ID Gypsy16-VV_LTR repbase; DNA; EDCOT; 814 BP. XX AC AM462489; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy16-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-814 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-814 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 713-713 (2007). XX DR Genbank; AM462489; Positions 8711 7898. XX SQ Sequence 814 BP; 235 A; 225 C; 175 G; 178 T; 1 other; tgtagggacc cctccccttg ggaaacacgt ggcatgcaac tcatggtgac gcgtggcacg 60 tgttatcagc cggaccatca tcatccggat tcccctaaag atatgcatgg tgcggctatc 120 ctatccggaa cccctcaagg aaaggcaaac gacgtttcag cttctcctat ccaaggaaga 180 gaaaacgayg ctggcagagc gtagacaccc ggatagtctc cacaacacat ccggataatc 240 agcatgatcc atccggatat aaatcgtctg gatggtcaat tacagtaaag cgagtcttac 300 acgcaatcac agcaagcagc catggcccac atcccattac ctgcagaatg agaagacaag 360 aggaagtgac agcaagtcac ttcccacgat cattctacat aaacactccc cacgatctct 420 gacaaccgca ttgcctacca tggtttctga cagccgttcg tagggtgata atgctcctac 480 taacacctat tgtcatcatc acaacagaaa atatctcctc accattaatg agaggaacag 540 tacccctgaa gctgtatata tatgccttcg catgaagaag aaagggatga tgatccccct 600 ggtaacctct tgatacctag taaaaggcca actgatttat atatctttct ctgaccatgg 660 ctaacaaaac catcggaggg tgcgtccgga caccctgtcc ggatgccctt ttttgcaggt 720 gcaactgctg aatcaagaac cccttgtgtg ttgagaatcg cgtgtccatc cacctagcag 780 caacgtggac caccggatac gcgaggtgac aaca 814 // ID LCCOPIA1_I repbase; DNA; EDCOT; 4267 BP. XX AC . XX DT 14-JUN-2005 (Rel. 10.06, Created) DT 14-JUN-2005 (Rel. 10.06, Last updated, Version 1) XX DE L. corniculatus copia-like retrotransposon internal consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; LTR-retrotransposon; integrase; gag-pol; KW LCCOPIA1_I; internal portion. XX OS Lotus japonicus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RP 1-4267 RA Gentles A. and Jurka J.; RT "L. corniculatus copia-like retrotransposon LCCOPIA1."; RL Repbase Reports 5(6), 150-150 (2005). XX DR [1] (Consensus) XX CC Generates 5 bp target sites duplications. The ORF is interrupted, CC with two parts coding for gag-pol and integrase domains. XX FH Key Location/Qualifiers FT CDS 97..1531 FT /product="LCCOPIA1_I_1p" FT /translation="FRPRSFVVILDTPFVFVFFLNLMATEKFDVLFVRLNG FT KNYSTWAFQFEIFVTGKDLWGHVDRSNPAPDKDKHKTEHAKWEVKDAQVKT FT WIISSVDPSIVLNLRPFKTAADMWDFLKKIYSQNNAARRFQLEHDIAISQQ FT ESLSISEFYSHFTNLWAEYTDIVHENLTADGLKSVQLVHETTKRDQFLMKL FT RSDFEGIRSNLMNRNPVPSLDSCLNELLREEQRLLTQTSMEQQKXTSVPVA FT YAAQGKPRGRDMSAVQCFCCKGFGHLAANCSKKYCNYCKKNGHIIKECPIR FT PPKRPVTAFTASVGSSFPSNSANSAFVQQNAPAPVQTLTPEIVQQMIISAF FT SALGISGKSFSTSSPWYFDSGASHHMTNNAQFLTDVTKYSGNLMIHTADGN FT QLPITATGDISSTLTDVFVSPGLTSNLISVGQLVDNDCRVEFSKSGCLVQD FT QHTGKMIVKGPKVGRLFPLHFFVSMSFIAFCFLX" FT CDS 1457..4259 FT /product="LCCOPIA1_I_2p" FT /translation="RGLKLDVFFHSISLSQCLSLPSVSCNSANVDYQTWHK FT RLGHPNSVVLHDLLKSGFLENKKIPSFSTIQFDCSSCKLGKSKILPFPTHH FT SNVEKPFDMIHSDLWGMAPVTSHANDKYFVTFIDDYSRFTWIYFLRSKAEV FT FSTFKFFHAYVQTQFSSKIKILRSDNGGEYTSHLFQEFLQNNGILSQRSCP FT STPQQNGVAERKNRHLLDVVRTLLLESFVPTRFWCEALSTAVYLINRLPSP FT SLNNDTPFTRLFGHPPTYTNLRTFGCVCYLHLPPQERTKLTAQSIECAFLG FT YSTHHKGFLCYDPSQCRIRVSRNVIFQENKYFFASHLDHSSPSISVLPLFS FT SSAIGPQSARPLLTYQRRGNVAPNLPPEPPRPLQDPSLQADPVQAALPDLL FT RRSSRVRKPPEKYGFTSPLSLTATLSSVSIPSSYKQAMEHECWQNAVETEL FT LALEENQTWDVVPCPPSVKPLGSKFVFSIKLRSDGSIDRYKARLVVLGNKQ FT QYGLDYDETFAPVAKMTTVRTILAIAASQSWTLHQMDVKNAFLHGDLKEEV FT YIKLPSGMPTLSPNEVCKLKRSLYGLKQAPRVWFEKFQSTLLGFSFTQSQY FT DPSLFLQRTSKGIVVLLVYVDDIVVTGSDQEVISTIKQLLHSTFRMKDLGQ FT LTYFLGLEVHYQPKGIFLNQHKYIQDLIQLASLTNVTSVDTPMEVNVKYRR FT DEGDLLEDPTLYRKLVGSLIYLTTTRPDISFAVHTVSKFMQSPRHLHLSAV FT HRIIRYLIGTSKRGLFFPTGSSLQLQAYSDADWAGCPDTRKSTTGWCMFLG FT DALISWKCKKQDSVSKSSTEAEYRAMSVACSEIIWLRGLLADLGFLQTQPI FT PLHADNTSAIQIAANPVYHERTKHIEVDCHSIREAYDRRVITLPHVSTAVQ FT IADIFTKSLTRQRHNVLASKLMLVDLPASIX" XX SQ Sequence 4267 BP; 1143 A; 1011 C; 791 G; 1321 T; 1 other; tggtatcaca gctggttttc gatcatatcc tagtctagcc agaaaattcc tagtctcttg 60 tcctagacca tgtttttttt ctcagccttg tcctagttca gaccacgttc cttcgtggtt 120 atcctcgata caccctttgt cttcgttttt tttctcaacc tcatggctac agaaaaattt 180 gatgtcttat ttgttcgcct taatggcaag aactactcaa cctgggcatt tcaattcgaa 240 atatttgtca cgggtaagga cctttggggt catgttgatc gcagcaaccc agctcctgat 300 aaagacaaac ataagactga acatgccaag tgggaggtaa aagatgctca agtcaagaca 360 tggatcatca gctctgttga tcccagcatc gttcttaatc ttcgaccgtt caagacggct 420 gccgatatgt gggacttcct aaagaaaatc tatagtcaga ataacgctgc tcgtaggttc 480 caactggaac atgacatcgc catttctcag caggaaagtc tctcgatctc tgaattttac 540 tctcatttca cgaatctttg ggctgaatat actgacatag tccatgagaa cttgactgct 600 gatggtctta aatcggtaca gttagttcat gaaactacta aacgagatca atttcttatg 660 aaattgagat ctgactttga aggcatcagg tctaatctca tgaatcggaa ccctgtaccc 720 tcattggatt catgtctcaa tgagctactt cgtgaagaac aacgcctcct cactcaaaca 780 tccatggaac aacaaaagty cacctctgtt ccagtggcat atgcagcaca aggaaagcca 840 agagggcgag acatgagtgc tgttcaatgt ttttgttgca aaggctttgg acatcttgct 900 gcaaattgtt caaaaaagta ctgcaattac tgcaaaaaga atggacatat tatcaaagaa 960 tgcccaataa gacctccaaa gcgaccggtc acagcattta ctgcctcggt tggttcttct 1020 tttcctagca attctgccaa ttcagcattt gtccaacaaa atgctcctgc ccctgttcaa 1080 actctgactc ctgaaatagt tcaacaaatg atcatttccg cattttctgc tttgggaatc 1140 tcaggtaaat ctttctctac ctcttcccct tggtactttg actctggggc ttcccaccat 1200 atgacaaaca atgctcaatt ccttactgat gtcaccaaat attctggaaa tctcatgatt 1260 catactgctg atggcaacca attacctatt acagccactg gtgatatttc ttcaactcta 1320 acagatgttt ttgtgtcccc tggtctcact agtaatctta tttctgttgg tcagttagtt 1380 gacaatgact gtcgggtaga attctcaaaa tctggttgtc ttgtgcagga tcaacacacg 1440 gggaagatga tcgtgaaggg gcctaaagtt ggacgtcttt ttccactcca tttctttgtc 1500 tcaatgtctt tcattgcctt ctgtttcttg taattctgct aatgttgatt accaaacgtg 1560 gcataaacgt cttggtcatc caaactcagt tgtacttcat gacttgctaa aatctggttt 1620 ccttgaaaat aaaaagatcc catcttttag tactattcag tttgattgca gttcgtgtaa 1680 acttggcaag agtaagattc taccttttcc aactcatcat tcgaatgtag aaaaaccttt 1740 tgatatgatc catagtgatt tatgggggat ggcccctgtt acatctcatg ctaatgacaa 1800 atattttgtc acttttattg acgactatag tcgtttcaca tggatctatt ttttgcgctc 1860 aaaagctgaa gtattttcta cattcaaatt cttccatgct tatgttcaaa cccaattttc 1920 atcaaaaatt aagattcttc gctctgacaa tggaggggag tacacatctc atttgtttca 1980 agagttcttg caaaataatg gtattctatc tcaaaggtct tgcccttcaa ctccccaaca 2040 aaacggggta gcagaaagaa aaaaccgcca tttgctcgat gttgtccgca ccctcttgct 2100 ggaatctttt gtgccaactc gtttttggtg tgaagctctc tccactgctg tgtatctcat 2160 taaccgcttg ccttctccat ctttgaacaa tgacactcct ttcactcggt tatttggtca 2220 tccacccaca tatactaacc ttcgcacctt tggttgtgtg tgttaccttc atcttcctcc 2280 ccaagaacgc acaaagctca ctgctcaatc tattgaatgt gctttccttg gatactctac 2340 tcaccataaa ggttttctat gttatgatcc tagtcaatgt cggattcggg tctcaagaaa 2400 tgtcatcttt caagaaaata aatatttttt tgcatctcac ctagaccata gctctccttc 2460 aatttctgtt ttgccattgt tttctagctc tgctatagga ccacaatcag caagacctct 2520 cttgacgtat caaaggcgtg gtaatgttgc tccaaatttg ccaccagaac ctccaaggcc 2580 tcttcaggat ccttccctgc aagctgatcc agtacaggct gcactaccag accttctacg 2640 acgcagttct cgcgttcgta aaccacctga aaagtatggt ttcacctctc ccttgtcttt 2700 gacagcaact ttatcttctg tttctatccc ttcctcttat aaacaggcaa tggagcatga 2760 atgttggcaa aatgctgttg aaacagaact tctagcatta gaagaaaatc agacatggga 2820 tgtggttccg tgtccaccat ctgttaagcc tcttggcagc aagtttgtgt tttctataaa 2880 acttcgttcg gatggctcaa tagaccggta caaggctcga ctggttgttc ttggaaataa 2940 gcaacaatat ggacttgact atgatgagac ctttgcacct gtcgccaaga tgacaacggt 3000 gcgtactatt cttgcaattg ctgcctccca gtcttggaca ttacatcaga tggatgtcaa 3060 aaacgccttc ttgcacggtg atctcaagga ggaagtttac atcaaacttc cgagtggtat 3120 gcccacactc tcccctaatg aagtttgcaa actgaagcgc tctttgtatg gtttgaaaca 3180 agcaccaaga gtctggttcg agaagtttca atccacacta cttggatttt ccttcacaca 3240 gagccaatat gatccatccc ttttcttaca aaggacttca aaaggtatcg tggtactcct 3300 agtttatgtg gatgatattg tggtgacagg gtctgatcaa gaggttattt ctacaattaa 3360 acaattgttg cattcaactt ttcgcatgaa agatcttgga cagctcactt acttcttggg 3420 gttagaggta cattatcagc ccaaaggaat atttttaaat cagcacaagt atattcaaga 3480 cctgatccaa ttagctagcc tcaccaatgt gacctcagtt gacaccccca tggaagttaa 3540 tgtgaagtat agacgggatg aaggtgacct tctagaagat cccactttat atcgcaagct 3600 ggtaggtagt cttatctacc tcaccaccac ccgacctgac atttcttttg ctgtccacac 3660 agtcagtaag ttcatgcaat cacctcggca tttgcacctt tcagcagtac accgcatcat 3720 tcgatacctc attggtacct ctaaacgtgg cttattcttt cctactggat catcacttca 3780 gctccaagca tacagtgatg ctgattgggc cggatgtcca gacacaagga aatctactac 3840 tggttggtgt atgtttctgg gtgatgctct aatctcatgg aaatgtaaga aacaagattc 3900 ggtctcaaag tcatcaactg aagcagagta tcgcgccatg tctgttgctt gctccgagat 3960 aatttggttg cgtggtcttc ttgcagatct tgggttcctt caaacacaac caattccact 4020 acatgccgac aacaccagtg ccatacaaat cgcagcaaat ccagtatacc atgaacgaac 4080 aaagcacata gaggttgatt gtcactctat acgagaagcc tatgaccgcc gagttatcac 4140 tctacctcat gtctcaactg ctgttcagat tgctgatatt ttcaccaaat ccttgacacg 4200 tcagcgccac aatgtcctag ctagcaaatt gatgcttgta gacttaccag catcaatttg 4260 agggggg 4267 // ID Copia-43_VV-LTR repbase; DNA; EDCOT; 181 BP. XX AC chr11; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-43_VV_; KW Copia-43_VV-I; Copia-43_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-181 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr11; Positions 7521287 7521467. XX SQ Sequence 181 BP; 53 A; 30 C; 27 G; 71 T; 0 other; tgcagaaaat cagcatcaga attcgtaact gcatttgatc agctagttta ggaaatctgt 60 acagctcatt ctttccttta ttttcacata tgttgttata cgttagcaca agtttaggag 120 taattttagt ttctcaaatc tgtatttata cctcttcttc taataagaat tgtgtgaatc 180 a 181 // ID MuDR-8_VV repbase; DNA; EDCOT; 10697 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-8_VV, an autonomous DNA transposon - a consensus sequence. XX KW MuDR; DNA transposon; Transposable Element; mutator; TIR; KW Mutavine-8; MuDR-8_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-10697 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 768-768 (2008). XX DR [1] (Consensus) XX CC MuDR-8_VV (Mutavine-8 in [1]) consensus is an autonomous element. CC Its individual copies are >90% identical to the consensus CC sequence CC MuDR-8_VV contains 80 bp-long TIRs which are 90% identical. XX FH Key Location/Qualifiers FT CDS join(3687..6198,6723..7468,7835..8269,8351..9163) FT /product="MuDR-8_VV_Transposase" FT /note="MUDRA transposase." FT /translation="MTDSTVEVLCYWNGTILRTETDLRYIGNNVEIEPIDV FT PIHTTFVELLKMIYDIIGVDRDYQLVLKCRHPTEMNKFQPLVVRNDRTVAR FT MLVVPSKYGMSSVQLFIEQTPNHYHLSNEMGHLTRLSTGDTDVDDENERDE FT EDDRDDAIDTDEIHLPNDDENCCQRENIDLVMVQQVVECESTRFVNLEVGD FT RSNNPEVEFEVENTSLVASPHGTQFNISNDNLEETFAPVSYHMPPTPQFLN FT MDEAINCVVSDWTPWKKPTLGNVDGELSIGQIFSSKSDLQHAVKMFSIKSH FT QEFTVYRSNASVLVLKCKKAPECQWRLRAMTVKDTGMFRITKYKGPHTCVN FT PCINQDHSQLDSSFVSEYIETLVKAEMTITVAAIQAVVAEQFGYQISYQKA FT MKAKRKAMTRLFGDWYKSYAELPRFFLALEQSNPGCIMYSKMVPGNNPNEE FT IFQRVFWAFAPSIKGFTHCRPVLSIDGTHLYGKYKGTLLIAMGCDGNNQLF FT PLAFAITEGENTDSWSWFLACIRVGVTQRKGLCLISDRHPGIIAAVNETYS FT GWTEPDAYHRFCMRHLASNFNTKFKDKTLKDLMCRAAMESKVKKFISHMDT FT IGRINAEARNWLEQIPLEKWALSHDGGRRYGIMTTNMSEVFNGVLKGARNL FT PITALVQLTFYRVNSYFTVRREHGASRLASGEEFTPHIDAKIKAKVVKAGS FT HEVLLYDHVAGRFHVKTRHSVGSSNRKPRTYHVTLQTGSCTCNKTLLLGFP FT CSHILAACHCRAIDFRQFVQGYYTTRAYLSTWAPLFYPIFDELEWPQYNGP FT IIVPSDSMKRLTSGRPKSSRLHNEMDARETRTPQTYMDTPLFRARPDPEDT FT SVLTLQHRHRSSTIRVDPDMGSVLTCRHRLLREWVLDDRVRPYIIQSGFYV FT FHRVGHVKVDWPLITALVERWRPETHTFHMPVGEMTITLQDVAILFGLRVH FT GHPVTGSTDIDWHALCEELLGVRPTETDIRGASLTVRFITTHFSHLPPGVV FT DEVTLQRHARAYLLLLVGGSLFPDKKGVYIQLAILPMLRDFGETAQYSWGS FT ATLAHLYRELCRASLDSAESIAGPLHLLQVLWQPYTDDILALLPDICLADQ FT DIWRTMSPLFFFYIVEWHRPERVLRQFGLIQGIPSTPPIDSDLHSIDRRGR FT PQFDWRLYHEHYVALWEARGDHIVTAEPIEPHMDYHAPYMTWYRRITRRFI FT TPMDDFGPMRYQATALSAHLLIETMTSIISRGGHALEDSDSDACRTGIVDI FT IRMATDVMCIIREDYRIPHVEHGGGRSPAQSTVARPPLVRGRSTSRGRGRY FT SSCQPITSSVSASLQPPTFLSSRLVQSPISSDVPSVQHPTSSDPPSVQPLT FT SSDPPSVQPPISLDLPPXQPPTSSDPPSAQPLTSSDPPSVQPPTSLDLPPL FT QPPTSSDPPSVQIDTSTQLDLPPAIPRGRRGLRRPRLLPPPPPLFPAPAPS FT QTDVLHVSHAVPATVREERPKRKRVPVTHRFSPCGGM" XX SQ Sequence 10697 BP; 3442 A; 1585 C; 1812 G; 3791 T; 67 other; gacttttggg ccaaaatggc ccatttttta aacttaacgt tgaaaacggg ctcattttca 60 aactattgtt caaaatggcc ctttgaagcc acatcagccc ataaatcaat gttttatacc 120 ctttttactt taccatttcc atccatcccc gtgctctgtt ctctcttctg tgcgattttt 180 ttttctaaac cctagcccca ccagtgggcc actaaaaaag acggtggagc tacaaagcat 240 aaagtttaag gtaagtccta atcttctttt tggcttgtat aaagtttttg gcactttcca 300 attttttttc ccatctcaaa atctcgattt ttagaaaaaa aaaaaatttc cattgttgtg 360 aatgattggt taaggagtgt ggttatggtg aattaatgac tattagtatc agattttggg 420 gcagtcgttg gggaggatta ggcttgcggt gttggcattg aggagctact caatctacgg 480 aaaaacaggt gagttgggtt gtgttgattg tgcttgtgtt gattgtgttt tgttgctctg 540 tttggttggt gagaattggc tacaaggaga gtaaattatt gttacaaaaa actgaggccc 600 tcccattgca acagttgggc ttaattaaaa tgagttttta atgttctaaa aaacaaaaca 660 agaayaggaa atragcatga aaaaratggt tgttgcttaa aaaaatggag gttttgggtt 720 tgtttttttt tttggtattt aagtccatgt ttgcaataac cttttgtttc aataagcagc 780 tggccaccaa aaaattatcc aatttctatt tcaataattw aaaatttgta ttatatttya 840 aatatttttt taggtatcyc aggattaata tttggaaata aaaaaaatat ttgttagaag 900 ttgtttccam tactttttcc argcaattgt tactgtttga agccattttt gttttacacc 960 ttttccctgc acctgacttt taaaggtgat tmaaaacttg cratgtgaaa tactaacaaa 1020 catatatgtk tgtgtattag agagagggta tgtctttatg tatttatctt tagaaacatg 1080 ttcagttgta tacacaaaca catgtatgtt aaaatctgtc atattcattt ttaagtattg 1140 ggcaaacatt tttgggaatt ctggcaatat agaataygtg gttagtttgc atttttaatt 1200 taaatttgta gkwwctataa gatgtaattg acttgttctr caatatagaa tacgtggtta 1260 gtttgyattt ttaatttaaa tttgraaata aaaaatatat aatattctat aatatttaaa 1320 taataaaagg atttatgagg atattatcat atatatgaaa ttaacttata agattttgta 1380 gttaagggga aaaaaattag gattaatcga aaagaatttt ttgaaattat tatggggcat 1440 taattaataa tattaatagc catagataac agatttaaaa aaaaaaaaaa atraaagttg 1500 taaataatga taaatatatt tgaatggaat gatttttaat tmtttttttc ttttttkaga 1560 atttgagtgg aatagggaat gtgytttcta agaatttcga ccgactcaat agataatgtg 1620 agtctccaag ccatgtttca gaaatctggc gatattttgt tttgtaaagt ggttgtgacc 1680 ttgrctgaac cgatgatatg ttggattgaa tctgttctta aagatgtctc caacttctac 1740 ttgttctgaa tgtgagacaa cmcattgtca ttaatatgat tgaatttagg atgttttatt 1800 tctgtgtcag tytacccatg cattcactta cactcattcc ttgtctttga aggaggaaag 1860 gcctcaacat tcaaaatatt ttatttttcc caaactgaag tgaagtattt gatagaagtt 1920 ctactattat ggaagtattg ttatgaattg ctcatctatt tgaggttata atataaaata 1980 ctagcttttt aaaagtaacg aattgaggtc tgggaaacgt gttctgttaa ytgtagaaat 2040 atttttatat attttatggt tatttaaata tattttttgg ttatctaaat ttaatgtttc 2100 tatcataaac tggatgtatc ttgyatgaat atatatatat atatatatat atatatatat 2160 atatatatat atatatatat atatatatat atatatatat atatatataa catgtttkct 2220 aggaaaaaaa tgattttgga tataaacaat ttcaaagtaa aaaatgaata aataattttt 2280 ttctgatcaa gagatcttga ataattttgt ctcaatagct cttaaatata aaatactcat 2340 ctagaatttt tttgccttga tatcaagaaa acttctcaaa tatgagtaaa cacttttttt 2400 twtaaaaaaa aaaaaaaaaa atccagattc ttaaagtaya gacattttct ctttaaaagg 2460 acttttgtat ttggttatat ccaaaaattt aatttttata taattatatt ttttaaagat 2520 atcaaaatta cccatacttt taataaaaat attattaaaa taaaatagta aaagtataaa 2580 atgaatggtc caactctaaa aaaacactat tataaaatat accatatacc tcatgtttga 2640 tgactccact tagactacta gattgtggat gtgatgggag tgraggagga tgaaagggag 2700 gccaaaagtg aacccatctg gaaaaacttt gattatgggt tggagaaatt gaatgtgggt 2760 agggaccata ttgtttatgt gatcctttgt caattgggtt gtacttcatt ttcgtgagtg 2820 cacactagac attattacaa atggtgtggc ccttggacac gtctagatgt tcaagtaggg 2880 tgtgatgcca gggaatataa aaaaaaaaat tgccaagaaa gcatttttat tattatacta 2940 gaatttagaa tcacaatcta catgctatct acattctgca gtgcaagcat aatagcaarg 3000 aaggttatca aatatgattt tcaggatcta attttttaaa ataattccaa atagaagatc 3060 aaagttttta attttatstt ccatatataa aacaatataa taaycttarg atatggtttt 3120 tatttmtgag atattgaaaa ttattttttt ttacaaggtt ctttagaaaa tctcattttt 3180 tttatttaaa ataacatatt taacatatat ttatttttaa aaatatattt aacagataat 3240 tttgagttgt aaaagaatta acataattaa cacatattta ttttaaaatt taatttttaa 3300 tataaaaata ttaatttcat tttatcaaaa aaataaatta aaagttaatc tcatcctaat 3360 tatgaaatta gaaaaataaa ytaaacgtgt ttgtaaccca aacacatgta aaacatttta 3420 ttggaccaca aaaataatat taattcatar tatcatccta ctctttactt atacacttat 3480 ttgcttatac attgctttca tttgagttga acttggtatt tagacatgaa gytttgttac 3540 attccaatat ttattaggtt tattattgta ttttatgaat cattgaccat aaagtattat 3600 tttttactta aataaatatt ttttttattt gaataaatat tttttttatg taataacctt 3660 ttgttattat ttatgtgaag gcmattatga ctgattccac agtagaagtg ctatgttatt 3720 ggaatggaac aattttgagg acagaaacgg atttgagata tattggaaat aatgtagaga 3780 ttgagcctat agatgtgccc attcatacga cctttgtgga gttgttgaag atgatatatg 3840 atatcattgg tgttgacaga gactatcagt tagtcttgaa atgtcgacat ccaactgaaa 3900 tgaacaaatt tcaaccatta gtggtgagaa atgatcggac agttgcacgt atgctagtgg 3960 tgccatcgaa gtatggaatg tcttcagttc aattattcat agagcaaact cccaaccact 4020 atcatttgag taatgaaatg ggtcatttga cacgattatc aacaggtgat actgatgttg 4080 atgacgaaaa tgagagagat gaggaagatg atagagatga tgcaatcgac acagatgaga 4140 ttcatttacc taatgatgat gaaaattgtt gtcaaagaga aaatattgat ttggtgatgg 4200 tccaacaagt tgtggaatgt gaaagcacaa gatttgtgaa ccttgaagtt ggtgataggt 4260 ctaataatcc tgaggttgag tttgaggttg aaaacacatc actagttgcc tccccacatg 4320 gcacccaatt taatatctct aatgacaacc tagaggaaac atttgcaccc gtttcatacc 4380 atatgccacc tacaccacaa tttttaaata tggacgaggc aattaattgt gttgtaagtg 4440 attggactcc atggaaaaag ccaactttag gaaatgttga tggggagtta tcaattggcc 4500 aaatattttc ctcaaaatca gatttgcaac atgctgtgaa gatgttttcc ataaagtcgc 4560 accaagagtt tactgtttat agatcaaatg caagtgtgtt agttcttaaa tgtaaaaaag 4620 caccagagtg ccaatggcga ctaagggcaa tgacagtgaa agatacgggt atgtttagaa 4680 tcacaaagta caaaggtcct catacatgtg tcaatccatg tattaatcaa gatcattcac 4740 agttggattc tagctttgta tctgagtata ttgaaacatt ggtgaaggca gaaatgacca 4800 ttacagttgc tgcaattcaa gctgttgttg cggaacaatt tggttaccaa atttcttatc 4860 aaaaagcaat gaaggcaaaa aggaaagcaa tgactcgatt atttggtgat tggtacaagt 4920 cttatgcaga gttgcctcgt ttcttccttg ctttggagca gtcaaatcct ggatgcatta 4980 tgtattccaa aatggttcct ggaaacaacc cgaatgaaga aatttttcaa cgtgtttttt 5040 gggcattcgc tccatctatt aaagggttta ctcactgtcg accagttctt agtattgatg 5100 ggacacattt gtatggaaaa tataaaggga ctttgctgat tgctatggga tgtgatggta 5160 ataaccaatt gtttccactt gcatttgcca ttacagaagg agagaataca gatagttgga 5220 gttggttttt ggcatgtatc agagttggag taacacaaag gaaaggcttg tgtctgatht 5280 ctgatcgtca tcctggcatt atagctgctg tnaatgaaac atattcggga tggactgagc 5340 cagatgctta tcatagattt tgcatgcgtc atttagcgag taacttcaac acaaagttca 5400 aagataagac tttaaaggat ctcatgtgta gggctgctat ggagagtaaa gttaaaaaat 5460 ttatttctca catggataca attggccgga taaatgccga ggctagaaat tggttggagc 5520 aaattcctct tgaaaaatgg gcactctcac atgatggtgg gcggagatat gggattatga 5580 caactaacat gtctgaagtt tttaatggtg tccttaaggg tgctcgtaac ttaccaataa 5640 cagctttagt ccagttaact ttctatcggg ttaacagtta cttcacagtc aggcgggagc 5700 atggtgccag tcggctcgct tcaggtgaag aattcactcc acatattgac gccaagataa 5760 aggctaaagt tgttaaggcg ggttcacatg aggttctttt gtatgatcat gtggcgggac 5820 gttttcatgt taaaactaga cactctgttg gaagcagtaa taggaaacct cgcacatatc 5880 atgttaccct tcaaacgggg tcttgcacat gtaacaaaac acttttgtta ggattcccat 5940 gttcgcacat tcttgctgct tgtcattgtc gagcaattga ttttcgacaa tttgtacaag 6000 gttattacac cacacgtgct tacctatcaa catgggctcc cttgttttat cccatatttg 6060 atgagttgga gtggcctcaa tataatggac cgataattgt gccttcagac tcaatgaaac 6120 ggctaacttc tggtcgacca aaatcaagtc gtttgcataa tgagatggat gcaagggaaa 6180 ctagaactcc acaaacatgt ggactttgca agcaatcggg tcacaatcga cgttcttgtc 6240 ctaatagaga aaccaatgat aggaggagtt gatgtacttc atgaacatct tattgtactg 6300 ttttttttaa atttactagt attgacctta atcgttttaa gatatatgta gaaactatct 6360 tattgaacat cttattgacg tttgtgttgt ttgaaattdt tattttttgt caattcattc 6420 ttattttgct tatatcaggt tacatgaaaa aaatattaat ctctattatt taggggagat 6480 gctgttcaaa tttttaaaat tttaataatg aaattcatgt tgttagaaat tgttgttttt 6540 tgtcaattca ttcatatttt dcttatatca ggttacattg aaaaattttg aatctctact 6600 gtttagggga aatgctgttc aaatttttac aattttaatc atgaaattca tgttgttaga 6660 tattgttgtt tcttgtcaat tcattcatat tttgtttata tcatgtattg atgtacatgc 6720 agacatggat actccgttgt ttcgtgctcg tcctgaccct gaggatacat ctgtgcttac 6780 tcttcagcat cgacatcgat catccaccat tcgtgttgat ccagatatgg gtagtgtttt 6840 gacttgccga cacaggttgc ttcgagagtg ggttttggat gatcgtgttc ggccatacat 6900 tatacagtca ggattttatg tctttcatcg agtgggccat gttaaggttg attggccttt 6960 gattactgca ctggtagaga gatggcgccc agagacgcac acattccaca tgccagttgg 7020 tgagatgacc atcacattgc aggacgtagc catcttattt ggattacgtg tacatggtca 7080 tcctgtcact ggttctacag atattgattg gcatgcactt tgtgaggagt tattgggtgt 7140 tcgaccgaca gagactgata ttcgtggagc atcccttaca gttcgtttta ttactaccca 7200 tttctcccac ttaccaccag gggttgtaga tgaggtcacg ttacagcgcc atgctagagc 7260 ttatctttta ttgttagttg gtggttcatt atttccagat aagaaggggg tttacatcca 7320 attagcaatt ctacccatgt taagagattt tggtgagact gcacaatata gttgggggag 7380 tgcgacacta gcacatcttt atcgagagtt atgtcgagct agcttagata gtgcagaatc 7440 tattgcagga ccattacatt tgttgcaggt ataactacaa gtcttattaa ttatgtaatt 7500 ttgtcataat tatgtgcatt taaacataat tttatttcat ttttagctat ggtcatggga 7560 gcgattacat gtgggtcgtc ctagtagatc acttccccat gcaccagtgc ctatagatga 7620 gagattccca ccagatgcac tagggagtag gtggagagtt cccttatctc atacagacac 7680 tcctcatcat gtgttggtca catacagaga tgagtttgat agacagcgat ctgatcaggt 7740 ttgggctaaa tattagtatt ctttaacaag attattaata ttaataatat aatttaaact 7800 ttattaaata catactaada tttgaatata tcaggtatta tggcagcctt acacagatga 7860 tatactagcg ttgcttccag acatttgttt agctgatcag gatatttggc ggacgatgtc 7920 accacttttt tttttttata ttgttgagtg gcatcgtcct gagcgtgtgt tgcgacagtt 7980 tggactcata cagggtattc cttcgacacc ccctatagat tctgaccttc actccataga 8040 tcgacgtggt cgacctcagt ttgattggag gttgtatcat gagcactacg tggcattatg 8100 ggaggctagg ggggaccaca ttgtcactgc ggagcctata gagcctcata tggactacca 8160 tgctccgtac atgacatggt atcgtcgtat tacacgtcgt tttattacac ctatggatga 8220 ttttggacct atgcggtacc aggctactgc cttatctgcc cacttattgg tttgtatcac 8280 tttaatatta tgtacatatt gtgtataata tttattccaa caaataatta tatatcattt 8340 tatgtgacag attgagacta tgacatctat catatctcga ggaggtcatg cattggagga 8400 ctctgatagt gatgcttgcc gcactggtat tgttgatatt attcgtatgg ccactgatgt 8460 tatgtgcatt attcgggagg attatcgtat cccacatgta gagcatggag gaggtaggtc 8520 accagctcag tcgacagttg ctcgaccacc acttgttcga ggtcggtcga catctcgagg 8580 gagaggtaga tatagtagtt gtcagcccat cacatcgtca gtatcagcat cattacagcc 8640 ccctaccttt ttatcctcac gattagtaca gtcacccatc tcttcagacg taccatcagt 8700 gcaacaccct acttcttcag acccaccatc agtccaaccc cttacctctt cagacccacc 8760 atcagtacaa ccccctattt ctttagacct acctccanta caacctccta cctcttcaga 8820 cccaccatca gcccaacccc ttacctcttc agacccacca tcagtacaac cccctacctc 8880 tttagaccta cctccattac aacctcctac ctcttcagac ccaccatcag tgcagattga 8940 cacatctact cagctagatt taccgccagc cattccgagg ggtaggcggg gcctacgtcg 9000 acctagattg ctacctccac caccacctct atttccagct ccagccccat cacagacaga 9060 tgttcttcat gtgtcacatg cagtacctgc tacagttaga gaggagcgtc caaaaaggaa 9120 gagagtacca gttacacata ggttctctcc ttgtggaggc atgtgagatt atatatgttt 9180 tttattttcc actatattaa tgtttagtgg atattttttg tgactttaat taaactatta 9240 aaaattacat tttgtagtag actttttgta attaatttca ttaactaatt ttgtaaaaaa 9300 atctatatat gacaactacg gcttaagagt atattattat tttgttaaag ataaatttgt 9360 cataatataa ataaattaat atattaaaaa ttaacaaatt aaatatctta aattaataaa 9420 ttatacaatt ttatatatta tttatatgtt atataaattt attattttaa gattattaat 9480 ttattaataa atcaaatatt catttataat atmttctatt tatcaattta tgtttgttga 9540 aataatacta gatttttaag tttaaatata aataatttat tatttaagta tatttttaaa 9600 atttcaatca taaattgtga tttaatagtt tttaattaaa ttggaaagta aaaaaaaawa 9660 taaaattata attgaaatct cagttattaa ctactatayt attatttcga taaagataaa 9720 tttatcataa tataaataaa ttaatatytt aaaaattaac aaattaaata tattaaatta 9780 ataawttata caattttata tattatttat atgttatata agtttattat tttaagatta 9840 ttaatttatt aataaatcaa atattcattt ataatatctt ctatttatca aatttatgtt 9900 tgttgaaata atactagatt tttaagttta aatataaata atttattatt taagtatatt 9960 tttaaaattt caatcataaa ttgtsattta atagttttta attaaattkg aaagtaaaaa 10020 aaaaataaaa ttataattga aatctcagtt attaactact ataytattat ttygataaag 10080 ataaatttat cataatataa ataaattaat atcttaaaaa ttaacaaatt aaatatmtta 10140 aattaataaw ttatacaatt ttatatatta tttatatgtt atataarttt attattttaa 10200 gattattaat ttattaataa atcaaatatt catttataat atcttctatt tatcaattta 10260 tgtttgttga aataatacta gatttttaar tttaaatata aataatttat tatttaagta 10320 tatttttaaa twtmawtmat wtattatttt taagtataag taatttaata attttttaat 10380 taaattttaa atttaaataa aaaattaact aaagccrcrt ttggcaamtg cggctttagt 10440 acaaaaatga agccgcgttt gccaactgcg gctttagtgc aaaaatgaag ccgcatttgc 10500 caactgcggc tttagtacaa aaataaaaat gaagccgcgt ttcccaactg cggctttcac 10560 tataatgacg aaaaaaatat attttttaat gatgtagcgc ctacgtggca tcaaagaggc 10620 cattttgaac aatagtttta aaatgtgccc gttttgaaca ttaagtttca aaaatgggtc 10680 attttgaccc aaaactc 10697 // ID MuDR-4N_Mad repbase; DNA; EDCOT; 1114 BP. XX AC . XX DT 07-OCT-2010 (Rel. 15.1, Created) DT 07-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW 8-bp TSD; MuDR-4_Mad; MuDR-4N_Mad. XX NM MuDR-4N_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1114 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1508-1508 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 46-bp long, imperfect. TSD is 8-bp long. XX SQ Sequence 1114 BP; 334 A; 178 C; 193 G; 408 T; 1 other; gagagctgtt attcccaccc caatgtctta tcttcccacc caccttttta tgaatttttt 60 aattacaaat ttgtccattt gtaaaatgac taataaggac cttagttacc cccttttgca 120 ttactttttt ttttataaaa aagaaaaaag aaaagtttgg gcgtgataac tctcacgcta 180 tgtttagaaa atttgtctcc cttaaaccct aactcatcat tcccatctcc tttcattcag 240 agaaagcaaa aagaatgaac ttagaagatg acgtttctat ggaagaagta gatgattatg 300 tttccgtcga agaggtaaaa gataatttta tgtgggtcat cttgatttgt cgacatcgta 360 caattgaagc atagctctgt gactttttat ttgaatttgc attaggttag ggtgcaattt 420 gtttcacgtt ttcctatgag aattcctgga attcgttttc attaggttag ggtaaatttg 480 tttttcatga gttttccttg aataaccgtt tccctctttt cctttctaca gtattgttga 540 attttatata attaattgcc cttcgaataa ccagaaggtg aaacacaaat ctcacaccat 600 ttgcttcata ctgggcacac attgtttcaa agccttttga tggtgatgaa ctccattgct 660 tcatccttgg ttcgttttcg aacatttggt ttcagttaat tattttaatt ttgaaaccga 720 agtgaactcc gaaaacaaat atatattcct atttctttat ttctgaactt ttccttggat 780 gagcccttgg aatttggaaa ggggaaatgc atatgaaaaa gaaaacaaaa ggggaaaagc 840 aacgaatgaa aacccagaat tcttcatccc cccccccaaa aagttggaat ttggaaagga 900 aacggttttt tttttttttg gcttttagaa gagagtaata ttatttgttt atattctttt 960 tttttaagak aaatttatct ctaattatat atagggttat tttaggaata atagtgggtg 1020 ggaaaataac attttaattt tttaactttt tatagtgggt gtaaatataa cgtgggtgga 1080 gaaataagac aacggggtgg gtctagcagc tctc 1114 // ID MTCOPIA2_I repbase; DNA; EDCOT; 4656 BP. XX AC AC147407; XX DT 29-DEC-2006 (Rel. 11.12, Created) DT 29-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Internal portion of Copia-type LTR-retrotransposon. XX KW Copia; LTR Retrotransposon; Transposable Element; KW internal portion; MTCOPIA2_I. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4656 RA Jurka J.; RT "MTCOPIA2: Copia-type LTR-retrotransposon from barrel medic."; RL Repbase Reports 6(12), 632-632 (2006). XX DR EMBL/GenBank/DDBJ; AC147407; Positions 17512 12857. XX FH Key Location/Qualifiers FT CDS 332..4654 FT /product="MTCOPIA2_I_1p" FT /translation="MAPRNNSPDTESVFFVHPSKDPNSLSITPKLTGSNYI FT AWNRTVQRSLGTKNKLGFINGAIPIPDVDDLNRSAWERCNHLVQSWLINSV FT SDSIAQTIVFYDTAFEVWHDLQERFSKVNRIRIANLRSTINNLKQGSKSVL FT DYFTEMKALWEELASHRPIPNCSCIHPCRCEASRVAKTHRNEDQIMQFLTG FT LNDQFSIVRTQVLLLDPLPSLNKVYSLVVQEESNNASLSSLSISDDSSIQI FT NASDARKFQGSGKNPSQPKPTRLCTFCNRTNHTVDFCYLKHGYPNVNKAQP FT RVNAVTYEDVDAGTSSSIGQGSSTSSNAGFSQEQLVQLASLLQQANLVVPA FT SPSSQASSNHISANPLISTTISAPESSSAGIIPKPSYWLLDSGANEHISCN FT LSFFSSFYRIPPVYVSLPNKTCVLVQYAGTVSFTSNFYLSHVLYSPAFTHN FT LISVAKLCESLSYSLHFTSAHCIIQDTMSLKMIGLAKQMDGLYKCTPSSCS FT SNSVFSSVSNKSCNVVAAISCNSSISIPSNALWHFRLGHLSHQRLHSMSLL FT YPNIINSNNKDACDLCHFAKHKHLPFNSSISHASTNFELLHLDIWGPLSIA FT SVHGHRYFLTIVDDHSRFLWVILLKSKAEVSTHVINFITMIQTQFHITPKF FT IRTDNGPEFILSTFYASHGIIHQKSCVETPQQNGRVERKHQHILNVGRALL FT FQSKLPPSFWSYAILHVVFLINRVPTPILHNQSPYFVLHHQLPALNLFKVF FT GCLCYASTLQSHRTKLQLRARKSIFLGYKSGFKGFTLYDIQSREIFVSRHV FT TFHETFLPYPHTSLSTTPDWEYFSSSHVYDVSNQPTPINSPTIIDDILPPS FT PPLNPPPPPPIPVVSPASRTSIRQTTTPSYLQDYVCKNIHTSPYPINNYIS FT HHNLSNNYSSFVLSLHTTTEPKSYAEASKHDFWKQAMQVELQALEKTGTWK FT LVDLPSNIKPIGCRWIYKVKYHVDGSIERYKARLVAKGYNQIEGLDYFDTY FT SPVAKLTTIRLVIALSSIHNWHLHQLDVNNAFLHGDLQEDVYMLLPPGIKS FT NKPNQVCKLQKSLYGLKQASRKWYEKLTYVLSHHHYIQASSDHSLFVKKTS FT FSFTILLVYVDDIIIVGDSLTEFTHIKSVLDASFKIKDLGQLKYFLGIEVA FT HSKLGISLCQRKYCLDLLADSGTIDSKPVSTPSDSSTKLHHDSSPSYADIP FT SYRRLVGRLLYLNTTRPDITFITQQLSQFLSQPTQAHHTAALRVLRYLKGC FT PGRGLFFPRNSSINLQGFSDVDWAGYLDTRRSISDQCFFLGNSVISWRTKK FT QITVSRSSSEAEYRALASATCELQWILYLLQDIYIACPKLPVLYCDNQSAL FT HIAANPVFHERTKHLEIDCHIVREKVQAGILKLLPVSSQDQVTDFFTKGLL FT PKPFNILLSKMGLINIYQPPSSGGLLH" XX SQ Sequence 4656 BP; 1260 A; 1029 C; 688 G; 1679 T; 0 other; taatatggta tcatgcgcct tctcccatgg gggaaaggta gttacgatcc tcaacggcct 60 ctaaccgttt ttctccgctg tgctttcttc tccgatcacc ttcgttgatc gtttctctgc 120 ttgattcatg gtgctagatc ctttcttctg cattttgaac tctgtttttc tggttcgatt 180 gaattcatat tcaatctcaa ttttcttctc gttctttctt cttgttgtga ttgattcaat 240 agttctttac tgtgatttca atcctctctt tttttttttt tttttgattc cttgaatttc 300 ttcatctttt tcgcaatttt tcaccatttt catggctcct cgaaacaatt ctcctgatac 360 tgaatcagtt ttctttgttc atccaagtaa agatcctaat tcactttcta ttactcctaa 420 gcttactggt tctaattata ttgcatggaa tcgaacggtt caacgttcat tgggaacgaa 480 gaacaaatta gggtttatca atggtgctat tccaattccg gatgttgatg atttgaatcg 540 ctcggcttgg gaacgatgca accatttggt acaatcttgg cttattaatt ccgtttctga 600 ttcaattgct caaactatcg tattctatga tactgctttt gaagtttggc atgatttgca 660 agaaagattt tctaaagtta atcgcattcg cattgccaat cttcgttcca ccattaacaa 720 cctcaagcaa ggttctaagt ctgtgttaga ctattttact gaaatgaagg ctctttggga 780 agagttagct tctcacagac ctatccctaa ttgttcatgc attcatcctt gtcgttgtga 840 agcttcaagg gttgctaaaa ctcatagaaa tgaggaccag attatgcagt ttctcacagg 900 tctcaatgat caattttcca ttgtaaggac acaagtgtta cttcttgatc ctcttccttc 960 attgaacaaa gtgtattcac tggttgttca agaagagagc aataatgctt ctctttcctc 1020 tttgagcata tctgatgatt cctctattca aatcaatgct tctgatgcca gaaaatttca 1080 aggtagtggc aagaatccat cacaacctaa acctactaga ttatgcactt tctgtaacag 1140 aactaatcac actgtggatt tttgttattt gaagcatggt tatccaaatg ttaacaaagc 1200 tcaacctaga gttaatgctg ttacttatga ggatgttgat gctggtacct cctcctctat 1260 tggtcaaggt tcatctacaa gttccaatgc tggtttttct caagaacaat tggttcaact 1320 tgcatcattg ttacaacaag caaacttggt tgttcctgca tcaccatcct cccaagcttc 1380 ttctaatcac atttcagcta accccttgat atccactacc atctctgcac ccgagtcatc 1440 ttcagcaggt ataataccta aaccctctta ttggttactt gactcagggg ctaatgaaca 1500 tatttcatgc aatctctctt tttttagttc attctataga attccacctg tttatgtttc 1560 cttaccaaac aaaacttgtg ttcttgttca atatgctggt actgtctctt tcacttccaa 1620 tttttatctc agtcatgttt tatattcacc agcttttact cataatctca tttctgttgc 1680 taagttgtgt gaatcattgt catactcttt acacttcact tctgctcatt gcatcataca 1740 ggacacaatg tctttgaaga tgattggttt ggctaagcaa atggatggct tatacaaatg 1800 cactccatct tcctgctctt caaattctgt ctttagtagt gtttccaata aatcgtgtaa 1860 tgttgttgca gctatttcct gtaattctag tattagcatt ccttccaatg ctttatggca 1920 ctttagactt ggccatctgt ctcatcaaag acttcattct atgtctctct tgtatcccaa 1980 cattatcaat agcaataata aagatgcttg tgatttgtgt cattttgcta aacataaaca 2040 tttacctttc aattcaagta tttctcatgc ttctaccaat tttgaattac ttcatcttga 2100 tatttggggt ccattatcta ttgcatctgt acatggtcac agatactttc ttactattgt 2160 agatgatcat agcagatttc tttgggtgat tttacttaaa tccaaagcag aagtttctac 2220 acatgtcatc aatttcatca ctatgattca aacacaattc cacattaccc ctaagttcat 2280 tagaactgat aatggacctg agtttatact ttccaccttt tatgcttcac atggaataat 2340 tcatcaaaaa tcttgtgttg aaactcccca acaaaatggt agagtagaaa ggaaacacca 2400 acacattctc aatgtaggta gagctttatt atttcaatcc aaactcccac cttctttttg 2460 gtcatatgct attcttcatg ttgtgttcct aatcaacaga gttcctactc ctattcttca 2520 taaccagtca ccttattttg tcttgcatca ccagttacct gctctcaatt tgtttaaagt 2580 gtttggttgc ttgtgttatg cttctactct tcaatctcac agaacaaaat tgcaacttag 2640 agctcgtaaa tctattttct taggttacaa atcaggtttt aaaggtttta ctctatatga 2700 tattcaatct agagagatat ttgtctcccg acatgtcact tttcatgaaa cttttcttcc 2760 ataccctcat acatctctct ctaccactcc tgattgggaa tacttctcct catcccatgt 2820 ttatgatgtt tccaatcaac ctactcctat taattcacct accataatag atgacatttt 2880 acctccttca cctcctctta accctccccc accacctccc atacctgttg tttcccctgc 2940 ttccagaact tccatcagac aaaccactac tccttcttac ttacaagatt atgtttgtaa 3000 gaatattcat acttccccat atcctataaa taattacatt tcacatcaca acttatctaa 3060 caattactct tcatttgttc tgtctcttca caccaccact gagccaaaat catatgctga 3120 agcaagcaag catgattttt ggaaacaagc catgcaagtt gaactgcaag ctcttgagaa 3180 aactggtacc tggaaacttg ttgatttacc atccaatatc aaacccattg gatgtagatg 3240 gatttataaa gttaaatatc atgttgatgg ttccattgaa agatacaaag ccagattagt 3300 tgcaaagggt tacaatcaga ttgagggact tgattatttt gatacttact ctcctgttgc 3360 taaacttact acaattaggc ttgtcattgc tctctcttct atacacaatt ggcatttaca 3420 tcaacttgat gtaaacaatg ctttccttca tggagattta caagaagatg tttatatgct 3480 cctccctcct ggcatcaaat ctaataaacc caatcaagtt tgcaagctcc aaaaatctct 3540 ttatggcttg aaacaagcta gtaggaagtg gtatgaaaaa ttaacatatg tgctttctca 3600 tcatcactat attcaggctt cttctgatca ttccctcttt gtcaagaaga catctttttc 3660 attcactatt cttttagtat atgtggatga tattataata gttggtgatt cccttaccga 3720 gtttactcac atcaagtctg ttttggatgc ttcatttaaa atcaaagact taggtcagct 3780 taaatatttt cttggtattg aagttgctca ctccaagctt ggaatttctt tatgtcaaag 3840 aaaatactgc cttgatttac ttgcagattc aggcactata gattccaaac ctgtttctac 3900 tccctctgat tcttctacta agcttcatca cgattctagt ccttcatatg ctgatatacc 3960 atcctataga agactagtag gcaggttact ttacctcaat acaactaggc ctgatatcac 4020 tttcataaca caacaactta gccagttttt atctcaacct acacaagcac atcatacagc 4080 tgctttaagg gttcttaggt acctcaaagg gtgtccaggc agaggtttgt tttttcccag 4140 aaattcttct atcaatttac aagggttttc tgatgtagat tgggcaggtt atcttgacac 4200 cagaagatct atttctgacc agtgtttttt cttaggcaat tctgttattt catggagaac 4260 aaagaaacaa atcactgtat ctaggtcttc atctgaagct gagtataggg ctttagcatc 4320 tgccacatgt gaactccaat ggattctata cctgcttcag gacatctaca ttgcttgtcc 4380 taaactacct gttctttact gtgataatca gagtgccctc catatagctg ctaatccggt 4440 ctttcatgaa cgcaccaaac atttggaaat tgattgccat atagtcagag aaaaggttca 4500 agcaggcatc ctcaaattgc tcccagtttc ctctcaagat caagtaacag attttttcac 4560 taaaggtttg cttcctaaac cattcaacat tcttttgtcc aagatgggat tgataaacat 4620 ttaccaacct ccatcttctg gggggctatt gcataa 4656 // ID Ogre-LE1_I repbase; DNA; EDCOT; 12262 BP. XX AC AC171735; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 16-APR-2007 (Rel. 12.03, Last updated, Version 3) XX DE LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-LE1; Ogre-LE1_I; internal portion. XX NM Ogre-LE1_I. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-12262 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC171735; Positions 64613 76874. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). CC Additional annotations: 5739..5901: putative intron. CC Note: ORF2+3 (gag-pol) disrupted by mutations generating several CC stop codons and the frameshift. XX FH Key Location/Qualifiers FT CDS 782..2086 FT /product="Ogre-LE1_ORF1" FT /translation="MTHPHFPNTQMVVKVNPILKTWWKDIQKNRELEANEL FT LGGLTALISVESDRHLIKALLKFWDTERLVFKFRDFELTPTIKEVGGFMGL FT AYKELEIIVPHKPSPRSFLKQMGMCHNPNLLCLKEGWISLEFLYSRFGDEE FT GHQNFHREFACSSAKWERYRLNAFAVVLLGSLVFPREGGKIHTGLCYVVRM FT LARGGKTLVPMILAEILRALTACTKGKRYFEGCNFLLQLWAVEHFYQRANK FT VDIVRWTMGNKIINHPLRMKHFISPVGTEDWFTYLKERSAVEIQWKYYWLK FT PRRAIIRGNELYFIELIGLNGVQPYAPLRVLRQFGQIQMIPLRSHMSHYGY FT DFGSELPQVNTILRRWKNVITIDVQEHRPFCTPEYYVWLLEDAEHRDLSEG FT GLPGFGDEKERRWARNLLNTDYDITLEMKKQIVPNIGEQHD" FT CDS join(2500..5738,5902..7759,7762..9366) FT /product="Ogre-LE1_ORF2+3" FT /note="gag-pol." FT /translation="MVDDNSTTERVEACEGGQLHSNLILRLERKISQLEEE FT VANMRDLAKLSISLGTQFGENIDNPPNQTATPDNPPIHISPPEPIRPNAFP FT PPHAQNTQFPFHHYYQHTKPTVPETTPNTNIPHTFENNNPNPIYVETAPLT FT HDLHESESHQKDILIKTLTERLDNLTNRVQHVEGNKKLGGLGYEDLCMHPD FT VELPEGYKLPKFETFNGIGDPKAHLRMYCDKLVGVGRDERILMKLFMRSLT FT GEALSWYIEQDSRKWIKWVDMATDFMNRFGFNIENAPDWFYIQNLKKKPSE FT SFREYAIRWRSEAARARPPMEESQMKDYFIRAQELQYYDRMMLVAEKSFAE FT IIKLGERIEEGIKNGTIINLEALQATNKALQSGGMTESRKKTGSVMMAHGT FT RTPLRHKTTNPPPSPYPHTPYLHTPYPQHPSAPPPISPQPMPIYYQNAPPQ FT YLHASYPVYNVQPTHF*TPPPTQTPNYRNRPSYERRPTKTYTPLAEPIAQL FT YERLKQAGYVSPIPALPVDVRAKWYDPNKVCAYHSGMKGHTTEVCRALKDK FT VQMLIDTKTIQLKDPTPNVANNPLPNHQVNMVEAGDVWDWEESIWAVETEE FT AMPTTAQAPLIVQGLAPFEVEVAAPRPPFAVYKASSPTQCDTHAVPWDYNK FT RETNVEETDVATGVTRSERIYTSENLVQGSSSKSKAPIVELEDQSIWKKVK FT AKEYSVIEQLSKTPSQISILELLQSSETHRDALLKILGEAYVPSNITHGEV FT SQMVGQVFEAYKISFHKDELPIEGTTHNKALYISVQYQDKVINKALVDAGS FT GLNICPLSTLTRLGVDSAKIQTWKMNVRAFDGSQRGTIGEITLDMLIGPVT FT FPIAFQILDIPSSYNLLLGRPWIHMAGAVPSTLHQCLKFEWDYEEVVVHGE FT KGHPVYTIEGRENMDGEMYHTVELVGNIELQPWFSQKIIDMMAWFGFELGK FT GLGAKLQGIVEPIQPVRHSTTFGLGYKYTTEEWLDWRPPRDGYYYPLKKPI FT PPLYQSF*SAGFMGDNIDEISDDLKGLSLTKEEGKVCNVVINEEEKGGPSG FT SKEAKISVSNWTSTPSRPRRASGFYYFFFLTSKIHYKNVESEIVAYNETAQ FT LNLNDLEEVEDNEVPEELIKRVEEFEEKPNPNLVETEVVNLGNAEVIQETR FT VSIHMTKEDKKEYTEFLIENKDIFAWSYADMTGLSTAIVAHRLPTDPACPP FT VKQKLRKYKPEMSLKIKEEVSKQLDVGILQVTEYPTWLANVVPVPKKDGKV FT RVCVDYRDLNKASPKDNFPLPNIHILIDNCAKHETQSFVDCFAGYHQIEMH FT KDDAEKTAFITPWGVYNYKVMPFGLKNAGATYMRAMTTLFHDMIHKEIEVY FT VDDVIIKSKESLNHLEDLRKFFARLRKYNLKLNPAKCVFGVPAGKLLGFIV FT SRRGIELDPSKIKAIRDLPPPKSKKEVMSFLGRLNYISRFIAQSTVICEPI FT FKLLKKDAAVKWTSECQQAFDKIKDYLSNPPVLVPPESGRPLLLYILVLDN FT AFSCILGQHDETGRKEQAIYYMSKKFTSCEARYSLLERTCCALTWVA*KLR FT HYLSSHTTYLISRMDPLKYIFQKPMPTGKLAKWQILLSEFDIVYVTQKAVK FT TQALADHMAENPVDDDYRPLKTYFPDEEVAFVGEDISEEYDGWRMFFDGAK FT NLNGCGIGAVLISPTGQHYPVSAKLRFLCSNMAEYEACILGLRRAIDLDV* FT EMIIIGDSDLLIHQVRGDWATKNRKLLPYLECVRRLCKRFVKTEFRHVPRV FT QNEFADALATLSSMIRHPDHNYIDPIHIHIHEQPAYCFHVEEEPDGKPWYD FT DIRRYLKSGEYTEDATSVQKRTIRRLATQFFLSGEILYRRTPDLGLLKCVE FT AREARRLVEEIHAGTCGPHMNGFTLAKKILRSGYYWLTMETDCIRYAQKCH FT QCQTHADMIRVPPNELHVTSSPWPFAAWGMDVIGPIEPTASNGHRFILVAI FT DYFTKWVEATSHKSVTKKVVDDFVKNNIICRFGIPESIITDNGTNLNSDLM FT RSMCEKFKISHRNSTAYRPQMNGAVEAANKNIKRILRKMIDNHKHWQEKLP FT FALLGYRTTIRTSTGATPYFLVYGTEAVIPAEVEIPSLRIIQEAKLSDADW FT IRGRAENLALIDGRRINAICHGQLYQNRMARAFNKKVKPRHFSPGQLVLKR FT IFPNQDEAKGKFSPNWQGPYIVSRVLTGGALILAEMDGEVWPKPINSDSVK FT KYYV" XX SQ Sequence 12262 BP; 3670 A; 2686 C; 2464 G; 3442 T; 0 other; gaatggcgac tctgctgggg atgttaggtt cttaccatta cgtgttaact gcttatttat 60 gtggggttta ttttatttat taggtgctta ccatgttttg ttgccctatt tattatctca 120 tcttcatgtt cctccctttc ccttttcctt aattgtttat tatcatgttt cacctcttcc 180 ctctcccctt atttgtttac atgtttaatc tcgtatcctc ttgttttatt tgcgtagttt 240 tcatgtctac tttcctttat ttatgcttat ttatttattg tttataaact gtctatatgt 300 taccgttttc caatttaaat gctaaatgtt tactgcttta ataaattggc atcccgctca 360 tacttccccc caattgggac cctcttcctt ttttattttg ttctcgtgat gttgtgcctt 420 tgcacctctc acaactactc caatcttata caaataccca ttatagagag tcggcatatg 480 cgtggacgta gtggatagtt ttactaccgc gaagccacga gcctctcgca tagaatccct 540 ttcaagtccg tgtcaagcca actcttagaa gtcctggtta agtcatacat gctgcataag 600 acctaggagg tttgaccctt ggtgtcaatc catgtaatta gtagccacct tctcgtctga 660 agggccccaa aacccttaga caaattgcat atttatgtgt caacgtgatc ataataatta 720 aatcaagcca acattgccaa aatggagttt agaagttgtt tgttactttg tttgcagagt 780 catgactcac cctcactttc caaacacgca aatggtggtc aaagttaatc ccattttgaa 840 gacttggtgg aaagatatac aaaaaaatcg agagttagaa gcaaatgaat tgttaggcgg 900 cctcactgct ttgatctccg tagagtcaga tcgtcactta atcaaggcat tgttgaaatt 960 ctgggacact gagaggttag tcttcaagtt cagggatttc gagctaactc caacaataaa 1020 agaagttgga ggattcatgg gtctcgcata caaagagttg gaaataattg ttccacacaa 1080 gccaagtcca agatcttttt tgaagcaaat gggcatgtgt cataatccaa atctactttg 1140 tctgaaagaa ggttggattt ctttagagtt cttatattca cgctttgggg atgaggaagg 1200 tcatcaaaac tttcatagag aatttgcttg ctcttctgca aaatgggaaa ggtatcgtct 1260 taatgcattc gctgtcgtcc tattaggctc attggttttt cctagagaag gaggaaagat 1320 acacaccggc ttatgttatg tggttcgtat gttggctcga ggtgggaaaa ccttggtccc 1380 tatgatactc gcagaaattc taagagcttt gactgcatgc accaaaggca aaagatactt 1440 tgaagggtgt aactttctgc tgcaactttg ggccgtcgaa catttctacc aaagagctaa 1500 taaagtagac atcgtcagat ggactatggg gaacaaaatt atcaaccatc ccctaaggat 1560 gaaacatttt atctcccctg tgggaacaga ggactggttc acatacctaa aggagcggtc 1620 agccgttgaa atccaatgga agtattattg gttgaagcca cgacgtgcca tcataagagg 1680 aaatgaactt tacttcattg agcttatcgg tttgaacggt gtgcaaccct acgcaccact 1740 tcgagtcctt cgacaattcg gacagatcca aatgatacct ctacgatccc acatgagcca 1800 ctatggatat gactttgggt cagaattacc gcaagtgaac accatactac gaagatggaa 1860 gaatgtgata actatcgatg ttcaagagca ccgacccttc tgcacacctg aatattatgt 1920 atggctttta gaagatgcag agcatagaga tttaagcgaa ggaggtcttc ctggttttgg 1980 cgatgaaaaa gagagaagat gggctcgcaa cctcctcaac actgattatg acattaccct 2040 agaaatgaag aagcagattg tgcctaacat tggagagcaa catgattaaa gcttttaatt 2100 attatttatt tctctttact ccccatatgt tatccctagc cctttagtta tctttagatt 2160 gatgtaataa acagaaatta tttcaataat cgaaagttgt tctattatct aactctaaac 2220 tccaaattgg caaataaggc ttgaattaat tattatgcat cacttatgtg tcgcttaggc 2280 ctacctctgg ctcaacgagg ttccttgcat ttagggcgtt tatttcaaaa caacgtgttg 2340 atattgtgat attatcttaa cccctaactc ttttcttttg attctattgt tttcacattt 2400 cctaaggttg atctgtcctt catcctggca catacacgat caaaagggac ccccccttct 2460 ccttcttctc aaagagcaag ctcaaacgac aaaggaaaaa tggttgacga caacagcacc 2520 actgaaaggg tagaagcttg tgagggagga caacttcata gtaatcttat cctaagactc 2580 gagcgcaaga tttcgcaatt ggaagaagag gtagccaaca tgcgtgattt ggccaagttg 2640 tctatctctc ttggaaccca atttggagaa aacatagaca atcctcctaa tcaaacagcc 2700 acgccagaca atcctccaat ccatatatcc ccacctgaac ccattcgtcc aaatgccttt 2760 ccaccacccc acgcccaaaa tacccaattt ccatttcacc actattacca acataccaaa 2820 ccaactgtcc cagaaacaac cccaaacaca aatatcccac atacttttga aaacaacaat 2880 cccaatccca tatacgttga aactgcccct ctgactcatg acctccatga gtcagagtcc 2940 catcagaaag acatcttaat aaaaaccctg actgagagat tagacaactt gaccaacagg 3000 gtacaacacg tggaaggaaa caaaaagttg ggaggattgg gctatgaaga tctgtgcatg 3060 catcctgatg tggaactgcc cgaaggatac aagcttccga agtttgagac gttcaatggc 3120 attggggatc ccaaagccca cctacgaatg tattgcgaca aacttgtagg ggtgggaaga 3180 gatgagagga tactcatgaa gttgttcatg aggagtctta ctggggaggc cctatcatgg 3240 tacattgagc aagactcgcg gaaatggata aaatgggttg atatggcaac tgacttcatg 3300 aataggtttg gtttcaatat tgaaaatgcg cctgattggt tttacattca gaacctaaag 3360 aagaaaccga gtgaatcctt cagagaatat gccataagat ggaggtctga ggcggctagg 3420 gccagacccc ctatggaaga atctcaaatg aaagactatt tcatccgtgc ccaagaacta 3480 caatactatg accgaatgat gctggtggct gaaaagagtt tcgctgaaat catcaaacta 3540 ggcgaaagaa ttgaagaagg cataaagaat gggactatca tcaacttgga ggctttacaa 3600 gcaaccaaca aggctctgca atctggtgga atgacagaga gtcgaaagaa aacaggttct 3660 gtaatgatgg ctcatggaac taggacccct ttgaggcaca agacaacaaa cccaccacca 3720 tccccatacc ctcacacccc ataccttcac accccatacc ctcaacatcc ctcagctcca 3780 ccccctatat ctccccaacc catgccaata tattaccaaa atgctcctcc tcaatatttg 3840 catgcctcat atcctgtcta taatgttcaa ccaacacact tctaaactcc accacccact 3900 caaacaccaa attaccgaaa cagaccttcc tatgaaagaa gacctacaaa aacctatacc 3960 cctttggctg aacccatagc acaactttat gagagactga aacaagctgg gtacgtctct 4020 ccaattcctg cattacctgt ggacgttcgc gcgaaatggt acgaccctaa caaggtctgc 4080 gcctaccatt ctgggatgaa gggccacacc accgaagttt gcagagccct taaggataag 4140 gttcaaatgt tgattgatac aaagaccatc caactgaagg atcctacacc gaatgttgcg 4200 aataatcctc tccctaacca tcaagtcaac atggtggaag ctggtgatgt ctgggattgg 4260 gaagaatcta tctgggccgt cgaaacagag gaagccatgc ctaccactgc ccaggcacca 4320 ctaatagtgc aaggactcgc cccatttgaa gtagaagttg ctgcacccag accaccattc 4380 gctgtctata aggcatcctc cccaacacaa tgtgacacac atgctgtacc ttgggattac 4440 aacaaaagag aaacaaatgt ggaagagaca gatgttgcaa caggggtcac cagatctgaa 4500 agaatttaca cttctgaaaa tttggttcag ggaagctcta gcaaatccaa agcgccaatc 4560 gtagagctcg aggatcaaag tatttggaaa aaggttaaag ctaaagaata ctctgtcatt 4620 gagcagctga gtaaaacccc ttcccaaata tcaattctgg agttactaca atcttccgaa 4680 actcatcgag atgcccttct gaagatcctt ggtgaagctt atgtcccgtc taacatcact 4740 catggagagg tatcccaaat ggtggggcag gtctttgagg cttacaaaat atcttttcac 4800 aaagatgaac tgccaatcga aggaacaact cacaataaag ctttgtacat ttcggttcag 4860 tatcaggata aggtgataaa caaagcatta gttgatgcag gttcaggttt aaacatttgc 4920 cctctgagca cactgacgag gctgggtgtg gatagtgcaa aaattcagac atggaagatg 4980 aatgtgaggg catttgacgg ctctcagaga ggcactattg gggagataac cttggacatg 5040 ctcattggtc ctgtcacttt ccccatagct ttccaaattt tggacatccc ttcatcgtac 5100 aacttattat tgggtcgtcc atggattcat atggctggag cggttccatc tactcttcac 5160 caatgcctga agtttgaatg ggattacgaa gaggttgtgg tccatgggga aaaagggcat 5220 cctgtataca cgattgaagg aagagagaat atggatggcg aaatgtacca tacagtggag 5280 cttgttggta atattgagtt gcaaccttgg ttcagccaaa aaatcataga tatgatggcc 5340 tggttcggtt tcgagcttgg gaaaggtttg ggggctaaat tacaagggat agtcgaacct 5400 atacagcctg ttcgacattc caccactttt ggtttgggtt ataaatacac caccgaagaa 5460 tggctcgatt ggcgaccacc tagagatggg tactactatc cattgaagaa acccataccg 5520 ccattgtatc aatcattttg atcagcaggt ttcatgggag acaatattga tgagatctca 5580 gacgacttga aggggttatc gctaaccaaa gaagaaggga aagtttgcaa cgtcgtgatc 5640 aacgaggagg agaaaggggg ccctagtgga agcaaagagg caaagatcag cgtcagcaac 5700 tggacctcga ctccatccag acctcgtcga gcatctgggt agctttggaa gatgtttttc 5760 tatcaaattt taattcaaat aaaggagttt ttaataaacg ttttaattcc cgtccatgta 5820 ttgctttcaa atgaggactt atgaaatttt caaatcttta tcaataaagt tcttttcccc 5880 atttttttgt cttgtattta atttttacta tttttttttt ctcaccagca aaattcatta 5940 taaaaatgtc gaatctgaga ttgtggcata caatgagact gctcagctta accttaatga 6000 cttagaagaa gtcgaagaca atgaggttcc cgaggagtta atcaaaaggg ttgaggaatt 6060 cgaggaaaaa cccaatccaa atttggtaga gacagaagtg gtgaatttgg gaaatgcaga 6120 ggtgatacaa gaaacccgag taagcatcca tatgacaaaa gaagacaaga aagagtatac 6180 cgagtttctc atagagaata aggatatttt cgcgtggtcc tacgcagaca tgacagggct 6240 aagtactgca atcgtagccc atcgactacc cactgatcca gcatgtcctc cggtaaaaca 6300 gaagctgaga aaatacaagc ccgagatgag tttgaaaatc aaagaagaag tatcaaagca 6360 attagatgtt gggatactcc aagtgacaga atacccaact tggcttgcaa atgtcgttcc 6420 agtgcccaag aaagacggca aggtcagagt ttgcgtggat taccgagatc tcaataaagc 6480 tagccctaaa gataactttc cattaccaaa catacacata ctgattgata attgtgctaa 6540 gcacgaaact cagtcatttg tggattgctt tgccggctat catcaaattg agatgcacaa 6600 agacgacgct gagaaaaccg ctttcatcac gccgtggggc gtctataact acaaggtgat 6660 gccttttgga ctaaagaacg ctggagctac gtacatgaga gcgatgacta ctttgtttca 6720 cgacatgatc cataaggaaa ttgaggttta tgtggatgat gtcatcatca aatcaaagga 6780 aagtttaaat catttggagg atttacggaa attctttgcc aggctacgca agtacaatct 6840 gaaactgaat ccggcaaaat gtgtcttcgg tgtgcctgct ggaaagcttt taggtttcat 6900 tgtcagtcgt cgaggtatag aattggaccc gtcaaagatc aaagccattc gtgatcttcc 6960 cccaccaaag agcaagaagg aggtaatgag tttcttgggg cgacttaact acatcagtcg 7020 tttcattgct cagtctactg tcatctgtga acctatcttc aagctgttaa aaaaggatgc 7080 tgcagtgaaa tggacaagtg aatgtcaaca ggcatttgac aagatcaaag actatctatc 7140 caatcctcct gtattggtgc caccagagtc aggtagacca ttacttttgt atattttagt 7200 attggataat gctttcagtt gcatcttggg acaacacgat gaaacaggga ggaaggagca 7260 agcaatatat tatatgagca agaagttcac gtcgtgcgaa gcccgatact ctctattaga 7320 gcgtacctgt tgtgctctaa catgggttgc ctaaaagcta cgacattacc tctcatcgca 7380 taccacttat ctgatttcaa ggatggatcc tttgaagtat atctttcaaa agcctatgcc 7440 cacaggtaaa ctggcaaaat ggcagatact gttgagtgag tttgacatag tgtatgtcac 7500 gcaaaaagca gtgaaaacac aggcactagc agaccatatg gcagagaatc ccgtggacga 7560 tgattacaga ccgctgaaga cctacttccc agatgaagag gtggcgtttg tgggagagga 7620 catttctgaa gaatatgatg gatggagaat gttttttgat ggagctaaaa atctgaatgg 7680 atgcggcatt ggggctgttt tgatctcacc caccgggcaa cattatccag tatcagcaaa 7740 actcagattc ctttgctcaa aaatatggcc gaatacgaag cctgcatact aggtctccga 7800 cgggcgatcg acttggatgt ctaggaaatg ataataatag gggattcaga cctattgatc 7860 catcaggttc gaggtgattg ggcaacaaaa aatcgaaagt tgttaccata tttggagtgc 7920 gtgcgcaggc tatgtaaaag gtttgtcaaa acagaattta gacatgtacc aagggtccaa 7980 aatgaatttg cagacgcctt agccactctg tcttctatga ttcgacaccc tgatcacaat 8040 tacatcgatc ctattcacat tcatatacat gaacaaccag cttattgttt ccatgttgag 8100 gaagagcctg atggaaagcc ctggtatgat gacattagaa gatatttgaa gagtggtgaa 8160 tacacagaag atgcaacaag tgtacaaaag cgtacaattc gaaggttagc aacccaattc 8220 ttcttaagtg gggaaatact ctatagaaga actcccgatt tgggactgct aaaatgcgtt 8280 gaagcaagag aggctcgcag gctggtcgaa gagatacatg caggcacctg tggtcctcac 8340 atgaacggtt ttacattagc aaagaagatt ctgagatcag gatattattg gctaactatg 8400 gagacagact gcattcgcta cgcccagaaa tgccatcaat gtcagactca cgcagatatg 8460 attcgagtac ctcccaacga actccatgtc actagttcac cttggccgtt cgcagcatgg 8520 ggcatggatg tcattggtcc aatcgagcca acagcatcca acgggcacag attcattctt 8580 gttgcaattg actatttcac caagtgggtt gaggccacct cccataaatc agtgacaaag 8640 aaagttgtgg atgactttgt caaaaacaac attatttgta ggtttggaat tcctgagtca 8700 atcatcaccg ataacggcac caacctaaac agtgacctga tgagatcaat gtgtgagaag 8760 ttcaagatca gtcatcgaaa ctctacagca tacaggccac agatgaatgg ggctgttgag 8820 gcggcaaaca aaaacatcaa aaggatattg cgcaagatga tcgataatca caaacactgg 8880 caggaaaagt tacctttcgc attgctgggg tatcgtacca caatcagaac ttccacaggg 8940 gccacacctt acttcttagt atacggcacc gaagctgtga tacccgccga agttgagata 9000 ccttccctaa ggatcatcca agaagcaaag ttgagtgatg ctgattggat acgaggtcgg 9060 gcagagaatt tggcattaat agatggaaga agaattaacg ccatttgtca tggtcagctc 9120 tatcagaata gaatggccag agctttcaac aagaaggtta aacccagaca tttctcacct 9180 gggcaactgg ttttgaagcg gatttttcca aatcaagacg aggcaaaggg taaattttca 9240 ccaaattggc aaggtccata catagtctct cgagtactga caggcggagc cctcatactt 9300 gcagaaatgg atggagaagt ttggccaaaa cctatcaatt cagattctgt gaaaaagtat 9360 tacgtctaga gattgattca tgctcttttg taatttggaa ctacgtcaga cctgattccc 9420 atttaagagg ggatacgtag gcgctcctat ggggttcggt cttattataa ataaaacttt 9480 catttctccc ttttctactg ataactgggg cagaattttt gagaggatct caaaaattcc 9540 atcaagactt ctcctggcac atcttcatac tggggcagaa attttgagta aactcaaaat 9600 ttcaccaaaa gtttcttctc aacaagcagt cagcttacaa cgaagattaa atgatagctc 9660 cacttttgag tcagacgttg taaagtctca acctatgcca tggtcaaaga ttcgacatca 9720 gcttttatta aatgataatt tcaaaatctt tgaaagtttt gtttttatta ttattatttt 9780 ttctctcctt ttcccttttt ttttatgaaa aaaaaaaaca aacgctcgaa gaggtgtgga 9840 tggcaagcca aaggagcacg ctgcgccaaa tcacggatac agatcaacct tcccccgttt 9900 aaactaacta tttttctttg aatgtagaaa atacaggtac atatacaaag gcaactgcaa 9960 caatcaacat cacaacattt gagcccgaca tatgacactc gatccttcca ataaggcgga 10020 cgcccaagct actgtatgcc ctcaagcaac tactgtgctg acaaattaca ttatgcccga 10080 tattgcatca tttcgcacct acgcttgata tcaccctatg ctcaaagaac tacatcatta 10140 tgttatgccc gagaatgccg aaatgcatca tttcatgtgc ttgacatcgc atgatcccga 10200 agaaacacat tattgcacgt gctcgatata tcatatgccc gaggaaatac atcatcgcat 10260 atgcccaata ttgacttatg ctcgaagaac cgcattattg catgcgctcg atattttatg 10320 tgcccgaaga aatgcatcat tgcatgtgct cgatatttca tgtgcccgag gaaacacatc 10380 atcgcatatg cccaatattg acttacgctc gaagaattgc attattgcat gcgctcgata 10440 ttttatgtgc ccgaagaaat gcaccattac atatgctcga tactgcatgt gcccgaagtt 10500 tgcataagct caagattgca tcgtgctcga agtttacatg tgcccgaatc aaatcaagtc 10560 ataagtatca acagacgtca aaaacagata cgctctcttt actcattagt tatattccaa 10620 aggcgtcatc ctccaaaggc gtcatctttc atggcctgcg gacttcatgt catgacctga 10680 ggacttattt tatgcatatc atgttcctaa ggcgtcatag tctaaaggca tcatcctcat 10740 ggcctgcgga catcatatca tggcctaagg gtttaatttc tgtctatcat gatccgacgg 10800 tgtcatagtc taaaggcgtc attttcatgg cctacagaca acatttttca tgacctgagg 10860 atacaccctg catatcatgg ccctagacat catagcctaa gacgtcattt tttcacgatc 10920 ttaaggcaaa cattcatggt caacatggga attgcatcat gtttacattt accgtttatt 10980 ttgatgtgta tgttctaatt actctacata ggttatatta caagttacag atgtgcagat 11040 tacagacaaa gtcgcctttt gaacggctgt tcacttgttt acaagcgacc ctccgacaaa 11100 ttcctggcta ctcgcaccat catttcactc ttcatctatc attcaggcta ccatgaagat 11160 atcttcagat tcaattcgcc actgtgacct actgtctctt catctaggct cgtccgcctt 11220 acaatgcgac atctaggttc gtccgcctta caatgtgaca tctaggttcg tccgccttac 11280 aatgtgacat ctaggtttgt ccgccttaca atgtgacatc taggctcgtc cgccttacaa 11340 taggatattt aggctcgtcc gcctcaaaac gacatttagg tttgtccatc ttatagaaca 11400 tttaggtcgt ctatcttaaa gggacattta ggcttgtccg cctcatagga catttaggtc 11460 cgtccgctta taagatattt tgttcgcttt ataaaacatt taggctgtct gccttaaaac 11520 gacacttagg ctcgtccgcc ttaaaatgac gtttagattc tccatataac tagatatttt 11580 cgtctattaa tatatcttta tagtgtcaaa tctattggag tttgacatca ttcttcagag 11640 atgggttcaa tttttcaaga agttacagac aatcaaggct tgcagtacgt ctcaaacaga 11700 tacgcctttt atcacctctt gtctatttaa tagaactcat attttattat tattggtcat 11760 actttattta tttataagct aacattttat ctagaatttg cagatatgat cgatcgcctt 11820 tgatcacaat tatatcgcta tcctctatca attcttcgcc tttcatactc cgaacccttg 11880 ttcagatgtt gataacccca ctctatcatg ctcttcacgc ttctctgtca tactctttta 11940 gcctctcaat ctctctcttc tcgttactct aatcttatcc attcaagccg atatcgtgcc 12000 ttccaaatac cttaccactc tttcaacttt taagagtttc atttgctctt gaatctagaa 12060 ctacacacga cctgattctc gtataaccag agatatgtag gcgacttaaa accaaagtct 12120 cggtcgtacc cttttttttt caactctact tcgcttcaat tgatccgctg acatctgtcg 12180 tcggtcggac aaaatcggct actaagtcaa cgttggttgc ctgacaattc attcttcatt 12240 ctcaatcaac caaggggcag ct 12262 // ID Gypsy8-VV_LTR repbase; DNA; EDCOT; 392 BP. XX AC . XX DT 10-SEP-2007 (Rel. 12.09, Created) DT 01-OCT-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy8-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-392 RA Obukhanych T. and Jurka J.; RT "Gypsy8-VV."; RL Repbase Reports 7(9), 833-833 (2007). XX DR [1] (Consensus) XX CC This is a 5' LTR sequence of Gypsy8-VV LTR retrotransposon from CC Vitis vinifera. LTRs of this retrotransposon are 96% identical. XX SQ Sequence 392 BP; 119 A; 53 C; 85 G; 133 T; 2 other; tgatgagcca agaagatcgc aacgtgttcc taagaaaaac ccaaggttca taacatgata 60 aacatgcaga gcaagtagga tgatcgtgca aggagctgtt agagattaat tgctggcata 120 gttctattag aagacttggt ctgatgtctg ttagctatta ttatgctatt tgaataagta 180 ttagctattt atttgctaat aatggttgag tccttatttt cagtagttat ggtcgtgaga 240 gtaggagaag gtgggttttt ccttgtatat ttaaactatt tcagtatgca gcaagargga 300 gaagttcatt traaatccaa atattgtggt tcattctcac ccgaagaaga attctattta 360 ctgattatat tagctttgat tgggacctat ca 392 // ID LINE1A1_MT repbase; DNA; EDCOT; 5657 BP. XX AC AC122166; XX DT 10-NOV-2006 (Rel. 11.11, Created) DT 06-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE L1-type family from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; LINE1A1_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5657 RA Jurka J. and Shankar R.; RT "LINE1A1_MT: LINE1-type family from Barrel Medic."; RL Repbase Reports 6(11), 571-571 (2006). XX DR EMBL/GenBank/DDBJ; AC122166; Positions 94200 99856. XX CC This is a relatively new sequence. TSDs haven't been found. It CC may be 5'-truncated. XX FH Key Location/Qualifiers FT CDS 746..1813 FT /product="LINE1A1_MT_1p" FT /translation="MIDGQLVDIKIVEEWGVNVGEDACLFEEEDEQQSQSD FT IKEVFRDPETSKNFNVAVDEIVKELEAEELHNVSELREEVGACVDVVDVNP FT EDTSDVGPIINLDNGKGATTQSSTVPGVVRKLSDGKDMANFDGESLPEVSV FT LNLVNQAGVVDSGGVGRGRRSGSKSVGDRHAISASGPPFDGKSVLSGPWST FT EWLKDHHGGVGISFSAKRKFIKVGKRKVQKSQEGVDATKRRKIGGELRHTV FT HTLKKVARLSSKDRNAVLRTLKRRASKKKQPSGVEGSQGNSDEVSSFASVN FT KEWNNWVVLHGKEKEAAEDVWGIGKAFGLQFQGDIHNMFGALARKGEGKKD FT SKRSVEGGSGAAK" FT CDS 1857..3683 FT /product="LINE1A1_MT_2p" FT /translation="MRIVSWNVRGLGGLEKRREVKELVREKKPFVLCIQET FT KLEVIDEFICTSLWGPTNHDFSFSPSVGASRGMVTIWDRVEVEVWSTVRGV FT HFLLIHGRFLKSNEEFYIFNMYAPCDRRAKQVLWNSLSSRLLSLGSSKVCV FT CGDFNTVRSVDERRSVRGSQVVDDCAPFNDFIEDRVLINLPLCGRKFTWYN FT GDGRSMSTLDRFLLSEEWCMVWPTCLQVAQLRGLSDHCPIVLTVDEKNWGP FT RPVRLLKCWQDMPGYSDFVREKWGSFQVSGWGGFVLKEKLKLMKAALKEWH FT VANTLNLPSKIVSLKNRRAVLDSKGEEEELSEEELGELHGISSDIHSLSRL FT NTSICWQQSRLNWLRDGDANSKFFHSVLAARRRINSLSSILVDGVVVEGVQ FT PVRQAVFTHSKNHFLAPIMTRPSVGHLQFRKLSSVERGGLIKPFHEEEIKA FT AVWDCDSYKIPGPDGINLGFIKSFWHEMKAEIVRFVTEFHRNRKLSKGINS FT RFIALIPKVASPQSLNEFRPISLVGSLYKILAKILANRLRQVIGSVVSEVQ FT SAFVKNRQILDGILITNEVVDEARKSKKDLLLFKVDFEKAYDSVDWGYLDE FT VMGSMTFPTVW" XX SQ Sequence 5657 BP; 1389 A; 722 C; 1729 G; 1816 T; 1 other; aagggttggt gatggagtta agtttgcgaa agatgtaggc aaaaggttat ggaacgggaa 60 agggcgtgag gaggagggaa atggtgttgc ggaagagcgt tgcgttaaag tggtgagggt 120 aggggatgtg gttgtgacga ttcgtgatgg taaaggaaat tatggaaagg aaagggggac 180 tagtgttgat gatggtaaga tggggacaat ggctaaggga tcgacggaga atgagttatt 240 tgttgtggag aagcagcaac cggatgctaa gaagatggta cggatgtata ggtcgaaagg 300 agatgattta aaatgggcac gttcaggtgt tttggctaaa gtggtgaatg gggaggtgat 360 tacggtggtt caaaatagga ttgaagatgc aggcttcgtg aaccttgaca tcattccttt 420 gggagcggat agagttttct tacgaagttc atcggagaag gatattttgg ctatgcttgg 480 ggaggcgaaa gatttttttg atcatttttt tacgaatgtg gttcgttggg ataaggaagt 540 ggtacctttt cgttggggtg cttgggtgag attgtatggt attcctattc acgcttggag 600 cgaggatttt tttaaattat gtgtgatgga ttgtggatat tatttgcgta ctgatgagtt 660 gtcgttagat agggtaagat ttgatttcgt gtgagttctt atttcaacgt cctctttaga 720 gtctatctct tgtgttgatc gactaatgat agatggtcag ctggtagata ttaagattgt 780 tgaggaatgg ggtgtgaatg tcggggagga tgcgtgcctt tttgaagaag aggatgagca 840 gcaatcccag tcggacatta aggaggtttt tcgtgatccg gagacgagta aaaattttaa 900 tgttgcggtt gatgaaattg tgaaagagtt agaggctgag gaattgcata atgtttctga 960 gttaagggaa gaagtgggtg catgtgttga tgttgttgat gttaatcctg aggatacgtc 1020 agatgtgggg ccgataatta atctggacaa tgggaagggt gcaacaacac agagttcgac 1080 agtgcctggg gtggtgcgaa agttgtcaga tggtaaggat atggctaatt ttgatgggga 1140 atcgttacct gaagtcagtg ttttgaattt agttaatcaa gctggtgtgg ttgattcagg 1200 gggtgttggt cgcggtagga gatctggttc taagtcagta ggtgataggc atgccatatc 1260 cgcgtctgga cctccatttg atggtaagtc ggtgttatcg gggccgtgga gtacagaatg 1320 gttgaaggat caccatggtg gcgttggaat tagtttttct gctaaaagga agtttattaa 1380 agtagggaaa agaaaagttc aaaaaagtca ggaaggagtg gatgcgacta agcgcaggaa 1440 gattggtggg gaactgcgcc atacggttca taccctgaaa aaggtggcac ggttgtctag 1500 caaagataga aatgctgttc tacgaacttt gaaaaggaga gctagtaaga agaagcagcc 1560 ttctggtgtc gagggctcgc agggaaactc tgatgaagtt tcttcgttcg cctcggtaaa 1620 caaagaatgg aacaattggg ttgtgttaca tgggaaagag aaggaggcgg cggaggatgt 1680 gtggggaata gggaaggctt ttgggttaca atttcaaggg gatattcata atatgtttgg 1740 agcgcttgca aggaaagggg aaggaaagaa ggattctaaa agaagtgttg agggagggag 1800 tggtgctgcg aagtaggggt agggggttgt aggtgttggg ggggggggtg tgtgcgatga 1860 ggattgtgtc ttggaatgtt cgggggttag gcgggttgga aaagcgtagg gaagttaagg 1920 aattggtgcg ggaaaagaag ccttttgtgt tgtgtattca agaaacaaag ttggaagtta 1980 tagatgagtt tatatgtact tcgttatggg gacccacgaa tcatgacttt tcttttagtc 2040 cgtctgtggg ggcgtctaga gggatggtta cgatctggga tagggtggag gtggaggtct 2100 ggtcaactgt tcgaggtgtg cactttctgt tgattcatgg caggtttctt aaatctaatg 2160 aagaattcta tatttttaat atgtatgccc cttgtgatcg gagggctaaa caagtgcttt 2220 ggaattctct ttcttcgagg ttgctttctt taggtagtag taaggtttgt gtgtgtgggg 2280 attttaatac tgtgcggtca gttgatgaaa ggcgctctgt taggggttct caggtggttg 2340 atgattgtgc accttttaat gattttattg aagatagagt tttaattaat ttaccgttat 2400 gtgggaggaa gtttacttgg tataatgggg atggccgttc gatgagtaca ttggacaggt 2460 tcttgctatc tgaagaatgg tgcatggtgt ggcctacttg tcttcaggtt gctcagttaa 2520 gaggattatc tgatcattgc cctattgtct tgactgtgga tgaaaagaat tggggtccgc 2580 ggccggtgcg tcttttgaaa tgttggcaag atatgcctgg ttatagtgat tttgttcgag 2640 aaaaatgggg ctcttttcaa gtgtctgggt ggggcggttt tgttcttaaa gaaaaattga 2700 aacttatgaa ggcggctctt aaagaatggc atgttgccaa tactcttaat ctaccgtcta 2760 agatagtttc gttaaagaac agacgagcgg tcttagatag taaaggggag gaggaggagt 2820 tgtcagagga agaactaggt gaacttcatg gtatatcgtc ggatattcat tctttgtctc 2880 gtcttaacac aagtatttgt tggcaacaat caagactaaa ttggcttcgt gatggtgacg 2940 caaattctaa attttttcac tctgttttgg ctgcaagaag aagaattaat tctttgtctt 3000 cgattttggt cgatggggta gtggtggagg gtgttcaacc tgtccgtcaa gctgtgttta 3060 cgcattctaa aaatcatttt cttgccccaa taatgacgcg gccgagtgtg ggtcaccttc 3120 agtttcgaaa gctctcttcc gttgaaaggg gaggtttaat taaacccttt catgaggaag 3180 aaattaaggc agcggtgtgg gattgtgaca gctacaaaat tccgggtcca gatgggatta 3240 acttgggttt cattaagtcc ttttggcacg agatgaaagc agaaattgtg cgttttgtta 3300 ccgaattcca taggaatagg aaattatcga aaggtattaa ttctaggttc atcgccctaa 3360 ttcctaaagt agctagtcct caatcgttga atgagtttcg ccctatttct ttggtgggga 3420 gtctgtataa aattttagcg aaaattctag caaacaggtt gagacaggtt attgggagtg 3480 ttgtgtcaga agttcagtct gcttttgtta aaaacagaca gattcttgat ggaattttga 3540 tcactaatga ggtggtcgat gaggctagga aatctaagaa agacctttta ttgtttaaag 3600 tggattttga aaaggcgtat gattctgttg attgggggta tcttgatgaa gttatgggaa 3660 gtatgacgtt tccgacggtg tggtgaaagt ggattaaaga gtgtgttggt accgctactg 3720 cctctgttct tgtgaatgga tgtcctactg atgagttttt tcttgaacgg ggtttacgcc 3780 agggtgatcc tttatctcct tttttatttt tattggcagc agaaggattg aatgttttga 3840 tgaaagcgtt ggtagacgca ggattgttta aggggtatag tgtggggcgc gcggatcctg 3900 tggttgtgtc acatttacag tttgctgatg atacgcttct tattgggaat aaaagttggg 3960 ctaatgtgcg ggcgttgagg gctggactca ttttgcttga agctatgtcg ggattgaaag 4020 ttaattttca taagagttct ttggtagggg ttaatattac tggttcgtgg ttgtcagaag 4080 cggcttccgt gttgggttgc aaagtaggta aaatcccgtt tctctatttg gggctctcga 4140 ttgggggtga tccgcgtcga ttattgtttt gggaacctgt tgttaatcgc attaaaaata 4200 gattgtctgg ttggcaaagt cggttccttt cttttggtgg tcgtttggtt cttcttaagt 4260 tcgtcctgac tgctctacct gtctatgcac tttccttttt caaagctccg tcaggtataa 4320 tctcttccat tgaatctttg tttaataaat ttttttgggg agggggtgag gataaaagaa 4380 aaatttcatg gattaggtgg gatactttga gtttgaggaa ggagtatgga gggttggggg 4440 ttacgaggtt gagagagttt aatttagctt tgttgggtaa atggtgttgg cggttgttat 4500 tggagaagga agctttgtgg agaaaggtgt tggtggctag gtatggtgtg gcggatggag 4560 gtttggagga tgggggccgg agttgttctt catggtggag ggagatagtg aggattagag 4620 atgggatagg tgagggtgga gagggttggt ttgggtcttg tgttaggagg agggtgggag 4680 acggtgcaga gacagatttt tggtgggatt gttggtgtgg agatgtttca ttgtgtgaac 4740 ggtttagtcg cctttatgac ttgactgtga acaaactaat ctctgttagg aacatgatct 4800 tgttgggggt ggatgtcggt ggggaggcgt tgaggtggcg taggcggttg tgggcttggg 4860 aggaagagtt ggtagaggag tttanggctt tattactaac agtttcattg caggaatcag 4920 tgacagatag atggatttgg ttaccaactc aggatgatgg gtattccgtt cgtggagcct 4980 atgacatgct gacatcacag gagcagcctc acttacatca aaacttggag ttaatttggc 5040 atacacaggt tcctctcaaa gtttctatcc ttgcatggcg acttctgagg gatcggttac 5100 ctacaaaaga taatttggca aaccgtggca ttttacctct ggaggcgcgg atgtgtgttt 5160 ctagttgtgg gaatgaagaa gatgttaatc atttgttttt gtcttgtgca acttttagtg 5220 ccttatggcc attggtgcaa gcatggcttg gagtggtagg ggttgactct caatcaactt 5280 cagatcattt agtgcaattt attaattatg caggatgttc gagagggcga tgttccttct 5340 ttcatttgat ttggctgctt gttgtttcgg tgttgtggaa tgataggctt tttagaaata 5400 gacaaagttc tttgccacaa atgctagata aagtgaaatc aacttctttg tggtggttaa 5460 aggcttgtaa tgttgttttt agttttggta ctcaccagtg gtggtcgagc ccgctttctt 5520 gtttgggtat tgactgattg gatgtattgt tgtttggaac ttgacacttt tgtgattttt 5580 ttggcacacc ttctacggta acaattacag tgtcagtatt aatatatctc attttcgctt 5640 gttcaaaaaa aaaaaaa 5657 // ID Gypsy-18_Mad-LTR repbase; DNA; EDCOT; 273 BP. XX AC ACYM01061902; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-18_Mad-I; KW Gypsy-18_Mad-LTR; Gypsy-18_Mad_. XX NM Gypsy-18_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-273 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1422-1422 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01061902; Positions 1292 1020. XX SQ Sequence 273 BP; 75 A; 38 C; 61 G; 99 T; 0 other; tgttacgatt gtggttatct gtttgcaatt agtaacttaa tagtactgta ataaatagta 60 atcaagttgt ggtagtcgtt gggccagctg gcatttggtg ttagtggaat catatatgta 120 atcaatttgg tgaggttatc ggtagaaaag ttatttggga aaattcaata caaaaataca 180 aaaacatttc tctctgtttc ctcctctctc ttcctccatt gctaactggt aacttgcagg 240 ttgagaaagg gttgttgagt ctgggtgtta tca 273 // ID GYPSY-LTR_MT repbase; DNA; EDCOT; 3495 BP. XX AC AC144893; XX DT 09-JUL-2004 (Rel. 9.06, Created) DT 09-JUN-2005 (Rel. 10.07, Last updated, Version 2) XX DE Medicago truncatula Gypsy-like LTR-retroelement (Long Terminal DE Repeat). XX KW Gypsy; LTR Retrotransposon; Transposable Element; GYPSY-I_MT; KW GYPSY-LTR_MT. XX NM GYPSY-LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1197 RA Jurka J.; RT "Medicago truncatula Gypsy-like LTR retroelement."; RL Repbase Reports 4(6), 148-148 (2004). XX RN [2] RP 1-3495 RA Toth G.; RT "Long terminal repeat of Ty3/gypsy-like retrotransposon RT GYPSY-LTR_MT."; RL Direct Submission to Genbank (09-JUN-2005). XX DR Genbank; AC144893; Positions 88443 84949. XX SQ Sequence 3495 BP; 1064 A; 667 C; 560 G; 1204 T; 0 other; tgttataccc tgtttttgga cctaaaaata ctgggcccaa tttcatttca aactttgtca 60 attatcaaat ttcaactgca cagttcaaat tgtctctgcc tcgcagtatt ttcaatcaca 120 atttcaccta tgtttttctt gcataaaacc ttttgaaata tctttacttg tcttgtaagt 180 cattcaaaag tgtctctgaa tcattacatt gctttttcta cagtttattt caaaatttgc 240 aaaaagtcat acagaagggt attttggtca tttcctgcag tgggacccat tttcatcctt 300 gtgactgtct ctgagtcttt tcagattgtt ttttttacat ttcatcagta aaccttgtta 360 aattcatttc aaacttgcat ctgagtcagt gtcaagtctg tttgagtcag tttaggtcat 420 ttttagccct aggggcattt tggtcatttc acacgaaatt ttggcataga gaggttactt 480 tgaaatacct catttaggtc attggttcgt tttagtccgt tttgtcaatt ttatttttgt 540 ttcgctttac gtttgatcaa attgcgtttt attcaatttt attttttatt gcattttggt 600 ccagtttctt ttccaatttg cattttagtc ctttttatta ttttcatatt agtcccttaa 660 tttttcaatt ttgcagaaag gtcccaaatt aattctaagt ccaaggccgc accattcttt 720 tttttcaagt ccaggtgtca ctttttcatt tgatcagatg cacacatgtc agctataaaa 780 gcagtgagtc agagtcaaag ccattgatca cacgccactt caccaaaaaa cagaatcaaa 840 ctttctcttt cttgtcagtt agatcaaacc aaaaaaatca cagagaaatc accaagaaca 900 caagaaccct aagatttcca gaacaaaatt cgtacacaaa ttcattgatt ttcacatcaa 960 tcctcagaga ttcgtgtgaa tcttcatcac cggattgaag aattccccta caattcaaag 1020 tgcgagctca cattgaagca agctcaagca ctgatcatag ggattttcca cgcagattca 1080 aaaacgttga agcaagctca agcacgtaat cacagagaag cagagaaaga atcagagaag 1140 atgaagatga accggtaaac cgatttattt tcggtccaaa agcaagcaaa atcatcaaaa 1200 ccgtcaagaa cattcaagtt tttttccaaa gattttcctc cattaaaagt ttcaaccaaa 1260 acttcaggta aaactcattt tcttctctta gaaagtatta atcacggttt aaacctgtag 1320 aagaaaaatc acgcaagcag cagatctaaa aatttccaga attcaaagat aagactgtaa 1380 ccgtaaacac aaaacctaga tccataagga tctaagtgtt gaaagcaaaa acaagcacta 1440 gagaggcaat aaacgacgaa acgatgtaga tccgtaaaga tctaaacgtt ttctttcaaa 1500 aaagatcaaa atcagtttca aaaccgtacg aagttttttc ccgatctacg tcgtttcaag 1560 attcgtttgt aaaaaccagt gccaaaatca tacttagaat aagaagacga atcgtttgat 1620 gtagaagttt tgaagttctg gaaatttagg tcaccggagg tgcttaggcg cgccggagaa 1680 gatgaagctt ccggcggacc ttcaaggtct ccgccgtggc ttcatcctca ccggcggtga 1740 gggtttagag agagatgaga gaagagagaa gagttagaga gagaaaggat ttgcaaaaat 1800 gaaataaacc ggtactcttc tgtttatata agccagcgaa ccggaccggt tcaatccggt 1860 ccattcccct ttgattcctg gccgtttgat ctagggtttt atgatcctgg atcaatcgtg 1920 tggctcctgt gcatccggac cttgtagttt tgggctttgg gttgggctca gttttctttc 1980 acgttttttt gctttttttg ctatttgcac tgtttttctt tgctatttga accaatgtct 2040 tgattaaaaa tcttgataaa tttcctagaa aatccatgct tacttcttga cattttcttg 2100 atgttttacg gtgtttttgc acgctggaat tggcaaaatt cttgtatgat taatccatgg 2160 cattttaatt ttttcttgga ttatttctta tgattatttt gtcaattcta tcattgattt 2220 gtgaatacgt gataaatgcc atttgacatg ttaatgagag gtgctcatgc ctacaatctt 2280 atgtttactt tgctgtttta gattgattca tgaaaccttg attgtatgag caatgtatgc 2340 atattctaaa agagggtaat aagatgataa ttctatctca aaattggtat gaagctaagc 2400 ttgtttgttt ctaatgatcc tatgtttata gcttgagata aaagaaacta ttttcaaact 2460 tgctatagca tgagaattag aagctacaaa tgccttgggt ttcatatcaa aattttaggt 2520 tttattacca ttttattact atctttatgg cattttatgc gttcttgcct cttgctactc 2580 tttatgcttt atttcactaa caagtttatt tccatgtttc atgcatctca tttagcattc 2640 cctccacttt ttttagccta gcatttattt tttgcaagtt ttaattcatt tggtaatgta 2700 atttgttatc attggtttgt agcttggcaa aggggccata gaatgtattt aggcaatttt 2760 tgtaatatgg actatggaca ctatgacgca ccgacacgca cacactcacc ttagatgtat 2820 gcataggatt gtatggttaa ataagcgttt aggttttaaa cacttagaga aaatccatct 2880 ttttttcaaa aaaaaacaat tgaacttcac ttcaaaaatt ttcataataa atatgaagtc 2940 aacacttcat ttttttttct tttctttttt cttaagaaaa attcaattca ccttaatcat 3000 ttagactttc tttttaatca ctaatcaaac ctcacttttt ttgctaaatc taatgccctt 3060 gaggcctctc atctctattc ttcaaaatct cttttcaaac ttaaaatcaa ccaataaaaa 3120 caaaaaccat ctttgagcaa gaactacgcc ggttttgatc ccgtaaaacg gtacgtaggc 3180 aatgagtcaa aactcatcca agccgaaata aaaatcaaat tctacttctt ctcaccccca 3240 ttcttaacta atcacacttt cttttttaca aataatcaat aaaattaaag cgtagaaata 3300 aacttaggaa agcggttctt atggaatacc ataatcgctc cgggtgccta acaccttccc 3360 gtagcgaaaa tgacccccga attcggaaac tcaagggttt ttctcctttt acccttccca 3420 agaaaaaaga gagatatcaa cggtcgaaag gttcaagtcc aattaatggc ttggcaccca 3480 aaaaccatga taaca 3495 // ID SONATA2 repbase; DNA; EDCOT; 253 BP. XX AC . XX DT 21-MAY-2006 (Rel. 11.05, Created) DT 24-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE Nonautonomous DNA transposon from Solanum - consensus. XX KW DNA transposon; Transposable Element; Interspersed repeat; KW SONATA1; SONATA2. XX OS Solanum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae. XX RN [1] RP 1-253 RA Jurka J.; RT "SONATA2: Non-autonomous DNA transposon from Solanum species."; RL Repbase Reports 6(5), 268-268 (2006). XX DR [1] (Consensus) XX CC This family is an old family. TSD is "TA". Variant subfamilies CC exist in other Solanum species. XX SQ Sequence 253 BP; 93 A; 32 C; 46 G; 80 T; 2 other; tactccctcc gtttcaaata gattgatctr gtttgacttg acacggagtt taagaaagta 60 aagaagactt ttgaatcttg tggtcctaaa ttaaagatat gtcaaatgta caaaaatgtc 120 ctttaatctt gtggtcttaa acatgtcatg tggaaagttg aaattaaaat gttaccaaaa 180 aaagaaagag rtcattcttt ttgaaacaga ctaaaaagaa aatgaggtca ttctttttta 240 aacggaggga gta 253 // ID Copia-16_Mad-LTR repbase; DNA; EDCOT; 600 BP. XX AC ACYM01086656; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-16_Mad_; KW Copia-16_Mad-LTR; Copia-16_Mad-I. XX NM Copia-16_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-600 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1361-1361 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01086656; Positions 7048 7647. XX SQ Sequence 600 BP; 173 A; 102 C; 130 G; 188 T; 7 other; tgttggtata tggtccagcc catgatcaat gttctagatt tattctagta agcaagagat 60 gaggctggag cttgctagac aattctagca tgttattaag ttgatggaag aagctagaga 120 gtactagctt ccttggttgc aaatggaaag atctagaagc cacacttttg tggctagtct 180 agatctttct atgctagagg tttgaagaat acactagaaa ctagtagaat gccaaaccct 240 cacctataaa tatgggtgtg atgttgtagt gaaccaacaa aaccaagaga gagtgagtag 300 caaaggatca agtccaaagc tagagttcca ctccaagagt gagagtgaga gtgttccact 360 acacattgtg tgagtgaagt ttagtgtkat agaaagtktg tgtcatactt tcttgtatcc 420 atcaagcctt gtctttggct tggtaagact actcttgttg tactcatatt yttcatatag 480 tgaagattra tcctygtttg gtggacgtag gcataaattg ccgaaccaca taaattyttg 540 gtgtccattt tctactttac yttgtgcatt ctctatcttg tagtaccgac attcctaaca 600 // ID COP8_LTR_MT repbase; DNA; EDCOT; 641 BP. XX AC . XX DT 01-JAN-2007 (Rel. 12.01, Created) DT 01-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of LTR retroposon, COP8_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; COP8_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-641 RA Shankar R. and Jurka J.; RT "COP8_MT: A copia type LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 20-20 (2007). XX DR [1] (Consensus) XX CC The LTR sequence flanks both sides of well conserved internal CC region, having an ORF for reverse transcriptase. XX SQ Sequence 641 BP; 214 A; 114 C; 109 G; 204 T; 0 other; tgttggtgat ttccaaaata atggaatcac tttagaacca aaagttgtaa ctcttcatgg 60 gaaccattca tatacattgg aacattatta tttattatta ataatgaacc atgacattga 120 ttcaagtata tatggttata acctttggca aaagggtgct taatgaatca tgacattgat 180 tcaagttaaa gaggtgcttt ctctcatgtg aagagtcata taatgcacta taaatgcttg 240 acatttgggc attagttgaa tatatacaaa aaccacacaa ctacacacaa cttggacaga 300 attttgttac attaacaaca taattcttca tcattctatt attctaaatc atccatcaat 360 tctctaatgc atgagtgaat tgctggaacc ataaatctgt aaaatactgt taggagatac 420 gcttggtgtg gttgtgcaat acacgtcaag gaactcatag tatcctgaag gggattcgcc 480 ggtcattcct attgcatcca atatacattt attggtgggg gcgaatcgaa cctaaaggtt 540 agtgtggcaa ccccatacgc tttgattttt acatgcatga tcattaaaca tttcaggttt 600 caagtgcagc agcctcttcc caacaaacaa gatatataac a 641 // ID Copia-42_Mad-LTR repbase; DNA; EDCOT; 252 BP. XX AC ACYM01024266; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-42_Mad-I; KW Copia-42_Mad-LTR; Copia-42_Mad_. XX NM Copia-42_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-252 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1392-1392 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01024266; Positions 5648 5899. XX SQ Sequence 252 BP; 66 A; 33 C; 46 G; 107 T; 0 other; tgatgactat gtggcagagt atcattggtt ataaggttga ataagattga gttagttagt 60 atgaagttgt tggtgagggt atttgagtct tttgtaatag atagttgtaa ctacaaaaag 120 gttgttgtaa gctcattttc ttcagtttat tgtattcgac ttttctgaaa gataaacaaa 180 gtcttttctc tcatcttctt cgttaattca tctttttctg ccattgtttc cttcttcaat 240 tcttcataaa ca 252 // ID COP2_I_MT repbase; DNA; EDCOT; 6302 BP. XX AC AC152405; XX DT 14-DEC-2006 (Rel. 11.12, Created) DT 04-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE Internal region of LTR retroposon COP2_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR retroposon; KW internal region; Interspersed; repeat; COP2_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-6302 RA Shankar R. and Jurka J.; RT "COP2_MT: LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 605-605 (2006). XX DR EMBL/GenBank/DDBJ; AC152405; Positions 36234 42535. XX CC The internal region has long integrase domain. XX FH Key Location/Qualifiers FT CDS 2604..6107 FT /product="COP2_I_MT_1p" FT /translation="MSSYGEMCLADSATTHTILKDKKYFSYLLKGESTVNT FT ISGTIKIIEGSGRANISLCGGTKLYIKNALYSPKSHRNLLSFKDIRLNGYH FT LETRNEVSVEYLCITKHDLDRKCVLEKLPTFSSGLYYTYISTIEANVIVNQ FT KFTNHDNFVVWHERLGHPGSIMMRKIVEHSCGHQLKSREILQSNKFSCTSC FT SQGKLITRPSPTKIGSESLNFLERIHGDICGPIHPPCGPFRYFMVLIDAST FT RWSHVCLLSTRNQAFARLLAQLIRIRAHFPDYPVKKIRLDNAAEFSSQTFN FT DYCMSIGIDIEHPVAHVHTQNGLAESFIKRIQLIARPLLMRSKLPISTWGH FT AILHAATLIRIRPTSYHDSSPLKLVFGQEPNISHLRIFGCAVYVPISPPQR FT TKMGPQRRLGIYVGYESPSIIKYLEPTTGDLFTARFADCHFDESNFPTLGG FT EKMQLKKEISWNELSLSHLDPRTNQCELEVQKIIHLQSLANQLPNAFTDPK FT NVTKSYIPAANAPIKMDAPVGLSHIANESQPRMKRGRPIGSKDKNPRARKG FT AKRKDGLNEDIETLKEPSDIINISVPEEPNQVPEIHENQEISINYVTSGRQ FT WNRHEVNVDDIFAYNIALNVMSDNEDHEPRSIKDCRQSENWPKWKDAIKAE FT LYSLNKRKVFGPVVRTPKGVKPVGYKWVFVRKRNENGEIARYKARLVAQGF FT SQRPGIDFNETYSPVVDATTFRYLISLIVYEGLNLHMMDVVTAYLYGSLDS FT DIYMKIPEGFNLPDTNSSGSREDYSIKLNKSLYGLKQSGRMWYNRLSEYLL FT KEGYKNDSVCPCIFMKRSENEFAIIAVYVDDINIIGTPEELPKAIDCLKKE FT FEMKDLGKTKFCLGLQIEHLNNGIFLHQETYIAKVLKRFYMDKSHPLPTPM FT VVRSLDVEKDPFRPREEGEELLGHEVPYLSAIGALMYLANYTRPDISFSVN FT LLSRYSSSPTQRHWNGVKHVLRYLRGTMDMGLFYPKVSKLELIGYADAGYL FT SDPHHGRSQTGYLFTSGNTAISWRSVKQTITATSSNHAELLALHEASRECV FT WLRSMIQHIQKNCGLSSGRMDATIIYEDNTACIAQLKEGYIKGDRTKHISP FT KFFFTHDLQKDGDISIQQIRSCDNIADVFTKSLPSKVFEKLVLRIGLRRLR FT DICLHEGEK" XX SQ Sequence 6302 BP; 2160 A; 1059 C; 1102 G; 1981 T; 0 other; acgttatcag cacgctctaa tcaccgaaaa ggtattaata taatatattt cactaattca 60 tagtttgttt tccattggat atcatgtaaa aaatgtagct gtgtatatac gtgaatagga 120 tcattagaaa ttggttttta ttcgttgtgc ctatttaatt gttgtgataa ttatactctt 180 gtatcgatga ttatatatta ctgttataat tccatcaaat ggaatcagta ccttatatat 240 agatacaaca atttttgtta tgcaaattat aatgtttatt tattttaatt taacattaat 300 gcatcattga aggactgctt aaaaagaaat aaagaaactc taatgaattc ttgaagaatc 360 caatactaat gcatccctga aggattgcat aaacaaaatt tcttaatgaa ttcttgaaga 420 attcaacact aatactaatg catccctgaa ggattgcaca tataaaattg tcttaatgaa 480 ttcctgaaga attcagcagt actactaatg catctctaaa ggattgcaca tacaatattt 540 cttaataaat tcctgaagaa ttcagttcta gtgcatcctc agttaaaaat caatttttta 600 tgaatttctg atgaattcaa cattaatgca tccttataca aataatttat caaacttaat 660 atatagtttt tgctgaactc aaatatttaa tccctgaagg attgcaaaag tactaccatt 720 ttcattatga ttgtcgtacg attgtccttg attatattta tgcatttttt gttgaatgac 780 atttgtatat gcataaacaa ctgccatggt aaaatataat ggttattaaa gtatgcaggt 840 tgcatgagta attgaattct tgtacaataa tatcagtagc agacttgata tttttctttt 900 ggatatgcat gagacaataa cattaaacgt gtatcatttt atcaactaat tatgagaatt 960 atacttctca tttataaaag aaggacacgt agttagtatt catgtgttgc atttatcaca 1020 ttagaaattg catcacttat tttgtaataa ttatcttata aataaattaa tattaactca 1080 agaagtgttt atcaatagta atgataggaa caaatcagca tacagttttt tttttatgca 1140 acaaatcagc atactattac acgtacttag catacaaatt tatggaacaa atattgacac 1200 caactacaac acatatttag gaacaaatca gcattttttt ttttaacaaa acgatggctg 1260 aaaaaatata acacaatttt tttttgcata gttatataac acagattgaa tagcattcct 1320 tttcattcca gagtctgatg aatctactta attttctttt cttactcgtt acattatcta 1380 acttgattaa tcttataatt tgatgatagt agtaagcatg tcaaatctct caaaactcca 1440 ttttgaggcc ctaaaaattt ctggacacaa ctatttgact tgggccgtag atgctgaaat 1500 gtacttagct gctgaaggaa atgcagatgc cataaaagaa ggaaataagg catccgaaca 1560 acaaaaagca aaagcattga tattccttcg tcaccatatt aatgaagcac ttaagaatga 1620 atacctcact gtgaaagatc cacttgtgct ctggaataaa ctaaaagata gatacgagca 1680 cttgaaagcc attatcctcc caaaagctag gtatgattgg atgcatttgc gcttacagga 1740 ctataaatct gtaactgcct ataattctga agtatacaaa attacttctc aattagaatt 1800 gtgtggtgaa aaggtaacag atgcggatct attagaaaaa acattttcaa cctttcatgc 1860 atccaacatg ctcctgcagc agcaataccg tgaaaagggg tttcaaaaat actctgattt 1920 aatttcttgt cttttggttg ctgaacaaaa caatgagctt ctaatgaaaa atcatgaagc 1980 tcgccctgct ggtgtagctc cattccctga agcgaatgca tcacaacaca accattttgg 2040 agaagctcgt ggtcgcggtc gtggtcgtgg tcatgcccac aatcctaatg gaaaattcaa 2100 aaccccattt ttccaccaga agtggaaaaa taatgaaaag attgaaaagg aaaaaggtgg 2160 acaaaataac aaaacaaatg aaaatatatg ctatcgatgt ggtggcaaag gtcattggtc 2220 tcgtacatgt cgtactccaa agcatttggt tgacctttat caacaatcac tgaaaaacaa 2280 aggaaaaaag gttgaaactc attatgctta taatgatggt gatgatgctg attatgatat 2340 ttatggtgac ctggatacta ctcctttgga tattggtgat ttctttgaag atccaaatgg 2400 aaaaattgat caccttattg gagatggaac cgtgaagaag tagttttttt tatgatagta 2460 ataaagtctt atgttttaga aagttttgaa tttctccatg ttaagtgtgt ctttgaattt 2520 ctcaatatta ttgacaataa aagttatttt cctcgtcgtt taaacaattt cttatcattc 2580 ttattcttct ttttttttat agaatgagta gctatggaga aatgtgtctc gctgatagtg 2640 caactaccca cacaattctc aaagataaaa aatatttttc ttacctatta aaaggagaat 2700 caaccgttaa taccatatct ggtactataa agataattga aggctccgga agagctaata 2760 tatcattatg tggagggaca aaattatata ttaagaatgc gttgtactca cctaagtctc 2820 atagaaattt attaagtttc aaagatattc gcctaaacgg ataccatctc gaaacaagaa 2880 acgaagtaag tgttgaatat ctttgcatca caaaacatga cttagataga aaatgtgtat 2940 tggaaaaact acctactttt tcctctggat tgtactacac ctacattagt acaattgaag 3000 caaatgtaat tgtaaaccag aagtttacaa atcatgataa ttttgtggtt tggcatgaac 3060 ggttgggcca tcccggatct ataatgatgc gaaaaatagt tgaacattca tgtggtcatc 3120 aattgaagag ccgggagatt cttcaatcta ataaattttc atgcacttct tgttcacaag 3180 ggaagttaat aactcgacca tcaccaacaa aaattggaag tgaatctcta aattttttag 3240 aacgcataca tggtgatatt tgtgggccaa tacacccacc gtgcggacca tttagatatt 3300 ttatggtttt aatcgacgca tcaacaagat ggtcacacgt ttgtttattg tcaactcgca 3360 accaggcgtt tgcgagattg ctagctcaat taattagaat aagagctcac ttccctgatt 3420 atcctgtaaa gaaaatacgt cttgataatg ctgctgagtt ttcatctcaa acattcaatg 3480 attattgcat gtccattgga attgacattg aacatcctgt agcacatgtt catacacaaa 3540 atggacttgc agaatcattt attaagcgta tacagttaat tgcaagacca cttctcatga 3600 gaagcaaact cccaatttcc acttggggac atgcaatttt gcatgctgca acattgattc 3660 gcatcaggcc aacaagttat catgactctt cccctttgaa attggttttt ggtcaagaac 3720 ctaatatttc ccatctacga atttttggat gtgcggtgta tgttccaatt tctccaccac 3780 aacgcactaa gatgggtcct caaagaaggt tgggaatata cgttggatat gaatctccat 3840 caattataaa gtatcttgag cccacaacag gagatttatt tacagctagg tttgctgatt 3900 gtcactttga tgaatcaaat ttcccaacat tagggggaga gaaaatgcag ctgaaaaagg 3960 aaatcagttg gaatgaactt tcattgtctc atcttgatcc tcgaactaac caatgtgaac 4020 tagaagttca aaagataatt catttgcaaa gcttagcaaa ccaattgcca aatgcattca 4080 ctgatccaaa aaatgtgact aaatcataca taccagctgc taatgctcca ataaaaatgg 4140 atgctcctgt tggactatct catattgcaa acgagtctca accacgcatg aagcgtggta 4200 gaccaatcgg ttccaaagat aaaaatcctc gagcaagaaa aggagctaaa agaaaagatg 4260 gtctaaacga ggatatagaa actttaaaag agccttctga cataatcaat atttcagttc 4320 cagaagaacc taatcaggta cctgaaatac atgaaaatca agagatctcc ataaattatg 4380 tcaccagtgg aagacaatgg aaccgacatg aagtcaacgt tgacgatatt tttgcatata 4440 atatagcgct aaatgtgatg agtgataacg aggatcatga accaaggtct attaaagatt 4500 gtagacaaag cgagaattgg ccaaaatgga aagatgcaat taaagcagaa ttatactcgc 4560 tcaacaagag aaaagtcttt ggacctgtcg tccgaacacc taaaggagtg aaaccagttg 4620 ggtataaatg ggtgtttgtg cgaaaacgta atgaaaatgg tgaaattgca agatataaag 4680 caagactcgt tgctcaagga ttttcgcaaa gacctgggat tgactttaat gagacatatt 4740 cacctgtagt tgacgcaact acttttagat acttaattag tcttatagtt tatgaagggc 4800 taaatttgca tatgatggat gtggttactg cctacttgta tggctcactt gatagtgaca 4860 tctacatgaa gatccctgaa ggatttaact tacctgatac aaatagttca ggatctaggg 4920 aagactactc cataaaatta aataagtctc tctatgggct aaaacaatct ggacgcatgt 4980 ggtataatcg cctcagtgaa tatttgctaa aggaaggata caaaaatgac tctgtttgtc 5040 catgtatttt tatgaaaaga tctgaaaatg aatttgctat aattgctgtc tatgttgatg 5100 acataaacat tattgggact cccgaagagc ttccaaaagc catagattgc ctgaagaaag 5160 aattcgaaat gaaagatttg ggaaagacaa agttttgtct cggattgcaa atcgaacatt 5220 taaataacgg aatttttctg catcaagaaa cttacatagc aaaagtgtta aaacgtttct 5280 acatggacaa atctcatcca ttgcctactc caatggttgt tagatcacta gatgtggaga 5340 aagatccttt cagacctcga gaagaaggtg aagaactact tggtcatgaa gtaccatatc 5400 ttagtgcaat aggagcatta atgtaccttg ctaattatac gcgtccagat atatcatttt 5460 ctgttaacct attatcaaga tacagttctt cacctacaca aagacattgg aatggggtca 5520 agcatgtact tcgttatctt cgaggtacaa tggatatggg tttgttttat cctaaagtat 5580 ccaaactaga attaattggt tatgcagatg caggttattt atcagatcct catcatggta 5640 gatcacaaac aggttatttg tttacaagtg gaaatacagc aatttcatgg agatctgtga 5700 aacagacaat aacagcaaca tcatcaaatc acgcggaact tttagcatta catgaggcaa 5760 gtagagaatg tgtttggtta agatccatga ttcagcacat ccaaaagaat tgtggtttat 5820 cctccggaag aatggatgca acaataattt acgaagataa tacagcatgc atcgctcagt 5880 tgaaagaagg atacattaaa ggagaccgaa caaaacacat ttctccaaaa ttctttttca 5940 ctcatgatct tcagaaggat ggtgatatca gcattcaaca aattcggtcg tgtgataata 6000 ttgcagatgt ttttacaaag tcgctcccaa gtaaagtttt tgagaaactt gtactaagaa 6060 ttggtcttcg ccgtctaaga gatatttgtc ttcatgaggg ggagaaataa atgtgttctg 6120 cactcttttt cccttcacca aggttttatc ccattgggtt ttcctggtaa ggtttttaac 6180 gaggcaattc aaactcaaaa ggatattgta ctctttttcc ttcactagat tttttttccc 6240 acggggtttt attttagtaa ggttttaatg aggcatatcc tcgatggaca tccaaggggg 6300 ag 6302 // ID LINE1A_MT repbase; DNA; EDCOT; 3278 BP. XX AC AC148776; XX DT 22-MAY-2006 (Rel. 11.05, Created) DT 26-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE LINE1 sequence from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; LINE1A_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3278 RA Jurka J.; RT "LINE1A_MT: L1 element from barrel medic."; RL Repbase Reports 6(5), 246-246 (2006). XX DR EMBL/GenBank/DDBJ; AC148776; Positions 41416 44693. XX CC The beginning of 5'-end is not confirmed. XX FH Key Location/Qualifiers FT CDS 23..1978 FT /product="LINE1_MT_1p" FT /translation="MSRIDRFLLSENWSLSWPNCFQMATSRGWSDHCSLLL FT CVDDANWGPKPVHMLKCWENFTGYKSFVCETWNSSHLEGWGSFVLREKLKL FT IKRDLSVWHRTHLNNLPARISVLKDRIGFIEVKGESSSLEEDEIAELHGLS FT EEVFALSRVNSSICWQQSRLQWLCEGGANSNFFHNFMSNRRRRNAIPFFLV FT NGVLVEGVQDVRAAVFDHFSSHYQAHRVHRPSMDGLFFRSLAVREGLDLIK FT PFSVEEVKNAVWDCESFKSPGPDGISFGFLKDFWDLLKGDVMRFLVEFHRN FT GKLAKGINSTFIALIRKVENPQSLNEFRPISLVGSMYKILAKVLANRIRLV FT IGSVISDAQSAFVKGRQILDGILIANEVVDDASKRKKELLLFKVDFEKAYD FT SIDWSFLEEVMVKMGFPILWRKWIKECVGTATASVLVNGSLTNEFSLGRGL FT RQGDPLSPFLFLLVAEGFNVLMEAMVARRLFHGYCVGSHDPLMVSHLQFAD FT DTLILCEKSWANIRALRATLLIFEELSGLKVNFSKSLLVGVNVPGSWLSEA FT SLVLNCKVGTIPFLYLELPIGGNASQLVFWKPLLNRINTRLLGWKSKHLSL FT VGRLVLLKSVLSYLPVYALSFFKDPSGIVSSIESIFNNKFLGGRADHRKII FT WVD" FT CDS join(2129..2602,2606..3109) FT /product="LINE1_MT_2p" FT /translation="MEDGFLRVGGRDGSVWWRNIAGLRSEGWFFNNVSHLL FT GDGTNVLFWTDIWLGELSLRDRFSRLYELSLFKGESVATMKALGWDEAGEA FT WKWKRRLFAWEEESVAELTLLLHNVSLQAQQKDMWIWKADSSSSSYTVQSA FT YKMIMTQAPLDQVTDMPSCHKDVSLKVVLFVWRLFRDRLPTKVNLHRRQVL FT DVEAQFCVADCGFLETSNHLFLHCNFSGSVWNVIVNWLGVVTVMPNDVQWH FT FIQFSLLGGVSRSKHSILQVIWFATMWEIWKERNNRIFNTKVSSVIQVVDK FT IKLLTYKWLKVKFVTLPFNYHGWWLSPFTLLGIG" XX SQ Sequence 3278 BP; 749 A; 446 C; 888 G; 1195 T; 0 other; tatcagaggt gatgggaggt cgatgagtcg gattgataga ttcttgttgt cagaaaattg 60 gagtttgtcg tggcctaatt gttttcagat ggctacatcg agaggttggt cagatcattg 120 ttctctcttg ttgtgtgttg atgatgcaaa ttggggacct aaaccggttc atatgttaaa 180 atgctgggag aatttcactg gttataaatc ttttgtttgt gagacttgga attcgtctca 240 tcttgaaggt tggggtagtt ttgtgttgag agaaaaacta aagctgatca aaagggattt 300 atcggtgtgg cataggactc acttgaataa tttaccagct aggatatcag tgttgaagga 360 tcgtattgga tttattgagg tgaagggaga gtcttcgtct ttggaggagg acgaaatcgc 420 cgaattgcat ggtctttctg aggaagtgtt cgctctatct cgggtcaatt ctagtatttg 480 ttggcaacaa tcacgtctgc aatggttatg tgaagggggt gcaaattcaa atttctttca 540 taattttatg tctaatcgga gacgccggaa tgctattcca ttctttttgg tcaacggtgt 600 tttagtggaa ggggttcaag atgtcagggc agcggtgttt gatcattttt cttctcatta 660 ccaagctcat agagttcatc ggccaagtat ggatggttta ttttttcgat ctcttgctgt 720 tcgtgagggg ttagatctga tcaagccttt ttctgttgag gaggtgaaga acgctgtgtg 780 ggactgcgaa agctttaaaa gccctgggcc tgatggtatt tcttttggtt ttttaaaaga 840 tttttgggat ttgttgaagg gtgatgtgat gcgttttttg gtggaatttc ataggaatgg 900 gaagttggct aaagggataa atagtacatt cattgctctt attcgaaagg tggaaaatcc 960 tcaaagtctt aatgaatttc ggcccatttc tttggttggc agtatgtata agattttggc 1020 gaaggtcctt gctaatagaa tccgtctggt cattggctct gttatttctg atgctcagtc 1080 ggcttttgtt aaaggtcgcc agattcttga tgggattttg attgcaaatg aagttgttga 1140 tgatgcttct aaacgtaaaa aggaattgct tctttttaag gttgattttg agaaagctta 1200 cgattcaatt gattggtctt tcttggagga agtgatggtg aagatggggt tcccaattct 1260 ttggcgtaaa tggattaaag agtgtgtggg gactgctact gcttcggtgt tggttaatgg 1320 ctctctaaca aatgagtttt ctttaggaag ggggctaagg caaggggatc ctctgtcacc 1380 tttcttgttt cttttggtgg ccgaaggttt taatgtgctt atggaggcta tggttgcaag 1440 aaggcttttt catggctatt gtgtgggtag tcatgacccg ttgatggtgt cccatctgca 1500 atttgcggac gatacgttaa tcttatgcga aaaatcgtgg gctaatattc gagctttgcg 1560 agctacttta ttgatttttg aagaactctc tggtcttaag gttaatttct ctaagagcct 1620 tttggtaggg gtaaatgttc cgggttcttg gttgtcagaa gcgtcgctgg ttttgaattg 1680 taaggttggt actattcctt tcttgtatct cgagttgcct attggaggga atgctagtca 1740 gttggtgttt tggaaacctc tccttaatcg tattaacact agattgttgg gttggaagtc 1800 gaaacacttg tctttggttg gccgcctggt gttactgaag tctgtcctgt cgtacctccc 1860 tgtttatgct ctttcttttt tcaaggatcc gtcaggtatt gtttcctcta ttgaatctat 1920 ttttaataac aaatttttgg gagggagagc agatcaccga aaaattatat gggttgacta 1980 gaaatctgtt tgtcggagtc aggaggttgg aggtttggga gtaaggagaa taaaagagtt 2040 taatttagca ttgttgggga agtggtgctg gcgggtgttg gtagataggg atagtttatg 2100 gtttagggtg ttagtggcgc gaaatgggat ggaggatggt tttttgagag ttggagggag 2160 agatggttct gtttggtggc ggaacatagc gggtttacgt tcggagggtt ggttttttaa 2220 taatgttagt catttgttgg gtgatggtac caatgtttta ttttggactg atatttggtt 2280 gggagagttg tcgttacgtg ataggtttag taggttgtat gagctttctt tatttaaggg 2340 agaatctgtg gcaacgatga aagctttagg ttgggatgag gcgggtgagg cgtggaagtg 2400 gaagcgtagg ttgttcgcgt gggaggagga gtcggtagcg gaacttacgc ttttacttca 2460 taatgtttct ttacaggctc agcaaaagga catgtggatt tggaaggctg attcttcttc 2520 ttcttcttac acagttcaga gtgcatacaa aatgattatg actcaggctc cgttagatca 2580 ggtgacagat atgccatctt gttgacataa ggacgtttcg ttgaaggtgg tgctttttgt 2640 atggcgtttg tttcgtgatc ggttgcctac gaaggttaat cttcataggc gtcaagtttt 2700 agatgttgaa gctcaatttt gtgttgcaga ttgtggcttt cttgaaacat ccaatcattt 2760 atttcttcat tgtaattttt ctggttcggt ttggaatgtt attgttaatt ggctaggtgt 2820 tgttacagtt atgcctaatg atgttcaatg gcactttatt caattcagtc ttttaggtgg 2880 tgtctctagg tccaagcact ctattctcca ggtgatttgg tttgcaacaa tgtgggagat 2940 ttggaaggaa agaaataata ggatttttaa tacaaaggtt agttctgtta tacaggtggt 3000 ggacaaaatt aagttgttga cttacaagtg gttaaaggtg aagtttgtaa ctcttccctt 3060 taattatcat gggtggtggc ttagtccgtt tacattacta ggcatcggct aaaggcattt 3120 tggtgttgtt ttgttttgtt ttgtggcgct tgtaatcttg tgtttttgta actttcatac 3180 tctgttcttc ttttgaggtt tttattcctt tgcacacctt gtgctaggaa ggcctcaggt 3240 gtgttaatat atttcatttt aatttcttaa aaaaaaaa 3278 // ID Gypsy4-PTR_LTR repbase; DNA; EDCOT; 397 BP. XX AC LG_III; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy4-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-397 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-397 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 333-333 (2007). XX DR Genome; LG_III; Positions 17538266 17537870. XX SQ Sequence 397 BP; 102 A; 58 C; 71 G; 166 T; 0 other; tgatgcattt tgcctttgct tcactacgtg gccatcaaga taataagtac tagcgtccgt 60 tttgttattt cctttaattg tcaataactg cccactaccc ttattaatta tcatttgtgt 120 ctgttttgct atttctttta ttgtgcccat taaagatggt ggaagtgggt actgttttat 180 gtaacggaca attaattact taattgtcaa tttcagttat ttgtaatttt cagttgtttg 240 taatttggct atttaaagcc tcgttctaat tagtaaaggg cagattaagt ttgtaaaatt 300 cttgttcatt atttggagag agtccaaatg aggtttcaga tattgatgag attctaattt 360 ctgagagcta atttgtttgt attttatcgc gacacca 397 // ID L1-1_PTr repbase; DNA; EDCOT; 6095 BP. XX AC . XX DT 04-DEC-2009 (Rel. 15.02, Created) DT 26-NOV-2010 (Rel. 15.12, Last updated, Version 3) XX DE Non-autonomous L1-type element - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW L1-1_PTr. XX NM L1-1_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-6095 RA Jurka J.; RT "L1 elements from black cottonwood."; RL Repbase Reports 10(2), 157-157 (2010). XX DR [1] (Consensus) XX CC The youngest sequences are >98% identical to consensus. XX FH Key Location/Qualifiers FT CDS 620..2218 FT /product="L1-1_PTr_1p" FT /translation="MSLCSSVENVPMVSSNIEQHNQVKSGHTLRLELQDML FT NSHGMRISQFQADSDVSIEKHSTVQASNVVPEMNHVLGSKVDEVKVGSHQQ FT EQLKLRPKLNFLNALKGSDVDDNEGSKTLGISSVRNLHFAPPTMTDGRVTV FT APPLDVFEDGCEFWKSTLVGHFVGQKLPYPVVNSIAKRIWSSYGLSEVLSS FT DNGFFIFNFDSVDHATNVLERAPWHMANRPLVLKRWQPNMQFLKDDLARVP FT VWVRLYNVPLEYWTIKGLSCVASAIGVPLHADHTTLLRKRLSYARVCVEID FT ASKTLVKEYDLRCPNGLFITISAEYEWIPSKCSNCNVFGHTTALCATNNID FT NLKVVAEGKRNLGAMNSKSADNKQNQFQWQVVGKRNKGSVSGENAPLASKV FT GNCNENGCSTSGIHMSDCNMIDHAASDVRNAACHEDENPSSPLVLKSLRED FT MKQEQGAASTALDQDMDAMGGDTDGEQTDKELTSTILTTPQTLNSTERETV FT NQLAIKARDSLEKKKKGSKASSKKNKKSGSSPGGTSR" FT CDS 2259..5906 FT /product="L1-1_PTr_2p" FT /translation="MIIGCWNIRGLNDPIKHSELRRLIHQERIALFGLVET FT RVKDKNKDNVSQLLLRSWSFLYNYDFSCRGRIWVCWNADTVKVDVFGMSDQ FT AIHVSVTILATNISFNTSIIYGDNNASLREALWSDIVSRSDGWESTPWILM FT GDFNAIRNQSDRLGGSTTWAGTMDRLDTCIREAKVDDLRYSGMHYTWSNQC FT PENLIMRKLDRVLVNEKWNLNFPLSEARFLPSGMSDHSPMVVKVIGNDQNI FT KKPFRFFDMWMDHDEFMPLVKKVWDQNSGGCPMYQLCCKLRKLKQELKLFN FT MAHFSNISDRVKDAKNEMDKAQQALHTAHENPILCMRERDAVHKYASTVRA FT EESFFKQKARIQWLSLGDQNTSYFHKSVNGRQNRNKLLSLTREDGEVVEGH FT EAVKSEVIAYFHRVLGVDQMPRVLNEEVMESAINLKLSSTQQHVLAQDVTR FT EEIKHAMFSLKNNKAPGPDGFNAGFFKRMWHIVGEDVINAVRSFFQTRRML FT KEMNATSISLIPKVANPTRLTDFRPISCCNTVYKCIAKILAGRIKVVLPSL FT VGPYQTAFISGRRISDNILLSQELMKGYHKSTGPARCAMKVDLMKAYDSVR FT WDFVDAMLIKMGFPRTVIDWIMVCVTSCQFSINVNGELAGYFQGGRGLRQG FT DPLSPYLFVLCMEILSGLFCKMSANQEFKFHWRCKKDKISHLCFADDLMIF FT SNGDVNSIRMIRTVLTKFQDLSGLYPNPNKSDIFLSGVLNAEREQIIHILG FT FREGELPMKYLGVPLLSSRLKAIYCKGLVDRITSKVRHWTCRTLSYAGRVQ FT LINSVLFSIQVYWASLFLLPGQVIKNVEQIMKSFLWSGSDMRTTGAKVAWD FT QVCLPKKEGGLGIKRITEWNKIALLKHIWNLCNDSDGSIWSTWIRSNLLRG FT RNFWTIKTPQNCSWAWGKILKLRSLAWPKMKYIIGDGMTTSLWFDNWHPHS FT PLADSYGERFIYDSGMAKNAKVNVLIQNSEWKTPTTQAIGWHPIIEAIPSN FT SNPKMGQKDEIVWLDSPNHRFSVKVAWEQLRRHRQMVEWHDIVWFKNAVPR FT HSFLLWMAVQQKLTTQDKLHRFGIHGPNRCSLCLRNNEDHNHLFFECSYTK FT AIWWDVCDRCDIPRMTKGWDEWIRWATVSWHGKSFVNFSRKLSFAATVYHV FT WQERNARIFAGMSRTSNLVFNQIECIIRDKLDLMRNVVPTNENKRIQRAWR FT VNTIDS" XX SQ Sequence 6095 BP; 1712 A; 1101 C; 1420 G; 1862 T; 0 other; gagtgtggtg ctgtcggagc tacatctact ccgtccaccg ttggattgtt ctcatttctg 60 actatgttgt tccttccaac cttctctcaa cattgaccga acggatttgt tatccaatca 120 acgaggtaag agatattgat ctcgcaatat ttctactatt ctgcattttc agttctggaa 180 ctatggagaa gtggtgaagt tgcagcatag tgaatggatt ttcttcatga tttctcttat 240 ggctgtcata gacatgaagg cctttgccat atgtgaagat taaatcacag ttctttggaa 300 aaagtttcat tttttcttgc tagtttcaga gtggtttgtc gtagcttgat ctcctttgtt 360 caccgttgga tcgttaccat ttttgagtat gttgttcttc ggaacctact ctacatcttg 420 accgaacgga tcattgttac aatcagtgtg ctgggagata ttggcctcgt aattctgtaa 480 ttctcttctt ccttcatgaa ctaatctgca tcttgttgtt tatgagttag gttgctgtta 540 tttctgagct taggttgctt cttggactca gtttatcttc ttagaatttt gttctctcta 600 gtatttgtat gctaccataa tgtctctatg ctcttctgtg gaaaatgttc caatggttag 660 ctctaacatt gaacaacaca atcaagttaa gtctggacat acattaagat tagaactgca 720 agatatgttg aatagccatg ggatgaggat ttctcagttt caagctgatt ctgatgttag 780 tatagagaaa cactctactg tccaagcttc taatgttgtt ccagaaatga accatgtgtt 840 gggttctaaa gttgatgagg tgaaggtagg gtctcatcaa caagaacaac taaaacttag 900 acccaaattg aattttttaa atgctttgaa gggttctgat gttgatgaca atgagggtag 960 caagaccctt ggcattagtt cagtccgtaa tctgcacttt gctcccccta ctatgactga 1020 tggtcgtgtg acagtagctc ctccacttga tgtgtttgaa gatggctgcg aattttggaa 1080 atccacccta gttggtcatt ttgtggggca gaaattaccg tatcccgtgg ttaattctat 1140 tgccaaaaga atatggagct cctacggtct atcagaagtt ttgtcttcgg ataatggttt 1200 cttcatcttc aattttgatt ctgtcgatca tgccactaat gtgctggaaa gagccccatg 1260 gcacatggca aacaggcctt tggtgcttaa acgttggcaa ccgaacatgc aatttttgaa 1320 agatgatttg gccagagttc cggtatgggt tcggctgtat aatgtccctc tcgagtattg 1380 gactattaag gggttgagct gtgtagcgag tgctattgga gtcccccttc atgcggatca 1440 tacgacattg ttgcgtaaaa ggcttagtta cgcaagagtt tgcgttgaga tagatgcttc 1500 gaagacgttg gttaaggaat atgatcttcg ctgtccaaat gggttattca taacaatttc 1560 agctgagtac gaatggatac cgtcgaagtg cagtaattgc aatgtctttg gacacaccac 1620 agcgctatgt gctactaata acattgataa tcttaaagtg gtggcagagg gtaagaggaa 1680 tctaggagct atgaactcta aatctgcgga taacaagcag aatcagtttc agtggcaggt 1740 agttggtaaa cgaaacaagg gttctgtgag tggggagaat gctcccttgg catctaaagt 1800 gggtaattgt aatgagaatg gttgttcaac atctggtata catatgtctg attgtaatat 1860 gattgatcat gcggcatcag atgtgcgcaa tgctgcttgt catgaagatg aaaatccttc 1920 ctctcctctt gtcttgaaga gtttacgaga agacatgaaa caggagcaag gggctgcaag 1980 tactgcttta gatcaagata tggacgcaat gggaggtgat acagatgggg aacaaaccga 2040 taaggagtta acgtcaacga tcctgacaac ccctcaaacc ctgaattcca ccgaaaggga 2100 aactgttaat cagttagcta ttaaggctag agactctcta gagaaaaaga aaaagggttc 2160 aaaagcctct tcaaagaaga ataagaaatc tggctcctct ccaggaggca cgtcaaggta 2220 atctttgtgt tgctgtttgt actcctctct attttcctat gattattgga tgttggaata 2280 ttagaggttt gaatgatcct ataaagcatt cagaattgcg tcggctcatc catcaagaga 2340 ggatagctct ttttggtctg gttgaaactc gagttaaaga caagaataaa gataatgttt 2400 ctcaacttct tctgcgttct tggtccttct tgtataatta tgatttctct tgtcgtgggc 2460 gtatttgggt ttgttggaat gctgatacgg tgaaggtgga tgtttttgga atgtcagacc 2520 aggctattca tgtttctgtc actatattag ctaccaatat cagtttcaat acttcaatta 2580 tttatggaga caataatgct tccttacgtg aggcattatg gtctgatata gtgagtcgta 2640 gtgatggatg ggagtcaacc ccgtggattc ttatgggtga ctttaatgct atccgcaacc 2700 agtcggacag gttaggaggg tctactacgt gggctggtac tatggacaga ttggatacat 2760 gtattcgaga agcgaaagta gatgatcttc ggtattcagg tatgcattat acttggtcga 2820 accaatgtcc tgagaatctg attatgcgga aactagatag agtgcttgtc aatgagaagt 2880 ggaatctgaa cttcccatta tcggaagcga gatttttgcc ttcgggtatg tcagaccatt 2940 ctcctatggt ggtaaaggtt attggcaatg atcagaacat aaagaaacca ttcagattct 3000 tcgatatgtg gatggatcat gacgagttca tgcccttggt gaagaaggta tgggatcaga 3060 attcgggggg ttgtccaatg tatcagctgt gttgcaaact aagaaagcta aagcaggaat 3120 tgaaactttt caatatggct cacttctcca acatttcaga tagagttaaa gatgcaaaaa 3180 acgaaatgga taaggctcaa caggctctgc atacagcgca tgagaatcca attttgtgca 3240 tgcgagaaag ggatgctgtt cataaatacg cttctaccgt cagggctgaa gagagttttt 3300 tcaaacagaa ggcaaggata caatggctta gcttggggga tcagaatact agctactttc 3360 acaaatcagt aaatggaaga cagaatagaa ataagcttct atcacttaca agggaggatg 3420 gagaggttgt cgaaggacac gaggcagtca aatcagaagt aattgcatac ttccatcgtg 3480 tgttaggagt ggatcagatg cctagggttc tgaacgagga agtgatggaa tcggcaatta 3540 acttgaaact gtcttcaacg caacagcatg tactcgcaca agatgtaaca agggaggaga 3600 ttaagcatgc tatgtttagt ttgaagaaca acaaagcccc tggtccggat ggctttaacg 3660 caggtttctt caaaagaatg tggcacatag ttggggaaga tgtaatcaac gctgttagat 3720 ccttctttca gactcgtaga atgcttaaag aaatgaatgc tacatccatt tcccttattc 3780 ctaaagttgc taatcctaca aggttgacag attttcgtcc tatatcttgc tgcaatacag 3840 tgtacaaatg catcgctaag attctagctg ggagaatcaa agttgttttg ccatccttag 3900 ttggtccata tcagactgct tttatctcag gacggagaat cagtgataac attcttttgt 3960 ctcaggaact aatgaaaggc tatcataaat ctacgggacc tgctcgttgt gctatgaaag 4020 ttgatctgat gaaggcttat gactcggtgc ggtgggattt cgttgacgct atgttaataa 4080 aaatgggatt ccctagaaca gtcattgatt ggatcatggt ttgtgttaca tcatgtcaat 4140 tctctatcaa cgtcaatggt gagcttgcag gttactttca agggggaaga gggctgagac 4200 aaggggatcc attgtcccca tatttgtttg tcctatgtat ggaaatcctt tcggggctat 4260 tctgcaagat gagtgccaac caagaattca agttccactg gagatgcaag aaggacaaaa 4320 tttctcatct ttgttttgct gatgacttga tgatttttag caacggggat gtaaactcaa 4380 ttcgtatgat cagaactgtg ctcacaaagt ttcaagatct atcaggtctg tatccaaatc 4440 caaacaaaag tgacatcttc ttgagcggtg tgttaaatgc tgagagggaa caaattattc 4500 atattcttgg gtttagagag ggggagctcc ctatgaaata tttgggagta cctcttctct 4560 cgtccagact aaaggctatt tattgtaagg gcctcgtgga tcgaatcacc tctaaagttc 4620 gacattggac ttgtagaaca ctctcgtatg caggacgggt acaactgatt aattcagtct 4680 tattttccat acaggtctat tgggcatctc tctttctctt acctgggcaa gtaattaaaa 4740 atgtggagca aattatgaaa tcctttcttt ggtcaggttc agatatgaga actactgggg 4800 ctaaagtggc ttgggatcag gtatgtcttc caaaaaagga gggggggcta ggaataaaaa 4860 ggataacaga atggaacaag attgctttgt tgaaacacat ttggaacctg tgcaatgact 4920 cagatggctc aatatggtct acttggatca gatccaatct gttgcgaggt aggaatttct 4980 ggacaatcaa gacgccacag aattgctctt gggcttgggg aaagattcta aagctcagat 5040 ccttagcatg gccgaagatg aagtacatca taggagatgg aatgacaacc tctctatggt 5100 ttgataattg gcatcctcac agcccactcg cggattctta cggggaaaga ttcatctatg 5160 attcaggtat ggccaagaac gcgaaggtga atgtgctaat tcagaactca gaatggaaaa 5220 ctcctaccac ccaagctatt ggctggcacc ccattataga agctattcct tccaattcta 5280 atcctaagat ggggcaaaag gatgagatag tttggttgga ttcgccaaat cacagattct 5340 cggtcaaagt agcttgggaa caactaagac gtcatcgtca gatggttgaa tggcatgaca 5400 ttgtgtggtt caagaatgct gttccaagac attcatttct tctatggatg gccgtccaac 5460 agaaactcac aactcaagat aaacttcatc ggtttggtat acatggtccc aatagatgct 5520 cactctgtct ccgcaacaat gaggatcaca accacttgtt ctttgaatgc tcctatacta 5580 aagcgatctg gtgggatgtt tgtgacagat gcgacattcc aagaatgaca aaaggctggg 5640 atgaatggat tcgatgggcc actgtctctt ggcatggcaa gagtttcgtc aatttttctc 5700 gtaaactgag ttttgcagct acagtgtatc atgtatggca agaacggaat gcaaggatct 5760 ttgctggaat gtctagaact tcgaatttgg tctttaatca aatcgaatgt atcattcgtg 5820 ataagcttga tttgatgagg aatgtcgtac caacaaatga aaacaaaagg atccaacgag 5880 cttggagggt gaataccata gattcttaat ttgttagtta gctggttgta ttggtttccc 5940 taacgaatct agtgaggttt cagttttatg gtcggtggct agcctgtagc catctgttgt 6000 tttatgtttc tgttatcatt gtaaatctgg ggtatgcccc ttataatgtt tgtatcttct 6060 tcttttaata catacgtcaa cttaccaaaa aaaaa 6095 // ID Copia27-VV_LTR repbase; DNA; EDCOT; 215 BP. XX AC . XX DT 07-SEP-2007 (Rel. 12.09, Created) DT 01-OCT-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia27-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-215 RA Obukhanych T. and Jurka J.; RT "Copia27-VV."; RL Repbase Reports 7(9), 787-787 (2007). XX DR [1] (Consensus) XX CC This is the 5' LTR sequence of Copia27-VV LTR retrotransposon. CC LTRs share 93% similarity and contain indel mutations. XX SQ Sequence 215 BP; 75 A; 18 C; 37 G; 85 T; 0 other; tgttgaaaaa gataggatca gctgagataa ttagcaagat attaggagat ttaatttatt 60 tttttgtaat ctgttagaca gttgtatatt gttaggttgt taagttgttt cctatttttg 120 tgttgagaaa aatctctata aagaggatgc cgtgtataca attttaaata tagaatagaa 180 taaaaaaaaa attatccttt cctattctgt ttaca 215 // ID Copia-22_Mad-I repbase; DNA; EDCOT; 5112 BP. XX AC ACYM01125589; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-22_Mad-I; KW Copia-22_Mad-LTR; Copia-22_Mad_. XX NM Copia-22_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5112 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1296-1296 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01125589; Positions 7237 2126. XX CC Positions [2300-2758] - Integrase core CC LTRs are 92% similar to each other. XX FH Key Location/Qualifiers FT CDS 395..1375 FT /product="Copia-22_Mad-I_1p" FT /translation="MAMNSVKIEGLLGMITVKLQEDNFVKWNYQFSSVLRG FT YDLFDFFTGESQCPPKYCITPEGGVTKEITQAYKQWIQKDLALLSLLIATL FT SDEVMDHVIGCKTAQEAWESLQERFASISVVRINQLKTEFHTAQKGSESVD FT KFLLRLKVIKDQLVAAGERITENDLMIAVLSGLPPEYEVIKTIILARDTSI FT SLKDFRAQLIGVEGSLETRLTNIAGPMSAMYVRGDSTHNQGSQGGYQSFEQ FT GESSHSQRFNGSSSFNGGFGFTGNGGRSFQQRSNFNNNRRFNGPNNNTRSY FT SNFGNRSYGFNDSNGSTSSNGSVDNQKGQYGSSNA" FT CDS 3296..4984 FT /product="Copia-22_Mad-I_2p" FT /translation="MLPVHTDSQLQVVLPFSLQSESSINTANSTDINNVGS FT VHQMVTRLKSGVIQRQDYSAFIASFPELQSLKLTTEDHFGGGYSFVSAITD FT ATEPTTFRKAALLPQWQQAMQEEYDSLRSQGTWVLVPSLSDRSIVGSKWVY FT KVKKNPDGSVSRYKARLVAQGFSQEQGIDYLDTFNPVVRHTTVRIMLALAA FT TNHWQLRQLDIKNAFLHGDLQEEIYMKQPQGFVDASYPTHVCKLIKSLYGL FT KQAPRAWNSKFTSYLAAMNFQASASDTSLFIKKDDSDIVILLLYVDDIILT FT GSNSVKIQKMIDELSEVFELKDIGQLTYFLGLQISYKDNGDIFINKSKYIR FT DVIHKAGMDSCKPATTPCKPHDQLVIFEGSLMTDPSLYRSIVGSLQYLTFT FT RPDIAYVVNTVCQFMQSPTEMHYAVVKRILRYLQGTQHHGILYSAAKVTTL FT TAFSDADWAADINTRRSITGYIVYLGNNPVSWQSKKQCSVSRSSTDAEYKA FT LAHTAADVAWVRGILKDLKVFLSLPPTIHCDNMSAIALTANPVFHSRIKHL FT DTDFHFVRERVQQGDL" XX SQ Sequence 5112 BP; 1524 A; 843 C; 1089 G; 1630 T; 26 other; tggtatccag agctcagaac gatcgcttgg gattcttccg ttgcagtttt gtgtatcagg 60 ccgactgaga tgattactgg ggagtttctg gaatctggta tttttgtttt tcgattgtat 120 ttttctgttc ttgaagttgt agatgaactg tttgatgaaa tgtcgctgtg aaatatatgc 180 tttgctgggt gtgaaatgat tgtaattggt ggtgagattt tttttttagt tcaaagattg 240 ttgattgtca aagtgttgaa gattgaaaga atgaaaatgg ttgattgttg agttgtgtac 300 tgcataaaaa aggccgaagc cagcagtgtg aagtgtgttt tgtgtataaa gattcagaag 360 tttgttgatt gttgagtgtt agttttgttt tacaatggct atgaattcag tcaagattga 420 agggttactt ggtatgatta ctgtaaaatt gcaagaagat aattttgtca aatggaatta 480 tcagttttct tctgttcttc gtgggtatga tctgtttgat ttctttactg gggaatcaca 540 atgtccacca aagtattgta ttacgcctga aggaggtgtt acaaaggaga ttactcaagc 600 ttataaacaa tggatacaga aagatttggc gttactgagc ttactcattg ctactcttag 660 tgatgaagtt atggatcatg tgataggatg caagactgca caagaagctt gggaaagttt 720 acaagaaaga tttgcttcta tttctgtagt gaggatcaat cagttaaaaa ctgaatttca 780 cactgctcaa aaagggtctg aatcggttga taaattcttg ctgagactga aggttattaa 840 agatcaactt gtagctgcag gggagaggat tactgagaat gatttgatga ttgcggtgtt 900 atcagggctg ccaccagagt atgaagtcat taaaactata attcttgctc gagatacatc 960 tatatctcta aaggatttca gggctcaatt gattggagtt gagggttctc ttgaaacaag 1020 attgactaat attgctgggc caatgtcagc tatgtatgtt cgtggtgatt caacacataa 1080 tcaaggaagt caaggcggtt atcagtcatt tgaacaaggt gaaagttctc attcacagag 1140 atttaatggt tcaagcagtt ttaatggtgg attcggtttt actggcaatg gtgggagatc 1200 ttttcaacag agatcgaact tcaacaataa caggcggttc aatggtccta ataacaatac 1260 caggtcctat tctaattttg ggaatagatc ttatggtttc aatgattcta atggttcaac 1320 tagttccaat gggtcagttg acaatcaaaa aggtcagtat ggtagttcta acgctytkcc 1380 rggtggaagt ggttttcgac aaggmagtaa ttggcatggt aatacaaatt acaaggctgc 1440 tatatctcca gagtgtcaga tttgttcaag aaggggtcat actgcaccaa attgttacta 1500 taggactgac agtgatcaag trttcaaggg gccagttttt tgtcaaatyt rtggcaagaa 1560 aggacatacg gctatacaat gctatcacag gaacaattat tcttatcaag gacctcctcc 1620 acctcagtca ttgaatccaa cacctgcggg aatggcagct cagtcatcaa attcaacaca 1680 agtagctcaa agtattcatg ggttttctaa tgccgataca taggtagttg acacaagtgc 1740 aagtcatcat atcacagcta atcttgagca tattaaccaa gtcactcctt acaatggtga 1800 atcaaaaatc acaataggaa atggagaagg tttgcttgtc aaaaacattg gtgtatctaa 1860 acttattact gatactcata cttttgtgtt gaatcatgta ctgcatgtcc cacttcttgc 1920 aatgaatttg ttatcagtca agaaattatg tagagataat ggttgttggt ttatttgtga 1980 tgatttggtg ttttttatcc aggacaaggc aactcgggtg attttgtacc aaggaaagag 2040 tgatgatggg gaattgttca agataccagc atctgttttc agaagttcat ttgctgcaaa 2100 attggagaag tgtagtgcat ttcttgggaa gaaagtgagm agttcarttt ggcacaagmg 2160 attgggacat ccatctgagg aagtattgtc tatcatgttg aagactgcak gtgtatctgt 2220 tcataaagat ccttgttcta ctatgtgttc agcttgtatt tcagggaaaw tgtgtagact 2280 gcctttttct gtaaagcaag ttaraacaac acatagrttt gaaaagatac attcggatgt 2340 ctggggtyca tcacctcara aatctataga gggatataga tactatgtca gctttgtaga 2400 tgatttttyc cgttttgtat ggatttttcc aatgatcaat aaatcagatg tgtttcakat 2460 ttttgcaacg tttcatgcgt ttgwtaacac tcagtttaat agctcaatta aatgtctgca 2520 aactgatggt ggtggagagt atgtmaataa tgtgatgaag agttttttkg atcaaaaagg 2580 tattacacat cagatttcat gtccttacac acctcaacak aatggagttg tagagagaaa 2640 acataggcat ttggytgaaa ctgytttgag tttaatgaca gamggttcaa ttcctgctat 2700 attttggtat catgcctgtt catatgctgc attcttgata aataggatgc catgcacakg 2760 attggataac aagtcacctt atcagatttt atttggtgaa aatgctgcaa tacataatct 2820 taaggtgttt gggacagcaa tatatccata tctcaggcct tacaatcaaa ataagttgca 2880 agcgagatta aagcagtttg tttttcttgg atttgcaatg ggatacaaat gtgtgatctg 2940 ttatgatatt cttagtagga aattcattat ttcacggcat gtaatacatg ataaggatgt 3000 ctatcctttt aaacattcgt ctgttttaaa gggtgttcat tcaagtggtt cttcaagttc 3060 acatcagaat catatagcta tttaggtacc tattccagtg tctagtatcc aagaggaaaa 3120 ttcaggatca catgctatca atgatgttga actgcaatct tcatctccga gtctcactat 3180 atcagctaca aatagtgaca cgggtacaca gtcaagggag tcaagggaat cagttttgga 3240 ctcacaacaa tatcaagctc aaaacacttc tcatcatcac tctggtacat catccatgtt 3300 gcctgtccac acggattcac aacttcaggt agttttacct ttttcattac aaagtgaatc 3360 atccattaat actgcaaatt ctactgatat aaataatgtt ggttctgtcc accaaatggt 3420 tacacgattg aaaagtggtg ttattcagag acaagattat agtgcattca ttgcatcatt 3480 tcctgaactc caatctctaa agctaaccac agaagatcat tttgggggag gctatagttt 3540 tgtgtctgcg attactgatg ccacagaacc aaccacattc aggaaggctg ctttattacc 3600 acaatggcag caagcaatgc aagaagaata tgactcactc aggagtcaag gcacttgggt 3660 tttagtacca tctctaagtg acaggtcaat tgttggaagc aagtgggtat ataaagtgaa 3720 gaaaaatcct gatggtagtg tttctaggta taaagcaagg cttgtggctc aagggttctc 3780 tcaagagcaa ggcattgact acttagatac tttcaatcca gtggttcgac atactactgt 3840 gagaatcatg ttggctttag cagcaaccaa tcattggcaa cttagacagc ttgatattaa 3900 aaatgcattc ttgcatggtg atttacaaga agaaatttac atgaaacaac cacaagggtt 3960 tgtagatgca tcatatccca ctcatgtctg caaattaatc aagtcattat atggcctaaa 4020 acaggctcca agggcgtgga attccaagtt tacatcttat ttggcagcta tgaattttca 4080 agcttcagct tccgatacta gtttattcat caagaaagat gatagtgaca ttgttattct 4140 cctcctatat gttgatgata tcatattgac aggttcaaac tcagtcaaaa ttcagaagat 4200 gattgatgag ctatctgagg tgtttgaact caaagatata ggacagttaa catacttcct 4260 tggattgcag atttcttata aggacaatgg ggatattttt ataaataagt ccaagtatat 4320 tagagatgtg attcataagg ctggtatgga ttcatgtaaa cctgcaacta ctccatgcaa 4380 acctcatgat caactggtaa ttttcgaggg ctctttgatg acagatcctt ctctttacag 4440 gagtattgta ggatcgttgc agtatttgac ctttactagg ccagatattg catatgttgt 4500 taatacagta tgtcagttta tgcagtctcc aacggaaatg cattatgcag tagtaaaacg 4560 catactccga tatcttcaag gcacacaaca tcatgggatc ctatattcag cagcgaaagt 4620 aacaacatta actgcgtttt ccgatgctga ttgggcggct gatatcaaca ctagaaggtc 4680 gataacaggc tatatagtgt atctgggtaa caatcccgtg tcttggcaat cgaagaaaca 4740 atgctcagtc tcgaggagtt caacagatgc tgaatataag gctcttgctc acactgcagc 4800 tgatgttgct tgggtgaggg gaatactgaa ggatctcaaa gtgtttttgt ctttacctcc 4860 tacaattcat tgcgataata tgtctgccat agctcttact gcgaatcctg tgtttcattc 4920 tcgaataaaa catcttgaca cggattttca ctttgtgaga gaacgtgttc aacaaggaga 4980 tctataagtg gtgtacattc caactgagga tcaaactgcc gatgttctta caaaaggttt 5040 gcacagtcca gcttttcttc gacattgtta caatcttagg ctgagtaccc cagccacgat 5100 tgagggggat gt 5112 // ID POPCOP1_LTR repbase; DNA; EDCOT; 331 BP. XX AC scaff_2371; XX DT 06-APR-2007 (Rel. 12.04, Created) DT 06-APR-2007 (Rel. 12.04, Last updated, Version 1) XX DE Copia-type LTR retrotransposon - long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; POPCOP1_LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-331 RA Jurka J.; RT "POPCOP1: Copia-type LTR-retrotransposon from black cottonwood."; RL Repbase Reports 7(4), 150-150 (2007). XX DR EMBL/GenBank/DDBJ; scaff_2371; Positions 2170 2500. XX CC LTRs are ~95% identical. XX SQ Sequence 331 BP; 116 A; 41 C; 48 G; 126 T; 0 other; tgttagttat taaacttatt tatcaagatt agtattaaag agtcataact attagtattg 60 aagagttgca tctattagta ttaaagagtc ataactatta gtattgaaga gttgcatcta 120 ttagtattaa agagtcataa ctattagtat tgaagagttg catctattag tattgaagag 180 tcacaactat taatgtctat atattgtatg aatctcataa tgaaaaagtg tgagagtacc 240 attttcatat gtattgtatt ctaccaaatt agagagtgtg caacctaaat ccttttcaat 300 tctattctct atttctgcca aatttccaac a 331 // ID RAM13_I_MT repbase; DNA; EDCOT; 2074 BP. XX AC . XX DT 27-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE Internal region sequence of RAM13 LTR retroposon, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR; retroposon; Interspersed element; internal region; KW RAM13_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2074 RA Shankar R. and Jurka J.; RT "RAM13_MT: LTR retroposon from Barrel Medic."; RL Repbase Reports 6(11), 590-590 (2006). XX DR [1] (Consensus) XX CC Flanked on both termini by intact LTR sequences. XX FH Key Location/Qualifiers FT CDS 504..773 FT /product="RAM13_I_MT_1p" FT /translation="METECHEVVVEENLKVRSVDIFPKSGSTEVKEITRVQ FT MDARHSLRWESLNSKRSTVSEWEYLILYAKFMEFLPNRRKKKGDIFILSFF FT PP" XX SQ Sequence 2074 BP; 639 A; 293 C; 423 G; 719 T; 0 other; agtttttggc gccgctgccg gggactgttg agtcatttca atttggtaat tttattttta 60 tttaggattt ctgtcattta tatttttgtt tctatataaa aaaaattata aaaaaaatat 120 gatttatgct cttctttttc ttctcattgt actgtgctac taaaaagttt attcaagtgt 180 tgcagctatg atagacaggt tatacctcca tgacacaaaa gagattggta tgttgaagta 240 tgaaaaatat atgctatctt tgaagatagg atatttggac aataaaatct caagattaat 300 gatagatgtg gtcgttatga gggggatcaa ccaggtagta attgtgaaga gaagaaagag 360 gtgatcaaca tcgattacaa tactcaactt caaaatattt tagatgattt cttggtgtca 420 aatcaagttt catttgagaa gtttgatgtt caattggtga tcttgttgag aaagaacatg 480 agtctcagag gaagctggtt cagatggaga ctgagtgtca cgaggttgtt gtggaagaaa 540 atctcaaagt gaggagtgtg gatatttttc cgaagtctgg atcaacggag gttaaggaaa 600 taactcgtgt gcaaatggat gcacgtcatt ctctaaggtg ggagagctta aattccaaaa 660 gatcaacagt gagtgaatgg gagtatctga ttctttatgc caaattcatg gaattcctac 720 caaacaggag gaagaagaag ggtgatatat tcattctatc attttttcca ccctaacagt 780 ggttgaagcg tcaagctcaa tgacgtaaaa gaaagcgctt ggtgggaggc aacccatcct 840 ttttattatg tctttatttt cagtaattta tttctattgt tgagtcaaac aatttgtctt 900 taatttttat tttggttgta tcccactgtt atgtgattga atctgaactt gtttattatt 960 gatgaatttg cttgtttgtt gactttttcc aatttagtaa caaatgtttg ttcaagtggt 1020 attccaaaag ttcaaaagga ggagtgactt gtgtttcaaa ggcgaaatgt acgacagtta 1080 aagatatcat aaccgtaagg ttcatgacca aattttattt ttccaattta cttataaaga 1140 gtgttccatg catttacatt tctagaactt gcaatttttc actactagtc gattgatctt 1200 tgtcattagc acactgaggc aaaagtgctt ggtcctgtaa gcctttttga agcctaccct 1260 gttattattt gaaatattat cctttttttt agtcaatttg agctggtagg tttagatctt 1320 tttgttcggt gacgaactac attacaagct tagagacttt taggatttat cccttattgt 1380 ttttctgagt taggctttgt agaatgttgc taaatattaa gtttggggtt gctattggaa 1440 tttgcaacca actaagtttg gggtgggggt actagagaac aaaagaaaaa gaaaaaaaaa 1500 acattctcat gaaaacaata tgccaaatgg tgtattcgga aaaaaaaaaa aaaaaaagaa 1560 tagaatgaaa aagggacaag atattgaaaa accgagtaac tttaaacacg attgtcccaa 1620 ttgttataaa taatctctag tacccttgca agaattgttg ttccaaaagg tgaatgaatg 1680 atgaattgaa ttttgtgctt aacttccgta ggaatgccta actcaaattt tgtgtagcct 1740 acttatccaa atattatccc gccttcacct aagccccgtt ataaccctta aagacctcaa 1800 agctgcattg acattgattt tgattgacgt ttagaaactt tccaagcgta tggtaatatg 1860 tagattgcat gtcgactgtg tgtgaaccct ttcatattgt tgcgtggagt tgtgaattgg 1920 tggttgctaa caagtcaaac tagctcatct ttagctagta aggtgttgaa cttttgggta 1980 ctatcgcttg atcaggtaat tgttattttg ctgtcgattg tcaatattac aagtaaattc 2040 cttgaggaca aggaatagtt caagtttggg gttg 2074 // ID Copia11-PTR_LTR repbase; DNA; EDCOT; 222 BP. XX AC scaffold_1749; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia11-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-222 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-222 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 195-195 (2007). XX DR Genome; scaffold_1749; Positions 692 471. XX SQ Sequence 222 BP; 72 A; 43 C; 30 G; 77 T; 0 other; tgaaagagat attgacagcc ttaggattct tgtaatccta tcacgattaa ttagccatga 60 tactctcctt atcatgctac ctataatctc tccatgatat ctgtaatatt tcatactgtt 120 tttagaatga ttagattacc atgtatatat gcgacaatca ctcttgtaac ctgctatata 180 tatgaataac aacaaaggca acagtaggtt agctttccta ca 222 // ID MuDR-18_VV repbase; DNA; EDCOT; 16580 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-18_VV, an autonomous DNA transposon - a consensus sequence. XX KW MuDR; DNA transposon; Transposable Element; mutator; TIR; KW Mutavine-18; MuDR-18_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-16580 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 773-773 (2008). XX DR [1] (Consensus) XX CC MuDR-18_VV (Mutavine-18 in [1]) consensus is an autonomous CC element. Its individual copies are >90% identical to the CC consensus sequence. MuDR-18_VV contains 255-263 bp-long TIRs CC which are 91% identical and flanked by 9 bp-long TSDs. Downstream CC of the transposase gene is a putative gene encoding for a CC ULP1-like protein similar to CAN67356.1 (region 7001-10155). XX FH Key Location/Qualifiers FT CDS join(3875..4143,4308..6216) FT /product="MuDR-18_VV_Transposase" FT /note="MUDRA transposase." FT /translation="MEGDIFCYIHEGGEVVKSADGSVQYKGGRTESIVVSG FT NITHAELVSKVCGELNIDPNXIKLEFTVKFDPSCLLPLHDEASVVKMFRFN FT DIGLTPIVASNSAQVISSHADPPTEINTHSPTIESFGFSQRCAESNVVQLE FT SSRFENAIMGSGQTFPNASEFHDVVYLMSMACRFRYSFTRNTPKHMTVVCT FT VTQCPWKVTARAIGDSKIVQVHTFRNVHNHSLEDVSSSQPLIRSNRASLVI FT DDVIRSTPNYQPSQICKDFVRQHGMQLTYLQAWQMKEKXKERIYGQPKYYY FT KLLPWMCDKMVTTNPGTVVELRHSSDEHFQQLFVAHAVSIQGFALGCRPXI FT AIDSSHMSGPYGGALFSATAYDANDSMFPLAFGVMSSENYEDWSWFLQNLK FT KVVAEKEVVIISDRHPALLRSVPXVFGLENHAYCYRHLKXNFSSFVSKQNT FT KGNKGKENALQFLDSIAYARLEHDYNVSMYELRKYNDALATWVEDNSPEHW FT AMSKFPKQRWDKMTTNLAESFNAWLRHERHHXICNFLMEHMAKLGSMLVKH FT KEQSNNWKXSLGPQIEEKVLQNIAKGEVYPVTPFMNGIFRVCIXRAFLNVD FT IMKRTCTCRGWQMFRIPCEHATTVILSIGHNVADFVDDCYKFPMQELIYAG FT SFSSIETHDMPIVDDHGVVQSITGQVFFSLKPXHTKRPPGRPXKKRIESQF FT QDKQTVHCSRCHMSGHNRKTCKNPLS" XX SQ Sequence 16580 BP; 5195 A; 2637 C; 3126 G; 5462 T; 160 other; gggaaacttg tgttttaggg cccttattta taaaaaatat gatattcaaa ccccaagttt 60 ttcaaatatg gaaaacaatc attaatgggc aaaataatat gagatttgtg cactctgtgc 120 tgagtcaatt ttatcttcca aaaatgccct caatgtctta tgcatcaaca gccaaatagc 180 ctccatgtca tacttaaaaa aaaaatttgt gaaaattgat aatttcttaa aaaaaccacc 240 cgacccgact tttggtgtcc ctttctctct ttctctcatt ttagtaaaaa aaaaccttaa 300 gtcaaacgac atctaacttt gctctcagta gccctaaatc tgccttttag tttggcaaca 360 accaaatcta agattttccc taagccagaa tctcaaaaac ttgccatttc agaaggttat 420 ttcaaatctg aatcagccaa aaccttcacg tccaacaaac ccaactgata cacatcttcc 480 ccgaatctca aacttctctg tttttctctt aacatcctaa ttagtcgaac gtgtttgtct 540 ctaaacgtct ggagtagctg aaactgatac ccatcttccc aatacgttga agtaaaccaa 600 acgggagaca tatcttgttt ttgcatcatc gaagttggaa ttccgttcag gtttctcaaa 660 atgaaactgg agttttcctt cttgtgcgtg ttttccgatt aatcaatcac atgtgagttt 720 tcatttacgg gtttgtttgg atggtgcaga tatcttaggg tttgaagtgt tttattttgg 780 ggtttcttat atttagcttc attttctgta gaatgaaata taggataaat tatttttggt 840 taaagatatg ttcgtattta gagaaaataa attattatta ttattattat tattattatt 900 attattatta tttattttta aatatttttt tttgctttcc aggaattcta ttgtcattag 960 atttttaggg aaattggttc atttgtatta ctactagtcg atggaaattt tctttcaatt 1020 ttaatggtat atatgagagt tactactaaa ccctaaacag attatttgct tggtcgtttg 1080 tcattgttat tgctttacta aatttgaata ccgatttcat tgtgtgtatg ttgttattat 1140 tttgtccttt gtctttgcat gatagaattg aatgtatgtt gttattgtta ttgttttatg 1200 aatttgattt gagacatgat aaaatgatag cagtaagcat gtaaaagatg aatgttgact 1260 acaaatttgg gatgaaaaat aagtgacaac attgtgaagt gttggtcatg ccttacttta 1320 tttgcagatt ttatttattt ttgaatcgtt taatgccttg ttgaggtaag aattggtacg 1380 cattttttct gagttatgtt ttggggacca cattacattc ctaagtcttt aaatttgaga 1440 tgagtatagt tttgtatttg cctttttatg agtggaaaat tgtattgtat ctatgccata 1500 aaattatttt caaaaacact aaccaaatag tatatttgct ttgtggggag taattgttga 1560 tgacatgaac aaactgaaaa tggtttgtta ggggcagtga tcataattat ggctttaata 1620 tattccacat gtgttgctat aatgtacagt gaaaaaaaaa attatgttgg agacttggtt 1680 ttgggacaga catatcttgc aagatgtaga aggcaaaatg attgagacca ctaactgagg 1740 catccttcaa atgagagtct gtacagcaaa aggaagagtt caaacaaaat ttagctttca 1800 atttgttaga aaatgaaatc aaactggaca aatcaataac acctctaaag gcatgtaaat 1860 ttattaggta aattactaag ttaaagatat agtgtagtgg tatgatagcc agagatacaa 1920 ggaggtctcc aaaaagtggt aaacaatttc tagactatct gatacaaccc ttgtaagatg 1980 aaacctctct tgaggcatct caaatactag ttactttcct tatttttgga agatgaaacc 2040 cttgtagctt ttatttaaac taaaattcac aagtacacca gttcatttca agtgytagcg 2100 gaagtatatg cctaaaatca aggcctaaag taatatccta tctaaagagg aagttataat 2160 ataccttaat aaaccgctgg aaacctaaaa attattggaa atgaaactaa aatcatttga 2220 agacaagttg gactttgaat ggaaattgaa tggctcacta tgaaaacaat gtatctgaag 2280 gtrcatagcc atcaacaaga aagtcataaa cgtgattrtg aaaaaataaa awaaaatcat 2340 cagaaagaat gacctcctta taggaaattg atcaatccct actaaaccta gattaaacac 2400 aaacaatgtt ttactttgtg cttaatggtt tgttgaatct tgctrttact tttgtgaatc 2460 gttgaggttt attgatgttt atgataacca atatgttcat tatggcaata aggaatggtc 2520 aatattgaaa tgggtccgaa aaaataatct tctaatttta ttatttatgc tatttccatc 2580 aacataagtt tgtctraagt aagacttaat aaatgaatat aaactaagtt tttagaatgt 2640 tatgactaca aattacatca ttctaatgaa gttgtgtttt gaacaatgaa tttgaatgtt 2700 tacttttaat tgtttttcta acttttccaa tctctaatac gtcatttcca atactaaatc 2760 tratttcgaa tgtgattgtg ctagacggtt gaaatccctt tgttatgatt tcttggatgg 2820 tgaatgctta ctctcataat aacattaaag tagacatgtt gttcattcta tatgttggtt 2880 gcaatttcct tagtggcaga gccgttggga aaaaatattt caaatggttg caagttatgc 2940 aacttgatta taatgtagag aacttttgca ctatagacta catcatgttt gaaataactt 3000 ctctttwgtt atttctgttc atatgagaca tgcacagaaa wgtcttatga taaagcgacc 3060 tyttatataa tatcgtcgtt ttctaaaaat tatggaagtt tgcagtatca tttatttgac 3120 aaacttcttt ttgttaaaca aaggttactt ggtcaaaggt tatacctcaa atctaaatct 3180 acattattac tccattacta aaccagtgaa ggtttgttct agattgtgtg gtcatgatgc 3240 trccatgtgt tgytgttgtt attgtacttt agttactacc ttaaccatgc ttagatacaa 3300 ccttaatcaa gctcaggtac tacaatagtg aaccgtaggt actaccttag tgtagtttag 3360 gtactacctc atcacacttt cacttaatat gtatgtgagc tctagttact ttgttcggca 3420 ctacttactg ctttattatt cttgttgtat tgtttgtaac ccattttgtt gttattaaag 3480 gaatrgaaga ggatattttt tgytacatac atgaagrcgg tgaggttgtt aagtctgttg 3540 atgggtccgt acaatacaaa ggtggtcgga cagaatccat tgtcgttart ggaaatatca 3600 cacatgcaga attggtttca aaagtgtgtg gtgaactgaa cattgaccca aacttaataa 3660 aattagagtt tacggtgaag tttgacccat catgtttact accgttgcat gatgagactr 3720 ycgttgtgaa gatgttcaga ttyaacgaca tgttttgtca tgtttatgtc ttcccacrta 3780 tagaagttgg tgaagggttg attgcacaaa ctaggtacat atggccttag ccccatcata 3840 ttaatttggt tgaatctttg ttgttattaa gggaatggaa ggggatattt tttgttacat 3900 ccatgaaggc ggtgaggttg ttaagtctgc tgatgggtct gtacaatata aaggtggtcg 3960 gaccgaatcc attgtcgtta gtggaaatat cacacatgca gaattggttt caaaagtgtg 4020 tggtgaactg aacattgacc caaactyaat aaaattggag tttacggtga agtttgaccc 4080 atcatgttta ctaccrttgc atgatgaggc ttccgttgtg aagatgttca gattcaatga 4140 catgttttgt crtgtttatg tctccccacg tacagaagtt ggtgaagggt tgatcgcaca 4200 aactaggtac atatggcctt agccccatca tattaacttg gttgaatcac tttccaaaca 4260 tttgttcata gatggttagc aaatttgttt ggatgtcttt tttgcagtgg gctaacacct 4320 attgttgctt ctaattcdgc acaagtaatt tcctcccatg cvgatccacc tacggaaatt 4380 aatactcact cccctacaat tgagtcattt gggttttccc aacgatgtgc agaatcaaat 4440 gtagttcaac ttgaatcaag tcggttcgaa aatgccatta tgggtagtgg acaaacrttc 4500 cctaatgctt ctgagtttca ygatgtggtc tatttgatgt ccatggcttg tagattccga 4560 tattcgttca ctaggaatac tccaaaacac atgacagtag tttgcacagt aacccaatgt 4620 ccttggaaag tcactgctcg tgcaataggg gattctaaga tcgttcaggt tcacacattc 4680 cgtaatgtcc acaaccatag tttggaagat gtctcctcct cccaaccttt aatcagatcc 4740 aatcgtgcgt ccttggtgat tgatgatgtc ataaggtcta ctccgaatta ccaaccaagc 4800 caaatttgta aggacttcgt aaggcaacat gggatgcaat tgacttatct tcaagcatgg 4860 caaatgaagg aaaaggmaaa ggagcgcatt tatggacaac ccaaatatta ttataaattg 4920 ttgccttgga tgtgtgacaa aatggttact actaatccag gaaccgttgt tgagttgcgt 4980 cattcgagtg atgagcactt tcaacaactc tttgttgctc atgcagtgtc aatccaaggg 5040 tttgcattgg ggtgtcgacc trtcattgct attgactcat cccatatgag tgggccatat 5100 gggggtgcgt tattttcagc cactgcatac gatgctaatg actctatgtt cccgttagct 5160 tttggcgtta tgagctcaga aaattatgag gattggtcat ggtttttgca aaacttgaag 5220 aaagttgttg cagaaaagga agttgttatc atctccgata gacatccagc cctacttcgt 5280 agtgttcccr aggtgtttgg ccttgaaaat catgcctact gttaccgtca cttgaaggad 5340 aatttcagta gttttgtgag caagcaaaat acaaaaggga acaagggtaa agaaaatgcg 5400 cttcaattcc tagatagtat tgcctatgca aggttagagc atgattataa tgtttctatg 5460 tatgaactac ggaaatacaa tgatgcttta gccacatggg tagaagataa ttcacccgaa 5520 cattgggcca tgtcaaaatt cccaaaacaa agatgggata aaatgaccac caaccttgcc 5580 gagtcgttta atgcgtggtt aaggcatgaa agacatcact ycatttgtaa ctttttaatg 5640 gagcacatgg ctaagttggg ttctatgctt gtgaagcata aagagcagtc caacaattgg 5700 aaakggtctc tagggccaca aattgaagaa aaggtattgc agaatattgc caagggtgaa 5760 gtgtatccag ttactccttt catgaatggc atttttaggg tttgtatcrg tagggcattc 5820 ttgaatgtgg acattatgaa gcgtacttgc acatgtaggg gttggcaaat gttyagaatc 5880 ccttgtgaac atgcgacaac cgttattctt tccattggcc ataatgttgc tgattttgtt 5940 gatgactgct acaaattccc aatgcaagag ttgatctacg cgggctcctt ctccagtata 6000 gagacccatg acatgccaat tgtggatgac catggtgttg tacaatctat aacgggtcag 6060 gttttcttct ctcttaagcc tyctcataca aaacgtcctc ccggaagacc aargaagaag 6120 cgcatcgagt cccaatttca agataaacag acagtccatt gctctcgttg tcatatgtct 6180 ggccacaata ggaaaacgtg caagaatcct ttgtcttaag tgcattgttg ttttatgtac 6240 ttctattact raacatttgt attaatgtac tttcatatgt wtttttggaa crcatgagta 6300 tgtgttgtta ccyagtatgc aatcttaatc atgtttgtta cttaactrgt tacrttataa 6360 cttatgttty ttttcctgta actagccatc ttgtgtgtga attagcatgc attaatatat 6420 tttaaagcat agtaatcaga attgaacatt ccagttgaag ttcagagacc atttttcctt 6480 gcatgtgttt ccattcattg tttttcatgt actctttact tacaccatga cctatttccc 6540 ttgtyagttg ttgcatgctt tgtttagttt catttgttat gaatagctaa cctaatggtc 6600 aastgtaaac ttttgaactg ttaatgttga atcacttcta acatttttca ttsgatggaa 6660 gtttggttta tatgtgaatt tacaagttca aatataagaa tctgctgtga ttttgaatga 6720 acakacaaca ctkacctatc agaagaaaat catttgcctt agtggagata catggttttt 6780 tttttttttt ttttgtggat gccatggtat taagatgttt tattttcttg ggaagtgtac 6840 aatctcatca gaattgttat ttccttacaa aataaatttt cctaggcatt tgctgttgct 6900 gttggtccta ccgttgctga tcattctatt cactttytgt actttgcaca gtccgygact 6960 aacattgaat accttgaaca cattcctcac taatatatag atggccactg ttyggcggaa 7020 aagaaaagaa cacctcccag ctacatgcag ccaggttgcc aacaaaatac attttgtaaa 7080 ctgaattgaa atttttttwa atttttttat ttatttcccc ctatattgat atgttttgat 7140 actgatagaa attgcccact gactgcaggt gaaactgcca aaatcatggt gttctggcaa 7200 aaaattcatt tcagtcatcg cgaggcttcc tgatgataaa cgagacgcca ttacakaaat 7260 gggatttgga ggacttctac acttggcttg tcgagaacta cgctacgagt tgtgttcttg 7320 gataatttct aattatgaca ctgcctacca tcaaytgaat atggctacyg gcrttgttgt 7380 cccggtaaca rcacaagatg tcrgcaatat tatgggcatc ccatgtartg gtgaggagay 7440 tgtggtgcat actaggagag gcacctctaa tcgcacctac accataagtc tattggagca 7500 aaatctagag aacttggcca ttggtgatga cttcaggaag actttcttga tttttgcatg 7560 tgccacccta ctygcaccta actccaagct tgaaggaata catgacctat gggacaccat 7620 atgggatggt gacgttggtg tccaaaagaa ttggtcaaaa tttgtcctac attacataga 7680 ggatggaatc agagaatacc agaaaaacca gccaacttac atacgcggyt gccttatttt 7740 tctccaggta cagttaagac ttaatgaatc tattgtttta attttgtcta ctacattctc 7800 tcmttttaat gtagtttcat ttaaattata atttatttta aaccgtattc aaagatgttg 7860 ttgaatgtgt ttcaactatt acattttcct gtcatttcac agytcttcta catgacaaaa 7920 ttttatttgc catccgtcac ggttgatgtc actatgccat tacttgctgc atggagtgat 7980 gacytaatca aaagacggtt atcagctgaa attgccacat ttggtggtta tggtcatgtc 8040 catgtaaggt ccaactgtac acttctttcg ttataaaaaa tttcttatcc aagttatctc 8100 catatttaaa aaaatatatt mtaatttttg tttaacgacc ctttccarac tcaacarcta 8160 ccagaatttg ctgmccactc ccatgcacar gcagcaggtg ggcagtcctc ggcttctgat 8220 gatgctactg aggttgtaaa tgtcttcatt gatagccaag cwcacatatg catagttgta 8280 ttrcagtaat gcaatttttt tcgcctcatt ccartcattg attttttgtt tcaaaatttt 8340 tcctcctcat cttaggtaat tcaagcaygt atggtagaaa actcagaaaa attgttgaga 8400 ttagcctctt cattagctga mgatgttgct gaattgmttt cccgtyagtt tgggtcgcaa 8460 taccgatgtt carctactcc arcccagcct tcagcccaag tctaagatga accagctcct 8520 atgacaggcr acattcagct ttcagctgaa gaatttgttg aacaacccaw cctaccatta 8580 gcaccgcatt ctccaaytga aagacatgaa tctgcatttg accatggacc ytcatcacta 8640 cacyaagaat ctcatgacca atcctatcct tacccacact tggaaagtgt agaagatgtc 8700 caaaatgttg gcacaatagc tactcacagc catttagaca taccaacctc aagtcacaaa 8760 tataaacrga ctggtaggcg gattgtgaaa aggcytgcca tttgtaaatc tccatttgtt 8820 gcacaatgcc ttaaactgtt cccgaaaata tcacataarg ataggttggt agctgatttt 8880 gctttrgacg aagatgctga tccaaggtag tttttgaatt tcatttgcaa ccatatttaa 8940 tgtgcataaa tatgcctcta ttgcatggtt taacataatc ttttatgaca tttcagcgag 9000 gttgtatgtg atatgcacgg actgtttatt acgagggtcg agctcgcttc tctcaatgga 9060 ggtcgatggg tgaamamcat tgtaagctac taatcctcca atttcctgaa taccyaattc 9120 acattatttt ttttccaata atagatgctt taaacttggc taataattga gtaccraatt 9180 tttttttttt ttttccagat tattggtgtt atgtctcgca tgttgaatgc taaccaacca 9240 catccacgac rytgccacta cttcgatcct tcattttcgg tacacacttt tcgagactta 9300 tttattacat taaggaaaag taaattgtat tcgtttatgt twttattgac taatccccaa 9360 cttgaacagg ttgttcttgc tagtctttta ccgaaagcya raaaagaaga aatacttgac 9420 agatcaygca tgtttcttca agctgacata gkgggacacg atgtagcgtc ytgtgaaatg 9480 gtacattaac atactccttt catagctacc taatrgtatg rcttatatct atcaacatag 9540 accctaacra ttcaattgtt gataatgtag ttgttcattc ccgtatgcga gaataaccat 9600 tggcaccttc atgtgctgaa cattctggct ggccgtatcg agatmctttc tagtctgcca 9660 ctacgaagag ggaactacat tagtgcttcc actaggcgat tgtcaatggc tttggagaga 9720 gcattgcatg cacatggaat tcatgtgaat rtggaggttt caaaattggt ccatgtacag 9780 ccagatctag tgcaacaaaa aaatgggtaa attttgttgt gaatgacagy tttggttgma 9840 ataaagttgt agttaaaatg cgttagacga ttratgtatg tgtatgataa tccaaacgtt 9900 atggtcttct aggtatgayt gtggtatttt tgcactcaag tacatgaaat attggaatgg 9960 ggctacctta acacaagcag ttgcggaggt tagtgttgcg ttacaacatg ttttaatcat 10020 atcttccaat tttgtataca cttgcaaata atttttaatg ttatttgtag gagaaaatgc 10080 atgtttacag gttggcaaat ggttgtgaca ttgctcctta atgaagccaa caatgttagg 10140 ggaaatatta tacaggcatg tggattgtga gaggttatcg gaccggaaaa tgtcaaaata 10200 aggtatttcg tagaatgaca cctagttttg catttgtaag tagtgaagtt agttgtgtta 10260 tccctttaat ttcctcttct gatcattttg atgaatttca gccatgtcaa gttatttatt 10320 catgacttta agttacaaag ttaataaagg taagttttgt ttttggacaa gaatggacaa 10380 taatttgcat attaacaaat tggagaaaat ggaaggtact gaatgacaac ggtatttttt 10440 ttcaaaaact gatgtgtctt gtgatttttt tgttagctag taaatatgtc aaattattac 10500 cctattgttc cttcattgga ggacctacca attgcacaac tctcaactta gttctttaaa 10560 gtatgaagtt ccctctgaaa tagttgttcc tttatttgca ttgaaaatga aacacttata 10620 atatttagta aataagctag agtttgacac tatttccagg cctttttgca tataagatag 10680 tattatgtga taaattccga agttgacctg tgtagttaaa attatgagtt ttttggttct 10740 tagttcagtt ttgttgagct cgcttttgaa cttaaatttt catttattat gaattgaact 10800 ctgaaaaatg atatgaaaaa tattatgtta caatggatta cacttgagaa gacaaagaaa 10860 tttgtatgcc acattgagtt gcatttggaa cgtgctttta taagcttggc catttatgtt 10920 tgattcataa ataaatgttt caaatacatt caattttaga cacaaataaa ttaatttaac 10980 aggaaatcgt actttgcttt catatgagag atgtggattt taagtcaatg cttgtaactr 11040 cttttgcttt gtcacctata gttttgttyg cttttatttg gtatccactt aaaaattatt 11100 gtagttttgg ttggtggtcc attggttgat tatgggatgg tttcygtgac tttttccagg 11160 tagagaacga agaaaattyg ggagatgggg tagaaaatga tggagatgga taaatgaatg 11220 cagaaaytgg agaaacacaa cctcaaagtg ctgaaaaaat gaggmacawc aggcagtgtt 11280 tgacgagagg acatgatatt aaattacayt gaaatgayga tgagaaaaat gtcaggacaa 11340 attcggttaa tatacaattg gaaagtatta attttggctt ctgaccattt gtatgccata 11400 tgtagtaaay agatatgttt caacttcatt gtgtctgtat ttgatgaatg gtatgtgggc 11460 cgctrcataa gccatttgtt tgaagaatta cagtccatag atgctaacaa tgtggctaat 11520 cagaaacttt tgtttcatta gattgactga aattgaattg ttaattaact tgagtaggat 11580 atcgctgctt tgtgcccagg tactttcatt tatattggaa tgagatgact atgttatgta 11640 gaacatagaa gcataattta atctatgaga taacagtgtg tttgatgata attttttttc 11700 cttctcttca gcctaataga agtacatgta ggtmrtagga gaataataag gayaattgga 11760 tgcatgtttc catggtagca attgaaagtg ctgytgaaaa ttttccagta gtttgtaatc 11820 tgaaccccac gaaatgtgta atgcaattat gatggacatg catttaatag taggacatga 11880 catgtagttg ttaatggtga taaaaagctt tatatagttg ttcaattgct rcattggaaa 11940 tattcctatg catgaatttt tacctatgca aaatatacat aaagcacaaa caggttattg 12000 aggatggacg atgttcagac acgatcraag taacaaatgg ttatcrctta gtattaaaat 12060 tacaattaca rcccacttcg cacttattat aatgaaaggg tatttttttt tttaacacat 12120 attcattagg cagtgttgat gtgaataaca cttatatgag aatcaggaaa atgattctaa 12180 taatgttgta taaaatatgt tgtataaata tgaaaatact gttaatagta ataaatcaca 12240 acaaakgaca tataattgta attacgaaaa cgacaatagt atgataaacg aaaaactttt 12300 aattataaca ctataatatg aaaaactcgt ttagagtatc cactttttga gctttaacag 12360 tgggccaatc aggcaaaaat gcaagcatat caggagtaga tgttagagcg gcaacaataa 12420 ttggaagcma ctgtgaargt tcacggaaaa gatgaatttg cattttggct tgtaatgatg 12480 attactacaa attacttggc agctgcatac ctgataaaaa aaaacaatta acattggtta 12540 aggaaagttg caaagacaac aargggacaa aaaatgaagc aaggaaagcy aacaaatgtg 12600 gagttcaaac caaaatgttc atatatggaa aaaatgttca cactggtgta taccacatat 12660 atgtgttatc gtacaaaatt atgtcatcat tatagtacca aatcatttta tacatatctt 12720 tatagtaata cagagatgtg gatgaaaaty tgtatacagg gacaactagg catcaaaatt 12780 ggttagtcca taatgcttgg acatatatct ttgtcagtgt gaaattatga tgaaattgaa 12840 tgtcaagtgt tggtmttatg gatgaggaat gtgctaccta ggattgataa acaamaaatg 12900 taaggtaata gtcgtaaggt taacttaggg tagtccctaa gatgtagaaa gatagtactc 12960 gtaaggttaa ataaggtagt actttagaca cattaaggta gtaccttacg cacattcagg 13020 tagtacctta gccacaataa ggttgtaact cggatgccat aaggtattac taggggtgga 13080 aaagatggct aacctattac aacacaacaa tgccattctc aatgaargaa attgtctatt 13140 cagtgtaatt gcttcgtttt ttataaacta ggtggaaatt gaatgycgaa gcatacatac 13200 taaggtttac catggttgaa cgttggaatc acaaattaac tacaccttgg gaaacaaagc 13260 tagtaggaaa gttgtggtya gttgcacgat ttaagtattg aactatggag agaaagtgtt 13320 atagtaacgt agtayctaag ggacatttaa gtartaccta tgatacattg agatagtacc 13380 tatagtacat taagatagta cmttcaaact attatgagta tataacgtac gaagtgacta 13440 accaattaac agaaagtaat gccattattg aatctgtaat ggaatgaaag aaatgtgtct 13500 tcagttcgaa agtgcaacag aaagtaatgc cattgtcaaa ttatgatgga attgaatgtc 13560 aagcatagga catatggtta aggaatgtgc tacctaagaa tgataaacaa cccaaggttc 13620 atgaactcac tacctaagct ccattaagtt aataactaag gttcacaatg gtagtcccta 13680 agytgcagta aggtagtaca attaatattc attagggtac tccctaagtt gyagtcaggt 13740 agtagtcgta aagttaacta gggtagtccc taagatgcag taagrtagta gttctaaggt 13800 taactaaggt agtaccttag acacattaag gtagtamctt aagcacatta aggtagtacc 13860 gtaggcattt tcaggtagta ccttagccac atcaaggttg taactyagat gccataaggt 13920 attaccagag gtgaaaaaaa tggttaacct attgcaacat aacaatgtca ttcttaatta 13980 aggaaattgt ytattcagtt taattgcttg ggtttttttt taaactagtt ggaaattgaa 14040 tatcgaagca tacatactat ggttgaccat ggtagtacrt tggattcata aattaactac 14100 tgattgggaa acaaagctag tagaaaagtt gtgcttgctt gcacaattca ggtactgaat 14160 tgtggagaga gtgttatagt aaggtagtac ctaagggaca tttaggtagt acatatgata 14220 cgttgagata gtacctaggg tacattaaga tagtaccttc acactattac ttgaaaatca 14280 tgtacgaagt gactaaccaa ttaagacaaa gtaatgccat tatcaaatct gtaatggaat 14340 caaagaaatg tgtcttgagt tcgaaagtgc aacatttctc caacgtgcaa taaggacaat 14400 aaccaattgg accttacaac ataaaaagta gtgagatacc acctatgatg cattaaagtt 14460 gaacctaaag tggatgacaa tagtaagtaa agtgcattag ggtagtacct aaggagaaca 14520 ttctmaaaaa taaattattt ttaactaatg ccaatgacaa ttcaagacat tgtgtactga 14580 gggaagatgt tggacatata tccattcagy gtcaaattar gatgaaattg aatgtgaagc 14640 ttaggtccta tggttgaggg aagtgctaac taggattgat gaacaaccca aggttcaaga 14700 actcacgacc taagcttcat taagttaata actaaggttr acaatggtag tccctaagtt 14760 gcartaaggt agtactccta aggttcaata gggtagtcca taagttgcag tcmagaagta 14820 ctcctaaggt tcactaaggt agtacttaaa ctaccttaag gtagtacctt aggcacatta 14880 aaggagtacc ctaggcacat taaactagta cctttgccac tttaaggtgg tgccttagcg 14940 acattaaggt agttaatcag gtgcaataag gtatgaacta aggtgaacgg gatgcataac 15000 ctattacaac ataacaatgt catgctcaat taaagaaact atcattttca accaaatggc 15060 ttggttatgt ttcaaactat gatgaaattg aatgacaaaa atacatccta tgattgacca 15120 tagtagtacc tagaattcac aaactaacca taaagtgttt atgaagctag tgcccaagtt 15180 gtgatcgggt gcattgttaa ggttccgaaa tatggagaca atgtggtaca gtcagttagt 15240 acctaaggga cattaaggca gtacctaaga gacattaagg tagtacctaa ggaacattaa 15300 ggtagtacct aaggggtatt aaggtagtac ctaagggaca ttaaggtagt acctaaggga 15360 cattaaggta gtacctaaag tttattacga tagtacctaa gggttactaa gataatacct 15420 aaggctcagt caagcagtgc tcacatctaa ggtgaactaa ctcacaaaaa ttgcaaaaca 15480 tgatgccaac tctaaataca aattaattac cttaagattt gggtggggtt taggccaata 15540 tgcaacccaa tcagatgaag aggatatttc ttcttcacga aggcaatatt tcacacttgc 15600 cgttttcatt ctggtttact caattgaacc agagatttga atcacactgt tgcaatattt 15660 cctcaaaccc tttttttaac tggatgttgt taccatgaag cgcttcattt gcctcttaaa 15720 aaactgcaca acaaagaaaa atgtagattc aggttttcga ttgaaggttt cttctcagaa 15780 atgtaccaca ttttgcaaat ttaaacatgg ttttccattc acggtttttt cactaaaata 15840 tgtgaaaatt ttctaattta aacacgctct cctctctagc ttactgcaga catgaaaacg 15900 aatgagagaa atgttcccaa actttgagag gacgaaagaa agggaaattt caatctcggt 15960 atcagttggg tttgttggac atgaaggttt tggccgattt agatttcaaa tgatcttcta 16020 aaatgtcaag tttttgagat tccggcttag ggaaaatatc aaatttggtt gctgataaac 16080 taaaatgcag atttagggct acgagagttt ttcagaagaa acttagatat ccattccagt 16140 tttgactgaa ggtttttttg gctaaaatga gagaatgaga gagaaagaga gagagagaga 16200 gagagagagt ggaacaatca aatgttctga tttgggagag gcaaattagg gatgaagaac 16260 tatcagattt gggaattttt tctagttcaa acagagaatt ggtttttttt tcyagttcca 16320 aatgtcggrt cgggtggttt tttaagaaat tatcaatttt cacaattgtt tttttttttt 16380 ttttaaagta tgacatggag gctatttggc trctgatgca taagacatta agggcatttt 16440 tggaagataa aattgactca rcacaaagtg cacaaatctc atattatttt gcccattaat 16500 gattattttc tatatttgaa aaacttgggg tttgaatatc atatttttta taaataaggg 16560 acctaaaaca gaagtttccc 16580 // ID Gypsy-39_Mad-I repbase; DNA; EDCOT; 4792 BP. XX AC . XX DT 14-OCT-2010 (Rel. 15.1, Created) DT 14-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-39_Mad-I. XX NM Gypsy-39_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4792 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1772-1772 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 1629..4748 FT /product="Gypsy-39_Mad-I_1p" FT /translation="MDWLSRHNAYVGCREKFVTFDRPGRPAITFQGERRIL FT QNSIISAIQTTKLLQKGCVGFLAHVVTRGEPSLCAGDVPVVNEFTDVFPED FT LPGLPPAREIEFTIDLLPGTNPISLAPYRMAPAELRELKIQLQELVDKGYI FT QPSMSPWGAPVLFVRKNDGSMRLCIDYRQLNRVTVKNRYPLPRIDDLFDQL FT RGAQVFSKIDLRSGYHQLLIRNEDVPKTAFRTRYGHYEFRVMPFGLTNAPA FT AFMDLMNRVFRPYLDRFVIVFIDDILIYSKSNAEHMKHLKLVLERLRKHQL FT YAKFSKCQFWLDQISFLGHVVSAEGISVDPQKISAVSMWEQPRNVTEVRSF FT LGLAGYYRRFVQDFSAIALPLTKLTRKGVKFEWDESCERSFQELKQRLTHA FT PVLALPDDGGEFEIYSDASLSGLGCVLMQHGKVIAYASRQLKTHERNYPTH FT DLELGAVVFALKIWRHYLYGEKCRIFTDHKSLKYVFTQNELNLRQRRWMEL FT ISDYDCTIEYHPGHANVVADALSRKSYGQLASLRAIHVPLLFSLRETGVAV FT TPDSQGALLAHFQIRPVLVDLVREAQELDQQCADLKEQVRNGSRRDLKIRR FT DGALVMGNRLFVPKDNEVVKKEILDEAHISAYAMHPGSTKLYHTIRPFYYW FT YGMKRDVAEYVKRCIICQQVKADRQRPEGLMQNLPIPAWKWEDITMDFVYG FT LPSTRSRFDGIWVIVDRLTKTAHFLPVRQTYTLEKLAQLFIDNIVKLHGVP FT VTIVSDRDPRFTSRFWRAFNDAMNTQLLYSTAYHPQTDGQSERTIQTLEDM FT LRVSVLQWKGSWDSYLPLIEFAYNNSYHSSIGMAPFEALYGKACRTPLCWT FT EVGERVLVGPEIVDTTNTNIQLIKRNLKAAQDRQKSIADRHSRDREYEIGD FT FVFLKLSPWKGVVRFGKRGKLSPRYVGPYRITERIGAVAYRLELPPELSQI FT HDVFHVSMLRKYVPDPSHVIQPEPLEVSQDASYVEEPVAIIDRQDKTLRNK FT VIPLVKVLWRNHAVEEATWETEELMRSQYPYLFI" XX SQ Sequence 4792 BP; 1148 A; 1018 C; 1349 G; 1275 T; 2 other; gattggtatc agagcatact taggacttca ttcttccatt tggtaatcat aagctttctt 60 gtggccataa tctttcgtcc ttctaaatct tgtttgcctc ttatcagaat catggatcct 120 actggtggga atgtacctcg acgacctcgt tctggtctaa tgggaggaat tcagcagttg 180 acctccgctc tacgaaatgc ttttcctggt agtaacaggc cgagtcgtac atatatggag 240 attgctcata gccacggcgt tacggaactt agtgtagttg gagcctgtga ggaggctgag 300 gattggttgg aaaagatgga ggacacctta gagagtatga gatgcccagc gtctgaatgg 360 gcgaataccg ctggttactt ccttcagggg aacgcgaggt attggtggaa gtcagtgacg 420 ggctctcgcc cacgtaattc tttgatgact tgggctacgt tcaggagact tttcagcgca 480 cactttttga gccccggtta tcagctgagg aagagacagg agttcctaga gtttcgccag 540 ggcaatctga gtattacaga gtttgatagc acttttcggc gcctgtcgag acaccatgag 600 ggaaccagcg ggagatgatg attcagctgc agattgctat gaaccaggac ttttgcgagc 660 ttctggcacc acagaggcat acatcatacg aggagatgat tgaggcggct ttgaggatcg 720 aacagacgag gtggaacaga cttaaccaga atcagcctca gagccagaac cagcctcgga 780 gccagaacca gctcggaacc agaatcagcg gggtcgtgga ttccgatccc ggagtatgag 840 ggagccttct acttcttcta attccttcgg ccctagacac tctcagtcgt tcaagcgaca 900 ggtcagggtt cgggatcatc tagtgagggc tcaggcagtg agtcggcgag gcgatctttc 960 agccacttta atccgagtgc ggctaatccg gccgtgtgtt acaggtgtgg cggctttgga 1020 cacatagccc gtgattgcgc tactccacgt ccatctgatg gttttgcttc tggttcgggt 1080 tacggtggga gtaataaccc gagtacttcg agttacggtg ggggtaatta ttcgactact 1140 cagagttatg gtgggagtag tagtcagagt actcagtttt ctgctcagag gcagccgcag 1200 twttctggag cagcttcagg cagtcgtgct caggggaacc gagcaggccg caacagccag 1260 ggtcctagga ctcgaggcgg ccgtaacagt ggttcgggac gtcaggtcca tgggcgtatc 1320 aacgccatga ctcagcagga ggcggagcag gatcccagag tcattactgg tacgttactt 1380 gtttgtggta attgggctcg tgttctgatt gattcgggtg ccacttattc atttatatct 1440 ccacmatttg cacgggttgt aaacccgcaa cctacatcgc tcggttttga tatgttcata 1500 caattgccac ctggagatct ttctgtgcac agtgggagtt taaggattgc ccagttattg 1560 ttgaagggga actcttggag gccaatttga ttcccttcaa acttgtggag ttcgatgtca 1620 ttctgggaat ggattggcta tctaggcaca atgcttatgt cggatgtagg gagaaatttg 1680 tgacatttga tcggcctgga cgaccagcga tcacgtttca gggtgagcga cggatccttc 1740 agaatagtat tatttctgcc atccagacga ctaagttatt acagaagggt tgtgtgggat 1800 tcttagccca cgtagtcacg cggggtgaac cttctctgtg tgctggagat gtgccagtgg 1860 tgaatgaatt caccgatgta tttcctgagg atttgccagg gttaccacct gcgagggaaa 1920 tcgaattcac cattgattta cttccaggta ccaaccctat ttccttggca ccataccgaa 1980 tggcaccagc tgagttgaga gaattgaaga ttcaacttca ggagcttgtg gataaaggct 2040 acatccagcc cagcatgtct ccctggggcg ctcctgtact gtttgtcaga aagaatgatg 2100 ggtcgatgag actttgcatc gactacaggc aactgaatcg ggtgacggtg aagaaccgtt 2160 atcccctgcc tcggattgat gatctgtttg accaactgag gggtgctcag gtgttctcta 2220 agatcgatct tcgttcgggt taccaccagc tgctgatccg gaatgaagat gtaccgaaga 2280 ctgccttccg cactaggtat ggacactatg agttccgtgt catgcctttt gggttgacga 2340 atgcacctgc agctttcatg gatttgatga acagagtctt cagaccgtat cttgatcggt 2400 ttgtgattgt gttcattgat gacatcctga tctactccaa gagtaatgct gagcacatga 2460 aacatttgaa gttggtgttg gagaggttga ggaaacatca gctgtatgcg aagttcagta 2520 agtgtcagtt ttggctagac cagatcagtt tcctcgggca tgtggtttcc gctgagggaa 2580 ttagtgtgga ccctcagaag atttctgcag tgtctatgtg ggaacaaccg aggaatgtta 2640 ctgaagtgag gagttttctg ggactggctg gctattaccg acgttttgtg caggatttct 2700 cggcaatcgc cctgcctctt actaagttga cccggaaggg ggtcaaattc gagtgggatg 2760 agagttgtga acggagtttt caggagctta agcagcgtct tactcatgcc cccgtccttg 2820 ctcttccgga cgatggcggt gagtttgaga tctacagtga tgcatccttg tcgggattgg 2880 gttgtgttct gatgcagcat gggaaagtca tcgcctatgc ttccaggcag ctcaaaactc 2940 acgagagaaa ctaccccact catgatctgg aactcggagc agtggtcttt gctctaaaaa 3000 tctggcgaca ttacttgtac ggcgagaagt gccgcatctt caccgatcac aagagtttga 3060 agtatgtctt cacccagaat gagctgaatt tgaggcagag aaggtggatg gaactcatta 3120 gtgactacga ttgcactatt gagtatcatc ctggtcacgc caatgtcgta gcggatgcac 3180 ttagccggaa atcctatgga caacttgcct cccttcgagc tatccatgtt ccgctattgt 3240 tttctcttcg agaaaccggc gttgcagtga caccagattc acagggagca ttgttggcac 3300 acttccaaat taggcctgtt ttggtggatt tggttcggga agctcaggag ctcgaccaac 3360 agtgtgcaga cctaaaggaa caggtgcgga atggttctag gcgagatttg aaaatccgga 3420 gagatggagc cttggtgatg ggaaataggc tgtttgtgcc taaggacaat gaagtggtga 3480 agaaggaaat tcttgatgaa gcccacattt cggcgtatgc catgcatccg gggagtacca 3540 aattgtatca cactatccgt ccattctact actggtatgg gatgaaacgg gatgtggcag 3600 agtatgtgaa gagatgtatt atttgccagc aggtgaaggc ggacagacag agacctgaag 3660 ggctaatgca gaatctccct ataccagcgt ggaagtggga agacatcacc atggatttcg 3720 tgtatggttt gccgagcacg cggtcgaggt ttgatggcat ttgggtgatt gtggatcgac 3780 tcaccaagac tgctcatttc ttacctgttc gacagaccta cacactggag aagttggcac 3840 agttgttcat tgataatatt gttaaacttc acggtgtacc cgtcaccatt gtttcggaca 3900 gagatccaag attcacctcc aggttttgga gagcattcaa tgacgccatg aatactcagc 3960 tgttgtacag cactgcctat catccacaga ccgatggtca atctgagagg acgattcaga 4020 ctttggagga catgttgaga gtgtctgttc tccagtggaa gggtagttgg gatagctatt 4080 tgccgttgat cgagtttgcc tacaacaaca gctaccactc cagtatcggc atggcaccgt 4140 tcgaggcact gtatgggaag gcgtgccgga caccgttgtg ttggactgag gtcggtgaac 4200 gggtgttagt ggggccagaa attgttgaca ccactaatac taacatccag ttgataaaga 4260 ggaacctgaa ggcggcacaa gatcgacaga agagcatcgc ggaccgacat tccagggatc 4320 gtgagtatga gattggtgac tttgtcttcc tgaagttgtc gccctggaag ggtgtggttc 4380 gatttggtaa gcgagggaag ttgagtcctc gatatgttgg tccctaccgg atcacagaga 4440 gaattggtgc ggttgcttat agattggagc taccaccaga gttgtcgcag attcacgacg 4500 tatttcatgt ttccatgctt cggaagtatg taccggatcc ctctcacgtt attcagccgg 4560 aaccgttaga agtgagtcag gatgcgagtt atgttgagga accagtggcg atcatcgacc 4620 gacaggataa aactctgagg aacaaagtca ttccgttggt aaaggtgttg tggaggaacc 4680 atgcagtcga ggaagcgacg tgggaaacgg aggaactgat gaggagccag tatccgtatt 4740 tatttatttg aggttgtaat ttcggggacg aaattctttt aagggggtag at 4792 // ID TAM3_AM repbase; DNA; EDCOT; 3629 BP. XX AC X55078; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 17-OCT-2006 (Rel. 2.02, Last updated, Version 3) XX DE Antirrhinum majus Tam3 gene for Tam3-transposase. XX KW hAT; DNA transposon; Transposable Element; AMTAM3TN; TAM3_AM. XX NM TAM3_AM. XX OS Antirrhinum majus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Lamiales; Plantaginaceae; Antirrhineae; OC Antirrhinum. XX RN [1] RP 1-3629 RA Nacken K.W.; RT "TAM3_AM."; RL Direct Submission to Genbank (25-OCT-1990)W.K.F. Nacken, RL MAX-PLANCK-INSTITUT F, ZUECHTUNGSFORSCHUNG, CARL-VON-LINNE-WEG, RL 5000 KOELN 30, FRG. XX RN [2] RP 1-3629 RA Hehl R., Nacken K.W., Krause A., Saedler H. and Sommer H.; RT "Structural analysis of Tam3, a transposable element from RT Antirrhinum majus, reveals homologies to the Ac element from RT maize."; RL Plant Mol. Biol 16, 369-371 (1991). XX DR GenBank; X55078; Positions 1 3629. XX FH Key Location/Qualifiers FT CDS 848..3094 FT /product="TAM3_AM_1p" FT /note="transposase." FT /translation="MDTSNIQPATTEDYIHNFNMGVGFSVWDTTLGIGPHV FT GNYQQEHVFGPGVGPSNNNPAVELGPHVGTSHHDTSANMAGETATGGASSA FT VGSDDDAAEGDNAEMDEDEIPDTPVEQMASTSRPPKKTKKATVWKWFSKVT FT GSNWAQCLLCPTRYSHKTGCGTGTLTRHLTAKHKNRDMDAPDMQRQPDGTM FT APWRYDQNYMRICLAQFIVQNELPFSFAQNELFENFLQKAVQCKFKKISRA FT TCFRDGVKQYEKEIIVLRNEFKNFNGRISLTSDLWQGSGSYHFSCITAHWI FT DKDWIMRKRIIEFAQLDSPHNGDCIRDATMSSLNYWGIKDKIMSISLDNAS FT NNVNAIKSLKPAMNLILGGQLFHVRCICHILHLCVKDGLSVLIQSIDRIRV FT CLSHINRYPPRVQAFNTVCETHGMPIKHIYLDVPHRWNATYRMLIEAKPYS FT EPITFFCHRSLGPNSILADDWNICDILVPYLVYFEEFTKIMSSCYTPTSNI FT MLLYMVSVVRLFHQHRNHATLKNIIKEMEKKWVKYYKKVPNVCILSSCLDP FT RVRLIGTLELLEKYHSALNNVYNGNEERNRILQLLYSLYDMYAPSTDMDES FT PTNASRGSGFSIFDELLSNQQSNQPSVGNYTEIHLFVQKPPQKFDKDFDIL FT KWWRQNESLTPVLARIARDLLSSQMSTVASERAFSAGHRVLTDARNRLKPG FT SVKFCMIWKDMLDQQYREKTLRKVETVLAMDGEEDNEDATMPYDFTNIH" XX SQ Sequence 3629 BP; 1105 A; 686 C; 703 G; 1135 T; 0 other; taaagatgtg aattgggccg tgccaattcg gcccggcacg gcccagctcg tgaaaaagca 60 cggcccggca cgcctatttt gcgtgccggg ccatgcgggc cattatattg cgtgcctggg 120 ccgattcggc ccaggcacgc atttggcccg tgaaacaagg ggccccgcgg gcccctttaa 180 aaaaaaaaat tattattttt ttttttttta ggcccagcct atggctgggc ctaaaagaag 240 ctgacccaca aaaaatgtgg gtcagctgtt aaagcgtggc tacaaagcca cgcttttaac 300 tcaatttcaa gtagccgttg ccaatggcaa cggctacttg aaatttaaac tcaacggtcc 360 aatttcagat tggacctcca atctgaaatt ggacgttctg attgctgcca tattcaggca 420 gcaatcaggc gccaatttta tttttaggtt atttattttt ttttttctta acttttgaaa 480 actataaata ccaccccatc tcttctattt tttcccactt tcaagtttca actatccaat 540 tctaatctac ttctagccaa attctactta tttcctcttt aaaattcctc acatttttat 600 ttcttagtgt tttatttaaa gttctagtat tttttttcat tgtcactttg tgtttccaca 660 caataccttc ataacatttt tcaattcggc aaacgaagaa aactcaaatc atcgtggcca 720 atccgtccca cctcatatcg atattaatga aataccgtca cgatacgaat ttccggtagg 780 gggagttcca agtaccgacc cgtacgtgcg atatcgtgca gatacaccat atgaagattc 840 acaatttatg gacacgagca atattcaacc cgcgactaca gaagactata tacacaattt 900 taatatgggt gttggctttt cggtgtggga tacgacctta ggaatcgggc cacatgttgg 960 taattatcaa caagaacatg ttttcgggcc cggtgtcggc ccttcaaata acaatccggc 1020 agtggaactt ggaccacatg taggcacttc ccaccacgac acgtcagcga acatggcggg 1080 agaaaccgcg accggtggtg cttcatcggc ggtgggctcg gacgatgacg cagcggaagg 1140 ggataatgca gaaatggatg aggacgaaat tccggatact ccagtcgagc aaatggcctc 1200 tacatcaaga cctccgaaaa aaacgaagaa agcgacggta tggaaatggt tttcaaaggt 1260 gaccggttct aactgggctc agtgtttact ttgtcctaca agatattctc acaaaacggg 1320 atgcgggacg ggaacactta caagacattt gacggcaaag cataagaatc gcgacatgga 1380 cgctccggat atgcaacgac aaccagacgg tacaatggca ccgtggaggt atgaccaaaa 1440 ttacatgcgt atttgtttag ctcaatttat agttcaaaat gagttgccct ttagttttgc 1500 acaaaatgaa ctatttgaaa actttttaca aaaagctgtg caatgcaaat ttaagaaaat 1560 ttctagggca acttgtttta gagatggtgt taagcaatat gaaaaggaaa ttatagtttt 1620 gagaaatgaa tttaaaaatt ttaatggtag aatttctttg acttctgatt tatggcaagg 1680 tagtggatca tatcatttta gttgcattac cgcacattgg atagataaag attggattat 1740 gcgtaaaaga ataattgaat ttgcacagtt agattcgcct cacaacgggg attgtatacg 1800 cgatgccaca atgtcctctt taaactattg gggtataaaa gacaaaatta tgagcatttc 1860 cttagataat gctagtaaca atgttaatgc tataaagtca ctcaaaccgg caatgaatct 1920 tatactcggg ggtcaattat ttcatgttag gtgcatatgt catattttgc atttatgtgt 1980 taaagatgga ctgtcagtgt taatccaatc aattgataga attagagttt gcttatccca 2040 cattaataga tatcctccta gagtacaagc atttaatact gtttgtgaaa cccatggcat 2100 gcccattaaa catatttatc ttgacgtacc acatagatgg aatgcaactt atagaatgtt 2160 aattgaggcc aaaccatatt cagaaccaat tactttcttt tgtcaccgat cacttggccc 2220 aaattctatt ttggccgacg attggaatat ttgtgatata cttgttccct atttagtgta 2280 ttttgaagaa tttactaaaa ttatgtcttc gtgttatact cccacatcta acattatgtt 2340 attgtatatg gtttctgtcg tgagattatt tcatcaacat agaaatcatg caactttaaa 2400 aaatatcata aaagaaatgg aaaaaaaatg ggtaaagtat tacaaaaagg tgcctaatgt 2460 ttgtatttta tctagttgct tagatccacg tgttagatta atcggaactt tagaactatt 2520 agaaaaatat cattcggctt taaacaatgt atataatggt aacgaagaac gtaatagaat 2580 attacaattg ctttatagtt tatatgacat gtatgctcca tccactgaca tggatgaatc 2640 tcctactaat gcttctagag gtagtggttt tagtattttt gacgagttat tgtcaaacca 2700 acaatccaac caaccaagtg tagggaatta tactgaaatc cacttatttg tacaaaaacc 2760 acctcaaaaa tttgacaaag attttgatat actaaaatgg tggagacaga acgagtcact 2820 aacccctgtc ttggctcgta ttgccagaga cttacttagt tcgcagatgt ctacggtagc 2880 atcggagcgt gcttttagtg caggtcatcg tgtgcttacg gatgcaagaa accgattaaa 2940 accgggcagt gtaaaatttt gcatgatttg gaaagacatg ctcgaccaac aatatagaga 3000 aaaaacttta aggaaggttg aaacggtctt ggcaatggat ggagaagagg ataatgaaga 3060 cgcaaccatg ccatatgatt ttacaaacat ccactaaaac acttgcaacc tattttttta 3120 agttaacctt ttatgttttt tttttagatt ttattttgaa gttcaccttt tatgtttttt 3180 ttttagttaa tatttttatg cacctttgtt gtagttgcta aaatttaccc ttttttattt 3240 ttaagttcac cttttatgta tttttttgta gaacaaaaat tttagtttac ctctttttat 3300 gaaagtttgc tacttattag ttagtttaat tataattcat caaatgttaa gttgtaacat 3360 ttacttattt tcacataaat tcaatgaaga agtctttttt ttatgcatgg ggtttttttt 3420 tccagcattt tttttatgct aaaatatgta tttgtagtaa aagataaaaa aaaaaaaaat 3480 gggccgtgct gggccgaacc ggctggagaa atggcccagc acggcacggc ccgggctcaa 3540 aaagcccagg cacggcccgg cacgcctaaa aggcgtgcct gggcgaatac gtgccgagcc 3600 ggcacggctc ggcacgtttc acatcttta 3629 // ID Gypsy4-VV_I repbase; DNA; EDCOT; 8883 BP. XX AC AM438099; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy4-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-8883 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-8883 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 692-692 (2007). XX DR Genbank; AM438099; Positions 23050 14168. XX CC Positions [4803-5306] - Integrase core CC 'ACTCC' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 249..2993 FT /product="Gypsy4-VV_I_1p" FT /translation="MPNWIQDSGGRLVKRDTPHNKELDLSLNIIEATPEDQ FT HSHHGHQDNPNAFRSMRDCMHPLRMSAPSCIVPPTERLVIRRHIVPLLPTF FT HGMESENPYAHFKEFEDVCNTFQEGGASIDLMRLKLFPFTLKDKAKIWLNS FT LRPRSIRTWTDLQAEFLKKFFPTHITNDLKRQISNFSAKENKKFYECWERY FT MEAINACPHHGFDTWLLMSYFYDGMSSSMKQLLETMCRGDFMSKNPEEAMD FT FLSYVAEVSRGWNEPNKGEVGKMKSQLSASNAKAGMYTLNEDVDMKAKFVA FT MTRRLEELELKKMHEVQAVAETPVQVQPCPICQSYEHLVEECPTIPVVKEM FT FGDQANVIGQFRPNNNAPYGNTYNSSWRNHPNFSWKPRAPQYQQPAQPSQQ FT ASSLEQAIMNLSKVVGDFFGDQKSINAQLSQRIDSVENTLNKRMDVMQNDV FT SQKIDNLQYSISRLTNLNTVQENGRFPSQPHQNPKGIHVVETHEGESSQVR FT DVKALITLRSGIKVELPTPKPHVEEEEEEETKKREEIKGKKKDISEGKEDH FT NSTVNANPEKVLIKEEMLKKHTSPPFPQALHGKRGIRNASKILEVLRQVKV FT NIPLLDMIKQVPTYAKFLNDLCTIKRWLNVNKKAFLTEQVSAIIQCKSPLK FT YKDPGCPTISVMIGGKVVEKALLDLGASENLLPYSVYKQLGLGELKPTSIT FT LSLADRSMKIPRGVIEDVLVQVDNFYYPVDFVVLDTDPIVKEVNFVPIILG FT RPFLATSNAIINYRNGLMQLTFGNMTLELNIFYMSKKLITPEEEEGPKEVC FT IIDTLVEEHYNQNMQDKLNESLGDLEEGLPEPSDVLATLQGWRRREEILPL FT FNKEEAQEADEEETPKLNLKPLPMELKYTYLEENQQCPVVISSSLLVIRKS FT VYLKFSRGVRK" FT CDS 4437..5339 FT /product="Gypsy4-VV_I_2p" FT /translation="MLLAKTPWYAHIANYLVTGEFPSEWKAQDRKHFFAKI FT HAYYWEEPFLFKYCADQIIRKCVPEEEQQGILSHCHESACGGHFASQKTAM FT KVLQSGCTWPSLFKDAHIMFRSCDRCQRLGKLTRRNQMPMNLILIVDLFDV FT WGIDFMGPFPMSFGNSYILVRVDYVSKWVEAIPCKHNDHKVVLKFLKENIF FT SRFGVPKAIISDGGTHFCIRPFETLLAKYGVKHKVATPYHPQTSGQVELAN FT REIKNMLMKVVITRRRDWSIKLHDSLWAYRTAYKTILGMSPYRLVYGKACH FT LPVEVEYKA" XX SQ Sequence 8883 BP; 2714 A; 1655 C; 1861 G; 2628 T; 25 other; aatggcgccg ttgccaggga aggtgccaac ttcacagtga tattatttca gagtacttgt 60 gattttcatc acaagttagg tgacttttct ttcattttac taattttttt ttaattaatt 120 gtttctttac ttgttcatat tctaatatat cttttaattt agttttagtt cattttagtc 180 tttttgtagt cttgttttct tttgttttct tttgtttttg ttttagttac agttgatact 240 agttgtgtat gccaaattgg atacaagata gtggaggaag gcttgttaaa cgtgatacac 300 ctcataacaa ggaattggat ttgagcttga atatcataga agctacacct gaagatcagc 360 atagtcacca tggtcaccag gacaatccca atgctttcag atcaatgaga gactgcatgc 420 atccacttcg tatgagtgca ccatcatgta tagtgccccc tacagagcgg ctagtgatca 480 gacgacatat tgttccactt ctaccaactt tccatgggat ggaaagtgag aatccctatg 540 cacatttcaa ggaatttgaa gatgtttgta atacattcca agaaggagga gcttcaatcg 600 acttgatgag gcttaagtta tttcctttca ctttaaagga taaggccaag atttggctta 660 attctttaag gccaaggagt atccgtactt ggactgattt acaagctgaa ttcctcaaga 720 agttttttcc tactcacata acaaatgact tgaaaaggca aatttcaaac ttctcagcta 780 aagagaataa gaaattctat gagtgttggg aaagatacat ggaagccatc aatgcttgtc 840 ctcaccatgg ttttgataca tggctattga tgagttattt ctatgatggg atgtcttcct 900 caatgaagca actcctcgag acaatgtgta gaggagattt catgagtaag aatccggagg 960 aagctatgga tttcttgagt tatgtggctg aagtttcaag gggatggaat gaaccaaaca 1020 aaggagaagt gggaaagatg aagtctcaac tgagtgcttc taatgctaag gctgggatgt 1080 acaccttgaa tgaagatgtt gatatgaaag caaagtttgt agctatgaca agaagattgg 1140 aggagctaga actgaaaaag atgcatgaag tacaagctgt tgctgaaaca ccagtgcaag 1200 tacagccgtg tcctatttgt caatcttatg aacacttggt ggaggagtgc cctacaattc 1260 cagttgtaaa ggaaatgttt ggagatcaag caaatgtcat tggacaattc aggcccaata 1320 acaatgctcc gtatggaaat acttacaact caagttggag gaatcatcca aatttctcat 1380 ggaagccaag agcacctcag tatcaacagc cggctcaacc atctcaacaa gcttcaagcc 1440 ttgaacaagc aataatgaat ctcagtaagg ttgtgggaga tttttttgga gaccaaaaat 1500 ccatcaatgc tcaactcagt caaagaattg acagtgtaga aaatactttg aataaaagga 1560 tggatgtgat gcaaaatgac gtatctcaaa agatagataa tctccaatac tcaatctcaa 1620 ggctcactaa cttgaacaca gtgcaagaga atggtagatt tccttctcaa cctcaccaaa 1680 accccaaggg tatccatgta gtggaaactc atgagggaga atcttcacag gtgagagatg 1740 ttaaagcctt gatcactctc aggagtggta taaaagttga gctgccaaca cccaagccac 1800 atgttgaaga ggaagaagaa gaagagacaa agaagaggga ggaaatcaaa ggaaagaaga 1860 aagatatcag tgaaggaaaa gaggaccata attcaacagt gaatgcaaat ccggagaaag 1920 tacttattaa agaagaaatg ctgaagaaac acacctctcc accttttcct caagctttgc 1980 atgggaaaag ggggattaga aatgcatcaa aaattcttga agtattgaga caagtgaaag 2040 tcaatattcc attgctagat atgattaaac aagttccaac atatgcaaaa ttcctaaatg 2100 acttgtgtac tatcaaaaga tggttgaatg tgaacaagaa agccttcttg actgagcaag 2160 taagtgctat catacaatgc aagtctcctt tgaagtacaa agatccagga tgtcctacca 2220 tttcagtcat gattggagga aaggtagtgg agaaagcttt gttagacttg ggagcaagtg 2280 agaatttgct accatactct gtctacaagc aattgggact tggtgaattg aagccaacat 2340 caatcactct atctttagca gatagatcaa tgaaaattcc aaggggggta attgaagatg 2400 tcttagttca agttgataac ttctactatc cagtagattt tgttgttctt gatacggacc 2460 ccattgtcaa ggaagttaat tttgttccta tcatccttgg aaggccattc ctagctacct 2520 caaatgcaat catcaactat aggaatggac ttatgcaact cacttttggc aacatgacac 2580 ttgagctcaa tatcttttat atgtctaaaa agctaatcac tccggaagaa gaagaaggtc 2640 caaaagaggt atgcattatt gacactctag tggaggagca ctataatcag aatatgcaag 2700 acaagttgaa tgaaagtctt ggggatcttg aagaagggtt gcctgaaccc tctgatgtgc 2760 ttgctactct acaaggttgg aggaggagag aagagattct acctttgttc aataaagagg 2820 aggcacaaga agctgatgaa gaagagaccc caaagctcaa tttgaagcct ctgcccatgg 2880 agttgaaata cacatacctg gaagagaatc aacaatgccc tgttgttata tcttcatcct 2940 tactagtcat caggaaaagt gtctacttga agttctcaag aggtgtaaga aagtaatagg 3000 atggcaaata tttgacttga aaggcattag tcctttggtt tgtacacatc atatatacat 3060 ggaggaagaa gctaaaccaa ttcatcaacc tcaaagaaga ttgaatcctc atttgcaaga 3120 ggtggtgcga gttgaagtgc tgaatctact tcaagcaggt attatctacc ccatatctga 3180 cagcccttgg gtgagtccta ctcaagtggt atcaaagaag tcagggatta ctgtggttca 3240 aaatgagaaa ggagaagaaa ttactacacg cctcacttca ggttggaggg tgtgtattga 3300 ttataaaaaa ttgaatgttg tgacaaggaa agatcatttt ccattgccat ttattgatca 3360 agtcttggag agagtctctg gccatccttt ctattgtttc ttggacgggt actccggata 3420 ttttcaaatt gaaattgatg ttgaagatta ggagaagacc actttcacat gtccgtttga 3480 aacatatgcc tacagcagaa tgccttttgg tttatgcaat gcacctgcaa cattccaaag 3540 atgtatgcta agtatcttta gtgatatggt agagcgaatt atgaaggttt tcatggatga 3600 catcaccata tatggaggta catttgaaga atgcttagtc aacttggaag cggttcttaa 3660 aagatgcatt gaaaaggact tggtgctcaa ctgggagaaa tgccatttta tggtacatca 3720 aggaattgtc cttggccata tcatctccga gaaaggcatt gaagttgata aagcaaaggt 3780 ggaacttatt gtcaaattgc catccccaac aaytgtaaaa ggagtaaggc tattccttgg 3840 ccatgtaggg ttctatagga gacttataaa agatttctct aatctytcaa mcctctttgy 3900 gaacttttgg ctaaggatgc taagtttatw tgrgatgaaa grtgtcaraa gagttttgat 3960 caaytgaagc aattyttgas arcmactcca atagtgaggg ctcctaactg gcaaytaccc 4020 tttgaagtaa tgtgtgatga cagtgacttt gctataggag ctgttcttgg ccaaagagaa 4080 gatggaaagc cctatgtgat ctactatgca agcaagacat tgaacgaagc tcaaaggaac 4140 tacacaacta cagagaaaga attgttagct gtagtgtttg ccttagacaa gtttcgtgct 4200 tatctggtag ggtctttcat cattgttttc actgaccatt cagccttgaa gtatttattg 4260 acaaaacaag atgcaaaagc aaggttgatt agatggattc tcttattaca agagttcgat 4320 ctccaaatca gagataaaaa aggagtggag aatgtggtag ctgaccacct ttcaaggtta 4380 gttatagcac acaattccca tgtcctacct attaatgatg actttcctga ggaatcatgt 4440 tgctagcaaa aactccttgg tatgctcata ttgctaacta tctagttact ggtgaatttc 4500 caagtgagtg gaaagcacaa gataggaagc acttctttgc aaagattcat gcttattatt 4560 gggaagagcc tttccttttc aagtattgtg cagatcaaat aataaggaag tgtgtccctg 4620 aggaagagca acaaggaatc ctcagccatt gccatgaaag tgcatgtgga ggccactttg 4680 cctctcagaa aacagccatg aaggtgttgc aatcagggtg tacttggcca tcactcttca 4740 aagatgccca catcatgttt aggagttgtg atagatgcca aaggctcggg aagctaacaa 4800 gaaggaatca aatgcctatg aacctcattc taatagttga tctctttgat gtttggggca 4860 ttgactttat gggacctttc ccaatgtctt ttggtaactc ttatatcttg gtgagggtgg 4920 actatgtttc taaatgggtt gaggcaatcc cctgcaaaca caatgatcac aaggtggttc 4980 tcaagtttct caaagagaac atcttctcaa gatttggggt gcctaaggcc ataatcagtg 5040 atggaggtac tcatttttgc attagacctt ttgaaaccct attagccaag tatggagtga 5100 agcataaggt agctacacct tatcaccctc agacttccgg tcaagttgag ctagcaaaca 5160 gggaaataaa aaatatgttg atgaaggtgg tgatcacaag aagaagagat tggtctatta 5220 agcttcatga ttcattatgg gcatatagaa cagcttacaa gactattctt ggcatgtctc 5280 catatcgcct agtttatggc aaagcatgcc atctccctgt ggaagttgaa tataaggctt 5340 agtgggcaat caacaagtta aacatggact tgatcagagc cgggacaaag aggtgcttag 5400 accttaatga gatggaggaa ttaagaaatg atgcttacat caattccaaa gttgcaaaac 5460 agaggatgaa gaggtggcat gatcaattaa tctccaacaa agaattccgg aaaggacaaa 5520 gagtcttact ctatgattca aggcttcata tctttcctgg gaagctcaat tcgaggtgga 5580 taggtccttt cattattcac caagtgcatc ccaatgaagt ggtggaatta ctgaattcca 5640 acagcactga tacttttaag gtcaatggcc atcgtctcaa gccattcatt gagtcattca 5700 agcaagaaaa ggaggaaatc aacctccttg agccatagaa agcctaatca gaaaagggtt 5760 agatgggctt ggtttcacca aagtccatat ttttgtttaa ttttgttaat ttaaaagctt 5820 tattaattct tttgatttta attttggtct taagttttgt tatttatatg taacttaatc 5880 tttttgaatg atctaatgta ggaggaattg caaagaaatc gaaagaaagt ctcttggagc 5940 taaaaaggag ttcaaaagca agggaaaatt catggcctgc gagatttcgc agccaaatga 6000 ggcctctgcg aaaatggccc ttggctgcga aattatttcg cagctccatg cccccctctt 6060 ggcacacgag tgccatttcg cagcatagtc ccatgctcac tcagccgccc attgagggta 6120 atttggattg cagggctagg tcattccact ccgagctcta ctttgacaca gccactttca 6180 gacttcagcc cgagctcaag gactccttcc atctactaca gaggtaccat atggagcatt 6240 tactgactcc cagggatttt ttctatcccc gtatagcaat ggacttctat cagtccatga 6300 ccacacacca ggtccaagat cctactgtta tccacttcac catagatgga cgtcatggta 6360 ttctgggagc tagacacata gtagaggcat tgcatattcc ctacgagcca gcccgtctag 6420 aggattattg agtctggact catcctgccc agagcgacat agttcatatt ctatctagag 6480 gagcatcctc acgccagtat ttgttgagaa agaagctcat tcctagcatg tttttcatag 6540 atgcactcct gcgtcataac atctttccac ttcagcatta ggtgcagagg agagaagttt 6600 tactagaggc attgttcagg atatctgagg aattcttctt tggcccgcat tatctcatta 6660 tggccgctct tctgtacttc gaagagaagg tccataggaa gaagctgctc agagcggatg 6720 ctattccact tctcttcccc agattgctat gtcagattct ggagcacttg ggctacccat 6780 caaagcctca acttgagcgc aaacgtattt gccgagagat attcactctc gaaaaatgga 6840 cgaatatgac aacctatagt gcagagtcgg gagccccagc tggagcagag cattcagaca 6900 ttccacatcc agagcagcca gaggagccac agccggttga gataccagct gacattacag 6960 agcctatacc agaggttgca ccttttgctc ctcgtgccac accacagact ccccctgtta 7020 ttccagctac atcaaagccc tctcatccat ctgagcctag gattgccatg tccatttctg 7080 agtacagagg tctatgtcac actttgcaga cattaaccac ttctcaaagc atccttagtc 7140 aggagatgac agttcttcat gatcatcagg agcagattat cgccattaag acttagcata 7200 ctgccatcct gaggtagatt cagcatcatc tgggtattcc atcagctcct gagcacccca 7260 tgcctatcct ctcaaaacac acagagccat cacaggcccc tcatttcata gagcaggctt 7320 tgccctctgg ggagtcaact acaggagatg cagagacatc cacctgagcc atcatcatcg 7380 tctcactatc tgatcattta catatttttc tttatgtatt ttctttatgt atttccttac 7440 taaagtagca cttgtaatcc catgcttttg atattttata tattgggatt ggatgtatta 7500 cttgttttcc tttatattgt actttcatga agtaatacaa atctatcaat tttttagcac 7560 tcttagcatt attttatttt aattcctcta ctcatatctt ttattgtttt tgaaacatgt 7620 ggtttctcct aatctactcg aacttcatat cactcaggag gcaccacttc ctccccgtaa 7680 tttcaatcgc tcatgccaca ttaaggacaa tgttcagctt ggttgggggg agagttgagg 7740 aaggaagttt tttgttgtta gtactaagta ttttggtaat ttagtttatt tttgtttaaa 7800 tttannnnnn nnnnngtttt tattccactc tccatggtta ttaaggaaaa attctcaaat 7860 taaaataaga taaatcgaat ctttgctttt acttgactta gagtttgtat tatgcttact 7920 aaagttgatg aattgttgaa cttatattga attcaaccgt agttcttcca ctttaagcta 7980 ttcacacact gtgcacaata ggtttcgatt ataagatgaa aatccatttc cctcttgact 8040 taggaaaatt tagacttggt acctttgacc tcatttaata gtgttgggac accttataaa 8100 aggccaatga gcctttgaaa agaaaagaaa gaaagaaaaa tgtttgcttg ccttgaaact 8160 cgagcaaggt ctgaggggta tatggtgaaa atctttaaaa cctggtgccc taagccttca 8220 ttggttggga gtcaccgacc tcaatgctca ttacaagggt gaataggtgg agtttaacat 8280 actgtaggtg cttgggtatt aaaaattcat tctcaaaagt ccggtgtaaa attcgaggag 8340 ttagcggttg aaagatcctt aaagcttgat gccctaaacc ttaattggtt aggagtcatc 8400 gatggacccc cgttacatgg acaatttaga aaagaatacc tttaagcctt gtactcctaa 8460 aaaaaaaaat gtgtgaaata aaagggtgcg tttttagcct attgaatttg gtcagtttgc 8520 taagtattga aaaagaacta ggttaggggg agagattagt ttagcatact atattcggaa 8580 gctatcaagt aacacttaga cttttgtgga agagtaaggt tgggtccttt ggaagtggaa 8640 atgattttaa agcttcaatt tgcataatac tttctcttta tgaattgtga ttaagtaaag 8700 tatttgataa ctcttgctga aatttgagtt ttatatcttt aatgtcccat gtgagagctt 8760 gatcatcatg ccacttaaat ttttttgaag tgatcagcat gattttgtaa agtatattac 8820 tgattagttt attttttctc tcctttattg ctaagggact agcaatatgt cggttggggg 8880 gag 8883 // ID Copia-69_VV-I repbase; DNA; EDCOT; 4024 BP. XX AC chr18; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-69_VV_; KW Copia-69_VV-LTR; Copia-69_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4024 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr18; Positions 16221632 16225655. XX CC 'TTAA' target site duplication CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1121..2590,2594..3568) FT /product="Copia-69_VV-I_1p" FT /translation="MHTPRVTIFKDLDKTYNSMVKVGNGGYVDVKGRGTVA FT IKTNSGIKLISDVLFVPDISQNLLSVGQMLEKQYSLQFKDNQCIIFDPYGE FT KLLCLKMKSKSFAINWENAAEYAYAGVTQSVSDLWHKRFGHYNQRSLVELK FT KLELVEDMPNVSNEAQICEICQQGKQSRLPFKNNQAWRATEKLQLIHTDVC FT GPMKTTSLSGNKYFILFIDDYTRMCWVYFIKLKNEVFSVFKQFKALVENQS FT NLSIKILRSDNGTEYTSSQFVEFCSTAGIKRQLTTPYTPQQNGVSERKNQT FT VKQMARCLLFEKKMPSNFWAEAVNTFAYLLNRLPTKSLKNKTPHEAWYGVK FT PFVNHLKIFGSICYYHVPKPKRSKLDGRAQKGILIGYGTSTKGYRIFCLQI FT NKVVLTRNVKVDEMTTWDWKNKKDAQSDADFDNHEDFQTSKFVDDFPVRGT FT RSLEDIYQRCSLSITEPKSYVEAKDSEAWRRAMQEELKMINKNETQLVERP FT KNHKVFEVKWVFKTKLNSDGSICKHKARLVVKGYAQQYGVDYQETFAPVAR FT YDTIRLLFVLSAQNSWHIHQLDVKSAFLNGFVDEEIYVEQPDGVVAPGKKD FT YVYLLRKALYGLKQAPIHCMTKLGFVRSQSEATLYVKTDDVQLLIISLYVD FT DMLVTGNHPKLIQSFKDEMNRVFEMTDLGVMKYFLGMEVMQSCSRIFICQQ FT KYAMDMLKKFKMQDCKLVSTPMTTSEKLSKDDGSEKINEGLYRSLIGSLLY FT LTTSRPDILFVVSVLSRFMHSPSEKHFSAVKRVLRYIKGTIDLGVQFSKSV FT EGDLKLLGYSDSD" XX SQ Sequence 4024 BP; 1387 A; 693 C; 846 G; 1098 T; 0 other; ttaacttgca gctttatacc tgtaatttct tgaacaagtg gtattagagc cacagttggt 60 cttacaggac ctgtgttttg agagaaaacc aagaaagttc acttcataac ccatttgaaa 120 ccacactaga aaatggcaac cagcagcatc tctttgttag ctcctcaaat ctttgtggga 180 gaaaactatc aaatttggtc cgtaaagatg caaacgtacc tggaagcatt tgatctttgg 240 gaagttgtag ctgaagacga accaatagct ccacttccgg cgaatcctac cttagcacaa 300 atcagagctc atactgacga aaagaccaaa agtttaaagc taagacttta atccaaaatt 360 cagttgttga ctcagtattt catagaatta tgaattgcag gacaaccaaa gaagcctggg 420 acaagcttaa attgaagtat caaggaagtg atagaaccaa acaaatgcaa gtgctgaatt 480 tgaaaaggga cttcgagttt ctaaccatgc aagaagatga aactatcacc aagtattctg 540 aaaaaattgc tttgattgtt aacaaaatca ggtcgcttgg tgaagaattt cctgatgcaa 600 atatcgtgga gaaggttctt gtgacacttc ctgagaggtt tgagtccaag atttcatctc 660 ttgaagaatc tagggacctt tcacaaattt cacttgctaa actaatgaac gtactccaag 720 cataagagca aagaagagat ttgaggcaag agaacgtcac agaaggtgct tttcaaatgc 780 agaccctaca atctaataaa gacaaaaacc agttcagcaa gaagaaaagt aaaaacagag 840 agaagagcag caaagaaggg gcccaacaga agaaatattc aacctgctca cattgcaaga 900 agactacgca tctagagaaa tattgttggt ggaggccaga tgcaatatgc ggcaattgca 960 aacagcttgg gcatgttacc aaagtctgga aatataaaaa taaaggtcct caatttcagc 1020 aagcacaagt tgctgatgca gattcacagg aggagaaact ctttgtagta tcatgtttct 1080 caagtcaaga ctcttataat gcttggctca ttgatagtgg atgcacacac cacgtgtcac 1140 aatattcaag gatcttgaca aaacctacaa ctctatggtg aaagttggga atggtggata 1200 cgtggatgtc aagggaaggg gcacagttgc tatcaaaaca aattcaggta tcaagctcat 1260 ctctgatgtg ttatttgtac ctgatattag tcaaaatcta ttgagtgtag gtcaaatgct 1320 tgaaaagcaa tattccctgc aattcaaaga caaccaatgc atcatctttg atccatatgg 1380 agagaaattg ctttgtttga agatgaaaag caagagcttt gccatcaatt gggagaatgc 1440 tgctgaatat gcatatgctg gagttactca aagtgtttca gacctatggc ataaacggtt 1500 tggacactat aaccaaagaa gcttagtaga gctaaaaaaa cttgagttgg tggaagacat 1560 gccaaacgta tctaatgaag ctcaaatatg tgagatttgt caacaaggca aacaatcaag 1620 gttgccattc aaaaataatc aagcatggag agccactgaa aagcttcaac tcatacacac 1680 cgatgtttgt ggtcccatga aaacaacttc tttgagtggt aacaaatact tcattctctt 1740 tatagatgac tataccagaa tgtgttgggt atattttatt aaattaaaga atgaagtttt 1800 ctctgttttc aaacaattca aagcccttgt agaaaatcaa agcaacttga gcattaaaat 1860 cttaaggtcc gacaatggta cggaatatac ctccagtcag tttgttgagt tttgtagcac 1920 tgcaggcatc aaacgtcagc taacaactcc atacactcca cagcaaaatg gtgtctcgga 1980 gaggaagaat caaactgtaa agcagatggc caggtgtctt ctatttgaga aaaaaatgcc 2040 aagtaatttt tgggcagagg cagttaacac ctttgcatat ttgctgaaca gattgcctac 2100 aaaatccttg aagaacaaaa caccacatga agcatggtat ggtgtcaagc cctttgttaa 2160 tcatcttaaa atatttggaa gcatatgcta ttatcatgta ccaaaaccta aaagaagcaa 2220 gctggatggc agagctcaga agggcattct cattggctat gggacatcaa ctaagggcta 2280 tagaatattc tgtttgcaaa ttaacaaagt tgtcttgacc aggaatgtaa aagttgatga 2340 aatgacaact tgggattgga aaaataaaaa agatgcgcaa tctgatgccg acttcgataa 2400 tcatgaagat tttcaaactt ctaaatttgt agatgatttt ccagtgaggg gcacaagaag 2460 tttggaggac atctatcaaa ggtgcagttt atcaataact gaaccaaaaa gttatgtaga 2520 agccaaagat tctgaagcat ggaggagagc aatgcaagaa gaattgaaga tgattaacaa 2580 gaatgaaacc tagcagcttg tggagagacc caaaaatcac aaggtgttcg aagtgaaatg 2640 ggttttcaaa acaaaactca attctgatgg ttcgatatgc aagcacaaag ctaggctagt 2700 ggtgaaggga tatgctcaac agtatggtgt tgattatcag gagacttttg ctcctgtggc 2760 aaggtatgac actatcaggc tactttttgt actttctgct caaaattctt ggcatattca 2820 tcagttagat gttaaatctg ccttcttaaa tggatttgtt gatgaagaga tatatgtaga 2880 gcaaccagat ggggttgtgg ctccaggcaa aaaggactat gtgtaccttc taaggaaggc 2940 attgtatggc ttgaaacaag ccccaataca ttgtatgact aaacttggtt ttgttagaag 3000 tcaaagtgaa gcaaccttat atgtaaaaac tgatgatgtc cagcttttaa taatctctct 3060 ttatgtagac gacatgcttg taacaggaaa tcatcccaag ttaattcaaa gcttcaagga 3120 tgagatgaat agagtctttg aaatgaccga tcttggagtc atgaagtact ttttgggaat 3180 ggaagtgatg caatcatgtt caagaatttt catatgccaa cagaagtatg ctatggatat 3240 gctgaaaaaa tttaaaatgc aagattgcaa gcttgtgtct actcctatga caaccagcga 3300 gaagttaagc aaggatgacg gctctgagaa aataaatgaa ggcttatata gaagcttaat 3360 tggtagcctt ttatacctaa caactagcag acctgacata ctgtttgttg ttagtgtgct 3420 ttctaggttc atgcactcac caagtgagaa acatttttcg gcagttaaaa gagtattaag 3480 gtacatcaag ggaacaattg atcttggagt tcaattttca aaatctgtag aaggtgattt 3540 gaagctgcta ggctactccg acagcgacta gggaggttgt gttgatgatt caagaagtac 3600 ttcagggtac ttattctcct taggctcagg ttttttcact tggagctcaa agaaacaaga 3660 aaccacaggc caattaacag cagaggcaga atacattgct gttgcatctg ctgtaaatca 3720 agctttatgg ttaagaaaaa tactgaaaga cttggggcaa gagcaagttg aagcaaccaa 3780 cattatgtgt aacaacattt ctgcagtatc aatttcgaaa aatcttgtgt ttcatggtcg 3840 aacaaagcat attaagatca agtatcattt tattagagaa gttcaacaat ccaatgaagt 3900 gttacttgtt cattgttcct ctgaaaatca acttgcagat atattcacaa agcctttacc 3960 aatggaaagg tttgaagctc ttaagcagaa gataggtgtt tgtcatccgg atgccaagga 4020 ggag 4024 // ID Copia9-PTR_I repbase; DNA; EDCOT; 4138 BP. XX AC scaffold_750; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia9-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4138 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4138 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 294-294 (2007). XX DR Genome; scaffold_750; Positions 4288 8425. XX CC Positions [1521-2024] - Integrase core CC 'AAAAA' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 446..1621 FT /product="Copia9-PTR_I_1p" FT /translation="MKNAESVNDYFGRTLTIANKMRIHGEQMNDVVIIEKI FT LRSMTSKYDYVVCSIEESNDLDTMSIDELQSSLLVHEQRISRHVNDEQALQ FT ITHGFQQGGRCGGRGTYQGRGRGRGRFGFNKSILECYYCHELGHFQWECPK FT RDKEQRVNYAETKDEMLLMAFVDSNETAMEHIWFLDSGCSNHMCGKQNMFF FT DLDKSFRETVKLGNDSSLTVQGKGNIRMEVNGCVHIITEVFYVPDLKNNLL FT SIGQLQEKGLTVLIQHGICKIFHKEKGLIMETEMTHNRMFTVHARYTPKES FT KCFSSLITDQADLWHCRYGHLSWNGLKVLQQKKMVKGLPLFTASKKVCEDC FT LVGRQHRDPFPRASMWRANNILQLVHADICGPINPVSNGKKTVSYYIHR" FT CDS 1551..4106 FT /product="Copia9-PTR_I_2p" FT /translation="MLTYVDQLIQFQMAKKRYLITFIDDYSRKTWVYFLME FT KSEAYSTFKSFKARVEKETGTYIRRLRTDRGGEFTSQDFTDFCNEHGIQRQ FT LTTAYTPQQNGVAKRKNRTIMNRVRSMLTAKQIPKTFWPEAVNWTVHILNR FT CPTLVVKNKTPAEMWNGHKPSVDYFRVFCCISHVHVPDSKRVKLDARSVKC FT ILLGVSDESKAYKLFDPISNKIIISRDVVFEEDQQWTWDDDHKQAIFTELE FT WENDTEGAVENEGGEPESDDSEESIFNEETGDSEPDGGNIEADGDNINISH FT EDINISHEEHETRTRRPPGWIRDYETGQGLSDEETVNLTHLALFTDGDPIT FT FAEAVKFEKWRKAMDQEIQVIEKNDTWDLTVLPSGGKTIGVKWVFKTKFNE FT HGEVDKYKARLVAKGYCQQHGIDYAEVFAQVARLDTIRIVISIAAQKSWVI FT YQLDVKSAFLHGEITEEVFVEQPPGYEQKGHEAKVYRLKKALYGLKQAPRA FT WYSRIETYFSKEGFIKCPYEHTLFIKTVGGGKILILCLYVDDLIFTGNDNA FT MFEEFKKSMKTEFDMTDLGRMKYFLGIEVLQKADGIFITQRKYAQEILERF FT NMAQCNSVHNPVVPGFKLTKDEEGVAADSTVYKQIVGILMYLTATRPDLMF FT SVSLISRYMERPTDSHFQAAKRILRYIKGTIVFGIFYKKGGKAELVGYSDS FT DYAGDQNDRKSTSGYAFLMTSGAVSWSSKKQPVVTLSTTEAEFVAAASSAC FT QVVWLKRILTILNQEQSNPTVVFCDNISAIKLSKNPVMHGRSKHIDVRFHF FT LRDLVKDGILELIHCSTQQQVADILTKPLKLDTFLKMRNLLGVHEYPGIN" XX SQ Sequence 4138 BP; 1368 A; 714 C; 963 G; 1093 T; 0 other; tttggtatca gagcctcctc acgaggtttg atcaaattct tttcaggtat taaagtgaag 60 agtcagagac atggcatccg aaaatagttt cgtgcaacct gccattccaa ggtttgatgg 120 tcactatgac cattggagta tgctgatgga gaatttcttg cgttccaaag aatattggaa 180 cttgatagaa acaggaatca ctgctgcagc agagggatca agtctaagtg agctacaata 240 gaagacgtat gaagatcaaa agctgaaaga tctcaaggcc aagaactatc tgttccaagc 300 cattgatcga tcgatactgg aaaccatctt gaagaaagat acagctaaag aaatatggga 360 ttcattgaag caaaagtatc aagggacagc tcgtgtcaag cgtgctcaat tgcaagctct 420 tcgcaaagag tttgaggtgt tgcatatgaa gaatgcagaa tctgttaatg attattttgg 480 cagaacactc accattgcaa acaaaatgcg aattcatgga gaacaaatga atgatgtggt 540 tatcattgaa aagattttga ggtctatgac ttcaaaatat gattatgttg tttgctccat 600 tgaggaatcc aatgatttgg acacaatgtc tatagacgag cttcaaagca gcctcttggt 660 gcatgaacaa cggatcagca gacatgtgaa cgatgaacaa gcacttcaga tcactcatgg 720 attccaacaa ggaggaagat gtggaggtag aggcacttat caaggacgag gaagaggaag 780 gggtaggttt ggattcaata aatccatcct agagtgttac tattgtcatg agttagggca 840 ttttcaatgg gaatgtccta aacgagacaa ggaacagagg gtgaattatg ctgaaacaaa 900 ggatgagatg ttgctgatgg cgtttgtaga ttccaacgag actgcaatgg agcacatttg 960 gtttcttgat tctgggtgca gtaatcacat gtgtggaaaa cagaatatgt tttttgatct 1020 tgacaaaagc tttcgagaga ccgtgaagct tggcaatgac tctagtctta ctgtacaagg 1080 gaaaggaaac attcgaatgg aagtaaatgg gtgtgtgcat ataatcacag aagttttcta 1140 cgtaccagat ctaaagaata atctgttgag tattggccaa ttgcaagaga aggggctgac 1200 agttctcatt caacatggaa tttgcaaaat atttcacaaa gagaaaggtt taatcatgga 1260 aacagaaatg acacacaaca ggatgttcac tgtgcatgct cgttacacac ctaaggaatc 1320 aaaatgtttc tcctcactga tcacagatca agcagacctt tggcactgtc ggtatggaca 1380 tcttagctgg aatgggctca aagtgctgca acaaaagaaa atggtgaaag ggttacctct 1440 gtttacagcc tccaaaaagg tttgtgagga ttgcctggta ggaagacaac atcgtgatcc 1500 atttcctaga gcaagcatgt ggagagctaa caacattctt cagttggtac atgctgacat 1560 atgtggacca attaatccag tttcaaatgg caaaaaaacg gtatcttatt acattcatcg 1620 atgattacag caggaaaact tgggtgtact tcttgatgga gaaatcagaa gcttattcca 1680 cattcaaatc ttttaaagcc agagttgaga aggaaactgg aacttacata cggcgcctta 1740 gaacagaccg tggaggagaa tttacatccc aggatttcac tgatttctgc aatgagcatg 1800 gcattcaaag acagctgacg accgcttata cacctcagca gaacggtgta gcaaaaagga 1860 agaaccgcac tattatgaat agggtgcgaa gcatgttgac agcaaagcaa attcccaaga 1920 cattctggcc tgaagcagta aattggacag tgcatattct aaatcgatgt ccaacactag 1980 ttgtgaagaa caaaacacca gcagaaatgt ggaatgggca caagccatca gtggactact 2040 ttcgagtttt ttgttgcatt tctcacgtgc atgtacctga cagcaaaaga gtaaagcttg 2100 atgccagaag tgtaaaatgc attttactgg gggtcagtga tgaatctaag gcttataagt 2160 tgtttgatcc aatttcaaat aaaataatta taagccgaga tgtggtcttc gaagaagatc 2220 agcaatggac ctgggatgat gatcacaaac aggcaatatt tactgagctt gagtgggaaa 2280 atgacacaga aggagcagtt gaaaatgagg gaggtgaacc agagtctgat gactctgaag 2340 aatctatttt caacgaagaa actggagaca gtgaacccga tggaggtaat attgaagctg 2400 atggagataa cattaatatc tcacatgaag acattaatat ctcacatgaa gaacatgaga 2460 cacgaacacg aagaccacca ggttggataa gagactatga aaccggacaa gggctctcag 2520 atgaagaaac tgtcaaccta acacatttag ctttgttcac tgatggagat cctattacat 2580 ttgctgaagc tgtgaagttt gagaaatgga gaaaagccat ggatcaagag atacaagtta 2640 tagaaaagaa tgacacatgg gatttaacag tgctgccatc gggaggaaaa actataggag 2700 taaaatgggt gtttaaaaca aaattcaatg aacatggaga agtggataag tacaaggctc 2760 ggctagttgc taaggggtac tgtcaacagc atggaattga ttacgctgag gtctttgcac 2820 aagtagctcg cctggacact atacgaattg ttatatccat tgctgcacag aaatcttggg 2880 taatctacca gcttgatgtc aagtcggcct tcctgcatgg agaaattact gaagaagtct 2940 tcgttgagca gccaccagga tatgaacaga aggggcatga agctaaagtt tatcgactga 3000 agaaggcatt atatggcctt aaacaggctc ctcgcgcctg gtatagtcgc attgaaacat 3060 atttcagcaa agaaggcttc atcaaatgtc cttatgagca tacattattc attaaaactg 3120 taggtggagg taaaattctg attttgtgtc tttatgttga tgatcttatc tttactggca 3180 atgataatgc catgtttgaa gaatttaaaa agtccatgaa aactgagttt gacatgactg 3240 atcttgggcg aatgaagtac ttccttggca ttgaagtatt acaaaaggca gatggtatct 3300 tcattactca acgaaagtat gctcaagaga ttctggaaag gtttaacatg gctcagtgta 3360 actcagtaca taaccccgtg gttcctggtt ttaaactcac gaaagatgaa gagggagtag 3420 cagctgatag caccgtttac aaacaaatag tgggaatcct aatgtatttg actgccacac 3480 gccctgattt aatgtttagt gtcagcttga tcagcaggta tatggagcgt ccgactgatt 3540 ctcacttcca agcagcaaag agaattttac gatatataaa gggcacaatt gttttcggga 3600 tattctacaa gaagggagga aaagcagaac ttgtaggata ttcagatagt gactatgctg 3660 gcgatcaaaa tgacaggaaa agcacgtcag gatatgcttt tctcatgact tcaggagctg 3720 tttcttggtc ttcaaagaag caaccggtgg ttactctctc taccactgaa gctgaatttg 3780 ttgctgcagc atcaagcgca tgccaggtcg tgtggttgaa aagaattctg acaatcctaa 3840 atcaagagca aagtaatcca actgtggtgt tttgtgataa tatatcagca attaaacttt 3900 caaagaatcc tgtgatgcat ggtcgtagta aacacataga tgtaagattc cattttctcc 3960 gtgatcttgt taaagatggg attctggagt taattcattg ttctacacag caacaagttg 4020 cagatattct aaccaaaccg ttgaagcttg atacctttct gaaaatgcga aatttgctgg 4080 gagtgcatga atatccaggt ataaactgaa tgataatggc attcagttta agggagga 4138 // ID BNTAN repbase; DNA; EDCOT; 177 BP. XX AC X16589; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 11-NOV-1996 (Rel. 1.1, Last updated, Version 1) XX DE B. nigra tandem repeat DNA (clone BN1G 9, BN1G 23, BG1G 14). XX KW BNTAN; tandem repeat. XX OS Brassica nigra OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-177 RA Lakshmikumaran M.; RT "BNTAN."; RL Direct Submission to Genbank (21-SEP-1989)Lakshmikumaran M., Tata RL Energy Research Institute, Biotechnology Group, 90 Jor Bagh, New RL Delhi 110003 (India).. XX DR GenBank; X16589; Positions 1 177. XX SQ Sequence 177 BP; 51 A; 42 C; 30 G; 54 T; 0 other; agcttcttac aaagtgattc atccgggttt gattggaacg acgcagaagc tgtcctattc 60 ccaaactggg aaactggaat cacctgattt aaaagtggga taacttcttc atcccaactc 120 ctatgagatt tattcaactt cctggtgatt ctccaccaca tttatgtatc caaatca 177 // ID COP6_LTR_MT repbase; DNA; EDCOT; 192 BP. XX AC . XX DT 28-DEC-2006 (Rel. 11.12, Created) DT 28-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Long terminal repeat sequence of COP6_MT LTR retroposon from DE Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Internal; Interspersed; repeat; COP6_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-192 RA Shankar R. and Jurka J.; RT "COP6_MT: A copia type LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 612-612 (2006). XX DR [1] (Consensus) XX CC The LTR flanks the internal region on both termini. XX SQ Sequence 192 BP; 72 A; 32 C; 19 G; 69 T; 0 other; tgttagagac acaatccctt aattattgga tcatatcaag tcaacacatc aagttataaa 60 taacaattat ctgcatatca agtcagcaca tcttatacat aattagcaat tatgtttcct 120 tatagcttat catattctgt tgtatatatt gtatgtctta ctcaacattt taaagataag 180 aaatacaata ca 192 // ID SHAMET repbase; DNA; EDCOT; 250 BP. XX AC . XX DT 22-JAN-2007 (Rel. 12.01, Created) DT 22-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW DNA transposon; Transposable Element; Nonautonomous; transposon; KW Inverted; Interspersed; repeat; SHAMET. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-250 RA Shankar R. and Jurka J.; RT "SHAMET: A putative non-autonomous DNA transposon from barrel RT medic."; RL Repbase Reports 7(1), 100-100 (2007). XX DR [1] (Consensus) XX CC The internal region coding of transposase is missing. 5 bp TSD is CC present. The sequence is present in low copy number in the genome CC and poorly conserved. XX SQ Sequence 250 BP; 87 A; 40 C; 31 G; 92 T; 0 other; ctccctccat ccttaatact tgacccattt ggaatttttt aattttgacc taactaactt 60 tgaccgtatt tttcaactaa tatacaaaga taaataacat catataagat gtcgttagat 120 tcgtctcgat gagtattttc aaaatatcaa attttcataa ttttttctaa tatattattc 180 aagatattta agctcaaagt tatgcattga catacgtaat aagatcaact gtattaaagg 240 acggagggag 250 // ID HARB-N4_Mad repbase; DNA; EDCOT; 361 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW HARB-N4_Mad. XX NM HARB-N4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-361 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1503-1503 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~97% identical to the consensus. 3-bp TSDs are usually TWA. This CC non-autonomous Harbinger is a derivative of autonomous Harbinger CC similar to HARB-3_Mad. XX SQ Sequence 361 BP; 109 A; 57 C; 73 G; 121 T; 1 other; gaccatctcc aacccttggg ctaaaagcca aattttttag cccagaaaca tcttttctgc 60 tccaaccctt ctgccctaaa attttagccc ggaattatta aagaatgaac ttaggctaat 120 ttttttctta aatcaatttt ttaaataaat aaatatgtag attattgtaa attaatttta 180 tgaacatttt aatctaaaaa aatttaaatt ccgataaaca tttggcattt agcccggggg 240 gaaagctggg gggtatttgg cccagaaata gcatttggca tttagcctaa aattttagca 300 tgggttggag agtgtttggg gggggggtaa tttggctttt agcccaggkt tggagatggt 360 c 361 // ID TNT1_I repbase; DNA; EDCOT; 4114 BP. XX AC X13777; XX DT 12-SEP-2002 (Rel. 7.08, Created) DT 09-APR-2007 (Rel. 12.05, Last updated, Version 2) XX DE Nicotiana tabacum retrotransposon TNT1_I, internal region. XX KW Copia; LTR Retrotransposon; Transposable Element; KW reverse transcriptase; endonuclease; protease; internal region; KW TNT1_I; internal portion. XX NM TNT1_I. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RA Grandbastien A.M., Spielmann A. and Caboche M.; RT "Tnt1, a mobile retroviral-like transposable element of tobacco RT isolated by plant cell genetics."; RL Nature 337(6205), 376-380 (1989). XX RN [2] RA Casacuberta M.J. and Grandbastien A.M.; RT "Characterization of LTR sequences involved in the protoplast RT specific expression of the tobacco Tnt1 retrotransposon."; RL Nucleic Acids Res 21(9), 2087-2093 (1993). XX DR Genbank; X13777; Positions 611 4724. XX FH Key Location/Qualifiers FT CDS 82..4065 FT /product="TNT1_I_1p" FT /translation="MSGVKYEVAKFNGDNGFSTWQRRMRDLLIQQGLHKVL FT DVDSKKPDTMKAEDWADLDERAASAIRLHLSDDVVNNIIDEDTARGIWTRL FT ESLYMSKTLTNKLYLKKQLYALHMSEGTNFLSHLNVFNGLITQLANLGVKI FT EEEDKAILLLNSLPSSYDNLATTILHGKTTIELKDVTSALLLNEKMRKKPE FT NQGQALITEGRGRSYQRSSNNYGRSGARGKSKNRSKSRVRNCYNCNQPGHF FT KRDCPNPRKGKGETSGQKNDDNTAAMVQNNDNVVLFINEEEECMHLSGPES FT EWVVDTAASHHATPVRDLFCRYVAGDFGTVKMGNTSYSKIAGIGDICIKTN FT VGCTLVLKDVRHVPDLRMNLISGIALDRDGYESYFANQKWRLTKGSLVIAK FT GVARGTLYRTNAEICQGELNAAQDEISVDLWHKRMGHMSEKGLQILAKKSL FT ISYAKGTTVKPCDYCLFGKQHRVSFQTSSERKLNILDLVYSDVCGPMEIES FT MGGNKYFVTFIDDASRKLWVYILKTKDQVFQVFQKFHALVERETGRKLKRL FT RSDNGGEYTSREFEEYCSSHGIRHEKTVPGTPQHNGVAERMNRTIVEKVRS FT MLRMAKLPKSFWGEAVQTACYLINRSPSVPLAFEIPERVWTNKEVSYSHLK FT VFGCRAFAHVPKEQRTKLDDKSIPCIFIGYGDEEFGYRLWDPVKKKVIRSR FT DVVFRESEVRTAADMSEKVKNGIIPNFVTIPSTSNNPTSAESTTDEVSEQG FT EQPGEVIEQGEQLDEGVEEVEHPTQGEEQHQPLRRSERPRVESRRYPSTEY FT VLISDDREPESLKEVLSHPEKNQLMKAMQEEMESLQKNGTYKLVELPKGKR FT PLKCKWVFKLKKDGDCKLVRYKARLVVKGFEQKKGIDFDEIFSPVVKMTSI FT RTILSLAASLDLEVEQLDVKTAFLHGDLEEEIYMEQPEGFEVAGKKHMVCK FT LNKSLYGLKQAPRQWYMKFDSFMKSQTYLKTYSDPCVYFKRFSENNFIILL FT LYVDDMLIVGKDKGLIAKLKGDLSKSFDMKDLGPAQQILGMKIVRERTSRK FT LWLSQEKYIERVLERFNMKNAKPVSTPLAGHLKLSKKMCPTTVEEKGNMAK FT VPYSSAVGSLMYAMVCTRPDIAHAVGVVSRFLENPGKEHWEAVKWILRYLR FT GTTGDCLCFGGSDPILKGYTDADMAGDIDNRKSSTGYLFTFSGGAISWQSK FT LQKCVALSTTEAEYIAATETGKEMIWLKRFLQELGLHQKEYVVYCDSQSAI FT DLSKNSMYHARTKHIDVRYHWIREMVDDESLKVLKISTNENPADMLTKVVP FT RNKFELCKELVGMHSN" XX SQ Sequence 4114 BP; 1335 A; 713 C; 1034 G; 1032 T; 0 other; actggtatca gagcacaggt tctgctcgtt cactgaaata ctattcactg tcggtagtac 60 tatacttggt gaaaaataaa aatgtctgga gtaaagtacg aggtagcaaa attcaatgga 120 gataacggtt tctcaacatg gcaaagaagg atgagagatc tgctcatcca acaaggatta 180 cacaaggttc tagatgttga ttccaaaaag cctgatacca tgaaagctga ggattgggct 240 gacttggatg aaagagctgc tagtgcaatc aggttgcact tatcagatga tgtggtaaat 300 aacatcattg atgaagacac tgcacgtgga atttggacaa ggttggaaag cctatacatg 360 tccaaaacgc tgacaaataa attgtacctg aagaagcagt tatacgccct acacatgagt 420 gaaggtacga attttttgtc acatttaaat gtgtttaacg gactaatcac acagcttgcc 480 aacctcggag tgaaaatcga ggaagaagat aaagccatct tgctattgaa ctcgttgcca 540 tcttcgtacg ataatttggc aacaaccatc ctgcacggta agactactat tgagttgaaa 600 gatgtcacat cggctcttct actcaatgag aagatgagaa agaagcctga aaatcaagga 660 caggctctca tcacagaagg tagaggcagg agttatcaaa ggagttcgaa caactatggt 720 agatccggag ctcgtgggaa gtcaaagaat cgatccaaat caagagtcag aaattgctac 780 aactgtaatc aaccaggtca cttcaaaaga gattgcccaa atccaaggaa gggcaaaggt 840 gaaaccagtg gccagaagaa tgacgacaac acagccgcca tggtgcaaaa taatgataat 900 gttgtcctct ttataaatga ggaagaggaa tgcatgcacc tgtcaggtcc agagtcggaa 960 tgggtggttg acacagcggc atctcaccat gccacaccgg taagagatct tttttgcaga 1020 tatgtagcag gtgatttcgg cacagtgaaa atgggtaaca caagttactc aaagattgcg 1080 gggattggtg acatttgtat caagacaaat gtcggatgca cattggttct aaaggatgtg 1140 cggcatgtac ctgatttgcg gatgaacttg atctcgggaa ttgctttaga ccgagatgga 1200 tacgagagtt attttgcaaa tcaaaagtgg agactcacta agggatcatt ggtgattgca 1260 aagggagttg ctcgtggcac gttgtacagg acaaatgcag aaatatgcca aggtgaattg 1320 aacgcggcac aagatgagat ttctgtagat ttatggcaca aaagaatggg tcatatgagc 1380 gagaagggat tgcagattct tgccaagaaa tcactcattt cttatgccaa aggtacaact 1440 gtaaaacctt gtgactactg tttatttggt aagcagcata gagtctcatt tcagacatcg 1500 tctgaaagaa aattgaatat acttgattta gtatattctg atgtttgcgg cccaatggaa 1560 attgaatcaa tgggcggtaa caaatatttt gttactttta ttgatgatgc ttcacgaaaa 1620 ttatgggttt atattttgaa aaccaaagat caggtgtttc aagttttcca gaagtttcat 1680 gctctagtag aaagggagac gggtcgaaag ctaaagcgtc tccgaagtga caatggaggt 1740 gagtacactt caagggaatt tgaagagtat tgttcaagtc atgggatcag acatgaaaag 1800 acagttcctg gaaccccaca gcacaatggc gtagccgaga ggatgaaccg caccattgtg 1860 gagaaggtga gaagcatgct cagaatggct aaactgccta agtcattctg gggtgaagca 1920 gttcagacag cctgttacct gatcaatagg agtccatcag ttccgttggc gtttgaaatc 1980 ccagagagag tctggaccaa caaggaggtg tcctactcgc atctgaaggt gttcggttgc 2040 agagcttttg cacatgtacc aaaagagcag agaacaaagc tggatgataa atctattccc 2100 tgcatattta tcggatatgg agatgaagag ttcgggtaca gactgtggga tcctgtaaag 2160 aagaaggtca tcagaagtag agatgtagtc ttccgagaaa gtgaagttag aactgctgct 2220 gatatgtcag aaaaggtgaa gaatggtata attcctaact ttgttactat tccttctact 2280 tctaacaatc ccacaagtgc agaaagtacg accgacgagg tttccgagca gggggagcaa 2340 cctggtgagg ttattgagca gggggagcaa cttgatgaag gtgtcgagga agtggagcac 2400 cccactcagg gagaagaaca acatcaacct ctgaggagat cagagaggcc aagggtagag 2460 tcacgcaggt acccttccac agagtatgtc ctcatcagtg atgataggga gccagaaagt 2520 cttaaggagg tgttgtccca tccagaaaag aaccagttga tgaaagctat gcaagaagag 2580 atggaatctc tccagaaaaa tggcacatac aagctggttg aacttccaaa gggtaaaaga 2640 ccactcaaat gcaaatgggt ctttaaactc aagaaagatg gagattgcaa gctggtcaga 2700 tacaaagctc gattggtggt taaaggcttc gaacagaaga aaggtattga ttttgacgaa 2760 attttctccc ccgttgttaa aatgacttct attcgaacaa ttttgagctt agcagctagc 2820 ctagatcttg aagtggagca gttggatgtg aaaactgcat ttcttcatgg agatttggaa 2880 gaggagattt atatggagca accagaagga tttgaagtag ctggaaagaa acacatggtg 2940 tgcaaattga ataagagtct ttatggattg aagcaggcac caaggcagtg gtacatgaag 3000 tttgattcat tcatgaaaag tcaaacatac ctaaagacct attctgatcc atgtgtatac 3060 ttcaaaagat tttctgagaa taactttatt atattgttgt tgtatgtgga tgacatgcta 3120 attgtaggaa aagacaaggg gttgatagca aagttgaaag gagatctgtc caagtcattt 3180 gatatgaagg acttgggccc agcacaacaa attctaggga tgaagatagt tcgagagaga 3240 acaagtagaa agttgtggct atctcaggag aagtacattg aacgtgtact agaacgcttc 3300 aacatgaaga atgctaagcc agtcagcaca cctcttgctg gtcatctaaa gttgagtaaa 3360 aagatgtgtc ctacaacagt ggaagagaaa gggaacatgg ctaaagttcc ttattcttca 3420 gcagtcggaa gcttgatgta tgcaatggta tgtactagac ctgatattgc tcacgcagtt 3480 ggtgttgtca gcaggtttct tgaaaatcct ggaaaggaac attgggaagc agtcaagtgg 3540 atactcaggt acctgagagg taccacggga gattgtttgt gctttggagg atctgatcca 3600 atcttgaagg gctatacaga tgctgatatg gcaggtgaca ttgacaacag aaaatccagt 3660 actggatatt tgtttacatt ttcaggggga gctatatcat ggcagtctaa gttgcaaaag 3720 tgcgttgcac tttcaacaac tgaagcagag tacattgctg ctacagaaac tggcaaggag 3780 atgatatggc tcaagcgatt ccttcaagag cttggattgc atcagaagga gtatgtcgtc 3840 tattgtgaca gtcaaagtgc aatagacctt agcaagaact ctatgtacca tgcaaggacc 3900 aaacacattg atgtgagata tcattggatt cgagaaatgg tagatgatga atctctaaaa 3960 gtcttgaaga tttctacaaa tgagaatccc gcagatatgc tgaccaaggt ggtaccaagg 4020 aacaagttcg agctatgcaa agaacttgtc ggcatgcatt caaactagaa gacagtgcta 4080 cctcctctgg atgaatgaga ctggaggggg agat 4114 // ID MuSHAN_MT repbase; DNA; EDCOT; 4702 BP. XX AC . XX DT 30-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative DNA transposon from Medicago truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW MuSHAN_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4702 RA Shankar R. and Jurka J.; RT "MuSHAN_MT: A putative DNA transposon from Barrel Medic."; RL Repbase Reports 6(11), 583-583 (2006). XX DR [1] (Consensus) XX CC A putative DNA transposon exhibiting mutator like protein CC translate with conserved domain for cysteine protease. The CC sequence is well conserved and abundant in Medicago genome. It's CC flanked on the both termini by ~145 bp long inverted repeats. XX FH Key Location/Qualifiers FT CDS 674..3619 FT /product="MuSHAN_MT_1p" FT /translation="MRKMFRERQNKILSKIPEMSNRLRLKRNQTLMELPSM FT LKLQSMLAAPVSSHFKPTRSTRLRFFSDDVKSKDRDELLEWVRRQANKAGF FT TIVTQRSSLINPMFRLVCERSGAHKVPKKKPKHARTGSRKCGCLFMISGYQ FT SKQTKEWGLNILNGVHNHPMEPALEGHILAGRLKEDDKKIVRDLTKSKMLP FT RNILIHLKNKRPHCMTNVKQVYNERQQIWKANRGDKKPLQYLISKLEEHNY FT TYYSRTQSESTTIEDIFWAHPTSIKLFNNFPTVLVMDSTYKTNMYRMPMFE FT VVGVTSTDLTYSVGFGFMTHEKEENFVWVLKMLRKLLSSKMNMPKVIVTDR FT DMSLMKAVANVFPESYAMNCYFHVQANVKQRCVLDCKYPLGFKKDGKEVSN FT RDVVKKIMKAWKAMVESPTQQLYANALVEFKDSCSDFPIFVNYAMTTLNEV FT KDKIVRAWTDHVLHLGCRTTNRVESAHALLKKYLDNSVGDLGTCWEKIHDM FT LLLQFTAIQTSFGQSVSVLEHRFKDVTLYSGLGGHVSRYALDNIALEETRC FT RETLCMDNDICGCVQRTSYGLPCACEIATKLLQEKPILLDEIYHHWLRLXM FT GEESNEVAFCVEVELKAIVERLKKLPFQMKLEVKEGLRQLAFPETTLMSPP FT PRKVPTKGAKKKVDIARSKGKITSTSRIPSSWEVVDSQNPDSQPSPSPTTS FT SYKRKKGARLGKTSLSPLPPPTRYPKPKAIPVMSPIDYMPRFMLPFIEKVV FT DVIGDGHCGFRAIAEFMGLTEKNHLMIRTHLIQELIDHRDDYVEVFAGEDR FT YNYILNGLHPPANTKTCAHLVDKWLTFPDMGHIVANYYKMCVVVLTNLEVG FT NSESFFPLRGPPPPGNQKTPILCLGAIPNHFVLISLKNGCPLPPSSTEWHN FT HKKEDAVTWEDEYLDQHELFRKLMAIESGNKPSKPQKESNKAAPILLDTPE FT KPKQQFEVIAEDEEDSMSLDLLQSLGL" XX SQ Sequence 4702 BP; 1425 A; 816 C; 1018 G; 1437 T; 6 other; gagaattgtt gttcccacat ttxataaggc tgtgccacac gagtaaatta cgyttttacc 60 ccctcggcag ttaactgccg aggaatttga aatccggctg cagttaactg ccgaggaaaa 120 cctcggtagt taactgccga gaaatatgtt tcatcagatg aaacagccac ctgctccccc 180 tacacactat tttcttcatc aacttcattt ccacctccat tcaatcccaa aatccaatat 240 tttttttytw taatcaattc ttgatccaaa atcattcaag catcaagcat aggaggtatc 300 aacacacttt tgacgtaaaa aaacaggtat tgtgcatttt attcgattca ttttttggtt 360 ttgttatggg tgttttaggg gtatctacgt cagttacgta gaaccctgtc atgggaatcc 420 tcggcagtta actgccgagg aaaacttcgg tagtttagtg ccgaggaaaa cctcggtagt 480 aaggtaccga ggaactcttg gtgaaaaatt ttcacaacga aaaaatggca gctactgcca 540 gattttcaaa aaaaaatttc ttttgttttt tttttgtttt tttttgtttt aattcattat 600 ggcattgatg tttatgcatt agttagttgt taattcatat ttatgtgttg tttaattata 660 gtaatggtag agaatgcgga agatgttccg ggagagacaa aacaaaattt tgtcgaaaat 720 tccggagatg tcaaaccgcc taaggttgaa gcgaaaccaa acattgatgg agcttccgtc 780 catgttgaag cttcaaagta tgttggcggc tccggtgtcc tcccacttca agcccacgag 840 gtcgacacgg ctaaggtttt tttcagacga cgttaagtcg aaagatagag atgaattgct 900 tgagtgggtg cgtcgtcaag caaataaggc gggatttaca attgttacac aaagatcaag 960 cttgatcaat ccaatgttcc ggctagtgtg tgaaaggagt ggagctcaca aagtgccgaa 1020 aaaaaaaccg aagcatgcga gaacgggctc aagaaaatgt gggtgcttgt tcatgattag 1080 tggatatcaa agtaagcaaa caaaggaatg gggattgaac attcttaatg gagttcacaa 1140 ccatcccatg gagccggctt tagaaggaca cattcttgcc ggtagattaa aggaggacga 1200 caagaagatt gtacgtgact tgaccaagag caagatgctt ccaagaaata ttttgataca 1260 tttgaagaac aaaagaccac attgcatgac aaatgtgaag caagtgtaca atgaacgtca 1320 acaaatatgg aaggcaaata gaggtgacaa gaagccgttg caatatctaa tctcgaagtt 1380 ggaggagcac aactatactt attactcaag aacacaaagt gaaagtacta caattgaaga 1440 tatcttttgg gctcatccaa catccattaa gttgtttaac aattttccaa cggttttggt 1500 tatggactcc acctacaaaa ccaacatgta taggatgcca atgtttgagg tagttggggt 1560 cacttcgacc gatttgacat attcggttgg gtttggattt atgacacatg agaaagagga 1620 aaactttgtt tgggttttaa aaatgttgcg taaacttctt tcgtcaaaga tgaatatgcc 1680 taaggtgatt gttaccgaca gggatatgtc tttgatgaaa gcggttgcaa atgtttttcc 1740 cgaaagttat gcaatgaatt gttactttca tgtgcaagca aatgttaaac aaaggtgtgt 1800 cttagattgt aaatatcctt tgggctttaa aaaggatggg aaagaggtga gcaatcgcga 1860 tgttgtgaag aagataatga aggcatggaa agctatggtt gaatcgccca ctcaacagtt 1920 atatgcaaat gcattagtgg agttcaaaga ttcatgtagt gatttcccaa tttttgtaaa 1980 ttatgccatg accaccttga atgaagtgaa ggacaaaatt gtgagggcat ggacagacca 2040 tgtgttgcat cttggttgca ggaccacaaa cagggtcgaa tcggctcatg ctttattgaa 2100 gaaatacttg gacaatagtg tgggtgattt gggtacttgt tgggagaaaa tacatgacat 2160 gttgttgctt cagttcactg ctatacaaac atcctttggt caaagcgtta gcgtgttgga 2220 acatagattc aaagatgtca ctttgtactc ggggttaggt ggtcatgtgt ctagatatgc 2280 tttggacaac attgctttgg aagagacacg ttgtagggaa acattgtgca tggacaatga 2340 catttgtggt tgtgttcaaa ggacatctta cgggctacca tgtgcatgcg aaattgctac 2400 taaactcctt caagagaagc caattttatt ggatgagata taccaccatt ggcttaggtt 2460 atstatgggc gaagaaagta acgaagttgc tttttgtgtc gaggttgagt tgaaggctat 2520 tgtagaacgt ctaaagaaac tccctttcca aatgaagctt gaggtcaaag agggtttgcg 2580 gcagttggca tttcctgaaa ccaccttgat gtctccacca ccacgaaaag taccaaccaa 2640 gggagcaaag aaaaaagtcg acattgcgag gtctaaagga aaaattacat cgactagtcg 2700 gatcccttct tcttgggagg ttgttgattc ccaaaatccg gatagccaac cgtcaccatc 2760 accaacaaca tcatcatata aaaggaaaaa aggtgctcgt cttggtaaaa catcactttc 2820 cccacttcca ccacctactc ggtatccaaa gcctaaggct atcccggtta tgagtcctat 2880 tgattatatg ccacgcttca tgcttccatt tattgaaaaa gtggtggatg ttatcggcga 2940 tggacattgt ggattccggg ctatagccga gttcatgggc ttgaccgaaa aaaatcatct 3000 catgatccgt acacatctta ttcaagagtt gatagatcat agagatgatt atgttgaagt 3060 atttgcgggt gaggatcgtt ataactacat tttaaacggc ttacatcctc ccgcaaatac 3120 aaaaacttgt gcacatcttg ttgataagtg gttgactttt ccggacatgg gacacattgt 3180 tgctaattat tacaaaatgt gtgtggtcgt gttgacaaat cttgaagttg gaaactcgga 3240 atcttttttc ccactaagag ggccaccacc gccgggtaat caaaaaactc ccatcttgtg 3300 ccttggggca attccaaatc atttcgtgct tatttccttg aagaatggtt gtccactacc 3360 tccatcatct acggagtggc acaatcacaa gaaagaagat gcggtgactt gggaagatga 3420 gtatttggat caacatgagt tgttccgaaa gctcatggct attgaaagtg gaaacaaacc 3480 gtccaaacca caaaaggagt caaacaaagc ggcgcctatt ttgttggaca ctcccgaaaa 3540 accaaagcaa caatttgaag ttattgcgga agatgaggaa gattctatgt cacttgatct 3600 tctccaatca cttggtcttt aatgagtgat ttttttgtcg gtgttagttc tttttttttg 3660 gtagaaatta caccgacgta tattttgggg tcgaaattgt aacgccaatt ttttggtggc 3720 caatatataa ctaacattat gtaatttata ttgatatata tatatatata tatatatata 3780 tatatgataa tatgactttt atgtggtgaa actaatgcaa tacttattta tagcttatta 3840 atgtttacgc atttgattta ttcgttatta cattccattt aattttgttc taatatatga 3900 ttcttttctt aaagcttttt tcaagtgaga catgtctgag gttgcacaaa ttgaagggcg 3960 tgttaggtac tccgcgttta aaaagacggt taaggttatg ataacgccga cggactctct 4020 tgacaatttg aaggcacaac ttaacactta ttttgagcat cttggtgaaa atcaatatac 4080 acgtcacttg tttggtcaaa tgccatgcat agacctagga gaagatagag atgaatacgc 4140 atggaaaacg gcaagctata tgcctttgct tattcgcgac gacggcgacg tcggatttat 4200 gtttcggaat atggtggaag ataatatatt atatatgtat gttcgttcca tatgcaattg 4260 cgttgaatgt aagtagggat ttaatttaat gatgtgtaat gagttgttta attatggaca 4320 ctttgtaatg ttttgatgaa tttcaaacgt ttgtttaatt ttaaccaaat gtcggtttaa 4380 tttaattatg aacaattgta aaagatattg tatttatctt gattatgtcc gagtttcaat 4440 cttgtatgaa ttattttgcc tttgaaaatg ctctggttta attacaggta aaaactggcc 4500 gaaaaaatgg cttggaaatg tttagaatta tgcagaaccc actgtctgca taatcagttt 4560 tcctcggcag ttaactaccg aggttttcct cggcagttaa ctgcagccgg wtttcaaaaa 4620 cctcggtagt taactgccga ggggtatttt ggtaatttac tcgtgtggca cagccaaaca 4680 acatgtggga acagcaattc tc 4702 // ID Copia-1_Mad-LTR repbase; DNA; EDCOT; 144 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-1_Mad_; KW Copia-1_Mad-LTR; Copia-1_Mad-I. XX NM Copia-1_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-144 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1649-1649 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 144 BP; 39 A; 23 C; 22 G; 60 T; 0 other; tgttgacttt tgtattttag gtaggatccc taattgatat gtaatcccat gtaatcactt 60 gtaattagtt ttctttcctt ttacgttagg gttgtacacc tataagttcc tcttattgag 120 aagaatatat catcattcaa agca 144 // ID Copia-68_VV-LTR repbase; DNA; EDCOT; 309 BP. XX AC chr18; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-68_VV_; KW Copia-68_VV-I; Copia-68_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-309 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr18; Positions 24282215 24282523. XX SQ Sequence 309 BP; 79 A; 40 C; 58 G; 132 T; 0 other; tgttaaagtt atcaacatca gcatgtgact gagaggatgt attgaacaag tcaagtttgt 60 ttttgtgtca aaaatatgcc tctgtttagt ttttcaatat attaggaatt gtccgagtct 120 tagggaggtt gttgcagcac gtttagagta attggttatc tttctattcc tatttttttg 180 gtatttttat ttctgttgat ggttttgcct ataaaaggct tgtatcaggt gaagtttaaa 240 ttatcaccat attaataaaa ttattttctt tcctcctctg tgtgtctctt ttataaagtg 300 ggttcaaca 309 // ID Copia-41_Mad-I repbase; DNA; EDCOT; 5072 BP. XX AC ACYM01025173; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-41_Mad-I; KW Copia-41_Mad-LTR; Copia-41_Mad_. XX NM Copia-41_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5072 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1311-1311 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01025173; Positions 9734 14805. XX CC Positions [1943-2470] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 926..2638 FT /product="Copia-41_Mad-I_1p" FT /translation="MALNSLPESYEQLKTSYNAQKEKWSLNDLISICVQEE FT ARMKRGKQEVVNVVSTDKGKKHDVFSGKPSKPFNFSHSAGNNTLSSKGPQG FT FRVDMEKVKCYFCKEYGHFKRDCPKRKKWGNKTGNKTKNVFVCVNINLVEV FT PPNSWWFDTGCSVHITNSLQGFTRREFARNEVYEVHVGNGNKVAVEAIGTL FT KLKLSTNFELELLDVLYVPSLTRNLISASKLVKTGYAFIGDDESIRIFKKC FT NLNLLLGICLLENDLWRLHCDVVTIPNCMQVSTVLKSKRSLVNEKSSMLWH FT RRLGHISQKRLELLVKENILPRLNFIDLQNCVDCWKGKLTNTKKIGSTRSQ FT KLLEIIHSDVCGPFPTKTICKNVYFVTFIDDFSRYAYVYLISEKNEVASCF FT KTYQNEVEKQLETSIKILRSDRGGEYYGRYTEEGQQKGPMARYLEENGIQA FT QYTTPGTPQQNGVAERRNRTLKEMVRCMMSRTNLPMFLWGEALKMTNYISN FT RVPSKSVNKTPFELWTSRKPSLNHLHVWGCLAEAKMYNPTERKLDSRTVTC FT HFIGFPEKSKGYRFFSPSLSTRIF" XX SQ Sequence 5072 BP; 1648 A; 755 C; 1134 G; 1466 T; 69 other; tttggtatca gagcaaggtt agtctacttg gattcaaaac tgttttttta gtttaaacat 60 atcacatata atcctcagtt gaagattttt aagggaacaa gactttgcac cgatgcacaa 120 atgcttagaa gatcacatca aaatgggatt ttgtcaagca ttgttgcatg aattaggtcg 180 caggacattg taattcattt atcataacat acatactgct ctcttcaaaa agggaatata 240 tgaatggttc gattaagtga attagggcat agtggttatt ttgatattaa attgatctaa 300 ttcttgtcca aagacctgag ttatgaagat gtttaatatt aaattaagta gctatgtcaa 360 tgaaacttgt agtaaagagt ttcttgccca aaggtgttac cttgtactgc atgcaatttt 420 cattgtttgt ttcactaaca aattaatgac gtcctcagtg aatcccatgt ccctgaattt 480 ttcctctatc gagccgctca atggaggaaa ttacaaaaaa tggagacaag atgttgagat 540 tattttggga ctgatggact acgatttggc acttagagaa gatgagccag caccagtgga 600 tgcaactagc acaactgctc aaaggttgaa atttgaaaaa tgggaaaaag ctaatcgcat 660 ggcattactt gtgataaaaa gatcaattgg ggaagctgtg agagggggac tacctgccag 720 tgacaaagca aagaatttcc ttgaaggcat tgaggcaaag ttcaaggtct ctgagaaagg 780 agagatagga aacctcatga caaccctgac tactctgaaa tttgatgaaa gtcacacagt 840 tagggagcac atactgaaaa tggtggaggy agcggcaaag ctcagtgatc ttgaagtgcc 900 tattgatgac tcttttgtgg ttcatatggc tcttaactct cttcctgaga gttatgagca 960 gttgaagaca tcctacaatg ctcagaaaga aaaatggagt ttgaatgatt tgatttcaat 1020 ctgtgtccaa gaggaggcaa ggatgaaacg aggaaaacaa gaggttgtca atgtggtgag 1080 cacagacaaa ggaaaraagc acgatgtgtt ttctggtaag ccaagcaaac cctttaactt 1140 ttctcactct gctggaaata atactctctc ctcaaaggga cctcaaggtt ttagggtgga 1200 tatggaaaag gttaagtgtt atttttgcaa ggaatatggt catttcaaaa gggactgtcc 1260 aaaacgtaag aagtggggaa ataaaacagg taataaaact aaaaatgttt ttgtttgtgt 1320 taatatcaat cttgttgaag tccctccaaa ttcttggtgg tttgacactg gttgttcggt 1380 gcatattacc aattcattgc agggattcac aagaagggaa tttgcaagaa atgaagtcta 1440 tgaagttcac gtaggaaatg gaaataaagt ggctgtggag gcaataggca ctctaaagct 1500 caagttgtca actaatttcg aattagaatt gttagatgtt ctttatgttc ctagtttaac 1560 tagaaattta atttcagctt ccaagcttgt aaagactggt tatgctttca ttggcgacga 1620 tgaaagtata aggattttca agaaatgtaa tctcaatctt ttacttggta tttgtttgtt 1680 ggaaaatgat ttatggagat tacattgtga tgttgttaca attccaaatt gcatgcaagt 1740 gtcaacagtt cttaaaagta aaagatcttt ggttaatgaa aagtcctcta tgctttggca 1800 taggaggctc ggacacataa gtcaaaagag attggaactt ctagttaaag agaacatact 1860 gccaaggtta aactttattg acttgcaaaa ctgtgttgat tgttggaagg gtaaattaac 1920 aaacacaaag aaaattggat caacaaggag tcaaaaactc ttggaaataa ttcattcaga 1980 tgtttgtggt cctttcccca ctaaaaccat ttgcaaaaat gtctattttg tgacttttat 2040 tgatgatttt tctcggtatg cttatgttta cttaatatcc gagaaaaatg aagtggctag 2100 ttgttttaaa acttatcaaa atgaggtaga aaagcaacta gaaacatcaa ttaaaatttt 2160 gaggtcrgac cgtggtggag agtattatgg caggtacact gaggaagggc aacaaaaggg 2220 tccaatggca agatacttgg aggaaaatgg catacaagct cagtacacta ctcccggcac 2280 accacaacaa aacggtgtgg ccgagagaag gaacagaact ttgaaagaaa tggtaagatg 2340 catgatgagc aggaccaatc ttccaatgtt cttgtgggga gaagcactta agatgacaaa 2400 ctatatttca aaccgtgtac caagcaaatc agtgaataaa actccttttg agttgtggac 2460 atcraggaag ccaagcctca accatcttca tgtgtggggc tgtttggcag aggcaaaaat 2520 gtataatcca acagaaagga agcttgattc aagaacagtg acttgccatt tcattggttt 2580 tccagaaaaa tcaaaagggt acagattctt ctcaccgagt ttatccacaa ggatttttka 2640 aactaataat gctaggttca ttgaagatca acaatctagc aatgaaggtt tgaaagaagt 2700 ggtttttgaa gaagaagatt tgattagttc gtcatctttc aaagaaactc caatgcatgc 2760 tgacacaatt gattttgggg acgtggraat tctaagycat gttgattgca tggatcagca 2820 tgaattggta racgtgcarc cacaaatatt agaaatgcaa gawaatgctc aacaaatcwc 2880 catgcagcaa gttccagtgc aaaggaggca gtcacaaaga artagraggt ctccwttctc 2940 gaatgactac ttagtatatg tgggagaggt tgagcatgag gaaggaattg acaatgatcc 3000 aatcacgtay ratcaagcaa ttaattgtga taaagctaat gactggaagg ctgsaatgaa 3060 ggacgaaatg gattcgatgt acttcaatga agtttgggaa ttggtggaaa gagacgaatc 3120 tataaaaccc ataggatgca aatgggtttt taagacaaaa agggactcta gtggggcagt 3180 tgaaaggtat aaagcgaggc tggttgcaaa gggttacaca caaaaggagg gtttggatta 3240 ctcggacaca ttctccccag tttcatcaaa agactcactc cgagtcattc ttgccctagt 3300 tgcacatttt gatcttgagc ttcaccaaat ggacgttaaa acggcgttcc ttaatggagt 3360 tctcgatgaa aatattcaca tggtacaacc acctggtttc rttaaagagg gcaatgagca 3420 catggtatgc aaactaarga aatcgatcta cgggttgaaa caagcatcra gacaatggtt 3480 tatgaagttt gatgaaaaag tcactggttt tggwttkgtt gagaacaaaa tcgatgactg 3540 tttrtatctc aaggtgtgtg gttccaagtt tattttcctt gtcttgtrtg tcgatgatat 3600 tttgttagca agtaatgatc taaacttgct gatagawacc aaaaggytgc tgtcaaatac 3660 tttckaaatg aaagacatgg gtgatgctac tttcgtgctt ggaatagaaa taattaggga 3720 caggaaaagg tgcttactag ggmtctcgca graakcttac atagaaaagg tcctgaaaag 3780 attcaatatg gagagttgtg caaaaggtga agccccaatg agcaaagrag acaagtttaa 3840 caaatctcaa tgtcctcaka atgatattga aaagcaaagc atgtccaaca gacccyatgc 3900 ttcacttgtt ggaagtttaa tgtatgcaca agtttgcacg akgccggatt tggcttttgy 3960 agtwagtgtg cttgggagat tccaagcaaa cccaggggaa tatcattgga ytgcygccaa 4020 gaaggttgtt cgatacttgy aaaggaccaa atcctacatg ttagtatatg gtaggattga 4080 aaggttggaa gtgattggtc attgtgactc araytttgcg ggatgtgagg atgatcgaag 4140 atcaacgagt gggtatgttt ttctaatggc tggaggtgmt atttcttgga gaagtgcaaa 4200 gcagaaaact ttggctactt caacaatgca ggcagaatat atttcatgtt ttgaagcaac 4260 ccaacaagyc atgatgttga agaatcttat ttcagaaatg aggatagttg acacaattgc 4320 gaagccactt gtaatatatt gtgacaataa agctgytgtg ttcttctcta aaaacaacaa 4380 gaaatcttat gcagctcgat taatggatgt caagtatcaa tcagtcaagg agaaggtraa 4440 ggcrggaatg gtgtctatag aacacattga cactacttta atgttggctg atccccttac 4500 aaaaccgttg gcagtgggag ttttcaagaa tcatgtggca aacatgggcg tggttgaatc 4560 ctttgattca gctacygtat ggaagtaagg gttatcttwm atwwrawwtm atmttttrtt 4620 awaaaaataa agcttgaatt catgtactct tgaatttkac cmtgttaatg gttgaggttt 4680 yatttcagct attgtatata tgtacaaata tatgtatgca atatattgaa atgttgtgga 4740 ctgaygaaag attcggacta awtgtgcttg gtattataag cattccattg gagctaaaca 4800 aaagcttgac aatggtggac tgctctgatc agtgggagca tggaaacaaa gttttgaatt 4860 tgtttcggta attatatcat gcataartta ttttgggtga tgtgatctta gggtgcttgt 4920 acgagttgat gtataagatt ttctaaggtt catttctttg aaataattta tggcagatwy 4980 gyaaagggtt aatkgttgtg ttgacaaaag tgatcactaa gggattaata cgttgataaa 5040 ggatatgatc artgataatt caagtgggag aa 5072 // ID SHACOP20_I_MT repbase; DNA; EDCOT; 4700 BP. XX AC . XX DT 26-JAN-2007 (Rel. 12.01, Created) DT 26-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP20_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; terminal; repeat; ORF; SHACOP20_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4700 RA Shankar R. and Jurka J.; RT "SHACOP20_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 66-66 (2007). XX DR [1] (Consensus) XX CC The internal region has a single ORF, containing intact domains CC for gag-pol polyprotein in Copia-like arrangement. Present in low CC copy number in the genome. It has LTRs identical to SHACOP2_MT. XX FH Key Location/Qualifiers FT CDS 33..4697 FT /product="SHACOP20_I_MT_1p" FT /translation="MSSPSSPVNNSETQRVTAAASKNFKQIISVKLDETNY FT LQWKQQVEGVLRGTKMVRHVVSPQIPPVFLNDAAREAGTENPAYTEWEEQD FT SLLCTWILSTISSSLLSRFVRLRFSHQVWDEIHNYCYTQMRTRSRQLRSEL FT RTITKGTRSIAEFIARIRSISESLMSIGDPVAHRDLIETVLEALPEEFNPI FT VATVNSQTEVISLDELESQLLTQEARNEKFKKALVGETASVNLTHAENSGE FT KNGHNQPQTGSYPDQQFNISGNPTGNNSSQYFNPNFGGRNGSRGRGFRGNR FT FRGRGGRNFGRGNIQCQICYKTGHDASICYHRLSVPPQYEGYGSLGGNFGG FT NLGSGYGPATGFGTHSNVWMQGVGQRNPSYGAPRAPFPPQFGNSRPPAPQA FT YITGNESTSSNSFNNGWYPDSGATHHVTPDANNLMDAASFSGSDQMYIGNG FT QGLAINSIGSMSFSSPFSPNTTLTLNNLLHVPSITKNLVSVSQFCKDNNVF FT FEFHSNICYVKSQDSTKILLKGHLGDDGLYQFDQPYVPSVSRTASSSSVAT FT SSLSLNNCFSPSSLSLSRSQCNNGSVYTPIHTSGSSNDSSNSLSLYKVWHN FT RLGHPHHEVVRSVMKLCNQQLPNKSFTDFCSACCLGKSHRLPSVSSKTVYN FT KPFELIFCDLWGPASVESHGGYSYFLTCVDAYSRYTWIFPLKLKSHTLITF FT QNFKTMVELQYNLPIKSVQTDGGGEFRPFTQFLTTLGITHRLTCPHTHHQN FT GSVERKHRHIVETGLTLLANAKLPLHYWDHAFLTATYLINRLPSPILNNKS FT PFFLLHLQIPDYKFLKSFGCSCFPFTRPYNNHKLELRSKECVFLGYSPSHK FT GYKCLDPTGRMFISKDVIFNEYKFPYSELFTSGQSSSPPTTSSDHTPLPSF FT LFPLNNKQCPTTQSSSTPTTTLHTASPHSSFPESNQSNHHHSIQDTHASSH FT SNHHNISPGPIFNPTPISTHPPSPSPSSHSHNTYHSISVEPVTSQPSTQAE FT PHRIHPNNTHSMATRAKHGIVQKRKHPTLLLTHIEPTGYRQAMKQPQWLQA FT MQLEHEALMKNNTWTLVPLPADRQAVGCKWVFRTKQNPDGSINKYKARLVA FT KGFHQMPGFDYKETFSPVVKPVTVRSVLTLAVTNKWCIQQLDVNNAFLNGY FT LEEEVYMTQPPGFEAVDPSLVCKLNKALYGLKQAPRAWFERLKSTLLKLGF FT CSSKCDPSLFILHANQHSTFMLVYVDDILITGSSASLIQQLVKKLNAEFSL FT KDLGKLDYFLGIEVHYSENGSLLLSQKKYIQDLLVKANMANANGIASPMAS FT STKLTKYGSNHVSDPTFFRSIVGGLQYVTVTRPEISYSVNKVCQFLSAPLE FT DHWKAVKRILRYLKGTIHHGLLINPAPMHQPLSLTAFCDADWASDPDDRRS FT TSGACILLGPNLISWWAKKQTLVARSSAEAEYRSLAQASAEVLWIQSLLKE FT LKVPTAIPQIFCDNLSTVSLAHNPVLHSRTKHMELDIFFVREKVISKDLIV FT SHIPAQYQVADILTKPLSASRFLELRNKLRVSDPMSLRG" XX SQ Sequence 4700 BP; 1311 A; 1095 C; 846 G; 1448 T; 0 other; tggtatcttg agctttttct tcgatccaaa ccatgtcttc gccttcgtca ccagtcaaca 60 actctgagac gcaacgcgtc accgcagcgg cctcgaagaa cttcaaacaa atcatctccg 120 tcaaactcga cgaaacgaac tatcttcaat ggaagcaaca ggtagaagga gtgttacgcg 180 gcacaaaaat ggtgcgtcac gttgtttcac cgcagatccc accggttttc ctcaacgacg 240 cggcgcgtga ggctggaact gagaatccgg cgtatactga atgggaagag caagattcgt 300 tgctctgtac gtggattctt tccacgatct cgtcttctct actatcgcgt tttgttcgac 360 ttaggttttc gcatcaggta tgggatgaaa ttcacaatta ctgctacact cagatgcgta 420 ctaggtcaag acaacttcgt tctgaactta gaactattac aaaaggaacg cgctcgattg 480 ctgagtttat cgctcgcatt cgttcaatct cagagtctct catgtctata ggggatcctg 540 tggctcaccg tgatctgatt gaaactgttc ttgaggcttt acctgaggaa ttcaatccta 600 tcgttgccac tgttaatagt caaacagaag ttatttctct ggatgagtta gaatctcagc 660 ttcttactca agaagcacgc aatgaaaaat tcaagaaagc attagttgga gaaactgctt 720 ctgttaattt gacacatgct gaaaattctg gagaaaagaa tggtcacaat caacctcaaa 780 ctggatctta tcctgatcag cagttcaata tttctggtaa tcctactggt aacaattcat 840 ctcagtactt taaccctaat tttggtggca gaaatggatc tagaggcaga ggttttcgtg 900 gtaatcgctt cagaggaaga ggaggacgta attttggcag aggaaatatt cagtgtcaga 960 tctgctataa gactggtcat gatgccagta tttgctatca caggctctct gttcctcctc 1020 agtatgaagg atatggtagt cttggtggaa attttggagg taaccttgga agtggctatg 1080 gtcctgcaac tggttttggt actcattcaa atgtttggat gcaaggtgtt ggtcagagga 1140 acccctcata tggtgcaccc agagctcctt ttcctcctca atttggcaac tctcggcccc 1200 ctgctcctca agcctacata actggaaatg agtccaccag ttctaactca tttaacaatg 1260 gttggtaccc tgactctggt gccacccatc acgttactcc tgatgctaat aacctcatgg 1320 atgctgcctc attctcaggt tctgaccaga tgtatattgg aaacggtcaa ggtttggcta 1380 tcaactccat aggctcaatg agtttctctt ctcccttctc tcctaacact actcttactc 1440 ttaacaattt gcttcatgtc ccttcaataa ccaaaaatct tgttagtgtc agtcaatttt 1500 gtaaggacaa taatgtattc tttgagtttc attctaacat ttgctatgtt aaatctcagg 1560 attctactaa gatccttcta aagggacatc tgggagatga tggtctctac caatttgatc 1620 agccatatgt gccttctgtg tcaagaactg cttcttcaag ttctgttgcc acttcttctc 1680 tttccttaaa taattgtttt tctccttcta gtctttccct atctaggtcc caatgtaata 1740 atggaagtgt gtacactcct atccatacta gcggtagcag caatgatagt tctaattctc 1800 tttcattgta taaagtctgg cataatagac ttggccaccc acatcatgag gtggttagaa 1860 gtgttatgaa attgtgtaat caacaattgc ctaataaaag tttcactgat ttttgttcag 1920 cttgctgttt gggtaaatct cacagattac cttctgtttc atcaaaaact gtctataata 1980 aaccttttga actcatattt tgtgatttgt ggggtcctgc ttctgttgag tcacatgggg 2040 gttactctta tttcttaacc tgtgttgatg cttactctag atatacctgg atatttcctc 2100 ttaagctaaa atcccacact ctcatcacat tccaaaattt taaaactatg gttgaacttc 2160 aatataacct cccaattaaa tccgttcaaa ctgatggtgg tggagaattt cgtcccttta 2220 ctcagttttt aacaacttta gggattacac atagacttac ctgtccccac acccatcatc 2280 aaaatggctc tgtggaaaga aagcacaggc acatagtaga aactggccta actctccttg 2340 ccaatgccaa actacctcta cactactggg atcatgcttt cttgactgca acctacctca 2400 ttaataggct gccttcaccc attctcaaca acaaatcccc atttttcctg cttcatcttc 2460 aaattcctga ttataaattt ttaaaaagct ttgggtgctc atgtttccct tttaccagac 2520 cctacaacaa tcacaaacta gaattacgtt caaaagagtg tgtgtttctt ggttattctc 2580 cctctcataa aggatacaaa tgcttagatc ctacaggcag aatgtttatc tctaaggatg 2640 ttatattcaa tgagtataag tttccctact ctgagttgtt cacttctggt cagtcttcct 2700 caccccctac taccagttct gatcatactc ctttaccttc atttttgttt cccttaaata 2760 acaaacaatg tcctacaact cagtcatcat ctactcctac tactaccctc catactgcca 2820 gtcctcattc ttcatttcct gagtccaacc agtctaatca tcatcatagc atccaagata 2880 ctcatgcttc ttctcattca aatcaccaca atatctcacc tggacctatc tttaatccca 2940 cacctatttc tactcatcct ccttcacctt ctccctcttc ccactctcat aatacttatc 3000 acagtatatc tgttgaacct gtcactagtc aaccttcaac tcaggctgaa cctcatcgta 3060 ttcatcctaa taatacacat tctatggcaa caagagcaaa acatggaatt gttcagaaaa 3120 gaaagcatcc cactcttctt cttactcata ttgagcctac tgggtacaga caagccatga 3180 aacagcctca gtggctgcaa gctatgcagc ttgaacatga agctttgatg aaaaacaaca 3240 cttggactct tgttcctcta cctgctgaca gacaagcagt aggatgcaaa tgggtgttca 3300 gaactaaaca aaaccctgat ggaagcatca ataagtacaa ggcaagattg gttgccaaag 3360 ggtttcatca aatgcctggc tttgactata aagaaacatt ttctccagtg gtaaagccag 3420 taactgtgag aagtgtgctg acactagcag tcacaaacaa gtggtgcatt caacaactgg 3480 atgtaaacaa tgccttttta aatggctatt tagaggaaga agtgtacatg acacaacctc 3540 ctggttttga agctgttgat ccctctttgg tgtgtaaact gaataaagcc ttatatgggt 3600 taaaacaggc cccaagagcc tggtttgaaa ggttaaaatc cactctgctt aagctgggtt 3660 tctgctctag taaatgtgat ccatctctgt ttatcttaca tgcaaatcag cacagcacct 3720 tcatgctagt ttatgttgat gatatactca tcacaggcag ctctgcctcc ttaattcagc 3780 aacttgttaa aaagttaaat gcagaattct ctctaaagga tctaggcaag cttgattact 3840 tcttaggaat tgaggtgcat tattcagaaa atgggtctct actcctatct cagaaaaagt 3900 acatacaaga tttgttagtt aaggcaaata tggcaaatgc aaatggaatt gcttccccta 3960 tggcctctag tacaaagcta acaaagtatg gctccaatca tgtatctgac cctacatttt 4020 ttaggtcaat agtgggtggc ctacagtatg ttactgttac tagaccagaa atctcctact 4080 cagttaataa agtctgtcaa tttctatcag cacctctaga ggatcactgg aaggctgtaa 4140 aaaggatcct cagatactta aaaggcacca ttcatcatgg tcttcttatc aatcctgcac 4200 ctatgcatca acctctttct ctaactgcct tctgtgatgc tgactgggct tctgacccag 4260 atgatagaag aagcacctca ggtgcctgta tacttctggg gccaaatctc atatcttggt 4320 gggcaaagaa acaaacactg gttgcaaggt ccagtgctga agctgaatac agaagtctgg 4380 ctcaagcttc tgctgaagtt ttatggatac aatctcttct taaagaactg aaagttccaa 4440 ctgctattcc tcagatattt tgtgacaatt tgagcactgt atcactggct cataatcctg 4500 ttcttcattc aagaacaaag cacatggagc ttgacatttt ctttgtcaga gaaaaggtca 4560 tcagcaagga cttgattgtc tctcacattc ctgcacaata ccaagtggca gatatcctta 4620 ccaagcccct ctctgcttcc agattcttgg aactaagaaa caaactaagg gtgtctgacc 4680 ccatgagttt gaggggggac 4700 // ID Copia21-VV_LTR repbase; DNA; EDCOT; 206 BP. XX AC AM479441; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia21-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-206 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-206 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 702-702 (2007). XX DR Genbank; AM479441; Positions 5252 5047. XX SQ Sequence 206 BP; 61 A; 30 C; 40 G; 75 T; 0 other; tggaagtgat ttacagcaat catcaagccg agtatcatgg cctggaattg atgtaattgt 60 tttattttta gtaaagcaaa tctgtaaccg ttgtacatga tatttcctta gctgtacaaa 120 ttccttagat aggtttgtaa acgtctgtat aaaggtttgc taaacagatc aatatatgtg 180 tgttgacatt tccattgtga gcttca 206 // ID Harbinger1_PTr repbase; DNA; EDCOT; 4082 BP. XX AC . XX DT 14-DEC-2009 (Rel. 15.02, Created) DT 14-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Harbinger-type DNA transposon - consensus. XX KW Harbinger; DNA transposon; Transposable Element; Harbinger1_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4082 RA Jurka J.; RT "DNA transposons from black cottonwood."; RL Repbase Reports 10(2), 110-110 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 647..1930 FT /product="Harbinger1_PTr_1p" FT /translation="MNHSNFNFYDAFDFDDDTPVFAFQVATAVVAEEESNN FT QGRRTGYRGSILGHNIVNRNRKEGELRLYNDYFAENPKFTESQFRRRFRMS FT RRLFLRIANAVEAHNPYFKQRTDALGVLGLSCLQKVTAAHRILAYGIPADL FT TDEYLRIGETTAIESLRAFVKAIVEVFGDWYLRAPNEADICRLLSIGEQRG FT FPGMLGSIDCMHWKWEKCPIAWHGMYTGHCREPTIILEAVASQDLWIWHAF FT FGMPGSLNDINVLDRSPIFAALAEGRTAPVNYTINGHEYTMGYYLADEIYP FT NWSTFVKTIPRPLGAKRKYFASKQESARKDVERAFGVLQSRFAIVRGPVRY FT WDEETLANIMKACIIMHNMIIEDEGAMNLGFDHEREVNSFISVSHGEIPEL FT HDFLQTHNRIRDRATSSQLQEDLVEHLWEQYGNE" XX SQ Sequence 4082 BP; 1382 A; 631 C; 632 G; 1437 T; 0 other; taagagcatc tccaatgaaa atgctatatt gaagagccaa attgataaaa tggctttttg 60 aatagtataa atatagcttt tttgattatg tgcattccaa cggtaaaaag ctatttagaa 120 aagccaatta tattttaata tatttcatgt taaattaatt ttaatataat tatataacta 180 atttagatat tttatatata atataattat gatgttatta attatataat taatatgagt 240 aatttataaa agtaatataa aattaatgaa gtaatatgaa agttaaaaga tataatttaa 300 aattaaattt aaaatttatt tatatgaata tttttaattt tcagttttat atgttactgt 360 taaaaattta attttttaaa agtaaattca aattcaaact ttgaaaaaaa ccgccaacat 420 tttaaatttt gattttcaat tttttttaaa aaaaattcaa gctttgaaaa aatgaccgcc 480 aacattttaa attttaaaat ttcaaatttt gaaaaaataa ccgccaacat tctaagattt 540 caaaatttga aaaaataatc catctataaa tattctcata taccttaaca ttttttctca 600 tcattttctt ctctccaatc tttattatat ttcattaaaa ttcatcatga atcattctaa 660 ttttaatttt tatgatgctt ttgattttga tgatgacact cccgtgttcg cttttcaagt 720 tgctaccgct gtggttgctg aagaagaatc gaataatcaa gggcggagaa cagggtatcg 780 tggctctatt cttggtcaca atattgtcaa tcgtaataga aaggaaggtg agttaaggtt 840 atataatgat tattttgctg aaaatcctaa attcactgaa agtcaatttc gaagaagatt 900 taggatgagt cgtcgtcttt ttcttcggat cgcaaatgca gtggaagctc ataatccata 960 tttcaaacaa aggacagatg ctcttggtgt tcttggttta tcttgccttc aaaaggtaac 1020 tgcagctcac agaatacttg catatggtat tcctgcagat cttactgatg aatatcttcg 1080 aattggagaa accactgcga tagaaagtct tagagctttc gtcaaagcaa tcgtagaagt 1140 ttttggtgat tggtatctaa gggcaccaaa cgaggccgat atttgtcgat tattatcaat 1200 tggagagcag cgtggatttc cagggatgtt agggagcatt gactgtatgc attggaaatg 1260 ggagaaatgc ccaattgcat ggcatgggat gtatactggt cattgtcgtg aaccaactat 1320 aattctagag gcggtggctt cacaagatct ttggatatgg catgcctttt ttggaatgcc 1380 tggatcatta aatgatatta atgttcttga tcggtcacct atcttcgctg cacttgctga 1440 aggtcgtact gctcctgtca attatacaat taatgggcat gaatatacaa tgggatacta 1500 tttagcagat gagatttatc ctaattggtc aacctttgtt aagacaatcc caaggccatt 1560 aggagcaaag agaaaatatt ttgcaagtaa gcaagagtct gcaagaaagg atgtggagcg 1620 ggcatttggg gtgctccaat ctcgttttgc aattgtacgt ggacctgttc gatactggga 1680 tgaagaaacg cttgcaaata ttatgaaagc ttgcataata atgcataata tgattattga 1740 ggatgaagga gcaatgaacc ttggatttga ccatgaacgt gaagtcaatt cctttatatc 1800 agtgtcacat ggtgaaatac cagaactaca tgattttctt caaactcata atcgaatcag 1860 ggatagagca actagctctc aactacaaga agatttggtt gaacatttgt gggaacaata 1920 tggcaacgag tagaatcatt agatttgaac ttcttatgtc atcataattt tcaagttttt 1980 tatgtttttt ttttcattat ggttgttatc ttttaagtta attaatccta cttattgttg 2040 ttaagtgtta gaagaacttc aaaaaagtat tatgaattga taccactttt ataacaatat 2100 atttaaaata accaagaaat ttctacatat ttaattaaaa atacattaca ttaaacaata 2160 aatcaatcta gttaattaaa aattaaaacc cctcttttgc ataatttcta actttctatt 2220 ttgaaaatac gctgcagaaa ttggatccaa attagaaata tccattttca taatttgttc 2280 ttctttctca atcctgtcca attcttgttt ctcttgactt tgttgaatca tcatagcttg 2340 ttgctctaac ataatttttc tgtcttgttt cttctgatcc tcaatttcaa ctagagtatc 2400 cctgaattgt tgtaagagat ttgttacagt tacctcccca actttatctt ttccttgtct 2460 acgtttaagt cgttcctttg cagccttctg accaattggt ctatcttgat aaatcaacgg 2520 ttcactgtct tctcctaaac taacagaatc aggggtagat ggagctgatg aagccggact 2580 tgcattgaca tgactttttt gtttcttgtt tgacctttga tgttgacttg cacgctcaaa 2640 ttgccatttg ggttcttttc ttaagataac ccaacaatgt tctagttgaa atcgtttgcc 2700 aacgcaagaa gcatacattt gtcgagcatc attaatctgg taaaaaatta gagaaattaa 2760 ataatgttaa aatatgtgtt aaacaattta acatggaaat gaatattaaa attacccttg 2820 attcttcggt cattccactt tgctgacgat tttcaatttg agtaacaaat ccaacaaatt 2880 taccgacttc tctatttatt tcttgccatc tacttgagat gcttatttgg gaacgattat 2940 tcaagtttcc tccattctct acaaagtaag catgtactcg agcccagaac tgttttgttt 3000 gttgttcaac tcctgtaatt ggatccttgc ttgtatttag ccatgcagag acaagtaaac 3060 aatcttcctc tggtgagaag tttttacttc tttgtgattt ttttattgta tggacattta 3120 aattcgagta tgttaagtca tcaattaatt gattagaatc acttggttga gagagaatat 3180 cttctgactc actcataaga aagttggtaa aagagcttgg aaaatttgaa tccatctaca 3240 ttaaaaaaaa aactcaagtt aaaaccttat aagagagtgt aaaagaagct cacattcaat 3300 gtctagcaat tttgtagttt ccatacatgt gaattaataa taagcattgc ctcctacttg 3360 ttctaacatt acaatttgac cattttttgg aactaaaaga ggattgatat actggtttaa 3420 ttgcattttc aacaagacaa aatataattg acctcaaatt aaaacagaca atcaaaaata 3480 aattttaaat atgtcactct atatttttat caatatcagc taccattatt acttcctctc 3540 aattttgtca aagataacaa cataaataaa aattgtcttc cttaacccat atcaaaaaca 3600 taaaataaca aagaaataaa aatcatcaca aatatcaaat taacaacaaa aggtctaaaa 3660 aatcaagaga tataaaagag aaaatagaaa aagcttttaa acaaacatac cttttaattt 3720 cagctaatta acacaaccga tgttattaat taaccggaga ataattgatt cttgtttttc 3780 taaatttgag agaagggtga ggcacaatac aagattttaa aatttacaag tttctttcct 3840 tctgctttta aagaaaaaaa ataaactgtt ggccaacggc tataaaaata gccgttggcc 3900 aacggtaatt ttcttttgcc atttctacag aaaaatgtag aaatggctct tcacgtatcg 3960 aatagctatt ttagctattc gtttgcctgc tccgttggag tgataaaaac agaaacaaaa 4020 gctaaaagta caatttttta aatttggctc ttcatttagc tctccggttg gagatgctct 4080 ta 4082 // ID Copia-56_PTr-LTR repbase; DNA; EDCOT; 157 BP. XX AC . XX DT 10-DEC-2009 (Rel. 15.02, Created) DT 10-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Copia-type LTR retrotransposon: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Copia-56_PTr-I; Copia-56_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-157 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 166-166 (2010). XX DR [1] (Consensus) XX SQ Sequence 157 BP; 52 A; 25 C; 27 G; 53 T; 0 other; tattatagaa tgtatagcat gtatatatct gaataggaaa ttaatgtagg attattccaa 60 tgttgtaatc cctacagtta ctgccgtgtt ctgccgcata tatataaata ggaaggttgg 120 ctaaggcaca acctaagaca ttctattatt ctcaact 157 // ID Copia20-PTR_LTR repbase; DNA; EDCOT; 228 BP. XX AC scaffold_180; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia20-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-228 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-228 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 215-215 (2007). XX DR Genome; scaffold_180; Positions 426753 426980. XX SQ Sequence 228 BP; 76 A; 38 C; 36 G; 78 T; 0 other; tgttaccgta tatgtataca attaggactc ttaatattaa ctatcaagat tatcttatca 60 tagactcctt gtatagcaaa ataaccttcc atgtagactc cttgtatggc aaaataacct 120 ggaatgtata aaaggctact ttatgccgag tgcaagggaa acattctgca aagttaataa 180 attgattaac tcttttggta ctctgctttt ggcttgaata gattaaca 228 // ID Gypsy-1_Mad-LTR repbase; DNA; EDCOT; 148 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-1_Mad_; KW Gypsy-1_Mad-LTR; Gypsy-1_Mad-I. XX NM Gypsy-1_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-148 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1733-1733 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 148 BP; 53 A; 35 C; 33 G; 27 T; 0 other; tggagccaaa aataatcaca aggcgacacg tggatttttg ggtaaagagg acaaaattac 60 ccttgaggca catcgggatt cctacgcgcg agcagcggac aatcatccct caaccaagtc 120 aaaagtgccc aaaataggta acaattca 148 // ID COP12_I_MT repbase; DNA; EDCOT; 4046 BP. XX AC . XX DT 02-JAN-2007 (Rel. 12.01, Created) DT 06-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE The internal region of COP12_MT LTR retroposon from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Internal; Interspersed; ORF; COP12_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4046 RA Shankar R. and Jurka J.; RT "COP12_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 7-7 (2007). XX DR [1] (Consensus) XX CC The internal region has a single ORF having domain for reverse CC transcriptase. It is flanked on both sides by LTRs. XX FH Key Location/Qualifiers FT CDS 76..4044 FT /product="COP12_I_MT_1p" FT /translation="MASGSNAVITVPQFSGESYHIWVVKMKSCLKSFGLWD FT YVDEDKQVPPLQANPTVAQMKHHEEEKLKKEKAVSVLHSALADDVFTGIMH FT LETAKQIWDELDERYAGDERVRSIKLLTLKREFEMLKMKEHESVKEYTSKL FT SHLVNQMRLHGEVVDDSKVVEKMLISLPDKFEAKVAAIEESCDLKKLTVSE FT MVSKLTAHEQRFSMRMDDVSDGAFQAKHKQFGVGQKKKNYKHGGDQKGKNK FT DDGSSSESAAKDKFPPCLTCKRTNHLTKDCFYKGKPQIKCNHCNRWGHREK FT FCRLKQNQSQPQHAHQVNFTDEQAHEDHLFMATHTSSSSSKDVWYVDSGCT FT IHMANEPSLFTSLDKAVQTKVKIGNGKYVQAKGKGIVSVHTSKGPKYIHDV FT LLIPDLSQNLLSVAQLLKKGYSISFKNNVCVIMDSTDSEVVKVEMCGNSFP FT LSLNQVNQTALVSKHDDSALWHKRYGHFNFNALKYLQSHDMVRDMPEINCI FT NDLCDACQLGKMHRKSFQSTNVTRAKEKLELVHTDLCGPMSVPSLSHNKYF FT LLFIDDLTRMTWVYFLTSKAQTFNVFKKFRAMVESQSGCKIKALRSDNGKE FT YTSNEFNLFCEDMGIVHQLTVSYTPQQNGVSERKNRTVMEMARCLIAEKQL FT PKSFWAEAVYTAVYLLNRLPTRAVQGKTPIEAWIGVKPSAKHLKVFGSICY FT VHVVAAKRSKLDDKAEMGIFLGYAASSKGYRVYNLKTKQIVISRDIDVDEN FT AYWDWENDEVQRSTKSAESAHDKQEHTTNEDENQIAESDSLILKSKSLSEV FT YENCNFVENEPSSFEEASLITEWKDAMKEELLAINKNGTWELTQRPKDKNV FT IGVKWVYRTKLNPDGSIHKHKARLVVKGYSQMAGIDYGDTFAPVARHETIR FT LIVALSAQCGWKIFHLDVKSAFLNGILEEEIYVEQPAGFIVAGYEDSVYRL FT HKALYGLKQAPRAWYSRIDSHFLQNDFRRSQNEPTLYVKKCGNGKRIIVSL FT YVDDLLITGNDIDEINKFKKSMLEVFEMTDLGLMKYFLGMELHQLDDGIFL FT SQKKYANDVLKKFKLESCKSVSTPLAVNEKLSKSDGDAKADVTQYRSLIGC FT LLYLTATRPDLMFSASLLSRFMHSPSVTHLGVGKRVLRYIRGTTDFGIWYN FT KGDSKIEGFVDSDWAGSIDDSKSTSGYVFSLGSGVFSWNSKKQDVVAQSSA FT EAEYIAAAAASNQAIWIKKVLSDLNHVQEEPIVLWCDNKSAIAIAKNPIQH FT GRTKHINVKFHAIREAEQNGDVKLQHCSSEEQLADILTKALPSAKFMELRS FT KLGVFQKSFKE" XX SQ Sequence 4046 BP; 1370 A; 615 C; 906 G; 1155 T; 0 other; tggtatacag agcagtgttc ttagaggctg tgagaaaaag aaaaacacac acccagaaaa 60 cttgttagaa atcaaatggc ttctggtagt aatgctgtaa ttactgtccc tcaattttct 120 ggggaaagtt atcacatatg ggttgtcaaa atgaaatcat gtttgaagtc ttttggctta 180 tgggattatg tagatgaaga caagcaggtt ccaccactgc aagctaatcc cacagtagct 240 caaatgaaac accatgagga ggaaaaattg aagaaggaga aagcggtttc agttctgcat 300 tcagccttgg cagatgatgt gtttacggga atcatgcatc tcgaaacagc caagcaaata 360 tgggatgagc tggacgaaag gtatgctggt gatgaaaggg taagatccat aaagttattg 420 actcttaaaa gggagtttga aatgctgaaa atgaaggaac atgaatctgt caaagaatac 480 acctcaaaac tatctcactt ggtgaatcaa atgagacttc atggtgaggt tgtagatgac 540 agcaaagtag tggaaaagat gctgatcagc ttacccgaca aatttgaagc caaagttgct 600 gctattgaag agtcatgtga tctcaagaaa ctaactgttt ctgagatggt cagcaaattg 660 acagctcatg aacaaagatt ctctatgaga atggatgatg tttctgatgg tgcttttcag 720 gccaaacaca agcagtttgg agttggacag aagaaaaaga actacaaaca tggtggtgat 780 caaaaaggaa agaacaaaga tgatggtagt tcaagtgaat ctgcagcaaa ggacaagttc 840 cctccttgtc taacttgtaa aagaacaaat cacttgacaa aagattgctt ttataaggga 900 aagccccaaa ttaaatgcaa tcactgtaat cgatggggtc atagagagaa gttttgtcga 960 ttaaaacaaa accaatctca accacaacat gcacatcagg ttaacttcac tgatgaacaa 1020 gcccatgaag atcacttgtt tatggccact catacaagta gctcttcttc taaagatgta 1080 tggtatgttg atagtgggtg cacaatccac atggcaaatg aaccaagtct cttcacctct 1140 ttggacaaag ctgtacaaac caaagtgaag attggaaatg gaaaatatgt gcaggccaaa 1200 ggaaaaggta ttgtttctgt tcacactagc aaaggtccaa aatatatcca tgatgttttg 1260 ttgattccag atctgagtca aaatttgcta agtgttgctc agttattgaa gaaaggatat 1320 tcaatttcct ttaaaaataa tgtttgtgtc ataatggatt caactgattc tgaagttgtg 1380 aaggttgaaa tgtgtggaaa tagttttcca ttaagtttga atcaagtgaa tcaaacagca 1440 cttgtttcca aacatgatga ttctgcacta tggcacaaaa gatatggtca ttttaatttt 1500 aatgcattaa aatatctgca atctcatgat atggtgagag acatgccaga aattaattgt 1560 attaatgatt tatgtgatgc ttgtcaactt ggaaaaatgc atagaaagtc ctttcagtca 1620 acaaatgtta cacgagcaaa ggaaaaattg gagcttgttc ataccgactt gtgtggtcct 1680 atgagtgtgc cctctcttag ccacaacaag tactttctat tgtttattga tgatctgact 1740 aggatgacat gggtgtattt tctgacaagt aaagctcaaa cttttaatgt cttcaaaaag 1800 tttagagcta tggtggaatc tcaaagtggc tgcaaaatca aagctttgag atctgacaac 1860 ggaaaggagt atacttccaa tgaatttaat ttgttttgtg aagatatggg cattgtacat 1920 cagctgacag tgagctacac acctcagcaa aatggagttt ctgagaggaa aaacagaaca 1980 gttatggaga tggcaagatg tttgattgct gaaaagcaat taccaaaaag cttttgggct 2040 gaagctgttt atacagcagt gtatctcttg aataggctgc caacaagggc tgttcaaggg 2100 aaaacaccaa ttgaggcatg gataggtgtg aagccttcag ccaaacattt gaaggtcttt 2160 ggatcaatat gttatgttca tgttgtagca gcaaaaagat ccaaattgga tgataaagct 2220 gaaatgggga tttttttggg ttatgcagca agctccaaag gttatagagt gtacaacttg 2280 aagacaaaac aaattgtgat cagcagagac attgatgttg atgaaaatgc atattgggat 2340 tgggaaaatg atgaggttca aagaagtaca aaatctgctg aaagtgctca tgacaaacaa 2400 gagcacacaa caaatgaaga tgaaaatcag atagctgaat ctgattccct aattctaaag 2460 agcaaatctc tgtctgaagt ttatgaaaat tgcaattttg ttgagaatga accttctagt 2520 tttgaagaag cttcattgat aacagaatgg aaagatgcaa tgaaggagga gctgctggcc 2580 attaataaaa atggtacatg ggaactcact caaagaccta aagataaaaa tgtgatagga 2640 gttaaatggg tttacagaac caagttaaat cctgatggct ccattcacaa acacaaagca 2700 aggcttgttg tgaaaggata ttctcaaatg gctggaattg attatggtga tacatttgca 2760 ccggttgcta ggcatgaaac aattcggttg attgttgctc tatcagcaca atgtggatgg 2820 aagatctttc atttggatgt caaatcggca ttcttaaatg gaatcctgga ggaggaaatt 2880 tatgttgaac aacctgctgg ttttattgtt gcaggttatg aagacagtgt gtataggctt 2940 cataaagcct tgtatgggct gaaacaggcg cctagagcct ggtacagtag aattgactca 3000 cattttctgc aaaatgattt caggaggagt caaaatgagc ctacacttta tgttaaaaaa 3060 tgtggcaatg ggaagaggat tatagtttct ctttatgttg atgacttgtt gattaccggt 3120 aatgacattg atgagattaa caagtttaag aagagcatgt tggaggtctt tgaaatgacg 3180 gacctgggat tgatgaagta ttttttggga atggaattgc atcagcttga tgatggaata 3240 tttctttcac aaaagaaata tgctaatgat gtgctgaaaa aattcaaatt ggagagttgt 3300 aaatctgttt caacacctct tgctgtaaat gaaaaactct caaaatctga tggagatgct 3360 aaggcagatg ttactcaata taggagtttg attggttgtc ttctttactt gactgcaact 3420 agaccagatt tgatgttctc tgctagtttg ctttctaggt tcatgcattc accaagtgta 3480 acacacttag gtgtgggcaa aagagtgttg aggtacataa gaggtactac tgattttggt 3540 atttggtaca acaaaggtga tagtaagatt gaaggctttg ttgatagtga ttgggctgga 3600 tctattgatg attctaaaag cacaagtggt tatgtttttt cacttggtag tggtgtattt 3660 tcatggaatt ccaaaaaaca agatgtggtt gctcaatcct cagctgaagc tgagtatatt 3720 gctgctgcag ctgcatcaaa tcaagctatt tggatcaaaa aggtattgag tgatctgaat 3780 catgtacaag aggaaccaat tgtgctatgg tgtgacaaca aatcagctat agcaattgcc 3840 aaaaatccaa ttcaacatgg aagaacaaag catatcaatg tcaaatttca tgctataaga 3900 gaagctgaac aaaatggaga tgtaaaactg cagcactgca gttctgaaga acaattggca 3960 gacattttaa caaaagcact tcctagtgcc aagttcatgg agctaagaag caagctagga 4020 gtatttcaaa aaagttttaa ggagga 4046 // ID DNA3-6_Mad repbase; DNA; EDCOT; 1057 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative non-autonomous Harbinger family DNA transposon from DE apple. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA3-6_Mad. XX NM DNA3-6_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1057 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1470-1470 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TSD is 3-bp long. TIR is 14-bp long. XX SQ Sequence 1057 BP; 282 A; 261 C; 223 G; 291 T; 0 other; ggcctcgttt ggcagctcgg actgtactga ctatttctgt cggataggat aaatagccac 60 cggatagtac tgactaaatt agtcgggcgt ttggtgcagt atcggactaa tgaccgtatt 120 atttatactg tgtttggtat tataccggat aggaggaatc aaacttaaaa taaaattaaa 180 aaaaaaaaac tgaaatcatc tctcttgttc ccagatctct ccgccgcacc cccccaaact 240 ccctccctct ctctcccttc ttcttcttcc ccgtctgctc ccctgaacta aaccccacca 300 caaaggcagc aacaagaaac ccagcaaaac ccacctttca aattctcatc gtttttttcc 360 caatccttct ctttttttta gctacaaatc aacccagcaa aaaaacacac cacaaaccaa 420 gaaaattcac acaaaggact ttgttttcta tttgtcctaa aaaacaattg gaaggaaatt 480 cacggaggac accttttttt caacaaacca agaacactca tcggagagaa aaatggggct 540 gactgtgatt ttgggcatta ggttggggaa aagcattgac aaaattcgat ttggaggagg 600 ggaagagctg agtgacgcct ccagttggcg aattcctcag cttccatccg cccctttctg 660 tatatccctg tggaatatgt tgtttcgcta ctggtctcct tttgtctctc tctcactctc 720 ttctttgttc ctctgtgtgc tttccgtcgg acgagacggg aaattagtcg gcgaatgact 780 gcagaggagt ggcgcccggg gtggagaact cgtcgaggaa ctgctcgaag gcccactttg 840 agaagtcgtt aacggcggct tcgtgaagtt ggagaggaca gcgccccgac taattatccc 900 gagcttttgg gctgttttaa tagtacggtg tcaaccgtat aaaatttgat gggccggata 960 attaagcggg tgcttattta gtacgagagt gcaccaaaca actgctcccg tattatttat 1020 cctatccgat gctttatacg gcgtgccaaa cgaggcc 1057 // ID Ogre-MT3_LTR repbase; DNA; EDCOT; 2224 BP. XX AC AC151524; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 10-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE Autonomous LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-MT3; Ogre-MT3_LTR. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2224 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC151524; Positions 76334 78557. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). CC In Medicago truncatula, there are distinct subfamilies of CC Ogres differing in their LTR sequences. XX SQ Sequence 2224 BP; 696 A; 434 C; 327 G; 767 T; 0 other; tgtcataccc taaattttga ccaaggatcc cacggacgcg tgtcgtttga ctctagccga 60 tctcatgatt cagtgaaaat ttcggcaggg aggtatttta aaatacctca ttttttgctc 120 cgattgcagg cactttcctc tcgttttatt tcattatcta atttccatct tttattttta 180 attttaaagt tagttacttt ttttttaata gttaataaat gtttattttc cagtttttgt 240 ccaataaagt taataagtcc aaaaattcca acaaagggtc cctttttttc ttttttcatt 300 tctcctccgt acgcctcgtg ttcagccaat ttcacagggt caattttttg tttccaaatc 360 tgggaacgcg gtagtaactt ctgcaagtta tttccttatt caatccaacc ctaatgctat 420 aaaagcaaac ctgcaaaata cagaaaagac agacaatttt ccacagccgc aaaccgagaa 480 accacagaat caccaatcag tagccgcaat catcaaaccc taattttctt tctctttcaa 540 aaaatttcaa aatcaaacac tcaaatccaa accgatttca accaacactt tattcaaacc 600 gaatctgttc ataagcacct caaataaatc aagtttcgca cttaaacatc accttttctt 660 ttgaatccgt cacttacaaa ctcgaatccg aacccacaac aataagagta acggatccga 720 tttaaacaaa ggttcaatcg ctccgtttca acaagtatca gaaccgagtt tgatgaacag 780 aagcgaattc aaagattaga gaagaagcag atcggaatcc gaggtaaaaa aaggtagtat 840 tttattttcg tgttgtttga atgtagatct agaacgtgtt gttgcttttc tttgaaatct 900 aagtccggat ctatcaccta tgcgaaaaag gatataataa tatgtaattg tttttgaaaa 960 aggagggttt tgaaaactcc ggcacggtgg tgcaccaccg gccaccgcgc cggaaaactc 1020 atgaaaagaa gaacagagaa gagggagacg tgagattaga gaagtgaaga gagagaaatg 1080 aatgaagaaa gtgaaagaaa tgggtcttac accctattta tataacctcg aaccgggcgg 1140 gtctaaccga cccgcccacg acccgtttct gcttaagccc agttgttcct ttttaatttc 1200 actacagttt tattaattac acctctgttt ttgctttctg cacccctttg ctgaaagaaa 1260 attatctaaa aaacttacaa aaatattgtg tttgttttaa ttttttattt actgttttta 1320 ttttataatt gccatttttt tatttactta gaatcatctc atgcatattt taatttcttg 1380 tcattttatt gtcattaatt tttttttttt tttttagtgt gtataattag gaaattgatg 1440 taatttattt tgcgcatttt tttatttctt attatatttc tcttgagacc atagaatgta 1500 tctaggaggg tatgtaatag tgtagtaaca cacgcaccga cactatgccg ctttatttac 1560 cgcttatttt atttttgctc cgttacgtta gttttaaggt tagtctaaaa aaaatcaaat 1620 atgcaaaact cccaaaatat tttcttaata aaccttggtt tgtaacccaa gtgttttcct 1680 ttttattttc ttaatcaaat gcttaattga attaatattc ataatagact tgacttcttt 1740 gtaattaaaa tttgaccaac ctcaccttat tttatctcat gccttgaggc ctcttatctc 1800 ttcttaaaac tattttcaaa aattaaaatc aacctaaccc accaaagaaa ttctttaggt 1860 gaactacatt ggttttgatc ccttttcttt aagggtatgt aggcatagga tttttatcct 1920 tccaaatcaa gtaaaaataa ccaaaaacat acttcttccc ccattctttc acttagattt 1980 tttaggtaat aaatttcaaa taagcaatga atttagcaca aagataaatt aggtaagagg 2040 ttcctacggg ataccgtaga cgcttagggt gctagcacct tcccttcgcg taaccaaccc 2100 ccgaatccaa agtctcgatg agggttttta ctcatttttt cccttcccac gaataaaaat 2160 cgagagttca aagattgacg attcaaatca attaatggtt tgatatccga aaatcacgag 2220 caca 2224 // ID TreLTRRT2-I repbase; DNA; EDCOT; 6103 BP. XX AC . XX DT 03-DEC-2010 (Rel. 15.12, Created) DT 20-DEC-2010 (Rel. 15.12, Last updated, Version 2) XX DE Gypsy-type LTR retrotransposon: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; TreLTRRT2; KW TreLTRRT2-I. XX NM TreLTRRT2. XX OS Trifolium repens OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Trifolium. XX RN [1] RP 1-6103 RA Hand M.L., Cogan N.O.I., Sawbridge T.I., Spangenberg G.C. RA and Forster J.W.; RT "Comparision of homoeolocus organisation in paired BAC clones RT from white clover (Trifolium repens L.) and microcolinearity with RT model legume species."; RL BMC Plant Biology 10, 94-94 (2010). XX RN [2] RP 1-6103 RA Laten H.M., Hand M.L., Cogan N.O.I. and Forster J.W.; RT "LTR retrotransposons in white clover, Trifolium repens L."; RL Repbase Reports 10(12), 2176-2176 (2010). XX RN [3] RP 1-6103 RA Jurka J.; RT "Classification as Gypsy."; RL Direct Submission to Repbase Update (20-DEC-2010). XX DR [2] (Consensus) XX CC Composite of internal region of two independent LTR CC retrotransposon insertions that are 97.1% identical at the DNA CC level, including LTRs and 98.4% identical excluding LTRs. LTRs CC from each element are 99.9% and 100% identical, respectively. CC Related to Ram4 from M. truncatula. Gag-prot ORF separated from CC RT-RH ORF by +1 frameshift. 143 bp region where ORF1 and ORF2 CC overlap does not encode identifiable protein domains. No CC detectable integrase. LTRs flanked by 5 bp target site CC duplications. CC Originally defined in ref 2 as: CC "LTR retrotransposon of unknown class from CLUSTALW alignment of CC two, full-length elements from T. repens L Genbank Accessions CC GU443965 positions 104389-112569 and GU443966 positions CC 61716-69898. XX FH Key Location/Qualifiers FT CDS 120..3752 FT /product="TreLTRRT2-I_1p" FT /translation="MHLRSGKSLPVFSNIPKRPRSRMVRPPNNPNPNNXNN FT NNNNGXETNPVXNXTGPPNQPVTGNPGANPTGGSTNPALNFTTSESIPXNN FT PNXGGTNPVISSGTIGASASGSTMSATTSSMAGGFVPPNXXGAMMTQMNVS FT SXPTNVSXXXGYTDGSQXGGTPSRPPWLPRNPQXGMPTTTMASLYNWPSXE FT SSPSSSAMGNRGNSLNLTNNSMNVLRQQMDESNHDMVNALTQQIGTIFNPV FT LQTANDNYLLLANQMGRMADFFGAPDAPNNQRIPRVNPEIQTGVQAQPVRI FT EREQQEPEVVLVNRNQDADNVLRQVRQENVAGQNNLANLVENILAQNGLNT FT GLHRPNFVSPLSEXVLQAELPRGWKIPKFTKFAGDTNESTVEHIARYLAEA FT GNLANNEDLKMKFFPNSLTKNAFTWFTTLPPHSIHTWTQLERLFHEQFYMG FT QSRISLKELASMKRKTSEAIDDYLNRFRLLKARCFTQVPEHELVEMAAGGL FT DYSIRKKLDTQHLRDMAQLADRVRQVERLRAEKVRNSKFHKKEKVAYIETY FT ESENEFDDGQDYIENNEVNVAELKPGPPYTCKMLKPSNGNNPVEPKNDRFV FT SKTYTFDITKCDEIFDLLVADGQIIVPKGLKLPPLDQRKKRGFCKYHNFLG FT HRTSQCVLFRDLVQKALQEGRLKFGEKPKSKQQVDEDPLQIADAAYTEPFE FT CLMLEALNLTEGGQLISIPEEEYENKVEEVYPQAGETLLDFLQRCKENDGE FT ATLCPHCSAMFDKKAAAGLNKFLPHSQNRNNWPNQKPTYSNILNSQQAPVH FT QRLGPQKSFVPSNRTPVNQWVHGRSMDYGQRNMERGNSSNSNPKKDPESRK FT YDYRNNYKGKNPMTRSQWRRYQRQKKVAAQQSPLTTDGNGRRPLELAKKPM FT KERLGESKIESSVADNVEDDHMEADDFLDSEPDLDIIVNVVSILPREFDVC FT SEVTDDEEESGMQMALHRPVCYYVTSNGALEDQMATFERPDEGMKSHLKPL FT FIQXKVNNVGINKVLIDGGAAVNLMPEFLLRKIGKSLVDLHPHNIVLSNYE FT GETGFSLGAIQLEVVVGSTVRPTLFLVVASKANYNLLLGREWIHGVGAVPS FT TLHQRLIIWREDGIVENIEADQSYFKTEVHHLTKHSFDKKLATISPCTEKD FT FAYRLARNGHHAIKLDPTHGFLWEREDGNSEDGEYESHKCPTGWDVKENYY FT V" FT CDS 3613..6093 FT /product="TreLTRRT2-I_2p" FT /translation="QEMVTMQSNWIPHMVSCGRERMETARMASMKATNAQL FT VGMSKKTTMSESQTWARITAYMAENRIKMALEANSFSENMADIANGEKIGK FT QEPELQKLDCIYDDEPLGFEKDPISQSHKMQAQDPLQEIDLGDGLMKRPTY FT ISANIPPDLKAKVVQLLVEYKDCFAWDYNEMPGLSRKLVEHELPVRPDKKP FT VKQLPRRFAPEIMSKIKEEIERLLRSKFIRTARYVEWLANIVPVIKKNGSL FT RVCIDFRDLNNATPKDEYPMPVAEMLIDSAAGFEYLSMLDGYSGYNQIFIA FT ENDVPKTAFRCPGALGTYEWVVMPFGLKNAGATYQRAMNLIFHEYIDTFMQ FT VYIDDIVVKSSSKVDHLDHLKKSFEKMRKYGLKMNPLKCAFCVNAGDFLGF FT VVHKKGIEINQNKTKAIMETKSPTTKKQLQSLLGKINFLRRFISNLSGKAQ FT PFSPLLRLKKEDIFTWGQDQQRAFDEIKSYLSKPPMLMPPIRNKFMKLYIS FT ASDSTLGSMLAQEDENGEEKAIYYLSRVLNDAETRYSSIEKLCLCLYFSCI FT KLKHYIKPVDVFVYSHCDIIKHMLSKPILHSRIGKWALALTEYSLTYKPLK FT AVKGQIVADFIADHSVIETPQNYVESRPWKLYXDGSKHKHGVGIGILIISP FT SKIPTKFKYKINGFCSNNEAEYEALIXGLEILLDLGAKNILIRGDSELVLK FT QLTKEYKCIKEHLMKYFVIAISLLKRFDQVXIEHVPRXENQEANDLAQIAS FT GYKISXEKLEELIEIKDKLIXDQPXXXELSMPKLVGADVPQDNGQDTTCRI FT GKGXXLQNCHFSLXYXTXSRNWHF*" XX SQ Sequence 6103 BP; 2024 A; 1099 C; 1277 G; 1606 T; 97 other; aattggcacg cccrgtggga cctctggatt gtgtaatttt tacttagtga atttttgaaa 60 attttycata caaaatttgt tgtttggtgt ttgtgctttg attgtgtcta tatttgtata 120 tgcatttgag aagtggtaaa tctcttccag tattttcaaa yataccaaag cgtcctcgtt 180 ccagaatggt gagaccacca aacaatccta ayccyaayaa tawtaataat aataayaata 240 atgggrcrga aaccaatcct gttcyraaty cgacaggacc accaaatcaa ccagtaactg 300 gcaatcctgg cgccaatcct actggcggat caacaaatcc tgccctaaac tttacaactt 360 ctgaaagtat cccargcaat aatcctaatg ktgggggtac aaatcctgtg ataagttctg 420 gaaccattgg cgcaagtgcc agtggatcaa caatgtctgc cactacktca agtatggcag 480 gagggtttgt tcctccaaat aygartggtg caatgatgac acaaatgaat gtatcatcca 540 trccaacsaa ygtatcacam ayryatggrt ayacagacgg tagtcaartt ggtggaacwc 600 cgtcragacc yccwtggttg ccyagaaacc cacaatwtgg ratgccaacr acracgatgg 660 caagcctgta taattggcct tckrtagaaa gttctccctc rtcttctgcg atgggaaata 720 ggggaaattc tctgaacttg acwaataatt ctatgaatgt acttaggcaa caaatggacg 780 aaagtaacca tgayatggtg aacgcgttga cccaacagat tggcacaatc ttyaatcctg 840 tgttacaaac agccaatgac aattatttrt tgttagccaa tcaaatggga aggatggcag 900 acttttttgg tgcccctgat gctccaaata atcaaagaat tccccgtgta aayccggaga 960 ttcaaacagg agtccaagcc caaccagtgc gcatcgagag agaacaacaa gaaccagaag 1020 tagttttggt taatagaaac caagatgctg ataatgttct taggcaagtt cgacaagaaa 1080 atgttgcagg gcaaaataac ttggccaatt tagtagaaaa tattttggcc caaaatggyt 1140 tgaatacagg gttgcataga ccaaattttg tgtcaccctt gtctgaawwt gtattacagg 1200 cagaattgcc aaggggatgg aagattccca aattcacaaa atttgctggt gatactaatg 1260 aatctactgt cgaacatatt gccagatatt tggcagaggc agggaatttg gcaaataatg 1320 aagatttaaa aatgaaattt tttcccaatt ccctcactaa aaatgccttt acgtggttta 1380 ccacacttcc ccctcattca attcatactt ggactcaatt ggaaaggcta tttcatgaac 1440 aattctacat gggacaatct aggattagtc tcaaagaatt agccagtatg aagcgcaaaa 1500 cctcagaagc cattgatgac tatctaaaca ggtttcgcct ccttaaggca aggtgcttta 1560 cccaagtgcc tgaacatgaa ttggttgaga tggctgctgg tggcctcgac tattccatta 1620 ggaaaaagtt agatactcaa catttgagag acatggccca attagcagat cgtgttcgac 1680 aggttgaacg cctcagggct gaaaaagtca gaaattctaa gtttcacaaa aaagaaaaag 1740 tggcatacat agaaacttat gaaagtgaaa atgagttcga cgatggtcag gattacatag 1800 aaaataatga ggttaacgtg gctgagttaa aaccaggccc tccttatact tgtaaaatgt 1860 tgaaaccatc aaatgggaat aatcctgtcg aaccaaaaaa tgatagattt gtttctaaga 1920 catacacttt cgacattact aaatgtgatg aaatttttga cttattggtc gctgatggcc 1980 aaataattgt gccaaagggt ttaaaattac cacctttgga ccaacgkaag aaaagagggt 2040 tttgtaaata ccataatttc ttgggtcata gaacctcaca atgtgttctt ttcagggatc 2100 tggtccagaa agccctacag gagggaagac tcaaatttgg cgaaaagcca aaatccaaac 2160 aacaggtgga tgaagatcca ttgcagattg ctgatgctgc atacacggag ccattcgagt 2220 gcctgatgtt ggaagcattg aacctcactg aaggggggca attaatttcc attcctgagg 2280 argagtacga aaacaaagtg gaagaggtgt atccacaagc aggggagact ttattggatt 2340 tccttcaacg ctgcaaagaa aatgatggcg aagctacatt atgtcctcat tgtagtgcca 2400 tgttcgacaa gaaggctgct gcaggcctca acaagtttct gcctcatagt caaaacagaa 2460 acaattggcc aaatcaaaag ccaacttatt ccaatattct gaatagccag caggcacctg 2520 tacaccagag gttgggacca caaaaatcat ttgtcccctc aaacaggaca cctgtcaacc 2580 aatgggttca tggaagaagc atggactatg gtcaaaggaa tatggagaga gggaactcca 2640 gtaacagcaa tcccaaaaag gatcctgagt caaggaaata tgattacagg aataattaca 2700 aagggaaaaa tcccatgaca aggtcycaat ggcgtagata tcaacgccag aaaaaagtgg 2760 ctgctcaaca atccccatta actactgatg gtaatggaag aaggcctttg gaattggcaa 2820 agaagccaat gaaagaaagg ttaggcgaat cgaaaataga gtcttcagtt gctgataatg 2880 tcgaagatga ccacatggaa gcagatgact ttttggattc tgagcctgat ctcgacataa 2940 tcgtcaatgt tgtgtcaatc ttaccaaggg aattcgacgt ttgctctgaa gtgacagatg 3000 acgaagagga atctggaatg caaatggccc ttcataggcc agtatgttac tatgtgacga 3060 gcaatggtgc tctagaagat caaatggcta catttgaaag gccagatgaa ggcatgaaga 3120 gtcacttgaa gcctctcttc atacagscya aagtgaacaa tgtggggatc aacaaagtgc 3180 taattgatgg tggtgctgct gttaatctca tgccagaatt tttgctcaga aagattggca 3240 aatctttrgt ggatcttcat cctcacaaca tagttctttc aaactatgag ggtgaaactg 3300 gtttctcttt gggagcaatc cagttagaag tggttgttgg aagcactgta aggccaacct 3360 tgttcttggt tgtggcctct aaggcaaatt acaatctact tctaggtcga gagtggattc 3420 atggagtagg ggcagttcct tctaccctgc accaacgcct cattatctgg cgagaggatg 3480 gaatagtgga aaatattgaa gcagatcaaa gctacttcaa aactgaagtc catcatttga 3540 caaagcactc cttcgacaar aaattggcaa caatttcacc atgcactgag aargactttg 3600 catatcgtct agcaagaaat ggtcaccatg caatcaaact ggatcccaca catggtttct 3660 tgtgggagag agaggatgga aacagcgagg atggcgagta tgaaagccac aaatgcccaa 3720 ctggttggga tgtcaaagaa aactactatg tctgagtccc aaacttgggc aaggattacg 3780 gcctacatgg ctgaaaacag aatcaagatg gctttggaag ccaattcatt ttcagaaaat 3840 atggctgata tagccaatgg tgaaaagatt ggcaaacaag agccagaatt gcaaaaactg 3900 gactgcatct atgacgacga acccttagga tttgaaaaag atccaattag tcaaagtcat 3960 aagatgcaag cacaggatcc tttgcaagaa attgaccttg gagatggtct gatgaaaaga 4020 ccaacatata ttagtgcaaa cattcctcca gatctgaagg cgaaagtggt gcaacttcta 4080 gtggaataca aagattgttt tgcttgggat tacaatgaaa tgccaggtyt gagcagaaaa 4140 ttggtggaac atgaacttcc agttcgacca gacaaaaaac cagtaaaaca attgcctmga 4200 aggtttgcac cagaaattat gtcaaagatc aaggaagaaa ttgagaggct gctgaggagc 4260 aaattcatca gaacagcaag gtatgtcgaa tggttagcaa atatagtgcc tgtgattaag 4320 aaaaatggtt ctcttagagt atgtatagac tttagagatt tgaataatgc tacaccaaaa 4380 gacgaatatc ctatgcctgt agcagaaatg ctaattgatt cagcagcagg atttgaatat 4440 ttaagtatgc tagatggtta ttctggctac aaccaaattt tcattgctga aaatgatgta 4500 cccaaaactg cttttagatg cccaggggca ttaggcacgt atgaatgggt agtgatgccc 4560 ttcggtttga aaaatgctgg ggccacttat caaagagcaa tgaatctaat tttccatgar 4620 tacatagaca cttttatgca agtgtatatt gacgacatag ttgtcaaatc ctcgtcaaag 4680 gttgatcatt tagatcattt gaaaaagtct tttgaaaaga tgaggaaata tggattaaaa 4740 atgaatccat taaagtgtgc tttttgtgtt aatgcaggag atttccttgg gtttgttgtg 4800 cacaaaaagg gcattgaaat aaatcaaaac aaaacgaagg ctatcatgga gacaaaatct 4860 ccaactacta aaaagcaact tcagtcccta cttgggaaga tcaatttctt gaggagattc 4920 atctcaaatt taagtggtaa agctcagcct ttctcgccac tacttcgtct caagaaagaa 4980 gatattttca cttgggggca agatcaacaa cgagcttttg acgaaatcaa gagttatttg 5040 tcgaagccac caatgttgat gcctccaata aggaacaagt tcatgaagtt gtatatatca 5100 gcatcagatt cgacactggg tagtatgctt gcccaggaag atgaaaatgg tgaagaaaaa 5160 gccatctatt acttaagtag ggtattaaat gatgctgaaa ctagatatag tagtattgaa 5220 aaactatgct tatgtttgta tttctcttgt ataaaactca agcattatat aaagcctgtt 5280 gatgtttttg tttattctca ctgtgatatc attaagcata tgttrtctaa accaattttg 5340 catagtcgaa ttggaaaatg ggccttagcc ttaacagagt attcattaac atataaacct 5400 ctaaaggcag tcaaaggcca aattgtrgct gattttatag cagatcattc tgtaatagaa 5460 actccacaaa attatgtaga atcacgaccc tggaaattgt atyttgatgg ttctaaacat 5520 aaacatggag ttggaattgg gattctaatt atttcccctt ccaaaatacc cactaagttc 5580 aartataaaa ttaatggrtt ctgctcaaat aatgaagcag artatgaagc tttaatarca 5640 ggcttagaaa ttttattgga cttgggggca aaaaatatyy tgatyagagg tgattcagaa 5700 ytggttttga aacaattrac aaaagaatac aagtgyataa aagaacactt gatgaaatat 5760 tttgtcatag caatttcttt gttaaaacgt ttcgaccaag tyaycattga acatgtrcct 5820 cgwrtagaaa atcaagaagc caatgatttg gctcaaatag cttctggtta yaaaatytcy 5880 artgagaaac trgargagtt gattgaratt aaagataaac tyattrttga tcaacctsct 5940 yctwtrgaat tgtcaatgcc aaaacttgtg ggggcagatg taccacaaga caatggtcaa 6000 gataccacrt gcagaattgg aaaaggtgam watcttcaaa actgccattt ctcccttkyg 6060 tatycgacay gcagtcgaaa ctggcatttt tgagggggca att 6103 // ID Copia-12_Mad-I repbase; DNA; EDCOT; 5277 BP. XX AC ACYM01088783; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-12_Mad_; KW Copia-12_Mad-LTR; Copia-12_Mad-I. XX NM Copia-12_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5277 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1355-1355 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01088783; Positions 13780 8504. XX CC Positions [2473-2973] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 610..1545 FT /product="Copia-12_Mad-I_1p" FT /translation="MTTSSLKIDGVLGMLTIRLQDDNFAKWSFQFQSVLEG FT YDLFDYFDGTNVCPPKYVVSLESGVTKEITNAYREWIKTDKALLSLLLATL FT GDEAIKYVIGSKTAHEAWTHLTDRYATVSRARINHLKTELHTIKKGVDSIE FT KYLLRLKHLKDQLLAAGENISENDLIVAALAGLPPEYNMIRTVIVARETPI FT TLKEFRAQLLSAERTAEEYQSVLHFPMTGMFSQGESSATGARRQFYHGESS FT TSHNHNGAGFVGQYQRNNGTFGGLNGNQGGNHHNGSQSNSNNSNAGNFSRT FT NTGFNGSRFYTKPRFTGGNS" FT CDS 1903..5247 FT /product="Copia-12_Mad-I_2p" FT /translation="MDTGATHHMTSNLEDLTMIAPFDGDQNITVGSGECLP FT VKNTGSSSIQTSSKPLNLYTVLHVPELTASLISVYTLCKDNNYDVILDEFG FT FWVQDKATKTILMRGKSSGGLYHIPKQFFKYNQLRQSTPKAFLGQLIKASL FT WHHRLGHPTNEVLHSMLSHSQITYTSDINKHVCSFCLKGKMSRQVFETRTL FT GSVKPFERISSDVWGPSSVVSIEGYRYYVSFIDDCTKFTWIFPLIYKSQVL FT EVFQSFYAFIQTQFQAVVKFFQSDGGGEYMSLVFQKFLSSKGILHLVSCPY FT TPQQNGTAERKHRHILETAITLLTSANLTHNFWYHACAHAVFLINRMPCKS FT LSMQSPFFQLFKVQPVLHSLKIFGTAMYPYLRPYNSSKLDARTDQCVFVGY FT ALGYKGVLCYHRAKRRLYISRHVIHDEQTFPFYYSSSPICAQNVVGPVSRH FT HPVIVPYVLPVHAEISQRDSSSSQSVSSENSVHDQVISAIQVSSQSSPDST FT GVQVTSQLQDSSPPTTLLSAPTLNSLLPVHNPASIEVGPPFYPNNDSSLVH FT TISPPVSSSEHPMQTRLKSGAIQRKDYSAYSAQSPFSSLSGDFAFCGYTAL FT LTITESDEPSSYKAAVKSEKWKEAMVDEFIALQRQGTWILVPPPLNRNIIG FT GKWVYKVKRDQHGVISRYKARLVAQGFSQEQGLDYEDTFSPVVRHSTVRLV FT LALTASQKWSLRQLDVKNAFLHGDLQEEVFMKQPQGFQDSEHPDYVCKLIK FT SLYGLKQAPRAWNSKFTTYLPTLGFVVSDSDTSLFVKTQGADIVILLLYVD FT DIIITGSSSLLVQQVIDALGDVFDMKDMGKLTYFLGLQITYQENGDLFISQ FT SKYVKDLLKMAGLESCKPCSTPCKPHTQLLKDEGTSLPDPTLFRSLVGALQ FT YLTFTRPDIAYAVNYACQFMANPTDVHFSLVKRILRYLQGTVACGLTYSAH FT SQLHLTAFSDADWASDINTRRSTTGYVVFLGLSPISWQSKKQGGVSRSSTE FT AEYKALANATADMAWVRLILKDLQVYLPTPPLLYCDNVSTLALCSNPVFHT FT RIKHLDTDFHFVRERVQKGDLQVEYISTKDQVADILTKGLHGPLFLHHCCN FT LKLGYPS" XX SQ Sequence 5277 BP; 1500 A; 994 C; 1087 G; 1696 T; 0 other; ttgttatgat ggtatcagag ctcaggttct tttctttttg gggcgcggtg atgatctgaa 60 tctatcggtg ctggtcggaa gtatctggcg gtgttttctt tttttttttg gttctgcgag 120 gtcggtggta gtcgaaacgt ctcatcaatg gcggtgtgtt ttccgattga gaatgatgat 180 caagttcagg ttctttcgtt tccgatttct ctaaattgct tgtgaattgt gatacataat 240 ctgaagcacg aagctgttag tgttgattga ttgttgaaat cttgagaaaa aaaaaaaact 300 atggaggcac aaagccatgt gttctgtatc ttgtgattgt tgtaagatac tctgagtttt 360 gtagcacgaa gctctttgca gtgacacgaa gtcttattgt tgttgattga aatcttgaaa 420 tttgttcaaa agattcttga ttggtcaaat tagggcaaaa tgctctctga attgacacaa 480 agtctgattg ttgtttgaag tattgtgatc tgtatgcaag attcttgatt gttcaagact 540 gattgcactt gcattctgtt tggagtatta gtataatctt gaagaaagct tgataattac 600 tgtgcaacaa tgacaacttc atcacttaag attgatggag tgttggggat gcttacaatt 660 cgtttgcaag atgataattt tgctaagtgg tcattccaat ttcagtctgt cttagaaggt 720 tatgatctat ttgactactt tgatggaaca aatgtttgtc ctcctaagta tgtagtatct 780 ttggaaagtg gagtaaccaa agaaatcaca aatgcttatc gtgaatggat taagacagat 840 aaggctctat taagtcttct tcttgctaca cttggagatg aagcaattaa gtatgttata 900 gggagtaaga ctgcacatga ggcatggaca cacctcactg atcgatatgc tactgtttca 960 cgagctcgga tcaatcacct taaaactgaa ctgcatacaa tcaagaaagg tgttgactca 1020 attgagaagt atttgctcag acttaagcac ttgaaggatc agttattggc tgctggagag 1080 aatatttcag agaatgattt aattgttgca gctctagctg gtttgcctcc tgaatataac 1140 atgatccgta ctgtgattgt ggcaagagaa acaccaataa cactgaaaga atttcgtgca 1200 cagttgctga gtgcagaaag aacagcggaa gagtatcaat ctgtactgca ttttcctatg 1260 acaggcatgt tctctcaagg tgaatcatct gcaacaggag ctaggagaca gttctatcac 1320 ggagaaagtt ctacttctca taatcataat ggtgccggat ttgtgggaca ataccagaga 1380 aataatggaa cttttggggg tctcaatggc aatcaaggtg gaaatcacca taatgggagt 1440 cagagtaatt ccaataattc caatgcaggg aatttttcaa gaaccaatac tggttttaat 1500 gggtctcgat tttacactaa accaagattc actggtggca attcttgagg ttttaatagt 1560 agaagcaatg gtaatttttc tggtccctca aacagtcaca gaagcaattc taactggaat 1620 gcttggaatg gaaacaatgg gcacaaatcc aatattattc ctgaatgcca gatctgtagc 1680 aaatgagggc acactacact caattgctac tacagaaatg aacagttacc atcttctaat 1740 ggtccaatcc ctgagtgcca gatctgtgga aaacgagggc atattgctct taactgttac 1800 catcgaagca attattcttt ccagggtgca ccttcacctc aatctctcaa tgcattgact 1860 gcacaatctt ctacagactt taacaataat caagcttgga tcatggatac tggggctaca 1920 catcacatga ccagcaacct tgaggacttg actatgattg caccatttga tggagatcag 1980 aacatcacag ttggcagtgg tgaatgtctt ccagtgaaga atactggttc ttcttctatt 2040 caaacatcct ctaaaccctt aaatctctat actgttttgc atgttcctga gttaactgca 2100 agtctcattt ctgtctatac tttatgcaag gataataatt acgatgtaat tcttgatgaa 2160 tttgggtttt gggtgcagga caaggcaaca aagacaatac tcatgagagg aaagagtagt 2220 gggggattat atcacatacc aaagcagttc ttcaagtaca atcagttgag gcagtctaca 2280 ccaaaagcat ttcttgggca gttaataaag gcttctttgt ggcatcatcg gttaggtcat 2340 cctaccaatg aagttctaca tagtatgcta tcccattctc agattaccta tacgagtgat 2400 ataaataagc atgtttgcag cttttgtctt aaaggcaaaa tgtctagaca agtgtttgaa 2460 actagaactt tggggtctgt aaaaccattt gagaggatca gcagtgatgt atggggacca 2520 tcttcagttg tatcaataga gggttataga tattatgtga gttttattga tgattgtact 2580 aaattcacat ggatattccc tttaatatac aaatctcaag ttctagaagt atttcagtct 2640 ttctatgcat ttattcaaac tcagtttcaa gcagttgtta aatttttcca atctgatggt 2700 ggtggagaat acatgagttt ggtttttcag aagtttctta gttcaaaagg tatattgcac 2760 ttggtatcat gtccttacac tccccaacaa aatggcactg ctgaaagaaa acacagacat 2820 atattagaaa ctgcaattac cttgcttacc tcagctaatc ttacacataa tttttggtat 2880 catgcatgtg cccatgcagt ttttcttatc aataggatgc catgtaaatc tttaagtatg 2940 cagtctccat ttttccagtt gttcaaagtt caacctgtgc tacattctct gaaaattttt 3000 ggcacagcaa tgtatcctta ccttagaccc tataactcat ccaaattaga tgcacgaaca 3060 gatcaatgtg tatttgtggg atatgcctta ggctataagg gtgtgctttg ttaccatcga 3120 gctaagagac ggttgtatat ctctagacat gtaattcatg atgagcagac atttcctttt 3180 tactacagta gctctccaat atgtgcacaa aatgttgttg ggccagtttc tagacatcat 3240 cctgtgattg ttccttatgt tctacccgtt catgctgaaa tttcacagag ggattcttct 3300 tcttcacaaa gtgtcagtag tgagaattca gttcatgatc aagtgatttc agcaatacaa 3360 gtttcttccc agagttctcc ggactccaca ggtgttcaag ttacttctca gctccaagat 3420 tcctcacccc ctactacttt actctctgca ccaactctca actctttgtt gcctgtccat 3480 aacccagctt caattgaggt aggtccacct ttttacccaa ataatgattc aagtttagta 3540 catactatat cacctccagt atcttcaagt gagcatccta tgcaaactag actaaagtca 3600 ggtgcaattc aaaggaagga ttatagtgct tattctgcac aatctccttt ctcttcttta 3660 tctggtgatt ttgcattttg tggatatact gctttactca ctattacaga aagtgatgaa 3720 ccttcgtcat ataaagctgc tgttaaaagt gaaaaatgga aagaagcaat ggtggatgag 3780 ttcatagctt tacaaagaca gggtacatgg attctagttc ctccaccttt gaacaggaat 3840 ataattggtg gcaagtgggt ctacaaagtc aagagagatc aacatggtgt aatttctaga 3900 tacaaagcac gccttgttgc ccaagggttc agtcaagaac aagggctgga ttacgaagat 3960 acatttagtc cagtggtccg acatagtaca gttcgacttg tgctcgccct tactgcatct 4020 caaaaatgga gtcttagaca attagatgtg aagaatgcct ttcttcacgg ggatttacaa 4080 gaagaggtgt ttatgaagca accccagggt ttccaagatt ctgagcatcc tgattatgtg 4140 tgcaaattaa tcaagtccct ctatggttta aaacaggcac ctagggcctg gaattctaaa 4200 ttcacaacct acttacctac attgggattt gttgtttcag attcagatac cagtcttttt 4260 gttaaaaccc aaggtgctga tatagtgata cttcttctct atgtagatga tattatcatt 4320 actggctcta gttccttact ggtacaacaa gtgattgatg ctttagggga cgtttttgac 4380 atgaaggaca tgggcaagct tacatatttt ttgggcttgc agattacata tcaagaaaat 4440 ggtgatttgt ttatatctca gtcgaaatat gttaaagatt tattgaaaat ggctggtctt 4500 gagtcttgta aaccttgttc tactccctgc aagcctcaca cccaactact caaggatgag 4560 ggtacatcat tgccagatcc aactctgttt cgaagtttgg taggagcact tcaatatctg 4620 acattcactc gtccggacat tgcctatgct gtgaattatg cttgtcagtt tatggctaac 4680 cctacagatg ttcatttctc ccttgttaaa aggatcctcc gatatcttca gggcactgta 4740 gcttgcggtc ttacttattc tgcccattcc cagctacact tgacagcttt cagtgatgca 4800 gattgggcat ctgatatcaa cacaaggcgc tctaccactg gttatgttgt gttcttaggt 4860 cttagtccca tatcttggca atctaagaag caaggggggg tatctcgaag ttccacagag 4920 gctgagtaca aagctttagc taatgcaact gcagatatgg cttgggtccg attgattttg 4980 aaagacttgc aggtgtactt acctactcca cctttgttat attgtgataa tgtctccaca 5040 ttggctctgt gctctaatcc tgtctttcat actcggatca aacatttgga cacggatttt 5100 cattttgttc gagaaagggt gcagaaaggg gatttgcagg tggaatatat ctccactaaa 5160 gaccaagtag ctgatatttt gactaagggc ttgcatggtc ccttgtttct tcatcattgc 5220 tgcaatctca aacttggtta cccaagttga gattgagggg ggggggggta ttaacca 5277 // ID Gypsy-9_Mad-LTR repbase; DNA; EDCOT; 239 BP. XX AC ACYM01139694; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-9_Mad-I; KW Gypsy-9_Mad-LTR; Gypsy-9_Mad_. XX NM Gypsy-9_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-239 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1412-1412 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01139694; Positions 17 255. XX SQ Sequence 239 BP; 77 A; 36 C; 33 G; 92 T; 1 other; tgcagattgt cttatcatta attcattaaa ttcgttttta ctttaagtag gttataaaat 60 caatcatcaa aatttctact ttacaatcat taattgaaat ctggtttgtt tcgatttatt 120 taataatccn tgtggagaat gaccttgcga gatccgttta tactacaata accttgtgat 180 tcttgcaagt aaaataggag gtttttatcg cattcacatg agcagtaaaa atcctatca 239 // ID Gypsy3-VV_I repbase; DNA; EDCOT; 8952 BP. XX AC . XX DT 10-SEP-2007 (Rel. 12.09, Created) DT 10-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW internal portion; Gypsy3-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-8952 RA Obukhanych T. and Jurka J.; RT "Gypsy3-VV."; RL Repbase Reports 7(9), 798-798 (2007). XX DR [1] (Consensus) XX CC This is an internal portion of Gypsy3-VV LTR retrotransposon from CC Vitis vinifera. Individual elements are 90% similar to their CC consensus. The internal portion is flanked by LTRs, which are CC 98% similar to each other. LTR sequence is deposited as CC Gypsy3-VV_LTR. Target site duplications are 5 bp-long. XX FH Key Location/Qualifiers FT CDS 51..1682 FT /product="Gypsy3-VV_I_1p" FT /translation="MATPSRSRSSGRGEEDNSEWRQAIERRQLASERQLKA FT LLQETERLREENAVLRIQASTSGPPRRQRSRGQVANSRPQQEPESIYPGTA FT GAIPGACNVRPHEPHTPMPRAPREESSDSTHFSAKRQRDRKSQLSNSMRAR FT LGPQEPGRPRPPVATTWAARPDPMVTPMVQNVLPHRDPMVTPMVRNVHSHL FT AVQQAGRNLPNEPPIGSISKRLDDMLSTPFCSHIIHYEPPRGFLVPKFSTY FT DGSSDPFDHIMHYRQLMTLDIGNDALLCKVFPASLQGQALSWFHRLPPNSV FT GNFRDLSEAFVGQYLCSARHKQNISTLQNIKMQDNESLREFVKRFGQAVLQ FT VEACSMDAVLQIFKRSICPGTPFFESLAKKPPTTMDDLFRRANKYSMLEDD FT VRAATQQVLVAGQASRGGAERNAKPPDRPRPSDRRQEGPSRPERPPLTPLS FT ISYEKLLPMIQGLSDFRWPRPLGTDPSKRDHSKRCAFHKEHGHTTETCRCL FT HYLVERLIKAGHLKQYLRSDAGGRDASQNHNSESPQGPSRPQGRYKLY" FT CDS join(1597..2340,2344..5604) FT /product="Gypsy3-VV_I_2p" FT /translation="MLEVETLPKITTLRAPRAPAAPKAVINYINGGPSDEE FT YDSKRKRQKLLRAASVRERINSIRPGLTGGGPRPIDGTIIFPPVDPTRTLQ FT PHRDALILSLEIGDFDVRRILVDPGSSADLVQASVVSHMGHSLTGLENPGR FT ILSGFNGSSTTSLGDIVLPVQAGPVTLNVQFSVVQELSPFNVILGRTWLHY FT MKVIPSTYHQMVSFLTNDGQIDLYGSQLAARQCYQIAREAGTSQEDASLPE FT PSHARDQQLLGPADKDPPAADPLQTIQISEESTHLTNISSLMTPEETQNMQ FT NALRQNHDIFAWAHSDMKGIHPSITSHRLNVFPTARPIRQKIRRFHPDRQK FT IIRNEIDKLLEAGFIREVDYPDWLANVVVVPKKEGKWRVCVDYTNLNNACP FT KDSFPLPRIDQIVDSTAGQGMLSFLDAFSGYHQIPMSPADEEKTAFITPHG FT LYCYKVMPFGLKNAGATYQRLMTKIFKPLIGHTVEVYIDDIVVKSKTREEH FT VLHLQEVFHLLRKYGMKLNPSKCAFGVSAGKFLGFMVSQRGIEVSPDQVKA FT VMETPPPRSKKELQRLTGKLVALGRFIARFTDELRPFFLAIRKAGANGWTD FT SCQNAFEKIKHCLMQPPILSSPIPKEKLYMYLAVSEWAISAVLFRCPSPKE FT QKPIYYVSRALADVETRYSKMELTALALRSAAQKLRPYFQAHPVVVLTDQP FT LRNILHKPDLTGRMLQWAIELSEFGIEFQPRLSMKGQVMADFVLEYSRRPS FT QHQESSEKEWWTLRVDGASRSSGSGVGLLLQSPTGEHLEQAIRLGFPASNN FT EAEYEAILSGLDLALALSVSKLRVYSDSQLVVRHVQKEYEAKDARMARYLT FT KVRDTLQRFTEWTIEKIRRTENGRADALAGIAASLPIKEAILLPIHVQANP FT SVAETSTCNTIEANQADGQEWTNNIIEYLRTGTLPEDPKQAHKIRVQAARF FT TLIGGHLYKRSFTGPYLRCLSHSEALYVLAELHEGVCGNHSGGRSLAHRAH FT SQGYYWPTMKKDAAAYVKKCDKCQRHAPIPHMPSETLKPISGPWPFAQWGM FT DIVGPLPAAPAQKKFLLVATDYFSKWVEAEAYASIKDKDVTKFVWKNIICR FT FGIPQTIIADNGPQFDSIAFRNFCSELNIRNSYSTPRYPQSNGQAEATNKT FT LITALKKRLEQAKGKWVEELPGVLWAYRTTPGRPTGNTPFALAYGMDAVIP FT TEIGLPTIRTEAAKQDDANAELGRNLDWADEVRESAAIRMADYQQRASAHY FT NRKVRPRSFKNGTLVLRKVFENTAETGAGKFQANWEGPYIVSKSSESGAYH FT LQKLDGTPLLRPWNVSNLKQYYQ" XX SQ Sequence 8952 BP; 2580 A; 2463 C; 2050 G; 1851 T; 8 other; ttggcgccgt ctgtgggaaa attttcactt tgattcagtc accagcaaag atggccacac 60 cttcccgaag ccgttcatct ggtaggggag aggaagataa ttctgaatgg cgccaagcca 120 tcgaaagaag acagttggca agcgaacgac aactgaaagc tctcctccag gagacagaaa 180 gattaagaga agaaaacgcg gtattacgca tccaggcttc aacatcaggg cctcctcgtc 240 gtcagcgttc aagaggccaa gtagcaaact caaggcctca acaagaacca gagtcaatat 300 atcctgggac agcaggagct atcccaggag catgcaacgt gaggccacat gagccacaca 360 cgcccatgcc tcgagctccc cgtgaggaaa gctcagactc tactcatttt tcagcaaaaa 420 gacaacgcga tagaaaatct cagttgtcaa attcaatgcg cgcaagacta ggcccacaag 480 agcctgggag accaaggcca ccagtagcca caacctgggc agcacgccct gaccctatgg 540 tcacccccat ggtgcagaac gtgctcccgc accgtgaccc catggtcacc cccatggtgc 600 ggaacgttca ctcgcaccta gcggtacaac aagctgggag aaacctccca aacgagccac 660 ccattggctc catcagcaaa aggctggacg acatgctctc cacgcctttc tgctctcata 720 tcattcatta cgagccccca aggggattcc tcgtaccaaa attttccaca tacgatgggt 780 ccagcgaccc cttcgatcat atcatgcatt atcgacagct catgacgctc gatattggca 840 acgacgcgct gctatgcaaa gtatttcccg ccagcctaca agggcaggcc ctctcatggt 900 ttcatcgcct acctcccaac tctgttggca atttcaggga cctgtccgaa gctttcgtgg 960 gacaatactt gtgctccgct cgacacaagc agaacatcag cactctgcaa aacataaaaa 1020 tgcaagataa cgaatcctta agggagttcg tgaagcggtt tggtcaagcc gtacttcaag 1080 tagaggcttg cagcatggat gctgtcctac agatcttcaa gcgaagcatc tgtccaggca 1140 ctccattttt cgaatcacta gctaaaaagc ctcctacaac gatggacgac ttgttcagac 1200 gtgccaacaa atattcaatg ctcgaagatg acgtacgagc agccacccag caagtcttgg 1260 ttgctggaca ggcatctaga ggtggcgcgg aaagaaatgc caaacctccg gaccggccaa 1320 ggccgtccga tcgaaggcag gaagggccaa gtcgcccgga aaggccgcct ctcacacctc 1380 tttccatatc atatgaaaaa cttctcccta tgatccaagg cttgtccgac ttcaggtggc 1440 ctagacccct cggaacggac ccatccaaaa gagatcatag caagagatgt gccttccaca 1500 aggaacatgg tcacacaaca gagacatgca ggtgcctcca ttatctggtc gaaaggctca 1560 tcaaggcggg acatttaaag caatacctcc gctcagatgc tggaggtaga gacgcttccc 1620 aaaatcacaa ctctgagagc ccccagggcc ccagccgccc ccaaggccgt tataaactat 1680 attaacggag gcccatctga cgaggagtat gactctaagc gaaagagaca aaagttgttg 1740 cgggccgcat cagtacgcga acgtatcaat tccatccggc ctggactaac tggagggggc 1800 cctcgcccca tagatgggac aatcattttc ccaccagtag accccacccg gacactgcag 1860 ccacatcgcg acgccctcat cctgtcccta gagataggag acttcgatgt gagacgcatc 1920 ctggttgacc caggcagctc ggccgatctt gtacaagcat cggtcgttag ccacatggga 1980 cacagtctca caggcctcga aaaccctgga cgaatcctgt ccggattcaa cgggtcatca 2040 actacgtcct tgggagacat tgtactgccg gtccaagctg gcccagtcac tctcaacgta 2100 caattctcgg tggtacaaga gttatcaccc ttcaatgtca tcttggggcg cacatggcta 2160 cactacatga aagtcatccc ctctacatat catcaaatgg tgagtttcct taccaacgat 2220 gggcaaattg acctatatgg cagccagtta gccgctcgcc aatgctacca gatagcacga 2280 gaagcaggga ccagccagga ggatgcatcc ctccctgagc ccagccatgc acgtgaccaa 2340 tagcaattat tgggtccggc ggacaaagat cccccggcag cagatccctt acaaacaatc 2400 caaatttcgg aagaaagtac tcaccttacg aacatcagtt ccctcatgac accagaagag 2460 acccagaaca tgcaaaacgc cctcagacaa aaccatgaca tcttcgcatg ggcacattct 2520 gatatgaagg gaattcatcc ctccattacc tctcataggc ttaacgtctt tccaacagcc 2580 agacccatcc ggcagaagat taggcgtttt cacccggaca gacaaaaaat catccggaat 2640 gagattgaca aattgctaga agccggattc atcagagaag tagattatcc ggactggttg 2700 gcaaacgtag tggtggtacc caaaaaagaa ggaaaatggc gggtgtgcgt cgattacacc 2760 aacctcaata atgcatgtcc aaaagacagt ttccctttgc cacgaataga tcaaattgtg 2820 gattccactg ctgggcaagg gatgctctct ttcttggatg ccttctccgg atatcaccaa 2880 attcccatgt ccccggctga cgaggaaaaa acagcattca taacgccaca cggcctctat 2940 tgctacaaag tcatgccatt cggactcaaa aacgctggcg ccacttatca gagactgatg 3000 acaaagatct tcaaacctct gataggccac acagtagagg tatatattga tgatatcgtg 3060 gttaaaagca aaacccgaga ggagcatgtt cttcacttac aagaagtttt tcacctcttg 3120 aggaagtatg gcatgaagct gaatccttct aaatgcgcct ttggcgtaag tgctggcaaa 3180 tttctgggat ttatggtcag ccaaagaggg atagaggtta gcccggatca agtcaaggca 3240 gtcatggaaa cacctccccc caggagcaag aaggagttac aacgcctcac aggcaagctc 3300 gtcgcgctag ggcgttttat agcccgcttc actgatgaat tgcgaccctt cttcttggca 3360 atacgaaaag ctggagcaaa cggatggacg gacagctgtc aaaacgcttt tgaaaagatt 3420 aaacactgtc ttatgcagcc gcccatcctg agcagcccca tcccaaaaga aaaattgtac 3480 atgtatctgg ctgtatcaga gtgggcaatc agcgctgttc tattccgctg cccctcaccc 3540 aaggagcaga aacctatcta ctacgtcagc agagcattgg cggacgtaga aaccaggtat 3600 tcaaaaatgg agctaacagc cttagccctt cgaagcgctg cccagaagct ccgcccctat 3660 ttccaagccc acccggtggt cgtgctgacc gaccaacccc ttcgcaacat tctgcacaaa 3720 ccagacttaa ccggaagaat gctgcaatgg gctatcgaat tgagcgaatt tggaatcgaa 3780 ttccaaccca gattgtccat gaaaggccaa gtaatggctg acttcgtgct ggaatattcc 3840 cgaaggccta gccaacacca ggaatcaagt gaaaaagaat ggtggacttt gcgagttgat 3900 ggagcctcac gatcatcagg atccggagtc gggcttctgc tacaatcccc aacaggggaa 3960 catctggagc aagccatccg gctgggattc cctgcctcta acaatgaagc agaatatgag 4020 gccatcttat ccggattgga cctcgccctg gctctatccg tctccaagct ccgggtctat 4080 agcgattctc aacttgtggt aagacacgtc cagaaggaat acgaagctaa ggatgcgcgc 4140 atggcgcgat atctaactaa agtaagggac accttacaac gattcaccga gtggacaatc 4200 gaaaaaatca gacgaactga aaatgggcgc gccgacgcct tggcaggcat agctgcctcc 4260 ctccccatca aagaagccat attattgcct atacatgtgc aagccaaccc ttctgtcgca 4320 gaaacctcca cttgcaacac cattgaggca aaccaagcag acggccaaga atggacgaac 4380 aacattatag aatacctccg gacaggcact ctgcccgaag atcccaaaca ggcacacaag 4440 atccgggtgc aagctgcccg tttcaccctg attggggggc acttgtacaa acgatccttc 4500 acaggtccct accttcggtg cctaagtcat tcagaggccc tgtatgtgtt agctgagttg 4560 cacgagggag tatgtggaaa tcattcagga ggacgatctc tggcacatag ggcccattcg 4620 caaggatatt attggcccac aatgaagaag gatgcggcag cctatgtcaa aaaatgtgat 4680 aaatgtcaaa ggcatgctcc cattccacat atgccatcag aaacattgaa accaatctca 4740 ggcccatggc ccttcgcgca gtggggcatg gacatagtgg gacccctccc agccgcacct 4800 gcccagaaga aattcctgct tgtcgccacg gattacttca gtaaatgggt ggaagctgaa 4860 gcatatgcta gcatcaaaga caaagatgtc accaagttcg tatggaaaaa catcatctgc 4920 cgctttggaa tcccccaaac cattatagcc gacaatggtc cacagtttga tagcatcgca 4980 ttccggaatt tctgttcgga actgaacatc cggaattcat actccacacc gcgttatcct 5040 caaagtaatg ggcaagcaga agccacaaac aaaactctaa tcactgcctt aaagaaaagg 5100 ctcgagcaag ccaaaggaaa atgggtggag gagctacccg gcgtcctatg ggcctatcga 5160 accacacccg gacgaccaac aggaaacact cccttcgccc tcgcatacgg tatggacgca 5220 gtcattccta ccgaaatagg gttacccact atccggactg aggcagcaaa gcaggatgat 5280 gcaaacgcgg agttaggaag aaacttggac tgggcagatg aagtaaggga aagcgcagcc 5340 atccggatgg cagactatca acaaagggca tccgctcatt acaatcgcaa agtaaggccc 5400 agaagcttca aaaatggtac gctggtcctt agaaaagttt ttgaaaatac tgctgaaaca 5460 ggagcaggaa aatttcaagc caactgggaa ggaccctata tagtatctaa gtcaagtgaa 5520 agtggagctt atcatctaca aaagctagac ggaactccat tactcagacc atggaatgtg 5580 tccaatttaa agcagtatta tcaataaaag aaagaagaca agtacaaatg tgaaaaaaga 5640 atgttttatt gatatttgtg aagttatgta caaagaggtc tccggactac aaaaagtaca 5700 gaaagaagat agcagcaaaa aattacaaaa agaaaagcta tcagggagca ggcttgtcga 5760 gcagcttctt ctcttcaccc ggaggaattg aagggacatc ccgcttgatg ccatgtttct 5820 tcatacagca gcgatagccg aagaagaaca tgtcatctac ttgcttttgg tagtccgctt 5880 caagctcctc cctctctgca gcaaactcac cctctagctc ttctttttgc gctgataagc 5940 gcagctgcaa atcttctttc tgcttcttct caatwgaaac ctccgtccgg agttgcctca 6000 cctcccccct cagcagggcc atctcatcct ccgcctcatg caggcgggca tccatcgatt 6060 cctcccggct ctttgcctca gctaaatccg cccggagagc ctcgttgtcc tctcgagcgg 6120 tggataaact ggcttcggcc tcctccagtc tcaagcgcag ctgatcttca ctatttttgc 6180 gctgagaggc gaaggccttc atgtaatcag cggtccgcag caggtcagta aatagatcgt 6240 gttgttgggc catgccgcga agaccactca ccagctgcag acaaacacac aaacaagaaa 6300 agcaaagtta caaaccatac cacaaacaca tcagtatgac aaaaaaaatc aagaagtaca 6360 aaacaakata taccgtttcc accacttcga acatttttgc tgaaggcatg gcaatggtcg 6420 agccgggtgg aatctgtttc agcttctctt ccaactccgc gtagctaaaa gggctagcgg 6480 agatgcaagc cgcatcatca acaggattcc cccctgatga ggcattagaa agtgactcct 6540 cctccggatc cggggcccca tcattttcgg ccggctgggt ctctccgggt gaaccctcat 6600 ccgggaccac caccgggacg gctggggtct cagttgccat ctccgcctcg ctcccctccg 6660 gatgatcatc ctggacggac gagcaactga cttcaatggt ttcctggaat cgatcttgaa 6720 gccgcccgat gaggccggac tttaggttgc gcgccgaacg cgacctcctt gaagctggcc 6780 ccttcaccgg tacaagggca agagggcttg gctcgcaaga aggcagactc tggctttctg 6840 cccccatttc ctccattggg gttgccatag gaggcaatgc tgccgcacaa aaggcctcgg 6900 ctgcatccgc atccggatgg ggagagccgg gttgatttat tgacgtagct tcttcagcca 6960 aaagagccaa acggccagcc gccgacattg agggccccga atggttcaga cccgcgagat 7020 gtccggggcc gcttgaaata gagggcggga caggattttc cggctccttt attgttacct 7080 ccttctcata agtaatagga ggaattacaa actccttcgg aggagtgggg agtttcactt 7140 ccttcccctt attgtgaaga accagcttct tctttttygc tggagctcca gcaggaggag 7200 aggatgcggt gcgtttttta ccaggagcct tccgcaaagt tccctctttt tttctcttct 7260 cccgatcatc aaggagtgct cggcgtttct cagcatctgc cttttgcacc tccttgtaga 7320 aagggagatc tttcagaatg taatgctccc caggcactac ctcctttggc agcttcctgg 7380 ggagaatgtt gatgacatac tcctgggact cccggacgac ggccattagg ttccgcgcag 7440 tgagcagcgt ctcataatgc ctctcggcag cggcaatctc aaataacttg ttcagacggg 7500 caaacgacgc cttttctacc cactcaacta cgtggcccct cttgtccgga cctgcattat 7560 cagcaaccaa agatatgaat gccatccgat aaamtcaaca aaaagaacaa caagataaaa 7620 gccggacaaa acccgcaaac tgacttaccc ggaagctcca acgaatggtt tggagaaaat 7680 ggcctctccg gatgctccaa aagacccgcc catgcacccc ggaccaccac atgtcccttc 7740 gctcctccct tcgtcgaatc cggcagctca gtcaccaatt gaagggaggg caggtgagca 7800 gccatgctaa agatgtcatt ttttcccttc ttsagggagt agacaaaaag aacctccagc 7860 agcgagaggt ccaggttgaa cagcatgttt agaatgctgc atcccatcag cacccggact 7920 atgttgggat ggatgaaggc tggtggaatc tgggtgaagt gaaggaattc cttgaacaat 7980 gacgggagag ggaaccggag cccagcgttg aattgctcct tkgagaaggt gatggcatgg 8040 tcttcagctt tctcagtcga cacggcctct ccatccataa attccacaak cacgccattt 8100 gggatgcaga aacgttcgcg gaactccttc acactcaatt tatccacaga tttctcagca 8160 tgagcatcgc cggacgggcc agatgaggta gcttccttgt ttgcagacat tttttagcct 8220 gaggctgaac tgaaatctgc atgcaagaag taccaacagt caaaacacag caatccaaaa 8280 ctcacaaacc ctaaacgaca aamaactctc aagaaaacct cacaccacca gtatacccat 8340 cccaaaaccc ttgactctac cccaaagaaa aaccctcaac ccacagaaaa cacagggggg 8400 caacaaaaac cctcgaaaac attgacaaaa cacccagtcg caagcaactt gcccaaacaa 8460 accagaaaca aaccaacaaa gaccaaagcg caaaaccaaa gagaaaaaca agacaaatgc 8520 acgtaccgag tgtaaacagg gaaaagaggg ttgaaaaccg caaatgcagt caccgtcacg 8580 acgcgaaaat caccggcaga aaagttctag ggcttcactc agaaaaagcg aaggtacaca 8640 gaaggtagaa gaagaaacac tctcagaaaa aaacgcagta ggaaaaaatg caacagaagg 8700 cacagtatgc tatttatagg gcgacagccc ctcggaaaac caaacgctca gctacgccat 8760 cattgaaacg acacgctgcc tgggaatacc cagagacgac ggctcatcat aaatgctttt 8820 ctctctcttg cacccccact cgccacgtgg cccaatgagc gcaaaaagta acctcagttt 8880 caaaaaaacc aattattttt taacccgccc atttttgctc aggcaaaata ggcaagttaa 8940 aaaggggggc at 8952 // ID Copia-52_Mad-LTR repbase; DNA; EDCOT; 218 BP. XX AC ACYM01039178; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-52_Mad-I; KW Copia-52_Mad-LTR; Copia-52_Mad_. XX NM Copia-52_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-218 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1402-1402 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01039178; Positions 233 450. XX SQ Sequence 218 BP; 63 A; 29 C; 39 G; 87 T; 0 other; tggatatatg atggttgtta tatggattaa gttggttaga atccggtgga aataagaagg 60 gtaatattgt aaatctacga aaggtagttt tactataaaa gaaagcttgt aagacatttg 120 agatcacttt tgtatattcc tttctgagat tttaatagaa cgatatcttc atccttcttt 180 cttccttctc tttcatatct ctaagcttgt gttcttca 218 // ID Gypsy12-VV_I repbase; DNA; EDCOT; 9132 BP. XX AC AM431879; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy12-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9132 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-9132 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 704-704 (2007). XX DR Genbank; AM431879; Positions 13161 4030. XX CC Positions [4798-5229] - Integrase core CC 'ATTAG' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(232..3219,3223..4149) FT /product="Gypsy12-VV_I_1p" FT /translation="MPYWIRDQEGRLVRIENPQDTELDICVNIMDPPSEDQ FT NSQQGQGGNPNAYLSMRDRMHPPRMSAPSCILPPLEQLVIRPHIVPLLPTF FT HGMESENSYSHIKEFEEVCNTFREGGASIDLMRLKLFPFTLKDKAKIWLNS FT LRPRSIRNWVDLQAEFLKKNFPTHRTNGLKRQISNFSAKENEKFHECWERY FT MEAINACPHHGFDTWLLVSYFYDGMSSSMKQIIETMCGGDFMSKNPEEAMD FT FLSYVAEVSRGWDEPNSREKGKFPSQQAQNPKAGMYMLSEDVDIKAKVATL FT ARRLEELELKKIHEVQAIFDTQVHVMPCTICQSCDHVVDECPTMPAVREML FT GDQVNVVGQFRPNNSASYGNTYNSSWRNHPNFSWKPRPPPYQPQGQTQVPQ FT QPSSVEQAIVNLSKVMGDFVGEQKAINSQLHQKIENVESSQIKRMEGMQND FT LSQKIDNIQYSISRLTNLNTVIEKGKFPSQPSQNPKGVHEVETQDGESSNL FT REVKAVITLRSGKEVDQPLPNVELDEELRSKRPLIKESKSQEEKSGKKSAS FT KSSIEEEPRIVIKEDMMKKHMPPPFPQALHGKKEIKNSSEILEVLRQVKVN FT IPLLDMIKQVPTYAKFLKDLCTVKRGLQVTKNAFLTEQVSAIIQSKSPVKY FT KDPGCPTISVNIGGTHVEKALLDLGASVNLLPYSVYKQLGLGGLKPTTMTL FT SLADRSVKIPRGVIEDILVQVDKFYYPVDFVVLDTDSTVKEENFVPIILGR FT PFLATSNAIINCRNGVMQLTFGNMTLELNIFHLCKRHLHPEEEEGFEEVCL FT INTLVEEHCDKSLEESLNENLEVLEDGFPEPFDVLAIMSPWRRREEILPLF FT NQEDSQGVTVEDPPKLILKPLPVDLKYAYLEDDEKCLVVVSSTLTSDQEDS FT LLGVLRKCKKAIGWQISDLKGISPLVCTHHIYMEEDAKPVRQPQRRLNPHM FT QEVVRNEVLKLLQAGIIYPISDSLWVSPTQVVPKKSGITVINEKGEEVSTR FT PTSGWRVCIDYRRLNSVTRKDHFPLPFMDQVLERVSGHPFYCFLDGYSGYF FT QIEIDLEDQEKTTFICPFGTFAYRRMPFGLCNAPATFQRCMLSIFSDMVER FT IMEVFMDDITVYGSSYEECLMHLEAVLHRCIEKDLVLNWEKCHFMVQKGIV FT LGHIISKNGIEVDKAKVELIVKLPPPTNVKGIRQFLGHAGFYRRFIKDFSK FT ISKPLCELLVKDAKFVWDEKCQRSFEELKQFLTTAPIVRAPNWKLPFEVMC FT DSSDLAMGAVLGQRENGKPYVIYYASKTLNEAQKNYTTTEKELL" XX SQ Sequence 9132 BP; 2688 A; 1847 C; 1981 G; 2592 T; 24 other; aatggcgccg ttgccgggga tggtgccaca atacagtgat gcaacctttt agaggctact 60 tgtgaatcca tcacaagttt ggtgaattcc tttttcatta acttcatttc ctttcattta 120 attcttgtta ggtttatttt cattttcttc ctaactttaa tttttttttt ctagtttcct 180 tgttgttttt atttatttat ttattattat tacaggaatt gtaacttgtg catgccctat 240 tggattaggg accaagaggg aagattagta aggattgaga atcctcaaga cacagagttg 300 gatatctgtg taaatatcat ggaccctcca tcagaggatc agaattctca acaaggtcaa 360 gggggtaatc ccaatgcata cctatccatg agggatagaa tgcatccccc aaggatgagt 420 gcaccctcat gcatcctgcc cccacttgag cagttggtta taaggcccca tattgtgccc 480 ctcctaccaa ctttccatgg aatggagagt gagaattcat attctcacat caaggagttt 540 gaggaggtgt gtaatacctt tagagaggga ggagcttcaa tagacttgat gagactcaag 600 ctattccctt tcactttgaa ggacaaggca aaaatatggc ttaattcttt aaggccaaga 660 agcataagga attgggttga tcttcaggct gagtttttga aaaaaaattt ccccacccat 720 aggaccaatg ggttgaagag acaaatctca aatttttctg ctaaagaaaa tgagaagttc 780 catgagtgtt gggaaaggta tatggaggcc attaatgctt gtcctcatca tggttttgat 840 acatggctct tagtgagtta tttttatgat ggaatgtctt cttccatgaa gcaaattatt 900 gaaaccatgt gtgggggaga ttttatgagt aagaatcctg aagaagccat ggacttttta 960 agttacgtgg ctgaggtgtc aagaggatgg gatgagccca actcaagaga gaaaggaaag 1020 tttccctctc aacaagccca aaatccaaag gctggaatgt acatgttaag tgaagacgtg 1080 gacataaaag ctaaagtggc aacattagct aggaggttgg aagaacttga gttgaaaaaa 1140 atacatgaag tccaagccat tttcgatacc caagtccatg ttatgccatg caccatttgc 1200 caatcatgtg atcatgtggt agatgaatgt ccaaccatgc cagctgtgag agagatgtta 1260 ggtgatcaag taaatgttgt ggggcaattt aggcccaaca acagtgcatc ttatggaaac 1320 acctataatt caagctggag aaaccaccca aatttttctt ggaaaccaag gccacctcca 1380 taccaaccac aaggccaaac ccaagtacct caacaaccat cttcagtgga gcaagccatt 1440 gtaaacctga gtaaagtcat gggtgacttt gtgggtgaac aaaaggcaat taactcccaa 1500 ttgcatcaaa aaattgaaaa tgttgagagt tctcaaataa agagaatgga ggggatgcaa 1560 aatgatctat ctcagaagat agataatatt cagtactcca tctctaggct taccaaccta 1620 aacacagtga ttgagaaggg aaagttcccy tctcaaccaa gccaaaatcc caagggtgtt 1680 catgaagttg aaacccaaga tggtgagtct tcaaatttga gagaggtcaa agctgtgatc 1740 actttgagaa gtgggaagga ggttgatcaa cccttgccta acgtggagct tgatgaagaa 1800 ctcaggtcaa agagaccctt gattaaagag agcaagagcc aagaagagaa gagtgggaag 1860 aagagtgcat ccaaatcaag catcgaggaa gaaccaagga tagtgattaa ggaggatatg 1920 atgaagaaac atatgcctcc cccttttcct caagctttac atggaaagaa agaaatcaag 1980 aattcatcag aaattcttga agttctgaga caagtgaagg tgaatatacc tttacttgat 2040 atgatcaagc aagtccccac atatgcaaag tttctaaagg acttgtgcac agtcaagaga 2100 ggtttacagg tgacaaagaa tgcattcctc actgagcaag tgagtgctat catccagagt 2160 aagtccccag ttaagtataa agatccggga tgtcccacca tatcagtcaa cattggaggg 2220 acacatgtgg aaaaagcttt attagatttg ggagcaagtg tgaatttgct cccatactct 2280 gtgtataagc aactgggact tggaggattg aagcccacaa ccatgaccct ctccttagct 2340 gataggtcgg tcaaaatccc aaggggagtg atagaggata ttctagttca agtggacaaa 2400 ttctactatc ctgtggattt tgtggtgctt gatactgatt ccactgtcaa ggaagaaaat 2460 tttgtgccaa ttatcctagg gaggcctttc ctagctacct ccaatgctat cattaattgt 2520 aggaatgggg tgatgcagct cacatttgga aacatgacat tggaattaaa catattccac 2580 ctatgtaaga ggcatcttca ccctgaagag gaggaaggat ttgaggaggt gtgcttgatc 2640 aacactttgg ttgaagagca ctgtgacaag agtttagagg agagcttgaa tgaaaacctg 2700 gaagtccttg aagatgggtt ccctgaaccc tttgatgtgc tagccataat gtctccttgg 2760 aggagacggg aagagatctt accactgttc aaccaggaag actcacaagg agttactgtg 2820 gaggaccctc caaagcttat tttaaagcca cttcctgtgg atttgaagta tgcatacttg 2880 gaggatgatg agaaatgtct agtggtagtt tcctcaaccc tcactagtga tcaagaggat 2940 agtcttttag gagtcctcag aaaatgtaag aaagccattg gatggcaaat ttctgatctg 3000 aaagggatta gccctttggt gtgcacccac catatttata tggaggaaga tgcaaaacca 3060 gtgaggcaac cccaaaggag actgaatcct cacatgcaag aagtggtgag gaatgaagtt 3120 ttgaagctac ttcaagctgg gatcatatat cccatttcag acagcttgtg ggtgagtccc 3180 acccaagtag tcccaaagaa atctggaatc actgtgatct agaatgagaa aggggaggaa 3240 gtctctacac gtcctacctc aggatggagg gtgtgtatag actataggag gttgaattca 3300 gtgactagga aggaccattt tccattgcct ttcatggacc aagtccttga gagagtctca 3360 ggacatcctt tctattgttt tctagatggt tattcagggt acttccaaat agaaattgat 3420 ttggaagatc aagaaaagac gaccttcatt tgtccctttg gtacttttgc atataggaga 3480 atgccctttg gactatgtaa tgctcctgca actttccaaa gatgcatgct aagcatcttc 3540 agtgatatgg tggaacgcat catggaagtt ttcatggatg acatcactgt atatggaagt 3600 tcttatgagg agtgtttgat gcatttagaa gctgttctcc atagatgtat tgagaaagac 3660 ctagtgctaa attgggagaa gtgccatttt atggtacaaa aaggaattgt cttaggacat 3720 atcatctcca aaaatggcat tgaggtagat aaggcaaagg tggagctgat tgttaagttg 3780 ccacctccta caaatgttaa aggaattagg caattccttg gacatgccgg gttctatagg 3840 aggttcatta aggatttctc aaaaatctca aaacctctgt gtgagctttt ggtaaaggat 3900 gccaagtttg tgtgggatga gaagtgtcag agaagttttg aggaattgaa acaattcctc 3960 acaactgcac caatagtgag agccccaaat tggaaattac cttttgaggt aatgtgtgat 4020 tcaagtgatc ttgctatggg ggctgttttg gggcaaagag agaatggaaa gccctatgtg 4080 atctattatg caagcaaaac tttgaatgag gctcaaaaga actacacaac tactgagaag 4140 gagttgttgr crgtagtttt tgccttggat aagtttcgtg cttatttggt agggtcctct 4200 atagtggtgt tcactgacca ttctrctttg aagtacttgc taaccaagca ggatgccaag 4260 gcaagattga taagatggat tcttttgctc caagaattca atctccaaat cagrgataaa 4320 aaggggrtag araatgtggt agctgaccac ttgtccagac ttgtgatagc acatgactca 4380 catggtctgc ctatcaatga tgacttccct gaggagtctc tcatgtcagt aratgtagct 4440 ccatggtayt ctcacattgc aaactttttg gttaytggag aagtaccaag tgagtggagt 4500 gctcaagaca agagrcattt cttggctaag atccatgcct attattggga ggaacctttt 4560 cttttcaaat attgtgcaga tcaaattata aggaaatgtg ttcctgagca agagcaatcg 4620 ggaattctyt cccattgcca tgatagtgca tgtggaggtc attttgcctc ccagaaaaca 4680 gctatgaaag tgatccaatc aggcttctgg tggccctctc ttttcaagga tgcccattct 4740 atgtgcaagg gatgtgatcg gtgtcaaagg cttggtaagc taacacgcag aaatatgatg 4800 cccttgaacc ccatcttaat agtggatatc tttgatgtct ggggtataga cttcatggga 4860 ccatttccaa tgtcatttgg acattcctac atcttggtag gagtggatta tatctctaag 4920 tgggtagaag caatcccatg taggagcaat gatcataaag tggtacttaa attcctcaag 4980 gaccacatct ttgcaagatt tggagtgcca aaagccatta taagtgacgg gggaacccac 5040 ttttgcaata aaccttttga gactcttcta gccaagtatg gggttaagca caaggtagct 5100 acaccttatc acccccaaac aagtggccaa gttgagttag ccaaccgaga gatcaagaat 5160 atattgatga aggtggtcaa tgtgaatagg aaggattggt ctcaagctcc tggattcctt 5220 atgggcttat aggaccgctt acaagaccat tctaggaatg tctccctatc gccttgttta 5280 tggcaaagcg tgccatcttc cagtagagat tgagtataaa gcatggtggg caataaaaaa 5340 gctcaacatg gatttgataa gagccgggtt aaagagatgt ttggatttga atgaattaga 5400 ggaaatgagg aatgatgcat acctcaattc aaaaattgca aaagcaagat tgaaaaaatg 5460 gcatgatcag ttggtaaatc agaaaaattt taccaaagga caaaaagttt tgctttatga 5520 ctctaaactt catctctttc caggaaaatt gaaatccagg tggacgggtc ctttcataat 5580 tcatgaagta catcccaatg gagtggtgga agtattcaat cccacaggca atcaaacctt 5640 caaagttaat ggccatcgtc tcaagccatt catagagcct tacagtacag acaaggagga 5700 gatcaacctc cttgaaccac cacaactctg agggaaagca ggatatcatg ggctaaataa 5760 gtccatgaat tttttgttat agttttatag ttatatcatt atttttattt ctttttatta 5820 taatttttcc tcaatcttag tttattttgt cttaattcaa gtcaattttg atgataaatt 5880 tcagaaaaaa atcatgaaag atggggagaa ctcttcaaaa gcaagacagg ggagtaaaac 5940 caagaaaatt tcgcacacct gattccaagg tgcgaaaatt tcgcacaccc caaaaccaag 6000 gtgcgaaatc ctcggtccaa agggagccat tttcgcacac cccaaaacta agtccagaag 6060 ctcaaaggac tcccccacga accagctgag aagcctctgg aatcccgaac agtcacccac 6120 ctccatttcg gccatggcga agaccagagg aggcctttct ggctccccat cctcaccgac 6180 acctcgacca catcgagctg ccatgggagt cgcagcttcg ccacctgttc aggccccggc 6240 cattccccca tctgaggggg aagccccttc tcagcgccga taccccacca ggaggccacc 6300 cacggaccca gtgccaccag ccgatcaagc cacgagctct gtttctcggc caccagcgaa 6360 gagaaccaag ttctcgggtc ctggagagcc atcccacgca cctcagccaa agccacctac 6420 agaggactct cggattcctg tggggattac tcctgagacc gttatcaggc gtcccatgat 6480 atccggacca ccgatagagg gcaacttgga ttgcagagat cgatccttcc attccgagac 6540 ctactttgat ataacggccc tcagacagca gccacagctc agagattcat tccgactact 6600 acagaggtat cacatggagg atcttctcac tcctaggcaa ttctactatc ccagagtagt 6660 tatagatttt tatcaatcta tgactactcg aggcctccgt aatcctaccc tcatccaatt 6720 taccatagat ggacgccagg gtgccattgg agctcgtcac attgytgagg ccctccgtat 6780 accttatgag cctgtgattc aggcagactt cagggagtgg tcctcattct ctcagagtga 6840 catggtccgc attttgtcca gggggacttc tacagcctca gtgttgacta ggagagagct 6900 tccatctrgg atgctcctta ttgatgtgct cctgcgtgcc aaccttttcc cccttcagca 6960 caaagttcag aggcgaggag ctatacttga ggcgttattt aggatttctg agggctattt 7020 yttcggccct catcatttga ttatgacttc tcttcttcat tttgaagaga aagtccatca 7080 gaagaagctt caaarggcag atggcatccc attactattt ycgaggctcc tctgccagat 7140 tttagagcac ctgggctatc ytgaacagcc ycgtcttgag aggcgccgcc attgccgaga 7200 ggacttctct ctygacaaat ggcatcactt ggtagcctac tttgcacccc agggagcccc 7260 agytgtgcct gcacctccag agctacccca agatgagcag atgcctcagg cccagcagga 7320 tgagattctc acagagacca cacctcctgc ccctgcaaca cacccctcag agcatattcc 7380 tgagcctata catcctattt ctcctatcac ttcgggtgct ccaccagtca tgccagctac 7440 cccagcacct cctccttcat ctgagcccac tgtcaccgtt tctcttacgg aattcagagg 7500 cttagagcgt tcattgcgga cactgagcac tgctaaggat tctattatcc accagatggc 7560 cactattcgg gcacaccagg atcagatcat tgctactcag gcccagcata ccacgatcct 7620 tcatcagatt cagcagcatt tgagtatgca gacacctttt gggcatgata ggtctgcacc 7680 atccgagcct ctagtgccag ataaggagag cttaccagct gagcagccca taccagagga 7740 ggagatcaga gcagagccat cacatgacac ccctcatatt tgatattttt atattttact 7800 tgttttttat tttagacttg taaatcccat cttttgcatg tgttataaac tgggattgga 7860 agtattactt gaaatcatac attgtatatt tcttttacaa gtaatatata tatatatata 7920 tatatatata tcctttttta ttatattccc ttttctcatt actyttttgt ccttggaaca 7980 tgtggtttaa ggtactccat acctccttta cactcagact ttgtctcact caggaggtac 8040 cacttcctcc ctttattttt aatcgcttty gaaacattga ggacaatgtt caacttggtt 8100 ggggggagag ttgagaaarg aagttttgtt gttaatacta agttattttg gtattttagt 8160 tgatttttgc ttaaaattta aaatttttaa aaaagttttt tgaatcattc tctatggttg 8220 ttaaagataa tttctcaaaa ataaaatagg ataagtcgag ttttaactta attatttaag 8280 tcttagagtt tgttttatgc tttcaaagtt gataatctat tgaagcctct ttgatttcga 8340 actttcttct tccatttcaa gctttacaca cactatgcac attagatccc gaatatatga 8400 tgtaaaactt tctcaccttc taagcttagg aaaattttga cttggttcat tacttaacct 8460 ctctttaata gtgttgggac acctcataaa gaccaatgag tctttgaaaa aaaaaaaaaa 8520 aaaaaaaaaa aaaaaaaaaa ggaagaaaga agaataagct tctattcttt ccttgaaacc 8580 taagcatgat ccgaaggggt ggcgaaagcc tttaaaaccc gatgccctaa accttgattg 8640 gttgggagtc atcgatcctc tgcttgctac ataggtgaat tggttaagat tagtaagtaa 8700 aaagaattgt gaataagaag gtgcgttcct aacctattaa gagttgatta actttgccaa 8760 tgttcgagaa aagcttaggt tggagggtga ggatagttgt atatactata tccggaagct 8820 aatctcatta acacttagct tattatggaa gagtttgatt tggaaccttg agagtagaga 8880 ttcttttgat acttaattgc ataatctcca ctctttgtac tttttgttta agttttaagc 8940 tttgacaact cctattgcat tttgaatctt catatcttta gttcaccagg tgagatgtgt 9000 ttggatatca gtcatgtctc tcaattattt tttggaatga attgcatgac ctcttttatg 9060 tatattatta cgtttgctta gtttttctct ccttaattgc taagggacta gcaatatgtc 9120 ggttgggggg ag 9132 // ID Copia-4_TC-I repbase; DNA; EDCOT; 4638 BP. XX AC CACC01004329; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-4_TC_; KW Copia-4_TC-LTR; Copia-4_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-4638 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01004329; Positions 17596 12959. XX CC Positions [1768-2301] - Integrase core CC LTRs are 95% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS 499..2658 FT /product="Copia-4_TC-I_1p" FT /translation="MALLQQEKSSISSYYGKLKTVWGELQASNPIPVCTCG FT CTCGAAQKMEDMREQEKVFDFLMGLDDTFSTVRSQILSVDPLPSLGKAYSI FT AAQEEKQRQVVANRVPTIEGAAFLAGQVIGDQAMTSRHAVANNKRSQNRRL FT KEKTEPVRCTHCGKPKHTKEQCFEIIGYPENWNRRPSDRSRSRGGRRVDQS FT SSSSALAATIGDSNSSIPTSGIKAQQQQILQVLAALGVGNTPNLQSASQAA FT NITNQNVGKKERHNDPWVIDSGATDHITKDLGLLTNVKHKPNFPPIQIPNG FT EMVPVQALGHVNLNKQLVLDQVLGIPNFNFNLLSVSKLTKDLNCVLTFWPT FT FCVIQDLPSRRPIGVGRVRDGLYYLEPIREGKALMASNMRHANMWHQRLGH FT LPMNRLSFIGDLSINVKENKFCDACCRARQHRLPFFASTYESSRIFELIHC FT DIWGDYKTPSLSGAFYFLTIVDDYSRATWVYLMKYKSETRDYLLHFYQWVR FT TQFNTQVKIVRSDNGMEFKHNDLLTYYNENGIERQTSCTNTPQQNGRVERK FT HRHLLEVARALRFQAHLPIKFWGECVLTASYLINRMPLSVLKNKTPYEILL FT GISPTYQHLRTFGCLCYGLITNKSRDKFAPRSKPGIFLGYPHGQKGYRIFD FT IEDKKIYTSRDVQFFENIFPSALTKGSNGIDGSPTTHIPASWTSTDPNIQV FT HTSDESFMCSYLNPSDKLVQ" FT CDS 2658..4625 FT /product="Copia-4_TC-I_2p" FT /translation="MIESHGDSGSHVETEPCESYDMARSGELNDIGTLDEI FT GQRHSLSNEECTIDSNGSLGQQIEQPSTTTGTTVIADTSVMTGKRARQIPR FT KLANYDFVLPPSLTSSSSTHTPTPKANSTVYPLSQFISYSRFSRDHNAFLA FT AILSTDEPTNFHQAIKHAHWRDAMAKEISALEENKTWVLSKLPPGKRAIDS FT KWVYKIKYNPDGSVERYKARLVAKGYTQIERVDFHETFASVAKLVTVRSLL FT AVASVQNWELHQLDVNNAFLHGDLNEEVYMKIPQGFTRKGEQRVCKLQKSL FT YGLKQASRNWYKKFTTTLLAIGFYQSDADHLLFLFHRGPAFIAILIYVDDV FT IITGNDSDHIVKLKRYLDKKFCIKDLGKLKYFLGIEVARSPSGIVLSQHKY FT VLDILSECGLMGSKPSSFPIDQQHKLASDTGPFCSNPELYRRLVGRLFYLT FT ITRPAISYVVHLLSQFMHNPRQPHLNAVFRVLRYLKNAPGQGLLLPSNNSL FT SLRAYCDADWAGCPTTRRSTTGYIIFLGSSPISWRSKKQTVVSRSFAEAKY FT RAMATISSEIIWLIRLLRDLQVPCSNPVPLFCDNQAAIHIAANPVFHERTK FT HIEIDCHFVRQHIQSQTLIPRPITSKFQLADIFTKALGRDRFHELLSKLGV FT STLHTPT" XX SQ Sequence 4638 BP; 1419 A; 966 C; 953 G; 1300 T; 0 other; taattttttt taagtcatgg cagagaatga agcaaatcaa gttaatgtgg ccttagtatc 60 atctgcaaac gcatcacaca acattgcaat tgatactaag tccccatact ttttgcattc 120 atcatatcat cctggcttaa cttttgtcac acatcctctt aacgagaatg gtgaaaatta 180 ttttacctag aggcgcagct ttctaaatgc attatgatcc aaaaacaaag caggattcgt 240 agatgggacc ataatcaaac cggatgtcaa ttcccaagat tacgacttat gggtccaatg 300 caatgccatt gcgcttccaa tgcaatgcca ttgcgcttcc aatgcaatgc cattgcgctt 360 tcctggttaa caaatgcgct tgcaaaggag atccaaagta gcacagctca tgcagacaca 420 actcatgagg tttgggcaaa tctgtaggaa agattcacac aaggaatagc tccacgtata 480 tacgaattga ggcgtgcgat ggcactattg caacaagaaa agtcatcaat ttcatcttat 540 tacggtaagc tcaaaactgt ttggggtgaa ttacaagctt ctaatcctat ccctgtatgt 600 acatgtggtt gcacgtgtgg agcagcacag aaaatggagg atatgcgaga acaagagaaa 660 gtatttgatt ttctcatggg attagatgac accttcagca ccgtgaggtc tcagatactt 720 agcgttgacc cattgcctag tttggggaaa gcatactcca tagcagcgca ggaggaaaaa 780 caaagacaag tagtagcaaa tcgagtccca actattgaag gtgctgcgtt tctggcagga 840 caggtgatcg gagatcaagc aatgacgtcg aggcatgctg ttgcaaacaa caagagaagc 900 cagaatcggc gtcttaagga gaaaacagaa ccagtgcgtt gcactcattg cggaaagccc 960 aagcatacaa aagagcaatg ttttgaaatt attggttacc cagaaaattg gaatcgtcgg 1020 ccatcagatc ggagtcgaag ccgaggagga agacgcgtgg atcagagtag cagcagttcg 1080 gctcttgcag ccacaattgg agacagcaat tcctcaatcc caacttcggg aataaaggca 1140 caacaacagc aaattcttca agtgcttgct gcgttgggtg tgggcaatac accaaacctt 1200 caatcggcat cacaggcagc caatatcacc aatcagaatg tgggtaagaa agagagacac 1260 aatgatccat gggtcataga cagtggggcc acagaccaca ttacaaagga tttgggcctt 1320 ctcactaatg tcaagcacaa gcccaatttt cctccaatcc aaatacccaa tggagaaatg 1380 gtccccgtac aagctttagg ccatgttaac ttgaataaac aattggtctt ggaccaagtc 1440 cttggcattc caaattttaa ttttaatttg ttatctgtta gcaaattaac caaggatttg 1500 aattgtgtgc tcacgttctg gcctacattt tgtgttatac aggacttacc ttcgaggagg 1560 ccgattggag tgggtcgggt gcgtgatgga ctctactact tggaaccaat aagagagggc 1620 aaggcactaa tggcaagcaa tatgaggcat gcaaatatgt ggcatcagag actggggcat 1680 ttgccaatga atcgcttatc ttttattggg gatttatcta ttaatgttaa ggaaaataaa 1740 ttttgtgatg cttgttgcag agcacgacaa catcgtttgc cattttttgc cagtacttat 1800 gaatctagtc gaatttttga acttattcat tgtgacattt ggggagatta taaaactccg 1860 tcattatctg gggcttttta ctttctaacc attgttgatg attacagtcg ggccacctgg 1920 gtatatttga tgaagtataa gtcagaaaca cgtgattact tactgcattt ttaccaatgg 1980 gtacgaactc aatttaatac acaggtgaaa attgtgcgtt ccgacaatgg gatggaattc 2040 aaacacaatg atttacttac ctactacaat gagaatggaa ttgaacgcca aacaagctgc 2100 acaaacacac cacaacaaaa tggaagagta gaaagaaagc acagacactt gttagaagtt 2160 gcacgagcgc tacgcttcca agcacatcta cccataaaat tttggggtga atgtgtctta 2220 acagcttcat acttaatcaa cagaatgcca ctttcagttt tgaaaaacaa aaccccatac 2280 gaaatcttgc ttggaatatc accaacctac caacatctca gaacttttgg atgcttgtgt 2340 tatggactca tcaccaacaa gtcacgcgac aaatttgcac ctcgctctaa accaggtatt 2400 ttcttgggct atcctcatgg acaaaaaggg tatcgaatat tcgatattga agataagaaa 2460 atctatactt cacgtgatgt gcaatttttt gagaatattt tccctagtgc attgaccaaa 2520 ggaagcaatg gaattgatgg gtctccaaca acacacatac cggcatcttg gacttcaaca 2580 gatcctaata tccaagttca cacttctgat gaatcattca tgtgttccta tctgaaccca 2640 tctgataaat tagtgcaatg atcgagtcac acggagacag tgggagccat gttgaaactg 2700 agccatgcga gtcatatgat atggctagat ctggcgaatt aaatgatata ggcacgttgg 2760 acgagattgg gcaacgtcat tcattaagca atgaagagtg taccattgat tcaaatgggt 2820 cacttgggca acaaatagag caaccaagta ctactactgg tactactgtt atagcagata 2880 cttcagtgat gacaggaaaa agagctcgtc agattcctcg aaaactagca aattatgatt 2940 ttgtcttgcc tccctctctc acatcgtcct cttcaacgca cactcccaca cccaaggcca 3000 actcaacggt atatcctctt tcacaattca tctcttattc tcgattttca cgtgatcaca 3060 atgctttttt ggcggccatc ctttcaaccg atgagccaac taattttcat caggcaataa 3120 aacatgctca ttggcgggat gctatggcaa aagaaatctc agccttagaa gaaaataaaa 3180 catgggtttt gagtaagtta ccacctggga agcgagcaat cgattctaaa tgggtgtaca 3240 aaattaagta caacccagat ggaagtgtgg aacgatataa ggctcgtctg gttgctaaag 3300 gttatactca aatagaaagg gtagactttc atgaaacttt cgcatcggtg gctaaattgg 3360 tgactgtcag aagcttgctt gcggtagctt cagtacagaa ttgggaatta catcaactgg 3420 atgtcaacaa tgcatttctc catggagacc taaacgagga agtttatatg aagattccac 3480 aaggattcac tcgaaagggg gagcaacgtg tttgtaagtt gcagaaatct ttatatggac 3540 ttaaacaagc ctcgagaaat tggtataaaa aattcactac aaccttgtta gccattggtt 3600 tttatcaatc tgatgcagat catttgcttt tcttgtttca tcgaggacca gctttcattg 3660 ctattctgat atatgtagat gatgtgataa tcacagggaa tgattcagac catattgtca 3720 aactaaagcg ttatttggac aagaagtttt gcatcaaaga tcttggaaaa ttgaaatatt 3780 ttcttggcat agaagttgct cgttctcctt ctggcatagt tttaagccaa cacaagtacg 3840 tattggatat tttgtccgaa tgtggtttaa tgggcagcaa gccttcatcc tttccaatag 3900 accaacaaca caagcttgca tctgacactg ggcctttttg ttctaaccct gagctttatc 3960 gacgacttgt tggacgcctg ttttatctca ctatcacaag gccagctatt agttatgttg 4020 tgcacttatt gagtcaattt atgcacaatc ctcggcaacc acacttaaat gcagtttttc 4080 gtgtgcttcg atatctcaag aatgctccag gtcaaggact cttattacct tccaataatt 4140 cattgtctct tcgggcatat tgtgacgcag attgggcagg atgccctaca acccgccgat 4200 ctactactgg ctacattata tttcttgggt catcaccaat ctcatggcga tcgaagaaac 4260 agacagttgt ttcacgctca tttgcagaag caaagtatag agcaatggcc actatttcta 4320 gcgaaatcat ttggttaata cgattactac gagacctaca agtgccttgt tctaatccag 4380 taccactttt ttgtgataat caagctgcca tccacatagc tgcaaatcca gtttttcatg 4440 aacgtacgaa acacatagaa attgattgtc attttgttcg ccagcatatt cagtctcaaa 4500 ctttgattcc tcgacctatc acttcaaaat ttcagctagc agatattttt actaaggcac 4560 ttgggcgtga ccgttttcat gagttactta gcaagttggg tgtttcaact cttcacactc 4620 caacttgagg gggagtaa 4638 // ID Harbinger-1N1_VV repbase; DNA; EDCOT; 734 BP. XX AC . XX DT 05-FEB-2009 (Rel. 14.03, Created) DT 05-FEB-2009 (Rel. 14.03, Last updated, Version 1) XX DE Harbinger-1N1_VV, non-autonomous DNA transposon - a consensus DE sequence. XX KW Harbinger; DNA transposon; Transposable Element; PIF; TIR; MITE; KW mPifvine-1.1; Harbinger-1N1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-734 RA Benjak A., Boue S., Forneck A. and Casacuberta J.M.; RT "Recent amplification and impact of MITEs on the genome of RT grapevine (Vitis vinifera L.). submitted."; RL Repbase Reports 9(3), 706-706 (2009). XX DR [1] (Consensus) XX CC Harbinger-1N1_VV (mPifvine-1.1 in [1]) is a non-autonomous DNA CC transposon which is a deletion derivate of the autonomous CC Harbinger-1_VV. Individual copies are >90% identical to the CC consensus sequence. TIRs are 20 bp-long (with 1 conserved CC mismatch) and flanked by 3 bp-long TSDs. There are approximately CC 50 highly conserved copies present in the genome which could CC place this family in the group of MITEs. XX SQ Sequence 734 BP; 251 A; 73 C; 80 G; 329 T; 1 other; gagcccgttt ggcagtgatt tttaaaagtg tttctaccct taaaaacact tttaagtgtt 60 tttgggatga aaataaagtg tttggcaaat tttaaaaaac acttttgaaa atctggaaaa 120 acacttgaag tgatttttag agaatcactt gacaggtgtt tttttaaaaa aacacttcaa 180 tttttttgaa atattccaaa aatgcccccc agtgataaat caattagaaa aatctttttt 240 ttttttttag aaattaatag gtggtcatat attgttttac ttttaaaatt atcttttatt 300 caatgttytt tttttttttt tattgattta gatgtttttt gtaaatattt tttaaaattt 360 tagtatagtg ataaaaaaat tattattttt aattagaaaa gtcttttttt tttttagaaa 420 ttaataggta atcatatatt gttttaattt taaaattatc ttttattcaa tgttattttt 480 tttagtgatt tagatgtttt ttcattaata aaaagttttt tttgtttatc ataccatttt 540 ttttaattaa aattgtatgt cctttttggt aatttattaa tattaaaagt gtttttatat 600 ttatacaata tattatcaaa aacactttag aatcattttt tctgattatc ataaaagtgt 660 ttttcacaga aacactatag cagaaaacac ttcaaataaa aacacttcca ctagaatcac 720 taccaaacgg gctc 734 // ID LycEPRV_I repbase; DNA; EDCOT; 7521 BP. XX AC . XX DT 16-MAR-2006 (Rel. 11.03, Created) DT 14-DEC-2010 (Rel. 16.01, Last updated, Version 2) XX DE Endogenous caulimovirus from Lycopersicon esculentum (internal DE portion). XX KW Caulimoviridae; Integrated Virus; Interspersed repeat; KW LycEPRV_LTR; LycEPRV_I. XX NM LycEPRV_I. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-7521 RA Mueller L.A., Giovannoni J.J., van Eck J., Stack S. RA and Tanksley S.D.; RG Tomato Genome Sequencing; RT "Sequencing of Tomato Chromosomes 1, 10 and 11."; RL Unpublished. XX RN [2] RP 1-7521 RA Staginnus C., Gregor W., Mette M.F., Teo C.H., RA Borroto-Fernandez E.G., Machado M.L., Matzke M. RA and Schwarzacher T.; RT "Endogenous pararetroviral sequences in tomato (Solanum RT lycopersicum) and related species."; RL BMC Plant Biology 7, 24-24 (2007). XX DR [2] (Consensus) XX CC LTRs are ~97% identical. No LTRs have been reported previously CC for this retrovirus. XX FH Key Location/Qualifiers FT CDS 1198..2970 FT /product="LycEPRV_I_1p" FT /translation="MNKEEFAVDEKTYENQDGMIIKIVFSNLGRRYKKIGN FT NLYLMLEKETAKLEDSLTAMVRITKENEEIDKSREIEKIKTQAKQEVQNLE FT EIKNTRISELEKELARLKLLYENKQKEKDKELELTNEIKQMEQKLNEDLNK FT DIEVNEIDGNENDQQSEISDISETYTEILEQINKSKKLEINTGDMNRPSTS FT RVKTPDNSPRNSPRRTPPTYYTESYQQSDRNNAIWNSRLNKNWTPKPANEQ FT YNFLDLDCVADINKAILIWIGNMSKQLIDNKIETAKTPRYIERTFVGTTKL FT WIENLPSESLEVLRNDKKMDGSASATNIDILDKYESAIRNEFGGMTTDIRE FT QNREKIINRQLMTKLAICKMCYLEEYTCAFKEYYYKAKYNLDEAKEIRKQY FT YTKLPEPFSTNVIKDWNNEGIIDTLGSRIKFLNQWFIQLCENQKEKLKMEK FT VLNKNLSCCKNKIAPQFGCTTKKQKSKRYKNYRKKKSIYKYKQPRRRYYVK FT NYKIKRPYRPKRKISQCTCYNCGKIGHIAKDCKLPKNPKRKQIAELIIDNE FT KYMQIEYIDYELSENDSIYEVSDIETENEEENINIDNNETDEEI" FT CDS 4224..5537 FT /product="LycEPRV_I_2p" FT /translation="MKIFILAKIIVEGYYNRYYTPMIDTGAEANICKYNCL FT PEDKWEKLKTPMVVTGFNNEGSMIKYKAKNIKIQIWDKILTIEEMYNFEFT FT TKDMLLGMPFLDKYYPHIITKTHWWLTTPCGNKIGAKRVNNKQRKTMEWIK FT GSEKINQEMENINNKQITQLEIIIFVIDKVKLINEQIEQLYSEDPLQGWEK FT HKTKVKIELIDENSIITQKPLKYNFADLEEFKIHINELLENNYIQKSNSKH FT TSPAFIVIKHSEQKRGKSRMVIDYRNLNAKTKTYNYPIPNKILKIRQIQGY FT NYFSKFDCKSGFYHLKLEEESKQLTAFTVPQGFYEWNVLPFGYKNAPGRFQ FT HFMDNCFNQLENCIVYIDDILLYSRTQDEHIRLLEKFIHIVKNAGISLSKR FT KAEIMKSQIEFLGIQIDKNGIKMQTHIVQKIITIDENIDTKKKL" FT CDS 6145..7320 FT /product="LycEPRV_I_3p" FT /translation="MENILKTLTTLCTKVDSMGLRIQKLEEKEESTSQQHD FT SKNVELRRSADGKKPELEGDVGKLDKTHDNVCLNAATASTSTTKGASGIRY FT TNLNMNKIFDKPFIPKNQKDSLFIPPQIHTYSESLNQDKKAYNHITRSYIE FT NLYKIQNYLNSTPRSPTTKNPNTDFITQKLQGYNKLIAQPGTNANLVKTCY FT SYGLLNTVYTQTGDEISTIPELYKAFMNYKRITKGTLFYIKFYSAPAEILF FT DEIKPIIQVIKIGLTRDMIIPEDIGIQQEIQKIEIPEFYANKRVIGIATIL FT NELTNNYLNGNSVWSYYVREQVMIYSNSKETREQDMEEIRQWILSLLKPEQ FT KPTTRALRKGFISEELLTRYCKIIGQKYPDHICSKCQGEDNVIPDVQIE" XX SQ Sequence 7521 BP; 3642 A; 865 C; 1103 G; 1911 T; 0 other; ttggtatcag agctagttaa ttaaataact atggaaaaca aatcaactat gacagatgat 60 ctacaagaac aggtatacca ttttatattt atgagtagct aaattaattt attcctgaaa 120 atctcttgtt aattataatt gtttataatg tttgaataat gttataataa ccatctttag 180 aaagtttgct acagaaatat tcttcaaaca agtattgcca gactatgcca tcctaaggtt 240 gaaaccggta ggcagagaag gccgtttagg ggagtaaaca aagttgaggc gctgttaggg 300 taactaatca aagaagaaaa ctgtagtagt gaccagacta gatgattatt aaatcattat 360 ttttgcataa taagcaagta taatttttta agaggttgaa aggaataaaa ttttagtgaa 420 aaataaaaat aataaaaatg gaaacctacc tattaaacga tgatgttgat tataagatat 480 tattattcta tatactaaaa aatttgaata ttgatataaa aagagaaatt tataataaat 540 tattaacata tgagataata gaaataacaa cccaaggttg gactgagtta accatacaaa 600 gtatacaaaa tgagctttat tatgatatgt atgatttata tgatgattta gatattggag 660 attaaatatg actgaatatt ggctaaagcg atatggtagg aattacaggt taaaaaagat 720 tagatatcca gataaattaa gtaggctttt taaaatatta tataaaaagc catgataaat 780 aaaaataaaa atactaaaat aaaaagaact aagatagata aaaagataag aaaaatatgg 840 aaaaaattaa gatctttata tatagaatat gaactatcac aactagtcaa aacagataat 900 gataggaaaa atcaattgat aaacataatt tcaaaaatag aatataaata tgtctgctat 960 ttgaaaaaac agtatgaaca aagaaatcta taaacaacaa ttaatagaag aaataatgga 1020 aataatggtt gaaaaagaac aagaattaca acatagaaaa agaagactag aagaaaacat 1080 attagcagga gtatgtaata aatcaatact agcacaaaga aaagatatat taacgttaga 1140 attagaatta gattgtcttg aatatgaatt acaacataat ataatacata gatcataatg 1200 aacaaagaag aatttgcagt agacgaaaaa acatatgaaa accaagacgg aatgataata 1260 aaaatagtat tttcaaattt aggaagaaga tacaagaaaa taggaaataa cttatattta 1320 atgctagaaa aagaaacagc aaaattagaa gatagtttaa cagctatggt aagaataaca 1380 aaagaaaatg aagaaataga taaatcaaga gaaatcgaaa aaataaaaac acaagcaaaa 1440 caagaagtac aaaatttaga agaaataaaa aatacaagaa taagtgaatt agaaaaagaa 1500 ttagctaggt taaaattatt atatgaaaat aaacaaaaag aaaaagataa agagctagaa 1560 ttaacaaatg aaataaaaca aatggaacaa aaactaaatg aagatctaaa taaagatatt 1620 gaagtgaatg aaatagatgg aaatgaaaat gaccaacaat cagaaataag tgatataagt 1680 gaaacatata cagaaattct agaacagata aataaatcga aaaaattaga gataaacaca 1740 ggagatatga atagacctag tacgtcaaga gttaaaaccc cagataatag tcccagaaat 1800 agtcctagga gaacaccacc aacttattat acagagagct atcaacaatc agatagaaat 1860 aatgcaatat ggaacagtag attaaataaa aattggacac ctaaaccagc aaatgaacaa 1920 tacaattttt tagatttaga ttgtgtcgca gatataaata aagcaatatt aatatggata 1980 ggaaatatgt ctaaacagtt aatagacaat aaaatagaaa cagcaaaaac accaagatac 2040 atagaaagaa catttgtagg aacaacaaaa ttatggatag aaaatctacc ctcggaaagt 2100 ttagaagtac ttaggaatga taagaaaatg gatggatctg catcagcaac aaatatagat 2160 atactagata aatatgaatc agcaataaga aatgaatttg gaggcatgac tacagatata 2220 agagaacaaa atagagaaaa aataataaat agacaactta tgacaaaatt agctatatgt 2280 aaaatgtgtt acttagaaga atatacttgc gcatttaaag aatattatta caaagctaaa 2340 tacaatttag acgaagcaaa agaaataaga aaacaatatt atacaaaatt accagaacca 2400 tttagtacaa acgtaataaa ggattggaat aatgaaggaa taatagatac tttaggatct 2460 agaataaaat ttttaaatca atggttcata caactatgtg aaaaccaaaa agaaaaatta 2520 aaaatggaaa aagtactaaa taaaaattta tcatgttgca aaaataaaat agcaccacaa 2580 tttggatgca caactaaaaa acaaaaatct aaaagatata aaaattatag aaaaaagaaa 2640 tctatatata aatataaaca accaagacga aggtattatg taaaaaacta taaaataaaa 2700 agaccataca gaccgaaaag aaagatatcc caatgtactt gttataattg tggaaagata 2760 ggacacatag ctaaagattg taaattaccc aaaaatccaa aaagaaaaca gatagcagaa 2820 ttaattatag ataatgaaaa atatatgcaa atagagtaca tagattatga attaagtgaa 2880 aatgatagta tatatgaagt atcagatata gaaactgaga atgaagaaga aaatattaac 2940 atagataata atgaaacaga tgaagaaata taatgtctga aaatgaaata aaaataatat 3000 ctaaggaaga atatcaaaat gaagaatcat cagaacagaa aattatattt gataatacga 3060 tatttgaaca aataaaagga aaagaattag atttaagtgt tgaaaaagta ttagaaatac 3120 ctattttaag aaatttgttt aaaagacaaa aagaagaata ctatgtagtt agccaaaaag 3180 aacatatcat agattgcaaa tacacaagag gaaaaacata tatacctata ataaataaaa 3240 gaatgataaa caaagaaata caagatataa aagctaaatc accaataaaa tatgtacatt 3300 taggaggaac agaaatatta ataaaagcct gctttagaga aggaatagat acacctatag 3360 aaatatattt agcagatgat agaattgtac accctataga aaaaagcgta attagtgcag 3420 taaaaggaaa cttgatatat caaaaattta aatttacaat aagtgctaat tatacagtat 3480 cattaacaga taaaaacata gatagatcat tagttctata ttggaaaatg tctggaatag 3540 aactagcacc aggaagcaaa ttatttacag caagatgtaa aaatttatat atactaacaa 3600 caaagcataa aataacagca aaaaataaaa ttaacaaaat aaaaatagaa aatccttttg 3660 aaaaaataat tactgtaata gacaataatg actatagcta taaagaaatt gatatagaag 3720 aagatttaga gatagtaaaa gaaagattaa gcacttcaag cgtaccaaat acattgacaa 3780 gagtcacctc atcaaggatg agtacatcta aaagaaaata tgaaattcca caaagcctat 3840 tagataaaga agaaataaca ccatatcatt atttcataac aggaataata gaccaaagaa 3900 aatataaaat attaataaat acaggacaag aagaaaatta tataacaaga gagttagtat 3960 tagaagaaga aattataaga acaggacata catgccctgg actacctagt gagatagtaa 4020 acacgaatga agaaacaaca gaaaaagaaa taattatagg aggaatactc ttaataatac 4080 aattcaaaat atgccaagga gatcataata ttacattagg aataaaatgg ttagaaaaag 4140 ttaaaccata caacatagaa aatgaacaat taacaataac ttgtcaaaat aagaaaataa 4200 ttataaaaag gacaaaatga ttaatgaaaa tatttatact tgcaaaaatt atagtagaag 4260 gatattacaa cagatattat acacctatga tagatacagg agcagaagcg aatatatgta 4320 aatataattg cctaccagaa gataaatggg aaaaattaaa aacacctatg gtagtaacgg 4380 gatttaacaa tgaaggaagt atgattaaat acaaagcaaa aaatataaaa atacaaatat 4440 gggataaaat actaacaata gaagaaatgt ataattttga atttactaca aaagatatgt 4500 tattaggaat gccattttta gataaatatt atccacacat aataacaaaa acacattggt 4560 ggcttactac accatgcgga aataagatag gagcaaaaag agtaaataat aaacaacgaa 4620 aaactatgga atggataaaa ggaagtgaaa agataaacca agaaatggaa aatataaata 4680 ataaacaaat aacgcaatta gaaattatta tatttgttat agacaaagtc aaattaatta 4740 atgaacaaat agaacaatta tatagtgaag atccattaca aggatgggaa aaacataaga 4800 caaaagtaaa aattgaatta atagatgaaa atagtataat aacacaaaaa ccattaaaat 4860 ataactttgc tgatctagaa gaatttaaaa tacatataaa tgaattgtta gaaaataatt 4920 acatacaaaa aagcaatagt aaacatacaa gtccagcatt tatagtaata aaacatagtg 4980 aacaaaaaag aggtaaaagt agaatggtca tagattatcg taatctaaat gctaaaacca 5040 aaacatacaa ttatccaata ccaaacaaaa tactaaaaat aagacaaata caaggatata 5100 attatttcag taaatttgac tgcaaatcag gattttacca cctaaaacta gaagaagaat 5160 ctaaacaatt aacagcattc acagtaccgc aaggtttcta tgaatggaat gttttacctt 5220 ttggatataa aaatgcacca ggtagattcc aacattttat ggataactgt tttaaccagc 5280 tagaaaactg tattgtatat atagatgaca tattattata ttctagaaca caagatgaac 5340 atataagatt attggaaaaa tttatacata tagtaaaaaa tgcaggtata agtttgagta 5400 aaagaaaagc agaaattatg aaatcacaaa tagaatttct aggaatacaa atagataaaa 5460 atggaataaa aatgcaaaca catatagtac aaaaaataat tactattgat gaaaatatag 5520 atacaaaaaa gaaattataa tcctttctag gattagtaaa tcaggtaaga gaatatatac 5580 caaaattagc agaacatcta aaaccattac ataaaaaact taaaaaagat gtagaatatc 5640 attttgatga taaagataaa aaacatataa gaaatattaa gaatttatgt aaaaaactac 5700 caaaactata ttttcctgat gaaaataaaa catttactta tattgtcgaa acagattcaa 5760 gtgatcatag ttatggagga gttttaaaat acaaatatga aaaagaaaaa atagaacacc 5820 attgtagata ttattcagga tcttatacag aagcacaaat aaaatgggaa ataaatagaa 5880 aagaattatt cgcattatat aaatgtttat tagcatttga accatatatt gtttacaata 5940 aatttattgt aagaacagat aacacacaag taaaatggtg gataacgaaa aaattagatg 6000 attcagttac aacaaaagaa ataaggagac tagtattaaa catactaaat tttacattta 6060 caattgaggt aataaaaact gacaaaaata tgattgcaga ctatttatca agacagagtt 6120 acacagccag gacaagataa tgttatggaa aacatactca aaaccctaac tacactttgt 6180 acaaaagtgg acagtatggg attgagaatt caaaagctag aagaaaagga agaatctaca 6240 agtcagcagc atgactctaa aaatgtggag ctacgtcgtt cggcagacgg taaaaagcca 6300 gaactagaag gagacgttgg gaaactcgat aaaacccatg acaatgtttg tttaaatgca 6360 gctacagcaa gcacatctac aacaaaagga gctagtggaa taagatatac aaatttaaat 6420 atgaacaaaa tcttcgataa accatttatt ccaaagaacc aaaaagactc attatttata 6480 ccaccgcaaa tacatactta ctcagaaagt ttaaaccaag ataaaaaagc ctacaaccac 6540 ataacccgct catatattga aaacctttat aaaatccaaa attatttaaa ctcaacacct 6600 agatctccaa ctaccaaaaa ccctaacact gattttataa cccaaaagct acaaggatat 6660 aataagttaa tagcacaacc gggcaccaat gcaaatctag taaaaacatg ttatagttat 6720 ggattactta atacagttta tacccaaaca ggagatgaaa tatctaccat accagagcta 6780 tacaaagcct ttatgaacta taaaagaatt actaaaggaa cattgtttta tataaagttt 6840 tattcagcac cagcagagat attatttgat gagataaaac caattataca agttataaaa 6900 attggtttga ccagagatat gataattcca gaagatatcg gaatacaaca agaaatacaa 6960 aagattgaga taccagaatt ctacgccaac aaaagagtta taggaatagc aactatccta 7020 aatgaactaa ctaacaatta tttaaacgga aactcagtat ggagctatta tgtacgagag 7080 caagttatga tatattcaaa ttctaaagaa accagagaac aagatatgga agagatacgc 7140 caatggatac ttagtctact caagccagag caaaaaccaa caacaagagc attaaggaaa 7200 gggtttattt cggaagaatt attgaccaga tattgcaaaa ttattggaca aaaatacccc 7260 gaccatatat gttcaaaatg tcaaggagaa gataatgtca taccagacgt acaaatcgaa 7320 taagtaaaaa aaaaattgta ttttattaaa attctgtgtc ggctgaatat cagccatatg 7380 tagaaagaaa taattttatt tttgtcgtgt tgcgtcggct ataaaaagcc aaattgtata 7440 aaagtcgtaa agtaaatagt ttgtcagcca atcatgtaaa aagtttgtcg gccaattata 7500 taaagtagta atagtaagta t 7521 // ID VLINE6_VV repbase; DNA; EDCOT; 6307 BP. XX AC . XX DT 13-SEP-2007 (Rel. 12.09, Created) DT 13-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE Non-LTR retrotransposon from grapevine. XX KW L1; Non-LTR Retrotransposon; Transposable Element; VLINE6_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6307 RA Obukhanych T. and Jurka J.; RT "VLINE6_VV."; RL Repbase Reports 7(9), 1005-1005 (2007). XX DR [1] (Consensus) XX CC This is a non-LTR retrotransposon from Vitis vinifera. CC Individual copies are ~87% similar to their consensus. XX FH Key Location/Qualifiers FT CDS 640..1587 FT /product="VLINE6_VV_1p" FT /translation="MELDSXKKWGERSWNLRKGVKVMKMGGPFFLLEFEDE FT EEAERVLKRGTRRFKDKVLHLERWSEEAGCLKVGSQTKEVWVRVVGLPLHC FT WSEEMFKRIGDCCGGFVEVDEETKNLSQLQWARILVKNRGNFFPGTLNLVV FT KSFCYAVRLWWEVQPRVSAVEPMKNLRXREGERVREEGDVGSRAGNSGGKG FT KERWRAAEADGAGSVRKNRGEEKGDGDKMXVSADGLAGYSKEEGEVGLSEK FT DGVDGLDSCKCGCEVXQPXNCQSLEHESPEVWVXKQKDINGXRACWEKGQS FT SRGGEWAAHEGPLSVQRIFGPDGQ" FT CDS 2665..6147 FT /product="VLINE6_VV_2p" FT /translation="MFGMGGFKFKGGGGGGGVFWDNRVLQLEEMEVGKYSV FT SCRFKNCEDGFCWIFSGVYGPTVKVEREDFLSELGAIRGLWNEPWCVAGDF FT NMIRFPSERSRGGRLSPTMRRFSEVVEELELRDLPLQGGMFTWSGGLNNRL FT KSRIDRFLISEDWEAHFQGAIQVVLARPVSDHSPILLDGGGMRRGPTPFRF FT ENMWLKEEGFKEVLRKWWEGIQVSGSASFILTEKLKALKPILRSWNKEVFG FT QIDSKKQNAWNLMDFWDKEERVRSLSLEEEEARKEAREMYKKWVLLEEVSW FT RQKSREIWLKEGDRNTRFFHQMANAHRRRNQMNRVKVNGRWFTEESEIKEE FT VSRAFQGLLADPGDWKPSIDGLIFERLEEGDVEGLEKPFSEEEVFGALSGC FT CGEKAPGPDGFSMAFWQFSWDFVKEEVMNFFRQFHETGSFVRSLNATFLVL FT IPKKGGAEDLKDFRPISLVGGLYKWLAKVLANRMKGVLAKVISTSQNAFVE FT GRQIMDAVLIANEAIDSILKSNRGAILCKLDIEKAYDHVDWSFLLAVLEKM FT GFGERWCRWIKWCLSTVRFSVMVNGSPTGFFQSSRGLRQGDPLSPYLFVVV FT MEAFSCLMKRAVAGGFLTPCLVRGRRGEGVQISHLLFADDTLIFCEAKEDQ FT LTYLCWLLMWFEAISGLRVNLEKSELIPVGRVENVEELADEFGYKVGKLPS FT TYLGMPLGAPFKSVAAWDGIEERFRKRLAMWKRQYISKGGRITLIRSTLSN FT LPIYFMSIFQLPRVVRMRLEKIQRDFLWGGGALEQKPHLVRWPIVCVDKRK FT GGLGVKSLGAFNRALLGKWVWRFANERKALWNQVIRRKYGEERGGWRSCET FT REAYGVGLWKAISKMGHLVTPFFGFVVGDGKNVRFWKDKWCGTIPLCEAFP FT SLFALATSKEAWVNEVWTAEGERGGSWTPCFNRPFNDWELEEVERLLCCLD FT GKKVRVDEEDRVRWMESKDGVFSVKSLYRALQPVSLASFPSKIIWNSCVQP FT KLSFFAWEASWGRVLTLDRLQKRGWVLANRCFLCQKCEESIDHLLLHCEKT FT REVWMLLLSFFGVSWVFPLSVKETLLGWRGSFVGKKRKVAWQLGPLCLFWV FT IWKARNSIAFEDCVLSIQRLKVSFVYLLWSETKLWIKDGPSTLIDFIDWVC FT MR" XX SQ Sequence 6307 BP; 1665 A; 786 C; 2119 G; 1708 T; 29 other; ggcaaagttt tgggtagcga ttgaatcgaa gacgtttgaa gtgtctatag aggaagtcaa 60 agggaaacta aaaggtatca ttgtggaaag gagtagaggt ttttcctctt ggatcaggtt 120 tggggtatca agtttgagaa agctactgga aggttttgaa gaatgttgta gggaggaaaa 180 gaaaggaaga ttggttaaag tctgggagga agagggaaga aagttccggt tggagaggcg 240 tgtaaacggg gcaggaagat acgtcttatg ctctgttgtt gatgtagagg ctaaaagatt 300 ctgtttagtc tttcctgaag gaaagggctt gataggagga tgggccattc tagctgagaa 360 actaagggct ttagggatag ttactaaaga ggaagcaaag gtgtagaagc aactcaaatc 420 aattcaaaaa agaaggatgt gacaatagat gatgaggaag aaaggtgcat tggaaagaag 480 gagcagggkg agaaaaagas cttcstagat gtggctaagg aaccggctgg aaggctagga 540 gaagmgttgt ggcttcaggt tggagggaga ggattgagga gtagggagga agttttgggg 600 cggtgcctag ttggtagatg ggaagggtca gtggtggaga tggagttaga ttcgkttaaa 660 aaatgggggg agcgcagctg gaatcttagg aaaggagtga aggtgatgaa gatgggagga 720 cctttcttct tgttggaatt tgaagatgaa gaggaggcag agagagtatt aaagaggggg 780 acgcgtagat ttaaggataa agtgttgcat ttagagagat ggagtgagga ggctgggtgc 840 ttaaaggtag gaagccaaac aaaagaagtt tgggtaaggg tggtgggact cccgcttcac 900 tgttggagtg aagaaatgtt taaaagaatt ggtgaytgtt gtggaggttt tgtggaggtg 960 gatgaagaaa caaagaatct ttctcaactt caatgggcca ggattttggt aaagaatagg 1020 ggaaattttt ttccaggaac tttgaattta gtggtgaagt ccttctgcta tgcagtccgc 1080 ctgtggtggg aggtgcagcc tagagtttct gcagtggagc cgatgaagaa cttgagakgg 1140 agagaggggg aaagggtgag ggaagaaggg gatgtgggct cacgcgcggg gaatagcggt 1200 gggaagggaa aggaaagatg gcgtgcagcw gargctgatg gagcaggttc agtcagaaaa 1260 aatagggggg aagaaaaggg tgatggtgac aagatggsag tttcagctga tgggttggca 1320 ggatatagca aggaggaagg agaggtgggc ttaagtgaaa aagacggtgt ggatgggctt 1380 gatagctgca agtgtgggtg cgaagtgrcc caacccagwa attgtcaaag cctggagcat 1440 gaaagtcctg aggtgtgggt wgwaaaacaa aaggatataa atgggycaag ggcttgttgg 1500 gaaaaggggc agtcaagcag aggtggggag tgggccgctc atgaaggccc tttaagtgtt 1560 caaagaattt ttgggccaga tggacaatag gggtgagaag cgggcttcaa gggtggatat 1620 ccctttmttg caaygggatg ggctgggtct tttggacaat aggcccaaag tggtagagaa 1680 ggatgggcaa gattggccca tcttcttttc aaaaggatgg gctgggccgg ytggaccaca 1740 gacccagagt ggcaggagga gaggggcagc ccatcctagc atcagtttgg gccccgtttg 1800 cttataagtc tccctgggat gagctcgwcg taaaagctag ggcttckttt tgccaastgc 1860 satctgagga rtggttcgca gaagagattc tggtcggcgg gatggggtct gcagcggaga 1920 gagggacacc agagagctgc tcaatagcgg acgagtgctt tttggaggaa gattccaggt 1980 attccctctt aaagccttct actgtttgcg tgtggggggg acgggtctct tcttcttctt 2040 ctcctttctc tggggtggrg ggctctttga ttgagatgga ggagagatgt ggtaatgagg 2100 tcgttctgaa ggaaagcgaa ggggagttaa gtgtcaatcc tctgagagtg tgtccggcgg 2160 aagaaagaat gggagagaag agtgcgagcg ggtctttccc gttaaaagag gggagggagg 2220 aaaggggtga gaaagaggaa gaggatgwgg agtcgtggag gtacagttgt ttggcaaagt 2280 tttgtcattg tttgggaatg cctacagagg gctttgaaag tgagattctg aaacttctca 2340 atagaatgag ggaaagaaga gatcgatctg agagggtaag cggaaaaaag aggaaaggac 2400 agagaccctc gagatttgac cgcgagttga agaaacttga atggtcggtg aattatggtg 2460 ggtcaggagg ggatcggggt catcaagagt gtgttagatg aggcttagaa ttctgtcgtg 2520 gaatgtaagg ggggcaaatg acagagacaa gagaaaattg ataaaggatg tgattaaaac 2580 acagaaggtg gacttagtgt gtctccagga aacaaaaatc caggagatga ctaatggaat 2640 tgtgagaagc ctcggggtag gaagatgttt ggaatggggg gctttaaatt caaggggggc 2700 ggcggggggg gtggtgtgtt ytgggataat agggtgttgc aattggagga gatggaggtg 2760 ggcaaatatt cagtttcttg tcgctttaag aattgtgagg atggtttttg ctggattttt 2820 tcaggagtgt atgggcccac tgtgaaggtg gagagagaag attttttgag tgagctgggg 2880 gccattagag ggttgtggaa tgagccgtgg tgtgtagcag gagacttcaa catgataaga 2940 ttcccttctg agcggagtag aggaggtcgt ctgtccccga caatgaggag attctcagag 3000 gtggttgagg agttagaatt aagggacttg cctcttcagg gggggatgtt cacgtggagt 3060 ggaggtctta ataatcggtt aaagtcgaga attgatcggt tccttatttc tgaagattgg 3120 gaagctcatt ttcagggggc tattcaagtt gttttggcta ggccagtatc tgatcactct 3180 ccgattcttc ttgatggggg agggatgagg agagggccca cgccttttag atttgagaat 3240 atgtggctga aggaggaggg ctttaaagag gtgttgagaa agtggtggga ggggattcaa 3300 gttagtgggt cagccagttt cattttgact gaaaaattga aggctttaaa accgattttg 3360 agaagttgga ataaagaggt ttttggtcag attgattcta agaagcagaa tgcttggaat 3420 ttaatggatt tttgggataa ggaagagagg gttcgctctt tgtctttgga agaagaagaa 3480 gctaggaagg aggcaagaga gatgtataag aagtgggtcc ttttagaaga agtgtcatgg 3540 aggcagaagt ctagggaaat ttggctgaaa gagggggata gaaacacaag gttttttcat 3600 cagatggcta atgctcatag aagaaggaat cagatgaata gagtaaaagt gaatgggagg 3660 tggttcactg aggaaagtga aatcaaagag gaggtgagca gagctttcca agggctgttg 3720 gcagatccgg gtgattggaa gcccagtata gatggtttga tttttgagag gctggaagag 3780 ggggatgtgg aggggctgga gaagcctttc tcggaggagg aggtttttgg ggcgctgtca 3840 ggctgttgcg gagagaaagc gccaggccct gacggtttct caatggcttt ttggcagttt 3900 tcttgggatt ttgttaagga ggaggtaatg aacttcttca gacagttcca tgagactggg 3960 agctttgtaa gaagtttgaa tgcaaccttt ctagtgttga ttcctaagaa agggggggct 4020 gaggacttga aggattttag gccaattagc ttggtgggag ggttgtacaa gtggttagct 4080 aaggtgttgg ctaatagaat gaagggagtg ttagctaagg tgatctcaac gtctcaaaat 4140 gcttttgtgg aggggcggca gattatggat gcagtgctga ttgctaatga ggcaatagac 4200 tccattttga aaagcaatag aggggcgatt ctctgcaaat tagacattga gaaagcctat 4260 gatcatgtgg attggtcrtt tcttttagcg gtgttggaga agatggggtt tggggaaagg 4320 tggtgtaggt ggataaagtg gtgtttatcc actgttaggt tttcagttat ggtgaatgga 4380 agccctacgg gttttttcca gagctcaagg gggttaaggc aaggagaccc cctttcgcct 4440 tacttattcg tagttgtgat ggaggctttt agttgtttga tgaagagagc agttgctgga 4500 ggttttttga cgccttgttt ggttcgggga agaaggggtg aaggggtcca gatctcacat 4560 ttgttgtttg ctgatgatac gttgattttt tgtgaagcaa aggaggatca gttgacgtat 4620 ttgtgctggt tgttaatgtg gtttgaggca atttcagggt taagagtgaa tctggaaaaa 4680 agtgagctga ttccggttgg tagagttgag aatgtggaag agttggctga tgagttcggt 4740 tataaggtgg gaaaattgcc ctccacttac ttaggaatgc cgttgggtgc tccttttaaa 4800 tctgttgctg cttgggatgg aatagaagaa agattcagaa agagattggc tatgtggaaa 4860 cgtcagtaca tttcaaaagg ggggaggatt accttaattc gaagtacytt gtccaatttg 4920 ccgatctatt ttatgtctat tttccagctg cctagggtgg ttagaatgag attggagaag 4980 attcaaaggg attttttgtg gggtggtggg gctcttgagc aaaaaccgca cttagtaagg 5040 tggccgattg tgtgtgtaga caaaagaaaa ggagggttgg gggttaagag tcttggggct 5100 ttcaataggg ctctccttgg caagtgggtt tggcgctttg caaatgaaag aaaggccctt 5160 tggaaccaag tgattagaag gaaatacggg gaggaaagag gagggtggag atcttgtgag 5220 actagggagg cctatggagt tgggttgtgg aaagcaataa gtaagatggg acatctagta 5280 accccttttt ttggctttgt ggtgggtgat ggtaagaatg tgaggttttg gaaagacaag 5340 tggtgtggaa ccatcccttt gtgcgaggct ttcccttctt tatttgcttt agcaacgtcc 5400 aaagaggctt gggtaaatga agtttggaca gccgaggggg aaaggggggg aagttggact 5460 ccttgtttca atagaccttt caatgattgg gagttggaag aagtggaaag gttgctttgt 5520 tgcttggatg ggaagaaggt tagggtggat gaggaggata gggtgaggtg gatggaatca 5580 aaggatgggg ttttttcggt aaaatctttg tatagggctt tgcagccggt gtctcttgct 5640 tctttccctt caaagattat ttggaactct tgtgtgcagc ccaaattaag cttctttgcg 5700 tgggaggctt cgtggggaag agttctaacc ttggatcgtt tgcaaaagag gggttgggtt 5760 ttggcaaata gatgttttct ttgccaaaag tgtgaggagt cgattgacca cctcctcctt 5820 cattgtgaaa aaacaaggga agtgtggatg ttgctccttt ctttttttgg agtttcttgg 5880 gtttttcctc tttcggtaaa ggaaaccctt ttaggatgga ggggctcttt tgtgggaaag 5940 aagaggaagg tggcgtggca attgggaccg ttatgcttgt tttgggttat ttggaaggct 6000 aggaattcaa ttgcttttga ggattgtgtg ctgtccattc aaaggctgaa agtttctttt 6060 gtgtatttac tttggtcgga aaccaaattg tggataaaag atggtccttc gaccttaata 6120 gattttatag attgggtgtg tatgcgttaa gggagagggt tttttgtttt tttgttttgc 6180 cttgtccytt gttgtttggg tccttttgta agggggtgag tttctctata ctgtaattct 6240 gtgggtcgct tctttagcgc ctctttgcaa tacaatctta tacttattga tcaaaaaaaa 6300 aaaaaaa 6307 // ID hAT-3_PTr repbase; DNA; EDCOT; 4533 BP. XX AC . XX DT 17-DEC-2009 (Rel. 15.02, Created) DT 17-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE hAT-type DNA transposon - consensus. XX KW hAT; DNA transposon; Transposable Element; hAT-3_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4533 RA Kojima K. and Jurka J.; RT "DNA transposons from black cottonwood."; RL Repbase Reports 10(2), 113-113 (2010). XX DR [1] (Consensus) XX CC ~85% identical to consensus. XX FH Key Location/Qualifiers FT CDS 1552..3717 FT /product="hAT-3_PTr_1p" FT /translation="MENLQNQNASSTGTTPTSTNAPTSNTNPTSTTAGSTT FT DNKGKQPQVLTSRKRNVDDKKKSQIWDHFTKLDGDPKTPRAECNYCGKDYA FT CHTIVNGTSNMWSHLKVCKKFPFVVDKKQKVLVLEPKKEEGESGDRNVGTL FT KAIGYNYDECRQALAKMVIIDELPFNFVEGKGFRLFSRTMQPRFDIPSRFT FT VMRDCLKLYVEEKERLRTALRGQRLCLTTDTWTSIQNINYMSLTAHWIDNE FT WNLHKRILNFCQVSNHMGETIGQVIENCLLEWGIDKLLTVTVDNASSNNVT FT ISYLKNVMKDWPTNILSNEHLHVRCCAHIVNLIVCDGLKEINVSVVKIRNA FT IRFVRSSPSRQLAFKKCAEKLHIECKKSLCLDVATRWNSTYLMLEAAEKFE FT KVFVRLGESEPRYMSYFLEVDSKGNKKNIGPPSLEDWENARTLVKFLKIFY FT MVTLRFSGSLHVTSNSFFNELIYMHTNLLQLCKSRDNLLSGMAMNMMLKFE FT KYWGCEANQNFLLYVANVLDPRLKLKYVKFCFGELYDYDKAQLLTKKVKDN FT LVSLYEFYLKADEVVDDNRHKQDVNDAIDDVEVDVNTLARFKRHLQEEDSV FT ENRNEVERYLVDGCEDPNDDKLDILGWWKSNASKYKILSKVAQHVLAIPIS FT TVASESAFSTGGRILDQFRSSLSPATVQALICCQNWLHHGPIPTDIRTLMN FT DFETYENLESGNFSYKLTPFIL" XX SQ Sequence 4533 BP; 1380 A; 699 C; 860 G; 1593 T; 1 other; taggggtgtt caaaaaaacc gataaaccga gtaaaccgat aaaaccgaaa aaattaaccg 60 aaaaaaccga accgaaaaat aaaaccgatt aaaccgatta gattatgtag aaaaaacccc 120 ggttcggttc ggttttcggt tttgtagtgc agaaaccggg ttaaccggac cggaccggtt 180 caaaaaaggg tccctaggta taaatagaaa atgttgcgcc gcgcccctct cttctctcca 240 gtctactctc cgctaaccct aaacctttca atttcaattt tcaaacaatc tctcctctca 300 ctactcagag ccacccgccg tccccctcgc ccctcgccct ctccggcctc cgctaaggcc 360 gcccccgtac cagagcaccc gcaacccgtc ccctctcgcc tcttcgcctc tccctctcca 420 ctctccttag actwagaaaa cataaacaca gatcgaccat cgacgtttcc tcagtctcaa 480 ctggaccaaa acagtctgtg tttccatcag accgacgttt cctcagcctc tcaaaaccag 540 tgagttttaa ttttttttct cctttctaat taattaatta attcggttaa ggttattgtt 600 atttttaata cagttaagct tattttttat acgtttcttc ctcagtctcc actggatcaa 660 cacagtcggt gctcgtgttt ccgtcggacc gacgtttcct gtcagcctct caaaaccagt 720 gagttttaat ttttttttct cctttctaat taattcatac agttaagctt attgttattt 780 ttaatcaatt ttgttgggtg atgaattttg gtttaggttt aaatcagaat ttagagctat 840 ttgggtgatt aaagcgaatt ttttttcctt tgtttgaata gaagggattt agcagtttag 900 gatatgatta tttttaatca aaattgttgc ttacttctta caattgtttg cagtttagga 960 ttagagctgt cttgtacatg taatttcaca gtttattttg ctgttttgta aatgtaattt 1020 caatatctgc tactgtaaac ttgtgttgat tctgttgttg tgcctgttgc tgtgttgatt 1080 ctgttgcttt gttggttgat tactaaaaac agatgaattg ttgatttttt tgctgtgttg 1140 gttgatttat aaggtcacac caagtagttt gattaaaatc atgtttataa gcctgtgttg 1200 attgacttga ttctgcaaac tagttttgtt ttgatgggtt tttttattcg gttttgtttt 1260 gtcattctgt aaaatgtatt cattattctg ttttggatga tcttgattgg cattttgtat 1320 tcattaaaat catgttattc ttgtattcat tgttctgtta cttctgtaat tatttttcct 1380 ccattgatag attttctaag cttgttttga cacattttct aagcttgttt tcatgttact 1440 tcttaatatt tgtttcattt taatttttaa acatgatttt aatctttatg tttattaagt 1500 ctgatataaa ttatgcatga ttattaacat gttttcattt ggtaattaca gatggaaaac 1560 cttcaaaatc aaaatgcttc atccactggc actaccccaa catcaaccaa tgccccaact 1620 tcaaacacta acccaacatc aaccactgca ggatccacca cggataataa aggtaaacaa 1680 cctcaagtcc ttacatcaag gaaaagaaat gttgatgata aaaaaaagtc acaaatttgg 1740 gatcacttta caaaacttga tggtgatcct aaaaccccta gagctgaatg taattattgt 1800 ggaaaagatt atgcatgtca tactattgtt aatgggacaa gtaatatgtg gagtcattta 1860 aaagtatgca aaaagtttcc ttttgtggtt gataagaagc aaaaagtttt ggtattagaa 1920 cctaagaaag aggagggtga atcgggagat cgaaatgtgg gaactcttaa ggcaataggt 1980 tataattatg atgaatgtag acaagcacta gcgaaaatgg ttataattga tgagttgcct 2040 tttaattttg tggagggtaa gggatttaga ttattttcta ggaccatgca acctagattt 2100 gacattcctt ctcgtttcac tgttatgaga gattgtttga aactttatgt tgaagagaag 2160 gaaagattaa ggacagctct taggggtcaa cgattgtgct taacaacaga tacatggaca 2220 tcaatccaaa acattaacta tatgtcctta acggctcatt ggattgataa tgagtggaat 2280 ttgcataaaa gaattcttaa tttttgtcaa gtttccaatc atatgggtga gacaattggt 2340 caagttattg agaattgttt gttagagtgg gggattgata aacttttgac tgttacagta 2400 gacaatgcaa gctctaataa tgtgactatt tcatatttaa agaatgtgat gaaagattgg 2460 ccaactaata tattgtcaaa tgagcatttg catgttagat gttgtgcaca cattgtaaac 2520 ctcattgtgt gtgatggctt gaaagagatt aatgtttcag ttgttaagat tcgaaatgca 2580 attaggtttg tgagatcttc accttctagg caacttgcat ttaagaagtg tgcagaaaag 2640 ttgcatatag agtgtaagaa atcattgtgt ttggatgttg caactcgatg gaattcaact 2700 tatcttatgt tagaagctgc tgaaaagttt gaaaaggtgt ttgtgaggtt aggtgaaagt 2760 gaacctaggt atatgagtta ctttttggag gttgattcaa aggggaataa aaaaaacata 2820 gggccaccta gtttggagga ttgggaaaat gctagaactt tggtgaagtt cttaaagatc 2880 ttttacatgg ttacattgag attttctggc tcattgcatg tcacatcaaa ttctttcttc 2940 aatgaattga tttacatgca tacaaacttg ttgcaattgt gtaaaagtag agataatctt 3000 ttaagtggaa tggcgatgaa catgatgtta aagtttgaga agtattgggg ttgtgaagca 3060 aatcagaatt ttttgttgta tgtggctaat gtcttggatc cacgtctcaa gttgaaatat 3120 gtgaaatttt gttttggtga gttgtatgat tatgacaaag cacaattgct aacaaaaaag 3180 gtgaaagata atttggtgag cttgtatgag ttttatttga aagctgatga agtggtggat 3240 gataataggc ataaacaaga tgttaatgat gctattgatg acgtggaggt agatgttaac 3300 actttggctc gattcaaaag gcatttacag gaggaagata gtgtggaaaa tagaaatgag 3360 gttgagaggt atttggttga tggttgtgag gatcctaatg atgataagtt agatattttg 3420 ggttggtgga agagtaatgc ttcgaaatat aagatacttt caaaggttgc acaacatgtt 3480 ctggctattc ctatatccac agtggcttct gaatcagcct ttagcacagg cggtcgtata 3540 ctcgaccaat ttcgaagttc tctatctcca gcaacagttc aagcacttat ttgttgtcaa 3600 aattggttgc atcatggacc aattccaact gatattagaa ccttgatgaa tgattttgaa 3660 acctacgaaa accttgagtc aggtaatttt tcttataaac ttacaccttt tattttatga 3720 tttattaatt aacgcgtttt caatctaaca tgtctaattt tttattttgt agaatttggt 3780 ggaaagttgc atctagcaac ggatgataat tagttcaaaa atcggatgca tttattgaaa 3840 actatggtaa aatactattt tttattttta tatcttctaa tttaatttat catgttataa 3900 ttctagattt tgaatttcag gaatcaaagt gcaatgttct tgatgtgctt tttgattgag 3960 atgatgtgca caatgaagat ttattttttt tggcttggag tgttttatga caatgttatt 4020 tgttgttttt tcttaagccc tttgaaggca atgctttgta atttggattt taacttattg 4080 gtgtgtgtgt tatttaaact tttcgaagca gaaaaatatt aggaagtcaa aaaatatatt 4140 gaacacaaga ttgacattaa taatttatat aaatgaatat tcagtggcaa aaaactataa 4200 acacaagatt gacactaaca atttaataca aatgaatatt tagtggtaaa aaaattaaat 4260 atatttggaa tcttgtaaga aaattagaca atattaacat taattacaag cccatcagaa 4320 atccattaga agcccattaa aaagcccatt aaaagcccaa aaaagcccaa aaaagcatat 4380 aggttttccg gtttttgata aaaaaccgaa ccgaaaccga accgaaaccg gtcggtttgg 4440 accggttccg gttcggtttc gggttttttt ttttttcagt ttggttgttt tttttaggta 4500 aaaaccgaac cgaaccgaaa atgatcaccc cta 4533 // ID Gypsy-74_PTr-LTR repbase; DNA; EDCOT; 988 BP. XX AC . XX DT 22-DEC-2009 (Rel. 15.02, Created) DT 22-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-74_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-988 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 183-183 (2010). XX DR [1] (Consensus) XX CC ~87% identity to consensus. XX SQ Sequence 988 BP; 268 A; 161 C; 216 G; 343 T; 0 other; tgatacgaac caagtcaggt ccgaatttgg ccttaaaata tctgctgacc agttttgcga 60 gatcagacat atctctcaaa ccgtacatcg gaacgagctg aaattttaca gggagatact 120 agacacatgg aactatattt tggtaaattt tcaggtcaaa tggagttcgg gaacatatta 180 ttttagaggg tcgaagttac tagacaaatc ttgtcaaatc tgtcagacta gacctttgtg 240 tactgtttgg gacatatctg gagctacagg tggaattttt ctgtgattca agttggtctg 300 gaaactagac atctcaagct ttccaaccat atatggtagg cccagtaatt catccagacg 360 agagagaacg acgtgtttga agtcaggact gaaaatctgc caagaatatg tgaaaattag 420 agattcgggc tacatggagg aattttagca tgaagacttt gtttttatta tcctattttt 480 atttatttat ttatttaatg ttgaataatt atttttaatt tgggtttgtt ctggcccatt 540 agacattgtt taggggttta tttcattatt ggaacttatg ttagttgatt actagtttag 600 gcccattagc ttgcaaccca aaaggggtcc attagggtta gttagaggag actatattat 660 gtttttttag ctgcaaattt cagcagcaag ttggagaata aacgtgagtt tttcttttgt 720 ttgtttgtgg caaaacaacc tttctttgca gggacaaaga tcgtacactg acttatcgaa 780 gattaactgg cttcgtggcg tcattcacat acttagggtt cttagataca aggttatctc 840 tgggtccaag tctttttcca atacctttgg ttcttaggta cagggttacc tctgggtcaa 900 ggttctatca aacctgattt ttggctttcc aggttgttat ctactttgtt gggggttgct 960 tgaccacgtg atcaagaggt tcgcatca 988 // ID Copia-63_Mad-I repbase; DNA; EDCOT; 5058 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-63_Mad_; KW Copia-63_Mad-LTR; Copia-63_Mad-I. XX NM Copia-63_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5058 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1664-1664 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [2272-2799] - Integrase core CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 484..4152 FT /product="Copia-63_Mad-I_1p" FT /translation="MSDKSVRIESLLGMLTVKLQDDNFVKWNYQFQSVLRG FT YDFFEFFTGESPCPPKFVINTESGVTTEITAAYKSWVQKDMALLSLLIATL FT SDDAMEYVIGCKTSHEAWVNLQDRYASVSRARINQLKIEFHTIQKGSDSID FT KYLLRLKAIRDQLVSAGERITDNDVVITALSGLPSEFDIVKAVVLARETSI FT PLKDFRAQLIGVESAMEARVTTLASGMAAMYVQGDRVTGGHQNSGYSQGES FT SNAGSRTGDTQGYQGNNRFQNRNGYNNSQGSNTSQNYNRSGYGSFNNSRPY FT YNGNRQRWGNNYNSSSTGNRSSWSGNTTFKTGPIVECQICSRRGHTAATCS FT NRSDGYQVLICQICGKKGHHALDCRHRNNYSYQGAPPPPSLTAFSAQAPSH FT MTAAEYGQNVQHFSAADTWVLDTGASHHMTSNLGNLNQPVQYNGDEKITIG FT NGEGLTVNHIGSTTLSTPQHLLFLKNVLHVPTITVNLLSVKKLCEDNHCWF FT ICDESVFFIQDKATGMMLYHGKSRGELYEIPVTVFSRRLVAGQNKAVALLG FT KAVKTSVWHKRLGHPSAEVLDVMLRNVGQPVSVDSSPSVCSSCLSGKMCRQ FT PFPVKETRASSMFEKVHSDIWGPAPVKSLEGFRYYVSFVDEFSRFVWIFPI FT INKSDVFQVFVKFFAFVTTQFNSVIKCLQTDGGSEYMSNRFQSFLALKGTA FT HSISCPYTPQQNGLAERKHRHIVETAITLLTEAEVPLQFWNYACNHAAFLI FT NRMPCKVLGMKSPYQLLFKQDPVLHTLKIFGSAVYPFLRPYTKHKLQPRSK FT QCVFLGFVAGYKGVVCYDLSSTKLVLSRHVVHDETTFPFKPRLQLSSGKFN FT KVQSTTMSPIIVQIPCFAPDPTASPTHAESYANPEIVEDRPMDSLQVPSSS FT SQVSQDLNAHTHSSPTLSTSTPSTISLLPVHSPSQLEVILPISSPVVETNE FT ESAHNMVTRLKSGAISRRSYTGYIGSFPELQTLQMDDECDFTGGFSFIAAI FT KDSEEPSTFRKASTSPHWQSAMQEEFNALKAQGTWQLVPSPPNRTIIGSKW FT VYKVKKNPDGSVSRYKARLVAQGFSQEQGIDYSETFSPVVRHTTVRLILSL FT AAINKWELRQLDIKNAFLHGDLQEEVYMKQPQGFVDQTKPHYVCKLIKSLY FT GLKQAPRAWNSKFTTYLPALGFVASSSDTSLFVKNDDKDVVVLLLYVDDII FT LTGSNASKVQQVI" XX SQ Sequence 5058 BP; 1423 A; 881 C; 1123 G; 1627 T; 4 other; aggttgattt tttttgggat tttcttccgc tgagtaattc ttggagattg atcgttgaag 60 gcsttgttgg agttcttgga ggattggtgc tggcttgctg aattttgggt cgagggtctt 120 tcaatcaggt tgttggtttc tttctttatt ctttgcacat caagtgtttg mgtttttgct 180 tcagtgaaga tatatggcga attgggctgt ttcttgtggt ttttcatata tgggttattt 240 gttggattcg attaaggctg atgccaagat ttgttgacaa tagcagaatt atatttgtgg 300 tgtgatatgg ttgaagttgt tcatttgtga cattgctgaa attttagctt ttgaagtata 360 tacatataga aggccgatgc caagaagtag tgcaaatatc ttgaagaggt gatcattgtt 420 gaagtttgga gttaaacaaa tttgtgattg agattgtttg cttgtcagta atacgtgata 480 aagatgtctg ataaatcagt acgcattgaa agtttgcttg gtatgttaac tgtgaagttg 540 caagatgaca attttgttaa gtggaattat cagtttcagt ctgttttacg agggtatgat 600 ttctttgaat tctttactgg tgagtctcct tgtccaccaa agtttgtgat taacactgag 660 agtggagtga ctacagaaat cacagcagct tataaatctt gggttcagaa agatatggca 720 ctattgagtc tgttaattgc tactttgtcg gatgatgcta tggaatatgt matagggtgt 780 aaaacgtctc atgaagcttg ggtaaactta caagaccggt atgcgtccgt gtcaagggct 840 aggattaatc aactcaaaat tgagtttcat acaattcaaa aaggcagtga ttctattgac 900 aagtatttgc ttcggttgaa agccattcgt gatcagcttg tgtctgcagg ggagaggatt 960 actgataatg atgttgttat tactgcttta tctggattac catcggagtt tgatattgtc 1020 aaggctgtag ttttagcaag ggagacttct attccactga aagatttcag ggcgcagttg 1080 attggtgttg aatctgctat ggaagcaaga gtcactactc tggcaagtgg catggctgca 1140 atgtatgttc aaggagatag agttacaggt ggtcatcaga attccgggta ttcacaagga 1200 gagagttcaa atgctggttc acgaactggt gatactcaag gctatcaagg gaacaacagg 1260 tttcaaaaca gaaatgggta taataattct caggggtcta atacttctca gaactataac 1320 agaagtggtt atgggtcttt caataattca aggccttatt acaatgggaa tagacagaga 1380 tggggaaaca actataatag ttcttctact gggaataggt cttcttggag tggtaatact 1440 accttcaaaa caggtccgat agttgaatgt cagatttgtt ctcgcagagg tcatactgct 1500 gcaacttgtt cgaataggag tgatggttat caggttctaa tctgccaaat ttgtggaaag 1560 aaaggtcatc atgctctgga ttgtagacat aggaataact attcctatca gggggcacct 1620 ccacctcctt ctcttactgc attttctgct caagctccat ctcacatgac tgctgcagaa 1680 tatggtcaga atgttcaaca tttctctgca gctgatacat gggtgttgga cactggtgct 1740 tcacaccata tgacatctaa tcttgggaat ctcaatcaac ctgtgcagta caatggtgat 1800 gagaaaatca ctattggtaa tggggaaggt ttgactgtta atcatattgg ttctacaacc 1860 ctttcaactc cacaacattt actgtttctc aagaatgtct tacatgttcc aaccattact 1920 gttaatctct tatctgttaa gaaattatgt gaagataatc attgctggtt catatgtgat 1980 gagagtgtat tttttataca ggacaaggca acaggaatga tgttgtacca cggcaagagt 2040 aggggagagc tatatgagat tcctgtgact gtgttttcaa gaagattggt tgctggtcaa 2100 aataaagctg ttgcattact tgggaaagct gtaaagactt ctgtttggca taagaggctt 2160 gggcatccat ctgcagaagt gcttgatgtt atgcttagaa atgttggaca gcctgttagt 2220 gtagattcat caccttctgt ttgttcttca tgtctttctg gaaaaatgtg tagacaaccc 2280 tttcctgtca aagaaactag ggctagttct atgtttgaaa aagtacattc tgatatttgg 2340 gggcctgctc cagttaagtc tctagaaggg tttagatact atgtaagttt tgtggatgag 2400 ttctcaagat ttgtatggat cttccctatt atcaataaat ctgatgtttt ccaagtattc 2460 gtcaagtttt ttgcatttgt tacaactcag ttcaattctg taattaagtg cttacagaca 2520 gatggtggtt ctgaatatat gagtaacaga tttcagtctt ttttggcact caaaggaact 2580 gcacattcca tatcatgtcc ttacacacct cagcagaatg gtcttgctga gaggaaacat 2640 aggcacatcg tagagactgc catcacactt ttaaccgagg ctgaagttcc attacagttc 2700 tggaattatg cttgtaatca tgctgcattt ctgatcaaca gaatgccgtg taaggttttg 2760 gggatgaagt ctccatatca gcttctgttt aaacaagacc ctgtgttgca tacattgaag 2820 atatttggat ctgcagttta tccattctta aggccgtata ctaaacataa attgcaacct 2880 aggtcgaagc aatgtgtttt tcttggtttt gtggctggat ataaaggggt agtctgttat 2940 gatttgagta gtactaaact agtattgtca agacatgtgg tgcatgatga gactacattt 3000 ccatttaaac caagactgca gttgtcttct gggaagttca ataaggtcca gagtacaaca 3060 atgtctccaa tcattgttca aataccatgt tttgctcctg atcccacagc ctctccaacc 3120 catgccgagt catatgcaaa tccagaaatt gttgaagacc gaccaatgga tagcttacag 3180 gttccaagct catcaagtca agtttctcag gatctcaatg ctcatactca tagctctcct 3240 actctctcaa catcaactcc aagtacaata tcattgttgc ctgtccatag tccttcccag 3300 ttagaggtaa tactaccaat ctcttctcct gtggttgaaa ctaatgaaga atcagctcac 3360 aatatggtca ccaggttgaa gtcaggtgcc atttcaagaa gatcttacac aggttatatt 3420 ggttcatttc cagaattaca aactctacag atggatgatg agtgtgactt tactgggggg 3480 ttttcattta ttgctgcaat aaaggattcg gaggaaccat caacattccg aaaagcttct 3540 acaagtccac attggcaaag tgcaatgcaa gaagagttta atgcactcaa agctcaagga 3600 acttggcagt tggttccttc tccaccaaac agaaccatta ttggcagtaa gtgggtatat 3660 aaggttaaga agaatcctga tggaagtgta tcgaggtata aagccagact tgtggctcaa 3720 ggtttttccc aagaacaagg cattgactac tcagaaactt ttagtccagt agtacgacac 3780 actactgtga gactcatttt gtccttagca gctataaata aatgggaatt gaggcagtta 3840 gatatcaaaa atgcatttct gcatggtgac ttacaagaag aggtgtatat gaaacagcct 3900 caagggtttg ttgatcaaac taaaccccat tatgtctgta agttgattaa atcgttgtat 3960 gggttgaagc aagcccctcg ggcatggaat tcaaagttca cgacctattt accagctttg 4020 ggatttgtag catcttcatc ggataccagt ttatttgtga agaatgatga caaggatgtg 4080 gtggttcttt tactatatgt ggatgacatc attttgacag gatcaaatgc tagcaaagtt 4140 cagcaagtta ttgawgattt ggcaggtgtt tttgacttaa aggatatggg cagacttact 4200 tacttcctgg gacttcagat tcactacaag gagaatggag acatatttgt gaatcaatca 4260 aagtatgtta aagatcttat tcataaagct ggaatggagt cttgtaaacc tgcaaataca 4320 ccatgcaaac ctcacaatca aatgctattg aatgagggaa taccattgca ggactctaca 4380 ttgtacagaa gtttggttgg ttccctgcaa tatctcacat ttacacgtcc tgatatagct 4440 tatgctgtga attcagtgtg tcaatttatg actgctccga cagatgtaca tctcacttct 4500 gtcaaacgaa ttattcgata tcttcaaggc actgcagagt gtggaattac atatgcagct 4560 gatactgaca tacatttgac agcattttct gatgctgatt gggctgctga tttgaacaca 4620 agacgatctg tgactggtta tgtggtttat cttggtggga atccaatctc ttggcagtca 4680 aagaagcaat cctccgtctc tcgaagttct acagaggcgg aatacaaggc acttgctcat 4740 actgcagcag atgtggctgg attcggctca ttttgaaaga tttgggagtt gcattacctg 4800 ttcaaccaac tatattctgt gataataaat ctgcaatagc actcagtgct aatccggtgt 4860 atcattcgag aatcaaacac cttgatacgg attatcattt tgtccgtgaa agggtgcatc 4920 atggtgatct gttggttgag tatctaccta ctgatgaaca gaccgctgat attcttacta 4980 aaggattaca tagtccgccg ttcactcgtc attgtttcaa tctcaaactt ggtttcccta 5040 gttgagattg agggggga 5058 // ID GYLES1_LTR repbase; DNA; EDCOT; 785 BP. XX AC AF119040; XX DT 02-SEP-2005 (Rel. 10.08, Created) DT 02-SEP-2005 (Rel. 10.08, Last updated, Version 1) XX DE GYLES1: Gypsy-type LTR retrotransposon from tomato (LTR portion). XX KW Gypsy; LTR Retrotransposon; Transposable Element; GYLES1_LTR. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-785 RA Parniske M., Wulff B.B., Bonnema G., Thomas C.M., Jones D.A. RA and Jones J.D.; RT "Homologues of the Cf-9 disease resistance gene (Hcr9s) are RT present at multiple loci on the short arm of tomato chromosome RT 1."; RL Mol Plant Microbe Interact 12(2), 93-102 (1999). XX RN [2] RP 1-785 RA Parniske M. and Jones J.D.; RT "Recombination between diverged clusters of the tomato Cf-9 plant RT disease resistance gene family."; RL Proc Natl Acad Sci U S A 96(10), 5850-5855 (1999). XX DR EMBL/GenBank/DDBJ; AF119040; Positions 13644 12860. XX CC LTRs differ by 2 base substitutions. XX SQ Sequence 785 BP; 229 A; 123 C; 196 G; 237 T; 0 other; tgttagaccc gcaatctact tgatctaact acatgcagac atgccaaaga cttgggcatt 60 ggtcttggca taaatgatgg caaaacagtg caacacaagt tcaaggtgct tgggtgttgg 120 caaggcagct tgaacgtgca tggtttacgt gcgggctaag ggcgttggca agacagcatg 180 ttgacttgat gaagcaaagc tgtgaagact tggcaaggtc aaagacaaag gcagttcacc 240 cgaaattgct gaaataaaac taagtgtgga agacagctaa aatattctaa gtgttggaag 300 ctggcaggat tattctaagt gttggaatga agcctgaaat attctaagtg ttagaatatt 360 agtatttcgt gtagataaga atgtaatttg aattagattc tatctgttgg aaatatagct 420 gttggaaagt tagttttgaa ccctgggctg acatgtgtcg gacaggtgtc atgtgtaacc 480 gccgcatgta accgcttgta actgccattg tgcagaattt tgatttaagg tggaaattcg 540 tctaagggaa gggacagaaa cttttctagc cttagactga tttgtgaagc cttccctttg 600 tattaattat tgattaataa aggttgggac ttagtcctgt aaacgctgcc tgtttattgt 660 ttgacattgc tgtttaagta tttctatact tagtcaattc tgtggatgta agtaggctga 720 agtattacag acgctgtaag actgcctaga gtggtgtgcg agaaaaataa atcgaccctc 780 tttca 785 // ID ALFARE2_LTR repbase; DNA; EDCOT; 1311 BP. XX AC . XX DT 03-JUN-2005 (Rel. 10.05, Created) DT 03-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE Alfalfa LTR sequence from copia-type retrotransposon - consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; LTR sequence; ALFARE2_LTR. XX OS Medicago sativa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1311 RA Gentles A. and Jurka J.; RT "ALFARE2 LTR sequence consensus."; RL Direct Submission to Repbase Update (03-JUN-2005). XX DR [1] (Consensus) XX CC 5 bp TSDs. 78% similar to LTR of autonomous element COPIA_MT. XX SQ Sequence 1311 BP; 402 A; 238 C; 259 G; 410 T; 2 other; tgttggaaca aaatgtgttt aacattaccc tttgagagtt ttgatgataa caaggtatta 60 aaaattgtca attggatatg ctaatatttg ttcaagtgta caggaccata gacaaaaatt 120 tgacatcttt attaggttct ggaagaacaa aagagagcaa aggaatcaac aaaaaggaag 180 cttaaagcat ctgaagagaa gtgctcctga agtcaaagtg ctcctgaagt gatgacgtca 240 tcagaagcaa gttcatcaga agcatctcat cagaagctga agatcaccag aagctgtagt 300 tcatcaggag atgcaagact taaagcttca aaggttgttc aatggattta atctcgtcta 360 agcattgcag aagactggaa gagtgaagca acgactattt tgaaaggatt tgaaggcatt 420 ggatgcttgt tctttgaaga gcgttgacaa agtacaattg tacgaagtgt acaaccacta 480 tctccactac tcagtttgtg tctctgctac aagacaagaa taacagctct gcctgcaaca 540 atgttcctwc atactgggaa tggatttgaa attgatcctt cataggacaa taaccatatc 600 aggcaaaaga tcattggtga ttgatcaaag cttcaaacga ctctattttg atgtgctggc 660 aattcacaac gtctctttca cacctctata taaaggagtg aagacttaga gaatggcaag 720 actcaacaac aatttgaaag cgccaaaact ctgctgaaat tgttctgcat caaaagttca 780 cttagaattt cttatcaaag ttcatatctt agaaattcta gagtcttaag agtctgtatc 840 tgatttgtat tgtgaacacc actgattgta tatcaagtgt tcaacctcaa acatttttct 900 ttgtaattct gtttgaattt agaagtctct tgcagttgtg cttgagcatt agaagtctct 960 tgattgtgtt caggagcata ggaagtctct tgcagttgtg cttgagcatt tgaagtctct 1020 tgctagtttt agcagtgagc ayttgtaatc agatattaca ttttagtgaa ctctccttgg 1080 aagtgcaagg gggacaggac tgacttccgg tttgtggaag gaacctgtat aattgctttg 1140 tgtctttctt ctctctctct ctctctctct gttttatccg ctgcatttag ttctgaacat 1200 cacttcagaa gcagaactct atttgcttct gatcagtgtt ttcagcttag gagaaaacga 1260 agaaaaagct aacacaattc aacccccctt cttgtgtttt tctcaccttc a 1311 // ID Copia-61_VV-I repbase; DNA; EDCOT; 4042 BP. XX AC chr14; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-61_VV_; KW Copia-61_VV-LTR; Copia-61_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4042 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr14; Positions 2120506 2124547. XX CC Positions [1526-2062] - Integrase core CC 'ATATA' target site duplication CC LTRs are 91% similar to each other. XX FH Key Location/Qualifiers FT CDS 47..2626 FT /product="Copia-61_VV-I_1p" FT /translation="MATTNGSMVSVSQPAIPIFKGECYEFWSIKMKTLFKS FT QDLWDLVENGYPYPDEEARLKENTKKNSKALFFIQQAIHESIFSKIAAATT FT AKEAWTTLKTAFQGSSKVITVKLQSLRRDFETLHMKNGESVQDFLSRVAAI FT VNQMRSYGEDILDQTVVAKVLRSLTPKFDHVVAAIEESKDLSTYSFDELMG FT SLQSHEVRLSRTEEKNEEKAFYTKGETSDQKNGGREATGRGRGKGGAHGRG FT GRGRGRGDAQGDQRQSTEKSRNKSNIQCYYCKRFGHVQAECWKKERQEKQA FT NYVEQEEDQVKLFMAYNEEVVSSNNIWFLDSGCSNHMTGIKSLFKELDESH FT KLKVKLGDDRQVQVEGKGTVAVNNGHGNVKLLYNVYFIPSLTQNLLSVGQL FT MVSGYSILFDGATCVIKDKKSDQIIVDVRMAANKLFPLEVSSIEKHALVVK FT ETSESNLWHLRYGHLNVEGLKLLSKKEMVFGLPKIDLVNVCEGCIYGKQSK FT KPFPKGRSRRASSCLEIIHADLCGLMQTASFGGSRYFLLFTDDHSRMSWVY FT FLQSKAETFETFKKFKAFVEKQNGKCIKVLRTDRGGEFLSNDFKVFCEEEG FT LHRELTTPYSPEQNGVAERKNRTVVEMARSMMKAKNLSNHFWAEGVATAVY FT LLNISPTKAVLNRTPYEAWYGRKPWVSHLKVFGSVAYTLIDSHNRSKLDEK FT SVKCIFIGYCSQSKGYKLYNPVSGKIIVSRNVVFDEKASWTWRVSEDGALV FT EISSESEVAQSEDQQPSVQIPASPTLSHSPSSPNLSSSSSSQSLEETPLRK FT FRSLRDIYETTQVLFVADPTTFEEAVEKEEWCSAMKEEIAAIEKNETWNWW FT SFLKTRM" XX SQ Sequence 4042 BP; 1239 A; 642 C; 1034 G; 1127 T; 0 other; atttttggta tcagagcaac caggttcctt ctgaactggg cgaataatgg caacaaccaa 60 cggcagtatg gtgagtgtgt ctcaaccagc aattcccatt ttcaaaggtg agtgctatga 120 gttttggagc atcaaaatga agactttatt caagtctcaa gatctgtggg acttggttga 180 aaatggctat ccttatccgg acgaagaagc taggttgaaa gaaaatacga agaagaactc 240 caaggcattg ttctttattc aacaggctat acatgaatca atcttctcaa agattgcagc 300 agcaaccaca gcaaaagagg cgtggacaac cttgaaaact gcatttcagg gttcctctaa 360 agtgatcacg gtgaagctcc agtccttgcg ccgtgacttt gaaaccttgc acatgaaaaa 420 tggagagtca gtgcaagatt ttttgtcaag agttgctgct atagttaatc aaatgaggtc 480 gtatggtgaa gatattcttg atcaaactgt cgtagcaaag gtgttaagga gtttaacgcc 540 taagtttgat catgtagttg cagccattga ggagtctaag gatctgtcaa cctattcatt 600 tgatgagctc atgggatcct tgcaatctca tgaagtgagg ctgtccagaa cagaggagaa 660 gaatgaagaa aaggcatttt acacgaaggg ggagacatca gatcagaaga atggaggcag 720 agaagctact ggtagaggac gtggcaaagg aggtgctcat ggaagaggtg gtcgtggcag 780 aggccgaggt gatgcacaag gtgaccaaag gcagtcaact gagaagagca gaaacaagag 840 taatatccag tgctactact gcaagcggtt tggacatgtt caagctgaat gttggaagaa 900 agaaaggcaa gaaaaacaag ctaactatgt cgagcaagag gaagatcaag tcaagttgtt 960 catggcctat aatgaagagg tagtatcttc caacaatatt tggtttttgg atagtggatg 1020 ttctaaccac atgacaggga taaagtcact ctttaaggag ctggatgaat cacacaagtt 1080 gaaggtgaaa cttggtgatg acagacaagt gcaagtggaa ggcaagggga ccgtggcagt 1140 aaacaatggt catggtaatg taaagctcct ttacaatgtg tactttattc ctagtttgac 1200 tcaaaacttg ttaagtgtgg ggcaacttat ggttagtgga tactccattt tgtttgatgg 1260 tgctacttgt gtgatcaaag ataaaaagtc tgatcaaata atagttgatg ttcgtatggc 1320 cgcaaacaag ttgtttcctc ttgaagtgtc aagtatagaa aagcatgctc ttgttgttaa 1380 agagactagt gagtctaatc tgtggcactt aaggtatggt catctaaatg tcgaagggtt 1440 gaagttacta agtaaaaagg aaatggtgtt tggactacct aaaattgact tggtgaatgt 1500 gtgtgagggc tgtatttatg ggaaacaaag caagaaacca ttccctaagg gaaggtcaag 1560 gagggcatct agttgtcttg agattataca tgctgatcta tgtggtctta tgcaaactgc 1620 ttcatttggt ggcagtagat attttttgtt gtttacagat gatcatagca ggatgagttg 1680 ggtgtatttt cttcaatcaa aggcagagac ttttgagacc ttcaagaagt tcaaagcatt 1740 tgtagagaag cagaatggca agtgcattaa ggtgttgcgg actgacagag gtggagagtt 1800 cttatcaaat gattttaaag tattttgtga agaggaaggc ttgcatagag agctgactac 1860 tccttattca ccagagcaaa acggtgtggc tgagaggaag aatagaacgg tggttgagat 1920 ggctagaagc atgatgaagg ccaagaacct ttcaaaccat ttttgggcag aaggagttgc 1980 tacagctgta tacttgttga atatttctcc aaccaaggca gtgttgaata gaactccata 2040 tgaagcttgg tatgggagga aaccttgggt aagccattta aaggtttttg gtagtgttgc 2100 ctatacgttg attgactcac ataaccgtag taagcttgat gaaaaatcag taaagtgcat 2160 ctttattggt tattgctctc aatcaaaagg atataagcta tataaccctg ttagtggtaa 2220 gataattgtt agcaggaatg tggtgtttga tgaaaaagct agctggactt ggcgtgtaag 2280 tgaagacggt gctcttgtgg agatttcaag tgaaagtgaa gtggcacaga gtgaagatca 2340 gcagccttct gttcagattc cagcaagtcc aactctctcg cattcaccta gttccccaaa 2400 tttgagtagc agcagttctt cacaatcttt agaggaaacc cctctaagga aattcagatc 2460 tttaagggac atctatgaga ctacacaagt cttgtttgta gctgatccaa caacctttga 2520 agaagcagtg gagaaggaag aatggtgcag tgctatgaaa gaagagatag ctgccattga 2580 gaagaatgag acttggaact ggtggagctt cctgaagaca agaatgtgat aggtgttaaa 2640 tgggttttca gaaccaagta cttagcagat ggtagtatac aaaagcacaa ggcacggtta 2700 gtggcaaagg gctatgcaca gcaacatgga gttgattatg atgacacctt ctcaccagtt 2760 gcacggtttg aaacagtaag gaccttatta gccttagcta ctcatatgca ttggtgtgtt 2820 tatcagtttg atgtcaagtc tgcttttctt aatggagagc tagtagagga ggtgtatgta 2880 tctcagcctg aaggcttcat agttcctggt aaagaagagc acgtgtatag actaaagaag 2940 gccctttatg ggttgaaaca agccccacga gcatggtaca gtaagataga ttcttacttt 3000 gttgagaatg gcttggaaag gagcaagagt gagccaaatc tttacctgaa aaggcaaggt 3060 aaaaatgatc ttcttattat ttgtctttat gtagatgaca tgatctatat gggttcatcc 3120 tcttttctta ttaatgagtt taaagcctgt atgaagaaga agtttgagat gtcagaccta 3180 gggctgttgc attctttctt ggtttagagg taaaacaagt agaggatgga gtctttgttt 3240 cacaaagaaa gtatgctgtt gatttgctta agaagttcaa tatgttaaat tgcaaagtag 3300 tagctactcc tatgaattca aatgagaagt tgcaggctga agatggcact gaaagagctg 3360 atgctaggag gtttagaagt ctggttggag gcctcattta tctgacacat acacagccag 3420 atatagcttt tgcagttggg gtgatctcca gatttatgca ttgtccttcg aagcaacatc 3480 ttggagctgc aaagagattg ttgcgataca ttgctggaac atatgatttc gggatatggt 3540 atggtcatgt tcaagagttc aaattggttg gctacactga tagtgattgg gcagggtgct 3600 tagaggatag aaaaagcact tcaggctata tgttttctct tgggtcaggt gcagtctgtt 3660 ggagttcaaa gaagcaagca gtgacagcct tgtccttttc tgaagctgag tatacagctg 3720 caacctcatc cgcatgccag gcagtgtggt tgaggcgaat tcttgctgat attaatcaag 3780 aacatgagga gccaactgta atttactgtg acaacaaagc tgccatagca atgaccaaga 3840 atccagccta ccatggaagg acaaaacatg ttgatattcg ggttcatttc ataagagatc 3900 ttgtggttga aggtaaagtt gttttgcagt attgtaacac aaatgagcag gtagcggatg 3960 tgctgacaaa agctttatct agagacaagc atgtctactt cagaagcaag cttggagttt 4020 gcaactttga atcaaggggg ag 4042 // ID M2_VM repbase; DNA; EDCOT; 757 BP. XX AC AJ391759; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-JUL-2004 (Rel. 9.06, Last updated, Version 2) XX DE Vicia melanops retrovirus-like DNA sequence fragment, M2_VM. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-like repetitive sequence; M2_VM. XX OS Vicia melanops OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Vicia. XX RN [1] RP 1-757 RA Nouzova M., Neumann P., Navratilova A., Galbraith D. RA and Macas J.; RT "Microarray-based survey of repetitive genomic sequences in Vicia RT spp."; RL Plant Mol. Biol 45(2), 229-244 (2001). XX RN [2] RP 757-1 RA Jurka J.; RT "Gypsy-like retrovirus fragment (classification)."; RL Direct Submission to Repbase Update (JUN-2004). XX DR Genbank; AJ391759; Positions 1 757. XX SQ Sequence 757 BP; 233 A; 156 C; 166 G; 202 T; 0 other; tcgatgcagg tttcctcgtc acttccgaat accgtcagtg gttagccaac atagtgcctg 60 ttccaaagaa agatggaaag gtccgaatgt gtgttgacta ccatgactta aacaaagcga 120 gtccaaagga ttattttccc ttaccgcata ttgacacctt ggttgataac accgctaagt 180 tcaatgtttt ctccttcatg gatggtttct ccggttataa tcagattaag atggctcccg 240 aagacatgga gaaaacatct ttcatcacac cgtggggcac cttttgctac aaagtaatgt 300 cgtttggatt aaagaacgca agcgcgactt atcaaagagc gatgactact ctctttcatg 360 acatgatgca taaagagatt gaagtgtatg tggacgacat gatagccaag tccagcacag 420 aagaggaaca tgttgaatac cttttgaagt tatttcaacg actaaggata tatcaacttc 480 gcttgaatcc taacaagtgc acttttgggg tgagatcagg aaaactccta ggattcattg 540 tcagccaaag aggttttgaa gtagaccctg acaaagtcaa ggctattcaa gaaatgcctg 600 caccaaaaac agaaaagcaa gtgaggggtt ttcttggacg attgaactac atctccagat 660 tcatctctca aatgactgct acttgtgggc cgatcttcaa acttctccga aagaatcaag 720 gggttgtatg gacagaagat tgccagaaag cgttcga 757 // ID Gypsy4-PTR_I repbase; DNA; EDCOT; 4692 BP. XX AC LG_III; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy4-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4692 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4692 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 332-332 (2007). XX DR Genome; LG_III; Positions 17542958 17538267. XX CC Positions [3568-4050] - Integrase core CC 'AGTGT' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 41..2980 FT /product="Gypsy4-PTR_I_2p" FT /translation="MPKTRSGHSYNIMDQGSNIPSSSNPNPNTDTFQASSS FT FQQQLDQFSQTLNVMMHRLDVIDERSNREVGRPPREARRVQRRREGVGDDE FT DEIEEVQMGGVRHRAIHGQPRDTDVQRNVWDELARRMKVEVADFYGKLNPE FT AFFDWITSLEDYFDWFSVPGERKVQFVKLKLKGPARAWWSSVEERLRRTRQ FT APMVEWEDMKARLEAKYLPINYEQLIYEDMLQWNQNNRTTVDQYTERFHEL FT TVRSKTNETESQVLARYLKGLKPDIRKDMLTARLYNVEEAYQLALQFERQT FT SNNTRRFYSADSGNFRFPVPTSAKPTVESTRGNVNGDFKGKEKAFGEGPQC FT YKCKGRGHFAVVCPTRDQRVAYICEKDLVFDDAEINHEEDHIQEETDSKEE FT RLQATDLPICVIQHVLTGHKTKEDVDHDWRRTNIFHTRVAYGDKALNVIID FT NGSSMNVVAKEIVERLGLSQETHPTPYQVRWINDNNSILVQSRCLVKFSFG FT KKYEDQVWCDVLPMTVCHLLLGRPWMYDRRVNYDGLENTYSFKMHDRKVVL FT EPLHISAFEGPKKSNLMLTMRQVKEAMQDGNILLFLVGRESKQLDGKVPES FT VKFLLQEFEDLMPEDLPQQLPPLRDIQHAIDFVPGSSLPNLPHYRMSPTEH FT AELQRQVQELLTKGFIRESLSPCAVPALLTPKKDGSWRMCIDSRAVNKITV FT KYRFPIPRLDDMLDQLGGAVIFSKIDLRSGYHQIRVKPGDEWKTAFKTKEG FT LYEWLVMPFGLTNAPSTFMRVMTQALRPFLGKFVVVYFDDILIFSKSVTVH FT LEHLRQVLETLRTEHLYINKGKCSFLEQKTNFLGFIVSHKGVEADSSKVQA FT IREWPEPQSFFDIRSFLGLATFYRRFVPGFSTITAPITECLKSKIFKWTPA FT AAKAFDEIKQKMSSAPVLKLPDFSKVFEIACDASNVGIGGVLSQEGHPIAF FT LAKNSTSLGANTQPMKWSFMLWFRL" FT CDS 3226..4692 FT /product="Gypsy4-PTR_I_1p" FT /translation="MKDDYASDKHFKDIWAALQSNTSTKTDFSVSGGYLTK FT NGRICVPGGSIRDFIIMELHGGGLAGHFGFDKTYLLVADRFFWPHMRRDVH FT TIISRCRICQVNKGTKQNTGLYTPLPIPHHPWVDISMDFVLGLPRTQRHND FT SVMVVVDRFSKMAHFVPCHKTYDASNVASLFLKEVVRLHGLPTTIVSDRDV FT KFISYFWKTLWAKLGTKLAFSSAFHPQTDGQTEVVNRSLGNLLRCLIDDHA FT TSWDLILPQAEFAYNNSVNRTTGSSPFQLVYGMTPRTPLDIISLPLPQRTS FT EAGLDFAAHMMSVHEEVRKKIALQTEVYAQRANLRKRDKQFEVGDQVLIRL FT RSERFPPGSYNKLHARRAGPFTVLKKLGPNAYVIDLPPTYAISPVFNIEDL FT TAFNGQNDFPSPLDDIPIRVPSTPSPSDGILAVLDHQFVSTRRGGYYKFLV FT QWAHKPLSDSVWLQGDEVHRLAPEVYRDYIQQYLPEASSLGGRQ" XX SQ Sequence 4692 BP; 1357 A; 1015 C; 1042 G; 1278 T; 0 other; aattggtatc agagccggtt ttgattttca aaacttcctt atgccaaaaa ccagaagtgg 60 tcattcatat aacatcatgg atcaaggttc caacattccc agctcttcaa atccaaaccc 120 aaacaccgat acttttcaag cctcatcaag ttttcaacaa caacttgatc aattttctca 180 aactttgaac gtgatgatgc atcgtttgga cgtaattgac gaacgcagca atagagaagt 240 ggggcgacca cctagggaag ccagacgtgt acaaagaaga cgagaagggg ttggggacga 300 cgaagatgaa attgaggaag tgcagatggg cggggtgaga cacagggcta tacatggaca 360 accacgcgat acagatgttc aaagaaacgt ctgggatgaa ttagccagac gcatgaaggt 420 ggaagtagca gacttctatg gcaaactcaa tccggaggca ttttttgatt ggattacttc 480 acttgaagac tatttcgact ggttctcagt acctggagaa cgcaaggttc agtttgtcaa 540 attaaagctt aaaggaccag cccgtgcttg gtggagcagt gtggaagaga gacttaggcg 600 aacccgtcag gcccctatgg tagagtggga agatatgaag gcacggttag aagcaaaata 660 cttacccata aactatgaac aactcatcta tgaagacatg ctccaatgga atcaaaataa 720 cagaactacg gtggaccagt atacagagcg atttcatgaa ctaacagtga ggagcaagac 780 caacgaaacc gagtctcaag tattagctcg gtatttgaag ggattgaaac ctgatattcg 840 caaagacatg ttgacggccc gactgtataa tgttgaggaa gcttaccagc tagctttaca 900 atttgagaga cagacctcga ataacacacg tcgtttttat tctgctgact ctggtaattt 960 tcgtttccca gtccctacca gtgcaaaacc aacagtcgaa tcaacaagag gaaatgtgaa 1020 tggtgatttt aaaggaaaag aaaaggcttt cggagaggga ccccaatgtt acaaatgcaa 1080 aggacgtgga cactttgcgg tggtatgtcc cactcgagat cagagagtgg cttatatatg 1140 tgagaaggac ctagtgtttg atgatgctga aattaaccat gaagaagacc atatccaaga 1200 agaaactgat tccaaggaag aacgattaca agccactgat ctacccattt gtgtgattca 1260 acatgttttg acagggcata aaaccaaaga ggatgtggac catgactgga ggagaaccaa 1320 tatcttccac acaagggttg catacggaga caaagctctg aatgttatca tcgacaatgg 1380 tagtagcatg aatgttgtgg ccaaggaaat agttgagcgt cttggtcttt cccaagagac 1440 acatcccacg ccatatcagg tgcgttggat taatgataac aattcaattt tggttcaaag 1500 tcgctgtctt gtgaaatttt catttggcaa gaagtacgaa gaccaagttt ggtgtgatgt 1560 attgccaatg accgtatgtc atctgttatt ggggaggcca tggatgtatg ataggcgtgt 1620 caattatgat ggtctggaga atacctattc gttcaagatg catgatcgaa aagtggtatt 1680 ggaaccactc cacatctctg cgtttgaagg tcctaagaaa tccaacctga tgctgactat 1740 gcgacaagtc aaagaagcca tgcaggatgg gaacattctt cttttcttag taggacgcga 1800 atccaaacag ctagatggta aagtccctga aagtgttaaa ttccttctcc aagaatttga 1860 agacttaatg ccagaagacc ttccccaaca gttaccacca ttacgagaca ttcaacatgc 1920 catcgatttt gttccaggtt cgtctctacc caatttacct cattatagaa tgagcccaac 1980 tgagcatgct gaactccaaa gacaggtaca agaattattg actaaaggat tcatccgtga 2040 aagtttgagc ccctgcgctg tacctgcatt actcacccca aaaaaagatg gtagctggcg 2100 aatgtgtatc gacagccgag cggtgaacaa aatcacagtg aaataccggt ttccaattcc 2160 acgcttggat gacatgttgg accaattggg tggtgccgtg atcttcagta agattgattt 2220 gcggagtgga taccaccaaa tccgagtaaa gcctggggat gaatggaaaa ctgctttcaa 2280 gacaaaagaa gggctatatg aatggttagt tatgccattc ggcctcacca atgctccaag 2340 cacgtttatg cgtgtcatga cacaagcact tcgacctttc cttggaaaat ttgttgtagt 2400 atattttgat gatatactca tttttagcaa gtctgttaca gtacatttgg aacacctacg 2460 ccaggttttg gagacgctaa gaacagaaca tctctacatc aacaagggta aatgctcctt 2520 ccttgaacaa aagaccaatt ttttagggtt cattgtatca cacaaaggcg ttgaagctga 2580 ctcctcaaag gtccaagcaa tccgtgaatg gcctgaacct caatcttttt ttgatatacg 2640 cagcttcttg ggtttggcaa cattttatcg caggtttgtc ccagggttta gcaccatcac 2700 agcccctatc accgaatgcc taaagtccaa gatcttcaag tggacgcccg cagctgccaa 2760 ggcatttgat gagataaaac aaaagatgtc ttctgccccg gttttgaagc ttcctgactt 2820 ttcaaaggta tttgagattg cttgtgatgc ctctaatgtt ggtatcggtg gagtattgag 2880 ccaagaagga catcctattg cttttttagc gaaaaactca acgagtctcg gcgcaaatac 2940 tcagcctatg aagtggagtt ttatgctttg gttcagactt tgaaacattg gcgcctttac 3000 ttggtacatc gtgaattcat tttatttact gaccatgact ctttgagaca cctcaactct 3060 caaaacaggt taaatgccaa acatgcaaga tggttcgact accttcagca atttaacttc 3120 actatttgac acactgctgg ccgtgagaat aaggtggcag acgccctcag tcgacgacca 3180 cataacctga ctacatttac tgttaatgct gccagtttcg aagccatgaa ggatgactat 3240 gcatcagaca agcatttcaa ggatatctgg gcagcactac agtccaacac atctaccaaa 3300 accgactttt ccgtatcagg tggatacctc acaaaaaatg gtcgaatttg tgttccagga 3360 ggttcaatac gtgatttcat cattatggaa ttgcatggag ggggattagc tggccatttc 3420 gggtttgata aaacatacct attggtggct gaccgttttt tttggccaca tatgcgacgt 3480 gatgtgcaca cgataatctc caggtgtcga atctgccaag ttaacaaagg tacaaaacaa 3540 aacactggtc tctacactcc tttgccaatt cctcatcacc cttgggttga tatcagcatg 3600 gattttgttc ttggcctacc ccgtactcaa cgtcacaacg actctgtaat ggtggtggta 3660 gatcgtttct ctaaaatggc tcattttgtt ccatgtcata aaacatatga tgcctctaat 3720 gttgcttccc tatttttaaa agaagttgtg aggttgcacg gcctccctac tactattgtc 3780 tcagatcgcg atgtgaagtt catcagttat ttctggaaaa cattgtgggc gaaattaggc 3840 actaaactgg ctttctctag cgcattccac ccacagactg acgggcagac tgaggttgtc 3900 aaccgcagtt taggaaattt gttgcgctgt ctaattgatg atcatgcaac cagttgggat 3960 ctgattctcc cgcaagctga atttgcctac aataattcgg tcaatcgcac cacgggtagc 4020 tctccattcc agcttgttta tggtatgact ccgcgaacac ctttggatat tatctcgtta 4080 cccttaccac aaaggacgag cgaagcaggg ttagattttg ctgctcacat gatgtccgtc 4140 catgaggaag ttcgtaaaaa aattgccctg cagacagaag tttatgctca acgtgccaat 4200 ttacggaaac gagataaaca attcgaggtc ggtgatcaag tgctgattcg attacgttca 4260 gaacgttttc ctcctggcag ctacaacaaa ctccatgctc gtcgtgcagg acccttcacc 4320 gttctgaaaa agctgggacc taatgcctat gttattgact tacctcctac ttatgctatt 4380 agtccggttt tcaatattga agatttgact gcattcaacg gtcaaaatga ctttccatcc 4440 cctttggacg acatcccaat ccgtgttcca tcgactcctt ctccatctga tggtatcctt 4500 gctgtgttag accatcagtt tgtctctact cgtaggggtg gttattataa atttttggtt 4560 cagtgggcac acaagcctct ttcggattct gtttggctcc aaggagatga agtacaccgt 4620 ctcgctcctg aagtgtatcg cgactatatc cagcaatact tgccggaggc aagttctttg 4680 ggagggcggc aa 4692 // ID Copia47-PTR_I repbase; DNA; EDCOT; 4250 BP. XX AC LG_XVIII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia47-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4250 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4250 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 272-272 (2007). XX DR Genome; LG_XVIII; Positions 10478572 10474323. XX CC Positions [1701-2081] - Integrase core CC 'GTGCA' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 417..2165 FT /product="Copia47-PTR_I_2p" FT /translation="MSWILGSVDPLIILNLRPYKTARTMWEYLKKVYYQDN FT NARHFQLENDISNYSQSNLSIQEYYSGFQNLWAEYTDIIYAQIPAESLSVV FT QKVHEQSKRDQFLMKLSSEFEITRSNFMNRAPFPSLDGCFGELLREEQRIL FT TQSSLKQDNPAAVAFAVQGRGRGRNMGNVQCYSCKEYGHIANNCRKKFCNY FT CKQQGHIIKECPTRPQNRKIQAFPAVVSESSSVTVATSSLTPEMVQQMIIT FT ALSALGLQGNTSNSQLWLADSAASNHMTNSSSMLKNVREYHGSSHIQVANG FT GHIPITKIGDIDPTFTNIFVSPELSTSLISVGQLVDDNCDVHFSRNGCLVQ FT DQVSGKVIAKGPKVGRLFPLHFSIPSCLSFACSNVLNKSEVWHKRLGHPNS FT VVLSRLLNSGLLGNKDKFSSFDALIDCSTCKLGKSKTLPFPSHGSRATKCF FT DIIHSDVWGPSPILSHAHSKYFVTFIDDYSRFTWVYFLRSKSEVLSVFKTF FT LAYVETQFSTGIKVLRSDSGGEYMSRDFHDLLLQKGIISHRSCPYTPQQNG FT VVERKNRLCWMSLEPYCLTRLFPLNSGLKHCLLLFI" FT CDS 2534..4240 FT /product="Copia47-PTR_I_1p" FT /translation="MYERRRPLLALPETNPPSDTASETASVPSPLQPALRR FT STRVSYPPDRFGFSATLSNIIVPSCYSQAVQHECWQTAMQEELCALQDNHT FT WDLVSCPLSVKPIGCKWVYSIKLRSDGTLDRYKARLVALGNRQEYGVDYKE FT TFAPVAKMTTVRTIIAIAASQGWPLHQMDVTNAFLHGDLKEDIYMAPPPGL FT VLSSKSVVCKLKRSLYGLKQAPRAWFDKFRTILLRFSFVQSQYDSSLFLCT FT TSTGYVFLLVYVDDIVITGTDSTLISKLQQHLRDSFHMKDLGSLTYFLGLE FT VHSSPSGIYVHQQKYTHDLIALAGLQASSPVDTPLEVNVKFQSDDGDLLPN FT PSLYRQLVGSLNYLTITRPDISFAVQQVSQFMQSPRHLHLAAVRRIIRYLL FT GSSNRGLFYPAGSPISLVAYSDADWAGCPDTRRSVTGWCMFLGDSLISWKS FT KKQDRVSKSSTESEYRAMSVACSEIVWLRGLLAEMGFHQTTPTLLHADNTS FT AIQIATNPVFHERTKHIEVDCHSIREAVDAHVISLPHISTDLQIADVFTKS FT MTRQRHQFLVGKLMLINHPASI" XX SQ Sequence 4250 BP; 1017 A; 898 C; 870 G; 1465 T; 0 other; tggtatcaga gctatacctt tgaatttgta ttccaaaatc aggttctttc ttgttgtttt 60 cggtttctgg gttattctgg attagtccta gatacatagg actctcgatc tcctggctct 120 ttgcaatcag tcctagatac agaggacttt tagtttcttg gttcttttgg tttggttctc 180 ggttgtcagc cgaggtttgt agtctccttg ttctgtgatt ttttgtgcat cactacaaag 240 atgtcaaaca attctgatct gtttggtgtc cgatttactg ggaagaatta ttctgcttgg 300 gaatttcagt ttcaagtatt tgtcacagga aaagaattgt ggggtcatgt ggatgggagt 360 gatccaaccc ctatgctaca aaactgtctt tatggaaggt caaggacgct cgggtaatgt 420 cctggatact agggtcagtt gaccccctta ttattcttaa tctgaggcca tacaaaacag 480 caagaaccat gtgggaatat cttaagaagg tttactatca agataataat gctagacatt 540 ttcaattaga aaacgacatc tctaattatt ctcaaagcaa tctttctatt caggagtatt 600 attctggttt tcagaaccta tgggcagaat atactgatat catttatgcc cagattccag 660 cagaatccct ctcggttgtt cagaaggtgc atgagcagag caagcgtgat caatttctca 720 tgaaattgag ttctgaattt gagattactc gctcgaattt tatgaaccga gctcccttcc 780 cttccttgga tggttgtttt ggggaattac tgcgggaaga acagcgaatc cttacacaaa 840 gttctctaaa gcaggacaac ccagctgcag ttgcctttgc tgtccaggga agaggtagag 900 gccggaatat gggcaatgtt cagtgttata gctgcaagga atatggccac attgctaaca 960 attgtagaaa gaagttctgc aattattgca aacagcaagg gcatattatc aaggagtgtc 1020 ccactcgtcc tcaaaaccgg aaaatacagg cctttccagc ggtggtatct gaaagctcat 1080 ctgtgacagt cgctaccagt tctcttactc cagaaatggt gcagcaaatg atcattacag 1140 ccctctcggc cctagggcta caaggtaata cttccaattc acaactttgg cttgctgatt 1200 ccgctgcttc aaatcatatg accaactcat ctagtatgct taagaatgtg cgagagtatc 1260 atggttcatc acatattcag gttgctaatg gtggtcatat acccatcact aaaattggag 1320 atattgatcc caccttcacg aatatttttg tatcaccgga actgtctact agccttattt 1380 cagttggtca actggtggat gataactgtg atgtgcattt ttctcgtaat ggttgtcttg 1440 tgcaggatca ggtgtcgggg aaagtaatcg cgaaggggcc taaagttgga cgcttatttc 1500 cgctgcattt ttccattcct agttgtcttt cttttgcatg ctcgaatgtt ctaaataaaa 1560 gtgaagtctg gcataaacgt ttaggccatc caaattctgt tgttttatcg cgattgttga 1620 attctggttt gttgggaaat aaagataaat tttcttcttt cgatgctttg attgattgtt 1680 caacatgtaa gttaggtaag agtaaaactc ttccttttcc ttctcatggt agtcgtgcca 1740 caaaatgttt tgatattatt catagtgatg tttggggacc ttcaccgata ctttctcatg 1800 ctcattccaa gtactttgta acttttattg atgattatag taggtttact tgggtatact 1860 tcctacgttc caaatctgag gttctttccg tctttaagac atttcttgcc tatgttgaaa 1920 cccaattttc tactggtatt aaggtattaa gatctgattc gggtggggaa tatatgtcac 1980 gtgactttca tgatttgtta ctacaaaagg gcattatttc acatcgttct tgtccatata 2040 cacctcaaca aaatggggtt gttgagcgta aaaatcgact ttgttggatg tcactagaac 2100 cttattgctt gactcgtctg ttccctctaa attctgggtt gaagcattgt ctactgctgt 2160 ttatttaatc aaccgtttgc cctcccaggt gttaaatttt gactcccctt attatcgtct 2220 atatcatgag gctcctagct actctgattt gcatactttt ggttgtgtct gttttgttca 2280 tttgccttct aatgaacgcc ataaactttc tgctcagtct gctaaatgtg cttttctagg 2340 ttatagtatt tctcacaaag gttttgtttg ttatgatcta agttgtagca aatttcgtgt 2400 ctctcgaaat gtggtcttct ttgaaaatca atattttttc cctactgcta ctcctgctgc 2460 atcttcattg catgctccta ttcttcctca ttttgaggac gtgtcgtcat ttgagcggtt 2520 taaacctgga attatgtatg aaagacggcg cccacttttg gctcttccgg agactaaccc 2580 accatctgat actgcttctg agactgcttc ggtaccttcc cctctgcagc ctgctcttcg 2640 tcgttctacg agggtttctt atcctcctga taggtttggt ttctctgcta ctctatccaa 2700 tattattgtt ccatcatgtt actcacaggc tgtccagcat gagtgttggc aaaccgccat 2760 gcaggaagaa ctttgtgcgc ttcaggataa tcatacatgg gatcttgttt catgccctct 2820 atcggttaaa cccattgggt gtaaatgggt atattccata aagcttcgct ctgatggcac 2880 tctagaccgc tataaagctc ggttggttgc tctggggaat cgacaagaat atggggtgga 2940 ttataaagag acttttgccc ccgtagccaa aatgactact gtgcgcacta ttattgccat 3000 tgctgcttca cagggttggc cacttcatca aatggatgtc acaaatgcgt ttcttcatgg 3060 tgatctcaaa gaggatattt atatggcacc tccaccgggt ttggttttat cttctaaatc 3120 ggttgtttgt aaattgaagc ggtccttgta tggtttgaaa caagctcccc gagcatggtt 3180 tgacaagttt cgcactatct tgcttcgctt ctcttttgtg caaagccaat atgattcttc 3240 attatttctt tgcacaacat ctactgggta tgttttccta cttgtttatg tcgatgacat 3300 tgtcattaca ggcactgatt cgacattgat tagcaaactt cagcaacatc ttcgggattc 3360 ctttcatatg aaggaccttg gttctctcac ttacttcttg ggtttggagg ttcattcttc 3420 cccttctggt atttatgtgc accaacagaa atacactcat gatttgattg ctttggccgg 3480 tcttcaagct tcttctccag tggatactcc tttggaggtg aatgttaagt ttcaaagtga 3540 tgatggggat cttcttccta atccatcttt gtatcgacaa cttgttggca gcttgaatta 3600 tcttactatt actcgacctg atatctcctt tgcagttcag caagtcagtc aatttatgca 3660 atctcctcgt catctacact tagcagcagt ccgtcgtatc attcgatatt tacttggttc 3720 ttctaaccgt ggtctattct acccagctgg atctcctatt agtcttgttg catatagtga 3780 tgccgattgg gctggttgtc ctgataccag acgctctgtt acaggttggt gtatgtttct 3840 tggtgattcc ttgatttctt ggaaaagtaa gaaacaagat cgagtctcca aatcctcgac 3900 tgaatctgaa tatcgtgcca tgtccgttgc ctgctcagaa attgtttggc ttcgtggcct 3960 gcttgccgag atgggatttc accagactac tcctactctc cttcatgcgg acaacacgag 4020 tgctattcag attgctacga atcccgtctt ccatgagcgc accaaacata ttgaagtgga 4080 ttgtcactct atccgcgaag ctgtcgatgc tcatgttatt tctcttccac atatctccac 4140 cgatctccag attgctgacg tgttcaccaa atccatgact cgacaacgac atcagttttt 4200 ggttggcaaa ttgatgctta ttaatcatcc agcatcaatt tgagggggga 4250 // ID MuDRASH3_MT repbase; DNA; EDCOT; 5455 BP. XX AC . XX DT 16-JAN-2007 (Rel. 12.01, Created) DT 21-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A DNA transposon from Medicago truncatula. XX KW MuDR; DNA transposon; Transposable Element; TSD; TIR; KW Inverted repeat; Interspersed repeat; ORF; MuDRASH3_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5455 RA Shankar R. and Jurka J.; RT "MuDRASH3_MT: A DNA transposon from barrel medic."; RL Repbase Reports 7(1), 40-40 (2007). XX DR [1] (Consensus) XX CC The DNA transposon has intact domain for transposase of MuDr CC family. Also it has well conserved TIR and "T" rich 9 bp TSD. CC Present in Medicago genome in few copies. XX FH Key Location/Qualifiers FT CDS 887..2812 FT /product="MuDRASH3_MT_1p" FT /translation="MEEHITLILHHGGDLVRNENRRLQYVGGEFCVWEKIY FT VDELCLWDIEKMVKHCKSYFKVSKLGYMKPYEGVSNDLNICLTPLTTDQHI FT LDMVQAARSNGNEVEIYAQHLVDNEEVEIVPLTTEEREEVEREMEKCLRSA FT KTREEEPIKVMEVDILTAEERNVVECLVASVQTRVGNEEEIVDDMQEGMEE FT DNVGATQGREEDNVGATQGREEDNVVDNEGGNVTQAEESQPQETVTQQETQ FT VEENVTKGAQKKARKSKGKEKQTAAPKRKRPVRYSRGTGVTINDDGPLVFD FT SSSDDTDFEADYVAGHRDSHCEVGNGSQVHIEMSEPNEVCSDNDSYVSEEL FT RSPISTDDEGDGNRNIVYPQFNENAGFGDVNLELGMEFATLQKFKDAVKDY FT TIHKGKDIKWLKNDKKRARAECKHETCGWVIYCARDEKRKCFQIRTFVSKH FT DCPTDFKNKQANRKWVVKMLEKVLRFDPEIKHREIFDLFKKDYKVILDDNL FT IFRATKEARDLVEGSEREQYGLLWDYANELLRSNPNSTVRMNTTPMPQSPP FT QFKRFYVCLDACKQGFKAGCRPLIGLDGCFLKGYYGGQLLSAVGQDGNNHI FT FPIAFAIVDVETKDNWNWFLKLLHKDLGDYERNGWNFISDMQKV" XX SQ Sequence 5455 BP; 1681 A; 809 C; 1273 G; 1691 T; 1 other; gagtgaacca tcaaattcgt ccctgaattt tcacgcgtcg gccaaattag tccctcaatt 60 atacgaaatt tcaatttcat ccctgaattt gtcaaacgtc catcaaaaag gtccctccgt 120 taacgggctc cgttagccat gctgacatgt cgtctggcat ggtgtgctgt cctgtacgcg 180 tggcaagaag gaagccacgt gttcagggac gaatttgatt gatttggaaa aagttcactt 240 ttcatttttc aatttaattt tttcgtgctt ttcccatttt gcccctgcat tacatattcc 300 ttcttcttca cattttactc agaaccatca aaaacatcct tgactcttct ccttcccgct 360 aaaacgttct ccattttcac ccctccaaaa tcatcctcat ctccatcgat tctggcgtgt 420 ttgaagttcc tgtgttcgac cgtgatcaaa ggtaacacct ttccttttgt ttatcaagat 480 tctggcgtgt ttcgttttgg caccgttttt gttcgttttt gttcgttttt atcatttcgt 540 tttggcgttt taagattctg tctgtgatca tttcgttttc attttgtcct tttgttgcgt 600 gtttgagaca aatggtttgg tatgattatt cgtttttagg gtttttggta aagttgtaaa 660 aatttgaaaa tttaattttt tttcctggtt ggttactaaa tttgatgaac atttaacttt 720 gtaatgaagg aaattacacg tttgtatttg agttttgcat tttagttttg tatttttttg 780 ttgttttgtt tgtgattaaa atcaaggttg ccgaattctg catcatggtg gtgagcatat 840 aacactaata ctgcatcatg gtggtgattc tgtgttgttt tgtaggatgg aagagcatat 900 aacactaata ctgcatcatg gtggtgattt agtgcgaaat gagaatcgga ggctgcaata 960 tgttggcggt gaattctgtg tatgggaaaa gatatatgtt gatgagttgt gtttgtggga 1020 cattgagaag atggtgaaac attgcaaaag ctacttcaag gtatctaaac tagggtacat 1080 gaagccgtat gagggtgttt ccaatgatct gaacatctgc ttgactccat tgacaactga 1140 tcaacatatt ttggatatgg tgcaagctgc aaggtctaat ggtaatgaag ttgaaatata 1200 tgcacaacat ttggtagata atgaggaggt tgaaattgtt ccattaacaa ctgaagagag 1260 ggaggaggtt gagagagaaa tggaaaaatg tctgagaagt gcaaaaacaa gggaggagga 1320 accaattaaa gttatggagg ttgacatact aactgctgag gaaagaaatg tggtagagtg 1380 tttggttgct agtgtgcaaa ctagggttgg taatgaagag gaaattgttg atgatatgca 1440 ggagggaatg gaagaagaca atgttggtgc tactcaagga agggaagaag acaatgttgg 1500 tgctactcaa ggaagggaag aagacaatgt tgttgataat gaaggaggaa atgtcactca 1560 ggctgaagaa agtcagcctc aagaaacagt cacccaacaa gaaactcagg ttgaggaaaa 1620 tgtcaccaaa ggagctcaga aaaaggcaag gaaaagcaaa ggcaaggaaa aacaaactgc 1680 tgcaccaaaa agaaaaagac cagtgagata ctcaagaggg actggggtga ccattaatga 1740 tgatggccca cttgtgtttg attcttctag tgatgacact gattttgagg cggattatgt 1800 ggctggacat agagactctc actgtgaggt aggtaatggt agccaggttc acattgaaat 1860 gtctgagcct aatgaagtat gcagtgataa tgacagctat gtttctgagg agttaaggag 1920 tccaataagc actgatgatg aaggtgatgg aaataggaat atagtttatc ctcaatttaa 1980 tgaaaatgct gggtttggtg atgtaaactt ggaacttgga atggagtttg ctactcttca 2040 aaaatttaag gatgctgtta aggattacac cattcacaag ggaaaagata ttaagtggct 2100 gaagaatgat aagaagaggg caagggctga atgcaagcat gaaacatgtg gttgggtaat 2160 atattgtgca agggatgaaa agaggaagtg ttttcagatc agaacatttg tgagtaaaca 2220 tgattgccct acagatttca agaataaaca agctaatagg aaatgggtgg ttaagatgct 2280 tgagaaagtc ttaaggtttg atcctgaaat aaagcataga gaaatatttg atttgttcaa 2340 gaaggattat aaggtgattc ttgatgacaa cttgattttt agggcaacaa aagaagcaag 2400 ggatttggtt gaaggcagtg aaagggagca atatggtctt ttgtgggatt atgcaaatga 2460 actgctgagg agtaacccaa actcaactgt gaggatgaat acaacaccaa tgccacagtc 2520 ccctccacaa ttcaaaagat tttatgtttg tctggatgca tgtaaacaag gttttaaggc 2580 tggatgtaga ccattgattg ggttagatgg atgctttctt aaggggtatt atggagggca 2640 acttttgtct gctgttggac aagatggaaa taaccatatt tttcccattg cttttgcwat 2700 tgtggatgtc gagactaaag ataactggaa ttggtttttg aaattattac ataaagatct 2760 tggagattat gagcgtaatg gatggaactt catctcagac atgcaaaagg tatgaataac 2820 catcttagtc tttttcatct ttcatgttat gtcccttttt ttcatgcatt ctgatgtata 2880 gtaatagctg aaaatagtaa gtaaaataat gcagggacta tattgatatt tattaatata 2940 attcagggac taatttgata gtaagttgta taattcaggg actagtgtga tagtaagttg 3000 tataattctg ggactagttt gatagtaagt tgtataattc agggactaat ttgatggata 3060 gtgatatata ttagggaata atgattctgt aattgttaaa attggcaggg tttgattcca 3120 gccatgcaag aagtgatgcc tggggtgcca catagatatt gtgcaatgca tctatggagg 3180 aacttcacaa aacaatggaa ggagaaggaa ttgagagggg tggtatggga gtgtgcaagg 3240 gcaacaactc ccactcaatt caaccgcatt atggagaggg tgaagaggct taatcagaag 3300 gcatgggagt atcttaacaa atggccaaag gaagcatgga ctaaagctta ttttagtgaa 3360 aattgcaagg cagataacat agtgaacaat gcttgtgagg ttttcaatgc aaagatcttg 3420 aactatagag ggaaaccaat actcactttc gctgaggatg ttaggtgcta tgttatgaga 3480 aaaatgagtc ataacaagat gaagcttgat gggagagctg gaccactatg tccttggcag 3540 caaagtaggc tagagaaaga aaagcttgcc agtcacaatt ggacaccagt gtggagtggt 3600 gataatccaa ggcaaaggta tcaaatagaa aattactcca gaatcaaagt ggatgttgat 3660 atatttaagc aaacttgcac atgcagattt tggcagttaa ctggtaagtg ttttctttta 3720 tttttctagc taaatatgtt ttatttttat actcattctg gtgtttttga tttgaactgg 3780 aatatgttgg atttgaatgc aacaggaatg tcatgtatgc atgcttgttc agcccttgca 3840 ttgagaggtt taaagccaga agaccattgt catgcttggt tgacccttgg atcttatagg 3900 gcaacataca actacttcat tcagccagtt aattcccaaa tatattggga atcaactcct 3960 tatgaaaaac ctgtgccacc aaaggttaaa agggctccag gaagaccaaa gaaagccaga 4020 agaaatgatg gtaatgagga acctgtttgt gggagtcaga tgaagaagac atacaatgac 4080 actcaatgtg ggaggtgtgg attgcttgat cataatgcaa gaagttgtat gatgcaaggt 4140 gttagtagga gaccaaagga aaatcctggc aatgtagatg atgtggatga aaatgctggc 4200 aatgtagatg ctgtggatga aaatgctggg aatactccta atgaagtgcc agaaaatgct 4260 cctaactttg tgcctggaaa tgctcctaat gaagtgccag aaaatgttgt gccagcaatt 4320 gatcctaatg aagtgcctgc aaatgttgtg ccagaaaatg ctccttactt tgtgcaacat 4380 aatgttgttg cacatgctgg acaggtatga cttttaattt ttaaggatcg ttttggcaat 4440 tagtatatta attgaaggac tgatatgatt gattctgtta tgattttagg gactaatttg 4500 attgaaattg aaatttcaga gtcttgcacc aaggaggtat ggccttagag gaccggttcc 4560 ttcagctaat aggccaaaga atacaccaat gaggggtcct gcaccagctc atccaactcc 4620 tgctggcatg attagggttc catatccaac ctatggtcca cccggttcga ctcaacctca 4680 attcatggag tttataccaa ctcccggatt tcccaagaag tgatgcttcc tgaagtttaa 4740 tagatgtttt ggatttgtaa tatgtaggct tatttgaatt atgccccata gttgggtttt 4800 tttttgctta acttgccatt taagtcttat gacttgttaa tgccccaaaa ttgggttgct 4860 tttgcttatg taatttctca gaattatgac ttattaccta tgacttttgc ctatgtaata 4920 tcacagtttt aatttctgtg ttctgtaatt tcaaggatca atttgatata tgattaaaat 4980 attcagggac taatttgatg gttttaaata tgatctgggg acgaatttgt gtgttctgaa 5040 tcatcttcaa cctcttttca taaccattaa acttattatt caaggaaatt taggtgatat 5100 tagaatgtag attatagatt gtgtaattag ggttccaatt ttatacaatt ggggaagaca 5160 aagtcgttgg ggaagaaaag agttgtttgg ggaaaaaata aaaaaaaatt ctgcaaatca 5220 atcaatttag tccttcaaaa tgtttggaat tatcagccaa attagtccct gcctacgtgg 5280 cgtatgacat gtaagaggtt aacggccacg tcagcaccgt taacagcccg tttgaccaga 5340 aggactaaat tgattgacaa ttaacaaatt cagggatgaa attgaaattt cgcataattg 5400 agggactaaa ttggccgacg cgtgaaaatt cagggactaa cttgatggtt cactc 5455 // ID MuDR-4_Mad repbase; DNA; EDCOT; 4222 BP. XX AC . XX DT 07-OCT-2010 (Rel. 15.1, Created) DT 07-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; 8-bp TSD; MuDR-4_Mad. XX NM MuDR-4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4222 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1509-1509 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TSD is 8-bp long. TIR is imperfect 46-bp long, imperfect. XX FH Key Location/Qualifiers FT CDS join(984..1571,1575..1994,1994..3256) FT /product="MuDR-4_Mad_1p" FT /translation="MRIEGILERKKCGCPFQLKGKKLATDDDWILTVVIGV FT HNHTAAGHLEGHSFAGRLSSEETSLLTDLSKSLVQPKEILTTLKRRDKRNV FT STLRTIYNARQRLRLLEKGGRSQMQQLMSKLSEHRYTEWHRSCPKTNTILD FT LFWTHPTCLELLHAFPHILIMDCTYKTNRYRMPLLEIVGVTSTDMTFSVGF FT VYLSAEEDNYVWALSILRGLMDGIVMPDVIVTDREMALMRAIELIFGTSKH FT LLCRWHINKNVLAKFKKLYKSKEDCDRFLEKWNTMVASSTEADFIRQTRQL FT CNEFSMYQEMLQYVIDTWLNPYKERFVAAWIDKFMHFGNTTSNRVSIYHLL FT LYFHFHFLVRLLNPCYFNRAESSHAKLKRHLGSSQGTFETSWESIHALLGL FT QHTEIKASFEKSLIVVHHDFRHSDFMELRGFVSISALYMVLKEYELSKMNS FT IDSEACGCVLRDTHGLPCAHEIVRYMRDGRPIPLESIDPHWRKLDMKCTPI FT RNAAEYDYDAEMELFHRRWIESDATARMVLKXKLMELVLPQTTSLVEPSVT FT TKTRGRPSKKTDKSTRRDPSLFEIVESEQGSYSLGDLYPEMSSKQKRRPKE FT KVHRARSVKPIELTNAFPVALRPYIILVKDVAADGHCGFRAIASLLGYNED FT GWVQVRKDLLQELETYSSCYSKLYGSENRVHELKHALRYFETHANIDRWMT FT MPDMGHIIASCYGVVLIHLSDVQCLTFLPLRTEPIPLAARKEIAIGFTNHH FT FVQVWI" XX SQ Sequence 4222 BP; 1290 A; 669 C; 886 G; 1375 T; 2 other; gagagctgtt attcccaccc caatgtctta tcttcccacc caccttttta tgaatttttt 60 aattacaaat ttgtccattt gtaaaatgac taataaggac cttagttacc cccttttgca 120 ttactttttt ttttataaaa aagaaaaaag aaaagtttgg gcgtgataac tctcacgcta 180 tgtttagacg atttgtctcc cttaaaccct aactcatcat tcccatctcc ttcattagag 240 aaacaaaatc attcagagaa agcaaaaaga atgaacttag aagatgacgt ttctatggaa 300 gaagtagatg attatgtttc cgtcgaagag gtaaaagata attttatgtg ggtcatcttg 360 atttgtcgac atcgtacaat tgaagcatag ctctgtgact ttttatttga atttgcatta 420 ggttagggtg caatttgttt cacgttttcc tatgagaatt cctggaattc gttttcatta 480 ggttagggta ataattcaag taaggcatgt ttgtcgcaac tgacactgat aatcgtccaa 540 cttgatgtgt tgtctccgaa acctacacac aaatcccttt cttaattagc actattttca 600 acttgatgta atgcccattt atttacgtat ggtggaattc gtttgcagca ggtagatgaa 660 tctggtaata attcagcatc tacacatatg gtggactgta ctagtgaatt taccacaaat 720 aaggtaatat ttgcttgact acgcaattga tttacttata ctcttgtatg tttattcata 780 atgtgcaatt ttggtacgta gttattcaag agtagagaag aattaataca atgggctcga 840 gaagttggga aggtcaatgg ttttgttatt gtgacgttac gatccgatca aggtggaaaa 900 gataacagga gccctagact tacattgggt tgtgaaagga atggacaata tgtaagtcga 960 attcacaaaa aaagacataa aggatgagga tagaaggaat tctggaacga aaaaaatgtg 1020 gatgcccgtt tcaattaaag ggtaaaaagc tagcaactga tgatgattgg atattgacgg 1080 tagttattgg agtgcataat cacacagcag caggccattt ggagggtcat tcatttgctg 1140 gtagattatc gtctgaagag acttcgttat tgactgatct gtctaaaagt ttggtgcaac 1200 caaaggagat tttgactaca ctaaaacgaa gagacaaacg aaatgtatct acactgagga 1260 caatttataa tgcacgtcaa cgtttgaggc ttttggagaa aggtgggagg tcccaaatgc 1320 aacaattgat gagtaagcta tctgagcata ggtacactga gtggcatagg agttgcccaa 1380 agactaatac tattttggac ttgttttgga cacacccgac ttgtttggaa ttgttacatg 1440 catttccaca tattttgatt atggattgta cgtacaagac caataggtat cgtatgccat 1500 tgttagaaat tgttggagtt acgtcaactg atatgacatt ttctgttggt tttgtttatc 1560 tttctgcaga atgagaagat aattacgttt gggccttgag tatattgcga ggactcatgg 1620 atggtattgt tatgcctgat gttattgtga cagatagaga aatggctttg atgagggcca 1680 ttgaacttat atttggtaca agtaagcatt tattatgtag atggcacatc aataagaatg 1740 tgctagccaa gttcaaaaaa ttatataagt ccaaggaaga ttgcgataga tttttggaga 1800 aatggaatac aatggttgca tcttctactg aagccgattt cataaggcag acaagacaac 1860 tatgcaatga gtttagtatg tatcaagaga tgcttcaata tgtgatagat acttggttga 1920 atccatataa agaaaggttt gttgcagcat ggatcgataa atttatgcac tttgggaata 1980 caacctcaaa taggtaagca tttatcactt gttactttat tttcattttc attttctagt 2040 gagattgcta aacccttgtt actttaacag ggctgagtct tcacatgcca aattaaaaag 2100 acatcttgga agtagccaag gaacatttga gacatcatgg gaaagtatac atgctctgct 2160 tgggttgcag cacactgaaa tcaaggcttc ttttgagaaa agtttgatag tggtgcatca 2220 tgattttaga cattcagatt tcatggaact tcgtggcttt gtctcaatta gtgcactata 2280 tatggtccta aaagagtacg agttgtccaa aatgaacagt attgactccg aggcatgtgg 2340 ttgtgtttta cgagacactc atggattacc atgtgctcat gagattgtta gatacatgag 2400 agatggtcga cctatwccac ttgagagcat tgatcctcat tggaggaaac ttgacatgaa 2460 gtgtacaccc ataagaaatg cagcagagta cgattatgat gcagagatgg agttgtttca 2520 taggcgttgg atagaatctg atgcaactgc aagaatggtc cttaaaakga aacttatgga 2580 gttagtatta ccacaaacta cttcacttgt tgaaccatct gtgacaacca agactagagg 2640 taggccaagt aaaaagacgg ataaatctac tcgtcgtgat ccgtcattgt ttgagattgt 2700 ggaatcggag caaggaagtt attcacttgg tgatctttat cctgaaatga gttcaaaaca 2760 aaagaggcga ccaaaggaga aggtgcatcg cgctcgttca gttaagccaa ttgagttaac 2820 taatgcattt ccagtagcat tgaggccata cattattctt gtaaaagatg tggcagctga 2880 tggacattgc ggtttcagag caattgcatc attattgggt tataatgagg atggatgggt 2940 acaagtgcga aaagatttat tacaagagtt agagacttac tcaagttgct actccaagct 3000 atatgggtct gaaaataggg tccatgagtt gaagcatgca ttgagatatt ttgaaactca 3060 tgcaaacatt gatcggtgga tgactatgcc tgacatgggc catattattg catcatgtta 3120 tggtgtggta cttatccacc tatcagatgt acaatgtctt acatttttac ctcttagaac 3180 agaacctata ccactagcag cacgtaagga gatcgccatc ggattcacca atcatcattt 3240 tgtgcaggta tggatataag gatttattgt tggaaatttt tgcaggtgat cttataagga 3300 ttgaatgcat ttactttaag tttaagttat aaatttcttg tagtctagtt taattaagtt 3360 gtacttttat gcaggtgttc ttgaaatcag gtcatccaat tcctcctata gcgacaaatt 3420 gggaaagata ctgtgaacca tggtgtttag aatgggctac tccgtacatt gctcgtatac 3480 aacagttcaa attcattgta gggtctactg ttataactag agagatcgtg gagcttgacg 3540 aaaattgaag ctggtaagca gcgccaccat gcttatccgt cagacaattc cagattctat 3600 tcatagtatt ttttttccca gtaaactccg cgtttcgatg cttttctgta tttttctgac 3660 taaattgctc ttggtttgtt cctcagggaa tatgaattgg gatttttttt ctgtcttgtt 3720 ttgctttaga attcgtgctc ttcttttaaa tccacgttta cggtttagtg tttttttttc 3780 ctggaataat tgctaaaatg tttttatccc taggattttg gcccaaatta gaacccacct 3840 tgcaaaacta ccagacactc tttgctgcaa attaagaaaa tctccaacat atctagcaaa 3900 atgacagttg catagaaaaa gaaaacgaag gggttcaagc aaagaatgac tacttgaaat 3960 tcttcattcc caccccaatt ggaatcagga tgaaaatcag aagaccgttt ttttcattgt 4020 tcttttttcc ggtttttaga agagtaatat tatttgttta tattattttt tttaaagaga 4080 aatttatctc taattatata tagggttatt ttaggaataa tagtgggtgg ggaaataaca 4140 ttttaatttt ttaacttttt atagtgggtg taaatataac gtgggtgggg aaataagaca 4200 acgggtgggt ctagcagctc tc 4222 // ID Gypsy-32_VV-I repbase; DNA; EDCOT; 4543 BP. XX AC chr15; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-32_VV_; KW Gypsy-32_VV-LTR; Gypsy-32_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4543 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr15; Positions 8379680 8384222. XX CC 'TAATC' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(288..1652,1656..4433) FT /product="Gypsy-32_VV-I_1p" FT /translation="MASDEMRRGGNGEWRGSRRVEMPVFTGENPDGWIFRA FT DRYFATYGLTEEEKLVAAAMSLDGDALSWYQWTDSREVFGSWENLKRRLLL FT RFRLTQEGSLCEQFLAVRQQGTVAAYWREFEILETPLKGISEEVMESTFMN FT GLLPEIRAEQRLLQPYGLGHLMEMAQRVEDRNLAMRAAREPNGPKSTKMLS FT TANRGEWKIGENFQTRAVAVGEKTMSQRREIPIKRLTESELQARREKGLWF FT KCEEKFSPGHRCKKELRVLLVHEDEEEDDNQFDDRATEEPALIELKDAVEL FT SLNSVVGLTTPGTMKIKGTIGSKEVIILVDSGATHNFLSLELVQQLTLPLT FT TTTSYGVMMGTGISVKGKGICRGVCISMQGLTVVEDFLPLELGNTDVILGM FT PWLGTLGDVKVNWKMLTMKIKMGKAVMVLKGDPSLSRTEVSLKAMARALQH FT HSQGVWVELCTSTTSDLSEGVQEVPKTVKEVLAQHQQIFEPITGLPPSRDI FT DHAIQLILGASPVNVRPYRYPHILKNEIKRLVQEMLEAGIVRPSLSPFSSP FT VLLVKKKDGGWRFCIDYRALNKVTVPDRFPIPVIDELLDKLHGATIFSKLD FT LKSGYHQIRVRQQDIPKTAFRTHEGHYEFLVMPFGLTNAPATFQSLMNRIF FT WPHLWKFVLVFFYDILVYSKDLKEHCDHLQTVLSILANHQLHVNGKKCLFA FT KLQLEYLGHLVSAKGVAADPNKISAMVEWPTPKSLKELRGFLGLTGYYRRF FT VEGYGAISWPLTQELKKDAFNWNLEAEVAFQKLKTTMTTIPVLALPNFSQL FT FIVEMDASGYGLGTVLMQSHRPVAYFSQVLTARERQKSIYERELMAIVLAV FT QKWRHYLLGRHFIVRTDQSSLKFLLEQRIVNESYQKWVAKLFGYDFEIQFR FT PGLENKAADALSRIPISMELAALMVPSRIDTSLISSQVEADPHLVKIKQRL FT LADPDAYPRYSLDHGILLYKGRLVLPKASPLVPALLQEGHASVVGGHSGFL FT QTYKRLTRDFFWVGMKNDIKEFVEKCLVCQQNKTLTLSPAGLLQPLPIPDK FT IWDDVTIDFIEGLPKSEGYNSILVVVDRLSKYAHFSLLKHPFTAQTVAAIF FT VQDVVKLHGFPRSIISDRDKVFLSRFWTELFRLQGTSLCHSTAYHPQTDGQ FT TEVVNRCVETYLRCFSYNKPRRWSTWISWAEYWYNTTFHSSTNTTPFRAVY FT GRDPPPLIRFGSDSTSVLAVDQLLQERDLILNELKDHLCCAQSKMKSSADA FT HRRAVQFEVGDFVYIKLRPYRLRSLAKRPNEKLSPRYFGPYKVVQQIGPVA FT YRLKLPSSTSIHPVFHVSQLKRALGSADLCQPLSPILTEDLEWLVEPDQVL FT DIRQSSNNNQLGTEVLIQ" XX SQ Sequence 4543 BP; 1245 A; 933 C; 1162 G; 1203 T; 0 other; atttggtatc agagcatcga tccagatggc tcagaaaagg aatgaaggtc gcgtggattg 60 tctagagaag gaagttggag aaatcagaga ggagatgcaa cgcttaccaa gaatggaaaa 120 gacggttatg gaccttgctc agaatgtaat gcgagtttct gcagtcgctg gaagagacgc 180 agaaggcagt ggcggcgttg tcattagggc ggaacacgac gactgctgct caacgagaag 240 atcgggctgg atggatccct ggagtttggg aacccagtgg gggggggatg gcgtcggatg 300 agatgaggcg aggtggaaat ggagaatggc gcggcagccg aagggtggag atgcctgtat 360 ttacgggaga gaacccggac ggctggatct tccgggccga tcgatacttt gcaacgtacg 420 gactcactga agaagagaaa ttagtcgccg ccgcgatgag tttagatggg gacgcactct 480 cttggtacca atggactgat tcgagagagg tgtttgggag ttgggaaaat ttgaagaggc 540 ggttgttgct tcgctttcgt ctgactcaag aagggagcct ttgtgagcag tttttggcgg 600 tgcgacaaca agggacagtg gcagcatact ggcgggaatt cgagattcta gagactccat 660 tgaaagggat ttcagaggag gtaatggaaa gcacgtttat gaatgggctg cttcctgaga 720 tccgggctga gcaacgtcta ttgcaaccat atgggctggg ccacttaatg gaaatggccc 780 aaagagttga agacaggaat ttagccatga gagcagcccg tgaaccaaat ggcccaaaga 840 gcaccaaaat gttgtcaact gcaaatcgag gtgagtggaa gattggggaa aattttcaga 900 ctagggcagt ggctgtcggc gagaagacga tgagccagcg acgtgagatt ccgataaaga 960 gactgacgga atcggagctt caagcccgta gagagaaggg gctctggttt aagtgtgaag 1020 aaaagttctc ccctggtcat cgctgtaaga aagaattacg ggttttattg gtgcacgaag 1080 atgaggagga agacgataac cagtttgacg acagagcaac cgaagaacct gcactcatcg 1140 agctgaaaga cgctgtggaa ttatctctaa attccgtggt cggtttaact acgccgggaa 1200 ctatgaagat caaagggacg attgggtcaa aagaggtaat catccttgta gacagtgggg 1260 ctacccacaa ttttttatcc cttgaattgg ttcaacaatt aacacttcca ttaactacaa 1320 caacgagtta cggggtgatg atgggaaccg ggatatccgt gaaagggaag ggcatttgta 1380 gaggagtttg tatttcaatg caggggctca ctgtagtgga agattttctt ccactcgaat 1440 taggcaacac tgatgtgatt ctaggaatgc cttggttggg gaccttagga gacgtgaagg 1500 taaactggaa gatgctaaca atgaagatca aaatggggaa ggcagtgatg gtgttaaagg 1560 gagacccgag ccttagtcgg actgaggtat ctcttaaagc aatggctaga gcactgcagc 1620 accatagcca aggggtatgg gtggaactct gttagacttc caccacttcg gatttgagtg 1680 aaggagtaca agaggtcccg aaaacagtta aagaagtatt agctcaacat cagcaaattt 1740 ttgagccgat aacagggtta ccaccaagtc gtgatattga tcatgccatt caattaattc 1800 tgggagcatc tccggttaat gtccgaccct accggtatcc acatattcta aagaatgaaa 1860 taaagagatt ggtgcaagag atgctggagg caggaattgt tcggcctagc ttaagcccat 1920 tctctagtcc agtgttgttg gtgaaaaaaa aagatggagg atggaggttt tgcatagatt 1980 accgcgccct caacaaagtt acagtcccgg atcggtttcc cattccggtg attgatgagt 2040 tacttgacaa acttcatggt gcgaccattt tttccaaact agacctcaaa tcaggttacc 2100 accagattcg agtccggcaa caagacatcc ccaaaacggc atttcgcacc catgaaggtc 2160 actacgagtt cttggtgatg ccttttgggc taaccaatgc accagcgact ttccaatcgt 2220 taatgaaccg tatattttgg ccacatcttt ggaaatttgt gctcgtattt ttttatgaca 2280 tattggtcta cagcaaagac ttgaaggagc attgtgacca tttgcaaact gtgctgtcca 2340 ttttggcgaa ccaccaactg cacgtcaatg gaaagaaatg tctctttgct aaactacaat 2400 tggaatacct aggccatttg gtttctgcca agggggttgc tgctgatccc aacaagattt 2460 cagccatggt agagtggccc acacccaaat cccttaaaga attacgagga tttcttggat 2520 tgactggata ctaccgtcga tttgtagagg gatatggagc tatttcttgg cctctcactc 2580 aggaactcaa aaaagatgct tttaattgga acttagaggc tgaggtagcc ttccaaaaat 2640 tgaaaacaac tatgacaaca ataccggttt tagctttgcc caatttcagc caactcttca 2700 ttgtagagat ggatgcctcg gggtatggtt tgggtaccgt tttgatgcaa agtcatagac 2760 cagtagctta ttttagtcaa gtcctcacag caagggaacg acaaaaatcc atatatgaaa 2820 gagagttaat ggctattgtc ttagcagttc agaagtggcg tcattacctg cttggtcgcc 2880 actttattgt gcgaacggat caaagtagct tgaagtttct actagagcaa agaatagtga 2940 atgagtcata tcaaaagtgg gtcgcaaaac tgtttgggta tgattttgaa attcagtttc 3000 ggccaggact ggagaataaa gcagctgatg ccttatctcg catccccatt tctatggagt 3060 tagctgccct catggttcct agtcgcatag acacttcgtt gatcagttca caagttgaag 3120 ctgacccgca ccttgttaag attaaacaga ggctactggc tgatccggat gcttatccta 3180 ggtattcctt ggaccatggc attctccttt acaaggggcg cctagtcctt cccaaggcct 3240 caccccttgt tccagcactt cttcaagagg gccatgctag tgtggttgga gggcattccg 3300 ggttcttgca gacttacaaa cgactcacaa gagacttctt ttgggttggc atgaaaaatg 3360 atatcaaaga gtttgtggag aagtgtctag tatgtcaaca aaataagacc ctaactttgt 3420 cgcctgcggg gttactacaa ccactgccta ttccagacaa aatatgggac gatgtgacaa 3480 ttgactttat tgaggggctt cctaagtctg agggttataa ctccatttta gttgttgtgg 3540 atcgattgag caaatatgct cacttctcac tgctcaagca tcctttcaca gctcaaacgg 3600 tggctgctat ctttgttcag gatgttgtca aattacatgg atttccccgt tccattatta 3660 gtgatcgtga caaggtattt cttagccgat tttggacaga gctatttcgg ttgcagggta 3720 cttctctctg ccatagtacc gcatatcatc cgcaaacgga tggacaaacg gaagtggtca 3780 accgttgtgt ggagacatac cttcgatgtt tttcatataa caagcctaga cgttggtcta 3840 catggatttc atgggcagaa tactggtata ataccacatt ccactcctcc actaatacga 3900 caccgtttcg agcagtttac gggcgagacc caccaccgtt gatacgtttt ggatcagatt 3960 ccacctctgt tctggcagtg gatcagttat tgcaagagcg tgatctaatt ttaaatgaat 4020 tgaaggatca tctctgctgt gcccaatcca aaatgaagtc atctgcagat gctcatcgac 4080 gtgcagtcca atttgaagtt ggggattttg tctatataaa gcttcgtccg tatcgacttc 4140 gttcccttgc caagcgacca aatgagaagc tctccccacg atattttggc ccttacaaag 4200 tagtgcagca aattggtcca gtggcgtaca ggttaaagct tccttcttcg acatctattc 4260 atccagtgtt tcatgtttcc cagctcaagc gggctcttgg ttcagctgat ttgtgtcagc 4320 cactttcccc tattcttact gaggatttgg aatggcttgt ggagcctgat caggtcttag 4380 atattcgcca atcttccaat aacaatcagc ttggtactga agtacttatt cagtagaaag 4440 gacttcctca gtttgaagct tcatgggaat cagttgacac aattaaagag cactttcctg 4500 acttccacct tgaggacaag gtgtctctca ttgagggggg taa 4543 // ID Copia-29-LTR_VV repbase; DNA; EDCOT; 500 BP. XX AC CU459380; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-29_VV, LTR retrotransposon Ty1-copia like, long terminal DE repeat from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Brand-B01; KW Copia-29-LTR_VV; Copia-29-I_VV; Copia-29_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-500 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL/GenBank/DDBJ; CU459380; Positions 609225 609724. XX CC LTR : 500 and 502 bp CC LTRs are 94.4% similar to each other CC Direct flanking repeats : aatat. XX SQ Sequence 500 BP; 153 A; 109 C; 72 G; 166 T; 0 other; tgttgggata tttataggtg aatggaaatt aagacatacc atttcaatta gatacaactc 60 ttcctaatgg acacaacttg tgtcaaagga tatgtcaagt atttaagaca catatcttct 120 aagagtcacc agaaaaccta taaatacccc ctcccctcct ccctcccccc catggcattt 180 ctgattcatt ccatcatcaa ttctctccac ttcttctcct ttcttccaag tgcttggtat 240 tcaagagagt tcaagtcatc aagtgattca ttgtttcttg tgatttggag tgctactatc 300 acaagaaagt gatcattata tcctaggaga cgattgtcaa caaaccgtaa gcaccagtgc 360 ggggcaaatt catcttaagg acatagagtc aaactctagc ctcgatcaac catttataag 420 atttaatatt tacttacctt cttgtttatt tattatacat aattatttga ccatacattt 480 gtgatagttc tagaataaca 500 // ID Copia50-PTR_LTR repbase; DNA; EDCOT; 333 BP. XX AC scaffold_1819; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia50-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-333 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-333 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 281-281 (2007). XX DR Genome; scaffold_1819; Positions 4762 4430. XX SQ Sequence 333 BP; 97 A; 43 C; 64 G; 129 T; 0 other; tgatagaatt aatcttgttg ttttatttca gtttgttttg ttttaattcc agcagagttt 60 aagagtagac gtaacctttc atatagaagt tatgatttag aggttattta gtggacgtaa 120 cctttcatat agcagttatg atttagaggt tatttagagg acgtaacctt tcgtatttgt 180 aacctttcgt atttgcttct atatataata agaaaatcag aaaatgatgc agtgagttaa 240 gcatcacaaa aggcctctgt tctttcatta ttttgtctct gtgattgtgt gagtttccca 300 aattgtgtga ctggccgtaa gaaagaataa cca 333 // ID L1-7_Mad repbase; DNA; EDCOT; 5985 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-7_Mad. XX NM L1-7_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5985 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1811-1811 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 1061..1699 FT /product="L1-7_Mad_1p" FT /translation="KIMGQPLHTFQKLQVLMIMHAVSQLAKAGLVSKNSLS FT SARGLDDASPSHFVEGLVDDNDTTCDHVSDTPMDTPLIGIQLNSSLVLSER FT CNANDSVQVVSQVQEASPPSLSPQVRSEIQKVNDWYTMVEEDALQNNVAGR FT ENNDLDGANNVSEDDMTLVLSKSQREDYEKKNRNLVIIPTSVRLFKLMLGL FT LLWLPMIHEDHLLEYSGLSKSPH" FT CDS 1653..5807 FT /product="L1-7_Mad_2p" FT /translation="MKTIYWNIRGLANRPTRQALRSLVRKHSPDFLCLAEP FT MTSTMKIRPFFWKSIGMHFLGVNDRGQRLPNIWVFHTANVLSPTVLSTSSQ FT HITIQFLVAGTAHCITFVYAATTVVERRPLWLSIAQVCAGFSGPSLILGDF FT NAVLGAHEKMGGILPRRIACEEFQAMVDTCGLVPIDVKGSPFTWTNGRGIS FT SHIEMLLDRCFCSTAWLDAWPITNCSTLVRHSSDHNPLLVSFQKFAAQGPT FT PFRFHRMWLDHPDFINLVKNSWQSIQVYGCPMFILQQKLKLLKPILRHWNA FT DVFGNVNVAVDNAREALEKIQLEISTEGFTDERHGAELQAHSTLSHALLVQ FT EKFWQDKTRSKWLRDGDRNTSYFHTLAKIRRTRNFISSLRIDSELVEDVEI FT LRNHVVEHFFNAFHDDGLAIDTGLVTRLIPPLVTTPENDTLLAIPTLEEIK FT QTVFSMNPDSAPGPDGFGGYFFHACWDFVGFEVSLAVQDFFKTGYILPNLN FT SSFVALIPKVQEADSISQFRPIAMANFIFKVITKILADRLALVATRIILPN FT QYAFLKGRHISDCILLASECVNLLDNKCFGGNVAIKFDVAKAFDTLNWDFL FT DRVLRAFGFHDTFVQWVRVILSSARLSILFNGSPVGFFGCSRGVRQGDPLS FT PLLFCLAEEVFSRGLVDLVNSGKVKPISSPRGVTAPSHILYADDIMVFCRG FT DKRSLMNLMHFIEEYGVNSGQRISKVKSRIYIGKSASVRRLRILSWLNVSE FT GELPFTYLGAPIFKGKPKRAYFQALADRIRSRLSQWQGHSLSMAGRVTLVK FT SVVVSMLSHTFSVYSWPPTVLNQVRSWTRNFIWTGCADSCGFSIVAWKKCC FT VPLNEGGLGIRNFSALNKAFLLKKFWDILVTSSMASRFFQGRFFNCLGQPC FT STYKSSSIWPGLRPLFSDIFHGSKWVIGNGQNINFWHARWLDFPIVDRLGI FT PPDLCKAFRAKVSDFIVDGCWIPPPTLHSWLAPIWDDISSIGLPSKYGIDD FT KMVWLSASNGDLSLSLAYDFKRNKQPVVQWDRWVWQSCFRPRNSVTLWKYL FT HGKMLTDDLLQRRGFAIASMCSLCCEGMETASHIFFECSFARQIWSTVLEL FT FRVQYLFQDIFSFFHYPLQQGFGTQVQLLWWGMIGVGFYSIWHARNAVRFH FT EEVVSINYVVRSIKCQLLEIDSLNSGCMKNYVEELCILHSIGVRGRPAKAP FT KIIEVLWRPPSQSWIKVNTDGAARGSPGVAAFGGIFRDFTGNSLGCFAGSI FT GLASSLDAELRAVIHAVSLAWDKGWHSLWIECDSSLVVHLLSSSSPSLTSI FT PWRLLVSWHNCRVLLSSMQVQISHIFREGNQVADCLANYGVDHPGVHWWDS FT CPPCAAAAYSHNLSKLPCYRFC" XX SQ Sequence 5985 BP; 1413 A; 1087 C; 1334 G; 2151 T; 0 other; gaaaaaatag cgctctgcta gggttttgcg gctgccacta tgacggctgc gccaaatctc 60 cactctggtc ctcgtttgcc tattgttcct tggagttttt taggcagcga tcccgatgtt 120 gccactgaga aacccgctcc ttccaagcaa tcgtttgccc agttgctcaa acaacctgtg 180 gtttctttat ctcaactccc cattccatgt gaaaagggtg gttatgtatc agtaaagatt 240 tctgaagatg ctttttccaa gggcttggat cgttgcaaac aatctttgat tggtcgtgtg 300 cttttaccta agggttctac accaattcaa atggttgatc ttagaaataa gcttgagacc 360 atatggggtt ttaaggcttg gcgtttaatc cctttgggga aaggtttttt ctctctgcgt 420 tttgaccacg tcgaggacat gagacgagtt tgggcagttg gtacactcaa tcttaatcct 480 ggattattta gaatttccca atggtcccca aatttctcac cctccaaaca gaagtcgacc 540 catgcgcaag tttggattcg tctatatgat ttgggattgg aatattggga acctcaaacc 600 ttaatggaaa tcgctcgagg agttggagta ccaatccaat tggacagggt gacagctttt 660 atgaattttg gtttgtatgc tagaatatta gtggatattg acctttctaa aaagcctccc 720 acttcactta tggttgaacg tgatagtgga gaggttttat ttgtggaaat aatatatgaa 780 aaacttcctg atttttgctc tgtttgtgga aatattgggc atctgcctgc tacttgtcgt 840 gttgctgcaa gggatattaa gcgtgggcat gtggttgaga aggaaggtgc aagatcatga 900 atagtgaagc gcaatgagaa caatcaggat aacattcgag ttgaaactga tatccgcaat 960 caaccggaag gtaaggttcg tgttaataat gtgtccaact cgagtgtgag aggtttggat 1020 gatggtgatg tttcgcccat acatgttgtg gatggtttag aaaataatgg gacaacctct 1080 gcatacgttt cagaaactcc aggttctcat gatcatgcat gcagttagtc aattggctaa 1140 ggctggtttg gttagtaaga actccctctc tagtgcgaga ggtttggatg atgcttctcc 1200 ctcacatttt gtggaaggtt tagttgatga taatgataca acttgtgacc atgtttctga 1260 tactccgatg gatactcccc ttataggtat tcagttaaac tcttctcttg tgctctctga 1320 gagatgtaat gctaatgact cagttcaagt tgtttctcaa gttcaagagg ctagtcctcc 1380 ttctttatct cctcaagttc gctctgaaat tcaaaaggtt aatgattggt acactatggt 1440 ggaggaagat gctcttcaaa ataatgttgc aggtagagaa aacaatgatt tagatggtgc 1500 aaataatgtt tctgaggatg acatgacttt ggttctctca aaatctcaaa gagaagatta 1560 cgaaaaaaaa aacaggaatc tggttatcat acctacgagc gtgagactat tcaaactcat 1620 gctagggttg ctgctatggc tccccatgat ccatgaagac catttattgg aatattcggg 1680 gcttagcaaa tcgccccact agacaagctt tacggagcct tgtcagaaaa cattctcctg 1740 attttctttg tttggcagaa cctatgactt ctacaatgaa aattcgtcca tttttttgga 1800 aatctattgg tatgcatttt ctgggagtaa atgatagagg tcagagattg cctaatattt 1860 gggtttttca cacagctaat gttttatctc ctacggtttt atctacttca agtcaacata 1920 ttactattca atttttagta gctggcactg cccactgtat tacttttgtt tatgctgcta 1980 caacagtggt ggaacgtcga ccactttggc tttctattgc tcaagtttgt gccggctttt 2040 caggtccttc acttattttg ggtgatttta atgcggttct tggcgcgcat gagaaaatgg 2100 ggggtatttt gcctcgtcga atagcatgtg aggagtttca agctatggtg gatacgtgtg 2160 gtttggttcc gattgatgtt aagggctccc ctttcacttg gactaatgga cgtggcatat 2220 catctcatat tgaaatgtta ttagatcggt gcttttgttc tactgcatgg ctggatgcct 2280 ggcctatcac caattgctcc acgttggttc gtcattcttc ggatcataat cctcttctag 2340 tttcttttca aaagtttgca gcacaaggtc ctactccttt tcgctttcat cgcatgtggt 2400 tagatcatcc tgattttatt aatttggtta aaaattcatg gcagtctatt caagtttatg 2460 gttgtcctat gtttattctt caacaaaagc tcaagttgct aaagcctatt ctaagacatt 2520 ggaatgctga tgtttttgga aatgtcaatg ttgccgtgga caatgctaga gaggctttag 2580 aaaaaattca gttagaaatc tccacagagg gttttactga tgaacgtcat ggggctgaat 2640 tacaagctca ttctactttg tctcatgcgc tgctagttca agaaaagttt tggcaggata 2700 aaacacgatc taaatggttg cgagatggag accgtaatac gagttatttt catactttgg 2760 caaaaattcg caggactcgt aattttattt cttctttgcg tattgattcg gaattggttg 2820 aggatgttga gattttgcgc aatcatgtgg tggagcattt ttttaatgct tttcatgatg 2880 atggtcttgc tattgacaca ggtttggtta ctcgtcttat tcctcctttg gttactacac 2940 ctgaaaatga tactttattg gctattccca cattggagga gattaaacaa actgtatttt 3000 ctatgaatcc ggatagtgct ccaggtccag atggttttgg tggttatttt ttccatgctt 3060 gctgggattt cgttggattt gaggtttctt tggctgtcca agatttcttc aagacaggtt 3120 atattttacc caatttgaat tctagttttg tggctctaat tcctaaagtc caagaggcag 3180 attctatctc tcaatttcgg ccgatagcca tggctaattt tatattcaaa gtcattacaa 3240 agattcttgc agataggctt gctcttgtgg ctactcgaat tattttgccg aatcaatacg 3300 catttcttaa gggcaggcat atttcagatt gcattttgtt ggcctcggag tgtgttaatt 3360 tattggacaa taagtgtttt gggggtaatg tcgctattaa gtttgatgtt gctaaagctt 3420 ttgatactct caattgggac tttctagatc gggtgcttag agcttttggt ttccatgaca 3480 cttttgttca atgggttcgt gtaatccttt cctcagcccg gctatctata ttattcaatg 3540 gttcacctgt tggatttttc ggatgtagta ggggtgttcg tcagggggat cctctatccc 3600 ctctcctttt ttgtcttgct gaagaggttt ttagtcgagg tctagtggat cttgtaaatt 3660 ctggaaaggt taaacccatt tcttcccctc ggggagtgac tgctccttct catattctct 3720 atgcggatga cataatggtt ttttgcagag gtgacaagcg cagccttatg aaccttatgc 3780 attttattga agaatatggt gtgaattctg gtcaacgtat tagtaaagtt aaatctcgta 3840 tttatattgg gaaatcggct tctgtgcgtc gtttgcgtat tttatcctgg ctcaatgtct 3900 ctgaaggtga gcttccattt acttatttgg gggctcctat ttttaaaggc aaacctaaga 3960 gggcatattt tcaagcatta gcagatagaa tacgttctcg tctttctcaa tggcaaggtc 4020 actctctctc aatggctggt cgagttactt tggtcaagtc agttgtggta agcatgttgt 4080 ctcatacttt ctcggtttat tcttggccac ctacggtatt aaatcaggtt cgtagttgga 4140 ctcgaaattt catttggacg ggatgtgctg attcttgtgg attttctatt gtggcatgga 4200 aaaaatgttg tgttccttta aatgaaggag gtcttggcat tcgtaatttt tcagctttaa 4260 ataaggcctt tttgttgaaa aagttttggg atattttggt tacctcatct atggcttcac 4320 ggttttttca aggtcggttt tttaattgtc ttggacagcc gtgttctaca tacaagagtt 4380 cctccatttg gcctggttta cgccctcttt tttcagatat ttttcatgga tcaaaatggg 4440 tgataggtaa tggtcaaaat attaattttt ggcatgcgag atggttagat tttccaatag 4500 ttgataggct tggtattcca ccagatttat gcaaggcttt tcgagctaaa gtttctgatt 4560 ttattgtgga tggttgttgg attcccccac ctactttaca ttcatggcta gcgcccattt 4620 gggatgatat ttcttctatt gggcttcctt caaagtatgg gattgatgac aaaatggttt 4680 ggttgtctgc ttcaaatggt gacctttctt tatctttggc ttatgatttt aagcgtaata 4740 aacaaccagt ggttcaatgg gatcgatggg tttggcaatc ttgctttcgc cctcgtaatt 4800 cggttacatt gtggaagtat ttacatggta agatgttaac tgatgatctc ttgcagcgaa 4860 gaggttttgc tatagcatct atgtgctctc tttgttgtga aggtatggaa actgcttcac 4920 atattttctt tgagtgctct tttgcacgtc aaatttggtc tactgttttg gaattattca 4980 gagttcaata tttatttcaa gatattttta gctttttcca ttatccttta caacaaggtt 5040 ttggtaccca agtgcaactg ctttggtggg gtatgattgg agttggtttt tattctattt 5100 ggcatgctcg caacgctgtt cgttttcatg aggaggttgt ttccatcaat tatgttgtaa 5160 ggtctattaa atgtcaactc cttgaaattg attctctcaa ttccggctgt atgaagaatt 5220 atgtggaaga gctttgcatt cttcattcta ttggtgttcg tggacgtcct gctaaggctc 5280 caaaaattat tgaggtgttg tggcgcccgc cttctcagtc ttggatcaaa gtgaatactg 5340 atggtgctgc aagaggttcc cctggtgtgg ctgcatttgg tggtatcttt cgggatttta 5400 cgggtaattc tcttggttgt tttgcgggtt caataggctt ggcctcttct ttggatgccg 5460 aactacgcgc tgttattcat gctgtatctt tagcttggga taaaggttgg cattccttat 5520 ggattgaatg tgactcctca ctggttgttc atcttctttc ttcatcctca ccttccttga 5580 catctatccc ttggaggctt ttggtcagtt ggcataactg tcgagtttta ctatcctcca 5640 tgcaggttca gatttctcat atttttagag agggtaatca agttgctgat tgtttggcca 5700 attatggtgt tgatcacccc ggtgtccatt ggtgggattc atgccctcct tgtgctgcag 5760 ctgcttattc tcacaacctt tctaagcttc cttgttatag gttttgctga aagaggtttt 5820 gaattgttgt tatgaattct ttaatggtct gggtttggcc tcatgtccct cctgacatat 5880 tgtatttttc ttgtttatca ataaattctc ctcaaagtct cttcccatga tagcaatgct 5940 ggagtgggac ggactttgcg gccaaattaa aaaaataaaa aaaaa 5985 // ID DNA9-17_Mad repbase; DNA; EDCOT; 1073 BP. XX AC . XX DT 27-OCT-2010 (Rel. 15.11, Created) DT 27-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-17_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1073 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1857-1857 (2010). XX DR [2] (Consensus) XX CC TSD is 9-bp long. Imperfect TIR is ~71-bp long: Pos 8-81 and CC 992-1065. XX SQ Sequence 1073 BP; 459 A; 144 C; 123 G; 347 T; 0 other; gagaaaatta gaattagatg cctcatttta gacttttgta gactaaacat ttatgctttt 60 tgagtttttg attaagcttt tgaaacattt gattaagata ctcagacttg aactacttca 120 gattaattga aattaattta catttaaata tctgctatat attttaaata atttcaacta 180 tatttaagtc taaaaattta aacttttcaa atctaaatgt acacccacgc caaatggaaa 240 cataccaaca ttaaatgaaa atgtaccaac gtcaaacgaa aacgtaccaa ccccgaatta 300 aaatgtaccc aattataaac tatattaaaa tgaatattca tctttttgga atgtttaaaa 360 atatgtttga ttcatacaca atgctctaga tagtcttgtt ttttggtaga taagtctctg 420 gaacaacttt tagttgatca gagataaatc cttattattg tagataatgc taaataataa 480 cgataaatca tataattttg aattaacaaa aaggttatta tccgttgatt aatgactctt 540 tctagaaaaa taaaattaat taaagtaatt taaactttta cattgttaac gactctttct 600 ataaaaaaaa ttaattaaag taattcctca ttattaggac aaaaagtaat aaaacttatg 660 ttttgaaaac aaacgtacca aaaattcaaa tgtaccaaaa actaaatgta ccaaaaattc 720 aaatgtacca agaagccaaa tggaccaaaa attcaaatgt accaagtaac taaatgtacc 780 attataatca aacgtaccga tataatcaaa cgtacctaac aacgagtttt gttacattct 840 atttaattta ctaaaataaa tattttaata aaaaatataa aaaaatctta aatcatcata 900 ataagagatg cataaaaata ggaggaaaaa agggaatgct aacgtgaata gacttctaat 960 gaaataaaat taaagtacca aaattgtagg gaaaatgttt aatcaaattt gcaaaaggaa 1020 tagatgttta gtctatgaca tttaaaaacg aggcgtctaa ttcaaaacgt ccc 1073 // ID TE-4_Mad repbase; DNA; EDCOT; 621 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative transposons from the apple genome. XX KW Transposable Element; Nonautonomous; TE-4_Mad. XX NM TE-4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-621 RA Kojima K.K. and Jurka J.; RT "Putative transposons from the apple genome."; RL Repbase Reports 10(10), 1829-1829 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >83% identical to the consensus. XX SQ Sequence 621 BP; 169 A; 115 C; 173 G; 162 T; 2 other; tgttggaacc aaattcgcgc acatccgcgg acggaggcga aatccagtcg gaattgccca 60 tgatctccgg cgaggggaga atggggttga ttgggggtgt ggttgaatcc ggatcggact 120 gcctacatat ctccgggaag gagaatcaaa ccacnggtgt agttctaaga aagaatggtg 180 tgatgtgcaa tacatcgtga accatccttg acgaatagcc tatggcgggg cgttaaggag 240 atgagttctc catggacgtg tctacgcgta gacggcggcg tgtatgcaag atgagcctnt 300 gttaggcgta gagagaatat aagagagatg tatcttcagt tgtgattgat tgattcattc 360 agagataaat gcccaggcta gagtatttat agagatcttg agagtccttg tagggaaagt 420 aatcccaatt aaatcgggag actatctagg agggaatcta ggataagata tccaatcctc 480 ctaggattat gattacgttg cctaatcccc aagatatcct aatttgactt gaattagggt 540 ttccttactt gggagacaag taatatcttc aatgggctta agcctagcct gtcggactaa 600 ggctgtcgga ctacgcttcg t 621 // ID Gypsy-28_Mad-LTR repbase; DNA; EDCOT; 1808 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-28_Mad_; KW Gypsy-28_Mad-LTR; Gypsy-28_Mad-I. XX NM Gypsy-28_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1808 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1751-1751 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 1808 BP; 514 A; 279 C; 453 G; 560 T; 2 other; tgttgtttgt aagaaagaaa gatggaactt tgagattgtg cattgattac aggcaattga 60 atcgggtgac gattaaaaac cgttatccct tgcctcgtat agatgatttg tttgatcagc 120 tcaaaggtgc ctgtgtgttt tctaagatcg atttgaggtc tgggtattat caattaaaga 180 ttaaagatga ggatgttcat aaaacagctt tcaggactcg ttatgggcat tatgagtttt 240 tggtgatgcc atttggattg acgaacgctc ctgcagcttt catgagattg atgaatgaag 300 tattccagga atatcttgac aggtttgtta ttgtttttat tgatgacatc ctggtatatt 360 ctaagtcgaa atcagaccat attcgacatc ttaacttggt gttaaggaaa ttgagggaac 420 accggttata tgccaagttt agtaaatgtc aattttggct ggatcaagtg gcatttttgg 480 gacatgtggt atcagctcag ggaattcaag tggatcctca aaagatagca gcagtggaaa 540 gttgggaaca acctcgaacs gtcactgagg tgcggagttt tcttggtttg gcaggttatt 600 atagacggtt tgttcaagac ttttctatga ttgccttgcc attaacgaag ttaaccagga 660 aggatgttaa gtttgagtgg gatgaaagtt gtgagcaaag tttccagcag ttgaagtatt 720 gccttactca tgcacctgtg ttagtacttc ctgatgataa tggtaacttc gagatctaca 780 gtgatgcttc tttgaatggt ttgggttgtg ttttgatgca gcatagtaga gtgattgcct 840 atgcttctag gcagttgaag actcatgaaa gaaactatcc gactcacgat cttgagttgg 900 cagctattgt gtttgctttg aagatttgga gacactatct ctatggcgag aaatgtaaga 960 tctttaccga tcataaaagc cttcagtacc ttttcactca gcatgatctt aatcttcgtc 1020 agagaagatg gttggaattg ttaagtgatt atgattgcac gattgagtac catccgggtc 1080 gtgcaaatgt ggtagctgat gctctgagta ggaaacctca agggcgactt aatgctttgt 1140 atgccagtcg tgttcctctt ctggcagagt tgagatctac tggagtagag ttagaatkgg 1200 aagagcaaag tgaagctttt cttgccaatt ttcaagtcaa gccaatttta attgatcggg 1260 tgcttgcagc tcaatcgttg gatgaagaaa ttcaagaatt gatcagttta agaaatgaag 1320 ggaagaagaa agatctcaag atccgaggat cagatggtat gcttatgcaa gagaacagga 1380 tgtatgtgcc taataatgag gaactgaaga aagaaatctt ggatgaagca cattgttcgg 1440 cttatgctat gcacccagga ggaactaaaa tgtatcatac cattcgacca ttctactatt 1500 ggccgggtat gaagagggag attgcggagt atgtaagtag gtgtattgtt tgccagcagg 1560 ttaaggctga aagaaagaag ccgtttggga gattgcaacc acttcccgtt ccccagtgga 1620 aatgggagaa tataacgatg gattttgtgt ataagctgcc acgtacacaa aatggttttg 1680 atggcatttg ggtggttgta gatcgactta ccaaatcagc acattttatt ccagtaaggg 1740 agaagtaccc tttaaataag ttggctcagt tattcatatc gaaggttgta aagtatcatg 1800 gtgtccca 1808 // ID Copia-9_TC-I repbase; DNA; EDCOT; 4791 BP. XX AC CACC01005488; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-9_TC_; KW Copia-9_TC-LTR; Copia-9_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-4791 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01005488; Positions 13303 18093. XX CC Positions [2049-2546] - Integrase core CC LTRs are 96% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS 2184..3683 FT /product="Copia-9_TC-I_1p" FT /translation="MKYKYDVSSIIPAFQNFVKNQFQTSIKIIRSDNGLEF FT KLPDFYAKTGIIHHLSCNENPEQNGLVERKHQHILTVARSLLHQSHLPMSF FT WGDFVMKAVHFINRIPTRLLSNKTPFELLYHALPTYDHFRVFGYLCFASTL FT SQHRKKFDKRASKCVFLRYPNGVKWYKVYDIDAHKVLVSMNVVFHENVFPF FT SLSKGYSSDVPTFYQTPGVLASIFDHFQVSSNVLPNYDPPLVSCQSGEHDI FT YLENHFSSNSIDSTQNFPIDSTDHVPNFSNHVTPSSVSVQPDVNSLPRRSY FT RARHVPKYLEAYHIDIPSSSNNVTSYPITDYLSAYKLSSTHESFTLALSQI FT HEPTSYHQAIQHSHWKDAMALELQALEDNKTWSVVPLPSHCHTIGCKWVYK FT VKMKANGNVERYKARLVAKGYSQVEGFDYQETFNPVAKQTTVRIFLAIAAA FT QGWCLRQLDINNVFLHGDLEEEVYMEIPPGYIVQGEYSSDTKLACKLHKSL FT YGLK" XX SQ Sequence 4791 BP; 1504 A; 790 C; 855 G; 1642 T; 0 other; tggtatcaaa gcgggtaatc ttgctatgaa tgtttttctt gatttaggca agtattttct 60 tcttcttgct ttttgaatca gtacaaattt gttgtttgag ttcttaattt tttttttggg 120 aatttcttgt ttcttgagat tttggtacaa atgacaaaca ctagaacaaa tttctcttct 180 tcatttgaag atttgcaaat ggcaaatcaa ttaggctcga agactagtgt ttcaccaacc 240 gagaaccctt aatcaccgtt ttatctacat catagtgatc atcctggatt actagtgata 300 aaccctaagc tgacaacaaa taattatgtg ccatggtgta gatcattcct acttgctctc 360 tctgttagga ataaagttgg atttgttaat ggaaatatcc ttaaaccaga acctgtggat 420 cctctgtttg agtcatggaa taggtgtaat gacttgattg tggcttggtt gttagactct 480 gtaacagcac atatagcctc aacaattttc tatatggata atgcgatgaa aatttggaat 540 acactgaaac agaactttgc acagctagac gatactaggg tgtgtaactt acagtacact 600 ttaggcaata taacaaaagg aagtaggtct gtggatattt acttcattga gctgaagggt 660 gtttaggaag aaatgaggaa ttttagacca ttaccacgtt gcgaatgtgg taagtgcaac 720 ccaaattgtt tcaagaaata cactgaacag taccagaaag acatgacatt caggtttttg 780 aatggtttaa atgattcatt ttctgggatc aggtctcaaa tcatattaat ggatccaata 840 ccttccttgg ataaggtcta tagcttggtg ttaagagagg aaactcaaag gaatttactg 900 atacaagggc agtcagttct ggaatctaca gcagccatag ccactatttt taaaggaaag 960 aggaaattaa aaagtgatgt catttgttct cactgtaaca aaaaaggcca tgtcaaggaa 1020 aggtgtttta gattgatagg ttttccaaat gattttaaat ttacaaaagg aaaaagatgt 1080 ggattcaaga aaggaaaatc tattgtgaat caagtttctg ctggtaataa tgttgatgca 1140 gaatacttgc agcaaaatca tgaagatggc attgaagttc ttgattttga ctcacagttg 1200 tttatgataa aacaacaaat tcataagctg gtggatcttc tcaatgggag tggtatgaat 1260 gtcaataatg ataaaagtcc ttcatcaatt ccttcttcaa gcaaccacca agcaaaacat 1320 tctttgatca actcatcttt tgcaggtatc atatctggaa tttcatgttt taatactgta 1380 aataaccttc ctactagata taaaaatgtg aatcctttca tgattaaata aagttcctgg 1440 atcatagaca taggggcaac agatcatatg tgttgtactt tagataaatt catttctatc 1500 aagcttgttg ttaatagata tgttcagctc gcaaacaata ctagagccat tgtttctcac 1560 attggcatag ttaaaataac ttctttgctt accttgtcaa atgtgttgta tgttcccagt 1620 ttcaaattta acttgatatc agtttctcag ctcattgatt ctacatcaaa ttctgtgttt 1680 ttcactgata aagtttgcat tattcaggac cttacctcat ggacaatgac tggtgtagct 1740 agagtttact caggccttta tctcatgcaa gatagcaagg atgaaaagga tttatcaaag 1800 ttcaatctga aaaaacttgt tgatttttca attgtatctt cttttacttc ttgtaactct 1860 ttttcaaaca agccttgtgc ttcagctcca agatcttttg acctatggca ttttagatta 1920 gaacatcctc ctatagaaat gatacgtgtg ttaaataaac aagttccaaa tattcactgt 1980 tcaaatgatt tgctttgtga aatatgtccc cttgctaaac agaaaaaaaa ctttcatttt 2040 ctattcatat tcaaagttca aagaatgctt ttgatcttat acatgttgac atatggggac 2100 cttatgaaat acctacattg tctggtcaac gatattttct cactgtagtt gatgatttta 2160 ctcgtttcac ttgggttttc ttgatgaaat ataaatatga tgtatcaagc atcattcctg 2220 cttttcaaaa ttttgttaaa aatcagtttc aaacatcaat caaaattata agatcagata 2280 atggattaga gtttaaacta cctgatttct atgcaaaaac aggtattatt catcatttgt 2340 cttgtaatga aaatcctgaa caaaatggtt tggtggaaag aaaacatcaa cacattttga 2400 cagtagctag gtccttgttg catcagtcac atctacctat gtcattttgg ggtgattttg 2460 ttatgaaagc agttcatttt attaatcgaa tacctactag acttctctcc aataaaacac 2520 catttgagtt attgtatcat gctttaccta cctatgatca ttttagagtt tttggctact 2580 tgtgttttgc atccacttta tctcaacaca gaaagaaatt tgataaaaga gctagtaaat 2640 gtgtgttttt gagatatcca aatggtgtta aatggtacaa agtttatgat attgatgctc 2700 ataaagtgtt agtgtccatg aatgttgttt ttcatgaaaa tgtttttcct ttttctttgt 2760 ccaaaggtta tagcagtgat gttcctacat tttatcaaac acctggtgta cttgcttcta 2820 tatttgatca tttccaagtt agttctaatg ttttgcctaa ttatgaccct ccacttgtta 2880 gttgtcagtc aggtgagcat gacatttatt tagaaaatca tttctcatca aattccattg 2940 attccactca aaattttcct attgactcta ctgatcatgt tccaaatttc agtaaccatg 3000 ttacacctag ttctgtgtct gttcaacctg atgtcaattc tttacctagg agaagttatc 3060 gagccagaca tgttcctaaa tatttggaag cctaccatat tgatattcct tcaagctcga 3120 acaatgtaac ctcatatcct ataacagatt acttgtctgc ttataaactg tcttcaactc 3180 atgagtcctt taccttggcc ttatctcaaa ttcatgaacc tacttcctat catcaagcta 3240 ttcaacattc tcattggaaa gatgcaatgg cacttgaatt gcaagcctta gaagacaaca 3300 aaacatggtc tgtagtaccc ttgccttcac attgtcacac tataggctgt aaatgggtat 3360 acaaggtgaa gatgaaagct aatggtaatg tggaaagata taaagcacgt ttagtagcaa 3420 aaggttacag ccaagttgaa ggttttgatt accaagaaac gtttaaccct gttgctaagc 3480 aaactacagt tagaattttt ctagctattg cagcagcaca agggtggtgt ttaaggcagc 3540 ttgacataaa taatgttttt cttcatggtg accttgagga ggaagtttat atggagattc 3600 caccaggtta tatagttcag ggggagtatt catctgatac aaaacttgct tgcaagcttc 3660 acaagtcttt atatgggcta aaataagctt ctaggcaatg gaatgcaaag tttacaactt 3720 ctctcatcag gtatggtttt aagcaatctt tgtcagacta ttctttattt actatgtcta 3780 ctggagatgg aaattttgct gcattgctgg tgtatgtaga cgatattgtg attggtagta 3840 catctgatca gttagttgac aacattaaag agtacttaag tacacaattc aagttaaaag 3900 atttaggtat agttaagtat ttcttggggt tggaaattgc tagatctcct gaaagaatat 3960 ctgtttgtca acgcaagtat gttttggata tgcttgaaga atatagtcta ctaggtgcta 4020 aaccagtgtc aacccctatg gattataatt acaagttgca gaaatccact aaagattacc 4080 gattgaaaga tcttactatt tacagacaat tggttggaaa gttattgtat ttgacattta 4140 caaggccaga tgtttgttat gctgttcaag tgttatctca atttatggac aaaccttcaa 4200 atgatcattt agctacagca ttcagagttt taagatactt gaaaggggca ccaggacaag 4260 gacttctact gcattcacag tcaaacttgc aaattcaagc ttattctgat agtgattggg 4320 caagttgtcc aaatactaga aaatctgtca ctggatatgc tttatttctt gaaaactcaa 4380 tggttagttg gaaggctaaa aagcaatctg tagttgctag aagttcagtt gaggctgaat 4440 atcgttccat ggcaacaaca tcttgtgaga taatatggtt gaaatccttg ttggcagagt 4500 ttggaatttg tcagacaaat gctattaaac tgtactgtga caatcaattt gccatttaca 4560 ttagcaagaa tcctatgttt cattaacgta caaaacacat tgagctcgat tgtcacttca 4620 ttagagaaaa ataattacag gtttaataga accagtatat atctcaacag cagatcaagt 4680 tgcagatata ttcacaaagg ctttacagcc taaggatttc tacagattac ttagcaagat 4740 gaatgtgtat gatatacaca gttcatcttg agggggagta ttagacttac t 4791 // ID LTR-8_Mad repbase; DNA; EDCOT; 2322 BP. XX AC . XX DT 15-OCT-2010 (Rel. 15.1, Created) DT 15-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR-8_Mad. XX NM LTR-8_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2322 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1792-1792 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 2322 BP; 532 A; 476 C; 565 G; 748 T; 1 other; tgtcacagcc cgtcccgaat gatattattt tatctcgatg gcgtggaaat gctaatttac 60 ccttggacgt tgagtacgtt atgtggtgtg tgtggtttga gtttgggttg tggaccaatt 120 tagttagttc ctaagttttt ggacccactt agagttaagt tttagttgtt tttggttggt 180 gacccaaagc tggaccacac actcacacac acacaccact cccgttgacc cttctctctc 240 ctccctctct cggattttct tccatttccg tacaactgta cggacaaccc tcaaaaccct 300 ttcagtcacg gatcgaggtt gtggagccgt ctttgtgctc cttgcaagct caggagctca 360 tctataccgt tggttggacg tgaaaccctc gaaaacccga gaacccagga accccgattt 420 tgagtactgt tcatgcagtc gtgatcgtgg acttttcagc gagttttaag gttctaggaa 480 gctttagaac atcttcacga agctcgggga agaaagttgg agtgttttgg acgtcgggaa 540 gctcagtttg gcgagtttca aattttggcc ggattatcga ggtttctccg gcgagattcc 600 gtggatttta gggcttaaaa ktggtaaggt tttgttctac tcgtcgtaag cttcattttg 660 gtacaaattt catgaatttt ggttgagaaa tgaagaagat attgaagttt taagattttt 720 ccagtttccg gcgatcgcag cggcgaccgg cgccggactc cggcgaacca aggaagaagg 780 aggagaatat tccgtcaaag ttgacggaat attctaacgc cgtcaggtaa ctttaacggc 840 atatgctgtt tttaacggaa tattccctaa cgccgttagg gaatccgttt ggtgtgccag 900 gcacgtgcct gcgcgtgagc cgcgcgtctg gccgtgcctt ggccggcgcg tgagggcgcg 960 tgggtgctcg gaaatttttt ctaaaaatat ggggatgttc ctgaggttga gtaggtcatg 1020 gtggtatatt caaatacccc atttgagcaa tgtatgagaa gttatttcct agttttgtgt 1080 atgtgcttta aataacgttt atttagttat ttcgcatata ggtgagacct atcctgagga 1140 cgagcgccat caatcgaggc tcgggggcta cgacccttcg acataccagt gagtgggctt 1200 ttggttttcc gtatatacct atatacttga gatttttccc agaaaatgaa tttgaatgat 1260 tatacgtttt gaaatgccat gcaaagtatc tgcctatttt atttatgcat tagtagttgc 1320 atatatttat gattggtgct gcggacgcac aggtaagtgc caggtaagtt cataaattaa 1380 agatatgaga ttgcttcagt tatgcgagat atgatgtgat gtattgagag ctcataaacc 1440 tgcaccccgg tgttagtgct cccgcccaga gttagggcac agtccttcac gtgatgttca 1500 cctcccgcac catatgctca ccttggatcc aagttaggtg cacaggcttg tcgtacagac 1560 cactttaggt ggttccgact cgtaggtgac ccgcgatcat tcgcacagtc ttcacgtgat 1620 cgtagcacta gagcatattt attttacacc tagtcttgtc gtacagacca ctttaggtgg 1680 ttccgactcg tgtgcaggat ttgatatgat tgagattggt tatgagctat agactcagcc 1740 gtgcaggtca cgttaggtgg atccggctga tatgatatct ggcattgata tattttaact 1800 ggattactta tggcatttca ttgagatact ttggcatggt atatttctat ggattttcat 1860 cctgagcatg atttctgata tagcatatat tattttctgg gaaattatac aggttttacg 1920 gcgaggggtt agaacttttg agaaatgaaa tgattttgaa aagctttgtt tttgcccact 1980 cacactttct gttttgcgcc cctccaggtt ttaggtagaa gtgctttggt ggctcacggg 2040 gatttcgacg gtggttctga cagaacatca caaatgtagg atcacctttg ggtgttgtat 2100 aattagtact tgtccagccg gactgcactt aggctattta tgctctgatt gtgtatttca 2160 cacttaatct cgcactagca ccttatctta gctagtactg ctggtagttt ggtttttatt 2220 cattcgtatt tccctatatc tttattgctt ccgcactgtg cacatggcta cgtcaccctc 2280 acgtgacggc cagcatgccc tgatttaggt cggggtgtgt ca 2322 // ID MUDRB_PT repbase; DNA; EDCOT; 4581 BP. XX AC AF506028; XX DT 29-MAY-2006 (Rel. 11.05, Created) DT 13-JUN-2006 (Rel. 11.05, Last updated, Version 1) XX DE MuDR-type element from Poncirus trifoliata. XX KW MuDR; DNA transposon; Transposable Element; MUDRB_PT. XX OS Citrus trifoliata OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Sapindales; Rutaceae; Citrus. XX RN [1] RP 1-4581 RA Yang Z.N., Ye X.R., Choi S., Molina J., Moonan F., Wing R.A., RA Roose M.L. and Mirkov T.E.; RT "Construction of a 1.2-Mb contig including the citrus tristeza RT virus resistance gene locus using a bacterial artificial RT chromosome library of Poncirus trifoliata (L.) Raf."; RL Genome 44(3), 382-393 (2001). XX RN [2] RP 1-4581 RA Yang Z.N., Ye X.R., Molina J., Roose M.L. and Mirkov T.E.; RT "Sequence analysis of a 282-kilobase region surrounding the RT citrus Tristeza virus resistance gene (Ctv) locus in Poncirus RT trifoliata L. Raf."; RL Plant Physiol 131(2), 482-492 (2003). XX DR EMBL/GenBank/DDBJ; AF506028; Positions 201351 205931. XX FH Key Location/Qualifiers FT CDS 786..2639 FT /product="MUDRB_PT_1p" FT /translation="MSQISILVRFLGKDVEDAYDPDCLSLVSLINDVLNNV FT FGRHKHYDESFKLTGIVPWSNEGIELNNDKDFQNLVNLIQAKGLNSINLEM FT DALSLASLSPVLAQTCPEDNHFASNAVNVDILDGESDDAISVESIDWSDED FT IGDIVKSDSEPEVDLGFDINEFDGDDGMSDCESDNEDVSIASDEEDDAVIL FT KMTRDLRKKRFKKPDGDDDIVLEVGQTFSCAQEFKNVLKDYDIQESRVLKR FT KKNDKCRVTAVCAGKDKEGKECPWRTHASLLVDKVTFQIKTLKGGEHKCKE FT LFKNPEVTSRWIAQKLYGFISFNPDIGCESMSDELRKRFSCSTTKKRLYMA FT KKRVLKIADSDYTKSYAKLHDYANVLLIKNKRAMVKIQYETQGVETYFKRI FT FISFDALQNGFIRGCRRFIGVDGCHLKTSFGGILLTAVTLDANNGIFPLAV FT CICEVECKDSWKWFLELLKEHLGIVNEMALTIMSDRQKGLIQAIDEVLPGC FT TTRHCARYIYANFRKEHSAEELRGMFWKAVRATNKVDFEKEMKKIKEFKKE FT AYEWLMHNEPETWACHTFDPFFKIDHVTNNMSESWNSLLNEYRKKPILQLL FT EFIRLKIMKRLIRRREKAAL" XX SQ Sequence 4581 BP; 1548 A; 608 C; 884 G; 1541 T; 0 other; gggtaaaagc ccatttagtc cctatatttt aagattagtg tccgtttagt ccctgtattt 60 ttaaaaatgc ctcaaaacac cctcggcatc acctccgtta ctgttaattc tagattcatg 120 agggtaaaaa tgtatttttc ttagtaaaat ttaaaatttt aaaaaattat tacgataacc 180 tagatccata gtggcaaaaa cgtattttaa ccctaatatt ctttaaaacc ctcgctttaa 240 gaacttaagt gacttgcttt tttaaaactc ataacaattt tcttgctata aaattttttc 300 tattggaaac gtagtcttgc agcagatgtc aaaaccgaca acgaaggaaa ttggcctatt 360 ctggtacgtc tcacgttggt cttgtttatt tatttatttt tttaatcttc catgtgttca 420 gtgaaaagaa attatttttc ttttcacttg aatgggtatt tcttcccaag actaaaattc 480 cataagaagt agactaacag ttgaacgatt tttgttttac agtaaactaa aagttgaaca 540 ggttttattt tctttctttt tttttaaccc tttcatggtt gtttcgtagc ttaatattgg 600 tagtggaatg gatttgtaat tgaaaagaaa ttattttaac ttcacttgat tgagtatttt 660 tttgtaaaaa aaaaaatcat aatcatataa agttctataa tgtcgatttt gtattttatg 720 aattcgtatg taatagtttt aagtttctga taattttttg ttcatcttta tgttggtaga 780 ttcaaatgag tcaaatcagc attttagttc gatttttagg caaagatgtg gaggatgctt 840 atgatcctga ttgcttgagt cttgtatccc tcatcaacga tgtcttgaat aatgtctttg 900 gaaggcacaa gcattatgat gagagcttta agcttactgg cattgtccca tggtccaatg 960 aagggattga attgaacaat gataaagact tccagaattt ggttaactta attcaagcca 1020 agggtcttaa ttctattaat ttggagatgg atgcgttatc cttggccagc ttgtcacccg 1080 ttttagctca aacttgccct gaagataatc attttgcctc aaatgcagtt aatgttgata 1140 ttttagatgg tgaaagtgat gatgcaatca gtgttgagtc tattgactgg tctgatgaag 1200 atattggtga tattgttaag tctgatagtg aacctgaagt tgatttaggg tttgatatta 1260 atgaatttga tggggatgat ggcatgtcag attgtgagag tgataatgaa gatgtatcta 1320 ttgcaagtga tgaagaagat gacgctgtaa tattgaagat gacaagggat ttaagaaaaa 1380 aaaggttcaa gaaacccgat ggtgatgatg atattgtttt ggaagttggg caaactttta 1440 gttgtgctca agagtttaag aatgtattga aggattatga tattcaagag tcaagagttt 1500 tgaaaaggaa aaagaatgac aaatgtagag ttacagccgt gtgtgctggg aaggacaaag 1560 aaggaaagga atgtccatgg agaacccatg catctttatt ggttgacaaa gttacattcc 1620 agattaaaac tttaaaaggt ggtgaacata agtgcaaaga gctgtttaag aatcctgaag 1680 taactagtag atggatagct cagaaattgt atggttttat tagttttaat cctgatatcg 1740 gttgtgaatc catgtcagat gaattgagga agaggttttc ttgttcaact acaaagaaaa 1800 ggttgtatat ggccaaaaaa agggttctaa aaattgctga tagtgactac acaaaatctt 1860 atgcaaagtt acatgactat gccaacgttc ttcttataaa gaataaaagg gcaatggtga 1920 aaattcaata tgaaacacaa ggtgtagaga cgtacttcaa gaggatattc ataagttttg 1980 acgcactaca aaatggattt atacgtggat gtagaaggtt cattggagtt gatggctgcc 2040 accttaagac atcatttggt ggtatcttgc tgacagccgt tacacttgat gccaataatg 2100 gcatattccc attggcagtt tgcatttgtg aggttgagtg caaggacagt tggaaatggt 2160 ttcttgaatt gttgaaggaa catcttggta tagtgaatga gatggctctt actataatgt 2220 ccgacagaca aaagggttta attcaggcaa ttgatgaagt tttgcctggg tgtaccacaa 2280 gacattgtgc aagatatatt tatgcgaatt tcaggaagga acactctgct gaggagttaa 2340 gaggaatgtt ttggaaggct gtgagagcaa caaacaaagt ggattttgag aaggaaatga 2400 aaaaaattaa agaattcaag aaagaggctt atgaatggtt gatgcataat gaaccagaaa 2460 cttgggcatg tcatactttt gatccctttt tcaagattga tcatgttact aataatatgt 2520 cagagagttg gaattctcta ctcaatgagt acaggaaaaa accaatcctt caattgcttg 2580 aatttataag attgaagatt atgaaaaggc tcattcgaag aagagaaaag gcagcgttgt 2640 gatattctga tttgcctcca agagtgcata gaaaattgac aaaaatatcg aaggctttaa 2700 ggaaattgat tgttgtgaaa gccagtaaag ctcagtatga ggtgttggaa tttatagatg 2760 atgaagagag acattatgtg gttgatttga agaaatttga atgtgattgt ggggcctggc 2820 aaattagtgg catgccttgc aagcatgcaa tggcatgcat ttcacgtaat agtcttgaac 2880 caatcgactt tattgatgag agtctgaaaa aagatgctta tttaaggact tactctgaga 2940 ccatatgccc aataccggac caatgtaatt ggccttcagt tgacaagcct atcctattgc 3000 ctccagtaaa atatgttaaa attggcaggc ctaagcataa caggaaaaga gaaagaaatg 3060 aaggaccagc tcgcaagaaa aggtacactt tgacatgcag ccagtgcaat aaacttggac 3120 acaataagag aagttgtcca ttgaataaag aggtacttaa tatgatttaa aatgtgttct 3180 catattgatt caggtcaata aatgttggga catgggttgc taacattata ttttcatttt 3240 gatgcagaat acaattacta attcatcttc cagcacaacc tatccatcag gtcattatga 3300 tttaattaat cttttaaatg tttatttagt agttagtagt tttgattagg ttattttaat 3360 ttggaggttg aaagttttag gtatatgttg ttgtacatgt ttttgtacgt aatttttaac 3420 agatgaaaat aaaattaatg tatgaaacaa attaataaat aaaataaaat ttaatataac 3480 tttttttaac ttcagcaagg taattgagtg gaggtgaaat ccaatctgga cctagtggaa 3540 gtcaaccgaa tgctaagaga caaaaacatc aaaaaaccaa tgtcggttca tcccctggca 3600 tagccaaaca agcaggtctt taaactattt tcatttttat ttttagattt actagtataa 3660 caatatgctc atccttttat ttattttttc tattatttca gcaacaattt caacaagata 3720 tatacaaagt caaccaaatc ctatgagaca aaagcaaaaa ggaaaaataa gggtttctct 3780 aacacaaccc tctcaaacct aaatgtgaac aacattatag aagtaaataa aaggtatgtt 3840 atatcttaaa ttccttgcga aatacacaca atattaattg aacttattta cttaaaacag 3900 cagcaatggt gatgcagctt tgatcaacga ttgtttattt gcttctgggg agcagtttga 3960 ctggaagtat ttcaagtttg actggaagta ttccaaaact ataaagccaa acataatcca 4020 cctgtcttcg tttattggtc tcttttattt tgtgctggtt gtagcattat tgatagttta 4080 ccgatggtga catttttttt ttaacttcta attgtaggta cttttttttt aatgatattt 4140 aatcaatggt tgtatcaaac ttatcattga ctttatttat caattgccaa tatatttatc 4200 ttttagcacc tcaataaata aagtttagac atgagaagtt tgaatgatga aaaactcaat 4260 cttgtgttga aaatttgaaa tttaattgtc caaaattgta tgcaaactat caagtgtgca 4320 aatggtgttt gcaaaaaaaa aaaattaata taatttttta aattttttag ggttaaattg 4380 gtaatttaat tattattttt tattaatatc taaaaaaatt attataaaag ggtaatattg 4440 taaaaataaa ccaaaataaa tgaaagataa cggtaggggt atcaatactt taacggtagg 4500 gatgttttga ggcattttta aaaatatagg gaccaaatgg atactaagct taaactatag 4560 ggactaaatg agcttttacc c 4581 // ID DNA3-11_Mad repbase; DNA; EDCOT; 861 BP. XX AC . XX DT 22-OCT-2010 (Rel. 15.11, Created) DT 22-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE Non-autonomous DNA transposon from apple. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA3-11_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-861 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1849-1849 (2010). XX DR [2] (Consensus) XX CC TSD is 3-bp long. XX SQ Sequence 861 BP; 215 A; 86 C; 292 G; 268 T; 0 other; gggccagttt gggattgctg tgctttttta aaaaaaactg cttctgttgt gctttaagaa 60 taatcagctg taaaataaag cagttgagcg tttgataaac tgtattttta aaagtgttgt 120 gagtatgaaa agcagtgtaa aagcgtttgg taaattttaa tgtaaaagtg atataattgt 180 atacaatgac aaaaatggac atggtagtgg gggtggtgac aacgacaatg gtggcaaggg 240 caatggtggt gatggtggtg gtggtgccaa tagggggtgt ggtggttggg ctgcagaggt 300 aacaatggtg gtaggggcgg cgacaacggc gatggtggcg gttgtggtgg tggtggtggt 360 ggtgcggttg tggttatggt ggcggtggtg gcggtggtgg ggtggtggtg gcaacgatgg 420 tggtggcagt tgtggtgtgg tggtagtggc ggtggtgatg gttgtggtgg tggtggtggt 480 ggtggtggcg gattgtggtg gtggtggtgg tggcaacaat ggtggtggta atggcaatgg 540 tgtagaggtt agtgtttgta gtggtaggtg gtggtggtca ctttgttctc caaggataaa 600 atgtgtgtgg aaggataaat aatgtcattt ttaaaaatta atgagggtat tacaggaatt 660 gaaaatattc attaaaggct caactccgct ttttattaaa gcagctttta aaagcaacct 720 acatgctgct tttaaaagct gttgtctgga ggccattgct tttaaaataa gcaggatatt 780 ttatttttac caaacacttt tttattgctt aactttaaag tgaagcagtt tttggtgaaa 840 aaaacaatac caaacggggc c 861 // ID VIHAT1 repbase; DNA; EDCOT; 5547 BP. XX AC AM444020; XX DT 28-MAR-2007 (Rel. 12.03, Created) DT 28-MAR-2007 (Rel. 12.03, Last updated, Version 1) XX DE hAT-type DNA transposon. XX KW hAT; DNA transposon; Transposable Element; VIHAT1. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5547 RA Jurka J.; RT "VIHAT1: hAT-type autonomous transposon from Vitis vinifera."; RL Repbase Reports 7(3), 139-139 (2007). XX DR EMBL/GenBank/DDBJ; AM444020; Positions 1 5547. XX CC TIRs are relatively short. The youngest copies are flanked by 8bp CC TSDs. XX FH Key Location/Qualifiers FT CDS 1752..2519 FT /product="VIHAT1_1p" FT /translation="MASEGGSAXPGRDPAWKYCSPIEGNRNATICNFCGLV FT MKSGGITRFKSHLMHKDPHNNTKKCPRVPPEVKEEIRLLVHDKQKAKAKKN FT ADIEEIRSQLRGTMGTHHTHLVNEDDDDEDAEEEDVYMYPTDMHPDERDAY FT RSAVRASKASNWEREQHENIVGSKRKSGESSTGIPSTMRKSQSMRHSHHSP FT PIAPSLYKSSAAKQKNIKDIFKGGAIKETMGRLISKFFIYESVAPAKAKSH FT HFKNMIIGAQQAGNY" FT CDS 2600..3523 FT /product="VIHAT1_2p" FT /translation="MGIEPPSPYEIKNKYLEMEYKEMEAYVNQQREKWKTY FT GCTIMSDGWTGPTKLSIINFMVYSKGTTVFLKSVDASNYIKDHKYIYELLK FT TIIKEVGKENVVQIVTDNGSAFMKAGKQLMKKYNLYWTPCAAHCIDLIFED FT IGKRPNVIEVINNARKITNFIYNHGWLLAQMRKYCGGDIVRPGATRFATNY FT IALDSLLKKRADLKKLFMSDEWAQHKLSRTKLGRELEQLLFDHTYWDRLTN FT IVSLYEPLYVVLRLVDSEVVPTMPFVYELMQVMKENLIRQGAGDWMFKIIQ FT DRWQKTLKHPLHAAGT" FT CDS 3973..5169 FT /product="VIHAT1_3p" FT /translation="MIIKFVAAEWWFMYGNQTPTLRKLAIKVLSQTASSSA FT CERNWSTFALIHTKQRNRLAYSRLEQLVFCYYNMRLKLXDMEAENDRVAEK FT DYLDLLDISAEVGEEEDNQLFQWVRPIHLDDEVGNPDPRIAAHAREFGVNV FT ERVLSEEVHSESFSKDTDDXLHATYSQQEIDSTSAGHSSRPSAAGTSASGY FT DGSRGGTDDGGDNGGGDIDERRHSQYPINQFTCENDFTHCTQDEDHGSRRA FT GPGIGAIGRPYRGRERMMEPYNEELLSGSFESMSIGTQFSDSSNEANVYPP FT HVMSYGQPSSSTDEEYGMSHYSPSRQMXYQIXYQMEEGFGVNTWVNFEYPI FT HVEAVGRTQEIYAWHVRIYNQYYRGSLTWYQYCLQQQAGVPSSINPIEPHR FT NSFWY" XX SQ Sequence 5547 BP; 1866 A; 847 C; 986 G; 1823 T; 25 other; caaggaggaa aaaatcggca aaaatcggcg aaatatcgcc gatatatcgc gtgtcggcgg 60 gtggcgacac gacaaatgga ggagataagt cggccggccg atatttctca aaaaatcgcc 120 aaaaattggc tataaatcgc cgatatatcg gcgacacagg aaaaatcggc gattttttga 180 taaaatcgcc tgagaatccc gtgtgtcgtc gatttattgg cgatttatcg ccgatttttt 240 ggcgattttt tgagaaaatc ggycctctct ctccagcgtg atctgacggc ccagatcacg 300 cccgtgttga tccaacgccc agatttgaat cccaacgtta acaaagagat ccaacggcca 360 gattgcttcc aaattgtgat ccaacggcca aaattaattt taaacggtaa cttaaggttc 420 caacggctat tttggcccaa atttcatcta taaatagcca attttgcatc aatttcatcc 480 atctttgctt tgattcttca tttcctctct tactactcca attttttcca agattgctca 540 attattcaat cattttaagg tatgtttgtt tgaaattata attaattttg tttgcaataa 600 ttaattcatg tatttttaat taattagtat gtttacattt aattgtaatt attttgtgta 660 tttttattga attaatttag gttatgatat atttatttta gatgattatt tgtgatttaa 720 attcgtattt agaattacat taaactaatt aacttagcta aattgtttaa ttaatttaat 780 taacatagta aattatgtaa ttaatttaat taacatggtt aattatggaa tattaaatat 840 gctcaatttt ttatattatc gcgatttttt tttcatattc aattataatt aatttcaaaa 900 tttagtaaat ttgtcataaa attacattta gattttaaaa attaacttag gtaatttatt 960 taattagcta aattaacatg aactactata tatggaatat taaatatgct caatttttta 1020 tattatcgcg attttttttt catattcaat tataattaat ttcaaaattt agtaaatttg 1080 tcataaaatt acatttagat tttaaaaatt aacttaggta atttatttaa ttagctaaat 1140 ttrwcatraa mttacattta katwtkraaw attaamtwwg stcaatttwt ttaattagct 1200 aaattaacat gaactactat atatggaata ttaaatatgc tcaatttttt atattatcgc 1260 gatttttttt ttcatattca attatratta atttcaawat ttagtaaatt tgtcataaaa 1320 ttacatttag attttaaaaa ttaacttagg taatttattt aattagctaa attaacatga 1380 actactatat atggaatatt aaatatgctc aattttttat attatcgcga ttttttttca 1440 tattcaatta tgattaattt caatatttag taaatttgtc ataaaattac atttagattt 1500 taaaaattaa cttaggtaat ttatttaatt agctaaatta acatgaacta ctatatatgg 1560 aatattaaat atgctcaatt ttttatatta tcgcgatttt ttttcatatt caattatgat 1620 taatttcaat atttagtaaa tttstcataa aattacattt agattttraa aattaactta 1680 ggtaatttat ttaattagtt aaattaacat agatttaaat ttaagtgtat ttttcttgca 1740 atagatttag catggctagt gaaggtggtt ctgccrtgcc agggcgagat ccggcttgga 1800 agtattgttc accaattgag ggtaatcgaa atgcaacaat ttgtaatttt tgtgggttgg 1860 taatgaaaag tggaggcatc acacgattca agtctcattt aatgcataag gacccgcata 1920 acaacaccaa aaagtgtcca agagtgccgc ccgaagtgaa agaagagata cgattgttgg 1980 tgcatgacaa acaaaaagca aaagcaaaaa aaaatgctga tattgaagaa attcgtagtc 2040 aattacgtgg cacaatgggg acgcatcata cacatttggt aaacgaagat gatgatgatg 2100 aagatgctga ggaagaagat gtgtatatgt atccgacaga tatgcaccca gatgagcgag 2160 atgcatatcg atctgcagtt cgtgcctcga aagcatctaa ttgggaacgt gaacaacatg 2220 agaatattgt aggaagcaaa cgcaaatcgg gagagtcttc tactggtata ccgtcgacga 2280 tgcgaaaatc acagagtatg cgacattcgc atcattcacc ccctattgcc ccttcgcttt 2340 acaagtcttc tgcagcaaaa caaaaaaata tcaaagatat attcaagggt ggtgcaatta 2400 aagaaacgat gggacgctta atcagcaaat tcttcattta tgagagtgtc gcacccgcaa 2460 aagcaaagtc tcatcacttc aagaatatga ttattggtgc acaacaagca ggtaattact 2520 aatttatcaa atgttatatt gtgttatact tttagtaagt atagtatttt gtgacatgtt 2580 ttacatatga agtgtaggaa tgggaatcga acctccatct ccatatgaaa taaagaacaa 2640 atacttggaa atggagtaca aagaaatgga agcttatgtg aaccaacaaa gggaaaaatg 2700 gaagacatat gggtgcacaa taatgtcaga tggatggaca gggcccacga aattaagtat 2760 tattaatttc atggtttatt ctaaagggac cacggtgttc cttaagtcag tcgatgcatc 2820 gaactatatc aaagaccaca agtatatata tgagcttttg aagactatta tcaaagaagt 2880 cggtaaggaa aatgtggtcc aaattgtcac agataatggg tcggcattca tgaaagcagg 2940 gaaacaattg atgaagaagt ataacttata ttggactccg tgtgcggcac actgcatcga 3000 cttaatcttt gaagacatcg gtaaaagacc caatgttatc gaggtgataa acaatgctcg 3060 caagataact aacttcattt acaatcatgg ttggttacta gcacaaatga gaaagtattg 3120 tggtggagac attgttcgac caggagctac aaggtttgct accaattata ttgctcttga 3180 cagtcttcta aaaaaaaggg ctgatttgaa aaaattgttt atgagtgatg aatgggcaca 3240 acacaaactc agtcgaacaa aacttggacg agaattggag caattattgt ttgaccatac 3300 gtattgggac agattgacaa atatagtttc attatatgag ccattatacg tggtgcttcg 3360 acttgtggat tctgaagttg ttcccacaat gccatttgtg tacgagctta tgcaagtgat 3420 gaaagagaac cttattcgtc aaggagctgg agattggatg ttcaaaataa tacaagatcg 3480 ttggcagaaa acactaaaac atccacttca tgcagcaggt acttaaatac tatatatctt 3540 tataagtttt tactttgtat ttaagtttct ttaaaaaaaa aatactaact ctactaaatt 3600 ttattstagc atacttcttg aatccaagat ttcaatatag gcgtggagtt ggtagtgatc 3660 cggaactact tcaagctgtc catgatgttt ttgcaaaatt agatccaact actgaatcgc 3720 ttggtcaatt tggaaatgag gtgaataaaa aattgttatt tttgtcaata aaacaataat 3780 ttcattcatc aatttatttg aacgtttact aacaaattaa atgttgaata catagcttgt 3840 actttttcga gatgcaaaaa gaggattcgg tgatcgagcg gcaattgcat caaggtcaac 3900 catggtgcct ggtgagtctt tataggaaaa aattgattat tattattgta agttcaccac 3960 ataagtattt atatgattat caaattcgtt gcagctgaat ggtggtttat gtatgggaat 4020 caaacaccta cattgagaaa gttagccatc aaagttctct cacaaactgc gtcatcttct 4080 gcatgtgaga gaaattggag cacgtttgct ctcatccaca caaagcaacg aaatcgtttg 4140 gcttactctc gattggagca attagtgttt tgttactata atatgaggct aaagttacrc 4200 gatatggagg cagaaaatga tcgagttgct gaaaaagatt accttgatct ccttgacatt 4260 tcagccgagg tgggtgaaga agaagataat cagttgttcc agtgggttag gcctatacac 4320 ttggatgacg aagttggaaa tcctgatcca cgaattgccg ctcatgctcg agaatttgga 4380 gttaatgttg aacgtgtgtt gtccgaagaa gttcactctg aaagttttag taaagatact 4440 gatgatyctc ttcatgcgac atattcccag caagagattg actccacaag tgctggccat 4500 agtagtagac ctagtgctgc aggtacttct gcttctggtt acgatggttc aagaggtgga 4560 actgatgatg gaggtgataa tgggggagga gatattgatg aacgtcgaca tagtcaatat 4620 ccaatcaacc aatttacttg tgaaaatgat ttcacacact gcacacagga tgaagaccat 4680 ggctctagaa gagctggtcc aggcatagga gctattggaa ggccttatag aggaagagaa 4740 cgaatgatgg aaccatataa cgaggagtta ctttcaggga gttttgaatc tatgagtata 4800 gggactcaat ttagtgactc ctcgaatgag gctaacgtct accctcctca tgtgatgagt 4860 tatggtcaac cttcaagttc aacagatgaa gagtatggta tgtcacatta ttccccttcc 4920 agacaaatgy cataccaaat tycatatcag atggaagaag gatttggcgt taacacatgg 4980 gtgaactttg agtatcctat ccatgtagaa gcagtaggca ggactcaaga gatatatgca 5040 tggcatgtta gaatttataa ccaatattat cgaggctcat tgacttggta ccaatattgt 5100 ctccaacagc aagccggggt tccttcatct atcaatccca ttgaaccaca tcgaaactca 5160 ttttggtact aaagggacat tgcaatgtaa tgtgtacaaa ttattgttat ttaatgaaat 5220 gaagtatttg atgtgacttt ataatgagaa caattacgaa attaacattt cttatagatc 5280 gacatgatat aattacatct aatatcgcaa attatatcat atatatatca aatttttcaa 5340 taaaacaatt ttaaaatgtc tattatactt ctaattatat tattatgagg tttttcttac 5400 atttccatga gtttttaaca attttaagcc taccaataat atccaccgat atatctccga 5460 tatatccaaa aatatctccg atatatccga tatatccgta aaatcgaatt accgatatat 5520 ccgtgattac cgatattttc atccttg 5547 // ID TOPSCOTCH_LP_I repbase; DNA; EDCOT; 4616 BP. XX AC AF220602; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 09-APR-2007 (Rel. 12.05, Last updated, Version 2) XX DE Lycopersicon pimpinellifolium retrotransposon TOPSCOTCH_LP_I, DE internal region. XX KW Copia; LTR Retrotransposon; Transposable Element; internal region; KW TOPSCOTCH_LP_I; internal portion. XX NM TOPSCOTCH_LP_I. XX OS Solanum pimpinellifolium OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-4616 RA Lavelle T.D., Oldroyd E.G., Dalhbeck D., Staskawicz J.B. RA and Michelmore W.R.; RT "Direct submission."; RL Direct Submission to Genbank (04-JAN-2000). XX DR Genbank; AF220602; Positions 30504 35119. XX FH Key Location/Qualifiers FT CDS join(882..2264,2248..3267) FT /product="TOPSCOTCH_LP_I_1p" FT /translation="MQYNKGKNVSGSYDPMAMYVGRGSNGNTGNSSNFKQK FT KNWHLVCDYCKLHGHTKDICFRLIGYPPDWKFKKKFGPGQDVQNAGKANHA FT YVDSQVRDEFESVKGLNNNSGSLEQATKVGKKGHESQLTTQPTFTPNQYNK FT ILQMISKEDSQEYMANTAGTYKPLSVSNTNVERKDNADWIIDSGATRHMTS FT KETKLDYSVSVKDLDKQVHLPNGQATSVIQIGSCKVSSGDTLTNVLVVPGF FT KYDLLSVSQLTRQLNCSVNFFPEFCVFQDLSNGKVKGIGKERNVLYYLPSQ FT IPKRDAHDEQNTLISSMVFNSEGLKWHNRLGHPSMKVLKSLSLIKRGEDIN FT ECNNCPVCPLAKQTRHPFPLSISKTFVIFDLLHLDVWGPYKSPTHVGYRYF FT LTIVDDYSRMTWLILMKFKSDVFQILQCFFVMVQTQFNKTVKKIRSNNGLN FT SSIVNVKHCLKNWSQSKIGVNHESICPHTPQQNGVVERKHRHILEVARALR FT FQGSLPIRFWGECVLAAIYLINRMPTSVLNGQSPFEMFHGMQPDLSHLRTI FT GCLCYATKLVKDDKFSTRADACVFMGYSSTKKGYVVYSLNHQKMLVSRDVV FT FKEDVFPFATKKMDKDVPLFNHQHITTYSQSVEDVITVQEPAVNNDTLEFT FT ETNNPNNSEDVELEDNMVPKIPVVAPISTRHSERSSNPPVWLKDYVTNVSD FT HPYSISKYVIYDHLSTGYQSFLGQFSEEVEPRTYEEAVKNPRWVEAMEQEI FT KALEDNGTWQIMKLPDRQSVIGCKWVFKIKYKADGMVDRYKARLVAKGYN" XX SQ Sequence 4616 BP; 1507 A; 691 C; 989 G; 1429 T; 0 other; tggtatcaga gccgtgagtc tacaacatca gattcacgtt ttttctttcc atttttccgc 60 cattgttaag tttgatagcc attgattgaa tttcagagcc atggtatcag aagttatcgc 120 aagttcaagt tcaagtgttt cagcaaatac tcttgaagga atagagaaga atcgcaatca 180 tcctctgtac ttacatccct cagatactcc aggcagtgta ttaacttcaa tccaactcac 240 aggaactgaa aactacttgt tatagagcag gtcgttgatg atcaatttgc gtgcaaagag 300 caaattaggc tttgtacttg gatcttgtcg aaagtcagat tataaacctg aattagggga 360 acaatgggag aagtgtaatg cgtttgtgtt ggcttggatt atgaacacag tttctaagga 420 gttgttgagt gggattgtgt atgcattaga tacagccgtg gtttgggaag atttgaatga 480 aagatttaac aaggttgatg gttcgagaag ctatcaactt catcgagaaa tatgtactct 540 tcatcaaggt aatcttacag tatcagctta tttcacaaaa ttgagactgc tatgcgacga 600 atttgatgca ttggtgcctc ctcctacctg cgattgtgat aaatgaaaga tgtatataga 660 tcatttacag tttctgcgat tgtttgcttt tctgatgggg ttaaatgaat atatagccat 720 gcaagaagcc aaatcttgat gatgaaccct cttccaaatg taaacaaagc atatgctatg 780 ataacttctg atgaaagcca gcgtatgact gctgtgaata gagttagtgg agatattcat 840 gagtcaatgg cattgtattc aaaaaggttg atgattctgt aatgcaatac aataaaggaa 900 agaatgttag tggtagttat gatcctatgg caatgtatgt tggacgaggt agcaatggaa 960 atacaggaaa tagtagcaat tttaaacaaa agaagaattg gcatttggta tgtgattact 1020 gtaagttgca tggtcataca aaggatatat gctttagatt gattggatat ccaccagatt 1080 ggaaattcaa gaagaagttt ggccctggtc aagatgtgca aaatgcaggg aaagcaaatc 1140 atgcatatgt tgatagtcag gtcagagatg aatttgagtc tgtgaaggga ttgaataaca 1200 attcaggaag tttagaacaa gctacaaagg tgggaaagaa aggacatgag agtcagctca 1260 caacacagcc tacttttact ccaaatcaat ataacaagat tctgcagatg ataagtaaag 1320 aggattcaca agagtatatg gcaaatactg caggtactta taaaccttta tctgtatcta 1380 ataccaatgt tgaaagaaaa gataatgcag attggataat tgattctgga gccactcgtc 1440 atatgacctc taaagaaaca aaattagatt attctgtttc tgtaaaagat ctagataaac 1500 aggttcatct acctaatgga caagcaactt cagtaattca aattggtagc tgtaaagtgt 1560 caagtggtga cacattgaca aatgtgttag ttgttcctgg ttttaagtat gatttgttat 1620 cagtctcaca gctaactaga cagttgaatt gttctgtgaa ttttttccct gagttctgtg 1680 tatttcagga cctctcaaat ggaaaggtga aggggattgg taaagagagg aatgttctat 1740 actacctacc cagccaaatt ccaaaaagag atgcacatga tgaacaaaat acattgataa 1800 gcagtatggt ttttaattca gaaggcttaa agtggcataa taggctggga catccctcca 1860 tgaaggtgtt gaaaagtttg tctttgatta aaagaggtga agatataaat gagtgtaaca 1920 attgtccagt ttgtccactt gcaaaacaaa ctagacatcc ttttccttta agcatatcaa 1980 agacctttgt catttttgac ttacttcatt tggatgtatg gggaccatat aagagtccta 2040 cacatgttgg ttatagatat ttcctaacaa ttgttgatga ctattctagg atgacttggt 2100 taattctgat gaaattcaaa agtgatgttt tccagatatt acagtgtttt tttgtcatgg 2160 ttcagactca attcaataaa actgttaaga agatcaggtc gaataatgga ctgaattctt 2220 caatagtgaa tgtaaagcat tgtttgaaaa attggagtca atcatgagag tatttgtcct 2280 cacaccccac aacaaaatgg ggtggtagag aggaaacata ggcacattct tgaagtagca 2340 agagctctaa gatttcaagg ttctttacca ataagatttt ggggagaatg tgtcttggca 2400 gctatatatc taattaatag aatgccaact agtgttctaa atggacagtc accttttgaa 2460 atgtttcatg gaatgcagcc tgatctaagt cacttgagaa caattggttg tctttgttat 2520 gcaactaaac ttgtcaagga tgacaaattt tcaaccagag ctgatgcatg tgtgtttatg 2580 ggatattctt ctactaagaa aggttatgtt gtttacagtt tgaaccacca gaaaatgttg 2640 gtaagtaggg atgttgtttt taaggaggat gtgtttccat ttgcaacaaa gaaaatggac 2700 aaagatgtgc cattattcaa tcatcaacat attactacat attctcaaag tgtggaggat 2760 gttataacag tccaagaacc agcagtgaat aatgatactt tggagtttac tgaaaccaat 2820 aatcctaaca attctgaaga tgttgagtta gaggataata tggtacctaa aattccagtg 2880 gtagcaccta tatcaaccag acattcagag aggtcaagta atcctccagt ttggttaaag 2940 gactatgtta caaatgtttc tgatcatcct tattccatat ctaaatatgt aatatatgat 3000 catttgtcta ctggatatca atctttcctt ggtcaatttt ctgaagaagt agaacctaga 3060 acttatgagg aagcagttaa aaatcctagg tgggtggaag caatggaaca agagattaaa 3120 gcattagagg ataatggtac atggcagatc atgaaactac ctgacagaca atctgttatt 3180 ggttgtaagt gggtattcaa aattaaatat aaagcagatg ggatggttga tagatataaa 3240 gcaagattag ttgctaaagg gtataattaa atagaaggga ttgattatca ggagaccttt 3300 gctcctgttg tgaagatggt cactgtaaga gccattattg ctttggcttc catagaggtc 3360 tggccaatat ttcaaatgga tgtgtttaat gcttttttac aaggtgattt atatgaagaa 3420 gtctatatgg aattacctaa aggattcaag ggtgcagagc aaaattgtgt gtgcaagcta 3480 gtcaagtcat tatatggtct aaagcaggcc tcaagacaat ggaatgctaa acttactaag 3540 gcattatgta aatcttgata tacacagagt tttttggatt actcattgtt tactaagaga 3600 agtgatacag ggatggtaat agttttggtt tatgttgatg acttgctgat cacaggtagt 3660 gatcctgtgt tagttaaggc tactaaacaa gtgttgcata atcacttcaa gatgaaggat 3720 ctaggagagt tgaaatattt cttaggaatt aaattttgca gatctgaaag tggtatagta 3780 atgaatcaaa ggaagtatgc attggaatta atttctgagg ctggccttgc aggagcacaa 3840 cctgttttta ctcctttgga atgtaatata aagctcactt cagttgcata taacacaagc 3900 agtgatgatc ctattttcct tgatataagc aggtaccaaa gaatgattgg taaactactt 3960 tacttgtcta atactagacc agatattgct tttgcagtcc agaatttgag tcagtttatg 4020 cagcaaccta aacattcaca ctggaatgct gctttgagag tgattaagta aattaaagga 4080 agtccaggtt tggggttact tatgagttca cataaagata caaagctaac tggattttgt 4140 gatgctgatt gggcagcttg tctgaatact agaaggtctg tgacaggtta tttgttgaaa 4200 tttggtgact cccttatctc ttggaagtct aagaaacaga atacagtttc tcgaagttct 4260 gctgaggcag aatataggag tctagcaacc ttgactgcag aagtggtctg ggtaactagt 4320 ttgttcaagg agttatgtgt aaagttggaa tcctcaacca taatacattg tgatagcaaa 4380 gcagctcttc agattgctgc taatcctgtg tttcatgaga ggacgaagca catcgaaata 4440 gactgccact tcattcgtga gaagatacta caagggctaa tacgaaccaa ttacataatt 4500 tccaaaaagc aacaggcaga tgttttaaca aaagctcttg gaagaactca acatgatttt 4560 ctgttatcca agcttggatt attgaatatc ttcaatacat ccagcttgag ggggat 4616 // ID GYPOT1_LTR repbase; DNA; EDCOT; 2117 BP. XX AC AC149480; XX DT 23-OCT-2006 (Rel. 11.1, Created) DT 24-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE Long terminal repeat similar to Gypsy LTR, from Populus DE trichocarpa: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; GYPOT1_LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2117 RA Jurka J. and Shankar R.; RT "GYPOT1: Gypsy-type element from black cottonwood."; RL Repbase Reports 6(10), 489-489 (2006). XX DR [1] (Consensus) XX SQ Sequence 2117 BP; 661 A; 252 C; 442 G; 762 T; 0 other; tgtgatgttt tgaataaatg agtaggaaaa tacaataaag tccttgaatg cttagatgta 60 ggaataaatt aaatgagggg tagatgatat atataaatag aaggaaaaaa aaaaaagaga 120 tctgaatatt ttgagtgaaa aaccgtgaga gagaagggag aagggagaaa gaagaagaag 180 aagagaaaag agggaaatta gaaaggaaat agaaaggagt tggaggaaat aagtaaaaag 240 gtaagattta ggttgttaaa tgtataaatt tgtattattg agcttttaat tttggttttg 300 ataaatgtta gggttttgaa aatttgtgtt ttgggtttaa ttgatgaatt aaattgaatg 360 ttataaggtt gattgttatg agtaattgat taatgagttg attatggaag attgtgatga 420 ttttgagtta tgaattgtgt aaatggtgaa tgttgagtta taaatttggc aagaacagta 480 ggtaatctgt gagaattctg ggttggaggt tgaagatgac aaaatttcgg tttggtccct 540 caattttgga aaattacaat ttagtccccg aactttggaa aattacaaat tggtccctgg 600 agcatattcc gagattctga acagaataac atatgaatta tggacagaat tcctgtatag 660 ataagagaat ttaacacttt caatttagtc ctccaatttg acaaaattac aatttgacac 720 taaaaatttg gtaaaattcc agaatggtcc ttggagtata atgagatgat ctggacagaa 780 atgaggacta attatggtca gaatttcagt atattcatgg atttatgata aatttcagtt 840 tggtccttca attagacaaa agttgcaatt tgacccttaa aaataggata aattacagat 900 tattccctag ctgtaatatt agcttttgca gattagtttg atgaataatt aaggtttatt 960 tagtgaatta ttgccaattt tattagttgt tttattatgg attagatttc ggaaaaaccg 1020 ttaaattttg ggtttttgag aaaattgact agttagttca aaaacatata gggttacgga 1080 atacatcatt agttaagttt attaaatagg ttaaatgttc tttcgagtcg ttcttaaata 1140 tgtctccttt atattcagat aatcctgata ttctaccggc gggacgtcag taggattttc 1200 ttcggtgtat gcttttggct tctgtttgct tttgagtcag gtgagtggat aattttccat 1260 atgcatgaga aatattataa atacttgatt tgttaatatg aattggatca tgcttcttga 1320 taatatatat gttgattatt atccttgtta tgataagcat gatcaattgt tgaatccgaa 1380 ttattgatat gaaccagtat atatattctg aattgatagc tcctcatttg attgatgtca 1440 tgagttgagc cttgagatat gaatatatct gtttgattat gattatgaac ctatggtatg 1500 tcagtcagaa tacccatgct aacagggtag tgttagtctt tgtgcacatc gtatctgaac 1560 cctagttggt cgggggagtc accaacctgt gtggactgat catcccacag tacggagcct 1620 catgctcatt gcattttgat tttctgacga gttttaccat atgacattct tgttatggcc 1680 aatttgagaa cacttccata agaacctaaa gccaattgta tatatatttc tcattgttgt 1740 attacctcgt gtgtgtgtat tgaacgttat ctactcactg agttgttgaa ctcaccatct 1800 cattatttat ccttttcagg cttatagctt gatagcaggt cattttgttg gaccttcaga 1860 acctgctttt tggttgtact ttgtaccttt cctttatgtc tagttagtgc tccaaaactc 1920 tgaacttata taaactcttc tattaagaca attcaattat attatgaagt taattttgtt 1980 gttactgctg cgttgaactc tgattgactt atttgaagaa taagtttgtg tgtaagtttg 2040 ggttcgcata ggtatggaac cttggagggg aaccttgcct atgtgccggt catggatccg 2100 ggattcgggt cgtgaca 2117 // ID Copia2-VV_I repbase; DNA; EDCOT; 4562 BP. XX AC . XX DT 29-AUG-2007 (Rel. 12.08, Created) DT 29-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW internal portion; Copia2-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4562 RA Obukhanych T. and Jurka J.; RT "Copia2-VV - LTR retrotransposon from grapevine."; RL Repbase Reports 7(8), 667-667 (2007). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 2849..3661 FT /product="Copia2-VV_I_1p" FT /translation="MDSTPLPISLDLDIPIALRKGVRNCTKYPIAKYLSYQ FT KLLRQYKAFTSNISHLFIPRNIQEALDDPKWKLAVLEEMNALKKNGTWEIV FT DLPKEKKTVGCKWVFTIKCKADGSIERYKARLVAKGFTQTYGIDYQETFAP FT VAKINSIRILLSLAVNFNWPLHQLDVKNAFLNGDLEEEVFMNLPPGFEEKL FT GKNKVCKLKKSLYGLKQSPRAWFERFGKVIKXYGYIQSQADHTMFYKHSKE FT GKIVMLIVYVDDIVLTGDDSLELERLKRKL" XX SQ Sequence 4562 BP; 1450 A; 761 C; 861 G; 1450 T; 40 other; tggtatcaga gccaagttaa ttggctattc cctttctttt tcctctcatt ctttctagtt 60 ctattcttct ttctttttcg tttctattgc tatctcttta ccatgtcaga aatttctttt 120 aagtcraatc tactccttcc cttactgttg gttccaattc ctcaaaatta cccacatcca 180 taattctgaa tcccactctg tccagatcac cacaattcgc cttaatgaga acaattttct 240 cagatggtct caatcagttc ggatgtacat tagagggcga ggcaaaattg gttatttgac 300 tggtgacaag aaggcaccar cgtagaggga ccctagctat gccacttggg atgcagaaaa 360 ttccatgatg atgacatggc tggtaaattc catggaggag gagattagct cgaattatat 420 gtgctaccct acwaccaaag atctttggga caacgtgatt cagatgtatt cagatcttgg 480 aaatcaatcc caaatctatg agttacaact caaacttggt gatatttgtc aaggtgagaa 540 ttcggttacc aaatatttta atgtgcttaa gcgtttatgg caggatcttg acttattcaa 600 tgactatgag tggaaaacta cggatgattg taactatttt aagaagatkg tagaaagttc 660 ataggatatt caaattttta gttgggctta atgttgagtt tgatgaagtt cggggtagag 720 gacggatcat tggtagacaa cctctccctt ctataggtga agtgttctct gaagtgcgaa 780 gtgaggaaag tcggaggaat gttatgctkg ggaagaaact ctmtggacct gtggaaaact 840 cagccttatt gggcactgta gcaacagctt ctcgcaatcc taataaccaa cgtcgtttgg 900 atgacaagcc aagagtttgg tgtgatcatt gtaataaacc atgccacact cgtgaaactt 960 gttggaaaat acatgggaaa ccagctaatt ggaagcccgt tgaatggaag actaataagc 1020 aaggcgactc taatcgtttc cctgctaaag cacatgctac tatcaatgag acaccctcaa 1080 gtcccttsag caaagaacaa ttagaccaac tkctamaact gctaaaayct gctctgccga 1140 cttctggtac tcctagtgtt tctctagcac aaacaggtag tgcacctttt gtgtgcatat 1200 tctctttcat tatctactcc atggatcata gattctggag cctctgacca catgactaat 1260 ttatctaatt tgtttatttc ttatacacct tgttctggaa ataaaaaaag tacgtattgc 1320 agatggtagt ttctcaccta ttgctggaaa aggctttata aaattatctg agaagataga 1380 tcttaaatct gttctacatg ttccaaaact ctcttgtaat ctcttatctg taagtaawtt 1440 atctaaagat tctaattgtc gtgttktttt ttatgactct cattgtgaat ttcaggacta 1500 gaactcgggg aagatgattg gcagtgctag gttgatcgat gatctctact attttgatga 1560 taatttgtct gagaataaac aagctcaggg tcttattggt agtgttagtt ctatttctgt 1620 tcatgatcaa ataatgtttt ggcacttaac acattaggac atcctagttt tttctattta 1680 aaacatttgt ttccaggttt atttaaagga ttggattgta cttcttttga ttgtgaaagt 1740 tgttttttgg ctaagagcca tcgcaatact tataatacaa aaccgtattk tgcctcaaaa 1800 ccattttatt tgatacatag tgatgtttgg ggaccttcaa aaattactac tttatctgga 1860 aaaaaatggt ttgtgacctt tatwgatgat catacactca cacacgtcta tgttgggttt 1920 atttaatgaa sgaaaaatct gargttgsaa aactttttca agatttttat watatgattg 1980 aaaaccaatt tcaaacaaaa ataagtattt ttcggaktga taatggaacw gartwtttta 2040 atgaatgttt gggtgatttt ttgawagaga aaggtatttt acatcaatca acttgtaggg 2100 atacccctcc tcaacaaaat ggaattgctg aamgtaaaaa taaacattta cttgaagtag 2160 ctcgagctat tatgttttac atgaatgttc caacatactt ttggggggat gcaattttaa 2220 caacttcyta tctgattaac agaatgccta caagaattct aaagtatacc acacctttag 2280 aatgttttaa aaatattttt ccaatayata craytyactt tagatttacc cttaaaaatt 2340 tttggttgca ctgtkttcgt tcacctgcca aatcatcttc gatccaaatt tgatccaaga 2400 gccgaaaaaa atgtgttttt ctaggttatg ctcctaataa aaaagggtat aaatgtttta 2460 atccccccac tagaaaaatt tatgttagta tggatgtctc ctttattgaa aatattccwt 2520 tttataacaa aactactctt cagggggaga atgatctaat ggaagaaaat ttttggcaac 2580 aagaacaacc aaaacctagt atttttcttc ctaaatataa atcaaaaaac agatgtttta 2640 attagtgaaa aaggggaaat actaatttat ctagtgccaa ataaaattgc atcacaaaca 2700 gggggagaaa ctctacaacc tatgtccact gagctctgtg ctttatacta ggcgcaggtt 2760 taattctaat actgagaata atcaagtcaa tcttgatcat ggtcaatcat caccttctgg 2820 agttctcaaa atcacaggta atcttcctat ggactccact cctttaccta tttctttaga 2880 ccttgatatc cctattgcac ttagaaaagg agttaggaac tgcactaaat atcccattgc 2940 caaatatctg tcttatcaaa aactcttaag acaatataaa gctttcactt caaatatctc 3000 acacttattc attcctagaa atattcagga agcactagat gacccaaagt ggaaattagc 3060 agttctagag gaaatgaatg ctcttaaaaa aaatggaact tgggagattg ttgatttacc 3120 taaggagaaa aaaactgtag gatgcaagtg ggtttttaca atcaagtgta aagccgatgg 3180 tagcattgaa agatataaag caagactagt agcaaaaggt tttactcaaa cctatggaat 3240 tgactaccaa gagacttttg cacctgttgc aaagataaac tccattagra ttttgctttc 3300 tcttgcagta aatttcaatt ggcctttaca ccaattagat gtgaaaaatg ctttcttaaa 3360 tggagatttg gaggaggaag tgtttatgaa tctaccacca ggtttcgaag aaaagcttgg 3420 aaaaaacaaa gtttgcaaat taaagaagtc cttatatggt cttaagcagt ctcctagagc 3480 ttggtttgag agatttggaa aagtaatmaa gcwttatgga tatattcaaa gtcaagctga 3540 ccatacaatg ttctataaac actcaaaaga aggtaagatt gttatgttga ttgtttatgt 3600 ggatgatatt gttttaactg gtgatgatag tctagaactg gagagattga aaagaaaact 3660 ttaactcgtg aatttgagat aaaggatttg ggwgccttaa aatactttct tggtatggag 3720 tttgctagat ccaaagaagg tatttttgta aatcaaagaa aatatgtact tgacttatta 3780 agtgaaacag gtttactagg atgtaaggct agcagaaaca cctatagaac cgaatttaaa 3840 actscaacca acaagtccag tagaggtgat tgacaaagag aaatatcaaa gcctagttgg 3900 gagacttatt tatctctctc atactcgtcc tgatattgct tttgcagtaa gcatggtgag 3960 tcaattcatg catgcaccta aacaagaaca ctttgatgtt gtttacagaa ttctaaggta 4020 cttaaagggg acactaggaa aaggacttct atataagaac cgaggacacc tccaagttga 4080 agcgtttact gatgcagatt gggctggaag tgtaattgat aggagatcaa cctctgggta 4140 ctgtactttt gttggaggca accttgtgac ttggcgaagt aaaaaacaga atgtggtggc 4200 tagaagtagt gctgaggctg agtttagagt agtagctcat ggcatttgtg aggttttgtg 4260 gattagacaa ctactggaag aatttaagat tkcaagtcct ttacctatga aggtgttttg 4320 tgacaacaaa gcagccattg ccattgctca taatccagta ctccatgatc gaactaaaca 4380 tgtggaggtt gacaaacatt ttattaagga gaaactggaa aatggactga tttgtatgcc 4440 ctatatacct actattgaac aagtggctga trtrctcact aaaggatttc caaaraagca 4500 gtttgatgat ttagtaagca agctggctat gaatgatatc ttcaagccag cttgaggggg 4560 ag 4562 // ID Copia-27_Mad-I repbase; DNA; EDCOT; 3568 BP. XX AC ACYM01133169; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-27_Mad-I; KW Copia-27_Mad-LTR; Copia-27_Mad_. XX NM Copia-27_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3568 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1300-1300 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01133169; Positions 4005 438. XX CC 'CCATC' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 30..3155 FT /product="Copia-27_Mad-I_1p" FT /translation="MGKRSASVPVADVSKAVHDRRFSQQQIITQLQDFRDK FT VTMTNHQLTDLQHSLADLAILSARQEQFQQTCLEELRSLKTQPTTLPQPTW FT STSPPQPITTFHPSRTPFAAGTSSPSPTTPPFHSSSHPVCHFPTSRYLPQS FT SSGSVFHPFDSDPHSFHHYPPPSPTHDPHFTHAYSTPPHSPTVSLQTTPHL FT PSQIPSSTPPQLRHHRVPPLPSTSPSLAAMATSSRTRASVTVESSRTTTRS FT GHASTQIKRSLQPISSVAMKRKPKSEVFGYRRSKNSSNFSSSSVGSTLCSY FT CCTDGLVHTVLIHDVTSSRWKSGSQTNCNGSRVMPPLGNPTHAIEDLFPKE FT DFIQIAHRVPRPKEPDKALCCQVPILYSPLQQARLHLAFIPHYMTFAMIVF FT NSYGSRRNILAHDVFDKRQKRAIDQNYVPHIFFLIRTVPRAIALIWGFQTI FT FFTGTFGWVSLCFVDSFDLNELYNQYIHTKFGEPIEYSAYLDTISQPQKIP FT HKLKSFRQYREYMETLLAYLIHFFQRPEPLPDCDRIFLKVEPEIEEQWAPG FT KVKEWENEKQANGHVQDQLTMLDLDYSSTGEELMAVGPEKLKDALALLGLQ FT TSGTVQRAVETTLGSPITLLTGTFARVSLCSMDIFFRMIGNAPTWEFPGRG FT SMICSTIWNNFLTLMANGIFSTFMSGLTKVISTFTLSRHMIDTMTSVCLVL FT SDCSTCAIKFIPGNTLSVFPTLYFLEYLFTNTFGSQLLHGRKMQHTAISID FT NLVLLSRWFWTSIIIASMPIQGSVLSSNLFVVVLSQDHMIGRAVPGSLVAV FT TTTTGHPMVAGTPTRADNAYAGIDAIADQIQLLMVIFYSLLHCIIHHDPTL FT ELFRHSRDAKTLEAIEFGLYACSVQPTKQLIKVVEDTCCLGPQIIQRPHGT FT KAYMYCDGLTTIVEKPRCGEHIRHVDCKVLLQLYCKLIIIPMATYLNAKSN FT LAFLAPPFVTSVCGSYDFESYFPEYLRLFKALLALHFQWYHVFATVVSMSM FT VLTAPRALALLSNDSKSVFVKYSLDLYLLVLLRLPW" XX SQ Sequence 3568 BP; 874 A; 901 C; 727 G; 1066 T; 0 other; tttggtatct agagcctagg tgtgcttcca tgggcaagcg gtcggcatcg gtgcccgtgg 60 ccgacgtttc gaaggcggta cacgaccggc ggttttcgca acaacaaatc atcactcaac 120 tccaggactt ccgtgacaag gtcacgatga cgaaccacca actcaccgat ctgcaacact 180 ctctcgcaga tctggccatc ctcagtgctc ggcaggagca attccaacag acttgtcttg 240 aagagctccg ttctttaaaa acccaaccca ccaccctccc tcagcctaca tggagtacgt 300 ctccgccaca gcccatcact acctttcacc cgtcgaggac ccctttcgct gctggtactt 360 cgtccccctc tcctaccacg ccgccattcc actcctcttc ccatcccgtt tgtcatttcc 420 ccacctcccg atatttaccc cagtcttcca gcggctctgt tttccatcca tttgactctg 480 acccacattc cttccaccac tacccgcccc cttccccaac ccacgacccc catttcaccc 540 acgcctactc aacccctccc cattcgccca cagtgtctct tcaaaccaca ccacatcttc 600 cctcgcagat tccatcatct acaccaccgc agctaagaca tcatcgtgtt ccaccgttgc 660 cttcgacatc tccgtcgttg gcagcaatgg cgacttcgtc cagaactcgg gcttccgtaa 720 cggttgagag ctcccgcaca acgactcgtt ctggccatgc ttctacgcaa atcaagcgtt 780 ccctgcaacc catttcttcc gtggcgatga agaggaagcc taagtcagag gtctttggct 840 accgacggtc caagaactct tcaaattttt cctcctcctc ggtaggatca actttgtgct 900 cttactgttg cactgatggt ctcgtccata ccgtgctgat tcatgatgtt acctcatctc 960 gctggaagag tggctctcag actaactgca atggcagtcg agttatgcca ccattgggta 1020 accctactca tgcgattgaa gatctctttc ctaaggaaga ttttattcag atcgctcacc 1080 gggtcccccg accaaaggaa cccgacaagg ccctctgttg tcaggtaccc atattgtatt 1140 ctccactaca acaggcacgg ttgcatttgg catttattcc acattatatg acctttgcaa 1200 tgattgtgtt taattcctac gggagtagaa gaaacatatt ggcccacgat gtgtttgaca 1260 aaaggcaaaa gagagcaatt gatcaaaact atgtgcctca cattttcttc ctgattagaa 1320 ctgttccgcg tgctattgca ctcatttggg gttttcaaac tatctttttt actggcactt 1380 ttggatgggt gagcctgtgc tttgtggata gttttgactt gaatgaacta tacaaccagt 1440 atattcatac caaatttgga gaacctattg agtactctgc ttaccttgat actatttcac 1500 aaccacaaaa gattcctcac aagctgaagt cgtttaggca gtatagggaa tatatggaaa 1560 ctctacttgc atatctgata cattttttcc agcggccaga acctttgcca gattgtgaca 1620 ggatattttt gaaggttgaa cctgaaattg aagagcaatg ggcacctggt aaggtaaaag 1680 aatgggaaaa tgagaagcaa gcaaatgggc atgttcaaga tcagcttact atgctcgatc 1740 ttgattattc tagcacgggg gaagaactta tggcagtggg tccggaaaag ctaaaggatg 1800 cactagcatt gttaggactg cagacgagtg gtactgttca gcgtgctgtt gagaccactt 1860 tgggttctcc cattaccttg ttgacgggca cgtttgcaag ggtaagtttg tgttctatgg 1920 atattttttt caggatgatt gggaacgcac cgacgtggga atttcctggt agaggttcga 1980 tgatttgttc tacaatttgg aacaattttt taactctgat ggccaatggt attttctcca 2040 ctttcatgag tggcttgact aaagttattt ccacctttac tttatctaga catatgattg 2100 atactatgac atcagtttgt ctagttctct ctgattgctc cacttgtgct ataaagttta 2160 tacctggcaa cacacttagt gtatttccta ctctatattt tttggagtac ctgtttacaa 2220 acacatttgg cagccaattg cttcacggac gaaaaatgca gcacactgca atttccattg 2280 acaatctggt gttactttca cgatggttct ggacatctat aattattgca tcaatgccga 2340 tacagggaag tgttttgagc agcaacttat ttgtagttgt tctttcccaa gatcatatga 2400 tagggcgagc tgtccctggc agtttggtag cagtaacaac aactacagga catccaatgg 2460 ttgctggcac tcctactcgg gctgataatg catatgcagg cattgatgca atagctgatc 2520 agattcaact tctcatggta atattctatt ctctcctcca ttgcatcatt caccatgatc 2580 cgacgcttga gctctttcgc cattccaggg atgcgaaaac attggaggcc attgaatttg 2640 gactctatgc ttgttccgta caaccaacca agcaattgat caaggttgta gaagacacat 2700 gttgtctggg ccctcagatt atacagagac cccatggcac aaaggcatat atgtattgtg 2760 atggtttgac cactatagtg gaaaagccaa ggtgtgggga acacatacgg cacgtggact 2820 gcaaagtcct tctacaactc tactgcaagc tcattattat tccaatggcc acatatttga 2880 atgctaaaag taatttggca ttccttgctc ccccgtttgt aacttcggtt tgcggctcat 2940 atgactttga aagttatttt ccagaatatc tacgtttatt caaggctctt cttgctttac 3000 actttcagtg gtatcatgtt tttgcaactg ttgtctcaat gtccatggta ttgactgctc 3060 cacgcgcact cgcactgtta tccaacgact ccaaatcagt ttttgtcaag tattctctgg 3120 atttgtacct cttggttctc ttgcgtttac cgtggtaact gactcgcaac agttggagct 3180 caatgtgaaa gttgagaagt tgctcgaaaa tcaaatctca ctattcactg attatatctc 3240 agaactttca tggattatag tagcaacaag agaatttctt acatggcatc atagtgtaag 3300 cttttctata ttccaccaat ggcctgccat cttctccact tcttccaggt cttttggttc 3360 tttgggttta ttgtttggca aaaattggct atattacatg cttgctggac ttgtggtcta 3420 tttggagatt cacactgcac tagttttggg agcatctatc atggtaattg ttttggcacc 3480 ccacggcttg ggagaacaag cagcagcgcc agcctctgca tgccaacttg acggcctgag 3540 gacatgcctt attttaaggg ggagggaa 3568 // ID Gypsy19-PTR_LTR repbase; DNA; EDCOT; 513 BP. XX AC LG_XIX; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy19-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-513 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-513 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 317-317 (2007). XX DR Genome; LG_XIX; Positions 4225131 4225643. XX SQ Sequence 513 BP; 167 A; 74 C; 106 G; 166 T; 0 other; tgataagcca cgcagatcaa ccagagccat taggccaaat tccaagtatg tatgatgaag 60 tgaacgtaat tgcatatggc atacgggaag atatcagacg tgaaataata gttgcatgtg 120 ccatgcagca atagttgaac gtgaacagta tttacatgga catgcagata tacagaagag 180 ataaagagtg tgttgaggag gagcggtttt aatacaagac tgggtcttgt acagttgcga 240 tttatcagtt gcttttattt caatttatta tagttgttgt gattaatatt cagtacgtgt 300 tattttcagt ttgtacgtgg gtaaactcac atcgtgagtt accaactttt ccttaatttt 360 agagttatct gtatcggctt tgcttattta aagcagctaa gaattatgaa gaggcagaaa 420 aatttgatat taaaataatt atggtccttt ctcacccgaa gagaaacaaa cagttctcag 480 caaatacttg ttaaatattt gttgaactta tca 513 // ID Copia-48_Mad-I repbase; DNA; EDCOT; 4967 BP. XX AC ACYM01033143; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-48_Mad-I; KW Copia-48_Mad-LTR; Copia-48_Mad_. XX NM Copia-48_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4967 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1318-1318 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01033143; Positions 175 5141. XX CC Positions [2068-2568] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 1756..4875 FT /product="Copia-48_Mad-I_1p" FT /translation="MFWVQDKLIRTILLKGLCRAGYYHIPFRTFQKSLSAS FT SLSHKCFLAQPVSTSLWHQRLGHPSNAIISTMLHQNKVSLSFDTCKSVCTS FT CLEGKFTKIPFVFPTTKSVHPLEIIHSDVWGPAPLLSYESFRYYVTFIDEC FT TRFTWIFPLKYKSEVFALFVKFHAFFNTQFSVKIKVLQSDGGGEYTSSQFQ FT SFLATNGIIHQKSCPYTPEQNGLAERKHRHIVETAITLLQTARLPNLFWFH FT TCATATYLINRMSCATLKMQSPYQMLYGQIPSITHLKIFGCACFPLLKPYN FT TSKLQPKTTTCVFLGYATNYKGFICLDVAKNQLYISRHVLFDESVFPYKQF FT SSSPKSSQPAIPSTSLNSCPSLPCITLTNQVTSSSHPHASPSHITCSISTT FT ASRASESLTASSASDSLPASRAPDSLETHASATSFFNPSFSSPSSNHIFQS FT DIPAPTPTQHPVPVDPDFQQEHLHVVLPIPMNVHPMVTRSKNGIIKRRALS FT ASVSSQAILSEPKSFKAASKVPQWQNAMQEEVDALHSQNTWSLVPLPRGKN FT LVGCKWVYRIKQNADGTVARYKARLVAKGYSQEEGINYGETFSPVIKPTTI FT CLVFALAAQFKWQLPQLDVKNAFLHGFLQEEVYMEQPPGFQSLNHPSTYVC FT KLQKSLYGLKQAPRAWNDRFTSFLPALGFKSSHADSSLFVLHSHHDIVILL FT LYVNDVILTGSSSQLISQVIKELTTEFEMKDLGNLHYFLGLQISHTDEGLF FT VSQSKYVTELIDKVDLQDCKPCATPCLPYHRLLKDDGKPYHSPEQYRSVVG FT ALQYLTFTRPDIAFSVNQACQFMHNPMESHVIAVKRILRYLKGTSNYGIHF FT KPGQIYLQSYSDADWVGDPNDRRSTSGFVIFLGPNPISWASKKQHTVSRSS FT TEAEYQALAITAAELAWIRQLFCDLHISLPQAPMLYCDNLSAISLSTNPVF FT HAKSKHIEIDYHFVRERVTMGDLQVQHVSSADQFADILTKGLSAPMFQQHC FT GNLWLSSITHEIEGGCKSVNKHKDENSSEESSRA" XX SQ Sequence 4967 BP; 1407 A; 1097 C; 902 G; 1561 T; 0 other; tggtatcatc gcctcgcatc gacctggcgc ttccgcacct taatcaacga atttctttct 60 cttctttatc ctctagtttg caatctgttg tgtgataaac aaaataattg gcttcttctg 120 atctccataa aacttcacga tattgttctt cgtttctgca taccaactgt ttgatcaatt 180 gtctcagtga aagaattcta tacaacatca ataatggtga ctgctgatca gttaaagatc 240 gttcaatctc cgatcactag ttttatttcc accatttcga catccgttac agtcaagctt 300 gatgattcta actatctcac atggagtttt cagataactc ttctcttcga aagtcatggc 360 attatgggct ttgtggacgg ctcaagaaaa tgtcctctgc ggtttgatga tgattctaca 420 agtgaaggga ttgagaccga tggttatctt gtctggaaga tgcatgaccg tgcccttatg 480 cagttgatca ttgtcacctt gtctccaatg gcgatgtcct gcatcattgg aagccgaagt 540 tctcatgaaa tgtgggttaa tcttgctgaa agattttcaa cagttacaaa agctacgatt 600 tttcagatga aaactgaact ccaaaacatc aagaaaggtt ctgagtctgt ctctgtatat 660 ctgcaaaaga tcaagtatgc caaagatcat cttgcagctg ctggtgttca tttcgatgat 720 gatgatcatc cttgctctga aaggtcttcc tgcagaattt aatacctttc gctgtgtcat 780 aaggggaaga gagaacacaa tttcgctaaa ggatttcatg tctcaattgt tggcagaaga 840 gactactatt ggtcaggcct ttgaaacatc aacatattgt ggctctgcaa tggttgctgg 900 tactgcgatt aacaaaggga aagctttagt tcttgatcaa gcttcctcct attctgttga 960 atttggttca agctcttgaa ccaatgacca aaactacaag agtaatggta gtggattatc 1020 ttcttctggt catagttttg gaggtcctta caacaatact ggcagtcaat ttttaacaat 1080 ggtggtcatt atcaaggagg gtacaaaggc aataacttca gaggcagagg ccgcgacaga 1140 tcatattatt ctggccccag attttattag cctccatcca acacgagtcc tgggattctt 1200 ggtgctccaa gaccatttca atcacattgt cctgatcatc cttctgagat cccaacatgc 1260 caaatttgta acaaaaaagg gcatgttgca gctgattgct ttcagagaca cagttcacag 1320 gtcacaagtc ctcaatctcc ggttcaatgc caaatttgct ggaaatttgg tcattctgca 1380 gttcagtgct atcacagagg caattttgcc tatcaaggca agtcaccatc ctccactcta 1440 gcagcaatgc atgtcaatca tcaaccatct gcacctatgg atcagttttg ggttgccgat 1500 actggtgcaa cctcacatat gacatctgag ctagccaact tggatctgtc aaatccatat 1560 cacggcagtg acacaataac catagcaagt ggtgcaggtt tgcaaatttc tcacattgga 1620 acttcaaaat tacacactcc tactcatagt cttgcattga agaatgtgtt atatgttcca 1680 aaaaatatct cagcatctat tatcagtttc tcaactatgt aaggataatc gatgcagatt 1740 catatgtgat gatctatgtt ttgggttcag gacaaactca taaggacaat ccttctcaag 1800 gggctgtgta gggctggcta ttaccatatt cctttccgca cttttcagaa gtcattatct 1860 gcatcatctc tatcacacaa atgctttctt gcacaacctg ttagcactag tttatggcat 1920 caaaggctag gtcacccatc taatgcaatc atctctacaa tgcttcatca aaataaagta 1980 tctctctctt ttgacacatg taaatcagtt tgtacatctt gtctcgaagg aaaattcacc 2040 aaaatacctt ttgtttttcc tacaactaag tctgtacatc cattagaaat tatccatagt 2100 gatgtatggg gacctgcccc tcttttgtca tatgaaagct ttcgatacta tgtaactttc 2160 atagatgaat gtacaagatt tacatggatt tttccattga aatataaatc agaagtgttt 2220 gctctctttg tcaaatttca tgcctttttt aacactcaat tttctgtcaa aataaaagtt 2280 cttcaaagtg atggtggtgg agaatatacc agttcacaat ttcagtcttt tctagccaca 2340 aatggtatta ttcatcaaaa atcctgccca tatacccctg aacaaaatgg tttagctgag 2400 agaaagcata ggcacattgt agagactgct attacactac ttcaaactgc aagattacca 2460 aatcttttct ggtttcatac ttgtgctact gcaacatatc tcatcaatag aatgtcatgt 2520 gctaccttaa aaatgcagtc tccctatcaa atgttgtatg gccaaattcc cagtattact 2580 catctcaaaa tttttggttg tgcatgtttt cccctcttaa aaccatacaa cactagtaag 2640 ttacaaccaa aaacaactac atgtgttttt ctgggttatg caacaaatta caaaggcttc 2700 atatgtctag atgttgctaa aaatcaactg tatatatctc gacatgtctt atttgatgaa 2760 tcagtttttc cttacaaaca gttttcaagt tctcctaaat cttctcaacc tgcaattcca 2820 tccacttcac tgaactcttg tccatctctg ccatgcatta ccttaacaaa tcaagtcaca 2880 tcatcatctc atcctcatgc atctccatca cacatcacat gttccatttc tacaactgca 2940 tctcgtgcct cagagtcctt gactgcatct agtgcctcag attctttgcc tgcatctcga 3000 gctccagatt ctttggaaac acatgcatct gccacctcat tcttcaatcc ttcattctca 3060 agtcctagtt ccaatcacat atttcagtct gacataccag cacctacacc tacacagcat 3120 ccagtccctg tggatcctga tttccaacaa gaacaccttc atgtggttct tccaatacca 3180 atgaatgtgc accctatggt tacacgatcc aagaatggta ttatcaaacg aagagcttta 3240 tctgccagtg ttagttctca ggccattctc tcggaaccaa aatcattcaa agctgcttct 3300 aaagtacccc aatggcagaa tgccatgcag gaagaggtag atgctcttca ttctcaaaat 3360 acatggtccc ttgttcctct tccacgtggt aaaaacctag ttgggtgtaa atgggtgtac 3420 agaattaaac agaatgccga tggtactgtg gccaggtata aggccaggct tgtagcaaag 3480 ggctatagtc aggaagaagg tataaactat ggagaaacat ttagtcctgt gattaagcct 3540 acaacaattt gccttgtttt tgctttagca gctcagttca aatggcaact accgcaattg 3600 gatgtcaaaa atgccttctt acatggtttt ttacaggaag aagtgtatat ggagcagcct 3660 ccgggttttc aaagtcttaa tcatccttca acttatgtct gcaagcttca aaaatcgctc 3720 tatggactta aacaagctcc gagagcttgg aatgatagat tcaccagttt tctacctgca 3780 ttgggtttta agtcttcaca tgccgattcc tccttatttg ttctccattc tcaccatgac 3840 attgtcatat tgctgcttta tgttaatgat gtcatattaa ctggaagttc gtctcagttg 3900 atttctcagg tcatcaaaga actcaccaca gagtttgaga tgaaagattt aggcaatctg 3960 cattattttc tggggttgca gattagtcac acagatgaag gattatttgt ttctcaatct 4020 aaatatgtta ctgagcttat tgacaaagtg gatttgcagg attgcaaacc ctgtgctact 4080 ccttgtttgc cctatcaccg acttctcaaa gatgatggca agccttatca tagcccggag 4140 caatatcgta gtgtggttgg agctcttcaa tatctcacct ttacaagacc ggatatagcc 4200 ttctctgtca atcaagcatg tcaattcatg cataatccta tggagtccca tgtcattgca 4260 gtcaaacgaa ttctccggta tcttaaggga acttcaaact atggcattca ttttaaacca 4320 gggcaaatat atcttcagtc ctatagtgat gcagactggg tcggggatcc aaatgatcga 4380 agatctacct cagggtttgt catttttctc ggccctaatc ctatctcttg ggcatcgaag 4440 aagcaacaca ctgtgtcacg atcgtccaca gaagcagaat atcaggccct cgctatcaca 4500 gcagctgaac tagcttggat aaggcaatta ttttgtgacc tccacatttc tcttcctcaa 4560 gcaccgatgc tttactgtga caacctctca gctatctctt tatctaccaa tcctgtgttt 4620 catgcaaaat ctaaacatat tgagattgac tatcactttg tccgtgaaag ggttacaatg 4680 ggtgatcttc aagttcaaca tgtttcatct gccgatcaat ttgctgatat actcacgaag 4740 ggtttgtctg cacctatgtt ccagcagcat tgtggcaatc tctggcttag ttccatcacg 4800 catgagattg aggggggatg taagagtgta aacaaacaca aagatgagaa ttcaagtgaa 4860 gagagttcaa gggcctagat gatgacaagt gtcacaagat ccaagggaag ttataaggat 4920 gttagaatct gttaggatct gttggtggtt agaatgtgta gttagtt 4967 // ID Copia21-PTR_LTR repbase; DNA; EDCOT; 119 BP. XX AC LG_X; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia21-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-119 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-119 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 217-217 (2007). XX DR Genome; LG_X; Positions 16196526 16196644. XX SQ Sequence 119 BP; 40 A; 25 C; 18 G; 36 T; 0 other; tgtaaataaa tctattatgc gctacctaga ctctccactg tcatgtattt atatcagctt 60 tcaaatgaat gacaggcaac gagaaacatg ctcatcaatt ctatcatggt atcagagca 119 // ID Helitron-N1_Mad repbase; DNA; EDCOT; 713 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous Helitron elements, consensus. XX KW Helitron; DNA transposon; Transposable Element; Helitron-N1_Mad. XX NM Helitron-N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-713 RA Bao W. and Jurka J.; RT "Helitron transposons from the apple genome."; RL Repbase Reports 10(10), 1641-1641 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~90% identical to the consensus. XX SQ Sequence 713 BP; 227 A; 112 C; 119 G; 255 T; 0 other; tctttatata taaagccaag ggcccaatga acagtgtttt ttggtgtcac aagcttcacc 60 aaaaataatt ggacaaaaat gcccctcaaa caaaaaactt caaaagcaac ccaaaataat 120 gcatcaaatg tggcaggggt attttcgtca ttttaacagt gttttttaat aattaatttt 180 tttgtacatt ttttttaata attagtacct cacaataggc tagcaataat gtgattcaat 240 cagttgttca ttaaatatta ttttctctat ttttaaacac gttcaaaaca tcttaagagg 300 cgtgtaatgc cggttataaa aaaggtcttt cgcacgcgga taataatgtg attaaattag 360 ttgtcaaatg attttttttt ttaacaaacg atattatcta cactaagggg ggggggtggg 420 cttagcctca caatgggcta gcaataatgt gattcaatca gttgtttatt aaatattatt 480 ttctctattc ttaatataaa ttcaatagag accgatttta ttatgtggat tcagctgctt 540 taattggttt atgaggggtt tcttctagca tgatctaaga ttattcattt acttcaaata 600 tttgactttc cttttgtcaa tttacgcata taaatacatt taaaacgtgt aagtcgcgcg 660 tagcacgccg tgattcaaaa aatgtcttct gcacgcgcgt gcatgaaggc tag 713 // ID Gypsy-35_Mad-I repbase; DNA; EDCOT; 1539 BP. XX AC . XX DT 13-OCT-2010 (Rel. 15.1, Created) DT 13-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-35_Mad-I. XX NM Gypsy-35_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1539 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1764-1764 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 47..919 FT /product="Gypsy-35_Mad-I_1p" FT /translation="MIYQDSNLAQRSRLYELLEELRKHNEECKRSLEVEKV FT LRGHGEMQKSFACMLRIKAPVTLQRQWVNEDRARFNAWLDEENFPYVSDYR FT SIPFEKWLGSKAGGQFFAPAVIRHRPKKIVNLAEEQRPPIFSVEAEDMVGH FT EEKPRPPIFSVETGSVVGLEEKVKVSEPQIDSENDSSEECSNDERGRDIGL FT AQESTPIDMIIGDKVDMEKSYSAKLFELNAEIMPGGHNTCSTHSAAENAKY FT FTKSEILGDDLLFGFGKCQSENFDVKRSWLGIKHRWPPPDYVSATFLFVC" XX SQ Sequence 1539 BP; 469 A; 283 C; 351 G; 436 T; 0 other; ttttggcacg cccagtggga cccagtgcta atactacgaa gttcatatga tatatcaaga 60 ttccaatctg gctcaacgta gccgattgta cgagctccta gaggaattga gaaaacacaa 120 tgaggaatgt aaaagatctt tggaagtgga aaaagttctt cgtggccatg gagagatgca 180 aaagtcattc gcttgcatgt tgagaataaa agctcctgtt accctgcaaa ggcaatgggt 240 aaatgaagac agggctcgat ttaatgcctg gctagatgaa gaaaattttc cttacgtttc 300 tgattacaga tcaattccat ttgaaaaatg gttaggctca aaggccgggg ggcaattttt 360 cgctccggcc gtaatcagac atcggcctaa gaaaattgtt aatttggccg aagaacaaag 420 gccacctatt ttttcggtcg aggctgaaga tatggtcggc cacgaagaaa aacctaggcc 480 acctattttt tcggtcgaga ctggaagtgt ggtaggccta gaagaaaaag ttaaagtttc 540 tgagccacaa atcgactcag aaaatgattc gtcagaggag tgctccaatg acgaacgagg 600 ccgagatatt ggcctagccc aagaatctac gccaattgat atgattattg gcgataaagt 660 cgatatggag aaatcctatt cggctaagtt gtttgaatta aacgccgaaa ttatgcctgg 720 ggggcataat acttgttcca cacattcggc ggccgaaaat gcaaaatatt tcaccaagtc 780 agaaatattg ggagatgatc ttttattcgg ttttggaaaa tgtcaaagtg aaaattttga 840 tgtaaaaaga tcttggcttg gaataaagca tcgttggcct cctcctgact acgtttcggc 900 cacttttctt ttcgtttgct aaaaatataa ttatatataa taaattattt tcttaaccat 960 tcggcccttg accgatactt aagaaaataa gaggggcaac aagtggtgtg ctcggcaaaa 1020 ttttggtcat tttgttttta gccgagctcg acaaacaagc cgacccgaga agagttattt 1080 tcgctgctat caatagtacc atgcctatgg ttaaagtgtg gggacaagtt tcaaaaccat 1140 ttaatcagga agatgctagg gtcaaagttt ggccgaataa gtcatggttg ctgttttgag 1200 gttatatata tatatatata tatatatata tatatatatg tatatagtca tgattgctga 1260 caatgggttt gatatgcata tatatgtagg caggccgagc tgccaagaaa agactcttct 1320 cgacctcggc caaatttatc ctcgacccca attccaattc ttctcgaccc tggttcataa 1380 ctgtttatct tcggccatga gttgttcttt ggtcgaaagg agccgtgagt aaacagcagc 1440 aagggatgac ggtcaaaagt acatctgatt aggctggaga tacttaattt ccttaatcat 1500 tcggcttacg agccgaagtt caaggaaact ggggggcaa 1539 // ID MtPH-M-2-IIa repbase; DNA; EDCOT; 5303 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 13-MAY-2008 (Rel. 13.05, Last updated, Version 1) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-M-2-IIa. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5303 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC An autonomous element representing subfamily M-2 of PIF/Harbinger CC transposons from Medicago truncatula, carrying 14 bp-long TIRs. XX SQ Sequence 5303 BP; 1869 A; 990 C; 767 G; 1677 T; 0 other; gcgtgtgttt ggttgtgcgg tgaaaaaaat tgattttggt agaattgatt ttggttaaaa 60 gtaagttgaa tgtaaagtga tttatgtttg gataccttca aaacaaaagt gatttgtatg 120 aaaaattttg tttggatgtt ttgagtcata attgctttta catgtataaa agaccaaaat 180 gggctttaaa atgtgagtgt gtgtgtttgt atatatgtat atataaattt tacatttatt 240 tgatttttca tccttcattt atttttgatt aactgacaat aaaattacta gattaatata 300 attgttaatc acacaatatt caaataaaaa tgcatgtagg gaatatatat aatttttttt 360 ttgaatatga accttcaaat agatttgaaa ttcatcaatt tgtccaattc ttacgatatt 420 atagtcaaca caagtatata atgattttga gcactgtaaa gaagaaagaa aaggatactg 480 taaggaacaa tacaacacct agatgaacat aataaagaga tagaatcatt tcagagttcc 540 acattgaatc agaagtaaac aatttcatca gacaatatta gcaatcttgg aaaacacaaa 600 attcattgca tccatttctt ttgagacaat cctctccatc tccctagcat aactaagtgt 660 ttggttgatg agttgcagag agggtgtttc tttgcaagat agtcatatgc cttctcaatg 720 catcctgtta tctcatctct gatggtcttt taaaattaaa cattactaca atactaatga 780 tttttgttga actttataat ttgatctcga accgagtttc gaacatgatt catctcagat 840 gaggaagcta tatttaaatt ttgagataaa tccaaattaa ctagtctacg ataatcatca 900 tgatcaaggg ttatgtcttc atcctcatac cgattgaaat cgacgtccat atcagcattc 960 cttctaataa agttatgtat agccattgtt gcaacaacaa cttcaacttg tgtcttaatt 1020 gtgaatttag gcatgcgtcg tagaattgca aatctattct tccatacacc aaaagttctt 1080 tctattgtgc accttaaact tgagtgataa taattgaata cctcgttgtt attttcaaac 1140 ccatgagaac gccgaaaatc agggaggtga taacgttcac atctgtatgg accaagatat 1200 cccatcggtg ttggataacc ggcatccacc aaataataca tacctaaaaa caaattaaat 1260 tataaattgt aaagaataat actaataaat aagttgtaaa agataatatt agtacctgga 1320 ggaggatgtg gaaaatttag atttgcattt gtgagagcat ggtcaaaaac acgagcatca 1380 tgggcagtac cttcccatcc ggctaaaaca aaagtaaagc acatgttcca atcacataca 1440 gccattacat tttgtgtcgg atatcccttt cgtccaataa atctagtttg gtcattggca 1500 ctaaccacac agggaatatg cgtaccatcg attgctccta tggcattctt aaaatatggt 1560 caataccgtg gatcactttg aatttttgca tgactatcac ggaacaaagg atcttgaggc 1620 tttatatatt cgatggacaa actcaagcaa gcaactaaca catcatgaaa acgtctactc 1680 acagtttctc ctaagtgttg gaacctttct tgaatcattc tattacccac tccatgtcca 1740 acaacaagta agaacattgc aaccatctct tctaccccta tgtgattagt gggctttaaa 1800 ccatgatcaa ctaatttagt gcaaagttta tgaaaaatat gtttttccat tcgaaacatc 1860 tcataacaac gagtgggatt tccttgcaat acttctttca cccatgcatg ccctgttagc 1920 tcactagttc tacatggctc tttacataaa tgtttcacag catactcacc cattagtgca 1980 gccactaaag aagcttgttc aaaaaaatca tcgtcttcat ttgattcttc attacaatag 2040 tccattttgc aatgagattt ggctactgtc aaaggtaaac aattagtaag aaaaacaaaa 2100 aaaaaaagtt aatttattat atcaggagct atcttgaatg tcacacaatc taaaacatga 2160 tattaaacat aagaaatcat aagaaacata acaatgatca gaacaatcag aaatcatgcc 2220 atttgaatta tagacaaata tagcgcatga gctttgtaga agaaattaat tatcctgtca 2280 gccatatatt gtatttttac tcggattacg tatatatact tgtctgcatt gtttttgcat 2340 cttatttgac atatgtgtct ttattgtgta cattcagaag gtactagcaa tgtaaataag 2400 tttaccagca aagtaaatct tatgtatttc attttgcaga aaactaccta atgcaaccca 2460 tatgttagtt ttctttattg tgtatatctg tgcattttgc agcaaactac ctaaacaaat 2520 atagtgcaga aatcatgtgc agaatatagt gcagaaatca taacaacatt gcaaataact 2580 atgataagga caatattttg acacaatcta aaaaggtgct aaaaactgaa caagaaaacc 2640 cgcaaatcag aaccaaaata gcagttaacc ctgaagcaaa aaaacaacat aagtgaacca 2700 taaatacgag cataattatc acacaacata agtcttcatt aagggataga aacattacat 2760 aagttactag tacttcataa gagtacttca tagttactac cacttcttag attacttcct 2820 aattgaaagg aaaaacataa cagtacttca aagttaccgg tacttcctag attacttctt 2880 aatttaaaga caacagagca ttacaacatt aaagactaaa caaaatagta cttcatagtt 2940 actagtactt cgtagattac ttcttaattc atagtacttc ctaggttaat tcccattaca 3000 tcctagtcac acaggttcca aattacatag tcatgaatgg caatgggtta tcaattgtat 3060 gcttaagcca attcaacctt ttctcctctg aacctcgtag ggaaataaaa atctcccttg 3120 caggcttaaa catcagcaag ttgcaacact gcgcatgcaa ataaagatca tttgagattt 3180 catccatggt gtgaagctca gccatcactt cgccaataga tgcattaccc gcagcatcat 3240 tgcgagaacg acatgtctct gctattaaac taactgcttc agctatcttt gatgatgcac 3300 ttgatttttt cttacttggc ttgtctgctc taacaactct tttcctcttc tcaccactct 3360 tttgaccatc aatttttttg tgaagaattc agcccaatat ttgcaaattc agttgttgct 3420 ccaacacttg catcctcgct atcgccaaat ccttctacaa ccactacatc attatcatca 3480 tcttcaaaca cacatggcaa taccccacat gatggtgccc aagtgtactc tccattagcc 3540 actacatcct taaaaagtgt ggttaactca ttggcaaatg gaagcccctt gttcctaaat 3600 ttttcataaa gagggttttc ctgcattttc atatctcatc atataagaaa cacgggtata 3660 catatctaag gcttatgaaa taacaatttt ctctattaca taccagctgt ttggtctccc 3720 accactcatc aggtgctaca acagtgttgt tcaccggatc ccaccctaat ccagtttctc 3780 tcccaaataa gttataccat gctctccaat cctttctcag actgtcatac ctattcttta 3840 attgagcctt ctcatacttc agtccggtta aattatgaaa ttgggcctta atattgttcc 3900 accctttttt tgtaaagctc gtaccaacac gttctctgtt ggaaacttgc tccaaacatg 3960 ctttcacaaa gttttcagtt gacttataat cccaattagc ttttgttttc tgccccccat 4020 cattaggtga ggaggaacgc acaacatttt tcttggtatt caccattcta tgtaaacaag 4080 gttaaatatt aatctatttg aatcaaacct atattcgaat aaccacttat ctaatgaggt 4140 gaaattggta aacaaaaatc actatcagtt caagtaaaac aatgaagcaa acaaagagag 4200 actttattat cattatcatt tgaagagctt attgagactg tttatattat catacagaaa 4260 aacagaacca aaatagtagc aaaactgaac caaaacatca gtaaaataaa gacatattct 4320 ctactaaaaa aacacaaaca tctaaaacct tgtcaaaagt aaatattaaa taacagacat 4380 gaataagtgg catttgtgct tgagagcttt ctcttcttgc aactatttca agatccatgg 4440 tcctaaacta ttcaaggtct tcatcatcaa ggttgacaga ttctttagat attatccttc 4500 gaaacttgta acttcagata taatacatgt gtttaagaga aaatttggta aaaagaaatt 4560 ataaaaccac atatgaacac catagatagc tcttccttta ttttctagag ttgacaaaag 4620 atagagaaaa aaaaaaaaat gaaaagccac ctatgaacat tccttctgtc aacaaagttg 4680 aaactatagt gataaatggt atagaacata actcaatcta aagtactcat acaatggaaa 4740 taatattcat tagtatcatt tgatgaaaag catagaagct attttcaaac tccatcaata 4800 tcattaatat ttcaggcaaa aaataaaata aacaatcata actaaggtca aggaaaacaa 4860 aagaaataaa ttgtttttat ttaggcattt tatcaaacac atcaaatgca atgttatcaa 4920 aattgaatta atagacagaa gatgagtgtt tgagcttacc cttgagtacc aaacactgca 4980 actatttggc tatttgcttg tttaagaatg aaagagtgac aaatgagcca acctatatat 5040 agaagtttgt atgaagagag taactacata gttaatgaaa ctatgaggtt gatgaccaat 5100 ttctacaagt tgtgaagaat taatgaaaat gtggaggccg cccttgatac aaagtggatc 5160 atatttccat taaggaattc cattaagtgg aggcctcccc aacataaatc actttatgtt 5220 caactcactt ttaaccaaaa tcaattctac ttaaatcaat tctaccaaaa tcaattcttt 5280 ccaccgcaca accaaacaca cgc 5303 // ID PEABODY_I repbase; DNA; EDCOT; 4507 BP. XX AC AF083074; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Pisum sativum Ty3/gypsy-type retrotransposon PEABODY_I, internal DE region. XX KW Gypsy; LTR Retrotransposon; Transposable Element; PEABODY_I; KW Ty3/GYPSY superfamily; gag-pol pseudogene; internal region; KW internal portion. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-4507 RA Volman P.G., Shilo J., Weinhouse H., Ohana P. and Benziman M.; RT "Direct submission."; RL Direct Submission to Genbank (09-AUG-1998). XX DR Genbank; AF083074; Positions 1721 6227. XX SQ Sequence 4507 BP; 1211 A; 648 C; 1265 G; 1383 T; 0 other; tagtggtatc agaacaggtc ggcctgtccg gccagttttc gtgtcgttac tgtctaacaa 60 ttgtgtattg ttactaatct aactttaagt tgtgttgtat tgataagttg aaatggctgg 120 aaggaatgac gatgcaatgg ctgccgcaat gcaagcaatg gcacaagctg tgcagaactt 180 gccaaatgct ggtggagatg ctggatcacg tagcttggcg acttttcaga gagagaatcc 240 gccggtgttt aaagggaagc atgatccaga tgcagccttg ggatggttga aagagattga 300 gagaatcttc cgtgttatgg attgcactcc agctcagaag gttcggtatg gtactcacat 360 gctagcagtc gaagctgatg actggtggct agagactcac gagaggttga ccgtggcagg 420 tgaagtcatt acttgggatg tattccgtag ggaattcatg acgaagtatt atccggaaga 480 tgtccgtggt aagaaggaaa ttgagttcct tgagctgaag caaggaaaca tgtctgtcac 540 tgattatgct gcgaaatttg tggagctatc caaattttat cctcattaca ctggtgctgg 600 tgctgaattt tcaaagtgca tcaagtttga aaacggactg cgctctgaaa ttaagaaggc 660 tgttgggtat caaaagatac gcatttttac tgaattggtt gatagctgca ggatatttga 720 agaagacaat aatgctcatt acaagattgt cagtgaccgc aggggcaagc aacatcaaaa 780 ccgtggaaag ccgtatgatg ctccagtggg aaaagggaaa caaggagctg ctccggctca 840 gaggaccagt aggggaggtg ctcctgctgg ttatagtttg tttccaatgt tggtccggct 900 ggtccataaa aataatgtta tgcactgcct gaaaataaaa aagtgttttc cctgtggtaa 960 actggtccat gcaatagctg attgcaagca caaggaaatg atttgtttta attgtggcga 1020 agaagggcat attggaagtc agtgtcagaa gccaaagaaa tctcagactg ggaaggtgtt 1080 cgcattgacc ggaactcaaa cctccagtga ggacagactt atccgaggta cgtgttatat 1140 taatggcttt cctcttgtag ctattattga cacaggtgcg actcattcct ttatatcttt 1200 ggattgtgct gtgaaactta agttagagat atctctggag atgtttggta gtatggtaat 1260 tgatactcct gcgaagggtt cagtgactac tacttcggtt tgtttaaatt gtcctttgag 1320 tatttttggt agggactttg ggatggacct agtgtgtctt ccactagtgc agattgatgt 1380 tattctgggt atgaactggt tggtgtttaa ccgagtttct atcaattgtt ttgataagac 1440 ggtggtattt cctgagattg aggaaggaaa gagtttgttt ctatcagcca ggcaggtgag 1500 tgaggaagta gctgatgggg cagagttgtt tatgctgtta gcgactttgg aggctaaaga 1560 taaactggtg gttggcgatc tagccgtggt gtgtgatttt cctgatgtgt ttccagaaga 1620 agtgaatgaa ttaccgccag agcgtgaagt ggattctcga ttgatttgta cctgtactag 1680 gccgatatcg atggctccgt accgtatgtc tgctgttgag ttaactaaat tgaagagtca 1740 gcgggaagat ctgttggata agaagtttat tcgtccgagt gtgtcaccgt ggggtgcacc 1800 agtgttgttg gttaagaaga aagaaggtac tatgaggttg tgtgtggact acaggcaact 1860 gaataaagtg acgatcaaga atcggtatcc tttgccgagg attgatgatt tgatggatca 1920 gttggttggt gcgagtgtgt tcagcaagat agatttgaga tcgggatatc atcagatacg 1980 ggtgaaaact gaggatattc agaagactgc tttcagaaca agatatggac attatgagta 2040 ttctgtaatg ccttctggtg tgactaatgc gcctggagta ttcatggagt atatgaatag 2100 gattttccat ccgtacctag ataagtttgt tgtggtgttt attgatgaca tattggtgta 2160 ttcgaaatct gaagaagagc atgttgagca tttgagagtg gttttaggag ttctacgaga 2220 aaagaagtta tttgctaaac tgtcgaagtg tgaattttgg ttagaagaag ttagttttct 2280 tggtcatgtg atttcaagag gtggtgttgc tgttgatcct tctaagatag aagcggtatc 2340 taagtgggaa gctccgaagt ctgttgctga gattcgaagt ttccttggtt tggctggtta 2400 ttataggaag ttcattgaag gattttctaa gttggcgtta ccgttgacaa tgttgactag 2460 aaaggggcag gcgtttgttt gggactcaaa atgtgaagaa ggtttccaag agttaaagag 2520 aaggttaact actgctccta ttctgatatt accgagttcg tcggaatcat ttgaagttta 2580 ctgtgatgct tcattgttgg gtttgggtgg cgtgttgatg caggataagc aggttatagc 2640 ttatgcttca agacagctga aggttcatga gaggaactat ccgacgcacg atttagagtt 2700 ggcggctgtg gtgtttgttc tgaagttatg gaggcattac ttgtacgggt caagatttga 2760 ggttttcagt gaccataaaa gtttaaagta tttttttgat cagaaagagc tgaatatgag 2820 gcagagaaga tggttagagt ttctgaagga ttatgacttt ggtttgaatt accatccggg 2880 taaagcaaac gtagtggctg atgcattgag tcggaaatca ttacatatgt ctatgctaat 2940 ggttaaggaa ttggatttaa ttgagcagtt tagagacttg agtttggtgt gtgagagtac 3000 tcacaatagt gttaaattgg gaatgttgaa gttaacaagt ggtattctgg atgagatcag 3060 agagggtcag aaatccgata tgcttttggt tgataagttg actctagtga atcaaggtca 3120 agaattcaga gttgatgaga atggtgttgt gagatttggt agtcgggtgt gtattccgga 3180 tgttatcgaa cttaagaaga gtattcttga agaaggacat cgtagtggcc tgagtataca 3240 tcctggagct acgaagatgt atcatgattt gaaaaagtta ttttggtggc cgggaatgaa 3300 aagagaaatt gcgagttttg tttattcttg tttgacttgt cagaagtcaa agattgagca 3360 tcagaagccg tctgggctaa tacaaccgtt ggctattcca gagtggaagt gggatagtat 3420 cagtatggat tttgtttctg gtttaccgat gacaattaag aattttgaag ctatttgggt 3480 gattgttgac agattgacaa aatcggctca tttcattccg atcagaatgg attatccgtt 3540 agagagatta gctgagttgt atattgagaa gattgtaagt ttgcatggta ttccgtcgag 3600 tattgtttcg gacagagatc ctagatttac atcgaaattc tgggaaggtt tgcacaaggc 3660 tttgggaact aaactgagat tgagctctgc atatcacccg cagactgatg gtcagactga 3720 gaggacgatt cagtcattag aggatctttt gagagcttgt gttttggaaa agggaggtgc 3780 ttgggattgt tatttacctt tgattgagtt tacctacaac aatagttttc attcgagcat 3840 tggtatggcg ccgtttgaag ctttgtatgg taggagatgt cggacacctt tatgttggta 3900 tgagtccggt gagagtgctg tggttggacc ggagattgtt caacaaacta cggaaaagat 3960 taagatgatt caggagaaga tgaggattgc tcagagtcgt cagaagagtt atcatgacaa 4020 gagaaggaag tcacttgagt ttcaagaggg agatcatgtg tttcttcgtg ttactccgat 4080 aactggggtt ggtcgagctt tgaagtcgaa gaagttgaca cctcgattta ttggtcctta 4140 tcagattttg gaaaggatag gggaggtagc ctatcgtatc gctttaccgc cgtcacttgc 4200 gaatttgcat gaggtttttc atgtgtctca gttgaggagg tacattcctg atccgtcgca 4260 tgtagtccaa gtagatgatg tacaggtgag agataacctg actgttgaaa catcacctat 4320 gaggatagag aatccagagt tgaagcaatt gcggggtaaa gagattgctt tggtgaaggt 4380 agcttgggga ggaccagcag gtggcaatgt gacttgggaa cttgagagtc agatgaagga 4440 gtcttatcca gagttattcg cttgaggtat gttttcgagg acgaaaactc ttttagtggg 4500 ggagagt 4507 // ID Gypsy11-VV_I repbase; DNA; EDCOT; 9491 BP. XX AC AM477421; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy11-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9491 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-9491 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 726-726 (2007). XX DR Genbank; AM477421; Positions 3051 12541. XX CC Positions [4701-5117] - Integrase core CC 'TCCAT' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS join(798..2708,2712..4574) FT /product="Gypsy11-VV_I_1p" FT /translation="MEAINACPHHGFDTWLLVSYFYDGMSSSMKQILKTMC FT GGDFMSKNSEEAMDFLSYVSEVSRGWDEPNSREKEKFPSQPTQNPKGGMYV FT LSEDMDMKAKVATIARRLEELELKKMHEVQAISETQAHVMPCTICQSCDHV FT VDECPTMPTVREMLGDQANVVGQFRPNNNAPYGNTYNSSWRNHPNFSWKPR FT PPPYQPQGQTQAPQQTSSVEQAIVNLSKVMGDFVGEQKTINSQLHQKIENV FT ESSQIKRMEGMQNDLSQKIDNIQYSISRLTNLNTMNEKGKFPSQPSQNPKS FT VHEVETQEGESSKLREVKAAITLRSGKEVDQPLPKVRQDEEPRKVIKEDMM FT KKHMPPPFPQALYGKKEIKHSSEILEVLRQVKVNIPLLDMIKQVPTYAKFL FT KDLCTVKRALHVTKNAFLTEQVSAIIQSKSPVKYKDPGCPTISVNIGGTHV FT EKALLDLGASVNLLPYSVYKQLGLGGLKPTAITLSLADRSVKIPRGVIEDV FT LVQVDKFYYPVDFVVLDTDPTVKEANYVPNILGRPFLATSNAIINCRNGVM FT QLTFGNMTLELNIFHLCKRHLHPEEEEGLEEVCLINTLVEEHCDKNLQESL FT NESLEMFEEGLPEPSDVLAIMSPWRRREEILPLFNQEDSGATVGYPPKLVL FT KPLPVDLKYAYLEENEKCPVVVSSILTSDQEDSLLGVLRKCKKAIGWQIYD FT LKWISPLVCTHHIYMEDDAKPVRQPQRRLNPHMQEVVRGEVLKLLQAGIIY FT PISDSLWVSPTQVVPKKSGIIVVQNEKGEKVSTRPTSGWRVCIDYRKLNSV FT TRKDHFPLPFMDQVLERVSGHPFYCFLDGYSGYFQIEIDLEDQEKTTFTCP FT FGTFAYRRMPFGLCNAPATFQRCMLSIFSDMVERIMEVFMDDITVYGSSYE FT ECLLHLEVVLQRCIEKDLVLNWEKCHFMVQQGIVLGHIISKKGIEVDKAKV FT ELIVKLPPPTNVKGIRQFLGHVGFYRRFIKDFSKISKPLCELLVKDAKFVW FT DEKCQKSFEELKQFLTTAPIVRAPNWKLPFEVMCDASDLAMGAVLGQREDG FT KPYVIYYASKTLNEAQRNYTTTEKELLTVVFALDKFRAYLVGSSIVVFTDH FT SALKYLLTKQDAKARLIRWIFLLQEFNLQIRDKKGVENVVADHLSRLVISH FT DSHGLPINDDFPEESLMSIEVAPWYSHIANFLVTREVPSEWSAQDKRHFFA FT KIHAYYWEEPFLFKYCADQIIRKCVPEQEQSGILSHCHDNACRGHFAS" XX SQ Sequence 9491 BP; 2656 A; 1979 C; 2005 G; 2836 T; 15 other; aaatggcgcc gttgccgggg atggtgccac aatacagtga tgcaaccttt taaaggctac 60 ttgtgatttc catcacaagt ttggtgaatt cctttttcac taacttcatt tcctttcatt 120 ttatttttgt taggtttatt ttcattttct ttctaacctt aacttttttc taggtttctt 180 ttgtttttgt tgtttttgtt ttatttcagg taagtagtaa cttgtgcatg ccttattgga 240 ttcgggacca agagggaaga ttagtaagga ttragaatcc tcaagacaca gagttggata 300 tttgtgttaa yatcatggac cctccaccag aggatcagaa ttctcaacaa ggtcaarggg 360 rtaatcccaa tgcatattta tccatgaggg atagaatgca cccaccaagg atgagtgcac 420 cctcrtgcat cmtrcctcct mttgagcagc tggttataag gccccatatt gtgccccttc 480 taccaaattt ccatggaatg gagagtgaga atccatatgc ccayatcaag gagtttgagg 540 aggtktgcaa tacctttaga gagggaggag cttcaataga cttgatraga ctcaagctat 600 tyccttttac tttgaaggac aaggcaaaaa tatggcttaa ttctttaagg ccaaggagca 660 taaggaattg ggttgatctt caggccgaat ttttgaagaa atttttcccc acccatagga 720 ccaatgggtt gaagagacaa atctcaaact tttctgctaa agaaaatgag aagttccatg 780 aatgttggga aaggtatatg gaggccatca atgcttgccc tcatcatggc tttgatacat 840 ggctcttggt gagctatttt tatgatggaa tgtcttcctc catgaagcaa attcttaaaa 900 ccatgtgtgg gggagatttt atgagtaaga attcggaaga agccatggac tttttaagtt 960 atgtgtctga ggtgtcaaga ggatgggatg agcccaactc aagagagaaa gagaagtttc 1020 cctctcaacc aacccaaaat ccaaaaggtg gaatgtacgt attaagtgaa gacatggaca 1080 tgaaagctaa agtggcaaca atagcaagga ggttggaaga acttgagttg aaaaagatgc 1140 atgaagtcca agccatttcc gagacccaag cccatgtcat gccatgcacc atttgccaat 1200 catgtgatca tgtggtggat gagtgcccaa ccatgccaac tgtgagggag atgttaggtg 1260 atcaagccaa tgttgtgggg caatttaggc ctaacaacaa tgcaccttat ggaaacacct 1320 ataattcaag ctggagaaac catccaaatt tttcttggaa accaagacca cctccatacc 1380 aaccacaagg ccaaacccaa gcacctcaac aaacctcttc agtggagcaa gccattgtga 1440 acctaagtaa agtcatgggt gactttgtgg gtgaacaaaa gacaatcaac tcccaattgc 1500 atcaaaagat tgaaaatgtt gagagttctc aaattaagag aatggagggg atgcaaaatg 1560 atctatctca gaagatagat aatattcaat actccatctc taggcttacc aacctcaaca 1620 ctatgaatga gaagggaaag tttccctctc aaccaagcca aaatcccaag agtgttcatg 1680 aagttgaaac ccaagagggg gagtcttcaa agttgaggga ggttaaagct gctatcactt 1740 taaggagtgg aaaagaggtt gatcaacccc tgcctaaggt gaggcaagat gaagagccaa 1800 ggaaagtgat taaagaggat atgatgaaga aacatatgcc tccccctttt cctcaagctt 1860 tatatggaaa gaaggaaatc aagcattcat cagaaattct tgaagtcttg agacaagtga 1920 aggtgaatat acccttactt gatatgatca agcaagtccc cacatatgca aagtttctaa 1980 aggacttgtg cacggtcaag agagcgttac atgtgacaaa gaatgcattc ctcactgagc 2040 aagtaagtgc tatcattcag agtaagtctc cagttaagta taaagatccg ggatgcccca 2100 ccatttcagt taacattgga gggacacatg tggagaaagc tttactagac ttgggggcaa 2160 gtgtgaattt gctcccatac tctgtgtaca agcaactggg acttggagga ttgaagccca 2220 cagccatcac tctctcctta gctgacaggt cagtcaaaat cccaaggggg gtgatagagg 2280 atgttctagt tcaagtggac aaattctact atcctgtgga ttttgttgtg cttgatactg 2340 atcccactgt gaaggaagca aactatgtac caaacatcct tgggagacct ttcctagcta 2400 cctccaatgc catcatcaat tgtagaaatg gggtgatgca actcacattt gggaatatga 2460 ccttggaatt aaacatattc cacctatgca agaggcatct tcacccagaa gaagaggaag 2520 gattggagga ggtgtgcttg atcaacacct tggttgaaga gcattgtgac aagaatttac 2580 aagagagctt gaatgaaagc cttgaaatgt ttgaagaagg gttacctgaa ccctctgatg 2640 ttctagccat catgtctcct tggaggagac gggaagagat cttaccactg ttcaaccagg 2700 aagactcata aggagcaact gtgggatacc ctccaaagct tgttttgaag ccgcttcctg 2760 ttgatttgaa atatgcatat ttggaggaaa atgagaaatg tccagtggtg gtttcttcaa 2820 ttcttactag tgatcaagag gatagtcttt tgggagtcct caggaaatgc aaaaaagcca 2880 ttggatggca aatttatgat ctgaaatgga ttagcccttt ggtgtgcacc caccatatct 2940 atatggagga tgatgcaaaa ccagtgaggc agccccagag gaggttgaat cctcacatgc 3000 aagaggtggt gaggggtgaa gttctgaagc tactccaagc tgggatcata tatcccattt 3060 cagacagttt gtgggtgagc cccacccaag tagtcccaaa gaaatctgga attattgtgg 3120 tccagaatga gaaaggggag aaagtctcta cacgtcctac ctcaggatgg agggtgtgta 3180 tagactacag gaagttgaat tcagtgacta ggaaggacca tttcccattg cctttcatgg 3240 accaagtcct tgagagagtc tcaggacatc ctttctactg ttttctggat gggtactcgg 3300 ggtacttcca aatagagatt gatttggaag atcaagaaaa aacaaccttc acttgcccct 3360 ttggtacttt tgcgtatagg agaatgccct ttggtctatg taatgctcct gcaactttcc 3420 aaagatgtat gctgagcatc tttagtgata tggtggagcg catcatggaa gtcttcatgg 3480 atgacatcac tgtatatgga agttcttatg aggagtgttt gttgcattta gaagttgttc 3540 tccaaagatg tattgagaaa gacctagtgc taaattggga gaagtgccat tttatggtac 3600 aacaaggaat tgtcttagga catatcatct ccaagaaggg cattgaggta gataaggcaa 3660 aggtggagct aattgttaag ttgccacctc ccacaaatgt taaaggaatt aggcaattct 3720 taggacatgt cgggttctat aggaggttca ttaaggattt ctcaaaaatc tcaaagcctc 3780 tttgtgaact cttggtaaag gatgccaagt ttgtgtggga tgagaagtgt cagaagagtt 3840 ttgaggaact gaagcaattc ctcacaactg caccaatagt gagagcccca aattggaaat 3900 taccttttga ggtaatgtgt gatgcaagtg accttgctat gggggctgtc ttagggcaaa 3960 gagaagatgg aaagccctat gtgatttatt atgcgagcaa aactttgaac gaggctcaaa 4020 ggaactacac aactactgag aaggagttgt tgacagtagt ttttgccttg gataagtttc 4080 gtgcttattt ggtagggtcc tctatagtgg tgttcactga ccattccgct ttgaaatact 4140 tgttaaccaa gcaagatgcc aaggcaagat tgataagatg gatctttttg ctccaagaat 4200 tcaatctcca aatccgggat aaaaaggggg tagaaaatgt ggtagctgat cacttgtcaa 4260 gacttgtgat atcacatgac tcacatggtc tgcctatcaa tgatgacttc cctgaggagt 4320 ctctcatgtc aatagaggta gctccatggt attctcacat tgcaaatttc ttggttacta 4380 gagaagtacc aagtgagtgg agtgcccaag acaagaggca tttctttgct aagatccatg 4440 cctattattg ggaggagcct tttctcttca aatattgtgc ggatcaaatc ataaggaaat 4500 gtgttcctga acaagagcaa tcaggaattc tttcccattg ccatgataat gcatgtagag 4560 gtcattttgc ctcctagaaa acagcaatga aagtgatcca atcaggcttt tggtggccct 4620 ctcttttcaa ggatgcccac tctatgtgca agagatgtga tcggtgtcaa aggcttggta 4680 agctaacacg ccgaaatatg atgcccttga atcccatctt gatagtggat gtctttgatg 4740 tttgggggat agacttcatg ggaccatttc caatgtcgtt tggacattcc tacattttgg 4800 tgggagtgga ttatgtctct aagtgggtag aagcaatccc atgtaggagc aatgatcata 4860 aggtggttct taaattcctc aaggacaaca tctttgcaag atttggagtg cctaaggcca 4920 ttatcagtga tggaggaacc cacttttgca ataaaccttt tgagactctt ctagccaagt 4980 atggggttaa gcacaaggta gttacacctt atcaccctca aacaagtggt caagttgagt 5040 tagccaaccg ggagatcaac aatatattga tgaaggtggt gaatgtgaat aggaaggatt 5100 ggtctattat gggcttatag gcccgcttac aagaccattc ttggaatgtc tccttatcgc 5160 cttgtttatg gcaaagcgtg tcatcttcca gtggaggttg aatataaagc atggtgggaa 5220 tcaaaaaact caacatggat ttgacaagaa ctgggttgaa gagatgtttg gatttgaatg 5280 aattggagga aatgaggaat gatgcttacc tcaattcaaa aattgcaaaa gagaggttga 5340 agaaatggca tgatcaattg gtaaatcaaa agaattttgc caagggacaa agagtcttgc 5400 tttatgactc taagcttcat ctttttccag gaaaattgaa atcaaggtgg acgggtcctt 5460 tcataattca tgatgtgcaa tcaaatggag tagtggaact actcaacttc aatagcactc 5520 aaactttcaa agtgaatgga catcgtctca agccctatat agaatcattt tcccgagaca 5580 aggaggaatt catcctcctt gatccacctc caacatgaaa atacttggtt yatggttgaa 5640 cttagtctct tcaaagacta aagagttcat cctctttttg ttttctttta agttgatttt 5700 artttaatct agtgtttttc ttgtgttttt ccatgttttg atttttattt ttgactttaa 5760 tgtcgttcta atgtgttttg aattggtttt ttttgtgtta acattcaggt gggaaagctt 5820 gaagaatgaa gtcatggtga aagcaaggca aaacagggga gaaaaaacca agactcggcc 5880 attttcgcac aacacttctt gtggtgcgaa atttttgcat aacacacccc ttgtgcgaaa 5940 atgcttttgt ggcaatttcc aaaaaaacat gctctcggtc ccttcccaaa gtcttttgtg 6000 cgaatttcac aggaatgcga accttgtgcg aattcatttt tgggacaaat tttcaaaacc 6060 atgctctctg tctgggtact cacaggaatg cgaaattttc gcataacaca agatgttatg 6120 cgaaatttgc atttcctctt taaagaccgt gttctcctct tccccatgct caatttcttc 6180 ttcatttctc ctagcacctc tcttcccaat caccaaatcc cttccttaag tttcttttct 6240 tcatcattcc ccactctcaa caccaccatg gcagcccatc tccataactc cacctcatag 6300 ccgcggcaat cactattcat caccatccac cccttcaatt ttcagctctt tccaccatca 6360 aaaacctccc aattcttcac tcaacactct aaatccatcc ctcaaccaat ttcagccttg 6420 tatctaccaa accaaagcct caagctaagg attcaagccg cgttttcttc aaagggaacc 6480 cattgccgcc gggtagagga gctccaattt tcaaattttc ttcgtgaaaa agctccaatt 6540 tccaagccta ttcaccatga aaaatccttt tcctacctta gccagcattt cccaccctca 6600 aaagccaaaa attttcacca tttgaacgag cttcaaaact tcaagtgggc gggtgaatag 6660 tgcatgtgcg aaattttcac ataacacgcg aaattttcgc ataacaccta ccttgtgtga 6720 atttttcagt ttttccatct ctgccctccc caatccaaag cctctgagcc tcatttcatt 6780 atttcattat gcctatgacc cgaggaggac atacctcagc tcccaaagta gtgagagagc 6840 cgcctctgtg cgagccccac tagatgcacc gccacattta gctgattctg cctctcagag 6900 caaataccat acgagaagag catctaccac acctgtgacc cctacttaga ttccaccttg 6960 gggttctcct acaaagaaag ccaagacttt agagccagga gagtccttta gaacacctcg 7020 ggattcacag tctcagccgc cttccaccag acgccctaga cccagctcac ccattgaggg 7080 caactcagat tgtcgatcca aagcatttca tgtcgaggca tattttgatc acactatttt 7140 gcgccagcag actgacttgc gggattcata cagcctactt gagaggtacc atcttgcacc 7200 ctttatgact ccgccccagt tcttttatcc tcgagtagtt ttagactttt accagtctat 7260 gactactcat ggcttcccgg taccagcctc gatacttttt accattgatg gacgccaggg 7320 tattttgggg gctcgacaga ttgccgaggc tttccatatc ccttatgcac cagctgatcc 7380 cactgcattt agacgctggg cctcactttc tgagtgggac atggttcgta gcctatctcg 7440 agggacatct tcccagagga ccattttcag gagggagctt cccccaggga tgctcctagt 7500 tgatgtggtg mttcgcacca acctttttcc tcttcagcat acagtacaga ggcgatgggc 7560 cattttagag gcattatttc gtatctctga gggctactac tttggtcctc atcatttgat 7620 tatggccgct cttctccatt ttgaggagaa ggtgcataag cgacatctta cgagggcggc 7680 ttccattcag ttacttttcc ctcggctgct atgccatgtt ttggcacata tgggttttcc 7740 tgcaaaccct caggctgagc cccgccgcca ttgtcgagag agcttctctc ttgaacaatg 7800 gaatcagcta tggctccatc agcattcccc agaacttctc gagccaaggg aagtccctcc 7860 tgctccatcc acttcagctc tctcggagcc tgtaccagag gcagcatcat ctgatgcccc 7920 acctgttgtt cctcctacct cagagccgcc catcactatc cctggttcag agtaccgtgc 7980 cttgctcgct tcttttcaga ctctaaccac tactcagacg gccattatgg agtggatgga 8040 ccacttccag attcagcagg accagcagac tctcattctc cgtgagattc agcagcacct 8100 tggtcttgta ccaccagctc cacctatagc ggtgccttcc tcaattccag caaaggaccc 8160 ctcctatcca ccagaggagc ctattacttg atcatacgat cactcctctc cttttttttg 8220 tatctatatt ctatgttttt ggatgtctta tgtattttgg accactttta tactgggatt 8280 ggatatattc catgtttgtc ttgtatattg tactctctca atttatatag acatcttcct 8340 ttttgtgtat tttagctatt cctttttatt tcctttaatc atcactctta tgatttttct 8400 tttcttatgc aacatgtggt ttctcctctc tattcagagt accttactat caagaggtat 8460 cacttcctcc cttttattac catttgcttt tggaacattg gggacaatgt tcatcctagt 8520 tggggggaga gttgaggaag taatttgttg aattttggtt aagttatatt gctaacaaat 8580 tttttgcaaa ctctccttgt tttcttaaag ataaattctc aaaaaaataa ataaataaat 8640 aaataggaga aattaaattc ttatcttatt gccatagtct tagagtttgt attatgctta 8700 ttaaagttga taaattgttg aagctccttt tgatttcaat cttaagtctt ccactctaat 8760 cttttcacac actgaacaca ttagattcta gttataagat ggaaaacttt ttcaccccct 8820 aaacttagga aatttttgac ttggtgccat tgacctcatt ctattagtgt tgggacacct 8880 tataaaaggc caatgtgtct tatgaaaaaa ttttgcttca cttgctttga aacccgagca 8940 aggtccgagg ggtatatggt gaaaatcttt aaaacctggt gccctaagcc ttcaatggtt 9000 gggagccacc gacctcactg ctcgttacat gggtggatgg gtggagtata tatatatata 9060 taaaaggtgc gttcttagcc ttctatttat gagttagtgt tgctaaagtt agagaaaaac 9120 cttagttggg gggagaatat agtttgacac actataactg gaaactaagc atcttaacac 9180 ttagattttt gtggaagatt aagagttggt cctttgggag tggaaattat tttgatactc 9240 aaatttgcat aatgtccgct ctttgcatgt tgtgataggt aagttatttg atgactcttg 9300 ttgatgattg agttttatat ccttgacttg ccacgagaga gtttgatcca atcatgccac 9360 ttggttattt tttttatttt tttatttttt ggagtgatca gcatgatttt gtaaattatt 9420 atattatcta tttttcttta tttttctttc cttcattgct cagggactag caatgtgtca 9480 gttgggggga g 9491 // ID Ogre-MT4_I repbase; DNA; EDCOT; 12091 BP. XX AC AC145061; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 16-APR-2007 (Rel. 12.03, Last updated, Version 3) XX DE Autonomous LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-MT4; Ogre-MT4_I; internal portion. XX NM Ogre-MT4_I. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-12091 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC145061; Positions 78938 91028. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). CC In Medicago truncatula, there are distinct subfamilies of CC Ogres differing in their LTR sequences. CC Additional annotations: 6055..6357: putative intron. XX FH Key Location/Qualifiers FT CDS 701..2110 FT /product="Ogre-MT4_ORF1" FT /translation="MRNLRQYSFRRPDLLSLRKLGKKVVCMDDFYKQHGNL FT MGVVKTDIDEGLLNAFVQFYDPGYHCFTFQDYQILPTLEEYSCWINLPVLD FT KVPFSGLEEIPKHSTIAAALHLETDEVKAHLITKGKLLGFSTDFLYERTTF FT FDKMGVAYAFNSILALLIYGLVLFPSLDNFVDIKAIQIFLSRNPVPTLLGD FT TYLSIHRRTQAGRGTILCCAQLLYRWITSHLPRTPRFTTNPENLLWSKRLM FT SLTPTEVVWYDRVYDKGTIIDSCGKFANVPLLGIEGGISYNPTLARRQFGY FT PMEGKPLSIYLENVYYLNVDDSKGTKEQVVRAWHTIRRRDKSQLGRKTGAV FT HESYTQWVIDRAVQIGMPYKISRFVSAITPAPPLPMTFDTEKEYQERLVEA FT EREVQKWKGEYQKKDQEYEAVMALLEQEAYDSHKKDVIIAQLKKSIREKDA FT ALDQIPGRKKKRMDLFDGPHSDFEE" FT CDS join(2590..6054,6358..9819) FT /product="Ogre-MT4_ORF2" FT /note="gag-pol." FT /translation="MLAAEQENAQLREELVNLKGEMERMALMMETMMAERE FT QAAISNSTPVVVVTAAPEGPPQPSPTTTTTIGLTQPLITDFSSGNMATMGN FT SGFRPLGPQGPFATPQYSMPSGYPWGMPIATNGVFGPGATEMPFAQGQQTS FT AHFQMSQPIPQATMTQAGPTVHVGPQHEEQIYHSDSIMGDDKAIDWEERFG FT ALEKKMSNMRGKEAVVQSIYDLCLVPDVNIPPKFKMPVFEKYQGDTCPQNH FT LTMYISKMIAYKNNVPLLIHCFQDSLTGPAHTWFMGLKGVTTFEQLAEAFM FT QQYKYNTYLAPSRKELQSLTQKDKESFKEYAQRFIQKAAQIRPPLDERELS FT DLFYETLSPCYSEKMIVCASQKFTDLVETGMRIEEWARKGAAVSGSSSGGS FT SGVSSSGNKKFGNGYPKRNAQEVGMVAHGGPQPVYSNHPFVANITPQMTAP FT QNPNYQSPRPQGPAPYYPPLYQPLYNLQQLSQQPYYPQQPYQQRPYNPPQQ FT QPRPQAPYNQQNQKQQFDPLPMTYGALLPSLLAQNLVQTIPPPRIPDPLPR FT WYRPDLHCIYHQGAPGHDVERCFALKKEVQKLINSKELTFTDPDAVAQNNP FT LPTHGPAVNMIQDDQEEARILSVGDIKTPLVPIHVKMCKATLFNHNHEACD FT ICLMDPRGCIQVQNDMQGLLNRRELVVTREPESKDVCVVTPVFRARRPLVI FT NPNSTKPVGTPLVICVPRPTPTTAQKAVPYKYEGTILEPGSETTSPVVVDN FT IAENSRILRSGRIFPTVGPKSVSVPVDEPVKERNAGKGKAGEQAKEFDFED FT ADEVLKLIKKSEYRVVDQLLQTPAKISIMALLSSSGAHRDALRKVLDQAFV FT DYDVTLGQFESIVGNVTACNSLTFSDEDLPAEGNKHNQALLISVLCRTDSL FT SNVLIDTGSALNVMPKSTLDQLAYSEAPLRLSKVTVRAFDGTRRSVYGEVD FT LPISVGPHEFQVTFQVMEIQASFSCLLGRPWIHDAGAVTSTLHQKLKFVSR FT GKLITVSGESAFLISNLSAFSVIGGSSSDGPSFQGFSAEESVGKIETCMAS FT LKDARRVIQEGKTGGWGQLVELPENKRKEGIGFLNSKPGMFDPTRGSFHSA FT GFIHDSPETNAILDDAPGGVTPVFVTPGGACCNWIAVDIPSVTPRSKLNIS FT ESVEHSDPMLSPNFEVPVYEAVAEEDEEIPNEIKWMLEQERKTIQPHQEEI FT EIINLGTEEDKKEIKIGALLDVSVKKRVIELIREYVDIFAWSYKDMPGLDP FT DVVEHRLPLKPECPPVKQKLRRSHPDMALKIKEEVRKQIDAGFLVTSEYPQ FT WLANIVPVPKKDGKVRMCVDYRDLNKASPKDNFPLPHIDVLVDNTAKCKVF FT SFMDGFSGYNQIRMAPEDREKTSFITPWGAFCYVVMPFGLINAGATYQRGM FT TKIFHDMIHKEIEVYVDDMIVKSGTEEEHVEYLLKMFQRLRKYKLRLNPNK FT CTFGVRSGKLLGFIVSQKGIEVDPDKVRAIREMPVPKTEKQVRGFLGRLNY FT ISRFISHMTATCGPIFKLLRKDQGVEWNDDCQKAFDQIKEYLLEPPILVPP FT VDGRPLIMYLTVLEDSMGCVLGQQDETGKKEHAIYYLSKKFTDCESRYSVL FT EKTCCALTWAAKRLRHYMINHTTWLISKMDPIKYIFEKPALTGRIARWQML FT LSEYDIEYRTQKAVKGSILAEHLAHQPIEDYQSIKFDFPDEEVMYLKAKDC FT DEPVFGEGPDPESEWGLIFDGAVNVYGSGIGAVLITPKGTHIPFTARLRFD FT CTNNIAEYEACIMGIEEAIDLRIKKIVIYGDSALVINQIKGEWETRHPGLI FT PYRDYARRLLTFFNKVELHHVPRDENQMADALATLSSMINVNGHNTVPVIN FT VQFLDRPAYVFVAEAIDDDKPWYHDIQVFLQTQKYPPGASNKDKKTLRRLS FT SRFFLNEDVLYKRNFDGVLLRCVDKHEAEKLMCEIHEGSFGTHSCGHAMAK FT KILRAGYYWITMHADCYNHAKRCHKCQIYADKIHIPPSMLNVISSPWPFSM FT WGIDMIGRIEPKASNGHRFILVAIDYFTKWVEAASYANVTKQVVVRFIKNN FT LISRYGVPNRIITDNGTNLNNNMMKELCDDFKIQHHNSSPYRPQMNGAVEA FT ANKNIKKIIQKMVVTYKDWHEMLPYALYGYRTSVRTSTGATPFSLVYGMEA FT VLPVEVEIPSLRVLMEAELSEAEWCQSRYDQLNLIEEKRMAALCHGQLYQS FT RMKQAFDKGVHPREFKEGDLVLKCIKSFQPDPRGKWTPNYEGPYVVKRAFS FT GGALILTNMDGEELPRPVNSDAVKKYFV" XX SQ Sequence 12091 BP; 3454 A; 2599 C; 2606 G; 3432 T; 0 other; gaaatggcga cttcactggg gacttagatc ctacgcgggt taaacccacc ttactttttt 60 tattttgtgc tttattattt gtttatgctt tgtaaatatt ttgcttacat gtttacttta 120 ttacgtgagt ggtgagataa gctctacacc cgagcttgag ggaaacttaa gataggacgg 180 tggtataatc atagttccat gccaagagta ctcttcggta ttggcacatg tgataacccc 240 actcaacgga gggatcttgg aagtatatgt tgtcaacgtg agtactcatg tttggcatgc 300 tattttcaag tgacctttga agttgaggac ctttagtcac ctttaaccca tcttggcctt 360 ttaggaacgt agtgcggtgg ctaatcgaga gtactcttga attagttgat acgcgatact 420 acacccaaac gagactttcc gacgaatata attggaatgg gagtactccc gttacccgat 480 aaatattcgg aagtggttaa agactttggg aacttggtag aacccttgtt acaagtgcaa 540 tctaaaaacc ttagtcctta ccaaatgacg ttgttaccct ttgactccaa catatgaatt 600 taacttcatc atgcatacat gcatccatcc ataaatattt tttccattca tcattttttt 660 ttgaaggact tataaaagct ttgttgtaaa cattgtagat atgaggaacc ttaggcagta 720 tagtttcagg aggccagatc tcttgagttt gaggaagcta gggaagaaag tggtttgtat 780 ggacgatttc tacaagcaac atggaaattt gatgggtgtt gttaagacag atatcgacga 840 agggcttctc aacgcttttg ttcagttcta tgacccgggc taccattgct ttacttttca 900 agattaccag attctcccca ccttggagga gtactcttgt tggattaatc taccagtgtt 960 ggacaaagta cctttcagtg gcctcgagga aatccccaag cactcaacca ttgccgcagc 1020 tctccatctt gaaacggacg aagtgaaagc acatctcatc actaagggaa aacttttggg 1080 tttctccacc gattttcttt acgaaaggac cacattcttt gacaaaatgg gggttgccta 1140 tgcctttaac tccatccttg ccttgcttat ttatggcctc gtactcttcc ctagcctcga 1200 caactttgtg gacattaaag ccattcaaat tttcttgtca aggaaccctg tccctacctt 1260 attaggtgat acttacctct ccatccatag gcgcacccag gctggtcgtg gaactatcct 1320 ttgttgtgca caattgctat atcgatggat cacctcgcac ttaccccgaa ctcctcgctt 1380 caccaccaat ccagaaaacc ttctttggtc aaaaagactc atgtccctga ctccaaccga 1440 ggtagtgtgg tacgatcggg tttatgacaa aggaactatt attgacagtt gtgggaaatt 1500 tgccaatgta ccacttcttg gtatagaagg aggaattagc tacaatccta cgcttgccag 1560 acgtcagttc ggatatccca tggaagggaa gccgctcagc atctatctag agaatgtgta 1620 ttacctcaac gtagatgaca gtaaaggcac gaaagagcag gttgtgcgag cttggcacac 1680 cattcgtaga agagacaaga gccagttagg gaggaagaca ggagccgttc atgaatcata 1740 tactcagtgg gtgatagata gagctgttca aattgggatg ccttacaaga tatcaagatt 1800 tgtatctgca atcactccag caccacccct acctatgacc tttgacaccg agaaggaata 1860 ccaagagcgt ttagttgagg cggaacgtga agtacaaaag tggaaagggg agtatcagaa 1920 aaaggatcag gaatatgagg ctgtgatggc cctactagag caagaagcct atgatagcca 1980 caagaaagat gtgataatcg cccagctgaa aaagagtatc agagagaaag atgccgcgct 2040 tgatcaaatt cccgggcgga agaagaagcg tatggatctc tttgatgggc cgcattctga 2100 ttttgaggag tagctcggtt cagaggcttg agagtctttc agtttgtttt gatgtttttt 2160 gtgtagttac ggagtctatc ccttggcttt gttgttagaa agggaattat ctcgttttat 2220 tttgaaagtt tttcccttgg ctttgttgtt agaaagggaa ttatcttgtt tttctttgaa 2280 agtttatccc ttggctttgt tgttagaagg ggaattatct tgtaatcaac tttgtttttt 2340 tatgatttgt ttaggttggt atgtttacaa aactgctttt ataggtcctt caataaaaat 2400 aaaaaaaaaa tatataaaaa tcgcatattt tggcatatag catatcatgc atcatattgc 2460 attcataaaa agtatcaaaa tccaagtctc atactctcct catttctgcc tcagaaaagc 2520 aaagtggccc ggcgtattca gtacaaaccc gctcgcattc acaacactcg agctcatatc 2580 aagaaaagga tgttagcggc agaacaggaa aacgctcagc tcagagagga actggttaac 2640 ctcaaggggg agatggaaag aatggcactt atgatggaaa ctatgatggc tgagagagag 2700 caagcagcaa tctccaattc aactcctgtt gtggttgtca cagctgcacc tgagggtcct 2760 ccgcaaccat ctccgactac tactacaact atcggcctca cccagcctct gataactgat 2820 ttttcttctg gtaatatggc aactatgggc aactcaggct tccgtcctct tggcccccag 2880 ggtccctttg ctactcctca atattccatg ccttcaggct acccttgggg catgccgatt 2940 gcaactaacg gggtttttgg tccaggcgct actgaaatgc ctttcgcaca gggtcaacag 3000 acttcggcac atttccagat gagtcaaccg attcctcaag ctaccatgac tcaagcaggt 3060 cctactgtgc atgttgggcc acaacatgaa gaacagattt atcactccga cagtataatg 3120 ggggatgaca aagcaatcga ttgggaagaa aggttcggtg ctctagagaa gaagatgagt 3180 aatatgcggg gaaaggaagc agtcgtccaa agcatatatg acctttgctt ggtaccagat 3240 gtaaacatac ctccaaagtt caagatgcct gtatttgaga agtatcaagg ggacacatgt 3300 ccacaaaatc atctaactat gtatattagc aagatgatag cttacaagaa taatgttccc 3360 ttactcattc actgcttcca ggatagtttg actggtccgg cacatacctg gttcatggga 3420 ttgaaaggag tcactacttt tgaacagttg gctgaggcct tcatgcaaca gtacaaatat 3480 aatacctatc tggcgccaag tcgcaaggag ttgcagtcct taacccagaa agataaagaa 3540 tcgttcaaag aatacgcaca acgcttcatt caaaaagctg ctcagattcg tcctcccttg 3600 gatgagaggg aactttcaga tttgttctat gaaaccctga gcccttgtta ttcagaaaag 3660 atgattgtct gtgcatcaca gaagttcact gacttggtgg aaacaggaat gcgtatcgag 3720 gagtgggctc gtaagggagc agctgtttcg ggaagttctt caggtggttc ttcaggagtt 3780 tcgtccagtg gtaataagaa atttgggaat ggttacccaa agaggaatgc tcaagaggtt 3840 ggcatggtgg ctcatggagg acctcagccc gtgtactcta atcacccctt tgttgccaac 3900 atcaccccac aaatgaccgc accccagaac ccaaactatc aatcacccag acctcaagga 3960 cctgcaccat actacccccc attataccaa ccactataca acctacaaca actctctcaa 4020 caaccctact atcctcaaca accataccaa caaaggccat ataacccccc acaacaacaa 4080 ccccgtcctc aagctcccta caaccagcaa aatcaaaaac aacaatttga ccccttgcca 4140 atgacctatg gagcattgct cccttcttta cttgcacaga atctggtcca aactatacca 4200 cctcctcgca ttccggaccc tctcccacgc tggtaccgtc cggaccttca ttgtatttac 4260 catcaagggg caccaggcca cgatgtggag cgttgttttg ctcttaagaa agaggttcag 4320 aaattgataa atagtaaaga gttaaccttc accgaccctg atgctgtagc tcagaacaat 4380 cctctgccta ctcatgggcc tgctgttaat atgattcaag acgatcagga agaggctcgc 4440 attctctctg taggtgatat caagactcct ctggtaccga tacatgtgaa aatgtgtaaa 4500 gcaactctct tcaaccacaa tcatgaagct tgtgacatat gtttgatgga tcctcgtgga 4560 tgtatacaag tccagaatga tatgcagggt ctcctaaata gaagggaact tgtggttaca 4620 agggaacccg agagcaagga cgtctgtgtt gtcactccgg tattcagagc caggaggcca 4680 ctggtgataa accctaacag tacaaagccc gttggtactc ccttggtaat ctgtgtgcct 4740 aggcccacgc ctactactgc tcagaaagct gtaccctata agtatgaagg cacgattctt 4800 gagcccggaa gtgagacaac ttcacctgtt gttgtggata atatcgcaga gaatagccgg 4860 attttgagga gtggccgcat ctttcctacg gtgggtccga agagtgttag tgttccggtc 4920 gatgagccag taaaagagcg aaacgccggt aaaggtaaag ctggggagca ggccaaagag 4980 tttgactttg aggatgccga tgaagtcttg aagctgatca agaagagtga atacagggtg 5040 gtggaccagc tgttacaaac tcctgcgaag atttccatca tggccctgtt atcaagttct 5100 ggtgctcatc gggatgccct gaggaaagta ctagaccagg catttgtgga ttatgatgta 5160 actctgggtc aattcgaaag cattgtgggg aatgtgaccg cgtgtaacag tctgactttc 5220 agtgatgaag atctcccggc ggaggggaat aagcataatc aagcattact catctctgta 5280 ctttgcagaa cagattcgtt atccaacgtc ttgatagata ccggctctgc acttaatgtg 5340 atgcccaagt caactctcga ccaattggcg tactccgagg ctcctttgag acttagcaag 5400 gtgacagtga gggccttcga tggaactagg agatcggtgt atggtgaggt agatttgcca 5460 atttcggtcg gcccacatga atttcaggtt actttccaag tcatggaaat ccaggcttct 5520 ttcagctgtt tgctcggcag accatggatt catgacgctg gggctgtgac atctactctc 5580 catcagaaat tgaagtttgt aagtcgtgga aagttgatca ctgtgagtgg cgagtcggcc 5640 tttttaatca gcaatttgtc tgctttctct gttatcggtg gtagtagttc ggacgggcca 5700 tcattccaag ggttctctgc cgaagaaagt gtcggtaaga tcgagacttg tatggcttcg 5760 ttgaaggatg cccggagagt aattcaggaa ggcaaaaccg gaggctgggg tcagctagtg 5820 gagttgccag aaaacaagcg taaagaggga attggtttcc ttaacagtaa gcctgggatg 5880 ttcgacccta ccagaggttc tttccacagt gctggtttca ttcatgattc gccagagacc 5940 aatgcaattt tagatgatgc acctggagga gtgacaccgg tctttgtgac gcctggagga 6000 gcttgctgca actggattgc tgttgacatt ccttctgtga caccccgctc taagtaatgt 6060 gtttgtcttg tcttttgttg tttttttgtt tttaagaaaa ctcctttcgt tctgcccaag 6120 gcgaaagtga aatcatgtag ggctttgttt tgcttctagt acttttatta caaataaaaa 6180 tcgtcgtttc tatcacggct tttattactt ttattttttt ttgttgcttt ttatggaaaa 6240 aatggtaata caaaaatcca aaaaaaaatc attctctttt tttttttttt ctcttttaaa 6300 tttcaaaacc aaaggtctgc atttactcat taaaatcaat catgaatcat gtgcagactg 6360 aacataagtg aatccgttga acacagtgac cccatgcttt ctcccaactt tgaggtcccg 6420 gtttacgagg ctgtggcaga ggaggatgaa gagatcccga atgagatcaa atggatgttg 6480 gaacaagaaa ggaagacaat tcaacctcat caggaggaga tagaaatcat caatctgggt 6540 actgaggaag acaagaaaga aatcaagatt ggggcattgt tggatgtatc tgtcaagaaa 6600 agagtaattg agcttatcag agaatatgtt gatatattcg catggtcata caaagacatg 6660 ccgggtctag accctgatgt cgttgaacac agactacctt tgaagcctga gtgtcctccg 6720 gtaaagcaga aattgagaag atctcatcct gatatggccc tcaagatcaa agaggaagtg 6780 cgaaagcaga ttgatgcagg tttcctagtc acatcagagt atcctcaatg gttggccaac 6840 atagtgcctg ttccaaagaa agatggcaaa gtcagaatgt gtgttgatta tcgggacttg 6900 aacaaggcta gtccgaagga taattttcct ttacctcaca ttgatgtatt ggttgataat 6960 actgctaagt gcaaggtttt ctccttcatg gacggtttct ccggctacaa tcagatcagg 7020 atggctcctg aggatagaga aaagacgtct ttcatcacgc cctggggtgc tttctgctat 7080 gtggtgatgc catttggttt gataaatgct ggtgccactt accaaagggg tatgaccaaa 7140 atctttcatg atatgattca caaagaaatt gaggtctacg tagatgatat gattgttaag 7200 tctggcacag aagaagaaca tgttgagtat ttgttgaaga tgtttcagcg gttgagaaag 7260 tacaagctcc ggttgaatcc taacaaatgt actttcggtg tcagatctgg taaactccta 7320 ggctttatcg tcagtcaaaa gggtattgaa gttgatcccg acaaggtcag agccatcaga 7380 gaaatgcctg ttccaaagac agagaagcaa gtcagaggtt ttcttggtag actcaattat 7440 atctccagat ttatctctca catgactgcc acatgtggac caattttcaa gttactccgc 7500 aaggatcaag gggtggagtg gaatgatgat tgtcagaagg cttttgatca aatcaaagaa 7560 tatctgttag aacctccaat tcttgttcct ccagttgacg gaagaccttt gatcatgtat 7620 ttaactgtac tggaagattc catgggctgt gttttgggtc aacaagatga aaccggaaag 7680 aaagagcacg ctatctacta tttgagtaag aagttcactg attgtgagtc ccgatattct 7740 gtacttgaga aaacttgttg tgctttaact tgggctgcca agcgtctccg tcattatatg 7800 attaatcata caacttggtt gatatccaag atggatccta tcaagtacat atttgagaag 7860 ccagctttaa ctggaaggat tgctcgctgg cagatgttat tgtccgagta tgatatcgag 7920 tatcgcactc agaaagcagt caaaggtagc atcttggcag aacatttggc tcatcaacca 7980 atcgaagact atcaatcaat caaattcgac ttcccagatg aagaggttat gtatctaaaa 8040 gcaaaagatt gtgacgaacc agtgttcggt gaaggtcctg atcctgaatc cgaatggggt 8100 ttgatatttg atggagctgt taatgtctat ggaagtggaa ttggtgcggt cctcattacc 8160 cctaagggta ctcacatccc ttttactgcg aggttacgtt ttgattgcac aaacaacatc 8220 gcagagtacg aagcttgcat catgggtatc gaggaagcca tcgatttgag gatcaagaaa 8280 attgtcattt atggagattc cgctcttgtg attaaccaga tcaaaggaga atgggaaact 8340 cgccatcctg gtttgattcc ctacagagat tatgcgagac gattgctgac tttcttcaac 8400 aaagtagagt tacatcatgt gccccgcgat gagaatcaaa tggcagatgc tttagctact 8460 ctatcctcaa tgatcaatgt gaatggtcac aatactgtgc cagtaatcaa tgtccaattt 8520 ctcgaccgac ctgcttatgt gtttgtagct gaagcaattg atgatgacaa gccatggtat 8580 catgatatcc aagttttcct tcaaactcaa aagtacccac ctggggcatc caacaaggac 8640 aagaaaacat tgagaagatt gtcaagccgt ttcttcctta acgaagacgt tttgtataaa 8700 aggaactttg atggggtcct acttagatgt gtggataagc atgaagcaga aaaattgatg 8760 tgcgagattc atgaaggctc tttcggaact cactcatgtg ggcacgccat ggcgaagaag 8820 atattgagag ctgggtacta ctggataaca atgcacgctg attgctacaa tcatgccaag 8880 agatgccaca aatgtcaaat ctatgctgac aagattcata taccaccatc tatgctcaat 8940 gtcatctctt ccccgtggcc cttctctatg tggggcattg acatgattgg tcggattgaa 9000 ccaaaggctt ccaatgggca tcgcttcata ttagtggcta tcgattattt caccaagtgg 9060 gttgaagcag catcttatgc caatgtgacc aagcaggtag tggtcagatt tatcaagaac 9120 aacctcatca gccgctacgg tgttcccaac agaatcatca cagacaatgg cacaaatctg 9180 aataacaaca tgatgaaaga gttgtgcgat gacttcaaga ttcaacatca caattcttct 9240 ccttacagac cacagatgaa tggggcagtt gaagctgcaa acaagaacat caagaagatc 9300 atacagaaga tggtagttac ttataaggac tggcatgaaa tgttacccta cgctttgtat 9360 ggataccgta cctcagtgcg aacctcgaca ggggcaaccc ctttctcttt ggtatatggt 9420 atggaggctg tactacctgt agaggttgag attccttctt taagagtctt gatggaagct 9480 gaattgtctg aagctgaatg gtgccagagc aggtacgacc agttgaattt gattgaggaa 9540 aaacgtatgg ctgctttgtg tcatggacag ttatatcagt caaggatgaa acaagcattt 9600 gataaaggag tccatccccg cgaattcaag gaaggagatc ttgtgctcaa atgtatcaaa 9660 tcctttcaac cagatcctag gggcaaatgg acgccaaact atgaaggtcc ctatgtggtg 9720 aagagagctt tctctggtgg tgctttaatt cttacaaata tggatggaga ggagttacct 9780 cgtcctgtga attctgatgc agtcaagaaa tactttgtct aaatatataa aagaacagct 9840 cggtaggtcg aaaacctgaa agggcggctt aaaccaaaaa tgagcgtctc ggtggatcga 9900 aaacccgaaa gggcggtcca ggcaaaaatt agagacagaa aaaaaaaaaa aaaaaaagaa 9960 gggaaattat cctgatagat cgaaaacccg caagggcgat ctatgcaaaa attaaggatc 10020 gagacaagta actgcatcag atgaaacatc actcgcccga gacaccttga ctgtcagaag 10080 ttctctaatg ttgaagcatc caaactgtgg aattcaaagt ggttaagaag tatagcggtc 10140 attgtgttca atgtacctat cccatataat taccatattc caactctttg taatctgtgg 10200 tgccatgcct ttagccggtc accatttcta ttaaatcaat ttgagcatgt gcccctttgt 10260 tggaattctt gtttattcta tgtgcaaaaa aatctttctt tcgtttttag tattagtatt 10320 tgaaacaaaa ttttgaaaaa aacttttcta aagattttat gttttctttc taaaaaaaaa 10380 aaaaaaaaaa aaaaaaaaaa aaaacaacaa aaaaaatgac aaacatatta tctttaaaaa 10440 catgtatcac ataagtatgt gtcaacagtt ggtccgaaac aagcaggttc aacaaagaag 10500 aaatagtcat tgcaaaaaaa aagagcgccc tggtggatcg aaaacccgaa agggcgatct 10560 aggtaaaaat taggggcata caaaaagaga aaaagaaaaa tgtctccccg gtggattgaa 10620 aatccgaaag gacgatccag gcaaaagtta gggatttcaa atataaatac aaaaagcaat 10680 gactattcag acaagacagt acggtgttgc attgatgaaa tggcgacttc taccacagtt 10740 tgtgaagact tacctcagca gtatgtttaa gggctgtacc ctaacaatgt ttgattcatt 10800 ccccgtgact ttatccccat tgaaggcttt gagtgttcgt acagtgatgc cgggccattc 10860 tcctcgtaga cctgcccagt cctgtctcaa caatcttacc attacaccat catatgagtc 10920 tcatacatat tcattcattc atgcatacat agcacgcata taaacaccat ccatacatag 10980 tttctttttt tacccaatat tttgcttcat tatcctcaaa atgggtctaa actcaggtat 11040 gttataaaac caatcgtgtt tcaaagtggc aggtctcgcc agtaaccagt ctatacagtt 11100 gccccatcgt cttcagacaa tttcattttt cccctcaggt gtatctttgt caagttaatc 11160 cccactcata tcaagcttta caatgtcttt actttagcca ctcgtcggcc catcatgtct 11220 ttactttcgc cactcgtcgg ccaatcatgt ctttaatttc gccactcgtc ggcccatcat 11280 gtctttaatt tcgccactca tcggcccgtc atgtctttac tttagccact cgtcggcccg 11340 tcttgtcttt actttagcca ctcgtcggcc cgtcatgtct ttactttagc cgctcgtcgg 11400 cctgtcttgt ctttacctta gccactcgtc ggcccgtcat gtctttacgt tcgccactcg 11460 tcggccaatc atgtctttac tttcgccact cgtcagcaat caatcatgtc tttactttcg 11520 ccactcgtcg gccaatcatg tctttacttt cgccactcgt cggcaatcaa tcatgtcttt 11580 actttcgcca ctcgtcggca attaatcatg tctttacatt cgccactcgt cggcaatcaa 11640 tcatgtcttt actttcgcca ctcgtcggcc aatcatgtct ttactttcgc cactcgtcgg 11700 caatcaatca tgtctttact ttcgccactc gtcggcaatt aatcatgtct ttacattcgc 11760 cactcgtcgg caatcaatca tgtctttact ttcgccactc gtcggccaat catgtcttta 11820 ctttcgcctt gaaacattgt catttatact tacctatcat ttctttcccc agtgatacct 11880 atccatttgg ctcccagtca gcctctgcat catcgttacc ttcatactta catcatattc 11940 agtcgtatta tcacattcat cagcattaca tctctggcgt ttcaaatggt ccaaaattgg 12000 cgtttttata tatttaagtc tctccgaccc tttggtttaa aaagttctct tttaaaacct 12060 ttgtgacgaa gaaacttaaa taggggcatc t 12091 // ID Copia-19_Mad-I repbase; DNA; EDCOT; 4218 BP. XX AC ACYM01079582; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-19_Mad_; KW Copia-19_Mad-LTR; Copia-19_Mad-I. XX NM Copia-19_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4218 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1364-1364 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01079582; Positions 18236 14019. XX CC Positions [1721-2041] - Integrase core CC 'TTTAA' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 392..2041 FT /product="Copia-19_Mad-I_1p" FT /translation="MAWDLLYGEYHGGDQVRSVKLQNLRREFEYARMRDDE FT CLSNYLTRLNDLINQMRTFGESLSNERLVQKVLISLSKPYDSIYLIIENTK FT CLETVELQEVVAILKSQEQRFDLHTVDTTGKAFSSLTISPKGQNNGGSQFG FT PSQLQKNWNSKGRKWDSRPKFQQKFSTNSAHNAYSSQSVNQSSTKPQCKVC FT SKFHFGECRFKGKPKCYNCERFGHWARECPVSKPVQKANSANQVEVTGNLL FT FANSTISESTVNGEWYIDSGCSNHTTVSEKLLVDIRRNVVGKVQMPTGELM FT NVAGMGTLVIDTSKGRKYIKEVMYLPELQENLLSVGQMDEHGYYLLFGGKM FT CSIFDGPSLDCLVIKVEMKRNICYPLTLLSNDQVALKTSLSRSTWIWHKRL FT GHLHQRGLKQLKEKEMVHGLPKLEEVDEICEGCQLGTQHREWFPKNQAWRA FT SNPLELVHVDLCGPMQTESIAGNKYFMLLVYDCTRMMWVYFLRYKSDALNC FT FRKFKSMVELQSGFKVKCLTSDRGGEFTSGEFNKLCDDEGIQRQLSMAYTP FT QQN" XX SQ Sequence 4218 BP; 1392 A; 678 C; 977 G; 1166 T; 5 other; tggcctcaga gccaggttgc gccatttaaa atctgggygt aaatctatga ggtcaccgag 60 ctctatcgaa gctcacgaaa ggtttgcaaa gatgtctgga tctggaggct cggaagtgag 120 aactccaatc ttctccggcg agaactacga gttctggaga attaagatgg taacaatctt 180 caaatctctt gggttatgga atctggtaga aaagggattg ccaacacccg atttgaaaaa 240 gaagaagaag gaagctgaag agtcatcgga agacgacagt gatgaagaaa tgattgatgt 300 gctcgtgagg gatgcaaagg ctctaggtat tatacaaaat gcagtttctg atcagatctt 360 tcctaggatt gccaackccg attcagccaa gatggcatgg gatctactgt atggagaata 420 tcatggtggt gatcaggtta gatccgtaaa acttcagaat cttagacgag aatttgagta 480 tgctagaatg cgagatgatg aatgtctatc taattatctc acaaggctaa atgatctaat 540 taaccagatg agaacatttg gtgaatctct ttctaatgag agacttgtgc agaaagttct 600 gattagttta agtaaacctt atgattcgat ctatttgatt atagaaaata caaagtgtct 660 agaaactgta gaattgcagg aagttgttgc gatcttaaag agccaagagc aacggtttga 720 tttgcacact gttgacacta ctgggaaggc attctcatcc ctcacaataa gtccaaaagg 780 acaaaataat ggtggatctc aatttggtcc atctcagctt cagaagaatt ggaattctaa 840 aggcagaaaa tgggattcga gacccaagtt ccagcagaaa ttttctacaa attctgctca 900 taatgcatat tcctcacagt ctgtgaatca gtcaagtaca aaaccacaat gtaaggtgtg 960 ctctaaattt cactttggtg agtgtagatt taaggggaag cctaaatgtt acaattgtga 1020 gagatttgga cactgggcta gagaatgtcc tgtaagcaaa ccagtgcaaa aggcaaacag 1080 tgctaatcaa gtagaggtga cagggaatct attatttgct aacagcacca tctctgaatc 1140 tactgtcaat ggtgaatggt atattgacag tggttgtagc aatcatacga ctgtaagtga 1200 gaagttattg gttgatataa ggaggaatgt ggtaggcaag gtacaaatgc caactggaga 1260 acttatgaat gtggctggaa tgggtactct agtgattgat actagtaaag gcagaaagta 1320 catcaaagaa gtaatgtatc taccggaatt gcaggagaac ttactaagtg tgggacaaat 1380 ggatgagcat gggtattatt tattgtttgg aggtaaaatg tgcagcatct ttgatggtcc 1440 ctcattagac tgccttgtaa tcaaagtaga gatgaagagg aatatatgct atccattaac 1500 attattatct aatgatcaag ttgcattgaa aacaagctta tctcggtcta cctggatttg 1560 gcacaagaga ttaggtcatc tacaccaaag ggggttaaag caactcaaag agaaagaaat 1620 ggttcatgga cttccaaaat tagaagaggt tgatgaaatc tgtgaaggat gtcaacttgg 1680 aacacaacat agagagtggt ttccaaagaa tcaagcatgg agggcaagca atccactaga 1740 gttagttcat gttgacttat gtgggcctat gcaaactgag tctattgcag gtaacaagta 1800 ttttatgctt cttgtatatg actgcacaag aatgatgtgg gtttatttcc tcagatacaa 1860 gtcagatgca ttgaattgtt ttagaaaatt caagtctatg gtagaattac agagtggttt 1920 taaagtgaaa tgtctgacaa gtgacagagg aggggaattc acatcaggtg agtttaataa 1980 actgtgtgat gatgaaggca ttcaaagaca actttctatg gcttatactc cacagcaaaa 2040 ttgagtggtg gaaaggaaaa acagagmtgt agttgaaatg gaaaaagcca tgctccatga 2100 taaaggatta ccttactatc tgtgggcaga atctgtacac acaaatgtct acttactgaa 2160 taggtgtcct acaagagctc tcggagatat aacctcattt gaagcattca gtgggagaaa 2220 accagggatt gcacatttta aaatctttgg ttgcttgtgc tatgtgcata tatcaagtga 2280 actgagacag aagctagatg ccaagagtac caagggcatc tttgtaggat atgcaacttg 2340 tgaaaaaggg tacagggtgt atgaccctat caagaagaga ctttggttgt caagggatgt 2400 agtatttgat gagggtgcag cttggaattg gaaggagatc tctgatactc atgtaattgt 2460 gccaaattat gaaaacttat ctgaacagtc acaattttca tcacctaaca caactcttgg 2520 aagtcatgac tatattcagt caccaagatt gtcatcttct catgaaacaa caggtgatat 2580 aattagcagt atgaaaaagt ctgaaacata tgaccacact ccactgaaat ggagaaattt 2640 ggatgatgtt ctrgcacaat gcaatctttg cattgtagaa cctgaaaagt ttgatgaagc 2700 tgccaaagat aaatcatgga tgaaagctat ggaagatgag ttgtcaatga ttgaaaagaa 2760 tgcaacatgg gaattggtag atagaccaat aaacaagctt ataattggtg tgaagtgggt 2820 gtttaaaact aaactcaacc ttgatggaac tgtgcagaag aataaggcac gacttkttgc 2880 aaagggatat gctcaaaaac cagggataga ctataatgag acttttgccc cagttgctag 2940 attggataca attaggactc ttgttgcttt ggctgcacaa aagaactgga aactgtatca 3000 actagatgtc aaatctgctt ttctaaacgg agtactagaa gaggaggtct atgtagatca 3060 gccggatggt tttgtagtca aggggagtga agacaaggtg tacaagcttc ataaagcttt 3120 gtatggttta aaacaagcac caagggcctg gtatagtgaa attaactcct attttgtgca 3180 gtgtggattt gttaaaagcc aaagcgaagc tactctctac acaaaagaaa agggagaaga 3240 attcctaatt gtttcactct atgttgatga cattgtgtac actgggaaca acaatgtgtt 3300 attgaatgaa ttctaggagg acatgaagat caaatatgaa atgacagatt tgggacttct 3360 tcaccatttt cttggcatgg gagtcattca aactcactcg agcattttca ttcatcaaag 3420 gaaatatgca gcctccttgt tgagtaagtt tgggctaagt gagtgcaaat ctgtggccac 3480 acctcttgtc ccatctgata aactgtgtaa agatgatggt agtggaccag caagtgagga 3540 acaatataga agaattgtgg gaagtttact ataccttact gtcactcgac cagacataat 3600 gtatgctgct agtctccttg ctagattcat gcatagtccc acaaataaac attttggtac 3660 tgctaaaaga gtgctaagat atattaaagg caccttggat tatggattgg aatatgtgaa 3720 aggaaagaat gcaatgctaa tcgggttttg tgatagtgat tggggaggat cagttgatga 3780 cagcaaaaac acttctggat atgctttttc ttttggtagt ggagtgttct cttgggcttc 3840 agtgaaacaa aattgtgtag ctctctccac tgcagaagca gagtatatca gtgcctctga 3900 agcaacagca caagccattt ggcttagatt cgtgcttgaa gatttcggtg aattacaaac 3960 tgaagcaact ccagtgcact gtgacaatac aactgcaatt gcaatcacta aaaatctagt 4020 tttccatcag aaaaccaaac acatcgacag aaggtatcat ttcattaagg gtgcacttca 4080 agaaggaata attgacttgg tgtattgtcc aacaaatgag caagtggcag atatattcac 4140 taaggcttta accaaggatc gattcaacta tcttagagac atgcttggtg tgaaatcagc 4200 tcaaaactta aaggggag 4218 // ID DNA8-7_Mad repbase; DNA; EDCOT; 783 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA8-7_Mad. XX NM DNA8-7_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-783 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1478-1478 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~93% identical to the consensus. TIR is ~25-bp long. TSD is 8-bp CC long. XX SQ Sequence 783 BP; 259 A; 135 C; 120 G; 269 T; 0 other; ggcttattat attaacaccc cacaaattgt tgaataaacc ccacatactt aatacacctc 60 acatttgctt tttcaatgaa aaattatctt aatacacccc acatacttcc ccataatacc 120 ctcacattct caatatacac cttacatttt ctacatgcac cccatatttt ctatacaccc 180 cacatttctc aaatcttata aagcttttaa tttggacaaa aaatgccgac tggaattttg 240 acaaaagatg ccgcctggga tttaaagcat atgtgggttg ttttcaattc caccattaaa 300 acccatgtcg tctgttttta atatttggtg gtaattttag gtgtttaatt cttcatgtaa 360 tccctgtgat ccctaaaaga tgaatacgaa catagaagct tgaataacgc agcaaaagca 420 agattaaata attatcgatg tcgtcaaaat cactaaaaca ataaagaata tgaagtctta 480 cctcatgtga agcttccgaa acatcgattt cgtgtttcat tcgtcaaaaa taatttttct 540 caatcaacat gtttgtagtt tcattggtta gggttttgtt caacaatgga gggtcggagg 600 ggttttgata gttgaagaag ataaataata cgttaaaagt gatttggggt gtatttagaa 660 tttttttttt ttaacctaat aaggtcaaaa ttgtcattgc atagtagggt aaataagtta 720 tttaatatta aattttaatg tggggtgcat tcaacatttt gtggggtgct aatataaaaa 780 gcc 783 // ID EnSpm-N1_Mad repbase; DNA; EDCOT; 1943 BP. XX AC . XX DT 20-OCT-2010 (Rel. 15.1, Created) DT 20-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous EnSpm elements, consensus. XX KW EnSpm; DNA transposon; Transposable Element; Nonautonomous; KW EnSpm-N1_Mad. XX NM EnSpm-N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1943 RA Bao W. and Jurka J.; RT "EnSpm-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1604-1604 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is ~89-bp long. XX SQ Sequence 1943 BP; 692 A; 287 C; 383 G; 580 T; 1 other; cactactaca aaaaacactt tgcgcgacga aataagtttg ttgcgcaaag tacaatttcg 60 tcgcgcaaaa ccttgcgcga cgaaattttg gtcgcgcatg gttcgtcgcg caaagctcgt 120 gacgataggg tttgcgcgac gaaaattaat cttcgtcgcg caaagtactt tgcgcgacga 180 aatattttgt cgcgcaaaga tttaatactt tgcgcgacga aatatttcgt cgcgcaaaga 240 tttttgtttt taatttttta attaaattaa ttaatttaat attttgcgcg acgaaatatt 300 ttgtcgcgca aggtttttga ctttttgttt tattatttct cttatttaat ttaattatat 360 taattgtttg cgcgacgaaa tatttggtag cgcaagattt ttcgaatttt tactttttta 420 atttaattta attgtatgat tttatttttt aattacttta atttaaattg acatattcaa 480 aataaaatta catatgaaaa atagtgatca aattatccaa tatatataat atattcaaaa 540 tgtacacata aattaacaaa gtacaataat aaaatcctaa tacaagtcta ttgtggtggt 600 agtggcgggg gatatggttc gatagcgtcc taatcctcaa ctttagccgt caaagtctcg 660 acgattccct acaaaaaaaa aaaaacaaac atggtcaaat aacaaaaaaa acataaaata 720 ataccaaaaa attggcataa tctcccctaa aattggtata ccccaaatcc gaccccaaac 780 tccacccctc accctatact cgaccccaaa ccccgcacca aactcaaaat taactccaaa 840 aacacatatt aatgaaaaaa aaattaaaat ttggggagaa tatacctttt ggcaagattg 900 agagtgagtg agaatgagag ggaggagtga gtgtgagaga attagaggag atagtgagag 960 agagatgaga gagtgagtga gagtgagaga tagtgaagag agagagaaga gagattaagt 1020 gagaggagtg agtgtgagag agagggtcgg atttggggag agggaaagag agaggagagg 1080 taagagaata gagaaagaca ttgagaaaat tgtggaggag ttattttggt tttaaaaacc 1140 gtatcacttt gcgcgacgaa atattggtcg cgcaaagtct taaaaaaaat tcccgcgtcc 1200 catttttggt gcccgcccaa atttttagag ttttgcgcga cgaagtgttg gtcgcgcaaa 1260 gttttgcgcg acgaagaatt ggtcgcgcaa agttttgcga cgaaattggt cgcgcaaagt 1320 cttaaaaaaa aaaattcccg cgtcccattt ttggcgcccg cccaaattta aggattttgc 1380 gcgacgaaat attggttcgt cgcgcaaaat ttataaaaat aattttattt tacaatttaa 1440 aatataaata aattaaaata aataaggttt aggcgaccaa atgtgtattc gtcgcgcaaa 1500 gaaaataata aagaaataat ttagtttaac aatataaaat ataaaaaaat aagtaaataa 1560 ggtttaggcg acgaaatatt gatattcgtc gcgcaaagtt tttaaaaaat aataaaaact 1620 tatgaaaata actatatttt aaaatttata atataaaatt aaataaaaaa caaaaataaa 1680 ttggtttagg cgacgaaata tttggattwc gtcgcgcaaa ggtttaaaaa aaaatttatt 1740 ttttttattt ttgtaaagac tttgcgtgac gaagtttaaa gtttcgtcgc gcaaagtaac 1800 tttgcgtgac gtgtgtttcg tcgcacaaaa tttcatcgcg caagactttg cgcgacgaag 1860 tttaaaattt cgtcgcgcaa agtgactttg cgcgacgatg tgtgtttcgt cgcgcaaaca 1920 aggggttttt ttttttacta gtg 1943 // ID Copia-5_SL-LTR repbase; DNA; EDCOT; 144 BP. XX AC AC243358; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the tomato genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-5_SL_; KW Copia-5_SL-I; Copia-5_SL-LTR. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-144 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the tomato genome."; RL Direct Submission to RU (22-JAN-2011). XX DR Genome; AC243358; Positions 96401 96544. XX SQ Sequence 144 BP; 41 A; 32 C; 14 G; 57 T; 0 other; tgtgtactaa tcctagtcct attaggatta gtactcctta attctagtcc tattaggatt 60 agtactcctt ccaatatctc ctatatatat ctcgcatgta ttcccttatt aggttaacaa 120 ttcaatacaa tcaatattcc ttca 144 // ID COP14_LTR_MT repbase; DNA; EDCOT; 171 BP. XX AC . XX DT 02-JAN-2007 (Rel. 12.01, Created) DT 02-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of COP14_MT LTR retroposon from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR; retroposon; Interspersed; repeat; COP14_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-171 RA Shankar R. and Jurka J.; RT "COP14_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 10-10 (2007). XX DR [1] (Consensus) XX CC The LTR sequence flanks the internal region of the LTR retroposon CC from barrel medic. XX SQ Sequence 171 BP; 53 A; 19 C; 19 G; 80 T; 0 other; tgttgaaata tataatattt ttttttattg ttattctatt ttttaatggt tgtttatttt 60 tcattatatc actccttaaa ttaaggagtt gattagttgt attctctcct attaaaggag 120 caccattttc attgaaataa attactctca agttatagag aaatttcaac a 171 // ID Copia-7_TC-I repbase; DNA; EDCOT; 7483 BP. XX AC CACC01015606; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-7_TC_; KW Copia-7_TC-LTR; Copia-7_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-7483 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01015606; Positions 10766 3284. XX CC Positions [1644-2174] - Integrase core CC LTRs are 96% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS 4699..6549 FT /product="Copia-7_TC-I_1p" FT /translation="MERTKGMGDERRSGRRWLDNLQSLFVDNLSKRLTWLA FT IKGAFEEYGNVVDVFIPRKVQQDPKREVNFAFVKYRERYELDRALKWGGHQ FT WIDGKHLVVKRAEPMRKGFKDRKIRGLQGKIQKLVFERQGFERRSYKEVVV FT GKGVMEKEQWKAKLNEKENLEKSLEGMADQKVAPKLRKIAVEQEQRNDDQN FT GRINVEKMNAHERPNLVKLGTEHRLKSKDNKLVFKDKIPVGDMEWMQRSIM FT GKLHKHVFPKIVQEELQCEGIRVQVRPAGGLHVVLVFTDDEDKEKTLKDHK FT EGLNEWFDCLYPCSEKNELCNSKVWVRVEGIPLHLWHQSFFQFLGNSWGSF FT SKVDRQTELKLRFDQALIQVETTNKANIPPIAKIWSCEKLWELPVHIVKAS FT DIEKMVLTEVMTPEVVDSADSVHHFMCEGENRQECGCCNLGTYKLSLARGK FT CLSGSIDLERREICEELFLNSNEIDELIKSRLKRQKEGEDSSAALVEREMM FT GMDLDMAGTKGPHGEEIEKVKGSSYSIGSLVCKMGQKDSNLLEYESWEGRS FT NSEGGLWTDSGLDPKRGVRESSTNVSSGDITQKIKVDIRPERVNKEDGNSS FT SLEAISRQGTKGIGRRVEN" FT CDS join(1179..3014,3018..4088) FT /product="Copia-7_TC-I_2p" FT /translation="MLDSNFHLRAEIGNGDFIQIVGKRTVSVQTTSGIKTI FT SNVLYFTEMSQNLLSVGQLLDDKYSLWFKDKSCTIYDPAGIEIITVAMKNK FT CFPIDFMKNEFIIYQCCANDAILWHKRLGHVNYGSLKLMASNNLVDGLPII FT GAVDHICEICQFGKQNRNSFPKSSDWRARTKLQLIHSDVGGPMRTPSLNGS FT LYYLIFIDDLTRFCWVYFMKKKSEVFDKFIRFKAMVENEIDLTMKILRTDN FT GQEFCSKEFEDFLTRYGIKHHRTVSYSPQQNGVSERKNKTLVEMARCLLLG FT KNLPTKFWVKTVNVVVNLLNVLPTKALDAMSPYEAWNGEKPSVAHLRVFGS FT IYYVKVPDEKRKKFDSKSQVAIHLGFSDTSKGYRLFNVHTNKVFISRDVKF FT DEDHKWNWEKGIVESSRNFNITADVLPQNFNDDEDIEDENLAVRGTRSLQN FT IYERCSSVIMEPNSFTKASKDKRWLQAMHDEIEMIKKNQTWHLVDRPANQK FT VIGVKWVFKTKLNADGTVNKYKARLVAKGYAQEYGVDFSVTFAPVARHDTI FT RLLTALVVKESWKIWHLDVKSAFLNGFITEYVYIEQPEGFVEKGSESKVCE FT LVKVLYGLKQAPRAYERIDCYLRSEGFNRSINEPTLYVLSTNGFVNLLVSL FT YVDDLLVISLDSYVVDDFKVKMNQEFEMTDLGEMTFFLRMEFIQKPGYIGI FT HQTKYAKELLKQFKMESCKAVDTLIVTGNKLCKDDGSSQADSSNYRSLVGC FT LLYLTTTRPYIMYAASVLSRFMQNPSELHLIAAKCVLRYIKGTYDYGLKYF FT KKESKELLGFCDSDWAGSLEDSRSTTGYCFSLCSAVFTWSYKKQEIVAQSS FT AEVEYIAAASAANHAVWLRKMLYDLGFEQNGGTKLLIDNQSALAIANNSVY FT HGRTKHIRVKYHAIQDAIKEGEIYMEHCLSKDQLADIMTNGLNKDLFVALR FT DRLGVTKLNLKEVC" XX SQ Sequence 7483 BP; 2536 A; 1070 C; 1774 G; 2103 T; 0 other; tggcatcaga gctgcatcaa ggatcttaag ggacccttgt aacacaaaca atgtcatttc 60 tttttttttt ccttcctcaa atagtccctg cttatcatcc ttctttttta cttgaaaatc 120 tcattgtctt taccaaggca tcatctagct ttaatgcaac aacacctcct atatttacag 180 gagaaaatca tgtgatatgg gctgtgaaga tgaaagctta tctcagggct tttgatttat 240 gggagatggt ggaggtggga ggtgatcctc cggtgatgag gcatgctaat cccactattg 300 ctcaacttaa acagcatagt gaggaagtag taaggagata taaagcactc tcttgcattc 360 aatctgctgt attggatatt attttcacaa gaatcatgac atgtgataac ccaaaagaag 420 cttgggatcg attgaaggat aagttccatg ggagtgaaag gactcgatag atgcaggctc 480 tcaacttgca tagagaattt gagatcctta gaatgaaaga ggataagaca attaaagagt 540 attctgataa aatcatgaag ctcgttaacc agctaaggct gctaggagag gatttatccg 600 agaggagaat tgtgaacaaa gtcttggtta gtcttccaga gaagtttgag gccaagattt 660 catctctaga agactcaaag gacctctctc aactcacggt tgctgaacta gtgaatgctc 720 tccaagctca agaacaaaga cgttccattc gaaatggtgg acaaatggaa ggcgctttta 780 tggttagaag ccatggcaaa gtagtaagta acagtcagag aagatatgac catgacaaga 840 aggagaaaga cagaagaaac agtaatgaaa aacaaggaaa aggtaaagcc aaattccaac 900 catgttcata ttgcaagaag cgtaaccatt tagaaaaatt ttgttggttt caccccaatg 960 tcaaatgcag atattgcaat cagatgggac atgttgagaa agtctgtaag gctaaggcga 1020 ataataatga agaaaaagtt actataatgg aggagaaaga agactgtgat gaagctctgt 1080 ttatgattaa aataacaaag aaacacataa ggaatgatgt ttggtagata aatagtggtt 1140 gctccaatca tataactggt gataaggaga ttttcatcat gcttgatagt aactttcatt 1200 taagggctga gataggaaat ggtgatttca tacagattgt tgggaaaaga accgtaagcg 1260 tccaaacaac ttcaggtatt aaaacaatct ccaatgtttt atattttact gaaatgagcc 1320 aaaacttatt aagtgttgga cagttgcttg atgataagta ctcactatgg ttcaaagata 1380 aatcatgcac aatttatgat ccagctggta ttgaaataat cactgttgcc atgaaaaata 1440 aatgttttcc tatcgacttt atgaaaaatg agtttattat ttatcagtgt tgtgcaaatg 1500 atgcaatact ttggcataag cgattgggac atgttaatta tggatcctta aagcttatgg 1560 cttcaaataa tctagtcgat ggattaccta ttattggagc tgttgatcat atttgtgaaa 1620 tctgtcaatt tggtaagcag aatagaaatt catttcctaa aagcagtgat tggagagcaa 1680 ggacaaaact tcaactaatt cactctgatg ttggaggacc catgagaact ccttcactca 1740 atgggagctt atattatctt atatttattg atgatctaac tagattttgt tgggtttatt 1800 tcatgaaaaa aaaatctgag gtgtttgaca aatttatcag atttaaagcc atggtggaaa 1860 atgagataga tttgacaatg aagatattaa gaacagataa tggccaagag ttctgctcca 1920 aggaatttga agattttctg actcgttatg gcattaaaca tcacagaaca gtgtcatatt 1980 cacctcaaca aaatggggtt agtgagagga aaaacaagac acttgtggag atggcacgct 2040 gcttgttgct tgggaaaaac cttccaacta aattttgggt aaagacagta aatgttgtag 2100 tgaatttgtt gaacgttcta ccaaccaagg ccttagatgc aatgagtcca tatgaagcat 2160 ggaatggaga aaaaccatct gttgcacatt tacgtgtatt tggttccatt tactatgtta 2220 aagtccctga tgaaaaaagg aagaagtttg attcaaagtc acaagttgct attcatttgg 2280 gatttagtga tacttcaaaa ggctacaggt tattcaatgt ccatacaaac aaagtgttta 2340 ttagtcgtga tgttaaattt gatgaggatc ataaatggaa ttgggagaaa ggcattgttg 2400 aaagctcaag aaactttaat atcactgctg atgtattacc acaaaatttt aatgatgatg 2460 aagatattga ggatgagaat cttgctgtga gaggtaccag gtcactccag aatatttatg 2520 agaggtgcag ttcagttatc atggagccaa actcattcac aaaagcttct aaagataaga 2580 gatggctaca agcaatgcat gatgagattg agatgattaa aaaaaaccaa acttggcatc 2640 ttgtagatag accagcaaac caaaaagtga taggagtcaa gtgggtcttc aagactaaac 2700 ttaatgcaga tggaacggtt aacaaataca aggcccgttt ggtagctaaa gggtatgctc 2760 aagaatatgg ggtagacttc tctgtgacat ttgcaccagt ggctagacat gataccattc 2820 gacttctaac agctttggta gtcaaagaaa gttggaaaat ctggcactta gacgtgaaat 2880 ctgcattctt gaatggtttc ataacagaat atgtttacat tgagcaacct gaaggttttg 2940 tagaaaaagg aagtgagagc aaagtttgcg aacttgttaa agtattatat ggtcttaagc 3000 aagcaccaag ggcctagtat gaacgaattg attgttattt aaggagtgaa ggcttcaacc 3060 gaagtataaa tgagccaact ttgtatgtac tgagtacaaa tggctttgtg aatttgttgg 3120 tctcactcta tgttgatgac ttgctggtta ttagtctaga tagttatgtt gtggatgact 3180 ttaaggtgaa aatgaaccaa gagtttgaaa tgacagatct tggtgagatg acatttttct 3240 tgaggatgga gttcattcaa aaaccaggtt atatcggcat tcatcagacc aagtatgcta 3300 aagagcttct taaacaattt aaaatggaat catgcaaagc tgttgacact ctaattgtta 3360 caggaaacaa attatgcaaa gatgatggaa gctctcaagc tgatagttca aattacagga 3420 gccttgttgg atgtcttcta tatctgacaa caactagacc atatatcatg tatgcagcta 3480 gtgttttatc tcgattcatg caaaatccat ctgaacttca tctcattgca gccaaatgtg 3540 tgcttagata catcaaggga acttatgatt atggtctcaa atatttcaag aaagaaagca 3600 aggaacttct tggtttttgc gatagtgatt gggccggtag tctagaggac tctcgaagca 3660 ccactggata ttgtttttcc ctttgcagtg ctgtttttac atggagctac aagaagcaag 3720 agattgttgc gcagtcctcg gcagaggtcg agtatattgc tgcagcttca gctgcaaatc 3780 atgcagtttg gctaagaaag atgctttatg atcttggttt tgagcaaaat ggaggaacca 3840 agcttctgat tgacaaccaa tctgcacttg cgattgccaa caattctgta tatcatggtc 3900 gtactaagca tataagagtt aaataccatg ctatacagga tgcgatcaaa gaaggtgaaa 3960 tctatatgga acattgctta tcaaaggatc agttggcaga catcatgaca aatggtttaa 4020 acaaagatct gtttgtggca ttgagagata gattgggagt taccaagctc aacctcaagg 4080 aggtgtgttg aagttgacgt taagcttgga gatttgctgg agagttgttg gtagttaaat 4140 tacttttgtt agatatactc caccctgagc agatgtagat gtagatttag aatccctata 4200 gtattttgca agtattgcaa ttgaatgatt cttgaatctt gagaatactt ctgcaagtaa 4260 tcttgaacat ggatatttat tcttatggat gaaagaataa gtacagtatt agagaatccc 4320 caccgtacaa ctcccatatt tcctaaggtt ctttctctcc gtagaagtca aaatccttga 4380 ttacttgttg atcaagatgc aacctggact tgccagtgat tttgctaaag agatagccta 4440 gtagcatggc gtcactaggc tgaaacctga gtcccaccaa caagggagcc gcagcattgt 4500 tgtcttccat caaagatcga tatatagttg tggaagggaa agcaaaagat tttcttgatt 4560 aatcagaaag aagagtagca ggctactaga tgacaacttc ttgtaagagg aaaaatattc 4620 gggttttatg agaggtaaaa ctcaagaaaa gaacaaatct gttatgctgc tgctaacgct 4680 tgttaagtag tggctcgaat ggagcgtacc aaaggaatgg gagatgagag gagatctggt 4740 agacgatggt tggacaatct tcaatctttg tttgtcgata atctgagtaa aagacttact 4800 tggttagcta tcaagggagc tttcgaggaa tatgggaatg tggttgatgt ctttatccca 4860 agaaaggttc aacaagatcc aaaaagggag gtaaattttg ccttcgtcaa gtatagagaa 4920 aggtatgaac ttgatagggc attaaagtgg ggagggcatc agtggattga cgggaagcat 4980 ctagtggtga aaagagccga gccgatgaga aaagggttta aagatcgaaa aatcagaggt 5040 ttacaaggaa aaatccaaaa acttgtgttt gagagacagg ggtttgaaag gcggtcatac 5100 aaagaggtag tggtgggcaa aggagttatg gaaaaagaac aatggaaggc taaacttaat 5160 gagaaggaaa atttagagaa gagcttggag gggatggcag atcaaaaagt ggccccaaag 5220 ctgcgtaaaa ttgcagtgga gcaagaacag aggaatgacg accaaaatgg tagaataaat 5280 gtggaaaaaa tgaacgccca tgagagacca aatttagtga aattgggtac tgaacataga 5340 ctcaaatcaa aggacaataa actggttttc aaagacaaga taccagtggg cgatatggag 5400 tggatgcaaa gaagtatcat ggggaaactt cataaacacg tgttccccaa gattgtccaa 5460 gaagaattac agtgtgaggg cattcgagtt caagttaggc cggcaggtgg gcttcacgta 5520 gttctggtct ttactgatga tgaggataag gaaaagactt taaaggatca caaagaaggc 5580 cttaatgagt ggtttgattg tctttatcca tgctctgaaa agaatgagtt atgcaactcc 5640 aaagtatggg taagggtaga ggggataccg ttacatttat ggcaccaatc ttttttccaa 5700 tttttaggta atagttgggg tagtttctcc aaggttgata gacagacaga gttaaagcta 5760 aggtttgatc aagctcttat tcaagtagag actaccaaca aagcaaatat ccctccaatt 5820 gcaaaaatat ggtcttgcga aaagctatgg gaattaccag tgcacatagt gaaagcttcg 5880 gacattgaga aaatggtgtt gacagaggtg atgacgcctg aagtagttga ctcagctgac 5940 tcagttcacc atttcatgtg tgagggcgag aatcgtcaag aatgtgggtg ctgcaatctt 6000 ggcacgtaca agttgtcttt ggcacgtgga aaatgcttga gcgggagcat agacttggag 6060 aggagggaaa tttgtgaaga gctctttttg aattcaaatg agattgatga gctgatcaaa 6120 tcaagattga aaagacagaa agaaggagag gactcaagtg cagctttggt tgaaagggag 6180 atgatgggta tggatttaga catggcaggg actaagggcc cacatgggga agagattgaa 6240 aaggttaaag gaagtagtta ctctattggg agcttagttt gcaaaatggg tcaaaaggat 6300 tcaaatttgc tagaatatga gtcttgggaa ggtagatcaa atagtgaagg tggactatgg 6360 actgatagtg gactagaccc aaaaagagga gtgcgtgaga gctcaaccaa tgtgtcaagt 6420 ggtgatatta cgcaaaagat aaaagttgat attaggccag aaagggttaa caaggaggat 6480 ggaaactcat caagcttaga agcaattagc agacaaggga caaaggggat aggaaggaga 6540 gtggaaaatt aaggcaagaa aaaagaaaga ctttctgtgg gaagagcagt ctgatacaga 6600 gaaaaataag gcttatgatg gagaaggaaa aatgaaaaaa aataatacag gctttgaagg 6660 attgggaaag ttgataaaaa agagatggta tgaagaggtt gatgagaaaa tagtgacgag 6720 caaaagggcg aatcaagtta gattcaaaaa gaaagggaga aaaattaaca gagggaaaag 6780 tagaagaaaa ggcaagaaaa ttggtaataa atttttatca aatggggatt tcaagaatag 6840 aaatgaagtg ctaatgaaag acgtgaaggt tgcttgctca attgagaata aattaggttt 6900 cacttgtgag gaagatgagg atatgttgct agcagacatg gtgagggagg cagcgaaaag 6960 agctaaagct aagaaaggaa caataaaagg gagcttcaaa tgacaagaga tggtttttta 7020 acatgagatg tctagctgat gttgttggaa gcgtgaaagt gtttttgatg ggttggtgtt 7080 tggcttcaaa agtgttgttt tacgtggaga agttttaagg aattgagcca gactgtctac 7140 ttaaagatgg atgcatgaat gttatcagag cctttgagat aaggataatt cctaaattga 7200 tatgttcaag tcaaccgatg tcaatcataa gtctattttt gagtgtgttg gagctttgct 7260 ttttctggat gttgtaagtc aaggcaatag gcttggatta tagtttcact tttgtgtgga 7320 gtagtgtggt cttcttgtat gtgtactact ctttttcttt caattgcttg acttcttatg 7380 tcactaaaag tcttttatct ataagattta aaacttttta tgacatgtaa gcttttgaaa 7440 ttaataaaat ttctactttt aaaataaaaa gttaaattac ttt 7483 // ID Gypsy-23_VV-LTR repbase; DNA; EDCOT; 1081 BP. XX AC chr11; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-23_VV_; KW Gypsy-23_VV-I; Gypsy-23_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1081 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr11; Positions 9297680 9298760. XX SQ Sequence 1081 BP; 274 A; 172 C; 202 G; 433 T; 0 other; tgtagaccct ctattttgtc ttcctcgcac atgtcgttta cagcaattcc ctggtggccc 60 attaatactc gtgtagccta tctactctaa gccaccttgg ggactatggt tgagggattt 120 atcgaactct attgcaactt ctggtagccc atttagactt agatatactt aagcaccacc 180 ctaggcccac ttaggccctt taagcccatt aggcaccatc ctaggcccgt ttagacactt 240 taggatcatt taggtacact tggcccatta ggcatcgccc taggtccatt tagacacctt 300 aggttcactt agtgcacctt aggcccatta ggcatcaccc taggcccatt tagacaccgt 360 aggttcactt agtgcacctt aggcccatta gacgcacttg gcccattagg cacggcctta 420 ggcccactta aacacttttc aaggtttagt ttcacttaga tttgttttct tgtttttatt 480 tatttattta ttttattgat tgcttttaag attaagtgag ttttgatata tttatattat 540 ttcatcatta ttattatttg tattttcgtt tatttatttt attttataat tgcatgaaat 600 gagttatttg tttatttatt atttttggtg gtttgagttt gacacttcga ctattattat 660 atgttgcatt agtttaattt tattattatt attattaaat atatctaata tttattaatt 720 aatttattta tttttaggta tatatcattt tatctatgta ttgatatttt cttatttggg 780 atttaaggac ttcttgaaat tttaatgaaa ggaatattga ctttgattta tgggaatggt 840 tctgacttta tggattattg ctttcttttt tggaattttt ttttattgtt atttttccat 900 gtaggtggag tcaatgggaa ggtgtgcaga ggatgctcat ggaaaagacc acactgtttt 960 tttgaaaggt agattcgggg cgggaaaacg gactataaat cagggatgaa tgcggatgat 1020 ttttagagga agatacagaa aggtttttta aaaggtattg cgctgatttt gggaggagac 1080 a 1081 // ID Gypsy-30_VV-LTR repbase; DNA; EDCOT; 348 BP. XX AC chr4; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-30_VV_; KW Gypsy-30_VV-I; Gypsy-30_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-348 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr4; Positions 9252073 9252420. XX SQ Sequence 348 BP; 99 A; 51 C; 69 G; 129 T; 0 other; tgatacaccg agaaggtcct ctaggattcc caagaaaaat cccaagtttt tagtttagga 60 ttgaattggt cttttctaaa tgattgtctc ttgaatttgt tttattttgt tttattgctt 120 ggtcatagtc ataggtggtt aggtggttag tcgtttccta aataatagct aagtcatggt 180 cttgcatagc tgaagtctag gagtcagttt tgcaaaaacc ttatttaaag agtttatgtg 240 gacctgaaac aaaaaaaaaa agatttttat tcaaacttgt ggttgtcttt cacccaaaga 300 aagtcaagta tcctgtgttt ttcattgtgt tctgacaggg acctatca 348 // ID Gypsy-20_Mad-I repbase; DNA; EDCOT; 4562 BP. XX AC ACYM01079178; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-20_Mad_; KW Gypsy-20_Mad-LTR; Gypsy-20_Mad-I. XX NM Gypsy-20_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4562 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1424-1424 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01079178; Positions 6768 11329. XX CC Positions [3444-3932] - Integrase core CC 'CAACC' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 41..1729 FT /product="Gypsy-20_Mad-I_1p" FT /translation="MPRHTTTPRFTVMEERMAALEDAFVSLQSSFSDTLDA FT KLAICFEQFHREQSYGGRNGGSASDPDHRVAPILENLPDPDERELIRTPRR FT EIYDGAHPPRQNFQHRIEFPRFTNGDNLIAWIYKAEQFFAHYGTAEHQKVV FT TVSFHLESEALQWFRWMDCLVTTPRWDDFTTAFCHEFGPSEFEDCTESLFK FT LRQTGTLKDYIAEFRRLANRTSDVGLILLKSCFLGGLKKELRFDVKLLRPA FT TVHEAISIAIQLDTKYVELKSGSPKSFPQYKPPIQPSTPHNAAYPRFPNLP FT FKKLSPDEIQKKREQGDCWFYDEKWVRGHKCGQNQLLMIDFLGTDEEIFKP FT PNDVLAEIQHMELSECAYFGTLSKHTPQTMKGGGFIGNQPVTFLLDLGSSP FT SFVDSRLVKQVGWKLWGTKPFEVLVANGGKVRSHGCYKESSISLGGYSCAH FT TLFTLPLGGCEVVLGVDWLSTISPILWDFQLLTMDFTVNDHHHTLSYSNPQ FT PVPTLQAISLPNVDKEFSNSTLGLVLYSVEGSTMEASELTPSQLHDLQQLL FT HDYESLFEVPTSLPPL" FT CDS join(2613..3440,3444..4421) FT /product="Gypsy-20_Mad-I_2p" FT /translation="MVSPQLLALPDFSVPFVLECDASGNGIGAVLQQRGKP FT IAFSSQALGPKNQALSTYERELIAIVQAVKKGQHYLQGRHFIIKTDHHSLR FT YFLSNRAHTSFQQKWVSKLLGFDYEIQYRSGSENVVVDALSRVVVFSQPQG FT DTNNQSEMIVTCHAISYPYMGWIDELRRFNENDDWILQKVQDLTKDVTTTS FT HYHVYNGLLKYKSRIVLSLTSIWRDKVLHEHHSTPTSGHEGVLKTYHQVKR FT GFYWTCMKSDVKRFGSECTVCQQHKYETITPPGLLPLPIPHGIWRDISMHF FT IGGLPLCSGKSVIMVIVDRLSKYAHFVALAHPYTASIVAQAFVNHVFKLHG FT MPSSIVSDRDPIFLSSFWNEFFKLQGSTLCLSSSYHPQTDGQTEVLNRCLE FT TYLRCFTSAQPKKWLHWLPWAEWSYNTSYHTSAHFTPFELVYGYPLPHIAA FT YESGTARVELVEQSLIARDQLLSQLKSNLEKARNRIKVQVDRHRTEREFVE FT GQLVYLKLIPYQLQSLASHSYHKLQPRFYGPFEVLEKIGSVAHKLKLPEGC FT KLHPVFHVSCLKQHLGPDIVPTTTLPSVHDDGLKQQMPMAVLQRRMYKKGN FT AAGV" XX SQ Sequence 4562 BP; 1226 A; 971 C; 980 G; 1385 T; 0 other; ttggtatcac ccattgtcga ttctggtttc ccttccgtgc atgccccgac acactaccac 60 ccctcgtttt acagtcatgg aagagcgcat ggctgctctt gaagatgctt ttgtttcctt 120 gcagtcttct ttctctgata ctctggacgc caagctcgcg atctgttttg agcagtttca 180 tcgtgaacaa tcttatgggg gacggaatgg cggttcagct tccgatcccg atcatcgtgt 240 agctccgatc ttggagaatc ttcccgatcc tgacgaaagg gaactcatcc gcactccacg 300 acgcgagatc tatgacggtg cacacccccc tcgacaaaac ttccaacatc gcatcgaatt 360 tcccagattc actaatggag ataatctgat tgcttggatt tacaaggccg agcaattttt 420 cgcccactac ggcactgcgg agcatcaaaa agtggtgaca gtctcttttc atttggagag 480 cgaggcacta caatggtttc gatggatgga ttgtttggtt actacaccac gctgggatga 540 tttcaccact gcattttgcc atgaattcgg accttcagag ttcgaagatt gcactgaatc 600 tctcttcaaa ctccgtcaaa cgggtactct caaggattat attgctgaat ttcgtaggct 660 tgccaatcga acttctgatg ttggtttgat tctacttaag agttgtttcc taggtggttt 720 gaagaaggaa ttgagatttg atgtgaaatt gctacgccct gccactgtcc atgaggctat 780 ttctatagct attcaattgg atactaagta tgttgaactt aaatctggtt ctccaaaatc 840 ttttcctcag tataaacccc caatacagcc ttctactccc cataatgctg cctatcctag 900 gtttcccaac ttaccattta agaaactctc acccgatgaa attcagaaaa agagggagca 960 aggtgattgt tggttctatg atgaaaagtg ggttcgtggt cacaagtgtg gccagaatca 1020 attattgatg atcgatttct taggtactga tgaggaaata tttaaaccac ctaatgatgt 1080 gttggctgag atacaacaca tggaacttag tgaatgtgct tattttggga ctctatccaa 1140 acacacacct caaaccatga aagggggggg attcattggc aaccaaccag tgacattctt 1200 actcgatttg ggtagttctc ctagttttgt ggattccagg ttggtgaaac aagttggttg 1260 gaaattgtgg ggaaccaaac cttttgaagt actggtggct aatggtggga aggtgaggag 1320 tcatgggtgt tataaggagt cttccatatc tttgggtggt tattcatgtg ctcatacact 1380 ttttactctt cctcttggtg gctgtgaggt tgttttgggt gtggattggt tatctaccat 1440 cagccctata ctttgggact tccagctttt aaccatggac ttcacagtga atgaccacca 1500 tcatacactc tcctatagta accctcaacc agtacctact ttacaagcca tctctctgcc 1560 caatgtggac aaagaatttt cgaattctac tttggggttg gtgctctact cagtggaggg 1620 ctctacaatg gaggcttctg agttgactcc ctctcagctc cacgacttgc aacaattatt 1680 gcatgattat gagtctctat ttgaagttcc tacttcttta ccaccactat gagtgcatga 1740 ccattggatt cccctcttgc caggttccaa accacctaac atctgaccct accattatgg 1800 gcctttccaa aagtctgaaa tagaaaaagc aatggctgag ttgttacaag caggttttat 1860 ccatccaagt cacatccctt tttcttgccc agtgttgctt gtcttaaaga aggaaggggc 1920 ttggcggctt tgtatggatt acagagagtt aaactctata accatcaaaa ataaatatcc 1980 tattcccttg atagatgact tgcttgatga gttgtatggg gctcagttct ttactaagct 2040 tgatttacga tctggttacc accaaattag gatgtgtgaa gaagatatcg agaaaactgc 2100 tttccgtacc catgagggac actacgagtt cctagtgatg ccttttgggc tcacaaatgc 2160 tcctgccaca ttccataatc taatgaatga tgtcttccgg ccttacttaa ggaaatttat 2220 acttgtgttc tttgatgata ttctcatcta caacaagtct tgggaggatc acatctcaca 2280 tttaacaaca acattccagg tactcacaca tcattagctt tttgtgaaaa aactaaaatg 2340 cttcttttgg ccaatctaaa gttgaatatt tgggacatgt ggtttcttga gagggtgtag 2400 ccgttgatcc ctccaagctg caagcaattg ttgattggcc tatacctgcg aatgtaaaag 2460 gattgagggg ttttttaggc ctcacatgtt actatcggaa gttcattccc ggttatggca 2520 aaatttgtca acccttttat gagttaacca aaaaggatgg atttcattgg aattctagtg 2580 ctcaggatgc ttttcttaca ctcaaacaag ctatggtttc tcctcaactc cttgcattgc 2640 ctgatttttc agtacctttt gtccttgaat gtgacgcatc tgggaatggc ataggggcag 2700 tgctgcaaca aaggggaaaa cctattgctt tctcaagtca agcacttggt cccaagaacc 2760 aagcactatc cacatatgag agggaattaa ttgcaatagt gcaggctgta aaaaaaggac 2820 aacattattt gcaaggaagg catttcatca ttaaaacaga ccaccatagt ctgcgctatt 2880 tcctaagtaa tagagcacat acatcttttc aacagaaatg ggtatctaag ttgcttggat 2940 ttgattatga aatccaatat aggagtggct ctgaaaatgt ggttgtcgat gccctttcac 3000 gggtagttgt tttctctcaa cctcaaggag acaccaataa tcagtctgaa atgattgtta 3060 cttgtcatgc tatctcatac ccctacatgg gatggattga tgaattaaga aggtttaatg 3120 agaatgatga ttggatcctg cagaaggtgc aagatttaac taaagatgtg acaaccactt 3180 cccactacca tgtttataat ggactgctca agtataaatc gagaatagtg ctcagtctca 3240 cttcaatttg gcgagataag gttctccatg aacaccattc cactcctact tcgggacatg 3300 aaggggttct taagacatat caccaggtta agcgtgggtt ttattggaca tgcatgaaaa 3360 gtgatgtgaa gcgatttggt tctgagtgca cagtttgcca acagcataag tatgaaacca 3420 ttactcctcc aggtttgttg taaccactgc ctattcctca tggtatttgg agggacatta 3480 gcatgcattt cattggaggt cttcctctgt gctctggaaa atctgtaata atggtgattg 3540 tcgatagatt atccaagtat gcccactttg tggcattagc acatccctac actgcttcta 3600 ttgtggctca agcatttgta aaccatgttt tcaaattaca tggcatgcct tcatcaatag 3660 taagtgacag ggaccctatc tttttgagtt ctttctggaa tgagttcttt aaacttcaag 3720 gttcaaccct ttgcctgagc tccagttatc acccccaaac cgatggccaa actgaggttc 3780 tcaataggtg tttggagacc tatttgagat gtttcactag tgcacaacct aaaaaatggt 3840 tgcattggtt accatgggca gagtggagct ataacacttc gtatcatacc tctgcacatt 3900 ttactccatt tgagttagtt tatggatacc ccctacctca cattgcagct tatgaaagtg 3960 gcacagcacg agtggaactg gtggagcaaa gtttgatagc cagggatcaa cttttgtcgc 4020 agctcaaatc gaacttggaa aaggcaagga acagaataaa ggtacaagtt gacaggcacc 4080 gaaccgagag agagtttgtt gaggggcaac tggtctacct aaagcttata ccttatcaat 4140 tgcagtcctt agcttctcac tcttatcaca aacttcagcc tcgtttctat ggtccttttg 4200 aagtattgga gaagataggc tcggtagctc acaagttaaa gcttcctgaa ggctgcaagt 4260 tacatcccgt ttttcatgtg agctgtttaa agcaacattt gggccctgac attgttccta 4320 ctactacttt accctctgtt catgatgatg gtctgaaaca acaaatgcct atggcagtac 4380 tacagcgaag aatgtacaaa aaagggaatg cagctggagt ttaattactt gtgcagtggg 4440 aagagggtac cagagacgat gcaacctggg aagattttga tgctttcact gcgagctatc 4500 cggggttcaa gttttgattg ccaaacaacc ttgtggacaa ggtcttttga aggggaggga 4560 aa 4562 // ID DNA9-20_Mad repbase; DNA; EDCOT; 1627 BP. XX AC . XX DT 28-OCT-2010 (Rel. 15.11, Created) DT 28-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-20_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1627 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1860-1860 (2010). XX DR [2] (Consensus) XX CC TSD is 9-bp long. TIR is 159-bp long. XX SQ Sequence 1627 BP; 444 A; 415 C; 341 G; 427 T; 0 other; gggtaaagta caaaaaacta cctcaactat tggtctcacg acactttcat acctcatctt 60 ttaaaaatga caatgtcata cctcatctta cgaatttgtg ccaatgtcat acctccgtca 120 gtttttctgt taatttctct gttaagtgct gacgtggcta gatacggggc cactcactaa 180 tccaactgga ttaaaatata attaaatata tttttaataa ttaaaaatta aaaattaaaa 240 aaaatatata ttaaatctct atctctctcc tctcttctcg cctctctctt ctctgccatc 300 cccaaaaccc cttcccaccc gacccccccc cccgtccccc caacccttcc tccaccaccc 360 tctctctctc gcatctccct ctcctctcca ccgtagtctc cttcctcccc acttctctct 420 ctcgccgtgc ccagaacccc ccaaacccac ctggattttt tcatccgccc tcctttctcg 480 gatctacctg caagctccga cccgcttccc tctcccactc cattgcccac cgccgatccg 540 ccgtcgttgc cgtctccgaa gctgtcaagg agaaagggag agagggagag ctgtcaaggt 600 cggggccgac gaggttgccg tcttccccta acccaaaccc agatcccacc ccaaaccagc 660 cactcccatt cccaccaggt gcctctcttc tcttcctccg ccgctctctc tatttctaac 720 ctacaagcat gcataaaaaa caaagcaccc accaatcctg agaacacacc attaacaaaa 780 gttcaaaaat ccatcttcca gtttacctca cttttctaag aaaatggaac cttcagaata 840 taaaaaaaat tcatttcctt tctcccacat tttccgagca accaaacaaa gcaaaaccat 900 tcaatttttc ccaaaaaaaa aacccaagtt gtattcacaa gagactcggc agcggtggtg 960 ggcgcgggat tgctgctgcg ttttgctggg cttgaagatg gtgctgggct gcgggagcag 1020 agggaggtgg cagaggcggt cctcaacttc tgcaaacccg acgacgaagt cgattacttg 1080 gtaatcgtgg ggcgacaagg ctgtcaagga ttcgcagaag tattcgaacc catatgggta 1140 gtttggtaag gaaggggagg agatcaatgg agggagtggg tacccggaga ggggtgaggt 1200 tggtgtgccg gagatcggcg acttcgatgt cgtcagttag aatggggaag aaggtgatgg 1260 tcgttggtgg atggagtcga cgatgaagag gagagaaggg agggtgagtg cgagttgcag 1320 atgagagaaa ggtgggtggg gttgcagatg agagaagggg aaagggggtg ggtccccatg 1380 taaaaaaata ttaaatgatt ttaatttttt tagtttttaa tatttaatta attttttaat 1440 attttattaa tttatttaag ccacgtcact atttaagcca agccacgtca gcacttaaca 1500 gaaaaactga cggaggtatg acattggcac aaattcgtaa gatgaggtat gacattgtca 1560 ttttaaaaag atgaggtatg aaagtgtcgt gagaccaata gttgaggtag ttttttgtac 1620 tttaccc 1627 // ID HARB-3N1_Mad repbase; DNA; EDCOT; 1956 BP. XX AC . XX DT 25-OCT-2010 (Rel. 15.11, Created) DT 25-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE Harbinger DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW HARB-3N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1956 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1862-1862 (2010). XX DR [2] (Consensus) XX CC TIR is 17-bp long. XX SQ Sequence 1956 BP; 596 A; 349 C; 339 G; 657 T; 15 other; gaccatctcc aatggtgact taaaacctaa aaatatttag yccagaaaat ttaggtttta 60 gcccawaaac agyttttcta ctccaacmct tctgayctaa aattttarcc ycagattatc 120 aaagaatgaa ttaaggctat ttttttwaaa ttaacttwaa aaaaawatgt agactatcct 180 arattaattt tatgaatatt ttaacctaaa aatatttaaa ttccgataaa ttttgaaaaa 240 tcactaaatc aatacatgaa aatyatgata aaccacataa actyaatacc aacratattt 300 aataaatcac ataaacttaa aaaaaaaaga caattaataa accacataaa cttaatacaa 360 tcgaaaactc atagactaca taaacttaat aatgatatct accatcttga cttggtaatg 420 gacttgggtg atagtcttga gatgaatcat catcttgaaa tatactcctt gtggcattcc 480 tttgtaaaat ttccttttgc ttaccacgta agtatttctt cctctctgga gtgtatttgt 540 cgaggtcctc cattataaaa ttagtttcgt acatttcttg ctccctatcc ctttgttcct 600 tcatggccaa aagcatttgg gccgattctt cttgcgacga cactggtttt tgttcattct 660 tgccatttcg ctagcaaatt gtgcacgtat tggatcttgg gacttccctt ttctctttac 720 ttcattttgc ttatctytac ccaggggcct tggaaaagaa gaagttgggc tcatttggtc 780 gacaccttca ttggcatcat ttgggggtgg ggcttcatta tgaaataatc ttccacattg 840 ttgattcgca tcggttcccc accttagaca atctttgagg atgttccaag catgatgcaa 900 ctttaaagct tgattttttg gtgtagttct tatcttgtaa attgtcattc ctttgtcacc 960 ctatgcaaca aatacataaa aacaattagt tgcaaaatac tattatgtac atgacaacta 1020 aaatatcaac aaagaaactc acaatttctg aggcgcccct tccactaggc atgtcaacca 1080 tggctctctc caagcttccc ttccacaaag tgtacgcttt gttgataatc ttccattgat 1140 cataaacacc accaacttcc cttcgaccag cgttggagtt ttcatggaac ttatcaacaa 1200 ttttacccac aaaacctttc tattttgatt gatgttgacg gcaccatctt cgctaacaga 1260 aatccatgcc aaacataaag caatatcttc gtcaaaggtc caattacgac ctctaacatg 1320 ctcttttacc atcttgaaaa ttttggaaat gagaagaaat ggtagaaaga aaaagtggaa 1380 gaattgtaga agaaaagtga gttttgtgtg aatgtttgaa caaatacata ggtatttata 1440 gagtttttgg ttgaatttta agttaaataa ttttttacaa ttattttagc cgttggattt 1500 aaatttggac tgctatatct ttcttttttt tttaccgtta gatttgatta tattcgatct 1560 aaaccgttag attcaataaa tatataaata tataaaaaaa aatttgaacg tccgttggat 1620 taaccaacgg tccaattaaa gtggtcgttg gatgaacaaa agtaattgtt gggctacagt 1680 aaccatgaca gcagagggga ccaacccacg tgggtgggcc ttcggctgga agaaagtggg 1740 cgcgtgaggt gagttgggtt ttggggtgtg ggcttcacag cccacttttc actctcacca 1800 gtgggtccca ttttattttg taagctaaat tgtggctgat atttgccttt taggttttaa 1860 gttttaggtt tggtttaggt tttgggttgg agtgggtttt tttggggggg ggggagaagg 1920 ggaattttag gttataagcc actattggag atagtc 1956 // ID GYPSY5MT_LTR repbase; DNA; EDCOT; 2216 BP. XX AC AC122730; XX DT 16-DEC-2006 (Rel. 11.12, Created) DT 04-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE GYPSY5MT_LTR - putative Gypsy long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW GYPSY5MT_LTR. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2216 RA Jurka J.; RT "GYPSY5MT: Putative Gypsy long terminal repeat from barrel RT medic."; RL Repbase Reports 6(12), 621-621 (2006). XX DR EMBL/GenBank/DDBJ; AC122730; Positions 42595 44810. XX CC This is a recent insertion flanked by 5bp TSD: CTATA. XX SQ Sequence 2216 BP; 721 A; 474 C; 325 G; 696 T; 0 other; tgtcataccc taaattttga ccaaagatcc cacggacgtg catcgtttga ctctggtcga 60 tctcatgatt cagtgaaaat ttcggcaggg aggtatttta aaatacctca tttttgttcc 120 gattgcaggc acttttctct cctttcattt cattatctaa cttccgtctt ttaattttaa 180 ttttaaagtt agttactttt taatatttaa taaatgttta ttttccgttt tttgtccaac 240 gaagtcaata agtccgaaaa tttcagcaag ggtccatttt tctttttttc atttcttctc 300 cgtacgccac atgtttaggc aaattcatag ggtcaaagtt ttgttgccaa atccagcaac 360 tcagtagtaa tctctgcaag ttatttcctt gttctatcca accctaatgc tataaaagca 420 aacctgcaaa atacagaaaa acaaaaaaaa agcctagccg caaacaaaga aaaacggaca 480 atttccacaa caaaaaaaac attagaaaac cctagccgca aactgcatcc caagaccgaa 540 tcaaagaaac ctgcatcaac aaaatttata acacaataac aatcccaaaa cctcacacaa 600 attcctcaca accaatcaac tcccaaatcc gaaccaaaag cacaaccgac gggtccaggc 660 cgagtttgac tcaacagccc ccaagtttaa accgaaggtg caacagacag atccggatcg 720 aatccaacct tgcaagttcc gatccaaaac accaccgttc cgacaaaggt aggttaaact 780 ttctctctta gatctaggtt cgaatgttag gttcttgaat gttttaaact taaaattgaa 840 accagaagaa ggagtagagt aaattagaaa gaaaaaaaaa ataaaaaaat agctttaggg 900 ttccggcgcg gaggtgccgt cgcaccggcc cggccaacca ccgccggaac cccccttacc 960 tccgccggag atgatgaaga ttcgccggaa tcttcatgta gaaacccaga aaagaagaac 1020 agaaaagaga gagaccgtga gtttagagga ggaagagaga gaaatgactt gagaaaatga 1080 aagaaaaagg gtcttacacc ctatatatat caatccgaac cgggcgggtc taaccgaccc 1140 gcccacgacc cgttttttgc ttaagcccaa tcgttttttt attcactaca gtttcgctag 1200 ttatacccct gttttacttt ctacacctct ttcatttttg aaaatctctc taaaaattac 1260 aaaaatatgt tttgctttgt gttaattgtt tatttactgt tttgtcatta ttattgtagt 1320 atatttgaat catctcatgc atatttaatt ttttgttatt ttatttcatt ggtattattt 1380 ttagtatgta taattagttt ttatttcttg ctattatatc tctcttgaga ccatagaatg 1440 tatctaggag ttgatgtaat aatgtaggta acacaagcac cgacacatgc accgacacta 1500 tcccacttta tttaccgctt tacgcttatt ttttattgtt ttacgccgtt acgctagtat 1560 accgtttagt ttagaaaaaa atcattttac caaaaaaaca aatatgcaaa actccaaaaa 1620 tattttctta ataaaccttg gcttgtaacc caagtgtctt tttttccttt tattttctta 1680 atcaaatgct taattgaatt aatattcata atagacttga ttttcttgta attaaaattt 1740 taccaacctc accttatttt ctctcatgcc ttgaggcctc ttatcccttc ttaaaaccat 1800 tttctaaaat ctaaaatcaa ccaacccacc aaaaagaaac tttttaggtg aactacattg 1860 gttttgatcc cttttcttta agggtatgta ggcataggat ttttatcctt ccaaatcaaa 1920 taaaaataac caaaaacata cttcttctcc ccccattctt tcacttagat cttttaggta 1980 ataattttca aataagcaat gaatttagca caagataaat taggtaagag gttcctacgg 2040 aataccgtag acgcttaggg tgctagcacc ttcccttcgc gtgaccaacc cccgaatcca 2100 aagtctcgat gagggttttt tactcatttt ttcccttccc acgaataaaa atcgagagtt 2160 caaagattga cgattcaaat caattaatgg tttgatatcc gaaaatcaag agcaca 2216 // ID Copia-38_VV-LTR repbase; DNA; EDCOT; 250 BP. XX AC chr1; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-38_VV_; KW Copia-38_VV-I; Copia-38_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-250 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr1; Positions 8897753 8898002. XX SQ Sequence 250 BP; 59 A; 37 C; 45 G; 109 T; 0 other; tgttagaatt catgagagtt tgcctttgaa aatgtcttag ttagacttag tctctgtttt 60 gctatctctg attttcagtt tttctgttag tagaagtagt catagcagct gagagttttt 120 agcattttca gtttggttgt aagcctataa ataggcattc tctttggtga aatatagtgt 180 gtgtctttct ccaactcagt actctaatat tttctgaaag ttttagttcc tttctccaga 240 ttttttaaca 250 // ID BvL1 repbase; DNA; EDCOT; 7663 BP. XX AC FM993986; XX DT 03-AUG-2009 (Rel. 14.07, Created) DT 03-AUG-2009 (Rel. 14.07, Last updated, Version 1) XX DE BvL1, LINE-type retrotransposon. XX KW L1; Non-LTR Retrotransposon; Transposable Element; BvL1. XX OS Beta vulgaris OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC Caryophyllales; Amaranthaceae; Beta. XX RN [1] RP 1-7663 RA Wenke T. and Schmidt T.; RT "The genomic organization and diversity of a non-LTR RT retrotransposon (LINE) family in Beta vulgaris."; RL Direct Submission to EMBL (28-JAN-2009). XX DR EMBL/GenBank/DDBJ; FM993986; Positions 1 7663. XX FH Key Location/Qualifiers FT CDS 139..1287 FT /product="BvL1_1p" FT /translation="MDLSEQTIKKKEMREKEKKEEREGEKKLSQILYPKSK FT NPRSSPLKSSPASPNPFGRSRYHNANLLITILESIIVVLVVFYSKLQPVGC FT ISGEFKVGREIVLSDSQNHSSQLLLVQSNHLWVSCFLPTHHRSKVRKIYDL FT GFLSFKYKRKGKVGDFELGAFNARSLIAFGVECIMLSSGNSMRVQEKEAFL FT KDCAFNAKVDSLLLFQNPFPSCRGVGKYLNSYINKPWLSKSSITGLCFHSL FT TSNFNYTNSFCFIGSLLMDPPSSFKEALISSSVVPHSSNLAENILNVDSGS FT VLAELPDKGDSLVADPVVPQFAQANVVLDELPQVKQDIVELTKSCLIGKML FT SSNIDTRTIISRTKADWKFVKGEVEYLEMGNGWLMLKCF*" FT CDS 2729..5233 FT /product="BvL1_2p" FT /translation="MKIACWNIRGCRRKNAFDEVKDFCKANSISICMLCET FT KCKSPPLNLYALKCGFKFLDFIPTIGMSGGLWIMWKQCSFNPFSLDVMYKS FT DRFISCQITLSKSSLQFLIIFIYAPANSLFKNEFWHELTMYCNSLSIPFVV FT MGDYNEIRNASDKNGGAPPSSKRFERLLNFTSLVPCKALPSQGSAFTWRKK FT AYGVDNIHEKLDHGYASIDWLSMFPNATIMNHIFSSSDHCPISLSLGLSFS FT LKSTPFRFEKMWCQRKDFDTLIKKTWCHKFHGSYMFCLVQKCKQLKANIKI FT WNKTRFGNIFTQQRKVDKDLGQIQARLFADPSSDGLQQKQKRLLDKKQQLF FT NYHHKYWKQKYRGQHLSLGDQNTKYYHAFASIRRNRNQIKSLKDVSGSSCS FT HPDEISRLLTQSFQDRFTSDSQCQFGNPLDFSLISPIITEEDNSLLTGLVT FT DEEIKCALFDLAPDKAPGPDGYPPFFFQKYWTLVGPSVNRAIKAFFHSGHL FT LSEINHTFLALIPKIDNPEIASHFRPISLCSTIYKVIAKILANRLKVVLGR FT IIHPLQGAFVPDRLIQDNILIAHEVFHSFRKKSGKEGWIAIKLDMEKAYDR FT LEWGFIFAMLHHLGFSQVWIDWIRACLSSVSFSVLANGVPGDRFFPSRGIR FT QGDPLSPYLFILCAELLARNLHYHSVSNGKLVGVVVGKSGVKVPFLTFADD FT TMIFAKANVDSCRAIRSILDKYCSMSGQLVNYSKSAFKCTDNVDQVKCEEF FT KNILGMSYSHSLENYLGCPIIDSRVTKETFAPIVHKVQAQLPKWKANSLSL FT RQVELFSFKLISPRKQIIKCRVSCCLRPSSPS*" XX SQ Sequence 7663 BP; 2024 A; 1474 C; 1577 G; 2587 T; 1 other; caggaataga tttatactct atcagtcaag cataaggata gagtatggag aagtgagaac 60 acgaagcatg atgctttttt ttgtcttcat aatttttgct attgtccttg gtcggcactc 120 ggcaatgatg tgtgaaccat ggaccttagt gaacagacaa ttaaaaaaaa agagatgaga 180 gagaaagaga aaaaagaaga gagagaaggc gaaaagaaac tttcccaaat cctctaccca 240 aaatcaaaaa accctagatc ttctcctctg aaatcttctc ctgcttcacc taatccgttt 300 ggcaggtcta gatatcataa tgcaaaccta ttgattacga ttctcgaaag tataatcgtt 360 gtcttagttg ttttctattc gaagttacag cctgttgggt gtatttcagg cgagtttaaa 420 gttgggagag aaatcgtcct ttccgattct caaaatcatt catctcaact gcttttggtt 480 cagtctaatc atctctgggt aagctgcttc ttacctactc atcacagatc aaaggttcgc 540 aagatttatg atctagggtt tctatctttc aagtacaaaa ggaagggtaa agttggggat 600 tttgagttgg gtgcatttaa tgctcggtct ttaatcgcct ttggagtgga gtgtattatg 660 ctgtcgtctg gtaattcaat gcgtgttcag gagaaggaag cgttcttaaa ggattgtgca 720 tttaatgcga aagtggattc acttctgctg tttcagaatc cctttccctc ttgtagaggg 780 gttggtaagt atctaaactc ctatataaat aaaccttggt tatctaaatc tagcattact 840 ggattgtgtt ttcactctct tacttctaac ttcaattata caaattcttt ttgctttatt 900 ggtagtctcc taatggatcc tccttcttct tttaaggaag ctcttatttc ttcttctgtt 960 gttcctcata gctctaacct tgctgaaaac attctgaatg ttgattctgg ttctgtcctt 1020 gctgagttgc cggataaggg cgattcttta gtggcggacc ctgttgttcc ccagtttgct 1080 caggctaatg tggttctgga tgaactgcct caggtaaaac aagatattgt ggagctcaca 1140 aaatcttgtt taataggtaa aatgcttagc tctaatattg atactcgtac tattatctct 1200 cgtactaagg ctgattggaa atttgtcaaa ggggaggtgg aatatcttga aatggggaat 1260 gggtggttga tgcttaagtg tttctaaccc tggtgacctc tcacttgtct ggaagtgaga 1320 ggccatggca tgttcaggga gatatttttg tgatctaccc ttggcgccct tcttttgatc 1380 cttatcttga ggagattaag tgggttgacc tgtggattcg tatccctagg ctccctgctg 1440 agctcctcaa ttttgattct gttgctagtc ttttatctgc taatggcatt ggtgctctga 1500 taaagcttga tcctaggtct ttgttaaggc ataaaatccg atttgctcgt gcatgtgtgc 1560 gtgtggatat taaagctcct tcgttatgag ttgctgaggt ttgtaggcat ggtgatcttg 1620 tccaaggcta tgttatatgg tatgaagatt tttcttccgg ttgttcattt tgtgggtctg 1680 aaaaccatgt tattgattgt tgtcctttgc taacctcccc taaaaaggaa atgaaagttc 1740 gtttaatgaa aaatccaaag caaaagtgtc tctatgacaa tctagctaaa gctggccaag 1800 ctaaccttga tactactgct gagcaagcaa atgtagttca agctcaggct aagcacttag 1860 ctaaccagtc attgagtaaa gctgataaga aggtggtccc tcctaagaag cgctttaacc 1920 ctgttaggag ctgcctctaa gaaaaagtct gtgttgtctg aaggttttga tgattctcac 1980 cctcttttgg gtattcctga aactgctccc ttgaaaggta gtcctggtat tgttcttaag 2040 gaacctgctg aggttccaag ggctgttggt aatgctggtg caagtgctaa tctttcttct 2100 cttcatggtg taagtaagct aagttcagat gctattcttg ataaaggtaa gggtaagctt 2160 tttatagctt ctcctactgt tgagatctcc tctgatgatg aggattcagg gaggctctcc 2220 tctgtgctcc ctctctctat tgtgggccct cctcagattg agcctggtga tggagacata 2280 gggtgtctag atttacctct ggtccctgct ctccccccaa tcaaagtgtt ccatacctct 2340 catcttttct ctgagagtta ttatgatgat atgctgtgtg aggatgagtt tgctgctgtc 2400 agatcccctc atgatagtga tgaaaggtct ggaagtgggg cattctttct ggatatgcct 2460 ctcaatgagg atgaagatgt taagactatt actgagaact cctttcagtc cctccactcc 2520 gataactcta ttgtgcagca aattgaacag ttgggggttg agcaggtttc ccctatggag 2580 cacacctctc aatctgagtc ctcgaagaga aaggttgagg aaccagagga agaaagtgcc 2640 tcctcttccc tgaagaggcc aagaacctga tctctacagc tctaaaggta ttcaaagttt 2700 tttgcgatgg ttttttgcta agttttaaat gaagattgct tgctggaata ttcgaggatg 2760 ccgtaggaaa aatgcctttg atgaggttaa ggacttttgt aaagctaatt ccattagtat 2820 atgtatgtta tgtgagacga agtgtaagtc tcctcctttg aacctctatg ctttaaagtg 2880 tggttttaag tttttggatt tcattcccac cattggtatg tctggtggtt tatggatcat 2940 gtggaagcaa tgctcattta atcctttctc tttggatgta atgtataaaa gtgatcgttt 3000 tatttcgtgt caaattactc tctctaagtc ttctttacag tttttgatta tatttattta 3060 tgctcctgct aattctttgt ttaaaaatga attctggcat gagctgacta tgtattgtaa 3120 ttcgcttagt attccttttg tggttatggg ggattacaat gagattcgta atgctagtga 3180 caaaaatggt ggtgctcctc cctcctccaa gaggtttgaa cgccttctga acttcacttc 3240 cttagttcct tgtaaagctc tcccttctca agggtctgct tttacttgga ggaaaaaagc 3300 gtatggagtg gacaatattc atgaaaagct ggaccatggc tatgctagca tagattggct 3360 atcaatgttt cctaatgcaa ctattatgaa ccacatattc tcttcctcgg atcactgccc 3420 tatatcccta tctttgggct tatctttttc gcttaaatct actccgtttc gttttgaaaa 3480 aatgtggtgt cagcgaaaag actttgacac actcattaaa aaaacgtggt gtcataaatt 3540 tcatggctca tatatgtttt gtctagtgca aaaatgtaaa caacttaaag ctaatattaa 3600 aatctggaat aagactcggt ttggtaatat cttcacacaa cagcgtaagg ttgataaaga 3660 tttaggccaa attcaagctc gattatttgc cgatccaagt agtgatgggc tccaacaaaa 3720 gcaaaagcga ctattagaca aaaaacaaca attatttaat tatcatcata agtattggaa 3780 gcaaaagtat aggggccaac atctctcttt aggggatcaa aatactaagt actatcatgc 3840 gtttgcttca atcagacgta atcgcaatca aattaaatcc cttaaagatg tttcgggttc 3900 ctcctgctct cacccggatg agatttctcg tttgcttacc caatcctttc aggatagatt 3960 tacttctgat tctcaatgcc agttcgggaa ccctttggat ttctcgctta tttcccctat 4020 tattacggag gaggataatt ctctgcttac gggtctggtg acggacgaag aaatcaaatg 4080 cgctttgttt gatttagcac ccgataaagc tccaggccct gacggttacc cccctttttt 4140 ctttcagaaa tattggaccc ttgttggtcc gtctgttaac cgagcgatta aagctttttt 4200 ccactctggg catctattat ctgaaatcaa ccacactttt ttggctctca tccctaaaat 4260 tgacaatccg gagatagcat cgcatttccg ccctattagc ttatgttcaa ctatttataa 4320 agtgatcgcc aaaattcttg caaatagatt aaaagttgtt cttgggcgga ttattcatcc 4380 tctccaagga gcttttgtcc ccgatcgtct tatccaggac aatattctta tagcgcatga 4440 agtttttcat tctttccgga aaaaatcggg taaagaaggc tggattgcca ttaaacttga 4500 tatggaaaaa gcttatgatc gattggaatg gggtttcatt tttgctatgt tacatcattt 4560 gggattcagt caagtgtgga ttgattggat ccgcgcctgt ctttcatctg tctcgttttc 4620 ggttttagct aatggtgttc ctggggaccg tttctttcct tctcgtggga ttcgtcaagg 4680 ggatcctctg tctccttatc tatttattct ctgtgcagaa ttgttagctc gcaatctgca 4740 ctatcatagt gtctctaatg gaaagttggt tggagttgta gtgggcaaat ctggagtgaa 4800 agttcctttc ctcacttttg ctgatgatac tatgattttt gcaaaagcaa atgtagatag 4860 ctgcagggct attcgttcta ttttagataa gtattgttct atgtctggtc agttagtcaa 4920 ttatagtaaa tcagctttta agtgtactga taacgttgat caagtaaagt gtgaagagtt 4980 taagaatatt ttagggatgt cctattctca ttcgctagag aattatctgg gatgccctat 5040 tattgatagt cgtgtgacaa aggagacttt cgcgcccatt gtgcataaag ttcaggccca 5100 actcccaaaa tggaaagcaa actctctctc tctcaggcag gtagagctgt tctccttcaa 5160 gctaatctcg cctcgaaagc aaattatcaa atgcagagtt tcctgctgcc tcagaccatc 5220 ctctccaagc tagattgctg ctatcgcaac tttttttgga ataaagctcc caactcgtca 5280 gctcctaatt tgattgggtg ggaccgtatt tgctccccga aggtggtagg tggtttaggt 5340 tttcgtaaag ctagtgtgaa caatatggct aaccaaatga aattgctctg gaagcttctc 5400 agaaatgaaa ataatctctg ggtggtgctg acaaaaagaa aatactgtaa aaataaggat 5460 ttcttggtga gcaaggttcc ttcttctgcc tcttggcaat ggaaaaagct gatgtcttta 5520 cgcccgattt ttaaatctgg gctccgttgg caagtgggta atgggaatac cattaatttc 5580 tggcatgata actgggtttt ccctcactct ttgagctcaa tgattcaaca tcccaggatg 5640 aataatttaa ctagggtaag tgagtttatt ttggaaaata ggacgtggaa tgttccgctt 5700 ttaagctctt tacttccttc ggatgtttgt ctcaagattt ccaatatttt tatccctaaa 5760 aataatgttg atgacgaggt cttttgggcc ctctcccctg atggtattta ttctgttaaa 5820 tctggggccc agctgattat taaccagaaa gttgggggtc tcacccaggt tgattttcag 5880 tggatctgga agtctaagct ttctcctaag attaaaaatt ttcttatgga aagcttgtaa 5940 tgatggcctc ccaacaaagg cccaggctgg aacaggtgca tgttttcact cctcagcagt 6000 gtgaattctg ctcttgctca gtggaaaccg cgtcgcatct tttctttcaa tgccaagtta 6060 ctcgtgacat tatgcatcag cttgatgctg attatgggtg gcctcaagtt ccggcagctg 6120 cgaatttgga ttcttttaga gccaatttgc aggtttgtgt agactcgctt ggaagactga 6180 agacttgtca actagctgtt gtttggtggt ttgtttggtt cacccggaat aaactcattt 6240 tttcctccga agctttttct gtccgtcaaa tcagcttcct agttcataaa tttgttgagg 6300 aaaataaatt gagtgatgag tttgctccta gctctcagcc ttgctctatt agtaagcctt 6360 tgagtcataa cgctttagcc cgtcggtgtg ctgtttgggt tccccctcct gagggtgttt 6420 ttaaagtaaa ttttgatggt tccaaatata gtgatgggcg agcctccttt ggttttgtta 6480 ttagaaattt cctgggtgaa gttattcttg caggttgtaa ctcgttgtct tctgattgtt 6540 ctattattca agcggaggct cttgggctta gggaagcaat taaggctgcc cttttttgtt 6600 ctctacctca gatcatcata gaaggagata atctctcggt tatcaacgca gttcttaaaa 6660 tttggaaacc tccctgggtt atcaactctt tattacagga tgtttggtgt gagttgggta 6720 attttaacag tgtctctttt actcattgtt tcagggaagc gaatagggct gcagatttta 6780 tggctcatca aggtcaggcg gctcagaatc tctgttactc gttcccgccg ttctctgttg 6840 atttctctct tgtcatccgt aaggatgttt taggctggcc tcccgattag gggcttgttc 6900 ctagtttttc tttcctgtat caaaaaaaaa aaaaaaaaca aagatgttct aaagactcac 6960 atgcttcttt acaccgtgtc taatttaaaa tgtacatata tacttgagtg taatataaat 7020 gcttggaggt aattcttatt atcgatcttt cagtaaatta aagtgaaaaa atctcaccta 7080 aaacaactta ctcttaatca caacacagtt tagcaccata gtatataaaa gcggattatt 7140 attatttgaa atttaacatt ttattcatca aatatactta aatttggcta ttgatcccaa 7200 attaaacatg aaaaaacaat gttagataat attctaactt gcattgtagt aataagttga 7260 aaacactctt ttagtatgtc tacaaattaa attgagatga atatcccttg taaatgaagg 7320 agggtacttg aaattctcac tttacagccc aatatcaaac ctttaccgca agatcagata 7380 aggactcgca aatcacaatc aactaaatca accttgattc ttaaatatac ccatattaca 7440 cataatgttt tgagttgaac ctcaaatcaa gtcgaatctg gcaacttcta cactccatgc 7500 aataaacata tattaanatg aacaaaataa acaaatggaa gaacctgaga tgaatcatgt 7560 tctccatctt ctaataaggg ggtcactcga taatctcaca atcccattat ttgtacccct 7620 ataagaccag gtgcggtgga acaatattat ttgttccccc ttt 7663 // ID GmOgre_I repbase; DNA; EDCOT; 10196 BP. XX AC . XX DT 16-SEP-2008 (Rel. 13.09, Created) DT 16-SEP-2008 (Rel. 13.09, Last updated, Version 1) XX DE GmOgre_internal; Ogre-related retrotransposon from Glycine max. XX KW Gypsy; LTR Retrotransposon; Transposable Element; GmOgre_I. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-10196 RA Laten H.M.; Gouvas,E.; Badal,E.B.; RT "Ogre-related consensus sequence based on a collection of 721 RT overlapping sequences from the Genbank Genome Survey Sequence RT database."; RL Repbase Reports 8(9), 906-906 (2008). XX DR [1] (Consensus) XX CC Consensus sequence of GmOgre from the primer binding site to the CC end of the coding region based on 721 overlapping BAC-end CC sequences from the Genbank Genome Survey Sequence database. XX FH Key Location/Qualifiers FT CDS 869..2734 FT /product="GmOgre_I_1p" FT /translation="MGTNQTGKRFYQVKVKSLDTTSIKELGRLMEPLQMQA FT FRKTYGKILELTIAEVSIEAIASLTQYYDQPLRCFTFGDFQLVPTIEEFEE FT ILGCPLGGRKPYLSSGCLPSLSRIATVVKDSARGLDRIKQTRNGIAGLPXK FT YLEDKARGMANQGDWVPFMDVLALLIFGVVLFPNVDGLVDLAAIDAFLAYH FT HSKESPVVAVLADLFDTFDRRCEKSSARIICCLPALCVWLVSHLFQQDTRH FT PCPLLSHRSCTEKRRIDWDQLLAGIGGRTIXWFPRWKEGKEGVLFSCGXYP FT NIPLXGTRGCINYNPALAIRQLGYPMRGAPTEESMSPFLVRDXGAQNSKTI FT QRIHKAWETPLRKDQELRGIRNGIIGGYHEWLKVHIRGLDWLAKLKVVSEE FT XFEAPEEDEEVQALKSELGKAKLAKEKFKLAATHVRKECAGLREENAITAR FT ALEQETKRARKEEYGRNKFRGALWGSNSELKLRREERDQSRAHSMVLKEEL FT XACSRSKRSLSQRLCETETNMLAIIAKYQEELGLATAHEHRIADEYAQVYA FT EKEARGRVIDSLHQEATMWMDRFALTLNGSQELPRLLAKAKAMADTYSAPE FT EIHGLLGYCQHMIDLMAHIIRNR*" FT CDS 6741..10196 FT /product="GmOgre_I_3p" FT /note="Exon 2 of gag-pol." FT /translation="NGRXDDESPEGTNTWDPXIXFEQEMNQTEDEGXEDVG FT LPXELERMVAHEDQEMGPHQEETELVDLGIGSGKREVKIGTGITAPIREEL FT IILLKDYQDIFAWSYQDMPGLSSDIVQHRLPLNPXCSPVKQKLRRMKPETS FT LKIKEEVKKQFDAGFLAVARYPEWVANIVPVPKKXGKVRMCVDYRDLNRAS FT PKDNFPLPHIDILVDNTANFALFSFMDGFSGYNQIKMAPEDMEKTTFVTLW FT GTFCYKVMSFGLKNAGATYQRAMVALFHDMMHQEIEVYVDDIIAKSKSEEE FT HLVNLRKLFERLKKYQLRLNPAKCTFGVKSGKLLGFXVSQKGIEVDPEKVK FT AILEMPEPRTERQVRGFLGRLNYIARFISQLTAICEPLFKLLRKNQTDRWN FT EDCQEAFGRIKKCLMNPPVLMPPVPGRPLILYMTILDESMGCMLGQHDESG FT KKERAVYYLSKKFTTCEMNYSLLERTCCALVWASHRLRQYMLSHTTWLISK FT MDPVKYIFEKPALTGRIARWQVLLSEFDIVYVTQKAIKGSALADYLAQQPL FT NDYQPMHPEFPDEDIMALFEEKLDEDRDKWTVWFDGASNILGHGVGAVLVS FT PDNQCVPFTARLGFDCTNNMAEYEACALAVQAAIDSNVKLLKVYGDSALVI FT HQLRGEWETRDPKLIPYKAYIKELAKTFDEISFHHVPREENQMADALATLA FT SMFQLTPHGDLPYIEFWCRGKPAHCCQVEEERDGKPWYXDIKRYVVSKEYP FT PEIADNDKRTLRRLAAXFFMSGXXLYKRNHDMTLLRCVDAKEANHMIEEVH FT EGSFGTHANGHAMARKILRAGYYWLTMESDCCVHVRKCHKCQAFADNVNAP FT PHPLNVMSAPWPFSMWGIDVIGAIEPKASNGHRFILVAIDYFTKWVEAASY FT TNVTRXVVVRFIKXEXICRYGXPRKIITDNGTNLNNKMMXEMCEXFKIQHH FT NSTPYRPKMNGAVEAANKNIKKIIQKMTVSYKDWHEMLPFALHGYRTSVRT FT STGATPYSLVYGMEAVLPFEVEVPSQKILAESGLEESEWAQTRYDQLNLIE FT GKRLTAMSHGRLYQQRIKNAFDKKVRPRKFNXGDLVLKKISHAVKDNRGKW FT APNYEGPFXVKRAFSGGALVLTNMDGEELPSPVNSDVVKRYYA*" FT CDS 2791..6570 FT /product="GmOgre_I_2p" FT /note="Exon 1 of Gag-pol." FT /translation="MSWSHVSTPKSLCKSNHSYISSLACIFFLYPLLTFGF FT LGKNTITKRAXRXPYRTRSKSRTMGDQEETQEQMKADMSALKEQMASMMEA FT MLGMKQLMEKNAATAAAVSSAAEADPTLLATXHHPPSNIVGRGRDTLGHDG FT SPHLGYNRAAYPYGLPPNYSPPXLQEDAGHIASPVXEXEPPQQPDEVHKDP FT QDYARRDVEFYPPIPEGPAPGTLPQPNIAAXPIVLSMEGPPPATEERRKLD FT LLEERLRAVEGFGDYPFADMTDLCLVPDVVIPPKFKVPDFDKYKGTTCPKN FT HLKMYCRKMGAHSKDEKLLIHFFQDSLAGAAVVWYTNLEASRIRTWKDLIT FT AFLRQYQYNSDMAPDRTQLQNMFKKEGETFKEYAQRWRDLAAQVAPPMVER FT EMITMMVDTLPVFYYEKLVGYMPSSFADLVFAGERIEVGLKRGKFDYVSST FT XXNAKRIGATGAKRKEGDAHAVSSTPAWVKPXQTPHGTHQYAQHHPSFSAH FT XGNASSSXPVQPKAPTQREAPQVPTPNTTRPAGNSNXTRNFPPRPXPEFTP FT LPMTYEDLLPSLIANHLAVVTPGRVLXPPFPKWYDPNATCKYHGGXPGHSX FT EKCLALKYKVQHLMDAGWLTFQEDRPNVRTNPLANHGGGAVNAVESDRPXR FT SKPLRDVATPRRFIFEALQKGGVIPHSGCKEDSCLLHSGEXHDMETCLXVE FT ELLQRMIDQGRLEVGIEGKEEQHICMQSTXGSXVAKPKPLVIYFTKSAASQ FT KPGHPLXAKPVPFPYQNSHAVPWRYTPPXXKEEEXTDVSSLSAKVTNITGL FT SGVTRSGRVFAPPDLPVQPADVKGKGKVVEEQDGEAPHASNKDIPAKGXPE FT KKDGXKEVSLEEASEFLRIIQQSEFKVIEQLNKTPARVSLLELLMSSEPHR FT ALLVKVLNEAHVAQDISVEGFGGLVNNITANNYLAFAEEEIPAEGRGHNKA FT LHVSVKCMDHIVAKVLIDNGSSLNVMPKSTLEKLPFNASHLKPSSMVVRAF FT DGTRREVRGEIDLPVQIGPHTCQVTFQIMDINPPYSCLLGRPWIHSVGVVP FT STLHQKLKFVVEGHLVIVSGEEDILVSCPSSMPYVEAAEESLETAFQSFEV FT VSISSVDSLFGQPCLSDAAVMMARVMLGNGYEPGMGLGKDNGGITSLIXTQ FT GNRGKYGLGYKPTQADMKRSIAGRKNSGQSSRWRQESEGSPPCHISRSFIS FT AGLGDXGQVFAICEDDXPSTLDLVRPCPPDFQLGNWRVEERPGIYATSIM" XX SQ Sequence 10196 BP; 2748 A; 2312 C; 2504 G; 2334 T; 298 other; gttggcgact ccactgggga ctgtttttta gagagttagg ccatttaatc ttgtgcaatg 60 ttttaycatg acttwcycct ttgttggttt ccctttcatt atgttcttgt gtatataaac 120 tctttgttgc ttttagtgyg ttttaaaatg tatgcatgag gtaaatattt attcatttga 180 tgcacacaaa caccaacact atttgcacac actgtgagtg aaaaagggcc ctatacccgg 240 gttcatggga acataaggag tggaggtgaa tctgtgatca tgctaggtct ccgacttgct 300 tgattacagt gaaccctcat ctagagcttt tctctttgaa aacwtattgt tgctagtagt 360 ccctactgct rcaatatgtt cttcgaaggg gatgatacct ctagaaacca tcaagagaga 420 tatgactacc ttggggrtta tyrctaaaag cctagttagt tctctccctt ataggtccct 480 taaatagggg cacggagcaa acacgctgcg tgccattttt cacactgcca tgcatragta 540 tcatataccc ttttgcttat gttcrgtraa tattgtcata ctgtgtacat tcccgcattg 600 tgycttttgc atakgcatyg catatgggtt ctgtcttgat ccctctctrt aaacaaacca 660 acggagggtc cgtgtcrcct tcttaaawac rtacgttggg gcactttgct acccctagac 720 gttgtrtcta agaaggrgac aaattycccg grcccccgca ttcctaratt gcatctgtgt 780 catatgcatt ccwtcatgca ttcatccatt ccacccatga gatatcggag ttttgatttg 840 caccagcttt tgtctcactt tagtaagcat gggaacaaat caaaccggca agaggttyta 900 ccaagtcaag gtyaaaagcc tagataccac cagcatcaag gaattagggc ggttgatgga 960 acctctccaa atgcaagcct tccgcaagac ttacggaaag atcttagagt tgaccatagc 1020 agaggtrtcc atagaagcca ttgcatcact yacccaatac tacgaccagc ctttgagatg 1080 cttcacattc ggagacttcc aattrgtacc aaccattgaa gaatttgagg aaattctagg 1140 atgtcctctc gggggaagaa aaccatatct ttcctccggg tgtctcccct ctttgagcag 1200 aattgcaact gtggtcaagg attcagcaag aggtttggac cgcataaaac agactcggaa 1260 cggcatagcg ggcctaccac rgaagtacct agaagacaag gcgaggggta tggccaatca 1320 aggagaytgg gtcccgttta tggatgtgtt agctttgcta atttttgggg tcgtcctctt 1380 tccaaacgtg gatggtttgg tggacctagc agcaatcgac gctttccttg cmtaccacca 1440 tagcaaggaa agtccggtgg tagctgtctt ggcagatyta tttgacacat ttgaccgaag 1500 gtgcgaaaag agtagcgcac ggatcatctg ttgcttrccc gcyctctgtg tttggttggt 1560 ttcrcacttg ttccaacaag acacaagrca tccatgtccg ctcctgagcc atcgctcgtg 1620 tactgaaaag aggagaatag attgggacca gctyttggcy gggataggag gtagaacaat 1680 carttggttc ccccgatgga aggaaggaaa agaaggagtc cttttctcat gtggargata 1740 cccaaacatt ccgctgrtag gaacgagggg ttgtattaac tacaatcccg cgctcgctat 1800 aagacaacta gggtacccca tgaggggagc accgacggaa gaaagcatgt ctcctttcct 1860 tgtgagggat ytcggcgcac aaaattccaa gactatacaa agaatccata aggcatggga 1920 aaccccgtta aggaaagatc aagagcttag aggcattcgt aatggcatca ttggtgggta 1980 ccacgaatgg ctgaaagttc atatacgagg tttagattgg ctcgccaagt taaaagtcgt 2040 cagcgaagag arttttgaag caccggaaga ggacgaagaa gtccaagctc tcaaaagcga 2100 gttaggaaag gcaaaacttg ccaaggagaa gttcaagttg gccgctacac acgttcggaa 2160 ggagtgtgcc gggttacggg aagagaatgc aattaccgca agagcccttg aacaagagac 2220 caagagggct cgcaaggaag agtatggccg gaacaaattt cgcggagctc tatggggtag 2280 caatagtgaa ctcaagttgc gaagggaaga aagggaccag tcgcgagcac atagcatggt 2340 tytgaaagag gagttarttg cttgttcaag gtccaaaaga agcttgtctc agcgtttatg 2400 cgagacggag accaacatgc tagctatcat cgccaagtac caagaagagt taggtctagc 2460 cacggcccac gagcatagra tcgcggayga gtatgcccaa gtatacgcgg aaaaagaggc 2520 tagaggaagg gtgatcgact ctttacacca agaggcaacc atgtggatgg atcggtttgc 2580 tcttaccttg aacgggagtc aagaacttcc ccgattgtta gccaaggcca aggcgatggc 2640 agacacctac tccgcccccg aagagattca tgggcttctc ggctattgtc agcatatgat 2700 agacttaatg gcccacataa ttagaaatcg ttaggaaact tgtatggtct ctcagacctt 2760 gactagatay gacttccttt ttgaaataaa atgagttggt cccatgtttc tactccaaaa 2820 agcttgtgca aatcaaatca ctcctacaty tcatctctag catgcatttt ctttctttac 2880 ccactcctca cgtttggttt tttagggaaa aacaccataa ctaaacgcgc crcaaggsat 2940 ccctatcgca ccagatccaa atctagaacg atgggtgatc aagaggagac rcaggaacag 3000 atgaaagccg acatgtcggc tctgaaagaa caaatggcct ccatgatgga ggccatgtta 3060 ggtatgaarc agctcatgga gaagaacgcg gccacygcyg ccgctgtcag ttcggctgcc 3120 gaagcagacc cgactctctt ggcaactrcg caccatcctc cctcaaacat agtaggacgg 3180 ggaagggaca cactggggca cgatggcagc cctcacctgg gatacaaccg agcggcttac 3240 ccttatggat tgccgcccaa ctaytcacca cccrtcttgc aagaagatgc gggccacatt 3300 gcttctcccg tccwtgaaar agagcctcct cagcagcccg acgargtcca yaaagaccct 3360 caagaytatg ctcgraggga tgtcgagtty tatcccccga tccccgaagg gccggcacca 3420 ggcacgttgc ctcaacccaa catcgcagca ycrccaatag ttttgtcyat ggaaggrccg 3480 cccccggcaa ctgaagaaag gaggaagctc gatctccttg aggaaagatt gagggcygtg 3540 gaaggatttg gggactatcc gttygcagac atgacggatc tttgcttagt acccgatgtt 3600 gttattcccc cgaagttcaa agtgccggac ttcgacaagt ataaagggac gacttgtccc 3660 aaaaaccatc tcaaratgta ctgccgtaag atgggcgccc aytctaaaga tgaaaagctg 3720 ttratacact tctttcagga tagcttggcc ggagctgcgg tagtgtggta cactaatttg 3780 gaagcttccc gtatccgtac ttggaaggat ctgattacyg ccttcctaag gcagtatcag 3840 tacaattctg atatggctcc ygaccgyact caactgcaga atatgttcaa gaaagagggt 3900 gaaaccttta aagaataygc gcagcgrtgg agrgatytgg cggcacaagt agctcctccc 3960 atggttgaga gagagatgat caccatgatg gtagacactc tgccagtgtt ctactatgag 4020 aagctagtrg gttacatgcc gtccagcttt gcggatctgg trttygccgg ggaaagaatc 4080 gaggtwggat tgaaragagg aaagttygat tacgtttcct ccacaarygy gaatgccaaa 4140 agaatcgggg caacaggggc aaaaaggaag gaaggagatg cccatgccgt ctcttcaaca 4200 cccgcrtggg tcaaaccccm gcaracacct catggtaccc atcagtacgc gcaacatcac 4260 ccragcttct cggctcatrc ygggaacgcc tctagttcar cacccgtgca gcctaaggca 4320 cccacccaga gggaagctcc ccaagttcca actccgaaca cgactcgmcc ggccggtaat 4380 tccaacrcra caaggaactt ccctccgagg ccattkccrg aattcacccc rctcccaatg 4440 acgtacgaag ayctyytrcc atccctcatc gccaaycatt tggccgtggt aactcccgga 4500 agggtcctcs aacccccttt cccraagtgg tatgacccta aygcaacttg caagtaccat 4560 gggggtgycc cggggcattc crtygaaaaa tgcttggccc ttaaatacaa ggtccaacat 4620 ttratggatg cyggatggct gactttccaa gaggatcggc ccaatgtgag aaccaacccg 4680 ctcgccaatc atggaggggg agcrgttaat gcmgttgart ccgataggcc gcrcaggtct 4740 aaacctttaa grgatgtggc aacccctagg aggtttatct ttgaggccct acaaaaggga 4800 ggtgtrattc cccatagtgg gtgtaaggag gattcctgty tgctacattc cggcgagmtg 4860 catgacatgg agacgtgttt ggragtagag gaattgttac agcggatgat agaycaaggt 4920 cgactrgaag tcggcattga aggaaaagaa gagcagcata tatgcatgca rtcyacggak 4980 gggagcrgtg ttgcgaagcc caaacccttg gtgatatact tcactaaaag ygcagcytcg 5040 caaaagcccg grcacccctt artrgccaaa cctgttcctt tcccgtacca aaatagycac 5100 gcggtcccrt ggagatatac acctccgrgg ragaaggaag aagaagycac ygacgtcagc 5160 tcgytgtcrg ctaaagtaac aaatatcacg ggactgagtg gtgtgacccg tagtggtcgt 5220 gtgttcgcrc ctccggacct accagtccaa cccgcsgacg tcaagggaaa aggaaaagtg 5280 gtggaggaac aagatggcga agcaccccac gcttcgaata aagatattcc rgcaaarggb 5340 cyyccggaga aaaaggatgg taraaaggag gtgtcgctag aggaagccag cgagttccty 5400 cgkataattc agcagagcga attcaaggtt atcgaacagc tcaacaaaac cccggcyagg 5460 gtctcgctgt tggagttact tatgagctcc gagcctcatc gggctctgct agtaaaagtk 5520 ctgaacgagg cycacgtggc ccaagatatc tcggtagaag gtttcggagg gctggtcaac 5580 aatatcactg ccaacaacta tcttgccttc gccgaagaag aaatccccgc cgaggggaga 5640 gggcataata aggctttaca cgtatcagtc aagtgtatgg accatatcgt agccaargtr 5700 ctcatcgata atggttccag tttaaacgtg atgcctaaga gcactttgga gaarttacca 5760 ttcaatgctt cccacttaaa rccaagttca atggtggttc gkgccttcga cggcactcgc 5820 cgagaggtta ggggagagat cgatctccca gtacaaatag gccctcacac ctgtcaagtc 5880 accttccaaa taatggatat taaccccccc tacagctgyc tgttggggcg cccgtggatc 5940 cactcagtgg gagttgtgcc ytctacactc caccaaaagy tgaaattcgt agtggagggg 6000 cacttggtca tcgtgtcagg cgaggaagay atcttggtaa gctgcccatc ctccatgcct 6060 tatgtggaag ccgcagaaga atcgttagaa acygctttcc agtcttttga ggtggtcagc 6120 atttcctccg tggactccct ctttgggcar ccttgtctgt ccgatgcagc ggtaatgatg 6180 gcccgagtta tgttggggaa cggttatgaa cccgggatgg gtttaggcaa agacaacggc 6240 ggcataacta gcctgataaa wacccaagga aatcgtggga agtatggttt aggctataag 6300 cccactcagg cggacatgaa aagaagcatc gcgggaagga agaacagtgg tcaragctcg 6360 cgttggagac aagaaagtga aggaagcccg ccctgccaca taagtagaag ctttataagy 6420 gcgggtctgg gagacraagg tcaagtgttc gcgatatgyg aagatgatrt tccragtact 6480 ttggatttgg tmcgaccatg ccctcctgat ttccagctgg gaaattggcg agtggaggaa 6540 cgccccggca tttacgcaac ragcataatg taaaccttta cggttttaaa agctctatag 6600 ttgggcctag gctttagagt ttttcmtttt gttaaggctt tgtgtctttt gtttttgaat 6660 ttataataca aggatctttc ttcatctgtt cctggtctct acccattctc attcatttgc 6720 atgtttactt ctttttctga aacggcagat ycgatgacga gtcccccgaa ggtactaata 6780 cctgggaccc gyctatcrac ttcgagcaag aaatgaatca aacggaagat gaaggaratg 6840 aggatgtggg acttccyycr gaactagaaa gaatggtcgc ccatgaggac caagaaatgg 6900 ggcctcatca agaagaaaca gagctagtag acttaggaat tggcagtgga aagagggaag 6960 taaagatagg tacaggyatt accgcaccta tccgtgaaga attaataatc ctgctaaaag 7020 actaccaaga catctttgct tggtcatacc aagatatgcc cggtttgagt tctgacattg 7080 trcagcaccg attacctcta aatcccgrgt gttccccrgt aaaacagaaa ytgagragga 7140 tgaagcccga aacatccttg aagataaaag aagaagtgaa gaagcaattt gacgctggat 7200 ttctggccgt cgctcggtat ccagaatggg ttgccaacat cgtaccagtt cctaaaaaag 7260 rtgggaaagt acgaatgtgt gtrgattayc gggacctgaa tcgggccagt cccaaggaca 7320 attttccktt accacacatc gatatcctcg tagataacac ggccaatttc gctttatttt 7380 ccttcatgga yggtttctcy ggttacaatc agataaagat ggcgcccgag gatatggaaa 7440 agactacytt cgtcaccctg tggggracgt tctgttacaa ggtgatgtcc tttggactca 7500 agaatgccgg ggcaacttat caacgggcca tggtagcttt gttccatgat atgatgcatc 7560 aagagatcga ggtctacgtg gacgacataa ttgctaaatc taaatcygag gaagaacacc 7620 ttgtcaacct gcggaagttg ttcgaaaggc ttaagaaata tcaattaagg ttgaaccccg 7680 ctaagtgtac ctttggggtc aaatcaggga aattgcttgg tttcrttgta agccagaaag 7740 ggatagaggt agaccccgaa aargtgaagg ctatccttga gatgccagaa ccccgtacag 7800 agaggcaagt ccgaggtttc ctgggrcgct tgaattatat tgccagattc atatcgcagc 7860 tcaccgccat ttgtgagccg ttgttyaaac tcttrcgcaa aaaccaaact gatcgstgga 7920 atgaggattg ccaagaggct tttggaagga tcaaaaagtg cctwatgaat cctcccgtgc 7980 ttatgccacc agtacctgga aggcctctca tyttgtacat gacaatcttg gacgagtcaa 8040 tggggtgtat gctggggcaa catgacgaat ccgggaagaa agagcgcgct gtttactacy 8100 taagtaagaa gttcacgacc tgtgaratga attactcctt gctcgaaaga acgtgttgtg 8160 ctttagtatg ggcatcccat cgcctaaggc agtacatgct gagccatact acctggttga 8220 tatccaarat ggacccggtt aagtacatct ttgaaaagcc agctctcacr ggacgaatcg 8280 cccggtggca agtcttgcta tcygagtttg atatagtcta cgtcacccaa aaggcgataa 8340 aaggaagcgc yttrgcagat tatttggctc aacagcctct taacgactay cagcccatgc 8400 atcckgaatt cccggatgag gacatcatgg ccttgttyga ggaaaarttg gacgaagatc 8460 gggacaaatg gacygtatgg tttgacggag cgtcaaacat tctaggycat ggcgttgggg 8520 cagtrttggt ctctccggac aatcaatgtg tacctttcac agccaggcta ggattcgact 8580 gcaccaacaa catggccgaa tatgaagcat gtgccctrgc cgtccaggca gcrattgact 8640 ccaatgtcaa actactcaag gtgtacggcg actcagcgtt ggtaatccat cagctgagag 8700 gggaatggga aactagagat cccaagctga taccctacaa agcctatatc aaggaattgg 8760 ctaagacctt ygatgagatc tccttccatc atgttccccg cgaggaaaat caaatggcgg 8820 atgcrcttgc tactttggcg tctatgttcc agctaacrcc gcacggggay ctaccctaca 8880 ttgaattttg gtgtcgtggc aaacccgcrc attgttgcca agtrgaagag gaacgggacg 8940 gaaagccttg gtattwcgac atcaagcgat atgtcgtaag caaagaatac ccgccagaga 9000 ttgccgacaa ygataaaagg acattgagra ggttggcagc crgtttcttc atgagcggar 9060 gcayactgta taagagaaat cacgacatga cactcctgcg rtgtgtggat gccaaggagg 9120 caaatcacat gatcgaggaa gtccatgagg gctcgtttgg aacgcacgcc aacgggcatg 9180 ctatggccag gaagatcyta agagcaggtt attactggct taccatggaa agtgattgtt 9240 gtgtccatgt gaggaartgc cacaaatgtc aagcattcgc agayaatgtc aatgcyccrc 9300 cacatcctct gaatgtcatg tccgcccctt ggcctttctc catgtgggga atagatgtca 9360 tcggggccat ygarcccaag gcctcgaatg gtcatcgctt catyctcgtr gcgatagatt 9420 atttcaccaa rtgggtcgar gcggcttcht ataccaatgt cacgaggart gtggtggtca 9480 grttcatwaa garrgagats atytgycgat ayggwytscc waggaagaty atyackgaca 9540 ayggcaccaa yctgaataac aaratgatgs rggaaatgtg cgaggaktty aaaatccagc 9600 atcayaaytc caccccytay cggccaaaga tgaatggrgc ygtrgargct gcmaataaaa 9660 atattaagaa gattattcag aagatgacgg tgtcatacaa agattggcat gagatgytgc 9720 ctttygccct rcayggatat cgaacctcgg tacgaacttc tactggggca acgccgtayt 9780 ccttggttta tgggatggaa gcggtactcc catttgaggt agaggtccct tcccagaaga 9840 tactagcgga atcaggccta gaagartcag agtgggctca aacacgctac gaccaactca 9900 accttattga aggtaagcgt ttgacggcca tgagccatgg gcgcctgtat caacaaagga 9960 taaagaacgc gttcgacaag aaggtacgcc cgcgcaagtt caaysagggg gaccttgtsc 10020 tgaaaaagat atcccacgct gttaaagata atcgagggaa gtgggccccg aaytacgaag 10080 grcctttcrt tgtgaaaagg gctttttctg ggggggctct ggtgctcacc aacatggatg 10140 gcgaggagct accctcrccc gtgaactccg atgtygtyaa gcgatattac gcttga 10196 // ID Copia-34_Mad-LTR repbase; DNA; EDCOT; 240 BP. XX AC ACYM01063166; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-34_Mad-I; KW Copia-34_Mad-LTR; Copia-34_Mad_. XX NM Copia-34_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-240 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1384-1384 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01063166; Positions 19 258. XX SQ Sequence 240 BP; 70 A; 35 C; 43 G; 92 T; 0 other; tgtgatttgt cgattggtta taaccactat cactcaagta gttagatggg tttagagagt 60 tagttacaaa agggggtagt attgtaatag tccatgtgtg ttgagaggct atataacaca 120 ttgtaaagac ttgtaatatt tttatacagt gaaatacaaa gcattctgaa accctttttc 180 ttctaagctt ctgctctcct tatttcattt ttccatagtc atatttctta agagttatca 240 // ID MUMT repbase; DNA; EDCOT; 3908 BP. XX AC . XX DT 22-DEC-2006 (Rel. 11.12, Created) DT 22-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE A mutator type DNA transposon, from Medicago truncatula. XX KW MuDR; DNA transposon; Transposable Element; transposon; KW Interspersed; repeat; mutator; MUMT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3908 RA Shankar R. and Jurka J.; RT "MUMT: A mutator type DNA transposon from barrel medic."; RL Direct Submission to Repbase Update (22-DEC-2006). XX DR [1] (Consensus) XX CC The sequence lacks any inverted repeat unlike other mutator CC transposons and shows three different protein domains of plant CC specific protein, transposase and a SWIM zinc finger domain. XX FH Key Location/Qualifiers FT CDS join(821..1411,1415..1960,1964..2578) FT /product="MUMT_1p" FT /translation="MGAQMKRRLELNDEAGINVSRNFQSLVVEANGYKNLT FT FGEKDCRNYIDKVRRLRLGTRDAEAIQKYFVRMQKQNSQFYYVMNVDDESR FT LRNVFWADARCRVAYEYFGEVITFDTTYLTNKYDMPFVPFVGVNHHGQSML FT LGCALLSNEDTETFTWLFKTWLECMHGRSPNAITTDQDRAMKNAIEIVFPK FT ARHRWCLHIMKKISEKFGSHSDYESIKTLLHDIVYDSFSKSDFMTRWENMI FT EFYKLQDNEWLKGLFVERHRWVPAYVRDTFWAGMSTTQRSESMNSFFDGYV FT SSKTTLKQSVEQYDNALKDKIEKENIADFRSFNTVISCISHFGFEFQFQKA FT FTNAKFQEFQLEIASMMYCHACFNRLEGLDSIFFVTSKKVYDQMKDIVFMV FT FFNEKDFMLKCTCCLFEFKGILCRHILRVLKLIGKTDFVSSNYILARWRKD FT IKWRYTLIKCGFDNLVGKTELQRAGKACDAFYEFASTRINSEDDLVKVMNL FT IQNMKIELPCNETSPRIVEEDCSAQNQATILDPKLARSKGRPPSKRKTSIV FT DQIVKKKLAXXXXXXXXXXXXXIRVQEEVSMKFIAIY" XX SQ Sequence 3908 BP; 1229 A; 518 C; 749 G; 1285 T; 127 other; ttaatagaaa tgataccctt cagtcttcac aaaaacaaaa ccacgttaac cacttccacc 60 gcaattgttt cctctttccc acgaaacaaa gactctggtt gatattcaac ttctattgtt 120 gtgaaatagt gtcgtcatcg atttctcgtt ttcatgctct tgcctctgta aatcagattt 180 catatgcatc ctcacataac tctgtttctg cttatcatca caacttccat tgattcatag 240 cactaaagca gagtatttca gttttaattt acttacaagt aagtatttgt gtatttgttg 300 tttttatata tcattagcag gaattttgag ccgattgatt gatttttcat ttacttaact 360 gcgttagtca attaatatag gnnnnnnnnn naatttgttg tattagtgca agaaggattt 420 gagtcctgtg atgaattgga aacttatgat tgtttagaag caaatggtac ttatgaagaa 480 gaaacacctt gtgatgggat gtcattcgga tatgaaaagg aaattactga gtattacaag 540 aattatgctg aacgggtggg ttttggagtt nnnnnnnnnn nnnnnnnnnn nggagatgaa 600 gggaaaatgt attttacttt agcatgtaat cgagctagaa agtatgtgag tcgctcaaag 660 aatctgttaa agccaaatcc tgtaactcaa acacagtgta aggctagatt gaatgcgtgt 720 atttatttag acggaacaac taaaattaaa agtgtannnn nnnnagcata atcatgatct 780 aagtccaggg aaagcacgat attttagatc gaacaagaat atgggggctc aaatgaagag 840 gaggttagaa ctcaatgatg aagctgggat taatgtaagc agaaattttc aatctctagt 900 cgttgaagca aatgggtata agaatctcac atttggagaa aaagactgca ggaactacat 960 agacaaagta agaagactac gacttgggac aagagatgct gaagcaatac aaaaatattt 1020 tgttaggatg caaaagcaaa acagtcaatt ttattatgtc atgaatgtgg atgatgaaag 1080 tcgattacga aatgtgtttt gggcagatgc aagatgtagg gttgcatatg aatattttgg 1140 tgaagtcata actttcgaca ccacttattt aacaaataaa tatgacatgc cttttgttcc 1200 ttttgttggc gtaaatcatc acggtcagtc tatgttgttg ggttgtgctc tgttgtcaaa 1260 tgaggatact gaaactttta cttggttgtt taagacatgg ttagaatgta tgcatggacg 1320 ttctccaaat gccataacta ctgatcaaga cagagcaatg aagaatgcaa ttgagattgt 1380 ctttccgaaa gctcgtcatc gatggtgctt atgacatata atgaaaaaga tttcagaaaa 1440 gtttggtagt cactctgact acgagtctat caaaacactt ttgcatgata ttgtatatga 1500 ttcttttagc aaaagtgatt ttatgacgag gtgggaaaat atgattgagt tttacaaact 1560 acaggataat gaatggctga aagggttatt tgttgagcga catcgttggg tccctgcata 1620 tgtaagggac acattttggg ctggaatgtc aactacacaa cgaagtgaaa gtatgaactc 1680 tttttttgat ggatatgtaa gctcaaagac aacattgaag caatctgttg agcaatatga 1740 taatgcattg aaagataaga ttgaaaagga aaacattgct gactttcgtt cttttaatac 1800 agttatttct tgtattagtc actttggctt tgagttccaa ttccaaaaag catttaccaa 1860 tgcaaagttt caggaattcc aattggaaat agcttctatg atgtactgtc atgcatgttt 1920 caacagattg gagggtttgg attcaatatt ttttgttaca tagagtaaga aagtatatga 1980 ccagatgaaa gatattgtgt tcatggtgtt cttcaatgaa aaagacttta tgttaaaatg 2040 cacctgctgc ttgtttgaat ttaaaggcat tttatgtagg cacatccttc gtgtgcttaa 2100 gctcattggg aaaacagatt tcgtgtcatc taattatatt ttggcacggt ggaggaagga 2160 tataaagtgg aggtatacac ttattaaatg tggttttgat aatttggttg gaaaaactga 2220 attgcaacgt gcaggtaaag cttgtgatgc cttttatgaa tttgcttcaa cgaggataaa 2280 tagtgaagat gatttagtga aagtgatgaa cttaattcaa aacatgaaaa ttgagttacc 2340 atgtaatgaa acatctccta gaattgtaga agaagattgt tcagctcaaa accaagctac 2400 cattcttgat cctaaactag ctcgaagtaa agggcgtcct ccttcaaaaa ggaagacttc 2460 tatagttgat cagattgtga agaagaagct tgcnnnnnnn nnnnnnnnnn nnnnnnnnnn 2520 nnnnnnnnnn nntattcgag ttcaagaaga ggtgagtatg aaatttatag caatttattg 2580 atattgtagg tataatagtt gagatgtcta atttaagaat ttttatggca gggccaatgt 2640 tcatctagag gtcaagaaat tgaacacgaa gtgttttaca gttctcaact tggtgataga 2700 attggaacac aagagagcat tcaagtaaac aaagcatata ctagtcatgc aaatcaggtg 2760 caaatataag attcatctaa ttatatatta ctatttatgt agttgaacat agtannnnnn 2820 nnnnnnnnct aattatagtt ttttctacga cagagactaa gattgcatgt agttcaaagt 2880 acttcaaatg aagagattat taggtatcaa attattgatg ggactgggtc acaagacaat 2940 attcatgtaa acatgatttc ttactttcat ttaattaaaa atgattggct ttttgttatt 3000 tgaaatattc aatatgatat tgcatactag ttatttatgt ttttgcatgt taatatctat 3060 aacaggagca taactatgtt tgtagtagtg aaaatggtag tgtgaatact ttagctccct 3120 tcaatccaaa tcaagaacat tttggtcaag taaacaaggt gtaaatatag attttggtgt 3180 tgttttgttt ttatttgaac atttttataa tgaacataaa tggttaatta tatattcttt 3240 gcaggctcct tattactctc aggtcacaaa ctataatgct acttgttctg atttgttgca 3300 ggtattggtt tgaagtcttc ttattgtatg aaaatacaat ctgttggttt tttattgtgt 3360 gggaatagaa gcaaatttta atacaaaaaa cactaatccc tttgtctctt tctgtaggaa 3420 caacaccaca tgatcaacac aataatctta gagacgcaag ttgaatgatc cagccatcaa 3480 aagacatgaa taagacacaa nnnnnnnnnn nnnnnnnnnn nnnnnnngtg ctagaacttg 3540 gatattttga tttgtaagga ttataatgtt gctgaaagta atattactta aagaattttc 3600 tgtcgcattt ttttgcttgg ttgggcttgt tttgttttgc tgttatgaca gctggggttc 3660 tgctatatcg gtccctgttg taattgtttt ctggtgtccg agttttagtt gtgcttcgcc 3720 cgcgctcgtt tttaataaat ttgctgattc tnnnnnnnnt taaagaattt aaagcttgaa 3780 atacataaaa tgatgtgtat gcaattttca ttcgatgaaa tgtataacat agatttgagt 3840 aatattacat tacatggata gtcttaatat tagagacttc tttcatggtc acatagactt 3900 tctaaaga 3908 // ID Copia34-PTR_LTR repbase; DNA; EDCOT; 229 BP. XX AC scaffold_342; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia34-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-229 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-229 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 245-245 (2007). XX DR Genome; scaffold_342; Positions 48967 49195. XX SQ Sequence 229 BP; 72 A; 41 C; 36 G; 80 T; 0 other; tgttaggaaa tgaaatattc ccgtgtatag aatagcagag ttgtataaaa tagaagatat 60 gtatttattc actttccatt gtaatgccta atatgtcgct actgaagcta caatgcagca 120 actgattcct gacttgtagg aatcagttgc agcctccctg tataagtata tgattcagta 180 tcaataacaa tcactctggt aaattcaatc tttctcttca ttcttttca 229 // ID Ogre-PT3_I repbase; DNA; EDCOT; 11092 BP. XX AC AC149300; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 13-APR-2007 (Rel. 12.03, Last updated, Version 2) XX DE Autonomous LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-PT3; Ogre-PT3_I; internal portion. XX NM Ogre-PT3_I. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-11092 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC149300; Positions 95335 106426. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). CC Additional annotations: 6475..6682: putative intron. XX FH Key Location/Qualifiers FT CDS 503..2851 FT /product="Ogre-PT3_ORF1" FT /translation="MLNSSIQVLNQIMTKYLSFQEFGQESELTQVAEGKCP FT RIDASRLPCITKINHMVNDLGKLVSIMEYIDETIFERRYGRIAQLMRLPVQ FT AAAIKALLNFWDPSYRSFTFGNIDMTPTLEEYERILDFPNNSHRIYLRQRF FT EDTASEVVSLLGLGKISQCRVAEGGFKWKVIEARMKKNAEEGKLGEERYRL FT VAFAIFGLVLFPSEIGVISLEAASVFIEYERDQINPSSAILGETMLSLNHC FT RMHGKGAMRCCTPMLYLWIISHIETPRDIFNNFWWFDLRPLKVTMDETWKN FT WDEKAWIDKYAALPRSNFKWKAPWMNNAICTMSCGNKIWVPLIGITGYISY FT APALVTRQLGGMQYAPRTLGLADFIGLFKHQPFLEEMKLIRQDWERPLMVK FT REEGSTFETSFSQNYAVWRNEELSEERGFSIPKHPESVIEQPKRKRTDIEE FT ELRKQLEQCRIDLSKSKGQLRLLENQLEEENTMRVYLNQQLEKQDKQLTSL FT KEWQKRAEVAEEIAKAVQAELRNRITEYDELSNKNGLTQKELAKVKRSTKG FT KMSADKEMVDSLKKGRSILLKKVEVEKEKNRLAHLDIEEERRIRAQYMMQL FT EEERSSRKAAESDMRDYQKRAESSKGRMMALQSEIEIREEKLKEIRSHYFE FT MEEELGKAKQERQECQDYMNNFTVQINSKIAELDLEKEELQRVRDKLARSE FT DMVRVLERSNEALGASNEVIIADNTVFHDKIRHITKQVEQVARYAERLQRQ FT ATQVGNDASKYREYMAAITCFIGDLANRGNAF" FT CDS join(3178..6474,6683..9394) FT /product="Ogre-PT3_ORF2+3" FT /note="gag-pol." FT /translation="MENEERAHLESHYQTELESVKNEVSRLTDLLEQLLRA FT KNGEGTSAQQPEGAPAAHIPQVSQNQGANSANEQHFVPITPIQPTHAPITV FT DLTAEGVPDNRSPSVMDQDKLFALEERLRAVEGNDWFDPIRAAEVCLVPNI FT VVPKDFRIPEFIKYTGLECPNTHLRSYCNKMAEVIRDDKLLIYFFQDSLAG FT SALSWYMRLDSIRIKSWRDLVEAFLKQYKFNMEIAPDRTNLMAMEKRSQES FT VRAYAQRWRDEAMHVQPPLIETEMVSLFANTFKAPYYEHLMGSSSQHFYDA FT VRKAERIEQGIKAGRIAMPVEKKGFIGRKREGDVNNLEGGYKGKRVDFHNP FT QVPTSQFSRINFNQPFSPNRTNNQSNYQNHYQRPHTKYTSEQLPPLPMPLK FT DMYAKLLSIGQIAPIPTLPLQPPFPIWYKPELACEYHGGNLGHGIETCYAF FT KKRLLELIKMGWVSFEDKPNVNSNPLPKHAPNSSGIGMIEVGNQCKVLKVS FT MKRLYDMLVQSRFLKTKVKSHLEGYDYCEYHGRDGHHIEDCIEFCEKIAKM FT LKIGELRIEPIKSSGEVSMMEGQDEMTGVCRVQQTAYGPPRLILVKPSYTK FT GNHNAMPYNYGYATNVRAPLPSFQPEISGLTRSGRCFTPEELRKAKGKEVV FT DLDKALEVNKPVTEDESNEFLKLIKHSEYCIVDQLKKTPARISLMSLILSS FT EPHRNALQKVLNEAYVPQDIEHKTMEHLVGRIHATNYLYFTADELDAEGTG FT HNKPLYITVRCKDCLIGKVLIDNGSALNVLPKHMLEEMPIDESHIKPSTMM FT ARAYDGSPRPIIGTLEVELYVGPQMFLVTLQVMDIHPSYSMLLGRPWIHAA FT GAVASSLHQCLKYIMNGMLVTVKAEETISMTKNVAVPFIEAGDCKGNNIHA FT FEIVNTDWVPENTVLRRPRISEAARMASLCFLNSEIPFQYNLIIGIPEGVN FT LEKMKSAAQRFGLGYQPNQEDYRWAAGWRRARRMARIKGRELEEEKLEIPP FT LSVSFPKAAYIMQHDKEAESLDQELSNMSINTLGENKMEGDDMKTVARKGD FT EALPQLTIYTIEEVSAKTFVRKLAQDEKFQNWVTQEAPVVFKRNPESGSPT FT TSHTFSIKNKWPNLNEHVIAMEEEEWDESNISEFTRLVEQQEQTWKPIAEE FT LETINVGSDQLKKELKIGTLITSEQRIKLITLLQEYSDVFAWSYEDMPGLD FT TNIVVHKIPLEEGCKPVKQKLMRAHPDVWIKVKAELEKQWDAGFLEVVRYP FT QWVSNIVVVPKKEGKIRVCVDFRNLNKASPKDDFPLPHIDVLVDNAARSST FT YSFMDGFSGYNQIKMAPEDKAKTTFVTPWGTFCYKVMPFGLKNAEATYQRA FT MVTLFHDMMHKEIEVYVDDMIAKSKRGEDHVEVLRKLFERLRKYELRLNPA FT KCSFGVKSGKLLGFVVSDRGIEVDPDKVRAIQAMSSPKTEKEVRGFLGRLN FT YIARFIAQLTTTCEPIFRLLRKKNPGTWNEECEEAFNKIKHYLQNPPLLVP FT PVAGKPLVLYLTVTEAAMGCVLGQHDETGRKERAIYYLSKKFTECESRYTE FT IERLCCALMWAAKRLRHYMLYYTTWLISKVDPLRYICNKPFLSSRIARWQV FT LLAEYDIVYMTRKAVKGSAIADHLADNARKALREVHEGICSTHASGRMIAR FT KIQRAGYFWMTLEKDCIDYVKKCHKCQVYSDKVNMPPAPLFNLISPWPFAM FT WGIDVIGSVNPKASNGHRFILVAIDYFTKWVEASSYAHVTQNVVKRFIEKD FT LICRYGPPEKIVTDNAQNFNGKMIAELCTKWKIKHSNSSPYRPKMNGAVEA FT ANKNIKKIIQKMVVTYRDWHEMLSFALHAYRTAVRTSTGTTPYSLVYGMEA FT VMPLEVEIPSLRVLMDSELEEAEWAKVRYEQLNLISEKRIAAICHHQLYQK FT RMAKAYDKKVRPRLFQEGDLVLKKILSLPGDDQSKWAPNYEGPYVVKKAFS FT GGALKLARMDGEDLARPVNSDSVKRYYA" XX SQ Sequence 11092 BP; 3577 A; 2024 C; 2685 G; 2806 T; 0 other; cagaatggcg actccgctgg ggaccttgtg gactaagctt tgtttttgtc tgaattgttt 60 ttgtttttgt gtgtttttaa tatacctttc cttttgttat ctgcttatat gttttaaata 120 ttttttacac atattgttca tgcatttgta tagaactgtc tcatgcatct tatagaactg 180 tcacatgcat cacatacttt gattttgaga agcacacaca agctttaagt taggtggggg 240 attagcgatt tgccctatga ctatcggtca gggttcagat gcgtgaaaca cccaactcat 300 atctgagtgc ctgcttggta atggtgggta tacttacctt aaccgttcct tgcgacgccc 360 ccatactgtc tttacgaaga acgtcactgg gcagatatga gaccctttta aagaccagat 420 agaaaaccta cccattctca cctaataatt agaacttgtc cttaggatat ctatcttatg 480 ttcatttgca tcatgattaa taatgttaaa ttcatcaatc caggttttga accaaatcat 540 gactaagtac ctatctttcc aagagtttgg gcaagaatct gagttgactc aagtagctga 600 aggaaaatgc ccaagaatcg atgctagtag gttgccttgc attactaaga taaatcacat 660 ggtaaatgac ttggggaagt tagtgtctat tatggaatac attgatgaga ctatttttga 720 aaggcgatat gggagaattg cacaactaat gaggttaccc gtacaagcag cagcaatcaa 780 agccctactg aatttttggg atcctagtta tcggagtttt acctttggga acattgatat 840 gacaccgact ttggaggaat atgaaaggat tctagatttt ccaaacaaca gccacaggat 900 ctatttaagg caaagatttg aagacacagc ttcggaggta gtcagtttat taggcttggg 960 aaagatcagt caatgtagag tcgccgaggg gggtttcaaa tggaaggtca tagaagcccg 1020 aatgaagaaa aatgctgaag aaggcaagtt aggagaggaa cgatacaggt tggtggcctt 1080 cgccattttt gggctagtat tgttcccttc cgaaatcgga gtcatcagtt tggaagcagc 1140 aagtgtcttc atagaatacg agcgtgacca gatcaatcct tcatcagcta ttttgggaga 1200 aaccatgtta tcactcaatc actgcagaat gcatggaaaa ggagccatga gatgttgcac 1260 ccctatgttg tatttatgga ttatcagtca tatcgaaaca ccaagggaca tttttaataa 1320 cttttggtgg tttgacctac gaccgttaaa ggttaccatg gatgagactt ggaagaattg 1380 ggatgagaaa gcatggatag ataaatatgc agcattgcca aggagcaact tcaaatggaa 1440 agcaccatgg atgaacaatg ccatctgcac aatgagctgt ggaaataaga tatgggttcc 1500 cttgattggt ataaccgggt acatcagtta cgcgcccgcc ctagtaacaa gacagttggg 1560 tggaatgcag tacgcgccaa gaactctggg tttagctgat ttcattggtt tattcaagca 1620 ccaacccttc ctcgaagaaa tgaagcttat ccgacaagat tgggaaagac ccctgatggt 1680 aaaaagggaa gaagggagca catttgaaac atcattcagc cagaattatg cagtttggag 1740 gaatgaagag ctttctgaag aaaggggttt ctccatacca aaacatccag aatccgtaat 1800 agagcaacca aaaaggaaaa ggactgatat tgaggaagag ctgagaaagc agctagaaca 1860 atgtagaatt gatctcagca agagcaaagg gcagctgcga ctgttagaaa atcaattaga 1920 ggaagaaaac acgatgaggg tttacttgaa ccagcagttg gaaaaacagg ataaacaatt 1980 gacatcttta aaggaatggc agaaaagggc cgaggtagct gaagaaatag caaaagcggt 2040 ccaggctgag ttaaggaatc gaataactga gtatgatgag ctgtctaaca aaaacgggct 2100 cacacaaaaa gagttggcta aggttaagag atctaccaaa ggcaagatga gtgccgataa 2160 agagatggtg gattccttga aaaaaggaag gagcattctt ttaaagaaag tagaagttga 2220 aaaagagaaa aatcgattag cccatctcga catagaagag gaaagaagga tcagagctca 2280 atatatgatg caactggagg aagagagaag ttcaagaaag gctgcagagt ctgatatgag 2340 agattaccag aaaagagccg agtcttcaaa aggaaggatg atggctttac aatcggagat 2400 cgagatacga gaagaaaagt taaaagagat aagaagccat tacttcgaga tggaagagga 2460 gctcggtaag gctaagcaag agcgtcaaga atgtcaagac tacatgaaca actttacagt 2520 ccaaattaac tccaaaatag ccgaactgga tctcgaaaag gaagaactac agagggtaag 2580 ggataagttg gcccggtcgg aggatatggt tcgagtattg gaaagaagta atgaagccct 2640 aggagccagc aacgaagtga taattgcaga taacactgtg ttccatgata agataaggca 2700 tataacgaag caggtcgagc aagtagcccg ttatgcggaa aggttgcaac gacaagctac 2760 ccaagttgga aatgatgctt caaagtatcg ggaatacatg gcagccatca catgttttat 2820 tggggactta gctaataggg gaaacgcctt ttaaagggta acaatgtata acgccctgtt 2880 ttgtaatcat tgtatgaatg acttctattt ataagaaggc catgacctat ctttctttct 2940 aaaaatgtgt tggtaagcta caatgataag aacttggcaa accctccttt acagtaatcg 3000 ggtcaactca gaaatcttgc ctaaaggatt acgaaagtca tgaatcaact ttaaaatata 3060 catttgcacg agcatcatat tttcatcacg catttgtttt taatttatca tatgcatgcc 3120 agatcgtgaa acataggtcc cacatccaaa gtccacaaca cccggtctag agcgagaatg 3180 gagaacgaag agagagctca tttagagtca cattatcaga ccgagttgga gtccgtaaaa 3240 aatgaagttt ctcggttaac tgacttactt gagcagcttc taagagctaa gaatggggag 3300 ggaacatcag cacaacagcc tgaaggagcg ccagcagctc acatccctca ggtatcccaa 3360 aaccaggggg caaactcggc caatgaacaa cattttgtgc ctatcacccc tatccagcca 3420 actcacgctc caatcactgt ggacttaaca gcggagggag tcccggataa taggtctccc 3480 agtgtgatgg accaagacaa gctatttgct ctggaagaaa ggttaagggc agttgagggt 3540 aatgattggt ttgaccccat acgagcagcc gaagtatgtt tggtaccaaa catcgtggta 3600 ccaaaagatt ttcgaatacc agagttcatt aagtataccg gtttggaatg cccaaacact 3660 caccttcgat cctactgcaa caagatggcg gaagtaatcc gtgatgataa attgctaatc 3720 tatttctttc aagatagcct agcaggatcc gctttaagct ggtacatgag gttagacagc 3780 atcaggatca agagctggag agacttggtg gaggctttcc tcaaacagta caagtttaac 3840 atggaaatcg ctcctgatcg aacaaatcta atggcaatgg agaaaaggag ccaggagtca 3900 gtaagggctt atgcgcaaag atggagggat gaagcaatgc atgtccaacc ccctttgata 3960 gaaacggaga tggtgagctt gtttgccaat accttcaagg caccttatta tgagcaccta 4020 atgggtagtt cctctcaaca tttctatgat gcggtacgca aagccgaaag aatagaacaa 4080 gggattaaag ctgggcgaat agcaatgcca gtggaaaaga agggttttat tggcagaaag 4140 agagagggcg atgttaacaa tctggaaggt gggtataagg gcaagagagt agatttccat 4200 aatcctcaag tacctacctc tcaattctca cgcataaact ttaaccaacc tttttcccct 4260 aatcgaacaa ataaccaatc gaactaccaa aatcactacc aaagacctca tacaaaatac 4320 acttcagaac aactgccacc cttacccatg cctttgaagg acatgtacgc caaacttttg 4380 agcattggac aaatagctcc tatccctaca ctaccactac aaccaccatt cccaatttgg 4440 tacaagcccg agttggcttg cgagtaccat gggggtaatc tcgggcatgg gattgaaacc 4500 tgttacgcct tcaagaagag gttgttagag cttattaaga tgggatgggt atcctttgag 4560 gacaagccca atgttaattc aaacccattg cctaagcatg ccccaaatag tagtggaata 4620 ggcatgatcg aagtgggaaa tcaatgtaag gtgttgaagg tgtccatgaa gaggttgtac 4680 gacatgttgg tacaatcaag atttctaaag acaaaggtga agagccattt ggagggatat 4740 gattactgtg aataccatgg aagagatgga catcatattg aggattgcat cgagttttgc 4800 gaaaagattg caaaaatgct aaaaataggg gagttgagga ttgaacccat aaagagcagc 4860 ggtgaggtga gtatgatgga aggacaagat gaaatgacag gagtatgcag ggtccagcaa 4920 acagcttatg ggcccccaag gctaatcttg gttaaaccgt cctacacaaa agggaatcac 4980 aatgccatgc catataatta tggttatgcc actaacgttc gagctcctct tccttcgttc 5040 cagcctgaga taagtggttt gaccaggagt ggtcgttgct ttacgcccga ggagttgagg 5100 aaggcaaagg gcaaagaagt ggtagatctg gacaaagcac tagaagttaa taagccagta 5160 acggaagatg agtcgaatga attcttgaag ttgatcaagc atagcgaata ttgcatagtg 5220 gatcaactaa agaagactcc agctaggatc tcccttatgt ccttgatact cagctctgag 5280 ccgcatcgaa acgccttgca aaaggtattg aatgaggcat atgtgcccca agacattgaa 5340 cataaaacca tggagcatct agtgggaagg atccatgcaa ctaattacct gtacttcacg 5400 gctgatgagc ttgatgctga aggtaccgga cataacaagc ccttatacat tacggttagg 5460 tgcaaggact gcctcatagg aaaagtactc attgataatg gctcggccct taacgtgttg 5520 ccaaagcaca tgctagaaga aatgccgatc gatgaatccc atattaagcc aagtactatg 5580 atggccagag cgtatgatgg atcgcctagg ccaataattg ggactttaga agtggagcta 5640 tacgtgggac cacaaatgtt cctagtaaca cttcaggtta tggatatcca cccttcctat 5700 agtatgttgt taggaagacc ttggattcat gcagcggggg cagtagcttc gtcattgcac 5760 caatgcttga agtatatcat gaatgggatg ttggtaactg tcaaggccga ggagacaata 5820 tccatgacaa agaatgtagc tgtgcctttt atcgaagcgg gtgattgcaa aggtaacaat 5880 atccatgcct ttgagattgt gaacaccgac tgggtgccag agaacacagt gctaagaagg 5940 cccaggatct cagaagcagc aaggatggca agtctatgct tcttgaacag cgagatccca 6000 tttcagtata accttattat cgggatacca gaaggggtta atctggaaaa gatgaaaagt 6060 gctgctcaaa gatttgggct agggtaccaa cctaaccaag aggattatcg gtgggctgct 6120 ggttggagaa gggcaagaag gatggctaga atcaaaggaa gagagctaga ggaagaaaaa 6180 ctagaaatcc ctccccttag cgtgtcattc ccaaaagctg catacataat gcaacatgat 6240 aaagaggccg aaagccttga tcaagaactg tcaaacatga gcataaatac cttgggggaa 6300 aacaagatgg aaggagatga catgaagaca gtagcaagaa agggagatga agcactccca 6360 caactgacga tctacaccat agaagaagta tccgccaaga cctttgtgcg caagttagct 6420 caagacgaga agtttcagaa ctgggtgacc caagaagctc cagtggtttt caaaatgtaa 6480 accaattttg tttgtcttaa catgcttttg tcattgctta tgtttgcttt tatttcctct 6540 agttgacaat caaggctcat gatgtcagct agattttatg cttttcatga agcccacctt 6600 ttctttaaat aaattgtgag atcatgcact tttcacaaat tgctttcttt ttatgcattt 6660 acaccaaaca cttcccgctt tcaggaatcc tgaaagcgga tctcccacaa catcacatac 6720 atttagcatc aagaataaat ggccaaactt gaacgagcat gtgatagcta tggaagaaga 6780 agagtgggat gaaagcaata tcagtgaatt caccaggcta gtagaacaac aggaacagac 6840 ttggaagcct atcgccgagg aactcgaaac catcaatgtg ggcagtgatc agcttaagaa 6900 agagttgaaa ataggtaccc taattacttc tgaacaaagg ataaaattga tcaccctatt 6960 acaagaatat tcagatgtct ttgcttggtc ctatgaagat atgcctggtt tggatacaaa 7020 tattgtggta cataagatac cgttggaaga aggttgtaag ccagtcaagc agaagctgat 7080 gagggcccac ccggatgttt ggatcaaggt caaggcagaa ctcgagaagc aatgggatgc 7140 tggttttcta gaagtagtta gatatccaca atgggtgtct aacattgttg tggtgcctaa 7200 gaaggagggg aagattagag tgtgcgtgga ttttcggaat ttgaataagg ctagtcccaa 7260 ggatgatttt ccgctaccac acatagatgt tttggtggac aacgctgccc ggagttccac 7320 atattccttt atggatggtt tttcaggata caaccagata aaaatggctc cggaggataa 7380 ggcgaaaaca acttttgtca caccttgggg gacgttctgc tacaaggtca tgccatttgg 7440 attgaagaat gccgaagcaa cctatcaaag agcaatggtg actttgttcc acgacatgat 7500 gcacaaggaa attgaggtgt atgtagacga catgattgcc aagtctaaaa ggggagagga 7560 tcatgttgaa gttttgagga agttgtttga gagattgagg aagtatgaat taaggctcaa 7620 tcctgcaaaa tgttcattcg gagttaaatc gggtaagctg ttaggatttg tggtaagtga 7680 tagaggtata gaggtggatc cagataaagt aagggccatc caagctatgt catcccctaa 7740 gacggagaaa gaagtaagag gattcttggg aaggttaaac tacattgctc ggttcatagc 7800 tcagttaaca acgacgtgtg aacctatatt ccgactacta aggaaaaaga atcctggaac 7860 ctggaatgag gagtgtgagg aggcattcaa taaaatcaag cattatttac aaaatccacc 7920 tttactggtt cctccggtag caggaaaacc tctagtatta tatctaacag taactgaagc 7980 agccatggga tgtgtattgg gtcagcatga tgaaaccgga aggaaggaaa gagctattta 8040 ttacttaagt aagaaattca ctgaatgtga gtctagatac acggaaatag aaaggctttg 8100 ttgtgcgttg atgtgggcgg caaagaggtt gcgacattat atgttatact ataccacttg 8160 gttgatttca aaggtggatc ctctgaggta catttgtaac aagccctttc tctcaagtcg 8220 aattgcaagg tggcaagttc tattagcaga atatgacata gtatacatga caaggaaagc 8280 cgtaaaagga agtgcaatcg cggaccatct ggccgataat gctagaaagg cattacggga 8340 ggtccatgag gggatttgct caacccatgc tagcgggcgt atgatagcaa ggaaaatcca 8400 gagggctggt tatttttgga tgacactaga gaaagactgt atcgactatg tcaagaaatg 8460 tcataaatgt caagtttaca gtgacaaggt caatatgcca ccagctcctc tatttaatct 8520 aatatcccct tggccatttg caatgtgggg aattgacgtg atcgggtctg ttaacccaaa 8580 agctagcaat ggtcatagat tcatcctcgt agctattgac tatttcacaa aatgggtaga 8640 agctagttca tatgcccacg taacacagaa cgtagtgaag aggtttatag agaaggactt 8700 gatttgtcga tatggtcctc ctgaaaagat agtgacagat aatgcacaga atttcaatgg 8760 caaaatgata gcggagctgt gtactaaatg gaaaatcaag cattcgaatt cttcaccata 8820 ccgaccaaag atgaatggcg cagtagaagc cgccaataag aacatcaaga agattattca 8880 gaaaatggta gtcacatata gagattggca tgagatgttg tcattcgcac ttcacgcata 8940 ccgcactgca gtcaggacct cgacagggac taccccatat tctttggtat acggtatgga 9000 ggcagtgatg ccgttggaag tggaaatccc atcgttaaga gtattaatgg attccgaact 9060 agaagaggct gagtgggcca aagtgagata tgagcaactg aacttgatca gcgaaaagag 9120 gatagctgca atatgtcatc accaacttta ccagaaacga atggccaagg catatgataa 9180 gaaggttaga ccgcggttgt ttcaagaagg ggatctagta ttgaagaaaa tattgtcgtt 9240 acctggagac gatcaaagca aatgggcacc gaattacgag ggtccttacg tagtaaagaa 9300 ggcattctca ggaggagcgc tgaagttggc tagaatggat ggagaagacc tagctcgacc 9360 tgtgaattct gactctgtaa aaagatatta tgcttgatgt aggctcctaa atcaataaag 9420 caaagtttgg ccattgactt ctttctcttt tgcattgatc tcacaacaat catttttttt 9480 tttttagggt ttagggttta gggtttaggg tttagggttt agggtttagg gtttaatccc 9540 aacagtgtgt cttgttatcg cacctaaaaa gtttagcatt ggctgaatga atttcttttt 9600 tatacaaaag cccagtttaa aatcacatcc ctacactggg ggcaataaga gatgttttca 9660 tgaaaagttt tacgaaagcc tatagatttg aaaaccaagc taaaagcatt tgacaaaagc 9720 atgacaaaga ggcaatgata agtcatacat tttgggaaaa ggactacttg aagaaagtca 9780 gagacttctt cttcaaggat atgataggag gcaacacgag agatgaatcc aaagcaagct 9840 tatgttaaga gggagtctca tgaactagaa gaagaggatg gggcctatgt ttcaaaacca 9900 ggtacgaatg catgcatggc atctaatcat gaatcattgc acatatgttt ttttggatcg 9960 ttacaggagg agaccttgat gcattccaac aagattggag acgaagaaag aatcatagag 10020 gatgatagca aagaatcacg gttttgaacc atagtgaatt ctggaacaac gagaagaaca 10080 agaaaaagag agaatgaaaa gttttgaacc ctgccatcag gaagaacgac atcaatatca 10140 gctttggtaa taaggaatca ccagatagga ttccaagttg tttgagatcg ccagaaggga 10200 tctcgtattt tgatattggt caaaggaggt cgccagacgg gacctcgtat ttcagctttt 10260 aataaaagga atcgccagat gggattccaa gttgacggag atcgccaaaa ggggtctcgt 10320 atttcgctat gtggaggtcg ccagatggga cctcatattt catgtttgtt aaaaggaatc 10380 gccagatggg attccaagtt gattaaaaga gatcgccaga agggatctcg tgtctcgcta 10440 tttagaggtc gtcagatggg acctcgtatt acctgttgaa caaaaggaat cgccagatgg 10500 gattccaagt tgaataaagg agatcgccag aagggatctc gtgtttcgct atttggaggt 10560 cgccagatgg gacctcgtat tacctgttga ataaaaggaa tcgccaaatg agattccaag 10620 ttgattaaaa gagatcgcca gaagggatct cgggtttcgc tatttagagg tcgccagatg 10680 ggaccttatg tttcatgttt gttaaaagga atcgccagat gggattccaa cttaagggag 10740 atcgccagaa gggatctcgt atttcgctat gtggaggtcg ccagatggga cctcatattt 10800 catttgaata aaaggaatcg ccagatggga ttccaagttg attaaaggag atcgccagaa 10860 gggatctcgt gtttagctat taggaggtcg ccagatggga cctcatattt catgttggtt 10920 gaaaggaatc gccagatggg atttcaagtt gaggaggatt gctgtaaaag acaagtttca 10980 gatcaatcaa gcttcaacca gatcagtttc gggagttccg ttttgggttt atctttataa 11040 aacttactgc gcaaaacctc tgctccgtaa gcattataaa gagggggcat ct 11092 // ID Copia-48_VV-I repbase; DNA; EDCOT; 4041 BP. XX AC chr19; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-48_VV_; KW Copia-48_VV-LTR; Copia-48_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4041 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr19; Positions 4829803 4825763. XX CC 'ATAAC' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 61..1035 FT /product="Copia-48_VV-I_1p" FT /translation="MDGNVGHMVSFNGTNWVTWKTKMEDLLFCKDLNGPIE FT GDSGKPEGMKDDEWKKLNRKAVGFIRQWIDDSVFHHVSTENSVHGLWTKLE FT SLYDRKTAVNKAFLFRKLVNSKYKEGTPIAEHLNEIKSIVNQLAAMKITFD FT DELQALLLLSSLTESWETLVVTVSNSTPDGVVTMSQVTSSLLNKETRRKSS FT GSSHSEALVIENRGRGRSKSKASHNRDKSRGRSSSISKKDVECYYCHKKGH FT MKRECRKLKFKEQNKEKNSEKKQNDTTVVTDGELMIIRDDVSVNLIGQETD FT WVIDSGASFHVTSRADFFTSYSQGDFWECPYGK" FT CDS 965..2617 FT /product="Copia-48_VV-I_2p" FT /translation="MLLRGLISLLLTRKVIFGNVRMGNEDVSKIVGMGDIC FT LETNTGCKLLLRDVRHVPDIRLNLISAGKLDDEGYNNNFSDGKWKLSKGSL FT VVAKGKKTCSLYIVQAKICKCVVSTLENDSSTDLWHRRLGHMSEKGLQVLS FT KKELLAGIKGTPLKTCVHCFHGKQNRISFRRNIASRKSHVLDLIHSDVCGP FT LKVMTLGGALYFVTFIDDHSRKVWAYTLKTKDQVLDVFKHFQAKVERETGR FT QLKCVRSDNGGEYIGPFDQYCTNHGIRHEKTVKKTPQQNGVVERMNRTILE FT RVRCLLSHSKLPRSFWGEAMRTAVDLINLSPSVPLNGDVPEKVWTGKEVSY FT DHLRVFGCRAFVHIPKDERSKLDPKAKQCIFIGYGHEEFGYRLYDPVDKKV FT VRSRDVVFLEDQAIEDIDKLESAESSTNDLVDLDPLNPPVVHDIDEEVQTP FT HDDAAEDDVEPEIEGEQSPQEPLSQTPLRRSTREKQPSKKYSSNEYVMISD FT QGEPETYQEVLKHENKTEWLKAMKEEMKSLHENHTYDLVKPPKGKKILKNK FT WVFR" FT CDS 2843..4021 FT /product="Copia-48_VV-I_3p" FT /translation="MEQLEGFIDKGNDQLVCKLKKSLYGLKQAPRQWYRKF FT DSFMTEHGYSRTTSDHCVFVKKYPDGNFIILLLYVDDMLIVGQDMSKISKL FT KSELSKSFAMKDLGPAKQILGIRIVRDRSHGLIWLSQENYVKKVLERFNMD FT KAKPVNCPLAGHFKLSSSQCPTSDEEKNEMQKIPYASAIGSLMYAMVCTRP FT DIAHAVGVVSRFMSNPGKEHWAAVKWILRYLQGTSKMSLCFGKGEPILDGF FT TDSDMAGDVDSRKSTSGYSITFAGGTVTWQSRLQKCVALSTTEAEFIAITE FT ACKELLWLKKFLQELGLKQERYVLHCDSQSAIHLSKNSSFHSRSKHIDVRY FT HWIRDVLNDKLLQLEKVHTDDNTSDMLTKALTKDKHEKCRLLAGMVESST" XX SQ Sequence 4041 BP; 1250 A; 621 C; 1001 G; 1169 T; 0 other; tctggtatca gagctgttgg ttaattcgat tccgattcgt tatatttgtg tgtgtgaatt 60 atggacggca atgttgggca tatggttagt ttcaatggca caaattgggt gacttggaaa 120 actaaaatgg aagacctttt gttttgtaaa gatttgaatg gacccataga gggtgatagt 180 ggcaaaccgg aagggatgaa agatgacgag tggaaaaagc taaaccgaaa agctgtcggt 240 tttattcggc aatggattga tgatagtgtc tttcatcatg tctctacaga aaattcagta 300 catggtcttt ggaccaaatt ggagagtctt tatgatagaa agacggccgt gaataaagct 360 tttttatttc gaaagcttgt gaattctaaa tataaggagg gtactcctat tgcagagcat 420 ttgaatgaga ttaagagcat tgtgaatcag ttggccgcca tgaaaattac ttttgatgat 480 gagttgcaag ctttgttact tcttagttca cttactgaaa gctgggaaac tttggtggtc 540 acagttagta actccacacc tgatggagtg gtaacaatga gtcaagttac tagcagcctg 600 ttgaataaag agacaagaag aaaatcatca ggttcttctc actccgaggc acttgtgata 660 gaaaatcgag ggagaggcag gagtaagagt aaggcttcac acaaccgtga taaatctaga 720 ggtcgttcaa gctcgatttc aaagaaagat gttgagtgct attattgtca caagaaaggg 780 cacatgaagc gggagtgcag aaaactcaag ttcaaggagc agaacaaaga gaaaaattca 840 gagaaaaagc aaaatgatac aactgtagtt accgatggtg aactcatgat tattcgtgat 900 gatgttagcg ttaatttgat tggccaagag acggattggg taattgattc tggagcttca 960 tttcatgtta cttcgcgggc tgatttcttt acttcttact cgcaaggtga tttttgggaa 1020 tgtccgtatg ggaaatgaag atgtgtcaaa aattgtcggc atgggtgaca tttgcttgga 1080 aacaaatact ggatgcaaat tgttgcttag agatgtgagg catgtaccgg atattcggct 1140 caatttaatc tctgctggaa agttagatga tgagggctac aacaacaatt tcagtgatgg 1200 aaaatggaag ctctctaaag gttctctagt ggtagcaaaa ggaaagaaga cttgttctct 1260 ttacattgtg caagcaaaaa tctgcaagtg tgttgtgagt accttagaga atgactcatc 1320 caccgattta tggcatagaa ggcttggaca tatgagtgag aaaggattgc aagttttatc 1380 taagaaagag cttctagcgg ggataaaagg tacgcctttg aaaacatgtg ttcattgttt 1440 ccatggtaaa caaaatagaa tatcattccg tagaaacatt gcatctagaa aatctcatgt 1500 tctagatttg atacattctg atgtatgtgg tcctttgaaa gttatgacac ttggtggtgc 1560 tctatacttt gtcactttta ttgatgatca ctctagaaaa gtttgggctt atacactgaa 1620 aactaaagat caagttctag atgtgtttaa gcattttcag gctaaggttg aaagagaaac 1680 tggtagacag ttgaaatgtg tccgctcgga taatggtggt gaatatattg gaccatttga 1740 tcagtattgc actaatcatg gcatcaggca cgaaaagaca gtaaaaaaga cacctcaaca 1800 gaacggggtt gtagagagaa tgaatcgcac cattcttgag agagtcagat gtttgctctc 1860 acattctaaa ttgccaagat ctttttgggg tgaggcaatg aggacagcag ttgatcttat 1920 caatttgtct ccttcagttc cgttgaatgg tgatgtgcca gagaaagttt ggacagggaa 1980 ggaagtctcc tatgatcact tgagggtatt cggctgtaga gcttttgttc atattccaaa 2040 agatgagagg tccaagcttg atccaaaagc aaagcagtgc atatttattg gctatgggca 2100 tgaagaattt ggctacaggt tgtatgatcc agttgataag aaagttgtca gaagccgaga 2160 tgttgttttc ttggaagacc aggctattga agacattgac aagcttgagt cagctgagtc 2220 tagtactaat gatcttgttg atttagatcc tcttaatcca cctgttgttc atgatattga 2280 tgaggaagtg cagacacctc atgatgatgc agcggaagat gatgttgagc cagagattga 2340 gggggaacag tcaccccaag agccactatc acagacaccg ttgaggagat ctaccagaga 2400 aaaacaacca tccaaaaaat attcttcaaa tgagtatgtg atgatatcag atcaggggga 2460 gccagagact tatcaagaag tcttgaagca tgagaacaaa actgaatggc tcaaggcaat 2520 gaaagaggaa atgaagtctt tgcatgagaa tcacacctat gatttagtga agccgcctaa 2580 agggaagaaa attttgaaaa ataaatgggt cttcagatga aagaatgatg ggaacaattc 2640 tcaaccgaga ttcaaggcac gacttgttgt gaaaggtttt gatcagagga agggagttga 2700 ttttgatgag atcttctcac cagttgtgaa gatgtcctcc attcgaactg tgcttggtat 2760 agctgcgagt atgaatttag aagttgagca gcttgatgtg aagaccgcat ttttgcatgg 2820 tgacttatga gaggaaattt atatggagca acttgagggc ttcatagata agggtaatga 2880 tcagttagtt tgcaaattga agaagagttt gtatggattg aagcaagcac cgaggcagtg 2940 gtacagaaaa ttcgattctt tcatgactga gcatgggtat tcaagaacca cttcagacca 3000 ttgtgtgttt gtgaagaaat atccagatgg taattttatt attctcttgc tttacgttga 3060 tgatatgctt attgtgggcc aagacatgag caagattagc aagttgaagt cagagttgag 3120 caagtccttt gccatgaagg atttgggtcc agcaaagcaa attcttggga taagaattgt 3180 tcgcgacaga tcacatgggc tgatttggtt atctcaagag aattatgtta aaaaggttct 3240 tgagaggttc aatatggaca aagcaaagcc tgttaattgt ccacttgcag gccacttcaa 3300 acttagctca agtcaatgtc ctacaagtga tgaagagaaa aatgagatgc agaaaattcc 3360 ctatgcttca gcaattggtt ctttgatgta tgccatggtt tgtactcgac cggatattgc 3420 tcacgcagtt ggggttgtta gtcgatttat gtctaatccg gggaaagaac actgggcagc 3480 agtgaaatgg attctgaggt atcttcaggg cacttcaaag atgagtttgt gttttggtaa 3540 aggcgagcct attcttgatg ggttcacaga ttctgatatg gctggtgatg ttgatagtcg 3600 aaaatctact tctggttatt cgattacttt tgcaggggga acagtgacat ggcaatcaag 3660 attacagaaa tgtgttgctc tctccaccac agaagctgag ttcatcgcca ttacagaagc 3720 ctgcaaagaa ttattgtggt tgaagaaatt cttacaagag ttgggtttga aacaagaaag 3780 gtatgtcctt cattgtgata gtcaaagtgc aatccacttg agtaagaatt cttcatttca 3840 ttcgaggtcg aaacacattg atgttagata tcattggatt cgtgatgtct tgaatgataa 3900 gttgttgcaa cttgaaaaag ttcacactga tgataacact tcggatatgt tgactaaggc 3960 attgactaag gacaagcatg agaagtgtcg actattggcg ggaatggtcg aatcctccac 4020 ataagtcggg agggggagaa t 4041 // ID Gypsy-13_Mad-I repbase; DNA; EDCOT; 11057 BP. XX AC . XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-13_Mad-I; KW Gypsy-13_Mad-LTR; Gypsy-13_Mad_. XX NM Gypsy-13_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-11057 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1336-1336 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [7103-7585] - Integrase core. CC LTRs are 97% similar to each other. CC The original sequence included a fragment of RTE non-LTR CC retrotransposon which was removed. Therefore the new sequence is CC artificial and labeled as "consensus". XX FH Key Location/Qualifiers FT CDS 673..1779 FT /product="Gypsy-13_Mad-I_1p" FT /translation="MASRKAQTVPAIGAKNKSVLVASGVTLGITTRSKTRA FT TSAASFTSASTLPREQEHPRHEPVITLASLRALRGESPRKYSESMLSDADS FT SGSSAMQVMTTGATSIDEQLAQMNEAIARLTRTVEEKDLQIAALVNRLEAQ FT DGEKPNPEDDPLKGGAGGEEEPPMKKIDVKSEPDQAAALMGSLSIQQLQEM FT ITNTIKAQYEGSSHASTLYSNPYSRKIDALRMPRGYQPPKFMQFDGKGNPK FT QHVAHYVETCNNAGTEGDYLAKQFVRSLKGNVFEWYTDLEHESINNWEQLE FT KEFLNRFYSTRRTVSMLELTSTKQWKEEPVMDYINRWRNLSLDCKDRLSEI FT SSIEMCIQGMQWGLQYILQGIKPRTF" FT CDS 3182..4945 FT /product="Gypsy-13_Mad-I_2p" FT /translation="MGMIRVDMTIGELKSSTIFHVIDARTSYDLLLGRPWI FT HANGVVPSTLLQCLKFYRKEVKVIYGDTKPFTEAESHFADAKFYMDEDMVP FT ETLLKEIKSIGKATPKKQEWQAVPKKQEEEVMPSLSKNDDELAKPATTRGS FT RMPSNGPNIPVFRYIPTSRRKNGQSPFETAASKTDAQRHMDNVKFLKTNAV FT LPLTQLGDTKVARPSQGFIKGLPKGVEPSFLPTKRTEEGCDPNAYKLMSKA FT GYNFTFSANLGNKDSNTVKDNKRDLTKTQKKLEKHGYGVNNNKARLGFTPN FT APVKISSKAKNASAQHISVSIIQDKDEPQPAPQTLVFDRINRSRPRVSAPK FT LINGQNRTSVFKRLNTSASRSSIFKRLSKSKKQSNITNFPPRQSVMERLEE FT AKEPSRRRKTTLEVEKIDRLAEKDDVRSSIPSRMKRQAILEVNTVGSLKVK FT RRTIIHTGQSSCQQAREVNIEEKAQDVFYITIQEGEEDEILEEDVIAAPSQ FT LEDEGQATVDDLKELNLSTSEKPNPIFMSALLSADKIEKYYQLLLEYKNVF FT AWTYKEMPGLDPIIVVHHLVVKPGTRPIKQTQRRYQSELIP" FT CDS 6914..7963 FT /product="Gypsy-13_Mad-I_4p" FT /translation="MEEAHSGICGAHQSGPKLHFQLKRMGYYWPSMVNDCL FT EHAKMCQACQFHANFIHQPPEPLHPTATSWPFDAWGLDVVGPIAPKSSAGE FT AYILAAKDYFSKWAKAIPLKEVKKETVVRFIKEHIIHRYGVPRYIITDNGK FT QFSNRLVDKLCEKYKLKQHKSSMYHAPANGLAEAFNKTLCNLLKKVIGRTK FT KDWHERIGEALWAYRMTYRTPTQATPYSLVYGVEAVLPLESQIPSLRIAIQ FT ESLTDEENAKLRLQELEALDEKRLEAQQHLECYQARLSKAFNKKVLPRSFQ FT MGDLVLSLRRPIITTHKTKSKFTSKWDGPYVIQEVYTNGAYLIMAEDGLKI FT GPINGIF" XX SQ Sequence 11057 BP; 3652 A; 2765 C; 2237 G; 2398 T; 5 other; tcgttcttcc aagatcaagc cccgacggcc cttgaagaaa gtgttcatcg ttcatcttcc 60 attcatccca aagaatcaag aaagccttcg tcgttcttcg ttcattgttc ttccaagatc 120 aagcctcgac ggcccttgaa tcaacaatca tccaccttca agatcaagcc ccgacgaccc 180 ctttgaataa cttccaccaa ttcaagatca agccctaaag gcccttgaag aacttccacc 240 aattcaagat caaaccccaa aagcccttga agatccgttc atcaccgtta ttcaagatca 300 agtctcaatg gcccttaaag aaacgctcat cctcaagatc aagccccaac ggctccttaa 360 agatccactc aaatccactt tcaagatcaa gcccacgacc cttgaagaac gttcttccaa 420 gatcaagccc cgacgaccct tggatcaatc gcacatccaa aatcaacacc ttacggagat 480 tgaatcagag gatcaagata gagagattgt aacccaaaat catcaaatac aaatattact 540 ttgtgcacgt tgttcttgtc tctttcgttt tcaggaaaat ttcgtgttca caaatttggc 600 acgcccagtg ggactatctt tacctctcat ctctttctcc gttcaagaaa tttaagcaca 660 cttccaaaat taatggcatc aaggaaggct caaactgttc ccgcaatcgg cgcaaagaac 720 aagagcgtcc tcgtcgcaag tggtgtcact ttgggcatca cgactcgaag caaaacaaga 780 gctacttctg ccgcttcttt cacctctgca tcaactctgc caagggaaca agagcaccca 840 aggcacgagc ctgtgatcac cttagcctca ttaagagcac taagggggga aagcccaagg 900 aaatactctg aatccatgct ctccgatgcc gattcaagcg gcagttcagc catgcaagtc 960 atgaccactg gagcaacttc aattgatgag cagctggctc aaatgaatga agcaatcgca 1020 aggctaaccc gaactgtgga agaaaaagac ttgcaaattg cagcactagt caaccgattg 1080 gaggcgcagg atggcgagaa acccaaccca gaggatgatc cactaaaggg aggagctggc 1140 ggagaagagg agcctccgat gaagaaaatt gatgtgaagt cagaaccaga ccaagcagca 1200 gcactcatgg gatctctttc tatccagcag ctgcaagaga tgatcaccaa caccatcaag 1260 gcacagtacg aagggagctc tcatgcctcc acgttgtact cgaatcctta ctccaggaag 1320 atcgacgcct taaggatgcc gaggggctat caaccgccaa agtttatgca atttgacgga 1380 aagggaaacc cgaagcaaca tgtcgcacat tacgtcgaaa cctgcaacaa tgcagggacg 1440 gagggagatt acctcgccaa gcagtttgtg cgctcgttaa aaggaaacgt ctttgagtgg 1500 tacacagacc tggagcacga gtccatcaac aactgggaac agttggaaaa ggaattcctc 1560 aaccgcttct acagtacccg ccgcactgta agcatgctag agctgacgag cacaaagcaa 1620 tggaaggaag aaccagtcat ggactacatc aaccgatggc gtaatctaag ccttgactgt 1680 aaggacagac tctccgagat ttcttcaatc gagatgtgca tccaaggcat gcaatggggt 1740 ttacaataca tccttcaagg tatcaaacca cgaacttttt gaagaattag ccagccgtgc 1800 ccacgacatg gagctgagca tcgcccacca tggaaagaat aagctaatca ccgatttcaa 1860 aagggataaa gtgtttactt caagagcaga caatcatggg aaaaaacccg ccaatgaagc 1920 ttttaccacc aataccaccc ctatcaagac ctcgtccgca cccattaaaa tctccttcaa 1980 taacaaagca aaggagataa aaagaagtga gccttcccac acccaagata ggtacaaaaa 2040 cactttgagg gaactggagc agaaggtata cccttttccg aactccgaca tggacgtaat 2100 gctggacgac ctgctgaaga agaaggtgat tgagttgccc gaatgcaaac gccctgaaga 2160 gatgaatcgc atcaatgatc ccaagtattg caagtaccat tgcatcgtgg gtcatcatgt 2220 gggcaaatgt ttcatcctaa aagaactcat catgaagtag gcacaacaag ggcggattaa 2280 gctcgactta gaagacacag ttgcaacgca caccactatg gtcgtgttcg gatcctttga 2340 tctcgtgcct cttcaagaaa tgtctgacca tgctcggcaa tactcaaacc acactgcacc 2400 ttctgcacca ccgtcattag gggcaagcaa ccaagatgca cctactgacg atgacaaatg 2460 atggacatta gcgacctata agaggacgag gaaaccgaga ccgcaaacta taaagccaaa 2520 gggggaacaa gggagaaagc accgccgccg cagcagtagg aagcctaaaa gaaacataag 2580 agctgctaag ccaatatatg ttggggaact tgcggagcaa aagccacgca ttcccgtctc 2640 cttgcatgag tacttcccgg aggacttctt ccaacattac actatcgttg catgtcatat 2700 ggtcgaagta gaaatggaag aaccctcaaa aggcaaagtt gtcgccactg agggagaaaa 2760 aactcttaca cctgaagaag gtctgccaac acactttagc gtcgaggaag cgctacaatt 2820 gccaaagaag atacgaaggg cactggcagc tgttttagca agtctaaaca accacgaagt 2880 gcaagaaagc aagaacgaag gcttgaggct tcggccacac gagtgtgcca catgttatgc 2940 tgccgaggac ataatccact tcatcgatga agacttgctg ctaggatcca agcctcacaa 3000 ccgtcctctt ttcgtctctg ggtacgtaaa ggagcacaaa gtcgaccaca tacttgtgga 3060 tggcggatca gccataaata tcatgccaaa gtcaacaatg accacaatcg gcatcaaggt 3120 ggatgaacta tccctaagtc gtctactaat ccaaggtttt aaccaatgag gacaaagagc 3180 gatgggcatg atccgagtag atatgaccat tggtgaactt aagtcaagca caatatttca 3240 cgtgattgat gcaagaactt cctacgattt gctcttagga aggccttgga tccatgcgaa 3300 tggagtagta ccgtccaccc ttctccaatg cttaaaattt taccgaaaag aagtgaaggt 3360 gatctatggc gacactaaac cattcaccga agccgaatca catttcgcag acgccaagtt 3420 ctacatggat gaagacatgg tgcccgaaac tcttctaaaa gagatcaaat ccataggcaa 3480 agcaacacct aaaaagcagg agtggcaagc cgtgcccaag aagcaagaag aagaagttat 3540 gccatcttta agcaaaaatg acgatgagct tgctaaacct gcaacaacca gagggagtag 3600 gatgccttca aatggaccaa acatacccgt ttttcgatac atcccgacgt cgagaagaaa 3660 gaatggtcaa tccccatttg aaactgcagc aagcaaaact gatgcacagc ggcacatgga 3720 taatgtaaag tttctcaaaa cgaatgcagt tttgcctctg acacagctag gcgacactaa 3780 ggttgcaaga ccatcacaag gcttcataaa aggcctgcca aaaggggtag aaccaagctt 3840 tctcccaacc aagagaaccg aagaaggttg tgatccaaat gcctacaaac tcatgtcgaa 3900 agctgggtac aacttcacct tctctgcaaa tttgggaaat aaggattcga acaccgtcaa 3960 agacaacaaa cgtgatctca ctaaaactca gaagaagttg gagaagcatg gttacggggt 4020 taacaacaac aaagcgagac ttggcttcac accaaatgca ccggtgaaga tctccagcaa 4080 ggcaaaaaat gctagcgctc aacacatcag cgtgagtatt atacaagata aagatgagcc 4140 tcaacctgcc ccccagacat tagtatttga tagaataaat cgttcaaggc ccagagtttc 4200 ggcacctaaa ctcattaacg gtcaaaacag aacttccgtc ttcaaaaggc ttaacacgtc 4260 agcatctcga agctctattt tcaaaaggtt gtcgaaatct aagaagcaaa gcaatataac 4320 taacttccct ccacgacagt cagttatgga aagacttgaa gaagccaaag agccttctag 4380 aaggagaaag acgacactag aagtagaaaa gatcgatcgt ctggcagaaa aggatgacgt 4440 tcgaagttcc attccttcaa gaatgaagcg ccaagcaatt ttggaggtta acacagttgg 4500 atcactaaaa gtaaaaaggc gcaccatcat ccacactgga caatcttcat gccaacaagc 4560 tcgagaggtc aacatcgaag aaaaggccca agacgtcttc tacatcacaa tccaagaagg 4620 tgaagaagat gaaatcctcg aggaagatgt cattgcagca ccgtcacaac tcgaagatga 4680 ggggcaagcc acagttgacg atctcaaaga actcaactta agcacaagtg agaaaccgaa 4740 tcctatcttc atgagtgcat tactaagtgc agacaagata gagaagtatt accagctgtt 4800 attagagtac aagaacgtct ttgcttggac ctacaaggaa atgcccggcc tcgaccctat 4860 cattgttgtg catcatcttg tagtcaagcc tggaacgcga ccaataaagc aaactcaaag 4920 acgctatcaa tccgagctca tcccataaat tgaggccgag attgacaagt tgatcgaagc 4980 agacttcatt cgagaggtgc aataccccaa gtggatctcc aacatcgtca tagtccttaa 5040 gaaatctgga taaatacgtg tttgcgtaga cttccaaaac ctcaatgatg cttgcgcaaa 5100 ggataacttc cccttgccaa tcattgaaat catggtggac gcgaccactg gccatgaggc 5160 actatcattc atggacggct cttctggata caatcaaatt cgtatggctc ttgaagatga 5220 tgaactaaca gccttccgca ctccaaaagg tatctactgc tacaaggtga tgccttttgg 5280 tctgaagaat gctcgagcta catatcaacg agcaatgcag aagatcttca ataacatgct 5340 acacaagaac gtagaatgct atgtagacga tgtggtggtc aagacaaaga aaatatcaaa 5400 tcacttgaag gatttgcgag tagtgttcga aaggttgcga aaatacaacc tcaagatgaa 5460 cccgttaaag tgtgcatttg gcgtcacatc tggaaagttc atcggcttca ttgtcaagca 5520 tcgtggcatt gaagtggatc aatcaaagat caaggccatt caaagcatgc ccgagccaag 5580 aaacctgcac gagttgaaaa gtctacaagg acgactagcc ttcatcagac gcttcatctc 5640 caaccttgta gggcattgtc aaccgttcag tcaactcatg aagaaagatg ttccgttcgt 5700 atgggacaac gcatgcaaca atgcttttga aagcataaag aagtatttat caagtccacc 5760 tatcctgggg gcacctatac tagggaaacc actcatatta tacattgctg ctcaggaaag 5820 ttcagttgga gcactcttgg cacaggaaaa cgaatcccaa aaagaaaaag cgatctacta 5880 cctcagtcga atgctcaccg gtgctgagtt gaactattcc ccaatagaaa aaatgtgcct 5940 tgccttaatg tttgccatct agaagctcag acattacatg catgcttaca ccatccattt 6000 ggttgctaaa gctgacccgg tcaaatacgt catgtccaag ccagttttga cagggcaact 6060 agctaaatgg gcattgcttc tcaatcaata cgagatcatc tacgtcccag ctaaagccgt 6120 caagggaaaa gcgctagcaa acttcctcac cgaccatcca atctcagccg attggaaaat 6180 ctcaaacgac ttgcctaacg aggaggtgtt ctacatcgac atattcccga catgaatgat 6240 gttcttcgac ggatctgcac gagcagacta agcgggggca ggagtagtat tcatgtcgcc 6300 acaaaggcaa atactacctt attcattcca actaagcgaa ttatgctcca acaacgtcgc 6360 tgagtaccaa gtactgatca tcgggctcca aatggcaatc aacatggaaa tcccagccct 6420 tgagatatat ggcgactcca aactcataat caatcaactc ctgactgaat atgaggtaag 6480 gaaagatgat ctcatcccat acttccggct ggcaacgcaa ttgctacgaa ggtttgaagc 6540 cttaacacta gaacacgtgc caagaaaaga gaatcaaatg gcagacgctc tcaccaacgt 6600 agctttgagc atgacattag aagaagatga agctgcaaac gtaccaatct gccaaagatg 6660 ggtaatcccg cttgttactg aaatggtact aagcgataca aacgttattt caatacttcc 6720 ggtcaacgtt gaagaatgga aacagccttt gatcagctac ttggagcatg gaatactcct 6780 agattatcta aaacaccgct ctgaagtacg tcgacgagca catcgcttcc tctattacaa 6840 agagacactc taccggcgat cttttgaatg agtacttctg agatgcctag gcgaggaaga 6900 agccaatcaa gccatggaag aagcacactc aggaatatgt ggggcgcatc agtccggacc 6960 gaagcttcat ttccagctca aaagaatggg ttactactgg ccaagcatgg taaatgactg 7020 cctagaacac gccaaaatgt gccaagcctg ccaatttcac gccaacttca tacatcaacc 7080 gcctgaacca ttacacccca cagctacttc atggccattc gatgcatggg gattggacgt 7140 cgtaggacca attgcgccaa agtcatctgc aggagaagct tacatcctgg ctgcaaaaga 7200 ttacttttcc aagtgggcta aagccatacc cctgaaggaa gtcaagaagg aaactgtcgt 7260 ccgtttcatc aaggaacata tcatccaccg atatggtgtg cctcgctaca ttatcactga 7320 caacggaaaa cagttctcca accgactcgt ggacaagctc tgcgagaaat acaagttgaa 7380 gcagcacaaa tcctccatgt atcatgctcc ggctaatggt ctcgcagaag cattcaacaa 7440 gacattgtgc aacctcttga agaaggtaat cggcagaaca aagaaagact ggcatgaaag 7500 aataggcgaa gcactttggg catacaggat gacatataga acacctaccc aagctacacc 7560 ttattctctc gtatatggcg tagaagctgt tctaccactc gaaagtcaga tcccctcact 7620 aaggatagct atacaagaaa gcttgactga cgaagaaaat gcaaagttgc gccttcaaga 7680 gctagaagcg ctggatgaga aaagactcga agcccagcaa catttggagt gttatcaagc 7740 acgactctcc aaggccttca acaagaaagt tctccctcgt tcttttcaaa tgggagatct 7800 cgtcctttca ttgcgtaggc ctatcatcac aactcacaag acaaagagca agttcacgtc 7860 aaagtgggat ggaccatacg taatacaaga agtctacacc aatggcgcct acttaatcat 7920 ggcagaagac ggcttgaaga tcggccctat caatggcata ttctagaagc gttactaccc 7980 ctaaaaggcg acaaactcct gctctttgtt cgtacgagcc taaactgcat gaaccaaagc 8040 tcctggccca caagagcata aactgtgtac ggcaaaatca tcatcaaaat cattgttaaa 8100 ttcatcgctc atttgaacta cgtcatgact tgatccctcc tcaaccgagg gtacgtaggc 8160 aacttgaaac ttcaaaactt caagtacagt tacatcacca acaaaaaaaa aacacaaaca 8220 ctttgaagaa taaaaagcaa gttcagaata tgaatacttt atttctttaa aaggaatgat 8280 ttggttacaa agccgtatta caaaggtgag catcacacca acgtcaccac cgacgaaatt 8340 tgtgaccaaa agacactaca tagcataaac tctgcagtct ttgacacaac ctcacacagt 8400 aaaaagtgac acactggaac aagctccaag cagcaacggc aaagagccca cgacaagcac 8460 caaggtcaat gtgcacacta acgccaccac caaggaaagt tgtgaccaaa aaacactaca 8520 cagcataaac ttgctgcagt ctttgacaca acctcacacg gtaaaagtga cacactggaa 8580 caagctccaa gtagtatgac gacaaacagt gcaataagga cagtgggcag cgcaatgatg 8640 cgcagcgaat aatgcaacga cagtggtgca gcaagcatgg taaaaaggca gctacaagac 8700 ggtccttcaa agcacactac agtaataaag aaaccaaaat gctacgcaac cccgcagtgg 8760 ttacgcaagc agtttcttgc actgcacaac gacgtcacca ccaatgggag aactgtgacc 8820 aaaaggcatt acatagcgaa gccccgctgc agtctcttgc acagcaccac acgacagtgc 8880 accaccaagg gaaaactgtg atcaaaaggc actatacagc gaaaccccgc tgcagtctct 8940 ggcacaagca ctaggcagct tgctcactct gccaccaact accacatctc tggaagcttc 9000 gtgaggtcct ggcaccatgc tctgtcttct caaaattaaa gattcctaac atttacaaaa 9060 aammaccaaa aaaaaaaaaa aaargraatc aaggttagca ggtggaactc aaggcccgag 9120 acataaactc ttatacatta ggctttggcg atggcctcca ttccaccact tcaatcctca 9180 aagtttaaga aaagcagaaa cccaaatcca ggccctggcc cagctctcaa agcccaatcc 9240 aggttttctc ctccagccat gccttcgact tgcagctcac cacacgccac gggatagccc 9300 aatgccatca tcgattccac tcccatagca gcacttcgcc aaattcctca ccgacatcat 9360 catccccagc ttgatcagag ctcacagtac aattggagta gccacagccg tttctctctt 9420 ttcccccaca aactcttcaa agtctctacc tttctctccc cccgtcactc tcgtcgtaat 9480 ccgtcaatct caagcccttc ttccttggac ctgtatcatc tttcaaacct acaaaagaac 9540 ccatcaagcg tcatggactc caaagcaaca ccaggcccaa gcctgagtca agaccaacac 9600 caggcccata gccgccatgc cagagaaagc ttttgcaaat gggtgtgcag agagattcaa 9660 agctcgacct cgaccacctt cgaggcttca ccgctgacaa acaccaccca agcctacctg 9720 ctgctcatcc accgcagcga ctatcgagca cgcgagctct atgctccgct ccaccaactc 9780 ctcgacgccg tcatccactc tgactctgtg gagttgtcac tgagcctcaa cctctccctg 9840 cgactccaaa ctgctcctct ccgtcaccaa ttccccagcc gaagtctatg gctatttggc 9900 ggatgcggga tacaaggtcc gctgcctctc tacccatctt ccaccgtagc acctggcctc 9960 cctcgagctc gtcacgtttc tcaccatgtt cctcatctcc gcgcctggcc ttctcagctc 10020 catgttctcc gtcgagttcc atccctgcaa agcaccatat ataaaagaaa aataataata 10080 aaaaaaaaga atggtggaac ttggtgcatc cgcactaaaa aaaaaagaga tattatatat 10140 atatatatat atatatatat atatatatat atatatatat atatgccaga agaataaaga 10200 aggaatggtg gagtctttgg tgctctagca ccatgtgaaa aaaatggaat cttgattcat 10260 catggcacca tgtgtaagta ccaccgaaag caaagaagaa aatataataa aaaaaatttt 10320 gtggtatgtg tgagtaccac caaaggcaaa aagaaaaaaa aaaagttaca aaagtttctg 10380 gaggtgcgca tgtgcaccat tctgaaagaa gaaaaaaaat atatatatat aataaaaaaa 10440 tgtttgatct ttggtgcgtc tcgcaccatg attaaaggca araaaaaaaa aagtttggtc 10500 tttgatgcgt ctggcaccat gtggaaaaat gggtgcacca tgattaaaga aaaaaaaaat 10560 atatatatat atatatgatt aaaaaaaaat aatttgggcg cttcctgcac gatagaatat 10620 atacatataa aattatatat atgtatatag gaaagatgaa tgggtggcat tttaaaaaaa 10680 aaaaaaattt acgctttaaa tacaatttga ggaatccaga aagtcctcca acccagttca 10740 agatcaaagc tgtggaaagt taacaagcgc aaaaacaaat acgtgccgat tcatccacta 10800 ccaaagccaa agatcatcta ccacatgaag ctctttgtgg tccaatttca accttcaaga 10860 tcaagcctcg acgtccattg aagaaatttc aaacaaagtt caagaacaag cctcaacggc 10920 ccttgaagaa aatttcagcc caattcaaga tcaagcccca acggcccttg gatcgacatc 10980 tacattaagg gatttcaaaa cgcatctcct acacgtgaca agcacatgta tacgacacgc 11040 cttgaagtgg gggcatt 11057 // ID RT_VM repbase; DNA; EDCOT; 228 BP. XX AC . XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Vicia melanops Ty1/copia-type retrotransposon RT_VM, reverse DE transcriptase gene - a consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; RT_VM; KW retrotransposon; Ty1/COPIA superfamily; reverse transcriptase. XX OS Vicia melanops OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Vicia. XX RN [1] RA Pearce R.S., Harrison G., Li D., Heslop-Harrison J., Kumar A. RA and Flavell J.A.; RT "The Ty1-copia group retrotransposons in Vicia species: copy RT number, sequence heterogeneity and chromosomal localization."; RL Mol. Gen. Genet 250(3), 305-315 (1996). XX RN [2] RP 1-228 RA Jurka J. and Drazkiewicz A.; RT "RT_VM: a y1/copia-type retrotransposon, RT gene from Vicia RT melanops."; RL Direct Submission to Repbase Update (18-SEP-2002). XX DR [2] (Consensus) XX SQ Sequence 228 BP; 78 A; 45 C; 42 G; 63 T; 0 other; ggtgaactgg aggaagaaat ctacatgaat caacctgaag gttttcaagt tcaaaaaccg 60 aatcatgtat gtaaactaaa aaagtctcta tatggtctga aacaagcacc caggcagtgg 120 tacaagaagt taactgcatt actcattgct caagggtaca gtcagtcaag ctcagattat 180 tctcttttta ctatatgcac taacactgac tttacagcca ttctagtg 228 // ID MARINER_MT repbase; DNA; EDCOT; 3921 BP. XX AC . XX DT 30-JUL-2005 (Rel. 10.07, Created) DT 30-JUL-2005 (Rel. 10.07, Last updated, Version 1) XX DE Mariner DNA transposon from Medicago truncatula - a consensus. XX KW Mariner/Tc1; DNA transposon; Transposable Element; MARINER_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3921 RA Jurka J.; RT "A new mariner sequence from Medicago truncatula - a consensus."; RL Repbase Reports 5(7), 182-182 (2005). XX DR [1] (Consensus) XX CC There are several copies in the available sequence data CC ~90% identical to each other. XX FH Key Location/Qualifiers FT CDS 1047..2537 FT /product="MARINER_MT_1p" FT /translation="MYKRVDAVFFGRLKRDIQNFVANCDHNVLILKHCFFL FT TVLYFFFLYLITIRTSFFNHAEAIIVEEIQQSNNKRSFLDNNQRKLVSHLL FT LNSSYNGKLCRGIVRTLASYFSVSQDVIYRIWRQVKKTGDPCHKKSKNCGR FT KRIQIDFDKMRNASLAKRSTLRSLQTVLGLKTKTTLLKYIKEGVLRRHSNV FT LKPYLNDNNLKARIEFCLDMLEESSIPHDPVFKPMYNVVHIDEKWFYITKK FT SSNYYLLADEDEPHRMCRNKNYIGKVMFLVVVARPRFDDDGNETFSGKIGC FT FPIVHKVPAQRSSINRPAGTLETKPITSINREVTRKMYIDEVLPAIKEKWP FT REYAHETIYIQQDNAPCHVPLDDEEFCRAACDGGFDIRLTFQPPNSPDLNV FT LDLGFFSAIQSLQQQEVTNSVDALIEAVQKSFDAFSAQSSNNIFLTLQSCM FT IEIMKVKGSNNYKIPHMEKEMLLRRGMLPTQLKCDPELFQETFEYLYNVEE FT M" XX SQ Sequence 3921 BP; 1285 A; 650 C; 691 G; 1294 T; 1 other; caccctccgg tcatatatat aagcaaaaaa aacagctttc acggtgatta agaaatgcag 60 ttaagtgtag ttgattttct aaattttgtg taaaacataa gttaaattga ctatattgcc 120 cttttcttaa aattaataca ccaacatgat tgtacaactg cattagagaa atttatcatt 180 ayaccttctg gtttcccacc tcacgtgaaa atatgcaagg cattggaaac atcaattcaa 240 ttatatcaag gcatttcagc ttcttaacac caaatatttg gtgtgccgcc aaaattttca 300 tttgaatgaa tgaaactaca attttcattc catgtcaaat ttcaaaagtt tttttgggat 360 gattcatttt ccttatcatg ttcctataaa tagctatgaa catttacact atcaccatct 420 atgagtgttc ttcaatatgg cttttgatat tgacttgaac gaaccttata atgatgccga 480 cggaatcgcc gatgaaaaca gagatgtgtt acccatcgac ttaaatgtgc agccttacga 540 tgaagattac attttcgact tgaacgttgt cccgtcactt gaagatgatt gtgtaaatga 600 tgctgaaaat gtcactggtg gaaatgaagc tgatgatata tttagaggta aattagttag 660 tttcattgaa gctgaggaat ctataatgta gtataatcaa atgagttttc tttttcttac 720 tttatttttt ataacttttt gtttcaggga cccaagatga tacaaatggt gaagatgaag 780 acatgggtga cttatttagt gaagaagatg aagatatggg ttatacatta aatgaaggtg 840 agacaattaa ttcaaactat tacacaccat tgtttgagat attatcattg cttgctatat 900 tatcattgct gggtgtatgt aattttattg gaatttttca ttaattaaag atattatcaa 960 gcatcatttt cttaataaat atggttaatt tcttaaaact agcatgtaga aagaaacctt 1020 aaacggctgt taattcgaaa cagagtatgt ataagagagt tgatgcagta ttttttggga 1080 ggctgaagag agatatacaa aattttgttg caaactgtga ccacaatgtt ttaattttaa 1140 aacattgttt ttttcttacg gttctgtatt ttttcttctt gtatttaata acaataagaa 1200 cttctttttt taatcatgca gaggcaatta tcgttgagga aattcaacaa tctaataaca 1260 aacgttcttt tctcgacaac aatcaacgga aacttgtttc tcatttattg ttaaattcaa 1320 gttataatgg aaaactttgt cgtgggattg tcagaacatt ggcatcttat ttttcagtct 1380 ctcaagatgt catttatcgg atttggaggc aagtaaaaaa aacgggtgat ccgtgtcata 1440 agaaatcaaa aaattgtggt cgaaaaagga tccaaataga tttcgacaaa atgcgcaatg 1500 cttcattagc taagcgtagc actcttcgat ctttacaaac tgtcttgggg cttaaaacca 1560 agacaacttt gctgaagtac ataaaagaag gggtcttacg ccgacattcg aatgtgctca 1620 aaccatattt gaatgataat aatttgaaag ctcgtattga attctgcttg gatatgcttg 1680 aggagagtag cataccacat gatccagtgt ttaagcctat gtataatgtt gttcacattg 1740 atgaaaaatg gttctatata acgaaaaagt catcaaacta ttaccttctt gcagatgagg 1800 atgagccaca tcgtatgtgt aggaacaaaa attacatcgg taaggtcatg tttttagttg 1860 ttgtggctag gccaagattt gatgatgatg gtaatgagac cttctcagga aaaattggtt 1920 gctttccaat agttcacaag gtaccagcac aaaggtctag catcaataga cctgccggga 1980 cacttgaaac aaaaccaatc acttctataa atagagaagt cactcgaaag atgtatatcg 2040 acgaagtttt accggcaatc aaagaaaaat ggccacgaga atatgcacat gaaacaattt 2100 acattcaaca agataatgca ccttgtcatg tgcctctaga tgatgaagag ttttgtagag 2160 cggcttgcga tgggggattc gacattcgtt tgacttttca acctcctaat tctcccgatt 2220 tgaacgtatt ggatttaggc tttttttctg ccattcaatc cttgcagcaa caggaagtaa 2280 ctaattcggt tgatgcactt attgaagctg tgcaaaaatc ttttgatgct ttttccgccc 2340 aaagttcgaa caacattttt ctcacacttc aatcttgtat gattgagata atgaaggtga 2400 aaggatccaa caactacaaa attcctcaca tggagaaaga gatgttgctt aggagaggca 2460 tgttacccac tcaactaaaa tgtgacccag aattatttca agaaactttt gagtacttgt 2520 ataatgttga ggaaatgtga gggcagaaac ttaaactctt aagtacttgt atttcatgat 2580 ttcttttggt gtacttgtat aatgttgagg aaactttttt atttcaagaa atttttcagt 2640 atttttagtg tgcctactga ataattattg tttcttcatt tacataaaga taaaataaca 2700 tggcagcttt agagggaaga taatttattt aaggctacac gtaatgccac acgtaatgcc 2760 actaacataa gaaagtccac ttttttatgt tccatgttag attcacacaa ttcatttcag 2820 tttatcttgc cacacgtagt gcaatgcatg taaacaaatg aacgcagacg tgaaagttga 2880 ggaattataa gtaaaagaaa gaaaataaaa tattataatc gggacaaata caattttata 2940 aagagatgtg tagtttcatt atgaaagaag gattaaccaa agataacagg ttacaaaaaa 3000 aactcattcc agtacccaaa aacatcaact ctttctatgc cacacctagt tcattgaatc 3060 tatgtatatt ttcagcacat cttcaatccc tttcctcaac tcttcattat tcaactcctc 3120 aatctcaagt ccattctcca actcttcatc cttcaactcc tcaatctcat ctccagagtc 3180 cattgtttct actggaactt cattcagatc aaagttttcc atgtttaagt ccagaaaagc 3240 tctctcacat ggttggacaa ttttttgacg cagatttttc actcttccag attgcattac 3300 ctctggaact tcaccacaaa cactcataga agacccatct tcattagggg ctttgttcaa 3360 gtcaaaattg ttcttgtact gccctccaaa tgctacatct tcaaacaccc atgtttgctt 3420 tgttgtgacc tcatcatcac tttttgacat cacttcacct tcaaacaaag tatcttgaat 3480 taggttggta tctccatccc catcaagtga gtcttcaaca acaagaaggg aaatatcttc 3540 cgagttgctg tcaatgccca aatcaaatga gggtacttca tcaaaccaat tttgtgggga 3600 tgccattttt ttttttgagt tgaaaagaag aagatgtatg ggtggtagaa gaccgtaaaa 3660 tgagttttta taattgaaaa gaaaagatgt attgggtata ccaagagtta tgaaaagctg 3720 ttgtgaagaa ttgaaatgaa tgcattatgg aaaattgtaa tgaaatgtat tggtgtacgt 3780 gtattccaat aggtgattga aaaccacaaa agactttaaa ggggtatatt aggaataaca 3840 gtgtaaaaag tggttagttt tgcttatatt tgtgaccaaa gattgatgtt tttttttgct 3900 tatatatgtg accggagggt g 3921 // ID Copia-65_VV-I repbase; DNA; EDCOT; 4460 BP. XX AC chr15; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-65_VV_; KW Copia-65_VV-LTR; Copia-65_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4460 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr15; Positions 15868722 15864263. XX CC Positions [1778-2251] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 27..938 FT /product="Copia-65_VV-I_3p" FT /translation="MEKSQQTLASSSSSHFVPISFNHSTSVKLENHNFLIW FT RKQIFSAIRGHNLQHFVIGVHDPSLKFRSSEDRSQGIVNQDFLDWEQQDQL FT LVSWLLSSMFEGVLSRCINCESAFQIWKTLEVYFASQTRIKISQYKTLLQN FT TKKESLSMNEYLLKIRGFVDLLALVGVNLSVKDHIDAITDGLLSEYDTFFL FT TINSRTEDYSIEEIESLLLAQEARIEKHNKRLLKLLLVILHKIQVTLEEAI FT FLKVEVSLVTISFTLILAEVIFLLEEGMVFKVEVVLTMVVGDPGTLGIIML FT LLMLKNQYAKCA" FT CDS join(1670..2251,2255..3229) FT /product="Copia-65_VV-I_1p" FT /translation="MSLCKLSKFNKILPNFVCKACCLGKIHMLPFPTSISE FT YQEPLQLVYSDLWGPSPVQSSNGYKYYVCFVDAFSRYNWIYLLRNKSNSFQ FT TFQNFKAQAKLQLGFKIKCLQSDWRGEFCAFTDYLTINGIIHRIYCPHTYQ FT QNGVAERKHRHIVENGLTLLARASMPFKYWDESFKTVVFLHNRLPSPVSHG FT KSPLLLFNHVPDYKALRFFGCACYPNTRPYNSHKLAFRSVQCTFLGYSLTH FT KGYKCLNPSDKIFISRDVIFYEHLFPFSESLSSQPQHSSISQPLSFRQSPP FT ILYSKQHVSSISTASLPFPIALIPPINTTTHLENCQDPNAPIVSSSILSTV FT GNIHSMITRSKKGIFKPKVYSVTKEPQSADEALQNENWKIAMIDEYSTLLR FT HNTWSLVDLLAGRKVIGCKWIFRVKENPDASINKYKARLVAKGFHQTAGFD FT YTETFSPIVKPTTIRVVLTIALSRNWKIQQLDINNAFLNGDLQEEVYMEQP FT KGFIEKSTSHLVCKLHKSLYGLK" XX SQ Sequence 4460 BP; 1380 A; 872 C; 759 G; 1449 T; 0 other; tggtatcaga gctctcaact tcagcaatgg agaaatctca acaaacccta gcttcttctt 60 cctctagtca ttttgtccct atttcattca atcattctac ctcagttaag ctggaaaatc 120 ataattttct gatatggaga aaacagattt tctcagcaat tcgtggtcac aatcttcagc 180 actttgtcat tggagttcat gatccatcgt taaaatttcg aagttcagaa gatcgatctc 240 aaggaatagt gaatcaagat tttcttgatt gggaacaaca agatcagctc ttagtttctt 300 ggcttctttc atcaatgttt gaaggagttc tttcgaggtg cataaattgt gaatctgctt 360 ttcaaatttg gaagacattg gaggtatatt ttgcttctca aacacgtatt aaaatctcac 420 aatataaaac cttgcttcag aacaccaaaa aggaatctct gagtatgaac gaatatttgc 480 ttaaaattcg tggttttgtt gatctacttg ctcttgttgg tgtgaatctc tccgtgaaag 540 atcacattga tgctatcaca gatggattgc ttagtgaata tgacacattc tttctcacaa 600 ttaattctcg aactgaggat tattcaatag aggaaattga gtctctttta ttagcacaag 660 aagctaggat tgagaaacac aacaagaggc tactgaaact gcttctagta atattacaca 720 agatccaggt aactttggaa gaggcaattt ttctcaaggt agaggtttca ctagtaacaa 780 tcagtttcac cctaattttg gcagaggtaa tttttctcct agaggaaggg atggttttca 840 aggtagaggt ggttttaaca atggtggttg gagatcctgg aacacttgga ataataatgc 900 tactgctaat gctgaaaaac cagtatgcca agtgtgcatg aagattggtc attctgcaga 960 taggtgttac tatagatatg atcctagttt tcagggtcct catacccctg gtttcactcc 1020 tagttttcaa aagtcacctc aaacacaaat tcaaggtggc aacaagccta acatgcaagt 1080 cttgatggct acaccggaaa acatttgtga tactaattgg tatccagact caggtgcctc 1140 aaaccatgtg actacaaatg ccaataatct ggttgaacac acaccatact atggcaatga 1200 gcaagttcgt gttggcaatg gtatgggaat ctctattaaa catattggtc tttcatagtt 1260 ttcctctcct ttcacttctc agcttttgtc tttaaatcat cttcttcatg ttcctgaaat 1320 cacaaagaac ttgttgagtg tatctaaatt tgctagagac aacaatgtat tctttgaatt 1380 ccatcctaat ttttgtcttg tcaaagatca agtttccaaa attgtggttc tggagggcaa 1440 acttaaaggt ggcttgtatg catttgattc atcacaaatt cagcttaaaa aatctgctcc 1500 atctcaagtt tctctttcac aaagtgtcac ttcccatcaa tctggtctta gagcaaactg 1560 tcaagtgtct atacatgttt cagatctcca atctcagaat ggtagctcta cagttggtat 1620 ttggcatgac agacttggtc atccatcttt caagattgta caaactgtta tgagtctttg 1680 taaactttcc aaattcaata aaattctacc taattttgtg tgtaaagctt gttgtcttgg 1740 caaaatacat atgctcccat ttcctacttc tatatctgaa tatcaagaac ctctacaact 1800 agtgtactca gacttatggg gaccatcacc tgttcaatca tccaatggct ataagtacta 1860 tgtctgtttt gtggatgcct tttctaggta taattggatc tacctcttaa gaaacaaatc 1920 taattcattt caaacctttc agaatttcaa ggctcaagct aaattacaat tagggttcaa 1980 aattaaatgc ctacaatctg attggagggg tgaattttgt gcttttactg attaccttac 2040 tataaatggc attattcata ggatttattg tcctcacact taccaacaaa acggtgtagc 2100 tgaaaggaag catagacata ttgttgagaa tggtcttacc ttacttgcta gagcctcaat 2160 gcctttcaaa tattgggatg aatcattcaa aacagttgta ttcttgcata ataggttgcc 2220 ctctccagtt tcacatggta agtctccctt atagcttctt tttaatcatg ttcctgatta 2280 caaggctctt agattctttg gttgtgcttg ctatcccaac actagaccat ataatagcca 2340 taaacttgcc tttcggtctg tacaatgtac atttctaggt tatagcctca ctcataaagg 2400 ctacaagtgt ttaaacccct ccgataaaat tttcatatcc agagatgtca ttttttatga 2460 acatctattt ccattttcag aatctctttc ctctcaacct caacattctt ccatttctca 2520 acctctctca tttcgtcaat caccaccaat tctttattct aaacaacatg tctcttctat 2580 ttctacagcc tcattaccct ttcccattgc tctcattcct cctatcaaca caaccactca 2640 cttggaaaat tgtcaagacc ctaatgctcc cattgtatca tcatctatcc taagtactgt 2700 tggaaatata cactctatga tcactagatc taagaagggc atatttaaac caaaagtata 2760 cagtgttacc aaagaacctc aatctgctga tgaagccttg caaaatgaga actggaaaat 2820 agccatgata gatgaatatt ctactctctt gagacacaat acgtggtctt tggttgacct 2880 tctagctggt agaaaagtaa taggatgcaa gtggattttc agagttaaag aaaatccaga 2940 tgcttctatt aacaaatata aagctagact cgttgcaaag gggtttcacc aaacagctgg 3000 atttgattat acagaaacat ttagccctat tgtgaagcct actacaatca gggtggttct 3060 cactatagca ttatcaagga attggaaaat tcaacaactt gatatcaata atgcattttt 3120 gaatggagat ctacaagaag aagtttatat ggaacaacct aaaggcttta ttgaaaagtc 3180 cacttctcat ttagtatgca agctccacaa atctctatat ggactcaaat aggcaccacg 3240 tgcctggttt gagaaactct acgaagcact tgtagatctt ggttttacat ctgctaaatt 3300 tgatcggtct ttattcacaa ggttcactat ggatcacact acctttctcc tagtatatgt 3360 tgatgatata ctggttaccg gcagcaatcc ttgtgtaatt caacaattaa tctcacaatt 3420 aaacaagagt ttttctctta aagatcttgg tgagatagac tatttcttgg gcatacaagt 3480 gaaacatacc actgaaggtc tacacttgtc tcatactaag tatgtgcatg atctcttatg 3540 caaagccaaa atgaacaatg caaatggcat gaagactccc atgatcagtg gtcaacaact 3600 tacacgtctg gaagtgatac tgtgaaagac attcaactct ctaggagtgt tgtaagtgca 3660 cttcaatatc tcactatcac caggccagaa atttcctttt gtgtcaatcg agtttgtcaa 3720 tatttgaagg atccacaaga agaacactgg caagtagtaa aaatgatact taaatacttg 3780 aaaaacacta tttaatatgg acttcaatat gtcactatca ccaggcaaga aatttccttt 3840 tgtgtcaatc aagtttgtca atatttgaag gatccacaag aagaacattg gcaagtagca 3900 aaaaggatac ttagatgctt gaaaaacact attcaatatg gacttcattt gacctgttca 3960 agtactttaa atttggtggg attttgtgat gctgattggg catcaagtct agatgataga 4020 agatctacat ccggttattg tgtctatctt gaaaacaatc tagtttcttg gtgctcaaag 4080 aaataacata ttgtctctag atcatctaca gaggcagaat acagaagctt aactggaata 4140 actgttgaga tcacatggtt aactacccta ctaagtgaat tgaggatcat attaccaaga 4200 actccagcag tatgttgtga taatctgagc acaatattgt tacctgcaaa tccaatttta 4260 cacgctagaa ccaagcatat taagcttgat ttgtattttg tgcgtgagaa agttattcaa 4320 aagcttattg atgtgagaca tgttccttca agtgaccaaa caacagatct ttttaccaaa 4380 gctataccta gctccagatt ttctctactt agaagcaaac tcaaagttct tgatttaagt 4440 actctaagtt tgagggggga 4460 // ID Helitron-N2_PTr repbase; DNA; EDCOT; 1675 BP. XX AC . XX DT 15-DEC-2009 (Rel. 15.02, Created) DT 17-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Helitron-type non-autonomous DNA transposon - consensus. XX KW Helitron; DNA transposon; Transposable Element; Nonautonomous; KW Helitron-N2_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1675 RA Kojima K. and Jurka J.; RT "Non-autonomous helitrons from black cottonwood."; RL Repbase Reports 10(2), 230-230 (2010). XX DR [1] (Consensus) XX CC >85% identity to consensus. XX SQ Sequence 1675 BP; 388 A; 258 C; 296 G; 729 T; 4 other; aattaactat aaactaaaag aggagggttt tactgtaccc ctcctcacaa agcactattc 60 attggaatag tgctttgctt tttttttttc tttttgtttt ttttcaatta attttttttt 120 ttttaatttc attttttaat attaattttt tttctattta gttatcacac tctcatgaca 180 cggatcccag gtttgacggg ttaacccggt tgactcagat tttttttttc ttaattagtt 240 tttttctttc aatttcatcc tttaatattg atttgattga gaattaaact tcatgatttg 300 ttttgtttac ttttcattag gttatcctga tctcatgacc cgagaataat gcttaacgga 360 ttaacccgag ttgactcggg ttgttttttg tgtcttttat ttaattgatt tttttcaatt 420 ttatcattca acattgggtc ggttgggaat tgagcttcat aatctatttt gatttgcttt 480 ttatgagaat atcttggtct caagatcaag gtcacgagtt ttggcatttt aaccctggtt 540 aaatcaggtc gtttttttta ttttctttct aagaggttat atcggtctca tgacccgggt 600 cacgagtcct tcaacattgg acttgctttt tattgggttg tcctcgtctc atgacccggg 660 tcgcgggtta acctaattga ctcatttttt ttttttaatt gacttttttt tccaatttca 720 tcaattaata ttgtgtttga ttgagaatta ggcttcatga tttgtttcgg tttgtttttc 780 attaggttat cntggtctca tgacccggta atagtgctta acggttaact cgggttaact 840 tggcttattt tttatgtcat ttttttaatt aagattttta caaatttcat cgttcaacat 900 taggtccgac agggacgatt gagaatcgag ctttataatt tgttttgact ttctctctat 960 ggggttatct cggtctcaag accaaagtcg cggatttgac aggttaaccc gggttaaatc 1020 angtcatttt tttttttttt tctataaggt tatctcggtc tgatgacccg ggtcatgagt 1080 ttggtggatt gactcaggtt gttttttatg ttcttttttt aattgatttt tttttaatct 1140 catccttcaa tattgggctg gttagggatt gaaattcgta atttgtttcg atttgctttt 1200 catggggtta tctcggtctt atgacccggg ttgcaagttt gacatgttaa cccgggtcgt 1260 tttttaggtc nttttttaat tgattttttt ttcaatttca tccttcaata ttgggttgat 1320 tgagaattag gcttnataat ttattttgat ttgctttcta tagggttatc atagtctcat 1380 aacccgggtc gtgaatttga cacgttaacc cgggttgtcc aaggtcaatc caatatgttg 1440 ttattttaat attaagaaaa aatatcatct tgaaattttg tttagtcaaa atttgttttc 1500 acgggttgta tgagttgttt ttggaccagt aaagtcaacc gggttacatc gggtaaaccc 1560 tcacacgatt taattttttt tccgctagaa aaaaaattag caacatttaa atattttttt 1620 tacgttcaag aaaaatttaa cttgacccgc agcgtagcgc gggtcaatca tctag 1675 // ID HAT-N14_Mad repbase; DNA; EDCOT; 886 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-N14_Mad. XX NM HAT-N14_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-886 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1636-1636 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is ~88-bp long. XX SQ Sequence 886 BP; 312 A; 136 C; 173 G; 265 T; 0 other; tagggatggg caaataccca ttggttatgg gtaaccgcgg ttacccgccc atttaaatta 60 aacggttacg gttatgggta accgtttaga taaataaacg gttatgggta taaccgttta 120 cccgcgaaat ttaaatgggc ggttatgggt attaaccacg gttataaacg ggtaaccgtt 180 tacccattta ttttatatat gtaaaactaa cacaaaccat gttctcgatc caataatact 240 tagcacccaa taaattagca aggaattcat cggtcattct ctcaataaca ctactacagg 300 aatgatgatt ctcatcatca aggaattggc caaattaatt taaattcctt gcgggtaacc 360 gtgaaattga cagaaatgct ttgacagaaa tgtcttctaa acaatttttg taacccaata 420 atacttagca aatattatat ttaccttcat tggtaacagt taaaaatatc gtccgtaaac 480 tattatttca attattggaa tggtataagg acttaaaaaa ttaaaatatg gaaatgtatg 540 atgaatgtac ctataacggt gtttaattgt caaaaaaaaa attatgacaa ttttttttta 600 attttcaagt tgttaaaaaa catgtagacg ggtgaaaaaa gggtaatggt aaaaaaaaaa 660 aagataaacg ggttaaaaag gataaatggg taaacgggta ttaaacggtt acggttaaat 720 gggtatgcgg ttatgggtat ggttaaccgt ttataaacgg ttatgggtat gggtataacc 780 gtttaggcaa ttacccaacg ggtaaacggt tatgcgggta tgagcataaa cggttatggg 840 taaattaacc gcggttaccc gcccgcataa ccattgccca tcccta 886 // ID Copia-61_Mad-I repbase; DNA; EDCOT; 4259 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-61_Mad_; KW Copia-61_Mad-LTR; Copia-61_Mad-I. XX NM Copia-61_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4259 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1660-1660 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1599-2105] - Integrase core CC 'AACA' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(129..2018,2022..4166) FT /product="Copia-61_Mad-I_1p" FT /translation="MAGDKDESVKKGSASSSSTSNRHPTTTTRLEVDKFNG FT SNNFGMWQCEVMDVLYQQELDMVLEDKPEDIDDKQWTRINLHACAAIRSFL FT DKELKYPYMKETSAKELWTKLEEKYMTKSAENRLFLKKRLFRFQYRPGISM FT HEHLNDYNKILADLANLDVKIPDEDKALCLLNSLPDDYDHLTTTLLYGKSE FT VKLDEVSAALVNHECRKKELKTHNSQTEAFVARGRTEERKSGKRGKSRSKS FT RGKFPAKDECAFCRQKGHWKKDCPKLKNKEKEKAGSEANIAKSGDDDDFEF FT ALASSYADGHSNEWILDSGCTYHMCPIREWFSNFEELDGGVVLMGNNNACK FT TQGIGKICLKMHDGTVRELSDVRYVPDMKKNLISLGALESKGLKITMEGGV FT LKAVYGALVVMKGTRRNNLYFLQGSTVIGGAAVTEAADADSTDTTRLWHMR FT LGHAGEKALQGLVKQGLLKGAKACKLEFCEHCVLGKQTRVKFGTAIHHTKG FT ILDYVHTDVWGPSKNASWGGSHYFVSFVDDFSRRIWVYTMKRKDEVLKIFL FT KWKKMIETQSGRKIKTLRSDNGGEYKSDPFLKVCQDEGIVRHFTVRETPQQ FT NGVAERMNRTLLEKVRCMLSNAGLGKAFWAEATYASHLINRLPAAANEGKT FT PMEVWSGKPCTDYKFLHIFGCPAYYYVRESKLDPRAKKALFMGFSTGVKGY FT RLWCPDEKKFVVSRDVTFDEAAMVNQNKHEGETEATETMSSSKQVELLKTP FT VVPVRSDVSNTSPTVNSDDEDEDDEEEAPTQEPPQQQDYIATRRSRREIRK FT PARFTDIVAYALPVIEDDIPSAYKEAVMSSECELWKKSMDEEMKSLHKNET FT WKLVQLPKGKKAIGCKWVYAKKMESLGKDNVRFKARLVAKGYAQKEGIDYN FT EVFSPVVKHSSIRILLALVVQFDLELAQLDVKTAFLHGDLEEEIYMSQPEG FT FKVAGKENWVCKLEKSLYGLKQSPRQWYKRFDRFMIGQKYTRSHYDHCVYF FT RKLQDGTFIYLLLYVDDMLIACKSKVEIERLKTQLSNEFEMKDLGEARKIL FT GMEIERDRAKGKISLCQKQYLKKVLQRFRMNENSKPVSTPLASHFKLSASM FT SPKTVEESQYMAQIPYANVVGSLMYAMVCTRPDISQAVSIVSRYMHNPGKG FT HWQAVKWILRYILGTVDVGLLFQQDKVTGQCVVGYVDSDYAGDLDKRRSTT FT GFVFTIAGGPVSWRSILQSTVALSTTEAEYMAVTEAIKEAIWLQGLLDDLG FT VQQDHVDVHCDSQSAIHLAKNQVHHARTKHIDVRFHFVREVIDEGDILLQK FT IGTADNPADMLTKPVSLHKFKHCLDLIGICKIC" XX SQ Sequence 4259 BP; 1267 A; 686 C; 1108 G; 1196 T; 2 other; agtggtacca gagcccagtt ccgtgaatag tgttggcgct acagttccgt gaacagtgaa 60 ctgctacagt atctgtgaac agtattgtac ctgtgaacag tgccgtattt gtgaacagtg 120 ccgagtagat ggctggagat aaagatgaat ctgtaaagaa ggggtcagca tcgtcttcgt 180 ctacatccaa tagacatcca accactacta caaggttaga ggttgataaa ttcaatggct 240 ctaataattt tggtatgtgg caatgtgaag ttatggatgt gttgtatcaa caagagttgg 300 atatggttct ggaagataaa ccagaagata ttgatgacaa gcagtggacg cgaattaatc 360 ttcatgcttg tgctgctatt cgatcgttcc ttgataagga gttgaaatac ccgtatatga 420 aggaaacttc tgctaaggag ttatggacga aattggagga gaagtatatg accaagagcg 480 cagaaaatcg tctcttcttg aagaagcgac tcttccgatt tcagtatcgt ccaggtatct 540 ctatgcacga acacctcaat gattataata aaatacttgc tgatttagca aaccttgatg 600 tgaaaattcc tgacgaggac aaggcactat gtttgttaaa ttcattgcct gatgattatg 660 atcatttgac aactactctg ttgtatggaa aatccgaggt gaaacttgat gaggtgtctg 720 cggcattggt gaatcatgag tgtcgtaaga aggaactgaa gactcacaat tcacaaaccg 780 aggcatttgt tgcaaggggt cgaacagagg aaagaaaatc tgggaagcgg ggaaaatctc 840 gttcaaagtc acgagggaag tttcctgcta aagatgaatg tgctttttgt cgccaaaagg 900 gtcattggaa gaaagactgc cccaaattga agaacaaaga gaaggagaaa gcgggttctg 960 aagcaaatat tgcaaaatct ggagatgatg atgatttcga gtttgctttg gctagttcat 1020 atgctgatgg tcactcmaat gagtggattt tggattcagg ttgcacctat catatgtgtc 1080 ccattcggga atggttttct aatttcgagg agctggatgg tggagttgtt ttgatgggta 1140 ataataatgc ctgcaaaaca caagggatag gcaaaatctg tttgaagatg catgatggaa 1200 cagtcagaga attaagtgat gttcggtatg taccggatat gaagaaaaat ctcatctcac 1260 tgggtgcatt ggaatccaag ggtctcaaga tcaccatgga gggtggagtt cttaaagctg 1320 tgtacggggc actggtggtg atgaaaggta caagacgaaa taacttgtat ttcttgcagg 1380 ggagtacagt tattggtgga gcagctgtca ccgaagctgc tgacgcagat agcacagaca 1440 ccacgaggtt atggcatatg cgtcttgggc atgctggtga aaaagcgttg caaggattgg 1500 tgaagcaagg cttattgaaa ggtgcaaagg catgcaaatt ggaattctgt gagcattgtg 1560 tgttgggtaa gcaaactaga gtaaaatttg gcactgctat tcaccacact aaaggcattc 1620 ttgattatgt tcacactgat gtttggggac cttccaagaa tgcatcttgg ggaggtagcc 1680 attattttgt ctcctttgtt gatgacttct ctagaagaat atgggtgtac accatgaagc 1740 gtaaagatga agtcttgaag atattcctga agtggaaaaa gatgattgaa acgcaaagcg 1800 gtcgaaagat caagactctc agatcagaca atgggggtga atataagtct gatcctttct 1860 tgaaagtttg tcaagatgag ggtattgtga ggcacttcac ggttagggag acaccgcaac 1920 agaatggggt ggcggagcgc atgaaccgta ctttgcttga gaaagttcgg tgtatgttgt 1980 ctaatgctgg attaggcaag gcattttggg ctgaggcamt cacttatgca agccatctca 2040 ttaatcgatt gccagctgct gcgaacgagg gcaaaacgcc catggaggta tggtctggta 2100 aaccttgtac tgattacaag tttttacaca tatttggttg tcctgcttac tattatgtca 2160 gagaaagcaa gttggatcca agagcaaaga aagctctatt tatgggcttt agcactggcg 2220 tgaagggata ccgactctgg tgtccagatg agaagaaatt tgttgtaagc agagatgtga 2280 cttttgatga ggctgctatg gttaatcaga acaagcatga aggtgaaact gaagcgaccg 2340 agaccatgag tagctcaaag caggtggagt tactgaagac tccagttgtt ccagtaaggt 2400 ctgatgtttc aaacactagt cctacagtta attctgatga tgaggacgag gatgatgaag 2460 aggaggcacc tacccaagag cctccacagc aacaagacta tattgcaacc agaagatcga 2520 gaagggaaat ccgaaagcct gctcgattta ctgatattgt ggcatatgca cttcccgtta 2580 ttgaagatga tattccatcc gcctacaaag aagctgtcat gagttcagag tgcgagttgt 2640 ggaagaaatc tatggatgag gagatgaaat ctcttcataa aaatgagact tggaagctgg 2700 ttcagttacc aaaggggaag aaagcaattg gttgtaaatg ggtgtatgcc aaaaagatgg 2760 aatctttggg aaaagacaat gtaagattca aagccagatt ggtagctaaa ggctacgctc 2820 agaaggaagg cattgactac aatgaggtat tttctcctgt agtaaaacat tcttctattc 2880 gtattctgtt ggctttggtt gtgcagtttg accttgagtt ggcccaactt gatgtcaaga 2940 ctgcgttctt acatggtgat ttggaggaag agatttatat gtctcagcca gaaggtttta 3000 aggttgctgg aaaggaaaat tgggtttgca aattggaaaa atcattgtat ggcttgaagc 3060 agtctccaag acaatggtac aagcgatttg atcgatttat gatcgggcaa aagtacacaa 3120 gaagtcacta tgaccattgt gtatactttc gcaaactaca agatggaacc ttcatttatc 3180 tgcttttata tgttgatgat atgcttatag catgtaagag caaagtggag attgaaaggt 3240 tgaagactca actaagtaat gaatttgaga tgaaggactt gggagaagct cggaagatac 3300 taggtatgga aattgaaaga gatagagcga agggcaagat tagtctgtgt cagaagcagt 3360 atttgaagaa ggtactacaa cgtttcagga tgaatgaaaa ttcaaaaccg gttagtacac 3420 ctcttgcctc tcatttcaaa cttagcgctt ctatgtctcc taaaactgtt gaagagagtc 3480 agtacatggc tcaaattcct tatgcaaatg ttgttggtag tttgatgtat gctatggtgt 3540 gtactaggcc tgatatttca caagctgtta gtattgtcag tagatatatg cataatccag 3600 gaaaagggca ttggcaagct gtgaaatgga ttctacggta tattctgggt actgtggatg 3660 ttggtttatt gttccagcag gataaagtta ctggtcaatg tgttgttgga tatgtggatt 3720 ctgattacgc aggtgatttg gacaagcgta ggtccactac tggttttgta ttcactattg 3780 ctggaggtcc agtaagttgg aggtcgattc tgcaatctac agttgctttg tcgactactg 3840 aggcagaata catggctgta acagaagcta taaaggaagc catctggctt caagggttgc 3900 ttgatgactt aggggttcaa caagaccatg tggatgttca ttgcgacagt cagagtgcta 3960 ttcatttagc aaagaatcaa gttcatcatg cacgtacgaa acacattgac gtgaggttcc 4020 attttgttcg tgaggttatt gacgagggag atattcttct tcagaagatt gggaccgctg 4080 acaatcctgc ggatatgtta acaaagccag tttcgttgca caagtttaag cactgcttag 4140 acttgattgg catttgtaaa atttgttgat tgccccatgg gggattggga gacgactatt 4200 aggagttcta cttagagggt ttgagccaag gtggagattg ttgattattg actcaaaca 4259 // ID Copia-57_VV-LTR repbase; DNA; EDCOT; 266 BP. XX AC chr8; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-57_VV_; KW Copia-57_VV-I; Copia-57_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-266 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr8; Positions 16571931 16571666. XX SQ Sequence 266 BP; 97 A; 45 C; 54 G; 70 T; 0 other; tgatagaaga tacctagctg atcaacaaga aagtaactgt ccggggtcag ctgcaacaaa 60 ccgagatcag gtgcaacaaa ctgaggtcag ctgcaacaaa cagaagccgg ttaagaacgt 120 cttgaagaag gaagttagtt agttaggttg ttgtagatat aaatataaga aaacgtcagt 180 gtaaaaatac tcatcatctt ttcttaatag acaatgagaa atattggttt ttcccagttt 240 ctgaaaccca gtttctaaaa ctttca 266 // ID Copia-76_Mad-LTR repbase; DNA; EDCOT; 587 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-76_Mad_; KW Copia-76_Mad-LTR; Copia-76_Mad-I. XX NM Copia-76_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-587 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1691-1691 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 587 BP; 162 A; 105 C; 127 G; 192 T; 1 other; tgagaattaa gctgcatact aagcttaaat caacctgcag atgacaatcc tgcaggttga 60 aagtgaagag aatgaagaat tcgaagagat gaagaacttg ctatttttag aagtagccgt 120 tagttcaaac ttgcaacggc tagtttcatt tcttgtttta gaaaccttac agctgttatt 180 cttatctgtt tgggttgtac tgtgttatcc gatcctcctc caagtggaag gatcgtagcc 240 tccgatggca tgaatggctg gagatgagtc cttgctccct gaaatgtagg atcttagcat 300 ttgaccggtt agaggaatat agtccttgta ttctctgctt ttttcagata tagaaaaata 360 tacagaaaca ttctcttact ctctgtgctc ttccttmtta gattttctgg ttttaaagct 420 tcaatctttg tgtattaatc aacctaaagc atcatgcctg ataccatttc aaacatggta 480 tcagagcact aggtctgatt ccagagaggg gcgtgaaact gtgagagagg ttcttcctga 540 aaaattccca gaaggggata aaggtggttc ctttattggt tggttca 587 // ID hAT-11N_VV repbase; DNA; EDCOT; 3498 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE hAT-11N_VV, a non-autonomous DNA transposon - a consensus DE sequence. XX KW hAT; DNA transposon; Transposable Element; TIR; Hatvine-11; KW hAT-11N_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-3498 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 778-778 (2008). XX DR [1] (Consensus) XX CC hAT-11N_VV (Hatvine-11 in [1]) consensus is a non-autonomous CC element. Its individual copies are >80% identical to the CC consensus sequence. Although the putative protein product CC contains a hAT family dimerization conserved domain, it appears CC to be only partial compared to other hAT-related proteins found CC in Vitis. Additionally, individual copies do not contain an CC intact ORF due to premature stop codons and/or frameshifts. CC hAT-11N_VV contains 20 bp-long TIRs which are flanked by 8 CC bp-long TSDs. XX FH Key Location/Qualifiers FT CDS join(700..2224,2365..2564) FT /product="hAT-11N_VV_Transposase" FT /note="hAT transposase; pfam05699:hAT family FT dimerisation domain." FT /translation="MLKTLTLVLMHVMNLILLKMTRPPPPLVSLPLTLPQP FT NPIGKRPRASRRTSIVWNHFTIINRQNTRGEVENLAECKYCKKKHIVCKAS FT GGTGHLKRHVEQCTKKHGALDPRQSQISQNEIGSSTSSMSPFIYNQQFLRE FT GLARMVASMGLPLTFGEDPRFVHFMQKYVQPAYHRIPRTTSRNDVIKCYKN FT EKQLIIEEFKNHSGIVSVTSDIWTNQSNEPFTCVTTHYTDSNWKLQKKILG FT FRKIFHPHDGPSIYDSLTSVFREYDIQSKIFSITFDNASNNKSVINLFVRT FT IREGPLSEIFHVRCVCHIINLIVQDGLKLISPSLQAIRSTILFLDSSNKLQ FT EFYTLCQSVGLKKRKFRHDIGHHWNSTYLMLKSCVGYHNILSDYVNSKTGE FT IIVTSDDWEKGFAFLKFLKVFYDTTNMCSIVYTPTSCITLRCICNMSDVFQ FT QYREHPLFSEICVQMFFFFVKYWKTIPPLYCLAACMDPRVKVEGVENILNF FT IAICMNQPSEPEVGPSSRCDLSKYLDTDYCSYLSPNEVQNFDIMKWWKSHE FT STFPILSKMTRDLLTPPVSTVASNLLFL" XX SQ Sequence 3498 BP; 1201 A; 567 C; 553 G; 1176 T; 1 other; tagaggtgtc cattgggtcg gcccacccat tttagcccgt ggcctagcat gccaaaagaa 60 caggccaggt cggcatgacc caataatgta gtgacctgac ccggcacgac ctaaaggagc 120 gagttgtgtt gggcctaagg aaacaactcg tcagcccact gtcccaatcc acttggccct 180 tttaaatttc acttttttct ttttactttt tccttttgat tacatgtcaa atgtttgtaa 240 tacctctctc aacaactata taacagctag tttgaggggt aaaaaagtaa atcaatatct 300 atttttattt tttttatgtc aaatgtgtat attacctctc ccaacaatta tataacaact 360 agttttaggg gtaaataagt aaatgactca ccaataattc tctataaata cctttcattt 420 taattatttc tcacaaaatt atctattctc tatctttata ttgtttacaa ttctctctaa 480 tttatctttc cacaattctc taagttgaaa ttccctacaa gtgctaaaga tatctactaa 540 ctctacaagt ggtcatcatt cacaaggttg aggtatttat atttagttat ttcatttatt 600 tattttaatt ctatatattt catttaattg ttctcttcct tttacctttc tttatttttt 660 attttcctct aaaattaaaa atggatcctc atcacctaga tgttgaaaac cttgactttg 720 gtattgatgc atgtaatgaa tttaatcctt ttgaagatga cgagaccccc acctcctcta 780 gtgtccctcc ctctaaccct tccccaaccc aatcccatag gcaaaagacc tagggctagt 840 agacgcacat ctatagtatg gaatcacttc actataataa atagacaaaa tacaagagga 900 gaggtagaaa atctagcaga atgtaaatat tgtaaaaaaa aacatatagt atgcaaagct 960 agtggtggca caggtcacct taaaagacat gtcgaacaat gtaccaaaaa acatggtgca 1020 ttagacccta gacaatccca aataagtcaa aatgaaatag gatctagtac atcttcaatg 1080 tcccccttta tatacaatca acaattccta agagaagggt tagctagaat ggtagctagt 1140 atggggcttc cattgacatt tggagaagat cctagatttg tacatttcat gcaaaagtat 1200 gtccaaccag cctatcatag aattcctagg actacttctc gtaatgatgt aattaaatgt 1260 tacaaaaatg aaaaacaatt aataattgaa gaatttaaaa atcatagtgg tattgtatct 1320 gtgacctcag atatatggac taatcaaagt aatgaacctt ttacatgtgt gacaacacat 1380 tatacagatt caaattggaa attacaaaag aaaatattag gttttcgtaa aatatttcat 1440 cctcatgatg ggccttccat atatgattct ttgacaagtg tttttagaga atatgacata 1500 caaagcaaaa tttttagtat tacctttgat aatgcttcaa ataataaaag tgtcataaat 1560 ttatttgtaa gaacaattag agaaggtcca ctaagtgaaa tatttcatgt gagatgtgtt 1620 tgtcatataa ttaatttaat agtacaagat ggtttaaaat taatatcacc ctcattacag 1680 gctatccggt ctactatact atttcttgat tcatctaaca aattacaaga attttatact 1740 ttatgtcaat cagtaggttt gaagaagaga aaatttcgtc atgatatcgg tcatcattgg 1800 aattctacct acctaatgtt aaaatcttgt gtagggtatc ataacatact atcagattat 1860 gtcaatagta agacaggtga aattatagta acttcggatg attgggagaa aggttttgct 1920 tttttaaaat tcttgaaggt tttttatgat actactaaca tgtgttctat tgtatatact 1980 cctacatctt gtataacact tagatgtatt tgcaacatga gtgatgtgtt tcaacaatat 2040 agggaacatc ccctttttag tgaaatatgt gtacaaatgt tttttttttt tgtgaaatat 2100 tggaagacta ttccaccact ttattgttta gctgcttgta tggatccaag ggttaaggtt 2160 gaaggtgtag aaaatatttt aaatttcata gctatttgta tgaaccaacc atccgaacca 2220 gagggtaaga tatacgaaca attaaacaac ttaatataaa tattatgaga ataaatatgg 2280 taatgtctct tcaagtacta taactccatc tacatttgga aatgatccat tctttataca 2340 attagctaag gggaaagcga caagttggtc cttcaagtag gtgtgatctt tcaaaatatt 2400 tagatactga ttattgttca tacctatccc ctaatgaagt acaaaatttt gatattatga 2460 agtggtggaa atctcatgaa tccacttttc ctatactatc taaaatgaca cgtgatctac 2520 taaccccacc ggtgtctact gtagcatcga atcttctttt tctatagctg caaatataat 2580 aggagacagg aggacaactc ttacaccaaa gatgctagaa gcttttgaca tgtttgaagg 2640 attgggaaga tggacgcatg ggacttcaaa ctttagagga tgaacttaaa agaagccttc 2700 aagaaattgc atctcaatgc agacaatgat gtttcaagag attgatgatg attgaagatg 2760 aaaaaagaag aatgaagatt gaataagaag acaaaagtga atatgataat tgaagaatta 2820 tatgttgttc gtttctttta aatctattaa atgtagctaa tttttaaagg ttgagtaatg 2880 catatgattg atarttgggt gggtgctaac ctagttggga tgtacttaaa ctatagtgat 2940 gcaattctga catttttttt tctccttatt ttttcatgta atttgttgaa atattgaata 3000 aaagaattat ttttttatat ttcatttcct tttatattcc attattttaa atttattgtt 3060 attttgataa aaaaaattca aatatatata ttttttacta tttttaaaag caaaaaacta 3120 atatttttat aaattttaca attacaaact cgataaatat aaatataaaa aaaaagtata 3180 attattagag gtgtttaaag taacaaaaaa aaaaatttaa taatgaaaaa aaacttaaga 3240 ccaaatgact taaaaaaatg aaattaaaaa ttttaacaaa gtgagtggtc catgggccac 3300 acgacacgac ctccgacaca gaacaacatg attagccctc gagcttatgg gtcgtgttga 3360 gtcacctatt tggcttgcat gggctggcca gtcacgacac aaattttaag tgggccatgc 3420 tagcccaaca tgttggctcg taatggcctg gtaaacatcg agttgtgcca gcccagcacg 3480 acccattgga cacctcta 3498 // ID SONATA3 repbase; DNA; EDCOT; 247 BP. XX AC . XX DT 18-OCT-2006 (Rel. 11.1, Created) DT 18-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE SONATA3: Non-autonomous DNA transposon from Solanum species. XX KW DNA transposon; Transposable Element; SONATA3. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-247 RA Jurka J. and Shankar R.; RT "SONATA3: Non-autonomous DNA transposon from Solanum species."; RL Repbase Reports 6(10), 508-508 (2006). XX DR [1] (Consensus) XX SQ Sequence 247 BP; 103 A; 21 C; 31 G; 88 T; 4 other; tactccstcc attccatttt atgtggtatt gtttgacttg acacgaagtt taagaaaaaa 60 atgaagattt tagaaaatta tagtctaaaa taatttttat atatttatat aattataaat 120 catttcatta attaagggta aaagaagaat tttaagttaa attattttca attataawaa 180 aatgacattc tttttaagac wgactaaaaa gaaaagagtg tcacataaaa tgggacaagr 240 aagtatt 247 // ID Copia-92_PTr-I repbase; DNA; EDCOT; 4098 BP. XX AC . XX DT 22-DEC-2009 (Rel. 15.02, Created) DT 22-DEC-2009 (Rel. 15.02, Last updated, Version 2) XX DE Copia-type LTR retrotransposon: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; internal portion; Copia-92_PTr-I; KW Copia-92_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4098 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 168-168 (2010). XX DR [1] (Consensus) XX CC >87% identical to consensus. ORF is disrupted. XX SQ Sequence 4098 BP; 1396 A; 616 C; 1009 G; 1075 T; 2 other; agtggtatca gagcttaggt ttgattattt gacatggtca atccaaactt cccacttcaa 60 tgtcctaggt tgacaaagga caactatgaa acttggtgta ttcgagtaaa agcttggcta 120 ggttcccaag atgtatgaga gacggttgaa aaaggctttg aggagcctat agatggagca 180 acgttgactt cagcccaaag ggaggccgtg caaaaggcac gaaggaagga tcaacaagca 240 ctcacaatca tccaccaatg tctggatgat gccacttttg agatagtggc caacgcaacc 300 accgccaagc aagcatgaga agttttgcaa gaatcaaacc aaggagctga caatgtgaga 360 aaggtacgtc tacaaaagct acgtggtgac tttgaaaagt tacatatgct tgaatcagag 420 aatatttcag aatactttgc aagagtattg gccatataca atcaaatgaa gagatatgag 480 gagaagatgg aagagacacg tgtggtagag aagatcctat gctcgctgca aaagaagttc 540 cattatgtgg tggtcgcgat agaggagtca caaaatatgg atkttctttc aatacaaggt 600 ctcatgggaa aattacaagc ccatgaggaa agagtcaatg agattcaaga ggatgtgggt 660 gcacaagcac tttttttcaa agcaagatgg ttctggatat tcccaagggg gtagaggacg 720 tggacaaagc aaaggaagag gaggaagagg cagatttgga agaggaggtc gaggcagcct 780 caacaggtca accggtcgac cgaatgaagc aaaccggtcg accggttaca ctgacagtgg 840 caatccgaga tccaggtttg acaaatcaaa agttaaatgc tataattgtc aaaagataag 900 gtcattatgc tagggattgc tggagtccaa ccaagagggt tgaggagaat gcaaatcttg 960 tgatagaaga ggagaaggaa gccaccctat tactagtgca tgatgagaga atgcaagaca 1020 aagagaacat gtggtatcta gacaatggag ccagcaacca catgtgtgga gacaaagaca 1080 agttcatgga gcttgatgaa gcaattagag gtaatgtcac ctttgcagat cattcaaagg 1140 tttccatcaa aggaaaaatg tatgattttg attaaattga aagatggaag tcatcaattt 1200 attggtgatg tctattatat accaacggtg aaaagcaaca tattgagctt aggacaattg 1260 ttggagaagg ggtatgagat taagatgaaa gatcgtactt tgacattact tgacactaaa 1320 ggagctatga ttgcaaaggt agccatgaca aagaatagaa tgttcttgct aaacatagag 1380 acggatgtgc ctaaatgcct aaatacatgt gtgaaagatg agacttggct ttggcatatg 1440 agacttgggc atgtaaactt tgatagcttg aagatgatgg cacaaaagga gatgttgaag 1500 ggtctaccat ccattataca tccaaatcag ttgtgtgaag gatgtttagt gggcaagcaa 1560 tttcgcaaga gctttccaaa ggagtctaca tcaagagcaa gtcaacccct acaagaaata 1620 catgtcgatg tttgtggtcc tatcaaacca tgtttgtttg gtaaaaattt atattttcta 1680 ctttttattg atgattatag tagaaaaact tgggtatact tcttaaaaga aaagtctaat 1740 gtgtttagtt gttttaagaa gtttaaggca ttagttgaaa aagaaagtgg ttattctata 1800 aaatcactta ggacggatag ggggtgaatt ttgttctaat gattttaatg agttttgtga 1860 agatcatggt ataaagagac tcctaacggt gcctagatcc ccacaacaaa atggcgtggt 1920 ggagagaaag aatagaagca tcctcaacat ggcgagaagc atgctcaaaa ccaagaagat 1980 gcctaaagag ttttgggctg aagctgtaga ttgtgttatc tacttgtcaa ataggtgtcc 2040 tactaaaggc ttgaatgaca tgactccaca agaagcatgg agtggaagaa agccaagtgt 2100 ttctcacttg aaagtttttg ggagcattgg ctatgtgcat gtagatgatc aagtaaggac 2160 caagctagat gacaagagca aaaagatgat ctttgtgggc tatgaccaaa agtccaaagg 2220 atacaagctt tacaacccta atgaaggaaa gatggtgatt agtagagatg ttgagttcaa 2280 tgaagaagga gcatgggatt ggaaggtaaa tgatggtgag aaatatgact tcctaccgat 2340 tcttgatgaa gaggaggaaa gatatgaaga tcatcaagaa cctatagtta cacctccaca 2400 aacaccaatg agctcaactt cttcttcttc tagtggaagc tcaagtagtg gcactccacc 2460 aagtccacca agaaagatga ggagccttga tgacttatat gaggtaacta atcctattga 2520 tgatgtaaca ctatattgtc accttgctac atgtgatcct atagtgtttg aagaagcaat 2580 aaaggatgca aaatggagaa ttgctatgga tgaggagatt gcatcaattg agaagaatga 2640 cacatggaga ttggttccta gaccaaaagg aaaagaagcc aataggtgtc aagtggatct 2700 acaaagaaaa gaagaatgtc aaaggagagg tggagaggta caaggcaagg ttagtggcaa 2760 aaggctatag tcaaaagcat gggattgact atgatgaggt ttttgctcca gttgctagat 2820 tggagaccat tcgattaatc attgccaccg ctgcccaaca tagatggaga atctatcaaa 2880 tggatgtcaa atcagccttt cttaatggtt ttcttgaaga ggaggtctac attgagcaac 2940 ctatgggtta tgaagtgaag ggacatgaag acaaggtttt aaagttgaac aaagccttgt 3000 atggattgaa gcaagcccca agggcttggt atagtcgcat tgatggctat ttcttaaaga 3060 atggatttgt taaatgcccc catgaatatg ttatctatgt aaagatcaaa gagagtggtg 3120 atactcttat tgtatgtttg tatgtggatg acttgatctt tacaggaaat aatccaaaga 3180 tgtttggaga cttcaagcaa gcaatgatca aggagtttga gatgacggat attggtctta 3240 tgtcctacta cttagggatt gagatcaaac aaggagaaga tggaatcttt gtgaatcaag 3300 agaagtttgc aagggaggtt ctcaagaagt tcaagatgga ggattgtgca aaagtgaata 3360 ctctagttga gtgtggagtg aagatgtcaa agaatgatga aggggagaag ataaactcta 3420 caacattcaa gagcttagtt gggagtttga gatatttgac atgcactcgt ccaaatattc 3480 tttttggagt aggacttgtg agtaggttta tggagacacc aactatgaca cacttcaaag 3540 cttgaagcga attcttcgat atatcaaagg tactgttgat tttggcttgt tctatggtta 3600 ttctaatagc tttgaacttg tgggttatag tgatagtgat tgggctggag atatggatga 3660 tagaaagagc actacaagtt ttgttttcta catgggagac acaacattca catggagttc 3720 aaagaagcaa tctatagtca cwttatcaac atgtgaagct gaatatgtag ctactacaac 3780 atgtgtttgt cattccatat ggctaagaag attattgaag gagttgtgaa tgccacaaga 3840 gaagcctaca aaaatttatg tggacaactc atcagtcatt gcattagcaa agaatccagt 3900 atttcatgat agaagtaagc acattgacac aagatttcat tacctacgag attgcattgc 3960 aaacaaggaa gttgaagtca agtatgtgaa gacacaagac caagtcgcgg atattttcac 4020 aaagccactc aaatatgatg tttttgccaa gatgagagat atgctgggag ttatgaagaa 4080 atcaagttta agggggga 4098 // ID MtPH-E-IIa repbase; DNA; EDCOT; 3382 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 13-MAY-2008 (Rel. 13.05, Last updated, Version 1) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-E-IIa. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3382 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC An autonomous element representing low copy number family E of CC PIF/Harbinger transposons from Medicago truncatula, carrying 22 CC bp-long TIRs. XX SQ Sequence 3382 BP; 1089 A; 450 C; 574 G; 1269 T; 0 other; gggcctgttt gaaacacttt ttaaaaacag ttttttaatt tttaaaaatt aaaaaattaa 60 aaacttgttt gattacctat ttttaaaata taatttttga aaagtgtttt gggtttttta 120 gttttggaaa ctaaaaaagt gaaagagcta aaatgggttt tgcttttcta ttttaagttt 180 taagttttta aaatcgtgta aaaaataaga aaagtgaaaa cacggagaaa agtgccagtt 240 ttctccaatg gcatagttgt aattatgttt gaagttcagg ggcatttcca tattttttat 300 caaaaatatt tggatcaaaa atcattcctc attttgcaga aaaactaacg tgagaacact 360 gagaagcgaa atggcaattt ccacggcgat tcttctccga tctccgccgt gatttttctt 420 cggtctacat ctcgcttctt cttctccacc gtgcttcttc ttctctgcgg ttttttcagg 480 ttacatctca catctaattg tttttcattt ttaaattaat ttctgttctt tgattcagaa 540 ttttgcacct aatatagtga tttcttactt gattttgtgt ttttagatct atgattttca 600 atattaggtt aatttgtaaa tttgagattg tggtagaatt cgaaatttgt aatgcttttt 660 atatgttgtt gtgtttgata aactctgatt cattttgata acttatttgc agcttatgtg 720 attgatattt gcagcttata gatctggatt aagttcctgt ctagataaaa aaaacttatt 780 tgcagcttat agtataagtg cttatcataa taagcactta tttataagca taagctattt 840 ttatagcaaa atagaaaata acgttaaatt atttttctaa ttgctattta taagctatat 900 taaagaacta agaaattatg aatataagtt gaaatcaact catgcaaatt gttaaacatt 960 atttaattat ggcttctatc aacttgtatc tttcaatgtc attaataagt tacaatattc 1020 acacggatac cagatacaaa actcaccgat ggaaaataat ttgaaaatct gaagtaattg 1080 aacgtaacat gagtcaatgt tgtgttagtg ctagatagtg gacattactt caatttgaac 1140 tgttgatgtt cttaagtgta attagatttc agctagtgtg gcatttaatt aatttgttaa 1200 tactgatagt tagttagtca agtgtaactt attgtactta ttagtgagtt gatatgagtt 1260 ataaatagtg ttgcatttga tttttagtca ttcagataga caatcaataa aatgagatca 1320 ttctcaagtt ttcataatat tcctttttct atttcttgtg tgcattgata tgcttgctcc 1380 ctaacagatg gctacatatt tgtttggctt acttaacata tgaattttga tccatgtatt 1440 gttgaatcat ttgttaacat agacatgtaa taatttgtta actgaacctt attgatatga 1500 ctctctcttt gcatatctgt tttagacatg aatctcatca tgaatcacga ttaattattt 1560 gaagtggtgc aggtagaagg atttgaagta gtatgaaaaa cactagccac cgtccacgtt 1620 tcactgctcc tgcctcctca tttgttgcgc ctgctgtttt gatcaagaga aagtaagaga 1680 aagttgaaga aagagtgttt tcaaacatat tgtgcttgtt gaagagaaag ttgctacatt 1740 cttattcata attggtcata atgttcgtca tagagttgct tcaaaccgtt ttcaacattc 1800 cacagaaaca atctcacgca atttcaagga agtattaagg gcagtgtgtc gattaggaaa 1860 agaactgata aagcaggagt ctatggagtt gcctaataga attaagaata atccaaaata 1920 ttatccttgg ttcaaggtat gtgtgtaatt catattattg ttattgtagt tgtatcttta 1980 tttggttgtt gtttaattat ccatataatt tggattgtgc cttgtagaat tgcataggtg 2040 caattgatgg gctcctgctg agaaacaaat ttcatgtaga ggtagaaaga caacaatcac 2100 tcagaatgtc atgtgtgctt atgatttcaa catgatattt acatatgtat attcggggtg 2160 ggaaggaagt gcacatgatt ctaaagtttt acttgatgca attacaaatc caaatgcagg 2220 atttccttgg ccacctaaag gtaagtatta atatctaaca taaagttatg cagttatatt 2280 gaggaaatta acaagtagag ctaacatgta ttttaattga tgaaggttca ttttatcttg 2340 ttgattctgg gtatccatgt accagaggtt ttcttccccc ttatagaggt gaaagatatc 2400 atgcacaaga atatcgaggt caaggtagac aaccaaaaag tccagaagag ttatttaact 2460 acaggcactc gtctttaagg atgacaattg agcgctgttt tggagtgttg aaaaacagat 2520 ttcctatttt aaagttaatg ccttcctaca aaccttcaag gcaaagactc atagtaactg 2580 cttgttgtgc tattcacaat tacatacgca agtggaattt gcctgatgag ttgtttagga 2640 tatgagagga aatggataat atagaacttg aggcggtgaa cgaggttcct aaccttgaag 2700 ggatgagctc gaatgttgaa aacttaacaa ggttatctga tgaaggtgca gctgagatgg 2760 caatggatag gaatcatctt agagatagga tgtgggtaca tcgtcataat taatcgaact 2820 aattacgctt tttttagatt ttcttatatg caacaatgga gtatggagtt ttgttagtta 2880 ttttgcggat gattgttttt gtttgcttat ttgatgttta tgttatcgac attaatatgc 2940 tataatattt ttatgtgttt cacatttttc aattttgtat cgcttgaaca aattatgact 3000 tcgtatctaa aaaaattatt tattttgtga ctaaattcta catttaacta tagtacttca 3060 aatttaattt gattggtaac taaggataaa gttgtaagaa aaatacaatt atataaaagg 3120 taatataatt tatataggtt aaaaaaaaga ttttaaaaat ttgattacca aacaagtttt 3180 ctaattttct attttttaaa actgtttttg aaaattatat caccaaatgg attttctaat 3240 ttttttcatt tctaaaacag ttttgaaaag tcacattacc aaacaagttt tttctttttc 3300 tcttcttgaa atcccttttc taaaattagt ttttaaaaac acattttgaa aactaaaaac 3360 aaaaagtgtt ccaaacaggc tc 3382 // ID LTR-3_Mad repbase; DNA; EDCOT; 3217 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR-3_Mad. XX NM LTR-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3217 RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-3217 RA Kojima K.K. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1786-1786 (2010). XX DR [2] (Consensus) XX CC ~87% identical to consensus. 5-bp TSDs. XX SQ Sequence 3217 BP; 846 A; 524 C; 789 G; 1056 T; 2 other; tgtgaaatcc cgttcctgga tttcactgtt ataatctacg tatttgtatt attgagattt 60 tatattattt tttgggaaat taattattta aaatccgtag accattcgag gtcacaagtt 120 atattttcga atagatatcg aggtcacgaa cgcataggcg aaagccgttt gcgagtccga 180 gttataacgg tatagttacg gacgtttgaa ggttgtgaac tatagaattt aggaattatt 240 tagaagctgc cattgtggga aagaggagag ggataaggga gttaaaagag ggagggaacc 300 aatcagattt taaaaggtga ggagcagccc aatcaggaga aggagaagga ggggaaagga 360 gagagacccg aaatgggtca ttttttgacc cgcgaaccac catttttgac ccggccatat 420 ctccttcata cgaactccgt tttgggtgat cttggtgtcc atggaaagcc cttgatgagc 480 cctacatcct ggtagtgtta gatttcccaa tttctttccc atttttccag ttcgaagcca 540 caaacccacg ggtgttccgg cggctttatc ccttttcccg gtggctccgg caagtttcac 600 catccatgac caccaccaaa agacttccct caaccccagg aacaaagccc aagcagtgtt 660 ggaggcgtcg gagttcgatt ggaagccgaa tcaaagcaca ccmttttcta gggtttcggc 720 gggtttgagt gaaattgaag tgtttcccgg ccaaattgga cttggccaca ggtataaagt 780 ttgctctact ctttgagatc ttcatttctg taatttttgg taatttttaa aaatagttga 840 attttccggc aagtcggggc ggccgaccgc cacccgcggc ggcgcgtgcg gcggcggcct 900 ggccagtggg ccgacgatgt ccttttaagt tcaattagat gccctgattt cataattgat 960 atccttatga tatggtttga ttgtttgaac ctaatttcat tacgatacgt ggttaggtca 1020 aaaatatgat tcgacgatcc gaccgttgga tcgtcaccaa accttaatgc gtgatagaac 1080 ataatatttt tggatcatag aaacttacgg atcgagaatc cgacgtacgg atcttcccta 1140 attggatttc taagtttgta aaattaaatg tcgaccgcca cttgaatttt gaaattggcg 1200 gagatccgac cgtcggatcg tgttgagatt ttagtatgtt gttatttgag cataatgtgg 1260 actttggaaa gttacggatc cgaaatccaa tgtgtggatc ttccggattg aattgtgtag 1320 aattgtggac cctacctttg accgaaagtt gacttttgat caacatgtct cgaaacgtcc 1380 taattactaa aattagtact acgggggact aagtgaagtc tagtgggcct acattggtta 1440 gatagcgact tgaatatatg aaatatgatt attatcttaa tttcttatat tagtatcatt 1500 tgtgaatatg aattggtctt ataaatatga tttctattga aatgtgaatt ttatatattt 1560 agccatagac ctatgctaat taaacatgat ttggcttgtg tactgatgat gtttgtgata 1620 tacgtgtgtt taattaactt ttagtaatgt gaatgataat tatgaagaat gttatgacaa 1680 ttatgggatc taaatattgt ttgataatta tttggatatg attgccaact gaatacttat 1740 ttgaacttgg cgctattacc tagcatgaga tggagatgaa agtcaggaga tgagttaggt 1800 actttattag atttttagta gaattagtaa ttgagggaat tccttgtgtt gtgctccata 1860 tgactagatg ctggttgata tgcggagtcg atagcatgta tgcgtataat tatgtataag 1920 gtgtgatgat gagactgcac catgtagacg tggtgcatgg ctggtcctgc ttggttaatc 1980 cgcgttgggg ggccatacta ttatggatcg tgcttggtta acgcgttggg atcctatggc 2040 cattatctta gggtgatcat gcttggttaa tccgcatggg tgatcactct aatagttgta 2100 ggatgacttg cttggttaat atatccgcgt tgggggacca tatgcattct agaagtgagg 2160 aggattagtt gtacttggta catttgatgg gggaatcata tgcttgtttg gattccgttg 2220 agtgatggtc cggaatccct tctattctgc gattccgttg agtgatggtc cggaatcgta 2280 tccacttgga tttcgttgag tggttgttat gcatcgtact ccgcgattcc gttgagtgat 2340 ggtccggaat cgtatccact cggattccgt tgagagatgg tccggaatcc ctcctactcc 2400 gcgattccgt tgagtgatgg tccggaatcg tatcctgttt ggattacgtt gagtggtccg 2460 ttatccctac tcttgctcat ttccataagt tagacttgtt ccctggattc gagtgaatgg 2520 gatgtaccca caatagatct tgtgaatata aattagaatt atcaagttat tactcgaaat 2580 ccaggcaggg aactatgtag agttccttta ttaattttgt gaattgatgt gtgatctgat 2640 tgattgatta acataattaa atgttaatat cgtgcctcct tgattcatgg aatgggttac 2700 ttgagatgat tgtggaatga tgttggatat gattgttatt aatatgatca gatcagttga 2760 ttaatgtgac tagaggatac tattgtgctt cgttggttct ttgatatgtt acatgatatg 2820 aatagcggtw ttatgttgaa acataatgat ttatatgatg gatgaaatgg aaaccttgat 2880 tgtcatgcgg gttgttatgt agtttgaatc gaataattca tgcttgtcaa gtccaaatgt 2940 ttgattgagg aatgttatgc attttggctt gaacagaatg tgttatatgt cgagttatag 3000 cgaagttgaa ctacgaatgg cttgatccct attgagggta cgtaggcagt ctaacgagga 3060 ggttagatgc agccataaag tataagaaaa attatcacga aattcgaatc ttgagttgtg 3120 cattgtccat atcccggagg cggggtatgt gagtgatacg ggtatttggt aacgtcacgt 3180 gtcgatcctg gacgtatgtc gggatcgggg cgtgaca 3217 // ID L1-2_PTr repbase; DNA; EDCOT; 6167 BP. XX AC . XX DT 14-DEC-2009 (Rel. 15.02, Created) DT 14-DEC-2009 (Rel. 15.02, Last updated, Version 2) XX DE Non-autonomous L1-type element - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW L1-2_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-6167 RA Jurka J.; RT "L1 elements from black cottonwood."; RL Repbase Reports 10(2), 158-158 (2010). XX DR [1] (Consensus) XX CC The youngest sequences are ~96% identical to consensus. XX FH Key Location/Qualifiers FT CDS 163..2316 FT /product="L1-2_PTr_1p" FT /translation="MASNPKLQTLKANTTHSITKQPTNHHQNIQNTASLTQ FT VRFLKSHESTNNQKSLSNSHLDPKQQPPPKHNRNIPSPKTQNNHSFNISVP FT QIYFEGFPIWADYHRIKASFNKFGSVLKLYVSRRVNKSGSLFGFVTIASNF FT SDKVLLESVNDIWFEYHRLKANFARHYKKIPRENKAPDRSKPKTTIRVPIS FT ERDVRSYKEVLSEGKAEQILLPVASGPKDYFEKLSLDIEEEDYAWLKRCLL FT GKIKKGSNYSSIRFGLIQHDIDFAGLRFLGASQVLVIFDNRDILMESWRKN FT NKCWDVFFEEVRPWVETDTTLNRMAWITITNLPIIGWNCRCLTKILERSGQ FT MIGYDKTTLKHFELSQLRILIGTQLDKVNKVIVLQLNNQTYQVKIEEMDQL FT HYPIAGSISYTMDDFQTSLEQGDEDDEEDSVDVADGVDTDEDRAGVSPSVT FT RTLGGGSSGWENSDLAQDGDKLSTSDDSSLIIFNALHLDVVQDQHVASSLE FT RFPEIMAYNLSFSDSSYIKSSPIPNALTVYTGRGTPILREDARNPAAALGL FT DSLVLAQIXSPVYGSGSQSPSDVLSISFGSNNDLALQSTYNPQAVVILEPQ FT HMNHPVILHSDANTKESATALSAKTRRKLRRTKMITADGSLNETVNKSEMD FT TEDSTIQRCNRRNLLAHGENNKPSEGDEVCLMLEIGEALQIEKPHNLDDFT FT SYINQQRRKEKADWEASQ" FT CDS 2366..6040 FT /product="L1-2_PTr_2p" FT /translation="MQILSWNSCGLGLARKKRTVSKLIRDFDIEVCFLFET FT KLQSYSDRLVFQLWSVSNVSWFGNEAEGTKGGILAMWDNSKFAVSSVEYGH FT GWIGLFGQNVLTGFSGAVVGVYAPCNQADRLLLWKDLRILKAAFECPWFLA FT GDFNETMLRSDRSSGFINKVGSTAFRLFIDDCNLIEYNMSEGLYTWFRGGS FT MSKLDRIFSSPCCHLQFPLLSLRRLPRGFSDHCPLILGVSPAEKGWIPFKF FT MDCWLHHPNFKDIVKGIWDEACNEFSGQFKLIKKLSFMATRLRQWNRVGFG FT HQETALASIQSNISAIEQKSEYGQLSTAEQNSLDSLIKKQWQCNLHIESMW FT RQKSRQIWCRLGDRNTRFFHLVANFRRAKNHLLKVVHNGSVVEGLPVIKDA FT AVSFFSNLFRSPDRFRIGLGPVGFKTLSASSSASLERDITLEELKQSVWDC FT DGSKSPGPDGFNFKFYRLAWNFIADDLLDLAKNFFKTGRLPKGVNHAYVHL FT IPKIASPVGFKDFRPISLIHGIYKIMAKVLSSRLKAVMHDLISENQTAFLA FT GRQIIDGFLVANEAVHSLKRYRVPSLIFKVDFHKAFDSVQWDYLEQVMRHM FT GFGEKWINWINTCISTAKLSVLINGSPSKEFLMGRGIRQGDPLSPFLFLIA FT AEGLSVLFQRAASNDLFKGIPFGDSFCLSHLQYADDTLIFMPANLHMVKTV FT KRILLWFAICSGLHINFHKSSLIGINVGEDTCASMAYSVFCRFDSLPCSYL FT GMPLGSNPKRLSTWKPIIENFRRKLSMWRGRMLSMAGRICLIKSVLSSLPV FT YYMSSFLMPKGVCNILTSIQRRFLWSGVAKQKKICKVQWRIVVKARKEGGL FT GLGSLMSKNISMLFKWIWRLSLPDHALWKQVTTHFYSPTFENGIPKLHGHI FT SPFWKDVLSILDPNSVIGLVLRENIKFMIGDGSSILFWSDVWIGSNALRSI FT FPRLYQISTFRNGLVNEMGQWVNDQWRWNLVWRRNLLSYEEQQYHHLLSML FT EPTIIRQGKDDKLIWPCNSDGSFSVKSCCTLIDNTSSANDRVFEANVWIKG FT APPKVQVFLWLAVQDKVSTRAFLHQRTVLSATQASCVFCSSDLETSEHLFI FT HCNFSRSVWMKVLDWWGIQCCLPRTLDSLLLQWPEMVHGKFQRSAWRLISS FT STIWGIWLLRNKIVFEEGTINLFDCFSTILHRVAIWLHTQDSNFTYTGNDL FT LRSSDGIKLWCNKKS" XX SQ Sequence 6167 BP; 1745 A; 1164 C; 1361 G; 1887 T; 10 other; gttttggtct aactccgatc tagggagatc caaccgttaa cttgagctga tatttggata 60 tgtnctgcat aagatgtgtn tttaccnttt caccgttggg atttgttatt nnttgaattg 120 ttggtgagta attgttgttt gaagctctgc ccagaatctg tcatggcttc caatccgaaa 180 cttcaaaccc tcaaagctaa caccacccac tcaatcacta aacaacccac aaaccatcac 240 caaaacatcc aaaatacagc ctccttaacg caggttaggt ttctaaaatc ccacgaatca 300 acaaacaatc aaaaatccct ttccaatagc caccttgacc caaaacaaca accaccccct 360 aaacacaatc gcaatattcc tagcccaaaa acccagaata accactcctt taacatttca 420 gtgccacaaa tttactttga agggttccca atatgggctg attaccatcg cataaaggct 480 tcttttaaca agtttggctc tgtactcaaa ctctatgtat ccaggcgtgt caacaaatca 540 gggagtcttt tcggttttgt aacaatagca tcaaactttt ctgataaagt tttgctagag 600 agtgtgaatg acatttggtt tgaatatcac agactaaagg ccaatttcgc cagacactat 660 aaaaagattc caagagagaa caaagctccc gacagatcaa aacccaaaac aactataaga 720 gtgcctatta gtgaaagaga tgtaagaagt tacaaagagg tactcagtga aggaaaagcg 780 gaacaaatac ttctgcctgt ggcttctgga ccaaaggatt actttgaaaa actctccctt 840 gatattgaag aagaggatta tgcttggcta aagagatgtc ttctgggaaa aataaaaaaa 900 ggatccaatt actcttctat acgttttgga ctgatccaac atgatataga ttttgctgga 960 ctgcgctttc ttggggcatc tcaggtcctc gtaatttttg ataatagaga catattaatg 1020 gaatcatgga ggaagaataa taaatgttgg gatgtatttt ttgaggaagt tcgcccttgg 1080 gttgagactg acacaacttt gaatcggatg gcctggataa caataacaaa tctacccatt 1140 atagggtgga attgcagatg cctcacgaag attttagaaa gatctggtca gatgataggt 1200 tatgataaaa ctactctcaa gcattttgaa ctatcacagt tacggatcct cattggtaca 1260 caactggata aggtgaataa ggtgattgtt ttgcaactca ataatcaaac atatcaggtt 1320 aagatagagg agatggacca gttacattac ccaattgctg gctctatttc atacaccatg 1380 gatgactttc agacatccct agagcaaggg gatgaggatg atgaggaaga ctcggttgat 1440 gtggctgatg gcgtagacac agatgaggac agagcaggtg tgtctccatc agtcaccagg 1500 actcttgggg gcggcagcag cgggtgggaa aattcagatc tggcacagga tggagacaag 1560 ctatcaactt ctgacgatag ctctcttatc atatttaatg ctcttcatct ggatgtggtg 1620 caagatcaac atgtcgcctc atctttagag agatttccag aaattatggc atacaatctt 1680 tctttttctg acagcagcta tataaaaagc agtcccattc ccaatgctct taccgtatat 1740 acgggacggg gcactcctat tttgagagaa gatgctagaa accctgcagc tgccttgggc 1800 cttgactccc ttgtattggc ccagattgna agcccagttt atggcagtgg atctcaaagc 1860 ccatctgacg ttctctctat ttcatttgga tcaaacaacg atttagccct tcaatcaaca 1920 tataatcctc aagccgtagt aattctggaa ccgcaacaca tgaatcaccc tgttatttta 1980 cactctgatg caaacacaaa agagagtgca actgctctat ctgcaaaaac aagaaggaag 2040 ttgcgacgta caaagatgat tacagctgat ggaagtttga atgaaacagt taataagagt 2100 gagatggata ctgaggactc aacaatacag aggtgtaaca ggaggaactt gctagcacat 2160 ggcgaaaaca ataaaccttc tgagggtgat gaggtttgtt taatgctgga aataggagag 2220 gctttgcaga ttgaaaaacc tcacaattta gatgacttca catcctatat aaatcagcaa 2280 aggcgtaaag agaaggctga ttgggaagca tcccagtgag cagatgttcc nctttgttct 2340 gtaaggattt taaatctctt ttcttatgca gattctttca tggaattctt gtggtttggg 2400 gttagctaga aagaagagga cagtttcaaa gttaatcagg gattttgata tagaggtttg 2460 ttttttgttt gaaactaagt tacaaagtta ctcagacaga ttggtttttc agttatggag 2520 cgtcagcaat gtttcttggt ttggtaatga ggctgaaggt actaaagggg gcattctggc 2580 tatgtgggat aactctaagt ttgcggtatc atcagtggag tatggtcatg gttggatcgg 2640 gttatttggg cagaatgtct tgacnggctt ctcaggggcg gtggtaggtg tttatgcccc 2700 ttgcaatcaa gctgacagac ttcttctttg gaaggacctt cgtattctga aggctgcttt 2760 tgagtgtcct tggtttttag caggtgactt caatgaaact atgttgcgaa gtgacagaag 2820 cagcggcttc attaacaagg tgggttcaac ggcttttaga ctttttattg atgattgcaa 2880 cctaatcgag tacaacatgt cagagggtct gtacacctgg tttcgtgggg gatccatgag 2940 taaactagac cgcatttttt ctagtccttg ttgtcatttg caattccccc ttttgtctct 3000 tcgacggctt ccaagagggt tctctgatca ttgcccttta atcctagggg tttcacctgc 3060 agaaaaaggt tggattcctt tcaaattcat ggattgttgg ctccatcatc cgaattttaa 3120 agatatcgta aagggtatat gggatgaagc ttgcaatgaa ttttcaggtc agttcaagct 3180 cattaagaag ctcagcttta tggcaactcg gctcagacag tggaataggg ttggttttgg 3240 gcatcaggag actgctttgg catcgatcca aagcaatatt tcagctatag aacagaaatc 3300 agagtatggg caattatcta ctgcagagca gaactcgctt gattcattga tcaagaagca 3360 gtggcaatgt aacttgcata tagaaagcat gtggcgtcaa aagtctcgcc aaatttggtg 3420 tcgcctgggc gatcgcaaca cgcgtttctt ccatctagtt gctaacttca ggagggctaa 3480 aaaccatctc ctgaaagtgg ttcataatgg ttctgttgtt gaaggcttac cggtcataaa 3540 agatgcggca gttagcttct tctccaactt attcagaagt cctgatagat tccgaattgg 3600 tttagggccc gttggtttta aaacactctc ggcttcttct tcagctagct tggagcgaga 3660 tatcactttg gaagaattaa agcagagtgt ttgggattgt gatgggagca agagtccggg 3720 tccagatggt ttcaatttca aattctacag gcttgcttgg aatttcattg cagatgatct 3780 gttagacctg gccaagaatt tcttcaaaac aggtaggctt ccaaaaggag tcaatcatgc 3840 ttatgttcat ctaattccga agatagcttc cccggttggc ttcaaagatt tcaggcctat 3900 tagtttgatt cacggcattt acaagataat ggctaaggtt ctttctagcc gtctgaaagc 3960 ggttatgcat gaccttatca gtgagaatca aacagctttc ttggcaggga ggcaaataat 4020 tgatgggttt ttggttgcca atgaagcagt tcattccttg aaaagataca gagtgccgag 4080 ccttatcttt aaggtggatt ttcacaaagc tttcgatagt gtgcagtggg attatttaga 4140 gcaggttatg aggcatatgg gttttggtga aaaatggatt aattggatca acacttgcat 4200 ctccaccgca aaattatcag tgctgattaa tggatctcct tctaaggaat tcttgatggg 4260 ccgtgggatt cgccaaggtg accccctttc tccgttcctt tttctaattg cagcagaggg 4320 attatctgtt ttgtttcaaa gagcagcttc aaatgatctt ttcaaaggta tcccttttgg 4380 agacagcttt tgcctcagtc acctacaata tgcagacgac actttgatct tcatgcctgc 4440 taatcttcat atggtcaaaa cagttaaaag gatcctgttg tggttcgcta tttgttcagg 4500 tttgcacatt aacttccata aaagctcttt aattggcata aatgttgggg aagatacttg 4560 tgctagtatg gcatattcag tcttttgcag atttgattcc ttgccttgct cttatctggg 4620 catgcctttg ggatccaatc ctaaaagatt gtctacatgg aagcctatta ttgagaattt 4680 cagaagaaag ttgagcatgt ggagaggtcg tatgcttagt atggcagggc gtatttgcct 4740 aatcaaaagt gtcttgagtt cattgccagt ntattatatg tcttcttttc ttatgccgaa 4800 aggtgtctgt aatatactaa catctattca acgaagattc ttgtggtctg gagtggcgaa 4860 gcaaaagaaa atctgcaagg tacagtggcg tattgttgtg aaagctagaa aagaaggagg 4920 cctcgggttg ggttctttaa tgtctaaaaa tatatccatg cttttcaaat ggatatggag 4980 gctaagctta ccagaccatg ccttatggaa acaggtaaca acccattttt actccccaac 5040 tttcgagaat ggaatcccaa aattgcatgg tcatatttcc ccattttgga aagacgtttt 5100 gtcaatcttg gatccaaaca gtgtcatcgg cttagtattg cgtgaaaaca ttaaattcat 5160 gattggagat ggatcctcca ttctcttctg gtctgacgtg tggataggat caaatgcttt 5220 acgtagcatt ttccctaggc tttaccaaat ttctactttt cggaatggtt tggttaatga 5280 gatgggtcaa tgggtgaatg atcaatggcg atggaatttg gtttggcgta ggaacctctt 5340 atcttatgaa gagcaacaat atcatcattt gctctcaatg ctggagccaa cgataattcg 5400 gcaaggaaaa gatgacaaac ttatatggcc atgcaattct gatggaagct tctcagttaa 5460 atcntgttgc accctaattg ataatacctc ctctgcgaat gatagagttt tcgaagccaa 5520 tgtttggatt aaaggggccc ctccgaaagt tcaggtgttt ctctggttgg cagtacagga 5580 caaagttagt acaagagctt ttctccatca acggactgtt ttgtctgcca cacaagcttc 5640 atgtgtcttt tgcagctcag atttggaaac ctcagagcat ctttttatac attgtaactt 5700 ttctaggagt gtttggatga aagttttgga ttggtggggt atccaatgtt gtttaccgag 5760 aacacttgac tcgctgcttc tgcagtggcc cgaaatggta catggcaaat tccaaagatc 5820 agcttggaga ctaatttcaa gtagtactat ttggggtatt tggttgctga ggaacaaaat 5880 tgtttttgag gagggaacta taaacttgtt tgattgtttc tccaccatcc ttcatcgggt 5940 tgctatttgg ttgcatactc aagattcaaa cttcacttat acaggaaatg acctcttaag 6000 atcttctgat ggcatcaaat tgtggtgtaa taagaaatct taggtagtct tcttgttgtt 6060 tgctgtagta gatcagtttt ttttttcttt tatctcttgt atttctcttt ggctattggc 6120 tttatggcct tctcaatata ctctcgatga ttatcaaaaa aaaaaaa 6167 // ID MTCOPIA1_LTR repbase; DNA; EDCOT; 269 BP. XX AC CT963078; XX DT 29-DEC-2006 (Rel. 11.12, Created) DT 05-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE Copia-type LTR-retrotransposon - long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; MTCOPIA1_LTR. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-269 RA Jurka J.; RT "MTCOPIA1: Copia-type LTR-retrotransposon from barrel medic."; RL Repbase Reports 6(12), 631-631 (2006). XX DR EMBL/GenBank/DDBJ; CT963078; Positions 62740 63008. XX CC This is a very young element, LTRs are identical. XX SQ Sequence 269 BP; 73 A; 46 C; 37 G; 113 T; 0 other; tgttaaaatt gtatcttagt ttgttataat tagatagctt ggagaacaag ttacttagca 60 actccataga atcttattgt acactagctg catttgatct taattctttt agaaagtttg 120 ttaggatctt aaacagctat atatagcttg ctgtaaccgt tttcttctca attcaatgaa 180 tctagctttt atctcaattt tctctctttc ttctttgtta agcttctgca tttcttcaac 240 ttccaccatg gatatggtga agtttaaca 269 // ID COP21_LTR_MT repbase; DNA; EDCOT; 290 BP. XX AC AC124966; XX DT 11-JAN-2007 (Rel. 12.01, Created) DT 11-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of LTR retroposon, COP21_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; ORF; Interspersed; repeat; COP21_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-290 RA Shankar R. and Jurka J.; RT "COP21_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 18-18 (2007). XX DR EMBL/GenBank/DDBJ; AC124966; Positions 16002 16291. XX SQ Sequence 290 BP; 105 A; 41 C; 39 G; 105 T; 0 other; tgttgagagt atatcatgga atgtggtcaa cactaatgat cattgacata taaatgcata 60 ttatggaatt aaagaagcac atcatgacat attccttgta cagcagttga ctcatgtaat 120 gtatttaata gtttttatat tataatcata ttataggtta gtcattatta ggtaatattc 180 ttgtattctt gtatatataa gatcttacat gaataagaac aaaaaaaaca cacaattctg 240 atatcaatac tgccatgcca tatttactat actagtcgac cttctttaca 290 // ID VLINE1_VV repbase; DNA; EDCOT; 6063 BP. XX AC . XX DT 20-AUG-2007 (Rel. 12.08, Created) DT 20-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE Non-LTR retrotransposon from Vitis vinifera. XX KW L1; Non-LTR Retrotransposon; Transposable Element; VLINE1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6063 RA Obukhanych T. and Jurka J.; RT "VLINE1_VV."; RL Repbase Reports 7(8), 766-766 (2007). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 2936..4627 FT /product="VLINE1_VV_1p" FT /translation="MGLCRGILPRPVSDHFPILLEGGGLKRGPSPFRFENM FT WLEEEGFKDQMKRWWGSLNFTGTFSFVLDAKLRALKDILKTWNKEVFGLIE FT TKKREALSQVVYWDEKEKYSALNLEDCEARKEARESYKTWVLREEISWRQK FT SRELWLKEGDNNTRFFHRMANAHSRRNWLSKLKVNGCWHTEENDLKNSVVG FT AFQKLYSEEGGWRPCIEGLSFMGLDSSEAEGLEIPFSEEEVFAALSDLGKD FT KAPGPDGFTMAFWLFCWDVVKVEIMGFFREFHERGRFVKSLNATFLVLVPK FT KGGAEDLKDFRPISLVGSLYKLLAKVLANRIKKVMGKVISESQNAFVEGRQ FT ILDAVLIANEAVDSRLKSNEGGVLCKLDIEKAYDHVSWKFLLAVLKKMGFG FT ERWIKWIDWCISTVKFSVLINGSPSGFFQSSRGLRQGDPLSPYLFVIAMEV FT FSCLLRRAISGGFLSGWRVRGRSGEGILISHLLFADDTLVFCEESQDQMTY FT LSWLLMWFEACSGLRINLEKSELIPVGRVHDIEDLALELGCKVGGLPSCYL FT GLPFGGTFQISGGVGWG" FT CDS 4656..5948 FT /product="VLINE1_VV_2p" FT /translation="MWKRQYISKGGRLTLIRSTLSSMPIYFMSLFYLPRKV FT RLRLEKIQRDFLWGGGALVQKPHLVRWNLVCLEKRKGGLGVRNLALMNKAL FT LCKWNWRFANEREALWKQVISHKYGVEEGGWCTRDVSGRNGVGLWKAIRKE FT WLFLDGRLAYHVGNGQRVRFWKDKWCGDEPLCESFPSLFSISLSKDAWVSD FT VWNPDGDGDGWTPLFSRAFNDWEIELVERFLQKIQAFRVQREEEDRVIWTA FT SKSGAFSVKSLYSILEPGGSSLFPSDSIWRASVPPKVAFFAWEASWGKVLT FT LEQLQRRGYSLANRCFLCLSEAETVDHLLLHCVKTRVLWNLLFSLFGVSWI FT LSCSVKETLLGWHGAFVGKTRKKAWQMAPLCIFWSVWKERNLLAFGNEEFS FT LQRLKYSFVCNLWSWVRVSIVLSPSSLVSFFDWLGSK" XX SQ Sequence 6063 BP; 1427 A; 851 C; 1983 G; 1780 T; 22 other; agagtatggg atggaggagt ccagaggagt ttcgaaaggt ggtaagtgtt ggtttgcagt 60 ggaatctaag acattcgaaa tctccattga agaggtccga ggtaaactga gagggactat 120 tttggaaagg agcaaaggct tctcctcttg gataagattt ggagaaaaaa gcttaagtct 180 atctgttgga aggtgtggaa gcttggtgtg gtgcagagga gagtcaagct cgaggcgtct 240 aaaagtttgg gaagaaggag gaagaaaatt taggctggag tgtcgttcta atgaagctgg 300 taggtttttg ctctgctcgg tgagagatgt ggaagctaag aagttttgtc tagtttttcc 360 agaaggaaaa ggcttagtag gggggtggtt yttgttggct aagaagttaa gggcccttgg 420 agtctccact ccagctgtga gcaaaggtag cttccagggt gcttccaacc tctgaaaagg 480 akgggtgtag tgtcaaaggg aaagagaaag ggacaggttc gtatgcagaa gtcgtgaaag 540 ggaagacagg ggaatcaggg gattctttat gggtgcatgt aggggatcgg gaactgcttt 600 gtagggaaga gcagcttagt cgttgcctgg ttggwtgttt tggtgatagt tttgagtctg 660 ttcctccttt gtcttccttg aaggggtggg cgtatgaaag ttggtttctk aaggggggtt 720 taaaaatttc caggttgggt ggggcccttg tgttgtttga gtttgaaaat aaatgggaag 780 ctgatatggt gcttttaagg gggagcagac gttttaagga gagagagttt ctcttgcaaa 840 gatggggacc tgaagtgggg tgtttttgga atgagagcca tgctaaggaa gtttgggtga 900 gagttgtagg acttcctctt cacctttgga gtagagaggt gttcaagagt attggagaga 960 gttgtggggg gtttgtagct gtggatgagg aaacagcttt cttctctcag ttgcagtggg 1020 ctcggatctt ggtgagagct tctgggaaga attggccagg gtctttgcag gtggtggctg 1080 gkaattcttg ttgggcggtt agtctgtggt gggaagcccc cccgtgggtg tcgcaggtag 1140 tgtcaaggtc ctggttgcag aagagaaatg ggcgggaggt tagggatgaa ggtgggggtg 1200 gtctcacgcg ctggtgttag cgtgcgggag cttcaaattg atattcaaaa aagggggtca 1260 gaagtgcagg ttgagtgtgg cagaaggcat agggatgcag mcggtgcagg gggtaggcwg 1320 actagtagct cctgtagtgg gctctttcag cgagtgggcc tgggcccagg acagctagtt 1380 gggaggcttt aaaaggaaaa ggtgggatgg gtttaagtgg tgaagcgggt tgggccgagg 1440 gcccatctcc cttcagccct gaggtggcgg gctggggtaa gggctctaag gggcctcttg 1500 ggcctwttat tmctgaggcc catttgggyc tttttgggga gcccttcctc ttctagggct 1560 ccccctgagc ccgtcggggg ctytgcgggg mtggagcagg agctcctggc cgtggaaggt 1620 gccgacgccg kggagtcgtc tctcggccgt ctgaagctca ccgacgaggc gctgttggag 1680 gaagcttcca ggtatcccgt taatcacaaa ctctcttttt tctctttggg gcttcgggtt 1740 tcttcttctt cttctccttt cttggggscc gatgatgttg tggtggggaa ggagggggtt 1800 tccagtgggt tgtttggggc agtggaaggg gcgatgrgca gggttcckct gcgtgaagag 1860 tggattgaag atttttcggc cctcgaaggt tggaacgagc ctccttgggc ttcgggtggc 1920 ggtgmaagtg ggactgagct agcaattgtc ccagttggat cggattttgc gagtccatta 1980 gtggaaasga tggcctttca gctggaagag ggggagggag atgaagggtg gagctccagc 2040 tgccttgcga agttcagtcg ctgcttgggt atgccgacag aagggtttga agaggaaatt 2100 ttgtacctct tgaggagaat gaaggggaga attgaacaaa agagtcagga cggggcgact 2160 agaaagacga agtcawcgtc ttcaaaatcc agtagggaac tcaagaagct ggagtggaca 2220 gtaagctata aaaaagctaa ggtgggttct agcgccaatg taggtatttt tggaggggct 2280 tctggatcag ggtgtaaatg aagataagaa ttttatcatg gaatgttaga ggggcaaatg 2340 atagtgataa aaggaagatc attaagtcag tcataaaatc ccaaagagtg gacgtggttt 2400 gtttgcagga aactaaaatt aaagaaatga ctacggggct tgttcgtagt cttggggtgg 2460 gaagacatct agactggaga gcagtcaatt ctaggggtgc agctggaggt attctggtgt 2520 tttgggacaa cagagtggtt gagttggttg agttggaaga aggggtkttc tcaatttcgt 2580 gtcggttcaa gaattgtgtg gatgggatga tgtgggtgtt cactggtgtg tatgggccgg 2640 tgtgcagtag ggatagagag gatttttggg aggagcttgg gtcaataaaa ggtttatgga 2700 gtgacccttg gtgtgtggga ggaggatttc aatatggtaa gatttccaga ggagcgtagt 2760 aggggaggtg ggttttctgc ttcaatgagg agattttcag aagtggtaga ggatttggag 2820 ctaagggact ttcctttaca ggggggtcct tttacttgga gaggcgggtt gaataaccag 2880 tcccagtcta ggcttgacag gtttttagtg acagataact gggacagcat gttcaatggg 2940 gctgtgcagg ggaattcttc ctagaccagt ctctgatcac tttcccatcc tcctagaagg 3000 aggaggtttg aagaggggtc cttccccttt cagatttgag aatatgtggt tggaggaaga 3060 ggggttcaaa gatcagatga agaggtggtg ggggagttta aattttactg ggactttcag 3120 ctttgtttta gatgcaaaat tgagagcctt aaaagatatt ttaaagactt ggaataaaga 3180 agtgtttggt ctcattgaga ctaaaaagag agaagctctt agccaggttg tgtattggga 3240 tgaaaaggag aaatattcag ctttgaatct ggaagattgt gaagcaagaa aggaggctag 3300 ggagtcttat aagacttggg tgttgaggga agaaatttct tggagacaga agtctaggga 3360 attgtggttg aaggaggggg acaataatac cagattcttt cataggatgg cgaatgctca 3420 tagtagaaga aactggttgt ccaagttgaa agtgaatggt tgttggcata cggaggagaa 3480 tgatttaaaa aatagtgtgg tgggggcgtt tcaaaagctg tattcagaag aaggggggtg 3540 gcgtccttgt attgaggggt tgtcctttat ggggttagat agcagtgagg ctgaggggct 3600 ggagattcct ttttcggaag aagaggtgtt tgcagctctt tcagatctag gcaaggacaa 3660 agcccccggt ccggatggct ttaccatggc tttttggctt ttttgttggg atgtggtgaa 3720 ggttgagatt atgggttttt ttagagaatt tcatgagagg ggcagatttg taaaatctct 3780 aaatgcaact ttcctggttt tagtcccaaa gaagggaggt gcagaagatt tgaaagattt 3840 caggccgatt agccttgtgg gcagccttta caagttgttg gccaaggtgt tggcaaatag 3900 aattaaaaag gttatgggga aagtgatttc ggagtcccaa aatgcctttg tggagggtag 3960 acagatttta gatgcagttt tgattgcaaa tgaggctgtg gactcaaggt tgaaaagcaa 4020 tgaaggaggt gtgttgtgca agttggatat agagaaggct tatgatcatg ttagctggaa 4080 gttcttgttg gcagtgctta aaaagatggg ctttggggag agatggataa agtggataga 4140 ttggtgcatc tctactgtga aattttctgt tttaataaat ggttctcctt ccggtttttt 4200 ccaaagttcg agggggttga gacaaggaga tcccctctcc ccttatttgt ttgtgatagc 4260 catggaggtg tttagttgtt tgttgagaag ggctattagt gggggcttct tatctgggtg 4320 gagggtgaga ggtaggagtg gtgaggggat tctaatatcg cacttgttat ttgcggatga 4380 tacgttggtg ttttgtgagg agtctcaaga ccagatgact tatctaagtt ggcttctcat 4440 gtggtttgag gcttgttcag ggttgagaat taacttggag aagagtgagt tgatcccggt 4500 gggaagggtg catgatatag aggatttggc cttggagttg gggtgtaaag tgggtggtct 4560 cccttcctgt tatttgggtc tgccttttgg gggcaccttt caaatcagtg gcggtgtggg 4620 atggggttga agagcgtttt cgaaaaaggc ttgctatgtg gaagagacag tatatatcaa 4680 aaggaggaag actcacccta attcgaagca ctctgtctag catgcctatt tacttcatgt 4740 ctctctttta tttgccaaga aaagtgaggt tgagattgga gaagattcag agggattttc 4800 tgtggggtgg gggagctctt gtccagaagc cacatcttgt taggtggaac ttggtttgct 4860 tggaaaaaag gaaaggtggt ttaggtgtga gaaatttagc tttgatgaat aaagctctct 4920 tgtgtaagtg gaattggcgg tttgccaatg aaagagaggc tttgtggaag caagtaatya 4980 gtcacaagta tggtgtagag gaggggggat ggtgtactcg ggatgtaagt gggagaaatg 5040 gtgttgggct ttggaaagca attaggaagg agtggttgtt tttggatggc aggttagcct 5100 accatgtggg taatgggcag agagtgagat tctggaagga caagtggtgt ggagatgagc 5160 ctctttgtga gtccttccct tctttatttt ccatttcctt gtctaaggat gcttgggttt 5220 cggatgtttg gaacccagat ggtgatgggg atggttggac ccctcttttc tcaagggcgt 5280 ttaatgattg ggagattgag ttggtggagc gttttttgca raagatccaa gcctttaggg 5340 tgcaaaggga ggaggaagat agagtgatat ggacagcttc aaagagtggg gctttctcag 5400 tcaagtctct ttattctatt ttggagcccg gaggttcttc tttgttccct agtgatagta 5460 tttggagggc aagtgtgcct cctaaggtag ctttctttgc ttgggaggct tcttggggta 5520 aagtcttaac tttggagcaa cttcaaagga gggggtactc tttggcaaat aggtgttttc 5580 tttgtctatc tgaagcagaa acggtggatc accttttact tcattgtgtt aagacgcggg 5640 tcctatggaa tcttcttttc tccctttttg gtgtgtcttg gattctctct tgttcagtga 5700 aggaaactct tcttgggtgg catggagcgt ttgtggggaa aactcgtaaa aaggcttggc 5760 aaatggcccc cttatgtata ttttggtcag tttggaagga aagaaatttg ttagcttttg 5820 ggaatgagga gttttcgctt caaaggttga aatattcttt tgtatgtaat ctttggtctt 5880 gggttagggt gtctatagtt ttgagccctt cttctcttgt aagttttttt gactggctag 5940 gctctaagta agggaaggtg gtgggcttct tttgtatact ccctgtatac ttagagggca 6000 ctggtttttg gtgtttcctc ttttcgttta atatacttct ttttcactta tcaaaaaaaa 6060 aaa 6063 // ID BoSB13 repbase; DNA; EDCOT; 225 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB13. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-225 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 225 BP; 42 A; 60 C; 69 G; 54 T; 0 other; caactcgagt tggcctagtg gtacttgagg gagcttcggc cccgatacgg tcccgggttc 60 gattcgcgtt ggccacgagg ggttttacat gggctgcctc tcgccctcca gaccacttcg 120 cgtaaccagg ggccctttag tggacgctta aaaatcctgt aatggcatgg gcttaggccc 180 ggtgggctag tcgatcacgc aaaagtggtc ggatactgga ttatc 225 // ID Copia17-PTR_I repbase; DNA; EDCOT; 4535 BP. XX AC LG_X; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia17-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4535 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4535 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 206-206 (2007). XX DR Genome; LG_X; Positions 4562950 4558416. XX CC Positions [1762-2061] - Integrase core CC 'CATCT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 46..2061 FT /product="Copia17-PTR_I_1p" FT /translation="MAAAGQSSLSEVTSQPGTASHGSLSGGTEGTSHQITR FT HKLNGYNYLQWSSSIMMFICGKGRDDYLTGDIIIPEKNDPMFRTWKTENHM FT VISWLINSMTNEIGENFLLYGTAKEIWEATIETYSSSENTSELFEIEAVLH FT DLHQGELSITQYFNILCRHWQHLDMFEIHSWNCPEDTVLYRRIVEQKRTFK FT FLLGLNKNLDEVRGRIMGTKPLPNLREAFSEVRREESRKKVMMGPHNSAHI FT MEGSALTARGYSNSNYYNRQRKGRPWCDHCNKPGHVKENCWKIHGKPADWK FT PSKSINDKDRRANNVISDNNRDKNTILPTETSPFSKEQLEILQKLFNQNSL FT SQPSMSTSGSGSGLSAQKGKFSAALTVSKKHSSPWIIDSGASDHMTRDATL FT LNEYNQCTNNSTVRIADGSSSQVKGIGLSRLSRDMILNSILHVPNLDCNLL FT SISKLTRDLNCVAKFFPHLCIFQDLDTGKKIGSAKMCSGLYLLKSEIPLKQ FT TQNRSYVSSKGQLALNFHVNKDSEVLLWHYRLGHPNSMYLEKLFPSFFSNK FT SSQSFKCEICQLSKNVRSSYPTISYKPSHPFAMIHSDIWGPSQVHNITGTQ FT WFVSFVDDHTRLTWLFLMKEKSEVSQIFQNFHAMIQTQFQTKIQILKTDNA FT KEYFNSSLNTYCLNQGIIHISSC" FT CDS 2816..4525 FT /product="Copia17-PTR_I_2p" FT /translation="METSDCENTAFVIDDSNIPIALRKGVRSCTSHPISKF FT VSYEGLSPTYHAFVSAIDSVQIPKSIEEALKDSGWRKAVSDEISALNKNRT FT WEISELPPGKKPVGCKWLFTIKHKVDGSIERLKARLVAKGFTQSYGIDYQE FT TFAPVAKLNTIRVLLSLAANQDWPLHQLDIKNAFLNGDLEEVYMEIPPGLE FT TSSNVNRVCRLKKSLYGLKQSPRAWFNRFTKTVAQYGYSQCQADHTLFVKT FT SPEKEIAILIVYVDDIILTGNYEEELVRLKKLLAKEFEIKDLGYLKYFLGM FT EVARSRKDIYVSQRKYVLDLLKETGMLGCKPADTPMDSTKKIGAENDSIPV FT DRGRYQRLVGRLIYLSHTRPDIGFAVSFVSQFMNNPTEDHMAAVNRILRYL FT KMTSGRGLLYKKCDNRIIEIYTDADWAGNIIDRRSTSGYCSYVWGNLVTWR FT SKKQHVVSRSSAESELRALALGICEGMWIQRLLKELGMESLTPIQMHCDNQ FT AAISIAKNPVHHDRTKHIEIDRHFITEKIEKNIVHLTYTPTRSQIADILTK FT ALPRTNFEELSHKLGMYNIYNPA" XX SQ Sequence 4535 BP; 1547 A; 965 C; 840 G; 1183 T; 0 other; tggtatcaga gcctactctt gaaccctaat ctgcttctct aaggcatggc agcagcagga 60 caaagctctc tctctgaggt gacctcacag ccaggaacag cctctcatgg tagcctttca 120 ggaggcactg aaggcacatc acaccaaatc acaagacaca aactcaatgg atataattat 180 cttcaatggt catcatcaat catgatgttt atttgtggaa agggcagaga tgactacctc 240 acaggggata tcatcatacc agaaaagaat gatcccatgt tccgaacatg gaaaactgaa 300 aatcatatgg taatatcatg gctgatcaat tcaatgacca atgaaattgg agaaaatttt 360 ctcctatatg gaacagcaaa ggaaatctgg gaagcaacaa tagaaaccta ctcaagttct 420 gaaaatacat cagaactatt tgagattgag gcagtgttac atgatctaca ccaaggagaa 480 ctttctatta ctcaatactt caacattctc tgccgtcatt ggcagcacct agatatgttt 540 gaaattcaca gctggaattg ccctgaagac acagtcctat atagaagaat tgttgagcag 600 aaaagaactt ttaaatttct tcttgggctc aacaagaacc ttgatgaagt cagaggaaga 660 ataatgggaa ccaaacctct tccaaatctc agagaagcat tctctgaggt tagacgtgaa 720 gaaagtagaa agaaagtaat gatgggacct cacaactcag ctcatataat ggaaggatct 780 gcccttactg ctcgaggcta ttcaaacagc aactattata accgacagag gaaaggaaga 840 ccctggtgtg atcactgcaa caaaccagga catgtcaagg aaaactgctg gaagattcat 900 ggcaaacctg ctgattggaa accatcaaaa tcaataaatg acaaagacag acgtgccaac 960 aatgttatct cagataacaa ccgagataag aacaccattc tgccaacaga aacaagtcct 1020 ttcagcaagg aacaacttga gatcttacag aaactcttca atcagaattc actgtctcaa 1080 ccaagtatgt caacctctgg ttctggatct ggtctgtcag cacaaaaagg taaattttca 1140 gcagccctta ctgttagtaa gaaacactca agcccttgga tcatcgactc cggagcatca 1200 gaccatatga caagagatgc cactcttctt aatgaataca atcagtgcac taataattct 1260 acagtccgta tagctgatgg gtcttcctcc caagtaaagg gaatagggct gagtagactc 1320 tcaagggaca tgatcctaaa ctctattctc catgttccta acctagactg caacctactc 1380 tcaattagca aattgactcg tgacttaaat tgtgttgcta aattctttcc tcatttgtgt 1440 atatttcagg atttggatac ggggaagaag attggcagtg ctaagatgtg ttctgggctt 1500 tatctcctca aaagtgagat tcctctaaag caaactcaaa acagaagcta tgtatcatcc 1560 aagggtcagt tagctttaaa ttttcatgtc aataaagata gtgaagtttt gttatggcac 1620 tatcgtcttg gtcatccaaa ctccatgtac cttgaaaagt tgtttccatc cttcttttcc 1680 aataaaagct cacaatcctt caaatgtgaa atatgtcaac tctctaaaaa tgttcgcagt 1740 agctatccca ccatttcata taaaccatca catccatttg caatgattca tagtgatata 1800 tggggcccct cacaagtgca caatataact ggaactcagt ggtttgtctc ctttgttgat 1860 gatcacacta gattgacttg gttattcctt atgaaagaaa aatctgaagt cagccaaatt 1920 ttccaaaact tccatgccat gatacaaacc caattccaga ctaaaatcca aatcctaaaa 1980 actgataatg ccaaagaata tttcaattct agccttaata cttattgtct aaatcaaggc 2040 attatccata taagctcgtg ttaacactcc acaacaaaat ggagtggctg aaaggaagaa 2100 tagacatctg ttggaagttg ctagatccct tatgctctct actcatgtgc caaaacaatt 2160 ctgaggagaa gctatactca cagcaaccta tctcatcaac agaatgcctt ccagagttct 2220 aaacttcaga actcccagcc aagtccttct acaagccttt ccacacacca aactactctc 2280 ttccttagac cctaaagtat ttggctgctc agtgtttgtt catatacacc atagagaaaa 2340 attagaccct acctctctca agtgcatttt tataggatac tctccacacc aaaagggtta 2400 taaatattac tctcctgttc tcaaaaagga ctatacctct atggatgtca cattttttga 2460 acaccaagta tactatccca agtctgatct tcacggggca accatgagag aatatcagaa 2520 ttgggatata caatctaatc atgtaattaa ctcaggagac aaccaataga gtcttgtcca 2580 aagtcatttg agtccttaca ctacacctcc agcctcaatc caatcagtcc cagcaccacc 2640 agcctcagtc caatctcctg accagattca tcctacacca aaacagatca caaatcatga 2700 gcttcttact tattctagaa ggaaaaaact tggaaaggag atagagcaca caatacctct 2760 tgcacatgac caagattcag aaccaagtcc agattctgcc ccgatatact caagtatgga 2820 aacttctgac tgtgagaata ctgcctttgt tattgatgat tcaaatattc caattgcttt 2880 gagaaagggt gttagatcat gcacaagtca tcccatcagc aaatttgttt catatgaagg 2940 gttatcacca acctatcatg catttgtttc agccattgac agtgtacaga ttcctaagtc 3000 tattgaagaa gctctcaaag attcagggtg gagaaaggca gtgagtgatg aaatcagtgc 3060 cttaaacaag aatagaactt gggaaatttc tgaacttcca cctggaaaga aaccagttgg 3120 gtgtaaatgg ttatttacta tcaaacataa ggttgatgga agtattgaaa ggttaaaagc 3180 tcgtctggtt gcaaaagggt ttactcagtc ctatggaata gattatcaag aaacatttgc 3240 tccagtggcc aaacttaata caatcagagt gcttctatcc ctagcagcta accaagactg 3300 gccattacat caactagaca tcaaaaatgc tttccttaat ggagacttgg aagaagtata 3360 catggagatt cctccaggac tagaaacatc ctccaatgtc aacagagtat gcagactgaa 3420 aaaatcacta tatggactca agcaatcccc tcgagcatgg tttaacagat ttacaaagac 3480 agtagcacag tatggatatt cccaatgcca agcagaccac acactgtttg taaaaacctc 3540 cccagaaaag gaaatagcaa tcctaatagt atatgtggat gacatcatct taactgggaa 3600 ttatgaggaa gaactggtga gactgaagaa actcttagcc aaggaatttg agatcaaaga 3660 ccttgggtat ctcaaatact tccttggcat ggaagtggca aggtcaagaa aagatatata 3720 tgtttctcaa cgaaaatatg tcttggatct gctaaaagaa acaggaatgc ttggatgcaa 3780 acctgcagac actccaatgg attcaacaaa gaagatagga gcagaaaatg atagtatacc 3840 agtggatagg gggagatatc aaagacttgt gggtcgactc atctatctct cacataccag 3900 acctgatatt ggctttgcag tcagttttgt aagccaattc atgaacaacc cgacagaaga 3960 tcatatggca gcagttaata gaatcttgag gtacctaaaa atgacttctg gtagaggcct 4020 tctatacaag aaatgtgaca acagaattat tgaaatctac acagatgcag actgggcagg 4080 aaacattata gataggagat ctacttctgg atattgctcc tatgtttggg gaaatctagt 4140 aacttggaga agcaagaaac aacatgtggt atctagaagc agtgcagaat ctgagctgag 4200 agctctagct cttggtatct gtgaagggat gtggatacaa agattactta aagaacttgg 4260 catggaatca ttgacaccta tccagatgca ttgtgataat caagcagcca taagcatagc 4320 aaagaatcca gttcatcatg acaggacaaa gcacattgaa atagatcgac acttcatcac 4380 agaaaagatt gagaagaaca ttgttcacct tacctacact ccaacaagat ctcagattgc 4440 agacatcctc accaaagctc taccaagaac taattttgaa gaattgagtc acaagctggg 4500 catgtataac atatacaacc cagcttgagg gggag 4535 // ID SHACOP12_I_MT repbase; DNA; EDCOT; 4616 BP. XX AC CR931729; XX DT 24-JAN-2007 (Rel. 12.01, Created) DT 24-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP12_MT, from barrel DE medic. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Internal; Interspersed; terminal; repeat; ORF; SHACOP12_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4616 RA Shankar R. and Jurka J.; RT "SHACOP12_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 53-53 (2007). XX DR EMBL/GenBank/DDBJ; CR931729; Positions 80700 85315. XX CC This element has just two intact full length exact copies in the CC genome. It has conserved a single frame ORF having intact domains CC for gag-int-pol as well as peptidase and CCHC zinc finger motif. XX FH Key Location/Qualifiers FT CDS 149..4615 FT /product="SHACOP12_I_MT_1p" FT /translation="MENPPFFDFATNPSNPYYLHPNENPSLVLVTPSLDNK FT NYQTWSRSMRVALISKNKLKFVDGTLNPPPVSDLLHEPWLRCNNMVLSWLQ FT RCISETIVKSIIWCDRASVVWKRLENRFAQGDIFRVADILEELAKFQQGNL FT DISSYFTQLTTLWEEIQNFRPIRDCTCAIPCTCGVASDLKKYNEQDKVIKF FT LKGLNEQYAHVRSQIMLINPLPELDKTFSLVLQQERQTHIPVFGEIPVDQQ FT STVNQVQQTNSNKGFARGGSSSYRGRGKGSYNGTRGQNQGITRTCSHCGRH FT NHTIETCFLLHGYPPGYQNKGPKSANLAVSEQKYTDAVQNQGSVSSPSLNS FT IHEQYNQILQLLQHSNLQASTSNTNATMPQPAVNSVISLPAAYTSTSTPII FT GKKSTLWVIDSGATDHITHCLQNFSSFYNIPPISMSLPNGNKIVTTIAGTI FT SLSNSLILHNVYYIPDFNINLFSISQFLKTSNASFLFSIDTCSIVQILNQR FT VIGTAKKFGGLYVLDSSLLNKSQNNGLVSASICNSVFPSLSSKSTDSANVW FT HYRLGHISDSIHKCISIQFPIVKYTSTHSPCDICHYAKHKKTSFPHSLIHS FT TQIFDILHVDIWGPYATPSVSEFKYFLTLVDDFSRFTWVIFMKCKGETRNH FT LMNFISFIDTQFHKKLKCLRSDNGLEFIMPSFYLSKGIIHQRSCVETPQQN FT GIVERKHQHILNVARALSFQSHIPTNFWHFSIQQAVHIINRIPTPLLQNKS FT PYECLHQQQPSLIHLKVFGCLAFASTIQSHRTKFDSRARKSVFLGYREGTK FT GYLLYDLHSHEFFLSRNVIFHESSFPFSTLHERCSPDSSTPHVSVDNSHLS FT SYHEPIQSSVIPNSSFPLSQNLDNSDTSTTHNSTPPNATSSATAIPDQTTT FT DVPIRRSARPKTTPAYLKDYHCSLLTSSESQLLSDSGKSAYPLSSVLTYDH FT CTPSYKKFCLTVSYNPEPKTYNQACKIECWKEAMKDELHALAATNTWSIVD FT LPPGKVPIGCKWVYKTKYHSDGSLERHKARLVAKGYTQMEGVDYFDTFSPV FT AKMTTVRTLLSLAAIKGWFLEQLDVNNAFLHGDLNEEVYMVLPPGLKLQNS FT DSNDLKVCRLNKSLYGLKQASRQWYAKLSAALVSLGYTPSVADSSLFTKLK FT GTNFTALLVYVDDIVLSGNDYAEIQHVKQFLDQKFRIKDLGKLRFFLGLEI FT ARSNKGISVNQRKYTLELLEDSGHMAVKPSSTPYDTSLKLHNSDSPPYHDE FT FSFRSLIGRLLYLTLTRPDIAFAVQQLSQFVSKPREVHFQAATKILKYLKN FT SPAKGLFYSSSSPVKLAGFADSDWASCPSTRRSVSGFCVFLGSSLISWKSK FT KQTTVSRSSSESEYRALASLTCELQWLSYLFKDLHINFQQPASVYCDNKSA FT IYLAHNPTFHERTKHIEIDCHVVRERIQSGLIHLFPVPSSSQIADLLTKPL FT LSPAFNSLVSKLSLCDLHSPACGG" XX SQ Sequence 4616 BP; 1304 A; 1002 C; 733 G; 1577 T; 0 other; ggtatcagtt gtgaatctct tcatcaattt ctcttgttga tcgattcatc tcaagaatcc 60 tctttattat tcaatttctg aatttttatt ttcagttttc attccgctgt tcatttgatt 120 ccttgattat ttgatttctt tcatctctat ggagaatcca ccattttttg attttgcaac 180 caatccttca aatccttact acttgcatcc taatgaaaat ccatcacttg ttcttgttac 240 tccatcattg gataacaaga attaccagac ttggtcgcga tctatgcggg tcgccttaat 300 ttccaagaac aaattgaaat ttgttgatgg caccctaaat cctcctcctg tttcagatct 360 ccttcatgaa ccatggttaa gatgtaacaa catggttctg tcttggcttc aacgatgtat 420 ttctgaaacc attgtgaaat caatcatttg gtgtgatcga gcctccgtgg tttggaagcg 480 attggagaac cgttttgcac agggtgatat tttcagagtt gctgatattc ttgaggaatt 540 ggctaaattt caacaaggta atcttgatat ctcctcctat tttacacaat taaccacttt 600 gtgggaagaa attcagaact tccggccaat tcgtgattgc acttgtgcca tcccttgcac 660 ttgtggtgtt gcttctgatc tcaaaaagta taatgagcaa gacaaagtaa ttaagttttt 720 gaaaggtttg aatgagcaat atgcacatgt gcgctctcag attatgctaa ttaatccttt 780 gcctgaactg gataagactt tttctcttgt acttcaacaa gaaagacaaa cacatattcc 840 tgtttttggt gaaattcctg ttgatcaaca atcaactgtt aatcaagttc agcaaaccaa 900 ttctaacaaa ggttttgctc gtggtggttc ttctagctat agaggtcgag gtaaaggatc 960 ttataatgga acaagaggac agaatcaagg cattactcgc acttgtagtc attgtggaag 1020 acataatcat acaattgaga cttgtttcct tctccatggc tatcctcctg gttatcaaaa 1080 caaaggtcct aagtcagcga atcttgcggt ttctgaacaa aagtatactg atgctgtcca 1140 gaaccaagga tctgttagca gcccttcact gaattctatc catgagcaat ataatcagat 1200 tttgcagctt ctacaacatt caaatttgca agcttcaacg tcaaacacca atgctactat 1260 gcctcagcct gctgtcaatt cagttatctc acttcccgca gcttatactt ccacatccac 1320 tcccataatc ggtaagaaat ctactctttg ggtcatagac tcaggagcaa ctgatcatat 1380 cactcactgt ttgcaaaatt tttcttcttt ctacaacatt ccacctatct ccatgtcact 1440 accaaatggt aataaaatag tgacaaccat agcaggcaca atatccttat ccaattcact 1500 tatccttcat aatgtttact acattcctga tttcaacatc aatttatttt caatatctca 1560 atttttgaaa acttctaatg ccagtttctt gttttctatt gatacatgtt ctattgtgca 1620 gattttgaat cagagagtga ttggtacagc taagaagttt ggaggactgt atgtgttgga 1680 ttcttcactg ctaaataaat ctcaaaataa tggtttagtt tctgcttcaa tttgtaattc 1740 tgtttttcca agtttgtcgt ctaagtcaac tgattctgca aacgtttggc attatagatt 1800 gggtcacatt tcggattcca tacacaaatg tatttccatt cagtttccca ttgtaaaata 1860 caccagtacc cactctcctt gtgatatatg ccattatgca aaacataaga aaacatcatt 1920 tcctcatagt cttattcatt ccactcaaat atttgatata ctacatgttg atatttgggg 1980 accctatgct accccttctg tttccgaatt taaatatttt ttaaccttgg ttgatgactt 2040 tagtagattt acatgggtca tttttatgaa atgtaaaggt gaaacaagaa atcatctcat 2100 gaatttcatt tctttcattg atactcaatt ccataagaaa cttaaatgct tgagaagtga 2160 taatggactt gagttcatca tgccttcatt ttatctttct aaaggcatca ttcatcaaag 2220 gtcttgtgtt gagactcctc aacaaaatgg tattgtagaa aggaagcatc aacatatcct 2280 taatgtggct cgagccctct cctttcaatc tcatatccct accaattttt ggcatttttc 2340 aattcaacaa gctgtccata tcattaatcg aatcccaact ccccttctac aaaataaatc 2400 cccatatgaa tgtcttcacc aacaacaacc ttctttaatt cacctaaaag tcttcggttg 2460 ccttgctttt gcctccacca tccaaagtca tagaaccaaa tttgattcta gagcaagaaa 2520 atcagttttt cttggatata gagaaggcac caagggttac cttctttatg atcttcattc 2580 acatgaattt ttcttatcaa gaaatgtcat ctttcatgaa tcatcttttc cattttctac 2640 attgcatgaa cgatgttccc ctgattcctc tacacctcat gtctccgttg ataattcaca 2700 tctttcttcc tatcatgaac ccatccaatc atctgttatt ccaaattctt cttttcctct 2760 ctctcaaaac cttgataatt ctgatacttc tacaacacat aattctaccc ctcctaatgc 2820 tacatcttct gcaacagcta ttccagatca gaccacaaca gatgtaccta ttcgacgatc 2880 tgcacgacct aaaacaacac cggcatatct taaagactat cactgcagtc tccttacttc 2940 ttctgaatca caattactct ctgactcagg taaatcggca tatcctctct cttctgtttt 3000 gacatatgat cattgcactc cttcatataa aaaattttgt ctaactgttt cttataaccc 3060 tgaacctaag acctataatc aagcttgtaa gattgaatgt tggaaagaag ctatgaaaga 3120 tgagttacat gctcttgcag ccacaaatac ttggtcaatt gttgatttac caccaggaaa 3180 agttccaatt ggatgcaagt gggtttacaa aactaaatac cactctgatg gttctcttga 3240 aaggcataaa gcccggttag ttgcaaaggg ttatactcaa atggaaggag ttgattactt 3300 tgatactttt tcaccggttg caaaaatgac tacagttaga acattacttt ctttggcagc 3360 catcaaaggg tggtttcttg agcaacttga tgtcaataat gcatttctcc atggtgacct 3420 caatgaagaa gtttacatgg tgttaccccc tggtctgaag cttcaaaatt cagattctaa 3480 tgatcttaaa gtttgtcggt taaataagag tctctatggc ttgaagcaag ctagtaggca 3540 atggtatgcc aaactttctg cagcgttggt ttctctcgga tacactcctt ctgttgctga 3600 ttcttctttg ttcactaagc taaaaggtac caattttact gccttattag tttatgtgga 3660 cgacatagtt ttatcaggaa atgattatgc tgaaattcag catgttaagc agtttttgga 3720 tcaaaaattt cgcatcaaag accttgggaa gctaagattt tttcttggct tggaaatagc 3780 aagatcaaac aaaggaattt cggtgaatca acgcaaatat actcttgagc ttcttgaaga 3840 tagtggtcac atggctgtta agcctagttc cactccctat gatacctcct taaagttgca 3900 taattctgat tcccctccat atcatgatga attctccttc agaagtttga ttggtagact 3960 tctctatttg acactcacgc ggcctgacat tgcttttgct gttcaacaac ttagtcaatt 4020 tgtttccaag ccccgtgaag tccactttca agctgctaca aagattctga agtatctcaa 4080 gaactctcca gccaaagggt tattctattc atcttcatct cccgtcaaac ttgcaggttt 4140 tgctgattca gattgggcta gctgtccctc tactagacga tctgtctccg gtttttgtgt 4200 gtttcttggc tcttccctca tctcatggaa gtctaagaag caaacaactg tttctagatc 4260 cagctctgaa tctgagtata gagccttggc cagccttact tgtgaattac aatggctctc 4320 ctatttgttc aaggatcttc atatcaactt tcaacaacca gcttcagtat attgtgacaa 4380 taaatcagcc atatatcttg ctcataatcc aacatttcat gagagaacaa aacacattga 4440 gattgattgt catgttgtgc gcgaaagaat tcaaagtggt ctcattcatc tctttcccgt 4500 gccatcttct tctcaaatag cagatttgtt gacaaaacca cttctgtctc cagctttcaa 4560 ttccttggtt tccaagctta gcctatgtga tcttcatagt ccagcttgtg ggggga 4616 // ID Gypsy-42_Mad-I repbase; DNA; EDCOT; 11574 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-42_Mad-I. XX NM Gypsy-42_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-11574 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1778-1778 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 2975..3997 FT /product="Gypsy-42_Mad-I_1p" FT /translation="MPESPIRSEPVRRRKDKTKPQHRASPRTTTERNRSSG FT HTTGTIPDEAKMIRPRMLKSKIPRSITRKTKTTTRWALRSSTTWKSAWSMS FT YLLNFSQPRPNQISWMATWLPRKQHKSILSPPKRRASSKEDKLKAALAELF FT PRSSSVNLHHLKPLYVTAHIEGYPVSKIFVDCGATVNIMPVSIMKALRRSN FT DELIPSGITMSSFVGDKSQTKGVLPLEVNIAGRNHMTAFFIVDSKTEYNAL FT LGRDWIHQTSCIPSSLYQVLIFWDGKSVVVHPADNQPFEANMIQARYYDDH FT VGYITLQGFNEEGRPTRISVQKAIEVGAETVHQDSARLGLADLITDPDV" FT CDS join(4281..5168,4961..5953,6086..7354) FT /product="Gypsy-42_Mad-I_2p" FT /translation="MKTELCKLLNEFKDCFAWSYHEMPGLDRTLVEHELRI FT KPGCKPFRQPPRRFSTEVQLGIKDELVRLLKAGFIRTARYVEWLANIVPVL FT KKSGALRICIDFRNLNLATPKDEYPMPISDLLIDAAANHEMLSFMDGHAGY FT NQIFIAEADVHKTAFRCPGALGTYEWVVMPFGLKNAGATYQRAMNTIFHDL FT IGTIIEVYIDDVVVKSKRRRTHLDDLRQAFLRMRQHNLKMNPPNALSAYRP FT ATSWVSLYIIVVSRWTKIRLEQSSTLHPRRPRSNYSLYSARLIFSAVSLLI FT RQEKPQNEPAKCAFGVSAGNFLGFLVHHRGIEVDENKARAIIDAPPPTTKK FT QLQSLLGKINFLRRFIANSAGKMKAFSTLLKLKDSDKFEWREEHQEAFTQI FT KVSLTTPPVLVPPRRGKPLKLYISAAEESIGCLLAQDNDVGREQAIFYLSR FT NLNSPEINYSAVEKLCLALFFAASKLRHYMLPSVTQVIAQTDVIRYMLTRP FT IVKGRIGKWTMALSEFSLQYVPQKAVKGQALADFLAQHPSPYGFGGNDVEI FT GMVETRDNYWTMYFDGSSTSASAGVGIVIQSPNHHRWYFSLKLDFDCTNNQ FT AEYEALIIGLSVLHDLRAARVLILGDSNLRDELAQIASGAQLLGGKLGRAI FT PVVRRPHPALVNQQVLQHDCVIRTRVMSLPSLLEREDPVDVCAVETLPDDW FT RRSIMRYLDNPSDKHDRRTRVHATNYVLYQNELYRKGEDGLLLLCLGPQEA FT AQAIAEVHEGICGAHQSGRKMRWLLRRHGYFWPSILKDCIEYARGCVQCQI FT HGPIQRVPAELLHSVTKPWPFRGWAMDVIGKITPSSGAAKHAWILVATDYF FT TKWVEAKSYAELTSKEVCNFVEENIVTRFGVPETIITDNGTIFTSDRFKEY FT TANLKIRLEQSTPYYPQANGQAEASNKVLIGILEKMIKEKPGMWHLKLNEA FT LWAYRTSLRSATGTTPYALTYGHDAMLPVELSINSLRVIEQSSLFSAEYNQ FT AMRQELEDLEEARLDAYNLLVAQKKIAERAYNQRVRQKTFGEGS" FT CDS join(10997..10602,10609..9674,9833..8823) FT /product="Gypsy-42_Mad-I_3p" FT /translation="MAANTFITKLIEECNKCQNITDRNTIKTIRFEDEPNV FT SHQTLGPLFKDDVPEAIIEMLKEHCLKPLFQGYDWSKWESAKPQGVWPSTT FT AAWAAWVTRMEPYFGDEWKALGIFDAIKLSTIEMNLDRELVMAAWLLKLLV FT LGHQHDGSSPRPPWPNGAGHHAILGTSPTGLPVDTSLSGYKFDLDLKTIFE FT ERAVEALTKGDQRPSKEDVQKLHKNFFNYNTLITHFAGSEGEDLKKGEHGA FT FLFYWYNKYIFCAKSNKCLAENMPVAEALASGHVLALSPAVLANLTRCLAE FT ATVGKIDPHQNGPLWVFQLWLQVYFSTLRPKSQASTLPKLMGLELASRPIP FT THSAEEIFKYFFGLEDLSDDEFQICRRRTYPSSIILPQSAWEEAEEADLRE FT SWGSFIMTRDLPYGCEARRGSWEVYHPNFLARQLGYLQGCPMPFLASRSFS FT SRVLGVIHHDSRPTLWLRSSARKLGSLPPQLPGSSTGLSPRVPHAIPCFSL FT LLSRERLSGSSERECEIAEKEFDERCAKFRLRPRTLESRCASTFAEWWDAY FT TKDFFSTPAEEISKKLFGDRPKKALAPKSKETAQGIYLLTFLVHLFSFELY FT LTQMFLGGRTIKRAEVVAMAAAKKKLAPPPKKAAAAAPTLPSKRLARKPKR FT QETLPGLKNASRNWPRKGSGRFTLSPAKPREQLLLVFLSLLLSSRPRPGTA FT DPMIEPAINPVVERLATSAPAAAHAEAGPVAATLEEATPSAEKNPPPNPKK FT TQRSSWKKRYKIYNVLLSKTPCLMTDPFFI" XX SQ Sequence 11574 BP; 3069 A; 2875 C; 2955 G; 2662 T; 13 other; tttttggcac gcccagtggg acccagtgct aaaactacga agttcatgac cattgagaca 60 cgatcggtta aaaagaaaac agtcatggga aagtcmacga ccaaccttcc agtccagaac 120 ccaggacaag atgacttgtc acaggcacag aatcctcctg ttgccgtgac acctgaggcc 180 acaagtgcga cacgccgaga aaaggaagtt tgtctcggcg gccagcctcg caatgcagaa 240 atccccaaca aaaccaaggg cgttttattg aagggatagt agaggactgc gatgaggatg 300 gtggtgaagg ctctgatcca ccaactaggt cgtttcttcg gagacgactt gaagagcaat 360 ctcggcatgt tcagccgaga agtaaaaagc atacttgagg wgatacgtag taatggtgat 420 acacacaaca gattgctcga actactggtt agtaaagcct acgaaggtgg acccgccgat 480 cgttcccgac aacttccacc caagaataat ccgttaccaa cgtacaggcc gagacaggat 540 ctgctcggct caaaatgatc gacttggaaa aaagaggagg atcaagcagc agatcagacg 600 gatccgacca gagagcagaa acaacatccg tcgatatggt cgaggtccaa agaatgatcg 660 attcggcctt gaaaaagggg ccgaagttcc caaaattcat ccatccatac ccagcttatg 720 tggaaaagtt tgaatatcct aaaggcttta aaatcccaga cttcagcctt tttgctggag 780 aatcgtccct gtcctcgtta gaacatgtgg ctcggttcac tgcgcaatgc ggagatgtta 840 atagtgactt ccataaactg cgactattca acttctcgtt gacgggctca gcattcgcgt 900 ggtacatcaa cctcccacct aactccatcc aaagttggga ggaactagtc gaaaagttcc 960 atgagcaatt ctatcggccg gggatggaaa tgtcagtttc ttcattggcc aggatggctc 1020 aagcatctga cgagtcacca atggaatacc ttacgaggtt taagtcggcc agaaactggt 1080 gccgagtacc tctccctgaa gtcgaattcg tcaggmtcgc tctgaacggc ctggatgtgg 1140 aatacaaaaa gaaattcctg ggggcaaact tccgagatat gtacgagctg gctcagcacg 1200 tcgagcaata tgattatttg ctccgagaag aaaagatctc gaagtcctca tcccgaggga 1260 cgatctacaa gaaccccacg gtcagttatg catcggccga aggcgaagat cccaatatgc 1320 cagtatagac gcggccgaga tagtgatcga taaaccgtat gtatgcaagg cattggctca 1380 cgccaattcc aaagatgcca aaacccgctc ggcctctgaa gagaccgtta aaacatcaaa 1440 agtttacact ttcgacatca ctaaggccga tgccatcttc gaccagttgc tgcttgcgaa 1500 aattatcaag cttcggccag gacataatat tcccaaggcc gaagagttga aagggaaaac 1560 gtattgcaag taccataact cgaacaagca tacgacaaac aactgcgtcg tgttccggat 1620 gccatccaaa gctggatcga taacggcaag ctcaagtttc ctgaaaagma aatgggcgtc 1680 gacaccgatc ccttccctac ggcgacagta agcatggtag atgctcgttt acccaaggat 1740 aaagggaaag ggaaggccga gttcgttcca atgcaacacg tcccaaagca gaactctcgg 1800 ccacgactca agattgattt attttcaaac gagccaccca aagatttttc aggaccagct 1860 attgtcgagt ccatgtcaga ctccagcgca gaggaaactg atgggccgat ggttttatgt 1920 agtcggtgca aagcaaacgt catcttaacc gagccaaaag agaaaccacc tcaggctcaa 1980 caccacgaca gccgcccacg gccgcgacga cacctcaaaa ggtgctcggc gcaggccaac 2040 gccagaaggt ktttgatagg cttggccctc aaacacgaat gacgagccac cctcagccag 2100 acggcgcctt gatttcgacg cgccgtttta taacgaggat tattatgcgc gcaactctag 2160 cagctcaagt tcatccgcga accagaaaac cttcaagcca cctgagccac gcgaccaacg 2220 ttggtatagc tacaattccc ctaccggcgt gtataccgcg ctatccaaat cgcagaaacg 2280 tcggcgccag cgaatagact gcatggctcg ccgacaagca gcccaggcta cctcggctac 2340 caaatggcag ccgaaagaaa cagcaggtaa tgaagatgac cgacaacccc cgacaatcat 2400 ggccgagtta cttcaaggga agaaggtgat cgatcgcgac tttgaaacca caattgaaga 2460 atccgagaag cgcatcaaac tccttcttcg gcccggggag atgaaagctc gtctcgagca 2520 cttcaggaag gaagccgaaa gcaaacttcc tccactaccc ccacaagagc cattaataaa 2580 agtccgacga aatctacacc cccattcctc ggcgaagcct tggagtacat gcgggagttt 2640 cacaagaagc attcgctaat gacttgtacg gcctaccaaa ggcgtgtcaa gagctcttga 2700 cctggcacta acttgccctg atgctgaaca gattatccaa aagaccactg atccggggat 2760 gaaggccagg ttccagcata tacgtgaagc tcgagtcctc ggcttcgagg tcgatccata 2820 tactgatata gacaccgccg agcttccttt ctctctcgag gacctccaat atttacgata 2880 ccatttcgaa gtcttctcag ccgttccctt ttcggcctta cgaccgatga gaaagaacgc 2940 gtggcacggt tagatgctta cctagacaca agggatgccc gaatcgccta tcaggagcga 3000 gcccgtaagg cgtcgcaagg acaagaccaa gccccaacac cgagcgagcc cgaggacgac 3060 gacagaacga aacaggtcca gtggacatac cacaggaaca atacccgatg aggcgaagat 3120 gatcaggccg aggatgctca aaagcaagat acctcgctcg ataacccgga agacgaagac 3180 cacgacccga tgggcccttc ggtcctcgac aacatggaaa tcagcatggt ccatgtctta 3240 cctgctgaat ttcagccaac cacgtcccaa ccaaatttct tggatggcga cgtggttgcc 3300 gaggaagcaa cacaagtcga ttttgtcgcc accgaagaga cgagcaagca gcaaagaaga 3360 caaactcaaa gcagctcttg ccgaactgtt tccccgctct tcctcggtta atctccatca 3420 tttgaagccg ttgtatgtta cggctcacat tgaaggatat ccagtctcca aaatcttcgt 3480 cgactgcgga gcaacggtca atatcatgcc cgtctccatc atgaaggcac tacgtcgctc 3540 taacgacgaa ctcattccat cagggatcac catgagcagc tttgtcggcg acaagtccca 3600 gaccaagggg gtgcttcctt tagaggtaaa tatcgcaggt cgcaatcaca tgaccgcgtt 3660 cttcatagtc gactcaaaga ccgagtataa tgcattgctc ggtcgggatt ggatccatca 3720 aacaagctgc atcccctcgt cattatatca agtcctcatc ttctgggatg gcaaatcggt 3780 cgtggttcat ccggccgaca atcagccgtt cgaagctaat atgattcagg cacgttacta 3840 cgatgatcac gtcggctaca tcaccttgca aggtttcaac gaggaaggac ggccgactcg 3900 gatttcagtt cagaaagcca tcgaggttgg cgccgagact gttcaccagg attcggcgag 3960 actcgggttg gctgacctca tcactgatcc cgatgtctga caccaaacag gacgaacgcc 4020 gggccgcggt ttcatctacc atggaacgac tgctggccca ctggtatact atttccaaac 4080 aaccgaattc gggcgtaaac ctcgtggagt ttctcgccga atgagacaat ggtccagtcc 4140 tttcacttga caaagtccaa gctgccccgg ccgagctcga agacagtcgg ccccaagtca 4200 aagacccatt agaggaaata aatgttggaa cggccgaaga ccctcgaccg ttatttatta 4260 gtgctttgtt accccaaccc atgaaaaccg aactttgtaa attactcaac gaatttaaag 4320 attgttttgc ttggagttac catgagatgc ctggtctaga tcgaaccctc gtcgagcatg 4380 aattacgcat caaacctggt tgtaaacctt tccgccaacc ccctcgacga ttctcgaccg 4440 aagtacaact cggcataaaa gatgaactcg ttcgactttt aaaagccggg tttattcgga 4500 cagctcgata cgtcgaatgg ttggcgaaca tcgtaccagt gttaaagaaa agtggtgctc 4560 tacgcatttg catcgatttt cgtaatttga atttggcaac ccccaaagat gaatatccaa 4620 tgccaatttc agatttgtta attgacgctg cagcaaacca tgagatgtta tccttcatgg 4680 atggccatgc tggctacaac cagatcttta tcgccgaggc cgatgtccac aaaactgcct 4740 ttcgttgccc gggggcactc gggacctacg aatgggtagt catgccattc ggccttaaaa 4800 acgctggtgc cacataccaa cgtgctatga ataccatctt tcatgacttg attggtacca 4860 tcatagaagt ctatatcgac gatgtggtag tcaaatcaaa gcgccgccga acacatttag 4920 atgatcttcg gcaggctttc cttcgtatgc gccaacataa cctcaaaatg aacccgccaa 4980 atgcgctttc ggcgtatcgg ccggcaactt cttgggtttc cttgtacatc atcgtggtat 5040 cgaggtggac gaaaataagg ctcgagcaat catcgacgct ccacccccga cgaccaagaa 5100 gcaactacag tctttactcg gcaagattaa ttttctccgc cgtttcattg ctaattcggc 5160 aggaaaaatg aaagcgttct ccacgctttt gaaactcaag gattctgaca aattcgaatg 5220 gcgtgaagaa catcaagagg ctttcacaca aatcaaggtc tccctcacaa ccccacccgt 5280 ccttgtgccg cctcggcgtg gcaaacctct caagctgtac atttcggcgg ccgaggaatc 5340 catcggttgc cttcttgcac aagacaacga tgttgggcgt gagcaggcca tcttttatct 5400 tagccgaaat ctcaactcac ctgagatcaa ttattcagcc gtcgagaagc tctgcctggc 5460 cttgtttttc gctgcgtcaa aactccggca ttacatgctc ccatcggtca ctcaggtcat 5520 cgcccagacc gatgttattc gttacatgct cactcggccg atagtaaaag gccgaattgg 5580 gaaatggaca atggcactgt ccgaattcag tttgcaatac gtgccccaga aagccgtcaa 5640 aggccaagca ctggccgatt tcttggccca acatccctct ccatatggtt tcgggggcaa 5700 tgacgtcgaa attggcatgg tggaaacacg tgataattat tggacgatgt actttgatgg 5760 ctctagtacc tcagcctcgg ctggcgttgg catcgtcatt caatccccaa atcaccaccg 5820 ctggtatttt tctctcaagc tcgatttcga ttgtacgaat aatcaggccg aatacgaagc 5880 ccttatcatc ggccttagcg tccttcatga cttgagggca gcccgcgtcc tcatcctcgg 5940 tgattcaaac ttgtgattaa ccaactcaat gggacttttc gttgcatgag ttgtactctg 6000 gcgccctatc acatggttgc cagctatttg gccgagtcgt tcgacggtat cacattcaaa 6060 cacatctcac ggttcgaaac actgacgcga cgaactggct caaatagcct ccggagcaca 6120 actcctgggg ggcaaactag gccgggcaat acctgtagta cgacgaccac acccggcctt 6180 ggttaatcag caagttctcc aacacgattg cgtgatccgt acacgagtca tgtccttacc 6240 ttcgttgttg gaacgagagg atcctgtaga tgtttgcgct gtcgagacat taccagacga 6300 ctggagaagg tcaattatgc gatatctcga taaccccagt gacaaacacg accgcaggac 6360 aagggtccat gccacaaatt atgtgttgta ccaaaatgag ttgtaccgga agggtgagga 6420 tggtttattg ttattatgcc tcggcccgca ggaggctgcc caagcaattg cagaagtaca 6480 cgaaggaatt tgcggggctc atcaatctgg acgaaagatg cgttggttgc ttcgtcgaca 6540 cggctatttc tggccgagta tattgaagga ttgtatcgag tacgcacgag gatgtgtaca 6600 atgtcaaatt catgggccta tacaaagagt cccggccgaa ttacttcact cggtcaccaa 6660 accatggccg ttcagaggat gggccatgga cgtaatcggc aaaattacac cgtcttccgg 6720 agcagcaaag catgcgtgga tacttgtggc gaccgactac ttcaccaaat gggtcgaagc 6780 aaagtcatac gccgagttaa cgtctaaaga agtttgtaat tttgtggaag aaaacatcgt 6840 gaccagattc ggcgtaccag aaacaatcat aactgacaac ggtacaatct ttacatccga 6900 caggttcaaa gagtatacgg cgaatttaaa aatccgactc gaacagtcca cgccgtatta 6960 cccacaagca aatggacagg ccgaagcaag taataaagtt ttgatcggca ttcttgaaaa 7020 aatgataaaa gaaaagcctg gtatgtggca tttgaagtta aacgaggctt tatgggcata 7080 tcggacttca ctccgatcag caacagggac gaccccatat gcgttaacct atgggcacga 7140 cgcgatgtta ccagtcgagc taagtataaa ctcgttgcga gtaattgaac aaagtagttt 7200 gttcagtgcc gaatacaatc aggccatgag acaagagtta gaagacttgg aggaagctcg 7260 gcttgatgct tataatttat tggtggcaca gaaaaagatt gccgagcgag cctataatca 7320 acgagtcaga caaaaaacgt tcggcgaagg gagttagttt ggcaaaccgt gttgcccgta 7380 ggaattaaag atcctagatt cgggaaatgg tcgccgaatt gggaaggacc gttcatcgtc 7440 cacaaagttc tcggcaakgg ggcataccac cttaaagatc gaaccggtct aattcataaa 7500 ctaccaatca atgggaaatt tttaaagaaa tactatccag tcacttggga gatgcgagaa 7560 taaaagttca tttcattaat tttgcaaaaa gggtgtacaa acagagctgg ccaaccaatt 7620 tacaactaaa caatcctaag gggtcgaagg aaggaaggct tcaagggcgg ccttcagctc 7680 caaccacctt acttcaccca ttgtgacttc ggcttgcctg ttcttttatc cakcttcagt 7740 tgctcaatct gcttcgcgcc agccgcgtak tctgtcaacg aggcttgctc gmctcaaaat 7800 ccttttcgag ctcgaagcaa cggccgacct ttgacgttgg agttcggcaa tttgatgatc 7860 gaggtcggcc agctgttctt tctttgcctt tatsgcctcg acctctggac gaakagcttc 7920 ttgagcaacc tttgcagcct taggtcgtct tcggcccgga gagccctctc gaaggtagca 7980 aagtattctc gggtccgctc caggatagaa gacaagcggg tgacatttcg gtgctcagca 8040 ggccaccggc tgcaaggtcg ttcaagcatt ctcctacaga gtcgaggcct ttgcgttcaa 8100 ggatttgtga ggccgagagg gataagagct cctgcagctt ggcgaaggca ttggactcgg 8160 ccgagtctgg cgtagcggca gaaggmccgg ccgccccaga agaactggaa aggagggcgt 8220 cgagctcgac ttcccatgaa ggctgcacat gaaaagatgt ttagaaaagt caagtcagaa 8280 aaatagcaaa aaaaggaaag tttgctctaa gacctgccga gaggagactt cggccatgtc 8340 tgctggttca ttgctcgaac ctagagaact tagtggccga gcccagtgtt taagagagcc 8400 tcttaattca cgcggccgat ggaggctatc tacattcgat ggccactgag gtggccaaga 8460 aatatagata acacccttcg gcgcatagaa ttttcggtga aatgagtaat tgggcacctg 8520 gcatttaata tttttcttgg tttagacttg taaagcagaa attaacaaga gaaagtgatc 8580 aaggtcctta caaaagccga agtaacttct tgaggaggaa tgccgagatt ctgatcctga 8640 ggatgaaccg gcgtctctgc cgtcgcttcc ggttcgacag gggtgccgct tcaggcccag 8700 gaccgcttcg gctgaggggg tcgacttgac cagccgcttc gaccaccggt tgaggattgg 8760 gggtggtatt tcggccggtc gaggcckcct caccagttgg ggccttcgct ctcatcctcc 8820 tagataaaaa aagggtcagt cattagacaa ggagttttag atagaagaac attataaatt 8880 ttatacctct tcttccagga tgatcgctga gtcttctttg gattaggggg agggttcttc 8940 tcggccgagg gagtcgcctc ctccagggta gcagccaccg ggccggcttc agcgtgagca 9000 gctgccggtg ctgaagttgc aagccgttcg acaactggat tgatggccgg ctcaatcatc 9060 gggtctgctg tacccggtcg aggcctcgac gacaggagga gggagagaaa cactaggagc 9120 agttgctccc gtggtttggc tggagataac gtgaatctcc cgctcccctt tcttggccaa 9180 tttcttgacg cgttttttag gccggggagc gtctcctgcc gtttcggctt ccgggcgagg 9240 cgtttgctcg gcagagtcgg tgcagcagct gccgcctttt tcggaggagg ggcaagtttc 9300 ttcttagccg cggccatcgc caccacctcg gccctcttta tggtacggcc acctaaaaac 9360 atttgggtta aataaagctc gaaggaaaat aaatgaacaa ggaaagtaag aaggtatata 9420 ccttgggccg tttctttgga ttttggggca agggcttttt tcgggcgatc gccaaaaagc 9480 ttctttgaga tttcctcggc cggagtgctg aagaagtcct tggtgtaagc atcccaccac 9540 tcggcgaagg tgctggcaca ccgggattct agggttctcg gccgaaggcg gaatttggcg 9600 caccgctcgt cgaactcctt ctcggctatc tcgcattccc tttccgagga gccagagagg 9660 cgttctcggc tcaaaaggag cgagaagcaa ggaatggcat ggggcaccct tggagatagc 9720 ccagttgacg agccaggaag ttggggtggt agacttccca gcttcctcgc cgagcttcgc 9780 aaccataggg taggtcgcga gtcatgatga atgaccccca ggactctcga agatcagctt 9840 cctcggcctc ttcccatgcc gattgtggaa ggatgatgga agatgggtat gtccggcgac 9900 gacagatttg gaattcgtcg tctgacaagt cctctaggcc gaagaaatat ttgaagattt 9960 cttcggccga gtgagtagga atggggcgtg aggccagctc caggcccatt agcttcggaa 10020 gagttgaagc ttgggacttc ggccgcagcg tcgagaagta gacttgcagc cagagctgga 10080 agacccagag cgggccgttt tggtgggggt cgattttccc cacggtagct tcggccaaac 10140 accgggtgag gttggcaagg acggctgggc tgagggccag gacgtgaccg ctggccaggg 10200 cttcggcgac tggcatgttc tcggccaggc acttattcga cttggcacaa aaaatatact 10260 tgttgtacca gtagaataag aaggccccat gttccccttt cttgagatct tccccttccg 10320 agccggcgaa gtgggtgatc agggtgttgt agttgaagaa gttcttgtgc agtttctgca 10380 cgtcttcttt cgacggcctt tgatctcctt tcgtcagggc ttcgacggcg cgttcctcga 10440 agatggtctt caggtccagg tcgaatttgt acccggagag agaagtatcg actgggaggc 10500 cggttggaga ggtgccaagt atggcgtgat gtccagcacc gttgggccaa gggggccgag 10560 gggaagaacc atcgtgttgg tggccgagca ccaaaagctt aagcagccat cacaagctct 10620 cgatccaagt tcatctcgat ggtcgagagt ttgatggcat caaaaatgcc gagagccttc 10680 cactcgtcgc cgaagtatgg ctccatccga gtaacccagg cagcccaggc cgcagtggtc 10740 gagggccaaa caccttgggg tttggccgat tcccatttcg accaatcgta cccttggaat 10800 aagggtttta ggcagtgttc cttaagcatt tcgatgattg cttctggaac atcgtccttg 10860 aacagtgggc cgagggtttg gtgggagaca tttggctcat cctcaaatcg gatggttttg 10920 atggtgtttc ggtcggtgat gttttgacac ttgttgcact cctcgatcaa cttggtgatg 10980 aaagtattgg cagccattga agatgaaggt tttctgggta ttgaaggttg gttttctgag 11040 aaatggcaag agatttgaga gcaaatggca aagagatttg agagttttga aagcgtaaaa 11100 gtttgaatga agagagttga gtatttatag gcgttttggg ggaagattca acggtttaaa 11160 atgagggata aaatcgaccg ggggatttgt aatcatgatg aatattcaaa gaatccaggc 11220 tgcacgatgg cgtgtgacgg cgagcttaat ggtgaaggga cgtttgagtg tctgcacgtc 11280 tcaaaagacc gaaaattcac gaatcaaggt tgtaatgatg gcgtgtgatg gggattcatt 11340 ttgagaaggc gtttcagtgt caagtgagga caagcatgcc gaggagatgc cacgtggcag 11400 ggcgtctgac aaaattaaga tcgtgcaatc gtgcttcata aatgcgcctg agtggatgga 11460 atattcgaga cttttcgttg tcctttaaag atatattaag ggtttgattt cacttcttca 11520 aggtcgaagc tcggccaaga gtttaggccg aagacctcag aagcgagggg gcaa 11574 // ID HAT-9_Mad repbase; DNA; EDCOT; 5108 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-9_Mad. XX NM HAT-9_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5108 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1625-1625 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~95% identical to consensus. XX FH Key Location/Qualifiers FT CDS join(2039..3916,3748..4161) FT /product="HAT-9_Mad_1p" FT /note="transposase." FT /translation="MDIDEENTEAMEMSTFNLSDTQGTTSAPSPSKRKAKG FT MRVGKIRQKRSRVWTLFEELPVGPDNKQHAKCKNCGIVYVCDSNCGTKNLL FT NHMDTCSKKHHIDMKKSQVGLRSPQFNHISFCELLIEAIVKHDLPFRFVEY FT EGIRTLFKYISPDIKLPCRNTVKKHVLRMFEDEKIRLRDWLNTVEGRICLT FT SDLWSSATTDGYLTLTAHFVDKEWKMHKRILNFCRMPPPHTGVALSEKINA FT LLVEWGIEKKLFSITLDNASANDCSVELLKKQLNFRGLLLMDGKFFHVRCC FT AHILNLIVQDGLKEIDGSVTKVRECIKYIKCSEGRKNKFFACVAQVGLAGS FT KRGLRQDVPTRWNSTYTMLDSAIFYRRAFLNLALVDSNFSSCPSLEEWDKI FT EKISNFLGYFYEVTCLFSGTNYPTSNLFFPKVFKVHYCIQDAMEDCDDFMR FT RMGSYMNLKFEKYWSEYSLILAIAVILDPRYKLQFVEWGYDKLYGKESREL FT KDVSGTLFALFGRYMDKFSHLLVSNPVNQTPTQIKVGDKLFEVVFIFVIPL FT FILFICIFILYVDLCFYFVFICRNLIIFIKMGQLQLKKLNYIYILKERDSI FT ENKSWIFFHGGNWSNFVIPYFLVWLLMCEFDNIYQDGSTSVEKTELHLYLE FT GKRLDRKQELDILSWWKLEQFRYPVLSRMASDVLTIPISTVASESAFSISG FT RVLDQYRSSLLPETVQALLCTRDWLFGKEGKFHISLYFFFFAYIIGYNCFS FT FFLFMFSFRERGC" XX SQ Sequence 5108 BP; 1373 A; 849 C; 1110 G; 1770 T; 6 other; taggcctggc attttcaacc caacccgtta acccgacccg acccgacccg ttaaaattag 60 tattcgggtg ggtggttaac gggtcgggtg gttaacgggt caacccgtta gtcacccgtt 120 aaataacggg tcagtttggg tgaacccgcg aaacccatta gccacccgtt aacacccgtt 180 agtaaggact tttgtgtaat ttcaatagtt aattcaaaac cctcaggttc ctagctctct 240 cgctagttgc tagtcgctgc ctcgcacgcc gttcgttgct ctctgagact gagagatcgc 300 tgtgcgccgc tccttccttc tggctccggt tatctccctc atcttcttcc ctcaaaaatt 360 ttactgaact ccaccactct ctctctggta agctccgatt cccttccacc tcttctttca 420 tttcgattac ttttcgtttc tgcagattag attcatctat tttttctcgg attttgcttg 480 agcttggttt aggtggtctc tgcagattag attcgaccct tttcgggttt ttttttgttg 540 tgttttggat attgggtttt gctttttgtt catgggtttg atgtgtggaa tttgttcatt 600 tgtatattct ccaattaaaa tttccatttt tgggtaaatt ggagctgtta attcaccccc 660 atgaagttaa aagtattgag ttcgttatgt tttggtaggt ttttggattg gaattgggtt 720 gttgtttttg cattatgtct gttgcttttg cattgattag gtctmtgcat ttttgggtaa 780 atcgcaggac ttcttgcact gatgttaggt cacaggatgc tgttgttttt gcattttatc 840 agaaaaacca ccactggtgg ccttgatcag cttacgaatg ctgaacaaaa gcacttcact 900 tttaaacagg ccaaacattt gagctaatat ttgcttagct ttttggaacc caaactaata 960 taatatttga gctaatgtcc atatctaata tctgggttcc tgtttagatt gaaatgtgag 1020 agaaaaccag aaatcaaaat ttaaggagtt cttttcgaat gttgagttcg gaagtcttct 1080 gattcttgtc ttagaagtgt cccgcttgat aggattggag tgggttgctg tctcgtwgct 1140 tgtttttgcg tatggatcgt ttatgcaatg ggattagacc caagagagtc gatccaacga 1200 gagtactatg taatcgaggg aggatcagga gcaggttcgg ttttcacagc atgctttgca 1260 atgcagtcgc tctgaaatct agtcctgaat gtagataaga tttccttccg agtwaattct 1320 agagaaccga ttgaacatgt ctaacggagg actgttgttt gttctttagc cagtaatttc 1380 ctttgaggcc ctaatcgawa gtgaggcgtt tcgcaggcga ctttttgctt aaacctcatg 1440 aagagctaat cattggttgt gagtaactag gtttggctca tgtcttggaa cccaatgtat 1500 aggttgattt aaatgattcc tcatgataat ttaggcatgc atgttctgat ttattggccc 1560 aacatatgcg aatttaaggg acggtttgtc acaaaattgg gaagtctttg cttccctaaa 1620 gttggtgttt aagctgcatg attcatgaac gttgtacatt catgccaatc acgtggtggt 1680 tcagttgatt gtctttttgt tgcatttatg attttatagg attagagaat cctatatcct 1740 cttcggttta tgtgcccagt gtcataggtg gcttagttct tccaagttaa attacagcta 1800 tgtaaggatt catgtttctt ggttgattgg tcagaattct taatatccag atgatgccat 1860 aaatgtttgc tgcgattgtc gtccctacaw ggtaatccaa gaggctttag attacgtggc 1920 ttcagttgct tctcttagtg tggaacttgt cataagccgt ttgatttcag acataaattg 1980 ttttgtagaa attaaactgc atcttccatt cacgtctttt cgtttatggt tagtgcagat 2040 ggatattgat gaagagaaca ctgaggctat ggaaatgtca acattcaatc taagtgatac 2100 gcaaggtaca acaagtgcac caagtccttc aaagagaaag gctaaaggta tgcgagtagg 2160 taagatacgt caaaagagat cccgtgtttg gactttgttt gaagaattgc ctgttggtcc 2220 tgataataaa caacatgcga agtgtaaaaa ctgtgggata gtttacgtat gtgatagtaa 2280 ttgtgggacg aaaaacctat tgaatcatat ggatacgtgt agtaaaaaac atcacattga 2340 tatgaagaaa tctcaagttg gattgcgttc tcctcagttt aaccatatta gtttttgtga 2400 gctattgatt gaggctatag ttaagcatga tttgcctttt aggtttgttg aatatgaggg 2460 cattagaact ttgtttaaat acatatctcc tgatatcaaa ctgccctgta gaaatacagt 2520 taagaaacat gtgttgagga tgtttgaaga tgaaaagata agacttcgag attggttaaa 2580 tacagttgag ggaagaattt gtttgacatc tgacctatgg tcttctgcta caactgatgg 2640 atatctcaca ctcacagctc actttgttga caaagaatgg aaaatgcaca aaagaatttt 2700 aaatttttgt cgtatgcctc ctccacatac cggggttgct ttgtctgaaa aaattaacgc 2760 cttattagtt gagtggggga ttgaaaagaa actgttttcc attactttgg ataatgcctc 2820 tgcaaatgat tgttctgttg agctattgaa gaaacaatta aattttagag gtttgctatt 2880 aatggatgga aagttcttcc atgttcgttg ttgtgctcac attctaaact tgatagtcca 2940 agatggacta aaggaaattg atggatcagt gacgaaagtt cgtgagtgca tcaaatatat 3000 aaagtgttca gaagggagaa aaaataagtt ttttgcttgc gttgcacaag tagggttggc 3060 aggtagtaaa agagggttga gacaagatgt gcctactaga tggaattcaa catatacaat 3120 gcttgatagt gctattttct atcgtcgtgc ttttctcaat ttggcacttg ttgattctaa 3180 ttttagttca tgtccttcct tggaagagtg ggataaaata gagaagattt ccaatttctt 3240 ggggtatttt tatgaagtta cttgcttatt ttccggaaca aattacccta catcaaactt 3300 gttcttccca aaagtgttca aagtccatta ttgtattcaa gatgctatgg aagattgtga 3360 tgatttcatg agacggatgg ggagttatat gaatttgaag tttgaaaagt attggtcaga 3420 gtatagtttg atccttgcca ttgcagtgat tcttgatcct cgctataaat tgcaatttgt 3480 agagtggggt tatgacaagc tttatggtaa ggagtcgaga gagttgaagg atgttagtgg 3540 cacattgttt gcactctttg gtcgttacat ggacaagttc tctcatcttc ttgtatccaa 3600 cccagttaat caaactccta ctcaaataaa agttggagac aaactttttg aggtagtatt 3660 tatatttgtt attcctcttt ttatactttt tatatgcatc tttatattgt acgttgatct 3720 ttgtttctat tttgttttta tatgtaggaa tttgataata tttatcaaga tgggtcaact 3780 tcagttgaaa aaactgaatt acatctatat cttgaaggaa agagactcga tagaaaacaa 3840 gagttggata ttctttcatg gtggaaactg gagcaatttc gttatcccgt actttctcgt 3900 atggcttctg atgtgttaac aattcctatc tcaactgttg cctcggaatc agcatttagt 3960 attagtggta gggtgcttga tcaatatcga agttctttgt tgcctgaaac cgttcaagcc 4020 ttgctatgta ctagagattg gctttttggc aaagaaggta aatttcatat ttctttgtat 4080 tttttttttt ttgcttatat aataggttat aattgttttt ccttttttct ttttatgttt 4140 agctttagag aaagagggtg ctgacttgga agaacttact gaagaaattt ttgacatgag 4200 ccttaacgaa aactcgggac aatgctccag tagtattagt cttgattaag tatggtatgt 4260 tttttaactt gttcttttaa agacaatgct tccagttaag ctaaggcaca gtgtgttaaa 4320 ggctatatag gtgatgagtg aagtgtagtt ggaaaatggc tcttctcgtt cagcatttct 4380 ccattttcct tattgttgtg ttctttatta ttgcaggtgg aagctaatta gaatgctgct 4440 aactttggct tgggaggatc aaccaagcaa ttatataggt gatgagtgaa gtgtagttgg 4500 aaaatgattg ccacacgtac attgtctggg tgaggaaggg ctacaagaag ttgaagcatg 4560 tatctgtttt aatagggcat tagacattac ctatagtaga acttgtactc gtgctctttt 4620 tactgcacta aagagcgtgt tttaaattaa tcgagcaaaa gcactttccc attatgatag 4680 cgttctgtta taatggctac atgagcaact cgaggtgagg gcatgcgctt ggtaccactc 4740 agtcgagcaa aagcactttc taacagcatt gacattacta tagatctctt gggttttcat 4800 atgggtccag catttttaat tgtaatctgc cattccatgt tggctcatga attgcattgc 4860 atcctctgcc ggatttttgc attgatttgg atgaaatgtg taaaaaaaac aaaaaaacaa 4920 aaaaaaccaa aaaaaaaaaa aaaaaacagt aacgggtgaa acgggtgacc cgttaggacc 4980 cgttaactta acgggttggg tttgggtgac ccgttagctt aacgggttgg gtttgggtga 5040 cccgttagmt taacgggtcg ggttaaaccc gacccaaacc caataaaccc gacccgttta 5100 caggccta 5108 // ID PIGMET repbase; DNA; EDCOT; 274 BP. XX AC . XX DT 24-JAN-2007 (Rel. 12.01, Created) DT 24-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW DNA transposon; Transposable Element; Nonautonomous; transposon; KW Interspersed; repeat; Inverted; terminal; PIGMET. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-274 RA Shankar R. and Jurka J.; RT "PIGMET: A putative non autonomous DNA transposon from barrel RT medic."; RL Repbase Reports 7(1), 44-44 (2007). XX DR [1] (Consensus) XX CC The element has ~35 bp terminal inverted repeats and lacks any CC transposase domain. It is present in multiple copies (~75) in the CC genome with a high degree of conservation. Asymmetrical TSDs are CC present of size ~4-5 bp. XX SQ Sequence 274 BP; 97 A; 39 C; 38 G; 100 T; 0 other; ctccctccat tctttttctt ttgatgtttt agaacttcaa ctatattcca aaacatttga 60 tgttttagtg aatttattat tgttttctca agtttaccct tgttggaaaa cacaataaac 120 tattaaagta gttgtgacct ttggtttatc acatgtgaat ttaatgataa ataaggacat 180 ttaagtaaaa aacacacaaa tgtttatata ctttaattac tccttaaaac ttgtgtcaag 240 agctaaaaca tcaaaagaaa aggaatggag ggag 274 // ID POTTEN1 repbase; DNA; EDCOT; 1109 BP. XX AC U91987; XX DT 19-NOV-1998 (Rel. 3.1, Created) DT 19-NOV-1998 (Rel. 3.1, Last updated, Version 1) XX DE Nonautonomous DNA transposon POTTEN1. XX KW DNA transposon; Transposable Element; Nonautonomous; KW nonautonomous DNA transposon; POTTEN1; SOL3; TIR. XX OS Solanum tuberosum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RA Oosumi T., Garlick B. and Belknap R.W.; RT "Identification and characterization of putative transposable DNA RT elements in solanaceous plants and Caenorhabditis elegans."; RL Proc. Natl. Acad. Sci. U.S.A 92(19), 8886-8890 (1995). XX RN [2] RA Oosumi T. and Belknap R.W.; RT "Characterization of the Sol3 family of nonautonomous RT transposable elements in tomato and potato."; RL J. Mol. Evol 45(2), 137-144 (1997). XX RN [3] RA Oosumi T., Garlick B. and Belknap R.W.; RT "POTTEN1."; RL Direct Submission to Genbank (05-MAR-1997)CIU, USDA/ARS, 800 RL Buchanan Street, Albany, CA 94710, USA. XX DR GenBank; U91987; Positions 361 1469. XX CC POTTEN1 is a nonautonomous DNA transposon; it is flanked by CC 10 bp long target site duplication and it has ~300 bp long CC SOL3-like TIRs. XX SQ Sequence 1109 BP; 386 A; 170 C; 159 G; 393 T; 1 other; gtaaaagggc ctaaaatatc ctcgaagtat tggaaatgat acaaaactac cctacatcca 60 cctattggct ccaaaatgcc cttctcatcc acatattggc tccaaaatac ccttgacatc 120 cacctttggg ttcaaaattg accacttatt taacgatttt gaatttaaac tatttaaata 180 acttttttaa atacttggcg ctcaactatt ggttataatt taatgtatta atatcattta 240 taaaccaacc cactacccac ccattactaa ttaaacccca cccaattaat aaaccaattc 300 taatatcaaa atcgccctaa acactactaa aacacgacga aattacagat tcctgaatat 360 gacatccaaa attattcgag atcgaactta agccccaatt aaatttaggt tggccgctta 420 tttaggagga cactttcaat aggattctct ttcaaccttg aattcaaaat ttatgattaa 480 aggtaaagaa gtagtatatc ctgaattaat tcatgcactt tttttaatat aattatataa 540 atagttatga tttgttttaa attttaaaac tttaatatat ttttttttaa aagttatcta 600 ttaagtaaca tcacataatt gagacgaagg aataattaag atcaacatag tcagactttt 660 aagtttatct gtaattttta attttgcact tgaattataa tatgttttaa ttgaggactt 720 gaatgtatga taatntactt cctatagaca ttttcgcctc aaatttttag aaacactcat 780 tggccgtagc tttcctgtta ttgcattagt aatggggtgg gtttattaat tgggtggagt 840 ttaattagta atgggcgggt agtggattga tttataaatt atattaataa tttaaattat 900 aaaaaatagt tgagcgtcac gtatttaaaa aaaacattta aatagtttaa atttaaaacc 960 tttaaataag tggtcaattt tgaacccaaa ggtggatgac aagggtattt tggagccaat 1020 aggtggatga gaagggtatt ttggagccat aggtggatgg tagtttttta ccatttctaa 1080 tacttcaagg gtattttaga ccattttcc 1109 // ID Copia-23_Mad-LTR repbase; DNA; EDCOT; 534 BP. XX AC ACYM01124502; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-23_Mad-I; KW Copia-23_Mad-LTR; Copia-23_Mad_. XX NM Copia-23_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-534 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1369-1369 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01124502; Positions 5591 5058. XX SQ Sequence 534 BP; 161 A; 78 C; 113 G; 178 T; 4 other; tgtaaaagtt ctagtgaatg acaatgagtg tttgatatta cttgaatgac aagtaacttg 60 ttttacgggt tatttgttat aaaagtgata tagttgatct ccaactcata aggattatgg 120 agtcttatat tcatgcagct aacttgatca aatcctgata agggtttaat gcaaagatat 180 tgaatcatga taggactctt tcatcattta gatgataagg gtatgcgacc gytgataggc 240 cggtggcgta accctaactg acatgtatat ataaatatat gaagttgtag tccctrctcc 300 cwtacgtgaa aaaccctaag aaattactga gacctattct gacagtaagg gagmtattga 360 gtagtgggag tagaagacca acttgcggct cagacatggc atcgaacata ggtaggtgtt 420 cttgctatta aattctggta tacactactt tatattctgt gtgagttagt tgtattgaaa 480 cctagtaccc tgttgttgta attttggttt atgagtctta tagaactgct taca 534 // ID Copia43-PTR_LTR repbase; DNA; EDCOT; 109 BP. XX AC LG_I; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia43-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-109 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-109 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 265-265 (2007). XX DR Genome; LG_I; Positions 10457121 10457013. XX SQ Sequence 109 BP; 43 A; 19 C; 12 G; 35 T; 0 other; tgtttgaaca ccatgaattc ctcaaatgac aaatatcctt atccaattag aagttccaaa 60 ttgaattttc attgatcggt caattgaaac aaataataat aattgacca 109 // ID Gypsy13-PTR_LTR repbase; DNA; EDCOT; 2944 BP. XX AC scaffold_132; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy13-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2944 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-2944 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 305-305 (2007). XX DR Genome; scaffold_132; Positions 396510 399453. XX SQ Sequence 2944 BP; 951 A; 645 C; 519 G; 829 T; 0 other; tgtcataacc caattctggg ttattcccta aaaattcatt atttttcaaa taaaaataaa 60 aaaataaaat aaaggctggt aacgtggaga aagcaggccg ggaaatcaag ctgcaatttt 120 tggaggaaat tcaaggccta attgtacccc attatgccca agaatggaga aaaaaaaatg 180 caaattcaag gtcaaattaa atgattattg gacgatttgc ataaaaatta agtccaatga 240 cataattaaa tttttaatag gccaatttga tttaatcatg ggcctaattg aattttaatt 300 atgtttaaga attaatttgg gtctaattga aggatttaat taagtgcaag gacttaatta 360 tactttaaat gggtcaaatt aattttattt ggggcttaaa tggtgaaaaa ttaagttttg 420 gggcctaatt tgggcttaat tgagaaaatt agaattttaa gagaccaaat ttatttttta 480 ccaagttatt tgattgaaat taggagccaa attgcaagaa aattgaagtt ttgaggtcaa 540 ttaggggtta aattgaagaa atccgagacc agggaccaat ttgcaaaagg cgccggacta 600 taggggccta attgacaaaa accggggact aaattgaata aagtgaaagt ttaattgtca 660 attaggggtt aagttgcaaa aattcgagac cagggactaa tgtgtaaaag gcgcgtaaat 720 ccagggttcc aattgaagtt cggcaagggt gtaattgcat taaatcaaaa gtttaggtca 780 attagaggta caattgcata aaagtgaaag ttggaggatt gctttgaact tcgaagaaat 840 ccctatttaa aacctaaaac ggcgctgttt tgagttaaaa aaaaaagaaa aagaaaaaga 900 aaaaagaggg accagacgac gcgtcgtctg gtcactattc attatcttct ttatttttcc 960 ggaaaaactg gtccagtcac ctcctttgca ggtgcattta atgcacttaa catccaccaa 1020 atttgccaaa ccgtgcacaa aaccgatcac aagacatccc tctacgtctg ggtatggtct 1080 tcaccggctc actggcacat aaacggatgt ggcaccactc caaggaggcc acctcaggca 1140 gcctgcagct gcagattaac agtgcaccat gcctactttg agccaacggt tgggatcctt 1200 cccaatcgaa tcaagggctg gaatttattc ccctgtgaag acaagattac cctcttccac 1260 cgcctataaa tagaggcttc gttgatgacc tgagggagaa gaaaatcgaa ctcaaagttg 1320 gccgaaaacc agccttccct gctcattttt cctgcaacca atcctttctc tgctttctct 1380 ctccaccgtg gcctttagcc accaccatct tcatcacccg tcttctcact atcatcccca 1440 cctccagtat ccatcaaacc atctcacgtg gtggttgcac cacctctctc tctctctctc 1500 tcttctgtaa aaatccccct tctctgccac tgtgacctcg gcagcagcgg caacagcaga 1560 agcagcggcc accaccttgc ccagaagctc ttttccttcc aaaaggcagc cagggtagca 1620 gctttctcct cagccactcc aacagctcca actgcgagct tcccttctcc ttcgcaggcc 1680 tctgtttctt cttcttcttc cagcggcgac cagagccagc catcggcctc accaccccag 1740 ccacaccgtg cgccaccagt caggccacga gctcccttaa cgctaggtaa gcctccctcc 1800 tctcttctta ttcttctccc tctctgccac tgccgtatga gaacaatgca acgtgaatta 1860 taattcacgt tgcactatct tatgcaactt agtcactggg ctgccagtga ctaagttgct 1920 ttgggctgga cctgtcctag cccagcccgt ccctaaattt aaaaaacaat atgttgggcc 1980 gagttcggcc caaccttttt gggctaatgc caacccacct gtttttgggc ctgtgcttgg 2040 cccagcccac atgtttaaat aattaattaa ttaattatat atatatatat aataataaaa 2100 taataataat aataaaaaaa ataaaaaaaa atttcaaaaa tcctttcaaa aaattgtgat 2160 tttctcaaat atttttctat taattttgca taatatcagg ttgtatattt acactataaa 2220 atacaaatct ggtattaaaa tacccggttt tctccgaaat atttttttaa aaaaatcata 2280 gcattttcaa aaataaaaaa aatatatttt gttgcatacg gctaaatcct aaaatatttc 2340 caagcatatt tttcataaaa aaaatgcatc tttttcatgt tttaaaaaaa ataaaaatgg 2400 atattgtaac cagtttatta ttatgcttta ggatttggcc aacatgtcaa aaatctcttt 2460 tcaaccttgt taggggtcta aatgtagact ttaatattta tggggtgtaa ttatacgata 2520 aagtacaccc tcaggtatta aagatacaag atgtaaataa atgcaatgct aaaattcaga 2580 ttttagaacg gttaagattt aacccgataa ggtagagact ccatcatgaa gggagatctg 2640 tcttgaacct taaaaaagac caacgaatag aaactcaacc tagaaaaaca atcaaacaac 2700 aatgcagctt accttaggta gggtgcacgg gggtgatgcg tcttcccctt gcacaaccag 2760 tcccttacat agactctcgc agaccatagg ttcctagtga ccataatact aggtagcgac 2820 tcctgaacct taatcataat tttatgatta aatccaaaaa ccctttccaa cacacgacac 2880 ctcatatagg aggcacgaca aagagcctcc gctgtcgcca gacgacgtcg cgccccccgc 2940 gata 2944 // ID Gypsy1-PTR_LTR repbase; DNA; EDCOT; 365 BP. XX AC LG_XI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy1-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-365 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-365 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 297-297 (2007). XX DR Genome; LG_XI; Positions 11637351 11636987. XX SQ Sequence 365 BP; 124 A; 53 C; 48 G; 140 T; 0 other; tgaaatttgt ttgtcgaaat aatttattga tgctcgagag agattaatat ttacattagg 60 aaaacctgat tatcaacatt aggagtaatt aatttaatcg agaaagttca cataagcata 120 gttacggtaa gtcagaaatc ctagaaccag tacaattgaa ttcattaata tttaatcatt 180 ttttgtttgt ttttttttaa tcattaattt ttgtttcata aactatctca ttcgattcct 240 caaatagatc ataatttaaa agactttggt aattagtagt aatttttaca aatcctcgtc 300 ggacgatact ctactcatca ctttattact tgttacgatt cgtgcacttg cgaaattaac 360 caaca 365 // ID MUDRAV3_MT repbase; DNA; EDCOT; 559 BP. XX AC . XX DT 30-NOV-2006 (Rel. 11.11, Created) DT 30-NOV-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW Inverted; repeat; TIR; TSD; Interspersed repeat; MUDRAV3_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-559 RA Shankar R. and Jurka J.; RT "MUDRAV3_MT: A Putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 580-580 (2006). XX DR [1] (Consensus) XX SQ Sequence 559 BP; 197 A; 109 C; 76 G; 177 T; 0 other; ggcttaatta caccacatgt cctttaagtt tgacgtttgt aacagatagg tcctttaagt 60 ttgttttgta acagataggt cctttaactt tgtaacactg tgcaactaag tccttccgtt 120 aacaaaacat ttattttctt aaaacaaaac acttaacaca ttacattaat gttacactca 180 acaatgtttc atcgtctaac atgattgcac gcttaaaatt aaactaaaaa aaacaacatg 240 ttacaaggat tgttcacttt acttgattaa atatcaagct tattgttgca ataacacaag 300 ttaaagccaa caacatgcaa gttacatcag caatcttcaa aaataatcat aacattttcc 360 aattaataac atgtttttgc cttttgcatg ccacatcaca gacttcacag ccacgtcagc 420 gtttttttga cggtgagtta acggaaggac ttagttgtat actgttacaa agttaaagga 480 cctatctgtt acaaaacaaa cttaaaggac ctatctgtta caaacgtcaa acataaagga 540 cccgtggtgt aattaagcc 559 // ID Ogre-LE1_LTR repbase; DNA; EDCOT; 4003 BP. XX AC AC171735; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 10-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-LE1; Ogre-LE1_LTR. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-4003 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC171735; Positions 60610 64612. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). XX SQ Sequence 4003 BP; 1138 A; 816 C; 557 G; 1492 T; 0 other; tgttgacacc caattttgac cgacctttga ccctttttag gaatactatt agattaaata 60 cgtattttaa actttaaaat ttttagtcga ctttgcttga aaattatata ttttagtatg 120 ttctacttta taaaattatc gtatatattt ttaaaatatt ttaaaattat taacgaattt 180 caaatgtttc aaagttaaat gatttttaca ctttccttaa aattatttaa attctagcct 240 attttattct aatttctttc aattctagcc acttgaatta gagttttatt tcattcatag 300 ccatctcttc ctttcaattc tagccaattt taattgcaat tttagtcatt ccgtacctaa 360 ctcatctaat ttcaagaagt catcttttga tctcatcctt ccattttaat taattcctag 420 atctaatcct aacccctcat ctcttctaaa atcaatggtc cagatttaat ctacatatta 480 taacctaaaa gaccctaatc cctaaaataa ttctgattct cttctccctc cctttttcag 540 ccgcctctcc cctctctctc tctctctcca gcccggcccc ctctctcctc gccacttccg 600 gtgaaagcca ccagaagaac cagccgccag tcgctcctct ctctctctct ctcttcgcca 660 cctcttcttc tccaagcagc cgctcccttc tctctccctc tcctccatct tttccggcaa 720 gggagacagc caggagacaa gcaacaacag ccatggcgga cagcatcagt agccatgacc 780 ggcgaggagt cagcagcggt cgccggcgaa aactcctgcg tccggccagc agctgcaaaa 840 agaggcgaac gaccacctct ctctcctcgt cgcctccctc tcgtcgctct cgcaaatggc 900 gagcaaccag acccaccagc gtgctgcaaa caacagccgc cggacgagca acgagcggcg 960 tcaaccatca gcccacagtc accggcagca tgtctccctc ctctacattc ctcttcctca 1020 cccgtctccc ctctcccgtc attcccctcc tcccgcttct cctctccctc ccgctctctc 1080 tctcctcccc gttttcccct tcttcttctc cttttctttt cctcttcttt tgcagagaca 1140 ggtagcatct ccgaccagca acgtctcgag gagacagcag cagcagcgtc tcgaggagac 1200 agcagcatcg actccggcga gcctttcctc tttctttgtt tccagccaac aagttcggct 1260 aatgaacgac gtggattcta tacatatctc aatattgcgg ctgattttaa gatgaatttc 1320 aacagatccg tctgggttag tttctgtttt agtttttatt attattttta atttagatgt 1380 ttaatttgcc taatgttctg cttgtttttc agaaatattt tgttatgaat ataaaaccat 1440 attgtgattt gcttgatctt atggactgtt cttgttgatt tttctcttga aaatttgcaa 1500 agtacatgtg ttttagccat gttgaaaaca atattgtatg ataatcagtt cctgtaagtc 1560 tgctaaatgt gatttgggta ttgacatgct aattgtatat tggtttcact ttgattatta 1620 tttgttatga taagtcttgt aattttcaat agtagttgca gatttcttat atcttttata 1680 aatattattg tcattttaat tgattatttt attttacctt gattgacttc aaatatattc 1740 ttggttgtta tatctctgga aagtgatatt taattaaggt aaaaagaatt gtactgattt 1800 tactctctac tagttaagga aaataagttt aattgattta tttttccttg tgaataaata 1860 ctgattcctt atttgtttgt attatggtaa tgaattattt tttttctgat ttggaataag 1920 gaaaagggaa tattaattga ttccttaaaa atatttcttt tccttatttg ttccctctcc 1980 tctactatat aaataagacc cctcctctat ttcatggacc attcactctc aaccaaaaaa 2040 aaattctctc atcactctcc ctcctctcat tgctcttttg ctacttttaa acaacattaa 2100 tatttcggtg aatattcaag tgcttttctt cgctattttc ctactttgtt cgagtaaaag 2160 gtgaatcatc ttgttttgtt taacaggtta gtattcttaa cattaatact attttcatat 2220 tcacatattt gtgtaaacca ttgtctgttt ttatatagaa tccgtcatta aacgattgca 2280 tattgtctca ccttaactaa caagtgtgat tacttgtgta gttatttaat tactttgaca 2340 tgtttcatat ttgaggttca agttgaagat taactgaaga aggatttgtt tatttgttga 2400 atgtacatat atatatatat ttttattttt tccgctattt tatttatttg aatgatgtaa 2460 caattgtaac cctaaagatc atataataaa gttatttggg ggtcgtctag gggaggggga 2520 tttatatgct tacttgctca ttattttttt ttttagaaat catgcctata ggtttgtctt 2580 taaccaccta gatttgatat ttgtaggtgt tataatctaa tcaattttca atttgcttga 2640 cgtttattta acaagtctta aaaaaataag aactagaatc cattaatttt ttaaatgtta 2700 aaatcaaatc ctaataaatc tagtaggttg ttagatgtta aaatattata aattctcatt 2760 tgtcttatca tgtagaaacc atgtctaagg tttaatttgt tcataccatt tacgaaatca 2820 tgcatatata tgttactttt ttttaacacc tagaaatcat gtctataggt ttgttaataa 2880 gagaataaaa tttgtttgtg catatttgag tcctccccta aaaataatta atattattta 2940 actagtaatc ccatttgttt tccacattcg tgatgcaata ttttcttctt aatactaaac 3000 taaaatcatt tcatgcattt aataaattat ttggctttaa atatatttca tcgtaaaacc 3060 tttgcattaa taaatttacc atcttaatgt tctactagtt ttagtactta taaagttttg 3120 caacataatt ttcttaaaag tcattattca atcttccttt gaaattttgg attgattgtg 3180 acattatttt taaaataaag tactatctcc taacctatcg ttagtgggaa agtcaaagga 3240 actatgaggt ctagttccaa tttttaaacc gacgcatcct cggaagtacc acctacccat 3300 gaatttcaaa agaattatgt gcatttatgt gtgcctacgt gtgaactaaa tcttttaaaa 3360 tcatttttca aaacataact attttttaga ccgacctcaa atcaaaattg tttctatggt 3420 ggaggagcgc gatcaacaat atcgtggcat cattcctata aagaaacaaa cattttttca 3480 aaaaaaaaaa aatcatattc aaaacttact caattttcaa aactttattt tttgcacata 3540 ttaattgctt aatatttgcc aattttgcct ataacatagt ctcgtatgtt aaataaaaaa 3600 aaaaaaatat aaacttggtt gtttattatt gctgtcttct agcctcgcat atttaaatta 3660 ataaaatagc cttaattgtt ttatacttgt tatcacttag caagcatatt aatgaataat 3720 aatgaagtga ccttgattgc tacttgtaac ccccacatag attgcatgag atacggccgg 3780 gacccacact tgtggacctc gagggatgcc taacaccttc cctcgaggta atttgaaccc 3840 ttacccaaat ctctggctca ttgaccttag ttagacttag ttagtttaga taggtgccct 3900 aacgcgcctt aactcgttag gtggcgactc caaagctcaa aaatcccaaa ggagttgtta 3960 ggtcgtgcac aaaacccgtt ttccgtgaaa atggggcgcg aca 4003 // ID Copia-70_Mad-LTR repbase; DNA; EDCOT; 102 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-70_Mad_; KW Copia-70_Mad-LTR; Copia-70_Mad-I. XX NM Copia-70_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-102 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1679-1679 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 102 BP; 29 A; 6 C; 32 G; 35 T; 0 other; tgataactat aatatgtgca tgtgtgtgag atggttagga tgtatgtgag gtagttaagt 60 tggttaagag tctatggtgt aaggttgtga caagtgtcaa ca 102 // ID MTCOPIA2_LTR repbase; DNA; EDCOT; 179 BP. XX AC AC147407; XX DT 29-DEC-2006 (Rel. 11.12, Created) DT 29-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Long terminal repeat of Copia-type element. XX KW Copia; LTR Retrotransposon; Transposable Element; MTCOPIA2_LTR. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-179 RA Jurka J.; RT "MTCOPIA2: Copia-type LTR-retrotransposon from barrel medic."; RL Repbase Reports 6(12), 633-633 (2006). XX DR EMBL/GenBank/DDBJ; AC147407; Positions 12856 12678. XX CC There is 1bp substitution between LTRs. XX SQ Sequence 179 BP; 58 A; 30 C; 22 G; 69 T; 0 other; tgaagagtac acagcagata ttacatagta ttctagctta gctgtaacct gaagtagtta 60 gttattctct agaatacact tacattacct tatcctgtta cttcaatata tgtatatata 120 ccttctgtaa caataattct agtaatgaga attcagtttt actattctac tgtatttca 179 // ID Copia6-VV_LTR repbase; DNA; EDCOT; 194 BP. XX AC AM431515; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia6-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-194 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-194 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 746-746 (2007). XX DR Genbank; AM431515; Positions 4487 4294. XX SQ Sequence 194 BP; 61 A; 41 C; 28 G; 64 T; 0 other; tgttggcgtg agctgttctc tgaaccatta aaggagaaaa atcaatctct gcaatcagtc 60 actgcaatcc ctcaacaatt gtagccgtaa tccatgtagt ccatgtatag ccttttcttt 120 tgtctatata tatacacctg tactctaatc agttgatata gaataaaaat atatgatttc 180 tccttagacc aaca 194 // ID Copia-35-I_VV repbase; DNA; EDCOT; 4699 BP. XX AC CU459357; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-35_VV, LTR retrotransposon Ty1-copia like, internal portion DE from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Wintz-B01; KW Copia-35-LTR_VV; Copia-35-I_VV; Copia-35_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4699 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL/GenBank/DDBJ; CU459357; Positions 77263 81961. XX CC Full size = 5281 bp CC LTR = 291 bp CC LTR are 99.3 % similar to each other. CC Direct flanking repeats = aaaac. XX FH Key Location/Qualifiers FT CDS 1032..2600 FT /product="Copia-35_VV_1p" FT /note="Incomplete putative gagpol polyprotein." FT /translation="PKTQNRDYKDNLWCTYCKKARHTRERCWKLHGKPPSR FT EWGQKGEQPSNNGQTHVTTVQQNGATPQETGSLNQEEVERVRSLICNLDKP FT TGTGLLAYSGKFPFSIGLNVLDITFANSWVIDSGATDHMTHSPNIFSTYFP FT CSSSRKIATADGSLTTVAGIGDVKINPSLMLKNVLHVPRLTTNLISIQKLT FT QDLHCNVVFYHSHCVFQDEDSGRMIGHARERDGLYYLKTPSQSNITKGKSS FT HSFVSEVFSFNKEKVWLYHRRLGHPSFRVIKIMFPSLFKGLDVEHFHCEVC FT ELAKHKRVSFPVSNKRSSIPFYLIHSDIWGPSPIPNITGAKWFVSFIDDCT FT RVTWIFLLKHKFDVSTVLPNFCSMIKTQFGVNIKRFRSDNAKDYFNQVLTP FT YFQREGIIHESSCVNTPQQNGVAERKNGHLLDSTRSFMFHKNVPKSFWGEA FT VLTAAHLINRLPSRILGFKSPMDILSTFYPNLHTTNNLVPRIFGCVAFVHV FT HNQNRGKLDPRTLKCVFVGYSSTHKRV" XX SQ Sequence 4699 BP; 1461 A; 885 C; 985 G; 1368 T; 0 other; tggtatcaga gctgaattag gatccttgga atttattttg tttcagcctt cattgctgaa 60 tacagtgccc aatttttctt ctgtttttga aactcaaaac agagcatttg tttcctctcc 120 tagaattttc attttcttct tggccttcat tgccattcat ttgccttttt tttgccttca 180 ttatcaatct gatctcttgg ctttcaaacg attgtctatt gttgacccac gtgctttgct 240 tgaatcacct agaaattgcc cttttttttc cgtaaaaaat gtcagagatt gcagaaacaa 300 ccactacagt ccattcagag gagattattc gaccccaaca ttccggagaa ttgcaaaata 360 tccaggctgc atataggctg gatggaaaaa attatctgaa atggtcccaa cttgttcgca 420 ccatgttgaa agggaaaggg aagattagcc atctcatggg tacagggccg aaactaggag 480 atcctcattt tgaagcatgg gatgaagaag actccatgat tatggcatgg ttgtggaatt 540 ctatgattcc tgaaatcagt gacacatgca tgttcctagc tactgccaag gacatttggg 600 atgcaatcca acagacgtac tctaaggcga gagatgcggc ccaagtatac gaggtcaagg 660 tgaaaactgt tactgagtat gctaatcaat tgaaatcttt atggcaagaa cttgatcatt 720 acagggtgat aaagaccaag tgtcccgaag atgctgctat tctcaaggat ttcatagaac 780 aagatcgagt ctatgatttt cttgttggac tcaatccaga atttgaccaa ttgcgaatcc 840 agattcttgg caagaaagaa gttccgtgct ttaatgaggt ggtggcatta attcgaggag 900 aggaaagcag aagatgcctg atgcttaatc cacagaacac ggacagctcg gctatggtgg 960 ctggcagtgg taacaattca gccacaaata tggaaagagt actagtttct ggcaatggaa 1020 gatctagtta accaaagact caaaatcgtg actacaagga caacttatgg tgcacttatt 1080 gtaagaaggc acgccatacg cgtgagcggt gctggaaact acatggaaaa ccaccaagtc 1140 gagagtgggg acagaaggga gaacaaccaa gtaataatgg tcagacccat gttacaacag 1200 tacaacagaa tggagcaaca ccgcaagaga caggcagtct taatcaagaa gaagttgaga 1260 gggtgaggtc tcttatttgc aaccttgaca aaccaacagg tactggttta ttggcgtatt 1320 caggtaagtt tccattctct attggattaa atgtcttgga tataaccttt gccaactcct 1380 gggtcattga ctcaggtgct accgaccata tgactcattc accaaacatt ttttccacat 1440 atttcccatg ttcaagcagt agaaaaatag ccacagccga tggctccttg accactgtag 1500 caggtatagg agatgtcaaa ataaacccat cactgatgtt aaaaaatgtt cttcatgtcc 1560 ctaggttaac cacgaacctc atttctatcc aaaaactcac tcaagattta cattgcaatg 1620 tggtttttta tcatagtcat tgtgtatttc aggacgagga ttcggggagg atgattggac 1680 atgctagaga acgggatgga ctctactatc tcaaaacacc aagtcaatca aacattacca 1740 aaggcaaatc atctcattct tttgtctcag aagttttttc attcaataaa gaaaaagttt 1800 ggctttatca tcgtcgactt ggacatccat catttagggt tattaaaatt atgtttcctt 1860 ctttatttaa aggtctagac gtcgaacatt ttcattgtga agtgtgtgaa cttgctaaac 1920 acaaacgtgt gtcttttcca gttagcaata aaagaagttc tattcctttt tatctcatac 1980 acagtgacat ttggggtcct tctcctattc ctaacattac tggggctaaa tggtttgttt 2040 cattcattga tgattgtact cgagtcactt ggattttttt gctcaaacat aaatttgatg 2100 tcagtactgt ccttccaaat ttttgttcta tgattaagac tcaatttgga gtcaatatca 2160 aaagatttag gtcggataat gctaaggatt atttcaatca agtcctaact ccatactttc 2220 aaagggaagg aataatacat gagtcatctt gtgttaacac tccacagcaa aacggagtgg 2280 cagaaagaaa aaacggtcac cttcttgact caacccgatc cttcatgttt cataaaaatg 2340 tgcctaaatc cttttgggga gaagcagttc ttacagctgc tcatctcata aatagattgc 2400 cttctaggat cttgggattc aaaagtccaa tggacatact ttcaacattc tatccaaacc 2460 tacacactac aaacaatctt gttcctagga tatttgggtg tgtggcattt gtccatgttc 2520 ataatcaaaa cagggggaag ttagatccac ggacattaaa atgtgttttt gtgggttatt 2580 cttcaactca taaaagggta taagtgttac catcctccat aaaaaagatt ctatgtctcg 2640 gtagatgtta ctttccatga acaagaatct tatttcacta ttccttatct tcagggggag 2700 aattcggtaa tggaagataa ggataggggg gattttttat tccttgatct gccatcactt 2760 cccttgtcaa aacaatctcg tcccattgat cctttgattg aaaccttacc taaattgccc 2820 gatcagcctg aacttgtgcc tgaaaatcca aaatctgccc ctgagaatgt gagatttgac 2880 aaagtgtttt cgaggaagaa gacagttgtc cctgaatctg tgcaagtcca agacttcaac 2940 ccaaattctg agaatgaggt aacaatttct aatccttcat tgcaatctga atctcatgtg 3000 aacaatgatg accaggacct ccctattgct gttaggaaag ggattagaga atgcacaaat 3060 cgacctctat accctcttac acacttccta tcctttaaaa aattttcacc atctcataga 3120 gcctttcttg ttagcctaaa cactatttct atccctacca ccgtatccga ggctttgacc 3180 gatgaaaaat ggaaacaagc tatgaatgtg gagatggagg cattagaaaa aaacaaaact 3240 tgggagttgg taaaattgcc gacaagaaag aaacccgtgg ggtgtaaatg ggtttatact 3300 gtgaaataca gagtagatgg atcaatagaa agatacaagg ctagattggt tgccaagggt 3360 tatactcaaa cctatgggat tgattaccaa gaaacttttg ctccggtcgc aaagatgaac 3420 actgttagag tcttgttgtc attagcagct aattacaatt gggatttgta gcaatttgat 3480 gtcaagaatg cttttttgca tggagaacta gaggaagaaa tttatatgga ggtcccgcca 3540 ggttatgaca ataatttggc tgctcatact gtatgtaaat taaaaaaggc cttgtacgga 3600 cttaagcaat caccacgagc atgatttgga agattcgcaa gagtgatgat aactatggga 3660 tataggtaaa gtcaaggaga tcatacgttg ttcattaaac actcatcttc ggggaaactc 3720 acagctctct tggtgtatgt tgatgacata atagtgacag gaaacgatga caaggagaga 3780 caggttctaa atcaatgttt ggctaaggaa tttgagatca aggcattagg gaggttgaaa 3840 tattttcttg gtattgaggt ggctcactct aagcaaggca tttttatctc ccaacagaag 3900 tatgttaaaa atcttctcaa agaaactgga aagaccgcat gcaaaccagc aagtactcca 3960 atagatccga atcttagact cggagaggca gaaaatgatg ttacagtaga taaagaaatg 4020 tatcaacgct tggtgggaag gctcatttat ctatctcata cacgaccaga tatagcatat 4080 gcagtgagta tgattagtca attcatgcat agtccaaagg aagctcatct gtaggtagct 4140 tatcgagtgt tacaatatct caaagggaca ccaggtaaag gtattctgtt taaaaggaat 4200 ggagggttag tacttgaggc atacacagat gctgactatg ctggctcaat tattgacaga 4260 aggtcaactt ttggatattg catctttctt ggtggaaatc tcgtaacatg gaggagtaag 4320 aaacagaatg tggtagcgcg gtctagtgca gaggcagaat ttcaagcaat ggctcagggt 4380 gtgtgtgaac tactatggtt gaagatcgtt ttagaagact taaagattaa atgggatggc 4440 ccaatgagac tctattgtga taataaatct gcaatcagca tagctcacaa cccggtacag 4500 catgatcgaa cgaagcacat tgaaattgac agacacttca tcaaagagaa gttggatagt 4560 ggattgatat gtacacctta tgtgtctaca catggtcaac ttgccgatat acttaccaaa 4620 gggctaagta gttcagtgtt tcaaagcttt gtatccaagc tgggtatggt gaatacctat 4680 tcaccagctt gagggggag 4699 // ID MUDSOLT1 repbase; DNA; EDCOT; 4342 BP. XX AC AC151957; XX DT 22-SEP-2005 (Rel. 10.09, Created) DT 22-SEP-2005 (Rel. 10.09, Last updated, Version 1) XX DE MuDR-type DNA transposon from Solanum tuberosum (a complete DE sequence). XX KW MuDR; DNA transposon; Transposable Element; MUDSOLT1. XX OS Solanum tuberosum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RA Buell R., Liu J., Zaborsky J., Tallon L., Wirtz U., Wei F., RA Kuang H., Zhang P., Wang X., Marano M.R. and Baker B.; RT "None."; RL Unpublished (2004). XX RN [2] RP 1-4342 RA Jurka J.; RT "MUDSOLT1: MuDR-type DNA transposon from potato - a complete RT sequence."; RL Repbase Reports 5(9), 271-271 (2005). XX DR EMBL/GenBank/DDBJ; AC151957; Positions 113309 108968. XX CC The protein-coding region was annotated as putative mutator CC transposable element-related protein in ref. 1. This entry CC describes a complete sequence, including TIRs. XX FH Key Location/Qualifiers FT CDS join(1004..1252,1200..1604,2130..3311) FT /product="MUDSOLT1_1p" FT /translation="MTYIHSSNAADNNRQQLVQENPLANDFSDSEVELTDG FT LLVDKHEKTAQYIVDEWEILSIEAQRKMTAPEGESDCVDSTDTEFAQLQKE FT SLIVLILRTQSLHSDSENEILNFPTFNPQTDRDNLILALECVFESKKDFKS FT AVVTHEIKNGKYIQWLKNDKERIKAVCIHSECKWEITACKMQRDTSFQIRK FT YIPTHNCKEWHYDNRKITSSFIARKYLTKGLIEAFNEVLPYVNHRFCARHL FT HNNFKRAGFGGFTLKKAFWAAAKATTVKEFDACMVRIRELDPNAVDWLNDK FT EPSQWSRSHLSSDAKCDILLNNICEVFNSMIFDARDKPIVTLLEKLRYLLM FT ARMLANREKAHKWSSNDVCPKIKDILHKNQTAAGEYIPRKSNQRKYEIIGA FT TIHDSWAVDLENRICSCTKWSIMGIPCKHAIAAIRAKKDNILDYVDDCYKV FT ETYRRIYEHAILSINGPQMWPKSTKVPPLPLTIVGNKKTGRKQKARRKEAD FT EVGASRTKIKRKQQSLDCSTCNKPGHNKKTCKYNVVSQETTSVHQKLHVLL FT YLNYIRIGFLSDNLKLTQFICELMIQVRRGLEEAGQEKTRQEGAGQEKTVG FT QEEVVDIDSGWIYY" XX SQ Sequence 4342 BP; 1488 A; 630 C; 819 G; 1405 T; 0 other; cttaaaatag tccattatct ttgagtttat actcaaaata gtcctatttg tttttagtgg 60 agcattaata gtcctgattc tttaataaag tggtgcattt tcagtctcca tcctaaccac 120 tgttagtttt ttaatagatc agtgggttat gcacgtgctt cgcatatgtt tccctccaaa 180 cttacagact cttgctgttg caatgctgtt tgggcttctc cttttgaaac attagtcttc 240 tttctaagtt ttccccctct ttatctctaa tctccaaata accctaaaat ctgaaacctg 300 cattatactt tcttcaataa tataatcaaa gcttggaagt tataatgttt ttaaggagca 360 acgatgacag agaatcacct ctaatttatg gtaagtacga ttttattttt aattctttta 420 atcaaatccc accatcgcaa aaaataattc aacacaagaa gcacatttat atatatatat 480 atatatatat atatatatat atatatatat atatataaag atgtcgcttt gtaagtttgt 540 taatatttta aaagttatat gacttaatca attcccttga aatttatact ttttgttatt 600 tgctttaata gtaatatcat gttgtatatg tattatttgt gttgattaga atataatttt 660 tgctatttta gaatcgacgg cagatacatc attttttagt atcaaaatac accacggagg 720 agttatgaaa cgtactccag aaaaacatta tgttgagggc aacatagact atattgatta 780 tgttaatgga aacaaattgg accttgatga gtttaagaag atggcagaga tttgtggata 840 cttaaagaat tcaattactt tttggcataa atgtggaagc tctagtaata gatggaggtt 900 ggtgtctaca taatgaagcc catgttgttc gtaaaaacat cccaaatgac aacatgatca 960 aaatttactt cgacacttgg attcatattt caatatagaa gatatgactt atatacatag 1020 ctcaaatgct gcagataata acagacaaca acttgttcag gaaaatccat tggcaaatga 1080 ttttagcgac tcggaagttg agttaactga tgggttactt gttgataaac atgaaaagac 1140 tgcacaatac atagtggatg aatgggagat ccttagtatc gaagcacaga gaaagatgac 1200 agctccagaa ggagagtctg attgtgttga ttctacggac acagagtttg catagtgatt 1260 ctgaaaatga gatcttgaac tttcctactt ttaatccaca aacagacaga gacaatctaa 1320 ttttagctct agaatgtgtt tttgaaagca agaaagattt taaaagtgca gtagttactc 1380 atgagattaa gaatggaaag tatatccagt ggctcaaaaa tgacaaagaa agaataaagg 1440 ccgtttgtat acattcagag tgcaaatggg aaatcacagc atgtaaaatg caaagggata 1500 catctttcca aattaggaag tacattccta cacataattg caaggagtgg cattatgata 1560 atagaaaaat aacatcatca ttcattgcaa gaaaatacct cacataaatt aaatcaaaca 1620 gggcttgaag cttagttgat tttagagata cagtaagtgt agatccacga gctcatgtaa 1680 ctctatctca agccaacaga gctaagatgt tagctattgc attgattgat ggtgatatca 1740 aggatcaata caaaatgatg tgggattatt gtattgaaat tgataggaca aatccaggta 1800 gtacaattca tatgaagttc actgagaatg agataccgaa caagccgtac agattttaaa 1860 ggatatacat ctgttttgct gcttgtaagc tagctttcaa ggtaggatgc agaaaaataa 1920 taggcatgga tggttgttgg ttgaagggtc caatgtatag gactcaactg ttaactgctg 1980 ttggaattga tggtaataat agtatatttc ccattgccta tgcaattgtt gagaaagaaa 2040 gtaaagagtc gtgggtttgg tttttgaact atttggcagc tgatttagat gtagataaga 2100 ctggttggac ctttatgtcc aacaaataaa aaggtcttat tgaggctttt aatgaggttt 2160 tgccatatgt caatcataga ttttgtgcga gacatcttca taacaatttt aagagagctg 2220 gttttggtgg gttcacatta aaaaaagcat tttgggctgc tgcaaaggct accactgtaa 2280 aagaatttga tgcttgcatg gtacgtataa gagagttaga tccaaatgct gtcgattggc 2340 tcaatgacaa agaacctagc caatggtcaa ggtctcattt atcttcagat gccaagtgtg 2400 atattttatt aaataacatt tgtgaagtgt ttaatagcat gatctttgat gctagagaca 2460 agcctattgt gacacttttg gagaaattgc gatatcttct catggctaga atgttagcaa 2520 atagggagaa agcgcataaa tggagttcga atgatgtttg cccaaagatt aaggatattt 2580 tgcacaaaaa tcagactgca gcgggtgagt atattcctag aaaatctaat caacggaagt 2640 atgagattat aggagctact attcatgata gttgggctgt tgatttggag aacagaatat 2700 gtagttgtac aaaatggagt atcatgggaa ttccttgcaa gcatgctatt gcagcaattc 2760 gggcaaagaa ggataacatt cttgactatg tggatgattg ttacaaagtc gaaacatata 2820 gaagaatcta tgaacatgca attctttcga taaatgggcc acaaatgtgg cctaaatcaa 2880 ctaaagttcc tccattgcct ctaacaattg taggaaataa aaagacagga agaaaacaaa 2940 aggcgagaag aaaggaagcc gatgaagttg gagcaagtcg aactaagata aaaagaaagc 3000 aacaatctct agactgcagt acatgtaaca agcctggcca taacaaaaaa acttgcaaat 3060 ataatgttgt gtcacaagag actacttcag ttcatcaaaa actacatgta ctactatatc 3120 ttaactatat cagaattggt ttcttatcgg ataatcttaa actaactcaa tttatatgtg 3180 aacttatgat tcaggttaga agaggacttg aagaagcggg acaagaaaaa actagacaag 3240 aaggagctgg acaagaaaaa accgttggac aagaagaagt agttgatata gattctggtt 3300 ggatatacta ttaacaaaca caaagttaaa atgaatcact ggtaatttag cttagtttga 3360 gtgctaatac gtgttcaatg ttaatggtag tttagcctta tccaagtgct tatctatgca 3420 tttttcaggt gttgatatct ccattttggt gctactatat tgctatcaga ttgttggtgg 3480 atatgatgct gcaactatat tgcattggtg ttcctctgtt tcattttcaa gtgttgttgt 3540 tatcaagtgt tgtattgttc taaatccgta ggtgttgcgg tgttgccaat atactgtact 3600 tttggagtta tttttatgca ttttcaagtg ttttgaactt taaaatgatg ttatagtttt 3660 gtttttttct ggtgttgcta atatgctgca tttcttagtg ttgttttgct gctattgctc 3720 tttagttttt ggtattttga tatctcttta cctctaaaat catgttatct ttgtgccctt 3780 ctagtatgtt agtgtcgtct tcaacttaac cattcattca gaaggtgcta atataattga 3840 aaactaaaat ctgaaatcaa tctaggtgaa ttgaaaatat attttttttc tcgaaaaagt 3900 atgaaacttt atagaataag taggctttcg gttacccttc tttcctttac tttcgtttat 3960 ttagcaagga aaactaatga accaaaatat agtctatgca attcttattt tccttcaaaa 4020 ttgccagaag ccccaaatta cagaaaggaa caaaaactag aaataggaag taaaagggac 4080 cgaagaacag taaaggagtt tctcaggtaa agaaattgga ttaaatgaac aaatataaga 4140 aagaaatgaa gaaaacccaa ttaattatca aatttaaatt caagtcacgt gcataaccca 4200 ctggtctgtt aaaaaactaa cggtggttag gatggagact aaaaatgcac cactttatta 4260 aagaatcaga attattaatg ctccactaaa aagaaatagg actattttga gtctaaactc 4320 aaagataatg gattatttta ag 4342 // ID HAT-2_Mad repbase; DNA; EDCOT; 3491 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-2_Mad. XX NM HAT-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3491 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1608-1608 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 12-bp long. XX FH Key Location/Qualifiers FT CDS 954..3362 FT /product="HAT-2_Mad_1p" FT /translation="MERYYKKQCLNPSPNIPDSPPLPSNIPGSPPPPSSIP FT SSAQQSEITELDEILANLPADPGLRRRMLDYPLNCREAIRRYYLQKEPCQP FT KSHIMPRKASDNRCFITGWFDNFKWLEYSIVKDAAFCRYCYLFKCDFDKAG FT GSGSDVFTTKGFTNWRKGPENFRVHEGGVGSLHNKAMQQAKDLMTQKQHIE FT TFVIKQTDEARVNYHTLLSGALDCTRWLLRQGLAFRGHDESLKSSNRGNYI FT ELMQFLADHNEKVRKVVFENAPKNLKYTSSDIQKDLVRACAIETINAITKD FT MEGTFFSLLVDGSRDASNKEQMAVVLRYVNKKGEAIEKFLGVQHVSSTTSS FT SLEEAIERLFATTNLSMSKLRGQGYDGASNMRGELNGLKTKILNKYPQAFY FT IHCFAHQLQLALVFVAKENEDVANFFINANRLVNLIGSSCKRRDALREKQQ FT EQIQKALHLGNLETGKGLNQESSLMRPCDTRWNSHYGTIVSIIVMFEAVVE FT VVEWIKSDRNQDNLGEATGLFKDIQTFDFVFHLFLMRLILGITNELSQALQ FT KKDQDIVNAMALVEVCKQRLQSLRDDDFGDLLHDVEKFCEEHDIVIPNMED FT LHFVPGKSRRKAPKITNFHYYRVDLYFQVLDMQLKELNDRFNEVNTELLLC FT MACLSPVNNFASFDKEKIVRLAQLYPQDFDRMDLMNLPIQLDNYIQDMKMH FT SEFSSLRGISDLAKELVKTGRCESYMLVYKLLTLALVLPVATASVERAFSA FT MKIVKTPLRNKMGDQWLSDSMVVYIERDVFAFIDNEPIMRRFHDMKPRRQQ FT L" XX SQ Sequence 3491 BP; 1065 A; 620 C; 713 G; 1093 T; 0 other; cagaggcgaa gctacgtagg agcgaagggg ggcgttcgcc cctccgctcg ccggaaaaca 60 aaggcaggag cgacgcttga acccccctgg ttcggccgga aactggggag caccgggagc 120 accgggttct gagttctgaa accagaaaca gagtagctct cggggaagac gacgggaggg 180 attttttttt taattttaaa atccaggcca aaacgacgtc gttttgggcc tggtaaaaaa 240 aaattaaaat tttttggtaa acgacgtcgt tttggttgaa tgaaaaaaaa aaatatataa 300 acggggggac cactggtccc catccccatc atctcaatcc ctatttcaaa ttaaaaaccc 360 ttcacccttt tccccatatc ccatcccgtc agtccccccc caccccacct tttcccccct 420 ttcccccccc ccacacgaca aaaccttcac tttccataat tccattggtt gttggcctcc 480 tccaagacca gacacatcag tctgcaactg caagcactgt gcactgtgca cagccactcc 540 aaattccaat taaggtaaaa tttttaattt atttcaaacc ctaattgatt attgaatata 600 aatttttgtt taattgatgt aggattatag ggttatacat tatatggtta ttgattatag 660 attattcata tgaatactat gattattgat tttttttttt gaagtacata aaagaggatt 720 gatacattat atatacatta acataatgaa ccccaattca actaactaaa accctcattc 780 aaatgcattg ttggtactta ttaattacat tcgtagtcta catactctac tgtagaataa 840 aaattgatta ttcatatgat atgattgttg gtactgatta attaaattcg tagtctactc 900 taggactaag agtctaagat atatttgttt ttctttcgtt atacagttac gtaatggaac 960 gatattataa gaaacagtgc ttaaatcctt ctccaaatat tccggatagt cctcctcttc 1020 cttcaaatat tccgggtagt cctcctcctc cttctagtat tccgagtagt gcacaacaaa 1080 gtgagattac tgagttggat gaaatattag ctaatcttcc ggcagaccct ggactgagac 1140 gtcgaatgct tgattatcca ctcaattgtc gtgaagcaat tcgtagatac taccttcaaa 1200 aggaaccttg tcaacctaag tctcacatca tgccaaggaa agctagcgac aatcgatgtt 1260 ttattacagg ttggtttgat aattttaagt ggttggagta tagtatagta aaagatgctg 1320 cattttgccg ttattgctat ctttttaaat gtgattttga taaagcgggt ggtagtggaa 1380 gtgatgtctt cactacaaaa gggtttacaa attggaggaa aggacccgaa aattttcgag 1440 tccacgaggg aggtgttgga agtcttcata ataaagctat gcaacaagct aaagacttga 1500 tgacacaaaa acaacacatt gaaacatttg tgatcaagca aactgatgaa gctcgcgtta 1560 attatcacac tttactgagt ggagcacttg attgcacaag atggttgttg cgacaaggtt 1620 tggcttttcg tgggcacgat gaatctttga aatcgagcaa taggggtaat tatatagagc 1680 ttatgcaatt tcttgccgat cataatgaga aagttagaaa ggttgtgttt gagaatgctc 1740 ccaagaatct caagtatact tcttccgata ttcaaaagga tcttgttcgt gcttgtgcta 1800 ttgaaactat taatgcaatc actaaagata tggaaggtac atttttttct cttttggttg 1860 atggatcacg tgatgcttcc aataaagagc aaatggcggt ggtattgcgt tatgtgaaca 1920 aaaaaggaga agcaattgaa aagtttttgg gtgttcaaca tgtctcctct acaactagta 1980 gctcacttga agaggctatt gagagattgt ttgctacaac aaatttgagt atgtccaagt 2040 tacgaggaca aggctatgat ggagctagta atatgagagg tgagttaaat ggtcttaaaa 2100 caaagatttt gaacaaatac cctcaagcat tttatattca ttgttttgca caccaactcc 2160 aactagctct tgtatttgtg gcaaaggaaa atgaggatgt tgccaatttc ttcatcaatg 2220 ctaatagatt ggtgaatctt attggatctt cgtgcaagcg tcgtgatgca ttgagagaga 2280 aacaacaaga acaaattcaa aaagctcttc atcttggtaa tcttgaaacg ggtaaagggt 2340 taaatcaaga aagtagcctc atgcgtccat gtgatacacg gtggaactcg cattatggta 2400 ctatagttag tattattgtt atgtttgaag ccgtggtgga ggtggttgaa tggattaaaa 2460 gtgatcgcaa ccaagataat ctcggtgaag ctactgggtt attcaaagac atacaaactt 2520 ttgattttgt gtttcacctt ttcttgatga gacttatatt gggaattaca aatgagttat 2580 cacaagcatt gcaaaagaaa gatcaagata ttgtgaatgc gatggcgtta gtggaagtat 2640 gcaagcaaag actacaatcc ttgagagatg atgactttgg ggacttgttg catgatgtag 2700 aaaagttttg tgaggagcat gatattgtca ttcctaacat ggaggatttg catttcgtac 2760 ctggaaaatc aaggcgtaaa gctccaaaaa tcacaaactt ccattactat cgtgtagacc 2820 tctattttca agtccttgat atgcaactaa aggaattgaa tgatcgcttc aatgaggtaa 2880 acaccgagtt gcttctttgt atggcatgtt tgagtccagt gaataatttt gcatcttttg 2940 acaaagaaaa aattgttcgt ttagcccaac tttatcctca agattttgat cgtatggacc 3000 tcatgaatct tccaattcaa cttgacaatt acattcaaga tatgaagatg catagtgagt 3060 tttcatcatt gagaggaatc agtgatcttg caaaagagtt agtgaagact gggaggtgtg 3120 aaagctatat gttagtgtat aagcttctta cattggcttt ggtgttaccg gttgcaaccg 3180 cttcggtgga gagagctttt tctgctatga agattgtgaa aacaccattg cgtaataaaa 3240 tgggagatca atggttgagt gatagcatgg ttgtttacat tgagagagat gtatttgctt 3300 ttattgataa tgagcctatt atgcgacgtt ttcatgacat gaaacctcgt cgacaacaat 3360 tgtaatttgt ttttattgat taattatgga agacattatt atatacaaag atttagttgt 3420 tgctattttt ttttaacctt gcactgtttt aaattcgccc ctccccccga gaaatcctgg 3480 cttcgccact g 3491 // ID Gypsy13-VV_LTR repbase; DNA; EDCOT; 1523 BP. XX AC AM436064; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy13-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1523 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-1523 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 707-707 (2007). XX DR Genbank; AM436064; Positions 29409 30931. XX SQ Sequence 1523 BP; 450 A; 299 C; 269 G; 505 T; 0 other; tgattactac ccaaaaagtg ttattttaca cctttaattc attatgtttt aagcactttt 60 gtgtagtagt tctccatctt tatcccaatt ggcatgttaa ggacctagca atgacttcta 120 atcatatttg tggctagttt tagtgttttg acagcttttt ggatcattaa aacaagccaa 180 gtaaaggaga gaagcaaaga ggaaaaacaa gcaaagagaa aatgaagaaa acagaggaca 240 gcagctgcag tcttcctttg cacttttgga gaactttctg atgtccattt tctacatgct 300 atataccatt tcaaagctca ggaagtcaag aatccaacgc ttcaaaccgt gtacgatttg 360 gagctgaaat gaggaagata tgtccttcgg aagacaactg ctccaggctt gtgcgaaatt 420 cgcacaacac cttgaaattc gcacaacacc ttcagcttgt gcgaagcttg tgcgaaattc 480 acacaacacc ttccaaattc gcacagccca tgcgtggtgc gaattttcct ctatttttgc 540 cgactccact ttagatcttt tcctatgtat tttttgatgt aatttccttt cttatccctg 600 taactaacca atcacaagct tttgcttttg taaagactat ataaggggtg gaaatcacct 660 cttggaacta acgaacatgt gttacgcttt acacttagtg aaatacagag ctctctcatt 720 tttccttttc tctctactat tttctttttc ttggaagcca aacaacctct gagaatgttt 780 tcccagagga tgagaggcta aacttttggt ttcttggagt gaaggaagct aggtgaaaag 840 tccagatgca aaggtggaaa actctcgtgc attaaataca ggtagttgta gttcataaat 900 ggcttctaaa tccaaagttt tgctttaaat cccttagaat cactttgaat ggccaataca 960 tggtaagctt caggtctcta tggatgctta ttgctagatc catatcagtc cattagttat 1020 catgtacgag ccattggaaa gtgactcaag gtgaagaccc atagtgtcta aagccattaa 1080 tggaccttga ctaccatttc tattgacttt ttatggatta aatcttcatt gttaaaccta 1140 taccggttcg ggaaataact ataggttaaa tccccaatgc gaggagaaaa atccggaatt 1200 ttccactttg tattttgaac ttgatcctag caacccttag ctccgggaga ctttctttct 1260 tccattttta cttagtttta tgttagttta gtttcaaaca cctttcaaaa caaatttcat 1320 tttcttttaa actttaagtt tttgataagg aaatcattaa attcaatttc taatctcgag 1380 tatatcacta gtagaatgaa aacgcatccc agagttcgac cctagagcca ctatgctata 1440 gtagctttgc tacgctagta tgaggtcata ggttttataa atgtttttta ttaaatgacc 1500 cgactggagt ttcatgcgaa tca 1523 // ID Copia13-VV_LTR repbase; DNA; EDCOT; 161 BP. XX AC AM455744; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia13-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-161 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-161 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 723-723 (2007). XX DR Genbank; AM455744; Positions 7847 8007. XX SQ Sequence 161 BP; 48 A; 20 C; 28 G; 65 T; 0 other; tggcaagaat atatttaggt actggtgtat atttggcaag aatatattta ggctgattta 60 gtgtgattac gattgtaata tgtgattcct tgtaattcct ttatatactg atgtactctg 120 caccaatgaa ttatgatgaa atatactttt cttctcaatc a 161 // ID Copia-52_VV-LTR repbase; DNA; EDCOT; 315 BP. XX AC chr2; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-52_VV_; KW Copia-52_VV-I; Copia-52_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-315 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr2; Positions 17869118 17869432. XX SQ Sequence 315 BP; 70 A; 39 C; 59 G; 147 T; 0 other; tgataaaata tcttcgtgca atgggtcatt tgaccaagtc tttaataaat tgttttatgt 60 tgagtcttat atctgttatg ttgtcttggt ctataggaaa ttgtttattg agtctcttta 120 ttatctcctg atttttgatg atggtggtag cagatttatt gaaacatggt ttcatggtcc 180 tatttttatg cctttgttgt tatggctttg tcaagccagt taattgtatt gcctatttat 240 tggttgtctc agtacaaata aagtgtagaa ttgtttctct gttctggttt tacttttgct 300 cagtttattt tatca 315 // ID BoSB9B repbase; DNA; EDCOT; 217 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB9B. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-217 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 217 BP; 36 A; 65 C; 71 G; 45 T; 0 other; ggacgagtta gtctggtggt atacggcttg cggctgcaag tacggccccg ggttcgattc 60 gcactggcca ccagggaatt tacatgcgga cttgctctgg cgcccgagac cgaagaccgt 120 tgcctggcca tgacccaccc tcgggtgtgc gtccgcgccg ctaaagggtt cggtctctag 180 tctggaccac cacggtgggg ccaggacact cggttat 217 // ID COPIA2-LTR_LC repbase; DNA; EDCOT; 1208 BP. XX AC . XX DT 24-MAR-2005 (Rel. 10.02, Created) DT 09-JUN-2005 (Rel. 10.07, Last updated, Version 2) XX DE L. corniculatus copia-like LTR retrotransposon - LTR consensus DE sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; COPIA1-LTR_LC; KW COPIA2-LTR_LC; copia-like retrotransposon LTR. XX NM COPIA2-LTR_LC. XX OS Lotus corniculatus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RP 1-1208 RA Gentles A. and Jurka J.; RT "COPIA2_LC: L. corniculatus copia-type LTR retrotransposon."; RL Repbase Reports 5(2), 34-34 (2005). XX RN [2] RP 1-1208 RA Toth G.; RT "Copia-type LTR retrotransposon from Lotus."; RL Direct Submission to Repbase Update (09-JUN-2005). XX DR [1] (Consensus) XX SQ Sequence 1208 BP; 363 A; 242 C; 236 G; 358 T; 9 other; tgtaagatca agttttgatc tagtagtaca actctatgtt ttgatgatta caagttaacc 60 ttttgatatg aacaattgtg gtactctaac gtgtttttct gagtgtgcta tttacaggct 120 ctgacctcaa ctcaatctca cacaaatcag aagcactgtg tataaagagt aacccaagca 180 acgctttcgc attcaccatg ttcagtatga acagtggaaa agcttcagaa gttctgaagy 240 tatacaaact ctgatgtgga ctcagtcgct agaagctctg aagatccaga agttctgata 300 accaagaaac actgaaggtt cagatgttct gatggtgtag aagactctga agatccagaa 360 gctgaatagt ggaaactctg aagtccagaa gcaagaaact ctgaaggcca tgttcttccc 420 tctgagttca gaatcagaag atacaatggt cagaggatct gtgctttccc tctgactctg 480 atcaaccggc ttcacaagtt ccaatatgaa gyattcccct gatcagaagt ctcctaggtt 540 waaaggtcaa gtcgctatcc aagtacaaaa gcaagtgtac cttcctgacg acctacctaa 600 cgttctcagc cacagcagaa gctggatttt ccagaactgc cctccaacgg tagcatttcc 660 catgcaacgc tcaaccctaa tccttggagt atatawagag gctgaagayt gaaagaagcg 720 gctagaagca twcacatacg cgcaagacat attcaaaatm ttctaagctt tctttcatct 780 gaaattcatt gagtttacta ttagcttttt agaagcaaat ctcttgtaaa caattctttg 840 ataaacagtt tgtttagttc ctttaggaga tcaaggttga tcggatccta gagaagacta 900 agagagtgaa tcttagtgtg agctaagtca gtgtaattgt tagtcacttg taggtttcaa 960 gtgcagttgt aactcttacc tgattagtgg attgccttca ttctaagaag gaagaaatca 1020 ccttaacggg tggactggag tagcttgagt gatttatcaa gtgaaccagg ataaaatcct 1080 tgtgtgcttt tctatctctt atctttagca cttaagttct cgaaagattt gtcaaaatct 1140 ttaaggtgga agytttrtac tgaaaacgtt attcaaaccc cccctttcta ccgtttttca 1200 taccttca 1208 // ID TPN1_IN repbase; DNA; EDCOT; 6412 BP. XX AC D37795; XX DT 04-MAR-1998 (Rel. 3.02, Created) DT 04-MAR-1998 (Rel. 3.02, Last updated, Version 1) XX DE Japanese morning glory Tpn1 gene - a transposon. XX KW EnSpm; DNA transposon; Transposable Element; En/Spm family; KW PHNTPN1; TPN1_IN; Tpn1; transposon. XX OS Ipomoea nil OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea. XX RN [1] RA Hoshino A., Inagaki Y. and Iida S.; RT "Structural analysis of Tpn1, a transposable element isolated RT from Japanese morning glory bearing variegated flowers."; RL Mol. Gen. Genet 247(1), 114-117 (1995). XX RN [2] RP 1-6412 RA Hoshino A.; RT "Direct submission."; RL Unpublished (1995). XX RN [3] RP 1-6412 RA Hoshino A.; RT "Direct submission."; RL Direct Submission to EMBL/GenBank/DDBJ (28-JUL-1994). Atsushi RL Hoshino, Science University of Tokyo, Department of Biological RL Science and Technology; Yamazaki 2641, Noda, Chiba 278, Japan RL (Tel:0471-24-1501(ex.4420), Fax:0471-25-1841). XX DR GenBank; D37795; Positions 1 6412. XX SQ Sequence 6412 BP; 2009 A; 1114 C; 1115 G; 2174 T; 0 other; cactacaaga aaaatgcaca tagacaacac tagaaagaca acagttttta agaaaagtgt 60 tgtcttttgt ataaaagaca acagtttggt ccaaaaccgt tgtctttgat gcaacacttt 120 tgtcaaagac aacggttttt acttaaccgt tgttgtaagt gtgttgtctt tgtgcatttt 180 gtgaaaagac aacaccacaa cgacaacggt tttttaaacc gttgtctatg tgcgtttttt 240 tttttttaaa agacaacggt ttttttaacc gttgtcgttg gtgtgttgtc tttaagcgca 300 ctggaataca caacactaga aagacaacgg ttttttaaaa ccgttgtctt tgtgcgctct 360 ttttttaaaa aagacaacgg ttttatttaa ccattgtcat tggtgtgttg tctttaagtg 420 tactcgaata cacaacacta caaagacaac ggtttttaaa aaccgttgtc tttgcacgct 480 cttttttatt taaaggacaa cggttttttt accgttgttg ttggtgtgtt gtctttaagc 540 gcactagaat acacaacact acaaagacaa cggtttttta aaaccgttgt cgttgcgcgt 600 tctttatttg tttaagacaa cggttttatt taaccgttgt ctttaaaata taaaaaaaga 660 tgttaacatc ttatgtatga atgtgcaaca tctggtatat aactgggttg cttctgtgtt 720 aggatgcccg caggaaaaat agaacctgag acctctaaca taataaactc taaacccatc 780 aagctacacc aacacttata tatttaagcg taacatctag gatataacca gtttgcttct 840 gtgttgtctc tgagaacaaa gacaatgatt gtataaaata ggttaaagat gctaccagga 900 aggatagaac ccaaaacctc taacataaca aacaaaacta aacccaccaa accacaccaa 960 cctttgttta ctaaagtgtt acaccttatc ttttacttat aattttgggc tggcagcttt 1020 gacctccggg catttgaaca aagaaagaat acaattcaaa agttaattta ataattatat 1080 tttcgttcat atttaaatat aaaattattc accaaaattt caattttaat taattaaagt 1140 tttattttca attacaatta agaccaatct atgaattcaa ataataataa taataataat 1200 tatcaagtat aaaaaataat agattatatc tataatattt ttttaaaaaa attgggggcc 1260 ctgtgcggtc gcgccggtcc gacatggcct agtacggccc cggcggtgcg gtgtggtgtt 1320 ccgaatggtg cggtatggtg tggatcggcg taagggcggt atgatagggg cctaggttgg 1380 taatcgatcc tttcggctag cgcatgacta acaaggttag ctatatgttg gtaatcaacc 1440 attccggcat gcatgggaca cgtggagaat ggatatgaaa gagtagttga tattgtacag 1500 ttagttatag cccatttctt ttgccgcgat ctttgtaata attgggccgc catctgtctg 1560 ggtaataaag gacaaattat gatgtgcaac tgtgtgcacc atggtgcaca ctgttctatg 1620 ttcataatta ccgaactata tattcataat ttttgaaatt catattcata atgattgaac 1680 tctatatata ttcacaatta cagaactcta tgttcataat tttcgatatt catattacca 1740 aatgttgaac tctgtattca caaatcacaa aactttagta tagaaattat gaatctacaa 1800 tataaaaatt ttgaatattt acactacaaa aaaaaaaaaa aacaattttt agtgacaaaa 1860 atttagtgat gggtagaaaa acccctcact aaatgtatta tttgtataat ttttgtgaaa 1920 gtaaaaaatt actctaatta aaagtttatg atttagtgac aaaattttaa ttatatattt 1980 attttaaaag tatactctga ctattgacat gaaagatatt gttaccatca tcattatctg 2040 aaaattattt cactcaaatc tcattcccac caaaacctta tttttaggcg cccaagtcta 2100 attgcttcta aaacactagt acaaaattga acataccacc ggcttcgcac ccatcgcaca 2160 actaccaccg gcttcacgtc acacccacca ccgttcacag ccaccgcgac aaagccacag 2220 ccaccaccgc gacgccgacg ccacagccgc tgccacgccg ttgatctgaa cccctccctt 2280 gccctgcgac gatggcggcc tccctgtgac gacgccacag ccgccggctc cgatgtgagt 2340 ttgtgagaaa ttttaattta ttgatttcct cttgcctata aataattaac cattcgcctc 2400 tgcatagtgt tcatgtatat tgttatgtta tttcatattg ttaatagttc ttcaatattt 2460 tcactctatt ttcctcgttt tctcgtatgt atatttaggt tttttttttt cttctatttg 2520 cttgattttg tttctactat tgcaatgatt ttatggtata caagagtgat ttccgcaaga 2580 attacaagga gaattttcct gataacaaat ctatggccat tgtgagattt cttaaagcat 2640 tgcatttaag ttattcttaa tactaattgc atagttgttt ggatgatacg atcataatgt 2700 tattattatt ttaagcatta tcactattgt gtttttgtat attaaaattg aaccaaagct 2760 tcaattgata gattatttcc tgtttaattt catttaaggt tgggaaagct ggtggtgaga 2820 aatggaaggc aatgtctgac tctgtgagct ctgatcttct gctttagagt tattattaag 2880 tttgtgtatt taaatttgaa ttaaattgct cgatacatct gtcacacgtt tgctatatgg 2940 actctactgt taggagaaag ctccatatgt ggcaaaggca tcacctctga agtctgagta 3000 tgagaaagct atgcaagagt tcaagaaaaa tgtctctgta attctctttg aaattgatca 3060 cttttgatat tttccttatt tcacatcatt attacattac tttttgctat gattttccgc 3120 taatggcttt ttaaattatc ctctacttct ctattgtaga agagtagcag ctcagaagca 3180 accgtgtctg aagaatctga gcagacttct gaggtgaaag acaactctga gcatgaagca 3240 agctgttagg tctgttgcaa caaagtttcc tttactgtag ggtttggtat ttcaattgtt 3300 tcacaattca gactaattcc tcatgatata gtctaccgtt tgcatgttaa tgagtgtagt 3360 acttagatgg ttttcatact tctgttgaat acatacttga caagaatgta tctacacata 3420 tatatacttt ctattatgag aatgcaaaca tgtcatcata ttattaagat gtgtggacaa 3480 tatcaatctt gaaatgtttt ccctcaacct ttagagcagc tttggtggtg ctacatctta 3540 ttatatactc acaggattcc agaatttccc ccggttactt gtctgtactt atattgtaac 3600 ttgtaaatgc tccgtaacta ttttctatat atcagatttg aagatctgaa ggaccaatta 3660 agaatgcgtt tattgaagaa gcgcaaagtt aaaagaatcc agtttgtaat tacaaatggg 3720 ggtttatcta tagaattgaa tacatatgct ttaatccgtc caaccaatcc aggtctgatt 3780 ttatttcttc atagtttcgt gaaccaaata tcttcaagat aattgataac taatttattt 3840 tcttctttct cagggactat tacttggctt gattctgtct ctaaccttcc tataaaggta 3900 atcaatctta atgtcttcta ttctcacaaa caagaataca agataaaact ttagccttga 3960 gatgatggtt ttaaatgaat caaaatgaac agcagtctct ggacagggta aactaagtgg 4020 aatttaataa agttgttgtt aattgacttc ctgtagtctg tctttgttta cttatgtgca 4080 actgggcaag atagaacaaa tcttacttaa gtgactactg atcattcacg tgttctcata 4140 ttctacgttt gatgtgatga gcattactag tttgctaaca aattaatact caaattttta 4200 attacttggt gacttcattt aacaatgatc tataggtctg ttgatctcat ggtcttacca 4260 gtgaatggtg acattgtatt atgtctaatt gatatccttg atctctaagg tatcaccatt 4320 gttcacttcg aaggttggtc cagggaactg tccattcact gttattgtgt tatgggtatt 4380 gcacgacctc ttcactggtg ttgcttgaat atgtttcaca actctaatca gtatcttcca 4440 gtttatgaga gccaaataca aaccaaatga aaatgaaaaa ttaaatactg agaaaagaga 4500 gcattgttag gatcaaattc ttacaacaaa ctggtgtttg tgaacttcag catttgccaa 4560 agaaaatgca tttgcataga gaaccaaaag gctaatgaac aagaaagggt agagcgattt 4620 agcaatgctg tggctgaatg cttccatgtt gcaattcaga gtttatcagg tatggtagat 4680 atatgtttta tgcttttact tggtgaagag aaaagtatca aggcctttct tttatacagg 4740 ggatgaggtt ggtagatttg gtttcagaat gattgtcagc ttaaagggca gacttagttc 4800 aaccctatag gagccggtgc atccactaac ctatcaaact actaaattct cataatactt 4860 tgcttccatt agatctaata taatctgcca ggttcataac ttttgcattt atggaaattt 4920 gttggcagca tctcttttgt tgtggctgga ttagttgatg aatgggctgc tctcttcttt 4980 gaagagcttg attacattaa tgagggagaa aatgtgacac tttttgtaga gattttgaag 5040 aaagtatact tcaaggaggt cacatatcta tgagaaacat gtctttgtta gtatcatgta 5100 catcatgata ctaattgaga ggcatcacac atggcttaat gatgagttaa ctaccaaagt 5160 caatgatctc ataaaccttc gtaaaactca ttccaaactt gaggcatata catgtctgtt 5220 aaactttctg atgtactttc tgatgtaagt tggtattgaa gagcatgtca tgcctactat 5280 ttattctttg gttcacccac acaacatcac tgatatgaat gtattgacaa attcaggtag 5340 agaggaagtt cagtgaaagt tctagctctt tgacatggta cacggacaga gtaaaggagc 5400 tgggtttgaa gttggcatcc ttagacttgg ttcgtgaatt ttttttgtag tattatgact 5460 tggatgatat atgattcgat tagaattgtt catggaagta tttagacttg ttaattagtt 5520 cttttgtaac tacacttggc catggtgaat ggataaattg atttttatat gattaaaatt 5580 tcagcaggtt aaaaatagtt aaaaccgttt agacaacggt taaaaaccgt tgtctatttt 5640 acaaaagaca acagtttgaa actgttgtct tttctacaaa agacaacact ttatgagtgt 5700 gacttttaac aatagcggtt tcaataacac aatagacaac agtttataac tgttgttttt 5760 taaagaaaag acaacagtta aaaaccgttg tctatgtgca tcacttttaa caacaccggt 5820 ttcaacaaca ttgaatagac aacgggtcaa aaactgttgt ctttgaaaga aacgacaacg 5880 gtttaaaacc gttgtctatg tacatgactt ttaacaacac cggtttcaac aacactcaat 5940 agacaacggt tcttaaaccg ttgttttttc tagaaaagac aacggttatt aaccgttgtc 6000 tatgtgtgtg acttacaaca acaccagctt caacaacact taatagacaa cggttaaaaa 6060 accgttgttg tttctagaaa agacaacggt tattaaccgt tgtctatgtg cgtgacatac 6120 aacaacaccg gcttcaacaa cacttaatag acaacggtta aaaaaccgtt gttgtttcta 6180 gaaaagacaa cggttattaa ccgttgtcta tgtgcgtgac ttacaacaac accggcttca 6240 acaacactta atagacaacg gttaaaaaac cgttgttgtt tctagaaaag acaacggtta 6300 aaaaaccgtt gtctatgcgc gggacttaca acaacaccgg cttcaacaac agaaattata 6360 cccctacgac aacggttatt aaccgttgtc tatgtgcatt tttcttgtag tg 6412 // ID Copia-80_Mad-LTR repbase; DNA; EDCOT; 169 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-80_Mad_; KW Copia-80_Mad-LTR; Copia-80_Mad-I. XX NM Copia-80_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-169 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1699-1699 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 169 BP; 57 A; 11 C; 37 G; 64 T; 0 other; tgtaaacagt taaggttgtt atggtagttt tgtaattagt gagtgattag ttgatgaagg 60 tgtaattagt tagttatcta atactagtga gtaactagta tataaggcat cattgtgtaa 120 ccttattgag ataatgaaat gaaaggataa ttttcctaat atggtatca 169 // ID RAS3_MT repbase; DNA; EDCOT; 816 BP. XX AC . XX DT 29-NOV-2006 (Rel. 11.11, Created) DT 29-NOV-2006 (Rel. 11.11, Last updated, Version 1) XX DE Putative non-autonomous DNA transposon from Medicago truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW non-autonomous; Inverted repeats; Interspersed Repeats; TSD; KW RAS3_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-816 RA Shankar R. and Jurka J.; RT "RAS3_MT: A putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 598-598 (2006). XX DR [1] (Consensus) XX CC A putative non-autonomous DNA transposon, preferably present in CC (AT)n regions. Flanked on both the sides by (AT)5-7, as TSDs. XX SQ Sequence 816 BP; 281 A; 115 C; 104 G; 316 T; 0 other; gggataggat caaatgacac catggtgtca aaattagttt gacaccaaat ctcatccatt 60 catttcattt aatccaaagg tttaaaacta tcaccaaatt aattaatata caccaaatac 120 tctctatcac ctaattaaga aacatatcta tcatcattaa tttataatca aacattccat 180 ttttatttcc ccaaatttat ttgttcctct tttttatttc cccaaattta taaattttcc 240 cagatttcta taatcatact caaacttctt ttctaaactt ttttataaaa tgaatggttg 300 aactcatata cctatggttg tttgagtcat catcaccatc aatgatattt ctttgtcttt 360 atctcatata ctcatatttt tttaataatt aattaaattg tattaaaaaa aaaaccaaca 420 agctcgacaa atgattcttg aattgttcat gctaattaga ttattttgtc actcataggt 480 ctaatgtttt ttttagagga ctcgttgtgt ctcatgttta actgaattaa gatttatcat 540 gattttataa aaattataaa gtttgagttt gtgcttatgg ccaaaagaaa aaaattaggg 600 gaaaataaaa agggtttgaa tctaccaaaa acaagaaggt attgtttgat tatgaattaa 660 tgatgataga tatgtttctt aattaggtga tagagagtat ttgatgtatg ttaattaatt 720 tggtgatagt tttaagcctt tggattaaat gaaatgaatg gataagattt ggtgtcaaac 780 taattttgac accatggtgt catttgatcc tatccc 816 // ID HAT2_MT repbase; DNA; EDCOT; 3946 BP. XX AC CR931739; XX DT 03-JAN-2007 (Rel. 12.01, Created) DT 04-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE hAT-type DNA transposon. XX KW hAT; DNA transposon; Transposable Element; HAT2_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3946 RA Jurka J.; RT "HAT2_MT: hAT-type DNA transposon from barrel medic."; RL Repbase Reports 7(1), 30-30 (2007). XX DR EMBL/GenBank/DDBJ; CR931739; Positions 58082 62027. XX CC The youngest sequences are ~99% identical to each other. XX FH Key Location/Qualifiers FT CDS 751..2910 FT /product="HAT2_MT_1p" FT /translation="MQENMDVDDVPTNAVENPIDVDSDHDLQGEAAGDVGK FT NRKRSRAWDHFVPDGKRAKCIYCNMTYAAEGNTHGTTNLNKHYKKCPKNPN FT RVIDKAQKTLVLGKQVEGDSNVSFKLVEFNQLECRMELAKMIIIDELPFKH FT VEGVGFKGFMSRAQPRLKIPSRVTVAKDCMELYKEEKVILRSLLSLNQQMV FT SLTTDTWTSIQNMNYMCVTGHFIDEGWELQKKILGFGLIANHRGDTIGKAL FT EKCLKDWGITKLCTVTVDNASSNNVALSYLTRNMSAWNGNTLLKGEYMHLR FT CCAHILNLIVFDGLSLIDSSISKIRAACKHVKSSPSRLALFKVCVKDANIS FT SSQKVVIDVATRWNTTYLMLEVASKYEEAFNRLEGEDPSYVSELEVVGGTP FT TVYDWNRARVFINFLKIFYDATLTFSSSLHISANCFFRKLVKIHTALSSWI FT QGEDVVLKNMALTMKAKFEKYWSDENINYLLFVAVYLDPRYKMEYLDFCFG FT WMYGVEKAKMIIAKLHELIGKLFDYYKSVQPIGFVSSDSSSSSTNTMQSDV FT VTFGVGGNVDMDALHRRRVKRRQSEHNSSELVRYLEDEVEDDYEGFEHLKW FT WKSKSTKYIVLSLIARDILSIPISTVSSESAFSTGGRVIDPYRSSLKAETV FT EALICTQNWIKPVTRSVLDESKAFDVLEFETGINCFLAFIFLFYLLVLFLH FT CLFFYVIRNVIFEWSRGVCS" XX SQ Sequence 3946 BP; 1171 A; 603 C; 774 G; 1398 T; 0 other; taggggtgta catgggttgg gttaatccgg aaaacccggt caaacccacc caaagaaaac 60 caaaaaaatg ggttgggccg ggtaaatggg tgaatgtggt tttaaaaatt gatataccca 120 taaaataaaa tgggttccgg gtaaaaccgg acccaaaccc aaaaacccat tttaacccgg 180 aagatgagca atcaatacat atattccaat ttttctcaaa cgttaatact gaaatttttt 240 tttcttctca aggagcattg atactataca cattccaatt tcataagttc agtttccaaa 300 tagtgttcac cgatacatat ttcattttgc caattttcaa ttcaatgttc aattcaatat 360 ataaagagac caacattaac caaccagtaa acccatctac caaaatcaaa ctcattcgtt 420 ccagcaataa catactattt atgaaagatt catttcacac attgcataac aataatttct 480 cgttccagca taccattttt cttaatccat agttgttttg catcatcaaa gtaagcttgc 540 ttcttgtggc taaattgaca gtaccatatc taactcatgt tcatttcttt ttttagtttg 600 cacaaaaggt gcttgatgaa atgtctactt catatcaata ttttttaatg tttatttata 660 gtatctactt ataagttaga attgaaaaat actttaatag tttgattttt cgattctctt 720 ttattttaat actgttgtac atgattgtta atgcaggaga acatggatgt tgatgatgtt 780 cctacaaatg ctgtggaaaa tccaattgat gttgattctg atcatgactt acaaggtgaa 840 gcggcaggtg acgtcggaaa aaatcgtaag cgttctcgtg cttgggatca ttttgtacca 900 gacggtaaaa gggcaaagtg tatttactgt aatatgacgt atgctgctga aggtaataca 960 catggaacca caaatctcaa taaacactat aagaaatgcc ccaagaatcc aaacagggta 1020 attgacaagg cacaaaaaac ccttgtactt gggaagcaag tagagggtga tagtaatgtc 1080 tcttttaagc ttgttgaatt taatcaatta gagtgtagaa tggagcttgc taagatgatt 1140 atcattgatg aacttccctt taaacatgtt gaaggtgttg gatttaaagg ttttatgagt 1200 cgtgctcaac ctcgtttgaa aattcctagt cgtgtcactg ttgctaaaga ttgtatggaa 1260 ttatataagg aagaaaaagt gatcttaaga tctttgttgt ctctcaacca gcaaatggtg 1320 tcattgacca ctgatacgtg gacctcaatt cagaacatga attacatgtg tgtgacaggt 1380 catttcattg atgaagggtg ggaattacaa aaaaagattt taggctttgg gttaattgct 1440 aaccataggg gtgacaccat aggtaaagcc ttagaaaaat gcttgaaaga ttggggaatt 1500 actaaactgt gcacagttac agtagataat gctagctcta ataatgttgc tctatcttat 1560 ttgactagaa atatgagtgc ttggaatgga aataccttgc ttaaagggga gtatatgcat 1620 ctgcggtgtt gtgcccatat cttgaatttg attgtttttg atggattatc tcttatagat 1680 tcatccattt ctaagatcag ggctgcttgc aagcatgtta agtcatctcc ttctagattg 1740 gcattgttta aagtgtgtgt gaaagatgca aacatttcta gctcacaaaa ggtagtaatt 1800 gatgtagcaa caagatggaa taccacatat ttaatgttgg aggtagcttc taaatatgaa 1860 gaggcattca accgcttgga gggtgaagat ccttcatatg tgtctgaact tgaggtcgta 1920 ggaggaactc caactgtgta tgattggaac cgtgcccgtg tgtttatcaa ttttctgaag 1980 atattttatg atgctaccct aactttttcc tcttctttac atataagtgc taactgtttc 2040 tttagaaagt tggtgaagat tcatactgca ctgtcatcat ggattcaagg tgaagatgtt 2100 gtgttgaaaa acatggcatt gactatgaaa gctaaatttg aaaagtattg gagtgatgag 2160 aatatcaatt atctgttgtt tgtagctgtt tatcttgatc ctaggtacaa gatggagtat 2220 cttgattttt gttttggttg gatgtatggg gtggaaaagg ctaaaatgat aattgctaaa 2280 ctgcatgaac tcataggcaa attgtttgat tattacaagt cagtgcagcc tattggtttt 2340 gtttctagtg attcctcctc tagctccact aatacaatgc aaagtgatgt tgttactttc 2400 ggtgttggag gtaatgtgga tatggatgct ttgcaccgaa gaagggttaa aagaaggcaa 2460 agtgaacata actcaagtga gttggtaaga tacttagaag atgaggttga agatgattat 2520 gaaggatttg aacatttgaa atggtggaaa agtaagagca caaagtacat tgttctttct 2580 ctcatagcta gggatatatt atcgattccg atatctactg tttcttctga gtctgccttt 2640 agcactggag gtcgtgttat tgatccatac cgtagttctt tgaaagctga aacagttgag 2700 gctttgatct gtactcaaaa ttggatcaag cctgtcacaa ggtctgtttt agatgaaagt 2760 aaagcatttg atgtgctgga atttgaaaca ggtattaatt gtttcttagc ttttatcttt 2820 ttattttatc ttttagtttt attcttacat tgtttatttt tttatgtcat tagaaatgtc 2880 atatttgaat ggtctcgagg agtttgcagc tgaatccctt gacgagtaac taggtaaaaa 2940 tctaatacca ttgtttcatg tttatactaa ttttgtcttg tgtgattggt gttcctgttg 3000 ttgatggggt agtctatttc ctgttgttga tgaagtttac gttttttagt tgcatactac 3060 tactatgtgt ttttcttatg tgccttcaat tagagcctga cttacatatt aatgaaggtt 3120 gtttgtcact gtcatgatgt cctggcaggt ttagcaactt gggttatatt gagtgatctt 3180 ttgaattggg attacacatg tttgtcttaa tttttcatta acatttcaga tttttcttgc 3240 tcattattat gtaatgtagt gctgagattt tcacaatgga taaatgtata tgtttcttgc 3300 tgcatacttt tgaactccaa tctatgacat aattatcact tatgtagtat ttatgacatg 3360 catacttttg aactccaaat tggtagtcta tgaactaatg ctttaatttt tattatcaca 3420 gtttggtgga gatggagaat ataaacgatg aagtcaggac tcttttgaat tgtggggaat 3480 gttaatgatg acatcaagac tcgtttcttg ttatgttttg ggctcttttt tgtatttgat 3540 gagacatgat tttggtttat tttgacttgg ttgttgcaat ttgtctcttg aacatttgtt 3600 gttttctttt gccaagactt tagctaattt aagatgatgc actctttgag tatttttatt 3660 ctaatgcaat tttatgttat gcaatgtctt taaatttttg agttattttt atgaaaaaat 3720 tatgatgact tgtcatttgg tttaatacta caaaaaaaaa gaagcaaaaa ttaattcggg 3780 taacccacta cccaacccaa tccaacccgg aaattagtgg gtttacccaa accggcccaa 3840 tagtttaacg gatggacatt ttatctcacc caaaccggag taccttatat ggtttgggtt 3900 ttggatttgg ccaaacccaa cctaaaccgg cccacttaca ccccta 3946 // ID Copia37-PTR_LTR repbase; DNA; EDCOT; 241 BP. XX AC LG_XV; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia37-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-241 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-241 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 251-251 (2007). XX DR Genome; LG_XV; Positions 7974942 7974702. XX SQ Sequence 241 BP; 61 A; 39 C; 39 G; 102 T; 0 other; tgttgtgttg atttagtatt aaccgttact gctatttaag ttaataatgt ccggatcctt 60 tggacttcag tttttaattc gattttcttg taaccgcttg accacgtctt tagtggttcc 120 gttatttcca ttattcctgc tgtgtaaagg ctgatataaa gccttaatct ctcatctgaa 180 ataatatagt tttcttgctt ttaacaattg tttgtataat taagagctta agaaactgtc 240 a 241 // ID Copia-58_Mad-I repbase; DNA; EDCOT; 4608 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-58_Mad_; KW Copia-58_Mad-LTR; Copia-58_Mad-I. XX NM Copia-58_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4608 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1654-1654 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1508-2029] - Integrase core CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS 23..4024 FT /product="Copia-58_Mad-I_1p" FT /translation="MDNKSDNMALKIINQDVYKLDKFDGSNFTRWKDKMRF FT MLTVLNVIYVLDPKLEPIREPSDKDSDNIVADRKKREEDELVCRGHILGTL FT SDRLYDLYAHIQSPKEIWEALEHKYTTEKRGTDKFLMFKYYEFTMFDNKPI FT LDQVHELLVLVSKLRELKIVIPDPMIVGAIMAKLPQTWNNYRKKLLHMVED FT ISLEDLQKGIQIEEETRNRDKNFANQDFSKVHIVEGNKYKKNFKVKIDKGK FT FKKTNSNNNQKNANGVCYHCGKKGHYIRDCRHRKASEEYANKTNSANMVEN FT SGIDNIVAMVSMMHIGMITELNMAAAIKSSDWWLDSGATIHVCNDKAQFKT FT YEASTDNQEVLMGNHNSAKVLGKGTVELQFTSGKKLTLLNVLHVPEIRKNL FT VSANLLCKNGIKTVLESDKLIMSKNGMFVGKGYSCDGMFKLSINNKVNSSA FT YIVESSSHLWHLRLAHINFRSLKYMRTLGLIACNDDYNDKCETCIQAKMTK FT KPFPTAERNTNLLDLIHSDICEFNGVLTRGGKRYFITFIDDCSKFTYVYLL FT SNKDEAFECFKRYKAEVENQKGRKIKCLRSDRGGEYFSHEFDIFCEEHGVV FT HQRTAPYTPQQNGLAERKNRTLTEMINSMMINANTPKYLWGEALFTACHIH FT NRITSTKTHVSPYEIWKGRKPNLSYLRVWGCVAFYKALDPKRSKLGPRGIK FT SIFVGYAENSKAYRLLNLDSNTIVESRDVEFIENKFYNDYSVSGKENDQTH FT FSNPSTSQSQGEKRKQSETVNEPRKSQRVRKEKTLGSDFISSQSIVFLVEG FT NRTKVLKKIPILLNVEDDPKSLSEALTSRDAAFWKEAIDDEFESLISNQTW FT VLVDLPQGSKAIGCKWVFRRKYNTNGSIQTFKARLVAKGFKQKKGIDYFDT FT YAPVARLTSIRILFALASLYNLHVHQMDVKTAFLNGDLDEEVYMEQPEGFV FT LPGNEKKVCKLVKSLYGLKQAPKQWHEKFDFVILSYGFRHNSADKCIYSKF FT TNDYGVVICLYVDDLLIFGTNMKGVSETKEYLNSKFKMKDLNEVDTILGIK FT VKKHSGGYALCQSHYIEKLLLKFKHLQIKEANTPYDPSETLLNNSGRSVAQ FT LEYASVIGSLMYAMHCTRPDIAFAVSKLSRYTSHPGTAHWKAINRIFGYLK FT RTINLSLTYSEFPAVLEGYSDASWITSANDNKSTSGWIFTIAGGAISWASK FT KQTCIAHSTMESEFIALAAAGKEAEWIRNLLLEIELWPQPMPSISLYCDSE FT ATLSRAYNKVYNGKSRHISLRHEYVKQLITDGVINIVYVKSSNNLADPLTK FT ALSRALVVSTSSGMGLKPFTEN" XX SQ Sequence 4608 BP; 1629 A; 658 C; 927 G; 1394 T; 0 other; atcttaaagt gttattttcg tcatggataa caaatctgat aacatggctt tgaagattat 60 caatcaagat gtctacaagt tagacaaatt tgatggatca aatttcaccc gatggaagga 120 caagatgcgt ttcatgctta ctgttctaaa tgtcatatat gtgttggacc cgaaattgga 180 gcctattcgt gaaccaagtg acaaagactc ggacaatata gttgccgatc gaaagaagcg 240 tgaagaagat gaattggtat gtcgaggaca catcttgggc acattatctg atcgtttata 300 tgacctgtat gcacacattc aatctccaaa ggaaatttgg gaagcacttg aacacaagta 360 cacaacggaa aaaagaggta ccgataaatt tttaatgttc aaatattatg aattcactat 420 gtttgataac aaacccatcc tagaccaagt tcatgaatta ttggtcttgg tctcaaagct 480 tcgtgaactt aaaatagtta ttccggatcc tatgatagtt ggggctatta tggcaaaatt 540 accccaaaca tggaataact atagaaagaa acttctacac atggtggaag atattagttt 600 ggaggatttg caaaagggta ttcaaattga agaggaaact cgaaatcgtg ataagaattt 660 tgcaaatcaa gatttctcta aagttcacat tgtcgaagga aacaaatata aaaagaactt 720 caaagtcaaa attgacaaag ggaagtttaa gaagaccaat tccaacaaca atcaaaagaa 780 tgcaaatggt gtatgctacc attgtggaaa gaaaggccat tacattcgtg attgtagaca 840 cagaaaagca agtgaggaat atgccaataa gaccaatagc gcaaatatgg tggaaaactc 900 tggaattgat aacattgttg caatggtatc aatgatgcat attggcatga ttaccgaact 960 gaatatggca gcggcaataa aatcctccga ttggtggctc gactcagggg ctactataca 1020 tgtgtgcaat gacaaggcac aattcaagac atatgaagca tcaacggaca atcaagaagt 1080 tttaatgggg aatcataatt ccgccaaagt tctaggaaaa ggaaccgttg aacttcaatt 1140 tacttctggg aagaaattga cgttgcttaa tgtactgcat gttccagaaa ttagaaagaa 1200 tcttgtgtct gcaaatttat tatgtaagaa cggtataaag actgttctag agtccgacaa 1260 gttaataatg tcgaaaaatg ggatgtttgt tgggaagggg tattcttgtg atgggatgtt 1320 caaactaagt attaataata aagtgaattc ttctgcttat attgttgaat cttcctctca 1380 tttatggcat ttacgtttag cacatataaa ttttagatct ttaaaataca tgcgcacact 1440 tggtttaatt gcttgcaatg atgattataa tgataaatgt gaaacatgta ttcaagcgaa 1500 aatgactaag aaaccttttc caactgccga aagaaataca aatttattag acttaataca 1560 ttctgacata tgtgaattta atggtgtttt aacaagagga ggaaaaagat attttatcac 1620 atttatagat gattgttcta agtttactta tgtttattta ttgtctaata aagatgaagc 1680 ttttgagtgt tttaagcgct ataaggctga agttgaaaac caaaagggaa ggaaaattaa 1740 atgccttcgt agtgatagag gtggtgaata tttttcacat gaatttgata ttttttgtga 1800 agagcatggt gttgtacatc aaagaactgc accctataca ccacaacaaa atggtttggc 1860 agaaagaaaa aataggacac tcactgaaat gattaattct atgatgatta atgctaatac 1920 tccaaaatat ttatggggtg aagcattgtt tactgcatgc catatacaca atagaattac 1980 atctacgaag acacatgtgt caccatatga aatttggaaa ggaagaaaac caaatttgtc 2040 atatttgaga gtatggggtt gtgtagcttt ttataaggca ctcgatccta agagatccaa 2100 gttgggtcca agaggaatta aaagcatatt tgtaggatat gcagaaaatt caaaggcata 2160 taggttgctt aatttagact cgaacacaat agttgagtct agagatgtcg aatttataga 2220 aaataaattc tataatgact actcagtgtc tggaaaagag aatgatcaaa cacatttctc 2280 taatccgtct actagtcaat ctcaaggtga gaaaagaaaa cagtctgaaa ctgttaatga 2340 accaaggaaa agccaaaggg taagaaaaga aaagactcta ggctctgatt ttatttcgtc 2400 tcaatctatt gtatttttag tcgaaggaaa tagaacaaag gttcttaaga aaatacccat 2460 attgttgaat gttgaggatg atcctaaaag tctaagcgaa gcattgactt caagagatgc 2520 agccttttgg aaagaggcta tagatgatga atttgaatca ttaatatcta atcagacatg 2580 ggttttagta gacttgcccc aaggatcaaa agcaataggt tgtaagtggg tatttagaag 2640 aaaatacaat acaaacgggt ctattcagac atttaaagcc aggctagttg ccaaaggttt 2700 taagcagaaa aaaggaatag actatttcga tacatatgca ccagtagcta ggctcacatc 2760 aattagaata ttgtttgcat tggcatcttt atataatttg catgtgcatc aaatggatgt 2820 gaaaacagca tttttaaatg gtgatttaga tgaagaagtc tatatggaac aaccagaagg 2880 gtttgttctc cctgggaatg aaaagaaggt ttgtaaatta gtaaagtcat tatatggatt 2940 gaagcaagca ccaaaacaat ggcatgaaaa gtttgatttt gtcattttat catatggatt 3000 tagacataac agtgctgata aatgcatata ctctaaattc acaaatgatt atggtgttgt 3060 tatatgttta tatgtcgacg acttgctaat ttttggtaca aacatgaaag gtgtatctga 3120 aactaaagag tatctaaatt caaaattcaa gatgaaggac ttgaatgaag tagatactat 3180 cttgggaatt aaagtaaaga agcatagtgg gggttacgct ttgtgtcagt cacattatat 3240 agaaaaattg cttcttaagt ttaagcatct acaaataaaa gaagcaaata ccccttatga 3300 ccctagtgaa actttgctta ataattctgg taggtctgtt gcacagcttg agtatgctag 3360 tgtaatcgga agtttaatgt atgccatgca ttgtaccagg ccagatatcg catttgcagt 3420 aagcaaactt tctagataca ctagtcatcc aggtactgct cattggaaag caataaatag 3480 aatttttggt tatcttaaaa gaactattaa cctgagttta acttactctg agtttccagc 3540 agtacttgaa ggatattcag atgcaagttg gataacaagt gctaatgata ataagtctac 3600 atcagggtgg atttttacaa ttgccggagg agcaatttct tgggcttcga agaagcaaac 3660 atgtatagca cattcaacta tggaatctga atttatagca ttagcagcag caggtaaaga 3720 agcggaatgg attagaaatt tgttattgga aatagagttg tggccacaac caatgccatc 3780 catttcttta tactgtgata gtgaggctac tttgtctaga gcatacaata aggtatacaa 3840 tggaaagtct agacatatta gcttgagaca tgaatatgtc aagcaattaa taactgatgg 3900 agttattaat attgtttatg ttaaatcaag taataacttg gcggatccgt taacgaaagc 3960 actttcaaga gctttggtag ttagtacatc tagtggaatg gggctaaaac cctttactga 4020 aaattagcca ccaataatgg taacccgact ttgtctagaa catcactagt ttaaaagttt 4080 aatgggtaat aacaagttat tgttaagtgg ttgtgaaagc actgaaaatt attatatagc 4140 tcattccagg atgatcagtg caagactgct acgtttagga ggatgagttt tatctcttaa 4200 tgaggttatt tgtagttatg tctatagtag cagggacatg ggaaggaacc tcacctatat 4260 gaacataaga agtggtgccg cttctaccaa gagttgggtt ttctcttgta aatgtttatg 4320 aaaccaggat gaagcacaag gccataatag tgcttaatta gttcagaaat ttctttaagg 4380 aaataagaca tagtcatgtg tgtagtgatt ccggttttaa cataagaata ggtggtttaa 4440 acttaggtca ccatcgcatt cgttataact ttgaattact tacactaatt aaaggtttaa 4500 ttcgaaagac acctttattg tatgcatgat tatatcggta tgcttgtgat aattataaag 4560 agagaattgt aatatcattt tctatatatt cttaaaatag ggaaggat 4608 // ID Copia3-PTR_LTR repbase; DNA; EDCOT; 257 BP. XX AC scaffold_1009; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia3-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-257 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-257 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 235-235 (2007). XX DR Genome; scaffold_1009; Positions 1694 1438. XX SQ Sequence 257 BP; 61 A; 39 C; 52 G; 105 T; 0 other; tgttgggaat attttcttat tcactgcata gttgtccagg tcaataggag tttgttagtt 60 agtggatgaa taaatggtat acgtgtccag ctctcattac ttagtggctg gtctgttggg 120 ttaagttggg ttagtgccta gtctttagtt aattctgttt tcgattattt gagtcattgt 180 aatgcctatt taaaggcact cttctttatt caataataca tagcaattca ttctcattct 240 ctactatgtg tgcaaca 257 // ID Copia-85_Mad-LTR repbase; DNA; EDCOT; 388 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-85_Mad_; KW Copia-85_Mad-LTR; Copia-85_Mad-I. XX NM Copia-85_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-388 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1709-1709 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 388 BP; 123 A; 54 C; 82 G; 129 T; 0 other; tgttgaatta taagtctcta gctgattgag tattagaaat aagatgagtt ttaatgtgtg 60 tattcacttg agcataaatg ccaagtgtaa ggttaaatga tgtaaggcca tgagtgccat 120 gtggtgtttg atccatgtaa ttaggtagat gagtggctaa gattaaaagt agtgtttagt 180 gtggtcctaa agctaaggcc atcagttaaa tgtaaagcag tgtgagtgct catttttctg 240 tgtagtacga aatattcctc tgcaatattt ttgcagtaga gaacaagaaa gaaaagaagc 300 aaccattttt cggttcatct tccatctttg cttttgcttc tgttcagcat tctaaaacaa 360 atccagctaa attagagtaa cactaaca 388 // ID Gypsy-23_Mad-LTR repbase; DNA; EDCOT; 285 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-23_Mad_; KW Gypsy-23_Mad-LTR; Gypsy-23_Mad-I. XX NM Gypsy-23_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-285 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1741-1741 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 285 BP; 73 A; 41 C; 60 G; 111 T; 0 other; tgttatggtt tgtgatcagt tttgatatta aataaatgtt ggggttaata tgttaacttt 60 tggggcaaaa ttgtaataga acttataagt tgttagattg ttttgcattt cgccatctgg 120 cattcgcaaa gcatatatgc ttttgtaatt cagttgcaat gtgtggttga aaatcaatac 180 agaaattgag aattgtgctt catctcatct tctccaattc ccttttcccc attgttgcta 240 gctgcaaggt ttggttgagc aggtctggag gtttgatctc taaca 285 // ID Copia11-VV_LTR repbase; DNA; EDCOT; 210 BP. XX AC AM443574; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia11-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-210 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-210 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 678-678 (2007). XX DR Genbank; AM443574; Positions 355 564. XX SQ Sequence 210 BP; 70 A; 23 C; 23 G; 94 T; 0 other; tgttgaatat aatgtattta tagtatatta tctctctttg ttaatatagg tcacatgtat 60 ggtagttagg actcctagcc ttgtatatat atatatatat atatatatat atatatatat 120 atatatatat atatatatat ctcttaattg taaatagaga ttacatgaat gagaattaag 180 gtttttctct tttctctctc tctctcaaca 210 // ID Copia-8_Mad-LTR repbase; DNA; EDCOT; 244 BP. XX AC ACYM01089008; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-8_Mad_; KW Copia-8_Mad-LTR; Copia-8_Mad-I. XX NM Copia-8_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-244 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1350-1350 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01089008; Positions 3785 4028. XX SQ Sequence 244 BP; 64 A; 44 C; 35 G; 101 T; 0 other; tgttaggata taacaatgcc aggtgttaca tgtatagctt atcatgtgtc tgtgtatcat 60 tggttaagtc ttgagttagt tatagttgtg tatttataag acaagtcaat gtattgtatt 120 gaattgaata gtgtggtaat aataattcag tttacaaaac tctctctcta ctttccctct 180 ctactttccc tctctaattt ccctctctac atttcacagc tcttacattt tcttacagtt 240 atca 244 // ID hAT-N3_Mad repbase; DNA; EDCOT; 660 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW hAT-N3_Mad. XX NM hAT-N3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-660 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1638-1638 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >92% identical to the consensus. TSD is 8-bp long. XX SQ Sequence 660 BP; 225 A; 131 C; 125 G; 179 T; 0 other; caaggttcta aaaatcgcta ggcgctagtc gggcggcggg caggggccta gcgcctaggc 60 ggctaggcgg ggcctaggcg gatttatgta aatttattat atatcttgta aataagtgcc 120 tatttacacc taaaaaaaaa ctatacttgt atggataata aaagaatgat aaaatgcaaa 180 aatagaagta gaagaataca caaattatat acatccaaaa agttcaatat ttaaaaaaca 240 gtaagcatat aatcataatg aggaggattt ggatgataga ctaaattctt cttgttcatg 300 aatcatgatc cttgcattgg attggacata gactaaatta tttaaccttg ttgtatctag 360 tttatttctt ttctttgtat gtatcccctc aaaagtgctc caattcgttt cactattgga 420 tgaacttgta gtaaatccat catttgcaaa ttaggtacac catttccata agtataccac 480 catgaaacca aaaaagaaaa aagcacacaa ttaataaaaa atatataaaa aaaaccgcct 540 aggagccgcc tagggccgcc tagcttccag ccgatttttc caaacgcctt gcccaaaatc 600 ggggcggggc tccaccgccc agcgcctagg cggccgccta ggccgatttt tagaacactg 660 // ID Copia-74_Mad-I repbase; DNA; EDCOT; 4417 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-74_Mad_; KW Copia-74_Mad-LTR; Copia-74_Mad-I. XX NM Copia-74_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4417 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1686-1686 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1753-2250] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 1408..2727 FT /product="Copia-74_Mad-I_1p" FT /translation="MLDNNCYITLFPSCFYIQDMETGTILFSGKSSNGFYP FT FSSSSPTAHGRAAFLGVRVGSDVWHSRLGHPSSSILKFLFSRHSNKLPVSG FT NLNLNTFMCHSCPLGKSVKLPFSASLSVTHAPLELIHSDVWSASNKSVSGF FT QYYVLFVDNFSRYSWIYPMKLKSEVFNIFTHFKTLVENQFSTKIKMFQSDG FT GGEYTSHQFKHFFLHHGIHHRLSCPHHPEQNGLAERKHRHIVDTGLTLMAH FT ASMPPAYWAEAMHTAVYLLNRLPSKVLGFMSPYQKLFLKEPDYSFLKTFGC FT ACFPYLRPYNNNKLQFRSTKCVFLGYSLNHQGYRCLDISTNRIFLSRHVVF FT DEGNFPFKAISGSLAPSSPASSPPPVLEITGPLPRAPRLSSSQPVVVSPSL FT ETHQSSPSSDPPQPALQVYSRDPHRRVLSFAQAATLCTPARLCRSL" FT CDS 2792..4417 FT /product="Copia-74_Mad-I_2p" FT /translation="MLTRSKTASLKPPKYVFSAAISSTGPIEPTCFSQANT FT FPEWRTAMADEFNALQRAGTWTLVPRTASMNILPNKWVFRIKQNSDGSIQR FT YKARLVANGFHQQPGLDYGETFSPVVNHSTIRLILALSVQFQWPVRQLDVQ FT NAFLHGSLSEEVYMHQPRGFVDPQFPHHVCRLRRSLYGLKQAPRAWFQCFS FT THLEDLGFRPSTADHSLFTYIHGSTRIYLLIYVDDILVTGNNPSHIVTLIK FT NLGIRFSMKDLGPVHYFLGMEVVRTPSGLSLSQQKYATDLLHRTKMHGAKP FT VPTPAVSGRRLSLQDGDPLPDPTEYRSVVGALQYLTLTRPDINFAVNQVCQ FT FLHQPTSTHWAAVKRILRYLVGTTSHGLIYKPGSFRLTAFSDADYAGDPDD FT RRSTGGYCLYLGSNLVSWSAKKQNGVSRSSTEAEYRQLAIAAATLSWFRML FT FRDLQFPLHCPTLFCDNISAISLASNPVFHARTRHVEVDYHYVREKVVRKE FT LDVRYLSTHDQIADIFTKGLSLPRFRLLVSKLPVLDCTVSLRGRKG" XX SQ Sequence 4417 BP; 802 A; 1232 C; 899 G; 1482 T; 2 other; attcctcctt tgagttatct tttatggtac tcagagccag tgactaacgt cttttttttt 60 cggattcttm ctactcttct ccatggctgc ctcaaccagt tcgactactc cttcctccga 120 catcttccct tctgtttctc atgcgatctc catcaaactt gactcttcca attatcctct 180 ttggttggct cagttgctac ctgttcttcg cagtcgtcaa ttgttggctt ttgttgatgg 240 tacttccatc tgcccctcgg cgttcttgtc cgacgctacc ggcaacgcct ctcccaaacc 300 caaccccgcg tatgctgact gggttcagaa ggaccagctt gttctttctt ggatcaatgg 360 ctctcttggt caccaggccc tcgccgccac tgctcgtcat tccactgccc gtgatgtttg 420 ggttgctctt cagcagcgtt ttgcttctac aaaccaaagt cgcattcttc agcttcgtac 480 tgctttcttc cagaccaaac gaggtgattc ttcaatttct gactttcttg ataagatcaa 540 tggtattgca gatcaattgg cccttgccgg ggcacctgtt tctsctgatg acatggtgcc 600 ggtcgtcatg tctaatgtcg gccccaaatt tgagaacact gttgctgctg ctcaggcccg 660 tgacaagccc atctcccttc ctgatcttga ggctcttctt ctcgctgctg aactccgcct 720 tgctgatcct cctgctccgc cggactccag cgtctcggcc ctggtagcct cccgcggctc 780 ttctgcctct cgtggccgct cctcttctga tcgcggcggc gatcgtggct ctggccgttt 840 ctcacgtggg ggtggtcgtc ctcaacatga tgggtctcgc aacaatggtg gtgacggcta 900 tcgtggctat cgcggtgctg gtggtttcca tgaccgtccg tttcgcgatc gtggtggtgg 960 tcgtcctcag cacgacggct ctcgcttccg tggctccaac aatgcttctg gggttcttgg 1020 tccagcccca tctcacggtt cctcccgtcc tcgctgccag atttgcaata cttttggcat 1080 ggtgctcttg actgtgctca acgccttaat ttggcttatg aaggtcgtcc tccttcttcc 1140 cgtctcactg ccttgactgc tcagcactcc cagccttggc tccttgattc cggggccaac 1200 tcgcatatca ccaatgatct caatactttg tctcagtccc gcgattatcg tggtggtgat 1260 tccgtcggtg gtgtcgttgg cggtacaggt ttgcccatta accgtattgg ctcctccact 1320 ctctctcata ataatatttc tttcaagctt aatgatgttc ttcattgtcc ggatgcttct 1380 acttctgtgt tgtctgctaa tcggtttatg ttggataaca attgttatat tacattgttt 1440 ccttcttgtt tctatattca ggatatggag acggggacga ttcttttttc gggcaagagt 1500 agcaatggct tttatccctt ttcctcttca tcaccgactg ctcatggtcg tgctgctttt 1560 cttggtgttc gtgttggtag tgatgtctgg cactctcgtt taggccatcc atcttcttcc 1620 attttaaaat ttcttttttc taggcattcg aataagttgc ctgtttctgg caacctcaat 1680 ctcaatactt ttatgtgtca ttcttgtccc ttaggcaaaa gtgttaagtt acctttttct 1740 gcatccttgt ctgttactca cgctcctctt gagcttattc actccgacgt gtggagtgcg 1800 tccaataagt ctgttagtgg tttccaatat tatgttcttt ttgttgataa tttctctcgt 1860 tattcttgga tttatcccat gaaattaaaa tctgaagttt ttaatatttt tactcacttt 1920 aagaccttgg ttgaaaatca attctccact aaaattaaga tgtttcagtc tgatggtggg 1980 ggcgaataca ctagtcatca attcaagcat ttttttcttc accatggtat tcatcatcgt 2040 ctctcatgcc ctcaccatcc cgaacaaaat ggtttggcgg aacgcaaaca ccgtcacatt 2100 gtcgacactg gacttacttt aatggcccat gcgtcgatgc ctcctgccta ctgggctgag 2160 gccatgcaca cagcggttta tcttctcaat cgcctcccct ctaaagtact tggttttatg 2220 tctccttatc aaaagttgtt tcttaaggaa cctgattata gttttttaaa gacctttggg 2280 tgtgcatgtt ttccctacct acgaccctat aataataata aactccaatt tcgttctact 2340 aaatgtgttt ttcttggtta ctctctcaat catcaaggtt atcggtgctt agacatctct 2400 actaatcgca tctttttatc acgccatgtt gtgtttgatg aaggtaattt tcctttcaag 2460 gccatctctg gctctcttgc cccgtcctct ccggcctcgt ctcctcctcc tgttttagaa 2520 atcactgggc ctcttccgcg tgccccccga ctgtctagca gccaaccggt ggttgtgtcc 2580 ccctctttgg agactcatca atccagtcca tcatccgacc caccacagcc ggccctccag 2640 gtttactccc gtgaccctca caggcgggtt ctttcttttg cacaagcagc caccctctgt 2700 actcccgccc gcctctgccg ttcactctga tgcgcctcca gaggctccat ctgctgctgt 2760 accacctgcc gtgccctcta cttcccatgg tatgctcacc aggtccaaaa cggcttctct 2820 taagcctcct aaatatgttt tttctgctgc catttcttct accggtccta ttgagcctac 2880 ttgctttagt caggccaaca cttttcccga atggcgtact gcgatggccg atgaatttaa 2940 tgcacttcaa cgtgctggta cttggactct tgttcctcgt actgcttcta tgaatatttt 3000 gccaaacaaa tgggtgtttc gtattaaaca gaattccgat gggtctattc agcggtataa 3060 ggctcgtttg gtagccaatg gttttcatca gcaacccggc cttgattatg gtgaaacttt 3120 tagtcctgtt gtcaatcact ctactattcg cttaattttg gctctttcag ttcagtttca 3180 atggcctgtt cgtcagttgg atgttcagaa tgcttttctt catggctctt tgtctgagga 3240 ggtctatatg caccaacctc gtggctttgt tgatccacag ttccctcatc atgtgtgccg 3300 ccttcgtcgt tctttatatg ggctcaagca ggcgccccgt gcatggttcc aatgtttttc 3360 cactcatttg gaagatttgg gttttcgtcc ctctaccgcg gatcactcgc tttttaccta 3420 tattcatggc tcaactcgta tttatctctt aatttatgtt gatgatattt tggtcaccgg 3480 gaataatccc tctcatattg tcaccctcat taagaatttg ggcatccgtt tctctatgaa 3540 ggaccttgga ccggttcatt atttcttagg catggaggtg gtccgcactc catcaggtct 3600 ctctctttcc caacagaagt atgccactga cctccttcac cgcaccaaaa tgcatggtgc 3660 caagccggtt cctactcctg ccgttagtgg gcgacggctc agtcttcagg atggtgaccc 3720 tctgccggat cctactgaat accgaagtgt tgtcggcgcc cttcaatact tgactctcac 3780 tcgccccgac atcaacttcg ccgtcaacca agtctgccaa tttcttcacc agccgacttc 3840 tactcattgg gccgccgtca aacgcattct tcgttacctt gtcggcacta cttctcacgg 3900 tcttatctac aagcccggtt catttcgtct tacggcattt tccgatgccg attatgccgg 3960 ggatcctgat gatcggcgtt ccaccggggg ctattgcttg tatctgggtt ccaatcttgt 4020 ctcatggagt gccaagaaac aaaatggggt ctctcggtcc agcactgaag ccgagtatcg 4080 tcaacttgca atcgccgctg ccactctttc atggtttcgt atgctgttcc gtgacctcca 4140 gtttcctctc cattgtccta cactgttctg tgacaatatc agtgctatat cccttgcttc 4200 caacccggtg tttcatgccc gcactcggca tgttgaggta gattaccatt atgttcgtga 4260 aaaggttgtt cgcaaggagc ttgatgttcg ttatctttct actcatgatc agattgctga 4320 catcttcacc aagggccttt ctcttcctcg ttttcgactt ctggtttcca agcttcctgt 4380 actcgattgt actgtcagct tgcgggggcg taaagga 4417 // ID SHALINE8_MT repbase; DNA; EDCOT; 5895 BP. XX AC . XX DT 01-JAN-2007 (Rel. 12.01, Created) DT 05-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A LINE sequence from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; LINE; KW Interspersed; repeat; ORF; Poly-A tail; SHALINE8_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5895 RA Shankar R. and Jurka J.; RT "SHALINE8: A LINE element from barrel medic."; RL Repbase Reports 7(1), 98-98 (2007). XX DR [1] (Consensus) XX CC The LINE sequence is well conserved in central and 3' regions CC compared to the 5'. It has two ORFs, of which the second one has CC intact exo-endo-phosphatase and reverse transcriptase domains. XX FH Key Location/Qualifiers FT CDS 2478..4256 FT /product="SHALINE8_2p" FT /translation="MSIIVWNCRGLGNLRVIPKIKFLVRYYKPDILFLCET FT MVDNNKIEEFRYLLGFDFSIAPTRNNRGGGIALFWRNTVNCSIINYSTNHI FT SAKIEEVNQSKWVFTGFYGYPDIARRRDSWNFIRSLANQISLPWCIMGDFN FT DILHSDXXXGRATRPNWLIKGFRQAIQEVELIDIHMEGYPFTWFKSLGTTR FT AVEEKLDRALATNPWMQLFPNARLENLVAPSSDHFPILLDRTPVIRSHRVE FT RSFKFENAWRIEDGVNDVVQGSWLGSTGHNVMEKLASCAEDLTHWSKTHCH FT KIQTDIEHCRKQLHRCRTTHGIQDETYFDNMRKKLDHLLVQEDMFWRQRAK FT KHWYRDGDLNTKFFHAAATSRKKVNKILSLENNEGVRTSDEGGMRVIAKEY FT FEELFESYESTCSPVTNMLNQVVDHEDNVQLTAPFCREEFRDAMFSMHPDK FT CPGPDGFNPGFYQHFWSICSDDIFNECCQWMNEGQFPSSLNSTNIALIPKG FT VEQKTMKDWRPIALCNVLYKLLSKVLANRLKKILHKCIADSQSAFVPDRSI FT LDNALVAIELVHYMKTKTKGKEKSVALKLDIVKHMIELIGHTSEML" FT CDS join(151..1689,1693..2478) FT /product="SHALINE8_1p" FT /translation="MSTICAFNLFLVNLPFECANLLLIWSLRKNPANHMSS FT SLPLLIVFSETYYPESKVIIDLHLGIYGAQSILLIVMIHELLAQIYRHDAL FT CFKLSYKSVILVVAGVHYPLLSIHYSMRYNLTLLSYITFLSLNFIIQMENL FT NLNSDSSAATQRPNLTQAELLDLCLIGRVMVNKPIHISTLETRLGPIWEPK FT YQMTLIQMEGNKFMVQLYSKADLTRILDRSPWLIDNNMLILKKVAIGEDPL FT MVALDTTEIWVQIHQLPFGFMDEKVGALVGSHIGKMIRFDEENNYGPWRKF FT MRVRVEISMDTPLQQELVIEREKGDNIKLVFKFEKLGKFCFVCGVIGHSEN FT FCSDKFESSSTDNEKRWGTHLRAENNAVGNGSKEANRWIVGGRSKVTGNRN FT GGGAANIDCHSKAITSQGVSNHRIFGRIKVGINSETRALTFFKYTECERSD FT GTGLVRWWTEIDPTKVIIDVDTSKEVRNTTALFVPNLTKSDKVNKVLAEGM FT TEKDEFLYANGGGAEALKLVDLEAQHRASPQLSRAGSKEARTGAEKKGARD FT AGAEVLPLADSWVPQRTSQQGQVVPFNDIQQQGAPRLSQPNQQLLQQSLPL FT KTMSAHVYRQLFAKETTPINVSFNTNNAVFQVQKVDKVHQLMSAGQTSVLV FT PTPNNTENCAEFAATREKTSQPSQHSRARAARLGKGPAAVQTHGKPKKPAI FT ARNPVQPDSFMASARGANRAGGPQDDSGPKKRSRTDTAKEGDRGQEVRKEM FT SVVNNPVYEKDETAGPAKQACREQ" XX SQ Sequence 5895 BP; 1751 A; 1122 C; 1354 G; 1659 T; 9 other; tttttctctc ctaaggtccc tttctctctg atctgtcctt tgtgagattc tgttgtcgat 60 tgattaccct taatctaatc gcttggtgga ttctttgtct ccttctatta gccttcatta 120 cgtccagatc tggtgaggcg tggtggtaat atgtcaacga tctgcgcctt taatttgttt 180 ttggttaatc ttccctttga atgtgcgaat ctgcttctga tttggtcttt aaggaagaat 240 ccggcgaatc atatgtcgag ttctttgcct ctcctgattg ttttttcgga aacttactac 300 ccagaatcaa aggtaataat agatttgcat ctgggtattt atggcgctca atcaatcctt 360 ttgattgtaa tgattcatga gttattggct cagatttacc gtcacgatgc actgtgtttc 420 aaattgtcct ataaatctgt catattagtg gttgctggtg ttcattaccc ccttctctca 480 attcactatt ctatgagata caaccttacc cttttgtcat acatcacgtt cctgagtctt 540 aacttcatca tccaaatgga aaatcttaac cttaatagtg acagcagcgc tgcaactcag 600 cgaccaaatc ttacccaagc cgaactgctt gatttgtgtt taattggtcg ggtaatggtg 660 aacaagccta ttcatatttc cacacttgag acacgactcg gtcctatctg ggaaccaaaa 720 taccagatga cactaattca gatggagggc aacaaattca tggtccaact atactcaaaa 780 gcagatctca ccagaatcct ggatagaagc ccgtggctga tcgacaacaa catgctgatt 840 ttgaaaaagg ttgctattgg agaagatcct ctgatggtag cactggacac cactgagatt 900 tgggtgcaga tacatcaatt gccttttggc ttcatggacg agaaggtggg cgcacttgtc 960 ggaagccata ttggtaaaat gataaggttc gacgaagaaa acaattatgg gccttggcgc 1020 aagtttatga gggttcgggt tgaaatttcg atggataccc cactacaaca agagctggtc 1080 atcgagcggg agaaaggaga caatatcaaa cttgtcttta agtttgaaaa actaggtaaa 1140 ttttgctttg tctgcggtgt cataggtcac tctgaaaatt tttgcagtga caaattcgag 1200 tcaagctcaa cagataatga gaagaggtgg ggcactcacc taagagctga gaataatgcg 1260 gtgggaaatg gaagcaagga ggccaacagg tggattgttg gtggtcggag caaggtaacc 1320 ggcaaccgga atggtggtgg tgcggccaac attgattgcc attcaaaagc aattactagc 1380 caaggcgttt caaaccacag aatattcggt cgcattaaag ttggtattaa ttcggagaca 1440 agagcattaa ctttttttaa gtacactgaa tgcgaacggt cggatggaac tggtttagtg 1500 cgatggtgga cagagatcga ccctaccaaa gtcatcattg atgtagatac ttccaaggaa 1560 gtcagaaata ctacagcttt atttgtccca aatcttacca agtcggataa agttaacaaa 1620 gttttagcgg aagggatgac ggagaaggat gaattcttgt atgctaatgg tgggggtgca 1680 gaagcactct gaaagttagt tgatttggaa gcccagcata gggcaagccc acaattgtca 1740 cgagctggaa gcaaagaagc gcgtacagga gctgaaaaga aaggggcgcg tgatgcaggc 1800 gctgaggtgc tgccactagc cgacagctgg gtccctcaaa ggaccagtca acaaggtcaa 1860 gttgtgcctt ttaatgatat tcaacagcaa ggggccccac ggttgagtca accaaaccag 1920 caattactac agcaatcatt acctcttaag acaatgtctg cacatgttta tagacaactg 1980 tttgcaaagg agacaacacc tataaatgtc tcttttaata ctaataatgc tgtctttcag 2040 gtccaaaaag tggacaaagt tcatcaatta atgtctgcag ggcaaacatc agtgctggtc 2100 cctactccta acaacacaga aaactgtgcg gaatttgctg ctacaaggga gaagacaagc 2160 cagccgagcc agcacagccg agctagagcc gcaagacttg gcaaaggacc ggctgcggtt 2220 caaacccatg gaaagccaaa gaagccggct attgcacgca acccggtgca gccagattcc 2280 tttatggctt ctgcacgtgg ggccaataga gctggtgggc ctcaagatga ttctgggcct 2340 aaaaaaaggt ctagaacaga tactgctaaa gaaggtgatc gtggtcaaga ggtgcgaaaa 2400 gaaatgtctg ttgttaacaa cccggtgtat gaaaaagatg aaacggcggg acctgctaag 2460 caggcctgcc gagaacaatg agtattatag tatggaattg ccgaggactg ggaaacctgc 2520 gagtgattcc taaaatcaaa ttccttgtcc ggtactataa accggatatc ctttttcttt 2580 gtgaaacaat ggttgataat aataaaatag aggaatttcg ctatcttttg ggttttgatt 2640 tttctattgc acctaccaga aataatagag gtggaggtat tgctttattt tggcggaata 2700 cggttaattg tagcatcatt aattactcaa ctaaccatat tagcgctaaa attgaagaag 2760 ttaatcaaag caagtgggta tttactggct tttatgggta cccagatatt gctagaagaa 2820 gagactcttg gaattttatt cggagtcttg ctaaccagat tagtctacct tggtgtatca 2880 tgggagattt taacgatatc cttcactcag atgnnnnnnn nggaagagcc actagaccaa 2940 actggcttat caagggcttc cgacaagcta tacaagaggt agagctcatt gatattcata 3000 tggaaggtta tccgttcacc tggtttaaaa gtttgggtac aacacgcgca gtggaagaaa 3060 agctcgaccg tgcgttagca actaatcctt ggatgcagct ctttccaaat gcaagactag 3120 aaaacctggt tgctccttca tcagatcact tccctatctt gctagataga actccagtaa 3180 ttagaagcca cagagtcgaa aggtccttca agtttgaaaa cgcatggaga attgaggatg 3240 gagttaatga tgttgttcag ggtagttggc ttggtagtac agggcataat gttatggaaa 3300 aattagcaag ttgtgcagaa gacctcacgc actggagtaa aactcattgt cacaaaatac 3360 aaacagacat tgaacattgc agaaagcaac tccatagatg tcgtactacc catggtatcc 3420 aggatgaaac gtattttgat aatatgagga agaaacttga tcatctgcta gtccaagagg 3480 atatgttctg gcgacaaaga gccaaaaagc attggtaccg agatggagac ctgaatacaa 3540 aattctttca tgcagcagca acttccagga aaaaagttaa taaaatcctc tctctcgaaa 3600 ataatgaagg agtccgtact tctgatgagg gtggaatgcg agtgatagca aaagaatact 3660 tcgaggaact gtttgaaagc tatgaaagca catgttctcc ggtcaccaat atgctcaatc 3720 aagtagttga tcatgaggac aatgtgcaat tgacagcccc gttttgtaga gaagagttta 3780 gagacgcaat gttctctatg caccctgata aatgcccagg ccctgatggt tttaacccag 3840 gcttttatca acacttctgg tctatctgta gtgatgacat cttcaacgag tgttgtcagt 3900 ggatgaatga aggacaattc ccgtcatctc taaactccac gaacatagct ttaataccaa 3960 aaggagtgga acagaaaact atgaaggatt ggcgacctat agctctgtgt aatgtacttt 4020 ataaactctt gtcaaaagtc ctcgctaatc ggttgaagaa gatcctacac aagtgtatag 4080 cggattcaca gtctgctttt gtgcctgata gatccatctt agataatgca ttagttgcta 4140 ttgaattagt gcattatatg aagactaaga caaaaggcaa agaaaaaagt gtggcactga 4200 aattggacat agtaaagcat atgatagaat tgattgggca tacctcagag atgttatgag 4260 taagttggga ttctcggcta aatggatcca gtggatcatg atgtgtgtgg aaacagtgga 4320 ttactctgtt attctaaaca aagagaaagt tgggcctatt attccaggac gtggtttaag 4380 acaaggcgat ccattatctc cctatctttt catcctctgc gccgaaggac tctcggcgtt 4440 aatcagaaat gctgaaagta agggagacct tcaaggcgtt cgtatttgcc gcaccgctcc 4500 aagggtttcc catcttttat tcgctgatga ctgttttctt ttcttccaag cgaatttgaa 4560 tcaggcgaat gtcatgaagc aaattttatt gcaatatgag gaagtatcgg gccaagcaat 4620 cagtctccca aagtctgaga ttttttacag caggaatatg gatgaccaac tcaagcaatc 4680 tatcaccaac attctgggag ttcgcgcggt cttagggacc ggcaattatc ttggtttacc 4740 atccatggta ggccggagca aaaaggcaac tttcagcttt atcaaagata gggtttggca 4800 aaaaatcagt agctggagca gtaaatgtct atccaaagca ggtcgagagg ttatgataaa 4860 gtctgttctt caagctatcc cttcctatgt tatgagtatt tttaggttac cacataccct 4920 cctggacgaa atagagaaga tgatgaatgc cttttggtgg ggacatggtg gctccagaaa 4980 tagaggcatg aattggctta cttgggaaaa gctctctgtt cataaaaatg atggaggtat 5040 gggctttaag gatttagcag cttttaacgt tgctatgctt ggtaaacaag ggtggaaatt 5100 acaaactaac cctgatagcc ttgtttccaa gattttcaaa gctagatact acccaaatag 5160 tagttatcta gaggctaaac tgggtcataa tcccagcttt gtttggagaa gcattcatag 5220 tgcaaaggtg gtggttagac aaggagctcg atggaaaata ggtacaggtg aacatattcc 5280 agtttgggat cacccttggc tcagtaatgt tgcacgaatt ttaccttcaa ctcatcatca 5340 attggagtgg ccttccatca ctgtttctga cttgttgatt atacaccaaa agcagtggaa 5400 tatggagctc attaatactt tttttgacgc tgatactgct aaaaatattt ttaatactcc 5460 gttgcttcct caggtaactc atgatagact tgtttggaaa tttgaaagga atggtaatta 5520 ttcagttaaa agtgcttata aagatattct gaatcatgat atggcaattg ttcaacaccg 5580 tgtaccaggt aattggaatg gtatttggag aytaaaagtg cccccgaaag ttaagaattt 5640 catttggcga gtttgtcgtg attgtttgcc cacgagaatt cgtttgcaat ctaaaggagt 5700 tcagtgtact gacaggtgtg caatgtgtga tgattttgga gaggatagca accatttgtt 5760 ctttatgtgt agtaaaagta tgctttgttg gcagcgtact ggcttatgga gccctttgat 5820 ggctgttttt gatattaatg tcagctttcc aaccaatgtg tttgctatcc tacaacacct 5880 ggatcagcag caaaa 5895 // ID Copia44-PTR_LTR repbase; DNA; EDCOT; 198 BP. XX AC scaffold_1239; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia44-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-198 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-198 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 267-267 (2007). XX DR Genome; scaffold_1239; Positions 5238 5435. XX SQ Sequence 198 BP; 61 A; 32 C; 34 G; 71 T; 0 other; tgtagcagat tgtaattatc tctaattgta attatcttct aaagagttgt gattagaact 60 cttagttgtt cagttatatt ccatgtctat cactgtccat atgtatctcc tattctgtag 120 gaagaaaccg gtacaaggga ctataaagaa gccttgtact tcttgtattg aaaacttgaa 180 tgaataacgt gaacctca 198 // ID DTPH1 repbase; DNA; EDCOT; 820 BP. XX AC S44589; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 11-NOV-1996 (Rel. 1.1, Last updated, Version 1) XX DE DFR-C=dihydroflavonol-4-reductase {exon 2, nonautonomous DE transposable element dTph1} [Petunia hybrida, lines W138, leaves, DE Transposon, 820 nt]. XX KW Transposable Element; DTPH1. XX OS Petunia x hybrida OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Petunioideae; Petunia. XX RN [1] RP 1-820 RA Gerats G.A., Huits H., Vrijlandt E., Marana C., Souer E. RA and Beld M.; RT "Molecular characterization of a nonautonomous transposable RT element (dTph1) of petunia."; RL Plant Cell 2(11), 1121-1128 (1990). XX DR GenBank; S44589; Positions 1 820. XX SQ Sequence 820 BP; 255 A; 164 C; 184 G; 217 T; 0 other; gaattctctt gtcagaagga gaggttccaa tttaatggca agagggttca aaacttgttt 60 taaatcatag atgtccaaat cttagctagg tgtgacatct aatatctttt ccacccactg 120 taatgtagca gtattagaag tatatattaa catacacgaa agatgattgt ttaaaattat 180 atatagatga caagagcttt aatttggaat tgtagacagg ggcggagcca agaattttaa 240 taagggggtt caagaggaca accgttcaaa tataaaagag gaaaaatcaa aaatatttgt 300 ggcagcccag attcgatcct gggtggtgag cccagcattg acaccccttc gccattgaac 360 taatgccaac acttgttcaa agggggttca acacacagta tatatccaat ctaaaccaat 420 tttatcacat atatgcagtg taaattttgc gcaaaggggg ttcaattgac acccctttgc 480 accaagtagc tccgcccctg attgtagaga acaagaagaa ggtgaaacac cttttggact 540 tgcctaaagc tgataccaat ctgacggtat ggaaagcaga catgacagaa gaaggaggtt 600 tcgatgaagc cattcaaggc tgtgaaggtg tatttcatgt ggccacccct atggtttctg 660 aatccaagga ccccgaggta gtaactaaat acttctatca atctctgtta aaaggctttt 720 ctggactcgc cctcgggctc gacccgggca ctagcaaaac gcaccgaggt ttacgggcgt 780 ggcttagatc cgttagctta cacttcggga ggccgattgt 820 // ID Copia-28_Mad-LTR repbase; DNA; EDCOT; 212 BP. XX AC ACYM01055761; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-28_Mad-I; KW Copia-28_Mad-LTR; Copia-28_Mad_. XX NM Copia-28_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-212 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1375-1375 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01055761; Positions 18616 18827. XX SQ Sequence 212 BP; 64 A; 30 C; 31 G; 87 T; 0 other; tgtaactgat aaaacttaga gatgttatat ttgttttatc tgttttggat atttaggaga 60 actgtccttt ctgttagata gatgaggtgt catgtataag gctttatatg gtttgtatat 120 ataccaacaa tgtaatctta ttcagcaaga aatgaaatca caattatatt ttactctctc 180 tctacaatct tttctctctc tagattctaa ca 212 // ID Copia23-VV_I repbase; DNA; EDCOT; 4084 BP. XX AC AM484507; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia23-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4084 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4084 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 688-688 (2007). XX DR Genbank; AM484507; Positions 9299 13382. XX CC Positions [1494-1994] - Integrase core CC 'CTGTC' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 684..3239 FT /product="Copia23-VV_I_2p" FT /translation="MLVSQTTSRGGRSGTRGRGQRPHCTYCNKLGHTRDRC FT YQLHGRPPRTAHMAQSSDSPLSQPPSSSASQTSQASIASVAQPGNASACLT FT HTSSLGPWILDSGASDHLSGNKDLFSSITTTSDLPTVTLANGSQTVAKGIG FT LALPLPSLPLTSVLYTPECPFNLISISKITRTLNCSITFSDKFVTLQDRST FT GKTIGIGRESQGLYHLTSDSSPAVCISTDAPLLIHNRLGHPSLSKFQKMVP FT RFSTLSSLPCESCQLGKHTRVSFPKRLNNRAKSPFELVHTDVWGPCRTAST FT LGFQYFVTFIDDYSRCTWLFLMKNRAELFSIFQKFYTEIQTQFNISIRVLR FT SDNAREYFSAQFTSFMSHHGILHQSSCAHTPQQNGVAERKNRHLVETARTL FT LLHSHVPFRFWGDAVLTACYLINRMPSSVLHDQIPHSLLFPDQPLYFLPPR FT VFGCTCFVHILTPGQDKLSAKAMKCLFLGYSRLQKGYRCYSLETHRYFISA FT DVTFFEDSPFFSTTSESLPVSEVLPIPIVSPPDVMPPRPLQVYHRRPRVVA FT PLPFPEAPADSLPIPSASPAPALPSPNDLPIAVRKGTRSTRNPHPIYNFLS FT YHRLSSPYSAFVSAISSVSLPKSTHEALSHPGWRQAMVDEMAALHSNGTWD FT LVVLPSGKSTVGCRWVYAVKVGPDGQVDRLKARLVAKGYTQVYGSDYGDTF FT SPVAKIASVRLLLSMAAMCSWPLYQLDIKNAFLHGDLAEEVYMEQPPGFVA FT QGESGLVCRLRRSLYGLKQSPRAWFSRFSSVVQEFGMLRSTADHSVFYHHN FT SLGQCIYLVVYVDDIVITGSDQDGIQKTKATSFYPLSDQRLGETQVFLGN" FT CDS 3121..4074 FT /product="Copia23-VV_I_1p" FT /translation="MWTTSSLQAVIRMVFKKLKQHLFTHFQTKDLGKLKYF FT LGIEIAQSSSGVVLSQRKYALDILEETGMLDCKPVDTPMDPNVKLVPGQGE FT PLGDPGRYRRLVGKLNYLTITRPDISFPVSVVSQFLQSPCDSHWDAVIRIL FT RYIKSTPGQGVLYENRGHTQVIGYTDADWAGSPTDRRSTSGYCVFIGGNLI FT SWKSKKQDVVARSSAEAEYRAMALATCELIWLRHLLQELRFGKDEQMKLIC FT DNQAALHIASNPVFHERTKHIEVDCHFIREKIASGCVATSFVNSNDQLADI FT FTKSLRGPRIKYICNKLGAYDVYAPA" XX SQ Sequence 4084 BP; 866 A; 1095 C; 818 G; 1304 T; 1 other; tggtatcaga gcaaaaggag aaaacctaat tttttttttc aacctcatcg ccgtcggatc 60 tccatcacgc cggcaacctt ttccggcgac attttccggc gacctttttt ccgggaaacg 120 accacatatt ccgaaccgcc ggaggctgat ctacacgcca gtggaaaccc caccggcaac 180 cggcatctca cgcgccccca cgcgccccca cgcgccgccc ttctcctccg gcctgtcacc 240 cacgcgccgg cgcgtgacgg cgcgtggccc actttccggc cacttccgac acctctccag 300 gctcgttcgg cgccgtcttg gccttctagc cctccggcag tcctccccga gccctgcatc 360 tccatttttt ccctgttttt ggccttcttg ccattccggc cacctccgac agggctcccc 420 ctccatcccc gaggcttggg tgctgcttct cttcctctcc aggcacgtca cgaccttttt 480 ttctccattg attgcacctc tcacagccgt ggtttcactg tttttctctc tccgccgaaa 540 tctgaaccca tcttagggct ctcttcgatc caaatacgtg aatatgacca ccaaaaatca 600 gatctttacg tctgttctcc cggggtctcc tccgtatctc gtccactcag actttgccat 660 ctgatagcgc ttcagattct tctatgttag tttctcaaac tacctctcga ggaggacgca 720 gtggtacccg aggtagaggc caacgtcctc attgcaccta ttgcaataaa cttggccaca 780 ctcgcgatcg ttgctatcag ttacatggaa gacctcctcg cactgcccat atggcccagt 840 cctctgattc tccgctgtct cagcctccga gctcctccgc atctcagaca tctcaggctt 900 ctattgcctc tgttgcccag cctggtaatg cctctgcctg ccttacccac acatcttctc 960 ttggaccctg gattctagat tctggagcat ctgatcacct atctggtaat aaggatcttt 1020 tctcctctat tactactacc tctgatttac ctactgttac cttagctaat ggttctcaaa 1080 ctgtggctaa aggtattggt ttggcccttc ctctgccttc tctacctctc acttctgtcc 1140 tttatactcc tgaatgtcct tttaatctta tttccatcag caaaatcact cgtactctta 1200 attgctctat taccttttct gataaatttg tgaccttgca agaccggagt acggggaaga 1260 cgattggcat aggacgtgag tctcaaggcc tctatcacct cacctcagat tcatctcctg 1320 cagtttgcat ttccactgat gctcctctcc tcattcacaa tcgtctgggc caccctagtc 1380 tctccaagtt ccagaagatg gttcctcgtt tttcaacttt gtcgtcgctt ccgtgtgagt 1440 catgtcagct tgggaaacat actcgtgtct cgttcccaaa gcgtttgaat aatcgggcaa 1500 agtctccttt tgagcttgtc cacactgatg tttggggtcc ttgtcggact gcgtctactt 1560 taggatttca gtattttgtc actttcattg atgactattc tcgatgtact tggttatttt 1620 taatgaagaa tcgagctgag ttattctcta ttttccagaa attttatact gaaatccaaa 1680 cccagttcaa tatttctatt cgtgtgttac gcagtgacaa tgccagggaa tatttttcag 1740 cccaatttac ttcgtttatg tctcatcatg ggattcttca tcagtcttct tgtgctcata 1800 ctcctcaaca aaatggggta gctgaacgca agaatcgaca tcttgttgag acagctcgta 1860 ctctcctcct ccatagtcat gttccttttc gcttttgggg ggacgctgtt cttaccgctt 1920 gttatttgat taatcgtatg ccctcctctg tcttacacga tcagattcct cactcccttc 1980 ttttccctga ccaaccactt tatttccttc ctcctcgtgt ctttggttgt acttgctttg 2040 ttcatattct cactcctgga caggacaagc tttccgccaa agccatgaag tgyctcttct 2100 tgggatattc cagacttcag aagggttatc gttgttattc ccttgagact catcggtact 2160 ttatctccgc tgatgtcacc ttctttgagg actcaccatt cttttccacc acttctgagt 2220 ctcttcctgt ttctgaagtc ttgcccattc ccattgtctc cccacctgat gttatgcccc 2280 ctcgaccact tcaggtttat catcgtcgcc ctcgtgtcgt tgctcctctc ccttttcctg 2340 aggcacctgc tgactcactt cctatccctt cggcttcacc tgccccggct ctgccttctc 2400 ctaatgactt acctattgct gttcggaaag gtactcgctc tactcgtaat cctcatccta 2460 tttacaattt tttgagttat catcgattat cttcacccta ttctgctttt gtttctgcta 2520 tatcctctgt ttctcttcca aagagcaccc atgaagctct ttcccatcca ggctggcgac 2580 aggcaatggt ggatgaaatg gctgctctgc actctaatgg cacttgggat cttgttgttt 2640 taccctctgg taaatctaca gttggttgtc gttgggtcta tgcagttaag gttggtcctg 2700 atggtcaggt tgatcgcctt aaggcccgtt tagttgctaa aggctatact caagtttatg 2760 gttctgatta tggtgacaca ttctctcctg ttgccaagat tgcttctgtc cgcttgcttc 2820 tctccatggc tgctatgtgt tcttggcctc tttatcagtt ggatattaaa aatgccttcc 2880 ttcatggtga tcttgccgag gaagtttata tggagcaacc tcctggtttt gttgctcagg 2940 gggagtctgg tttagtgtgc aggttacgcc gttctctata tggcttgaaa caatctcctc 3000 gagcatggtt tagccgtttt agttctgttg ttcaagagtt tggcatgctt cgcagtacag 3060 cagaccattc agttttttat catcataact ccttggggca gtgtatttat ctggttgttt 3120 atgtggacga catcgtcatt acaggcagtg atcaggatgg tattcaaaaa actaaagcaa 3180 catcttttta cccactttca gaccaaagac ttggggaaac tcaagtattt cttgggaatt 3240 gagatagctc aatctagttc tggtgtggtc ctttcccaaa ggaaatatgc tttagacatc 3300 ctggaagaaa ccggtatgtt agactgcaaa ccggtagaca cacctatgga tccgaatgtc 3360 aaacttgtac caggacaggg ggagccttta ggagaccccg ggagatatcg acggctcgta 3420 ggtaaattga actatctcac cattactcgt ccagacattt cttttcctgt gagtgttgtt 3480 agtcaattcc tacagtcacc atgtgatagc cattgggatg ccgtaatccg tatccttcga 3540 tatatcaaaa gtacaccagg ccaaggtgta ttgtacgaga acagaggtca tactcaagtt 3600 attggttaca cagatgcaga ttgggctggc tcacccacag atagacgttc cacttcaggg 3660 tactgtgttt ttattggagg taatctaata tcttggaaga gtaagaaaca agatgtagtg 3720 gccagatcta gcgctgaagc cgagtatcga gctatggctt tggcaacatg tgaactcata 3780 tggttgagac atcttcttca ggagttgaga tttggaaagg atgaacagat gaaactcatc 3840 tgtgataacc aggccgcatt acatattgca tccaatccag tctttcatga aaggaccaag 3900 catattgaag ttgactgtca tttcattaga gagaagatcg catcaggatg tgttgctaca 3960 agttttgtca attcaaatga tcaactagca gacatcttca ctaaatctct cagaggtcct 4020 aggattaaat atatttgtaa caagcttggt gcatatgacg tatatgctcc agcttgaggg 4080 ggag 4084 // ID SHAMUDRA_MT repbase; DNA; EDCOT; 5645 BP. XX AC . XX DT 11-JAN-2007 (Rel. 12.01, Created) DT 11-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A DNA transposon from Medicago truncatula. XX KW MuDR; DNA transposon; Transposable Element; transposase; KW Interspersed; repeat; TIR; SHAMUDRA_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5645 RA Shankar R. and Jurka J.; RT "SHAMUDRA_MT: A DNA transposon from barrel medic."; RL Repbase Reports 7(1), 105-105 (2007). XX DR [1] (Consensus) XX CC The transposon looks autonomous and contains intact transposase CC domain. It has inverted repeats on both terminal with 9 bp target CC site duplications. XX FH Key Location/Qualifiers FT CDS join(1831..2514,2533..2886,2890..3234) FT /product="SHAMUDRA_MT_1p" FT /translation="MRFSRVPPQTYYVLSSYNSAHKCNNTGRVRLLRTKLL FT AKKLVPILRHTPDMTIKALQDLCKHKWYVIFSRFQMYRAKLKALEMIHGAS FT DEQYAHLRNYAEELLRSNPGSTVKIKCKETAAGFVFQRIYVCFDACKRAFV FT QNCRPLIGLDGCFLKGRYGGQLLSAIGKDGNNQMIPIAFAVVEAETKXSWD FT WFIELLLSDLNGIQCKRWSFISDQQKVIFVTFYLFLCSINFVLFVMMKGLV FT NTIASIGDNVEHRLCVRHLYGNFRKRHPGEHLKEALWDAARATTMPDFNKA FT MXXLKRFSEAAWEEMRQYPPGMWCRAGYSTHTCCDLQVNNMCEAFNSAIIE FT LREPIISLVEGLKFYITNRIVRLRDYMLRYXGDICPMIKKILXKAKKDANG FT WSPIWXGDREYAQFTVSDGSDTYVVNLKEKTCACRKWDLSGIPCPHAIAGI FT YYNSQNPDDYVAHWYR" XX SQ Sequence 5645 BP; 1869 A; 832 C; 1196 G; 1726 T; 22 other; ggctaaactg cagttttccc cccctaactt tcaaaacggt gcgattttgg ccccctagta 60 aaaaaaatta aattttaaac ccctatgttt tagccccttt gcaaaacaga ccttttggtc 120 aattttgacc tggtcaacgc ggatgtgtca tgccacatgt gtatttaccc atttattttt 180 atttaaaaag ccaattgtgt aattctttaa aaaaataaaa aagaaaaaag aaaatataaa 240 agggtttggc acgtgagagc tgcattttca gattcaaatt ctagggttaa accacaaacc 300 cttaagtttc caaatccatt gttcttcaat aatctccttc caaaatcgtt accgaaatca 360 aatatccatc acaaatcgaa ttccaggtga ttgttcatct ctgtttgttg cgaaaatgaa 420 gtggaaagaa gatggaaagg cgacggcgac ggcgagtacg ggttctaggg tgaagaagaa 480 cgattcgatg gcgactgaag gttcagagaa gaagaaagat tcagagaata tggaagttct 540 atcatctcaa ggaaacgtgt tctctggaca gattcccgac atggatgctt caaagtaagc 600 gtttttttgg tttcatatat ctgtttaact ataaagcaaa gctcatgtta cattatttct 660 gaataaaaaa agggttgttg gaagtattga atactgtatt taattatgca cagttgaaaa 720 ctagaaaatg ttaattttat actgcttttt tggtttacat tgctatgaaa ggagtatgag 780 tataaatatc gtatgaaaat acagtattca tatagtataa atacggtata aaaatacagt 840 attcatacag ttgtaataca atatgaatta aatattaaat gatatttatt caatctttgt 900 agggctgttg aggaccattc attgaagata aggtttcacc acaaaggtta tttcatttct 960 gaccctgtta tagcttataa gaagggtgaa gtatatgaat ttggtggtga gttagacata 1020 gatgagacaa acctcaaaga tttggacaac ctggtgagag agattggtgt ggaaggtgag 1080 tataagttgt tttatgtcag tccaggttgg gagttgagtg atggtcttag gccgttgaaa 1140 actgataggg atgtcattag attcataaat gatcatataa atcatggagt tgctgatttt 1200 tatgttgaag ctgataagga ttttgaagga cttgatagca ggtatgtgag tgatgaggaa 1260 gttgttgtgt tagataaagg gaaagaacca gctgaacttg aagaggaaga agaatctgat 1320 cctgagtatg ttggtgatgg ggatgatgag ggtgatgagc atgagtctga agctgaaatt 1380 ggaagtgttg atggggtgtc aattgatgac agtgattttg atgaagaatg ggactggact 1440 tctgtgctgc ctaaacaaac tttgaaccca actcctgttg ctcagtcatc caactcttgt 1500 caggctattg ttggtgttga agcatcaagg aacactgagg cgacaactga ggaagatttt 1560 gaagatgaga atggagactc tgattttcta gaaagttgtg aatcaagtga ggatgatggt 1620 attcaaagga aaaagaagaa atacaatagg tttaagtttc ctgaaaatga tgagactgtg 1680 atatttgaag agggacagat atttgcaact gctttgttaa ttaaaactgc tgtgaaagaa 1740 tatgctttac agaacaagaa gaatgttcac ttgaagaaaa gtgagaaaaa gagaattatt 1800 gtgaagtgta gtgatggatg tccatatcac atgagattta gtagggttcc acctcaaact 1860 tattatgtgt tgtctagtta taattctgca cataaatgca ataatactgg tagagttaga 1920 ttgttaagaa caaagttgtt ggctaagaag ctggtaccaa tcttgagaca cacacctgat 1980 atgaccatta aggcactaca agatttgtgt aagcataagt ggtatgtgat ttttagtagg 2040 tttcagatgt atagggcaaa attgaaggct ttagaaatga tacatggtgc tagtgatgag 2100 caatatgctc atcttagaaa ctatgctgaa gagttgttaa gaagtaatcc tgggagtact 2160 gtgaagatta aatgtaaaga gactgctgct ggttttgtat ttcagagaat atatgtttgt 2220 tttgatgctt gcaagagggc atttgtccaa aactgcagac cattgatagg gctggatggt 2280 tgttttctga aagggaggta tggtggacag ctattatcag caattgggaa agatggtaac 2340 aatcaaatga tacccatagc atttgctgtt gtggaagctg aaaccaaaga wtcatgggac 2400 tggtttattg aactactgct ttcagatttg aatggcattc aatgcaaaag atggtctttc 2460 atatcagacc agcaaaaggt aatatttgta actttttact tatttttatg ctcttaattt 2520 aatattatgt agattaattt tgtattgttt gtaatgatga agggtctggt gaatacaata 2580 gcttctattg gtgataatgt tgagcacaga ttgtgtgtga gacatttgta tggaaatttt 2640 aggaaaagac atcckggtga gcacttaaaa gaagctttgt gggatgcagc tagggcaact 2700 actatgcctg attttaacaa ggctatggas rawctgaaaa gatttagtga ggcagcttgg 2760 gaggagatga ggcagtatcc accaggtatg tggtgtaggg caggatatag tactcacaca 2820 tgttgtgact tacaagtcaa taacatgtgt gaggcattta actctgcaat cattgagtta 2880 agagagtaac caattatttc acttgttgag ggattraagt tctatataac aaataggata 2940 gttagattaa gggattacat gttgaggtat kaaggtgata tttgtccaat gataaaaaag 3000 atattggana aggctaagaa ggatgcaaat ggttggtcac caatttggyg tggtgatagg 3060 gartatgctc agtttactgt ktctgatgga agtgayacgt atgttgttaa tctcaaagag 3120 aagacatgtg catgtagaaa atgggattta agtggtattc cttgcccaca tgctattgcw 3180 ggaatctact acaatagcca aaayccagat gattatgtgg cacattggta caggtgagtt 3240 gtgatcttaa tttatatgct ttctgcttta tgtaatctta atttaagtgg ttaattaagt 3300 ataatttggt tacatatgac aggaaacaaa ctttcttgga tacatatgat aattttatca 3360 tgccttcaaa tggaccaaag ctatggccag aagtgaacct tccaccaata ctaccacctc 3420 cagtcagaag ggcacctggg aggccaaaga agctaagaag gaaggataat gatgagccta 3480 agccaacaac tagcaagaag ggaaagagaa atcaggaaac tgtgaggtgc agaagatgta 3540 aagagcttgg acataatatg aggacttgta agggtaaaac agctgctgat aggacgatta 3600 cacctggagg gaacaaggta ataacgcagt ttctgctgtt ataacacttt ctgatagata 3660 acacaagatc tgatatttaa cacactttgt gatattgtag gataatactg cacaayttca 3720 acaccctgag gcttcaaatg cacaaggtac aaacaacaat gctggttctg caactgctgc 3780 tcatgtgaac aaccatgctt caaatacaca agactcaaat gcacatgcaa ctgctactgc 3840 tggtacaaac aaccatgctg gttctgtaac tgctgctcct gtgaacaaca ttgctacaga 3900 tgcacaacac tcaaatgcac aacgctcaaa tgctcatgta actgctgcaa ctagtaacac 3960 atctggcaag catgttattg ttggtgattc atccttgttt gtgcctagaa agtcaaggtt 4020 tgctggagct aaaaggaaaa gtgatgagat ggcaactgtg gggactcaac aatctgtgaa 4080 caaaacttaa gttaggaatg acaattaatg acaatgagac tgatgttata ttttgattaa 4140 tttaggttat ttaatgtcaa gtactctatc tgatattttg gttaattttg gttatgtaag 4200 gttaagtact ctaaagtact ggttatgatg ttttggttaa gtactctaat gtcaagtact 4260 cttcatgtat tttgtatttg gtgaatgtga agtaatacta tgttaactcc aatgtcaagt 4320 actctttaaa tgtcatgtgc caaagctagg atgcatttct attcttgatc aatggttgat 4380 gtgctattgt taagaaattt aaaagaagta caatgtcaat aatgtgcgtc tgttcacaaa 4440 ctcagggagc attattattt ggattctaat catgctttca tttgatgtgc catagcattg 4500 ttatttraat ttawaatgaa agcatgattt cattttacat tgracttttg ttatttataa 4560 catacataca atttattctt tcaaagatgt tacttttgtc actttgattt tagaacaaat 4620 caccccaaac tcagggaact ttcataaagt ctcctgagaa atagctttca ttacaattgt 4680 agtctccttc ctcaggcaac attacagaac tgatagaaat tctttkctaa yattcattaa 4740 ttcttgccaa tagcaraaat tacattccat aayaacataa catagcaaca ttacataact 4800 tatacattaa tcataccaag cttaatgaaa atcacaaaca aacttaaaaa caacaacatc 4860 cctaaaacaa caattgttaa ctccaacttt ttctccttct tcttcaatgc atcattcttc 4920 ttcaacagtc ctctaattaa tttcttctgc ctatcaggaa cttctggatc aaaccatctg 4980 aaaaaactgc attttcttct ctggaaatac tttccacatc catggaacct ccttcctgga 5040 ttttcatctg tccaagctgt gaccagaggt gattcaacac cacaataaca aaccaacctc 5100 gatttggcca tacatgatga cccactaacg gttgaagatg aattgttacc aaacattttc 5160 tgttttcaga tatgcaaaca cacaaaacaa atcgatgtgg aactaagaaa ggaggtagag 5220 gaagaatcga tgtggaagaa aggagaagaa ttgtcgaata agatggttga ataagaacag 5280 atgaaggttc ggtttatgga gaagaacaga tgaaggttcg gttatggtgg aaaaaaaaca 5340 agaagaagag atgaagaaga agggttgaag agttggagtt ttttaacgtt ggaagctctc 5400 acgtgccaaa ccttttatat ttttttttta tttttttaaa gaattacaca attggcattt 5460 tgaataaaaa taaatgagta aatacacacg tggcatgaca catcagcgtt gaccaggtca 5520 aaattgacca aaaggtctgt tttgcaaagg ggctaaaaca taggggttta aaatttaatt 5580 ttttttacta gggggccaaa atcgcaacat tttgaaagtt agggggttaa aagtgcagtt 5640 tagcc 5645 // ID BNINTMO repbase; DNA; EDCOT; 632 BP. XX AC X99804; XX DT 30-MAY-2000 (Rel. 5.04, Created) DT 20-SEP-2007 (Rel. 12.1, Last updated, Version 2) XX DE B.napus DNA fragment with retrotransposon integrase motif. XX KW Gypsy; LTR Retrotransposon; Transposable Element; integrase; KW BNINTMO. XX NM BNINTMO. XX OS Brassica napus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-632 RA Elborough M.K. and Storey E.S.; RT "Direct submission."; RL Unpublished. XX RN [2] RP 1-632 RA Elborough M.K.; RT "BNINTMO."; RL Direct Submission to Genbank (06-AUG-1996)K.M. Elborough, RL University Of Durham, Biological Sciences, South Road, Durham, RL Co. Durham, UK. XX DR GenBank; X99804; Positions 1 632. XX CC This is a fragment. XX SQ Sequence 632 BP; 160 A; 132 C; 179 G; 161 T; 0 other; tgatccgtag tggttggaag tttcctacct gccagttcgt aaaggccgaa catcaagtgc 60 ccaatggtat gtttcagaac ttcctatacc agagtggaag tgggatcaca tcacaatgga 120 tttcgtgacc ggttttccta tgactaggaa ccgtaaggat gcggtgtggg ttgtggtcaa 180 tcggctaacc aagtcggctc atttcttact ggtccggaag ggggatggag tggatcagat 240 cgtaaggatt tacttggacg agatagtacg tctgcatgga gtgccggcta gtattgtctc 300 gaatagagat cctaggttca cctcttatct ctggcaggct tttaaaaaag ccttaggaac 360 aagagtgaac atgagcacaa cttatcatcc tcagacggat gggcagtcag agaggacgat 420 ccagacgttg gaggacatgc tgagggccgt ggtattggat tggggcgact catgggagaa 480 acatctaccc ttggtcgagt ttgcctacaa caacagtttc cataccaaca ttggtatgtc 540 accttatgaa gctttgtatg gacggccttg caggacacca ttatgctgga cccaagtggg 600 ggagagaagc atatttggcc ccgtggatcc ag 632 // ID Copia-93_Mad-I repbase; DNA; EDCOT; 4479 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-93_Mad_; KW Copia-93_Mad-LTR; Copia-93_Mad-I. XX NM Copia-93_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4479 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1724-1724 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1749-2276] - Integrase core CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS join(87..1337,1341..3611) FT /product="Copia-93_Mad-I_1p" FT /translation="MADSDNTIIKKGDGESFADPYFLHPSDHPGLILVSKK FT LTGDNYNTWCRAMEISLGAKNKIGFINGKVNMPSETKQPDAYAAWQRCNNM FT LLAWIINSIESDISDSILYLKTAYEVWEDLRERFSQSNAPRIFQLQREIAS FT LTQGQQSVAVYYTKLKGLWDELASYSSSTICTCGAQHETNRLMQFLMGLNE FT SYSAIRGQILLMNPLPSYRQAYSSIIQEEKQRELGTGSRSLTEPAAMAVRH FT QQQSSKKQHQQSQTSSNSRPPLHCSYCDAKYHTVETCWQKNGYPPDHPRHN FT PNTTRNSKQNGGGSGFSRGSSSAHHVASTPTIKDLQAAVPNLSEKQYADIF FT SALTSKNDKSQAANEAPQAHAALTSPPPSGLSPLVPGRWIIDSGATDHITC FT SSSLLTNSINNTSLPPVSLPSGEASITSIGNIQLSDLLQLKDVLCVPSFQV FT DLLSVGKITDGLHCSVTFFPSWCILQDLISKVTIGVGKRRGNLYYLVALAS FT TSSLQNRPSCHLITVSADLWHRRLGHPSLGRLQYLANQTLNFPFDSSHRCH FT VCPLAKQTRQPFSRSSISTSSFFELLHCDIWGPHKTASLTGAHYFLTIVDD FT FSRFTWVFLMRHKHETQPTLKTFFAYIETQFHTKIKQIRVDNGGEFYSMRD FT FFSDNGIIYQHSCVYTPQQNGVVERKHRHILETARALRFQSHLPVKFWGEC FT ILTAAYLINRLPTPLLSKKSPFEILYNKPPSYSHMRVFGCLAYATSVHPSS FT KFSPRAHRCVFLGYPPGQKAYKLYDLETHKIFTNRDVIFLEDTFPFDPSTT FT AAPSPPLSDLPHSTPLPIPLDPTTLDHSTTTPLDIVPHTSTPLDPPLDPSP FT PPDSSSHPPTFHPLTDPPTDPTPDLPISTQPTRFSTRHKEPNVRLRDYVCS FT QVMLPPLQSSSPSSSGSTKGTRYPICNFISYHRYSPLHLSFVAHISRGVEP FT SSFAEAIQDPHWHEAMDSELEALSSNNTWTLTPLPPGKRPIDCKWVYKIKH FT HADGSIERYKARLVAKGFTQAEGIDYHDTFSPTAKMTTVRCLLALAAGQSW FT SLQQLDVNNAFLHGDLQEEIYMSPPPGLRRQGENLVCRLNKSLYGLKQASR FT QWFAKFTEAVHAAGFVQSKADYSLFTRKSGKSFTALLIYVDDIINHRQRCR FT CHQFPQTVSSHSLSY" XX SQ Sequence 4479 BP; 1110 A; 1186 C; 852 G; 1326 T; 5 other; tggtatacag agcaggttcc aaaccctagc tcttttctcc gccgaaacca ccagaacctt 60 tttttcgttc gttgtcctcc ttctccatgg ctgacagcga caacaccatt atcaagaagg 120 gcgacggcga gagttttgcc gacccttatt ttcttcatcc ttcagatcat cctggtttga 180 ttttagtctc caaaaaattg actggggaca actacaacac ttggtgccga gctatggaga 240 tttctttagg tgccaagaac aaaattggtt ttattaacgg caaggtgaac atgccatctg 300 aaacaaagca acccgatgct tacgccgcat ggcagaggtg caataacatg ttacttgcat 360 ggatcatcaa ttccattgaa tctgatattt cagattcaat tctttacttg aagacagcct 420 atgaagtttg ggaagatctt cgggaaagat tttctcaaag caatgctcca cgaatttttc 480 agcttcaaag agagattgcc tctctcaccc aaggccaaca atctgtggct gtttattaca 540 caaaattgaa gggtctttgg gatgagttag catcctatag ttcttcgaca atctgcactt 600 gtggcgcaca acatgaaacc aatagactta tgcagttcct catgggattg aatgagtctt 660 acagtgctat tcgtggacaa atcctattga tgaatccact tccctcctac cgacaagcgt 720 attcctcgat catccaagaa gaaaaacaac gggagttagg cactggatcc cgcagtctaa 780 ctgaaccagc agccatggcg gttcgccatc agcagcaatc ttccaagaag cagcaccaac 840 agtcgcagac cagcagcaac agtcgacctc ctcttcactg ctcttactgc gacgctaagt 900 atcataccgt tgagacttgt tggcagaaga atggttatcc accggatcat ccccgtcaca 960 atcccaacac gacacgcaac tccaaacaaa atggtggtgg cagcggcttc tctcgtggaa 1020 gttcttctgc tcatcacgtt gcttctactc ccaccatcaa ggatcttcaa gctgctgtgc 1080 ccaacctgtc cgagaaacaa tatgcagaca tcttttctgc cttgacttcc aagaatgaca 1140 aatcacaagc tgcgaatgaa gcaccacaag cccatgccgc tctcacttct ccaccaccct 1200 caggtttgtc tccgcttgtt cccggtcgat ggatcatcga cagcggagca acggatcaca 1260 tcacttgctc gtctagttta ttgacaaatt ccattaacaa tacctctttg ccgcctgtct 1320 cactgcctag cggagagaak gcttctatta cttcgattgg caatattcaa ttaagtgatt 1380 tactacaatt gaaagatgtt ctatgcgtgc cttctttcca agttgattta ttatctgttg 1440 gaaaaattac agatgggtta cattgttcag tgactttttt tccctcttgg tgcattttac 1500 aggacctgat ttcgaaggtg acgattggtg ttggtaagcg acggggcaat ctctattacc 1560 ttgtggcgtt ggcttctact tcctctctgc aaaaccgacc ctcctgtcac ctcattaccg 1620 tttctgctga cctttggcac cgccgtctgg ggcatccttc tcttgggcgt ctacaatatt 1680 tagcaaatca aaccttaaat ttcccttttg attcaagtca tcgttgtcat gtttgtccgt 1740 tggcgaaaca aactcgccaa ccttttagtc gtagctccat ttcaacttct agtttttttg 1800 aacttttgca ttgtgacatt tggggtcctc ataagactgc ctcccttact ggtgctcatt 1860 atttcttaac tatcgttgat gatttttctc gtttcacctg ggttttctta atgcgacaca 1920 aacatgaaac acaacctacc ctcaaaacct tttttgctta tattgaaact caatttcaca 1980 ccaaaatcaa acaaattaga gtcgataatg ggggtgaatt ttattccatg cgggatttct 2040 tctctgacaa tgggatcatt tatcaacact cttgtgttta cacaccacaa caaaatggtg 2100 ttgtagaacg caagcatcgc cacatcctag aaactgcccg agctttgcgt tttcagtctc 2160 atttaccagt taagttttgg ggggagtgta ttctcaccgc cgcttatctc ataaaccgtc 2220 tccctacacc attactttcc aaaaaatcac catttgagat actatacaac aaaccaccct 2280 cttattccca tatgcgtgtt ttcggttgtc ttgcctatgc cacgtctgtc cacccttcct 2340 ccaagttctc tcccagggct catcgatgtg tttttcttgg ttatccccca ggtcaaaagg 2400 cttataagct ttatgatctt gagacacata aaattttcac caatcgggat gttatttttc 2460 ttgaagacac ttttcctttt gatccatcca ccaccgctgc accatcccct cccttatccg 2520 atttacctca ttccacacct ttacccatcc cacttgaccc caccaccctt gaccattcca 2580 ccactactcc actagatatt gtcccccaca cttccacacc gcttgaccca ccgcttgacc 2640 catccccacc gcctgactca tcctcacatc ctcccacctt tcaccccctc acggaccccc 2700 ccacggaccc cacccctgac cttcccattt ctactcaacc cacccgtttt tccacacgcc 2760 acaaggagcc caatgtccgt ctccgtgact acgtttgctc gcaggtgatg ctgcccccac 2820 tccaatcttc gtcgccttcg tcatccggtt ccaccaaagg tactcgttat cccatttgta 2880 attttatttc ctaccacaga tattcaccat tgcatctttc ttttgttgct cacattagtc 2940 gaggtgtaga accctcttct tttgcagagg ctattcaaga ccctcattgg cacgaagcca 3000 tggattcaga acttgaggca ctttcttcca acaatacctg gactcttact ccgcttcctc 3060 ccggcaagcg tcccattgat tgtaagtggg tctacaaaat caagcatcat gctgatggtt 3120 ctatcgagcg ttacaaagct cgtctwgttg ccaaaggatt cacccaagcc gagggcattg 3180 attaccatga cactttctct cccactgcca aaatgaccac tgttcgttgc ctgcttgctc 3240 ttgccgctgg tcaaagttgg tctcttcaac aactcgatgt taataatgca tttcttcatg 3300 gcgaccttca ggaagagatt tacatgtctc ctcctcctgg tcttcggcga cagggggaga 3360 acctwgtgtg tcgcctcaac aagtccttgt atggcctcaa gcaagcctct cgacaatggt 3420 ttgcaaagtt cacagaagct gttcacgccg ctggttttgt tcagtccaaa gcggattatt 3480 ctctcttcac ccgtaagagc ggtaagtcct tcacagctct gttgatttat gttgacgaca 3540 ttattaatca caggcaacga tgtagatgcc atcaattccc tcaaacagtt tcttcacact 3600 cgctttcgta ttaaggacct tggcgatctg aaatactttc tgggtattga agtttctcgt 3660 tcaaagaaag gaatatgtat ttcacaaaga aagtatgccc ttgatataat caaagatggc 3720 ggccttttgg gtgcamgacc gtggatttcc aatggaggaa aacaagcttt cagataaagg 3780 tgaattactc aaagacccat ctctgtatcg aagattggtt ggacgcttga tttatcttac 3840 cgttactaga ccggacatca catactccgt gcatgtactc agccgtttta tgcatgaacc 3900 gcgtcaacca catatggatg cagcacttcg aattgtgcgg tatttgaagt ctgctccagg 3960 tcagggctta tattttcagt cagataataa gttaaatttg agagcttttt gtgattcgga 4020 ttgggcggtt gtccgataac tcgacgtcca cactgggtat tgtatatttt tggggaattc 4080 gttgatttcg tggaggacta agaggcagaa aacggtctca ctttcttstg ctgaagccga 4140 atatagggcc atggctggga catgttgcga gctcacttgg ttgcggtatt tgttaacaga 4200 tttgcatgta cccatttcag gacctgccat tatgtcttgt gataaccagg cagcattgca 4260 cattgctgct aatcctgtct ttcatgagag aacacgcaca tagagatgga ttgccatttc 4320 attcgggaca agattttaga cggctctata gctactcgat atgtcagttc ttctcaacaa 4380 ccggcagacg tatttacaaa ggccttaggc aaggaaaatt ttcatccatg ttgcgcaagt 4440 tgggagttct tgacatccac tctccaactt gagggggag 4479 // ID L1-14_Mad repbase; DNA; EDCOT; 5978 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-14_Mad. XX NM L1-14_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5978 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1818-1818 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 5978 BP; 1399 A; 934 C; 1910 G; 1726 T; 9 other; ttctctaggg tttctctagg agagcggtag ggttaggaat tacggcggcg gccgtagagt 60 tctgggtgct gtgctcgagg gtctgtaggg atcgagctga gagtgtggac taggtttggg 120 tggatgtttc tcaggtagta ggcaattggg gggaaaatct gtggggttta tcgaacaggt 180 ttgcaagtgg tgcaagggtg atggaggata tggtgatgaa gtttgcagat agattggctc 240 tcactgctga ggagcaaagg gtggtggtga tcgatgataa ggagagtgct ttctcagagc 300 caataaggtt ttcctagttg ggagggtgct twcacgtaag gcsttcaaca aagaaggttc 360 aaacgacaaa tgttgaatct ttggcgccct aaggctaggg ttacgatagt ggagttggat 420 gatgggttgt tctcatttgg ttttgatagt gacgggaaag gcgatggtgc agaaaggagg 480 gccatggctg tatgatggtg ctttgctggt gttggcggag gcagataacc tggcgcatcc 540 gcaagtattc cgctgtggtc tcaggagttt tgggttcaag tcaagggttt acctcttgcg 600 tatatgactc gccatatggg gcagtttatc ggtaatcaga ttggagttca tgttctaact 660 gatcagagta ggaagggtga actctttggt agtatattac gcattmgggt tgcggtggat 720 attacgaaac cgttacgcga agtctgctgc tctcattcag ggcacggagg tgggggttga 780 tttgcggtat gagaaactcc caataacctg tttcttatgt gggattattg gacatatgga 840 agagcagtgt gtgcagttca aagggaagaa tgatgatgac ctttcgaagc cgtatggcga 900 tggttccaga atgatgtttt gggagataat tatcgtaggc cgcaaggtaa gcgttttggg 960 ttggaggcgt cgcatgggtg gtctatgaaa gcccggtgca tgtgaggaag ggagagtatg 1020 aatagtgtgc agtggagatc agggaggctg gaggacgccg gtggtggctg tagagggatg 1080 gccagacagc gagactagtg gggagggaac ggatgatgcc atcattaatg gcgacattaa 1140 ttgccagatt tgaatgttgc gttgacctgg aggagatgat ggagattcta tggcaattat 1200 ccatttcagc aaactcctac aaatcaggaa gcaggggggt tgacgttgtt tggtttgatt 1260 tgaatgtccc gccagctgtg atggggagat actcaggttc aatcaactta gtagtggggg 1320 ggatagggaa tgatcaatac gatgaggtga gttcattggg cctcggggtg gagataaggt 1380 tgtgtgggcc agcaggtggg cttatggggc ggatgtggct taggcaaatt tggggggggg 1440 actcggtgct accagttggg gtgtcgggct gggtcagacc cattcaacct tatgcctatt 1500 attgagcatc atcagagggc aggaagagga ggcaagaaaa ggagtcaaga gggttgtgtc 1560 gagcaccttc agcccatgca cgggatcgtg ggggtgcaat gttacctgaa cttgggaaaa 1620 ggttggtacg agaggatgag gatgtggtgg cacggcgtgg aggtcgaagg aggttggtgg 1680 ctagtttggt gttgtccagt tcatcggcgg aggttgacgg gggtcaaccc cgccgtcagc 1740 aatgagttgt ttaagttgga actgccgggg gcttgggaac ctccgggcag ttcatgcgct 1800 ccaacgttta atttctagtc aagatcccac tgtagtgttc ttgtgcgaga caaaaagtaa 1860 tkctcgttac atggaccgtt tacgtttaaa gttgaatttt gatcgtagtt ttacagttga 1920 tagtagaggt agttcagggg gtttgtgtgt tttatggaag gatgaaataa atttatgttt 1980 aaggtcttat tctcagaacc atgttgattt tgatgtgggt gttccggggg atacagacta 2040 ttggcgattt actgcttttt atggttttcc agccacgtgt gataggtata agtcttggag 2100 gttgttggag tctcttgctg gcaatgagtc taaaccttgg ttgtgtattg gtgattttaa 2160 tgaaatcctc caagccaatg agcaggaagg gggtaatgtt cgacaagata ggcaaatgga 2220 gggtttcgga atgcggtgga gcattgtcgg ttgatggacc ttggcttctc agggaataaa 2280 tttacgtggt ttacgacgaa agggggtgga atcaaggtga ggctggatag agctttgggt 2340 aatcaagaat ggatggattt gttccctcgt tttaaagtgc aacatttgaa taagacttcg 2400 tcgatcatgt gccggtctgc ttaattggtc gggacgcact ccaatccgag ggaagaagca 2460 gtttcgttat gaggaatgtt ggcatatgca gaagggtgaa gggtacggga tgggtggaac 2520 catggtgggg ctcgccaatg ttccaggtta cgagaaaatt aagatgacga ggatgaagct 2580 caataactgg gctcgagcaa tgcaaggtcg gggccaagag agattaggga agtggaggat 2640 aagcttacga gtttgttggg gcaaccgttc actgatgagt ctattgagca gaaaaatgag 2700 cttattggga agttgaacag attgcttgaa caagaggagc aattttggag acaacgatcg 2760 aaggagaatt gggttaaact tggggatcgc aataccaaat attttcatca gaaggctaat 2820 aggagacaaa aacgtaactg tttatatggg ttaatggatg ataatggggt ttggcgtgag 2880 gaccgtaggg ggatggagga ggttgtggtg tcgtatttca caaagctttt agttcaaatg 2940 gagtggagaa ttttgatgat atcttatgcc atatcgccca ggtgacggag gagatgaata 3000 cctcccttga tagcccattc acggatgagg agattaaatg tgctgttttt caaatgcatc 3060 ctacgaaagc ccgggscctg acggtatgtc tccggggttt taccaaaagc attggggagt 3120 ggtggtacgg atgtgtgtaa tggggttcgg tccatgctcc tatctggtca attctacgga 3180 aaattaatta tacccatgtc acgttaatcc ccaaagtcaa ggatgctacg atgatgacac 3240 aacttcgccc tattagtttg tgcaatgtgt tgtacaaaat agtggcgaag gtctcacgaa 3300 caggttgaag gttattcttc cacatgttat ttctcctact caaagtgctt ttgttccggg 3360 gcggttaatt tctgataatt atttggtagc tgctgaagtt gctcactata tgcataaacg 3420 gtctcggggt ccaatggtct tatggcgttg aagctggata ttagtaaggc atatgatcgt 3480 gtggaatgga agtttcttga ggctatgatg catcggttgg gattctctga taggtggatc 3540 cgtatggtca tgttgtgtgt tacaacggtg acttactcct ttaagttgaa tggggacccg 3600 gtgggttatg tgcatccaga aagaggaata agacaagggg atcctctctc cccctattta 3660 tttgttatgt gtgcagaggg tctctcggca ttattgacaa gggcagagct tgatggagat 3720 ttgcagggga tcaaggtgtg tcgtgctgct cctagcatcc atcatttgtt tttcgctgat 3780 gatagctttc tttttgcccg aggtaccgtt ggtgagtgtc agaacattaa acaggtgttg 3840 cgaagtatga gtggcttctg gacaagcggt gaattttgag aagagttgtg tttcgttcag 3900 tcccaatctc actagttatg ataagcagtt attggctgat tgtctcggta tgaggagagt 3960 ggattttcat gataaatatt tgggtttgcc ggtgctagtc cggaagtcga agaaggaaac 4020 tttgcgtatg tgaaagatag ggtgtggaaa aagttgcaaa gttggcgagg tggcctactg 4080 agtagtgcgg gtcgtgagtt attggtgaag acggtggctc aggctttacc tatgtattcc 4140 atgcaatgtt tcctgctccc taaatcgttt tgtgaggagt tgaacatgat gatagctaag 4200 ttttggtgga gtggtgatcc gggtaaaagg aaaatacatt ggcttaattg gagggtttgt 4260 gtaagcctaa gcatgaggga ggtcttgggt ttagagacct ttatgcattt aatctggctt 4320 tgttggccaa gcaagcwtgg cgttttctgc atgatcctga ggcccttgtg tatcgggtgt 4380 tcaaggcccg atactttcct acgacagatt ttctggaggc tcgggtgact tctaatagtt 4440 catatgttgg agaagtattg cagcctcgag accggtgctt caaaagggac ttcggtggca 4500 ggtgggtaat gggaagaagg ttcgcatatg gaaggataat tgggtgccga gggagtcttg 4560 cttccggatt ttgaccccgc caccggtgca ttgggatgtk gaggccacgg tggagggttt 4620 attttggacg gagtcaaagc agtggaatgt tcagttgttg aatgagcttt tttctcagga 4680 ggaagtggag ttaattcgag ggattccact tagcttacgg gatattgctg atcgtaggat 4740 ttggcattat gaacgacatg gcaagtttac agtccggagt gcataccatg ttgcacgggg 4800 gttaatgtcg ctagtgggga aggggcagcg gctctcttcg tcttctagta tgtggggaga 4860 agttatggaa gaagctgtgg atgcttgtgt tcctgggaag gtgaagattt gtgcttggcg 4920 tgcatgtttg gattctttgc ccacaaggtt gaatctttgc aaacggagag tgacgattga 4980 ggaggtgtgt gtagtttgtg gtggccaggt ggaatcaacg gagcatgtct tgcgggattg 5040 caatgtggcg gtgtggtttc gaggtttggg taagggtgga atgggcakgg ggtgtctttt 5100 atgaattggt tagccaattt acagttacag ggtcctacgt cggggtttga gctttgttta 5160 atgttggttt ggtctctgtg gaagcatagg aatgaggttc tttggaacgg caagtcgtta 5220 ccccgcatga gattgtgctt cgaaccgagg gttggatgca ggagtttcac aagtggcata 5280 agccagaggc aagaaggcta gccgagaggt tcagaagtgg aggaaacctg cggagggttg 5340 ggtcaagtgc aattttgatg gagcttggag tcaaagggga accggggagg ttttggggtg 5400 gtgattcgta atcacttggg ggagtttctt gctgctgctg caggtcctat tgagaggcca 5460 tgttctgctt tgcacgctga gttcattgca gctcggcaag cgttctgttg gtcaagagtt 5520 tttgtccagc ggatgtgaag gttcagtttg aaggagatgc tagtttggtg ttggcgccat 5580 gaagggtcaa ggggatgatt gctctgcttt cggtcccata ataaatgatt tgagatgctt 5640 tctctggagt ggccgaattt gatggttagt catgttcaac gggaaggtaa ctcggcagcg 5700 catcggcttg ctcggatggg gattagtagt gctcaggagg tkgtgtggtt cgaggagcct 5760 ccggatttga ttcaggatat tctgtttgag gaaggattgt aagttcgttc tattgttcat 5820 ttgaggatag gtctattgtt gtgcgggaca ctcttttcct tcgaccgggt tgaaatcccc 5880 ggcaaggttt ttatcgaggc ccattatgca cactatcctc agtttgtacg tattctgatt 5940 tgcttaatga atatcgtact ttcttcaaaa aaaaaaaa 5978 // ID Gypsy-40_Mad-I repbase; DNA; EDCOT; 3731 BP. XX AC . XX DT 15-OCT-2010 (Rel. 15.1, Created) DT 15-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-40_Mad-I. XX NM Gypsy-40_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3731 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1774-1774 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 3731 BP; 1007 A; 791 C; 681 G; 1251 T; 1 other; tattttggca cgcccggtgg gatccttata tgaagttaga tcatgaacaa tccttatgtt 60 catgattttt ctgctttttc ggagtatgag gaggatgacg gtgtggaaga gcgcccaagc 120 tatggctatc acatagagcc aacctatgag ttgccaactt atgggtacat ggctgaagag 180 tactcaagtc ccatggaaca tgattgtcgg ccaactaatg gccatcaaat aaataataat 240 cttgaagatt ggccaactta tggctatgat gaaggttatt attcttttga agacaatcac 300 attcatgaat actatgatag gccaacaaat ggctttgagt atcaaaatgc ttccaatgag 360 tacatagagc caatatatga gatgccaact catgatcatc cggatgaaaa gctctacaaa 420 gaggatgtgg gcaaattaga gaaggtgtcc aaactccatg tggcaagcat cgaatatggt 480 gaagaggtga ctaagtgttt taaaagggtg gaggaaagct atacaacttt tggagaaact 540 ttgagaaagt tgatagatca aatgtgtcaa atcccctcta caaagcacac tcaccctact 600 acaaccaagg aagaacaaat catacacgtt gatgaaggcc aaacaatggc cccacccaat 660 gaaaaatcca tgaaaatgga tatggttgta gaagaccaag ccgacatatc gaaaccgata 720 acggctaaga tggagcttat ggctattgta ggccaaacac caacgctcgg ggggctcgag 780 cccacacctc atgtggagcc cgaagaagaa gaaaatagct catacactct tccccgccaa 840 cacaagcatg ttgtccacat cgagatctca aggagggcaa agcttgggat caaacatgaa 900 tggccacctc ctatggttcc caagctacat ggcatggcca atttaaatgg tggatctgat 960 ctctctacac tcaattttaa aaagagaaaa agatttgagt gttgagagaa aaataacact 1020 tgggcagcca aggggcttca tccaattatg cccgaatagg gctttctttt gtgttactct 1080 tttgcccgaa gtgactccct ctcttccttt tcttctttct ttctctcctc tttccttttc 1140 ttttcctccc tccttctttc tttttctttt ttttatttct ttctctttgt cttgtctgtc 1200 ttttactttg cccgaaaggg ctatatattt atatatatat atatatatat atatatatat 1260 atatattata tgtaaaagag ggaaatggaa gtactttgcc cgaatgggct ttatatatat 1320 atatattata tatattatta taatatagtt ttgaaaaaaa aagacaacaa agaaaatata 1380 aaaattaaaa ttgtttgttt ttttgcccga aaagggctct ctctcctttt gcttttaaaa 1440 atatgggtac ctttttaact ttgcccgagt gggcatttct gttgcccgac taagggcttt 1500 ctttttgttg tttggttcgc ccgaaagggc tttgtctttt atgttttact gttttagtag 1560 cctgacaagt ctttcttttt atttgttttt attccacttg cccgcagggg ctttaatttc 1620 ttttttctgt ttgcccgaaa gggctctgtt ttctttgtgt gtttcttgtg ctgttacaaa 1680 gaaaaagata taaaaattaa aaattccaaa aatcacaaaa acattttgct ttcttgcttt 1740 tgtttttctt tcttgctttc tttccctttt tgttttcttg ctggggagct ttacagaaaa 1800 tataaagagt tgggcagttt gtgagtagcc atttttaccc ttctttccac ttttctctta 1860 tccaatggat gtatttagcc cgaacccaaa aaagttgaaa ttagaaaacc atccagtggc 1920 tgtacccaaa ttcatggaat gaggagtttc ataaaaagcc gaaactatgg ctttcctgct 1980 gaaaagcatg tcatctgttt ctcaatggct attgcaagag agcatggggc tatcttgccc 2040 gactggtggt gcccgatgga accataacca tgcctgacgg gaatgacgtc ttccctgctc 2100 accaccaaca gactctgcat gtctccctaa ctctcaccag ctcctacgac caagggtcgg 2160 gctacttcgg caactaccat tggaggctac agtaagagct tttgatgtgg ctactattaa 2220 tcactggaga ctagttttca tgggtgagaa aatagaaaaa tggagctgca tctaaatgtg 2280 aaatccgaaa gctggaggaa gatgacagaa aattatgttg ctgtggcccg acggagctac 2340 aatcttgccc gaggggcatg acatcttctc tgctgcaatt ggtttagatg ttgtcaatca 2400 gatgtggggc cccacgtttg atctggcaaa catatttgaa gtgttcttgc cacaactgct 2460 gcagctccaa agatatgttg ccaagctgct tataaaagaa ttaaaggttc gaatgagagc 2520 actgaaactt cttgtagata ccagcaccgt cctcgaccaa cagtactcca acagcttgat 2580 catcctttgc atctcaattt ttgaattttg ggatggatag caacttcccc aaaagaacta 2640 tttcaaaata cctcaggagt tcaaaatcag aagtctgatg aagcaagaaa gaaattcaca 2700 aatgcagaat ctgtccattc cgcacaaatt tctgggtaac caaagcagat atgctgagtt 2760 ggtactcaga cctccttgcc gaagttcttg agctctgcag ccatttccag tgctgacctg 2820 tttgcttcct tttctctttt ttataccctt ctctctattc ctctttttca ttttctttct 2880 ctctctcccc ttttcccttt tctttcttat ctcttctgtc ccccttttgc ccgaaaagag 2940 ggtctccctc tttctttctt tttcttttta ttatttctct ctctctctcg ccatttttgt 3000 tgttcccgaa agtttctgtc ttttattttt gcccaaagag acgactctct ctctctctgt 3060 atatattctt tttattgtat atatctcttt cttccctttg cttgatcggg ctatgtgtat 3120 atatatatat tatatgtaca tatatattat atatatatat atatgtggcc gaaaagccaa 3180 agaaaggcat tgcttggctg tctctatctt tctttttgtc tttcttccct cttctctctt 3240 tctctctctc tctctttttc cttttctttt tctttctttt ccttcctttc tctttcttcc 3300 tgtctctttc tgtccttact ttgcccgaaa gggcatagtc tatatatata tatatatagt 3360 atattatatt atattatatg aaaaagaggc aaaaagaaaa agaacaataa aaaggatagt 3420 tgcccaagtt tatttatctc ttatccctct tttccagttt gcccgacttc gggcattttt 3480 ccagtttact atctatgtaa ccagtgagga tgctcccatg ttttttggta tcaacaagaa 3540 ggagcacaag ccagacaaca ttctttccaa tgctagttgc actaccaatt gccttgctcm 3600 tcttgccaag tttatcaacg acagaaggac cgaagaggta gacgtgcctc ttccttcgac 3660 atcaatctct ggcagcattg gagttgtaag tttcacaaac tttgctcaaa tttgtaaaac 3720 ttggggggca c 3731 // ID Gypsy14-PTR_LTR repbase; DNA; EDCOT; 368 BP. XX AC LG_V; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy14-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-368 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-368 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 307-307 (2007). XX DR Genome; LG_V; Positions 10698992 10698625. XX SQ Sequence 368 BP; 112 A; 64 C; 88 G; 104 T; 0 other; tgggacgatc gttggttgac acctggacta gccatgcaga gaagccatgc agataagcca 60 tgagaagaat cagtctaggc aagagtaatt ctcggcacga gattagccta gttggttagt 120 atcccacgtc cccatacagt ggagaaagat agtggagaaa gactagttcc ataggaatga 180 gtcaacctga tttggtggga ttgcccacta tagtaagcct agactctata tatagagata 240 gggaacccac gtaaaagggg gtaatcagtg aagtattcac atagcaagta tcaaataaaa 300 tcatttgttc ttgcaaattg attctgtgtt atcgtttttc ttttcttttg tttcatagtg 360 gttgaaca 368 // ID BoSB5A repbase; DNA; EDCOT; 182 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB5A. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-182 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 182 BP; 31 A; 49 C; 59 G; 43 T; 0 other; ccgggcctcg tggtctggtg gtaaaggaac ctcggctgag gtgtccgcca tcacgagttc 60 gagccccggc cacagcggat ttaacatggt ttccgtttgg cctccaggac cttcttcgcc 120 agttccggtt ggacgcggtg ggatagtcgg actaagtgag aggtccggat acctggatta 180 tc 182 // ID SHACOP4_I_MT repbase; DNA; EDCOT; 4025 BP. XX AC . XX DT 12-JAN-2007 (Rel. 12.01, Created) DT 12-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP4_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; ORF; SHACOP4_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4025 RA Shankar R. and Jurka J.; RT "SHACOP4_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 74-74 (2007). XX DR [1] (Consensus) XX CC The internal region has intact domains for gag-pol polyprotein CC having gag-int-pol pattern of Copia-type LTR. Present in Medicago CC genome in poorly conserved copies. XX FH Key Location/Qualifiers FT CDS 81..4022 FT /product="SHACOP4_I_MT_1p" FT /translation="MASNNITLPAPPVFTGKKYEIWSVKMKTHLRAYDLWE FT VVETAAEPPPLQENPTVAQMRYHSEQVAKRAKALTILHSAVNDDVFMRISH FT LETAKQVWEKLEEEFFGNERTKQMQVLNLKREFEALKMNEAENIIDFMTKV FT MKVVNQIRLLGEQFLDSRIVEKVLVVLPERFESKISALEESKDLSKITLTE FT LINALQAQEQRRLLRQEEASETALQVKHKGKSIATKGEKKFVGEHSGKDTK FT KKERFPKCGICKRTSHKESDCWYKGKTPPPFQCRYCNKTGHIERFCRLKQQ FT HQNQQNHTSQKANVTEIEDSEELLFMANTTRSSEDGDTWFIDSGCTQHMTS FT KPELFSEIKPAAGSVKIGNGQKVAITGRGTVKIHTATGIKYISDVLLVPEL FT DQNLLSVGQMIEKGYCLLFKEGSCVVTDVNGHELFEVNMRKRSFPINWNLV FT SEHECNMSKAELDSKLWHKRFGHYNLKSIQFAQKQELVKDLPNIQTFSEVC FT EGCQLGKQHRLPFPSSATWRASDKLELVHSDVCGPMNTSSLNGSKYFILFI FT DDFTRMTWVYFLKQKSEVFSVFKKFKIFVENQSGCLLKKLRTDNGKEYTSA FT EFNKFCDDLGVERQLTVSYSPQQNGVSERKNRSVLEMARCMIFEKKLPKSF FT WAEAINTAVYLQNRLPTKAVEGMTPIEAWGGFKPSIKHLRVFGSLCYTHIP FT DVKRSKLDEKAEKGILIGYSSKSKGYKVYGIDSNKIFINRDVKVDEDAYWN FT WETSQVDRGSTLSSLEDANEDQDEEVDDDFAVRGTRPLSEIYQRCNSAVLE FT PTSFEDASKVDEWYQAMKEEMDNIEKNKTWQLVDKPRDKNVIGVKWVYRVK FT MNPDGSINKYKARLVVKGYVQQSGIDYTETFAPVARMDTIRILVALAAQMK FT WKIWHLDVKSAFLNGNLDEEIYVAQPAGFLVKGREDKVYKLNKALYGLKQA FT PRAWYSKIDSHFLNQGFKRSENDATLYVRRLLDGGSLIVSLYVDDLLVTSN FT NQQEVQQLMEEMKNQFEMSSLGEMNYFLGLEVHQSENGIFLNQEKYAREVL FT KKFKMESCKSAPTPLVWNLKLSKEDEAEKIDASRYRSLIGSLLYLTSSRPD FT LMYAASLLSRFMQNPTKTHFAAAKRVLRYVKGTTQFGIWYKPSENESLLGY FT VDSDWAGNIDDMKSTTGYAFSLGSGMFSWNSRKQEIVAQSTAEAEYVAAAA FT AANQAIWLRKILDDLGIQQLEATVLYCDSKSAIAIAENPVQHGKTKHIQVK FT YHAIREAVKNQEIKLIHCCSDSQVSDILTKSLPRAKFEKFRELLGVSIQNL FT KE" XX SQ Sequence 4025 BP; 1360 A; 636 C; 896 G; 1133 T; 0 other; atggtataca gagcttcttt gttcttaaag ggcctgtgat taaaaaccct tgctttcttg 60 acacccaacc atttttcttg atggcttcaa acaatattac ccttccagca cctcctgtat 120 ttacaggaaa gaaatatgaa atctggtctg tgaagatgaa gactcatttg agggcatatg 180 atctttggga agtggtggaa acagctgctg aaccaccacc tttgcaagaa aatccaactg 240 ttgctcaaat gagataccac agtgagcaag ttgccaagag agctaaggct cttaccatcc 300 ttcactctgc tgtgaatgat gatgttttca tgagaatctc acacttggag acagcaaaac 360 aagtttggga aaagctagaa gaagagtttt ttgggaatga aagaaccaag cagatgcagg 420 ttctaaatct caaaagagag tttgaagcct taaagatgaa tgaggctgaa aacataattg 480 atttcatgac gaaagttatg aaagttgtga atcaaatcag attgttggga gaacaatttc 540 ttgatagcag aattgtagaa aaagtcttgg tggttttacc tgaaagattc gaatcaaaga 600 tttctgcact tgaagaatca aaagatcttt ccaagataac cttaacagag cttataaatg 660 ctcttcaagc tcaagagcag agaagacttt tgagacaaga ggaagcatca gaaacagctt 720 tacaagtcaa acacaaagga aaatccatag caaccaaagg tgaaaagaaa tttgttggag 780 agcactctgg gaaagataca aagaagaagg aaagatttcc aaaatgtgga atttgcaaaa 840 gaaccagcca caaggaaagt gattgttggt acaaaggaaa aacaccacca ccatttcaat 900 gtagatactg caataaaact gggcatattg agaggttttg taggctgaaa cagcagcacc 960 aaaatcaaca aaatcatact tctcaaaagg caaatgtaac tgaaattgaa gatagtgaag 1020 aactcttgtt catggccaat actacaagga gttcggagga tggagacaca tggtttattg 1080 atagtggctg cacacaacac atgactagca aaccagaact gttttcagag atcaaacccg 1140 ctgcaggatc tgtaaagatt ggaaatggac agaaagttgc catcacaggt agaggaacgg 1200 tgaaaattca cactgcaaca ggtattaaat acatttctga tgtactttta gttcctgaac 1260 ttgatcaaaa cctgttgagt gtgggccaaa tgattgaaaa aggttattgt ttgttattta 1320 aagaaggaag ttgtgtggtt actgatgtta atggtcatga attatttgaa gtaaatatga 1380 gaaaaagaag ttttcctatt aactggaatt tagtttctga acatgaatgt aatatgagta 1440 aagctgaact tgattctaag ctttggcaca aaagatttgg ccactataat ttgaaatcta 1500 ttcaatttgc tcaaaagcaa gagttagtca aagacttgcc caatattcaa actttttcgg 1560 aggtgtgtga aggttgtcaa cttggtaagc aacataggtt gccttttcca agttcagcaa 1620 catggagagc aagtgataaa cttgaattgg ttcactcaga tgtttgtgga cctatgaata 1680 cttcttcact caatggaagc aagtatttta ttctttttat tgatgatttt acaaggatga 1740 cttgggttta ttttctgaaa cagaagtctg aagttttttc tgtttttaag aagtttaaga 1800 tctttgttga aaatcaaagt ggttgtttat tgaagaaact tagaactgac aacgggaagg 1860 agtatacttc tgcagaattc aataaatttt gtgatgattt gggtgttgaa cgtcaactta 1920 cagtcagcta ctcgcctcaa cagaacggag tttctgaaag aaagaataga tctgtccttg 1980 aaatggctag atgcatgatt tttgagaaga aattgccaaa gtccttctgg gcagaggcaa 2040 taaacactgc tgtctatctc caaaatcgac ttcctacaaa ggcggtagaa gggatgacac 2100 ctattgaggc ttggggaggc ttcaagccgt ctatcaagca tctgagagtg tttggttcgc 2160 tgtgctacac tcacatacca gatgtgaaaa gaagcaaatt ggatgaaaag gctgaaaaag 2220 gaattttaat aggctatagc tcaaagtcta agggctataa agtctatgga attgattcaa 2280 ataaaatttt cattaataga gatgttaaag tggatgaaga tgcatattgg aattgggaga 2340 cctctcaagt tgatagaggt tcaactttgt cttctctcga ggatgcaaat gaagatcaag 2400 atgaagaagt tgatgatgac tttgctgtta gaggtacccg acctctttca gagatttatc 2460 aaagatgcaa tagtgctgtc cttgaaccta ccagctttga agatgctagt aaagttgatg 2520 aatggtacca ggctatgaaa gaggagatgg acaacattga aaagaacaag acatggcagc 2580 tggttgacaa gcctagagac aagaatgtca taggagtgaa atgggtctat agggtcaaga 2640 tgaacccaga tggatccatc aacaaataca aggccagact tgttgtcaag ggctatgttc 2700 aacaatccgg gattgactac acagaaacat ttgcaccggt agcaagaatg gatactattc 2760 gaattcttgt agcgttggca gcacaaatga agtggaaaat ttggcattta gatgtcaaat 2820 cagcattctt aaatggtaac cttgatgaag aaatttatgt tgctcaacct gctggttttt 2880 tggtgaaagg gagggaagac aaggtgtata agcttaataa agctttgtat gggctgaaac 2940 aggcccctag agcttggtat agcaaaattg atagccactt tcttaatcaa ggattcaaaa 3000 ggagtgaaaa tgatgcaact ctttatgtaa gaagattgtt ggatggtggt tccttaattg 3060 tctctttgta tgttgatgac ttgctagtaa caagcaataa tcaacaagaa gttcaacaac 3120 ttatggagga gatgaaaaac cagtttgaga tgtctagctt aggggaaatg aactattttc 3180 tcggcttgga agtgcatcaa tctgagaatg gaattttttt gaatcaagag aagtatgctc 3240 gtgaagtttt gaagaagttt aaaatggaaa gctgcaaatc tgctccaact cctttggtgt 3300 ggaatttgaa actctcaaag gaagatgaag ctgaaaaaat tgatgcttct cgttatagaa 3360 gtttgattgg gagtctactc tatcttactt catctagacc tgatcttatg tatgcagcaa 3420 gcttactctc aagatttatg cagaatccta ccaagacaca ttttgctgca gcaaagaggg 3480 tacttagata tgttaagggt actactcaat ttggaatatg gtacaagcca agtgaaaatg 3540 aaagtttgtt aggctatgtt gatagtgatt gggctggaaa tatagatgac atgaagagta 3600 ctacaggcta tgctttttct ttaggctctg gcatgttctc atggaactcg aggaaacaag 3660 aaattgtagc tcaatccacg gctgaagcag agtatgtagc cgcagctgca gcagcaaacc 3720 aagctatttg gttgaggaaa atactcgatg acttgggaat acaacagctg gaagcaactg 3780 tgctttattg tgatagtaaa tcagcaattg ctattgctga aaatccagtt caacatggaa 3840 aaacaaagca tattcaagtg aagtaccatg ccatacgcga ggctgttaaa aatcaagaga 3900 tcaaacttat tcattgttgt tctgactctc aagtttctga tatattgact aaatctcttc 3960 caagagctaa gtttgaaaag tttcgagaat tgcttggagt gtccatccaa aatctcaagg 4020 aggag 4025 // ID L1-2_Mad repbase; DNA; EDCOT; 6555 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-2_Mad. XX NM L1-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6555 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1806-1806 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 719..2761 FT /product="L1-2_Mad_1p" FT /translation="MQQGVVRLSERRGSNKNCSTWNSSHEKLPDVVLSGWW FT DSINSNHRKAVSYGGWVALEGLPPHLWTNNFFQKIGEACGGLVEIDRRTAN FT FGFLLEAKLKLKPNDTGFIPEFVDVADGESVFRVKIRQLSPAKRPNLSAED FT GGATKSPXGSLKKDLKIQRLTGATLPAKADMQQSVPSPGTRVSFRIGEFEC FT PVTVGADRKYGLNRLLTEDARHEXSATHDFTFSISKHGRPLQTECLTDSAS FT FIEEQENADAKDNFKNSKRKESLRQRCFLEXGKGMEVSGRAGGGGGMSTEE FT AQSSTSGYYFNRSXKEVSLKSKEKALMVRGPLVHKDFDLSDFVRLVGLVPQ FT NNYAGSCLGPLILNYDGLRYHFQLGRELSNKIFWHSAMSAEPKLSFRVSNM FT PNFTTEILSQRQRAKEAHFDGVPKRSPTCFNLKFLGRFGEIDKLGKRLKLL FT LPHEFGSNQTPVERPEMMEIHSPNLTILDSVCELEEEKESDVDENPVRPPG FT GSTEEEPFDQRMRWTEALGLDSSLLSDSAEEEYMSQSSDSDEENGDSSQDE FT KEPSDVFDRFNGELHNLFTDTNLETEATXEEXPSQTHHVVALEDVEQSDFK FT DIGKNKKMLKYSRRKRSACVSVKREAQDQXSKFLSKMKVSLFPLKRSLFHE FT MKTGKVKVSKSEGGSKGDKKLQRGIIRLNEDN" FT CDS join(2751..4592,4511..6412) FT /product="L1-2_Mad_2p" FT /translation="MKIISWNVRGLGSRQKRLTLKQQFRRLQPDIIILQET FT KKTSIDRRLVASVWGSRFKEWIYAPAQGSSGGIAVIWNTKNISVTESLIGV FT FSVSIKIKALNGLEWWLSGVYGPCKSRERREFWEEMAGLYGLCGPRWCVGG FT DFNVVRFVNEKSNGGRLTTSMRNFNDFIRETELKDLELLNAQFTWSNFREE FT PVCRRLDRFLFSAGCEEIFPEVRQMALARVISDHCPIQLDSNKVKWGPSPF FT RFENMWLQHPEFRNKFNLWWQSEQVEGWEGYKFMIKLKAIKKKVQRWSKES FT FGEVEKDFKEAEASLEELDRREGMEGLDVDARRKREELLFLVGDLAYKEEV FT KWRQRSKVEWAKEGDGNTKFFHRVASGRRKRNYIERLEPDVGGVIEDAKEI FT EEHIVNFFKSLFSSNEEACWGLEGINWAPISELEANWLERPFEEAEVQRAV FT FDCGKDKSPGPDGYSLQMFQHCWDILKADIMKIMEEFYETGIINAVTNETF FT ICLIPKKSDSLKVTDYRPISLVTGLYKIMAKTLASRLKEVLGSTISPNQGA FT FVKDRQILDAVLIANEVVEEVRQKKEEGLVLKIDFEKAYDHVSGDFWTKSY FT KEKALAIDGGNGCRDASCEWRFLDEVLQRKGFGNRWRKWMQGCLSSANFSV FT LINGRPRGKFQASRGLRQGDPLSPFLFTLVVDVLSRLMEKAQENXLIKGLC FT IGQEKVEISHLQFADDTIFFLAEDEGVWNNLLXVLNLFCSVSGLKINKAKC FT XLAGINSDXEKLNRLADSWGCEVGSWPIKYLGLPLGGRPRAXKFWDPVVEX FT MERRLQSWKKAFLSRGGRLTLIQSVLGSLPIYYMSLFKIPCGVXGRLEKLM FT KGFLWEGVEEGKKXHLVKWELVTKSKEEGGLGVGNLRNRNEALLAKWLWRF FT PREPQSLWHKVIRSKYGLQANGWNALPPMRGSSRSPWKDISSGSQQFLSCC FT KFEVGNGERVRFWEDGWLAGGPLKEQFPRLFLLSRKHNQNISSFVEVSTNS FT LSWNFDFRRNLNEVEIEEAATLLQKVEEVRLSPSRMDNRRWNLEASGLFTC FT KSYRSLLSNNGIVHYFPPYSQIWKSKVPPKVKILVWLVAKGKLNTCDRIQR FT RNPLMCLSPHWCSLCKAKEESVNHIFLHCSYSIQLWWKLFQEVRASWVIPK FT GCFELLSTKFQALGKGRKXKALWGCLVSAVFWNIWLERNKRIFEDYTGVGA FT EVLWGRVKYWAALWASVTKEFNNYSLSQILWDLLAAVK" XX SQ Sequence 6555 BP; 1986 A; 1094 C; 1782 G; 1664 T; 29 other; taaggatgag ctacagacat ttatccaggg atttcaaagt tgagcaaaag gttttcatct 60 tagaggttga agataagtct tttggcgaaa ggattcgaat aactgagaga actagaatca 120 gagggtacca gatttctttc gatttgggtt gtgctgcatg gctcgtcgat caggtaaagg 180 aggcaatagt taaaggtggt cagagtttct tcagaaaata tagaggacat aactaccagt 240 tttgggtcga aagatttcat aacaaaaacg gggatttcct tgttatttcc aaatcagaaa 300 aggaaggctt tgtcagaaat atcctcgtcc ctaaaggttt taactttttc ggatggagaa 360 gtttggagga cttactgtct gaaatcctcc gtgggggaaa gagagcgggg gctactcaga 420 ggaaagtgaa gagagtcgga aaagagtttg tgagcagcca gacgggtgca ggccctcagg 480 tttcgtatag ggacgctgtc ctcggaggca agacggcgac aatagtggca cccattcgaa 540 acgccaaaga ggaaatatgg atgaagaaaa tctggaataa gagagacatt tccaaggaat 600 cctacagttg ggggagcgta gttgtttgcg agagacaggt ggtacatcaa ccttggagag 660 aggtggaggc ctcacttcga aatcttctgg gaatggaaat aaggctctcg cccttccaat 720 gcaacaaggc gttgttcgtt tgtcagaacg aagaggaagc aacaaaaatt gctcaacttg 780 gaactctagc catgaaaagc taccagacgt ggtgctgtct ggatggtggg acagtatcaa 840 ttcaaatcac agaaaggcgg ttagttatgg cggttgggtt gctctggaag gattaccgcc 900 acacctttgg accaataact ttttccagaa gattggagag gcctgcggag gtctggtaga 960 aatcgaccga agaaccgcta actttggttt tctgctcgaa gcaaaattaa aattgaaacc 1020 caacgacaca ggctttattc cagagttcgt tgatgtggca gatggagaat cagttttcag 1080 ggttaaaatt cgtcaacttt cgccagcaaa gagacctaat ctttcggctg aagacggtgg 1140 agcaactaaa tcaccaamtg gatctttgaa gaaggacctg aaaatacaga ggctcaccgg 1200 agctaccctt ccggcgaagg cggatatgca acaatcagtc ccctctccgg ggacacgtgt 1260 ctctttccgg attggtgagt ttgaatgccc tgtcactgtc ggagctgaca gaaagtatgg 1320 tctgaacagg cttttgacag aggatgcacg gcatgaggwg tctgcaaccc atgactttac 1380 tttctctatw agcaagcacg ggaggccact tcagacagaa tgtctgacag attcggcgag 1440 ctttatagaa gaacaagaaa atgcagatgc aaaggataat ttcaagaatt caaaaaggaa 1500 agaaagtctc agacaaaggt gctttttgga aaawggcaaa ggcatggaag taagtgggag 1560 agcaggtggc ggtggtggta tgtccaccga agaagcacaa agctctacaa gtgggtatta 1620 ttttaataga tcaaamaagg aggttagtct aaaaagtaaa gaaaaagctt tgatggtgcg 1680 tgggcccctg gttcacaagg attttgatct aagtgacttt gtaaggctcg tgggtcttgt 1740 tccacaaaat aattatgctg ggtcatgtct aggcccactt attctaaact atgatgggct 1800 gagatatcat tttcagttag gaagggaact atcaaacaag atcttttggc actcagccat 1860 gtcggcagaa ccaaagttgt cgtttcgggt gagcaacatg ccaaatttta ctacagagat 1920 tttatctcag cgacaacggg ctaaggaagc tcatttcgac ggtgtcccaa aaagatcccc 1980 cacttgtttc aatttgaagt tccttgggag atttggtgaa atagacaaac ttggaaaaag 2040 gctgaagctt cttctcccac acgaattcgg atctaaccag actcctgtcg aaaggcctga 2100 aatgatggaa atccattccc ccaatctcac catcttagat tctgtttgtg aattagagga 2160 agaaaaggag agtgatgttg atgaaaatcc tgttcggcca ccgggcgggt cgacagagga 2220 ggaaccattt gatcaaagga tgagatggac agaggctctt ggmttggatt cgtctctttt 2280 gtcagatagt gctgaagaag aatacatgtc acaatcatca gattcagatg aggagaatgg 2340 tgactcttca caagacgaaa aagaaccatc tgatgttttt gatcggttca acggggagct 2400 tcacaacctc ttcacagata caaatttgga aacagaggcg acgkcggaag aggmaccaag 2460 tcaaacgcat catgtagtag cattagaaga tgtggagcag tccgatttca aggatattgg 2520 aaaaaacaag aaaatgttaa agtacagtag aaggaaaaga tcggcttgcg tatcagtcaa 2580 acgcgaggca caagatcaaw cttccaaatt tttgtcaaag atgaaagttt ccttgtttcc 2640 tctgaaaagg tctttattcc atgaaatgaa gactgggaaa gttaaagtca gcaagagtga 2700 gggtggaagc aagggagaca agaaacttca aaggggtatt atcagactta atgaagataa 2760 ttagctggaa tgttagagga ttgggaagta gacagaagag actgacattg aaacagcagt 2820 tccgacgttt acagcccgat atcattatat tacaagaaac taagaaaaca tcaatcgata 2880 ggagacttgt ggccagcgtg tggggaagca gatttaaaga gtggatttat gcccctgctc 2940 aaggaagttc tgggggcata gcagtaattt ggaacaccaa aaacatctca gttactgaat 3000 ctctgattgg agttttctct gtctccataa aaattaaggc cctcaacggg ttggaatggt 3060 ggttatcagg ggtctatggc ccttgcaaaa gtagagagcg aagggagttc tgggaagaaa 3120 tggctggcct ttacggactg tgcggaccaa gatggtgtgt aggaggggat tttaacgtgg 3180 tgagatttgt aaacgagaaa tcaaatgggg gaaggctgac tacaagcatg aggaatttta 3240 atgatttcat tcgagaaaca gaactcaagg atttggaact gctcaacgct caatttacat 3300 ggtcaaattt cagagaagaa cctgtgtgtc ggaggctaga cagatttctg ttctctgcag 3360 gttgtgaaga gatttttcca gaggtaagac aaatggcttt ggcaagggtc atttctgatc 3420 attgccctat ccagctagac tccaacaagg tgaaatgggg gccaagtcct tttagattcg 3480 aaaacatgtg gctacaacat ccagagttca ggaacaagtt caatctatgg tggcaatctg 3540 agcaggtgga gggatgggag ggttacaagt ttatgatcaa gttaaaagcc ataaaaaaaa 3600 aggtgcaaag atggagtaag gagagtttcg gggaagtcga gaaagacttt aaagaagctg 3660 aggctagctt agaggagtta gataggagag aggggatgga agggctagat gttgatgcta 3720 gaagaaagag ggaagaacta ctcttccttg tgggagattt ggcttacaag gaagaagtga 3780 aatggaggca gagaagtaaa gtggaatggg caaaggaagg ggacggtaat actaaatttt 3840 tccatcgagt tgcaagcggg agaaggaaga gaaactatat agaaaggttg gaaccggatg 3900 ttgggggagt gatagaggat gcgaaagaga tagaagagca tatcgtcaat ttcttcaagt 3960 ccttgtttag tagcaacgaa gaggcatgtt ggggcttgga aggtatcaat tgggctccaa 4020 taagcgaact tgaggcaaat tggcttgaga ggccttttga ggaagccgaa gttcaaagag 4080 cagtttttga ttgtggaaag gataaatcgc caggaccgga tggctattct ttgcaaatgt 4140 ttcaacattg ttgggatatc ttgaaggcgg acattatgaa gattatggag gagttctacg 4200 agacagggat aataaatgcg gtgacgaacg aaacttttat ttgcctaatc ccgaagaagt 4260 cagattcttt gaaagtgacg gactacaggc ccataagtct agtgactggg ttgtataaaa 4320 ttatggcgaa aaccctggcc tcaagattga aggaggtttt gggcagcaca atctctccga 4380 atcagggggc gtttgttaag gatcgacaaa ttttggatgc tgtcctcatt gcaaatgaag 4440 tggtagaaga ggtcaggcag aagaaagagg agggattggt gctcaagata gactttgaaa 4500 aagcgtatga tcatgtgagt ggagattttt ggacgaagtc ctacaaagaa aaggctttgg 4560 caatagatgg aggaaatgga tgcagggatg cttaagctcc gcaaatttct ccgttttgat 4620 caatgggagg cctaggggaa aatttcaagc ttcaagaggt ttgagacaag gtgatccact 4680 gtcacctttt cttttcacct tagtagtcga tgttttgagt aggttaatgg agaaggctca 4740 agaaaatsat ctcatcaaag gcttgtgtat cgggcaagaa aaggtggaga tttctcatct 4800 tcaatttgcm gatgacacca ttttcttctt ggcggaagac gagggagttt ggaacaacct 4860 attasaggtg ctcaacttat tctgttckgt ctcagggttg aaaatcaaca aagctaagtg 4920 ctwtttggct ggaataaatt cagatwgtga gaaattaaac aggttggcag attcttgggg 4980 ttgcgaggta ggcagctggc ctataaagta tttgggactc ccccttgggg gtaggccaag 5040 agcamtaaag ttttgggatc cagtggtaga aamgatggaa agaagacttc aaagttggaa 5100 gaaggccttc ctatccagag gaggtagatt aactctgatt caatcwgtct tgggaagctt 5160 gccgatttac tatatgtcct tgttcaaaat tccttgcggg gtgakwggac gcctagaaaa 5220 actaatgaag gggtttctgt gggaaggcgt ggaggaaggw aagaaaamcc acctggtmaa 5280 atgggagtta gttactaaaa gcaaagagga aggaggtcta ggggtgggga atttgaggaa 5340 tcggaacgaa gcattactgg ctaagtggtt gtggagattc ccaagggaac ctcagtctct 5400 stggcacaag gtgataagaa gcaagtatgg gctacaggct aacggatgga acgcacttcc 5460 tccaatgagg ggttcaagcc gtagcccatg gaaagacatt tcgagtggtt cccaacagtt 5520 tcttagctgc tgcaagtttg aggtgggcaa cggggagagg gtgaggtttt gggaggatgg 5580 gtggttagca gggggaccgc tgaaggagca attccctaga ttattcctgc tatcgaggaa 5640 gcacaatcag aacatctcga gcttcgtgga agtttctaca aattctttga gttggaactt 5700 tgattttagg agaaatttga atgaggtgga gatagaagag gcggccacat tattacagaa 5760 agtggaagag gttcgattgt ctccatcaag aatggataac agaaggtgga atctggaagc 5820 ttcaggtttg ttcacatgca aatcctatcg ttcattactg agcaacaatg ggattgtgca 5880 ctattttcca ccctactcwc agatttggaa atcaaaagtt cctccgaagg ttaaaatact 5940 tgtatggctk gtggccaaag ggaagctcaa cacttgcgac agaattcaaa ggagaaaccc 6000 tcttatgtgc ttatccccac attggtgcag tttgtgcaaa gccaaggagg agagtgtaaa 6060 tcacatcttt ctccattgct cttactcgat ccaactgtgg tggaaactgt ttcaggaggt 6120 tagagcaagt tgggtcattc ctaaggggtg tttcgagcta ctaagcacaa agtttcaggc 6180 acttggaaaa gggaggaaak ccaaagcttt gtggggttgt ctggtmtcgg cagttttttg 6240 gaacatatgg ctggagcgca acaaaaggat ttttgaggat tatactggag tgggggcaga 6300 agtactttgg gggagagtaa aatattgggc agccctttgg gcttcggtca ctaaagagtt 6360 taataattac tctctatctc aaatactgtg ggatttgtta gcagcagtta agtgagctag 6420 gtctagaaat ggctgctgta gccaaatcct agtgagagtt ttttcttgtt tcctgttaat 6480 ggtggatttc ttatccactt cwgtgtattt ctcttttctt ttataaaatg ttttgtttct 6540 tctcaaaaaa aaaaa 6555 // ID Gypsy21-PTR_LTR repbase; DNA; EDCOT; 374 BP. XX AC LG_XIV; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy21-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-374 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-374 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 323-323 (2007). XX DR Genome; LG_XIV; Positions 14275177 14274804. XX SQ Sequence 374 BP; 126 A; 75 C; 57 G; 116 T; 0 other; tgagtctcct agttttaggg actgatgtca tttttaacgt gtctcctatt tgtaggaacc 60 gacgttaacc atttttaaaa aaacaaaatt gcaaataatc tcaaaatata atagcattta 120 aatcaaataa aaaacacaca agtaagggta acctttctct tgaaaggatg ttttaaaggt 180 ggtgtctacc ttcccttaat cataactaac cccgtacctg aatctcttgg accagtgtct 240 aatttgggat ttctaattcc ctcaaattac tagatggcga ctccaataaa atcttcattt 300 ctcccaatcg agaaaaaaac ctttttgtta aataaacaaa aagtggagtc gtcgcccgac 360 gtcgtgtatc gaca 374 // ID MEGY-I_MT repbase; DNA; EDCOT; 6550 BP. XX AC AC146683; XX DT 09-JUN-2005 (Rel. 10.05, Created) DT 29-MAR-2007 (Rel. 12.04, Last updated, Version 2) XX DE Medicago truncatula LTR retrotransposon MEGY-1 (internal). XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Metaviridae; MEGY-I_MT. XX NM MEGY-I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-6550 RA Neumann P., Pozarkova D., Koblizkova A. and Macas J.; RT "PIGY, a new plant envelope-class LTR retrotransposon."; RL Mol Genet Genomics 273(1), 43-53 (2005). XX RN [2] RP 1-6550 RA Lin S., Dixon R., May G., Sumner L., Gonzales B., Cook D., Kim D. RA and Roe B.A.; RG Department Of Chemistry And Biochemistry, The University Of RG Oklahoma, 620RL Parrington Oval, Room 208, Norman, OK 73019, USA; RT "MEGY-1 LTR retrotransposon."; RL Direct Submission to EMBL/GenBank/DDBJ (12-DEC-2003). XX RN [3] RP 1-6550 RA Toth G.; RT "Medicago truncatula LTR retrotransposon MEGY-1."; RL Direct Submission to Genbank (09-JUN-2005). XX DR Genbank; AC146683; Positions 117789 124338. XX CC Internal sequence of Ty3/Gypsy-like retrotransposon MEGY-1. 5bp CC target site duplications. XX SQ Sequence 6550 BP; 2064 A; 1334 C; 1285 G; 1867 T; 0 other; agtttttggc gccgctgccg gggagtaaac taatttaatt aattctttct ttgtgattag 60 aactcttttc tctcccctct ttttcccttc ttctttttcc tacacttgat tcgggtggct 120 taaagataat agataacatg gctgaggaac gcactcttaa ggagtattcg atcccttctt 180 cggatgagcc atgcactatt atagtctacc caacagttca aggtagcaac ttcaaaataa 240 aacctgcact actaattctg gtgcaacaaa accagttctc tggatcacct tccgaggacc 300 caaatttaca tatctcaacc ttttggagac ttagtgtaac ttgcaaagac gaccaagaaa 360 ccgtcaggct atatctcttc cctttttctc taaaagataa agccagcaat tggttcaatt 420 ctttgaagcc tggttccatt acctcatggg accaactgag gagagaattc ctttgtcgtt 480 tctttccccc atccaaaact gcccaactta ggggaaaact ttaccaattt actcaaaaga 540 atgaggaatc tcttttcgat gtgtgggaac attttaaaga aatacttaga cgttgtcccc 600 atcatggtct agaaaaatgg ttgatcatcc acacctttta taatggtcta acatctagca 660 ctaaattgac tgttgataca gctgcaggtg gtgccctaat gaacaaagac ttcacaacag 720 cttatgcgtt aattgagaac atggctctaa acctcttcca atggacagaa gaaaaagcaa 780 ccatcgatcc ttcgccctct aaaaaagagg caggtatgga tgaaacctct tccattgact 840 atttatctac caaggtgaat gcattatctc aaagacttga tcgcatgagc acacctacct 900 tctcgcctcc ttgtgaaaca tgtgacctat ctagtcattc taacaccgat tgcaacctaa 960 gtagtgttga gcagttaaat tttgttcaga atggccaaag agttgttcaa aagtctcaca 1020 ttgaactttt aatggaaaac tattttctta aacaatccga acagctccaa gagctcaagg 1080 accaaactag acttttgaac aactctcttg ctactctcac aacaaagata gactctatct 1140 cctctcacaa caaaatttct gaaactcaac tctcccaggt agttcgtaag gttaaccacc 1200 ccaataaaat gaatgctgtc acacttagga gtggtaagcc actcgaagac cccataagga 1260 gaaccgagac cgataacagt gagaaagaaa tctgcgaacc accatctagg gaaaccagag 1320 cagaaagaga gaaaccacga gttgaggaaa acttgccacc tccctttaag ccaaaaatcc 1380 ccttccctca aaggtttgcc aaatcaaagc tagatgagca attcaaaaag ttcatagaga 1440 tgatgaacaa gatatatatt gatgtgccat ttaccgaggt cctaacccaa atgcccacat 1500 atgctaaatt tttgaaagaa atcctctcta aaaaaagaaa gattgaggaa agtgagacgg 1560 ttaaccttac agaagaatgc agtgccatca tccaaaataa attgccacca aagcttaaag 1620 atccaggtag tttttccata ccttgtgtca tagggtcgga agttgtgaag aaagctatgt 1680 gcgatctagg agccagtgtc agcctaatgc ctttatcact ttatgagagg ttgggaatag 1740 gggaacttaa atcaacaagg atgaccctac aactagcaga ccgttctgtt aagtatccag 1800 ctggaatcat agaagatgtc cccgttaagg taggagaggt atatatcccc gccgattttg 1860 ttgtgatgga aatggaagaa gacaatcaag taccaattct tttgggaaga cctttccttg 1920 ccactgcagg agctatcatt gatgtaaaaa agggtaagct tgccttcaat gtaggtaagg 1980 aaactgttga atttgaactt gctaaactaa tgaaaggtcc ctccattaag gactcttatt 2040 gcatgataga cataatcgac cattgcgtga aagaatgctc tttagcatca actgcacatg 2100 atggtttgga agtatgcttg gttaacaatg caggtacaaa actggaagga gaggcaaagg 2160 cttatgaaga actgttagat agaactcttc caatgaaagg tctaagtgtg gaggagttag 2220 taaaagaaga accaacactt ctacccaagg aggcaccgaa agtagaactc aaaacacttc 2280 catcgaatct aaggtatgaa ttcttgggcc ctaactccac ctatcctgtt attgtaaatg 2340 caagtctcga tgaagtagaa actgaaaaat tgctttatgt cctcaagaaa tatcctaaag 2400 ccataggtta caccattgat gacattaaag gaataaatcc ttcattatgc atgcatagga 2460 tacttcttga agaagactat aaaccctcca ttgagcacca aagaagacta aatcccaata 2520 tgaaagaagt tgtgaaaaag gaagtcttaa aactcctaga tgcaggtgtt atttatccaa 2580 tttctgactc caaatgggtt agccccgtgc aagttgtacc aaagaagggt ggtctcacag 2640 ttattaaaaa tgataaaaat gaatccattg ccactagaac cgtcaccggt tggagaatgt 2700 gtattgatta taggaagctt aataaagcaa cccgtaaaga tcacttccct ctccctttta 2760 tagaccaaat gttagaaagg ttagctaagc attcgcattt ttgttaccta gatggctatt 2820 ctggattttt ccaaataccc attcacccta atgaccaaga aaagacaact tttacatgtc 2880 ccttcgggac ctttgcctat agaagaatgc cttttggtct gtgtaatgcc cctgctactt 2940 ttcaaagatg catgatgtct attttttctg acttcgttga aaagataatg gaagtcttta 3000 tggatgattt ttctgtgcat ggttctaatt ttgatgattg tttgactaac cttgaaaaag 3060 ttttggaaag atgtgaacag gtgaacctag tcttaaattg ggagaaatgt cacttcatgg 3120 taagagaagg aattgtccta ggacacttgg ttttcgacag aggtatagag gtagatagag 3180 caaaaatcga aattattaaa aaaatgctac ctcccacctc agttaaagaa attagaagtt 3240 tcctaggaca tgcagggttc taccgtcgtt tcatcaaaga tttctcatca atcactaagc 3300 cactaaccag cctgcttctc aaagatgcag actttacctt tgatgattct tgtttgcagg 3360 cattttgcag gttgaaggaa gcactaatta ccgccccaat catacaacca ccggattgga 3420 acttgccttt tgaaataatg tgtgatgcaa gcgactatgc ggttggggca gtattaggtc 3480 aaagaaacga caaaaagatg catgccatat actatgccag taagacccta gatggggcac 3540 aggtaaacta tgccacgaca gaaaaagaat tgctagcagt tgtctacgcc attgacaaat 3600 ttcggcaata cttggtggga tcaaaaatca ttgtttatac agatcactcg gccataaaat 3660 acttgctaaa caaaaaagat gccaaaccga gattgatccg atggattttg ctcctccaag 3720 aatttgacct tgaaataaaa gataaaaagg gcgtagaaaa tgttgtcgct gaccacttgt 3780 cccgacttcg ggagaccaat aaggatgagt tacccttgga tgactcattc ccagatgacc 3840 aactattctt attggcacaa actgacgcac cttggtatgc agattttgtt aactttcttg 3900 cagcaggagt actaccgccc gagttaaact accaacaaaa gaagaaattc ttcaatgatc 3960 tcaagcacta ctattgggac gagccctacc tcttcagaag aggctcagat gggattttca 4020 ggcgatgcat tcctgaaaac gaggtaagta gtattctaac tcattgtcac tcctcttctt 4080 atggcggcca cgccagtaca caaaagactt ctttcaaaat tcttcattct ggtttctggt 4140 ggccatcact tttcaaagat gtgcatctct ttatctctaa atgtgacaaa tgtcaacgca 4200 ccggtagcat cactaaaaga aatgaaatgc ctttgaataa catccttgaa gtggaaattt 4260 ttgatgtttg gggtattgac tttatgggac ctttcccttc ctcttttggg aatcagtaca 4320 tattagtagc cgttgactat gtgtccaaat gggttgaggc cattgcttcc cccactaatg 4380 atgcacaggt ggttataaaa atgtttaaga aagtcatttt ccctagattc ggagtgccac 4440 gagttgtgat aagcgatgga gggtctcact tcatttcaag acattttgaa aaacttttgc 4500 aaaaacttgg agtgagacac aaaattgcga caccctatca cccccaaact agcggacaag 4560 tggaggtctc aaacagacaa attaaagcta tccttgaaaa aactgtttcc acctctagaa 4620 cagattggtc aaataagctt gatgatgccc tttgggccta tcgaacggct tataaaaccc 4680 ctattgggat gacccctttt aaacttgtct atgggaaatc ttgtcacctt cctgttgagc 4740 tcgagcataa ggcctattgg gcaattagaa acctcaactt agatcccaat ttagccggtg 4800 acaaaagaaa acttcaatta aacgagctag aagaacttag gatggatgct tatgagaatg 4860 cccgcattta caaagagaga actaagacct ggcatgacaa gaaaatcatc aaaagacact 4920 tcaaaagtgg tgaccttgtg ctgctcttta actctaggct aaagctcttt ccaggtaaac 4980 tgcgatcacg atggtccggt cctttccaag ttcgcacagt ctacccttat ggggcgattg 5040 aaatcttttc tgaagaaaca ggatccttca cggttaatgg ccaacggctt aaaatctata 5100 ataccggaga agtaaatgaa gtagtggctg atttcaccct tagtgaccca ccttaaggat 5160 ttttcatcct caccttcgtc aagctagtga cgttaaaaga gcgcttcgtg ggaggcaacc 5220 caccaattta attgctttct ttgttttctg ttatttctct ttattttgta ggtaagtgtc 5280 cgagattgat taagaaacgc aagaaaatca aagttccaag aaccagaagg gcggcacggc 5340 ccgtgcttga cttggcacgg ccgtgccaag aaacacaacc acatcttcaa taaagttggc 5400 agaatgatag cacggcccgt gctacatctg gcacggccgt gccaacctga aggcctccgg 5460 agtttaaaat ttcgacaaat tgtgagcttt cctcaccctt tctcactttt tccttatttc 5520 tcctaagtgt ggggggagcc taataaagaa agtgtcttta gtcgtagtgt ttccaaactc 5580 ccttgaactt tattcttttg tttcgtttta ttgtgaaagg catgtttaag tagctaattt 5640 ttattaaaaa tatcatgaca caaaaaattt cattgtctcc tcttattttg ttgattcttg 5700 tacatgaaag caaactcttg tgttttaagt cttcttgata taaccacatc ttgttttaaa 5760 gtgaataaaa ttctccaatg agaaaaacac aaagttgctt cccttgagta aatgtatgaa 5820 taggtatttt aagaaaacgc gttctaatct tagtggtgca ttaaccttta aaaattctca 5880 aagcgccagt agtataagtg agtataaggg agatcataaa aagccaaaaa gccaaataat 5940 ttcaagatct catcactgaa tctagattgg ggaaggaggt aggccctccg acttcctacg 6000 tgaaggtgat tgttatcttg agaaaaactt taaaaagcat tgttgaaact agattgggga 6060 aggaggtagg ccctccgact tcctacgtga agacgatgtt ttaaggaata ccattgaatc 6120 tagattgggg aagggggtag gccctccgac ctcctacgtg aaaatgtttt tccttaaata 6180 aagaacttaa aatgtgcata tggcaaaaga acaaagattc tcaaaaactc ccatctctct 6240 tatatgaatt gtagaaggaa tttttcttgg ttagtttagt gctaggatta gaccatgttt 6300 cctcattata cctatcttat acatgagcaa gaaaagggtt ggacttcaca cacacactca 6360 cttgaaactt gattgttggg tagaataaag atttcaggaa atacttgagt ttgtgattag 6420 tgtacatttt gggatttaag cccttgagga gacatgtgct ttaattaatt gtcatttgat 6480 ttaactgttg atgctactat gtttatgcct tttgcttgag gacaagcaaa gattcaagta 6540 tgggggagtt 6550 // ID Copia-9_Mad-I repbase; DNA; EDCOT; 4753 BP. XX AC ACYM01100325; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-9_Mad-I; KW Copia-9_Mad-LTR; Copia-9_Mad_. XX NM Copia-9_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4753 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1287-1287 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01100325; Positions 5133 9885. XX CC Positions [2018-2515] - Integrase core CC 'GTATA' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 2480..4531 FT /product="Copia-9_Mad-I_1p" FT /translation="MQSPFQMLYHTVHDIKHLRVFVCACFPILKPYNTSKF FT QPKTATCVFLGYASQYKGYICLDVITGKIYVSRHVLFDETCFPYLNPICAS FT DQMFPASSQSHSSHSQMHPSQLTPIITLSNQVSSPSSHSSSSQTTEYLPVH FT SSSASESFSASRASDSLDTVASRASESISLPSHEYTAVHTPRDLSPSPMIL FT SSAGTQPPIPVDPDFHPESLSVVLPIPLNVHPMQTRSKNGVFKPKVFLATV FT TAEPKSFKHAAPIPEWQNAMKEEIAALHSQKTWTLVPLPPDKNLVGCKMIY FT KIKKHADGSVARYKARLIAQGYSQEEGVDYLETFSPVVKPTTIRLIFALAA FT QFKWTFRQLDVKNAFLHGILQEEVYMAQPPGFESPTQPSNYVCKLHKSLYG FT LKQAPRGWNERFTSFLPSLGFQVSPADPSLFVQQSTQGTVLLLLYVDDVIV FT TGSSSHLINKVIIAFTAEFEMTDLGLLHYFLGLHISYTSEGLFVSQAKYIH FT ELVDKVDLQDSKPCATPCLPYHRLLKDDGQPYPRPEQYRSVVGALQYLTFT FT RPDIAFAVNQACQFMHNPMISHVIAVKRIIRYLKGTSTYGIHFKPGPIHLQ FT SYSDADWAGDPNDRRSTSGFVVFLGSNPILWASKKQHTVSRSSTEAEYRAL FT AITATELAWIRQLLCDMHVPVYSSPMIFCDNVFAI" XX SQ Sequence 4753 BP; 1286 A; 1091 C; 878 G; 1497 T; 1 other; tggtatcctc gccggacgtt ctggtgcttc cgcttccaac acattgtctt ctcttctcta 60 ccctctagtt tgcttctttc tgtgataatt ggcgttggaa acataccagt cgcttcaaca 120 gttggcttct tctcttctgc ccaccaactg tttgttcaaa agtctcaatc aaagttcgtc 180 acgaaaatct gcaaaatggt cactgctgct caattgcaaa ttgttcagtc tcctatcacc 240 ggtctcctct ccaccgtctc tacttctgtt acagtcaaac tcgacgattc aaactatctc 300 acatggagct ttcaagttcg attgcttctg gaaagtcatg gcattatggg gtttattgat 360 ggttcaagaa aatgtccacc aagattcaat gaagattcta acactgaagg gattgaaact 420 gatgactatt tggtttggaa aatgcacgat cgtgcactaa tgcaattgct catcgccaca 480 ttatcaacga ctgccatttc ctgcatcatt gggtgccaga gttctgcaga aatgtggttg 540 aatcttactg agcgtttttc tgccgtgaca aaagctacaa tctttcagat gaagacagag 600 cttcagaata tcaagaaagg gtctgaatcc gtttctgttt atcttcaaaa gattaaagat 660 gcaagggatc atcttgctgc agctggagtt ctatttgatg atgaagatat cattattctt 720 gcattgaaat gattaccttc ggatttcaac acgattgttt tgtgatcaga ggcagggaaa 780 atggaatatc tctcaaagat tttaggtctc aacttttggc agaagaagca atcatcaatc 840 aatcttttga cagttctccg ggtttgtctt ttggtagtgc tatggctgct ggcatttcat 900 ctgacaaagg gaaggcactt gctcttgatc aagatcaacc caacacttct tctgatcatt 960 ccttcaaata caatggagga ccaagttctg ctagtcatag tccaggttct gctccgagta 1020 gtggatcgta taacaatttc actggtggct atcacaatta tggtaaaggg agttctttca 1080 gaggcagagg gaaaggccgt tttcagtaca attcacatcc aagattttct aatggtaatc 1140 ccggtattct tggtacttca aaaccatacc agtcctactg cccggatcac ccatcagaaa 1200 tccccacctg tcaaatatgc aacaaaaagg gtcatgttgc tgcagattgt ttccaaagac 1260 ataacaacac tgccactgga ccaactccta ttcaatgtca gatatgatgg aaatatggac 1320 actccgccct tcaatgctac cacaagagta attttgccta tcaagggcgg cctccaactc 1380 ctaatctcac cgctatgcat gcaaatcatc aaccttcagc accaactgag catttttgga 1440 ttgccgatac tggggctaca tcacacatga cttttgactt ggcgaacctg gatctatcta 1500 ctccttatca agtgtctgat acaataacta ctgctagtgg cgcaggtttg catatttcca 1560 atattggcac ctctaaattg gttgtcccac atcattctct cactctccag aatgttttac 1620 atgttccaaa gctttcccag catttattat cagtttatca actctgcaag gacaataagt 1680 gccaattcat ttgtgatgat gtttcttttt gggttcagga caaatccaca gggaaaatcc 1740 tcctccaggg gctgtgtaaa gctggttact atcctattcc cttcatcaca tcccacaagc 1800 agtcatcctc atcatctgca tctcattcat gtttccttac aaaaccagtt cattcaagaa 1860 tatggcacaa aaggctaggg cacacatcca acgcaatcac ttctgcaatc ctacatcaat 1920 ctcaagttct tgcatcatta gatccatgtt catcaccttg tacaccatgt ttagagggca 1980 aatttaccaa attacctttt aatgttcctg tccttaaatc tgtacaccct ttagaaaaat 2040 ccatagtgat gtatggggcc ctgctccttt gctatcctat gaaggattta gatactatgt 2100 aaccttcata gatgattgta ctcgttatac atggattttt ccattacgaa ataaaacaga 2160 agtttttgca acatttgttc agtttcatgc ttatttgagt acccaatttt ctgctgtggt 2220 aaaaatattc caaagtgatg gtggtggtga atatacaagt actaagtttc aacagttttt 2280 agcacaccat ggcattttac atcacaaatc atgtccatat acacctgaac agaacggttt 2340 ggcagaaagg aaacataagc acattgttga aactgcaatc acccttcttc aaactgcaca 2400 cctgcctaac caattttggg ttcgtgcttg tgttactgct tcttatttga tcaatcgaat 2460 cccatgtgct ttattacata tgcaatcacc atttcaaatg ctatatcaca ctgttcatga 2520 cattaaacat cttcgagtct ttgtttgtgc atgttttcct atcctcaaac catacaatac 2580 ctctaaattt cagcctaaaa ctgccacttg tgtgtttttg ggatatgcta gtcaatacaa 2640 gggatacata tgtctagatg ttattactgg aaaaatttat gtctctcgac atgttttgtt 2700 tgatgaaact tgttttccat acttaaatcc catctgtgct tctgatcaaa tgtttcctgc 2760 atcatctcag tcacattcat cacacagtca aatgcatcca tcacagttaa caccaatcat 2820 taccttatcc aatcaggtat catcaccctc atctcattca tcatcatctc agaccacaga 2880 atatttgcct gtgcattcat ctagtgcttc agaatctttt tctgcatctc gagcctcaga 2940 ttcattggat acagttgcat ctcgagcctc agaatctatt tctttacctt cacatgaata 3000 cactgcagta catacaccca gagacttgtc accaagtccc atgatcttat caagtgccgg 3060 tacacagcct cctattcctg tggatcctga tttccatcct gagagcctaa gtgtggtttt 3120 acctatacca ttgaatgttc atcctatgca gacccgatcg aagaatgggg tgttcaaacc 3180 aaaggtgttt ttagccacag ttactgctga acctaaatcc tttaaacatg cagccccgat 3240 tcctgaatgg cagaatgcaa tgaaagagga aattgcagct ttgcattctc aaaagacctg 3300 gactttggta cccttacctc ctgataagaa tttagtgggg tgtaaaatga tttacaaaat 3360 caagaaacat gcggatgggt ctgtggcacg gtataaggca aggcttattg cacagggata 3420 tagtcaagaa gagggggttg attacttaga gacttttagt ccggtagtaa aacctacgac 3480 tatacgcctg atttttgcct tagctgctca attcaagtgg acttttaggc agttagatgt 3540 taaaaacgcc tttctccatg gcattcttca agaggaagtc tatatggcgc agcctccggg 3600 gtttgaaagt ccaacacaac cttccaacta tgtttgcaaa cttcacaaat cgttatatgg 3660 tctcaaacag gctcctcgcg gctggaatga acgatttacc agtttcttac caagtttggg 3720 atttcaggtg tccccggcgg atccgtcttt gtttgtacaa cagtctacac agggcactgt 3780 gctattgctt ttgtatgttg atgatgtcat tgtcactggc agtagctctc atttgatcaa 3840 caaagttatc attgctttta ctgctgaatt tgaaatgaca gatttgggat tattgcacta 3900 ttttttgggc ttgcatatta gttatacttc agaaggttta tttgtgtccc aggcaaagta 3960 tattcatgag cttgttgata aagttgatct ccaggactcc aaaccgtgtg ctacaccatg 4020 tctaccgtat catcgactcc tcaaggatga tgggcagcct tatcctcgtc ctgaacaata 4080 tcggagtgtt gttggtgctc tccaatatct tacttttaca cgtcccgaca tagcttttgc 4140 agtcaaccaa gcttgtcaat ttatgcacaa tcccatgatt tctcatgtca ttgcagtaaa 4200 gaggatcatt cggtatctca aagggacatc tacctatggt atacatttta agccaggtcc 4260 gatacatctg caatcttata gtgatgcaga ctgggcaggt gacccaaatg atcgcagatc 4320 tacttcaggt tttgtggtgt ttcttggttc aaatcctata ttatgggcat ccaagaagca 4380 acataccgtc tctcgttcat ccaccgaagc tgagtatcga gccctggcta tcacagctac 4440 tgaacttgcc tggattcgcc aacttttatg tgatatgcat gtccccgtgt attcttctcc 4500 catgatcttt tgtgacaatg tttttgctat tgytctttct acaaatccgg tttttcatgc 4560 aaaatcaaag cacattgaga tcgactatca ttttgtccga gagagggtca ctcgagggga 4620 tcttcaggtt caacatgtgt cttcctcaga tcaatacgcc gatatcctca caaagggttt 4680 atcagcgcct ttgtttcagc accattgcag caatctgatg cttagtgcac tagagcatca 4740 gcttgagggg gaa 4753 // ID Copia1A-VV_I repbase; DNA; EDCOT; 4533 BP. XX AC CU459238; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 08-SEP-2008 (Rel. 13.1, Last updated, Version 1) XX DE LTR retrotransposon Ty1-copia like, internal portion from Vitis DE vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Huben-B01; KW Copia1A-VV; Copia1A-VV_LTR; Copia1A-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4533 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL; CU459238; Positions 1040047 1044579. XX CC Size = 4944 bp CC LTR = 206 bp CC LTR are 100 % similar to each other. CC Direct flanking repeats = atata. XX FH Key Location/Qualifiers FT CDS 622..3720 FT /product="Copia1A-VV_1p" FT /note="Incomplete putative gagpol polyprotein." FT /translation="TASLMTLGVGFSVARPLPSIREVFSEVRREESRRRVM FT LDHSVGPEGSALLTYGPHGPHGPYAIAGRGHSVGLEGSALLTYGPHGPHGP FT YAIAGRGPSVAGSSGPSPRQSKRTYCEHCKKLGHTKDTCWALHGKPADWKP FT RQPNKAHSHQASTEAQADKTPTEVCQSTSSVGFNSNQIAKLYELFSNFQAS FT GQSSTTLSSGSLAKKGTFLTALSTMSQTIPWIVDSGASDHMTDAHHLFSTY FT SPCAGNLKVKIADGTLSPVAGKGSIRISESITLNPVLHVPNLSCNLLSISQ FT LTKKSNCSAKFLSSHCVFQDLSSGKTIGSAKEREGLYYFDETDVLGQSSPT FT VCNSTSYSKDSELLLWHKRMGHPSFQYLKHLFPSLCSNKTILDFQCEVCEL FT AKHHRTSFPKSKYKPSIPFTLIHSDLWGSSRTPNRTHKKWFITFIDDHTRL FT CWVYLLTDKTEVRSVFMNFHYMIQTQFHTKIQILRTDNGTEYFNHSLSTYL FT QENGIIHQSSCVDTPQQNGVTERKNRHILEVARALLFSSHMPTQFWGDSIL FT TATYLINRMPSRVLSFVTPLQKFHEFFPHSRLDAHLPLRVFGSTVFVHIHG FT PKRNKFDPRALKCVFLGYSSTQKGYKCYDPISQKLYVSLDVTFFEHTPYYS FT LQGESMSETRPSLTSDYLDVAMFESTPCFISNPSHNTEGHLNLGGDMELQT FT NRETLVYSRRPKSKFNETLISEALQESESVIVPTPREYDFNSDQVTDDLPI FT AIRKQPRSCTLHPISNFVSYNSLSAKCRAFTTNLDRIQLPKNIQEAFEIPE FT WKEVVMEEIRALEKNETWEVMNLPRGKKPVGCKWIFTVKYKADGTVERYKA FT RLVAKGFTQTYGIDYTETFAPVAKLNTIRVLLSLAANLDWPLHQFDIKNAF FT LNGELEEEVFMMLPPGFCKEEEETRVCKLKKSLYGLKQSPRAWFDRFAKVI FT KNQGYQQGQSDHTMFFKQSNDGRMTILIVYVDDIILTGDDTGEVERLKKVL FT ATEFEVKDLGQMRYFLGMEVARSRKGN" XX SQ Sequence 4533 BP; 1354 A; 949 C; 1003 G; 1227 T; 0 other; tggtatcaga gccaggtttg ctctaaaacc ctaatctgtc catggatgcc caaagaggaa 60 gcaaccacga aagagtgtcg gagatacact cttcgatggg tcccgtcggt gcattcgaca 120 actccccact ccaccttacc attgaaaaat tgaatggtaa gaattacaga gagtgggctc 180 aagcaatcaa actcgtaatt gacggaaagg gaaagttagg gttccttacc ggcgagactc 240 gacgaccacc tccgaccgat gtagcagcat ctcagaaatg gcggtcggaa aactccttta 300 tcacctcgtg cttgagtaat tccatgaaac catccattgg aaagacttac atgtttctcc 360 caacggcaaa ggacgtgtgg gatgcgatac aggaaacgta ttccgatgct gagaatgctt 420 cccaaatctt tgaaatcaag acgcggcttt ggcagatgaa gcaaggagat cgggaagtca 480 cggaatacta caccgagatg ctgggtctgt ggcaagagct cgatcttagt tgcgaagaag 540 agtgggagtg cacgggggac agcgtgcgct tcaagaagaa gatggagaat gagagggtct 600 tcgagttcct agcggggttg aaccgcgagc ttgatgacgt taggagtagg gttctcagtc 660 gcccggccgt tgccctccat ccgagaagtc ttctctgagg tgcggcgaga ggagagcaga 720 aggagagtga tgctggatca ctcagttggg cctgagggct cagccctttt aacttatggt 780 cctcatgggc cccatgggcc ttatgctatt gctggacgtg gtcactcagt tgggcttgag 840 ggctcagccc ttttaactta tggtcctcat gggccccatg ggccttatgc tattgctgga 900 cgtgggcctt ctgttgctgg atctagtggg ccaagcccaa gacagtccaa gaggacttat 960 tgtgagcatt gtaagaagtt gggccacact aaagacactt gttgggcctt acatggcaag 1020 cccgcagatt ggaagcccag acagccgaat aaagcccaca gtcatcaggc ctccaccgaa 1080 gcccaggcag acaaaactcc tacagaagtt tgtcagtcaa cttctagtgt ggggtttaat 1140 tccaaccaga ttgcgaaatt atatgagctt ttttctaatt tccaagcctc tggtcagtct 1200 tctaccactt tatcctctgg ttctttggca aaaaaaggta cctttttgac agcacttagc 1260 accatgtctc agactattcc ttggattgtt gactctggtg catctgatca tatgacagat 1320 gctcatcatt tattttctac atattctccc tgtgccggta atttaaaagt aaaaattgca 1380 gatggtactt tatcaccagt tgctggcaaa gggagtattc gtatttctga gtcaattact 1440 ctcaaccctg tcctacatgt acctaatttg tcttgcaatt tgctgtctat tagccagtta 1500 accaaaaagt ctaattgctc agctaaattc ctatcatctc actgtgtttt tcaggaccta 1560 tcatcgggga agacgattgg cagtgctaag gaacgtgagg gtctatatta cttcgacgaa 1620 actgatgtgc ttggacagag ttctcctact gtttgtaatt ctacatctta ttctaaggat 1680 agtgaacttt tgttatggca caaaaggatg ggtcatccta gttttcagta tttaaaacat 1740 ttatttccct cgctatgttc aaacaaaacg atattggatt ttcagtgtga agtgtgtgaa 1800 cttgccaaac atcatcgaac gtcttttcct aaatctaagt ataaaccatc cataccattt 1860 actctgattc acagtgatct atggggttcc tcacgtaccc ctaataggac ccataaaaaa 1920 tggtttatta cttttattga tgatcatact cgcctatgtt gggtatattt gttgactgat 1980 aaaactgagg ttcgatcagt cttcatgaac tttcactata tgatacaaac tcagtttcac 2040 accaaaattc aaattcttcg tactgataat ggtacagagt attttaatca ctccttgagc 2100 acttaccttc aagaaaatgg tattatacat caaagttctt gtgttgacac acctcaacaa 2160 aacggggtta cagaacggaa aaatagacat attcttgaag ttgctcgtgc tttgttattt 2220 tcatctcaca tgccaacaca attttggggt gactccattt tgacagccac atatcttatt 2280 aaccgaatgc ctagtcgggt cctatccttt gtcacacccc tccaaaaatt ccatgagttt 2340 tttcctcatt cgagacttga tgcacacctt ccacttcgtg tctttgggtc cactgtgttt 2400 gtccacattc atggacctaa gcggaacaaa tttgatccca gagcacttaa atgtgtcttt 2460 cttggctact cttccacaca aaaaggctac aaatgctatg acccaatttc acagaagcta 2520 tatgttagcc tagatgtcac attttttgag catactccct actactcgct tcagggggag 2580 tccatgagtg aaactagacc ttccttaacc tctgactatc ttgatgttgc tatgtttgaa 2640 tccactccgt gctttatatc taacccttca cataatacag aaggacactt aaacttaggg 2700 ggagatatgg aattacagac aaatagggaa acacttgtct attcaaggag gccaaaatcg 2760 aagttcaatg agacactcat ctccgaagca ctacaagagt cagaatcggt gatagttcca 2820 acccctcgag agtatgactt caattctgat caggtaacag atgacttacc cattgctatt 2880 aggaaacaac ctcgttcatg tactctccat cctatctcaa actttgtgtc ttataattct 2940 ctttctgcaa agtgtcgtgc ctttacaact aaccttgaca gaatccagct tcctaaaaac 3000 attcaagaag ctttcgaaat tccagaatgg aaagaggttg tgatggaaga aataagggca 3060 ttagaaaaaa atgagacttg ggaagtgatg aatttaccaa gggggaagaa accagtgggc 3120 tgtaaatgga tattcacagt gaaatataaa gcggatggca cagtagaacg atacaaagcc 3180 cgcctagttg caaaggggtt cactcagacc tatggcatcg actatactga gacatttgca 3240 ccagtagcaa agctgaacac tatacgagtt cttttatcct tagcagcaaa cctcgactgg 3300 ccactccatc agtttgatat aaagaatgcc tttctgaatg gagaactaga agaagaagtg 3360 tttatgatgt taccaccagg gttctgtaag gaagaagaag aaaccagggt atgcaaattg 3420 aagaaatctc tttatggtct caaacaatca cccagagcat ggtttgatag atttgcaaag 3480 gtgattaaga atcaaggata ccaacaggga cagtcagatc acacaatgtt cttcaaacag 3540 tccaatgatg gaaggatgac cattctaatc gtctatgtcg atgacatcat tctcactgga 3600 gatgacacag gagaagtgga aagattaaag aaggtcttag ccacagaatt tgaggtgaaa 3660 gatctgggtc aaatgcggta tttcctagga atggaggtcg ccagatcaag aaagggaaat 3720 tagtatttcc caaagaaaag tatgtacttg atttgttgac tgagactggc atgctgggat 3780 gcaagccaag cgatacccct atcaaggcaa gaaacagaat ggaaagtgac ggaaagcctg 3840 tggatagaga gaaatatcag cgactagtag gtagactgat ctacctttct cacactagac 3900 ctgacattgc tttcgccgta agcgtggtta gccaatacat gcactcacca aaggaaagtc 3960 atctggaagc agtgtataag atcctcagat acctaaaagg ttctccaggg agaggactat 4020 tctttaagaa gagtgacagt aagaaagtag agatttacac agatgcagat tgggcgggag 4080 cagcagatga cagaaggtct actacaggtt actgtaccta tgtctggggc aatttagtaa 4140 catggagaag taaaaagcag agtgtagtgg ctagaagcag tgccgaagct gaattcagag 4200 cagttgcaca aggtatgtgt gaaggactat ggttgaaaaa actgttggaa gaactatgca 4260 ttacaataga gctccccatt aaactctatt gtgacaacaa agctgccatt agtatttctc 4320 ataatcctgt tcagcacgac agaaccaaac atatagaagt ggacagacac tttataaagg 4380 aaaaattgag aaagggatta tttgcatgac ttatatccct acaagggaac aattggccga 4440 tattttcacc aaggggttac agaaatcaag ctttgaagac tttattggca agttggacat 4500 gattaatatc tatgatccaa cttgaggggg agt 4533 // ID BNR1 repbase; DNA; EDCOT; 6700 BP. XX AC EU564339; XX DT 08-NOV-2010 (Rel. 15.11, Created) DT 08-NOV-2010 (Rel. 15.11, Last updated, Version 2) XX DE Beta vulgaris LINE BNR1, complete sequence. XX KW L1; Non-LTR Retrotransposon; Transposable Element; BNR1. XX OS Beta vulgaris OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC Caryophyllales; Amaranthaceae; Beta. XX RN [1] RP 1-6700 RA Heitkam T. and Schmidt T.; RT "BNR - a LINE family from Beta vulgaris - contains a RRM domain RT in open reading frame 1 and defines a L1 sub-clade present in RT diverse plant genomes."; RL Plant J 59(6), 872-882 (2009). XX DR EMBL/GenBank/DDBJ; EU564339; Positions 89 6788. XX FH Key Location/Qualifiers FT CDS 1457..2284 FT /product="BNR1_1p" FT /translation="MVVNVSDNEKTESHFLKNDELIINVKIPENTSLLGND FT DAPAGNKKSDKTTDEVPCTEKIVDNDDVQYPSNVKLTPSKNGARDLENKKK FT SQPSNDFNIIETNKTSIQNPPGPSPELGLISCNASSPPIPIQSIHQTSPTQ FT PHSSPPTSPLSPIHLTNRFKALVRPSSSMSSSSSLSGPLFPPGFENDIPLT FT IKAIHKKKREKKIQKKKKPPFLPLPNQSSPSLTRALIPSSSENSVSSILEV FT GKKLGMRFNGPETILEERIESILQQHKASWKANQN" FT CDS 3077..5317 FT /product="BNR1_2p" FT /translation="MHENYLRHLGLNPQNMTFMDKLRLLKTNLEEWNAAEF FT GIIEEKISFFENKIHEYDLIANNRMLDKAELEERKAAQIELWQWSKRNESF FT WAQHSRAKWIREGDRNTRYFHVMASIRRRKNNIEYLKEGEHMIEDPTEIKM FT AATNFFKNLFTEEHEIRPVFEGLDFKRLGEQHEHILTDPFSTAEIDAAVAA FT CDSSKSPGPDGFNFMFIKNSWDLIKEDIYAIVFEFWQTSHLPKGCNTALVA FT LIPKTNPPNGFKDFRPISMIGCVYKIISKILARRLQQVMAHLVGSHQSAFI FT KGRQILDGALIAGEVIESCKRNKVDATIFKIDFHKAFDSVSWGFMEWTLTQ FT MNFPKQWREWIRACVLSASASILINGSPTSPIKLRRGLRQGDPLSPFLFTL FT IAEPLNLLIKKAVSLSLWEGVEICRGGLKITHLQYADDTVLFCPPKLEFLE FT NIKRVLILFHLASGLQINFHKSSLMGINIEPKLLDHMASQLLCKVGSLPFV FT YLGLPIGGSASRINLWEPVIAKIEKKLASWKGNLLSIGGRVTLIKSCLASL FT PLYYMSLLPMPKGVIEKIIQLQRNFLWRGSLEKKALPLVSWNVLELPKQYG FT GLSIGNLHNKNTALLFKWLWRFIHEPNSLWRQIVQAKYDIGPTFTIRDLTT FT PPHGGPWRGICNLIQSSSHAYQIATHMIRKNIGDGSSTMFWHDVWVGEHPL FT KEVCPRLFLLSLSPNALVSSCGFWDGQIWHWSLHWKRNLRPQDRCES" XX SQ Sequence 6700 BP; 2107 A; 1511 C; 1310 G; 1772 T; 0 other; aaaaaatata agtcttattt ctaagataga gaaactgtat aagaatcgag gagagatgga 60 ggagaatacc cctagagaga gaaaccccac cagagaccat gaaaacccaa tcaaaatcct 120 tgaaaaccca tggataacca tcaaaagaag aaaatccaag cctccaaacc accaagcttc 180 tcgaacctgt tttgtaaatc atctcccccc ctccataact ataccagaaa tagctagaat 240 cttcagaacc catggggcaa tcgcagaaat aacaatccca aaaacccaga accaaaccag 300 ccacaaattt gcttttgttc aatttcatta cccacaatcc cttactacag ccatacgaga 360 tgaaaacaaa agaaaagttg aaaccatggt aatttctgtg cacccagcaa aatatgataa 420 aaacctctat gctcgagcca acaaccctcc aaccaccctc acatactcat ctcgcgtagc 480 aaatacaaaa caaattagcc aaaacccgaa aaaagcatat accagagacc ttcgcacata 540 caaagaagct gcaaatccca caaaaaccac tgaaaacaaa aaaacaaatc acccgcaaac 600 ccgacctcca aagccaacgc caattctgca gttccataat cccaataacc cagttcttcc 660 tttcgaggag tatgtcccca caacaacctc ctgtaaacct gaaccatcgg cacatcgaaa 720 aatgagctca cgagctcttg gagaagacac cgaaaaaatc agaagcacac tgggagccat 780 tgatatggaa agtgattttg ctgctgcctt aaaaggcaag agatgcaaag aaaatgaaga 840 catgctccaa agaagttcaa tagccttctc cccgtcttcg caatcatctg aaattattat 900 ggatcacatc ttggccgagg gagttaactg cctcacaatt agacccatgg gaggaatgtt 960 acaccttcta acttttgaca catttgaaaa taagaaagca atgattgaga gtggatggct 1020 ccaaagatgg ttttcaaaaa taataaacgt caatactaga agtgcatccc tgtggaggga 1080 aacatgggta aatatatatg gagtgcctct cattgcttgg ggatatgaga gcttttacaa 1140 cattggaagt atgctgggga gagttttatc agtcaattac aaggactttg attgtgcaag 1200 agttctcctt ttcacagatt gcttctttga cataagttgc aagatatctt ttgagattga 1260 agatgagaaa tacccagtct ttatttcaga gaagcaacaa ctctggcaga acaaaacgag 1320 cccagagtac aaaattagca agatcaatga tgcaaatgac ggaaatccac taggtacaat 1380 caaagatgca aagggacctg atgatgacga aagtcagtaa tcctcatgca gccaacttca 1440 ggtaagccta ctcctcatgg tcgtgaatgt ttctgataat gagaagacag aaagccactt 1500 tttgaaaaat gatgagttaa ttattaatgt gaagattccc gaaaatacct cattattggg 1560 aaatgatgat gcccctgctg gcaataaaaa aagtgacaag accactgatg aggtcccatg 1620 taccgaaaaa attgtcgata atgatgatgt gcaataccct agcaatgtca aactgacacc 1680 ctcaaaaaac ggcgcacgtg acctagaaaa caaaaaaaaa tcccaacctt ctaatgattt 1740 taacatcatt gaaaccaaca aaacctccat ccaaaatccc cctgggccct cgccagaact 1800 gggcctaatc tcctgcaacg cttcctcccc acctatacca atccaaagta tccatcaaac 1860 aagcccaaca caacctcact cttcacctcc tacctcccct ttgtccccaa ttcacctaac 1920 taatagattc aaagccctag ttaggcccag ttcctccatg tcatcatcct catcactatc 1980 tgggcctctg ttcccgccgg gcttcgaaaa tgacattccc ttaaccatca aagccattca 2040 taaaaaaaag agagaaaaga aaatccaaaa aaagaaaaag cctccctttc tccctcttcc 2100 aaatcaatcc tccccatccc ttacaagagc tcttatccct tcatcttcgg aaaactcagt 2160 ctcatccata ttagaagtgg gcaaaaagct tgggatgcgc tttaatgggc ctgaaactat 2220 ccttgaggaa cgaattgagt cgattcttca gcagcataaa gccagctgga aggctaatca 2280 gaattagcct ctctccactc caatccataa aacaaaaaaa tctttaatga ttcttctatc 2340 ctggaattgt cgtggactag gcgctagaat taagcgcaat gcagttagga aattgataca 2400 aaaaaatgat ccccacttga tattcatcca agagtcgaag ctagaatcaa tcagcccgaa 2460 agtcatgaaa tccatctgtg atgtcaatga catgaactcc gcaataagtc cctcaaatgg 2520 tccttcaggg ggcctaatat ccatatggaa gaatagcctt cttcatggtt gaagaatcaa 2580 gatgtgagtg taatggatca tactcacacg gctctatact atcaatcaac atgaaatgca 2640 gatttattaa tttgtacaac ccatgtgatg ttcagaggcg tacagaagta tggcgcgaat 2700 taatccaaat ttgcgaatca tcaccactcc cgtgcctttt cataggcgat tttaatgaag 2760 tccttgaggc ttctgagaga ggtagccaac atattttaac taacagttcg acagaattta 2820 aagatttttt gcaggtcctt catctcatag aaataccatc ctcaaattcc aaattcactt 2880 ggtttcgtgg ccaatctaaa agcaagcttg accgagtctt tgttcaggct cagtggatat 2940 ctgcataccc tcttattcga gtctctcatc tacaaagagg attgtccgat cactgcccta 3000 ttctagttca atcaaaagaa aagaattggg ggccgaggcc cttccgattc cttaattgct 3060 ggctctctca cccaggatgc atgaaaacta tctcagacac cttgggctaa atccccaaaa 3120 tatgaccttc atggacaagt tgagattatt gaagaccaac cttgaagaat ggaatgctgc 3180 agaatttggt atcattgagg aaaaaatttc tttcttcgag aacaagattc atgaatatga 3240 ccttattgca aacaatagaa tgcttgataa agctgaactg gaggaacgca aagcggctca 3300 aatagaactt tggcaatggt caaagcgcaa tgaatccttt tgggcccaac actcaagggc 3360 caaatggatc cgagaggggg accgcaatac ccgctacttt catgtgatgg cctcaataag 3420 aaggaggaaa aataacattg agtatctcaa ggaaggtgaa catatgattg aagatcccac 3480 tgaaatcaaa atggccgcga caaatttttt taaaaatcta ttcacggaag agcatgaaat 3540 cagacctgtt tttgaaggtc tcgacttcaa aaggctcggt gaacaacacg agcatattct 3600 cactgatcct ttctctactg cggaaataga tgcagcagta gccgcttgtg acagctcgaa 3660 atctcccgga ccagatggtt ttaatttcat gtttatcaag aactcttggg atcttatcaa 3720 ggaagacatc tatgctattg tgttcgaatt ttggcaaact tctcaccttc cgaaaggatg 3780 caacactgct cttgttgcct taatccctaa aaccaatcct ccaaatggtt ttaaggactt 3840 caggccgata agtatgatag ggtgtgtcta taaaataata tcgaaaatcc tcgctaggag 3900 attgcagcaa gttatggcgc atctagtagg ttctcaccaa tcggccttca taaaaggaag 3960 gcaaatcctg gatggtgcct tgattgcggg ggaagttatc gaatcttgca aacggaacaa 4020 agtggatgcc acaatattca aaattgactt tcataaggcg tttgatagcg tctcctgggg 4080 atttatggaa tggactctca ctcaaatgaa ttttccaaag cagtggcgtg aatggattag 4140 agcttgtgtc ttatctgcct ctgcaagcat tctcattaat ggttctccta cttctcccat 4200 taaacttcgt cgtggcctga gacagggaga tcccctctcc ccgttcctct ttactctgat 4260 tgcggagcca ctaaatctcc ttattaagaa ggcagtttct ctaagcctat gggagggggt 4320 cgaaatttgc agaggtggcc tcaaaattac ccatcttcag tacgcagacg acactgtgct 4380 cttctgcccc ccgaaattgg agttcctgga aaatataaaa agagttctaa tactctttca 4440 ccttgcttct ggactacaaa taaatttcca caagagttcc ctcatgggga tcaacattga 4500 accgaaactt cttgatcaca tggcatctca actgctatgc aaagtgggtt cacttccctt 4560 tgtctattta gggcttccaa ttggtggcag cgcatctcgt attaatctat gggagccggt 4620 catagcaaaa atcgagaaaa aattggcctc atggaaaggc aatcttcttt ccattggagg 4680 aagagtcaca ctcataaaat catgccttgc aagcctccca ttatactaca tgtctcttct 4740 cccgatgcct aaaggggtga ttgaaaaaat cattcaactg caaagaaact ttctttggcg 4800 tggtagtttg gagaagaaag ctctccccct tgtgtcgtgg aatgtgcttg aacttcccaa 4860 gcaatatgga ggactgagta ttggtaatct tcataataaa aacactgctc tcctattcaa 4920 atggctttgg agattcattc atgagccgaa ctcattatgg cgtcaaatag ttcaagcaaa 4980 atatgatatt ggaccgacct tcactattcg ggacttgaca accccaccac atggtggccc 5040 atggcgaggt atctgtaatc taatccaatc ttcttctcat gcgtatcaaa ttgcaactca 5100 catgataaga aagaatatag gtgatggttc aagcactatg ttttggcatg atgtttgggt 5160 tggtgaacat cctctcaaag aggtatgccc ccgcctcttc ctcctctctt tatctccaaa 5220 tgctctagtc tcctcctgtg gtttttggga tggacaaatc tggcattgga gtctccattg 5280 gaagcgaaac cttcgtccgc aagatcgatg cgagtcgtga atccttgcaa gtccttctag 5340 atagagcagt gctctaccag gatggtcatg atcaaaccat ctggacccca gctaaatccg 5400 ggaaattctc agtgaaatct ttcacattgg aactagcaaa aaaagatgta ccgcaaaact 5460 ttgatgcttc aaaaggattc tggaagggcc ttgtcccttt tagaattgaa atatttgtgt 5520 ggtttgtact tcttggtaga ttgaatacaa aagaaaaact atggagattg ggaatcgttc 5580 cagaatcgga aaaaaattgc gtgctctgta atattcaccc ggagtcagtt aatcatctat 5640 tcatgggttg tacagtggcg tcggagcttt ggctgtggtg gttgagtatt tggggagttt 5700 cgtgggtttt tccctcgact ttaaaaagcc tccataatca gtggcacgct ccgttcagag 5760 gatctatcat taaaaaatca tggcaagcaa tatttttcat catcttgtgg accatttgga 5820 aggaaagaaa cgggcgaatc tttgaaaata aagaatgctc catgtctcag ttgaaagatc 5880 taattcttct aaggctaagt tggtggttga aagggtgggg agatttcttc ccctatagtt 5940 ctactgatac tccttcgaaa cccgcaatgt ctcctatgga attccaagcc gtgcccaagt 6000 aatcacctgc ctagccgcct actgctgtcg agtcgtggtc tcctcctcca tttgggtcgt 6060 tgaagtggaa tgtagatgca tcatgcagct caatatttga atcctcatca attgggggtg 6120 tgctccggga tcacaatggt aattttaatc tgcatgtttt ccgaggccta tccccggttt 6180 atggaaatca ataatcgccg aagtgctagc tatccatcgt gccacttaaa aatatcagca 6240 tcttgtgaaa gatctcatga acctgcccat aatgattgag tcggactccg ttaatgcagt 6300 gaaatggtgc aagcaagata agggtggccc atggaacatg aattttatac tcaacttcat 6360 tcgaggggag tcgagaaaga gcccgggcat gtcaattacc tacaaaggtc gagcatcaaa 6420 tatggtggca gacgcattag ctaagcaagg gttaagtaga agggatgaat ttattgcctt 6480 ggctctaaaa atcacatgta tttcatttta tctagtttgc ttcatagtat aagagagttg 6540 taatatggtg tatgaacatt ttaaggatgg aaatcctcct cctcttcggg tgtgagtatt 6600 cactatgaaa gtttccctcc ttctgaggag gaatacctgg gttgagtcga ggttttctac 6660 ccttaactat aaatgaataa aaccaaatta tcaaaaaaaa 6700 // ID RAGYPSY4_LTR_MT repbase; DNA; EDCOT; 3185 BP. XX AC . XX DT 22-NOV-2006 (Rel. 11.11, Created) DT 28-NOV-2006 (Rel. 11.11, Last updated, Version 1) XX DE Long terminal repeat sequence of LTR retroposon RAGYPSY4, from DE Medicago truncatula. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW RAGYPSY4_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3185 RA Shankar R. and Jurka J.; RT "RAGYPSY4: LTR sequence from Barrel Medic."; RL Repbase Reports 6(11), 588-588 (2006). XX DR [1] (Consensus) XX CC Internal region contains intact Integrase and RNAse domains. The CC internal region is ~86% identical to GYPSY-I_MT. XX SQ Sequence 3185 BP; 955 A; 616 C; 481 G; 1132 T; 1 other; tgttataccc tgattttgga cctaaaaata ctcgttcaaa tttcttttct accactgata 60 attgtcaatt tactgttgtt ttactttgaa tcttcacttt attttcatct gcatatttta 120 ctgtctctgt ctcaaggtat tttcaaatca tgattttgcc tgtgtttttc ttgcataaga 180 tcatccaaag tgtctttctt acattacaag tcatttgaaa actctctgaa tcattgcatt 240 gcttttcttg cattttaatt cattgcaaaa atcatacaaa aagggtattt tggtcatttc 300 ctgcagtgga acccatttta gtccctgtgt ttgtctctga gtcttttcaa cttgttttac 360 aaatcattgt tgagtctttg ttaaaaaatc atttcaaaaa ttgcatctga gtcagtttga 420 gtcagtttag tccctagggg cattttggtc ttttcctgtc aaaatttcga cagagaggta 480 ttttaaaata cctcattttt gtaattggtt cattttagtc cttttgttga ttttattttt 540 aggtttcact ttactttttt tccaacttac caattttaat tcaattttat ttttaattgc 600 attctggtcc ctcaaacaar tttccagaat tgcactttag tccaaaactt tttaaaattg 660 cattttagtt cattattatt aattgcagtt tagtcctcaa ttttacattt ttgcagaaag 720 gtccctaggt cacaacaagt ccaaggccga gccatacaag tccaggtgtc accatttcat 780 tggatctcaa gtacaagtgg cagcttataa atagtgcaca gtgtcagaga aatccacaga 840 gacccattca atcaatgcca catcacaaac agaactccag tttctctctc cattcagtta 900 gatcaaaaca gaaaccatca agaacaagca aaaaccctaa ttctccagaa ccaaaattca 960 taaacaaatt catcaaattc gcgtcaattc tcagagattc atggtgaatc ttcatcattg 1020 aatcgttttc tctgcaattc aagtgcgaat tcatcaccgg tggtgacaaa ctcaagcacg 1080 atcacagagt ttttttgaag aagaagagga aagaaagaag atgaagaata tgaaccggtg 1140 aagaagaaga aggaatcaaa ccagccagaa acaccgattt attttcggtt tcaagtcaaa 1200 aatcaacaaa cagaatcaaa tcgaagtttt ccaaagaatc tcgttcgaaa tctccgatta 1260 aatcacaggt aaacataaaa cttcatcttt atttctcaag aacattaaca aggacgaatc 1320 aatgtagatc ttcaaggttt caaatagttt ctttcaaaaa atttaaaaac ctaaaaaaaa 1380 ttttcaaaac cgtaagaaaa atttagatct acgttgattc aagccttgca tgtgaaatcc 1440 agtgttagat tcgtgtttag ggtgaagaaa cgagtagatt gatgtaaaaa ttttggattt 1500 ctggtgaggt taaggctcgc cgaaatctgg agttcacgcc ggagttgatg aagattccga 1560 tgaatcttca tcttctccgg ccgttccttc cagaatccgg cgaagagaag agggagacga 1620 gaggttagtg agagaagtga gaagttagag agagaaagaa cattagcaaa tgaaaaaacc 1680 cgctcccctc cttttatagg ccagtgaacc ggaccggtcc aagaccggtc catttccctt 1740 cattcctggc cgtttgatct agggtttgat cccctggatc aatcctgtgg ttcctgtgca 1800 tccggacccc ttaggcttgg gcttgggctt tttccttttg gttttgctgc gtttttgcta 1860 ttttcttgct attcacacca tgctttcttg ctatttgaac cactgttcgt tctaattttc 1920 tcgtaaaaat tcctaaaaaa tttctatgtg tttcttgata catttttgac ttttttgtga 1980 tttttttaca tgttataaaa ttgataaaaa tatatgtatt gctttcttga ttattttctt 2040 ttctttagtt gaatttcatg caatttctcg ttttttccgt tcgtgatatc ttgatctatg 2100 atatgaatgt tcgatgtgca atttcatgat gaatgccact gtttgtgtgt gtgttttgct 2160 gttttcaaca tgatttgtta atttcttgcc ttgcaagtat tgctttcctc tttgtattgt 2220 ggttattgtc gtcattttta ccgtttacca tatattcctt tgtttgctct ctttgccata 2280 ttttcatgcc ttattttact aaccattttt tgttctatgt ctcatccatt ttatagcatt 2340 tcatcatttc attcctattc atttttttta tgttaagtgg acatgtaata attctaggta 2400 gtttaatttc cttttaattt cttgcaagac catagcatgt aaattagggc aaagtgtaaa 2460 ggacaatgga ctctctataa tgatgtacac cgacacaagc accgacacgc aaacacgttg 2520 tatgtttacc gcttagatgt atgcttagga aacgcaatac ttagaaaaat atcatttttt 2580 ttcccaaaaa ataactccat aactcaaatt ttttctctaa taaaccttgg agtcaacact 2640 ccattgtatt ttccctttat tttcttaatc aaaacttcaa tgaatcttaa tttctactta 2700 gacactcttt ctttaataat tgaaccaacc attcactatc tttttctctc atgcctttac 2760 ggcctctttc tcttcttcaa aaccattttc aaaaactaaa atcaatcaaa cacacaaaaa 2820 ccatttttga aagagaacta catggaattt tgatccctta aaagggtatg taggcaagag 2880 gtcaaaacct ctccaagtcc aataaaataa aatctcaaac attttctccc tccattctta 2940 aactaaataa actttctttt caataaataa gcataaagcg tagacataaa gctaggaaaa 3000 cggttcctat agaatactat agtcgttacg ggtgcttaac accttcccgt aacgaaaacg 3060 acccccgaac ttagagtttc taagggtttt ctcaatttta cccttcccaa gaaaaaatag 3120 agaatatcaa agattgaaag gttcaagcct aattaatgac ttgatacccc aaaatcgtga 3180 taaca 3185 // ID MUMET1 repbase; DNA; EDCOT; 5337 BP. XX AC AC187466; XX DT 19-DEC-2006 (Rel. 11.12, Created) DT 04-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE MuDr-type DNA transposon. XX KW MuDR; DNA transposon; Transposable Element; MUMET1. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5337 RA Jurka J.; RT "MUMET1: MuDr-type DNA transposon from barrel medic."; RL Repbase Reports 6(12), 637-637 (2006). XX DR EMBL/GenBank/DDBJ; AC187466; Positions 147077 152413. XX FH Key Location/Qualifiers FT CDS join(689..2164,2168..2773) FT /product="MUMET1_1p" FT /translation="VLLAYSFRVGFGVRVRFANKKEDGSVSSCRLVCCKEG FT LKRKEKRYAYEGKYTRADVRTNCPVRITLSRKNGKLVINDFEEEHNHDLQN FT SETKHMLRSHRKITEVQAYEIDLANDSGLRQKSTFQLLSTQAGHRANVGFT FT EVDVRNYITARRKRSMAYGEIGCLSKYFQRQLLENPSFFHAYQMDVEEHIT FT NVFWCDAQMILDYGYFGDVVSLDTTYCTNYANRPLAFFSGFNHYRGSVIFG FT AALMYDETSESFRWLFDTFLQAHNNKKPKTIFTDQDQAMARAVADVMPETH FT HGLCTWHLLQNGVKHLGNMMKGGSSLLSDIKKCMYDIDIEANFEKLWFDMI FT HKFNIHDKSWIISTYELKKKWASCYMKGVLTLGMRSTQVSESLNAHFKSCM FT KPNVNILEFFNHFEIVVEEKRAKELSCVYESSHKLARLAYETAPILIQMGK FT TYTHTVFELFQDEFKLFLTLSVPIRHESDSLCEYVITKAKHEGSWRVFNRV FT SNSITCSCRKFDTFGILCSHALKVFELNDVKVIPDNYILKRWTREARYGVV FT QDFRGKEVEGDPNLSRNRMFRQVVSKFIKAATEASPKEEWLKFLDNGVDDM FT FKKIIELRTQAMDNNGDNGARPEVVSLDFMQAKGFRVRPGSKRIKRHKSCL FT EKQHSRATSRRAPPKEKSSQVYELLFKVLVLVLLVLVTAIILHVS" XX SQ Sequence 5337 BP; 1592 A; 817 C; 1053 G; 1875 T; 0 other; gggctccact tgtgtaacat agtggatttt aagttatata acattgtcca atcagggtgt 60 gccacgtggc acacccttta aaaaaaaata attcaccgcc accatcatca tcatcatcat 120 catcagttta ccgtccaccg tcgatcaccg ccaccgccgt caacctgcca tgactgtggc 180 atcataaggt tttctttttc ttttatcttt ttctttagaa tgattgaaat gttcatagaa 240 atgagattaa cccataataa aaatcaaaat ttctatgaaa atagagaata acaacggttg 300 atcaagagat aaaacaattg tttttgaact agtttcaatt tattaggatt tgattttagg 360 aaatttaggg ttttatttaa ggatgtatat aacccattgc aatgtttact aaactctgtt 420 tctttttttt aaaaaagctt gactcatgtt gttgttgttt tgaaaaaagg caaaggggat 480 tgattgatcc ttgaattttt ttgttcttat cattcattct gtttcaatgt tttctttctt 540 aatgttttgt atgaattgtt ttttatgcct tatgttcttt atttactttt taggttcttt 600 ggatagtttg atcaaatatg acatcttcag atgttgattg gaaaccaaag attggaatgg 660 gatttgattc tatggaagag gctaataagt tttgcttgct tatagtttcc gtgtgggctt 720 cggagttaga gtacgtttcg caaacaaaaa agaagatggt agcgtatcgt catgtcgatt 780 ggtttgttgt aaggaagggc taaaaaggaa ggagaaaaga tacgcatatg aaggaaaata 840 tacgagagcc gatgttagaa caaattgccc tgtaagaatt acactttctc gtaagaatgg 900 aaagttggtc atcaatgact ttgaagaaga acataaccat gatctacaaa attctgagac 960 aaaacacatg cttcggtcac atagaaagat aactgaggtg caagcatatg agattgattt 1020 ggctaatgac tctggattaa ggcagaagtc aacatttcaa cttttgagca cacaagcagg 1080 gcacagagct aatgttggat ttacagaggt ggatgtaaga aactacatca ctgcaagaag 1140 aaaaagaagt atggcatatg gtgagattgg atgtctttca aaatattttc aacgacaatt 1200 gttggagaat ccatccttct ttcatgcata tcagatggat gtagaagaac atattacaaa 1260 tgtgttttgg tgtgatgcac agatgatttt ggattatggg tattttggcg atgttgtttc 1320 tttggacacc acatactgta ccaactatgc caatagacca cttgcttttt tttctggttt 1380 caaccattat agaggttcag tcatatttgg ggcggcacta atgtatgatg agacaagtga 1440 gtcatttaga tggttgtttg atacattctt acaggcacac aacaacaaaa aaccaaagac 1500 gatcttcact gaccaagatc aagcaatggc aagggcagtt gcagatgtga tgcccgagac 1560 tcatcatggt ttatgcacat ggcatttgtt acaaaatgga gttaaacatc ttgggaacat 1620 gatgaaggga ggatcttctt tgcttagtga tatcaaaaaa tgcatgtatg atattgacat 1680 tgaagcaaat tttgagaaac tttggtttga catgatccac aaatttaata ttcatgacaa 1740 atcttggatc atttcaactt atgagcttaa aaaaaaatgg gcttcatgtt atatgaaggg 1800 agtgttaaca cttggtatgc gaagtacaca agttagtgaa agtttgaatg ctcacttcaa 1860 gtcttgtatg aaaccgaatg tgaatatcct agaattcttc aaccattttg aaatagttgt 1920 tgaggagaag agagcaaaag aattgagttg tgtgtatgaa tcctcccata agcttgcaag 1980 gttagcatat gaaactgcac caatactaat tcaaatggga aaaacataca cacacactgt 2040 atttgaattg tttcaagatg agtttaagtt attcttaact ttatctgtac caattagaca 2100 tgaatctgac tctctttgtg aatatgtcat cacaaaggca aaacatgaag gatcttggag 2160 agtttaattt aaccgtgttt caaattccat cacttgtagt tgtaggaaat ttgatacttt 2220 tggcatactt tgttcacatg ctttaaaagt gtttgaattg aatgatgtta aggtaattcc 2280 tgacaactat attttaaaaa ggtggacaag agaagcccgt tatggcgttg tgcaagattt 2340 taggggaaag gaggttgaag gagatcctaa cttgtctaga aatcgaatgt tcagacaagt 2400 tgtctctaag ttcattaaag cggcaactga agcatcaccc aaggaagaat ggctcaagtt 2460 tcttgataat ggtgtagatg acatgttcaa gaaaataatt gaacttcgga cacaagctat 2520 ggacaataac ggtgataatg gtgctcgtcc agaagttgtg agtttggatt ttatgcaagc 2580 aaaggggttc agggtacgac ccggttcaaa gcgaattaag cgacacaaaa gttgtctgga 2640 aaaacagcat agtcgcgcta catctaggcg cgctccacct aaagaaaaaa gttcacaggt 2700 atatgagttg ttatttaaag tacttgtttt agttttactt gttttggtga ctgccataat 2760 tttacatgta tcttagctta ataatttgac ataatcattt taggttgatg gagtatcttg 2820 ttctgcgcct acaacttatg agcccccaca agcacatgag tctcaagtca attacacagc 2880 catgctaatg gtaatttcaa aaacaaattc ataatgaact attcatacat tcaacaagta 2940 tcgtgatgct aatttttaag ttgttattaa tgtaggaaat aggggggcca acctatttga 3000 atggaatgaa tgcatagggg gcactggcgt tgctgcattt ttgttgttat taagttttct 3060 ggtttgatac ctgggggggt tccggtttgc atgtagtttt ttgctgttca ggcgcggttt 3120 tttggagcat gggaactgtg tttttgctgt taaaaccact tagtaatgtt attttggatc 3180 ctgttagtgt gctgtcttag gattgtgcag ccacacctct gctaagttgt tatagcagca 3240 actttagttc cccatgttgg gtattttttg gggtttgtcc catttttttc ctgctgaatt 3300 atagcagcac ttttatagca gcttctgcca tacattgact ttgtattttg aatggaatat 3360 acaatatttt gctagcttaa ttgtgttata gcagcctctg tcatttgttc gtttctattt 3420 atgctagcat aattttagag tgtgtaacaa atcttaattg tgttatagca gcctctgtca 3480 tttgttcgtt tctattttgc tagcataatt ttagagtgtg taacaaatct tgattctttt 3540 gtttttggat tgtgtgttaa ctctactgga ttgtagcctg ttgaacttga ctgtctgccc 3600 ataggagttt gagcttttac tgaatctggt gttttttttg ggtgttctat gcatacttca 3660 atgctggttc aaggtaattt tctgtatatc tcagatcaag tttgaggtaa ttctctacgt 3720 agttcaaagc tggttttccg cctgtggact gttgtggtgc tgcagctacg ttgtggcatt 3780 tcttccaccc ctaggttctg attagtatca ttgtgttcca gctgcaacat attggttttg 3840 ttttcttctc tttgctttgg tcttcaagtg tttggtttat tttacagatt tttattgtct 3900 gttttagctg gatgtattgg tctcttttga tatagaaaag gtttagtttt attcattttt 3960 agcattcatc ataatgtaac ttatagaata gaattaaaac tataacgaga tacttttgta 4020 gatcttttgg ctatgttaga tacattagag agcaatacct attttatttt tcttccatac 4080 ttttttcctc atctctctct ttcattttta atccttatga catattaatt actactattg 4140 tttccttatg tttgtctttc taaacttatt tccttttttt tttcttcaca gatttcactt 4200 ctatggatct ctttatatct ctatattttg ctcttgatat aaagggtatc aggacaaatt 4260 agtttgtaat tactgtatgt attagacaca tggttttgtt acaatgaata gggaatgaaa 4320 attggacata aagaattgtg aagtgttgat gtgtcattga attctgatgt attttcatat 4380 gataattagt aactattctt atattagaca aacataatat aggtaaagat gataaaacgt 4440 tggatttgga ttttatgtaa cctcaagaaa ttatcaagtg cttctagcaa gtgttaatat 4500 cttaccggtg gcataaaaaa gaaaaaaatt accggtggca taaactttaa atgaacatta 4560 tgtatccaat ttccataaaa aatttgtagt taaggtgtct aaagtcagga tcattctcag 4620 acaaagttct tccaacaaaa catttttttg tcattatatc acaaactgct atttttaatt 4680 ttgataaccg gtgaagatga tgaatttcaa atgtgttcta taaaaaagct tttcataatt 4740 tattactaag tactttaatg tattatcaat tgtattatac ggcttattta acctcaaatc 4800 ttatatactt aattaaccct cttttcacta tttttgtcac aattcaaaaa atcacaaatc 4860 aacccacctc tcaagagaca attgaaagga tatttgttgt tattagtcta ctgatcttta 4920 caataacaac cctcaatgaa tcccttaatg aatctcaaaa ttaattccaa atcaaattca 4980 tcaataattc caaatcaaat tcatcaaatt tgaaaaagag tgttgcagaa gagaaagtga 5040 agaggaacgg tggccgttgg tggagaggac ggcggcggcg gaggcggagg gaagcgtcgg 5100 cggtggggga gaaaagttga tggtgggtgg gtgggtggtg ggttcgtcgt actggagaag 5160 agaagaggag aagagaagag gaatgtgttt ttgatttttc actcttctct cagtcacgtg 5220 ttctctctta ttctccttta attgattttt ttttttttaa agggtgtgcc acgtggcaca 5280 ccctgattgg acaatgttat ataacttaaa atacccaatg ttacacaagt ggaaccc 5337 // ID SHAMUDRAV_MT repbase; DNA; EDCOT; 6806 BP. XX AC . XX DT 15-JAN-2007 (Rel. 12.01, Created) DT 16-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A MuDr like DNA transposon from Medicago truncatula. XX KW MuDR; DNA transposon; Transposable Element; ORF; Interspersed; KW repeat; TIR; TSD; SHAMUDRAV_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-6806 RA Shankar R. and Jurka J.; RT "SHAMUDRAV_MT: A MuDR type DNA transposon from barrel medic."; RL Repbase Reports 7(1), 104-104 (2007). XX DR [1] (Consensus) XX CC The complete sequence is present in very low number and rarely of CC full length. The sequence has characteristics of MuDr transposon CC in terms of TIRs as well as an ORF containing completely intact CC MuDr class transposase. Also this sequence has another ORF in CC antisense, an another feature of MuDr type transposons. Also the CC sequence is flanked by 9 bp TSD, rich in poly-T. XX FH Key Location/Qualifiers FT CDS 1353..472 FT /product="_2p" FT /translation="MTQYHVIDKRFKTWYKSNGFRFPQESEHWDNRRSHTL FT PRMRPRSLTHTHAYIEWLTTTCNPRLRISIETNPSNSDPDEAEEEEPEHEP FT EIRNNQTPIHDDFWDQDIFSQLQDHQSQPHTTQNIHGSVMYEFLDTPQQNI FT IQPPPYTSPRNAYEPHYQSTYQQNSMPNYGYNDPNQAGASNNNYFSYNDPN FT QAGPSNTNYPPYSNPQYPMYTNQNYNHPPTPTNLLSHFSPASLNSSDQFLD FT MGWPTREHDVSLSLGYGSQIQSAADNNDEDQHDPQVNRGRNRRRRGCGTAG FT HL" FT CDS join(3157..3369,3373..3522,3526..5421) FT /product="_1p" FT /translation="MTIACKKYINFLGEIFHQNDTCMVDHVMHAVHEKAVP FT LMANPAGAWGACCPTSQLQLAGYPPAGAWGRVGAPATTSCVVPQPFFFLKF FT RFKFYLTKYYKCGLHVTSILHQTTLLHTRLLISDQTKSMASNINVFVYYNG FT EVKQNDSGIFFQSQYTKGFKVSMASTYLHLKKRIAEKICLGDNMVVSEIMC FT RNPMFVGATAIHYQALRITDNDDVEFMFNVHKSHSSLSYIELYVTFEMKNP FT TSNFELNYPSSSSQHQNLPQQQYNTQHCNPSSSSSQPHYNPSSQPFQSQWS FT QNVYEPPQLITQPHPSQTPSRSTQPETLNDEINIFTSQFQDQPTDEVQDDE FT DNDDEELLAAQNGDENEEDDEDDLPQLPILPIRASYNPPRSMRNVNDDHST FT ELYHSMALPVDQGIAPGMQFHNKNDCILAIKYYHMKKSTDYIVKKSDPERY FT VIKCKDTKCGFKLRASWRKKTDKWEIGNMNDHTCVSTEMTQDHHKLSYNVI FT CESVKSLLYMDASITVKVIIAHIREKFNYTVSYRKAWRARNKAIESIYGNW FT EESYEELPQWLMVMEKDLPGTIIDFQSDPSTEVANETVFKRLFWAFRPCIS FT GFEFCKPIVQIDATWLYGKYKGTLLLAVAQDGNNKIFPIAFAIVEGETKEA FT WSFFLKNLRQHVTPQENICLISDRHVSIKSAYDDPQNGWHDAPTSHVYCVR FT HIAQNFMRSFKDGELKKKVECMGKNHISFHVNSTFYLFKMTHLTFFKTMQV FT TP" XX SQ Sequence 6806 BP; 2242 A; 1188 C; 1315 G; 2058 T; 3 other; gaaatttttt tttttctgcc cttatttaat tccaaaaata caaaaatgcc ctagttttga 60 aaaaaattgc ataaatgccc tacttttcag aattttctgg taccttgcaa cccccacttg 120 cggggtacct taaaaaaatt ttaaaaatta actaccccgc aagtgggact tgcggcctcc 180 tttttttttt tttttttttt tttaaaaaaa attaaataac tataactaca ctacatgcct 240 atattttttt tttttttttt ttttaaaatt aatagattgc tacccccact tgcggggtat 300 gcttaatttt tttttaaaat ttttttaata ccccgcaagc cccacttgcg ggtttgtttt 360 ttgttttttt ttttaatttt taaaataaaa aaaaataata aaaaaaaaga aggaaaaaaa 420 ataataaaca tattaaatat catgatatct acaattatta taaatgcccg gctgtcccac 480 accctcgtct tcgacgattt cttccgcgat ttacttgagg gtcatgttgg tcttcgtcgt 540 tgttatctgc agctgattgt atttgactac cataacccaa tgacaatgac acatcgtgtt 600 cccttgttgg ccatcccata tccagaaatt gatcactaga gttcaacgaa gccggagaaa 660 agtgagataa taggtttgtt ggtgttggtg ggtggttgta gttttggttg gtgtacattg 720 ggtattgtgg gttgctgtag ggggggtaat tggtgttgga cggtccagct tggtttgggt 780 cattatagga gaagtagttg ttgttggatg cgccagcttg gtttgggtca ttgtaaccat 840 aatttggcat tgaattttgt tggtaagttg actgataatg gggctcatat gcatttctcg 900 gggaggtata tggtggtggt tggatgatgt tttgttgggg ggtgtcgaga aattcataca 960 ttacagaacc atgaatgttt tgggttgtat gtggttggga ttgatgatct tgtagttgag 1020 aaaaaatgtc ttgatcccaa aaatcatcat gaattggtgt ttggttgttg cgaatttcag 1080 gttcatgttc cggctcttct tcttcggctt cgtctggatc tgaatttgat gggtttgttt 1140 caattgaaat ccttagacgt gggttgcatg tggttgtcaa ccactcaata tacgcatgag 1200 tgtgggtgag tgatcttggc cgcatgcgtg gtaaagtatg actccgtcgg ttgtcccaat 1260 gttcgctctc ttgtggaaag cgaaaaccat ttgatttgta ccacgtcttg aaccgtttgt 1320 ctattacatg gtactgtgtc atgtctcgtg ggggccctgg tatttcttgt ggcagaccaa 1380 attggagctt gaccctatca gttggatgcc attcaacttt gtcaaaacat ataaggtaac 1440 ttgttgcagt ccactcccaa tattcttcag gcaagttgtg tggaacattc ttgtatggtc 1500 tccatttaaa ctagcacaag agataagatg tagtgtaagg ttaacaattt tgatatatat 1560 atatatatat atatatatat atatatatat ataaagtcat aattaaaaaa tcaattataa 1620 tattacatca tggggtagta tgtcatcaaa cttttttcgg taagaaatag tgtcatggct 1680 tggattttca tagtatcttg aacctgcacc tgtccatcta acaaatgata taaacaattt 1740 agtaactaat ttatcaaata ataatattaa taagaagtga gaaaatgtga cgaaataaat 1800 attaaaaaaa aaattgatca cgattacttt aatccaagcg gccactggag tgggttatca 1860 tttttcggag cgatataact caaccgacaa tatccccaaa cttgtaacag gaaatgacat 1920 cctgttagtg cttttatatt tgggtgtgat gcctcacaca agccacgata aaggtaagtc 1980 aacactgccg atccccaact atagtttctt gttagattaa aatccattaa caaatacaac 2040 caggagttgt gcacaaataa tccagttgta ttaggaaaca agaaccctcc aaagaggtat 2100 agtaggtacc tcctagtgtg ttgtattttt acctccggag gagattgttc actgaagtta 2160 ttatcgacca gattatcctt taaccacgac aatgagaggg taaaaccatc agttttattt 2220 gctggaggag ttattcccaa caattgagca caaatgttcc acgcaagatt tggaggagcc 2280 gtaacaaatg gtccgcaaaa aggtaatccg agtaacatat atacgtcttc caacgtgatt 2340 gtgcattcac ccgttcgaaa atgaaaagta tgtgtttcag accgccacct ttctacaaga 2400 gcggttacga tgtgtctatc gattttgtaa cgccctattt gagaaacctc aaaaaatccg 2460 gtttgacgta gatactcttc aatatgagga cttggtatta tgtgttgtct tgtacgggtg 2520 acgagaggtg caccctctgc atcctaacaa aaaataaaaa gaaatgaata caattaaaac 2580 ataatcaaaa tataaattta aatagttcaa tatatattga aattaatatt gaactataat 2640 attaagagta gtattaataa ttaaaaaatg aaaacgacat taacaaatta atatttatat 2700 atacccatct tctgatatgt tcttcattgg atctgtgatc attttccaac cacaagtatg 2760 ccattacttt atataatttg tttgaaatat tggttgtatg tgagtgagta aggaaaggaa 2820 tgtgagtgag taaggaaagg attgagataa ctagaatatg tctgaagagt taaaatatag 2880 ttctagtatt tataatgtaa agttatgtgt aaatagggtg aagtagttgt gtggtatcgt 2940 aatgaatgaa gtgaagaatt caattcatat cttttactaa ttcaacacct gcaaagcaac 3000 aacacatgca aagcaacagt cttaaaataa atatagaagt gacaactgca tcaataaata 3060 tagaagtgac tactgcatca gaagcacaga agcatggtgt tcaacaagca tgctactcaa 3120 cagtatcata ttaatcaagt aagatatgac tattgcatgc aaaaaataca ttaatttctt 3180 gggagaaatt tttcaccaaa atgacacatg catggttgat cacgtgatgc atgcagtcca 3240 tgaaaaagca gtacctttaa tggccaatcc agctggcgcg tggggcgcgt gctgtcctac 3300 ctcgcaactc cagcttgcgg ggtaccctcc agctggcgcg tgggggcgcg tgggggccta 3360 acccgcaact acaagttgcg tggtacccca accatttttt tttttaaaat ttcgttttaa 3420 attttacctc acaaaatatt ataaatgtgg tctgcatgtt acgagtatat tgcatcaaac 3480 cactctactt catacacgct tactcatttc ttaagaccaa accaaatcaa tggcatcaaa 3540 tataaacgtt tttgtgtact ataatggaga agttaaacaa aatgattccg gtattttttt 3600 tcaaagtcag tataccaaag gttttaaagt cagcatggct agtacttact tgcatctcaa 3660 aaaaagaatt gcggagaaaa tatgtctcgg agataatatg gttgtgtctg aaattatgtg 3720 ccggaatccc atgtttgttg gagctaccgc aatccactac caggcgttaa gaataactga 3780 taacgacgat gtcgagttta tgtttaacgt acataaaagt catagttcgt tgtcctacat 3840 agagctttat gttacgtttg agatgaagaa tccaacatct aattttgagt taaattaccc 3900 ctcaagttct agtcaacacc aaaatctacc acaacaacaa tataacacac aacactgcaa 3960 tccctcatcg tcatcgtccc aaccgcacta caacccgtca tcgcaaccgt ttcaatcaca 4020 gtggtcacaa aatgtgtacg aaccaccaca actaataact caacctcatc cctctcaaac 4080 accatcccgt tcaacacaac ccgaaacttt gaacgatgaa atcaatatat tcacctccca 4140 attccaagac caaccaactg atgaagttca agatgatgaa gacaatgatg atgaagaact 4200 ccttgccgca caaaacggtg acgagaacga agaagacgat gaagacgatc tgccacaact 4260 accaatttta ccaattagag cttcttacaa cccaccaagg tccatgcgca acgtcaacga 4320 tgaccactca actgaacttt accattcaat ggctcttccg gtcgatcaag gtattgcccc 4380 agggatgcaa tttcataaca agaatgattg cattctcgca attaaatatt atcacatgaa 4440 aaaatcaacc gattatattg tgaaaaaatc agatcctgaa aggtatgtca tcaaatgtaa 4500 agatacaaaa tgtggtttca aattgcgggc ctcgtggagg aaaaaaactg ataaatggga 4560 gattgggaac atgaatgatc atacatgtgt ctcaacagaa atgacacaag atcatcacaa 4620 acttagttac aatgtgatat gtgaaagtgt taaatcacta ctatatatgg atgcctcaat 4680 tacagtgaag gttataattg cacacatccg agagaaattt aattacacag tttcatacag 4740 aaaggcatgg agagcaagga ataaggcgat tgaatcaatt tatggtaatt gggaggagtc 4800 ttatgaagaa ctaccacagt ggttgatggt catggaaaaa gatttgccag gaacaataat 4860 tgattttcaa tcagacccat caacagaagt ggcaaatgag accgtcttca agcgtctctt 4920 ttgggccttt cgtccgtgca tctcaggttt cgaattctgc aaaccaattg tccaaattga 4980 cgcaacttgg ttgtatggta aatacaaggg aacattgttg ttagctgttg cgcaagatgg 5040 gaacaacaag atatttccca tagcttttgc aatcgtggaa ggcgagacca aggaggcatg 5100 gagtttcttt ttgaaaaatt taaggcagca tgtcacccca caagagaaca tatgcctcat 5160 ttctgataga catgtgtcga taaagagcgc gtatgatgat ccacagaatg gatggcacga 5220 tgctccgaca agccatgttt attgtgtccg acacattgca caaaacttta tgagatcatt 5280 caaggatgga gaactaaaga agaaagttga atgcatgggt aaaaatcata tctctttcca 5340 cgtaaattcg acattttatt tgtttaaaat gacacatcta acttttttca aaacaatgca 5400 ggttacgcca tgaacatccc tacattcgaa tactaccgtt ctgaaattgc tgttgcagac 5460 cgaaaggctt tagcatgggt cgacaatatt cccaaacaaa agtggactca atcacatgat 5520 gatggtcgac gatggggcca tatgacaagt aacttggtag agtcacaaaa caacgtgtat 5580 aagggtattc gaggacttcc gatcacagct atcgtgaaag catcatatta caggttggcg 5640 gccttgtttg ctaaaagagg acatgaggca gcggcaaggg taaattctgg tgagccattc 5700 tccgaaaaca gcatgaaata tctcaggaat gaggtgatta aatccaacag tcatcatgtc 5760 actcagtttg accgggatcg atataccttt tccgtccgtg aaaccatcga tcataaagaa 5820 ggattgccaa agggagaata caaagtggac ctgcaaaata aatggtgtga ctgtggacgg 5880 tttagagcgt tacacctacc atgctcacat gtcattgccg catgttctag cttttgtcac 5940 gactacaaga cttttgtcga taacaaattc acgaatgagt gtgtatacgc cgtatacaac 6000 atccacttcg acgtggttca ccaccagaca tattggccta attatgaagg accgaaggtg 6060 gttcccaaca agtcaatgcg tagggcaaag aaaggtcgtc caccaattac tcgcattagg 6120 accgagatgg acgatgtgga aactgagaga agatgcggtg tttgtaggat gcctggtcat 6180 tcccgcaaag attgcattaa tattagacat cagtagaaat ttagtcttta tttcatgttt 6240 ataggatgtc gtatgtgatt aatattatta ttattattat tattattatt attactttwt 6300 tattaataat aattactatt attaatataa gttaaaatgg tatgataaat tgaaaaatta 6360 ttattawtat taataataat tactattatt attattatta ttattattat tattattatt 6420 taaaaaatwa aataaaaaaa acaaaaaaca aacccgcaag tggggcttgc ggggtattaa 6480 aaaaatttta aaaaaaaatt aagcataccc cgcaagtggg ggtagcaatc tattaatttt 6540 aaaaaaaaaa aaaaaaaaaa aatataggcg tgcagtgtag ttatagttat ttaattttaa 6600 aaaaaaaaaa aaaaaaaaaa aaaaggaggc cgcaagtccc acttgcgggg tagttaaaat 6660 ttttaaaatt tttttaaggt accccgcaag tgggggttgc aaggtaccag aaaattctga 6720 aaagtagggc atttatgcaa tttttttcaa aagtggggca tttttgtatt tttggaatta 6780 aataagggca gaaaaaaaaa aatttc 6806 // ID Ogre-PT2_LTR repbase; DNA; EDCOT; 2775 BP. XX AC AC182676; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 03-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-PT2; Ogre-PT2_LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2775 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC182676; Positions 36607 39381. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). XX SQ Sequence 2775 BP; 937 A; 510 C; 597 G; 731 T; 0 other; tgttgtaacc catttttggg tccccacaaa atatatatat aaaaatatgt atatagccaa 60 aggaggttaa gaaaaaataa taggaggcag aagcgctcag aaaatggttg gaaaattggt 120 caatgaggtt aaaaatacaa agattggatt tttgacagta tattcttgaa ggaggagagc 180 cctgttgaga aggaaaattt gaaatttgag gagaaaagcc caaatttgga tgtttatgga 240 cttaatttga tttttaaatg aatttatagg ggatttgatt gcaagaaaaa ttgattttta 300 agtcaatttg ggctttaatt agaagaaatt taagttctgg ggccaaaata tattttttag 360 gaatttatta ggtcaaatca ggggcctaat tgcataaata ttgaagttta agggccaatt 420 ggggacttaa ttaagaaaat ttgaaaccaa ggaccaaatt gaagaaggcg cgcaagtata 480 ggggctggaa ttaattgatt caggggccta attgaagaaa ttagaagttt tttgatcaat 540 taagggctca attgcataaa tcagagacca aggactaaag tgaaaaacgc ggccaacaag 600 agggacggag accgaaattg gcagggatgc aattgaagaa agaaaagatg attgagggct 660 gatttgaaat ttggcgcgtt ttggcgccac atttaaatga aacggcgtgt tttctccaaa 720 acgacgtcgt ttcatacatt caaaaacaaa aaaaaagaaa agaaagagca gaacggtgtc 780 gttttgaacg acactgttca tcttcttccc ccgatcacgc agcggggaag aaggagaaag 840 ggaagcttta atttgaattt ctgccggcca ctctctcgcc tggagcccac cgaccggaca 900 caatggccga ccacccaccg cgcaccaccc accgaacctc ggcaaccacg cccaatggcc 960 gaccagccgg ctgctccccg tgagagctgt aaaaaacagc gcccttggcc tctataaata 1020 gaggccaaga acgctgagtt aaggggagga aaaacagagg aaaaacaggg gaaaaacaga 1080 gaaagaaagg agagaagaga ggggaggaag aaggagaaaa aacaaaaaaa acagaggaga 1140 gagagaggaa gaatcgaaag aagagagaaa ccgagaggag agaaaaacat aaaaaataac 1200 agaggaaaga aaaacagact gagagaagag agggaaggga aggaaaagag aagaccgaaa 1260 cataggaaga aaaggggaaa cggacgttcg gaacagctgc agcgccgcct ggagccgccg 1320 tccgagagct acgccaccgc caccagcctc tgccgcagca ccgccagcga cgcacagcct 1380 cctccgcgcc aggtaacttt tcttctcatt ttcgcgttca tttctttttc cttccccgca 1440 tgcagaacga gtagcgttct gcatgcaggg gtggggggaa aataattctg ggccgggtct 1500 ggcccagaag aaaatgtttt tttttgggcc gagatcggcc caacccagtt tgggccgaaa 1560 tcggcccaca attttgggct gagcccggcc cagtggtttg ggccggacca accctgtctt 1620 ctgggccggg tctggcccag aagagtcttt ttgggccgag atcggcccaa tacattttgg 1680 gccgaatcgg cccaccaatt ttgggctgag tccggcccag tagtttgggc cggcccagcc 1740 cgatttaata ttatatttat tatatatata tatatatatt atattttgta ttatttatat 1800 atatatatat gaaaaaaaat tataaaaatt tgcaaaaatt atagaaaaat atatgtgatt 1860 ttgttgtaat tttattactg tattttgatt aatattggtt ggttttttat actgtaaaga 1920 tacaaaatcc ggtattaaaa tacccggttt tcatcaaaac atcaaagatt ttcaaaacaa 1980 aaaatgtctt ttgctttcaa aaattttcta aaaatatctt tgaaaatatt gttgattttt 2040 aggcatttat tttatcaaag tgaattaata tttggttgta ttttttacaa acccagtatt 2100 aaaatacccg atttgcgtca aaccgtacaa aatacatagt taaaaaatgt tttgttttaa 2160 atacagccta gtctctccaa tatatatata taaatattat aacatcatat tttcacaaca 2220 aaagaaattt caaaacaata tatgtattag catgcatttt ggctttaata accagtttat 2280 tcaagtcatg agaactaggc caatatttca aaaattctaa aaaaaatctt tttgtccttg 2340 ggattgctaa tttatacata aaacgttttc ctgatattaa aaatgttttt tttttacata 2400 gacattagaa cggttaggtt ttacccgata agataaggac ctccttatta aggaggactt 2460 ttcttgaacc atagacggac caacaactag gaaacacaac gaaactttga attttatcag 2520 acaaataaac aatgcagctt accttaggta aggcgtattt ggggtgctaa taccttccct 2580 ttacgcaacc agtccccgta cccaatctct gagaccagtt agggttccta tgtggcgact 2640 cccacaccat ttttcactgc taagagacaa cgaattcctt gtctccccac attgaccaga 2700 tatatatccc ccatccccca ttacatttat ttttttgtgg gtggacgatc gccgcgacgt 2760 cgcgcacgtg cgaca 2775 // ID Copia-11_TC-LTR repbase; DNA; EDCOT; 420 BP. XX AC CACC01006392; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-11_TC_; KW Copia-11_TC-I; Copia-11_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-420 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01006392; Positions 25959 26378. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 420 BP; 108 A; 61 C; 85 G; 166 T; 0 other; tgttaaaact ggaatatatc tcagcttcaa tggagggtga cttgatgatg gtttgaatag 60 gtggagatga ggtcacgagc agcagcatgt gactagtcta aagtagcagt ttatgtgttg 120 gttattttca gttttttgtc ttcagaatta tgtcaattta gcaacatgga tttaccatgt 180 tgagttgtgt ttgttaggat gtcagccact aatatcatgc tacagctaaa cagttattgg 240 tggtttaatt gcttagttat gtactggttt tttgttttgt attttctctc tctcggttct 300 gtaactactg catatatata tattcaatga aaaacagaac agcaagtgtc tttgtcttca 360 taattttctc ttggcctgat taagtctcaa tgcttgtata actcattcct tttttgaaca 420 // ID Copia-66_VV-I repbase; DNA; EDCOT; 4390 BP. XX AC chr18; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-66_VV_; KW Copia-66_VV-LTR; Copia-66_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4390 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr18; Positions 14100805 14105194. XX CC Positions [1830-2351] - Integrase core CC 'GAGAT' target site duplication CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS 1989..3521 FT /product="Copia-66_VV-I_2p" FT /translation="MKTKTETRAILTNFLAYVHTHFNTNIQTLRSDNGQEF FT NMPTFYQEHGIIHQLSCVETPEQNGRVERKHQHLLNVVRSLMFQSKLPLSH FT WTNYVLTATHLINHTPSYILNNQTPYQLLFQKPPNYNYFEVFDCLCFASTI FT TNNRGKFHPRATKCIFLGYPPNIKGYKVLDLTTLKTFVSRNVLLHESTFPS FT IPNTIHKPFVFPDFPQIYESKSYKPNNSISITSGSTNSTDPTSVIESSIPE FT NTIHANNDANSLRRSERTKHLPKYLQNYYCGNMTKIDSATQAPSSCSSSGK FT PYCIFSFLSDSRLSSKHKAFIYVISSTFEPKTYKQAVSIPHWQTAMTDEIK FT ALKHNKTWDLAILPPNKTAIGCKWVYRVKFKADGSVERYKARLVAKGYTQQ FT EGLDFFDTYSPVAKMTTVRVLLAIAAAKQWYLHQLDVNNAFLHGDLNEEVY FT MQLPPGFSTPNDPRVCKLKKSLYGLRQASRQWYSKLSSSLLSLVSVKQRQI FT QAFLSNKHQLVLLLY" XX SQ Sequence 4390 BP; 1400 A; 873 C; 668 G; 1449 T; 0 other; tggtatcaga gcttcatatt ttccgctgtt cttgatcttt cttgattctt cttcatcttt 60 cctggttgat tgttacttca caatgactaa ggaagagcat gcttctatgg ctaactctca 120 ttcatcaaat ggacctatac agaatctttc agatgattca tccagctact attacttaca 180 tccatctgat aatcctggtg cacttctagt ttccgagata ttcactggtg agaattatat 240 tgcatggagt cgatctatgt caattgctct aacagtgaaa aattaaattg catttgttga 300 tggttctctg gttcaaccga tcactaatga tcctcatctt cgtgttgctt ggctaagagc 360 caataatctt gtcctgtctt ggctaatgaa ttcaattgcc aaagaaatcc gtggtagtct 420 tctctatttc acaaatgctt ttgatatctg ggaggagctg aaaatcagat atctcagaag 480 tgatggacca agggttttct ccctggaaaa atccttaagt tccatttctc aaaattcgaa 540 atctatcact gaatatttta gtgaattcaa ggctttatgg gatgaataca ttagctatca 600 tcctatcccc agttgcaaat gtgggaacct taatcgttgt tcttgtaata ttttgaagga 660 cttgactgat agacagcaat caaactatgt aatgaaattt cttatgggcc ttcacgattc 720 ttattcagca attagaagtc aattgctacc gcaatctcct ttactatcta tgagcagagt 780 tttctcccta cttttacaag aagagagtca aagatcatta actaatgcag ttggcatttc 840 cattgattca caagcaatgg ttgttgaaca atcatcaaga atcgtttcaa caagtaatac 900 tcaattcaca aagcagaaag gaaagtctaa tgcaatctac tctcattgtg gttattcggg 960 tcacttagtt gataaatgtt ttcagctaat tggatatcct cctggatgga aagaaccaag 1020 aggaaaaaga ttcaactcta caccaactac aaccaaaaat tttcaaagat tgcccactgc 1080 aaataatact aatattttgg agcaaaattc aagtaattcg aacatgattt ttttctcaag 1140 aacaaatcca aaatctgctt actctagcaa acaacctttc tagctcaaac acaaattcta 1200 atgcaactgc caatgttgca tccaccttag gtaattcctt tttctgcaat atagtttctt 1260 catcaaagaa ccagtttact tggattcttg atataggagc aacagatcat atgatatgtt 1320 ctccccttct atttgactcg attgttttac ctaaaacatc ttccaaagtt catttaccaa 1380 atggacaaac agttccaatt atcttcactg gatctgtaaa attctcacct gatattactt 1440 tacacaatgc tctttatgtt ccatctttca atatcaatct tgtttctgca tcaagattaa 1500 ctaaagataa tttaattgga ttattttttc ttcaatccaa atgtatcttg caagacctca 1560 acaaatggag gatgattgtg cttgttgaag ttcaatctag tttataccat cttcaacaat 1620 tatctgctca aacaaataaa gaaatgcttt ctagttcaat tggtttacct tctagttctt 1680 tagttgagtc ttgtactgtt aattctaatc tatggcattt tcatttaggt catattccaa 1740 atgcaaaaat acaactcata aatagttctg attcttttgt aaaggctatt cataacaaag 1800 tttgtgagat ctgtccatta gctaaataga aaaagctacc atttcctata tcaaatagtc 1860 aatcaaataa agcttttcaa ttggttcaca ctgacatttg ggggcctttt tccattcctt 1920 catattctgg ttacagattc tttctaacta ttgttgatga tttcacaaga ttcacttggt 1980 tattcttaat gaaaaccaaa acagaaactc gagctatact taccaacttt ctagcttatg 2040 ttcacactca tttcaacact aatattcaaa ctcttagatc agataatggt caagaattta 2100 atatgcctac tttctatcaa gaacatggca ttattcatca attatcatgt gttgaaacac 2160 ctgaacaaaa tggaagggtt gaaagaaaac atcaacacct attgaatgta gttagatctc 2220 tcatgtttca gtcaaaatta cccttatccc attggacaaa ttatgtatta acagccacac 2280 atctgataaa tcatactcca tcatacattc taaataatca aacaccatat cagttattgt 2340 ttcaaaagcc acctaactac aattacttcg aagtcttcga ttgtttatgc tttgctagta 2400 caatcacaaa caatcgaggc aaattccatc caagagcaac aaaatgtatt tttcttggtt 2460 atccaccaaa cattaaagga tacaaagttc ttgacttaac aactctcaaa acttttgttt 2520 ctcggaatgt acttcttcat gaatctacat ttccctctat tccaaacaca attcacaaac 2580 cttttgtttt tccagatttt ccccaaatat atgaatccaa atcctacaaa ccaaacaact 2640 caatttctat aacttctggt tctacaaatt ctactgatcc aacctctgtt attgaatctt 2700 caattcctga aaatacaatt catgcaaaca atgatgctaa tagtcttaga aggtctgaaa 2760 gaactaagca tttacctaaa tacttgcaga attactattg tggtaatatg actaagattg 2820 attcagcaac tcaagcacct tcaagctgct cctcatctgg taagccctac tgcatattct 2880 cctttttatc tgattccaga ttatcctcca aacacaaagc cttcatttat gttatttcat 2940 ccacttttga accaaaaact tacaaacaag ctgtctcaat tcctcattgg caaactgcca 3000 tgactgatga aataaaagct cttaagcata ataaaacttg ggatcttgca attttacctc 3060 caaacaaaac tgctataggt tgtaagtggg tatatcgagt gaaatttaag gcggatggaa 3120 gtgtagaaag gtacaaagcc aggcttgtag ccaagggcta cactcaacaa gaggggcttg 3180 atttttttga cacatactct cctgttgcaa agatgacaac agttagagtg cttcttgcta 3240 ttgcagcagc taaacaatgg tatttacatc aacttgatgt aaataatgcc ttcttacatg 3300 gagacttaaa tgaggaggtc tacatgcaat tgccaccagg tttttcaaca ccaaatgacc 3360 ctcgagtttg taaactcaaa aagagtttat atggtttgag acaagcttcg aggcagtggt 3420 actcaaagtt gtcttcatct ttactaagtt tggtttcagt caagcaaaga cagattcaag 3480 cctttttatc aaacaaacat caactagttt tattgctcta ttaatctatg ttgatgatgt 3540 tataatagct tcaaatgatc tcaaggaaat agatgttgtg aaaaagtttc tccatgaatc 3600 ttttactata aaagatttag gtgaacttaa atattttgta ggcattgaag tagccagatc 3660 agcaaaaggt attgtgttgt ctcaacgaaa gtatgctctg gatgtattga aagatagtgg 3720 tttctttggc tctaaaccaa ttggttttcc tatggaatca agtttaaaac ttactgccaa 3780 tgattcaagt cctttattgt ctgatcctgc atcatataaa agactcattg gcaaacttct 3840 ttacttaaca atcactagac ttgacttggc atatgcagta caagctctca accagtttat 3900 gtctaatcct cattcaacac atttacaagc tgcagaaaga gttcttcgat acattaaggc 3960 aacactgggt caaggtttat tcctaaaggc ttcatctgat ctacatttaa aggcatattc 4020 tgatagtgat tggggtggct gcatcaacac taggcgaagt gttactggtt tcacagtttt 4080 cataggagac ttggtttatt tgttggttga tttgaatgtt aagcatcctc aaccagcact 4140 gctatatact gacagcaaac ctgcttcaaa aatagcttcc aacccagtac accacgaacg 4200 aacaaaacat atacagctcg attgccatct agttagagag aaattgcaag agggtttgat 4260 caaaataatc cacattcctt ccaagcatca actggcggat atattgacca aacctcttgg 4320 atgtctcaat tttcatcatc ttatcagcaa gatgggaatg ataaacattc attctcatct 4380 tgaggggggg 4390 // ID Gypsy-4_Mad-LTR repbase; DNA; EDCOT; 267 BP. XX AC ACYM01134511; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-4_Mad-I; KW Gypsy-4_Mad-LTR; Gypsy-4_Mad_. XX NM Gypsy-4_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-267 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1407-1407 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01134511; Positions 1549 1283. XX SQ Sequence 267 BP; 66 A; 66 C; 47 G; 88 T; 0 other; tgataagccc actcacgtga gcccattact cctcctcttc gagaacggcc cataccagct 60 tttccatcgg gtccaagtag ctagggtttt ctcactttgg aagagatata aatatgtaat 120 gttgtggaca gaaagggcta tgaaatgaat gataaaaact gcctcttttc cctcaaactc 180 ctctttcttt attctctctt tcattcctgc actattttct gttaagattt ccctttttag 240 gcaacctgaa ccgattgggg tgtacca 267 // ID Copia-94_Mad-LTR repbase; DNA; EDCOT; 232 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-94_Mad_; KW Copia-94_Mad-LTR; Copia-94_Mad-I. XX NM Copia-94_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-232 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1727-1727 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 232 BP; 71 A; 31 C; 42 G; 88 T; 0 other; tgttagagat aatgtacaca taggattgtg acacttgtaa acagattaag agagttagtt 60 atagttgtta agaatatgca aatgtaagta gggtgtagta tatatactct tatagtgtaa 120 tagcttggtg attaagaaaa gaaatagaaa tatctttctc tctctatgaa tctctctctc 180 tgacttctct ctctaagatt actgtctgtg attctcttct tcttggttta ca 232 // ID Copia-64_Mad-LTR repbase; DNA; EDCOT; 349 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-64_Mad_; KW Copia-64_Mad-LTR; Copia-64_Mad-I. XX NM Copia-64_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-349 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1667-1667 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 349 BP; 99 A; 50 C; 78 G; 122 T; 0 other; tggtgtataa atgtatttgc tgtgttagtt tcattataag caagtgtagg atttaatgtg 60 agcctttgga tcatattcca tatggtattt agattagatt agattgtaat gagtcatagc 120 tcatgacaag tgtaagcatc ttacatgatg acttagaaat gaatggttgt gatggatttg 180 taatgttgtg agagagtgaa gttgtttctc actcctccaa cggtaaaaca tgctctttga 240 gctctttgct tagagagcga gttgaataca ctgaaacctt gaagaaagct ctgctctctg 300 tgcgtgtgtg cattttactg ttccattgaa tctaccagga aatcaaaca 349 // ID SHALINE14_MT repbase; DNA; EDCOT; 4346 BP. XX AC . XX DT 23-JAN-2007 (Rel. 12.01, Created) DT 02-AUG-2010 (Rel. 15.09, Last updated, Version 2) XX DE A long interspersed element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; retroposon; KW repeat; ORF; Interspersed; Poly-A; SHALINE14_MT. XX NM SHALINE14_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4346 RA Shankar R. and Jurka J.; RT "SHALINE14_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 91-91 (2007). XX DR [1] (Consensus) XX CC The sequence has 5' truncated end. It exists in Medicago genome CC in multiple copies. It has intact domains for CC endo/exo-phosphatase, reverse transcriptase and RNAse H. The 3' CC end is very well conserved across the copies. XX FH Key Location/Qualifiers FT CDS join(4..186,190..4110,4114..4170) FT /product="SHALINE14_MT_1p" FT /translation="MNILFWNVRGIGNSDTRTALKNLCLSHKPSLIFVAEP FT MVNFAQIPDWYWHSIGVSKYCINNGPFLPNLWALWGNELIATVIFVSDQCI FT ALEISCYQSSVYIAAIYASTYYVKRRQLWANLTHFQGCFQGPWFFMGDFNA FT VLGAHEKRGRRPPPPLSCEDFLNWTNANILNHLPTLGTFYTWTNGRFGNEN FT VALRLDRAVCNEEWINFWRSSTCSALVRHQSDHHPLLLSLIYSTVKHASPF FT KFFKAWISHDDCRQLVSDTWSKDVRGQGMARLQSKLNNVKNAFKIWNRTIF FT GDVDRQVKLAMDEVNRIQHLIDSEGFSDNLYLQDLEAQLSLTKALNVQDEL FT WKEKARHHQFINGDRNTAYFHRVSKIRATTKSISFLQDGDNVITDPTAIEM FT HILSYFQDIFSVDNNCAQNTLVDETIPSLVSEEDNNMLXRIPXYDEIKEAV FT FALNADGAPGPDGFGGHFYQTFWDIVGLDVVHSVHEFFLHGELPPNINSNM FT IVLIPKIPGAKAMGDYRPIALANFQFKIVTKILADRLASITSRIISVEQRG FT FVRDRNISECVIIASEAINSLDKRQYGGNIALKVDISKAFDTLDWNFLIMV FT LXHFGFSPIFINWILAILQSARLSILVNGKAVGFFSCSRGVRQGDPLSPLL FT FCLAEEVLSRAXSTSAARGRIVPMSYCRGISLPTHILYADDVLIFCTGLKS FT NIRWLLRIFHNYSEVSGQLINNAKSRFFTGAMTGSRTNMIANLLGFSVGSV FT PFQYLGCPIFQGKPKVIHFQMIADRIKMKLATWKGXILSIMGRVQLVKSII FT HGMLVYSFHVYLWPRRLLRLLDTWIKNFIWSGDVLTRKVCTVSWKVLCRPW FT DEGGLDLKPTRLINXALILKLSWNLIAQDSQWSHLFKSRYFSNGQPSMRYF FT KSSVWSGVKLHIGTVMNNSLWIVGNGDNINFWTDNWLGEPLVDLLNIDADF FT HAHIKGMLSEVIVNGTWXIPAAIADFGDIKERLDVVILPRTHLPDVLVWKH FT ASDGVFTSKLAHSFMRPPSHVWPWAASIWXACIPPSHSFIFWRLSHGKMPT FT DENLQTRGCIVVSVCSFCLKPAETSDHLFLHCNFAFRLWTWLGVKLNCVID FT SSSVDSLLDCRPVSCSSQVSDIFVAAVXHTIHTIWWARNAVRFSXXTPTIH FT AAKIRIHSFIAMSGNVSKGKCLLSYFAFLDSFAVSPHCRSVKDIILVFWKP FT PSSPWVKVNTDGSVIGGNAACGGLFRDXLGTFCGAFSCNIGIQTVFEAEVF FT GFILAMEYAAHKGWRHIWLESDSTSALLIFSNPSLVPILLRNRWHNAQVLG FT VQVISSHIFREGNSCADKLASLGHEITDAVWLDTLPARVCLDFFRDRCGLP FT NYRFPFVFGGLCFSLFSLFCFXFC" XX SQ Sequence 4346 BP; 978 A; 754 C; 933 G; 1652 T; 29 other; tcaatgaata ttctcttctg gaatgttcga ggtattggta attctgacac tcgaactgct 60 ttaaaaaatt tatgtttatc ccacaaaccc tctctaattt ttgtggcgga accaatggtt 120 aattttgctc aaattcctga ttggtattgg cattccatag gcgtatctaa atattgcatt 180 aataattgag gtccttttct tccgaattta tgggctcttt ggggaaatga attaattgca 240 actgtgattt ttgtgtctga tcaatgcatt gctttggaga tttcttgtta tcagtcttct 300 gtttatattg ctgccattta tgctagtaca tactatgtga agcgtcgaca gctttgggct 360 aatctcactc attttcaagg atgttttcaa ggtccatggt tttttatggg cgatttcaat 420 gctgttttag gtgctcatga gaaaaggggc aggcgccctc ctcctccttt atcatgtgaa 480 gattttttaa attggacaaa tgctaatatt cttaatcact tgcctactct gggtactttt 540 tacacttgga ctaatggtag gtttggcaat gaaaatgttg ctcttcgtct tgacagggcg 600 gtttgtaatg aagaatggat caatttttgg cgtagttcta cttgttcagc tttagtccgt 660 catcaatctg atcatcatcc tttattgctt tctcttattt attcgacggt gaagcatgca 720 tctccattta aatttttcaa agcatggatc tctcatgacg attgtaggca gctggtgtct 780 gacacttggt cgaaggatgt tcgcggacaa ggaatggctc ggttacagtc taaattaaat 840 aatgtcaaaa atgctttcaa gatttggaat cgcacaattt ttggtgatgt ggataggcaa 900 gtgaagcttg ctatggatga agtgaatcgc attcaacact taattgattc tgaaggtttt 960 tctgacaatc tttatttgca ggatttagag gctcaactgt ctttgacaaa agctttaaat 1020 gttcaggatg aattatggaa agaaaaagcg agacaccatc agtttattaa tggtgaccgc 1080 aacactgcct attttcatag rgtctccaaa atccgagcaa cgacaaaatc tatttctttt 1140 ttacaggatg gtgataatgt tataactgat cccactgcta tagagatgca tattctttct 1200 tattttcagg atatttttag cgtggataat aattgtgctc agaatacttt ggtggatgaa 1260 actattcctt cgctggtgtc ggaagaggat aataatatgt tgatkcgtat tcctttktat 1320 gatgaaatta aggaggcggt ttttgctctt aatgctgatg gtgcaccggg tccggatggg 1380 tttggaggac atttytatca aactttttgg gacattgttg gtcttgatgt ggttcattct 1440 gttcatgaat ttttccttca tggtgagctg cctcctaata ttaattctaa tatgattgtg 1500 ttgattccaa aaattccagg tgctaaggct atgggtgatt accgacctat tgcactggca 1560 aactttcagt ttaaaattgt tactaaaatt ctggcagata ggcttgctag catcacttct 1620 cgaattattt ctgttgagca acggggtttt gttcgtgacc gtaacatttc tgagtgtgtt 1680 attattgctt ctgaggcgat caattcgcta gacaaacgac agtatggtgg gaatatagct 1740 ctaaaggttg acatttccaa ggcttttgac actttagatt ggaatttttt gattatggtg 1800 ctgcancatt ttggtttctc ccctattttt atyaattgga ttcttgctat tttacaatct 1860 gctcgtctat ctattttggt taatggcaag gcngttggtt ttttttcttg ctcccgtggt 1920 gtgcgtcaag gggaccctct ttctccactt ttattttgtc tagcagagga ggttcttagt 1980 cgagctntat caacttcagc agcaagggga cgaattgttc ctatgtctta ttgtcgtggt 2040 atttckttgc cgactcatat tttatatgcg gatgatgtct tgattttttg tacaggtttg 2100 aagagtaata ttcggtggct tcttcgtatt tttcataatt attcwgaagt ttcaggtcag 2160 cttataaata atgcaaagag tcgtttcttc actggtgcta tgactggttc tcggacaaat 2220 atgattgcta atttgttagg tttttctgtg ggatcagtgc cttttcaata tcttggctgc 2280 cccatctttc aaggaaagcc aaaggtaatt cattttcaaa tgattgctga cagaattaaa 2340 atgaagctag ccacttggaa aggtrgtatt ctatctatta tgggtagggt gcaacttgtt 2400 aaatctataa tccatggtat gcttgtttac tcttttcatg tttatctttg gcctagaagg 2460 ttgctccgtc ttcttgatac atggattaaa aattttattt ggagtggtga tgttcttacg 2520 agaaaagttt gcacggtttc ttggaaagtr ctgtgtcgtc cgtgggatga aggtgggctt 2580 gatctcaagc ctacgcgctt gattaatgam gctttgattc tgaaattatc ttggaatctt 2640 attgcacaag actctcaatg gtctcatctt ttcaagagcc gttatttctc taatggtcag 2700 ccctccatgc gctattttaa atcttctgtt tggtcgggtg ttaaacttca tattggcacg 2760 gttatgaaca attcattgtg gatagtgggt aatggtgata atattaattt ttggactgat 2820 aattggctag gtgaaccttt ggtagatttg ttgaatattg atgctgattt tcatgctcat 2880 attaaaggta tgctgtcgga agttattgtt aatggtacct ggaakatacc tgcagctatt 2940 gctgattttg gwgacattaa agagcgccta gatgttgtca tcytacctcg tactcatctc 3000 ccggatgtgc tggtttggaa gcatgcttct gatggagtct tyacttccaa gcttgctcat 3060 tcttttatgc gkcctccttc acatgtttgg ccttgggcag cctctatttg gagmgcttgc 3120 atccctcctt ctcattcttt tattttttgg aggctttctc acggtaagat gcccacagat 3180 gaaaatcttc aaactcgtgg ctgcattgtg gtatctgttt gtagtttttg cttgaagcct 3240 gctgaaactt ctgatcattt atttcttcat tgtaactttg cgtttcggct ttggacttgg 3300 cttggggtga agctcaattg tgttattgac tcttcctctg tagactctct tcttgattgt 3360 cggccagtta gytgctcctc ccaagtgtcg gatatctttg ttgctgcagt tttkcatacg 3420 attcatacta tttggtgggc taggaatgca gttcgattct cagwttygac tcctactatt 3480 catgcagcaa aaatacgtat tcattctttt attgctatgt ckggtaatgt ttckaaaggt 3540 aagtgcttac tgtcatactt cgcttttctt gattcttttg cagtttctcc tcattgccgt 3600 agtgtcaagg acattatttt ggtgttttgg aagcctcctt cctctccttg ggtgaaggtc 3660 aatacggatg gttcsgttat tggtggtaat gcggcttgtg gkggactgtt tcgtgattwt 3720 ctaggtacct tctgcggtgc tttttcttgt aatattggta tacagactgt ttttgaagca 3780 gaggtttttg gttttattct tgctatggag tatgctgctc ataaaggatg gcgacacatt 3840 tggctggaga gtgactccac tagtgctctt cttatttttt caaatccttc tttagttcct 3900 attcttcttc ggaaccgttg gcataatgct caggttcttg gtgttcaggt tatctcttct 3960 catattttcc gtgaaggtaa cagttgtgcg gataagctag cttctttggg tcatgaaata 4020 actgatgctg tttggttgga cactcttcca gctagagttt gtcttgattt ctttagagat 4080 agatgtggtc tgcctaatta cagatttcct tagtttgttt ttggtggact ttgtttctct 4140 ttattttctt tgttttgttt tttsttttgt tgagggtttt ggcctagtcc cccctctttt 4200 gtaattattt tttccccttt tttaataaat tttttcgagt gtggtggcat aggatggagg 4260 tgtctcgggg tgccaaccta gttgggatgt cgatgatgcc ccttgatgtc tttcctctct 4320 ccttgcttat caaaaaaaaa aaaaaa 4346 // ID PSAT28 repbase; DNA; EDCOT; 195 BP. XX AC AF155765; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-JUL-2004 (Rel. 9.06, Last updated, Version 2) XX DE Pisum sativum dispersed repetitive DNA, PSAT28. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy retrovirus-like; PSAT28; Repetitive sequence. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-195 RA Neumann P., Nouzova M. and Macas J.; RT "Molecular and cytogenetic analysis of repetitive DNA in pea RT (pisum sativum L.)."; RL Genome 44(4), 716-728 (2001). XX DR Genbank; AF155765; Positions 1 195. XX SQ Sequence 195 BP; 48 A; 34 C; 49 G; 64 T; 0 other; tcgatactca atgcttgaga agactgttgt gctttggctt gggctgctaa gcgcttacgc 60 cagtatatgt tgaatcacac gacttggttg atatccaaaa tggatccaat caagtatatc 120 tttgagaatc ctgctttaac tgggaggatt gcccgttggc agatgttgtt atctgagtgt 180 gatattgagt atcga 195 // ID ENSPM1_PT repbase; DNA; EDCOT; 9166 BP. XX AC . XX DT 16-APR-2007 (Rel. 12.04, Created) DT 16-APR-2007 (Rel. 12.04, Last updated, Version 1) XX DE EnSpm-type DNA transposon - a consensus sequence. XX KW EnSpm; DNA transposon; Transposable Element; ENSPM1_PT. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-9166 RA Jurka J.; RT "ENSPM1_PT: EnSpm-type DNA transposon from black cottonwood - a RT consensus sequence."; RL Repbase Reports 7(4), 140-140 (2007). XX DR [1] (Consensus) XX CC Present in several hundred copies in the genome. XX FH Key Location/Qualifiers FT CDS 1106..3412 FT /product="ENSPM1_PT_1p" FT /translation="MDDRSWMYRDSPQGLRRMDYCNGVQGFINFATSIPRN FT FTGGGIRCPCRKCQNKKYLHPDVVMMHLLHKGFMENYLCWYAHGEVFVRNK FT SMGERVVGSTSSASNVHEVANDNTNPYRNMVMDAMRMNQGNVSQCPIVEEE FT PNADATRFFDLLKDSDEPLWDGCTNHSKLSAVAQVFTIKSDHGLSEAGYDK FT IIEWARSILPEGNRLKENFYAAKSMMKPLGLGYQKIDMCPNFCMLYYLENA FT EMTECMTCGHSRYKPRTGRGKTLVAYKKLRYFPITPRLQRLFMSPRTAEHM FT TWHQSHDAVDGVMVHPSDGEAWKHFNSVHPHFSAESRNVRLGLCTDGFNPF FT GSFAAPYSCWPVILTVYNLPPGMCMRPEFMFLSTVIPGPSSPGRNIDVCLR FT PLIDELTQLWSSGALTYDISRKQNFLMRAALMWTINDFPAYGMLSGWSTHG FT KLACPYCMENNKAFTLTNGGKASFFYCHRRFLPLNHRYRKNRKDFFVGRVE FT KDVASPRLSGEELHDVVSEYGDIVFGLQSGKQKFPGFGLTHNWVKRSIFWE FT LPYWKTNLLRHNLDVMHIEKNVFENIFNTVMDVKGKTKDNIKARLDIALFC FT NRKNMELVYDESRVAKPRASFVLEKNAQLLVYKWLKSLRFPDGHASNISRL FT VNIEECRLYGMKSHDCHVFMQTLIPLAFRDLLPKGIWDALTEISHFFRDIC FT SSKLNVDHIERLETNIVETLCKLEMIFPPSFFDSMEHLPIHLPFEAKVGGP FT VQYRWMYPFERLDITVAM" FT CDS 4047..4877 FT /product="ENSPM1_PT_2p" FT /translation="MHVITRFSFIYCLLMYITYKVYQMGRSAAKSLSSLSL FT GPERKVKCYNGYFVNGYVFHTEEYGHGRKTYNSGVCVKGSTSSELEVDYYG FT RLEEVVELQYHSEQNRVFLFKCYWYDTTDRGIRVDPHYGLVEINSKARLRN FT VNDVFVFAKQCQQVYYTYTPSFRKDRSRVDWLSVLKTKPRGRVEVVQDENE FT DTSVRDEVFQVSELVEPYRVAPSIDLEENSNFRVFDDSLVDVDAEELNVVL FT SSSGQANVDEEDDIHIEDCDEGDDNSIDDEEEENSD" XX SQ Sequence 9166 BP; 2719 A; 1623 C; 1884 G; 2926 T; 14 other; tcactaccag aaattcgcta aataccaacg gatttaccga cggaatattt ctgtcggtaa 60 tttgaggtcg aaattaccga cggaaacttt tccgtccgta attcagtcgg taactaccga 120 cggaaacttt tccgtcggta ataccgactg aattacggac ggaaaatgtt tcgaattaaa 180 aaaaaaggcg ggtcgctgac gtggaggttt tggcggagtt atttttaccg acggaatcac 240 cgagggattc aaaatgrcag cccgtacagt gacgtgaccg gttcaccgtt taaattaccg 300 acggaatcac cgagggattc gaaatggcag atccgtacag tgacgtgtcg atttttccga 360 cggaatcacc gacggaaaat ccgtcggtga wtccatcgga aaaagttaat atatgtccac 420 tctgccgacc ctctcctccc ctatttctcc ttcttcttcc caatcccaac tctccccatc 480 tgcaaacaac cagccccccc tcccccccaa acaaaaatct ccctcatctc agcacaacaa 540 gttatatttc ttgaagtttt gtggtcacaa catccgtgtt ctgatttacc gatggatttt 600 atcatttttt gtaagtaatt ctatcttttt aaattttaac atttaattaa atgtcaattt 660 tattgttttt ttagtatatg tattttgtta gtatatgtac atgttttatt gttatttctc 720 aaacaaactt gtagtatatg aatgtataat tttatacttg ttatggtttg ttttagattt 780 tgtaaaattg tatttgtttg taaattgttg aaactttatg gaattaccga attacatgtg 840 ctgttttgaa ataattaata gcttgtttaa tgggtccgtt taaattttta tcaatggtat 900 tgcggagttg taatttccgt aaatttatat atataaattt gtatggacgt tgataattga 960 taatgaatat ttaatattta tgagaagttg tgattagttt gttggataat ctcgaggtaa 1020 agtaatattt ttgcaagttt atttacctaa catagttaat taatacatgt tgtcatcata 1080 attttataga ggttcgatag aagtcatgga tgatcgttca tggatgtatc gagattcacc 1140 ccaaggattg cggaggatgg attattgtaa cggggttcag ggttttatta atttcgcaac 1200 atctattccc agaaatttta ctggaggcgg tattaggtgt ccatgcagga agtgtcaaaa 1260 taaaaagtat ctgcatccag atgttgtaat gatgcatctt ctacacaaag ggtttatgga 1320 gaattacctg tgttggtatg cacacggaga agtatttgtt cgtaataaga gcatgggaga 1380 aagggtggtt gggtcaactt ctagtgctag caacgtgcat gaagttgcaa atgacaacac 1440 taatccttac aggaatatgg ttatggatgc aatgagaatg aatcaaggta atgtcagtca 1500 atgtccaatc gtagaagaag aacctaatgc agatgcaact aggttttttg atttgttgaa 1560 agattctgac gaaccattat gggatggctg cacgaaccac agtaaattat cggccgtagc 1620 acaggtgttc accatcaagt cagatcacgg gttgagtgag gccgggtatg acaagattat 1680 tgaatgggcg agaagcattt tacctgaagg gaacaggctg aaagagaact tctatgctgc 1740 gaagtccatg atgaaacccc tcggtttagg ataccagaaa attgacatgt gccctaactt 1800 ctgcatgtta tactaccttg aaaatgctga gatgaccgag tgcatgacat gcgggcattc 1860 ccgttacaaa cccagaactg gcaggggaaa gactctagtg gcatataaaa aacttagata 1920 cttcccaatc acacctagac tgcagaggtt attcatgtca ccaaggactg ctgagcacat 1980 gacatggcac caatcacatg atgcggttga tggagtgatg gtgcatcctt ctgacggcga 2040 agcgtggaaa cactttaaca gtgtgcatcc tcacttttca gctgaatcaa ggaatgtgcg 2100 tcttgggttg tgtacagacg gattcaaccc attcgggtca tttgctgctc cttattcttg 2160 ttggccggtc atactcacag tttataactt gccaccggga atgtgtatga ggccggagtt 2220 catgttttta tctactgtca tacccggtcc gagcagcccg gggcggaata tagatgtttg 2280 tcttcgaccg ttgattgatg agttgacgca gttgtggtcc tccggagctt tgacttatga 2340 tatatcgagg aaacaaaatt ttcttatgag ggcggctttg atgtggacta tcaatgattt 2400 tccagcttat ggaatgcttt ctggttggag cacgcatgga aaactagcat gtccatactg 2460 catggaaaac aacaaggcat tcacgctaac aaacggaggt aaagcttctt ttttttactg 2520 tcaccgtcgc ttcttgccac tgaatcacag gtacagaaag aacagaaaag atttctttgt 2580 tggcagagtt gaaaaggatg ttgcatcccc gcgtctttct ggtgaagaat tgcatgatgt 2640 tgtatcagag tacggtgaca ttgtgtttgg tcttcaatca ggtaagcaga agtttcctgg 2700 ttttggtttg acccataatt gggtaaagcg aagtatcttt tgggagcttc cttattggaa 2760 gaccaatctg ctccgccata accttgacgt catgcacatt gaaaagaacg tgtttgagaa 2820 cattttcaac accgtcatgg atgtgaaggg gaagacaaag gacaacatca aggctagatt 2880 ggatatagct ttgttctgta accgtaaaaa tatggagttg gtttatgatg agtcacgggt 2940 cgcaaaacca agagcaagct tcgtgttaga gaaaaacgca caactactag tctacaaatg 3000 gcttaagagt ctgcgttttc cggatggaca tgcctcgaac atatcaaggc tggttaatat 3060 agaggaatgc agattgtatg gaatgaagag tcatgactgc cacgtgttta tgcaaacact 3120 catcccatta gcttttcgtg atttgttgcc aaaggggata tgggatgcac tcacggagat 3180 cagtcatttc ttcagagata tatgctccag caagttgaat gttgatcaca ttgagaggct 3240 tgaaacgaat atcgtcgaga cactatgcaa acttgagatg atattccctc catcattttt 3300 tgactcaatg gagcatctcc ccatacatct accgttcgag gcaaaagttg gaggaccggt 3360 ccagtataga tggatgtacc cattcgaacg gttagatatt acagttgcaa tgtaattcat 3420 atataaaagt attttctatg tttttcttaa ttgaaaatat ttgattaatt caatgcaggt 3480 acttgtttaa tctcaagaaa aaggttaaga acaaggcgca tgttgaggct tcgatatgtg 3540 aggcctatat tgttgaggag atctcaacat ttatctcgta ctatttcgaa cctcatctga 3600 gaacgagaat caatcgcgtt ccacggcatg atgatggcgg tgaagtgcct tccagtggga 3660 acttgtcaat attctccaat cctggacgac ccacacctaa aaatgccgta agaggaagat 3720 atttgtcgga aatagagttc aaacaagcac acaattatgt tctatttaac tgtgatgagc 3780 tgagaccttt tattcagtaa gtttatatat gtgtaatact aattaaactt tgttaataat 3840 atactattaa ttatatattg taatatcata cactcattta atttggatca accttgcagg 3900 caacatcgac aatatttgct gtccaataac tcacagctga ccgaatccca gatctttcaa 3960 ttacaagatg aacaatttgc cacgtggttc agaacacatg taagtactat cacaaactca 4020 ttatcwcttg caaaattact gtacgtatgc atgtcattac gagattctcg ttcatttact 4080 gtttattgat gtacattaca tacaaggttt atcaaatggg aaggagtgct gctaagtcat 4140 tgtcttcact aagcctgggc cctgaaagaa aagttaagtg ctacaacggg tattttgtca 4200 atggatatgt tttccatact gaagaatacg ggcatggaag aaagacatac aacagcggtg 4260 tttgtgttaa gggatcgact agtagtgagt tagaagttga ctactatggt agattagaag 4320 aggtcgtcga actgcaatat catagcgagc agaatagagt gtttttattc aaatgctatt 4380 ggtatgacac gactgacaga ggaatcagag ttgatccgca ctatggtctg gtcgaaatca 4440 actcaaaagc tagactccgc aacgtaaacg atgtctttgt tttcgcaaag caatgtcaac 4500 aagtttatta cacatacacc ccttccttta gaaaggatcg atcaagagtt gattggttat 4560 ccgttttaaa aacaaaaccc aggggtcgtg tcgaggttgt tcaggatgag aacgaagaca 4620 caagtgtgcg agatgaagtc tttcaagtta gtgagttggt tgaaccatat cgagttgctc 4680 cttcgattga cttggaagaa aattcaaatt ttcgtgtttt cgatgatagt cttgttgatg 4740 ttgacgcaga ggagttgaat gttgttttga gctctagcgg acaagcaaat gtcgatgaag 4800 aagatgatat ccatattgaa gattgcgatg aaggtgatga caattcaatt gatgacgaag 4860 aagaagaaaa ttctgactaa ctatcaaaat gaagccctgt gtaaaaccct ttttttcatg 4920 taatttagat tatggatgat atattttgta acacgaaata tttattactt gaaataatta 4980 cttgaaatgc cacaatcacg aaataattac ttgaaataat tatgtatcat ggatgatata 5040 ttttgtaaca cgaaataatt acttgaaatg ccacaatcac cgacgttcat accgacagaa 5100 taagtccgtc ggcatttcac agagagttcg aaaataatta cttgaaatgc cacaatcacc 5160 gacgtccata ccgacggaat aagtccgtcg gtatttcaca gagagttcga aaataattac 5220 ttgaaatgcc acaatcaccg acggccatac cgacggaata agtccgtcgg yatttcacag 5280 agagttsgaa aataattact ggaaatgcca caatcaccga cggccatacc gacggaataa 5340 gtccgtcggc atttcacaga gagttcgaaa ataattactt gaaatgccac aatcaccgac 5400 gtctataccg acggatatat gtccgtcggt aagttgtcgg cgggtcaata ttaccgacaa 5460 aattaccgac ggactgtgcg aattccaaag ggttgtgcat taaatgcatc tctgaccgcg 5520 tcatcttgcc gacggaatta ccgacggacc acgaaaaata tggagggtca ttaaaaattt 5580 tggtgcgaaa ttcaaaaatt accgacggat ttttgacact tcaccgacgg aataaattaa 5640 aataataatt aattttatat ccgtcggtga atccgtcggt aaaactgcca tataaatccc 5700 agcgaccgcc ccttcagttc attttttctt ctcctcagtt tttcatcttt aatttcgatt 5760 cttttcctct ccattcttca aagctttctc ctgcaatctc tagcaagttt tcttgtgaat 5820 cttcatcagw ttaaaaggta tgtgtttctt ctatttcatt ttactttaag ggtttttttt 5880 ttgctatttt tttttgttat gttttttgtt ttggtgtatt ttttgtaatg tagataaagt 5940 cttgaaatca acacattatt aaggtaagca tatttcattc ctaaagtcta tagttttttt 6000 tttgaattta ttgaatattt tttattgttt gtattggcat aattattatt agttaatttg 6060 ttgaatattt attgttaatg ttgaatttac cttagaatta gtaattgaat atgttggaat 6120 aattattaat tttactctat tattgcatga tttgtgttta attttttcca tttattttga 6180 ttgttaktct agagtttttt ttgaatttat tgttttgttg tattggcata attattgaat 6240 aattttttga attgtaattg ttaatgttga atttacctta gtattagtaa ttgaatattt 6300 tggaataatt gttaatttta ctctattatt gcatgattta tgtttaattt tttccattaa 6360 ttttaattgt tagtctagag tttttttttt tattgaatat attttattgt tgtattggca 6420 taattattga ataatttgtt gaattgtaat tcttaatgtt gaatttacct taggattagt 6480 aattgaatat gttggaataa ttagtataga ttgggtcaat tggttgtggc tattgttaat 6540 atgtgcaggt ttgtagattt gggtagtctc cagtataggg gaggtgctgt cgaatttttt 6600 tttaacattc gaatttaatt atataattat tcgtataaaa ttgtgtagat gcgtagaatg 6660 aaatccacag ctcgtcgctc acatatggtc gcagctagtt cttctagcag cgaggatgac 6720 atatccttag gtgccgatca agaagaggca cctacgccac ctgcgtcgtc aaccgatgct 6780 gcctcttcca gcgcggtttc acagcgcaga ggcggcgtgc cttcacagcg gaatcaattc 6840 acccgcaagt acgaggcaca gtggaaggay gacctttcaa tgtaagtttg ttwaggtttt 6900 agtttttttt taaaaaaaat acttataaca taatttatga acaactaatc aatatttaat 6960 taatttcatt tattttcagg ttcacaaaca ttgaggccgc ccgagtaata tcatcggcgt 7020 ttaaatcgtc gatggagatt ccattgtttc aatggagtca ggtatccaga catcctgaat 7080 ggatacctca aatcgatgca tggtttgaca gatttgaggt tggtgttaat ttataatttt 7140 cagcttattt ttaataaatt attaatataa ttgtaaataa attattattt ttatttaaaa 7200 ttaattattt atacacagaa caaattcgac tgggacagtg cgcataacaa tgttgtgagg 7260 agggtgtggg aaaatcacgc ggcaactagg taacatcgaa aacaatacaa gatttttttt 7320 agataaaaat ttatgtttta aaatctaatt tgtkactatg tgaagtaggt tgcgtgattt 7380 ttggtatgaa gcacaaaaaa aggcaaaaaa aaacgcgaga gataagggtc tccaaggctg 7440 gaacgatgtg gcggtttgga gggatttcaa accgatatac atcccggaag atatatggcc 7500 gcaatatctt gagcacgtga cgtctgagcg gttcacacga cgctcacagt ccggtgctgg 7560 caaccggaac cggccaattc atggttcggt gacaacgcac actggcggct ccgttccgtt 7620 tgctgcacat gcgaaacgga tggtaagatt aatttaaatg aaatatatcg ttaaattaat 7680 ttgttgttcc ttataataaa tcttttttca ttataggcta cgtctcttgg acgtgagccg 7740 agcccaatgg agctgtttgt ggagacgcac gtgcggagtc aagaccgcca aaagggggtg 7800 caacagttcg ttgacaaccg tgctcaacat ttcgtggtat gtttgttcaa ccattttatt 7860 ttgtaagtta ttatgtttat tgaattgaat atgatgatta ctttttttat tttcaggaga 7920 cctataatag tcggttgagg gagagatatg gggacgatcc tttgacccat ccggatttcg 7980 atccggattt gtggatggag gttggatcgt ctggtggacc cgataaaaat cgggtttacg 8040 ggctctccaa cactacggcc gacaacttgc ggtcgacccg tagtgtctca accgttggga 8100 gctcccaatc aatatcgagc acccaatcta aggagttcgt ggccttgcag caacacacgg 8160 ctcagctcac cgaaaaatac gaccacctat cagcggagta cgcacaactc aaagcgtctc 8220 atgcacaaca aagagcggag tctgaacaac tcaaagcgtc tcaagcacaa caaaaagcgg 8280 agtctgaaca acaaaaagcg gcttatgaac agcttcgcca aatggtcatg aacatgacat 8340 cacagatggg tggatacatg tgcgcctaat cctttttggc cgtatggtcc cgggaacaac 8400 cagcctcctc ctcctcctcc tccagctcca cctttatwtt aatttgtaat aaayattatt 8460 tacctttaaa ayttcattta atattttttt gaaacacatt caatttgtaa tgaatattat 8520 ttaactttat ttttttattt ttgatgttta atayaaattt tatttgcata attggttttt 8580 attactatta atttatataa ttttatatta tatattctaa ataatttttt aaaaacaaat 8640 ttagaaaaaa ctattaccga gggttttacc gacggaatta atccgtcggc atttgacagt 8700 aagttcaccg acgcatttac agacggatat attcggtcgg tatttcatac actcaccgac 8760 agatttaccg acggacttaa tccgtcggca tttgacagta gctgccacaa ttaccgacga 8820 atttacagac ggatatattc ggtcggtatt tcaaacactc accgacagat ttaccgacgg 8880 taattagccg tcgataaatc acgatatcac cgacggaata aaatccgtcg gtatatttca 8940 agcgggaaat ttttttttgg cgcgcaaatt ccgtctgtaa aaccatcggt aaatggtttt 9000 tttgtttttc cgacagatat agcgacggaa tggggaatta ccgacgaacg gaaagccgac 9060 ggacgtattc cgtcggtgat gacgtcggta aaaaaattac cgacgaactt ttaatctcac 9120 accgacggaa tatttccgtc ggtaaaactg tgaaatcttg tagtga 9166 // ID Copia7-PTR_I repbase; DNA; EDCOT; 4133 BP. XX AC LG_I; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia7-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4133 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4133 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 290-290 (2007). XX DR Genome; LG_I; Positions 26421044 26425176. XX CC Positions [1397-1915] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 52..1203 FT /product="Copia7-PTR_I_1p" FT /translation="MSGDEDQRFLEQNRSSMSFRTSETWENSNHPLFLHHA FT DQPGAVLVSQMLMEDNYTTWVQSMSMTLTIKNKKGFVDGTLRRPTHNSNEQ FT QQWDRCDILVRTWLLGSISKDISGSVIHCKDARGIWLELKERFSQTNTVSL FT FHIENVIHDCEQGTNSVTTFFTKLKCLWDEKDALNSFPPCNCEVATTVKTF FT LETQKTMKFLMGLNESYAQTRSNIISMDPLPNLNKAYAMVLRHEKQAETFT FT GKLNTPPEASAFTIKKVTRDFASTNGEIKFCEKCNMNNHNTKNCRAHLKCT FT YCNGKGHTYDYCRRRRNATAGGQGRSKANHVAPQNHDKEDLPEFPFSREEC FT HQLLSQLLANTKSASANLVGNIPNYEELSGPTIGEDDWDGH" FT CDS 1154..3250 FT /product="Copia7-PTR_I_3p" FT /translation="MRNSQDLRSGKMIGTGTEKEGLYCLNLSSTATCNAVY FT INTDNLWHQRLGHPSTKISSLFSFIANKACISRNCYICPLAKLTRQPFPLS FT TIRSASCFDLIHIDIWGGYHVPSSTGAKYFFTIVDDHSRSTWVYLMKHKSE FT ARTLLIHFIQMVANQFSKSIKVIRSDNGSEFKIPEFYSSKGIIHQTSCVNT FT PQQNGVAERKHRHLLNVARALLFQATLPKHFWGDAILTAAYLINRTPTPLL FT KGKTPFECLFHTKPSYSHLKVFGCQCFVSTHPTHPSKFDPRAHECVFIGYP FT HGQKGYKLYLLTTKNIRVSRYVIFFEHVFPFQPSPVLTSRSHSPKLIPTIS FT HTPSMHISILILYPPTSQSSAVPYSHHPILSPDLISSPPTDNNPSIPSAYN FT NTPDPPLPLIPSPLPTQPLPPNPRRSSRATKLPTALQGFHIDAALPSRPDR FT SDSSTEVLSPGQAHSLSNVLSYANLSSPYRTFTANMTIPREPLSFSQALQD FT PKWRDVMQQEVQALHANKTWSFVPPPAHKRPIGCKWVFKIKYNPNGTIDRY FT KVRLVAKGFSQVEGIDYRETFAPVVKLTTVRILLSLAAMQNWHLHQLDVNN FT AFLNGDLDEDVYMQLPPGFRRKGEHRVCKLHKSLYGLKQASRQWFLKLSSA FT LKSVGFTQSWSDYSLFVRNHQGIFTALLIYVDDVILAGNNLDDITKTKRF" XX SQ Sequence 4133 BP; 1266 A; 993 C; 771 G; 1103 T; 0 other; ttctctcttt atggtatcag agcagtggtt ctaagaaccc agaaatacct catgtcaggt 60 gacgaagatc aaaggttcct tgaacaaaac aggagctcaa tgtctttcag gacctcagaa 120 acatgggaga actccaacca tccactcttc ctccatcacg cagaccaacc aggggccgtc 180 ctcgtctcac aaatgctgat ggaagataat tacacaacat gggtgcagtc aatgagcatg 240 acacttacta ttaaaaacaa aaaggggttt gtagatggaa ccctcaggag accgacccac 300 aactctaatg agcaacaaca atgggaccga tgtgatatcc ttgtaagaac atggctgctt 360 ggatccatat cgaaagatat ctcaggcagt gtcatccatt gcaaggatgc aagaggtata 420 tggctggaat tgaaagaaag attttctcag actaacacag tttccttgtt tcatatagaa 480 aatgtcattc atgactgtga acaaggcaca aactcagtca caacattttt cacaaaactc 540 aaatgcctat gggatgagaa ggatgcactt aattcctttc ctccttgcaa ttgtgaggta 600 gccaccacgg tcaaaacctt cctggagaca cagaagacca tgaaattttt aatggggctc 660 aacgaaagtt atgcacagac ccgaagcaat atcataagta tggatcctct tccaaatctg 720 aacaaagctt atgccatggt tttacgccat gagaagcagg cagaaacctt cactggaaaa 780 ttgaatacac caccagaagc atctgcattc acaataaaga aagtgacccg tgattttgca 840 tcaaccaatg gagaaatcaa attttgtgaa aaatgcaaca tgaacaatca caacaccaaa 900 aattgcagag ctcacctcaa atgcacatat tgcaatggaa aaggtcatac ctatgattat 960 tgccgaagga gaaggaatgc tactgcaggt ggacaaggaa gatcaaaggc caatcacgta 1020 gctcctcaaa atcacgacaa ggaagatttg ccagaattcc ctttttcacg agaagaatgc 1080 catcaacttc tcagccaact tttagcaaac acaaagtctg catcagccaa cctagttggt 1140 aacattccaa attatgagga actctcagga cctacgatcg gggaagatga ttgggacggg 1200 cactgagaag gagggtcttt actgcctcaa tttgtcatcg acagcaacgt gcaatgcagt 1260 atacatcaac acagacaact tgtggcatca aagacttggt cacccctcaa ctaaaatatc 1320 ttcattattt tcgtttattg ccaataaagc atgtatttcc agaaattgct atatctgtcc 1380 tttagccaaa ctcactaggc agccttttcc attgagcact atacgtagtg catcatgttt 1440 tgatttaatt cacattgaca tttggggtgg ttatcatgtt ccatcttcca ctggtgcaaa 1500 atattttttt accattgttg atgatcattc acgaagcaca tgggtatatt tgatgaaaca 1560 caaatctgag gcacgaactt tactcattca ttttattcaa atggttgcaa atcagtttag 1620 caagagtatt aaggtcatac gtagtgacaa tggctcagaa tttaaaatcc ctgaattcta 1680 ttcatctaaa ggcattattc atcaaaccag ttgcgtcaac acaccacaac aaaatggtgt 1740 ggctgagcgc aaacatagac atttgttgaa cgttgcaaga gccctacttt ttcaagcaac 1800 tcttccaaaa cacttttggg gggatgccat actcactgcc gcttacttga tcaataggac 1860 accgactccg ctccttaaag ggaaaacacc atttgaatgc ctttttcaca caaaaccaag 1920 ttactctcat ttaaaggttt ttggatgtca atgtttcgtg tccacacacc ccactcatcc 1980 cagcaaattt gatcctaggg ctcatgaatg tgttttcatt gggtatccac atggccagaa 2040 agggtataag ctttaccttt taacaactaa aaacattcgt gtttcaagat atgtgatttt 2100 ctttgagcat gtgtttccat ttcaaccaag tcctgttctt acctcccggt ctcattcacc 2160 aaaactcatc cctacaattt ctcatacacc ttccatgcat atctccatcc ttatcctata 2220 tcctccaact tcccaatctt ccgctgttcc ttactctcat catcctatcc tatcaccaga 2280 tttaatttct agcccaccaa cagacaacaa tccctccatc ccttctgcct acaataacac 2340 acctgaccca cctcttcctc tcatcccctc acccctacca acccaaccgt tacccccaaa 2400 cccacgccga tcttctcgag ccacaaaact tcccactgca ttgcagggct ttcatattga 2460 tgcagccctc ccctcacgcc ctgatcgatc agactcttcg accgaggtcc tttctccagg 2520 tcaggctcat agtctctcca atgtcctctc ttatgccaat ctttcttccc cttacagaac 2580 atttactgct aatatgacaa ttcctagaga gcctctctct ttttctcagg cacttcagga 2640 ccccaaatgg agagacgtca tgcagcaaga agtccaagca cttcatgcta ataagacttg 2700 gagttttgtt ccccctccag ctcacaaacg ccccattggt tgtaaatggg tttttaaaat 2760 caagtataat cccaacggca caattgaccg ttacaaagtc aggttggtag ccaagggatt 2820 cagtcaagtt gaagggattg attaccggga aacttttgcg ccggttgtta agctcaccac 2880 agttcgcatc ttactcagtc ttgcagccat gcagaattgg catcttcatc aattggacgt 2940 caataatgcg tttcttaatg gagaccttga tgaagacgtt tacatgcagc tccctcctgg 3000 cttcagacga aagggggagc atcgagtttg caaactacac aaatcattgt atggcctgaa 3060 gcaagcttca cgacaatggt ttcttaaact ttcctcagca ctcaaatcag ttggcttcac 3120 acaatcatgg tccgattatt ccttattcgt ccgaaaccat caagggatct tcacagcctt 3180 gttgatatat gtcgatgatg ttattctagc agggaacaat ttagacgaca tcacaaagac 3240 caaacgcttc taaaggatat gggacaattg aattacttcc ttgggataga ggtagcaaga 3300 tctaagcatg ggatttcttt gtgccaaagg aaatatacat tggaaatttt ggaagacaca 3360 ggttttcttg gtgctaagcc ttcatgtttc tcagctgaac aaaacataac acttacacaa 3420 gaagatgggg acttactaga agacgcctct caatatcgga gattggttgg acatctcatt 3480 tacctaacta tcacacggcc agatcttgca tacgcagttc atatacttag ccagttcatg 3540 gacaaaccca ggcagcctca cttagaagca gcacacaagg tattgaggta catcaaacat 3600 gcacctggtc aggggattct tttaccgtcc aaagggccat tggaattgag ggcatattgt 3660 gatgcagact gggctcgctg taaagacact agaagatcaa caactggcta ttgtattttc 3720 cttggacatg ctcccatctc atggaagacg aagaagcaaa gcacagtgtc acgttcaagt 3780 gccgaagctg agtatcgttc catggccact acgtgctgtg aaataatgtg gttgctatac 3840 attttaaagg atttgaatgt taagcatgag cagctagtta aattgttctg cgacaataag 3900 gcagcaatac atatagcctc caatcctgtc tttcatgaaa aaaccaaaca tatagaaata 3960 gattgccatg tggtgcgaga caaagtgcaa aaagaattgg ttaaaccaga acacataggg 4020 accaaggagc aaccagcaga catattcaca aagccactga gttcgaacca gtttgccaca 4080 ttactaggca agttgggagt gatcaatata cactccaact tgagggggag tat 4133 // ID Gypsy13-VV_I repbase; DNA; EDCOT; 9473 BP. XX AC AM436064; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy13-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9473 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-9473 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 706-706 (2007). XX DR Genbank; AM436064; Positions 30932 40404. XX CC Positions [4785-5279] - Integrase core CC 'TTGTT' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 4410..5717 FT /product="Gypsy13-VV_I_3p" FT /translation="MSIEVAPWYSHIANFLVTGEVPSEWSAQDKRHFFAKI FT HAYYWEEPFLFKYYADQIIRKCVPEQEQSGILSHCHDSACGGHFASQKTTM FT KVIQSGFWWPSLFKDAHSMCKGCDRCQRLGMLTRRNMMPLNPILIVDVFDV FT WGIDFMGPFPMSFGHSYILVGVDYVSKWVKAIPCRSNDHKVVLKFLKDNIF FT ARFGVPKAIISDGGTHFCNKPFETLLAKYEVKHKVATPYHPQTSGQVELAN FT REIKNILMKVVNVNRKDWSIKLLDSLWAYRTAYKTILGMSPYHLVYGKACH FT LPVEVEYKAWWAIKKLNMDLTRAGLKRCLDLNELEEMRNDAYLNSKIAKER FT LKKWHDQLVNQKNFAKGQRVLLYDSKLHLFPGKLKSRWTGPFIIHNVQSNG FT VVELLNFNSTRTFKVNGHRLKPYMESFSRDKEEFILLDPPPT" FT CDS join(225..2390,2394..3899) FT /product="Gypsy13-VV_I_1p" FT /translation="MPYWIRDQEGRLVRIENPQDTELDICVNIMDPPQEDH FT NSQHGQGDNPNAYLSMRDRMHPPRMSAPSCIVPPLEQLIIRPHIVPLLPNF FT HRMESENPYAHIKEFEEVCNTFREGGASIDLMRLKLFPFTLKDKAKIWLNS FT LRPRSIRNWVDLQAEFLKKFFPTHRTNGLKRQISNFSAKENEKFHECWERY FT MEAINACPHHGFDTWLLVSYFYDGMSSSMKQILETMCGGDFMSKNPEEAMD FT FLSYVSEVTRGWDEPHSREMGRMKGPVNPKGGMYMLSEDMDMKAKVATIAR FT RLEELELKKMHEVQAISETQAHVMPCTICQSCDHVVDECPTMPTVREMLGD FT QANVVGQFRPNNNAPYGNTYNSSWRNHPNFSWKPRPPPYQPQAQTQAPQQT FT SSVEQAIANLSKVMNDFVGEQKAINSQLHQKIENVESSQIKRMEGMQNDLY FT QKIDNIQYSISRLTNLNTVNEKGKFPSQPSQNPKGVHEVETQEWESSKLRE FT VKVVITLRSGKEVDQPLPKVRQDEELMSKKTLVKESNNQEEKSGKKSASKS FT SIEEEPMIVIKEDMMKKHMPPHFPQALHGKKEIKNSSEILEVLRQVKVNIP FT LLDMIKQVPTYAKFLKDLCTVKRGLHVTKNAFLTEQVSAIIQSKSPVKYKD FT SGCPTISVNIGGTHVEKALLDLGASVNLLPYSVYKQLGLGGLTPTAITLSL FT ADRSVKIPRGVIKDVLVQVDKFYPVDFVVLDTDPTVKEANYVPIILGRPFL FT ATSNAIINCRNGVMQLTFGNMTLELNIFHLCKRHLHPEEEEGLEEVCLINT FT LVEEHCDKNIEEILNESIEVLEEGLPEPSDVLAIISPWRRREEILPLFNKE FT DSHGAAVEDPPKLVLKPLLVDLKYAYLKEDEKCPVVVSSTLTSDQEDSLLG FT VLRKCKKAIGWQISDLKGISPLVCTHHIYMEEDAKPVRQPQRRLNPHMQKV FT VRGEVLKLLQAGIIYPISDSLWVSPTQVIPKKSGITVIQNEKGEEVSTRPT FT SGWRVCIDYRRLNSVTRKNHFPLPFMDQVLERVSGHPFYCFLDGYSGYFQI FT EIDLEDQEKTTFTCPFGTFVYRRMPFGLCNAPATFQRCMLSIFNDMVERIM FT EVFMDDITVYGSSYEECLLHLEDVLQICIEKDLVLNWEKCHFMVQQGIVLG FT HIISKNGIEVDKAKVELIVKLPPPTNVKGIRQFLGHVGFYRRFIKDFSKIS FT KPLCELLVKDAKFV" XX SQ Sequence 9473 BP; 2670 A; 1985 C; 2021 G; 2793 T; 4 other; aaatggcgtc gttgccgggg atggtgccac aatacagtga tacaaccttt tagaggctac 60 tagtgatttt catcacaagt ttggtgaatt cctttttcac taacttcatt tcctttcttt 120 taattgtaga attccttttg ttttctttct aaccttaact tttttctagt tttcttttgt 180 ttttgttgtc tttgttttgt tttcaggtaa gttgtaactt gtgtatgccc tattggattc 240 gggaccaaga gggaagatta gtaaggattg agaatcctca agacacagag ttggatatct 300 gtgtaaacat catggaccct ccacaagagg atcataattc tcaacayggt caaggggata 360 atccaaatgc atatctatcc atgagggata gaatgcatcc accaaggatg agtgcaccct 420 catgcattgt acctcctctt gagcagctga ttataaggcc ccatattgtg cccctcctac 480 caaatttcca tagaatggag agtgagaatc catatgccca catcaaggag tttgaggagg 540 tgtgcaatac ttttagagag ggaggagctt caatagactt gatgagactc aagctattcc 600 cttttacttt gaaggacaag gcaaaaatat ggcttaattc tttaaggcca aggagcataa 660 ggaattgggt tgatcttcaa gccgaatttt tgaagaaatt tttccccacc cataggacca 720 atgggttgaa gagacaaatc tcaaactttt ctgcaaaaga aaatgagaag ttccatgaat 780 gttgggaaag gtatatggag gccatcaatg cttgtcctca tcatggcttt gatacatggc 840 tcttggtgag ctatttttat gatgggatgt cttcctccat gaagcaaatt cttgaaacca 900 tgtgtggggg agattttatg agtaagaatc cagaagaggc catggacttt ttaagttatg 960 tatctgaagt aacaagagga tgggatgagc cccactcaag ggaaatggga aggatgaaag 1020 gtcctgtaaa tccaaagggt ggtatgtaca tgttaagtga agacatggac atgaaagcta 1080 aggtggcaac aatagcaagg aggttggaag aacttgagtt gaaaaaaatg catgaagtcc 1140 aagccatttc cgagacacaa gcccatgtca tgccatgcac catttgccaa tcatgtgatc 1200 atgtggtaga tgagtgccca accatgccaa ctgtgaggga gatgttaggt gatcaagcca 1260 atgttgtggg gcaatttcgg cctaacaaca atgcacctta tggaaacacc tataattcaa 1320 gctggagaaa ccatccaaat ttttcttgga aaccaagacc acctccatac caaccacaag 1380 cccaaaccca agcacctcaa caaacctctt cagtagagca agccattgcg aacctaagta 1440 aagtcatgaa tgactttgtg ggtgaacaaa aggcaatcaa ctcccaattg caccaaaaga 1500 ttgaaaatgt tgagagttct caaattaaga gaatggaggg gatgcaaaat gatctatatc 1560 agaagataga taatattcaa tactctatct ctaggcttac caacctcaac acagtgaatg 1620 agaaaggaaa gtttccctct caaccaagcc aaaatccaaa gggtgttcat gaagttgaaa 1680 cccaagagtg ggagtcttca aagttgaggg aggtcaaagt tgtgatcact ttgaggagtg 1740 ggaaggaggt tgatcaaccc ttgcctaagg tgaggcaaga tgaagaactc atgtcaaaga 1800 aaaccttggt taaagagagc aataaccaag aagagaagag tgggaagaaa agtgcatcca 1860 aatcaagcat tgaagaagag ccgatgatag tgattaaaga ggatatgatg aagaaacata 1920 tgcctcccca ttttcctcaa gctttacatg gaaagaagga aatcaagaat tcatcagaaa 1980 ttcttgaagt cttgagacaa gtgaaggtga atataccctt acttgatatg atcaagcaag 2040 tccccacata tgcgaaattt ttaaaggact tgtgcacagt caagagaggg ttacatgtga 2100 caaagaatgc attcctcact gagcaagtga gtgctatcat tcagagtaag tctccagtta 2160 agtataaaga ttcgggatgc cccaccattt cagtcaacat tggagggaca catgtggaga 2220 aagctttact agacttaggg gcaagtgtga atttgctccc atactctgtg tacaagcaac 2280 tgggacttgg aggattgacg cccacagcca tcactctctc cttagctgac aggtcagtca 2340 aaatcccaag gggggtgata aaggatgttc tagttcaagt ggacaaattc taatatcctg 2400 tggattttgt ggtgcttgat accgatccca ctgttaagga agcaaattac gtgccaatca 2460 tccttgggag acctttcctg gctacctcca atgccatcat caattgtagg aatggggtga 2520 tgcagctcac atttggaaac atgaccttgg aattaaacat attccaccta tgcaagaggc 2580 atcttcaccc agaagaggaa gaaggattgg aggaggtgtg cttgatcaac accttggttg 2640 aagagcattg tgacaagaat atagaagaaa tcttgaatga aagcattgaa gtgcttgaag 2700 aagggttacc tgaaccctct gatgtgctag ccatcatctc tccttggagg agacgggaag 2760 agatcttacc actgttcaat aaggaggact cacatggagc agctgtggag gaccctccaa 2820 agcttgtttt gaagccgctt cttgttgatt tgaagtatgc atatttgaag gaagatgaga 2880 aatgtccagt ggtggtttct tcaactctca ctagtgatca agaggatagt cttttgggag 2940 tcctcagaaa atgcaagaaa gccattggat ggcaaatttc tgatctgaaa gggattagcc 3000 ctttggtgtg cacccaccat atctatatgg aggaagatgc aaaaccagtg aggcagcccc 3060 agaggaggtt gaatcctcac atgcaaaagg tggtgagggg tgaagttctg aagctacttc 3120 aagcagggat catatatccc atttcagata gcttgtgggt gagccccact caagtaattc 3180 caaagaaatc tggaattact gtgatccaga atgagaaagg ggaggaagtc tctacacgtc 3240 ctacctcagg atggagggtg tgcatagact acaggaggtt gaattcagtg actaggaaga 3300 accatttccc attgcctttc atggaccaag tccttgagag agtctcagga catcctttct 3360 attgttttct ggatggttac tcggggtact tccaaataga gattgatttg gaagatcaag 3420 aaaagacaac cttcacttgc ccctttggta cttttgtgta taggagaatg ccctttggtt 3480 tatgtaatgc tcctgcaact ttccaaagat gtatgctaag catcttcaat gatatggtgg 3540 aacgcatcat ggaagtcttc atggatgaca tcactgtata tggaagttct tatgaggagt 3600 gtttgttgca tttagaagat gttctccaaa tatgtattga gaaagaccta gtgctaaatt 3660 gggagaagtg ccattttatg gtacaacaag gaattgtctt aggacatata atctccaaga 3720 atggcattga ggtagataag gcaaaggtgg agctaattgt taagttgcca cctcccacaa 3780 atgttaaagg aattaggcaa ttcctaggac atgtcgggtt ctataggagg ttcattaagg 3840 atttttcaaa aatctcaaag cctctttgtg aactcttggt aaaggatgcc aagtttgtgt 3900 aggatgagaa atgtcagaag agttttgagg aactgaagca attcctcaca actgcaccaa 3960 tagtgagagc cccaaattgg caattacctt ttgaggtaat gtgtaatgca agtgatcttg 4020 ctatgggggt tgttttgggg caaagaggag atggaaagcc ctatgtgatt tattatgcga 4080 gcaaaacttt gaacgaggct caaaggaact acacaactac tgagaaggag ttgttggcag 4140 tagtttttgc cttggataag tttcgcacct atttggtagg gtcctctata gtggtgttca 4200 ctgaccattc crctttgaag tacttgctaa ccaagcaaga tgccaaggca agattgataa 4260 gatggatcat tttgctccaa gaattcaatc tccaaattcg ggataaaaag ggagtagaaa 4320 atgtggtagc tgaccacttg tcaagacttg tgatagcaca tgactcacat ggtctaccta 4380 tcaatgatga cttccctgag gagtctctca tgtcaataga ggtagctcca tggtattctc 4440 acattgcaaa ttttttggtt actggagaag ttccaagtga gtggagtgcc caagacaaga 4500 ggcatttctt tgctaagatc catgcctatt attgggagga gccttttctc ttcaaatatt 4560 atgcagatca aatcataagg aaatgtgttc ctgaacaaga gcaatcagga attctatccc 4620 attgtcatga tagtgcatgt ggaggtcatt ttgcctccca gaaaacaact atgaaagtga 4680 tccaatcagg tttttggtgg ccctctcttt tcaaggatgc ccactctatg tgcaagggat 4740 gtgatcggtg tcaaaggctt ggtatgctaa cacgccgaaa tatgatgccc ttgaacccca 4800 tcttgatagt ggatgtcttt gatgtttggg ggatagactt catgggacca tttccaatgt 4860 cgtttggaca ttcctacatt ttggtgggag tggattatgt ctctaagtgg gtaaaagcaa 4920 tcccatgtag gagcaatgat cataaggtgg ttcttaaatt cctcaaggac aacatctttg 4980 caagatttgg agtgcctaag gccattatca gtgatggagg aacccacttt tgcaataagc 5040 cttttgagac tcttctagcc aaatatgagg ttaagcataa ggtagctaca ccttatcacc 5100 ctcaaacaag tggccaagtt gagttagcca accgggagat caagaatata ttgatgaagg 5160 tggtgaatgt gaataggaag gattggtcta ttaagctcct ggattcctta tgggcttata 5220 ggaccgctta caagaccatt cttggaatgt ctccttatca ccttgtttat ggcaaagcgt 5280 gtcatcttcc agtggaggtt gaatataaag catggtgggc aattaagaag ctcaacatgg 5340 atttgacaag agccgggttg aagagatgtt tggatttgaa tgaattggag gaaatgagga 5400 atgatgctta cctcaattca aaaattgcaa aagagaggyt gaagaaatgg catgatcagt 5460 tggtaaatca gaagaatttt gctaagggac aaagagtctt gctttatgac tctaagcttc 5520 atctttttcc gggaaaattg aaatcaaggt ggacgggtcc tttcataatt cataatgtgc 5580 aatcaaatgg agtagtggaa ctactcaact tcaatagcac tcgaactttc aaagtgaatg 5640 ggcatcgtct caagccctat atggaatcat tttcccgaga caaggaggaa ttcatcctcc 5700 ttgatccacc tccaacatga aaacacttga ttcatggttg aacttagtct cttcaaagac 5760 taaagagttc atcctctttt tgttttcttg taagttgatt ttagtttaat ctagtgtttt 5820 tcttgtgttt ttgcatgttt tgatttttat ttttgacttt aatgtcgttc taatgtggtt 5880 tgaattggtt ttttgtgtta acatgcaagt aggaaagctt gaagaatgaa gtcatggtga 5940 aaacaaggga aaacagggga gaaaaaccaa gactcggcaa ttttcgcaca acacttcctg 6000 ttgtgcaaaa ttttcgcaca acacatccct tgtgcgaatt cgtttttgtg acaaaatttc 6060 aaaaccatgc tctctgtctt ggagaacctc aggaatgcga aattcacatt tcctctttaa 6120 aagccatttt ctcatcttca attctaagct ttttcttctt catttctctc aacacctctc 6180 ttccgatcac ccattcccat ccttaagctc ttctccttca tcattcccca tcctcaacac 6240 caccatggca gcccatctcc atagctccac tccatagccg cggccttcac tattcaccac 6300 agtccacacc ttcaattttc agctctttct cctctttcca ccatcaaaaa cccttcaatt 6360 cttcactcaa cactctaaat tcatccctaa accaatccca accttgattt taccaaacca 6420 aaacctcaag ctaaggattc aagccacggt ttcttcataa gaaacccatt gcccccgagt 6480 agaggagcct ccaaattcca aattctcttc ttgaaaagct ccaatttcca agcctagcca 6540 ccatgaaaaa tccttttcct accttagcca gtatttccca ccctcaaaag ccaaaaaatt 6600 tcaccatttg aacaagcctc aattttgcaa aagggcgggt gaatagtgtc ttgtgcaaaa 6660 aattcgcaca acaccccctc ttgtgcgaaa tttttgcaca acacccccct tgtgcgaatt 6720 tttcagtttc tccatcccta ccctccccaa tcccaagcct ctgagcctca ttttatcgct 6780 tcttcatgcc taagacccga ggaggatata cctcagctcc cagagcagtc agagagctac 6840 ccctgtgcgg gccccactag atgcacctcc acatttacct gattctgccc ctcagagcag 6900 ataccatacg aggagagcat ctgccacgcc tgtagcccct actcaaattt cacctcaaag 6960 tcctcataca aagaaagcca agacttcaga gccaggagag tcatccagag catctcggga 7020 ttcacagtct cagcctcctt ccaccaggcg ctctagagcc agctcgccca ttgagggcaa 7080 ctccgattgc cgatccagag catttcatgt cgaggcatgt tttgatcact ctattttggg 7140 ataacagccc gagttgcagg attcatacag cctacttgag aggtaccatc ttgtaccctt 7200 tatgactccg ccctagttct tttatcctcg agtagcttta gacttttacc agtctatgac 7260 tactcgtggc gtcccggtac cagcctcgat actttttacc attgatggac gccagggtat 7320 tttgggggct agacagattg ccgatgcttt ccatatccct tatgcactag cagatcctac 7380 tgcatttaga cgttgggccc cattttctga gtgggacatg gttcgtatcc tatctcragg 7440 gacatcttcc cagatgacca ttttgaggag ggagcttccc cctgggatgc tcctagttga 7500 tgtggttctt cgcgccaatc tttttcctct tcagcataga gtacagaggc gaggggctat 7560 tctagaggca ttattccgta tctctgaggg ctactacttt ggcccccatc atttgattat 7620 ggccgctctc ctccattttg aggagaaggt gcatacgcgg cgtcttgcga gggcagacac 7680 tattcattta cttttccctc ggctgctatg ccatgttctg gcgcatatgg gttttcctgt 7740 agaccctcat tctaagcccc gccgccattg tcgagagagt ttctctcttg accaatggaa 7800 tcaggtatgg ctccatcagc attccccaga acttcccgag ccaagggaag tccctcctac 7860 tccgtccact tcagctccct cggagcctgt actagaggca gcatcgtctg acgctccacc 7920 tgctattcct cctaccttag agtcgcccat tactatccct ggtgcagagt actgtgcctt 7980 gctcgcctct ttccagactc tgaccactac tcagacggcc atattggagc ggatggacca 8040 cttccagcgt caacaggacc agcagactct cattctccgt gagattcagc agcacctcgg 8100 tctttttcca ccagctccac ctgtagcggt gccttcctca gttccagcag aggacccctc 8160 ctatccacca gaggagccta ctacttgatc atatgatcat tcctctcctt ttttgtatct 8220 atattctccg tttttggatg tcttatatat tttggactac ttttatactg ggattggatg 8280 tattccatgt ttctcttgta tattgtactc tctcagttta tatggacatc ttcctttttg 8340 tgtattttag ctattccttt ttatttcctc taatcatcac tcttatgatt tttcttttct 8400 tatgcaacat gtggtttctc atgttcattc agagtcctta ctatcaagag gtatcacttc 8460 ctctctttta ttatcactag cttttggaac attggggaca atgttcatcc tagtgggggg 8520 ggagagttga ggaagtaatt tgttgaattt ttggttaagt tattttgcca acaaaatttt 8580 tttgcaaact ctcttgattt ctcaaagata atttctcaaa agtaaatggg agaaattaaa 8640 ttcttatctt attgccatag tcttagagtt tgtattatgc ttattaaagt tgataaattg 8700 ttgaagctcc ttttgatttc aatcttaagt cttccactct aatcttttca cacactgaac 8760 acattagatt tcagttataa gatggaaaac tttctcaccc cctaaactta ggaaattttc 8820 gacttggtac cattgacctc attctattag tgttgggaca ccttataaaa ggccaatgtg 8880 tcttataaaa attttttttg cttcacttgc tttgaaaccc aagcaaggtc cgaggggtat 8940 agggtgaaaa tctttaaaac ctggtgtcct aagcctttac tggttgggag tcaccgacct 9000 cactgctcgt tacatgggtg gataggtgga gtatatacat cttaaaaaaa aaaaaaaaga 9060 ggtgcattct tagccttcta tatatgagtt agtgttgcta aagttagaga aaaaccttag 9120 ttggggggag aatatagttt gacatactat aactggaaac taagcatctt aacactaaga 9180 tttttgtgga agattaagag ttgacccttt gggagtggaa attattttga tactcaaatt 9240 tgcataatgc ccgctctttg catgttgtga taggtaagtt atttgatgac tcttgttgat 9300 gattgagttt tatattcttg acttgccatg tgagagtttg atccaatcat gccacttgat 9360 tattttttgg agtgatcagc atgattttgt aaattattat attatctatt tatttttctt 9420 tctttttctc tccttcattg ctcagggact agcaatgtgc caattggggg gag 9473 // ID Gypsy-5_Mad-LTR repbase; DNA; EDCOT; 325 BP. XX AC ACYM01109377; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-5_Mad-I; KW Gypsy-5_Mad-LTR; Gypsy-5_Mad_. XX NM Gypsy-5_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-325 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1408-1408 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01109377; Positions 1184 860. XX SQ Sequence 325 BP; 76 A; 78 C; 37 G; 134 T; 0 other; tgatgcagaa tgcatctcct aattctactt ggattagctt tccttttatt tagttttcct 60 attttagtta agaattcccc gttgttaaag gatttcttat tagttaaatt gctttcctaa 120 tttttcaaag tttgtctcta taaatagagc agattgtaat cttttaattt aattttgatg 180 aatgaaaaat ctccttacta gaatcccctg atttcttccc ctttcccttc gtctcctcaa 240 cccctaattc gtctcctcga tcttttactt cttctcggtc ccgtcacacc cttgttcacc 300 ctaatactac ggcagttcta catca 325 // ID LTR-17_Mad repbase; DNA; EDCOT; 608 BP. XX AC . XX DT 04-NOV-2010 (Rel. 15.11, Created) DT 04-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE Putative LTR-retrotransposon from the apple genome: long terminal DE repeat. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR-17_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-608 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 2007-2007 (2010). XX DR [2] (Consensus) XX SQ Sequence 608 BP; 140 A; 182 C; 147 G; 139 T; 0 other; tgtggaaatt ttcaggtcga cgggccgagg gcccactcta acaacaccga tactgtcccc 60 acttaaccac ctgcacaatc ctcaggtgtg gggttttatc acaaaaggcc tcgatgttag 120 ttagagaggg gtatttctat ttaaagcact cttctcttct ccctctgtcc gatgtgggac 180 aatgggggtt ccaacactcc cccgcacgtg agaccccact tatgggtcac acgtgaattt 240 ccacacatcg gcaaccacgt ggagccatgt cgggactcac ccaatcacgc ggggccaatg 300 gggacccacc caaacacgtg gcatctttgg cctacgtgga caatcacgcg gggccaacgg 360 ggacccaccc aatcacgtgg cagtacgggc ccgcctcctg gctctgatac catgtggaaa 420 ttttcaggtc gacgggccga gggcccactc taacaacacc gatactgtcc ccacttaacc 480 acctgcacaa tcctcaggtg tggggtttta tcacaaaagg cctcgatgtt agttagagag 540 gggtatttct atttaaagca ctcttctctt ctccctctgt ccgatgtggg acaactgggg 600 ttccaaca 608 // ID Copia-49_Mad-LTR repbase; DNA; EDCOT; 308 BP. XX AC ACYM01035317; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-49_Mad-I; KW Copia-49_Mad-LTR; Copia-49_Mad_. XX NM Copia-49_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-308 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1399-1399 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01035317; Positions 3030 3337. XX SQ Sequence 308 BP; 100 A; 38 C; 62 G; 108 T; 0 other; tgttggaaga atgcatgcaa gtcatatctt gtgttaaaat gcatgcatga aataaacatg 60 ttggatgact agtgaagtta ggctagtcaa cattctttgt gtaaaatgca tgcatgaaat 120 aaacatgttg gatgactagt gaagttaggc tagtcaacat tctttgtgta aattaggcaa 180 gttaggaaat taggtaagtt aggcaagtta ggcaagttag gcttatgtct actttctttt 240 cctatatata tgtttcattt gtaattgttt cttcatgaaa tacacatcaa aaattctaca 300 tggtatca 308 // ID Copia18A-VV_LTR repbase; DNA; EDCOT; 249 BP. XX AC CU459284; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 08-SEP-2008 (Rel. 13.1, Last updated, Version 1) XX DE LTR retrotransposon Ty1-copia like, long terminal repeat from DE Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Kastel-B06; KW Copia18-VV; Copia18-VV_I; Copia18A-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-249 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL/GenBank/DDBJ; CU459284; Positions 574040 574288. XX CC LTR = 249-231bp CC LTR are 89.2 % similar to each other. CC Direct flanking repeats = gtaaa. XX SQ Sequence 249 BP; 71 A; 31 C; 34 G; 113 T; 0 other; tgttgagcta taaatagaat aggagaatat ttttttttcg tattatgtta gtttcctatt 60 tctgtaaata gataggttta ttagtttcct atttctgtaa ataaatagtt ttatgattta 120 gaaataagtt agtttcctat tatgtctctt gtttcctatt tcttctcttg taatctccta 180 tataaaccgt gtgtatagtc aatctaaaag agagagaact tattattttt catcccatat 240 ttcgtgtca 249 // ID GYPSHAN4_LTR_MT repbase; DNA; EDCOT; 177 BP. XX AC AC131249; XX DT 28-JAN-2007 (Rel. 12.01, Created) DT 28-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of LTR retroposon, GYPSHAN4_MT, from Medicago truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; terminal; repeat; GYPSHAN4_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-177 RA Shankar R. and Jurka J.; RT "GYPSHAN4_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 27-27 (2007). XX DR EMBL/GenBank/DDBJ; AC131249; Positions 98053 98229. XX SQ Sequence 177 BP; 57 A; 30 C; 17 G; 73 T; 0 other; tgtcaaaatt aatcccaata cataattttc gtttcttgtt ggcacaccct ttcattaaca 60 atatttttag ttcatttctt gtgttttgtg cttttaatta aactttcagc aagcaacttt 120 tatcaattca tgattaaaag tcaaatatga acaattttca caaaatagtg ttcatca 177 // ID DNA6-1_Mad repbase; DNA; EDCOT; 686 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA6-1_Mad. XX NM DNA6-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-686 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1474-1474 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~85% identical to the consensus. TSDs are likely 6-bp. XX SQ Sequence 686 BP; 196 A; 135 C; 155 G; 200 T; 0 other; taggggtgca actcgggcgg gttggatggt caacccaatc ctaacccaac cttcacaatt 60 cgggtttggg ttgggttcgg gttcatgcgg gtttagtcgg gttcgggttt taattgggtt 120 cgggtttatt cgggttgggt tcgggttcgc ccaactttat cgagttcaat cttataacac 180 cttattttgc atgatttttc aaattttgaa ccaaacaacg tcaatattag ttaaaatttc 240 atttacacat catcatccac acaaaagtta aagcaaacaa cttggagact atttctaatg 300 tttcaaccat gcaaagttga aattaaatta caagacgtat accaaagctt caaccaaaag 360 aaatgtaaaa gtaacactat cattcattat ccatatgaaa accgacaata aacttcaagt 420 atagtcattc caaaacttat acataactta tataatatga agtgggatgg gtaatatgtg 480 catgagcgaa ttcgggctca aaatcgggtt gggtttgggt tgacatgggc gggcaaggca 540 tcaacccaac ccaacccaat aaatgatcgg gttgaggtcg ggttgggttt gggcgggttt 600 tttcttcatt ctaacccgcc cgatcggatt tgaaatcggg ttgggcatgg gcggattcgg 660 gttgacccaa cccaagttgc ccccta 686 // ID Copia18-VV_LTR repbase; DNA; EDCOT; 257 BP. XX AC AM451396; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia18-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-257 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-257 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 698-698 (2007). XX DR Genbank; AM451396; Positions 4554 4298. XX SQ Sequence 257 BP; 77 A; 29 C; 35 G; 116 T; 0 other; tgatgagcta taaatagaat gggagaatta ttttcctatt atgttagttt cctatttctg 60 taaatagata gatttattag tttcctattt atgtaaatag atagttttat gatttagaaa 120 taaattagtt taggaataag ttagtttcct attatgtctc ttgtttccta tttcttctct 180 tgtaatctcc tatataaact gtgtatagtc gatctaatag atagaaatta ttatttttca 240 tcccatattt cgtgtca 257 // ID Copia-78_Mad-I repbase; DNA; EDCOT; 4275 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-78_Mad_; KW Copia-78_Mad-LTR; Copia-78_Mad-I. XX NM Copia-78_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4275 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1694-1694 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1737-2237] - Integrase core CC 'GGGAG' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 114..1229 FT /product="Copia-78_Mad-I_1p" FT /translation="MSGSGGSEVRTPIFSGENYEFWRIKMVTIFKSHGLWN FT LVEKGVKTSDSKKKKSEGSSEDDGDEEMAAVLMQDAKALGIIQNAVSDQIF FT PRIANAESAKMAWDLLYGEYHGGDQVRSVKLQNLRREFEYARMRDDESLSS FT YLTRLNDLINQMRTFGESLSNERLVQKVLISLSKPYDPICLVIENTKCLET FT VELQEVVAILKSQEQRFDLHTVDATERAFSSLSVNPKEQNKSGGHSSSSRS FT QRNWNSKGKKWESKPKFQQKSPLHNYQSANAPQSVGQEVAKPQCKVCSKYH FT FGECRYKGKPKCFNCDKFGHWARECNVGRSVQKANNASQLEMTGNLFYANN FT AVTEPKVNGEWYVDSGCSNHMTGNVDLLV" FT CDS 1785..3653 FT /product="Copia-78_Mad-I_2p" FT /translation="MKTESIAGNKYFMLLIDDFTRMIWVYFLRYKSDAFNC FT FKKFKAMAELQSGFKIKTLRSDRGGEFKSAEFDQFCEKEGLQRQLTLAYTP FT QQNGVVERKNRTVIEMAKSMLHEKRMPYFLWAEAVHTSVYILNRCPTKALN FT NITPFEAYSGRKPGIAHLRVFGSLCYVHVPSEQRHKLEPKSLKGVFVGYAT FT CEKGYRVFDPLSKKLFLSRDIVFDEEAAWNWEENSGSTFLNTGSFVHGDIS FT AESNDRMVLSPTSPILPQSRRALSSEDYETESRSPILGESSSMSNAIEGQN FT QAFDNTPLKWRNLNDVLAQCNLCIMDPEKYEDAKQDESWLKAMEDELFMIE FT KNGTWKLVDRPTEKPVIGVKWVYKTKLNLDGSVLKNKARLVAKGYAQKPGL FT DYNETYAPVARLDTIRTLIALAAQKSWKLYQLDVKSAFLNGVLQEDVYVEQ FT PEGFVVKGKEEMVYKLHKALYGLKQAPRAWYGEIDSYFSQCGFEKSLSEPT FT LYIKARGEDILIVSIYVDDIVYTGSCKPMLEEFKEDMKMKYEMTDLGLLHH FT FLGMGVIQTDSCIFINQKKYASSLLSKFGLNEAKTVSTPLVATEKLSKDDG FT SGSASENCIGALWEAFYISLLQGRI" XX SQ Sequence 4275 BP; 1349 A; 697 C; 1073 G; 1151 T; 5 other; tggcctcaga gccaggttgg attataacaa tctgggcgta aatctgtgaa gtcgtcgagc 60 tcaatcgaag ctctcttgaa gctctgtgaa ggttgtcgat tcagatcaaa accatgtctg 120 gatctggagg ctcggaagtg aggactccaa tcttctccgg tgagaactac gagttctgga 180 gaatcaagat ggtgacaatc ttcaaatcac atgggttgtg gaatctggtg gagaagggag 240 ttaaaacgtc cgattcgaag aagaagaagt ctgaaggatc gtcggaggat gatggagatg 300 aagaaatggc agctgtgttg atgcaagacg caaaggcttt gggaatcatt cagaatgcag 360 tctcggatca aatcttccct cgaatcgcca atgccgagtc agcgaagatg gcatgggatt 420 tgttgtatgg agagtatcat ggtggtgatc aggtacgatc tgtgaaattg cagaatctta 480 gaagagaatt tgaatatgct aggatgcgag atgatgagtc tttgtctagc tatcttacac 540 ggctgaatga tctaattaat cagatgagaa catttggtga atctttgtcg aatgagagac 600 tagtgcagaa ggtcctgatt agtcttagta aaccttatga tcctatctgt ttggttatag 660 agaatacaaa gtgcttagag actgtagaat tgcaggaggt agttgcaatc ttaaagagtc 720 aagaacaacg gttcgatttg catacggttg acgcaactga gagagcattc tcttcactct 780 ctgtgaatcc aaaggagcag aacaagagtg gtggtcattc tagttcatct agatctcaga 840 gaaattggaa ttctaaaggc aagaaatggg aatcaaaacc caaatttcag cagaaatctc 900 ctctgcacaa ttatcagagt gcgaatgcac ctcagtcagt gggtcaggag gttgcaaagc 960 ctcagtgcaa ggtgtgttct aagtatcact ttggtgagtg tagatacaaa gggaaaccaa 1020 agtgcttcaa ctgtgataaa tttgggcatt gggctagaga gtgtaatgta ggcaggtcag 1080 tgcaaaaggc aaataatgca agtcaactgg agatgacagg gaatctgttt tatgcaaaca 1140 acgcagtcac agaaccaaag gtgaatggag agtggtacgt tgacagtggt tgtagcaatc 1200 acatgacagg aaatgtggat ttgcttgttg akgtkagaac caacgtagct ggcaaagttc 1260 aaatgccaac tggagatctt gtgaatgttg caggaatggg atctttggtt attgatacaa 1320 ataaggggag aaaatatgtt agagaagtaa tgtaccttcc cgggttaaag gagaacttgc 1380 tcagtgttgg tcaaatggat gaacatggat acttcttggt gtttggwggt ggaatgtgca 1440 atgtgtatga tggtccatca ctagaatgct tggttatgag agtgaaaaag aaagtgaata 1500 ggtgttatcc actgactttg ttctctgaaa atcaaatggc gctgaaagct agtgtcactc 1560 actccactga gatttggcac aggagactcg gacatctaca ttttggtggt ctcaaacaat 1620 tgagagacaa ggaaatggta catggtttgc cacagcttgc agastacaat ggagtctgtg 1680 aaggatgcca atttggtaaa caacacagag aagaattccc aagaaatcaa gtgtatagag 1740 caactgctcc acttgaactg attcatgtcg atttgtgtgg acctatgaag actgagtcaa 1800 ttgctggaaa taagtatttc atgctgctga tagatgattt taccagaatg atttgggtct 1860 atttcttgag atataagtca gatgcgttca actgttttaa gaaattcaaa gctatggcag 1920 aattacaaag tggtttcaag attaagacac tgagaagtga cagaggaggg gagttcaagt 1980 ctgcagaatt tgatcagttc tgtgagaaag aaggtttaca aagacagctt actcttgcat 2040 atactccaca acaaaatgga gtagtggaga gaaagaacag aacagtgatt gagatggcga 2100 aatctatgtt gcatgagaag aggatgccat actttctctg ggcagaagct gtgcatacat 2160 ctgtgtatat tctgaataga tgccccacaa aggccttgaa caacattaca ccttttgaag 2220 cttattctgg tagaaagcca ggaatagctc atctgagagt atttggatct ctgtgttatg 2280 ttcatgttcc aagtgaacag agacataaac ttgagccaaa aagtctaaaa ggagtatttg 2340 tggggtatgc aacttgtgag aaggggtata gggtgtttga tccattatcc aagaagctgt 2400 tcttgtcaag agacattgtg tttgatgaag aagctgcctg gaattgggaa gagaactcag 2460 ggtcaacatt tcttaatact ggaagtttcg ttcacggtga tataagcgca gagagtaatg 2520 acagaatggt gttgtcccct acatcaccta tactacctca gtctagaaga gctcttagta 2580 gtgaagacta tgaaactgaa tcaaggtcac ctatcttagg tgaatcttca agcatgtcaa 2640 atgcgattga aggacaaaat caagcatttg ataatacacc attgaaatgg agaaatctga 2700 atgatgtatt ggctcaatgt aatctgtgta tcatggatcc agagaagtat gaggatgcca 2760 aacaagatga gtcttggtta aaagctatgg aggatgagct gtttatgatt gaaaagaatg 2820 gcacctggaa gcttgttgac agaccaactg aaaagcctgt cataggggtt aaatgggttt 2880 acaaaaccaa gttaaacctt gatggttcag tgttgaagaa taaagcaagg ctggtkgcaa 2940 aaggctatgc acaaaagcct ggtttggact acaatgagac ttatgcaccg gttgctaggt 3000 tggataccat tagaacctta atagccttgg ctgcacaaaa gagctggaaa ctgtatcagc 3060 tagatgtgaa atcggctttt ttgaatggag ttctacaaga agatgtctat gttgagcagc 3120 ctgaaggttt tgtagtaaaa ggcaaggaag aaatggtgta caaacttcat aaggccctct 3180 atggtctaaa acaagctccg agagcttggt atggagagat agacagttat ttctcacagt 3240 gtggtttcga gaaaagcttg agtgaaccaa cactgtatat aaaagcaagg ggagaggata 3300 ttctgattgt ctctatctat gtagacgata ttgtctacac tggcagttgc aaaccaatgc 3360 tagaagagtt caaagaagat atgaaaatga agtatgagat gacagattta ggtctccttc 3420 accacttcct tgggatggga gtgatacaaa ctgattcctg catcttcatt aatcagaaga 3480 agtatgctag ctctttactg agcaaatttg gtttaaatga agcaaagact gtctcaactc 3540 ctctggtagc tacggaaaag ttgtctaaag atgatggaag tggatctgca agtgagaatt 3600 gtataggagc attgtgggaa gccttctata tctcactgct acaaggccgg atataatgta 3660 tgcagctagt ttattggcaa ggtacatgca ctgtcctacc aatagacact atgggactgc 3720 aaagagagta ctcagataca tcaagggaac tctggattat ggcttggagt atgtgaaagg 3780 aagaaaatca tgtttaattg gcttctgtga tagtgattgg ggaggttcat tggaagacag 3840 caaaagcaca tcaggatatg cattctcctt tggcagtggt gtgttctctt gggcttctgt 3900 caaacaaaac tgtgtggcat tgtccacagc agaagcagag tacataagtg catccgaagc 3960 cacagcacaa gcaatatggc tgagatttgt cttggaagat tttggagaat tacaaactgt 4020 agccactcct cttcactgtg ataacacatc tgccattgct atcacaaaga attctgtgtt 4080 ccatcaaaag acaaaacaca ttgataggag gtatcacttc attaaggatg cactgcaaga 4140 aggaatcatt gatttgatat actgtcccac tgaagaacag attgcagata tcttcacaaa 4200 acctttggct aaggatcggt tcaactttct cagggatatg cttggtgtga aatcagctca 4260 aaacttaaag gggag 4275 // ID Copia19-PTR_LTR repbase; DNA; EDCOT; 306 BP. XX AC scaffold_130; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia19-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-306 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-306 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 211-211 (2007). XX DR Genome; scaffold_130; Positions 593945 593640. XX SQ Sequence 306 BP; 99 A; 65 C; 45 G; 97 T; 0 other; tgaaagaagg acaacaaact cctactccaa cacggattgc aaatcctcct gcaatttaga 60 ttgtagaatc agaccttaac acagcttcca gagttttagt ttaactccaa cacaagttgc 120 agagcttccc tcctactgca atgttacgtt gccctgcata caattgttag gataatagtt 180 aatagagata gactttgatt tgatcataaa catagcttca tctactgtaa cagaaagtgt 240 atatataccc ctgttgctgt aacagaagat tacgaataaa tattcttctt tccttttatt 300 tcttca 306 // ID Copia28-VV_LTR repbase; DNA; EDCOT; 218 BP. XX AC . XX DT 12-SEP-2007 (Rel. 12.09, Created) DT 01-OCT-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia28-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-218 RA Obukhanych T. and Jurka J.; RT "Copia28-VV."; RL Repbase Reports 7(9), 789-789 (2007). XX DR [1] (Consensus) XX CC This is 5' LTR of Copia28-VV LTR retrotransposon. 5' and 3' LTRs CC are 98% identical to each other. XX SQ Sequence 218 BP; 69 A; 39 C; 29 G; 81 T; 0 other; tgttggaaag tcaatcttcc taaatcttcc atattaagaa tagatgatct gtatatgtta 60 gttttcctat tgtaattcct gacttatagc tggatagtct agaatatggt aagctgattc 120 ctgacttgta gaaaaagatc tcaaacctcc ttgtataaat acacacttca acatcaataa 180 tattaattca gccaattctt cttcttttca tggtatca 218 // ID TAM2_AM repbase; DNA; EDCOT; 5187 BP. XX AC X06266; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 25-MAR-1997 (Rel. 2.02, Last updated, Version 2) XX DE Antirrhinum majus DNA for transposon tam2. XX KW AMTAM2; Chalcone synthase; TAM2_AM; Tam2 element; nivea locus; KW transposon. XX OS Antirrhinum majus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Lamiales; Plantaginaceae; Antirrhineae; OC Antirrhinum. XX RN [1] RP 1-5187 RA Krebbers E.; RT "TAM2_AM."; RL Direct Submission to Genbank (17-NOV-1987)Krebbers E., Egelspfad RL , D-5000 Koeln 30, West Germany.. XX RN [2] RP 1-5187 RA Krebbers E., Hehl R., Piotrowiak R., Loennig E.W., Sommer H. RA and Saedler H.; RT "Molecular analysis of paramutant plants of A. majus and the RT involvement of paramutant transposable elements."; RL Mol. Gen. Genet 209, 499-507 (1987). XX DR GenBank; X06266; Positions 1 5187. XX SQ Sequence 5187 BP; 1892 A; 976 C; 855 G; 1464 T; 0 other; cactacaaca aaaaacccct attgggacac agaaatgtgt cccaagatag atctattgca 60 acacttacta tatcttggga cacttgcaat atctgtcgca taaaacctat gtcccaagag 120 tgcatgggtc acttttttaa atgtccctac atctattgtc taaggacatt tatatatgtc 180 ccataggtaa gcttttggga cacaaataaa tgtcccaaaa taattatgtt aggacacatg 240 aatatgccac atgcttctta tgcttgagga catttatata tgtcccatag gaaagctttt 300 gggacacaaa taaatgtccc aaaataatta cgttaggaca caaataaatg tctcaaaata 360 attatgttag gacacataaa tatgtaccat gcttcttatg tcctaagata tctagtatct 420 tatagttaag acatttaagg ctccaacatt gcaatttttt tttctctttt caactttgaa 480 cttttcaacc caacatcaag ccaatatgaa accaactttt atataaatca aatatgttca 540 ttcaattatt aacaagacca ataaactata aacatcaaat atgttcattc aaatattaag 600 aaaatcagta actatagtct caaactaaaa gaatgtcaca ctattgacaa cataaacgaa 660 cagtcaagct gctctaacat gacattaaat ctccgatcga cttcaaagcc tcgacaataa 720 cttgtcatgt ggaaacttag gaacatcgtt catctgatca tcttgaaaat cttactggtt 780 agaatcttga cagcagcatc ctgcaagaac aaataatagt tctaatcacc ttaatgccat 840 aagttgatct acagtccata gtaaatatac tgcaatcttc actatccatt ttcactgata 900 tatatttgtc tgtaaattgt ttaagctgca aacatgaact catagtcttc acacagaaag 960 gtacctttga acgctcaaaa caatctgttt cattgtgtta aatgtccagt atacagtata 1020 cagtttgacc atataacaat gttacttcag atttctgtaa tgaaacaata gcacaatgca 1080 ggaaaacaca attcctccat aaagtgcaca aatactataa gactgtgatt cgaaaaaaca 1140 ctatatgtag ctaacaactc aaatgtagca gaaattaaac agaagtttca tatcaatttc 1200 aaccaaaatc atataacata gtccatacca acatatatca actcactaac taaagataaa 1260 ttacattctt ccaatagcca tgtagagtaa gctatcatga acgttagcaa aagattgcat 1320 catacctcac agataccgtg cagttggtgg ctggtagaat tgtagaggaa tagaggtaaa 1380 ccagagtctc gatatcttgg tggtaaacct atagaaattt caataggggc caacctcagt 1440 atataaaaaa tttgaatact taacacaata tatagtgaga atcagcagaa atcagcaagt 1500 atcaaattta agacataaga aagcaaataa aataaacaca atagttactt ttttaaatat 1560 aattcaggat tcaagttttc acaaaaatcg aaataggtta acatctccaa cttcatccaa 1620 tataatgttc tagaatttaa aagcataggg ttgatgtttt gtaaacacac accttgacta 1680 ggccaatgat tcaaaccatc cgttccacat tcagatagta acactatcat attgctctcg 1740 acgaatttta ttatatattc aaaataaaca ttgacttatt tgcttcacaa gaggaaagga 1800 cagggacatt acattagcct gtagtaattc aagctggaaa atttccagct aactattcgt 1860 tgtccagaca gtgagctaaa taataagcat aacagaatct agaagctgga acaatcaact 1920 caacatgcaa tcaaaacagg atcaagaaaa aatggagtgc gacaaagata gtctaaagct 1980 gcaatttatg aaggattaag gtattaaaaa ctgcaatcta catgtaggag aaagaaaata 2040 aagatgaaaa catatacgct gcaaacttgt aaaacagacc tggagtaacg ccttgctgga 2100 gaaggactgt gaaataagct gccagagatg aaaccacaac attttagcat gataattcca 2160 ctaatacaca tgaaaagagg ttcactatta ttccgagaca ctgaaaaatc agcattttct 2220 ttcattgaaa aaaatgtgaa aaggcaggtt ttcaatataa tcaatctcaa tatgatgcca 2280 aattaaagag gtttgaaata atcaactgac agtgatggcg tcgtctaaga ggtaatgacg 2340 gactccgtct cctgtggcgc ctaaaaggag ataatgcaac tctacgcatt ttttgaggtg 2400 tcttcctgtt ctcctcagca aaaacaatcc ttatttcacg tccaccaata actgaacgat 2460 tcaggtagct ttttgcttca gctgcatctt caggatataa aaactttacg aatccaaagc 2520 cacgtggttc cttatattat cgtgaccatg tgtaatagaa agtgaatttg cataatagca 2580 tgaattaagg ccaccaaaac gagcttggga gatctcaatg gtttatgaaa agatagcata 2640 ccctgtatag taattcttgg gcagatatac atccttcata gggccaaatc tttcaaaagg 2700 atccctaagg tcttctggcc tgcacaacga gtacctcatt atagattctc cgtagtacat 2760 ctaaatagtt aaacccgaac atcattaaag acagagatta acaatattgg catagaaagg 2820 cgttagctta tccagggtag gattgcaaat tcttaaccca tgttccatac acttcaagat 2880 tctccaacaa acaccctaac tccagaaaag ttttcacata ctattgaatt tctcatataa 2940 tcataaactt aaccaacgag gcaaaaatac gcataaaata gcaacatata catatgaaga 3000 aacttaataa aaccatacac acaacgggta cctaatgatc ttcctagcta gacaatgatg 3060 gcaagaacat aaaccaccct cacggagttg atctatgaga actcagcact ttttttcttt 3120 tcaaattcct ttctttctac tagttcttac atattaaata agatgttgca tctaattacc 3180 tcaatgactt tcattggtgt ccacccaact ccagatcttc ttggctactg tcttgctacc 3240 ataattagaa acatcagttt tcagcatgat aagtaacaca cataatcata acatagaaag 3300 agcagtctca accttcaaag ctgatttctg gaatgactga atgcattttg tggcttcttg 3360 tgaacttttt gctgccaact gcagattaaa acttaacatt cttcttagta taaaagaata 3420 acaagaatta tttcgaggat gctaattctt ctggaacttg agaaagtggt gatgagatct 3480 ttcatggaaa cggatgatgc ctctgcaaat tcatgctcat tgagtcctca ctgtgctctg 3540 gcacaactgc actgattgca atcaaaaacc aatatttaca aatgcaggca tgtgaatata 3600 tacttgttat tcacaacctc acaacaaaat ctcataaaat aaataaggcc tatcaccttt 3660 aagaatatag accaaaagca gctcactatt gagctgcaaa gccttactac actccttgat 3720 cacatgctgt gcaattccaa tttgctgtag cagaatgctc gattgctaaa atgcacagca 3780 gaaaatagat aacaaaatcc aacagatcaa tgtaccaatc aagtcaacaa tttgacaatg 3840 aaactagcac cattaaataa taaaacaaac taaatgagat gtctttcgtc aattatagca 3900 taaagtaatg taaaaatagt tataatagct cattcaaata agtcataagt caacataaca 3960 gaggcaattg ttcataccta ggcctgcaag tgtcctcacg gattcaggcg actacatcat 4020 atataagtga gtggcaaatg aaaacgaata gaaaataaaa aacgaataga gagaagtcat 4080 ataggtacac gccgacgtta ggaaagcgaa gaaaataaaa aactggagga tagagagaat 4140 atggcagaga tgccgtaaat acctggaggt gagggtgaac cgactgcgta aatctgtact 4200 tgtgaatcta tatcaaaaaa tcaatctatc ttcaaatatt ttttgataat ttatgcggat 4260 cttaatctga aataatcaaa attcgaatga ttctaattaa ttgcttttag tcaaaccaca 4320 atatgtggcc aacaaatatc acgaagatga tacactgaaa ttccaataca gagcatcctt 4380 aataagtttc catcaattca atctcttcct tcttcaagcc atttcatcgt aatcatgtaa 4440 cgctaacaat tcatggaaat taatcaatca atcgcgatga ttaatttccc ataattgttc 4500 ggctccactt caattcatat caaaatcaaa aaaattgaaa atcatccaca gatctacacc 4560 gatcgatcgg ttttttaaat caacagtgga tccaactgaa cttcaccgag tattcgcatt 4620 atccgatcgg aacgacgatg gtagaatcag tcgcatggaa ttaagcgaat cgctctagaa 4680 attagggatc gacatacctg aagacgaaat ggcgcagaag atcgagaaga tcgacacgaa 4740 caacgatgaa ttcgtcgatg cggacaaatt tagggcgatt tacacggcga ttaatgtacg 4800 gaggacggcc ggacgatcga agagcggagg accgatgacg aagtaccatg gagaagctcc 4860 aataggaaag caaatcggcg ggggagatga gattagagag aattcagaga gctacggttc 4920 ttcggagatg gagaaattta gagattttct gtgaatgtgc gaagaaaatt ttggacatga 4980 gagggaggga gtgtgggcct tttttttttt tttttttttg tttgatagaa gtgtgggcca 5040 tctcttcaaa ttaaaatttc tgtgaaatat attagaggct tttcttggga caaataataa 5100 aaaagccctg tggttgatat gtaacgacac ttattagtgt atgtctctaa aaaattgtcc 5160 caatagctac tttttgttgt agtggta 5187 // ID Copia-54_PTr-LTR repbase; DNA; EDCOT; 166 BP. XX AC . XX DT 08-DEC-2009 (Rel. 15.02, Created) DT 08-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Copia-type LTR retrotransposon: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Copia-54_PTr-I; Copia-54_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-166 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 162-162 (2010). XX DR [1] (Consensus) XX SQ Sequence 166 BP; 52 A; 20 C; 20 G; 74 T; 0 other; tgttaaataa tatttatgta gtcttattta ttaagggtag aatagtactt tcagtttaac 60 ctatatatac tttatttgta tttaggttaa gactaagcac tcataatata cagattattc 120 agaattctag cctccttttc tgtgtttgat cttaattatt ttaaca 166 // ID Gypsy-26_Mad-I repbase; DNA; EDCOT; 4235 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-26_Mad-I. XX NM Gypsy-26_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4235 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1746-1746 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 4235 BP; 1158 A; 867 C; 863 G; 1344 T; 3 other; gtttggtatc agagcataag tttgggcagt attgcgttca tcacacgcgt gatgtaagca 60 ttctcggttc ttgagcctaa atgttgaatc ttgccacctc gtcgagtacg aaaaatgtgt 120 tagcttttcc taagttttgg gcggcttagg cgacttatcg acattctaga agatcgtttt 180 ggcgaccgcc tctagacttt aagcgaagaa cctccctgcc aaggaaaaat cccgatttga 240 gacaagttga tggccctgaa gcagggctaa tgtatcgata gttgtgtatc accggagatt 300 taccatcaat tccactacca tctagtcatt tctaccaacc ctttcgagtt aggaaaccag 360 aaatagtttt gattccttgg cagtacccgt tagtatacca cctattagaa ttcctacgaa 420 gtttacttcg tcaaaattcc agaaatgtct tgagtgacaa tgtggtgcta aagtggtagc 480 actcgacgga agaacatctg ggggacaatc acttttggtc cccgatagca ctaatctttt 540 caaacgcact agtgatcatt ccggatcttc aggaggaaga tcgacttccg tttaagtccg 600 ttctaaagta gattattagc aaattccttt tccggcctta ggacattcca accaatacta 660 gtttccagaa tttcttttgg tgatgtactc gtcatttcga cgagcatagg cacaggtgta 720 cgagttgtta tacctacggt cagtagaaat ccccgaagta gtaagtattt tccctagaat 780 taatgaaacc acctcatagg accagttcct taccaatcat ctgaaaccat ccacccgagc 840 gggctctaac ctgtaatcag cctacggtgg cgctactaat tgacgatatt gtccgatatc 900 caggaactgt caaccagtat tcaggcggta tgatttctga taccggacac atgtactagt 960 atctgggagt gataccttta tgccagaacg ccggttcaca gtttcagggt aacgaacaat 1020 atcaaaatat catatatgcg ttaattagcg gcgcgactga tagactgatt aacagtgact 1080 acctgagccg aagaaactaa atcatggaaa cttaggagca agccttgtag gaggacagta 1140 aactcatagt tgtgttaacc atattaccca tctaggtaac caaaacattc tcgaccagcc 1200 atccttscga tcacttccac agacaaacat tagaattgaa gcacgagtta atttcccgct 1260 gtaagagcga attgagtatc gagaaagctg tgaagaccta ttagcacgtg tcgtagtgaa 1320 aggaagtagt atggtacgtt tcgaggacgt atacctttgg cgtcatttct caaaatttta 1380 cctgggatat caccaaatgg tgaagtgaag tacaccatcg atccactttc tcgtactaca 1440 ccagttttcc ttgcgtcttt tcgaacaact cctacatcat tgagagaact tagttacaaa 1500 agcttaccga ttaggaattt acccaaccaa acaccttatc tagggaacct caaacctatc 1560 cgcgaaggcg aaagactgaa ccttaggatc gtacctagat tttagcaact caatcgggtg 1620 acgattaaaa ccgttaaccc atacttcgaa ttgatggtct acccgaccaa cctttggaac 1680 ccgagttttc ttccatagcc tgacgaattc gtagtggtct taccgacgac tttctcacct 1740 acctcagcaa cgagaccaaa ttttctaaac accgacagtc agctttatac caaattcctc 1800 aaatgttaac tttgtttagt tggtactttt cttgggagac gtgatctcag tagacgatat 1860 tcttttcttt ttccaaaaag gttgtagcgg aagaaagttg aaattctcac aaagtgttgt 1920 gaaattcgag atatccttgg tcttgtcgat tttatcgaca atttgttagc gatttttcgg 1980 ctatagtgtt tttcctcact tatcgaccga ggaaagttag tttagttgga tgttgaatat 2040 gaataaagtt tctgacaact gaactgttgt ctcatctcac ctttgtttta cacctttcga 2100 tgacattgat cattttggaa atccacgatg acgttttctt tggatgtttt ggctgtgtag 2160 atgcagcatg acggagtatc gcttatattt cccaacggtt agaaccgttc gaaatgaacc 2220 atcttactca tgacttagag tcaacagtta ccatctttac ttgaaaaccg gatgacactt 2280 ctctgtggag aaacgtgtcc aaaatcttta ccaaccttag acctctcaaa tacatcttca 2340 tttgaaaaga actagatttc tgacaacggc gatggaagaa ccaaatcaac gtctacgatt 2400 gcactatcgt gtatcacccc ggttgtgcaa acgtaattac tgtttaccgc agcaaaagac 2460 atatctaccc ttgaacactt tcagcctgtc ctatcccatt tcagttggaa ttcacgagca 2520 ttgatttgac gttacttaca aatcatcaag aaatcgttcg agtggttata atcacttcct 2580 gtatccaaat ggagatgggg aatatcacca taagctcccg gtacgaggta tcttgtacat 2640 gtggagatta tgatgatgtt tcggtgatta tcgaccgact tgacaagtca gctcactttc 2700 cgttggtcca gagggactac attttagacc acttggtaaa attactcatt cttgaattta 2760 tcagattttt ctggcgtttc gatcaacatc tactctgact gtgattccat attcaccttt 2820 tgtgctggaa ggcattccag tcaaccttgg gtacgtgtct accctactgc acttcgtatt 2880 atttttgaag cagacagacc gtctaggaga atcgctcgga cattgaaatt ttagttgtga 2940 ccattaattc ctcaatcacc caacaaatac tctgctgaac gaatctttac cgttggtgat 3000 tgaatattcc agaagctacc gttgtagcga gatgtcatgc attaattcca gttaccttgt 3060 attctagatt tgatggactt gttttgaccc tcaaattctt gattgttctt ttagccttct 3120 cgacatagtt tttgctaaat tcgagggaaa ttcaatatga atctgctcgc tatggcgttg 3180 tgaactgcat tgttcggcta catggtgtgt gtgtcactac tgtatctcac cgtgatacgt 3240 gtttcacttc caagtcttgg gaagtcttct tgaaggccat ggtactaagt tttgtccaat 3300 accacatttc accctcagac taacggctag tctgaaacga actatccaga ccttagtgga 3360 catgttgcgt tttgtccgtt ctacagtttt agcatggttg taacagacac ttatctttgt 3420 twgagttgcg tgtaactacg gttacaattt ttggttttgg gtatggcacc gtttgagacg 3480 tggtatggag attttatgca cagtacatga ttgacagaag agtattgcga acaggtattt 3540 gaatgatcga gattacgatg tagcaaattg tgtgctattg gcgttgtcgc ccgagagggt 3600 agtacgtgag cgcgatcgag gcgctaatca gacgatttat gtgtatttcc caatgagggg 3660 caagatggta atattgcacc ctcgggaatt tkttgcttgc ttatcgagac aacagtgagt 3720 tgtcggtatt gcgggctgca gaccgtaata tcgataactt attcgttgga ttcgttaagc 3780 aagtggacaa gtaggccgtt tacgttagtt tatttattta ttgtttgggc ttgacccaaa 3840 gatactacac acttattctc ggagtacgtg acgctacgag tgcgtaggtg aaatttttct 3900 atgttcagtt ttgatttcag tacaattatt ttaactttac gttatattat atacgtattt 3960 tgacgatatg ttactatata tctatttttg actttatgtt tttataaagg attttatatt 4020 gtagtattgt actgaaggag aaggaaagta tgagtttgga ggcatgaaag aggaatcatt 4080 gcaatccgat cgcgacggaa tgacattctc ttttatgcaa ccgctctaac ttgatttctt 4140 ccttatatat atattttctt cctatctttt gagtatttta tgtatagcaa atgatttcaa 4200 atttcgggga cgaaattttt ttaaggtggg tagat 4235 // ID Copia-2_TC-I repbase; DNA; EDCOT; 4165 BP. XX AC CACC01006997; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-2_TC_; KW Copia-2_TC-LTR; Copia-2_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-4165 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01006997; Positions 17624 13460. XX CC Positions [1607-1963] - Integrase core CC LTRs are 95% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS 2229..4019 FT /product="Copia-2_TC-I_1p" FT /translation="MGVFIGYSQHSKAYRVYHVDSGKISISRNVSFDEGSS FT WNWDKPQHTRVSATNTLSAFQNISDIELDEDELIDKAPVRGTRTIQDIYKR FT CQVALSDPVSFEDASQHEEWIKAMKEEINMIEQNHTWSLVDRPINGHVIDV FT KWIFKRKFNSDGSLNKNKARLVAKGYSQLAGIDCRDTFAPVARLDTIKLLI FT DLSAALDWKIYHMDVKSAFLNGKPNEEIFIEQPRGFEVGDRQNKVYKLHKA FT LYGLKQAPRAWYSRIDAYILAKGFYKSLNEATLYVKKIKNEVAVIVSLYVD FT DTLITGADQASIGEFKSTMKKEFHMSDLGQMKYFLGLEIHQSKESITLSQI FT NYIQEVLKRFKMAECKPTSTLLVAHEKLSLNSGEILESPNDYRSLTECLLY FT ICSTHREIMFAVSYLSRFMQRPSQLHLVAAKRVLRYLRGTTCHGINFIKNE FT TIELVGFSDSDRGGCNDDGRSTSGYIFSLGNGLFSWNSHKQNTVAQSSSEA FT EYVAAAEASNQAIWLRKILQDLGMDQTNPTKLFIENKFAISMTKNPVFHGR FT TKHINIKQIRQNSRKERGDTCAILQIRRPGCGHNDQASVLSQGLNLTKIS" XX SQ Sequence 4165 BP; 1404 A; 748 C; 852 G; 1161 T; 0 other; tggtatcaga gctaaaacta agctcttaag ggacctgaaa cataccacca accaaattca 60 caactttaac aacactgtaa attgatagca atatgtctta tctccaacac agcttcacac 120 ccgtcacctc ccaccttcaa tggtgaaaac tacacatcca ggtcacttaa aatgaaagcc 180 tacttatagg cttatgacct atgggacatt gttgagacag attcagaacc ccctgccttg 240 aaagaaacga caacatttgc tcaaatcaaa cagcatgggg aagaagttgc taaacggtat 300 tgagctctgt cctttctcca tgcatgtgtc acgaaatcgg tgtttgcaag aattatggct 360 tgttccacgg caaaggaggc ttgggacaga cttaaagatg agttccaagg ttctgacagg 420 acaaggcaac ttcaaattct taatcttatg agagaatttg aaattcttcg gatgaaggag 480 tctaactcag tgaaggagta cattggaaaa gtgatgaaaa tagtcaatca agtaagactt 540 ttgcgagaaa atctacctga aaaagagttg tagagaaagt gttgatatcc ttacccgaaa 600 ggtttgaacc cacaatttca tcacttgaag gttcaaagga tctcttacaa ttgtaactca 660 caaatgtagt caatgctctc caagcatcag acagtaggag agccatgcgt ctcgacagct 720 acataaatca tgctatggtg gtcaacatga aaggaaaagg ctcagttgat gtttacatca 780 gtaaaggttc aaacgaacag aaagacaaag ggaaaaagaa ttctcaaaca atagatcatg 840 gggtaagaag aataaccatc aaatgtgttc ccattgcaaa aagcgtaacc atgcagaagc 900 caactgctgg tttagacctt caactaagtg ccgaatctgt aattagcatg gtcatataga 960 aaaggtgtgc aagaataagt ttgaaaatcg agagaaatct cctcaagcat ctaagagagc 1020 tgagattgct gaagaaacac ttctgatggc tcagacagaa ccaaaagttg ttgaagcaaa 1080 tcagtggtta ttagatagtg gagcttcaag tcacatgaca ccatatgttg agctcttcgc 1140 agaacttggc actcaacacc gatcgtatgt gaagataggt aatggggtgt atctgcaagc 1200 aattggaaaa ggatctgtgg aaacatgaac ctcttctggt gacaagtatg catttaaagt 1260 acttcttgta cttgaaatta cccaaaatct cttaaatgtg ggacagatgg tcgatgatgg 1320 ttatgaatta ttgtttaaag accattcatg caagatatat gatccaagag ataagtacct 1380 catgacagtt gcaatgaaaa ggaattgctt tccaatagat ttcaatgatg tgtgtttgca 1440 tgcttctaaa aatgagatga atttgacctc tttatgccac agacgccttg ggcattataa 1500 ttattcctcc ttaattcagg ccagcacctc tggtttaatg gaaaacttac cctcactcac 1560 aaaatccaag catgtttgca gcacttgtca atttggaaaa ctcaccagga aaccatatcc 1620 tcatgcaagc tcaagtcgct ctgttggaaa acttgattta gtgcacatcg atgttggagg 1680 cccaatgagt gaagtatctt taaatggcaa taagtttttc ttgatctttg ttgatgattt 1740 atcacgcatg tgctggattt actttatgaa agcaaagtct gaggtgttta gtcacttctt 1800 gaaattcaaa gcacaagttg aaactgaaat aggaaaaaag attaaatcaa tcagatctga 1860 taatggtggg gaatacacat ctcgagagtt cactcaattt ctagaaaaag aagaaatatt 1920 tcatcaaact cacagcccct tattgcccac agcaaaatgg tgttagtgag aggaaaaatc 1980 gaacaataaa tgagatagtg aaatgtctct tgctagaaaa aggacttccc aaaagcttct 2040 gggttgaggc tgccagtaca gctatttatc tgttaaatcg gttgcctttt cgtgcactta 2100 aaaataccca tccttatgaa gtatgatttg aaaaaaaacc atctgtatca catctcagag 2160 tctttggatg cctttgttac cagcatatac ctgaagagca caaagataag ttgcaatcca 2220 aagttgtaat gggagttttt attggttata gtcagcactc aaaggcatac agagtgtatc 2280 atgttgattc tggtaaaatc tctatcagca ggaatgtatc gtttgatgaa ggaagcagtt 2340 ggaattggga caaacctcaa cataccagag ttagtgccac aaacacttta tctgcttttc 2400 aaaatatttc tgatattgag ttagatgaag atgagcttat tgataaagca ccagtcagag 2460 gtactcgcac aattcaagac atttataagc gatgtcaagt ggccttatct gatcctgttt 2520 ctttcgaaga tgcctcacaa catgaagaat ggataaaagc tatgaaagag gagattaaca 2580 tgatagagca aaatcatact tggtcattgg tagacagacc aatcaatggc catgtaattg 2640 atgtcaaatg gattttcaaa cgaaaattca actctgatgg aagccttaac aaaaataagg 2700 cgagattggt cgcaaaaggt tattctcaac ttgctggaat agactgccgt gatacttttg 2760 caccagtggc aagacttgat accatcaaac ttctcataga tctctctgct gcgcttgatt 2820 ggaaaatcta ccacatggat gttaagtctg cttttttgaa tggtaaaccc aatgaagaaa 2880 tattcatcga gcagccaaga ggatttgaag ttggtgacag acaaaacaaa gtatataagc 2940 ttcataaggc attatatggc ctgaagcagg caccacgtgc ttggtacagt aggattgatg 3000 cctacatatt agctaaaggt ttttacaaga gcttgaatga agctactttg tatgtgaaga 3060 aaataaaaaa tgaagtggca gtaattgtgt ctctttatgt tgatgatacc ttgattactg 3120 gtgcagatca agcaagcatc ggggaattta aatcaacaat gaaaaaggag tttcacatgt 3180 ctgatttggg tcaaatgaaa tattttcttg gtcttgaaat tcatcagtcc aaggaaagta 3240 ttactctttc tcaaatcaac tacattcaag aagtcctcaa acgtttcaag atggcagaat 3300 gtaagccaac ttcaactctt ttagttgcac atgaaaagtt atctctcaat tctggtgaaa 3360 tactagagag tcccaatgat tatcgaagtc ttacagaatg tctcctatat atttgttcta 3420 cccatcgaga gataatgttt gctgtaagtt atctttcaag attcatgcag agaccaagtc 3480 aacttcattt ggttgctgct aaaagggttc tcagatattt gagaggtaca acctgtcatg 3540 ggataaattt catcaaaaac gagactattg agcttgttgg attttcagat agtgaccggg 3600 gtggctgcaa cgatgatggt agaagcacat caggctacat attttctctg ggaaatggtc 3660 ttttttcatg gaactctcat aagcagaata cagtggcaca atcttcatct gaggcagaat 3720 atgtggcagc agctgaagct tcaaatcaag caatctggct aaggaaaatt ctacaggatc 3780 ttggcatgga tcaaaccaat cctacaaagt tgtttattga gaacaagttt gcaatctcca 3840 tgaccaagaa tcctgtgttt catggaagaa ccaagcatat caacatcaag caaatcagac 3900 aaaatagcag aaaagaaagg ggagatactt gtgcaatatt gcaaatcaga agaccaggtt 3960 gcggacataa tgaccaagcc tcagttttaa gtcaaggttt gaacttaaca aagataagtt 4020 gatgatgcag gttgcaagca ttaaggagga gtgttgttga taatgcaggc aacaagttac 4080 tgtcagttga aaatagcagc acgacttgta catggaagtt gaaaacatga cgctgtatta 4140 agttattttt aatcatgctt ttact 4165 // ID GmGYPSY10_I repbase; DNA; EDCOT; 6515 BP. XX AC . XX DT 01-JUL-2008 (Rel. 13.07, Created) DT 01-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE Gypsy-like retrotransposon from Glycine max. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW reverse transcriptase; gag; integrase; consensus; soybean; KW GmGYPSY10; GmGYPSY10_LTR; GmGYPSY10_I. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-6515 RA Mogil L.S.; Laten,H.M.; RT "Intact, full-length transposable element consensus sequences in RT Glycine max assembled from robust collections of BAC-ends."; RL Repbase Reports 8(7), 685-685 (2008). XX DR [1] (Consensus) XX CC Complete consensus sequence based on alignment of 320 GSS entries CC with an average overlap density of 35 sequences (range: 17-48). CC LTRs (composites): 1-982; 7498-8479. XX FH Key Location/Qualifiers FT CDS 1920..6512 FT /product="GmGYPSY10_1p" FT /note="Gag-pol." FT /translation="MSLHSSSSVNGEGSTPKDPLYKILDELRSLKLWKEKQ FT ERKEKGKKRVEEISQDEREKIREEERRKIMKEMKREKHASYSSHDSCKSLS FT EELSDYYRGRHSSHTKHHSQRREKDRRPQEVNISLPYFHGKDNVEAYLDWE FT MKVEQLFACHHISEERKVPLATLSFQGYALYWWTSLVXERRIHGDPPVEYW FT NDLKSALRKRHIPSYYERELMDKLQRLRQGSMSVEEYRQQMELLLLRAGLR FT EEERTSIARFLSGLNMEVRDKVELLPYRDLDELVQLCIRVEQQLKRKPSSK FT SYGSHSYPRKDQAHGILGAAPSKPKEDKGKTIEKYTPKTSSQERTSNIKCF FT KCLGRGHIASQCPTKKTMIMRGQDIYSSQEETTSCPSSSGSEDEVRGEESS FT EEVYPHEEGDLLMVRRLLGGQSCDLSQSQRENIFHTRCKILDKTCSLIVDS FT GSCCNCCSTRLVSKLNLTIIPHPKPYKLQWLNEQGEMIVNQQVKVPFSIGT FT YKDEVNCDIVPMEAGHILLGRPWQFDRKIIYNGLTNEITLTHLGTKFVLHP FT QTPSQVAKDQLTMKDKRDEEEKLEKQKKKKDSKALSSKAKGKEKEEKDSSK FT KIVKKENHFATKGDIKRALLLKQSFYLLLSRETSLSTATIPTFETLPPKVQ FT ELLHEFGDIFPKEIPPGLPPLRGIEHQIDLVPGASLPNRPAYRTNPQETKE FT IESQVKELLEKGWVQESLSPCXVPVLLVPKKDGTWRMCTDCRAINNITVKY FT RHPIPRLDDLLDELHGANIFSKIDLKSGYHQIRMKKGDEWKTAFKTKFGLY FT EWLVMPFGLTNAPSTFMRLMHHVLRDFIGRFVVVYFDDILVYSRSLDDHLG FT HLRQVLSVLRKNTLYANIEKCTFCVDNIVFLGFVVGRNGVQVDPEKIKAIQ FT EWPTPKSVGDIRSFHGLASFYRRFVPNFSTIASPLNELVKKNVAFTWGEKQ FT EQAFALLKEKLTKAPVLALPDFSKTFELECDASGVGVGAVLLQGGHPIAYF FT SEKLHSATLNYPTYDKELYALIRALQTWEHYLVSKEFVIHSDHQSLKYIRG FT QSKLNKRHAKWVEYLEQFPYVIKYKKGKTNVVADALSRRHTLFCSLGAQIL FT GFDNIRDLYALDEHFSPIYESCGKKAQDGFYLAEGYLFKEGKLCIPQGSIR FT KLLVKESHEGGLMGHFGIDKTLVLLKEKFYWPHMKKDVHKHCTRCVACLQA FT KSRVMPHGLYTPLPIPSAPWVDISMDFVLGLPRTQRGVDSIFVVVDRFSKM FT AHFIPCHKVDDASHISKLFFXEVVRLHGLPRTIVSDRDAKFLSHFWKTLWA FT KLGTKLLFSTTCHPQTDGQTEVVNRSLSTLLRALLKGNHKSWDEYLPHVEF FT AYNRGVHRTTKQSPFEVVYGFNPLTPLDLIPLPLDTSFIHKEGESRSEFVK FT KLHERVKNQIENQTKVYSTKGNRGRKELVLNEGDWVWLHLRKXRFPTKRKS FT KLSPRGDGPFQVLERINNNAYRLDLPXEYGVSTTFNISDLIPFAGGADIEE FT EEXTDLRSNPLQGXG" XX SQ Sequence 6515 BP; 1992 A; 1170 C; 1353 G; 1957 T; 43 other; tgtggtatca agagcatctt catctaggtg atgttctttt gcttcctcta tctttttgtt 60 cggtgaattc tctttaattc cttgttcttc atcttattct ccatgtatat cctccattgt 120 cttgtggttt ggtgctgttt agagtagatt aaaaaaaaaa aaccgattaa atcttagatc 180 tacacttgtt cttgcatttc tatggttcaa attttgtaga tctactcttg aatcttgttt 240 ttgtgttgat tttaggttct atcawttttc attcataata ttcttgtgct gaacctttag 300 atctaaattt tsttccaaaa tattgattag aaaaaaaaaa cacaaaaatc taagtgtaaa 360 tcacttaatc catgttgtct tagagtcatg tttagtcata gtaattgtca cattatgctc 420 taagtttgtg ttgaattttt attttgttkw ttgaattcta gatacatttk ttcatgtatt 480 cttgtcattc ttagcctatc ttttgaattt tgagtctaat tcatgcatgt tatttagttc 540 ataacatgtt ctaaatcaat tcctagaagt agtcttgtts ttgaactctt ttttgttttc 600 taagwttcct acatgatgcc tatgatgaag ttgagwtgtg gtgytgagtt gtggctggat 660 ttgtgaatca aataagtctt aagctctctt gaattgtgtt attcaagata attgagcata 720 agcaaacaca aattgtaact atccaagcct taagcaacat aaacactact cttgatttct 780 aggttgaaat cgctggtgct ggcagcttga acatacraam ttgtataaat tactgggaat 840 tggtcactac gttttttgag ctgaaacttt tactgaattt tctagacatc tggaccaaaa 900 ttataaaaaa agaaccaagc gatttggatt aaaggaaaaa ataagaaaaa tctcacaagt 960 tggcagaaaa atcagtgtcc aggaaaaaaa aaaaaagtga aaggaaagtg tgcttgttgt 1020 tttggctcaa aatttgttct ataattggtg cctattttat accaatccta gttctgaaat 1080 ttcaattgaa aattattgtg aaaacaagtg ccaaaactag aggtttcttg agtctttttt 1140 tttwkagttt ttctactcta ctctagagcc attctaggtt tctctttgag tcctagcttg 1200 ctttttgtgc ttttcattgc tttaattgtt gaataatcct tggaaatttg tcttgttaaa 1260 actctattgg tttagctttc atttcatttt ttttkgtctt tggttattgc ttgtctcttt 1320 gtttccttgc ttgtgagttg ccatataggg aattggaaag gaggattggt gccatatctt 1380 gaagaatttg agtcaagaag caaggggcca accaccttaa gagctattgg actaagaagc 1440 actccaaatt gagtgaaaca ctaaagagag aatagccacc acaattgagg acttttttyt 1500 ttgtaatttt gtaattggca atttgctttg ctttcaaatt ttgtaacaaa aaggcctttc 1560 attggaagta agttgggagc ctccgctagg tcaccctact tccatttgtg tgtaataatt 1620 ttaggcaatt tycccttagg atagtgagtg ttttgttggg aaccttaaat gaggtcatcc 1680 aaacactctt aggatccgcc tagtttgcat ttcttgcact ttaatttctt gcttactttc 1740 atagcttatt tcctttaccc tccattgtca aaccgcctag atagcttkcc ttttaccaat 1800 tagtttttac cttatctttc acacctcttt tagtgtttat tttggctagt ttcaaccata 1860 gtttctttta cctttttttc aaacccccaa caagaaagaa ccataactta ggaaccaaca 1920 tgagtcttca ttcttcatct agtgttaatg gtgagggttc tactcctaag gaccccttgt 1980 ataagatatt agatgagttg agatccctta agttgtggaa agaaaaacaa gagagaaaag 2040 aaaaaggtaa aaaaagagtg gaagaaataa gtcaagatga aagagagaaa ataagagagg 2100 aagaaagaag aaaaataatg aaagaaatga aaagagaaaa acatgcctcc tatagtagtc 2160 atgactcttg caagagttta agtgaagaac ttagcgacta ttatagaggg cgtcatagtt 2220 cacatactaa acatcactcc caaagaagag aaaaggatag aaggcctcaa gaggttaaca 2280 ttagcctccc atatttccay ggaaaagata atgttgaggc ctacttagat tgggaaatga 2340 aggttgaaca actctttgct tgccatcata ttagcgaaga gagaaaagtt ccattggcta 2400 cccttagctt tcaagggtat gccctctatt ggtggacttc ccttgttarr gaacgaagga 2460 ttcatgggga tcctccagta gagtattgga atgatcttaa gagtgccctt aggaagaggc 2520 acattccctc ctactatgaa agggagctta tggacaagct ccaaaggctt agacaaggga 2580 gtatgagtgt tgaagaatat agacaacaaa tggaactact ccttttaaga gctggactta 2640 gggaggagga aagaacaagc atagctaggt tccttagtgg gctyaatatg gaagtgaggg 2700 acaaggttga actccttcca tatagggacc tagatgagct agtccaactt tgtataagag 2760 tggagcaaca acttaaaaga aagccttctt caaaatctta tggctctcac tcttatccaa 2820 ggaaggacca agcccatgga attttagggg ctgcaccttc aaaacccaag gaagataagg 2880 gtaagaccat agagaaatac acccctaaga ctagttccca agaaaggact agcaacatta 2940 aatgcttcaa atgtcttggg agaggtcaca ttgcctctca atgccccaca aagaaaacca 3000 tgatcatgag gggtcaagac atttatagta gtcaagagga gactacttct tgcccttcct 3060 ctagtggaag tgaagatgaa gtaaggggtg aagagtctag tgaggaagtc tacccycatg 3120 aagaaggtga cctcttaatg gttagaaggc tccttggagg tcaatcttgt gatctatctc 3180 aatcccaaag agagaacatc tttcatacaa gatgcaaaat tttagataaa acttgttctc 3240 tcattgtgga tagtggatct tgttgcaatt gttgtagcac aagattagtt tccaagttga 3300 acctcactat cattccccac ccaaaacctt ataaacttca atggctcaat gagcaagggg 3360 aaatgatagt taaccaacaa gtgaaggtac ctttctccat tgggacatat aaggatgaag 3420 ttaattgtga tatagttccc atggaggcag gacatattct tttaggaagg ccrtggcaat 3480 ttgataggaa gatcatttac aatggcctaa ctaatgagat taccctcacc catcttggca 3540 ctaaatttgt gttgcatcct caaacacctt cacaggtggc caaagatcaa ctaactatga 3600 aagataagag ggatgaggaa gaaaaactag aaaaacaaaa gaaaaagaag gatagtaagg 3660 ccttgtcttc aaaggccaag gggaaggaaa argaggaaaa ggattcctcc aagaagattg 3720 ttaagaagga aaatcatttt gcaacaaaag gtgatattaa aagagcactc cttcttaaac 3780 aatctttcta ccttctccta tcaagggaaa catcccttag cactgccaca attcctacat 3840 ttgagacctt acccccaaag gtccaagaac tcttacatga atttggtgat atatttccca 3900 aagagatacc ccctgggcta cctcctttaa ggggaataga acaccaaata gatttagtcc 3960 caggagcaag ccttcctaat aggccagcct ataggactaa ccctcaggag actaaggaga 4020 tagagtctca ggttaaagaa ttgttggaga agggctgggt ccaagagagc ctaagcccat 4080 gtgytgtgcc agtgttgttg gtgcccaaaa aggatggtac gtggagaatg tgtacagatt 4140 gcagggccat caacaacatc actgtaaagt ataggcaccc cattcctaga cttgatgatt 4200 tgcttgatga gttgcatggt gccaatatct tttcaaaaat tgatcttaaa agtggttatc 4260 accaaatcag gatgaaaaag ggtgatgagt ggaaaacygc tttcaagacc aagtttggtt 4320 tgtatgaatg gctagtgatg ccttttgggc tcactaatgc accaagcacc tttatgaggc 4380 ttatgcatca tgtcttaagg gatttcatag gtagatttgt agttgtttat tttgatgata 4440 ttttagtgta yagtaggagc ctagatgatc acttaggaca tctcagrcaa gttctttcag 4500 tccttaggaa aaacaccctc tatgcaaata tagagaagtg taccttttgt gtagataata 4560 tagttttctt aggktttgta gttggtagaa atggggtcca agtggaccct gagaaaatca 4620 aggccatcca agaatggccc accccaaaaa gtgtgggaga tattaggagc ttccatgggt 4680 tagcaagctt ctatagaagg ttcgttccta atttctctac aattgcatca cctctcaatg 4740 agctggtgaa gaagaatgtg gcatttacct ggggtgaaaa acaagagcaa gcctttgctt 4800 tgctcaaaga aaagcttact aaggcacctg ttctagctct tcctgacttt tctaaaactt 4860 ttgagctaga atgtgatgcc tctggagtgg gagttggagc tgtattgtta caaggtgggc 4920 accctattgc ttattttagt gaaaaacttc atagtgccac cctcaactac cccacctatg 4980 ataaagagct ttatgcctta ataagagccc tccaaacttg ggaacattac cttgtttcca 5040 aggaatttgt cattcatagt gatcatcaat cacttaagta cattagaggg caaagcaagt 5100 taaacaagag gcatgcaaaa tgggtagagt acctagagca atttccatat gttatcaaat 5160 acaaaaaggg aaaaacaaat gtggtagctg atgccctctc taggagacac acattgtttt 5220 gctccctagg agctcaaatt ttaggatttg ataatattag ggacttgtat gctttagatg 5280 aacatttctc tcccatttay gagagttgtg ggaaaaaggc ccaagatgga ttctatttgg 5340 ctgaggggta tttgttcaaa gagggaaagc tttgcatacc ccaaggatcc attaggaaat 5400 tacttgtgaa agagagccat gagggtgggc tcatgggcca ctttgggata gacaagaccc 5460 ttgtcttact caaagaaaag ttttattggc cccatatgaa gaaagatgtc cataagcatt 5520 gcactaggtg tgtggcttgt ttacaagcca agtctagggt gatgcctcat gggctataca 5580 cacccttacc catcccatct gcaccttggg tagacattag tatggacttt gtccttgggc 5640 ttcctagaac ccaaagaggt gtagactcta tctttgtggt ggtggatagg tttagcaaga 5700 tggcacactt tataccatgc cacaaggtgg atgatgcttc ccacatctca aaactctttt 5760 tcarggaagt tgtgagactc catggtttgc ctaggaccat tgtgtcagat agagatgcta 5820 agttccttag ccacttctgg aaaaccttat gggctaagyt aggaactaaa cttcttttct 5880 ctaccacttg tcatccacaa actgatgggc aaacagaggt agtgaatagg tctttatcca 5940 cccttttaag ggctcttctg aaaggcaacc ataagtcttg ggatgagtat cttcctcatg 6000 tagaatttgc ctacaacagg ggggttcata gaaccaccaa gcartcccct tttgaggttg 6060 tctatgggtt caatccccta acaccsttag acctcattcc cctcccactg gacacttctt 6120 ttatacataa agaaggggaa tctaggtcag agtttgtaaa gaagttgcat gagagggtta 6180 agaaccaaat agagaaccaa acaaaggtgt attcaactaa rggcaataga ggaagaaarg 6240 agctagttct taatgagggk gactgggttt ggctccatct taggaaggaw agattcccta 6300 ctaaaaggaa atccaagctt agccctagag gggatggacc ttttcaggty ttggagagga 6360 tcaataacaa tgcctatagg ttggacctcc caraagagta tggagtcagc accactttta 6420 ayatttctga tttaattcct tttgcaggtg gagctgatat tgaggaggag gaacyaacag 6480 atttgaggtc aaatcctctt caaggggrag gggat 6515 // ID EnSpm-1_Mad repbase; DNA; EDCOT; 4174 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous EnSpm elements, consensus. XX KW EnSpm; DNA transposon; Transposable Element; EnSpm-1_Mad. XX NM EnSpm-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4174 RA Kojima K.K. and Jurka J.; RT "EnSpm-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1601-1601 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~93% identical to consensus. Both termini are incomplete. XX FH Key Location/Qualifiers FT CDS join(569..2836,2878..3399,3399..4151) FT /product="EnSpm-1_Mad_1p" FT /note="transposase." FT /translation="MDRQWIHNHNRCDVEYLDGIDEFIEFATRHNLGSTHI FT RCPCRRCNNSMWETFENVRFHLVRNGMMETYTTWYHHGERLDQASSSYVTR FT VETVESNVDPNEQVMNILNDVYPYASSNTNQEGGDDGRPTMDSEAFKNYEK FT LLKNAKQELYPGCENFSVLTAIVELMHGKIKFRLSNKCFDYFLGVIKRMLP FT KENCLPEDHKSAQKVLKGLGLGYEKIHACVNNCILFYKENKQLDKCPVCNE FT PRFKMTSQNRKTKIPQKVMRYLPLKPRLQRLYMSMHTATDMRWHKEGRVND FT DVMRHPADGEAWKEFDRMYPDFAADPRNVRLGLATDGFNPFGVLNQTHSTW FT PVVVFPYNLPPWKCMKKEYMMLTLLISEDPGKSIDVYLRPLVDELKDLWEN FT GVRTYDKYTGQMFTMRAAVMWTVNDFPAYAMVSGWMTKGYLACPICKENVT FT SSWHARKVCYLGHRRWLPWDNEWRQNDKAFHGTKETRPRPREWSGDEILDQ FT LNRLEFGHFGKGVSKPRPTTHLNWTHKSMLFELPYWSKLKLRHNLDVMHIE FT KNVFDTLVGTILDIEGKTKDTIEARLDLERMGIRSSLWMKSVGGTLKKGHP FT FFTVKPNGKKEFFNFISSVKFPDGYASNISRCVNVKGCKFSNMKSHDCHVI FT LQRLLPVGIRHLLPLDVVKPIVLLSRFFSQLTARCLRKSDVKQLQDDIVNV FT LCKFEQIFPPAFFTSMIHVMIHLPDEALLAGPVNCRWMYPIERYLIKRVIY FT IYIYIHTFYLCRYLGELKKCVRNKAKPEGSLVEAWVAYESLTFCAMYLEDV FT ETAFNRPQRNNDGGVRKEKLSVFAQIARPFGDPVKGESFTKKDMEVAHWFI FT LNNCDEALPYLEEHEQLMKREHPSHLYAKKHRDLFPSWFHAHVSCMWFELS FT IFSNLFMPVFKFGYTNRLTFCICYIRMNKLKELNSPSYDEELYNLARGPLH FT VELFSGCHVNGIKFLGATRDDKLSTQNSGVHVPGAGDSEDIDFYGKLTSVV FT QLLYKDRCQVILFKCLWFDTNPHNRTSVKRDHGLLSVNTTRRWYDEDPYIL FT ATMAKQIFYLDDPKAGNGWKVVQKIDRRGLYDIPELDHDDNDDNVADQQLS FT SSIEIGEETLRDTNIVQEPFDVPGVPEFEISIDLGDLPQYNAPEEANEDED FT EWESGNDSSEDSESYYCSSDED" XX SQ Sequence 4174 BP; 1248 A; 718 C; 988 G; 1220 T; 0 other; aattgatctt tattaatttt atctatttta tttagtttta gtaattattg tgatttagtt 60 tatttgtatg cacatatttt tgtacatcac gtacaaaatt gttttgtgtt gtacgaagtt 120 aatactactt aacttcgtac acttttttca agaaaagctt agtttcccgt ttgagaatta 180 gttggatttc gtgcatggat gcgaaagcat gactgcggtc caattaattc ttgaattgtc 240 ccattttttg gacagtttgg gaatgcatag ttatgtgttg tagtttgcgg ttcacggatt 300 aggtttcgat agtggaaatt ttggtaacat ttcctgatgt tcttcgagta cacggtggat 360 attatgtatc tacggcgtgc acttgaagaa ctgtaaggag atgctgccga aattagccca 420 cgtcgaaatt taatccattg gaatcgtaaa ttacggcaca taactgtgca ttcctgaatg 480 ggatagggcc cttaccggag gaataaggtg acaagacaat agttgaagtt gttgtaattc 540 ttgtactttt attgggattg cagacaaaat ggacagacag tggatacata atcataatag 600 atgtgatgtt gagtacttgg atggaataga tgagttcatt gaattcgcaa ctagacacaa 660 cctaggttca actcatatcc gatgtccatg taggaggtgt aacaactcaa tgtgggagac 720 attcgaaaat gttcgatttc atttagtaag aaatgggatg atggagacct atactacttg 780 gtatcatcat ggagaacgat tagaccaagc ttcgtcttca tacgtgacac gagtggagac 840 tgttgaatct aatgtggatc ctaatgaaca agttatgaat attctaaatg acgtttatcc 900 atacgcctcg agcaacacca atcaggaagg gggagatgac ggtcgtccaa ccatggacag 960 tgaggcattc aaaaactatg aaaaactatt gaaaaatgcc aagcaagaat tatatccggg 1020 ttgcgagaac ttttcggtgc tcacagcaat tgtggagttg atgcatggca agatcaagtt 1080 tcgtttgtca aacaagtgtt ttgattactt tttgggagtt atcaagagga tgcttccaaa 1140 ggagaattgt ttacctgaag atcataaaag tgcccaaaaa gtgttgaagg gtctcggatt 1200 ggggtatgaa aaaattcacg catgtgtaaa taattgtata ttgttctata aggagaacaa 1260 acagttggat aaatgccctg tctgcaatga gccgaggttt aaaatgacat cacagaatag 1320 aaagaccaag attccacaaa aagtaatgcg ttatcttcca ttgaagccta ggttgcagcg 1380 attgtacatg tcgatgcata ccgcaaccga catgagatgg cataaagaag gacgggtaaa 1440 tgacgatgtt atgaggcatc ctgcagatgg agaggcatgg aaagaattcg atcggatgta 1500 ccctgatttt gcagctgacc cgcgcaacgt cagattggga cttgccaccg atggatttaa 1560 tccgttcggg gttttaaacc aaacccacag cacttggccg gtcgtcgtgt ttccttataa 1620 tctgccacct tggaagtgca tgaaaaaaga atacatgatg ttgactctat taattagcga 1680 agatccagga aagtccattg atgtttattt gcggccgttg gttgatgagc taaaagattt 1740 atgggaaaac ggtgttcgta catacgataa gtatactggg cagatgttca ccatgcgagc 1800 ggcagtgatg tggacagtaa acgattttcc cgcgtatgca atggtttctg ggtggatgac 1860 taagggttat ttggcatgtc caatatgcaa ggagaacgta acatcgtctt ggcatgcgag 1920 aaaagtttgt tatcttggtc atcgtagatg gctcccttgg gacaacgagt ggcgtcagaa 1980 cgataaagcc ttccacggca caaaagagac tcggccaaga ccaagagaat ggtccggaga 2040 tgagattttg gatcagttaa accgtttgga atttggtcat ttcggcaaag gggtcagtaa 2100 gcccagacca actacacatc tgaactggac gcacaagagt atgttatttg agctcccgta 2160 ctggtcaaag ttaaaattga gacacaacct cgatgttatg catattgaga aaaatgtgtt 2220 tgatactttg gtcgggacaa ttctagacat tgaaggaaaa acgaaggaca cgatcgaagc 2280 tcgcctcgat ttggaacgaa tgggcattag gtcatccttg tggatgaaga gtgtcggtgg 2340 tacattgaag aaaggccatc ctttttttac agttaagccg aatgggaaga aagagttttt 2400 caactttatt tcttctgtaa agtttccaga tgggtatgct tccaatatct cgcgttgcgt 2460 gaacgtgaag gggtgtaaat tttcaaacat gaagagtcat gactgtcatg tgatactcca 2520 acgccttctt ccggttggta ttcgacactt attgcctctt gatgtggtga aaccaatcgt 2580 gttgttgtcg agattttttt cgcagttgac tgcaaggtgt ttgcggaagt cggatgttaa 2640 acaattgcag gacgacattg tgaacgtctt atgcaagttc gaacagatat ttcccccagc 2700 tttctttaca agtatgattc acgtgatgat tcacttgcca gatgaggcat tgcttgccgg 2760 accagtgaac tgtcgatgga tgtatccaat agaaaggtac ttaattaagc gtgttatata 2820 tatatatata tatatataac atattcatga tcaacgaacg ctttgaataa tttgtagcat 2880 accttttatt tgtgcagata tcttggtgag ttgaaaaagt gtgttcgaaa caaggcaaag 2940 cccgaaggat cacttgtgga ggcatgggtc gcatatgagt cacttacttt ttgtgcaatg 3000 tatcttgaag atgttgagac agctttcaat cgtcctcaac gcaataatga cggtggtgtc 3060 agaaaagaga aactgtctgt ttttgcccaa attgcgcgac cattcggcga tcctgtaaaa 3120 ggcgaatcgt ttaccaaaaa ggacatggag gtagcgcatt ggttcatact caacaattgt 3180 gacgaggctt tgccatacct tgaagagcat gaacaattga tgaagcggga acatccttca 3240 catttatatg ccaagaagca ccgtgacttg tttccttcgt ggtttcacgc acatgtaagt 3300 tgtatgtggt ttgaattgag catattttcc aacttgttca tgcccgtctt taaatttggt 3360 tacactaaca ggttaacttt ttgtatatgt tatattagat gaacaaattg aaggaattga 3420 attcaccctc ttacgatgaa gaattatata acttggcgag aggaccgctt cacgttgaat 3480 tgttctcagg ttgtcatgtc aacgggatca agttcttggg ggcaacacgt gatgacaagt 3540 tgtctactca aaatagtggt gtccatgtcc cgggtgcggg cgacagtgaa gacattgatt 3600 tttatggcaa actaactagt gtagtacaat tgctttacaa agacaggtgt caagtgatac 3660 tgtttaagtg tctttggttt gatacaaacc cacataaccg aacgagtgtt aagcgagacc 3720 atggtttact atcagtaaac actacgagac gttggtacga tgaagaccca tacattttgg 3780 caactatggc gaaacaaata ttctatctag acgaccctaa agccggcaat ggttggaaag 3840 ttgttcagaa gattgatcga agagggctat atgatattcc ggaactagat catgatgaca 3900 atgacgacaa cgtcgctgac caacagttat catcttcgat agaaattggt gaagaaacac 3960 tccgggatac taatattgtc caagaaccgt ttgacgtacc tggagttccc gaattcgaaa 4020 tatcaattga ccttggtgat ctgcctcaat acaatgcacc ggaagaggca aacgaagatg 4080 aggacgaatg ggaatccgga aatgatagta gtgaggatag cgagagttat tattgtagtt 4140 cggatgagga ttaatataaa cttgtaaagg aaaa 4174 // ID Gypsy-26_VV-LTR repbase; DNA; EDCOT; 2555 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-26_VV_; KW Gypsy-26_VV-I; Gypsy-26_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-2555 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 13419547 13416993. XX SQ Sequence 2555 BP; 645 A; 469 C; 502 G; 939 T; 0 other; tgtttggtta ttttgggtag agatccgagg gctgttggag agattagcta gagaaggagg 60 tttttgcttt ttgagaggcc gttatagata ttttgaggag cagactggtt ctggagaggt 120 tttccattgg agaagcaagc tgagagaacc ggagtgctgc ctggagatat tagacgagag 180 agagagaaca gggaggtttg gggttggagc agagaggtga gcttttggga gaagaaaaaa 240 gaggtatgga taccataaat caggggattt actttatcag tagatagtct tgttattttt 300 ctctcagtag tggtggtaga ttgtttgatt atgtgtttga tttcatgatt catatttgag 360 ttaatggttt attactgcta cattcttcac ttctctgatt ggttttttga gagtggctct 420 gttctagctt caccatatat catatagaaa tctttgtttt gtttcatttt gcttgcaaca 480 ccaagtgata tttggcttga tttcactcac catcatcaaa gctcgttgat aaaaatacgg 540 aacttggctt gtatgaacct ttttttttgt ctctaccatg tgtgccctgt tttagctacc 600 ttcccctgtt tctgatattg gtcctggtga gcatctattt tctcatctct gctcgaagga 660 gcaaggaatt tccaataata tatttcagca gcaatcctgg gtctcaatac tactgttatg 720 gttctgaggt tgtttgcaag ccttgtaaag ttttggtact agggtcgccg gtgccattat 780 cgccggtgtc accgccgtca gtttctccac cgtcgtcccc gtccatagct ttatccaggg 840 gtttattagc ttttgccatt gttggatcag tcggggcctt ttcgggcatt tgcaccataa 900 tttattactt gtggactgga gtctgttgtg ggcacaagaa gatccacaac tctgtgcagc 960 caataattgc tcgaggcaat tctaatgggg atgctgatat taatttagtg cagtccgtga 1020 ttaatcccga tactaggctc gtatcggtga tggcagtaag taatgagatt ggcgtgattc 1080 aaccggtcga agaaataagg gatatatgta gagagttgtt ctgtttcatg ctgatgtggc 1140 tcaggctttg agcaagattc ctggtgatgt atagaagacg cagtttagct ggcactaaag 1200 gtactgagca agacaatgga cagcacgggc cttacttcgg actgctggag ttgttctggg 1260 gtgtaacgaa gatcaaccag gcgcgggcca tcgcgtgcct tgctgctaag tggcatatat 1320 gcgccacaat agacacattc gaatccaatg aatccgagag ccccaaagac ccggattccc 1380 tatccatgtg ccccgttcct ctattcccat acatactttc aaaacggatt tcataaaaat 1440 ctcattctta ttggtttttt ttattcttta tctctcattg tttcttgatc ttaaataagt 1500 ctaatttcaa taaatcaact cttgctattc tcctcagggt atgccttttt cattttgctt 1560 atttatttat tttctattat tgttactata tttattttca tctcttttat tttattttat 1620 ttcatttatt ttatctttta ttattattat cattattact ccctttatta tcattattat 1680 tttatctttg ttgattttaa aatactccat taaattctag ctttcaaata gtttttccaa 1740 attccatttc tatcaaacaa ttttatttta tttttattta tttaatttat ttttcaaatt 1800 ttcatcttta gaatttttag gatcacttaa aaatctcttt tccaataaaa tattgttgcc 1860 atctttcctt ctggcaaaat attttcacac ttccttgatt ttaaaatgtt ttaaaataag 1920 taaggattaa attccgtaat tccaagtgat ggaatttatg gaattaattc atgcaaaaat 1980 gaattgggtc ttggtggggg ccctacatat gagattccat gattgattga tttatttgtc 2040 atgcatgatt gatttactct attccttgat atgcgcttaa ttatatctgt tcataattca 2100 ctaaccctgt tccatgatag cgcgttgctg tttgccgccc aggtgcgcat ctattcatat 2160 ttcgcctatt ctttatacat gctttacttc tcatattgtg catgatcgat ttgagtattc 2220 atcgttttcc tcattgattg ccacgtcagc ttcattctat tagtagagac ccgactttag 2280 ggacttagag gggtgctacg gtctttaccg taccttcccg ataagtaacc tgacccccga 2340 acctagtccg gtttttcaca gaccgccttt tccaaaataa ggagtcacac ttagggtttt 2400 tctttcttat tttgtttacc ctttaaaaat aaaacaaaaa taagtggtga ctccaagtca 2460 ttttcttaat caataaaaat caaattttga aataaaaatc gagtttcgcc atcgagtggg 2520 aaacgcattc gagcaatcga aatgcggggt ccaca 2555 // ID HAT-4_Mad repbase; DNA; EDCOT; 5449 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-4_Mad. XX NM HAT-4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5449 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1615-1615 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~94% identical to consensus. XX FH Key Location/Qualifiers FT CDS join(1839..3506,3869..4570) FT /product="HAT-4_Mad_1p" FT /note="transposase." FT /translation="MSSGVTKRDPAWEHGDPIDGNKHGTICKYCGRVMKSG FT GVTRLKYHLSGLDPANNVQRCDNVPPEVKAFITTLLKNKKQQKEKITHGME FT NIRAGLRGEVIGQAVDSDDDDDEDECDDDMGPEERRSLKQALRASKQSAWE FT REHLHKIPNRAQGSGTSGGAQMRRGGSLRESQPTPPIAPSLYKSSKARQKS FT VWSYFTGGNVKEGMGRLISKFFIYENVPAEKASSHHFKNMVVGCQQAGVGV FT QPPTPYEIRNKYLDMEYKDIGEYVNKLRSKWETNGCTIMCDGWTGPTRLSI FT INFMVYSKGKTIFLKSVDASDHIKNYKYIYKLLRDVIMEVGEHNVVQVVTD FT NGSAFVKAGKKLMKHHNVFWTSCAAHCIDLMFEAMGKRENVATVVKRARTI FT TNYIYNHGWLLAKMREFCKGEIIRPATTRFATNYIALDSLLKKKAGLKQLF FT TSDDWANHNFSRSNAGRMVESIVLDHAFWTQSEHVCQVFEPLYKVLRIVDT FT EVYPTMGAIYELMRVVKDELERKHGARWVIKIIEDRWYKTLYHDLHAAGIN FT YVIICNSFLNLLELLGLSTLFFIVAEWWIMYGTDAPTVRKLAIKVLSQTAS FT SSACERNWSTFALIHTKQRNRLAHSRLEKLVYCYYNMKLQIRDKEAEIDHV FT DRGDPLDVFDIVGEDDDTEGNQLYQWIRPLHLDDDEGNPAPRVAEEARNEG FT INVERVLEEEVGSSSADSLEELLRPRPRNTGIPPSSNPTQPQHRADTNDSS FT STRSGDSPTTGGGNDEGYSGAGGSGGGYGNYVGHHLPDL" XX SQ Sequence 5449 BP; 1669 A; 958 C; 1249 G; 1571 T; 2 other; cagtgtatta aatatcgata atatcggcga tatttcgccg atattatcgt ttttcagagg 60 caccgatatt ttcccacgta tccgtctcat tatcgtcaaa atatcgcgat attatcgata 120 atatcgcgat atattcgata ttatcgaaaa agtcgtcgtg gatccgtcgt cggaaaggca 180 gccgaggctg cgtcgtccca gctgcccaga tctctctgca atccatgctc aaacccaaga 240 tctgcgcctc aacgacgccg attcccccgc cgttgtcgaa gtcgcggcga aagagctcgc 300 agaacggatc gcagttgtag atccagaacc cgtggtctgt ccccacggcg aagcaggcgt 360 ggtcttggtt gaagcagacg tggaacagag acggaggcga gcgcggcgcc ggcggggcag 420 gctccggggg gaggaggaga atgggtggtt gttgtggagg ttgaggttgg ggtttggggg 480 cgattggggg tcgtggtggt cgtcgctgga gtcaacgaca gaggtggggt tgttgtcggt 540 gggatcggtg aggaaggcgg agaaggatca agagaactcg ccagagagtt cctgggttcg 600 ccgacgaggc ggaakacgcg gacgaggagg aaggcgaggg aggaggagaa ggccatgtgg 660 gagaaggatc gagaaaggtc tctgtgcgtg tgtgtgggag aagggagaag agagaaggat 720 cgagaattcg agagatctgt gagattgtgt gtgtgtttgt gggagaaggg agaagggaga 780 agagagaagg atccagagac gactgacgtc tctgtgtgcg tgtgttgttg tgcgtgtgtg 840 gtgtgcgtgt gtggtggcgt gtgtgatccc tgtgtgtgcg tgtgtgtgtg tgtcggtggc 900 gtgtgtgtgt gtgtgtgtgg tgtgtgacgg tgtgagaaaa gaaaagcatc taaataattc 960 aacttttaca gcttttagga atggtacaat ttttgacaag acaaaaataa tggtggtttc 1020 atgcatcaag attcaaaacc gtgtgccacg cgtgatattc tttcacattc tcagaggtgg 1080 agtatcagat gatcacacat tttttgacca tggacaaaaa taatggtggt ttcattcaaa 1140 agcatctaaa taattcaaaa cccagacaac ttttacaatt acaacttgta caatttcaga 1200 ccatggacaa aaataatggc ggagtatcag accatggaca acttttacaa tttcagacca 1260 ttcaaaatcg tgtgccactg tgttattctt tcacattctc agaggtggag tatcagatca 1320 tcacacattt ttttgaccct tcgaaaatta aaacctctat tacacatttt cgtttcttct 1380 tcttccctta cccctttcag agccattcca gatctattcc agaggttcaa cacaaagggt 1440 tccatattta aggtaagttt acgaacttat atttatatta ttgtaattta tacaacaaat 1500 tgtgtggacc aatacttgca tgttaatttt ttgaagtaat taagtaatgt tgtataatta 1560 ttccctagaa taattttaat atgtttaatg ttatttatta ttttattatc aaattggatt 1620 attattcatt aatattaggt tttattattc catattattt ttataattac ttaaattctt 1680 acaatcattt tctttacttc ctatttaatt cttctgtaga ataactttac ttcctatttt 1740 ctttacttcc tatttaatat gtttccgtca ctactatatt ttttggccaa aaaataattg 1800 cctaattttc atgaaaaata aatataggta cgtttaagat gtccagtgga gttactaaac 1860 gtgatccagc ttgggaacat ggagacccaa tagacggaaa caaacatggc acaatttgca 1920 aatattgtgg tcgggtaatg aagagtggcg gagtgacacg acttaagtac catcttagtg 1980 gattagatcc agcaaataat gtccaacgat gcgataatgt ccccccagaa gtgaaggcat 2040 tcatcaccac attattaaaa aataaaaaac agcagaagga aaagataaca catggaatgg 2100 aaaatattcg agctgggcta cgaggagaag tcattggcca agcggttgac agtgatgatg 2160 atgacgatga ggacgaatgt gatgatgaca tgggacctga agaacgacgc agtttgaaac 2220 aagcattacg tgcctccaaa cagtcagcat gggaaagaga acaccttcat aaaattccta 2280 atagagcaca aggttccggg acaagtggtg gtgcacaaat gagacgggga ggcagtctta 2340 gagaatcaca accaacacca ccaatagccc caagtttata taagtcatcc aaagcacgtc 2400 aaaagagtgt ttggagttat ttcactggag gtaatgtgaa ggagggaatg gggcgtctaa 2460 ttagcaagtt ctttatctat gaaaatgtcc ctgctgagaa ggcatcatca catcatttca 2520 aaaatatggt agtgggatgt caacaggccg gtgttggagt acaacctccc actccctatg 2580 agataagaaa caaatatttg gatatggagt ataaagacat tggcgagtat gttaacaagt 2640 tgaggtcaaa gtgggaaact aatggttgca caatcatgtg tgacggatgg actggcccga 2700 ccagattgtc tatcataaac ttcatggtat actccaaggg aaagacaatt tttttgaagt 2760 ctgttgatgc ttcagaccat ataaagaact acaagtatat ttacaaatta ttgagggatg 2820 taatcatgga ggtgggagag cataatgttg tccaagtcgt gaccgacaac ggttctgcat 2880 ttgtcaaagc tggaaaaaag ttaatgaagc atcataatgt gttttggaca tcatgtgcag 2940 cacattgtat tgatctcatg tttgaggcaa tggggaagag agagaatgtt gctactgtgg 3000 taaaaagagc tagaacgatc acaaattata tttacaatca cggttggttg ttggcaaaga 3060 tgcgtgaatt ttgcaaagga gaaattattc gtccagctac cactcgattc gccaccaact 3120 atattgcatt agacagccta cttaagaaga aagcagggtt gaagcaacta ttcactagtg 3180 acgattgggc caaccacaat ttcagccgct caaatgcagg tcgtatggtg gaaagtatag 3240 tgcttgatca tgctttttgg actcaatcag aacatgtgtg ccaagtgttt gaacctcttt 3300 acaaagtttt acggatcgtt gacacagaag tgtatcctac tatgggggca atatatgagt 3360 tgatgcgtgt agtgaaggat gaattggaaa gaaaacatgg tgcaaggtgg gtcataaaga 3420 taattgaaga ccgatggtat aaaacattat accacgattt gcatgcagca ggtataaatt 3480 atgtcataat ttgcaattca tttctttagt tgcataagta ttatttctct tattagagta 3540 tgtgtttctt tgaacagcat attatttgaa tcctcgatac caatacagac ccggtgttgg 3600 agatgatggt acccttatac gtgctgtaca taatgtatac tctaaattag accctgcatc 3660 accagcagtt ggccaatttg gaaatgaggt acacaattac ttaaattata ataattactt 3720 tgttggatta aactaacacg atttattgaa ttcagctaac atggtttaaa gatgcaagaa 3780 gaacttttgg agaaccaaca tcagttgctg ctcgaacaaa aatgtctcct agtgagtgta 3840 aacatatttc actataagtt tataatagaa tttgttggag ttattaggct tatcaacatt 3900 gtttttcatt gtagctgaat ggtggatcat gtatgggacc gatgcaccaa ctgtgagaaa 3960 gttagcaatc aaagtattat cacaaacagc ttcctcatct gcttgtgaaa gaaattggag 4020 cacatttgca ctcatacaca caaagcaaag aaataggttg gctcatagta ggttggaaaa 4080 attagtttat tgctactaca acatgaagct tcaaattcga gataaggaag cagaaataga 4140 tcatgtcgac cgtggtgacc cactagatgt gtttgatatt gttggtgaag atgatgatac 4200 agagggtaac caactttatc aatggattag acctcttcat ttagatgatg atgaaggcaa 4260 cccagctccc agagttgctg aagaagcacg taatgaaggg ataaatgtag aaagagtatt 4320 agaggaggag gtgggatcta gcagcgctga ctctttggaa gaacttttgc gcccaagacc 4380 aagaaacact ggaattccac cttcttccaa tcctacacaa ccacaacatc gtgctgatac 4440 taatgatagc tctagtacaa gatcaggaga ctcacctacc accggaggtg ggaatgatga 4500 aggatatagt ggagctggag gtagtggtgg tggatatgga aactatgttg gacaccacct 4560 cccggattta tgagcccctt cactggtgag gcaaacttca cgcatgcaac acaggatgat 4620 gaccatggca gtaggcgggc aggaccagga attggtgcca tagggaagga ctatactcgc 4680 agagaaagag gcaaggggat tttgtcaagt caagaagatg actcgttatc tataacttcg 4740 gactctgttg gagtgggaag tagtaactat ggttatactc ataaccaacc atttccctac 4800 ccttcatatc ccattcctgt tgggatggaa tcgagcgact catggaaaca atccgagact 4860 caatcttcaa atgattttgc ttatggacaa cgtcaaccaa tctcggatcc atatgggtgg 4920 catgttaaca attacatgca aaactatttt ggggatttat catttgataa ctactcttca 4980 caatacactc actctacaca tagagatgat gaagatagtg aaaaatttga acctcatagg 5040 aactctatgt ggtactaagt cactcatgta tcttaccatg caatgtataa agtgtaaaat 5100 attgtactaa ttcattatat ataaatgatt atggtgtgtt taaacttctt tcattaatta 5160 ctacatattt tctacactca caatgtttgc cagctcgcta tataatcaac ttgatwatgt 5220 taaatccatc atgcaatgca tttccttcca attttttgtg ataaactaat agataattga 5280 ctaaataaac atcctgcaaa gtttcaataa aaatttccaa gtttttctta caatttccgt 5340 ggtttccata ttatttttat cgatatcgat attatcccga tatttccatc gatatttccg 5400 tgttttcgga ctaccgatat ttccgatatc atcgatattt tataccttg 5449 // ID EGLN2_SM repbase; DNA; EDCOT; 410 BP. XX AC AB016143; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 23-SEP-2007 (Rel. 12.1, Last updated, Version 2) XX DE Solanum melongena LINE retrotransposon EGLN2_SM, endonuclease DE region. XX KW L1; Non-LTR Retrotransposon; Transposable Element; endonuclease; KW LINE; EGLN2_SM. XX NM EGLN2_SM. XX OS Solanum melongena OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-410 RA Noma K., Ohtsubo E. and Ohtsubo H.; RT "Non-LTR retrotransposons (LINEs) as ubiquitous components of RT plant genomes."; RL Mol. Gen. Genet 261(1), 71-79 (1999). XX DR Genbank; AB016143; Positions 1 410. XX SQ Sequence 410 BP; 163 A; 67 C; 85 G; 95 T; 0 other; ttggaatgtg cgaggtctaa atcaagaggt caagcattaa aaaatgaggt attcataaga 60 agaaataaaa taagatgtat agtaatatat gagcatagag ttagaagtga tagggtaagg 120 aaaactatca ataaaaccat gccaagatgg gattggaacc ccaatgcaga tagcaatacc 180 agaggaagaa tttggataga ttaggatagt acgacagtca agttttaaaa caaagaaaca 240 ttaccacaac acatacatga caaactaaca ctgatccaag agggaaagga attttagttc 300 actgcagttt atggaataca cattattgct acaagaagac ctctatggga taccttacac 360 aacctgaatc tgtgcatatc agagccttgg ctcatccccg gggacttcaa 410 // ID MuDr1_MT repbase; DNA; EDCOT; 286 BP. XX AC . XX DT 14-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A non-autonomous DNA transposon sequence from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW Inverted repeat; MuDr1_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-286 RA Jurka J. and Shankar R.; RT "MuDr1_MT: A non-autonomous DNA sequence from Barrel Medic."; RL Repbase Reports 6(11), 575-575 (2006). XX DR [1] (Consensus) XX CC Self-complementary sequence, flanked by 9 bp TSDs. XX SQ Sequence 286 BP; 100 A; 48 C; 34 G; 104 T; 0 other; gggttaatta agtttttagt ccctataaat attcacaatt ttgtttttag tccctacaaa 60 ataaaatcac actttttagt ccctataaaa ttttccatca gcatttttag tccctataaa 120 atttttccat cagcattttt agtccctgta aaaaatttcc atcaacattt ttggtcccta 180 aaatgcttaa ggaaaatgtc acagggacta aaaagtgtga ttttattttg tagggactaa 240 aaacaaaact gtgaatattt atagggacta aaaacttaat taaccc 286 // ID Gypsy9-VV_LTR repbase; DNA; EDCOT; 554 BP. XX AC AM487024; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy9-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-554 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-554 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 740-740 (2007). XX DR Genbank; AM487024; Positions 25941 25388. XX SQ Sequence 554 BP; 163 A; 112 C; 134 G; 144 T; 1 other; tgtcacaaga tgcttcaaat gaccctcccc atggcttata taggaggtga gaagtttcta 60 gagacccttg gagacatcca cacttagcca ctagtgggaa gagtgtggaa ggttctagaa 120 atgcctagag aagtccacac aactctacac tatggtagaa ggcatgagaa gggtccaaag 180 ctttctagag aaatctagaa gtctcttgta tataggyttg tacatagaat agtgtaggac 240 attctagaat attcatgaat tgtaaggaac cctccaaggt tctagagagt tccattggtg 300 cctataaata ggtgagggcc tcatttggcc aaggcaccaa gcaagtgagc ttccaagcac 360 ttgtaaaggc ttccttgagt taataagagc ttccattctt taaggaattg cctaccaagc 420 ttcttaagct tttgagtcgc aagtgtctta gcctagcaag ctaagcattg gggagcaagg 480 ctgacttagc aagatcaagc gtcttggctt gtctaagtgc cgcacgagct tagtgaacga 540 ctaagtccgt gaca 554 // ID Gypsy9-PTR_I repbase; DNA; EDCOT; 4486 BP. XX AC LG_VIII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy9-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4486 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4486 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 342-342 (2007). XX DR Genome; LG_VIII; Positions 13551946 13556431. XX CC Positions [1899-2324] - Reverse transcriptase CC Positions [3403-3882] - Integrase core CC 'CACAT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 477..2588 FT /product="Gypsy9-PTR_I_2p" FT /translation="MALCWHQSYMSFMLQVWGREKPELIELKQKNDLETYI FT KDFDILWNRSEISEKNALVFFIGGLDVEVKNMIKMFEPKSLKQAYTLARLQ FT DNTLTHRRYGSNPNKQTYHPTTFAYPNKPATPSSYNKNFPTRFPSTSLKPP FT QAGLLPNPPPYNPNITQRTTRPIRNRDVDERRAKGLCFWCDEKFIPGHRCQ FT NKKLYSLCVMEESGECSEDEGATDLDPDTYQPHISLNALEGVTGLNTLRVT FT GRVEKQPLVILVDSGSTHNFISNHVADRLHCNLTNIKALTVQVADGGIMAC FT TSVCSNFQWSIQGVDFVTDVFTLDLKNCDMILGIQWLATLKTIVCNYEEMW FT MAFIWQGQEVFIKGNDPVTMETVRLKQLNGLLCSASLVSEINLCSLGSINS FT QEQEKNPTSTGLQPGLAENTAFTNLQAEYQELFEEPKGLPPPRSHDHSIPF FT KEGSNPVNLRPYRHSSLQKDVVEHMVKEMLGLGTIQHSHSPFSSPVVLVKK FT KDRSWRLCIDYRALNQLTIKDKFPIPLIDELLEELVGASVFSKIDLRSGYH FT QIQMAPESIYKTAFKTHNGHYEFLVMPFGLTNAPATFQSLMNDLFRDQLRK FT FILVFFDDILIYSHSMTEHLGHLRTVFTILQTNMLYAKASKCVFCSPQVEY FT LGHVISAAGVSTDPHKIEGILNWPLPCNIKQLRGFLGLTGYYRRFVKGYGI FT ICKP" FT CDS 3433..4485 FT /product="Gypsy9-PTR_I_1p" FT /translation="MDFVEGLPKSEGREVIFVVVDRFSKYAHFMAIPHPYT FT ACSVARVFLDNVYKLHGFPATIVSDRDTVFLSLFWKELFARQGVKLCYSTA FT YHPQSDGQTEVVNKCLENYLRCMKGTSPTRWVQWLPLAEWWYNTNYHTATK FT STPYEIIYGYPPFLHIPYFPKDSPVDAVDNFLCKREQILHAVKKNLQNARH FT RMIQLANKHRSERQLAIGDLVYLKLQPYRQKTLGHRHSKKLASKYYGPYEV FT LARIGTVAYKLKLPISTSIHPVFHVSLLKKKVGNREVHPTLPDLPSEPLLL FT PQAILDRRMVKKNLQAATQLLVHWAGLTLAEATWEFADELALRFPQFNLED FT KVYLKEGQ" XX SQ Sequence 4486 BP; 1329 A; 1040 C; 932 G; 1185 T; 0 other; agtggtatca gagctgcatc ttcaaactca aaatgcctcc tgaaacgaga tcccaagatg 60 caagaagggt ggatgaaacc accaatctgg agcaacccca agcatatgat cacatccaac 120 aacagcttaa tgataccagg gccgatgcta atacacgctt cagagaactt aaagaagcta 180 tggatgccct tgtttctcgg gtagacacaa cattgcaaaa gacccaactt tcttcagggg 240 agtgcagctt acctaaagct cctcagttcc cccccccaag agattcccct gctcgtttca 300 actggattaa tgaaggtact cctcctcaat atcaattacg tagaccaaaa cgagagtttc 360 ctatttttga gcgataggat gtccttaaat ggatttataa gtgtaaccag tactttgatg 420 tagaagaaat tgttgagcaa gataagctca aattagcttc ctattaccta gatggcatgg 480 ccttatgttg gcatcaaagt tacatgagct ttatgctgca ggtttggggg agagaaaaac 540 ctgagctcat tgaacttaaa cagaaaaatg acttagaaac ctatatcaag gatttcgata 600 tcctctggaa tcgatctgaa atttctgaga aaaatgcttt ggtattcttc ataggagggc 660 tggatgtaga ggttaagaat atgatcaaga tgtttgagcc aaagtccttg aagcaagcat 720 atactttggc tagattacag gacaacaccc tcacccatag acgttatggc tctaatccta 780 acaaacagac ttatcaccca accacctttg cttacccaaa caaacctgct accccttcca 840 gctacaacaa aaatttcccc accagattcc caagtaccag ccttaaacca ccacaagcag 900 gtctcttacc aaacccccca ccttacaacc ccaacattac ccaaagaacc actagaccca 960 taagaaatag ggacgtggat gagaggaggg ctaagggcct ttgtttttgg tgtgatgaga 1020 agtttatacc ggggcataga tgccagaaca agaaactgta ttccctatgt gttatggaag 1080 agagtgggga gtgtagtgaa gacgagggag ccactgacct ggaccctgac acctatcagc 1140 ctcatatatc cctcaatgcc ttagaaggag taactggcct taacacattg cgggtcacag 1200 gcagggtcga aaaacagcct ctagttatct tggtagattc tggcagtaca cacaatttca 1260 tcagcaatca cgtagcagac agattgcatt gtaatcttac aaacattaag gctctaacag 1320 tgcaggtagc tgatggtggg atcatggctt gcacttctgt gtgtagcaac ttccaatggt 1380 ccatccaggg agttgatttt gtgactgatg tatttacctt agatcttaaa aattgtgata 1440 tgatattggg cattcaatgg ctggctacat taaaaaccat tgtatgcaac tatgaagaaa 1500 tgtggatggc gtttatatgg caaggtcaag aggtttttat caagggaaat gatccagtaa 1560 ccatggaaac tgtcagacta aagcaactta atggtttgtt atgtagtgct agtctggttt 1620 ctgaaattaa tctgtgcagc ttaggctcta ttaacagtca ggaacaggag aaaaatccaa 1680 catccactgg gttacaacct ggccttgctg aaaatacagc tttcaccaat ctgcaagcgg 1740 aataccagga gctgtttgaa gaaccgaagg gcttgcctcc tcctcgcagc catgatcaca 1800 gtataccttt taaggaaggc tctaatccag tcaatctcag accctatcga cattctagtc 1860 tacaaaagga tgtggtagaa catatggtta aagaaatgct gggcttagga accattcaac 1920 atagccatag ccctttttct tccccagttg tcctagtcaa gaagaaggac agatcatgga 1980 gattatgcat tgactatagg gcattaaacc agctcacaat caaagataag ttccctattc 2040 ctttaataga tgaactccta gaagaattgg tgggtgcctc agttttttct aagattgatc 2100 tccgctctgg ttaccaccag atccaaatgg ctcctgagag catctacaag actgcattta 2160 agacacacaa tgggcactat gaattcttgg tcatgccttt tggcttgact aacgcccctg 2220 ccacctttca aagtctaatg aatgacttat ttagggacca attgaggaag tttattcttg 2280 ttttctttga tgacattctt atttatagtc actccatgac agagcaccta ggccatctca 2340 ggactgtctt tacaattcta cagactaaca tgttgtatgc caaggccagc aaatgtgttt 2400 tttgcagccc ccaagttgag tatctcggcc atgtcatttc ggcagcaggg gtgtcgactg 2460 atccccataa gatcgagggt atcttgaatt ggcctctccc atgcaacatt aaacaactaa 2520 ggggtttttt gggtctcact ggatactaca ggagatttgt taagggttat ggtatcattt 2580 gcaaaccctg aacccagctg ctgaagaagg atgcttacag atggaatgag gaagccactt 2640 tagcgttgcc agacttgact caacagttca tcatcgagac agatgctagc aacagaggaa 2700 tgggggcagt cctcatgcaa gcaggccacc caatcgcatt cattagtaaa tcatttgggg 2760 tttaacaaca agcactttcc acctatgaaa gggaactact tgctattcta ctggcagtta 2820 ctaaatggcg acattactta tggggcaaac attttattat acgtactgat catcttagtc 2880 tcaaatatct gttggaacag aaggtgactt gcccatcaca acatgtgtgg ctcgccaaac 2940 tccttgggtt tgactatgag attgagttca aaaaagggaa ggacaatgtg gttgctgatg 3000 ccctctcaag ggtgtcctgt ggaactctca gtaccatgac agtctcttct cattctacta 3060 cactcttgga agccatcaaa caatcctggc agaatgtaca gcttctcatt caggaattaa 3120 ccctgcagcc taactctcat cctcactact cttgggtcaa gtaggaaagg taagcttgtg 3180 gtaggccaac atggacctct tcaaactcaa atcatttctc tatatcatga ttcagctaca 3240 gggggacatt caggcactac tgttacagca aaaagggtgg ccaataggtt tcattggaag 3300 ggccagcaaa agcatgttag acaatacatc agggaatgcc ccatttgcca acaaaacaag 3360 tctgaaaaca cacgcactcc tgggttacta caacccctcc ctatacctac agctcctttc 3420 attgatatta gtatggattt cgtggagggg ctccctaaat ctgaagggcg ggaggttatc 3480 tttgtggttg tggacagatt tagcaaatat gcacacttca tggctattcc acacccctat 3540 actgcctgtt ctgtagcccg agtgtttcta gacaatgtct acaaattgca tgggttccca 3600 gccaccattg ttagtgacag ggacactgtc tttcttagtc tcttctggaa ggagctattt 3660 gctagacaag gcgtcaagtt atgctattca acagcctacc acccccaatc agatggccag 3720 acagaggtgg tcaataagtg tcttgaaaac tacctgcgtt gcatgaaagg tacttcacca 3780 acacggtggg ttcagtggct tcccctagcc gaatggtggt acaacaccaa ctaccatacg 3840 gccaccaaat ccaccccata tgaaatcatt tacggttacc ctcccttttt acacattccc 3900 tacttcccaa aagactcacc tgtcgacgca gtggataatt tcttatgcaa aagggaacaa 3960 attctacatg cagtcaagaa aaacctacag aatgcaaggc atagaatgat tcaacttgca 4020 aacaaacaca gaagtgaaag acagcttgct attggtgatc tagtctacct caaactgcaa 4080 ccatacagac agaaaactct aggccacaga cattctaaaa aactagcttc aaaatactac 4140 ggtccatacg aagttttagc aagaattggt accgtggctt ataaattgaa gttacccatc 4200 tctacatcca tccaccctgt gtttcatgtg tcactgttga agaagaaggt gggcaatcgg 4260 gaggtgcacc ctacattgcc tgatctgccc tctgaacctc ttctccttcc acaagctatt 4320 ttggatcgcc ggatggtcaa gaagaatcta caagcagcca cccaactcct cgttcattgg 4380 gcaggtctta cacttgcaga agctacctgg gagtttgctg acgagctagc tctccgattt 4440 ccacaattca accttgagga caaggtctat ttgaaggagg ggcaat 4486 // ID Copia-21_Mad-LTR repbase; DNA; EDCOT; 472 BP. XX AC ACYM01138139; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-21_Mad-I; KW Copia-21_Mad-LTR; Copia-21_Mad_. XX NM Copia-21_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-472 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1367-1367 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01138139; Positions 30062 30533. XX SQ Sequence 472 BP; 145 A; 57 C; 101 G; 169 T; 0 other; tgtaagaatg tgaacatgag ataagatgat ctgatattag ttgtttgagt ccaatctgaa 60 taagaaagcc tctaagaaga tggatatcag tttttgtcag tgaaggtttc tgttacagtg 120 ataaactgat ttgaattagg aaaacttaag tagttttcca taaggatttt aatagggaat 180 ccatattcta atatgagaag gatatgtatg tatatatata tatatatggt gttctcttca 240 ctcacagggt gtgctctttt tggaactaag ccctattctt actttgagtg ataaataccc 300 tgacagagag aagaagaatt gctgtgctat tcaggttggt tgagatccac cattactgca 360 tcaaacggga gttcttcagg ttagtataat taggttttat ttggattgat attttgcatc 420 tacttggttg tggtttaagt aactgaatct tgtagctaga ttaaggttaa ca 472 // ID DNA9-9_Mad repbase; DNA; EDCOT; 171 BP. XX AC . XX DT 15-OCT-2010 (Rel. 15.1, Created) DT 15-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-9_Mad. XX NM DNA9-9_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-171 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1490-1490 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TSD is 9-bp long. TIR is 45-bp long. XX SQ Sequence 171 BP; 49 A; 23 C; 34 G; 65 T; 0 other; gggtaatgct agggagacca aatttttaaa ccaaattttg taaaccaaat gatgtggttg 60 ttgatgattg gattattact taagtgttga ttaacgtgct tatttcctat tggtgacaca 120 tcatttggtt tgcaaatttg gtttaaaaat ttggtctacc tagcattacc c 171 // ID CAULIV-1B_Mad repbase; DNA; EDCOT; 7676 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Caulimovirus-like sequence. XX KW Caulimoviridae; Integrated Virus; CAULIV-1B_Mad. XX NM CAULIV-1B_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-7676 RA Kojima K.K. and Jurka J.; RT "Integrated Caulimovirus-like sequences from the apple genome."; RL Repbase Reports 10(10), 1645-1645 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >86% identical to the consensus. This consensus is ~78% identical CC to CAULIV-1_Mad. XX FH Key Location/Qualifiers FT CDS 217..2031 FT /product="CAULIV-1B_Mad_1p" FT /note="movement protein." FT /translation="MSRLFRSNSMASTSSRSSLGTIPDIVNEEQKLDFQTD FT XSVDFGDWNIPKVSSKNIYKKKWSVASFRSEHHVKTVEKAYALSKEHETCQ FT LFSPEQIKTHRKDGHNYIHIGLVQIAVKPLTRRGLNTSILLCLRDARFTNF FT SDSILGMIESSLYNGPIHFDCFPDLTISLSDPHMLKALTLNIKTSGYQVLE FT GTQPLALIYRVYYKVTGTNMNFQALTKSPRDHTLLIQTNQENANIKVPRTI FT RWSDISLPSDWCLINESKPVAIQNSLVNLDNIEQYFDGTVKINFDRPARRS FT CESVHSHKSFAPSRNSFSGSIPTDRMGQDQELINSLANRKLKAVDTSSSVT FT QQELINDLINIKLKSVETTSQVTHPVYQPQTQDQGEQTSPTESDFEAGQVN FT HQLLVLNKPFKXNXKRLNADIEAXENIPRRNIFRNKYTXEEKLEIYKKWTN FT FMETHRFEVFFFDYVEKYYESEKKLEVITKENWLKEDKTIVSSSHPPQETI FT LITTANTQIPATPFKLPKEDAGVKPVIEQNNFTNQSLHTIGKQLDKIETKX FT DKLSQPKPTIREKPLVNFPESSSSAVALKTTRFHKSKNXPNVTRIKTRKNS FT XCFXTSX" FT CDS 1979..5782 FT /product="CAULIV-1B_Mad_2p" FT /note="retropepsin and reverse transcriptase." FT /translation="MLXELKQEKTVXVLXHPDESQXETTSTSSESETDTDS FT IRKVEQAFQNLELKRITNKRVNPTSLTKNWYPRPTPPDIQFEERNIQNQFS FT VSSDKLYEWNIDGLSEQELLNKLQHISMVANSYITNHNLSQTQVVDLLVTG FT FTGMLHSWWEKHLTEQSRNEIKNAVKRDEEGIPIFDEXXGQGVPDAVNTLL FT FTIIEHFIGTPSNVTSRIHDQLSNLRCPTLSDFRWYKDVFMSRVMLREDSN FT QPFWKEKFXNGLPNLFAHKIRNVLVNEEGIIPYHTLTYGNIINIIQKEGLK FT MCIDMKISKQVNKDKSIAKYELGTFCEQYGLPPIAPSNKKKRSDAYNRYPX FT RYSSRRHPKYKNKNFETNEFYEKPKTNKWKRKPSGKFHPKEQKGKCYKCGK FT FGHYANKCRVKKTINQLKISEEEKLQLIQVLELRDTDHSQSEDDLELSSSD FT NNSSSNSSSPDIKVGCTDACCNNKISVLNKQEEQEDLLIELXSKVDDPELK FT SFYLKKLKKLVSPEEPGTSQTQSTPKISLSTTLERFNKSKKEITVKDLQRE FT VNKIKDEIRFLKSENLEVRTXLSRVQTQSLVNPHEEEXXSSSSGPDSGSQS FT EKSTENLVLGLLDKIRIQKWYSKIKIIIEDFHLETIALIDSGADLNCIQEG FT LXPTKYFHKSTEILSAANQSPMQLKYEIPKAHVCQNNICFKTPFVLIKNIS FT DPVILGLPFXALIYPFKVHHNRITTRVLGQKVTFEFCLETDLKKLRHLQKN FT NISKTISIITNKSQHINFLKEEINHKXIEEQLTNKSLLETIDNFQKKLINE FT VCSDIPNAFWHRKQHIVKLPYIKEFNESKIPTKARPIQMSQEVMEFCKTEI FT QELLNKGIIRKSKSPWSCPAFYVQKNAELERGTPRLVINYKPLNEVLEWIR FT YPIPNKRDLIKRLSQAVIFSKFDMKSGFWQIQIHEXDKYKTAFVTPFGHYE FT WNVMPFGLKNAPSEFQNIMNEIFNQYSHFSIVYIDDVLIYSKSIDEHWKHL FT HXFARIIKSNGLVVSASKIKLFQTNVRFLGYNIHQSTIQPIDRVIQFADKF FT PDQITDKTQLQRFLGSLNYVSEFYPHLRQQCKPLFDRLKDNPPXWSTIHTS FT IVKQIKXHVKTLPCLGIPTPNSFKIVETDASDIGYGGILKQXTSSGSPEQI FT VRFHSGVWNPAQTNYSTIKKEILSIVLCISKFQDDLLNQKFLVRVDCKSAK FT HVLQKDVQNIASKQIFARWQAILSIFYFXIEYIKGSXNCIPDFLTREFLQG FT KNVRKQQ" FT CDS 5766..6935 FT /product="CAULIV-1B_Mad_3p" FT /translation="MSGNSNSQRRLPATLPPPPPVKQESIPDSSSALAITN FT RFAPLGSTVGQFRPNYQTALASPYDPYSSMPSPSTPKTPSFAKTSPYVKKN FT PMEYLFSIPXHINKKQXPXKIAKTIXPPNFHYXPTESXKTLKYYQAILSET FT EXIXIKPIYSTTHQNKILYHSLHIGKFLTEQEWGXPLYXTKXLHTQHXLIP FT NNKYNYFDYIQAWTNXFLHQTXDFSHSWFVTFDKSFRLNFPAWFPXWWSAH FT GPTASLLPEDLMQVLSSGFQKKFDRSRFDDRITLLSLFMAKYKVPWIXKWN FT YEVETGEVYRARWVKWWDKFDYGKIISLVSSEFPIXPVPTVSPPATQQRHC FT QKSQKIPNXYQTLVLHXPSKENPNHPSPPKXQVRRRKRNPPAXENGR" XX SQ Sequence 7676 BP; 2751 A; 1581 C; 1159 G; 2054 T; 131 other; gttcattttc agtctttcaa tttacagtct atcttatctg ttaatcttct aagtcgtttg 60 ttcgactccc caaccaaaca gtaaggcgtg ttccaaacaa taagtcccag gagaggcatg 120 agcggatcgc atgagcgggg aaggagttta gctaatacgc gaggaaggtg anncatataa 180 gttttctgta ttttgtttgc ctgtattgtg aactttatga gtagattatt tagatctaat 240 tcaatggcca gcactagctc tagatccagt ttaggnacaa ttccagatat tgttaatgaa 300 gaacaaaaac ttgattttca aactgatgan agtgtcgact ttggagattg gaatatcccc 360 aaggtttcaa gtaaaaatat ttacaaaaag aaatggtcag tagcctcatt tagaagtgaa 420 catcatgtca agacagttga aaaagcttat gctcttagta aagaacatga aacttgtcaa 480 ttgttttcnc cngaacaaat caaaacccat agaaaagatg gtcataacta cattcacata 540 ggcttagttc aaatagccgt aaaaccntta acacgnagag gccttaatac ctctattttg 600 ttatgtctcc gagatgctag attcactaac ttcagtgata gcatacttgg aatgatcgag 660 tcaagtcttt acaatggacc tatccatttt gattgtttcc cagatctcac cataagtctt 720 tcagaccccc atatgctgaa agcactcaca ttaaacatca aaacttcagg ataccaagtc 780 cttgaaggaa cacagccctt ggcattaatt tatagagtct actacaaagt cactggcaca 840 aatatgaatt tccaggcctt aaccaaaagt cctagagatc atacactctt aatccaaacc 900 aaccaagaaa atgcaaacat caaagttccc agaaccatta ggtggtcaga tatcagtcta 960 ccttcagatt ggtgtttgat taatgaaagt aagccagtag ccatccaaaa cagtctagtc 1020 aacctagaca acatagaaca atattttgac gggacngtca aaatcaattt tgaccgtcca 1080 gccagaagat cttgtgagtc tgtccactca cataaatcat ttgctcctag cagaaattct 1140 ttttctggat ccataccaac cgataggatg ggtcaagatc aagagttaat caattcatta 1200 gccaatagga aattaaaagc agtagacact agttcatctg tcacccaaca agaattaatc 1260 aatgatttga ttaatatcaa attaaaatca gtagaaacaa cctctcaggt tacacatccg 1320 gtntaccaac ctcaaaccca agatcaagga gaacaaactt ctcctacaga atctgatttc 1380 gaagcaggtc aggttaatca tcaactttta gttttaaata aaccattcaa aangaatagn 1440 aaaaggctca atgctgatat tgaagccgna gaaaacattc ccagaaggaa tattttcaga 1500 aataaatata canaagaaga aaaattggaa atttacaaaa aatggactaa tttcatggaa 1560 acncacagat ttgaagtatt tttcttcgat tatgttgaaa agtactacga gtctgaaaaa 1620 aaattagaag taataaccaa agaaaattgg cttaaagaag acaaaaccat tgtctcttct 1680 agtcatcccc cacaagaaac nattctnatc acaactgcna atacgcaaat tccagcnact 1740 cctttcaaac tcccnaaaga agatgcagga gtcaaaccag tcattgaaca aaacaatttc 1800 acnaaccaga gtctncatac natcggaaaa caattagata aaattgaaac naaaatngat 1860 aaactttctc aaccaaaacc aacaatcagg gaaaaaccct tagtcaactt cccagaatct 1920 tcttcnagcg cagtagcctt gaaaacaact cgcttccaca agtcaaaaaa tngaccaaat 1980 gttacnagaa ttaaaacaag aaaaaacagt cnatgtttta naacatccng atgaatctca 2040 ancagaaaca acttctacat catctgagtc agaaactgat acagattcca ttagaaaagt 2100 ngaacaagct tttcaaaatc ttgaactcaa aaggattacc aacaaacgag tcaatccaac 2160 atctcttacn aaaaactggt atcccagacc aacncctcct gatattcaat ttgaagaaag 2220 aaatatccaa aatcaattct cagtctcttc tgataaactc tatgaatgga atatagatgg 2280 tttgtcagaa caagaacttc tnaacaaact ccaacatatc tctatggttg ctaatagtta 2340 tattaccaat cataatctca gccaaacaca agttgtcgac cttttggtca ctggatttac 2400 nggaatgctt cattcctggt gggagaaaca tctcactgaa caatccagaa atgaaataaa 2460 aaacgcngtt aaaagagatg aagaaggaat acccatcttc gatgaacana tnggacaagg 2520 cgtccctgac gcagttaaca cattactttt cacaatcata gaacatttca taggaacacc 2580 tagtaatgtc acctctagga tccatgatca actcagcaat ctgagatgtc caactctaag 2640 cgactttaga tggtacaaag atgtnttcat gtctagagtc atgctcagag aagacagtaa 2700 tcaaccattt tggaaagaaa aatttatnaa tggattacca aatctttttg cncataaaat 2760 cagaaatgtt ttagtnaacg aagaaggtat cataccatat cataccctta cttatggaaa 2820 tataattaat attatccaga aggaaggntt gaaaatgtgt atagatatga aaatttcaaa 2880 acaagttaac aaagataaat ccatcgctaa gtacgaatta ggaacgttct gtgaacaata 2940 cggattacct cctattgctc cntccaacaa aaagaaaagg tcagatgcct acaataggta 3000 tccaancaga tactccagta gaagacatcc caaatataaa aacaagaatt ttgaaacaaa 3060 tgaattttac gaaaaaccca agactaataa gtggaagagg aaaccttcag ggaaattcca 3120 ccccaaagaa caaaaaggaa aatgctacaa atgtggcaaa tttggtcatt atgccaacaa 3180 atgtcgngtn aagaaaacna tcaaccagtt gaagatctct gaggaagaga aacttcagtt 3240 aatccaagtt ttggaattaa gagacacaga ccatagtcaa tcagaagatg atttggaatt 3300 atcctcttcc gataacaatt cntcgagcaa tagctcatcn ccagacatca aggtaggatg 3360 taccgatgct tgttgcaata acaagatttc agtcctcaat aaacaagaag aacaagaaga 3420 tcttctnatc gaattaatna gtaaagtcga tgacccngaa ctnaaatcnt tttatctcaa 3480 gaaactaaag aaattagttt ctccagaaga acccggcact agccaaaccc aatcaactcc 3540 aaaaatctct cttagcacaa ccttggaaag gtttaataag tctaagaaag aaatcacagt 3600 caaagatctc caaagagaag ttaataaaat caaagacgaa attaggtttc taaaatccga 3660 aaacctagaa gtccgnacac anctcagtag agttcaaaca caatcgttag taaaccctca 3720 cgaagaagaa cncgntagtt cttcctccgg tcccgattca ggttctcagt cagaaaaatc 3780 cacagaaaac ttagtcttag gtcttttaga caagataaga atccagaaat ggtattctaa 3840 aattaaaata ataatcgaag attttcattt agaaacaatt gctttgattg attcgggtgc 3900 agacttgaat tgtattcaag aagggttaat ncctactaag tattttcata agtcaacaga 3960 aatacttagt gctgcaaacc agtcgccaat gcaattaaaa tatgaaatac cnaaagcgca 4020 tgtttgtcaa aacaatattt gttttaaaac cccatttgtt ttaataaaaa atatttcnga 4080 tccagtcata ttaggtctcc cttttntagc actcatatat ccttttaagg ttcatcacaa 4140 taggattacc accagagtct taggacagaa agtcacgttt gagttctgcc tggaaacaga 4200 cctcaaaaaa ttaagacatt tacagaaaaa taatatttca aaaaccatta gtattatcac 4260 taataagtca caacacatta atttcttaaa agaagaaatt aatcacaaan gaattgaaga 4320 acagctaaca aataaatctt tgttagaaac tattgacaat tttcaaaaga aacttattaa 4380 tgaagtctgt tctgatattc ccaacgcctt ttggcaccgn aaacaacaca ttgttaaact 4440 tccttacata aaggagttta atgaatcnaa aataccnact aaggccagac caatccaaat 4500 gagtcaagaa gtcatggaat tctgcaaaac agaaatccaa gaacttctta ataaaggaat 4560 tattagaaaa agtaaatcac catggtcatg ccctgcattt tatgttcaga agaacgcaga 4620 attagaaaga ggaactccca gattagttat taactataaa cctttgaatg aagttttgga 4680 atggattcgg tatccaattc ccaacaaaag agatttgata aagagacttt ctcaagcagt 4740 tattttttca aaatttgata tgaaatcagg cttttggcaa attcaaattc atgaanatga 4800 taaatacaaa acagcttttg taactccttt cggncattat gaatggaatg taatgccttt 4860 cggccttaag aatgcaccaa gtgaatttca aaatattatg aatgagattt ttaatcaata 4920 tagccatttt tcgattgttt atattgatga tgtncttatt tattcaaagt cgatagacga 4980 acattggaaa catttgcatn tgtttgctag aataattaag tccaatggat tagttgtttc 5040 tgcntctaag attaaactgt ttcagactaa cgttaggttt ttaggataca atatccacca 5100 gtctaccatt caaccnatag atagagtcat tcaatttgcn gataaattcc cagatcagat 5160 tactgacaaa acccaattac aaagattcct tggatcatta aattatgttt cagaattcta 5220 tcctcatctt cgncagcagt gtaaaccntt gtttgatcgt ctcaaagata atcctccanc 5280 atggtctacc attcatactt ccattgtcaa acagatcaaa ncncatgtta agacattgcc 5340 ctgtcttggc attccaactc ccaactcatt taaaatagtt gaaactgatg catctgatat 5400 cggttatgga ggtatcctca agcagnnaac ttcttccgga tctcctgaac aaattgttcg 5460 tttccattca ggagtatgga atccngcaca aactaattat agtactatta agaaagagat 5520 attatctatt gtattatgca ttagcaaatt tcaagatgat ttattaaatc aaaaattttt 5580 agtccgagtc gattgcaaat ctgcaaaaca tgttttacaa aaagatgttc aaaacattgc 5640 atcnaaacag atttttgcac gatggcaagc catattaagc attttttatt ttganattga 5700 atacattaaa ggcagccana attgcatccc ngatttccta acaagagaat ttctgcaggg 5760 gaagaatgtc aggaaacagc aatagtcaga ggaggcttcc agccactctn ccacctccac 5820 caccagtaaa acaggaatct attcccgatt cctcatcggc cctagccatt accaacagat 5880 tcgctccctt aggatcaacc gtaggacaat tccgaccaaa ctaccaaacg gcattagcca 5940 gtccatatga cccatattca tcaatgccat caccttcaac ccccaaaaca cctagctttg 6000 ctaaaacatc tccntacgtc aagaaaaacc caatggaata ccttttcagc atccctnacc 6060 atattaacaa aaaacaancg ccaganaaaa tagccaaaac gatcttnccn ccnaatttcc 6120 attatntncc aactgaatct tncaaaaccc tcaaatatta tcaagccatt ctcagtgaga 6180 ccgaangcat tnctatcaaa ccnatttaca gcaccaccca tcaaaacaaa atcctttacc 6240 attccctcca cattggaaaa tttctnaccg aacaagaatg gggantcccc ctctatcana 6300 ccaaacnact tcatacccaa catgntctca tccccaacaa caaatacaat tattttgact 6360 acatccaagc atggaccaac atnttccttc accaaacanc tgactttagt cattcatggt 6420 tcgttacntt tgataaaagt ttcaggttaa acttcccagc atggtttccn aantggtggt 6480 cagctcacgg cccaacagcc agcctactac cngaagatct catgcaagtt ctntcatccg 6540 gtttccagaa gaaatttgac agaagccgnt tcgacgacag aatcaccctt ctctcgttgt 6600 tcatggcaaa atacaaagtc ccttggatcn tgaaatggaa ttatgaagtt gaaacaggtg 6660 aagtttacag agcccggtgg gtcaaatggt gggacaaatt cgattacgga aaaattatca 6720 gtttggtctc atcngaattt ccaattgnac ctgttccaac ggtatctcca ccagcaacac 6780 aacaaaggca ttgccagaaa tcccagaaaa tacccaatcn ttatcagaca ttagtccttc 6840 atcntccctc aaaggaaaat ccaaatcatc caagtcctcc aaaacntcaa gttcgaagaa 6900 gaaagagaaa tcctccagct cangaaaatg gcagataagc ttatagcaga agcagctttg 6960 ctncgcagtg aagacgaaga ctcaagttca gactcatcag acgcttcgtc tcaaccagcc 7020 aagtgggcag attaccagga ttcccaagac ccgtttgatt tgtaaaatta aaatgtaata 7080 atttgtaatc atttaagttt ttacccatgt aaattncaca gtagaagcca tgtgattttc 7140 acagaaagca gcatcagcag tagcagcaat cattcagaca antcactatt catgaatagt 7200 aaaatcactt tttactattc atccatcatt tcagccagca gcagcgtgan tccacagtaa 7260 aagcacatca ttcgccagcc tttacagcct ttggcacatg caacgacaga cagcagcggg 7320 attcccggcc tcaatcatcn nacctctccc tacaaaagaa actcattcca gaagaagggg 7380 acttcgtcga aagctgagac tctctgcgaa ttctctnaag aacagaagtc atgttcagct 7440 ccattccnca tccagcaaaa ttatcaaaca cttgtatttt aattttcaat caaggatgcc 7500 tgcgagcncc accgttttcc ttatcaatcg tcagtagacg aaattgtaag tcggtttcca 7560 atttgaaata aaattatttt caaattatat ccgcatcatt aattttaatt cattattttc 7620 attatgaaga atattttcat aactactgat tttgaatggc ataaaattct tactca 7676 // ID Gypsy6-PTR_LTR repbase; DNA; EDCOT; 404 BP. XX AC scaffold_916; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy6-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-404 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-404 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 337-337 (2007). XX DR Genome; scaffold_916; Positions 12194 11791. XX SQ Sequence 404 BP; 105 A; 68 C; 71 G; 160 T; 0 other; tgatgtggac cgggtagcaa gacaacaaaa tggctgatta ttgttgcaca atcaagcacg 60 tttaattttc ttacgtaata gttggagttt cctctcattt cattatttag cttttactct 120 cccaattaat tcgggacgtt tctttctgtt ttttagcttt tatttcctca ttaattctag 180 actgtttccc gatttaatga agctgtttta ggtctctaag aattctgttt tctctattta 240 tttggttgta agcactttgt gagggataga cagaataaaa aaaaaaccaa aactcttttg 300 agtagttaac tcaaatacct ttctttcttt gtttttctgc ggaattacag attgaaaaaa 360 ccttgtgtgt tagaacgcgt gtgagttccg tttggtctgc atca 404 // ID HARB-5_Mad repbase; DNA; EDCOT; 5480 BP. XX AC . XX DT 28-OCT-2010 (Rel. 15.11, Created) DT 28-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; HARB-5_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-5480 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1865-1865 (2010). XX DR [2] (Consensus) XX FH Key Location/Qualifiers FT CDS join(2937..3461,3641..4321,4306..5070) FT /product="HARB-5_Mad_1p" FT /translation="MEDKLDRMFSNTVATGEHAWAPSSGVLPPETREESIG FT QIDSDDEEESETMQDLRQATRKGKKRAANQGELQKKKVDKKGKKIGGAAKL FT CGQIDRLVEVYETRSSANSLMRKLHIGSSISEVLAAVAQLPGCEPPSELWL FT FATCLFCSAEKREVFATMKDPEVQLTWLKYMFNKEQLLSDCWIMTCGMLNY FT VLGYRCIFNMNTSDDDVEDLEDGVIICAVARAVETYYLKYVHKTPCMNSSQ FT TGNIWLMEVLQGNDVRCYRMFRMNKDVFYRLSNDLQTNYGLKGSRRMNAIE FT ILGMFLHMLGHGVKNRLAQERFQHSGETVSRYFGVMLDIVCKMAIDIIKPM FT DSEFRGIPQEIRRDTRYMPYFKVKFDSSSNLFANYKCLQTKCRLTVFFYVI FT IFRIVLVPDCIGAIDGVHVEASIPPPDQVPYIGRKGIPTQNVMAACNFDMQ FT FTFACAGWEGTAHDTRVFLSVLRNPNLNFPKPPNGNLHTYIITFYILALYN FT YYNTKQNFQXSGKYYLVDAGYPQMRGYLGPYKGERYHLPDFRRGAEPTGHK FT EVFNHMHSSLRSIIERTFGVWKKRWAILRDMPNYPFNKQVKIVIATMALHN FT YIRRYSERDRHFDDPRDYCEESDSSDDDDEEYQNYQVEGSHEIEALRNRIA FT ASLMNASN" XX SQ Sequence 5480 BP; 1695 A; 805 C; 1167 G; 1810 T; 3 other; gccccagttt ggtagtgagg tgcttaaaaa aaaagctagg gtgaaaaaaa gctagaagga 60 tttgaggtgt ttggtaaatt ttccaaaagc agctttgttt taaagctgag ggtgaaaaga 120 agcccaaaac cggaagctgc tatttgcagc ttcccaaaaa cagctgcagc ttcccaaacc 180 aaaaacacgg gtgaacagtg taggtttaat gaatttttca ataatccaaa attgccctcc 240 ttccttacag tctctcctct ccgcctctct ctccttctcg ccttcctcct ttctttcctt 300 cagtctactc tcctctcgca tacccgaacc aggaaaccag atctctctcg ttctctcgtt 360 ccaaaaccag cgttctccct tgttctctcg ttctccaggt tcgtttggta agtttctctt 420 gtaaatttta tttatttatt tgtttggatt tttaactttg gggatgggag agggaaaaag 480 gggtgggaag agcaaaggga tgagggtatg ggtgtcggga aaaacaattg gggatggagg 540 gtggggaaaa attaattggg gaaggtgata tggtttgtgg aaaaaaataa ttgggaaaaa 600 aataattggg gaaaaattag ggtttgtgga ggaaacaaga aaaattgaga aggtctgctt 660 ctgatttggg tttaggtaaa ggataatttt ttataaagct ttgctctggt tctaatctgt 720 gaactgtgct tctgatttgt catccctttg tcagtgttcg tatcgtatct ctctggaagg 780 aagtgggttt ctgaggacat cgctgaggct gtactcgaac aggtggatta tttttgtctt 840 ggtacaaaat tcggttttca tgtttttgat aaatctgttt tgtgattgca tttaaatggt 900 atttggttta tgtgtttacg tattagtttg cacttgaaat gagttttctt tcaagcattt 960 tgtaattttc gtgattatat tcgattagtg gtacatatcc tctcgtgaaa cctagggatt 1020 aaagtagaag accaaaactt gaaagaatga aattagggta gctgatttct gttaaatttg 1080 agcatggagt gtttgcagca cgttgactat caagttgccc ctgtatctac aagagaaact 1140 tgagataatt catacgcaag caatttacac tctagatcag gctttgtgaa gtacttacag 1200 gttatgtttc taactgtctt atagttttag gagaaaatga atktcaaaca gaggagtgat 1260 tctacaaaaa acatatgatg caatgaagtc caagatgaga tattttgatc atatagttgg 1320 tgcaaatgct tccaaaagca ttcagcccgc tggattatgt ctttaatcta ttgctaaatt 1380 cacatgcaac ttgtacactg agagccactg aaacactatg aaaatgaaaa ctgcacattc 1440 actacaaaaa cattgttaaa accagactct gtcacttacg tgtactgatk aagatgatgc 1500 ataatcagac aatttggtcg cctgaagaat ttagattaat gtaaccaaag tctttccacc 1560 caaggccttg ttcttagtat tgcaatgttc ctgagattga atgattcaag aacaaattaa 1620 gcaggagtaa agagagataa agaatgaaat aggtagaagt ggttaggtgt ttgttggtta 1680 ggattaaaga gattagataa agaatgaaat aggtagaagt ggttatatgt tctggtgtgt 1740 tcatcttctt ttcttttagg ttttttggtg tttgttggtt tggctttcag ctcttacttg 1800 aaacaaggtt tttcagagat taggattaga tagactactt gtttcatttc tcagtcttct 1860 tgtctactaa aaaaataata atagtcaagt gaatattttt tatcttattc atcgtgtgaa 1920 ttttcatgta ttttttggtt gatctatcat ttttatggtt gatctatgtg ttaatgaatt 1980 ttcatgtatt tttatggttc atcgtgtgaa ttcttcaagg atagttgaca ttacattctg 2040 aaatttcaaa gaataatcga accacttttc gaacttatat gttgatcaac ataatttttt 2100 ttctttctat aatgtggtcc tttttattat aagtattctc ttctgttcaa actaaattcc 2160 acttaatgaa ttagtgtgat gaaatgttta tttagtctag aatgctttaa tggtcgtaaa 2220 ttgttgtgtc cagtagtctt atataataaa tagttgtatg gaaaatcaca tggactagaa 2280 ttacatttgg taaacctgtg gggtatccat ataagcatgt gttggtaaac ctgtggggta 2340 tccatataaa cctgtgcaat ttaatcttgt gattaatggt ccagtttttt tcccaaactg 2400 tgatgtaatc ttttgtagtt gtatgtggat cgtttattgg ttatttcttg gttatatata 2460 caaatcagta gttggtatcg atggcaaaga agggggcatc ttcgtcaaat cctacagcta 2520 catggaatgc ccacaatata tctatatttt gtgatgtttg catcaaggag gttgaggccg 2580 gacatcgtcc gggcactcac tttgacaaag atggatatgc aaatattaga gctaacttca 2640 aggcagagac agggcatgat tatgaaagaa agcaactgaa aaataagtgg gatgcactta 2700 aaaatgagtg gaagttgtgg aaagagctag ttggtaaaga aactggccta gggtggaatt 2760 cgagcaaggg taccgttgat gcctctgagg agtggtggaa taataaaatt caggtttgtg 2820 tatttatctt ttaatatgta ttatgatatc atgcaatatg tattaaccat attctttctt 2880 acttgtagat aaacaaagaa tatggaaaat tgcgaaaaaa gggcattagt cctgagatgg 2940 aggacaagtt agataggatg ttctcgaaca cagttgctac cggtgaacat gcctgggcac 3000 cttcatctgg agtactacca ccagagacaa gagaggaatc tataggacaa attgattcag 3060 atgatgagga agaaagtgag accatgcagg atctaaggca agctactagg aagggaaaaa 3120 aaagagcggc taaccaagga gaattgcaaa agaagaaggt tgataagaaa gggaaaaaaa 3180 ttggaggtgc tgcaaaactt tgtggtcaaa ttgaccgtct tgttgaagtt tatgaaacta 3240 ggagttctgc aaactcattg atgaggaagc tgcatatagg cagtagtatt tcggaagtgt 3300 tagcggctgt tgcacaattg cctggttgtg agccacctag cgagttatgg ttgtttgcta 3360 catgtttatt ttgtagtgca gagaagcgag aggtgtttgc cacgatgaaa gatcctgaag 3420 tccagctgac ttggttgaaa tatatgttca acaaagaaca atagggagct aaaacctaaa 3480 actatgaatt aggactatat gtgtggtttg tactttgcat taagattatg tgttgaatgt 3540 tgctacatgt ttattgaatg ttggattata tgttgaatgt tggattatga tttcttgtta 3600 aacgttggat tatgacttgt tcttgaatgt cggattatga cttcttagtg attgttggat 3660 tatgacttgt ggaatgttga attatgtgtt aggttacagg tgtatattca atatgaacac 3720 ctctgatgat gatgttgagg atttggagga tggtgtaatt atatgcgctg tagcgagagc 3780 tgttgaaaca tattatttaa aatatgtcca caaaactccg tgtatgaatt cttcccaaac 3840 aggtaatatt tggttgatgg aagtactaca aggaaatgat gtgcgatgct atagaatgtt 3900 taggatgaac aaagatgtct tttatagatt atccaatgac ttgcaaacta attatggatt 3960 gaaaggttca aggagaatga atgcaattga aatattagga atgttcttgc atatgttggg 4020 acatggtgtg aaaaatagat tagcgcaaga gagatttcaa cattctggtg agactgttag 4080 tagatatttt ggtgttatgt tggatatcgt atgtaagatg gcaatagata ttatcaaacc 4140 gatggattcg gagtttcgtg gcattcccca agaaataagg agagatacaa gatacatgcc 4200 ttattttaag gtaaagtttg actcgtcttc taacttattt gcaaactata agtgtttgca 4260 aacaaagtgt aggttgacgg ttttcttcta tgttattatt tttaggattg tattggtgcc 4320 atagatggag tacatgttga ggcttcaata ccacctccgg atcaagttcc atacattggt 4380 aggaaaggaa taccgactca aaatgttatg gctgcatgta attttgacat gcaattcaca 4440 tttgcttgtg ccggatggga aggcactgca catgatacaa gggtttttct atccgtgcta 4500 cggaatccaa atttaaactt tcctaagcct ccaaatggta atcttcatac ttatattata 4560 acattttaca tacttgcttt gtataattat tacaatacaa aacaaaattt tcaattktca 4620 ggaaaatatt acttggtaga tgcggggtac ccacaaatga gaggttattt gggaccatat 4680 aaaggtgaaa gatatcatct cccggacttt cgtaggggtg ccgaaccaac gggtcataaa 4740 gaggtattca accacatgca ttcttctctt aggagcatca ttgaacgaac ttttggggta 4800 tggaagaaaa gatgggcaat tttaagggat atgcctaatt acccgttcaa taagcaagtg 4860 aagattgtca ttgctacaat ggctcttcat aactacatac ggaggtattc tgaacgtgat 4920 cgtcattttg atgaccccag ggactattgt gaagagagcg atagtagtga tgatgatgat 4980 gaagaatacc aaaattatca agttgaagga tcacatgaga tagaagcatt aagaaataga 5040 atagcggcaa gtttgatgaa tgcatctaat tagactactt tcaagtacat taacaatatt 5100 gtactaatga atcctagcta ttcagtctaa aatatttcaa ttgaagtagt ttgtcatact 5160 aattaatatt taagataaag tttataaata tttttctttt aaaaataaag tatatttagt 5220 aattcacttt tatttgttaa gaaaattaaa ttaatagcac atctagtatt ataccctttt 5280 tggtcatttc acacagtcac agctgtttta cataaaagtt taccaaacac tatcatactg 5340 cttttttttt ccaaaagcac ttttacaaaa aagtttacca aacactctgc tgctttattt 5400 cacagccgct tattctcaca gcacagccgc ttattctcac agcagctttt tttcaaagca 5460 cagcaatacc aaaccagccc 5480 // ID Copia-14_Mad-LTR repbase; DNA; EDCOT; 207 BP. XX AC ACYM01113852; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-14_Mad-I; KW Copia-14_Mad-LTR; Copia-14_Mad_. XX NM Copia-14_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-207 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1358-1358 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01113852; Positions 1614 1408. XX SQ Sequence 207 BP; 57 A; 27 C; 36 G; 87 T; 0 other; tgttaaggaa agtatctcca cagattagtc aatattatta attgatattg ttgttattta 60 cttccttgtt tagtccttga cgatccttgt gtctaggctt tagtttagga tcttgttcac 120 tgtattcttg tatataaggt gtaaacctag ttggagaaat atataatgaa agctatattc 180 cattatacgt tttctatgat ggtatca 207 // ID Copia-17_Mad-I repbase; DNA; EDCOT; 4844 BP. XX AC ACYM01116382; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-17_Mad-I; KW Copia-17_Mad-LTR; Copia-17_Mad_. XX NM Copia-17_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4844 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1292-1292 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01116382; Positions 649 5492. XX CC Positions [1997-2497] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 569..4834 FT /product="Copia-17_Mad-I_1p" FT /translation="MFYDGSDESQYYELRCKATRTRQDDRPVNLYFTELKG FT VWQDLDRWRPIKMVCTVDLRTRKEELSKDRVYDFLAGLDNGFDQVRSEILR FT MKPIPAIEECFSLVRREAQRQTTMLGTKAITTSSSMAMITKSPSPSLRPSA FT TEAPRPNRTQEDIDKDKLHCNHCNGKRHTEETCFEIHGYPEWYWERKKELK FT AKGRRTSQAKLAESGAGVTVVAAGRMGPKSNQEHNSDLGKAAVAAGQSGPK FT SNILAHNQEGKMEPAAVHEDTDQMLSLIRQISHNDPGKIGTVLIASTKRDS FT GWIIDSGATDHMTYDASLFHHKTFPPKENVITANGEIASVTGAGSIALTPS FT LSLHNTLLVPSLSNHLLSVGQVTEQLDCVVLMFPTFCLLQDIQTRAIIGRG FT TKRRGLYYVEDVVPGRVNQVRSSNNNKTKAVWLWHRRLGHASFGYLKKLLP FT SLFSGVSDSDFHCNDCILAKSHRTSYRLSLNKRTMPFELVHSDVWGPSPII FT TQHGIRWFVIFVDDCTRMTWLYTMKQKSDVGQIFQQFYRMIGNQFSLPIKV FT LRSDNGGEYLNFELSQFFREHGILHETTCPQTPQQNGVAERKNRHILETTR FT ALLIGAHAPNTYWADAVTYSVYLLNRMPSRVHNFRTPMEVLTDHVTLPSSL FT QLSPRIFGCVAYVHLQKNQRSKLDPCAVRCVFLGFNSQQKGYKCYHPSSKH FT FYITMDVTFSETEMFFATDQTHPTRQGEIDCIVDDYRWLDLPFELGSSSGL FT SKGQPCERQLIKDAVSLGDRSPSTEACDAGPCVMEHAAKSSGGYCTPRETP FT VQPIDGPEICELASGLTDSAEVAAPTHNNPHPPMLVHAHVPEDIQEVRSYN FT SDIGENSYILPPRQNRGKPPDRFSPDGKVRYAIAQYMSTHRLSPKYQALVN FT QMAGIKIPTKVEEALQDPRWKEAMEVEMEALQKNETWNVVPLPHGKRPVGC FT KWVFTIKHKADGSIDRYKARLVAKGYTQTFRVDYQETFAPVAKMNTIRVLL FT SLAANFDWPLKQFDVKNAFLHGDLEEEVYMDFPPGYDVPNGAGKVCRLLKA FT LYGLKQSPRAWFGRFTQAMKSYGYKQGNADHTLFMKRMGGKVTLLIIYVDD FT MVVTGDDTEEIKRLQNYLSAEFEMKDLGGLKYFLGIEVARSRDGIYLSQRK FT YVLDLLSETGMLACKPAETPIVQNHHLAIYQDQTPTNKERYQRLVGRLIYL FT SLTRPDIAYAVSVVSQFMHSPSEDHMAAVMRILSYLKGAPGKGLIFKKHGH FT MEIKGYTDADWAGNISDRRSTSGYFTFVGGNLVTWRSKKQNVVARSTAEAE FT YRGMAHGICELLWIRILLTEIGFKPRETMLLHCDNQAAREIANNPVQHDRT FT KHVEVDRHFIKEKLDVKLIDIPYVRSEEQLADVLTHAVTAKVFKDSLDKLG FT LGDIYAPT" XX SQ Sequence 4844 BP; 1465 A; 979 C; 1132 G; 1266 T; 2 other; aagactttta tcttggtatc aagagcaggt tttcggcctg tctcttccca aaccaaaccc 60 taaaaccaga caaacgtaca aactgcaacc aaggttgcat cagaagcaac ttctggtgtt 120 cttaaaagtt gaacccagga atccaaaatc tgtggcgttg taatcatcaa ggctgcatca 180 aattcaacct tattaaawta aaaaaaaaaa aamccaattt ggtctgatgg ctgaagaaag 240 aaaaactggt gagttggtta ccatccaatc cttgtccatt ccaaatgagc ctaccaacat 300 cagcggcatt ctgtttggat acagattgaa tgacacaaac tggaaagtgt ggtcgaagat 360 gatggaggtt catgcttcag gcctcggcaa gcatgggtat ttaactggaa aaatcccagc 420 tatcacagaa gactctccag gatacaccaa gtgggtcact gaagatgcta ttgtgcgagg 480 atggctattg aaaaccatgg aaccacacct gttgagtctc ttcatcgatt taccgacagc 540 caaggacatc taggaaagtg caagccagat gttctatgac ggatccgacg agtctcagta 600 ttatgaattg agatgcaagg cgacacggac tagacaagac gatcgtccgg taaatttata 660 tttcacagaa ctgaagggag tatggcaaga tcttgataga tggcgtccta tcaagatggt 720 atgcacggtt gaccttcgaa cccgcaagga agagttgtca aaggacaggg tgtatgattt 780 ccttgccgga ctggataatg gattcgacca agtccggagt gagatcctaa gaatgaaacc 840 catccctgcg attgaagaat gcttcagttt agttagacgt gaagcacaaa gacagaccac 900 catgcttgga acaaaagcca ttacaacaag ctcctctatg gcaatgatca ccaagtcccc 960 gtcaccatcc ctccgtccat cagccactga agcacctcgt ccaaaccgta cccaggaaga 1020 cattgacaag gacaagcttc attgcaatca ttgcaatgga aagaggcaca ctgaagaaac 1080 ttgttttgag atccacgggt acccagagtg gtactgggaa aggaaaaagg aattgaaggc 1140 aaaggggaga cgcacgagtc aggccaagtt ggccgaatct ggagctggag tgactgttgt 1200 ggcagcaggc cgaatggggc ctaaatccaa ccaagagcat aattctgacc ttgggaaagc 1260 agctgtggcc gctggccaat ctgggcccaa gtcaaatata ttagcccaca accaggaggg 1320 aaaaatggag cctgcagcag ttcatgaaga taccgatcaa atgttgtctt taattaggca 1380 aatttcacat aatgatccag gtaaaatcgg tactgtactt atagcatcta ctaaacgtga 1440 ctctggctgg ataatagact ctggggctac cgaccatatg acatatgacg catcattgtt 1500 tcaccacaag actttcccac caaaagagaa tgtgattact gccaatggtg aaattgcttc 1560 tgttacggga gctggttcta tagcccttac tccttctcta tctctgcaca acacgttact 1620 tgttccatca ttgtcaaatc atttactttc ggtgggtcag gttacggaac agttagattg 1680 tgtagtacta atgttcccta ctttttgcct acttcaggat atccagacac gggcgatcat 1740 tgggcgtggt actaagagga gagggttata ctatgtggaa gacgtcgttc caggccgagt 1800 caatcaagtg cgtagcagca acaataataa aaccaaggca gtttggttat ggcatcgtcg 1860 actaggacat gcatcttttg gttatttgaa gaagttactt ccgtctttat ttagtggtgt 1920 atcagattct gattttcact gtaatgattg cattctcgca aaaagtcatc gtacttcgta 1980 ccgtttgagt ttaaataaaa gaacgatgcc ttttgagtta gttcactctg atgtgtgggg 2040 tccttcacca ataattacac aacatggcat tcgttggttt gttatctttg tggatgattg 2100 cactagaatg acatggctct atacgatgaa acagaaaagt gatgttggtc aaatctttca 2160 acaattttac cgcatgattg gaaatcaatt ttctctccct attaaagttc tccgatctga 2220 taacggtgga gaatatctta atttcgaact ctctcaattt ttcagggagc atggcattct 2280 gcatgagact acttgccctc aaactccaca acaaaacggg gtagcggaac gtaagaatcg 2340 acatatcttg gaaaccactc gagctcttct gattggggct catgctccta acacctattg 2400 ggcagatgct gtcacctatt ctgtttatct cctaaaccga atgccatcaa gagttcataa 2460 ttttcgcacc cctatggaag tcctaacaga tcatgtcact ctaccatcct ctctccagtt 2520 atcacctcgc atttttggat gtgtggcata tgtgcacctt caaaaaaatc aacggagtaa 2580 attggaccca tgtgcggttc ggtgtgtgtt tttgggattc aatagccaac aaaagggata 2640 taagtgttat catccatcgt ctaaacattt ttacatcacc atggatgtta cattctctga 2700 aaccgagatg ttctttgcta ctgaccaaac ccaccctact cgtcaggggg agatagattg 2760 tatagttgac gattacaggt ggcttgatct gccgtttgaa ttgggcagtt cgagtgggct 2820 tagcaaaggg cagccttgtg aaagacagct cataaaggac gctgtcagcc taggtgaccg 2880 aagcccaagc actgaagcat gtgatgctgg cccatgcgtg atggagcatg ctgcaaaaag 2940 cagcggtggg tattgcacac cgagagagac acctgtgcag cccatagatg ggcctgaaat 3000 ttgtgagtta gcaagtgggc taacagacag cgccgaagta gcagctccaa cacataataa 3060 ccctcatcct cctatgctgg tacacgctca tgtccccgag gatattcaag aggtacgttc 3120 ttataattca gatattggtg aaaattctta tattttacct cctaggcaaa atcgtgggaa 3180 accacctgac aggttctctc cggatggaaa agtgagatat gcaattgcac aatatatgtc 3240 aacacatcga ctatcaccca agtatcaagc cttggtgaat caaatggcgg gaatcaagat 3300 tccaacaaaa gtggaagaag ccttacaaga tcctcgttgg aaggaagcca tggaggttga 3360 gatggaggct ttacagaaaa atgaaacatg gaatgtggta ccactaccgc atgggaagag 3420 accagtggga tgtaaatggg tattcaccat aaaacacaaa gcagacggat ctatagatag 3480 atacaaagca agattggtag caaaagggta cacacagaca ttcagagttg attaccagga 3540 aacgtttgct ccggttgcaa aaatgaatac tattcgagtt cttttgtcct tagctgcaaa 3600 ctttgattgg ccattgaaac agtttgatgt gaaaaatgct ttcctacatg gagatctgga 3660 agaagaagta tacatggatt ttccacctgg atatgacgta ccaaatggag caggaaaagt 3720 gtgtagactt ctgaaagctc tctatggact caaacagtca cccagagcgt ggtttggaag 3780 gttcacccaa gcaatgaaaa gttatggcta caaacaaggg aatgcagacc atactctgtt 3840 tatgaaacgt atgggaggta aagttacttt gttgatcatt tatgtggatg atatggtggt 3900 tacaggtgat gatacagaag agataaaaag actgcaaaat tacctttccg cagaatttga 3960 gatgaaagat ctagggggct tgaaatactt tctgggaatt gaagttgctc gttctcgtga 4020 tggtatttac ttgtctcagc ggaagtatgt gcttgatctt ctttctgaaa ctgggatgtt 4080 ggcatgtaaa ccagcagaga ctcccattgt gcagaatcat catctggcaa tataccagga 4140 tcaaactcct actaataaag agaggtacca gaggttagta ggaaggttga tctacttatc 4200 gctcacaagg ccggatattg catatgcagt tagtgttgta agccagttta tgcactctcc 4260 tagtgaagat catatggcag ctgtgatgcg tatattgagt tatctgaaag gtgcacctgg 4320 gaaaggattg attttcaaga aacatggaca tatggagata aaagggtata cagatgccga 4380 ctgggctggg aatattagtg atcgtcgctc cacatctggt tactttacat ttgtgggagg 4440 gaatcttgta acttggagaa gcaaaaaaca aaatgttgtg gccaggtcca cagctgaagc 4500 ggaatatcga ggtatggcac atgggatttg tgaactatta tggatccgga ttcttctcac 4560 cgagatagga ttcaagcctc gggaaactat gttattacac tgtgataatc aagcagcgag 4620 agagatagcg aataatccag tccaacatga tcgtacaaaa catgtggaag tggatagaca 4680 cttcatcaaa gagaagttag acgttaagtt gattgacatt ccgtatgtga ggtctgaaga 4740 acagttagct gatgtgttaa ctcatgcagt gacggcaaaa gtctttaaag actcacttga 4800 caagttgggt ttaggagata tctatgcacc aacttgaggg ggag 4844 // ID Copia-59_VV-I repbase; DNA; EDCOT; 5285 BP. XX AC chr13; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-59_VV_; KW Copia-59_VV-LTR; Copia-59_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5285 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr13; Positions 23519462 23524746. XX CC 'GTAC' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 1095..3182 FT /product="Copia-59_VV-I_1p" FT /translation="MTSFNPLANILTQKKLEGPNYVDWKRNLDILLTAEEY FT KFVLSEVCLEKPGEGATQDQIKAHQKWVKADEMARCYILASMSNVLQHQHQ FT KMDTAYDILENLKEMFGDQTSAARQNTLREILTSKMEEGTQVRTHVLKMMS FT LLNDMEVLGAEVDKATQIEMVLNTLPPSFQQFRLNYNMNKMDFTLSKLLNE FT LVAAQTIIKQGAAPVVLNIERVFSSVQKKGKKKKNVKPNNNGAANGVNGVV FT KKPKGKCFHCKQPSHWKLQCPTWLAKKKQGTSPFHLLVVETCLAVLTTHQW FT CVDLGATNHVCNSLQGFQETRQLSKGEVNIFLGNGSEVAVLAVGNIALNFK FT NNRTLFLKNVLYVPSIRRNLIPISSLSKNGYSVCFNEFYDDSVVIKFREQM FT ICSGSLIDSLYILKVTPELQLTNSEVNNFDIVAPLKRKRPIELSYTYLWHL FT RLGHINLDRISLLVKDGPLSSLKVEALPTCESCLEGKMTKRPFPLKGNRAN FT DVLELIHSDLCGPMSVQARGGFEYFVTFTDDYSRYGYIYLLCRKSECFEKF FT KAFKAEMEQRHGKYIKTLRSDHGGEYISREFITFLSEQGITSQLSAPGMPQ FT QNGVAERRNRTLMEMVRSMMSYSDLPISLWGHAIETAAYILNLVPSKSVPK FT TPTELWTGRKPNLKHVRMWGCPTHVLKGKTDKLETKTELCFFIGYPR" XX SQ Sequence 5285 BP; 1633 A; 819 C; 1148 G; 1685 T; 0 other; attggtatca gagccaggtc tgaaactcgt ttggaggtat tattcgtact gtcgtttttg 60 atttgttatg gaaaaagagt tatatgcgtt ggattaaaga gactcaattt tgaaaatgca 120 agagataatg gctgcagttg ttatatgaat atgcatatgt tcattgatgt taacacgcag 180 attgggtttt gttaacatta ccacaattat taatattata ttgctcttgg tttgttcttt 240 ttgaattcaa caaagattgg catgatgatg ggtgttttat attataatat tatattgcat 300 ataaggatgt taatggctgc cgttttcatc aaatgcttca attataatat tgtattgttg 360 aatgcttcta attaccgcaa atcaagagtg ataatggttg caatttttta aatataagtg 420 cataagttca ctgctgttca tccgaatgtc atgcataatt tcatttgtga ttttggtgat 480 ttgccatgcg agtttctaca ataagattgt actattgtag actgcgcaaa agacaataat 540 tagaatgcta catggctgaa cattggtgtt tattgctgat ttttgtaagg ttatttttct 600 atcgcaaatc agaacatgct tgctgcaatt ttggttttga taacatgaat gttttagtaa 660 accagcagct catttatttc cattaatttg tgagtatttc aagagttgct agttgtgatt 720 acttacattt tcttcctcat cggcagatga tatgttttga tgtaatcact gtaactcttc 780 tagtattgtc tatatttatt tatctctcta tctgagtaaa ttaattaggg acatagacta 840 gaagtaataa tttcacattt atatttaaga ggcatgtttt ctcccatcga gtggtacatg 900 ttgatcttat gttgctttta tatgcataac atatgtttag tttagttctc ccatcgagat 960 tactgtccat ggatgttatg atgcatatat gaattttgct gtcattattg ttattatgca 1020 atcttggttt aaattcagtt tttgattatt attgaattgc tgtaatttta ttttatgcat 1080 aatcttgtga cagaatgaca tctttcaatc ccttagccaa tatcctaacc caaaagaagc 1140 ttgagggtcc taactatgtt gattggaaaa gaaatttgga cattttgctt actgcagaag 1200 aatataagtt tgtgctcagt gaagtgtgtc ttgaaaaacc cggtgaaggt gccactcaag 1260 atcaaattaa ggctcaccag aaatgggtta aagctgatga gatggcgcga tgttacattt 1320 tggcatctat gtcaaatgtt ttgcaacatc agcatcagaa aatggataca gcttatgaca 1380 tcttagaaaa tctcaaggag atgtttggag accaaactag tgcagcaagg cagaacacac 1440 taagggagat cctgacttct aaaatggagg aaggaactca agtaagaact catgttttga 1500 agatgatgag tcttctgaat gacatggagg ttctaggtgc tgaagttgac aaggctactc 1560 agattgagat ggtcttgaac actctgcctc ccagttttca gcagtttcgt ttgaactata 1620 acatgaataa aatggatttt actttgtcta aactgctgaa tgagctggta gctgctcaga 1680 ctattattaa gcaaggagct gcacctgttg tgcttaacat tgagcgagtt ttttcatctg 1740 tccagaaaaa gggtaagaaa aagaaaaatg ttaagccaaa caacaatggt gctgctaatg 1800 gtgtaaatgg tgttgtgaaa aagccgaaag gtaagtgttt tcactgcaag caacctagtc 1860 actggaagct acaatgtccg acatggctag ccaagaaaaa acaaggtaca tctccttttc 1920 atttactggt tgttgaaact tgtttagcgg tgttgactac acaccaatgg tgtgtagact 1980 taggagccac taatcatgtc tgcaattcat tgcaggggtt tcaggaaaca cgccagctaa 2040 gtaaagggga agtgaacatt tttctgggaa atggctctga agttgcagtt ttagctgtag 2100 gaaacattgc tttgaatttt aagaataata gaacattgtt tttaaagaat gtcttgtatg 2160 ttccttcgat tagaaggaat ttgattccaa tttctagttt gagtaagaac ggatattctg 2220 tttgttttaa tgaattttat gatgattctg tcgttattaa atttagagaa caaatgatat 2280 gttctggctc tttaattgat agtttatata ttcttaaagt tacacctgaa ctgcaactta 2340 ctaattctga agtaaataac tttgatattg tcgcaccatt gaaaagaaag cgtcctattg 2400 aattgagcta tacttatctt tggcatttga gacttggtca tattaattta gatagaattt 2460 ctttgttggt taaagatgga cctttgagtt cattgaaagt ggaggcacta ccaacgtgtg 2520 aatcctgtct agaaggaaaa atgactaaga gaccttttcc cttaaagggt aatagagcca 2580 acgatgttct tgaattaatc cattctgatt tgtgtggtcc aatgagtgtc caagctaggg 2640 gtggttttga gtattttgtg acattcacag atgattactc aaggtatgga tatatttact 2700 tattgtgccg taagtctgag tgttttgaga aattcaaagc attcaaggca gaaatggagc 2760 agcgacatgg aaaatatatc aagacattac ggtctgacca tggtggagaa tacatctcta 2820 gggaattcat taccttttta tcagaacaag ggattacttc acagttatct gcacctggta 2880 tgccacaaca gaatggtgta gcagaaagaa gaaataggac acttatggaa atggttagat 2940 caatgatgag ttattcagat ttgccaattt cattatgggg acatgcaatt gagacagcag 3000 catacattct gaatttagtt ccttctaagt cagtacctaa gactcctaca gaattgtgga 3060 ctggacgtaa gcccaacctg aaacatgttc ggatgtgggg ttgtccaaca catgtgttga 3120 aagggaaaac agataagttg gaaacaaaaa cagaattatg tttctttatt ggatatccta 3180 gatgaacgaa aggtggttta ttttatagtc ctaaatataa aaagatcatt gttagcacca 3240 atgcacatta tcttgaggaa aactatatta gaaaccatat tcccaaaagc caattagcct 3300 taaatgagtt gagaggagac accataccag ctagaatttt tccatcagaa catgaacctg 3360 aaccattcat ggtcggagct gacattccgt tacctcaacg tagtgggaga aatgttagtg 3420 gaccgaaatt tgaaacttct gacatttcat tgcctgttgg tgatgaagaa aatgttgaag 3480 caccagtaca tgtgccgttt gaagaatata ttgatgaagt acaggatgtg gtcccaccag 3540 tcataaactt gccggcctta cagccacagc aagatgaagg tgtggctgaa caacctgtag 3600 tacttcgtcg tagtgggaga acaagacgac caccggttca atatacactc ttgggagaag 3660 catttgatag aatccctgaa gaagtgaata ccgaaccagt atgttacgac gatgcactac 3720 aagataaaga tgctgataag tggcttgtag ctatgaaatc tgagatggag tctatgtact 3780 ctaatcaagt ctgggaactt gtagaaccac ctaaaggggt gaaacccatt ggatgtaagt 3840 agatctataa gaaaaagaga ggtatagacg gaaaagtgca aacttataaa gctaggcttg 3900 ttgcgaaatg gtatactcag aaagaaggga tcgattatga ggaaactttt tcgccagtag 3960 ccatgcttaa gtctattaga attctcttat ccattacagc ttatttcgat tatgaaattt 4020 ggcaaatgga tgtcaagata gctttcttaa atggaagtct tgatgaatgc atctatatga 4080 agcaaccaga aggtttcata acaaatgggc aagaacattt gctatgcaaa ttgaataggt 4140 ccatttatgg ccttaaacag acatctagat cttggaatac ttgttttgac cagacgatca 4200 agacttttgg ttttgatcaa tgtcatgatg agtcttgcgt gtataagaag tggaatggta 4260 agaaggtggt gtttttggta ctatacatgg atgatattct acttatagga aattgtatag 4320 gtatgttgac ttcggtcaag gactggttgt ctcagcgttt tgatatgaag gacttgggag 4380 aagctgctca tattcttggg atcaagctta tgtgaaatcg caagaaaatg atgataggct 4440 tatcccaggc actttatatt gatactattc tcaatcgttt caacatgcag ggttcaaata 4500 agggttttct tccttttaga catggaatcg ttctatctaa ggatcagtct cctaagactc 4560 ctgaagagat agaaagcatg aaggcagttc cttatgcttc tgcagtagga agtctcatgt 4620 atgcgatgtt gtgtactaga cccgatatct gttttgctgt tggcatggta agcagatttc 4680 agtttaaccc gggaagagaa cattggactg cagttaaaca tataatcaag tacttaaaaa 4740 gaaccagaga ttatatgtta gttttccagt cagaaaatct tgtgcccata gggtatacag 4800 attcagattt tcaatctgat caggactctc ggaaatctac ctcgggaaat gtttttgtct 4860 taggaagtgg agccattagt tggaggagta tcaagcaaac ttgtgttgct gactccacca 4920 tggaagctaa atatgtggca gcctctgagg cagccaagga agttgtgtgg cttagaaact 4980 tccttttgga tctaggtgtg gttccttcgg ttcaatcgcc tattacactt tattgtgata 5040 atagcggggc ggttgcaaac tcgaaagagc cacggagcca taaaagggca aaacacatag 5100 agcgtaagta tcacttgata cgagacatag ttcaaagggg tgatgtggtg gtgatgaaga 5160 ttgcatcgga aaacaaccta gcagatcctt ttacaaagag cttatcgtcc acgacttttg 5220 aaagacatgt agaaggaatg ggggttaaag tagcagatgc atggttataa gtctaagtgg 5280 gagat 5285 // ID Copia-31-LTR_VV repbase; DNA; EDCOT; 373 BP. XX AC CU459240; XX DT 01-SEP-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-31_VV, LTR retrotransposon Ty1-copia like, long terminal DE repeat from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Edel-B05; KW Copia-31-LTR_VV; Copia-31-I_VV; Copia-31_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-373 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL; CU459240; Positions 3626259 3626631. XX CC LTR = 373 bp CC LTR are 100 % similar to each other. CC Direct flanking repeats =ggagc CC UTL size = 39 bp CC gagpol putative polyprotein size = 1298 aa. XX SQ Sequence 373 BP; 73 A; 67 C; 90 G; 143 T; 0 other; tgttgggctt tgtggagcct agttttgttt gatccggttt gacgacccga cccgaataat 60 attgcatggc ctttttaatg ggagatttat tgaggcctgt tgggcccgtt tagcccattg 120 tggaaccacc ttttgtaatt agggtttttt agtatggtag ggttgccgtg ctatatatat 180 atagagaata ttgtagccgc tatgttgtac tctgtattct tccctgataa tagtgatatc 240 cctgcaactc cgtggacgta ggcaaattgc cgaaccacgt aaatactgtc ttgtgtgtga 300 ttgtttttct ttggcgtgtg ttttctctaa tttttgtttc tcacgggttg ggaattcggt 360 ttaattccct aca 373 // ID OGRE-I_PS repbase; DNA; EDCOT; 12496 BP. XX AC AY299398; XX DT 09-JUN-2005 (Rel. 10.05, Created) DT 09-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE Pisum sativum gypsy-like LTR retrotransposon Ogre (internal). XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Metaviridae; OGRE-LTR_PS; OGRE-I_PS. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-12496 RA Neumann P., Pozarkova D. and Macas J.; RT "Highly abundant pea LTR retrotransposon Ogre is constitutively RT transcribed and partially spliced."; RL Plant Mol Biol 53(3), 399-410 (2003). XX RN [2] RP 1-12496 RA Toth G.; RT "Pisum sativum gypsy-like LTR retrotransposon Ogre."; RL Direct Submission to Genbank (09-JUN-2005). XX DR Genbank; AY299398; Positions 19541 32036. XX CC Long terminal repeat of Ty3/Gypsy-like retrotransposon Ogre. 5bp CC target site duplications. XX SQ Sequence 12496 BP; 3350 A; 2528 C; 3126 G; 3492 T; 0 other; gctggcgact ctgctgggga aatagtgaag ttgacctgtg ctggtccatc ttccctgagc 60 gagtctctcc tagcgctctc taggttagga ttttggttgc tttgtgctgt gtttatttat 120 tgcattcatt atttgttcat ttcatttatt gattgcattg attgtgtgca ttaatgtttg 180 cattcatatt cattattcat tctgcctggc tggttgtctg tttttctttg tggggtggga 240 gtcagttgag gtaaaaggtc caatacccag accatgagtg aaatctagga tgattaggaa 300 tagagtgatt catgggaagc gagtggtatt gcgccactta gcggaacatt gatatcacga 360 gcagttcaga ccctggtggg atattgtcgt tacatacttc aggtgtgtat atgatggtat 420 tctgcgaaag gttatttatg ctgcgtttct ctcgacttta ccctggccta gacgacaccc 480 gtgagtaggg aagggttgat tattacaggt accgttggtg acttgtggtt ctgttggtga 540 ctttgggttc agacaacagt gtattcagtt gaccttgggt ttttcaagtt ggatttgggt 600 tctgattttg actgaagctt cgacctagtg atcagtttgc acaaccagcc agtcgagtct 660 gcatcatgtg catcatagca tatttatttt tcaaaagaaa tgcaaaaaga aaaaacgaaa 720 aaaaatgaaa aatgaaaaaa gaaaaaaaaa agagaaaaaa aactaatctc tgcatgcata 780 tcatttctca ggtacattct agagcttggt ctactgatag agatggcaac cgtcccagag 840 tcgaagcgga agacctgttc ctacagcttt tatcgtgagc cactgacttc attgatcgag 900 ttgggtagtc ttatgcctag tgaccaactg aagggttttg ttgggcagtt tggggatatt 960 ctgacgttgt tgaagacggt agttgatccg gtgccgctgc agacacttct tcagttctac 1020 gacccggagc tcagatgttt tacctttcaa gactatcagt tggcgcctac tctcgaggag 1080 tattctattc tgatgagcat tccgattcag catcaggttc ctttcctgga tgtaccaaag 1140 gaagttgact tcagggtgat tgccagagct ctccggatga gtgtcaaaga agtttgtgat 1200 aattggaagc ccagtgggga agtcgtgggt atgcctttga agtttctgtt gagggtagct 1260 agagaagaag ccgagaaggg gaattgggaa gtttttcatg cccagcttgc tgctatgatc 1320 tatgggatcg tcctattccc aagcatgccc aattttattg accatgcagc tatcagtatc 1380 ttcattggag ggaatccagt ccctaccctg ttagctgaca cttactatgc catccacagt 1440 aggcatggta agggtggagc catcaggtgc tgtctacctc ttctgctcag atggttcatg 1500 tcccttctgc cagccagtgg accctttatg gatactcaga gcactcttaa gtggactcag 1560 agggtcatgt cgctcacctc ctatgacatc agatggcagt cttaccggat ggatgtaaag 1620 gatgttgtta tgagttgtgg agaattccgt aacgtgccac ttgtggggac caagggttgc 1680 atcaattaca acccagtgct ttctcttcgc cagttagggt tcattatgag tagaagacca 1740 cttgaagctg agatagttga gagtgtgtat tttgagaagc gtactgaccc tgttagattg 1800 gagcagatag ggagagcttg gaagtctatt ggtgtgaagg atggatccgt cttagggaag 1860 aagtttgcca ttgcaatgcc cgattacact gattgggtaa agaagagagt ggaaacttta 1920 ttgctaccct acgataggat ggagccattg caagagcaac cacctttgat tcttgctgat 1980 agtgtgcccg ctgagcacta taagcaagcc ctgatggaga atcgtcggtt gagagagaaa 2040 gagcaagaca cccggatgga gttgtacaaa gccaaagctg ataagttgaa cttggcccat 2100 caactcaggg aaatgcaagg agaagatgct agcagagcaa ggagcaagaa gagatcttac 2160 aaggagatgg aatccatgtt ggatacagag catagggagt gtttgaggtt gcagagagca 2220 gaagtcaact atcaaaagaa gatcagagac ctagaaaagc aactcaaaga caaagacact 2280 cagttgaaga aagagatgga gttgagacag aaatcaaagg actatcttga agaagaagtc 2340 ttggagctta gaagacaact gaaggagaag atcacccctc taccagaatg ttcagaatgc 2400 acactgttga tagaccagtg ccattaccta aagaccctca ttccggaaga ccgactgtct 2460 tagactgtgc ctttgattat atttgttgag aatcacctcc aggcttgttg gaagggattc 2520 atttgcttgt actccgtctt ttggatcttt tttgttgaga atcacctcca ggcttgttgg 2580 atgggattca tttctttgta ctctgtttat tcgaatgttc tgtcgacttg gttgtatgac 2640 ctgtttaccc ttatttatag ataaggatgt cagtatttcc ctgttgttct catatttccc 2700 tgtatctgtt gttctcttgt cgctgcaggt tgccatcttt tcaggatggg tcaggctctt 2760 tgaatgcctg agaaatgagc acatcatgtg catcatacgc atcatttaat atcatactca 2820 tctcatttgc ataacaggtg ttcttgtgcc gacttctcac tttgattccg tgtccaggca 2880 ggatagctga tcaaagaccg caccgctact caacgagact caaccatcag aggaatatgg 2940 accaggttca aactgagtta gctgagatga gggctaacat ggcccagttc atgcacatga 3000 tgcaaggggt tgcgcaagga caagaagaac tccgagctct agttcagagg caagaagctg 3060 taactccacc gcccaaccag gctctgccag agggaaaccc agtccatgac actcctgctg 3120 ctgccattcc cgtcaacaac tatgctgtgg gtgaagagtt gatgggtatc cgagtcgacg 3180 gtcaaccaat tgctccagat gctgctaatg ccagagtcat tcatgctccg gcccgtaaca 3240 gaatcccgat tgttgacaga caagaggatt tgttcactat gttcagtgaa gacgaagata 3300 ttccgggaag aaatgatgcg agagatcgta aagttgacgc ccttgctgag aagattagag 3360 ctatggaatg tcagaattct ctcggttttg atgttaccaa tatggggttg gtggaaggtt 3420 tgaggatccc ttacaagttc aaagcaccgt ccttcgataa atacaacggt acttcttgcc 3480 ctcgcaccca tgtgcaggct tattatcgaa aaatctctgc atacaccgat gatgaaaaga 3540 tgtggatgta ttttttccaa gatagtctat ctggggcttc tttggactgg tacatggaat 3600 tgaagagcga ttctatccgc tgttggaggg atctgggtga ggcctttttg aggcaataca 3660 aacacaacat ggacatggca cctagccgga ctcagctgca gagtctatgt cagaaatcca 3720 atgaaagttt caaggagtac gcccagaggt ggcgtgaact ggctgctaga gttcaacccc 3780 ctatgctgga gagggagttg acagacatgt ttatcggtac tcttcaaggt gtgtttatgg 3840 accggatggg gagctgccca ttcggtagtt tttctgatgt tgtcatttgt ggagagagga 3900 ctgagagctt gattaaaact gggaagatcc aagatgttgg ttcctcttct tctaagaagc 3960 catttgctgg ggcacctcgt cgaagagagg gtgaaactaa tgctgttcaa caccgcagag 4020 atcagaacag aattgaatac cgtcaggctg ctgcagtgac tattccggca cctcaacctc 4080 gtcaacaaca acaacaaaga gttcaacaac cgcaacaaca acaacagcaa cgtccgtatc 4140 aacccagaca aaggatgcct gatcgacgtt ttgactcgct acctatgtcg tacgccgaac 4200 tgctgcccga actactcagg ttggggttgg ttgagttgtg tacgatggct ccgcctacag 4260 tattgcctcc tggatacgac gccaacgtcc gttgtgactt tcactctggg gcaccagggc 4320 atcatactga gaagtgtcgg gctctccagc ataaggtcca agatttgatc gatgccaacg 4380 cgatcaactt cgctccagtg cctaacgtcg taaacaaccc tatgcctcag catggtgggc 4440 atagagtgaa caatattgag gggaaagaag ctgaagatct ggttgataat gttgatgatg 4500 ttcagacttc tctgctagtt gtgaagagcc gtctgctgaa tgagggtgtc tactcgggct 4560 gtgatgagga ttgtttgggc tgtgcagaat cagagaatgg ttgcgaccag ttaagggccg 4620 gtatccaggg tatgatggat gagggttgtt tgcaattcag tagggctgta aaagatcgtg 4680 ggacagtgtc aactatcacc atttacttta aaccgtctga aggacatgga caaagggtcg 4740 tcagtgcacc tgcaacaaat ggtaccccag ttaccattcc cgtgcctgta accatcagtg 4800 ctccaactac tatcgttgcg tctggaagaa gggctgttga gaatagtaga gccgtgccgt 4860 ggaagtatga taatgcttat cgcagtaaca gaagggttga aagtcagaca aaaccagtga 4920 atcaaactcc agtgacaatt ggtttagcga atagagttcc tgcaactgtt ggtccagctg 4980 tggacaatgt ggggggtcca ggaggtttta ccagaagcgg tcgtctgttc gcaccgcagc 5040 ctttgaggga caataatgct gaggctctcg ccaaagcaaa gggcaaacag gctgtggttg 5100 aggaagagcc tgtccagaag gaagcgcctg aggggtcatt tgagaaggac gtggaggagt 5160 ttatgaagat gatcaagaag agtgactaca agattgtaga tcagttgaat caaactccgt 5220 ccaagatttc tatactttca ctgttgttgt gttctgaagc acaccgtaat gccttgctga 5280 agatgttgaa tctggcttac gtacctcagg agatttctgt caatcaactg gagggtgtga 5340 tggccaatgt gagcaccagg catggagtag gattcaccaa cctggactta ccgcctgaag 5400 ggcgaaacca taacaaagcc ttgcacatca ccatggagtg caagggggca gtgttgtctc 5460 acgtattggt agacaccggg tcgtcgctga atgtgctgcc taagcagatt ctgaagaaga 5520 ttgatgtgga agggtttgtg cttactccca gtgacctgat cgttcgtgct ttcgacagat 5580 ccaaacgttc tgtgtgcggg gaagttacct tgcctgtgaa gataggccct gaggtattcg 5640 atatcatctt ctatgttatg gacatccagc ccgcctatag ttgtttattg gggcgtccat 5700 ggattcatgc agcaggggca gtctcgtcga ctcttcatca aaagctcaag tatgtctgga 5760 acggtcagat tgtgactgtg tgcggtgaag aagagattct ggtgagtcat ctatcctcgt 5820 tcaaatatgt tgaggtggat ggcgagatcc acgaaacctt atgccaggtg tttgagactg 5880 tggctctcga gaaggtggcg tatgctgagc agaggaaacc aggtgtttca attacttctt 5940 acaagcaggc taaggaggtt gttgattctg gcaaagctga aggctggggc aagatggtgg 6000 atttgccggt taaagaagac aaatttggcg ttggttacga gcctctccaa gcagagcaga 6060 atggtcaagc gggtccgagt acctttacca gcgctgggct gatgaatcat ggcgacgtct 6120 ctgcaaccgg tagtgaagac tgtgacagtg attgtgattt ggacaactgg gttcgcccgt 6180 gtgcaccagg ggggtctatt aacaactgga cggctgaaga agtggttcaa gttactcttc 6240 tgacagagta attttctgtt gttttgtcat tttgcatgaa aatcctacgt tctgcccaag 6300 gcgtagtggt tcattgtagg gcctcatcat gttttaatga ttatcattaa tgaaggacat 6360 tttttgcaat caaactttat gatccctgtc tttctacttt ttgttttcat cctttttcaa 6420 aaacaataaa aatggcaatg tttttgtttt ttgtgacttt cttgaactct ttttctaaaa 6480 caaagcatta aacatgcaga agcgatctta tggcattcac tatgaacggt tctgttatag 6540 ctcagtatga tttcgacaat cccatctacc aagctgaaga ggagagtgag gaagactgtg 6600 aactccctgc agaattggtc agattgctga agcaagagga aagggtcatc caacctcacc 6660 aggaggagtt ggaggttgtt aatttgggta ctgaggacgc cacaagagaa atcaagattg 6720 gggctgcttt agaggactct gtcaagagga ggctgattga gatgctgaga gaatatgtgg 6780 agatattcgc ctggtcatat caagatatgc ctgggttgga tacagatatt gtggtgcatc 6840 gattacctct tagagaagga tgtccttcgg tcaagcagaa gcttcgtaga acgagtcctg 6900 atatggcaac taagatcaag gaagaggttc agaagcagtg ggatgctggt tttttggctg 6960 ttacaagtta tcccccatgg atggccaaca tcgttcctgt accgaagaag gatggcaaag 7020 tcagaatgtg tgtcgattac cgggatttga atagagcgag tccgaaagat gatttcccat 7080 tacctcacat tgatgtattg gttgataata cggctcaatc ctcggtattc tctttcatgg 7140 atggtttctc tggatataat cagatcaaga tggcgccaga ggacatggaa aagacgacat 7200 tcattacacc ttggggcacg ttctgctata aggtgatgcc atttgggcta aagaatgctg 7260 gtgctaccta tcagagggca atgacgactc tttttcatga catgatgcac aaagaaattg 7320 aagtgtacgt agatgatatg attgcaaagt cacagacaga agaggagcac ctggttaatt 7380 tgcagaagct gtttgaccgt ttgagaaagt tcaaactgag gctgaatccg aacaagtgta 7440 cgtttggggt gagatcaggg aagcttttag gcttcattgt cagtgagaaa gggattgagg 7500 ttgatccagc aaaagtcaaa gctattcaag agatgcctga accgaaaacg gagaagcaag 7560 tccgtgggtt tttagggagg ttgaactaca ttgcaaggtt catatctcac ctaactgcca 7620 cgtgtgaacc aattttcaaa ttgctaagaa agaatcaagc gatcaagtgg aatgatgatt 7680 gtcagaaagc ttttgacaag ataaaggagt atttacagaa acctccaatt ctgatacctc 7740 cagttccagg gagacctctg ataatgtacc tgtcagtgac tgagaactcg atggggtgtg 7800 tattgggacg gcatgacgag tctggtcgaa aagagcatgc catatactac cttagcaaaa 7860 agtttaccga ctgtgaaaca agatattcac tgctcgagaa aacttgctgt gctttggcct 7920 gggctgctcg ccgactgagg cagtatatgt tgaaccatac taccttattg atttctaaga 7980 tggatccagt gaagtacatc tttgagaaac cggccctcac cggacgcgtt gctcgttggc 8040 agatgattct aacagaatat gatattcagt acacgtcaca aaaggccatc aaaggcagta 8100 ttctgtcaga ctacctcgcc gagcaaccga ttgaagatta tcagcctatg atgtttgaat 8160 tccctgatga agacatcatg tatcttaaga tgaaagattg caaagagcct cttgtcgagg 8220 aaggaccgga cccggatgac aaatggacac tgatgtttga tggggctgtg aatatgaatg 8280 gtaacggtgt tggggcagta ttgatcaatc ccaaaggtgc tcatatgcct ttttctgcca 8340 gattgacgtt tgacgtcacc aacaacgaag ctgagtatga ggcttgtatc atggggatag 8400 aagaagccat tgatctgagg atcaaaactc tcgatatatt tggagattcc gctctagtgg 8460 tcaatcaagt caatggagat tggaatacga atcagccgca tttgattccg tatagagatt 8520 acaccagaag aatactgacg ttcttcaaga aggtgaagtt gtatcatgtc ccccgggatg 8580 agaatcaaat ggctgatgcc ttggctactt tgtcgtctat gatcaaagtt aattggtgga 8640 atcacgtgcc acatgttgca gtgaatcgac tcgagaggcc tgcgtatgtg tttgcagccg 8700 aatctgttgt gattgatgag aagccgtggt attatgacat caagaacttc ctcaagactc 8760 aagaatatcc tgaaggtgcg tcgaagaatg acaagaaaac cctgagaagg ctagctggaa 8820 gcttctattt gaatcaggat gatgtgctgt ataagagaaa ctttgacatg gtcttgctca 8880 gatgcatgga cagacccgag gcagacatgt taatgcagga agttcatgaa ggttcctttg 8940 gcactcatgc cggcggacac gcaatggcta agaaactgtt gagagcgggt tattactgga 9000 tgactatgga atccgattgt ttcaagtatg ctcggaagtg ccataagtgt caaatttatg 9060 ctgatagggt gcatgtacca ccaagccctc tgaatgtcat gaattcgcct tggccgtttg 9120 ccatgtgggg cattgatatg attgggaaga ttgagcctac tgcttcgaat ggacatcgct 9180 tcatcttggt tgcgattgac tatttcacca aatgggtgga agcagcttcc tatgctaaca 9240 ttaccaaaca agtggttacc cggttcatca agaaagaaat catatgtcgt tatggagttc 9300 ctgagagaat catcactgac aatggttcga atctcaataa caagatgatg aaagagcttt 9360 gtaaagattt caagattgaa catcacaatt cttctcctta cagaccgaag atgaatggtg 9420 ctgtagaagc ggcgaacaag aatatcaaga agattgtgcg gaagatggtc gttacgtaca 9480 aggattggca tgagatgctg cctttcgctt tgcatgggta ccgtacctca gtacgtacgt 9540 cgaccggggc aaccccttac tcccttgtgt atggtatgga agctgtccta cctgttgaag 9600 tggagattcc ttctttgaga gttttattgg atgtcaagtt ggacgaagcc gagtggattc 9660 gaacaaggtt taacgagttg agccttatcg aggagagacg gctagcagtt gtatgccatg 9720 gacagttgta tcagagaagg atgaagcgag cctttgatca gaaagtgcgt cctcgaagct 9780 atcagatcgg tgatctagtt ttgaagagga tcctccctcc cggtacagat aacaggggca 9840 agtggactcc taattacgaa ggtccatatg ttgtgaaaaa ggtattctcc ggtggagcct 9900 tgatgcttac aactatggat ggtgaagact ttccgtctcc tgttaactca gatgtagtca 9960 aaaaatactt cgcataaatt gacccgctgg acaaaaagaa aaaagagtcc aggcaaaaaa 10020 agggcatccc ggcgaaccaa aaaacagaaa gaaaaggttc gggcaaaaat tagggataaa 10080 atgaaaagaa tttgtacacc cggtaagtcg aaaacccgca agggcggctt aggcaaaaat 10140 gggtatcccg gtggattgaa aacccgaaag ggcgatccag ccaaaagagg gatcaaagcg 10200 aagactacag tctgagttgt ctgtacttca tcaagctttg tcgtctgcca tctcgaaaga 10260 tgtgatccgt ccagtcattc ttctcaaaaa gcaagaagtt gggaggaaaa ctgatgatct 10320 atgagttata acagaattgg gaaatagtgg atgccgtgtt cacattgcca ttaggataga 10380 tttttccttt tgtgcgcaat tacctctttc taggaattgc ctcccaatgt atttgccttt 10440 tcaggcgcat tttcaatcaa taaaagtcgt tattcagata aatggctctt ttgttttatt 10500 tttactgttt tgtttgcaaa aatgtccgaa tttttgataa gcattgcata taagaacatg 10560 aaggctacac aataatgtgc agaaagataa aacatttgaa aatcattttg aatgttgagg 10620 acacttgagc gtatcttgtc catgtatccc ctgggggcat tttgttgtgc tgtttttcag 10680 gttggcatct gtaaggacgt ttcctcagca gatattttcc ccaagcaagt ttggaagcta 10740 tcagagctat gttcccctgc ggagacgtct gtggatagcg ccttctattc cccaacagat 10800 ctaaggattg cctattccca gcaggcctgt atttgccgat tttcctcccc gagtgaggca 10860 ggttcattga aatttatctc cagcagttat cttatctgtg gactgaagga tatccccggc 10920 ggagtttacc tttccccagc agcagtgcta tcctccaaca cgagtgagaa gtcgttgctc 10980 tccctgcaga gtctccccgc agagttggag tacccgatca gttttggctc cccagccaga 11040 gtttttcatc attttttgca tttttgcatt tttagtgatc attgcatcct caaactgcgt 11100 agcattccca ttcaatatgg agcattacgc catagaaaaa ttcaaacata tgcattcatg 11160 tgttaacctc accagaccat atccccggca gaggcggatc atttcactca acatcagcac 11220 aacaagtctg ctacagttgc tctcgacaac attcaggatt gatatccccc acagaggttt 11280 atttcctcgc ccgttggtga cagaaagttt gtttctccca agtgagaccc cctgcaagtg 11340 gtcaaccttg ccctgacata tctaagatgt cgttcttgtg ataccagtaa gtgtcatgcc 11400 agcacccgcg tgtgtctcct tgtttggtgt tggtaaacac cattgtttcg gtgtctgtaa 11460 acatcgggta ttctccccag tcatcagtaa atgtctggtc atcactgttg cggtgtctgt 11520 aaacatcgag tctcactcca gtcatcagta aatgtctgat catcattgtt ttgatgtcag 11580 taaacatcga gtctcaatcc agtcatcagt aaatgtctgg tcatttttga tgtcggtaaa 11640 catcatcttt cgatgtcagt aaacgtcgag tcttttctac agtcatcggt aaatgtctga 11700 taatccccaa ctagagatcc ccagtagagt catcggtaaa tgtcctatct ggtttccagt 11760 tacaaacatt tgttttttcc cttagtgaag tgttccccgg tcatcggtaa atgtctggtc 11820 gtttgttttg atgtcggtaa acatcatctt tcgatgtcag taaacatcga gtctcatccc 11880 agtcatcagt aaatgattgg tcatgctttg tttccttgtt gataaaatca agatccccag 11940 aagtcgtcgg taaacgtctt gtctgattac accacgaaga ttttgttcct cctcaagtgg 12000 agacgccatc ggtaaatggc cccgtatgtt tcgatatcgg taaatattga atgcccagtt 12060 ttatccgcca tcgataaatg gccccgtatg cctcgatatc ggtaaatatc ggatccccag 12120 ttgcagtagc catcggtaaa tggtcgagtt gaagttgata tcggtaaatg tcaagttttc 12180 cttgaagctg ccatcggtaa atggttttgc ttccttttac atcagagttg tttcccagca 12240 gccatcggta aatggtcttg ctgaagttga tatcggtaaa tatcaagttg ccagtttcta 12300 accatcggta aatggtttcg cttttctgaa gttgtcactt gcaggcgtca tcagtaaatg 12360 acgtggttca tcttgtatca tatccggcag agtgcaaatt tctacggtcc ttggtattca 12420 atccctgttt accctgaagg tctgacagtc gttgctctca tccattcggg ttcccagctg 12480 attgaatagg ggcagc 12496 // ID Copia52-PTR_LTR repbase; DNA; EDCOT; 223 BP. XX AC LG_VII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia52-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-223 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-223 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 285-285 (2007). XX DR Genome; LG_VII; Positions 11315503 11315725. XX SQ Sequence 223 BP; 73 A; 36 C; 34 G; 80 T; 0 other; tgttaggaat cctgttagag atatattagg aatgaataac ttacatgagt tccctactgt 60 aatactaagt ctataggaca atgaattccg aggaagtgtt ggattcctag tagatgagaa 120 taactgtata tactcttgta taaatatgcg atgcaatcaa taataattct cattccagca 180 aattctattc ttctcaattc tattcttctc ttatcgattt aca 223 // ID Copia-47_Mad-I repbase; DNA; EDCOT; 5021 BP. XX AC ACYM01034867; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-47_Mad-I; KW Copia-47_Mad-LTR; Copia-47_Mad_. XX NM Copia-47_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5021 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1317-1317 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01034867; Positions 11448 16468. XX CC Positions [2336-2614] - Integrase core CC 'AAAAG' target site duplication CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS join(2558..3379,3383..4360) FT /product="Copia-47_Mad-I_1p" FT /translation="MPTSVLLDKSSFEVLFGVVPQISHLRIFGCACYPLLK FT PYLSTKLQPKTIKCVFLGYASQYKGYICYDVSGNITYISRHVIFDEHDYPF FT PDLSISKSSHTPSVMSQPPSFLPTFTNTNVVVLPVSHVPSTIDTTHTLSNS FT IESSLPTPQPSPMSSLSSPFVQPSPLSITGTSESSPSVPVVLESNAEAISS FT VHMHQGSSFQPEVLQVVLEIPPMNLHPMQTRSKSGIVKKNALLTTLQESGG FT VDLSLVEPLNYKNALTVLVWMKVMTEEIDALHSGTWSLVSLLANKNLVGCK FT WIFKIKKHADGSIARHKARLVPKGFSQEPGQDYGETFSHVVKPTTVRIVLA FT LAAHFGWSLRQLDVKNAFLHGIIQEEVYMVQPLGFVDPNHPHLVCKLHKSL FT YELKQAPRAWNERFTSFLPTLGFKSTYSDSSLFVKQVHYEIVILLVYVGDT FT IITGSASNAIQDVIHSLTIEFEIKDLGDLHYFLGIQISKTKTGLFLSQAKY FT VQDLLLKTEMNKSKSCDTPCLPYNRLLKDDGQPYGNPKLYRSIVGALQYLT FT FTRPAIAFSLHQVCQFMQNLMVAHFTAVKRILRYLQGTLHLGINYHIGALN FT LT" XX SQ Sequence 5021 BP; 1340 A; 1064 C; 911 G; 1706 T; 0 other; tggtatcaat cgcctatgat gcttgcgcat gatacgtcga tccatcttct tgctttcgct 60 gctttcgatt tctgtcttcg gctgcctctg atttctgttt cttgattctc aaggatttct 120 tcgtcttcgt gcacctacat tgtctagggt ttggctcgat cttgtgtggt ggtcgatctt 180 tccttgatat ctctctgtcg tgttcattcc aagtgtttgc gatttgttct cagtgaagtt 240 ttttcttgca cagtgatctg atttggttgt tttctgcaac aatagtgact gctgctcaac 300 ttacgattat tcaatctcca attacgtccc tcatttctac tatctccacg tccgtgaatg 360 tgaaattaga tgattccaac tacctgaatt ggcattttca gatgcaactc atgctggaaa 420 gcaatggcat tatgggattt gttgatggat ccaatcacta ccctgtgccc aatgtctctg 480 ctgcttctgg tatcaattct tctgactctt ctacttctaa gaaatgtgat aagttgctcc 540 atatggaaaa tgcatgatag gactgttatg caacttatta ctgcgacttt gtctccggtt 600 gctatgtctt gtgcgattgg taaccaaagc tcccaagaac tttgggttcg tcttaaagaa 660 caattttcca ttgtgtcaag aactagcata tttcaaatga agtctaattt gtagaacacc 720 agaaaagggt ctgataatgt cagtcagtat ttacataaaa tcaaagaggc tagagattac 780 ttggcagctg caggggttta ttttgctgat gaagacattg taattctagc cttgaatgga 840 ctccctcctg agtataatac cttccgatgt gtggttaggg gtagagaaag tgtgatttcc 900 cttaagtttc gatcccaatt attggctgaa aaaaaagtat tgtggataat gtttctgttg 960 ctccttcata tcccactact atggctgcta actctggacc tcctatgtct taagccccat 1020 tacttcagca gtctactggt tctcatggtc aatcttccta acctaatggt ggctacaagt 1080 cttttaatag gaacaaaggc aagggaaaat ttaattaagg tcagaggtca tttaactcaa 1140 gacctcaact ttacacacag actcatgttt tgcctacacc aacccctggt gttcttggtc 1200 aatctccagg tcaatactat tcttctccat ctgcccctct tattcctaca tgccaattgt 1260 gcaacagtga aggtcatact gcaccatttt gtggttctaa acctcctgag agatccaaat 1320 gtcacatctg tggcaaaaca aatctttcca catggtactg tttttataat gacaaaggtc 1380 caaattatat tggtggtggt tcctatcaga gttatcctcc gatgtcttct cagacttatg 1440 gaacttcttc tcaacatttc caatctcaac catcttctat gcatgctatg tatactgcag 1500 ttcaaccatc tcaggcatcc acctcttaag gcctccctca agtctggctt actgactctg 1560 gtgccacaaa ccatatgact gcagatctgt ctaacttgtc tttggcgact ccttatccat 1620 ccaatgaaac gattcaaaca gcaaatggtg aaggtttgtt agtatcacac attggtcaat 1680 tctgattaac accagagtga aaccaataac tttgaattct atcatttgtg taccaaaact 1740 tgttgtcagt acatcggatc tgtttggata acacctgctg gctaattttt gacacgtttt 1800 gcttttggat tcaggacaag gccataggga ggattctcta caaagggttg tgcagtaatg 1860 gactatatcc cattcctctt gcatcttctc catctatctt aaaaaataca acacaacaac 1920 ctcaagcata tattggtcag ctagcactat cttctacttg gcatcataga ctaggtcacc 1980 ctacaaataa aattgttaca ttgatgttgc ataaagctca tatccaatgt aaacaggtct 2040 cttcaccagt catatgtcac agtcgtctat aaggtaagtt ttgtaaactt ccttttcacc 2100 acagtgtcaa taagtttgtc caaccttttc acaccataca tagtgacctt tggggtcatt 2160 ctccttgtat ttccaaagat ggatataggt actatgtgat tttcgttgat gaatgtacaa 2220 ggccctattg gttatttcca ttaatcaata aaaatgactt gttctctgtg tttgttacat 2280 tttataacta tgttcaaact cagttctcaa gtcgtgttca gattttccaa agtaatgggg 2340 ggggggaaag tatattagca aacagtttca atcttttctt aaagataagg gtatccttca 2400 tcagaaatca tgtccctata ctcctgaaca aaatgggttg gctgagagaa aacataggca 2460 tcttatagaa acctcaatcc ctttattgca gaatgctaag ttaccttcct atttctggtc 2520 ctatgttgtc caaactacat catacctgat taatcgaatg cccacatccg ttctccttga 2580 taagtcttcc tttgaagttc tatttggagt tgttccacaa atttcccatt tgagaatatt 2640 tggttgtgcc tgctatccct tgttaaaacc atatctcagt accaaacttc aacccaaaac 2700 cattaaatgt gtgtttttag gttatgcttc acagtacaaa gggtatattt gttatgatgt 2760 atctggaaac ataacctaca tttctaggca tgttatattt gatgaacatg attatccatt 2820 tccagactta tccatttcca agtcctccca tacaccttct gtgatgtctc aacctccatc 2880 ttttttgcct accttcacaa acactaatgt tgttgttcta cctgtgtctc atgtcccttc 2940 cactattgat acaactcata cccttagtaa ttctattgag tcttctcttc caacaccaca 3000 accatcaccc atgtcatcct tatcttctcc atttgtccaa ccctcacctt tgtccattac 3060 tggtacatct gaatcttctc cctcagtccc tgtggtactt gagtccaatg ctgaagcaat 3120 atcatctgtt catatgcatc aaggttcttc atttcaacct gaagttttgc aagtagtact 3180 ggagattcct cctatgaatt tgcatcccat gcaaactaga agcaaaagtg gaattgtgaa 3240 gaagaatgct ttgttgacta ctctacaaga atctggtggt gttgatttgt ctttggttga 3300 gcctcttaat tacaaaaatg cattaacagt tcttgtttgg atgaaagtta tgacagaaga 3360 aattgatgcg cttcattctt agggcacatg gagtttggtg tcattacttg caaataaaaa 3420 tttagtcggg tgtaagtgga tatttaagat taaaaagcat gccgatggct ctattgctag 3480 acataaagct aggttagtgc ctaagggctt cagtcaagaa ccaggtcaag attatggaga 3540 aacttttagt catgttgtca agccaactac tgtcagaatt gttttggccc ttgcagcaca 3600 ctttggttgg agtttaaggc agttggatgt caagaatgca tttctgcatg gaattatcca 3660 agaagaagta tatatggttc aacctcttgg atttgtggat cccaatcatc cacatttggt 3720 ctgcaaactt cataaatctt tatatgagtt aaaacaagct cccagagctt ggaatgaaag 3780 gtttacttca tttctaccaa cactgggatt caaatctaca tactctgatt cttccttatt 3840 tgtgaaacaa gtgcattatg agattgttat cctattggtg tatgttggtg acaccattat 3900 tactggcagt gcatccaatg ctattcagga tgttattcac tctctcacaa ttgagtttga 3960 gatcaaagac ttaggcgatt tgcattattt tctgggaatt caaatttcca aaaccaaaac 4020 tgggttattt ctgtctcagg ccaaatatgt tcaggatttg ttactcaaga cagaaatgaa 4080 taagtctaaa tcttgtgata ctccatgtct accctataac agattgctta aggatgatgg 4140 tcagccgtat ggaaatccta agttgtatag aagcattgtg ggggcattac agtaccttac 4200 ttttaccagg cctgctattg ccttctcttt gcatcaggtt tgccagttta tgcagaatct 4260 aatggttgct catttcacag ctgtgaagcg catactcagg tacttacagg gcacattgca 4320 cttgggaatc aactatcata taggagcttt gaatctaaca tagtgatgct gattgggcag 4380 gagacccaaa tgatcaacga tccactactg ggttcgttgt tttttcttgg accaaatcct 4440 gtgtcttggt cttctaagaa acaacaaatt gtttccaggt cctctactga ggcataatat 4500 catgctttgt ctactacttc tgcagaactc gattggatca aacaattact tgtgtttcag 4560 catgttccta tatctcaagc tctagtattg ttttgtgaca atctctccac tactgggttc 4620 gttgtttttt cttggaccaa atcttgtgtc ttggtcttct aagaaacaac aaactgtttc 4680 caggtcctct actgaggccg aatatcatgc tttgtctact acttctgcag aactcgattg 4740 gatcaaacaa ttacttgtgt ttctgcatgt tcctatatct caagctctag tattgttttg 4800 tgacaatctc tccattattg ctctttcatt taatttggtt cagcatcaaa agaccaaaca 4860 tattgaaatc gatgtgcatt ttgttaggga acgagtggcc aagtgtttcc tccagagaac 4920 agtttgcaga tatcttgacc aagggattga gtgctccttt gtttcgaaca cattgtgaga 4980 atctcatgct tagcttatca aagcaagaga ttgcgggggg a 5021 // ID RAS_MT repbase; DNA; EDCOT; 848 BP. XX AC . XX DT 29-NOV-2006 (Rel. 11.11, Created) DT 01-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW Interspersed repeat; Inverted repeat; non-autonomous; RAS_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-848 RA Shankar R. and Jurka J.; RT "RAS_MT: A putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 602-602 (2006). XX DR [1] (Consensus) XX CC A putative MuDR like non-autonomous DNA transposon from Barrel CC Medic, which is present in the genome in large amount as well as CC well conserved. It has got 9 bp TSDs, flanking both termini. XX SQ Sequence 848 BP; 295 A; 142 C; 131 G; 280 T; 0 other; gagtttttct atttacaccc catgtttttc tggttacacc caaattttct taaaattttt 60 ttataatacc aaaattgccc ttttatataa attttcttaa aaccctaatt ttattcattg 120 tcagtgagtt tcaccctctt tcaccccaca aagcgatcga tcaaacaatt tgatgttcaa 180 tatcaatctc catgaaaatt aaagagtgaa tcaaaatatt tttcatccat actcaattgg 240 atataagtaa gtgaatttct tcttctattt gctagtttca atttttttcc ttcaactgca 300 atgatgcact gtacgattac ggttttaatt tacattggca aggttaactt aaattcagtt 360 taagtaggtt catgtaaact aagtttacat gaacctactt aaactgagtt tacatgaacc 420 tacttaaatt gagttaacat gaacctactt aaactgagtt tacatgaacc tacttaaact 480 gagtttacat gaacctactt aaactgagtt tacaaaatcg cagaactgtg aatcgcagaa 540 caaggaaaac acaaaatcag aactgagaac ccataacaag aaaaacacaa tcgattgaag 600 aacaacactt gctaacctga tttgcttcga attttctttg aaatcatgaa tggacgtgag 660 aaagtatggt tttgaaaatc ttcgcagaac acaatcgatc gattggagaa ttatggtttt 720 ggaagaaggg ttttggggtg taaccaaaaa agaaggaata ggctttttga aaatcaaatt 780 ttatgaaagg gtaatcttgt cattttgggg tgcaaccatg attaactagg gtgcaagtag 840 aaaaactc 848 // ID CAULIV1 repbase; DNA; EDCOT; 6042 BP. XX AC . XX DT 30-MAR-2007 (Rel. 12.03, Created) DT 30-MAR-2007 (Rel. 12.03, Last updated, Version 1) XX DE Caulimovirus-type sequence. XX KW Caulimoviridae; Integrated Virus; CAULIV1. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6042 RA Jurka J.; RT "CAULIV1: Caulimovirus-like sequence from Vitis vinifera."; RL Repbase Reports 7(3), 126-126 (2007). XX DR [1] (Consensus) XX CC This is a basic module of the virus. XX FH Key Location/Qualifiers FT CDS 21..3761 FT /product="CAULIV1_1p" FT /translation="MSRRSSDSQDTVVNSEEINYPKIQNDLDDWKLPKVSN FT QEIYKKGTFKFFTDYTIKTSEMTVSLEQDDQVIRLLDNRSVEKHKKDGYNF FT IHFGMIQVAAKPLTRLGLNTAIVMCLRDNRHLEYRDSIIGAVQAGLNDGPV FT YFQCYPNFTVRLRDADILDSVVLHIKTHGFKIKPGNSPVSIITRFAYKSMN FT TSVGSGALCTSPKGETTYFHSDMLDKSDFIIPKKILWKDVDFPENWHFANA FT VPAIAQRSESIEQIVQYPDGGGELVFSKSFRHSSSPRVSVYEPSRASSSSI FT PVRTTREEEGSSSGNPKNVKLTGVRSYTNVARPFYSEENESTQESQQDESP FT VMSPTYSQMINTISLSDEDFEINKDLLRKDFYSEVNKQRNDWFFSTVPKVI FT RTIYQEEFYAYLRQEKKNIKFWIWFELFKQEEYPDYPFKRIKVTSSNNENK FT PYEFSKDFQENPQVNQAFVDRINQKIKDNLVTPLTVQPDKRINMVKGDISS FT EEEADELIKMFEEPHNQIINNLETFKTRNYYPRPTFPDMQFEERNQYTQAS FT YTSGTIYEWNIDGMTEYNILTKLQEMTMVSTAYKLNNRLPDHAVAQTIVAG FT FTGQLKGWWDNYLTFDDKNSILKAYRINESNEVVKDEDGQDIEDAVATLIY FT SISKHFIGDPAKIKDKTADLLTNLKCPKLHDFRWYKEVFLTKVMLRSDCNQ FT SFWKEKFISGLPKLFSERIRIKIREQYNGQIPYDKLTYGEIISIVTGEGIK FT LCNDFKLKQQMKNEQKIYKNEFGSFCSQFGFSQKETMPPSKQKPSRKPSKD FT KFYHSKRGTHDNYRMNDTKHSRHVQRRVNKDTQKKVETPLDVKPIICFKCG FT KVGHYKKDCRVKQKINNLSVSDDLKNMLCKVMLNSDSESRTDSDNEDDINQ FT LDSSGDVSSQSSSDQDVCIKGNCNCRPKTINVISQDQEFILDTLRKVEDEK FT TKQNLYEVFKKSVVKVEAKKTVNPYNLNDILNRFDQQSPKDVSIKELHEEV FT KQHKKEIKELRQFISLGLSDLQDQINRIGNQEIHTDIPESSHVNDNETNTF FT LNTVSRVIFQRWEISLTIVVKDKFVFDIIALIDSGAAENCLQESLVPIPLC FT EETSESLFGANGQRLAIKYKLTDVHIRNHDICIKQTFILVKNLKEKALLGI FT PFLSSIYPLWVDNQGIRTKLFDKEILFEFANPIGCITPLNQEINLVGLDVP FT SKIIGNQFMHNDIINDILSISLCISKFQIGILNQEFY" FT CDS 3931..5289 FT /product="CAULIV1_2p" FT /translation="MAPKKNTQASSSQKSQSSQANQSPSTHKMLWSQQVEE FT EEAQLLAKLHSSKPMHESSHMPNKMLTLYYDPSDHSKPIKATQYPATSGSQ FT TFKQVTMANPSQKELATSSSFSSKQIVVAANPTPLSTKSRYWQNDLNQSLL FT VIEREFFSENPREIAAKAFQENFHYPSGDILKTREFYEAVLIETGSVKIKH FT NADKFSNMGLAFSTCHIYKILTVKQWGGNPNLSREFSEPSKPRFFNYWDYQ FT RAWFNAFLIQNRDFHHSWMFYFPSKNQLSSFPFWFYSWWTYYGPTIKILPK FT PILDGFELFRSSFNIPRELSAFPPLLFFFSNFGLAWIVQWDYIIITDESAA FT FPSLGRTFKTKWWDALKNDASTDAVKQYFLKNPSQVSASDDMSQFLLKKQQ FT LQAMLAAAKTPQEFQKILDEGSSSFSQENSYAESDDSTSYLPDNGDDCEGI FT LPPIRRSK" XX SQ Sequence 6042 BP; 1943 A; 1136 C; 1073 G; 1883 T; 7 other; tgagttcaat tttccgaacc atgtctagga gatccagtga ttctcaagat actgttgtaa 60 acagtgaaga gatcaattat cctaagattc aaaatgattt agatgattgg aaattaccca 120 aggtgtctaa tcaagaaatt tataagaaag gaacctttaa gttcttcaca gattatacca 180 ttaagacctc tgaaatgaca gtcagtttag aacaagacga ccaagtcata agacttctag 240 ataacagatc cgttgaaaag cataagaaag atggctataa tttcatacac tttggtatga 300 ttcaagtagc agctaagcct ttgacaagat taggtttaaa caccgctatt gtcatgtgtt 360 taagggataa taggcatctc gaatatmgag attctattat aggcgcagtc caagctggac 420 tgaatgatgg cccagtttat ttccagtgtt atcctaactt cacagttaga ttaagagatg 480 cagacatctt agattcagtt gtcctgcata ttaagactca tggctttaag atcaaaccag 540 gaaacagtcc tgtttctatc ataaccaggt ttgcctataa gagcatgaac acaagcgtgg 600 gatccggggc tctttgcacc agtcctaaag gtgagaccac ctattttcac tctgatatgc 660 tagataagtc ggatttcatc atccccaaga agatcttgtg gaaagatgtt gatttccctg 720 aaaattggca ttttgctaat gctgttccag ccatagcaca gcgttctgaa agtattgaac 780 aaattgttca atatccagat ggaggaggag aactggtctt ctccaaatct ttcagacatt 840 ccagcagccc tagagtttct gtttatgaac cctctagagc ttcaagctct tccatcccag 900 ttagaaccac tagggaagaa gaaggatcca gctcaggaaa tcctaagaac gttaagctaa 960 caggtgtcag aagttacacc aatgtggcta gaccatttta cagtgaagaa aatgagtcta 1020 ctcaggaatc ccaacaggat gagtcccctg ttatgtctcc tacctattcc cagatgatta 1080 acacaataag cctaagtgat gaggactttg agatcaacaa ggatctctta agaaaggact 1140 tctattctga agtcaataag caaagaaatg attggttctt tagcactgtc cctaaggtca 1200 ttagaaccat ttaccaagaa gaattctatg cctacttaag acaagaaaag aaaaatatta 1260 agttttggat ctggtttgaa ctcttcaaac aagaggaata tccagattat ccctttaagc 1320 gtataaaggt taccagtagt aataatgaaa ataagccata tgaattctct aaggatttcc 1380 aagaaaatcc ccaagtcaac caagcttttg tcgataggat taatcagaag attaaggata 1440 atcttgttac tcctttgact gttcagcctg ataagagaat caacatggtt aaaggtgata 1500 ttagttcaga agaagaagct gatgaactaa ttaagatgtt tgaggaaccc cataatcaaa 1560 ttattaacaa cttggaaacc tttaagacta ggaattacta tcctaggcct acttttcctg 1620 acatgcagtt tgaggaaaga aatcagtata ctcaagcctc atacaccagt ggtactatct 1680 atgaatggaa catagacggt atgaccgagt ataacatact cactaagctt caagaaatga 1740 ccatggttag tacagcctat aaattaaaca atagactgcc agatcatgct gtagctcaga 1800 ccattgttgc tgggtttaca ggtcagctta agggttggtg ggataattat ctcacttttg 1860 atgataagaa tagtatcctt aaagcctata ggatcaatga gagtaatgaa gttgttaagg 1920 acgaagatgg ccaagatatt gaggatgcag tggctactct aatctactca atatccaagc 1980 acttcattgg agatcctgca aaaattaagg ataaaactgc agatctctta accaacctta 2040 agtgtcccaa gcttcatgat tttaggtggt ataaggaagt cttcctaacc aaagtcatgc 2100 taaggtcaga ttgtaaccag tctttttgga aagaaaaatt catctcagga ttacccaagc 2160 ttttctctga gagaattagg atcaagataa gggaacagta taacggtcaa atcccttatg 2220 ataagctaac ctatggtgag attataagca ttgtcacagg tgaagggatt aagttgtgca 2280 atgacttcaa gcttaagcaa caaatgaaga atgaacaaaa aatctacaag aatgaatttg 2340 gatcattctg tagccagttt ggtttcagcc aaaaagaaac tatgcctccc tctaagcaaa 2400 arccaagtag gaagcctagc aaagataagt tttaccacag taagagaggt acccatgaca 2460 actataggat gaatgatact aagcattcaa ggcacgtcca aagaagggtc aacaaagata 2520 cccagaaaaa ggtagaaact cctttagacg tcaagccaat tatctgtttt aaatgtggca 2580 aagttggcca ttataaraaa gattgtagag ttaagcaaaa gattaacaac ttaagtgtct 2640 cagatgacct aaaaaatatg ctttgtaaag taatgttaaa ctcagactct gaatcaagga 2700 ctgattcaga taatgaagat gatattaatc aactagatag cagtggcgat gtttctagcc 2760 aatcttctag tgaccaagat gtttgtatta agggtaattg taattgtcgt cctaaaacca 2820 taaatgtcat aagccaagat caggaattca tcctagatac tttaagaaaa gttgaagatg 2880 aaaaaactaa gcaaaatctt tatgaagttt ttaagaaatc tgttgttaag gtagaagcca 2940 agaagactgt taatccttat aaccttaacg atatcttaaa caggttcgac cagcagtctc 3000 ccaaggatgt cagcattaag gaacttcatg aagaagttaa gcagcataaa aaggagatta 3060 aggagttaag acaattcata agtctaggtc tctctgatct ccaagatcaa atcaatagaa 3120 ttggcaacca agaaatccat acggatattc cagaatcktc tcatgttaat gataatgaga 3180 caaatacttt tttgaatact gtragtaggg ttatcttcca gaggtgggaa atctccctta 3240 ctatagtagt caaagataaa tttgtctttg atattattgc cttgattgat tcaggagcag 3300 ctgaaaattg ccttcaagaa agtctggttc ctattccttt atgcgaagag actagtgagt 3360 ctctatttgg agccaatggc caaagacttg ccattaagta taagttaaca gatgttcata 3420 tccgtaacca tgacatctgt attaagcaaa cctttatcct tgttaagaac cttaaggaaa 3480 aagcccttct aggaataccc ttcttaagct ctatttatcc cttgtgggta gataaccaag 3540 gtataagaac taagcttttt gataaggaaa ttctttttga atttgctaat ccaattggat 3600 gcatcacccc tcttaaccaa gaaattaacc ttgttgggtt agatgtccca agtaagataa 3660 taggcaacca gttcatgcat aatgacatta taaatgatat tttaagcatt tctttatgca 3720 tttcaaaatt tcaaattggg attttgaatc aagaatttta ttaaaagttg ttttcaaaga 3780 ttttggaaaa ctattaaata tataactttt aagtatgatt taattcactg gtatattatt 3840 ttaaaatcta agtttcaaag ttactttatt aaaggagatt atttcaaccc taatcagcta 3900 tctcgtgaat tttgcagggt tcatgagatc atggccccta aaaagaatac ccaagcttct 3960 agctctcaaa aatcccaatc cagtcaagct aaccaatctc cttctaccca taaaatgctt 4020 tggagtcaac aagttgaaga ggaagaagca caacttttgg caaagcttca ttcttctaaa 4080 cctatgcatg aatccagcca tatgcctaac aaaatgttaa ccttatacta tgatccttct 4140 gatcattcta aacctattaa ggcaacacaa tatccagcta cctcagggtc tcagaccttt 4200 aagcaggtta ctatggctaa tccctctcaa aaggaattag caacaagctc ttctttttca 4260 agcaaacaaa ttgtggtggc tgccaacccc acacctcttt caacaaaatc aagatattgg 4320 caaaatgatt taaatcaatc tcttttagtt attgaaagag aatttttctc tgaaaacccc 4380 agagagattg ctgcaaaagc atttcaagaa aattttcatt atccctctgg tgatatttta 4440 aaaacaagag agttttatga agcagtcctt atagaaactg gttctgttaa gattaagcat 4500 aacgctgata aattcagcaa tatgggcttg gcattctcca cctgccatat ctataagatc 4560 cttacagtca agcaatgggg tggaaatcct aatctttcaa gggaattttc tgaaccatct 4620 aagccaaggt tttttaatta ttgggattat cagagagcat ggtttaatgc ttttctgatc 4680 cagaataggg acttccatca ttcatggatg ttctattttc catctaagaa tcagctttcc 4740 tctttcccat tttggttcta cagttggtgg acttattatg gtccaactat taagattctt 4800 cctaagccca ttctggatgg ctttgagcta ttcagaagtt cttttaatat tcccagagaa 4860 ctttcagctt ttcccccttt actattcttt ttcagcaatt ttggcctggc ttggatagtc 4920 cagtgggact atattattat tacagacgaa tcagcagcct ttccatctct gggaaggact 4980 tttaaaacta aatggtggga tgcattgaaa aatgatgcat ctactgatgc agtcaagcag 5040 tatttcctca agaacccctc acaagtctca gccagtgatg atatgtctca gtttctcctc 5100 aaaaagcagc agttacaagc catgctcgca gcagctaaga cccctcaaga gtttcagaaa 5160 atccttgatg aaggaagctc aagcttttcc caagaaaatt cttatgcaga gtctgacgat 5220 tcaacaagct accttccaga caatggtgat gactgtgaag gaatccttcc tcccataaga 5280 agatctaagt aatcatcagc cttttgtctt ccatcaaaag ttttttacaa gctttgcagt 5340 atctgttcca aaagcagcaa gcatgtgtct tcacagtata aagcagcttg ccagaagtct 5400 tctcagccga aaaagggtgt ttcggggttt ttcggtataa tagtgaatct tactattcac 5460 tgttcactat tcactattca agcacgggtc tactgttcat ggttactgtt caagattcct 5520 tttttgccta tttaaggagg ctcgggcctc atttgtaagc acgttcattt ttaagctgaa 5580 gctctccctt ctctcttctt tctctctctt ccttctctct tctctctctc tcatcatgta 5640 acctcttcaa gtcttcaagc tttcttcaag ctttcctacc cttgtccatt gtaagatatt 5700 tctccttatg tataatataa gtatgttttg attacctcct atatggatgg tttttaatta 5760 agttttaatt tttattttat ttttcatttt attttatgtt ctkataccgc ctatatggtc 5820 ggttttaatt aagctttatt tttaagttta tgtttttatt ttgtaccgcc tacatggtcg 5880 gttttaagct tattatgaac taacaagttt tttggttcyt tctctttaaa tttctttgtt 5940 ggatatcttg tttgatttct aaccctcttc tttgttttga atcactggca taattcattt 6000 gttcatttgc atatgacctt gtcctgggtg tctatggtat ca 6042 // ID Gypsy24-PTR_I repbase; DNA; EDCOT; 4612 BP. XX AC LG_II; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy24-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4612 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4612 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 328-328 (2007). XX DR Genome; LG_II; Positions 21467597 21462986. XX CC Positions [3532-4011] - Integrase core CC 'CTAAC' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 37..4611 FT /product="Gypsy24-PTR_I_1p" FT /translation="MTHETRSQDIKKLEGAIATTNKEQGLWNDKMAKLLEQ FT QGQQQLSSDTRLLRLEELISGISLQQNTLLQKLQLPTGATSSNQEYHRSSQ FT EGMLYKNDWQQSGSYKFHKPRRDFPSFEGEDVHKWLYKCNQFFEMEEVPET FT EKLKLASYYLDGVALYWHQNFMRSKVGQLVTWKEYVEGLCGRFGGHKEPLE FT ELKDLKQEGDLETYIRNFDILWNRAEIDERYALIFFLGGLETEIKNLVKMF FT EPKSLNQAYNLSRLQENTNLYKSSHNQPIKQPTSPFSNNQTSNQQQSPYKP FT NKFLESTSQHSTQPGLLPTPQTHNGIQPMRRPTRNVRSTEMEERRVKGLCF FT WCDDKFTPGHKCRTRKLYSICLVGDDEGETDNMVESGQESGVLIDTDPHIS FT MNALEGVPGCYTLKVTGRVDKLPIFILIDSGSTHNFMNTWVASQLQCVLSP FT INPVTVKAANGGKMLCSSICRGFRWKMQGIHCEADVFVMELEACDMVLGVQ FT WLATLGDIVCNYKSMWMSFEWQGQQTTLRGEEPVKLQSVQFGQMSGLLSNR FT TSIAGINLCSLRMIQDTPDTATSTSAKNLNKEEKAALQQLLHLYQDVFIPL FT VGLPPSRSHDHTIPLKEGAQPVNLRPYRYSSLQKDTVEGLISEMLEAGTVQ FT PSHSPFASPVVLVKKKDLSWRLCIDYRALNRLTIKNKFPIPLIEELLEELT FT GASVFSKIDLRSGYHQIRMNSGDIHKTAFRTHNGHYEFLVMPFGLTNAPAT FT FQSLMNEVFRAYLRKFVLVFFDDILIYSKSYTQHQAHLQTVFELLRSHQLV FT AKESKCVFCDDRVEYLGHIISKEGVATDPEKLQAIKNWPLPQSIKQLRGFL FT GLTGYYRKFIRSYGIICRPLTRLLKKDAVGWDQEATVAFEALKKEMMNPPV FT LALPDLSKIFIVETDASGAGIGAVLMQEGHPIAFISKALGPRQQSLSTYER FT EMLAIIMAVHKWKQYLWGRSFKIRTDHVSLKYLLDQKLSFPSQHLWLTKLL FT GFDYEIEFRSGRENIAADALSRISSNELHTLTLSTIEAPVLDNIKQSWQED FT NKIQAIIQDLIKDPATHPHYKWSNNYLFRKGKLVVGHNPTLQHQLISMYHD FT TSLGGHSGSTVTTARLASMFYWRKQQKQVRQYVRECPTCQRCKTENVASPG FT LLQPLPVPTAPFTDISMDFITNLPKSEGKEVIFVVVDRFSKYAHFMALSHP FT YSATTVAKTFMNSVYKLHGMPATIVSDRDTIFLSKFWKELFALQGVNLHYS FT TAYHPQSDGQTEVVNRCIEGYLRCMTGDNPSQWCKWLALCEWWYNTNFHTA FT TKTTPYNILYGFNPPIHIPYFPKDSALEAVDHYLTTREQLLQTVKLNLTKA FT HNRMRQLANKKRSDRVLEVGDSVYLKLQTYKQRSILHPHHKLAAKYYGPYT FT VIKKIGEVAYKLNLPSSSTIHPVFHVSLLKRSRGNRMVHHSLPDSPHEPLL FT QPQVIMDRRMVKRGTQAATQVLIHWKGLSPAEATWEFIDDVQLRFPTFNLE FT DKVTLKDGD" XX SQ Sequence 4612 BP; 1455 A; 1012 C; 1001 G; 1144 T; 0 other; agtggtatca gagcttctat cttcggaccc tgaacaatga ctcatgaaac taggtctcaa 60 gatattaaga aattggaagg ggcaatagca acaactaaca aggagcaagg tctgtggaat 120 gacaagatgg ccaaactgct agaacaacaa ggacaacagc agctgtctag cgatacacgc 180 ctcttgaggt tggaggagct catttcaggt atttcacttc agcagaatac cttactacaa 240 aaactacagt tacctacagg agcaaccagc tccaaccagg agtatcaccg cagcagccaa 300 gaaggaatgt tatacaagaa tgactggcag cagagtggat cttacaagtt ccataaaccc 360 aggcgagatt ttccatcatt tgaaggggaa gatgtacaca aatggttata caagtgcaat 420 cagttttttg aaatggaaga agtccctgaa acagagaagc ttaaactggc ctcatattac 480 ttggatggtg tggctttata ttggcaccaa aatttcatgc gaagcaaggt tggccagcta 540 gtaacttgga aggaatatgt ggaaggctta tgtggcaggt ttggtggcca taaagaacct 600 ttggaagaat taaaagatct gaagcaagaa ggcgatttgg agacttacat caggaatttc 660 gatatcctgt ggaatagagc tgagattgat gaaaggtacg ctttgatttt cttccttggt 720 ggacttgaga cagaaattaa gaacttggta aaaatgtttg aaccaaaatc ccttaatcaa 780 gcctataatc tgtcccgttt acaagaaaac acaaacctct acaaaagttc tcacaaccaa 840 ccaatcaagc aaccaacctc accttttagc aacaatcaga cttccaacca gcaacaatct 900 ccatacaaac caaataaatt ccttgaatcc acttcccaac actctactca accagggttg 960 ctacctaccc ctcaaacaca caatggaatc cagccaatga gaaggcctac ccgaaatgtt 1020 cgaagcactg agatggaaga aagaagagtg aagggcttat gtttttggtg tgatgataag 1080 tttacaccag ggcacaaatg cagaacacga aaactttatt ccatatgctt agtgggtgat 1140 gatgaaggtg agacagacaa tatggtagaa tcggggcagg aatcaggagt gttgatagac 1200 acagaccccc acatttccat gaatgcatta gaaggggttc caggatgcta caccctcaag 1260 gtgacaggta gggtagacaa actaccaatc tttatattga tagactcggg tagcactcat 1320 aatttcatga atacttgggt tgctagccaa cttcagtgcg tcctaagccc catcaaccca 1380 gtaacggtca aggctgccaa tgggggaaaa atgttatgtt cttctatttg caggggtttt 1440 agatggaaga tgcaaggaat acattgtgag gctgatgtat ttgtcatgga attggaggcc 1500 tgtgacatgg tcctaggggt ccagtggtta gccaccctgg gagacattgt gtgcaattac 1560 aaaagcatgt ggatgagttt tgaatggcaa gggcaacaaa ccaccttaag gggagaagaa 1620 ccagtgaaat tacaatcggt tcaattcggt cagatgagtg gtctactgag caacaggact 1680 agcattgcag gtatcaatct ctgcagcttg aggatgattc aggacacacc tgatactgca 1740 acatccacct ctgcaaagaa tcttaacaaa gaagaaaagg cagccctaca acaactactt 1800 cacctctacc aggatgtctt cattcctttg gttggactac cacctagtcg gtctcatgac 1860 cacaccattc ccttaaaaga aggagcacaa ccagtcaacc tacgtcctta caggtattcc 1920 agcctacaaa aggatacagt ggaagggcta atctctgaaa tgttggaagc aggcacagtc 1980 caaccaagcc atagcccatt tgcatcaccg gttgtattgg ttaagaaaaa ggatctttcc 2040 tggcgattgt gtattgacta cagggctctt aacagactga ctatcaaaaa caaatttccc 2100 attcccctga ttgaagagct gctggaagag ctgacaggag catcagtctt ctccaagatt 2160 gacctacgtt cgggttacca tcaaattcga atgaactcag gagacatcca caaaacagcc 2220 ttcagaacac acaatggcca ttacgaattc ttagtgatgc ctttcggtct tacgaatgcg 2280 ccggccacct ttcaaagctt gatgaatgag gtgtttcgag cttatttaag gaagtttgtt 2340 cttgtgtttt ttgacgatat tttgatttac agtaagtcct acacgcagca tcaagcacat 2400 ctgcagactg tttttgagct gctcagatca catcagttgg tagccaaaga gagcaagtgt 2460 gttttttgtg atgatagggt ggaatacctc ggccatatta tatctaagga gggggtagca 2520 actgatccag aaaagctaca ggccatcaag aattggccac tgcctcagag catcaaacaa 2580 ttgaggggat tcttgggact cacggggtac tatcgcaaat ttataagaag ttatggcatt 2640 atttgtcgcc ctctgaccag gcttttaaag aaggatgcag tgggttggga ccaagaggca 2700 acggtggcct ttgaagctct taaaaaggaa atgatgaacc ctccagtcct agcactaccc 2760 gatttgagca aaatttttat tgtggagact gacgcttcag gtgctggtat tggagcagta 2820 ctcatgcagg aaggacatcc aattgcattt attagcaagg cattgggacc aagacaacag 2880 tcgttatcta catatgagag ggaaatgcta gctatcataa tggcagtaca caagtggaag 2940 cagtatttgt ggggcagatc cttcaagatc agaaccgatc atgttagctt gaaatactta 3000 ctagatcaaa aactatcttt tccttctcag catttgtggc tcaccaaact attggggttt 3060 gattacgaaa ttgaatttcg tagtggaagg gagaatattg cagctgatgc tctttccaga 3120 ataagtagca atgaactcca taccctcact ctatcaacaa tagaggctcc agtactggac 3180 aacatcaaac aatcatggca agaagataac aagattcaag ctatcatcca ggatctcata 3240 aaggacccgg ctacacaccc tcactataaa tggagcaaca actacctttt cagaaaaggc 3300 aaattggtgg tgggacacaa tccaactctt cagcatcaac tcatttccat gtatcatgat 3360 acttccttag gcggacattc gggttctaca gtcactaccg caaggcttgc cagcatgttt 3420 tactggagaa aacagcagaa acaggttagg cagtatgtta gagagtgccc cacctgtcaa 3480 cgttgcaaaa cagaaaatgt ggctagccca gggttgttgc aaccacttcc agtgccgaca 3540 gcacccttca cagatatcag tatggatttc ataacaaacc tcccgaaatc agaaggcaag 3600 gaagttatct ttgtagtggt ggatcggttt agcaagtatg cccactttat ggcactttca 3660 catccgtatt cagctaccac cgtggcaaaa accttcatga actcagttta caaactgcat 3720 gggatgccag caaccatagt aagtgatcga gataccattt tccttagtaa attttggaaa 3780 gagttattcg ccttgcaagg agttaatctc cattactcca ccgcctacca tccccaatct 3840 gacggacaaa cagaagtggt caaccggtgc atagaaggct acctcaggtg catgactggc 3900 gacaatccct cgcaatggtg caaatggttg gctttgtgtg aatggtggta taatacaaac 3960 ttccataccg ctacaaaaac tacaccctac aacatattat atggttttaa tccacccata 4020 cacatccctt atttcccaaa agattcagct ttggaagcag tcgatcatta cctcactact 4080 agggaacaat tgctgcagac agtcaagctc aacctcacca aagcacataa tcgaatgcga 4140 caactggcta acaaaaagag aagtgacagg gtcttggagg taggcgattc agtctattta 4200 aaattacaaa cttacaaaca gagatccata cttcacccac accacaaatt agctgccaaa 4260 tactatggcc cctacactgt catcaaaaag attggggaag tagcatacaa actcaacctt 4320 ccatcttctt ccaccatcca tcccgttttt catgtatctc tattgaaaag aagcagggga 4380 aatcgaatgg tacaccacag tttacctgac agcccacacg agcctctgct acagcctcaa 4440 gttatcatgg atagaaggat ggtcaaaagg ggaacacaag ctgctacaca ggttttaatt 4500 cattggaagg ggttatcgcc tgcagaagca acatgggagt tcatagatga tgttcagtta 4560 aggtttccaa ctttcaacct tgaggacaag gtgactttga aggatggaga ct 4612 // ID Gypsy-3_Mad-LTR repbase; DNA; EDCOT; 2351 BP. XX AC ACYM01138405; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-3_Mad-I; KW Gypsy-3_Mad-LTR; Gypsy-3_Mad_. XX NM Gypsy-3_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2351 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1406-1406 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01138405; Positions 2050 4400. XX SQ Sequence 2351 BP; 644 A; 426 C; 496 G; 784 T; 1 other; tgtgacagcc cgtcccgaat tatggttttc gaaagtgtga agttaataaa ttatcattaa 60 gtgttttaac gatttagaac attagggttt atttagttac cctagtttta aaaaaaggat 120 gattttggac gttttgtttg tttgtgttga tgagtgtggc ttttggaacc catacactca 180 cggacacact cattcccttt ttctttcttt cccgtgattc cctcaacctc actcacactc 240 tctcttcctt cgaaaattct cattctctct ctctctacac acggacaacc tcaaggatca 300 tcaaatcttc acagatcgaa gaaacaaaga ccaccatcgt cttcatctcg tcgatacgag 360 ttcatccata cccatttcag gtaagaattt caacgttttc acgtcgaacc actcacttcc 420 gttttgtgca ctattcatca actttgtatt ggttgatttt ttaggagttt ttaagctcat 480 agggagctta agaaggttct taggaagctc ggagtgcttc gttggaagtt tttagacgta 540 agaatatcga gatcgaaaag ttcaagtttg acccgtgcct tttgagccaa tttccggcca 600 aaccatggcg atttggccga catgcaaggt atcaatctct tcatctcgtc gagtaataca 660 actttccttt ttgtttcact caatttcgtt gagtattgaa cacgttatac tcatttgaat 720 cttacccagt ttccggcgac ctctgaggct ttcgaggaat attccggcca aaagacggcg 780 agctagatgt cgtgtgaggt accattctct tcgtctcttc aagggctata actttcattt 840 ttgaatcact tgatttagtt gagaaatgac aaagttatgg caatttgaaa aactgcccag 900 aaacaggaaa aaaccagtcc ggcgagccga ggaagaagac gcacgtgggg gcgcgtaggt 960 ccgtgccacc cacggtgcgt gggggcacgt gacaagccca aaaattattt taaaaatatg 1020 tcgacgtccg tgacgtcgag taggtcacga tggtatattc atatacccaa attgagcaat 1080 gtatgagaag ttattagtga atgttgtgta tgtgctttta aataatgttt ttataattat 1140 ttctcttata ggcgagacct atacggagga cgagcgtaac cagactaggc gtgggggtta 1200 cgaaccggct acatatcagt gagtgggcag ttattttcag tatatatata tatacgtata 1260 cttgacgttt ttcccagaaa acgtatttaa aggaaatgtg atttaagtat cttgtcatat 1320 atgcatcata ttttagtatg tgcattatca taattatgca tattgttgca tggtgctgaa 1380 gaggcccagg taagctacat gtgagtatat tatgctggta acgattatga gatacgatgt 1440 tggttatgat taagatatgg ttatgatatg atggagatat gatgaattat atgattgaga 1500 tatgattgag agctcattca cttgcacacg tatattagtg ctccgcctag agttaggggc 1560 acagtctttc acgtgatgtt cacctctcgc accacatgct cgccttggat ccaagttagg 1620 tgcacagtcc tgtcgtatag accactttta atggattcga ctcgtaggtg acccgcgaat 1680 tatcgtacag tcttcacgtg attgtagcac tagagcatat tatgttatat acagtgatga 1740 attgcagacc acgtgaggtg gtattgaatg tgtgcaggat atacatatat acatgatgtg 1800 atgagatgat tatgagctat atatgcagtc gatggctgag ttgattacga tgaaagagta 1860 taaactatat tcatagccga ggattgaatt gattatatgt tattccatca tattcgcata 1920 gagatgatga gcatttagtt gtgatatttg gcatgacata cgttcataat gtctagtatg 1980 attttgagat atattacgtc tatatatact ttatttttgg gaaattatac ttattttatg 2040 gcgaggggtt agtatattca aagagaaaag aaggttttga ataagtttgt tatactgacc 2100 cactcaactt tgttttgcgc ccctccaggt tttaagtagc gttgttggtg gatctcgagg 2160 tttccagctg aagttctgac aaaccatcac tcatgtagga ccatctttga gtgttgttaa 2220 attagtacat cttatgtttg actgcactta gaccttgtgc tctggttgtg tattcacagt 2280 taaacttact tgagaaccta tggtatttgg ttttaattat tcgtactttc cttaaaaata 2340 tckcttccgc a 2351 // ID Copia1-PTR_LTR repbase; DNA; EDCOT; 332 BP. XX AC LG_XI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia1-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-332 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-332 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 191-191 (2007). XX DR Genome; LG_XI; Positions 13092016 13092347. XX SQ Sequence 332 BP; 102 A; 69 C; 44 G; 117 T; 0 other; tgcacctgca aagacaatta catcagcaaa tcatataaaa tctgctagtc ccatgcaatc 60 tgctgattct actacatcag ccttggaagt ctcctaatcc caagaaactg cattccttag 120 ttagaatgat taattgacat tccctttgta atacatgtaa ttgattggac ttaccttaca 180 ttgctgagtt tctgtaaata gaaaagtcta cctatgtact aatatttata ctgcatacaa 240 cttaatagaa gacacggttg tgtagcaata attctcaatc tctctgctct catctttttc 300 tcttccattg agtttataat tcttatatgg ta 332 // ID EnSpm-3_VV repbase; DNA; EDCOT; 15169 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE EnSpm-3_VV, an autonomous DNA transposon - a consensus sequence. XX KW EnSpm; DNA transposon; Transposable Element; CACTA; En/Spm; TIR; KW Cactavine-3; EnSpm-3_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-15169 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 755-755 (2008). XX DR [1] (Consensus) XX CC EnSpm-3_VV (Cactavine-3 in [1]) is an autonomous element. Its CC individual copies are >80% identical to the consensus sequence. CC It is questionable whether individual copies contain an intact CC ORF due to premature stop codons and/or frameshifts. EnSpm-3 CC contains short TIRs which are flanked by 3 bp-long TSDs. CC Downstream of the TPase gene (region 8938-12854) is another ORF CC encoding for a ULP1-like protein similar to CAN73872.1 (aa CC 839-1482). Although ULP1 (or Peptidase C48) -like proteins are CC usually found in Mutator elements, our study shows that such CC proteins are common in CACTA elements as well. This feature is CC not restricted only to Vitis as similar examples were found in CC rice [1]. XX FH Key Location/Qualifiers FT CDS join(4947..7411,7502..7607,7691..8344) FT /product="EnSpm-3_VV_Transposase" FT /translation="MDRSWISKDRRSKEYEDGVERFITFAIQNSANKNSIK FT CPCLQCGNMIFHTPQKIREHMFFHGIDQSYHTWYWHGEVAPSGPPTTRAEH FT YDRVQFDDVHSTIEMVQAAQEDCKNDPESFQRLLKDAEKPLYPGCRNFTKL FT SALIKLYNLKARFGWSDKSFSELLEMLGNMLPVNNELPLSMYEAKKTLNTL FT GMEYEKIHACPNDCILYRNELKDASSCPTCGTSRWKTDKTGTKKRKGVPTK FT VMWYFPPVPRFRRMFQSLKIAKELIWHAEERDFDGKMRHPSDSPSWKLVDH FT RWPEFSSEPRNLRLAISADGINPHSSLSSKHSCWPVLMIIYNLPPWLCMKR FT KFMMLSLLISGPRQPGNDIDIYLAPLIEDLKTLWEVGVQAYDAHQREFFTL FT RVVLLWTISDFPAYGNLSGCTVKGYFGCPICGEETYSRRLKHGKKNSYTGH FT RRFLPCNHPFRKQKKAFDGEQEFRPPPQILSGEEILRKINVICNSWGKKKF FT NRGKSKVSNPNCWKKKSIFFDLEYWKYLHVRHNLDVMHIEKNVCESIIGTL FT LNIPGKTNDGLNCRLDLVDMGLRSELAPKFESKRTYLPPACYSLSKMEXKV FT FCQTLSQLKVPYGYCSNLRNLVSMEDLKLYGLKSHDYHTLMQQLLPVSLRS FT ILPKHVRNAICRLSSFFNALCSKVVDVPTLDELQNEVVVTLCLFEKYFPPS FT FFDIMVHLTVHLVREVRLCGPVYLRWMYPFERFMKVLKGYVRNRNRPEGCI FT VECYIAEEGIEFCTEYLSNVEAIGIPSTSNIDQKVGASIFGGHTMKVDSNL FT WLQAHHYVLENTTIIQPYVEDHMKWLKMKYPRQAKRQKWLQDEHMRTFTYW FT LRQKVEVAIGNEEPVSETLKWIAHGPSHYVFKYHGYVINGCHYHTKERDDL FT RATQNSGVSIVATTMQIASAKDKNPVFGELCFYGVITEIWDLDYTMFRIPI FT FKCDWVDNKNGIRVDDLGFTLVDFSKMAHKSDPFILASQAKQVFYVQDELD FT PRWSVVLSTPQQDFLERDEGDDLMDNSIEHHPVISSLPQVESFDAMDDSDA FT ICMRGDCEGIWVENKSYM" XX SQ Sequence 15169 BP; 4935 A; 2123 C; 2610 G; 5420 T; 81 other; cactactaca aaaattgtaa ataatggcgt ttaaatcctt ggcrcttcta aaaagtgaca 60 aggaatgcaa tgaacagtaa ttgtataaaa gaataatggc ggtttataaa catggtgttt 120 tatgtaagcg tcattattgc acttcatcat tcttggcagt tgtaagaagt gtcattgtct 180 cctattattt atatatagtt atatttcccc atttctcaaa catcccgctt tgtctcaaca 240 aatatcccgc ctcatatgaa aaaacctaga aaactaaacc catcatccct gatttcttgc 300 ctttagcaaa ctcgtcggag atgccctgat ttcttgcctt tagcaaactc gtcggagacg 360 cccaactatc gaacgatcaa ctactgactg gtgataatga gagcacctca tcggagacac 420 ccaaaaacac tccattgtgt caggtaattt ctaacagtgg gtaaaaaaac aataataaaa 480 aaaatagaat tggaatcatg cattttcaaa gcttgaacgc agtcaatcta ttagagtttt 540 caagatctgg tatttcagtt ggaaaggtta aattttttgg tttgtttgag tgcattttga 600 tttaggttgt agttggttgg tattcagagt ggtgtagaga acgtcaatgt ctggaaatgg 660 agaagagggg aaagccttgg ctgggagcat tggtggtggt gtctttgttg tttcaaaatc 720 ttagggtttc gttggtctct caagattgaa gtaagcggtt tttcattttg agtgtttggt 780 tgtagggaaa gtggataaat cagttacaaa tatgcagaaa atttatttca aaattgattt 840 tggggctttg aattttaatt tagtttgatg tttatttggg tatgtacagg tttggctgct 900 ttgttccaat ttcaaagaga aagagagtgg tgagagaaat gtttgggctt tggtgaattg 960 ggataatgag agcttcatct ctgttcgtgg tttgaagtgg agtgctccaa ttggaaagca 1020 gcaatttgtg agtgattctt ccctaaaaaa aaaacaatta tggaataatt ttctattgtg 1080 ctttggaatg aaatgattct tgttgctttt tcttggagga gctttgcaac atcccctgtt 1140 gatagcttct tcccaagaac gaaatgaatg tgtttgagga tgattttgaa acatggagtc 1200 ttaagggcag tcctagcagg actcgagagt acatgttgga tggccacaac cctttggagc 1260 ccagaataag ttccgaatgg aactatgggc ytgagcactg agacatcatt tttgcataga 1320 gtgttttcty agcaaggatt aattaattaa aaattctggc aataaagaaa ttggcactat 1380 tctactttag ccataatcca agtgattttg ttaaaatgaa cacaaaagtt tcttaatgat 1440 aatcatggca taactgtttg tagactagga agaattcaac tttttacttg gttataagtg 1500 tcattagcaa ggaktttggg ggaacttcct ttaacattat ttcaatagat gtggttatat 1560 gtagaacatg gagtaaataa attatcacat gccaatacaa gtttagtttt gatggatact 1620 atttgggtaa tctgatgcga gctggcatcc aagggactag caaaacctct agccacgaga 1680 taatgaagaa ctttaagctg actagttttg gtttactacy aaggctgaaa ttttgacctt 1740 ttttgaaggc ttgaaagakg tcctttccta gsggatgata ttttcccttt tgaaagatat 1800 tcttccatgg tcatttcctt tgccyaatac caagagacat gacttctaga gctasaatca 1860 ttagatgata gakatgtttg atttatcaga atacatggaa atttctttct attggaagcc 1920 tagattagct aatcatgmaa ttaatggaac ctacacatgg aattgggcta aaaaaaaaat 1980 gattcactaa aaagttctag cttgttaccc tctgattttt atttttttta atgggcaata 2040 aaagcttaaa ctgtaattcc aactgttagg atattcaata ccttatttag agatttcatt 2100 tggtcaaagc atttaaaact tgcaaaaatt ttcttatata tctttctctt gatggcaaaa 2160 tttgggctat tttttttkgt gaatatatca atgttttatt ccatttttka gactttttac 2220 tttatttgat ctsgaatcct taatgaagtc aaaagagtga caattgtgga tcacttagtg 2280 tgtgcacgtc tatatatgat aaattctata tggcaatata tagaaagcat ttcaaagaat 2340 taaaaataaa ccttaaatat ttttggtttt ataggaatat tctatatagg ataaattcta 2400 tatggcaata ttttggtttt atttccattt aatagaaaat ggaattgacg ccctaatatt 2460 ttttaattaa atgttcctat gttatcttta tactattttt aaatattttt tatgaattaa 2520 ttaaatattt agtaaattta atattactat atatatatat atattaatta aatatatatt 2580 tcattaatta caatattttt taattactat atttaattaa ttaaatatta ccatatatac 2640 attaattcaa tattttgata caatgtagta cgttaaaaat tgaattaaaa tttagatgtt 2700 cattaaattt agtttwattt acacttttct tcttctactt tctatatttc ctataaatct 2760 attttgattt tggwaaaaag gatgggaaaa atataatttt agtaaatata ttaattctct 2820 aatccaaata aataaaatca atttaataaa taaatataat tataacacaa atactattga 2880 ttctacctaa aatatattga aggtagtttg gaagcattta tcataatgtt ggaagtcytt 2940 ggtaataatc gaaaaatgtt tttctcataa acatttaaca tttggtaaat tttaattgtg 3000 attttgaaaa tttgtattac caaatgataa tttttgaact aactcatgaa atatgcattt 3060 ttcacaaatt attttttggt agcctattat atatatatat atatatatat atatatatat 3120 atatattata agttattaaa ataatttact tgattgatta taaatatatt aaaataattt 3180 accaaaccat ttgaaaatag aaaatagtac aaataaaatt gataacacaa aatttaatta 3240 taacctaaaa acaattttag gatatttggc tctaaggggt atttgggata aatttcctat 3300 taccatgatt acttagtwta gatacttaaa aggttaaaaa ttataatttc aaaatttttt 3360 tattaawttt ttwaaattat gaacactatg ttccatgtcc atgttcatta ctrtgtgctc 3420 ctatattatg atatatgstt taaaaattaa ttctcgattt ctccattacg atgcactatt 3480 tatttatttt acataggcat ctagaatttc ttcacatttt atttagatgt atattatatt 3540 agttttataa taaagagatt aaaattttaa tcaaacaaaa aatattttta ttttcataat 3600 ttttatttta aatgaaaaag atatatgtta aaccatatat tatccctata atgcttgtga 3660 attcttctca aaaacacaaa tctaaaaaaa aaaaaccaaa tgcaaaagca caacatagag 3720 acaagtttaa attatatagt tcacaaaata ccattatagg ctaaaattta gacaaaaata 3780 aaattaatta ttaaatattg attgtcttat tatttgtttt gtaggataat tacttgatgt 3840 gtatttaaaa ttgtyaattt agattatttt gattaaattt ggtgtggacc tttttgtaga 3900 agatgttgct ctctaagttg tgaaaaggct tttaggcctc catgttaaat gttacatatt 3960 taagatawac atgatagaat gagagttatg ttgttttgtt gtaatattcc aattagtaat 4020 catgttttaa ttttactcaa ctatgcttgc atgcaacctt agagttcccg ttcaagtatc 4080 attgtgagac aaaagtttat gttattacat agtaaagaca ttttagttgt caaaaggtga 4140 aaatggtttt atctatgcta gtttcacgtt gacaactttt aaattgtcta ccatgtgata 4200 aagatctttt ctctacaaat gatgcttgaa ttgtccgatt ggayagtgta ggaaaacata 4260 atatctatga agttaattgc ttgttcttaa tttattttaa ataaattttg gtactatttc 4320 ctcttgttct ctrggtacat acttggacaa ggtgacatat tatgttttgt ccattttgtg 4380 tacttggaga accataggga aatgctgcca aaattttttt waaattaaat tgagcacatt 4440 ggcagttgac acatagagat tatgtattcc tatatgggat aggaaccact ccctaattta 4500 caatgttgga gatgttagat ggcataaaac atgcaacata gcttgaattg tatatgytaa 4560 taatattaat atgcacttgt ttaattgagg ttatgcatca cctttaatgc aagtactcaa 4620 ggtcaataac atttatagct tcgtaatcac tactacatat aacacataca atgacctttt 4680 kttttttctt ggctttttta aaaattgtca ataattagcg tgttattcca atagtgtaaa 4740 tatatgtaca aaagtcataa tgattagaaa attaatgctc accctttttc tcttaaatct 4800 agcctcttaa acaaatgttg tattaaattg attattgatt attctttgaa cagaagaaag 4860 mgaggttgct aaacgaatga cacakaaaat gttgatattt tcttcaattt gaagtttgat 4920 cactattgga agtttgttat taaaaaatgg accgttcatg gatctcaaag gatagaagat 4980 cgaaggagta tgaggatggg gtagaacgtt ttatcacatt tgcaatacaa aattctgcaa 5040 ataaaaactc cattaaatgt ccatgcttac agtgtggtaa tatgatattc catactcctc 5100 aaaagattag agagcatatg tttttccatg gaattgatca aagttaccat acatggtatt 5160 ggcatggaga ggtagctcca agtggaccac caactacaag agcagaacat tatgatagag 5220 ttcaatttga tgatgtgcat agtacaatag aaatggttca agctgcacag gaggattgta 5280 aaaatgaccc agaatcattt caaagattat tgaaagatgc agaaaaacct ttatatcctg 5340 gttgtagaaa ctttacaaaa ttgtctgcat tgattaaatt gtacaacctg aaagcacgct 5400 ttgggtggtc tgataaaagc ttttcagagc ttttagaaat gcttggaaat atgttgcctg 5460 taaataatga gttgcctttg tctatgtatg aagcaaaaaa gacattgaat acattgggaa 5520 tggaatatga gaaaatacat gcatgtccca atgattgtat cctttatagg aatgagttga 5580 aagatgcatc ctcatgtcct acttgtggaa cttcaaggtg gaagacagat aaaacaggaa 5640 ctaaaaagag gaagggagtt cctacgaaag taatgtggta tttccctcca gttccaagat 5700 ttagaagaat gtttcaatca ttaaaaatcg caaaagagct catatggcat gccgaagaaa 5760 gagattttga tggtaaaatg cgtcatccat cagactcacc atcatggaag ctagttgacc 5820 atagatggcc cgagttttcc tcagaaccta gaaacttgag acttgccatt tcagcagatg 5880 gcataaatcc tcacagttca ttaagtagca aacatagttg ttggcctgtt ctcatgataa 5940 tttataacct tcctccatgg ttgtgcatga agagaaaatt tatgatgtta tctttgttaa 6000 tttcaggtcc acgacaacct ggtaatgaca ttgacatcta tttagcaccg ttgatagaag 6060 atcttaaaac attgtgggag gtcggagtcc aggcttacga tgcacatcaa cgagagttct 6120 ttacattaag agttgttcta ttatggacaa tcagtgactt ccctgcgtat ggaaacttgt 6180 ctgggtgcac agttaaagga tattttggtt gtccaatatg cggggaagaa acatattctc 6240 gtagattgaa acatggaaaa aagaactcat atacaggaca tagacgattt cttccatgca 6300 accatccatt taggaaacaa aagaaagcat tcgatggtga acaagagttt aggccacctc 6360 cacaaatatt aagtggagag gaaattctca gaaaaatcaa tgtcatttgt aattcatggg 6420 ggaaaaaaaa gtttaatcgt ggtaaatcca aagttagcaa tccaaattgt tggaagaaga 6480 agtccatatt ctttgatctt gagtactgga aatatcttca tgttcgtcat aatttggatg 6540 taatgcatat tgagaaaaat gtttgtgaaa gcatcattgg taccttactc aacattccag 6600 gtaagacaaa tgatggactc aactgtcgtt tagatcttgt agacatgggc ttaaggagtg 6660 aattggcacc aaagtttgaa tcaaagagaa catatctccc tcctgcatgt tattcacttt 6720 cgaaaatgga aaanaaggta ttttgccaaa ctctttcaca attgaaggtt ccttatggat 6780 actgctctaa ccttcgaaac cttgtgtcaa tggaagactt gaagctttat ggcttgaaat 6840 cccatgacta ccatacatta atgcagcagt tattgccagt ttcattacga tctattttgc 6900 caaagcatgt gaggaatgcc atttgtagat tgagttcctt tttcaatgct ctctgtagta 6960 aagtggttga tgttcctaca ttagatgagt tacaaaatga ggttgtggtg acattgtgct 7020 tgtttgaaaa gtatttccca ccttcattct ttgatatcat ggtgcatctt actgtgcatc 7080 ttgtaagaga ggtgagactt tgtggaccag tttaccttag gtggatgtac ccatttgaaa 7140 ggttcatgaa agtgttaaaa ggctatgtac gaaatcgtaa tcggcccgaa ggttgcatcg 7200 ttgaatgcta tattgcagaa gaaggcattg agttttgtac agagtactta tcaaatgtag 7260 aggcaattgg aattcctagt acttcaaaca ttgaccaaaa agttggggca tctatatttg 7320 gaggtcatac catgaaggtt gattccaatt tatggttaca agcacatcat tatgtgttgg 7380 agaatacaac aatcatccaa ccttatgtcg agtaagtggg acacactttt gtttctttgt 7440 ttatcatgct tataataaat ataggatact aactataaaa ttattataca tgacttcata 7500 gagatcacat gaaatggttg aaaatgaaat atccacgtca agctaaaaga caaaagtggc 7560 tacaagatga gcatatgcgt acttttactt attggttgcg acaaaaggta ctagagtggt 7620 agtaaaactt actgtattct ttacactcat ggttaactat gttagtaata actataactt 7680 atctatacag gttgaagttg ccattggtaa tgaagaacct gtatctgaaa cccttaaatg 7740 gatagctcat ggtcctagcc actatgtttt taagtatcat ggctatgtca ttaatgggtg 7800 tcactaccat accaaggagc gtgatgattt acgagctacc caaaatagtg gagtcagtat 7860 tgtagctaca acaatgcaaa ttgctagtgc caaggataaa aatccagtat ttggtgagct 7920 ttgtttctat ggggttatta ctgagatttg ggatcttgat tataccatgt tcaggattcc 7980 aatcttcaag tgtgattggg ttgataataa gaatggaatc agagttgatg atcttgggtt 8040 taccttagtt gacttcagca aaatggctca taaatcagat cctttcattt tagcctccca 8100 ggctaagcaa gttttctatg tacaagatga acttgatcca agatggtcag ttgttttatc 8160 aactcctcaa caagacttct tggaaaggga cgagggtgat gatctcatgg acaactctat 8220 tgaacaccat ccagtcattt cttctttgcc acaagttgaa tcatttgatg ctatggatga 8280 ctctgatgca atatgtatgc gaggcgactg tgaggggatt tgggttgaga acaaatctta 8340 tatgtaactg aagtgtagcc ctgttataat gatgttttca aatttatact ttatttcaaa 8400 atgcatttta gtttttatta taacatgtat ttgtctaact aagtagttgt tgtttgtatt 8460 ttatgcggtg acctgatatg ctactacagt tttctataag gtaaacctta tgcttattgg 8520 ttcatttgtc tgtactatta gatgattgtt atggttttag ttttagttaa cgtcagattg 8580 gctttagaaa aacattgaca gatctatttt caatattatg ttcgaaatag atcaattcat 8640 taggtaatgc cttatgcaat tgaaattttt atacttaaaa ttttgtttag atatttcata 8700 caaaatttgt atggatttat ggatatttta taaacttact tttaaacttt ataatttttt 8760 tttattacag gtatggatct agagcaagaa gaaaaaccac ctacaaaaag gaggtgtaga 8820 gggataacta gaaagtcwat gattatcaag aatcggagca aaggggtaaa gttggtgata 8880 aaagtacaat cctgatggca tttatgttgg acaagcttct gtgcatctta ccagtttttt 8940 aggcgtattg gcacgtacta tggtgccgat tagatataat agttggagag atgtacctat 9000 acaagtgaag aataacctat gggacaccat tgaggtaaaa tagttttttc ggtatataat 9060 ctttttccaa ttcagtttat gaaacatttt taattactaa taactatatt aatgatttat 9120 aggcttcttt tacactggat agtaaaagta ggaggaattg tatgctaacg atgggcaaat 9180 gctttcgatc attcaagaac atgttgactg tcaagtatgt tattcctttc aaagaccaac 9240 cagaggtcct gaagaaacca ccaattgaat atatttttat tgaagatgaa gattggacta 9300 tatttgtgaa ggaaagattg tctaaaagat ttcaggtcaa cttaaactca tcttcatgcc 9360 ttatactcat attcacattt actaaatata aaataaaatt tgtaggattt tagagaagtt 9420 caaaaagaaa gaaggaagaa gcatatttac aatcatcatc ttagtaggaa gggatatgct 9480 ggtcttgagg atgaaatggt aggttaatga tagtttctta ttttctttta ttttatgcat 9540 aaattgatta aagactcatt acagtacatt ctaatatctt aatagatggc aacaastggc 9600 tatacagaaa tcattgatag aagcatatta tggaagaaag caatggagaa gaaagatggc 9660 acttatgatg aagttgtcat accagtggtg gagaagattg taagtataca ttttctaaca 9720 tatatttcat ttattttaag actttattta tagtaaccaa tatgacattg aagttaataa 9780 catcattgtg gttttaggac aagatgttga aagagtcacg agaaagtggt cgaattttta 9840 gtggcaataa tgacatactt acagaagcac tgggcactcc cgaatacagt ggtcgagtac 9900 gggctaaagg caagcattat acaccacacc aatatttcca ttctatggcg aatagtgcta 9960 tgcgggaatt tgtgaaagaa tctcaagagc gacaatctaa gtttgaggca aatattttag 10020 cccaactttc tcagatgatg cctagcacac ctcaatctga tgttagcagc tctaatgtta 10080 agcaaaatca aattgtcctg cctcaagcta ttgagcaacc taagtgtcaa gttgatgacc 10140 atctcccaat agtgcaaaaa gcaaacaagg tatgttgtga ttaatattat gttctataat 10200 tcctatgtga taacacataa agttagaaat ttcatttcat tcatctagtt gaaactattc 10260 aaataccaac tcattaagag acattttcat ccttcaagaa tgaaagttat ggggtttaaa 10320 tatagttttt acttgtctag gtttgtccca cctacatgat gaatgagcta actatggaaa 10380 aaacttttca tatggtacaa gcactagttt tttaatttag ggtttatagg gtttaaaacc 10440 tttatgtaaa taagcatcat atttgacctt gatgaatcaa ttttcctcaa ctaactctta 10500 cattcctagt aaaattctaa attttcaatg gttgcatata agtaaacaat cttgtttaat 10560 tttataggtt aggaaatgcc aattggccat agggacaaag gaaaatgtag ttgcagctgg 10620 cacaattata cttgaatgtg gtgttaactt cttagttgtt gtggatgctt cttatgagcc 10680 aaatgcacca cttcctgtgc ctattcctaa ccaaattaaa actattggag aggctcttgg 10740 gtatcaagtt ttgtggcctg cccaaatggt cagtcttact actcatccca tccaggtata 10800 gttttttttt tttttttttt tttcaatttt cattaacagt ttcttggtag taattataac 10860 ttattttwtc aaggacaata attatatatg caatcataca ctttgtttta taggattcaa 10920 agaaatttaa gaaacaaagg aataaagaaa cacgattaag ttctaaggat gagaaccccg 10980 tagacattaa gaactttgct acattggttg gactactgct caaggaaggg aaagtacatg 11040 cagtaaacat cacaaaggat gtttttggag agtcttgtaa gagctttctc atgaatgatg 11100 atatggatat gataatttca tcaacagagg tgtcatctaa ctgtcttatg ttctatatat 11160 ggtgagggaa catttatttt gttttttttt tttcatatat tttagttgct tcattatagt 11220 ttaactttta attataatca tattaggaga gttgaaatgt tagttgcatt aaaatattaa 11280 cttcttgtta atggtatgtg aaattaaatt aggcatttgc ataaaaagat ggttgatgcr 11340 aagatggcag gacgatttgc ttttgtaaat ccagctttgg tttccaaagc tggaatgggg 11400 gaagcaagca aggaaagtag gtcaagggtt attgctaatc gattgatgaa tgcaaatcat 11460 gctgacttta ttttcattcc atacaaccca gggtaagtta tagaacttaa gtaagctatg 11520 ttggtaaact tatcaatcat aattaatata taactaaatt tatgtaaaat tttgtagcta 11580 tcattgggtt ttggtggcac tggaaacaag gactatgatt gcatattacc ttgactcatt 11640 rgaagaccaa ccttctgatg atctcaagga gattgttaat atgtaagttt ttctctcaat 11700 acaagagcat gaagcataat tggtaacaaa tattattttc ttcatgtagg gcccttagaa 11760 ttcatccacc acaaaagcat aagtcatcaa agagggagcc tacatgggtt gtagtagggg 11820 tgagtaattc atataaatta ggtaatgcaa tttttaatac catttcttaa tgtttaatta 11880 agtacaagat atcctacaac taactataaa attggtgtat tctacaatga tttattttta 11940 tgcataaagt gtttaattaa gtacaagatr tcctacaact aactataaaa ttggtgtatt 12000 ctacaatgat ttatttttat gcataaagtg cccaatacaa ccaggtagtg ttgaatgtgg 12060 atactatgtg atgagatata tgagagatat tattgctgat caaggatgtc ttacatcaaa 12120 ggtatgcacc agtttattaa tttccaatat atcaattttt accttttttt tcaatgtaat 12180 tgattaaatt gtttacatta ctccttaata gtttcacgga aaaaaaatcg tatagcaaag 12240 atgagttgaa cgaagtacga tcagaatggg taatgctggt cactcagttg atactctctt 12300 ctgtttgaag gctttgaaga cacttttttg tatggaaata gatcatactt ttgcccaatc 12360 caactatcac ttttgttgag gttaatattt twatwttttt tttctctttt gaaccaaact 12420 atgattataa gtaaattgtt tgatggaatc acaaccaagt tgataatatt ttctttctat 12480 tgtcatgata tttctccaat ttcccataac tgaactaagt tgttaactgc atgcatgact 12540 cacaggcatc caaagggaag gactttttga agctgaaagt tggaagtttt tccaagtttc 12600 taatagttca tgagctactg ccacaaaaaa ggtttttttc atagggatat caagtttatt 12660 atttcttgcc tcctattaaa gatcttctac aaggggatat acacttggaa ttttgttgtt 12720 ctcatgtgat catttgtttt cattctcaac tacagaatgt tcttgttggt tcaaaaggga 12780 acatgaagat ttctaatttt ggccatggtg ttataccaca acattgtaag ttacatcatc 12840 accctcataa aacataaaga tttcttcata aaataaattt tttgtttcat tgcttaactt 12900 atttattttt caatgaattt aaaactacaa gatgatggat tactatatat ttatatacaa 12960 ccaatggaag ttcaaattac attgcttaat taacttctaa ttaagttttt tcaagtgtcg 13020 aaaatgtggt ttgtagttta attttcattt cattcaaatt aactgttcta tttttatctc 13080 ttcaaccaat ttgtagacta ggtaagtgat tgagcatagc tctagaagct gccaatgaag 13140 tatctctatg aacataatcc ccctcatgag ttgcagaaat tttaagacca acatcatact 13200 cttagaggta tggtctctac tactcaaaaa ttaccattat attttgttca ttcagaaaat 13260 ttatattggt gatgaagttt ttattatttt acatcattgg cttgataacc atgcttttta 13320 aatttagtat acatgagaaa tagcaattaa gaattccggt ttctcacttt atgtgtttgt 13380 attatggaca tttttaagct aaagttcctt aagctttact tttgtgtaat gtattgcatg 13440 ataggctgat gtttgaatct ctatttagct tcatagataa cctgaattta ttgttaaatt 13500 tttatgcatt aatcatatct gtgccatata gttgtcactt tggatcgctc acacataatt 13560 ctagatattt tcccaaatat gttttatttt aaaaaataat cataatcttt ttaaatatga 13620 aatatgagct ttcattaaaa aatattcatc attagaagat gtttatctac cattaagttg 13680 tagatattct tctctacatt ttttttatgc atgccaattt atttattgtt aagttctaga 13740 attcatatag ttgttgctac ccttgatagt gataaataag atgaatgata agtatgatac 13800 aatkgrcyay trttttkgat rywmtsttgy mmcgcaywts rtwtgktkkk mwatgttaat 13860 tcttttcact twacwaaaaa yttagttgat aaagtatcwt ggtgtkmwcc ttattccgta 13920 tttcatgtwa caccatattc cswrwcyttc ctattgycaa tgttgcacat tcgatgaggt 13980 ytattactat tagatgatgc ctaattgaat acacatttgt tttaatggac tattgatgtt 14040 gatattctct tgtcccaaac ttggtttgtt tttctatttt tttttttggg gctatactaa 14100 agatttaatg gattattgat gttgatgttc tcttatcccg tatttgatta atctcttgtt 14160 ttgtgtttta actattgata gtaattttgt tgtaattatt cttagggtca catatgtcaa 14220 ttggtataca catttgtttt cctattatat tttcattgac atttctttct ctctatttct 14280 agaagtcttc acttatatat cttttctgaa attgtaattg attttagttt tttgtgcatg 14340 taggtcattt ttttgggaaa ttaaccttgt rgttggataa gctagcatga aggagtatgt 14400 tgaaggccaa agcacaattg ggttgcatgt aaagaaaaaa tggactatgt caagggacta 14460 aacattaaag ttatgacatt ttttgtggtt attttaatat attttagctt ttttgtgttt 14520 cttgtttatg aaatacaact tctttatttg tgattaaata ctgcaatttg gaaatgtatt 14580 accaggtgaa aaattaggtg caacaactaa tttcattggt atataatttt ttttcttatg 14640 tgtatgcatt atttcaataa caggtgaaaa attaggtgta acaattatta aactaaaact 14700 aaatttaaaa ttaagcaatt atcttccttg acgcttttac taagtgtcaa ggaatgagag 14760 taactactag taacatttat acaacccaat aatgacacta ataaatgtgt caatatagtg 14820 tgaacaacta acaatgatac tttttaagtg tcaaggttct cttcaatgac gctttttaga 14880 aatgtcctta tagttcgata tttgaaactg ctaaacaatg acacttatat aaagtgtcaa 14940 ggtttcttct actcaacaat ggcgcttata aagtgtcaat gtagtttgat ataactaatg 15000 atgacacttt ttttaagcgt caaggttctc ttcaatggcg ctttctagaa gcgtcattgt 15060 agacaaatac ttattatgac aggctagtag atgacgcttt ggggaagcgc cattgaatgt 15120 gtttctcgac acttaaaaag cgtcatggtt aatgtttttt cttatagtg 15169 // ID DNA3-2_Mad repbase; DNA; EDCOT; 819 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA3-2_Mad. XX NM DNA3-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-819 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1466-1466 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~99% identical to the consensus. 3-bp TSDs are usually TWA. XX SQ Sequence 819 BP; 293 A; 108 C; 131 G; 287 T; 0 other; tggcgcgttt actaatccgt aatcaaattg agaggaattg gattgagggg gaattggatt 60 gaggaggaat tgaaatgagg tggaatcaga atcagattcc tgttgaagtt gtttactaaa 120 actgtcagga atcggagtag gaatgatgtt gagtccatat aagttgttta ctaattcatt 180 tcaatcggaa tgaaaactag gttgattact atattgccct tacataaata aattattttc 240 atactaatta atttaattaa attcttaatt aaatttatat aataaaattc atctatataa 300 gcatgtataa ataggtttta tttatttatt aaaagatggc aaaaatgata ttgagtctat 360 ataagttgtt tactaattca cttcaatcgg aatgaaaact aagttgatga ctaaattgcc 420 cttacataaa taaattattt tcatactaat taattaaatt aaattcttaa ttaaatttat 480 ataataaaat tatctatata aaaaaatata aataggtttt atttatttat taaaaatgac 540 ataatgagtg tcaaatgaag ggcaatgttg ggataataag aaacaagtga gggcataatt 600 ggaataaaag atgcattcct gattcccttg cccttaggga attcaaatac ctcacaaaac 660 tagggaatcc ggttcctcca atttcaggaa ttggattcct tgtttcgtgt gggctccacc 720 acttttttga ttccttaata tttagtaaac accggaatac tccgtaatcg gaattcaatt 780 ccctttcttt attccgatta cccttacgta aacgtgcca 819 // ID SHALINE15_MT repbase; DNA; EDCOT; 6372 BP. XX AC AC147498; XX DT 21-JAN-2007 (Rel. 12.01, Created) DT 21-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A LINE element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; ORF; LINE; KW Interspersed; repeat; SHALINE15_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-6372 RA Shankar R. and Jurka J.; RT "SHALINE15_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 92-92 (2007). XX DR EMBL/GenBank/DDBJ; AC147498; Positions 47111 53482. XX CC The LINE element is poorly conserved across the genome. Almost CC all instances are of incomplete length and the copies are present CC with heavily truncated 5' end, mostly. This sequence has domains CC for RNA recognition motif, ORF1p of CCHC zinc finger binding CC protein, endo/exo-phosphatase and reverse transcriptase. XX FH Key Location/Qualifiers FT CDS join(125..976,980..1027,1082..1105,1124..1171, FT 1196..2482) FT /product="SHALINE15_MT_1p" FT /translation="MREFRREGARPAGFRQPSRRSPSPVTRSNGGEGPYAG FT EAEKGGTYGEWVWVRNRRRKSLRPEQDGRSGQRRFNGHGGKGHVQERRFDQ FT SGRVFDRFRFDSRLGACASSPMVRVFSGSVRGRSLTSKQGRPFSCSRDASN FT RHKSRYSSVKIPARRFFPLGSVQQRSRGHSNGVYNYADQGSRDDNGSGSNV FT SHDSAVFYITNFPDRLLFVDLKKVLEVCGILADVYLSQFRNVRGQRFGFAK FT FLKVRDVDKLKKALNNVFFWDLRLFENVAKFDRFVEGDVEKRLGENNRGNK FT EGKNRGSCRWQPFVVSSKWGMLFVVERWRGWWRRKGGRKWLLGKEVSLFVV FT CVASEVVREYLPYHDDVVWANKCLLAKVKDGICFSGIQQSFLDAGFLDFNL FT ISLGGDNVVLSPGLDGDVTELFSSAAAFLGNFLCDCRPWSKDSNVQYERGA FT WIRCYGVPLHAWNDNFFLELASTRGRLLKIDEITVNKGRLEYARFLIATPE FT LQELNFFAHFVIDGRKYPIRFIEDLEFGLAVDACLSEFEDDNKSQCSVPEG FT IPHEEPVIDALVHHIHEDIVKYSKEGDSAAVPAICSSIQGMSENIVKKENA FT ASSHSIHEAENTTLKNDVEVFNGTKKCAPIRRKVAPSLLGLKKLARLSELD FT RKELIRSLKKDKKSKRLFLKGKSSKTSSNFSSSKTNKVSLSAGSGNSGKSK FT DWENWVVLHGNAKEVEEDIIEVGKKIGIQCNNSFQALSRSGVHGGLEGCGR FT GV" FT CDS join(4244..4987,4991..5545,5549..5572,5576..5641, FT 5645..5707,5744..5884) FT /product="SHALINE15_MT_2p" FT /translation="MMQNIMIKSYLCSKWTLKKAYDLVDWRYLDEVMDKML FT FPRLWCSWIMECVTTATASVLVNGCPTDEFHFERGLRQGDPLSPFLFLLAA FT EGLNVMMSAVASNGLFTSYSVGTQILVSVSHLQFADDTLLVGIKSWANVRA FT MKAVLLLFEAISGLKVNFHKSMLFGVNITESWLHEAAVVMHCRHGRLPFIY FT LGLPIGGDPRKLIFWYPLVERIRRRLSRWKSKNLSLGGQLVLLKSVLSSIP FT VYFLSFFAPSCIISTLDSIFLNFFWGGGEDSRKISWIKWDNICLKKENGGL FT GVKRLREFNLSLLGKWVWRVLEDKESLWNVVLRAKYGEFGGRVRFCEGVGS FT IWWRQLNQVRAGVGLVESTWLVDNIGRKVGDGSTTLFWEDSWLLNVPLSVA FT FSRLYELSENKGVMVGVLGGGDGYYLHGRRSWWRSVWSSLILFFRLTLTDG FT CGDSTHHKYTRCILLILTQRWILTSLQILINFYGLKRFPIDLLQRIIFVRG FT ISLRQPMFLVVLYVVTRRTWIICFSNATIMVVYGL" XX SQ Sequence 6372 BP; 1662 A; 880 C; 1695 G; 2135 T; 0 other; ggaggggagg tttacttttc atttttaaat tatagacact atgaaatgtt ttataagaag 60 ttaacatatt aacatgataa acaatcatat aatacatcaa tccattgaat aatatttaca 120 cgttatgaga gagtttagga gagagggcgc acgacctgct ggcttccggc aaccatcacg 180 ccggtctcct tcgccggtca cgcgttcgaa cgggggggaa gggccatatg ccggggaggc 240 agaaaagggt gggacatatg gggaatgggt ctgggtgaga aataggagaa ggaaatcatt 300 gagaccggaa caggacggac ggagcggaca gcgtcgtttc aacggacatg gaggtaaggg 360 gcacgttcag gagaggcggt ttgatcagtc tggaagggtt tttgatcgct tcaggtttga 420 cagtagactg ggagcatgtg catcttctcc tatggttagg gttttttctg gttctgtacg 480 cggacgctcc ctgacttcca agcaagggcg tccgttttct tgctcgcgtg atgcatcaaa 540 cagacacaag tctaggtact cttcagttaa gattccagcg cgcagattct ttcccttggg 600 gtctgttcag cagcgttctc gtggacactc caatggtgtc tataactatg cagatcaagg 660 aagcagggac gataatggca gcggcagcaa tgttagtcat gactcagctg tgttttacat 720 tacgaatttc ccggatcgtc ttctgtttgt ggatttgaag aaagttttgg aggtgtgtgg 780 tattttagcg gatgtgtatc tttcccagtt tcgtaatgtg cgtggacaac ggtttggttt 840 tgcaaaattt ttgaaggtac gtgatgttga caaattgaaa aaagcactca ataatgtttt 900 cttttgggat cttagattgt ttgaaaacgt agctaagttt gataggtttg ttgagggtga 960 tgtagagaag aggctttagg gagaaaataa taggggaaat aaggaaggaa aaaaccgagg 1020 gagttgttag ttagagagac tgagaaaggt gatagtagga aattggtact aggaaaggtg 1080 aaggtggcag ccattcgtag tgagttagag agggagagcg tgatcaaagt gggggatgtt 1140 gtttgtggta gaaaggtgga ggggatggtg gtgaaggaga aaccagaggt gttgaaggag 1200 gaagggaggt cgaaaatggt tgttggggaa ggaagtgagt ctgtttgtgg tatgtgttgc 1260 atctgaagtg gttagagagt atttacctta tcatgatgat gttgtttggg ctaacaaatg 1320 tcttttagcc aaagttaaag atggtatttg cttctctggt atacaacaat cttttttaga 1380 tgctggtttt ttggatttta atttaatttc tctgggaggg gataatgtag tgttatctcc 1440 gggtctggat ggtgacgtca cggaattgtt tagttcagcg gctgctttct tgggtaattt 1500 tttatgtgat tgtcgtcctt ggtcgaaaga cagtaatgtt caatatgaga ggggtgcttg 1560 gattagatgc tatggggtac ctttacatgc ttggaatgat aattttttct tggaattggc 1620 atcaactaga ggtcgtcttc tcaaaattga tgagattact gtgaataaag gtagactgga 1680 atatgctcgt tttttgatag caacacctga attgcaagaa ctgaattttt ttgcacattt 1740 tgtgattgat gggaggaagt atcctatacg atttattgaa gatttggaat ttggcttagc 1800 agtggatgct tgtttatctg aattcgaaga tgacaataaa tcacaatgct cagttcccga 1860 aggtatacca catgaagagc ctgtaattga tgctcttgtt catcatattc atgaggatat 1920 tgttaaatat tcgaaggaag gtgatagcgc agctgtacca gccatttgtt caagcattca 1980 aggtatgtca gagaatattg ttaagaagga aaatgcagct tcttcccatt ctattcatga 2040 ggccgagaac acaacattga agaatgacgt tgaggtgttt aatggcacta agaaatgcgc 2100 acctataaga cgtaaggtgg cgccgtcgtt gcttggtttg aaaaagttag caagactctc 2160 agaattagac agaaaggaat tgatcaggtc tttgaaaaaa gataagaaat ctaaaagact 2220 atttttgaaa gggaagtcgt ctaaaacatc ttccaatttt tcttctagca agacaaataa 2280 agtttccttg tcagcaggat caggtaattc tggtaagtct aaagattggg agaattgggt 2340 tgtgcttcat ggaaatgcga aggaagtgga ggaagatatt atagaggtgg gaaaaaagat 2400 tggtattcag tgtaacaaca gttttcaggc tctttctcga agtggagttc atggagggtt 2460 ggaaggttgt ggacggggag tttgattgtt tagtgtggag ggagcggctg gggaggtgtg 2520 tgaggtgttg atgctttttt gatgaagatt ttatctatta atattagggg gcttggagct 2580 tccgaaaaaa ggagggaggt taacagatta gttgccgaga ggaagccgtc aatgttatgt 2640 gtacaagaat cgaaggtgga agtggttgat gagtacttgt gtcgatctat ttgggggcct 2700 gatcccatgg ccttttcttt taaaccttct gttggtgcgt caggtggtat tattactgtg 2760 tgggatccta gtgttttgga tgtttggttg acggtaaata ttgcaaattg tttaatgatc 2820 aaggggtcgt ttattaagaa tcacgaaatg ttttgtttag ttaatgttta tgctccttgc 2880 aataataggg ggcgacaaat tttgtgggaa gccatttcta atttgttctt tgtccatggt 2940 gatgtggctt ggtgtgtgct tggtgatttc aatgttgtgc gtaatagtga agaaaggaga 3000 ggccgagttg aaaatatagt gtcaactgac tgtgattttt tcaatcagtt tattgacagc 3060 aattctctca ttgatttacc tttgtgtggt cgtaatttta cttggtatcg gggagatggt 3120 gtttcgatga gtcgcctaga ccgatttctt ttatctgaat catggtcgac tttatttcct 3180 aattgtattc aagttgctct tcctagaggg ttgtcggacc attgtcccat tctgttgact 3240 attgatgagg aaaattgggg gcctaaacct cttagaatgc tcaaatgttg ggcggatatt 3300 ccagggtatg gtgagtttgt taaagaaagt tggcagtcgt ttcaggttca aggttggagt 3360 ggcttcattc tgaaggaaaa acttaaaaga ttaaaggaaa ggttgaggag ttggcattcg 3420 aatcatactc ttaacattaa cagtaagatt caaggggcta aacaaagaat ggcaacattg 3480 gatgctatag gagagaatag tcctctgagt gatgaggaag tgaacgaaat tcatatgctt 3540 tcggctgata ttatggcttt ttcgaaactt caagctagta tgcattggca gaaatcaaga 3600 attaattggt tgaaggaagg tgatgcaaat tcaaagtttt ttcatggtat catgtcatcc 3660 agaagaaggt cgaactctat catttctttg tcaaccgagg atggtattat tgagggtgtg 3720 gggaatgtgc gtcatttgat ctttcaacac tttcaaaatc atttcaagag acgtccacaa 3780 ccgtggccag atatgagtgg tttggttttc aaatcgttgt caatggcgga tggggcggat 3840 ctcatcaaac ctttcttgtt ggaagaaatt aaagcagcag tatgggattg tgatagtttt 3900 aaatgtcctg gaccagatgg tattaatttg ggctttttca aagacttttg ggacatttta 3960 aagattgatt tattgaactt ttttgcggag ttttaccatc atggtaagtt aactaaaggc 4020 cttaattctt ctttcatagc tttgattcca aaggttgaaa gtcctcaaag ggtagctgat 4080 tttcgtccta tagccttggt gagtagtgtt tataaaattt tgtctaaagt tttggccaat 4140 cggttgagaa aggtggttgg tagtgtggtg tcggcttctc agtgtgcttt tgttaagggt 4200 agacagattt tggatggtat tctgatagca aatgaattgg tagatgatgc aaaacataat 4260 gataaagagc tacttatgtt caaagtggac tttgaaaaag gcgtacgatt tggtggattg 4320 gaggtactta gatgaagtga tggataaaat gttatttccg cgtctgtggt gctcttggat 4380 tatggagtgc gttacaactg ctacagcttc agtactagtg aatggttgcc cgactgatga 4440 gtttcatttt gaaagaggac tccgtcaagg ggatcctcta tctccgtttc tgtttctgct 4500 agcggctgaa ggccttaacg tgatgatgtc tgcggttgcc tccaatggat tgtttacatc 4560 gtattcagtt gggacgcaga tacttgtgtc ggtgtctcat ttgcagtttg ctgacgacac 4620 tttattggtt ggtattaagt cttgggctaa tgttagagca atgaaggctg ttcttttatt 4680 atttgaagct atatcaggtc taaaagttaa ttttcacaaa agcatgttgt ttggtgtgaa 4740 tattactgag tcgtggttac atgaggcagc agtggtaatg cattgtagac atggacggtt 4800 acctttcatt tatttaggtt tgcctattgg tggagatcct cgtaaactta tcttttggta 4860 ccctttggta gagagaattc gtcgtcggtt atctaggtgg aagtctaaaa atttatcgtt 4920 gggaggtcag ttggttttac taaagtccgt tctgtcgtcc attccagttt atttcctttc 4980 cttcttctaa gctccctcat gtatcatttc tacccttgat tctatttttc ttaatttttt 5040 ttggggtggt ggtgaggatt ctaggaaaat ttcttggatt aaatgggata atatttgttt 5100 gaaaaaggag aatggaggtt tgggtgtgaa aagattacgg gagtttaatt tgtctttatt 5160 aggaaagtgg gtgtggaggg ttttggagga taaggaaagt ttatggaatg tggtgttgcg 5220 tgctaaatac ggagagtttg gggggagggt gcggttttgt gagggtgttg gatcgatttg 5280 gtggcgtcag ttaaaccaag ttagagctgg tgtggggttg gttgagtcta cgtggttggt 5340 tgataacata ggcaggaagg taggtgatgg gagtactact ttgttttggg aggactcttg 5400 gttgttaaat gttcctctgt cagtggcttt ctctagactt tatgaattgt cagaaaataa 5460 aggagtgatg gtgggggtgc ttggaggtgg agacggatat tatttgcatg ggaggaggag 5520 ttggtggcgg agtgtgtgga gcagttgatt aattttgttt ttcaggttga catagctgac 5580 agatgggtgt ggagactcca ctcatcacaa gtatacacgg tgcattctgc ttattcttac 5640 ttaacagcgg tggatactaa catcactgca gattttgatc aatttctatg gcttaaagcg 5700 gttcccttaa aagttaatat ttttgtttgg cggctttttc tgaatagact tgctacaaag 5760 gataatcttc gtaagaggaa tatccttgag gcaaccaatg tttcttgtgg tgctttatgt 5820 ggtaacgagg aggacatgga tcatttgttt ttccaatgca actattatgg tcgtttatgg 5880 cttatgattt cggattggtt aggttttgtt acggttctca atggcaattt atattctcat 5940 gctcatcagt tttgcgctct aggtgggttc tcaaagaatt ctatgcaagc ttttactatc 6000 atttggattt cggtcttata tactatatga aaagaccgca acaggaggat tttccaaaat 6060 caaagtgctc ttttggagtt tctacttgaa agagtcaaac tccaaacata ttggtgtttg 6120 aaagctaatt tcatcttgtt cgttttttat tattcgtatt ggagaattaa tcctttacct 6180 tgtttacaga ctgttttgta aagtctgttt ttggtttctg tttcatggct tacatagcct 6240 ttttgtattg tatttaactt tatcagattt ctcaggcaat tgtatttaac tttatcagat 6300 ttctcaggca catcttgtgc ttgagggatt gattttatta tatttctatt agtttcttca 6360 aaaaaaatat aa 6372 // ID LTR-11_Mad repbase; DNA; EDCOT; 718 BP. XX AC . XX DT 27-OCT-2010 (Rel. 15.11, Created) DT 27-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE Putative LTR-retrotransposon from the apple genome: long terminal DE repeat. XX KW LTR Retrotransposon; Transposable Element; LTR-11_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-718 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 2002-2002 (2010). XX DR [2] (Consensus) XX SQ Sequence 718 BP; 208 A; 164 C; 200 G; 146 T; 0 other; tgttaacgtt gggcccattt aggcccaccc aaggacataa gcccaaggaa aggccaagaa 60 gcccaaggcc caaggagttc gaagagggcc gacccgagtg ctcaggccga ccgagacaaa 120 agaaggacta cccgaccgcg agaacacgtg ggcgcgctga caactttatg gcacaagtct 180 ccaaggacag aactactcaa gtgctactta gactattcaa cgacgtgcag gcaacaacag 240 aggcctagga tgggacataa aggcagtcgg ggcagtgctc ggcaaggcga ggcagagtaa 300 ccgaggtccg agcgggacgc tcgggccacc tgggccttaa aaggcgtgcc atccgactgc 360 tagaacgtca cttcgttgac aaaggcctgg ccgagtaggt gaaaagttgt cagtaagcta 420 gtacaagtgg ttggcacatt aaatgccggt ttgagaggcc tcaagggggc gaggcctata 480 taaaggggta gagacctcca ttatgggggt cagacgaatc agagagaata gagtgaatgt 540 attagccgag cgctatttag tcttgaaatc aatatattga gagcaacaca gtggatgtag 600 cccagttttg aggggtgaac cacttacatc tttgagtcca tttaatttca gcccatctcg 660 tagcccatct aatgtcattt aattaagttt gttaacctta caattttgag cgttaaca 718 // ID Copia-10_Mad-LTR repbase; DNA; EDCOT; 205 BP. XX AC ACYM01115773; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-10_Mad-I; KW Copia-10_Mad-LTR; Copia-10_Mad_. XX NM Copia-10_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-205 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1352-1352 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01115773; Positions 13247 13451. XX SQ Sequence 205 BP; 72 A; 26 C; 34 G; 72 T; 1 other; tgttaaagga agaaaattgt taatgagtga ttataggaat caggaagata gtcaacgatt 60 tggctccaga gattttagga gtaaatgtaa ttagcatcaa attaggattc ttttacctat 120 aatagttctc agctgtttgt ataaatcctt gtattctctg tacaaagtca tatcartaaa 180 agatcactaa ttctacattt ttaca 205 // ID Gypsy9-PTR_LTR repbase; DNA; EDCOT; 371 BP. XX AC LG_VIII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy9-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-371 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-371 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 343-343 (2007). XX DR Genome; LG_VIII; Positions 13551575 13551945. XX SQ Sequence 371 BP; 97 A; 77 C; 68 G; 129 T; 0 other; tgttataggg cagcaactaa ctaatgggtt cacacgggag aaattcaaat taagggaaca 60 gttgataaaa cggtgtgttt tagagtaagt cattaagtcc aaaacgatgc gttttataga 120 gtttataatt ttgttatgag tcacgtggaa aggaaagaaa tcacgagctg gttgttaggc 180 tcctctgtat atataatagc atctgttgca acagatgcag gcatgcaata atagtgaacc 240 aattcctttt ctttcggtaa ttcttccctc acaccttctc tgtgttttca ccgctccttc 300 tccttcttcc ttcttcttct cttcgtctac ttcttctgct ttatctcttg acaaccaagt 360 tagttgctcc a 371 // ID Gypsy-49_Mad-LTR repbase; DNA; EDCOT; 2460 BP. XX AC . XX DT 29-OCT-2010 (Rel. 15.11, Created) DT 29-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-49_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-2460 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1996-1996 (2010). XX DR [2] (Consensus) XX SQ Sequence 2460 BP; 662 A; 429 C; 591 G; 778 T; 0 other; tgtcacagcc cgtcccggga tttttatatc tgggacgtga attgacgtaa ttacccttgg 60 cgggcattaa ggtacgtgtg tgtgtgacat tatttgaatt aattttgtaa gttttgggat 120 taaacttttg gaatttgaat ttttgtggtt agggatttgg atggatggtg aggattgtgt 180 tgggccacac aatcacacac acacgcactc cctgtcttct ctccctctcg tagcactctc 240 tgtctctctc cctcgacctc acacacaccc acacccaatg tgtacggcac acacccaaac 300 cctccaaaaa ctcgacggat cgaggcaacc aaggtatgca tcttcatcct ttcgacgttc 360 tgagttcatt ggtactagtt ttaggaagtg aaaccctcga aatcacggga aacccgaacc 420 tccatttttg agttactgtt catgcacacg taaaatgtcg tgtttcaggg aattctaagc 480 ttgtagtgag cttagtgaag tcctaaggag gctcggagta cttcgtttga aggatttgga 540 cgtcgggatc acgtggttcc attttggccg aatttcttgg gaattttccg gtgagatttc 600 ttgattttta gagccttaaa ctagtctatc gtgattctac atgtttgggg cttcaatttg 660 atataaaata cgaagaaaat gggtgaaaaa cgaaggagaa caagaggttt taaaattggc 720 cggaaaacgg tcgccggaaa aaccagtccg gcgacccaag gaagaagaag ggcgcgtggg 780 gggcgcgtag gcccgtgcca cgtgcggcgc gtgggggcgc gtggcacatc aaaaaaataa 840 tctaaaaata tgtcgacgtt cgtgacgtcg agtagatcac tgtggtatat tcatataccc 900 aaattgagca ccgtatgaga aagttattac gattattggt taggtgcttt aaataacgtt 960 ttatagtttt cgcatttagg tgaaaatgtg aattgacgat ccgaccgttg gatcgtcacc 1020 aaactttgat acgttgtaat acgtaatatt tgaggattat tggaacttac ggattgggaa 1080 tccgagttac ggatcttcca gaattggagt tgtaagttca taaaataaaa tgttaaccgt 1140 cacttagttt tggaaattga cggagatccg accgttggat ggtaatgaaa tttcaggatg 1200 ttgtcctaga gatatattgt ggacctctgg aagttatgga tttaaaatct gagttgcaga 1260 tctttcggat cgaactgcgt agtgatgtgt tttatataag ttatattcta tcgatatgat 1320 ttctgaggtt ggatttgatt attgttctag gcggcgatcg tcatgacgcc ttgatgtgtt 1380 gtgctaggga gttgtagggc gaactccagg tgagtgggca gttttgtttt cgtattacct 1440 atatactatt gagttttccc agaaattgaa tttaaatgaa agtatgattt aaaatgccat 1500 ggatagattt atatgaaaag tatgatttga aatgccatgc atagaagtat atgaaaagca 1560 tgaattgata tatgatgcat atatatatgt gaattggtgc tgtggacgca caggtaagta 1620 tcaggtgagt tttatattat tcatgtgcat tgttgatgtg tatattgtgg atagctcata 1680 acctgcaatc atggtgttag tgcttatatt attcaccaca ccgcacgctc gtcttggatc 1740 caagtaggtg gatgtcgtac agaccaagtg agggttccga catgctagtc gtatagatta 1800 ctagatgtga ttccgactag tgggtgacct tagattatgt gcacagatga ttgatgagag 1860 aagcactaga gcgtattatt acaccatcca tgtcgtacag actacttcag gtagttccga 1920 cttatctgca gtgtagtgcc gtacaggtca tcgaggtgac tccggttgga ttggatgttg 1980 agctatggaa ttaaccgtac aggaccaact gcagggtctc cggttaattc aacttttcac 2040 ctgttacatt gatgcatcat ttattttgtt ttcgaaatta aaacatggca tactttcggg 2100 ttttaaagaa aaattgatga ttcgagattt atgaaaagta ttatgttatt atactatttt 2160 ctgggaaaag tatacaggtt ttacagtgag gggttagaat tatttttggc gaaatgtttt 2220 tgaaaagctt ggttttactg acccactcaa ttttgttttt cgcccctcca ggttcttgat 2280 agcagagttt tggtggccac gaggaatcca acggtattct gacagaattc acaaaagtag 2340 gactcaccct cgagggtttc cattttaata attgtatttt aaaagcttcc gaactgtgta 2400 aatggttacg tcactctcat gtgacggcca gcatgccctc cttcgggacg gggtgtgtca 2460 // ID Gypsy-16_Mad-LTR repbase; DNA; EDCOT; 577 BP. XX AC ACYM01047118; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-16_Mad-I; KW Gypsy-16_Mad-LTR; Gypsy-16_Mad_. XX NM Gypsy-16_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-577 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1420-1420 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01047118; Positions 802 1378. XX SQ Sequence 577 BP; 157 A; 131 C; 92 G; 197 T; 0 other; tgcattttgg agcattttgg agcaattttg ggcttggaat gaatatcaca tgcttggagc 60 aagggagatg gacgaaattg aagacctaaa gatgctagga ttcctaatta aagaaggatt 120 cctagaagaa tgaggattcc tatttgaagt acgaaagtta agccaaggtt tcctattttg 180 gtttgacctt tcctaatctt aaatgtccct aagttccagc aacattgcag atctcttatg 240 cattttagga cacaaaacaa agtatccttg caccaaacaa ggccttgttg tggggtctcc 300 ctttcctctt ccttgccgtg caagggagcc atcccttttc tatcttttgc cataaatcac 360 attccctttt caattaaaag cctttccctt tctttcctaa acccaccagc accttcctta 420 cctttccctt aggattttga ctttaattct tatttaactt ttagttttga attaattcat 480 gttacctaaa ttattttcct agctttaatt accctaaagg ccttaaataa tcatccttgc 540 cgtgggaatc aggaccattc atcatcaccc acttcca 577 // ID Copia-55_Mad-LTR repbase; DNA; EDCOT; 244 BP. XX AC ACYM01042437; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-55_Mad-I; KW Copia-55_Mad-LTR; Copia-55_Mad_. XX NM Copia-55_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-244 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1405-1405 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01042437; Positions 28095 28338. XX SQ Sequence 244 BP; 68 A; 40 C; 46 G; 90 T; 0 other; tggatatata tgccaggtgt attggatatt atgataggtg tattgaatgt atgctaggtc 60 attaaagact gccacatcag cagcagctta ggacatagac cattgtttgg tgaaccgcct 120 atatagagta atagctcctt gtattagata agtttggttg taataacagt tttttgagat 180 atcagaaata catctttctt ctcctctaag cttcttcatg cttttcaatt ctgcaattct 240 ttca 244 // ID Copia-41_VV-I repbase; DNA; EDCOT; 4496 BP. XX AC chr10; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-41_VV_; KW Copia-41_VV-LTR; Copia-41_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4496 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr10; Positions 5083276 5087771. XX CC Positions [1729-2229] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 1054..2733 FT /product="Copia-41_VV-I_1p" FT /translation="MFQQTLQSTGTTIGTASVAQKGIFSHALNVRQENHTT FT WIVDSGASDHMTGNLMVFHEYTPCHNNSSIRIADGTLSRVFGTGSVIISKD FT ITLHSVLYVPKLDCNLLSISRLTQDLNCVTKFIPHMCEFQALNSGKRIGNA FT EVRAGLYLLRAEEIQRLPMKTACVVSNPSTKTDSVVMLWHYRLGHPKFSYL FT EKLYPSLFNKNSKNFQCEICQLSKHTRNSYSIQPYKPSHPFSLIHSDVWGA FT SRINNITGSRWFVTFVDDHTRVTWVFLMKKKSEVREIFENFNNMVQTQFQA FT KIQVLRTDNAREYYHNILGSYLLENGIVHQSSCIDTPQQNGVAERKNRHLM FT EVARSLMIASNVPKQLWGEAALTATYLINRMPSRILQFKTPCQILLAAYPS FT ARIISSIPIKVFGCTAFVHIHKSQRSKLDPTATKCIFLGYSPNQKRYKCYS FT PTTKKFYTSMDVTFFENQPFYPKTAIQGENWSTDEFQFWETEISTTSPLSS FT SLPPQTDTTLSVPENNSLDVPSVTPKSTTQGSKEVIVYSRKNLKEKPEKPP FT QKEPEDSTSPEQN" XX SQ Sequence 4496 BP; 1487 A; 946 C; 923 G; 1140 T; 0 other; tggtatcaga gcattcagat ctaaaccacg tataaaaaaa aaaaatcatc tttttccatg 60 gagagcagaa cggaaggatc aaactcggag gtgatgtcca gacttgaagc agttcactcc 120 ggcagtgcca gcaccacaga cggcatcatt cttcccataa caggtcataa actcaatggg 180 cagaatttta ttcaatgggc tcagtctgtt cggatcttca tctgcgggaa aggtaaggaa 240 gaatacctta cgggagccat tgttcagccg aaggaagatg atccaggata ccgaacctgg 300 aagttggaaa atagtatggt gatgtcttgg ttaattaact ctatgaccaa tgacatagga 360 gaaaacttca tgtattatgg cacagcaaag gagatatggg atgtagctag agagacctac 420 tccaacatcg ataatacctc ggcgattttc gaaatcaaga gtattctcca ggatcttcga 480 caaggagatt caactgttat cgaatatttt aatatcctta cacggtattg gcaacaactc 540 gatatttatg aagaattggt ttggaagtgt cccgaagatg gactcctata caagaaggtc 600 attgaaaagg aacgcatcta caaattttta cttggcctta ataagaattt agatgaggta 660 cgtggtagag ttctaagtat taagccatta cctagtgtta gggaagtttt ttttgaaatt 720 cgcagagagt aaagcagaca aaaagtgatg ttgggaaccc aaaattcctc caaaaatctt 780 gagaactcag ccctagttgc acgaggaacc caatccaaca acaacaacca ccaaacgaag 840 aagaatcgtc catggtgcga ccattgtaga aaacctagac acacgaaaga gacttgctag 900 catctacacg gtaaacctgc tgattggaaa ccttctcggc cacagcaaaa cagagaaggc 960 cggggttaca ccgctacaac cgaagaagac acatctggca ctagctcaaa tcctggaccg 1020 tttagcaaag agcaattaga ggcactgcag aaaatgttcc aacaaactct tcaatcaact 1080 ggaacaacta ttggtaccgc atctgtagcc cagaaaggta ttttttccca tgccctaaat 1140 gttagacagg aaaatcacac tacatggata gtggactcag gagcttcaga tcacatgact 1200 gggaatctca tggtttttca tgaatatact ccttgccata acaattcctc tattcgaatt 1260 gccgatggaa ccctttctag ggtattcggc acaggttcag ttattatttc caaggatatt 1320 actcttcact ccgtgctcta tgttccgaaa ttggattgca acctattgtc tataagtaga 1380 ctaacacagg atcttaattg tgttactaaa ttcattcctc acatgtgtga atttcaggcc 1440 ttgaactctg ggaagaggat tggcaatgct gaggtgcgtg ctggacttta ccttctgaga 1500 gctgaggaaa ttcaaaggct accaatgaag actgcttgtg tagtttccaa ccctagtacc 1560 aagacggata gtgttgttat gttatggcac taccgattag gtcacccaaa attttcctat 1620 cttgaaaaac tatatccatc attattcaat aaaaattcca aaaattttca atgcgaaata 1680 tgtcaattgt ccaaacatac tcgcaactcc tattccattc aaccatacaa accatctcat 1740 cctttttcct tgattcacag tgatgtttgg ggggcctcta gaatcaacaa cattacaggt 1800 tctagatggt ttgtcacctt tgttgatgac cacactcgag tgacttgggt attccttatg 1860 aagaagaaat cagaagtgag ggaaatattt gaaaacttca acaacatggt tcagacgcag 1920 tttcaggcaa aaattcaagt ccttcggaca gataatgctc gagaatacta tcacaacatt 1980 cttgggtcat atcttctgga gaatggcatc gtacatcaaa gctcgtgcat tgatactcca 2040 caacaaaatg gagttgcaga aaggaaaaat agacatttga tggaggttgc acgatccctc 2100 atgatagctt caaacgtgcc taaacaatta tggggtgaag ctgcactcac agcaacctac 2160 ttgatcaacc gaatgccttc taggattctt caatttaaaa ccccgtgtca aatcctcctt 2220 gctgcatatc catccgctcg aataatctcg tctatcccaa tcaaagtctt tggttgtact 2280 gctttcgttc acatccataa gtcccaacgt agtaaacttg atccaacagc cactaaatgc 2340 atctttctcg ggtactcacc aaaccaaaaa agatacaagt gctactctcc aacaaccaag 2400 aaattctaca cttccatgga tgtcactttc tttgaaaatc aacccttcta ccccaaaact 2460 gcaattcagg gggagaactg gtccacagat gaattccaat tctgggaaac cgaaatcagc 2520 actacttctc ctttgagttc atcactgcct cctcaaacag atactactct ttctgtcccc 2580 gaaaacaatt ccttggatgt cccttctgtc acacctaagt caactacaca aggcagtaaa 2640 gaggtaatag tttattctag aaaaaattta aaggaaaagc ccgagaaacc tcctcaaaag 2700 gagcccgagg acagcacttc acctgagcag aactaagaat tggaccagga tccaagcaac 2760 ccaaactcat aaccaggtaa cacaatttat gatctaaatt ccagtaatga ctttgatgat 2820 cttgatcaac ccattgcttt aaggaaaggt gtaagatcct gcactcagca tccaatcaat 2880 aatcatgtgt cctatggaaa gctttcacag aatttccaag cattcatcac ttctcttgaa 2940 gatgatcgta tcccatccaa catccaagaa gcacttcaac aacctgaatg gaagactact 3000 gttcaggaag aaatacaagc attggagaaa aatgggacat gggaaatctc agaattacca 3060 gagagtaaga ggcctattgg atgcaagtgg atatttaccg tgaagcacaa tctagatgga 3120 agtataaaca ggttcaaggc tcgactagta gctaaaggat ttactcaatc ctatgacatt 3180 gattatgaag agacatttgc accagtagca aagctcaact ccatcagagt gttattgtca 3240 gttgcaataa atttggactg gaatctgcac caacttgatg tcaaaaatgc atttctcaac 3300 ggagaactag aagaggaagt ctacatgaag attccaccta gtatggaaac tccagaaaat 3360 tcaggaaaag tgtgtaaact gagaaagtcc ctatacggtc taaaacagtc acctagggcc 3420 tggtttgatc gactgactag agttgtgaaa aaacatgggt tcatccaatg tcaagcagct 3480 cacacactgt ttatgaagca ctctaaggaa ggtgaaatga ctttgttcat tgtctatgtt 3540 gatgatatta taattaccag agacgatgaa gaagggatag ggaatctcaa gaagctgcta 3600 gcaagagaat ttgaaatcaa agatcttgga caactcagat actttcttgg catggaagtt 3660 ggcagaacta aggagggaat tgtggtcacg caaaggaagt atgtccttga tctacttcag 3720 gagactggaa tgctaggttg taagccagtg gacacgccta tggatcctat tggtaagata 3780 aagataatga cagtcatcca actgaaaaag acaggtacca gaggttagta ggaaagttga 3840 tctccttaac tcacacaagg cccgatatta gtttcgctgt gagcatggta agccgctaca 3900 tgaacaatcc cactgaaaga cacatgaaag ccgtatatag aattttacag taccttaaaa 3960 agagcccggg tagaggactc tacttcaaga aaacctcaag tagggaagtt gaggtattca 4020 cagatgctga ttgggcagaa tccttgacag atcggaggtc aactactggg tattgttcct 4080 atgtgtgggg aaacttggtg acttggagaa gcaagaagca gtccgtagtg gcgagaaaca 4140 gtgcagaggc aaaattcagg gcaatggctc atgggatatg tgaaggaatg tggctccaaa 4200 gaatactcaa ggaacttgga attatatcaa actccactat gacagttttg tgtgataaca 4260 aggctaccat aagtattgca aagaatccag ttcaacacga cagaaccaag cacgtggaga 4320 taaaccgtca cttcatcaag gagaaacttg aagggggaac aatcagactt atgtatattc 4380 cttcaagtcg tcaaacagca gacattctga caaaggcact tccaaaggcc acctacgaaa 4440 acatgaaaag caagttggga atgctagaca tctactaccc aacttgaggg ggagcg 4496 // ID Gypsy17-PTR_LTR repbase; DNA; EDCOT; 436 BP. XX AC LG_XIV; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy17-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-436 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-436 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 313-313 (2007). XX DR Genome; LG_XIV; Positions 4332411 4332846. XX SQ Sequence 436 BP; 138 A; 95 C; 73 G; 130 T; 0 other; tgttacaagc ggaagaaaga gcataagtca atggcgggct ttaattcaaa aggaagttac 60 tggtcacttt attataaact gcaccgtttt aattaccttt aaacgcaccg ttttgttgtt 120 attaaaactc atcgtttgga tgagtcaata ctcaccgttt cagtaaggct ttttattctg 180 ttacaattct gttgtaagaa gaagtatata acgtgcatct gtgcatgaaa agataaaaga 240 aatataatga gaaatgaatg acttcctaga attacggaac acccctattg caccttctcc 300 tgttccttat cattccccac aacaatggct aagtggtaaa actgactccg gccatctctc 360 aactcatcac tgcactccta catcccagct gcagaactcc atagttatag gatcattaag 420 tgtctcacac gcaaca 436 // ID LTR-6_Mad repbase; DNA; EDCOT; 2364 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR-6_Mad. XX NM LTR-6_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2364 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1789-1789 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 2364 BP; 579 A; 456 C; 543 G; 785 T; 1 other; tgtcacagcc cgtcccggag atgtacgtta attatgttat cgacggcgtg aaattaccta 60 aatatccttg gacgttgaga attattatgg gatgttgtgg tttaaactta agattttgga 120 ccaattagtt atattcctct tttattggac ccaattagaa ctaagtgttc tcttagttgt 180 gattggtgtg cattttggga ccacacacac acccctaccc tttctctctc ttctctcccg 240 tactctctct ctctcggttt cactctctct ctccttggct atacgtacgg acaagggcaa 300 gaacacccca aacctcgcag atcgaagacg ataatggtac cattgcgttc ctcgtgacct 360 tacgagttca ttggtaccaa tttcaggtaa ggaaaccttc gatatcccgt ggaaacccta 420 gccccgattt tggtgcactg ttcacgcgga cgtaaaactg tttgtttcag ggaatttcaa 480 gctcatagag agctttagga ggtcctaagg aggctcgggg tagttcgttg gaagaatttg 540 gacgtcggag ggccgagatc gaagttttca aagttgaccg gattatcgag cttcctcagg 600 taaattctag tggatttcaa ggcttaaaaa tggtataacg tgattctaca cgttgttagc 660 tttccaatgg ttcaaatttc atgaaaaatg gtggaaaaat gagtgagaac aaaggttttg 720 aagtttttcc cagtctccgg cgaccggcga ctcgccggag aagacggggg aatattccgt 780 cagttttgac ggaatatgct gacgccgtca gttagtttgg acggttaccg ttgggtttta 840 acggaatatt ccgaggaata ttcctaacgg cgttactgat tccgtcacgt gtgcctggca 900 catggccgcg cgtggggggc gcgtcttgcc gtgcccttgc cggcgcgtgg cggcgcgtga 960 gggctccaaa aatttatcta aaaatttggg gatgatcctg aggttgtgta ggtcactgtg 1020 gtgtattcat atacccattt tgagcaatgt atgagaagtt attagctagt tttgcctatg 1080 tgctttaaaa taacgttttt atagttaatt cgcatatagg tgagacttat cccgaggacg 1140 agcgtatcca agggcgactc gggggttacg acccgtcgac ataccagtga gtgggctttt 1200 ggttttcagt atatatttat atacttgata tatttcccag aaatacgtgt ttaaatgata 1260 gtatgccatg aaatgccatg catataagct tataattcat acatgaattg gtatgtgatg 1320 ctttatatat ataaatgtgg tgctgtggac gctcaggtaa gctcaggtaa gttgtgtttg 1380 gttatgtgaa tcatcgatga tgtgatatgt gattgaataa tgttgagctc ataaaactgc 1440 acctagggtg attgtgattt agccatagat atgaagcaca tgcctgttta tttatgtcac 1500 ctcccgcacc atatgctcat attggatcca acttaggtgc acagtcttgt cgtacagacc 1560 ttatttatgg ttccgactcg taggtgacta gcgatttatc gcccggctat tatgtgagag 1620 tagaattgag catgattata ttacacccaa tmttgtcgta cagacctttt tgtttggttc 1680 cgactcttgt gcagtatatt gccgtatagg tcattgtagt gactccggct agattgactt 1740 ttgagctatg aattcagccg tacagactac cacaggggtt ccggctaaca tgtcatattt 1800 ctatgaaatt attcttacct gaattgctta ctctgttata tcttggcatg gcatacattt 1860 gaatatgatt atgtgaagca tgaattgaat tgatatgatt tcatatatat atattatgta 1920 tatgcttata tcttgattct gggaaaaatt atacatgttt tacagcgagg ggttagatat 1980 gttgataaat gaaatggttt tgtaaaacat ttgtttttgc ccactcacgt tttctgtttt 2040 gcgcccctcc aggttttaag taagcttgtt gttggtggct tgaggacgtc ggcagttctg 2100 acctatctaa ataatagtag gacattcctg gtactgtata actagtactt gtcctactgg 2160 actgcaccta gacttattat gctctgatta ggagtgttta ctgttgtaac taactcctat 2220 cacttcctgt ttagtagtgc actctagtaa ttcggttttt aattattcgt atatttctta 2280 tctttattgc ttccgcactg tgcacatggc tacgtcactc tcacgtgacg gccagcatgc 2340 cttgatctcg gtcggggtgt gtca 2364 // ID Copia-29_Mad-LTR repbase; DNA; EDCOT; 349 BP. XX AC ACYM01054283; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-29_Mad-I; KW Copia-29_Mad-LTR; Copia-29_Mad_. XX NM Copia-29_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-349 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1376-1376 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01054283; Positions 25579 25231. XX SQ Sequence 349 BP; 100 A; 47 C; 65 G; 137 T; 0 other; tgatgagtat ggttacatgg caatattaca tatatttgcc atgtcagcaa atcagttgga 60 tttggttgta aggtcagttg gatatagttg taagatttag ttaattggat aagatttgat 120 aagatttagt gagatatgtt gaggggtagc ttagtcatta agaaagtagt ggtagtcctt 180 tatattggat tctcttgtaa taactctctc aattaacaaa aatacaatag tcgtgaagta 240 cttttcctct ctaagttttc tgagattttc cttggctctt taaccttcct tcattctcta 300 agattcttca tcaatgtcaa actctgtatt tctagttaat agttagtca 349 // ID hAT-1_PTr repbase; DNA; EDCOT; 3494 BP. XX AC . XX DT 14-DEC-2009 (Rel. 15.02, Created) DT 14-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE hAT-type DNA transposon - consensus. XX KW hAT; DNA transposon; Transposable Element; hAT-1_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3494 RA Jurka J.; RT "DNA transposons from black cottonwood."; RL Repbase Reports 10(2), 111-111 (2010). XX DR [1] (Consensus) XX CC >96% identical to consensus. XX FH Key Location/Qualifiers FT CDS 973..3336 FT /product="hAT-1_PTr_1p" FT /translation="MSLDKYFKRKSLEDEESIKASSHVTQSSSKKSHIEIN FT PDTLLADPGLRRPIYEYHINDRDAIRRAYLQKGPCQPSHCDFPQKQFGNIS FT TLRRFNPAWFGAYPTWLEYSIAKDAAFCLYCYLFKSKGGVDSFVGDGFSNW FT KKKERFDLHIGKSNSSHNAARIKCENLMNEKQSIMTLLSEQTVKSQSDYRT FT RLNASIECARFLLHQGLPFRGHDECECSSNQGNYLELLHFLSRNNEAIKRV FT TFSEAPRHNKLTSPDIQKDITQAAAEEITNVIIKDLGDSLFSILIDESRDI FT SIKEQMAVVLRYVDNNGHIIERFLGIQHVRDTTASSLKAAIEALFSKHGLS FT ISRLRGQGYDGASNMRGEFNGLKALILNSNPSAYYVHCFAHRLQLTLVAVT FT KKHNEVGDVFNFISSIINIVGASCKRMEVIREKQYARIIEGLENGEISSGR FT GLNQETSLRRYGDTRWGSHYVTIIRLLAMFSSVLDVLEIIREDGMNSEQRT FT EAVVLTDIMESFNFVFMLHCLRRILAVTNEFSQALQRKDQDIENAMSLLKT FT SKERFKMMRENDWESLLEEVSSFCIKHDIDILNMDDEYKLRGRSRRKSQGI FT TNLHHFRYELFNNIIDMQLTELDDRFTETSTELLLCVACLNPSDSFSAFNK FT EKLXRLALFYPSEFSIVDLMVLGDQLDTYIIDLRGDDEFSGIEGIASLAEK FT MVKTKKNLIFPLVYMLIKLSLLLPVATATVERVFSAMHIVKSRLRNRMGDK FT WMNDSLVVYIEKDIFDKIDNEAIMKRFQNMKTRREQL" XX SQ Sequence 3494 BP; 1135 A; 510 C; 643 G; 1204 T; 2 other; gcagtggcgg agccacggag ggacaaaagg gggcaattgc ccccttaatt tttttttata 60 ttaaaatatt aatatattag tttagggaat tgttactgca gggaaggaaa aagaaagttg 120 ttattgttta taattgttga cttatatgtt aatataatat aatataatat aatatacaca 180 gctcattcca caattttttc ctttttccct tttgtttcta tatctccgct taaaatccct 240 gactaacaaa gtttttttgt tccttttcat gagctgtcgt tccctgcctc tctcgtatgc 300 aaatttctca tcaagtatag ttaagcaatt aatctttttt gccttttgct ttatacttta 360 ggtaaatttt ctttattttt tctatttatt tcattgttta attttagttt tattctttta 420 taattagtta ttaaaaatat tagggtttat gataatttag gggttttgat atgaatatgt 480 tcaaatgttc aaaataaatg tttaaatctg ctaatttaat caattaaatg tttcttttct 540 tattataaag gaataaatta atattcatgc aaaaccacta ttcttgacat ctcttgcatt 600 ggcagagtag tttattgaaa tttaatattt tcacatgact tgtttgtaag taaaatatca 660 agtagaaagc atgtttttca agaattgttc ctcttacaca tacactaggc attgctcctc 720 aattaaatat ctagaaatga ttaagtataa tttaatcaac atacttatta tatgcatata 780 gatatgaatt gaaataggtt ttgattttga tgaattgacg tgtattttgc tatgaatttc 840 atatggaaga tttagaatta ttgtgtaact caactgactt ttatttaaca gtgaattatt 900 gtgtagttgt gttaattatt atgtagacac taatgatgat aaaaaaatcc agcaggttca 960 tattaaatta acatgtcact agacaagtat ttcaagcgta aatcccttga ggatgaagag 1020 tcaatcaaag cttcaagtca tgtaactcaa tcaagttcaa agaaaagtca tattgaaatc 1080 aaccccgaca ctctccttgc tgaccctggc ttaagaagac caatttatga ataccatata 1140 aatgataggg atgcaatccg aagagcttat ctacaaaaag gtccttgtca accttcacac 1200 tgtgattttc ctcaaaaaca atttgggaat atatcaacac tacgacgctt taatccggct 1260 tggtttggtg catacccaac atggttagag tacagcatag ccaaagatgc tgccttttgc 1320 ttgtattgtt acctcttcaa gtcaaaaggg ggtgttgatt cgtttgtggg tgatgggttt 1380 tcaaattgga aaaaaaagga aagatttgat cttcatattg gaaagtctaa tagtagtcac 1440 aatgcagctc ggataaaatg tgagaatttg atgaatgaaa aacaaagtat catgactttg 1500 ttatctgagc agacagtaaa gagtcaaagt gattatcgaa ctcgattgaa tgcttcaata 1560 gagtgtgctc gttttttgtt gcaccaagga cttccatttc gtggccatga tgaatgtgaa 1620 tgttcaagca accaaggaaa ttatctagag ctcttgcatt ttctttccag aaataatgaa 1680 gctattaaaa gagttacttt cagcgaagct cctagacata acaaattgac ttctccagat 1740 attcaaaaag acattactca agctgctgca gaggagatta caaatgtgat tatcaaagat 1800 ctaggtgact cattattttc aattttaatt gatgagtcac gtgacatatc aatcaaggaa 1860 caaatggcng ttgttctacg atatgtagac aacaatggac atataattga acgttttctt 1920 ggcattcaac atgtgcgaga tacaactgct agttcactca aggcagctat tgaagctttg 1980 ttttctaaac atgggctaag catatcaaga ttgcgtggtc agggatatga tggagctagt 2040 aacatgcgag gtgaattcaa tggcttgaaa gcacttattc taaatagcaa tccaagtgca 2100 tattatgtac attgttttgc tcacagactt caattgactc ttgtggctgt tacaaagaag 2160 cataatgaag ttggagatgt cttcaatttt atttctagca ttataaacat agttggagca 2220 tcatgtaaaa ggatggaggt gattagagaa aaacaatatg ctagaattat tgaaggactt 2280 gaaaatggag aaatttctag tggacgaggc ttgaatcaag aaacttctct tagaaggtat 2340 ggtgataccc gttggggctc ccactatgtt acaattattc gtctacttgc aatgttttca 2400 tcagttcttg atgtgcttga gattataagg gaggatggga tgaactcaga acagagaacg 2460 gaagcagtcg ttttaacaga tattatggaa tcatttaatt ttgtgttcat gcttcattgt 2520 ttgagaagga tactagcagt tactaatgag ttctcacaag cattacaaag aaaagatcaa 2580 gacatagaaa atgctatgag tttattgaaa acatcaaagg aacgattcaa aatgatgaga 2640 gagaatgatt gggaatcttt actggaagaa gtgtcatctt tttgcatcaa acatgatatt 2700 gatattctaa acatggatga tgagtacaag cttcgtgggc gttcaaggcg aaaatctcaa 2760 gggattacaa acctacacca tttccgttat gaattgttta acaatatcat tgacatgcaa 2820 cttactgagt tggatgatcg ttttactgag acgagtacag agttacttct ttgtgtggca 2880 tgtttaaacc caagtgactc tttctctgct ttcaacaaag aaaagcttnt tcgccttgct 2940 cttttttatc ctagtgaatt ctctatagtg gaccttatgg tacttggtga ccaacttgat 3000 acgtatatta ttgatctacg tggtgatgat gagttctctg gtattgaagg tattgctagt 3060 cttgcagaga aaatggtaaa aacaaagaag aatttgatat ttccattagt atatatgctt 3120 atcaaattgt cattacttct accagttgca actgctacag tggagagagt tttttctgct 3180 atgcatattg tcaagagtag attgcggaat aggatgggag ataagtggat gaatgatagt 3240 ttggttgtat acattgagaa agatatcttc gataagattg ataatgaagc tattatgaag 3300 cggtttcaaa atatgaaaac tcgaagagaa caattataat gtaagttttt tcagtttaaa 3360 agtattttta aattaatttt acttgatatg aattagtata tatgtttcga attgatttct 3420 aatgcatatc tatataatat agtatttgtt aataatttgc cccctcatta aaaaaactct 3480 ggctccgcca ctgc 3494 // ID Copia-41_Mad-LTR repbase; DNA; EDCOT; 448 BP. XX AC ACYM01025173; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-41_Mad-I; KW Copia-41_Mad-LTR; Copia-41_Mad_. XX NM Copia-41_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-448 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1391-1391 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01025173; Positions 9286 9733. XX SQ Sequence 448 BP; 136 A; 73 C; 94 G; 145 T; 0 other; tgttaggact ctattgaatt atcattgggc ataataagga ctatcatacg tggaattaat 60 taattaaagt caaaaccatt taaaggataa aatcccttat ttgtaggaca ctaaatgcgt 120 gcttcagttg tggtttaaca actgacaaac gtggagattt tttaggctta gacgatccca 180 cgatagttgg gatgcagttg ggtttataag cctatacagg aggtgtccct actcacggga 240 agattacatc aaaaacaaga tctagaacta tcgctagggt tttgatatca ggttcctcag 300 tgagtagaag actctctgtg ttgctgtttt gttgcttgta tcatgacgtc ctcaggtatg 360 atcatactca gactcctcaa atatatatat gtatatgtga atgttaattg tgatccttgg 420 caaagactaa tcagttgtag gtctaaca 448 // ID SHACOP15_I_MT repbase; DNA; EDCOT; 4152 BP. XX AC CR931743; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP15_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Internal; Interspersed; repeat; ORF; peptidase; integrase; KW SHACOP15_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4152 RA Shankar R. and Jurka J.; RT "SHACOP15_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 57-57 (2007). XX DR EMBL/GenBank/DDBJ; CR931743; Positions 33334 37485. XX CC The internal region has intact domains for gag-pol polyprotein CC with integrase and cysteine peptidase. This internal element is CC present in three complete and intact copies in the genome and CC exhibits Copia-like arrangement for various domains. XX FH Key Location/Qualifiers FT CDS 172..4086 FT /product="SHACOP15_I_MT_1p" FT /translation="MAAKFEIEKFNGRNFSLWKLKIRAILRKDNCLDAIDG FT RPADITDEKWKEMDDNAVANLHLAMADSVLSSIAEKKTAKEIWDTLIKLYE FT VKSLHNRIFLKRRLYTLRMGESTSVTDHINTLNTLFSQLTASDFKIAENER FT AELLLQSLPDSYDQLIINITNNNITDTLHFDDVAGAILEEESRRKNKEERS FT ESSKQAEALTMTRGRSTERGPSGSQNHGRSKSRRKKNIKCYGCGMKGHVKK FT ECWNIKKNGEKNSEASTSQGCVASTSDDGEILYSEAATSSKGERRLNDVWI FT MDSGATWHMTPHRDWFFSYEPISEGSVYMGNDHALEIAGVGTIRLKMHDGT FT VRKIQGVRHVKGLKKNLLSVGQLDDLGCKIHTESGILKVVKGNLVVMKAEK FT ITSNLYMLLGDTLQEADASVAASSQEETTMMWHQRLGHMSERGLKVLAERN FT LLHGLKAVNLPFCEHCVISKQHRLKFARVTTRSKHILDLIHSDVWESPEIS FT LGGARYFVSFIDDYSRRLWVYPIKKKSDVFPVFKAFKAQIELETRKKIKCL FT RTDNGGEYIDGEFLAFCKQEGIVRQFTVAHTPQQNGVAERMNRTLLERTRA FT MLKTAGMAKSFWAEAVKTACYVINRSPSTAIDLKTPMEMWKGKPVDYSSLH FT VFGCPVYVMYNSQERTKLDPKSRKCIFLGYADNVKGYRLWDPTARKVVVSR FT DVVFAENELQSEQKNDSTSKETAIVQMEEKSKESDSSEAESVHEEQEPDDV FT NDGVRRSTRQTQKPSWQSDYVMTSHDAYCLITEEGEPSTFHEALNGSDASQ FT WMTAMHEEMEALHRNKTWELVELPKGRKAIGNKWVYKIKRDGNDQVERYRA FT RLVVKGYAQKEGIDFNEIFSPVVRLTTIRVVLAMCAALDLHLEQLDVKTAF FT LHGELEEEIYMLQPEGFKEQGKENLVCRLTKSLYGLKQAPRCWYKRFDSFI FT ISLDYSRLSSDHCTYYKRFDGNDFIILLLYVDDMLVVGPNKDRVQELKAQL FT AREFDMKDLGPANKILGMQIHRDRKDMKIWLSQKNYLRKVLRRFNMQDCKP FT ISTPLPVNFKLSSGMSPSNEAERMEMSRVPYASAVGSLMYAMICTRPDIAQ FT AVGVVSRFMADPGKEHWNAVKRIMRYIKGTSGVAVCFGGSELTVRGYVDSD FT FAGDHDKRKSTTGYVFTLAGGAVSWLSKLQTVVALSTTEAEYMAATQACKE FT AIWMQRLMEELGHKQEQITVYCDSQSALHIARNPAFHSRTKHIGVQYHFVR FT EVVEEGSVDMQKIHTNDNLADVMTKPINADKFVWCRSSYGLLET" XX SQ Sequence 4152 BP; 1343 A; 704 C; 1051 G; 1054 T; 0 other; gtggtatcag agccgctggt tcgtagctgt tattccgctg tgataaacta gtggagtggt 60 aagaaaaatc ttagtatgct ctgtggttgc ggtttaaact gatcttccac atcagaaaag 120 aattcttatt attccggtct agtttgaaag aaaaatattt ggtgtaaaac catggcagcg 180 aaatttgaga tagagaagtt caacgggaga aatttttccc tatggaaatt gaagataagg 240 gcaattttaa gaaaagataa ttgtctagac gcaatagatg gcagacctgc agatatcact 300 gatgaaaagt ggaaagagat ggatgataat gccgttgcca atttgcacct agcaatggcg 360 gactcggtat tgtcaagtat tgctgaaaag aagacagcaa aggagatctg ggatacacta 420 ataaaattgt acgaggtcaa atcactccac aacagaatat tcttaaagag aaggctctac 480 actcttcgaa tgggtgaatc cacatccgta acggatcaca tcaacaccct gaatacgcta 540 ttttctcaac tcacggcttc tgatttcaaa atagcggaaa atgagcgtgc tgaacttcta 600 cttcagagtt taccagattc gtatgatcaa ctcatcatca acattacaaa taataacata 660 actgatactc ttcactttga tgatgtcgcc ggtgcaatcc ttgaagaaga atccaggcgc 720 aagaataagg aagaaaggtc agagagttca aagcaagcag aggctttgac gatgacgaga 780 ggcagatcaa cggaacgtgg ccccagtggg agtcaaaatc atggtaggtc aaaatctcga 840 agaaagaaga atattaaatg ctacggttgt ggcatgaaag ggcacgtaaa gaaggagtgt 900 tggaatatca agaagaatgg agagaagaat tctgaagctt caacatctca aggatgtgtt 960 gcaagtacct cagatgacgg ggaaatcctg tatagcgagg cagcaaccag ttctaaaggc 1020 gaaagacgac tcaacgatgt ctggataatg gattcaggtg caacatggca catgactcca 1080 caccgagatt ggtttttctc ttatgagcct atctcagaag gatctgtgta catgggaaat 1140 gatcatgcct tagaaattgc tggagtcggt actatcagat taaagatgca tgatggtact 1200 gttagaaaaa tacaaggagt gcgtcatgta aaggggttga agaagaattt attgtctgtt 1260 ggacaattgg atgatctcgg gtgtaagatc cacactgaaa gtggaatctt gaaagtagtg 1320 aaaggcaatc ttgtggtgat gaaagcagaa aagatcacaa gtaatctata catgcttctg 1380 ggagatacgt tgcaagaggc cgatgcatca gttgcagcat caagccaaga agaaacaacg 1440 atgatgtggc atcaaagact aggccatatg tcagaacgtg gcttgaaagt ccttgcggaa 1500 cgcaatctcc ttcacgggct caaggcagta aatttaccat tttgtgagca ctgtgtgata 1560 agcaagcaac atagattgaa gtttgctaga gtaactacta gaagcaaaca catactagac 1620 ttgatacatt ctgatgtgtg ggagtcacca gaaatatctc taggaggagc aagatatttt 1680 gtgtcattca ttgatgacta ttccagaaga ttatgggtgt acccaatcaa gaagaagtcg 1740 gatgtgtttc cagtattcaa ggcattcaaa gcacaaatag agcttgaaac taggaagaaa 1800 attaagtgct tgaggacaga taatggagga gaatatatag atggcgagtt tctagcattt 1860 tgtaaacaag agggtattgt aaggcaattc acggttgcac atacacctca gcagaatggt 1920 gtggcagagc ggatgaatag aactctccta gaaagaacaa gagctatgct gaaaacagcg 1980 ggaatggcca agtcgttctg ggcagaagca gtgaaaaccg cctgttatgt aataaatcgc 2040 tcaccatcaa cggcgattga tttgaagaca ccaatggaga tgtggaaagg aaagccagta 2100 gattattctt ctctgcatgt ttttggttgt cctgtgtacg tgatgtacaa ctcccaagaa 2160 agaacgaagt tggacccaaa gtccaggaaa tgtatcttct tgggttatgc tgacaatgtt 2220 aaggggtatc gcctgtggga tcccactgcc cgcaaggttg ttgttagcag ggatgtagtc 2280 tttgcagaaa atgaactgca aagtgagcag aaaaatgaca gcacttctaa agagactgct 2340 atagtgcaga tggaagaaaa atccaaagaa agtgattctt ctgaagctga atcggtgcac 2400 gaagaacaag aaccagatga tgtcaatgat ggtgttcgtc gatcaacgcg tcagacgcag 2460 aaaccgtctt ggcaatcaga ctatgttatg acaagccatg atgcatattg tcttataact 2520 gaagaaggtg aaccgtcaac ttttcatgag gcgttgaatg gttcggatgc ttctcaatgg 2580 atgacagcaa tgcatgaaga aatggaggcc ttacatagga acaagacatg ggagcttgtt 2640 gaacttccaa agggtcggaa agccattgga aacaaatggg tatacaagat caaacgtgat 2700 ggcaatgatc aagtggaacg gtatcgtgca agactggttg taaaaggata tgctcagaaa 2760 gaaggtattg acttcaatga gatattttct ccggttgtca gacttactac tatcagagta 2820 gtgttggcga tgtgtgctgc gttggattta catcttgaac agctagatgt aaagactgct 2880 tttcttcatg gagaacttga agaagaaatt tatatgctcc aaccggaagg atttaaggaa 2940 caaggaaaag aaaacttggt ttgcaggttg accaaatctc tgtacggtct aaagcaggcg 3000 cccagatgtt ggtacaagag atttgattct ttcataatta gcctcgatta cagcagactt 3060 agttcagacc attgtacgta ctacaaaagg tttgatggta atgattttat cattttgctg 3120 ttgtatgtgg atgacatgtt ggtggtaggc cccaacaaag atcgagtcca ggaattgaag 3180 gcacagttgg ctagggagtt cgatatgaaa gacttgggac cagcaaacaa gattttaggg 3240 atgcaaattc accgagacag aaaagacatg aagatttggc tttctcaaaa gaattatcta 3300 aggaaagtct tgcgccgctt caacatgcaa gactgtaagc caatctctac cccacttcct 3360 gtgaatttta aattatcctc aggtatgagt cctagcaatg aagcggagag gatggaaatg 3420 tctcgagtac cgtatgcatc ggcggtggga agccttatgt atgccatgat atgtacaaga 3480 ccagacattg cacaagcagt gggagtggtt agtcggttta tggcggatcc gggtaaagag 3540 cattggaatg ctgttaagag aatcatgagg tacattaaag gaacctcagg tgttgcggta 3600 tgtttcggag gatcagagtt aactgtcagg ggttatgttg attcagattt tgcaggtgat 3660 catgataaaa gaaaatctac tactggttat gtgttcacgc ttgcaggagg agcagtaagt 3720 tggttgtcca agttacaaac ggttgtagct ctgtcaacga cagaagcgga gtacatggca 3780 gctactcaag catgcaagga agctatttgg atgcaaaggt taatggagga actcgggcac 3840 aagcaggaac aaattactgt gtattgtgac agtcagagtg ccttgcatat tgcaaggaat 3900 ccagcttttc attcaaggac gaaacacata ggcgttcaat atcattttgt tcgcgaagta 3960 gtagaggagg gaagtgtgga catgcagaag attcacacca atgataatct agcagatgta 4020 atgacaaagc cgatcaacgc tgataagttt gtatggtgtc gatcctcgta tggcctattg 4080 gaaacgtagc aactggagtt ggcaaggtag agagattttg gaagctcaca aaagtgactt 4140 taagtgggag at 4152 // ID MuDr4_MT repbase; DNA; EDCOT; 533 BP. XX AC . XX DT 14-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; TSD; KW Interspersed repeat; Inverted repeat; transposon; MuDr4_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-533 RA Shankar R. and Jurka J.; RT "MuDr4_MT: A putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 576-576 (2006). XX DR [1] (Consensus) XX CC The sequence is self-complementary and flanked on both termini by CC 9 bp TSD. XX SQ Sequence 533 BP; 185 A; 75 C; 67 G; 206 T; 0 other; gggttaaata tgtttttggt ccctataaaa ttgggacctt ttaagtttag tccttactta 60 attttaatag ttcttttagt cccttaaaaa attctgcact cagtattagt ccctcctcaa 120 ttcaaatttg tttaatttat gcttaaactc ttgagttttt gaacaatttt ttgcagacgt 180 gttaagaaca ttactaaaag ttcctctgca aaaaattgtc gcaaaatttg atttctacgt 240 ccagattttg ttaattttat ctttaacttt tgtcgtttta aaaaattcat atttaattcg 300 tttcatgtta aaaaattcta aattttagta aatgaacctt tcatagtgtt ctaaacttgt 360 ctcaaaaaaa tcgttcaaaa atttaagagt ttaaggataa ttaaacaaac tttgttgtaa 420 cagggactaa aattagaagt aatttttgta gggactaaaa aacctattaa aattaagtaa 480 ggactaaact tagaagttcc caattttata gggaccaaaa acatatttaa ccc 533 // ID Copia-25_Mad-I repbase; DNA; EDCOT; 4227 BP. XX AC ACYM01078046; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-25_Mad_; KW Copia-25_Mad-LTR; Copia-25_Mad-I. XX NM Copia-25_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4227 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1371-1371 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01078046; Positions 9499 5273. XX CC Positions [1716-2207] - Integrase core CC 'GCAGT' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 2474..4000 FT /product="Copia-25_Mad-I_1p" FT /translation="MCDQNVEGNSSEKSDVNDEFLASSSETNESIENGSRL FT VQMQSNTGLQDYDHTPLKFKSLTKIYAKCNLCIIEPENFEEVTKDKSWQKA FT MEAEIGMIEKNCTWELVDRLFDKPVMGVKWIYKTKLNLDGSIQKNKARLVA FT KGYSQKLGIDFNETFAPVARLDTIRTLIRLAAQKGWKLFQLDVKSAFLNGV FT LNEEVYVDQPLGFVIKGKEDKVYKLKKAFYGLKQAPRAWYKEIDSHFCSFG FT FHRSPSEATLYIKATEAGILIVSLYVDDIIYTGSSGALMDEFKAEMMGKYE FT MFDLGLLHHFLGLGVIQTEGSIFLHQKKYARTLLEKFGLKECKPVATPLAT FT NERLSKQDGSEIADENLYRQIVGSLLYLIATRPNIMFAASLLVGFMHNPTR FT KHMGTAKRVLRYIQGTLDYGIAYEKGKDDVLIGYCDSDWAGSEDDMKSTFE FT YAFSFGSGAFSWAPIKQSSVALSSAEAEYISAAKATAQAIWLRFVLSDFGE FT EEVEPTQILCDNT" XX SQ Sequence 4227 BP; 1400 A; 610 C; 1004 G; 1163 T; 50 other; tggcctyara gccaggttgc atcatctgca actgggcgtg aatctgtgaa gcttgcartg 60 aagaactcga actgatcgtc ragcttcctc actgaagaaa actyggagaa gaaatcgtag 120 tgatcttgaa tctagtctca tatggctaga tcgagtggtg ccgatsttcg tgcgccrgta 180 ttcaatgggg acaatttttt ctggcagatt cggatgaaaa aaatattycg atcgcacrag 240 ctccgggata ttgtcgaaaa gggtctcgat actycggtga aggagggtga agaacttact 300 gcagctraga gcaagctatt gaaggataat ataatcagag atgcaaaggc acttggaatc 360 attcaagggg ccgtttctga tcagatattt ccgagaatcg ccatycaaga gactgcaaat 420 gctgcttgga atgtgctgaa acaagaattt gtgggagata aacaggtacg rgctgtgaaa 480 ctccaaggct tacgccgtga ttttgaatat actagaatgg gtgaaaatga agcattctct 540 gsatatctag ttagattatt tgatttgatt agtcaaatga gaagctatgg traggatata 600 agtawtcaga gaatcgttca aaagttgytg ataagtttac ctaggtycta tgatagtatt 660 gcttmtgtga ttgaaaatac taaggatcta gataytgttg atgttcaaga tgtggtagct 720 attctcaagg gctatgagca aagaattgac aggcatgatg aatctcacac tgagaaagca 780 tttgttagtc tcagtattgg tccaaagcag aataagtaca atggraatca agggttcaaa 840 ccacagaaga attggaagtc caaatggaag aaaggagwwa atagacytgc aaatyaaact 900 sgaaaagttg caggtacttc tgatggagct aagaatcctt gtatacattg tgataaaytg 960 cattttggtg aatgttggtt caaagataaa ccaaggtgcc ataattgtca taagttgggg 1020 catattgcaa gagattgccg agtcaagaag gagaaggcta accaacatgt gaattttgtt 1080 aatcaagtaa atgatactcc taccatgttc tatgtctgta atatgtcact gtgacgaaaa 1140 gtgaagatat atggtatgta gacagtggtt gyagtaacca tatgactgga atggaggatt 1200 tactgattga cattgataga aatakaactg ctaaagtaga aatgggtact rgacarctca 1260 ttgaagtcac akggaaagga agtttaggag ttgataccaa aatgggaagg agatatatca 1320 aggaagtgat gttaattcca ggtttaaaag aaaatttgct yagtgtaggg maamtgatgg 1380 aacacggtta ctttcttgtg tttrgaggta caactgcaga aatatatgat gatggttcaa 1440 tgtctaatct ratagctaga gtaccaatra agggcaatag aagttttccc ttgaaactta 1500 aacctragat ryaggttgct ctaaaggcta gtgtgtatca gtcttctaca atctggcata 1560 ggagattagg acatttgaat gtaggcagtt tgaagcaact caaagaacat gatatggtat 1620 tgggtttgcc tgatcttgaa atgacaaatg agatatgtga aggatgtgct cttgggaagc 1680 attgcagaga tacatttcca aaggaagcat catggagggc ctcactacct cttgaactca 1740 ttcactctga catctgtgga cctatacaaa cttctacaaa ggctgggaat aggtattttc 1800 ttacctttat agatgactgc actcggatgt gttgggttta cttcttaagg aacaagtcag 1860 aggtgtttag tatattcaag aaatttaagc tcacagttga attgcaaagt ggatataaat 1920 tgaagaagtt gagaagtgac agagaaggag aatatgtatc tgttgaattc agggaatttt 1980 gtgaagaaat gggcatggaa agacaactta cagtgggata tacacctcag cagaatggag 2040 tagctgagag gaagaatata accatagttg agatggcaaa gtgtatgatg attgaaaagg 2100 gtgttccatt tgaattctgg gcagaagctg ttaacacagc agtatatatt ttgaacagat 2160 gtcctaccaa gtctcttgat aagaagactc atttcgaggc atatagttga agaaaaccaa 2220 ggatcaaaca cttaaagatt tttggttctg tgtgttatgc atatatccca agacaaatta 2280 gacagaaatt agatgaaaca agtactaaat gcattttctt gggatatggc acatgtgaga 2340 aagaatatag actctatgat cctatctcaa agaaaataat tgtgtcaagg gatgtaatag 2400 ttgatgaaaa tgcctgttgg gattggaagt ctcaatctga gaaaaccatc agtgtatcta 2460 tacctagaaa aaaatgtgtg atcagaatgt ggaaggaaac tcaagtgaga aaagtgatgt 2520 aaatgatgaa ttcttagcat cttcatctga aaccaatgag tcaattgaaa atggctcaag 2580 gctggtgcaa atgcagagta acacaggtct tcaagactat gatcatactc ctttaaagtt 2640 caaaagcttg acaaaaatat atgcaaaatg caatttgtgc attattgagc ctgagaactt 2700 tgaggaagta acaaaagata agtcatggca aaaggcaatg gaagcagaaa taggcatgat 2760 agagaagaat tgcacctggg aacttgttga tagactattt gataagccag ttatgggtgt 2820 caagtggatc tataaaacaa aattgaacct agatgggtct atacagaaga ataaggcaag 2880 gttagtggct aagggatact ctcaaaagct tgggatcgat ttcaatgaga catttgctcc 2940 tgtggcaagg cttgacacca ttagaacctt aattaggctt gctgcacaga aaggatggaa 3000 gctttttcaa cttgatgtaa agtctgcatt tctgaatgga gttctaaatg aggaagtata 3060 tgtagatcaa ccacttggct ttgtgattaa gggcaaggag gacaaggttt acaagctcaa 3120 gaaggccttc tatgggttga aacaggcacc aagggcctgg tacaaggaga ttgactctca 3180 tttctgcagc tttggttttc acagaagtcc aagtgaagca actctctaca tcaaagcaac 3240 tgaggcagga atacttattg tttctttgta tgttgatgac atcatataca cagggagttc 3300 aggtgcatta atggatgagt ttaaagcaga aatgatggga aagtatgaaa tgtttgattt 3360 gggactattg catcatttct tagggcttgg agttattcaa acagagggta gtatttttct 3420 gcatcaaaag aaatatgcaa ggaccttgtt ggagaaattt ggattgaagg agtgcaaacc 3480 tgttgcaact ccacttgcaa caaatgaaag attaagcaaa caagatggaa gtgaaatagc 3540 tgatgagaat ctttacaggc agattgttgg tagcttgtta tatttaatag ctacaagacc 3600 taatatcatg tttgctgcaa gtctacttgt tgggttcatg cataatccaa ccaggaaaca 3660 tatgggaact gcaaagagag tgctaaggta tattcaaggc acactggact atggaattgc 3720 atatgaaaag ggcaaggatg atgtgcttat tggatactgt gatagtgact gggcaggaag 3780 tgaagatgac atgaagagca ctttcgaata tgcttttagc tttggttctg gagcattttc 3840 ttgggcccca atcaaacaaa gcagtgtagc tttgtccagt gcagaggcag agtatattag 3900 tgctgcaaaa gcaactgctc aagccatctg gttaaggttt gtcttatcag attttggaga 3960 rgaagaagtg gaacctactc agattytatg tgataacact tyagctattg caatctctaa 4020 gaatccagtg gcacatcata agacaagaca cataaacaga aggttccatt tcatcagaga 4080 tgcactgyag aatggtgaag ttgatmtgat ttactgcaaa actgaagaac aagttgctga 4140 tatctttaca aaagcattgg cmagggatag atttgagtrt ttraggaagg ctttrggagt 4200 gatttcagct aaacacttag aagggag 4227 // ID ALFARE1_I repbase; DNA; EDCOT; 4927 BP. XX AC . XX DT 25-MAY-2005 (Rel. 10.05, Created) DT 26-MAY-2005 (Rel. 10.05, Last updated, Version 1) XX DE M. sativa (alfalfa) putative retrotransposon, internal consensus. XX KW LTR Retrotransposon; Transposable Element; internal portion; KW ALFARE1_I. XX OS Medicago sativa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4927 RA Gentles A. and Jurka J.; RT "M. sativa putative retrotransposon ALFARE1."; RL Repbase Reports 5(5), 98-98 (2005). XX DR [1] (Consensus) XX CC There are only 4 complete copies of this element in currently CC available alfalfa sequence, along with numerous copies of the CC 1358 bp LTR. The complete elements are flanked by 5 bp target CC site duplications. Although the full-length copies contain CC several substantial ORFs, they have no similarity to any known CC proteins. Therefore it is not clear if this sequence represents a CC true autonomous retrotransposon. XX SQ Sequence 4927 BP; 1538 A; 911 C; 913 G; 1437 T; 128 other; tcaaaatggc gccgctgccg gggactggcg tttagatatc gtagacatcg cgactatttt 60 atcattttaa gcatcagtat atactctgta aatatatttt ctttygtata gttattgkta 120 ctaacccctc tttgcataca aagaaaaatt tcttgttagt tatatccgtt tcagattctc 180 tacataaatg aaatyatggc ttcatggtta taacaacttc tacactccac tggaatatga 240 atcatatcaa cagtatcaac aatatccctc tgaagatgaa cgaatatcaa agatggaaaa 300 tactttgaat atcttcatgc agcaaatgat aaacatgcag gataccaatc agagattgaa 360 gaatctattt caratggaaa tgatgcaaga acaaatcatg gatattcaag ccaacattca 420 tccactcacg gaaaacaaga aaataattca aatacattga ggaagtcgga aagatgttga 480 aaaggtgttg agataccgag gaagacataa tactagaaga atgtagcaca atraaaatga 540 cggaagaatt agagccacta catccarwag aayttcctca agaamggtca tatrctgaag 600 aggccraaac tgttgataat gragmagtgt tgatagttac agagaaacag gaatggatac 660 twakcaagaa agaatcaagk gaasraaagg ggaagacaac garcgaggcr aagattgatc 720 gartcataga cgaaatwtgy gccttgttca acaaaccmag gttagggagg atatggactc 780 cacatcaatt atacttcaaa ttcatggaat tcctcccaac acgcaggatt acaaragatg 840 atgtgttgtc cgtttcattt tggccaccct aaygaaaaag gcgtcgagct aacgacgtta 900 aacaagcgct tgttgggagg caacccaact ttgtaagtta tttacgttwt aatgcatata 960 ggtgtargag tcatgtgcay accaaaacca ttcamaaatc agaagccaaa agaaarcagt 1020 ctgaactgtc atactcgcga ggcgagtaaa acwactcgcc atggcgagta aactggtcat 1080 tgactkcgtt gaccaccaaa ytactcgcca cggcaataca taygctcgcg aggcgaatgr 1140 cagcagttct gaaactccct cattaatytc tcttaaccac ccwttaccaa ctttaattat 1200 cattttcttt tgmtytctct ctcaycaaca aattttatta ttctctcaaa ccctaacaca 1260 tcaacactac cctttttyaa wtatcaagtc aatccaagtc aagcttattr yatactcttt 1320 tctgcactta gattctttra ttcaggtwyg tattgatttg ttgyatwgat ttyaragtta 1380 awaaaaaaac cytaggagwa rattraawgt cttgaaaatg atacccacat gactgagatg 1440 aaacaaaatc atgccaaatt cgtaatttyc tattccaatc cacawttttg wtaccctttt 1500 gtamaawtta aaaattwggg tttttgtgga acaaatcaat ttaaccaaat gcatgattta 1560 gttcatctct tgtcatatca gggtcgaatg ctatattagg gttargaats taaaactgaa 1620 aaattttgaa aaagggtcga tttttgtyat tttctgggca actcgccatg gcgagcttca 1680 tcactcgccg aggcgagtgt gcacttgaaa cccagaaaat tatctctact cgccatggcg 1740 agttcaagct cgcgaggcga gttgcaayag aacmtgaata tttttaatac actgttccat 1800 actgatttta attgtctatt tgtgggtgtg gaattcctgg ttrttttgca ggtatggctc 1860 caaagaaacc crtgaaacyg gaaaaaggaa gaaaggtgaa acatccacat ctcaaccccc 1920 acctagaaac caaccatttg accgagagag atttaaatct cgttaccacc aagacagata 1980 cagggagttg cttaaacaga gcatgtggcc cgagaaagtg tttaacataa accctcaagg 2040 accctaccaa gacctcttga agcttttaac tgaccaaggg tggggaagac tgctccaacc 2100 tatcaccgca atcaatgctg agctcgtgcg tgaattttac gccaatgctc ttcctgaaaa 2160 cctcaccgat ccatttgtct atgaaacctt tgtgagaggt cgcaccatcc gcttcgatcg 2220 cgaagctatt aacatctatc tcggtaacac ttcccactaa gtgatgagga tgagatggat 2280 gaattccatg acaaccaaaa tcgaggcacc tttaacattg agccaatgag agaaacaatc 2340 aaaagggcta tcttactagg gggtgaaact tatgacgtga gtaatgctgg aagacatcac 2400 agagcacaat ataaactcat gaacaaaact tgcaaattca tcctraartt tatccttcac 2460 aatgtcagac ctaacagcca cttgtccgat tgcactgtgg atgtatgccc actcatatac 2520 tacattctca agggcttcaa ggttgacata gcccgcacat tagcatggga gttaaggctg 2580 gtcaccctca aggaaaaagt garccaaaaa cccgcctagc ttttcctgga ctcatcatgg 2640 gcttgattaa agattcacga atgaagttgc ccaccgctgt acatgaggaa ctccggaacc 2700 ccgttgatga tgacttcatc agacgwtaca tcatgagtga cccaaagccg gawaaaggma 2760 aacaagcmtc atcttctsrg gcacmtcawc cacaaycmsr styysmacca ywtcwrrwsc 2820 camacacwrc tgcytttgac tttgcmagct wcrctcaatg gcaataccag tgccataccc 2880 atacwtggaa yatgctggam gcwacmaacc gtgctaatac wtatcttcag cagtctcagt 2940 atktrrtgca gcagcaggcw gggtacccwc cggaggtgat gtcacaattc atgacaccag 3000 aggcctwtca ggctcatgtt tcttggcctg agggcaggcc agatccttac ggagggggtg 3060 gctcatcgtt cgggacgctt tctgacgata tattgatggg agattctgac agagacgatc 3120 cagacagagt cccaagtgca actggtggtt cagatgatga tgacatgcag ggttgaggag 3180 gaaragaaga gacgtgaaag ctcaccttta ttgagtgaca ttttataagc tttcagtcga 3240 ttctttcctt ctctttcatt tcctttattt gctttcattc cagctatttt gacaaatatt 3300 tgcttctgtt gttttatctt ggcacttatg actcataatt ttgtttaayt attaytttgt 3360 tcacttattg tggatattat gtttaaacaa ttgctttaat tagtattgtg atgttcacat 3420 tgttcaagtt gtattgtgtt gttttakwtt agcacttttg gtttatatca agtactttct 3480 tttgaaaatt gtggaagttt ctytagttta tcactcttgc ttattgaaaa gaaaatgctc 3540 aaagcttcaa atttcaaagc gcttgaaaga tagccaaaac ttgagcaaaa ttctcagatg 3600 attgataata acagatagtt tgtgataaag cgcaaagcca aggtacaagt ttccagtttt 3660 tctaggtttt acttgaatag gaaaygagta ctttgcacaa atttcaattc atttagttct 3720 cctcgataat gtgtttgttt gtgaaccact tagtactagc caaaaagtga ggaaacctca 3780 aatatttgta ctatatgcaa ggagaccggc attcattgtt ttaactcggt cattttatgt 3840 taaatctaat atttgttttr aattgtgtaa agacatggaa aggatcaagg catattttgt 3900 ttaatgagag aaacatactt gaccacaaat agcctacctt gtgagaagag cgagtatttg 3960 ttaacccact tgagccaaat gaagcaaggt cctcaattat gaactgtcaa ttcataagca 4020 caatgcttga tgaattcgcc ctatattttt caaaatccag ttcatttttg ttgcactatc 4080 ggaccttgat atgttttaat tgttgaaccc taaaccttca tygttatttg tccctttttg 4140 ccatagatta agggaacatt caaatagggt atgttttcat tcaagttggg gagaaaaagg 4200 tagatgtcat catttgtcaa gtgaattggt gtaatcagaa attttgatca agacaacatt 4260 gtttgtatat gaaaaaagaa agaaaaagaa aaatgtgtac atgataaaaa tgagaaaaga 4320 agaaaaagaa aaagaaagaa aaatccaaaa atagaataag ttgtcaagat caaggagtat 4380 catgttttaa caccaagggt ttgttaggga atttagtaaa tttgtctttt gaatgtgaat 4440 agaaggaatg ttcccttatg cttggccatt tgaattcaat tgacccacaa atgtcctttc 4500 ttttgtagcc aagccaaatt acaaccctaa aagacctttt gatccatgtt tttatgcttt 4560 ttgaaatgat aattggatgg acatataact tgatttggat gttaacttga ttgccggatg 4620 tgtgttcata accctcactc atttgatttc aattgcatat ctacttacaa agaagtgtgt 4680 taggtgtggt tcgtgaataa atattttatt gacttgaact atttgacatg aactttgtgc 4740 ataggactca tttcatattt gtggtagaat tccagattag ttggaaactc agacttgccc 4800 gcgcattcac tttgaatcat tcatctgaaa atgttttcaa accttttgta cttgtgtctt 4860 gtcatattaa cttgtttgat tttcaatntt ttgtttgagg acaaacaaag agttaagttg 4920 gggagag 4927 // ID MuDRASH_MT repbase; DNA; EDCOT; 1607 BP. XX AC . XX DT 05-DEC-2006 (Rel. 11.12, Created) DT 05-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW Interspersed; repeat; TSD; MuDRASH_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1607 RA Shankar R. and Jurka J.; RT "MuDRASH_MT: A putative non-autonomous DNA transposon from barrel RT medic."; RL Repbase Reports 6(12), 636-636 (2006). XX DR [1] (Consensus) XX CC The sequence is present in high copy and well conserved. The TSD CC is not conserved across the sequences but for individual CC sequences, with 9 bp flanking both termini of the sequence. The CC sequence contains region showing similarity to transposase. XX FH Key Location/Qualifiers FT CDS 137..394 FT /product="MuDRASH_MT_1p" FT /translation="CAVLACTRGKKKTTCTGTKLMENTKISIFTFLTSFFC FT NSFFTPMFAITIHPHISYRTHQLSLCLFFFPPFSLLQDHHPLRRSRLHF" XX SQ Sequence 1607 BP; 465 A; 324 C; 254 G; 564 T; 0 other; gagtgaacca tcaatttcgt ccctgaatct ttaggggtct gccaaattcg tccccaaatt 60 taacgaaata tcaaaatagt ccctgaattt gtttgacgtc catcaatttc gtccctccgt 120 ccaaaaggtc cgttagtgtg ctgtgttggc ttgtacacgt gggaaaaaga aaaccacgtg 180 tacagggact aaattgatgg aaaatacgaa aatttcaatt ttcacttttt taacttcatt 240 tttctgcaat tcctttttta cccctatgtt tgccattacc atacatcctc atatttcata 300 cagaacacat caactaagtc tctgtctgtt cttcttccct ccattttcac ttctccaaga 360 tcatcatcct ctccggcgat caagattgca tttttgaagg aagatttcgt ttgttttgaa 420 ggtaactttg ttcatcttct tctccttttt ctctgttcgt tttcgcccat attttttccg 480 tttttatgat tttcgttttc atgtttttat catttagtta tgacttatta ctattttgat 540 tagtatctac tgcctttttt tatgttgttc tgcaaattta tgcctcaagg atcaacttga 600 tttctgttaa tataatttag ggactttttt tatggttttt aaaataattc agggatcgat 660 ttaatagtaa cacaaataat tcagggacta atctgatggt aaaattataa cagatatgca 720 acatttcatt catcttcaac ctcttttcat ggtaaaatca ttacaactct acacaacctt 780 agaaatatac attagcatgt tgcaaaactc aaacaagcat attataacta tcataaactt 840 aatcacccta agctcacttt ccatcaacct tgccctccaa acctcgtcat tgccactttc 900 cttagcctta agcatggact gaaccttctc catcattctt gtctttcttc catgagcagc 960 acaaattcca ttgtttttaa aagtaaccta gttcttcagc ttcatcaacc cacacaacat 1020 tcaagcactc tcacatcacc attaaacatg gaggatgaag atgaagcttg actttgatag 1080 ctctttttgc ccatatgacc acctcccatc attttagatt caatttcaac agttttgctt 1140 gaatgaattt tgcagatttt ggttttcaga ttcaattaaa aaaaattagg gtttgcaatt 1200 ttttgatttg gggaagaacg tgacccttaa ttattggaag aaaatttgga gattttgggg 1260 tgtagattac acattgtaaa attagggttc caattttata tatttgggga agaaatagtc 1320 gttggagaag gaagagaacc gttggggaag aagagcaatt tcctgaaatt caatcaactt 1380 agtccttgaa aatttagatc attatcggcc aaattagtcc ctgcctacgt ggcgtctgac 1440 atgtgagagg ttaacggcca cgacagcccc gttaacgctc cgtttgaact gaaggactaa 1500 cttgattgac atttaacaaa ttcagggatt aaattgatat ttcgcataat tgagggacga 1560 agttggccga cccgtaaaaa ttcaaagacg aagttgatga ttcactc 1607 // ID METRAHAT repbase; DNA; EDCOT; 5202 BP. XX AC . XX DT 28-JAN-2007 (Rel. 12.01, Created) DT 28-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A DNA transposon from Medicago truncatula. XX KW hAT; DNA transposon; Transposable Element; transposon; ORF; KW Inverted; terminal; Interspersed; repeat; METRAHAT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5202 RA Shankar R. and Jurka J.; RT "METRAHAT: A DNA transposon from barrel medic."; RL Repbase Reports 7(1), 37-37 (2007). XX DR [1] (Consensus) XX CC The sequence is present in few complete and several disrupted CC copies. It contains intact domain for hAT like transposase as CC well as it has 15 bp long hAT-type terminal inverted repeat. Also CC it has domains for zinc binding motif. XX FH Key Location/Qualifiers FT CDS 1357..3477 FT /product="entry_name_1p" FT /translation="MFSVMESISQNLSSTLTSGSANVAEPTEQVAVATQVP FT VVGLPPLPCLAKRRKPNAGGPRRTSPAWDHFIKLPDEPEPTAACIHCHKRY FT LCDPKTHGTSNLLAHSKVCFKNPQNDPTQASLMFSNGEGGTLVAASQRFNP FT AACRKAIALFVLLDEHAFRVVEGEGFKLLCRQLQPLLTIPSRRTVARDCFQ FT LFLDENLRLKTYFKSDCVRVALTTDCWTSGQNFSYMTLTAHFINNDWKYEK FT RILSFCTVPNHKGDTIGRKVEEILKEWGIRNVSTITVDNASSNDVAVAYLK FT KRINNMGGLMGDGSFFHLRCCAHILNLVVGDGLKQNELSISSIRNAVRFVR FT SSPQRSAKFKECIEFARITCKKMLCLDVQTRWNTAYLMLDGAEKFQPAFEK FT LEGEDSGYLEFFGEAGPPSIHDWENVRCFVRFLKIFYDATKEFSSSQEVSL FT HKAFHQLASVHCELKRSAMNLNTVLASMGSDMKQKYNKYWGKIENINKLIY FT FGVILDPRYKFSYVEWCFNDMYGDQPTFFTDLIAVIHTQLFKLFNWYKDAY FT DQQHNSGHPSASPSESSYVSENVIPAEVPSHLARAEAFKEHLKLKESIVKK FT NELERYLDEERAEDVNFEILLWWKQNSCRYPVLSSMVRDVLATPVSTVASE FT SAFSTGGRVLDTYRSSLNPQMAEALICAQNWLKPTLNQFKDLNINEEFELS FT ATVVSGI" XX SQ Sequence 5202 BP; 1473 A; 864 C; 1028 G; 1837 T; 0 other; ggggtggaca acaatagtcg acccgacccg aacccggcaa acccgttgga aaattgaaag 60 tctgggtggg tagcgggtcg gtttccgggt tgggcggatt gaaggaatgg tttcagatgg 120 gtttagatgg gcgggctcgg attgaatttt caggcccatc gaaacccaaa tccgaccgag 180 cccaactaat attcaatcag tattttttta cccctaaggc cctattcttg ttaagttgct 240 ggacttttgc ttggatcaaa tttaagccca attctttaga tccattgaca acaaactagg 300 gttatatcaa aacacacact catacttatc cattcattga gagaaagaga gagaacgagt 360 tctggaagtt gaaggaaagc cagtttcact gcgccaccgt cgtaaacata ttgaccacca 420 cttcctccct ctctctcgat cgatttcatt ttgaaaccca aagaagatgt ctgtccattt 480 tcgttttcgt tttcgtaagt gttcattttc gtaagttcat tttcgttttc gttttcttca 540 cttaatctct tgatttttct gttatccatc taattaagtt catcttttgc ggatgtgttt 600 gacagatgtt tggtactagt agatcgattt tcacaaaggt acgtgttgta tcgtattcac 660 tattttgttg gctagggttt gcattttttc atcatagaag aaatcaaagt ttacttatcc 720 atctaaccaa gttttctttt ttactttgta tgttcatttt ctcttatctg aagaacaaat 780 caaagctcaa cttaaagaaa tagaaggtat atgactatat gcttgtgttc attatttttc 840 ttttttggtt tgtttttact tttttggttt gttcttactt tatttctaat aaattcaaac 900 tgggttttaa tttgtaattt ttgttagaaa tgtaaaaaaa actttttcta aactaaatca 960 aacaagtttt tgtaattctt ttttgttttg gtagtttctt tactgttttc tttcaaagta 1020 aacgcaagga ctgtcatgat aatcttgaat caaagagttg ctgaagcatg ctttattttc 1080 aatgttcaat tcaagctcaa caaatatatt cgtgcaaaaa tgatttaaca ataaatttga 1140 gagtaaaaaa caattctaga aacaagcttt actaacaatt atccttttta tttttgaagg 1200 ttattggctt tttggtggta tttaagtttg tagtgattat tgattaagct gttgaaaagg 1260 taagtttttt aatccatcct ttttgaacat gtaaatataa agctatgaaa tatttaagtt 1320 gatgtggttg acgttttttt tacttaatct tcatgttttc agtaatggag agtataagtc 1380 aaaatttgtc ttctacctta acatctggaa gcgctaatgt tgctgagcct actgaacaag 1440 tagcagttgc tactcaagtt cctgttgtcg ggcttcctcc tctcccttgt cttgcaaaaa 1500 ggaggaagcc taatgctggt ggtcctagga gaacctctcc agcctgggac cacttcatta 1560 agttacctga tgaaccagaa cctactgctg catgcataca ctgtcataaa agatatttat 1620 gtgatccaaa aactcatgga acttctaact tgctggccca ctcaaaagta tgctttaaaa 1680 atccacaaaa tgatcctaca caagcttctc ttatgttttc taatggggag ggtggtactt 1740 tagttgctgc tagccaaaga tttaatcctg cagcttgtag gaaggctata gctttatttg 1800 tacttctaga tgaacatgct tttagagtag ttgaagggga aggttttaag ctcttatgta 1860 gacagttgca acctctctta accattccat ctaggaggac tgtggctagg gactgtttcc 1920 agctctttct tgatgaaaat ctgagattaa aaacatattt caaatcagac tgtgttaggg 1980 tagctttaac cactgattgt tggacatctg gtcaaaactt tagctatatg accctcactg 2040 cccatttcat taacaatgac tggaagtatg aaaaaagaat cttgagtttt tgcacagtcc 2100 ccaatcataa gggtgacaca attggtagga aagtggaaga gattttgaaa gagtggggga 2160 taaggaatgt gtctacaata acagtggaca atgcatcttc taatgatgta gctgttgctt 2220 acttgaagaa aagaattaat aacatgggag gtttaatggg tgatggttct ttctttcatc 2280 ttcgttgttg cgctcatatc ctaaaccttg tggtggggga tggtttaaaa caaaatgagc 2340 tctctatttc ttcaattaga aatgctgtta ggtttgtgag atcgtcaccc caaagatctg 2400 caaaatttaa agagtgcatt gagtttgcta gaattacttg taagaagatg ttgtgtcttg 2460 atgtccaaac aaggtggaac acagcgtatt taatgctaga tggtgctgag aaattccaac 2520 cagcctttga gaagttggag ggtgaagatt ctgggtattt ggagtttttt ggggaagctg 2580 gtcctcctag tattcatgac tgggagaatg ttaggtgttt tgtcaggttt ctaaaaattt 2640 tctatgatgc taccaaggag ttttcctcat ctcaggaagt gtctttgcac aaggcattcc 2700 accaactagc ttctgttcat tgtgagttga aaagatcagc catgaacctg aacacagttt 2760 tagcttcaat ggggtctgac atgaagcaga aatacaacaa gtattggggt aaaattgaaa 2820 acatcaacaa gcttatttac tttggtgtga ttcttgaccc tcgatacaag tttagctatg 2880 tggagtggtg cttcaatgac atgtatggtg accaacctac attttttact gatctgattg 2940 ctgtgatcca tactcagctg ttcaaactgt tcaattggta caaggatgcc tatgaccagc 3000 aacataattc tggtcatcca tctgcaagtc catccgagtc tagttatgtt agcgagaatg 3060 tgatcccagc tgaagtccca tctcatttgg caagggctga agcttttaag gagcatctta 3120 aactgaagga atcaatagtt aaaaaaaatg agcttgaaag gtacctagat gaggagcgtg 3180 cggaggatgt caactttgag atccttcttt ggtggaaaca aaactcttgt cgttatcctg 3240 ttttgtcatc catggtgagg gatgttttag ctacaccagt ttcaactgtg gcttctgaaa 3300 gtgcctttag cactggagga agagttttag atacatatag aagttcattg aacccacaaa 3360 tggcagaggc attgatctgt gcacaaaatt ggttgaaacc cactttgaat caattcaaag 3420 acctcaacat aaatgaggaa tttgagctgt ctgccactgt tgtatcaggt atttaatatg 3480 tttattttaa cttttaaatg tgtggcattt attcttgttt aaatgccatt aactaatcat 3540 attgcttggt ccttgtattt gtatatagaa tttgatggac catcagctaa tggatcaaca 3600 tcttgtggtg ttagagcagc tgttgtacaa ggagatgcat catcatctca atcacagcca 3660 atgagctgtg attgaaaaaa ctagtgttag tgattatatt atttttcatt atttgtgttt 3720 atgttattat ttattttatt aagttatgcc attgtttatt ttattaatgt agttattgtt 3780 tttatttaca ggttcttaac ccttttttgg tgtcattaat cataatgatt aatgactttg 3840 cttagtgcat tttttgggag aatctacttt ttgtggaata tacacaacaa ctctttttgg 3900 aagcatctgg aggatgatga aggattttaa tccaacttgt atgtttgaag acattttgaa 3960 atgtagatgc ttgcttgctt ggctccatgg tctcacattt ttgcttgatt gatagcatat 4020 acactgctgt ttaaacgatg tttaatgctt atgctaaggt atgttaggct tagtaagtgt 4080 tacttgataa tgcttgtagt tatcatggtt ttaaatccct tactgtttgt tttattcttc 4140 tttttttcaa gtcagtgatg cagttataaa tctagaggtc agctctagtg atggtaatgt 4200 aggagagttc actgttttta tcccaaactg ttgcacaaag gtacaataat gtaggatgca 4260 taatgatttt attgtgatga ttttactgtg atgaaatgtg ttggtaacac attgcttttg 4320 attttcatta ttcaagcaga ttattgatgt taacttgggt gtggctactc ttgtacttgc 4380 tgaaatgatg agatgtgata ttaatttgaa cacaatcaag gttagtttta gtttatttat 4440 tgaatttagt cttgattcta acttcatcta taaaaaaata caaaatttat atcttataac 4500 attttgtccc tcttgttgtg cagctatatt tgtgtgacca tgttgcagca tcagcaactg 4560 caagcatctc ctgccaatgt atttgtagaa ttatggatga ttgtaattat ggcattgtaa 4620 agtttaagtt gttggttgtg ttgtgcagtc ttatcaactc taaacgtatt gcacagtcgt 4680 acttttattt atttgaagtt tgtaatatta tgatacagga ataccggata cctatcacat 4740 ggatgatgaa ttatcatgaa tgatgtagtt gggcttcttt aaaccaacta aattcatgtt 4800 tatttcctat tacagggctg aatcatgaat gatcaaatga tgtaattagg cttttctaag 4860 ccaacttaac tcttgtatga tatgacaaga aaatatgctt aatttatttg tatttcattg 4920 gcaacttaga ttgagagggg atggaatcat gaactgatcc aatttggaaa ttatggttaa 4980 aaatatttga aaaacagcga tgggccaaaa atccatcacc ggcccaatgt tggcctcatc 5040 cgacataacc cacccataac atccgctgaa accgattaac cgagacccgc cataaccgtt 5100 gcttcatttg ggtgaaattg ggccttgaat tctcaaccgt ggattgtttc ggattgagct 5160 ttctgagccc gaacccaccc atacccgacc gttgtccacc cc 5202 // ID Copia1_LTR_MT repbase; DNA; EDCOT; 816 BP. XX AC . XX DT 24-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A copia type LTR sequence from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR; retroposon; TSD; Interspersed repeat; Copia1_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-816 RA Shankar R. and Jurka J.; RT "Copia1_MT: LTR retroposon from Barrel Medic."; RL Repbase Reports 6(11), 558-558 (2006). XX DR [1] (Consensus) XX CC The LTR sequence resembles features of RAM LTRs as the closest CC one. It's internal region contains integrase domain and resembles CC Copia-like LTR retroposon. Intact 4 bp TSD (TCAA) is present. XX SQ Sequence 816 BP; 200 A; 132 C; 221 G; 263 T; 0 other; tgttgagatt gtcttcaaat ttgtggtttg gaagaacagg gaaatcgtga cacgattttg 60 ggatcgcgac acgatttcga gatgccgtga gctagggttg caggggtgca aatcgtggca 120 cgatttcggg aaaatcgtga cacgatcaag aaacttgctc gttaagtatc cttgataagg 180 actggtcgtt ccttgggacg gacgcaaatc gtgacacgat tgggaaaatc gtgacacgat 240 tggaacagag gaagactagt acttaagtgt tcttgtgcag atttgaagag agaggagttg 300 gaagagagag acttgggaaa tcaaagggga agctctaggg tttagggttc tttgattaga 360 gtatctcttg ggttgaaaac atgggaaaca ccttgtagag agaatcattg agtgtcttgg 420 tgagattggg aaaggggtag aaattagggt ttgttcatag tgaacattgt caagctaatt 480 tcttgtaacc tcttgtatcc cttttgtaaa gaactcattt gatagtggat tggagagtac 540 aaactctcct ccagagtagg tcaagtttgg accgaactgg gtgaacaatc tctttgtgtt 600 tattgttttc ttcttccctc tcctttgtgt atcttgtgat tagttgcttt gtgtttcaca 660 cttggttcct agattagatc taggtggtgt tttgttgttt cttgcttgca caataaactt 720 tgtttggtgg ttaccactct ccgtcgctcc acacatcatt attctttgta ttggtgtggt 780 tcgatccggg tcttggaggc ccggggattc acaaca 816 // ID HAT-3N2_Mad repbase; DNA; EDCOT; 710 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-3N2_Mad. XX NM HAT-3N2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-710 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1611-1611 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 25-bp long. XX SQ Sequence 710 BP; 202 A; 160 C; 123 G; 225 T; 0 other; cactggcgga tccatatagg gacccggggg gtcccgggac ccttcggaag cccgaagaaa 60 cacttgtgat cgaccttcgg gaccctccaa caatttgggc aggtgcagtg gagaggcttg 120 ttgcctccat ggatgtgcag gcagcagtgc ttataacaaa gaagaagaag aggtttttaa 180 tttttgtttt aaaagaccta gccaaaacga caacgttttt tagccaggtc attataaaaa 240 atttaaaaac taaaatatct ctgttttctc tacagagccc gagaaccccg gtcttttcca 300 gtatccccaa attatattta agaactccca gccccaatcg tcgcaacctt ccaactttaa 360 acccaagtta ccctattccc caccaccatt tgccgttcca ccgcctttag ctgcctaatt 420 ttatttcttc caaattcata taagtttttt aatcctagac tctagtccca actcccaatt 480 aataatatat atgttacatt aacaaatttt atctttgtag agtcactaat tgcgttatgt 540 tgctgaggag aatttgttgg ttttattacc tttgagatta atcttgattt attcaatgaa 600 ccaaattcag tagaaaatag tgatatggaa ccaaattagt ctaatatatt tttttttttt 660 gagcttttat gttgggaccc cccgatcttg aaatcctgga tccgccactg 710 // ID SHACOP8_I_MT repbase; DNA; EDCOT; 4139 BP. XX AC AC174297; XX DT 16-JAN-2007 (Rel. 12.01, Created) DT 06-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP8_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; terminal; ORF; KW SHACOP8_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4139 RA Shankar R. and Jurka J.; RT "SHACOP8_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 80-80 (2007). XX DR EMBL/GenBank/DDBJ; AC174297; Positions 72170 76308. XX CC The internal region sequence contains intact domains for Arginine CC methyltransferase and integrase. The sequence is flanked on both CC sides by intact LTRs. It is present in only two copies of full CC length sharing identity about 90%. XX FH Key Location/Qualifiers FT CDS 54..4136 FT /product="SHACOP8_I_MT_1p" FT /translation="MASTNNPSATYSNVKVPLFEGVNYDFWAVKMETLFTS FT LDVLEYVKNGYEEPTPTEAEISKEKAEESSKQPEELKKKITDAGVLGMIQR FT GVSLSIFLRIRRAKTSKEAWSILQQEFEGDSKVRTVKLQSLKRDYENERMK FT ENENLNEYFNRLSELVNQMKSHGDTIEDRRIVDKILISLTARFDPMVGVIE FT ETKDLSTLTIQGLMGSLRSYEQRMLRHSEKSIESAFQSKLNIQPNNGENKP FT QIQTRGESSRGGRFGRGRGRGRNSRGRSGRSANGGRWNEASNKWCKICNSG FT THDEKDCWYKGKPQCHNCKRFGHLQKDCRLAKQQHASYAEGESDEGNLFYA FT CQKALHEEEKNVWYLDSGCSNHMTGQKGAFINIDSSCGSKVKLGNGEHVEV FT KGKGSIGVTTKQGSRVIHDTLYVPELDENLLSVGQLLEHGYSLNFENRECR FT IFDSERRSVAIVKMTSNRSFPLSFDYEKNVSMMAREENDSCLWHRRLGHLN FT YESLKLLYQKKMVYGLPRIEEKSGVCEGCVFGKHHRKPFPKEGAWRAKQVL FT ELVHTDVCGPMNTLSHGKNRYFILFIDDFTRMTWVYFMRQKSEAFVIFKKF FT KALVEKQSGRFIKMLRSDQGKEYTSNEFHKFCEDEGVERQLTVGYTPQQNG FT VSERKNQTVMEMAKSMLLEKGLPKTFWPEAVNTAVYLMNRCPTKAVWKKTP FT FEAWSGRTPSVNHLKIFGCVCYAQIPKQKRTKLEETSEKCVFIGYSSMSKG FT YRLYNLKTNKVIISRDVVFDENASWNWEEDKMKEKTVPAIILQQQNSAAEN FT EQPTPCTPSSSSSPSSPNSSSSTPSSTPIKLKDLSDIYARCNYCVVEPENF FT DEAIKEDAWRNAMQEEINAIEKNKTWQLVERPNDKEAIGVKWVYKLKHNPD FT GSIQRAKARLVVKGYAQQPGIDYSETFAPVARLDTVRTVIALAAQREWNLY FT QLDVKSAFLNGELKEEVYVQQPQGFVTKGQEEKVYKLKKALYGLKQAPRAW FT YSEIDSYFIQQGFERSQSEHTLYVKRQGKDDIFLVALYVDDLVYTGNNKKM FT VENFKIEMMKKYEMSDLGLLHHFLGIEVYQDEYGVFICQKRYAENILKKFG FT MNGCKPADIPLVVNGKLKKEDGGRLVDANMYRSLVGSLFYLTATRPDLIFA FT ASLLSRFMSKPSHLHLGAAKGVLRYIMGTMEHGIRFQNNSKLEVKGYCDSD FT WAGSVDDMKSTSGYVFSLGSGVISWCSKKQDTVAQSSAEAEYLAAGLATQQ FT SLWLRRILEDIGEKQEESLLLHCDNKSAIAMAKNPVFHSRTRHINIKHHFI FT RSVIEDGDVQLVFCNSQEQLANIFTKALPRGRFQQLREAMGVKEQHIKG" XX SQ Sequence 4139 BP; 1446 A; 670 C; 979 G; 1044 T; 0 other; gagtggtatc agagctgcag atccttgcag ctgtagcaaa aacaacaaaa gttatggctt 60 ccacaaacaa cccttccgca acttacagca atgtcaaagt tcctctattt gaaggagtga 120 actatgattt ttgggctgtt aaaatggaga ctctattcac atctttggat gttctagagt 180 atgtcaaaaa cgggtatgaa gaaccgacac caacagaggc tgaaatatca aaagaaaagg 240 ctgaagaatc aagcaaacaa cctgaagagt tgaagaagaa gatcacagat gctggagttc 300 tcgggatgat tcaaagagga gtctctctat ccatcttcct aaggattagg agagctaaaa 360 catcgaaaga agcctggagt atcctacaac aagagttcga aggagattca aaggtgagaa 420 cggtgaagct tcaatctctt aagagagatt atgaaaatga aaggatgaag gagaacgaga 480 acctgaacga atacttcaac agactctccg agttggtgaa tcagatgaag tcacatggtg 540 atacgataga agatcgcaga attgttgaca aaattctgat cagtttgaca gcaagatttg 600 acccaatggt gggtgtgata gaagaaacca aggatctatc aaccttgact attcaagggt 660 tgatggggtc tttgagatcc tacgagcaaa ggatgttacg acattctgaa aaatcaattg 720 agagtgcctt tcaatctaaa ctcaacattc agcctaacaa tggtgaaaat aagccccaaa 780 tacaaactag aggtgagtct tctagaggtg gcagatttgg aagaggcaga ggcagaggtc 840 gaaactcacg tggcagatct ggaagaagcg caaatggcgg aagatggaat gaagcatcaa 900 acaaatggtg caaaatttgt aacagtggca ctcatgacga gaaggactgt tggtacaaag 960 gcaaaccgca atgccacaat tgcaagagat tcgggcacct tcaaaaggac tgtcgtcttg 1020 caaagcaaca acatgcttcg tacgcagaag gagaatctga tgaaggaaat ttgttttatg 1080 cttgtcaaaa agcattgcat gaagaagaaa aaaatgtatg gtatttggac agcggctgta 1140 gcaaccatat gaccggacag aagggagcat ttataaacat tgattcttca tgtggctcaa 1200 aagttaaatt gggaaatgga gaacatgtcg aagtgaaagg gaaaggaagc attggagtca 1260 ccacgaagca aggaagcaga gtcatacatg acacgctcta tgtcccggaa ttagacgaaa 1320 atttgcttag cgttggacaa cttctggagc acggctattc tctaaacttt gaaaatagag 1380 agtgcagaat ttttgactca gaaagaagaa gtgttgccat tgtgaagatg actagcaaca 1440 ggagctttcc actatctttt gactatgaga aaaatgtaag catgatggcc agagaagaga 1500 atgactcgtg tttatggcac aggagacttg ggcatttgaa ttacgaaagc ctcaagttac 1560 tctatcagaa aaagatggtg tatgggctgc caagaatcga agaaaaatct ggtgtgtgtg 1620 aaggttgtgt gtttggcaaa caccaccgga aaccatttcc aaaggaaggt gcatggagag 1680 ctaaacaagt gttggaactt gtacacacag atgtgtgtgg tcctatgaat actttgtccc 1740 atggcaaaaa taggtacttt atcttgttta ttgacgactt tacccgcatg acttgggtat 1800 atttcatgag acaaaaatct gaagcatttg taatctttaa gaaatttaaa gcattagttg 1860 aaaaacaaag tggcagattt ataaagatgc tgagaagtga tcaagggaag gagtacacct 1920 caaatgaatt tcacaaattt tgtgaagatg aaggtgttga aagacaactc actgttggat 1980 atacacctca gcaaaatggt gtatctgaaa gaaagaacca aaccgtgatg gagatggcga 2040 agtctatgct acttgagaaa ggtctgccta aaaccttttg gcccgaggcc gttaacactg 2100 ctgtgtattt gatgaacagg tgtccaacaa aggccgtgtg gaaaaagact ccatttgaag 2160 cctggagtgg aagaacaccg tcggtgaacc atcttaaaat ttttggatgt gtttgctatg 2220 ctcaaattcc taaacaaaag agaacaaagc tggaagaaac aagtgaaaaa tgtgtcttta 2280 ttggctatag ttccatgtca aagggctata gactttacaa cttgaagaca aacaaggtga 2340 tcattagccg ggatgttgta tttgatgaga atgcttcttg gaattgggaa gaagacaaaa 2400 tgaaggagaa aacagtccct gcaatcatat tacaacaaca aaattcagca gctgagaatg 2460 agcaaccaac cccatgtaca ccaagttcct catcctctcc aagttcacca aattcaagtt 2520 catcaactcc cagctcaact ccaataaaat tgaaggattt gagtgatatt tatgcaagat 2580 gcaactattg tgttgtggaa ccagaaaatt ttgatgaagc aatcaaagaa gatgcttgga 2640 ggaatgcgat gcaagaagaa ataaatgcta ttgagaaaaa caaaacatgg cagctagttg 2700 aaaggccaaa tgacaaagaa gctattggag taaaatgggt gtacaaattg aagcataatc 2760 cagatgggtc aattcaaaga gccaaggcta gattggtagt aaaaggttat gcacaacagc 2820 ctggaattga ctatagtgaa acttttgccc cagttgctag attggatact gtacgaacag 2880 ttattgcatt agcagctcag agagagtgga acctgtacca acttgatgtg aagtcagctt 2940 tcctgaatgg agaactaaaa gaagaggtat atgtgcaaca acctcaaggc tttgtgacta 3000 aaggccaaga agaaaaagtt tacaagttga agaaagctct ctatgggttg aaacaagccc 3060 cgagagcatg gtatagtgaa attgacagct acttcattca acaaggattt gaaagaagtc 3120 aaagtgagca tactttgtat gtgaagcgtc aaggtaaaga tgatatcttt cttgttgccc 3180 tttatgttga tgatttggtg tatacaggta acaacaagaa aatggttgaa aattttaaaa 3240 tagaaatgat gaaaaaatat gagatgagtg atcttggctt gctgcatcat tttcttggta 3300 ttgaggttta ccaagatgaa tatggagttt ttatttgtca aaagagatat gctgaaaata 3360 tcttgaaaaa gtttggcatg aatggctgta aacctgctga tattccttta gtggtgaatg 3420 gaaaattaaa gaaggaagat ggtggaagat tagtagatgc aaacatgtat agaagtttgg 3480 ttggaagttt gttttatcta acagctacac gacccgattt aatatttgct gctagtttac 3540 tctcaaggtt tatgagtaaa ccgagtcact tacaccttgg agcagcaaaa ggagttctaa 3600 ggtatatcat gggaaccatg gagcatggaa tcaggtttca aaataattct aaactcgaag 3660 ttaaaggcta ctgtgacagt gattgggctg gaagtgttga tgacatgaaa agcacttctg 3720 gttatgtgtt tagtctgggt tcaggagtaa tttcttggtg ttcaaagaaa caagacactg 3780 tagcgcaatc ttcagctgaa gcagaatatt tggcagctgg tttggctaca caacaatcat 3840 tgtggttgag aagaatactt gaagatatcg gagaaaagca agaagaaagt ctgctgcttc 3900 actgtgacaa taaatcagca atagccatgg cgaagaatcc agttttccac agtcgaacaa 3960 gacatattaa tataaagcac cacttcattc gaagtgtgat cgaagatggc gatgtgcagt 4020 tagtgttctg caattcacaa gagcagcttg caaacatttt tactaaagca ctaccaagag 4080 gaagatttca gcaacttaga gaagcaatgg gagttaaaga gcaacacatt aagggggag 4139 // ID Copia-32-I_VV repbase; DNA; EDCOT; 4428 BP. XX AC CU459295; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-32_VV, LTR retrotransposon Ty1-copia like, internal portion DE from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Gans-B08; KW Copia-32-LTR_VV; Copia-32-I_VV; Copia-32_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4428 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL; CU459295; Positions 604386 608813. XX CC full size = 4922 bp CC LTR = 247 bp CC LTR are 100 % similar to each other. CC Direct flanking repeats = gtagt. XX FH Key Location/Qualifiers FT CDS 79..3708 FT /product="Copia-32_VV_1p" FT /note="Incomplete gagpol polyprotein." FT /translation="KGDEFTFFFLGTRDRSGDFITPTRLRGENYDDWASDI FT QLALEARRKFEFLEGTITGPQPPYTQSDWNTVNAMLVSWITNTIDPEVKST FT LSKFRDAKRLWEHFKQRYAMVNGPRIQQLKTSIAKCEESKSMSVTTYYGKL FT NVLWEELFKHEPLISCTCCSSCTAASLHQARREQGKLHDFLMGLNTDLYAQ FT LRTNILSQDPLPSLDRAYQLVIQDERVRLAKAVTEDKLAEVLGFAVRTGAG FT RGRGKTERPVCSHCKKTGHETSTCWSLVACPHCHKHGHDKNNCYEIVGYPE FT GWLDQNKADGSVGRSRQQAGRGRGSARANAASSIIGASSTKSSTDQLFTPE FT QWKALAGLIGNAQVPDDRLNGKFDTKSWIIDTGATHHVIGDLSWLFDTIAL FT FECPVGLPNGESVVATQSGSVRLSNNITLKNVLYVPKLNCNLLSVSQLTDD FT LHCIVQFNSYMCAIQDHTRELIGTGVRQDGLYYFGGAESDSVQHVSVHNAA FT STLELWHKRMRHPLEKVVKLLPPVSNLKGSLNKACEICFRAKHPRDKFPLS FT DNKATRIFEKIHCDLWGSYKHVSSCGARYFLTIVDDFSRAMWIYLLVDKTE FT VFRMFMSFIAMVDRQFSQTVKVVQSDNGTEFKCLLDYFSATGILFQTSCVG FT TPQQNGRVERKHKHILNMGRALRFQANLPIYFWDESVLAAAHLINRTPSPL FT LHNKTPFEILFGTPPSYAAIHTFGCLSFAHDKKSKDDKFASRSRKCVFLGY FT PFGKKGWKLFDLDTKELFVYRDVKFFEDVFPFGNPGAVNIIPDNIVPTVNV FT EIDSDFADFVDDDADLPNPQAQTQNPNLIQPEPQAHQDLSPGPEVVPTVGL FT DSLGLDNTSNGQSAPMGKGMRDKFPSVLLRDFVTHTVVVESPSPATPSPQH FT PSGTPYPIAHYINCDNFSVHYRKFLAAIISSNDPKSFKEAMKDVGWQKSMH FT EEIRALKENGTWTLEPLPKGKRALGSQWVYRTKYFSNGDIERLKSRLVVLG FT NHQEAGIDYHETFSPVAKMTTVRAFLAIVASKNWELHQMDVHNSFLHGDLE FT EEVYMKLPPGFESSDPNLVCRLRKSLYGLKQAPRCWFAKLVTTLKGYGFLQ FT SYFDYSLFTYTKDNVQINVLVYVDDLIISGNDSAALKTFKAYLSDCFKMKD FT LGVLKYFLGIEVARSSAGLFLCQRKYTLDMVSEAGLLEPSRVASRSSKIID FT " XX SQ Sequence 4428 BP; 1190 A; 883 C; 1015 G; 1340 T; 0 other; tggtatcaga gcactaacat gcacacacaa taaaacaatg gccgacgacg atgaacaacc 60 accattgccg ccacctaaaa gggagatgaa ttcacctttt tttttctcgg cacaagagac 120 cgatcaggcg acttcatcac tcccactcgc ttacgaggcg aaaattacga tgattgggct 180 tccgatattc agttggcatt ggaggcacgc cgcaagttcg aatttttgga aggcactatc 240 accggaccac aacctccata tacccaatct gattggaaca ccgtcaatgc aatgttggtt 300 tcttggatta caaacacaat cgatcccgag gtaaagagta ccctatctaa atttcgtgat 360 gcaaaacgct tatgggagca ttttaagcaa cgatatgcta tggttaatgg cccaagaatt 420 caacagttaa agacttcaat tgctaagtgt gaggaatcga aatctatgtc tgttacaact 480 tactatggca aattgaatgt attatgggag gaattattta agcatgaacc actaatttct 540 tgcacttgtt gttcgtcttg tactgccgca tcattgcacc aagcaagacg tgaacaagga 600 aaattacatg acttcttgat gggactcaac actgatctgt acgctcaatt acgaaccaat 660 atcctttctc aagatccctt gccttcgctt gatcgagcat accaactggt gatacaagat 720 gagcgtgtgc ggctcgccaa ggcagtcaca gaagacaaac tagcagaggt ccttggcttt 780 gctgtccgta caggtgctgg aagaggacga ggaaaaacgg agaggcctgt gtgtagccac 840 tgcaagaaga cggggcatga gacttcaact tgctggtccc tcgttgcttg tcctcactgt 900 cacaagcatg gccatgacaa aaataattgt tatgaaatag tgggttatcc tgaggggtgg 960 ttggatcaaa acaaggctga tgggagtgtt ggacgtagtc gtcaacaggc tggtcgtggg 1020 cgtggttcag ctcgtgctaa cgcggcaagt agcataattg gagcatcctc tactaaaagt 1080 tctaccgatc aactcttcac acccgaacaa tggaaagctc ttgcgggctt aattggtaat 1140 gctcaagttc cggatgatag gttgaatggt aagtttgaca cgaagtcatg gatcattgac 1200 accggggcaa ctcatcacgt gatcggtgat ttatcttggt tatttgatac tatagcgttg 1260 tttgagtgtc cggttggcct tcctaatggt gaatctgttg ttgcgaccca atccggttcc 1320 gttcgtttgt cgaataacat cactcttaaa aacgttcttt atgtgccgaa actcaattgc 1380 aatttacttt cggtttcaca attgactgat gacttacatt gtattgtcca atttaactct 1440 tatatgtgtg ctatacagga ccacaccagg gagctgattg gaacgggagt taggcaagat 1500 ggactttact acttcggtgg agctgaaagt gattcggtac agcatgtttc tgtccacaac 1560 gcagcctcca ctttggagtt gtggcacaaa aggatgagac atcctttaga gaaagtagtg 1620 aagttacttc ctccagttag caatcttaag ggtagtttaa acaaagcttg tgaaatatgt 1680 tttcgtgcta agcatcctag agacaaattt cctttaagtg acaataaggc aactagaatt 1740 tttgagaaaa tacattgtga tttgtggggc tcttataaac atgtctcttc ttgtggagct 1800 cgttattttt taactattgt tgatgatttc tcaagagcta tgtggattta tttgttggtc 1860 gataaaacag aagtttttcg gatgtttatg tcttttattg caatggtaga tcgacaattt 1920 tctcaaacag tgaaagttgt tcaaagtgat aatggtacgg aatttaaatg cctacttgac 1980 tatttttctg caactggcat tttattccaa acttcttgtg tgggaactcc gcaacaaaat 2040 gggagggttg agagaaaaca caagcatatt ttaaatatgg ggagggcatt acgctttcaa 2100 gcaaatttgc ctatttattt ttgggacgaa agtgttcttg ccgctgctca tttaataaac 2160 cgcactccct ctcctttgtt acacaataaa acaccatttg aaatcctatt tggcacccct 2220 ccttcatatg cggcaattca cacctttggt tgtcttagtt ttgctcatga taaaaaatcc 2280 aaagatgaca aatttgcaag tagaagtaga aaatgtgtgt ttttgggtta cccgtttgga 2340 aagaaggggt ggaagttgtt tgatttggac accaaggaat tatttgttta tcgtgatgtc 2400 aagttttttg aggatgtttt tccgtttggt aacccaggtg ctgtgaatat tattccggac 2460 aacattgtgc ctacggtaaa tgttgaaatt gatagtgatt ttgctgattt tgtcgatgat 2520 gatgctgatt tacctaaccc acaagcccaa acacaaaatc ccaacctcat ccaacctgaa 2580 ccccaagccc accaagatct ttcacctggg ccggaagttg ttcccactgt tgggcttgat 2640 tcacttgggc ttgataatac aagcaatggg cagtctgctc ctatgggaaa gggcatgagg 2700 gataaatttc cttcggttct attacgagat tttgttactc atacggtggt tgttgaaagt 2760 ccatctcccg ccactccgtc tccacagcat ccctcaggta ctccttatcc catagcacat 2820 tatataaatt gtgacaattt ttctgtacat tatcgaaagt ttcttgcagc tattatttcg 2880 agcaatgatc ctaagtcatt taaagaggct atgaaagatg tcggttggca aaagtcaatg 2940 catgaggaga ttcgggcttt gaaggaaaat ggtacgtgga ctcttgaacc tcttccaaag 3000 ggtaagcgtg ctttgggaag tcagtgggtt tacagaacca agtacttctc aaacggtgat 3060 attgaaaggc tcaaatccag attagtagtt ttggggaatc atcaagaagc cggtattgat 3120 tatcatgaga ctttttctcc agttgccaaa atgactacgg tgcgtgcttt cttggctatt 3180 gtggcttcga aaaattggga acttcatcag atggatgttc acaattcctt tttgcatgga 3240 gatcttgagg aggaagtgta tatgaagcta cccccaggat ttgagagttc cgatccgaac 3300 ttggtttgca ggttacggaa atcactttat gggttgaaac aggctccgag atgttggttt 3360 gccaagttgg tcacgactct taaaggatat ggtttcttac aatcctactt tgattattct 3420 ctttttactt acactaagga caatgttcaa ataaatgtgc tagtgtatgt cgacgatctt 3480 attatctctg ggaatgattc cgctgcactt aagaccttta aagcctatct cagtgattgt 3540 tttaagatga aagatcttgg tgttttgaag tatttcctcg gaatcgaggt ggccaggagt 3600 tcggctggtt tgttcttgtg tcaacgcaag tacacacttg acatggtatc ggaggccgga 3660 ttactggagc caagccgtgt ggcttcccga tcgagcaaaa tcatagatta ggactcgcaa 3720 atggggagct cttgtcgaac cctgagtcct atcgcagatt agtaggttga ctcatttatc 3780 tggcagtgac ccgtccagat ttggcctact cggttcatac attatctcaa tttatgcagg 3840 agcctagaat tgagcattgg gaggcggctt tgagagtcgt tcgttatttg aaaggtactc 3900 ctggtcaggg tatcttgtta cgtacagata gtgatctgtc cctgcagggt tggtgtgatt 3960 ctgattgggc agtatgtcca gtcactagac gctctttgtc cggatggctt gtgtttcttg 4020 ggcaatctcc tatttcttgg aagacaaaga agcaacacac agtttcccgc tcgtctgcag 4080 aagcggaata ccgagctatg gcagcagtta cttgtgagct caaatggttg aaggggttgc 4140 ttctgagctt gggtgtgcac cacccaaagg caatcaagct cttttgtgat agtcagtcag 4200 cccttcatat ggccaaaaat ccagtatttc atgaacgcac caaacacatt gaggttgatt 4260 gtcactttgt tcgggatgcg ataacagatg gtttgattgc tccatcatat gttcctactg 4320 ttacacaatt ggcggatatt tttacaaagg ctcttggaaa gaaacaattt gattatcttc 4380 ttgccaagtt gggcattttt gaacctcatg ctccaactta agggaggg 4428 // ID Copia-54_Mad-LTR repbase; DNA; EDCOT; 152 BP. XX AC ACYM01040376; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-54_Mad-I; KW Copia-54_Mad-LTR; Copia-54_Mad_. XX NM Copia-54_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-152 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1404-1404 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01040376; Positions 4527 4376. XX SQ Sequence 152 BP; 42 A; 28 C; 27 G; 55 T; 0 other; tgtgtaaagt atgggtgtta gaatattagt gtgtgaagca tggtgtgtga tgttcatcgg 60 gtgactcacg acatccttct ccacttgtat aagttctctt tcttgtaacc ttacacattt 120 tcaatacaaa caattctttc aaaactatca ca 152 // ID SHALINE16_MT repbase; DNA; EDCOT; 5758 BP. XX AC . XX DT 23-JAN-2007 (Rel. 12.01, Created) DT 02-AUG-2010 (Rel. 15.09, Last updated, Version 2) XX DE A long interspersed element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; retroposon; KW repeat; ORF; Interspersed; Poly-A tail; SHALINE16_MT. XX NM SHALINE16_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5758 RA Shankar R. and Jurka J.; RT "SHALINE16_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 93-93 (2007). XX DR [1] (Consensus) XX CC The sequence is present in multiple but variable copies in the CC genome in very few complete or nearly complete copies. This CC element is having intact domains for CCHC zinc finger protein in CC its first ORF as well as endo/exo-phosphatase, reverse CC transcriptase and RNAse H in its second ORF. XX FH Key Location/Qualifiers FT CDS 1611..5732 FT /product="SHALINE16_MT_2p" FT /translation="MSLVAWNCRGVGSPSAIPDLKYLVRHFNPDLLFLSET FT LAHRNKIEELRFLLGYDSCFPVDRTGRGGGFALFWRNSLNCXLVDFSNNHI FT TVEIVDSXLGTWRLTGYYGYPNGGRRTAAWNFLRQLSAQFTGPWCIFGDFN FT DILDASEKRGRTTRPPWLINGFRQAVLDAGLSDVPXEGYPFTWFKSLGTPR FT AVEERLDRALANNXWFNMFPNANVETLVAPASDHYPIFVNLAPLPRPHISK FT RHFRYENAWQLEPGFKDLVTNSWQEHSSHTLIPKLSSCAEDMCEWKKNHCN FT KLKKDIEDCRKQLHDTRLESSGEDQIRMVELRKRMQRLLSQDDAYWRQRAK FT THWYKDGDRNTKFFHASATARKKVNRILSLDDDGGHKITNEHGLQEVARNY FT FVNIFQQNSDFSPVIDVINPSVSDNDNDLLTAPFSKAEFSDAIFSMHPDKC FT SGPDGYNPGFYQHFWNLCSDDIFKECCGWLDTGQFPPDLNITNIALIPKGS FT SQVSMKDWRPIALCNVLYKIISKVLANRLKKVLPKCISDNQSAFVPGRSIL FT DNAMVAIEVLHFMKTKTRGEDRYVALKLDISKAYDRMDWNYLRAVLNKMGF FT HNRWIHWMCMCVESVDYSVLVNGEQVGPIIPGRGLRQGDPLSPYLFIICAE FT GLSSLIRDAETRGVLTGTKVCRQAPSVSHLLFADDCFLFFKAKEDQAHVMK FT NILSTYELASGQAISLPKSEIYCSRNVPDDLKTTITDILGVQVVLGTGKYL FT GLPSMIGRDRNATFAYIKDRVWQKINSWSGKCLSKAGREVMIKSVLQAIPS FT YVMSIFQLPTTLIDSIEKMMNSFWWGHGKTTQRGIHWMNWEKLSAPKIHGG FT MGFKDLSAFNLAMLGKQGWKFITEPDSLVSRIFKARYFPSGSYLTANVGHN FT PSYVWRSIMRARFIVRGGARWSIGSGATIPILNEPWLPNGEFISSDIPGAH FT FVHNFTVNSLMNLYDKSWNEQVIRQVFSADIADKILHTPLISQVDEDRIIW FT KAERHGRYSVRSAYRLCVSELIDSSYLWRPGYWSGIWNLKVPPKVKNLIWR FT MCRGCLPTRVRLLDKGVNCPTNCASCDSTHEDLLHVFFDCPFAVQVWNRTG FT LWSSVHHALSHTNSATDAIFYLLETLSAELXQRMSSVIWSIWKHRNLRVWE FT DVTETSAMVVERARNMVADWQLANAPDVLVSTSYPQHAMPTQMGASTSQHH FT NQVLWQPPTAGRYKCNIDAAFSSHLNRTGIGICIRDAEGTFVLAKTMTYPC FT IVSVDVGEALGLHSALQWLSEMQFDNVDFESDSKLTADAFLSTRNDXSEFG FT SIISSCRSLYRTFFSNSRVEFVRRQANXVAHALAREATSLASPAVYYDIPN FT CIETIIINEML" FT CDS join(15..80,93..149,153..167,171..308,312..1169, FT 1173..1247,1251..1322,1326..1388,1395..1472, FT 1476..1511) FT /product="SHALINE16_MT_1p" FT /translation="MLNICYKLQRQHNLCSPRVSSTRLPFLGCRRILGRIP FT LVRSSTSDPSRCFYPDVYIQPNTSFLQNPSLVLSSPSFSCVFLSVSFLSFS FT VSSCPVVFMDPVNLNLAGLTLSEEGLTLNLESEPETAAVLEHCLIGRVLAD FT REIQFAYFSERMSRAWKPGKRVTITKSVPDRFLFQFHHRVDAARVLEEEPW FT LYDNYHIVMDRISPGVVPSCVPLNHIDFWVQIHGLPFGFIQPKVGQGIGSF FT LGTLKTYDDRNTIHSSYMRLKVAIDVTIPLKREWRVRASNGSFVTINFKYE FT KLGVFYYRCGLLGHTDKVCPELFELEADDGIRHWGVGLKPVTQSLGTTATN FT RWLHDPIPAVAPKPSQVLFLLVVKLLLALVILHLSPHACFSVTTYCYETRC FT ARCPQLNASKRYRCKFCFSSAAVALFFHRYFSVLAARPPFGAWFTCCPFSK FT RLHNTRGKWFGFEETETYAGPSEWGNICCRGNGKFCNWFKC" XX SQ Sequence 5758 BP; 1424 A; 1110 C; 1290 G; 1905 T; 29 other; accaaaataa aataatgcta aatatatgtt ataaattgca aagacaacat aacttatgct 60 ctcctagggt ttcctccacc tagggtttct agcgccttcc ttttttgggc tgccgccgca 120 tcttgggccg gattcctctt gtgagaagtt gatctacatc tgatccatga tctagatgct 180 tctatccaga cgtttatata cagccaaata ctagctttct tcaaaaccct agtcttgtgc 240 tttcttctcc ctcgttttcc tgtgttttcc tgtctgtcag ttttctttcg ttttctgtca 300 gttcctgtta gccagtcgtc ttcatggatc ctgttaacct taaccttgct ggcttgacct 360 tgtctgagga gggtttaacc ctaaacctag agtccgaacc tgaaactgct gctgtacttg 420 aacactgttt gattggtcgt gtccttgctg atcgtgagat tcagtttgcc tatttcagcg 480 agcgcatgtc tcgtgcttgg aagccaggca aacgggtcac gatcactaag tctgtgcctg 540 accgtttttt gttccaattc caccatcgag tcgatgccgc tcgtgttctt gaggaagaac 600 catggcttta cgataattac catattgtca tggaccgcat ctcccctggt gtcgtaccta 660 gctgtgttcc cttgaatcac attgatttct gggttcagat tcatggtctg ccttttggct 720 tcatccaacc gaaagtaggt cagggaattg gtagcttttt aggtaccctc aaaacctatg 780 atgatcgcaa cactatccac agttcctata tgcgtctcaa agttgctatc gatgtcacta 840 tcccattgaa aagagaatgg cgtgttcgtg ctagtaatgg ttcttttgtt actattaatt 900 ttaaatatga gaaactgggt gttttctatt acaggtgtgg cttgctcgga catacggaca 960 aggtgtgtcc ggagctgttt gaattagaag ctgatgacgg cattcgtcat tggggagtcg 1020 gcctgaagcc cgtcacacaa agtcttggaa ctactgctac gaatcgctgg ttacatgacc 1080 ccattcctgc tgtcgcacca aaaccatccc aggtgctgtt cctgctggtc gtaaagctgc 1140 tgctggcgtt ggtaattctg catctttcat gaccgcatgc ttgcttttca gtcacaactt 1200 actgctatga aacacgatgt gctcgctgcc cacaactcaa tgctagctaa aaaaggtatc 1260 ggtgcaaatt ctgtttttca agtgcagctg ttgccctctt cttccacagg tacttcagcg 1320 tctagcttgc tgccaggccg ccctttggtg cttggtttac ctgctgcccc ttttccaagc 1380 gactccactg atgaaacacc cgaggaaagt ggttcggatt tgaagaaacg gaaacgtatg 1440 ctggcccttc agaatgggga aacatttgct gctgaagggg aaatgggaaa ttttgtaatt 1500 ggttcaaatg ttagtcatgg ggaggatatt gatatgaatg taattgctac atctttaggt 1560 gatgaacaaa ttgtaacggc aggccctgat gatcaggcct gcctagataa atgagtctag 1620 tggcgtggaa ttgtcggggt gtaggtagcc cgagtgcaat tcctgacctt aagtacctag 1680 ttcggcactt caatccggat cttcttttct taagtgagac tctagctcac cgtaataaaa 1740 ttgaagaact tcgttttttg cttggttatg attcttgttt tcctgtagac cgcaccggta 1800 gaggcggggg ttttgcttta ttttggcgta attctttaaa ttgtcawctt gtygattttt 1860 ctaataatca tattactgtt gagattgtag atagtgwtct tggtacttgg agacttactg 1920 gttattatgg ctatcctaat ggaggtcgta gaacagccgc ttggaatttt cttcgacaac 1980 tttctgctca atttacaggt ccttggtgta tttttggtga ttttaatgac atcctggatg 2040 ctagtgagaa aaggggacgc accactcgac ctccttggct tattaatggc tttcgtcaag 2100 ctgttcttga tgctggttta tctgatgtcc cgrttgaagg ttatccgttt acttggttca 2160 aaagtctagg tactccacgt gcygtggaag aaaggttaga tcgtgcactt gctaataatt 2220 tktggtttaa tatgtttcca aatgctaatg ttgaaacttt ggtggctcca gcttctgatc 2280 attatcctat ttttgttaat cttgctcctt tacctcggcc tcatatatct aaacgccatt 2340 ttcgttatga aaatgcgtgg caacttgaac cgggytttaa ggatctcgtt actaattctt 2400 ggcaggaaca ttcgtcacat actcttatwc caaagttatc ctcttgtgcg gaagacatgt 2460 gtgagtggaa gaaaaatcat tgtaataagc taaaaaaaga tattgaagat tgtcgtaaac 2520 aattgcatga cacgcggttg gaatcttcgg gcgaggatca aattcgcatg gttgagctta 2580 ggaaacgaat gcaacgattg ctgtcccaag atgatgccta ttggcgtcaa cgtgctaaaa 2640 ctcattggta caaggatggt gaccgaaata caaagttttt tcatgcwtcg gctacagctc 2700 ggaagaaggt aaatcgtata ctttctcttg acgatgatgg aggtcataaa attactaatg 2760 aacatggttt gcaagaagta gcaagraatt attttgtgaa tatttttcaa cagaatagtg 2820 atttttctcc tgtgattgat gttattaatc cgtctgtctc tgataatgat aatgaccttc 2880 ttacggcacc tttctctaag gcagagttta gtgatgctat tttctctatg catccagaca 2940 aatgttcagg ccctgatggt tacaatccgg gtttttacca acatttttgg aatttatgta 3000 gtgatgatat ttttaaagaa tgttgtggtt ggttagatac aggacagttt ccccctgatt 3060 tgaatattac taacattgct cttattccta aaggttcttc gcaggttagc atgaaggatt 3120 ggcgmcctat agcactttgt aatgttttat ataaaattat ttcgaaagtg ttagcaaaca 3180 ggttgaagaa agtgctgcct aagtgcattt ccgacaatca gtctgctttc gtcccrggac 3240 gctccatttt agataatgct atggtagcaa ttgaggttct acattttatg aaaaccaaga 3300 cacgagggga agacaggtat gttgctctaa aacttgatat tagcaaagcc tatgatcgta 3360 tggattggaa ttatttgagg gctgtcttga ataagatggg ttttcataat cggtggattc 3420 attggatgtg tatgtgtgtc gaatcagtgg attattctgt gcttgttaat ggtgaacagg 3480 ttggtcctat tattccaggg cgtggtctcc gtcaagggga tcctctytct ccgtatttgt 3540 ttattatttg tgcagaaggt ttatcctcgc ttatcagaga tgccgagacc agaggtgtcc 3600 tcacgggtac naaggtttgt cgtcaagcac cmtcagtttc tcatctttta tttgctgatg 3660 attgttttct ctttttcaaa gctaaggagg atcaagcaca tgttatgaag aatattttat 3720 ccacttatga attagcttct ggtcaagcga ttagtttacc aaagtctgag atatattgca 3780 gtcgaaatgt ccctgatgat ctcaaaacta ccattacaga tattctaggc gttcaagttg 3840 tgttgggcac aggtaaatac cttggcttac cttctatgat aggccgagac cgaaatgcta 3900 cttttgctta catcaaggat cgtgtttggc agaaaattaa ttcctggagt ggtaagtgtc 3960 tmtctaaagc aggtcgtgag gttatgataa aatctgtttt gcaggctatt ccttcttatg 4020 ttatgagtat ttttcagctt cccactactt taattgactc aattgaaaag atgatgaact 4080 ccttctggtg gggtcatgga aaaacaactc aacgagggat acattggatg aattgggaga 4140 agctgtcagc accaaagatt catggaggta tgggtttcaa ggacctatct gcttttaatt 4200 tggctatgtt aggtaaacag ggatggaaat ttattacaga accrgattct ctggtgtctc 4260 gaatttttaa agctcgttat ttcccctctg gttcctatct cacggctaat gttggccata 4320 atccgagcta tgtttggcgt agtatcatgc gtgctagatt tattgtgcgt gggggygcac 4380 gatggagtat aggctcaggt gcgactattc ctattcttaa tgaaccttgg ttgcctaatg 4440 gggaatttat tagtagtgat attccaggtg cacattttgt tcataatttt actgttaata 4500 gtttgatgaa tttatatgat aaaagttgga atgaacaggt gattagacaa gtttttagtg 4560 ctgatatagc agataaaata ctacatacgc cacttatttc tcaggttgac gaggatagaa 4620 ttatctggaa agcggaaagg catggacgtt actctgttcg tagtgcttac agattgtgtg 4680 twtcagaact gattgattct tcttatctyt ggagaccggg gtattggtct ggtatttgga 4740 atcttaaagt tccaccgaaa gttaagaatt taatttggcg matgtgtcgt ggttgtttac 4800 cgacccgtgt acgtttgctg gataaaggtg ttaattgccc tactaattgt gctagttgtg 4860 actcyactca tgaagacctt ttacatgttt tttttgattg tccttttgct gtacaggttt 4920 ggaataggac aggtctttgg agttcggtgc atcacgccct ttcgcatacc aattcagcta 4980 cggatgctat attctatctg ttggagacgt tgtcggctga attaratcaa cgtatgtcat 5040 ctgtcatatg gagtatatgg aagcatcgca atctcagagt ttgggaagat gtaacagaaa 5100 caagtgctat ggttgtcgag cgagctagaa acatggttgc ggattggcaa ttggctaatg 5160 ctccggatgt tcttgtatcc acttcgtatc ctcaacatgc catgccaacg cagatggggg 5220 cttccacctc acaacatcac aatcaagtct tgtggcagcc tcccactgcc ggtagataca 5280 aatgtaacat tgatgcagcm ttctcatctc acctcaaccg tacaggtatt ggtatttgta 5340 ttcgcgatgc agaaggtacn tttgttctgg ctaagactat gacttaccct tgtattgtct 5400 cggtggatgt gggagaagcg ttagggttgc actctgcttt gcaatggttg agtgaaatgc 5460 aatttgacaa tgtggatttc gaatctgact ctaaattaac agctgatgcc ttcctttcta 5520 ctcggaacga cktgtccgaa tttggatcta ttatttcctc atgtcgttct ttgtaccgta 5580 ctttcttttc waactctagg gtggagtttg ttaggcgaca agccaacgwg gttgctcatg 5640 ctcttgcaag ggaggccacg tctttagcta gtcccgctgt ttattatgat atacccaatt 5700 gtattgaaac tattattatw aatgaaatgc tataagcatc tttccttcaa aaaaaaaa 5758 // ID SHACOP17_LTR_MT repbase; DNA; EDCOT; 405 BP. XX AC AC127428; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of LTR retroposon, SHACOP17_MT, from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; terminal; repeat; SHACOP17_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-405 RA Shankar R. and Jurka J.; RT "SHACOP17_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 62-62 (2007). XX DR EMBL/GenBank/DDBJ; AC127428; Positions 43014 43418. XX CC Exists in the genome in very low copy number. XX SQ Sequence 405 BP; 143 A; 42 C; 70 G; 150 T; 0 other; tgatgactgt gagaataagt gaaatattta gtgtttacta aatatggaat aatctaaaga 60 tggaaagtgc aaagaataat gcaaaggaat gtttactcta ggataagagt aataatagga 120 tggagagtac atgagaggtt tataattgtt tgaagtattg ttcactcaat ttttagcatg 180 tacattatta taaaatgttt aggagttttg taatttagat atcacaacaa aacaagtaga 240 gtgtaacaaa gtgaatttat ttattagaag ttcatctttc tttttagaca ttttttcata 300 caaatttatt gttctaacta cattcgtgtt caactttagt gagtgcatag ttcatattat 360 tattagaagt ctatattttc cgctgctact caacaattgg catca 405 // ID Copia40-PTR_I repbase; DNA; EDCOT; 4239 BP. XX AC scaffold_2111; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia40-PTR_I; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4239 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4239 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 258-258 (2007). XX DR Genome; scaffold_2111; Positions 4713 475. XX CC Positions [1660-2127] - Integrase core CC 'ATATA' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 699..1739 FT /product="Copia40-PTR_I_2p" FT /translation="MFEASLQAASKGVNFSPTTHLSSRNQSRYPFNNVGRY FT TSNNSGGNWRPSTSQHHRYTGQVLTTHGTSNSSRSQPRPYLGYCQICGIQG FT HTAKKYPSFRLVPLHSNQNSSPTPWQPQANLADTSSQTQSPWLLDSGASHH FT ITADLQNLAHQLPYTGTDDVMIGDGKSLRITHLGSSTLHSSAHSFKLNNIL FT CVPDIKRNLLSIYQFCVDNNVSVEFLPWCFLVKDLLTGEIRVKGKTKESVY FT KWSCVVTPHAFSSLKTAPINWYLRLGHPAVSVLKTILSKHNLNSSSVSKDF FT VCNACHCNKSHKLPFSVSTLTSHKPLEIIFSDVWTSPILSVDGFKYYVFFC FT GSLH" FT CDS 1669..4239 FT /product="Copia40-PTR_I_1p" FT /translation="MYGHHLFCLLMVLSIMFFFVDHFTKYVWFYPLQKKSD FT VKTTFIRFKAVVENYFKTKIMTLYSDNGGGYIALKEFLVMHGISHLTSPPH FT TPEHNGFAERRHRHIVETGLSLLTHASLPRIFWSYAFATAVYLINRMSTTK FT LQNLSPYAVIFQHSPNYEKLHSFGCLCYPWLRPYTAHKLDPRSKPCIFLGY FT SLSQSAYLCFEPESSKIIVSRHVSFIEHIFPYHDLHKQEPPCISTSVDMWI FT PPVITIPSSTSTHSSAAAPEARTPPLVILHPSSGLANPSETPSLPSSTISI FT SAPVILNPIATTPTPTAPLPCHPMTTQSKNNIHKPIQKLTYTTTLTTQPQE FT PTTLAQATEDPHWQSAMNEEYSALLRNGTWTLVPPVCASNLVGCRWIFRIK FT RNADGTVARYKARLVAKGFHQRPGLDYHDTFSPVMKPTTVPLVLSIAVSNG FT WTLRQLDINNAFLQGTLVEDVYMAQPPGFHDLDKPEFVCKLRKAIYGLKQA FT PRAWYHELRNFLHASGFSNSLADTSLFVFHQQSHLIYLLVYVDDIIVTGDN FT QHAVNQFIQRLAARFSLKDLGSLQYFLGVEIQSHPTGGKLLSQHRYIMDLL FT HRTNMAHVKPTSTPLPPGCKLSLDMGAHLADPTHYRATIGSLQYLSLTRPD FT VCFAVNKLSQFMHKPTDVHWKLVKRLLRYLLGTVNHCLLLHRHSPCSVYAF FT SNADWGGNMEDLSSTSAYVIYLGRNPISWSSKKQHTTTRSSTEAEYRAVAD FT TAAEISWVCSLLSELHFPVSHTLVIYCDNIGATQLSSNLVFHSRMKHVAID FT FHFIRQRVQPGALRVSHVSSNDQLADALTKSLPRLQFWLLKDKIGLIDPVH FT LEGA" XX SQ Sequence 4239 BP; 1158 A; 1114 C; 737 G; 1230 T; 0 other; tggtatcaga gcagttgcac taaattgcat tgtttttttt ttctcttcac tcccttcttc 60 ccttcttctg ttctatctaa atcactatga gtgattcctc aaacacaacc cttgttacta 120 ttaatgttac agctcaggct ccagtgaaac tcaacatcac caactatctg tcatgacgac 180 ttcagtttca tactctcttc attggttatg atctgcaagg ctacatagac ggcacaaaac 240 catgcccata acaatatctt accaccaata cagacaaccc caccactcaa accttaaatc 300 cagaatatca tacctggata cgtcaaaacc aactgatttt gaacgccatc ataggatcaa 360 ttacaccaac cattattcct tttattgctc gcgccacaac agctcgcgca acatggaata 420 tccttgcagc cacatatgcc actccatctc ggggtcgcat caaacaggta aaagccaatc 480 tcaaatcgct aaccaaaggc aatctcagca tcacagactt cctgcaatca gtcaaggcta 540 gagctgatga acttgcagtc ctaggggccc ctgtagacaa tgaagacctg acggacaaaa 600 tcgtagaaaa actaggtgat gactacaaag aattggtgag agcagtgcaa gccagagacc 660 attccattag ctttgatgaa cttcatgaaa aattattaat gttcgaagcc tcactccagg 720 cagccagtaa gggtgttaat ttctccccca caacacatct ctccagtcga aaccaaagca 780 ggtatccctt caacaacgtt ggccgatata catccaataa ctcaggtgga aattggcgcc 840 cctctaccag ccaacaccac cggtacacag gacaagtttt aaccactcac ggcacctcca 900 acagcagccg atctcagcca aggccatatc tggggtattg ccaaatttgt ggcattcaag 960 gacacacagc gaaaaaatat ccctcatttc gtcttgttcc cctccacagc aaccaaaatt 1020 ccagtcctac tccgtggcaa ccgcaggcca accttgcaga tactagttcc cagactcagt 1080 ctccatggct tctggatagt ggggcatccc accacatcac ggcagatctc caaaatttgg 1140 ctcaccagtt gccctacacc ggcacagatg atgttatgat aggggatggt aaaagtctgc 1200 gtattacaca cttgggttcc tctactcttc attcatctgc tcactctttt aaacttaaca 1260 atatattatg tgtgcctgat attaaacgca atttactctc tatatatcaa ttttgcgttg 1320 ataataatgt ttctgttgag ttcttaccct ggtgttttct tgtgaaggac ttattgacgg 1380 gggaaattcg cgtaaagggt aaaaccaaag aaagtgtgta caaatggtcg tgcgttgtca 1440 cccctcatgc cttttccagt ctcaaaacag ctcccataaa ttggtatctt cgattaggac 1500 atccagctgt ttctgtttta aaaacaattt taagtaagca taatttgaat tcgtcttcag 1560 tatccaaaga ctttgtctgc aatgcatgtc actgtaataa gagtcacaaa ctaccatttt 1620 ctgtctccac tttgacttct cataaaccgc ttgaaataat attttctgat gtatggacat 1680 cacctatttt gtctgttgat ggttttaagt attatgtttt tttttgtgga tcacttcact 1740 aaatacgtat ggttttatcc gctacaaaaa aaatctgatg tcaaaaccac ttttattcgc 1800 tttaaagcag tagtggaaaa ttatttcaag acaaaaatta tgactttgta ttctgacaat 1860 gggggtggat atattgcgtt aaaagaattc cttgttatgc atggaatatc tcatctgaca 1920 tcacccccac acacccctga acacaatggc tttgctgaac gccgtcatcg gcatattgta 1980 gaaacaggcc tctcactttt aactcatgca tctttgccac gtattttttg gtcttatgct 2040 tttgctaccg cggtctatct catcaatcgc atgtcaacta ccaagttaca aaatctttcg 2100 ccttatgcag ttatttttca acattcccca aattatgaaa aacttcatag ttttggatgt 2160 ttatgttatc cttggctacg cccgtacact gctcataaat tagatcctcg ttccaaacca 2220 tgcatttttc taggatattc tctatcacaa agtgcttatt tatgctttga acccgagtcc 2280 tcaaaaatca ttgtgtccag gcatgtgtcc ttcatcgagc atatttttcc ataccatgat 2340 ttacataaac aggagccacc atgcatatcc acttcagttg acatgtggat tccaccagtt 2400 atcaccattc catcatccac ttctacacac tcttctgcgg cagcacctga agcaagaact 2460 cccccgctag tgatccttca tccctcatca gggctggcta acccatcaga aaccccttcc 2520 ctcccatctt ccaccatttc tatatctgcc ccggtcatcc tcaacccaat agcaaccaca 2580 cccacaccga cagcacctct tccttgtcac cctatgacaa cccagtccaa aaacaatatt 2640 cacaaaccca ttcagaaact cacgtatact accaccctta ccactcagcc tcaagaaccc 2700 accacccttg cccaggccac agaagaccca cactggcagt ctgccatgaa tgaagagtat 2760 agtgctctgt tacgcaatgg aacttggact ttagtcccac ctgtttgtgc ttctaacttg 2820 gttggctgta ggtggatttt caggatcaaa cgaaatgcag atggaaccgt ggctcgttac 2880 aaagccagac ttgtcgccaa aggttttcat cagcgtcctg gactggacta tcatgacaca 2940 ttcagtccag ttatgaaacc tacgacagtc cccctggttc tcagtattgc tgtcagcaat 3000 ggatggacac ttcgccaact tgacattaat aatgcatttc tacaaggcac tcttgttgag 3060 gatgtttaca tggcccaacc tccgggcttt catgatctgg acaaacctga gtttgtctgt 3120 aaacttagaa aagcaattta tggcctgaaa caggcacctc gtgcgtggta tcatgaacta 3180 cgcaattttc tgcatgcatc gggtttttct aactccctgg ccgatacttc acttttcgtc 3240 ttccatcagc aatctcacct catttatctg ctggtttatg tggacgatat tattgttaca 3300 ggggataatc aacatgctgt caatcaattc attcagcgtt tagcagctcg gttctcctta 3360 aaagatttgg gctctctgca gtattttctg ggcgttgaaa ttcagtctca tcccactggt 3420 ggcaagcttc tctcacagca caggtacatt atggacctgc tacatcgcac caacatggct 3480 catgtaaaac ccacgtcaac tccgctgcct cctggttgta aactaagctt agacatgggt 3540 gctcatctgg ctgatcctac acactatcgt gcaacaatag gaagccttca gtatctatct 3600 ctaactcggc ctgatgtttg tttcgctgta aacaagctct cccaattcat gcacaagccc 3660 acagatgtcc actggaaact ggtgaaacgt ctccttcgat atttacttgg cactgtcaac 3720 cactgtctgc tacttcatcg tcattctcca tgttcagttt atgccttttc taatgcagac 3780 tgggggggaa acatggaaga tttatcctcc accagcgcct atgtaatcta tcttggtcgg 3840 aatcctatct cctggtcttc caagaagcaa cacaccacga cacgttcatc cactgaagct 3900 gaatacagag cagttgcaga cacagcagct gaaatcagct gggtatgctc tttactgtct 3960 gaactacatt ttccagtgag tcatactcta gtcatctact gtgacaatat tggtgccacc 4020 cagctgagct ctaatcttgt gtttcactca agaatgaaac atgttgctat tgattttcac 4080 ttcattcgac aaagggttca accaggtgct ctacgagtgt ctcatgtatc ttcgaatgat 4140 cagttagctg atgcactgac gaaatcacta ccccgcttgc agttctggct tcttaaagac 4200 aagattggac tcattgaccc cgtccatctt gagggggca 4239 // ID DNA-9-1N_Mad repbase; DNA; EDCOT; 310 BP. XX AC . XX DT 07-OCT-2010 (Rel. 15.1, Created) DT 07-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; KW DNA-9-1N_Mad. XX NM DNA-9-1N_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-310 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1462-1462 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Imperfect TIR is 85-bp long. TSD is 9-bp long. XX SQ Sequence 310 BP; 108 A; 47 C; 44 G; 111 T; 0 other; gagtaatgct attcttacca caattttata ccacatttct ttaccatctt aggtggcaga 60 tgagttggac aagctacatc atttaatttc aatcttttta ttaattaaaa cacttaaata 120 atcttaggtg gaagaaggag actcctcgta taccacaatc atcatttaat taacaatctt 180 tttattaatt attgattaac attttgaaat taaatgctaa ttaatttaga tgatgtggct 240 gtccacatca gatgccacct aaggtggtat acaattgtgg tacaaaaata tggtaagaat 300 aacattattg 310 // ID Gypsy-27_PTr-LTR repbase; DNA; EDCOT; 1059 BP. XX AC . XX DT 09-DEC-2009 (Rel. 15.02, Created) DT 09-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-27_PTr-I; Gypsy-27_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1059 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 174-174 (2010). XX DR [1] (Consensus) XX SQ Sequence 1059 BP; 301 A; 192 C; 235 G; 331 T; 0 other; tgatgcggat cagcccaaca ccaagcgtaa tcatgccaac gacccattgg aggtgccaat 60 tgggccaatc acaagagcta gggcaaagaa gcttaaagaa gcattgaatg ggcttgttca 120 gaacatatgg agcaaaatgg acctagaggg gcttgggaca tttaaggagc atgaaggaca 180 acctttaatt catctagttc aggtccaaga agagcccaat tcgtgtggaa caaggggttg 240 atgtgtccgg cccaatacca gccttgttag gcttgttttt ttcctaatgc tacaaggata 300 aaaagtcagc aatttattct cctaattaag taaggaagtt ggccatatct tattcctaaa 360 gaggggagga ctatttaatg cttttcctaa cttaggaagg aaagtaatta aatcagcaac 420 aaaggaggaa atttgttttc ttatttgtcc aagttaaaca aggaaatcca agctaatcaa 480 ggacatcaag ggggcagcaa cacaaatttt ccaaatcaga tttttcctag tttatttagg 540 acttcttaag ggtgacaaat ctgattctag catatttagg atgataattt ttggattttt 600 attattttct tcttagtttt tgggttatta ttacttattt gggtcaattg taagtgggct 660 tcatataagt ccacctaagg ggggtccatt agggtttctt taagtctaga gtcagtataa 720 ataaaggcat aaccaaacat gtaaggttac gcaattttca gatcaataaa cttctttgct 780 gcacttattg tgtgttggtg ggataatctc ccttccttgg ttctctaaag aactgaaaac 840 gacttatcga agaacaactg tcttcgtggc gtcatcctta tacttctcgt tcgcgaatca 900 atattcgttg ggtgggggtc tccgtttcca atagtgctgg tgcctaggta caagttatct 960 ttgtgtcaca ctcctatcaa acctgattta cttggctttc cgggaattgg tgtctttgcg 1020 tgtgggttgc gtgaccatgt gatcacgagg ttcgcatca 1059 // ID Gypsy18-VV_LTR repbase; DNA; EDCOT; 2226 BP. XX AC AM476928; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy18-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-2226 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-2226 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 717-717 (2007). XX DR Genbank; AM476928; Positions 11058 13283. XX SQ Sequence 2226 BP; 727 A; 228 C; 512 G; 755 T; 4 other; tgtaatgacc gggtatttta tgccacgtta gcaattttag tttgaaaagt cttaatttat 60 gtgatggttg aaaagtaaaa aagaaaagcg tttggagaac acgtgtcaat ttcggattgg 120 tgaatttcgt tttattgcgt cgrtcaatta aacgagttga aattttatgc catgtcagcc 180 ttaggataga aaattcttag gattttagaa attggaaatt tccgggaacg aaaaacgaaa 240 aygaaaaatg aaaaataaat aaattaagat taattagaat taattaagaa aaataaatta 300 attaattaaa ttaaattgat gaataataat attgagaaaa ttagttttta tttggtgtta 360 ataaataaaa ttgtatgtta aaatgaaaaa aaaaatgaat gaaaaatgaa ttggaaatca 420 aataaaacaa ttagaataaa gaaaagaaaa gaaaataaaa taaaataaat aatagcaata 480 ataatggatt gggcttagtt ttgagttggg cttggattaa gtgggctggt ggcttttaaa 540 aagcaagtgg gctggtggtt ttttttaaaa gccatgtgag tgggctgatt aaaataaaaa 600 gaaatgggct taagtgaaga agagggaaca gtagcagatc tggaagaaag gggggcggcg 660 gcactgtagc aatctcacct cgccggagct ttgaccgacc gtttgggtgg tcaaatgacc 720 tctgtttacg gctcagattt ggagggggtg ttctactcga cgaggggaat aatcctacgg 780 tggccaatcg tattgttagc ggctaaattc ttagatctgt ggtaggggac cctaacccta 840 aaacttaaat ttttatgttt ttcccttgga aaaaaattat agatattgtc attttgagtt 900 aattgggaat tatggatgtt gtgtaaattt tttctagaat atttggaatt tgtttggaat 960 ttttggaatt tcgggaaatt gattttgatt gataattaat tgttttgaaa ggttaaaaat 1020 tattagatgg gttggaaaat tccaaatttt gggttaaatt ttaaatataa tgatttgtga 1080 atttttaggc attggttaga atattttcga aaattttagg gtaaatagtt agttaatttt 1140 ggatattaga aattattata atggttgaaa aattttgtaa gtgtggtaaa atctcaagat 1200 tgttgatatg caattttttt taatatttat ttgggatatt atcggaaatt gtaatgtgtg 1260 aaattgtttg attggattat tggggaatgt tgagattgtt gaattattga ggaacattgg 1320 aattgtggca ttcattgcat catggttatg tgaaaaaaat aaataaataa ataaaatcat 1380 gaagattgtg aaaagtgtat gaaatggaaa aaaaaaatga aatagagatg agaagtggaa 1440 gcccgtgtga ggtgaattaa gaagggagag agatccctag ggtgaaagac ccaaaagttt 1500 accccgggaa gactccgaat ggggagtgta tttgggtgcg gacgcgtaty cttcggtgaa 1560 agcccgagaa caatagtgca ttgtatgact gtgtgtcaca cgttcatgtg cattcatgta 1620 attgttgaat attgtgaaat tgtgtataat atcatatatt aaactatgtg attgattgat 1680 attgttgaat tgttcctttt gtgttgaagt gtcctttccg tattctttga aacatagtaa 1740 tccccttaac cccttgggtg ctaggcatcc tactgagcaa tgtggaaatg ctcacccctt 1800 ccttgttaca cctttttaga tgcagatatc tctcctgagg atccacaggt gggacaggga 1860 ggacttcagg atgctcctgg agcggcctag tggagtgtgg catttatttg ttattgtgtt 1920 cctttttgga ttttggggaa ttgttttagc aattatgact catggatttg ctatgaagct 1980 ttatttgatt aagttgttaa ttgtgaactt ttattttgga ctataatgaa tatttattta 2040 atcttgttgt tttgagtagt tttgggatat tgtaatttat gagaattcta gtgagatgta 2100 tgaaaaaaaa aaatccagag tgttttggtt gactgccaac atggaatagg aggaaccctt 2160 agggtcaaac ctttgacctg grgtcacggg tcaaattttg ggtcacccgg aatttgggtc 2220 gtgaca 2226 // ID Copia5-VV_I repbase; DNA; EDCOT; 6442 BP. XX AC AM470769; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia5-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6442 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-6442 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 743-743 (2007). XX DR Genbank; AM470769; Positions 7564 1123. XX CC Positions [3235-3702] - Integrase core CC 'GATCT' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 3334..5382 FT /product="Copia5-VV_I_1p" FT /translation="MFKVFRTEVEKQLGKVIKIVRSDRGGEYYGKHGDVGQ FT QKGPFARYLQDNGIVAQYTMSGSPEQNGVVERRNRTLMEMKRSMMGRSNFL FT EYLWGEAIKTATYILNRVPSKSVPKTPFELWIDRKPSLNHFKVWGCPAEMK FT IYDPSLKKTDSRTIRCYFIRYPSHSKGYKFYCSTRGTRIVESQVAKFLELD FT VADSIPSQSNERVEPMDVISLRLPVSDVNLDVGAFDSGIQQGVAAVNFPTV FT EISPIVDEIPPVEMRRSQRTRRPALSNDYYVYLGEGEYDIGEEVDPTTYCE FT ALSSDKTNEWLIAMRDEMQSMSDNDVWELVILPKGYKPIGCKWVFKTKRDN FT KGNVERYKARLVAKGYTQREGIDFTETFSPVSTKDSFRLVMALVAHFDLEL FT HQMDVKTAFLNGDLSEKVYMSQPEGFKENGKENMVCRLKRSIYGLKQASRQ FT WYLKFDKIVTSFGFIENKFDQCVYMKVNGIKYIFMVLYIDNILLSSSDVNL FT LNDTKHILFANFNMKDIGEAFFVLGIEIYRDRSRNLLGLSQKAYINRVLKR FT FNMQTCKAGDVPVVKGDKLSNEQCPKNDLEKDAVKTIPYASAIGSLMYAQV FT CTRPDITFIVNVLGRYLSNPGHDHWVAAKKVMRYLQRTKDFMLVYRRVDNL FT EVVGYLDSDLVVVLMIANLLQCQIEPNCILDHVC" XX SQ Sequence 6442 BP; 2022 A; 907 C; 1302 G; 2196 T; 15 other; tgtggtatca gagcctgatt tacatgattt aggatctaca tttggaaatc gaaaataaaa 60 tttttagttt cttattttat tttcttttcg aagccaaatc tgtgatccat gaatgtgcat 120 gtttttttag tttcttttga ttatgaaact ttaggctttt tgttcctttt gtcacaagct 180 tcaaattgat atatcatatg ttcaatttcg ttgtttaaat tgggagtaat taaatttttg 240 gaattttctt gtttaaagat tcaagaaaaa ttttatttga tcaaattatt gtgttttact 300 caaattaaac tcttagattt tgttgtttac atatattata gttgatatgt agcatcaatt 360 tcggtttttt ggctcaattt ggtgaaaatt gaaaatttga aaatatgggt atgaacccta 420 aaaaattcgt tttatttttt ttttttaaaa aaaaaatttg agcaagattg agaagttttt 480 tttttgttta attaattgtt gtaaagagac ttcttatatt gttaatgtaa aaatacatgt 540 aaaatgaggc cgaaataggt gttaaaatag agtttttcaa tcttggctat ggaggtatga 600 aaaaccgaat tttgttaatc aattatggag atctttaagt tgtttttttg atgattaaat 660 gtcctagaat tgttagaaac aacctaaagt ttaaaagccc tcaagatcct gatcaaaaaa 720 acattttttt ttttattgtt tgtaatccgg gttgcaaccg ggtcatttga cccgtattgc 780 agaattttgg acccaatgct ggaggttgaa gatgacctcc agcacatgcc acacgtgcca 840 catgtaccac acattcctca ctcgcaggtc aagtgtgtga ggcgcgtata acctcatccg 900 gtgttcgttt tgagccccgt tttttcctgt gcgctcattt ttttgtaatc tatttttcta 960 gatatattat tatatttttt gggggtcaaa aatatttatt aaataattat tacttattta 1020 tgtgatttaa ttagcttaaa attatttttt ggtataattt tctgttgaga atttaccaga 1080 aattatgcta atatatatgg aataggagtg tagtactcac tctctctata ttgaaacttt 1140 ttcatgcata ctctcctact tggtctaaat cacataaact agttaaataa ttaatttaaa 1200 gtgtaataaa taaataaaaa ttgttgttca aattcttgca actataattg atcatatgca 1260 tatatatcgc taatatgcac tattgttgtt gggcaatttt ttttaattta cccaattttg 1320 gaacgttgca tgtgaattgt tgaggttatt ttaccaaagt gatttaacca tcaaaatttg 1380 caagtttatg agttcctatt ttgttgatgg ggaaaatttt agattaattt gtacaatcgc 1440 ctgcccaaag ggggttattg tgcaaattaa tttaacaaca tgaggatatt gaatgagata 1500 aataatttga caaatttatt tgcccaaagg aaataaattt taatgaatta tttgttgatc 1560 ttcatgctta gagaatagtt gtttattgtg gactctgccc aaaggggagt ttatgatagt 1620 acaattgatt cttgtattgt attgcttatg attatttaag ttttttttta cctattgccc 1680 ataattgatc tagttgcaaa attttgtcaa tcagtttcct ttgctgtgaa caacaataat 1740 gctacaattg aaattctaag tgggtcgaac tataagagat ggagatcaga catagagttt 1800 gttttaggaa tgatggactt ggacatggct ctacgtgaag atgaacctcc taagcctact 1860 aatgaaagca ctgaagctat gagagctcat tatgcgaaat gggaaagatc gaaccgtttg 1920 agtcttattt caatcaagag gtccattgtt gagcatctcc ttggaggaat acctgagagc 1980 aacaatgcta aggaatttct cgttactgtg gcaaaataga taccaaacat ctgacaatgc 2040 tgaagctggg cattttatgg atgaattgat gaatatgaga tatgatgata tgaaaggggt 2100 tcgtgagtat atcctaaaaa tggtgcatct tcagactaga ttgaaagcac tagacattcc 2160 cattcccgat aagtttattg ttcatcaagc cctcaatact ctgccatctt cttttagcca 2220 aatcaagact gcatacaaca ccctgaatca gtcttggggt gtgaatgacc tgatcactaa 2280 gtgtgtggtt gagaaagaaa agctgaaaag agaaaagaat gaatctgctc atctcgttgc 2340 tcttggagaa ccgaataata aaaaaagagt tgaaaagact agaaagccca acttccatag 2400 taataagaaa aataagaact tcaagaarag tgggagtgaa aagmagaaka atggaaatgc 2460 caagaacaca gaccttaagt gctatcactg caacaaaaag ggtcacaaga gggttgattg 2520 ctttamgttt aagaattggc tagagaagaa aaagaaggaa carggtatgt tatctgycta 2580 tgtctgtttt gaatctaatt tagttaatgt tcctttagat tcatggtggc ttgayagtgg 2640 tgctactgtt catgttgcaa cttctttaya gggkataaga aatctgagra agccaagtga 2700 aaaagagtca aagcttaaag ttggcagtga catcrggatt ratgttgagc atattggggt 2760 tgctgtttta gaattagatt ctggttttca gcttgttttg gacaatattt tctatgtacc 2820 ttcgtttaga aggaatttaa tttccctttt agtacttgat aaagctggat atagtttcac 2880 ttttgaaaat aaaagagttg atgtgattta tgactctaaa gtgattggaa attgtgtttt 2940 atctgatggg ctttatagat tgtcgttgtt atctacttgt tcttacaatg ttgaaaacaa 3000 tgttgctaaa agaccattga ctaaggaaag atcttcattg ttatggcata agcgtttagg 3060 gcacatttct aaagaacgag tagaacgctt aattagtttt gggattcttc cctgccttga 3120 ttctgatgac ttagaaattt gtgctgattg tgtgaaagga aaattgacaa agaataagaa 3180 aaagggtgca actcgtagtc aaaatttgtt ggagattgtt catacagaca ttagtggacc 3240 ttgtgtggca acaagtactt cattacattc attgatgatt tttcccgtta tggctatgta 3300 ttttttatca aagaaaaagc agatgctctt gaaatgttca aagtcttccg aactgaagtt 3360 gagaaacaat tggggaaagt catcaaaatt gtgagatctg atcgaggtgg tgagtattat 3420 gggaagcatg gtgatgttgg acaacaaaaa ggaccttttg caaggtactt acaagataat 3480 ggtattgttg ctcagtatac tatgtctggt agtcctgaac agaatggtgt agtagaaagg 3540 cgcaatcgca ctcttatgga aatgaagagg agcatgatgg gtagatcaaa ttttctagaa 3600 tacttatggg gtgaagccat taaaacagca acctacattt tgaaccgtgt tcctagtaag 3660 tctgtgccta aaacaccgtt tgaactatgg atagacagaa aacccagttt gaatcatttt 3720 aaagtatggg gatgtccagc tgagatgaaa atctatgatc cttctttaaa gaagacggat 3780 tcgagaacta ttaggtgcta ctttattagg tatcctagtc actcaaaagg atataagttt 3840 tattgttcga ctcgtggcac tagaattgtt gagtctcaag tggcaaagtt tttagagttg 3900 gatgttgctg atagtatacc ctctcaatcc aatgaaagag tggaacccat ggatgttatt 3960 tctttacgtt tgccagtctc agacgttaac cttgatgttg gagcttttga ttctgggatt 4020 caacaaggag ttgctgctgt caatttccct actgtcgaaa taagccctat tgtggatgag 4080 attcctcctg tggaaatgag gagatcacaa agaactagga gacctgcctt atctaacgat 4140 tattatgttt accttggaga gggagagtat gacattggag aagaagtgga ccctactact 4200 tattgtgaag ctctcagtag tgataagaca aatgaatggt tgattgccat gagagatgag 4260 atgcaatcta tgtcagacaa tgatgtttgg gaacttgtta ttcttcccaa aggatataaa 4320 cccattggat gcaaatgggt attcaagacc aaaagagaca acaaaggaaa tgttgaaaga 4380 tacaaggctc ggttggttgc taaagggtat acacagcgag agggcattga tttcacagag 4440 actttttcac cagtctctac caaagattcc tttaggctag ttatggcgtt ggtagctcat 4500 tttgacttag agcttcacca gatggatgtc aagacagctt ttctcaatgg tgatttgagt 4560 gagaaggtct acatgtcaca acctgaagga tttaaggaaa atggaaaaga gaacatggta 4620 tgcagattga aaaggtcaat ttatggtctc aagcaagctt ctcgccagtg gtacttgaaa 4680 tttgacaaaa ttgtgacgtc ttttggtttt atagagaaca agtttgatca gtgcgtttac 4740 atgaaggtta atgggatcaa atacattttc atggttcttt atatcgataa cattctactt 4800 tctagtagtg atgtgaatct cttgaatgat accaagcata ttttgtttgc taattttaac 4860 atgaaggata ttggagaagc attttttgtg ttgggtattg agatttatcg tgatagatct 4920 cgaaacctcc ttgggctatc tcagaaagcc tatatcaatc gtgtgcttaa aagattcaat 4980 atgcagacgt gcaaagctgg tgatgtacct gttgtgaagg gagataaact cagtaatgaa 5040 caatgtccaa agaatgattt ggaaaaggat gccgtgaaga ctattcctta tgctagtgcc 5100 attggtagcc tgatgtatgc acaagtatgt acaagacctg atatcacatt cattgttaac 5160 gttcttggta gatatttatc caaccctgga catgatcatt gggttgctgc aaagaaagtc 5220 atgagatatc tacaaagaac gaaggatttt atgcttgtgt ataggagggt ggataatctt 5280 gaggtagttg gatacttaga ttctgatttg gtggttgttc tgatgatcgc aaatctactt 5340 cagtgtcaaa tagagcctaa ttgcatcctc gaccatgtat gctgagtttg tagcttgtta 5400 tggtgcatca tctcaagctg tttggctaag aaatttgatt tcagagttgc caagttgttg 5460 attccatctt tcgacccatt gtgatttatt gtgacaataa tgcagttgtg ttctacttta 5520 agaacaataa gattagtacg ggttctaagc atatggaaat caagtacctt acagtcaagg 5580 acttagtgaa gaaaggagat attgtgattg agcacataag aactgagtcc atgctagctg 5640 atcctctaac caaaggttta aagcccataa cgttcaagga acatgttgtg aatatgggtg 5700 ttattaagtc ttttgattct ttggtttagt gggagctttt gtgatttccc ttatttcaat 5760 tattgtttta tgcaaacatt gatcattatt gttctgcaac ttgcaaaatt aaaatmtttt 5820 tattatgatc atcataatta agtattatat tatagcatgt cgtaattgaa ttacatacaa 5880 catggtatct tgagatattg aaccttaaga attwcagttg tatactattg gatgtcacaa 5940 ataccactat tttgagattt tgtggtgcat tgttggtgac atatgacttg ttaaagtcaa 6000 gcaatttcat attgtttaga aattgcagca atttcatttt gttgagaaat tgcaattaca 6060 atttcatttt gctggtaaat tggaatgagg actgataaga aacaatgcat atagatgatg 6120 atcacatgtt ggcattgatt tcttactaca ctactgggtt tacgatccat gtcgatatgg 6180 ttataaatat tygtgactat aaggggcatt atgtttgttg agattaacat atagaccatt 6240 atagtccaat attaagacca tgttggaccg gataagttta acaagatgct atttatagac 6300 tatcatttct ttcaaaaaaa aaaaaaaaaa aaaaggtgtg gccacacaaa ataaactttt 6360 ctgtatttaa cccgagagtc ttattttcaa aatgaattta atgaatcctc aaaaaacaat 6420 taatgtagcc caagtgggag aa 6442 // ID Copia-51_Mad-I repbase; DNA; EDCOT; 5263 BP. XX AC ACYM01038468; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-51_Mad-I; KW Copia-51_Mad-LTR; Copia-51_Mad_. XX NM Copia-51_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5263 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1321-1321 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01038468; Positions 9693 4431. XX CC Positions [2516-3016] - Integrase core CC 'TGTA' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 426..1475 FT /product="Copia-51_Mad-I_2p" FT /translation="MLTIKLNDDNFIKWNFQFCSVLRGYDLFDHFTGESVC FT PPKFLITLELGVTNEISTAYKAWVQTDMALLSLLIATLSDDAMEYVVGCKT FT THEAWTALQDRYMFVSSATVNHLKAELHTIKKGSDNVDKFLLRLKTIKDKL FT IAAGEKITDNDLVIAALTGLPADFDTIRTVVLARDTPISLKEFRAQLLEAE FT KIIEARMQSLVHSMAVMYGNGSVPFSSGGNSAYQSVSHVSSPSTGSDSTVP FT QSSNFGFGLVAPDSSNSGGSTSQTCQQFPPHNANVFSEPRNNFGKQGPRSF FT GHNNGHTSFGNTYSTQSGHSGYNSSGHNYGNSSRGKGYKGKGNGGYRPKFN FT GNRSGNY" FT CDS 1517..3673 FT /product="Copia-51_Mad-I_1p" FT /translation="MSDLFKERTYGSDLSVQNETTPVVQECQICGKRGHIA FT IDCRHRGNFAYQGAHPPPSLSANYAFQDYPSQFQYPGVPPPIQFPDLSGYQ FT GVSFTTPQVPPDFQASVNQGQSSLILSSSQDHDVSSDIPALNAQTSSGDGS FT WILDTGASHHMSPNVNLLDTVIPYTGDKRIVVGNGDGLTVNHIGTAFLPTS FT SHTLCLRNVLHVPMLTVNLLSVQQLCKDNHSWFICDDTQFYVQDKATGLIL FT YQGKSNNRELFRIPIHLFPKVLTLDDSSCSAFVGKAVKSSLWHHRLGHPSN FT DVLTAMLRSSNISFSHDVPDQPCSHCFSGKMSSLPFVERLDRVEIPFHKIH FT SDVWGPSPIASIEGLRYYVSFVDEATRFVWLFPLMNKSEVFGTFVKFFAYV FT ENQFNTKIKVLQSDGGGEFLSTAFKDYPANHGIVHFISCPYTPQQNGLVER FT KHRHIIETAITLLTAASLPHKFWYHVVAHAVFLINRMPSKTIGMVSPFQKL FT FHTLPEISSLKVFCSAIYPYLRPYNDHKLQPRSTQCVFLGYFSDYKGAICF FT NRLTHKFFLSRHVLHDENCFPFATTLSDTRCSDTGVSSTSNLSCPIVVHLD FT ALNLSHSGIDSYVQPHNVSVSSSLSTHGLESTSSPYIVVGAQNHHISSSSV FT ASQSFSMLHVPDSLQLEADLSQSSSSIPQGIQTRLKTGAITRRDYSALSAT FT FPEVHSLTLHEDTHFSGGF" XX SQ Sequence 5263 BP; 1348 A; 972 C; 1051 G; 1863 T; 29 other; tacaagaatg ttaagatggt atcgagagcc agatatgctt gcgcgattga ttctgggtgt 60 gttctttccg ctgctccgtg agattttctt gattctttct ctcgattaag aaaatttggg 120 aatttttttt ttcgaatttc ttggattcat ctgtgttaaa ggccgatgcc tcgatgaatc 180 atcacatatt gtgttttttt tttagttgaa gatttgactg ttttcttgaa ggtcgatgcc 240 aattaatttc atattggttg atgaactaag gtcgataacc aattgttcat caagattgta 300 gattcttgtt gttgaattct gtgttttgga agaagatttc tctgggtttt tctgttccca 360 tttctgtgtg gtgtcaattt atactcacgc atgatgactc ggttaaactt gaaaatcttt 420 tgggaatgtt gactattaag ttgaatgatg acaatttcat caagtggaac tttcaattct 480 gttctgttct tcgtgggtat gatttgtttg atcattttac tggtgaatca gtttgtcctc 540 ccaaatttct tattactctt gaattagggg ttaccaatga aattagtact gcatataaag 600 cttgggttca aactgatatg gctcttttga gtcttcttat tgccactttg agtgatgatg 660 ccatggaata tgttgttggt tgtaaaacta ctcatgaagc ttggactgcc ttacaagata 720 gatatatgtt tgtctcgagt gctactgtga atcatttgaa agctgagtta cacactatta 780 agaaaggaag tgataatgtt gataagtttt tgttgaggtt aaagacaatt aaagacaaac 840 ttattgcagc tggtgaaaag attacagaca atgatttggt kattgctgca ttgactggtt 900 tacctgctga ctttgatacg atcagaactg tggtattggc cagagataca cctatctcgt 960 tgaaagaatt cagggctcaa ctcttagagg ctgaaaagat tatagaagct aggatgcagt 1020 ctcttgttca cagcatggca gttatgtatg gtaatggttc tgttccattt tcttctggtg 1080 gtaattctgc atatcaatca gtttcacatg tatccagtcc ttctactggt tctgattcta 1140 cggtgccaca gtcatccaat tttggctttg gtcttgttgc tcctgattcc tctaattcag 1200 gtggctcaac ttctcagact tgtcaacagt ttcctcctca taatgctaat gtttttagtg 1260 agcctagaaa taattttggt aaacagggac ctaggtcttt tggtcataat aatggccata 1320 cttcttttgg taatacctat agtactcagt ctggtcatag tggttataat tcttctggtc 1380 ataactatgg caattcatct agaggtaagg gttacaaagg caaagggaac ggtggctatc 1440 gacctaagtt caatggtaat cgatctggta attactagtc aggtaacact accactagac 1500 cgaatatagt tcctgaatgt cagatttgtt caaggaaagg acatacggca gtgacttgtc 1560 tgtacagaat gaaactactc cggttgtgca agaatgtcag atttgtggta agaggggcca 1620 tattgccatt gattgtcgac acaggggtaa ctttgcttac caaggggctc atcctcctcc 1680 ttccctcagt gccaactatg cctttcaaga ttatccttct caattccagt atcctggtgt 1740 tccacctcca attcagtttc ctgacctttc tggttatcaa ggggtttctt tcactactcc 1800 acaagttcct ccagattttc aagcttctgt aaatcaaggc cagtcttctc ttattttatc 1860 tagttctcaa gatcatgatg tttcatctga tatacctgct ttgaatgcac aaacttcttc 1920 tggtgatggt tcttggattc ttgacactgg tgcctcacat cacatgagtc ccaatgttaa 1980 tctgttagat acagttattc cttatactgg agataaacga attgttgttg gcaatggtga 2040 tggtttaact gtcaatcaca ttggcactgc cttcttacct acatcttcac atactttatg 2100 tcttcgaaat gtcttgcatg tgccgatgtt aacagtcaat ttgttgtctg ttcagcagtt 2160 gtgtaaagac aatcacagtt ggtttatttg tgatgatact cagttctatg tgcaggacaa 2220 agcaacgggg ctgattcttt accaaggaaa gagtaacaat cgtgagcttt ttcgcattcc 2280 tatccatcta tttcccaagg tgttgactct agatgattct tcttgttctg catttgttgg 2340 caaagcagtt aagtcatctt tgtggcatca cagacttgga catccttcta atgatgtctt 2400 gacagctatg cttaggagtt caaatatttc ttttagtcat gatgtaccgg atcaaccttg 2460 ttctcattgt tttagtggta aaatgagtag tttaccattt gttgaacgac tagatagagt 2520 tgagattcct tttcataaga ttcacagtga cgtttggggt ccttcaccaa tagcatctat 2580 agaaggctta agatattatg tgtcatttgt agatgaagca actcggtttg tatggctctt 2640 tccattaatg aataaatcag aggtttttgg tacatttgtc aagttctttg cctatgttga 2700 gaatcaattt aacacaaaga ttaaggtgtt acaatctgat ggaggaggag aatttctgag 2760 cactgcattt aaggattatc ctgctaatca tggtattgtt cattttattt cttgtccata 2820 tacaccacag cagaatggtt tagtggaaag aaagcatcga cacatcatag aaactgctat 2880 tactttgttg acagctgcta gtcttcccca taagttttgg tatcatgttg tggcacatgc 2940 ggtgttttta ataaatcgaa tgcctagcaa gactattggt atggtttcac cttttcagaa 3000 gttgtttcac actttaccag agatttcatc tttaaaagtc ttttgctcag ccatttatcc 3060 ttatctcagg ccatacaatg atcacaagct tcaaccaaga tccactcaat gtgtttttct 3120 aggttacttt tctgattata aaggagctat ttgctttaac aggttgacac acaagttctt 3180 tctttctcga catgttctac atgatgagaa ttgctttcct tttgccacca ctctttctga 3240 tacaaggtgt tctgatactg gtgtgtcttc cacttctaat ctttcctgcc ctattgtagt 3300 tcatttggat gctttaaatc tgtctcactc tggtattgat tcttatgttc aaccacataa 3360 tgtctctgtg tcctcttcat taagtacaca tggcttggag tcaacatctt ctccttatat 3420 tgttgttggt gctcaaaatc atcatatcag ctcaagttca gttgcttctc agtctttttc 3480 tatgttacat gtgcctgatt cccttcaact ggaggctgat ttgtctcagt ctagttcttc 3540 tattcctcag ggaattcaaa cgagactcaa aactggtgct ataacaagaa gggattattc 3600 tgccctttca gcaacatttc ctgaagttca ctcaytaacc ttacatgaag acactcattt 3660 ttctggtgga ttcaycttca ttgccgatat tacagattct gctgaacctg caacttttaa 3720 acttgcttct caattgcctc aatggcaatc tgcgatgcaa gatgaatatg atgcacttca 3780 aacccaaggt acatggcttm tygttccttc tccttctgat aaaaacatca ttggatgtaa 3840 gtgggtgtat aaaatcaaga ggaatcctga tgggactatt tctcggtata aagcwcgact 3900 tgttgctcag ggttttagtc aagaaaaagg cttrgattat acagagacct ttagtcctgt 3960 ggttcggcac ayaactgtac ggatgattct tgcattggct acaacttata aatggtctct 4020 ctgacaactt gatgtgaaaa acgccttttt acatggagag ttaaatgagg aggtgtacat 4080 gaagcaacct ccagggtttg tcaatcttca gtgtccaaca catgtgtgta agttggttaa 4140 gtctttgtat gggcttaagc aagctccccg agcatggaat gctaaattta caggttattt 4200 ggcagccgtg ggttttcata cttcttcctc agattccagt ctttttgtta aacaagtggg 4260 tactgatgtg gttatactac ttttctatgt cgatgatata atccttacag gctccaatac 4320 tactttaatt caatctgtta ttgatgatct tgctggtgtt ttttctctca cggacatagg 4380 tcaattaaca tattttttgg gtttgcaaat ccaatacaag tccaatggtg ctatgtttgt 4440 tyatcaggag aagtatatta aggacttgat tcataaagca ggcatggata attgtaaatc 4500 atgtgctact ccttgcaagc ctcatagttc tgttttggtt gctgaagggg aattgttgac 4560 agaccctact ttgtayagaa gccttgttgg atcattgcaa tatctaactt ttacaaggcy 4620 agatattgct tttgcggtta atactgtgtg tcaatttatg catgctccta ctgatgttca 4680 tcttggtttg gtaaagcgaa ttattcggtt tttacaaggc acaatgaaat gtggattgac 4740 ttttacttct ggtagtggga ttgatatmag aggttatagt gactctgatt rggctgctga 4800 tgttaatacy akacggtcta tcacaggtta tgtggtctat cttggtgcca atcycatctc 4860 ctggcaatcc aagaaacaaa gttytgtttc tcgyagttcc accgaagyak aatataaagc 4920 tcttgcacat gctgctgctg atattgcatg gattcgrttg atattgtgtg atttgtgtgc 4980 tattgtttcc aatccaccty ttttgctgtg tgataatcaa tctgccattg cattgagctt 5040 gaatcctatt catcactcam ggatcaagca tttagaaaya gattttcact ttgtccraga 5100 gcgtgttcaa aaaggagata tggatgtgya gtatgtgcct acccaagacc aaatcgcaga 5160 tatwcttacc aaggctttac atggccccga ttttcttcga cattgtmaca atcttaatct 5220 ggggtatccc agtkaagatt gagggggggg tattggatat aca 5263 // ID GYVIT1_LTR repbase; DNA; EDCOT; 1902 BP. XX AC AM448663; XX DT 25-APR-2007 (Rel. 12.04, Created) DT 15-AUG-2007 (Rel. 12.09, Last updated, Version 2) XX DE Gypsy-type LTR retrotransposon - long terminal repeat (LTR). XX KW Gypsy; LTR Retrotransposon; Transposable Element; GYVIT1_LTR. XX NM GYVIT1_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1902 RA Jurka J.; RT "GYVIT1: Gypsy-type element from Vitis vinifera."; RL Repbase Reports 7(4), 141-141 (2007). XX DR EMBL/GenBank/DDBJ; AM448663; Positions 12875 10974. XX CC LTRs show no similarity to other Gypsy LTRs known to date. XX SQ Sequence 1902 BP; 554 A; 356 C; 383 G; 592 T; 17 other; tgattactac tcaaaaagtg ctatttgata gcctttaatt aatccttttt aacacttttg 60 agtagtagtt taggcctttt aactcaattg acatgttaag gatcctttaa agcaattttg 120 atcactttgt gtaagttttg gtgtttttgt tagtattttg atcaccaaag caagtcaaga 180 atgaggagag ctatgaggaa tcttgggcaa agttgagaat tcaattgcca agagtgaatc 240 cggattgcaa ggagaaaaag caaagaggat cagtcatgga gcatattctt gatgacagtc 300 gtagcagcca cttttggagc actttctgaa gtccaaatga tgcaagctat ataccatttc 360 aaagctcagg aagtcaacaa tccaatgctt caaacggtgc gcgatttgga gttgaaacga 420 agaagttgca gccattacaa gccagtcact ctgaagtgct gcggaatcaa ccttttgttg 480 cgagaatttc gcaacacttt tgtacagtaa ggtgtttctc cttctgacga tgcacgaacc 540 atgccgcgag agggaagcta gaaacttcaa gatggaagcc aactttgcag cctggtgaag 600 atagctcggt cttgcgaaat aatttcgcag ccctcttggg tgtctgcgaa atttcgcaga 660 caccactttt ctcctgcgaa atggctcctg aagcctcccg aagcttgcta ccgacattgg 720 gagatatttt ccattagatt tttgttgtct aaatcccaaa atactccttg taaaccacca 780 attacatgat tccttagttt ttaagttagt aaaaagacca aatatctttg taagaattag 840 ttttatatta gtttgatata aatacctctc gggagcctgt tctcagaaag gagttccttc 900 tgtaaccttt tggtaagcaa gtaaagtatt ttctttctac tgccttacct tctcactttg 960 tattttcatt ttatttctaa gttatgaatt ctctgaggag ttttccccag agaatgagta 1020 actaaacctc caattccttg gagctaaggt tgccggggaa ggttccaagt gcaaaaatgc 1080 aaaactctgt ggttttagct aataatgaag aggaagtgaa atcctttagt gatttcaatg 1140 gtttttttta gttaacttaa aaaacacttt ggagtcacct aggccaacac ttggtaaggc 1200 aagtgatttc caaccgtgga aatgcactag tttacccctt gcgagcctct ggtaggtgac 1260 ttcaaggtag gattttctgg aattaccaac acttrgtaag cttttggact cctaggagac 1320 atccattagt tatctcttgc gagtttgtga agggrartcc aaggttaaag atcaccttga 1380 atggtaagtg ctcgtgagag gcatgaacca ttgcaagttg tatcagtgag agaattaaag 1440 tgaaatctaa ttgaaggagt ctctgtacat caccggttag agrattgact ataagttgaa 1500 tctctaatgc gaggaaatga accatytgac cggagctatg tcttttgcat gaggaaccac 1560 cycagtgaac ctaaatctcc aaggaatgct tttcttccta aattattcca aacttctgtt 1620 aagattagtt agtttaagtc tmaaccttta ccaatcaaas tttgtgtttt ayttcttaar 1680 ctaaccgtga aatgaaacaa raccaattca cttggaattg gtatccttga ttgcttgywm 1740 atcattccya gtgaacgatc cttagagcca ctatactata gtagctttgt atttgctacc 1800 ctagtgtatg gtgttatagg tataaattty gttgatcact tcctcaatca aggagcwcca 1860 gctgaacaca aatcagctga gacaccaatt gggcatgagt ca 1902 // ID Gypsy-7_Mad-I repbase; DNA; EDCOT; 3082 BP. XX AC ACYM01142332; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-7_Mad-I; KW Gypsy-7_Mad-LTR; Gypsy-7_Mad_. XX NM Gypsy-7_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3082 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1330-1330 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01142332; Positions 5387 8468. XX CC Positions [2217-2438] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1203..1835,1839..2813) FT /product="Gypsy-7_Mad-I_1p" FT /translation="MMRDCPQKKALKAMAFKEDKAEESNDASMGCIRLLNA FT IQTTLPQPKAQVGGGSLFVDVKTGDKTTRVLVDTGATHNFMTSEEATRLGL FT RVTKEPGSVKTVNSAATPIVGVARNVHVDIGTWKGTIDFTVVKMDDYGVVI FT GLEFMDKVRAFPIPFYNIFCILADGRQPCLVPLERQAKKCTQHLSAIQFAK FT SWKKGEATFLATLMLNEGEEKGPLPKQVEDVLVEFADVMPKELPKKLPPRR FT EVDHAIELEPGAKPPSKSPYRMSPPELEELRKQLNELLDAGYIQPSKSPYG FT APVLFQRKKEGSLRLCIDYRALNKITIKNKYPLPLIADLFDQLGEARYFTK FT LDFSTAFHPQTDGQTERVNALLETYLRHYVSANQRDWAKLLDVAQFSYNLQ FT RSESTGKSPFELAIGQQPLTPNTVVTGYTGNSPAAFKTAKEWQLAHELARA FT HLEKASKKMKKWADRKRRNVEFQTGDQVFVKLNASQHKSTRGLHKSLLRKY FT EGPFPIIKKVGKAAYVVELPPRLKFHPVFHVSNLKPYHAD" XX SQ Sequence 3082 BP; 901 A; 682 C; 844 G; 631 T; 24 other; gctggtatca gagccaagct cgtgaatcac ttgaaggaaa gtaggatatg gcaagtggag 60 agatggtgtc cggagtctcc gacctaaggg agcgtactgc agaggtccaa gacgttgcca 120 agagcaagcc aaagttaaaa gacttgcaag catcgatgga gaccatggaa gagcgactcg 180 agaaggtgga acgaaccata ctcgagttcg atactcgact cgatgaggac gttgtcgaca 240 aggaggaaat ccaaaccatg gtggacaatg gtaaggatga actgcgtggc ttggtggaag 300 ggctacgaga tgagctcctt ggcgctctca acaccatggc agacaagatg cggagggaag 360 tccargttca ccttgacaac atagaggcaa ggtttgtggc gcttcaagaa gagataaagg 420 acacaaggga acttaaggga gatgtggcgt tttgtaaaga agcagtcgtg aagcaattcg 480 tgcaagggyc gagggaaatc aaggcgttgg actccaaggt aatmgactcc tttaaaccca 540 aatcctataa tgggaagagg gaagcaaagg agctcgacac attcgtgtgg aacgtggagc 600 gatacttcaa gtacctaaag cttgaagatg acgagtccaa aatctcaacg gcaaccatgt 660 tcttagctga caatgccctt atgtggtggc gtcgccgaag catggagatt gagcaaggta 720 cgttctctct caccacttgg gatgaattta agaaagatct tatgttgcac ttctatcccc 780 aaaatgccaa gtacgaagcc aaggagaaac taaggtggct caagcaaacg gggagcgtca 840 aagaytaygt caacgccttc gtgagcttrt tattcgaggt gcccaacatg ttagaggaag 900 acaagctcat gtacttcatg agtgkactgc aaaattgggc aaaactcgaa ctacaaagga 960 ggcacgtgca aacattgtct gatgccattg ccgccgctga atccttgatt gagtttaaat 1020 caagccacca aggtgattcc aagtccacgg ggaagagggg taaccatgag agaagtgggg 1080 gagaacayaa gccgaaggay aaggccgaga caagcaaacc gaaggagaag aaagccgata 1140 agcatgacaa aggcaagggt aagtcttggc aacccaaytg ttacctatgc gacgaccctc 1200 acatgatgcg agattgccca caaaagaagg cccttaaggc catggctttc aaggaggaca 1260 aggccgagga gagtaacgat gcaagcatgg gatgcatccg tctactgaat gccatccaga 1320 caaccctccc acaacctaag gctcaagttg ggggaggatc attgttcgtc gacgtcaaga 1380 ctggtgacaa gacgacgcgt gtgttggtgg acacgggagc aacacacaac ttcatgacgt 1440 cggaggaagc cacaaggctk ggcctccgag tcacmaagga gcctggtagc gtgaagacgg 1500 taaattccgc tgccaccccc attgttggag ttgcgcgtaa tgtgcacgta gacattggca 1560 catggaaggg aacgatcgac ttcaccgtag tcaagatgga cgactatggc gtagtcattg 1620 ggttagagtt catggacaag gtacgagcct ttcccattcc cttctacaat attttctgta 1680 tcctagccga cggaagacaa ccttgcctgg tgccattgga aaggcaagcc aagaagtgta 1740 cccagcactt gtcggcaatt caatttgcca agtcttggaa gaaaggcgag gccacatttc 1800 ttgcaacyct aatgttgaat gaaggggagg agaagyaygg gcctttgccg aaacaagtgg 1860 aagacgtcct tgtggagttt gcggacgtga tgcctaagga actgccaaag aagttgccac 1920 caaggagaga ggtcgaccat gcgattgagt tggagcctgg tgctaagcct ccctccaaat 1980 caccttatag gatgtcgcca cccgagttgg aggaattgag gaagcaactc aacgagctac 2040 ttgatgctgg ctacatccaa ccctccaagt ccccatatgg tgcacccgtc ttgttccaac 2100 gcaagaaaga aggtagccta aggttgtgca tcgactatag agcattgaac aagattacsa 2160 tcaagaacaa gtacccactt ccgttgatcg ccgacttatt cgatcaactt ggtgaagcaa 2220 ggtacttcac aaagttagac ttctccacag cttttcatcc ccaaaccgat ggacaaacgg 2280 agcgggttaa tgcattgttg gagacttatt tacggcacta tgttagtgcc aatcaacgag 2340 attgggctaa gttacttgat gttgcccaat tctcttataa cttgcaacgt tcggagtcga 2400 cggggaaaag tccgttcgag ttggctatag ggcaacaacc cttgaccccg aacacggtcg 2460 tgactggcta cacggggaat agtccagccg ctttcaaaac ygctaaggag tggcaattag 2520 cccacgaact tgctcgagct catttggaga aggcttcaaa gaagatgaag aaatgggcrg 2580 atcgcaagcg aaggaatgtg gagttccaaa ctggcgacca agtctttgtg aagctcaatg 2640 cgtctcagca caagagtact cgtggcttgc ayaagagctt gttgcggaaa tatgagggac 2700 cattccctat catcaagaag gttggcaaag ccgcgtatgt tgtggaactc ccaccccgcc 2760 tcaagtttca cccggtgttc catgtragca acttgaagcc ttatcatgcr gacratgarg 2820 aaccaagtcg aggtgagtct catcgagcac cccctttgat gacgraggca tttgacaaag 2880 aagtggagag cattgaagcc aagcgtgtcg tggtgcgacc aagacaacca aagcatgtgg 2940 agtactttgt caaatggaag gggctaccat actccgaagc aacctgggag aaggagacgt 3000 ccttatggca atataaggac ttgattcaga cattcgagag gcaagagtcg acgaggacgt 3060 cgacggctta agtgggggag ga 3082 // ID Copia-37_Mad-I repbase; DNA; EDCOT; 4381 BP. XX AC ACYM01138943; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-37_Mad-I; KW Copia-37_Mad-LTR; Copia-37_Mad_. XX NM Copia-37_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4381 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1307-1307 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01138943; Positions 2355 6735. XX CC Positions [1736-2230] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 104..1621 FT /product="Copia-37_Mad-I_1p" FT /translation="MGDEMIPHVSDPLILHHSDSPSLVLVSQLLDGHNYGQ FT WSRSMRIALSAKNKLGFVDGSIKNPATTDAKYSIWQRCNDMVLSWIWQSVQ FT GNIAHSILYCKTATAAWRDLEDRFSQGNDSRIYQIRQEIVEHRQGQLFVSD FT YYTKLKALWDELASYHEPIACECEGSKAHADREEKERVMQFLMGLNENYST FT IRGSILMMSPLPDTRRVHGLVLQHERQLDVVNRREPTAHAMQASRSTAPKG FT GYGAHNPSSRKTFKCSYCDGGHPVERCFFLIGFPEGHKWHGKNVQPRNRRT FT PPASNNVETLPLTTAQIDTTKAPISSNQPTFTTEEYHQLMALLCNKNGTNL FT PLVHAAGIYTPNCNFTQHSLHSPLYWIVDSGATYHISHSSPIHNHTRPQHD FT FVGLPNGGQAAIESIGSIKLSPKITLDRVLHVPQFRVNLLSVSKLTWALKC FT VVIFYPGFCVVQDMATKKMIGLGKLFNGLYYLTPTQNPHLANHVNHTSTLW FT HQLLGHPSSA" FT CDS 1865..3622 FT /product="Copia-37_Mad-I_2p" FT /translation="MRFKSDTQTIIHSFFSWVKTQFNRDIKTLRADNRGEF FT ISLRSFLDTHGTFFQHTCAHTPQQNGVVERKHRHLLNVARALRFQANLPLK FT FWGESVQTAYYLINRLPTPLLSHQSPYKLLHRTPLVYTHLRVFGCLCYATN FT LTPSHKFNARARRCLFLGYPLGQKGYRVYDLDSKRIFTSRDVTFHEHLFPI FT ANLPPEPDHNTPVLPVPHDDPTPAPSDLLPTIDLPASLTPSLPPDIPPPTP FT ATTTSPTPAPSSPSMPLIPLRRSERIKQPPAHLRDYQTHHAALLQHNVNSS FT TMSGTRYPLHRYVSYARLSPAHRSFVHNVSHLVEPASYEQARHDPHWLVAM FT NSELEALEANHTWTLVPLPLHQCPIGCKWVFKIKYHSDGTIERYKARLVAK FT GFTQREGIDYKETFAPVAKLITVRCVLSIAAVRSWSLHQMDVQNAFLHGAL FT HEEVYMLPPPGYRRQGETMVCRLHKSLYGLKQASRSWFQRFSSTIQEIGFQ FT QSHADYSLFTKVCGHSITVVLLYVDDMIIAGNNEEAISQLKQFLSGCFRIK FT DLGPLKYFLGVEVARSKAGISISNESILWTYWRKLACLA" XX SQ Sequence 4381 BP; 1174 A; 1181 C; 837 G; 1184 T; 5 other; aatattaaga tggtatcaga gcactgatct tggtgactct agaaggctca tctttgcttc 60 cgccacaaac acaaccagtt cctcttcatc aaacccagcc accatgggcg acgagatgat 120 acctcatgta tctgatcctc tcattctaca ccattcagac tcaccaagtc ttgttttagt 180 ctcacaactt ctcgatggac acaactatgg acaatggagc cgctctatgc gaattgccct 240 cagcgccaaa aacaaactag ggttcgttga tggatcaatc aagaaccctg caaccactga 300 tgctaaatat tcaatttggc agagatgcaa cgacatggtc ctatcttgga tttggcaatc 360 tgtgcaaggc aacattgctc acagtatact ctactgcaaa actgcgacag cagcatggag 420 ggaccttgag gatcgattct cgcaaggcaa cgattccagg atctatcaaa ttcgacaaga 480 gattgtcgaa caccgacaag gacagttatt tgtttcagat tattacacaa aattaaaagc 540 tctttgggat gaattagcat cataccatga gcccattgct tgtgaatgcg aaggatccaa 600 ggcacatgca gacagggaag agaaagagag agtcatgcag ttcttaatgg gactgaacga 660 gaaytactcc accatacgag gctctatatt gatgatgagc ccactcccgg atacacgacg 720 tgtccatgga ttggtcctcc aacacgaacg ccaattggat gtggtgaatc gtcgtgaacc 780 cactgcccat gcaatgcaag ccagtcgttc aacagcacca aaaggaggct atggcgccca 840 caaccctagt tcacgaaaga ctttcaaatg cagctactgt gacggaggac atccagttga 900 acgttgtttt tttcttattg gcttccctga aggacacaaa tggcacggaa agaatgtgca 960 gcccagaaat aggcgtacac ctccagcctc caacaatgtt gagacactac cattgacaac 1020 tgctcagatt gacacaacca aagcacccat ctccagcaat caaccaacgt tcacaaccga 1080 ggaatatcat caactcatgg cccttctttg caataagaat ggtaccaatc tgccacttgt 1140 acatgcagca ggtatctata cgcccaattg caactttaca caacattctc tgcattcacc 1200 attgtattgg atcgtggata gcggggccac atatcatatt tctcactcat cacccatcca 1260 taatcacact agaccccaac atgattttgt tgggttacca aatggtggac aggctgcgat 1320 tgaatccatt gggtctatta aactgtcgcc caagataacc cttgatagag ttttgcatgt 1380 accacaattt cgtgtgaacc tattgtctgt gagtaagtta acttgggcat tgaagtgtgt 1440 tgtgattttc taccccggtt tttgtgttgt gcaagacatg gctacgaaga agatgattgg 1500 cctgggcaag ctgtttaatg gactctacta cctcactcca acacaaaacc ctcatctcgc 1560 caaccatgtc aaccacacct cgacactgtg gcaccaactt cttgggcacc catcctcggc 1620 tcytcttcac tctttatccc agaccattcc agaaatcaty tttgattcta cacatgtttg 1680 tgatatttgt cctttagcaa agcaaactcg ttcatctttt gtttccagtt yaataaaatc 1740 aattgcacct tttgatttga tccactgtga tatttggggg ccgcaccaaa cacataccmc 1800 ctctggggca cgttacttcc tcaccattgt agacgacttc actcgattca catgggttca 1860 tctcatgcga tttaaatccg acacacaaac cataatccac tcgttctttt cttgggtgaa 1920 aacacagttt aatcgtgaca ttaaaaccct tcgtgcagac aatagggggg aattcatatc 1980 tctgcgatcc ttcttagaca ctcatggcac attttttcaa cacacctgtg cccacacccc 2040 tcaacagaac ggagtcgttg aacgcaaaca ccgtcacctt ttaaatgttg cccgagcctt 2100 acgctttcaa gctaacctac ccttaaaatt ctggggggag agtgtacaaa ctgcctacta 2160 ccttatcaat cgccttccaa cacccctgct ttcccatcaa tctccctata aactcttgca 2220 taggacacca cttgtctaca ctcatcttcg agtttttggg tgtttatgct atgctaccaa 2280 ccttactccc tcacacaaat ttaatgctcg tgctcgtcgc tgccttttcc tgggatatcc 2340 ccttggtcag aagggctatc gtgtttatga ccttgatagc aagcgcattt ttacctctcg 2400 cgatgtcacc ttccatgaac atcttttccc tattgctaac ttaccaccag aacctgacca 2460 caatacccca gtcttacctg ttccccatga cgaccccact cctgcacctt cagacctcct 2520 tcccactatt gatctacctg cctcactcac tccctccctt cctcctgaca tacctccccc 2580 aaccccagcc actactacct cgccaactcc tgcaccatcg tctccttcga tgcccctcat 2640 tccccttcgt cgctccgaac gcattaaaca accacctgcc caccttcgtg actatcagac 2700 ccatcatgct gctttgcttc agcacaacgt caactcttcc accatgtccg gcacacgata 2760 tcctcttcac cggtatgttt cttatgctcg tctctctcct gctcatcgct cttttgttca 2820 caatgtctct cacttagttg aaccagcctc ttatgagcag gcacgccatg accctcactg 2880 gcttgtagct atgaattctg agcttgaagc ccttgaagcc aatcacacct ggactttggt 2940 tcctttaccc ctccaccaat gccccattgg atgtaaatgg gtcttcaaaa tcaagtatca 3000 ttccgacggt accatcgaac gctacaaggc tcgccttgtc gccaaagggt tcacgcagcg 3060 cgaaggtatt gattacaaag agacgttcgc ccccgttgct aagctcatta ctgtccgctg 3120 tgtcttgtcc attgctgctg ttcgcagctg gtctcttcac caaatggatg tccaaaacgc 3180 tttccttcac ggtgcactcc atgaggaagt ctatatgtta ccacctcctg gttatcgtcg 3240 acagggggag actatggttt gtcgacttca caagtcatta tacggactca agcaggcatc 3300 tcgcagctgg ttccaacgtt tttcatcaac cattcaagaa attggctttc aacagtctca 3360 tgcagactac tcattattca ctaaggtttg tggacactcc attactgtag tattgctcta 3420 cgtcgatgac atgatcattg caggaaataa tgaggaagcc attagtcaac tcaagcaatt 3480 tcttagtgga tgttttcgaa ttaaagacct cggaccatta aaatattttc tgggtgtcga 3540 agttgcacgg tccaaagctg ggatctccat ttccaacgaa agtatactct ggacatattg 3600 gaggaagctg gcttgcttgg cgtaagacct gccaaggtac ctatggaacc agatttagtg 3660 ttgacaacaa caggtgatga tgccctcaag gacccgactc gatatcgacg tttggttgga 3720 aaattaatat accttaccat tacaaggcca gatattacat atgcagtgaa taatctcagt 3780 cagttcatgc aagaaccaac actccatcac cttaaagcag cacatcgtct cctccaatat 3840 ctgaaagaag caccaggaca agggttacta tttcctacgg agaaccaact taatttgatt 3900 ggctactgtg atgcggattg ggctagatgt ccgatcacac gtcgatcagt gacaggtttt 3960 tgtatcttcc ttggtaaatc acttgtatcg tggaaaagta aaaagcaagt cacgatggca 4020 agatcttcag cagaagccga gtatcgctcc atggctgcaa ccacttgtga gcttacttgg 4080 ctgaggaatt tgttgaatga tttacgtgta aaccatcctg agccagcaag gttgttttgc 4140 gacaatcaag ctgctctaca tattgcagcg aaccctgtgt atcatgaacg aaccaaacac 4200 atagagctgg attgtcatac tgttcgtgaa aggattcaaa ggggagagat caagacctct 4260 catgtgcaga cgggacgtca aatagcagac atgtttacaa agccactgag agcacctacc 4320 ttccattcac atcttggcaa gttgggtgtt attgatatcc atactccaac ttgaggggga 4380 g 4381 // ID Copia1-VV_LTR repbase; DNA; EDCOT; 200 BP. XX AC . XX DT 13-AUG-2007 (Rel. 12.08, Created) DT 31-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia1-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-200 RA Obukhanych T. and Jurka J.; RT "Copia1-VV - LTR retrotransposon from grapevine."; RL Repbase Reports 7(8), 666-666 (2007). XX DR [1] (Consensus) XX SQ Sequence 200 BP; 53 A; 19 C; 40 G; 88 T; 0 other; tgtggaaatc cggtataatt ttgaatgatg atttgtagga tattagggaa agattgaggc 60 cccaattgtg ggtaatttgt gttttccata tttgtatttt ttcctttttt gtttgctctc 120 tgtgtatttg ttaaataggg atccgtttat gtaaaaaata cagttttgaa tgaattttaa 180 aatgattctt agtttctaca 200 // ID RAGYPSY_LTR_MT repbase; DNA; EDCOT; 3350 BP. XX AC . XX DT 07-NOV-2006 (Rel. 11.11, Created) DT 07-NOV-2006 (Rel. 11.11, Last updated, Version 1) XX DE A gypsy like novel LTR, from Medicago truncatula. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed element; LTR; Endovirus; retroposon; RAGYPSY_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3350 RA Shankar R. and Jurka J.; RT "A novel gypsy like LTR from Medicago truncatula."; RL Repbase Reports 6(11), 589-589 (2006). XX DR [1] (Consensus) XX CC This sequence is a consensus sequence of a novel LTR having very CC similar internal region to internal region of Gypsy retroposons. XX SQ Sequence 3350 BP; 1004 A; 635 C; 543 G; 1168 T; 0 other; tgttataccc tgattttgga cctaaaaata ctcgtttcaa atttcttttt taacactaat 60 atttgtcaat tttctctgtt attttactct caatctttac tctcttttta aacgtattat 120 actgcctctg tcttttctga cattacaagt catttaagaa ctctctgaaa cgtcgcatta 180 cttttcttgc actttatttc aaaaaatcat acaaaagggt attttggtca tttcctgcag 240 tggaacccat ttttgtccct gtgtttgtct ctgagtcttt tcaacttgtc tgtacaaatc 300 atcgttgatt ctttgttaaa aatcatttca aaattgcatc tgagtcaatt tgagtcagtt 360 tagtccctag gggcattttg gtcttttcct gtcaaaattt tggcagagag gtattttgaa 420 atacctcatt tcagtatttg gttcgtttta gtccttttgt tgattttatt tttggtttca 480 ctttacgttt tgtcaagtta cccattttat tccaatttta tttttatttt tattttgcat 540 tttggtcctc aaagaagtcc aaaattgctt tttagtccaa aactttttat tttacatttc 600 agtccttttt ggttaattgc agtttagtcc ttaagttttt atttttgcag aaaggtccca 660 aattcatttc aagtccaagg ccgtgccatt ttcatacaag tccaggtgtc acctttccat 720 tgggtctcaa gtacacatgt cagactataa atagtgcaca gtgccacaca aagccattaa 780 tcacacgcca actcaacaaa cacaatcaag ttttctctct cctttctgtt aggatcaaaa 840 catcaaaaat tcccaagaac acgaagaaca taaaccctaa ttttctgcag aaatcataga 900 aattcatcag aaatcaacga atttcacatc aattctcaga gattcgtgtg aatcttcatc 960 atcgaattgg agatttccct acaattccaa gtgcgagctc acattgaagc aaactcaagc 1020 actgatcaca ggaattctca cgtggatcta agaagcagga aacaagctca agcacgtaat 1080 cacagagaaa gaatcggaga agatgaagaa accaagccag taaaccgatt tattttcggt 1140 tcaaaaagca accagaaatc atcaagaaca aatcgaagtt ttccgaagaa actcagcaga 1200 atctccatta aaactcaggt aaaactcatt ttttctcttt aatggcgtta atcatagttg 1260 aacctgcatg caaacgaaca aaccagatct aaaaagtttc cagaacagaa aacgaactga 1320 accgtatgcg taagatctag atccataagg acttagactt tgcaagcaag aacaagcacc 1380 agagaagtaa caaacacgaa acgatgtaga tccttaagag tttgaacgta ctcattcaaa 1440 accctaaaaa aaaaaaaaat tcaaaaccgt atgaaaattc tccgatctac gtcgattcag 1500 gctttgtttg tgaaaatcaa tgtcagattc gtgtttaggg tttaaaaacg aacaagaaaa 1560 tgtaaaaaaa tttgaattct gggtattttg ctcgtcggaa ccctgacttc tcaccggaga 1620 agatgaagtt tccggtggaa ccttcatctt ctccggccaa caaccaccgg agaagggagg 1680 agagaggtga gagctctgag agaagagaga ggtttagaga gagaaagaga tgaaagaaat 1740 gaaataaacc ggtgtccaca tgcttatata gacgcctgaa ccggtccggt tcattttgtt 1800 ttcatcctgg accgtaggat ttagggtttt gttatttgaa tggctgtgat gctttgttcc 1860 atgtgcttga tctgtgttac catgcgctgc ttgttttgaa ccgtcagatc taggtctgga 1920 tcaatctaac gcctctgagg cctttggatg atccaggccc agtctgcatt gggttttggt 1980 ttgggcttaa ggttcctttt acgtttttgc ttttttcttg ctatttgcac ccctattttt 2040 tgctgtttga acctgtttct tgcttaaatt tttttacaaa aattcctaaa aatcctagat 2100 gtttcttgat acatttttgg tatttttatg gtgttttgca tgtaaaaaaa aatggtaaaa 2160 ttgcatgaat taattcccat gtgtttttac atttttggta ttcttttggt tatattttct 2220 tgttcatgaa acgttgacat gtgatatgga tgattgatat gcaatattgt gatgaatatg 2280 tctctgatca tgtgtccttt ttgctgtttg tggatatgat tttgtaactt tcttgttttg 2340 caaataatat gtgtttttct taaggaataa agtgccaaat ttctctatga atgtggtgtg 2400 atactttgct tgcatatgtc tctattaatt tcatgtcatg gctcgaaaca aaacctcttt 2460 caaaattgcc atgatgaggg aattatgggt cataagcatg tttaagtatc atatcaaatt 2520 ttttaggtac attttgccac tttattactt tccttttttg cctttcctat gcaatttctt 2580 tttgtttact tcctactatt ttatgcctta tgattactaa ccatttcatc tcatgtgcca 2640 tacatttcat aagcatttca caattccatt cctattcctc atagtttagg gtttatttct 2700 tttatttcaa tgttactttg gcatgtaata ttttagatag ttttcatttc tttttagatc 2760 tttgcaagac catagaatgt atttaggaca atgtaaagga ctatggacac tctaataatg 2820 tacaccgaca cgaacaccga cactcgcaca cacgttgcat gattgtcgat ttagatgtat 2880 gtttaggaat tcgacgccta gtgaaatttc tccttcgaaa taggctaaat tttccaaaca 2940 aactttggag tcaaaactcc aatgcctttt tgtgaaataa aaataaagat caaattcgac 3000 atttttcttc tatgccttac ggcttctctc ctccttttca aaaatcattt tccaagtaaa 3060 ataaaaacct caatcatctt ctcccctcat tcttcactca aataaaatat cttcttttca 3120 ataagtaagc aataaaaaat aaagcgtaga aataaactta ggagaacggt tcttatggaa 3180 taccataatc gctccgggtg cctaacacct tcccgtagcg aaaacgaccc ccgaatctag 3240 aatctaaggg ttttttctca attttgccct tcccaaaaaa aatagagaat atcaaagatt 3300 gaaaggttca agtcaaatta atggcttgac acccgaaaat cacgataaca 3350 // ID Gypsy-78_PTr-I repbase; DNA; EDCOT; 6049 BP. XX AC . XX DT 23-DEC-2009 (Rel. 15.02, Created) DT 23-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: internal DE portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-78_PTr-I. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-6049 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 187-187 (2010). XX DR [1] (Consensus) XX CC ~94% identity to consensus. XX FH Key Location/Qualifiers FT CDS 71..5011 FT /product="Gypsy-78_PTr-I_1p" FT /translation="MVRTRQGTRTEPPSLERRGGNQGAQGWQDEDPLDDTT FT SHAPVIPPETLQGEAAVAGEGRRPNQTEGVPPVAAEQQERSEAQPSTIPTG FT VPPQYVDAGLLVQIVKAVMEGMAGSATQTTPTTQIPQAAPMTGTTTDNVVP FT LVRLVKSMREMGCEPYMGEQDAEIAGRWIRKVEKTMIQISIPEGLRVNCAT FT QLLSDRAMTWWETVQLRRATETLTWSDFKTEFENQFYSRYHRKVKEQEFLA FT LRQGDMSVLEYERRFHDLSLFAPHYVPTEEHMIEKLRDGLRQDLRQGLIAL FT RFKSVRELIEAAQALEACIGESQGGHQGIGKKRDGDYFSGRPPLPKKGKSG FT VFEQYRKKGSLMLPPHQQSGGRVMVGQSHSRANSSTGTGDRKGVDYPFCVK FT CGQKHPGDCSVSPGRCFVCRGEGHRWRNCQYLGQGCHYCGGRGHYKRDCPK FT RNTGQVQSYRQPSQSHQQSVTVNRPVRSSQSGANSSRGRPRAQNDRTPGRV FT FHLTQEEVRAASDVVAGTLLMNNFNVHVLFDPGATHSFIAKRIVTKLRKGV FT EIVEKGFVIGTPMGNMVETNIVYVDVGVSLSGYETEVDLIPLELHDFDIIL FT GMNWLSKYKALIDCYAKTVTFQTPEGERMIFEGERILKPIALISVVTAQKL FT LRKGCMGYLAYILNSDDEGPRLKDIPVVKEFPDVFPEELPGLPPEREVEVS FT IDTFPGVPPIAQQPYRMAPAELNELKTQLQELLDKGFIRPSNSPWGAPVLF FT VRKKDGTHRLCIDYRQLNKITMKNKYPLPRIDDLFDQLKGARAFSKIDLRS FT GYYQMKIKEADVAKTAFRTRYGHYEFLVLPFGLTNAPALFMDLMNRVFQPY FT LDKFVVVFIDDILVYSNSFEEHEEHLRQTLQTLRDHQLYAKLSKCEFWLKR FT VTFLGHVISAEGVFVDPQKVEAVLKWERPTSVTEIRSFLGLAGYYRRFIEG FT FSLIATPLTQLTRKNKKWVWSEECEKSFQELKRRLTTAPVLTLPSGTEGFV FT VYSDASGKGLGCVLMQHGKVIAYASRQLKTHEVNYPVHDLELAAVVFALRI FT WRHYLYGSRTQIFTDHKSLKYLMSQKELNMRQRRWIELIKDYDCTIEYHPG FT KANVVADALSRKNKATLGRLTVGKERQLAELKEMGADLGINAGGGLVAQLL FT VRPTYREQILHAQFRDKEGSKIRKNVEAGVEMKFRVADDGSLMMGQRLYVP FT NDETVKRMVLQEAHESKFSIHPGSTKMYRDLKHLYWWPNMKREIAEYVSKC FT GICQQVKVEHQRPAGPLQPLQIPEWKWEMITMDFVSGFPKGRKGNDAIWVI FT VDRLTKSALFLPIKMTDSVDKLAKIYINEVVRLHGIPVSIVSDRDPRFTSR FT LWPSIQHALGTRLDMSTAFHPQTDGQSERVIQVLEDLLRACVLEFGGNWEE FT HMALVEFTYNNSHQATIGMAPYEALYGRRCRTPLCWEEIGDRKLYGAELVQ FT VTTEKVRTIRDRIKAAQDRQKKYADVRRRPLEFSTGDQVFLKVAPWKNMLR FT FGLKGKLTPRFIGPFKILQRVGPVAYKVDLPPQLAKVHDVFHVSLLRKADV FT DPARVLPQVPVEVKEDLTLELRPIRILDQEVKELRSKKIPIVRILWRNAQI FT EEETWEREAEMRKKYPNLFELPGMEYETS" XX SQ Sequence 6049 BP; 1831 A; 1164 C; 1665 G; 1389 T; 0 other; gttggtatca gagcacttgg tctggatcct gaggatcact gataattgtg ttgttgtggt 60 gaatttcagg atggtacgca cccgacaagg gacacgaact gagccgccct ccttagaaag 120 gaggggcggg aaccaaggtg cccaaggttg gcaagacgaa gatcccttgg atgatacgac 180 atctcatgct ccggtaatac cacccgaaac cttgcagggg gaagccgcgg tagcggggga 240 aggccggagg cctaaccaga cagagggagt acccccagtt gcagcagagc agcaagaaag 300 atcagaagca caaccgtcaa ctattccaac tggtgtgccc ccgcagtatg tagacgcggg 360 actccttgta caaatagtta aagcagtgat ggagggcatg gctggttcgg cgacacaaac 420 aactcccacc acgcagattc cacaggcagc ccctatgact ggcacgacca cggacaacgt 480 ggtgccactg gtgcgactag tcaagagtat gagggaaatg ggctgtgaac cgtatatggg 540 ggaacaagat gcagagatag ccgggagatg gattaggaag gtagaaaaga ccatgattca 600 aataagcata cccgagggtt tgagggtaaa ttgtgcaacc cagttactgt ctgatagggc 660 catgacatgg tgggaaacag ttcagctgag gcgtgcaacc gagacactaa cttggagtga 720 cttcaagaca gagtttgaga atcagtttta ttccaggtac catcgcaagg tgaaggaaca 780 agagttcttg gcattaagac agggtgatat gtcggtattg gagtacgaaa ggaggttcca 840 tgatctctca ttgttcgccc cacactatgt gccgacagag gaacatatga ttgagaagtt 900 gagagatggt ttgcgacagg atttgagaca aggattgatc gccttgcggt ttaaatccgt 960 gagggagttg attgaggctg cacaagctct ggaggcttgt attggagaaa gccaaggggg 1020 acatcagggt ataggcaaaa agagagatgg ggactatttc agcggcagac caccactccc 1080 gaagaaagga aaaagtggag tgtttgagca gtacaggaaa aaggggagtt tgatgttacc 1140 gccccaccaa cagtcaggtg ggagagtgat ggttggacag tcgcactcga gggcaaactc 1200 ttcaactggg accggtgacc gcaagggtgt tgactatcct ttttgtgtaa aatgtggaca 1260 aaaacaccct ggggactgct cagtttcccc cgggcgatgc tttgtgtgca gaggagaagg 1320 tcataggtgg aggaactgcc agtatctggg tcaagggtgt cattactgtg gtggaagagg 1380 tcattacaag agggactgcc ccaaaaggaa cactggacag gtacagagct ataggcagcc 1440 cagtcagagc caccaacagt cagtcaccgt gaataggcca gtgagatctt ctcaatcagg 1500 agcaaactcc agtcgaggga gaccgagggc acaaaatgat cggaccccgg ggagggtctt 1560 ccacctgaca caggaggagg tcagggctgc atcggatgtg gtggcaggta cactactaat 1620 gaataatttt aatgtgcatg tgttgtttga tccgggtgcc acccactcat tcattgctaa 1680 gagaattgtc actaaactga gaaagggagt agaaatagta gagaaggggt tcgtaattgg 1740 aactccaatg ggaaacatgg ttgaaacaaa tattgtgtat gtggatgtgg gggttagtct 1800 atctgggtat gaaacagaag tagacttgat tcccttagag ctgcatgatt ttgacataat 1860 cctaggcatg aattggttga gtaaatacaa ggctctaata gattgttatg ctaaaactgt 1920 tactttccaa acacctgagg gcgagaggat gatttttgaa ggagagagaa ttctcaaacc 1980 gatcgcctta atatcggtgg taacagccca aaaactttta agaaagggat gtatgggata 2040 cctcgcatac atcttaaact ctgatgatga aggtccacga ctgaaggata ttcctgtggt 2100 gaaggaattc ccagatgtgt ttcccgaaga actaccggga ctacccccgg agcgagaggt 2160 agaggtgtct atagacactt ttcctggagt cccacccata gcccaacaac cgtaccggat 2220 ggctccggca gaactgaacg agttaaagac tcaactacag gaattgttag acaaagggtt 2280 catacggccc agtaattctc cttggggagc accggtccta tttgtaagaa agaaagatgg 2340 aacccataga ctttgtattg actatcgaca gttgaacaaa ataacaatga aaaacaagta 2400 tccgttacct cggatagatg atttgtttga tcaattaaag ggagcgaggg cattttcgaa 2460 gatagatctg agatcagggt actatcagat gaagattaaa gaagcggatg tagcaaagac 2520 cgcatttaga actcgttacg gacactatga atttttggtg ctaccgttcg ggttgacgaa 2580 cgccccagcc ctcttcatgg acttgatgaa tcgggttttc caaccatacc ttgataagtt 2640 tgtggtggta ttcattgatg atatactggt gtactcgaat tctttcgagg agcacgaaga 2700 acacttgagg cagaccttac aaaccttgag agatcaccag ttatatgcaa aactgagtaa 2760 atgtgaattt tggctgaaga gagtgacgtt tctgggacac gtcatttcag ccgaaggtgt 2820 tttcgtagac ccccaaaaag tcgaagcagt cttgaaatgg gaaagaccga cttcggtcac 2880 cgaaatacgt agcttcctgg gacttgcagg atactatcgg agatttatcg aaggtttttc 2940 cctgattgca acccctttga cccagctaac taggaagaat aagaaatggg tgtggtcgga 3000 agaatgtgag aaaagcttcc aagaattgaa gaggaggctc accactgctc cagtgttaac 3060 ccttccctca gggaccgagg gttttgtggt atatagtgat gcctcgggga agggattggg 3120 gtgtgttttg atgcaacatg ggaaggtgat cgcctatgca tcaaggcagt taaagactca 3180 tgaggtgaac tacccggtgc acgacctgga gttggctgct gtagtatttg ccttgaggat 3240 atggagacac tatttgtatg ggtctcgaac ccaaattttt actgatcata agagcctgaa 3300 gtatctgatg tcgcaaaagg agttgaacat gcgacaaaga aggtggatag agctcattaa 3360 ggattatgac tgcaccatag aataccaccc ggggaaagca aacgtggtgg cagatgccct 3420 cagtcgcaaa aataaagcca ccctgggaag gttaacagtg ggaaaggagc ggcaattggc 3480 ggaattgaaa gagatgggtg cagatttggg cattaatgca ggaggtgggt tagtagccca 3540 actattggtg cgaccaacgt atcgggaaca gatactacat gcccaattcc gtgacaagga 3600 ggggtccaag attaggaaga atgtggaggc cggggtagaa atgaaattcc gagtagcgga 3660 tgatggatca ttgatgatgg gacaacggtt gtacgtgcct aatgacgaaa cagtcaaacg 3720 gatggttcta caagaagcac atgagtccaa gttctccata catcctggca gcactaagat 3780 gtatcgagac ctgaaacacc tctattggtg gcctaatatg aaaagggaaa tagctgagta 3840 tgtgtctaag tgtgggatat gtcaacaagt caaggttgaa caccaaaggc ctgcgggacc 3900 attacaacca ttacaaattc cagaatggaa gtgggagatg atcaccatgg atttcgtgtc 3960 aggatttccc aaagggagga aaggaaatga cgcgatatgg gtcatcgtag atcggttgac 4020 gaaatccgca ctattcttgc ctataaagat gaccgactcg gtggacaagc ttgccaagat 4080 ctacataaac gaggtggtac ggctccatgg gattccggtg tccattgtat cggatcgaga 4140 tcccaggttc acctctcgac tttggccgag catacaacat gccttgggga caagattgga 4200 catgagcact gcgtttcacc ctcaaacgga tggccaatca gaaagagtca tccaagtctt 4260 ggaagaccta ttacgggcat gtgtgctaga atttggagga aactgggagg aacacatggc 4320 attggtggag ttcacgtata acaatagtca ccaagccaca atagggatgg ccccatatga 4380 agccttgtat ggtaggaggt gcaggactcc tttatgttgg gaggaaattg gggaccggaa 4440 gttatatggc gcggagttgg tccaagtcac cacggagaaa gtgagaacta tcagggatcg 4500 catcaaagcc gcacaggata gacagaagaa gtatgctgat gtgaggagaa gacctctcga 4560 gttcagtacg ggggaccagg tgttcctgaa ggtagcccca tggaagaaca tgttacggtt 4620 tggattgaaa gggaagttaa ctccccgctt catcggaccc ttcaaaatct tacagcgagt 4680 ggggccagta gcctacaaag tggacttgcc cccacagtta gccaaggtcc atgatgtgtt 4740 ccatgtctcc ttgttaagga aggctgacgt ggaccccgcc cgagtcctac cccaggttcc 4800 agtagaagtc aaggaagact taacactgga attgaggccc ataaggatac tagatcagga 4860 agtgaaggag ctacggagca aaaagatccc catcgtcaga atcttatggc gaaatgctca 4920 aatagaagag gaaacttggg agagggaggc tgagatgagg aaaaagtacc ccaatttatt 4980 tgaactacca ggtatggagt atgaaacctc ttaaatttcg aggacgaaat tcatattaag 5040 ggggggagaa tgtaaacacc caaaagaaaa tatatatata tatatataat atattatatt 5100 gtattatata gaattgacga cgcagttttc gctgccgatt tctggatcgg cagcgacgca 5160 gttttcgctg ccgatttctg catcggcagc gacgcagttt ttgtttttaa aaaaaattaa 5220 ttaacttaag gagctgggag ggaggggtaa aaccggtttt agatagacca aaacaaggat 5280 aagaacacat ctaaaccaac ccccaaacaa cccacctcat ttgatgggga gtataaatac 5340 aaggaggaga gagaggatga tccatcctct tcccaaacag cagctgcatg tcgttcttcc 5400 cttcctcttt cacaacagaa acctaaacca aaccagtaga gagtgctttg tgaacgtgtg 5460 agggaaagat gagaccttga gagaagattg gacagctgcc tagagggaaa ggaaaaagag 5520 ggctggaaaa cgtgagagga agaagaagga ggagaaccag caggagaaga gaaagaatag 5580 tgtcaaacct tcctcaaact tagttagatt cgaaaggtat gggtcatgaa actcccttcc 5640 tcttctcctt aagaccagaa acggaaatga agaagaaaac cctaagaaaa ttgacctaag 5700 acctaagcta gctgtgaagg aaactgaaat taactaggag gacaaggaaa cagaaatgaa 5760 atgaagccaa tttcagaaca tctaacaaag aaaaatgaat aaaatggaaa taacaaatca 5820 tggtagaggg ctggctttaa ctatggggtt ggccagcatg catgtgtgtg ttctgctggg 5880 atttgttgaa ggattatgtg ctgaaattga tggtttcaat gtgtgtgttc tgctggaatt 5940 tattgaaaga ttatatgctg taattgatgg ttttcaatgt gtgtgttctg ctggaactta 6000 gtgacagtgt atatgctggg gttgttacag catgtgtggt gtgtgttca 6049 // ID TONT2-LTR_PV repbase; DNA; EDCOT; 280 BP. XX AC AY341443; XX DT 04-JUL-2005 (Rel. 10.07, Created) DT 01-AUG-2005 (Rel. 10.07, Last updated, Version 1) XX DE Copia-like retrotransposon from common bean (long terminal DE repeat). XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; TONT2-I_PV; TONT2-LTR_PV. XX OS Phaseolus vulgaris OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Phaseolus. XX RN [1] RP 1-280 RA Jurka J.; RT "Copia-like LTR-retrotransposon from common bean."; RL Repbase Reports 5(7), 193-193 (2005). XX DR Genbank; AY341443; Positions 6329 6608. XX CC LTRs are 99% identical. ORF first identified by automatic CC screening in Genbank annotation. XX SQ Sequence 280 BP; 79 A; 63 C; 73 G; 65 T; 0 other; tgttgtaaaa aagaacctaa tatagcaaaa caaaaacgaa aaacagagtg tgtgaaacgg 60 aaatggtttg tgcgtggaaa accctagctt tttgattctg ttggaggaga tctcggaagt 120 gcagtagaaa ctggaactta ccgagatctt cgcactcgtt gccctctcca ccctggatcg 180 tggccgcatg actgggaaag cactaccttg cccttcgaaa gttgaagaac gttgctccgc 240 ttccgcgcac gctgtgccgc agttgcaagg ttggacggaa 280 // ID Copia49-PTR_I repbase; DNA; EDCOT; 4499 BP. XX AC scaffold_3530; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia49-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4499 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4499 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 276-276 (2007). XX DR Genome; scaffold_3530; Positions 5112 614. XX CC Positions [1757-2257] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 74..3823 FT /product="Copia49-PTR_I_1p" FT /translation="MASDKTESSSVPVIQVQSENSSFSTNVTLTESNYDVW FT SQIMEMQIAGREKLEYLVSNTIPEKTDPSYAKWYAENQKIKGWLLTSMSPE FT IMKRYLRLPTAHEIWNALAKAFYDGADESQLFTLNQRAFSTKQVGRPISTY FT YGDLVEIFQELDHRDKIVMKDPDDVIAYKKSVERLRVHIFLNGLDEEFEQI FT RGEILRRDSALDLEETYAYVCRDSIRRNTLNGEPGHSEPSAMIARRSKYQR FT PQNLKPDRASGSLNHNHSIGSQNRSYEIRAARPERMCTHCGETGHTKLCCY FT ELIGYPEWWDFSKAPRKRNLKANPHVSVAVAEPNHMFGKKSGKDSSSGAIT FT GNARDTAENTGADAVNAGKAFHTSTSVRNSEWIIDSGATNHMTFNNNIQTI FT QPSNHHEIFTANGTPSSVSGEGTVTLTKNLSLESVLIVPSLNHNLLSVAQI FT TCALMCVVIFWPNLCIFKDIQTRKTIGYGTRRGKLYYLDLIPASSNQLAQV FT FSTNTANEHQKSEIWLWHRRLGHASFGYLQKLFPQLFSQLIVSDFKCDVCE FT RAKSHRVSFPISMNKSPAPFMVVHSDVWGPTNTHSLNGSRWFVSFIDDHTR FT MTWICLMKSKSEVSSLFQQFHKMIATQYQTNIQVIRTDNGGEFINHSLKDY FT LNTHGIIHQTTCPYTPQQNGVAERKNRHLLEVVRAFLFEAHMPTSYWGEAV FT TAGAYIINRVPSSSLQFQTPFEVLHRLVSAPTMPNLPPKVFGCVAYVHLHK FT GLRTKLEPRGLRCVFVGYALHQKGYRCYHPPSRQLYVILDVVFHETTMYYS FT SQTKENDEVQIATKPTDNVDIIAHGNQLIDTLDSLETNEECPVNENTEEHQ FT DREEYTSENGPEIVDGNQDTLEGPTASHSVPVNQLSSPVDSRLESHDIHPV FT ESLKELPNRVTRGKPKVNYEPTLHSKLKYPMNNYVSYHRLSNEKMAFVHQL FT SVVSIPNNVQEALVDPRWREAMNEEMKALQKNSTWDIVDLPKGKKPVGCRW FT VFTIKYKADGTIERCKARLVAKGYTQTYGIDYMETFSLVAKLNTVRIILSL FT AVNLDWPLHQFDVKNAFLHGTLQEEVYMELPPSCKQQTEGNKQVCRLRKSL FT YGLKQSPRAWFGRFTNFMKTVGYTQSNSDHTLFLKHNEKHITILIVYVDDI FT IVTGDDSGERKRLHEHLAREFEMKDLGELKYFLGIEVSRSDKGIFLSQRKY FT VLDLLSETGMTACSPASTPMEENLKLHGDSNQVPTNKERY" XX SQ Sequence 4499 BP; 1404 A; 890 C; 933 G; 1272 T; 0 other; gagcaggttt attatctgct ctttatatca ccacacaaac cttataaatc ttacgaatcc 60 tccttctcgt accatggcca gtgacaaaac cgaatcatca tctgttccag ttatccaggt 120 tcaatcagag aattccagtt tctcaaccaa tgtcaccctt actgaaagca actatgatgt 180 ctggtctcaa atcatggaga tgcaaattgc aggacgagag aaacttgaat atcttgtaag 240 caacacaatc ccagaaaaaa ctgatccatc ctatgctaaa tggtatgctg agaatcaaaa 300 gattaaagga tggttgttga cctccatgtc accagaaatt atgaaacgct atcttagact 360 gcctactgca catgaaatct ggaatgctct agccaaagca ttctatgatg gggcagatga 420 atcacagcta tttaccttga accaacgtgc gttctccacc aaacaggttg gtcgtcctat 480 ctctacctat tatggtgatt tggtagaaat atttcaagaa ctagatcatc gtgacaagat 540 tgttatgaaa gatcccgatg atgtcattgc ctacaaaaaa tcagttgaga gactgcgggt 600 gcatattttt ctgaatggcc ttgatgaaga atttgaacaa attcgtggtg agatcctaag 660 gagagattct gcactagacc ttgaagaaac atatgcttat gtttgtcgtg actctatccg 720 tcgaaacaca ctgaatgggg aacctggaca ctcagagcca tctgctatga tagctcgccg 780 aagtaagtat caacgaccac agaacctgaa accagatcga gcttctggtt cactgaatca 840 taatcattca attggatcgc aaaatcgcag ctatgaaata agagctgcac gaccagaacg 900 catgtgcact cactgtggtg aaactgggca cactaagcta tgctgctatg aattaattgg 960 atatccagaa tggtgggatt tttccaaagc accccgtaag agaaacttaa aggcaaatcc 1020 tcatgtgtct gttgctgtgg cagaaccaaa tcatatgttt ggcaagaaat ctgggaaaga 1080 ctcctcttct ggtgctatta ctgggaatgc acgcgacact gctgagaaca caggtgctga 1140 tgctgtaaat gcaggtaagg cttttcatac ctccacttct gttagaaata gtgaatggat 1200 aattgattca ggtgccacaa atcatatgac gtttaacaat aatattcaga ccatacaacc 1260 ctcaaaccac catgaaattt tcacagccaa tggaactcct tcttctgtgt caggagaagg 1320 cacggttact cttacaaaaa atctgagttt agagtcagtt cttattgttc cgagtctcaa 1380 tcataattta ttatctgttg ctcaaataac ttgtgccttg atgtgtgttg taattttttg 1440 gccgaacctt tgcatattca aggacattca aactcggaag acaattggtt atggtactag 1500 gagagggaag ctctactacc tggatctgat tccggcaagc tcaaatcagt tggcacaagt 1560 cttctcaact aatacagcta atgaacacca gaagtctgaa atttggctat ggcataggcg 1620 tttaggccat gcatcctttg gatatttaca gaaattattc ccacaattat tttcacaatt 1680 gattgtttca gattttaagt gtgatgtatg tgaacgtgct aaaagtcatc gtgtttcatt 1740 tcctattagt atgaataaaa gccctgcacc ttttatggtt gttcactcag atgtatgggg 1800 accaacaaac actcattctc taaatggatc acgttggttt gtttcattca ttgatgatca 1860 cacccgcatg acttggattt gcttaatgaa atcaaagagt gaagtgagtt ctttattcca 1920 gcaattccac aaaatgatag caacacagta tcagaccaat attcaggtga tcaggactga 1980 taatggggga gagtttatca atcacagctt gaaagattac ttgaacacac atggcattat 2040 tcatcaaaca acttgccctt acacccctca acagaatggg gtggctgaac ggaaaaatcg 2100 tcatctcctt gaggtcgttc gtgccttctt atttgaagct cacatgccta ctagttactg 2160 gggagaagct gttactgccg gagcatacat tatcaacagg gtaccttcta gttctctgca 2220 attccaaacc cccttcgagg ttctccatcg ccttgtaagt gctcctacaa tgccaaactt 2280 acctcctaaa gtttttggat gtgtagctta tgtacatctt cataaaggtt tgagaactaa 2340 gttggaacct cggggacttc gatgtgtgtt cgttggctat gctctgcacc aaaaaggcta 2400 tcgatgttat caccctcctt ctcgccaact ttatgttatt ctggatgtgg tcttccatga 2460 aactactatg tattattcat ctcaaactaa ggagaacgat gaagtgcaga tagcaactaa 2520 gcctacagac aatgtggata tcattgcaca tggtaaccaa ctgattgata ctttagatag 2580 cttggagact aatgaagaat gtccagttaa tgagaacaca gaggaacacc aggacaggga 2640 agagtatacc agtgaaaatg gtccagaaat cgttgatggt aaccaggata ccttggaggg 2700 gccgacagct tcccacagtg taccagttaa ccaattgtct tccccggttg attccagact 2760 tgagtctcat gatattcatc cagttgagtc cctaaaagaa ctacctaatc gagtcacaag 2820 aggtaaaccc aaggtgaact atgaaccaac ccttcactca aaactcaaat accctatgaa 2880 taactatgta tcctatcata gattgtcaaa cgaaaaaatg gcatttgtac atcaattatc 2940 cgttgtatct attcctaaca atgtgcagga agccttggtt gatcctagat ggagggaggc 3000 aatgaatgaa gaaatgaaag cccttcaaaa aaactcaaca tgggacattg ttgacttgcc 3060 gaaaggaaag aaacctgttg ggtgtaggtg ggtcttcacc attaaataca aagctgatgg 3120 aactattgaa cggtgcaaag caaggctggt agccaaggga tatactcaaa catatggaat 3180 tgattatatg gagacttttt cactggtggc caaacttaat actgttcgta ttatactatc 3240 tctagcagtt aatcttgact ggccgctaca tcaatttgat gtaaagaatg catttctaca 3300 tggaactctc caagaagaag tatatatgga attacctcct agctgtaaac agcaaacgga 3360 aggtaataaa caggtctgca ggttgagaaa atccctatat ggtttaaagc agtctcccag 3420 agcgtggttc ggaaggttca caaattttat gaagacagtt ggttacacac agagtaactc 3480 ggatcacact ttattcttga agcataatga aaaacacatt acaattctca ttgtgtatgt 3540 tgatgatata atagtaaccg gagatgattc aggagagagg aaaagattac acgagcacct 3600 tgcccgtgag tttgagatga aagaccttgg agagttgaag tatttcttgg gcattgaagt 3660 gtcacggtca gataaaggta tttttctttc acaaagaaaa tatgtcttag acttactaag 3720 tgaaacaggt atgacagcat gcagtccagc tagcactcct atggaagaga acttgaaact 3780 acatggtgat tccaatcaag ttccgactaa caaagaacgc tattagaggt tggttggaag 3840 gttaatgtat cttgcacata ctcgacctga tttagcttat tcattgagtg tggtcagtca 3900 atttatgcac tctccaagcg aagaacacat gaatgttgtc acccgtatct tacgctactt 3960 gaagtcgtct ccaggaaaag gaattttgtt cacaaaagga cacaatttgg atgttaatgg 4020 ttatacagat gctgattggg ctggttctat tcaagatcga cgttctactt ctggttattt 4080 cacgtttgta ggaggaaact tggttacatg gcgaagtaaa aaacaggagg tagttgctag 4140 atcaagtgct gaggctgaat atagagggat ggctaaagct atatgcgaat tgttgtggat 4200 tagaaatctg atgatagatt tacatattaa gcaagtcaat cctatgaagt tgtattgtga 4260 caacaaggca gcatgtgata ttgctcataa tcctgttcaa catgatcgta ctaaacatgt 4320 tgaagttgat aggcatttta tcaaggaaaa gctagaagaa aagctaattg aagttcctca 4380 tgttcgatct caagatcagc tcgctgatat actaaccaag gcactgtcaa accacgcgtt 4440 tagtacaatt ctcagcgaaa ttggaatgag tgacatctac gcaccaactt gagggggag 4499 // ID HELITRON1MT repbase; DNA; EDCOT; 14080 BP. XX AC . XX DT 16-DEC-2006 (Rel. 11.12, Created) DT 04-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE HELITRON1MT - helitron transposon. XX KW Helitron; DNA transposon; Transposable Element; HELITRON1MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-14080 RA Jurka J.; RT "HELITRON1MT: Helitron transposon from barrel medic."; RL Repbase Reports 6(12), 624-624 (2006). XX DR [1] (Consensus) XX CC The sequence is relatively new. It contained a transposon CC insertion which was removed. Therefore, it is a processed CC sequence labeled as "consensus" rather than an original sequence. XX FH Key Location/Qualifiers FT CDS 6066..6959 FT /product="HELITRON1MT_1p" FT /translation="MIAALQKMLDENNVHAKSFRMARDRLSEGDVQNLKLK FT LISERTTDGRIYNQPTVSEVAALILGDVDYAPRRDIIMETQCGELQRIDEF FT HPAYLAYQYPLLFPYGEDGYRDDVMHRDKKTGKKPKRVHLTIREWLAFRLQ FT SRLFEPMTILCARKLFLQFLVDCFTMMEADRLSWLRKNQSKLRVGKYKSLS FT ENQNKDQPESSKQGKRVVLPSSYTGGRRYMDQLYFDAMAISSAVGFPDLFI FT TFTCNPNWPEIQRYVTSKGLKPHDRPDIIARVFKIKFDQLLKDLTKKHLLG FT KVIACE" FT CDS 8636..10189 FT /product="HELITRON1MT_2p" FT /translation="FIILTQILLIFETDEQRNIYHKIMSSVSKEKGGVYFL FT HGYGGTGKTFMWRTLAARIRSRGKIVLTVATSGIASLLLPGGRTAHSKFKI FT PVPAFENSSCNIDGTSELAQLLKMTKLIIWDEAPMAHRFCFEALDRTLRDI FT MSSDKIFGGKVVVFGGDCRQILPVIPRANRSDIINATINSSYIWDSCEVLT FT LTKNMRLQQNAMSSDNQELKNFSDWLLKVGEGKLSEPNDGIVEIDIPAEFL FT IHDFDNPIQAIFQSTYPDFLNYYNDPQYLQSRAILASTIECVEEINDYILS FT LIPGNFSNEYITLFMYLHLKEKHDSNPYLLYCIGEEQEYLSSDEIDRSEIN FT DECQSFDILTPEFLNSLRCSGLPGHKLKLKVGTPIMLMRNIDQSMGLCNGT FT RLIITRMANHVLEAKIMSGTNIGSMTYIPRMDMSPSQSPWPFKLTRRQFPI FT IVSYAMTINKSQGQSLDSVGLYLPTSVFSHGQLYVAMSRVKSKAGLKILIH FT DKDKIPLSTTMNVVYKEVFENL" FT CDS 11430..11819 FT /product="HELITRON1MT_4p" FT /translation="NYAEVDQRFVNKNHHCLRGTWKLLNEEGGFHELKFNK FT NSYIPTITDGWAEIKEYHEIPDNAEVVFSFYDIDLFAICMLREIDDPKTLP FT KFHSRSLLPKETFFFDQGVNDMLLKRPTIVKFINYIIITIHF" FT CDS 12947..13672 FT /product="HELITRON1MT_3p" FT /translation="IICELDPLFVAEYFDELQEQWMLQDGIGNCHQVEFNK FT ILTIPILTTGWHQFRDFYHITLNPLMSFTYLGHSVFQIKIFDGSTPKNEYP FT RYHRLTTCITRDLTYQLTVPENSIVSSKLVSLYIFIFYFLILLITDSILYN FT SINISLCYIISLVLQILPTDLGNFLQAKNHEYLRLCGTANNVTICKLLFIN FT DPQTNTTIVIIGSGWRRFCLSNRIAPGTLLEFKCDSVMAKNIIIVFRLTRQ FT Y" XX SQ Sequence 14080 BP; 4599 A; 2378 C; 2317 G; 4786 T; 0 other; tcaacttaca atatatgaaa ggaagtaact accattttta cttatttacc catgcctgat 60 tttgcagtaa atttttcact taccatttac aaggttatat atgtctatta tggctgtcaa 120 aaccactttt ggactaatta gtgcaaatta ctgcagctac tccctattgt ccaacggcta 180 tacaattctc cctcctatta tacccttttt tcttcattga gaaggaaacc aaactgttca 240 ccatcatatc agttgcagtg agataaaact actccattat tgtatatttt cactctctct 300 taactttcaa tattcttctc agaatcaaac cggtcaccgc aagcatcttc taaaatctgc 360 tttcctcttc taaaatcgat ccaactgcct ccctccaagg tatgaaaaat caatttcgtt 420 ttgtttcctc cgtattccgc tttcctttcg tgatgcatgt tgattgttac acatttattt 480 ggtgattttc aatctatttc atgaagaaca tttagatctg taaaagtata atggttattt 540 ttcttcttct ttttgtcatt ttcgtttatt aatggttgca tgtaagttta agtgtttcaa 600 agttttcatt tatgagttaa aaagtttgta aaagccttta tttggatttt ttggtgtgtt 660 tattaatggt ttttgttgta atccttcaaa ctccttcagg agctgtgtgt gtttttggtt 720 caagctatca tttttaaaac ttaatccttt gtaaaagtta tgatctttca tcaatctttg 780 tgtttttttg gtctgtggcc ggttgtatgt ttcatgatga gcagatgata gttgtttgat 840 gattttgctg gatttatgaa caatctgaat gtctatacgt ttctttatat aatcatcgat 900 gaaagttgtt tttcatattg tgaactacac taatctatgt aagcccactg ttaggatgaa 960 caagggaaag aagattgcta ttactcgtcc ttatgacaat gtgaaggatg tgaatgactc 1020 caaagatgtt tggagtcttg ctgtcagggt catggatctt tggtgtgtta ctggtaagta 1080 cagacaggag cagtacttgg agatggtaat tgctgataag gaggtgatat tctattcctt 1140 aaatacatta ttttaaatac tgcattttta gtaagaatga ttcaagatta agacaagata 1200 tatttatgca gaatgacatg atccagctga ctgttccata tgaggaactt gctaaatgga 1260 aagaaatctt gaaggagaac aatacttata caatgctaaa ttttaaggta ttgaaaaacg 1320 atgttgcggt caaagcttcg actcatcctt tcagacttgc agtttcagga gcaaccatta 1380 tcaaaccagt tgattttcct accatccctt tagcctcttt cagatttaaa gactttggag 1440 agattctggc tggaaactac aggaatgatc tgctcatagg ttaatatttt agtgctttct 1500 ctgttattgt gcatatagat gtaccaacac ttatattttt tgtgtgtgtg tgcttgccag 1560 atgtcattgg agctttccaa gatattacta atacaaataa aaagggaaca atcataagat 1620 cagtcacttt tcttcttaag gatgctaggt ggtttttagt taaacttatt aatttatcca 1680 tattctaagt atatactaac tttatttgat atcatgcgta taaatacagt ggcctaatga 1740 ttcatgccac actttgggat gagtttgcaa agcaattctt tgatgctttt aaccaggcaa 1800 atggacctga aacaatcttc attgttctca agcatgtgag ggctagagaa gcacaaggtt 1860 cgcataataa tccttaatct atttattgtt atgcaagtgt ttacaccata gttataatcg 1920 taatactgtg tcttgatgtc tattttggct gttaggtatt tatcctttgt gtgtcaccaa 1980 tacctggtct ggaactaagg tcataatcaa tgctgagatt cctgaaattg ctgagtttaa 2040 gactaggtat gttttacaca attttgctta cacaataaat tttcgagaac atttgttact 2100 atgtttttaa atacttcaac acagatttgc agaacttcca attgatgatg tcaatgcaag 2160 ccaacaattg tcacaactta cccaaggatc tcagataact caacaagggg atatcatgaa 2220 taaggctcat tttctcactc tttctgaggt caatcatgtg atgcatgtaa gatattattc 2280 ctattatcaa caatatcaat attgttttga actattgtat aactgttttg gttattgttg 2340 tatgtttaag gaaaccattt gtgtaactat tgctgaaatc aaaaagatca atgccaacaa 2400 atatggatgg atctatgatg gatgcaattt ttgtactaaa ggtgtgagga tggataatgg 2460 ccaactcaaa tgtagaggaa accatattaa tgatgaagca aaacccaggt aggtagagtt 2520 gatatttata agaatttgtt agtatggtta tagttgcaca taagtttcat ttacctcaga 2580 ttcaatatta ttcgatcggt catataagtt atgcaattat ctaactttaa cattaactaa 2640 ttagatgagt tacacattca tattaaagcc taaaatatga gcattattat tttcaggttt 2700 agggttgagg ttgaagctgt ttacaagaat gataaggcaa agtttttgtt atgggacaat 2760 gatgttgcat ccataatagg aatgtctgct caggagctga aagaacagtt ggttgaggtt 2820 aacattttcc attacttcta aatatagtgt tgttcctttt tagatatgtg tctaatgttt 2880 atgagttcat agattggtca gtttcatcca acggcttatc ccccaattct ggatcaagtt 2940 gtgtgcccac agaaggtttt caaaatcaaa gcttgtcctg aatcaagtcc gtactctgtt 3000 attcaaatta gtgacaatga agggcttttg aaaaatcttg aaaaacaatt tggattggga 3060 gaggtatata acctcgtgat tgtagtcaat attttgaagt ttctatacaa atatatttta 3120 aattttttcc atcaatgatt gtaggccagt tcaaagcttg cccttcttga tgaggtgaag 3180 gttgatgaag tgaaggagtc tcaagagtta gttgttgata ctttgaacac tgtaagttat 3240 ttatttgtat acatgtcatt ttcaaaatag tttttccaaa tgtttaacaa ctagcaacct 3300 acataaaata ctcaaattat agagaatcct catatattcc attgaatgat tgtgcagcaa 3360 tccctctgtg atgaaaccga tccttcctgc agttctgcga cccctcctcc caaaagaaac 3420 tcgcaggaag atgttgattg ggttggttct acacaggatg ttgaggcaac ccaactttct 3480 tcaactaagc ttgccaaaca acccaagtta gagccaaaga actaatcaaa tcaccttaac 3540 aagaacacct tttatctacc tttttttggt taactttgac ctttggttct gaacaattat 3600 ctaagtacca tatgttggtc ttttgcactt atcttggctg atgtaatata ttatctaacc 3660 tatccaaaca tcggtgactt ttgttaaatg acttcactca caagctattt tgaatgacta 3720 ctactactta tgtgcttgaa ttcaaatgca atattaacta ctacatttat aatacaatat 3780 tgactgacaa actgtttata tatatatgtg acacctaata atctttttac taaaattaca 3840 tcattatagt atcagatatt atagaacatt agttaccata tatagatgaa attatattaa 3900 ccatatttca ataatgaaca tcattaaacc ataaattctc ggttttctaa acataatgat 3960 aattatatta cacttagcca caatattaca aatatcttaa attgataaaa cgatataata 4020 atttatgcta tcttttatgt attcatatga agttaaatgt gataataatt tatgctatct 4080 tttatgtatt catatgaagt taaatgtgat tgaaaaagta gattatagat ttggtattgt 4140 acaccatact ttgctgcaat tgttgtagac tctaccaaaa attgttccct ctatatcatt 4200 tttataatag tttccagcta aactctagct ttggaagacg tgatcacaca aaaaagccta 4260 tggctgatct gacttctaga tgtaatcatg taatctatat gttgtctttc caaggctgat 4320 ttcaagtaag aaataatata aacaatttat aataataatt agatttattt tttttgttaa 4380 ttatctatag cctattttgg tgtaatctct tatttctaga ccgtgttcaa tcacatttga 4440 caagtaggag ggaaagtgaa atttttgaaa tcaattttaa atttagattt caaatgttaa 4500 ctattacaaa tatatcattt tacttagata tggagggaaa caaaaatgtt taaaagtgct 4560 aattcactca aatatcattt cacatactaa tggtttgttc ttttgcattt caactcaaac 4620 ttcaaacatg gtggatgaag gaaaagatga tgctcatgtc aaagatgcta aagcaagacg 4680 acttagaaga aaggaaattc ttctgtctag gtttcccaag agacgaaaat catctctttc 4740 agcttctaca actccattag ctgatatcac caacactaat tttacatcac agaacacaca 4800 atcatctacc aacaggaacc acaaacttat tcctccattt aggttaataa gagacaatca 4860 gaaaccaagt tcaagtgata taacctctgc aagaccgttt tcatccttca atccaaatcc 4920 ttctgtgtca aatatttctg cattatacaa acatggaaca caaactagct tgccacaatt 4980 gcatagtcct gttccaaatt caaaaaatgc atccagaggt aatccattct acagaccaaa 5040 gcatcctttt ccaatcaatt ctccaaatta tcatcgaaca aattcaacat tacagcaaag 5100 gccattttca atggattctc catctattct tagaagtcat gatctaatgt caaagagtcc 5160 gcctaaaacc acaactccaa atttcacgca accaacatca tccaacttcc agattcgaaa 5220 tccaagaaaa gcctctactt ctcatatgac tggaataaat ttattaaata gatttgagat 5280 gattgataca aatattgcat catcttcaac tgctgctgaa aatgttgaca tcaatgatga 5340 gagtgatggt tctgctaata gtgaagattt cgaagcatac aatgcagttc accagagtga 5400 gagtgaatct tctgatgaag atgatttaac aggcagtcaa ttcagagata gtgctcaata 5460 ccatactcaa ggtagttttt tgcactattt aaatttagat aaaactgaag gcagtcaaat 5520 tgattatttt ttaccacatt cctaatacat gtctatttat tgagaacatt attttagttc 5580 ttatattcaa gtatcctaat ttatataaat acatgtagga tattatgata ttggtgatcc 5640 tgtcatagag tgtcaacgat gtggagcatg tatgtggtat caagagagga aaaataaatc 5700 tagagaaagt gcaaatccta agtttggact gtgttgtggt gatggaacta ttcaattacc 5760 atatttaagg aaacctcctg cattgctcag ccatatcagg agaggtagag gaccacctac 5820 aattaggatt caaggacaag catgtcaccg aattggcagt atgattccaa tgcctggacg 5880 tcccccaaag tttgcccagt tatatatata tgatacagaa aatgaattgc aacatcggct 5940 acaaggtctc aggtacataa caagtttata gtttattaaa tattaactat gatattagaa 6000 ttgatataga atgttgatat gttttttgtt cttaatgtag caatgcaaac ctgctggata 6060 tacaaatgat tgcagcattg caaaaaatgc ttgatgaaaa taatgttcat gctaagtcat 6120 ttagaatggc tcgcgatagg ttgtccgaag gtgatgtcca aaatttgaag ttaaagctca 6180 tctctgagag gacaacagac ggacgtatct ataatcaacc tacagtttca gaagttgcag 6240 cacttatact tggtgatgtt gattatgctc ctagaaggga tatcattatg gaaacacaat 6300 gtggtgagct acaaaggata gatgaatttc atcctgcata cctcgcctac cagtatccac 6360 ttttgtttcc gtatggtgag gatgggtata gagatgatgt tatgcacaga gataaaaaga 6420 caggcaaaaa accaaagagg gttcatctca caattagaga gtggttggca tttaggttac 6480 aaagcagact ttttgaaccg atgacaatct tgtgtgcaag aaagctattt ctacagtttt 6540 tggttgattg ctttaccatg atggaagctg ataggttgtc atggttaagg aaaaatcaat 6600 ccaagctaag agttggtaaa tacaagtctt tgagtgagaa ccaaaacaaa gatcaaccag 6660 agtcatcaaa acaaggtaaa agagttgtgt taccttcgag ctataccggt ggtcgaaggt 6720 acatggatca actttacttt gatgctatgg cgatatcgag tgcggttgga tttccagatc 6780 tgttcataac ttttacttgc aatccaaact ggccagaaat tcaaagatat gtaacatcaa 6840 aaggtcttaa accacatgat agacctgata ttatagcaag agtgttcaaa atcaagtttg 6900 atcaactact taaagatttg acgaaaaaac acctccttgg aaaggtcatt gcatgtgagt 6960 agctatcaac tctctaatat actattaact cctatttata attgccatat gtttgctaac 7020 aaataatttc attttctaaa tttcagacat gtacactatt gaatttcaga agagaggtct 7080 cccacatgca caccttctta ttttcttgca cccgtcaagc aaatatccta ccccagaaga 7140 catagacaag attatttcag ctgaaatacc aagtccagat aacaatccac aattgtacac 7200 attggtgggc aatcacatga tgcatggtcc gtgtggatta gcaaataaaa aatccccttg 7260 catgaataac aaagaccgtt gtactaaatt ctatccaaag aaatttcagg aatcaagtat 7320 tgttgatcat gagggttatc ctgtctatag aagaagggat aatggcagtc atattttaaa 7380 gaatggaatt gcattggaca atcggtcagt tgttccatat aatccgcatt tgttaatgaa 7440 gtatgaagct catataaaca tggagtggtg caaccaatcc agctcaatca agtatctctt 7500 taaatacatt aacaaagggt atgatcgaat aactgcagct gttgtgtctg atggttcaac 7560 aagtagaagt ccagataaca gtcaggatga aatcaagaag taccttgatt gtagatatgt 7620 ttcaccaagc gaagcttgct ggcgcatatt taaatatcct attcatggaa gaaaaccatc 7680 tgttgaaagg ttattttttc atttgcaagg cgaacactca gtatatttca atgattatga 7740 acatatagat gatgtgatgc tgagaccttc ggttacagag tcgatgttta catcgtggct 7800 gcagtgcaat gctaagtacg ctgaagctaa gacacttaca tatgccaaat ttgtgtctaa 7860 atttgtatat gtcaaagcta aacgtacttg gacaccaagg aaaaggggtt ttgcaatagg 7920 aaggttgatg tgggtgccac caaccacagg agaattgttc tacttgagac tgatgttaac 7980 caaagtccaa ggaccaacct cttatgagga catcagaact gttaacaatg tttgttacga 8040 cacctataga gaggcatgtt ttgcaagtgg atttttgatg gatgacaagg aatacattgc 8100 tgctattaaa gaagcaagtg tttggggttc tggacttttt cttagattgt tttttgttac 8160 tttgttgatc gcaagttcaa tgcacaggcc aaaacaagtt tgggaaaaaa catggcaatg 8220 gctaagtgat ggtattcttt atgaacaaag aagattggca aacaatccag gtaaacatgc 8280 cttttttgct tatcatctct taataattat atgatcttca aatgtaaaaa tcaatttcta 8340 gatttggcat ctaattactt ttatcatgtg caaggtttaa tgcttactga agaacaaatt 8400 aaaaacttaa cattgaccga gattgaaagg cacatggaaa gaaatagaag gagtttgaag 8460 gattacaaag gatttccata tcctgaagga tacattgtcg aacaacttgg aaaccgactg 8520 atttatgatg aattaaatta caatgtcaac gagttggatg cagaatttca acaactcttt 8580 gctacattaa caggtataca ctaatttagc attttctgga acattttcaa aatagtttat 8640 tatattgaca caaattttac ttatttttga aacagatgaa caacgcaaca tctaccataa 8700 aataatgtca tctgttagta aagagaaagg aggtgtgtat tttttacacg gttatggtgg 8760 tactggtaaa acatttatgt ggcgaacttt ggcggcaagg ataaggagcc gtggtaagat 8820 tgttttgaca gttgctacaa gtggtatagc atctcttttg ctaccaggag gaaggacagc 8880 acattctaag ttcaaaatac ctgtacctgc ctttgagaac tccagctgta atatagatgg 8940 tacaagtgaa cttgcacaac ttttaaagat gaccaaattg atcatatggg acgaggctcc 9000 catggctcat aggttttgct ttgaagctct agatagaact ctcagagaca ttatgtcctc 9060 agataaaatt tttggtggaa aagttgtggt atttggaggt gactgccgac aaatattacc 9120 ggttataccc agagccaatc gctcagacat aattaatgct acaataaatt cctcctacat 9180 atgggattca tgtgaagttc ttactctgac caaaaatatg cgtcttcaac agaatgcaat 9240 gtcatcagat aatcaggaat tgaaaaactt ctctgattgg ctcttgaaag ttggcgaagg 9300 aaagctatcc gagccaaatg atggaattgt ggaaattgat ataccagccg agtttttaat 9360 acatgatttt gataatccaa tacaggctat attccagagt acatatccag atttcttgaa 9420 ttactacaat gatcctcaat acttacaatc aagagcaatt ctggcttcaa caatagaatg 9480 tgttgaagaa ataaatgact acatactctc attgattcca ggtaactttt caaacgaata 9540 tattacatta tttatgtatt tacacctgaa agagaaacat gactccaatc catatttatt 9600 atattgtata ggagaagaac aagaatactt aagttctgat gagattgaca ggtcagagat 9660 caatgatgaa tgtcaatcat ttgatatctt aacaccagaa tttttaaatt ccctgagatg 9720 ctcaggtctg cctggtcata aacttaagtt gaaagtagga actcctatca tgcttatgag 9780 aaatattgac caatcaatgg gattatgcaa tggtactaga cttattatta ctagaatggc 9840 caaccatgtt cttgaagcga aaatcatgtc aggtacaaat ataggaagca tgacttacat 9900 tccaagaatg gatatgtctc cttcccaatc cccatggcca tttaagctta ccagaagaca 9960 atttcctatt atagtttctt atgccatgac tatcaataaa tctcaaggtc aatcactaga 10020 cagtgtaggt ttatatcttc caacatccgt atttagtcac ggtcaattgt atgttgctat 10080 gtcgagggta aagagtaagg ctggattaaa gatattaatt catgacaagg acaaaatccc 10140 actgtcaact accatgaatg tagtctacaa ggaagttttt gaaaatctat gatgtaagtt 10200 aactcattcc tacaatttcg ttttaaattt atgatgcact gattttatct acctatgatc 10260 ataaactaca cttacttatc ttcttccttt ttaaatttag gtgcacaaga gattaatgga 10320 ctcacatagc aacaacgtag aagttgactt catttctttt tttggttgga cctgatatag 10380 gtgcataatg gattaatgga ttcacatagt aacaacatcc aagttcaatt gaacttttcc 10440 acagttatca tttaacttgg acattgttgc tattttgatt gaggaaacat taattcagtt 10500 tactatgtgt aactaatgac atatattatt atcttataag tgcaactata aagtttatat 10560 ttaagtcttg aaaagtggtt gcagctaaat caattcataa ttatttatat tacacatgaa 10620 gtagtataat tgcatccaaa ttccactata tgacaagtta ctgataaacg catgctacac 10680 acctgcactt tgtaagtacc caacttgcat gcataacaca tcttctatac ttgaatagta 10740 ttacaacttg aattgtcaaa tcatcaataa aaccaacatg tatgttttct tatttttagt 10800 caaagtacca gtaagatgtt ggagaaatat aggacatgtg aatggttgta gtggcaccaa 10860 acaaagtaca caaatataac acctgcagct ttgaatttgt cttattgtac accattcact 10920 actacatttc ttgaatttgt cctattgtgc acacattcac tactacattt cacaatatca 10980 cgtgcttata ccatgtgcta tccgtcaaaa gtttaagaga gcacagtcta gctatttgaa 11040 ttggcaaatc acctacattt atgttcttat ttttagtgaa atgtattgta cgatcttatc 11100 acaaggtgag agacgatttt ggtttcatcc ttaccaaatc aactacaaaa atttataaca 11160 tattcaatta tataatttaa taatatttat atttcctcta tatatagtag tgaatgcaat 11220 atcataccat tcatcaactc aaaattgcca gagaaaaatg aatgcacaac aaattataac 11280 gaaacttcaa actgatccaa ttgaggtttt ttcggtggtt cgattagcat ttcaggtttt 11340 aattcattct tcttataaat tatttttgcc tcattcatac ttcttaatca ataataacat 11400 ctatataatt tttttttatt tcaaattaga actatgctga ggttgatcaa aggtttgtca 11460 acaaaaatca tcactgcctc aggggtacat ggaaactttt aaacgaagaa ggaggatttc 11520 atgaactcaa gttcaacaaa aactcatata ttccaacaat aacagatggc tgggcggaga 11580 ttaaggaata ccacgaaatt cctgataatg ctgaagttgt gttctctttc tatgacatag 11640 atctctttgc catttgcatg ttaagagaaa ttgatgatcc aaagacatta ccgaaatttc 11700 atagtcgtag tctccttcca aaagaaacat ttttctttga tcaaggggtt aatgatatgc 11760 tcttgaaaag gcctacaatc gttaagttca tcaattatat aattattact atacattttt 11820 aatatttttt attttgtttt ctatatttta atattagtgt attaatattc cttatttcct 11880 ttaatttttt gttttctata ttttaaatat aattacatgt tctgtctaac tttaattttt 11940 ttattctaca gagaatttca aaccattttg gtgagtttct aaaaaaaaaa aagtatgaga 12000 tgcttgcttg ctgccatgat caaggaacat ttgaagcgtt tcaagtcttt atttgtaaca 12060 atgaaaaatc gactgttgaa ttgggagtgg gctgggacaa attatgccga gcaaataatt 12120 tccagccagg aatcatccga ttcaaattta ctacaaatag tcctcattgt atgtgccatg 12180 tttatcaact ctccatccat ggatcagggt ctacttcaaa tactattcag tgaaacttat 12240 gtatttatta tgtgctttta ttaaataaat taacaattat gtaatgttgt tgtgttaact 12300 agactatttt tttttatttg aacctaatta ttgtctaata ttttagtaca actcttttaa 12360 ttagcatttt atttgtgtaa cttaaacatt ataatgtttg tatattacct tatattatta 12420 acaactttta taaataatgt ttattgctta ttacacgtaa gctttaatgc agctcataca 12480 ctgttacaat atgccaacca accgtgattg actattcagc caccaacaga gacgtgttca 12540 gccttatttc agcctttgca tcttccaata agtgtaacag ttgcttttca catatcttat 12600 tctactactt ttcattatct ctacttcata catataaata gaccttccat caaaaaccaa 12660 ctcacttatc tcagtatcat atttttcatt caaattgttg taaacattta actttcagtc 12720 cactaacaat ggagtccagt gcttcctcta tcagtgaact accatcaaat caaagaaaag 12780 ggcaatccag cagagctcca ttgatgacaa ttgaatccaa tagaccttct ttcttagctg 12840 tttgcacaga ggtattacta acataactta ataaattttc tcaatatctc tttcttcagt 12900 tttatttaca tgctacacca ctaacatact tttttttatt ttctagatta tttgcgaatt 12960 agatccactt tttgttgcag aatatttcga tgaactacaa gaacaatgga tgctacaaga 13020 tggtattggc aattgtcatc aagttgaatt taacaaaatc ctcaccatac caatacttac 13080 taccggttgg catcaattta gagattttta tcatatcaca ttgaatccac ttatgtcttt 13140 cacatattta ggtcatagtg tattccaaat caaaatattc gatggttcta caccaaaaaa 13200 tgaatatcca cgttaccata gattgactac ttgcattact cgagatctaa catatcaact 13260 cacagttcca gaaaattcaa ttgttagttc aaaattggta agcctttata tatttatatt 13320 ttattttcta atattactta ttacagattc cattttatac aactctataa atatttcact 13380 atgttatatc atttctttgg tgttacagat tttaccaact gatcttggca actttttaca 13440 agctaaaaac catgaatatc ttagattatg tggaacagct aacaacgtca caatatgtaa 13500 attgctattt ataaatgatc cacaaacaaa taccacaatt gttataattg gaagtggatg 13560 gagaagattt tgcttaagca atcgcattgc tcctgggact cttctagaat ttaagtgtga 13620 ctctgtcatg gcaaaaaaca tcattattgt atttagatta actagacaat attaaaagtc 13680 tactattctt attgctaaat ttattgtgta actttgacta tcaaatgttt tcctatgtac 13740 ttcttacaat aaatttatat ttccttttct ttataattat tactactgtt gtagcagggt 13800 cttttgaaat gatcaaattg gtgcctaata aagcaacttt ccgcaagtat ctacttctaa 13860 tatatgaaag caactcattt tttcactatc cgcaataaac gtaattattt tggaacgtac 13920 cctgtcgata agcgcggcga agccgcgccg tacagcgcgg caaagccgcg ctacccgtgc 13980 tgtagcacgg gtatctcgac tagttttata taaaagagta aattttatag tttgagtcaa 14040 atgttggggt caaggtataa atgtgggggt tttgggtatg 14080 // ID Copia-59_Mad-LTR repbase; DNA; EDCOT; 256 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-59_Mad_; KW Copia-59_Mad-LTR; Copia-59_Mad-I. XX NM Copia-59_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-256 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1657-1657 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 256 BP; 80 A; 65 C; 34 G; 77 T; 0 other; tgtaaacatt cctagtttaa gtatgattgt gtaaatccta gataagattt gattctagtt 60 atcctttcct attacaactt gtattacttg gaggagaagg aatatcttct ctccctttac 120 tactataaat aaaggcacaa tgtaggaggg ataacaacac acacattccc ctacaattct 180 acaaacacac atctctctcc tctctccctc tgccgccggc cctagtccct ctgtcagata 240 aaaatagacc acaaca 256 // ID Copia-62_VV-LTR repbase; DNA; EDCOT; 204 BP. XX AC chr14; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-62_VV_; KW Copia-62_VV-I; Copia-62_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-204 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr14; Positions 23405304 23405507. XX SQ Sequence 204 BP; 66 A; 31 C; 35 G; 72 T; 0 other; tgataaacca gacattgtaa taggcagtta caaggaagaa gttttagaag acaaaggaag 60 cttttataag ataattctgt tacacaattt gttattcaat ttacagctgt tataacagct 120 tttgtgtgta atactgatgc tataaataga tcttccttag cctctagcta ctcacttttt 180 gtgagagcag agtttcactt ttca 204 // ID VHARB-N3_VV repbase; DNA; EDCOT; 413 BP. XX AC . XX DT 10-SEP-2007 (Rel. 12.09, Created) DT 10-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE Non-autonomous DNA transposon from grapevine. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW VHARB-N3_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-413 RA Obukhanych T. and Jurka J.; RT "VHARB-N3_VV."; RL Repbase Reports 7(9), 1001-1001 (2007). XX DR [1] (Consensus) XX CC This is a non-autonomous Harbinger-like DNA transposon from Vitis CC vinifera, with 3-bp target site duplications. Individual copies CC are 88% similar to their consensus. XX SQ Sequence 413 BP; 161 A; 52 C; 46 G; 153 T; 1 other; ggccctgttt gacaactgtt ttcaagaaca attttctgtt ttttagaaca aaaaaaaact 60 gaaaaacacg tttgacaatc agaaactgtt ttctattttt ttttctgttt tctattatca 120 aaaaacagaa aatagggtgt tttcagagaa cttcttttag ttgttttcag ttgttttttt 180 tagagttgtt ttaaagaata attatacaaa catatataat gattaaaaat aaagttatgg 240 acataaaaat tatttttaaa acatatttaa aaatattaaa aacaggttaa aaacaatttt 300 aggttcccaa acagactttt gttctacaaa acatcatara acagttttca aaaactgttc 360 ttaaaaacta tttttttcag aactgtttta aaaaacagtt accaaacaag gcc 413 // ID Copia-34-I_VV repbase; DNA; EDCOT; 4705 BP. XX AC CU459252; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-34_VV, LTR retrotransposon Ty1-copia like, internal portion DE from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Rangen-B07; KW Copia-34-LTR_VV; Copia-34-I_VV; Copia-34_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4705 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL/GenBank/DDBJ; CU459252; Positions 1408916 1413620. XX CC Full size = 5020 bp CC LTR = 168-147 bp CC LTR are 91.9 % similar to each other. CC Direct flanking repeats = aatgc. XX FH Key Location/Qualifiers FT CDS 3393..4697 FT /product="Copia-34_VV_1p" FT /note="Incomplete putative gagpol polyprotein." FT /translation="EYGIDYEETFAPVAHISSIRALLAVAAARQWDLFQMD FT VKNAFLNGDLSEAVYMQPPSGLSVESNKVCHLRRALYGLKQAPRAWFAKFS FT STIFRLGYTASPYDSTLFLRRTDKGTILLLLYVDDMIITGNDLSGIQELKD FT FLSQQFEMKDLGHLSYFLGLEITHSTDGLYITQAKYASDLLSQAGLTDSKN FT VDTPVELNAHLTSSGGKPLSNPSLYRRLVGSLVYLTVTRPDISYAVHQVSQ FT YLSAPRSTHYAVVLRILRYLKGTIFHGLFYSTQSPLILRAFSDADWAGDLT FT DCRSTTGYCFLLGSSLISWRSKKQTFVARSSTEAEYRALADTTSELLWLRW FT LLKDLSVSTSSATPLYCDNQSAIHIAHNDVFHERTKHIEIDCHFIRYHLVH FT GALKLFFISSKDQLADIFTKSLPTRRTRDLIDNLKLVSHPP" XX SQ Sequence 4705 BP; 1085 A; 1171 C; 887 G; 1562 T; 0 other; gagccactgc tctgaccctt tcttagcagt ctgtcttcat tagtgtgact tcctttcttt 60 ttaacgcttc cgccaatcac aactgccgcc gcagcctttt gccgttgaac ctccgacgtc 120 atccaagcgt cgtccttggg ttccagacct gcagccacta tccttaagga gtttcacacc 180 gcacaagatc actgtttttt catcaccact gcgaatattg ctccgatttc aattttgacg 240 gtaccattga gatcgtccag cgccgatcta cacattcgtg gaaacctcgt cgccatcgga 300 gcccgtactt cattctctct gccacgtcag ccctagctac gtcaccactg ctgacgtgtc 360 agtgccacgt tagccctagc tgacataatc tccacgtcat ccgttgacca gcgttgaccg 420 ttgaccacac gtggactagc gttgaccgtt gactttgacc agtgttgacc gttgactttt 480 ccagggttga ccaggttctc cttacccagt ttttcgtgta gattccactt ttgcagtctg 540 ttttttgcat attgtgtctc taaatggata aaaatgatat ttttctttct cgccccatca 600 atactgtatt ggagggaaat aaaaattact tatcttggtc tcaagctatg cgcagttttc 660 ttaagggtcg catgctctgg cattattgta ctggtgtaat gactattcct atcaagggag 720 caagtgaagg agatgctgtt tttcttaatc gcatgattga atgggatagt cataaccaca 780 tgatcctcac atggattcgg aacacttcca ttccctctat ttccaatctg atgggcagct 840 ttgatgatgc aaaatctgca tgggatatgt tggccaaaag gtactccact actcatggat 900 ccctgaaata tcagttagta gttgaattac atcaactcaa gcaagaacca gggcaaccat 960 caatgactat tatgatcagc ttcgctttat ttgggaccaa attgaccttt ctgatccaac 1020 ttggacatgc tcaaaagatg cacagcaata tgcttccatt agagatgaat ttcgcctcta 1080 tgaattcttg atgtcacttc acaaggactt tgagcccatt cgtggtcagc tactcaatcg 1140 cagtcctgct ccctctcttg atactgctgt aaatgagttg gttagagaag aagctcgtct 1200 tgcaaccctt caagcctaga ataagttcaa tgttttggct attactccat ctactccact 1260 catagagcaa ccccaacaat caggtgattc ttatggctct agcaatcgtc gcaagcagac 1320 caacaaaaag ttctgcaact attgcaagcg tcctggccac accattgaga cttgttaccg 1380 tcgtaacaaa tctactgcta cagttgctaa tattgagcct actccgccaa tggcttccac 1440 ctcagttgag tccaagtctt ctggatctac tatcaacctc tcctccactg aactacagga 1500 gatcatagct caggctgttc atatggctgg taatgcatct ctttccactg ccttatctgt 1560 tctacctggt aagtctcaaa cttggctttt tgattctgcc tgctgcaatc acatgacacc 1620 tcactcatcc ctattctcca aacttgaccc tgcaccacat cctctaaata ttcatatagt 1680 taatggttcc accatgcatg ggaatagtct aggttttgtt tcaacctcta atctttctgt 1740 tcctggagtc ttccatgttc ctgacctatc ctataatttg tgctctgtgg ggcagttagc 1800 taaactaggt tatcgcctta ttttttacta ttctgggtgt attgtgcagg atccgaggac 1860 ggggcaggag cttgggaccg gtcctagagt tgggcgtatg tttcccgtga gcaatcttca 1920 tcttccacct gttgctcctg tttctattgc tactgcagct actgcagttt cttccttacc 1980 ttctcttgca ctttggcatt ctcgtcttgg tcatgcatca tcttctcggg tacaacagtt 2040 agtgtctagg ggtctgttgg gttctgtgtc taaagacatt tttgattgta cttcttgtca 2100 gttaggaaaa tagccagctt tgccttttaa taacagtgaa tccatttcta atagtatttt 2160 tgagttaatt cattctgatg tttggggacc ttctcctgtt gctagtattg gtggatctcg 2220 atactttgtt gtttttattg atgattattc tcgttatagt tggattttcc ctatgaaatc 2280 tcgttccgaa attttatcaa tatatagcaa ttttgcaaaa atgattgaaa cacaattctc 2340 caaacgtatc aaaacttttc gatctgataa tgctcttgaa tatactcaac atgcgtttca 2400 agctctgtta cattcctatg gcactgtaca tcatctaact tgtccaagta cctctcagca 2460 aaatggtcga gccgaaagaa aacttcgtca tattcttgac actgttcgtg ctctgcttct 2520 ttctgccaaa attcctgccc cattttgggg tgaagcggct cttcatgctg ttcatgcaat 2580 taaccgtatt ccaagtgctg tcatccataa tcagactccg tatgagcgtc tctttgggtc 2640 accccctgtc tatcatcacc ttcactcatt tggatctgct tgttttgttc ttcttcagtc 2700 tcatgagcac aacaaacttg agcctcgctc tagactctgt tgtttccttg gttatggtga 2760 aactcaaaag gggtataggt gttatgatcc tgtctctcat cgtcttcgtg tttctcgtaa 2820 tgttgtcttt tgggaacatc gattgtttgt tgaactctct cactttcgtt cttccttgac 2880 taactcctct gttttagaaa tctttccaga tgagtccctt gttccttcta caaatacttt 2940 tgatcctcct ttggacttct ctccagatat ttttgatgct tctcctagac aggttgcaga 3000 tgaacagatt gatgacgagc taccccactt tgagactggg tccccgctcc tactctgcct 3060 gaagatcctc cacaagacat tccacctcgc cactcaaccc gggtaagatc cattcctcca 3120 cacctacttg actatcattg ttacactgcc cttgctacac ttcacgagcc tcaaacctat 3180 cgtgaggcct ctactgaccc tttatggcag atttctatga aagaggaact tgatgcatta 3240 accaaaaacc atacttggga cctggttcct ctccttccta gacagtctgt ggttggttgt 3300 aagtggatct ataagatcaa gactcgctct gatggatccg ttgagcgcta caaggctcgt 3360 cttgttgcca aaggctttac ataggaatat gggattgatt atgaagagac ttttgctcca 3420 gttgctcata tctcatctat tcgtgctctc ttagctgttg ctgctgctcg tcaatgggac 3480 ctttttcaga tggatgttaa aaatgccttc cttaatgggg atctaagtga agcagtctat 3540 atgcaacctc cttctggtct ctctgttgaa tcaaacaagg tttgtcatct tcgacgtgca 3600 ctttatggtc ttaaacaagc cccacgagct tggtttgcca agttcagctc cactattttt 3660 cgcttgggtt acactgccag tccgtatgat tctaccttat ttcttcgtcg tactgataaa 3720 ggcactattt tgcttcttct atatgtggat gatatgatca taactggtaa tgaccttagt 3780 ggcattcaag aactcaagga ttttctcagt cagcagtttg agatgaaaga tcttggacat 3840 ctcagctatt tcctaggtct tgaaattact cattccacag atggtcttta tattactcaa 3900 gccaagtatg cttctgatct gctgtctcaa gccggactca ctgacagtaa gaatgttgac 3960 actccagtcg aacttaatgc gcatctgaca tcctccgggg ggaaaccatt gtccaatcct 4020 tctctttaca gacgattggt tggcagctta gtttatctca cagttactcg tccagacatc 4080 tcctatgctg ttcatcaggt gagccagtat ttgtctgctc cacgatcaac tcactatgct 4140 gttgttctgc gcattcttcg atacctgaag ggtaccattt ttcatggcct tttctactca 4200 actcaatctc ctcttatact ccgtgcattc tctgatgctg attgggcagg agatcttact 4260 gattgcaggt ccactacagg ttactgcttc cttcttggtt cttctttgat ttcttggaga 4320 agtaagaaac aaacttttgt ggcccgctct agtactgaag cagaatatcg tgcccttgct 4380 gataccacat ctgaactcct ttggctaaga tggcttctta aggatttgag tgtgtccacc 4440 tcctctgcta ctccccttta ttgtgacaac cagagtgcca ttcatattgc tcacaatgat 4500 gtctttcatg aacggactaa acacatcgag attgattgtc attttatccg ttatcatctt 4560 gtccatggtg ctcttaagct tttcttcatc tcctccaaag atcagcttgc agatatcttc 4620 accaagtcac ttcctacaag acgcactcgt gatttaattg acaacctcaa gttggtctca 4680 catccacctt gagtttgagg ggggc 4705 // ID MITRAV repbase; DNA; EDCOT; 372 BP. XX AC . XX DT 26-JAN-2007 (Rel. 12.01, Created) DT 14-APR-2008 (Rel. 13.05, Last updated, Version 2) XX DE A putative non-autonomous miniature DNA transposon from Medicago DE truncatula. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW MITRAV. XX NM MITRAV. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-372 RA Shankar R. and Jurka J.; RT "MITRAV: A miniature DNA transposon from barrel medic."; RL Repbase Reports 7(1), 38-38 (2007). XX RN [2] RP 1-372 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC The element is present in a high copy number across the Medicago CC genome as well as it is highly conserved. It has features of CC Harbinger type miniature transposons with 3 bp TSD (TAA) as well CC as ~34 bp terminal inverted repeats. Classified as Harbinger in CC ref. 2. XX SQ Sequence 372 BP; 142 A; 72 C; 57 G; 101 T; 0 other; gggggtgttt gtttcctggt ttaaaaaatt attcccagga acatggaggt tggaattata 60 gattcctatg tttgttacaa agttaaaaaa ataactcccg ggaataaaga attcctagga 120 aaaaaataac ttccacttac ccatgatttt attcccaaag aaagtgggcg ggaataaaag 180 attcccatgt aaatggtact aaaatggaaa taactaccca tatacccact atcacaaaca 240 attcccatga atctgacaat tatttaccaa acacaatttt ctaaaaatac tcaggaataa 300 gatgcccatt attatttccc aggaaaggtt aatcccagga atgaaatttt aaaccgtcaa 360 acaaacgccc cc 372 // ID Gypsy6-PTR_I repbase; DNA; EDCOT; 4383 BP. XX AC scaffold_916; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy6-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4383 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4383 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 336-336 (2007). XX DR Genome; scaffold_916; Positions 16577 12195. XX CC Positions [3464-3946] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS join(35..1360,1364..4381) FT /product="Gypsy6-PTR_I_1p" FT /translation="MAPKRRANLPNLREQPLDEVYERDEIARLQQQVETLT FT QQLAASMAQHQDPNPQDVEKESEDDENPFAHQPVQRRPAHDESRRWETGLK FT VDIPEFHGGLQADEYLDWINTVDEVLEFKQFLEDRRVALVATRLRGRAGAW FT WQQVKKTRTLQGKGKITCWDKMKKNMRSAFLPYNYTRTLYQRLQNLRQGNR FT SVDDYTTEFYQLVSRDAIAEDEESRVARYIGGLRIQFQDVLNMFDVLSVSD FT AYQRAVQLEKQLVRRNTGGLNFGGFGANTSNNSGRTGSMNFGGTGAGSASS FT SSTRTAVPPSPITKPTMPTHVTTPNTGFRCFNCGEPGHRFAECKKGQRRGL FT FSDVEEINREQEGDVEAEPVYDEEERLEGDAGPMLMIRRSCLAPHVVEDDW FT LRTNVFQSTCTISGKICRFIVDSGSCENIVSEEVVRKLHMATESHPRPKLT FT WLDKKNDVTVSRRSLVSFSIDTTYKDQIWCDVVSMDACHLLLGRPWLYDRH FT VMYDGFLNTCTFIFNSIKVVLLPKKEVTGGIPTGENNNLLTMAKFEAEVKE FT SGVVYVLIGKMEAENGIIPSNVEPLLQEFGDIFPAELSETLPPLRDIQHQI FT NLVPGANLPNRPHYRMSPKEHEELRRQVEELLTKGHIRESLSPCAVPALLT FT PKKDGTWRMCVDSRAINKITVRYRFPIPRLDDLLDQLSGATIFTKLDLKSG FT YHQIRIRPGDEWKTAFKTREGLFEWLVMPFGLSNAPSTFMRVMNQALRPYI FT GKSVVVYFDDILIYSVDPRMHLQHLREVLTVLRKEQFFAAKGKCVFLSDQV FT LFLGYIVSSKGLSVDETKIEAIKQWPQPQTMTDVRSFHGLTSFYRRFIPHF FT SGIMAPVTDCMRNNNKFVWTIEAETAFQEIKRRLTTTSVLVLPDFSNPFKL FT HCDASKLGIGAVLSQNGRPIAFFSEKLSGAKLRYNTYDVEFYAVVQAVRHW FT RHYLFLQDFVLFTDHDALKHMGSQDKISSRHACWAAYLQQFTFVIKHKAGT FT LNRVADALSRRKNMLVDMRVKVMGFDSFQNLYASDPFFAVVIENIQNNQQS FT DFVLHDGFVFKGTQLCIPECSLRTKIIQELHREGHVGRDRTYLLVAASYFW FT PSMRKEIGRFVERCRVCHVAKGGATNAGLYMPLSVPVRPWTDISMDFVLGL FT PRTQRGFDSIFVVVDRFSKMVHFIPCKKTTNAVNVAELFFREVYRLHGLLE FT SIVSDRDTRFLSHFWRSLWKMVNTHLNFSSAYHPQSDGQTEVVNRSLGNLL FT RSLVGDQLKSWDKKLGQAEFAHNHAVNRSTKLSPFKIVYGFLPRCPLDLAN FT LPNNTKVNHKAEDFVTQLQDIHNLTRQNLLESIAKFKHDADRKRRLVNYEV FT GDFVWAVLTKDRFPIGEYNKLSARKIGPVDIIEKINSNAYRLKLPSHLRTA FT DVFNVKHLLPFHGDLSSEEEDLLNSWSNSSQLGE" XX SQ Sequence 4383 BP; 1267 A; 904 C; 1085 G; 1127 T; 0 other; ggttggtatc agagctcggt tagttatcgt cgttatggca ccaaaaagac gcgcgaacct 60 accgaacctt cgtgaacaac cattggatga agtctacgaa cgcgatgaga ttgcacgact 120 acaacagcaa gtcgagacgt taacgcagca gttagcagca tcaatggctc aacatcagga 180 tccaaatcca caagacgtgg aaaaggagtc tgaagatgat gaaaatccat tcgcccatca 240 accagtgcag aggagaccag cgcatgatga atcaaggcgc tgggagacag gcctcaaggt 300 tgacatacca gagttccatg gtggtttgca agcggatgag tacctcgact ggatcaatac 360 ggtagatgaa gttttagagt ttaaacaatt tctagaagac agacgagtag cactggttgc 420 aacaaggctt agaggtcggg ctggggcttg gtggcaacag gtgaagaaga caaggactct 480 acaaggaaaa ggaaagatca cgtgctggga caagatgaaa aaaaatatgc gttctgcatt 540 tctaccatac aactatacac ggacgctcta ccaacggtta caaaatctaa gacagggaaa 600 ccgttcagtt gatgactaca ctactgagtt ttatcagtta gtatcgcgag atgcgattgc 660 agaggatgag gagtcacggg ttgcgcgata tattggcgga ctacggattc aattccaaga 720 tgtcctaaat atgtttgatg tattgagcgt gtcggacgcc taccagagag cagtgcagtt 780 agagaaacaa ctagtgcgca gaaatacagg gggtctgaac tttggaggtt ttggtgcaaa 840 tacaagcaat aacagcggac gaacagggag tatgaatttc ggggggaccg gtgcaggcag 900 tgcaagtagc agtagcacac gaacagccgt tccaccatct cctattacca agcctactat 960 gcctacacac gtaacgacgc ctaacacagg ttttcgttgt tttaattgcg gggaaccagg 1020 acacaggttc gcagagtgta agaaaggaca gcggagaggt ttgttttcag acgttgagga 1080 aattaacagg gaacaggaag gcgatgttga ggcagaacca gtttatgatg aggaagaacg 1140 tttagagggg gatgctggac caatgttaat gatccggcgc agctgtttag caccacatgt 1200 ggtagaggat gattggttgc gcactaatgt attccagtcc acttgcacaa ttagtggaaa 1260 aatctgtcgg ttcattgttg attcaggtag ctgtgaaaat atagtgtccg aggaggtggt 1320 ccgtaaacta cacatggcaa cggaatcaca tcctcgaccg taaaaattaa catggctaga 1380 taagaagaat gatgttacag tatcaagacg cagcttggtg tctttttcaa tcgacacaac 1440 atacaaagat cagatttggt gtgatgtggt ctccatggac gcctgtcatt tattattggg 1500 cagaccgtgg ttatatgatc gacatgtgat gtatgatggg ttcttgaata catgcacttt 1560 catattcaat tcaatcaagg ttgtgttgtt accaaaaaag gaagttacag gcggcattcc 1620 aacaggagaa aacaacaatt tattgacaat ggctaagttt gaagcagaag tcaaagaatc 1680 tggagttgtt tacgtgctga tcggaaaaat ggaggctgag aatggcatta ttccaagcaa 1740 cgtggagcca ttattacagg agtttggaga tatatttcca gctgagcttt ctgaaaccct 1800 acccccatta agggacattc aacatcaaat taatctggtc cctggtgcca acttgcctaa 1860 caggccacat tatcggatga gtccgaaaga gcatgaagag ttacggcgcc aagtagagga 1920 attgctaaca aaggggcata ttcgggaaag tcttagccca tgtgcggtgc ctgcccttct 1980 aaccccaaaa aaagatggaa cgtggagaat gtgtgtcgat agcagggcca ttaacaaaat 2040 tacagttcgt tacaggtttc caatcccgcg gttagatgac ttgctggatc agttgagtgg 2100 agccacaata ttcacgaagc tggacttgaa gagcggatat caccagattc gtatccggcc 2160 aggagatgag tggaaaacag ccttcaaaac tcgggaagga ctctttgagt ggttggtcat 2220 gcctttcgga ctgtctaatg ccccaagcac attcatgcga gtgatgaatc aagccttgcg 2280 gccttacatt ggtaagagcg tggtggttta ttttgatgac attttaattt atagtgttga 2340 tcctagaatg cacctacaac atctccggga agttttgacc gtgttacgta aagaacaatt 2400 cttcgcagca aaaggaaagt gtgtgttctt aagtgaccaa gtcttgtttt tgggatacat 2460 tgtgtcttct aaggggcttt cagtagacga gacaaaaatt gaagcaatca aacagtggcc 2520 acagccgcaa accatgactg acgttcgaag ctttcacggg ctgacatcat tctaccgccg 2580 cttcattccc cacttcagtg gcataatggc cccagtaact gattgtatga ggaacaataa 2640 caagtttgtg tggacaattg aggccgagac agccttccaa gaaatcaaaa ggagattgac 2700 caccacctca gtacttgtcc taccagactt ttcaaaccca tttaagctac actgtgacgc 2760 ctcaaagcta ggaatcgggg cagttctgag tcaaaatggc aggcctatag ccttttttag 2820 tgagaagctt tcaggggcaa aattacggta taacacctat gatgttgaat tttatgcagt 2880 ggttcaagca gtgaggcatt ggcgacatta tctgtttctt caggacttcg tcctatttac 2940 tgaccatgat gccctcaaac atatggggag tcaagataag atttcatctc gtcatgcatg 3000 ttgggctgcg tacttacaac aattcacatt tgtcatcaaa cacaaggctg gtacactgaa 3060 ccgggtggct gatgccctca gtcgtcgaaa aaatatgctg gttgacatgc gagtcaaagt 3120 aatgggtttc gactcttttc aaaatttgta tgcatctgac cctttttttg ctgttgtaat 3180 agagaacatt cagaataacc agcagagtga ctttgtcctc catgatggat tcgtcttcaa 3240 aggcacccaa ctatgtatac ccgagtgtag tctccgaacc aaaatcatac aagaactgca 3300 cagagaagga catgtgggaa gagaccgaac ttacttactg gtggctgcgt cctatttctg 3360 gccatccatg cggaaggaga ttggtcgttt tgttgaacgt tgtagggtct gtcacgtggc 3420 caagggagga gccaccaatg ctggtttata catgccactt tctgttccag tacgaccatg 3480 gaccgacatc agcatggatt ttgttctagg cctcccgcgt acacaacggg gattcgactc 3540 cattttcgta gtagtagaca ggttttcaaa aatggttcac tttataccat gcaagaaaac 3600 gacaaatgct gttaatgtgg ctgaattatt ctttcgagaa gtgtatcggt tgcatgggct 3660 gttagagtca attgtgtcag atagggacac tcgtttcctg agccatttct ggcggagtct 3720 ttggaagatg gttaatactc acctaaactt cagcagtgct tatcatcctc agtccgatgg 3780 acaaactgag gtggtgaacc ggtcgttggg taatctcctt cgtagtttgg tgggtgatca 3840 gttaaaatct tgggacaaga aacttggcca agcagagttt gctcataacc atgcagtcaa 3900 tcgtagcacc aagctcagcc ccttcaaaat cgtgtacggg tttctcccac gatgtccact 3960 tgacttggct aatctcccga acaacactaa agttaatcat aaggcagagg attttgtcac 4020 ccagctgcag gacattcaca accttaccag acagaacttg ctggaatcta ttgccaaatt 4080 caaacacgat gcggaccgca agcggcgtct tgtcaattat gaggtggggg actttgtttg 4140 ggctgtgcta acgaaggatc gctttcctat aggtgagtat aataaactgt ccgcacgaaa 4200 gattggtcca gtagatatta ttgagaaaat taattcaaat gcataccgcc ttaagctgcc 4260 cagtcatctc cggacagcag atgtatttaa tgtcaaacac ttgcttcctt tccacgggga 4320 tttatcatca gaggaggaag atctcctgaa ttcgtggtcg aattcttctc agcttgggga 4380 gga 4383 // ID Copia-67_Mad-I repbase; DNA; EDCOT; 4117 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-67_Mad_; KW Copia-67_Mad-LTR; Copia-67_Mad-I. XX NM Copia-67_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4117 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1672-1672 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1516-2046] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 3172..4086 FT /product="Copia-67_Mad-I_3p" FT /translation="MFTKFKQSMMNEFEMTDLGKMRYFLGIEVLQQVDGIF FT ICQKKYAQEVLERFKMENCNPVHNPIVPGTKLTKDVTGEKVDSTFYKQIVG FT SLMYLTATRPDTMFVVSLISRFMECPTEMHLAAAKRVLRYLKGTISLGILY FT KKGGHAELRGYSDSDYAGDLDDRKSTSGYLFMLSSGAVCWSSKKQPVVTLS FT TTEAEFIAAASCACQATWLRRIMKELGQAQQDSTTIFCDNSSAIKLSRNPV FT MHGRSKHIDVRFHFLRELTKDEIVQLVHCNTQEQVADILTKPLKTDAFLKM FT RELMGVCLEPGVN" FT CDS join(463..1233,1237..2397) FT /product="Copia-67_Mad-I_1p" FT /translation="MLHMKTGETVNEFFGRTLTIANKRRINGDKLTDVEVI FT EKILRSMTPKYDYVVCSIEESKDLDILSIDELQSSLLVHEQRMIGHVVEEQ FT ALKVAYEENSGGRGRGRGSFRGRGRGRGRQNFDKSTIECYNCHELGHYQYE FT CPKKDKEAKANYAEASEEMLLMAYVDTQEIKEDIWFLDSGCSNHMCGKREL FT FSDFDGSFRETVKLGNNTSMAVLGKGNIRLQVNGMTQVITGVFYVPALKNN FT LLSIGQLQEKGLAILIHGRCKIYHPERGLIMETVMAANRMFILVAQYQLNV FT QACFNALTDDPVQLWHCRYGHLSLGGLKTLQQKQMVSGLPQIKDSSRVCEN FT CLVGKQPRDPFPKRSTWRACQILQLVHADICGPIKPTSNSKKRYLLTFIDD FT FSRKTWIYFLIEKSEAFRTFKAFKSLVENETDASIKSLRTDRGGEFTSHEF FT VEFCVENGIQRQLTAAYTPQQNGVAERKNRTIMNMVRSLLTEKKMPKTFWP FT EAANWTVHVLNRSPTFAVKNKTPEEAWSGTIPSVSYFRVFGCISYVHIPDN FT KRTKLDDKSMKCVLLGVSEGSKAYRLFDPVSQRIIISRDVRFDENSSWDWD FT EHHHEAVIADLEWDDDEDKAIEADEVDSQGGDEDGSDGNGNEHKQQ" XX SQ Sequence 4117 BP; 1265 A; 688 C; 1100 G; 1061 T; 3 other; ctcgggttta acatttggta tcagagcccc cacctggggc tcttgatcga agcttgagag 60 atagcaatct tttgagtgaa gaggtacgag aatatggcag gagaaggaag tggttttgtg 120 caagcatcca ttccaaaact ggatgggcat tatgaccact gggcgatgct tatggaaaat 180 ttcctacgtt caaaggaata ttggagtmtt gtggagcatg gaatccctgc agcagcagaa 240 ggagcctcac tcgcggaggg gcaacggaag gtgctcgaag atcaaaagtt gaaagatcta 300 aaggctaaga actacttgtt tcaagcaatt gatcgagctg ttttggaaac aatcttgaac 360 aaggatacgg ctaaggagat ttgggattcg ttgaagcaga agtatcaagg gactgctcga 420 gtcaagcgag cacagttgca ggcacttcga aaggagtttg agatgcttca catgaagaca 480 ggagaaactg tgaatgagtt ttttggtcga actctgacca tagccaacaa gagaaggatc 540 aatggtgaca aattgacaga tgtagaagtc attgagaaga tcttgagatc gatgactcct 600 aaatatgact atgtggtttg ttcaattgag gaatccaaag atttagatat tctctcaatt 660 gatgaactgc aaagcagttt gttagtgcat gagcagcgga tgattggaca tgttgtggag 720 gagcaagcac taaaggtggc ctatgaagag aactctggag gaagaggacg tggtcgagga 780 agctttcgtg gaagaggcag aggaagaggt cgacaaaact tcgacaagtc aacgattgag 840 tgctataatt gtcatgaatt agggcactat cagtatgagt gtcctaagaa agacaaggaa 900 gcaaaggcca actatgcaga ggctagtgaa gagatgttgc taatggcgta cgtggatact 960 caggagatca aagaagacat ttggttcctc gactcgggtt gcagcaatca tatgtgtggt 1020 aagagggagt tattctctga ctttgatgga agttttagag aaactgtgaa actagggaac 1080 aatactagta tggctgtttt ggggaaagga aacattcgac tacaagtgaa tggaatgact 1140 caggtgatca caggagtttt ctatgtgcct gctttgaaga ataatcttct aagtattggt 1200 cagcttcagg agaaaggtct tgctattctc attmaacacg ggaggtgcaa gatctatcac 1260 cctgagagag gactgatcat ggagaccgtt atggctgcaa accgcatgtt cattcttgtt 1320 gctcagtatc aactcaatgt ccaggcatgt ttcaatgctc tcacagatga tccagttcag 1380 ttgtggcact gccgttatgg gcacttgagt cttggtggct taaagactct acaacagaag 1440 cagatggtga gtggactgcc tcagataaag gactcctcaa gagtgtgcga gaattgcttg 1500 gtaggcaagc aaccgagaga tccttttcca aaaaggagta cctggagggc ttgtcaaatt 1560 ctacaactcg ttcatgcaga tatatgtgga ccgataaagc ctacatccaa cagtaagaag 1620 aggtatctac tcacctttat cgatgatttt agtcgtaaga cttggatcta ttttttaatt 1680 gagaagtcag aagcctttcg aacctttaaa gccttcaaaa gtcttgttga gaatgaaact 1740 gatgcaagta ttaaaagttt gcgcacggat cgtggagggg agtttacatc tcacgagttt 1800 gttgagtttt gtgttgagaa tgggattcaa cgacaattga cagcagctta caccccgcag 1860 caaaacggag tagctgagcg taagaatcgg accatcatga acatggttcg aagcttatta 1920 accgagaaga agatgccaaa gactttttgg cctgaagcag caaactggac agttcatgtg 1980 ctcaacagga gtcccacatt tgcagtaaaa aacaaaacac ccgaggaggc atggagtggt 2040 acgataccgt cagtaagtta tttcagggtt tttgggtgca tttcatacgt acatattcca 2100 gacaacaaga ggaccaagct agatgataaa agtatgaagt gtgtgctact tggggttagc 2160 gaaggatcga aggcctatcg gctatttgat ccagtctcgc agaggatcat aatcagtcgt 2220 gatgttagat ttgatgagaa tagtagctgg gattgggatg agcatcatca tgaagctgtc 2280 atagcagatt tggaatggga tgatgatgaa gataaagcaa ttgaagctga tgaagttgac 2340 agtcagggag gagatgaaga tggatccgat ggaaatggaa atgagcacaa gcaacaatag 2400 tggatcagat gaagtctcag aagcaagttt atccagtcca gaagaaagaa gacctagggc 2460 tccgccggtg tggatgagag attacgtgac gggagaggga ttatctgaag aagaagacat 2520 ggtgcacttg gctcttttag cagacagtga tccaattcat tacaatgaag ctgtgaagag 2580 tgctaaatgg aggaaagcta tggatgtcga aatagcagct atcgagagga acaacacttg 2640 ggaattgaca gatttacctc aaggagggaa gacgattgga gttaaatggg tttacaagac 2700 taaactgaat gagaatggag aggtggacaa gtacaaagcw cggctggtgg ctaaggggta 2760 tgctcaagaa tatggggttg attatgctga agttttgctc ctgtggctag gttagatacc 2820 attcgagttg taattgcact tgctgctcaa agggaatgga caattcatca attggacgtg 2880 aaaagtgcct tcttacatgg agaaatcgat gaagaagtgt ttgtagaaca gccacctggg 2940 tatgtgcaga gaggtaagga gcataaagtt tacaaattaa ggaaagcttt atatggactt 3000 aaacaagccc ctcgtgcttg gtatagtcgt atagaagctt atttcttgaa ggaagggttt 3060 gtgaagtgtc cctatgaaca cactttgttc atcaaagctg gagatggagg taaaattctc 3120 attgtttgtc tttatgttga tgatctcatt tatactggca atgatgaatg catgttcact 3180 aagtttaagc agtcgatgat gaatgagttt gaaatgaccg atcttggtaa gatgaggtac 3240 ttccttggaa ttgaagtatt gcagcaggta gatggaatat ttatctgcca aaaaaaatat 3300 gctcaggaag tgttggaaag gtttaaaatg gagaactgca atccagtgca caatcctatt 3360 gttccaggta ccaagctaac gaaggatgtg actggtgaga aggtcgacag cactttctat 3420 aaacagatcg tggggagcct catgtatctc acagccactc ggcctgacac tatgtttgtg 3480 gtaagcttaa tcagcaggtt tatggagtgt ccaacagaaa tgcatttggc agcggcaaaa 3540 agggttttga ggtatttaaa aggcacgatc agccttggaa ttctttacaa aaagggagga 3600 cacgctgagc tcagaggcta ctcagatagt gattatgcag gtgacttaga tgatagaaag 3660 agcacatcgg ggtatttgtt catgctaagt tcaggagctg tgtgttggtc ttccaagaag 3720 caacctgtgg ttacgttatc aacaactgaa gccgaattca tagcagcagc ttcatgtgct 3780 tgtcaggcaa cctggttgag aaggataatg aaggagttag gtcaagctca gcaagactct 3840 acaacgattt tctgtgacaa tagctcagca ataaagctct ccaggaatcc tgtaatgcat 3900 ggtcgaagca aacacataga tgtacgtttc cactttcttc gtgagctgac taaggacgaa 3960 attgtgcagc tggttcattg caacactcag gagcaagtag cagacatatt aaccaagcct 4020 ttgaagactg atgcctttct gaagatgcgt gagcttatgg gagtgtgtct ggaaccaggt 4080 gtaaactgat tgctatagca atcagtttaa gggagga 4117 // ID Copia-1_TRe-I repbase; DNA; EDCOT; 4577 BP. XX AC GU443966; XX DT 20-NOV-2010 (Rel. 15.12, Created) DT 20-NOV-2010 (Rel. 15.12, Last updated, Version 1) XX DE Internal region of an LTR retrotransposon. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; KW reverse transcriptase; integrase; Ribonuclease H; retrotranspon; KW white clover; Copia-1_TRe-I. XX OS Trifolium repens OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Trifolium. XX RN [1] RP 1-4577 RA Hand M.L., Cogan N.O.I., Sawbridge T.I., Spangenberg G.C. RA and Forster J.W.; RT "Comparision of homoeolocus organisation in paired BAC clones RT from white clover (Trifolium repens L.) and microcolinearity with RT model legume species."; RL BMC Plant Biology 10, 94-94 (2010). XX RN [2] RP 1-4577 RA Laten H.M., Hand M.L., Cogan N.O.I. and Forster J.W.; RT "LTR retrotransposons in white clover, Trifolium repens L."; RL Repbase Reports 10(12), 2166-2166 (2010). XX DR EMBL/GenBank/DDBJ; GU443966; Positions 22070 26646. XX CC Internal region of a Copia-like retrotransposon possessing a CC single, intact gag-pol ORF encoding conserved domains for gag, CC prot, int, rt and int. Flanked by identical LTRs. CC Genbank Accession GU443966 position 22070 to 26646. XX FH Key Location/Qualifiers FT CDS 142..4539 FT /product="Copia-1_TRe-I_1p" FT /note="Gag-pol polyprotein." FT /translation="MVRPSQNTVAIPALTDPSQNPYYVHPNESATAALVSP FT LLDGKNYHVWSRSMKKAVIMKNKLRFLDGSCPMPDDFDPTYEPWIRCNNLV FT LSWLMNSVTPAICQSLVYTDSAAQAWEDLKARFSRVDRVRVSSLQREIYAL FT RQESSSVTEFFTKLKGMWEELLLYRPIPNCTCTFRCVCESMINAKKFREED FT LVLLFLTGLNDHYSMVRSQILLMEPFPLLNSAFGMVIQHENLNSLDTSDDQ FT ASISVNLAKKTYGKNPSFKSDKQCTHCGKSNHTIDNCFRKHGFPPGYRFRD FT GTVVGSKNQGQVNVNYAEADDSDARSTVDNRVATFSTEEYQALMSLLRSNT FT KPVEGPSQVNNITKCIASSYNNAKQGIVPNHLDTWIIDSGATDHVCAALSL FT FTSYTKVKAIPVKLPNGTIVTTDIVGNVVLTSELTLKNVLYMPHFSFNLIS FT VSRVAQDLNCVFAFTDDLCFIQNSLQRMIGSGRMINGLYYLEGTHSMIQPL FT SGKQCNSVAIPKTAIWHFRLGHTSLHRLELMKQLYPDIQVNKTDFCCDICH FT FAKQRKLPYDLSYSRASTCLELLHMDIWGPFSTPTPHGHKYFLTIVDDFSR FT FTWIILMKAKSETACKIQEFIQFVESHFSHKVKILRSDNGPEFISLSKFYL FT SKEIVHQTSCVGTPQQNGRVERKHQCILNIARALLTQSHLPSTYWGYVVLH FT SVFIMNRVPSTAVNGRIPFDILHAKLPDISQLRVFGCLCYVSTQDSHRSKL FT DPRARKCVYLGVKAGMKGYIALDLHNHEIIVSRNIHFEETILPYPINNSTP FT NWEYMVPPTNTQPSPIAPTQTTNSHETTNNHSTNPHNTASTPTLYYEPPIS FT TYTSDQVFSSSESHHNGNDSLVTLEPDIASNTEVAPMPAPPSPPTTNNYPP FT PNPPITLRQSIRTRHLPTHLLDYHCNSIIQKTPYPISHYISHSNLSSSYYT FT FCLSLLTEQEPNNYAEASQHDCWTKAMKAELTALANNNTWKIVDLPTGVKP FT IGSKWVYKIKRKPDGTIDRYKARLVAKGYNQIEGVDYFQTFSPVAKMTTIR FT TVLAVASIQNWHIHQLDVDNAFLHGDLDEDVYMKVPQGLEGTTDKQVCKLI FT KSLYGLKQASRQWYDKLSKFLITIGYVHMPSDPTLFTKKTETSFTTLLVYV FT DDIVLTGDCLTEIQSTKSQLHQTFGIKDIGTLKFFLGLEVAHSQQGIALCQ FT RKYCLDLLTETGTLGCKPSSIPMDPSNRLHHDDSAPHSNVTEYRALVGKLL FT YLTSTRPGIEFPVQQLSQFLDTPTSAHFKAAHKVLRYLKGNPGTGLFFPRN FT TTLQLSGFSDADWGGCPDSRRSITGYCFFIGKSLVCWKSKKQLTVSKSSSE FT AEYRALASATCELQWLSYLLADLHIISDKLPALYCDSQSALHIASNPVFHE FT RTKHLDIDCHIVREKLQGGLMKLLPISGYNQIADILTKALHPANFIVYFPS FT *" XX SQ Sequence 4577 BP; 1339 A; 991 C; 830 G; 1417 T; 0 other; tggtatcaga gcaactctct tgaggagctc tgctgcgcca tattcatttc atttcttcct 60 tctttcttcg ttttttcttc cattttctcg attccccttt cgtttttctt tcactttctt 120 gcattttcat tctctgttac aatggtgcgt ccatctcaaa acacagtggc aattcctgct 180 cttactgatc cttctcagaa tccatactat gttcatccta atgagagtgc cactgctgca 240 cttgtttcac ctcttcttga tggcaagaac taccatgttt ggtctcgttc gatgaaaaag 300 gccgtgatca tgaaaaacaa acttcgtttc ttggatggat cgtgtccaat gcccgatgat 360 tttgatccga cgtatgaacc atggattcgt tgcaacaatt tggttctatc ttggttgatg 420 aattcggtta ctccagctat ctgtcagagc ctcgtgtata ctgattctgc agcacaagcg 480 tgggaggatc ttaaggctcg tttttctcgt gttgatcgtg tgcgtgtctc atctttgcaa 540 cgtgagatct atgctcttcg tcaagaatca tcttcagtca ccgaattttt cacaaaattg 600 aaaggcatgt gggaggaatt actgctgtat cgacctattc cgaattgtac atgcactttt 660 cgttgtgttt gtgaatctat gatcaatgcc aaaaagttca gagaggaaga tttagttttg 720 ctatttctca caggtttgaa tgatcattac tccatggttc gttctcaaat tttattaatg 780 gaacccttcc ctctacttaa ttctgctttt ggtatggtga ttcaacatga aaatttaaat 840 agtttagata ctagtgatga ccaagcttct atttctgtga atcttgctaa gaagacttat 900 ggtaagaatc catctttcaa gagtgacaaa caatgcactc attgtggtaa gagtaatcac 960 accatagata attgttttag gaagcatggc tttccaccag gttataggtt cagagatggc 1020 actgttgttg gtagcaagaa tcaaggccaa gttaatgtca attatgctga agctgatgac 1080 agtgatgcta ggagcactgt ggataaccgt gtagcaacat tcagcactga agagtaccaa 1140 gccttgatgt ctttgctcag atccaacacc aagcctgtag aaggaccttc acaagtgaac 1200 aacattacaa agtgcattgc ttcttcttac aacaatgcta agcaaggtat tgtccctaac 1260 catttagata catggatcat tgatagtgga gccactgatc atgtatgtgc tgcactgagt 1320 ttattcactt cttacacaaa agttaaagct attcctgtca agttacccaa tggaactatc 1380 gtgaccactg atatagtagg caatgttgtc cttacatctg agcttacgtt gaagaatgtg 1440 ctgtatatgc cccattttag cttcaatctt atttctgttt ctagagttgc acaggatttg 1500 aattgtgtat ttgctttcac tgatgacttg tgcttcattc aaaattccct acagaggatg 1560 attggttcgg gtagaatgat caatgggctg tattatcttg aaggaacaca ttctatgatt 1620 caacctttat caggtaaaca atgtaactct gtagctattc ctaagactgc catatggcat 1680 ttcagacttg gccacacatc tttacataga ttagagctta tgaaacaatt gtatccagat 1740 attcaagtga ataaaactga tttttgttgt gatatctgtc attttgccaa gcaaagaaag 1800 ctaccatatg atttaagtta cagtagagct tctacttgtt tagaattgtt acatatggat 1860 atttggggtc ccttctcaac tcctactcca catggacata agtatttttt gactattgtt 1920 gatgacttta gtcgttttac ttggataatt ctcatgaagg caaagtctga aactgcttgt 1980 aagatacaag aatttataca atttgttgaa agtcacttta gtcacaaagt taaaatacta 2040 aggagtgata atggaccaga gtttatctcc ttgtccaaat tctaccttag caaggaaatt 2100 gtacatcaga ccagttgtgt agggacacca caacaaaatg gtcgtgtgga aaggaaacac 2160 caatgcattc tcaatatagc tagagctttg ttaactcagt cacacttacc ttccacatat 2220 tggggctatg ttgttcttca ttctgttttc atcatgaata gagtcccctc aactgcagta 2280 aatggtagaa ttccatttga tatcttacat gccaagttac ctgatatttc acagttaagg 2340 gtatttggat gtttgtgcta tgtatctact caagacagtc atagatctaa attggaccct 2400 agagcaagga agtgtgtata tcttggtgtt aaggctggca tgaaaggtta catagctttg 2460 gaccttcaca atcatgaaat aattgtgtcc agaaatatac actttgaaga aacaatcctc 2520 ccttacccta taaacaactc cacacctaac tgggagtaca tggtgcctcc caccaataca 2580 caaccttcac ctattgcacc tacacaaact acaaacagcc atgaaaccac aaacaaccat 2640 tcaacaaacc cacataacac agcttctaca ccaactttat actatgaacc acctatatct 2700 acttacactt ctgatcaagt tttctcttca tcagaatctc atcacaatgg taatgatagt 2760 cttgtcacac ttgaaccaga cattgcttct aatactgaag tagctcctat gcctgcacct 2820 ccttcaccac ctaccacaaa caattatcca ccacccaatc ctcccataac acttaggcaa 2880 tccatcagaa caagacattt gcctacccat cttctggatt atcactgcaa ctccataatt 2940 cagaagacac catatcccat ttcacattac atcagtcact ccaacctctc atcatcttac 3000 tacaccttct gcttatctct tctcactgaa caagaaccta ataactatgc agaagcctct 3060 caacatgact gttggactaa ggcaatgaaa gcagaactca cagctctagc aaataacaac 3120 acttggaaaa ttgtagattt acctacagga gtgaaaccca ttggcagcaa atgggtgtac 3180 aagataaaga gaaaacctga tggcactata gacagatata aagccagatt agtggccaag 3240 ggatacaatc aaatagaagg agttgactat tttcaaacct tctcaccagt agctaagatg 3300 actacaatca gaactgtgtt agctgttgct tctattcaga actggcatat tcatcaatta 3360 gatgtagaca atgccttcct tcatggtgat ctcgatgaag atgtatatat gaaggttcca 3420 cagggattgg aaggaacaac agacaaacag gtttgcaaac tcatcaaatc tctttatggc 3480 ctaaaacagg caagtcgaca atggtatgat aaattgtcaa agtttctcat caccattgga 3540 tatgtacaca tgccctctga ccctactctt tttaccaaaa agacagaaac aagcttcact 3600 actctcttag tctatgttga tgatatagtg cttactggag attgcttaac agaaattcaa 3660 tccactaagt cacagttaca tcaaacattt ggtattaagg atattgggac tctgaaattc 3720 ttccttggtt tagaagtggc tcattctcaa caaggaatcg cattgtgtca gagaaagtac 3780 tgcttggact tgttgactga aacaggtacc ttaggctgca agccatctag cattcccatg 3840 gatcctagta acaggctgca tcatgatgac agtgcacctc attctaatgt cactgagtat 3900 agagctttgg ttggtaagct gctctatctt acatctacta ggccaggcat agaattccct 3960 gtacaacagc taagtcaatt tctagataca cccaccagtg cacattttaa agctgctcac 4020 aaagtgttga gatatctcaa aggcaatccc ggcactggtt tattcttccc tagaaacact 4080 acactgcaac tatcaggttt cagtgatgcc gattggggag gttgtccaga cagcagaaga 4140 tctatcacgg ggtattgttt ttttattggc aaatccttgg tttgttggaa gtctaagaag 4200 cagttaactg tgtcaaagtc ttcttctgag gcagagtatc gtgccttggc ttcagcaact 4260 tgtgagcttc agtggttatc ctacctattg gctgatctac acatcatctc tgacaagctt 4320 cctgcactct attgtgacag tcagagtgct cttcatattg ctagtaatcc cgtgtttcac 4380 gaacggacca agcatttaga catagactgc catattgtca gagaaaaact gcaaggagga 4440 ctgatgaagc tgctacctat atctggctac aatcaaatag cagatattct aactaaagca 4500 ttacatcctg ccaatttcat cgtttatttt ccaagctagg ccttatcaac atcttccggc 4560 ctcagcttga gggggag 4577 // ID Copia-69_Mad-I repbase; DNA; EDCOT; 4558 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-69_Mad_; KW Copia-69_Mad-LTR; Copia-69_Mad-I. XX NM Copia-69_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4558 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1676-1676 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1803-2300] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 90..4355 FT /product="Copia-69_Mad-I_1p" FT /translation="MAEELSETESSMDAPAFSDVEVNPNQRLSSVLLNEFN FT YLPWSRAVSLALGGRSKLGYVNGAIEAPVVTSSTYESWLCKDQLVMSWLLN FT SMERRIAEIFSYSESSMHLWKQVKEMYGNQNNAARVFQLKKDLASLQQGSK FT AFVQHLGSLTNMWNELDVYRPHTTDATVLIKRAEEDKIFQLLASLGPEFED FT LRSHVLMNAELPSFTGVCAIIQREEVRRKVMNQETKDSVSETRAYVSSNKR FT PEGKVYKGKRPDLKCNYCDSLGHTKDRCWILHPELKPKFLKETKGPEIKGT FT QKYLNNNSYKANHAATLSTEGMVNFTTNPAALINDFAAYLHSKQVLNDRDE FT APVAEEKNHTALLGKFAGFLAKHDHVSQKDIPGIFSAFSTALNASNEHDYW FT IIDSGATDHMTNKINNLHDFTKMTNPSQVSVANGKGATVVGKGKINLLSKH FT IESAALYVPSFPFQLLSVGAITNSLNCLAIFSPHNVVFQDIITKRTIGEGF FT LLNGLYYLAKDTKNPKFFQVSSSVSQDQQLWHQRLAHPSDKVMSFLFPKIC FT KDKLKCDVCHLSKFSRLPFDSSTSRASHPFEIIHSDIWGPILESFDGYKYF FT VTFVDDFTRMTWLYLLKFKSELSNVFQDFHKLVGTQFASKIHILRSDNGTE FT YMSHNMSQYLSIHGILHQTTCVGTPQQNGIAERKNRDLLEKTRSIMFHMNV FT PKKFWSQGVLTAAYLINRLPSKVLSFKSPYEVLKDRQNDLSHLRVFGSTCF FT VHNQSLHRDKLDPRATKCVFFGYSSTQKGYKCYNPITKKIMVSRDVRFDEN FT MPYFSKKLSDADQGEFLSDMFPLPSVPLYQESPISRNPPTLLHELPSSQTT FT DIEPQVPIRRNPSRVRQPPLRLHDYVTYTSRYPLTNFVSYKQFSPSHTSFL FT STLDNTHEPQTFQEANELEIWQKAMRDELQALHDNRTWSVVKLPEGKKSVG FT SRWVYKTKFNSDGTIERHKARLVARGFTQTYGLDYKETFAPVAKMNTVRVL FT LSVAVNKSWPLYQMDVKNAFLHGELEEEVYMKLPPGHPQSDDPDMVCKLHK FT SIYGLKQSPRAWYAKLSSILEEFGFQRSSADSSLFVRDGLVGKVIVLIYVD FT DLIVTGDNAEEIHSLKLALQNKFAIKDLGRLKYFLGIELANSQEGLFLNQR FT KYILDLLKDSGLIDSKPARTPLDSKLQLSTHSEALSDITKYQRLVGKLIYL FT TITRPDISYAVSIVSQFMHAPTLAHMRIVKRILRYLKGSIGRGLLMTKNDS FT TAIMGYTDADWAGNSLDRKSTTGFCTFVGGNLVTWRSKKQTVVARSSAEAE FT YRAMASTACELIWLKSLLSDLGFPSNEPMSMFCDNQAAMHIASNPVFHERT FT KHIEVDCHYVRAQVQSKIITTYYTRSHDQLADIFTKSLPTVPFLCILSKLG FT SRDPLDPA" XX SQ Sequence 4558 BP; 1354 A; 942 C; 913 G; 1349 T; 0 other; tcaaaaattc aatatggtat cagagcagga actctaaatt cctgactcta gtaatcgttt 60 ccgctaagtt tcttttgctc taagccaaga tggctgaaga actctctgaa actgaaagct 120 cgatggatgc tccagcattt tctgacgttg aggtcaatcc taatcaacgt ctcagttctg 180 ttttgttgaa tgaattcaac taccttccct ggagtcgtgc agtatctctt gcacttggag 240 gaagatcaaa gcttggctat gtaaatggtg ctattgaagc tccagtagtc acttcttcta 300 catacgagtc gtggctgtgt aaagatcagt tggtcatgtc ttggttgctc aattcaatgg 360 agcgaaggat tgctgaaatt ttcagttatt ccgagtcatc catgcatctc tggaagcaag 420 taaaagagat gtatggaaat caaaataatg ctgcccgtgt cttccagctt aagaaggatc 480 tggcaagtct acaacaagga agcaaagcat ttgttcaaca ccttggcagt cttacaaaca 540 tgtggaatga gctcgatgtt tatcgtcctc ataccactga tgccactgtg ttgatcaaga 600 gagcagaaga agacaagatt tttcaactct tggcaagctt aggtccagag ttcgaagacc 660 tcagaagtca cgtcttaatg aatgctgaac tcccttcctt cactggtgtg tgtgccataa 720 tccaaaggga agaagtaagg aggaaagtca tgaatcaaga gactaaagac agcgtttctg 780 agactagggc ttatgtctct agcaacaaac gtcctgaagg caaagtttac aagggaaaaa 840 gaccagattt aaagtgcaac tactgtgatt ctcttggcca tacaaaagac agatgttgga 900 ttcttcatcc ggaattgaag cctaagttct tgaaggagac aaaaggtcca gagataaagg 960 gtacacaaaa atatctgaac aacaatagct acaaggccaa ccatgcagct accttgtcga 1020 cagaaggaat ggtgaacttc actaccaatc ctgctgcatt aatcaatgat tttgcagcat 1080 atctccacag caaacaggtg cttaacgata gagatgaagc tcccgtagct gaagagaaga 1140 atcacacagc tttacttgga aaatttgctg gttttctggc taaacatgac catgtttcac 1200 agaaagatat cccaggtatt ttcagtgcct tctctactgc cctaaatgct agtaatgaac 1260 atgattattg gatcattgac tcaggagcca cggatcacat gacaaataaa attaataact 1320 tacatgattt tacaaaaatg acaaatcctt ctcaagtgtc agtagctaat gggaagggtg 1380 ccacagttgt aggaaaagga aaaatcaact tactgtcaaa acacatagag tcagcagccc 1440 tttacgtacc ttcttttcct tttcaacttc tatcagtagg agccatcacc aattctctaa 1500 actgtctagc cattttctcc cctcacaatg tcgtttttca ggatatcatc accaagagaa 1560 cgattggtga aggtttcttg ttgaatgggc tttactactt ggctaaagac actaagaatc 1620 ccaagttttt tcaagtcagt tcaagtgttt ctcaagacca acaactttgg catcaacgtt 1680 tggcacatcc ttctgataaa gtaatgtctt ttttgtttcc aaaaatatgt aaggacaagt 1740 taaagtgtga tgtttgtcac ttgtctaagt tttctaggtt gccttttgat tcttccactt 1800 ctagagctag ccatcctttc gaaatcattc attcagacat ttggggtcca atactagagt 1860 cctttgatgg atataaatac tttgtaacct ttgttgatga ttttacaagg atgacttggt 1920 tgtatctttt gaaatttaag agtgaacttt caaatgtttt tcaagatttt cacaaactgg 1980 ttggtactca atttgcatca aaaattcata tattaagatc cgacaatggc actgaataca 2040 tgtcccataa catgtctcaa tatcttagta ttcatggcat actgcaccaa acaacatgtg 2100 ttggcacacc ccaacaaaat gggattgccg agagaaagaa tagagacctt cttgagaaga 2160 caagatcaat catgtttcat atgaatgtgc caaagaaatt ttggtcacaa ggagtactta 2220 cagccgccta cctaatcaat agattgccta gtaaagtact cagtttcaag tctccatatg 2280 aagtgttgaa ggacagacag aatgatctct cacacttgag agtttttggg tccacttgct 2340 ttgttcacaa ccaatctctc caccgtgata aactggatcc tcgagcaacc aaatgtgttt 2400 tctttggtta ctcatctacc caaaagggct acaagtgtta caatccaatc acaaagaaaa 2460 taatggtttc aagggatgtg agatttgatg aaaacatgcc ctacttctcc aagaaactaa 2520 gtgatgcaga tcagggggag tttttgagtg acatgtttcc attacctagc gttcctctct 2580 atcaagaaag tcccatttca cgtaacccac caactctatt gcatgagcta ccttcatctc 2640 aaaccacaga tattgaacct caagttccaa ttcgtcgaaa cccttctagg gttcgacagc 2700 ctccacttcg actacatgat tatgtcacct acacttctag gtatcctctt acaaactttg 2760 tttcctataa gcagttttcc ccctctcata cttcttttct tagtaccttg gacaatactc 2820 atgaaccaca aacatttcaa gaagcaaatg aacttgaaat ttggcaaaaa gcgatgaggg 2880 atgaactgca agctcttcat gacaaccgaa cctggagtgt agttaaactt cccgaaggga 2940 agaaatcagt tggcagccgt tgggtgtaca agactaagtt caactcagat gggacgattg 3000 aaaggcacaa agctcgtttg gtggctcgtg gatttactca gacttatggc ttggattaca 3060 aggaaacatt tgctcccgta gccaaaatga acactgtaag ggttctatta tcagttgccg 3120 taaataagtc ttggcctctt tatcaaatgg atgtgaagaa tgcttttttg catggggaat 3180 tagaggagga agtgtacatg aaactaccac ccggacatcc tcaatcagat gaccctgaca 3240 tggtttgtaa actgcacaaa tccatttatg gattgaaaca gtctccacgt gcatggtatg 3300 caaaactgag ctccattctt gaagagtttg gctttcaaag aagtagtgct gattcctcac 3360 tatttgttcg tgatggctta gttggaaaag taatcgtttt aatctacgtt gatgatctta 3420 tagtgacagg tgacaatgct gaagaaattc actctctcaa gctcgctctt caaaacaaat 3480 ttgcaatcaa agatttggga cgtctcaaat atttcctagg tattgagctt gcaaattcac 3540 aggaaggcct ctttctcaat caaaggaaat acattcttga tcttttgaag gactctggct 3600 taatagatag taaacctgca cgtactcctt tggatagcaa gctacaactt agtactcaca 3660 gtgaagctct ctccgatatt actaagtatc aaagacttgt aggaaagctt atttatctca 3720 caatcacgcg tcctgatatc tcttatgccg tgagtattgt gagtcaattt atgcatgctc 3780 ctacattagc tcatatgcga attgtgaaga gaattcttcg ttatctaaaa gggtctattg 3840 gtcgaggact ccttatgaca aaaaatgata gcactgccat catgggatat acagatgctg 3900 attgggctgg gaattctctt gatcgcaagt caacaacagg tttttgcacc tttgtaggtg 3960 gcaatttggt aacatggcgc agcaagaagc aaactgtcgt agctcgatcc agtgcagagg 4020 ccgagtatcg agctatggcc tccactgcgt gtgaacttat ttggctgaaa agccttctgt 4080 cggatctagg ctttcccagc aatgaaccta tgtctatgtt ctgtgacaat caagctgcca 4140 tgcacattgc ttccaatcca gtcttccacg agagaacgaa gcatattgaa gtggattgtc 4200 attacgttcg agcacaggtt caatccaaaa tcataaccac ctactacact cgcagtcatg 4260 atcagttggc tgacattttt accaaatctc ttcctacggt tccgtttctg tgcattctgt 4320 ccaagcttgg ctcaagggat cccctagatc cagcttgagg gggagtgttg gaagaataat 4380 gcaagctttt gtctagtttt gatggataac agctcagctt tcggctagtc ttagtgctag 4440 tgttagctgt ttgttttagt catggtgcat ctcttattta atgtttactt taggcatagt 4500 taagtgataa tattccctcg tcattgtaaa gctagttagt ggcttaagtt agagagag 4558 // ID COPIA4_LTR_MT repbase; DNA; EDCOT; 2034 BP. XX AC . XX DT 24-AUG-2005 (Rel. 10.08, Created) DT 30-AUG-2005 (Rel. 10.08, Last updated, Version 1) XX DE M. truncatula copia element, LTR sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; COPIA4_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2034 RA Gentles A. and Jurka J.; RT "COPIA4: Copia-type LTR retrotransposon from Medicago."; RL Repbase Reports 5(8), 196-196 (2005). XX DR [1] (Consensus) XX SQ Sequence 2034 BP; 695 A; 385 C; 376 G; 578 T; 0 other; tgttgaggca aaatccctaa ttaattttaa agataataaa caaatatgat taaagaatta 60 atggactttg attaattcct tggtatttaa cttgtgctct tgagtgtttt cactaagaca 120 ggaacaaggt ttgaatcata ccaagatgca taaaatcaaa ggacattgaa tccatgaact 180 aattctaaag ttcagaaagt tagttcagaa tgttgatcag aaagttgatc agaacgttct 240 gatgagagct cagaagcaac cctgttcaga agcaaccttg ctcagaagca accctgttca 300 gaagcaacct tgttcagaag caaccctgtt cagaagcaac ccagttcaga aggttgttca 360 gaacccagtt cagaaggttg ttcagaagca accagttcag aagcaaccta gttcagaagg 420 ttgttcagaa gcaacctagt tcagaaggtt gttcagaagc aaccagttca gaagcaacca 480 gttcagaagc aacctagttc agaaggttgt tcagaagcaa cctagttcag aaggttgttc 540 ttatacaagc caagaatctc aagaactgtg atcaaggtca tgcaaggcac atgtgacatg 600 aatatatgtc caggaaagta catttgcatg gatcaatcaa gcaataaagg catatacaag 660 agttatgtca aagaaggcat tcaatgttca tttaagacta tgaacattga tgtactagga 720 atatttcaca aaggaatatc atcctagatg ttatcatcac tgctcttcat tattgtttca 780 ctattaggat ttgattacat caaatgatag tcttacaaat catcctaagt gaaacagatg 840 gaacattctg atgatcagaa tgttcaagct cagctcatgc ttactttatg aacagtatag 900 taggtgaaaa gcaaaaagca aaagcaaagc aaatctgtca tctccaacaa gagatagaca 960 cgtctgagag ttggtactga tcaaggacaa cacaatctct caaagcatgg gcatgaagat 1020 gcagaatccc actaaatcct cctgcaccgg ttccaagaca aaatctggga aaggaacatt 1080 ctgatgtatg aagaaaagtc catacattgg ttattgtcca gaaattcata tgaaaagcat 1140 atgcatagcc cagaacttca tgtgttcatt catacatgat gaacccagat gaagatcatc 1200 atgaacacaa caacattctg atgttaatca gagatcagaa tgtttgccca gaatttcaag 1260 ttaaagcttg tgggacccag gacacatggc ataacaccat tggacaccct acaacggcta 1320 tatgagccca aggactctat aaatagaggg cttggcctta gcaaaacttg caccattgca 1380 aagcatacaa gaaaacaact ttgattttgt ttgaagcttt tgcaaactga aattgatcaa 1440 tctctaagtc tttcatcaac ttagtgcaaa tcaatactct tgttatctgt aggataacct 1500 cttcttcttc tttcattgtt tgttttacaa acacccaact tccatacaaa ttgtaacaaa 1560 gtctcatcta gcttttagag gtcctaaagt gttaggttga gcaaaggttg taaaagtcta 1620 agtggttaac ttagcaagaa ggtgcaagcc tgctgaggct tagagaatac aggagtgtaa 1680 ttgttcaggt gaacaagatt gtaaggtgca ggacttgaga ggttatctca agcatcttag 1740 tggaaactct cacaggattg tggggagtgg actagcccac attgggtgaa ccactataac 1800 tctttgtgtg ttctttcttt cttctctata cctttttatt tacagtatac acaacacaca 1860 cttacactta tactttatta agcaattttg tttatgaact tcagaacatt ctgaagtcag 1920 aaagttaaca taattccaag taaacaactt gagaatcact tttaagtttc aggataattt 1980 ttaaagggtc acaattcaaa cccccccttc cttgtgacta ttttatctac ttca 2034 // ID GYPSODE1_LTR repbase; DNA; EDCOT; 2963 BP. XX AC AC150162; XX DT 31-AUG-2005 (Rel. 10.09, Created) DT 31-AUG-2005 (Rel. 10.09, Last updated, Version 1) XX DE GYPSODE1: Gypsy-type element from Solanum demissum (LTR portion). XX KW Gypsy; LTR Retrotransposon; Transposable Element; GYPSODE1_LTR. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-2963 RA Jurka J.; RT "GYPSODE1: Gypsy-type element from wild potato."; RL Repbase Reports 5(9), 247-247 (2005). XX DR Genbank; AC150162; Positions 77604 80566. XX CC There are only 2 bases substituted between the LTRs. This appears CC to be a recent insertion. XX SQ Sequence 2963 BP; 592 A; 569 C; 727 G; 1075 T; 0 other; tgtaatgacc ctcttggtca tttctgtgtc ttgccttctg tgtgtcgttt agagcgttcc 60 tatagcgacc ccaagtcatt tatgacttgc tgggactgat agttcggtca cctggtcgtt 120 cgtttggtct tggtgtgagt ttttgtgttt tggagcttat gaaccttgaa cgatcatttt 180 cgatcaaaag ttctagaaga tgacatcgga atccaattct gacgatttca tcagctccga 240 aagggtcatt ttaggctagt agcatggtcg acatgactcc cgaggttttc agtgtgagtc 300 ggtgcgatta ggcgttttag cctttgattt ttgacataag gttgactttg gtcaacattt 360 tgagtaaacg cgctcggatg agaattccgt cagcgtggtt agctccggaa tgtcgagttt 420 ggtctagatt gacctttctt ttgtgtctgg aggttttcga tatctttccg agcccttttg 480 agggttttga cttaaaaggg ctttccgaag tgggacccaa tttttatcga aatgacctct 540 gatggaaatt tcgactgcgc cgttgagtct ggaatatcga atttggtatg attgcatatc 600 tcgtctgcgt gcacggggtt tcgaacgagt tcggggcacc ccgtcgggat tttaattttg 660 gaaatgttgc agaaaatcag caacatttct caaatttcaa accctcatct ctctctcatc 720 tctcaaccaa tttgggtgat ccaaaaggct aagttgtgag atttttcgag gacaacgcgt 780 tggtgatctc ggatagtgat ttggagtccc cgtttgaggt aattttcgaa aaatacctgc 840 tgccagacct ctttttgtga cttgattttg gaaattttga gacttgtttt cttagccatt 900 ttagatccga ttttggtgat ttttgaggct atcttgagtg gtttttcgag gagaacattg 960 tggtgttgtt agattttact gtagatcgct cgtttttggt aaatacactg ctgtcccatt 1020 ttgaattttg agaaaaattg ggttttagtt gcttgttgat attgtgttgt tcccgagccc 1080 cgaattgtgt cccattttgg gacatgagct gggggaactg gttaggaccc acttttgggg 1140 ttaatttcgg aatttcctgt gcgggtccca cgattcccgt tttgactcca aaattgaccc 1200 gtctctgttt gttgtgattt tggtgtctaa acgaccgtat taacgttgtg atactatttt 1260 tgatagcggg gaagcgtttc gagaccgttc ataaagggaa agctccgaag gagtgatttt 1320 ggagcgcgtg tgatcggcct acaggtaggc tacggttttc ctctcttaga ttgagctcga 1380 gaatgtgaat gcatgttgat tagttgggat ttgggttggt agttattgaa tcttgcatag 1440 gtgttaagaa atcatgtttt cggcctattt tgggaattat cggttaactg tgagcatgct 1500 ttgtgttatt aacggaccct tctcgctatg tggagtgctt gcatgcttaa ttactattta 1560 tttgaagcat gttgggcctt agtttaggtt tgactagggc ttgccttaga aatacatgat 1620 tcggatccga taggccttag ttttgccccg acgtcgctcg gccggcttag atccctgtag 1680 actggtgtag cagacttgag tctgatagtt tgggccttag ttagatgata cgcttgctcc 1740 gactttagtt attcttattt tccccgatgt tacggcttca cgagttacat cggcgacgct 1800 agtcctgctt cgcgatttga atttgatttt cgatttggtt ccaaggactt acattgattg 1860 gctaagtatg gacggcgttc catggacatt tatgagtgtg gatcgattag gactctttca 1920 gcagctacat tggcacattt atagagcatc cggtttaagg tccggcctct attgcccata 1980 tacttatata gagcatccgg tttaaggtcc ggcctctatt gcccagatac ttatatagag 2040 catccggttt aaggtccggc ctctattgct cagataccta tatagagcat ccggttagag 2100 ttccggcctc ttatacttgt tacttgtgat tggttacttg gatacttctg gtgagcatcc 2160 ggttcgaggt ccgacctccg tactgtcaga ttttactaat tagggttgag gttctgattc 2220 gtgttcttcg ttcttgggtt cgtatatgca attctcttta gttatagtta ttctgtgtac 2280 tcgtcgggct tatgggggtc cgttcgggtt tttatttaac ttgcgcacga gtgtaccttc 2340 tgggcttatg ggggtccagt taggtgtagt tagcttatag attactttag ttagttcttt 2400 gtacactcgt gtgcaatcca ttgttactta gatttccgct cttgaccctc ggtttgtatt 2460 attccttctt ttcatattgc ctttactttt caagttcagt cggcctatga tgcctactgg 2520 gtacctgttg ttttggtact tatgctacgc tctgcatctc tttcgtgatg caggtccggg 2580 cactagtagc cagcgttgat cgagcttgga gcagactgat ccggagacag gagtgagtac 2640 acggcgtttt gtactatttc agtctccatc tgtatatata gacttgtctt ttacctttcg 2700 agacagtcca gtctatgttg tccacttttg ggacttgtac tcattttgtt agtagctctg 2760 tactagtgac ttccaggttc tgggagggat ctttatttgt atatatgctt ttggtttgct 2820 tccgcctgtt atattgttat ttgcctactc ttgtttagtt tctaccctca gacccattac 2880 ttattgttcc gggttacggg ttggcttacc tactggtggg ttatagtagg tgccatcatg 2940 acttgagaaa tcgggtcgtg aca 2963 // ID Gypsy-24_Mad-I repbase; DNA; EDCOT; 4786 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-24_Mad_; KW Gypsy-24_Mad-LTR; Gypsy-24_Mad-I. XX NM Gypsy-24_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4786 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1742-1742 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [2140-2565] - Reverse transcriptase CC Positions [3697-4185] - Integrase core CC 'AGATA' target site duplication CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS 361..4257 FT /product="Gypsy-24_Mad-I_1p" FT /translation="MVSLSFPTLPNNPTPGISPHGRALIPSLHPNTTTTQA FT PNRPSTSRYLPPSTTGPTTSFVPPEPSYTHTPQPTSPTFPGHKHLKIELPR FT FFGDDPYGWIAMAEEFLDYHEITEHRRVTVAGLHLGGDAAHWLRWFKIRFP FT LSSWATFTTQLLQRFGPTDSLNINMALSHITQTTTVEAYVGQFIRLSCRTP FT DWTEAQLLGAFLGGLKDELQDDVVAQGPSSLARAIELARIYEHKQGRRPVV FT RPGHYRSSPYISKQPFFPSPTPPNQPTTSRPPPTTPTPPLPKPILRLTQAE FT MRNRREQGLCFNCDDQYRPGHRCRQSHILLLLADEEDPDPVPATEIPAPPP FT PPVVEHPEHPIALNAISATKRARGRAMRLDGFIFQTPIQVFIDSGADQSFL FT NPQVATRLGLHVDPSRTEAVMVATGRCFRTKGVAHQVSVRLQGYTFTSDFH FT LLAVAGCDMVLGVDWLETLGFIGWNFLLKIMEFSIHGTNYRLVGSSNPPVL FT RSPVPTSIEIVPGKPLHAVSQLSSLTHPSHQPTPPPALLQSILTKYHSLFQ FT PPTSLPPHREIDHRIPLLPGTGPINVRPYRYGHAQKAELERQVDEMLAAGI FT IRPSSSPFSSPALLVAKTDLSWRFCVDYRELNAVTIKDCFPVPIIDELLAE FT LKGAMIFSKLDLRSGYHQIRMHEADIHKTAFRTHEGHYEFTVMPFGLTNAP FT ATFQALMNSISKPLLRKSVLVFFDDILVFSDSLDRHVSHLTAVFDILQLHQ FT LQLKPSKCTFGQDSIAYLGHIISASGVQVDPSKIAAIVEWPTPTSLRGLRG FT FLGLAGYYRKFVRHFGLIAKPLTDLLKKDSFLWSPAADTAFSALKLALSTT FT PVLALPDFTKPFTLECDASNVGIGAVLAQDNHPIEFLSKPLAPKHQTLSVY FT DKEMMAVVFAVQKWRPYLIGHHFKILTDHQTLKYFLDQRLTTPAQQKWLLK FT LLGYNYTLEYRPGASNAAADALSRRSDLLSLMGISQPLFDCVSEIQNSYAA FT DPSTAKLLQDLQHNPHSTGSFKLQGDLIYYKTGIFVPSTSQWRARLLQEFH FT ASHSSGHSGFLRTYKRITHNFNWPGIKKEVKSFVAACDVCQRTHYETIKPP FT GLLQPLSVPTQVWTDIAMDFVEGLPSNHGKNAILVVVDRLSKYGHFIPIQH FT PYSAPQIAEVFIQEVFRLHGMPASIVSDRDPIFLSEFWTAFFKHQHTALCK FT SSAYHPQTDGQTEVLNRTLEHYLRSFAMDKPTTWIRWLPWAEWWYNTTFQS FT TIKMTPFQAVYGYPPPTVQSYLPGSSGGCHSQEPRHPS" XX SQ Sequence 4786 BP; 1114 A; 1503 C; 1001 G; 1164 T; 4 other; tttggtatcc agagccaggt tggagaccat gggcaaaagt aaggcgtccg ttacggtggc 60 ggatgtacca gaggacgaat tggaccgtga gtttcaacag caccagatac tcacccagct 120 acaggagttt caggaatcca tctcgctgtt gaatatccgc tacgacgacc tgcagcacac 180 catggccgat ctctcgatcc accgggttcg tcaggaccaa ctgcagcaaa cgattttaga 240 cgaagttcgt gccctmaaaa accctcccct acccaaccca caaattccaa tcggctccat 300 tcccgtttcg ctaggaccca cccccttctc tgccgtccac acccccatac caccaccgac 360 atggtctctc tctccttccc cacccttcct aacaacccaa cccccgggat ctcacctcac 420 ggccgggccc tcatcccttc ccttcacccc aacaccacca ccacccaagc tccgaaccga 480 ccctccacct cccgctacct tcccccatcc acgactgggc ccaccacctc ttttgttccc 540 cccgaaccgt cttacaccca caccccccaa cccacttccc cgacctttcc tgggcacaaa 600 cacctcaaaa tcgaacttcc tcgtttcttt ggagacgacc cttacggatg gattgcgatg 660 gctgaggagt ttttagacta tcacgagata accgagcacc gccgcgtcac agtggcaggt 720 cttcatcttg gaggagacgc ggcccactgg ctccgttggt tcaagatacg attccccctc 780 tcctcatggg ccaccttcac gacccagctg ctgcaacgat ttggcccaac tgactccttg 840 aacattaata tggccttgtc scatatcacg cagaccacca cagtggaggc gtatgtgggc 900 cagttcattc gcctctcctg ccgcactccg gactggaccg aagctcaact actgggcgcg 960 tttttgggag gcctcaaaga cgagctgcaa gatgatgtcg tggcccaggg accttcctct 1020 ctggcacgag caattgaact cgctcgcatc tacgagcaca aacagggtcg ccggccagtg 1080 gtccgtcccg gacactatcg ttcctcccct tacatttcta aacaaccctt tttcccctca 1140 cccaccccac ctaaccaacc cactacatct cgacctcctc ctacaacacc aacccctccc 1200 ctaccaaagc caatcctacg gctcacccag gcagagatgc gcaaccgtcg cgagcaggga 1260 ctctgcttca actgtgatga ccagtatcga cccggtcacc ggtgtcgtca atcccacata 1320 ctactgttac tagcggatga ggaagatccc gaccctgttc cagcgacaga gatccccgca 1380 ccaccgcccc ctcccgtggt ggaacatccg gagcatccca tcgccctcaa tgccatatca 1440 gccactaagc gtgctagggg ccgtgcgatg cgcttggacg gattcatttt ccaaacaccg 1500 atccaagtct tcatcgactc cggtgctgat caaagttttc tcaacccgca agtggcgact 1560 cgtttgggct tgcacgttga cccgtctcga accgaggcag tcatggtcgc cacaggacgt 1620 tgttttcgca ctaaaggggt ggctcaccaa gtttcagtgc gccttcaagg ctatacattt 1680 accagtgact ttcaccttct tgcggtggcg ggatgtgaca tggtattagg agtggattgg 1740 ttggaaacac tgggtttcat cggatggaat tttttgttaa aaattatgga attctcaatc 1800 catggaacca attaccgatt ggttgggtcc tcgaatcccc ctgttctgcg ctctcctgtg 1860 cctacaagta ttgagattgt tcctggcaag cctctccatg ctgtatccca gttgtcaagc 1920 cttactcacc cctctcacca acctactcca ccaccggccc tacttcaatc catcctcact 1980 aaatatcaca gtctcttcca accaccaaca tccttgcccc ctcatcgcga gatcgatcat 2040 cgaattccct tactcccagg tacggggcct atcaatgttc gaccatatcg atacgggcat 2100 gcccagaaag ccgaattgga gcgccaagtt gacgagatgc tagccgcagg cattatccgc 2160 cccagctcga gtcccttctc gtccccggcc ttattagtgg ccaaaactga cttgtcatgg 2220 cgtttttgtg tggattacag agagctaaat gcggtcacca tcaaagattg cttcccggtc 2280 cctattattg atgaactatt ggctgaattg aaaggcgcta tgatattttc taaattggat 2340 ctccgctccg ggtaccacca aatccgaatg cacgaggcgg acatccataa gacggcgttc 2400 cgcacacatg aaggccatta cgaattcaca gtcatgccat ttggcctgac caacgcgcca 2460 gccaccttcc aagcactgat gaattcaatc tcgaagcccc tgctccggaa atccgttctc 2520 gtcttttttg atgatatttt agtcttcagt gactccctag accgccatgt ttcccacctc 2580 acggccgtgt tcgacattct ccagttgcac caattgcagt tgaaaccatc caagtgtact 2640 tttggtcagg actcgattgc ctatttaggc catatcattt cagctagtgg ggttcaggtt 2700 gacccatcca aaattgcagc tattgtggaa tggccgacgc ctacaagtct taggggcctt 2760 cgcggattct tgggtctggc aggatactac cgcaaatttg tccgccattt tggtctcatt 2820 gccaagcctc tcacagactt gctcaaaaaa gacagtttcc tttggtcccc ggcagccgac 2880 acggcgttct cggccctcaa acttgcactg tccaccacac cagtgctggc tctcccggac 2940 ttcaccaagc cgttcactct cgagtgtgac gcctcaaacg ttggtatagg agcagtgttg 3000 gcacaagata accatcccat cgagttcctc agtaagccct tggcccccaa acaccaaacc 3060 ttgtcagtgt atgataagga aatgatggct gtagtgtttg ctgtacaaaa gtggcgccca 3120 tacttgattg gtcatcactt caaaattctc acggatcacc aaacactcaa atatttcttg 3180 gaccaacgac ttactactcc ggcacaacaa aagtggctgt tgaaactact tgggtacaac 3240 tataccttgg agtatcgtcc aggggcttct aatgcagctg ccgatgcact gtcccgccgt 3300 tccgaccttc tatctctaat ggggatatca caaccactat ttgattgtgt atccgagatt 3360 cagaattcct atgcggcgga tccttccacg gccaagctcc ttcaggactt acaacataac 3420 ccccacagta caggctcttt taagctgcaa ggtgacctga tttattacaa gaccggtatt 3480 ttcgtacctt ccacatctca gtggcgtgcc cgccttctac aggaattcca tgcttctcat 3540 tcttccggac attccgggtt cttacggaca tacaaacgca tcactcataa ctttaattgg 3600 cccggcataa aaaaagaggt taaaagcttc gtggccgctt gtgatgtctg ccaacgaact 3660 cattatgaaa ccattaaacc accaggactt ctacagccac tctctgtgcc gacccaagtg 3720 tggactgata ttgctatgga cttcgtcgaa ggtcttccct cgaaccatgg caagaatgct 3780 attttggtag tcgtggatcg tctctctaaa tacggtcact tcattcctat ccagcacccc 3840 tactccgctc cacagattgc tgaagtcttt attcaggagg tgttcagatt gcacgggatg 3900 cctgcttcta ttgttagtga tcgmgacccg attttcctta gtgagttttg gacggccttc 3960 ttcaaacacc aacatacggc actttgcaaa agctccgcct atcacccaca aacggatggc 4020 cagacagaag ttcttaacag gacattagag cattatcttc gcagctttgc catggacaaa 4080 cccactactt ggattcgatg gctgccatgg gcggaatggt ggtataacac cacctttcag 4140 tcaaccatca aaatgactcc attccaggcg gtctacggct atcctccacc cactgtgcag 4200 tcctaccttc ccggctcatc tggtggatgt cactctcagg aaccgagaca cccttcttaa 4260 gcatctcaag gagaacatgc acatggcaca gcagcgcatg aggcaacagg cagacaagca 4320 tcgatcggaa atgacttttc aattggggat tgggtcttcc tcaaactcca accgtatcgg 4380 caaacctctg tgtccaaaac tcaccgccca aaactggccc cgcgctatta cggaccattt 4440 caagtgctcg ctcgcgtcgg ccaggtcgcc tacacattgg accttcctcc tcagtcccgc 4500 attcacccca cttttcatgt gtcactgctc aaacccaagc tcggtgctca ttctgtgact 4560 tcagcaacac tacccccagt ggccgctgat ggctcccttc tatggtttcc agagcgcatc 4620 ctgcaacgtg gcatgttcaa aagacacaac aaggcsgtca ctcgctggtt aatcaaatgg 4680 caaggtctac cggagcatga cgcaacatgg gaagatgctg actccatagt cactcgtttt 4740 ccagattttg acgcctgagg acaggcttgt tctatggggg gtgccc 4786 // ID hAT-10N1_VV repbase; DNA; EDCOT; 1309 BP. XX AC . XX DT 05-FEB-2009 (Rel. 14.03, Created) DT 05-FEB-2009 (Rel. 14.03, Last updated, Version 1) XX DE hAT-10N1_VV, non-autonomous DNA transposon - a consensus DE sequence. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; TIR; KW MITE; mHatvine-10.1; hAT-10N1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1309 RA Benjak A., Boue S., Forneck A. and Casacuberta J.M.; RT "Recent amplification and impact of MITEs on the genome of RT grapevine (Vitis vinifera L.). submitted."; RL Repbase Reports 9(3), 714-714 (2009). XX DR [1] (Consensus) XX CC hAT-10N1_VV (mHatvine-10.1 in [1]) is a non-autonomous DNA CC transposon which is a deletion derivate of the autonomous CC hAT-10_VV. All copies contain a central region (positions CC 319-943) that is not related to hAT-10_VV but to a cellular CC non-genic region (82% identity). It seems that this region was CC captured and transduplicated by this element. Individual copies CC are >90% identical to the consensus sequence. TIRs are 11 bp-long CC (having 1 conserved mismatch) and flanked by 8 bp-long TSDs. CC There are approximately 20 highly conserved copies present in the CC genome which could place this family in the group of MITEs. XX SQ Sequence 1309 BP; 438 A; 217 C; 241 G; 395 T; 18 other; cagggttcaa aatatcggcc gagtccggta cgactcggcc gagtcgtatc cgcctcgacg 60 ccgaccgcga cgagtccgat accagataca ttttatacct aractcggct ttgaatcggt 120 tggactcgga tgactcgacc gatattccga gttaactcgg tcgactcgga aaaaaaaaaa 180 maatcaacag attctctaca aaagaaaccc atcacaacaa gaatcaacat tttyagagaa 240 atcaggagtg aagatttttc atctttggtg cgctgctggt gccgcaacgg tgactgaacg 300 ccggctaaac aaccctcmtt ccgagtttgg gagcagagaa gagctttgtg cagtgaagaa 360 aataggattt gayggcacca ccggcrgaac caacgtcgtg agcgtccacg gtggagggca 420 agataggaga agagagaggt gagagtagag agrtggccat ggcggtttca ctctctgcag 480 atcgcactct ctgctttcag tggagggcaa gataggagaa gataggtctt gaggctragg 540 attggtgatc ctatgtggct cagcaccatg acatattttt gacgggttca gcccaccaga 600 ttaggcccag cccaagttca attcataaaa gcctgtggtc catgtatttc tgtataaaaa 660 aataaaaaaa taaaaatttg gtgttttaag cttatggaaa aaaaatgatt tcttcaaaaa 720 tatattaaga aaaataaaat tttcatgcat gattttttat aaaaatatat awaaaaaaaa 780 atcaaatata attaaaatta attatatata aaaaaaatta aattaaaatt tgtttaaaga 840 atcatataag aataatgtat taatattacc tcggaaggag rttrataatt taagtaattg 900 cttaaaataa taattatgtt gatgtattag tctaaattga taaawwwdww tttatttatg 960 cacccccgtc tatagatctt acctctaaag atcatattga ttatagttga cttcaagttg 1020 atttcgagac cgatatattt atttttatta gcattattat aaataacttt gagcaaatac 1080 ttttataact atttaaataa tgttaaatgt aatacaattt tattttatta attttttgag 1140 tttatttaat tgtatatatt tttctgatga tttacataat atttttataa ttttttgaat 1200 tttctaatta gcttatttta cgtatcgtcc gataccaaac cgatacaccg agaccgatay 1260 gcctcgggac cctccgagtc aatgaccgat accgcgactt tgaaccatg 1309 // ID Copia-55_VV-LTR repbase; DNA; EDCOT; 184 BP. XX AC chr6; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-55_VV_; KW Copia-55_VV-I; Copia-55_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-184 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr6; Positions 19922825 19922642. XX SQ Sequence 184 BP; 63 A; 27 C; 36 G; 58 T; 0 other; tgttggcgtg agctgtctaa tgagataagt ataaaaatat gtatgtaaat cccatacttc 60 aagggatggc cttatttttt gccgcaagat atgtataggc tagaatagat tcctatgctc 120 tgaatctata tagtattgta ttcaacacac aaggaaataa tggaaaagag actacctttt 180 gaca 184 // ID SLIDE repbase; DNA; EDCOT; 3733 BP. XX AC X97569; XX DT 24-FEB-1998 (Rel. 3.01, Created) DT 24-FEB-1998 (Rel. 3.01, Last updated, Version 1) XX DE Ac-like DNA transposon Slide. XX KW hAT; DNA transposon; Transposable Element; DNA transposon Slide; KW hAT-superfamily; SLIDE. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RP 1-3733 RA Grappin P., Audeon C., Chupeau C.M. and Grandbastien A.M.; RT "Molecular and functional characterization of Slide, an Ac-like RT autonomous transposable element from tobacco."; RL Mol. Gen. Genet 252(4), 386-397 (1996). XX RN [2] RP 1-3733 RA Grappin P.; RT "SLIDE."; RL Direct Submission to Genbank (22-APR-1996)P. Grappin, INRA Centre RL de versailles, Laboratoire de Biologie Cellulaire, route de St RL Cyr, 78026 Versailles cedex, France. XX DR GenBank; X97569; Positions 1 3733. XX SQ Sequence 3733 BP; 1243 A; 680 C; 691 G; 1119 T; 0 other; taatgctgct cggtgggccg ggcctgaacc ggaccggacc gggcccgcgg tcctaacggg 60 cctggtgggc ctggtgggcc ggtcctgggt gggccggtct tggtgggcct ctgagcccgt 120 aacgggctgg tctccatggt tgagcccacg agcccgggac cgtttggccc gggaccggca 180 ggcgggcctg ggccggtcct ggcgggcctg gcgggcccaa cggctattta aaaaaaaaaa 240 aaaaaaaaaa aaaaaaaaaa atcaaacggc catatttaaa atctagccgt ttgggctgaa 300 aatatgaccg ttttttaagt taaaaaaatg gccatttggc ccccaaactt tattttaacc 360 ccaaacttta tataattaca cttttcccca tttctcaact ataaataccc cctcattctt 420 tcatttttat tcaccaattc atcaatatct ctcaatatct ctcaatctct ctcaatctct 480 ctactacaat tacttaattt attgttgaaa tttcgtgaaa aattgtgaag ttgttgaatt 540 gaagttttca agtgttcaac gattttcaat tttcaagaag ttgttcggca atccggtaaa 600 ctcgtttcaa ctcttacgtt tttataatat atttttgtgt ggtttagttt gcataattat 660 aattaatatg gcatttactt tgaaaaaaat gtttggtaaa ggaaaagata aaaccggtga 720 aagtagtggc caaccaacta cccttccccc ggctccccga cctagaaaag ataagcaagt 780 tgaaagtagt cgccaaccta gacgtcctcc tccttccgta attcttgata gtgatcaccc 840 ttgttttcaa tttaccgata gtgaaattta tcataatgtt gcaccaggtg atagattaga 900 tgatgaaatt atgaatgctc tttatcctaa tgaaaccatc ttagaaaata atgaggaaaa 960 tgaggatgat gatgaaactc aaacaccgga tttagatgat acacctacta gtcctcttaa 1020 taacccaagt gatgcaccgg tcgacccacc tgtagaaact cctactttta atagagaacc 1080 tgctaaacgc ttagaaacat cattagtttg gaattttttt actcaagtaa ggagaaaaaa 1140 taaggctaag tgtaaaactt gtgggaaatt aatgtcgcat aaatatgtag gagaccgtag 1200 cggcacaggt agtttgacta ggcacataaa aacacaccct agagataagg ctagattttt 1260 tcaaatgaaa gcgccatcta gaggggacaa gtgtagattc tgcgattaac cctagtacag 1320 gttcaaatct agttcaacca ggaattaaca ctgtcactgg aggtatttta tattacgatc 1380 caaatagaga tcgtgaagaa ttagcaaaga tgattactgt tatgtgctta ccttatactt 1440 ttgcttctaa tcctaattgg gttcattata ttagaagagt gtttaatcct acttataaag 1500 gttggcctcg cgcaacagtt aagagtgata tttataaatt caaacatgaa tatgaacaat 1560 atttgcgtta tttatttact catataccta atcggatttc tattactact gatattggta 1620 gaagtggtaa tgattgtgat tacctaactg ttacaagtca ttggatagat gaagaatgga 1680 taatgcaaaa tcgcataatt gcatatagaa taattaattc gcgtcacaca ggtaaattta 1740 tagctaacac tgttgcagat atttgtaaca aatgcatttc ctgggcaata ttatcctact 1800 atttcaaact gtttagttta tattgcagca ctatctgatt tgtttgttga atttagtgag 1860 ggtggggata tttatgaact tgctataaat gaaatgaaac aaaagtttaa aaaatatttt 1920 tttcctatcc ctcctattta tggtcttgct gcaatgctaa atcctacaat gaaattggga 1980 ggtcctcatt tttggtattc aaatatttat aaggctttag atctttcaaa tgaggaaatt 2040 gcgacacttg cagatgcaaa agcttcaatt aagattaacg ctcaaacagt ttataatgct 2100 tatcaacttg ccttagagca tgctaggcca actattccaa cccctacttc gtctagctca 2160 caatcctcta aaagagttgc gggcttaaaa gctcttaaat cttggacgga gttcaggggg 2220 tctcaaggtg aaaattatga tgaaacttca catctaaatg agcttcaagt ttatttgtct 2280 cagggacttg aaaaggagaa tccagacggc tcttttgatc ttttggaatg gtggaaggca 2340 agggaaaaac attttcctgt tcttgcaagg atggctcggg atattttatc aattcaagct 2400 tcaactgttg catcagagag cgctttcagt caagcaagac tgcaaatagg tgatcataga 2460 gcgtctatga gggatagctt ggaaaaatca gtattgttta gagattggat ccgctcggaa 2520 agaagaaact ttggaattgc agaagcacaa ccggcgatag atgaagctta tgaagaaatg 2580 atagcggaac ttacggagga ttcgcttcgc ccggaagtgg tgatgaacaa gcttcttttc 2640 caccaccacc aacgcaacct cctccgaacc ttgaaggatt tatgagattt gttagagata 2700 atacatagaa taatatgtaa cttgtatttt ggcacatctt ccttagtttt tttccttcta 2760 atggtggtat tagtaccttg ttgtgctcat tccattgggg gaaggatgac taagaaagat 2820 atgtcatttt ttggtaataa aatttattgc ttctacccat gagcttcttt tcgcaatatt 2880 tctttgtcta tacttagaat tatttatatg ctacaatata tacataatat acaatatata 2940 tactacaagg aaaatatatt tataagctac aatatataca taatatacaa tatatatact 3000 acaagaaaat atataagaga atatatatac ataagataca atataatata ctacaaggaa 3060 atatattatg ctacaatata tacataagat acaatatata tactacaagg aaatatatta 3120 tgcgaatata tatacataag atacaatata tatactacaa gaaatatata agagaatata 3180 tatcataaga tacaatataa tatactacaa ggaaatatat tatgctacaa tatatacata 3240 atatacaata tatatactac aaggaaatat atttataagc tacaatatat acataagata 3300 caatatatat actaaaagga aatatataag agaatatata tacataagat acaatataat 3360 atcaagaagt gatatttatg catgacaatt tagtgtttta ctattgtttt gttattttct 3420 ttttcgtcaa gcactttaat aattagatat acatatatac tacatattaa tatagccatg 3480 atactacaag aaattgtctt taaaaaaaaa aaaaaaaaaa cccgctaggc ccgcgaagcc 3540 cacgagcccg gcccgttaag cacaggacca tgtgggctta ggcccgtcac gggccggttc 3600 cacccattag gcccacgaag accgggaccg ccaggcccgg gaccgccaga gcccgggacc 3660 acgaagcccg ggaccgcgag gcccggcccg ttaggcccac taaggcccgg gcccgggaca 3720 aaatacagca tta 3733 // ID GmCOPIA10_I repbase; DNA; EDCOT; 7059 BP. XX AC . XX DT 27-JUN-2008 (Rel. 13.06, Created) DT 30-JUN-2008 (Rel. 13.06, Last updated, Version 1) XX DE Copia-like retrotransposon from Glycine max. XX KW Copia; LTR Retrotransposon; Transposable Element; soybean; KW extra ORF; consensus; internal portion; GmCOPIA10; GmCOPIA10_LTR; KW GmCOPIA10_I. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-7059 RA Wright L.N. and Laten H.M.; RT "Intact, full-length transposable element consensus sequences in RT Glycine max assembled from robust collections of BAC-ends."; RL Repbase Reports 8(6), 646-646 (2008). XX DR [1] (Consensus) XX CC Complete sequence with extra ORF of unknown identity downstream CC of pol. Related to retrotransposon V14 from Vitis vinifera. XX FH Key Location/Qualifiers FT CDS 53..1786 FT /product="GmCOPIA10_1p" FT /note="gag." FT /translation="MASANSLFPEGNSINRPPIFNGEGYHYWKTRMQIFIE FT AIDLNIWEAIEIGPYIPTTVERVSIDGSSSSESITIEKPRDRWSEEDRKRV FT QYNLKAKNIITSALGMDEYFRVSNCKSAKEMWDTLRLTHEGTTDVKRSRIN FT ALTHEYELFRMNXNENIQSMQKRFTHIVNHLAALGKEFQNEDLINKVLRCL FT SREWQPKVTAISESRDLSNMSLATLFGKLQEHEMELLRLHQNEENDKKKKG FT IALKASSSIQEESDQDNDADDDDDLSXFVKRFNKFLKVRGNQRRPNFKSKR FT RTENSSSTLKCFECNQPGHLRVDCPIFKKKMEKSEKKNHSEKKLKKAYITW FT DENDLESSDDSENEEINLCLMAKSYESDEEVTSSNNLSISFDELQDAFADL FT HKESIKLAKLVSSSKKTISNLENEISKLNKELDLLRNEVSISKTNEKVNIS FT TINDKKITDSCSCCDKYVKEIKELKNSLAKFSYSRNNLDVILSKQRYVSNK FT NGLGYKSEKLQKVHKNFSTSTQKCNSNSITCFYCGRRGHGISTCYFKKNYS FT NIKMIWVPKGSSVYTNMQGPNKIWVPKSKT*" FT CDS 1774..4875 FT /product="GmCOPIA10_2p" FT /note="Pol: prot, int, rt." FT /translation="VKNLIMQVSLRKKWYIDSGCSKHMTGDASNFTHISPK FT KSGHVTYGDNNKGRILGVGKIGTNSSNSIENVLLVEGLKHSLLSVSQLCDK FT GYLVSFDSQKCLIEHKHDINIKHVGHRVNNVYMIDLSIKQENNHCFLSKDD FT DPWLWHKRIAHINMDHLNKLISKDLVVGLPKLKFEKDKLCDACQKGKQTRV FT SFKSKNVVSTTRPLQLLHMDLFGPSRTMSFGGNYYALVIVDDFSRYTWTLF FT ITHKSDSFXAFRKLAKVIQNKKNLKIASIRSDHGGEFENKDFELFCDEHGI FT EHNFSAPRTPQQNGVVERKNRSLEEIARTLLNDTSLPKYFWAEAVNTACYI FT MNRALIRPILKKTPYELFNGRKPNISHLHVFGCKCFVLNNGKDNLGKFDAK FT SDEGIFLGYSLQSKAYRIYNKRTMNIEESIHVTFDESNAILSXKNMLDDIA FT DSLEHMNIHEQDSKGNDKGNNEDPPEEGKSNDXLPREWKTSRDHPLDNIIG FT DISKGVTTRHSLKDLCNNMAFVSMIEPKNIKEAIVDDNWIIAMQEELNQFE FT RNNVWKLVEKPENYPVIGTKWVFRNKLDEHGIIIRNKARLVAKGYNQEEGI FT DYEETYAPVARLEAIRMLLAYASIMNFKLYQMDVKSAFLNGLIQEEVYVEQ FT PPGFEISDKPNHVYKLQKALYGLKQAPRAWYERLSNFLLEKEFSRGKVDTT FT LFIKRXHNDILLVQIYVDDIIFGSTNDSLCKEFSLDMQSEFEMSMMGELKY FT FLGLQIKQTQEGIFINQSKYCKELIKRFGMDSAKHMSTPMSTNCYLDKDES FT GQSIDIKQYRGMIGSLLYLSASRPDIMFSVCMCARFQSNPKQSHLSAVKRI FT MRYLLGTINLGLWYPKNSTCNLIGYSDSDFAGSKTDRKSTSGTCQFIGSAL FT VSWHSKKQNSVALSTAEAEYISAGSCCAQILWMKQQLSDYGIILDRIPIKC FT DNTSAINLSKNPVQHSRTKHIEIRHHFLRDHVLKGDCVLEFVDTKNQLADI FT FTKPLPKEVFFSIRRELGLLDVRDLEK*" FT CDS 5330..6586 FT /product="GmCOPIA10_3p" FT /note="Unknown." FT /translation="NFKPSILTQFFTKSRPVKPNLPLFHSSFTSTDQNPEK FT LHQMAEPSKKRKGSSSTATAAAHRRHGPSGAPTAPIPPSLSSPRSSTLFSS FT DDQRLRYLSQFSSRIILDPKYLDVEFFNDETFDCYQVFQNSGLVDFMSLKL FT PYYPELVKVFYCNLKIQDGIIMSEVHGXSMVIDQSLFFSLTHLPSQGAPFE FT GTIVDDWKFDYSSHDARRMVCNDQAEMTGRLLAGSLTFDNRIMHYIIVRIL FT LPRSSNLAQASEEDLILMWAFLTGRQIDWAHLVRYRMHKALRANAPLPYPH FT LITLFLRHFQIPLDDEPFVQVKRSFAIGAGAVTSFGYRKDRNGQWLKKDAL FT PPQDERTPSPPPQREDSALMNEVLSELRGLRSYVGDRFDSLDSRFAGMDIR FT LTQLEEDVGYIRQSFDLPPPPPSS*" XX SQ Sequence 7059 BP; 2415 A; 1136 C; 1271 G; 2192 T; 45 other; agtggtatca gagcttcatt cttgtacaaa gtttagaagc ttcaagaaaa agatggcctc 60 agcaaattcc ttatttccag aagggaattc tatcaataga cctccaatct ttaatggaga 120 gggttaccac tactggaaaa cccgaatgca aatttttatc gaggcaatag atctaaatat 180 ctgggaagcc atwgaaatag ggccttatat acccaccaca gtagaaagag tttcaataga 240 tggtagttca tcaagtgaaa gcataaccat agaaaaacct agagatagat ggtctgaaga 300 ggatagaaaa cgagtacaat acaacctaaa agccaaaaac ataataacat ctgccctagg 360 aatggatgaa tatttcagag tttcaaattg yaagagtgct aaggaaatgt gggacactct 420 tcgattaaca catgaaggaa ctacagatgt taaaagatct aggataaatg cactaactca 480 tgagtatgaa ttatttagaa tgaatrcaaa tgaaaatatt cagagtatgc aaaagagatt 540 tacacatata gtaaatcatc tagcagcctt aggcaaagaa tttcaaaatg aagatcttat 600 aaacaaggtg ctaagatgtt taagtagaga atggcaaccc aaagtaacgg ctatttctga 660 atcaagagat ttgtctaaca tgtctcttgc cactttattt ggtaagttgc aggaacacga 720 gatggaacta ttgagattgc accaaaatga agaaaatgac aagaaaaaga aaggaattgc 780 tcttaaagca tcatcctcaa ttcaagaaga aagtgatcag gataatgatg cagatgatga 840 tgatgatcta agtytctttg taaaaagatt caacaaattt cttaaagtaa gaggaaatca 900 gaggcgacca aattttaaat caaagagaag gacagaaaat tcatcctcta ctctaaaatg 960 ctttgaatgc aatcaacctg gacatctgag ggttgattgt cccatcttca agaaaaagat 1020 ggaaaaatct gaaaagaaaa atcatagtga gaagaaacta aagaaagcat acatcacatg 1080 ggatgaaaat gatttggaat cctctgatga ttctgaaaat gaagagataa atctttgcct 1140 tatggcaaaa agttacgaaa gtgatgaaga ggtaacatct tcaaacaact tatctatttc 1200 ttttgatgaa ttgcaagatg catttgctga tttgcataaa gaatcaatta aacttgcaaa 1260 attagtttca tcatcaaaga aaacaatttc aaatttagaa aatgaaattt caaaattaaa 1320 caaagaatta gatcttctta gaaatgaagt ytcaatctct aaaacaaatg aaaaagttaa 1380 tatctccact attaatgaca agaaaataac agattcttgt agttgttgtg ataaatatgt 1440 aaaagaaatt aaagagttaa aaaattcact tgcaaaattt tcatatagta gaaataattt 1500 agatgttata ttaagtaaac aaagatatgt gtctaataaa aatggactag ggtataaatc 1560 tgaaaaacta caaaaggttc ataaaaactt ttccacttcc acacaaaaat gtaattctaa 1620 ttctatcact tgtttttact gtggaagaag aggacatggc atatcaactt gctacttcaa 1680 gaaaaattac agtaayatta aaatgatatg ggtcccaaaa ggatcctcag tttatactaa 1740 catgcaagga cccaataaaa tttgggtacc taagtcaaaa acttgattat gcaggtatct 1800 ttgagaaaga agtggtacat agatagcgga tgctcaaaac atatgactgg agatgcatca 1860 aattttacac acatatctcc aaagaaaagc gggcatgtaa catatggtga caacaacaaa 1920 ggtagaattc ttggagtggg taaaataggt acaaattctt caaactccat tgaaaatgtt 1980 ctacttgttg aaggccttaa gcatagcctg cttagcgtta gtcaactatg tgacaaaggc 2040 tatctagtat catttgattc tcagaaatgt cttatagaac ataagcatga cattaatata 2100 aagcatgtag gacatagagt caataatgtt tacatgatag acttaagcat aaaacaagaa 2160 aacaatcatt gctttcttag taaagatgat gatccatggt tatggcataa aagaattgct 2220 cacataaaca tggatcactt aaataaatta atttcaaaag atttagtagt tggtttgcct 2280 aaattgaaat ttgaaaaaga taaaytatgc gatgcatgtc aaaagggcaa acaaacaaga 2340 gtctcattca aatctaaaaa tgttgtttca accactcgac cattacagtt attgcatatg 2400 gatytatttg gtccatctag aaccatgagt tttggaggaa attactatgc tttagttata 2460 gttgatgatt tctctagata tacttggaca ttatttatta cacataaaag tgattcattc 2520 cawgcattta graaacttgc taaagtcata caaaacaaga aaaatctcaa gattgcatcc 2580 attagaagtg atcatggggg tgaatttgaa aataaagatt ttgaattatt ttgtgatgaa 2640 catggtattg aacataattt ttctgcacca agaacycctc aacaaaatgg agttgttgag 2700 aggaaaaata ggtcattgga agaaattgca agaactttat taaatgatac ttctcttcca 2760 aagtattttt gggctgaagc tgtcaatact gcatgttaca tcatgaatag rgccttgata 2820 agacctattt taaagaaaac cccatatgag ttatttaatg gtagaaaacc taatatttct 2880 catctacatg tttttggktg caagtgcttt gtrcttaata atggtaaaga taatctagga 2940 aaattcgatg caaaatctga tgaaggcatt tttcttggat attcwttaca aagcaaagca 3000 tatagratat ataataagag aactatgaat atagaggaat ccattcatgt tacctttgat 3060 gaatctaatg ctatattgtc aasaaagaat atgctagatg acattgcaga ttctttagaa 3120 catatgaaca ttcatgaaca agattccaaa ggaaatgaca aaggaaacaa tgaagatcct 3180 ccagaagaag gcaaatccaa tgatgyactc ccaagagaat ggaaaacttc aagagatcat 3240 cccctcgaca ayattattgg tgatatctca aaaggggtaa caactagaca ttctcttaaa 3300 gatttatgca ataatatggc ttttgtatct atgattgaac ctaaaaatat aaaagaagcc 3360 atagtagatg ataattggat cattgccatg caagaagaac taaaccaatt tgaaagaaac 3420 aatgtatgga aattagtaga aaaacctgaa aattatcctg tcattggaac aaaatgggtt 3480 tttagaaata aattagatga acatggkata attattagaa ataaagcyag rttagtagca 3540 aaagggtata atcaagaaga ggggatagac tatgaagaaa catatgctcc tgttgcaaga 3600 ttagaagcca ttagaatgct tttggcatat gcatccataa tgaactttaa actttatcaa 3660 atggatgtta agagtgcctt tytaaatggc ttaattcaag aagaggtata tgttgaacaa 3720 ccccctggtt ttgaaatttc tgataaacca aaccatgttt ataaattaca aaaggctctt 3780 tatggtttga aacaagcccc tagggcatgg tatgaacgat taagtaattt tcttcttgaa 3840 aaagaattct ccagaggtaa agtggatacc acattattca taaagagaar gcataatgat 3900 attttgttgg ttcaaatata tgttgatgat ataatttttg gatccactaa tgattcattg 3960 tgcaaggagt tttcccttga tatgcaaagt gaatttgaaa tgtcaatgat gggagaacta 4020 aagtactttc tgggattaca aatcaagcaa actcaagaag gtatattcat caatcaatcc 4080 aaatactgca aggaattgat caaaagattt gggatggata gtgcaaaaca catgtctaca 4140 ccgatgagca ctaattgtta cttagataaa gatgaatctg gtcagtctat agacataaaa 4200 caatatcgag gtatgatcgg atctcttctt tatttatctg ctagtagacc tgatattatg 4260 tttagtgtat gcatgtgtgc taggtttcaa tccaacccca aacaatcaca tctaagtgca 4320 gtaaagagaa tcatgagata tctattagga acaatcaatt taggattatg gtatcctaag 4380 aattcaacat gtaacttaat aggatattct gattctgatt ttgccggatc taaaactgat 4440 agaaaaagta caagtggaac ttgtcaattt attggatcgg ctcttgtctc atggcatagt 4500 aagaaacaaa acagtgttgc tttatctact gctgaagcgg agtatatctc tgccggtagt 4560 tgttgtgcac aaattttatg gatgaagcaa caattatctg actatggcat cattcttgat 4620 cgcataccta ttaagtgtga taatactagt gccataaatc tatccaaaaa cccagttcaa 4680 cattcaagaa ctaaacatat agagattaga caccactttc ttagagatca tgtcttaaag 4740 ggagattgtg tattagaatt tgttgatact aagaatcaac ttgctgatat tttcactaaa 4800 cctctcccca aggaagtgtt tttctctatt agaagagaat taggtctctt agatgtaaga 4860 gatttagaaa aataggaatt gattggttga ttgattrgtt gattgattgr ttgatttact 4920 ttttaccttt tgattgtaga ttattttgtt tgatcttgtt tgaattcttg tttttatgat 4980 agaatttatg atttcttgtg tatatagtaa ttgaatgatt gaatttagtg tattagtagt 5040 gaaaattagt catataggat gtatttgagc ataaatatag atattctctt agaaactagc 5100 ctaggatagg ctctggtaat cgattaccay ycagtgtaat cgattacaca tgaacaggca 5160 gcctgtaatc gattacaaca tcctgtaatc gattaccaga aggcttattg ggcctgtaat 5220 cgattaccaa tacctgtaat cgattacaat gcgtcatctt ctataaatac tcacgaaatc 5280 agagctsstg cgcagccaaa gcttcctcca cgttttcctc catacctaga acttcaaacc 5340 ttcgattctc actcaattct tcaccaaatc acgtcccgta aagcccaatc ttcctctttt 5400 tcactcctct ttcacttcca ccgatcaaaa tccagaaaaa cttcatcaaa tggcagagcc 5460 atcaaagaag agaaagggat catcytccac cgcyaccgct gctgcccatc gccgtcacgg 5520 cccatccgga gcacccacag cacctattcc tccttctttg tcatctccaa gatcatcaac 5580 aytgttttca tccgatgatc aacgtctacg gtacctttct cagttttctt ctagaataat 5640 cttagaccct aagtacctag acgtagagtt ctttaatgat gaaacgtttg attgctatca 5700 agtgtttcaa aattctggtc ttgttgattt catgtcatta aaattgccat attatcctga 5760 acttgtaaag gtcttctact gcaatttaaa aattcaggat ggtattatta tgtctgaggt 5820 gcatggtayt tctatggtca ttgatcagtc actwttcttt tctttgactc atttacccag 5880 tcaaggtgca ccttttgagg gcaccattgt tgatgactgg aaattcgatt attcgagtca 5940 tgatgctcgt cgcatggtct gcaatgatca agctgaaatg accggtagat tgytggccgg 6000 gtcattaaca tttgataatc gcatcatgca ttatatcatt gttagaattt tgcttcctcg 6060 gtcttcaaat ttagcacaag cctctgagga ggatttgatt cttatgtggg cttttctwac 6120 cggtcgtcag atcgactggg cccatttggt tcggtaccga atgcataagg cattacgggc 6180 caatgcacct cttccttatc cacatttgat tactctgttt ttgcgtcatt ttcaaattcc 6240 gcttgatgat gaaccctttg ttcaagtcaa gcgttccttt gcaattggtg ctggtgcagt 6300 gacctccttt gggtatcgta aagatcggaa tggacaatgg ctgaagaagg atgcactccc 6360 tcctcaagat gaacgtactc cttcacctcc tcctcaacgt gaagattccg cactcatgaa 6420 tgaagtcctc tccgaattac ggggtcttcg ttcgtatgtt ggtgaccgct tygactcgtt 6480 agattcacgc tttgccggta tggacattcg tcttacacag cttgaagagg atgtcggata 6540 cattcgtcag agtttcgatc ttccaccacc tcctccgtct tcttagattt tagattctga 6600 ttatttatct tttataagcc gtgtattttg gcttttagtt tcttagaatt tacattatta 6660 tgctaagtac tttgcttatt tatcttgtgk ttttaaattt cagtcttgga trttttgtgg 6720 ttgttgacat tttmwgttat ttgrattctg gtttgattat ttcttgtttr tgagtttggc 6780 ttattgtatt taatactctg atrcttatat cttgctactc cattgttata actgtgttga 6840 tttccgagtt ctttggcttt ttgatgttgc caaaggggga gaaaaaggtt gtagcaaaaa 6900 gcttaagaaa aagcttaaca aacttagaaa tcaagtgatc atgtattccg aaatataggg 6960 ggagaaaacg gatgcacatt ttatctatat acaattgttt gttgcttgct tgaatcttga 7020 tttcaggtat tgtattgtca tcatcaaaaa gggggagat 7059 // ID Gypsy2-VV_I repbase; DNA; EDCOT; 4572 BP. XX AC . XX DT 04-SEP-2007 (Rel. 12.09, Created) DT 04-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW internal portion; Gypsy2-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4572 RA Obukhanych T. and Jurka J.; RT "Gypsy2-VV."; RL Repbase Reports 7(9), 796-796 (2007). XX DR [1] (Consensus) XX CC This is an internal portion of the Gypsy2-VV LTR retrotransposon CC family from Vitis vinifera. Its individual elements are about 91% CC similar to their consensus. The internal portion is flanked by CC 95% identical LTRs, deposited as Gypsy2-VV_LTR. Target site CC duplications are 5 bp-long. XX FH Key Location/Qualifiers FT CDS 26..4570 FT /product="Gypsy2-VV_I_1p" FT /translation="MAGGSAMDALRERMTRMEEALGEWPREDGTVASWAEH FT TMGEIQVQRSLLETHDNFFEEKFVGFKTEMQSLMDDFKETLQSYGEDIAVL FT KKAVLQGSSSGPEAPSSKVRVPEPKGFNGNRNAKELENFLWDIEQFFKAAH FT VPDGEKVSITSMYLTGDAKLWWRTRMEDDAESGRPQITTWETLKKELKDQF FT LPTNTAWVAREALKRLRHTGSVREYVKEFSSLMLDIKNMSEEDKLFNFMSG FT LQGWAQTELRRQGVRDLPAAMAAADCLVDYKMGGAISTTQRPKSDGGKKAK FT AEGKASKKSGWKKQGKKPAVGGKPVEKTTKFVQQTTRMAGCFICNGPHRAR FT DCPKREKLSALVTADDKGDSDSETPPRVNPLQLLNVINGETPVQKSLMHVH FT AVVNGVQVKALVDSGATHNFVATREATRLGLKLEEDTSRIKAVNSKAQKIQ FT GVAKNVPMQIGDWKGTCSLLCVPLDDFDLILGVDFLLRAKVALIPHLGGLM FT VLEEKQPCFVKALRTKDGGKGQPEMLSAIQLKKGLKKGQETYVAALIEIKE FT GQSMEVPDSVVKILKEFKDVMPAELPKELPPRRPIDHKIELLPGTKAPAQA FT PYRMPPAELLELRKQLKELLDAGLIQPSRAPYGAPVLFQKKHDGSLRMCVD FT YRALNKVTIKNKYPIPLAAELFDRLSKASYFTKLDLRSGYWQVRIAAGDEG FT KTTCVTRYGSYEFLVMPFGLTNAPATFCNLMNDVLFDYLDAFVVVYLDDIV FT VYSKTLTEHEKHLRLVFQRLRENRLYVKPEKCEFAQEEITFLGHKISAGLI FT RMDKGKVQAIMEWTVPTKVTELRSFLGLANYYRRFIKGYSKRVSPLTDLLK FT KDNPWDWSMQCQMAFEGLKEAISTEPVLRLPDLDLPFEVQTDASDRALGGV FT LVQEGHPVAFESRKLNNAEQRYSTHEKEMTAVVHCLQQWRHYLLGSIFTVV FT TDNVANTFFKTQKKLSPRQARWQEFLADFKFEWLHRPGRHNTVADALSRKE FT VIAYITALSEVISDFNEKIKLAAEQDAAYGRLKQQVKEGVIRRYWLEGDLL FT VAKGGRWYVPAGGLRKDLLRETHDSKWAGHPGEERTLALLARSYYWPKMGE FT DVQAYVKSCLVCQMDKTERKKAAGLLQPLPIPERPWENISMDFITGFPKVR FT DFKSVFVVVDRFSKYAVFIPAPDACPAEEAAKLFFSNVVKHFGLPKDIVSD FT RDARFTGRFWVELFKLLGSELKFSTANHPQTDGQTERINALLEEYLRHYVT FT ATQKNWVDLMDTAQLCYNLQRSSATGMSPFELAIGVQPRMPLEVAKQKAGG FT SSPAAYKMAQSRQEMFDEARDSLEKAARRMKKYADRDRRPLEFQVGDRVLL FT KLTPQIWKKISSKTRQRGLIPKYDGPFEVIKRVGQVAYMLKLPERLKLHPT FT FHVSFLKPYHEDLDAERVQTKRAPPLVMKQFDREIEKILDHRTMGHSRKNR FT RTDFLVQWKGISEAEASWERDVTLWQFEKEVQAYWQSKSTRASTSAGGGG" XX SQ Sequence 4572 BP; 1223 A; 965 C; 1341 G; 1043 T; 0 other; attggtatca gagcaagcac cagagatggc tggtggtagt gcaatggacg ccttgcggga 60 aaggatgact cgaatggaag aagcgttggg agaatggcca cgtgaggatg gcactgtggc 120 ttcgtgggca gaacacacca tgggagaaat ccaagtgcag aggagtctgt tggagaccca 180 tgacaatttc tttgaggaga aatttgttgg gttcaaaacc gagatgcagt ccctgatgga 240 tgacttcaag gagaccctgc agtcctatgg agaggacatt gcagtcctta agaaggctgt 300 gttgcaggga tcttcctcag gccctgaagc cccttcctct aaagttcgag tcccagagcc 360 taaaggcttc aatggcaaca gaaacgcgaa ggagttggag aacttcttgt gggacatcga 420 gcagttcttt aaggctgctc atgttcctga tggcgagaag gtttccatca ccagtatgta 480 tctgactggt gatgccaaac tatggtggcg aaccaggatg gaagacgatg cagagtcggg 540 aaggccccaa atcaccactt gggagactct gaagaaggaa ttgaaggatc agttccttcc 600 caccaacact gcgtgggtgg ccagagaagc attgaaaagg ctcagacaca ccggatctgt 660 gagggaatac gtcaaggagt tcagttcctt gatgctggac ataaagaaca tgtcagagga 720 ggacaagctc tttaacttca tgtcgggatt gcaaggatgg gctcagacgg aacttaggag 780 gcaaggagtt cgtgatctcc ctgctgccat ggctgcagca gactgcctgg tggactacaa 840 gatgggtggt gccatctcca ccacgcagag acccaagtca gatggaggca agaaggctaa 900 ggctgagggc aaggcttcta agaagtctgg gtggaagaaa caaggcaaga agcctgctgt 960 aggaggaaaa ccagtggaga agaccacaaa gtttgtgcag cagaccaccc ggatggcagg 1020 atgtttcatc tgcaatggcc ctcatcgagc cagagactgc cccaaaagag agaaactctc 1080 agcccttgtg actgcagacg acaagggaga ctctgactcg gagacccctc ctagagtcaa 1140 cccactgcaa cttctgaacg tgatcaatgg tgagacccca gtccagaagt ccctgatgca 1200 tgtccatgca gtggtgaatg gtgtgcaagt gaaggccttg gtggacagtg gtgccactca 1260 caatttcgtg gccaccagag aagcaaccag gttgggactt aaattggaag aggacaccag 1320 tcggatcaag gcagtcaaca gcaaagccca gaagatccaa ggggtagcca agaacgtccc 1380 catgcagatt ggtgactgga agggtacgtg tagtttactt tgtgtgcctt tggatgattt 1440 tgacttgatc cttggtgtag acttcctctt aagggccaag gtggccttga ttccacatct 1500 tggtggactg atggtgctag aagagaagca gccttgcttc gtgaaggcct tgaggacgaa 1560 ggatggtggt aagggacaac ctgagatgtt gtctgctatt caattgaaga aaggattgaa 1620 gaagggccag gagacctatg ttgcagcctt gatcgagatc aaggagggac agtctatgga 1680 agtccctgat tcagtggtca agatccttaa ggagttcaaa gatgtgatgc ctgcagaact 1740 ccccaaggag ttgccacccc ggcgacctat tgaccacaaa atcgagttgc tacctggaac 1800 aaaggccccg gctcaagccc cttaccggat gcctcctgca gagttgctgg agttacgtaa 1860 gcaactgaag gagttgctgg atgcaggtct gatccagccc tccagggccc catatggtgc 1920 accagtgctg ttccaaaaga agcatgatgg ctcactccgc atgtgtgtgg actacagagc 1980 cctcaacaag gtgaccatca agaacaagta cccgatcccc ttggctgctg agctatttga 2040 cagattgtca aaagcttctt acttcaccaa gttggacctg agatcgggct attggcaagt 2100 tcgaattgca gcaggagatg aggggaagac cacttgtgta actcggtatg gatcatacga 2160 gtttctggta atgccttttg gattgacaaa tgctcctgct acattctgta atttgatgaa 2220 tgatgttctg tttgattatt tggatgcctt tgtggtggtg tatctagatg acattgtagt 2280 ttacagtaaa actctaacag aacatgagaa acacttgaga ttggtgtttc agagattgag 2340 ggagaatagg ctttatgtga agccagagaa atgtgagttt gctcaggagg agatcacatt 2400 tctaggacat aagatcagtg caggcctgat caggatggac aagggcaagg tgcaggctat 2460 tatggagtgg acagtcccta ccaaagtgac ggagttgcgg tccttccttg gcttggccaa 2520 ctactacaga aggttcatta aggggtattc aaagagggtg tctcccctta ctgacctatt 2580 gaagaaggac aacccgtggg attggagcat gcagtgtcag atggcctttg aaggcttgaa 2640 ggaagccatc tccactgagc ctgtgctgcg gttgccagac ttggacttac cctttgaagt 2700 ccaaacagat gcctctgata gagccttggg tggagtcttg gtgcaggaag ggcaccctgt 2760 ggcgtttgaa agcaggaagc tgaacaatgc agagcagagg tactccactc acgagaagga 2820 gatgactgct gtggtgcatt gcctgcagca gtggaggcat tacttgctgg gaagtatctt 2880 cacagtggtc actgataatg tggccaacac cttcttcaaa acccagaaga agctgagtcc 2940 cagacaggcg cgatggcagg agttcctggc cgacttcaaa ttcgaatggc tgcatcgacc 3000 aggaaggcat aacactgtgg ctgatgcctt gagtaggaaa gaggtaattg cctacatcac 3060 ggccctctca gaagtcatct ctgacttcaa tgagaagatc aagctagctg cggagcagga 3120 tgctgcatat ggcaggctga agcagcaagt aaaggaggga gtgatcagga ggtattggct 3180 agagggtgac ctccttgtgg caaaaggagg aagatggtat gttcctgcag gcggcctgag 3240 aaaggatttg ttgcgggaaa ctcatgattc gaagtgggca ggccatcccg gagaagagag 3300 gactctggca ctgctagcca gatcctatta ctggcctaag atgggtgagg atgttcaggc 3360 atatgtgaag tcctgcctgg tttgtcagat ggacaagact gaaaggaaga aggctgcagg 3420 gttgctgcag cccctcccca ttccagagag accttgggag aacatttcca tggattttat 3480 cactggattc ccaaaggttc gtgatttcaa atctgtcttt gttgttgtag atagattttc 3540 taagtatgct gtgtttatac ctgcccctga tgcttgccct gcggaggaag ctgctaagtt 3600 gtttttcagt aatgtggtga aacattttgg gttgcctaag gacatagtca gtgatcgaga 3660 tgcacgattc acaggccggt tttgggttga gctgttcaaa ctcttgggtt cagagttgaa 3720 gttctctaca gccaaccatc ctcagactga tgggcagacg gagaggatca atgccttgct 3780 ggaggaatac ctcaggcact atgtgacagc aacacaaaag aactgggtgg acttaatgga 3840 tactgctcag ttgtgctaca acttgcagag aagctcagca acagggatga gtccctttga 3900 gctagctatt ggggtgcagc cacggatgcc tttggaggtg gctaagcaga aagcaggagg 3960 aagtagtcct gcagcataca agatggctca gtcccggcag gagatgtttg atgaagcccg 4020 ggacagtcta gagaaggcag ctagacgaat gaagaagtat gcggatcgtg accgcagacc 4080 cttggaattt caggttgggg acagggtcct cctgaaattg actcctcaga tctggaagaa 4140 gatcagcagc aagacaaggc agaggggtct aattcctaag tatgatggac cattcgaggt 4200 aatcaaacga gttgggcagg tggcctacat gttgaagctg cctgagaggc tcaagcttca 4260 cccgactttc catgtgagct ttctgaagcc ttaccatgag gatctggatg cagagagggt 4320 gcagacaaag cgagcccctc ccttggtcat gaaacaattt gatcgagaga tagagaagat 4380 cttggatcat aggaccatgg gacatagcag aaagaaccgg cgaactgatt tcttggttca 4440 gtggaagggg atttcagaag cagaagcttc atgggaaaga gatgttacct tgtggcaatt 4500 tgagaaggag gtccaggcat actggcagtc taagtcgacg agggcgtcga cttcagcagg 4560 cgggggtggg tt 4572 // ID Copia26-VV_I repbase; DNA; EDCOT; 5721 BP. XX AC . XX DT 05-SEP-2007 (Rel. 12.09, Created) DT 05-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW internal portion; Copia26-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5721 RA Obukhanych T. and Jurka J.; RT "Copia26-VV."; RL Repbase Reports 7(9), 784-784 (2007). XX DR [1] (Consensus) XX CC This is an internal portion of the Copia26-VV LTR retrotransposon CC from Vitis vinifera. Its individual elements are 93% similar to CC their consensus. The internal regions is flanked by LTRs, which CC are 99% identical to each other. LTR sequence is deposited as CC Copia26-VV_LTR. Target site duplications are 5 bp-long. XX FH Key Location/Qualifiers FT CDS join(2020..3699,3703..4998) FT /product="Copia26-VV_I_1p" FT /translation="MDLSHTLVHHTTSNVDACLADCATTHTILRDKKYFSN FT ISLVKSNVNTISGPVDLIQGSGRATIILPRGTKIHINDALYYAKSKRNLLS FT FKDIRRNGYHIETMNDDSNEYLLITSIIYGEKHILEKLPSYSCGLYQTIIR FT PIESYVVMNQKFCDLKTFMIWHERLGHPGLSMMRRIINNSLGHPLKNQKIL FT MPNDYNCVACSQGKLIIKPSFTKVEYESPTFLERIQGDICGPIHPPSGPFR FT YFMVLIDASTRWSHVCLLSTRNIAFARLLAQIIRLKAQFPDHPIKTIRLDN FT AGEFSSQTFLDYCMSVGIDVEYPVAHTHTQNGLAESLIKRLQLIARPLLLR FT TKLPLSAWGHAILHAATLIRIRPTTNHDCSPLQLALGSQPNVSHFRIFGCV FT VYVPIAPPQRSKLGPQRRLGIYVGFNSPSIIRYLEPFTGDVFTARFADCHF FT DENVFPPLGGDKSIPKEWRDITWYVPSLSHLDPCTRQCELEVQRIVHLQGL FT ANQLPDAFTDIKKVTKSHVPVVNAPTHIDVPEGQLENVIANESKTRLKRGR FT PIGSKDLIPRKKKTTYEKLSTLEEFTNMKGSNDETQLDKQLAPEEAQIDQI FT PVSRTEEISMSHTGETKDRSDIIIDNIFAFQVAMDIMRNDEYQEPQTVNEC FT RKMNDWPKWKEAIQTELNSLTKREVFGPVVQTPGNIKPVGYKWVFVKKRNE FT NDEIIRYKARLVAQGFSQRPGIDYEETYSPVMDAITFRYLISLTVSEGLDM FT RLMDVVTTYLYGSIDTDIYMKIPEGFKLPEATNPKPRNMYSIKLQRSLYGL FT KQSGRMWYNRLSEYLLKEGYVNNSICPCVFIKKSKFGLTIIAVYVDDLNLI FT GTPEELTKATNYLKKEFEMKDLGKTRYCLGLQIEHCSNGILVHQSTYIEKV FT LKRFYMDKSHPVNSPMVVRSLEVNKDPFRPKEENEELLGPEVPYLSAIGAL FT MYLANCTRPDIAFSVNLLARYSSAPTKRHWNEIKHIL" XX SQ Sequence 5721 BP; 1907 A; 1005 C; 1009 G; 1799 T; 1 other; cgttatcagc acgactagtc tctacaaaag aaatagaaag atttttctct atttagagaa 60 atagaaagac gtttttctct tcaragaaat agaaagactc ttctctcttc tttctcacaa 120 aaaggtatgt gataaactta tatcatgatt ttctatttta ttaccctttg atctctattt 180 tcatttattt tatttgaata cataaatatg tataatccct ataaccagaa gttatggggt 240 aaattataaa ttatggggta aattcataac cagaagttat gaaaaatatg tgcaattcct 300 ataaccagaa gttatgggga aaaattacag aattacaaat acatgaccag aagttatgta 360 tatgatccct aattatttat ttttaattat acggtataac tggatgttat accaaacaat 420 attatatagc cagaagctat aaaataaata aataaataaa tgttcatagc ctgaagctat 480 gtacaaattt acataatgaa agttcatagc ccgaagttat gcacaaattt acataaaata 540 attcatagct tgaagctata tattactttg cacatttttg ttatgataaa ataatcatag 600 cccgaagcta tgaaaaagaa aatatatatt aaattttaat tcttatttca tatttataca 660 tttttaccat atttataatt gataaatttt aggtcattat atttttagat attgtttact 720 tgaaatattg ttaaagcatt ttattaatag attcatagtt tattataata attgaaatat 780 ttctctgatt aatattattc tatatatagc tttcagataa tgtcaaacct tgcaaagctt 840 gaatttgttg ccctcgatat ttcgggcaag aactacttat cttgggttct agatgctgaa 900 attcatctag atgcgatgaa tcttggaaat accattaaag aaggaaatga cgcatccctg 960 caggatcgcg ccagagcttt gatattcctt cgccatcaca ttgatgaagg attaaaaggt 1020 gaatacctta cggttaaaga tcctttcatc ctttggaata atctaaggga acgatatgac 1080 caccaaaaga ccgtaatcct tccaaaggca cgctatgatt ggatgcactt gagattacaa 1140 gatttcaagt ctgttagtga ctacaactcg accctattca aaattagctc acaattaaaa 1200 ttgtgtggag aaaaggtcac tgaagaagat atgcttgaaa aaacattcac gacttttcat 1260 gcctcgaatg tgctcctaca gcagcaatat cgagagcgtc gtttcactaa atattcagaa 1320 ttgatctcat gtcttcttgt ggctgaacaa aataatgagc tattattgaa aaaccatcaa 1380 tctcgtccta ctgggtctat gtcattgcct gaagccaatg ccacatctgt tcaaaccctt 1440 ggacatggac aaggacgtgg atatggacga ggtcgaggta gaggacgtgg tcgcggtcga 1500 ggtcgtggta aacacaattc ttctcatcgt agtggttctc aaagtaaaaa agaacaactc 1560 aaaccaccag aagtggaata attcagaggc acaacctgaa aaggggatag aaccacaaag 1620 taaacatgct cgtgagaata agtgtcatag atgtggcatg aaaggacatt ggtcacgtac 1680 ttgtcgtact ccaaaacatt ttgttgacct ttatcaagcc tcaataaaag caaaaggaaa 1740 ggaagttgaa atgaacttca ttgatagtga tggcccagtg gatctaaccc atttagatgt 1800 ttcagatttc tttgagaatc ctaatgggaa aattgaccat ctaattggtg atggaaatgt 1860 ttgttatgat taaatgttat gttcttattt agttctttgc aaataggttt attttgttat 1920 catctttgaa cacattgttt attattcatc ttttatagtt tatttcacat tttattattt 1980 cttatttaaa ttcttctctt tatttatact tgaagataca tggatctttc tcataccttg 2040 gtacatcata cgacatccaa tgtagatgca tgtcttgcag attgtgccac aacacacaca 2100 atccttcgtg ataaaaaata tttttccaac atatcgttgg ttaagtctaa tgttaataca 2160 atatcaggtc ctgtagactt gattcaaggc tccggaagag caactattat tttacctaga 2220 ggaactaaaa tccacattaa tgatgccctt tattatgcta aatccaagcg aaatcttctt 2280 agtttcaagg atattcgccg aaatggatat cacattgaaa ctatgaatga tgatagtaat 2340 gaataccttc tcattacttc aattatttat ggggaaaaac acatcttgga aaagcttcct 2400 tcttattctt gtgggttata tcaaacaatc attagaccca ttgagtcata tgttgtcatg 2460 aaccagaagt tctgtgactt aaaaactttt atgatatggc atgaacgtct tggtcatcca 2520 ggattatcca tgatgcgtcg tatcatcaac aattctttag ggcatccctt gaagaaccag 2580 aagattctga tgcccaatga ttacaattgt gttgcttgct cacaaggcaa attaattatt 2640 aaaccatcat ttaccaaggt tgaatatgaa tcaccaacct ttctagaacg tattcaaggt 2700 gatatttgtg gacctattca tccacctagt ggaccttttc gttattttat ggttttaatt 2760 gatgcatcaa ctcgttggtc tcatgtttgt cttctttcaa ctagaaatat tgccttcgcc 2820 aggttacttg ctcaaataat tcgactcaag gcacaattcc ctgatcatcc tattaagaca 2880 attcgtcttg ataatgctgg tgaattttcc tctcaaacat ttcttgatta ttgtatgtcg 2940 gttggtattg atgttgaata tcctgttgct catacccata ctcagaatgg attagctgaa 3000 tctctaatta agcgtttgca actgattgca agaccattac tcttgagaac aaaattgcct 3060 ttgtctgctt gggggcatgc tattcttcat gctgccactt taattcgaat tcgccctaca 3120 actaatcatg attgctcacc tttacaactt gctttaggct cccaaccaaa tgtttcacat 3180 tttcgtattt ttggttgtgt tgtctatgtt cccatagctc cacctcaacg ttccaagtta 3240 ggacctcaac gtcgacttgg tatatatgtt ggttttaatt ctccctccat tattcgttat 3300 cttgaaccat tcacaggtga tgtttttact gcccgctttg cagattgtca ttttgatgaa 3360 aatgttttcc cgccattagg gggagacaag tcaattccaa aagaatggcg agacattaca 3420 tggtatgtac cctccttgtc tcatcttgat ccttgcacaa gacaatgtga gttagaagtt 3480 caaaggattg ttcatttgca aggacttgca aatcaattac ctgatgcttt cacagatata 3540 aagaaagtaa caaagtcaca cgtgccagtt gtgaacgccc caacacatat tgatgtccct 3600 gaaggacaat tggagaatgt catagcaaat gaatctaaga cacgcctgaa gcgtggtaga 3660 cctattggct caaaggattt aattcctaga aaaaaaaaat gaacaacata tgaaaaactt 3720 agtactcttg aagagttcac aaatatgaaa gggtcaaatg atgaaaccca acttgacaaa 3780 cagttagctc ctgaagaggc acaaattgat caaataccgg tatctagaac tgaagagatc 3840 tcaatgagtc acacgggaga aacaaaggac cgtagtgaca ttatcataga taatatattt 3900 gcattccaag tggctatgga catcatgaga aatgatgaat atcaagaacc acaaactgtg 3960 aatgaatgtc gaaaaatgaa tgattggcca aaatggaaag aagcaatcca aacagagcta 4020 aactcgttaa caaaacgaga ggtatttgga cctgtagttc aaacacctgg aaacataaag 4080 cctgttggat ataaatgggt ctttgtgaaa aaacgaaatg agaatgatga aatcataaga 4140 tataaagcac gacttgttgc tcaaggtttc tctcaaagac ctggtataga ctatgaggaa 4200 acttattccc ctgtaatgga tgcaatcaca tttcgatact tgataagttt aacagtctct 4260 gaaggactag atatgcgtct tatggatgtt gttacaacct atttatatgg gtctatagat 4320 actgacatat atatgaaaat ccctgaagga ttcaaattgc ctgaagcaac taatccaaaa 4380 cctcgaaaca tgtactcaat caaactacaa agatctttgt acggattaaa gcaatctgga 4440 cgtatgtggt ataatcgttt gagtgagtat ttgttaaaag aaggatatgt gaataattca 4500 atttgcccat gtgtttttat caagaaatca aaatttgggc ttacaataat tgcagtgtat 4560 gtggatgatt taaaccttat aggaactcct gaagagctca caaaagcaac caattattta 4620 aagaaggaat ttgaaatgaa agacttgggg aaaacaagat attgtctcgg cctgcaaatc 4680 gagcattgtt caaatggcat attagtccat caatcgacat atatagagaa agtattaaaa 4740 cgattttata tggacaaatc acatccagtc aattccccta tggttgttcg ttcacttgaa 4800 gtgaacaaag acccatttcg tcctaaagaa gaaaatgaag aattgcttgg tccagaagta 4860 ccatatctca gtgcaatcgg tgcactaatg tatcttgcaa attgtactag accagacata 4920 gcattctctg tcaacttact agcaagatac agttctgccc caactaaaag gcattggaat 4980 gagattaaac atatattgtg ataccttcgt ggaacaagtg acatgggttt atattattca 5040 aaagaatcaa aatcacaatt gattgggtat gcagatgcag gatatctttc agatcctcat 5100 aaagctcgat ctcaaacggg atatgtcttt acttatggtg gaacgacaat atcttggaga 5160 tcagtcaagc aaacaatggt agccacatct tcaaatcatt cagaaattct tgcaattcat 5220 gaagcaagtc gtgaatgtgt atgactaagg tcaatgatcc aacatataca agaaacatgt 5280 ggactacctt ccatcagagg caatgcaacc gtgttacatg aagataatgc tgcttgtatt 5340 gcacaaatta aaggaggatt cataaaaggt gacagaacta agcatatctc ccctaaattc 5400 ttctatactc atgagctcca aaagaaatgt gagattgatg ttcaacaaat tcggtcatgc 5460 aataatctag cagatctatt cacaaaggcg ttaccttcga ccacattgaa aaagttaagg 5520 tatgacattg gaatgcgaag attgagagat ctaccatttg aaatgttgaa gaaatcataa 5580 tcatgtttac atgaggggga gaatgctaat atggatatat tgcactcttt tttccttcgt 5640 ccaggttttg tcccattggg ttttactggc aaggttttta atgaggcagt taccatattc 5700 ttatgatcat ccaaggggga g 5721 // ID RASH4_MT repbase; DNA; EDCOT; 756 BP. XX AC . XX DT 30-NOV-2006 (Rel. 11.11, Created) DT 01-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW Interspersed; repeat; Inverted; TSD; TIR; RASH4_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-756 RA Shankar R. and Jurka J.; RT "RASH4_MT:A putative DNA transposon from Barrel Medic."; RL Repbase Reports 6(11), 600-600 (2006). XX DR [1] (Consensus) XX CC The sequence is flanked by AT rich regions which define TSDs, CC poly(AT). XX SQ Sequence 756 BP; 299 A; 110 C; 99 G; 247 T; 1 other; gggataggat caaatgacac catggtgtca aattaaattt gacaccaaat cataaccatt 60 aattcaactt taatccgacg tctctcatca attcattaaa tgctcacatg cttgatcaaa 120 tgatctaaat tttaatttta gaaacaattt attctttctt tttttgatta attatttacc 180 aaaaattctc taatggtatt attatggttt ctttaccaaa aactattcac tgtcattctt 240 tttttaaggg cttatcatcc ttatttcttt ttattcctat taaccttttt tatttttatt 300 tttcttagaa gaacccaaag aaaattgatt tataaagagc accagaamta atgaatgaac 360 gattgcacca aaaaataaaa aagaacttat gctactaaac gaaagcaaaa cacaaatgct 420 agaacatccg atacaagaat attagcagca tgcatgaact caagaatact accataccaa 480 caaatgaaag agtagccaat acaaagagga tacaaagatg attgaacaaa gattagtaaa 540 tagaatctct aaaaaaattg tagggagaaa tcaaatggta aataattaat caaaaaaaga 600 aagaataaat tatttctaaa attaaaattt agataatttg atcaagcatg tgagcattta 660 atgaattgat gagagacgtc agattaaagt tggattaatg gttatgattt ggtgtcaaat 720 ttaatttgac accatggtgt catttgatcc tatccc 756 // ID Gypsy-32_Mad-I repbase; DNA; EDCOT; 3142 BP. XX AC . XX DT 08-OCT-2010 (Rel. 15.1, Created) DT 08-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-32_Mad-I. XX NM Gypsy-32_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3142 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1758-1758 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 3142 BP; 952 A; 833 C; 668 G; 689 T; 0 other; tttggcgccg tctgtgggaa acgacacgaa aagctatgtc ggttctcttt cattttttca 60 cctcaccacc gtgagaccca caaactccac cgtgaatctg cagaaaccca aaaaccaaaa 120 acctcactct ttgggctttt ccagaaaaat ttcgcaaacc tccaaccacc tctctctctt 180 ctctcagcca gtcacacatg gaaaccaaaa caaaagaaga aaaacgagaa agacagaaat 240 ccatggagct aggtctgaga aagtccaatt ctctctctct tacctcctct gcaatgatca 300 acaccactcg tccggcaact gattcctcaa gaaggagatc acaaagacac agagagcagc 360 catcgctttc ctgaagaaga agcgtcttca atggcttcct cacctgccct ccgtcgcctc 420 ctctccgcga actgcttccc caagtccttc gccactccgc tatccgccca ctcgccatca 480 cccgctcccc cgtttccaag ctcttcgaca ccaacgcctc cgcagctccg acgatcgcaa 540 caatgaaagc ggcctcaact ttgaccaccg ccccggccgt catttctctc gtcgaggcga 600 tgttcttccg ggtgcattca cttcgttctc gccgaggccc aacctgagcc acgtgctgaa 660 cctgatggcc aagtctcgga tgatcccatc ctttaggcgg caagactgga agtgcaagga 720 gaccggaact gaagctcgct cgtcggccac cggtggctga gagtcgacgg ccagagccac 780 accgcctctc tctcaacgcc cagcctgggc tcctaccttt catgcttgct ccccaaccgc 840 aacttgcagt gactcatcca gatctggtct accgctccgg caaaggatcc gacggcattg 900 aggatagtct ctcttgcttg ataaagcgag tggaggttag attggtccac taagagcagt 960 gaagctgctg tccaagaatg tggaggtcca aaggttgcat tgcagtatta tcaggcggtt 1020 cccatgtgcg tggtgtgaag gagaaggcga atgagatcaa ggataaggtg aagctgctta 1080 gagggttgtc gagaaacttg gcggcgtttc tcagatgggt tttggaccgt tggattctca 1140 agagggtttg gtcgatcaac ttcaggggaa gttgatctcg gaaagcgctg aggaattatt 1200 gctgaaacaa ttggaacagc tgagagtaga ggaaaagaat gttcagaagg aaaaaagaaa 1260 agaggaagaa atggacagag aaggagcggg gagatcaagc aaaagcagaa agaaaagcat 1320 aagcaaaagc aaagcagaaa gacaaaagca atcagtggga tgcggcacaa aagcaaaaga 1380 gaaaggcgca gtggaaagca agcagaagat aagctgtctt acaaaatcca ttatcatcgt 1440 gctgccatct gcaaaagaga aaagagaaag aaaggagagg aaaagcaaaa gcagaaagca 1500 aaagaagata aaaagaagca gacataattg cggtggtgat ggcatgcaga aaagggaatt 1560 atgggcgtga cccattgagc agagggtcgg atttattttt gaatgatgta atttattttt 1620 cttatctttc ggagacatct gtataacccc atcagagggt aatataaaaa ataaaaaaaa 1680 aaaaagggca agcccaaaat aatgggctgg aatgttatgt ggagggcgaa ggcccatatg 1740 cccaaaagag ccaggccctc tattatcacc aaccaggtga tcaaaagtac gtccagtact 1800 ccaaaattat tcggcagcct gccgctatta tcaccaacca ggtgatcaaa agtacgccca 1860 gtactccaaa aaattattcg gcagcctgcc gctattatca ccaaccaggt gatcaaaagt 1920 acgcccagta ctccaaaatt attcggcagc ctgccgctat tatcaccaac caggtgatca 1980 aaagtacgcc cagtactcca aaattattcg gcagcctgcc gctattatca ccaaccaggt 2040 gatcaaaagt acgtccagta ctccaaaatt atacatgagc atcactcatg tcaatcatac 2100 ataaacattc atgagcatca ctcatgtcaa tcatacataa acattcatga ccatcattca 2160 tgtcaacatt catgagcatc actcatgtca acattcatga gcatcactca tgtcaacatc 2220 catgagcatc actcatgtca atcaacataa acattcatga gcatcactca tgtcaatcag 2280 cttcgaaagc ttcatttaca gagctccagc ttcgagagct ccagcttcaa aagcttcatt 2340 tacaaagctc cagcttcaaa agcttcactt gcaaagcttc acctacaaag cttcagtgca 2400 gggtatacaa ataccgcctc cgaacaaccg ccacttcggc ccatacatgg attcaatttg 2460 aagtctccag ccaacagact ctattgactg aagacttggg ggactacatt atgtaccata 2520 tattgggcct caactgggcc tcatgaaaaa tacttggggg acttagccca ttatttatgt 2580 attgaggagc gagcccttat tctataaaag ggactccctc actttcatta gagagcaccc 2640 attattcatg tactgaggag cgagccctta ttctataaaa gggactccct caccatcatt 2700 agagagcatc gccgccagct gagcaaccgc ctcgccgcga gcatcactcc taacccatca 2760 cttatgtatt gaggagcgag cccttattct ataaaaggga ctccctcacc atcattagag 2820 agcatcgccg cctgctgagc aaccgcctcg ccgcgagcat caactctagc ccatcattta 2880 tgtattgagg agcgagccct tattctataa aagggactcc ctcaccttca acgccacaag 2940 ccgagccaac caaggcaaca taagccacaa gccgagcagc ctcgcaacat gtgctacttc 3000 tagttgagca tcatttcaga ttgagcaccg cctcatatcg agtatcagtt ctagacgaca 3060 tctagttact tcggcccaca catggactga atttcaagtc tccagccaaa agactctctt 3120 gactgaagac ttgggggact ac 3142 // ID Gypsy-15_Mad-I repbase; DNA; EDCOT; 4572 BP. XX AC ACYM01037991; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-15_Mad-I; KW Gypsy-15_Mad-LTR; Gypsy-15_Mad_. XX NM Gypsy-15_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4572 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1337-1337 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01037991; Positions 28699 24128. XX CC Positions [3456-3950] - Integrase core CC 'CAAAG' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 1137..4361 FT /product="Gypsy-15_Mad-I_1p" FT /translation="MRFLWHHCSLNTANNEGRGSVERTFCKDTIGFRKYSQ FT FVDSKLLKQWGYQAQTTRPFEVMIADGGKVKSSGCCKAMPLSLGGYKCSVD FT LYALPLGGCDAVLGVQWLSSVSPVLWDFQLLTMEFSKGAQKFKLVHSSPTV FT PFIQELPLHHVDKELNSSNLGLCLYSLETQKLEASVLNSKQLQELQELLGE FT FEDIFEIPIKLPPSRSLDHSIALVPGAKPPNLRPYHYGPLQKTEIEKAVQE FT LLDAGFIRASHSPFSFPVLLVKKKEGTWRMCIDYRELNALTIKDKYPIPLM FT DDLLDELHGSKYFSKLDLRSGYHQILMKPEDVGKIAFRTHEGHYEFLVMPF FT GLTNAPATFQNLMNDLFKPFLRKFVLVFFDDILIYSTSWQQHLVHLKVVLT FT VLHKNQLYLKKSKCSFGQNSVEYLGHIVFKDGVAADPSKLKAIQEWPQPRN FT VKELRGFLGLTGYYRKFIPGYGKVCQPLYNLTKKEGFVWNDSASEAFTQLK FT SIMSSPQVLALPNFSQPFVVECDASGNGIGAVLQQNQRPIAFFSQALGPKN FT QTLSTYERELIAIVHAVRKWQNYLQGRHFVIKTDHSSLKYFLGQRTNTQFQ FT QKWVAKLLGFDYEIQYRSGNENIVADSLSRIPDHQGIAAGDTMEFAAISYP FT YFGWMDDLRRYNENDDWIMDKIREVTEYKLKGTINPALAKYSVDNGFLCYK FT KRVVISPNSQWRTKLIEEHHCTPAAGHQGVAKTYQRTKKGFYWQGMKGDIR FT KFIAECAICQQNKFETIAPPGLLQPLPLPQRVWSDISMDFIVGLPNCKGKS FT VIMVIVDRLSKYSHFIALAHPYNASIVAQLFVEHVFRLHGMPNSIVSDRDP FT VFVSAFWRELFRLQGSKLCMSSGYHPQTDGQTEVMNRCLETYLRCFVGGQP FT RKWVQWLAWAEWCFNTSYHTSSKYTPFEVVYGFSPPHIAPHEIGSTKVAFV FT EQCMIERDGLLSVLRNNLQLAQNRMKVQADKKRTERHFNVGDMVYLKLVPY FT QLHSLVNHSYHKLQPRFYGPYAVLEKIGDVAYRLQLPEGSKVHPVFHVSCL FT KKQIGNNVTLQVELPLGV" XX SQ Sequence 4572 BP; 1239 A; 886 C; 1088 G; 1359 T; 0 other; ttggtatcag cctctggtcc tggttccctt ccgcgcatgc cccgtgctac taccaccaat 60 cgtatctctg tgatggacgg ccgcgttgct gagcttgaga attccatggc ttcgctcaaa 120 gcgtccgtcg atgcttccat ggcttctctt ccttccttgg ttgacaatgc ggtggctact 180 actctcgaca ctaaattgta gctctacttc gagcaattcc gtcgcgagct gcaatttcgc 240 ccgggcggta gtggtcttcc cgttcctgtg ggtcatgact gtcctgatcc tcgtgcatct 300 gcacatgctc cccgacctcc gagtccgaat cgttttggcg atgatcatcc gccacgaccg 360 ccatggattc agcgggtaga gttccctcga tttgttgatg gcgacgatcc gcttgcctgg 420 atctacaaag ccgagcagtt attctcctac tacaacactc cgcttgattc tcgcgtgctt 480 acagcttcct tccatttcga gggggaagtg ttgcagtggt ttaagtggcg cgattgtgtg 540 cgcactacac cgacctggga ggagtttact cgcgccttgt gcttggagtt tggaccactt 600 gaatttgagg atacggcgga agcacttttt aagctgcgtc acacaggtac tttgaaggat 660 tatatctctg aatttaggcg tttggccaat cgtacttccg atattagtcc tgtgttgctt 720 aagagttgtt tcataggagg gttgaaaaaa gagcttaagt ttgatgtgaa attactcaaa 780 cctgctactg tacatgatgc gattgcaatt gcagtacaat tagatgccaa atttactgag 840 tttaagagta gtcaggctaa gtcctcccct gtgttaaaaa accagtttgt tcctaccact 900 gcttctcctc ccattatccc gaaacccggt aatttgccag tcaagcgact gtcccttgaa 960 gaagttcaac ggaagaggga gagaggagag tgttagtttt gtttggataa gtggacaaag 1020 gggcacaaat gtgggttaaa acaacttctt atgttagatc tcatggatgg tgttgatgag 1080 tgtgttaatg aggagcagct ggaggctgct gaattgtctc atatggcact tagtgaatgc 1140 gctttttatg gcaccactgc tcgctaaaca ctgcaaacaa tgaaggtcga gggtctgttg 1200 aacggacatt ctgtaaagat actattggat tccggaagta ctcacaattt gtggattcca 1260 agcttctgaa gcagtgggga tatcaagctc aaactacaag gccttttgaa gttatgattg 1320 cagatggggg taaagtgaaa agttccgggt gttgtaaagc tatgccccta tcattgggtg 1380 gctataagtg ctcggtggat ctttatgctt tgccattagg aggatgtgat gcagtgttgg 1440 gtgtacaatg gctttcttct gtgagtccag ttttgtggga cttccaactc ttaactatgg 1500 aattctctaa gggtgctcag aagtttaagt tggttcatag ttctccaaca gttccattca 1560 ttcaggaact acccttgcat catgttgata aggaacttaa cagttctaat cttggtttat 1620 gtctttattc tctagaaact caaaagttgg aagccagtgt tctcaattct aagcagttgc 1680 aggagttaca agaattgttg ggagaatttg aagacatttt tgagatacct attaaactgc 1740 caccatccag atcacttgat cattctattg ccttagttcc tggtgctaaa cctccaaact 1800 tgaggcctta tcactatggt ccccttcaaa aaacggaaat tgagaaggct gtgcaggagc 1860 ttttggatgc aggattcata agggcaagtc atagtccctt ttcatttccc gtacttttag 1920 tcaagaagaa ggaaggcaca tggagaatgt gcattgacta tagggaactg aatgcactca 1980 caattaaaga caagtatcct attcccctca tggatgactt gttggatgaa ttgcatggct 2040 caaaatattt ttctaagctc gatttgagat ccggatatca tcaaattcta atgaagcctg 2100 aggatgtggg aaagatagca tttagaaccc atgaaggtca ctatgagttt ttggtgatgc 2160 cttttgggct cactaatgca cctgcaacat tccaaaattt gatgaatgat ctgtttaaac 2220 cattccttag gaagtttgtg cttgttttct tcgatgatat actcatctat agcacctctt 2280 ggcagcaaca cttggttcat ctaaaggtag tactcaccgt gctccataaa aatcagttat 2340 atctcaaaaa gtctaagtgt tcttttggtc aaaatagtgt tgagtatctg ggacatatag 2400 tgtttaagga tggggtggct gcagatccat ctaaactcaa agcaattcag gagtggcctc 2460 aaccaagaaa tgtaaaggag ttaaggggat ttttggggct tactgggtat tatcgaaaat 2520 ttattcccgg ttatgggaag gtatgtcaac ccttgtacaa tttgacaaaa aaagagggtt 2580 ttgtttggaa tgattcagct agtgaagctt ttacacagct caagagcatt atgtcctcac 2640 cacaggttct agcacttcca aatttttctc aaccctttgt agtagaatgt gatgcttctg 2700 gaaatggtat aggtgctgtt ttgcaacaaa atcaaaggcc aattgcattt ttcagtcaag 2760 cactcgggcc taagaaccag acattatcta cttatgagag ggagcttatt gccatagttc 2820 atgcagtaag aaaatggcaa aattatttgc agggaaggca ttttgttata aagactgacc 2880 atagcagttt gaagtatttc ttggggcagc gaaccaacac tcagtttcag caaaaatggg 2940 tggctaaact tcttgggttt gattacgaaa ttcagtacag aagtggaaat gaaaacatag 3000 tggcagattc actctctcga attccagatc atcaaggaat tgctgctggg gacactatgg 3060 aattcgctgc catatcgtat ccatattttg gatggatgga tgacttgaga cgatataatg 3120 agaatgatga ttggattatg gacaaaatta gggaggtgac tgagtacaaa cttaagggta 3180 ccatcaaccc tgctttagct aaatactctg ttgataacgg atttttatgc tacaagaaga 3240 gggtagtaat tagtccaaat tctcaatgga gaactaagct catagaggag catcattgca 3300 cgccagcagc aggtcatcaa ggggtagcta aaacttatca gagaactaag aaagggtttt 3360 attggcaagg aatgaaaggg gatataagga agttcattgc tgaatgtgcc atatgtcaac 3420 agaataagtt tgaaaccatt gcaccacctg gattgcttca acccttacct ttaccacaaa 3480 gggtttggtc ggatattagc atggatttta tagtgggatt gcccaattgt aagggaaaat 3540 cagttatcat ggtgattgtg gacagacttt caaagtacag ccatttcatt gcacttgctc 3600 acccctataa tgcctctata gttgctcaac tattcgtaga acatgttttc cgattgcatg 3660 gcatgcctaa ttccattgtg agtgatagag atccagtgtt tgtaagtgcc ttttggagag 3720 aactttttag actccaagga tccaaactct gcatgagctc gggatatcat ccccaaactg 3780 atggacagac tgaggttatg aatcgatgtt tggagaccta cttaaggtgc tttgttggag 3840 ggcagccgcg gaagtgggtt cagtggttag catgggcaga gtggtgcttt aacacttcat 3900 accatacctc ttcgaagtat actccctttg aggtggtgta tggtttttcc ccacctcaca 3960 ttgctccaca tgaaattggt tccactaaag tagcttttgt ggaacaatgc atgattgaaa 4020 gagatgggtt gctatctgtg ttaaggaata atttgcagct agctcaaaat cgcatgaaag 4080 tgcaagcaga taaaaagagg actgagagac actttaatgt gggagatatg gtttatttga 4140 agttggtgcc ctatcagtta cactcattgg tgaaccatag ctatcacaag ttgcaaccac 4200 gtttctacgg tccttatgca gttcttgaga agattggtga tgtggcatac agattgcaac 4260 ttcctgaggg gtccaaagtt catcctgtgt ttcatgtcag ctgtctcaaa aaacagattg 4320 gaaacaatgt gactctccag gttgaacttc ctttgggtgt atgaggatgg cttggttcag 4380 gacatacctg cagcaattct gtctagaagg atgtataaaa aggggaatgc ggctggagtt 4440 caacttctag tgcaatggga agggcaagga agctgcagat gccacttggg aagattttga 4500 tgagtttcag aaacgatttc caaattttgc agtataacct taaggacaag gttgctctga 4560 aggggaaggc at 4572 // ID Copia-60_Mad-I repbase; DNA; EDCOT; 6708 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-60_Mad_; KW Copia-60_Mad-LTR; Copia-60_Mad-I. XX NM Copia-60_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6708 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1658-1658 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [3279-3785] - Integrase core CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 3099..4094 FT /product="Copia-60_Mad-I_2p" FT /translation="MPGFQSTLLLWHDRMGHPGRDMMRRILKSSHGHHLHP FT YVGLPPCKACSLGKLNTQPSITKIIHDPPKFLQRIQGDICGPIQPTCGPFR FT YFMVLVDASTRWSHVCLLSTRNAAFAKLLAQIIKLRAHHPDYPIKSIRLDN FT AGEFTSQTFDDYCMSVGIEVEHHVPHVHTQNGLAEAFIKRLQLIARTLVMR FT TKLPVSAWGYAILHAAMLVRLRPTATQPHSPLQLVTGYEPDVSHLRVFGCA FT VYVPIAPPLRTKMGPQRKMGIYVGYDSPSIIRYLEPLTGDLFTARFADCHF FT DETVFPSLGGDKNANVPVERRELSWYAPTMSHLDPRTASV" FT CDS 4144..5892 FT /product="Copia-60_Mad-I_1p" FT /translation="MPDAFTDLAKVTRSHIPAANAPARIDVPSVRRNTAWE FT GRTVPEGGAAAPSTRHGTLAASQSSAPTLKRGRPPGSKDSQPRKRKTAQTS FT DPSLNPTIAYSSVPTHEVILDYGDVLDETNRPPENREISVHYAVLDEVWNR FT NEMIVDDAFAYTVATDIMLSDDIEPRSVDECRRRTDWSNWKQAIQVELDSL FT AKRKVFGPVAPTPPHVKPVGYKWVFVRKRNEKNEIVRYKARLVAQGFSQRP FT GIDYEETYSPVMDVITFRYLISLVVSEKLNMQLMDVVTAYLYGDLDTEIYM FT KVPEGLPLTGSNSSRPRNTLSIRLRRSLYGLKQSGRMWYNRLSEYLTSQGY FT VNNELCPCVFIKKSHSGFAIVAVYVDDMNLIGTPAELEEIAVHLKSEFEMK FT DLGKTRYCLGLEIEHCSDGILVHQSNYTQKVLRRFNEDKAKPSSTPMVVRT FT LDAKRDPFRPKEDEEEILEPEVPYLSAIGALLYLAQCTRPDISFAVNLLAR FT YSNAPTRRHWNGVKDIFRYLKGTTDLGLFYTHESSRAAAPSVLGLILALLV FT TQMLDICLTHIGHVLKRVMSLPLETPLYLGGLPSKR" XX SQ Sequence 6708 BP; 1742 A; 1660 C; 1473 G; 1827 T; 6 other; acacgttatc agcacgctct tgccagaagc taaggaactg aaggatcgta ggaggaggct 60 ctcttctaca aaattcaaag gctttcattt gttttctgcc aatcaggtac gcttaaaata 120 aattaagata tttgaaacga ccatgaagca tgaaaacatt ccccatgatg catgaacccc 180 ctatatttat attttccttc cgatatatat atatattgta tatgtattca tatattatat 240 tttatatata tatatatatg tttcatgcat tacgcaatta tttgctatgt ggaatttgtg 300 agtcaaagca tataaataaa ttagaagcaa ttagggtttt tcaaacccta gagaagttcg 360 aaaaaaaaaa tctgggaatt atgcggcacg ccgccgcaca ccaccatggc ccaccggacc 420 accggctggc ctgagcccag ccgcgtggag cacaccatag gacgacgtcg ttttgacacc 480 tggacctatg gcagcagccc tttgggcttt gctgcaccac acggacacca ggccttcggc 540 ctggtgggtt ccacgggcct gaagccctag cccagccaag caagcctgca gccttcttgg 600 gcttgtccca tggtcctcgg cccaactcca gcaagccgtt tgctaggctt gcctttgtcc 660 catgacttgg cccgcccaca gcagcccatg ttgctgggct ttgccccagc ctcagcccgc 720 ttaccgcagc cttgctgctg ggcttgaccc gcctcggccc aaaaacatga acccagcttc 780 ggctgggctt ccccgcacca cccaggccag cttggcctgc acccgtgcct tttttggccc 840 aaagccactg ggcttcccat cactcagccc aggcatgctg ccttaccagg cccattagcc 900 tacggtcgaa ccgaagccca tttttttttt caccgtatgt tattattttt gcttccacga 960 tcgaccccgt ttggtcccga tctattgaat taattaaaag tgacctgcag tccattaatc 1020 tgataattaa tccaaaatta ttgacctgaa gatcactttt ggacattaac gattcaataa 1080 tttatttttc tactttgaac cgttgacatc ctttcgtagt cccgaagctc tcacacttgg 1140 gttcccgaag caatcctcaa atccactaca cttaattagc atattgcatt ctgtgttctt 1200 gcaggaacct ctcctttatg aactaatcgt tcataaaact aaatcgaacc tgtagtttca 1260 aatttagtgc ctttgaaacc cgaagttttc attcaaaact taccacatga aacctgtagc 1320 tttcatgctt aaattaaacc aatacatgtc tatagaaccc gaatgttcta cgatgtatgt 1380 ctatggctta ccatatgact aaccacgttt tgttgtaccc tccgttttag ggacatgtcg 1440 aacttgaaca agctcgattt caccgctctg gaagtmtctg gaagaaacta cctgaagtgg 1500 gttcaagacg tgaagctcca tcttactgca aagggtatta gagccaccat cgaggaacct 1560 accgacgacg aacccgtcga cgaagctcag aaagctactg caatgatctt cattcgaaga 1620 cacatccatg atgcactgca gaccgagtac ctcgctgagg aggacccacg caccctctgg 1680 cttgctctgg ccgatcgttt cgatcaccag aaagacattt acttgcctga agcaagacac 1740 gactggcagc atctacgctt ccaagacttt aagtctgtga atgaatacaa ctctgaagtt 1800 tgtagaatcc gatcactgct taagttctgt aaagtggact taaccgaaca agatctcctg 1860 gagaagacct attcgacctt caatgccacc aatattgtcc tgcagcaaca atatagggca 1920 cagaagttca ccaaattttc ggatttgatc tctgttttac ttctcgctga aaagcagaac 1980 cagcttttga tgaagaatca tcaagctcga acgctcgcct gaagcgcatg cgaccaattc 2040 tagcagccac aaacgacgga aamaccgtcg tggccgtgga atgggcggca agcccaacca 2100 cgggcccaag gtcaacagag caaaggccca cccaagggag gaaatttgac ccagaagcgc 2160 caaccccttg cccctaaggc cccaaacttc aagaacaagg gaaaagctac cgttcaatcg 2220 gcttccactg aactggacat gtgctaccgc tgtggatcaa aggatcattg gtcacgcgta 2280 tgccgagcta cccccgaggc tattgccaag tatcattccc gtcgtgagtc taactttgcg 2340 catgtggaac atcccgaaga tgctactaca tccatggaga tatcagattt tcaggaggca 2400 tcagctccta tggaagaata aattttagac atgtttttag ggcgttttac ccctagtggc 2460 cgaacccact aggagtggcc gaaccctacc cccccctcta tttttctagg tttatggttt 2520 aattttggac aatttttcta agtmtttgga atatttgttt ggttttggtt tgttttgaat 2580 tatggataat tattttatgg atattatttc tcgaattgat taattgaatg aatggaatta 2640 tatttatgca tgtgaccaat tcaattaatt tatttctagg tatgactagt ggggaagtta 2700 gttgtctggc tgatagtgct accacgcaca ccatattgcg tgagcgacac tattttacta 2760 acttcgtacc taagaatgca cctctgacaa ccctctcagg cccatccaac ctgattgaag 2820 gatacggaaa ggcccgtatm atgttgtcta atggtactgt cttaaccatt aaagaggcac 2880 tctattctcc acgttccgga agaacgttgc tgagttttag agatattcga gataatcaat 2940 atcatgttga aaccactgaa gakaatggtt ctgaatttct ttgtatcact tcttacgaat 3000 atggccagaa gcgtattcac gagaagctgg aacgtctccc gagtgggttg tacatcacaa 3060 ccattcgcgg catagaggcc caccatgtgg ccggccctat gcctgggttc cagagcactt 3120 tgctgctttg gcatgaccgt atgggacatc ccggacgtga catgatgcgc cgtatcctca 3180 aatcatcaca tgggcatcac ttacatcctt acgttggact cccgccatgc aaagcgtgtt 3240 ctttggggaa gttgaatact caaccctcaa ttacaaagat tattcacgac cctcctaagt 3300 ttcttcagag gattcaaggg gatatttgtg gacctatcca accaacatgc ggaccattta 3360 gatactttat ggtgttggtt gatgcatcga cacgatggtc acatgtctgc ttattgtcca 3420 cacgcaacgc tgcatttgcg aaactcctag cacaaattat taagcttagg gctcaccacc 3480 ctgattatcc gatcaagtcg attcgactgg ataatgctgg agagtttacg tcacagactt 3540 ttgacgatta ttgcatgtca gttgggattg aagttgaaca tcatgtaccc catgttcaca 3600 cccaaaacgg cctggcagaa gctttcataa agcgccttca attgatagct cggactttgg 3660 ttatgcgaac caaactgccg gtatctgcct ggggctatgc aatattgcac gcagctatgt 3720 tggtccgcct gaggcccacc gctacccaac ctcattcacc gttacagttg gttactggat 3780 acgagcctga cgtctcgcat ttacgtgtgt ttgggtgcgc agtctatgtg ccaatagcgc 3840 cgccactacg taccaaaatg ggtcctcaga gaaaaatggg aatctatgtc ggttatgatt 3900 cgccatcaat tattcgctac ttagagccct tgacaggaga tctctttacc gcacgttttg 3960 cggattgtca ctttgatgag acagtcttcc cgtcgttagg gggagataag aacgctaacg 4020 ttcctgtaga acgccgcgaa ttgtcgtggt atgctcccac tatgtctcat ttagatcccc 4080 gcactgcctc agtctgaaac tgaagtgcga cgtattatag atcttcagag cattgctcaa 4140 agcatgccag atgcttttac tgatctagca aaggtgacga gatcacatat acccgctgca 4200 aacgcacctg caaggataga cgtacccagc gtacgtcgta acaccgcctg ggaaggccga 4260 accgtccccg agggtggggc ggccgcacct tccacgcggc acggtacatt ggcggctagc 4320 caatcatctg ctcctaccct gaagcgtggc agaccccctg gttcaaagga ttcacaaccc 4380 cggaagagga aaacggcaca aactagtgac cctagtctga atccgaccat cgcttactca 4440 tctgttccaa cgcatgaggt tattctagat tacggtgatg tcttagatga gacaaaccgg 4500 cctcccgaga atcgcgagat ttcggtccac tacgcagtat tggatgaggt ttggaatcgg 4560 aatgagatga tcgtcgacga tgcattcgcg tacacagtag ctactgacat catgcttagc 4620 gatgacattg aaccacgttc cgttgatgaa tgccgacgta gaacggattg gtcaaactgg 4680 aaacaagcaa tccaggtcga actcgattcg cttgcgaaac gtaaggtgtt tgggcctgta 4740 gctcctactc caccacatgt gaagcccgtg ggctacaagt gggttttcgt gaggaagcgt 4800 aatgagaaga atgaaatagt gcgatacaaa gcacgcctcg tagcgcaagg cttctctcaa 4860 cgccctggga ttgattacga ggagacgtat tcccccgtaa tggacgtcat aacgttccgc 4920 taccttatca gtttggtagt ttccgaaaaa ctgaatatgc agcttatgga cgtggtaacc 4980 gcgtatctct atggggatct agatacggaa atctacatga aagttccaga aggacttcca 5040 ttgactggtt caaatagttc tagaccacgg aacactctct cgattagatt gaggagatca 5100 ctctacggat tgaaacaatc cgggcggatg tggtataacc gtctgagtga atatttgaca 5160 agtcagggtt atgtgaacaa cgaactatgc ccatgcgtgt tcataaagaa gtcacattcc 5220 ggatttgcga tcgttgcagt ttatgtcgac gacatgaacc tcatcggaac tcccgcagag 5280 cttgaggaaa ttgccgttca cttgaaatcg gaatttgaga tgaaagatct tgggaaaact 5340 cgatattgtc tcggcctgga gatcgagcat tgttcggatg gaatcctagt acatcaatcg 5400 aactacaccc aaaaggtgtt gcgacgtttt aatgaggata aagcgaagcc ttcgagtact 5460 cctatggtcg ttcggactct agatgctaaa cgagatccct tccgtcccaa ggaggatgag 5520 gaagagattt tggagcctga agttccatac ctaagtgcaa ttggtgcttt attgtacttg 5580 gctcaatgca ctagacccga catctccttc gctgttaatc ttttggctag atacagcaat 5640 gcgcctacac gcagacactg gaatggtgtt aaagacattt tccgctacct caagggtacg 5700 acggatttgg gcttgttcta cacccacgaa tcctcgagag ccgccgcccc ctcggtcctc 5760 gggttgattc tcgccttgtt ggttacgcag atgctggata tctgtctgac ccacataggg 5820 cacgttctca aacgggttat gtctttaccg ttggagacac cgctatatct tggaggtcta 5880 ccaagcaaac gctagttgcg acttcttcga accatgctga gattctcgcc ctgcatgaag 5940 catcgcgtga gtgcttttgg ttgagagcag tcatggaaca tattcgaagc actagtggtc 6000 ttacttccgt cgttgacctt cctacgacga tctttgaaga caatgcagca tgtatcgagc 6060 agttaaagaa gggatacatc aagggagaca acaccaagca catagcgccg aagttctttt 6120 attctcacca gcaacaacag catcagaaca ttgaagtcaa gcaaatccgt tcccaggaca 6180 acctggccga tctcttcacc aagtcattgc ccaagtctac ttttcagaag ctcgtccaag 6240 gaatcggtat gcgtaaatta tctgagttga attgcttgta gttctcttat ttggaagtta 6300 tgtctaactc agggggagta tcctgaagca tactcacttg atcttaatgt actctttttc 6360 ctacgattag gagcattttt cccactgggt ttttgctacc taacgaggtt ttgatgaggc 6420 acccatcctg ggatgatcat actccgttga gttcactact ttcgtcctgt ttgacgtttg 6480 ttttagacat tatgcatact tctcactttt ctccttagtc tatgggtttt cacmtgcctt 6540 gggttttacc atagcgaggt tttgtgagtt ttactaccaa tgcatacttt ctttaaattt 6600 gagactcgca ttcacccgtt gtgccgacga cttcatcaac tgttctacct catctgctga 6660 agatctgatg cgatgttttg tttgagtatt tacacactca agggggag 6708 // ID DNA-3-1_PTr repbase; DNA; EDCOT; 1004 BP. XX AC . XX DT 08-DEC-2009 (Rel. 15.02, Created) DT 08-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Non-autonomous DNA transposon - consensus. XX KW DNA transposon; Transposable Element; Nonautonomous; TSD 3-bp; KW DNA-3-1_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1004 RA Bao W. and Jurka J.; RT "Non-autonomous DNA transposons from black cottonwood."; RL Repbase Reports 10(2), 191-191 (2010). XX DR [1] (Consensus) XX CC TSD is 3-bp long, TIR is imperfect, 11-bp long. XX SQ Sequence 1004 BP; 285 A; 162 C; 136 G; 421 T; 0 other; ggccatgttt gtttcccgga attcactttc cgggaaacca ctttccaaac tttcctgtgt 60 ttgtttgcca ttaggaaagt tggtcaacgg aaaacacttt ccggtcaacg gaaacacttt 120 tcggtcaacg gaaaacactt tccagtcaaa gaaaaatttg gtttggtttc caggaaagtg 180 ttttcccttt tggctgtgtt tgttttccgg aaagtggttt ccgggaaacc actttccaaa 240 ctttcctgtg tttgtttgcc attagaaaag ttggtcaacg gaaaacactt tccagtcaaa 300 ggaaaatttg gcttggtttt caggaaagtg ttttcctgga aaatttgggc ggaaaacact 360 ttccggaagt tgtgaaaaat ttagaaatgt cattatttgc tgattatatc aaatttgatc 420 ctcaaacttt tgattgctat atataatttg ttttgaatat ttatttttca attccatctc 480 ttaaaattta atttttatat taattttggt ccttattttt ataattgcta tttgcttttt 540 ccttatcatt tttttattga aattttttat ctatcaaatt tggtcctcat tcttttgatt 600 gttacttatt ttatttgaaa taatttatga aatgttaatt attattattt taatttcttc 660 accttttatt tttttttaat tttttagatt tgatctctat tattttgatt attatttatt 720 ttatttgaga taatttatga aattatattt tttttcaatt tcattctcat tcaacttttt 780 aatttgtaag atttgttcct cattatttta ataaacttga gaaaaataaa acattaataa 840 gttattttcc agctcatttt ccatgacata accaaacact ggaaagtgtt ttccaactta 900 ttttccatta cactaccaaa catcggaaaa tactttcccg gaattcactt tccccggaat 960 tcactttcca aaaggaaact actttccagc aaacaaacgg ggcc 1004 // ID Copia-37_Mad-LTR repbase; DNA; EDCOT; 252 BP. XX AC ACYM01138943; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-37_Mad-I; KW Copia-37_Mad-LTR; Copia-37_Mad_. XX NM Copia-37_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-252 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1387-1387 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01138943; Positions 2103 2354. XX SQ Sequence 252 BP; 75 A; 51 C; 53 G; 73 T; 0 other; tgttaaaggt gatccactac atcacaaact ggacagaagg aatattatca ttccttgaca 60 gctaggttag catgtgtaga tgcacatgca tcatggacag caaggccact gcatgtggtt 120 tctgactgct gcaacaagga cagcagggat gccacttcca gtccttttgt ttattgcatg 180 cgtatgttaa aatgatgtat ataaactctg ctgcaattgc agcagatcat tcattcaaat 240 atattggatc ca 252 // ID HAT-N13_Mad repbase; DNA; EDCOT; 511 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-N13_Mad. XX NM HAT-N13_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-511 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1635-1635 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is short: Pos 5-16 vs 496-507. XX SQ Sequence 511 BP; 136 A; 89 C; 159 G; 127 T; 0 other; caaggttcta aaagtcgcta ggcgctagtc gggcggcggg ctggggccta gcgcctaggc 60 ggctaggcgg ggcctaggcg gggcctaggc ggactaggcg gatttaagta aatctatcat 120 atttcaggta aataagtgtc tgcttctact tgaaatatat ataatttcat cataaactac 180 aaaatagaat gcatatatat catgaagtat tggaacataa tgaaaacatg tgaaataagg 240 atataatgtt tgttcattca agtatgcaac aagtctctta caatttattg gaaaaaaaca 300 aaatgcaaaa tgaaagttat gtattttctg tctaagtgag ttgcaaccta ggcgggtcta 360 ggcgggctag gcgggtgcct aggcgggcta ggcgggtgcc taggtggtct aggcggtggg 420 ctggggccta ggcattaatc ggggcggtgg gctggggcct agcgcctagg cggggcctag 480 gcggcgctag gcggggattt ttagaacagt g 511 // ID COPIA-I_MT repbase; DNA; EDCOT; 9359 BP. XX AC . XX DT 07-DEC-2004 (Rel. 9.11, Created) DT 07-DEC-2004 (Rel. 9.11, Last updated, Version 1) XX DE Medicago truncatula copia-like retrotransposon COPIA_MT, internal DE sequence - a consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; COPIA-I_MT; KW copia-like retrotransposon; gag-pol domain. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-9359 RA Gentles A. and Jurka J.; RT "Copia-like retrotransposon COPIA_MT."; RL Repbase Reports 4(11), 287-287 (2004). XX DR [1] (Consensus) XX CC COPIA_MT is a Copia-like retrotransposon with ~1240 bp LTRs, CC and a 5 bp target-site duplication. Average similarity to CC consensus is 94%. It is most similar to Copia-like CC retrotransposons TORT1 (Lycopersicon esculentum) and PREM2_ZM CC (Zea mays). CC Genscan_predicted_2378aa: CC MSGDEESVTTKYTSVKHDYDTADKKTDSGKAPKFNGDPEEFSWWKTNMYSFIMGLDEELWDILE CC DGVDDLDLDEEGAAIDRRIHTPAQKKLYKKHHKIRGIIVASIPRTEYMKMSDKSTAKAMFASLC CC ANFEGSKKVKEAKALMLVHQYELFRMKDDESIEEMYSRFQTLVSGLQILKKSYVASDHVSKILR CC SLPSRWRPKVTAIEEAKDLNTLSVEDLVSSLKVHEMSLNEHETSKKSKSIALPSKGKTSKSSKA CC YKASESEEESPDGDSDEDQSVKMAMLSNKLEYLARKQKKFLSKRGSYKNSKKEDQKGCFNCKKP CC GHFIADCPDLQKEKFKGKSKKSSFNSSKFRKQIKKSLMATWEDLDSESGSDKEEADDDAKAAVG CC LVATVSSEAVSEAESDSEDENEVYSKIPRQELVDSLKELLSLFEHRTNELTDLKEKYVDLMKQQ CC KSTLLELKASEEELKGFNLISTTYEDRLKSLCQKLQEKCDKGSGNKHEIALDDFIMAGIDRSKV CC ASMIYSTYKNKGKGIGYSEEKSKEYSLKSYCDCIKDGLKSTFVPEGTNAVTAVQSKPEASGSQA CC KITSKPENLKIKVMTKSDPKSQKIKILKRSEPVHQNLIKPESKIPKQKDQKNKAATASEKTIPK CC GVKPKVLNDQKPLSIHPKVCLRAREKQRSWYLDSGCSRHMTGEKALFLTLTMKDGGEVKFGGNQ CC TGKIIGTGTIGNSSISINNVWLVDGLKHNLLSISQFCDNGYDVTFSKTNCTLVNKDDKSITFKG CC KRVENVYKINFSDLADQKVVCLLSMNDKKWVWHKRLGHANWRLISKISKLQLVKGLPNIDYHSD CC ALCGACQKGKIVKSSFKSKDIVSTSRPLELLHIDLFGPVNTASLYGSKYGLVIVDDYSRWTWVK CC FIKSKDYACEVFSSFCTQIQSEKELKILKVRSDHGGEFENEPFELFCEKHGILHEFSSPRTPQQ CC NGVVERKNRTLQEMARTMIHENNLAKHFWAEAVNTSCYIQNRIYIRPMLEKTAYELFKGRRPNI CC SYFHQFGCTCYILNTKDYLKKFDAKAQRGIFLGYSERSKAYRVYNSETQCVEESMHVKFDDREP CC GSKTSEQSESNAGTTDSEDASESDQPSDSEKYTEVESSPEAEITPEAESNSEAEPSPKVQNESA CC SEDFQDNTQQVIQPKFKHKSSHPEELIIGSKDSPRRTRSHFRQEESLIGLLSIIEPKTVEEALS CC DDGWILAMQEELNQFQRNDVWDLVPKPFQKNIIGTKWVFRNKLNEQGEVTRNKARLVAQGYSQQ CC EGIDYTETFAPVARLEAIRLLLSYAINHGIILYQMDVKSAFLNGVIEEEVYVKQPPGFEDLKHP CC DHVYKLKKSLYGLKQAPRAWYDRLSNFLIKNDFERGQVDTTLFRRTLKKDILIVQIYVDDIIFG CC STNASLCKEFSKLMQDEFEMSMMGELKFFLGIQINQSKEGVYVHQTKYTKELLKKFKLEDCKVM CC NTPMHPTCTLSKEDTGTVVDQKLYRGRTMSIEEWELIIQAENPVDFASLTHHGCDLVRFYKKQK CC LMSYFSLLNGPTYEVLVRQFWVRASVFDIEAAKQEEAQLILVDPTLKGKTREEMGLLSFTGTEI CC RSNVMGIPVTXNEQVIAQAMRRDASGKYFGEEIPNPRTSXWKEIVNETIYGSKDAKPYSTLSME CC KKMLLKIQNENIFPKGGGSDQPSLGHKVFLHHTITQETTMNVPKYMFKYMIKELKKSQMENRKF CC VPYGRLLSVIFQEGGLLSALKDVGIYDNQKLGAVTGKIINAATLVKMKLIPANARKKLDTDMHE CC SDAISDLVTHHIPICKKDPLDVQRAYILDFYKTYNKKISLKDVPEEMYGGDLPVAKGRKSKKKQ CC ITKEEYLAEDATEEGAQKHKKAKKEKSAMSTILEEVEDLDDVPLIRKRTRSAQETAEQPASEQT CC GSEQAASEKPPSPKKKREAALQTIKRKRSXRNLKTAEGRRAEMLEELEENWDEDSSPKKAKRTI CC TSEPIVMPSFEMTEELKQYAREYSASKIAEKKRMKELYEKERDERLKAAGYVPTPDIAALASEL CC EQETVQYGATLLSQALKNKQASGATSSEPASKAPEAVHPEAXSSGNPSKAPTNTQIPSLPSSPS CC SSSTESDDQPLSQHIDKLLKTKPTKLTEFGTLDYERTQIEFSKNRIKLCEKFNLPTTHPLYPDI CC PEPVSVQQPEPNQTNPPNNQTPQKASEVVSEATTSETPQQQESSTLHXLEKHLGGEMQPTPTKA CC SKTVPGKTVLENQQTQTIPEQTVPEQTASEQVAPDQTTSEQIASDQTTEPEQQPEPPIIDLTSD CC QPSTSNTTQTEPSPIPDHILESEYIEEQLIRLSDEIQALILRRTVPVPPIHYYDQWMDLKKSFD CC ELLDQLRTKX. XX SQ Sequence 9359 BP; 3262 A; 1700 C; 1857 G; 2532 T; 8 other; accccccctt cttgtgtttt tcaccttcaa ttggtatcag agcttgctct gttatcacag 60 cacttaaccg tgttacagtt caagatctat tagaaaaaca tgtctggaga tgaggaatca 120 gttactacaa aatacacaag tgtcaagcat gactatgata ctgctgacaa gaaaacagac 180 tctggaaaag ctccaaagtt taatggagat ccagaagagt tttcatggtg gaaaactaat 240 atgtacagct ttatcatggg attggatgaa gagttatggg acatactgga agatggagtt 300 gatgatctgg atttggatga agaaggagct gctatagaca gaagaataca tactcctgct 360 cagaagaagc tttataagaa acaccacaag ataagaggaa tcattgtggc ttctatacct 420 cgcaccgaat acatgaaaat gagtgacaaa tctactgcga aggctatgtt tgcttctcta 480 tgtgcaaact ttgaaggcag caagaaagta aaagaggcta aagctttgat gctagttcat 540 cagtatgaac ttttcagaat gaaggatgat gagagtatag aagaaatgta ctcaagattt 600 caaactttag tttctggatt gcaaatactg aagaaaagct atgttgcttc tgatcatgtt 660 agtaagattt tgagaagctt accttcaaga tggagaccca aagtaactgc tattgaggaa 720 gctaaggatc taaatacttt aagtgttgaa gatcttgtta gctcactcaa agtgcatgaa 780 atgagtttaa atgagcatga aacctctaag aagagtaaat ccattgcttt accatctaaa 840 ggaaagacct caaaatcttc caaagcctac aaagccagtg aatctgaaga agaatcacct 900 gatggagatt ctgatgaaga tcaatctgta aagatggcta tgctgtccaa caagcttgag 960 tatctggcaa ggaagcagaa gaaatttttg agcaagagag gtagctacaa gaactccaag 1020 aaagaagatc agaagggatg cttcaattgt aagaagcctg gtcatttcat tgctgattgc 1080 cctgatcttc agaaggagaa gtttaaaggc aaatccaaga aatcaagctt caactccagt 1140 aaattcagaa agcaaatcaa aaagagcttg atggcgacct gggaagattt ggatagtgaa 1200 tctggttctg ataaagaaga agctgatgat gatgctaagg cagccgtggg gttagtggca 1260 acagtatcat cagaagcagt atcagaagct gaatcagatt cagaagatga aaatgaggta 1320 tattccaaaa tccctagaca agaacttgtt gattctctaa aagaactttt atcactgttt 1380 gaacacagaa ccaatgagtt gacagattta aaagaaaaat atgttgattt gatgaaacaa 1440 caaaagtcaa ctctattgga actgaaagct tctgaagaag aactcaaagg gtttaacctc 1500 atatcaacaa catatgaaga tagactcaag agtctttgtc agaagctaca agaaaaatgt 1560 gataaaggtt caggcaataa acatgagatt gccttggatg attttattat ggctggaata 1620 gacagaagca aagttgcttc tatgatctac agcacataca agaacaaagg caaagggatt 1680 ggatattctg aggagaaatc caaagaatac agtctcaaga gctactgtga ttgtatcaag 1740 gatggattga aatccacctt tgtgcctgaa ggtacaaatg ctgtaactgc tgttcagtca 1800 aaacctgaag cttctggttc acaggctaag atcacatcaa agccagaaaa ccttaagatc 1860 aaggtaatga caaaatctga tcctaagagt caaaagatta aaattctgaa aagatcagaa 1920 cctgttcatc agaatctgat taaaccagaa tctaaaatcc caaaacaaaa ggatcagaag 1980 aacaaagcag ctactgcttc tgagaaaaca ataccaaaag gtgtcaaacc taaagtattg 2040 aatgatcaga agccactcag cattcaccct aaggtacaag ggaggaaaag taaaacctcc 2100 aaaactaacc caaaaggacc catgaagata tgggtaccta aatctgaatt ggccaaaaat 2160 gcaggtgtgc ttaagggcaa gagagaaaca aaggtcatgg tacctagaca gcggatgttc 2220 aaggcacatg actggagaga aagctttgtt ccttaccctt acaatgaaag atggaggaga 2280 agtgaagttt ggtggcaacc aaactggaaa gatcattggt acaggtacta ttggtaattc 2340 ctccatctca attaataatg tgtggctagt agatggtctg aagcataacc tattgagcat 2400 tagtcaattt tgtgacaatg ggtatgatgt aacgttcagt aagaccaact gcacactagt 2460 caacaaggat gacaaatcca ttacattcaa gggaaagaga gttgagaatg tctataaaat 2520 aaatttctct gatctggctg atcagaaggt agtttgcctt ctgtcaatga atgataaaaa 2580 atgggtatgg cataaaaggt tgggacatgc taattggaga ttaatttcta aaattagcaa 2640 gttacaactg gtcaaaggat tgcctaacat tgattatcat tcagatgcac tttgtggtgc 2700 atgtcagaaa gggaaaattg tgaaaagttc tttcaaatct aaagacattg tatcaacctc 2760 cagaccctta gaattactcc atattgatct ttttggtcca gttaacactg catctttata 2820 tggaagtaaa tatggattag tcattgttga tgattacagc agatggactt gggtaaaatt 2880 cattaaaagt aaagactatg catgtgaagt gtttagcagc ttctgcactc aaatacaatc 2940 tgaaaaagaa ttgaaaattt tgaaagtcag aagtgatcat ggtggagaat ttgaaaatga 3000 gccatttgaa cttttttgtg aaaaacatgg gattctccat gagttttctt ctcctagaac 3060 tccacaacaa aatggggttg tagagagaaa gaacagaacc ttacaagaaa tggccagaac 3120 catgatccat gaaaacaact tagctaaaca tttttgggca gaagcagtca atacttcatg 3180 ttatattcaa aataggatct atatcagacc tatgttggag aaaacagcat atgaactctt 3240 taaaggaaga agacccaata tctcttactt tcatcagttt ggatgtactt gttacatctt 3300 aaacactaaa gactatctga agaaatttga tgccaaggct caaagaggaa tctttttagg 3360 ttactctgaa aggtcaaagg catacagagt gtataattca gaaacacaat gtgttgaaga 3420 atctatgcat gtaaaatttg atgatagaga gcctggaagt aaaacttcag agcaaagtga 3480 aagtaatgca ggtacaactg attctgaaga tgcatcagaa tctgatcaac cttctgattc 3540 tgaaaagtat acagaagttg aatctagtcc agaagctgaa atcactccag aagctgagtc 3600 taattcagaa gcagaaccta gcccaaaagt acagaatgaa agtgcttctg aggactttca 3660 agataacact cagcaggtta ttcaacctaa attcaagcac aaatcttcac atcctgagga 3720 gctaatcatt ggaagcaaag atagtcctag aagaacaaga tcacatttta gacaagaaga 3780 gtcattaata ggactgcttt caataattga gcctaaaact gttgaagaag ctctctcaga 3840 tgatggatgg atattagcta tgcaagaaga gctaaatcaa ttccaaagga atgatgtgtg 3900 ggatctggta cccaaacctt ttcagaagaa cattattgga acaaaatggg tattcagaaa 3960 caagctgaat gaacaaggag aagtaaccag aaacaaagcc agacttgttg ctcaaggcta 4020 cagtcaacaa gaaggcattg attacactga aacatttgct ccagttgcaa gattggaagc 4080 aatcaggtta cttctatcct acgcaattaa tcatggcata atattatatc aaatggatgt 4140 caaaagtgcc tttcttaatg gtgtcattga agaagaagtg tatgttaaac aacctcctgg 4200 gtttgaggat cttaagcatc ctgaccatgt ttataaactt aagaaatcac tatatggctt 4260 gaaacaagct cccagagctt ggtatgatag actaagtaat ttcttaatta aaaatgattt 4320 tgaaagagga caagttgaca caacactctt cagaaggact cttaagaaag atattttgat 4380 tgtgcaaata tatgttgatg atataatatt tggttctact aatgcatctc tttgcaaaga 4440 attttctaag ttaatgcagg atgaatttga aatgagtatg atgggagaat tgaaattctt 4500 tcttggaatt caaatcaacc aaagtaaaga aggagtatat gttcatcaaa caaaatatac 4560 aaaggagctt ctgaagaagt tcaagctaga agattgtaaa gtgatgaaca ctccaatgca 4620 tccaacctgc accttaagca aagaagatac tggaacagta gtagaccaga agctatacag 4680 aggtatgatt ggttctctgt tatacctcac tgcatctaga cctgatattt tattcagtgt 4740 atgcttgtgt gcaagatttc aatcagatcc tagagaatct catttaactg cagttaagag 4800 aatcttcagg tatctgaaag gaacaactaa tcttggactc ctgtatagga aatccctaga 4860 ttataagttg attggattct gtgatgctga ttatgctggt gataggattg aaagaaaatc 4920 aaccagtgga aattgtcaat tcctgggaga gaatctgata tcctgggcaa gcaaaagaca 4980 agcaactatt gctatgtcta cagcagaagc agaatacatt tcagctgcaa gttgttgcac 5040 acaactactt tggatgaaac atcagttgga agactatcag attaatgcta acagtattcc 5100 catttattgt gataatactg ctgctatttg tttgtcaaag aatccaattc tacattcaag 5160 agccaagcat attgaaatca aacaccattt tatcagagac tatgttcaaa aagggatttt 5220 agatatacaa ttcattgata ctgaacatca atgggctgat atatttacaa aacctttatc 5280 tgttgaaaga tttgatttta ttaagaaaaa tttgaacatg cattttgtgt ctgattgaaa 5340 aattgcttgc ctctgaataa gaagtttggt tctgaagttt attcagaagc attttggttc 5400 atcagaagct cttaactgag gttctgagga aaatgtgctt ctgaagatga cgtcagcact 5460 aaaacttcag aagtgttatt ctttgcttct gaatagcttg gttagtggga acgttggtag 5520 ttactttatg taacagctgt cccattaccc aaaaggtagt tttctgaaga gtctctgacg 5580 tggtctattt gtattggagt ataacaaaaa gggcaatgat gttttattcg ctttttaaca 5640 tacttacacg cgcccccaat ttgtcattaa tgctgtgttt gtttgtccct tctgaattgc 5700 aaacgtttta ataaaaacac taagtcaatt cacacacttc tcacttcaca acaaacactt 5760 tctattttct tctcaaccct ctgcgaaagt aagcgcattc actcatcctc tcaaaacacc 5820 ttagaaccct aaaactactt caaatcaatg gcatcttcaa gttctgctgg tggttcttca 5880 tcaaatatgg atatagatac tcctgcttat gayatcaaag gaagaactat gtctattgag 5940 gaatgggagt taatcattca agcggaaaat ccagtggatt tcgcttctct aactcaccat 6000 gggtgcgact tggtaaggtt ctacaagaag cagaagctga tgagttactt cagtcttctc 6060 aatggtccta cttatgaagt gctggtcaga caattctggg taagggcttc agtctttgac 6120 attgaagctg ctaaacagga agaagctcaa ctgattctgg ttgatcctac tctgaaggga 6180 aaaaccagag aagaaatggg tctactctcc ttcaccggga cagagattag atcaaacgtc 6240 atgggtattc ctgtaaccat kaatgagcag gttattgctc aagccatgag aagggatgct 6300 tctggcaaat actttggaga agagattcct aatccaagaa ccagcrcttg gaaggaaatt 6360 gtcaatgaga ctatctacgg atcaaaggat gctaagcctt acagcacctt aagcatggaa 6420 aagaaaatgc tgctgaagat ccagaatgaa aacatctttc ccaaaggtgg aggaagtgat 6480 caaccttcac ttggtcacaa agtctttctg catcacacca tcactcagga aacaacaatg 6540 aatgttccca agtacatgtt taaatacatg atcaaggaac tcaagaagag tcagatggag 6600 aacaggaagt ttgttcctta tggaaggctg ctctctgtaa tctttcaaga aggaggactt 6660 ctaagtgcct tgaaggatgt gggcatctat gataatcaga agctgggagc agtaacaggg 6720 aagataatca atgcagcaac tcttgtgaag atgaagctga ttccagcaaa tgctcgcaag 6780 aaactagata ctgatatgca tgaatctgat gccatatctg atctagtcac tcatcacatc 6840 cccatctgca agaaagatcc cctggatgtg cagagggcct acatcttgga cttctacaaa 6900 acctacaaca agaagatcag cttgaaagat gtccctgaag aaatgtatgg tggtgatctg 6960 cctgtggcca aaggcagaaa atctaagaag aagcagatca ccaaggaaga ataccttgct 7020 gaagatgcta ctgaggaggg tgctcagaag cataagaaag ctaagaagga aaaatctgct 7080 atgtccacca ttcttgagga agtggaggat ttggatgatg tccctcttat cagaaaaagg 7140 acaaggagtg ctcaagaaac agcagaacag cctgcttctg aacaaactgg ttctgaacaa 7200 gctgcttctg aaaagcctcc aagtcccaaa aagaaaagag aagctgctct tcagaccatc 7260 aaaaggaaga gatctwcaag aaatctgaag acagctgaag gacgaagggc agaaatgttg 7320 gaagaactgg aagaaaactg ggatgaagac tcaagcccca agaaggcaaa aaggactata 7380 acttctgagc ccatagtcat gcccagtttt gaaatgactg aagaattaaa gcagtatgct 7440 agggagtatt ctgcatccaa gatagcagaa aagaaaagga tgaaggaatt gtatgagaaa 7500 gaaagggatg agcgtctcaa ggctgcaggg tatgtgccta ctcctgacat tgctgcttta 7560 gcatctgagt tagagcaaga aactgttcag tatggagcaa ctctgctttc tcaagccttg 7620 aagaataagc aagcttcagg agcaacttca tcagaaccag cttcaaaagc tccagaagca 7680 gttcatccag aagctcaytc ttcaggtaat ccatctaaag ctccaactaa tactcagatt 7740 ccatctctac cctcttcacc ctcttcatca tcaacagaat cagatgacca accccttagc 7800 caacacatag acaagcttct aaaaaccaaa cctaccaaac taacagaatt tggaacactt 7860 gactatgaga gaactcaaat agaattttcc aaaaatagga ttaaactgtg tgagaaattc 7920 aatttgccta ctactcatcc actatatcca gatattccag aacctgttag tgtacaacaa 7980 cctgaaccca accaaacaaa cccaccaaat aaccaaactc cacaaaaagc ctctgaagta 8040 gtttcagaag caactacttc agaaaccccc caacaacaag aatcctcaac ccttcacaar 8100 ttagaaaaac atttaggtgg tgaaatgcaa ccaacaccca caaaggcctc taagacagtc 8160 cctggaaaga ctgtgttaga aaaccaacaa acccaaacca ttcctgagca aactgttcct 8220 gaacaaactg cttctgaaca agttgctcct gaccaaacaa cttctgaaca aatagcttct 8280 gaccaaacaa cagaaccaga acaacaacca gaaccaccaa taatagactt aacctctgac 8340 caaccttcca catcaaatac aactcaaact gaaccttcac ccatccctga ccatatcctt 8400 gagtctgagt atatagagga acagctgatc agacttagtg atgagattca ggcactgatt 8460 cttcgcagaa cagttcctgt acctcctatt cactattatg atcagtggat ggatctgaag 8520 aagagctttg atgagctgct ggatcagctt agaactaaat gtgtgtcatc tcactctgct 8580 atgctgaaga agctgttgga tgatatgcat gaagcagcta aggagaaaga gctgaattwt 8640 gtgcctctgc tggacatcac tcctttctat ccagaagaag agtacatcac aagggctgca 8700 agaattcatg ctgggtataa aagaagaatg agggaaaagg atgagctact tkagaagaag 8760 gatgatcaga tcaagtatct cttagaacag ttgtataagc aagcccaacc ttagttgcac 8820 acccaactct agcttgtttt tacttttgtt cttagtagct ttgtctttgt atcttaacct 8880 ttctttatat atattatcat tgtttctgga tcttgtgctt tttcaccttc aatatgtttt 8940 acaagcttta actctgatga tatttactgt ttttaatgct gcttgctctg aaatactatt 9000 tttaaagttt atatgtttat tcttttgttt ttttgctctg atactctttc ttttgttttt 9060 attctttttg ttgatgacaa aagggggagt aaatgtatag tatttttaag gcactgagcc 9120 ccactataac cacttctaaa tttcttttaa atacttctga tttgattttt atgagtattt 9180 tattgaaatt taattaataa gaatagaact tagggggagc ttacaaacct caccttaaag 9240 atctattaga ctcaggggga gcttacaaac ctctatccca gtggtcaact tattaattag 9300 atcaacaaca attgaacatt ttaaatacta ttgtttgtca tcatcaaaaa gggggagat 9359 // ID SINE-2_Mad repbase; DNA; EDCOT; 208 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative SINEs from the apple genome. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Nonautonomous; SINE-2_Mad. XX NM SINE-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-208 RA Kojima K.K. and Jurka J.; RT "Putative SINEs from the apple genome."; RL Repbase Reports 10(10), 1822-1822 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~83% identical to the consensus. 9-13 bp TSDs. Relatively long CC TSDs and polyA tail indicate that it is a SINE. XX SQ Sequence 208 BP; 47 A; 57 C; 65 G; 39 T; 0 other; aaccaccacg gggtggccca gtggttgggg acgaattcca ggcccgtatt ccacacggca 60 cgtcctgagt tcgattcctg gcgctggtga atcgcacgat ggtggccagg gggaggctga 120 aatgcctctg tgagtctttc cggcccccgg aagggtggac tgccgtggcg aagccaccag 180 ctggtcccct tttaaaaaaa aaaaaaaa 208 // ID Copia-3_SL-LTR repbase; DNA; EDCOT; 276 BP. XX AC AC209587; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the tomato genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-3_SL_; KW Copia-3_SL-I; Copia-3_SL-LTR. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-276 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the tomato genome."; RL Direct Submission to RU (22-JAN-2011). XX DR Genome; AC209587; Positions 131794 132069. XX SQ Sequence 276 BP; 79 A; 47 C; 39 G; 111 T; 0 other; tgttataaat ccattgaatt gtgtggattg tcctttagat ttactcaaga cttaattgta 60 ttcatgtata catgttccca aggtgataag aatcatttgg ataactatgt acctactaat 120 tggccattta tcacgggggc ctttggggtg atatctcaac tctataaata gagatatcat 180 tcaccttttg taatacatac ttgaataaga aaattatctc atctatctta tacttcttgt 240 ctttttcttc ttatattctg agctttcttt acaaca 276 // ID Copia-39_Mad-LTR repbase; DNA; EDCOT; 307 BP. XX AC ACYM01026927; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-39_Mad-I; KW Copia-39_Mad-LTR; Copia-39_Mad_. XX NM Copia-39_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-307 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1389-1389 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01026927; Positions 14191 13885. XX SQ Sequence 307 BP; 81 A; 39 C; 59 G; 128 T; 0 other; tgataagtga ggacacatgg caagtttgta ggtatatctg ccagctagga tttgttgaaa 60 agtggttatt ttagataaga tttggttgga ttggatctgt taagatttgg ttagattgga 120 taaaagtttt ctagtcatta agtcagttgg tagcctttat atgttagttt tctgattgta 180 ttgaacaatt acattgaatg aatattcatc ttttgagtgc actattctct ctctctgagc 240 tcttctttct tacttcattt ttcagctttc ttgatcaaac attcttagat ttacagtagt 300 taataca 307 // ID Copia-36_VV-LTR repbase; DNA; EDCOT; 256 BP. XX AC chr1; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-36_VV_; KW Copia-36_VV-I; Copia-36_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-256 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr1; Positions 11070387 11070642. XX SQ Sequence 256 BP; 73 A; 52 C; 32 G; 99 T; 0 other; tgttagtgaa ctagttgagt tagttgtgaa gtccaattag tttcaaccaa tcatttctgt 60 ttaaaaccaa cctctcaagt cagttatagc tatcaacaac taagtgtata aatactacag 120 aagtgtaatg atacgagcac tggaaataac agcaagaaat ttcactatgt ttttctctaa 180 ctttactctg tttttctctt actctgtttt ctcttcctct tcttctaatc gtttctgtta 240 ctccatttct tcaaca 256 // ID Copia-84_Mad-I repbase; DNA; EDCOT; 4367 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-84_Mad_; KW Copia-84_Mad-LTR; Copia-84_Mad-I. XX NM Copia-84_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4367 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1706-1706 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1808-2338] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 154..1257 FT /product="Copia-84_Mad-I_1p" FT /translation="MASPSATASPSESVPIPNPSSNPNSSPYTSLTIQNIG FT SMVPIKLKRSNYLPWCALFAPILRRYRLLGIVDGTEPCPPPLMPDRTLNPA FT FEIWYEKDQNLLIWFNSTLSEEVIPFTVGVSSSRDLWLKLEQRFGGISDAH FT VHQLRSRLQSIQKGSQSMSDYLQELKEISDSLTAAGAPISDRDLIAATLAG FT LPDDFESFTDSIMLRLSSTSLDELHGLLLTKELSMIRRKKAASSNITEPFH FT ALSVQTQPPLLPTPPQAYVIQNQPLQQSFRYNSNRGKNNRFSNNRGNRGNY FT RGNNFTSSFNRTNTAAHSRGSSSGPRAPCQICGNSSHEAIDCFDRMNPEIS FT GRIPSCQAPSNVCTLQCQVLSYLVD" FT CDS 1214..3094 FT /product="Copia-84_Mad-I_3p" FT /translation="MCARYNAKSSPTWLIDSGATSHITNDISNIHSPTPYN FT GEEKVYIGDGKGLSISHVGSSTLRTPATSFKLNNVLHVPHMKHNLLSAFQF FT LRDNYCSLTLDSNGSVVKDRSTGKTLLRGSVKDGFYPLQSSTSNRSFSGNV FT PPSLTASAFVSIKAPVKIWHSRLGHPSPPIFRKVLSRNKLAVQGASSVEFF FT CSDCAIAKNHKLPFKAASSSASHSLALLHCDVWGPAPVLSVSGFRYYLLIV FT DDHTKYSWFFPLKAKSEVYSTFVTFKTYVENTVGNKIKAIRSDSGGEFVSS FT SFQAFLQLHGISHQLSCPHTPEQNGCVERKHRHLVETARTLLVASHVPQKY FT WVEAISTALYLINRLPISGLLCSPWELLFHTSPDYTRLKIFGCSCYPWLKP FT YVSSKLDGKSKECVFLGYSLQHKGYRCLDLLTDRVYISRHVLFNEKSFPFS FT QVHTSQFLQSTVPVPPIIDLHFPLSSSSHSPTPQPPPPVVPHVSSPSPSQS FT PDQSIAHPSSAAVTNHHPMVTRSKNGIFRPKAYSATKHPLPSTLDYIPTTY FT NQASKHSEWRLAMQNEFNALQTTGTWSLVPSSPSQNVVGCKWVFRIKKRPD FT GSVERYKARLVAKGFHQQQGLIIKKPLAL" FT CDS 3214..4365 FT /product="Copia-84_Mad-I_2p" FT /translation="MQQPPGFTDSNLPNHVCKLKKSLYGLKQAPRAWFDKL FT FQALKSFGFTQSCSDASLFVIKDPVLVIVLVYVDDILISGQQFIQKLGSLF FT PVKDLGPLHYFLGLEVQRSSKGLFLHQSKYLLDLLQKTKMEGAKPCCTPLG FT TTKLDHSGIPLSNPTEYRSLVGALQYLTWTRPDISFAVNQVCQFMHTPTDL FT HLQAAKRILRFLKGTSDHGLWFQKSSLHLSAFSDADWAGCLFDRRSTSGFC FT VYLGTNLISWSAKKQPTVARSSTEAEYRSLAHTAAEITWICKVFHDFGFPL FT SSKPTIWCDNISAISLASNPVFHARTKHVEIDYHYIRELVLANLLQVQYVC FT TEDQIADIHTKSLTKNRFLLLQSKLSLGTPTSSKLSLRGCK" XX SQ Sequence 4367 BP; 1064 A; 1086 C; 770 G; 1445 T; 2 other; gtttctttat ggtttcatcg ccaaccgcct cacggcctct ctcgatcctc ttctcttccg 60 ctctacttct ctgatctcta cccaaattcg atcgaatttc ttgctgattt tgtactccga 120 tcttcgatca tcgatctgtt ttcttgatct tcaatggcgt ctccgtctgc gaccgcttct 180 ccttctgagt cggttccaat tccaaatccc tcttcaaacc ctaattcctc tccttatacc 240 tctctcacga tccaaaacat tggcagcatg gtgccaatca agctcaagcg gtccaattat 300 ctcccatggt gcgctctgtt tgccccaatt cttaggcgct atcggcttct tggtatcgtc 360 gatggcaccg aaccttgtcc gccaccactt atgcctgatc gcactctgaa tccggcgttc 420 gaaatttggt atgagaaaga tcaaaacctc ctgatctggt tcaattccac attgtctgag 480 gaggtgattc cgttcaccgt tggwgtttcg tcatctcgtg atctctggct caaactcgag 540 caacgatttg ggggcatttc tgatgcgcat gttcatcagc ttcgatcgcg acttcaaagc 600 attcaaaaag gttcacaatc catgtctgat tacctgcaag agctcaaaga gatctctgac 660 tctctcactg ctgctggagc cccaatctct gatcgagatc taattgcagc cactcttgct 720 ggtcttcctg atgattttga gtccttcact gactcaatca tgcttcgctt atcctccaca 780 tctttggatg aattgcatgg attgttactc accaaagaac tctctatgat tcgtcgcaag 840 aaagctgcct catccaatat tactgaaccg tttcatgctt tatcggtcca aactcaacca 900 ccactacttc ccacaccgcc tcaggcgtat gtcattcaga atcaaccact gcagcaatct 960 tttcggtata attcgaatcg tggaaagaac aatcgcttct ccaataatcg tggtaatcga 1020 ggaaattatc gaggcaataa tttcaccagt agcttcaatc gcaccaatac cgcagctcac 1080 tctcgaggct cttcttctgg tcctcgagcc ccttgtcaaa tctgtggaaa ttcaagtcat 1140 gaagccattg attgctttga ccgtatgaat ccggagatct ctggtcgaat tccctcctgc 1200 caagctccaa gcaatgtgtg cacgttacaa tgccaagtcc tctcctactt ggttgattga 1260 ctctggagct acctcgcaca tcaccaatga catmtccaat attcactctc ctactcccta 1320 caatggtgaa gaaaaagtat acataggtga tggtaaaggt ttgtccattt ctcatgttgg 1380 ttcctctaca ttacgtacac ctgctacttc ctttaaattg aacaatgtcc ttcatgttcc 1440 tcacatgaag cacaatttgt tgtctgcttt tcaatttctc cgagacaatt attgttcatt 1500 aacccttgat tctaatggat ccgttgttaa ggatcgttct acggggaaga cgcttttgcg 1560 gggttcagtt aaagacggtt tctatcctct gcagtcctct acatctaatc gttctttctc 1620 tggtaatgtt cctccttcac tcactgcatc agctttcgtc agtattaaag ctccagtcaa 1680 gatatggcat agtcgtttgg gccatccttc tcctcctatt tttcgcaagg ttctctctag 1740 gaataaactt gctgtgcaag gtgcatcttc agttgaattc ttctgctctg attgtgctat 1800 agctaaaaac cacaagcttc ctttcaaagc tgcaagttcc tctgcatccc acagcttggc 1860 attacttcac tgtgatgttt ggggacctgc tcctgtcctt tcagttagtg gttttcgcta 1920 ttatttgttg atagtagatg atcatactaa gtatagctgg ttttttccat tgaaagcaaa 1980 atctgaggtg tattctacat ttgtaacctt caaaacatat gtagaaaata ctgttggaaa 2040 taaaatcaag gctattcgtt cagattcagg gggtgaattt gtcagttctt cttttcaagc 2100 ttttcttcaa ttacatggca tttctcatca acttagttgc ccacatactc ctgagcaaaa 2160 tggttgtgta gaaaggaaac accgacatct tgtagagaca gctcgcactc tcttagttgc 2220 atctcatgtt cctcaaaaat attgggttga ggctatatct actgccctct atttgattaa 2280 tcgattgcct atatctggtc ttctttgttc tccgtgggaa ttgttatttc atacttcacc 2340 agattatact agacttaaga tctttggctg cagctgctac ccttggttaa agccctatgt 2400 ctcttctaag ttggatggta aaagtaagga atgtgttttc cttggctata gtctacaaca 2460 taagggctac agatgcttgg atctcctcac agatcgggta tacatatcca ggcatgtctt 2520 gttcaatgag aaatcctttc ctttttcaca agttcatact tcacagttct tacaatccac 2580 tgttcctgtt cctcccatca ttgatcttca cttccctctt tcttcatcct cacattcccc 2640 tactcctcaa cctcctccac ctgttgttcc acatgtttcc tcaccctccc cttctcaatc 2700 tcctgatcaa tctattgctc atccctcttc tgcagcagtt actaaccatc atcccatggt 2760 tactagatcc aaaaatggta tctttcgacc taaagcttac tctgctacta aacacccttt 2820 gccatccact cttgattata ttcccactac ttataatcaa gcttccaagc acagtgaatg 2880 gcgattagct atgcaaaatg agtttaatgc tcttcaaact actggaactt ggtctctagt 2940 tccttcttca ccttctcaaa atgtggtcgg ttgcaaatgg gtatttagaa ttaagaaaag 3000 gcctgatggt tctgttgaaa gatacaaggc tcgattagtt gccaagggct ttcaccaaca 3060 acaaggactg attatcaaga aacctttagc cctgtagcta aaccagtcac tattcggatt 3120 ttgttaacct ttgcagttca atataattgg tttctaaatc agcttgacat aagcaatgca 3180 tttcttcatg gtgacttaca agaagaggtg tttatgcaac aacctcctgg ttttactgat 3240 tctaatctgc caaatcatgt gtgtaaactc aaaaagtctc tatatggcct caaacaggct 3300 cctcgggcat ggtttgataa actctttcaa gctctcaagt cctttggttt cactcaatct 3360 tgttctgatg catctctctt tgtcatcaaa gatcctgttc tagttatagt attggtttat 3420 gtcgatgaca tattgatcag tggtcagcag tttattcaga aacttgggtc tctgtttcca 3480 gtcaaggact taggtcctct tcactatttt ctggggttgg aagttcaaag atcatccaaa 3540 ggtttatttc ttcatcaaag caaatatctt ctggatttac ttcagaaaac aaaaatggaa 3600 ggtgccaagc catgttgtac ccctcttggt actactaaac tggatcacag tggcattcct 3660 ctatcaaatc ccactgaata tagatccctg gtgggtgcct tacagtattt gacttggact 3720 aggcctgata tctcttttgc tgtcaatcaa gtatgccaat tcatgcatac tcccactgat 3780 cttcatctgc aagctgccaa aaggattctc cgattcctca aaggcacctc tgatcatggt 3840 ttatggtttc agaaaagttc tcttcatctt tctgcatttt ctgatgccga ttgggctggt 3900 tgtctatttg atcgacgttc caccagtggc ttttgtgtat atcttggaac aaacttaatc 3960 agctggagtg ctaagaagca gcctacagtg gctagatcct ccactgaagc tgaatatcga 4020 tctctggcac atactgcagc tgaaattaca tggatctgca aggtttttca tgattttggt 4080 tttcccttat cttccaaacc tacaatctgg tgtgataaca tatctgctat ctctcttgcc 4140 tccaatcctg tctttcatgc tcgaacaaag catgttgaga tcgattatca ttacattcga 4200 gagttggttc ttgctaatct gcttcaagtt cagtatgtgt gtactgagga ccaaattgct 4260 gatattcaca ctaaatcttt gaccaagaac cggtttcttc ttcttcaatc caagctatct 4320 cttggaactc caacttcttc caagctcagc ttgagggggt gtaaaga 4367 // ID MUDRAVI1 repbase; DNA; EDCOT; 17723 BP. XX AC AM455875; XX DT 13-APR-2007 (Rel. 12.04, Created) DT 03-MAY-2007 (Rel. 12.04, Last updated, Version 1) XX DE MuDr-type DNA transposon. XX KW MuDR; DNA transposon; Transposable Element; MUDRAVI1. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-17723 RA Jurka J.; RT "MUDRAVI: MuDr-type autonomous DNA transposon from Vitis RT vinifera."; RL Repbase Reports 7(4), 148-148 (2007). XX DR EMBL/GenBank/DDBJ; AM455875; Positions 29096 11374. XX CC There are only two copies of this size in the database. They CC carry a DNA fragment homologous to Copia-like protein (masked by CC a string of Ns). XX FH Key Location/Qualifiers FT CDS 2832..4634 FT /product="MUDRAVI1_1p" FT /translation="MSVHLKVKVSSKRGAVVVEDVFRTTPDYLPRQICKDF FT ERDHGVQLTYNQAWHLKEKAKERIYGVPRDSYTFLPWLCHRLREINPGTIA FT EYTSQEGHFMQLFIAHAFSIQGFIMGCRPVLAIDSCHLSGPYKGALLSAIA FT YDADDGMFPLALGVVSSENYEDWYWFLDKLKGVLDGKEVVIISDRHQGILR FT SVSELFGTGNHAYCYRHVKENFSSFFNKQTIRGKKGKEDALLLLDSIAYAR FT LEIDYNEAFEKLVRFNENLAKWVAENNPEHWAMSKFLKKRWDKMTTNIAEA FT FNAWLREERHQTIYTLLLMHMDKLVAMLDSHMRDTQKWKSVVGPKTEEKLM FT SNIMRSGPISVLPYLGGTFKVFTGEVYLVVDMNQRTCTCMTWQMSGLPCAH FT VCAVIRTLRHDVYDYIDPCFHVSMQDLIYSGQFQPLPTHNMPKLCDDRGYV FT IDCAGNSFPACQPPHVRRPPGRPRRLRIESQFCHKRAIHCSRSRIEIGRNR FT SNFGDISEKYRLSVGSDTIFVTDYRSTDISIIFQKYLRYFGIYRYSYRFFG FT KFPDISYQSSPRTGNKICPIFFKTLLFGNLIMICRQRLCFSAWLKNRGFRV FT REI" XX SQ Sequence 17723 BP; 5132 A; 3083 C; 3239 G; 5279 T; 990 other; gggagaattg tgttttgggc ccagctagac ccaaaaatta acaaatggtc catctatgta 60 acaaaattaa gcccaacacc cagtcaaagt ctcaaaattg ataagaaggc tatacaattt 120 ataatatgcc gaaaatgccc tttggctggc taatgwaaaa amaaaaacaa aatccacgtt 180 ggatwtcaat tcgttttccc caaaattagc ggtgttttca cattcstrag tgtttsccts 240 rttmssgccc aaagaatgcc ctaatcctct cttcatctsg agtttgccra ccatccgatt 300 aaaaacaaaa tygacgttgg atttccaktt cgttttyccc aaaattgaga ggcgttttca 360 cattcctgag tgttccctcg tttccgccca aagaatgccc taatcctatc ttcatgtgga 420 gtttcccggc catccgattt taggtgtaga cggtggagtt tttcacctct gtgaatccat 480 tgttgtcgac gatcascacc ggatttgggt tccgtggcga agtagttgag agttgaggtt 540 agtaggttca acaatttcag tttatgcttc atttcggcta tcccgaccaa ttcatttcag 600 cccaaataca ttgcccaaat ttatctggcg atttcagtgt gccattaatc cccaccgtgg 660 gtgtcgtccc gtgctgagca ttgagaaggg agcttctctg accatcaggt aaagtagtat 720 tttattttaa gcttaaagct taaaccccgt aactggctct aagacatggc gtgggttatg 780 gtgtttttaa gacatggctc acagtttgaa atagtgagga tccgcatggg ctaattgcat 840 atgcatgtcg tggtatgaaa aaagttattg tttagataat tatgtttgtg ttcgatttac 900 atgattgata gccttgacat ggaaaaatca cttcttttta ttaaactgtg atgtcaccat 960 gattcacttg tttgtccatg aatatgagaa ccctcgattg ccattcatga taattgtgat 1020 gctgaagatg acataaaaat atattttgat tttccatgca ttttacttgg ttcasttatg 1080 tttgtttggt ttagcattgc atattgaatt gaaaagttag tttgataggt gcaattttat 1140 tctaatatat cataagtaaa tgcaaataga ttctcttttg caaacatatt ttttgtcctt 1200 tcgttcaaat tatatcattg agcattatat ttacttcctc gtgcggcaat ctagttgagt 1260 tcgctagttc gcctgttacc tattttcgaa aaaaacccaa gttctttgaa ccctctagta 1320 tgagatattg tgggatacct agtatgtgta gatagattat catttcgaac ttcatgaaat 1380 ctgtagctaa catgaatata aatgcgaaat aaagaaacag atcagttcaa aggcagttta 1440 atgagtctta attctatttt tgaaatccaa tattaaggga gtcaatacat aagaaaccaa 1500 ttaagggatt tctcgttgaa atccagaatg gtttccaaca atcattgtag tggccaaata 1560 cctctttcca tgtttactat tcacaattgc taaatatcaa atgcatgcaa atgcaatatt 1620 attttcagca tacaattgaa gcaaattgaa attaagttaa atttgaagtt gtctattgag 1680 tatgagccaa aacactaatg acattggcat gatgtgtcca tttataagtc tgaaaagtaa 1740 ttgtgatgtt cctattggga tctagagggt catagcaatc tgcaaaaaac agaggaagag 1800 tcgaccaacc agtgaaaaat agaataagtg aagtaacatt tggaaaagta tatgcataaa 1860 tgatgcgtga taatctggac atgacgacta gtaatagtct gaacttgaaa gcaaaaggcc 1920 aaatgagaga aaatatgaag gccattttct ataatatgca taattgtttg atctataata 1980 tgatatttgt gctatgtttg tataggttaa tggacgcaac taataggata tattgttaca 2040 tttttgtggg tggcaaactt gtccaaaaaa aatgatgggc aatgggaata cttgggtgga 2100 agaagcaaag gtattcacat atataaagga atggcatttg aagatttcac caaaaaaatc 2160 atggagaaat ttgacatttc ccttgacgtg atgaagatgc actacacgtt gaagttcaat 2220 cccagagtca tccaagattt agaagatgag gatgatttgg ataacgtggt ttcccatagt 2280 gatgactttg caaatgtata cctagtagac ttaccctctg tggaagccat tgaagcaaat 2340 atcccgaatt cacagttggc atttcggtaa tggactttaa catcaatgtt tatttaaaaa 2400 attgtgaata tcaattttac acatcacgta gtctaattat gttaatatat gtcaatgcag 2460 agatccacct atcacgttcc cgtcctctaa tgcatcatgc gatccaattc gtaacactat 2520 gatgctatca agaggttttg cgtcgcgtgc tgcagatact gagtacatcc ctttggaatc 2580 gattcgtttt cgtgaggcaa tattagggtc gggacataca tttaaaaatg ccgaggagtt 2640 tcgcaatgca atttaccaga tgtcattagg tggaaggttt gaatacaagt acacgaaaaa 2700 ttcccctacg catatgtctg tcaagtgttc ggttgatggt tgtccttgga agataacagc 2760 tcacgctgtc gagggaaatg tcatcttgcg agttcatact taccaagtga atcataatca 2820 tatagctcag gatgagtgtt catcttaagg tgaaggtttc ttcaaagaga ggtgcggttg 2880 ttgttgaaga tgtgtttaga accactccag actatcttcc tcgtcaaatc tgtaaggatt 2940 ttgaacgtga tcatggggtt caattgacat ataaccaagc atggcacctt aaagagaagg 3000 caaaagagcg catatatgga gtaccacgcg actcttacac gtttctccct tggttatgcc 3060 ataggctaag agaaataaac ccgggcacaa ttgcggagta cacttcccaa gaaggtcact 3120 tcatgcaatt gttcattgcc catgcatttt caattcaagg gttcatcatg gggtgtcgac 3180 ctgtattggc tattgattcg tgccacctaa gcggtccata taagggagct cttttgtctg 3240 ccattgcata tgatgcagat gatggaatgt tccctctggc ccttggtgtg gtaagttcag 3300 aaaattatga ggactggtat tggtttttgg ataaattaaa gggggtatta gatggtaaag 3360 aagttgttat tatatcagat agacatcagg gaatcttgcg tagtgtttcc gagttgtttg 3420 ggacaggaaa tcatgcgtat tgttatcgac atgtgaagga aaacttttct agcttcttca 3480 ataagcaaac gattcgagga aagaaaggaa aagaagatgc tttgctactt ttggacagca 3540 ttgcgtatgc taggttggaa atagactaca atgaggcatt tgaaaaactt gtgcgcttca 3600 atgagaacct agcaaaatgg gttgcggaaa acaatcccga acattgggca atgtcaaagt 3660 ttcttaaaaa gcgctgggac aaaatgacaa ctaacattgc agaggcgttc aatgcgtggt 3720 taagagaaga gcgtcaccaa acaatttata ctttattgtt aatgcacatg gataaacttg 3780 tagccatgtt ggacagccat atgcgtgata cacaaaagtg gaagagcgtg gttggaccga 3840 aaactgaaga gaagttaatg tcaaatatca tgaggtctgg tccgattagt gtgctaccct 3900 atttgggagg gacgtttaag gtgtttactg gagaagttta tttggttgtc gatatgaatc 3960 aacggacgtg tacttgcatg acatggcaaa tgtccggttt gccatgtgca cacgtatgtg 4020 ctgtcatccg cacactgaga cacgacgtgt atgactatat tgacccatgt tttcatgtct 4080 ccatgcaaga tttgatttac tcgggtcagt ttcaaccatt accaacacac aatatgccga 4140 aactttgtga cgatcgagga tatgttatag attgcgcggg caactccttt cctgcttgcc 4200 aaccccctca tgtgagacgc cctccaggaa gaccccgacg attgcgcatt gaatcacagt 4260 tttgtcataa gagagcaatt cattgctctc gatcaaggat tgaaataggt cgaaaccgct 4320 ctaatttcgg cgatatttcg gagaaatatc gcttatcggt cggctccgac acgatattcg 4380 tcaccgatta tcggtcgacg gatatttcga taatttttca aaaatatctc cgatatttcg 4440 gtatttatcg gtattcttac cgatttttcg ggaaatttcc cgatatttcc taccagtcca 4500 gtccccgcac aggaaacaaa atctgtccaa ttttttttaa aacattgcta tttggtaatc 4560 tgatcatgat ttgcaggcaa aggttgtgtt tttcagcatg gctcaaaaat cgtggattta 4620 gggttcgtga aatttaaatc caatgccaca acagcaaaga gaccctagaa cagatccaga 4680 aagcacaagg agcaaaaaaa aagcaatttt tttggttttc attgggggtt ttgcatggat 4740 tttctcagaa atcaaacgag gatgaatttt cccgaaaatc gaatgaggga tggattttct 4800 tgggaatcaa acggggtttg aaaaaaaaaa catgattaga ttagtacctg gcaacctgcg 4860 aggattgaga gtggcagagg aaaataggcc tttttaggga ttctctcgtc tggagggcaa 4920 cttcagaaaa gggcttcttc atgcccatgg cccgagtgag agaagacggt gccccttttg 4980 aatttttaga tttggtaaaa ataaaaataa aaataaaaaa acaaatcatg agaacaattt 5040 tctatctata tataaataat tattaactat ccatatttat tttaattaaa tcactaccat 5100 atattgaaat ttagattttt atccacaata ttttatgaat taaaattaat gtaataagat 5160 aaattattaa taattttaat tatttaaata aattaatact aataaaaaaa aattgttact 5220 acatattttt aataaaattt taaaaattaa atcttaaata aaatatttta tataaattaa 5280 tttaattttt catttaaaat gtaataaaat atattttaat aaaagttttt aaaaataaat 5340 atttaaaatg aatatatcat tttaaaactt taaaatgtgt atttttacat tattttatca 5400 ttttttccga aagttttttc aaatatttct attaatttta aataattttg gcaactctat 5460 cgatatttgt gaaaaaatat ccaccgatat ttcctccagg atatttccga tatatccgta 5520 aaatcgaagt accgatatat ccgtaaaaac cgatatttca atccattgct ctcgatgcaa 5580 tggaataggt cacaaccgct ctaaatgtaa taatccattg ccgtgacatt tgcattttat 5640 ttggttgtac aatttcctca ttttgtatca ttccatacat gctgttgtat ggtatatggt 5700 aatggggttg ttgactctcg ttgttctgta ttgccctatt tataggcacg atgcactatt 5760 ttggaatttt tcttatttag agttgctttc aataaccaac ttaattgaaa gtgcactttg 5820 aatgtggttt ctttttagtt gttatttaat tccatctctg tctctacatt atcgagcatt 5880 tattatttgg agcctcatta aggatgacaa tttctgttac attattttac gtattggggt 5940 gacaaaattt attttttcaa taaagcgaga ctaccccttt atttatttcc aagttgtgaa 6000 ttagtcctct tatcacatta tcttctgctt gcacctattt taatgtgcca tcaatttcta 6060 agacgtcata aaaattgtct ttcaatttgt cctcaattag atatacttgt tacacacgtt 6120 gtccatatgg ttattatcta gtaatttatc tggttgctgg ttggataatc gatcatacac 6180 gtgtttcctt ccaaactcta cgcgttttcg taaaatgtca tattgttatg tatttcattt 6240 atttttccct tacaactatg attatggaac accattacca aattaatcaa aaagattaat 6300 tgtccaaata gtcaattgac ctttcccttt attattagtt cctccacgtc atcattaact 6360 gctataacat gcatttccag gtgcccgttc ttccaaggtt gaatcttaca acaatcattt 6420 cattcttcta tggccactac ggaggtgatg cattctttct tctttttaaa tattgataag 6480 ttatttcgga tacttcatat ttttcccaac ttacgaccta tagttgtttt tgatgttaaa 6540 gattgaataa cataaacatc caatcgtaaa ttatgatccc acatgaatat gtttgtttgt 6600 tcattcaatt ttattgcttt attcacaacg cttacgtatt cctattgatg ttaatttttt 6660 tcatatataa aattcatktg taaactacta mtgacctcca accatttcaa tgcagtccac 6720 cagattatac acacgttgtt catcttcwmg gtttctaaaa ctatgcaaca ggctcccwcc 6780 tgagaaattg gacgtggttc gagaccttca atttggaggt cttcttcact taaattgcaa 6840 ggagatccgg cataatmtct gtacatggct gattgcccat tttaatgttg ggtacaaacg 6900 cattgagatt acatcccaca taaggtatga tytgacagct gctgatgtcg gccttgtctt 6960 tggcctcccg acgactggcc ggattctaca tattgctact accccgtctg atcatccatt 7020 cggtaccctc aacacatgtg aggagagact cctcaactta cctattgggg aggagttccg 7080 taratgcttc atttactacg cttgtgcgac gctattagcc cccacctcaa ggattgatgg 7140 atgccgaaac ttgtggcata ccatccatga agatggtttc aagaaatgat gttaattggg 7200 gccaatttgt tgttgaccag cttgtggagg gtataagacg atttaagcaa gggaacagcg 7260 tctgggttca tggttgcatt attttcctcc aggtattggc ctgctttaac attcattaat 7320 tggtaacttt gactttgtta acatcagtac caacaagtaa gaattataca tatgtttatt 7380 tccattgtgc agctccatta cgtaatgaaa ttcaaaattc cttccgttca tgttccgatg 7440 acagcgcccc tactctcagc atggtcagat gagttgataa aggagcgctt atctgctgag 7500 ataagtgagt ttgggagttt tggacatggc gaggtagtca tttattcggc atgaagtttg 7560 ttatatattg atttacatgc aatttgaata cctccaatgt ttctatgttc ttaacatgcc 7620 tgatgttctc ataatgcagg cgtttgctga atcgtcaccg ccccgtacac atgtcgagga 7680 tgacagtgga ccgacaagta gtaatgtatg ctaaaactac ttgttacttt atgcattgag 7740 tccatctgaa tcacataaca atttggttat catcgctata ttgttaataa cttctaacca 7800 attttctttt aactagtttg aaattaaatt tgcctatgcc aattcgttct catgtgacag 7860 gaaatcttgg ataagtacta cgcagctgaa cgccaaataa attcttatca aaagggcatt 7920 cagcamcagc ttggcatcat gcgtggtctg atccaaagat tggatggtcr aagaaaaaga 7980 agtgtacatt cacctactgc tggtcactcg ggctatgcag cggatgagtt tcccgatgcc 8040 gagcatgatt cacccgctgc ccgatatgac atgccaaccc attgcaccga acaagtaccg 8100 gacactccta ttcgccatcc acctattatt ggtaacattt tgggccacat tcattactgc 8160 attagtgggt agaaaatatg tcaaattgta ctggggttca gttaactaat ctgttgatac 8220 tccaaacaaa cagctgatga cgaagtagtc gtccttgacc ccttaccttt gcgttctatg 8280 aytgtggccc gatcccatag cattgggagg caacggagag tgcgtcggat ggctcccaat 8340 gtattgtcac cattcatagc gcaggcacaa acgcgacatt ctgccataaa gatggaccta 8400 aaagcggcag ctgcaactgt atttgatggg gagttggacc cyaggcatgt tatatcatat 8460 actactccaa tttcaagtgt ttccacatgc aacaaatggt attaccctaa catatatggt 8520 tttgttggca gcgaggagct tgtttccatg cacgacacaa gtttaaccag aggcaacctc 8580 gcgtctttcc agggagactc ttggattggc aatgatgtta atatttcaat ttttccacta 8640 gtttgccaat tatttttaat tttaatgtga tgtaacatct cattagtcaa tctgaatatc 8700 gattacattt taatcatttc ttcttttagg tcgtggatgc attttgccga atgttgcaat 8760 tcgatgatga atcaaggaca aaactatttc tctcccccta catagctgta acgaatgctt 8820 ttaatggccc ctacatctga atttcccttg ttatgayaac atgtccacac gtttgcacat 8880 gtttccatgc attaagtact ttcatttgat atacaggaca tggtgattcg ttccaatgca 8940 aaatatttga cgcacgatgc aattgttgcg cgttttgatc catatatgta tgcctttgat 9000 ggttcgtatc agaatgttac tcaggtcaga cttgcattcc aatgttttat gtggcatcat 9060 ctgatctcct tgacccatta tattttctaa tccattgtat gtggcatcat gcaggtctac 9120 ttaycggtcc ttttcaaaaa ccattggaca ctttatgtct atgacttgca taataagcga 9180 atccagctcc trgattctcg gcctggacga aaaagragtt gtatgagtgg aatacaacaa 9240 aaattggtaa ggttccttct actcccctaa tattagttgc attgtacagc ataytgtaag 9300 tttgaatgtc aattactttg cttctttaag gccaaggttg ttctaatgct tgttgccgac 9360 aagaaagaaa tggttgytgt agacttgaac atgtacagtt ttgtcatgcc agacgtacca 9420 tgccaaccaa atgagttagt gtttwccaca attaagttta atttgatttc atagcatttt 9480 ccaaatttta tactccccat ttcacgcttt ttaagttctt acacattact ctttgtgtta 9540 gcaatgactg cggcgttttt attatgaaat tcatggacaa ctggtccaat gggggactct 9600 ccaaatcgat cgatgtggta tgtacatata ggctttcact atgccatcat ttatataaaa 9660 attgcatagc atcggcaact tatttaacct ttccttatat gtcttttaaa catgaatgag 9720 tgcaggccaa gatgaagaag tatagattga agctactrgg cagattattg ctttcatcac 9780 ataatgcgca tcggcatcga ttcatggcag tttgagatac acttttcaat aggatgtgac 9840 gaggattttt aaagctgatt gtacattata caggaaaaag tacatacaca tgacaatgta 9900 ttgcgaatat tatggcttat atatttaatg aaggttttga tgaagtcgyt ttttccctyg 9960 ctctctcaaa acatctaata aaaggcaccr ccwttacaaa ctataaaaaa cctatgcakc 10020 aacacgcgta catagcgttt acaatttatt cagtgtgaag rtgtttgtat ggcgacccca 10080 cgaaccgtyc catgaccttg ctttaaccat ttaattgcat tccccttcca acaaaacatt 10140 ccactatttg acaaataaaa aaacaaatta tccatctatc ttacataagt attttcactt 10200 tgataacttg cattttggag gagagactgt atgargggta ctacgtcagc aagaaaaatt 10260 tcatacaaaa cattttgaaa aaaaagaaga taacagttgc cgcggccggg tatcgactgg 10320 gtttacgacy ggggaaacaa atccggtcga ccggttacta aaccctcgac argtattcga 10380 ccgggtaacg tccggtcaat ggtgtacaca cgaccgggaa gccaccatcc tcaaccggtc 10440 acatacagcc actgggagag agagaatgta aaaaatacty ccgaccggta ttcgaccggg 10500 tatcgaccgg ttcaccaccg gtaacaacca gccactggga gagagagagt gtcgaaaatg 10560 cactcgaccg gtacctcgac ctatgatcga cckccaatcg accggacgat ctgattcctc 10620 aaccggtcac acacagctac tgggagagag agaaaatgac atgcggtctt gcgacygggg 10680 atcaaccrgt tgaagtgggc cggtcgaccg gtcggttcac ctaccgcgca tgtcttcgac 10740 cggtcgaaca tattttgaca ttgtttttgc tatgaaaaaa ttgatgtttt gtatgtaatt 10800 attgataaaa catataatag ctagagaaaa aagaagttag cgttatgttg tatttwatga 10860 tttaagcaaa attgtgatgc taagaaatag aggatttgwg ttggttttat aaaaaatggt 10920 cattaatgtt aaaatakaaa gtatccaata taaagaaatt gattaaaaay taaatattaa 10980 gttagtcyaa gatcctaaaa tggttattta caatttagtt tgtaacatst taattayttt 11040 taaaaattta ggagtggtaa atgttatttt ttaagaataa aaacaaaata tccattaaat 11100 caatattatt atattcaata ataagattta aaatagaaaa taaacattaa gccaacccca 11160 aaagaawawa aataaaawaa aacaaatttc caawawtttt ttattttatc ttagtttaat 11220 ttacaaaatg taattatctt ctactattcc aacaatttaa gaaaacttta tatctcaata 11280 tgaaatttcc ttwaattatt taattattta tttataaatt taaattatca cttatatata 11340 tatatatata tatatatata tatatgtttg cactcatagg tattcaattt aaatcaatta 11400 gaaatgaaaa ttcaatttca tataattgtt atagagtctc ggaattctaa gagtcaaagc 11460 aactctcaca ctttccaagc caaagcgact gttcggcttc ttacttacag agggggtcaa 11520 ccgcgagtgg agcgagcgag ccattcgtgg ggttgtcttt tgaaataccc cccgcgcgrc 11580 attttgacat tctcaggctt caagggtttt gggtattcag cttggtggga aacctacttt 11640 gaacggcatt gcagctattt catggcttyg gagtgggttt tgaagggtgt ggaatgatat 11700 ttgggaggtc ggccgtgtgt attggaaggg gtccttgatc agcgcgcgtc aaaggcggtt 11760 tctcacctgt tccagcgcsc caatctcctt tgcttcggtt tgttatcact ttgagctgct 11820 cctgtatttc tctaccaccg tcgtcccatt cagtttcact ctctcatgcc gcctaggaga 11880 gatacggctg cctctnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 11940 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12000 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12060 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12120 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12180 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12240 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12300 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12360 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12420 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12480 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12540 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12600 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12660 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12720 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 12780 nnnnnngagg cggagattgg ggagatggag ggtggggttg cccatcagag ggattatgag 12840 catacacaga ctgaggttga aatacctgca cagcagtccg agggctgcca gttgcggccr 12900 actgtatcag gggggatgac gtttaaggca atgcacacag ccgraacatc ttcgcagcca 12960 tcattcactg atccacctca tgcgcaaaga tcacctcata aagctccata cggacctagt 13020 caggcttgga ttgatttagg tgcttagatc agctcactgg gcgctcggat tgaggagcta 13080 gcaattgtca aggatatgcg attccactct atggaggatc gcatggatca ttatcagaca 13140 ggcttcaccg agcaattcca gtstatgcag caragatttc agagtattga ggatcgcatg 13200 gatcagcagc aggctacctt tgcgcatatc ctccagaggc ttgatcgcca ggacagtcag 13260 catgaggaca tgatggctta catccgatcc gtgtttccac caccacctcc taagtcgtga 13320 tagcagcgag agctatttag gattagcata mgtacatgca aatcattgcc atctttgtgt 13380 ctgttgtcta tgtttactct atatttcact tgackatata tatatgtcta tgtttatgtc 13440 tatatatgtc tatgtytcct ctatatttca gctgactata tgtatatata tatgatttct 13500 tttgtcttat gtgaattata cgtttacttt tgattagtat tatatgacct ttgattaacg 13560 cgtgataaat ggattatcgt gtgatggaac tcattctaat aaatactgga aaattatagg 13620 tgaagctttg tgttgtcagg aagttggtct aatgggattt taaaaaaata aatagaaaca 13680 gactactcat tgtatagaaa actaatgtaa cagtaccaaa aaataggytg aactataaca 13740 attatccttc aaagagggat atcgktgttt ggttgcaaaa tcaatgaatt catttatggg 13800 ttcaatgaag gcatactcaa gagragttgt ttttattatt attattatta ttattattat 13860 tattattatt attattatta ttattattaw tattattatt atttttaatg attatcattt 13920 taatgggccc aagtgcaatt tttttaacta tttgtttcca aaatcaaaac attaagtatg 13980 tcaaaaaatt atgtgggtgc taaaaatttt tgtatgatat agtacaacct ccatctttca 14040 cctgatccat ctgatcggct gttacaggcg agggtgtgtg cgacggggcg tccaratagg 14100 tgaccggtcg accggttaca ctttcccggt cgaataccgg tcgtgtaccg gtcgtgtacy 14160 ggtcgaggtg gccgactcat tatctctcac gtagttcctt gcatcttggg gagtcaacag 14220 tgtatgactg tggttttgca ttaaatgggg ttaaattatg aactagaaat catgcatatt 14280 gaaatgacat cgctttgtaa gttttcaatt tgatttscct tcgatccatg tccgaagggc 14340 ctgagacagg gccggtgaag gggataatgg aaggcaccat tcgaaagtta tcactgccct 14400 cacataaagg ctagggctag gggttacttc aattatgcaa ccatatatgg aaggggtcct 14460 tccaattata tycagttata taatgcattc ggataaaatt tcaaagattc taaatacaat 14520 aactaataga tcaacatgtc cattatgtca agacttaagt aatggtaata attcaaaaaa 14580 cattatgaaa tatgtatatc aattgatatg ttgttgttgt ttatatttaa ttgaaaactc 14640 ctaacacaac tatgatcgta acatgttaat tcagttttgt tcgttgtagt ctccacaatc 14700 gctttcctca gctgtwgcaa ccatcacctc ataaaarttc tcagtcgtgc gaaccaaaaa 14760 ttcaatctga gagcgaacaa aacaaaaagc ttaaagtcag tctcgcatcc tccaaggtgc 14820 cttgaaacag taggaattaa tcactcataa taaattaata tgacatcatg tcacaacttg 14880 gatgttttct tcccattttt tatgcacaca tacaacactt acataaatca aggcatttag 14940 aagatactat gtcactcgaa agtaaggagg gtgaatatag gaaggaggga ggtttgaaag 15000 aatattgaaa aaataaatga gcaaagaatt tttcgaaaat crtttgraaa cccttaagtt 15060 aggtagcctt gtacaccctt gtacagttag cacattggcc ttgtacactt agtgtaaatg 15120 ccttgtacag ttggagaaat ccataatagg gacgaccaaa caagtgyata tgggtgggaa 15180 aacaatgctt ccactctcat ggataaggga aaaggatgaa aaagytaatc ctcgttttgc 15240 ttcatatgca tcattagtag gggagctaat aaaattaatt aacatggtag ccatcacata 15300 aaatgcgtgc aatgaggcac cattcaagta atatgtgtga ggaatgtccc tgaaaattgg 15360 aaaaaagtaa atgagtaagt tcttcaaaat cacttgaaaa cccttaagtt aggtagcctt 15420 gtacaccctt gtacagttag cacattggcc ttgtacayyt agtgtaaatg ccttgtacag 15480 ttggagaaat ccataatagg gacgaccaaa caagtgcata tgggtgggaa aacaatgctt 15540 ccactctcat ggataaggga aaaggatgaa aaagttaakc ctcgwtttgc ttcatatgca 15600 tcattagtag gggagctaat aaaattaatt aacatkgtag ccatcacata aaatgcgtgc 15660 aatgaggcac cattcaagta atatgtgtgw ggaatgtccc tgaaaattgg aaaaaagtaa 15720 atgagtaagt tcttcaaaat cacttgaaaa cccttaagtt aggtagcctt gtacaccctt 15780 gtacagttag cacattggcc ktgtacactt agtgtaaatg ccttgtacag ttggagaaat 15840 ccataatagg gacgaccaaa caagtgyata tgggtgggaa aacaatgctt ccactctcat 15900 ggataaggga aaaggatgaa aaagttaagc ctcgwtttgc ttcatatgca tcattagtag 15960 gggagctaat aaaattaatt aacatggtag ccatcacata aaatgcgtgc aatgaggcac 16020 cattcaagta atatgtgtgw ggaatgtccc tgaaaattgg aaaaaagtaa atgagtaagt 16080 tcttcaaaat cacttgaaaa cccttaagtt aggtagcctt gtacaccctt gtacagttag 16140 cacattggcc gtgtacactt agtgtaaatg ccttgtacag ttggagaaat ccgacatagg 16200 tacagctgaa tgagtgtaaa tgggtgggat agccacttgc cgatgttatg ggtcagtgaa 16260 aagggggaaa atgaaaccca atttaggttc ccattcatca tacgtgtgct agcatattcc 16320 aatgaatgtg tacgaaggga aatgaggagg gagtacgagg catgtccccc tttgaaaaaa 16380 gaaatgagca aagaattttt cgaacatcgt ttgaaatcct tcaagttagg tagccttgta 16440 cacccttgta cagttagcac attggacttg tacacttagt gtaaatgcct tgtacagttg 16500 gagaaatcca taatagggac gaccaaacaa gtgcatatgg gtgggaaaac aatgcttcaa 16560 ctctcatgga taagggaaaa taatgaaaaa gttaagcctc gatttgcttc atatgcatca 16620 ttagtagggg agctaataaa attaattaac atggtagcca tcacataaaa tgcctgcaat 16680 gaggcaccat tcaagcaata tgtgtgagga atgtccccga agattggaaa aagtaaatca 16740 gtaagttctt caaaatcact tgaaaaccct taaaatacac gcccttgtac acccttgtac 16800 atttagtaca ttgaccttgt acacttagtg taaatgcctt gtacagttgc aggaaattga 16860 cctaggtaca ccttaatgac tgcatatggg ccggttaacc acttcccaat gtcatggctc 16920 agtgaaaagg gcgaaaatga aactcaattt ggtttcctat tcatcataag tgcactaact 16980 agtccccaca gctcaccttc tgcaccatac ccatttattc tgtagaatat aaacccacca 17040 accagattat aaagtgagga attttcaaac agctgaaatg ccaattttga ggatatcttt 17100 tccgatggat taactggaag tttctttcat ttacttagct tgtgtttcat ttgtatgagg 17160 caagatggat atgatcaaag cctcatttat accccaccct caaccctaaa acacgctgtt 17220 agtaagttca acatttttta agaacacccc aacaccagat caaaacggac gtctttcctc 17280 aaaccttgta aacaaacatc caccacatca tcaaaggaac caacatgaaa tcaaaatctc 17340 agaaaattta atcacaccca ccctcatttc gatttgggaa tgatgatgat cacatacatg 17400 cgaaggcttt tctgagttgc tcacaatcct cggctgcaca attgggagac attcatagtt 17460 ggcttcgtct ttaaccatgg tgtttacgga gggagagaaa ggggcaggag agtggtgacc 17520 atttttgcca ttatttgaga tttttcagtc agcatgacat ggcatttcaa gtgtaaccac 17580 tttaatttac caaccagctg acttggaact aatgaagggt atattagtca gttaatatct 17640 catagccttc ttattaattt tgttacatag atggaccatt tgttaatttt tgggcccagc 17700 tgggcccaaa acacaattct ccc 17723 // ID Gypsy-25_VV-LTR repbase; DNA; EDCOT; 525 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-25_VV_; KW Gypsy-25_VV-I; Gypsy-25_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-525 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 10087840 10088364. XX SQ Sequence 525 BP; 159 A; 85 C; 87 G; 194 T; 0 other; tgatggggga aatcctttta aagtttattc aaggaagaaa gggaaaacct aagtaaactt 60 taagtaggat taatattaat tagaattgaa ttgggattgg tatttgttgg agtctaatta 120 ggattagcta gttgagttat aatataatta gaatttgagt catgataggt tattagagtc 180 ctagtagact ttggatttct tagagaagcc tataaatagg ctaatcaata taaatcaaag 240 gaatgaattt gatgaataat attatacttt ctttcattgc aaggttgcaa ccctcaatga 300 tgagactcca ttgattttct tctaggtgag actcctagaa ggccttagtg agactctaag 360 gttttccatc ttttcttcat tctttcttct ttctttctat ttcttatctt ataattttct 420 ctaccatcaa atttattctt tgttcctctc cttacacctt aaaagtaaaa ccctagccca 480 cctacccttg agtgtaggca accatcctag ggttatccta catca 525 // ID COPIA4_I_MT repbase; DNA; EDCOT; 8382 BP. XX AC . XX DT 24-AUG-2005 (Rel. 10.08, Created) DT 30-AUG-2005 (Rel. 10.08, Last updated, Version 1) XX DE M. truncatula copia element, internal sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; COPIA4_LTR_MT; COPIA4_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-8382 RA Gentles A. and Jurka J.; RT "COPIA4: Copia-type LTR retrotransposon from Medicago."; RL Repbase Reports 5(8), 195-195 (2005). XX DR [1] (Consensus) XX CC This Copia-like element from Medicago truncatula has 2034 bp CC LTRs. There is a second ORF downstream of, and in the same CC orientation as, the normal gag-pol coding region. It potentially CC encodes a >620 aa protein that has no significant similarity to CC known proteins. XX FH Key Location/Qualifiers FT CDS 6077..7936 FT /product="COPIA4_I_MT_2p" FT /translation="REESEEKAEKEEEKGSSKKHGKGKDITKLAATLKASR FT AEKIALRPMCRTKYFNLESLETKAWNMKEFTEPQGWTNFITLQEHTYEDLV FT REFYTNLSVQEKKNGNEKFLISSVKGVKIKMTQEFVSEAFKIPNEGNQLYS FT SFWFDESRVNRNKLIVKYTKENHTFNSTNLEDTPKILHNMIRHCLLPRCGS FT FELVSDIDLCFIYHLMKKIKLNLCFIIIQHMIDSCLAIKQTSAGLPYGMHL FT TSIFQKAKVPLEGEKRKLDFMTFSSKTLGQLHITSSNMPASKTSGPSGSGK FT RNSDQNVQKAVKKRRVEEITDTKTPSPPAENLFSEVSKLAKEIVDGETQEV FT AELLASNMNIEEEAQDVEFSTGFDLNIEDINIDFNSELFQDGQETTQQAPE FT GQNVEIPAVQNVQKVETSAGQNVAVTEAQNDEGIHVMADQDNQELDDQHAS FT NELPPDGQLSVDPMPLASGSLPSEEVQLMAQNGQNVNPSSSSMDSVAGATN FT FLVSDLPTPPFIPSSTPPPPQMKTTTRSKLPNMAALFDSLNTFVSANRVQA FT VASGPAEPAKPSRAEKIASRALRVSTKTHKIACVLADWTVKVHAPGLAIPP FT PVFDDPSIFEAEPSSDSGDSTP" FT CDS join(70..1881,1885..4950) FT /product="COPIA4_I_MT_1p" FT /note="gag-pol" FT /translation="MSKVKYIAEGGSSNRPPLFDGSNYYFWKGKMELFLRS FT QDNDMWAVITNGDFVPTNKEGAVKAKSAWSTDEKAQVLLNSKARLFLSCAL FT TMEESERVDECTNAKGVWDTLKIHHEGTSHVKETRIDIGVRKFEVFEMSEN FT ETIDEMYARFTTIVNEMRSLGKAYSTHDRIRKILRCLPSMWRPMVTAITQA FT KDLKSMNLEDLIGSLRAHEVVLQGDKPVKKVRTLALKASQQTSSVDDEDVQ FT EPQELEEVHEEEAEDELALISKRIQRMMLRRNQIRKKFPKTNISIKTEADK FT SQVTCYGCNKTGHFKNECPDIKKVQRKPPFKKKAMITWDDMEESDSQEDAD FT TDMGLMAQSDDEEEVIIYKTDSLYKDLENKIDSLLYDSNFLTNRCHSLIKE FT LSEIKEEKEILQNKYDESRKTIKILQDSHFDMSEKQREINRKQKGIMSVPS FT EVQKENILLKKEVETLKKDLTGFIKSTETFQNIVGSQNKSTKKSGLGFKDP FT SKIIGSFVPKAKIRVKCCFCDKYGHNESVCHVKKKFIKQNNLNLSSERSHL FT NRSESSQKAEKAKKTCFYCNKSDHKRQNVTFRKDLLEELTFKDPTLHGYLK FT FLSCQMVLPQGARTKPWYLDSGCSRHMTGDRDCFLTFEKKDGGLVTFGNND FT KGKIRGKGTIGNLNSARIENVQYVEGLKHNLLSISQLCDSGFEVIFKPNIC FT EVRQTSSNKLFFSGSRRKNLYVLELNDMPAESCFMSLEKDKWIWHKRAGHI FT SMKTIAKLSQLDLVRGLPKISFEKDRICEACVKGKQVKSSFKTIEFISTQK FT PLELLHIDLFGPVQTASLTGKRYGFVIVDDFSRFTWVLFLKHKDESFEAFQ FT NFCKRVQNEKGYNIITVRSDHGGEFENASFKTFFDENGIKHNFSCARTPQQ FT NGVVERKNRTLQEMARTMLNESNVENYFWAEAINTSCYILNRVSIRKVLNK FT TPYELWKNIKPSISYFHIFGCYCYILNNKEKLGKFDPKSDKAIFLGYSTTS FT KGYRVYNLKTQTVEISMHIIFDEYDEHSKPKENEDTEVPTLQNVPVQNTEN FT TVEKEDDQNAQDQSFQSPPRSWRMVGDHPTDQIIGSTTDGVRTRLSFQDNN FT MAMISQMEPKSINEAIIDDSWIKAMKEELSQFERNKVWNLVPNNQDKTIIG FT TRWVFRNKLDEEGKVVRNKARLVAQGYNQQEGIDYDETFAPVARLEAIRIL FT LAYAAHKSIKLFQMDVKSAFLNGFLNEEVYVSQPPGFINKEKPNHVFKLTK FT ALYGLKQAPRAWYDRLSTFLIENGFSRGKIDTTLFRKTHNTDLLIVQVYVD FT DIIFGATKIKMCEEFSNLMQSEFEMSMMGELGFFLGLQIKQHSNGIFISQE FT KYVKDILKKYKMNEAKIMSTPMHPSSSLDKDESGKSISEKEYRGMIGSLLY FT LTASRPDIVFAVGLCARFQTCAKESHLTAVKRIFRYLVGTTDLGLWYRKGS FT SFDLVAYCDADYAGDKVERKSTSGSCQFLGQALIGWSCRKQNTIALSTTEA FT EYVSAASCCSQILWVRNQLEDYSLRYTSVPIYCDNTSAINLSKNPIQHSRS FT KHIEIKHHFIRDHVQKKNIALSFVDTENQLADIFTKPLVEDRFNFLKEKLL FT IMKNPNKD" XX SQ Sequence 8382 BP; 2969 A; 1484 C; 1525 G; 2404 T; 0 other; attggtatca gagcctggtt ctaagggttt gaacacttaa acaagtgtta gagaaaagat 60 tcaggaagta tgtctaaagt caagtacata gctgaaggag gatcttcaaa tagaccacca 120 ctctttgatg gatcaaacta ctatttctgg aaaggcaaga tggaactctt tctcagatct 180 caagacaatg atatgtgggc agtcatcaca aatggagact ttgttccaac aaacaaagaa 240 ggagctgtca aagcaaaaag tgcatggtca acagatgaaa aagctcaggt attactaaac 300 tctaaagcta gactctttct atcatgtgca ctaaccatgg aagaaagtga aagagttgat 360 gaatgtacaa atgctaaagg agtatgggat actctgaaaa tacatcatga gggtacttct 420 catgtcaaag aaactagaat tgacattgga gtcagaaaat ttgaagtctt tgaaatgagt 480 gaaaatgaaa ccattgatga gatgtatgca agatttacta caatagtaaa tgaaatgaga 540 tctcttggaa aggcatattc cactcatgat agaattagaa aaattctgag atgtcttcca 600 agtatgtgga gacctatggt cactgcaatc actcaggcca aagatttaaa atctatgaac 660 ctggaagatc tcattggttc actaagagct catgaagttg tacttcaagg agacaaacca 720 gtgaagaagg taagaacact tgccttgaaa gcatctcagc aaacctcatc agttgatgat 780 gaagatgtgc aagaaccaca agaattagaa gaagttcatg aagaagaagc tgaagatgaa 840 cttgcactaa tctctaaaag aattcaaagg atgatgttga gaagaaatca gatcagaaag 900 aagtttccaa agaccaacat cagcatcaaa actgaagctg acaaaagtca agtcacttgc 960 tatggatgca acaaaactgg acatttcaaa aatgaatgtc ctgacatcaa aaaggttcag 1020 agaaaacctc ccttcaagaa gaaagcaatg atcacatggg atgacatgga agaatcagat 1080 tctcaagaag atgcagatac agacatggga ctgatggctc agtcagatga tgaggaagag 1140 gtaattatct ataaaactga ttctttatat aaagatcttg aaaacaaaat tgatagtctc 1200 ttatatgatt caaacttctt aactaataga tgtcactctt taatcaaaga actttctgag 1260 ataaaagaag aaaaagaaat acttcagaac aagtatgatg agtccagaaa gaccataaaa 1320 attctgcaag attctcattt tgacatgtca gaaaaacaaa gagagataaa cagaaaacaa 1380 aaaggcatta tgtctgtacc ttctgaagta caaaaggaaa acatactttt gaaaaaggaa 1440 gttgaaacat tgaaaaagga tctgacaggg tttataaaat ctacagaaac ttttcaaaac 1500 atagtaggat ctcaaaataa aagtactaag aaatctggct taggctttaa ggatccaagc 1560 aaaattattg gaagttttgt acctaaagct aaaataagag ttaaatgttg tttttgtgat 1620 aagtatggac ataatgaatc agtatgtcat gttaagaaaa aatttatcaa acaaaataat 1680 ttaaatctta gttcagaacg ttctcatctc aatagatcag aaagttcaca aaaggctgaa 1740 aaggctaaga agacatgttt ctactgtaac aaatctgatc ataaaagaca gaatgttact 1800 ttcagaaaag atctcttaga agaactaacc ttcaaggacc caacattaca tgggtaccta 1860 aaatttttat cttgtcaaat gtaggtcttg cctcagggtg caagaacaaa accatggtac 1920 ctggatagtg gttgttctag gcacatgaca ggtgacaggg attgttttct aacttttgaa 1980 aagaaggatg gaggactagt gacatttgga aacaatgaca aaggtaaaat cagaggtaaa 2040 ggtactatag gtaatcttaa ctctgctaga atagaaaatg ttcagtatgt ggaaggttta 2100 aaacataatc tacttagcat aagtcaattg tgtgatagtg gatttgaagt tatctttaaa 2160 cctaatatat gtgaagtcag acaaacctcc tctaacaaat tgtttttctc tggttcaaga 2220 agaaagaact tatatgtttt agaactaaat gatatgcctg ctgaatcttg ttttatgtct 2280 cttgaaaaag acaaatggat ctggcacaaa agggctggtc atataagcat gaaaaccatt 2340 gctaaacttt ctcaacttga tctagttaga ggtttgccta agattagctt tgaaaaggac 2400 agaatctgtg aagcatgtgt taaaggtaaa caagtaaaaa gtagttttaa aactattgag 2460 tttatctcaa ctcagaaacc tttagagctt cttcacattg atctgtttgg tcctgttcaa 2520 actgcaagtc taactggcaa aagatatgga tttgttattg ttgatgattt ctccagattt 2580 acatgggtgc tatttttaaa acataaagat gaatcttttg aagcatttca aaacttttgc 2640 aaaagagttc aaaatgaaaa aggttataat atcatcacag ttaggagtga tcatggagga 2700 gaatttgaaa atgcatcctt caaaacattc tttgatgaaa atggtattaa acataatttt 2760 tcttgtgcaa gaactccaca acaaaatgga gttgttgaaa gaaaaaatag aaccttgcaa 2820 gaaatggcaa gaacaatgtt aaatgaatca aatgttgaaa attacttttg ggcagaagcc 2880 attaacacat cttgttacat tttgaataga gtttctataa gaaaggttct taacaaaacc 2940 ccatatgaac tctggaaaaa tattaaacct agcatatctt actttcacat tttcggctgc 3000 tattgttaca tactgaacaa taaagaaaaa ttgggtaagt ttgatcctaa atcagataaa 3060 gctatctttt taggatactc tacaacttct aaaggttata gagtgtacaa tctaaaaacc 3120 cagacagttg aaattagtat gcatatcata tttgatgaat atgatgaaca ttctaaacct 3180 aaagagaatg aagacactga agtaccaaca cttcagaatg ttccagttca aaatactgag 3240 aacacagtag agaaagaaga tgatcagaat gctcaggatc aatcttttca aagtccacct 3300 agaagctgga gaatggtagg ggatcatcct actgatcaaa tcattggaag cacaactgat 3360 ggtgtaagaa ccagattgtc ctttcaagat aacaacatgg caatgatttc tcaaatggaa 3420 cccaagtcaa tcaatgaagc cattattgat gactcttgga ttaaggccat gaaggaagaa 3480 ctttctcagt ttgaaagaaa caaagtttgg aacttggttc caaataatca agataaaacc 3540 atcattggaa caagatgggt ttttagaaac aagcttgatg aagaaggtaa agttgtcaga 3600 aacaaagcaa ggttagttgc tcaaggttac aaccaacaag aaggtattga ctatgatgag 3660 acctttgcac cagttgcaag gttagaagcc atcagaattc ttcttgctta tgctgcacat 3720 aaaagcatta aactttttca aatggatgtg aaaagtgcat ttttaaatgg ttttctaaat 3780 gaagaagttt atgtaagtca accacctgga ttcataaaca aagaaaaacc aaatcatgtt 3840 ttcaaattaa caaaagctct ttatggtctt aaacaagctc ctagagcttg gtatgacaga 3900 cttagtacat ttttaattga aaatggtttt tcaagaggaa aaattgatac cacacttttt 3960 agaaaaacac ataatactga cttgcttatt gttcaagtat atgtggatga catcattttt 4020 ggtgctacta aaataaaaat gtgtgaagaa ttttccaacc ttatgcaaag tgaatttgag 4080 atgagcatga tgggtgaact tggttttttc cttggtttac aaatcaaaca acattcaaat 4140 ggaattttca taagtcaaga aaagtatgtc aaagatattc ttaagaaata taaaatgaat 4200 gaggcaaaaa tcatgagcac ccctatgcat ccatcttcaa gtttagataa ggatgagagt 4260 ggaaaatcta tttctgaaaa agaatataga ggcatgatag gttcattatt atatttgact 4320 gctagcagac ctgatatagt gtttgcagta ggattatgtg ctagatttca aacatgtgca 4380 aaagaatctc acttaactgc agttaaaaga atctttagat atctagtagg tactactgat 4440 cttggccttt ggtatagaaa aggttctagt tttgatcttg tagcctattg tgatgctgat 4500 tatgctggag acaaagttga gaggaagagc acaagtggat cctgtcaatt cttaggacaa 4560 gcattgattg gatggtcttg cagaaaacaa aacactattg cactctccac aactgaagct 4620 gagtatgtat ctgcagctag ttgctgctct caaattttat gggtaagaaa tcagctggaa 4680 gattactctc taaggtacac aagtgttcct atttattgtg acaatacaag tgcaattaat 4740 ctttctaaga atcctattca gcattctagg tctaaacata ttgaaataaa acatcatttc 4800 attagagacc atgttcagaa aaagaatatt gcattaagct ttgttgatac tgaaaatcaa 4860 ttggctgaca ttttcacaaa accccttgtt gaggatagat tcaattttct taaagaaaaa 4920 ttgttaatca tgaaaaatcc taataaagat tgattactga tcactaaggg ccttaaacta 4980 aaccccttga tgtcatctga tacaaatcag atagatccat ctttatctca ctctcatcag 5040 aatgttcctg agttcagaac gttcatcagg tcagaatgtt caaatgatca gaatgttcat 5100 tgcaatattc atacgatcag aacaatcaag tatgttcatc tgagtttatc cattcatgac 5160 gttcttgaaa cttatttttt gttctgaacc caaattctgg gtcaaacaat ctcaggcgtg 5220 agatcttgtt ttgacttgtt caaaaaatcc atccataatc ttaagcattt aatgcttggt 5280 tataagaagt catgtttaag gtttaaccac catgtaatgg cttaaccatc aaatcatcca 5340 aaatccattc atcttcccaa acggctactt tttcctttct ctctcctagg cgttgctttt 5400 tgacagtttt tcatccttcc caatgctaac tgtcatcata tcactactat tctttttctc 5460 ttgcacgttt tgtctatata gtcagttacc aactctgatt atttcacttc catctcattt 5520 cccaaaaatt caaactgctc tgttcttcat tttctgaaaa aatggctaga accaaaacta 5580 ccccaagact ttccgaagaa cattttcaac caccaccatc caacaccgct gctgatcaaa 5640 cctctgatca acaacttttg agtgaaaccc ctgtacgcac cattcttcag gacgtaatca 5700 ttcctgcttc tgaaaatccc aaatcttcca aaaccagatc ctctaagaaa cccatcatca 5760 aacccagacc aatacctacc agacgatcaa caaggatgaa gaaacctttg aagaaaccaa 5820 aggtatctca cgtgaatcta gattctgacg aagaaaaaga agatgatgaa gactctgagg 5880 atgaaacaga ggaagatcca gaagaagagg atgaagactc tgaacaaact ctttctgacg 5940 caatgaaatc agtaaaagct tcctcaaaaa gggataagga acttacaaag ataatacttc 6000 aaaggaggaa ggagattgct gctgaagcta tgcccttatc tgaggaaaag acctctgaag 6060 atgaagaagc aagtgaagag aagaatctga agaaaaggct gaaaaagaag aagagaaagg 6120 ctcttctaag aagcatggga aaggtaaaga tattaccaaa cttgctgcta ccttaaaagc 6180 ttcaagggca gaaaagattg ctctcagacc aatgtgtaga accaagtatt tcaaccttga 6240 aagtctggaa accaaggcat ggaatatgaa agagttcact gaacctcaag gatggaccaa 6300 cttcataact cttcaagaac acacctatga agacttggtc agagagttct acaccaacct 6360 atcagttcag gaaaagaaga atggaaatga gaagtttctc atatcatcag tcaaaggtgt 6420 aaagatcaag atgactcagg aatttgtctc tgaagcattc aaaattccaa atgaaggtaa 6480 tcagctatac tctagcttct ggtttgatga gtctagagtt aaccgtaaca aactcatagt 6540 taaatacacc aaagaaaatc acacctttaa ctccacaaac ctggaagata ctcccaaaat 6600 tcttcacaac atgattaggc attgtctttt acctagatgt ggatcttttg aacttgtctc 6660 tgacatagat ctttgtttca tctaccatct catgaaaaag attaagttaa atctgtgttt 6720 tatcattatt caacacatga ttgattcatg tctagccata aaacaaacat ctgctggact 6780 accctatgga atgcatctca cttccatttt tcaaaaggca aaagtgcccc ttgaaggaga 6840 gaaacgcaag ctggatttta tgaccttttc ttccaagacc ttaggtcaac tccatattac 6900 ttcatccaac atgccagcct ccaaaacttc tggaccctct ggatctggta aaagaaattc 6960 tgatcagaat gttcagaaag ctgtgaagaa aagaagggtt gaagagatta cagataccaa 7020 aactccctct ccaccagcag aaaatttgtt ctctgaagtc tccaagcttg caaaggagat 7080 tgttgatgga gaaactcagg aagtggctga gctcttagct tcaaatatga acattgaaga 7140 agaagctcaa gatgtggagt tctcaactgg ttttgatctc aatattgaag atatcaacat 7200 tgacttcaat agtgagttgt ttcaagatgg acaagaaaca actcagcaag ctccagaagg 7260 tcagaatgtt gaaattcctg ctgttcagaa tgttcagaag gttgaaactt ctgccggtca 7320 gaatgttgca gtaactgaag cccagaatga tgaaggtatt catgtcatgg ctgatcaaga 7380 caatcaagag cttgatgatc agcatgcctc aaatgaactt cctccagatg gccagctgtc 7440 agttgatccc atgcctttgg catcaggatc tctgccctct gaggaggtac agctcatggc 7500 ccaaaatggt caaaatgtta acccatcatc ctcctccatg gattctgttg caggtgctac 7560 caacttcttg gtctctgacc ttcctactcc acctttcatt ccttcatcca ctccaccacc 7620 accacaaatg aagaccacca caagaagcaa acttccaaac atggctgctt tatttgactc 7680 tctcaacacc tttgtgtctg caaacagagt gcaagctgta gcctctggtc ctgctgaacc 7740 tgctaagcct tcaagagcag agaagatagc ctcaagggca cttagagtct ccaccaagac 7800 ccacaaaatt gcttgtgtgc tggctgactg gactgtcaaa gtccatgctc ctggtttggc 7860 cattccacct ccagtatttg atgacccctc catctttgaa gcagaaccct cttctgattc 7920 tggagactcc actccatgaa tcttttcaaa aatcctccct atcctttttg cagatgacaa 7980 aagggggaga agctttagga ttcaaagtct ttaagttttt tttagttata ggccctaagt 8040 aggtctaggt gatcaattga tattggaatt tataaattcc atcttttgct tttcttgatc 8100 acatgcactt tgattttctt ttttgttttt gaaccatctt ttcatgtaat gtacttcatg 8160 ttatatcaaa tgaatgaata ttgaatttgg ttcagtcttg catattttta ctttatgcaa 8220 aagattatga aattgagggg gagcttttta aagttcttaa aaactctgca taatggatta 8280 taaaaatgag ggggagcatt aaaataaatt ttttagctct gttatataat caaaatcctt 8340 aatcctaaat cataagttta tcatcttcaa aaagggggag at 8382 // ID Gypsy-11_Mad-LTR repbase; DNA; EDCOT; 259 BP. XX AC ACYM01129965; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-11_Mad-I; KW Gypsy-11_Mad-LTR; Gypsy-11_Mad_. XX NM Gypsy-11_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-259 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1414-1414 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01129965; Positions 2052 2310. XX SQ Sequence 259 BP; 82 A; 43 C; 50 G; 84 T; 0 other; tgttatgatt ataatagtgg ttagaataat agtggaaaac tatttagcta catgtcgtta 60 ttgttagtag ccagctggca ttgtgagaag gatggttgta taagaaccaa attgtggcat 120 tgttctgcag gattgaatta gaaaaacaat attacaagaa actttctatc tctctctatt 180 ttccttccca ctcactcacc gccattacta tcagctacta gcaggtcgag aaagggaatt 240 tagaagtttt gacctaaca 259 // ID GYPSY1GM_I repbase; DNA; EDCOT; 4524 BP. XX AC AF541963; XX DT 30-AUG-2005 (Rel. 10.08, Created) DT 31-AUG-2005 (Rel. 10.08, Last updated, Version 1) XX DE GYPSY1GM: Gypsy-type LTR retrotransposon (internal portion). XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; GYPSY1GM_LTR; internal portion; GYPSY1GM_I. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-4524 RA Graham M.A., Marek L.F. and Shoemaker R.C.; RT "Organization, expression and evolution of a disease resistance RT gene cluster in soybean."; RL Genetics 162(4), 1961-1977 (2002). XX DR Genbank; AF541963; Positions 39060 34537. XX CC LTRs are identical. XX FH Key Location/Qualifiers FT CDS 20..4522 FT /product="GYPSY1GM_I_1p" FT /translation="MADNTRMKEVYAELKKNADAITRVSDDLQNHIERLEA FT TNHAQMEKIEVMQSTNDSQFSQLNAVMSQVLQRLQNIPMSSHGASNSQKEQ FT QRSSFQVRSVKLDFPRFDGKNVMDWIFKAEQFFDYYATPDADRLIIASVHL FT DQDVVPWYQMLQKTEPFSSWQAFTRALELDFGPSAYDCPRATLFKLNQSAT FT VNEYYMQFTALVNRVDGLSAEAILDCFVSGLQEEISRDVKAMEPRTLTKAV FT ALAKLFEEKYTSPPKTKTFSNLARNFTSNTSATQKYPPTNQKNDNPKPNLP FT PLLPTPSTKPFNLRNQNIKKISPAEIQLRREKNLCYFCDEKFSPAHKCPNR FT QVMLLQLEETDEDQTDEQVMVTEEANMDDDTHHLSLNAMRGSNGVGTIRFT FT GQVGGIAVKILVDGGSSDNFIQPRVAQVLKLPVEPAPNLRVLVGNGQILSA FT EGIVQQLPLHIQGQEVKVPVYLLQISGADVILGSTWLATLGPHVADYAALT FT LKFFQNDKFITLQGEGNSEATQAQLHHFRRLQNTKSIEECFAIQLIQKEVP FT EDTLKDLPTNIDPELAILLHTYAQVFAVPASLPPQREQDHAIPLKQGSGPV FT KVRPYRYPHTQKDQIEKMIQEMLVQGIIQPSNSPFSLPILLVKKKDGSWRF FT CTDYRALNAITVKDSFPMPTVDELLDELHGAQYFSKLDLRSGYHQILVQPE FT DREKTAFRTHHGHYEWLVMPFGLTNAPATFQCLMNKIFQFALRKFVLVFFD FT DILIYSASWKDHLKHLESVLQTLKQHQLFARLSKCSFGDTEVDYLGHKVSG FT LGVSMENTKVQAVLDWPTPNNVKQLRGFLGLTGYYRRFIKSYANIAGPLTD FT LLQKDSFLWNNEAEAAFVKLKKAMTEAPVLSLPDFSQPFILETDASGIGVG FT AVLGQNGHPIAYFSKKLAPRMQKQSAYTRELLAITEALSKFRHYLLGNKFI FT IRTDQRSLKSLMDQSLQTPEQQAWLHKFLGYDFKIEYKPGKDNQAADALSR FT MFMLAWSEPHSIFLEELRARLISDPHLKQLMETYKQGADASHYTVREGLLY FT WKDRVVIPAEEEIVNKILQEYHSSPIGGHAGITRTLARLKAQFYWPKMQED FT VKAYIQKCLICQQAKSNNTLPAGLLQPLPIPQQVWEDVAMDFITGLPNSFG FT LSVIMVVIDRLTKYAHFIPLKADYNSKVVAEAFMSHIVKLHGIPRSIVSDR FT DRVFTSTFWQHLFKLQGTTLAMSSAYHPQSDGQSEVLNKCLEMYLRCFTYE FT HPKGWVKALPWAEFWYNTAYHMSLGMTPFRALYGREPPTLTRQACSIDDPA FT EVREQLTDRDALLAKLKINLTRAQQVMKRQADKKRLDVSFQIGDEVLVKLQ FT PYRQHSAVLRKNQKLSMRYFGPFKVLAKIGDVAYKLELPSAARIHPVFHVS FT QLKPFNGTAQDPYLPLPLTVTEMGPVMQPVKILASRIIIRGHNQIEQILVQ FT WENGLQDEATWEDIEDIKASYPTFNLEDKVVFKGEG" XX SQ Sequence 4524 BP; 1468 A; 851 C; 954 G; 1251 T; 0 other; ttggtgcttt catctcacca tggcagacaa cacccgtatg aaggaggttt atgcagaatt 60 gaagaaaaac gctgatgcga ttactcgtgt tagtgacgat cttcagaacc atattgaacg 120 gttggaagct acaaatcacg ctcagatgga gaagattgaa gtgatgcagt cgacgaatga 180 ttctcaattc tcacaactga atgcagtaat gtcacaggtg ctgcagcgtc tacaaaacat 240 tccgatgtct tcccatggtg catcgaactc acagaaagag cagcagagaa gttcgtttca 300 ggtgagatct gtcaaacttg attttcctcg ctttgatgga aaaaatgtga tggattggat 360 attcaaggct gaacaatttt tcgattacta tgcaacacca gatgctgata gattgattat 420 tgcttcagta catttagatc aggatgttgt cccttggtat caaatgcttc aaaaaactga 480 accattcagt tcatggcaag catttactag agccttagaa cttgattttg gaccatctgc 540 ttatgactgt cctcgtgcta ctttgtttaa actgaatcaa tctgcaactg tgaatgaata 600 ttatatgcaa ttcactgctc tagtaaatag agtagatgga ttaagtgcag aggcaatttt 660 ggattgcttt gttagtgggt tgcaggaaga aatcagcagg gatgtgaaag caatggaacc 720 ccgtacctta accaaggcag ttgcattggc caaattattt gaagaaaaat acacttcacc 780 acctaaaaca aaaacattct caaacctagc cagaaatttt acctcaaaca cttcagccac 840 acagaaatat ccaccaacta accaaaaaaa tgacaatcca aaaccaaatt taccaccact 900 tctacctaca ccatcaacca aaccattcaa ccttcgaaac caaaacatca aaaaaatttc 960 ccctgctgag attcaattga gaagagaaaa gaatctgtgt tacttttgtg atgaaaaatt 1020 ttcccctgca cacaagtgtc ctaatagaca agttatgctg ttacaactgg aggaaacaga 1080 tgaggatcaa actgatgaac aggtaatggt gactgaagaa gctaacatgg atgatgatac 1140 tcatcatttg tccttaaatg ctatgagagg atcaaatggt gtgggcacta ttcgatttac 1200 tggccaagtg ggaggcatag cagttaagat attggtggat ggaggtagct ctgacaactt 1260 cattcagcct agagtggctc aggtgcttaa gttaccagtg gaaccagctc ctaatcttcg 1320 agttttagtg ggaaatggac agattctgag tgcagaagga attgttcagc aattaccatt 1380 acatattcaa ggccaagaag tgaaagtgcc agtgtacttg ttacaaattt ctggtgcaga 1440 tgtgatattg gggtccacat ggttagcaac attaggtcct catgtagctg actatgcagc 1500 attgaccttg aaattcttcc aaaatgataa attcattact ttacaaggtg aaggtaattc 1560 agaagcaaca caggctcagc tccatcattt cagaagattg caaaacacaa agtcaattga 1620 agagtgcttt gcaatacaat tgattcagaa ggaagtacca gaagacactt tgaaggattt 1680 accaacaaat attgatcctg aattggccat cttactccac acttatgctc aagtgtttgc 1740 agtaccagca tcactgccac ctcagaggga acaggatcat gctataccac tgaaacaagg 1800 gtcaggcccc gttaaagtaa gaccatacag atatcctcac acacaaaagg atcagattga 1860 aaagatgata caagaaatgt tggttcaagg catcattcaa ccaagtaaca gtccattttc 1920 cttacccata ctgcttgtta agaagaaaga tggaagttgg agattctgca cagattatag 1980 agctttgaat gcaatcactg tgaaggatag ctttccaatg ccaacagtgg atgaactgct 2040 agatgaacta catggagctc aatatttttc aaaactggat ttgaggtcag gataccatca 2100 aattctggta cagcctgagg atagagagaa aactgctttt agaacacatc atggccatta 2160 tgaatggtta gtgatgccat ttggtcttac taatgcacca gccacattcc aatgcttaat 2220 gaacaaaata tttcagtttg ctctcagaaa atttgttctt gtgttttttg atgacatctt 2280 gatatatagt gcttcttgga aggatcatct caagcacttg gaatctgtgc tacagacctt 2340 gaagcaacat cagttatttg ctagattgtc caaatgttca tttggagata cagaagttga 2400 ttacttgggc cacaaggtat ctgggttagg agtttccatg gagaatacaa aggtacaagc 2460 agtattagat tggcctactc caaataatgt caagcagtta aggggatttc taggcttaac 2520 aggctattat agaagattta ttaaatctta tgccaatatt gctggaccat taactgatct 2580 tttacaaaaa gacagtttct tatggaataa tgaagcagaa gcagcatttg tcaagctcaa 2640 aaaagccatg acggaggctc cagtattatc actaccagat ttttctcaac catttattct 2700 ggaaactgac gcatcaggta ttggtgtggg agcagtgttg ggacagaatg gccacccaat 2760 tgcttatttt tcaaaaaaat tggcacctag aatgcagaaa caatcagctt ataccaggga 2820 gttgctagct attactgagg ctctatccaa attcagacac tacttattag gcaacaaatt 2880 cattatcagg actgatcaaa gaagtttgaa aagtttgatg gatcagtctt tacaaacccc 2940 tgaacaacaa gcttggttac acaaattctt agggtatgat ttcaagattg aatataagcc 3000 tgggaaagat aatcaagcag ctgatgcttt atcaagaatg tttatgctag catggtcaga 3060 acctcattct atcttcttgg aagaattgag agctagacta attagtgatc ctcatttgaa 3120 acagttgatg gagacataca agcaaggtgc tgatgcaagt cattatacag ttagggaagg 3180 cttactgtat tggaaagata gagtagtaat acctgctgag gaagagattg tgaacaaaat 3240 actccaagaa tatcatagct cacctattgg agggcatgca ggtataacta gaactctggc 3300 aaggctgaaa gctcaattct actggcctaa gatgcaggaa gatgtcaaag cttatataca 3360 gaaatgcttg atttgtcaac aagctaaatc aaacaataca ctgccagcag gactactcca 3420 acctttacct attcctcaac aagtttggga agatgtagcc atggatttca tcacaggttt 3480 accaaattcc tttggattat ctgtcataat ggtagtcatt gatagactca ccaaatatgc 3540 tcatttcatt ccattaaaag ctgattataa cagtaaggtg gtagcagagg catttatgag 3600 tcacatagtc aaattacatg ggataccaag atctatagtg tctgatcgag atagggtttt 3660 taccagtact ttttggcaac atttattcaa gttacaaggt actacattgg ccatgtcatc 3720 agcttatcat ccacagtcag atggacaatc tgaggtgctg aataaatgtt tggagatgta 3780 tcttagatgc ttcacgtatg aacatcctaa aggttgggta aaggcattac catgggcaga 3840 gttttggtat aacactgcat atcatatgag cttaggcatg actccattca gagccttgta 3900 tgggagagag cctcctacac tgaccaggca agcctgttct atagatgatc ctgctgaagt 3960 gagggaacaa ttaactgaca gagatgcatt gttagctaag cttaaaatta atttgacaag 4020 agcacaacag gtcatgaaga gacaagcaga caagaagagg ttggatgtgt cattccaaat 4080 aggagatgag gtactggtga aactgcagcc ttatagacag cattctgctg tcctgagaaa 4140 gaatcaaaag ctgtccatga gatactttgg accatttaag gtgctggcca agattggtga 4200 tgttgcttat aagttggagt tgccttctgc tgcacgaatt catcctgttt ttcatgtgtc 4260 ccagctgaag ccattcaatg ggactgctca agatccttac ctgccattgc ctttgacagt 4320 cacagaaatg ggaccagtta tgcagcctgt gaaaatacta gcaagtcgaa ttatcatcag 4380 agggcacaat cagattgagc agatactagt gcagtgggag aatggcttgc aagatgaagc 4440 tacttgggag gatattgaag atatcaaggc aagctatcct accttcaacc ttgaggacaa 4500 ggttgttttt aaaggggaag gcaa 4524 // ID COPIA3-LTR_LC repbase; DNA; EDCOT; 871 BP. XX AC . XX DT 09-SEP-2005 (Rel. 10.09, Created) DT 15-APR-2011 (Rel. 16.04, Last updated, Version 2) XX DE Copia-like retroelement from Lotus corniculatus - LTR sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; gag-pol; COPIA3-I_LC; COPIA3-LTR_LC. XX NM COPIA3-LTR_LC. XX OS Lotus corniculatus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RP 1-871 RA Gentles A. and Jurka J.; RT "L. corniculatus copia-like element."; RL Repbase Reports 5(9), 239-239 (2005). XX DR [1] (Consensus) XX CC LTR corresponding to COPIA3-I_LC. XX SQ Sequence 871 BP; 220 A; 137 C; 203 G; 308 T; 3 other; tgttggaaca tgttgtcttg cattttgtca aaacaactga ttgtcgaagc agatgycgtg 60 gcatctgayt tcgtgaagct aggacatcag tcctcagctt gagtttctgt tgtgggccct 120 ctgaagattt gctgaagata tgtttttgag ttacttgagg agcaagtagc tatttcagaa 180 gggttttaat tgtgggttgt tatttgttga aacaatcttt gttaaaagat ttgtttctat 240 ctttacttgt gcaaaaagaa accagatctt tgaagattgc gttttgaatt gctgttgttg 300 caatctgttt cttcagccca tgcaaaccct agagcccatg ctaccgctgc tgaagtctat 360 aaaaggatga agacctaaaa cttgaagacc accgaagcta tagagagaga tcaagtgttt 420 taggatttgt cattgtgctt tgtccttgtt agttgtgaat catctttgct cactgattct 480 ataaagcaaa gawgggttct gtgttgtttg attcttcaaa ctctgattgt tgattgtgtt 540 taccaatcac tgtggcagtg attgagagaa agtgagaggg gctctcatac ttaggttgag 600 atactaagta gaaatacact gggtagatta ggaagtgaac tatgaactgt ggtgttcatg 660 agtgtctgta attcctgaat cttgagatag tggatttcct ttctttgggt gcaaaccctc 720 cagacgtagg tgaaagtttt cactgaactg ggttaacaat ttctgtgttt tattgttttt 780 gtttttaggt tttgttttac tgttaagcga ttgtcgaacc tattgtccca gcatcgtgca 840 ggacattcgt cctataggga acctgaattc a 871 // ID Copia-46_Mad-I repbase; DNA; EDCOT; 4785 BP. XX AC ACYM01031533; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-46_Mad-I; KW Copia-46_Mad-LTR; Copia-46_Mad_. XX NM Copia-46_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4785 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1316-1316 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01031533; Positions 16871 12087. XX CC Positions [2171-2575] - Integrase core CC 'CCAGA' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 262..1746 FT /product="Copia-46_Mad-I_1p" FT /translation="MVTANQLQILQSPITSLISSVSTSVTMKLDDTNYLTW FT HFQMQLLLEGHGIMGFVDGSTPCPSRFLTLNSGDTELSPRQQSDQSCACKE FT SDEYMVWRMHDRALMQLITVTLSPPAISCAIGSTSAQDLWTRLREQFSTVT FT RTSIFKMKSKLQTIKKGTDSINVYLQRIKEARDYLSAAGVYFEDDDIVILT FT FNGLPSEYNTIRSVIRGRESVIFLKDLRSQLLAEEVMIETLHPTPMLNALV FT AHSPNFTQRPSNVQSQAQSGRPYTSHNSNSGYKSFTNKNKGKFNSNNRFNH FT SKQVFNNGNPGSGILGAAPQFGHPPVIPCQICGKTNHLADTCRFRNVSQMC FT QICGKNNHMAATCRFRDASQSHGCQICRNPNHSAEFCFQKGSSPMIIMYVN FT NASGNSISTPLPSAPPPQVWITDTGATNHMTTDLNNLSLTTSYPSHETIHT FT ANGEGLSISHVGSSTLQTPLQSFQLKSVLYVPKLTQNLLSVHRICLDNNC" FT CDS 2171..3943 FT /product="Copia-46_Mad-I_2p" FT /translation="MSVLGFVGFSQYAIKVKLALLLSLSITLLSTNLMLLL FT KCFRVMVGGGIYRQILSIFLVDKGIIHHMSCPHTPEQNRLVERKHKHIIEM FT SITLLRTASLPPSFWSYACQASVYLINRMLSSTLENKSPFEVLFNSIPEIN FT HLRVFGCSCYLLLRPYNHTKLQPRTSKCIFLGYASKYKGYICFEVQKIRVF FT ISHHVLFDETEFPYITLVSQCSKVSTPLPIGLTSTPVFTPNLNNVLITPQS FT NFVPTIPSVSHTPSLASVPLSTDVSSTDLHAHSSATLHDSSSSLSTDTPPI FT TGTAHQSSHSLPVVPEFQGDQLQVVLSIPPLNNHPMQTRSKNGISKKIALL FT ASVHESRGTDLTQVEPTTYKSALKSPVWLAAMQDELSALHTQGTWSLVPLP FT PHKNLVGYKWVFKIKKNADGSIGRYKARLVTKGFNQEEAIDYGETFSPVVK FT PTTVRLVLTLAAHFNWGIRQLDVKNAFLHGVLQEEVYMAQPPGFLDSTHSD FT YVCKLHKSLYGLKQALRAWNDIFTSFLPTLGFQSTYSDSSLFVKAVNGTIV FT ILLLYVDDIIITRNASQAILDVIHALTQEFDIKDLGPLHYFLGI" XX SQ Sequence 4785 BP; 1280 A; 1016 C; 882 G; 1607 T; 0 other; tggtatcaat cgccatttaa gcttcatcaa ctctctcacc ggtacaagcg tatagacttg 60 acggttcttc gatcttggaa tttttgcttc cgctattact tcaatcttct cgtgctatgt 120 tcttgttctt cgatcgcagg ttctttcttt ctgctttagg gttctgcatc tctaattttg 180 ggatactttc ttcgttgcaa gttgtgcaca ccaactattt gtgttttgtt ctatgtacat 240 cactttcttg aagattcaac aatggtgacc gccaatcagt tacagatatt gcaatctcct 300 attacttctc taatttcatc ggtctcaacc tctgtaacca tgaaattgga tgataccaat 360 tacttgactt ggcatttcca aatgcaactt ttactggaag gtcatggaat tatggggttt 420 gtcgatggtt caacaccatg tccatctcgg tttcttactc taaattctgg tgataccgaa 480 ctctctccta gacaacagtc tgatcagtct tgtgcttgca aggaatctga tgaatatatg 540 gtttggagga tgcatgatag agcattgatg cagcttatca cagttactct atcaccacca 600 gccatttcct gtgccattgg aagcacaagt gctcaggatt tgtggactcg tctcagggag 660 caattttcta ctgttactcg gacaagcata tttaagatga aatctaagtt gcaaactatc 720 aagaaaggta ctgattccat taatgtgtat cttcaacgaa tcaaagaagc tagagattat 780 ttgtctgctg ctggtgtcta ttttgaagat gatgatattg tgatccttac atttaatggt 840 ctaccatccg agtataatac aatcaggtct gtgataaggg ggcgtgaatc tgttattttt 900 ttgaaagatc ttcggtcaca attgcttgct gaagaagtga tgattgagac tcttcatcct 960 actccaatgc ttaatgcatt agtggctcat tcacctaatt ttactcagag accttccaat 1020 gttcagtctc aggcgcaatc tggtcggcca tacacttccc ataactccaa ctctggttac 1080 aaatctttca ccaataagaa caagggcaaa tttaattcga ataacaggtt caatcactca 1140 aagcaagttt tcaataatgg taatcctggt tctggaatcc ttggtgctgc tccacagttt 1200 ggccatcctc ctgtcatccc ttgtcaaatt tgtgggaaaa caaatcattt ggctgatact 1260 tgtcgattca gaaatgtatc tcaaatgtgt caaatttgtg gcaagaacaa tcacatggct 1320 gctacttgca gattcagaga tgcatctcaa tctcatggtt gtcaaatatg taggaatcca 1380 aatcatagtg ctgagttctg ttttcagaaa ggatcctctc caatgattat aatgtatgtc 1440 aacaatgctt ctgggaattc aatatcaact ccattgccct ctgccccacc tccacaagtt 1500 tggattactg atacgggtgc tacaaatcat atgaccaccg atttgaataa tctttctctt 1560 actacatcat atccatctca tgagactatt cacacagcca atggtgaagg tttatccatc 1620 tctcatgttg gctcttccac tcttcaaact ccactgcagt catttcaatt aaaatctgtt 1680 ctctatgttc cgaagttgac acaaaatttg ctatctgtcc atcgcatatg tttggataat 1740 aattgctgat taatttttga tgctttttgt ttttggattc aggacaaaac cacatggaag 1800 attttgtaca aagggcagtg ccgtaatggg ttatatccga tcatttctcc aacagatcca 1860 gtttcaacac aaaaggctta tgtggctgca tatcttggac atcaagttac atcaagactt 1920 tggcatcacc gattaggtca tccctctaat accattgtat ctcagattct tagaaaatct 1980 aatgtctctc atacccctga ttctttacct attgtttgtt ctccatgtct cgaaggcaaa 2040 tttagtaaac ttccatttcc cgtgtcttca tccaaatctg caaaaccttt tgagataata 2100 catagtgatg tttggggccc gactccttgt atttctattg aaggcttcaa atactatgtt 2160 actttcatag atgagtgtac taggttttgt tggattttcc caatatgcaa taaaagtgaa 2220 gttggcacta cttttgtctc tttctatcac tttgttgtca accaatttaa tgcttttatt 2280 aaaatgtttc agagtgatgg tggggggggg aatatatagg caaatccttt caattttttt 2340 ggtagacaaa ggcattattc accacatgtc ttgtccacat accccagagc aaaacaggct 2400 tgtcgagagg aaacataaac acatcattga gatgtccatt accttattac gaacagcttc 2460 tttaccacct tcattttggt cttatgcttg tcaagcttcg gtctatctca ttaataggat 2520 gctttcttca actttggaaa ataaatcacc ttttgaggtc ttgtttaatt ccattcctga 2580 gattaatcat cttagagtat ttggttgttc atgctatctt ttgcttagac cttataatca 2640 tactaaactg caacctcgaa cttccaaatg tattttcttg gggtatgctt caaagtataa 2700 gggctatatc tgttttgagg ttcagaaaat aagagtgttt atatctcatc atgttctatt 2760 tgatgagaca gaatttccat acatcactct ggtttctcaa tgctccaaag tatctactcc 2820 attgcccata ggtttgacat ccacacctgt gttcacccca aatcttaata atgttcttat 2880 cacacctcag tctaactttg tgcctactat accatcagtc tctcatacac caagcctagc 2940 ctctgtgcct ctatcaaccg atgttagttc tacagatttg catgctcaca gttctgcaac 3000 gttacatgat tcaagctcca gtttatctac ggacactcca cccattactg gcactgcaca 3060 tcaatcttct cattccctac ctgtggttcc tgaatttcag ggagaccaac ttcaagtggt 3120 tttgtccata ccaccattaa acaatcatcc tatgcagact cggtccaaga atggtatttc 3180 taaaaagatt gctctactag cttctgttca tgaaagtagg ggtactgatc ttacccaagt 3240 tgaacctacc acatataaat cagcactcaa atctccagta tggttggctg caatgcaaga 3300 tgagttgagt gctcttcata cacaaggaac ctggtctctt gtacctcttc ctcctcacaa 3360 aaacttggta ggctacaagt gggtgttcaa gattaaaaag aatgcagatg gttctatagg 3420 gaggtataag gctcgtttgg ttacaaaggg gttcaatcaa gaggaagcta tagactatgg 3480 cgagacattt agtcccgtgg ttaaaccaac cactgtgagg ttagtgctta ctttggctgc 3540 tcattttaat tggggtattc gacaacttga tgtgaaaaac gcttttctgc atggtgtttt 3600 acaagaggaa gtctatatgg ctcaacctcc tggttttctt gattccactc atagtgacta 3660 tgtttgtaag ttacataagt ccctatatgg tctcaagcaa gccctaaggg cttggaatga 3720 catattcact agtttcttgc cgactttggg ttttcaatcc acctatagtg attcctcttt 3780 atttgttaaa gctgtgaatg gtaccattgt gattctcctc ttatatgtgg atgacattat 3840 catcacgagg aatgcatctc aagcaatatt agatgttata catgctctta ctcaagagtt 3900 tgatatcaag gacctcggac cattgcatta cttccttggt atttaggttt tgcataagaa 3960 ggatggttta ttcctctctc aggacaaata tgttactgat ttgcttatta agtctggaat 4020 ggagttgtct aaaccgtgtg ctactctttg cctaccttac aataggttgt tgaaggatga 4080 tgggaagcct tagaataatc cagctttata tagaagccgc gtaagagcac tccaatacct 4140 cacttttact cgacctgata atgcattcgt tgtgtatcag gtttgtcagt tcatgcagtg 4200 tcttatggaa gctcactttg tggcagttaa acgaattctg aggtatctca aggctactaa 4260 agggtgcggc cttcattaca tcaaaggagg attggattta caagcattca gtgatgctga 4320 ttgggtagga gatcccaatg acaggagatc cacgacaggg ctagttgttt ttcttggctc 4380 aaaccccatc tcatagtcct tcaagaaaca aaatactgtc tctcgctctt ctactgaagc 4440 tgaatatcgc gcactgtcta caacggctgc taagattgat tagattaaac aattgttaca 4500 gtttttgcaa gttcctgttt ctggaccacc tactctctat actgtgataa tctttcagcc 4560 attgctctta cgtgtaatcc tgtccaacat cagcgcacaa aacatattga aattgatgtt 4620 cattttgtgc gggaacgggt ggcaaaacag gtgttgttgg tccaatttgt ttcttcactt 4680 gagcagtttg ctgacatatt cacttaaggc ttgtctgcac ctttgttcaa gactcattgt 4740 gacaatctca gactcagttt aactatccct gagtttgagg ggaga 4785 // ID HINDIII_VF repbase; DNA; EDCOT; 1794 BP. XX AC . XX DT 29-MAR-2005 (Rel. 10.03, Created) DT 29-MAR-2005 (Rel. 10.03, Last updated, Version 1) XX DE V. faba HindIII interspersed repeat, consensus. XX KW Transposable Element; Interspersed repeat; HINDIII_VF. XX OS Vicia faba OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Vicia. XX RN [1] RP 1-1794 RA Nouzova M., Kubalakova M., Dolezelova M., Kolblizkova A., RA Neumann P., Dolezel J. and Macas J.; RT "Cloning and characterization of new repetitive sequences in RT field (Vicia faba L)."; RL Ann. Bot 83, 535-541 (1999). XX RN [2] RP 1-1794 RA Gentles A. and Jurka J.; RT "V. faba hindIII repeat."; RL Direct Submission to Repbase Update (29-MAR-2005). XX DR [1] (Consensus) XX SQ Sequence 1794 BP; 616 A; 271 C; 338 G; 566 T; 3 other; aagctttttg aaaagtgtgt tggtgtgaaa agattatttt tgagtttgtt tttgaaattt 60 agagcaagta tctnagagtc gtctacctac cctaaggaat tcgtctgtgt anatgtcctt 120 taaagtagtg ccatcccacc attgagaggt aggtagcacc accgttggag gtgttcgggt 180 caattcgaag gtgtcgggac atggtgatca ccagagcaat gggaagacac cttagaagct 240 accctcatga tccaggttcc cggatcatga gggtacttac taagacatcc tcccattact 300 ctgacgatca cctttcgaag gcaaggcaac agtgaggcgt accctagggg tggtgtgtgc 360 gattcgtgtg tcgtgttcat ttatttttta tcttgttcat gttcattaag gtgttctacg 420 gcgtttgatt ttatttaagg ccattcattc ttgcatgcat tttgtttaac agtttaaaan 480 atttgcgagg aaaagtaaag ttctaaagct attacaaatg gcgcgggtcc acatcgccaa 540 aattaaaccg gacccgattt gacagaaaag taaagaaagg aattaaaaga attaaaagtg 600 cgagaaataa ttatattaca aggctttggg agaagtacat aattatttaa acgaaataaa 660 ataaatacgc gaaattaaac aattaagaac gtgggcgttg gacccttttg caaaatatta 720 aaattaacga ggaattaaaa attaaaagag catgtttttg gtatttttat gttttttaag 780 atttaatgaa aaagagaatt aattaaaatc aaaattgaat gcaaacccta attctaaagg 840 cttttaaatt tattatgaaa gtattaaaat ttgacctaaa ttaaacctaa tttttacatg 900 caattttaat tgtgaaaata aataaaataa tgttaaatat ttatgaaaga aaaaatagaa 960 aaaaagatga aaaattgttc aaaccctagt tctatgtatt tttagatttt tattgaaaag 1020 agttaaaatt aatcctaatt taaaaaaaac taatcaatta aagttaatta tttaaaaata 1080 cttaaaataa aatatttatt atattttttt tgtcttttct gatttttagg cattttttat 1140 attttataga aataattaat taatttaaac aataaagaaa ataatacaat aattaaaaat 1200 aaaatataag aaaaagatgg aaaattgcaa accagggggg gtggaagtcc caaatatgga 1260 ggtttgatta tgaaattctg gcccaataac cttgatccat ttgacctttc catgcagcgt 1320 gcacatgcgt tgaccatggt atatgatgtg ccttcaattt tgcacccttg gattgcttct 1380 gatggacgcg tggctgttga tctttgagga tgcatggtgt gtcttaacct ggaaattgca 1440 tgtgaacgca tatggaaaaa tattagtgag ataatgcaga cctggggctc gaacccaggt 1500 catgtacctt caccaccaat cctgcttgcc agctgagcta agtgcgcatt caattaatat 1560 acaaacaaac aaataatata aaaagaagca atgcgttagt ggattgaagc gcgcgaaatt 1620 caaagcagcc tatcacgtct tgccacgatt tcatcttcct caccatccct gaaacataaa 1680 atatgaggca acggtttttg ggacgttctc ttaggcatgc tatcagaaaa tagcgattag 1740 gcctgtgtta ctcataaatt gatcgcggat atgggttctt cttcgtccaa gctt 1794 // ID Gypsy7-VV_I repbase; DNA; EDCOT; 9732 BP. XX AC . XX DT 29-AUG-2007 (Rel. 12.08, Created) DT 29-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW internal portion; Gypsy7-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9732 RA Obukhanych T. and Jurka J.; RT "Gypsy7-VV - LTR retrotransposon from grapevine."; RL Repbase Reports 7(8), 673-673 (2007). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 249..5753 FT /product="Gypsy7-VV_I_1p" FT /translation="MPYWIRDSGGRLVKIETPHKTELELCLNIMEATPEDQ FT HSHHGHQDNPNAFRSMRDRMHPPRMSAPSCIVPPTEQLVIRPHIVPLLPTF FT HGMESENPYAHIKEFEDVCNTFQEGGASIDLMRLKLFPFTLKDKAKIWLNS FT LRPRSIRTWTDLQAEFLKKFFPTHRTNGLKRQISNFSAKENEKFYECWERY FT MEAINACPHHGFDTWLLVSYFYDGMSSSMKQLLETMCGGDFMSKNPEEAMD FT FLNYVAEVSRGWDEPNKGEVGKMKSQPNALNAKAGMYTLNEDIDMKAKVAA FT MTRRLEELELKKIREVQAVSETPVQVMPCSICQSYEHLVEECPTIPAVREM FT FGDQANVIGQFKPNNNASYGNTYNSNWRNHPNFSWKPRALQYTQPGQASQQ FT ASNLEQAIVNLSKVVGDFVGDQKSINAQLSQRIDSVENTLNKRMDGMQNDL FT SQKIDNLQYSISRLTNLNTVQEKGRFPSQPHQNPKGIHEVEAHEGESSQVR FT DVKAMITLRSGKEVELPTPKPHDETEEEEEETEKREEIKGKKKGSSGRKED FT HDSTVNEDPEKIVINGDVMKKHMPPPFPQALHGKKGISNASEILEVLRQVK FT VNIPLLDMIKQVPTYAKFLKDLCTIKRGLNVNKKAFLTEQVSAIIQCKSPV FT KYKDPGCPTISVMIGGTLVEKALLDLGASVNLLPYSVYKQLGLGELKPTSI FT TLSLADRSVKIPRGMIEDVLVQVDNFYYPVDFVVLDTDPIVKETNYVPIIL FT GRPFLATSNAIINCRNGLMQLTFGNMTLELNIFYMSKKPINPEEEEGPEEV FT CIIDTLVEEHCNQKIQEKLNESLGDLDEGLPEPSDLLATLPGWRRIEEILP FT LFNEEEAQEAVKEEAPKLNLKPLPTELKYAYLEENKKCPVVISSSLTTPQE FT ECLLEVLRRCKKAIGWQISDLKGISPLVCTHHIYMEEEAKPIRQPQRRLNP FT HMQEVVRAEVLKLLQAGIIYPISDSPWVSPTQVVPKKSGITVVQNDKGEEV FT ATRLTSGWRVCIDYRKLNVVTRNDHFPLPFIDQVLERVSGHPFYCFLDGYS FT GYFQIEIDVEDQEKTTFTCPFGTYAYRRMPFGLCNAPATFQRCMLSIFSDM FT VERIMEVFMDDITIYGSTFEECLVNLEAVLNRCIEKDLVLNWEKCHFMVQQ FT GIVLGHIISKKGIEVDKAKVELIVKLPSPTTVKGVRQFLGHAGFYRRFIKD FT FSKLSKPLCELLGKDAKFVWDERCQKSFEQLKQFLTTAPIVRAPNWQLPFE FT VMCDASDFAIGAVLGQREDGKPYVIYYASKTLNEAQRNYTTTEKELLAVVF FT ALDKFRAYLVGSFIVVFTDHSALKYLLTKQDAKARLIRWILLLQEFNLQIK FT DKKGVENVVADHLSRLAIAHNSHGLPINDDFPEESLMLLEDAPWYAHIANY FT LVTGEVPSEWKAQDRKHFFAKIHAYYWEEPFLFKYCADQIIRKCVPEQEQQ FT GILSHCHESACGGHFASQKTAMKVLQSGFSWPSLFKDAHTMCRSCDRCQRL FT GKLTRRNQMPMNPILIVDLFDVWGIDFMGPFPMSFGNSYILVGVDYVSKWV FT EAIPCKHNDHRVVLKFLKENIFSRFGVPKAIISDGGTHFCNKPFETLLAKY FT GVKHKVATPYHPQTSGQVELANREIKNILMKVVNTSRRDWSVKLHDSLWAY FT RTTYKTILGMSPYRLVYGKACHLPVEVEYKAWWAIKKVNMDLNRAGMKRCL FT DLNEMEELRNDAYINSKVAKQRMKRWHDQLISNKEFQKGQRVLLYDSRLHI FT FPGKLKSRWIGPFIIHQVHFNGVVELLNSNSTDTFKVNGHRLKPFMEPFNQ FT DKEEVSLLEPQQS" FT CDS 6483..8225 FT /product="Gypsy7-VV_I_2p" FT /translation="MAKTRGAQAASPSARNPRPRASPARDSMSEAPQAPAI FT PPSEGGVPSSPPQRRYETRRPPTTPGASTSRPKKSVRRPPTKKARVSGPGE FT SSAPPQPQPPTTESQIPSGMTPEVIIRRPMVTQPPIEGNLDCRARPFHSEL FT CFDMETFRHQPELRDSFHLLQRYHLEHLMTPRDFFYPRVALDFYQSMTTHR FT VRDPTVIHFTIDGRHGIFGARHIAEALHIPYEPVSPADFREWAHFSQRDMV FT HILSRGTSTRSFLLRKELPPGMFLLDVVLRSNIFPLQHMVQRRGAILEALF FT RISEGFYFGPHHLIMTSLLYFEEKVHRKKLQRADAIPLLFPRLLCQILEHL FT GYPSEPQLERRRICRELFTLDKWNHLTAYVAPPGAPARPAPPELPQDEQPQ FT QAQQXEIPTEIIPPAPAAPSTVPTPEATSSAPPTTPETPPVVPATSAPPPS FT ESTITISTSEFRGLCHTLQTLSTTQSVLAQQMAVIRAHQDQLIATQTQHTA FT ILRQIQQHLGILPPPEHDMPGPSEPTAPSEEATPAEQAIPSQEATPAEQTM FT PHEETTTVEIETPIQSTQETTAEPSSPHDPPTTT" XX SQ Sequence 9732 BP; 2905 A; 1959 C; 2111 G; 2744 T; 13 other; aatggcgccg ttgccgggga tggtgccaac tttacagtga tataaccttt tccaaaacac 60 ttgtgatctt catcacaagt ttggtgattt ttcttttmtt ttactaactc tttttaattg 120 tttcttttac ttgttcatat tttagcctat cttttaattt agtttttagt taatcttagt 180 tttttttttt ttgtagtttt gttttctttt gttttctttg tttttgttac agttgttact 240 agttgtgtat gccatattgg atacgagaca gtggaggaag acttgtgaaa attgaaacac 300 ctcacaaaac agagttggaa ttgtgcttga acatcatgga agctacacct gaagatcagc 360 atagtcacca tggtcaccag gacaatccca atgcattcag atcaatgagg gaccgcatgc 420 atccacctcg tatgagtgca ccatcatgca tagtgcctcc tacagagcag ctagtaatca 480 gaccgcatat tgtgccactt ctacctactt tccatgggat ggaaagtgag aatccctacg 540 cgcatatcaa agaatttgaa gatgtttgta atacattcca agagggagga gcttcaatcg 600 acttgatgag gctaaagcta tttcctttca ctctgaagga taaggccaag atttggctta 660 attctttaag gccaaggagt atccgaactt ggactgattt gcaagctgaa tttctcaaga 720 aatttttccc tactcatagg accaatggct tgaaaaggca aatttcaaac ttctcagcta 780 argagaatga gaaattctat gagtgttggg agagatacat ggaagctatc aatgcttgtc 840 ctcaccatgg ttttgataca tggctattgg tgagytactt ttatgatggt atgtcttcct 900 caatgaagca actcctagag actatgtgtg gaggagattt catgagtaag aatccggagg 960 aagccatgga tttcttgaat tatgttgctg aagtttcaag aggatgggat gaaccgaaca 1020 agggagaagt gggaaaaatg aagtctcaac caaatgctct taatgctaag gctgggatgt 1080 ataccttgaa tgaagatatt gacatgaaag caaaagttgc agctatgaca agaagattgg 1140 aggagctaga actgaaaaag atacgtgaag tgcaagccgt ttctgaaaca ccagtgcaag 1200 ttatgccttg ttccatttgt caatcttatg agcacttggt ggaggagtgt cctacaattc 1260 cagctgttag agaaatgttt ggagatcaag caaatgtcat tggacaattc aagcccaata 1320 acaatgcttc atatggaaat acctacaatt caaattggag gaaccatcca aatttctcct 1380 ggaaaccaag agcacttcag tacacacaac caggccaagc atctcaacaa gcttcaaatc 1440 ttgagcaagc aatagtgaat ctaagcaagg tcgtgggaga ttttgttgga gaccagaaat 1500 ccatcaatgc tcaactcagt caaagaattg acagtgtaga gaatacattg aataaaagga 1560 tggatggaat gcaaaatgat ctatctcaga agatagataa tctccaatac tcaatctcaa 1620 ggctcactaa ccttaacaca gtgcaagaga agggaaggtt tccttctcaa cctcaccaaa 1680 accccaaggg tatccatgaa gtggaagctc atgagggaga atcttcacag gtgagggacg 1740 tcaaagccat gatcactctg aggagtggta aagaggttga gctgccaaca cccaagccac 1800 atgatgaaac agaggaagaa gaagaagaga cagagaagag ggaggaaatc aaaggaaaga 1860 agaaagggag cagtggaagg aaagaggacc atgattcaac agtgaatgaa gatccggaga 1920 agatagttat caatggagat gtgatgaaga aacacatgcc tccacctttt cctcaagctt 1980 tgcatgggaa aaagggaatc agcaatgcat cagaaattct tgaagtattg aggcaagtga 2040 aggtcaacat cccattgcta gacatgatca aacaagtgcc gacttatgca aaattcctga 2100 aggacttgtg cactatcaaa agagggttga atgtgaataa gaaagccttc ttgactgagc 2160 aagtaagtgc catcatacag tgcaagtctc cagtgaagta caaagatccg ggctgcccta 2220 ccatctcagt gatgattgga gggactttag tggagaaagc tttgttggac ttgggggcaa 2280 gtgtgaattt gctaccatac tctgtctaca agcaattggg acttggtgaa ttgaagccaa 2340 catcaatcac tctatctcta gcagatagat cagtgaagat tccaagaggg atgattgaag 2400 atgtcttagt tcaagttgac aatttctact atccagtgga ttttgttgtt cttgatacag 2460 acccaattgt caaggaaact aattatgttc ctatcatact tggaagacca ttcctagcta 2520 catcaaatgc aatcataaat tgtaggaatg gactcatgca actcacgttt ggcaacatga 2580 cattggagct caatatcttc tatatgtcca agaagccaat caatccggaa gaagaagaag 2640 gtccagaaga ggtgtgcatc attgacactt tagtggagga gcattgtaat cagaaaatac 2700 aagagaagtt gaatgaaagt cttggggatc ttgatgaagg gttgcctgaa ccctcagatt 2760 tgcttgctac tctaccaggt tggaggagga tagaagaaat tctacctttg ttcaatgagg 2820 aggaggcaca agaagctgtt aaagaggagg ccccaaagct taatctgaag ccactaccca 2880 cggagttgaa gtatgcatac ctagaagaga ataagaagtg ccctgttgtt atatcttcat 2940 ctcttaccac tcctcaggag gagtgtttac ttgaagttct caggagatgt aagaaagcaa 3000 taggatggca aatatctgac ttgaaaggca tcagcccttt agtctgtaca catcatatat 3060 acatggaaga agaagctaag ccaattcgtc aacctcaaag aagattgaat cctcatatgc 3120 aagaggtggt gcgagctgag gttcttaagc tacttcaggc cggtattatc taccccatat 3180 cagatagccc atgggtgagt cctactcaag tagtgccaaa gaaatcaggg atcacagtgg 3240 tgcaaaatga taagggagaa gaagttgcta cacgcctcac ttcaggttgg agggtgtgta 3300 ttgattatag aaaattgaat gttgtgacaa ggaatgatca ttttccattg ccatttattg 3360 atcaagtgtt ggagagagtc tcaggccatc ctttctattg tttcttggac ggctactccg 3420 ggtattttca aatagaaatt gatgttgaag accaggagaa gaccactttc acatgtccat 3480 ttggaacata tgcctacaga agaatgcctt ttggtttatg caatgcacct gcaacattcc 3540 aacgatgtat gttaagcatt ttcagtgata tggtggagcg tattatggaa gtttttatgg 3600 atgatatcac catatatgga agtacatttg aggaatgctt agtcaacttg gaagctgttc 3660 tgaaccgatg cattgaaaag gacttagtgc ttaactggga gaaatgccat tttatggtac 3720 aacaaggaat tgtccttggc cacatcatct ccaagaaagg cattgaagtt gataaagcaa 3780 aggtggaact tattgtcaaa ttgccatccc caacaactgt aaaaggagta aggcaattcc 3840 ttggccatgc tgggttctac aggaggttta ttaaagattt ctctaaactt tcaaagcctc 3900 tttgtgaact attgggtaag gatgctaaat ttgtatggga tgagagatgt caaaagagtt 3960 ttgagcaact gaagcagttc ttgacaaccg ctccaatagt gagggctcct aactggcaac 4020 taccttttga agtgatgtgt gatgccagtg actttgctat aggagctgtt cttggtcaaa 4080 gagaggatgg aaagccctat gtgatctact atgcaagcaa aacattgaac gaagcgcaaa 4140 gaaactacac aaccacagag aaagaattgt tggctgtagt ttttgccttg gacaaatttc 4200 gtgcttatct agtagggtct ttcattgtgg ttttcactga ccactcagct ttgaagtact 4260 tattgacaaa gcaagatgca aaagcaaggt tgattagatg gattctctta ctacaagagt 4320 tcaatctcca aatcaaagat aagaaaggag tggagaatgt ggtagctgac cacctttcaa 4380 ggttggctat agcgcataat tcccatggtt tacctattaa tgatgatttt ccggaggagt 4440 cactcatgtt gttagaagat gctccttggt atgctcatat tgctaactat ctagttactg 4500 gtgaagttcc aagtgagtgg aaagcacaag ataggaagca cttctttgca aaaattcatg 4560 cctactattg ggaagaacct tttcttttca agtattgtgc agatcaaata ataaggaagt 4620 gtgtccctga acaagagcaa caggggatcc tcagtcattg ccacgaaagc gcatgtggag 4680 gccactttgc ctctcagaaa acagccatga aggtgttgca atcaggtttc agttggccat 4740 cacttttcaa agatgctcac accatgtgta ggagctgtga tagatgccaa aggcttggga 4800 agttaacacg taggaaccaa atgcctatga accccatttt aatagttgat cttttcgatg 4860 tttggggcat tgacttcatg ggacctttcc ctatgtcttt tggtaactct tacattttgg 4920 tgggggtaga ctatgtttct aaatgggttg aggcaatccc gtgtaaacac aatgaccaca 4980 gagttgttct caagtttctc aaagagaaca tcttctcaag atttggggtg cccaaggcca 5040 taatcagtga tggaggtact catttttgca acaagccttt tgaaactctt ttagccaagt 5100 atggggtgaa gcacaaggta gctacacctt accaccctca gacttctggg caagttgagt 5160 tagcaaacag ggaaatcaag aatatattga tgaaggtggt gaacacgagc agaagagatt 5220 ggtctgttaa gctccatgat tcactatggg catatagaac aacttacaag actattcttg 5280 gcatgtctcc ttatcgccta gtctatggca aagcatgcca tctccctgtg gaagttgaat 5340 acaaggcttg gtgggcaatt aagaaggtaa acatggactt gaacagagcc gggatgaaga 5400 ggtgcttaga ccttaatgag atggaggaat tgagaaatga tgcctacatc aattccaaag 5460 ttgcaaaaca gaggatgaag aggtggcatg atcagttaat ctccaacaaa gaatttcaaa 5520 agggacaaag agtcttactc tatgactcta ggctccacat ctttccagga aagctaaaat 5580 caaggtggat aggccctttc attattcacc aagtgcattt caatggagta gtggaactac 5640 tcaattccaa cagcacagac actttcaaag tcaatggcca ccgtctcaag ccattcatgg 5700 agcctttcaa tcaagacaag gaggaagtca gtctccttga gccacaacaa tcttaaccaa 5760 aaaggggtta gatggactta gtctttctga agactaacca aagtccatgt ttttttgttt 5820 taattttgtt gatttaaaag ctttattatt tgttttaatt ttaattttag ctttaattta 5880 ttttattttg atctaactta gactttttgg atgatcaaaa ttaggaggaa cttcaaagga 5940 attggaggaa agccttaaag aaccaaagaa ggagaaaaag cctgaaaaac agagcaatat 6000 ttctaacttg cgaaaatttc gcaagttgaa awwycaactt gcgaaaatga gggccaactt 6060 gcgaaatcct caccttaaag ctyaaattcg caagtccact attcaacttg cgaaaatttt 6120 cgcagcctgc gaaagcacct ctaggcacac gtgtgccatt tcgcaagttc aaaatccaat 6180 ttcgcagcct gcaaatcaac ttgcgaatca agttgcgaaa tggggcaacc tgcgaatcaa 6240 gccaacttgc gaaaatgcca accgtcattt aaattcctat ttaaacctct aattttttca 6300 attttcattt cgcacagcca ttccaagttg cgaaaaagcc ctatcaagtt gcgaagccca 6360 aaaatctcag agcatcccct ccataggaag cccagaggtc gtgcgtctga agaagaacca 6420 ccccgcgcac ctcacgcgca ccctgtggaa cacaagccaa gcaattcctc tccatttcag 6480 ccatggccaa gacaagagga gcccaagccg cgtctccatc agctcgcaac ccaagaccga 6540 gagcttcacc tgcgcgggat tccatgtctg aggctccaca ggcccctgcc attccacctt 6600 ctgagggtgg agtgccatct agccctcctc agcgcaggta tgagacgagg agaccaccca 6660 ctacacctgg ggcaagcact tcgcgcccca agaaatcagt tcgtcgccct cctacaaaga 6720 aagccagagt ttcaggccca ggagagtcat ctgcacctcc acagcctcag ccgcctacta 6780 cagagtctca gattccttct gggatgactc cagaagtgat tatcaggcga cctatggtta 6840 cacagccacc tatagaggga aatttggatt gccgagctag gccattccac tccgagctat 6900 gctttgatat ggagactttc agacaccagc cggagctcag agattcattc cacctactgc 6960 agagatacca tttggagcac ctgatgactc ctagggattt cttctatccc agagtagcat 7020 tagactttta tcagtctatg actacwcatc gcgtccggga tcctactgtc atccacttca 7080 ctattgatgg acgccatggt atctttggag ccagacacat tgcagaggcc ctgcacattc 7140 catatgagcc tgtgagtcca gcagatttca gagagtgggc tcatttttct cagagggaca 7200 tggtccatat attgtccagg gggacatcta cacgctcatt tcttcttagg aaggagcttc 7260 cacctgggat gtttcttctg gatgtggtgc tgcgctccaa catatttcca cttcagcata 7320 tggtgcagag gagaggagct atattggagg ctttattccg gatatcagag ggtttttact 7380 ttggccctca tcatttgatt atgacctctc ttctttactt tgaagagaag gtccacagga 7440 agaagctaca gagagcagat gccattccat tactttttcc taggctgctc tgtcagatat 7500 tagagcattt gggctatcct tctgagcctc agcttgagcg tcgacgcatt tgccgagagc 7560 tattcactct cgacaaatgg aatcatttga cggcttatgt tgcacctcca ggagccccag 7620 ctaggccagc acctccagag ttaccacagg atgagcagcc acaacaggca caacaggytg 7680 agatacctac agagatcata ccacctgccc ctgcagcacc ttctacagtg cccacgcctg 7740 aggctacatc ttctgctcct cctaccactc ctgagactcc accagttgta ccagctacat 7800 cagcacctcc tccatctgag tcyactatca ccatatccac ttcagagttt agaggcctat 7860 gtcatacatt gcagacattg agcaccactc aaagtgttct cgcccagcag atggcagtca 7920 tacgtgcaca tcaggatcag cttattgcca cgcaaaccca gcatactgcc atccttaggc 7980 agatacagca gcatttgggt attctgccac cacctgagca tgatatgcct ggcccatcag 8040 agcctacagc tccatctgag gaggctactc cagctgagca agctattcca tctcaggagg 8100 ctactccagc agagcagact atgccccatg aggagactac tacagtagag atcgagactc 8160 cgatccagag cactcaggag accacagcag agccatcgtc tccacatgat cctcccacca 8220 ctacctgatc atctatctac ttttgttttg tatttactta ttatagtaga actcttaatc 8280 ccatgttttt ttatgtttta tatactggga ttggatgtat tacttgtgca tatttcatat 8340 tgtactttct taaagtaata catatccatc attttttagt atacttggca tatttttatt 8400 ttatttcctc tactcattat ttttttgttg ttttttgaat catgtggttt ctcctataca 8460 attcaaactc tattccactc aggaggtacc acttcctccc tttattttca attgctcttc 8520 aaacattgag ggcaatgttc agcatggttg gggggaagag agttgaggaa ggaagtattg 8580 tttataatgc taagttatwa atggtaattt agttactttt tgcttaattt taaaawtatt 8640 ttttaaartt tttattctac tcttcatggt tatcaaggaa aaattctcaa aatgaaatgg 8700 gagaaattga atttttgtct ttttacttga cttagagttt gtattatgct tattaaagtt 8760 gatgaattgt tgaaacttct attgaattca accttatttc ttccacttta agcttaccac 8820 acactgtgca cactaggttc cgattataag atgaaaaact atttcacccc cttgacttag 8880 gaaattttag acttggtacc tttgacctca ttttaatagt gttgggacac cttataaaag 8940 gccaatgagc ctttgaaaaa aaaaaagaaa gaaagaaaga aaaaaatgtt ttacttgcct 9000 tgaaacccga gcaaggtctg aggggtatat ggtgaaaatc tttaaaacct ggtgccctaa 9060 gccttcattg gttgggagtc accgacctca atgctcgtta caagggtgaa taggtggagt 9120 ttaacatact gtaggtgctt gggtattgaa ttccaatctc aaaagtccgg ggtaaaatcc 9180 gaggagttag tggttgaaag atccttgaag cttgatgccc taaaccttaa ttggttggga 9240 gtcatcgatg gacccccgtt acatggacaa tttagaaaag aataccttta agctttgtac 9300 tcctacaaga aaaaaaaagt gtgaaataaa tgaggtgcgt tcttagccta ttggaggttg 9360 tcagtttgct aagatttgaa aaagaactag gttgggggga gagattagtt caacatacta 9420 tattcggaaa ctaataagta acacttagat ttttgtggaa gagtaaggat tgaccctttg 9480 ggagtggaaa ttcttttaaa gcttaaattt gcataatgcc ttctctttat gaattgtgat 9540 taggcaagtt atttgataac tcttgttgaa gtttgagttt tatatcttta atgttccatg 9600 tgagagtttg atcatcatgc cacttgaaat tttttggagt gatcagcatg atgttgtaaa 9660 ttatagtact gtttattttt atttttctct ccttcattgc taagggacta gcaatatgtc 9720 ggttgggggg ag 9732 // ID Copia-7_Mad-I repbase; DNA; EDCOT; 7291 BP. XX AC ACYM01099170; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-7_Mad-I; KW Copia-7_Mad-LTR; Copia-7_Mad_. XX NM Copia-7_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-7291 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1286-1286 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01099170; Positions 7824 15114. XX CC Positions [4205-4729] - Integrase core CC 'TTGTA' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS join(3065..4837,4841..5770) FT /product="Copia-7_Mad-I_1p" FT /translation="MKYDGVASVREHILKMVDLAQKLKDLEVPMTDQFLVH FT MALNSLPPKYGQLKVSYNTQKDKWGIDELISMCVQEEDRLKKDKVVDVNLV FT QAEKRKRDSTFGSTIPAGKKKKKENFSSFKSTNPFKGSHKIKYVNVEIEKE FT KECYFCKETGHLRKNCSGFKNWLVTKGKIINVFVCVESNLVFIPPQSWWFD FT TGCSIHITNSLQGFTKTREINNEVYNVYVGNGNKVVVESTGRVELVLSSGF FT VLELSPVLYALSMRRNLISASKLVKSSFTFVGDDHCVKFYHSNNINEMLGK FT AYLEIDMWQLDCSYTNECFNVQAVGSKSWSTSEKSSMLWHKRLGHISKERI FT LTLTKQNLLPQLDFSDFKECVDCFKGKLTNTRKLGSNRSQSLLEIIHTDIC FT GPFPNKTICGKSYFISFIDDFSRYAYVYLISEESEALECFKSFHLEVEKQL FT EKQIKIVRSDRGGEYFGRYTEVRQHKGPFATYLEQNGIVAQYTTPGTPQQN FT GVAERRNRTLKDMIRSMFAHSHLPIFLWGEALKTATYILNRVPSKSVNLVP FT FETWTGRKPSFNHFHVWGCKAEVRFYNPMEKKLDPRTTSCRFIGFERSKGF FT KFYCPNSHCRIMETHNAKFLEHLDGDDDNSSRSISFDFEELPQEGELLEQQ FT AIAVSIPFEPQAFTSPDSLPEQQVEGTMNENQTLHDEEQGPNIAEMEHDNI FT NDHIEGIDAALIQAPVRKSQRVRKAVTLPNFVYLNEVEYNVGDDDDPTSYY FT QAISSTRSKLWNEAMHEELQSMEKNRVWTLVPKQMEVHKLVGCKWVFKINR FT DSEGNIDKHKARLVAKGFTQREGVDYNETFSLVSTKDSMRIILDLTTHFDL FT ELHQMDVKTTFLNGDLEEDIYMSQPPWFVERGKELMVCKLNKLIYGMK" XX SQ Sequence 7291 BP; 2427 A; 1178 C; 1529 G; 2147 T; 10 other; tgtggtatca gagccattca acgtggctag ggttcttcgc tctcattaaa gactatgata 60 gagttttgat aactgcaaaa tcaaacataa tcctagacaa aaattatgct tccgctgtat 120 gttgttgctt tatcaattag tgacttacct atcaattaaa atatgataat aggctaccta 180 ggttttctcg agttgtgttt gttatatttt gcaggaaacc tattttcatt agatgaggac 240 aacgttgaaa aaccaacaaa tgcagaagaa cttttgggtg cataatatgc ttgtcaataa 300 tgaactgaca aacataatat gaattataaa caaggattac aacatctaat ctgctcaaaa 360 gtgtttggat tgttgttttt ggcttattga tcaactgatt ggatatgtga tttatttgta 420 ttaagtgaat aataatttgc tcaaaagtgt ttaattattc aagtcaaacg agtaaatcaa 480 tgtataatga gtcattaaac tgacaagatt acactcttca tctgctcaaa agtgttgaag 540 ttgtgtaaat tgcccttgtg tttaattact cagttataca aacctaatat aaatggtttt 600 tgtctaaaga tgataccatg gttatatgac tttggatggg gaaatattga aacaatagtt 660 ttccttgttt gataaattag ctagtgaatg atgcgaaata tattaagcac acaaattaaa 720 ccctcttttg acaaatgtag taaagtatgt aagtagggat cgttctagac cggggattag 780 gagggattgc taaacacttg gaaactgact taaaaactca aaaacaaagt ttaaaacact 840 aaactagact caaagaatgc aaaactaaag gttcaaacac ttaaacaaac ctaaaactca 900 aaacagcaac ctaatgactc aaaactgcct aaaaaccact tcctgggcag ttttgagaac 960 ctaacaagaa cttggacgaa tttgggtgaa aacttgaatc aaaacactta gaaacacaaa 1020 tcaaaacacc ttctaactaa tctaagactt caaaataaag ggggatttgt tttggacgaa 1080 aattgaaaac aaaacagaaa ctttaaacta aacagattgt agaacgtttt tggataaaaa 1140 ggatggataa aaggctagtt aggaggttyt tctccacaca tgtcacactt gcaaacaaaa 1200 cgattttcag ttgttcttcc aataaattat aaatactcaa cgccccaaat taaccgtgaa 1260 ttgcactaat taaccctcag tttttccaca agttattaag ttggatgatt gcatgcgaca 1320 acccgaaaca ttccctacaa gttccctaca tgaattgcat aatagagata caagcaagaa 1380 tcattaagtt ctatgaaaaa cataagcatt gacgaagcat tcgttactat gaattgcatg 1440 aaacttatgc taagaattca ttcaacgcga tcgttttcaa gcgaccttca ctacttgtga 1500 ttataagatt gtaactatta ggtgaaactc cctcataatc tagcatcata ttcatgcatg 1560 aaaactaagc gtgcactctc aatcaacata cacaaataag ttatcaatca aatagatgaa 1620 cgaattgaat ccacaactta tgaaataaca actgaatgta atcaaatcat attgcaagca 1680 tgtacatggt ttcgaattac cccccaacta agggggttta gttcctcata ctcacaacac 1740 aaagtttatt gaattgaaac atcgaagaca taagaaagat tacacctaaa acgcccaaga 1800 attccacttt gaatttctgc acgtcaagct cctcttcttc ttctccttgc tgcggcagag 1860 atggttaaag ggatttttgg wtgtggtttt ggtttaggaa tggagttagg atgatatggt 1920 ggtgcggcaa ggggtatgga tggtgtatgg aggtgtataa tggtggctgg agtaaaggat 1980 ggttgcggca aggagggatt aaggtgatgg tggctgcggc aaggtgggga aaagggttgg 2040 atgattttct gatttgtgga gagggatcmy ytttgcggca wggtggtaaa acacatatat 2100 ataggcagcc aaaccctaaa gaaatcaggt taggcaaata ggctagggtt tgggtgcrgc 2160 argggttgga aatccaccag aaaatarggt ttctagaaca ttaggtgcgg catgggctta 2220 gggtagatar attagggttt aacttggcag aaattaaatg attaggccct agggtgtggc 2280 tgattaagtg ggctaggatt agggtttagg tgcggcatag gcttagggtc cacaaggagt 2340 ttagggttta tgtcatctaa aagcccaaag ccaagaatag aaactcacga aaatggaaac 2400 ctcaaagaat agaaacttcc aactttagaa actttggttg ccaattccga cttctttgtt 2460 cttcacttcc atttcttcat ttcttaagct cctttgactt tcaaactcgt ccattccttg 2520 tgctccatta gcatacactc cattccagct caattttgct ctaaaatgct ccatttcgca 2580 cctctttgca tactttgccc ttagaacctg aaaacacata aaactagctt aaaagactac 2640 tttactaagt aaaaacacta taaatgcaca agaacaagct aaactaaggt gcataaatat 2700 gctcctatca gtgaataata ttgtttttgt gatcttcttc agcacctcac atgacgtctc 2760 tcaacttcaa caatatagag accttgactg gctccaactt caagaaatgg aaggaggatg 2820 tcgagattgt gctcggtctc atggatcttg atctggcact gagggaagaa aaacctaaag 2880 ccatcactgc cgagagtaat gtagatgaaa aagtgaagct tgaaaaatgg gagagggcaa 2940 atcgaatgtc taagggggaa ttcctaagac tgacaatgca agggaattct tggctgcagt 3000 aggaaagaag tttaaggagt cagaaaaggc agaaactggg acttttctta cataactcac 3060 atcaatgaag tacgatggtg tggcaagtgt cagagagcac atattgaaga tggttgatct 3120 tgcccagaaa ctcaaggatc ttgaggtacc tatgaccgac caattcttag tccacatggc 3180 tttaaattct ttacctccta aatatgggca gctcaaagtc tcatacaaca ctcaaaagga 3240 taaatggggt atcgatgaac tgatttcgat gtgtgttcaa gaagaggatc ggctcaaaaa 3300 ggacaaggtt gtggatgtga atcttgtgca agctgaaaaa cgcaaaagag actccacttt 3360 tggttcaacc atacctgctg gtaagaagaa gaagaaagaa aacttttctt catttaaaag 3420 tactaacccc tttaaaggat ctcacaaaat taagtatgtt aatgtcgaga ttgagaaaga 3480 aaaagaatgt tatttttgca aagagacagg tcacttaaga aagaattgca gtggattcaa 3540 aaattggctt gttactaaag gtaaaatcat aaatgtcttt gtatgtgttg agtcaaattt 3600 agtttttatt ccccctcaaa gttggtggtt tgacactggg tgctccattc atataactaa 3660 ttccttgcaa ggattcacaa aaacaaggga gataaacaat gaagtctaca atgtctatgt 3720 aggaaatggg aacaaagttg ttgttgaatc cacaggaaga gtcgaattag tcctttcatc 3780 tggttttgtt ttagaattga gtccagtact ttatgcactt tccatgagaa ggaatttgat 3840 ttctgcatct aagctagtta agtcaagctt tacctttgtt ggtgatgatc actgtgtgaa 3900 gttttaccat tcgaataata ttaatgaaat gcttggaaaa gcttatcttg aaatcgatat 3960 gtggcaatta gactgttcat atacaaatga atgctttaat gttcaagctg ttggttcaaa 4020 atcatggtcc acttctgaaa aatcctccat gctttggcat aaaaggttgg gacatatatc 4080 taaagaaaga atcctcacct tgacaaaaca aaatttgttg ccacaacttg attttagtga 4140 tttcaaagaa tgtgtcgatt gtttcaaagg aaaactcacc aacactagaa aattaggttc 4200 aaaccgtagt caatccctgc tagaaatcat acatactgac atatgtggac cttttccaaa 4260 caaaaccatt tgtggaaaat cttatttcat atcctttatt gatgattttt cacgttatgc 4320 atatgtttat ctcatctcgg aagagtctga agctttggag tgttttaaat cttttcattt 4380 agaggtcgaa aaacaacttg aaaaacaaat taaaattgtg agatccgata gaggtggtga 4440 gtattttggc aggtacactg aggttagaca acacaagggg ccttttgcaa catatcttga 4500 acaaaatggc atcgtagcac aatataccac tccagggact ccccaacaga atggggtggc 4560 agaaagaaga aatcgtactc tcaaggatat gataaggtct atgtttgcac actcacatct 4620 tcctattttt ctttggggag aggcgttaaa aacagcaacg tacatcttga accgagtgcc 4680 aagcaagtcc gtcaacttgg tgccatttga aacatggact ggaagaaaac cgagtttcaa 4740 ccacttccat gtttggggat gtaaagccga ggtaagattc tacaatccaa tggagaagaa 4800 gcttgatcca agaactacaa gttgtaggtt cattggataa tttgaaagat caaaagggtt 4860 taagttttat tgccctaaca gtcattgcag aattatggaa acacacaatg ctaaatttct 4920 cgagcatttg gatggggatg atgataactc ttcacgttca atatcatttg attttgaaga 4980 actgccacaa gaaggtgagt tgcttgagca gcaagcaatc gccgtgagca ttccttttga 5040 gccacaagca tttacttcac ctgatagtct tcctgagcaa caagtagaag gaacgatgaa 5100 tgaaaaccaa actctccatg atgaagagca aggtcccaac attgcagaaa tggaacatga 5160 taatattaat gatcacatcg agggtataga tgctgcactg attcaggcac cagtcagaaa 5220 gtcacagcga gttcgcaagg ctgtgacgtt accaaatttc gtgtatctta atgaggtaga 5280 atataatgta ggggatgatg atgatcctac atcctattat caagcaatct cgagtacaag 5340 atcaaagtta tggaatgaag ccatgcatga agaattacag tctatggaaa agaatagagt 5400 gtggacctta gtaccaaaac agatggaggt tcacaaactc gtgggttgca agtgggtctt 5460 taaaataaat agagactcag agggtaatat tgacaaacat aaagcaaggt tagtggcaaa 5520 aggctttaca cagagagaag gagttgatta caacgagaca ttttctcttg tctcaaccaa 5580 agactccatg agaataatac tagatctcac aactcatttt gatttagagc ttcatcagat 5640 ggacgttaaa acaacttttc ttaatgggga tcttgaagaa gacatataca tgagccaacc 5700 accatggttt gttgaaaggg ggaaagaatt aatggtttgt aagctgaaca aattgattta 5760 tgggatgaaa taggcttcga ggcaatggaa caaaaagttt gatagtgtga tggagaagtt 5820 aggttttcaa gagaataaac tggatgagtg tgtatacttt aaagtttatg gtaccaaggt 5880 aatattcttg gtattgtatg tagacgacat attaatggcg ggctcaggta tgtttttgtt 5940 acagtcgact aagggcatgt tagctcagaa cttcgatatg aaagacttgg gagaggctcg 6000 attcgttttg gggatagaaa tcattcggga tcgtgccaag agatcccttg gtctttcaca 6060 aagacaatat attgataggg tgactaaaag atttaacatg gataaatgtt caaacggaga 6120 gctacctatt ggaaaatgag acaagtttac ttgcgagcag tgccctaaga atgatctgga 6180 gaaagaagga atgaaagaca agccgtatgc gtcgctagta gggagcttga tgtatgcaca 6240 tgtatgtata agaccggatt tagtctttgc ggtaagtgta ttgggcaggt ttcaatcaaa 6300 tcctggtgca tctcattggg ttgcagctaa aaaggtcttg aggtatctta aaagaactag 6360 ggattttatg ttaacataca gtcatgtgga caaacttgag ttggtggcat tgcaggatgt 6420 atagatgata ggaggtcaac taatggttac atcttcctgc tagttaatgg agcaatttcg 6480 tggaagagtt taaagcaaaa gagtattgca tcttccacga tggaggctga attcatgggg 6540 tgttatgcaa caattcaaca agccatttgg cttaaaaatt tgatgaaggg actgatgatt 6600 attgacaata ttgaaaggcc actcaaactt tattgtgata ataaagttgc agtcttcttt 6660 tcgaagaaca ataaaaggtc ttatgcgagc aggttaatgg atataaagtt tctgaaagtg 6720 agatgaagtg aagaagggga ctattgatat tgagtatatc aacacaagtt tgatggttgc 6780 tgatccaatg acaaaggcct taccagtagg aatcttcaag aggcatgttt ttaacatggg 6840 agtaagagag tcctttgatt cagttaatga gtgggagtaa gcactctaaa gactgtgttg 6900 aacttgtttt tatttagttg tttcttttga tgtcatcagc tagttgcaat gcaatgcaat 6960 aaaatattat tattgttttg ataatttatg cattttatca tttcaaacag ttttggtact 7020 gaaagtaatt tcagtttgtt ttgaggaacc agcgtttttg tttgttggtt ctcaacatcg 7080 tgattctagt agtaacttag tgtttcatga taaatgtgta tgtaattata gaatatcaag 7140 tacatgttat tcgtacttgg gctttctatg gttcttcatt tttcttggaa tgacaagtta 7200 ctaactagag tggttgcaag cttttgtaaa ctcaatgatc atcatgattc ttattgtatt 7260 gaggaatatc attgacattc aagtgggaga a 7291 // ID Copia-5_TC-LTR repbase; DNA; EDCOT; 288 BP. XX AC CACC01013735; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-5_TC_; KW Copia-5_TC-I; Copia-5_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-288 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01013735; Positions 9741 10028. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 288 BP; 81 A; 53 C; 42 G; 112 T; 0 other; tgttagaaga taaccctgca tggacacgtg taaacctttt gtacagcatg atctacatac 60 ttctagctgt caatattttg atattaatgt gttgttttca ttttgaaaga acacctataa 120 gcggtttgta acaagtgtca tctacactat cattttgtaa tgtatatatg atcactgtgt 180 gatcatcatg tgatataaga tgaatattcc gcttctgtcc agcagcttac tagttcactc 240 tttacttctt tctttctcaa ttcatatgtt tttaccatga cattaaca 288 // ID Copia-38_VV-I repbase; DNA; EDCOT; 4098 BP. XX AC chr1; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-38_VV_; KW Copia-38_VV-LTR; Copia-38_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4098 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr1; Positions 8898003 8902100. XX CC Positions [1819-2175] - Integrase core CC 'CTTTC' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(136..1815,1819..4098) FT /product="Copia-38_VV-I_1p" FT /translation="MTPSSNISSVIPVFNGEHYHIWAVKMRFYLRSQGLWN FT VVMSEADTPPLGANPTVAQMKAYEEEKLKKDKAITCLHSGLADHIFTKIMN FT LETPKQVWDKLQGEFEGSERVKNVRLLTLKREFELMKMKDDESVKDYSGRL FT MDVVNQMRLLGEAFTDQKVVEKIMVSVPQKFEAKISAIEESCDLQTLTIVE FT LTSKLHAQEQRVLMRGDEATEGAFQANHKGKNSGNLQGKKFFKNSRGKAEG FT SSRKGKFSPCSHCKRTNHAEKDCWHKGKPLFNCNFCNKLGHSEKYCRAKKK FT QSQQQPEQHASVTEEDKNDDEHLFMASQALSSHELNTWLIDSGCTSHMTKH FT LSIFTSIDRSVQPKVKLGNGEVVQAKGKGTIAISTKRGTKIVTNVLYIPDL FT DQNLLSVAQMLRNGYAVSFKENFCFISDVHGTEIAKIKMNGNSFYLKLDLV FT EGHVFSAKIDESVVWHKRYGHFNLKSLRFMQEAGMVEDMPEISVNAQTCES FT CELGKQQRQPFPQNMSKRATHKLELIHSDICGPMSTTSLSNNVYFALFIDD FT FSRMTWVYFLKTKQVLSMFKSFKKMVETQSGQNVKVLRTDNGGEYTSKEFS FT LFCQEAGIVHQLTAPYSPQQNGVSERKNRTVMEMVRCMLFEKKLPKLLWAE FT AVNTSVYLLNRLPTKSIQSKTPIEAWSGVKPSVKHLKVFGSFCYLHVSSVK FT RGKLDERAEKGVFVGYAAESKGYRIYSLSRMKIVISRDVHFDENSYWNWDL FT KKVHKCDQTTPSILEPAIESTIIEGPLDVEATSDTPVLKMRPLSDVYERCN FT LVHAEPTCYKEAARFLEWIEAMKAEIDAIERNGTWKLTELPEAKNAIGVKW FT VFRTKFNSDGSIFRHKARLVVKGFAQVAGVDYGDTFAPVARHDTIRLLLAL FT AGQMGWKVYHLDVKSAFLNGILLEEIYVQQPEGFEVIGHELKVYKLHKALY FT GLKQAPRAWYSRIDSHLIQLGFRRSENEATLYLKQNEDGLQPVVSLYVDDM FT LVTGSNVKLLADFKMEMQDVFEMSDLGIMNYFLGMEIYQCSWGIFISQRKY FT AMDILKKFKLESCKEVATPLAQNEKISKNDGEKLEEPSAYRSLVGSLLYLT FT VTRPDLMFPASLLSRFMSSPSNVHMGVAKRVLKYVKGTTNLGIWYLKTGGV FT KLDGYADSDWAGSVDDMKSTSGYAFTIGSGVICWNSRKQEVVAQSTTEAEY FT ISLAAAANQAIWLRKLLADLGQEQSSPTELYCDNKSAISIAQNPVHHGRTK FT HINVKFHSIREAEKNSLVKLHYCSTDEQLVDIMTKGLPKSRLEFLRLKLGM FT SKANLKEE" XX SQ Sequence 4098 BP; 1356 A; 698 C; 931 G; 1113 T; 0 other; gtggtatcag agcaaaattc ctacgggctg tgaggcaaag tttttgagtg ttttgagtac 60 taaacacagt gaggttgagt gcaaacacta gtgaggttga gtgatctatt tttttcaggc 120 aactgtggtg caaacatgac tccttctagc aatatttcct ctgtaattcc agtgtttaat 180 ggtgagcact atcacatttg ggctgtcaag atgaggtttt acttaaggtc tcaaggtttg 240 tggaatgttg tgatgtcaga agctgataca ccaccattgg gagcaaatcc tacagttgct 300 cagatgaaag catatgagga agaaaaactc aagaaagaca aagccatcac ttgcctacat 360 tcaggacttg cagaccacat cttcaccaaa atcatgaact tggaaacacc taaacaggta 420 tgggacaagc tccaaggtga atttgagggc agtgaaagag taaaaaatgt tagactcctc 480 acattgaaga gagagtttga gttgatgaag atgaaagacg acgaatctgt caaagattat 540 tctggcaggt taatggatgt tgttaaccaa atgcggcttc ttggtgaggc atttacagat 600 caaaaggtgg tagaaaagat catggtttca gtgcctcaaa agtttgaagc caagatttct 660 gcaattgaag agtcttgtga cctgcaaact ctcacaattg tagagttaac cagcaagctt 720 catgcacagg agcaaagggt cttaatgaga ggtgatgaag ctactgaagg tgcttttcaa 780 gcaaatcaca agggaaagaa ttctggaaac ttgcaaggaa agaagttctt caagaacagc 840 agagggaaag ctgaagggtc ttcaagaaaa ggaaaatttt cgccttgctc tcattgcaaa 900 agaaccaacc atgctgagaa agattgttgg cacaaaggta aacctctctt taattgtaac 960 ttttgcaata aacttggcca cagtgagaag tattgcagag ccaagaaaaa acaatctcaa 1020 cagcaaccag aacaacatgc aagtgtgact gaagaagaca aaaatgatga tgagcattta 1080 tttatggcat cacaagcact cagttctcat gaactgaata cttggctcat tgacagtggc 1140 tgcacaagtc acatgaccaa acatctgtca atatttacct ccattgatag atcagttcaa 1200 ccaaaggtca agttgggaaa tggtgaagtt gtgcaagcca aaggaaaagg gacaattgct 1260 atcagcacca agagaggtac aaaaattgtc actaatgttc tttatattcc agatttagat 1320 cagaatcttc ttagtgttgc acaaatgcta agaaatggat atgcagtctc tttcaaagaa 1380 aatttttgtt ttatctctga tgtacacgga acagagatag caaaaattaa aatgaatgga 1440 aatagttttt atttgaagct tgatttagtt gaaggtcatg tctttagtgc caagattgat 1500 gagagtgttg tttggcacaa aagatatggt catttcaact tgaagtcatt gaggttcatg 1560 caagaagctg gtatggttga agacatgcct gaaatctcag ttaatgctca aacttgtgaa 1620 agttgtgagc tagggaagca acaacgacaa ccattccctc aaaatatgtc caagagagct 1680 actcacaagc tggaattaat ccattcagat atttgtggac caatgagcac aacctcattg 1740 agcaacaatg tgtattttgc gctatttatt gatgatttca gcagaatgac ttgggtttat 1800 tttctaaaaa ccaagtaaca agtgctctct atgttcaaaa gcttcaagaa aatggttgaa 1860 actcaaagtg gtcagaacgt taaggtgctc agaactgata atggaggtga gtatacctca 1920 aaagagttta gtctcttttg tcaagaagct ggaattgtac accagctaac agctccatac 1980 tcaccacagc agaatggagt ctctgagagg aagaacagaa ccgtgatgga gatggtaagg 2040 tgcatgctat tcgagaagaa gctaccaaag cttctatggg ctgaagcagt caacacctca 2100 gtgtatttgc ttaacagact accaactaag tctattcaga gcaaaacacc aatagaggca 2160 tggtctggtg taaaaccttc tgtcaagcac ctgaaagttt ttggctcatt ttgttatctt 2220 catgtgtcat ctgtcaagag agggaagctt gatgaaagag ctgagaaagg tgtctttgtt 2280 ggttatgcag cagaatcaaa aggttacaga atttatagct tgagtagaat gaaaatcgtg 2340 ataagtagag atgtgcactt tgatgaaaac tcctattgga attgggactt gaagaaagtt 2400 cataaatgtg atcaaaccac tccatctatt cttgaaccag caatagaaag tacaatcatt 2460 gaaggtccac ttgatgttga agcaacttca gacacaccag tgcttaagat gaggccatta 2520 tctgatgtgt acgagaggtg caatcttgta catgctgagc ctacatgtta caaggaagct 2580 gcaagatttc tagaatggat tgaggccatg aaagctgaaa ttgatgctat cgaaagaaat 2640 ggaacctgga agttgacaga actacctgaa gctaagaatg caattggtgt aaagtgggtt 2700 ttcagaacta aatttaattc agatggttca atcttcaggc acaaggctag attggttgtg 2760 aagggttttg ctcaagttgc tggagtggac tatggtgata catttgcacc agtagctaga 2820 catgacacta taaggctact acttgcactt gctggtcaaa tgggatggaa agtgtaccat 2880 ttagatgtca agtcagcttt tctaaatggt atacttcttg aagaaattta tgttcaacaa 2940 ccagaaggct ttgaggttat tggccatgaa ctcaaagtgt acaagctaca taaggctctc 3000 tatggtttga agcaagcacc aagggcctgg tatagcagaa ttgattctca tctgatccaa 3060 cttggattta ggaggagtga aaatgaagct actttgtatt tgaaacaaaa tgaggatggt 3120 ttgcaaccgg tagtatcact ttatgttgat gacatgctag tgaccggaag caatgtaaaa 3180 ttgctagctg atttcaaaat ggaaatgcag gatgtatttg agatgtctga ccttggcatc 3240 atgaactact tccttggaat ggaaatatac caatgcagct ggggtatctt catttcacaa 3300 agaaaatatg ctatggatat tctcaagaaa ttcaagctag aatcatgcaa agaagtagca 3360 actccgctgg cacaaaatga gaaaatttca aagaatgatg gtgagaaact tgaggaaccc 3420 tctgcatata gaagcttggt gggcagccta ctatacttga cagtaaccag acctgacttg 3480 atgtttccag ctagtttgct ttcaaggttc atgagttcac caagcaatgt tcacatggga 3540 gttgcaaaga gggtgctaaa gtatgttaaa ggtacaacaa atcttggcat ttggtattta 3600 aagacaggag gagttaagct agatggttat gctgatagtg attgggcagg aagtgttgat 3660 gatatgaaga gcacttcagg ttatgcattt acaatcggtt caggtgtcat atgctggaat 3720 tcaagaaagc aagaagtagt ggcacaatca actacagaag ctgagtatat ctccttagca 3780 gctgctgcaa atcaagcaat atggttgaga aaattgcttg ctgatttagg ccaggaacaa 3840 agctcaccaa ctgagcttta ctgtgacaat aagtcagcca tttccattgc tcaaaatcct 3900 gtccatcatg gcagaaccaa gcacataaat gtaaaattcc actccataag ggaagctgaa 3960 aagaattcac ttgttaagct gcattattgc tcaactgatg agcaacttgt tgacataatg 4020 actaaaggac ttcctaaatc aaggctggag ttcctaaggt tgaagcttgg tatgtccaag 4080 gcaaatctca aggaggag 4098 // ID BoSB14A repbase; DNA; EDCOT; 156 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB14A. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-156 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 156 BP; 32 A; 42 C; 47 G; 35 T; 0 other; taaccggggc gtctagctct ggtggtaaag gactcacagc tgtgagcacc gccacctggg 60 ttcgattccc ggccactgcg gatttaacat tcgggccgca gcgacacaga ttagtccctt 120 gggcctggaa agccgttggg gaaactgtgt ttaatc 156 // ID TRAMET1 repbase; DNA; EDCOT; 258 BP. XX AC . XX DT 16-DEC-2006 (Rel. 11.12, Created) DT 16-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Putative non-autonomous DNA transposon. XX KW DNA transposon; Transposable Element; Nonautonomous; TRAMET1. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-258 RA Jurka J.; RT "TRAMET1: Putative non-autonomous DNA transposon from barrel RT medic."; RL Repbase Reports 6(12), 644-644 (2006). XX DR [1] (Consensus) XX CC Present in >800 copies in barrel medic genome. TSD: TA. XX SQ Sequence 258 BP; 88 A; 35 C; 41 G; 94 T; 0 other; ctccctccgt cccttaataa atgactcagt tgacaatata cattattgac ttgacatact 60 ttgaccatac ttttatacta attcacaaag ataaataata tcatgtaaga tgttgttgga 120 ttcgtctcga tgagtatttt taaaatatta aatttttata atttttttta ctagataatt 180 gaagatatca aagataaaac atatgcattg gtatgtgtgt cagagtcaac tagatcattt 240 attgagggac ggagggag 258 // ID Copia32-PTR_LTR repbase; DNA; EDCOT; 230 BP. XX AC scaffold_516; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia32-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-230 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-230 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 241-241 (2007). XX DR Genome; scaffold_516; Positions 36195 35966. XX SQ Sequence 230 BP; 77 A; 31 C; 37 G; 85 T; 0 other; tgttggaaat tatattaata gtgttttgat gtaaatagga aagctgtatc ttgagataag 60 taggaaagat acgtaagaat attttgtatc aatctgcatt caattagctg tcattcctta 120 tcagtctctg atttataagg gaaccctaat gtatcttgta tatatattga acttaatcaa 180 tacagaaaag cattccgctt gaatagtttt ttacttatac tatacccgca 230 // ID Copia41-PTR_LTR repbase; DNA; EDCOT; 250 BP. XX AC LG_XI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia41-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-250 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-250 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 261-261 (2007). XX DR Genome; LG_XI; Positions 13416856 13417105. XX SQ Sequence 250 BP; 63 A; 20 C; 55 G; 112 T; 0 other; tgttaaagtt tatttattta attcattgtt ttatttaatt atttatttta tgttgattta 60 gtcataatgg acctagtctt taggaatgtg tttaggtggc taagagagtg gtgattgtgt 120 tgctagaatc atgggttagt ggggtaatgg tgatgtgggt tagtgggttc attatgcact 180 atgtaatgcc tatttatagg ctctttatca ttaattgaat tacctagtag agtattattt 240 tttatcatca 250 // ID Gypsy15-VV_LTR repbase; DNA; EDCOT; 427 BP. XX AC AM435517; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy15-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-427 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-427 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 730-730 (2007). XX DR Genbank; AM435517; Positions 23389 23815. XX SQ Sequence 427 BP; 98 A; 80 C; 96 G; 153 T; 0 other; tgatgcgaac agctggtaaa cgacaccgtg aggagaacca tgttagtgat gcgatgcgtt 60 tcatgcaaac cagaaaagtg atgcggtgcg ttttatgcga aaggaatgga taggcacgtc 120 agctagcact tatttcattt ctttctgtca tttccttatc ttttcctttc ttcatttcta 180 ttattcctgt gagaagcggc ttagcgatat tctcgggagt ttgttagaga agttgttgca 240 atttgttata gagatagtat atgagtgtga gagagaggaa gggtcaggga tgttgtggga 300 attgtgtgaa ttgctcatct cctctctgct ctgttatctt tcatattgtc atcaataaga 360 ttgcctattc tctctccatc cgcctctctt cttcttctta tgtcgcattt catttaagtt 420 tgcacca 427 // ID RT_BC repbase; DNA; EDCOT; 331 BP. XX AC AJ430549; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Brassica carinata retrotransposon RT_BC, pseudogene for reverse DE transcriptase. XX KW Non-LTR Retrotransposon; Transposable Element; RT_BC; KW retrotransposon; pseudogene; reverse transcriptase. XX OS Brassica carinata OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-331 RA Alix K.; RT "Direct submission."; RL Direct Submission to Genbank (04-FEB-2002). XX DR Genbank; AJ430549; Positions 1 331. XX SQ Sequence 331 BP; 93 A; 52 C; 87 G; 99 T; 0 other; cagatgtgtg ttgattaccg tttggcagaa gaacaagaag ccacggttca tcaacggggg 60 ggtgtgggag cagttgatag ctcattggga gagggaagac actgcagaga cgtcttctag 120 gaactccagg aaccggaaga gcgatcgtgg cgggaaaggt atgtatgtgc acaacctcgg 180 cgcttgctcc atgtctacta aggaggatga acttgtaagt tttttattat tatttatctt 240 tatatttttt aaataaatat tttatatatt ttttggctaa taatggcggt ttttttagat 300 cgaagcaaat gacggtaatc aacgcacatg c 331 // ID Copia-43_VV-I repbase; DNA; EDCOT; 4150 BP. XX AC chr11; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-43_VV_; KW Copia-43_VV-LTR; Copia-43_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4150 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr11; Positions 7521468 7525617. XX CC Positions [1777-2019] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 2520..4148 FT /product="Copia-43_VV-I_1p" FT /translation="MNNIFRPKQLHTTTKHPLPEPPEPSCVSQALKDPHWR FT KAMSEEVTTLLQHGTWELVPPTPGQNLVGCKFVFRKKRNPDGTISRYKARL FT VAKGFHQRPGIDYSQTYSPVVKPATIRLLLTIAVMHGWPLRQLDINNAFLH FT GNLEETVFMHQPPGFEDPSQPQHVCKLKKSIYGLKQAPRQWYKALRDALLS FT FGFIHSATDNSLFIYKSHDILCYCLVYVDDIIVTSNTLSFVNNIINKLGST FT FSVKDMGSLHYFLGIEVIPTPQGLFLSQHQYIRDLLSRTSMENAKETLTPM FT STTTKLTVQDNSECVDSTEYRKIIGALQYLGLTRPDIAFAVNRLSQFMQKP FT TTNHWAAAKRLLRYLKQTMFHGILLQKHDQFQLKTYSDADWASNTDTRVST FT TAFITFIGPNPISWSARKKRAVSRSSTEVEFRALATATSETIWLHSLIKEL FT GLTLIEAPQMFCDNIGANHFSLNPVQHTRMKHIEIDLLFVRDLVQKGTIRV FT QHIHTIDQLADLLTKSLSRQRFQLLRSKIGVADGTSILRGHIRTASI" XX SQ Sequence 4150 BP; 1170 A; 1106 C; 671 G; 1203 T; 0 other; ttttgtctaa acctctatat ggtatcagag cccacctcaa aactccaacg agtatttcct 60 gtctttctca cttctgctat ggccacttct tcctttgata gttttccaat agccatcaat 120 gccacccagc aaattattgc acgtctcaca ccaaccaact tcccttcatg gcatgcccaa 180 tttgagtctc tcctcctcgg ctataacctc tttggctatg tcgatggcac tcatacctgc 240 ccacccctac cgacgtcaac tgatgcagct gccactaccg ctcatcacct ttggttccgt 300 caggacaaac ttattctaag tgcaattctg acttcagtgt ccccagctgt gataccactc 360 atagcaacct cccagacgtc atatcaagcc tggactaaat tgacaaaact gtatgctagt 420 cgatccagga ctcgtgtcat gcagctcaaa gaggatctca ccctcatgca acgtggcaat 480 cgcaacatta cagagtacct acactctgta aaaaccattg ccgatgagct tgctctcatc 540 gatgccccat tatctcaaga tgacatcacc ctatatgttc ttcatggctt aggatcagat 600 tttcgtgaca ttgttgcccc gattcgagcc tgagagtctt cactctcatt tgaagaatta 660 catgatctgc tacttggtca tgaggcatat cttcgaaggc ttgactccac tgctcaatcc 720 ttggtagtta ctgccaatac cactcaacgc agggactcac gctcctcaaa gaatcagtct 780 ttatcaactt atcaacaatc caagaatgac tccagatcaa agtctcgaca gtcgaaacaa 840 tacaaatacc ctccaaggtg tcaatattgt gatcaacaag gccacattgc aaaatactgt 900 ccgaaattga aaccctctga agccactgtg aactgcacaa ctactacttc tagtctagac 960 aaacgttggc tcattgattc tgcggcttcc cataatatca cttctcaggt ttcaaattta 1020 caatttcact ctgaatatga tggtactgat gaagttatta ttggagatgg atcaggtttg 1080 cccattactc attccggttc tcttactctt tcatttccaa acagaaaatt tcaagttgaa 1140 gatactctat gtgttcctac cattaacaaa aacttgatat ttgttcacca cttcacaaag 1200 caaaacaatg ttatcctgga atttcaccca acttattttc ttgtgaagga tcggagaacg 1260 ggggagattc ttcttcaagg accgtgtgaa aatgaagtct accctctacc ctcatcgcct 1320 gctgctactc caattgcttt tgtccatgaa cgcacatcag tagctggttg gcatcagcgc 1380 cttggtcatc catccttcaa agttgtcact cgcctcatta gttctttctc ccttcccacc 1440 acttcatatc tttctagttc taataattgt cattcgtgtt ctaccaataa agctcattag 1500 ttaccctttc ataaacacgg tctaactagc acaacaccat ttgatttact ttacactgat 1560 gtatggggac cttctcccac tcctagtctc aatggccaca gatattatgt tatttttgtt 1620 gatcacttta ccaaatatgt gtggttcttt ccattgcatc aaaaatcaga tgttaaaacc 1680 atatttcctc atttctacaa aatgattgaa actcgtttta acataaaaat taaaggagtt 1740 tattccaata atggaggaga gttcactgtt ctttgaccct ttttcacaac ccatggcatt 1800 agtcattata caacaacccc ttatacaccc caacaaaatg gagtgtctga gcgtcgtcat 1860 cgccatattg tggagacagg tcaaaccctt ctaagtcatg cctctcttcc atcagaatat 1920 tgggcttatg cttttgcaac agccacatat ctaatcaatc gacttccatc acctgttctt 1980 catcataaat cacctcttca agctctcttc aagcaacaac ctcggtatga aaaattacgt 2040 tcctttggat gtttctgctt tcccttgatg aagtcgtata acacaaacaa atttcaaaag 2100 aaatctgttc cttgtatctt tgttggctac tctactagcc aaagtgcata tctatgtctt 2160 catctacaaa gtcaacgcat atacacctcc aaacacgtaa cctttgatga atctgtttac 2220 cccttcaaac aggtttccat gccatcaccc actgactcat ccccaccaga aacctcttct 2280 tttcaggacc aattttgcag cttgcttcca gggagcttcc agcaatcaca cgggctcaag 2340 gagatatccc ctctgcttct tcgactccaa gtgaagatcc agctcttgtg caacctcaag 2400 aggcaccact ctccacttca gatcaggtac ctcttagacc ttctacttct gtttctcaac 2460 cagaaaattc aataccatcc tctccaccac catgtccacg aaccatcatc actcgctcca 2520 tgaacaatat ctttcggcca aaacaactcc acactaccac caagcacccc ttacctgaac 2580 cacccgaacc aagttgtgta agtcaagctc ttaaagatcc tcactggcgc aaggctatgt 2640 cagaagaagt gacaaccctc cttcaacatg ggacgtggga actggttcct cccactcctg 2700 gccagaatct tgttgggtgt aaatttgtgt ttcggaagaa acgaaatccc gatggaacaa 2760 tcagtcgata taaagctcga cttgtcgcta aaggatttca tcaacggcca ggtattgact 2820 actctcaaac ctacagcccc gtcgtaaagc cagcaacaat taggcttctt ttaaccattg 2880 ctgtcatgca tggctggccc cttcgtcagt tagacatcaa taatgcattc ttgcatggta 2940 atcttgaaga aacagtcttc atgcatcaac ctccaggatt tgaagatcca tctcaacctc 3000 agcatgtttg caagctaaaa aagagtatct atggtcttaa acaagcccca cgacaatggt 3060 ataaggccct tcgggatgca ctcctcagct ttggttttat tcactcggcc actgacaact 3120 ctttgttcat ctataagtct catgatatct tgtgctactg ccttgtttat gttgatgaca 3180 taattgtcac aagcaacaca ctcagctttg tgaataacat tatcaacaag cttggctcta 3240 cattctcagt caaagatatg ggctccttgc attatttctt gggaatagaa gtgattccaa 3300 cgccacaggg gctctttcta tctcaacatc agtatatacg ggatctcctt tcacgaacct 3360 ccatggaaaa tgctaaagaa acactcactc caatgtccac tacaaccaag cttacagttc 3420 aagataattc tgaatgtgtt gacagcactg agtatcgcaa gatcattgga gcacttcagt 3480 atttgggact cactcgtccc gatattgcct ttgcagtcaa cagattatct cagttcatgc 3540 agaagccgac aacaaaccat tgggccgcag caaaaagact actcagatat cttaaacaga 3600 ccatgtttca tggtatcctt ctccaaaagc atgatcaatt ccaactcaag acctatagtg 3660 atgcggactg ggcatcaaat acggacactc gtgtttcaac cactgctttc atcacattca 3720 ttggtcctaa tccaatctca tggtctgcac gcaagaaaag ggcagtctca agatcatcta 3780 cagaagtaga gtttcgggca ctagctactg ccacatcaga aacaatttgg cttcattctc 3840 ttatcaagga acttggtctc actctcatag aagcacctca aatgttttgt gataatattg 3900 gcgccaacca tttcagttta aatccagtcc agcacacacg gatgaaacac attgaaattg 3960 atctcctctt tgtacgagat cttgtccaaa agggaactat tcgtgttcag cacatccata 4020 ccattgatca actagctgat ctccttacaa aatcactctc acgtcaacgc tttcaactat 4080 taagatccaa gattggtgtt gcagatggca cctccatctt gagagggcat ataaggacag 4140 ctagtattca 4150 // ID SHACOP11_I_MT repbase; DNA; EDCOT; 4392 BP. XX AC . XX DT 19-JAN-2007 (Rel. 12.01, Created) DT 19-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon SHACOP11_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; terminal; repeat; ORF; KW SHACOP11_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4392 RA Shankar R. and Jurka J.; RT "SHACOP11_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 51-51 (2007). XX DR [1] (Consensus) XX CC The internal region is of Copia-type, exhibiting a single ORF for CC gag-pol polyprotein. XX FH Key Location/Qualifiers FT CDS 66..4382 FT /product="SHACOP11_I_MT_1p" FT /translation="MADSDSNTEDTSSSSILAELTAKMTEVLNRAAAPSQV FT NVNSDHTVVAPIGIKLDGSNYPLWSQVVEMYISGKDKLGYINGDLPQPPQT FT DPTFRRWRTDNAIVKGWLINSMDTSLISNFIRFSTAKLVWDAIATMYFDGS FT DTSQVYDLRRRVSRLKQAGGSIEKYYNDLQGLWREIDFRRPNPMECPIDIQ FT HYNTLLQEDRVYVFLDGLDDRLDNIRSDVLQMKPFPSVEQAYAHVRREALR FT QAVMTDNSDEIPGAVLASKSLRLHTGKASSNSKHKSSYISTKCSHCGGTRH FT TRETCFKLHGYPDWWTDFQARKHRDTSTSDSDPGTAAVASAEPHLSLIPSS FT SSHLTQGNALIFSNPVDDRNAWILDSGATDHMTFDVADFSKRSTPRRKSIS FT NANGGLSSVTGAGTVMLSPSLLLSNTLLVPSLSHKLLSVSQVTNDLNCVVL FT IYPSFCFLQDILTKEIIGRGTKKGGLYYMEDFSVGQAHHMRHPENLKVEQI FT LLWHRRLGHPSFGYLKHVFPDLFIGTSLLDLKCEACILAKSHRVNFPLSMN FT KIDVPFALIHSDVWGPSPKSSVFGFRWFVIFIDDCTRMTWIYSLKHKNEVF FT QKFQQFHKMIQTQYLSKIRILRSDNGGEYVNQQFREYFQQHGHIHETTCPQ FT TPQQNGTAERKNRHILETARALLLGAHVPSHHWADAVTTAVYLINRMPSKV FT LDFKTPLQTLSTFVSLPTIQMLPPRVFGCVAFVHLHKNQRTKLDPCAIRCL FT FLGYGVHQKGYRCFDPINRHTYVTMDVTFLEFDTFYAPPSSNSSLQGETRE FT EESNWMMFDWFNHIDTPSHEVSDEAPQTFFPSLEVEATNPPLSPVSNDSSL FT ENIVEVSSPVTLDNNVDINVGYELPYRHNRGKPPKRYSPEVEDQRSRYPIT FT NYVSTEELSEPLKKFANELSSHSVPTNVEEALEDPRWIQAMNEEMEALNKN FT TTWNLVPLPKGKKPVGCKWVFSIKYKADGSIERYKARLVAKGFTQTYGVDY FT QETFSPVAKLSTVRVLLSLAVNLDWPLHQLDVKNAFLHGYLDEEIYMDIPP FT GYMTSSKTEVVCKLQRSLYGLKQSPRAWFGRLSLAMRKYGFQQSNADHTLF FT LKHREGKVTALIIYVDDMIITGDDSKEIERLQKQLATEFEMKNLGGLKYFL FT GIEVARSKQGIFISQRKYILDLLSEVGLLDCKPVDTPIIQNHHLGEYPDQV FT PTDKGRYQRLVGKLIYLSHTRPDIAYAVSVMSQFMHNPSEDHMNAVIRILR FT YLKSSPGKGLMFTKNNHLQVEGYTDADWAGDITSRKSTSGYFTFVGGNLVS FT WKSKKQKVVALSSAEAEFRGMAKGLCELLWLRRLLTEIGFAPNCEMKLFCD FT NKAAINISHNPVQHDRTKHVEVDRHFIKQNLETKIIQFPFVKSEDQLADIL FT TKAVCSKNFFNSLDKLGIQNLCAPT" XX SQ Sequence 4392 BP; 1301 A; 925 C; 900 G; 1266 T; 0 other; tggtatcaga gcttctgatc caaaacctaa tataactctg aaaccctaaa aatccacctc 60 cttccatggc cgactctgat tctaatacgg aagacacatc atcgtcctcc atcctagctg 120 aattgacggc gaaaatgacg gaagttttga accgagctgc agccccgtca caagttaatg 180 ttaattctga tcatacggtg gtggcaccaa tcggcatcaa attagacggc agcaactacc 240 cactttggtc ccaggttgtc gagatgtata tctcaggcaa agacaagctg ggttatatca 300 atggagatct tcctcaacct cctcaaactg accctacttt tcgacgttgg cggactgaca 360 acgcgattgt aaaaggatgg ctgattaact ctatggacac ctccctcatc agtaatttta 420 ttcgattctc cacagccaag ttggtgtggg acgcaattgc aaccatgtac tttgatggca 480 gtgacacctc tcaggtgtac gatcttcggc gtcgggtaag ccgtctcaag caggctggtg 540 gatctattga gaaatattat aatgatctcc aaggactttg gcgtgagatc gacttccgtc 600 gtccaaatcc gatggaatgc cccattgata tccaacatta caacaccctc ctccaagaag 660 accgagtata tgtatttttg gatgggcttg atgaccgctt agataatatt cggagcgatg 720 ttttacagat gaaaccattt ccatcggtgg agcaagccta tgcacatgta cggagggaag 780 ctctgcgtca agcggtaatg acagacaact ctgatgaaat acctggagca gttcttgcat 840 ctaaaagtct cagattacat accggcaaag cgagttccaa ctcaaaacat aaaagctcat 900 acatcagtac taagtgctct cactgtggcg gaacaagaca tacacgtgaa acatgcttta 960 aacttcatgg ttatccagat tggtggacag attttcaagc tcggaagcat cgagatacaa 1020 gcacttctga tagcgatcca ggaacagctg ctgtagcttc tgcagaacca catttgtcac 1080 tcattccatc atcaagctcc caccttacac aaggtaatgc tctaattttc tctaatcctg 1140 tcgacgaccg caatgcttgg atacttgatt ccggtgctac cgatcacatg acatttgatg 1200 tggctgattt ttccaaacgc tcaactcctc gacgcaaaag tatttccaat gctaatggtg 1260 gcttatcgtc ggtaacaggg gctgggactg tgatgttatc accctctctt ttactatcta 1320 atacgctgct tgttccatct ctctctcata agttgctatc cgtgagtcaa gttacaaacg 1380 acttgaattg tgttgtgctg atatatccat ctttctgttt ccttcaggat attctcacca 1440 aggagatcat tgggcgtggt actaagaagg gggggctcta ttacatggag gattttagtg 1500 taggacaagc acaccacatg cgccacccgg aaaatcttaa agtggaacag attttacttt 1560 ggcatcgtag gctaggccat ccttcatttg gatacttgaa acatgtgttt cctgatttat 1620 ttattggtac atcattgttg gacttaaagt gtgaggcttg catcttagcc aagagtcata 1680 gagtcaattt tccattaagt atgaataaga ttgatgttcc ttttgctttg attcattctg 1740 atgtatgggg tccatcccca aaatcctctg tctttggctt tcgttggttt gtgatattta 1800 ttgatgattg cactcgaatg acttggattt actcgttaaa acacaagaat gaagtgttcc 1860 aaaaatttca acaattccat aaaatgattc aaactcaata cttatcaaag attcgtattc 1920 ttcgttctga taatggtggc gaatatgtga atcaacaatt tcgtgaatac ttccaacaac 1980 atggacatat tcacgaaacc acttgtccac aaactcccca gcaaaatggc accgcagaac 2040 gtaagaatcg ccatatcctt gaaactgctc gtgctctttt acttggagct catgtgccta 2100 gccaccattg ggctgatgct gttactacag cagtgtatct cattaatagg atgccatcga 2160 aggttcttga ttttaagact ccgctgcaaa ctttgtcaac atttgtgtca ctacccacaa 2220 tacaaatgct cccacctcga gtctttggtt gtgttgcatt tgttcaccta cataaaaatc 2280 agcgaacaaa acttgatcct tgtgccattc gctgcctttt tttggggtat ggtgtacacc 2340 agaaagggta ccgttgcttt gaccctatca atcggcatac atatgtaact atggatgtga 2400 ctttcctcga atttgacact ttctatgcac ctccctcatc caattcttct cttcaggggg 2460 agacaagaga agaagaatcg aattggatga tgtttgactg gttcaatcat atcgatacac 2520 catctcatga ggtttccgat gaggctcctc aaacattttt cccttctcta gaagttgaag 2580 caacaaaccc ccctctctct ccagtatcca atgactcttc tttagaaaat atcgttgagg 2640 ttagctctcc tgttactctt gataataatg ttgatatcaa tgttggctat gagcttcctt 2700 acaggcataa tcgggggaaa ccaccaaaaa gatactctcc tgaggtggaa gaccaaagat 2760 cgaggtatcc aattactaat tatgtctcta cagaggagtt gtctgaacct cttaagaagt 2820 ttgcaaatga gctctcatca catagtgttc ctaccaatgt tgaagaggct cttgaagacc 2880 cgagatggat tcaagctatg aatgaagaaa tggaggcatt aaataagaat acaacatgga 2940 atcttgtacc tctaccaaag gggaagaaac ctgtaggttg taagtgggtt ttctcgatca 3000 agtataaagc tgatggatct atcgaaaggt acaaggcaag actagtggct aaagggttta 3060 cacaaacata tggtgtagac tatcaagaaa ccttttcacc tgtagctaag ttgagcactg 3120 taagagtcct tctatctctc gctgtaaatc ttgattggcc attacatcaa ttagatgtaa 3180 aaaatgcttt tctccatgga tatctcgatg aagaaatata tatggatatt cctccaggat 3240 atatgacaag ttctaagacc gaagtggtgt gcaagttgca acgttcatta tatggtttga 3300 agcaatcccc tagagcatgg tttgggcgat taagcttggc aatgagaaaa tatggctttc 3360 aacaaagcaa tgcagatcat actttattct taaaacatcg tgaaggtaaa gttacagctt 3420 tgatcatcta tgtagacgat atgatcatta ccggagatga ctctaaggaa atagaaaggc 3480 ttcaaaagca attggcaaca gaatttgaaa tgaaaaatct aggagggctc aaatattttc 3540 tagggattga ggttgctagg tccaagcaag gcatctttat atctcaacgg aagtatattc 3600 tagatctttt atcagaggtt ggattactag attgtaagcc agtagatact ccaatcattc 3660 aaaatcacca ccttggagaa tatccagacc aagtgccaac agataaagga aggtaccaaa 3720 ggttagttgg aaaacttatt tatctatctc atacacgacc tgacatagcc tacgctgtaa 3780 gtgtaatgag tcagttcatg cacaatccaa gtgaagatca catgaatgca gtaattcgga 3840 ttctccggta cttgaaatcc tcgcctggaa aaggattaat gttcacaaaa aataatcatc 3900 ttcaggttga aggctataca gacgccgact gggcgggaga tatcacaagt aggaaatcca 3960 cttcaggcta ttttaccttt gttggaggaa atttggtttc atggaaaagt aaaaaacaga 4020 aggttgtagc attatccagt gctgaagctg aatttcgggg gatggctaag ggtctttgtg 4080 agctcctttg gctgcgaagg ttgttgacag aaattggatt tgctccaaat tgtgaaatga 4140 aactattttg tgacaacaag gctgctataa acatttctca caatccggtt caacatgatc 4200 gaaccaaaca tgtggaagta gatcggcact ttattaaaca aaatctggag accaaaataa 4260 ttcaatttcc atttgttaaa tctgaggacc agttagcaga tatactcaca aaagccgtat 4320 gcagcaaaaa ctttttcaac tcacttgaca agttgggcat tcagaatctc tgtgcaccaa 4380 cttgaggggg ag 4392 // ID TND1_LTR repbase; DNA; EDCOT; 327 BP. XX AC AF059674; XX DT 02-JUN-2000 (Rel. 5.05, Created) DT 02-JUN-2000 (Rel. 5.05, Last updated, Version 1) XX DE Long terminal repeat from TND1, a copia-like LTR retrotransposon. XX KW Copia; LTR Retrotransposon; Transposable Element; TND1_I; KW TND1_LTR; COPIA superfamily. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RP 1-327 RA Kenward D.K., Ban R.M., Bai D. and Brandle E.J.; RT "Isolation and Characterization of Tnd-1, A Retrotransposon RT Marker Linked to Black Root Rot Resistance in Tobacco."; RL Theor. Appl. Genet0-0 (1999)In press. XX RN [2] RP 1-327 RA Kenward D.K., Ban R.M., Bai D. and Brandle E.J.; RT "TND1_LTR."; RL Direct Submission to Genbank (15-APR-1998)Southern Crop RL Protection and Food Research Centre, Agriculture and Agri-Food RL Canada, 1391 Sandford St., London, Ont. N5V 4T3, Canada. XX DR GenBank; AF059674; Positions 1 327. XX SQ Sequence 327 BP; 82 A; 70 C; 75 G; 100 T; 0 other; tgttaggtac ccgtaaactt aacagagaag tctttgaggt gaggaacctc cgagcaagtt 60 gtctgaggct tatgtgactt aagctctcag gttgtaaagg tttgttgagc acccgtaagc 120 tcgacagggt atagtggaaa tctcgagaga gtctctcggg gactggactg gccacaaggt 180 gtggtaaacc agtatacatc ggtgtgttct ttccttgctc tctttaattc ctgcagtatt 240 ttatttgcgc aacagaattt ttaattccgc ataattctcg taaaacgcta ttcacccccc 300 ctctagcgtt gagcatatat tctaaca 327 // ID Gypsy2-PTR_LTR repbase; DNA; EDCOT; 421 BP. XX AC scaffold_41; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy2-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-421 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-421 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 319-319 (2007). XX DR Genome; scaffold_41; Positions 2371908 2372328. XX SQ Sequence 421 BP; 141 A; 82 C; 87 G; 111 T; 0 other; tgtcacgact ggaaccaaag aagatgaggg ctagcgcaga agaagaggga tttaattcaa 60 agcaagcata aaacgacagc gtgggaagga agcggtaaag aatttaaagc attagttaaa 120 cggttgcgtt tcatgcagcc cggatagttt aaatgaaata atcaagccac gtgtaatggc 180 taggggaaat atagaattaa gggaacaatt tggtttatga taaataccca aggatgtaac 240 agaaacatgc caacttttga tataacagaa ttcagtatct tttcctaaat tctctccctc 300 tcaatcagtg tgtagggaaa accccatgct gaacgtatga cctgttcttc ctcactcctt 360 caaaacttct tcttccctcc catggtagtt tgatcatcct ctggaaaatt aacttgcagc 420 a 421 // ID GAG_CA repbase; DNA; EDCOT; 269 BP. XX AC AJ411828; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Cicer arietinum retrotransposon GAG_CA, partial gag gene. XX KW Non-LTR Retrotransposon; Transposable Element; GAG_CA; KW retrotransposon; gag gene; gag polyprotein. XX OS Cicer arietinum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; OC Cicer. XX RN [1] RP 1-269 RA Staginnus C.; RT "Thesis (2001) Department of Plant Molecular Biology, University RT of Frankfurt / M., Frankfurt a.M., Germany."; RL Direct Submission to Genbank (22-JUN-2001). XX DR Genbank; AJ411828; Positions 1 269. XX SQ Sequence 269 BP; 75 A; 53 C; 54 G; 87 T; 0 other; ttctgtgttt ggttcccgat gtgactatcc ctccaaaatt caaggttccc gagtttgaaa 60 aatacaaagg tgccacatgt cctaaaaatc ctctgactat gtattgcagg aaaatggatt 120 ctcatgctca taacgacaaa cttctcattc actttttcca agatagtttg agtggggcat 180 cgttaagttg gtatatgcca cttgagcgaa atcaaatttg ttcgtggaaa gacttggttg 240 atgctttctt gaggcattac tagtacaac 269 // ID DNA9-11_Mad repbase; DNA; EDCOT; 1309 BP. XX AC . XX DT 20-OCT-2010 (Rel. 15.1, Created) DT 20-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-10_Mad; KW DNA9-11_Mad. XX NM DNA9-11_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1309 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1492-1492 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Termini are similar to those of DNA9-10_Mad. XX SQ Sequence 1309 BP; 507 A; 251 C; 189 G; 362 T; 0 other; gggagcttta atgaaaaggg cttgggccaa caaatattta accaaaaacc atcccaaaat 60 gttatttaac caaaagggct caaagtttaa taaaaaaatc atccaaaact attgtccacg 120 ggtcaaactt acaagcccaa cccgctacaa atctacactt ccgtaaatac ccctaaatga 180 ttcgatattg tcttgactct tcaccaacct caacccagca cgaaaccgcc ataataactc 240 cctgtcttcc tatcaaatcg aattccccca tttcaaaaac aaccaaatca aagttcaaat 300 caaagttgaa aaaggaagca ttcatcggaa caaagccgcc gaaacaagtt caaagaagtt 360 taatggcaga aaccggcgaa aaaagtgtct ggaaaaaaaa aagaaccaaa acataaaact 420 gtttctggag aacccaaaac ataacactgt ttctggaaaa aaaaatcaga tacagtgttt 480 gttttgtctg tgcacaaaca aacactgtat ctggaaagaa aagaaccaaa atccagaaac 540 agtgacttaa attccagaaa cagtgactta gattccagaa acagtgactt agattccaga 600 aacagtctat gttttaacct ttgactgttt cttttctttc atgcatcagt tgattatatt 660 taagaaacat ggtgcttatt ttgctttgaa tccaaataca gtgaatttca ctatttcttt 720 tctagcttac atttaagaaa cagtgtgtct atttcatttg gatccagaaa cagtgactta 780 gattccagaa acagtaactt agattccaga aacagtgact tagattccag aaacagtgtt 840 acttaaaatc cagaaacagt ttatttttac agtccagaaa cagtgacccg tcgttattat 900 tgaatagcat gcagatctca aatttatttt ctggagaaac aaacgatgaa ctccactgac 960 gaagaaaaat tgaaaaacag tacctcgaat acactatgaa taataacgac gatcacattt 1020 caacgaaata atacaaaata taaattaaat agcatgagga tctatatttt tgtttcaaag 1080 aaaaagaaga aggtctgcaa aacaacgatg aactccatta acgacgaaaa tctggaactc 1140 aacctaaaaa agttaggggt aaaatcgaca aatcataatt tattatagtt gggccatttt 1200 tagttggact actttaatat gggccttgta ctaatcatta aacaaaactt ataacatggt 1260 tttttttatt aaaactaaaa cttttcaagc cattttcatt agttttcct 1309 // ID Copia-72_Mad-LTR repbase; DNA; EDCOT; 260 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-72_Mad_; KW Copia-72_Mad-LTR; Copia-72_Mad-I. XX NM Copia-72_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-260 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1683-1683 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 260 BP; 64 A; 53 C; 38 G; 105 T; 0 other; tgtcaacaat agctgctaga cattattggt atagacaata gacttgtaat tattcctcta 60 gctagccatc attactttac tttatagcta gccatcatta ctttgctttg ctttcctttt 120 ctccttattt tcctcttcgg tgttttcctc atgtaatcat catttggctt gtccacttgt 180 taggactagt tgtgtagttt ttggccctct ataagagagg acttccctct tgtaaacaaa 240 taataatgaa gtatattaca 260 // ID Gypsy18-VV_I repbase; DNA; EDCOT; 4844 BP. XX AC AM476928; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy18-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4844 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4844 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 716-716 (2007). XX DR Genbank; AM476928; Positions 13284 18127. XX CC Positions [3704-4201] - Integrase core CC 'GTACA' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 2063..3607 FT /product="Gypsy18-VV_I_1p" FT /translation="MAPLELKELKTQLDELLGKGFIRPSTSPWGAPVLFVK FT KKDDTLRLCIEYRKLNRVTVKNKYPLPRIDDLRTGYHQLRVREDDVSKTAF FT RTRYGNYEFLVMPFGLTNAPAAFMDLMNRVFRAYLDRFVIVFVDDILIYSR FT SLEEHKQHLVTTLGTLRRHQLYGKLDKSEFWLTEVNFLGHVVSEAGIAVDH FT SKVEAIQEWQRPTNVFEVRSFLGLAGYYRRFVEDFSRIAAPMTQLTRKWVK FT FDWNEECENAFQELKQKLTTAPVLTAPISGELFMIYCDASTVGLGCVLMQQ FT GKVVAYASRQLKQHERNYLAHDLELAAMVFALKTWIHYLYGEKFEVYSDHK FT SLKYIFTQKDLNSRQRRWMETLEDYDFALHYHPGKANVVADALSRKSYGQL FT FSLGLREFEMYAVIEDFELCLVQEGRGPCLYSISARPMVIQRIVEAQVHDE FT FLEKVKAQLVAGEIDENWSMYEDGSVRFKGRLCVPKDVELRNELLADAHRA FT KYTIHPGNTKMYQDLKRQF" XX SQ Sequence 4844 BP; 1361 A; 735 C; 1368 G; 1374 T; 6 other; gcatggtatc agagccaagg ttgcgataat accttggggt caatgtttgt gggtgtttat 60 gtgtgttgta atgttatgat ttttgtatgt gttaatcaac aagttaatga ttaattgaat 120 tatgtattgt gagtgtatga aattgaaagt tttgataatt gttgaagttg ctaagtgtgt 180 atatgtgaaa tttattgttg ctcaccttag tagtgtgatt gaattagggt ttgttaaact 240 tgaaatgacg ggaaggacca gaggaggaag atcagagagg aatgaggagt tggagacggt 300 aagagaagaa ctccaagaag taagaagaga gttgagagaa actgttgaat tgatgagagg 360 ccagggttcc aggagagmag gaggtaccca gggccatgag gattcaggcc actcacattg 420 gaggagccgc actgagaggc cagtaatgag ccaaatggaa acaatgaaga ggttcatggt 480 gatgcagcct ccatctttta atggagagcc tagtgctgaa gcatctgagc attggttgag 540 gaggatgaga agaattctgg tgggactgga catacctgag gaaagaaggg taggtctggc 600 aacatatatg cttgtggaca aagctgattt ctggtgggaa tcaatgaaaa gggtgtatga 660 cactgaggtt atgacctggg aggaatttga gagaatcttc ctaggcaagt attttgggga 720 agtggctaag catgccaaga ggatggagtt tgagcacctc atccaaggaa ccatgttagt 780 gctggagtat gagtcacgtt tctcagagtt gtctcgtttt gctttgggga tgatcagtga 840 ggaaggagaa aaggctagga ggttccagca ggggttgagg cctattatta ggaacagatt 900 agtcccactg gcaataaggg attattctga gttggttaag agggctttgt tggtggagca 960 ggacattgac gaaaccaacc aaattcgaga gcaaaagggg gacaaaaaag ggaaacaaag 1020 aatgggggaa agttctcagg ggccacagca gaggcagagg actcagcagt ttgagaggcg 1080 tccctcgttc tacgcaggag aggggcagat tgctcagagg gcggctacta atagagtatg 1140 ttatggttgt ggagcaggag accatttatg gagggcttgc ccattgcgag gcgcacagya 1200 ggctcaacct cagtctcagg gaagttctca gcaacaaccg gtagtgtctt tccagcctcc 1260 ttagtttcag ttgccttact atcagatgcc acaattaccc ccagctgcgc agggaaccag 1320 gacaactact atgaatagtc agacccgttc atctcaaggg tcgaatgcta gaggtagggg 1380 aaggccggca gcaggaagag tttttgcctt gaccccaaca gagccagata aggacgccct 1440 tttggtggaa ggtatgattt tggtatatag tacttgggtg cgtgttttgt ttgatactgg 1500 tgcaactcat tctttcattt ctgcatcttg tgctaatgca ttggggttga aatcggaaag 1560 ggtagagaat ttgttactta ttgagtctcc tatgggtacg aactctagag ttgatagaat 1620 atgcaagggg tgtgttatta ccttggcaga tagagcatta aatgtggatt tgaggatttt 1680 ggatatgact gggtatgatg ttattttggg aatggattgg ttggcagtgt atagrgcggt 1740 tattgattgt catcgccgta ggataatatt ttgtttgcca gagggatttg aggtttgttt 1800 tgttggaggg aagtgtgtta gtttgccttt ttcgtagtcc gatccgtgct atcggtatgt 1860 gttgaggaag ggatcaataa atttcctagc ttgccttcgt ggtaaggaga aagcccagaa 1920 ggacattaca gaaattccag tggtgaggaa gtttcaggat gtattcccag atgagttacc 1980 aggtttacca ccgcatagag agtttgattt ctctattgaa gtatacccag gaactgatcc 2040 tatttcagta tccccttata ggatggcccc tcttgagttg aaagaattga aaactcagtt 2100 agatgaattg ttgggtaagg gttttattcg tccaagtaca tcgccatggg gagccccagt 2160 gttgtttgtg aagaagaagg atgacacact aaggttatgt attgaatata ggaagttgaa 2220 tagagttact gtgaagaaca agtatcctct tccaaggata gatgacttga gaactgggta 2280 tcatcaattg agggttaggg aagatgatgt ttctaaaacc gcttttagaa cgagatatgg 2340 gaattatgag ttcttagtca tgccttttgg gttaactaat gcccctgctg ctttcatgga 2400 tttaatgaac agggtatttc gtgcttactt ggatcggttt gtgattgtct ttgtggatga 2460 catcttgatt tactccagga gtttggagga gcataagcag catttggtga ccacccttgg 2520 aactttgaga aggcatcagt tgtatgggaa gttggacaaa agtgagtttt ggcttactga 2580 agtgaacttc ttaggccatg tggtttctga ggcaggaata gcagtagacc attcaaaggt 2640 ggaagctata caggaatggc aaaggcctac caatgtattt gaggttagaa gtttcttggg 2700 gttggctgga tattatagga ggtttgtgga agacttctct agaattgcag caccaatgac 2760 tcagttgact agaaaatggg tgaagtttga ttggaatgag gagtgygaga atgctttcca 2820 ggagttgaag cagaaattga ccactgctcc agtgttaact gctcctatta gtggagagtt 2880 gtttatgatt tattgtgatg cttctacagt ggggctaggg tgtgtgctaa tgcagcaagg 2940 caaggtggta gcttatgcct caagacaatt aaagcagcat gagcggaatt atctagcaca 3000 tgatttggag cttgcagcaa tggtgtttgc ccttaagact tggatacact atttgtatgg 3060 agagaagttt gaggtgtact ctgatcataa gagtttgaaa tacattttca ctcaaaagga 3120 tctgaactct aggcagagga gatggatgga gacattggaa gattatgatt ttgcccttca 3180 ttaccatcct gggaaggcga atgttgtagc agatgctttg agtagaaaga gctatggcca 3240 gttgtttagc ttggggttga gagagtttga gatgtatgca gttattgagg actttgagct 3300 atgtcttgtt caggaaggac gtggtccatg cttgtacagc atatcggcta gaccaatggt 3360 tatccaaaga atagtggagg cccaagttca tgatgagttt ttagaaaagg ttaaagccca 3420 gttggtagca ggtgagatag atgaaaattg gtctatgtat gaagatggga gtgtgaggtt 3480 caaagggaga ttgtgtgtgc caaaagatgt ggagttgaga aatgaacttc tagcagatgc 3540 tcatagggcg aagtatacca tccaccctgg gaataccaag atgtatcaag acttaaagag 3600 acagttttrg tggagtggga tgaagagaga tattgctcag tttgtagcca actgtcagat 3660 ttgtcagcaa gtgaaggctg aacaccaaag gcctgcagag ttgttgcaac ctttacctat 3720 acctaagtgg aagtgggata atatcactat ggactttgtg atagggttgc caagaactag 3780 aagcaagaaa aatggagttt gggtgatcgt ggaccgtctt actaagtcag ctcattttct 3840 agccatgaaa actactgatt ccatgaactc tttggctaag ttgtatatac aggagattgt 3900 gagattgcat gggatacctg tatctatagt gtctgacagg gaccctaagt ttacttctca 3960 gttttggcag agtttacaaa gggctttggg cacccaactg aattttagca ctgtttttca 4020 ccctcagaca gatggtcaat cagagagagt gatccagatc ttagaagaca tgttaagggc 4080 ttgtgttttg gattttggag gaaattgggc agattactta cctttggcag agtttgctta 4140 taacaacart taccaatcta gtattggcat ggcaccttat gaagcactct atgggagacc 4200 ttgtagatcg cccttatgtt ggatagagat gggtgagagt catttgttgg gacctgagat 4260 tgtccaagag actacagaga agatacaact catcaaggaa aaacttaaga ctgcccaaga 4320 tagacagaaa aattatgcag acaaaaggag aaggcccttg gagtttgagg aaggggattg 4380 ggtgtttgta aaagtgtccc ctcgaagagg catatttcga tttgggaaga aggggaagtt 4440 agcccctagg tttgtgggac catttcagat tgataagaga gttggaccag tgacatacaa 4500 gttaattttg cctcaacagt tgtcccttgt gcatgatgtt ttccatgtgt cgatgctaag 4560 gaagtgtact ccagatccaa cttgggtagt ggacttgcaa gatgttcaga ttagtgaaga 4620 tacttcttat gtggaggaac ctttacgaat tctgtaagtt ggagagcata ggtttaggaa 4680 caaggtgatt cctgcagtca aagtgtggtg gcaacaccat gggatagaag aagccacttg 4740 ggaacctgag gaagaaatga gacgacacta tccgcaactc ttctacgaat tttaaggtaa 4800 gctagtttaa atttcgggac gaaatttctt ttaggggggt agga 4844 // ID DNA9-3_Mad repbase; DNA; EDCOT; 995 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-3_Mad. XX NM DNA9-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-995 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1484-1484 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >97% identical to the consensus. 9-bp TSDs. XX SQ Sequence 995 BP; 309 A; 118 C; 100 G; 467 T; 1 other; gggaaaatta ggttcacatc cttctttttg ttactccatt gattaaaatc ctattcattt 60 tcaatttttg atcaaggtcc ttgggtatta ataacatcat taattatttg aataataaaa 120 tatttttatt tttaaatata ttcctttagt gttaaaaatg ttacaattag tatatttata 180 tttatggcta aattttttat catatatttt tatttttagt ttgtacctat ttttaatttg 240 caaatatttt ttaatttgta ccaattttct tttcattttt aatttgtacc catatattag 300 tttctttttg tgcccatatt ttttaaagtt ttatttgtgt ttgtacccat gtgtataccg 360 tcacgtgaca ttgtatattt aatcaatgat agaaaaatta catatggtat atttatgttt 420 tatgcctaaa ctttgtatca tatatttata tttttagttt gtacccactt ttaatttgca 480 acattttttt ttaaatttgt agtattttct ttttagtttt attttgtacc catgtattaa 540 tttcttttag cgcctatatt tttaaaaatt catttgtact cataattttt aatcttttat 600 ttgtacccta atttatttat aatgtaccca ttcttcttta ttaatgtacc actttgttat 660 atgtgaaatg taccaatttt tttaacacta tggatacatt cttttgccat ttattatttc 720 ttatttttac atagttttta tccatttatt caatcaaaat gtttgaattt ttttattgta 780 accgtttcta atagtattat aatgagggat tttaaattta taggattata aatctcataa 840 aatatcaaac aattaatgtc aaaactataa aaatataaat attaatagta atataatgag 900 gtgtacaaag tcaagggacc ttgatcaaac tttgaatact attaaggttt taatcaaaga 960 atgttaagga ttagggaccg catccaaant atccc 995 // ID SHACOP14_LTR_MT repbase; DNA; EDCOT; 1008 BP. XX AC AC169177; XX DT 24-JAN-2007 (Rel. 12.01, Created) DT 24-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of LTR retroposon, SHACOP14_MT, from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; KW Interspersed; terminal; repeat; SHACOP14_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1008 RA Shankar R. and Jurka J.; RT "SHACOP14_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 56-56 (2007). XX DR EMBL/GenBank/DDBJ; AC169177; Positions 108005 109012. XX CC The LTR exists in moderate copy number in the genome. XX SQ Sequence 1008 BP; 257 A; 167 C; 233 G; 351 T; 0 other; tgttggatat ttgtatgttg gcttcttttt gcctaaaaca aatattcata tcggatgtgg 60 aacacaatgt tctgacatca aggtctggct gtgtgttctg cgcctcgcct tcttttacgc 120 acgcgcctgc gctatttaag gaagtccacg ccaatctatg attggtcaaa cctgcgtgtt 180 taaggagaag atcagaacaa ctttaagttc ctgagattgt gcaagcttct taggaatatc 240 ttttaaggtg atcataatgt ccaattaaat ttgccaagcc tgttatggta agtttcctta 300 tttggacctt tgacttgtaa ctgatcgccc gattgtttct ggagcccgtg attcatgatg 360 atcagatcgc ttcagtataa gagaagagga ctgcaagacc tgaagaccat tcaagccgtc 420 actaagcaaa ttagagtgtc tagggttttg agtcattttt gtgagccttt cgtgtgtctt 480 ttgatacatg ttaaggactg tcacttgagt tgtaattgtg cactactcca gagcttttaa 540 gcaaggagat aggtagttgt aaggctgcac caatgttgtg aaacaaaggt gtatgttgtt 600 attgtgttgg aaggtaactt ctattgtgct ttgataattg aattgtaaat cacatggttt 660 gtgattagag agataaggaa gtgggatggg atctcaagtc taggagttct taggctgaaa 720 tcattacggg tagagtctag gtcatcaagt gcaaacgtgg tttgttgaga gctttttgaa 780 tacaatctac tagtggattt ccttcatggc ttggtagccc ccagagtagg tgacgttgca 840 ccgaactggg ttaacaaatt attgtgtctc ctttcctttc tgtttgttta tgcttttgtt 900 gtttgatgtt agtttaatgt ttcaatcttt tgttaaacat ctgaatctgt ttgattaagt 960 gttgcaacat cgtgtgaaac atcttaagct aacgaagcca gaatttca 1008 // ID L1-6_Mad repbase; DNA; EDCOT; 4832 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-6_Mad. XX NM L1-6_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4832 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1810-1810 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS join(584..2317,2316..3167,3171..3851,3844..4656) FT /product="L1-6_Mad_1p" FT /translation="MMGMRSVNIFRGGCLVLDDVGSLPSQSVLLLSMNIVV FT WNSRGSGCTKFQNNVTNLKQNHKMEILAICKPRISGTRAFYVVKSLGFPSF FT EIVDANGFSRGLWLLWDNSKVHIDVIGTTDQSISACVRGAGFNPWLFTFIY FT ASPCIAKRRKLWDYLNGVADCHQMPWMLAGDFNEMLEVGDKLGGAPLCRIK FT DFKSWVDTNSLLDLGYVGPKFTWTNKKTLERIDRGLCNMAWRNLFPEACVF FT HLPRTKSDHCPLKISLQSXHVPNPLQRPFRFEAMWLRHDTFDELIAENWGN FT SHGSAMDKTCALVEPLKRWNIHVFGHLKQKKKKLLGRIAGIQKALCRGPNN FT FLLNLERELISEFNEILNQEAVFWHQKSRLKWLQDGDRNTKFFHLTMIVRR FT RRNRIEGLKNDQGEWIVDPDDLKSLVVEYFQTLFSHGQWSRQVTSLPKLFP FT SIHLDDIGSLNREIDHAEVKDSLFSIGGTKAPGIDGFPACFYQAQWGRCAS FT DIVDMVKIAFQTHRLPHGLNSTLIALVPKIENPQRMLNFRPISLCCTLYKV FT ITKIIVARLRPLLPELISPNQASFVPGRHITRDNILIAQEILYKFRKSKGK FT KGFLAWKIDLSKAYDRLNWSFISGVLYEIGLPESLIHLIMDCISSVKYQVC FT VNGELTESFTPSNGIRQGDPLSPYIFVLCIEKLSHIITNEVNSGQWKXVKA FT SQFGPGVSHLFFADDLMLFADATPKQARVMKRCIXKFCLASGQAVNFEKSM FT LYCSPNTCANEAREISAICGSPLSDNLGNYLGMPLIQCRVSKSTYKGVIDK FT VQSRLSSWKSNVLSMAGRATLIQAVTSAIPVYAMQTTKLPVSVCEHLDKLN FT INFFWGDSQKKKIHLCQWNLVCRPKCVRGVGLKKTAEMNQALLAKIGWRIH FT AKDTGLWAKIYEAKYLQGNSILDTKLHEKSDCSYTWKGILYGTDLLRKGMK FT WRIGKGDGVKFWKDPWVLNDPLINYVDANNFPEEDFPISYFLRDGWWDVSK FT LRYAFPENLVQKIISWPAGTIGAGEDKLIWGCTSNGTFTIKTAYNVLYDCE FT RSLFFIGLGFGLSKSPPNLNSSSSSLVKVSYYVTTNEQRTKRNLTVDSSCN FT LCSWPLETITHILRECSRAECIWDILRIPSQLRNTFNLDLKAWLMANVTSK FT VMWSDKIAWNCLFVFACWYIWKWRNHQIFDVDFSLPSDPKKVIVGAASEWM FT DSLLKIDKPPSRMHVMLKWEPPIFGWHKLNVDGSRKMVSSNIGAGGILRDH FT NGDCLGGFSINLGQGQIIXAEVWGLYFGLQLAIEKGISKLIIEMDSSSAVL FT LLNQSVQDTFHPLATLLKSCRDLMRRIEHCELKHIFREVNNVADQLAK" XX SQ Sequence 4832 BP; 1283 A; 896 C; 1052 G; 1582 T; 19 other; ccatctcttt tgtgagaact cccctcatct gtgagcttct tcstgctgtt ccttttcccg 60 gtgagccctc aacccwtctc ctcatctccc ccagatctgc cctctcgatc caacctwctc 120 tcatgactct ccctcgttwg ccmttttccc ctattctttc tagttcctgc tttctataca 180 ktgttcttgk cccctctaam aatctcctcc ccawatccca gtcaaatcat mcatctcttc 240 caccttttca agcacacmtt cctattaaaa tatttccttt ttgcttgtgg agwtttttct 300 cctctctccc ttgcaataaa ttctctctcc tcagtgaaag caaactagcc tcctactaat 360 cgaaggaaaa tccttctttc aatccttgtt gctatgcctc agttgttgat gcagatggtt 420 gcggcctagt aacccatctg agttaatttg gtaattcgtc ccaaatttmt gtaattttcc 480 acaattttgt taatctgtac ctgcaaaatt ctagggtttt ctgtgttctt gattttctgg 540 gtatcctggc ctttgatttg tcgggtgata gtgtcgaatt tttatgatgg gtatgcgttc 600 tgtcaacatt tttagaggtg ggtgcttggt attagatgat gttggctctc tgccttctca 660 atccgtatta cttttaagca tgaatatagt tgtgtggaat tctagaggat ctggttgcac 720 caaatttcag aataatgtta ctaatttaaa gcagaaccac aaaatggaga ttcttgcgat 780 ttgtaagcct agaattagtg gtacgagagc cttttatgtg gtcaaatcgt tgggctttcc 840 ttcatttgaa atagtggatg ctaatgggtt ctctagaggg ctgtggcttc tttgggataa 900 cagcaaggtt catattgatg tcattggcac cactgatcaa tccatctcgg cttgtgtgag 960 gggagctggt tttaacccct ggttgtttac gttcatttat gctagccctt gtattgcgaa 1020 gagaagaaaa ttgtgggatt accttaatgg tgtagctgac tgccaccaaa tgccatggat 1080 gctagcaggg gattttaatg aaatgttaga ggtgggtgat aaactaggtg gtgctcctct 1140 ttgtaggatc aaggacttta aatcttgggt ggatacaaat agtctgctgg acttgggata 1200 tgttggtcct aaattcactt ggactaacaa gaagactcta gaaagaattg atagaggctt 1260 atgtaatatg gcttggagaa acttattccc agaagcwtgt gttttccact taccacgtac 1320 taaatctgat cattgtcctc tcaaaatcag tcttcaatct wctcatgtcc ccaatcctct 1380 tcaaagacct tttagatttg aggctatgtg gcttaggcat gacacatttg atgagcttat 1440 tgcagaaaat tggggtaatt ctcatggttc tgccatggac aaaacttgtg ctctagttga 1500 gcccctgaaa agatggaata ttcatgtctt tgggcactta aagcagaaga agaagaagct 1560 ccttggacgc attgctggta tccagaaagc actgtgtaga ggcccaaaca attttcttct 1620 caacttggag agggaattaa tttcagagtt caacgaaatt ttaaatcagg aagctgtctt 1680 ctggcatcaa aagtctagat tgaaatggtt acaagacggt gatcgtaata ccaaattttt 1740 tcatcttacc atgattgtga gaagaaggag aaatagaatt gagggactga agaatgacca 1800 aggtgaatgg attgtagacc ctgatgacct gaagagtctt gttgtggagt actttcaaac 1860 actcttctct catgggcaat ggtctagaca ggttacttct ctacctaaac tctttccttc 1920 tattcatttg gatgatattg gatcacttaa tagagagatt gaccatgctg aagttaagga 1980 tagccttttc agtattggag gtactaaagc accgggtata gatgggtttc ctgcttgctt 2040 ttatcaagct caatggggca gatgtgcaag tgatattgtt gatatggtta aaatagcatt 2100 tcaaactcat agattgcctc atggtttgaa cagtacgtta attgctcttg tgcctaaaat 2160 tgagaaccct caaaggatgc tgaattttag accaatcagt ctatgttgca ctttatataa 2220 ggtcataact aagattattg tagctaggct caggcctctt ctccctgaat tgataagccc 2280 aaatcaagct agttttgtgc ctggcagaca tataacgtga taatattctc attgcacaag 2340 agattcttta taagtttaga aagtccaagg gtaagaaagg ttttttggct tggaaaattg 2400 atttgtccaa ggcttatgat cgcttaaact ggagctttat cagtggtgtg ctctatgaga 2460 ttggcctgcc tgaaagtttg attcatctta ttatggactg catatcctct gttaaatacc 2520 aggtctgtgt taatggtgaa ttaactgaga gctttacgcc tagtaatggt atcaggcaag 2580 gggatccttt gtccccttat atttttgtac tttgtattga gaagctgtct cacattatta 2640 ctaatgaagt caattctggt cagtggaaac mtgtcaaagc ttctcagttt ggtcccggcg 2700 tctctcacct ttttttcgca gatgatctta tgctwtttgc agatgcaaca ccaaaacaag 2760 ctagggtgat gaagagatgt attgamaaat tctgcttagc atctggccaa gcagtcaact 2820 ttgagaaatc tatgttgtat tgttctccta atacttgtgc aaatgaggct agagaaatta 2880 gtgctatttg tggatctcct ttatctgata atcttggaaa ttatttgggg atgccattga 2940 tccaatgtag agtctctaag tcaacttaca agggtgtgat tgataaagtt cagagtagac 3000 tttcttcttg gaagagtaat gtcctttcaa tggctggaag agccacctta atccaagcag 3060 tcacctctgc aataccggtg tatgctatgc aaaccactaa gcttccagtt agtgtttgcg 3120 agcatttgga taagttgaac ataaacttct tttgggggga ctctcagtag aaaaagaaaa 3180 ttcatttatg tcaatggaac cttgtttgca ggcctaagtg cgttagaggt gtgggattaa 3240 agaaaacagc agagatgaat caagctttgt tggctaaaat tggatggaga attcatgcta 3300 aggatacagg tctctgggca aaaatctatg aggcgaaata cttgcaaggg aactctattt 3360 tggatactaa attacatgag aagtctgact gctcctacac ttggaaagga attctttatg 3420 gaactgactt gttgcgcaaa ggaatgaaat ggagaattgg gaaaggtgat ggtgtcaagt 3480 tttggaaaga cccttgggtg ttgaatgatc ctttaattaa ttatgttgat gctaataact 3540 ttcctgagga ggactttcca atctcttatt tccttcggga tggttggtgg gatgtcagta 3600 agctaagata tgcttttcca gaaaacttgg tccaaaaaat aatcagttgg cctgctggga 3660 ctattggtgc tggagaggac aaacttatat ggggatgcac ttcaaatgga actttcacca 3720 taaagacggc ctataatgtg ttatatgatt gtgaaagaag cctgtttttt attggtttgg 3780 gatttggact ctcaaaatcc cccccaaact taaattcttc ctctagctca ttggtcaagg 3840 taagttacta ctaatgagca aagaaccaaa agaaacttaa ctgtggattc ctcttgcaac 3900 ctttgttctt ggcctttgga gaccatcaca catattctaa gggaatgtag cagagctgaa 3960 tgcatttggg atattctacg gattccttct caattgcgca atacttttaa tttggacttg 4020 aaagcctggt tgatggctaa cgtgacgtcc aaggtaatgt ggtctgacaa gatagcatgg 4080 aattgtttgt ttgtctttgc ttgctggtat atctggaaat ggaggaacca ccagattttt 4140 gatgtggatt tctccctccc tagtgatcct aaaaaggtta ttgttggagc tgcatctgaa 4200 tggatggatt cccttctaaa aattgataaa ccaccttctc ggatgcatgt tatgttgaag 4260 tgggagcctc ctatttttgg ttggcacaag ttgaatgtgg atggatctag aaaaatggtt 4320 tcgagcaaca tcggtgctgg aggaattctc cgtgaccaca atggtgattg cttgggaggt 4380 ttctctatta atctagggca agggcagatt atagawgctg aagtttgggg tttgtatttc 4440 ggacttcagc ttgctattga aaaaggcata tctaagttaa tcattgagat ggactcttcc 4500 tctgctgtat tattgttgaa ccagtctgtg caagatactt ttcaccccct tgctaccctt 4560 ttgaagagtt gtagggattt gatgagacga attgagcatt gtgagctaaa gcatattttc 4620 agggaagtga acaatgttgc agatcagcta gccaaataga gctacaattt ggaccttggg 4680 ttgtattctt ttcagtttcc tccccaatgg cttatgcaac atctaatgga tgatcttgta 4740 ggtgccccta tgggccgctc tattgttatt aatgctatgt attagttcgt ctggggtgtc 4800 ttcaccccct ctattcacca aaaaaaaaaa aa 4832 // ID ATLANTYS_LC_I repbase; DNA; EDCOT; 12848 BP. XX AC . XX DT 20-SEP-2005 (Rel. 10.09, Created) DT 15-APR-2011 (Rel. 16.04, Last updated, Version 2) XX DE ATLANTYS-like LTR retrotransposon from Lotus corniculatus, DE internal consensus. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW reverse transcriptase; RNase H; internal portion; gag-pol; KW Atlantys; ATLANTYS_LC_I. XX NM ATLANTYS_LC_I. XX OS Lotus corniculatus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RP 1-12848 RA Gentles A. and Jurka J.; RT "An ATLANTYS-like LTR retrotransposon of the legume Lotus RT japonicus."; RL Repbase Reports 5(9), 235-235 (2005). XX DR [1] (Consensus) XX CC This retroelement is similar to various Gypsy, but shares the CC characteristic, with other ATLANTYS sequences, of putative coding CC ORFs of unknown function on the complementary strand. The coding CC strand contains two overlapping ORFs for gag-pol/RNaseH, and CC reverse transcriptase. The ORFs on the complementary strand are CC separated by ~600 bp, and occur in the position opposite the CC normal env gene. They putatively encode sequences of 447 aa and CC 763 aa. The 763 aa ORF is similar to predicted CC aminotransferase-like proteins in rice (Oryza sativa). The CC shorter ORF shows no similarity to known proteins. There are 6 CC full-length copies in currently available sequence, which are CC >96% similar to the consensus. XX FH Key Location/Qualifiers FT CDS 117..3746 FT /product="ATLANTYS-I_LC_1p" FT /translation="MHLRSGKTISMASNRGRTSPQGSNVGNQGSPGGSSGN FT NNEEVSTGMGHGTTMPTQNVAISAVAEMPVSTSVQAQIVPTXTRENMPYGM FT PTSMMQGIQGTYSTFPENVPPFXIPPFGANGTMLNLGSRVSPXIPGSSSQI FT YLSTGMNTGSLQAIRQQVDDSNHEMVNMLSRQIGELINPVLQNNNANNQHL FT ARQMDRLATALGAPVEIQXAPGINQIPLPNHVPAPVRYQXPQHQEMRANPL FT YEAVQPPLQNVYMVNREEHADGVLERIRHQNAGGQQNVAAVVEQLLNQHGF FT NVGFANRPHFVSAFTEEVLESELPRGWKVPKFTKFSGDSGESTVEHIARYQ FT IEAGDLAINENLKMKYFPSSLTKNAFTWFTTLAPRSVHTWAQLERIFHEQF FT FRGECKVSLKDLASVKRKPAESIDDYLNRFRMLKSRCFTHVPEHELVVLAA FT GGLEYSIRKKIDTQYIRDMSLLADRVRHIELLKAEKSEERAKTTKWPKKEK FT VAYIDADSVCQNPCVYREVPADVDLNDVNLAELQPGDPYVCKALKPRENKL FT GEENPKNTIPAVKTYTFDVTKCDAIYDILVSDGLLVVPKDQKLPSPEQRKG FT KKYCKYHNFFGHWTSQCVRFRDLVQGALDSGRLKYDEKAKSQMKIDSDPLQ FT VAEANYVEPFYIGMVDISEKLNLGLTLEEAKEENTAVEEPDVVKEVSLEEV FT YPKAGETLVEFLSRSKDXEKEVMLCPRCSAVFDKSAAKAYQDSEMKRHYQX FT KMPVSRRLKYPHEEWVERDQELDGHKGQXSRIKDKTYVPDAGLPKNQWFRP FT APPRPKPYPKWQKIDLGQGSSYINNSRVSRXYSYGSGNYYAPEQMTRTQFR FT RFLRKRKAERERGGKFRSLWDIKPEDNPRNEPSVASIINQLDHAIKQGTXV FT PPNPAKEKGKDVXEDEDEDMLDDFDDSDGEDLNIICIVSILPAEFDRISEV FT TEXEEDYYDEEEPDDNPLCYYVMQKGSVEDERAIFQRPTEQMKSHLKPLFV FT WAKVDEKGVNKVLVDGGATINLMPKFMLKKLGKTEADLIPHDMVLSDYEGK FT TGSSLGAIMXNITVGTVARSTLFIVVPSKANYNLLLGREWIHGVGAVPSTL FT HQRISIWKADGVVENVQADQSYYLAETGYVXKKNFEKSLATIAPLDTVAXQ FT YFNPYSEYSVTLDPIRGLNLNEAYKPDAMSGWHSDEEKDATTEWQNXVKDD FT " FT CDS 3682..7314 FT /product="ATLANTYS-I_LC_2p" FT /translation="VDGTAMKKRMPXLSGKMXLKMINSSLARISAYAAENR FT IRTALEAARIAKEMATDEANASILPVEMTSQEEAXXXKDNTCIXXNEQSVD FT ECEFEDLCNLRLDCIYDDGPLGFEKPVVDMSKKMEAQDPLEEVDLGDGXEK FT RPTYISALIDPELKDXMVKLLKEFKDCFAWDYDEMPGLSRELVELKLPIKE FT DKKPVKQLPRRFHPDVLVKIKEEIERLLRCKFIRTARYVDWLANVVPVIKK FT NGKMRVCIDFRDLNAATPKDEYHMPIAEMMVDSAAGHEYLSLLDGYSGYNQ FT IFIAEEDVSKTAFRCPGALGTYEWVVMPFGLKNAGATYQRVMNTIFHDFIE FT TFMQVYIDDIVVKSPSRDDHLSHLRKSFERMRKYGLKMNPLKCAFGVIAGD FT FLGFVVHKKGIEINKNKAKAILDTSPPTSKKQLQSLLGKINFLRRFITNLS FT EKTKSFSPLLRLKKEDVFRWEAEHQKAFDELKKYLSNPPVMVPPIKGRPMK FT LYISATDETIGSMLAQEDEDGNERAIFYLSRVLNSAETRYTMIEKLCLCLY FT FSCVKLKYYIKPIDVMVFSHYDIIKHMLSKPILHSRIGKWALALTEYSLTY FT TPLKAIKGQAVADFLADHTMPREIITYVGIQPWKLYFDGSSHKNGTGIGMF FT IMSPQGIPTKFKFRIKSNCSNNEVEYEALISGLEILLALGAKNVVVKGDSE FT LVVKQLTKEYKCVSEHLAKYYVKASNLLAKFDEAGIGHVPRIENQEANELA FT QIASGYMIDRLKLTELIKIKEKLSPSDLDIMVIDNLTPDDWRKPIVEYLQN FT PVGSTDRKVKYRALSYTILGNELFKKNVDGTLLKCLSEDDAFIAVSAAHDG FT LCGAHQAGAKMKWILFRQGLYWPTIMKNCIEYAKGCQDCQKHSGIQHVPAS FT ELHSIIKPWPFRGWAIDLIGEIHPASSKQHKYIIVAVDYFTKWVEAIPLQN FT VTQETVIEFIQNHIVYRFGLPESITTDQGTVFVGRKVAAFAESWGIKLLTS FT TPYYAQANGQVEAANKVLISLIKKHVGRKPKSWHESLSQVLWAYRNSPREA FT TGTTPFRLAYGQEAVLPAEVYLQSCRIQRQEEIPSDVYWNMMLDEMVNLDE FT ERLLALDVLTRQKDRIAKAYNKKVRDRSFITGDYVWKVILPMDKKDRVYGK FT WTPSWEGPFTVEKTLPNNAYVIKELGNQSQCVTINGKYLKAYKPMLHECKI FT E" FT CDS 12544..10253 FT /product="ATLANTYS-I_LC_4p" FT /translation="CSFTSDYSLAYKYAIVGLLQALPFFQSLTLSNXQAFE FT HSNFCLILLVTAFHRLVSVFPVYSLNISMASGSGSDNVIPLAAACEMNEAK FT RTPIPDPPYDVEKRAIWKSQVFIPISVNGNLRAILGPLKKAKKGRPNSLPE FT DYEHFHPSIRGDELILAFQPSYRFPFLKDPKRAFRSAPPNPSAGEGAYLRW FT LNRVEASKSGHWKVTGIFDLIQLSRSPITYNPAMLLSSLFFWERSTNSFHV FT PFGMLSPTLLDVAAITGLWVVGDDYHSSAAPTDPIAIPTDNIAFSKFIKDH FT YVENGEVSDAEHVAFLLYWLSAYVFCTKSLRIPAKLLPLANLLHEGRIIAM FT ARLVLGNLYQMINEAIADIRDPKVASLNAAGPFWLLQLWMNAVFEPSLPAK FT NSPPVVSNTRIDAFRLEALTPPYDASTFEFDFKKYFTMFFELKRFRSSFAP FT YHKPSYGPRWLRNSYPNLPGSENLSQHQVELWQTILSPRVLTINFASNDFT FT LCGYNPQLVSRQFGLSQDLPNTLFDKSLILYPGTITKRSVFDTTIGYYNNE FT ELLGLSPFSFTPSFYVTQAFKAWWSAYWHDISTPIEDCFQRITNVFLLQRQ FT APKKTKGMHTSEINAFQQFFGVVYFPGPRLQETVAKAAQVLRRMWEAKAKK FT TRLSLPSDEDGLSFIIRKTGFRFPPLPTCKYALAFPVVLPKWVDHVSIKNF FT YHSALPPRKRVTWTKRYLWNYPLHVPVEIFNHISIKSLIGQGNHFDLASLR FT YLWLNPPLFSFCS" FT CDS 9746..8391 FT /product="ATLANTYS-I_LC_3p" FT /translation="GESLXHILFQFASFSSFSIIFTXILQRVGMSKMAVPR FT ATWFSSKPPPIALSSSSSGLESSSSSLDSTESDPVWDKLTFYFNSKPIAWQ FT HPGCEPYYTKECRDNLSNFPPQDMQNLPSPAREEXXPHDEVQGGEDPIIQP FT DQVIGVMPPPKADVLASAHSEPSPRQLQTSPQQPRLSPQRFQQDARAALIS FT PHAKGGSASSKTAASSHTSSERLSALLVEDPLSIFQSFFDGTLDLESPPRQ FT AEIAETAQSGGVPDDSRIEAALVKLKGLVFDTGFIGSVRVTPQLGQEVKEL FT LAFLLSQQLDQIQADALVELQTLVVDXVATLDKAIAVEQSIETKKAQVVSN FT TNGLLPAKEEALKLTARRTLIAAELSSVDARLDELHREVARLEKQKAMLID FT EGPAVNSRLNALAAECTGVMLSTSQLSKEVAAEQRMKQSLDCRIAAAGVQL FT EAFKSRI" XX SQ Sequence 12848 BP; 4006 A; 2657 C; 3096 G; 2975 T; 114 other; aattggcaca cctggtggga ccatttttgt gaaaactaag ttttacagaa gcgttttgtg 60 tgttttgttt gytgcatgct atttggtatt tgctacttgc cttgattgtg atttatatgc 120 acctgagaag tggtaagact ataagtatgg caagcaatcg aggaagaacy tccccccaag 180 ggtctaacgt gggcaatcag ggtagycccg ggggaagtag tggtaataat aatgaagaag 240 tgtctactgg aatggggcat ggcaccacta tgccaaccca gaatgtrgca atttctgcag 300 ttgcagaaat gcctgtatct acatcagtac aggcacaaat tgttccaaca rttacgaggg 360 aaaacatgcc ttatggtatg cctacgtcta tgatgcaagg catacaaggc acgtattcga 420 cgttccctga aaatgttcct ccattyrgca tacccccttt tggggcaaat ggaacaatgc 480 taaatttggg gagtcgagtt agccctycta ttcctggatc tagttcacaa atttatttat 540 ctacaggtat gaayactggt tcacttcaag ccattaggca gcaagtagat gatagtaacc 600 atgaaatggt taacatgyta tctcgacaga taggtgagct aatcaaccct gtgctccaaa 660 ataataatgc caataatcag catttggcac gacagatgga tcgtttggcg acagccctgg 720 gggcaccagt cgaratccaa ycggcrccag ggattaacca aatcccgttg cctaaccatg 780 tccctgcccc tgtgcgctat caggygccgc aacaccaaga gatgagggca aaccctttgt 840 acgaggcagt gcagccrcca ttgcaaaatg trtatatggt aaacagggaa gaacacgctg 900 atggtgtgct agaaagaatt cgacaccaga acgctggggg gcaacaaaat gttgctgctg 960 tggtggagca aytgttgaac caacatggtt tcaacgtggg tttcgcgaat agaccccatt 1020 ttgtgtcagc ctttacagag gaggttctcg aatcagaact tcctcgaggc tggaaggtcc 1080 ccaaattcac taagttctcg ggggattcag gagagtccac tgtagaacac atagccaggt 1140 accaaatcga agcaggagac ytagccatca atgaaaattt aaaaatgaag tacttcccga 1200 gttctttaac caagaatgca tttacctggt tcaccaccct cgctcctagg tcagtccata 1260 catgggcyca gttggaaaga attttccatg aacagttctt taggggagag tgcaaagtaa 1320 gtttgaagga tctggctagt gttaaaagaa agccagcaga gtctattgat gattacctaa 1380 acaggtttag gatgcttaaa tctcgatgtt tcacccatgt ccctgaacac gagctagttg 1440 tcttagccgc tggtggtcta gagtattcya ttagaaagaa aatcgacact cagtatattc 1500 gagatatgtc tttactcgca gatagagtga ggcacatcga attactaaag gccgaaaagt 1560 ccgaggaaag ggccaagact actaagtggc caaagaagga gaaggtagcg tacatagacg 1620 cggattcagt atgtcaaaat ccatgtgtct atcgagaagt ccctgcagac gtcgatttaa 1680 atgatgtcaa tctggctgaa cttcagccag gggatcctta tgtttgtaaa gcattgaaac 1740 cacgtgaaaa caaacttggg gaggaaaacc ccaagaacac gattcctgct gtgaaaactt 1800 atacttttga tgtgaccaaa tgtgatgcaa tctatgatat acttgtgtct gatggtttgc 1860 ttgtggtccc taaagaccaa aaacttcctt ctcctgaaca aaggaagggg aagaaatatt 1920 gcaaatatca caactttttt ggtcattgga cctcacaatg tgttcgtttc agggatcttg 1980 tgcagggggc attggactcr ggaaggctca agtatgacga aaaagccaaa agycaaatga 2040 agattgactc cgacccactg caggtagctg aagccaacta cgtggaacct ttctacattg 2100 gcatggttga catttctgag aagctgaatc tgggcctgac actcgaggag gcaaaggagg 2160 aaaacacggc tgtcgaagaa ccagacgtcg tgaaagaggt gagcytagar gaggtttacc 2220 ccaaggcwgg rgaaactctt gtcgagttty trtcmcgaag caaagatrgc gagaaagagg 2280 tcatgctktg ycctcgatgy agygccgttt tcgacaagtc agcagcyaaa gcctatcaag 2340 attcwgarat gaaraggcat taccagarca aaatgcctgt gtctagaagg ttgaagtayc 2400 cccacgagga gtgggttgag agrgatcaag aactcgatgg ccayaaaggc cagargtcaa 2460 gaatcaagga caagacttat gtccctgatg ctggtttgcc aaaraatcaa tggttyaggc 2520 cagcaccycc aagrccaaaa ccatacccca agtggcagaa aatcgactta ggccaggggt 2580 catcttacat caacaattcc cgygtgtcgc ggarctaytc ctatggctct gggaaytayt 2640 atgctcctga rcaaatgacc agaactcart tcagacgttt cctgaggaaa agaaaagctg 2700 agagagaaag aggtggcaag ttccgttcat tatgggacat aaagccagaa gacaaccctc 2760 gcaatgaacc tagtgtggcg tcgattatca accagctcga ccacgccatc aaacagggaa 2820 cartygtgcc accaaacccg gccaaagaaa aagggaaaga tgtggyygar gatgaggatg 2880 aagacatgct cgacgatttc gaygacagtg atggggaaga tctyaacatc atctgcatag 2940 tgtctatctt acccgctgaa ttcgacagaa tctcrgaggt caccgaaart gaagaagact 3000 actacgacga ggaagagcca gatgacaacc ccttgtgcta ctacgtgatg caaaaaggat 3060 ccgtcgaaga cgaaagagct attttccaga ggccaacgga gcagatgaaa agccacttga 3120 agccgttatt cgtttgggcc aaagtcgacg aaaaaggagt caataaagtt cttgtcgacg 3180 gaggggccac ratcaattta atgcctaagt ttatgctcaa gaagctaggc aaaactgaag 3240 cagacytaat ccctcacgac atggtccttt ccgaytatga agggaagaca ggttcttctt 3300 taggagcaat tatgwtgaac ataaccgtag gaacggtrgc ccgttccaca ttgttcatcg 3360 tggtgccctc aaaagccaac tacaacytgc tattggggag agaatggatc cacggcgtgg 3420 gggcagtgcc ctcaactctg caccaacgta tttccatttg gaaagcagat ggagtcgtcg 3480 agaacgtgca agcagatcag agctactact tagcggagac aggttacgtc rgcaagaara 3540 atttcgaraa gagtttagcc acaattgctc ctctagacac agtggcywct caatatttca 3600 acccgtaytc rgagtactcg gtgacgttgg atcccatcag gggtttaaac cttaatgaag 3660 catacaaacc tgatgccatg agtggatggc acagcgatga agaaaaggat gccacwactg 3720 agtggcaaaa tgakgttaaa gatgattaat tcgagcctag ctcgaatttc ggcttacgca 3780 gccgaaaaca gaataaggac ggccttagag gccgcaagaa tagccaaaga aatggctact 3840 gacgaagcca atgcctcaat tctkcctgtc gaaatgacat ctcaggagga ggcaamarca 3900 magaaggata acacgtgcat arrrraaaac gagcagagtg tcgatgaatg cgaattcgag 3960 gacctttgca atttgaggct agattgcatc tacgatgacg gcccattagg cttcgaraag 4020 ccagtggtcg acatgtccaa gaaaatggaa gcacaagacc ctttrgaaga agtggacctg 4080 ggtgatggct yagaaaagag gccaacatac atcagtgctc ttattgaccc agaattaaag 4140 gatargatgg tgaaattact caaggaattc aaagactgtt tcgcttggga ttacgatgaa 4200 atgcctggcc tcagtcgaga attggtggaa ttgaagttac ccatcaaaga agacaagaaa 4260 ccagtcaagc aattacccag gaggttccat ccagatgtgt tggtraaaat caaggaagaa 4320 atygaaagrc tccttaggtg taartttatc agaacggctc gatatgtgga ctggttagcc 4380 aacgtggttc cagtgatcaa raagaacggc aagatgagag tttgcattga ttttcgagat 4440 cttaacgctg ccactccaaa agacgagtat cacatgccta ttgctgarat gatggtggat 4500 tcagctgctg gtcatgaata cttaagcttg ttggatggtt actcaggcta caaycaaatc 4560 ttcatagcag aagaggatgt gtcgaaaaca gcttttcgat gtcctggtgc cttagggaca 4620 tacgagtggg tggtcatgcc attyggattg aaaaacgctg gcgcgaccta ccaaagggta 4680 atgaatacca tttttcatga ttttattgaa actttcatgc aggtttacat tgatgatatt 4740 gtggtaaagt ccccatcaag ggatgaccat ttatctcatc traggaaatc ctttgagagg 4800 atgaggaaat atggcttaaa gatgaatccc cttaaatgtg cttttggtgt tattgcaggt 4860 gattttttgg gttttgtggt gcacaaaaag ggcatcgaga tcaacaaaaa taaagctaaa 4920 gccattctcg acacaagtcc accaaccagc aagaagcaac tacaatcgtt attggggaag 4980 attaacttcc taaggagatt cattaccaac ctcagtgaaa agaccaagtc attttctccg 5040 cttcttcgac taaaaaagga agatgtgttc cgctgggagg cagagcacca aaaggcattc 5100 gatgaactca agaagtactt gtccaatcca cctgtaatgg taccacccat caaggggagg 5160 ccaatgaagc tgtatatttc tgccacagat gaaaccatcg ggagcatgct ggctcaggaa 5220 gatgaagatg gcaacgaaag agccatattt tatttaagta gggtgttaaa tagcgcagaa 5280 actcgataca ctatgatcga gaaattgtgt ctatgcctgt acttctcttg tgtaaagttg 5340 aaatattata taaagccaat cgatgtaatg gttttttctc attatgatat aataaagcac 5400 atgttatcca aaccaatctt gcatagtcga attggtaaat gggctttggc cctaaccgaa 5460 tattcattaa cttacacccc attaaaagcg attaaagggc aggcggttgc tgatttcttg 5520 gcagatcaca ccatgcctag agagatcata acctatgtgg gcatacagcc ttggaagtta 5580 tatttcgacg gttccagcca taagaatgga actggaatcg ggatgtttat catgtccccg 5640 cagggcatcc ccactaaatt caaatttagg atcaagagta attgctcgaa caatgaggtc 5700 gagtatgagg cactgatatc aggcctcgag atcttgctag ctctcggggc aaagaatgty 5760 gtcgtgaaag gggattctga gttggtagta aagcagctta ccaaagaata caagtgcgtt 5820 agtgagcatc tagccaaata ttatgtgaaa gcaagcaatt tgttggctaa attcgacgaa 5880 gctggaatag gacatgttcc tagaatagag aaccaagaag ccaatgaatt ggcgcagatt 5940 gcttctgggt atatgataga tagactaaag ttaacagagt taatcaagat caaagaaaaa 6000 ctgagtcctt cagatctcga cattatggtc attgataatc taactcctga cgattggaga 6060 aagccaattg tcgaatacct gcagaaccca gtggggtcaa ctgatagaaa agtcaagtat 6120 agagctctaa gttacaccat tttaggcaac gagttgttya aaaagaacgt cgacggcaca 6180 ctgttgaaat gcttaagcga agacgacgca tttatagcag tatcagctgc tcacgatggc 6240 ctgtgtggtg ctcaccaagc aggggccaaa atgaaatgga ttctatttag acaaggtttg 6300 tattggccaa ctatcatgaa aaattgcatc gagtacgcaa aaggttgtca agattgccaa 6360 aaacactcag gaatccagca tgtgccagct agtgaattgc actctattat caagccatgg 6420 ccttttaggg gatgggcaat agacttaatt ggcgaaattc acccagcttc atcaaagcag 6480 cacaagtata tcattgtggc agtcgactat ttcactaaat gggtcgaagc catcccacta 6540 caaaacgtaa cacaggaaac ggtgatcgag ttcatacaaa accacattgt atatcgattt 6600 ggattgccag agtccattac aacggaccaa ggcacggtgt ttgtgggacg caaagtggca 6660 gccttcgcag aatcttgggg catcaagctt ttaacctcga ccccttacta cgctcaggct 6720 aatggccaag tagaagcagc caacaaagtc ctaataagct tgatcaagaa gcatgtgggt 6780 cgaaaaccaa aaagctggca tgaatcttta agccaagtcc tatgggctta ccggaattca 6840 ccaagggaag cgacaggaac gacgcctttt cgactggcct atggccaaga agccgtattg 6900 cccgcagagg tatacttgca atcatgtcga attcaaaggc aagaagaaat cccaagcgac 6960 gtttactgga atatgatgct agatgaaatg gtcaacctcg acgaagaaag gctcttggca 7020 ctagacgtct taacaaggca aaaggatcgc atagctaaag catacaacaa aaaggttaga 7080 gatcgatctt ttattacagg ggattatgtg tggaaagtta ttctcccaat ggataaaaag 7140 gatagagttt atggaaaatg gacccccagt tgggaagggc catttacagt cgagaaaacg 7200 ttacccaata atgcttacgt gattaaggaa ttgggcaatc agagtcaatg tgttacgata 7260 aatggcaagt atttaaaagc atataagcca atgttgcacg aatgtaaaat cgaatgaaac 7320 atgaacgata aaattgccaa attatattca ttaatcgaaa aacgttacaa gtatggcaaa 7380 atacaagtaa aactagaaac ctaaaaagga aaaatggctc tgtatccgtc atatttagct 7440 tgcatgggtg ctaatcgacc caccagcgcc accatctggc cctcaagtcg agccttcttt 7500 tgacgagcaa ccaggtcttc aagggaggct gcaagaatcg cgacaactga ctgaacaaga 7560 ccttcaggat cttgctgatc caaagaggcc tggagaaaat cgaatttctc cctccactca 7620 tctatttggt gttcttgaaa gaacaccatt actgaaagtt cccggaactc ttcaaacaga 7680 ggcttggcct ccaagagaag cccctggaac tcctgaagag gaattctaac gcgcgcaacg 7740 attggcctat gaagcagttg atcaatgagc cctaaaagct catcaaggcc agcagaggag 7800 tcatacaggt tctggaaaag gttctcttgg aaagccaagt ccttgatacg acgaagaatt 7860 agtctgctat ccatggtgaa gaatgaaagg ttcttggatc gcagaaagaa gggaagaatg 7920 gaaagaaaag agttgctgtt gaaagacgag tagaaaactg cttcatttat agtagggaag 7980 taacaaacag acgtattaat gcaagcatgc agttaccaaa gcgtcagcca aacacggcaa 8040 gccacgtcaa ccactaccac aagtgaagga agttcttgag tcgttgaaca gaaacgtgat 8100 aaaagcgtta taaattatcg tggttttcca agaaacttgg aagytgaaag gttagattaa 8160 gcaccaagtt aaatggtgag gcttagcaat tcaatgcaag gagtaatgta gcgaaagctg 8220 attcaacgat aaaatgcaaa tcgagaaata aagcatgtcg agcattgcca atacaaagtc 8280 attcattaat tagaaatcga atagagttac aggacaggaa tgataaagtt ggcaacaaag 8340 gccataatag atccatggcc attacaataa agcaacaatt atgaagccta aattctcgac 8400 ttgaaggctt caagctgaac cccagcagca gcaatcctac aatccaagct ttgcttcata 8460 cgctgttcyg ctgctacttc tttagaaagt tgagatgtcg agagcatcac gcccgtgcac 8520 tcagcagcca gcgcattcag tcgagaattc acagctgggc cttcatcaat caacatagcc 8580 ttttgcttct cgagtctggc tacctccctg tgaagctcat ccagtcgagc atcaacactc 8640 gacaactcag ctgcaatgag agtcctccta gcagtcagct tgagagcctc ttcttttgcg 8700 ggcaataggc cattggtatt ggaaaccact tgtgcctttt tagtytcaat agattgctcc 8760 actgcaatgg ctttgtcaag cgtggccaca ayatcgacca cgagagtttg caattcgacg 8820 agagcatctg cctgaatttg atcaagttgt tggcttaaga ggaaggcaag cagttctttc 8880 acttcttggc ctaattgagg agtgactcgg acactgccaa tgaagccagt atcgaaaacc 8940 agccctttta acttaacaag agccgcttca atccggctat catcgggcac tccaccagac 9000 tgagcagtct cagcaatttc agcttggcgc ggcggagact cgagatccaa agtaccatca 9060 aagaagctct ggaagatrga aagaggatcc tcgaccaaaa gagcactgag cctttcacta 9120 gaagtatgag aagaagcagc cgtcttagaa gaagctgaac ctcccttagc atgaggtgag 9180 atcaaagcgg ctctagcatc ttgttgaaat cgctgaggag aaagtcgagg ctgttgaggg 9240 gaagtttgaa gctgtcgagg agaaggttcg gaatgagcag aggccagaac atcagccttg 9300 ggtgggggca ttacgccaat cacttggtca ggctgaatga ttggatcctc accaccctgc 9360 acttcatcat gcggyatgyt ttcttcacga gcaggggaag gcaggttctg catatcctgt 9420 ggaggaaaat tagaaaggtt atctcgacat tctttggtat aatagggttc acaaccagga 9480 tgttgccaag caattggttt cgagttaaaa tagaatgtca gtttgtccca cacagggtct 9540 gactcagtag agtctaaact cgagctagag gactctaaac cgctcgaaga actagatagg 9600 gcaattggtg gaggtttaga agaaaaccac gtggcccgag gtacagccat tttagacatg 9660 ccaaccctct gaagaatmaa agtaaaaatg attgagaaag aggaaaagga agcaaattga 9720 aacaagatgt garctaatga ttcaccttag ggccagatgc tctgagggga ctggaactgg 9780 ttgaactctt agaatggtgg gaagaggagc tgccagattt gcgactagac cttttcccgg 9840 aggtcttctt ggcttgagcc atctcgacag gaattggtgt agtaccttga agcagaggat 9900 tagaagcctg ctcatcaaca ccttgttcam caccttgctg cacttcctca cgttgactgg 9960 ctgatttagc cggggaggga tttcccacag aagattcacc agcrccttta gccctctttt 10020 ggctcgcaga agtagttggg gtggctcccc gttttcgact ctgaaacaaa agcaaatgat 10080 cacaaagata tacacgtcga gtaaaagtca gagtttcaca aggttcagta ttaccttagg 10140 aatcttgagc ttatcagcca aggcaacatc atcatcatca tcatcctcca cttcgacaat 10200 cgcagaggcc acccgaggag aagcctgagg ggtcggtcga ggaattggtt cagctacaaa 10260 aagaaaacaa aggaggatta agccataaat atcgcaaaga tgccaggtcg aaatgattac 10320 cttgaccaat aagcgatttt atcgatatgt ggttgaagat ttcaaccggc acatggagag 10380 gataattcca taggtaacgc ttggtccagg tcacccgctt ccgagggggc agtgcactgt 10440 ggtaaaagtt tttgatactt acatgatcaa cccacttagg aagcactacc ggaaaagcca 10500 aagcatactt acaagtaggc agtggtggga acctaaagcc agtttttcga ataataaaag 10560 aaagaccgtc ctcatcagaa ggaaggctca atcgggtttt cttggcttta gcttcccaca 10620 ttcgcctgag aacttgagct gctttggcaa ccgtttcctg aagtcgagga cccggaaagt 10680 acactacacc gaagaattgt tgaaaagcgt tgatctcaga tgtatgcata cctttggttt 10740 tctttggggc ctgcctctgc aaaagaaaaa cgtttgttat gcgctggaag caatcctcaa 10800 ttggcgtcga aatatcatgc caataagcag accaccacgc cttaaacgcc tgggtgacgt 10860 aaaaggatgg agtgaaactg aaaggactaa gaccaagtag ctcctcattg ttatagtaac 10920 caatggtagt gtcgaaaaca ctacgtttgg tgatggtacc aggatagagg atgagggatt 10980 tgtcgaacaa ggtattgggc aaatcttgac tcagcccaaa ctgtcgagac acaagctgag 11040 gattgtaacc gcaaagagta aaatcattac tggcgaagtt gatggttaac accctgggag 11100 acaatatagt ctgccaaagc tcgacttggt gttgagaaag gttctccgaa ccgggaagat 11160 taggatatga attccttagc caccgagggc cgtaagaggg tttgtgatac ggtgcaaagc 11220 tcgagcggaa acgtttcagc tcgaaaaaca tggtgaaata cttcttaaag tcaaactcga 11280 acgtggaggc atcataagga ggggtgagag cttcaagcct gaaagcgtcg atccttgtgt 11340 tagacaccac aggaggagag ttcttggctg gaagagatgg ttcgaaaacc gcattcatcc 11400 aaagctgaag aagccagaaa ggaccagctg cattcaaaga cgccacctta ggatctcgaa 11460 tatcggcgat tgcttcattg atcatttggt agagattacc gagcacgagc ctagccatgg 11520 cgataattcg accctcgtgc aacagattgg ctaaaggaag gagtttagcc ggaatcctca 11580 aagatttggt gcagaacaca taggcagaaa gccaatacag tagaaacgcg acatgctcag 11640 catcggagac ttcaccattc tcgacataat gatctttaat aaacttactg aaagcaatgt 11700 tatctgtcgg aatggcgata ggatcagtgg gagcagcaga agaatgataa tcgtcaccca 11760 ccacccaaag gccagtgatg gcagcaacat cgagaagagt aggagaaagc atcccaaagg 11820 ggacatgaaa gctattggtg gaccgctccc aaaagaaaag agaactcaga agcatggcag 11880 ggttgtaagt aatcggcgac ctcgacaact gaatgaggtc gaaaatgcca gtcactttcc 11940 aatgcccaga cttactggcc tccaccctgt tgagccatct cagataggct ccttcaccag 12000 cagatgggtt aggaggcgca gacctgaaag cccttttggg atctttcaga aaagggaagc 12060 ggtaagaagg ttggaatgca agaatgagct catccccacg aatgctgggg tgaaaatgct 12120 cgtagtcctc agggagactg ttaggcctgc ccttcttcgc cttcttcaaa gggcccaaaa 12180 tggcacgtaa attgccattc acagaaatag gaataaatac ctgggatttc cagatagccc 12240 gtttctccac gtcatacggc ggatctggaa tgggagtgcg cttggcttca ttcatctcac 12300 aagcagcagc caaagggatg acattgtcag aaccagaacc agaagccatg gaaatgttca 12360 gagaatacac cgggaaaaca gaaaccaaac gatggaaggc ggtcacaagc aaaatcaggc 12420 aaaagtttga gtgttcgaaa gcttgargat ttgaaagcgt gagtgattga aagaacggta 12480 aagcttgaag aaggccaaca atggcgtatt tataggcaag cgaatagtcg gacgtgaagc 12540 tgcattacag ggtgatgcat aaaatttttg aaatccaacg gttattttat tatataaccg 12600 caaaccctaa tgaaaaggct agraaaaggc catgattact ctaaagtaga gacggcacac 12660 ggcagacgag gtcagacgtc aaagcctctg attggagcaa aagtcaaacg attggatctc 12720 tgatgggact tgaaatcaga aaaggaaaag tcgcgaacag ccgtcaagct ccgtcgaaat 12780 gcacgggcga aaaatgcttg atctctccaa ggactggtag tcgagaatca acatttttgg 12840 ggggcatc 12848 // ID L1-10_Mad repbase; DNA; EDCOT; 5437 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-10_Mad. XX NM L1-10_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5437 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1814-1814 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 5437 BP; 1314 A; 700 C; 1944 G; 1454 T; 25 other; cgtwatgstg ggggawtgca cagatagaag mgaggmacga tggggkgmac tgtcswtagg 60 ggacatgtgg gtgcagatwc ataaggtgcc gccgctgagt atgacggckg cggtkgctac 120 ggcaatwggg ggmamgmttg gtagggtkgt atsggttgat aaatccgcca gcagggaatg 180 cattggaaga tttcttaggg tacgtattcg ctttaacctg cgggaaccac tgatgcgggg 240 gatgatggtc acgtttccag atgaaggacg agtgtgggta caatttcaat atgaagggtt 300 gcctaattat tgtttgtact gtgggaaact tgggcatgtg agcagggttt gtaaggcaca 360 tggattgcat gaggtgcatg gcttggggga ggaagacgaa tcacagagaa agagaggtca 420 attgccatat gagggtttgg aggctcgagg ggatttgcgg gggaatgcga ttcgttcacc 480 gtcgcgtaga tcgaaaagtc aaatkatggg agagggcagt tggagatcta tggagtcacg 540 agaggtgggg atgkgatgag gggatgcatg gggtggtggg gaagggatac gggagacggg 600 ggtagggttg ggcaggaggt acatgtccag cagggtaggt gggggagaca tgaatgatac 660 acataatcag cagatgcctt gggttgggaa tggtagtggg gaaggaatga gctaatcgct 720 aaacgtcgag tagcggaaga ggaggctcga aaggcgcggg aaagagcttt tgatgcgggg 780 ctcattggac ggggaggggt tgtgcgccgg gagtgagaat gtgwgttgtt tgattttgtt 840 gaacctgggg gcgagatggg ggggatgagg aagggagtaa gaagggtttg caggtggatt 900 tgaatgctcc agtgagtatg gaggaggaag gacacccggg tgaggtgcag cagagcggga 960 tgatgcgggg agcatcaggg gggggaggtg aatggtgtga gatggtaggg gctgttcagg 1020 gcggacccaa gattcggacc cttttgagtt gggtcctatt attgctgccg tgagtaggga 1080 gagtaggaga cggaagcgga ggattgagaa gtggaggagg aggtggaggg gatgggtagg 1140 gaggatagta gtatcggaat aagcgagctc ttattttttc tgaggcggag gagaccagcc 1200 gtgaagggtc tccacggtcg ccatgaaaac attatgttgg aactgtcaag gaattggggg 1260 ttccttgaca gttgatgcct tggtggagca ggtgcggctt cacaaccccg aggtggtgat 1320 cttacttgag acaaaaaata agagtgatcg ctacaagtat ttacttaagt tgttacggat 1380 ggattttatg caaccggtgg aaccaaaagg tattggtggg ggtttgtgtg ttttttggaa 1440 agatgaggtg gacatttcta gcattgtttg gagtagtttt tatattgaat tgggtgttgg 1500 tggtgatccg attcattcgg attggaggat gttagcggta tatgcaagta cggatgataa 1560 acggaggagg gggcaatggg agagcttagt aagaggatta gtagctcaca ggggaaatgt 1620 attgtgattg gtgattttaa tgatattgtg gatgacgaag agaaggaagg aggtaactat 1680 cggtctatgg cgagtacgag ggactttcgg gatttcctgg cagaaaatga gcttcttgat 1740 ttgggctttg aaggctatcc ttttacatgg aggaataagc gggatgatgg gttgattcaa 1800 caaaggcttg atagaggggt ggcgacttca ggatggatgg atttatttcc taatgcgaaa 1860 attaagcatg tggtgttgga gggctcagat cattctatgt taattctttc ctctgatgga 1920 accattctga aagggccgcg cggttcatct atgattctag gtgggggaag aatccggagt 1980 gtcgagatat tattacggat gcttggaggg aatcggtgga gggatctttg gcgtttaaag 2040 tgagtgagaa attgaagggg actcggcacc ggctgggtgt gtggaagaag actacgaaac 2100 cgaattctaa acggcgtatt gaggaactta gggaagagat taggaagggg attgtggatg 2160 cgatgtgcgg caagagtata ttagggggaa ggagaaagag ttggcagtgg caattaagga 2220 ggaagaattt attggaaggt gaaatcacgg aatacatggc tccgagaagg tgataaaaat 2280 acaagttttt tcatgctcaa acggttcaac ggaggagaag taatcggatg caggggctgg 2340 aagataatac tggagtatgg cagaaggatc cggtacgtat gcaggacatt gcggtaatta 2400 ttttactgcc ttatttcagt ctggtggctc tcggcaggga ggggaggtgg cggcatgtgt 2460 gggggcgaag gtggatgacg ggagaatgag gagcttattc ggccattctc ggctgaggaa 2520 attcgggaag ctgtgtttca aattccggct actaaatcwc ctggtcctga tggatttacg 2580 gctggatttt ttcaggatca ttgggaggtg gtgggtggtg atattattcg gatggtgcag 2640 gcctttcatc attcggggcg gttgctgcag aagattaacc atacacatat tgttttaatt 2700 ccgaaggtga aggctccgcg gcggatgacg gagctgaggc ctatttcttt atgtaatgta 2760 gtgtataaga ttattgctaa ggtcttgacg agaagactga aaaaaagtga tggaccgggt 2820 tattagtttt aatcagtcgg cttttgttcc gggcggcaga ttcatgataa tattttggtt 2880 gttcatgaaa ttttgcattc tttaaagcaa ggtgtggagg gggaggatgg taggatggcg 2940 attaaactgg atatggcgaa agcgtatgat cgagtggaat ggggtttttt gattgaggtt 3000 atgagtaatt tggggtttca tcctaaattt tgtgcttgga ttcgtgaatg catctctacg 3060 gtgtcgtata gtgtgatggt gaatggtgtt ccctcgggtt atttccgacc tgagaggggg 3120 ttgaggcagg gtgatccatt gtcacctttt tttatttctc ctatgtgcgg aagctctttc 3180 ggcgtatatt cggaagcatg aaatggaggg gctgattagt ggggtgcggg tggcgccggg 3240 agcaacgccc atcactcact tgttttttgc ggatgattcg gtggtttttt gtaaagcgga 3300 tgagacggag gcagggaacg tgattaagat tttggaggat tatggtaagg tctctggcca 3360 aattattaac ttggagaaaa gttctatatt ctttgggaag ggttgttcga agaagaataa 3420 aaagcgtatt gtgtcgagaa tgaatattca ggctagagac ggatttggta aatatttggg 3480 gattcaggca gattttgggc attcgaagaa ggcggtgttt gaatcggtwc gacgtggtat 3540 tgaaagtcgt attgatggtg ggcgagcaat ttttgtctcc ggcggggaag gaaattttga 3600 ttaaatcggt tgcaatggcg atgccgaatc atgctatggc gtgttttaaa ttgccggtga 3660 stacgtgtaa ggaaatggag cgagttattg ctcaattttg gtggaggggt caatcgaaga 3720 ctaggggatg tcattgggtg gcatgggata aattgactga gagtaagaag gttggagggt 3780 tgggtttccg tgaccttatt gggtttaatt tggctatgct tgccaaaatt agttggaggg 3840 tgttagataa gccggagtcg atgcttggta tggtgcttag ggataaatat tttcctaact 3900 cttcattctt ggaggcaagt aagcaaaata aatcgtcgtg ggggtggaaa ggattctgtt 3960 ggggagacaa gttctgaacc gtgggcttcg gtggagggtg ggtaatgggg agtcgattag 4020 ggtggctgat ccatggattc ccaagcccca ttcgttcaaa ccggtgttgc ggaatggggc 4080 tcctaattaa aggtgtgtga gttgatgacg gcggataggc aggggtggaa ttggaggagg 4140 ttgcgacggt ggtggcaccg gaggatttgg aattgattcg aactattccg attagtagac 4200 gtgggtgtga ggataaacga atttggcatt acacaaagaa tggggtgtat tcggtaaggt 4260 cgggatatca tgttgcgatg gagatgatga aaaatgggag tttgggagga aagggagggg 4320 atgtcgagtt cttcgggttc gttgggaggg gtgtggaaga ggatttggtc tctcgcggtg 4380 ccgaataaac ttcggttctt tatttggaag gctgtaggaa ggcgttggcg gtgaggcata 4440 atttggagcg cggcggattc ggtggtgaat aagtgtgagc tgtgtggagc ggtgatgaaa 4500 ctgaggctca tcttttcttt ggttgtgagt ttagccgtgc ttttggtttg ggacgtcgtt 4560 gcaaattaat atggcggcta tgggggtgaa ggattttttg gagggatggc agagggtagt 4620 ggagcgaatg gagaaggagg aggatgcgga tttgatttgc agcaggtggt gtttgggttc 4680 tggcgtatct ggaagtgtag gaatgaggcg gtcttcaaag ggattcggat cctgccacat 4740 gtggctgttg agctatggca gcggcaagtg gaggagttta gggaggctat gatggtacgg 4800 tagtggaggg aggggagcaa cggaggggta gggggtcagg gaggggggag gcctggggag 4860 ggatcggggg ggagagggtc aatggaagaa acctgtgttt ggaggttgaa gttgaattgt 4920 gatgctgctt ggaggaagga cacgaaggtg ggaggggttg ggtgggtgct tcgggacttt 4980 gctgggmttc ctaagcttgc gggaggggtg ggtggggaac ggtttgcggc tgcaattatg 5040 gcggaggcgg aggcggttag acaggggttg gagatggttg ttgggagtga ggttatggag 5100 gctggtacta ggttggtggt ggaatcggat tctaagggat tgattcagat gcttaataag 5160 gaggtcacgg ctgatgtgac tcttgagatt tatctccaag atatttggag gatggcgagc 5220 ttattccagt tggtgaggtt ttgctttacc cctcggcaat gcaatcgtgc agcccattcg 5280 gtggcggcgt acgttgttaa gcatggcggg agatttggct gggatgagtt aggtccagag 5340 tttcttttta atattttagc agaagatgca aatgtaactg ttcgtattta aatttaataa 5400 aatttctatc tttcgacaaa aaaaaaaaaa aaaaaaa 5437 // ID Gypsy-2_TC-I repbase; DNA; EDCOT; 7095 BP. XX AC CACC01024994; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-2_TC_; KW Gypsy-2_TC-LTR; Gypsy-2_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-7095 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01024994; Positions 693 7787. XX CC Positions [3717-4172] - Reverse transcriptase CC Positions [5277-5774] - Integrase core CC LTRs are 91% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS 1974..2891 FT /product="Gypsy-2_TC-I_1p" FT /translation="MEKIFKALGCSSTRSVELAAFRLEDVAQEWYVSLRRG FT RLTDAMPLTWKELSIAFLDRFLPLIVRNAWAREFEALVQTPGITVSEYDIK FT FTQLARYAPYLVSTEEMKIQRFVDGLVEPLFRAVASRDCNTYSAVVDCVQR FT IDMRTSESRAARDRAKRVKIEGYQGRRDFSSDVSSSSCQGPQRDSRLPQRG FT SDLTSANVGSRQKTFSRGRQQDSRQGSQAIDRCNNCGVWHSGLCFHTMRVC FT YGCGQLGHIKRNCPIAHQSQDSAHNSTQPVLSAPSVVASSDRGASGSMGKG FT AVTSSQTRSSRSGR" FT CDS 4215..6353 FT /product="Gypsy-2_TC-I_2p" FT /translation="MEKWPRPTSVTKIRSFLSLAGYYRHFVKDLSKIVTLL FT TKLTRKDTKFKWSSACEDSFEKLKACLTTALVLSLSQGTRGYTVFCDASRV FT GLGCVLMQHGKVIAYASRQLKRHEQNYPTHNLEIAVIVFALKIWRHYSYGE FT TCKIYTDHKSLKYIFQQRDLNLQQRRWMELLKDYDCTILYHPDKANVMADA FT LSQKSMGSLAHISTDRRSLIREIHSLGDMGVHWKVSEENALLAHFRVRPIL FT MDQIKETQSKDEFVAKALEDPQRKKGKMFTKDTDGVLRYGTRLYVLDSDGL FT RREILEEAHMVAYVVHPGATKMYQDLKEVYWWEGLKKDVAEFVSKCLVCQQ FT VKAKHQRPVGLLQPLPVLEWKWEHVAMDFVMGLPRTSGGYDSIWIIIDRLT FT KSAHFFLVKTTYRAAQYALVYVDEIVRLHGIPISIVSDKGAQFTSQFWGKL FT QEALVTKLDFSMVFHLQTDRQSKRMIQTLEDMLMACVIDLGVRWDQYLPLV FT EFAYNNSFQASIQMAPFEALYGRRCRSPIEWLEVGERKLLGLELVQDTTEK FT ICMIRQNMLSAQSRQKSYADNRWRDLEFQVGDHVFFKVSPTKGVMRFDKKG FT KLSHRYIRPFEILKRVEVVAYHLALPPDLSNIHLVFHVPMLRKYNMDPSHV FT IRYETIQLQDDLTYEEQPVAILDKQVKKLRSKDVALVKVLWRNHTSEEVTW FT QAEEEIQTKYPHA" XX SQ Sequence 7095 BP; 2100 A; 1232 C; 1670 G; 2093 T; 0 other; tgatgatgat agagtgtgcg agtagggagt gcacacatga tgatgttgaa gtgtgcgagt 60 agggagtgca cacatgatga tgatattgct ttgagttgag tgtggtggga tggtgtgcat 120 gatgatgaat gtatatacaa atatatatat atgttataga aagtttatga aaataattgt 180 gattgtgtta tgtgttggta atgttaattg ctcccaaatt gcttttcatt tcaacaagaa 240 aatggctttt gatgtaacaa gacccatttc acttaaaatg ctctgtttct cgctgcagca 300 agattcattt tcgctacagc gataaactct cgggttttgg gggtcacaat ggcctgattc 360 ttgctgcagc gagaaactat cgggttctag tgcaatgctt tcactttgat aaagattttg 420 accaccttcc ctttcgaact aggaaaagtg gtaaacataa aagttgtatc tctgcctctt 480 atctttctaa tggtccaaaa attaggtcaa tttcactttt gtagcgagag atatgctaga 540 aaaactgaaa cacatgaaaa ctaacactat ttttctttgc agcgagaaac ttcctgccat 600 gcttgctacc ttgcttgatt ttgacatatt tttcacccat ttaacttcat ggattgatca 660 taggtttttg gaacactatt aggttattaa tcaaagtttg agaggagggg ttttaagtaa 720 gaaattaaat caattgcatt attttcgaaa caagtgcatc atgaattcca aattctttct 780 atcgatcgct tgttcccttc ttatattcac tcactgagtt tatactcacc tttttcaaat 840 tcatgttttt agatcaagag gcagtcggta actaggtcaa ggtgttatca tagatttgta 900 tccttggtag gtatcttggc acttcgtagc cgcaacttca ccttgggcac tccgctggaa 960 gcccaaagtc atttttgttg taaatacgta cctgtgatgt atagtactaa gatgtatacc 1020 ttagaccata tatgtacatt ttgattggta aagctaccat gagtggtaat agttaatgtt 1080 attttgggat aatataaatg tagttttgat tgttataatt tactattaaa gtacttaaag 1140 ggttgagatt atgagatgta aatgtaaaaa tagttgacag gataatgagt acaattatat 1200 aaataggtgc ttaggcttag tgggctacgt ccattaggcc catgctctgg tcatggccca 1260 aaaattgggt cataacagac ttagtatcag agccctaggc tgtttaggtc ctaggatttc 1320 ctttttgttg gttcaacgga gtgtcgggtc attatgtgga aacttcagtt gtgaagtgaa 1380 cagcggcaca ttttacaacc aaaggaccgc atagattccc tatcttagaa accacatttt 1440 cctttatgta tgattataga aaaatgtgtt taataattgg tgtttgctct tgtctaggta 1500 agaatgccac ttaagacatg agctgcctca agacgaatag gggagcaaga tgcccataat 1560 gagatgacag attggccaca aacatccacc tgtaggggaa gaggtagaca tggtggggcc 1620 actaagtttg tgagggtgga tacgcttgtg agcagacacg aggagggaca atcttcaggt 1680 gatgtgggta gacaaccaac cgagggtatt accgtcgagg acttggcagc aggcctacag 1740 agagttaaat gggttgtaga gatgatggca acccgtatgg atgatataca aaggatagtg 1800 gaagggaaac ctacaataca aaatccctta gctcccaaag acaagtcgac cgccaacatc 1860 atgaggttga gaggggtcat ttagagattt cccttcctga tttcttgaag cttaagcctc 1920 catcattttt agggtttgat gcatcgaaga aaccccaagt tttcttagat aagatggaga 1980 aaatttttaa ggccctagga tgctctagta ctagatcagt cgagttggcc gcctttcgat 2040 tagaggatgt ggcacaagaa tggtatgtct cgttgcgtag aggtaggctg acagatgcaa 2100 tgccgttgac ttggaaggaa cttagtatag ccttcttaga tcgattctta ccactcattg 2160 tacgtaatgc atgggctagg gagtttgagg ccttagtaca gaccccaggt ataacggtgt 2220 cagaatacga catcaaattc acgcagttgg ctcggtatgc gccctatcta gtttctactg 2280 aggagatgaa gattcagagg tttgtggatg ggctagtgga gccactgttt agggctgtgg 2340 catctcgaga ttgcaatacg tactccgcag tagtggattg tgttcagcgg attgacatga 2400 ggaccagtga gagtagggct gcgagggata gagcaaagag ggtcaagata gagggctatc 2460 aaggtcgcag ggacttcagt agtgatgttt cgtcttctag ctgtcaaggc ccacagaggg 2520 actcacgatt accccaacgg gggagtgact tgactagtgc caacgttgga tcaaggcaaa 2580 aaacttttag tcggggaagg cagcaagatt caaggcaggg tagtcaagct attgatcgct 2640 gcaataattg tggagtgtgg catagtggac tatgtttcca tactatgaga gtttgttatg 2700 ggtgtggtca acttgggcat attaagagga attgcccaat agctcatcaa tcacaagatt 2760 ctgctcataa ctctactcag ccagttttat ctgctccttc agtagtcgcc tcatctgatc 2820 gaggggctag tggatctatg ggtaaaggtg ctgttacttc ctctcagacc aggtcgtcta 2880 ggtccggacg ttaaagttct gctggtaggg gccaagcgaa ggtatatgct ttaacactcc 2940 aagaggccct gacatccaat gtagtggtct caggtactct ttttgtttgt aatatggatg 3000 ctagagtatt gtttgatctt ggagctaccc attcttttat ttctccatgt tttgcacttc 3060 gtctaggtta ggatcgtgtt agaagataag aacaattagt ggtgtctact cctttaaaag 3120 agctatttac agtcgaatgg gaatatgagt cttgtgtagt tcgagtcaat gacaaagaca 3180 ctttggtgaa tctagtggtg ttagacacct tagactttga catgatcttg ggaatggatt 3240 agctatcacc ctgccatgcc aacgtggatt gttatcataa attggttaga tttgatttcc 3300 tgaatgagcc accatttagt attcaagggg atagaagcaa tgcttcaact aatttgatat 3360 cggtcatgtc taccagaagg ctattacgac agggttgttc aggttatttg gttgtggtaa 3420 gggatactca ggtgaaggtt ggagatataa gccaagtgtc ggtagtgaac gagttcatgg 3480 atgtatttct cgaggaacta ccaggtttgc ctcccaagcg agagattgaa ttttacatat 3540 atttgattcc aaacactaga cctatatcca tacccccata tagaatggca cctatgaagc 3600 ttaaagagct taaggatcag ttagaagatt tgttggataa aggcttcatc catcctacaa 3660 tctcaccatg gggagcaccg gtggtatttg taaagaagaa agatgggtca cttatgttgt 3720 acattgacta tcgacagctt aacaaagtga cggtgaagaa taagtacccc cttccaagaa 3780 tagatgattt atttgatcaa ctacaaggag cacaatgttt ctctaagata gatctgcgat 3840 atgggtacta tcagttgagg atccgaaatg aagatatacc aaagaccgca tttcgaacaa 3900 gatatgggca ctatgagttc ttagtgatgt cttttgggct tacgattgcc cctgcggcct 3960 ctatggattt gatgaaccaa gtgttcaagc cctatttgga caagttcgtg gtggtgttta 4020 ttgatgacat cttgatctac ttaaagagcc gagaaaagca tgaatagcat cttaagatag 4080 tgttccaaac tttgagaaac catcaattgt atgccatgtt ctccaagtga gagttttgga 4140 ttgaaagcgt tgcattttta ggacatgtgg tatcccagga tggggtacaa gtcgatccaa 4200 agaaagttga ggcaatggaa aagtggccaa ggccaacatc agttacaaag attagaagct 4260 ttttgagttt ggctggctat tatcgtcact ttgtgaagga cttatccaaa atagtcaccc 4320 ttctaactaa gctgacacgt aaagatacaa aatttaagtg gtcaagtgct tgtgaggata 4380 gctttgagaa gcttaaagca tgtcttacca cagctctagt attaagccta tcgcaaggca 4440 caaggggtta tacggtattc tgtgatgcat cacgggttgg tttagggtgt gtattaatgc 4500 agcatgggaa ggtgattgca tatgcatcaa ggcaacttaa aaggcatgag cagaattacc 4560 ccacacacaa tttggagata gcagtaatcg tgtttgcctt aaagatttgg agacactact 4620 cgtatggtga gacttgcaag atatatactg accataaaag tttaaagtat atatttcagc 4680 agagggatct taacttgcaa caacgtaggt ggatggagtt gctaaaagat tatgattgta 4740 ctattctcta ccatcccgat aaggcaaatg taatggcaga tgccttgagt caaaaatcta 4800 tggggagttt ggcacatatc tctacagata ggagatcctt gattagggag atccatagtt 4860 tgggagacat gggtgtgcat tggaaagttt cggaggaaaa tgcattgcta gcacatttta 4920 gagtgaggcc tattttaatg gaccagatta aagaaacaca aagtaaagat gagttcgtag 4980 ctaaggcctt agaggatcct caaagaaaga aaggaaagat gtttactaaa gacacagatg 5040 gagtattgag gtatggaacc agactttatg tgctcgatag tgatggattg aggagagaaa 5100 tattggaaga ggcgcacatg gtagcctatg tggtacatcc aggggctaca aagatgtatc 5160 aagatttgaa ggaggtatat tggtgggaag gacttaagaa agatgtagct gagtttgtct 5220 ccaagtgcct agtttgtcag caagttaagg ccaagcatca aaggcctgta gggctactac 5280 agccattacc agtgcttgaa tggaagtggg agcatgttgc aatggacttt gtaatgggct 5340 tgcctcgaac tagtgggggc tacgactcga tttggatcat aatagatcgg ttaacgaagt 5400 cagcccattt ttttttggtt aagactactt acagggctgc ccagtatgct ctagtttatg 5460 tggatgagat agtacgactg catggtatcc ccatttctat agtatctgat aaaggagcac 5520 aattcaccag tcagttctgg ggaaagttgc aggaagcatt ggtcactaag ttagatttca 5580 gcatggtttt tcaccttcag actgatcgac aatctaaacg gatgatacaa acattggaag 5640 atatgttgat ggcctgtgta atagaccttg gggttaggtg ggatcaatat ctacccttgg 5700 tggagtttgc ctataacaac agttttcaag ctagcatcca aatggcacca tttgaagcat 5760 tatatggacg gaggtgcagg tcacctattg aatggctaga ggtgggagaa aggaaactct 5820 tggggcttga gttggtgcag gacaccaccg agaaaatatg catgattcga caaaatatgt 5880 tgtcagcaca aagtagacag aaatcatatg ctgataacag atggagagac ttggagtttc 5940 aggtaggaga tcacgtattt tttaaggttt caccaacaaa gggggtaatg agatttgaca 6000 agaagggaaa attgagtcat cggtatataa gacccttcga gatcttaaaa agggttgaag 6060 tagtggctta ccatttagcg ctaccaccag acctctcaaa tattcacctc gtattccatg 6120 taccaatgct taggaaatat aacatggatc catctcatgt aatacggtat gaaaccatcc 6180 agttgcaaga tgatttaacc tatgaggagc aaccagtggc tatccttgat aagcaagtca 6240 aaaagcttcg ttctaaggat gtagccttag tgaaagtgtt atggcgaaac cacactagtg 6300 aagaggtaac gtggcaagcc gaggaggaga tacaaaccaa gtatccacat gcataaaagg 6360 tatgctacct tatagtttga tttaaattcg gggatcaaat ttcttttagt gggggagaat 6420 gtgagacctc gacctctata gcctcataat taggtgtaga cacgataacc cgagccaggg 6480 gtaatttcat catttcttta gtgagccctt agaagtatac tttcaaatat ttttaaggcc 6540 taagtaggcc taaagcataa tgaatgatga aaataatgat taaatgacga aggaaaaaaa 6600 aataaagatg atttccaaag taaaggcaaa atggcatttt tcatctcaag tcaaaatttt 6660 aatttttcat aaacccaagt atttttagac cattgtggac ttggcctcag tgtcaaaaga 6720 gtaaaaaaat tacacaaagg attggacaag aataagctaa cttgctaagg gcattttcat 6780 aatttaagtg gagttggata aggttgagct ataaatatca tcttccaata gcttcttctc 6840 acattttcca gcagcttctt cttcttcttc cttcttccct ctcatgtttc ttcatcctct 6900 atgggagttc tcttcaagct tccataacta tctcaagcta actccacttt tcatgctttt 6960 gtgcactctt tcatagaacc tttgtgctct ttcactctct cactttaaaa cccttgaaaa 7020 aaaaaatctt acttccatac tttctctcac tagctaggtg tttagagaga gaaagagaga 7080 gcttccataa tagct 7095 // ID SHALINE17_MT repbase; DNA; EDCOT; 4137 BP. XX AC . XX DT 23-JAN-2007 (Rel. 12.01, Created) DT 23-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A long interspersed nucleotide element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; ORF; KW Interspersed; repeat; Poly-A tail; retroposon; SHALINE17_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4137 RA Shankar R. and Jurka J.; RT "SHALINE17_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 94-94 (2007). XX DR [1] (Consensus) XX CC The LINE element seems to be truncated at the 5' end while the 3' CC end is well conserved. In the genome, very few similar length CC copies are present while shorter copies are present in large CC number. This element has intact domains for endo/exo-phosphatase, CC reverse transcriptase and RNAse. XX FH Key Location/Qualifiers FT CDS join(277..297,301..315,319..435,439..2961) FT /product="SHALINE17_MT_1p" FT /translation="MLKLMIXGVNGDLVFMVCRKVVEEESLGIFLDIYXIF FT LNFLGVLLEILMISMQMKKKGRSDRQPWLIQGFRQAVLDAGLADIHMDGYA FT FTWFKSLGTARAVEEKLDRAMANNSWFDIFPNARLECLTTTSSDHYPLLLD FT CAPQPASSSGQRRFRFENAWLVEPEFKPFVSQSWXGYGDHPIMQKLNQCAE FT DLSKWSMNINQNTRQEIRKTQRKLEAIRSHVDASNVNYFNMLRNRLDKLLV FT KDDMFWKQRAKTFWYRDGDLNTKFFHAAATTRKKVNRIEHLEDENGXECRT FT EDGLKHIARDYFMHLFQKSPSSRASVINMVPTSITGDDNDMLTATFTLEEF FT KDAAFSMQADKCPGPDGFNPGFYQHFWNICGHEVYQAGCDWLASGAFPPHV FT NSTNITLIPKGDSQTSMKDWRPIALCNVVYKIVAKVLANRLKKVLDKCISI FT NQSAFVPGRSILDNAMVAIEIVHYMKAKTKGKKGDVALKLDISKAYDRLDW FT DYLRDVMIKMGFSSRWXXWIMLCVETVDYSVLVNGAQVGPIVPGRGLRQGD FT PLSPYFFIICAEGLSSLISDAESRGDIRGTSICTNAPVISHLLFADDCFLF FT FRACENEAXGMKNILTTYEEASGQAINLQKSEIFCSRNTPDDLKNLIATTL FT GVRQVLGTGKYLGLPSMIGRSKNATFKFIKDRIWNRINSWSSRCLSQAGRE FT VLIKSVLQSIPSYVMSIFLLPGTLIDEIEKMINSFWWGHNSTNSRGIHWLS FT WERLSVPKIFGGMGFKGLRAFNLAMIGKQAWKLITNPDSLITRLLKAKYFP FT HSDYFGATIGHNPSYVWRSIWSARDVIRHGFKWSIGTGENIPVWNQPWISN FT VARILPSTHYQVEWPSITVAXLLITHQKEWNVELIRYFF" XX SQ Sequence 4137 BP; 1185 A; 665 C; 878 G; 1372 T; 37 other; tgccaagaat watgagtktt attrgttgga attgtcgggg tctgggtagc ccgagtacaa 60 ttcctaatct taagtaccta gtccggacct ataawccgga tgtaatattt ctatctgaaa 120 caatgacaac gtctaataaa attgaagaat tgaagtatat tttgggtttt gatttttgtt 180 tyactgtcta ccgaatcggt agaggtggag gtttggcttt tttttggaat aatactttta 240 attgtaatat cacwaatttc tcacaaaatc atattgatgt tgaagttaat gattwtttga 300 ggggtaaatg gagattaact ggtttttatg gtatgccgga aggtggtaga agaagagagt 360 cttggaattt tcttagacat ttatcwaatc tttctcaact tccttggtgt attattggag 420 attttaatga tatcctaaat gcagatgaaa aaaaagggaa ggtcagaccg tcaaccatgg 480 cttattcaag gcttccgaca agctgttttg gatgctggkc tkgctgatat tcatatggat 540 ggttatgctt tcacttggtt caaaagtctt ggaactgcsc gcgctgtgga agagaaattg 600 gatagagcta tggctaataa tagttggttt gatatatttc cgaacgcaag acttgaatgt 660 cttactacca catcttctga tcattaccct cttttgttgg attgtgctcc gcagcctgcg 720 tctagttccg gtcaacgtcg ttttcgtttt gaaaatgcgt ggcttgttga acctgagttt 780 aagccttttg tttctcaaag ttggcakggt tatggtgatc atcctattat gcaaaaactt 840 aatcaatgtg ctgaagatct atctaaatgg agtatgaata ttaaccaaaa caccagacaa 900 gagattcgca agactcaacg taaacttgaa gccatccgtt cacatgtgga tgcctctaat 960 gtgaactatt tcaacatgtt aagaaatagg ttggataagc tgctggtcaa agatgatatg 1020 ttttggaaac aacgtgctaa aacattttgg tatcgagatg gggaccttaa tacgaagttt 1080 tttcatgcag cagcaaccac caggaaaaag gtgaatagaa ttgaacatct cgaagatgag 1140 aatggtwtyg aatgtcggac tgargatggt ctgaaacaca ttgcacgtga ttatttcatg 1200 catctctttc aaaaatcacc aagctcgcgt gcaagtgtca ttaatatggt tccaacttca 1260 atcactggag atgataatga tatgttgact gcgactttca ctttagaaga gttcaaagat 1320 gcagctttct ctatgcaagc agataaatgt ccaggtccag atggytttaa cccaggtttc 1380 tatcaacatt tttggaatat ttgtggtcat gaagtttatc aagcaggttg tgattggcta 1440 gcaagtggcg ctttcccacc acatgtgaat tctactaata ttactcttat tccaaaaggt 1500 gattctcaga cttcaatgaa ggattggcga cctattgctc tctgtaatgt tgtgtacaaa 1560 atagtggcca aagtgcttgc taacaggcts aaaaaagtgc tagacaaatg tatatctatt 1620 aatcagtcag cttttgtccc aggtcgatct atcttagata atgcaatggt ggctattgaa 1680 attgttcatt atatgaaggc taagacaaaa ggtaagaaag gtgatgttgc acttaaattg 1740 gacattagta aagcatatga cagattagat tgggattatc tacgagatgt tatgattaag 1800 atgggttttt catctagatg grttcrttgg attatgcttt gtgttgagac agttgattac 1860 tcagtgttgg ttaatggtgc acaagttggt cctattgttc caggacgcgg tctccgtcaa 1920 ggggatcctc tctcacctta tttttttatt atttgtgctg aaggactctc ttcccttatt 1980 agtgatgctg aaagtagagg tgatattaga ggtacttcga tttgcacaaa tgctccagtt 2040 atttctcatc ttctctttgc agatgattgt tttctcttct ttagagcttg tgagaatgag 2100 gctrttggta tgaagaatat tttaactact tatgaagaag cttcgggtca agcgatcaat 2160 ctccaaaagt ctgaaatatt ttgcagcagg aatactcctg atgatttgaa gaatctcatt 2220 gctactactc tcggtgttcg tcaagtgttg ggtacaggta aatatcttgg tctaccatct 2280 atgattggtc gaagcaaaaa tgcaactttt aaatttatta aagatcgtat ttggaataga 2340 ataaactcct ggagtagtag atgtctctcg caagcaggta gggaggttct tatcaaatct 2400 gttctgcaat ctattccttc atatgtgatg agtattttcc ttcttccggg taccctcata 2460 gatgaaatag aaaaaatgat aaattccttc tggtggggtc ataattcaac aaactctcga 2520 ggcatacatt ggctatcttg ggaacggctt tcagttccaa agatttttgg aggtatgggt 2580 ttcaagggcc tccgagcttt taatttggct atgattggta agcaggcttg gaagttgatt 2640 actaatccag attctctgat cactagatta ctcaaagcta aatattttcc gcatagtgac 2700 tattttggag ctaccattgg acataatcct agttatgttt ggcgaagtat ttggagtgct 2760 agagatgtga ttagacatgg ttttaagtgg agtataggta caggcgaaaa tatcccagtt 2820 tggaatcaac cttggattag taatgttgca cgaattttac cttcaactca ttaycaagtg 2880 gagtggcctt ccatcactgt tgctsacttg ttgattacac accaaaagga gtggaatgtg 2940 gagctcattc gatacttttt ttgattctgg aactgccaat aatattttaa awactccgct 3000 tcttccttca gtaactcatg tagataaacc tatttggaaa tttgaaaaga atggcattta 3060 ttcagttaga agtgcttata gagatattct gaatcatgat atggcaattg ttcaacatag 3120 tgtaccaggg aattggaatt gtatttggaa cctaaaastc ccaccgaaag ttaagaattt 3180 cwtttggcga gtttgtcgaa attgcttacc aactcgaatg cgtttgcaat ctaaaggagt 3240 tcagtgtcct aacagttgtg taatatgcga cgattatgaa gaagatagca aacatytgtt 3300 ctttgtgtgt agtaagagta tgctttgttg gcaacgtact ggtttttgga gccctttgat 3360 tcrgctgact ttgatatcaa tgtcagcttt ccaacygata tgatttttwc tttmctacaa 3420 cacctrgatc agcagtcaaa agcaaatttt castgttacc ctttggagta tatggaagca 3480 tagaaacaat aaagtgtgga ataatatcac tgatacagct caagatattt gtgagcgtgc 3540 agggactttt cttactagtt ggaggaatgc tcaagatatt cggaatccta gctcatcaga 3600 aaccctccac cccgaatgat ttgaagtgga ctaaaccaag tgctggragg ttcaagtgta 3660 atgttgatgc gtccttttct catgctcgca atagagttgg tattggtgtt tgcattcgag 3720 atgcagaagg taattttgtt ttagccaaga ctgaatggat tactcctcta cttgatgtcg 3780 atatgggaga agctttgggt ctgttatcag caatgcaatg ggttaaagat ctgcaattag 3840 ktaatgtgga ttttgagact gactcwaaaa ttgtggtaga cagtctttat ggcagtaaaa 3900 gtggcgtctc tgattttagc gcaattatta atgattgtag acatctatta gtttctgatt 3960 tagtaaactc tgatgttaag ttcattagga gacaagccaa tgakgttgct catagtcttg 4020 ctagggaagc mctacgtcat gctagtttcc atattcatat taatattcca cattgtattt 4080 atactattat tattaatgaa atgctataag tttctttttg tcaaaaaaaa aaaaaaa 4137 // ID Copia-14_Mad-I repbase; DNA; EDCOT; 4463 BP. XX AC ACYM01113852; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-14_Mad-I; KW Copia-14_Mad-LTR; Copia-14_Mad_. XX NM Copia-14_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4463 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1290-1290 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01113852; Positions 6077 1615. XX CC Positions [1767-2222] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 1860..3536 FT /product="Copia-14_Mad-I_1p" FT /translation="MKHKSDTRDLLVQFIHLVETQFTTKVKMIRSDNGPEF FT RLDNFYAQNGIVHQTSCVNTPQQNGVAERKHRHLLNVARALLFQAKMPQRF FT WGDAILAAAYLINRTPTPVLKGKTPYEKLFNKIPHYSHLRVFGCLCFASTH FT PLKPSKFDPRARRCVFLGYPYGQKGYRLLDLQLNKVFVSRDVIFFEDQFPL FT DTSDAPDNSHALANSPTTSHPLFHFDMASFPDTPPMPSAPSDPPSHALSSS FT DPTPQALSSPDSPTNPAPSTTNLLSDPTSPDPLPSPIPNAPPTPPPRRGTR FT PTKPSTFLQDFHIEVPLPSRPDPMSSLNVVQSSSGTSHPLSHYLTYDRLSP FT HHKAYTATLTLLKEPTSFSQAVRDPHWRDAMQREIAALQANHTWTLVPLPL FT HKRPIGCKWVYKIKLKPDGTIERYKARLVAKGYSQIEGVDYQETFAPVAKL FT TTVRVLLSVAAVQGWHLHQLDVNNAFLHGDLDEDVYMNLPPGFGRKGENRV FT CKLNKSLYGLKQASRQWFIKLSNALMAAGFHQSRSDYSLFVRSHHGNFVAL FT LVYVDDVILAGN" XX SQ Sequence 4463 BP; 1237 A; 1088 C; 869 G; 1242 T; 27 other; gagtgattga tatctgggca aacaaaaagc aaacacacaa acaaacccta gcaaaacgca 60 gccatgggtg atagagaaaa gaagtcaacc tccgcaggca tgacctcgca ttcgaagtgg 120 gagaatccta atcacccact ttatctccat cattcgracc aacctggtgc agtgcttgtg 180 cctcagccac tggtggaaga caattacagt acatgggttc aatccatgac catggcttta 240 acagtcaaaa ataaactarg gcttgtcgat ggaacagtcg agaagcctac tgaagacaaa 300 catgaagaac tgcagcagtg gaatcggtgt aataatctgg ttaagacgtg rctcctagga 360 tctatgtcca aagaaatctc aagtagtgtc atccactgta aagatgcaag gcagatgtgg 420 cttgatttgc aagaaaggtt ttcccatgtg aacattgttc aattgtttca catagaaaat 480 gagatccatg gctgtgtaca aggcaacatg acggtgagtt cgtacttcac taaattaaaa 540 gggctttggg acgaacgtga tgtactgtgt tctatccctg catgtagttg cgacacgaaa 600 aaggagatta tttcttatgt tgaaacccag aaaaccatga agtttctcat gggtttaaac 660 gattcmtatt ccaccgttcg aagtaatact ctcctccttg agcctttacc aacagtgaac 720 aaggcctatt ccyttgttct tcgtcatgag aggcaggcag aagtctcaac tggaaagcat 780 ytttctcaac ctgaagcggc agtctttgcc gtgaaaaatg gtggccgaga aaatgaacaa 840 gaagacggaa atcttcgttg yggraaatgt aacaagacga accataytac caagcactgc 900 cgagcacacc tcaagtgcac tttttgtgga tggaaaggyc attcattcga atattgtcgc 960 aagcgcaaag cagctgctga acytgaacaa aatcgcccat cttctgctaa gggtaatcat 1020 gttgcagtgc atgacaagaa rgacgggatg cccaattttc ccttytctca ggaggattgc 1080 aarcagatac ttkcgatgtt aaacaagaac aagtcatcct ttgcgaatca cgttggtaat 1140 tcatcaaaca atgaaraact ctcaggtaaa gctttttcat gcatgcacaa tggtattaca 1200 actgtttgga tcttggatag tggtgcaacg gaccacatcr tttgcagccc taattctctc 1260 acatcatcga ggcctgtttc taaccatact gttgaactac ccactggttc tcttgccacg 1320 gtcacccaca ttggacaagt cgttttctca cccacattgg tgcttgatca tgttttgtgt 1380 gtaccatttt tcacgttaaa tctaatatcc attagtaagc tcgcccatga ttctttctat 1440 attaccattt ttctcagaca aatttgtgtt atacaggacc tacgctcggg gaagatgatt 1500 gggatrggay ttragcgaga ggggctatac tacctcgatc caccacagaa aagaacatgc 1560 aatgtcattc aagcttccaa cccttgtctt tggcatcaac gtctaggcca tccatcccaa 1620 actgtttcca tgttatttcc cttcttgaat aataaacctt gtgattctaa taagtgcttt 1680 atttgtccat tagccaaaca aaccagagca ccattttcat taagttctat atccactaaa 1740 tcytgttttg aactgattca tattgayatt tgggggggta tcacgttcct tctctttctg 1800 gtgcmcgmta cttyctcaca attgttgatg actacactcg aagcacatgg atttacttga 1860 tgaaacataa atctgataca cgggatctcc ttgtgcaatt tattcatttg gttgaaacac 1920 aattcaccac caaggtcaaa atgattagaa gtgataatgg gcccgaattt cgtcttgaca 1980 atttttatgc tcagaacggc atcgtccatc aaacgagttg cgtcaacaca ccacaacaaa 2040 atggtgttgc tgaacgtaag catcgtcact tattaaatgt tgcccgagcc ctcctttttc 2100 aagctaaaat gccacaacgt ttttgggggg acgccatcct tgctgcagcc taccttatca 2160 atcgcacccc cacacccgtt cttaaaggca agacacctta tgaaaaactg tttaacaaaa 2220 ttccccacta ttcacactta cgcgtatttg gttgtttgtg ttttgcttcc actcatccac 2280 ttaaaccttc caaatttgat ccccgtgccc gtcgctgtgt atttctggga tatccctatg 2340 ggcaaaaagg ctatcgttta cttgatcttc aacttaataa agtttttgtc tcccgtgatg 2400 tcattttctt tgaagatcag ttccccttag acacttccga tgcccctgac aactcccatg 2460 cccttgccaa ctcacccacc acatcccacc cacttttcca ctttgacatg gcttcttttc 2520 ctgacacacc tcccatgcct tccgcaccct ctgaccctcc ctcacatgca ttatcctcat 2580 ctgaccctac accacaagcc ttatcttcac ctgactctcc taccaaccct gcaccgtcca 2640 ccactaacct cctctctgac cctacatctc cagatccttt accttctccc attccaaatg 2700 ctccgcccac ccctccaccc cgacgtggaa ctcgtcctac taaaccttcc acttttttgc 2760 aggattttca tatcgaggtt cctctcccgt ctcggcctga tcccatgtct tctctgaacg 2820 tcgtccagtc atcgtcaggt acttctcatc ctctctcaca ttacttaaca tatgatcgtc 2880 tttcacctca ccataaagct tacactgcca cactcaccct cctcaaagaa cccaccagct 2940 tttcccaagc tgtccgagat ccacactggc gtgatgccat gcagcgtgaa atcgctgctc 3000 ttcaagccaa ccatacatgg acacttgtgc ctttgccgtt gcataaacgt cccattggtt 3060 gtaaatgggt ttacaagatt aagctcaaac ctgatggcac aatcgaacgg tacaaggcgc 3120 gcctcgttgc caagggctac agtcaaattg aaggtgttga ttaccaagaa acctttgctc 3180 cagttgctaa attaaccaca gttcgcgtgc ttcttagtgt tgcggctgtg caagggtggc 3240 atctccatca actagacgtg aacaatgcgt tcttacatgg tgatcttgac gaagatgttt 3300 acatgaattt acctcctggt ttcggacgaa agggggagaa tcgagtatgt aagttgaata 3360 aatccctata tggcttaaag caagcttcca ggcagtggtt cattaagcta tccaatgccc 3420 tcatggctgc tgggttccat caatcacggt ctgattattc actattcgtc cgaagtcatc 3480 atggtaactt tgttgcttta ttagtctatg ttgacgatgt gatactggcg gggaatmatc 3540 tgcatgaaat tgaagagact aagcagttcc tctctcaacg gttcaagctg aaagacttgg 3600 gacaactcaa gtattttttg ggaatagaag ttgcacgctc aaaacgtgga atcactctat 3660 gccagcgcaa atacgcacta gagatattgg atgatgctgg ttttctagga gttaagcctt 3720 ccaggtttcc tatggatcaa aatttgtctc tcacacaaat ggaaggaaag gagttgaaag 3780 atccttcgtc atatagacga cttgtgggca ggttaattta cttgaccata acgagacctg 3840 atttagcata tgccgtccac atactaagtc agttcatgga gaaaccacga cacccacatc 3900 ttgaggcagc acataaagtt ctcaagtaca tcaaacaagc accaggacaa ggaatctttc 3960 ttccttccac aggatcactg gaattacaag cgttttgtga tgctgattgg gctagatgta 4020 gagatactcg aaggtcgata actggctact gtattttgct tggtcaagcg cccatttcct 4080 ggaagactaa gaaacaatat atctcgttct agtgcagagg ctgaataccg ttccatggcc 4140 accacatgtt gtgaaatcat atggttgaag aatattttga aagatctgaa agtgagtgac 4200 tcamaacctg ctaagttgtt ttgtgacaat caagcagcat tacacattgc ctccaatccc 4260 gttttccatg agcgaacgaa gcatatagag attgattgtc acctagtacg agagaagatt 4320 caggaaggga tgatacgtac ggcgtacgtg aggacaagtg atcaaccggc tgacatattc 4380 accaagccat tgagttcaac acagtttgaa ggattactta gcaagttggg tgtcattaac 4440 atacactcca acttgagggg gag 4463 // ID HARB-2B_Mad repbase; DNA; EDCOT; 4588 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; HARB-2B_Mad. XX NM HARB-2B_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4588 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1497-1497 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >91% identical to consensus. 3-bp TSDs are TWA. ~76% identical to CC HARB-2_Mad. XX FH Key Location/Qualifiers FT CDS 711..2114 FT /product="HARB-2B_Mad_1p" FT /note="transposase." FT /translation="MSSSRRVYKQLQEQQKRLLAQQAELANLEEGGGGDEA FT FFMEEDEDDHHRRQRASHSRRVMEAVGQIAKPRRAANLDRKRERRGKDLLE FT DYFIPNSIFPDHVFRRRFRMQRNLFDKIMSAICNHDPYFVQKEDAFHVLGL FT IPEQKITASLRMLAYGASADQVDEIARMGKTTVLESLMRFCSAIEALYTNE FT YLRTPTPRDMRRLLRKGEMRGFPGMIGSIDCMHWTWKNCPSAWQGAYGDRK FT *AKSIILEAVASFDTWIWHAFFGVPGAQNDLNVLAQSPVFDELLQGKSPRC FT TYWVNGTQYEGSYYLADGIYPRWSTFVKTVPHPQTEKEKHFAKCQEGCRKD FT VERCFGILQARWAIVRAAARMFDVEALRSIMMTCIILHNMIVEDEYDYDAV FT DEYEPDPMNNSRTRIYCAHDRTEDPVQHEPLERDGRYNELIVQRYTDVQEP FT YWHVTRQNDLIEHQWGLHEGEDN" XX SQ Sequence 4588 BP; 1362 A; 893 C; 957 G; 1374 T; 2 other; gagcaagtcc acccctaagg actttgtgcc agcacccagc ccatttatcc actccagtga 60 acagtaacag actccaatga acagtaatag gccaatgcat ctccacccct aaaaaaatgc 120 gctggcaccc agtgaaaaaa tgcgctggca caaacgatct ccacccctac aaaatgcgct 180 ggcacccagc ccatttaaaa tatttttaaa ttttttctaa aagaataaaa aaataaaata 240 gttttaattt cggataggat ttttaaccaa tctcgtcacg ccacgtgtca ttatccgaac 300 gtactatttt gtgaatagat ttccgctaag attttcaacc aatcccgacg cgccacgtgt 360 cacttccgtt ttacaataat ttagccaaga tttcgataag attttcaacc aatcacgtca 420 tgccacgtgt cattatccga acgtactatt ttgtggatag atttccgata akattttcga 480 ccaatcccga cacgccacgt gtcacttccg gtttacaata atttagccaa gatttcgata 540 agattttcaa ccaatcacgt agtgccacgt ggcattgtcc agaacctcat cctttctttt 600 tttgtccata taaaccctac atccctacat ccatcctcac accaagctca atccttcttt 660 ttagctcaga atccttgttc atcgttttca aatcttgagt tcttattaca atgtcttctt 720 caaggagagt gtataaacag ttgcaggagc aacagaaaag gttgttggca caacaggcag 780 aattggccaa tctcgaggaa ggtggaggtg gagatgaggc tttcttcatg gaggaggatg 840 aggatgatca ccatagaagg cagagggcct cacattcccg ccgtgtcatg gaagccgtgg 900 gtcagatagc caaaccaaga cgtgctgcaa acctcgatag aaaaagggaa agacgaggta 960 aagatctatt ggaagattat tttattccca acagcatatt ccctgatcat gtttttagac 1020 gtcgttttag aatgcaacga aatttgttcg acaaaatcat gagtgctatt tgcaaccatg 1080 atccatactt tgtgcaaaaa gaggatgctt ttcatgttct aggtcttatt cccgagcaaa 1140 aaattacggc atccttgcga atgcttgcat atggagcatc tgcagatcaa gtggatgaga 1200 tcgcgaggat gggaaaaaca actgttctgg agtccctgat gcggttttgc tctgcaattg 1260 aagccctcta caccaatgag tacctccgga cacccacgcc aagggacatg cgaaggcttc 1320 tgaggaaggg tgagatgcga ggcttccctg gcatgattgg aagcatcgac tgcatgcact 1380 ggacttggaa aaactgtcca agtgcgtggc aaggagctta tggcgacaga aaatgagcca 1440 aaagcatcat tttggaagcg gtggcttcat ttgatacatg gatttggcat gctttttttg 1500 gtgttccagg agctcagaat gacctaaatg tccttgccca atccccagtg ttcgacgaac 1560 tgctgcaagg aaaatcgccg agatgcacat attgggttaa tggtacccaa tacgagggat 1620 catactacct tgcagatggc atttacccaa ggtggtcaac atttgtcaaa acagtgccac 1680 atccacagac tgaaaaggaa aaacacttcg caaaatgtca agaagggtgt aggaaggatg 1740 tcgagcgttg ttttggtatc ctgcaagctc gttgggcgat tgtcagggct gcagctagaa 1800 tgtttgatgt cgaggctctt cgatccatca tgatgacgtg tattattctc cacaacatga 1860 ttgttgaaga tgagtatgat tatgatgccg tcgatgaata tgagccggat ccgatgaaca 1920 actcaagaac acgtatctac tgtgctcatg accggaccga agatcccgtg caacacgagc 1980 cgttggaacg cgatggacgt tacaatgaat tgatcgttca gcggtacact gatgtgcaag 2040 agccatactg gcacgtaacc cgccagaatg acttgattga gcaccagtgg ggattgcatg 2100 aaggcgaaga taattaaaat gaggcttgtg gttgaagaat aaattgtatt tttttttaag 2160 tttatgtaat tctatgtagt gtgttttgtt tttaagttta tttggtgagt ttatgtaatt 2220 ctatgtagtg tgttttgttt ttaagtttat ttggtgagtt tatgtaatct tatttggtga 2280 gtttatgtaa ttctatgtag tgtgttttgt ttttaagttt atttggtgag tttatgtaat 2340 cttatttcat gtgtttaaat aaagtacaaa aaaataaagt tttaaaaata aataaataat 2400 tacattaaaa ttgcataata aattaaataa aaataaataa agttttaaaa ataaataaga 2460 aataacataa aaattacata agaaattaaa taaagttcaa aagaaaaaaa aaaaaaatac 2520 ataagaaatt aaataaagtt ctaaagaaaa aaagaaaaaa aaacataaaa aatacataaa 2580 aattatacaa agtctctcga gttaggatat gtggtgctag gatcttggtt gccacgattt 2640 gtgtagctag aacccccttg acttgtttcc gcatctcttg cacgcctcct tcgcatgaca 2700 tctctttttt ccgatgtcca aaaatattta gaattcggag acagtcctac tagagacttg 2760 ctcatagtgt cacgatctgc ttgagccatc ctttcttctc taagcatttc attttctcga 2820 tgaagtgctt ctctaaccag ctcgttctct cgattaacta cttctctttg tctctcagcc 2880 gccgcatcac gggcctcagt agctgctatt attgctgcca tagcagcaac tttttcctca 2940 tctctagcct tttcccgtgc catgttcagt tcaccttggc gagcaagttc ctccatatat 3000 ttagtgtagt catttttgga agaactacct tttttctttg atgccttttt accttgaggc 3060 ctgagggact gacgagtcgg ttgggtctcg ggcacttgtt caggcgtccc ttccgtgtct 3120 tgaaatgtgt cggcttcttg ttcggccgtg tctggttctg gagaactatg tagacccatg 3180 ccgtgcatga caacttctgg accggttgcc acaattttgt atttagggca atctttgaca 3240 atttgccaac attcccatct ggtgaatgat ttgttctggt tctttgaatt gtagaatgct 3300 tgagcttgta gtgtctataa aaatgtggga taagatagtg ttaaaaaatg cgggtgtaac 3360 acaaataaat aaattcaaaa tattgatacg ggtggaatgc atataaatta cataaaaatg 3420 acataagaaa ttaaataaaa attacataag aaattaaata aattaaaatt ttgatgcggg 3480 tggaatgcat ataaaaatta cataagaaat aacataaaaa ttacatacga aattaaataa 3540 atcaaaatat tgatgtgggt ggaatgcata taaataaata aaaatattgt cacctgatcc 3600 gctaaacttg tcccactacg gaggttaccg gaagcatgag agatggcgtt tttccaacaa 3660 gtaaaggatg cgttgagttt tttccaacga ccttgaagac cttgactagt tctggcgtct 3720 tttccatgta catcgcaaaa cgctttcgta attttactcc acatttctcg cttatccatc 3780 tcattacccg taatcgggtc atgagtagtg tgaacccaac attcacacaa cgtaacatct 3840 tcaatgagct tccacgaaga catttttttc tcttaaagtg tagaaaatat tgaaatgtag 3900 atagtataga aagtgtagaa aatattgaaa tgtggtgtaa aggtggaaga tgagggttag 3960 gtatttatag gaaaaaaaat taacattttt aaaattttct gtattttttt aaaatttttg 4020 tattttttaa taatttttct gtatttttta ataattttta atgaatttta atatagttaa 4080 ttaatctgga ccgttggatt tgaaaaatat tcaaatccaa gagccaagga gttgccacgt 4140 ggccaacggt catatttctg accgttgggc cttttttttt ttttttttac tttttgtgga 4200 aaaaacgtgg accgttgatc tgtgatcgga cggtccattt taaaagtaaa atttaaattt 4260 tttttaccgt tggaaatcca acggtctaga aaactagccg ttggaaatcc aacggcacag 4320 agsgggccac gtcgccaact cggggggtgg accgagtgcg cctgcagcgg gccccgcctc 4380 tgaaaccctg tcggctactc gcgccacgcg cgcgtgagtg cacgcgccag ccaaataggc 4440 cggctcctgg gtctgtcaaa attgggctgg tccgtagccc ggctcgggct gggtgccagg 4500 caacttgacg ggctggagcg aattgacagg gccccggcct gttatttgga ctgggtgctg 4560 ggcaatgttc actccggtgg acttgctc 4588 // ID Gypsy-44_Mad-I repbase; DNA; EDCOT; 5564 BP. XX AC . XX DT 22-OCT-2010 (Rel. 15.1, Created) DT 22-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-44_Mad-I. XX NM Gypsy-44_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5564 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1782-1782 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 5564 BP; 1606 A; 1118 C; 1188 G; 1649 T; 3 other; aatttttggc gccgttgccg gggattagca actttgctaa tcccccgttg tttctttttc 60 atgtcttttg ttttagttac tgactttgtt tctatttgtg tcttttattt ttacttatga 120 tatttgattt agttttgttt ccttgatttc aggtactaga gaagtaagac atggattttg 180 ctaccattca agctcaattg gcgaaactta cttctcaatt gtcacaatat gccgaaagga 240 ccacaatgca aagtgtccct acatatggtg tgtcctatgg gcaaggatat ccaactcatc 300 aatgttctca attcgctgcg aatgaagatg cttggggtta tcaaggccat agccaatcat 360 gggacaacat gttttccaac gcttacaatt cggattggag agattattca gattacatgt 420 ggggagaacc tcaacaattc caacaagatg ggtattggca gcaagaagag gagttctatt 480 caagacctat gacagccacc acaacaatct gcccaattca attcaggtac gtctttggat 540 aatgatatgt ttaataagtt actcacctct ttgaaccagg aagtagaaaa tggaaacaaa 600 gagatgcaaa atcaagccaa gaagacgggt gaattggaga agcaaattgg gcagattatg 660 gagttcatgg cacaaattca agagcaaagt gaactctcca actcaactat tgaaaatttg 720 aaggaagatt ttgaaatcca tgatgctatc actttgggaa gtgctatgga ggttggaggt 780 gaacccaaga catccaaacc aagccaaaac atggatgaac agctgctgct cgaagaagag 840 gagaataaca aggccacggc aagggaagaa ccacccttgc cgcagcccca tatgccctct 900 atgccgtcca ctacaaccaa ggtaagccta aattcaattt gtcctgaccc cgtttcacca 960 aatgtcctta ttccttgcag gatcatgcaa tccaaggaag aagagggtga gaaaggcatc 1020 ttcgaaacct ttccaaagaa tcaagagcaa gaagtggatg gggaatgtct agaattcatc 1080 aaagaagata cacttgagac gaaaattccc aaagaagttg gattttatga cacgggacaa 1140 gtcataactc tcaaaacacc aaatctggcc aagtcccata tccctgcaac cttcaaagat 1200 gtggtgttcg taattgagtt tgtgttggag caagcaagta agccatcttc tccaacttcg 1260 attttattat atactaactt gctgattttg atgattcagg cacctacact agaatttaaa 1320 ccattgccgg atcacgtcaa gtatcaccgt ccattcaagg atcaattcca tgctatgggc 1380 cctatccaag tttagaagga agtttcgtcc ggctggaaga cgttaaagca agcgcttctt 1440 gggaggcaac ccatgtattc aaataaggaa gatttttgaa ttgctccaca atcagttttg 1500 cgtttctaaa aaccttccct tttctgcagt tttattttgc catgattgtc atttttattt 1560 gttgcttgtt taattgtttt tggtgtgggt ttatttttga aacactgaca gttatgcaag 1620 gtatttttac attcattttc aaaaaaaaaa ggaacattaa gcagaaaaat acaagaggga 1680 gccttcacaa aggctgctta ggagaagtct cagtagtcgg cggagcctca gcagtcggcg 1740 gagccccaga aggaggaggc atcggaggtt gatcatttgg agcttcatta cgcggtacag 1800 ccccagaaga cgaaggcaaa tgctgttgga acaaacccac aaacctctga tgatcaagta 1860 aaatctgacc atcagattcc tgcatctggt caatcttcct cttcatgttt gtagcatagt 1920 tatgtgcgag cctgtgcaac tgtttattct catgcttgag ccctctaatc tcctgtttga 1980 gactcatcac ttcagccgcc aatgattcaa cttgacgggt tcgagcaaat aggcgttggg 2040 ccatattaga cacagaacct gcacactgca cactgagagc cagagaatcc ttaacagcca 2100 actcatcaga ccgtttggca agtagtctgt tatctttggg agtgacaagg ttcctggcca 2160 ccaccgcagc tgtcatatca ttcttcatca ccgaatcccc aacggtaagg ggaccagtag 2220 gggatatgaa ggatgggcgc catatgttgt ctggagaagg cggggctgcc tcttcaccaa 2280 ggttcaagtc aaaacgacgg tcggaggggc cagacatttt cagaggtgtt aaagaaagaa 2340 gaggtcggac aagtcaagat cgtagaagtg caagaaggga gtttctacag gcagaaattc 2400 aagtgtgctt tgaaacgtcc tgcgtacctc tataaaaatc agcactcgac gggatttcag 2460 agatcgaaga ggcgagctca gaaatcgaag aggccaactc aaaaatcgaa gaggcgctag 2520 ctttctcaaa agctgggctt gctcagaaac cacggccaat cttcttttcc agatttgtcc 2580 gcacttgtca catgcaacct ctgcactcga cgggatttca gagatcgaag aggcaagctc 2640 agaaatcgga gaggcatctg cttttccaga cgtgtcagca tctgtcacat gcagagtcag 2700 ctttgcggaa atcacgggca gtttgtcgaa gcgccgattc cagatatcgg agaggcatct 2760 gcttttccag acgtgtcagc atctgtcaca tgcagatcag ctttgcggaa atcacgcaca 2820 agtcagcttt gcggaaatca cgggcagttt gtcgaagcgc cgattccaga tatcgaagag 2880 gcacttgctt ttccagacgt gtcagcgcct gtcacatgca cactcagcct tgcgaaaatt 2940 acgggcaatc tgtcgaagat ctcttgtgaa gtagaaagca cgtgaagttt actattaaat 3000 catccaacgg ttgctgacaa gagtgaaaga atagtaccgg ttattaattc ctataaatgt 3060 cacccttcac cctccattgc aaggcagaca tacataaccc ttcttcttct ccgagaatgc 3120 ctttccaaca aaccctctcg agtcactcag tgttccttat tccttggggt acctctgcaa 3180 acaactcatc caaagcaaaa gtatttcata tcatgaaggt tgaaagcaag agtatctcat 3240 atcatgcttt ctccctgtcc ttctccttgt cgttgttttg ggacaaggag aaagagagca 3300 atcagccagc acttggtatc aatcttccga tctggaaccg actgcctgga accccttcct 3360 gattgcttac ctagccttgc tctcgagtac tcatcttcaw catcttatgc ttcctcttcg 3420 tctaccacat ctgcctgggg aacagataag ggaagtgaaa atgatacctc gaagcatgtg 3480 gagacaatkt gccaattcat cctcagctag ggacaaggag aaagaaagca agaggtgggc 3540 acttggaaag attgaagaaa gaaacagacc awcacctcta cctcgtgcct gcctgccgtg 3600 cagaagaaac aagcagagaa gaatgcagac tgcacaatca aatcaaccca gcagaaggag 3660 tctgatttga aaccaaggaa ctctcatatt cctcgctcag aattccaaac cagttcgaga 3720 tcaaagctgt ggaaagtcaa caagatcatc tatctccaaa accagatttg cgttcttaaa 3780 ctctactctg tctggttttt actttgccat acttgtcatg tttattcgtt gtttgtttgt 3840 ttgcttgttt ttgtgtgagt ttatgcttga aacattgagg acaatgtttg atttaagtgt 3900 ggggggggta accaagttgt tttgcatgaa attcgtagga gtttatcacc cattacttct 3960 agtgttgttc cttgctgttt taagtgtttt taagctgttt tggagtgttt tagtgtgttt 4020 tgacataaaa atccgaaaat ctcataaaaa tttgaaaaat tgttttgaaa aacccaaaaa 4080 gagttgtttt tgtgtgttta tttgtgtctt agggtacctt ccaacacaat gatgaggatt 4140 tggtttttaa ttacatgact gttaaagaga gttataaaca tggatgaaaa tttgatttac 4200 tctttggtgt atgcttggtt gtggttataa tttatgaatt cacatgcaat cataaaggaa 4260 aaatcagttt ttgtaacatg cttgaaggaa ggaactcaaa tgaacgctac aaccttgtga 4320 gacttgagcc taaacgttta tttggagagt taataatctg tgcatcattg ttttctaaag 4380 tcgttgcatg atctcattat tctttgcttg gttgctactt agaaggcgtt tcatcattta 4440 gttccaaatg ctagaactca tgcctatttc attcaaagca tgctattgat ttgcataaca 4500 catattcaag atgaagttgt gtagtgacca ccaaagccaa attgccgtgc ccctatttca 4560 ttatgtgttt aagtttaacc ccgttgagcc ttgttaagcc tatgttcttt gttaacccac 4620 actatcctta cctagcctag ttttaggacc atccataccc ttgttcttga agcatagtaa 4680 agcatgactt aaaatgaact ccttttttat caatgtattg cagaaagcaa gtgtggggga 4740 agtgattctt gtgtgtgtgt gtgtgccaaa gtccttaata aggcacgggt agaaaagaaa 4800 aaaaaagagt gaaaagaaaa aagtaagttt gttaaaaaag ggtccaaaac attgaattcg 4860 gccctaagtg ttgcatgaat cttccctttg tatttaaaag ttgattctgc attctaaagt 4920 gaattccaag tgtctatttc attgctttgc ttgctatcgc tttaagaacg tttgttattc 4980 ctatcctttc tttgttagcc attaccccca agccctgtta caacccttga cttcaatctt 5040 gagtgttgtg tgtttcaatt tgtggagttc gaaattggta tgagcatatg gtgtcactgg 5100 ttctcgcatc taagtagtag cattccattc atgagatcat atctaaacat gcttaataac 5160 tccagaaaat tgctttcttt gttataacat atgtgagtcc tagtctttcg tgtttacatc 5220 aatcttctca catatactag tgtagggtgt gtagtcagaa aatgtgtgtg aaaatagaga 5280 gtatcttgta aggaattgag caaattctct aaggcatgtt actacattca aaacatcgtt 5340 ttaattggtt aattgtgaac tagtaagtgg tgactgtgat taagtatgtg ctcaagtgta 5400 aagatgacca aaatctgtgg gaatgatgat ttttaacatg tcatgtttca ttgaaaatcc 5460 ctgaggcaaa tgttggaagg tctaggttgt gttttgtttg ttttgtttcg ttttgtttct 5520 tttgttttgc tcgaggacta gcaaaagcta agtgtggggg aatt 5564 // ID Gypsy11-PTR_LTR repbase; DNA; EDCOT; 358 BP. XX AC LG_XII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy11-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-358 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-358 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 301-301 (2007). XX DR Genome; LG_XII; Positions 4349641 4349284. XX SQ Sequence 358 BP; 99 A; 72 C; 73 G; 114 T; 0 other; tgatatggac aaacagccca tcatgcatac ctgcgccatg caaaggatcg tggggggaaa 60 gtaaccacaa ctggtcgtgg gttgtgggga ttaattagtt gcagttattt ttcttagatg 120 tctgttatgc agggaattca tggtcattca tgaccacgtg tgaagtggaa cagccatgat 180 cacttagtga cacatattcc tcttttattg cttttaatat gcttgtaact tccagaacca 240 aaggcctata aaagttgtgg cctacgggag agaagatatc atgaaataaa ctgttcttct 300 ttaaactctt cttcccctat tcctttctct caaattctgt tatgtcaagt acacatca 358 // ID POPGY1_I repbase; DNA; EDCOT; 8434 BP. XX AC AC182679; XX DT 29-MAR-2007 (Rel. 12.03, Created) DT 02-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE Gypsy-type retroelement - internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; POPGY1_LTR; internal portion; POPGY1_I. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-8434 RA Jurka J.; RT "POPGY1: Gypsy like sequence from black cottonwood."; RL Repbase Reports 7(3), 137-137 (2007). XX DR EMBL/GenBank/DDBJ; AC182679; Positions 5627 14060. XX CC There are only 4 single-base substitutions between LTRs, CC indicating CC that this is a relatively new sequence. XX FH Key Location/Qualifiers FT CDS 161..5488 FT /product="POPGY1_I_1p" FT /translation="MRVWSRTLSGRLCRVSSSFSENMAEEDNQSLHNENNE FT NIRVRTLRDHMNPTRTSAPSCIVFPPDASHFNFKTGIIQLLPSFHGFDLEN FT PYLHLREFEEVCNTYNDSNCSMNTIRLKLFPFSLKDKAKTWLQNLRPGSIR FT AWDEMQQQFLKKFFPSHRTNSFKRQIITFTQKPGETFYQCWDRYRDLLNTC FT PHHGFETWRLVSHFYEGLTPRDRQMVELMCNGTFEDKDPNEAMEYLDLLAE FT NAQNWDTTGTYEAPSKTQPHTSSGGMYNLREDHDLQAKFASLARKVEALEL FT KKSGQLKSVQDIACQICETNEHSTNDCPTLPSFKECLHEQAHALNSFQRPN FT HNPYSQTYNPGWRNHPNFNWKNENNNAQTSQPPFQAHHNFQNSHGYAPPYA FT PPPRRNLEETLHAFMEKQEAINTQLAQSMTDFKDTLAKFTSALSFQEKGKF FT PSQPQQNPKGQYHANASSSGSQHMDHVKSVITLRSGKVIEKPILEPCENDD FT ESISEGKEGVESDHCKEKTDSPLALPFPHAMTKQRKVNHNSEIFETFKQVR FT INIPLLDAIKQVPSYAKFLKDLCTVKRKLNVKKKAFLAEQVSAILQNNNAL FT KYKDPGCPTISCFIGEHKIERALLDLGASVNLLPYSVFQSLNLGELKPTSV FT TLLLADRSVKVPRGIVEDVLVQVDKFIYPVDFIVLDTQPVEACNSFPVILG FT RPFLATSNALINCRNGLMKLSFGNMTLEMNIFNICKQPGDDNDLQEVDFTE FT KLVHDQFQTTSSEIEIDESEDLQMVYFQEESKENSWRPKIEKLPPRSIDSI FT PSSVQPPKPDLKPLPFNLKYSFLGENETFSVIISSKLNAHQEGKLLQTLKM FT HKNALGWTIADIKGISPLICTHRIYLEENAKPSREMQRRLNPNMKEVVKNE FT VIKLLDNGIIYPISDSKWVSPTQVVPKKSGVTVITNKKNELIPTRTITGWR FT MCIDYRKLNSMTRKDHFPLPFMDQILERVAGHEFYCFLDGYSGYNQIEIAL FT EDQEKTTFTCPFGTFAYRRMPFGLCNAPATFQRCMLSIFSDMVERFLEIFM FT DDFSVFGDSFDDCLTNLEKVLSRCEEKNLVLNWEKCHFMVTNGIVLGHIVS FT SKGIEVDKSKIELIANLPTPKSVKDVRSFLGHAGFYRRFIKDFSVISKPLS FT NLLTKDNIFEWNEHCEEAFVKLKNLLTSAPVIQPPDWSLPFEIMCDASDYA FT VGAVLGQRKDKKPYVIYYASKTLNRAQMNYTTTEKELLAVVFACEKFRSYL FT VGSPVVVFSDHAALKYLLSKKDSKARLVRWILLLQEFDITIKDKKGTENVV FT ADHLSRLTTDSRSDITPIDDYFPDESLFSVSTMPWYANIVNFLVSGQLPAH FT WSTQDKRKFLNEVKNFYWDDPYLFKYCPDQIFRRCIPDNEVSSVIKFCHSE FT ACGGHFSSRKTTAKILQSGFYWPTMFKDSHAFCKTCENCQKLGSISKRHMM FT PLNPILVIEIFDCWGIDFMGPFPPSFGFLYILVAVDYVSKWIEAIPSRNND FT HKIVIKFLKENILSRFGIPRAMISDGGTHFCNNPFESLMKKYGITHKVATP FT YHPQTSGQVELANREIKQILEKTVNPNRKDWSLRLNDALWAYRTAYKTSLG FT MSPYRLVYGKPCHLPVELEHKAYWAIKAFNSNLDDASQLRKLQINELEEIR FT NDAYENSKIHKARIKEFHDKRILRKTFDVGQKVLLYNSRLHLFPGKLRSRW FT SGPFIVKRVYPYGACDIENPKNGNVFKVNGHRLKVYFDNFSVENDSIKLSD FT PVYKE" XX SQ Sequence 8434 BP; 2730 A; 1471 C; 1583 G; 2650 T; 0 other; agtttttggc gccgttgccg gggaggtaaa ttcttgtaca aattatagtg tttattttat 60 tttctctttt tacttttctt gtatttaact ttgtttcttt tgtgttgttt ctttttctat 120 tgtttttctt ttctttcttt tattctcttc ctgcacgtgc atgagagtgt ggtcacgtac 180 attaagtggt agactttgta gggtatcctc atcattttca gaaaatatgg ccgaagaaga 240 taaccaatcg cttcacaatg agaataatga gaatattcgg gttagaactc ttagagacca 300 catgaatccc acaagaacaa gtgcaccttc atgcatagtt tttcctcctg atgcatctca 360 ttttaatttt aagacaggca ttattcaact tttaccatct tttcatggct ttgatttaga 420 aaatccatac ttgcatttaa gggaatttga ggaggtttgc aacacgtata atgactcaaa 480 ttgtagcatg aacaccatta ggttaaagct ttttcctttt tcactaaaag ataaagctaa 540 aacatggcta caaaatttga gacctggatc cattcgtgct tgggatgaaa tgcaacaaca 600 atttttaaag aagttttttc cgtcccacag aacaaactct ttcaaaagac aaatcatcac 660 tttcactcaa aaaccaggag aaacatttta ccaatgttgg gatagatatc gagacttgct 720 taatacttgc ccccatcatg gttttgaaac atggagatta gtttcacatt tctatgaagg 780 attaacacct agagataggc aaatggttga attgatgtgc aatggaactt ttgaagataa 840 agaccctaat gaagcaatgg agtacttaga tttgctagct gaaaatgcac aaaattggga 900 caccacaggt acttatgagg caccaagtaa aacccaacct catacatcta gtgggggtat 960 gtacaacctt agggaagatc atgacctcca agccaagttt gcatccttag ctagaaaagt 1020 cgaggcacta gaattgaaaa agagtggtca attaaaatct gttcaagaca ttgcgtgtca 1080 aatctgtgaa accaacgaac attcaaccaa tgactgtcca accttgcctt cttttaaaga 1140 atgtctccat gaacaagccc acgcattaaa cagtttccaa aggcccaatc ataacccata 1200 ctcgcaaaca tacaaccctg gttggagaaa tcacccaaat ttcaattgga agaatgagaa 1260 caataatgct caaacttcac agccaccgtt tcaagcacac cataatttcc aaaattctca 1320 tggatatgca cctccttatg ctccgcctcc tagaagaaat cttgaggaaa cattgcatgc 1380 atttatggaa aagcaagagg caattaacac tcaacttgct caaagcatga cagattttaa 1440 agatactctt gcaaagttca catctgctct cagtttccaa gagaaaggta agtttccatc 1500 tcaaccacaa caaaatccca aggggcagta ccatgcaaat gcaagtagtt cgggaagcca 1560 acacatggat cacgtaaaat cagtcatcac tcttcgcagt ggtaaggtta ttgaaaaacc 1620 cattcttgaa ccttgtgaga atgatgatga gtcaatctct gagggtaagg aaggggttga 1680 atctgatcat tgcaaagaaa agactgattc tccgctagca cttccatttc ctcatgccat 1740 gaccaaacaa aggaaagtta atcacaactc tgaaatcttt gaaactttca aacaggtaag 1800 gatcaatata cctttgttag atgctattaa acaggttcct tcttatgcta aatttttgaa 1860 agatctgtgc actgtgaaga gaaaattgaa tgtgaaaaag aaagcctttt tagccgaaca 1920 agtaagtgcc attcttcaga acaataatgc attgaaatat aaagaccctg gttgtcctac 1980 aatttcttgc tttattggag aacataaaat tgaaagagcc ttacttgatc ttggagctag 2040 tgtgaattta cttccatatt cagtttttca aagtctcaat ctaggtgagt taaaaccaac 2100 ttctgtgact cttttacttg ccgatagatc tgtaaaagtg cctagaggaa tagttgaaga 2160 tgtgttagta caagtcgata aattcattta ccctgtagat tttattgtct tggacacaca 2220 acctgttgaa gcatgtaatt catttcctgt tattttagga cgtccgtttc ttgcaacttc 2280 taatgcattg attaattgta ggaatggact gatgaagcta tcttttggaa acatgacatt 2340 ggagatgaat attttcaaca tttgcaagca acctggagat gataatgatt tacaggaagt 2400 ggactttact gaaaaattag ttcatgacca atttcaaacc acttccagtg aaattgagat 2460 tgatgaatct gaagatttgc aaatggttta ttttcaggaa gaatcaaagg aaaatagttg 2520 gagaccgaaa attgagaaat tgccaccacg atcaattgat tccatacctt caagtgttca 2580 accaccaaaa ccggatttga agccgttacc attcaatctc aaatactcat ttttgggaga 2640 aaatgaaact ttttcggtaa taatctcttc caaacttaat gcacatcaag aaggtaagtt 2700 attacaaact ctgaaaatgc acaaaaatgc attaggatgg accatagctg acataaaagg 2760 aattagtcct ttgatttgca cacacaggat ctatttggag gaaaatgcta aaccctctag 2820 agaaatgcaa cgaaggctta atcctaatat gaaagaagta gtgaaaaatg aagtcattaa 2880 gcttctagat aatggaatca tttatcctat ttctgacagc aaatgggtaa gtcctaccca 2940 agttgtaccc aagaagtctg gagtcactgt gataacaaac aagaaaaatg agttaattcc 3000 aactaggact attactggtt ggcgcatgtg cattgactat aggaaactaa attcaatgac 3060 tagaaaagat cattttcctt tacctttcat ggatcaaatc ctagaaagag ttgcaggtca 3120 tgaattttat tgtttcctag atggctattc aggttacaac caaattgaaa ttgcattgga 3180 agatcaagag aagactactt tcacatgtcc atttggtact tttgcatatc gaaggatgcc 3240 ttttggatta tgtaatgcac cagccacgtt tcaaagatgc atgctcagta tatttagtga 3300 tatggttgaa cgttttcttg aaatttttat ggatgatttt tctgtttttg gcgattcatt 3360 tgatgattgt ttgactaact tagaaaaggt tttgagcagg tgtgaagaga agaatcttgt 3420 actgaattgg gaaaaatgtc actttatggt aacaaacggc attgtacttg gtcacattgt 3480 ttcatccaaa ggaattgagg ttgacaaatc taaaatcgaa ttaattgcta acttgccaac 3540 accaaaatct gttaaagatg ttagatcatt cttaggacat gctggttttt ataggaggtt 3600 catcaaagat tttagtgtga tatctaagcc cttgagtaac cttctaacaa aggataatat 3660 ttttgaatgg aatgaacatt gtgaagaagc ctttgttaaa cttaaaaacc tgcttacttc 3720 tgctcctgtc attcaacctc ctgattggtc attacctttt gaaataatgt gtgacgctag 3780 tgattatgcc gtgggtgctg tcttgggaca aagaaaagat aagaaaccct atgtgattta 3840 ctatgcaagt aaaactttga atagagctca aatgaattac accaccactg aaaaagaatt 3900 acttgcagta gtatttgcat gtgaaaaatt caggtcttat cttgttggct cacctgttgt 3960 tgtttttagt gatcatgcag cattgaaata tcttctttct aagaaagatt ctaaggctag 4020 attggttcgg tggattttgt tacttcaaga atttgatatc acaatcaaag acaagaaagg 4080 caccgaaaat gttgtcgcag atcacttgtc aagattgaca acagattcga gatctgacat 4140 cacaccaatc gatgactact ttcctgacga atctttattt tctgtctcta caatgccttg 4200 gtatgctaat attgttaatt ttcttgtttc aggacaatta ccggctcatt ggagtaccca 4260 agacaaaaga aagttcttga atgaagtaaa gaacttttat tgggatgacc cttatttatt 4320 caaatattgt cctgatcaaa tatttcgaag atgcattcct gacaatgagg taagtagtgt 4380 cattaaattt tgtcattctg aggcatgtgg gggtcatttc tcatcaagaa agaccactgc 4440 aaaaatccta caaagtggat tttactggcc caccatgttc aaggactcac atgcattttg 4500 caagacttgt gaaaattgtc aaaagttggg atctatttca aaacgtcata tgatgccctt 4560 aaatcctatt cttgtcattg agatctttga ctgttggggt atagatttca tgggtccatt 4620 tcctccatca tttggtttct tgtacatatt agtcgcagta gattatgttt caaaatggat 4680 agaggcaatt ccaagtcgaa acaatgacca caaaatagta ataaagttct taaaagaaaa 4740 tattttgagt cgatttggaa tccctcgagc catgataagt gatggtggaa cacatttctg 4800 caacaatcca tttgagtctt taatgaagaa atatggaatc acacacaaag ttgccacccc 4860 ttatcaccct cagacaagtg gacaagtaga gcttgctaat agggagatca aacaaatctt 4920 ggagaaaaca gtgaacccta ataggaaaga ctggtcttta agacttaatg atgcactttg 4980 ggcttatcga actgcttata aaacatcatt aggtatgtca ccttatagac tagtctatgg 5040 aaaaccttgt cacttgcctg tggaacttga acataaagct tattgggcta ttaaagcttt 5100 caattcaaac cttgatgatg ccagtcagct gcgtaagtta caaataaatg agcttgagga 5160 aataagaaat gatgcatatg agaattcaaa aattcataaa gcaagaatca aagaatttca 5220 tgacaagaga atcttgagaa aaacatttga tgttggtcaa aaagttttgc tttataattc 5280 tcgactccat ttatttcctg gaaagctaag atcaagatgg agcggtcctt ttattgtgaa 5340 acgtgtgtat ccatatgggg cctgtgatat cgagaatcca aagaatggca atgttttcaa 5400 ggtaaatgga catcgtttga aagtttactt tgacaatttt tcagttgaaa atgactctat 5460 taaattgagt gatcctgtat ataaagaatg attctttttc tcatattatt ttgtgttttg 5520 ttttggtgtg aattttgttt tgctagtctc tctcaccccg gtcaaatggc ggataacggt 5580 actccgtgac ttcagtcggt tctttcagtt tcccataata actgatattt gtatatattg 5640 tgcaattctt ggctctttct ctcttctttg actctcttct ccaattctca ttgaaaatgg 5700 acaccactct tgaaaaattg aaaaagtact ttcccgctct acctcagaat gcgattacaa 5760 aaatttacct tgctaggtgt gcaagattaa ggttgttaat gaatcatgga attcctgaag 5820 atattcgttg gctgattgaa gcaaaggtcc gattatcagg tgagtcctct aattctttca 5880 tttcacacat gcctggaaca ggtaaaagca cttttgcaaa gaaacgtcgt gcaaaacgac 5940 tgaaagtctg tcaccgatgt gctagatgga cttgtaatgc aacatgtcgt tctttaggaa 6000 tggtatctat aaaccgtgaa gataaaatac aattcattaa ggatggcctg agtaaggggt 6060 ctttagataa tcttctatta acccttgaga cgcatcctag tggagatgtg catcgtgcta 6120 ttcatgattt atggccacaa ttccataaag aacatgatcg agttagtctt gggaatctga 6180 ctaaaaaaga ccctgtttgc cagtttttaa gaaaactgga tgggaagcct atccccgacc 6240 catagagggc gtttaagccg ttcttggacg taaaaccaag ggaagatgtg agccacaatc 6300 acaactacct gtacatacac atgcttttca aaataaataa atacataaag agagagagag 6360 agtgtgagac tccagctggc ctatatctag gtgatatgat tgcattttca aatcctcatc 6420 tataaaatct tctcttcctt cccctcattt ctactcaacc cttacattac acagatatag 6480 aagtgtgtag aaatggcagg tccctcaagt tatcacataa aaaatatttg tgtttttggt 6540 ggatccagtc ctgggaagga aatagctttt ttggaagcag caaatcatct tggtcaggta 6600 ctagctgaga aaaagattca tttagtgtat ggaggaggca accttgggtt aatggggggt 6660 gtggcaatag ctgcattttt aggaggtagt caagtcttgg gggtcgtccc cgaagcttta 6720 acaaaagggg acatcattgg aagaacaatt ggagaggaac tacaggtctc cacaatgtct 6780 gatcgattga atgcaatgtt taaccatgct gatgccttca ttgccttacc aggtggtttg 6840 ggcacattgg aagagatctt tcatatttcc tcttgggccc aacttcacat tcaccataaa 6900 cctataggtt tgctcaatgt taatggtttt tatgataaat tgttgtcttt tcttgatcaa 6960 gctgtggaac aggaatttct aacatcttcg gcacgacaaa tcataatctc tgctgctact 7020 gctgaacaat tgatcgacaa actacaatct ttcacccctg taattgatcc ttccatgagt 7080 cgcataaatt ggtcaactac agaaagccgt aaaaagctta gattggattt gagccttcgt 7140 ttgtgaatcc ttgtgtcttt tggttttatt aatagcatat tattttgttt tgttatttct 7200 tatatttgtt taagtgtgtt tcaggtttgt cagtgttcgt tgtttcaggt gatgtcttct 7260 atactctatc tttctatctt atgacattga ggacaatgtc ttgttctggt tggggggaga 7320 gggtagtagt tgacaaaaaa aaaaaaaaaa aaaaaaaaac ttactaactg tttttgctat 7380 tagtaaaacc atttgacaaa actgttatta ctaggatggc agagtaaggg gaaattttat 7440 tgactcttga gacgcatctt agtaaacatt ttctaatggt tatttgcaat attcataaca 7500 aggcctatta gaatacttct tgaaatattc aggtttacaa actctcgcat tattatcact 7560 tgattctgct catatactca tttaacaagt attcttaaac cttcattttc acacacacac 7620 tttaacatat gattgtgggt tgcacattgg attattacat tatttatgtt cttttgttaa 7680 aggtaacaac taagggatag ggatagtcta taatttaaaa aaaaaaaaaa aaaaaaaaca 7740 acaacaaaaa ttgatgataa taaaagcgta gataagtttg gtttcgtagc ctccctaacc 7800 taagtaatta agcccgaagg ggtgttttaa cacctaatac cctaaagtca actgacttgg 7860 gagctattgg cccaaagctt gttacatggg ttaaggagaa aagcttaagg gaatcaaaca 7920 ttgcactatc tacgtatcag tatctgcaac ccgagttact aagctcgtag gggtgtctca 7980 acacctaatg ccctaagacc aactggtctg ggagtcatta gccgaaagct cgttacatgg 8040 gttaaagatg cattgtgttt taagtatatg tatatataca ttgaaaaaaa ataccaaaaa 8100 aaaaaagaga aaaagaaaaa aaaaaaaaaa aaaaaagaag ataataatcc caacccaagg 8160 aagttaacct taaacattag aacagaatat tgttttcttc caataaaagc cccatcatct 8220 atgttttcat acattgagca cataaaaagg aaggtttaat aatattttgt ttaagaggta 8280 ttgagcagat atataaaatt taatgagagt ttgtttatct ggatagatta atggaagttg 8340 aatgatgaat gccttgcttt gtgaaatttg caaatagttt ttctatttta acgctttgat 8400 tactagggac tagtaataag ctggttgggg ggtg 8434 // ID Copia15-PTR_I repbase; DNA; EDCOT; 4619 BP. XX AC scaffold_320; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia15-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4619 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4619 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 202-202 (2007). XX DR Genome; scaffold_320; Positions 35149 39767. XX CC Positions [1855-2373] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 22..4617 FT /product="Copia15-PTR_I_1p" FT /translation="MANAHTENDSQSFNDTNPKNKYLNFSDPFNPFRIENG FT DNPAAALVSELLTADNYVSWSRAISRALRAKNKLAFVNGTLSKPTDISDPL FT FEAWERCNDLVVSWLQNYVSSSVKSSLALVEDSRVLWLELRDRFTHQNGPR FT IFQLKRDLASLSQNQDNISTYFGHLKALWDELAIYDPLPDCVCGKLKILHD FT RYDRDCVIQFLMGLSDSYSNTRDQIMLLDPLPSLNRVFSMIQQQERQHLMI FT PSIKSPDLMAMMAKPFFNSSKNFSKATSQKTNRPYCSYCKLPVHSLENCFK FT VGNADPPQCTHCNMTGHIAERCYKLHGYPPGHKLHGKTKGIAATITQSRAL FT SDGDHEEDSTESMMLTRSQYQQLLSLLHSKETSSAMASLSVTQPSSSSPTP FT HVSNSRVSGMATCFSTSTHSSHPTHISPWIIDTGATDHMICCTSLFTSITA FT TVSYQVKLPNGQDVPVTHIGVVRLSEHLVLTHVLCVPSFNFNLLSAKQLTQ FT HHSCCLIFLSNACFFQDLASWTTIGMGEVRTGLYHLLRSRVSPSALVDALP FT HLHSSTSFPSASATHTTSLCDLWHYRLGHIFLSRLALITDPIITHNRTFHN FT PIPCSICPLAKQRRVSFPTSAHSALNNFDLVHCDIWGPNSVIAVDGSRFFL FT TIVDDHSRTTWVYMLRNKSDTRSCFMAFYSLIETQFHTKIKIIRSDNGAEF FT RMTDFFQTKGIIHQRSCVDTPQQNGRVERKHQHIMNIARALMFQSHLPPQH FT WTDCVLTATYLINRTPTPLLHNKTPYESLFQTPPQYKHLRVFGCLAYASTL FT SHGRKKFDPRGRACVFLGYPFGVKAYKLLDLQTDQIFLSRDVHFHESIFPF FT HSSFSPSVLPSNSITHPLPSSLPSSISIPTSPSSPPSLSSLTPSPALPANQ FT SSSQNFLAPGSPPPTPSPPQTFISPPTLSPATVASPPSSVSPFRRSTRTRR FT APEYLQDYHCHQTTLTPPISLLNQLLCSPSGTSSPLHTTISYQHFSPTYKA FT FSTSISTHIEPKTYKQALKDPGWCKAMDTELAALEANQTWQLTDLPPGKVP FT IDCKYVYKIKYNSDGSVERLKARLVARGFTQLEGVDYHETFSPVAKLVTVR FT CLLATASVKGWHLHQFDVNNAFLHGDLHEDIYMNKPPGYIKGSPTQVCKLL FT KSLYGLKQASRQWYSKFSNVLFAAGFSQSKADYSLFTRDINGTFVVILVYV FT DDILVASSDIAAVHELKSIFHRHFQIKDLGTLRYFLGIEVARSSQGIYLCQ FT RKYTLDILADSGTLGSTPAKVPMQQNLNLTQTTGTPLSDPSVYRRLIGRLL FT YLTVSRPDICYSVNNLSQFMANPTDAHLHAAHKVLRYLKGAPGQGLLFSSS FT SSLHLEAYCDSDWASCPDTRRSISGYCIFLGSSLISWKSKKQSVVSKSSAE FT AEYRSMAVTCAELTWLKYILSALHVQHFQPVSLHCDNQAAMHIAANPVFHE FT RTKHIELDCHLIRDQIQAGHICTRYVSSSNQLADIMTKALSSSVLNFHLSK FT MGVVNLYTPSCGGVLE" XX SQ Sequence 4619 BP; 1176 A; 1171 C; 769 G; 1503 T; 0 other; tggtatcaga gctgccgatc aatggccaac gctcatacag aaaatgattc tcagtccttc 60 aacgatacaa accccaaaaa caaatacctc aatttctctg accctttcaa tccattccga 120 attgagaatg gtgataaccc agctgctgct ctcgtttctg aactcttgac tgctgataat 180 tatgtcagtt ggtctcgtgc gatttctcga gctcttcgcg cgaagaacaa acttgctttt 240 gttaatggta cattgtctaa acctactgat atctcagatc ctctttttga agcttgggag 300 agatgcaatg acttggttgt ttcgtggcta caaaattatg taagttcttc tgttaaatct 360 agtcttgctt tagttgagga ttcaagagta ttgtggctgg aactcaggga tcgttttacc 420 catcaaaatg gccctcgaat ttttcaactc aaacgtgatt tagctagctt atctcaaaac 480 caagataata tcagcaccta ttttggtcac ctcaaagcat tgtgggatga acttgctatt 540 tatgaccccc ttcccgattg tgtatgtggg aaattaaaaa tccttcatga tcgatatgac 600 cgagactgtg ttattcaatt ccttatgggt ttgtctgatt catactcaaa caccagagat 660 cagataatgt tacttgatcc tctcccatcc cttaaccgtg tattttccat gatccaacaa 720 caagaacgac aacatttgat gattccttct atcaaatccc ctgaccttat ggcaatgatg 780 gccaaaccat tttttaactc tagcaaaaat ttctccaagg ctacttccca gaaaactaat 840 cgcccatact gctcttactg caagcttcct gttcattctc ttgaaaattg ttttaaggtt 900 ggaaatgccg atccaccaca atgcactcat tgtaatatga ctggccatat tgccgagaga 960 tgttataaac tgcatggcta cccacctggt cacaaactcc atgggaaaac taaaggcatt 1020 gcagcaacta ttactcaatc ccgagcactc tcggatggtg atcatgagga ggattcaact 1080 gaatcaatga tgcttaccag gagtcaatac cagcaattac tttctctttt gcattccaag 1140 gagactagtt cagccatggc ttcactatct gttacacaac catcttcttc ctctcccact 1200 cctcacgtca gcaactctcg tgtttctggt atggccactt gcttcagcac aagcacacac 1260 tcatctcatc ccacacacat ctcaccttgg attattgaca ctggtgcgac ggatcatatg 1320 atctgttgta cctccctttt tacatctatc acagccaccg tttcctatca agttaaactt 1380 ccaaatggcc aagatgttcc tgttacccac attggtgtcg taagattatc tgagcacctt 1440 gtcttaactc atgttttgtg tgttccttct tttaacttca atttgctttc tgccaagcaa 1500 cttactcaac atcattcttg ttgtctcata tttttatcca atgcctgttt ttttcaggac 1560 ttagcatcat ggacaacgat tgggatgggt gaagttagaa ctggtctgta ccaccttctc 1620 aggtctcggg tgtcaccctc tgctttggtt gatgcactgc ctcatcttca ttcctcaact 1680 tcatttcctt ccgcttccgc tactcacact acttcattgt gtgatttatg gcattatcgt 1740 ttaggacaca ttttcctttc cagattagct ttaatcactg atcccattat cacacacaat 1800 cgaacatttc ataatccaat accatgttcc atttgtcctt tggctaagca gcggcgtgtt 1860 tcttttccaa cttctgcaca ttctgcttta aataattttg atcttgtcca ctgtgatata 1920 tggggtccca actcagttat tgcagtggat ggatcacgtt tttttcttac aattgttgat 1980 gaccactctc ggacaacatg ggtttatatg cttagaaata aatctgatac ccggtcttgt 2040 tttatggctt tttacagttt aattgaaact caatttcaca ctaaaatcaa aatcattaga 2100 agtgacaatg gagccgagtt ccgcatgaca gatttttttc aaactaaggg cattatccac 2160 caaaggagtt gtgtcgacac accccaacaa aatggaaggg tcgagagaaa acatcaacac 2220 ataatgaata ttgcccgagc cttaatgttt caatcccacc ttccacccca acattggact 2280 gactgtgttc tcacagcaac ctaccttatt aaccgtactc ctacccctct tcttcataac 2340 aaaacaccat atgaatctct cttccaaacc cctccccagt acaaacactt gagagttttt 2400 ggttgccttg cctatgcctc taccttgtcc catggacgta agaagtttga tcctagaggc 2460 agagcatgtg tgtttttagg ctaccctttt ggagttaaag catataaatt acttgatcta 2520 caaactgatc aaattttttt atctcgagat gttcattttc atgaatctat ttttcccttc 2580 cattcatctt tttcgccttc tgttctacct tccaactcta ttacacatcc tttaccttct 2640 tcactgcctt cttctatttc tattcctact tcaccatcct ctcctccttc tctctcctcc 2700 cttactccct cccctgccct tcctgctaac cagtcttcat ctcaaaattt tttagctcca 2760 ggttctcccc ctcctacacc ttccccacca caaactttta tttctccacc tacattatct 2820 cctgctaccg tagcttctcc tccttcttca gtttcccctt ttcgcaggtc aactagaacc 2880 cgacgtgctc ctgagtacct gcaggattac cattgccatc agactactct aactcctcct 2940 atctcgttgt tgaaccagct gctatgttcc ccttcaggta catcttcacc tcttcatact 3000 actatttctt accagcattt ttctcctact tataaagctt tttcaaccag tatttccact 3060 catattgaac caaaaacata taaacaagct cttaaagacc ccggatggtg taaggccatg 3120 gacactgaat tagcagcctt ggaggcaaat cagacttggc aacttacaga tttacctcct 3180 ggcaaggttc ctattgattg caaatatgtt tataaaatta agtataattc tgatgggagt 3240 gttgaacgac ttaaagcaag acttgtggct cgcggtttca cccaacttga gggagtggac 3300 tatcacgaga ctttttctcc tgtggctaag ttggttactg tgaggtgtct cttggctact 3360 gcatcggtta aaggatggca tttacatcaa ttcgatgtaa ataatgcgtt cttgcatggg 3420 gacttgcatg aagatatcta tatgaataaa cctcctggct acataaaagg atcacctact 3480 caagtctgta aattgctcaa gagcttgtat ggtctcaaac aagcttcaag gcaatggtat 3540 tccaaatttt ctaatgttct ttttgctgca ggtttctctc aatccaaggc tgattatagc 3600 cttttcaccc gtgacattaa tggcacattt gttgttatcc ttgtttatgt cgacgatata 3660 ttggttgcaa gcagtgacat tgctgctgtg catgaattga aatctatttt tcacaggcat 3720 tttcagatca aggaccttgg caccttacgc tactttctcg gcatagaggt tgcaagatcc 3780 tcccaaggca tttatctctg ccagaggaag tacacactgg atattcttgc agattctggc 3840 accttaggca gcacccctgc taaggttccc atgcagcaaa acctcaatct tactcaaaca 3900 actggcactc cattatctga tcccagtgtt tatcgacgtc ttattggcag gctcctttat 3960 cttacagtct ctcggccaga tatttgctat agtgtcaaca atttgagcca attcatggct 4020 aatcctactg atgctcattt acatgcagcc cacaaagtcc ttcgctacct taagggtgca 4080 ccaggacaag gacttttgtt ctctagttct tcatctttac atcttgaggc ttattgcgat 4140 tctgattggg cttcttgccc cgataccaga cgttctatta gtggctactg tattttcctt 4200 ggctcttcct tgatctcttg gaaatccaag aaacaatctg tggtctccaa gtcctcggca 4260 gaggccgaat accgttccat ggctgtcact tgcgctgaat taacttggct gaaatacatt 4320 ctgtctgccc tccatgtcca gcattttcaa ccagtttcat tacactgtga caaccaagct 4380 gctatgcata ttgcggcaaa tccagtcttc catgagagga ctaaacacat tgaactcgac 4440 tgccatctaa ttcgagacca gattcaggcc ggccatatat gcactcgtta tgtctccagc 4500 tccaatcaac ttgctgatat tatgacaaaa gctttatcat cctcagttct taattttcac 4560 ttatccaaga tgggagttgt aaatctttac actccatctt gcgggggggt attagagga 4619 // ID SHACOP23_LTR_MT repbase; DNA; EDCOT; 209 BP. XX AC CT030234; XX DT 30-JAN-2007 (Rel. 12.01, Created) DT 30-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of LTR retroposon, SHACOP23_MT, from barrel medic. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; terminal; repeat; SHACOP23_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-209 RA Shankar R. and Jurka J.; RT "SHACOP23_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 70-70 (2007). XX DR EMBL/GenBank/DDBJ; CT030234; Positions 55180 55388. XX SQ Sequence 209 BP; 64 A; 31 C; 26 G; 88 T; 0 other; tgagctagta aataaatgca catattatgc ctaaaattgt gcatacgttt gctgttattt 60 tgctttttac gttactacta attaatggca attgttacat tgtaacaaat atatatatgc 120 cttttcatta tactgagttg acattgagaa ataattcaat tattggaaac ctaattggtt 180 atcccttttt catcttttac ttattctca 209 // ID BoSB6A repbase; DNA; EDCOT; 288 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB6A. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-288 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 288 BP; 82 A; 54 C; 73 G; 79 T; 0 other; gtggaagccc ccttagtcca gtggtttgac taagggttca ttaatgcttc tacaccagga 60 ggtctggggt tcaaacccca gaaaacgcaa acttatgcag attatggaga aaaaaggtta 120 caagaggtct tcagcatggt gcaaggcgta tcatcgaaca tggatctcat agggcggctc 180 ggagtgatgc agtcagacgt gcattctcat atgatggtag aattgtcggc tgtagaatcg 240 tctatgtaat atttctcatc gttgtaatag cataattaat cagacgtt 288 // ID HAT-N8_Mad repbase; DNA; EDCOT; 532 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-N8_Mad. XX NM HAT-N8_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-532 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1630-1630 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >96% identical to consensus. 8-bp TSDs. Both termini are similar CC to those of hAT-9_SBi and hAT-9N_SBi. XX SQ Sequence 532 BP; 152 A; 105 C; 92 G; 183 T; 0 other; ctatgatgca cggatacttc tgtttggtcc cgtatcccgt atccgatact tgatcggata 60 cgatacttgc ccgatactct cggatactcg tccgacacgt atcctggttg atggacacga 120 atttgacatg atggatatgc gtatcctaca tttaggatac acgtatcctg cttttaagat 180 acatttacac tttcaaaaaa aggtaatgag gaggagaaaa ttaataggag acatctataa 240 ttgaaagttg ctaaatacaa agagcttccc tctaattaaa accatgaata cgactctcac 300 acttcttcta ctgtataaag aggattagat ttcgaacttt ccttctctaa caactcaaat 360 gtacttgaat ttgaatgatg aattatgttt taaaatgtat atttttgttg ctatatacat 420 ttttatttgc cgtatccata gcgtatcgta tcttaatttt tagagatttt ccgtatcgcc 480 gtgtcgtgtc gtatcgtatc gccgtatccg tatccgtatc catgcttcat ag 532 // ID MUDRAV2_MT repbase; DNA; EDCOT; 421 BP. XX AC . XX DT 27-NOV-2006 (Rel. 11.11, Created) DT 01-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE Putative non-autonomous DNA transposon, from Medicago truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW non-autonomous; Inverted repeats; Interspersed Repeats; KW MUDRAV2_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-421 RA Shankar R. and Jurka J.; RT "MUDRAV2_MT: A putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 579-579 (2006). XX DR [1] (Consensus) XX CC A new transposon family from Barrel Medic, which lacks the CC transposase domain. It is close to another putative CC non-autonomous DNA transposon family, MUDRAV, though differences CC between these two families have been mainly due to A->T CC transversion in large. CC The sequence is flanked by 9bp TSD (TTAAT[A/T]ATA). XX SQ Sequence 421 BP; 126 A; 76 C; 82 G; 137 T; 0 other; ggtttaaata tgtctttagt ccttgcactt tcatcagatt ttggcattgg tccctacact 60 ttttttttgt ttggaattgg tccctgcact ttgtaaaaat attggtattg gtccctctat 120 taactttctg ttaaaaaaaa aaccacaaaa ctattggtat tggtccctgc actttgtaaa 180 aaatattggt attggtccct gcactttgta aaaaatattg atattggtgc cacgtggcgt 240 gaaatgattg ggccacgtgg cactccgttg gttttgtgtg ttttttttta acagaaagtt 300 aacagaggga ccaataccaa tatttttaca aagtgcaggg accaatgcca aacaaaaaaa 360 agctgcaggg accaatgcca aaatctgatg aaagtgcagg gaccaatgac acatttaaac 420 c 421 // ID COP18_LTR_MT repbase; DNA; EDCOT; 238 BP. XX AC . XX DT 10-JAN-2007 (Rel. 12.01, Created) DT 10-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of LTR retroposon, COP18_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; COP18_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-238 RA Shankar R. and Jurka J.; RT "COP18_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 14-14 (2007). XX DR [1] (Consensus) XX CC The element exists in low copy number. XX SQ Sequence 238 BP; 58 A; 55 C; 34 G; 91 T; 0 other; tgttagatta tgtggttcta attctccact tttacaagtc attgaatcaa ttacttatga 60 ggtaagttac tcttggattt aatgtgccta caatctttga ccaagagaaa ccatgctttt 120 cttcaagcat ccatgtcatg cttgctgcat gttccacacc tcatgctttg ttacttactt 180 ctctttaatt ctcaattgca tcgatcctgt gcttccgcat tgcgctaata ccttaaca 238 // ID U_LTR_MT repbase; DNA; EDCOT; 2966 BP. XX AC . XX DT 13-JUN-2006 (Rel. 11.06, Created) DT 21-JAN-2007 (Rel. 12.02, Last updated, Version 2) XX DE Putative long terminal repeat from Medicago truncatula - DE consensus. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW U_LTR_MT. XX NM U_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2966 RA Jurka J.; RT "U_LTR_MT: Putative long terminal repeat from an unclassified RT retroelement present in barrel medic genome."; RL Repbase Reports 6(6), 359-359 (2006). XX DR [1] (Consensus) XX CC The consensus is on average ~89% identical to individual CC sequences. Many incomplete copies are present in the genome. Open CC to re-classification pending data. XX SQ Sequence 2966 BP; 797 A; 325 C; 683 G; 1155 T; 6 other; tgtaacagcc cgattttcgc tagaattatt tttaattgtt ttaatatgtg tttatatgtg 60 cttgtgtgtg attatttatc attgggtgca tttttatggg ttttcgtgtt agaagggtaa 120 tttagtcatt ttgtgagtaa gggtaattta gtaaattcat ggtgaggatt atttttagtg 180 tttcaagtga gaaccattat tttactaagt tactagtgtg gtaattagtt gtgagccggt 240 aagtgatcgt tgttattatt ttaccgttaa gtgagtagaa acattttaga attagtgaat 300 gagtgagtta agcccactaa ggcattaggg ttaagcccat ttgagaggag cctatataaa 360 ctcttgtctt tagagaaaaa taggttttca tttcatttca taagaatttt gagagaggta 420 gagagagaaa gttcaagaga agaggaaaag ggttagaagg gagaaagctt gaagacccaa 480 gaggtgatag agattctagg agctaaattg aagcttttgc taggattatt gcttattgag 540 gtaagggggt tagatttcaa tcataatcac ttagttgtaa tttttcccta attgtatgct 600 taagtgctta attgaataag tgattatttt gctcttagtt gttgaaattc gtgctcttgt 660 tatgatgata tgtttgagta catgaaattg gtgataattg aattgttgtt ggtgaaattg 720 catgttcata gtatgtgaaa atgatatatt gtgaattgtg ctctaattgt tgaattgtgc 780 tatgttgttg ttgatttgtg atgagaatca tgtttaattg atgttgttgt tgttaagaga 840 tattgttgtt gatgattcat agcttgggtg ttcataaatc atgagtttgt gatgtgaaat 900 aagttgttgt tgttggtttt gtgaaaatgg gttgatttgg tgaattatgt ttaaatgaca 960 tttgttttca tgtttgatgt gttcttgaga gcccttttaa gtgctaagac ctgtaaacaa 1020 actttggaaa catatttggg cattgggaga tcaaaattgg gaattttggg tgaaaaaggg 1080 ttgaaacccg aaagtttttc tgcagaactg atgactgttc gcttaagcga acgcgtaagc 1140 gaacaatcac agtaggttct ggaactcggt cgcttaagcg aaccggtaag cgaacagcaa 1200 gcgaacagct actgtaagct tatggaacct ggtcgcttaa gcgaacaagc ccagtttcag 1260 caacttttga ttttcgttcc gggctttagg gggccaatcc gagctttgta aaacacttct 1320 ttcaacttgt ttaatctctg tttgtactcc taaacctact ggaacatgat ttactcattc 1380 aaacttggga ttttctaatt gggttgaaac ttgaactttt gataatttcg gattttgtcg 1440 gaaatgaact tttgtgaact aaaagggatt acaagtttgg tctacagtcc atgtggactt 1500 aggcaaggct tgtaaagttg gttaaatgtc ttaatcatgt caaacttgat tttcgggtgg 1560 gattgtggaa tatgtgaact tggggttttc tcatacgaac ttaggctaat ctttgaacta 1620 atgtttaata gttcgtaagt ggcttaagct catgactaca tgattgatta agattgattt 1680 gtgagttttc aaacttgaat aagttacctt gttttgaaaa ttatcaatgt tggccgtttt 1740 gccacttgat acggactttg tcgaaaacga ttctttaaag ccaattacct tataaatctt 1800 tcgtgactag ctttatatga ttaaatgaag atatgtgaat gaattgttag gtgttgaata 1860 tgatgtttat cataaggtgt tgtattttct ctttacttgg aatgtgagaa atatttggag 1920 tggttgaact atattatata gttgatgttg attaatgtat atatatcaat tgatgttgat 1980 atattatgat gataatttgr tgatgactct taattgaatt atgacttgat tgattgtgtg 2040 gacgtaaata cttgataatg caattgttgt tgaggttgat caatataatt ggaggtkawc 2100 ctttayattg ttgttgatat atttatgagg tgattttgca ttrtcgagtc tttgcttgta 2160 tgtccatgca tcatagtcat gttgagtctt gatgagaatt gtaaaaggag gtgtactctt 2220 ttacatcggt gataatgtaa gacgggtgtg aaatcttaca tatgatgttt ttgttgcatc 2280 atgggtgacg accttgatgt tatttggtac cacatgcata tatgtgttgg gattaggcgc 2340 atatcatatt ggcatgagtc ttatttgttg catgtgaatg atgaatgttg atgataagtg 2400 tgtttgatga atgcttaatt gtgatatttg gaattgttgy atgaatgtgt atatggaaat 2460 taattgctta tgtttaatta attgatactt gatttgattc atttatgttc aaattgttta 2520 tgttgattat gattgatgta aagcttaccc ccctagtggt tttgaccacc tacctgtctg 2580 tatggatggg tagacgaagt gcaggattag ttgcttttgg tgagttgctt ggatatcggg 2640 agctatctcc gttatcgttt ccttagagtc ttagggtagg ctctgatcta ggatgtctgt 2700 cttatgatta ttctagattg tttattctgg atttatttat gttgtggaga tttacccatt 2760 tgtcgggatt tggagaattt ttatgatgat gtattttgat atcatgacat gtatactttt 2820 gaggtgtatg gtttatatcc gctgcgactg ttgagaattt ttatatatgc atgttgattt 2880 ggtttttgtt gatgacgtgg cgtctatttc ttgaatattt atattattcg cgtgttttat 2940 cactttaata gaaatagggc gttaca 2966 // ID Copia8-VV_LTR repbase; DNA; EDCOT; 256 BP. XX AC AM467700; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia8-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-256 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-256 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 734-734 (2007). XX DR Genbank; AM467700; Positions 2849 3104. XX SQ Sequence 256 BP; 67 A; 32 C; 48 G; 109 T; 0 other; tgaagaggtt gtttacttgg tctattttct atttcaataa atcctagtct ttaggatgag 60 tcctagtttt taggcatatt gttattcact ttattttgtc aatcacgtag ctgagataaa 120 gcaaacgtgt gctaatttta tgctttctgt tggagttgta aatggttata aaagccaagt 180 tgagttttca ataaaggtgg tcaagtcatt tagtcttttt gttgagctct tattatttca 240 tcaaattgat tttgca 256 // ID LINE1C_MT repbase; DNA; EDCOT; 5782 BP. XX AC AC137081; XX DT 23-MAY-2006 (Rel. 11.05, Created) DT 26-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE L1-class element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; LINE1C_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5782 RA Jurka J.; RT "LINE1C_MT: L1-type element from barrel medic."; RL Repbase Reports 6(5), 248-248 (2006). XX DR EMBL/GenBank/DDBJ; AC137081; Positions 27821 22040. XX CC This is a recently retroposed element. 5'-end not determined. XX FH Key Location/Qualifiers FT CDS 4..1596 FT /product="LINE1C_MT_1p" FT /translation="MSSEFVFSALSDQNLQATNKPPDPYKPSSPKISFRDK FT LLGPSQEPMLREKEDMIEKNLVRIEHENGNRLLPKVYLEPSVFQELCTPWK FT DAIVVKLLGKNLGYHTMKERLQRTWKPQGGFEIMDNDNGFYMVKFDQAANK FT EKVITGGPWLIFDHCLAVTHWSPEFASPNTKVDKTIVWVRFPGLNLVYYDE FT SFLLAMASALGRPIKVDTNTLKIERGKFARVCVEIDLTMPVVGKIWVNGHW FT YKVQYESLHLICTNCGCYGHLGRNCSSTRHLQPSTSSEPTPSAVHQPAVVS FT QQTRSTPTSDEHLIQNVQKGTTVTISSKDSLPNDDQLNAIDGDNHVLHGEW FT SLVTRKKKPTKNIIINPQKTVTTKNNRFNALNHLTTRNKTGLPLPNNQSRP FT IIVQRCILQVPKDTKHRRHDTMATDEPVFDFSQVNPLVLSPPHSHKTTPEP FT HVPKTTQQLPTKQTTTNEVQENDPTLVNNPTPEPDPNSSFMLATPIPNDQE FT ANHPTKDQIGETSYHKDDVHQNLDTQETQDEEMVT" FT CDS 1481..5710 FT /product="LINE1C_MT_2p" FT /translation="MTKKLTTPQKTKLVKLAIIRMMFIRTWILKKLKMRKW FT SRSTFLLLFFSDYVVMEALLDITILSWNIRGAQNNNGRRNLKELMRKHNPT FT FIAIYETHVPYHRLSTFWANTDYTPVHIIEANGHSGGIWLLKHSATNILTT FT ITNSNPHSISFTINRGHASSFCTCIYASPNPTQHPILWNHLINLNHSIDAP FT WMIIGDFNETLLPSEQRGGVFHHSRAASFSNFMNSCNLLDLTTTGGKFTWH FT RNSNGIRILSKKLDRGLANVNWRLNFPEAFVEVLCRLHSDHNPLLLRFGGL FT PLSRGERPFRFEAAWIDHGEYESLVKNSWQPRTHNIISALNNVKENSVNFN FT HEIFGNIFQRKKHIENRLKGIQNYLERVDSIQHSHLEKELQKEYNHILFQE FT EMLWYQKSREKWVKFGDKNTAFFHTQTIVRRKRNRVHRLQLPCGTWSSDSD FT TLQQEAQNYFKLFFTASQDNRDRTFTEGTHLSITEEGRNSLTAPITKNEVY FT AALNSMKPYKAPGPDGFHCIFFKQYWHIVGNDIYHMVQTAFQTGHFDPEIS FT NTLIALIPKIDPPTTYKDFRPITLCNITYKIITKVLVHRLRPILTNIIGPY FT QSSFLPGRGTADNSIVLQEIIHFMKHSKRKKGYVAYKLDLEKAFDNVNWDF FT LSNCLHDFGFPNITIKLIMHCVASPSYSILWNGKGLPPFEPSHGLRQGDPL FT SPYLFILCMEKLSAAINSAVAQGRWAPIQITPTGPHLSHLLFADDVLLFSK FT AKTSQVHLIHDLFERFSQASGLRINIAKSRAFYSSGTPHGKITSLTTISGI FT QSTSSLGKYLGFPMLHGRPKKSDFNFIIEKMKSRLATWKNRLLNKTGRLTL FT ATSVLSSIPTYYMQINWLPQSICDSIDQTTRNFFWKDTNNKGVNLVNWKKL FT TTPKQSGGLRIRRAREANTCLLGKLVWDMVQSTNKLWVNILSNKYTTGSNI FT LQATCSSNSSPTWSSIIKAKNVLRNGYLWRAGSGTSSFWFHNWSPHGLIGS FT HVPIIDIHDIQLTVKDVFTHNGQHTHALYTNLPPAIAYYINNTNFRFNERI FT EDTIIWSHNINGVYTANCGYAWLLRNSDTDTNPLSTHSWSWIWKLKSPEKF FT KLFIWLACHNAIPTMSLLEHRHMAPSSTCSRCGEDEETIMHCLRDCRFSSI FT IWHRLGFTDTAFFNEAFPSSWIKQHATGNNSSLFLSGLWWSWRNRNLMCLS FT NESWSTHRIMLNIHNSISAINASYQAATAQSSQTLVRWNNSNFSGVVLNVD FT GSCLGAPIRAGYGGILRNSAGFFLQGFSGFIEATTDILFAELTAIHKGLLM FT AAENGIEEMICYTDSLLSVKLLTNSSSRFHAYAVLIQDLLLSTNFSIQHCH FT REGNQCADFMAKLDAISNEEFARHTTPPYDLIPLIRLDAMGTAFPRA" XX SQ Sequence 5782 BP; 1745 A; 1476 C; 1018 G; 1543 T; 0 other; gcaatgagtt ctgagttcgt tttctctgct ctgagtgacc aaaaccttca agccaccaat 60 aaaccacccg atccttacaa gccatcttcc ccaaagatct ctttccgaga caaactccta 120 ggaccatctc aagaaccaat gctacgtgaa aaggaagaca tgatcgagaa aaatcttgtt 180 cgcattgaac atgagaatgg taaccgactc cttcctaaag tttaccttga accatctgtc 240 ttccaagaat tatgcacgcc atggaaggac gctattgttg tcaagttgct ggggaaaaac 300 ctcggctacc ataccatgaa agaaaggcta caacgaacat ggaaaccaca agggggtttc 360 gaaatcatgg acaacgataa cggtttctac atggtgaaat ttgatcaagc ggcaaacaaa 420 gagaaagtca tcacgggagg tccttggtta atatttgatc actgccttgc agtcacacac 480 tggtcacctg aatttgcatc tccaaacacc aaagttgaca aaacaattgt ttgggtgaga 540 ttcccaggtc tgaacttagt atactatgat gagagtttct tgctagccat ggcttctgct 600 cttggccgcc ccatcaaggt cgacacaaac accctgaaaa ttgaaagagg taagtttgcc 660 agagtctgtg tggaaattga tctaactatg ccggtggtag ggaaaatttg ggtcaacgga 720 cattggtaca aagttcagta cgagagtctc cacctaattt gcaccaactg cggatgctat 780 ggtcacttgg gaagaaactg ctcatcaaca cgccacctcc agccgtccac ctccagcgaa 840 ccaacacctt cagccgtcca tcaaccagcc gttgttagcc aacaaactcg gtcaacaccc 900 acctccgatg agcatttaat tcaaaacgtc caaaaaggta caaccgttac tatttcgtct 960 aaggattcat taccaaatga tgaccaatta aatgccattg acggagataa tcatgtgcta 1020 catggggaat ggtcacttgt cactagaaaa aagaaaccaa caaaaaacat catcataaat 1080 ccccaaaaaa ccgttacaac aaaaaataac aggttcaatg cccttaatca tctaacaact 1140 agaaacaaaa ctggcctacc ccttccaaat aaccagtcac gccccattat tgtccagaga 1200 tgcatccttc aagtgcccaa agacacgaaa catcgtagac atgacaccat ggccactgat 1260 gaaccagtct ttgacttctc ccaagtcaac cctttagtgt tgtcgccccc acacagccac 1320 aagaccacac ctgaaccgca cgtgccaaaa acaacccaac agttaccaac taaacaaact 1380 accacaaatg aagttcaaga aaatgatccc accttagtca ataatccaac acctgaaccc 1440 gaccctaatt caagtttcat gctcgccacc cccattccaa atgaccaaga agctaaccac 1500 cccacaaaag accaaattgg tgaaactagc tatcataagg atgatgttca tcagaacctg 1560 gatactcaag aaactcaaga tgaggaaatg gtcacgtagc acctttcttc tcttgttctt 1620 ttctgattac gttgttatgg aagctctcct tgatatcacc atcctctctt ggaatattag 1680 aggggctcaa aataacaatg gaagaagaaa cctaaaagaa ttgatgagaa aacacaaccc 1740 aaccttcata gcaatttatg aaactcatgt cccttatcat agactatcca ccttctgggc 1800 taacactgat tatacccccg ttcacatcat agaagctaat ggacattccg gaggtatatg 1860 gcttctaaaa cactcagcta caaacatctt aacaactatc actaactcca acccccactc 1920 catttccttc actatcaacc gcggccatgc ttcctctttt tgcacttgca tctatgcaag 1980 ccctaaccca actcaacacc ccatcctttg gaatcattta attaacctca accactccat 2040 tgatgcgccc tggatgatca taggagattt caacgaaact ctcctaccta gtgagcaaag 2100 aggtggcgtc ttccaccata gccgagctgc ttcattctca aacttcatga attcttgcaa 2160 cctccttgat ctcacaacca ccggtggaaa gtttacttgg catagaaaca gtaacggcat 2220 ccgcattctc tccaaaaagc ttgatagagg attggctaat gttaactggc gcttgaactt 2280 cccggaagcc ttcgtcgagg ttctttgtag gctccattcc gaccacaatc ctcttctcct 2340 acgttttgga ggccttcctt tatctagagg tgagcggcct tttcgctttg aggcagcttg 2400 gatcgatcat ggtgaatacg agagcttggt aaaaaattct tggcaaccac gcacccataa 2460 catcatctcg gccttgaata atgtcaaaga gaattccgtc aacttcaatc atgaaatctt 2520 tggaaacatc ttccaaagga aaaagcatat tgaaaaccga ctcaaaggaa ttcaaaatta 2580 tcttgaaagg gttgattcca tccagcactc ccaccttgag aaagaactcc aaaaggaata 2640 taatcatatt ctattccaag aagaaatgct ttggtatcaa aaatcaagag aaaaatgggt 2700 gaaatttgga gataaaaaca ctgctttctt ccacactcaa accatagtta gaagaaagag 2760 aaatcgagta catagacttc agctcccctg tggtacttgg tcttccgata gtgatactct 2820 ccaacaagaa gcacaaaatt acttcaagct cttcttcacg gctagccaag acaatcgtga 2880 ccgaactttc actgaaggta cccacctttc cattactgaa gaggggagaa attccctaac 2940 cgccccaatc accaaaaatg aagtttatgc tgcccttaac tccatgaaac cctacaaagc 3000 ccctggtccg gatggtttcc attgcatctt cttcaagcag tactggcaca ttgttggcaa 3060 tgacatttac cacatggtcc aaaccgcttt ccaaacaggt cactttgatc cagagatttc 3120 aaacactctc attgcactaa tcccaaaaat tgacccaccc accacttaca aagacttcag 3180 acctattacc ctttgtaata ttacttacaa aattattaca aaggtcctgg ttcacaggct 3240 tcggcctatt cttactaaca ttattggtcc ctatcaaagc agctttctgc ctggtagggg 3300 cactgcagat aactctattg ttttgcagga aattattcat ttcatgaaac actctaaaag 3360 gaagaagggt tacgtagctt acaagcttga cttggagaaa gctttcgaca acgtcaactg 3420 ggattttcta agcaactgcc tccatgattt tggatttccg aacatcacca tcaagctcat 3480 catgcattgc gtagcttctc ctagttactc tatactttgg aacgggaaag ggttgccgcc 3540 tttcgagcct tctcatggcc tgcgacaagg tgatccgttg tccccttatc ttttcatcct 3600 ttgcatggaa aagctttcag ctgctatcaa ctcagcagtc gcccaaggaa gatgggcacc 3660 catccaaatc acccctacgg ggccgcattt atcccatctc ctatttgcag atgatgtcct 3720 tcttttttct aaggctaaga cctctcaggt tcatcttatt catgatttgt ttgaaagatt 3780 cagtcaagcc tcggggctaa gaatcaacat tgctaaatca agggcatttt actcgtcagg 3840 cactcctcat ggtaaaatca ctagcctcac tacaatatcc ggaatccaaa gcacatcctc 3900 acttggcaag tatttgggtt tccctatgct ccatggacgt cctaagaaga gtgatttcaa 3960 cttcatcatt gaaaaaatga aatcgcgctt ggcaacttgg aagaataggc ttctaaataa 4020 aacaggtaga cttactttag caacatctgt tttatcctcc atacccacct actatatgca 4080 gattaattgg cttcctcaga gtatttgtga tagtattgat cagacaacca gaaatttctt 4140 ttggaaagac actaacaaca aaggagttaa cttggtaaat tggaagaaat taactacccc 4200 aaaacaatct ggaggtttga gaatcaggag agctagagaa gccaacactt gtctccttgg 4260 aaaacttgta tgggacatgg ttcaatcaac aaacaaatta tgggtaaaca ttctttccaa 4320 caaatatacc acagggtcaa acatccttca agccacctgc agtagcaaca gttcacccac 4380 ttggtcttcc atcatcaaag caaaaaatgt cctccgtaat ggttatctat ggcgcgctgg 4440 ttcaggtacc tcctcctttt ggttccataa ttggagcccc catggactga ttggctcaca 4500 cgttcccatc attgacatcc acgatattca actcacggtt aaagatgttt tcacacataa 4560 cggtcaacac actcatgctc tctacactaa tctgcctcca gcaattgcat attacattaa 4620 taacaccaac ttcagattca atgaaagaat agaagatacc atcatatgga gccacaatat 4680 caacggggta tacacagcaa actgcggcta tgcttggcta cttcgcaact cggatactga 4740 caccaatccg ctttctaccc actcttggtc ttggatatgg aagctaaagt cccctgaaaa 4800 attcaaactg ttcatttggt tagcttgcca taacgccatc ccgactatgt ctcttctcga 4860 acaccgtcat atggccccct cttccacctg ttccagatgt ggagaagacg aagaaaccat 4920 tatgcattgc cttcgggatt gtcgtttctc ctccattatt tggcaccggc tcggtttcac 4980 ggataccgct tttttcaacg aagcttttcc atcaagctgg atcaaacaac acgctaccgg 5040 taacaactct tcccttttcc tttccggtct ctggtggtcc tggcgaaacc gcaatttaat 5100 gtgccttagc aatgagtctt ggtctaccca tcggatcatg ttgaacatcc acaactcaat 5160 ctctgctatt aatgcttcat atcaagccgc aacggcccag tcctcacaaa ctctggttcg 5220 ttggaacaat agcaatttct ctggtgtcgt gttaaatgtg gatggcagct gcttgggagc 5280 tccaatccga gccggttacg gaggtatttt acgaaactca gctggttttt tccttcaagg 5340 tttctccggt tttattgaag caacaacgga cattttgttc gctgaactta cggcaattca 5400 caaagggtta ctcatggcag ccgaaaatgg aattgaagag atgatctgtt acacagattc 5460 gctgctttca gtcaagctcc tcacaaacag tagctcccgc ttccatgctt atgctgtttt 5520 aattcaagac ttgctattat caacaaactt ctccatacaa cattgtcata gagaaggaaa 5580 ccaatgtgca gatttcatgg caaagcttga tgcaatttca aacgaagagt ttgcaagaca 5640 tacaacccca ccttatgatc tcattccttt gattagatta gacgccatgg gaactgcgtt 5700 tcctagagct taggcgtgtt tttacctttt tctttcctat cttgtttttt cttttcttag 5760 ctttgtaacc aaaaaaaaaa aa 5782 // ID Copia-69_Mad-LTR repbase; DNA; EDCOT; 123 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-69_Mad_; KW Copia-69_Mad-LTR; Copia-69_Mad-I. XX NM Copia-69_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-123 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1677-1677 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 123 BP; 23 A; 26 C; 16 G; 58 T; 0 other; tggaggtcat cattatgctt gcttagctgc cattgtcctc taccttttgt cctccatttt 60 tctttcccgt ttcttcttct atatatgttt gatcttgtaa ctgttttata tatgaaatat 120 aca 123 // ID TLC1_LTR repbase; DNA; EDCOT; 579 BP. XX AC AF279585; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Lycopersicon chilense Ty1/copia-type retrotransposon TLC1_LTR, DE long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Long terminal repeat; TLC1_LTR; Ty1/COPIA superfamily; KW retrotransposon. XX OS Solanum chilense OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-579 RA Ruiz-Lara S., Bratti S., Yanez M., Verdugo I. and Gonzalez E.; RT "Expresion Especifica de Retrotransposones LTRs en Lycopersicon RT chilense Inducidas por Heridas y Congelamiento."; RL Biol. Res. 32, R146 (1999). XX DR Genbank; AF279585; Positions 1 579. XX SQ Sequence 579 BP; 180 A; 75 C; 120 G; 204 T; 0 other; tgaggagtcc atccgcgaga accaaacttt gaataacttt gtgccaattt caaagtttgg 60 tagagttggt aatctatgaa gaagaaaaat ttgttttgtg ccaatttcaa agtttggtag 120 agtaggtgag ctatgaagaa gaaaaaattg tttttcttct atagcacatt tggagggtag 180 tgtatttgtt ctctataaaa gggaggacaa ttcttcattc taagtacacc aaaaagaatt 240 acaaaggaga gaaaaaaaga gtgaggcatc acagaggaaa ataatttgtg aggaaaaata 300 gagagtgtga gttatattgt aatgaggtgg aaaaatcaaa agagtgttat ttcttttgag 360 tgtgtagtag tcactttgag tgttgtattc gtgattacac actgtaaaat tccttactat 420 agtaatatca gttgctcctc ttggcgtgtt tcctattaga ggttcacgta atctgtgtca 480 tattctcttt tattctcgtt gtttaccgca ttgttgtgtt ctatatttat tgcctttatt 540 accgcaaata ttatttatgt tacggattta ttcccaaca 579 // ID ENSPM2_MT repbase; DNA; EDCOT; 11099 BP. XX AC AC135415; XX DT 19-DEC-2006 (Rel. 11.12, Created) DT 19-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE EnSpm-type DNA transposon. XX KW EnSpm; DNA transposon; Transposable Element; ENSPM2_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-11099 RA Jurka J.; RT "ENSPM2_MT: EnSpm-type DNA transposon from barrel medic."; RL Repbase Reports 6(12), 619-619 (2006). XX DR EMBL/GenBank/DDBJ; AC135415; Positions 58952 70050. XX CC This is a relatively new insertion with intact ORF. XX FH Key Location/Qualifiers FT CDS 2872..6063 FT /product="ENSPM2_MT_1p" FT /translation="MDRSWMKANRLSEKYEKGVEEFLQYCENLPNNNGKFH FT CPCVKCGNRLPLLSVEELRNHLICEGVCETYTNWIWHGESSNIPDVLERDD FT MDVEMDNQMEDMICDIGQEDFQRAHAHNNLRANNELILYPGCKNFTQLSAV FT LRLFNLKAKNGWTDKSFTELLELLCEMLPKGNTLPKCNYDAKKILCPMGME FT YKKIHACPNDCILYRNEFEDEKQCPTCGLSRYKVKDGDDDESLKRPPAKVL FT SYLPIIPRFKRLFANENDARNLRWHACDREDDGKIRHPADSLQWKKIDELY FT SDFGKEARNLRLGLATDGMNPYGNLSSNHSSWPVLLVIYNLSPSICMKRKY FT MMLSMMISGPKQPGNDIDVYLSPLIEDLRMLWEEGVDVFDGYSRQNFKMRA FT MLFCTINDFPAYGNLCGYSVKGHKGCPICEEETCFKQLKHGKKTVYLGHRK FT FLKPNHPYRKLRKAFNGEQEFETAPQALTGEQVYQRVKDINVKFGKKEKKK FT KQKTTEKKIWKKRSVFFDLPYWSSLDVRHCIDVMHVEKNVCDSVIGTLLNI FT HGKTKDNVNARLDMVEMGIRQELAPHSADNKKTYLPPACHTLSKQEKTSFC FT ECLHTLKVPRGYSSNFNSLVSMEDLKLIGTKSHDCHVLMQQLLPVAIRGIL FT PKKVRAILTRLCIFFNVICSKVIDLRKLEELENEAAIILCHLEMYFPPSFF FT DIMVHLIVHLVREIRLCGPVYLRWMYPVERYMKILKGYVKNQHHPEASIVE FT RYIAEEAVEFCNTNYMPEEEAIGIPKPQYDGRCGGIQGLKLKSLDSVEVLQ FT AHLYILNNIDEVQPYISTHKRIVKEKNSRMNEKWVLKEHNKTFLKWFKETI FT SNDNTCSENLKCLARKPQSDAISWTIYNVNNFTFYTRTKDDKSTVQNSGVM FT VVAESMHFSSSKDKNPIMASIPYYGIIEEMWDIDFVTLKVPIFKCKWIDIN FT NGVKIDEFGYTLVDLGKIAYTNEPFIMASQAKQVFYVSDPSNKKWSVVLQG FT KISHEPNNDNLHSTLYTYETPFTQRQSTSMEETLVDDVYATRDDHREGIWE FT NIQSNQS" XX SQ Sequence 11099 BP; 3628 A; 1681 C; 2073 G; 3717 T; 0 other; actagtacaa aatatacttt atagattcgt gcttaagtcg gttcgttctg ccacccgtct 60 taagaattga tgcggtggca gtttcgtaat tattttaaac ttccttaagt cggttataag 120 attacccgac ttacgattga tagaataatg aaaaaaattt tttttaataa attccttaag 180 tcactaggct gaccaattga cttaagaagt ctttttctta agtcggtcgc ttcaacaccc 240 gacctaagga tttttctctc tatttctagg tgaatcatca actttcacta tttttattta 300 tttattaatt aaataaataa actaattaaa tttattaatt aaattaatag ttgtttttaa 360 taaagaaatt aattaatagt tatatgtttg acaaaaaaat agttatatga ccttttttcc 420 gtaacaaaaa aaaaacaatt ttttttatgt ctcaacaaaa aaaaacagac atttttttct 480 tcaaaagaag tttctcttgc ttcagtctac ttagtactgt gagattgaga ttcatcgcag 540 caacaacaac accattgtcc ttttcatcgc gatcgattaa caaaaaataa acattttttt 600 cttaaaaaga agttcgtctc gcttcagtct acttcgtact gtgaggttca tcgcagcaac 660 aacagcaaca tcgtcctttt catcacgatc gatcattgtt ccagattcac ctcaactgtt 720 aggtatttaa tttaatccac ttgattatta gaatgattct cgtaattatc attggaattt 780 ttctatgata gtagtggtga cagtgattaa tttgatttcg tgtgatttcc atattgacca 840 ttaagtgttt gattatttgt ctaacccaaa gtttcctcca atgggttttg ttgttttgtt 900 tgattgatcg agatttgaaa cccctttttt agattttaaa ctctaagtac tcactagtta 960 gttttagctt aagtggtggc tttgttaggg aattgtgtta agccctgttt ggacacaatg 1020 tttaatttga aacccctttt ttagatttta aactctaagt actcgctact tagttttagc 1080 ttaagtggtg gctttgttag ggaattgtgt taagccctgt ttggatacaa tgtttaatta 1140 agtgctcata gcattagggc attttattcg aattctgcta gtatttgact ccctgctagt 1200 aattgatact aaattaattg actttcttca acttagagac tacaatatat aaacctcaat 1260 tgattagtga aaatttcctt tatcttgttc tgttttgatt taagtcttat gatttggaac 1320 tcatttgaat agtcatgaaa atagttgtgt gtataaattg ctaaaaaact ttgataattt 1380 tgagttgaat gagtgaacat atggtaggaa aggtgaaaaa ttcatttatc ttgttctgtt 1440 ttgatttaag ccttatgatt tggaactcat ttgaatagtc atgaaaatag ttgtgactag 1500 tataggacat cgtcaatatt gttagaagct agagacataa tggataaaat ggtgttacat 1560 aaatgtatca gagtgtataa catagctagg aagtgcttgg atccacctta tcaatgatct 1620 tgtgtctggt ctataatctg aaggttgaat gcacttgcac aaaaatctta aattatgaaa 1680 ctctaaccac cctacatact attaatacct tgatatttat tttttgtcat cttagctata 1740 catagaacta ttgtatgata cttttgtgct aacaaaattg cacaaaatca gagaaattca 1800 aaaatcataa tatgtccaaa ttacaactaa aactaaggta ggaaccagtt tcttttgata 1860 tgttcaaaaa tctaaattga tttacaaaga tctaaattga catacacaat tcagtggctg 1920 cagctgaaaa gaaaaaaaaa aggataaaac caaaataaga tggtatgaga ggtgtccata 1980 aaaaaaattg aaggtcctta tagtagtaag aatctctata aacagatttc atttttctag 2040 tagggaaagg gaacggtaaa tgtagatatt acccaatgtg tttcaactga aatatgttca 2100 acatatacaa aagaaacata agtaaatgta ctagaatgaa gattatgcca agtgcaacat 2160 tcttgtgcat acttcttttt tattattcac cattcatctt cattcaaaca agattaatta 2220 accgagtcaa attgttgtaa tttaagccta tgtagtcaaa aaggtattat ttatttatta 2280 gaggctaaag atattattta tttttaatac aaactataag caaaaatata tgtatgtggg 2340 gcgtcatttt ctaaaagcaa aggttttaga aacaatgtct tcaattaggc atttaatctt 2400 ttagaagaaa aacaaatata tggacatatt gaactttcaa ttttctttca atcattaaca 2460 aagtataatt atgtgagctg taaaacaaaa aatttaattt aatttaacag acttattaga 2520 tatagtcatg gactttaaaa agaaaacttt aggcatatat gagatgtgtg aacttatctt 2580 ctagaatcat tcagttccta tgagaaagca tatgctgaag ttattacttt aggcctccaa 2640 aaatattcac tcactttttt tttgttttga aggcacgtaa ttaggacctt tggcacccca 2700 ttggctacac atagtctttc cactagcttc agtcttttgg actgataact agactaatct 2760 ctgcctaggt gtaagtcaca tactaagtga cttacataac gaaggttcac accttctaaa 2820 ctgacagact tctactcact tccttcaagg aggttttttc agaaacaata tatggatcgc 2880 agttggatga aagctaatcg tttgagtgaa aagtatgaga aaggagtgga agagttttta 2940 caatattgtg aaaaccttcc taacaataac gggaagttcc attgtccttg tgttaagtgt 3000 gggaatagac ttccattact ttcagttgaa gaactacgga atcatctaat ttgtgagggc 3060 gtttgcgaaa cttataccaa ttggatatgg catggtgaat cgtcaaacat cccagatgtc 3120 ttggaaagag atgacatgga cgttgagatg gacaatcaga tggaggacat gatttgcgat 3180 attggacagg aggattttca gcgtgcacat gcacataaca atttacgcgc taacaatgaa 3240 ttaatattgt acccagggtg caagaacttc acgcagttat ctgcagtgtt gagattgttc 3300 aacttgaagg cgaaaaatgg atggacagat aaaagtttca ctgaacttct tgagctgttg 3360 tgcgaaatgc tcccaaaagg caacacatta ccgaaatgta actatgatgc aaagaagata 3420 ttatgtccga tgggtatgga gtacaagaaa atacatgctt gtcctaatga ctgcatattg 3480 taccgaaacg agtttgagga tgagaagcag tgccctacat gtgggctatc acgctacaaa 3540 gtgaaggatg gtgatgatga tgaaagctta aagcgtcctc ctgcaaaggt gttatcgtat 3600 cttccaataa ttccaaggtt caaaagatta ttcgctaatg aaaatgatgc aaggaatctt 3660 cgatggcatg catgtgatag ggaagatgat ggaaaaattc gtcatccagc tgattcattg 3720 caatggaaga aaattgatga attgtattcg gatttcggta aagaggcaag aaaccttagg 3780 cttggacttg ctacagatgg aatgaatcca tatggaaact taagtagtaa ccatagttca 3840 tggcccgttc tcctagttat ctacaattta tctccttcga tatgcatgaa acgaaaatac 3900 atgatgttat ctatgatgat atcgggccca aagcagccag gaaatgatat agatgtgtat 3960 ctaagtccct tgattgaaga cttaagaatg ctttgggaag aaggtgttga tgtgtttgat 4020 ggctattctc ggcagaattt caagatgcgt gcaatgttat tttgcactat caatgacttt 4080 cctgcatatg ggaacttgtg tggttatagt gttaaaggac ataaaggttg ccctatatgt 4140 gaagaagaaa catgcttcaa acaattaaaa catggaaaaa agactgttta tcttgggcat 4200 cgaaaatttc tcaaacctaa tcacccatat cgcaagttga gaaaagcgtt taatggagag 4260 caagagtttg aaactgctcc gcaagcccta actggagagc aagtttatca acgagtgaag 4320 gatatcaatg ttaaatttgg aaagaaagaa aagaaaaaaa aacaaaaaac cactgagaaa 4380 aagatatgga agaagaggtc tgtgttcttt gatcttccct actggagcag tctagatgtt 4440 agacattgta tcgatgtgat gcatgtggag aaaaatgtgt gcgatagtgt aattggaaca 4500 cttctcaata ttcatggtaa aacaaaggac aatgtgaatg ctcgtttaga catggttgag 4560 atgggcatac gacaagagtt agctccgcat tcagcagata ataagaagac atatttgcct 4620 ccggcttgtc atacgttgtc taaacaagag aaaacaagct tttgtgagtg tctacataca 4680 ttaaaagttc cacgaggtta ctcttcaaat ttcaatagtc ttgtctcaat ggaagattta 4740 aaattaattg gcacgaagtc tcatgattgt cacgtattga tgcaacaact actaccggtg 4800 gctattcgtg gcatattgcc taaaaaggtc agagctatct taactaggtt gtgcatattc 4860 ttcaatgtta tatgcagtaa agtaattgat cttcgaaaat tagaggagtt ggaaaatgaa 4920 gctgctataa tcttatgcca tttagagatg tattttcctc cgtctttttt tgatatcatg 4980 gttcacttaa ttgttcatct agtgagagag attagattat gcggtcctgt ttatttgagg 5040 tggatgtatc cagttgagcg atacatgaag atcttaaaag ggtatgtgaa gaatcaacat 5100 catcccgaag catctattgt tgaaagatac atcgcagaag aagctgttga gttttgtaat 5160 actaactata tgccagaaga ggaagcgata ggaattccca agcctcaata cgatggaaga 5220 tgtggaggta tacaaggttt aaaacttaag agtttggact cagtggaagt acttcaagca 5280 catttgtata ttttgaataa tattgatgaa gttcaacctt acatttctac tcacaaaagg 5340 attgtcaagg aaaaaaattc tcgaatgaat gaaaaatggg tgttaaaaga gcataacaag 5400 actttcttga agtggtttaa agaaactatt tcaaatgaca atacgtgttc tgaaaattta 5460 aaatgtctag cacgaaaacc tcagtctgat gccataagtt ggaccatcta caacgtgaat 5520 aattttacat tctatacaag gaccaaggat gacaagagta cggttcaaaa tagtggggtt 5580 atggttgtag ccgagtctat gcacttctca agttcaaaag ataaaaatcc tatcatggca 5640 tcaatacctt actacgggat cattgaagaa atgtgggata ttgatttcgt tacacttaaa 5700 gttcctattt tcaaatgtaa atggattgac ataaacaacg gtgtcaaaat agatgaattt 5760 ggttatacat tggtggacct tggtaagata gcttatacga acgagccttt cattatggca 5820 tctcaagcaa aacaagtgtt ttatgtttct gatccttcta acaaaaagtg gtcagtggtt 5880 ctccaaggta aaatcagtca cgaacctaac aatgacaatc tgcattcaac gctatatact 5940 tatgagactc ctttcacaca acgacaatct acttcaatgg aggaaacttt agtggacgat 6000 gtgtatgcca ctcgtgatga tcatcgcgaa gggatatggg aaaatattca atcaaatcaa 6060 tcttagttaa taaaatggtg acttttgttt caattgtatc atagagattc caaactttgg 6120 agtatcagtc cattagagaa gtagttaata gttttacttg tgaatttgca gtccattaga 6180 gaagtagtta atagttttgt tttcacatag aagcatatga ctgtgattgc tgggatatta 6240 ctttgtaaac aaagtgactt ctcaaatggt gcttaccaca attcatgtca tttaaattat 6300 gaaactactt gatcttgctt ttgcattttt atttttaatg ttttcgctcg ttttatttgc 6360 aaactcatct gacttctata ttaataaaaa aaaaaaaata tttttgccct taacgaatga 6420 cttctagttt tatgtagaag taacttacat atggaaaaat ttataatttg ttgagataca 6480 aatccatatt tgaattttca ttctattatg acactgtgta tcaagtttgt agtttgggtt 6540 ttgctactgt tatgataatg aatagtttga cttcaattta ttagtgtcaa acctcagtat 6600 aatctcattt tttgcctact gttctatttt catttccttg gtgagtttaa tatgcagttt 6660 ttaattgatt cttggttgtg cactatatta atggtattga gcttgcattg ttactaactg 6720 ttgttatgtt tctttttaaa cagacatatg ggtgatccag caggtccttc acaaagtggg 6780 tcgaatactc aatctaatcg aaaaagggga agaggtcgca cccgtatgaa gaatttgaaa 6840 atgaaaactg cacatggtga gaaattacca attgaattcc aatctaatgg attaccttca 6900 ggggaaaacg cgaaaaggtt caagctccag gtggcttcct ttgctcgaga gtgtacaagt 6960 attctgataa gtgattggaa tagtgttcct gatgccacaa aggatgagat ttggaaatca 7020 atcacagtaa tttttaattg tgtttatcaa tattgtactt aactttaatt ttgtcataca 7080 ctaactccta tatttgttgc gtaatgtagg ctaaatggga tatgccgaat gataagattg 7140 tgaaaaagaa aactatatcg tacgcgggtg agcgatggaa agcattcaaa tatagtttaa 7200 caagtaggta tttatttgat ggtgaaaata ttgacaagtc tcctatggag acttatgatt 7260 ttattgatga ggacatatgg caggagttta ttaggacgcg agccgaacct tcctttctgg 7320 ttagtttgat ttattatgta gttcttgtat caagtttcat tttagtatta cctaatgaat 7380 caatgtgttg tttatatagg agaaaagact gaatgcacaa cagactcaag ctcataataa 7440 atatcctcat agattgtctc aagggggata tgaattactt gagaaaaaga tgatggaaga 7500 aaaattaaaa gaaagacaag aagcagctgg agacatagaa gttccacctc catctccacc 7560 tcaacgtcat gagaagtgga aaagagccag aataaaacca tcaggagagt atacatcaga 7620 agacactcgt gttgttgcag agacaattgt aagtaaatgc ttaagttctt ttttccaact 7680 tgtaaatata ttggatcaaa gtaatgattt gaagaaaagc aaaaagatat ttttaaaagc 7740 acttaggatc caacaaaaat gatctatata aaaacaatca atggaaattc tcactgcctt 7800 atcttggtag aacattagaa atttgatagc tataattttt ctttttattg ttgattgtgt 7860 ttgtgattat gtattggcta ttggtcaatt ccacggtcca gttgaaacta atggaggttg 7920 tgtagttgtg ctcatgctag tttattaaca agcaattgtt ttgtcatata ttttattaat 7980 agaaactacc tataagattg tgatgataga tcaggaaagt agtattccat tgtattgtga 8040 tacaaaaaat gagcaaaaaa atgtgtaatc atatataggg attcttattt atagaccaat 8100 atgtaatacc atattttaac atcgataaaa gtgaaagttt atttactctc tcatgtagct 8160 tttaagttgt atttcttcta tggaatggtt gcatcatcca tcatcattca aattattaaa 8220 tcattgaatc acaaacagaa atgctaattt tccaataatc acaggacaaa tgttattgcc 8280 tagtagaacc acgttgattc atgaaagtgt gttaaactag cacaaaattc ttcatatcta 8340 ctactattta atttaacgca tttgagggga catatggatt tgtatttgac catgaaacat 8400 gtgagctgca attttctttt tctaaattgg ttattatata tatatgcata gtttcattgt 8460 cagtcttgtg tgtattataa agaatgataa atatgataaa tttgatgttg taggattctc 8520 tagtgtcaga cggatttgtg caaaatggac gtgaggacat cttggtgaaa gcccttgggc 8580 aagatgaaca ccctggtcgt gttcgtgctg ttggtcgagg tgtgggaatt cgagaatact 8640 ttggatcaaa atctcattcc accccgtctg ttatcagtgg tgcccaacta gcagcattga 8700 ctaagaagat tacacaggac gtgctgcaga ctcttcgcac tcaaccaaat caaaatttcc 8760 caatttattc tcctaatacc actcaacatg ttagctcaaa agacagttgc tctactgttc 8820 cacagacacc agatgatgaa gaggatatcg atatcccaga agagtgtgaa ttgtatgttg 8880 atggaagcaa ttatgtggtc gcacatgcta atgtgtacaa cctagggccc actatacaca 8940 atcaggtgct agctaatgat atggttagag tggctgttac taaggtgata gatgcaaaag 9000 ctcaagtacc tgtgcccact gatgaggtga caacaattgc tcaggccgtc aacactttca 9060 ttaaatggcc aaaaagactt ttgcgagtta tcactaataa ggtatttatt atctttgtgt 9120 ctatcactat ttacacttca tactgtttag acttgtgtaa tgttttatta taatggttta 9180 ggatgttgat atacctatga aagttgatgt tccacaaaaa aagtcagaac ctatttgtca 9240 aaaattgata gtgaaggcaa tgtacatgga acaagatttg aagtttaagg ctaaacatag 9300 tgggattgat attgagctac caagggatga tatcatggac ttgtgtttgg gtaaaaaaga 9360 attacacttg actattttgc aagtgtggct cacgtaagta tattttgttt gtaaatttaa 9420 tggtcattca attacttaat tttatttata atgaattttg ttgcactatc ttaggtatct 9480 acaccgtcgt tgtgttgaat tgggcaaaag tggaatgtac ggatttcttg atccgtatta 9540 cactcttgct caaaatgacc gagttagtgt tcaaacctac attcaaaaca caatggacca 9600 taataaaaag gatttgtacc tagctcctta ctttaacaag taattttttc ccctctcttt 9660 atattcaatc acttgtaata tagagatttg aattttacaa ataatttaat tttttaatgc 9720 ccttgtagtc gtcactggca gttgctcata attaatccta agaagcgtga ggtaaccttt 9780 ctctgttcat taggaaagaa gccgtcggat aaaaatttac cagtcattgt tgattcgtaa 9840 gtattcaatt tatttattat acatgaactg tcatatgttt aatgatataa gtttaacgat 9900 taagtattga ttattgtaga gctttggaag gttattataa tctacaaggg gtgagaaagc 9960 atagtaaagt agtatggttt tatcccaccg taagttgttt acacatgcta ctacttcatc 10020 tatcatcttt gtcgtgtttc tatattaaat agcttctgtt tgtaataata tttaccgatt 10080 agtcggtcac atttgatcat attcaatttc agagtcgaag gcaatcagtt tcttacgaga 10140 gcggatactt tgtcatgcta catatgttga acatcatatc cagtggtgtt gtggattcat 10200 ggatgcaagt atgtataaga tttttttaac aaatattata aattaattaa ttttattctt 10260 acatgctaat atgataaact aatattatgt catcatttat ttatttagat atttgcggat 10320 tcaactccct ttcaaaagga tgaagttaaa aatgttcaag aacgctgtgc aaatttgatt 10380 ctggaactta tcgaagcaaa tgaggattca ttgtagtgcg agattggttt ctggagcagg 10440 tggggggagt aagctttagt gagactggtt ttcttttttt agcaattggg gttttagctt 10500 agtgttagcc ctgttttgag ttttatatta tttgcatttt ggttctaata tgtactttaa 10560 tctgtcggtg cacagtggca atatttactt tctaatgaca ttgaagttca atggtttatt 10620 ttaaatagta catgtgtatt ttggttatgc actttaatgt atcttcctat tacactgcaa 10680 tatagtgcat tggatattct gcatgcatgc agtggacaaa aaaaaaatgg aagccaattc 10740 tgcatgtgtg ctatataaaa aaaaaaaagt attaactttt taagacggtt aaaactgtgc 10800 gacttacaaa gttaatatct taggtcgggt aaatattaac tgacttacac attgaggcct 10860 taagtcggtt gctaaatccg acttcaaaag ctgaaacttc ttactacggg agctgttagg 10920 tcgaacgcat gcccgactta caaagctttt ttaactgact taaacaagga ggccttaagt 10980 cggttgctat acccgactta aaaggaagaa acttcttact acgggagctg ttaagtcagc 11040 cgcgcgcccg acttaaaaag ccttttttaa ccgacttaaa aagggttttt tgtactagt 11099 // ID Gypsy1-VV_I repbase; DNA; EDCOT; 4419 BP. XX AC . XX DT 31-AUG-2007 (Rel. 12.08, Created) DT 31-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW internal portion; Gypsy1-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4419 RA Obukhanych T. and Jurka J.; RT "Gypsy1-VV - LTR retrotransposon from grapevine."; RL Repbase Reports 7(8), 671-671 (2007). XX DR [1] (Consensus) XX CC This is an internal portion of the Gypsy1-VV LTR retrotransposon CC family. Individual elements are on average 80% similar to the CC consensus. The internal portion is flanked by 95% identical long CC terminal repeats (LTRs). 5'LTR sequence is deposited as CC Gypsy1-VV_LTR. Target site duplications are 5 bp-long. XX FH Key Location/Qualifiers FT CDS 26..2314 FT /product="Gypsy1-VV_I_1p" FT /translation="MGTNKERIEQLEAGLGXVQDGXHRMELGMTDKLHQME FT ETXNRLSEVLLANPENPILGXIPTNREGNGGGQQMVXSKIAKLEFPRFSGD FT DPTEWFNRVDQFFEFQDTPEDQKVSLASFHLEGEANQWWQWFRRTFHEEGR FT VXSWEDFEEELWARFGPSECEDFDEALSRMRQMGSLRDYQREFEKLGNRVQ FT GWTQKALVGTFMGGLKXEIADGIRMFKPQSLKEAISLARMRDDQLARQRRF FT TRLAPPTRAPLTLPHTQLATPPTPATPVKRLSWEEMQKRRAQGLCFNCNES FT FTAGHKCQGPQILLLEGYEDNDDMICDEVTEEQPAGERSMKELLKPEITLH FT ALTGWTAPKTMRITAKIGAHEVVVLIDSGSTHNFISERVANMLRLPVVPTE FT TFTVRVANGERLRCQGRFEKVQVNLQGTTFSLTLYSLPLTGLDIVLGIQWL FT EILGSVVCNWKKLTMEFMWENQTKKLQGIDMQTIQAASLKELSKEFRQGHA FT LFALCLQVAQTKPQQNIHPSMQELLKEFSDLFTEPSSLPPAREVDHSITLK FT EGTEPINVRPYRYAHFQKTEIEKQVQDMLQSGLIRPSTSPFSSPVLLVKKK FT DGTWRFCTDYRALNAATIKDRFPIPTVDDMLDELHGASYFTKLDLRAGYHQ FT VRVNPPDIPKTAFRTHNGHYEYLVMPFGLCNAPSTFQAIMNSIFRPYLRKF FT ILVFFDDILIYSPNWDKHLVHVKQTFEILRQHQFFVKASKCAFGQQELEYL FT GHIITTSRRESG" FT CDS 3053..4417 FT /product="Gypsy1-VV_I_2p" FT /translation="MASWATAIQREWSLFLTMPPYGLNCCMKCMTPKWGGH FT SGVLRTFKKLAQQFYWPKMHKAVQDYVKGCEVCQKIKSETLAPAGLLQPLP FT IPCQVWDDITLDFIEGLPTSHGKDTILVVVDRFSKSAHFLTLTHPFTAKIV FT AEKFVEGVXKLHGMPKSIISDRDPIFISKFWQEFFKMSGTKLKLSSAYHPQ FT TDGQTEVVNRCVEQYLRCFVHQWPRKWSTYLPWAEYWYNTTYHASTGMTPF FT QALYGRLPPPIPPYKXGLSPVHEVDQKLLNRDELLRQLKTNLESSMNRMKQ FT MADXKRRDISFEVGXLVLFKLHPYRQQTVFKRAHQKLASRFYGPYQILEKI FT GPVAYKLQLPAGAHIHPVFHVSLLKRYXDNGGLAETQPVELPPFTDEGVVI FT LEPQDILDTRWIKQGTQLVEESLVQWKHLPXEEATWEPTNMLQELFPNLDL FT EDKDPLDGGG" XX SQ Sequence 4419 BP; 1341 A; 961 C; 990 G; 1100 T; 27 other; ttggtatcag agccaggtta cacttatggg aaccaacaag gaacgtattg agcagttgga 60 ggctgggctc ggtgragttc aagayggamt acaccgaatg gagctcggta tgaccgacaa 120 gctgcatcaa atggaagaaa ctmtcaaccg actatctgaa gtwttgcttg caaatccaga 180 gaatcccatc ctaggcagsa tccccaccaa ccgagaaggc aacggtgggg gacagcagat 240 ggtctyttcc aaaatagcaa agcttgaatt tccaagattc tctggagatg atccgacgga 300 atggttcaat cgtgtggacc aattctttga atttcaagac actcccgaag accaaaaggt 360 gtctttagct tctttccacc ttgaaggaga ggccaaccaa tggtggcagt ggtttcgcag 420 gacgttccat gaagaaggac gagtartctc gtgggaagat tttgaagagg aactatgggc 480 tcgttttgga ccttcagagt gtgaagattt tgatgaagct ctrtcaagga tgagacagat 540 gggatcattg cgagactatc aaagggaatt tgaaaagcta ggcaatcggg tacaaggatg 600 gacgcaaaag gctctggtgg gaacgttcat gggtggcttr aagycggaga ttgcggatgg 660 gattcggatg tttaagcccc aatcattgaa agaggcaatt agcttggcaa gaatgaggga 720 cgatcaactt gctagacaaa ggaggttcac acggcttgca ccaccaacgc gagctcctct 780 aactcttccc catactcaac tagcaactcc accaacacct gccactcctg tgaaacgact 840 gtcttgggaa gaaatgcaga aaagacgagc acaaggccta tgtttcaact gtaatgaaag 900 tttcaccgca ggacataaat gtcaaggacc gcagatactc ctgttggaag gttacgagga 960 taacgacgac atgatatgtg acgaggtcac cgaagaacag ccagctggag aaagatcaat 1020 gaaggaactc ctgaagcccg aaattacctt acatgcacta actggatgga ctgcgcccaa 1080 aaccatgcgg attacagcta aaattggtgc ccatgaggtg gttgtcttaa tcgatagtgg 1140 atccactcac aacttcatta gtgagcgtgt ggccaacatg ctgcgtttac cagtggtgcc 1200 aacggaaaca ttcactgtcc gagtggccaa tggagaaaga ctaaggtgcc aagggaggtt 1260 tgagaaggta caagtgaatt tacagggtac tactttctcc ttaactcttt actctttacc 1320 tctaacaggg ttggacatag tgctaggcat tcaatggctt gaaatactgg gttctgtggt 1380 ttgtaattgg aaaaagttga ccatggaatt tatgtgggaa aatcagacca agaaactgca 1440 aggaattgac atgcaaacca ttcaagctgc atcattraaa gagttatcta aggaatttcg 1500 acaaggacat gctctgtttg ctttatgcct ccaagtagct caaacgaaac cacaacaaaa 1560 tattcatcca agcatgcagg aattgttgaa ggaattttca gatttgttca cagagccctc 1620 aagcttacca ccagcacgag aggttgacca cagcattact cttaaagaag gaaccgaacc 1680 gattaatgtg cggccttaca ggtatgccca ttttcaaaaa actgarattg aaaaacaggt 1740 ccaagacatg ttgcaatcgg ggcttattcg accaagcact agtccttttt catcacctgt 1800 attattggtg aaaaaaaaag atggcacttg gcgattttgc acagactatc gagcacttaa 1860 cgccgcaacc atcaaagatc gatttccaat tccaacagtg gatgatatgt tggatgagct 1920 ccatggtgct tcttacttta ctaagcttga tctgagagcw ggataccatc aggtacgagt 1980 aaatcctcct gatattccta aaactgcttt ccgtactcat aatggtcatt acgaatactt 2040 ggttatgcca tttggcctat gtaatgcacc atctacattt caagcaatca tgaactctat 2100 atttcgacct tatcttcgaa aattcatatt agtttttttt gatgatattt tgatttatag 2160 tcccaattgg gataagcatt tggtgcatgt taaacaaacc tttgaaatat tgaggcaaca 2220 ccaattcttt gtcaaagcta gcaagtgtgc atttggccaa caagaattgg agtatttggg 2280 gcacattatc actacatcaa ggcgtgaaag tggatgaaaa taaaattgca gcaatggtag 2340 cttggccacg acctactaat atttctgaac tacgtgggtt tttaggctta acagggtatt 2400 accggaagtt tgttcaaaac tacggcatca tagctcgacc cctcaccaat cttctcaaaa 2460 aaggacaatt cggatggaat gaggaagctg aaacagcctt cctagctctc aaacaagcca 2520 tgacaaccac tcctacatta gccatgccta acttcaatga acctttcacc attgaaacgg 2580 atgcatctgg ggaaggaatt ggcgcagttc taactcaaca aggcaaacca atagcctata 2640 tgagtcgagc cttgggagtg accaaaaaat cttggtcaac ctatgccaag gaaatgctgg 2700 ccattgtgga agccatacgc atgtggcgac cttatctact aggccaaaaa ttctatattc 2760 aaaccgatca acgtagcctc aaatattttc tagagcaacg aatagcaact ccggagcagc 2820 aaaaatgggt ggccaagcta ctgggctatg attatgaaat tatttacaaa ccaggccgtg 2880 agaactcagc agcagatgct ctctcacgaa agcaaggcag tcccattctt catgatattt 2940 tttttccgca ggttacttta tgggatgaaa tcaaaaaagc tgctgaagaa gayccataca 3000 ttcagtcgaa aattcgtaaa ttggccacgg awcaacctgr aggatcatat acatggcgtc 3060 atgggctact gctatacaaa gggagtggtc attgttccta acgatgccgc cttacgggct 3120 aaaytgttgc atgaaatgca tgacaccaaa gtgggggggt cattcggggg tcttacggac 3180 attcaagaag ttggcgcaac aattctattg gccaaaaatg cataaagcag tgcaagacta 3240 tgtcaaggga tgtgaggtat gccaaaaaat taaatctgag actttggctc cagctgggct 3300 tcttcagccg ttgcccattc cgtgccaagt atgggacgac atcaccttag actttattga 3360 agggctaccg acttcccacg gcaaggacac aatcctggtg gtggtcgata gatttagtaa 3420 gtctgcacat tttcttacct taactcatcc ttttactgca aaaattgtag ctgaaaaatt 3480 tgttgaagga gttrtcaaac ttcacggcat gcccaaatcc atcattagtg atcgggaccc 3540 aatcttcatc agcaaatttt ggcaagaatt cttcaagatg tcgggcacca aactaaaact 3600 tagttccgca taccacccgc aaacggatgg ccaaacggaa gtcgtcaatc gctgtgtcga 3660 acaatatctt cggtgttttg ttcatcagtg gccacggaaa tggagcacct atcttccttg 3720 ggcagaatat tggtacaata caacttacca tgcttcaaca ggaatgaccc cttttcaggc 3780 tctgtatgga cgtctaccac cccccattcc accttataag ratggccttt caccagttca 3840 tgaagtggac caaaaactcc taaatcgaga tgaactgtta cgccaactca agaccaattt 3900 agaaagttcc atgaatcgaa tgaagcagat ggcagattma aarcgaagag atatttcgtt 3960 cgaagttggy ganctggtcc tttttaagct acatccatat cgccagcaaa cggtcttcaa 4020 acgagcccat cagaaactag ctagtcgttt ttatggaccc tatcagattt tagaaaaaat 4080 cggaccagta gcatacaaat tacaactccc agcaggagca cacattcacc ccgtgttcca 4140 tgtgtcactg cttaaacgat accakgacaa tgggggactt gctgagaccc aaccagttga 4200 gttgccacct tttactgatg aaggagtagt tatcctggaa cctcaagata ttttagacac 4260 acgctggatc aagcaaggaa cccagcttgt tgaagaaagc ttggtgcaat ggaagcatct 4320 accagyagag gaagcyacgt gggagccaac aaacatgctg caggagctgt tccctaatct 4380 ggaccttgag gacaaggatc cacttgatgg gggaggtat 4419 // ID GYPSY2-I_MT repbase; DNA; EDCOT; 4619 BP. XX AC . XX DT 31-JUL-2005 (Rel. 10.07, Created) DT 21-JAN-2007 (Rel. 12.02, Last updated, Version 2) XX DE Internal consensus of M. truncatula gypsy element. XX KW Gypsy; LTR Retrotransposon; Transposable Element; GYPSY2-I_MT. XX NM GYPSY2-I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4619 RA Gentles A. and Jurka J.; RT "Gypsy-like retroelement from Medicago truncatula."; RL Repbase Reports 5(7), 175-175 (2005). XX DR [1] (Consensus) XX CC 1619 bp LTR deposited as GYPSY2-LTR_MT. XX SQ Sequence 4619 BP; 1423 A; 957 C; 802 G; 1430 T; 7 other; tgagcctaac ttggctttat ttaattcttt gtgctataac ttgcttaaaa aaaaaaaaaa 60 aaataaaaga tggaaatact tgtatatatg ttcttccttc ttcttccttc tttctaaacg 120 tgagtggtga gataagtcct acacccgggc ttgagagaaa tttaagatag gacggtggta 180 taatcatagt gccattccaa gagtcaactc ttgggtattg gtacatgtgg tataacccca 240 ctcaacggag ggatcttgga agtaatatgt tgtcaacrtg agtagtcatg tttggcacta 300 ytattttcaa gtgaccgtcg aagttgagga cctttagtya cctttaaccc atcttggcct 360 tttaggacgt agtgcggtgg ctaatcaaga gtagtcttga attagttgat acgcgatact 420 acactcaaac gagactttcc tacgaatgtt aattggaacg ggagtagtcc cgtmacccga 480 taaatattcg gaagtggtta atgactttgg gaacttggta gaacccgtga tacaggtaca 540 atttgaaacc atagtcctta ccaaatggcg ttgttaccct tgactccaac attgtggact 600 taacctcacc atgcattcca cgttctttag cataatcatg catacatgca ttcattcata 660 aaaaattttt ctcactaata tcgaaggact tagataagtt yttgtaaaca tcaaagatat 720 ggaccttgta agaaggaaca ccaagaaata caacttcaaa aatcttaact aagctttagc 780 ttttgttaag aacttttttc cttggtttcg ttcttacttt tgaaaaggga accaattgca 840 acatcttcac aattttcaaa taaaacaatg ttccttatca agtttacaat tactttgaca 900 agtccttcaa aaaaaatgtg tctatttttg cataagcata gcatgcatca ttttgcattc 960 ataatttcaa gtctgagtct tacactgtgt cttttctact aaaggtcaat ccatctcaaa 1020 rgtgtcccaa ctgtcctcgt ccaaagccaa ctcgcactta caacactcgt gcaaacaaaa 1080 agaaagaaca tatcagtttg aacaagaaat ccacgagcat tcgtgaagag gtaacaacac 1140 tattgactcc cagcattgct aaagaagtat ttggttcctt ccaccactta tttgttcaaa 1200 taatgttatg tttgttgctt ttctcttttc aaaaaaaaca tcctttcgtc ccgcccgaga 1260 tgaaagtgaa ctggtgtagg gctttttgct ttaagaattg tcatcattaa taaaaaggtc 1320 gttttgatcc cgactttgtt ttcattttgt gcttttttct ggaaaaatgg taatacaaaa 1380 aacccaaaaa atctttcaat aatcattctc aaatatctgc ataatcataa cttgtactta 1440 cttgtcaaaa tcaataaata aatcatgcat taataaaccc gttgaacaca ataaccatgt 1500 actctcttcc aactttgagt tccttgtatc cgaagctgaa gaagacaaga atgaagagac 1560 tcccgacaag atctctcgca tactggggca tcttagccgt caaagctgca aacaaaatat 1620 caaagaagat tgtccagaag atggctttca tttacaaaga ctggcacgag atgctaccat 1680 ttgcacttca tgagtattgt acttcagtac acacttcaac aggggcaacc ccctctttcc 1740 ctcaagtata caacatgaag gtcatgcttc ccgtggaggt cgaagtcccg acaataggag 1800 ttctgccgaa atccaagctt gattgaactt aaaatgcatg acgaccttgt acaaccatgt 1860 caaaagaggt tgaaacaaac ttccaacaag aaggttcgtc cccgtgaaat tcaagaaaga 1920 gactttgtgc ccaaaaaggt actatctttc caaccagact ccaggggcaa gtggacgcct 1980 aactatgaag gctcatgtgc aatgactttt acaactatgg atggtgacaa acttgcactt 2040 cctatgaatg ccggtgcagt caagaaatac tctgtcaaaa tataaaagct cgataagtcg 2100 caaacctgaa aaggcggctt aggcaaaaat gagcgtctcg gtggactgaa aacccaaaag 2160 ggcggtccag gcaaaagtta gagacatgaa caaaaatgat tatcctgata gattgaaaac 2220 ccgaaagggc gatctatgca aaagttaagg atcaaaagac aaagtaactg catccggtcg 2280 ggcacaatcc acttggggca tccagctatc aaaagacctc cgattcgaag catctgcaga 2340 tcaaagactc ggaacagggg cattcaaagt tgttagggag aatagcggtt atttgtgttc 2400 aatgtaccct tcccattaca tttaccattt ttccaaaaat tttcaaaaaa tccgtggagc 2460 catgcccttg gcaggtcacc actcaattca tcaaaatttg agcctgtgcc catttatttg 2520 gaactctcat ttattctatt tgcataattt cttctatttt tgatggcaat acttaaagca 2580 aaaattttca aaaatacaaa aacttgtttt acatcttttg aaaagtgtga acaacaaaca 2640 cactctcttt gaactcgtga gtaggtgaag cgtacatcaa cattcgcctc gagaacggtt 2700 acactccgga agagaaacat ggctaagcac tatggaaagg acctctactt tgagcaagat 2760 gctgtcacag tcaaaaaata caaaaaaaaa aaagaaatac aaaaaaaaaa atcaaagctc 2820 gctaagttga aaacctgaaa aggcggctta ggcaaaagag agcgtcccgg tggactgaaa 2880 acccgaaagg gcggtccagg caaaaattag gggcacaaaa aagaatatat tcccggtgga 2940 ctgaaaaccc gaaagggcgg tccaggcaaa agttagggat ttttctataa aaaaaaaagc 3000 atgactgctg aagcatacca atggaaggac actctgtgcc ggtttacaaa tggcgacttc 3060 ttccaaactt tttatcaaca atgggcttta cccccaggag gcatcagttg ctaccttgtg 3120 ccaggttctt acaccgtcaa cggctcgatt tgttcacaat agtatcatct ccaaggaagt 3180 ttgccgagtg tttgtactgc gatgtcagtc cgtctcccat cttacctgtc ttgtctcggt 3240 tcatcgagtc acatgtcata tacagtcatg cagtcataca ttcacacagt cacacattca 3300 tacattcata caatcatgca ttcatcaata ttttcacata ttcatacgtt tatacgtaca 3360 catcatatgc acaacatcaa ttcacacata attgcatcag tcgtccagaa tctcgattcg 3420 gtcgtgtctc ttcagttcag tcttaactta ccattgtgtc aagccgcaag tttctacaaa 3480 taagcctctt ccatttacct tcttattgtc aaagtgtcat ccccggcgtg aagccgtgct 3540 agtcatgaca ctaatcaaac ttcaatttca actctcaata gtgtcatccc cagtgtgact 3600 gaccaagttg tcctttcatt cttacctttg ttaagctatc tcatcgatag ttaggtaaaa 3660 gtatcatttg tctttgttaa gctatcattt caacgatagt tagacgatgg tttttctttc 3720 attcttacct ttgttaagct atctcatcga tagttaggta aaagtatcat ttgtctttgt 3780 taagctatca tttcaacggt agttagacga tggtttttct ctcattctta cctttgttaa 3840 gctatctcat cgatagttag gtaaaagtat catttgtctt tgttaagcta tcatttcaac 3900 ggtagttaga cgatggtttt tctttcattc ttacctttgt taagctatct catcgacgat 3960 ggtttttctc tcattcttac ctttgttaag ctatctcatc gatagttagg taaaagtatc 4020 atttgtcttt gttaagctat catttcaacg atagttagac gatgattttt ctctcattct 4080 tacctttgtt aagctatctc atcgatagtt aggtaaaagt atcatttgtc tttgttaagc 4140 tatcatttca acgatagtta gacgatggtt tttctctcat tcttaccttt gttaagctat 4200 ctcatcgata gttaggtaaa agtatcattt gtctttgtta agctatcatt tcaacgatag 4260 ttagacgatg gtttttcttt cattcttacc tttgttaagc tatctcatcg atagttaggt 4320 aaaaatatca atcgtctttg ttcagctatc aatacgatag tagacaatca ttttccccag 4380 tgaaactata ttcccctagc ggagtcggat ccctttttct tcaamgaatt tgggtatccc 4440 gttattgttt ctcattccag tcaaatcatc tttgtcgtcc tgcattcata attgcatcac 4500 atgcattcat aacatcttag gtcaaaaatg gtgtactttt gtatttaagt ctcttcgact 4560 cgtcaaatca aagatttcat cttcaaatct ccggacgaag aaacttaaat aggggcatc 4619 // ID MELS3_IN repbase; DNA; EDCOT; 182 BP. XX AC AB041764; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Ipomoea nil mobile-like DNA transposon MELS3_IN. XX KW DNA transposon; Transposable Element; MELS3_IN; mobile-like. XX OS Ipomoea nil OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea. XX RN [1] RP 1-182 RA Hoshino A., Johzuka-Hisatomi Y. and Iida S.; RT "Gene duplication and mobile genetic elements in the morning RT glories."; RL Gene 265(1-2), 1-10 (2001). XX DR Genbank; AB041764; Positions 1 182. XX SQ Sequence 182 BP; 52 A; 38 C; 30 G; 62 T; 0 other; cactactgga aattttgaaa tttccgacca cctgaaagtg atcttaaatc aagtcaaaag 60 tcttgttccg accacttttg gtatccggaa aaacctttgt tgctatttcc gatcactttt 120 tggtatcaac ttaatttaag accattttca ggtggtcgga aattccataa tttccagcag 180 tg 182 // ID TIP100 repbase; DNA; EDCOT; 3873 BP. XX AC AB004906; XX DT 09-MAY-2005 (Rel. 10.05, Created) DT 09-MAY-2005 (Rel. 10.05, Last updated, Version 1) XX DE Ipomoea purpurea transposable element Tip100. XX KW hAT; DNA transposon; Transposable Element; transposase; Tip100. XX OS Ipomoea purpurea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea. XX RN [1] RP 1-3873 RA Habu Y., Hisatomi Y. and Iida S.; RT "Molecular characterization of the mutable flaked allele for RT flower variegation in the common morning glory."; RL Plant J 16(3), 371-376 (1998). XX DR Genbank; AB004906; Positions 1 3873. XX CC Terminal inverted repeats are at positions 1-11 and 3863-3873. CC This is Ac-like transposable element (hAT superfamily). XX FH Key Location/Qualifiers FT CDS 1329..3755 FT /product="TIP100_1p" FT /note="Transposase" FT /translation="MKKTQKIDLFFKRKNSEDSTSQVNPFASIEPLNSESR FT PEKAQRVEINEKFDIQALERDPGLRLPIWKCPIEKRDEVRRAYIKAGPYQC FT LLSKYPKSGEKHPRSFQASWFKLFPSWLEYSPSKDAAFCLPCYLFHTQDGP FT SGLDAFTINGFRSWKKVRDGKNCSFLAHIGKDLTSPHRNAEKACADLMNQQ FT SHIAQHIEKFTSQEIAENRLRLRTSIEATRWLAFQGCSFRGHDESITSTNR FT GNFLELLSFIASFNDEVTKVLDKAPRNASYTSPTIQKQILQVLATKVKSAI FT REEIGDAKFCIIVDEARDESKKEQMSIVLRFVDRDGFIQERFFGVVHVKDT FT SASTLKEGIFSILSRHNLDVQNIRGQGYDGASNMRGEWNGLKALILDECPY FT AYYVHCFAHRLQLALVASSKEVIPVHQFFTKLNSIINVVGASCKRNDQLKA FT AHASNISHLLSIDELESGRGLNQIGSLQRPGDTRWSSHLKSISSLMRMFSA FT TCEVLLNIIEDGTTHAHRGDADAAYEVLTSFEFVFIMHLMKKVLEISNMLC FT QALQLQSQDILNAMHLVSSTKLLIQTLRDSGWDELVASVKSFCETVNITVP FT DFDAQYIARRGRARHQQDELTIGHHYKVDIFYAVIDSQLQELSNRFDHKAM FT ELIVLSSSLDPKEMRISFRIDDVCKLVEKFYPQDFEDYETLQLRVQLEHFE FT HVQQLPDFRTLESISDLCRWLVKTRKSNIYPLVFRVVTLVLTLPVSTATTE FT RSFSAMNIVKTTLRNKMEDEFLSDCLLVYIEKQIAKQFSIDSIIDAFRDMQ FT ERRSKF*" XX SQ Sequence 3873 BP; 1254 A; 598 C; 729 G; 1292 T; 0 other; caggggcgga ggcacatatt atatgcaggg ggccttggcc ccccccccca acaaaaaaaa 60 ttttaatgca tgcaattagt atagcctatt aggcaatagg ggccttggcg gcttggcccc 120 cccccaaaaa aaaaaaaaaa aaaaatatta gtagtgtaat taattgtggc ccttcaccaa 180 tcagtaatca tccaatattt tccctcccca aacaaagctt cctttgtaag ctttcactta 240 acccaatttc aaaccaaacc tgcaacccgc atatacgcaa atcaaatttg gaagaagata 300 ataaatacac tcaaatcacg aatcaaagca atacacacaa gccatttctc ttccattttc 360 aagcagcaaa tgtataggta attttacatt tcttttttat tatttaaatt tttgaatttt 420 ttttttatga attattcttt attggagata aattcatcat tcttcactac aataaaaagt 480 ctagatattg tagttcaagg gtagctaaat gcctaaattc tctctttcgt ttcttcagtt 540 gacgacggca accgtggtga actcgggcta ctggctacga gtagtgccga ctggaagctg 600 gatcctgttt ggagtgtcgg cgttctcctt ttgttggtgt atgtttatac ttttaagagt 660 tctataagat ttgctagaat ttaaatacta gtgcataatg aaatgggtca tttgatgagt 720 tttgaaaatg atagtattag ttgaggatta tatgccattg ttgtggattt gagatgatgt 780 tataattaca gaaagggtca gtgttatata tgatgatatt agcttggaga aagagattag 840 aagctagcat attcaattca tgcagacaaa aaattagata attagaatgc caaatcaact 900 taaattaata tttagttaag aagaagttag aaccattgat gttactactc tatcttttca 960 taaacaacat aatatataat ttatatagta tatatagttt atgcatgagg agtaattagg 1020 tgatttaatg agttttgaaa atggcagtac acagtattaa ttaggattta tttgtcttta 1080 ttaatttggt gatttgatgt gtttatttac tcctgtatta tatagttaat ataattgtgt 1140 ttaattagta tattaattga caatacacaa tattgatttt gatgagtatt aattgtatta 1200 attgtattta ttataattag tatattaatt ggcacttggc agtacacaat atctttgttt 1260 gtttattttt tttcctcaat taatttgtca aaatattaac agtgtgaaca tgagaagatt 1320 gagttgaaat gaaaaagaca caaaaaatag atcttttctt taaaagaaag aattctgaag 1380 attcaacatc tcaagtaaat ccatttgcaa gtattgaacc attgaattca gaaagtcgtc 1440 ctgaaaaagc tcaaagagtt gaaatcaatg aaaagtttga tattcaagca ttagaacgcg 1500 atccaggatt gcgactacca atatggaagt gccccattga gaagcgtgat gaagttagga 1560 gagcttatat caaggctggc ccatatcaat gtttgctttc aaagtatcca aaatcgggag 1620 aaaagcatcc tcgtagtttt caggcatctt ggtttaagtt attcccttct tggttagaat 1680 attctcctag taaagatgca gcattttgtc taccatgtta tttgtttcat actcaagatg 1740 ggccttccgg attggatgct tttactatca atgggtttag atcatggaag aaagttagag 1800 atggaaaaaa ttgctcattt ttagcacata ttgggaaaga tctcacctcc cctcaccgaa 1860 atgccgagaa agcttgtgcg gatctcatga accaacaatc acacattgca caacatattg 1920 agaaattcac atctcaagaa atagcagaga atagacttcg cttgagaact tcaattgagg 1980 caacaagatg gcttgcattt caaggatgtt cttttagagg tcatgatgag tcaataacat 2040 caacgaaccg tggaaacttt ttagagctat tgagtttcat tgcctctttt aatgatgaag 2100 taacaaaagt tcttgataaa gctccacgaa atgcatcata tacatcacca acaatacaaa 2160 agcaaatttt gcaagtgttg gcaactaaag taaaaagtgc aatccgagaa gaaattggtg 2220 atgcaaaatt ttgtatcatt gttgatgaag ctcgagatga atcaaagaag gaacaaatgt 2280 caattgtctt gagatttgtt gatagagatg gctttataca agagcgtttc tttggagttg 2340 ttcatgttaa ggacactagt gcatcaacat tgaaagaggg catcttttct atcttatctc 2400 gtcataatct tgatgttcaa aatatccggg gacaaggtta tgatggtgca agtaacatgc 2460 gtggagaatg gaatggattg aaagctttaa ttttggatga atgtccttat gcttattatg 2520 ttcattgttt tgcacatcga ttgcaattgg cattagtagc ttcatcaaag gaagtcatcc 2580 ctgtccatca gtttttcact aagttaaact ccattattaa tgttgttggg gcttcatgta 2640 agcgcaatga ccaattaaaa gctgctcatg cctcaaatat ttctcatttg ctgagtattg 2700 atgagctaga aagtgggagg ggccttaacc aaattggttc tttacaaagg ccaggtgata 2760 ctcgctggag ttctcatttg aaatctatat caagtttgat gagaatgttt agtgcaacat 2820 gtgaagtttt acttaatatt attgaagatg gaactacaca tgctcaccgt ggagatgccg 2880 atgcagctta tgaggtactc acttcttttg aatttgtatt cattatgcat ctcatgaaaa 2940 aagttttgga gatttctaat atgctttgcc aagctttgca acttcaatct caagatatat 3000 tgaatgcaat gcatcttgta tcatctacta aattgcttat tcaaacttta agagatagtg 3060 gatgggatga attagttgca agtgtgaagt ctttttgtga aactgttaat ataactgtgc 3120 cggattttga tgctcaatat attgcaagaa gaggaagggc tagacatcaa caagatgaat 3180 taacaattgg gcatcattac aaagttgata ttttttatgc ggtgattgat tctcagttgc 3240 aagagttgag caataggttt gatcataaag caatggagtt aattgttctc agttcatcgt 3300 tagatccaaa agagatgcgt atatcattca gaattgatga tgtttgcaag ttggtagaga 3360 agttttaccc acaagacttt gaagattatg agactttgca attgagagtg caacttgaac 3420 attttgaaca tgtgcaacaa cttcctgatt ttagaacact agaaagtatt tctgatctat 3480 gccgatggtt ggtaaaaact agaaaatcga acatttatcc tcttgtgttc agagtagtaa 3540 ctctcgttct cacacttcca gtatctacag ctactacaga acgatctttt tctgctatga 3600 atatagtcaa gactacactt cgtaacaaga tggaagatga atttcttagt gattgtttgt 3660 tagtatacat tgaaaagcaa attgcaaaac aatttagtat agattcaatt atagatgctt 3720 ttcgtgacat gcaagagaga cggtctaaat tttagtagat ttgtaatata atgatgtatt 3780 ttggaacatg ttaaatgaat attattatat ttcagtattc tgtcttaaat tgtgattggc 3840 cccccgcatt ggttaatcct ggctccgccc ctg 3873 // ID RAVLIN2_MT repbase; DNA; EDCOT; 5608 BP. XX AC . XX DT 16-JAN-2007 (Rel. 12.01, Created) DT 06-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE A LINE element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; retroposon; KW LINE; Poly-A tail; ORF; RAVLIN2_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5608 RA Shankar R. and Jurka J.; RT "RAVLIN2_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 47-47 (2007). XX DR [1] (Consensus) XX CC This LINE element shares closest proximity with RAVLIN LINE CC (~85%). It's present in Medicago genome in multiple copies whose CC central domain is well conserved and moderately conserved tail CC region, while in most of the cases 5' end is heavily truncated. CC This sequence has characteristic features of L1 as well as it CC exhibits a RNAseH domain after RT polymerase domain, a feature of CC I-elements of drosophila, though this sequence has poly-A tail CC end. Also it has CCHC zinc finger protein domain in 1st ORF. XX FH Key Location/Qualifiers FT CDS join(4120..4224,4228..4374,4387..5388) FT /product="RAVLIN2_MT_1p" FT /translation="MNSXISXITLFGSLVMVKISIFGLIIGVENPFLKPVF FT LMQYQFIYLQLLVITLIIVNGIFLKLFVKCFLILSQLDSTSYYSTGRIGLE FT AFSNNGFLSLKEAYVFKXNNXQNMKWAKFIWXPDIPPSKSLLVWRLMHDKI FT PTDDNLMDRGCKLPSMCNLCCKNSESSFHLFFECSFALKLWNWLSASLNXN FT IQFTDMDDIWNICERAWSPQCKIVIKAALINLLNTIWFARNQARFKNKIIH FT WKSAISIIIAKASLSGNFTSKASTSSIREFIILKAFNVKIHPPKAPIIKEV FT IWNPPLFNWIKGNTDGASMGNPGLASCGGIFRNSEGNCMGCFAENLGIVNS FT YHAELCGAMRAIEIAYQKHWNFLWLETDSQLVVLAFKNSTLVPWQLRNRWN FT NVQLKLTNMNFMVSHIYREGNXCS" FT CDS join(190..264,358..786,811..927,1003..1353) FT /product="RAVLIN2_MT_2p" FT /translation="MAQRGNPSYCFCFEKLSVVCLEEFRNLNPGVLKLFAW FT SQDFKPNLQNNSTAQVWVRLHGLPQEYWRPRIFFAIANSVGTPICTDSAST FT KPMIDRTFGQYARVLVDMDITKDLRYNVLVERKGYAFFVELEYENLPDYCV FT HCKKIGHDVEICRFAIKTVQARTASKLINRWEKKNVAIIVEEAALKEVEVI FT NKNKDKQKDPAAEEGMEKKRSMMIVKKVKQALKALSLLMLHNSTMMSMIKK FT MLKLNSPERVQNDMEFLKQSWANIVDDTAAEDRLSEELEQRQAAVEEEQQH FT IFAEVSASYNKKSEKKQPKRRESEDCSASSQS" XX SQ Sequence 5608 BP; 1785 A; 975 C; 1006 G; 1813 T; 29 other; caaacaagcc acccaaacat ttgtccaacc caaaactttt gcccaggctc tgtcaaacat 60 ttgtgatatt ccctcatcac aactacctca gcctgtcatc aaaggagaca atctatccat 120 ttcaatccca gaagaagaat atgaagcagg tatggcatct tgcaaactca accttcatgc 180 cagggtcata tggcccaaag gggcaacccc tcttactgtt tttgctttga gaaattgtct 240 gttgtctgtt tggaagaatt taggtaagtg gggggtttcc tcaataggaa gaggatacta 300 tgaatttgtt ttttcagctt ggaggatgta aagagagtta gatcagttcc ttcttgaaat 360 cttaatccag gtgtcttaaa gctttttgct tggtctcaag attttaaacc taatttacaa 420 aacaattcca ctgcacaagt atgggttagg ttacacggcc ttccacagga atattggaga 480 ccaaggattt tctttgctat tgcaaatagt gttggaacac ctatttgcac agactcagcc 540 tcaaccaagc caatgataga cagaacattt ggccaatatg ctagagtttt ggttgatatg 600 gatattacaa aggatctaag atacaatgtt ttggtagaaa gaaagggtta tgctttcttt 660 gtggaattag aatacgaaaa tttacctgat tattgtgttc actgcaagaa aataggacat 720 gatgtggaaa tttgcagatt tgctattaaa actgtacagg ccaggacagc ttcaaagcta 780 attaactgaa caaattcatg ttatagctag agatgggaga aaaagaatgt tgccataatt 840 gttgaagaag cagctttgaa agaggtagag gtaatcaaca aaaacaagga caaacaaaag 900 gatcctgctg ccgaagaggg aatggagtaa aaaacacaaa agaatcaaca agttaacgaa 960 gatccaatca gtccaagagc cgtaatgagg atcagaattt agaaaaagag atcaatgatg 1020 atagttaaga aagtgaagca agctctcaag gctctgagtt tgttgatgct acataactca 1080 acaatgatgt caatgatcaa gaagatgttg aaactaaact ctcctgaaag agttcaaaat 1140 gacatggaat ttctcaaaca gtcatgggcc aatatagtgg atgatacagc cgctgaagac 1200 agactctcag aggaactaga gcagcgacaa gctgcagttg aagaggagca acaacatatt 1260 tttgctgagg tttcagctag ttacaacaag aagtcagaaa aaaaacagcc aaaaagaaga 1320 gaatctgaag actgttcagc atcaagccag agctaaggtt tcaaaaacct ttcaaatgaa 1380 gtgtttgttc tggaatgtta ggggtatagc taatcacccc tcaagattag ccttaaaaag 1440 actaattatt ttgcataagc ctgacattgt aattatttct gaaccctgga tgtgcttcaa 1500 tactttccct aatagatggc attctaacct taacctaaaa ctttttgcca tgaattctag 1560 acctaatcat ctccctaatc tctggtgctt ttgtaaatca ccttgaccct atccttcttg 1620 ctactgatga tcaacaggtt accttctctt taactataga ttccaaagta gtggccttta 1680 cagctatcta tgcatcaacc agttacatca aaagaagaca attatggtcc tctttgaatt 1740 cccttcaatc acaacattct attccctggt gttttattgg ggactttaat gttgttattg 1800 gatcccatga acatagaggt tcttatcctc ctgccagact tccaatggag gattttcttg 1860 gatggtcaga agctaataat ctctttcaca ttcccactag aggtgcagag tttacttggt 1920 ccaatgggag gagaggaaat agaagcactg aaagaagatt ggacagatca atctgtaatc 1980 aacaatggtt agatttgtgt tgttcccttt cttgttcaac tttaacaaaa caaaaatcag 2040 atcactatcc ccttttactt gagttccaag tgaccacagt cagttttgtt tcccaattca 2100 aattcctaca aatgtggacc cttcaccacg attgtaaaaa cattatcacc agtagttgga 2160 atacaaatat tgtaggatgt cctatgttca ttcttaatca caagctcaag aacctcaaaa 2220 caaaattgaa agtttggaat aagaatgtct ttggaaatgt gcacactatt gtkaaagctg 2280 cagaagataa ttttaatcaa attcaaaatg atatcaactt gcaaggttcc tctgacactc 2340 ttctggatsa agagaaagat gcwcaaatya accttgaact ttgcttgaaa caacaagaaa 2400 ctttttggaa agagaaatct aaaattactt ggcactcaaa tggtgacaga aacacaaaat 2460 atttccacag actaaccaaa atcaaaaaaa cctctaaact yatcactact ctgcaagatg 2520 gtgataatat gcttactgat cctgatcaaa tttcaaatca tattgtaaat tattataaga 2580 ctttattttg tactaacttt gttttgcagg accagttact tgtagatgaa gtaatcccta 2640 aactaatckc tgatgacata aatgcagttc tcaccactct tcctaatcat cattagagat 2700 caaggcagca gtttttggtc tgaacaagga tagcgctcct ggtcctgatg ggtttggtgc 2760 aattttcttt caaacttatt gggagattgt caagaaggat gtcataaatg cagttttaga 2820 wttcttcaca aaaggatgga ttcttccaaa tttcaattct aatatcattg ttcttattcc 2880 aaaaaatcca gatgcaactt cagtggatca atatagacca atagctatag caaatttcaa 2940 attcaagatc atttctaaaa ttctagcaga tagattagct catwttatgc caaagatcat 3000 ttctacagag caaagaggtt ttattcaagg taggaacatt agagattgca tttgcatcac 3060 ctcagaagct atcaatctac ttcataacaa atcttatgga ggtaacttag ttttcaaggt 3120 agatatttct aaagcttttg acactttaga atggcacttc cttcttaatg ttttaagagc 3180 ttttggtttt aatgaaacat tttgcaactg gattcatact attttaaaat ctgcaactct 3240 ttcaatttct gtcaatggaa aaccacaagg ttattttaat tgtaatagag gggtgagaca 3300 gggtgaccct ctatcccctc ttctcttttg catggctgaa gatgttttaa gcagagagat 3360 ttctaaatta gtggatgaag gaaagcttga actcattaaa ggtactagat atgttaatgt 3420 tccttctcac tctttttatg ctgatgatat gatgatattt tgtaaaggca aaaattcatg 3480 tatctcaaat cttatrgatt twtttatcaa atatgctctg gaatctggtc aaatggtcaa 3540 tcctgcaaaa tcaactgtgt atcctggttc catttctgtt tctaggattg aacataytct 3600 ccacaatgtt agacttcaat ataggatctt tacctttcac ttatcttggg gttcctattt 3660 tcaaagggaa accaaaagtt tctcatcttc aaccaattgc tgacaaaatc aaagcaaaac 3720 tatcagcttg gaaagcttct cttctatcta ttgctggtag agttcaactg gttaaatctg 3780 tcattcaaag tatgctgatt catactattt ctatatactc ttggccaata tctctgctca 3840 aggatattga aaaatggata agaaatttca tttggagtgg tgatgttgat aaaagaaaac 3900 tggtgactgt tgcttggaaa aaagtttgca wgcctttctm tgaaggtggt ttaggtatga 3960 gatctcttaa tactctaaat gaagcaacaa acctgaaact ttgctgggac atgttgcatt 4020 cwaaagaaga ttgggcaatc ttgttaagaa gtagagtttt gagakgcaga aaaccaattt 4080 atcatcacat tttctcctct atatggagta gtatcaaaaa tgaattcaat ratatcaakg 4140 ataactctat ttggctcctt ggtaatggtg aaaatatcaa tttttggatt gataattggt 4200 gtggagaacc cytttctcaa gccttaagta ttcctgatgc aatatcagtt catttatctt 4260 caactgttag tgattacatt gataattgtc aatggaattt tcctsaagct ctttgtcaaa 4320 tgtttcctca ttctcagtca acttgattca acaagttact attccactgg aagataaaga 4380 wgataaattg gtttggaagc attcagcaat aatggtttct tatctctcaa agaagcttat 4440 gtgttcaaaw ataataattr tcaaaatatg aagtgggcaa agtttatttg gtstccggat 4500 attcctccct ccaagtctct gttggtttgg aggctcatgc atgacaaaat tcctactgat 4560 gataacctwa tggatagagg ttgtaagctg ccttccatgt gtaatctytg ttgtaagaat 4620 tctgaatctt cttttcatct attctttgaa tgctcttttg ctttgaaatt gtggaactgg 4680 ttatctgcat ctttaaatat raatattcaa tttacagaca tggatgacat ttggaacatt 4740 tgtgaaagag cttggtctcc tcaatgtaaa attgttatta aagctgctct gatcaattta 4800 cttaatacta tttggtttgc aaggaaccaa gctagattca aaaacaagat aattcactgg 4860 aagtcagcca tttcaatcat tattgctaaa gcttctctat ctggtaactt cactagcaag 4920 gcatctacca gttctatcag agaattcata attttaaaag ctttcaatgt taaaattcat 4980 cctccaaagg ctcctataat caaagaagta atttggaatc ctcctttgtt taattggatt 5040 aagggtaata ctgatggagc atcaatggga aatcctggtt tagcatcttg tggtggaatt 5100 ttcagaaact ctgaaggtaa ttgtatgggt tgctttgctg aaaatttggg tattgtcaat 5160 tcttatcatg ctgaactatg tggtgctatg agagctattg aaattgctta tcagaaacat 5220 tggaactttc tttggttgga aacagattct cagttggtgg ttctagcttt caaaaattcc 5280 actctagttc cttggcaatt aagaaacagg tggaacaatg ttcaacttaa attaactaat 5340 atgaatttta tggtttctca catttatagg gaaggaaatr cttgtagctg atacccttgc 5400 taattttggt ctgtctctgg atcactttga ttttttggat catatacctt tgtttgctag 5460 ggaagagtac gttaggaaca gattrggttt gcctaatttt aggtttttaa cttcttgaga 5520 aagttttttg gtttggtccc ccttctctty tttgtttcct tttctctttt aatctatcct 5580 ttgtgggttt gctaaaaaaa aaaaaaaa 5608 // ID Gypsy-19_Mad-I repbase; DNA; EDCOT; 4989 BP. XX AC ACYM01061158; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-19_Mad-I; KW Gypsy-19_Mad-LTR; Gypsy-19_Mad_. XX NM Gypsy-19_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4989 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1341-1341 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01061158; Positions 15989 11001. XX CC Positions [3818-4312] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 770..2224 FT /product="Gypsy-19_Mad-I_1p" FT /translation="MAERFLDYYEVPPHQWVLVAACNFGADASIWMRGFEQ FT RYGRDNWGLFVDLLLQRFGGGDRANIESQLTHIQQIGSVDEYIADFTKLSC FT RVLDWTESQLKHVFLGGLRDDIRHDVLALEPDSLHQAQKLAKIFESKNQAK FT RSFRPSFPRHLQPSANSRPPTSPPSLPHQIRPSPSHYPTAPFKRLTPVEVQ FT DKIKKKKCFHCTEPFTPGHKCKTPMIVLLDIDNPDDEPTEFHDCPSEEDPT FT TDHPVLPCHMLELFSIPGLGMGHPMRLQGSIGSIIIRVLIDSGAACNLLSL FT DIVQKLDLAIENINPVQFTTASHKKVHTHMRAHNVTINLQDYTLLGSFLLL FT NIPSYDLILGAEWLESLGYIGWHFRNKTMLFTVNDKTYTLQGLVTTQPAIR FT PCTSAHSSSHYSLPIMTTDNTIIPPPQPLPVDTHFTLPPNTHPAITSLLSQ FT YSHMFTTPLGLPPQRQIDHKIPILPNTTPINVCPYRYPHS" FT CDS 3206..4894 FT /product="Gypsy-19_Mad-I_2p" FT /translation="MFAIVFAVQHWRPYLLGQHFQIVTDHQPIKYFLEQRI FT STPQQQKWLVKLLGYNYSVEYRPGSQNGAPDALSRKVELLPLLGVSSPIFE FT CIPTFAQFYTTDPVVKDIWPALLQSTATTIRGFSIINVVIHYKNRIYVPSN FT SPWRSTILEEFHSSLQGGHSNFLRMYHRLKRSFLWPGIRRDVKLFIAHCNV FT CQRQKHETIHPPGLLQPLPIPTGIWQDIALDFVEGLPSSNGYTVIFVVVDR FT LTKYGHFIPLKHPYTSASIADTFIKEIFRLHGMPKSIVSDRDPTFLSNFWK FT EFFKHQGSKLCHSTAYHPQSDGQSEVLKRTLEHYLHCFSTDKQSKWSTLLP FT WAEWWYNTTFQSAIKMSPFQALYGVSPPSIQTYLPGTTVVQSVDAALQDRD FT RVLRLLRTNLQLAQNRMKQLYDKGRTEREFMVGDWVFLKLQLYRQQSVTKR FT HSHKLAPKFYGSFQIQERIGSVAYRLLLPHDSKIHPVFHVSLLKKKIGDAV FT SPNPTLPPFDSTGFFTWQPETILNRGMFKKKNTAVTKWLIKWAGLPTEDAT FT WEEADDIIARYPGFQT" XX SQ Sequence 4989 BP; 1286 A; 1513 C; 890 G; 1298 T; 2 other; attggtatca cagccaggtt gttcgatggg aaaaaacmac tcaatctgcc acctcttccg 60 accctgatgc ggtcgccgcc gcgatggatt ctcgtcatga gcacctgcgc aatcaagtgg 120 agggcgtctg tgactccatg gcaaccttgg aaacccaaca ggctactctc caaaaatcgt 180 tcgatcacat gaacacgtcg acctccgcct ttcaaaacca catgacttcc cagttcgcag 240 cctttcaatc tttgttgctt gacgaacttc gccttttgaa atcagccaac cccaaccccc 300 caacaccaca accccaaccc caacccacca cggctccacc caccccaaac ccaaccccgg 360 tgctcaaccg tccgtccact tccgttccag caccgtcatt tcgttcctta ttcgcccatt 420 cccccaacac attatcgggt ttgggtctct ctaaccctcc ctcaccgaac cttgggcctc 480 ttccccccta tttctccgcc gcccgcacca cgccgtcgcc caccaccatc cacagtcgcc 540 catcttattc cccacaccaa accgcatctt cttctttttt aacccaaacc cactttcccc 600 aactccctcc ccaacccccc agccttccat ataactcctt ccaccacccc aattcccaca 660 caacccaccc cccatcccaa ccacacccca tcacacacac tcgaatttca aaaccataaa 720 aatggagtta cctcgtttta atggggatga tccatatggt tagttagcca tggccgaacg 780 gtttctggac tattatgagg taccaccaca tcagtgggtg ttggtggcag cctgtaactt 840 tggggctgat gcctctatct ggatgcgagg gttcgaacaa cgttatgggc gagacaattg 900 gggtctcttt gtggatttat tgttgcagcg atttgggggt ggtgatcgag ccaacatcga 960 gtcccaactc acacacatcc aacaaatagg ctcggtggat gagtacatag ctgatttcac 1020 taaactctca tgtcgagtgc tcgattggac agaaagccaa ttgaaacatg ttttcctcgg 1080 gggtttacga gacgacattc gtcatgatgt ccttgctctc gagcctgact cccttcacca 1140 agcccaaaaa ctagccaaaa tatttgagtc caaaaaccaa gccaaacgtt ctttccgtcc 1200 tagcttccct cgacacctcc aaccttcggc aaattcccga ccccctactt cacccccttc 1260 cctaccacac caaatccgtc cgtcaccatc ccactacccc actgctccct tcaaacgtct 1320 caccccagtt gaggtacaag acaaaataaa aaaaaaaaag tgtttccact gcacagaacc 1380 ctttacccca ggtcacaaat gcaaaacccc catgatagtg ttgttggaca ttgataaccc 1440 agatgacgaa cccactgagt tccatgattg tccctccgag gaagacccca ctactgacca 1500 cccggtatta ccgtgccaca tgcttgaact attttccatt ccaggccttg gcatgggaca 1560 tcccatgcgc ctgcaaggct ctattggatc catcattatc cgcgttctta tcgactcagg 1620 cgctgcatgc aacttgttga gcttggacat tgtacagaaa ttggacttag ccatagagaa 1680 tatcaaccct gtccagttca ctacagcttc ccacaaaaaa gtccataccc acatgagagc 1740 ccacaatgtt actatcaacc tacaagatta cacacttctt ggttcatttc tccttttaaa 1800 catcccaagc tatgatttga ttttgggtgc cgaatggtta gagtccctcg gatacattgg 1860 gtggcatttc cggaacaaaa caatgctctt cacagtgaat gacaaaacct acaccctgca 1920 aggccttgtt acgacccaac ccgccatccg cccatgcacc tcggcccact ccagctccca 1980 ctattcccta cccataatga caaccgacaa caccattatt cccccaccac aaccactccc 2040 cgtcgacacc cattttacac taccccctaa tacccatccc gcaataacat ctcttttgtc 2100 gcaatactcc cacatgttca ctacccctct tggtctcccc ccccagcgtc aaattgatca 2160 caaaataccc attcttccca ataccacacc catcaacgta tgtccatatc gttacccaca 2220 ctcttagaaa gtcgaaattg aaagacaagt gcaggaactc cttgaatcta gagtcattcg 2280 caatagtagc agcccattct cttcccctgt tcttttggtt aagaagaaag acgagtcatg 2340 acgcttatgt attgactata gagcactcaa tgctgccacc atcaaggatc ggtycccaat 2400 ccctgtggtc gatgagttgt tagacgagtt acatggtacc tccatttttt ccaagcttga 2460 ccatcactca ggctatcacc aaatacgcat gtgcacagaa gacattgcaa aaacggcatt 2520 tcgtacacat gacggccact ttgaattcat ggtaatgcct tttggtctat ccaatgcccc 2580 ctctacattt caagctttaa tgaattccat cttccgtccg tacttacgta agttcgtctt 2640 agtgttcttt gatgatatac ttgtgtatag cccttccttg catactcaca tttcccattt 2700 ggagcttgtt ttcaacattc tatccaccaa cagcttgaaa atgaagctca gcaaatgctc 2760 atttggccaa caccatattg attacttggg acactccatc tcgggccaag gggtttcagt 2820 ggatgcttcc aaaatccagg ccatcattga ttggccacaa cctgcttcca ttaagagtct 2880 gcgaggattt ttgggtttta acagggtatt acagaaaatt tgttcaccat tacggcctgc 2940 tcgccaagcc cttgacaaaa atgttgcaac aaggcaattt tttcctggtc tccagaatcc 3000 attgctgact tcgagaaact caaacaggct ttgacatcta ccccagtact tgctcttcca 3060 gatttcacca agacattttg ttgtcgaaac cgatgccttg gggctagtca taggggccgt 3120 gttatgccag gaaggccacc caattgccta cctcagtaaa gccttgtctg gatgcaattt 3180 gtctctctcc acctacgaca aggaaatgtt cgccattgtc tttgctgtgc aacactggcg 3240 gccatatttg cttggccaac attttcaaat tgttacagat caccagccaa tcaaatactt 3300 ccttgagcaa cgtatttcca ctcctcaaca acagaaatgg ctcgtcaaac tgttagggta 3360 taactactcc gtggaatata gaccgggttc ccaaaatggt gctcctgatg ccctctcccg 3420 caaagttgag ttgttgcctc tccttggcgt ttcatctccc atttttgagt gcattcctac 3480 ctttgcacaa ttctatacca cagatccagt cgtcaaagat atatggccag ccttgctgca 3540 gtccacggcc acaactattc gaggattttc catcattaat gtcgtcatcc actacaagaa 3600 ccgaatatac gtcccttcca actcaccatg gcgttccaca atactcgaag aattccattc 3660 ttctctgcag ggaggccatt ctaatttcct ccgaatgtat caccgcctga aacgcagctt 3720 cctttggccc ggaatacgac gggacgtgaa actttttatt gcccactgca atgtttgcca 3780 acgacagaag catgagacaa tccaccctcc aggtctcttg caaccattac cgattccaac 3840 cggcatttgg caagatattg cactcgactt tgtggaaggg ttaccctcat ctaatggata 3900 cacagtcatc ttcgtagtcg tggatcgatt aaccaaatat ggccacttca tccccctcaa 3960 gcatccctac acgtcagctt ccattgccga tacattcatc aaggagattt tccggctaca 4020 tggcatgccg aagtccatcg tatctgatcg tgacccaacc ttcctcagta acttctggaa 4080 agaatttttc aaacaccaag gtagcaaact ttgccatagc acggcatatc accctcaatc 4140 tgatggacaa tccgaagtcc tgaaacgaac tttggagcac tacctccatt gtttttccac 4200 tgacaaacag agcaagtggt ccactcttct cccgtgggcc gaatggtggt acaacaccac 4260 cttccaatct gctatcaaga tgtcgccctt ccaggctttg tacggggtct ctcctccatc 4320 aattcaaact tacttaccag gcaccacagt cgtccaatcc gttgatgctg cattgcaaga 4380 ccgtgacagg gtacttcgcc ttttacggac taacttacag cttgctcaaa accgtatgaa 4440 acaactctat gacaagggcc gaactgagcg tgaattcatg gtgggtgatt gggtcttcct 4500 caagctgcag ctttataggc aacaatctgt aaccaagcgc cattcgcaca aactggcacc 4560 caagttctat ggttcttttc aaattcagga acgtattggt tctgtggcgt atcgccttct 4620 gctcccacat gactcgaaga ttcatccagt ttttcatgtg tctttgctca aaaagaagat 4680 tggtgatgct gtgtccccaa accccaccct cccaccattt gactccacgg gtttctttac 4740 ttggcaacca gaaacgatat tgaatagagg catgtttaag aagaagaaca cagcagtgac 4800 taaatggttg atcaaatggg cagggctgcc aactgaggat gccacttggg aagaagctga 4860 tgacatcatt gcccgttatc caggtttcca gacctgagga catgtctcat ctcaagcagg 4920 gggagttgtt acacccacat cactgggcct cgtaacttcc ctccagccca tacttattac 4980 ctgctattt 4989 // ID Copia-46_VV-I repbase; DNA; EDCOT; 5414 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-46_VV_; KW Copia-46_VV-LTR; Copia-46_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5414 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 12372630 12378043. XX CC Positions [2908-3222] - Integrase core CC 'GTCAT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 1372..3222 FT /product="Copia-46_VV-I_1p" FT /translation="MTFMQLFIENISYFCSANMSNPIFSLLASQVLTGENF FT VKWKSNMNILLINENYHFVLKEVCPPVPPANASKAVSEEYNRWIIANNKAC FT CYLLAAMDEVLRTKHEGLETASEIMESLQQMFGRPSEQARHEAVKAVMNSK FT MKNGSSVCEHVLKMIHHFNEAEINGAKIDENTQVGMILETFSPSFLQFRTN FT YIMNHKKCNLTEFLNELQSYETLIDDKEGKTNIAKANAVVGKASSSRNKKK FT RNVRNQKDKKKIQKKKRKAVEPKPKGKCFHCNQDGHWKRNCKKYLDELKQK FT KKQGKLDLLVMETCLVENDFSSWIIDSGASNHVCISLKMLESSKDLEEGAF FT MMRVGSGARVSATAVGTVRLSFANNKYLLLHNVYFIPDFKRNLISVSKLHE FT QFISVSFDVDSVSIYKNGMNICSGYVDNGIYFVKPIFNNLLQTEMFKVAEP FT TPKRRKISNDKNDTYLWHLRLGHINIDRIERVAKDGPLRELKVGTLPVCES FT CLEGKMTKMPFSAKGERAKVPLEIIHTDVCGPLNVKARGDYEYFVTFIDDY FT SRYGYVYLIQRKSEAFEKFKEFRAEVEKQLSKSIKTLRSDRGGEYLVYEFK FT DYLIENGILSQLTAPGTPQ" FT CDS 4093..5397 FT /product="Copia-46_VV-I_2p" FT /translation="MLKSIRILLSIAAYYDYEIWQMDVKTAFLNGHLEETI FT YMVQPEGFVVKDQEQKVCKLQRSIYGLKQASRSWNIRFNEAIKSYGFEQNL FT GEPCVYKQIGGDKVVFLVLYVDDILLIGNDVESLSKVKNWLASQFQMKDLG FT EASYILGIQMTRDRKNRLLALSQATYIDKVLVKFAMENSKKGNLPSRHGVH FT LSKEQCPKTPQNEEKMRRVPYASAVGSLMYAMLCTRPDICFAVGVVSRYQS FT NSGLDHWVAVKHILKYLRRTRNYMLVYSGRELIPIEYTDFDFQLDRDSQKS FT TSRAVFTLGGGAIVWRSVKQTCVADSTMEAEYVAACEAAKEAVWLREFLKE FT LEVVPNMHEPIRLYCDNSGAVANAKEPRNHRKGKHIERKFHLVREIVSRGD FT VLVEKIASANNIADPFTKTLPARSFEQHLEGMGLRDMPHLL" XX SQ Sequence 5414 BP; 1717 A; 851 C; 1146 G; 1700 T; 0 other; attggtatca gagcaggttg atactctgta ttaatttaat gaatgattat ttgataatct 60 ttgcatggtt ttcggtaggc acttttgcat attgatgttt gtttgttttt tttttttttt 120 tttatgttca tggtgatgaa tgtttgtggg aatggattgg tcgttttttt tttttattta 180 ttggttccat ggattttgtt atttttgcaa taattatttt attagatctt ttgtaaatag 240 gattcttgct gtaattccta ttttataaga tcttttgtaa ataggtttgc tgctgtaatt 300 gtaaatcggt tttgggttgt atttaatgtc catggaacct ggccatttcc gtttttatat 360 ttataaagtt gatgattact ttgtcttgca aggagtggag ccaggggatt caaacccatg 420 aaggatgggt attccctgat tgtaccacca ggctatggct cctagctggt tatgtatatg 480 aagaaggttt atttcacgtt gcccctgaac tttatccctg gctccaccac tacccttgtt 540 ttagcatgtc attttagtta gaaaagtgcc tacctatttt tgtatgtcat gcattcatgc 600 gtttatttta ttttgctaaa attgttttac ttaattaatg tgatggacct tgtaacaaat 660 ttaatgagat taaatttgtt ttttaagtgg gtcaaatgtg atcattataa ttttttttta 720 ttattttatt ttatataatg tcacagatga cttaatttat aattttaaat tgtttaaaat 780 tataaaggct tagtaattta aaatgtttaa attgtctaag gtttatgaaa caatagttgt 840 tttataaatt aaatacacct tttgcaatat aatgagtggg agcgggtaat attacaatat 900 aaaccctagg tctccaccat taatacaaca ctgtgagttt ttagtagcgc ttagagacgc 960 tttgatttcg tcctccctac ggaaagtgtc tactaatttc aataacaagg ttgtcttcca 1020 tgagacagga ttttaagatg tattttagaa ttgacctacc ctacggcggc aatttctaaa 1080 ttaagtctta aaaatctgat atggtgggtt acactcataa agatataatt aaattggtta 1140 attattttct tgaccgaact taaaggaaat taataagtat tagaaatatg agatattttg 1200 gataatattt attaattgag aaagtctcac tttaattagc aattatttga cctaccctac 1260 gacgacactt agttgtggta attaaaattc cttaggatgt taaagtatat tttttggtgt 1320 attttatcat gagcattctt gcttcatatt tactttgcct ttaattttct tatgacattt 1380 atgcaattat ttattgaaaa tatttcttat ttttgttcag caaatatgtc aaacccaatt 1440 ttctcacttc tcgcctctca agttttaact ggtgaaaact ttgtaaaatg gaaaagcaac 1500 atgaacattc ttctcattaa tgagaactac cactttgtcc ttaaggaggt ttgtcctcca 1560 gtgcctccag ctaatgcctc caaggctgtc tcagaagagt ataaccgttg gattattgca 1620 aataacaagg cctgctgcta cttgttagca gcaatggatg aagtgcttag aactaagcac 1680 gagggccttg aaactgcaag cgagattatg gaatctctac agcagatgtt tggacggccc 1740 tctgagcagg cccgccacga agctgtgaaa gctgttatga acagtaaaat gaagaatggt 1800 tcttcagttt gtgagcacgt ccttaaaatg attcatcact ttaatgaggc tgaaatcaat 1860 ggagctaaaa ttgatgaaaa tactcaggtt ggcatgatct tagagacgtt ttctccttct 1920 ttcctccaat tcaggacaaa ctacatcatg aaccataaga aatgtaattt gacagaattc 1980 ctaaatgagc tgcaatctta tgagaccctt atagatgata aggaaggcaa gacaaatatt 2040 gctaaggcta atgcagttgt gggaaaggct tcttcttcaa ggaataagaa gaagagaaat 2100 gtgagaaatc aaaaggacaa gaagaagatc caaaagaaga aaaggaaggc tgttgagcct 2160 aaacctaagg ggaaatgttt ccattgcaat caagacggcc attggaaaag gaactgtaag 2220 aagtaccttg atgagctgaa acaaaagaag aaacaaggta aattagattt attagtaatg 2280 gaaacatgct tagttgagaa tgatttctca agctggatta ttgattcagg agcatctaac 2340 catgtttgta tttctttgaa gatgcttgag tcatctaagg atcttgaaga gggagctttc 2400 atgatgagag ttggcagtgg ggcaagagtt tcagcgacag cagttgggac agtacgactg 2460 tcatttgcta ataataaata tttgttattg cacaatgttt attttattcc ggatttcaaa 2520 cggaatttga tttcggtttc aaagttacat gaacaattta tttctgtttc ttttgatgtt 2580 gactctgttt caatctataa gaatggaatg aatatttgtt caggttatgt tgataatggt 2640 atatattttg ttaaaccaat tttcaataat ttacttcaaa ccgaaatgtt taaagtcgct 2700 gaaccaaccc ctaaaagaag aaagatttct aatgataaaa atgacacata tttgtggcac 2760 ttaaggcttg gtcacattaa catagataga attgaaagag tagcaaagga tggtcctttg 2820 agagagctaa aagttggcac tctaccagtt tgtgaatctt gcttagaagg caaaatgacc 2880 aaaatgccat tttcggctaa gggtgaaaga gcaaaagtac ctctagagat catacatact 2940 gatgtatgtg gacctttgaa tgtcaaagca agaggggact atgaatattt cgtcacattt 3000 attgacgatt attcaagata cggatatgta tacctgatac aaagaaaatc cgaggctttt 3060 gaaaagttca aagaatttcg tgctgaagta gaaaaacaac ttagcaaatc aatcaaaact 3120 cttcgatcag atcgaggagg agaatacttg gtttatgaat tcaaggacta cttgattgaa 3180 aatggaatat tatcacagct cacggcacct gggacacctc agtaaaatgg tgtagccgaa 3240 agaagaaatc gcactttgct tgacatgatg agatcaatga tgagctattc ttctctgcca 3300 acctcatttt ggggatatgc attacaaacg gtagtatata ttctgaacat agttccatct 3360 aagtcaatcc ctaacactcc cttagagtta tggaatggtc gcaaacctag tttgagacat 3420 attcgcatat gggggtgccc tgcacatgtg ttaaagggaa agattgggaa actagaacct 3480 cgctctgagg tatgcatgtt tataggatat cctaaaggaa caagaggagg tctgttttat 3540 agcgctcagg ataacaaagt atttgtgtca acaaatgcta cgtttctcga gtataactat 3600 atggcagatt ttaaacctag aagtaaagta gttctggaag agttgctagt tgatgagatc 3660 agccccacgc caacaacagt tgttgaacga caaagaaaag aaaccactgc tcgagatcta 3720 acaccaccgc caccatgacg tagtgggagg gaaataagat tgcccattcg ctatcgtgaa 3780 aatagagaag cacaagttgc agtcactgat ggcagtgatg atgatccatt gacattcaaa 3840 atggcgatgg atgatgttga tcaagagaaa tggcaggaag ctatgaaact cgaaatagag 3900 tctatgtact caaattcagt ctagaagctt gtagatctac cagaaggcat taagcctatt 3960 ggttgcaaat ggatctataa gagaaaaaga ggacctaatg ggaaagtaga gactttcaag 4020 gcaagactgg tggcaaaggg ttttacccaa aaggaaggag tagactatga ggatactttt 4080 tcaccagtcg ctatgctaaa atccattagg attctcttgt ccattgctgc ttattatgat 4140 tatgagatat ggcaaatgga cgtcaagaca gcatttttga atggccatct tgaagagact 4200 atttatatgg tccaaccaga gggtttcgtg gtcaaagacc aagagcagaa agtgtgcaaa 4260 ctacaaaggt ccatttatgg acttaagcaa gcttctagat cttggaatat cagatttaac 4320 gaagccataa aatcttatgg ttttgaacaa aatctgggtg aaccttgtgt ctataagcaa 4380 ataggaggag ataaagtggt tttcttagtt ctttatgtgg acgacattct actcattgga 4440 aatgatgtag aatctctatc caaggtaaag aactggctag ccagccaatt ccaaatgaag 4500 gatttgggag aggcaagcta cattcttggt atccaaatga ctagggatcg taagaatagg 4560 cttctggcat tgtctcaggc aacatacatt gacaaggtgc ttgtcaagtt tgcaatggag 4620 aactctaaga aagggaattt gccttctcga catggagttc atctctctaa agagcagtgt 4680 ccaaaaacac cgcaaaatga ggagaaaatg agacgagttc cctacgcatc agcagttggt 4740 agtttgatgt atgcaatgtt gtgtacaaga cctgacatat gctttgcagt gggagtggtt 4800 agtcgatacc agtcaaactc aggattagat cattgggtag cagtcaagca tatacttaaa 4860 tatctgagaa ggacgagaaa ctatatgttg gtatactctg gtagggaatt aattcctatc 4920 gaatatacag attttgattt ccaattagat agagactctc agaagtctac ttctagggcc 4980 gttttcactt tgggaggtgg agccattgta tggaggagtg tcaagcaaac ttgtgttgct 5040 gattcaacca tggaggctga atatgtagcg gcttgtgaag cagctaaaga ggcagtctgg 5100 cttcgcgaat tcttgaaaga actggaagtt gttccaaata tgcatgagcc aattagacta 5160 tattgtgata atagtggagc agtggctaat gccaaagaac ccaggaacca tcgcaaagga 5220 aaacacatag aacggaaatt ccacctggta agagagattg ttagtagagg agacgtttta 5280 gttgaaaaga tcgcatctgc gaacaacata gctgatccgt tcactaagac tttaccggcc 5340 cggagttttg agcaacatct tgaagggatg ggacttagag acatgccaca tttgctttag 5400 ggcaagtggg agat 5414 // ID Gypsy-25_PTr-I repbase; DNA; EDCOT; 5037 BP. XX AC . XX DT 08-DEC-2009 (Rel. 15.02, Created) DT 08-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: internal DE portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; internal portion; Gypsy-25_PTr-I; KW Gypsy-25_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-5037 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 172-172 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 60..4994 FT /product="Gypsy-25_PTr-I_1p" FT /translation="MCFRMVRTRQGARTDPSPVRGSGQSFRNESDPDWDPL FT ADTSSHIPATSVYSEGGESVRLRDDSSSRQADVSMPEVSDRQGGDNIPPPV FT APVAGSNPFSDPAFMEHIVRAVAAGMVAGASSTAPRSGGVVTIVQWVKGMR FT EMGCMTYRGEEDAEVAGHWLRKVERVINQMQVPEELRVDCVTQLLVESAHS FT WWETIRERRSGEVLRWRDFREEFEERYYSWEHRREKEQEFLXLRQGDLTVL FT EYERRFQDLAAFASTYLPTERHRVERFRDGLRRELRMILIAMQFQSVRELV FT RAAQGMERVIKDTPKPVVEQSQAXGAKRRDFEFXTGRPPLPKKGKSGXSSG FT QFQRRGGSFTPGGSSGGSRQVSGRGAWGGQSRQGVKTAGGSTEQKGPVYPF FT CQRCEQRHPGDCSAMPGRCYICRGEGHRWRECPHVGRGCYYCGDTSHRKKD FT CPRRTTEGAHGQRIEVQSQQQSVTVNRPIRPTQSGTSATRGRPRNQEGRTQ FT GRVYHMTYEDVGVVPDVVAGTLQLDTMQVYALIDPGASHSFVSYRIVNNLH FT VLSSNLGVGVTVSTPLGENIHIDDIYRGVKLYIGGLELRADLMPLELYDFD FT VILGMDWLSKHKAQVDCFTKTVTIQGIGDKRVVFKGERKVIPSCVISVLVA FT RKLLRKGCSAWLAHVRELEKGSIDLASIPVVREFRDVFPEELPGLPPVREI FT EVSIETIPGVSPIAQSPYRMAPMELAELKVQLQELLDKGFIRPSNSPWGAP FT VLFVKKKDGTLRLCIDYRQLNKVTVKNRYPLPRIDDLFDQLKGARVFSKID FT LRSGYHQLRIKEQDIQKTAFRTRYGHYEFSVMPFGLTNAPAMFMDLMNRVF FT RPYLDQYVVVFIDDILVYSNSHLEHEQHLRVVLQTLRENQLYAKLDKCEFW FT LKEVVFLGHVISAEGIFVDPRKVEAVLKWERPTNVTEIQSFLGLAGYYRRF FT IEGFSTIASPLTKLTRKEVRFVWSEECEASFQELKERLTSAPVLALPSGTE FT GFVVYSDASKRGLGCVLMQXGRVIAYASRQLKSHEVNYPVHDLELAAVVFA FT LRVWRHYLYGTQVQIFTDHKSLKYLMSQKELNMRQRRWVELIKDYDCVIDY FT HPGKANVVADALSRKGKTVMNDMELKEQESIVELKKMGLRLSVGPEGSLLA FT QLKIRSVLRDRVLVAQQADGKVKEIKERVNKGIETSFQMLSDGLIAMGRRI FT YLPEDKILKDEVLREAHESRFATHPGSTKMYRDLKEXYWWPNMKREIAEFV FT SNCGICQQVKIEHQKPAGELQSLSIPEWKWEDISMDFVTGLPRGKKGNDAI FT WVVVDRLTKSALFLPMKMTDSVDKLAKLYVNEVIRLHGVPVSIISDRDPRF FT TSRLWPSLQRAMGTKLNLSTAFHPQTDGQSERTIQTLEDLLRSCVLEFGGN FT WEDLLPLVEFTYNNSHQTTIGMAPYEALYGRKCRTPICWEEVGERKLLGPE FT MVQLTTDKVRVIKKRMKEAQDRQKSYADSRRRPLEFQVGDKVFLKVAPWKG FT IIRFGVKGKLAPRYIGPFEIKERIGPVAYRLELPVYLDKIHNVFHVSLLRK FT AKIDPSRVLPQVPMKIKGDLTMKAKPVKILDRDEKLLRNKRVPLVRVLWRS FT SRIEEETWERESEMKEKFPHLFSDIGT" XX SQ Sequence 5037 BP; 1443 A; 819 C; 1480 G; 1286 T; 9 other; ttttggtatc agagctcagg ttgctattcc ggggacagga atgattatat ggttttgaaa 60 tgtgtttcag gatggtgaga acaaggcaag gagccaggac tgatccatcc ccagttcggg 120 gaagtggcca gagttttcgt aatgaaagtg atccagactg ggatcccttg gcagacacct 180 cctctcatat acctgcaaca tcagtgtact cggaaggggg cgagtcagtg agacttcgag 240 atgattcgtc gtcccgtcag gcagatgtat ccatgcccga ggtatcagac agacaggggg 300 gagataatat acccccacca gtggcaccgg tagctggatc aaacccattt tcggatcctg 360 cttttatgga acatatagtg agagctgtgg cagcaggaat ggtagcgggg gcctccagta 420 cggctcctag atcaggggga gtagtcacca tagtgcaatg ggtgaagggt atgagagaga 480 tgggttgtat gacttaccgt ggcgaagagg atgctgaggt tgctgggcat tggctgagga 540 aagtggaaag agttataaat cagatgcagg tgccagagga gctacgggtg gattgtgtga 600 ctcagctatt ggttgaaagt gcccactctt ggtgggagac cattagagag aggagatcag 660 gggaggtatt gagatggagg gattttcgtg aagagtttga ggagaggtac tattcttggg 720 agcataggag ggagaaagaa caggagtttt tggawttgag gcagggagat ttgacagtkc 780 tggagtatga gaggagattt caggatttag cagcttttgc ctccacttac cttcccacag 840 agcgccacag ggtggagagg ttccgtgatg gactgaggcg ggaattgagg atgatattga 900 tagccatgca gtttcagtcg gtgcgggaat tggtacgtgc tgctcagggt atggagaggg 960 taataaagga taccccgaag ccagtggtcg agcagagtca ggcaatkgga gctaagagga 1020 gagattttga gtttwtgact gggagacctc ctctcccaaa gaaggggaag agcgggcmat 1080 catcaggaca gttccagaga aggggtggga gtttcacccc aggagggagc tcaggaggat 1140 ctagacaggt cagtggaaga ggagcttggg gaggacagtc tagacaggga gtcaaaactg 1200 ctggagggtc tacagagcag aagggaccag tatatccgtt ttgtcagagg tgtgagcagc 1260 gacaccckgg agattgctct gcgatgccgg ggagatgtta tatttgtaga ggtgaggggc 1320 atcgatggag agagtgcccg catgtaggaa gaggttgtta ctattgtggg gacacgagtc 1380 accggaagaa ggattgtcct cgtagaacta ccgagggagc ccatggtcag aggattgagg 1440 ttcagagcca gcagcaatcg gtgacagtca atcgtcctat caggcctacc cagtcaggga 1500 cgagtgctac tcgtgggagg cccagaaatc aggaggggag gactcagggt cgggtatatc 1560 acatgaccta cgaggatgtg ggagttgtac ctgatgtggt ggcaggtact ttacagttag 1620 atacaatgca agtttatgct ttaattgatc ctggagctag tcattccttt gtatcttata 1680 gaattgtgaa taacttgcat gtgttatcta gtaacttggg tgtaggggtg acggttagta 1740 cacctttggg agagaatata catattgatg atatttatag aggggtaaaa ctatatattg 1800 gaggattaga gttgagggca gatcttatgc cgttagagtt atatgatttt gatgtgattc 1860 tgggcatgga ttggctaagt aaacataagg cacaagtgga ttgtttcacc aagacggtga 1920 caatccaagg aataggtgat aaaagagtag tgtttaaagg ggaaagaaaa gtaattccaa 1980 gttgtgtaat ctcagtcttg gtggctagaa aattactgag gaaaggttgt tctgcttggt 2040 tagcccatgt aagagagctg gaaaagggta gcatagattt ggctagtatt cctgttgtga 2100 gggagtttcg agatgtattc ccagaagagt tgcctggatt acctccagtt agagaaattg 2160 aagtttccat agaaactatt ccaggagttt ctcctatagc ccagtctcct tataggatgg 2220 cacctatgga attggcggaa ctgaaggtcc agcttcagga attgttagat aaaggcttca 2280 tccggcctag taactcgccc tggggagctc cggtattgtt tgtaaagaag aaggatggca 2340 cccttcgttt gtgcattgat tatcgtcaat tgaataaagt gacggtgaag aacaggtacc 2400 cactcccacg aatagatgac ttgtttgatc agttgaaggg tgctagggtg ttctctaaga 2460 tagatctgag atctggatac caccagttga gaatcaagga acaagacata caaaagactg 2520 ccttccgaac ccgttatggg cattacgagt tttcggtgat gcctttcggg ttaaccaatg 2580 ctccggccat gtttatggac ttgatgaatc gggtgtttcg gccttacctg gaccaatatg 2640 tggttgtatt tattgacgat attttggtgt attcaaactc tcacttggag catgaacaac 2700 atctaagggt tgtgctacag actttaaggg agaatcaatt atatgcaaag ctggataagt 2760 gtgagttctg gctcaaggaa gtggtatttt tgggccatgt aatatccgca gaaggaatat 2820 ttgtagatcc aagaaaggtt gaggccgtgt taaaatggga aaggcctacc aacgtgacag 2880 aaatccagag tttcttgggt cttgctggat attaccggag gtttattgag ggattctcca 2940 ccatagcatc acctttaact aagctgaccc gcaaggaagt cmggtttgtt tggtcggaag 3000 agtgtgaagc aagctttcaa gaactgaagg agaggctcac ttctgctcct gtgctggccc 3060 ttccatcagg gacagaaggg tttgtggtat atagtgatgc ctcaaaaagg ggtctgggat 3120 gtgtattgat gcaamacggg cgtgtgattg cttatgcatc aagacagtta aagtcgcatg 3180 aggtgaatta cccggttcat gacctagaac ttgcagcggt ggtgtttgcc ttaagagtat 3240 ggagacatta tttatatggg acacaagttc aaatctttac agaccataaa agtttgaagt 3300 atttgatgtc acagaaggag ttgaacatgc ggcagagaag atgggtagag ttaataaaag 3360 attacgattg tgttattgac taccatcctg gtaaggctaa tgtagtagcc gatgccttga 3420 gtaggaaggg aaaaacagtg atgaatgata tggagcttaa ggaacaagaa agtatagtgg 3480 aattaaagaa aatgggcttg cggctaagtg tagggcccga gggatcactg ttagctcagt 3540 taaagatccg atctgtgctt cgagacaggg tcttggtggc tcaacaagca gatgggaaag 3600 taaaagagat caaggagagg gtaaacaagg gtatagagac atcatttcaa atgttatccg 3660 atgggctaat agctatgggt aggcgaattt atttgcctga ggataagatt ttgaaagatg 3720 aagtattaag agaagctcat gaatctcgat ttgctactca tcctgggagt acaaagatgt 3780 atagggattt aaaggaawac tactggtggc caaatatgaa gagggaaata gcagaatttg 3840 tgtcgaattg tgggatctgt caacaagtaa agatagaaca ccagaaacct gcaggggaat 3900 tacagtcatt atcaattccg gaatggaaat gggaggatat ttctatggat tttgtgacgg 3960 gattacccag gggaaagaag gggaatgatg ccatatgggt ggtcgtggat cgactaacaa 4020 aatctgcttt gtttttgcct atgaagatga ctgattcggt ggataagctg gcaaaattgt 4080 atgtaaatga agtaatcaga cttcacggag tgccggtttc aattatatcg gatcgggatc 4140 caaggttcac atcaagattg tggcctagct tacaacgggc aatggggaca aagttgaatc 4200 tgagcacggc atttcatcct cagacggatg gtcaatctga aaggaccatc caaactcttg 4260 aggatctctt gaggtcctgt gtgctggagt ttggagggaa ttgggaggat ctcctgccat 4320 tggtggagtt tacttataat aatagccatc aaactactat tggtatggct ccatatgaag 4380 cattgtatgg gaggaaatgt cgtaccccaa tttgttggga ggaagtagga gaaaggaagc 4440 ttttgggacc tgaaatggtg caactgacaa ctgacaaggt gagggtgatc aaaaagagga 4500 tgaaggaagc ccaggataga caaaaaagtt acgcagatag ccgaagaagg cctttggaat 4560 tccaagtggg ggataaggta tttttgaagg tggctccttg gaaaggcatc attcgatttg 4620 gagtaaaagg gaaattagcc ccgagatata ttggcccttt tgagattaag gaaagaatcg 4680 ggccagttgc ctatcgatta gaattgcctg tatatttgga taagattcac aatgtgttcc 4740 atgtgtcatt gctgcgaaag gccaagatag acccctcacg ggtattgcca caagttccta 4800 tgaagattaa aggggatcta accatgaaag ctaagcccgt caagatctta gatcgagatg 4860 agaagttgtt gaggaataag agagttccct tggtgagagt attgtggaga agctctcgaa 4920 tagaagaaga aacatgggaa agagaatccg agatgaagga gaagtttccg cacttattct 4980 ccgacatagg tacgtaactt gaatttcgag gacgaaattt ttattaggag gggagaa 5037 // ID DNA8-1_Mad repbase; DNA; EDCOT; 424 BP. XX AC . XX DT 27-OCT-2010 (Rel. 15.11, Created) DT 27-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA8-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-424 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1851-1851 (2010). XX DR [2] (Consensus) XX CC TSD is 8-bp long. TIR is 15-bp long. XX SQ Sequence 424 BP; 141 A; 72 C; 100 G; 111 T; 0 other; cagtggcgta gccaggattt tcaaataatg gggtcataat atcaaccaaa aagcttcatt 60 gggccatttc gtcgagcacc tagtaggcac ctgccaattc ctgtcaacat atgccgaaag 120 tttatgccaa catatgtcga caactactat tacttgtaga ggcttgtcga gggtggatgc 180 aggatactgt ggagtaatgt tgaagactgt caaggctttt caactaaagt atttcataca 240 agaagagaga aaaggaagac aaatatgata gaagaaaata gaagaagtag gaagatgagg 300 ttgtaattta gtttgcctta gctgtttata ggggtcaaat acaatataca aacaaatata 360 catggggttt ttgaagttat tggggtcaag gacaaccaat gaccccatgc tggctccgcc 420 actg 424 // ID BoSB7A repbase; DNA; EDCOT; 352 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB7A. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-352 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 352 BP; 83 A; 64 C; 93 G; 112 T; 0 other; gtggaagcac cttagcctat tggttaaggt ttaaaggctt ctacacccag gtctggggtt 60 caaatcccag actatgcaat ttcttgcaga ttataggatg cgaagctttc ggaggttcca 120 gagtactgta agcagagccg ttcgttgtgg tcgcctgttg tggtgagagc ctgtccatcg 180 aggatgtcgt acatgcagaa ccgtctgtgg tttcaagtgt ttcggggaga gcttcatcgt 240 ggaatcatta ttcgtggagc tattcatcat tatcgcatat gttgcaggta gttgatcatc 300 atatctaata gatttagaga ttatatgatg atgtaatgtg ttacccagcg tt 352 // ID Gypsy-29_PTr-LTR repbase; DNA; EDCOT; 942 BP. XX AC . XX DT 09-DEC-2009 (Rel. 15.02, Created) DT 09-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-29_PTr-I; Gypsy-29_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-942 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 178-178 (2010). XX DR [1] (Consensus) XX SQ Sequence 942 BP; 245 A; 153 C; 214 G; 330 T; 0 other; tgatgcgatc caaccatcaa aggatccatt ggaggttcca gttggtccag ttactaggct 60 tagggctaag aagttcaaag aagctttcaa tggacttctt caagatacat gggctaaggt 120 ggacttcaag aggatttgta ataataaaga gcaagccttg attaatctga ttcatgttca 180 agaggggctt gttggtggaa ccaagaccat tacacaagga ttgggagaag aagactagat 240 tcggacagtt tgacctttcg ttactctttt ggtcataact ggagctacag atcgaatttt 300 gatgtgattc tagttgggct ggaaactaga cttccatacc tttccaacgg tatatggcac 360 gccttctaat tcattaagac gagagagaac catccatttt aagttgggcc ttgctgctgc 420 cagacagaat gcggaaacaa cgaacttgtc ttatttaatt agttgggcta tcaaacttta 480 tttattttga gaggagacaa tttgtttggg ttttagactt gtttattttg tttattttaa 540 ttagtttggg ctagttttag cttgggttga ttattattta aattgggttt atgtgagacc 600 cattagggaa actagggttt tggcttggag tttaaatact ctttaggaat aattttaggt 660 cagacttttg atgatatttt cagcattgta gccgactttt ggttgctcaa tcttggttct 720 tgattgaact ttcaactctt caaagaattg accattcttt gttgtgaatt tatacttcct 780 ttgctcgtct ccaggtgtag gcgttgtgat cgagttggtt tatagtcttg ttgccttgga 840 gcaagtcttc cattgtgata agctcattca aatctcaaca aacttgggtt agattgatct 900 tggggtcgcg aataccatta aattccgcta gggttcgcat ca 942 // ID Copia-32_Mad-LTR repbase; DNA; EDCOT; 295 BP. XX AC ACYM01014620; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-32_Mad-I; KW Copia-32_Mad-LTR; Copia-32_Mad_. XX NM Copia-32_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-295 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1381-1381 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01014620; Positions 17250 17544. XX SQ Sequence 295 BP; 92 A; 66 C; 44 G; 92 T; 1 other; tgagaaacat atgcctctga cgaagccatt atctcagtca tctcctgaaa ttaggcaaac 60 acaagaaagt ccaccctcac aagaatctgg cttatttcct tcccttgtaa ttgctgattt 120 actttccatg taatcactca attagtttga ttatatttat atactttctg taaatgggac 180 tgtgtggtcc acgcttgtaa ctatatatat aaatgaatac catgactgat agaacagtca 240 agaattccag catagaacct ttcttgccgt aacactcyaa aacctcagtg gtcca 295 // ID Copia-50_VV-LTR repbase; DNA; EDCOT; 219 BP. XX AC chr20; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-50_VV_; KW Copia-50_VV-I; Copia-50_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-219 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr20; Positions 25308036 25307818. XX SQ Sequence 219 BP; 65 A; 36 C; 36 G; 82 T; 0 other; tgggaaagga atcaaggatc tcgtaatttg aggatgatat ttgattgtat atagaagatt 60 attttgattg attgtaactg atatgtttgc tcttagattc ctagaatagg ctaaccaata 120 ctttgtatat atgcatcttc ttccctgtaa gttcatacac ggaatataca ccagatttcc 180 agatttccaa aacactctgt tctactctgt tttcttaca 219 // ID Gypsy-38_Mad-LTR repbase; DNA; EDCOT; 631 BP. XX AC . XX DT 14-OCT-2010 (Rel. 15.1, Created) DT 14-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-38_Mad-LTR. XX NM Gypsy-38_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-631 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1771-1771 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 631 BP; 195 A; 157 C; 115 G; 164 T; 0 other; tgtggagcct aaaataatcc caaaaattct agaggcgaca cgtggacttt tgctcaagaa 60 agacaagatt gccctcaata aatgggcagg ctcctcagat actcccacgc gcagctcaca 120 cccctgaagg tctcagcagc tgaatacgac tgcccacagc tcacctgccc ttggcaagga 180 aaagtcaaag cattaaagat aaggattaat tacccaaatc ctatctttaa tacattccca 240 attgaagatt gactccaatc aagtaagtaa tcccaattta aatcaattag ggataattac 300 tccattatct caagatatta tttcctattt aatatcttga gaatatcttg gccaatagga 360 tgccgccatg tgtagggtaa aaccctaaca ctatggccgg ccctatccct ataaataccc 420 catattctac caaatttcag gagcttttgc taccctaaaa aagccctaaa cactttactc 480 tctcagagaa actaacttag gcatcggaga tccattggcc taaccccccc acctcgtggg 540 cgcgtgaggc ttaggtcttt gatcaaaggt gttgattgtt ttgcaggtgc attttcgtca 600 agactgaaga cggcggaaat ttgcatcgac a 631 // ID HAT-11_Mad repbase; DNA; EDCOT; 3422 BP. XX AC . XX DT 03-NOV-2010 (Rel. 15.11, Created) DT 03-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-11_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-3422 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1900-1900 (2010). XX DR [2] (Consensus) XX CC TSD is 8-bp long. TIR is 11-bp long. XX FH Key Location/Qualifiers FT CDS join(854..2137,2058..3251) FT /product="HAT-11_Mad_1p" FT /translation="MFFYFSVMERYFKRKTQPEILEPSPKSPKNNESSSKQ FT TCVDSMEINSETLQYDPGLRRPILSYHPNVRDQVRRAYLQNKPCQPKTHAF FT PYTNFGTKPRRFNPAWFTQFPNWLEYSTSQDAAYCLCCYLFKPDIGDQSGG FT DTFVGVGFKNWKCKKKLEIHVGGPNSSHNNAWRNCEALLNQKQHIETVISK FT QTDQDRIDYRTRLGASVGVSRILLQQGLPFRGHDESENSLNQGNFLEILRW FT LRHYNEGIKAVTLENAPENLKLTSPDIQKDISSAISYEIISAITSDINDSL FT FSILVDESRDKSSKEQMAIVLRFVDKGHVIERFVGIEHVADTKASSLKLAI FT DDFFSRHGLSISKLRGQGYDGASNMQGEFNGLKALILNENESAFYVHCFAH FT QLQLALVAVAKKKFRNWRSLYYGFFCGECCGGIFQWQKKNSEIGDLFTMVS FT SVVNVVVASSKRRDILREKHAHVVLEALENNELSSGQGLNQETTLKRASDT FT RWSSHYNCLISLAHMFSSTIEVLEIVRKDGTSSEQKFEAKVLLTFIQSFNF FT IFGLHLMKKVLGITNDLSQALQKKDQDIVNAMNLVNICKGRLQRMRESGWE FT SLFDEVSSFCDKNRIKIPSMDDIFTSGERPNRKAHPITNVHHYRVDLFTDV FT IDKQLTELNDRFTEKNTELLLCVACLSPSNSFSAFDKEKLMRLAQFYPSDF FT SEHDLELLKEQLENYIWDMTSNSEFADLKGISDLAQKMVGTKKDHTYPLVY FT LLLTLALILPVATASVERVFSAMNIVKNTLRNRMGDLWMNDCLVAYIEKDI FT FNSIEDEAIMQRFQNMKTRRGQLF" XX SQ Sequence 3422 BP; 1065 A; 598 C; 615 G; 1144 T; 0 other; caggggcgga gggaccatag gaccacagta gtcctaggcc catcctgctt ttgtttataa 60 aaaaaaatta gtactactta ttattttaat tattttatca ctttttcatg actctttcac 120 ttaaaccatt ccaatttcct agacaaaata tccggccctc tttaaatatt ttaagaatat 180 ttatgtaatc tagtctaacc ctaaagccta cctattccaa cttccaacac ttccattcct 240 tttcccaata ctaaaaatta gtattttttt actcttattt ctagccctag ccgactgcgc 300 ctgctgctag tctgaaaaaa aaatagtcag gaacagtaca taactttaaa gaggcccctg 360 catgaagcac cattgtcttt cagttctttg ccgttgatct gtacttttta cccgtagtac 420 acaaccctgc tgcttctctc atctatagca tgtcacagtc ttctatcagt ctatcagtct 480 tcaataattc aatttccatg atcctcaaag gtatgaactt cgaatctcca aagttgtcat 540 tttcaatttt tttttaattc atatatgttg tcatctacaa ttgtaaatta atttaacaaa 600 taatattttt tttttgcaga ttaaagaatt ccattattcc atcattccat caaaaaaaga 660 catattgaag tttagttaat tggtcaacaa cccaaagtat gtattttact ctcaattcct 720 gttacaattt tttgtttata aattatgatt aaattgatgt cttgcaattt ctcttaacta 780 ttgcctaatt tgttttagtt tgtaaaatta gcatatatgt tcatatttct tttaatttaa 840 agttagtcaa tctatgtttt tttacttttc agttatggaa agatatttca aaagaaaaac 900 acaacctgag atattagaac cgtctccaaa gagtccaaag aacaatgaaa gtagttcaaa 960 acaaacttgt gtggattcta tggaaattaa ctcggaaact ctccagtatg atcctggatt 1020 gcgtagaccg attttgagtt atcatcctaa tgttcgagac caagttcgaa gagcctatct 1080 ccaaaataaa ccttgtcaac caaaaaccca tgcatttccc tacacaaatt ttgggacaaa 1140 gcctagaagg ttcaatcctg cttggtttac tcaatttcct aattggttgg agtatagcac 1200 atcacaggat gctgcctatt gtttatgttg ttatctcttc aaacctgata ttggagatca 1260 atctggtggg gatacttttg ttggagtcgg attcaagaat tggaagtgca agaagaaact 1320 agaaattcat gttggaggac ctaatagttc tcataataat gcttggagaa actgtgaagc 1380 cttattaaac caaaagcaac atattgaaac agttatctca aaacaaactg accaagatcg 1440 aattgattat cgaactcgat taggtgcatc agttggtgtt agtagaattc tcttacaaca 1500 aggtcttcca tttcgtgggc atgatgaatc tgaaaattca ctcaaccaag gaaactttct 1560 tgaaattcta cggtggctac gtcattataa tgagggtata aaggctgtca cgctagaaaa 1620 tgctcctgaa aatttgaaat tgacatcacc tgatattcag aaggacatct caagtgctat 1680 ttcatatgaa atcatcagtg caatcactag tgatattaat gattctttat tttccattct 1740 tgttgatgaa tcacgagaca agtcttcaaa ggagcaaatg gccattgtat tgcgctttgt 1800 ggataagggt catgtgatag agcgctttgt aggtattgag catgttgcag atactaaagc 1860 ttcctcactc aagttagcca ttgatgattt cttttctaga catggattga gcatatcaaa 1920 attgcgtggg caaggctatg atggggcaag taatatgcaa ggtgagttca atggccttaa 1980 agcactaatt ttaaatgaga atgagtctgc cttttatgtt cattgttttg ctcatcaact 2040 tcaattagct ctagtagcag tggcaaaaaa aaaattcaga aattggagat ctctttacta 2100 tggtttcttc tgtggtgaat gttgtggtgg catcttctaa gcgtcgtgat attcttagag 2160 agaaacatgc tcatgtagtt ttggaagcac tagaaaataa cgagctttca agtggacaag 2220 gtttgaatca agaaactact cttaagcggg ctagtgacac gcgatggagc tctcactata 2280 attgtttaat cagcttggct cacatgttct catcaacgat agaagtgctt gagattgtaa 2340 gaaaagatgg aacaagttct gaacaaaaat ttgaagcaaa ggttctattg acttttattc 2400 aatctttcaa ctttattttt ggtctacact tgatgaaaaa ggttttgggg atcacaaacg 2460 atttatcgca ggcattgcaa aagaaggatc aagatattgt gaatgcaatg aacttggtca 2520 atatatgcaa aggaagattg caaaggatgc gagaaagtgg ttgggaatcc ttatttgatg 2580 aagtttcatc cttttgtgac aagaatcgta ttaaaattcc tagcatggat gatattttta 2640 cgagtggaga gcgaccaaac cgaaaagctc atcccatcac aaacgtgcac cattatcggg 2700 ttgatttatt caccgatgtc atagataaac aactcactga gttaaatgat cgatttactg 2760 agaagaatac tgaactactt ctttgtgtgg catgtttaag tccaagtaat tctttctctg 2820 cctttgacaa agaaaaattg atgcgtcttg cccaatttta tccaagtgat ttttcagagc 2880 acgatcttga gttactcaaa gaacagcttg agaattatat ttgggacatg acctctaata 2940 gtgagtttgc agatttgaaa ggaattagtg atcttgcaca aaagatggtt ggaaccaaga 3000 aagatcatac ttacccgtta gtgtacttgc ttttgacact ggcactcatc ttaccggttg 3060 caacagcaag tgtagagcga gtcttttctg ctatgaacat tgttaagaac accctacgca 3120 atcgaatggg tgatttgtgg atgaacgatt gtttggttgc ttatattgaa aaggatattt 3180 ttaatagtat agaggacgag gctatcatgc aacggtttca aaatatgaaa actcgtcgag 3240 gacaattatt ttaattattg ggaatatgta atattatcaa tgctatgtta ttttgaattt 3300 tggttacttt tcatatacat actatgatgt tttggttaac agttttgtaa ctactatcga 3360 tttaattttt tttaatattt gtgagaggcc cctcctaacc cgaaatcctg gctccgccac 3420 tg 3422 // ID Copia15-VV_LTR repbase; DNA; EDCOT; 474 BP. XX AC AM451502; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia15-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-474 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-474 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 709-709 (2007). XX DR Genbank; AM451502; Positions 22263 22736. XX SQ Sequence 474 BP; 123 A; 83 C; 92 G; 171 T; 5 other; tggaaaaaag ggatgaatga aattaagtaa atccattgaa ttaagtaaat tcattcattt 60 ttccagaatt ctaagagtct caagaagcca aattcwtttt ggttttctga acctgtctgt 120 gttcttccct ccttgaagtc tataaatagt ggtwgacttt ctttcaaaaa aaatacagaa 180 aaactttgga gtattgtcag agtgttgaag agttccttcc ttccgtgtcc gtgatagagt 240 tgaacaattt ccagttcgcc ggagtagctg tagagtgttg ttgctgccat tcgaagatcg 300 ttttatcctg ggagacagac gccttgcgat tctcaaagca cctgtggaga aggcgaatct 360 gttttaagga gattgtgttt tccacaagac tcggtctaat cttcttcctt aattctctgt 420 tttttttttt tccmrwtttt cttttatttt cttatgaact aaccagtgtg tgca 474 // ID HAT-1N_Mad repbase; DNA; EDCOT; 951 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-1_Mad; HAT-1N_Mad. XX NM HAT-1N_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-951 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1605-1605 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 14-bp long. XX SQ Sequence 951 BP; 251 A; 225 C; 193 G; 281 T; 1 other; cagtggcgga tccaggaaat aatgtttgtg gggtcatagc gcgcgcagcg cgaaattttt 60 ttttagcctc gtttggtact tcggactgta ctgactattt cagtcggata agataaatag 120 tcgtcggata gtactaactc cattagtcgg gcgtttggtg cagtgtcgga taagttaaat 180 ggctttaata catagctgat acagtttcta ccaaactact gcatgcaaca caggagaaga 240 gaaaagaatt aaaagataca aaaattatgg caattgaatt tctaccagca cgcatagatt 300 aagcatcccc gctcgatctg tcttctcttc taactctttc atcttccaaa acgtagaaaa 360 ttgatgacgc ttacgccatg gaaagaatgg aactggaaaa aaaaaaaaac ccgaaaacag 420 ttttgtatta atcaactctt gagcttagtc ttcacctttg tcacaattct gtcactaccg 480 cttttactct tgttactctt attcctcttt ttctgtttct gtttctttcc actctgtttg 540 tgatcctcta cttttccttg aggattcacc tcctcaaact cgagcggtct tataattaca 600 ccgggtctct tcatcacctg cacacaattg catttaaggt gaggaatgag aagcgccata 660 gcatccaaca tccggcttag ggaaacaaaa gacggatcaa atgtggtatt gcagaaktca 720 tcaatggatg caaactcaag catatccgta tggcatagta atagcttgct tcttcttctt 780 cctcttcctg cagtgccgag cttcgttcag gatttttgtc gaacacttgg cgtgtgactc 840 cgaccccgac gaccccagct ccaagaggtc gcgtatggga gcttcaaggt tgtttccatg 900 ctttccaagg ggtcgtgcga ccccgacgac cccactgtgg atccgcccct g 951 // ID Gypsy-73_PTr-LTR repbase; DNA; EDCOT; 2690 BP. XX AC . XX DT 22-DEC-2009 (Rel. 15.02, Created) DT 22-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-73_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2690 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 181-181 (2010). XX DR [1] (Consensus) XX CC >87% identity to consensus. 5-bp TSD. XX SQ Sequence 2690 BP; 861 A; 627 C; 498 G; 702 T; 2 other; tgtcataacc catttttggg ttattcccca aaattcactt ttttttcaaa ataaaaaaat 60 aaaaataaat aaagactggc aatttggaaa aagcaggccg ggaaatcaag ctgcaatttt 120 tggaggaaat taagagccta attgtacccc attgtaccca aaactggaga gacaatgcag 180 attcaaggtc aaattaaatg attattggac gaatctgcat aaaaattaag tccaatgaca 240 taattagatt tttaataggc caatttgatt taatcatggg ccaaattaaa gtttaattat 300 gtttaagaat taatttgggt cmaattaaag gatttaatta agtgcaagga cttaattata 360 ctttaaatgg gtcaaattaa ttttattagg ggcttaattg gtgaaaaatt aagtttggga 420 gcccaatttg ggcttaattg agaagattgg aattttagag gaccaaactt aatttttaca 480 aagttaattg gttgaaatca ggggtaaaat cgcaagaaaa tcgaagtttt ggggtcaatt 540 aggggttaaa ttgaagaaat tcacagccaa ggaccttttg aaaaggcgcc gaactctggg 600 gactaattga ctgaaatcag gggtgaaatt gaagaaattg aaagtttaat ggtcaattaa 660 gggttaattg cataaatcca agaccaagga ccataatgaa aaaggcgctg aaattcgggg 720 ctgatattga agttcggcag gggcaaaatt gcataaaatt aaaagtttaa ggtcaattag 780 gggtgcaatt gaaagaaatc gaaagtcgga ggactaaatt gaactttggc aaatccctaa 840 attaaaccaa aacgacgccg ttttaattaa aaaaaaagaa gaccagacga cgcgtcgtct 900 ggtcactgtt catctcttct tcttttcccg aaaaagctgc tcgggtggct acttttcagg 960 tgcatttaat gcttcatctc tccaccaaat ttgacaaaac atgcaccaaa atgatcacct 1020 gacatttcac tacaccccag tatggttctt tccggctgat tgacaccaca acggccccgg 1080 cgccggccta aagaggccaa ctcaggcagc cttttacctg caaatttgac agttcatgat 1140 gcccactttg agccaacggt tgggatcctt cccagccgaa tcaagggcca agatttgtcc 1200 ccagtaaaga caaaatgtcc ctcttccacc ccctataaat aggggtggat ttcatggcct 1260 gagggaggag aaaatcgggt ccaaagttgg caaaaaacca gcctcctccc cagttttttt 1320 tctctttttc ttctctctct cccctctctc tcaccgtgcc ctcagccacc aagccaccgc 1380 caccagcttc cccaccctcc accacacacc cctccaccga gcacctcttc cccacaccag 1440 cagccaccgc gcctcttttt ctcttctttc ttctcctacc gcacaccgac tccaccagac 1500 gccgccacca gcccaccgga ccacctccaa cctcactcca ggccagtgac acagctcttc 1560 tcccccccag gttgctcccg ctccctccgc cggctgcaac tgcgaagttg catgcagaac 1620 gtgaattact gtcacgttct gcacataatc atcgttgggc cgggccagtt ccggcccacc 1680 gatgttgggc cgggcccagc cccaaaaaga agagaaagaa ggtctgttgg gccgtatcgg 1740 cccaaccgac ttcggcccac tgttagcccg gcccaggctg ggccggccca gcccaatttt 1800 aatatttatt taataaataa tattatatat atatttaaaa aaaaaaaaaa aaatttcaaa 1860 tttcaaaggg catttaaaaa atttgtggtt cctcgcatgt ttttccamca attttgcata 1920 atatcgggct gtatacttac actgtaagat acaaatccgg tattaaaata cccggttttc 1980 tccgaaattt tcaaaaaaaa aaaaattaaa atattctcaa aaaaaaaaat attttgtttt 2040 cgtgcatacg gccaaatcct aaaagttttc caagcatatt tttcattaaa aaaaaaacaa 2100 aaattgcatc tttctcatgt ttaaaaaatc caaaaatgga tatcgtaacc agtttatgat 2160 tatccattag ggtttggcca aaatatcaaa aacctttttc caattttttt aggatccaga 2220 tgtagacttt aatatttgtg ggtgtaaaat tacacgtaaa gtacaccctc aggtattaaa 2280 gatacaaggt gtaaaaatgc gatgctaaaa ttcggacttt agaacggtta ggatttaacc 2340 cgataaggta gagacttcct catgaagaga gatctgcctt gaaccttaga aaagaccaac 2400 gaatagaaac ccgacttaga aaaaacaatc aaacaacaat gcagcttacc ttaggtaggg 2460 tgcactgggg gtgatgcgtc ttccccttgc acaaccagtc ccttacccag actctcgcag 2520 accataggtt cctagtgacc ataatactag gtggcgactc ctgaacctta taatcataat 2580 tttatgatta aatccaaaaa cccttcccaa cacacacaca cctcacacag gaggcacgac 2640 aagagcctcc gccgtcgcca gacgacgtcg cgccgcgcgc ccccgcgaca 2690 // ID Copia23-PTR_LTR repbase; DNA; EDCOT; 222 BP. XX AC LG_VII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia23-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-222 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-222 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 221-221 (2007). XX DR Genome; LG_VII; Positions 12645329 12645108. XX SQ Sequence 222 BP; 72 A; 34 C; 41 G; 75 T; 0 other; tgttagcgtg agctgtacag tttaggaatt aatattagca tgagctgtag agtccaatat 60 aggaattatt ccgtaactga tcctaattca ttgtatcccg atttgtaggg attctttaat 120 tacttgccgt ttcatagtca tcttgtaaag cttctctata agagaaagag tctgtaacct 180 aatttcaaaa taagaaagaa agtgaaattc ccagaattgt ca 222 // ID HAT-2N_Mad repbase; DNA; EDCOT; 1090 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-2N_Mad. XX NM HAT-2N_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1090 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1607-1607 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 12-bp long. XX SQ Sequence 1090 BP; 311 A; 219 C; 184 G; 376 T; 0 other; cagtggcgaa gctacgtgag ggcgaggagt ggcggccgcc cctcccctcg ccggaaatca 60 agcccaggag cggtggttcc gcccctccgg tctcgtcgga agtgatgaaa ttccgtctgg 120 ttttctggcc ttttgggttt ccctgctcta tcgcagcaca ggctgatcgc gggctctctt 180 ttttttccaa aaaaaaaaaa acctaggcca aagaaaggag gaacgaagat ctgcattttg 240 cagcttctgg aaattggaaa tgttctggtt tggttctaac gaagaagaag agaaaggaag 300 aagagagaga ctttctctct ctcccatccc accccacgtg acctttacaa tttgtttttt 360 ttttaaatat tggccaatca atttgcgcca cctaacctgc ttttgctgat ttatattgga 420 atttgttttg ttttttaatt attgtccaat taatttgacc actctttcaa tattttttaa 480 gccacttgtt tgacactgtt atttatctta aaattcacta taaatttata cgagcttcaa 540 aaaataattt gtaaaatatt acgaactcgt aattatttgt ttttttttct cttaccatca 600 aattcaacaa agtaataaag aaaatttgtc aatattttta tatattatat gttttataat 660 caatgttttt tggatattat aagctatata ataaatagac aattatttat acggtatata 720 ataaatttat tcaaatttgc ctaggtcctc gcctaagtgt aaagtcatgt ccatcgcctg 780 actagagctt agcatctttt aaaactttgc taattataca gttaagtaat aggacgatac 840 aacgagaaac ggtgctaaat catccttcaa ataatattgt tgttcaaacc ctccttcgac 900 tattttgagt agtccaaatc ctcttttgaa tatttcggtt agtgcaaatt ctcctatgaa 960 tattacgggt agttcaaata atcttcttgc aaatcctgga cttagacctc gaatgaatgt 1020 tcacattttt cgggacccta aactttttaa atttcgcccc tccccccgag aattcctggc 1080 ttcgccactg 1090 // ID MuDR-11N_VV repbase; DNA; EDCOT; 4011 BP. XX AC am433943.2; XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-11N_VV, a non-autonomous DNA transposon (incomplete). XX KW MuDR; DNA transposon; Transposable Element; mutator; Mutavine-11; KW MuDR-11N_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4011 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 770-770 (2008). XX DR EMBL/GenBank/DDBJ; am433943.2; Positions 333 4343. XX CC Partial sequence. CC MuDR-11N_VV (Mutavine-11 in [1]) is a non-autonomous element. CC Individual copies are >90% identical to this sequence. It CC contains a MUDRA-like transposase gene which is not functional CC due to premature stop codons and/or frameshifts. It does not CC contain TIRs. The element has low complexity (AT rich) regions CC toward its ends. We did not find TSDs and therefore we cannot CC confirm exact borders of the element. XX SQ Sequence 4011 BP; 1524 A; 469 C; 652 G; 1336 T; 30 other; tatatataaa gtaatttaac acaaatataa aatagtaacc gtgactatta aatgtatata 60 atatatattt aaatattaaa atattaaaat attatataca tttaaatatc cattttaaca 120 aagaaaaaaa aaaagatata attgtaaaat gttagaatat ataatattat tagtgtgaaa 180 ttattttttt gcatacatta ttattattat tattatatat atatatatat atatatatat 240 atatatatat atatatatat atatatatat attaaaatat aagaaatata agtagaacat 300 tattcaaaat tttgaatttg tattctatat tttataaaaa ttaacattag tcttaaatta 360 ttgaaaaaat tcttgtaaga tattgagagc taaaaattaa aaataaatta aagtagaaat 420 aaatttaaaa tattatttga tttatttaat tggatatttt aatgtatata atatatatat 480 atatatatat atatatatat ataatttgta taatataaaa taagaactgt gagtattaaa 540 ggtatattat gtatatttaa atattcaaat attatataca tttcaatatc tattttaaaa 600 aagaaaagaa atagawaatc gtaaaatgtc agaatatata ataaaagaaa ataaataaat 660 ttagtwatag ytgttagtat taaattattt ttttgcatac aatattaatt aaaaaaatat 720 aaaaatataa gaaatataag tagaacatta tccgagagtt ggtcttatct aatataatat 780 gtaaatgcac atttaaaatg ttatattata tacatttaaa tattcatttt twaaaaagaa 840 aagaaatata ttgtaatgga caatgcacca taatattagt aaaatagatt tgcaaaatat 900 atattttgtt tattatcata aagtttattg ataatgatac ttttttgttg atcttttgaa 960 taggtttgat aatggacagt tacaccacgg tattgtgcta tactaggagt aaaattattg 1020 attgtgaatt tggggtaagt tataatcgtc ctcctgataa aggtgtttta atcaatagta 1080 tgataacatt tgatgagtta aaaacaaaat tgtrtcrtgc tctgaatatt aatcstactt 1140 ayaccaagtt aaatatggtg ttkcaatatc cagttccctt tycaaatgga aawggtactg 1200 ktaattatgt ccctttgcct attcgagatg atggtgatgt aaggataatg ttyaccgttg 1260 tcgcacaatc tcctcctcca aatactattg aaatgtattg tcaaacttct tccattgatt 1320 atcacccygt gcctagtagc tttactaccc cattgcatat tgaaagtcta ggtccaagtc 1380 aacatatggt agaaaakaac acatcttccc ctawgtatat gcaaagttat gataatgata 1440 tggaacctay agttagggta gatatggcag gggttactga gtcaattgta atgacagttg 1500 gaaattatgt tgatatttta cctggaaatg atraygacaw tgtrgagtta tttgatgaag 1560 atgatggtaa tgaggatatt atggacatgg aggataatga aaatacagaa aatgatgcat 1620 cattgctagg tggtggtgaa catgatgtcc cttccccaat atttagagaa ttgaattggg 1680 atgtaattaa ctccatsgct racaaggatt taatagcacg yactggctta tggaatgaat 1740 cagatgaatt gtttaagggt ttgcggtttg agagtaaggt agacttacaa tatgctgtta 1800 aacgttattc tatatgtagg aatcaacatt tgattgttat tgaatctgag ccagatattt 1860 gggttgtaaa gtgtaaaaaa tggtttgagg gttgtaattg gaggcttcgt gcatgtcgtc 1920 gtaaatgtca tggtttgttt gagataacaa agtacatagg tcctcacact tgtgtttacc 1980 ttaaactatc acaagaccac tcacaattag actcaatctt cattgcacga gaagttcaaa 2040 atgtagtaca aaatgatcac acaatttcaa ttgttgcatt acatcaaata gtgaaagata 2100 aatttggtta tagtgttcat tacaagagga tttgggaagc aaagaggaaa gcaatcataa 2160 ggatatttgg tgattgggat gaatcttacc aaactttacc taggtggatg aatattgtta 2220 aacttactaa ccatgggact aaggttgttt ggaagacatc cgtactagca ggttgcaatg 2280 gaaatatacg ttttatgcgt gtgttttggg cttttggggc atgtgttgaa ggatttaaac 2340 attatagacc agtaatacaa atagatggta tttttttata tggaaaatac atagggaaac 2400 ttttgattac aacatcaatc gatgttaatg gtcatatctt ccctctaaca tttgcaatag 2460 ttgaagagga atcatcagat agttggtctt ggtttcttta tacattaagg actcaagtca 2520 cacaaagaga aggcatatgt ctyatttcag atcgtcatgc aggaatacaa gccgccatta 2580 gggatcctag tgttggttgg agcccgcctt atgcacacca tcgatattgt cttaggcatg 2640 tggcaakcaa tttcaatgat aaatatagaa ataagatgtt aaaagaytta gtgtataaag 2700 cagggtctca acatcaacca cgaaagtatg aggcatgtat gactaagtta aaacaattag 2760 atgagaaatg cttagaatgg tttaacaggt tagacacaaa gaaatggact ttggaacatg 2820 atkgaggaca tcggtatggg tggatgacta maaatattgc tgaatgcata aatggagtgc 2880 tcaaaggggc tagaatgttg cctatcactg ctcttgttcg attaactttc tatcgttgtg 2940 tttcatattt cgagactcgt cgaacagaga tacaaactcr aatggcaaat ggagatttgt 3000 atacttccta tgccattaac aaaataacaa aatatgaatc aagagttagt tgacacactg 3060 tcaatatttt tcaccgttca aatgagatat ttgaagttac aactgctccc cataggtttc 3120 atatggataa aggaaacaat atacaaattg tgaagttgaa agaaagaaca tgtacttgta 3180 ataaatggca atcatttggt ataccatatt cacatgtgtt ggttgtatgt gcacgtgcaa 3240 ggattgatag ttggcaattt gttgacaaac attataggat ggatgtatat gcttgttgct 3300 atacacttca attcaatcca attccacatc aagcctattg gccagagcct aattttccaa 3360 ttgttcatcc taatccaatt ctagtacgtg ataaaagaag accaagatct tcaaggatta 3420 ggaatgaaat ggatttgaga gaattaagtg tcaaaatgca atatgggcat tgtaaacagg 3480 agggtgacaa tcggcgaaaa tgtcctaata gagagaagtc ttctaataca accactcgat 3540 attgtaagtt ccaattgaaa atttaactat ttaaatgaaa gtttttttta acattaaaga 3600 tgaacattga gttatttcca tataatgtca ttcaaatgtc ttataataaa cttatgaaat 3660 catttaaatg aagtaggaaa tttcaaaatt taattggaat tggtaccatt aattatatat 3720 attataaaaa gaaataatac aatctaatat aaaaatatat taaaaatgca ttttcaaatt 3780 aaaaaattaa atatactcat acaattatta taaatatata ttataaaatt caatccaaag 3840 ggaaatcgtc tcttcattaa aaaaaaaatc ccaaaaaatt ggaaatgatt ttccaaaata 3900 aaaaaaataa aaaaatccga aagggaattc ccttaaaaaa aaattcccaa tttgatatga 3960 tttcccaaaa aaaaaaaaat taaataccaa agggaaatcg tctcttgaag a 4011 // ID Copia-53_Mad-I repbase; DNA; EDCOT; 4087 BP. XX AC ACYM01039013; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-53_Mad-I; KW Copia-53_Mad-LTR; Copia-53_Mad_. XX NM Copia-53_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4087 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1323-1323 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01039013; Positions 18247 14161. XX CC Positions [1567-2067] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1465..2322,2326..3387) FT /product="Copia-53_Mad-I_1p" FT /translation="MVRGLPCISHPDQVCEGCLLGKQFRKSFPKESTTRAK FT KPLELIHTDVCGPIKPNSLGKNNYFLLFIDDFSRKTWVYFLKQKSEVFGAF FT KKFKAAVENESGCKIKAMRSDRGGEFTSKKFQEFCEEHGIRRPLIVPRSPQ FT QNGVAERKNRTVLDMVRSMLKSKRLPKGMWAEAVACAVYLSNRSPTRSVWG FT KTPQEAWSGRKLGISHLRVFGSIAHVHVSDEKRTKLDDKSEKFIFIGYDSN FT SKGYKLYNPNNGKTVISRDVTFDEEGEWDFGPHAGDLHFFPQFEENEQRMM FT EQVREVQQESTTSPASPTSTNHGNSPASTSSSRSLNEREVPRTRNLRDLYE FT VAERLDNPTLFCLFADCEPVDFQEAVQDTKWREAMDDEIEAIQKNDTWELA FT ILSKGHKAIGVKWVYKMKKNANGKVERYKARLVAKGYSQRAGIDYDEVFEP FT VARLETIRLLISLAAQNKWKIQQMDVKFAFLNGVLEEEVYIQQPSGYEIKG FT HEDKVLKLKKALYGLKQAPRAWNSHIDKYFQENNFTKCPHEHALYVKIKDE FT DILIVCLYVDDLIFTGSNPSMFEEFKRVMTKEFEMTDIGLMAYYLGIEVKQ FT NKEGIFISQESYTKEILKKFKMDDCKPISTPVECGVKLTKHD" XX SQ Sequence 4087 BP; 1439 A; 743 C; 929 G; 976 T; 0 other; aagtggtatc agagccatgg cgaacaacgt tatggctgcc ttccaagttc cagtggtcaa 60 caacaacaac ttcgataatt ggagtatcaa aatgaaggcc cttttgggag cacatgatgt 120 atgggaagtt atggagaaag gctacatcga gctagaagat gaagatactc taatccaagc 180 ccagaaggag agtttgaaag attcaagaaa gagagacaag aaggttctct acttcatcta 240 ccaagcatta gatgacaatg gctttgagaa ggtctcgagt gcaacctcca ccaagtaagc 300 atgggagaag cttcaaacct cttacaaagg agccgaacaa gtgaaaaggt ttgtcttcaa 360 gtattaagag gtgagttcga atctctacaa atgaaagggt ctgaatcaat ctctgattat 420 ttctcaagag tcttagtcgt ttctaatcaa ttaaaaagaa acggtgaaaa gttagatgtt 480 agaattatgg aaaaaatact acgctcgtta gacccaaaat tcgagcacat tgttgtgacg 540 attgaagaaa caaaagactt gaaagaaatc agtatagagc atttaatggg ctcgctacaa 600 gcatatgaag agaaacataa gaacaggcaa gggaatgatg agcagctcct caaaacgcat 660 gttcagccaa agaagaaaga agaaaccttc aacaacgaga gaagccaata cgaaagaagt 720 cgtggccaag gtcgcggacg tgggcgtgga catggacgtg gacgcggttg gaacttcaac 780 aaccatagca actacgaaag atcaacaaaa ggtggtgaaa gaggacgctc aaacttgagg 840 tatgaaaaat ctcaagttca atgttacaat tgtcaaaagt ttgggcatta tgcctgggaa 900 tgtagagctc caagtaacag acctgatgag aaggtcaatt atgtgaaaga agagaatggc 960 gttatgttac tagcatgcaa acaatgatgg agaccaagac tatacatggt atcttgacac 1020 cggcgccagc aaccacatgt gcggaagaag aagcatgttc gtagagctaa atgaatcggt 1080 gagtggcaat gtttcttttg gaaacgaatc caaaatacct gtaaaaggaa aaggtaacat 1140 ccaaattccc ttgaaaaatg ggggtcacca attaatttca aatgtctact acgtgcccaa 1200 tatgaaaagc aatattttga gtttgggtca actcttagaa aagggttatg atattcacat 1260 gaaaaattat agcctttttc ttagagatga ccaaggaaga ttaatagtca aggtgaaaat 1320 gtcaaagaat aggatgtttc ctatgaatat tcaaaatgat attgcaaagt gcctcaaaca 1380 ttttacaaag acatatcctg gctttggcat cttcgctttg ggcatcttaa ctttggggga 1440 ctggagttat tatccaagaa ggagatggtg agaggcttac cgtgcatcag tcaccctgat 1500 caagtttgcg aaggatgttt acttgggaaa cagttcagga aaagttttcc aaaggagtcg 1560 accacaagag ccaagaagcc actcgagctc attcataccg atgtgtgcgg tccaataaaa 1620 ccaaactctt tgggtaaaaa taattatttc cttctcttca ttgatgattt ttcaagaaaa 1680 acctgggtat atttcttgaa acagaaatca gaagtctttg gagcattcaa gaagttcaaa 1740 gccgctgtag aaaatgagag tggttgcaag atcaaagcca tgagatctga tcgaggtgga 1800 gaattcactt cgaagaaatt tcaagaattc tgtgaagaac atggaattcg tcgacctttg 1860 atagttccaa gatcccctca acaaaacggt gtggcagaaa gaaaaaatcg aactgttctc 1920 gacatggttc gaagcatgct caaaagcaaa agattgccta aggggatgtg ggcagaagct 1980 gtagcatgtg ctgtctactt atcaaatcgg tctccaacaa gaagtgtgtg gggaaagact 2040 ccgcaagaag catggagtgg aagaaagcta ggtatctctc atctaagagt ttttggaagt 2100 atagcccatg tacatgtatc agacgagaag agaaccaaac tcgacgacaa aagtgagaag 2160 ttcatcttta tcggctatga ctcaaattca aaaggttata agttgtataa tccaaacaat 2220 gggaagacag tgatcagtcg agacgtgacg tttgatgaag aaggagaatg ggattttggc 2280 ccacatgcag gtgatcttca cttctttcct caattcgaag aatagaatga acaaaggatg 2340 atggagcaag taagagaggt tcaacaagaa tccactactt cacctgcttc accaacatca 2400 accaatcatg gcaattcacc agcatcaaca tcgtcaagta ggagtctaaa tgaaagagaa 2460 gtaccacgca caagaaatct acgagatctc tatgaggtag ctgaaagact tgataatcct 2520 acacttttct gtctctttgc tgattgtgaa ccagttgact tccaagaagc agtgcaagat 2580 actaagtgga gggaagcaat ggatgacgaa atcgaagcaa tccagaaaaa tgatacatgg 2640 gaactcgcta ttctttcgaa aggacacaaa gccatcggag ttaagtgggt gtacaagatg 2700 aagaaaaatg ccaatggaaa ggtcgaaaga tacaaagcga gactagtggc gaaaggttat 2760 agtcaaagag ctggaatcga ctatgatgag gtatttgaac ctgttgctcg tttggaaact 2820 ataagattac taatttcttt ggcagctcaa aacaaatgga agattcaaca aatggatgtg 2880 aagttcgcct tcctaaatgg tgtgcttgaa gaagaagtct acattcaaca accatcaggc 2940 tatgaaatca aagggcatga agacaaagtt ctgaagctga agaaagccct ttatgggtta 3000 aaacaagcgc caagagcatg gaatagtcac attgacaaat acttccagga gaacaacttc 3060 accaagtgcc ctcatgaaca tgctctctac gtcaaaatca aagatgaaga tattctgatt 3120 gtgtgcttat atgtggatga tctaatcttt accggaagta atccaagcat gtttgaagag 3180 ttcaaaagag tgatgaccaa agaattcgag atgacggaca ttgggctaat ggcatactac 3240 ctaggcattg aagtcaagca aaataaagaa ggcattttca tctcccaaga aagctacaca 3300 aaggagatac tgaaaaaatt caaaatggac gactgcaagc ctataagcac gccagtggaa 3360 tgtggagtga aactaaccaa gcatgactaa ggagaaagcg tagatccaac atttttcaaa 3420 agtctagtgg gaagcttgca ctacttgaca tgcacaagac cggacatttt gtatgtcgtc 3480 ggattaatca gtcgctacat ggagaatccc acaactacac acttgaagac cgccaaaaga 3540 attcttcgat accttagagg tactgttaac tttggcatgt tctattcaaa ttctgatagc 3600 tacaaacttg ttggatacag cgacagtgat tgggcaggag attccgatga tagaaaaaac 3660 actactggat ttgtgttctt catgggagac acggcattca catggatgtc gaagaagcaa 3720 ccgattgtca cactatctac ctgtgaagct gaattcgtag ctgctaccgc atgtgtttgt 3780 tatgcaatct ggctgagaaa cttgctgaaa gaattaagca tgccacaaga agaaccaaca 3840 gagatttatg tcgacaataa gtctgcaata gctctagcaa agaatccagt attccatgat 3900 aggagcaagc acatagatac ccgctatcac tacataagag agtgcattac aagaaaggat 3960 gtgcaagttg agtacgtgaa gtctcaagac caagttgcag acatattcac caagccactc 4020 acacaagaag actttatcag actgagaaac tcaatcggcg tcacaagaca agattaaggg 4080 gggatgt 4087 // ID L1-11_Mad repbase; DNA; EDCOT; 5843 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-11_Mad. XX NM L1-11_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5843 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1815-1815 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 2..1657 FT /product="L1-11_Mad_1p" FT /translation="MAEQVEPGGQAKGKSSRMDGESVSSPIEFGANGVDSS FT RSGKRSRGIDGPNLDAERDMAALHLEPNVSFKDKLMKSSRRLVSVAVSDFD FT FDPDLVDGDVSFSREVKGPIVTFSEKAVTKFGKDWHDALVIKLLGRSHTYN FT FLLNRLRQKWQLKGGMQLIDIDHDFYIVKFDLEEDKEFVLTGGPWIIAGQY FT LTIQKWRPGFVPATEVXTRMAVWVRIXGVPIEYFNVWAMRKIGSVLGKLLK FT IDVNTNSQYRGKFARICVEIDVTKPLEAFIQINDRWYNLEYEGMPEICFGC FT GRYGHKRESCXWSVDPMAEKVDGGENESNXMNMDEPIVKXAQSSDDVSAIH FT GXWMQVKPRGRPRKINNGQRGVDXXFNGQGSRFSALNGEDKSLNEGNVGSG FT TDGEKGEGSIERKIWGVRKKKEASDRDALADISNCGGKPSTHNLGQLRQPL FT VRRSSSSSISNVEDQPFKFNVNAFKTDMYYGSNMSKGTYIFGHQPSNASGS FT DVELAACDLDPGEEMMNTDHAIPGSIIQRSRSTEDXCSAKSXEXCASHVEX FT TLMGC" FT CDS 2144..5797 FT /product="L1-11_Mad_2p" FT /translation="TWWCSIMQRLKGFKSWVDRNYMIDLGFIGPKFTWTNK FT KVLERIDRGICNMSWRSLFPEAYVHHLPRTKSDHCPIKICLNSHXSFSPXH FT RPFRFEAMWLRHENFKEFVDGYWSNGGGSVVDKTCALVEPLKKWNIQVFGH FT LKQRKRKLLARIDGIQKALCRGPNKFLSKLEDELISEYNEVLNEEAIFWHQ FT KSRLRWLQEGDRNTKFFHLTTIVRRRRNRIEGLINNQGAWISESSDLKKLA FT VEYFQTIFSHGQKSKQMESLPNLFPDIHXADREALTKDIDMVEVKESLFNI FT GGLKALGIDGFPACFYQSQWNICANDIFEMVWNAFHSRRLPARLNSTLITL FT VPKIDNPQKMLNFRPISLCCTLYKVISKIIVARIRPLLPHLISPNQASFVP FT GRQISDNVLIAQEILHKFRXSKGQKGFLAWKIDLSKAYDRLNWKFIEYVLN FT EVGLPSNLVQLMMECVSTVRYQICFNGELTDGFTPQNGIRQGDPLSPYLFV FT LCIEKLSHLISATVNKGRWKPVKASQSGPGVSHLFFADDLILFSEATPKQA FT RLMKRCLEKFCKASGQAVNFEKYVLYCSPNTSRAVVNSISAICGSPVSESL FT GNYLGMPLIQTRVSKATYSGVIDKVQKRLATWKSKVLSMAGRITLIQAVTS FT SIPVYAMQTTKLPASVCEELDKLNRDFLWGDTDQKKKVHLCQWSMVCRPKS FT KGGLGIKRACVMNQALLAKLGWRIHAKDSGLWSQIYQAKYLKGYSILDPKI FT HERTECSYSWKGILYGANLLKKGMTWRIGNGESVKFWKDSWVLNVPLXETI FT DVANISNIDCVVSEFLXNGWWDXDKLRDVLPEDMVQKVICRPAGTTGAGMD FT KIIWRCASNGVFTVKLAYNLFFDGEDLPDSCWDFIWRVNVPPKLKVFLWLM FT SKGRLLSNEQRVRRQXTSDSSCMTCCGPIESIAHIFKDCSRAMCIWKSMGV FT PWQLRNAQNLEFKAWLLANLKVSSKGTNEGAWCTLFLFICWHIWKWRNKQI FT FDVNFVMPMYPKAIIERDVDEWLKACVKYSVKLVKRQISLSWDHPDVGWCK FT LNVDGSRRTNSGRIGAGGVLRDHNGNWLGGFAVNLGQGQVCDAELWSLYFG FT LQLAIDKGATELHIEMDSKAVIMLLKQSQVDNFHPLETIMHSCRLMMRQLR FT RCELNHVYREKNIVADQLANWSYNMDIGVLVFDEPPVWIRSALIDDAAGVP FT RTRFAVGL" XX SQ Sequence 5843 BP; 1569 A; 848 C; 1477 G; 1913 T; 36 other; tatggcggag caggtggagc ctggtgggca ggcgaagggg aagtcctcga ggatggatgg 60 agaatcagtt tcttcaccga ttgaatttgg agctaatggt gttgattcgt ccagatctgg 120 taagagaagt cgtggaattg atggaccgaa tttggatgct gaacgtgaca tggctgctct 180 gcacctggag cctaatgtga gtttcaaaga caagcttatg aaatcatctc ggcgacttgt 240 ctcggttgct gtatctgatt ttgattttga tcctgatctc gttgacgggg acgtgtcatt 300 ctctcgtgag gtgaaagggc ctatcgttac gttctctgaa aaagctgtga cgaaatttgg 360 taaggattgg catgatgctc tggtcatcaa acttcttggg cgatcgcaca cttataattt 420 tttgttgaac aggctgaggc aaaaatggca attaaaagga ggtatgcagc ttattgacat 480 tgatcatgat ttttatattg ttaaatttga tttggaagag gataaggagt ttgttttaac 540 tggtggacct tggataattg cgggtcagta tttgacgatt caaaaatgga gaccaggatt 600 tgtgcctgca actgaggtta tkactcgtat ggctgtatgg gtcaggatam tgggtgttcc 660 aattgagtat tttaatgttt gggcwatgag gaagataggt agtgtgctgg gaaaactgtt 720 gaagattgat gtaaacacca attctcaata caggggcaaa tttgctagaa tttgtgttga 780 gattgatgtg actaagcctc ttgaagcgtt tattcaaatt aatgatagat ggtacaattt 840 ggagtacgag ggtatgccag aaatttgttt tggatgtggt cgttatgggc ataagaggga 900 gagctgtmct tggagcgttg atcctatggc ggaaaaggtt gatggtggtg aaaatgagag 960 taatatkatg aatatggatg agcctatagt aaagkctgct caaagtagcg atgatgtttc 1020 tgctattcat ggtamwtgga tgcaagttaa gcctagaggt agacctcgga aaataaataa 1080 tggacagaga ggtgtkgatg ktkcttttaa tgggcagggg tcaaggttca gtgcgctcaa 1140 tggggaagat aaaagtctga atgagggmaa tgtgggaagt ggcacagatg gtgagaaggg 1200 tgaaggttct attgaaagga aaatttgggg ggttaggaag aagaaggaag ctagtgatcg 1260 ggatgcactt gctgatatat ctaactgtgg tggaaagcca tctacgcata atttggggca 1320 actaagacaa cctttagtga gaaggtcaag ttctagttcg attagtaatg ttgaggatca 1380 gccgttcaaa tttaatgtta atgccttcaa gactgatatg tactatggtt caaatatgtc 1440 gaagggaacc tatatttttg gtcaccaacc atctaatgct agtggtagcg atgttgagtt 1500 agctgcgtgt gatctggatc caggtgaaga gatgatgaat actgatcatg ctattccagg 1560 ttcaattatt caacgatctc gttcaaccga ggattmttgt tcagctaagt ctgmtgagak 1620 gtgtgcctcc catgtggagg maacccttat gggttgctag gctktatgcc ttggttttat 1680 ctwtctcatc catctttatg atgaatattg tagtatggaa ctctagaggt gctggttgca 1740 ccaagtttaa agataatgtt gcagaattaa ttaacattca ccaaatggag attttggtta 1800 tttgtgagcc caggattagt ggtcagaaag ctatttcagt wgtgaaatct cttggttttc 1860 cgtgctttga gattgtggat gctgttggct tctctggtgg tttgtggatg ttgtggaagg 1920 attctagatt aaaggtggaa gttatcggta ccactgacca agctatttct gttgttgtgg 1980 gwggtgttgg tcagaaccat tggattttca ccgctgtcta tgctagccct tgtgttacta 2040 aaagagagag attgtgggat tatttggatt ttgtagccga ttgtcatcaa ttgccttggt 2100 taattgctgg ggatttcaat gacatgttgt gtgtggawga taaacttggt ggtgctccat 2160 tatgcagcga ttaaaaggct tcaaatcctg ggtggatagg aattatatga ttgatttggg 2220 ttttattggt cctaaattta cttggactaa taaaaaagtk ttagaaagaa ttgatcgwgg 2280 gatttgtaat atgagttgga ggagcctttt ccctgaagct tatgttcacc atctcccgcg 2340 aaccaagtca gatcactgcc cwattaagat atgcttaaat tctcatmakt cattttctcc 2400 caakcatcgt ccttttcgtt ttgaagctat gtggttgagg catgaaaatt ttaaggagtt 2460 tgttgatggt tattggagta atggtggagg ttcggttgtt gataaaactt gtgctcttgt 2520 tgaaccgctt aagaagtgga atattcaagt ctttggtcat ctcaaacaga gaaagcgcaa 2580 acttctagca agaattgatg ggattcaaaa agctttgtgt cgtgggccta ataaatttct 2640 ttctaaattg gaggatgagt tgatttctga atataatgaa gttctgaatg aggaggctat 2700 attttggcat caaaagtctc ggttgaggtg gcttcaagaa ggtgatcgta atacaaaatt 2760 ttttcatctc actactattg taaggaggag aagaaataga attgaggggc tcattaacaa 2820 tcaaggtgct tggatatcgg agtcttctga tctgaaaaag ttggcagtgg agtactttca 2880 aactattttt tcgcatgggc aaaagtctaa gcaaatggaa tctcttccta atctttttcc 2940 tgatatacat gwtgctgatc gtgaagctct taccaaagat atcgatatgg ttgaagtcaa 3000 ggaaagcctc tttaatattg gaggccttaa agctctaggt attgatggkt ttcctgcttg 3060 cttttatcaa agtcagtgga atatatgtgc taatgatatc tttgaaatgg tatggaatgc 3120 ttttcactca aggagattgc ctgcgaggtt aaacagtacg ctgataacat tggtccctaa 3180 aattgataat cctcaaaaga tgttgaattt taggcctatt agtctttgtt gcactcttta 3240 taaagtgatc tctaaaatca ttgttgctag aatcagacct ctcttgcctc atctgattag 3300 tcctaatcag gctagttttg ttcctggtag acaaatttct gacaatgtcc tcattgctca 3360 agaaattctt cacaagttca gaatktcaaa aggccaaaaa ggatttttag cctggaaaat 3420 tgatctctct aaggcgtatg acagacttaa ttggaagttt attgagtatg tgctgaatga 3480 ggttgggttg ccttcgaatt tggttcaact tatgatggaa tgtgtatcca cagttaggta 3540 ccaaatttgt ttcaatggtg aattaacaga tggttttact cctcaaaacg gtattcggca 3600 aggggatcct ttgtcccctt atttgtttgt tctatgtatt gagaaactct cccatttaat 3660 ttctgcaact gtgaacaaag gaaggtggaa acctgttaag gcttctcaat ctggacctgg 3720 ggtctctcat ctctttttcg ctgatgattt aattttgttt tctgaagcta ctccaaagca 3780 agcaagatta atgaagaggt gccttgaaaa attttgcaaa gcttctggtc aagctgttaa 3840 ctttgaaaaa tatgttcttt attgttctcc aaacacgtcc agggctgttg ttaatagtat 3900 tagtgcaatt tgtggttctc ctgtctctga gagtcttggg aattatttag gaatgcctct 3960 aattcagact agagtttcaa aggctactta ttcgggcgtt attgataaag ttcagaagag 4020 gttggcaact tggaagagca aggtattgtc catggctgga agaattacct taattcaagc 4080 tgttacctcg tccataccag tttatgccat gcaaacgacc aagcttcctg ccagtgtgtg 4140 tgaagagtta gacaagttga acagggattt tttgtggggg gataccgatc aaaagaaaaa 4200 agtccatctg tgccaatgga gtatggtttg cagacctaaa agtaagggtg gtttggggat 4260 taagagagct tgtgtaatga atcaggctct tttggccaag ttagggtgga ggattcatgc 4320 taaggactct ggtctttggt ctcaaattta tcaggccaag tatttgaaag gctattctat 4380 tttagacccc aaaattcatg aaagaaccga gtgttcttat tcttggaaag gaattctgta 4440 tggagctaat cttcttaaaa agggcatgac ttggagaatt ggcaatggtg agagtgtgaa 4500 attttggaag gattcatggg tcttaaatgt ccctttaatk gaaactattg atgttgctaa 4560 tatctccaat attgattgtg ttgtctctga gtttttaagw aatggttggt gggatmttga 4620 taagctcaga gatgtgttgc cagaggatat ggttcaaaaa gttatatgtc ggcctgctgg 4680 tactactggt gcaggtatgg ataaaattat ttggagatgt gcttctaatg gagttttcac 4740 cgttaagtta gcttataatc ttttctttga tggagaggat ttgcctgatt cwtgctggga 4800 ttttatttgg agagttaatg ttccacckaa gctaaaagtt tttctttggt tgatgagtaa 4860 agggagattg ctttctaatg agcaacgagt tagaagacaa wtaacttctg attcttcttg 4920 tatgacttgt tgtggaccaa ttgaatccat tgctcatatt tttaaagatt gttccagggc 4980 tatgtgtatc tggaaaagta tgggagttcc atggcaactg aggaatgccc agaatcttga 5040 gtttaaggct tggttgctgg caaatctgaa agtaagttca aaagggacca atgagggtgc 5100 ttggtgtact cttttccttt ttatttgttg gcatatttgg aagtggagaa acaagcagat 5160 ttttgatgtc aattttgtca tgcctatgta tccaaaagcg atcattgaga gagatgtgga 5220 tgaatggttg aaggcttgtg tgaagtattc tgtcaaactt gtaaagaggc aaatttctct 5280 ctcttgggat catcctgatg taggttggtg taagctaaat gtggatgggt ctagaaggac 5340 aaattctggt cgaattgggg ctggtggcgt tctaagagat cataatggca actggttagg 5400 tggctttgct gtgaatttgg gacaagggca ggtttgtgat gctgaattat ggagtttata 5460 ctttggttta cagcttgcta ttgataaggg tgctactgag cttcatattg agatggattc 5520 caaggctgtt attatgttgt tgaagcaatc ccaagttgat aatttccatc ctttggagac 5580 aattatgcat agctgcagat taatgatgag acaattgagg aggtgtgaat tgaatcacgt 5640 ttatagagag aagaatattg tggcggatca gttggctaat tggagttata acatggatat 5700 tggtgttctt gtttttgatg agcctcctgt gtggattaga tcagctctca ttgatgatgc 5760 tgctggagtc cctcggactc ggtttgctgt tggtttgtag ttctttttgg gttgtgttcc 5820 ccgttcttca ccaaaaaaaa aaa 5843 // ID BoSB9A repbase; DNA; EDCOT; 212 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB9A. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-212 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 212 BP; 37 A; 62 C; 66 G; 47 T; 0 other; caagttgctt tggtctagtg gtataggagc tccagctgga gtgcccgccc ctgggttcga 60 gccttggcca ctgcggaatt tacatgtggg ctgcagcacc cgagaccgaa gaccgttaca 120 cggtgagcca catggtgacg ccctggcagc gtccatgctc acttcggtct ctagtctgga 180 ccacctcggt ggggccagga tactcggtta gc 212 // ID Copia-89_Mad-I repbase; DNA; EDCOT; 4073 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-89_Mad_; KW Copia-89_Mad-LTR; Copia-89_Mad-I. XX NM Copia-89_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4073 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1716-1716 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1582-2082] - Integrase core CC LTRs are 92% similar to each other. XX FH Key Location/Qualifiers FT CDS 40..2451 FT /product="Copia-89_Mad-I_1p" FT /translation="MVTIFKSLGLWNLVEKGITTPDSKKKKEAEGSSEDAV FT DEEMAAVFMKDAKALGIIQNAVSDQIFPRIANAESAKMAWDLLYGEYHGGD FT QVRSVKLQNLRREFEYARMRDDESLSSYLTRLNELINQMRTFGESLSNERL FT VQKVLISLSKPYDSICLVIENTKCLETVELQEVVAILKSQEQRFDLHTVDT FT TGKAFSSFSVSPKGQNRGGGQSGSSQFQKNWNNKGKKWGSKPKFQQKFPAS FT PAHNAQSMGQIGTKPQCRVCSKFHFGECRYKGKPKCYNCEKFGHWARECTV FT GKSVQKANSANQVEVTGNLFYANSTITESKVNGEWYVDSGCSNHMTGDSKL FT LIDMKTNVVGKVQMPTGELMNVAGFGTLVIDTSKGRKYVKEVMYLPGLKEN FT LLSVGQMDEHGYYLLFGGKMCSIFDGPSLDCLVLKVEMKKNRCYPLTLIPN FT DQVVLRAGISKSTWIWHKRLGHLHLRGLQQLKNKEMVHGLPVLEEVDEVCE FT GCQLGKQHREWFPKNQAWRASKPLELVHVDLCGPMQNDSLAGNKYFMLLVD FT DCTRMMWVYFLKYKSDALICFRKFKSMVELQSGFKVKCLRSDRGGEFTSCE FT FNKLCEDAGIQRQLSMAYTPQQNGVVERKNRAVVEMAKAMLHDKGLPYYLW FT AESVHTAVYILNRCPTRALGDVTPFEAFSGRKPGIAHLRIFGCLCYVHIPS FT ELRQKLDAKSVKGVFVGYATCEKGYRVYDPLTKKLILSRDVVFDENAAWEW FT KKASENYVTVLNHDELSELPKVSSPETTPEGMTMLCHQVWHLLMNQQAMRV FT AA" XX SQ Sequence 4073 BP; 1265 A; 676 C; 1059 G; 1070 T; 3 other; attttctccg gtgagaacta cgagttctgg agaattaaga tggtaacgat attcaaatcc 60 cttgggttat ggaatctggt agagaagggg attacaaccc ccgactcgaa gaagaagaag 120 gaagctgaag ggtcatcgga ggatgcagtc gatgaagaaa tggctgctgt gttcatgaag 180 gatgcgaagg ctctaggaat cattcagaat gcagtctcgg atcagatctt cccacgaatc 240 gccaatgccg agtcagctaa gatggcatgg gatttgttgt acggggagta tcacggtggt 300 gatcaggtac gatctgtgaa attgcagaat cttaggagag agtttgaata tgctaggatg 360 cgagatgatg agtctttatc tagctatctt acacggctga atgagctaat taatcagatg 420 agaacatttg gtgaatctct gtcgaatgag agacttgtgc aaaaggttct gattagtctt 480 agtaaacctt atgattctat ctgtttggtt atagaaaaca caaagtgtct agagactgta 540 gaattgcagg aggtagttgc aatcttaaag agtcaagaac aacggtttga tctgcatact 600 gttgatacta ctgggaaagc attctcatct ttctcagtga gtccaaaagg gcagaatagg 660 ggtggaggtc aatctggttc atctcagttc cagaagaatt ggaataataa gggcaagaaa 720 tggggttcaa aacccaagtt tcagcagaaa tttcctgcta gtcctgcaca taatgcacag 780 tcaatgggtc agataggtac aaaaccacag tgcagggtat gctctaagtt tcactttgga 840 gagtgtaggt ataaggggaa gcctaaatgc tataactgtg aaaagtttgg acactgggct 900 agagagtgca cagtaggtaa atcagtgcaa aaggcaaaca gtgctaatca ggtagaggtg 960 acagggaacc tgttttatgc aaatagcaca atcactgaat caaaagtgaa tggagaatgg 1020 tatgttgaca gtggttgtag caaccatatg acaggggatt cgaagttgtt gatagacatg 1080 aagacaaatg tggttggcaa ggttcaaatg cccacagggg aactcatgaa tgtggcaggt 1140 tttggtacac ttgtgataga tactagcaaa ggcagaaaat acgtcaaaga agtaatgtac 1200 ctacctgggt tgaaggaaaa cctgctaagt gtggggcaga tggatgaaca cggttactac 1260 ctgttgtttg ggggaaagat gtgtagtatc tttgatggtc cttcactgga ttgtcttgta 1320 ctcaaagttg aaatgaaaaa gaacagatgt tatcctttga cactgatacc aaatgatcag 1380 gttgtactga gagcaggtat ttctaagtct acttggatat ggcacaagag actaggccat 1440 ctgcatctta ggggtcttca acagctcaag aacaaagaaa tggtgcatgg tcttccagtt 1500 ttagaagaag tggatgaagt ttgtgaaggt tgtcagcttg ggaaacagca tagagagtgg 1560 tttccaaaga atcaggcatg gagagcaagc aaacctctag agctggtgca tgtggatttg 1620 tgtggtccta tgcagaatga ttcccttgcg ggtaacaaat atttcatgct tcttgtagat 1680 gactgcacaa gaatgatgtg ggtttatttt ctgaaataca agtcagatgc attgatctgt 1740 tttagaaaat tcaagtccat ggtggagtta caaagtggtt ttaaggtaaa atgtctgagg 1800 agtgacagag ggggtgaatt cacatcttgt gagttcaaca aactgtgtga agatgcaggg 1860 attcaaagac agctatctat ggcctatact ccacaacaga atggagtggt agagaggaag 1920 aacagagctg tagttgaaat ggcaaaagct atgcttcatg acaaaggact accwtactat 1980 ttgtgggcag aatctgtaca cacagctgtc tacatactga acaggtgtcc tacaagagct 2040 ctcggagatg taactccatt tgaagcattc agtggtcgaa aaccagggat tgcacatctt 2100 agaatctttg gttgtttgtg ttatgtacac ataccaagtg agttgagaca gaaactagat 2160 gcaaagagtg tcaagggcgt atttgtaggt tatgcaacct gtgaaaaggg gtacagagtg 2220 tatgatcctc tcactaagaa gcttatactc tcaagggatg ttgtgtttga tgaaaatgca 2280 gcctgggagt ggaagaaagc ctctgagaat tatgtaactg tgctcaatca tgatgagtta 2340 tctgagctgc ctaaagtatc atcaccagag acaactccgg agggcatgac tatgctctgt 2400 caccaagtct ggcatcttct catgaatcag caagcgatgc gagtagcagc atgagaaagt 2460 ctcaagcctt tgatcacact ccattgaaat ggaggaacct agatgatgtt ctggcacaat 2520 gcaatctctg cattatggaa cctgaaaagt ttgaagaggc agccaaagat gaatcatgga 2580 tgaaggctat gaaagatgaa ctgtcaatga ttgagaagaa tgcaacatgg gagctggtgg 2640 acagaccaag tgataaacct ataattgggg ttaagtgggt gttcaagacc aagcttaacc 2700 ttgatgggtc agtgcaaaag aataaggcaa ggctggtagc caagggatat gctcagaaac 2760 caggtgttga ctacaatgag acctttgcac ctgtggctag actggataca attcgaactc 2820 tagttgcttt ggcagcacag aagagttgga aactatacca actagatgtc aaatctgctt 2880 ttctgaatgg agtactcgaa gaagaggttt atgtagaaca accagatggt tttgtggtca 2940 aggggagtga agacaaggtg tacaagcttc ataaagcttt gtatggttta aaacaggcac 3000 caagggcctg gtatagtgaa attgacactt attttgctca atgtgggttt gagaaaagtc 3060 aaagtgaagc cactctttac accaaagcaa ggggagaaga aattctgatt gtttcatata 3120 tgtggatgac attgtgtata ctgggaatag caatgagatg ttggaggagt tcaaggaaga 3180 catgatgaca aagtatgaga tgacagattt ggggctcctt caccattttc tgggaatggg 3240 agtcattcaa actcacacaa gcatttttat tcatcaaagg aagtatgctg cttctttgtt 3300 ggataagttt ggcttgagtg agtgtaaatc tgtgtctaca cctctggttc aactgagaag 3360 ctgagcaaag atgatggcag tggtccagca agtgaggaac aatatagaag gattgtggga 3420 agtttattgt atctcacagc cacaagacca gatataatgt atgcagctag tctactagct 3480 mgattcatgc actgtcctac maataaacac tatggaacag ccaaaagagt gctcaggtac 3540 gtcaagggaa cattgactat ggtttggagt atgtgaaggg aaggaatgca atgctaatcg 3600 gtttctgtga tagtgactgg ggaggatctg ttgatgacag caaaagcacc tcaggtatgc 3660 attttccttt ggcagtggag tgttctcatg ggcctcagtg aaacagaatt gtgtagcact 3720 ctctactgca gaagcagagt atatcagtgc ctctgaggca actgctcaag ccatttggct 3780 cagatttgtt cttgaagatt ttggtgagtt gcaaactgaa gcaactccac tgcagtgtga 3840 caatacagct gcaattgcaa tcaccaagaa ccctgtgttt caccagaaaa ccaagcacat 3900 tgacagaaga tatcacttca tcaaggatgc tctacaggaa gggataattg atttggttta 3960 ctgtcctaca aatgagcaag tggcagacat cttcacaagg cattggctaa ggatcggttc 4020 aactatctca gggataagct tggagtgaaa tcagctcaaa acttaaaggg gag 4073 // ID MuDRASH4_MT repbase; DNA; EDCOT; 381 BP. XX AC . XX DT 17-JAN-2007 (Rel. 12.01, Created) DT 19-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; TIR; KW MuDRASH4_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-381 RA Shankar R. and Jurka J.; RT "MuDRASH4_MT: A putative non-autonomous DNA transposon from RT barrel medic."; RL Repbase Reports 7(1), 41-41 (2007). XX DR [1] (Consensus) XX CC The sequence exists in Medicago genome in multiple copies without CC region for transposase.Large portion of this sequence is MuDr CC type TIR CC with 11 bp TSD. XX SQ Sequence 381 BP; 140 A; 58 C; 60 G; 123 T; 0 other; ggggtaatag tcattttggt tcctgaatgt gtagcaagta gtcacaatag tccttcaatg 60 tatcaaaatt tcaaaaaagt ctctgatagt ccactttgtt agtcaaaata gtctctaacg 120 cttaaataat tccttaatac tcacaataac tcttttgata tagaaactaa aatgacaata 180 aataagtacg tataaggact aacatgataa taagtaagta tattgaagga ctaatatgac 240 aatattaacg aaatatttta atatcaagga ctattttgat taacaaagtg cacaatcagg 300 gactattttg gaattttgat acattgaggg actattgtga ctacttgtta ctcattcagg 360 gaccaaagtg actacttccc c 381 // ID Copia-99_Mad-I repbase; DNA; EDCOT; 6100 BP. XX AC . XX DT 25-OCT-2010 (Rel. 15.11, Created) DT 25-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome, consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Copia-99_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6100 RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-6100 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1983-1983 (2010). XX DR [2] (Consensus) XX SQ Sequence 6100 BP; 2010 A; 923 C; 1174 G; 1989 T; 4 other; agtggtatca agagcctagg tctagtagtt ggtgaatcct tttgggtttt gtattttcat 60 agtttatgat ttgaatgttg taattgttac aagctttatt cttgcttctt tgaatgtaaa 120 ttttgttaga aaatttgcca tctcaaatgt tgtagatgta gttcatatga gcatgaattt 180 tggagctaaa atttggtgcc atgtttttgg ggaaattcgg ccaaatccaa agggtggatt 240 tttgggttca tgtttgtctt gttaaaagtg ttttaaagtg acattaggaa cccctaagta 300 ccctagtatg gtaatatgtt ttttccctta agtttgagag tttttggggt gtctttgggt 360 gaaaaatgtt catggagctc ttatgggttt tcatggatgt tcttcattgt tcttgttatg 420 tttttggcaa gaacaaaaag gttgggtatt ttgattcaaa gtttttggtt gtttacataa 480 agtttttgtt tgtgatggat ggtttgaatt tattgtaatm aatggtatga catgtttgtc 540 tttttcaatc aacaccatac caatcactta cacattttcc ttgtttcaag gaaccatgtt 600 ttatggaaat cactttttca aacctaccca tcacctttca cttttgttga aaaattcaaa 660 agttttatga caccatctct catccaaaac cggccaccct attaaatagg gtacttttgg 720 ggcttttatg caattacata aagttttgat acttttgtgt atttgtactt tgacccgaaa 780 gtttacgttt ttacgtaaag gcccaaaatc actaaaggac aaattgtttt gctcctttaa 840 tgaagttttt gtatttgatg aaatttttgg gttctagttg taattacatg aagtagtgga 900 cttttgtgtt tttacaaagt gacctcaaaa gtttgtgttt tgcaacatag cccaaaaagt 960 tgaggttatt gcatttcggc ccaaattagg ttgagaacaa aatggttttg tatctttaaa 1020 tgagaattgg attttcattt catttagctc catttaaatc aattctatgg atacaaaaac 1080 caaatgaaaa tgttgcattc aagtttaatt agttaaagcg ttaattaatt aaagaaaggg 1140 tgattatgaa cctaagccta cgataattga gctatgtgaa aggccgtctc aaatttgttt 1200 gaaccatggg aatgtgtaga ttagattttg gttgtaattt gatatgatca aatgttgtaa 1260 aagagcataa gctcttcttt actttaaagt aatttgtttt gatcaaatgt tgtaaaagag 1320 cataagctct tctttacttt gaagtactcc tttcttgttt tatttgatat gcatgaaatt 1380 ggagtagttg ggtccaacgc ccaataggaa aaacacgcct taatgtgatt aaacgcgtaa 1440 ctaaaatcaa tcaccatccc tagaccgaga ttcaacacta ggctcgtgtt ggatctaatc 1500 aaaggttcat agtcatccta aggccctaag gcaactatat agtccatcaa tgaatgcaaa 1560 ccttatgtta gtagtaccat atactcttgc tttaaaaacc gttttacaag catagtggga 1620 gtatcatata caactaaatc aatcacatgg accaatagtt gtaataggac caaattgttt 1680 taataagatt aaaatgcatg cttatatgtg atgagaccta aaaccctcaa ccaaaccatt 1740 attaagttga taagcgtgag agtgctttga acactctttc gtggccttcc accgtggtag 1800 gctccgatcg tttgtgactc gtacaccgac ttcaccctat catgggggag tacaaagtgc 1860 gtgcttacac tcaggaggag ttctatatgc atacatgatg ttgtgaaggt aggcaacgag 1920 aatgatcaac atcatatcat tgtgaggttg ttcttgaacc cctactcgaa cttgcatggt 1980 gggaatgact taactaagtg caatggagcc aacatcatat cattgtgagg cttcattctc 2040 tagaggccaa ataagatggg tacttgcaag agatgcaaat gagtaagcgt actctctcat 2100 tattattgat gctagccaac atcatatcat tgtgaggtgg gcttggtaat gatgagtctc 2160 ccatacccta ctaagagttt cctccaaaac tctcgaattc cgatgaggga tatggaattt 2220 gccaaaaata gtgggtggtg ctatttgatt taaagacccg gatcaaatgg cttaaaatca 2280 atcaatttat attcgttatg tatttgttta ccaatatatt tgcaaacgct atccaaaact 2340 tgacaaagaa aaagccgaaa gctttagttt ccggacttgg taccacaatc ccatagattg 2400 tctttaatgg cttgtatatg tacctaagta gtctcatcct cacaatcttc ctattgataa 2460 tgtatcattg gaagaacatg ttagataagt ctatcataaa gaggacaaca cttttaatgt 2520 cataattctt caattacaaa tcgttgtatg aagaaataag agttgctttg aacaaccctt 2580 agctaacgca aacattagtg cttgtttctt tgttacatga acaaggaact tgagaagtaa 2640 gcacaagggc atggacactt tatgtgccat gattcttcac ttacaaattg ttgtatgaag 2700 aaatgagagt tgccttgaac aactcttgaa agtttgtaat tatgtttaga acataatggt 2760 tggttgacaa aaatagtcca tcaacatgga cttatgatga ttttgaatca ttgagtgttg 2820 aagtgttaaa ccacttctag agacggaaac taggcaagga cttcaccttt gtgtccctat 2880 ccaaatggtt cactaagttt attgtaaact atatagtgaa caataaccac acgctctcca 2940 aatcgtttga tgtgtataac acaattgaaa taagtttcaa gagagatagt gggagtttag 3000 ggaccatgac tattgtagtc aaaggagaag tcaaatgaag aaggcgaaat aactccaagg 3060 gaacaaactt tctttatgaa aggatggaca ttggaagggg tatttgcaag aaatgtcttg 3120 caagtgtcaa gaacacacct ttcgaaggtg ttgtaaattg ttcttgaawa gttcaaaaca 3180 gttggttctt ctacttgaat gcttgattcc gtattagtaa ctatgtttta caatcgttgt 3240 aaaagtgtgg ctaataagaa gtagaagatt aatgagagaa gagaaagtac ttcacattcg 3300 gaacgtgaat caaatgtaga tctctgcgaa agcagatagt acttacttcc tcatatgaac 3360 taccaaagaa attggaaaaa ccaaagattg tctttacatt ccaattttaa ggaacttaat 3420 tccgtcacta tagagagatg gatgaatgtt ttgtttgaca aaacattgtt ctttattaat 3480 gaatgattag attattgtaa tctaattgat tgtctctata gtagagatga tatggtagtg 3540 ttaactgttt agaatataac gatgcttaaa acccaaaagg ttgcaaggta gtgactaatc 3600 ccaactgagt tgtgatacct ctaaaacata aattacgagt tggtcataga tggatgcttt 3660 ggatcgttag atccggatcc aataccttct tgttaaaatt gtatagaggc gaaatgttcg 3720 aatctttatt cttttggaaa gaagaaagaa tcacaaagtt gttgaggtta attcacttag 3780 atgttagtgg cacttgtcca caacataata ctactcatgt tgtatgacat tcaccgaaga 3840 tcgctctcgg ttggactata gtttattttg aataaacaca agtccgaata ctttgcaaaa 3900 ggtttcaaag aattcaagaa atgtaagttg atgagtaaga cgtctaaagt atttacctcc 3960 ttagatttga tccaaggaaa ggtaacactt tagaacagtt tccttgaaag atatcaagga 4020 aagaagcatc ataagataat ggatttctcc attaggagaa gaacgaactc gaataagatt 4080 tagttcgttg gatgttatca attacccata tataggatat atacttctaa gacaatatga 4140 ttgtcaatta gaagatcttc caaaattttc atgactccat aggatgtagt tggaaagaaa 4200 gacaaatctt aatcatgtta agatttgggg ttgtgtgcta ataagcaata tttgtttgag 4260 aattatcttg tgggtatcct taaattaaca tttggatatc acttctataa accaactaac 4320 aaatgttgtt tgttgggtag ttcattgtaa tcctacacta ggatttgcct aagatagagc 4380 aaatgaacga gagatagaac tcaaagaatg ggttctttga gagacaagat ggtaatcaac 4440 aaatataaca acctagttcc tataccacaa gctccaaggt agtcgagaag gatttataaa 4500 ctgtctcagt tgaatggttt gaactttatg actatgtcat agagttacac ctcttaattc 4560 gaaagaaata agaatgaaaa tccttatgac tacattgagt gtatatacga catatactca 4620 aggaaatggt aaagtaccat ttgacccgaa ataatgaaac ctttatagct aattggtagc 4680 ttaaggtgac tacaatcaaa gagawtggtt gactttgaag aaaccatctt tgacgtagtc 4740 ttggtttcaa ttaattcgaa gattgctagc tacaactaaa tggtgattca atgtttggac 4800 ataatatggg tttccgaaac cattattaag atagtcttga taatatatgt ctaaaactat 4860 gaatcacaag acatgtaagt tgtagagatc catccatcat ggatcttagc aagctagtgg 4920 gagctataag cgtcttatga gagaaagatc aaatcgtttg atttctcata aagatgtaaa 4980 tgaatctttt gtttactagg tttacaaaag attagtggga gttaatcatg ttcctaaatt 5040 tgaatatata tatatatata tatatataca catatatgat atattaattt tggaaatgaa 5100 aagaatactt cttcgttaaa gttatgactt taaacattct ataacgatag aatgtatatg 5160 ggagacatag tctatataca tgggatggaa atctataatg atagatttca agatataatt 5220 ggattatatc aatccctaat aatagacaag agatgctagg aagtttctca tatgatgata 5280 aacttcaatt agaaggacga ctctagtgag actagcaagt tgcccttctc aaagggaacg 5340 taccctttga ctcccaaaga aataatgcgt aaatagaatc ctttatgcat acgcagaaag 5400 gtgatttatg tatttcatat tgtatgaaaa acattgatat gagttgtacc tagaamggta 5460 caagacgata tcagtgcaag cccaggatca gaaccatggc aactgtcaag tgagtcctta 5520 agtatttaag aaatactaaa ggatagattc ctcaaagaat gaggaagaat tagagtaacg 5580 taatggaagc gtaaatgtat tagattatga atctaatcca tcattggatg tttcttcatt 5640 atgaatgaag agataatcag atatctcttt attatgacta aagagatatt tggatggaaa 5700 cattaaaagt aatgacttta gtgtgttcca ttatgaatgc aaaatatatt gccatataga 5760 agcttacaac aatgttgttt ggatgggaaa gttcatttat gaactctcta ttcggttcca 5820 accagaaagt gtctctagtg taccgacact acgacactaa tggggcgata gctcaagcca 5880 gggaatcaag gtctcatcaa gatccgaact caaatgagag actgaaccac atgattgaga 5940 atcatgtata atggtgacgt cgttattctc aaggttgctt ctatggataa catatagata 6000 tccattgtct aggcctacta ctcagccatt tttgaaatga ctacagaaga ggtatcatca 6060 ctgatgacca agctgattgg ctctagtgca agtgggagat 6100 // ID Copia-57_VV-I repbase; DNA; EDCOT; 4200 BP. XX AC chr8; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-57_VV_; KW Copia-57_VV-LTR; Copia-57_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4200 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr8; Positions 16576131 16571932. XX CC Positions [1667-2161] - Integrase core CC 'GAGGC' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 92..4198 FT /product="Copia-57_VV-I_1p" FT /translation="MMSSTQSSGLQAGTLPSSTGATQTMQMLNHALPIKLD FT RNNYILWRTQMENVVFANGFEDHIEGLKICPPQKTSSGETNPDFVMWRRFD FT RMILSWIYSSLTPEIMGQIVGYQSSHAAWFALERIFSASSRARVMQLRLEF FT QTTRKGSLTMMEYILKLKSLADNLAAIGEPVTDRDQILQLLGGLGADYNSI FT VASLTAREDEMSLHSVHSILLTHEQRLSFQNSVAEDNVISANLATPQYQHF FT NNKRSSGQNRQSGFNTRRGTNGGRSQSSQHRPQCQLCGKFGHTVVRCYHRF FT DINFQGYNPNMDTVQTNKPNAKNQVQAMMASPSTISDEAWFFDTGATHHLS FT QSIDPLSDVQPYMGNDKVIVGNGKHLRILHTGTTFFPSSSKTFQLRQVLHV FT PDIATNLISVSQFCADNNTFFEFHPRFFFVKDQVTKKILLQGSLEHGLYRF FT PARFVPSPAAFVSSSYDRSSNLSLTTTTTLWHSRLGHPADNILKHILTSCN FT ISHQCHKNNVCCACQFAKSHKLPFNVSVSRASHPLALLHADLWGPASIPST FT TGARYFILFVDDFSRFSWIYPLHSKDQALSVFIKFKSLVENQFNSRIQCLR FT SDNGGEFKAFSSYLATHGIKSQFSCPYTPEQNGRAERKLRHIIETGLALLA FT TASLPFKFWLYAFHTTIFLINRLPTKVLNYQSPFQILFGKSPNYHIFKIFG FT CLCYPYIRPYNKNKLSYRSSQCVFLGYSSNHKGYMCLNPLTGRLYVTRHVV FT FHETVFPFQSTPDQSSSVVTIPTPAFLPCSSPPVSSLRSHTTPSTSSPPLT FT NMPSSTISLPDLIQVPFADISTSEPHPTNQHPMVTRAKNGISKKKVYFSSH FT ISEPTTFTQAVKDSNWVLAMEKEFSALQRNNTWHLVPPPSNGNIIGCKWVY FT KLKYKPDGTVDRYKARLVAQGFTQTLGLDYFETFSPVVKASTIRIILAVAL FT SFNWSVHQLDVQNAFLHGDLEEHVFMQQPPGFINSQYPSHVCKLNKALYGL FT KQAPRAWYNKLSTSLLGWGFQASRADSSMFIHHSTHDVLILLIYVDDILVT FT GSSSAQVSSFITRLNYSFALRDLGYVNYFLGIEVVSSGTMFHLSQHKYTQD FT LLSRTAMLDSKPATTPGLLGQTLSHLDGEPFSDATLYRSTVGALQYLTLTR FT PDISFAVNKACQFMATPTTTHWLAVKRILRYLKGTLSYGIQMQQSTSLDIH FT GYTDADWASCPDDRRSTGGYGIFLGPNLVSWSSNKQKVVSRSSAESEYRAL FT ASATSEMIWIQYVLQELCLSSSSPPLLWCDNKSAAHLAANPVFHARTKHIE FT MDLHFIRDHVLRKQLVIQYLPSAEQVADIFTKHISSSQFLSFRTKLSVVPS FT PVSLRG" XX SQ Sequence 4200 BP; 1103 A; 1020 C; 734 G; 1343 T; 0 other; tggtatcaga gctttggtat tttttttttt tacaagactt cttcttcttc atatcagttt 60 tagttctttg tagataacct ctattctatt catgatgagt tcaacacagt catcagggtt 120 acaagctggt accctacctt catctaccgg tgctactcaa acaatgcaga tgctgaatca 180 tgcactgccg atcaaacttg atagaaacaa ttacattctt tggagaacac aaatggagaa 240 cgttgtcttt gccaatggtt ttgaagatca tattgaaggt ctgaaaattt gtccacctca 300 gaaaacaagt tctggagaaa caaacccaga ttttgttatg tggcgacgat tcgatcgcat 360 gatccttagc tggatctact cctcactcac tcctgaaatc atgggccaga tagttggcta 420 tcaatcctct catgcagcct ggtttgcttt agaacgaatc ttttcggctt cttcaagggc 480 tagggtgatg caactacgcc tagagttcca aaccacaagg aaaggttcat tgacaatgat 540 ggaatacatt cttaaactaa agagtttggc cgataatttg gcggccattg gagaacctgt 600 gactgataga gatcaaatcc tccaacttct tggaggtctt ggggcagact acaactccat 660 agtagcctct cttacagcac gtgaagatga gatgtctctc cactctgtac acagcatttt 720 actcacccat gaacaacgac ttagctttca gaattcagtt gcagaagata acgtcatctc 780 tgctaatctt gctacaccac aatatcaaca ttttaacaat aaaagatcct ctggtcaaaa 840 taggcagtct gggttcaaca caagaagagg tacaaatggt gggcgctcac aatcatctca 900 gcatcgacca cagtgccagc tttgtggcaa gtttgggcac accgtcgttc gctgctacca 960 taggtttgat attaacttcc aaggctacaa ccctaatatg gacaccgttc aaaccaataa 1020 accaaatgcc aagaatcaag tacaagctat gatggcatct ccttccacta tatctgatga 1080 ggcatggttt tttgacactg gtgctacaca tcacctatca caaagtattg atccactctc 1140 agatgtacag ccatacatgg gtaatgacaa ggtgattgtt gggaatggta agcaccttcg 1200 tattttacat acaggcacta ctttctttcc ttcctcttct aaaacctttc aactgagaca 1260 agtacttcac gttcctgata ttgctactaa tctcattagt gtctcacagt tttgtgccga 1320 taataatact ttctttgagt ttcatcctcg attctttttt gtcaaggatc aggtcaccaa 1380 gaagatactt cttcaaggaa gtcttgaaca tggcttatat agattccctg ccagatttgt 1440 gccttcacct gcagcttttg tttcttccag ttatgacagg tcttccaatc tttctttaac 1500 aaccacaact acactttggc attctcggct tggacaccct gctgataata tcttgaaaca 1560 cattcttacc tcttgtaata tttcacatca atgccataaa aacaatgtct gttgtgcttg 1620 tcaatttgca aaaagtcata aattgccttt caatgtgtct gtttctagag cttctcatcc 1680 tttagcttta cttcatgctg atctttgggg ccctgcttcc attccgtcca caactggtgc 1740 acgctacttc attttgtttg ttgatgattt ctctcgtttc tcttggattt atccattgca 1800 cagcaaagat caagcattat ctgtattcat aaagttcaaa agtctagttg aaaatcagtt 1860 taattctcgg atacaatgtt tacggtctga taatggtggt gaatttaaag ccttctcttc 1920 atatcttgct acgcatggta ttaaaagtca gttttcttgt ccatacacac ctgaacagaa 1980 tggtcgagcg gagcgcaaat tacgacatat aattgaaact ggtcttgctc tattagccac 2040 tgcatcctta cctttcaagt tttggctata tgcatttcat acaactattt tccttataaa 2100 tcggctacct actaaggttc tcaattatca atctcccttt caaattcttt ttggcaaatc 2160 accaaattat cacatcttta aaattttcgg ttgcttatgc tacccttata ttcgaccata 2220 caacaaaaat aaactctcct atcgctccag tcaatgcgtt ttccttggct atagttccaa 2280 tcacaaaggc tatatgtgtc ttaacccctt gacaggccgt ctctatgtta ctaggcatgt 2340 tgtgtttcat gaaacggtat tcccatttca gtctactccg gatcaatcct catctgtagt 2400 tactatcccc actccagcct ttcttccttg ctcatctcct cccgtgtcct cactacgttc 2460 tcatacaact ccttccacct caagcccacc gttaactaat atgccttcct ccactatttc 2520 tttaccagac ctgatacaag ttccttttgc tgacatctcc acttctgaac ctcaccctac 2580 taatcagcat cccatggtca cacgtgcaaa gaatggcatc agcaagaaga aggtctactt 2640 ctcatctcac atctctgaac ctactacatt cacacaggct gttaaagatt caaattgggt 2700 tcttgccatg gaaaaagagt tttctgctct ccaaagaaac aacacgtggc atctagttcc 2760 accaccctcc aatggcaata taattggttg taaatgggtc tacaaactca aatataaacc 2820 cgatggaaca gttgatcgct ataaggcccg gttagttgca caaggattta ctcaaactct 2880 gggtctcgat tattttgaga cttttagtcc agttgtcaag gcttctacta tccgcattat 2940 acttgcagtt gcactctcat ttaactggtc agttcaccaa cttgatgttc agaatgcctt 3000 tctccatgga gatcttgaag agcatgtgtt tatgcaacaa cccccgggct ttatcaattc 3060 tcaatatcct tctcatgttt gcaagcttaa caaggcttta tatggcctta agcaggcccc 3120 ccgggcatgg tataacaaac tcagcacttc acttcttggc tggggatttc aagcttctcg 3180 agctgacagt tcgatgttca ttcatcattc aacacatgat gtccttattt tactcattta 3240 tgtagacgac atactagtaa ctggcagcag ttcagctcaa gtttcctcat ttattactcg 3300 gctgaattat tcttttgctc ttcgtgacct gggctatgtc aattattttc tgggcataga 3360 agtagttagt tctggtacta tgtttcatct cagtcagcac aagtacacac aagacctctt 3420 atctcgcaca gccatgttag actccaagcc tgctactact ccgggactgt taggacaaac 3480 attatctcat ctggatggtg aacctttctc ggatgccacc ttatatcgca gcacggttgg 3540 tgcgcttcag tatcttaccc ttaccagacc agacatttct tttgctgtta ataaggcttg 3600 tcaattcatg gctacaccca ctactactca ttggcttgct gtgaaacgga ttttacgata 3660 tctcaaaggc actttatcct atggcattca gatgcagcag tccacctcgt tggatattca 3720 tggctatact gatgccgact gggcatcttg tccagatgac agaagaagca ccggtggcta 3780 tggcatcttc cttggtccga atttagtgtc atggtcttcc aacaaacaaa aggttgtgtc 3840 tcgcagcagt gcagaatctg agtatcgtgc tcttgcgtct gctacttcag agatgatttg 3900 gattcaatat gttctacaag aactttgtct ctcttcctcc tctccacctc tactttggtg 3960 tgataataaa agtgcagctc acttggctgc aaatcccgtg ttccatgcta ggaccaaaca 4020 cattgaaatg gatcttcact ttatacggga tcatgttctt cgtaaacagc tcgtcattca 4080 gtatcttcct tccgctgaac aggttgctga cattttcact aaacatattt caagctccca 4140 gttccttagt ttcagaacga agctatctgt tgttccctcc cctgtgagct tgcgggggga 4200 // ID Gypsy15-VV_I repbase; DNA; EDCOT; 4551 BP. XX AC AM435517; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy15-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4551 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4551 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 711-711 (2007). XX DR Genbank; AM435517; Positions 23816 28366. XX CC Positions [3456-3716] - Integrase core CC 'AATGT' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 1368..3212 FT /product="Gypsy15-VV_I_1p" FT /translation="MFRLQVENARARIYCGGLCSALETYDLILGTQWLATL FT GDISWNFNTLQMGFELNGKPYLLQGKNKLQERMSPWADKLKGLVEQPGLFA FT IQDLSDATLWAIQVAENTHLEETLTPQQQEELQKMLQAFTDVFEEPTGLPL FT VRDYDHQIDLKDEAGPINCRPYRYAAVQKDAIEKLIGEMLHAGVIRQSRSP FT YTSPVVLVKKKDGSWRLCVDYRALNQVTVKDKFPIPVIEELLEELGGSTIF FT SKIDLRSGYWQIRMHEPDVPKTAFKTHEGHYEFLVMPFGLTNAPSTFQSLM FT NNIFQPYLRKFIPVFFDDILIYSRSFSDHIHHLSIALQVLRENLLYAKSNK FT CFFGHSSIEYLGHVISSGGVYTDPQKVVAVRDWPTPITLKQLRGFLGLTGY FT YRRFVKDYGKIAKPLTDLLKKDAFHWTEGSNQAFMALKQAMITAPVLALPN FT FSKEFIIETDASGQGIGAVLMQEGHPIAYISKALSDRFQTLSTYEKEMLAI FT LMAIKKWESYLVDRHFVIKTDHQSLKYLLEQRVTTPTQQALVAKLMQYDYE FT IRYKQGKENVAADALSRIQPAELFVLSTTILNTQLYDLIKESWGVDPELQK FT IIKAKEADPSAYPKYSW" XX SQ Sequence 4551 BP; 1342 A; 944 C; 1029 G; 1236 T; 0 other; gttggtatca gagccgacgt ttcttcgcct gtggaaggaa cgatggcaga agcaactcgt 60 tcacaggaag tcagacgcaa aatgcttgag atgatgaaag agttcgaaag gaaacaggag 120 ttgtggcatc gcgaatcaga agaaaaagct atcaaatctt ttgctgatct caaaagtttg 180 atcggaggct tgaaccttca gaaccaggag gtgatgacca ataggggaga agaacgtagg 240 tgggagaatc aactcggtca ttcgaccaag gtggactttc caaagtttaa tggaggtgga 300 ttagatggtt ggttacttcg ggtggagtat ttcttaaaag tcgatcggac tcctccggaa 360 gctagagtgc gcctggcagc tcttcactta gagggaaaag cgatccagtg gcattcaggg 420 ttatattaag actaaaggta atgaagccta ccttgattgg tctgaatatg tcattgcttt 480 gaatgctaga tttgggcaac atgtttttga tgatccgatt gcggatctgc gcaatttaag 540 gcaaacaggt tcactgcaga gctatatgga tgaatttgat gaattgtatc ctagagctga 600 tatcaaagaa tcccatgcct taagtttttt cttgtctggt ttgattgatg aactccagat 660 gcccgttcga atgttcaaac cacaaacact tgctgatgct tactctctgg ccagattaca 720 agaaaagcag tagccgcttt gcagaacaaa ccaaaaccag tctccaaagg acctagccta 780 tactcaccca ccactaacca ttaccacaaa gccacgccaa tcacctctat ttcccaaaat 840 gctaccaacc tcagtaacac cactttcccg aaaactacaa atgccggact gctaccctta 900 ccaccatcaa ccaatatacc taaaaccaat cctggaatca ccactagaaa ccatcgaaat 960 ttctctaaca gagacctaga cgagcgtcgg gctaagggtt tatgtttctg gtgtgatgag 1020 aaatttactc ctggccataa atgcaaaagg aaacaactgt atgttatgca gattcaggtg 1080 gagacagatg gtgaggggcc tgaagggaat ttacaaatgg aaggcttggg tgaggaggat 1140 gaacagattc agctgtctct taatgctctt atgagcaatg aagactcaca aactatgacc 1200 ttgaatggaa attacaaggg gcgctcctta tttgtgctaa tagactcagg aagctctcat 1260 aatttcctga gttctaaggt ggcaaaaagg gttgactgtt gttggcagaa ggctagaggg 1320 ataagggtga ccgtagcaaa tgggcacgaa cttcactgta cagctctatg ttcagacttc 1380 aggtggagaa tgcaagggca agaatttatt gcggaggttt atgttctgcc ttggagactt 1440 atgatcttat cttgggaact caatggcttg ccactctggg agatatctcg tggaacttta 1500 atacattgca gatgggtttt gaattaaatg gcaaaccata tctcttgcag ggcaaaaata 1560 agcttcagga gaggatgtca ccttgggcag ataagctaaa aggcttggta gaacagcctg 1620 gcttgtttgc aatacaggac ctttcagatg ccactctctg ggctattcag gtggctgaaa 1680 acactcattt agaggaaact ctcaccccgc aacagcagga ggagttgcaa aaaatgttgc 1740 aggcttttac ggacgtcttt gaagagccca caggattgcc cctggtccgg gattatgatc 1800 accagattga tttaaaggat gaagcgggac caattaattg cagaccttac aggtatgctg 1860 cagtgcagaa agatgctatt gagaaactga ttggtgaaat gttacatgca ggagtaatta 1920 gacaaagcag gagcccttac acaagtccgg tggttctagt aaaaaagaag gatggatcgt 1980 ggagattatg tgttgattac agagctttga accaagttac tgtcaaggac aaatttccaa 2040 tacctgttat tgaagaactt cttgaagaat tgggaggttc aacaattttc tccaaaattg 2100 acctacgctc tggctattgg caaatcagaa tgcatgaacc tgatgtgcca aaaactgcct 2160 tcaagacaca tgagggccac tacgaatttt tggtgatgcc ttttggcctc acgaatgctc 2220 catccacctt ccagagcctt atgaacaata tcttccaacc ctatcttcgg aagttcattc 2280 cagtgttttt tgatgacatt ttaatataca gcagaagctt ctctgaccac atacatcatt 2340 tgagtattgc cttgcaggtc ttacgggaga atttgcttta tgccaagagc aacaaatgtt 2400 tctttggcca ctctagtatt gagtatctgg gccatgtgat ttccagcggt ggagtttata 2460 ctgatcctca aaaagttgtt gctgttagag actggccaac tcccattaca cttaagcaac 2520 ttcgtggctt tctcggcctc acggggtact ataggcggtt tgtaaaggat tatggaaaaa 2580 ttgcaaagcc actgacagat ctgcttaaaa aggacgcttt tcactggaca gagggaagta 2640 atcaagcttt catggctttg aaacaggcga tgataaccgc accagtgctt gccctgccaa 2700 atttttcaaa ggagttcata atagaaacag atgcttctgg tcagggtatt ggagcagtcc 2760 taatgcaaga aggacatccc attgcataca tcagcaaggc cttatctgac aggtttcaaa 2820 ccttatccac ttatgaaaaa gagatgttgg ctattcttat ggccatcaaa aagtgggagt 2880 catatctggt agatcgccat tttgtaatca aaacagacca ccagagtctg aaatatcttc 2940 ttgaacagcg agtaactaca cctactcagc aagctttggt tgccaagctt atgcaatacg 3000 attacgaaat tcgctataag caaggaaaag agaatgttgc tgcggatgct ttgtctagaa 3060 tccaaccagc agagttgttt gttctatcta caacaatttt aaacactcag ttgtatgact 3120 tgatcaaaga atcttggggt gtagatcctg aattacagaa gatcattaag gctaaggaag 3180 cagacccctc tgcttatccg aaatattctt ggtgaggaga ggaacttcgg agaaagggga 3240 aattggtagt tggagtcaat gaacaactgc gacgagagat cttaaacagc tttcatgatt 3300 cgccaactgg aggccattct ggcgtgtatg tgactacaaa gcgaatatct gtagtagttt 3360 attggaaggg tttgaggaag tttgtccgag aatatgtgag aaattgctct gtatgtcagc 3420 gcttcaaacc agaaaataaa ccttattctg gcttactgca gccattgcct gttccagagg 3480 gagtcttcac agacatcaca atggacttca tcgaaggcct ccccaaatct aatggtaaaa 3540 tgacaatttt tgttgttgtg gacaggctta ccaagtatgg tcactttatg ctgctaccac 3600 acccatatac aaccaagatg gttgcccaag tgttccttga cagtgtatat aaacttcatg 3660 gtcttcctca ctccatcaca tgtgacagag accctatttt caccagtgtt ttttggtagg 3720 aatttttcaa attacagggc gtctcattgc agctatctac tgcgtaccac cctcaaacgg 3780 acggtcagac agaagtggtg aataggtgta ttgaaaccta tcttcggtgc atggcaggcg 3840 ataacccagg ccaatgggca aactggatct cattagcaga gttttggtat aatacttcat 3900 accattcctc tttaaagatg tcaccgtttg aagctttgta tggttatgcc cctccgctac 3960 aaattcccta ttttccaaag gactcaaatg ttgaagctgt tgatagagtg ttaaatgaaa 4020 gagagagttg gctgcaactg cttaaacacc atctctccat ggcacagcag aggatgaaaa 4080 ttcaagccga taagaacagg tttgacagag aattcaacat tggagatatg gtgttactaa 4140 aactccaggc ttataagcaa gtcagtatgc attcaggagg tcccaaactc caaccccgct 4200 attatggccc gtttaaggtg attgacagaa ttggaacagt ggcttatcag ctccagttgc 4260 ctcctgatgc tcaaatacac aacgtattcc acgtgtccct tctcaagcca gctcatgcat 4320 caattcaagc ttgctcatct ttacctatct ctaataccag caccaccttg ctcccacaag 4380 ctattctgaa ccgtcgttta gtcaaaagac acaatgtccc aactgttcaa ttactgatac 4440 attgggttga taaatcacca gctgatgcgt cttgggaatt tgcagatgat ttgaagagga 4500 ggtttcctgc tttcttcctt gaggacaagg aagtttctta gaagggagta t 4551 // ID Copia39-PTR_LTR repbase; DNA; EDCOT; 225 BP. XX AC LG_II; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia39-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-225 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-225 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 255-255 (2007). XX DR Genome; LG_II; Positions 17680085 17680309. XX SQ Sequence 225 BP; 76 A; 30 C; 39 G; 80 T; 0 other; tgttgtaaat atagtaaatc aattatagga ttgattattg ttctaaatag agtaagtcaa 60 ctatagggct gtcagttata gggctgattg cagggctgat ttatatgcat tcaattatag 120 cttgattcta gggatttaga ttaatcctag acctgtatat atacatactg tactcatgca 180 tcaagaatga gagaaatatc attttcatac tctaacaatt ctaca 225 // ID SHACOP_I_MT repbase; DNA; EDCOT; 4160 BP. XX AC . XX DT 10-JAN-2007 (Rel. 12.01, Created) DT 10-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; SHACOP_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4160 RA Shankar R. and Jurka J.; RT "SHACOP_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 84-84 (2007). XX DR [1] (Consensus) XX CC The internal region has domains for zinc knuckle, gag protein, CC Integrase, RT polymerase and transposase. XX FH Key Location/Qualifiers FT CDS join(199..3807,3811..4092) FT /product="SHACOP_I_MT_1p" FT /translation="MAADEGKVKIEKFDGADFGFWKMQIEDYLYQKKLHQP FT LTEKKPDSMKDDEWNLLDRQALGVVRLSLSRNVAFNIAKEKTTAGLMKALS FT SMYEKPSASNKVHLMRRLFTLRMAEGASVAQHINELNIITTQLSSVGIEFD FT DEVRALILLSSLPDSWSATVTAVSSSSGSKKMKFDDVRDLVLSEEIRRREL FT GESSSSSVLHTESRGRNSTRGNGRGKSKARRSKSRNHRSSHNSKSIECWNC FT GKTGHFKNQCRLPTKNQEEKDEANVASTSGGGDALICSLESKEESWVLDSG FT ASFHASSQKEFFKNYVPGNLGKVYLGNEQSCKVVGKGEVKIKLNGSVWELK FT NVRHIPGLTKNLISVGQLADEGYTTVFHGDDWKISKGAMTIARGRKSGTLY FT KTAGACHLIAVATNENPNLWHKRLGHMSEKGMKVMHSKGKLPSLRSIEIDI FT CEDCILGKQKRVSFQTSGRTPKKEKLELVHSDVWGPTTVPSIGRKHYFVTF FT IDDHSRKVWVYFLKHKSEVFEAFKRWKAMVENETDLKIKKLRTDNGGEYED FT TKFKKFCYEHGIRMERTVPGTPQHNGVAERMNRTLTERARSLRVQSGLPKN FT FWAEAVNTSAYLINRGPSVPLEHKIPEEVWSGKEVKLSHLRVFGCVAYVHI FT SDQGRNKLDPKSKKCTFIGYGEDEFGYRLWDDENKKMVRSKDVIFNERVMY FT KDRHNTTTNDSGLSEPVYVEIDDVPGSPTDKSPQSGELTESSIRQPSDTLV FT HPTPVPVLRRSSRPHAPNRRYIDYMLLTDGGEPEDYDEACQTTDASKWEHA FT MKEEMKSLISNQTWELAKLPIGKKALHNKWVYRVKEDHDGSKRYKARLVVK FT GFQQKEGIDYTEIFAPVVKLNTIRSVLSIVASENLYLEQLDVKTAFLHGDL FT VEEIYMHQPEGFLEEGKENMVCRLKKSLYGLKQAPRQWYMKFESFMHKEGF FT QKCNADHCCFFKRYKSSYIILLLYVDDMLVAGSNIDEIKNLKIQLSKEFDM FT KDLGPAKKILGMQITRDKQKGVLQLSQAEYINRVLQRFNMGDAKLVSTPLA FT SHFRLSQEQSPQTEEEKELMAKIPYASAIGSLMYAMVCTRPDIGHAVGVVS FT RFMSNPGKAHWEAVKWILRYLRGTTEKCLYFGKGEIKVEGYVDADFAGEVD FT HRRSTTGYIFTVGTGAVSWMSRIQKIVALSTTEAEYVAVTEASKLIWLQGL FT LTELGFMQEKSALYSDSQSAIHLAKNSTFHSRTKHIGLRYHFIRSLLEDEV FT LTLIKIQGSKNPANMLTKVVTIDKLKLCSTLVGLLE" XX SQ Sequence 4160 BP; 1367 A; 719 C; 1013 G; 1061 T; 0 other; acgtaactgg tatcagagca cctgattcgg tatccttgtt aatttttggc aaaagtacta 60 ttcacgtgaa tagtaatttt cgtgaatagt gaaatattgg tcagcgttac caatttgttc 120 acagaggtgt tctaaagcac attagttcac aaaaattgtc aaagaagatc caaaggaagt 180 tagattcaag tggaagtcat ggctgcagac gaaggaaagg tgaaaattga aaagttcgat 240 ggtgcggact ttggcttttg gaagatgcag atcgaagatt atttgtatca gaaaaagcta 300 catcaacctc tcacagaaaa gaaaccagat tcgatgaagg atgacgagtg gaaccttctc 360 gatagacaag cacttggtgt tgtgcgattg tcgttatctc gaaatgttgc ttttaacata 420 gcaaaagaga aaaccactgc tggtcttatg aaggctcttt ctagcatgta cgaaaagcct 480 tcagcatcaa ataaagttca tttgatgagg cggttgttta cgcttcggat ggcagaaggc 540 gcgtcagtgg cgcaacatat caatgaactt aatattatca caacccaatt aagttcagtt 600 ggtatcgaat ttgacgatga ggtacgagcg ttgatacttt tgtcttccct accagatagt 660 tggagcgcta ctgtcacggc tgtgagtagc tcatcgggaa gtaaaaagat gaaatttgat 720 gatgttcgtg atctagttct cagtgaagag atccgacgga gagagttggg tgaatcttct 780 tcctcttcag tattgcatac agagtcaaga ggaagaaatt caaccagagg aaatggacgt 840 ggtaaatcaa aggccagacg atccaaatcc agaaatcatc gtagttctca caactcgaaa 900 tctatcgagt gttggaattg tggaaagacg ggacacttca aaaatcagtg tagactccca 960 acaaagaatc aagaggagaa agatgaggca aatgttgctt ccacctcagg aggaggtgac 1020 gcgttgatat gctctttgga gagcaaggaa gagtcttggg tgttagactc tggagcgtct 1080 tttcatgcta gttctcagaa agaattcttc aagaattatg tccccggtaa ccttggtaaa 1140 gtttaccttg gaaatgaaca atcttgtaag gttgtgggca aaggtgaagt taagattaag 1200 ttgaatgggt ctgtatggga attgaaaaat gtcagacata ttcccggcct cacaaaaaac 1260 ttaatctccg taggccagtt ggctgacgaa ggctacacaa cagtcttcca cggtgatgat 1320 tggaagattt caaaaggtgc aatgacaata gctcgtggta gaaagagtgg tactctttac 1380 aagacagctg gagcatgcca tttgattgca gttgcaacaa atgaaaatcc taatctatgg 1440 cacaagagac taggccatat gagtgaaaag gggatgaagg ttatgcactc aaaaggaaaa 1500 ctaccaagtc ttcgttcaat cgaaattgac atatgtgaag actgtatact tggaaagcag 1560 aagagagtca gctttcagac aagtggaagg accccaaaga aagagaaact cgagcttgtt 1620 cactctgatg tttggggtcc aacaactgtc ccatccattg gtaggaagca ttacttcgtg 1680 acttttatcg atgatcactc tagaaaggta tgggtatact ttctgaagca taagtctgaa 1740 gtatttgaag ctttcaagag atggaaagcc atggtggaaa atgagacaga tttgaagatc 1800 aaaaagctca gaaccgacaa tggtggtgaa tatgaagaca ccaaattcaa gaagttttgc 1860 tacgagcacg ggatcagaat ggaaagaact gtgccaggta ctccccaaca caatggtgta 1920 gctgagcgta tgaatagaac attgactgag agagccagaa gcttgcgtgt gcagtcaggc 1980 ttaccaaaga acttctgggc agaagcagtc aacacatcag cttacttaat caaccgaggt 2040 ccatcggtgc cattggagca taaaatacca gaagaggtat ggagtggaaa agaggtaaaa 2100 ctctcacatc ttagagtttt cggttgtgta gcatatgtgc atattagtga tcaaggtaga 2160 aataaacttg atcccaaatc caagaaatgc actttcatcg gttatggtga ggatgagttt 2220 ggctaccgcc tctgggatga tgaaaacaaa aagatggttc gcagtaaaga tgtgatcttc 2280 aatgaaagag tgatgtacaa agacaggcat aacacaacca ccaacgactc aggattgagc 2340 gagcctgttt atgtagagat agacgatgtt ccaggaagtc ccacagataa gagtccccaa 2400 tcaggggaat tgacagaatc aagcatcaga caaccatctg acacactagt gcatcctact 2460 ccagttcctg tattaagaag gtcttctaga cctcatgctc caaacaggag atacatagac 2520 tacatgttgt taactgatgg aggagagcct gaagattatg atgaagcatg tcagaccacg 2580 gatgctagta agtgggagca tgcgatgaaa gaggaaatga agtctttgat ctccaatcaa 2640 acatgggagc tagctaagtt acccatagga aagaaggcac ttcacaacaa atgggtgtat 2700 cgagtaaagg aggaccatga tggctcaaag agatacaaag cccgactagt ggtcaaagga 2760 ttccagcaaa aggaaggaat tgactacact gagatttttg ctccagtggt gaagctcaat 2820 actatcaggt ctgtcttaag tattgttgcc agtgaaaatc tctatcttga gcagttagat 2880 gtgaagactg catttcttca tggagactta gtggaggaaa tatacatgca ccaacccgaa 2940 ggattcttag aagaagggaa agagaatatg gtgtgcaggc taaagaagag cttgtatggc 3000 ctaaaacaag ctccaagaca atggtatatg aagtttgaaa gcttcatgca caaggaaggt 3060 ttccagaaat gcaacgccga ccattgttgc ttcttcaaga gatataagtc tagttatatc 3120 attttgctac tttatgttga tgatatgtta gtagcaggct caaacattga tgagatcaaa 3180 aacttgaaga ttcaattgtc aaaagaattt gacatgaagg atttaggtcc agcaaagaaa 3240 atccttggta tgcaaatcac gagagataag caaaaaggtg ttttgcagtt atctcaagcg 3300 gagtacatca accgtgtttt gcaaagattc aacatgggcg atgccaaact ggttagcaca 3360 cctttggcaa gtcattttcg cctatcccaa gaacaatcac ctcagacgga ggaagaaaaa 3420 gaactcatgg ccaagattcc atatgcttca gcaattggaa gtttgatgta tgcaatggtt 3480 tgtacaaggc cagacattgg ccatgcagtg ggagttgtta gcaggtttat gtcaaatcca 3540 ggtaaagctc attgggaagc ggttaaatgg attttgaggt atctaagagg caccacagag 3600 aaatgtttgt actttggcaa aggagagata aaagtagaag gctatgtaga tgcagacttt 3660 gctggtgagg ttgatcaccg aagaagtaca actggatata tatttactgt tggtactgga 3720 gcagttagtt ggatgtcgcg aatacaaaag attgttgctt tatccactac agaggctgag 3780 tatgtggcag taacagaagc cagcaaataa ttgatatggc ttcaaggatt gttaacagag 3840 ttaggattca tgcaggagaa aagtgctttg tacagtgata gtcagagtgc gatacatctg 3900 gcaaagaatt caacatttca ttcgagaaca aagcacatag gtcttcgtta tcacttcatt 3960 agatctctac ttgaggacga ggttctaaca ttgattaaaa ttcaaggaag taagaatccc 4020 gcaaatatgt taacaaaggt ggtgactatc gacaaactaa agttgtgctc aactttagtt 4080 ggtctgctag agtaagaggc cggagaaggc tgctgcatga tcaggtgtga agaccgattg 4140 aaatcagtct tcaagtggga 4160 // ID LTR-7_Mad-I repbase; DNA; EDCOT; 111 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR-7_Mad-I. XX NM LTR-7_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-111 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1790-1790 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~91% identical to the consensus. XX SQ Sequence 111 BP; 23 A; 34 C; 33 G; 21 T; 0 other; tggtatcaga gcaaggttgt ccacgtgtga agcccaacgg ccacacgcgc tccacgtcac 60 ccagttgttg tccacgtgta ggcttgaaaa tccgccacac gtgcgggggc g 111 // ID POPGY2_LTR repbase; DNA; EDCOT; 1548 BP. XX AC . XX DT 29-APR-2007 (Rel. 12.04, Created) DT 29-APR-2007 (Rel. 12.04, Last updated, Version 1) XX DE Gypsy-type sequence: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; POPGY2_LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1548 RA Jurka J.; RT "POPGY2: Gypsy-type sequence from black cottonwood."; RL Repbase Reports 7(4), 153-153 (2007). XX DR [1] (Consensus) XX CC Complete internal portion currently unavailable. XX SQ Sequence 1548 BP; 571 A; 252 C; 265 G; 460 T; 0 other; tgacacgacc aaaaaattga tgtcttctcc caagtgtagg agtgtcgaag taataaataa 60 cccggcaaga ccggggtcga accacaggga ggttaactat ataaattaca aataaagaaa 120 tagataataa cagaaaagga gttgaagaga gctttgagat gtgatattga tgtaaggatt 180 aaacaaggat aaaataattg tcaaggttag aggatccact aatggtattt caaacaagta 240 tagtataaac tctttttatt actcaactgg aaaccacaca caaaggaggt tccaatcgga 300 ttataaattg ttaacatgat tacattagtt atcttattcg aataatgcta atacttgtaa 360 atgttgtcag gtattcatga ttataactta tgttaacaac aaatcaagtt cctttcatag 420 cacaggtgtc ggttatacca tacggttggg ctatgaaagt gccaagtatt tgttgtacca 480 agggttatac aacataaatc tagattaacc atttaacaag caaagtatta aagtgaacaa 540 gataacaaat acaaaacatg ttagtatcaa acattaaagt ccatgttgag tttatactat 600 acttattctt acaccattag tgtaaccttt tcaccttgac ataataaact tagctaaaca 660 taatgaaaga gagaaacata aataaacaag ataagaacat aaataagata taagttaact 720 aagtaaagga aaggaaatga aaagcataaa caagagatta atataaacaa aacttaagca 780 ttacaaaaat ataaagaaag agagcaagaa catgatcttg atctgaaaac caagatgcct 840 aaatgcatgg caaatgcctc cttttatagg ccaaaatttg gaactattga tttgatgact 900 aattgttgag tgggtggcca catcttgact tggtgacaat ccttatcttc ttgtctgaac 960 aaaacgtcat tgctaacgtc agaatttgaa cagattgtct tcatgaaagt tctaggaaat 1020 tgtctcagct ttccaacaaa aaaagaatcg gtgcatttgg acttctagaa ctcgagatat 1080 gggctgaaca ctgaacagtg tctgggctgc aggacagatt ctgacttctc tgttgttgct 1140 acaatttgga cttgaaaacg gcagttttga atcttggact cctcatgaaa gttttaggcc 1200 tatgtcttag ctttctatcc atataaacca gacctaaatc caagatctac agctccagat 1260 atgacccaat gactgaacag tgttccagtt tggactgaac cagcatctct tttctaagct 1320 tagccctctc tttgtcttct caatttcagt agttaaactc atcaatcaat cctttgattt 1380 atgtgatagg cctgcattta agatgaacat ttaccataaa ttaaaggtat cttatagtat 1440 cagacttgtt attataaaac atgctttagt taaggagtta ttgatacttc aagtgcaaaa 1500 tgatgatata aaaccttgat aaaaatgcac ttttaagtac taatcaca 1548 // ID Copia-38_Mad-LTR repbase; DNA; EDCOT; 103 BP. XX AC ACYM01018656; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-38_Mad-I; KW Copia-38_Mad-LTR; Copia-38_Mad_. XX NM Copia-38_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-103 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1388-1388 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01018656; Positions 2068 1966. XX SQ Sequence 103 BP; 38 A; 18 C; 12 G; 35 T; 0 other; tgttgtacaa agtcaactac aggcttgtat atatcttgta tcaatatgat aaacaaatca 60 tcaaggaatt tattcaaata caaaactgct tctttctgtc aca 103 // ID LTR-1_Mad repbase; DNA; EDCOT; 3448 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR-1_Mad. XX NM LTR-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3448 RA Kojima K.K. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1784-1784 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >86% identical to consensus. 5-bp TSDs. XX SQ Sequence 3448 BP; 945 A; 628 C; 828 G; 1042 T; 5 other; tgtgacaacc cgtcccaaat tttacaattt tataaatttt aaaagtgtga atttacgaaa 60 atgcccttag aggcgagggt cttgactttc gttgaccaac gtatagtgag gcgtatgaat 120 tattccttta gcgtattcct gaagtactcg acgtacggac gcgtaggcgc aagcagaagt 180 gaatttggag ttacggttaa agttttacgg aactacaaat ccgagaagta cgttggtaaa 240 gcactattta tatattttat acatttatca tatttatatt tattatttta atattagttg 300 atagaaaaat gggaaaaaag aagagggaat agggagaagg gaaaaagagg aagaaagagg 360 gggtgggctg cccaatcaga gaagaggaag gggagaggag agagaagaga ctggccaatc 420 agagaagagg aaaggagggg aaatgagaga agaaagtggg ggaaaccggg tttcccgctt 480 gacccgcccg acccgactca caccgccaat tcccgcgatt ccgccatttt tccggcgatt 540 caaacctcca ccacctgcaa acaactcctt aaccttccct cttccatttc catccaaaat 600 taaaggattt gggcgtgaat ttgggaagaa cgaaaccggt gggttccgtg ggtgccatgg 660 cgaaatccac caatttgaaa ctatctcatc caattaccac caccaaaaca ctcccctaga 720 acccaggaac aaagcccaag caatkktggg ggcgtcggag ttcgattgga ggcgaatttg 780 gagaacaccc aattctaggg tttccgacgg gttttagcaa aattggggct cttcccggcc 840 aaattggact tggccacagg tataaagttt actctactca ttgagatctt cattcctgta 900 aattttggta atttttggaa atagttggat tttccggcga gtcggggcgg ccgaccgcca 960 cccgcggcgg cgcgtggcca gggggccgtc gatgttattc ttaggctaaa ttagatgcct 1020 tgagttcagt tttggtaatt gtatgacgta ggttgattgt tggaacctaa attctctacg 1080 ttacgttaat aggtcattat atgaatcgac gatccgaccg ttggatcgtc accaaacttt 1140 aatatgttat agtacgtaat atttgaggac cataggaact tacggatcgg gaatccgata 1200 tacggatctt cccgaattgg atttgtaagt tcataaaata aaatgttgac cgccacttgg 1260 ttttggcaat tggcggagat ccgaccgttg gatcgtaatg aaaccttagg atgttgttct 1320 agaagtataa tgtggatctt tggaagcaac ggatcggaaa tccgtgatgc agatcttccg 1380 aattgaatta cgtagggatg tgttttatgt aaattatgta ttttatcggt aagaactctg 1440 agatgtgatt tgataattgg tcataggcga cgatggttcg tgatgtctcg atatgcgtgc 1500 tagggagtcg tagcgcggac ctcaggtgag tgggtctttt cctttctatc gtatattata 1560 tatatatata tatatatata tatatatatg attgacaatt ccacaaacgt ttataaattg 1620 attattgcat ataattactg tgaatgcttt gaagtactaa tgtgaactac gaatggcttg 1680 atccctgttt agggtacgta ggcagtctaa cgagacgtta gatgcagcca tacaataaat 1740 gagactaaat aattgagaca atagccttgt ttggggaatt gagcaatgtg agggacattg 1800 gtggaaaatg tgagatttaa ccttatgatt tggtgattaa atgttggtca taaatcaatg 1860 tgtgaagaat caagaawttg aagtaaggaa acgtaagtaa tgatagttaa ttaaactagt 1920 gtctagttgg gcttatcacc gataattatt tccgaaaata aatagttcgg gagtagggcg 1980 ttacagctta tgcattttta tgccatatta tatatatata tatatatata tatatgtata 2040 taattgaaaa tgctatgaca tggttgagta ttagattgca tcatggtata tccatatgta 2100 tattacctgc acataattat tgtgaacgct ttgaagtgca aaggtgaacg caggacaccc 2160 aggtaagttc aggtgagttt atggtattag ttgaaatgat ggagttatgg catgactaca 2220 tgtatgtttt aggcaactcc gaccttgtcg tacagttgca atgataggca actccgacac 2280 tgtcgtacag gttgcccatg agtcgtacat gttatawtag atgcatttag agctcataaa 2340 cctgcacccc ggtgttagtg ctcccgcccg tggccagggc acagtccttc acgtgatgtt 2400 cacctcccgc accttacgct caccttggat ccaaggtagg tgcacagtcc tgtcgtacag 2460 accactatag gtggttccga ctcgtaggtg acccgcgatt attcgcacag tcttcacgtg 2520 atcgtagcac ttgagcgtac ttatttacac ccagtcctgt cgtacagacc actataggtg 2580 gttccgactc gtgtgcaggg atatgtgatg agctatgggt tcagccgtac aggccacaga 2640 ggtggtccgg ctgacatatt actgagatat tgattgatga gatatggata agtcgtacag 2700 gtcactatag gtgactccga cttatgtgct agcattgatg tgatgagata tggataagtc 2760 gtacaggtca ctataggtga ctccgactta tgagctagca ttgattgatg agatatggat 2820 aagtcgtaca ggtcactata ggtgactccg acttatgtgc tagcgttgat tgatgagata 2880 tgggtgcagt cgtacaggtc accataggtg actccgactt gcgtgctagt atgggttatt 2940 aakcacatga ttattgatat tgctgatgag atgctgtgtt gtggtatatt tatggattta 3000 ctgttgatat acttttgatt tcacattgat acgtggtatg atttttctgg aaactataca 3060 ggtgttgcag cgaggggtta taatgtttta tatggtttct attaaaattt tatttctagg 3120 gccactcacc cttgttttgt tttcaccctc caggttttat tagctgagct ttcttatcgt 3180 cgaggattcg tggcgattct tagtattgga gattctttcg agggtacgat tcttaatcca 3240 ctctactgta cttacttatg ctctaacgtc acgtgtgaag tgggttcatt cccgctcacc 3300 agcgcactct ggtatttagg cactcttagg tttaaattta ttcacatttt tccacatcat 3360 cacactttat ggcttcgtca ccttccaggt gtcggccagc acagctcgat tcggagtcct 3420 agtggacatc ccgggtcggg gtgtgtca 3448 // ID Helitron-N1_PTr repbase; DNA; EDCOT; 3051 BP. XX AC . XX DT 10-DEC-2009 (Rel. 15.02, Created) DT 10-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Helitron-type non-autonomous DNA transposon - consensus. XX KW Helitron; DNA transposon; Transposable Element; Nonautonomous; KW Helitron-N1_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3051 RA Bao W. and Jurka J.; RT "Non-autonomous helitrons from black cottonwood."; RL Repbase Reports 10(2), 229-229 (2010). XX DR [1] (Consensus) XX SQ Sequence 3051 BP; 632 A; 448 C; 430 G; 1541 T; 0 other; taagaataaa ctaaaactgc tcagtgtttt actgtgcaag tccacagtga aacgctgagc 60 agtctttttt ttttcttttt tttttttttt ttattttttt tttttttctg ttcttttttt 120 ttttcttttt tttttttttt ttttattttt tttttgtttt ctatgccttt atgggttttt 180 ttttttgctt ttttctttgt gtatttttct tttaatgaat tttttttgtt taatttagtt 240 tgttaatgtt aattttttta tttagttatc agattttcat aacacagatc ccgggtttga 300 cgggttaacc ctttttcttt ttaattaata acataaacta aaactgctca gtgtttcact 360 gtgcaagtcc acagtgaaac gctgagcagt cttctttttt ttttttgttt tttttttttt 420 tttttgtttt tttttttttt tttttttttt tttctatgcc tttatgggtt tttttttttg 480 cttttttctt tgtgtttttt tcttttaatg aatttttttt gtttaattta gtttgttaat 540 gttaattttt ttatttagtt atcagatttt catgacacgg atcccgggtt tgacgggtta 600 acctggtttg acgagttaac ccgaattttt tttcttttta attaataaca tatactaaaa 660 ctgttcagtg tttcactgtg cagtccacag tgaaacgcta agctgttttt tttttttttc 720 tgttttattt attttttttt ttgcttttta tgcctttatg ggtttttttt ttgctttttt 780 ttctctgtgt tttttttctt ttaatgaatt tttttgttta atttagtttg ttaatgttaa 840 tttttttttt agttatcaga ctttcatgac acggatcccg ggtttgacgg gttaacctgg 900 tttgacgagt taacctggaa tttttttttt ctttttttaa agtttgacga gttaacccgg 960 aatttgtttt ttgctttttt tctttttaat taattttttt tgtttagttt agttttttaa 1020 tgttaaattt ctttctattt aattatcaga ctttcatgac acgtatcccg ggcttgacgg 1080 gttaacccgt caatttgttt ttctatttag ttatcaaact ttcatgacgc gaatcccagg 1140 tttgacgggt taacctggtt tgaagggtta acccagttaa ttcagatttt ttttcttttt 1200 cttcattagt ttttttcttc ctgttggttt tttttctttg ttttttttaa ttaatctatt 1260 taattatcac acttttatga cacgaccttg cagccagacc cacattcaag gctcttgggt 1320 ccggtgttgc agccagactc acttaaactt gagtcatgta agtttaatat tattattaat 1380 attataaata ttactcttgg gtcaagcgtt gcagctaaac caaaggctct tgggcatatc 1440 tttgcagaaa gacctaacac tcttagatct tagccttttt tgatattttt tatgcaagaa 1500 aaaaaattta acccgtggcg tgtgcctttg tttttttttt ctctcttttc ctttttaagc 1560 cttttactgt ggattgcaca gtacagtcca cagtgaaaaa gctgatgcct ttagtttttt 1620 ttttcttttt tttaattttt tttttaattt agtttcttaa tattaaattt tttctattta 1680 attatcagac tttcatgaca tggatcccag gtttgacggg ttaacccagt ttattcagat 1740 ttttttcttt ttcttgatta gttttttttc ttcctgtagg ttttttttct ctttgctttt 1800 tcctttttaa ttaatctttt ttttaattta tttcattaat aataaatctt ttttctattt 1860 agttatcaca ctttcatgac acgaattcca ggtttgacgg gttaacctga tttggcgggt 1920 taacccggtt gattcagatt ttttttcttt ttcctcatta gttttgttct tccgatttca 1980 tcttttaata ttgtatgcag tccacagtga aaaggctgaa gcctttagtt tttttttttt 2040 ttttttttta tgcctttcac tgtggactgc acagtgcagt ccacggtgaa aaggctgatg 2100 cctttttttt ttctttttaa ttaatttttt tatttagttt gttgatatta aatttttttc 2160 tatttagtta tcagactttc atgacacgga tctcaggttt gacgggttaa cccagttaat 2220 ttagattttt tttttctttt tcttcattag tttttttctt cttataagtt tttttttctt 2280 ttattgtttc tttttattta atattttttt atttaattta gttcatcaat attaaatttt 2340 tttctattta gttatcgact gatgccttta gtttttcttt ttttttcttt ttgctttttt 2400 gctgttttta tgcctttaac tgtggactgc acactggagt ccacagtgaa aaggctgatg 2460 cctttttgtt ttttgttttt tcctttttaa ttaatttttt tcgtttaatt tagtttgtta 2520 atgttcaatt tttttctatt tagttatcaa attttcatga cacggatccc gggtttgacg 2580 ggttagccca gttaattttg tgttaacccg tcaatttttt ttttctattt agttatcaaa 2640 ctttcacgac atgaatccaa ggtttgacgg gttaacctgg tttgaagggt taacccagtt 2700 aattcagatt ttttttcttt ttcttcatta atttttttct tccttttggt ttttttcttt 2760 ttaattaatc tatttaatta tcacactttt atgacacgac cttgcagcca gacccacatc 2820 caagactatt gggtctggta ttgcagtcag acccacttaa acttgggtca tgcaagttta 2880 atgttattat taatattata aatattactc ttgggtcagg cgttgcagcc acacccaaga 2940 ctcttgggta tagctttgca aaaagaccta atacttttag atcttaactt tttttgatat 3000 tttttatgca aaaaccattg acccgcggca tcgcgcgggt catgtaacta g 3051 // ID Gypsy-31_Mad-LTR repbase; DNA; EDCOT; 2637 BP. XX AC . XX DT 08-OCT-2010 (Rel. 15.1, Created) DT 08-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-31_Mad-LTR. XX NM Gypsy-31_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2637 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1757-1757 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 2637 BP; 700 A; 479 C; 670 G; 787 T; 1 other; tgtgacagcc cgtccctgat tttaagagtt tttaaagttt taataaagga ttttacaaaa 60 atgccctttg aggcacgcgc attattcgag gttaatcgtt gtgtcgtgcc atctaagatt 120 tgttttcttg acatatcctc gtagtactcg tcgctacgga cgcgtgggcg cagacggttc 180 gtgatttgga gttataacga aaaagttatt aacgtttgaa gtttgggcat tttaggaatt 240 ataatttagt aaaatctgga atttctttta tgaaaatgga cggcccagat ttaatgaaga 300 attaaatgga tggctgggat gagaagaaag aaggtttgtg tgtgtgtgtg cgtgagaaga 360 agaagaagaa gaagagattg ggcaaaactg cccaaccaga ggaagagaga gcaggagctc 420 cgggagagaa aggagagagt gctggcgaat ggggagaaga gagagaggag actggccaat 480 cggaacagag gaaaggagga aaggagagag ggcgagaagc ggaggagaga aggaagaaaa 540 acgggtcttc acccgtgacc cgtttcgacc cgcggcaccc acgcccattt tccgacgatt 600 ttcacccgat ttctcgcgaa ttgcttcaag aaaccacttg gaatcaacac tctaggcctt 660 ccctcttccc attccacccc aaaattcgag agatttggck ttgaatatgg agaaaaccgc 720 acacgggggt gccgcggctt tgtcgttcaa attcacccaa tcccgaagca atttcttcca 780 attgccacca cccatagcat ccccttgagg cctagaacaa agcccaagca ttggttggga 840 cggcggagtt gatttgaaga cgaattggaa ctcacccaat tctagggttc cgcacggatt 900 ttggtgaaat tgaagtgttt ccaggccaaa ttggccttgg cctcaggtat aaagtttact 960 ctactcattg agatcttcaa ttctgtattt tttgagaatt tttggaaata gttggatttt 1020 ccggcgagcc ggggcggcca accgccaccc gcggcggccc gtgcggcggc gcgtggccaa 1080 tggcccgcca atgtcattct tagcatgtgt ttaaggttct aggttcagtt ttgataattg 1140 atggacgtaa attgagtaat tgaacctaag ttcgttacga ttcgtggtta ggtgaaaatg 1200 tgaattgacg atccgaccgt tggatcgtca ccaaactttg atacgttgta atacgtaata 1260 tttgaggatt ataggaactt acggattggg aatccgattt acggatcttc cggaattgga 1320 gttgtaagtt cataaaatag aatgttaacc gtcacttggt tttggaaatt gacggagatc 1380 cgaccgttgg atggtaatga aattttagga tgttgtccta gaggtatatt gtggacctct 1440 ggaagttatg gatttgaaat ctgagttgca gatcttccgg atcgaactac gtagtgacgt 1500 gttttatata agttatatat tctatcgata tgatttctga ggttggattt gattattgtt 1560 ctaggcgccg atcgtcatga cgccttgatg tgttgtgcta gggagttgtt gggcgaactc 1620 caggtgagtg ggcagtattt ctgtttatac ctatatacta ttgatatttt tcccagaaat 1680 tgagtttaaa tgaaagtatg ttttaaaatg ccatgcatgc atattatgag atatatgaat 1740 tgataattga tgcatatata tatatgtgaa ttggtgctgt ggacgcacag gtgagtatca 1800 ggtgagtttt atgttattca tgtgaatcat tgatgatgtg aattgtgttg agagctcata 1860 acctgcaccc ctggtgttag tgcttatatt attcaccccg caccgcacgc tcaccttgga 1920 tccaagtagg tgcatgtcgt acagaccatg agagggttcc gacatgctag tcgtacagac 1980 cactagaggt ggttccgact ggtaggtgac cttagattat gtgcacagat gattgatgag 2040 agaagcacta gagcgtatta ttacaccatt cttgtcgtac agactacttc aggtagttcc 2100 gacttatgtg cagagtagtg ccgtacaggt caccgtggtg actccggttg gattggatat 2160 tgagctatag aattaaccgt acaggaccaa ctgcagggtc tccggttgat tccttatttc 2220 acctgttata ttgatgcatc cttattatgt ttttgacatt atagcatggc atactttctg 2280 gttttgataa agattgatga tttgagatat ttgaaggtat atgctattat gctattttct 2340 gggaaagtat acaggtttta cagcgagggg ttagaaatgt tttaaatgaa atgttttcga 2400 aaaactttgt tttactgacc cactcaattt tgttttgcgc ccctccaggt tctagatagc 2460 agagctttgg tggccacgag gaatccaacg gtgttctgac agaattcaca aaagtaggac 2520 tcaccctcgg gtgtttcatc ttagtaattg tattttttaa agcttccgaa ctgtgtaaat 2580 ggttacgtca ctctcacgtg acggccagca tgccctcctt cgggacgggg tgtgtca 2637 // ID HARB-N3_Mad repbase; DNA; EDCOT; 617 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW HARB-N3_Mad. XX NM HARB-N3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-617 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1502-1502 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~91% identical to the consensus. 3-bp TSDs are usually TWA. This CC non-autonomous Harbinger is a derivative of autonomous Harbinger CC similar to HARB-3_Mad. XX SQ Sequence 617 BP; 214 A; 97 C; 96 G; 208 T; 2 other; gaccatctcc aacccttggg ttaaaaccta aaatttttag cccagaaaat ttaggtttta 60 acccagaaac agtttttttg ctccaaccct tctgggttaa aattttagcc ccagattatt 120 aaagaatgaa tttaggctaa tttttttttt cttaaagtaa cttttttaaa agaaaaaaaa 180 ttatgtagac tatcctaatt taattttatg aacattttaa cctaaaaata tttagattcc 240 gacaaatatt gaaaaatcac taaccgacac catgaaactc gtgaaacact atgaaagaat 300 atgaaacaca taaaagaatt tttttttaat tactttagcc gttggattta aatttggacc 360 gttagatntt tttttttacc gttggatttc atcaaattag atcttaaccg ttggattcaa 420 tgaatttata aatataaaac taaaaaaaat atacatatat ggtgggccag ccccactaac 480 ccagggggaa tcctgggcta aatttggccc anaaatgagt tttgagtttt aactcatatt 540 tgccccaagg gttggagcaa gttggggtaa gtttagaacc taaaatttga gttttactcc 600 aagggttgga gtaggtc 617 // ID SHACOP4_LTR_MT repbase; DNA; EDCOT; 276 BP. XX AC . XX DT 12-JAN-2007 (Rel. 12.01, Created) DT 12-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of LTR retroposon, SHACOP4_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; SHACOP4_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-276 RA Shankar R. and Jurka J.; RT "SHACOP4_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 75-75 (2007). XX DR [1] (Consensus) XX SQ Sequence 276 BP; 72 A; 34 C; 48 G; 122 T; 0 other; tgttgagaca ttgagatttc agatgtacac aatagtattt tgtgatattt tatgttttct 60 tttattttaa tgtagtagtt gaagttacct ctgcagaagt atggtgaccc atacttgtta 120 gagtgtttaa gactttgtaa tcttggttag gtgacagact actatgctgt cctgctgttc 180 actttttctg ttttttctat atattgtatc agaaacttta ttttgatgta gaatgaaatt 240 atcttcaagt ttctgaaata acttttagtt cttaca 276 // ID BoSB5B repbase; DNA; EDCOT; 162 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB5B. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-162 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 162 BP; 31 A; 49 C; 51 G; 31 T; 0 other; aaccgggcct cgtggtctgg tggtaaagga acctcggctg aggtgcccgc catcacgact 60 tcgagccccg gccacagcgg atttaacatc ccttccgttg gggcgctgga ccccctacgg 120 ggggatagtt gggaatgtgg ctgcccagat accagaatta cc 162 // ID Copia12-PTR_I repbase; DNA; EDCOT; 4578 BP. XX AC LG_III; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia12-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4578 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4578 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 196-196 (2007). XX DR Genome; LG_III; Positions 6461870 6466447. XX CC Positions [1944-2258] - Integrase core CC 'ATAAC' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 2202..3845 FT /product="Copia12-PTR_I_2p" FT /translation="MPSKVLHFKTPLQVLSSHVALPTVLLLPPRVFGCVVF FT VHLHKNQRSKLDPCAVKCLFLGYRPTKKGYKCFDPINKRLYITMDATFIES FT EHFYSPTVPNLALQGECKREELNELNWYLTAPATVSTTDNSTNPAATSIGD FT SPAQAGERELEEAENDVKGIHENQLKETENDVEGIHENRLNGELVNQESQP FT TPLSAVPESPTENNLEVSSSTVPPYTSDLNTPVEYVLPFRHNRGKPPNRYS FT PDTEERRSKFPIANYVSTQHLPDPIQSFTEVLSSCHTPDNIADALADPKWA FT QAIQEEMEALQQNNTWKLIPQPEGKKTVGCKWVFSIKYKADGSIDRYKARL FT VAKGFTQTYGIDYVETFSPVAKLNTVRVLLSLAANLDWLLLQLDVKNAFLH FT GDLEEEVYMDIPPGFTSSSGTGVVCKLERALYGLKQSPRAWFRRFSSAMRR FT YGFVQSNADHTLFLKHRQKRLTALIVYGDDMIITGDDTEEMSKLQEQLSAE FT FEMKNLGGLKYFLGIEVARSQKGIFLSQRKYVLDLLSEVGLLECKPVDTPI FT I" XX SQ Sequence 4578 BP; 1450 A; 993 C; 966 G; 1169 T; 0 other; tggtatcaga gcatagtcta gggatttcta taacctaaac agagaattaa cccaacgact 60 tcgacttcat ggctgaatat tccactgaat tgattcagcc acaaaatccc ataacagact 120 ccatgcttga caacttcacg accaagatga cggaggcttt gacaaaagcc caggctacct 180 cacaaccaat tatcaatgac tcttctgcag caccaaccag cattaagttg gatggatcca 240 actatgcttt atggtcccag gtggtagaga tgaacatctc agccaaagac aaactagggt 300 atattaacgg agacttacct caaccctcag aaacagaccc aacattccgt aaatggcgca 360 ctgaaaactc cgtggtgaaa gggtggttga ttaattcaat ggaccaatca cttgttgcaa 420 acttcatccg ctttctaaca gcaaaacagg tgtgggacgc cattgcaact acatattttg 480 atggaactga cacatcacaa gtttatgaac ttcgacgcag ggtaactcgg atgagacaga 540 gaggaggatc aatcgaaaaa tattacaatg atttacaagg aatatggcgg gagatagact 600 ttcgacgccc caatcctatg gaatgtgcaa cagacattca aaaatatctc tctgatacag 660 gaggaaagag tttatatttt tttggacgga ctggatgatc gacttgacaa cattcgtagt 720 gacattctcc aactgaaacc gtttcctaca attgagcagg cctatgctca cgtttcctat 780 gctcacgtca gaagagagga tactcgacag gcagtgatga cagcaggggc agagaccaca 840 accagtggtg ctgttatggc cattaaaggc tcaaggtttg gccaaccacc aacgctggta 900 atgggaaagc atcacctatc ctctaaaccg aagggtcctt ttgatggagg gaaatgtaca 960 cactgtggaa acacaaaaca cactcgtgag acatgcttca agttgcatgg gtaccctgaa 1020 tggtggcatg aactacaagc taggagaaaa aaaggtaaca ctttacctga tgaaggcata 1080 ggtagagccg caacagtcac ggcagaacct caactctcac tcatccctat ggcagactcc 1140 tccacttcta aagcaacagg taactgtgga caaagtttct atagttctag ccatcaaaat 1200 gaaagtgagt ggattattga ctctagggct acggaccata taacatttga tcctgcggac 1260 ttctcacaca caactcaacc acaaaggact tgtattgcaa atgcaaatgg agtcgcgtac 1320 ccagtcacgg gagctggaac cgtgtcgcta tcatcctcac tcactttgtc ccacactctt 1380 cttgttcctt cattatcaaa caaattaatg tctgtgagcc aagtaaccga agaactcaat 1440 tgtgtggtat tgatatactc taatgtttgt tttcttcagg atgttctcag caggagatta 1500 ttgggcgtgg tactaagaga ggggggttat actacctaga tgatttcaac catgggaaag 1560 caaatcacgt acaccatcaa ctcagtagca aggaacgaga aatatggtta tggcatcgtc 1620 gtcttagaca cccatcattc ggatatctaa gacatctatt tccgaactta tttttacaat 1680 caaaggatgt tgattttaat tgtaagactt gtattctggc taagagccac agaaactctt 1740 accatgcaag tttgaataaa agcagtattt cgtttgctct tatacactct gatgtctggg 1800 gaccttcccc acgaacgact gtaactggtt atcgttggtt tgttatattt gtcgatgact 1860 ccacccgaat gacttggctt tacctgatga agacaaagga ggaggtgttc ccaatattcc 1920 aagcatttca caccatgatt tagaatcaat tttcagccaa aatacaagtg cttcggtcag 1980 ataatgaagg ggagtttgtc aaccaacgat tcaaagcatt cttccagcaa caaggtctcc 2040 tccatgaaac ctcgtgtgcc cagactcctc aacagaacgg tgttgctgaa cgaaagaatc 2100 gccacatctt ggaaacaacc cgtgctcttc ttctcggcac aaatgtccca actcaccact 2160 gggatgatgc aataagtgct gcagaatact tactcaacaa aatgccctct aaagtcctgc 2220 acttcaaaac tcccctgcaa gtgctctcct ctcatgttgc actacccaca gtgttgctgc 2280 tcccaccacg tgtgttcggc tgtgtggttt ttgttcatct ccataagaac caacgctcca 2340 aacttgatcc gtgtgctgtt aaatgtctgt ttctaggtta tagaccaact aagaagggct 2400 acaaatgttt tgatcccatt aacaagagac tttatatcac catggatgct acctttattg 2460 agtctgaaca tttctattct cctacggtcc ccaatttagc tcttcagggg gagtgcaaaa 2520 gggaagaact gaatgaattg aattggtact taacagctcc agccactgtt agcaccactg 2580 ataattcaac aaaccctgca gctacatcca ttggtgacag tccagcacaa gctggagaaa 2640 gagaacttga ggaggctgaa aatgatgtta aaggaataca tgaaaaccaa cttaaggaga 2700 ctgaaaatga tgttgaagga atacatgaaa accgacttaa tggagagctt gtgaatcaag 2760 aaagccaacc aacccctctc tctgcagtac ctgaatctcc tactgagaac aaccttgagg 2820 taagctcttc cactgttccc ccatatactt ctgacttgaa tactcccgta gagtatgtgt 2880 tacctttcag acacaacaga ggaaagccac caaacaggta ctcccctgat acagaagaaa 2940 ggcgatccaa attccccatc gctaattatg taagcacaca acacctacct gatccaattc 3000 agagtttcac agaggtatta tcctcttgtc atactccaga taatatagca gatgccttgg 3060 ccgaccctaa atgggcacaa gccatacaag aagagatgga agccctacag caaaataata 3120 catggaagct gataccgcaa cctgaaggga aaaaaacggt agggtgcaaa tgggtgttct 3180 caattaaata caaggcagat ggatcaattg accggtacaa agcaaggcta gtagcgaaag 3240 gattcacaca gacatacggt atagattatg ttgagacttt ctcaccagtt gctaaattaa 3300 atactgttag agttttacta tcccttgcag caaatctaga ctggctgtta ctccaacttg 3360 atgtaaagaa tgccttcctc catggtgacc ttgaagaaga agtttatatg gatatcccac 3420 cgggctttac atcatcttca ggaactggag ttgtatgcaa gttggagcga gctctatatg 3480 gattaaaaca atctcctcga gcatggttta ggagatttag ctcagccatg agaaggtatg 3540 ggtttgttca aagcaatgca gatcacaccc tcttcctgaa gcatcgacaa aagaggttga 3600 cagccttaat cgtctatgga gatgatatga ttatcaccgg ggatgacact gaagaaatgt 3660 caaaattaca agagcaattg tcagccgaat ttgagatgaa gaatctgggt ggacttaaat 3720 atttcttggg aatagaggtg gcaaggtcac agaagggtat attcttgtcc caaagaaagt 3780 atgtgctaga tctactgtct gaggtggggt tattagagtg caaaccagta gatactccca 3840 tcatttaaaa tcacggactc actgaacaca cagaccaagt accaacggat aaaggacgat 3900 accaaaggct ggtgggaaaa cttatttact tgtcacacac tcgccctgat attgcttatg 3960 ccgtaagtgt tgtgagccaa tttatgcata atccaagcga agaacatatg aacgcggtga 4020 ttcgaatact tcgttacttg aaatcctcac caggaaaggg tctaatgttc tctaaaaaca 4080 accgcttgga tgttgaagga tacacagacg cggattgggc agggagtatt ctagatagaa 4140 aatccacgtc agggtacttt acatttgtgg gaggaaactt agttacatgg agaagtaaaa 4200 agcaaaaggt ggtggctcgg tcaagtgctg aagccgaatt tagggggatg gcaaaagggc 4260 tttgtgaatt actatggctt agaaggttac taatggaaat aagctacggt cctaacatag 4320 agatgaactt gttttgtgac aataaagctg caatcgatat ctcacaaaat cctattcagc 4380 atgatcgaac aaaacacgtt gagatagaca gacattttat taagcaaaac cttgaagaaa 4440 agatcatcca gttcgttttt gtcaaatcag aaaatcaact ggcagatata ttgacaaagg 4500 cagtttccaa tagaattttt catgactcac ttgacaagtt gggcatcaaa gatatttatg 4560 caccaacttg agggggag 4578 // ID Gypsy15-PTR_LTR repbase; DNA; EDCOT; 367 BP. XX AC scaffold_523; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy15-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-367 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-367 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 309-309 (2007). XX DR Genome; scaffold_523; Positions 22488 22122. XX SQ Sequence 367 BP; 95 A; 56 C; 84 G; 132 T; 0 other; tgatgcgttc attcctacgt gggtaaatgc atggggcagg gacgtgggac gaatgaggaa 60 tgggtctttg ttccacgtgg gtaaatgcat ggtgcaacat ggggtgaata aagaatgagt 120 ctttgttagt tactggtcat ggctgaaaac tagtgtagtg ggaggagtat ttccttatta 180 ttagtttcgt attgttagtg ctttcctatt cttaagcagg tagtttattc ttctcagttt 240 agtcggctat aaaatatagc caataggttg ttttgaatta tgcagaaaat aaataacatc 300 catcctactc tgtctcttct tcccttctgt cttaattctt tcatagttga tagaaaatta 360 cttatca 367 // ID BoSB6C repbase; DNA; EDCOT; 321 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB6C. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-321 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 321 BP; 95 A; 62 C; 83 G; 81 T; 0 other; gtggaagcac cgtggcctag tggtcaaggt ttaaaggctt ctacacccag gtctggggtt 60 cgaaccccag acaacgcaat tttctacagg aagaggtctg ggtttcaatt cccggagaag 120 gcgaattatg cagaaaatta gggaaaatgc ttacaagaga tcttcagcat ggcgcaagga 180 ataccgtcag gaatggatct catagggcta ctcagggtga tgcagtcaga cgtgaatcct 240 tcataaggca ggtagaattg tcggctgtaa tatcgtctat gtaatgtttc tcataatttg 300 taatagcata attaaccaga c 321 // ID Tvv1_LTR repbase; DNA; EDCOT; 169 BP. XX AC . XX DT 31-AUG-2007 (Rel. 12.09, Created) DT 04-NOV-2009 (Rel. 14.12, Last updated, Version 2) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia25-VV_LTR; KW Tvv1_LTR. XX NM Copia25-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-169 RA Pelsy F. and Merdinoglu D.; RT "Complete sequence of Tvv1, a family of Ty 1 copia-like RT retrotransposons of Vitis vinifera L., reconstituted by RT chromosome walking."; RL Theor Appl Genet 105(4), 614-621 (2002). XX RN [2] RP 1-169 RA Obukhanych T. and Jurka J.; RT "Copia25-VV."; RL Repbase Reports 7(9), 783-783 (2007). XX DR [2] (Consensus) XX CC Long terminal repeats (LTRs) of the Copia25-VV family are 97% CC identical to each other. The 5'LTR contains a 18-bp internal CC deletion. The deposited sequence represents the 3'LTR. XX SQ Sequence 169 BP; 51 A; 26 C; 25 G; 66 T; 1 other; tgttagctgt atatatctgt acataccata atttggttgt ttcctttctt gtaggctgat 60 tcttagggat aataccttcc taatttagga ctctcaattg tatatatata caagtattat 120 tcctctaata aasatacaag gaattgagaa ataccttgat tcggttaca 169 // ID LTR-9_Mad repbase; DNA; EDCOT; 2371 BP. XX AC . XX DT 20-OCT-2010 (Rel. 15.1, Created) DT 20-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR-9_Mad. XX NM LTR-9_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2371 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1793-1793 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 2371 BP; 580 A; 464 C; 570 G; 757 T; 0 other; tgtgacagcc cgtcccgaga aataattatc gttgatgtga aaagactaaa atgcccttag 60 gcgttgagat gtgttgtgtg tgacatgcta ttagaagtgg actaatatgt taaattccta 120 agtttttggg accaattgga actaaaggaa attggtggtg attggttggt tgtttgtaaa 180 ccacacacac acaaaagtac cactttctct ctctcaccct cccgtgctct ctctctctca 240 gactcactct ctctctcttc tctcttgtac ggaccacacc caaaacccgc caaaacgtga 300 cagatcgagg ggttaaggtc accattgtgt tcgtgaggac catacgagtt gaatggtacc 360 attttcaggt aagaacctcc tttgaaaact cgtgaaatcc gaaccccgat ttgaggcact 420 gttcatgcac acgtaaaatc ttgggtttca gggaatttca aggtcatagg gagcttcagg 480 aggtcccaag gagctcggag tagttcgttg ttttggacgt cgggatcgtg agtttcaagc 540 ttggccggat tttgtggaat ttctccggcg agatcccgtg acttttggag cttcaaattg 600 gtaaggttgt gttcttcatg ttgtaagctt cattttggtg caaatttcgt ggaaaatggt 660 tgagaaatga ctgagatata agggtttgaa aatttcccag ttttccggcg acggcgacgg 720 tcgccggagt ctgaggttga agacgacgga atattccgtc agttctgacg gaatattctg 780 acgccgtcag ttaagtttaa cggaatctgt taggatttaa cggaatattc ccttactgcc 840 gttactgatt ccgtcagggt tccctgcgcg tggccgcgcg tcttgccgtg cactcgccgg 900 cgcgtggcgg cgcgtggtgg tcgaaaaatt attttaaaaa tatggggacg atcctgagat 960 tgtgtaggtc actgtggtat attcatatac ccaatttgag ctatgtatga gaagttatta 1020 catagtttgg tatatgtgca ttaaagtaac gtttatttcg gtacttctcc tataggcgag 1080 acctatccgg aggacgagcg tagccaggct aggcatgggg gttacgaccc agctgcatat 1140 ctgtgagtgg gcagttattt tcagtatata tatatatata tatacttgac gtttttccca 1200 gaaaacgtat ttaaaggaaa tgtgatttaa atgccatgtc atgtatgcct catattttag 1260 tatatgcatt atcataatta tgcatattgt tgcatggtgc tgtggaggcc caggtaagct 1320 acaggtgagt acattatgct gataatggtt atgagatatg atgatgatga tgttgagatg 1380 tatattagag ctcataatct gcaccccggt gttagtgctt ccgcccagag ttaggggcac 1440 agtccttcac gtgatgttca cctcccgcac cacacgctca tcttggatcc aagttaggtg 1500 cacagtcctg tcgtatagac cactatgggt ggttccgact cgtaggtgac ccgcgattta 1560 tcgcacagct ttcacgtgat cgtagcacta gagcgtacta ttattttaca cccagtcttg 1620 tcggtcagac cacgtgaggt ggttccgact cgtgtgcagt tatgtatata catgatgaga 1680 tatgtgacgt atatacatga tgatttatat gatgagatat gagattgacg ttgtgattga 1740 gatgagctct agattccgcc gtatagatca cgtcaggtga cttcggctag cagatggtta 1800 ttgtgaattg catcacctgg cttacttttg gtatttttat gttattgggc atggcatacg 1860 catggcatat attatacaaa tatgaatctt gatttattga gcatgatttg agatatatac 1920 atatttatgt attctatttt ctgggaaagt atctatatac ttgttttacg gcgaggggtt 1980 agtatattca aaggaaaata aggttttcgt gtaaatgtgt tttactgacc cactcaactt 2040 tgtttttcgc ccctccaggt tttaggtagc agagtttggt ggccacgagg aatccaacgg 2100 tgttctgaca gaatccgaaa aagtaggatt caccttcggg tgttgtatct tagtaattgt 2160 cctacttgac tgcaactaga ctttcttatt gctctgaaag tgtatttata cacttagact 2220 ctcactagca tcctttctta actgggattg ctagttgctt ggttttaaat tgttcgtatt 2280 tccttactct ttatcgcttc cgctttgcgc acaaggctac gtcacgctca cgtgacggcc 2340 aacacgtctc gacttcggtc ggggtgtgtc a 2371 // ID DNA3-10_Mad repbase; DNA; EDCOT; 571 BP. XX AC . XX DT 22-OCT-2010 (Rel. 15.11, Created) DT 22-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE Non-autonomous DNA transposon from apple. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA3-10_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-571 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1848-1848 (2010). XX DR [2] (Consensus) XX CC TSD is 3-bp long. XX SQ Sequence 571 BP; 204 A; 82 C; 91 G; 194 T; 0 other; gtactggttt ggtactgagg tgcttttata aaaagtgggt ataaaaaaaa gctgagctca 60 aaaaggtgtt tggtaaacac ttaaaaacag cttattttca cagttttggg tgaaaaaaaa 120 aagctgaaaa cgtgaagcag caaaaatgag ctttgaaaaa aagctgaaaa cgtgaagcag 180 cataaatgtt ggattatatg ttgaatgttg gattatgatt tcttgttaaa cgttggatta 240 tgatttcttg ttaaacgttg gattatatgt ttaagataaa gtttataaat atttttcttt 300 taaaaataaa gtatatttag taattcacct ttatttgtta agaaaattaa attaatggca 360 catctagtat tataccattt ttggtcattt cacacagtca cagctgtttt acataaaagt 420 ttaccaaaca ctataatact gctttttttt tccaaaagca cttttacaaa aaagtttacc 480 aaacactctg ctgctttatt tcacagctgc ttattctcac agcacagcag aagcagtttt 540 ttttcaaagc acagcaatac caaaccagcc c 571 // ID PIGY-I_PS repbase; DNA; EDCOT; 9248 BP. XX AC AY299398; XX DT 09-JUN-2005 (Rel. 10.05, Created) DT 29-MAR-2007 (Rel. 12.04, Last updated, Version 2) XX DE Pisum sativum LTR retrotransposon PIGY-1 (internal). XX KW Gypsy; LTR Retrotransposon; Transposable Element; envelope; KW Metaviridae; PIGY-1; PIGY-LTR_PS; PIGY-I_PS. XX NM PIGY-I_PS. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-9248 RA Neumann P., Pozarkova D. and Macas J.; RT "Highly abundant pea LTR retrotransposon Ogre is constitutively RT transcribed and partially spliced."; RL Plant Mol Biol 53(3), 399-410 (2003). XX RN [2] RP 1-9248 RA Toth G.; RT "Pisum sativum LTR retrotransposon PIGY-1."; RL Direct Submission to Genbank (09-JUN-2005). XX DR Genbank; AY299398; Positions 10891 1644. XX CC Internal sequence of envelope-class Ty3/Gypsy-like CC retrotransposon CC PIGY-1. XX SQ Sequence 9248 BP; 3045 A; 1940 C; 1681 G; 2582 T; 0 other; gtggggaagc gaccgaacaa tggtagaaaa acctcaaaca aaagggggca tgtacgagat 60 aagtagcctt gatcatgtta atgcaaaagt ggatgctctt gcccagaaaa tcgaaagttt 120 aaatgtatca cctccagcca ccgtggttgc cgtaactcaa aattgcgaag tctgtggaat 180 tcaaggtcac actcctacag attgtcaact cctaacagga atccaagcag agcaggtgaa 240 ctatgctcaa ggaaatcctt actcgcatac ctataactca aactggaaga accatcctaa 300 ttattcatat aaaagtaaca acactttata cgcaccagga caagctccca gtcaagcccc 360 agctatacca cctggatatc aaaagccgac cccatctaca cctaacaata acgttcctag 420 gaaatccaat ttggaaatca tgatggagaa cttcatagct tctcaacagc agaccaataa 480 agagttctta aaccagaatg tacacactaa cgaacagatt aaacaactag caagtaaagt 540 agatgccctg gctacccata acaaaatgct ggaaacacaa atctcgcaag tagctcaaca 600 acaagcgcct actgctgccc caactagtac ctttcctgga cagccccaac ctaacccgaa 660 aggccatgct catgcaatta tattaagaag tggaacagag gtagaaggac catctgaccc 720 aaggattgag aaccaaaact ctaaaaagtc aactgaggaa gaaggtagac ctaaggaaaa 780 ggaagagtgt aataaagaaa ccgtagaaaa caaagaacct tatgtacctc cgccacctta 840 caaaccacct atcccttatc ctcaaaggct aattaaaacc aaagacgcgg gccaatttaa 900 aaaatttgtt gacctactga aacaattaaa cgtcacgatt ccttttacaa aagctattac 960 acagatgcct tcatatgcta agttcttaaa agaaatttta tctaataaaa ggaaacttga 1020 agatagcgaa actgttacac tcactgctga gtgtagcgca ataatccaga atatgcctcc 1080 taaacttaaa gaccctagta gtttttctat accctgtcat ataggaaaat ttgtcataga 1140 taaagcttta tgcgatttaa gagccggtat cagtgttatg cccttgtcca tatgcaagaa 1200 acttgaaatg ggagaattaa gaccaactaa aatgtttgtg caattagcag atcgttccgt 1260 tagatatccc gtaggaattc ttgaaaacgt tcccgtgcgc ataggtcaat tctacattcc 1320 caccgatttt ataattatgg acataagaga agatgaagtt acccccatta tattgggaag 1380 acccttctta gcaaccgtcg gtgctatcat agacgtaaaa cgaggacgac tcactttcga 1440 agtaggagaa gtgaaaattg agttcattct ttccaaattt ctgaaagcac ctgcaataga 1500 agacacatgt tacttcatgg atatcatcga tgaatgcata aaagaaacaa aattagaaaa 1560 tgacgatttg tccgactatc gtgtagaaga tagactgaac caaagtttag caataacatc 1620 ggatcctacg caatgcctta agaaaccaac cctcgacctg aaaacacttc ccaaaaatat 1680 gagatatgaa ttcctagact tagaacttga acgaccagtg atagtcaatg cagacctagg 1740 aaaacttgaa accgaaaaac tcctacatat cttaagaaaa tatccaaccg cactaggata 1800 caacatcacc gatcttaaag ggataagtcc ttctatttgt atgcaccgca tcatgctaga 1860 agaagactgt aaaacttcta gggaacatca gaggagacta aacccgatcc tgagtgaggt 1920 agtgaagacg gaagtaacga agttattaga ggcaggtatc atatatccta tatccgatag 1980 caaatgggtt agtcctgtac acgtagtacc aaagaaagga ggtataacag tgatcaaaaa 2040 tgaaaaagga gaaactataa ccaaacgaat tgaatcggga tggagaatgt gcattgacta 2100 taggaagcta aacaaagcaa cccgaaaaga tcattttcat ttaccattca tagaccagat 2160 gttagagcga ctagccaagc attctcattt ctgctatcta gacggttact caggcttctt 2220 ccaaatacca attcatcctg atgaccaaga aaagacaacg ttcatatgtc cctttggtac 2280 cttcgcttat cgacgaatgg cgtttggctt aagcaatgct cctgcaacct tccaaaggtg 2340 catgatggca atattcgccg attttctcga aaacatcatg gaagtcttta tggatgactt 2400 ttccgtatgc ggacaaagtt tcgaagaatg tcttgaaaac ctagaaagag ttctagaacg 2460 acgtgtaaaa gtaaacctag tacttaattg ggaaaaatgt cactttatgg tacaagaagg 2520 aattgtttta ggacacatca tatcaaatag aggaattgaa gtagacaaag ccaaaataga 2580 agtaatcgaa aaccttcaac ctccgaaaac tgtgagagaa atacgaagct tcttaggaca 2640 tgccggtttt taccgacgat tcattaaaga tttctctaaa ataactaaac ctttaactgg 2700 attattaatg aaagacgctg aattcatctt cgacaataaa tgtttagaag catttcaaac 2760 acttaaacaa gcattgatct ccgcgcccat aatgcagacc ccggattgga atgaaccatt 2820 cgaaataatg tgtgacacaa gtgactacgc cgtaggcgct gttttaggac aacgaaagga 2880 taaaaaactt cacgtcatat attatgcgag tagaactcta gatgaagcac aaatgaatta 2940 cgccacgacc gagaaagaac ttttagcagt agtatttgca ctagataaat ttcgttccta 3000 cttggtcgga gctaaaataa tcgtttacac tgatcacgct gccattaagt acctcttaac 3060 aaaaaaggat gctaaaccta gactcctaag gtggatcttg ttgctacaag aatttgattt 3120 ggaaatcaaa gataaaaaag gaactgaaaa catagtagca gatcaccttt ctagacttga 3180 aaacctggaa ccggaaagaa catcgatcaa cgatgattta tcgtacgata aacttatagc 3240 taatttggaa gaaaatagag ttgatgaaca ggtagagacc accttggctg tatgcgttac 3300 accatggtac gccgattttg tcaattattt agccgccgga gtggttccac ttgatttatc 3360 ctaccaacaa aagaaacgat tcttccatga cataaaacat tattactggg acgacccttt 3420 acttttcaaa agaggcctcg atggtatttt ctgtcgttgt atacctgaag aagaggtaga 3480 aagtataatc caacattgtc attccgctcc ttatggtgga cacgtaagta catccaaaac 3540 ctgctctaaa atcctacaag ccggtcttta ttggccaaac atatggaagg atgtgcatgc 3600 cgctgtcaag aaatgcgata ggtgtcaacg cacaggaaac atatctagac gtgacgagat 3660 gccacaaaaa ggcattttgg aagtagaaat tttcaatgtg tgggggatag atttcatggg 3720 accttttcca ccttctttcg gtaacaagta catactcgta gcggttgatt acgtatcaaa 3780 atggattgag actatagctt ctccaacaaa cgacacacga gtagcaatta aactctttaa 3840 gaatataatc tttccaagat ttggtgtccc aagaatagta gtcagtgacg gtggatcgca 3900 tttcatatct aagatactcg aaaaattatt gtttaagtat ggtgtaaaac atcgagtagc 3960 aacaccttac catcctcaaa ctagtggaca agtggaagtg tctaatagaa aaattaaaca 4020 gatagtggaa aaaactgtcg ctacatcgag gaaagactgg tcatcaaaat tacccgaagc 4080 tttatgggca tatcgaaccg cttacaaaac tcccatagga acaaccccat ttaagcttat 4140 ttatggtaaa tcttgccacc tcccggtgga gttagaacat aaggcctatt gggctattaa 4200 aaatttaaat ttaaactata aggccgccgg tgaaaagcga attcttgata taaacgaatt 4260 agaggaactt agacaagacg catacgaaaa tgccagaatc tacaaggaaa gaacgaaaaa 4320 atggcatgat aaacgcatat caagaaaaac tttcaaacaa ggcgatgtag tcctattgtt 4380 taactctaga cttaagttat tcccaggaaa gctacgatct agatggtcag gccatttcca 4440 agtcactaat gtctttccca gtggagctgt agaaattaaa ggaaaatcta ttgaatcatt 4500 tatcgtaaac gggcagcgtc taaaacatta tcactatgat gaaaacaatg aagactcgca 4560 agtcctgcac ttagacgtat tgtctccaaa attaatagat taacatttaa tagttttatg 4620 tcgagcttgc gacattaaac aaagcgcttc gtgggagaca acccacaaat ttttattttt 4680 ttctttgatt attctttttg attttattca gttttcattc ttcatattct ttattttaat 4740 taaatttttc ttcttttctt ctttcggcat ctggccaaat cctgactaaa ttcttgtttt 4800 tcttttcttt agttaacact aacctaatgg gacatattga tcgcatgggt atcaaattcc 4860 gagggagagc tcagagacaa aaatttgaag aactagctga gagagagatg cacccaagtt 4920 tttatgctga tgattatgca atgaccgttc ttgggttaag agatagtgtc ctatatctgc 4980 tgagtcaaag agggtgggaa accaccccta ttcgaagaca atttgttact taccggaggc 5040 taactctaga attccttagc tccctgattt atttaccaaa ccatggaaaa ggaataaacc 5100 gaggtttcat tcaattcagg atgttcaata tggagtatca gtttaacatt taagaattta 5160 ctaacctttt agggttccct acttcttttg acacattcac catgagccaa gaagaccttt 5220 ttgaatatag agagcttaag catttttggg gaagtttgac gggaaatgac gaccctgagg 5280 aacatgagtt tctttctgga aacatacata tcccggcttt tcgttatttc cacaagatcc 5340 tagcacacac tctttttggg aagagatcaa acattaccac aatatcatgt gatgaactct 5400 tcataatatt ttgtgcttcc cagaaccgtc cagtgaatgg tgccacttat atgttggcga 5460 gttttgacct ccttattcaa gatgatcgtg caccgatcca aataggagga ttgataacta 5520 tgattgctaa tgctattgga ttgcgccaac ccatgcttga tttgaaccct ttttgtggta 5580 ttgagcctat gaatatactt ttcctcttca acactatgtt tataggaaac cttggacctg 5640 aagagtttga actattaatt aataaccaag ctttttacct attcaccatg cctagcccga 5700 tgactagtgt ccataaccga aataattggc tttacaacct ggatggaata ccttctcctg 5760 ttagatctgt tgaaaccatc caagattatg agattcttga caaccagatt ccttatgctg 5820 agtctgatcc gcagacacca actggttacc atgatgctgc ctctccacat catcctatcc 5880 cgtctgcaga atcggcgata cctgatctta gacatcatat gcccggaact gattataata 5940 ccgctattca agccttgatg tcagaacaag atgccattag agaagagtta actaagatgg 6000 gacatgaatt tctggaatac atgagtggaa tgacaaatca attccacgag ttgctacacc 6060 gtgtcaattc ctttgctcct ccgacgagag attctaccag tggctagaag aattgcagtt 6120 aattagtttt agttttagga aatttatagt ttcgtttaac attactttta atcttaggat 6180 ttatttttcg catgttttat ttttcagtca aatattacat tatgtttatt tttatgaagc 6240 tattggcatt attggttaaa ttaaatttta ttttgattta tgcattatct aaaattccca 6300 atgatgatat atattgtatg ctactactta catggtttat cagaaaaaat atatatatac 6360 tatgatgtgt agtagagtag catccatggc aattcaaaaa taaaacaata gcaaatatta 6420 taaacaaaac taaaaaaata ataataaaaa aaaattataa aagcttccac gcatgccatg 6480 tcacgagcgc agtgaccgtt gcatgctcac cagcgtgacg agcgtcacac atactgtcat 6540 ggtcgccacg caacccatga cgcccgtaac acactctgtc acgagcgtga caacgtgatt 6600 cctcgtaaac gttgatgacc gttagggtca tgaccgttac tccccacctt tttattttcc 6660 ccattcaacc cacctcttta ctccattcca ctcacattca tccacattta tttttctctc 6720 acccactcct cttcccaact tcaaaactct tcgtataaat acccacaata catttcttcc 6780 tacaccacat cattccaaca agccattcta tacaaatata tttcatcctc ttttccttct 6840 ttctacctac ctatcaatat ggcggagaac taacatcaag aagtgcaatt cggaaatatt 6900 attttccgat ctgaagatag caactatcaa cgagagcagt tcgttcggtt ccaacaacgc 6960 gatgtcatat ctaccaggta cccagattta aattgcttac aagaattagg attactttaa 7020 ggtgtgcaat ggctgcttag gctttctgat ttaacttttc tttgcacaca aaatcaccca 7080 acatacccat cactcacctt ggagttttta agttcttatt cctacaccac tccacccggt 7140 gagaacgaat acttaaccgg taccgcaaat ttccgcatgt tcaacactga gtactcacta 7200 tctcaggacc agttgagtgc catgctacac tttcctgtag gagaccaagt ccacccaaga 7260 atccctccaa actcagagtg gaacacgaac gcattcgacc tctttggaaa aatatccggt 7320 gtggaaacca ctaattggga tgcattactt gcttcgcaca tacacaaccc cactatccgg 7380 tattttatct gtattctgca aaacaccatt tttggaagac ccaacaacag taaagtcaac 7440 acgaaagaat tattcttcct ccactgcatc ttttcagccg acacaaaggt aaacgccgcc 7500 tctttcttac ttcaccatat tcgtaccttt tgtgctccag gccgccaacc ttttgtgatt 7560 ggaggattaa taaccaccat cgcactcggc ttaaatctag gggaccgact tcagaatttg 7620 caatctttgc cacccctgtt tatggatata agctattgtc tctccagccg cttaatcaaa 7680 aatagggtag gcgggaagta ttatcttatg gtgaataacc aagaagtccc aagcgttgtt 7740 ttgcccaaca ttaccctcac cgatgtcacc aaccccaacc gattcatata cgatctgaat 7800 gctcccgaac ctaccaagcc tacacaagca aacccgcccc cagacgagtt tgatgaaatg 7860 gagcaaggtg atcaaggtcc tgaacaacat tcggtcccac ataatccttc cgataatgtg 7920 gctggtccat cctcccggcg tcgtcgaaga agaaggcccg caacaaatga tgacatcatg 7980 gatgctattg aacatcaagc ccaacggctt gatgccatgc atgcgcagaa taacgaagta 8040 atgcaactga tgcgccagat gcaacaacaa caagaagaga ggaatgcaat aaccgaccag 8100 cggttcactg acttgcttaa caagtttgat gacttggaag tacgtcaacg atcaccaggt 8160 ccgagaacaa gaggacgcag gcagaattga gtttgggttc cttctttttt tttctatttc 8220 ttttgttttt tgaaacattg gggacaatgt ttcatttaag tgtagggggg aaaactttgt 8280 ttcagttata tttattttcc tttcaatatt tccctttcaa gtatgttatt tccctttcat 8340 ataaaaaaaa tatataattt attttaagtc aagtccctag tgtggaattt ttttattatc 8400 tattcccctc aattttcttg agccataaca aaattcaaca cactcaataa gtataaagga 8460 tgcttatttt ataaaacttg agtgaaatta agacaaaatt attaccgccc cagcactcta 8520 aaaacctcag catgttagac caggataagt acttattata ccaattcctt gcacttttag 8580 ttttatagta accccgagta gtttatacga gaagtcggca ccatcttaat agcaaactac 8640 gtggagagcc gatgaatata agtgaatgat tcccaaaaca acatattaaa aatcaggaaa 8700 tgcactaatt aagttaggtg atccttaccc gatcatttaa tccaaaggtt gcggacccta 8760 caaaacatag tatgaacgat ccattgtgag ttggttcagc ggtttctggt gctgaacttg 8820 gtagggcgga ctacggtccg atcccccgca atttgcaatg gactaaataa cgaggttatc 8880 caacttatgt accagaactt ctagctaaaa ggggatcaga atcgctaacc ggttactcca 8940 ctatgtgcgc gaaaagataa agggcttaat gtgatttcgc tagaatgaaa acgggtgaaa 9000 taagagtaaa agaactaggc tagctataat agcatgactc gaactggttt gcataaggtg 9060 gggttatctg atgttgtaac ggtagttgtt gatgttaaga ctaaactcag gttatttcta 9120 aacgagattt acttgcaacc tagtacgaat tgatgtgtgt ttggaaattt catctggcta 9180 atattttaaa atgatttcta cattgtatct tgcttgagga caagcaaaag tctaagtgtg 9240 ggggagtt 9248 // ID Gypsy-48_Mad-I repbase; DNA; EDCOT; 3528 BP. XX AC . XX DT 29-OCT-2010 (Rel. 15.11, Created) DT 29-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-48_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-3528 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1993-1993 (2010). XX DR [2] (Consensus) XX SQ Sequence 3528 BP; 1052 A; 621 C; 740 G; 1101 T; 14 other; aattttggcg ccgttgccgg ggattagcaa mwttgctaat cccccattgt ttcttttttg 60 tgtcttttgt ttagttactg attttgtttt tttgtttctt ttacttttga tatttgattt 120 agttttgttt ctttgatttc aggtactaga gaagtaagac atggattttg ctaacmttca 180 agctcaawtg gcgaatctta cttctcaatt gtcgcagtat gccgaaagga ccacaakgca 240 aagtgtccct acatttggtg cgtcttatag gcaaggatat caagccaatc aacatccaca 300 aagagattgg agtgatcatt caaactctat gtggtgggaa cctcaacaag ttcaacacga 360 agsatattgg cagccatatg aggagttcta ttcaagacct atgcagccac cacaacctca 420 tatacaatat gcccaatcaa actcaggttc gtcaatagat tataatcaaa ttcttaatga 480 attaaattct ttggtgcagg gctcacaaaa tcaagccaag gaggctcaac aagatgcata 540 ttggcagcca tatgaggagt tctacaccac gcctatgcag ccaccaccgc atcccccaca 600 acaattccaa tcgaattcaa gtatgtccat ggatagtgac caaattcttc aattactaac 660 ctctttggcg caggaccaac aaaatcaaga caagaagttg ggcaaattga agaatcaaat 720 gggagagatc gtggagttca tggcacaaat tcaagagcaa agtgaactct ccaactcaac 780 tattgaaaat ttgaaggaag attttgaaat ccatgatgct atcactttgg aaagtggcat 840 ggaggttgga acaagcccaa aaacgtccaa accaagccaa gaggaggacg aacagctgct 900 aatcgaggag gaggaagaag acacacccac ggcaagggta gaacaaccct tgccgcagcc 960 tcctaggscc cctatgccgt ccamcwcaag taaggtggtc ccaaattcaa ttmattctaa 1020 ccccattcca ccgaatgtcc cttttcctcg caggtttttg attcccaagg aagaagagag 1080 tgaaaaagac atcgtggaag cctttccaaa ggtgcaaaat gatattccaa ttcttggtgc 1140 aacaaacaag ttccagattg tgttgaattg ttcaagggac tttgtacacc aagaagaatg 1200 attcaagaga aagaagtggc tggggaatgt caagaattca tcaaagagga tgtatttgas 1260 acaacgaagc ccaaagaagt tggattttat gacacgggac aagtcacaac catcacacta 1320 aatctggccg agtccaatat ccctgaaact ttcaaagaag tggtgtttgt cattgagttc 1380 atgtcggagc acacaggtaa gccacctcct cgaatttcaa ttttgtttta tactaatatg 1440 ttgttaatga ttcaggcacc cactctagaa tttaaaccat tgccggatca tttcaagtat 1500 cacctcccat tcaaagatca attccatgcc gtgggaccta ggggagctta aatggaggta 1560 tcgtccggct ggaagacgtt aaagcaagcg cttcttggga ggcaacccat gcaaataaag 1620 aagacctagg aagctccggc atcacaacca gatttgcgtt cctaaaccct actctttatt 1680 gcttttactt tgccatattt gtcatgtttg ctagttgtgt tatttgcttg tttttgtgtg 1740 agtctatgtt tgaaacattg aggacaatgt ttggtttaag tgtggggggg gggtaaacaa 1800 agtgtttttg ttgcaaaatt cgtaggattt taccacctaa catttcaaag gttgtttttc 1860 attgtttttg agtgttttta gtgtgttttg atgtgtcttt atgtggcttt aacaggaaat 1920 acgaaaattc gaaaaaaaaa ttagaaaaag ttttgaaaaa cccaaaaaga gtcgttttag 1980 agttgttttt gtgtgtttgt gtcttagggt accttccaac acaatgatga ggatttggtt 2040 tttaattgca tgactgttaa agaaagttac aaacatgggt ggaagtttga tatgctcttt 2100 ggtttatgct tggttgtagt tgtcgtttac gaattcacat gtaatcacaa aaggaaaaaa 2160 aaatcagttt ttgtaacatg cttgaaggaa ggaactcaaa ctaacgctac aaccctgaga 2220 gacttgagcc taaactttat ttggagagtt attaatctgt gatttcttgt tttctaaagt 2280 cgttgcatga tctcattatt ctttgcttgg ttgctactta gaatgcgttt tatcacttta 2340 gttccaaata ctagaactca tgcccgtttc attcaaagct taaaattgag tgcataacat 2400 ataacaagat gaagttgttt agtagttacc accagagcca aaaagccttc atcccatgca 2460 tttgttttgt aggtttaacc ccttttgagc cttatttagc ctattttctt tgttagccac 2520 attatcctta cctagcctag awtaggacta tccataccct tgttcttaaa gtatagtgga 2580 gcatgactta gagggaattc cttttgatca acatattgca gaaaaacaag tgtgggggaa 2640 gggatttttg tgtgtgtgtg tgtgccaaag tcttaaagag gcacgggtag aaaagaaaaa 2700 gaaaaaaaat tcgtggaaaa tagaaagaaa aaaagaaaag ttgtgaaaag aatgaagaag 2760 agttgaaaaa tatgtgagaa aagctctaaa gtgttggttg ttgaagaaag ggtccaaaaa 2820 gcttgaattt gaccctaagt gttgcatgaa ctttcccttt gtgtttaaag tggatttttt 2880 gcattcaaaa gtgaattcta agtgtcaatt tcattacttt gctcactatt gctttaagaa 2940 cstttgttta cccttacctt tctttgttag ccaataccct tagccccgtt acaacccttt 3000 gacttctatc ttgggtgtta tgtgtttcaa tatgtggagt ttgggattgg tatgagcata 3060 tggtatccct ggttctcgcg tctaagtagt ggcattccat tcatgagatc atatctaagc 3120 atgcttaata actccagaaa atgctttctt tgttatacat atatgtgagt gttcgtctac 3180 atgtttacat caatcttctc acatataact agtgtagggt gtgtagtcag aaaatctgag 3240 tgaaaattga gtgcctatct agtaaggaat tgagggaatt ctctaaggca tgttactaca 3300 ttcaaaacgt cgttttaatt ggttaaatgt gagctagtga gtggtgacta tgattaagta 3360 tgtgctcaag ggtgaggatg actaaaatct atgtgagtgg tgatttttaa cgtgtcatgt 3420 tkcattggaa atccctgagg caaatgttgg aaggtttagg ttctgttttg tttgttttgt 3480 ttcctttgtt ttgctcgagg actagcaaaa gctaagtgtg ggggaatt 3528 // ID Copia-29-I_VV repbase; DNA; EDCOT; 4517 BP. XX AC CU459380; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-29_VV_I, LTR retrotransposon Ty1-copia like, internal DE portion from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Brand-B01; KW Copia-29-LTR_VV; Copia-29-I_VV; Copia-29_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4517 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL/GenBank/DDBJ; CU459380; Positions 609725 614241. XX CC size : 5519 bp CC LTR : 500 and 502 bp CC LTRs are 94.4% similar to each other CC Direct flanking repeats : aatat. XX SQ Sequence 4517 BP; 1622 A; 654 C; 910 G; 1331 T; 0 other; atcttaaggt gaatttcttt ttaatttttt gcttatattt gtgttttaaa cacagttaat 60 aacatggcct ttgcaaatat tattgatacc cctattgtta cacctactac tatccatggt 120 gagaaaccag agaaattcat tgggttggac ttcaagcggt ggcaacaaaa gatgttgttt 180 tatctcacaa cacttaactt ggccaaagtg ttgcatgaag atgcacctac tttaaaggag 240 ggagagactg acaagcaaat tgtggaaaca attgaagcat ggaaacattc atattttcta 300 tgcaaaaatt acatcctcaa tggacttaac aacacgatgt atgatgtgta tagtcaagtg 360 aagatagcca aagagctatg ggagtcattg gcgaagaaat ataagattga agatgctggc 420 atgaaaaaat tcatagttgg caaatttcta gattacaaaa tagttgactc taagacagtg 480 acaaaccaag tccaagagct ttaaataatt ttgcatgaat tacatgttga gaagatggaa 540 ttaagtgagt ccttttaagt tgcagcaatt gttgaaaaat taccatcatc ttgaaaggac 600 ttcaagaatt atctaaaaca caagcacaag gaaatggggc ctggggactt gattttgaga 660 ctgaaaattg aggaagataa tcgtgtttct gagaagaaag tgggaaaaca tcccatggag 720 tccaaggcaa acttggtgga atcaaagact aataaaaagt gaaagcactt tggtgaaggt 780 ctaagtcaaa gaaagaacaa atacaagaag tttgttggga agtgttacat ttgcaataag 840 caaggtcata gggccaacga ttgtcgcttg aaatgacaag gtaaggaaaa taaagcacat 900 gtgactgagg aagaggagtt ggcaaacatg ctttttgcat tggtattgct tgaagccaac 960 atggtagata acctaaatga atagtgggtt gacataggtg ccacccgtca tgtttatgga 1020 gaaagaaaca tgttctttac atatgtacca atcaatggta gaaatttgat catgggaaat 1080 tctgccacat atagggttgt gggaattgga aaagtggtgc taaagatgac ttctggaaaa 1140 gaacttgttc tcacatatgt gctacatgtg cctgatattt gcaagaatct tttttctgat 1200 tctatgctta gcaaaaatgg gttcaagtta gtttttgagt ctgacaaatt tgtattcatg 1260 aaaaatggta tgtatgtggg caagaggtat atgaccaatg gcatgtttaa gatgaatgta 1320 atgactgtta agcgtgattt caataataat aaagcaagta cttctgttta cttgattgag 1380 tcttttactt tgtggcatga taggttagga taggttaaca acaaaacttt aaaaaggttg 1440 attaacatga atttgttgac tttttttagc attgatttta aacagtaatg tgaagtgtgt 1500 gtggaagcca agatggctaa gccaatgttt cattcaattg aaagtaacac atgacctttg 1560 gatttatttc atagtgacat ctgtgactca aagtttgtac aaacaagagt agggaaaagg 1620 tttttattac ctttatagat gattgtacaa aatactgtta tgtgtatatg ctaagaagca 1680 aagatgaggc cttagatgtg tttaaacact acaagaatga ggttgaaaat caacttagca 1740 gaaagattaa ggcaataaga agctatagag ggggagagta tgaagctcct tttggagaat 1800 tttgttcaaa acatggaaca atccaccaaa ctactgctcc ttattcacct caatcgaacg 1860 gtcttgctga gtgcaagaac tgtacattaa aggaaatgat gaatgctatg ttgataagtt 1920 tggatctacc ccaaaactta tggggggaag caattctttc tacaaaccac attcttaaca 1980 agataccaca caagaataag gatgtaactt catatgagtt atggaagggt cacaaaccct 2040 cttacaaata tttgaaagtg tgggggtgtt tggctaaagt aggagtgcca aaacctaaac 2100 aggttaagat tgggcctaaa actattgatt gtatatttat tggatatgca aacaatagta 2160 gtgcatatca ttttcttgta cataagtctg gcattcctga tataattatt gagtctagga 2220 atacatcatt tttttagaat atttttcctt gtaaagaaaa gcaagaagta agttcaaata 2280 agagaactta tgatacttca aatggtaatc atcaaaatga ggaagaacca agacgtggta 2340 agagaggcaa gaagacaaag tcttttggcc cggattatct aacttacatg ttagataata 2400 aaccaaagac attcaaagaa gcaatgtcaa cacaaaagcc ccattttgga aagaggctat 2460 caatagtgaa attgaatcca tcatgcataa ccacacatgg aaattggtgg atttaccacc 2520 aggaaataaa cctttgggtt gtaaatggat cttaaagaaa aatatgaagc ctgatggaac 2580 aatagataag tacaaggcta gattggtagc caaaggattt aaacaaaagg aaggccttga 2640 tttctttgat acatattcac cagttacgag aataacattt attagagtgt taattgcaat 2700 taaaacattg cataatttgg aaattcatca aatggatgtt aagacaacct ttttaaatgg 2760 caagttagaa taagaaatat atatggaaca acctaaaggg tttggtgctc ctggacaaga 2820 aaagaaggtg tgtaagttga taaagtccct atatgggcta aaacaaacac caaaacaatg 2880 gcatgagaaa tttgacaaag taatgttgtc aaatgatttt aaaattaatg aatgtgataa 2940 atgtgtatac ataaagtgag tatgtcattg tgtgcctgta cgtggatgat atgttaatta 3000 ttggtagcaa taatgatgtc attaaagcta ccaagaaaat gctgaccaat tattttgata 3060 tgaaagacat ggatgtcata gacgtgatct taggtataaa aataactaag acatctagtg 3120 gactaatatt atcttaatgt cattacattg agaaaattct taaacagttt aaccaatatg 3180 atgatagtct aattaagaca ccagtagatt taaatctaca tttagctaaa aataatggtc 3240 caacaattga ccagttggaa tattctcgta tcattggcag tttaatgtat gtcatgaact 3300 gcacgcgtcc aaacatagcc tatgcagtta ataaactaag taggttcact aataatcttg 3360 aaaaagacca ttagaaagcg ttggttaggg ttcttagcta tctaatatac accttaaact 3420 atggacttga ttatttaagg tatccagtcg tactagaagg atatagtgat gcaaattgaa 3480 tatctgatat gaagaactca aagcccacaa gtggatatat attcacaatt agtggcgctg 3540 cgatatcatg gaagtcatct aaacaaacat gtattgcaag atcaacaatg gaatctgaat 3600 ttaatgcttt agataaagca ggggaagaag cagaatggca tcataatttt ctagaagaca 3660 ttccatgtta gccaaaacca attcctgcaa tatgtataca ttgtgatagc aaatcaacga 3720 ctggaaaggc acaaagtagc atgtataatg gtaagtcttg acacatccgt cgtagacata 3780 atagtgtaag gcagttactt gcaaatagga ttatttccct tgattatgtt aagtcaaagg 3840 acaacctggc ggatccacta actaaaggat tgtctagaga tcaagtaaac tgcccatcga 3900 ggggaatgag attaaggcct atcactaaag agtttcataa tggaaaccca acctagctga 3960 ttggaggtcc caagatctag gttcaatgag gaccactaaa ttatgaaata ctctatgaag 4020 agcactagaa aaaaataaat tcctacccat tcctatggtg aactagtgtt atacaagatg 4080 tgtttatgat aagttatgct tttaatgatt ctaataattt gaaagagatc aagtaaagta 4140 tggtagaata ctcgcgatag gaatcaccta tgtgagtgtg aaatggggtc atttctatga 4200 gaatttttaa ggttgaaatt ctctaaagca ctcatgaaac tgggaattgt ttagggccaa 4260 aatgaacaca actgtgagaa tcaatggtga tccaaaaagg aattgtgtga atactattgt 4320 cttgatttac atcaatagtt gaacagttca agacatcaca ttcactaatt agctagtaaa 4380 tccaatagta tttcactgag gaaggttcaa agccacaaac tacctatcat gatgcaatca 4440 ctttccaatt ttgtactacc tcgattgttt agttttccat tgcctttttt aagtcaattt 4500 ccattcatgt gggggat 4517 // ID MtPH-A6-3-Ia repbase; DNA; EDCOT; 4845 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 13-MAY-2008 (Rel. 13.05, Last updated, Version 1) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-A6-3-Ia. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4845 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC An autonomous element representing subfamily A6-3 of CC PIF/Harbinger transposons from Medicago truncatula, carrying 22 CC bp-long TIRs. The element contains a TA microsatellite in the CC first intron of its transposase. XX SQ Sequence 4845 BP; 1590 A; 694 C; 831 G; 1730 T; 0 other; gggtccgttt ggttcgagcg ttttggaggg gagaggaggg aaggggaggg gagattttta 60 atttgaagtg tttggttcta tttttagaag ggaagggaag gggaggggag gggagcaaat 120 ctctttaaaa ttttattgca ttgccataat tatccttaaa ttaatttcaa atctcaatat 180 taaccttgta acaactttta ttattattag attatattat ttttgtaaca atcttattat 240 tattattagg ttatcttatt cttgtaacaa ttattattat tattttgtta tattttcctt 300 gtaacaattt ttattattat ataatctacc actcttattt gttagatgta caaaccgctc 360 ttactactac tttgttgttg tcaacgactg cttgaggctt cctccaaagt gaattgtgag 420 taatttcatc atctcattgt ctatatcgta gtattattaa ttacatcgtt attgattcgc 480 tactttatta tccttgttta atcgttatcg ttgttggaac tttattgttt aaattgttgc 540 tttatcctta cggtggcttg tttgtttcat agtgtgtttt ttcttatggt attgatccat 600 tcatttgaga gtattgtttt tttttcactt ttaaaatcgt tgaagtcttt tttttttttt 660 ttatgaaatc gttgaagttt tattattatt attattattt tattttaatt cagcttatta 720 tacttgttgt tgcttgtttt tttttcacag ttaattcacc tatccatgtc ttgttgtgta 780 aaatcttgac caaatttttt tttcactaca caaccttact attatcggat tagctgaata 840 taactcgtaa tcattgaatc aaattgaaaa tgaaattcac taaaaacgca catagtttta 900 aaaaaaaaaa aaaaaaaatt taccatgaga acagaaatat acaaataaaa ttttgcataa 960 aatagctaca gcctacaggc aaacgaacag taaaaactca ggacatgttt acatttcaca 1020 tgttcccact taaaacctct ctcaagcatg caggccattt attttatttt tttaaaggct 1080 gatgctgcct attgaacttg ttcctgttgg cacactacat tatccatcct caaagctgtg 1140 cattattttt attgatactt attgttgttg gagtatcaga tacagcttat ataaaatgca 1200 aatcttcact tctagctaaa ataggataat cacaacctag tagtgttttt tttcactgtt 1260 aattcaccga tcctacatgt cttgttgtgt aaaatcttgg ctttattttt ctgtacatta 1320 atctatatgc tttgtttcat tttttttatc ttccatatat ctatacatta atcatgattt 1380 tttttttctt ttttacgttc tgcttttctt tctatatgct ttgtttcatt tttttttctt 1440 ccatatattg atcatgacct cgtttatata taaatatgtt tgttgtagtt tattacatgt 1500 ctatatgtaa ttgtagtata agagttatat aatctagaaa ttaattttat gcgattagat 1560 ggatcatcaa gatcagaaaa ttgctatcaa tagatggttt gatttgcgcc gaagagctat 1620 agctcagctt atgtgtgctg ttgtcttttg ttatattcga atctctcgta aaaaaaaaaa 1680 taagttatag tatgagctct cagagagaaa gggtgcgtga agaagtaatg tatcgactta 1740 aaaatagtga aactagtaga aatataataa gaatgggtcc tcaaactttt ttaaagttat 1800 gcgatatgtt agaaagagaa gggggcttac gacctacaag atggtcaagt gtggaagaac 1860 aagttgcaaa atcactttac atactaaccc ataatgctaa aaatcgtgaa gtcaactttt 1920 ggtttcgtcg ttcgggtgag acaattagcc gtcatctcca tcaagttttg aaagctattc 1980 ttgaattgga agaaaagttt attgtacaac ctgatggatc aacgatcccc ttggaaattt 2040 ctagtagcac tagattctac ccatatttta aggtacattt ttatattaat aaaatattag 2100 caagacttga ataaattata tatatatata tatatatata tatatatata tatatatata 2160 tatatatata ttgatagaaa aatactatat tgtgtcagga ttgtgttggt gctatagatg 2220 gaacacatat acgagtcaag gtatctgcaa aagacgcccc tcgttatcgt ggtaggaaag 2280 agtatccaac acaaaatgtt ttagcagcgt gcacttttga tttaaagttc acgtatgtgc 2340 ttgcgggatg ggaaggctcc gcctctgact caagaataat aaagaatgca ttaacacgag 2400 aagataaact taaaattcct caaggtaata taagaatcaa cataaagtta taactactta 2460 tattatatac ttcaaactat cacatttatt atttaccttt actataggaa aatattatct 2520 agttgatgct ggtttcatgt tgacaagtgg acttattacg ccttatagag gagttcggta 2580 tcacttgaaa gaattttcgg caagaaatcc acccctaaat tataaagaat tgtttaatct 2640 ttggcatgcg tctttacgaa atgcaattga aagagccttt ggtgtattaa aaaaaagatt 2700 tgagatttta tcaaattcaa cagaacccgc ttatggagtc aaagctcaga aattaatcat 2760 ttttgcatgt tgcattcttc acaattatct aatgagcgca gaaccaaatg aagaccttat 2820 agctgaagta gatgccgaac ttgcaaatca aaatgtatcc catgacaatc atgaggcatc 2880 aagaagtgat atggatgaat ttgctcaagg tggaattata aaaaatggtg cagcgcatca 2940 aatgtggtca aattatgaaa ataatggtca aacctaaatg gattacattg caatttatat 3000 tattattttg attttggttt ttctttgatg aagtagtact gaatttatta aattatggtg 3060 ttttttatat atgtgtgtgt ttggactaaa tgtatatttg aaattgatgt caagtgaatg 3120 atattggaac ttcatgttaa ttatatttat taatgtagtt atgttataat tgaccatttt 3180 tatagattat gacatcgaaa aagcaattgt caaccaacaa tggtaattct gggtctttga 3240 cctggaataa agccatggat gatgctcttg ttgatgctct catgcaagaa tttgaaaacg 3300 gtaacaaagt taacggtacc tttacgtcaa tagcatataa aaatgttaca gatgaactcg 3360 tgagattgtt tggtgaccaa attgataagg tgaagataca aaatcgttgg aaaactttga 3420 aaagaaacta cagtgagtat cacgaaaatt ttaaaggtgg tatgagtggg ttttcttgga 3480 attcaactac acagttatgg gatgcggaag aaccagtttg ggctgctcta attgaggtaa 3540 attttgtaaa tcttgtattt tgaaatattt tttgattgat caaaaatttt acaacttgtg 3600 tcaaacttac ttttcagtcg aaaccaaaag cagcacattg gagagttgat tcatttccaa 3660 actataaaaa gatatcaata cttcatgggc ctaaccgagc tgatggagat gaatctggaa 3720 cttttaaaga gaccggaaaa cgaggggcat cgatcactga ggaagatttt gttgaaacta 3780 ttcaagatat tgatgaccgt gttgctcgga atgaggtaac tttggagagc tttgatgctc 3840 ctgattatga ctttacttta cctgaaacac aatcatatga tccttcaacc atggcaagtg 3900 gtggaaaaag gaagagattg aaagtggcta agaataaaga gacatataat gatattattg 3960 aacttaaaga gtcaatgaaa gtggttgcag aggcactcag agaaggaaat gttgcaatac 4020 gggaaggaaa tgaaataacg agagaacgtc ataaacacga gttgcctcca atttcaggag 4080 aagagacttg gaatttatta gaggagtgtg aatgtgaccc aaattcattg cctaagatat 4140 atcgtgttgt catgaaagat gtagacatac ttagaatgat tcttcagtgt ccacccaaag 4200 cacgcaaagc agtcataatg gaaactgtct ttggttcttc tgattaatca tactatgatg 4260 gtgttatgat gtttatgtgt ttttttaggg agactgtttt gttatgatgt ttatcattat 4320 tttttttaag gagaaatagt taacaatagt catagtcact ttcatgtgtc ttatttgttc 4380 atatgcaaca aatttcattt atcttacaat tgttaattaa taagcactat ccatgatttt 4440 gaaaattctt atgtcatata tttaagagct atgctatttt ttacaaaagt aattggaaaa 4500 aaatgcaagg attacaaaga attgctctta taaaaaaaat attacaaaga attgctccga 4560 taaaaaaagc caaaaaaaaa aaacaatatg atgcttggag caaaatacat gagccagttt 4620 aagataaaat agcggcttag atgtgtgctt gtctttgtca gtttctgaaa tcgtaaaaac 4680 aaacagtttc ttttatttaa ttaagtttaa gggtaaaacg gtaaaataca gttaaaatcc 4740 ctccccttgt gaaccaaaca cacttttaat taaaaatatc tcccctccac tcccctccgt 4800 aaaaatccct cccctcccct cctaattctc gaaccaaacg gaccc 4845 // ID Copia-47_Mad-LTR repbase; DNA; EDCOT; 249 BP. XX AC ACYM01034867; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-47_Mad-I; KW Copia-47_Mad-LTR; Copia-47_Mad_. XX NM Copia-47_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-249 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1397-1397 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01034867; Positions 11199 11447. XX SQ Sequence 249 BP; 65 A; 45 C; 42 G; 97 T; 0 other; tgttaaagta tgagttagtg agtgtaggat tgttacactt gtcacaagaa taagagatgt 60 gggatgatta ggtagttaag tctgttgtgt ataaatagtg atgtacattg cattacttgg 120 agattaagga aaatcatata caacttcttt cttctctctc tctctctctc tctctctctc 180 tctctctctc tctctctctc taaaaatgtt cttcgtagat cacatatctt ccattgatat 240 tggttaaca 249 // ID LTR-13_Mad repbase; DNA; EDCOT; 2656 BP. XX AC . XX DT 02-NOV-2010 (Rel. 15.11, Created) DT 02-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE Putative LTR-retrotransposon from the apple genome: long terminal DE repeat. XX KW LTR Retrotransposon; Transposable Element; LTR-13_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-2656 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 2004-2004 (2010). XX DR [2] (Consensus) XX SQ Sequence 2656 BP; 653 A; 565 C; 656 G; 780 T; 2 other; tgtaacgacc cgtccccaat tattacggtt tttataattt taaaatgtga atttacgaaa 60 atgcccttcg aggcaaatgc gttgactttt gttgaccgcc ttgtcgtgtc acgtaagatt 120 cgttttcttg gcgtatcctc gtagtactcg tcgctacgaa cgcgtgggcg caaacggaac 180 gtgatttgga gttataacga aggagatatt aacgtttaaa gttgggggca tattagtaaa 240 ttaattattt tctagaatgc tccagatttt tggagcaaaa tctggtaaag ccacgtgtgt 300 ggcccagatt aaaggaaaag aagatgggcg gtggagatgg aaaataaagg agagaaaggg 360 agggaagtgg aggaatcagg aaaggagaga gaagggagcg accaatgagg gagaggggaa 420 agaggggaaa ggagagagga gaggaaaggg ggaaacggac ccccccttga cccgtgaccc 480 gacccgaccc ggtttattcc gaccgatttc cgccattttt cgcaaattca ccatccacca 540 cctggaaacc actccacgac cccccatctt ccatttcacc ccaaaattca ggggatttgg 600 cctcgatttc atgaaagaag aagcacggtg ccgacggcac cattgtcggt gatccgccaa 660 tcctgaagca atcctgtcga ccaccaccac caatagactc cccttgagcc caggaacaaa 720 gcccaagcaa tggttggggc gtcggagctg tttggagtcg aatcaaagca cacccaaatc 780 tagggttccg acgggttttt gtggaattga ggcttttccc ggccaaattg gacttggcca 840 caggtatgaa agttgctcca ctcactgaga tcttcatttc tgtgaagttt gagaattttt 900 agaaatagtt gatttttccg gcgagtcggg gcggcgcgtg ggccgaggcg tcccctgacc 960 ttcctaggct aaatttgaat accctgattc catatgtgat gtccgattga cgaaatttca 1020 ttgtttgaac ctagtttcat taaggtccgc cacttgatta ttataggaat cgacgatccg 1080 accgttggat cgtcaccaaa ctttaatacg ttatagtacg taatatttga ggacatagga 1140 acttacggat cgggaatccg acgtacggat cttcccgaat tggatttgta agttcgtaaa 1200 ataaaacgtt gaccgccact tgaatttgca attggcggag atccaaccgt tggatcgtaa 1260 tgaaacttta gtatgatgtt ttagaagcat aatgtggatc tttggaagtt acggatcgga 1320 aatccgaggt gcggatcttc cggatcgagt tacgtagggt tgtggaccct accgtcgatc 1380 tttgaccgac ggttgacttt tggtcaatgg gtctcaaatc attctagaac gtccttgggg 1440 atgtgtttta tgtaagttac gtgttctatt gataaggatt ctgagatgtg atttgataat 1500 tgttctaggc gccgatcgtt cgtgacgcct cgatattcgt gctagggagt tgtagcgcgg 1560 actccaggtg agtgggcttt tgtttttata tatatatata tgctttacga tttccaagaa 1620 atgtttttaa atggatttac gctttaaatg ccatgtcaat tgcattacat tttagtatat 1680 gcattagtat agttatgcat aatattgtat gatgctgcgg aggcccaggt aagcttcagg 1740 tgagtacata ttgatgatag tggttgcatt gtgtatggtt atgcgtagat gcatttagag 1800 ctcattatcc tgcaccccgg tgttagtgct cccccccgag gccagggccc agccttcacg 1860 tgatcgttca cctcccgcac cgcacgctca ccttggatcc aagkttggtg ccagcctgtc 1920 gtacagacca cawtaggtgg ttccgactcg taggtgacct gcgatacttc gcacagcctt 1980 cacgtgatcg tagcacttga gcgtacttat ttacacccag cctgtcgtac agaccacatt 2040 aggtggttcc gactcgtgtg caggaattgg ttgatgagct ataggttcag ccgtacaggt 2100 cacgttaggt gactccggct ggcatatcat tttatattga ttcatatcac ctggcttaca 2160 tattttatta ctgagatact tgacatggca catacttcgg ttttcactgc tctcgagcat 2220 gatttctata tacgtatgta ttattatttt ctgggaaatt atacgggttt tacggtgagg 2280 ggttattatt tttggaaaga gaaatggttt caaaaagctt tgtttttggc ccactcacgc 2340 tttctgtttt tcgcccctcc aggttttagc tgctgaaagt tcgtatcgac gaggattctt 2400 ggcgaatctc agtataggtg gctacctctg agggtatgat ccttacccac actactgtac 2460 tttacttatg ctctgacgtc gcgtgtgaaa tgggttcatt cccgctcaca gcgcactctt 2520 gtctttaggc acttttaggt ttaaatttat tcacattttc cacatcacta tactttatgg 2580 cttcgtcacc ttccaggtgt cggccagcac agctcgattc ggagtcctag tggacattcc 2640 gggtcggggt gtgtca 2656 // ID Gypsy23-PTR_I repbase; DNA; EDCOT; 4573 BP. XX AC LG_XVI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy23-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4573 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4573 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 326-326 (2007). XX DR Genome; LG_XVI; Positions 13230230 13225658. XX CC Positions [2201-2656] - Reverse transcriptase CC Positions [3650-4147] - Integrase core CC 'TGTCT' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 38..4573 FT /product="Gypsy23-PTR_I_1p" FT /translation="MARDDIGSSRSTDDDQRIRAIATGVVTAAINDIRPLF FT DGVPLLQAQLEEVLQRLEALSPNGNRIDDQRRGRADEITHGSTSLTRNPEN FT IPQYQNTRSLPVMSSTNCQVIETEDRAPRRTQGDRDYKLNVEMPTFKGTQN FT VDEFFSWIDEVETGFGVMDCSEDRKLKVVANKLRGSAAAYWKYLKNKRVLD FT GKPPIATWEKMKSKFMSKFLPPDYEQRLYVQLQNCKQGNRTVEEYIDEFIR FT LNSRNLLPDNENMQIARFRGGLKQDIQDQMKMLNTFTLGQAFDLARKAEEP FT IRAPSVRPRFTNQQYQAGPSRVTPTTEPSNGTVATENRPRRAAPQQAPNPY FT ARPMPSLCYRCHQSGHRSNQCPQRPAVNFVEGDYEVEGDDDHNTEVVDGIE FT ECEEDEFIGMVMRQPCDIQKKKLAASNQHSLVENLKAEKGGDEKFNYIVQR FT VFLTPKKGPEISTRHQVFRTNAIVNGVIAKVVIDTGSSENLVSKELVRRLK FT LTTEKHPQPYGLRWIRKVEGAADVVNEVCRVPLSIGKNYQDEIVCDVVVMD FT ACQILLGRPWQYDVDIGFKGKTNTYEFWWKGKHIFLKPPILKTGARQEEGE FT SFLTIATKHVAEECQACALLAQEEDTTEETIPEKVLPLVTEFSDLAPTELP FT MGLPPMRDIQHHIDLIPGASLPNLAHYRMSPQQHKILQDQVDDLLCKGYIQ FT ESKSPCAVPALLVPKKDGTWRMCIDSRAINRITIRYRHPIPTIQDMIDQLG FT GAKVFSKIDLRSGYHQIRIRPGDEWKTAFKTREGLYEWTVMPFGLSNAPST FT FMRLMNQVLRPFSCKFVVVYFDDILIYSPDEETHLRHLREVLIVLRKNHLY FT VNKKKCNFLQDRLVFLGFVVGKDGVQVDETKVKAIREWPTPSTVADVRNFH FT GLATFYRRFIRNFSSLAAPLTECKKKGGFRWEEEQETSFAILKEKLSTTPV FT VALPDFDKLFEVDCDASGKGIGAVLSQEGRPVEFFSEKLSAARLRWTTYEK FT EFYAVFRALMHWQHYLIQKEFVLYSDHQALKFINNQHHMNNMHARWITFMQ FT KFTFSLKHKAGLMNKVADALSRRTTLLVTVEIEITGFETLKEQYINDEDFK FT EVWNKCSTHQNVSDFLIHGGFLFKANKLCIPKGSLREKIIRELHGGGLGGH FT LGRDKTITLITDRYYWPQLKRDVGKIVQHCRVCQEAKGQTQNTGLYTPLPI FT PKTIWEDLSMDFVLGLPRTQRGKDSIMVVVDRFSKMAHFVACKKTADASHV FT ADLFFREVVRLHGVPKTITSDRDVKFVSHFWRTLWKKFDTKLQFSSAFHPQ FT TDGQTEVVNRTLGNMLRCISGEKPKRWDLDLAQAEFAYNSMTNRSTGKPPF FT EVVYTQQPKHALDLVTLPIQPKVSRAGENLAERVQQLHSEVRASLETANAA FT YKSAADQHRRKKEFTEGDLVMAYLRKNRLPGTRTKLQQRKYGPFRVAKKIN FT DNAYTLQLPDDWNISKTFNVADLSEYHEDVPLYADNSGRVCFQEEEN" XX SQ Sequence 4573 BP; 1434 A; 974 C; 1136 G; 1029 T; 0 other; agtggtatca gagcctacgc tctcagcaaa atttctgatg gcacgcgatg atattgggag 60 tagtcgttcg actgacgacg atcagcgaat aagggcaata gcaaccgggg ttgttactgc 120 cgccatcaat gacatacgtc cactattcga tggggttccg ttactgcaag ctcagcttga 180 agaggttctt cagagattgg aggcgttgtc tcctaatggc aacaggatag acgaccaacg 240 acgaggaagg gcagatgaga tcactcatgg ctcgacgtcc ttgacccgta atcctgaaaa 300 cataccacaa taccaaaaca cacgatcatt acctgtgatg tcgtcaacaa actgtcaagt 360 tattgaaact gaagatcggg ctccaaggag aacccaaggt gaccgagatt ataaactcaa 420 tgtggagatg ccaaccttca aaggaacaca gaacgtggat gagtttttct cttggatcga 480 cgaggttgag acgggatttg gggtgatgga ctgctcggag gatcggaaac tcaaagtagt 540 ggccaataaa ctaagaggat cagctgcagc ttattggaag tacttaaaaa acaagcgagt 600 gctagacgga aaacctccga ttgcaacatg ggagaaaatg aagagcaagt tcatgagcaa 660 gttcttacct cctgattatg agcaacgttt atatgttcaa ttacagaatt gcaaacaggg 720 gaatcggacc gtggaagaat acatcgacga gttcattcga ttaaattcac gaaacttact 780 accagacaat gaaaacatgc aaatcgcaag gtttagagga ggtttgaaac aggacataca 840 agaccaaatg aagatgctta atacattcac actcggacag gctttcgatt tggcacgaaa 900 ggctgaagag ccaatccgag caccatctgt acgacccagg tttacaaacc agcagtatca 960 agcaggacca agcagagtga ctcccacgac tgaaccaagc aatgggaccg tggctactga 1020 aaatcgacca aggagagctg caccacaaca agcaccgaac ccctatgcta gaccaatgcc 1080 ctcgctatgt taccgatgtc atcaatcagg acaccgttcg aatcagtgtc cgcaaagacc 1140 tgctgtcaac tttgtggaag gtgactatga agtagagggg gacgatgatc ataacacaga 1200 ggtggtcgac ggtattgagg agtgtgaaga ggacgaattt attggaatgg tgatgcgtca 1260 accgtgtgat attcaaaaaa aaaaattagc agcatcaaat cagcacagtt tggtggaaaa 1320 tctgaaagca gaaaaaggtg gggacgaaaa attcaattac atagttcaaa gggtcttctt 1380 aacgcccaaa aagggaccag agatttcaac tcgccatcag gttttccgaa ccaatgccat 1440 tgtcaatgga gtgatagcga aggtagtaat cgacacagga agttctgaga acttagtgtc 1500 caaagaactg gttcgaaggt tgaaactgac cactgagaaa cacccgcagc cctatggtct 1560 acgttggatt cgaaaggtgg aaggcgctgc tgatgtagtc aatgaagtat gtagagtacc 1620 gttgtcaatt ggtaagaatt accaagatga aattgtgtgt gatgtagtgg tgatggatgc 1680 ttgccaaatt ttgttaggaa gaccatggca gtacgatgtg gacatcggct tcaaaggaaa 1740 aaccaatacc tatgaattct ggtggaaagg gaaacatatc tttttgaaac cacctatttt 1800 gaaaacaggg gcacggcaag aggagggaga aagtttccta accatagcaa caaagcatgt 1860 ggctgaggaa tgccaagctt gtgcgttact agctcaagag gaggatacaa cagaggaaac 1920 catacctgaa aaggtcctcc ctttagtgac cgaattttct gatctggcac ctacagagct 1980 accaatgggt ttgccaccaa tgagggacat acaacatcat attgatctga ttccaggagc 2040 cagcttacca aacctagcac actatagaat gagcccccaa caacacaaga tattacagga 2100 tcaagttgat gacttgttat gcaaaggata tatccaggag agcaagagcc cgtgtgcagt 2160 accggcatta ctagtaccca agaaagatgg cacctggcga atgtgtatcg acagccgagc 2220 aatcaataga atcaccatcc gttaccgaca tccaataccc actatccaag acatgatcga 2280 tcaattggga ggggcaaaag tgttctccaa aatcgatcta cgaagcgggt accatcaaat 2340 tcgaattaga cctggggatg agtggaaaac tgcgttcaaa acacgcgaag ggctgtacga 2400 atggaccgtg atgccgttcg gtctctccaa cgctccaagc acttttatga gactcatgaa 2460 tcaagtgctg agaccgttct catgcaaatt tgtcgtcgtt tacttcgacg atattcttat 2520 ttacagccct gatgaggaga cacacttgag acacctgagg gaagtgctga tagtactgcg 2580 gaaaaatcac ttgtacgtga acaaaaagaa atgtaacttc ttgcaagacc ggctggtctt 2640 cttggggttt gtcgtgggaa aggatggggt tcaagtggat gagaccaagg ttaaggcaat 2700 tcgtgaatgg ccgacccctt caactgtagc agacgtgcga aacttccatg ggttagcaac 2760 attctaccga aggttcattc gaaacttcag cagcttggca gcaccgttga ccgagtgcaa 2820 aaaaaaaggt ggtttccgtt gggaagaaga gcaagaaacg agtttcgcta tactgaaaga 2880 gaaactaagc acgacacccg tcgtcgcgtt accagatttt gacaaattat tcgaggttga 2940 ttgtgatgct tcagggaagg gaattggggc cgtgttatct caagagggca gaccggtgga 3000 attctttagt gaaaaattaa gcgctgcaag gctgcgatgg acaacttacg agaaagaatt 3060 ttacgctgtc tttcgagctc tcatgcattg gcaacattac ttgatccaaa aagaattcgt 3120 gttgtacagt gatcatcaag ctctgaaatt catcaacaac caacaccaca tgaacaatat 3180 gcatgcccgc tggatcacat tcatgcagaa attcaccttc tccttaaaac acaaggctgg 3240 actgatgaac aaggtcgcgg acgcattgag taggcggacc acactgttgg tgacagtaga 3300 aattgagatc acgggttttg agactctgaa agagcagtac atcaatgatg aagacttcaa 3360 ggaagtgtgg aacaagtgca gcacccacca aaatgtgagt gacttcctga tacacggtgg 3420 cttcttgttt aaagccaata aactgtgcat tccaaagggg tctttgcgag agaaaatcat 3480 acgggaactt catgggggtg gattgggcgg ccacctagga cgtgacaaga caatcacgtt 3540 gatcaccgac cgttattact ggccacagct gaagagagac gtagggaaaa tcgtccaaca 3600 ctgtcgagtt tgtcaggaag caaaaggaca gacccaaaat accggtttat acactcccct 3660 gcccattcca aagacgattt gggaggattt atcgatggat ttcgtgcttg gattaccacg 3720 aactcagagg ggcaaggatt ccatcatggt ggtggttgac cggttttcaa aaatggcgca 3780 tttcgtcgcc tgcaaaaaga cagcagatgc cagccatgtt gccgacttgt tctttcgcga 3840 agtagtgcgc ttacatggag ttccaaagac catcacgtca gatcgtgacg tcaagttcgt 3900 aagccatttt tggaggactt tgtggaagaa atttgacacc aaactgcagt tcagcagtgc 3960 attccatccg caaacggacg gacaaacaga ggtggtgaat cgtactctgg gaaacatgtt 4020 gcgatgcatc agtggagaaa aaccaaaacg atgggacctt gatttggctc aagcagagtt 4080 cgcatacaac agtatgacca atcgctcgac aggaaaaccc cctttcgagg ttgtatatac 4140 tcagcaacca aaacatgcgc tggatctggt cacattacca atccaaccaa aagtcagtag 4200 agctggggaa aatctagctg aaagggttca acaactacat tcggaggtac gagctagctt 4260 ggagactgct aatgctgctt acaaatctgc tgcagaccag catcggcgca agaaagagtt 4320 cacagaggga gatttggtga tggcctacct gcggaaaaat cggctccctg gaacacgaac 4380 taagctacaa caacgaaaat atggaccctt cagagtcgcc aagaaaatta atgacaatgc 4440 ctatacctta cagctaccag atgattggaa catttccaaa accttcaatg tggctgatct 4500 gtcggagtac catgaggacg tgcctttgta tgcggataac tcggggcgag tttgtttcca 4560 agaggaggag aac 4573 // ID CPTAN repbase; DNA; EDCOT; 351 BP. XX AC M17141; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 11-NOV-1996 (Rel. 1.1, Last updated, Version 1) XX DE C.pepo tandemly arranged repetitive DNA, copy F. XX KW CPTAN; Repetitive sequence; tandem repeat. XX OS Cucurbita pepo OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Cucurbitales; Cucurbitaceae; Cucurbiteae; OC Cucurbita. XX RN [1] RP 1-351 RA Leclerc F.R. and Siegel A.; RT "Characterization of repetitive elements in several Cucurbita RT species."; RL Plant Mol. Biol 8, 497-507 (1987). XX DR GenBank; M17141; Positions 1 351. XX SQ Sequence 351 BP; 109 A; 59 C; 69 G; 114 T; 0 other; aagcttagga caatctttag tggatatggt atgatactaa aacgagaaaa caacttttca 60 gatcgagtta acgaccctgt cccaatgggc caaaaagttc ctatgttaac acctatggat 120 tttgggtgaa aaatggcccg gaagcgaaag tgaaaaaatt tcgtatttta accatttata 180 tgtgtaagac tcttaaactt gagcgtttcc ttacagattc atcgaaaaac atcgaaagaa 240 acaaaggttt ttcacatagt cattttggtg cctccacgag ggtcttttcg taatggttga 300 ggttgtgaag tcttttcgac acgagtaaat gttttttttc ttccatattt t 351 // ID Copia3-PTR_I repbase; DNA; EDCOT; 4407 BP. XX AC scaffold_1009; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia3-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4407 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4407 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 234-234 (2007). XX DR Genome; scaffold_1009; Positions 6101 1695. XX CC Positions [1891-2376] - Integrase core CC 'TATTT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 3374..4336 FT /product="Copia3-PTR_I_3p" FT /translation="MLIVCLYVDDLIYTGNNYAMFEKFKESMMIEFEMTDL FT RMMHYYLGLEVVQSTTCIFISQKKYVQEILERFQMNNCNSVGTPTEVGVKL FT FKDPEGKRVDSTNYKQIVGSLMYLTATRPDIMYAVSLISRYMENPKEIHLL FT AAKRIFRYLQGTADFGLLYKKGEHSDLMGFTDSDYAGDQDDRKSTSGYVFM FT LGTGVVSWSSKKQPIVTLSTTEAEFVAAASCACQAIWLRRILEEIQFKQQG FT ETSIYCDNSSTIKLSRNPVLHGRSKHIDVKYHFLRDLAKDEVINLIFCRSE FT DQVVDIFTKPLKTPLFHKLRELLGVCSLG" FT CDS join(280..1887,1891..3261) FT /product="Copia3-PTR_I_1p" FT /translation="MASENNFVQPSIPRFDGHYDHWSMLMENFLKSKEYWS FT IVDSGIPELTEGVVLTNAQRTEREGLQLKDLKAKNFLFQAIDRSILETILC FT KDTSKHIWDSMKKKYQGSTRAKRQQLQALRSEFETLRMKSGESVTNYFSRT FT MVIVNKMRTHGDKTEDVIIVEKILRSMTPKFNFVVCSIEESNNIEELSIDE FT LQSSLLVHEQKISQQDKEEQLLKASIDYHPTPVKAYRGRGRGRNDYKRNDN FT RGHIQQFQHHRGHHQQNQHHENHFHERGRRRGGHQNGGRSEHHSISADKSN FT VECYRCHRYGHFQSDCKTNMTRGYGEKLNFAEKEEEISLLMVCHAKEETNR FT NLWYLDTGCSNHMCGDKSVFSVLDESFRDDVKFGDNSKVSVMGKGRVSIQT FT KEDSTHNISNVLYVPDLKTNLLSVGQLQERGYEISIKNGVCQIRDDNLSLI FT AQINMTTNRMFPLYLNSTIQSCFLATMNNDAWLWHLRYGHLNFGGLKTLQK FT KRMVTGLPKIAAPSSVCEECVVSKQHRKPFPKFKSLRAKMLELVHSDLCGP FT INPTSNGGKRYIITFIDDFSRKIWVYFLQEKSEAFASFKHFKALAEKEVGL FT PIKILRTDRGGEYNSLEFTEFCKDHGIKRQLTAAFTPQQNGISERKNRTIL FT NMVRSLLNMSGIPRDFWPEVVTWSIHILNRSPTFAVQNMTPEEAWSGKRPA FT VDYFKIFGCIAYAHIPDVKRKKLENKGEKCVFLGVSDHSKAYKLYNPNTKR FT IVISRDVIFDEDQFWSWHSSVPNKPLVLDTDIDNDNEEGLQAQPTVESSQL FT VDDQRPLHARTRPAWMADYEVAGIAQDEDPLTYFALFSDCDPTTFEVAVKT FT STWRQAMNEEIAAIERNNTWELTQLPEGHKTIGVKWVYKTKLKENGEIDKH FT KARLVAKGSKQEFSVDYKEVFSPVARMDTIRLVLAMAAQNSWSIFQLDVKS FT AFLHGELEEQVYIDQPPGYVKLGAEDKVYKLKKGALWT" XX SQ Sequence 4407 BP; 1454 A; 776 C; 998 G; 1179 T; 0 other; gtggtatcag agcgtggtta gagtgaaatt aaaagaattg aaattgagag ttttgtgagg 60 gagagacagc agtagcttca cccactaaat tgagagagaa cgaagctttg tgaaagttca 120 cccactaaat tgagagcttt gtgagagaga acggagcttt gtgagagaga acccactaaa 180 ttgagagctt tgtgagagag aatccaccaa atttgtgaga gagaacccac caaattgaaa 240 gctttgtgag agaaacaaca gtagcttcat caagcatcaa tggcgtcaga aaacaatttc 300 gttcaacctt caattccacg gtttgatggt cactacgacc actggagcat gctaatggag 360 aatttcttga aatcgaaaga gtattggagc attgttgatt ctggaatacc agaattaacc 420 gaaggggtcg tgctgacaaa tgcccagaga actgaacgag aagggttaca attgaaggat 480 cttaaggcca aaaattttct atttcaggcc atagatcgct caattctgga aaccattttg 540 tgcaaagaca catcaaagca catttgggac tccatgaaaa agaagtatca agggtcaaca 600 agagcaaaaa ggcagcaact tcaagcactt cgttctgagt ttgaaacact ccgaatgaag 660 tcaggggaat cagtcacaaa ttacttctca cggacaatgg taattgtcaa caagatgcga 720 acccatggag acaaaactga agatgtcatc atcgtggaaa agattcttag atccatgaca 780 ccgaagttca attttgttgt ctgttccatc gaagagtcta acaatattga agaactgtca 840 atcgatgaat tacagagttc tttgttggtt catgaacaga agatcagcca acaggataaa 900 gaagaacaac tgttgaaagc ctcaattgac tatcacccta ctccagtcaa ggcttacaga 960 gggcgaggca ggggacgaaa tgactacaaa aggaatgaca atcgtggtca catacagcag 1020 tttcagcatc atcgtggaca tcatcagcag aatcaacatc atgaaaatca ttttcatgaa 1080 agaggaagaa gaagaggagg tcatcagaat ggtggcagat cagaacatca ctcaatctca 1140 gcagacaaat ccaatgtgga atgctacaga tgtcataggt atggtcattt tcagtcagat 1200 tgtaaaacta acatgactag aggctatggt gagaaattaa actttgctga aaaagaagaa 1260 gagatttcgt tgttaatggt ttgccatgca aaagaagaaa cgaataggaa tttgtggtat 1320 ttagacacag ggtgtagtaa tcacatgtgt ggagataaat ctgtgttctc tgtcttggat 1380 gaatcatttc gtgatgatgt gaaatttgga gacaattcta aggtctctgt gatggggaaa 1440 ggaagggtct caattcagac taaggaagat tccacacata atatttctaa tgtgctttat 1500 gtaccagact tgaagactaa tttactcagt gtagggcagc tgcaagaaag ggggtatgaa 1560 atttctatca agaatggggt atgtcaaatt cgggatgata atttgagctt aattgctcaa 1620 ataaacatga caaccaaccg aatgttccct ctctacctga acagcaccat tcaatcttgt 1680 ttcttagcaa caatgaataa tgatgcatgg ctatggcatc ttcgttatgg tcatctaaat 1740 tttggtggac tgaagaccct acaaaagaag aggatggtga ctggcttacc aaaaattgca 1800 gccccttcat cagtttgtga agagtgtgtt gtcagcaaac aacaccgaaa gccatttcca 1860 aagttcaagt ctttgagagc aaagatgtag ctggaactgg tgcattctga tctttgcgga 1920 ccaattaatc caacctccaa tggtggtaaa aggtatataa ttacctttat tgacgacttt 1980 agtcgaaaaa tttgggtcta tttcttgcag gaaaaatctg aggcatttgc ctctttcaag 2040 catttcaaag cattggctga aaaagaggtt ggattaccaa tcaaaattct tcgcacggat 2100 cgtggaggag aatacaactc tcttgaattc acagaatttt gcaaagatca tgggattaaa 2160 agacagctta ccgcagcctt tactccccag cagaatggga tttctgagag gaaaaaccga 2220 accattctaa acatggtgcg aagtctgctg aatatgagtg gcattccaag agatttctgg 2280 cctgaggtgg ttacttggag cattcatatc ttgaacagaa gtccaacatt tgctgttcaa 2340 aatatgaccc cagaggaggc ttggagtggc aaacgaccag cagtggatta cttcaagatt 2400 tttgggtgca ttgcttatgc ccatattcca gatgtgaaga ggaaaaagct ggagaacaag 2460 ggagaaaaat gtgtttttct tggtgttagt gaccattcca aagcctacaa gctttacaat 2520 cctaacacta agagaattgt gattagccgt gatgtaatct ttgatgaaga ccaattctgg 2580 tcatggcaca gcagtgttcc caacaagcct ttggtgctag atactgatat tgataatgat 2640 aatgaagaag ggctgcaagc acagccgaca gtagagagtt cacaactagt ggatgatcaa 2700 aggcctttac atgcaaggac aaggcctgca tggatggcag attatgaagt cgctggaatt 2760 gcccaagatg aagacccact cacctatttt gccctatttt ctgactgtga tcctacaacc 2820 tttgaagttg ctgtcaaaac atccacatgg cgtcaggcaa tgaatgaaga gattgcggca 2880 attgaaagga ataatacctg ggaattgact cagcttccag aagggcacaa aaccattggt 2940 gtcaaatggg tgtacaagac caaattgaag gaaaatggtg aaatcgacaa acataaggcc 3000 cggttagtag ccaagggctc caaacaagaa ttcagtgtgg actataaaga ggtgttctct 3060 cctgttgcac gcatggacac aatcagattg gtgcttgcaa tggcagctca gaactcatgg 3120 tctattttcc agctagatgt gaaatcagcc ttcttacatg gagagctaga ggagcaggta 3180 tatatcgatc aacctcctgg ttatgttaaa cttggtgctg aagataaagt atataagtta 3240 aaaaaaggcg ctctatggac ttaaacaagc tcccagagct tggtatagtc gcatagaggc 3300 ttatttttta cgggagggat ttcagaaatg cccacatgag catacatttt ttgtcaaaac 3360 tgaaaatgga aaaatgctga ttgtgtgcct atatgtggat gatttgattt acactggaaa 3420 taattatgcc atgtttgaga agtttaaaga gtctatgatg attgaattcg agatgactga 3480 tctcaggatg atgcattact atctcggcct tgaggtagta caatcaacaa cttgcatttt 3540 catttcgcaa aagaagtatg ttcaagaaat cttagaaaga tttcaaatga acaattgtaa 3600 ctcagttggc acacctactg aagttggtgt gaaacttttc aaggatccag aagggaagag 3660 ggttgacagt acaaactaca aacaaattgt agggagccta atgtatttga cagcgacgag 3720 gcctgacata atgtatgctg tcagtctcat tagtagatac atggaaaacc ctaaagagat 3780 tcatcttctt gctgcaaaaa gaatctttcg ttacctacaa ggtactgctg attttggatt 3840 actctacaaa aaaggagaac attcagattt aatgggtttt actgatagtg actatgctgg 3900 ggatcaagat gatcggaaaa gcacttcggg gtatgttttt atgctgggta caggagtcgt 3960 ctcatggtca tccaagaaac aaccaatagt taccttatca acaaccgaag ctgaatttgt 4020 agctgcagct tcatgtgcat gtcaagcaat ttggctaagg aggattcttg aagaaattca 4080 gttcaaacaa caaggagaaa cttcaattta ttgtgacaac agctcaacaa taaaactatc 4140 aagaaatcct gtgctacatg ggagaagcaa gcacattgat gtcaaatacc atttcttaag 4200 ggatctcgca aaagatgaag taattaatct tattttctgc aggagtgaag accaagtggt 4260 tgacatattc actaagccgc ttaaaacacc attgtttcac aagctaaggg agttgcttgg 4320 agtgtgttct ttgggatgat tgtattaaaa gctatcttat tattctttaa actgaatgtc 4380 tgaaattgtt cagtttaagg gagggat 4407 // ID PAP22_BP repbase; DNA; EDCOT; 582 BP. XX AC AJ414553; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Beta procumbens AluI family repetitive DNA, PAP22_BP. XX KW SINE1/7SL; SINE; Non-LTR Retrotransposon; Transposable Element; KW AluI family; PAP22_BP; Repetitive sequence; dispersed. XX OS Beta procumbens OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC Caryophyllales; Amaranthaceae; Beta. XX RN [1] RP 1-582 RA Dechyeva D.; RT "Direct submission."; RL Direct Submission to Genbank (10-SEP-2001). XX DR Genbank; AJ414553; Positions 1 582. XX SQ Sequence 582 BP; 139 A; 111 C; 151 G; 181 T; 0 other; ctttagagca tttagagtta ggatagcatg gtttttcctt cctttggatt taaattatac 60 ttcacgagtg tttggttgtt tttgatgtat ttcaagagaa ttggcacatg ttggagtact 120 tttgtgatct agggacttgg ggcatgttcg agggtgcgtg gctcgtactt tggagatgct 180 cgagtgagtc aaccttgggg gaatttaagg aaaaaggcca ccacggccgt ggcacataca 240 ccacggtcgt gggcacctgt agcaagcaaa acagaagatt gaagaattgg gactgattcg 300 acgaagtcag gtcaccatgg ccgtggtgat tttgccacga ccgtggctcc tgactctcat 360 agaatcagta cgtttgaagt acagttactg cctggacaat tttaaggcgc cacgaccatg 420 gctcctgact ctcatagaat cagtacgttt gaagtatagt tactgcctgg acaattttaa 480 ggcgcacgac cgtggcgacc tgaattcggg ttttgaccct gtttttccgt cttagtttaa 540 tgaacctttt atttagtttg tagagttttt agtcgacatt ag 582 // ID GmCOPIA11_LTR repbase; DNA; EDCOT; 374 BP. XX AC . XX DT 21-JUL-2008 (Rel. 13.09, Created) DT 21-JUL-2008 (Rel. 13.09, Last updated, Version 1) XX DE GmCOPIA11 LTR. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; KW retrotransposon; soybean; GmCOPIA11_LTR. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-374 RA Wright L.N. and Laten H.M.; RT "Intact, full-length transposable element consensus sequences in RT Glycine max assembled from robust collections of BAC-ends."; RL Repbase Reports 8(9), 904-904 (2008). XX DR [1] (Consensus) XX CC Internal region is related to AtCOPIA78. XX SQ Sequence 374 BP; 112 A; 61 C; 57 G; 143 T; 1 other; tgttgaaata taaacttgat ttgggcctaa attaattatt tggttccttg gacttagtta 60 ttttgggctt aagtaattat gggtcatgtt tctagagaat tcttgtagtg tttggagtgt 120 ctagatattt cttatggttk taatattctc tagaatactc tttggatctc tagagttgag 180 aactctctag aattagtgtg tctagagttc tccttagagt agtataaata gagatgtaat 240 cctacacatt tgtatcaagc aaaaatacaa agttctctcc tccataaaga attctccttc 300 ctatcaagtt tctattcaaa gtctccaata ttcctaaaca cttttcctaa acataaaaag 360 ccttatttcc aaca 374 // ID Gypsy-8_Mad-LTR repbase; DNA; EDCOT; 281 BP. XX AC ACYM01138672; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-8_Mad-I; KW Gypsy-8_Mad-LTR; Gypsy-8_Mad_. XX NM Gypsy-8_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-281 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1411-1411 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01138672; Positions 548 268. XX SQ Sequence 281 BP; 81 A; 43 C; 56 G; 101 T; 0 other; tgttaggctc gtgattatct taatcacagt ttattagtta gtaagttttt aatgagtttt 60 attaagcttt gtttagttgg gttgttatgc cagctggaag tgagagtttg agaaagaata 120 tatgtagcca attgtgggtg aaaagaagtc agtcaatttg ataaaagaaa atacattaca 180 aaaaatatcc ttctctctct agcccttctc tcgacatact ccctccgcca ttgttacata 240 cttgcaggtt tgagttaagg tcctgagatt ggatcttatc a 281 // ID HELMET4 repbase; DNA; EDCOT; 5649 BP. XX AC AC134242; XX DT 19-JAN-2007 (Rel. 12.01, Created) DT 20-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Helitron-type sequence. XX KW Helitron; DNA transposon; Transposable Element; HELMET4. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5649 RA Jurka J.; RT "HELMET4: Helitron-type sequence from barrel medic."; RL Repbase Reports 7(1), 33-33 (2007). XX DR EMBL/GenBank/DDBJ; AC134242; Positions 41269 46917. XX CC Based on well-preserved ORFs, it appears to be a relatively young CC element. The sequence may be incomplete. XX FH Key Location/Qualifiers FT CDS 481..1959 FT /product="HELMET4_1p" FT /translation="MDLGHPNFECEKCGSTMWYNERADKPRRPRNPTFSLC FT CLKGDVSLEFLEQPPDYLKELLAYKGGRHSVKFREKIRAYNSIFAFTSMGA FT KIDNTVNLRPGPYVYKISGQNYHRIGGLIPGQGKQPKFSQLYVHDTENEIQ FT NRLSSLNGGKTARDLDADIVRRLKDMLDMNNSVAKLFRMARDRLSAPDNKE FT VRIRLIGTRSNDSRQYTTPTATEIAGLIVGDFGESNGRRDIVIEHKTDGLQ FT RIKEYHPKFMAMQYPLLFPYAEDGFHLDIYYSQNHAKRKKKKKRKKVTLRE FT YYAYRIQQRPCEANTLIIGGRLFQQYVVDAFTAIEEERLRWVRQNQTVLRT FT DLYRNVCDAVVRGDTIAAATGKRIVLPSSFTGGPRYMVQNYQDAMAICRTF FT GNPDIFMTFTANPKWPEIQYMLQKIPGQSVDDRPDIKTRVFKMKLDQLMKH FT IVEGQYFGKIISGKSTWNKCSHILKKKKIKDQFDSNCLFNLYDTYMLY" FT CDS 3984..5342 FT /product="HELMET4_3p" FT /translation="MLACINIFSIFFLISFLTGIASLLLPGGRTAHSRFKI FT PLEIYEDSTCSINQNTHLADLMVQTDLIIWDEAPMTQRYAFEALDRTLKDI FT IGFKFPDRAEQPFGGMTVLLGGDFRQILPVIPKGRIHDIIQSCINKSFLWD FT YCTIFSLSKSMRVRNTTSTGKEHDVIREFNKWLLQLGDGNIQAQSRRGEDF FT ASWTTIPDQYLIPPMGDPLKQIVDNTYPELKSHLWDEEYFRERAILTPLNE FT TVDEINNYIVQFTDGETKQYRSSDEIDKTTDNISDQELMYPVEFLNSLNIN FT GFPRHCLELKEGMPIMLLRNINPALGMCNGTRLIITHLGERVIEAKIITGS FT NVGSKVLIPRIVLTSNDSKWPFLLRRRQFPIKVCYAMTINKSQGQSLNYVG FT LYLPRPVFSHGQLYVAFSRVTSPEGLKILIVERDENYVQYTKNVVYHEVFS FT GLPQCKYI" FT CDS join(1940..2629,2633..3736) FT /product="HELMET4_2p" FT /translation="MIHTCYTNKDLFFFSLFKLTAIYTIEFQKRGLPHAHI FT LLWLHPSNKYPTPEDIDKIITAEMPSKEDDPECFNAVKQFMLHGPCGDANI FT NAPCMIDGICSRKFPKSFFDETTIDRDGFPTYRRRDDGRHVKKGDINLDNR FT YVVPYNRGLLLAFQAHLNVEWCNKSRAIKYLFKYLHKGPDRAIMVIEDNVL FT GNRSTNATHITMVDEVKTFLDCRYVKVVIGNTLIMITMNLPFHLLCIIHCR FT YVSACEACWRIFNFDIHYRNPAVMRLSFHLPEEHSITLRDSEQLSDVISKE FT GVEHTMFTEWMLMNSMSSEARTLTYSEFPKKFVWDETKKKWKKRKAGRTIG FT RIYYAHPTSGEKYYLRILLNIVHGPTSYEEIKTVGGVTYQTFKETCNALGL FT LNDNREWNDALNEASQWATGTQLRELFVTILLYGEVADIGKLWETNWKTLS FT DDIVYKKRILFQHSRLELNDEQIQSYCLIEIDKILVRAGSYLSDFDGMPLP FT NSESFEATENRLIVEELSYNVDDLKKEHERCHPLLNEQQIDIYNNVINAVN FT TNIGGLYFVYGHGGTGKTFLYRTIIAKLRSEKKIVLAVASSGNPSLFQSLI FT " XX SQ Sequence 5649 BP; 1992 A; 980 C; 1048 G; 1629 T; 0 other; taaaaatcta acatttacta cttctattac atctgcttac tcttcgacag gaaataagac 60 atccaaaccc ataacaacac ataaaaggac aaataccaaa agtattcaca gtacacatcg 120 aatccaacac aaaagtggtt agtgttatct ctttgcatga ccaatttaat agtagcttat 180 aatatttaaa tacaatattt aaatgcacaa tgaaaccatc atagctgcat ttattacctt 240 ttctgactcc cggtgcttaa gactctaaaa aacgactaac gtgaactgat aatattcgat 300 atatatactc tcaacaggaa acaacaacca acaaactggg tcagtcgcat ctagaacaca 360 cgacagaagg atgaatccaa caaatggtta gtgtggctta tttctttaaa caacttagca 420 ttgcaaaaac caataatctt tcactttaaa atctcatttg cagaccatgt ccaaacttat 480 atggatctcg gccatccaaa ttttgaatgc gaaaaatgtg gaagcacaat gtggtataat 540 gagagagctg ataaaccacg tcgaccaagg aacccaacat tctctctttg ttgcctgaaa 600 ggggatgtct ccctagagtt tttagagcaa ccaccagact acttgaagga acttttagct 660 tacaaaggtg gcagacactc cgttaaattt agagaaaaaa tacgggcata taattctatt 720 tttgcattca catccatggg tgctaaaata gacaacacag tgaacttacg tccaggccca 780 tatgtgtaca aaattagtgg tcaaaactat catagaattg gtggactcat acctggccaa 840 ggaaaacaac ctaaattctc ccagctttat gtccatgata cggagaatga gatccaaaat 900 cgattgagtt cgctgaatgg tgggaagact gcacgagacc ttgatgcaga tattgtccgg 960 cgcctaaagg atatgctcga catgaataat tctgtagcca aattatttag aatggcaagg 1020 gatagattat ctgcaccgga caacaaagaa gttcgcataa ggttgattgg cacaagatca 1080 aatgattcaa gacaatatac aacacctacc gcaacagaaa ttgctggtct cattgttgga 1140 gattttggtg aatcaaatgg acgaagagat atagttattg agcataaaac agatggcctg 1200 cagagaataa aagaatatca tccaaaattc atggcaatgc aatatcctct gttatttcca 1260 tatgctgagg atggatttca cctagacatt tattattctc aaaatcatgc aaaaagaaag 1320 aaaaagaaaa aaagaaaaaa agttaccctg agagaatatt atgcttaccg gatacaacag 1380 aggccctgtg aagcaaatac tcttattatt ggtggtcgac tgttccaaca atacgttgtt 1440 gatgcattca cggcaataga agaagagcga ctgcgctggg ttagacagaa tcaaacagtg 1500 ttgcgtacgg atctgtacag aaatgtatgt gatgcagttg tgcgtggaga tacaatagct 1560 gctgctactg ggaagagaat cgttttgcca tcttctttta caggtggccc tcgatatatg 1620 gttcaaaact atcaagatgc catggccata tgcaggacat ttggaaatcc tgatatcttc 1680 atgacattta ctgctaatcc aaagtggcca gagattcaat acatgcttca gaaaatacca 1740 ggtcaatctg tcgatgatag accggacatc aagacaagag tttttaaaat gaaacttgac 1800 cagctaatga aacacatagt ggaggggcaa tattttggta aaattatatc aggtaaaagt 1860 acatggaata aatgttctca cattctaaaa aaaaaaaaaa ttaaagatca atttgattca 1920 aattgtttat tcaatctata tgatacatac atgttatact aataaagatt tgtttttttt 1980 ctctcttttc aaattgacag ccatttatac catagagttt caaaaaagag gtctgccaca 2040 tgcacacata ctattatggt tgcacccaag caataagtat cccaccccgg aggatataga 2100 taagattatt actgcagaaa tgccatctaa ggaagatgat ccagaatgtt ttaatgcggt 2160 aaaacagttc atgctgcatg gaccgtgtgg agatgcaaat ataaatgcac cttgcatgat 2220 tgatggtatt tgtagtcgaa aatttcccaa aagttttttc gatgaaacaa caatagatag 2280 agatgggttc ccgacgtata gaaggaggga cgatggaaga catgtgaaaa aaggagatat 2340 caatttagac aatcggtatg tggttccata caatcgaggt ttgttgctgg catttcaagc 2400 acatctaaat gttgaatggt gcaacaagtc aagggccata aagtacctat ttaaatatct 2460 tcacaagggc ccagatagag caataatggt aatagaagat aatgttttgg gcaacagaag 2520 cacaaatgca actcatataa caatggttga tgaggtcaaa acattcttgg attgtaggta 2580 cgtcaaggta gttataggga atactctaat aatgatcaca atgaatttat aaccatttca 2640 tcttttatgc attattcatt gtaggtatgt atcggcatgt gaagcatgtt ggaggatatt 2700 caattttgac atacactaca gaaatccggc tgttatgaga ttgagctttc atttgccaga 2760 agaacactca atcactctaa gagattcaga gcaattgtca gacgtaattt caaaggaagg 2820 agttgaacat actatgttta cagaatggat gctaatgaat tcaatgagct cggaagcacg 2880 tacattaacg tattctgagt ttcccaaaaa atttgtttgg gacgagacaa aaaaaaagtg 2940 gaaaaaacgg aaagctggaa gaacaatcgg aagaatttat tatgcacatc caactagcgg 3000 ggagaaatat tacctcagaa ttttactgaa tattgttcat ggtccaacaa gctatgaaga 3060 aataaagaca gtgggagggg tgacttatca gacattcaaa gaaacatgta atgctcttgg 3120 gctattgaat gataacagag agtggaatga tgcattgaat gaagcatcac agtgggccac 3180 aggcactcaa ttaagagagt tatttgttac cattttgctt tatggagaag tggcagatat 3240 agggaaacta tgggaaacta attggaaaac gttgtctgac gatattgtct acaaaaagag 3300 aatattgttt caacactcca gattggagct taatgatgaa cagattcaat catactgctt 3360 gattgaaatt gacaagattt tggttcgtgc tggaagttac ctttctgatt ttgatggaat 3420 gccgttgcca aatagtgaat cctttgaagc cacggaaaac cgacttattg tggaagagct 3480 tagttataat gttgatgacc tgaaaaaaga acacgaaaga tgtcatccat tgttgaacga 3540 acagcagatt gatatatata ataatgttat aaatgctgtc aacactaata ttggtggact 3600 ctacttcgtg tatggccatg gagggactgg caagactttt ctatacagaa caattattgc 3660 aaaactcagg tcagaaaaaa agatagtact tgctgttgct tcttcaggta acccatcact 3720 ttttcaatcc cttatataaa tttacatgtt gtctatttgt acttataaat atgtcagtcc 3780 atacaccctt atttctgcgc ttcattgcaa tatttattgt acaaattact atatgtacca 3840 aattagcaac tattatatgc tataatctat ctaatattat atgcttttct tctacacaaa 3900 atataaaaaa aaacatacaa tttttattca aatatataaa tatatatata tatatataga 3960 tagatagaca tagacacaca catatgcttg catgcataaa tatattttca attttttttt 4020 taatttcatt cttgacaggt attgcatccc tcttgcttcc tggaggaagg accgctcata 4080 gtagatttaa aattcctctt gagatctatg aagacagcac atgctcaata aaccaaaata 4140 ctcatctagc tgatctaatg gttcaaacag atctcataat ctgggatgaa gcaccaatga 4200 ctcaaagata tgcttttgaa gctcttgata ggacacttaa agacataatt ggtttcaaat 4260 ttccggatag ggcagagcaa ccatttggag gaatgacagt tcttcttgga ggagatttta 4320 ggcaaatact tcctgtaata ccaaaaggtc gaatacatga tataattcaa tcatgcatca 4380 acaagtcttt tttgtgggac tactgtacaa tattttcatt gtccaaaagc atgagggtca 4440 gaaatactac ctctacaggc aaagaacatg atgtgatacg tgaattcaat aaatggctac 4500 ttcaacttgg tgatggaaac attcaagcac aaagccgacg tggtgaagat tttgcatcgt 4560 ggacgacgat accagatcaa tatcttatcc caccaatggg tgatccactc aaacaaattg 4620 tggataacac ttacccagaa ttaaagagcc atctgtggga tgaagaatat ttcagggaaa 4680 gagcaatact cactcctcta aatgaaacag ttgatgaaat caataattat attgttcagt 4740 ttactgatgg agaaacaaaa caatacagaa gctcagacga gattgacaag acaactgaca 4800 acatatcaga tcaagagctc atgtatcctg tggaatttct aaactcctta aatattaatg 4860 gatttccaag acattgtttg gagcttaaag aaggaatgcc tattatgtta ttgaggaata 4920 tcaatccggc attaggaatg tgtaatggaa caagacttat tattacgcat ctaggagagc 4980 gagtaataga ggctaaaata attacaggat ctaacgttgg ttcaaaggtg ctaatcccca 5040 gaattgttct tacttctaac gactctaaat ggccttttct gttgcgcagg aggcagtttc 5100 caattaaggt gtgctatgca atgacaataa acaaaagtca aggccagtca ttaaattatg 5160 tgggattata tttgccaaga cctgtattta gtcatggaca actatatgtt gccttttcaa 5220 gagtcacttc cccagaggga ctgaaaattc taattgttga gcgtgatgag aattatgtac 5280 aatacacgaa aaatgtagtg taccatgagg tatttagtgg tcttcctcaa tgtaaatata 5340 tttgatgcac tgttttcaaa tctatctatc attcacaata actttagcaa ctacgttatt 5400 cattgttaac taacacactt cgatttgtac cattgatttt ttacaataat aaccgcgaat 5460 cccaagtaat cggacttttt ataacagaat ttaaacttca gaaccttaat aaagtaaaat 5520 cctacaaaca caacaataac catttgaatc gtttcaatgg tgaaaaaact tattaatggt 5580 tacaaccgta agtttctatc tacacatcaa ctaatagcat aaatggttcc aaatgagcag 5640 ccaatgtta 5649 // ID Copia-71_Mad-I repbase; DNA; EDCOT; 4522 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-71_Mad_; KW Copia-71_Mad-LTR; Copia-71_Mad-I. XX NM Copia-71_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4522 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1680-1680 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1833-2360] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 120..2696 FT /product="Copia-71_Mad-I_1p" FT /translation="MAANSSNSSSPVAAHPSSPAIADPSSSLPPHLNPSPM FT NPNSSFQASINSITIQNIGSMIQTKLKRHNYLVWRSLFEPIFRRYKLTGMV FT DGSEPPPPQFLADLSGNLSSIPNPAFEIWYEKDQNILIWINSTLSEDLIPF FT TVGVQSSRELWQNLEKRFGGVSRSHIHQLRSNLQLMSKGTSTISEYLQRIK FT EVSDALAAAGAPVEESDLLHLILNGLPDDYDSFVDSIQFRLADTTVDDLHG FT FLLSKEMALARRKQSQGSSEPYQAFTSIPAASNAPPLLPTPPPHQAYNAQS FT NGSQNSYPGNNRGNFQRNTSQRPYNNRNRSNRFNNSSTNRGGNRGGNRGFR FT SFTSAVIPCQICEDTGHLAIDCSHRMNPNFQGRVPPAKLAMYASSSTSSPP FT PWLLDSGASSHMTNNIHHLQNPQPYTGPDKVYIGDGQGLPILHTGSTLLKT FT PSADFQLKNVLHVPHLKHDLLSANMFLRDNWCSLTLNPFDFHVKDLTTGRM FT LFRAPVSNGLYPFYASSSPAPKVHAHSAIRTSSHVWHQRLGHPTFKTFRSL FT LSKSILPVSNNVQQFFCSNCVLGKCAKLPFQESLCTTSRSLELVHADVWGP FT APVCSVSGYRFYVIFVDDFTKYTWLYPLKHKSEVFHIFVQFQALVENLSGY FT KIGTLRSDSGGEFTSSNFKHHLSLHGIQQQFSCPYTPQQNGCAERKHRHIV FT ETARTLLIASQVPHKFWVEGFLTAVYLINRLPPVNKSSPWEQFFKKVPDYK FT SLRVFGCQCFPWLKPYTNSKLDPKSKMCVFIGYSLAHKGYRCLDPFTNRVY FT LSRHVHFDEHTFPFHDPHLLKSSTPHTPELTHLFPLPFPIFILLILSLPVF FT HHPYLP" FT CDS 2877..4523 FT /product="Copia-71_Mad-I_2p" FT /translation="MQTRSKSGIYKPKALTATTHPLPSHFDSEFIPTTYLQ FT ASKHSQWRAAMQDEFNALQSTGTWQLVPSTSTHNLVGCKWVFRIKRKPDGS FT VDRYKARLVAKGYNQQEGIDYGDTFSPVAKPVTIRIILTLAVQSNWFLHQL FT DVSNAFLHGSLKENVYMAQPPGFIDQDHPTHICHLKKSLYGLKQAPRAWYE FT KLQSALFSMGFQASHSDHSLFVLHKPTLVLVLVYVDDIIVTGPSSSVCNTI FT ISQLSSKFPIKDLGDLHYFLGLEVQKSTSGAFIHQSKYILDLLKRTKMDGA FT KPCATPLSSVKLDHTGSLLSNPEDYRSIVGALQYLTWTRPDLSFAVNLVCQ FT FMHSPREPHFQAVKRILRYLKGTLGFGLWFPKTTSPLLLNAYSDADWAGCS FT WDRRSTGGFCIFLGPCLVSWSAKKQHTVARSSTEAEYRSLAHTAAEITWIC FT QLFSDIGFKLSSLPQIWCDNVSAIALASNPVFHARTKHVEIDYHYIRELVL FT AKLLTVKFVCSADQLADIHTKSLPRPRFLHLRSKLSLQPSPFSLRGCEEQV FT TV" XX SQ Sequence 4522 BP; 1056 A; 1212 C; 801 G; 1451 T; 2 other; atatggtatc actcgcttaa gtccaccgac ttcgatcctc tttctgctat tttctcgctt 60 attttcttac ctaccaaaca ccatagcttc cgtctgcaga tcttcgatct tgttcatcaa 120 tggcggcaaa ttcttcgaat tcttcctctc ctgtggctgc gcatccttct tctccggcga 180 tcgcggatcc ttcctcttcg ctgcctccac atctcaatcc ttctccgatg aaccctaact 240 cctcctttca agcttcaatc aactccatca cgatccaaaa cattgggagt atgattcaaa 300 caaaactcaa gcgtcataat taccttgttt ggcgttctct gttcgaaccg atcttccgcc 360 gctacaagct caccggcatg gttgatggat ctgaaccgcc accgcctcaa tttcttgctg 420 atctttctgg aaatttgtcc tcgattccga atccagcctt cgagatctgg tacgaaaagg 480 atcaaaacat cctcatttgg atcaattcca ctctctctga ggatttgatt ccctttactg 540 ttggtgttca atcctcccgt gaactttggc aaaatcttga gaagcgattc ggtggagtct 600 ctcgttctca cattcatcag ttgcgatcga atttgcaatt gatgtcgaaa ggcacttcca 660 caatatctga atatttgcaa cgcatcaaag aagtttctga tgctctcgct gctgccggtg 720 ccccagttga ggagtcagat ctccttcacc tcattcttaa tggcttgcct gatgactatg 780 attccttcgt ggattcaatt caatttcgtc ttgctgatac tactgttgat gatctacatg 840 gatttcttct cagcaaagaa atggctcttg ctcgtcgcaa gcaatctcaa ggttcctctg 900 aaccgtatca ggcattcacc tccattccag cagcttccaa tgctcctcct ttgcttccta 960 cacctccacc acatcaggcc tacaatgctc agtctaatgg ttctcagaat tcttaccctg 1020 gcaataatcg cggtaatttt cagcggaaca cttctcaaag gccctacaac aaccgtaatc 1080 gttccaatcg gtttaataat tcctcaacta atcgtggtgg aaatcgaggt ggaaatcgtg 1140 gcttccgttc tttcacttct gcagtcattc cgtgtcaaat ttgtgaggac actggacatc 1200 ttgccattga ctgttcccac cgcatgaatc caaattttca aggccgtgtt ccgccagcca 1260 aacttgcgat gtatgcatct tctagtactt cttctccacc accatggcta ctggattccg 1320 gcgcaagctc ccatatgacc aataatattc atcatcttca gaatccacag ccctatactg 1380 gtccagataa agtctacatt ggagatggcc aaggtttgcc aattctccat actggttcta 1440 ctttacttaa aacaccttct gcagattttc aattaaagaa tgtgttacat gttccccact 1500 tgaagcatga tcttctttct gccaatatgt tcttgcgtga taattggtgt tcattaaccc 1560 tcaatccttt tgacttccat gtcaaggatc ttactacggg gaggatgctt tttagagctc 1620 ctgtcagcaa tggtctctat ccattttatg cttcttcttc acctgcaccg aaggttcatg 1680 ctcattctgc aataaggacc tcttctcatg tgtggcatca acgtttgggt catccaacgt 1740 tcaagacttt tcgatcactg ttatccaagt ctatactgcc tgtttctaat aatgttcaac 1800 aattcttctg ctccaattgt gttttaggca aatgtgccaa gttaccattt caagaatctc 1860 tctgtactac ttctaggtct cttgaattgg ttcatgcgga tgtttggggg ccagctccag 1920 tatgttctgt tagtggctat cgcttttatg tcatatttgt agatgatttt accaaatata 1980 cttggctgta tcctctcaaa cataaatcgg aagtgtttca catttttgtg caattccaag 2040 ctcttgttga gaatctgtct ggttacaaaa ttggcacttt aagatcagac tcagggggtg 2100 agtttacaag ttctaacttc aagcatcatt tgtctctcca tggcattcag caacaattca 2160 gttgtcctta cactcctcag caaaacggtt gtgctgaaag gaagcacaga catattgttg 2220 agactgctcg aaccctcctt attgcctcac aagttcctca caaattctgg gttgaaggtt 2280 ttcttactgc mgtctatctt atcaatcgcc tacctccagt caacaagtct tccccttggg 2340 aacaattttt caagaaagtt ccagattaca agtctcttcg ggtctttgga tgtcaatgct 2400 ttccttggtt aaaaccatac accaattcca aattagatcc caagagcaag atgtgtgttt 2460 tcattggcta cagcttagct cacaaggggt atagatgtct agatcccttc actaatcggg 2520 tttatctctc tagacatgtt cattttgatg aacatacatt tccctttcat gatccccacc 2580 ttctaaagtc ctccactccc cataccccag aacttactca cctttttccc ttacctttcc 2640 caatctttat tctcctaatt ctctcccttc ccgtgttcca ccacccatat cttcctcmcc 2700 tactcaacct gcgccagtta ctcaactgag caagttctca acctgagcaa gttcattctc 2760 ctgctccttg tcctgcacct ctgcaacctc cctcacctcc ctcttctcct ctaccagcct 2820 ctcattctct acaccctgca ccacatcctg tacctcctat ttcctctgtt cacccaatgc 2880 aaacccgctc taagtcaggc atatacaaac ctaaggccct tactgccaca acacatcctc 2940 tgccttctca ttttgacagt gagtttatac ctactacata tctccaggct tccaaacatt 3000 cacagtggag ggctgctatg caggatgaat tcaatgcttt acaaagtaca ggcacttggc 3060 agcttgttcc ttctacctcc actcataatt tggttggctg taaatgggtt ttccggatta 3120 agaggaaacc agatggctct gtggatcgtt acaaggctcg actcgttgca aaaggttaca 3180 atcagcaaga gggcattgat tatggtgata cttttagccc ggttgctaaa cctgtgacta 3240 tacgcatcat tctcaccctt gccgtccaat caaactggtt tttacaccag ctggatgtaa 3300 gtaatgcttt tctacatggt tctttgaaag agaatgtata tatggctcaa ccacctgggt 3360 tcattgatca ggatcatcct actcatatct gtcacttgaa gaaatcctta tatggcttaa 3420 agcaagcccc tcgtgcttgg tatgaaaaac ttcaatctgc tcttttctcc atgggatttc 3480 aagcttcaca ctctgatcat agtctgtttg tgctgcataa acctaccttg gttttggttc 3540 ttgtgtatgt cgatgatatc atagtgaccg gaccttcttc tagtgtctgc aacaccatca 3600 tttctcagtt gagctctaaa tttccaatca aggatctcgg cgatcttcat tactttctcg 3660 gtctggaagt tcagaaatcc acctcaggag ccttcattca tcaatccaaa tacatattgg 3720 atcttctcaa gcgtaccaaa atggatgggg caaagccatg tgccactccc cttagttctg 3780 tcaagcttga tcacactggt tccttgttgt cgaatcccga ggactatcgc tctattgttg 3840 gcgccctcca atatcttaca tggacccggc ctgatttatc ctttgcggtt aatctggtgt 3900 gtcagttcat gcactctccc cgggagcctc actttcaagc cgtgaaacgc atcctccggt 3960 atctaaaagg gacacttgga tttggcttat ggtttcccaa aaccacatct cccctacttc 4020 tcaacgccta ctccgatgct gactgggcag gatgttcgtg ggatagacgt tccactggtg 4080 gcttttgcat ctttcttggt ccttgtctag ttagttggag tgcaaagaaa cagcacacag 4140 ttgcccgatc ctctaccgaa gctgagtacc gctcccttgc acataccgct gctgagatca 4200 cttggatctg tcaactcttc tctgatattg gtttcaagtt gtcctccttg ccacaaattt 4260 ggtgtgacaa tgtttctgca attgccttgg cttcaaatcc ggtttttcat gctcgcacaa 4320 agcatgttga aatcgattat cattacatcc gtgagcttgt tttggctaag cttcttactg 4380 tcaaatttgt ttgcagtgcg gatcaattag cggatattca caccaaatct ctgccaaggc 4440 cacgttttct tcatcttcga tccaagcttt cacttcaacc ttctccgttc agcttgaggg 4500 ggtgtgaaga gcaagttacc gt 4522 // ID GYPSY1GM_LTR repbase; DNA; EDCOT; 370 BP. XX AC AF541963; XX DT 30-AUG-2005 (Rel. 10.08, Created) DT 30-AUG-2005 (Rel. 10.08, Last updated, Version 1) XX DE GYPSY1GM: Gypsy-type LTR retrotransposon (LTR portion). XX KW Gypsy; LTR Retrotransposon; Transposable Element; GYPSY1GM_LTR. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-370 RA Graham M.A., Marek L.F. and Shoemaker R.C.; RT "Organization, expression and evolution of a disease resistance RT gene cluster in soybean."; RL Genetics 162(4), 1961-1977 (2002). XX DR Genbank; AF541963; Positions 39430 39061. XX CC LTRs are identical. XX SQ Sequence 370 BP; 115 A; 58 C; 79 G; 118 T; 0 other; tgtaacgaat ggaatgtcac gtggggagaa ggttaacaat actgctgagt catcaagtga 60 gagaggattg cataacaaac ttgctgattt tgaggaattg ggacgtggga agagagagaa 120 gaaaccaagt tggaaaataa cggaatccca ctagtgtata agggaaagta gtgggagtgt 180 gataggcatg atgtatgatg aatgaaaatt ctcttcctct ctgattattc tctcttccat 240 tctgaatttc ttttgcatct tgtacttttg ctcttatttt cacactgaaa actaagagtt 300 gtatccatca ataaaagtac ttcgtccctt tccaattgaa ttactgtttc attaattact 360 tagcattaca 370 // ID Copia19-VV_LTR repbase; DNA; EDCOT; 259 BP. XX AC AM447619; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia19-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-259 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-259 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 686-686 (2007). XX DR Genbank; AM447619; Positions 1705 1963. XX SQ Sequence 259 BP; 86 A; 48 C; 38 G; 87 T; 0 other; tgttaagcta accaatttca gttaggaagt tagctaacct gtaactatgg tcaggtcagt 60 tagtaactaa agtcagttgg taaccaaagt taaactccag aagttttgat ataaaaacaa 120 atgtaaatca atcagatgag ttagtaaaaa aagcaagaat acatttcagt tccagagttt 180 ccaatactct gttttctctt cgtcatactc tgtttttctg ctacagccct gttcttttca 240 ttttctcttc aacaaaaca 259 // ID Copia50-PTR_I repbase; DNA; EDCOT; 4285 BP. XX AC scaffold_1819; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia50-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4285 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4285 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 280-280 (2007). XX DR Genome; scaffold_1819; Positions 9047 4763. XX CC Positions [1643-2044] - Integrase core CC LTRs are 88% similar to each other. XX FH Key Location/Qualifiers FT CDS join(35..2044,2048..4273) FT /product="Copia50-PTR_I_1p" FT /translation="MAGVEGDQSKTLAVVKPTTRGASIPIHYPMLSETNYG FT IWAVKMKIILRSLGVWSVIEGADTDDDKDQGAMVAISQAVPDDVMMAIAEK FT QTAKEAWDALREMRIGEDRVKKARVQVLKRQLYKVHMQDSETVNEYSMKLT FT ALVGEIRSLGAKLEESEVVEKLFSSVPDRFLQIIGTIEQFGDVDTMSVSEA FT IGRLRTFEEGLKGRSHTESTGEQLLFTQAEREARTPKAKKYESFSNNKRGG FT RHWRGHGSGRGYGGGRGNGERTNEDRKPRNFDKSKVKCFNCNEFGHFAKDC FT SKPNRRERANFVTTQTDDEPALLMAETCVISHSIQNEHVLLHEDKVVPKIK FT GTREKAWYLDTGASNHMTGCIEKFAEIDTTITGSVKFGDGSTVKIQGRGSV FT LLEDFTGEHRILTNVYYIPMLKSNIISLGQLDENGCKVVIEGGVMTILDRL FT QRLLAKVKRSSNRLYVLNIAPALPECFLVRSKEEAWRWHARYGHVNFHALK FT SLSQKQMVHGLPIIEHEDRICDGCLIGKQQRKPFPAESNFRAEYPLELWHI FT DLCGPITPTTNGGKRYFMLIVDDCTRFMWQVLISSKAEAFESFKRIKAAAE FT MEKGCKLKAFRSDRGGEFTSNEFKGFCELNDIKHYLTAPYSPQQNGVVERR FT NQTVVGMARSLLKSKSVPGEFGEAVSTAIYLLNRAPTKSLVDKTPYEAYYN FT RKPRVEHLRIFGCIAHVKNVTPHLPKLADRSKPMVFIGYDLNTKGYRMFDP FT KTKQVVVTRDAVFDEEKKWDWTDSSATESKPAKDIFTVLYFPVAVSSDAAH FT QRIEEEMLYPNMASPQPGFYQSGEPENTSAGSNRADGFGSGNAQTPVSFPV FT EQRASEFIHPEASEVGPRGKRDLNSLYDKTIPTELDYSGLCLLGEEEPTSY FT EEARTDSAWRKAMEEEISSIQENATWRLVALPENQKPIGLKWVFKLKKDTQ FT GRIIKHKARLVAKGYVQKHGIDFDEVFAPVARLETVRLLISIAAQKGWQVH FT HMDVKSAFLNGELEEDVYVLQPPGFEIKGEEYKVLKLYKALYGLRQTPRAW FT NSKLDKSLKALGFERCLLEHAMYTRKEGNLTVGVYVDDLIITGGCIRDIDK FT FKSQMKGLFRMSDLGLLSYYLGIEVCQTPTRITLKQSGFAKKVLEKCGMKD FT CNSTQIPMEPRLKLNKDSLEPPVDVTLYRSIVGSLRYLLHTRPDLAFAVGM FT VSRFMEKPTLEHMAAVKHILRYVKGTLNFGFVYEKKEGDLELIGFSDSDLA FT GDNNDRKSTSGLIFFLGANPISWCSQKQKVVALSSCEAEYIAGCAAACQGV FT WLSRLLGELLKAEPKKVVLKMDNQSAIALTKNSVHHERSKHIDTRFHYIRD FT CVKSGLVEVQHVRTEDQLADILTKSLGRIKFQEMRGKIGVLDINKEQQA" XX SQ Sequence 4285 BP; 1349 A; 749 C; 1136 G; 1051 T; 0 other; tcattttggt atcagagcca aggttgtcaa agcaatggcc ggtgttgaag gagatcaatc 60 taagacgctt gcagtcgtca aaccgacgac aagaggagcc tcaatcccga tccattatcc 120 aatgttaagc gaaacgaact acggcatatg ggctgtcaag atgaagataa tcttgcgttc 180 gctaggagta tggtcagtga tcgaaggtgc agacacagac gacgacaaag atcaaggcgc 240 catggtagcc atctctcaag ccgtgccaga tgacgtgatg atggcaatcg cagagaagca 300 gacggcaaag gaggcttggg acgcactcag ggagatgcga attggcgaag atcgtgtcaa 360 gaaggcacgt gtacaagtac tgaaacgaca attgtacaag gtgcatatgc aagattcaga 420 aaccgtaaat gagtattcga tgaagttgac tgccttggtt ggtgagatcc gatcacttgg 480 cgcgaaactt gaagaaagcg aagttgttga aaagctgttc agttcggttc cagatcgatt 540 tcttcaaatc attgggacaa ttgagcagtt tggagatgta gacacgatgt cggtttcaga 600 agctattggg cgtttgagaa catttgaaga gggattgaag gggcgatctc atacagagag 660 tacaggagag cagttgctat tcacccaagc cgaaagggaa gcaagaaccc caaaggcaaa 720 gaaatatgaa agtttcagca acaacaaaag aggaggacgt cactggagag gacatggtag 780 tgggcgtgga tatggtggag gtcgaggaaa tggtgaacgc actaacgaag accgaaagcc 840 acgaaacttc gacaaatcca aggttaagtg tttcaattgt aatgaatttg gacacttcgc 900 aaaagattgt tccaagccaa accgaagaga gagggctaat tttgttacaa cacaaaccga 960 tgatgaaccg gcactactga tggccgaaac ttgtgttatc agccactcaa tacagaacga 1020 gcatgtgtta ctgcacgaag acaaggtggt gccaaagatt aaaggcaccc gagagaaggc 1080 ttggtattta gataccggcg caagtaacca catgaccgga tgtattgaaa aatttgctga 1140 aattgacacg actattacag ggtcagtcaa atttggggat ggctcgactg taaaaatcca 1200 aggaagaggt tcggttttgc ttgaagactt cacaggtgaa catcgaatac ttactaatgt 1260 ctactacatc ccaatgttga agagcaacat aataagcctt ggccagttgg atgaaaacgg 1320 atgcaaggtt gtgattgaag gaggtgttat gactattttg gacagattac aaaggctact 1380 agcaaaagtg aagaggtcaa gcaaccggtt atatgtgctt aacatagcac cagctctacc 1440 cgaatgcttt ctggtaagga gcaaagaaga agcatggcga tggcatgcaa gatacgggca 1500 tgtgaatttt catgctttga agtctctaag tcagaaacag atggtgcacg gcttgcccat 1560 aatcgagcat gaagatcgca tttgtgatgg atgtttgatt ggaaaacaac aacgaaaacc 1620 attccctgct gaatcaaatt tcagagccga gtaccctctt gagttgtggc atatagattt 1680 gtgcgggcca atcacaccga ctacgaatgg gggaaagcgt tattttatgc taattgtcga 1740 tgattgcaca aggtttatgt ggcaggttct gatctcaagc aaagccgagg cgttcgaaag 1800 ttttaaaagg atcaaagctg cagccgaaat ggagaagggg tgtaagttga aagcttttcg 1860 aagtgatcgt ggtggtgaat tcacatcaaa tgagttcaag ggcttttgcg aattaaatga 1920 tattaaacac taccttactg caccttattc tccgcagcaa aatggtgtcg tggaacggag 1980 aaatcagaca gtggttggca tggcaagaag tttgctgaaa agtaaaagtg ttcccggcga 2040 attttaggga gaagcggtgt caacggcaat ttacttgctg aacagagcac caactaagag 2100 tctagttgac aagacaccct atgaagccta ctacaatcga aagccaagag ttgaacactt 2160 gcgaattttt ggatgtattg ctcacgtgaa gaatgtcaca cctcaccttc cgaaactagc 2220 agatcgaagt aaacctatgg tgtttattgg atatgatttg aataccaagg gttatcggat 2280 gtttgatcca aagacaaaac aggtggtagt gactcgtgat gccgtgtttg atgaagaaaa 2340 gaagtgggac tggactgatt catcggctac agaatctaaa ccagcaaagg atatctttac 2400 tgttctttat tttcctgttg cagtttcaag tgatgctgcc catcaacgaa ttgaggaaga 2460 gatgctgtat ccaaatatgg cgtctccaca gccagggttc tatcaatctg gcgagcctga 2520 gaatacatct gctggtagca acagagcaga tggattcggc tctggaaatg cacaaactcc 2580 agtgtcgttt cctgttgagc agagggcatc cgaattcatc catccagagg catcagaagt 2640 gggaccaaga gggaaacgag acctaaacag tttgtacgac aaaactattc ctactgaatt 2700 ggattattcg gggctatgtt tgctaggaga ggaggagcct acgagttatg aagaagcaag 2760 aaccgattca gcatggagaa aggctatgga agaagaaatt tccagcatac aggagaatgc 2820 aacatggagg ttagttgctt taccagaaaa tcaaaagcca attggtttga agtgggtgtt 2880 taaattgaag aaagatactc aagggagaat aatcaaacac aaggcgaggt tagtagcaaa 2940 ggggtatgtt caaaagcacg ggatagattt tgacgaagtt tttgctcctg ttgctcgatt 3000 ggaaactgta cggttgttga tatcaatcgc tgcacaaaag gggtggcaag tgcatcacat 3060 ggatgtaaaa tccgctttcc ttaacggtga attggaggag gatgtgtatg ttctgcagcc 3120 accgggtttt gagataaaag gagaagagta taaggtgctg aaactgtata aagccttgta 3180 cggtttgcga caaacgccta gagcatggaa ttccaagttg gataagtcgt tgaaggcact 3240 cggttttgag aggtgtcttc tagaacatgc gatgtacacg agaaaggaag gaaatttaac 3300 tgttggagta tacgtagacg atttaattat cactggagga tgtattcgag acattgacaa 3360 attcaaatct cagatgaaag ggctatttag aatgagtgat cttgggttgc ttagctatta 3420 tttgggaatt gaagtgtgtc agactccaac aagaatcacc ttaaagcaat cgggttttgc 3480 aaagaaggtg ctggagaaat gtgggatgaa ggactgtaac tcaacacaga ttcctatgga 3540 gcctcgcctg aaattgaaca aggacagcct tgaacctcct gtagatgtaa ctttgtatcg 3600 aagtatcgtt ggcagtttga gatacttgct gcacacacgt ccagacttgg cgtttgctgt 3660 tggaatggta agtcgattta tggagaaacc cacgctggaa cacatggcag cagtaaagca 3720 catactgagg tacgtgaagg gaacattgaa ctttggtttt gtgtatgaga agaaagaagg 3780 agatttggag ctgatcgggt tttcggacag tgatctggct ggtgacaata atgatagaaa 3840 aagcacttca ggattgatat tctttcttgg ggcaaatccg atcagctggt gttcacaaaa 3900 gcagaaagtg gtggcgctgt cttcatgcga agcagaatat attgctggtt gtgcggcagc 3960 gtgtcaaggt gtgtggctaa gtcgattgtt aggagaattg ctaaaggctg aacctaagaa 4020 agtggtgcta aaaatggata atcaatccgc aattgctcta accaagaact cagttcatca 4080 tgagaggagt aaacatattg acactcggtt tcattacata agagattgtg tgaaatcggg 4140 attggttgaa gttcagcatg ttcgtaccga ggaccagctt gctgatatct taacaaagtc 4200 actgggaagg ataaagtttc aggagatgag aggaaagatt ggtgtactgg acatcaataa 4260 agaacaacaa gcttaaggag gagaa 4285 // ID DNA3-5_Mad repbase; DNA; EDCOT; 2540 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous DNA transposon from apple. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW DNA3-5_Mad. XX NM DNA3-5_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2540 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1469-1469 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~82% identical to consensus. 3-bp TSDs. XX SQ Sequence 2540 BP; 910 A; 534 C; 463 G; 632 T; 1 other; gggtgcgttt gttgcaccgg actaactcgg actggactag cttcagggac taagctggat 60 tggcttggcc tggactaagc agtactaaaa ttgtgaagcg tttggtgcag tgccggacta 120 gccaggacta aatttttatt ttttattttt ttatatttaa ttatgaaaac ttccactttc 180 ttgtctaatt ttttttttaa gagataaaag atgctttatt gaaaatatta ttcatctcat 240 aaacaaaatg gggaaaggat tttgctttac atgaaagtct acatattttt ttcaccatca 300 gctatcaata catttacaag ttgcaactac ttgtgcttaa acttgagttc cttcacatat 360 tcttcaatgc ccttcaacta cttatgtaga tcttgagtgc ttcaattgca actgcacagg 420 ctatggggtg tccagaatat gtaaacccat gagaaaaaga accaagcttg ctgctctgag 480 agtgtatgac atctgaaact tctgggctca caagaacgct gattggcata tattcagaag 540 aagagccttt gccacagata caaggtctgg tttaatgttg tatttgtcac acctatacac 600 gtagccaagc ctttcaaatg catagattac atcgttccaa atgcacagat tacatcgtca 660 taaatagaac gcaacaattg tccctggtcc ctctggtccc tcagtgtgca atacaaatgg 720 agctggaaga tcaaactttt gtgggcagtc agtgtgcaat acaaagggaa ccataaagag 780 atgctcatgt agacttctag atacaaatgc caactagaac acatgagcaa tgaacaataa 840 tttggtagat aatattttga gtgtcattta tgaacactaa agttaaacta atgccaccac 900 ggccacggca ataaaaataa ctgactaata aacaatgtag cacaaagtaa atgtttgcag 960 gttaatgaaa cagaaagctg ttgagaataa aagctaactg tgtcgcaaag acctgtaaac 1020 ttctatgtac gccctgttaa acgaaatgtc cagccacaga taataaatct ggacatcaga 1080 taccatgggc aaacaactcc aaaaagatac aacagcaata catattcaca cagacgacca 1140 catattagac acaacaggag caagaaatca caaatgagaa tgaactaatc gttcaaactg 1200 caatctcagt cgaaagatgg tgattttaac ttactaatca cagaatatca ttaacgttaa 1260 atatttgcat catagattgc agacttactt ccaaaaagat acaattgaaa agttaataat 1320 cctaagcaaa caaaataaat tactgaaatg gtgctaagca aaataaatca tttggtaaaa 1380 agctcccaga cttttattgc tctgaaagat cagatagtcg atcactaatt caccccattg 1440 catctagatg caagtaagac aggtcgtaat agctatcctc atatccataa aaaaccaagt 1500 tcaaataacg aaatggtaaa cataataccg cacccaccac cgccaccaat tcaaccatta 1560 aattaaccca cttcacacct acctacatca ttggaattta aatcaattct aagattctaa 1620 aaatacatac agagcatcaa ttctaagaat catgcacaag caattgtacc tctcatagag 1680 ctacagaaca atgtccctgc aaaattcagt gattcatgag atgcagggga tactaaatgc 1740 aatcaaatac aagcaagact gacaagttca accaatttgc ttaatccaaa atctctaaac 1800 acaaaatacc caatcgattg agcaaaccat gaacaacaac aaaaaacacc gggataataa 1860 tttccactga aagattcttg caccatctta aaaacccaac cccaattaca caaactaaga 1920 aagcaatcca acgcagcaaa cgaaaattaa gaaatcaata ttatgtagaa aaggtattta 1980 gagttcaaac acctctgagt ccgtcaagca tctctaccca actacaattc aacagagatc 2040 gacatgaaag acaagaaaat ccaaacgaat ttagaaatca gaaagctagg gccccaaaat 2100 ccaacgcaga cttgttcgtc ttcttttcct tccgctgccg ggactcctat ttcacgacgc 2160 agcagaaagc accaaacgaa gaccatcgcc acagatacaa gtccatcgtc gattgtttat 2220 atgttggacg gctaccaggt ggtggacaag gaaggagaag ggaaagggcg aaggtgcgaa 2280 tggacgatga gcaagatgca gtcgcaacgg ttgatgtgcg aaggtgcgaa ggagaaggga 2340 gatgacggga ttagagggcg gcttagcagt cctctccgaa tctggggttc tcgctaagac 2400 ctgttagcga gggactcagt cgaggcgagt ccctgctaat sccactaaac ttagtccggg 2460 tagggaacaa acacgagact ggactaaaac ttagtccagt ctagtccagt gaaagacagt 2520 gagtccaaac aaacacaccc 2540 // ID Gypsy6-VV_I repbase; DNA; EDCOT; 9598 BP. XX AC AM424945; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy6-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9598 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-9598 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 694-694 (2007). XX DR Genbank; AM424945; Positions 4756 14353. XX CC Positions [4643-5137] - Integrase core CC 'GGCCG' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 774..2057 FT /product="Gypsy6-VV_I_3p" FT /translation="MEAINACPHHGFDTWLLVSYFYDGMSSSMKQLLETMC FT GGDFMSKNPEEAMDFLSYVADVSRGWDEPTKREVGKMKSQLSVFNAKAGMY FT TLKEDDDMKAKLAAVTRRLEELELKKVHEVQAVVETPVQVKLCPNCQSYEH FT LVEECPAISAEREMFRDQANVVGQFKPNNNAPYGNTYNSSWRNHPNFSWKA FT RATQYQQPDQPSQQSSNLEQAIANLNKVVGDFVRNQEAINAQINQRIDRVE FT STLNKRMDGMQNDMSQKFDNLQYSISRLTNLNTVQEKGRFPSQPHQNPKGV FT HEVESLEGESSQMKDVKALITLRSGKKIEKPTPKPHVEKEEEIKKEEEMED FT KKREISEKKEDYDSTMNAIPEKELLKEEMLKKSTSPPFPQALHGKKVIRNA FT SEILEVLRQVKVNIPLLDMIKQVPTYAKFLPFQS" FT CDS join(2057..3274,3278..5170) FT /product="Gypsy6-VV_I_1p" FT /translation="MIEEKVVEKALLDLGASVNLLPYSVYKQLGLGELKPT FT TITLSLVDRSVKIPRGVIEDVLVQVDNFYYPVDFIVLDTDPTVKEANLVPI FT ILGRSFLATSNAIINCRNRLMQLTFGNMTLDLNIFYMSKKKTTLEEEEGPE FT EVCIIDTLVEEHCNQNMQDKLNESLVDFEEGLSEPPNVLATLQSWRRIEEI FT LPLFNKEEEVAAEKETPKLNLKPLPVELKYTHLEENNQCPVVISSSLTSHQ FT EKSLLEVLKRCKKAIGWQISDLKGISPLVCTHHIYMEEEAKPIRQLQRRLN FT PHLQEVVRAEVLKLLQAGIIYPISDSPWVSPTQVVPKKSGITMVQNEKGEE FT ITTRLTSGWRVCIDYRKLNAITRKDHFPLPFIDQVLERVSGHPFYCFLDGY FT SGYFHIEIDVEDEKTTFTCPFGTYAYRRMPFGLCNAPATFQRCMLSIFSDM FT VERIMEVFMDDITVYGGTYEECLVNLEAVLHRCIEKNLVLNWEKCHFMVRQ FT GIVLGHIISEKGIEVDKAKVELIVKLPSPTTVKGVRQFLGHAGFYRRFIKG FT FSSLSKPLCELLAKDAKFIWDERCQNSFDQLKKFLITTPIVRAPNWQLPFE FT LMCDASDFAIGAVFGQREDGKPSVIYYASKTLDEAQRNYTTTKKELLAVVF FT ALDKFRAYLVGSFIIVFTDHSALKYLLTKQDAKARLIRWILLLQKFDLQIK FT DKKGVENVVADHLSRLVITHNSHSLPINDDFPEESLMFLVKTPWYAHIANY FT LVTGEIPSEWNAQDRKHFFSKIHAYYWEEPFLFKYCVDQIIRKCVPEDEQQ FT GILSHCHENACGGHFASQKTAMKVLQSGFTWPSLFKDAHIMCRSCDRCQRL FT GKLTKRNQMPMNPILIVELFDVWGIDFIGPFPMSFGNSYILVGVDYVSKWV FT ETIPCRQNDHRVVLKFLKENIFSRFRVPKAIISDGGVHFCNKPFEDLLAKY FT GVKHKVATPYHPQTSGQVELANREIKNILMKVVNASRKDWSIRLHDSLWAY FT RTAYKTILGMSPYRLVYGKACHFPVEVEYRA" XX SQ Sequence 9598 BP; 2925 A; 1852 C; 2066 G; 2755 T; 0 other; aatgacgtcg ttgccgggga aggtgtcaag tttatagtga tactatttca gagcacttgt 60 aattttcatc acaagtttgg taacgtttct ttcattttac taattcataa tccaaattta 120 tcttttaaat tcagcttagt ttaatttttt tgttgtagcc ctgtttcctt ttgttgtcct 180 ttattttcat tttagttaca gatagatact agttgtgtat gccaaattgg atacgagaca 240 gtggaggaag gcttgttaaa cgtgatacac ctcataacaa ggaattggaa ttgagcttga 300 atatcatgga agctacacct aaagatcagc atagtcacca aggtcgtcaa gacaatctca 360 atgaattcag atcaatgagg gaccgcatgc atccaccatc atgtatagtg ccccttacag 420 agcagctagt gatcaaaccg tatcttgttc cacttctacc aactttccat gggatggaaa 480 gtgagaatcc ctatgcacac atcaaggaat ttgaagatgt ttgtaataca ttccaagagg 540 gaggagcttc aatcgatttg atgaggctta agttatttcc ttttacttta aaggataagg 600 tcaaaattta gcttaattct ttaaggccaa ggagtatctg cacttggact gacttacaag 660 ctgaattcct caagaaattt tttcccactc atagaacaaa tggcttgaaa aagcaaattt 720 caaacttctc agctaaagag aatgagaaat tctatgagtg ttgggaaaga tatatggaag 780 ctataaatgc ttgccctcac catggttttg atacttggct attggtgagc tatttttatg 840 atgggatgtc ttcctcaatg aagcaactcc tcgagacaat gtgtggagga gatttcatga 900 gcaaaaatcc ggaggaagct atggatttct tgagctatgt agctgatgtt tcaaggggat 960 gggatgaacc aaccaaaaga gaagtgggga agatgaagtc tcaactgagt gtttttaatg 1020 ctaaggctgg gatgtatacc ttgaaagaag atgatgatat gaaagcaaaa ttggcagctg 1080 tgacaagaag attggaggag ctggaactga agaaagtgca tgaagtgcaa gctgttgttg 1140 aaacaccagt gcaagtgaag ctttgtccta attgtcaatc atatgaacat ttggtggagg 1200 aatgccctgc aatttcagct gaaagggaaa tgtttagaga tcaagcaaat gttgttggac 1260 aattcaagcc caataacaat gcaccgtatg gaaatactta caactcaagt tggaggaatc 1320 atccaaattt ctcatggaag gccagagcaa ctcagtacca acagccggat caaccatctc 1380 aacaatcttc aaatcttgaa caagcaatag caaatctcaa caaggtagtg ggagattttg 1440 ttagaaacca agaagccatc aatgctcaaa tcaatcaaag aattgacaga gtggagagta 1500 ctttgaataa aaggatggat ggaatgcaaa atgatatgtc ccaaaagttt gataatctcc 1560 agtactcaat ttcaaggctc acaaatttga acacagtgca agaaaaggga agatttcctt 1620 ctcaacccca ccaaaacccc aagggtgtcc atgaagtgga aagccttgag ggggaatcat 1680 cacagatgaa agatgtcaaa gccttgatca ctctaaggag tggtaaaaaa attgagaagc 1740 caacacccaa gccacatgtt gagaaagaag aagagataaa gaaagaggag gaaatggaag 1800 acaaaaagag agaaatcagt gaaaagaagg aggactatga ttcaacaatg aatgcaattc 1860 cagagaagga actcctgaag gaagaaatgc tgaagaaatc aacttctcca ccttttcctc 1920 aagcattgca tgggaaaaag gtgattagaa atgcatctga aattcttgaa gtattgagac 1980 aagtgaaagt caatatccca ctgctggata tgattaaaca agttccaaca tatgcaaagt 2040 tcctaccatt tcagtcatga ttgaagaaaa ggtagtggag aaagctttat tagacttggg 2100 agcaagtgtg aatttgcttc catactctgt ctacaagcaa ttgggacttg gtgagttgaa 2160 gccaacgaca atcactctat ctctagtaga tagatcagta aaaattccaa ggggggtaat 2220 tgaggatgtc ctggttcaag ttgataattt ctactatccg gtagatttta ttgttcttga 2280 tacagaccct actgtaaagg aagctaattt agttcctatc atccttggaa ggtcattcct 2340 tgctacctca aatgcaatca tcaactgtag gaataggctt atgcaactca cttttggcaa 2400 catgacactt gatctcaata tcttctatat gtctaaaaag aaaaccactc tggaagaaga 2460 agagggtcca gaagaggtgt gcattattga cactttggta gaggagcact gtaatcagaa 2520 tatgcaggac aagctaaatg aaagtcttgt ggattttgag gaaggtttgt ctgaaccccc 2580 caatgtgctt gctactctac aaagttggag aaggatagaa gagattctac ctttgttcaa 2640 taaagaagaa gaggtagctg ctgaaaaaga gactccaaaa ctcaatctga agcctctgcc 2700 cgtggagctg aaatatacac accttgagga aaataatcaa tgtcctgttg taatatcttc 2760 atctctgacc agtcatcaag agaagtcttt actggaagtt ctcaagaggt gtaagaaggc 2820 aataggatgg caaatatctg acttgaaagg cattagtcct ttagtttgca cacatcatat 2880 atatatggag gaggaagcaa agccaattcg tcaacttcaa agaagattga atcctcattt 2940 acaagaggtg gtgcgagctg aggtgctgaa gctacttcaa gcaggcatta tttaccctat 3000 atctgatagc ccttgggtaa gtcctactca agtggtacca aagaagtcag ggattaccat 3060 ggtccagaac gaaaaagggg aagaaattac tacacgcctt acttcaggtt ggagggtgtg 3120 tattgattat agaaagttga atgctataac caggaaagat cattttccat tgccatttat 3180 tgaccaagtg ctggaaagag tctctggcca tccattctat tgtttcttgg acgggtattc 3240 agggtatttt catattgaaa ttgatgtgga agattaggaa aaaaccacct ttacatgtcc 3300 atttggaaca tatgcttaca gaagaatgcc atttggttta tgcaatgcac ctgcaacatt 3360 tcaaagatgc atgttgagta tcttcagtga tatggtggag cgaattatgg aggttttcat 3420 ggatgacatc accgtatatg gaggtacata tgaggaatgc ttagtcaatt tggaagcggt 3480 tcttcacaga tgcattgaaa aaaacctggt gctcaattgg gagaaatgcc attttatggt 3540 acgtcaagga attgtccttg gccatattat ctccgaaaaa ggcattgaag ttgataaagc 3600 aaaggtggag cttattgtca aattaccatc cccaacaact gtgaaaggag taagacagtt 3660 ccttggccat gcagggtttt ataggaggtt tataaaaggt ttttcaagtc tttcaaaacc 3720 tctttgtgag ctgttagcta aggatgctaa gtttatatgg gatgaaagat gtcaaaatag 3780 ctttgatcaa ctgaagaaat ttttaataac aactccaata gtgagggccc ctaactggca 3840 attacccttt gaactgatgt gtgatgccag tgactttgct ataggagctg tgtttggcca 3900 aagagaagat ggaaagccct ctgtaatcta ctatgcaagc aaaacactgg atgaagctca 3960 aaggaactac acaactacaa agaaagaatt gttagctgtg gtatttgcct tggacaaatt 4020 tcgtgcttat ttagtggggt ctttcatcat tgttttcact gaccattcag ccttgaagta 4080 tttattgaca aagcaagatg caaaagcaag gttgattaga tggattcttt tgttacaaaa 4140 attcgatctc caaatcaaag ataagaaagg agtggagaat gtggtagccg accatctttc 4200 aaggttagtt ataacacata attctcattc cttgcctatt aatgatgact ttcccgagga 4260 atcactcatg ttcctagtga aaactccttg gtatgctcat attgctaatt atctagttac 4320 tggtgaaatt ccaagtgagt ggaatgcaca agacaggaag cacttctttt caaaaattca 4380 tgcttattat tgggaagagc ccttcctttt taagtattgt gtagatcaga ttataagaaa 4440 gtgtgtccct gaagatgagc aacaagggat tctaagccat tgtcacgaga atgcatgtgg 4500 aggtcacttt gcctctcaga agacagctat gaaggtgttg caatcagggt ttacttggcc 4560 atctcttttc aaagatgccc acatcatgtg tagaagttgt gatagatgcc aaaggcttgg 4620 aaagttaaca aaaaggaatc aaatgcctat gaaccccatt ctaatagttg agctatttga 4680 tgtatggggc attgacttca tagggccttt cccaatgtct tttggtaatt cttacatctt 4740 ggtgggggtg gattatgttt ctaaatgggt tgagacaatc ccctgtagac aaaatgatca 4800 cagggtggtt ctcaaattcc ttaaagagaa cattttctca agatttaggg tgcccaaagc 4860 cataatcagt gatggaggtg ttcatttttg caacaaacct tttgaagatt tattagccaa 4920 gtatggagtg aagcataagg tagctacgcc ttatcatcct cagacttctg ggcaagttga 4980 gctagctaat agggaaataa agaacatatt gatgaaagtg gtgaatgcaa gcagaaaaga 5040 ttggtctatt aggcttcatg attcattatg ggcgtataga acagcttata agactattct 5100 tggcatgtct ccctatcgtc ttgtctatgg caaagcatgt catttccctg tggaagttga 5160 atacagagct tagtgggcaa taaagaagct gaatatggac ttgatcagag ccggagcaaa 5220 gaggtgccta gaccttaatg agatggagga attaagaaat gatgcttata tcaattccga 5280 agttgcaaaa cagacgatga agaagtggca tgataaatta atctccaaca aagaatttca 5340 gaaaggacaa agagttttac tttatgacac aagactttat atctttcctg gaaagctcaa 5400 gtcaaggtgg atagggctgt tcattattca ccaagtatat gtcaatggag tggtggaatt 5460 attgaattcc aatggcaaag atacctttag agtcaatgga tatcgtctca agccattcat 5520 ggagccattc aaaccagaaa atgaggaaat caacctcctt gagccacaaa aagcctaagc 5580 aaataagggt ttgatggact tggttttacc acagtccaaa atttttgtaa attttgtaaa 5640 tttcaaagtt tttttccatt cttttcattt taatttttga tcttaaagta tgtttttata 5700 tgtaatttaa tgtttttgaa tgatctcagg tgggataaaa tgcaaagaaa tttaaaggaa 5760 taaatcggag cgaaatcgga ccaaaatcag agtgtgaaca gagcaaaaac aaggctctgt 5820 gagactttgc agcctaagga aatcctctac gaaattagca cttctctacg aaaccatttc 5880 gcaacttaaa tgaagccgct gcgaaatcag catgtctctg cgaaagcggc catcctttgc 5940 gaaatcattt tgcaactcat tttactcctc tgcgaaaatt ttcgcagctg cgaaaccaag 6000 tttggcacac gagtgccact tcgcaacaca ggaaccccca attcgcagct gcgaaacggc 6060 tgcgaagcta taaagcgtga aaatccctgt tttcgcagtc aaagctccat tccgcagggt 6120 atttcgcaat tgcgaaaccg attttggcac acgagtgcca tttcgcagca cagtgacact 6180 cctttcgcag ctgcgaaacg gactgcgaag taggctgcga aaacggcttt ttgctgcgaa 6240 atcgacgttc ttttgagaaa ctcaaaatga cccttaatat tccgttattt ttatatatac 6300 cggtcatttg agctgcgaaa gggtttcaaa aagagagcgc gtcatagttg ctgactgttc 6360 atctccttgc ccgagcccga cgatgagcga acctccggtc atcttctctg atcatcattt 6420 ccggctaaat ttcggcaatc tgaaatggcg cgaaccagat gagctaagtc ttcctctcct 6480 tctagccgca aacgagttcc gcgagaggag cccgttccag atcccacctc tgaacctccg 6540 cggccaaaag ttgtttcccc tccggcgaag ctcgcgccac agaagcctcc gatgaggcgt 6600 tgtctcacta ggtcaggggg tcggtccctg caaaagaagg ccagggttga aagctcagag 6660 cccatagact taacagagca gtccccggtt ccctcaccag agccctctcc agcgccatct 6720 ccgactctgc cagcacagcc tcaggagctc cagtcaccac tttctgaacc ccaaattcca 6780 tctcgggtag ctcctgaagt gataattaag tgtccgatgc ttactcagcc gccaatagaa 6840 ggaaatttgg attgcagagc gcgaccattc cattctgagc tgtactttga cacaacatcc 6900 ttccaattga ggccggagct agcggattct ttccgcctat tgcgtagata tcatatggag 6960 cagctgttgg cccctagaga cttcttctac cccaaggtag ccatggattt ttatcagtcc 7020 atgactacca agtaggtcag agatcctact ttaattcatt ttactataga tggtcggcct 7080 ggcattttgg gagctcgcca tatagcagag gccctgcata taccatatga gccaactcat 7140 tttgaggatt tcagattgtg gactagtccc actgagctgg agatggtaca taccttgtcc 7200 agaggagctt ccacacgtcc acatctgttg aggggggaac ttcctccaag catgtttctt 7260 attgatgcat ttctgcgtca taacatctac ccactccagc attagactca gaggagagga 7320 gtacttttgg aggccctatt caagatttct gagggatact tctttggccc tcaccaccta 7380 attatggcta cccttctcta ttttaaagag aaggtgcata agaagaagct gcagagagtt 7440 gatgccattc cacttctctt cccacggctg ctatgccaga ttctggagca tctggggtat 7500 ccaacagatc ttcagttgga gcgcaaatgt atttgccgag aggtcttcac tctcgacaaa 7560 tggaacaata tgacagcata tagagtggag cagccaggac ggccacaacc agctgagata 7620 ccagctgcca ggagagcatc cccacgtcat atacctgagg gtatacccat tgcctctcct 7680 gtcatatcca gagcccctcc agtcactcca gcctcatcac aaccatcttc ttcagctgag 7740 cccaggatgg ccattcccat ttctgagtat agggagttat gtcgctcact acagactctc 7800 actgcatctt agagcagcct tgctcaggag atggcagcca ttagagcatg ccaggagcaa 7860 atgttcgcca ctcaggccca gcacactgcc atcctgaggc agattcagca tcatctgggt 7920 attatatcac ctcctgagca ctccattcct atcccaccag agccatcaca ggcccctcct 7980 tttgtacatc agactatgcc tcctgaggag ccgactacag gagaggcaaa ggcagctgag 8040 ccatcatccc cacatcatcc tccagccacc atctgatcat tttcatagtt tcctttatat 8100 atgtcctcta tgtattcctt tatgtatttc ccttatattt tccttactgg agtagctcta 8160 gaaatcccat gcttttgata ttatatactg ggattaattg tattacttgt tctctttttg 8220 tattttcatc aaatgaagta ttacaaatct atcaattttt tagtactctt agcattattt 8280 tatcctaatt tcctctactc atatctttta ttgtttttga aatatgtggt ttctccaatc 8340 agtatttgaa attgatatca ctcaggaggt accacttcct ccctttaatt gcaatcaccc 8400 atatcacatt gaggacaatg ctcagttcgg ttgggggggg gggagagaga aatgaggaag 8460 gaagtatgct aagttaaagg aagtatgcta agttattttg ttaatgcaat tatgttgata 8520 aattagttgt aatcttttac agtccactct aatctccatg gattttgagg aaaaattttc 8580 aaattaaatc aggagaaatt gaactgttgc ttttcacttg acttagagta tggattatgc 8640 ttgataaagt ggttcaattg ttgaagcttc ttttgaaatc gagtttagtt cttccacttt 8700 aagctattca cacactgtgc acaataggtt ccgagtataa gatgaaaaaa tatttccctc 8760 ttgacttaga aaaattttgg gacttggtac ctttgacctc aattgataaa gttgagacac 8820 cttatgaaag ggcaatgagc ctttgaaaaa ataaaataaa ataaaataaa ataaagaaag 8880 aaaaatgttt gcttgccttg aaacccgagc aaggtctgag gggtatttgg tgaaaatctt 8940 taaaacctag tgccctaagc cttaattggt tgggagtcac cgacctcaat gctcgttaca 9000 agggtggata ggtggagtta gcatatggta ggtgcttggg tattaaaaaa tcaatcattc 9060 tcaaaaatcc ggggtaaaat ccgaggagtt ggtggttgaa agatcctcaa agcttggtgc 9120 cctaagcctt aattggttgg gagtcatcga tggtcccccg ttacatggac aattcagaaa 9180 gaatacccct taagccttgg tgtgttctct gcctattgaa tttggtcagg ttgctaagtg 9240 ttgaaaagag ataggttggg gggagagatt agtttagcac actatattcg gaagctaagg 9300 aatcatacac ttagattttt gtggaagaat aaagtttggt tctttggaag tgaaaatgat 9360 tttaaaactt caatttgcat aatgcattcc cttgatcaat agtgtttagc aaagtttgag 9420 ataactcttg ttgaaatttg ggtttatatt tctttaatgt ctcatgtgag agttagatca 9480 tcatgccact taaaattttt tgaagtaatc agcatgatgt tgtaaattat agtaattttt 9540 atttttattt ttctctcctt cattgctaag ggactagcaa tatgtcggtt ggggggag 9598 // ID RTE-1B_Mad repbase; DNA; EDCOT; 7630 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE RTE retrotransposons from the apple genome, consensus. XX KW RTE; Non-LTR Retrotransposon; Transposable Element; RTE-1B_Mad. XX NM RTE-1B_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-7630 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1820-1820 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Compared to RTE-1_Mad, RTE-1B_Mad lacks the internal duplication. XX FH Key Location/Qualifiers FT CDS 117..3272 FT /product="RTE-1B_Mad_1p" FT /translation="MTMNPERNRAKARTSPVSGALCGPSTVISEQGSLYLH FT RHPDAVLNEQGGHRNFFSNDSTQSCLGAYAPINFTQDTQKKYFDPIRRGMV FT KKLGQKGRVQESRMRLGTWNIGTLTGKSMEVVEVMVRRRINIMCLQETKWV FT GLKAKDLENSGFKLWYSGTNRTRNGVGIIVDKTLTQDVVDVKRVGDRIMAI FT KIVIGQELINVISAYAPQVGLDTSSKEKFWEDLGDLVQGIAQTEKLFIGGD FT LNGHVGRETGNYGGFHGGHGFGERNEDGEAILDFAMAYDLFLANTFFKKRE FT EHVITYKSGSSKTQIDFLLMRKGDRITCKDCKVIPGESLANQHRLLVMDVH FT IKRVRKKNKTWKCPKTRWWNLKGEKQVIFKEQVITQCVWDREGEASQMWDS FT MASCIRKVAKEVLGESKGFAPHQKESWWWNEEVQTKVKAKKECCKALYKDR FT TDENGERYRRAKQEAKKAVREAKLAAYDDMYKRLDTKEGELDIYKLARARE FT KKTRDLNQVRCIKDEDGKVLATENAVKDRWRGYFHNLFNEGHERSTPLGEL FT SNSEECRNYSFYRRIRKEEVVVALKKMKHRKAVGPDDIPIEVWKALGETGI FT AWLTDLFNRILKTKKMPNEWRKSTLVPIYKNKGDVQNCMNYRGIKLMSHTM FT KLWERVIEHRLRQETRVSDNQFGFMPGRSTMEAIYLLRRLMERYRDGKKDL FT HMVFIDLEKAYDRVPRDILWRILEKKGVRVAYIQAIKDMYEGAKTAVRTHE FT GQTESFPITVGLHQGSSLSPYLFALVMDELTGHIQDDIPWCMLFADDIVLI FT DETQEGVNAKLNLWREVLESKGLRLSRSKTEYMECKFSANGGQNELGVRIG FT DQEIPKSDRFRYLGSILQKNGELDGDLNHRIQAGWMKWKSASGVLCDRRMP FT LKLKGKFYRTAIRPAMLYGTECWAVKHQHVHKMGVAEMRMLRWMCGHTRKD FT KIRNEDIRGKVGVAEIEGKLRENRLRWFGHVQRRPTDAPVRRCDYGTEVQG FT RRGRGRPRKTLEETLRKDLEYLDLTEDMTQDRAQWRSKIHIADPTQ" XX SQ Sequence 7630 BP; 2417 A; 1513 C; 1927 G; 1773 T; 0 other; gttaactccg cctatgtaag tttatcttac attgccggtc ccaagcccgg ataaaggagg 60 agggggaggg cgtcaggtag tcgacagccg gcactccaca gttacgtcga atccttatga 120 caatgaatcc agaacgaaat cgcgctaaag ctaggacgtc acccgtaagt ggcgcgctgt 180 gtggcccgag cacagtgata agtgagcaag ggtcgctgta tctccatcgg cacccggatg 240 cagtgttaaa tgagcaaggg ggccatagaa acttcttttc gaacgactcc actcaaagtt 300 gtttgggagc atatgctcct atcaacttta cacaggacac acaaaagaag tactttgatc 360 ctattagacg ggggatggtg aagaagctag gacagaaggg tagagttcaa gagagtagaa 420 tgcgtttagg aacgtggaat ataggaacct taacgggaaa atctatggaa gtagtggaag 480 ttatggtgag gagaaggata aatattatgt gcctacaaga aactaagtgg gttggtctta 540 aggcaaagga tctagaaaac tcagggttta agctttggta ttcgggcaca aatagaacga 600 gaaacggtgt tggcatcatt gtggacaaga ccttgacaca agatgttgta gatgtcaaga 660 gggtaggaga tagaatcatg gcaatcaaga ttgtaatagg acaagaactc atcaatgtga 720 ttagtgcgta cgcacctcaa gtagggttgg atacgagttc gaaggagaaa ttttgggaag 780 accttggaga cttggtgcaa ggaattgctc agacggagaa gttatttata ggaggagatt 840 taaatggaca cgtgggcagg gagacaggca actatggagg ttttcatggt ggccatggtt 900 ttggggagag aaatgaggat ggggaagcta tcttggattt tgcaatggca tatgatctct 960 tcttagccaa caccttcttt aagaagagag aagaacatgt gatcacctac aagagtgggt 1020 cgtcaaaaac acaaatagat tttcttctaa tgaggaaagg ggatcgtata acttgtaagg 1080 attgcaaagt tataccgggg gagagcttgg ctaatcaaca tcgcttgttg gtgatggatg 1140 tacatatcaa aagagtgaga aaaaagaaca agacttggaa gtgcccaaag actagatggt 1200 ggaatctaaa aggagaaaaa caagtcattt tcaaagagca agtaatcacc cagtgtgtgt 1260 gggatagaga gggggaagct agccaaatgt gggattccat ggctagctgt atccgaaaag 1320 tagcaaaaga ggtattagga gagtccaagg gctttgctcc acaccaaaag gaatcttggt 1380 ggtggaatga ggaggtacaa acaaaggtga aggctaagaa ggaatgttgt aaagccttat 1440 acaaggatag gaccgatgaa aatggtgaaa ggtatagaag agcgaagcaa gaggcgaaga 1500 aagctgtgag agaagctaag ttagcggctt atgacgatat gtataagcga ctagatacca 1560 aagaaggaga gttggatatc tataaactag ctagagcaag ggaaaagaag acaagggacc 1620 taaaccaagt gaggtgcatc aaggatgagg atggaaaggt tcttgctaca gagaacgcgg 1680 tcaaagacag atggagaggt tattttcata atcttttcaa tgaaggacat gaaaggagta 1740 ctcctttagg ggagttgagt aactcagaag agtgtagaaa ctactccttt tatcgtcgaa 1800 tcaggaagga agaagtggtt gtagctttga agaagatgaa gcatagaaaa gcagtgggcc 1860 cagacgatat accgattgaa gtgtggaaag ccttgggaga gacaggtata gcatggctca 1920 ctgacctttt caataggatt ttgaaaacga agaagatgcc aaacgagtgg cgaaagagca 1980 ccttggtgcc tatttacaag aataagggcg acgtacaaaa ttgcatgaac tataggggta 2040 ttaagctaat gagtcataca atgaagctct gggagagagt cattgagcat agattgaggc 2100 aagagacacg ggtttcggac aaccaattcg ggttcatgcc agggcgctca accatggagg 2160 caatctatct cttacgaaga ttgatggaaa gatatagaga tgggaaaaag gatttacaca 2220 tggtctttat agatttggaa aaagcgtatg atagggtccc aagagacatt ctttggagga 2280 ttttagagaa gaaaggagta cgagtagcat atatccaagc tataaaggat atgtatgaag 2340 gagcaaagac tgccgtaaga actcatgaag gacaaaccga aagcttcccc ataactgtag 2400 gattacatca aggctcatcc ttaagtcctt acctttttgc gttggtaatg gatgagttaa 2460 caggacatat tcaagatgat attccttggt gtatgctttt cgcagacgat atagtgttga 2520 tagatgaaac tcaggaaggg gtaaatgcga agcttaacct ttggagagaa gtgttggaat 2580 ctaaaggtct tcgcctaagc cgatcaaaga cagaatatat ggagtgcaag ttcagtgcaa 2640 atggaggcca aaatgagtta ggggtgagga tcggagatca ggaaatacca aagagcgacc 2700 gttttcgcta cctaggatct atcttgcaaa agaacggaga attagatgga gatctcaacc 2760 atagaataca agctggatgg atgaagtgga agagtgcatc cggcgtgttg tgtgatcgtc 2820 gtatgccact gaagcttaag ggaaaatttt ataggacggc aataaggccg gcgatgctgt 2880 atggcacaga atgttgggcg gtgaagcacc aacacgtaca caaaatgggt gtagcggaga 2940 tgaggatgct tcgttggatg tgtgggcaca cgagaaagga taagattagg aatgaggata 3000 tccgaggtaa agtaggagta gccgaaattg aaggaaaact gagagaaaat cggttacggt 3060 ggtttggaca tgtgcaaaga aggcctactg acgctccggt tagaagatgc gactacggga 3120 cagaggttca gggccgaagg ggtagaggaa gacctaggaa aactttggaa gagactctaa 3180 gaaaagactt agagtacttg gatctaacgg aggacatgac acaggatcga gcacaatggc 3240 gttctaagat tcatatagcc gacccgactc agtgacttgg atttttcaag tctccaatcg 3300 agaagttttc cccactcggg aaattaaggg aacactacct caacctacat gctccactca 3360 caaagcttca acatacaagc ttcaacaaaa gaaaaattca aagaacttag tgaagaaggc 3420 tttggtgtat ttaacacaat acgttgaaat gaaacaaagc ttatttattg atatctctaa 3480 gaagttacaa atatgtacat atacacgagt caaaataaac aaacaagagg gagccttcac 3540 aaaggttgct taggagaagt ctcagcagtc ggcagagccc cagaaagaga aggcaccgga 3600 gggggatcat tcggagcctc agtactggac agcaccctag aaggaggagg catcggaggt 3660 tgatcatttg gagcttcatt acgcggtaca gccccagaag acgaaggcaa taaatgcctt 3720 tggaacaaac ccacaaacct ctgatgatca tgtaaaatct gaccatcaga ttccttcatc 3780 tggtcaagct tcctcttcat gtttgtagca tagtcatgag cgagccggtg caactgttta 3840 ttctcatgct tgagccctct aatctcctgt ttgagactca tcacttcagc cgccaatgat 3900 tcaacttggc gggttcgagc aaataggcgt tgggccatat tagacacaga acctgcacac 3960 tgaacactga gagccagaga atccttaaca gccaactcat cagaccgttt ggaaagtagt 4020 ctgttatctt tgggagtgag aaggttcctg gccaccaccg cagcggtcat atcattcttc 4080 atcacggaat ccccaacggt aagaggacca gtaggggata agaaggatgg gcgccatatg 4140 ttgtctggag aaggcgtggc tgcctcttca acaaggttca agtcaaaacg acggtcggag 4200 gggccagaca ttttcaaagg tgttgaagag aaaagaggtc ggacaaatca agatcttaga 4260 aatgcaagaa gggagcttct actggtggag attcaagtgt gctttggaac ttaataccag 4320 cctctataaa aatccgcact cgatggagct tcagaaatcg aagaggcgcc tgctcagaaa 4380 tcgaaaaggc gtttgctttc tcaaaagctg ggctgctcag agaccacgag ggccgatctc 4440 aggaatcgaa gaggcgtttg ctttctcaaa agctgggctg ctcaaagacc acgaaggtcg 4500 atcgcagaaa tcgaagaggc gcttgctttc tcaaaagctg ggctgctcag agaccacgag 4560 ggccgatctc agaaatcgaa gaggcacctg ctttttcagc cttgtcagca cctgtcacat 4620 gcacactcaa ctttgcggaa attacgggca ttctgtcgaa gatttctagt gaagtagaaa 4680 gcacgtgaat gttactgttc aatcattcac tttccacacg caacatcagc tcacgggtac 4740 cacagataac tttgccaaaa atctctgaca aagtttagac acgtgaagct tgcagctccc 4800 attacatcgc tatgaccaag aagggtaaaa gaatagcaaa gaaacagcac taacaaagtt 4860 tagacacata aattttgaag gtctagctac catattatta cccacaaggg taaaggaaca 4920 ggaccattgc tggataattg gaaagtccct gtgggtcaac ctctgtgctc cgtggcaagg 4980 tagactagca aacaggccta acctttactc acattcgaga aaacactccc aacaagattg 5040 cttgcttcaa gatcgaagag gcaccgtcct ccgaatctcg agagccagac tcccaacatg 5100 attactttct caaaaagcga cgagacaccg ctctccgaat ctcgagagcc agactcctag 5160 caggattgct ttctcaaaaa tcgaagaggc accgttctcc gaatctcgag agacagatcc 5220 ccgacaggat tgcttgttcg aaaaccgaag aggcaccgct ttctcaactt cgagagcccc 5280 ttagataaag cttgtctgta atcctcacac cgctttctca acttcgagag ccagatctcc 5340 ttggataaag cttgtctgta atcttcacac gtaacatcag ctttccagat accacagacc 5400 actttttcaa agtgctctga cagagttaaa acacgtgaag ctggcagctc ccactaccgt 5460 gctatgacca agcagggtaa aagaatagta ttactccttg ttagggagac tcctatatat 5520 gtcgacctcc atcctcaacg gacaggcaga cctgcaaaaa tgctcaaccc ttcctcatat 5580 ctgagagggc actcccaacg aagcctctcg aaatactcag ctttctttcc ccccgagaat 5640 acctctgcaa acaagctaca ctagagcaag aatatctcat atcatcaggg ttaaaagcaa 5700 gagtatccca tatcatgctt tttccctgtc ttttcctttg gccttgttct tacctgcaag 5760 acaaggagaa agagagcaat cagtcagcac ttggaatcaa gcttccagtc cggaactgac 5820 tgcctggaac cccattgctc tcgagtactc atcttcaaca tcttatgctt cccgagaaga 5880 taccacatct gcctgaggaa caaatagggc aagtgagaag gatacaagga agcatgtgga 5940 gacaagcgca acagaacacg tgccgataca tccactactt tgtcaacagc aaaagtatcc 6000 catatcagca gggtcgaacg tactctagat ttgatggact tgttttgacc ctcaaattct 6060 tcagtcggcc ttatactctg gcggaaacaa gaaaaccctc cagcccagtt caagaataag 6120 cctgtggaaa gttacttctt caaaagcaaa agtatctcat atcacctttt ctccttttct 6180 tctctttatc cttcatgcta cctgcaagat aaggagaagg ataacaatca gccggaactc 6240 gaaatcaaac ttctgatctg ggactgattg cttggagctc tgattgctta ccttgtctgt 6300 cacctctttc agcagatccc ctagctcggc gacttggggg actcctacta catggtttgt 6360 atcgcgcttg accaagcctg aaactacaag taagcgtcaa gtgaaattga tacattacct 6420 tgtgcatctc caccagttaa agataccacc cctggaggga ggaagagtac ttccaaagaa 6480 gatgccacat ctacctatga gacagataag gcaagtgaag acgataccac acttcggtac 6540 ttaaaagttt cgtgattacg agatcattct tccacaatat ttcctaatgt catttgtact 6600 aaatcattca cttgtactca ctaaaggaga gcttgaacct atatactgtg taaacccttc 6660 acaattaatg agaactcctt tactccgtgg acgtagccaa tctgggtgaa ccacgtacat 6720 cttgtgtttg cttcctgtct ctatccattt acatacttat ccacactaat gaccggagca 6780 atctagcgaa gatcacaaac ttaatattta agatgatatt ctttggtgta tgcttttcgc 6840 aaacgatata gtgttgatag atgaaacgca ggaaggggta aacgcgaagc ttaacctttg 6900 gagagaagtg ttggaatcta aaggtcctcg cctaagccga tcaaagacag aatatatgga 6960 gtgcaagttc agtgcaaacg gaggccaaaa tgagttaggg gtgaggatcg gagatcagga 7020 aataccaaag agcgaccgtt ttcgctacct aggatctatc ttgcaaaaga acggagaatt 7080 tgatggagat ctcacccata gaatacaagc tggatggatg aagtggaaga gtgcatccgg 7140 cgtgttgtgt gaccgtcgta ggccactgaa gctcaaggga aaattttata ggacggcaat 7200 aaggccggca atgctgtatg gcatagaatg ttgggcggtg aagcatcaac acgtaggtgt 7260 agtggagatg aggatgcttc gttggatgtg tgggcacacg agaaaggata agattaggaa 7320 tgaggatatc cgaggtaaag taggagtagc cgaaattgaa ggaaagagga gagaaaatcg 7380 gttacggtgg tttggacatg tgcaaagaag gcctactgac gctccggttc gaagatgtga 7440 ccacgggaca gaggttcagg gccgaagggg tagaggaaga cctaggaaaa ctttggaaga 7500 gaccctaaga aaagacttag agtacttgga tctaacggag gacatgacac aaaaccgagc 7560 gcaatggcgt tctaggattc atatagccga ccccacttag tgggaaaagg ctttgttgtt 7620 gttgttgttg 7630 // ID Copia5-PTR_I repbase; DNA; EDCOT; 4673 BP. XX AC LG_XIII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia5-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4673 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4673 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 278-278 (2007). XX DR Genome; LG_XIII; Positions 3997748 4002420. XX CC Positions [2150-2650] - Integrase core CC 'ATAA' target site duplication CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS join(911..3607,3611..4663) FT /product="Copia5-PTR_I_1p" FT /translation="MKASESISDYHTRIMVIVNQMRRNGEALTDAWITKKI FT LRSLDPKFDFVVVAIEESKEVDKLMVDELMSSLQAHKQKIVKRNGDKAIEH FT ALQVKLSLKDRYKQRETSTSGYTTQGRSPQRRRGFQQFQGRGSWNTGFRGR FT GGRNTTRGGQGQQAFTPRGRGGGYNNRDKRNIQCYRCNQFGHYSTECQGKA FT PLEIREHANYADEDANSRGATALFVQQGLDENQENIWYLDSGASNHMCGQR FT ELFGDLDKTKQGLVTFGDTSKVPFKGKGSIPIKLKNGDSSYIADVYYVPAI FT KQNLISLGQLMERGYTFYSKNCHLTIRDNNWRLIAYVKMSKNRMFPLNIQY FT DAAKCLSAITNSEEWLWHLRLGHLNFTSLKMLASKKMVKGMPHIDHLDEVC FT ESCVLSKHHRSSFAKEVNWKAKRPLELVHTDVCGPIKPMSTGQNRYYLTFI FT DDFSRKTWIYFLKRKSEVFNCFKEFKAIVEKQSGYKIRTVRSDQGGEYTAN FT DFEAFCTQQGIRHQTTPAYTPQLNGVAERKNRTILDMVRSLLKAKKLPKQY FT WAEAVSCAVYLLNRCPTKSLQVVTPQEAWSGHKPSVTHLRVFGCVAYAKIS FT DARRTKLDDKSEKCIFVGYGERRMGYKLYNPITKKVIMSRDVIFEEDKTWQ FT WKDDQEAVKWISTDLILEDEVEVPPVLAEGPILPADEPQSPVHRFPVFNRR FT NTPESSSASSSEGPRRMRNVDELYDSTQVMEDTTLFCFFADSDPLSFNEAI FT TEEKWIEAMDEEIHVIEKNDTWKLTYLPENKKAIGVKWVYKTKKNAKGELQ FT RYKARLVAKGYKQREGIDYGEVFALVARLETIRLMILLAAQHRWKIYQLDV FT KSAFLNGFLEEEIYVEQPLGYSEAENESKVYKLKKALYGLKQAPRANTRID FT RYFQDNGFEKCPYEHVIYVKKGADGSILFACLYVDDLLFTGNNPTMFEAFK FT KSMVQEFEMTDIGLMAYFLGLEVVQKEEGIFVSQSSYAKDILERFKMESCN FT PVSTPVENGVELRKSKVRNVDPTYFKSLVGSLRYLTCTRPDILYGVGLISR FT YMETPDQSHLNAAKRILRYIKGTINEGMFYTSSKNFNLVGYSDSDWGRDLD FT ERKSTTGFVFFMGNTSFTWSSKKQSIVTLSSCEAEYVAANLAVCHLIWLRN FT MLKHLGFPQEDPTEIYIDNQSAIALAKNPVYHERSKHIDTRHHFIREHVKN FT KEVKLISCNTNDQIADIFTKPLKGEIFTRLKFMLGMTSLD" XX SQ Sequence 4673 BP; 1614 A; 864 C; 1053 G; 1142 T; 0 other; acaattggta tcagagcccc gttcgtcaga aaacagaagt gttttgggag atatccgaat 60 tttcaaagtt gtcaaaaaca agttttgatc attccacagt gtagatctca tccatacgaa 120 ctcactggtg caaaaatcag cttgatcgga gacggaggta gaacacacgc gccacctgaa 180 tattctgcac tgtttgacca cgcgcctccc acgcgcccag aggtagacga cgactgagac 240 acacgcgcgc catattcaag ccgcgccgag cctctaagcc gacttcaaag tcgagccgct 300 cgatagccgc agccgagccg atagaatatt ctgcagaata ttcccggttc aaccccagcg 360 aaccgcctga tgcccagaat tggtgttttg accggttcac cccatttcgg acccattttc 420 aacaaagtca gaccggttcc ctacgttttg aagcattccg gatcgatcta tagtgtccgt 480 tttgccaaat tcaactccca gaaggtgata tagtcattaa aggagcaaaa tgactacaga 540 aaatgcacat gcactcatcc cgaagctaac caaggacaac tatgatagtt ggtgcatcag 600 attgaaggca tttcttggtt ctcaagagtg tatagagatt gtgcaatatg gttatgatga 660 accagagtct aaagaagcag aagatactct acaagaggca gaaaagcaag tcctcaaagc 720 aaatagaaag aagaacaaca aagcaaagac catcatctat caaggtcttg atgaagctat 780 attcgagatt attgcttccg tagaaacatc aaaagagata tgagaggctc tccaataaaa 840 atacaaaggt gctgacagaa tcaagaagat tcgtctccaa tctttgcgaa gtgagtttga 900 attattgcaa atgaaggcct cagaatctat ttctgattat cacacaagaa ttatggtgat 960 agtcaatcag atgagaagaa atggagaagc cctcacagat gcttggatta ctaagaaaat 1020 tttgagatcc ctagatccaa aatttgattt tgttgttgtc gctattgaag agtccaaaga 1080 agtggacaag ttgatggtgg atgaacttat gagttctttg caagctcata agcaaaagat 1140 tgtcaaaaga aatggagata aggcaattga gcatgcctta caagtaaaat tgtcactcaa 1200 agacagatat aagcaaaggg agacctcaac aagtggatat actactcaag gaagaagtcc 1260 acaaagacga cgaggatttc agcaattcca aggaagagga tcttggaata caggtttcag 1320 aggaagaggt ggtagaaaca ccaccagagg aggtcaagga caacaagcat ttactcctag 1380 aggaagagga ggcggttaca ataaccgtga caagagaaat atccagtgtt atagatgcaa 1440 tcaatttggg cactatagca ctgaatgtca agggaaagct ccattagaga tacgtgagca 1500 tgccaactat gcagatgaag atgccaacag cagaggagca actgcattat ttgtccaaca 1560 aggactagat gagaatcaag agaatatttg gtatcttgat tctggagcca gcaatcatat 1620 gtgtggccaa cgagagttat ttggtgatct agataagacc aagcaaggtc tagttacttt 1680 tggagatacc tcaaaggttc cattcaaagg taaaggcagc atcccaatca agttgaagaa 1740 cggcgattcc agctacatcg ccgatgttta ttatgtccca gccataaagc agaacctgat 1800 cagcttaggt caacttatgg agagaggtta tactttttac tcgaagaatt gtcatctgac 1860 aattagagac aacaattgga gattaattgc ctatgtgaaa atgtccaaga ataggatgtt 1920 tcctttgaac atccagtatg atgcagcaaa gtgtttgagt gccatcacca atagtgaaga 1980 atggctctgg cacctgaggc ttggacatct gaatttcacg agcttgaaga tgctagcaag 2040 caagaagatg gtcaaaggta tgcctcacat tgatcatcta gatgaagtct gtgagagttg 2100 tgtcctcagc aaacatcaca gatccagttt tgccaaagaa gtcaactgga aagcaaagag 2160 gccactagag ttagtgcaca cagatgtgtg tggtcccata aagcctatgt caactggaca 2220 aaataggtac taccttactt ttattgatga ttttagcaga aagacatgga tatacttttt 2280 gaagaggaag tcagaggtgt tcaattgttt taaagagttt aaagcaattg ttgagaagca 2340 aagtggctat aagatcagaa ccgtgagatc tgatcaaggt ggagaatata cagcaaatga 2400 ctttgaagcc ttttgtacac aacaaggcat cagacatcag acaacacctg cttatacacc 2460 acagctgaat ggtgtagctg agagaaagaa tcgaacgatt cttgacatgg taagaagtct 2520 actcaaagca aagaagctgc ccaaacaata ctgggctgaa gctgtatcat gtgcagtgta 2580 tctactgaat cgctgtccaa ctaaaagttt gcaagttgtc actccacaag aagcatggag 2640 tggtcacaaa ccaagtgtta ctcatcttcg agtctttggt tgtgtggcat atgcaaagat 2700 ctcagatgca agaaggacca aactcgatga taaaagcgag aaatgcatct ttgtaggata 2760 cggtgagaga aggatgggat acaagctgta taatcccatc acaaagaagg taattatgag 2820 tagagatgtt atctttgaag aagataaaac ttggcaatgg aaggatgacc aagaagcagt 2880 caaatggatc agcactgatt tgatccttga agatgaagtg gaagtaccac cagtacttgc 2940 agaaggtccg atattaccgg cagatgagcc acaaagtccg gtacacagat tccctgtatt 3000 caacaggaga aatacaccag aatcatcatc agcatcctca tcagaaggac caagaaggat 3060 gagaaatgta gacgagttgt acgattccac tcaagtcatg gaagatacaa ctctattttg 3120 tttctttgca gatagtgacc cacttagctt caatgaagct atcacagaag agaagtggat 3180 agaagcaatg gatgaagaaa tacatgtcat tgagaagaat gatacctgga agctgactta 3240 tctaccagaa aacaagaaag caataggtgt caaatgggtc tacaagacaa agaagaatgc 3300 aaaaggagaa ctgcaaagat acaaagcaag attagtggca aaaggctaca aacagagaga 3360 aggcattgac tatggagaag tatttgctct agtagcccgg ctagagacaa tcagactgat 3420 gatcttacta gctgcacaac atagatggaa gatctatcaa ctcgatgtga agtcagcatt 3480 tctgaatggc ttcctagaag aagagatcta tgttgaacaa ccacttggat acagtgaagc 3540 tgaaaatgaa agcaaagtat acaagttgaa gaaagccctc tacggtttga agcaagctcc 3600 gcgtgcttga aataccagaa ttgacaggta ttttcaagat aatggatttg aaaaatgtcc 3660 atatgaacac gtaatatatg tgaagaaagg agcagatggc agcatattat ttgcgtgcct 3720 atatgttgat gatttgctat tcaccggcaa caaccctacc atgtttgaag ccttcaagaa 3780 aagcatggta caagagtttg agatgacaga cattggtctg atggcatatt ttcttggctt 3840 agaagtggtg cagaaagaag aagggatttt tgtatcccaa agcagttatg ccaaagacat 3900 tcttgaaaga ttcaagatgg aaagctgcaa tccggtatca actccagttg agaatggagt 3960 agaattgagg aagagtaaag ttagaaatgt tgatccaact tacttcaaaa gcttagtagg 4020 aagcttaagg tacttgacat gtaccagacc ggatatacta tacggagttg gtcttatcag 4080 cagatacatg gagacaccag accagtctca cttgaatgca gccaagagaa ttcttcgcta 4140 catcaaaggc acaataaatg aaggtatgtt ttatacctca agcaaaaact tcaatcttgt 4200 tggctactcg gatagtgatt ggggaagaga tctggatgaa aggaaaagca caacagggtt 4260 tgtctttttc atgggaaata catctttcac atggtcatcc aagaagcaat cgatagtaac 4320 gttatcaagc tgtgaagctg agtatgttgc tgccaactta gctgtatgcc atttaatatg 4380 gttaagaaat atgctgaagc atttgggatt tcctcaagaa gatcccacag agatttatat 4440 tgataatcaa tcagcgattg cattagcaaa gaacccggtg tatcatgaac gaagtaaaca 4500 cattgataca cgtcatcact tcatccgaga acatgtgaag aacaaagaag ttaaattgat 4560 atcctgcaac acaaatgatc aaattgcaga tatctttaca aagccattga agggagaaat 4620 atttaccaga ttgaagttca tgcttggcat gacatccctc gattgagttt aaa 4673 // ID HAT-7N2_Mad repbase; DNA; EDCOT; 824 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-7_Mad; HAT-7N1_Mad; HAT-7N2_Mad. XX NM HAT-7N2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-824 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1619-1619 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~96% identical to the consensus. 8-bp TSDs. Both termini are >90% CC identical to those of hAT-7_Mad and hAT-7N1_Mad. XX SQ Sequence 824 BP; 260 A; 178 C; 134 G; 252 T; 0 other; taggggtggg cacttagaac cgaaaaccga aaccgaaaca cgaaccaaat cgaaccgcac 60 cgaacggttt ggttttgcgg ttttgaaacg gtttcggttt tgaaaccgaa ccgcaacata 120 gaaaacggtt tggtttcggt tttggctttt gaaaaccgca ccgaaaccga accgcaccgc 180 aaatattaat aaacatttaa ttaaatgtcc atattagatt tcatgtttta attggttgtt 240 tgttagaatc catacactta gtatgggact caaccacact agaatatcat cattcatcac 300 tttctttcgt tcattaactt gaaggacctt tgttatttta taccatcaca cacacatata 360 tgtacaaggg tggactaatc ttgttatcaa gagtcgaaca atgatctaat gaagtccact 420 catttgaagc atgatatcac atattctagt atcaaagttt cgctcacgtt taatgaattc 480 aaatttattc aacttgtttt atgataaaca ttgtaaggga cacccttttg ttgcacaaac 540 atgttttaac atcacaactg catgcaacat gctaattgtt tacataacaa atgtcttttt 600 cctattgcta ttgggaaatg cttattaata tgttaaattg caaattgtac attttttctt 660 aaaaaccaaa ccgaaaccgt ttgaaaccgc accgaaccga accaaacggt ttggtttcat 720 ttcggttttg gcttcaaaac cgcaccgaac cgaaccgcaa aaaatttcgg tttcggtttc 780 ggtttcactc aaaaccgcac cgaaccaaac cgcgcccacc ccta 824 // ID RT_AC repbase; DNA; EDCOT; 284 BP. XX AC AF232943; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Aegiceras corniculatum Ty1/copia-type retrotransposon RT_AC, DE reverse transcriptase. XX KW Copia; LTR Retrotransposon; Transposable Element; RT_AC; KW retrotransposon; Ty1/COPIA superfamily; reverse transcriptase. XX OS Aegiceras corniculatum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; Ericales; Primulaceae; Aegiceras. XX RN [1] RP 1-284 RA Chen H. and Sun M.; RT "Direct submission."; RL Direct Submission to Genbank (09-FEB-2000). XX DR Genbank; AF232943; Positions 1 284. XX SQ Sequence 284 BP; 95 A; 46 C; 57 G; 86 T; 0 other; ggaattcgat gttaaaactg cttttctaaa tggagaactt gaagaagaaa tttttatgga 60 gcaaccagaa ggcttccagg tgaaaggtaa agaaaattta gtctgtcggc ttaagaaaag 120 cctttatgga ctaaagcaag ccccgaggca atggtacaaa aaatttgact ccttcatggc 180 taatcactgt tttagaaaaa caagtggtga tcattgcgta tatattaaga attttgatga 240 tgattttatc attcttttta ctctacgtcg accacatgga tccc 284 // ID ENSUPMET repbase; DNA; EDCOT; 9226 BP. XX AC . XX DT 26-JAN-2007 (Rel. 12.01, Created) DT 26-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A DNA transposon from Medicago truncatula. XX KW EnSpm; DNA transposon; Transposable Element; CACTA; transposon; KW Interspersed; terminal; Inverted; repeat; ORF; ENSUPMET. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-9226 RA Shankar R. and Jurka J.; RT "ENSUPMET: A DNA transposon from barrel medic."; RL Repbase Reports 7(1), 21-21 (2007). XX DR [1] (Consensus) XX CC The element is present in the Medicago genome in moderate copy CC number. It has intact domain for Tnp2 En/Spm transposase, flanked CC by characteristic short exact TIRs of ~ 20 bp. XX FH Key Location/Qualifiers FT CDS join(2701..3420,3424..4974,4996..5544) FT /product="ENSUPMET_1p" FT /translation="MDKSWISNKSITKEEYIRGVLSFMDFAFANSSENGKI FT FCPCKKCVNCYKRTRMDVYEHVINHGFLKGYIHWIFHGEKENPSNPLCASE FT VEHEFDHDMDALIHDAFPMHTNSDNDDDAYTNIEDRGSEAFTNNHNAQQSE FT EDDDAKKFYKLLKDAEQDLYPGCTRXYSKLSFIVHLYHIKCLYGWSDKSLS FT MLLELLNDAFPDENTLPNSFYETKKIITXLGLSYEKIHACPNDCMLYWRDD FT HXNACPKCGLSRWKVNSDDVEGRKKIPLKVLRYFPFKPRLQRLFMSSKTAY FT FMRWHQDDRSKDGIMRHPADSFAWKDFDRRHSDFARDPRNVRLGLATDGFN FT PFKTMSXXSHSTWPVVLIPYNLPPWMCMKQPNFILSLLIPGPNSPGNNIDV FT YLQPLIEELKELWEIGVRTFDASKKESFQMHAAIMWTINDFPAYAXLSGWS FT TKGRFACPCCSFDTTSKWLRHSRKFCYMCHRRLLEPDHKWRYNKGHFDGNQ FT EFRAPPELPNGTIALKQMEEHGIGTPSPWKKKCILFTLPYWEYNVLRHNLD FT VMHIEKNVCDNIIGTLLDLERKSKDNDKARYDLIDMNIRSQLHPRIHQCNG FT KKYLPRACYQMTSKEKESFLEVLKNLKAPDEYLSSISRCVQVKQRKISGLK FT SHDNHLLMQELLPIAMKGCLPDKVTKVISELCNFFKELCGKVLNEHNLDGL FT EHRIAKTLCQLEKIFPPSFFTVMVHLAIHLAYEAKVAGPVHYRWMYPVERY FT EICLFIKKMILSYFNIKSFCRFLFTLKSFVRNRAHPEGSIAESYIAYEGLI FT FCSRYLPGVETRFNRPSRNDDSFFVENSSLFNPRGRPLGRKSHIGFKVKKR FT RRVSRVSLDKKTLIQAHRYVLFNNNNVDPFQREHIDLIKRQNRNRRLSPYE FT LDRIHCQTFSDWFRERVSFTKLFHYQYCVSFHNHFK" XX SQ Sequence 9226 BP; 2943 A; 1426 C; 1789 G; 3059 T; 9 other; cactacaaga aaagtaccct gtccctacag ccatttttta aagcgggtag tttttaccaa 60 cggacatatg aaaaactgtc actaaaacca ttttatttat tttattattt ctattatatt 120 attatataat tattattgtt atatttttta caaatagagt gagatttttt tttcacaaac 180 acgtaccgta ccattcacac tcacacgctc atcaatctca aaatggcttt ttcttcatca 240 atctaaaatc tcacaaactc cattgatctc aaacctcaca aactccattg atctcaaacc 300 tcacaaactt aagctgtatc gattccctca caaacctaga aactccattg atcaatctca 360 cctcacaaac ctcatcaagc tctgaatcga ttccctactg tatcgatttt caaatcgatt 420 ttgttgttcg tattttgttc aaattgattt agggatcttc aaatcgattt tgctcttaat 480 cgttctcaag ctcacaatcg attctgcgtg caatttggac gtgatattga aaagctatat 540 attcaagctt aagctgaaac gcgcgtgcat tctgccgtca aaacaaacac aacatcaatc 600 tgtatcgatt ttgttcaaac tgtatcaatc tcaatcgtcg ccttcatcga ccgtcggacc 660 gccgatcttc gaactcgctc tggatcattt tcaatcgctg tgagtaattt tcgttctctt 720 tgttttaatt tttgatatga atgtggtaat taggtatagt gttgttattc ttgaaattag 780 tatacgtaga tgtgtttttg aactagattt tgggaaaatt ttgaaatcag ttcatgtgta 840 tgtgtttttg aattggattt tggtagaatt ttggaatcag tttatgtgcg tgtgttttta 900 actgaatttt gggaaaaatt ttgaaatcag attatttgta tgtgtttttg aacttgattt 960 tggtagaatt ttgaaatcag tttatgtgta tgtgtttttg aactgatttc agcaccacgt 1020 ctgtgtcagc atatttgtta aagtagtgag agttgaaatc cttgtatttg aaggacttga 1080 aaattggtgg attatgttca tcagtgatag cttgtgctgg ctcgacgtta caatcatccg 1140 aatgagctac aaaaaatgca gcagttgtac gagcatggct tgaatttgtc acagccctat 1200 gctcaacact tttacattga ttttccacat ataaactaac tattgaaaca tatacattat 1260 tctgctcaat taataaggaa aacaaaacag aattcaataa acttttaggt cctatatact 1320 ttttttctct cctagagctc gctcgatttg gatgaacttg tttgtaccta tatacaaaac 1380 agaattcaaa acagaatcca gcagttgtac gagcttgttt gtttgtatta tgagtgtttt 1440 ccgaaccctc tcctagattt aatacctttt agtggatcaa gtaccccctt gcaagccaca 1500 tgaatattta gacctgagct gctggctgtg gttccaaatt tggaggcaga ggagcaatag 1560 cagcagcatt tgaacgtgta gaacggaaga ggtctagtct acgacgtgag tgttcacaca 1620 ctaattcaat gcagttggtg tggaagacta aagtaactac taaaacgaat gacttgataa 1680 tacaccaata cgagatccgg gagacgatta tcaacaaaag cgtctcgcaa ttaaaagaaa 1740 ctcttgtaat ttgtcatacc ttagtggggg taggggggtg ttctatattt tgttaccctt 1800 cacaattatg atgattttag tacttgtatt actgttccaa tcattaatga tatgttgcag 1860 ctcttctttt gtaaaaaaaa agaaaaagaa aaagggtttg tattctaaaa caacagtgtt 1920 gtatgcatgt acggcatata tgccatctac agctacttgt atataatagt taaaaagaag 1980 ttatatggtg ctagattgca atgaatattt ccttcataaa tatatgaatc aattctcaca 2040 taacattcat gatatatttc atcttttatt taaaactttt gaagggttgt ttatgcacca 2100 aaaaacatga atgagtctat aaaaggaatc actctacaag caaatttgaa tatgacattt 2160 ctctagttta tgcacttgaa ttcactataa tgataaaaat ttggataggg aaaacatatg 2220 atatgagtgt gtaaatcaaa gttaagagct agaattggag ttcaaaacta tattcatcaa 2280 tcattagtag cctgttacat atgtgaaaat gaggattttt ctatcagcat caatcaaatt 2340 gattccagag tttatttcta ttgcaggttg ctaagaagat ttgtatagaa gtcaagtctt 2400 cgaaagattt tttggaacag ctctggttgt tgttctgtgt ctgtcatagt ctacgaggat 2460 cacggcaaac cagctttgtt agatttagca ctcaaccgta agtggactat gactcttttg 2520 gataaataga ttaaaatcct aggtatgatt atgtagtgca actgattttg catgaagtat 2580 tactgttgaa tttattacta gctagctacg aaacctcgag agatttttgg gttttataag 2640 ccttattggc tcataaataa ggtgcagagc tcacggctcg actctctcct gttttataca 2700 atggataaga gttggatatc aaataaatct ataactaagg aggagtacat tagaggggtt 2760 ttaagtttta tggattttgc ttttgctaac tcatctgaaa atgggaaaat attttgtccc 2820 tgcaaaaaat gtgtcaattg ctacaagcgt actcggatgg atgtctatga acatgtaatc 2880 aatcatggat ttctaaaagg ttatattcat tggatctttc atggtgagaa agaaaaccct 2940 tctaaccctc tatgtgcatc tgaagtagaa cacgaatttg atcatgacat ggatgcatta 3000 attcatgatg catttccaat gcatacgaat agcgataatg atgatgatgc atatacaaat 3060 atagaggaca ggggttctga agcattcaca aacaaccata atgctcaaca atctgaagag 3120 gatgatgatg caaaaaagtt ttataagtta ttgaaggatg cagaacaaga tttgtatccc 3180 ggttgtacaa gaktttactc aaaattatcc ttcattgtac acttgtacca cataaagtgt 3240 ctgtatggat ggagtgacaa aagcttgtca atgttgctag aactgttaaa tgatgcattt 3300 cctgatgaaa atactttgcc taattcattt tatgagacaa agaaratyat tacgganttg 3360 ggtttatcat atgaaaaaat tcatgcttgt ccaaacgatt gtatgttgta ttggagggat 3420 taggatcats ataatgcatg tcctaaatgt ggtctttcaa gatggaaagt taactcagat 3480 gatgtggaag gtagaaaaaa gataccttta aaggttcttc gttattttcc ttttaagcct 3540 agattgcaaa gactttttat gtcatcaaaa acagcttatt ttatgagatg gcatcaagat 3600 gatcgatcta aagatggaat catgaggcat ccagctgatt cttttgcttg gaaagatttt 3660 gatcgtcgac attctgattt tgctcgtgat cctcgtaacg tacgacttgg gttagctact 3720 gatggcttta atcctttcaa aaccatgagt wcaawttctc atagcacttg gcctgttgtt 3780 ttgattccat ataatcttcc accatggatg tgtatgaagc aaccaaactt catactctcg 3840 ttgcttattc ctggtccaaa ttctccagga aataatattg atgtgtattt gcaacctctt 3900 atcgaagagt taaaggaatt atgggaaatt ggagtcagaa catttgatgc wtctaaaaaa 3960 gaatcatttc aaatgcatgc tgcgatcatg tggactataa atgacttccc tgcgtatgct 4020 atkttgtcag gttggagtac aaaaggtcga tttgcttgtc catgttgtag ttttgacaca 4080 acctctaagt ggttgcgtca tagtagaaag ttttgttata tgtgtcatcg gcgtttgtta 4140 gagcctgatc ataaatggag atacaataaa ggacattttg atggaaacca agagtttcga 4200 gctccacctg agctacccaa tggaactatt gctttgaaac aaatggaaga acatggaatt 4260 gggacaccgt caccatggaa aaagaaatgt attttgttca cattgcctta ttgggagtat 4320 aatgttcttc gtcataatct tgatgtgatg catattgaaa aaaatgtatg tgataatatc 4380 attggaacct tgctggattt agaacgaaag tcaaaggaca atgataaggc tcgttatgac 4440 cttatagaca tgaacataag aagtcagcta cacccaagga tacatcaatg taatggtaaa 4500 aagtatttgc ctagagcttg ttatcagatg acatcaaagg agaaagaatc attcttggaa 4560 gtgctgaaga atttgaaagc tccagatgaa tatttgtcta gtatttcaag atgtgttcaa 4620 gtgaagcaac gcaaaatatc tggcctcaaa agccatgaca atcaccttct aatgcaagag 4680 ttgcttccaa tagctatgaa aggttgtttg cccgacaaag tgactaaagt tataagtgag 4740 ctttgtaatt tcttcaaaga gctatgtggc aaggtgctta atgagcataa tttggatggc 4800 ttggagcatc gaatagctaa aacgttgtgt caattagaaa agattttccc tccatctttt 4860 ttcactgtaa tggtgcattt ggcaatccat ttggcatatg aggcaaaagt tgctggtcca 4920 gttcattacc gatggatgta tcccgttgaa aggtatgaaa tttgtttatt tatttaacag 4980 tattctaatt tataaaagaa aatgatatta tcttatttta atataaaatc tttttgtagg 5040 ttccttttta ctctaaagtc atttgtacgt aatcgagcac atcctgaagg gtctattgca 5100 gagagttata tagcttatga aggcttgata ttttgttcac ggtatctccc tggagtggaa 5160 actcgtttta atcgacctag tcgaaatgat gattcctttt ttgtcgaaaa ctcaagtctt 5220 tttaatccta gaggtagacc attggggaga aaaagccaca ttgggttcaa agtaaagaaa 5280 agaagaagag tttctcgagt ttctcttgat aaaaaaacat tgatacaagc acatagatat 5340 gtgcttttca acaacaataa tgtggacccc tttcaaagag aacacattga tcttatcaag 5400 agacaaaatc gaaatcgtcg gctctcacca tatgaactcg acagaattca ttgtcaaaca 5460 ttttctgatt ggtttcgtga acgagtaagt tttacaaagc ttttccatta tcaatattgt 5520 gtttcatttc ataatcattt taaataaaat tgtgttaggt cgcacgattg gaagagcaag 5580 gaagtgttat tgtcacagat gaaatcaaat ggttagcacg tggtccacta gaaatagtga 5640 gaaactatag tggttatatt gttaatgggg ttagattcca tacaaagaag cgtgaaaggt 5700 gcttaaagac tcaaaacagt gggatttgtg ttactgttaa gacaagaagt tatgctagtt 5760 caagagacaa acaccctaaa gaaggagaaa taaactacta tggtgcattg acagatatag 5820 ttcagttgga ttatgcaggg aaatataaag ttgtactttt caagtgtgat tgggttgaca 5880 taaatagggg ttgcagcatt gataatttgg gcttgccatt agtaaatttt aattatttgc 5940 aacatacagg caatgatata tgtgatgacc catttatttt tgcttctcaa gccaaaaaag 6000 tattctatgt ggagaataag agacaaaagg attggtttgt cgttgtgcac gctaaggtta 6060 gagatgtata tgatttgggt gatcttcaat ccaatgctat agataatgga aatgaacaag 6120 tcttggaaga aataaatgat aatgacttga ttagaccaga agctgatgat agtgatgata 6180 tcattgaagt tcaaattaat atggaggaca ttccccgaag tgacatcccc caaaatgatg 6240 aggattgtga tacaggggat gatagtgagg aagactatgt ttgttttcct gttattaatg 6300 atggttttac tgattttgtt taaggtgtgt attgctagtt ttagatcatt gtatttcaat 6360 tgaagaggta attattgttt tacatactct tattttgaat tttcagcaac taattcttat 6420 tttacattct cagcaactaa actgattgtt tgatctttta gttaaagcaa gtaccatggg 6480 cagacggaga aagttgaagg ttgttcaaac tgatggccca tcactagaaa aagagcaatc 6540 agttgatagt tctaatgaag tcaacaaaga gggaagtcat agtgagaccc attgtgaaaa 6600 gaagactaga ggttatacac atatgttaga tgtatgggac atgcctgatg gagaatttat 6660 acttattgaa gtggatagtt tgggtaatcc catgggttgg gaagggaaga ctctactgaa 6720 tgcaataggg agcttggtaa ggagacacca atgtgctcct atcaaccata tttcttggaa 6780 agacatgctt gagactgata ttaccaacat gtttgattta attaaggtct ttgtagaatt 6840 tttgaagttt tatttccatt tatttattgt gatattttat tactttacaa aatgtctaac 6900 aatttggctt tttaataaat agagtaagtt ccgatttgtt cctgaattga ccgagcaaac 6960 aacacaaata ctaaaggata acatgagcag taagtggaga caatttaagc atgatttgaa 7020 atcaaaaggg tatgatgaaa gcaaaactga agaggaaatg gcttctatca tccctgacac 7080 aagagttgat ccgtcccaat atcgtgcttt agtgcaccat tggtgttcca aggaagggaa 7140 ggtatatgtt tgttttcaat gcactgccta ttttcaatgc tgaatttatc taagaatatt 7200 gcttctgtca cgtcttttta tttacatccc actattttac tctgtaattg tgttggtaat 7260 tagactagtc agctactgca acaagagcta ctacaacaat aacaacaatg atttatttga 7320 actgtgtttt aatgcttcgt attttattgt ttatagaaaa taagtcaaat caacaaaagg 7380 aatcgctcaa aatatgagga tttacattgc atgggaacca agaatcttcc gaggctaatt 7440 catgagatgg tatgtttctt tgtatgactt ttattagtat tttcaactag gttgttttgc 7500 aaatagaatg cttactgttc ttattcaaaa ttttagacaa cgaaggctat aggagtgcaa 7560 ccttctcgag ctgaaattta tattgaaacc cgaactcgaa aagacgggag cattgtgact 7620 gaaaaggcag cttcaacaat tgtaagatat atttatttag agtaaggaac tgtgtaaaat 7680 ttcatgaaag gtgtactgtc tagtaacttg cttaagttta gtttccttgt aactaataac 7740 ttgaacctta cttggattac aagaagaaaa ttcactgtaa cgttcttcat gtaggaggag 7800 ttaaagaagc atatggcaga ggtagaaaat tcagaaaatt ttcaagtcac tgaagattct 7860 acaaattgga tgaatgatac atactcaaaa gtgaaagggc ctgaaagaag aggacgtgtg 7920 cgttgtcttg gcaaacttcc acgacatgct agttcaaata tttcatctca acgcactaat 7980 tcagaagata gacttcaaaa agtagaaagt gtacttggaa atcttgttgc tgtgcttcaa 8040 atgcgatttt ctgatgatcc acaaattaat gctgtcttac aggctgtagc tcaagaggta 8100 ataaatctta tttttcaact tcaagaatgt ttttcaagaa aataaaatac actttttttc 8160 acttaggtac ctgatgttgc aagtgctcca aatggttcta ttggtaataa tcaacaaact 8220 acaagtggca ctggttcact gcacttttaa ggtattatct ttcaatgagg gcaaatgtgc 8280 gttcactaat tatatgctag ctgcaacttt tttccttctt ctttgtcatg aattaaaact 8340 tacgtgactg cgagtttggt aaagatgtct gtgcaagata agtttatcac ttggcagatg 8400 actttgtgtg tttgcacatg cgcacatgca cggacgtaac gtgcatgttg aatttggcaa 8460 cttattgcat gacaacgtat ccatctctct aactgttaat tgtttttggt cttattttaa 8520 ggtgcattga tggagaagag gaagatgatc tggttttggc ggaacatgat gtgaagaaaa 8580 gtatatgatt gttcttgata gggtagaacc atataaaaac tgtgtctgtc agtttctgca 8640 tcttataagt agtaaaactc attttgtgta atttggtgtt gtctttagtt atatgatttg 8700 tccacattgg tgaataatac cttgagaata tattctggtg ttgtttttag tttatatgat 8760 gattggtgaa taataccttg agaatattaa tccaccaatt ttttttatga aatataactg 8820 tttttatagt tattaaccag tttgtatgat ggagaaaaat ataatacagt gcaacaacaa 8880 taaataatat ctcaaaaaat atttgggggt ttcacgtttt taaaaaaaaa gggggacatt 8940 ttataaaaaa aaaaattgtg ggattgattt ttacccacgg ccagagacgc tgtaggtaaa 9000 agtactagtc tgtagaaaaa tcttgtagag acacacaacc cgtccgtagg taaaggtact 9060 gtccgtaggt aaaacatgca cttacagaca aaaatccgtt gcaacttgct aagtatagtg 9120 cacggccaat atggccgtgg gtgaaagttt tggccacata tacctacgga aaatagcctt 9180 tagtgacggt ttttgcccgt cactagaggt caagtttctt gtagtg 9226 // ID BoSB1A repbase; DNA; EDCOT; 159 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB1A. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-159 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 159 BP; 31 A; 42 C; 63 G; 23 T; 0 other; acccaggacc tcgtagtcca gtggtactac ctccgggagg ggaggtcggc tgttcgactc 60 gcggggaggg ggaggcgtgc ccagggcccg taaaaaggta caggcaaagg ctggcgccgg 120 gcctaggtgg ggggccgcaa ggtcaacacc tggttaatc 159 // ID MuDR-7_VV repbase; DNA; EDCOT; 5853 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-7_VV, an autonomous DNA transposon - a consensus sequence. XX KW MuDR; DNA transposon; Transposable Element; mutator; TIR; KW Mutavine-7; MuDR-7_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5853 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 767-767 (2008). XX DR [1] (Consensus) XX CC MuDR-7_VV (Mutavine-7 in [1]) consensus is an autonomous element. CC Its individual copies are >98% identical to the consensus CC sequence. MuDR-7_VV contains 720 bp-long TIRs which are 97% CC identical and are flanked by 9 bp-long TSDs. XX FH Key Location/Qualifiers FT CDS join(1710..2864,2999..4093) FT /product="MuDR-7_VV_Transposase" FT /note="MUDRA transposase." FT /translation="MDESPLSLPGNSPSMPNVQAPQSQYDFIEADGQSEIV FT NVPIDVEDDEDDEDYNLSDFSESDDDIIEDFGMEDDGINRAIGGKQLEGVW FT NGEGDSDHGDSDELRSAEGSSDDEGNSRPRFPEFNQRIGMENVQLVKDQKF FT ASHVIFKEALKEWCIKEKHDFEYKHNDKWRVTAVCKKKCGWKIHASQTQMG FT DAFQIKSFKSIHTCGKDHKNSKISSRWLANKYLPFFRDDHTWTANALKGAV FT FRDHEVDVTLDQCYKAKRMAFKMIHGAEEKQYERLWDYAAAIRKWNVGSTV FT KIQTTNDVFERMYICLDACKRGFLAGCRPLIGIDGCHLKGTTGGQLLVAVG FT KDGNDNIFPIAFAIVEIENKSSWTWFLQCLLDDIGHVDENGWGLVETFKDL FT MPNAEHRFCVRHLHANFKKDFPGKVLKDAMWSAARATTKNSFDFHMDELKK FT LDVKAYEWLVKLDVRTWSRHAFNPRSKSDTLVNNIAESFNAWILEARDKPV FT LTMMEIIRVMLMQRLQTKRDHMRRYEGRVCPRIYKKLERIKSEVGHCISRW FT NGESKYEVEYIYGGRYVVDLNERTCGCGRWGLSGIPCFHAAAAIIEHGEQL FT ETYVDIAYTKETFLSCYQWMISPLPSHEQWPKTPYDLIKPPKFTKKVGKHK FT KVRKREAGEPINAFRVSKKGTAMKCGNCFQWGHNQRTCKAPDNPNKKAYKK FT KKKGQLEQSSTSGAKGSKKLLVNFKYYFVELFIQISSTTLLNFFNFFGFL" XX SQ Sequence 5853 BP; 1866 A; 920 C; 1227 G; 1838 T; 2 other; gggaaaaatg cccatacacc ccttaaactt ttaactactg gtcaaaagac ccccttaact 60 tttttattga ccaatttact ccttaaacta ttcacaactg ccaaattaat acttcagtta 120 gtcacacgtt aaaatactaa cggaataaac acatgccact cacgtggctt ttaaatacaa 180 actaaaaaaa acccaaacat ccaaaaccca acggaagaga agagaaccag tccaggtccg 240 gcagagagag agagagagag agagagagag agactgcacg ccgttcatag ccactgccaa 300 gcttctctcc gccgtctcgc cgcccttgtc ccggcggcgc cttggtggtt ccgccgcact 360 gttcaatctg ggtatgtctt tttttttttt tttcttcttc ttcttacgtc ttgctattta 420 aatcttctaa gaacttttat ttttttttta atctccatgt gcgaattttt attgtagaaa 480 ttcttgtttt ggtttaattt ctgggttggg tctctatgaa attcttggtt ttttactttc 540 tccatgtgcc tttcaccaac tgttgcattt gaggatgcca tagagctgtt tgattaaatg 600 cctgagagag atatggctac tgctaagggg gtttggttgc ttggttatcc aattttccaa 660 atatgctggc cttccaagtt tcccttgcaa cccatttgct acaaaaaaat atcaaacaca 720 ataattggtt ctgtaatgat ccagaagcca ataactaaat cttcaattag agaaatttca 780 ttaattttgt cacttgcaaa tatgccttgt atccatccaa gaaataatgc agagctacat 840 aaggattgat catgaacatc caaaatcctg tttatgaatc ccttggtatt tttagtgtgt 900 tccagtttgg tccaaacttg ccatgtctaa ttacactata gaattagtgt agcacttttc 960 ttttttatta tgagaagata atgtagtttt tccatatgtt caggcaaggt cactttgtaa 1020 gtaagcctta cggtcttaat gtcttaacaa ccatcttatg caacatttgc aatgacgaag 1080 cagttgatac tgaaaaatca taaacatagt ttcaaaattt gcattaagtc actaaagatt 1140 ttacctagtt tgatccaaat aagtttattt tttatgataa ttcattagtt gggatagagg 1200 gaatttgatc gccgaatgtc tttgtaactc aactgattta aggtttctaa atactttgga 1260 atatggatcc attcaaaaga atattattaa tttttacatt tttctactgt tgctaggtgc 1320 atcttttttt tttttttttt tcccctaaag atgctgggtg cagctaagta atattaatat 1380 gtaatatata gtttactgtt aaagatatgg cttttggtta gtgttaaaga tactgggtct 1440 cggtgtaatg attccagcca tatggtctac tgactaagct agcatgttgt aatattttga 1500 attatgtgaa ttgaactagc agcaatcatg cacatgtgca tgagcaaatt gttatatttt 1560 ttttctcact attctctata ttgttttttt tttgtgcatg agcaaattgt tatatttttt 1620 ttctcactat tctctatatt gttttttttt tttaattatg ttttctccag ctcttctatt 1680 aatgttcttg ttaattttgt attgtagcca tggatgaaag tccactgtca ctccctggaa 1740 attcaccttc tatgccaaat gtacaagccc ctcaatccca atatgatttt attgaggctg 1800 atggccaatc tgaaattgtt aatgttccaa ttgatgtgga ggatgacgag gatgacgaag 1860 attacaattt gagtgatttt tctgaatctg atgatgatat aattgaagat tttggtatgg 1920 aggatgatgg aatcaataga gcaattggag gcaagcagct tgagggagtt tggaatggtg 1980 aaggagattc agatcatggg gatagtgatg agttaaggag tgcagaaggg tcatctgatg 2040 atgaagggaa ttcaaggcct aggttccctg agtttaacca gcgcattggc atggagaatg 2100 tacagctagt gaaggatcaa aaatttgcat cacatgtcat cttcaaggag gcactaaagg 2160 agtggtgtat taaagaaaaa catgattttg agtataagca caatgataag tggagagtga 2220 cagctgtatg taaaaaaaaa tgtggttgga agatacatgc atcccaaaca caaatgggag 2280 atgcctttca aatcaaaagt tttaaaagca ttcatacgtg tggcaaggat cataagaata 2340 gtaagatttc ttcaaggtgg ctagccaata aatatttgcc attctttaga gatgatcata 2400 cttggacagc aaatgcattg aaaggtgcag tgtttaggga ccatgaagtt gatgtgactt 2460 tggaccaatg ttataaggct aagagaatgg cattcaagat gatacatggt gctgaggaga 2520 agcagtatga gagactttgg gactatgcag ctgctattag gaagtggaat gtgggtagca 2580 cagtgaagat acaaactacg aatgatgtgt ttgagagaat gtatatttgt cttgatgctt 2640 gcaaaagggg atttttagca ggttgtaggc cacttattgg gatagatggt tgtcatttga 2700 aggggacaac aggtggacag ttgctggttg ctgttggaaa ggatgggaat gataatatct 2760 tcccaatcgc ttttgctatc gttgaaattg agaataaaag ctcttggacc tggtttctac 2820 aatgcttgtt ggatgacatt ggacatgtgg atgagaatgg atgggtcttt atctcagacc 2880 gacagaaggc aagaaacaat taatgtgcat gtgaattatt tatttatttt ttaaaaatat 2940 catgatctat aacctgaata tgaataacta atgtatattt gcgtattttt tatggcaggg 3000 attagtagag acctttaaag atttgatgcc taatgcagag cacagatttt gtgttaggca 3060 tttacatgca aatttcaaga aggattttcc tgggaaggta ctcaaagatg caatgtggag 3120 tgctgctagg gcaacaacaa agaattcttt tgacttccac atggatgagt tgaagaagct 3180 agatgtgaag gcatatgagt ggcttgtgaa gttagatgtg agaacatgga gcagacatgc 3240 ttttaatcca agaagcaaga gtgacactct agtaaacaat atagcagagt ctttcaatgc 3300 ttggattttg gaggctaggg ataaaccagt gttgacaatg atggagatca taagagtgat 3360 gttgatgcaa aggttgcaaa ccaaaagaga tcatatgaga aggtatgaag ggagggtttg 3420 tccaagaatc tataagaagc ttgagaggat aaaaagcgag gttggacatt gcatttctcg 3480 ttggaatgga gagtccaaat atgaggtgga gtatatttat ggtggaagat atgtggtgga 3540 cttgaatgag aggacttgtg gttgtgggag atggggattg agtggaatcc catgttttca 3600 tgctgctgct gcaataattg agcatggaga gcaacttgag acttatgtag acattgctta 3660 cactaaggag acattcctaa gttgttacca atggatgata agcccacttc caagccatga 3720 acaatggcca aaaacaccct atgacctaat caagccccca aaatttacaa agaaagtagg 3780 caagcataag aaggtaagaa agagggaggc aggagaacct attaatgcat ttagggtgag 3840 caagaaagga actgccatga aatgtgggaa ttgtttccag tggggccata atcaaagaac 3900 ttgtaaagct cctgataacc ccaacaagaa ggcttataaa aagaaaaaga aagggcaatt 3960 agaacaatca tctacatctg gagctaaagg gagtaaaaaa ttattggtaa atttcaagta 4020 ctactttgtt gaacttttca tccaaatttc aagtactact ttgttaaact ttttcaactt 4080 ttttggcttt ttatagggta ctcagcaatc aaatataggt actcaacagt caagtcaaag 4140 tcgtacaaag gacaacacta gtggaagcaa gaaggataag ggaaaggcta aggtttagtg 4200 gcagcaagaa gataaataat tttttagttc aataatttgt ttagtgatac acagccttct 4260 aaaaatattg atggagccag tatacttttg tttttcaata ttgcttggaa agtgtaatta 4320 ttgattcatt gagtgttatt tttttggcaa acaatatacc atttgtgaac acttatttga 4380 tatttcaatt catggcatat tgagatcctt ttaagaatac tgatggagcc agtatacttt 4440 tgtttttcaa tattgctgga aaagtgtaat tattgattta ttttcttaga gttattgcat 4500 aaagttcaat tcatggcaga ttgggacaca ttcatttttg gtggttattg cataaagaga 4560 agaagtacgc atcaaccaaa tcactcatac aacttgaatc aaaataaaga gaagaagtaa 4620 gatcatccca agattgttta ctttccttgt tgactacttg aattattaca gtgtcaaatc 4680 tacatcacac aactcaaacc ctccatagca gcctctcaat ttaatggctg taagagaacc 4740 tataacagaa gggggacata tcccattggc ttctattttt cattgctcct atatgacttg 4800 aaacctttac aagtatcaat ggaagaagaa aaaaaatgta actatacatt tcttccatct 4860 aaagaataga aacagatttc ataattcttg cagtcacaag gttcctaaag atctggtagt 4920 gttatcttcc caaagttgtt gcgatcaagc ttactgaagt aatcgcagat cagcaatata 4980 tctttctccc caatctttcc catctctttg agcttgtaaa ttacattatc tgatttgctg 5040 aaacaaataa gggaaatatt tagggttgat ttctacatga agaaggagaa aattaagaaa 5100 taataattga agtgcaaatg ggaagaaata ataattcgtg tttgatatgt ttttgttgca 5160 aatgggttgc aagggaaact tggaaggcca gcatatttgg aaaattggat aaccaagcaa 5220 ccaaaccccc ttagcagtag ccatatctct ctcaggcatt taatcaaaca gctctatggc 5280 atactcaaat gcaacagttg gtgaaaggca catggagaaa gtaaaaaacc aagaatttca 5340 tagagaccca acccagaaat taaaccaaaa caagaatttc tacaataaaa attcgcacat 5400 ggagattaaa aaataaaata aaagttctta gaaaatttaa atagcaagac gtaagaagaa 5460 aaaaaaaaaa aaaagacata cccagattga acagtgcggc ggaaccacca aggagccgcc 5520 gggacaaggg cggcgagacg gcggagagaa gcttggcagt ggctatgaac ggcgtgcagt 5580 ctctctctct ctctctctct ctctctctgt gccggacctr gactggttct cttctcttcc 5640 gttgggtttt ggatgtttgg gtgtttttca gtttgtattt aaaagccacg tgagtggcat 5700 gtgtttattc cgttagtgtt ttaacgtgtg actaaytaga agtattaatt tggcagttat 5760 gaatagttta aggagtaaat tggccaataa aaaagttaag ggggtctttt gaccggtagt 5820 taaaagttta aggggtgtat gagcattttt ccc 5853 // ID Gypsy-30_VV-I repbase; DNA; EDCOT; 4378 BP. XX AC chr4; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-30_VV_; KW Gypsy-30_VV-LTR; Gypsy-30_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4378 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr4; Positions 9252421 9256798. XX CC Positions [3270-3764] - Integrase core CC 'TTTTA' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 3186..4268 FT /product="Gypsy-30_VV-I_3p" FT /translation="MYKNIQDYIQQCATYQKTKSETLAPAGLLQPLPIPCL FT VWDDISLDFIDGLPSSQGKDSIMVVVDRLSKYAHFIALSHHFSAKMIAEKF FT VENIIKLRGMPKSIISDRDPIFVSKFWQEFFTMSGTQLKLSSAYHPQTDGQ FT TEVVNRCLEQYLRCFVHQWPRKWFSYLSWAEYWYNTTYHCSTGMTPFQALY FT GRLPPSIPHYADGLSRVNEVDQSLLTRDEVLQQLKTNLELAATRMKHVADQ FT KRREVEFQIGDLVLLKLHPYRQHSVFKRAHQKLANRFYGPFPVEQKLGKVA FT YRLSLPPEAKIHPVFHVSLLKKYVGTSLPALVDLPPISDEGQLQVTPEKVV FT NTRWIKRGTKFIEESLVQ" FT CDS join(18..1589,1593..3164) FT /product="Gypsy-30_VV-I_1p" FT /translation="MTTNKERIEILEQGVGGLQDEVQRLGLGMNDRMQRLE FT ESLKALSDVVLSSKAAQPSHSSHSVKQGHTPQYQHEETESSRLNIPSLRTK FT IEFPRFAGDDPMEWFNRVAQFFEFQRTPEDQKVSLAAFHMEGEANQWWQWL FT NRTYKEENRTVTWTMFADELWARFGPTDGEDFDEALSHIKQSGSLRDYQRE FT FEKLGNRVHGWTQKALVGTFMGGLKPEIADGIRMFKPKMLKEAISLARTRD FT EQLTRQRRFACPIPPNRPAAAVTSINQRTSIVPKRLGWEEMQKRRAQGLCF FT NCNERFTPGHKCQGPRLLLIEGHDEVQDKEEEAEISDNREDELEVSIHALT FT GWASPRTMRVAATIKSQLIMVLIDSGSTHNFLSDKVARTLRLPVVPTKSFT FT IHVANGERLLCQGRFEKVPIDLQGIPFSLTCYSLPLAGLDMVLGIQWLEML FT GSVVCNWQYLTMDFNWENQARRLQGIQGPIQATSLETIAKEHRQGHMVFTV FT YVQTVEGPSWDGTQPDMQQILGEFEDVFEPFKLPPLREIDHHIPLKEGTQP FT INVRPYRYAYFQKAEIEKQVQAMLDVGIIRPSTSPYSSPVLLVKKKDDTWR FT FCTDYRALNAATIKDRFPIPTVDDMLDELYGATYFTKLDLRAGYHQVRVHA FT PDIPKTAFRTHNGHFEYLVMPFGLCNAPSTFQAIMNSIFRPYLRKFILVFF FT DDILVYSPTWELHLNHVRKTLEILKKHSFFVKATKCDFGKQELEYLGHIVT FT NHGVKVDGKKIEAMIAWPQPTTITELRGFLGLTGYYRKFVRNYGVLARPLT FT NLLKKGNFKWDEDAAAAFTMLKQALTTTPTLAMPNFNEPFTIETDASGDGI FT GVVLTQQGRPIAYMSRALGVTKRSWSIYAKEMLAIVEAIRTWRPYILGRKF FT FIRTDQRSLKYFLEQRVATSEQQKWVAKLLGYDYEIIYRPGKENSAADALS FT RRPNSPLLNPIFISQVSLWDDIRKAAATDLYMKKIFQQAAHDPTGHYVVKN FT GLCFYKQRVVVSTALRGQLLQEFHDSKVAGHSGVLRTFKRLA" XX SQ Sequence 4378 BP; 1302 A; 898 C; 1008 G; 1170 T; 0 other; ttggtatcag agccacaatg acaaccaaca aagagcgtat tgaaatatta gagcaaggag 60 tgggaggctt acaggatgag gtgcagcgac ttggacttgg aatgaacgat cgtatgcaac 120 ggctggaaga gtctttgaag gctttatctg atgttgttct ctcctcaaag gcagctcaac 180 cctcgcattc ctcgcactca gtgaaacagg gacacacgcc tcagtaccaa catgaagaaa 240 cagaaagttc tcgtctgaac ataccctctc ttcgaaccaa aatcgagttt ccgcgatttg 300 caggggatga tcccatggag tggttcaata gagtagcaca gttctttgaa tttcaaagaa 360 ctcctgaaga tcaaaaggtg agcttggcag ctttccacat ggaaggtgaa gcaaaccagt 420 ggtggcaatg gctgaatcgg acatacaagg aagaaaatcg aaccgtaacc tggactatgt 480 ttgccgacga gttgtgggca cgattcggtc caactgatgg agaagacttt gatgaggctc 540 tttcacatat aaaacaaagt ggttcacttc gggattacca aagagaattt gagaaattag 600 gcaatcgggt acatgggtgg actcaaaagg ctctcgttgg aactttcatg ggaggattaa 660 aaccagagat agctgatggg atacgaatgt tcaagccaaa aatgttaaaa gaggccatca 720 gtttggctag gaccagagat gaacaactta ctcgacaaag gagatttgct tgcccaatcc 780 caccaaatcg tcctgcggca gccgtcactt cgatcaatca aagaacatcg atagttccta 840 aacgattggg ttgggaagaa atgcaaaaac gacgagctca ggggctatgt ttcaactgca 900 atgagcgatt cacaccaggc cataaatgcc agggacctag actgctgctc attgaaggcc 960 acgatgaggt ccaggataaa gaagaagagg cagaaataag cgataacaga gaagatgaac 1020 ttgaagtttc tatacatgct ttgacgggat gggcatcccc aaggaccatg cgagtagctg 1080 ccactatcaa atcccaactc ataatggtgt taatcgatag tggatctaca cataatttcc 1140 tgagcgacaa agtggcaaga acattgcggc ttccagtagt tcctacgaaa tccttcacaa 1200 tccatgttgc caatggggaa cgactcttgt gtcaagggcg atttgagaag gtaccgatag 1260 atttacaagg cataccattc tctcttacgt gttactcctt gccgttagca ggactagaca 1320 tggtgttggg aatacaatgg ttggagatgc ttgggtctgt agtttgtaac tggcagtatc 1380 taacaatgga tttcaattgg gaaaatcaag cacgaagact acaagggata caagggccca 1440 ttcaagctac ttcacttgag accattgcaa aggagcaccg acaaggtcac atggttttta 1500 ctgtatatgt gcaaacagtg gaaggacctt cctgggatgg cactcaacca gatatgcagc 1560 aaattttagg cgaatttgag gatgtctttt aagagccctt taagctgcct ccactacgag 1620 aaatcgatca tcatattcct ctcaaggaag gaactcaacc catcaacgtt cgaccatatc 1680 ggtatgcgta ttttcaaaag gcagaaattg agaaacaagt gcaggcaatg ctggacgtag 1740 ggatcatccg accaagcact agtccatatt catcccctgt ccttttggtg aaaaagaaag 1800 atgatacttg gaggttttgc acagattaca gagcactaaa cgcagctacg attaaagatc 1860 gatttcctat tccaacagtg gacgacatgt tggacgagtt gtacggagct acctatttta 1920 ccaagctaga tcttcgagct ggttatcacc aggtacgagt tcatgctccc gacattccaa 1980 aaactgcatt tcggacgcat aatggacact ttgagtatct tgttatgccc ttcggcttat 2040 gtaacgctcc atcgactttt caagccataa tgaactctat ttttcgtcct tacctccgaa 2100 aattcatatt agttttcttt gatgacatat tagtctatag tcctacatgg gaattgcatt 2160 tgaatcatgt aaggaaaaca ttagagattt tgaagaaaca cagcttcttc gtcaaagcaa 2220 ccaaatgtga ctttggaaag caggaattgg agtatttggg ccatattgtg acgaatcatg 2280 gggtcaaggt agatggtaag aagattgaag ctatgatcgc atggccacaa cccactacta 2340 ttactgaatt gcgtggcttt ttaggcttga cagggtatta taggaaattt gtccgaaatt 2400 atggagtatt agctcgtcct ctcaccaacc tgctcaagaa ggggaacttc aaatgggatg 2460 aagatgctgc tgctgcattc acaatgctca aacaagctct gacgactaca cccactcttg 2520 caatgcctaa tttcaatgag ccattcacaa ttgagactga tgcttctggg gatggaattg 2580 gagtggttct aactcagcaa ggaagaccaa ttgcatacat gagtcgagct ttgggggtta 2640 ctaaacgtag ttggtcaatc tatgccaaag agatgttagc aattgtggag gccattcgga 2700 cttggagacc atacatcttg ggtcgaaagt ttttcattcg aaccgaccaa cgcagtctca 2760 agtatttttt ggagcaacga gtagccactt ctgagcaaca aaaatgggtg gctaagcttc 2820 ttggatatga ctatgagata atatatcgac ccgggaaaga aaattcagca gctgatgcat 2880 tgtctcgccg ccccaatagc cctctcctca acccaatatt tatttcacag gtttctttat 2940 gggatgacat tcgaaaggca gcagcaactg atttgtatat gaaaaaaata ttccagcagg 3000 cagcacatga tcctacaggc cattatgtag taaagaatgg actgtgtttt tacaaacaaa 3060 gggtggtggt ttccactgca ttgcggggtc agttgctcca ggagtttcat gacagtaagg 3120 tggctggaca ttctggagtt ttaagaactt tcaagagact agcttagcag ttttattggc 3180 cttctatgta caaaaatatc caagattaca ttcaacaatg tgcaacctac caaaagacta 3240 aatctgagac actagcacca gctggattgc tccaacccct cccaattcct tgtttagttt 3300 gggatgacat ctccttagat tttatcgatg gattgccatc ttcacagggc aaggatagta 3360 tcatggtggt ggtggataga cttagcaagt atgctcattt cattgcttta tctcatcatt 3420 tctctgcgaa aatgattgct gaaaaatttg tggaaaatat tattaaactt cgtgggatgc 3480 caaagtccat cattagtgat cgagacccca tttttgtaag caaattttgg caggagtttt 3540 ttaccatgtc gggtactcag ttgaagctaa gttcagctta ccatcctcag acggatggac 3600 aaacggaggt ggtgaaccgt tgtctagaac agtatctgag atgttttgtc catcaatggc 3660 ctcgaaaatg gtttagctat ctatcatggg cagaatattg gtataacacc acctatcatt 3720 gttcaaccgg gatgacacca tttcaagcct tatatggtcg ccttcctcca tcaattcctc 3780 attatgcaga tgggttgtca cgtgttaatg aggtcgatca aagtctcctt acacgggatg 3840 aagtattgca gcaattgaaa acgaatttag agttggctgc cactagaatg aaacatgtgg 3900 ctgatcaaaa gagaagagaa gtggagtttc aaatcggaga tctggtgcta cttaaattgc 3960 atccttaccg ccagcattct gtgttcaaac gtgcccatca aaaacttgct aatcgtttct 4020 atggtccatt tccagttgag caaaagttgg gcaaggtagc atatcgtctc agtttaccac 4080 ctgaagctaa gattcatccg gtgtttcatg tttctctctt aaagaagtat gtgggaactt 4140 ctctgcctgc gcttgttgat ctgccaccaa tttctgatga agggcagctt caagttacac 4200 cagagaaggt agtcaataca agatggatca agcgtggtac caagttcatt gaagaaagct 4260 tggtgcagta gaagaatttg cctgtagaag atgctaccta ggaagatacg cagatgctca 4320 agcatcaatt ttgtacactg aaccttgagg acaaggttcc acttatgggg gggagtat 4378 // ID Copia-82_Mad-I repbase; DNA; EDCOT; 4265 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-82_Mad_; KW Copia-82_Mad-LTR; Copia-82_Mad-I. XX NM Copia-82_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4265 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1702-1702 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1464-1964] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 36..4037 FT /product="Copia-82_Mad-I_1p" FT /translation="MSKGKMNADQGPALKPFDGKDDFTDWQRMMKNVLIQQ FT DLDDALDGEKPENMTEAAWTKVLKKAKSSIEIHLTRSVRSHITEKMTAQEA FT WEKLENVYMGKTVSNKLFLKDELFGLRLEEGGDIEDHVCRFQNCIANLQKV FT EETYKDDDMAIILLRSLPSSFKHFRTTLMFGKESLKLEDVIQALQSYAKLD FT DITESSQGLYAKGKERGREKTKEEKIGNRGRSKSKKKKEKKEGCFECGSAD FT HWKRNCKIWKEKKAKMEGSSGSASAVTEHESDGELLSVTSGSKAFTNWILD FT TGCTFHMCAVREWFDTYKEVSSGEVLMGDDSSCPVRGIGTVRIRMFDGMIR FT ALGNVRYVPRLRKNLISLGTLDEAGYGYKSKKGRLRVTKGSLVVMRGDLQP FT NKLYKLIGTTIVGGAAVSVNQSVEDKTELWHHRLGHISQKGLQELHKQGLL FT EGVSSCKLDFCEYCVLGKQRKVSFASSSADNRSKEQLSYIHSDVWGPAPTK FT SNGGARYFVTFMDDFSRKVWVYFMKQKSEVFAKFKEWKTETENQTGRKIKY FT LRSDNGGEYTSNEFADYCKQEGIIRHFTVKKNPQQNGAAERMNRTLMERER FT SMRFHAGLPDSFWAEAVNHASYLINRSPSTVLGFKSAEEVWSEKPVDYSKL FT RVFGCSAYAHIPSDERSKLKPKSTHCIFLGFEKGVKGFKLWDFNNRKKVVS FT RDVVFDETTMPLNKVESSREKTDDAEIEATKIPLISSDEEEAQVEQIEQEA FT ESDGFEEEEEHQHRSPVRNQVEQETGQIEGTPIRQTSQRVRTPTNNPPAFQ FT RCIALDKPNRNKKKPDRFGFDQDEVNYALNISQGDPTTYREAIASDERDSW FT ISAMTEEMESLYKNSVWELVPKPKDRKLVGCKWVFRKKEGLHEQDAVRFKA FT RLVAKGYSQKEGVDYDEIFSPVVKHTSIRLLLAMAAQHDMEIEQMDVKTAF FT LHGDLEETIFMAQPEGFVEYGKENLVCQLRKSLYGLKQSPRQWYKRFDSFM FT LKINFRRCLYDCCVYYHVFQDGMIILLLLYVDDMLIACQDKSRIQDLKKML FT SEEFDMKDLGAAQKILGMEIQRDRTAGRIWISQAKYIQKVLEKFNMQEAKV FT VSTPLAAHFRLSGQQCPTSEEEQQVMKNVPYANAVGCLMYAMVCTRPDIAQ FT AISVVSRYMANPGKQHWDAVKWILRYLKGSWRQRIMFERQKENAGVLGYVD FT ADYAGDLDKRRSTSGYVFTCAGGPISWRALLQPITALSTTEAEYIALAEAG FT KEAIWLSGLVSQMGITQDCVKLKCDSQSAIHLAKNQVFSGRSKHIEARYHR FT IRDWVESKEIWIEKVHTDDNAA" XX SQ Sequence 4265 BP; 1360 A; 734 C; 1140 G; 1030 T; 1 other; attggtatca agagctagga tcaaggtgtt ctacgatgtc aaaagggaag atgaatgcgg 60 atcaaggacc tgcgttaaag ccctttgacg gcaaggatga cttcacggac tggcaaagga 120 tgatgaagaa cgtactgata caacaggatt tggatgatgc actcgatggt gagaagccgg 180 aaaacatgac agaggcagca tggactaagg ttctcaagaa ggccaagagt tccatcgaga 240 tccatctcac aagatcagtt cggtcacaca tcaccgaaaa gatgactgcc caggaagcat 300 gggaaaagtt ggagaatgtt tatatgggca aaaccgtgtc caataaactt tttctaaagg 360 atgaactatt cgggcttcga ctagaagaag gaggtgatat tgaagatcat gtatgcaggt 420 tccagaattg catagctaat cttcagaagg tcgaagaaac ttacaaagat gatgatatgg 480 ctatcatctt gctgaggtct ctaccttcgt ctttcaagca ctttcgaaca actctaatgt 540 ttggaaaaga gtccctgaag cttgaagacg taattcaagc tcttcagtca tatgctaaac 600 tggatgatat aactgaaagc tctcaaggcc tttatgccaa aggcaaggag agggggcggg 660 aaaagacaaa ggaagagaaa atcggcaata gaggtaggtc aaaatccaag aagaaaaagg 720 aaaagaagga aggttgcttc gaatgtggtt cagccgatca ttggaagagg aactgcaaga 780 tttggaaaga gaagaaagcc aagatggaag gaagctcagg ttcagctagt gcagtcaccg 840 agcatgagag tgacggggag cttctttcag taacatcagg ctccaaggct ttcaccaatt 900 ggattttgga taccggatgc acttttcata tgtgtgcagt aagggaatgg ttcgatactt 960 acaaagaagt cagcagcggg gaagtcttaa tgggggacga ttcttcatgt cctgtaagag 1020 gaatcggcac tgttcgaatc agaatgttcg atgggatgat acgagctttg gggaacgtca 1080 ggtatgtccc tagactaaga aagaatttga tttccttggg tactttagac gaggccggtt 1140 atgggtacaa gtctaaaaaa ggaagactca gggtaaccaa aggatcgcta gtggtaatgc 1200 ggggtgacct acaacccaat aagttgtata agttaattgg gaccactata gtcgggggag 1260 cagctgtttc cgtaaatcag agtgtagaag acaagactga actctggcat cataggctcg 1320 ggcacataag ccagaaaggg ttgcaagaat tacacaagca aggcctgttg gaaggcgtgt 1380 catcttgcaa actggacttt tgtgaatact gtgttctcgg aaagcaaaga aaggtatcat 1440 tcgcaagtag cagtgcagat aaccgaagca aggagcaact cagctatatt cactcagatg 1500 tttggggccc tgcaccaact aaatcaaatg gtggagccag gtattttgtt actttcatgg 1560 atgatttttc taggaaggtt tgggtttatt tcatgaagca gaaatccgag gtttttgcaa 1620 agttcaagga atggaaaaca gaaaccgaga atcaaactgg aagaaagatc aagtacctga 1680 gaagtgacaa tggaggtgaa tatacaagta atgagttcgc cgattactgc aagcaggaag 1740 gcatcataag gcacttcaca gtaaagaaga atccccaaca aaatggagct gctgagagga 1800 tgaaccgaac tctcatggag agagagagga gcatgcgatt tcatgcagga ttgcctgata 1860 gtttttgggc agaggctgtt aatcatgcaa gttatttgat taacaggtca ccatctacag 1920 ttctcggttt taagagtgca gaagaggtat ggtctgagaa gccggtggac tattccaagc 1980 tcagggtgtt cggctgtagt gcttatgcac atattccaag tgatgaaagg tccaagctca 2040 aaccgaagtc tacacattgc atattcttag gttttgagaa aggagttaag ggtttcaagc 2100 tttgggattt caacaacagg aaaaaggttg tcagtcgaga tgttgtcttt gatgagacaa 2160 ccatgcctct taataaagtc gagagcagta gggagaagac ggacgatgct gaaattgaag 2220 caacaaagat tccattaatc agttcagatg aagaagaagc tcaggtggag caaatcgagc 2280 aagaggccga atctgatggt tttgaggaag aagaagagca tcagcatcgt tcaccagtta 2340 ggaatcaggt ggagcaagaa acagggcaga ttgaaggcac tccaatccgc cagacatccc 2400 aaagggttcg aactccaacc aacaatccac ctgcattcca gagatgcata gcactagaca 2460 aacctaatcg gaacaagaag aaacctgaca gatttgggtt tgaccaagac gaagttaatt 2520 atgctcttaa cattagtcaa ggagatccga ctacttatcg agaagctata gctagtgatg 2580 agcgagatag ttggataagt gctatgacag aagaaatgga gtctctttac aagaactctg 2640 tttgggagtt ggttcctaag cccaaagaca gaaagctagt tggatgcaag tgggtattta 2700 ggaaaaagga aggactacat gaacaagatg ccgtgagatt caaagcaagg ctcgtggcta 2760 aggggtactc acaaaaggaa ggggtggatt atgatgagat cttttcacct gtagtcaagc 2820 atacttctat cagattgctt ttagcaatgg cagctcagca tgacatggag attgagcaga 2880 tggatgtgaa gacagcgttt cttcatggag atctagagga gacgattttc atggctcaac 2940 cagaagggtt tgttgaatat gggaaagaga acctagtatg tcagctaagg aagtccctgt 3000 atggcctgaa acagtctcca agacagtggt acaagaggtt tgattcattc atgctgaaaa 3060 tcaattttag aagatgttta tatgactgtt gcgtgtacta tcatgtgttc caagatggga 3120 tgatcatatt gctattgcta tatgtggatg acatgctaat tgcttgtcaa gacaagtcta 3180 gaattcaaga cttgaagaag atgttgagcg aggagtttga catgaaggat ctaggtgctg 3240 cacagaagat ccttggcatg gaaattcaga gagataggac cgctggaagg atctggatat 3300 cacaagccaa gtatattcag aaggttcttg agaagttcaa catgcaagaa gcaaaggtag 3360 tttcgactcc tttggcggct cacttcaggt taagtgggca acagtgtcct acgtccgagg 3420 aagagcaaca agtaatgaag aatgtgcctt atgctaatgc agtgggctgc ctcatgtatg 3480 caatggtatg cacacgtccc gacatagctc aagcaatcag tgtcgtttcc agatacatgg 3540 caaatccagg aaagcaacat tgggatgcag tcaagtggat tttgcgttat ttgaagggtt 3600 cttggcgaca aaggattatg tttgagaggc aaaaggaaaa tgcaggggtg ttaggatatg 3660 tggatgccga ttatgcaggg gacttggaca agagaaggtc aacttctggt tatgtgttta 3720 catgcgcagg aggaccaatc agttggaggg cactactgca accaattaca gctttgtcga 3780 ccacagaggc agagtatatt gcattggccg aagctggaaa ggaagcgatt tggcttagtg 3840 gcttggtaag tcaaatggga atcactcaag attgtgtgaa gctgaagtgt gatagtcaaa 3900 gtgccattca cttggcaaag aatcaggttt tttctggaag atcaaagcac attgaagcaa 3960 ggtatcacag aatcagagat tgggtggagt ctaaggaaat ttggattgaa aaggttcata 4020 cggatgacaa tgccgcakat ttccttacaa agatagtgcc ggccaagaag ttcaagcatt 4080 gcttgaactt gatcaatctc gttgattgat taaagtggag cacctcctca cttgaggtgc 4140 aatgaggcaa gaagaagatt gccaaggtga agactcttga agatttccag agctgcttca 4200 agaaggttca aagatactct ggggtgcaac gatcaagact tggtttgact caccaaggtg 4260 gagat 4265 // ID Copia28-VV_I repbase; DNA; EDCOT; 4733 BP. XX AC . XX DT 12-SEP-2007 (Rel. 12.09, Created) DT 12-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW internal portion; Copia28-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4733 RA Obukhanych T. and Jurka J.; RT "Copia28-VV."; RL Repbase Reports 7(9), 788-788 (2007). XX DR [1] (Consensus) XX CC This is an internal portion of Copia28-VV LTR retrotransposon CC from Vitis vinifera. Individual copies are 96% similar to their CC consensus. LTRs, deposited as Copia28-VV_LTR, are 98% identical CC to each other. Target site duplications are 5-bp long. XX FH Key Location/Qualifiers FT CDS 72..2567 FT /product="Copia28-VV_I_1p" FT /translation="MAKSEIPTDFSKADLSNPYFTHHSDHPGLVLISKSLN FT GDNYLAWKRAMILALNSKNKLGFVNGSIKAPSEEIDPEGYATWSRCNDMVH FT SWIVNTLNPEIADSVIYYSTAHEVWEDLCERFSQSNAPRIFEIQRDIACLR FT QEQLSVSAYYTKLKGLWDELASYNAAAHGAQQDQQKLMQFLMGLNESYSAI FT RGQILLMNPLPSVRQAYSSVSQEEKQRLLTSTNAAAESAASAAMAVRSNGK FT SSATWKDGIDRSNTGRMEPTDRPSGSQNFRVNRSSQGQDGRPFFDQDRRRM FT GSGRGRPQCSYCGDMGHWVQKCFQLHGYPPGHPKARMNLGSNSNRNKSFSA FT ANQVSEADEGKPAVALSEAQLKQLLSLLNNQDENSSSKVNAVTKPGLSKVA FT SRNWIIDSGATDHITSSSKLLHKDKNCSLPPVLLPSGEKTNIVTKGTLPLN FT SVYYLHDVLSVPTFKVDLISVSRLTRGLNCSVTFFPYWCILQDLATRRTIG FT LGKQRDGLYYLVALATEKSLTNHSSSTNQPACNLAISSTDLWHSRLGHVSP FT SRLSFIAKNFLNFSVQSNNACPICPLAKQSRLPFGTSAISSTKPFEIIHCD FT IWGRYRHPSLFGAHYFLTIVDDYTRFTWIFLMRHKDEAQSLLKRFFSYVFT FT QFEFRIKTFRSDNGREFTSLRSFFQDNGVIFQHSCVYTPQQNGVVERKHRH FT ILQVARALKFHAQVPTQFWGECALTAVHIINRLPSPVLSFKTPFELLYSKP FT PSYSHLRVFGCLAYATNVHTSHKFDYRAMPCHPSSSVILLVRKHTNYLIYQ FT PKRSLLAEMSNFMKIFFLMSLSSPTLLSLR" FT CDS 2414..4723 FT /product="Copia28-VV_I_2p" FT /translation="MPSIFIGYPVGQKAYKLFDLSTKKVFTSRDVKFHEDI FT FPYVSLKPNSTLPSLTHNSGPIPLVAHDISSSLDSTSHALSPLLSNHTSTP FT SPTTENDDFSSPSRPSELVPSSPVLAPTPPSILRTYTRSPKPSSLLNNPTP FT IEPSSQIDPNPSPPPSTTLVSPSPVPPFASIPSAPPAETPIFSPETHSPKP FT ATPLRRSSRHIAPPIKLHDYVCSHVSSNQSSSLIPGPTKGTRYPLANYVSY FT HRYKPAYRSFVAQHSAVTEPRSYSEAAAHPEWQEAMRSELQALQANGTWSL FT TPLPAGKTPIGCRWVYKIKHRSDGSIERYKARLVAKGFTQLEGVDYQDTFS FT PTAKIISVRCLLALAAARGWSLHQMDVNNAFLHGDLHEEIYMSPPPGLRRQ FT GEENLVCRLHKSLYGLKQASRQWFAKFSEAIRSAGYAQSRADYSLFTRKQG FT KSFTALLIYVDDILITGNDPVSIATTKKFLHSHFHLKDLGDLKYFLGIEVS FT ASKNGIFISQRKYALEIIEDAGLLGAAPIDTPMERGLKLSDKSDLLKDQGR FT YRRLVGRLIYLTVSRPDITYAVHVLSRFMHQPRKAHMEAAFRVVRYLKNAP FT GQGLFFSSNNDFRLRAYCDSDWAGCPLTRRSTTGYCVFLGPSLISWRSKRQ FT KTVSLSSAEAEYRAMTGACCELTWLRYLLKDLGVLHQEPALLYCDNKAALH FT IAANPVFHERTRHIEMDCHYIRDKIQDGSIITRHVSSAHQLADILTKPLGK FT EIFAPMIRKLGVQDIHSPT" XX SQ Sequence 4733 BP; 1219 A; 1167 C; 943 G; 1404 T; 0 other; gagcaggact aaaatcctga ttcattgctg cactctaatc tctcgtgtag catctctttt 60 cttcaatcat catggcaaaa tcagagattc ctacggattt ctcaaaggca gatctctcca 120 atccctattt cactcaccat tcagatcacc caggtttggt tttgatttcc aaatctttga 180 atggagacaa ttatttggct tggaaaaggg ctatgattct agctttaaat tccaagaaca 240 aattgggttt tgttaatggc tcgatcaagg ctccttcaga agaaattgat cctgaaggtt 300 atgcgacttg gtcacggtgt aacgacatgg ttcactcctg gatcgtcaat actctcaatc 360 cagaaattgc ggacagtgta atctattatt ctactgctca tgaagtttgg gaagatctct 420 gtgagcgatt ctctcagagc aatgcgcctc gcatctttga aattcagcga gatattgctt 480 gtcttcgaca agagcaactc tctgtctctg cctattacac aaaattgaaa ggcctgtggg 540 atgaactggc ttcctacaac gctgcagcac atggggcaca acaagatcaa caaaaattga 600 tgcaatttct gatgggtttg aatgaatctt acagtgctat tcgcgggcaa atcctcctga 660 tgaatcctct cccttctgtc cgccaagcat actcctctgt ctctcaagaa gaaaagcaac 720 gcctcctcac ttcgacgaac gcagcagcgg aatctgccgc aagtgctgct atggccgtgc 780 gcagcaacgg caagtcttcg gcaacttgga aggacggaat agatcgatcg aacacaggaa 840 ggatggaacc gactgatcgc ccctctggtt ctcaaaattt ccgggtgaat cggtcttctc 900 aaggacaaga tggcagacca ttttttgatc aagatcggcg ccgcatgggt tctggaagag 960 gacgccccca gtgctcgtat tgtggagata tgggtcattg ggtccaaaag tgttttcaac 1020 tacatggata cccaccaggc catcctaaag caagaatgaa cttaggctca aactcaaatc 1080 ggaataaaag tttttctgcg gctaaccaag tttctgaggc agatgaaggg aaacctgcag 1140 ttgcattgtc agaagcccaa ctcaagcaac ttttgtcact tcttaataac caagatgaaa 1200 actctagttc caaagtgaat gcggtaacaa agccaggttt gtccaaagtc gcttcccgca 1260 attggattat tgatagtggg gcgacggatc atattacttc atcctctaag ttattgcata 1320 aagataaaaa ttgctcgtta ccgcccgtat tgttgcctag tggagaaaaa acgaatattg 1380 ttacgaaagg gactttgcct ctgaattccg tctattatct gcatgatgtc ttatctgtgc 1440 ctacattcaa agttgattta atatcagtta gtcgtttgac aagaggtcta aattgttcag 1500 tgacgttttt cccttattgg tgtattttgc aggatctggc tacgaggagg acgattggtt 1560 tgggtaaaca acgtgacgga ctatactatt tggtggcact agcgacggag aaatctttaa 1620 ccaaccattc ctcatccaca aaccaaccag cctgcaatct cgccatctct tccaccgatc 1680 tctggcacag tcgcttaggc catgtatcac cttctcgttt gagtttcatt gccaagaatt 1740 ttttgaattt ttctgttcag tccaataatg cttgccctat atgtcctttg gctaagcaaa 1800 gtcgtttacc ttttggtact agtgctattt cttctacaaa accttttgag attattcatt 1860 gtgacatttg gggtcgttat cgacaccctt ctctgtttgg tgcccattac tttctcacta 1920 ttgtcgatga ttatacacgt ttcacttgga tatttttaat gcgacataaa gatgaagcac 1980 aatcactttt aaaacgtttc ttcagctatg tgttcacaca atttgaattt cgcattaaaa 2040 cttttcgaag tgacaatggt agagaattta cctcacttcg ttcctttttt caagataatg 2100 gtgtcatctt tcagcattct tgtgtttaca cgcctcaaca aaatggggtt gtggaacgca 2160 aacatcgtca tattttacaa gtagcccgag ctttgaaatt ccatgctcaa gttcccactc 2220 aattttgggg ggagtgtgct ctcactgccg tacacatcat caatcggtta ccttcaccag 2280 tattgtcttt caaaactcct tttgaattgc tttactcaaa accaccttct tactcccatc 2340 tccgtgtttt cggatgttta gcctatgcca ccaatgttca cacctctcac aaatttgatt 2400 accgtgccat gccatgccat ccatcttcat cggttatcct gttggtcaga aagcatacaa 2460 attatttgat ttatcaacca aaaaggtctt tactagccga gatgtcaaat ttcatgaaga 2520 tatttttcct tatgtctctc tcaagcccaa ctctactctc ccttcgttga cccataattc 2580 tggtccaatc cccttggtgg cccacgacat ctcttcctcc cttgactcta cttctcacgc 2640 actttcccct cttctttcca accacacaag cacaccgtct cccaccacag aaaatgacga 2700 cttttcctct ccttctcgac cttccgaact cgttccctct tctccggtgc tggcaccaac 2760 cccaccctcc attcttcgta cctatacccg aagcccaaaa ccttcctcct tactaaacaa 2820 tcctaccccg atcgaacctt cttctcagat tgatccaaac ccttcaccac cgccttctac 2880 aactctagta tcgccttctc cggtgccacc gtttgcatcc atcccgtccg ctcctccagc 2940 cgagacaccc atcttttcac cagaaacaca ctcacccaaa ccagccactc cgctccgtcg 3000 ctccagccgc catatcgccc cgccaatcaa gctccacgat tatgtttgct cccacgtttc 3060 ctccaatcaa tcgtcttcct tgattccagg tccaactaaa ggtacacgat atccactggc 3120 caattatgtt tcttatcaca gatataagcc tgcatataga tcttttgttg ctcaacatag 3180 tgctgtcaca gaacccaggt cttattcgga agcagccgct catcctgagt ggcaggaggc 3240 aatgcgttct gaattgcagg ctctccaagc taatggcact tggtctctca ctccacttcc 3300 ggccggcaag acaccgattg gctgtcgatg ggtgtataaa attaaacacc gttcagatgg 3360 gtctattgag cgttacaaag cacgattggt agcgaaaggc tttactcaat tagaaggtgt 3420 cgattatcag gatacctttt cccccactgc caagatcata tctgtccgct gcttgcttgc 3480 attggccgca gcccgtggct ggtctcttca tcaaatggat gttaacaacg cttttcttca 3540 tggcgactta catgaggaaa tatatatgtc tccgccgcca gggcttcggc gacaggggga 3600 ggaaaacttg gtatgtcgcc ttcataaatc actctacggt ctgaaacaag cttctcgcca 3660 gtggttcgcc aagttctcag aagctattcg atccgccggt tatgcacaat ctcgagccga 3720 ttattctttg ttcaccagaa aacaaggcaa gtcctttact gccctcttga tatatgttga 3780 tgatattctg attactggaa atgatcctgt gagcattgct acaacaaaaa aatttctgca 3840 tagtcatttt catctcaaag atctgggtga tttaaaatac tttcttggca ttgaggtttc 3900 tgcttctaaa aatgggattt ttatttccca acgtaagtat gcattagaga ttattgagga 3960 tgcaggattg ttgggcgctg cccctattga tacacctatg gaacgaggat tgaaattgtc 4020 tgataagagc gatttgctca aggatcaagg tcgttatagg agattggttg gaaggttaat 4080 atatctaact gtgtcgaggc cagatatcac ttatgcagtt catgtgttaa gccggtttat 4140 gcatcaaccg agaaaggctc atatggaagc agcgttcaga gttgtgcgtt atctcaagaa 4200 tgcacctggt cagggtctgt tcttctcttc gaataatgat ttcagattga gagcctactg 4260 tgattctgat tgggcaggtt gtccacttac tagaaggtcc actacaggct actgtgtatt 4320 ccttggacct tcactgattt cttggagatc aaagcgacag aaaacagtgt cactctcttc 4380 agccgaagca gagtatcgtg caatgacagg agcttgttgt gagttgacat ggcttcggta 4440 ccttttgaaa gatttgggtg ttttacatca ggaacctgcc ttgctgtatt gtgacaacaa 4500 ggcagcgttg cacattgcag ccaaccctgt tttccatgag cgtactagac acattgagat 4560 ggattgtcac tatattaggg acaagatcca agatggttcc attattacaa gacatgtgag 4620 ctcagcgcac caacttgcag acattctgac taaaccattg ggaaaggaga tttttgctcc 4680 tatgattcgc aagttgggag tgcaggatat ccactctcca acttgagggg gag 4733 // ID PSAT3_PS repbase; DNA; EDCOT; 459 BP. XX AC . XX DT 23-MAY-2005 (Rel. 10.05, Created) DT 03-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE P. sativum satellite sequence - a consensus. XX KW Satellite; Simple Repeat; satellite repeat; PSAT3_PS. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RA Neumann P., Nouzova M. and Macas J.; RT "Molecular and cytogenetic analysis of repetitive DNA in pea RT (pisum sativum L.)."; RL Genome 44(4), 716-728 (2001). XX RN [2] RP 1-459 RA Gentles A. and Jurka J.; RT "A consensus of P. sativum satellite sequences."; RL Direct Submission to Repbase Update (20-MAY-2005). XX DR [2] (Consensus) XX SQ Sequence 459 BP; 152 A; 133 C; 107 G; 67 T; 0 other; cgacgtagtt cgggacaggg gaaaacgggc tcgctaggat gtcgcatcct atgcctacgt 60 atctcctctg gaaggagaat cagagctccc gtagttcggc tcacgcacgc caaacaaaac 120 cacacaggaa accgactgcc aatcgctgga cttacgtcag actccacaca aacaggcaaa 180 catggaaacc gaatgccaat cgctggactt acatcagact ccgagccaac aaacacacgc 240 acaggaaacc gactgccaat cgctggactt acgtcagact ccaacacgca aacacaaaga 300 aggttgaaaa acaaaaaggg cgcacgaaga gatccgctca tctcctgcct acgtacctca 360 tctggcatga ggatcagggc aacgtagttc ccctacgcag ggaaaaagga ctagcctaac 420 cagagacaaa gggagacaca actagggaga ctaactcga 459 // ID COP7_I_MT repbase; DNA; EDCOT; 4058 BP. XX AC . XX DT 28-DEC-2006 (Rel. 11.12, Created) DT 28-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Internal region sequence of a copia type LTR retroposon, COP7_MT, DE from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; retroposon; LTR; KW internal region; terminal; repeats; COP7_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4058 RA Shankar R. and Jurka J.; RT "COP7_MT: A copia type LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 613-613 (2006). XX DR [1] (Consensus) XX CC The internal region contains a single ORF showing domains for CC peptidase, subtilisin as well as integrase. Exists in multiple CC copies with varying LTRs but conserved internal region, in CC Medicago genome. XX FH Key Location/Qualifiers FT CDS join(44..892,896..3973) FT /product="COP7_I_MT_1p" FT /translation="MGSKWDIEKFTGSNDFGLWKVKMQAVLTQQKCVEALK FT GEAAMPATLTQEEKREMVDKAKSAIVLCLGDKVLRDVAREATAASMWAKLE FT SLYMTKSLAHRQLLKQQLYSFKMVESKSISEQLTEFNKILDDLANIEVNME FT DEDKALLLLCSLPKSFEHFKDTILYGKEGTTTLEEVQAALRTKELTKFKDM FT RVDEGSEGLNVTRGRNEHRGKGKGKSRSKSRSKGFDKSKYKCFLCHKQGHF FT KKDCPDKGGDGSPSVQVAEASNEEGYESAGALVVTSWEPEKSVLDSGCSYH FT MSPRKEYFETLILKEGGVVRLGNNKACKVQGMGNVRLKMFDGREFLLRDVR FT YVPELKRNLISISMFDNLGYCTRIEHGVCKISHGALITVKGSRMNGLYILD FT GSIVIGNASVASVASHNNSELWHLRLGHVSERGLVELAKQGLLGKDKLDKL FT EFCEHCILGKQHRVKFGSGMHHSSRPFEYVHSDLWGPSKTPTHGGGSYFLS FT IIDDYSRRVWVFVLKNKSDTFEKFKEWHTLIENQMGTKLKGLRTDNGLEFV FT SEQFNEFCRLKGIKRHRTVPRTPQQNGLAERMNRTLLERVRCMILGAGLPK FT SFWGEAVTTAAYLINRCPSTGIDFKTPMEVWSGKPADYSSLKVFGALAYAH FT IKQDKLEPRALKCVFIGYPEGVKGYKLWKLESSGRSRVLISRDVTFDETRM FT GMKCKDLETQVPETMVERTQFEVELPNEEEEDVEDEASTSDTSGTQPVVDP FT EYLLARDRERRTITAPKRFGYADLVCFALNAAEDVQDSEPRNFKETFESKE FT SKYWLKAVNEEMDSLERNQTWKLVKLPNHQRVVGCKWIFKKKDGIPGVEGP FT RYKARLVAKGFTQVEGIDYNEIFSPVVKHCSIRILMAIVNQFNLELEQMDV FT KTAFLHGDLEETIYMEQPEGFVEDKSKVCLLKKSLYGLKQSTRQWYRRFDE FT FLLKTGFVRSGYDSCVYMLKKNEKVILYLLLYVDDILMASSSKDEIMKLKE FT RLNGEFEMKDLGPAKRVLGIDIKRNRDKGELFLSQLGYLKKVVERFRMSNS FT KTVSTPLGHHTKLSIQQCPQSEDEKQLMEGTPYASGVGSIMYGMVCSRPDL FT AYAVSIVSRFMANPGIVHWQALKWVLRYLNGSLKGGLKYTRAAQDEDALEG FT YVDADYAGNVDTRKSLSGFVFTLYGTAISWKANQQFVVALSTTQAEYIALV FT EGVKEAIWLKGMIGELGITQECVKIHCDSQSAIHLANHQVYHERTKHIDIR FT LHFVRDMIESKEIVVEKVASEENPADVFTKSLPRSRFKHCLDLIKFVE" XX SQ Sequence 4058 BP; 1217 A; 610 C; 1136 G; 1095 T; 0 other; tggcgcccac cgtggggcat aggcgtgatt gataggaagt atcatggggt caaagtggga 60 catcgagaag ttcaccggaa gtaatgattt cgggttatgg aaggttaaga tgcaagcggt 120 attgacacaa caaaagtgtg tagaagcatt gaagggtgaa gcggcgatgc cggcaacctt 180 gacacaagag gagaagcgtg agatggtaga caaggcaaag agtgctattg tcttatgtct 240 cggagataag gtcttaaggg atgtcgcgag ggaagctacc gcggcatcga tgtgggcaaa 300 gttagagtca ttatatatga cgaaatcttt ggctcatagg caactcttga agcaacaact 360 ctattcattt aagatggtgg agtctaaatc gatctcggag caactaacgg agtttaacaa 420 gattcttgat gatttggcca acattgaggt taacatggaa gatgaggata aggctttgtt 480 gttactttgt tcattaccaa agtcctttga gcatttcaag gataccatcc tttatggtaa 540 ggagggcact actactttgg aggaggtcca agcggctttg agaaccaaag aattgaccaa 600 gttcaaggac atgagggttg atgaaggtag tgaaggcttg aatgttacaa gagggaggaa 660 tgagcataga ggaaaaggca aagggaaatc aagatccaag tctaggtcca agggctttga 720 caaatcaaag tataaatgct ttctttgtca caagcaaggt catttcaaga aagattgtcc 780 ggataagggg ggcgatggta gtccttcggt tcaagttgcg gaggcttcga atgaagaagg 840 ttatgagagt gcgggtgcac tagtggtaac aagttgggaa ccggagaaga gttaggtttt 900 ggactcggga tgctcttatc acatgagccc tagaaaggaa tattttgaga ctttgattct 960 aaaagaagga ggagttgttc gactcggaaa taacaaagct tgcaaagtcc aaggcatggg 1020 aaacgttcgt ctaaagatgt ttgatggccg tgaattcctt ttaagggatg tgaggtatgt 1080 tcccgaactt aagcgaaatt taatttccat aagcatgttt gataatctag gttattgcac 1140 tagaatagag catggggttt gtaaaatttc gcatggtgca ttgattacgg taaaggggtc 1200 tagaatgaat ggtttataca ttttagatgg ttccatagta attggtaatg catcggtagc 1260 tagtgttgca tctcataata attctgaatt gtggcatttg agattggggc atgttagtga 1320 gaggggttta gttgaactag ctaaacaagg tttgctaggg aaagataaat tggacaagct 1380 agaattttgt gaacattgca tactaggcaa acaacatagg gtgaagtttg gaagtggcat 1440 gcatcattct agtagacctt ttgagtatgt gcattcggat ctttggggtc cttctaagac 1500 tcctactcat gggggaggtt cctattttct ttctatcatt gatgattatt ctaggagagt 1560 gtgggtcttt gttttgaaaa acaaaagtga cacctttgaa aagttcaaag aatggcacac 1620 tctcatagaa aatcaaatgg gaactaaact aaaaggttta agaactgaca atggcctgga 1680 gtttgtttca gagcagttta atgagttttg caggttgaaa ggaatcaaga ggcatagaac 1740 cgtaccaaga acacctcaac aaaatggtct tgcggaacgc atgaatagga ctcttttgga 1800 gcgtgtgagg tgtatgattc taggagctgg gttacctaag agtttctggg gtgaagccgt 1860 gacaacggct gcttatttga tcaatagatg tccatcaacg ggaatagact tcaagacacc 1920 tatggaggta tggagtggga aaccggcaga ttactcctct ttgaaggttt tcggagcttt 1980 ggcatatgcg catatcaagc aagacaagct tgagcctaga gctttgaaat gtgtcttcat 2040 tggttatccg gaaggtgtga agggatacaa gttgtggaaa ttggaatcta gtggaagatc 2100 aagagtcttg ataagtaggg atgttacctt cgatgagacc cggatgggga tgaagtgtaa 2160 agacttagag actcaagtac cggaaactat ggtggagaga actcagtttg aggtggagct 2220 tccaaatgaa gaagaagaag atgtagaaga tgaagcttca acatcggata caagtggaac 2280 tcaaccggta gtggatcctg agtatctatt ggcaagagat agagaaagaa ggaccattac 2340 ggctcctaag agattcggtt atgcggactt ggtgtgtttt gctctaaatg cggcggagga 2400 tgtgcaagac tcggagccta gaaacttcaa ggagacattt gagagcaaag agagcaagta 2460 ttggttgaag gcggtgaatg aagaaatgga ttcattggaa aggaaccaaa cttggaaact 2520 tgtgaagcta cctaatcacc aaagggtagt tggatgcaag tggatcttca agaaaaagga 2580 tggcattccg ggtgttgaag gtccaaggta caaagcaaga cttgtggcaa agggtttcac 2640 tcaagtggag gggatcgact acaacgagat cttttcaccg gtggtgaaac attgttccat 2700 aaggatactt atggctatag tgaatcaatt caatcttgag ttggaacaaa tggatgtgaa 2760 gaccgctttc ttacatggtg accttgaaga gacaatctac atggagcaac cagaaggttt 2820 tgtagaggac aagtctaagg tgtgtctttt gaagaaatct ttgtatgggt tgaagcaaag 2880 cactaggcaa tggtatcgtc ggtttgatga gtttcttttg aagaccggtt ttgtgagaag 2940 cggatatgat tcttgtgtgt acatgttgaa gaagaacgag aaagtcattc tctatcttct 3000 tttatatgtg gatgatatct tgatggcaag ctctagcaag gatgagatta tgaagctcaa 3060 ggagagacta aatggtgaat ttgagatgaa ggatcttggt ccggcgaaga gagttcttgg 3120 gatagatatc aagaggaatc gtgacaaggg cgaacttttc ttatctcaac tcggttattt 3180 gaagaaggtg gtggagcggt ttagaatgtc aaactctaaa accgtgagca ctcccttggg 3240 tcaccacaca aagttgtcca tacaacaatg tcctcaatcc gaggatgaga agcaattgat 3300 ggaaggtact ccctatgcaa gtggggttgg aagcatcatg tatggaatgg tttgtagtag 3360 gccggacttg gcttatgcgg ttagcattgt gagtcggttt atggcaaatc cgggaattgt 3420 gcattggcaa gctttgaagt gggttttgag gtatttgaat gggtcgttga agggcggttt 3480 gaagtacaca agggcagctc aagatgaaga cgctttggag gggtatgttg atgcggatta 3540 tgcgggcaac gtagacacta ggaaatcctt gtcgggtttt gtgtttactc tctatggcac 3600 ggcgattagt tggaaggcaa atcaacaatt cgtggtggca ttatctacaa ctcaagcgga 3660 gtacatcgca cttgttgaag gtgtgaagga ggccatatgg ttgaaaggga tgattggtga 3720 gttaggaatt actcaagaat gtgtgaagat acattgtgat agtcaaagtg ccattcactt 3780 ggcaaatcat caagtgtatc atgaaaggac aaagcacatt gacattcgcc tgcactttgt 3840 tagagacatg attgaatcaa aagagattgt ggttgagaaa gtggcatcgg aggagaatcc 3900 ggcggatgtg ttcaccaagt cattgcctcg atcaagattc aagcattgct tggacttgat 3960 caagtttgtc gaatagtaat tcccttttgg agagagcagc atggtggttg atggttaaat 4020 tgacatcacc accaaattag aagtcaaggt ggagaaat 4058 // ID COP2_LTR_MT repbase; DNA; EDCOT; 203 BP. XX AC AC152405; XX DT 14-DEC-2006 (Rel. 11.12, Created) DT 14-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Long terminal repeat sequence of LTR retroposon, COP2_MT, from DE Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; COP2_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-203 RA Shankar R. and Jurka J.; RT "COP2_MT: LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 606-606 (2006). XX DR EMBL/GenBank/DDBJ; AC152405; Positions 36032 36234. XX SQ Sequence 203 BP; 59 A; 37 C; 26 G; 81 T; 0 other; tgttataaat attaatattg gatgtccaaa tagcaaatgt gttagtgggc catactacta 60 ggttttgggc ttagttcata agctactcta tttccctata aatagagctc atttgtaaca 120 ttgatacaca ctagtgaata agaatatttc tctcttcttc tccttctctc tattactgtc 180 tctatttact tatattcata aca 203 // ID Ogre-SD1_I repbase; DNA; EDCOT; 13767 BP. XX AC AC146506; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 13-APR-2007 (Rel. 12.03, Last updated, Version 2) XX DE LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-SD1; Ogre-SD1_I; internal portion. XX NM Ogre-SD1_I. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-13767 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC146506; Positions 57519 43753. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). CC Additional annotations: 3869..10754: ORF2+3 (gag-pol; CC contains multiple mutations generating stop codons and CC frameshifts); 7235..7395: putative intron. XX FH Key Location/Qualifiers FT CDS 1194..3104 FT /product="Ogre-SD1_ORF1" FT /translation="MNPYGKGDKRPKEDQSPRVMILDKAPTLLKAWYENMT FT NHGKEVVFKRLGFLRSLLYVEPRRDLIEALVHFWDPIKNVFHFSDFELTPT FT LEEIGAFIGRGKNLHEGEPMIPKHINGRRFLELLHINENEIGGCLDNGWVP FT LEFLYKRYGRKDGFELYGKKLHNNGCRLTWETHSYDAITVAFLGIMVFLKR FT GGKININLAAVITAFEKKPNITLVPMILADIYRALTICKNGGDYFEGCNML FT LQLWMIEHIRHHPYVVDFKVECNDYIGGHEERIKDHSFPKGIEAWKKYLNN FT LTADKIVWNYHWFPSAEVIYMSTFRSFIVLMGLRGVQPYMPLRVMRQLGRR FT QFLPPNEDIREFMYEFHPEIPLRKSEIFKIWGGCMLSSPHDRVEDRTKGEV FT DQAYLEWVHDQPSPKVLPEGSVKGPVDREAEIEVRIKQARLEVERSYRSTL FT DCLSNDLKNAKEELAQRDAIFEVRVRKHRSTILTLQEDLGIVISAMEQQEE FT EYTKEKVQVICTQSRLQNQVKASMEREREITRRFSAYQAECEVERGQRIAE FT RDALHLQIEELQEQRENLTHEVNTTRHWLQNCYDNMNEARDRVLQLRDALN FT DVYAGYFHQNNERLGRQTHVLAPHLPKALARIYKGLGDD" FT CDS join(3869..5053,5105..5518,5798..6286,6323..7234, FT 7396..7656,7660..9183,9187..10023,9951..10751) FT /product="Ogre-SD1_ORF2+3" FT /note="gag-pol." FT /translation="MNGQAPPSSIREYLNVNMPFPIQVSTNDLIYPPGFGP FT YTNTSNVAETSTVRPLNTPMMSNPLFVPTAPTNSTSNPTVVPKSNNDPSFQ FT VLHDHGYTPEEALKIPSSYPQTHQYSSPFKIEKTVKNEEHEEMTKKMKSLE FT HSIRDMQGLGGHKGISFSDLCMFPHVHLPTGFKTPNFEKYDGHGDPIAHLK FT RYYNQLRGAEGKEELLMAYFGESLVGIASKWFIDQDIANWHTWDDLARCFV FT QQFQYNIDIVPDRSSLANMRKKTTENFREYAVRWREQAARVKPPMKELEMI FT DVFLQAQEPDYFHYLLSAVGKTFTEVIKVGEMVENGIKSGKIVSQAALKAT FT TQALPNGSGNIGGKKRREDVATVVSAPRTYAQDNHTQHYFPPQIPQYLVPY FT PWRAPLPQNHPSALQNHQNTTRIPFRPRKEYKKGNGAKDEFTPIGESYASL FT FQKLRTLNVLSPIERRMSNPPPRNLDYSQHCAYCSDAPGHNIERCWYLKKE FT IQDLIDTRRIIVESPNGPNINQNPLPRHTETNILDDEASVPLPMTNPKAVP FT WKYEPTVVTYKGKEINEKVDEIEGMTRSRRCYAPAELRKNNNDQMQVKSPV FT TEREAEEFLRKMKLSDYSIVEQLRKTPAQISLLSLLIHSDEHRKVVMKILN FT EAHVPNEGTMSQLEKIAGRIFEVNCITFSDDELPVEGTGHNQGLHILLTEG FT LGQIYCPLSTLQKLNVNVERVRPNKVCVRAFDGSKTDAIGEIELILKIGPV FT DFTVNFQVLNINASYNLLLGRPWVHRAGAVPSTLHQMVKFEYDRQEVIVHC FT ERDLSVYKDSSLPFIKANNENEALVYQAFEVVVVEHNLEGNLISKPQLPMA FT SVMMVNEMLKHGFKLGKGLGIFLQGRAYPVSPRKSLGTFGLGYKPRVEDKM FT KAKKQRRDVWSLTKPIPPIYKSFNKARTIESSKSLLPEPVLEVHEELINYF FT QDLFVEADMIELEEGTSDRDVQFIGPDVQLNNWEATPLPIKNESWSFYADS FT SDMTCIQNYSPDLKIQSNLRPNPEILSQEIEYDEDEVFEEVSRDFKSFENK FT SNPNMSETETINLGDHENIKETKISVHARHKEDKIQALLDYKDVFASSYDD FT MPGLSTDMVVHKLPIDPKFPPVKKKLRKLKTDMSVIIKEEITKQLEAKVIR FT VAQYPSWLANIVPVPKKDGKVRMCVDCRDLNKASPKDDFPLPNSHILLDNC FT AEHEIASFVDCYAGYHQIIMDDEDAEKMSFITPWGTYCYRVMPFGLKNAGA FT TYMRAMTTMFHDMMHKEIEVYVDDVIIKSKKQSNHVQDLRRFFERLRRYNL FT KLNPAKCVFGVLSGELLGFIGSRRGIELDPLKIKAIHELPPPKNKTEVMSF FT LGRLNYISRFIAQLTTTCEPIFKLLKKNATVEWTEECREAFERIKNYLLNP FT PVLVPPEPGRPLILYMSVLDNSFGCVLGQHDGTGKKEHAIYYLSKKFTVYE FT SKYTLLERTCCALTWVAQKLKHYLSSYTTYLISRMDPLKYIFQKPMPTGRL FT AKWQILLTEFDIIYVTRTAMKAQALADHLAENPIDDEYEPLKTYFPDEEVS FT CIDEVIHNKDQGWKLFFDGAANKKGVGILVLMSESGEYFPITAQLRFYCTN FT NMSEYEACILGLRLAADMGIQKLLVLGDSDLLVHQIQGEWETRDPKLIPYQ FT HCLQDLCQQFVSIKFRHIPRVHNEIVDALATLSSMLQHPDEAHIDPLYIQI FT RDQNAYCNLVEEEFDGKPWFHDIKTYLQSGECPTNATSNQKRTIRRLDSGF FT FLSGGILYKKTPDLGLLRCVNAKEASTIMIEVHSGICGPHMNGYVLAKKIL FT RAGYYWLTMERDSIRFVRKCHKCQIHGDLIHSPPSELHAMSALWPFVDGEW FT MFDTFSSLRVTCDVCSMAFRGWGMDVIGPIEPKASNGHRFILVAIEYFTKW FT VEAVTFKSVTKKVVVDFIHFNIICRFGIPKAIVTDNAVNLNSHLMQEVCRQ FT FKIEHRNSTPYRPKENGAVEAANKNIKRYFVYGTEAVLPAEVEIPSLRIVV FT EAGIDDDEWVRTCLKQLSLIDEKRMTSVCHGQLYQKRMAQAYNKKVRPRRF FT EEGQLVLRRILPHQAEVKGKFSPNWKGPFIVKKVLSNGALYLADIEGKMTE FT MVINADAVKRYYI" XX SQ Sequence 13767 BP; 4465 A; 2428 C; 2876 G; 3998 T; 0 other; gatggcgact ctggctgggg ataaccagaa ttcgagcttc aaaatattga cttgcgtatg 60 actttgatct ttatttttat tattattctt tttggatatt gtgttgttag tatcatgtgt 120 tatttgctac ttgtttatcg ctttgatatt atgtgaattg ttatatatct gtctctcctc 180 gcgcacccat ctgagtcttt tgagatactt tattcggaga tgcgattacg ctcctgagcc 240 atgagatacc agagatgcga caacgctcct gggaaggatt ctatagtaac acatgtctta 300 agatgggaag gactaatagt gaggccggaa agccctgcta ccggtaagct atcccttccc 360 aactcgagta gtccactcgt tttacgacca gtctagacac tcattccatt aggttgctaa 420 cttagtaaaa caagtctcag cgatgattat tcctaatagg atccgattta tctgcatcat 480 gcatattttt aaactaatgg ggctcgacac aagggtcgag tccttctagg acaggtaccc 540 cccacttaag acgttcatgt acattttttg ttctacttgt tgcactatta ggaagactat 600 acaaaatgtc gaccgacttt ggatgaatta attaaaaaaa aaaagaagga aaattctaaa 660 aatacaaagg tcttagtgtc cttcttttat taaacacttt tactttgtca aaatttgtac 720 ttctttcata aatataagat tttttttttt ttagttatta ttactatcat ttttttttta 780 aaaaaggggt aaagataaat taagaaaaaa taaaataaaa ccaactatac tattgttttt 840 taaaagtcta gcaggattat ctaataaaga ggggtttaga ctataacaaa aagatttgag 900 tgcttatttt tcttatgtgt tttttttaat ttttttttca ctcttcttat aataataatt 960 atttagaaaa aaaaagaaat ttatactaat tttgttttct cctttcaact ctactcagat 1020 tatttaatag gagatttgaa aaaaataaat aaaatgtgat ggtttgtttt ccttagtgtc 1080 caatcatgtt tttactatta tatacaataa tttttacttt atttttaatt ttataaaaaa 1140 taaaaatgtg ttttattaag tcctaatttg tcattatcat aatataggaa aatatgaatc 1200 catatggaaa gggagataag aggccaaagg aggaccaatc acctcgcgtc atgatattag 1260 ataaggctcc gacacttttg aaggcatggt atgaaaatat gacgaatcat gggaaagaag 1320 tggtattcaa acgcttggga tttctgcgaa gccttttgta tgttgagcca cgacgggact 1380 tgatagaagc actagttcat ttttgggatc caataaaaaa tgtattccac ttttctgact 1440 ttgaactcac tcccacacta gaggagatag gcgcattcat aggaaggggt aaaaatcttc 1500 acgaaggaga acctatgata ccaaaacata tcaatggtag gaggtttttg gagttattgc 1560 acataaatga gaatgaaata ggtggttgcc ttgataacgg atgggttccg ttagaatttt 1620 tgtacaaaag atatgggcga aaggatgggt tcgagttata tggaaagaaa cttcataata 1680 acgggtgtcg tttgacctgg gaaacacaca gttatgatgc catcacagta gcttttttgg 1740 ggatcatggt gtttctgaaa aggggaggaa agatcaatat aaatttggct gcagtcatta 1800 cagcttttga gaaaaagcct aatatcaccc tcgtacccat gattctagca gacatctacc 1860 gcgctttgac aatttgcaag aatggaggag attactttga gggatgcaat atgttactac 1920 aactatggat gatcgagcac attcgtcatc acccttatgt agtggacttc aaagtagaat 1980 gtaatgatta cattgggggc cacgaggaaa gaatcaaaga tcatagtttt ccgaagggta 2040 ttgaggcttg gaagaaatac ctcaataatc tgactgctga caagattgtg tggaattatc 2100 attggtttcc atcagccgag gtgatataca tgtctacctt tcgatcgttc atcgtcctaa 2160 tgggccttcg aggtgtccaa ccttacatgc cacttagagt tatgcgacaa cttggtcgac 2220 gccaattttt accacctaat gaagatatac gggaattcat gtatgagttt catcccgaga 2280 ttcctttaag gaaatcagag atattcaaga tttggggggg atgcatgctc tcaagtcccc 2340 acgatagggt agaggatcgc accaagggtg aggtggacca agcatactta gaatgggttc 2400 atgatcaacc ctctcctaag gtattgccag aaggatcggt gaaaggacct gtagatcgag 2460 aagcagaaat tgaggttagg attaagcaag ctcgcctcga agttgagaga agctatagat 2520 ctactctgga ttgcctgagt aatgacctga agaatgctaa agaagagttg gcccaacgtg 2580 atgcgatatt tgaagtaaga gttagaaaac atcgttctac cattctgacc ttacaagaag 2640 acttgggcat tgtcataagc gctatggagc aacaagagga ggagtataca aaagaaaagg 2700 ttcaggtcat ctgcacacaa tctagactcc agaatcaagt taaggcttct atggaacggg 2760 aaagggaaat aacaaggcgt tttagtgcat atcaggcaga atgtgaggtt gagagaggtc 2820 aaaggatagc cgagcgagat gcactccacc ttcaaattga agagctccaa gaacagaggg 2880 agaatttgac gcatgaagtc aatactactc gacattggtt acagaattgt tatgacaata 2940 tgaatgaagc cagagatcga gtacttcaac tcagggatgc actcaatgat gtttatgctg 3000 gttatttcca ccagaataat gagaggttgg gccgccagac acatgttctt gctccacatc 3060 taccaaaggc cttggctagg atttataagg gtcttgggga tgattgagat ctgaggattt 3120 agtttctttc cgagtctgtt ttcttttctt agttattagt tgttgctttt atttatttat 3180 atttttgtta atcattttga gtctatctta gtcttagcta cttctattct catgttttat 3240 tcaaatcatt gtgttaagaa tatttgaaaa tgaatgaaaa tgatttactt ttggtcaact 3300 catgtacatt tattattcta aaaaaaaaaa ttaaaaaaaa attaaaaaaa taaattaaaa 3360 aaataaaata ataatatatt attatctttc acgaactacg taatgatctg attcatgttc 3420 aacatgatac gtaggcaacc ctcaacgggt tcgatcgaaa tgcatttcaa aattattcaa 3480 ataagtaaaa tataagacta agagacataa tcaagtagtc taaagccggg atgaaacata 3540 aaagccttcc gaaactcatt ttagaaacat aaataattta aggtgcataa catacaacgt 3600 gtgattatcg tttgcaaaac actaaaccct atcatgtttg ttttttttgt aaaagaaaag 3660 aaaaaaaaag agttttaagg tggttggttt gtgattagag ctgacatctc atcaatacta 3720 caccacatca aaagggaaag ggaagatgac gcgcaaggag ggaacagagt cgggaaatga 3780 cgacgtccaa atagttgcac aagaatcggt gtctgtggaa gaggtaaaaa tgttacgaca 3840 acaaatggcc gaaatgtatg aagcttagat gaatgggcaa gctcctccat cttcgattcg 3900 ggaatacctg aatgtgaata tgccattccc tatccaagta tcgaccaatg atctaattta 3960 tccacctgga ttcggcccct acactaacac atcgaacgtc gctgaaactt ctacagtgcg 4020 tcccttgaat acacctatga tgagtaaccc gttatttgtg ccaactgcac cgactaatag 4080 cacttcaaat ccaacagtgg tgcccaaatc caacaatgat ccttcattcc aagttcttca 4140 tgaccatggc tacacccctg aagaggctct taaaattcca agttcttatc cccagactca 4200 tcaatatagt tcccccttca aaattgagaa gacagttaag aatgaggagc atgaagaaat 4260 gactaagaaa atgaagagtt tggaacatag tataagagat atgcaaggac tagggggcca 4320 caaaggcatc tcattcagtg atttgtgcat gtttccccac gtccatttgc ctactggttt 4380 taaaaccccg aattttgaga aatatgatgg tcacggagac cccatagctc atttgaagag 4440 atattacaat caattgagag gtgcagaggg caaagaagag ttgctcatgg cctattttgg 4500 ggaaagccta gtaggaattg cgtctaaatg gttcatagat caggatatag ccaactggca 4560 tacgtgggat gatttggctc gatgttttgt gcaacaattc caatataata ttgatattgt 4620 gccagaccgc tcctcacttg ctaacatgag gaaaaagacc acagaaaatt ttcgtgaata 4680 tgccgttaga tggagagagc aagctgctag ggttaaacca ccaatgaagg agttagagat 4740 gattgacgtt tttctccaag ctcaagaacc tgattacttt cattacttgc tttctgctgt 4800 tgggaagaca ttcaccgaag ttatcaaggt tggggaaatg gtggaaaatg gcatcaagtc 4860 tgggaagatc gtaagccaag ctgctttaaa agccacaaca caagcgcttc caaatggttc 4920 tggaaatatt ggagggaaga aaagaaggga agatgtagcc accgttgtat cagcacctcg 4980 aacctatgcc caagataatc atacacaaca ctactttcct cctcaaattc cacaatatct 5040 tgtcccatat ccttaatatc ccatttttag cgcacatcca attgttcccc cttcttatcc 5100 gtaatggcgt gcaccacttc ctcaaaatca tccatcagcc ctacaaaatc accaaaatac 5160 aactagaatt ccttttcgtc ctagaaaaga atacaagaag ggaaatggag ctaaggatga 5220 gttcacccct attggagaat catatgctag cttgtttcaa aaattaagaa cgttgaatgt 5280 tttgagtcct attgaaagaa ggatgtcgaa tcctcctccg agaaatcttg attattccca 5340 acactgcgca tattgttctg atgccccagg gcacaacata gaaagatgct ggtacttgaa 5400 aaaagaaatt caagatttga tcgatactcg tcgaattata gttgaaagcc caaatggacc 5460 gaacatcaat caaaatccac tgcccagaca tactgaaaca aacatcttag atgatgaatg 5520 accacgaaga agttgcagtc ccatacaagc caatccttaa ggatgaaact ggcattgaaa 5580 gttcagcaaa tgtcgttgac ttaacaaaaa tgatgccttc aggggcggaa agtacgtctg 5640 aaaagttgac cccatcaagc gcacccattc taactgtaaa gggagcactt gaagatgttt 5700 gggcaagtca gagagaggca agattggttg ttccaagagg gccagactag cctatcttga 5760 tcgtgcaagg agcctatatt ccacttgtga tcattaggcc agtgtcccac ttccaatgac 5820 taatcccaag gctgtccctt ggaaatatga gcctaccgtc gtgacataca aggggaaaga 5880 aatcaatgaa aaagtagatg aaatagaagg aatgactcgt tcgagaagat gctatgcccc 5940 ggctgaatta aggaaaaata ataatgacca aatgcaagtt aaaagtccag tcactgaaag 6000 ggaggcagag gagttcttaa gaaagatgaa attgtcagac tactccattg tggaacagtt 6060 aaggaaaact ccagcccaaa tctctttgtt gtcattgtta atacattcag atgaacatcg 6120 taaagttgta atgaaaattt tgaacgaagc acatgttcct aatgaaggta caatgagtca 6180 gttagagaag attgctggga gaatctttga ggtaaactgc atcacctttt cagatgatga 6240 actaccagtg gaaggtacgg gacataacca aggcctccat atactgtaaa atgtgagctt 6300 tcatatgtca ctcgagttct aattgacgga gggtctgggg caaatatatt gtccattgtc 6360 aactctacaa aaattgaatg ttaatgttga aagagtacga cctaacaaag tatgtgttag 6420 ggcgtttgat gggtccaaaa cagatgccat tggggagata gagctcatac taaaaatagg 6480 gcctgtcgat ttcaccgtga attttcaagt gctgaatatt aatgcatcct acaatctatt 6540 gttgggaaga ccatgggtac atagggctgg ggcagtcccc tctacgttgc atcaaatggt 6600 taagtttgaa tacgatcgac aagaagtgat tgttcattgt gagagggatc tgtcagtcta 6660 caaggactct tccctccctt ttatcaaggc aaataatgag aatgaggcac tggtttatca 6720 agcttttgag gtagtggttg ttgagcataa cctcgaaggg aatctcattt caaaaccaca 6780 actgcccatg gcatccgtga tgatggtaaa tgaaatgctg aagcatgggt ttaaactagg 6840 taaaggcttg gggattttct tgcaagggag agcttatccg gtgagtccac gaaagagcct 6900 cggtactttt ggcttaggat acaagcccag ggtcgaggac aaaatgaagg ccaagaagca 6960 gaggagagat gtatggtcac ttaccaagcc tataccacct atatacaaat ctttcaacaa 7020 agcccgcaca atagaatctt ctaagtcact actcccagag ccagtgctag aggttcacga 7080 agaattgatc aattattttc aagatttatt tgtcgaggct gatatgattg aactcgaaga 7140 aggcactagc gacagagatg tgcaattcat tggtcctgat gtccagctga acaattggga 7200 ggccactcct ctccccatta agaatgagtc ttggtagtct gtcttgtttt ctttttgtca 7260 tccgatttat tcaagggttg taattcggat tttgtctcgt cgttttattt caaactctct 7320 attttccttt tcaataggat gtaattgtgt ttttatttca gtctaatata tttattttgt 7380 tttcttctat acagttcttt ctatgccgat tctagtgata tgacatgcat ccagaattat 7440 tcaccggatc ttaaaatcca atctaatctt cgacctaatc ctgaaatact gagtcaagaa 7500 atcgaatatg atgaagacga agtatttgaa gaagtaagca gggatttcaa atcttttgag 7560 aataaatcaa acccaaatat gagtgaaact gagacgataa atttagggga tcatgaaaat 7620 attaaagaga ctaagataag cgtacatgct cgacattaaa aggaggataa aattcaggct 7680 ctgcttgatt acaaagatgt ttttgcgtca tcttatgatg acatgcctgg attaagcact 7740 gacatggtgg ttcacaagtt gccgattgat cctaagttcc ctccagtaaa gaaaaagttg 7800 agaaagctta aaactgacat gagtgtaata attaaagagg aaatcacaaa gcaacttgag 7860 gccaaagtca ttcgagtcgc tcaatatcct tcttggttag ccaacatcgt acctgtccct 7920 aagaaagacg gcaaagttcg aatgtgtgtt gattgtcgtg atttgaacaa agcaagtcca 7980 aaagatgact ttcctttgcc caacagccat attttgttgg acaattgtgc tgaacatgag 8040 attgcatctt ttgtggattg ctatgcgggt tatcatcaga ttattatgga tgatgaagac 8100 gcagaaaaaa tgtcttttat cacaccatgg ggtacatatt gttatcgagt catgccattt 8160 ggattaaaaa atgcaggagc aacttatatg agggcaatga caaccatgtt tcatgatatg 8220 atgcataaag aaatcgaagt ttatgtggat gatgtgatca ttaaatcaaa aaaacagtca 8280 aatcatgtgc aagacttaag aagattcttt gaaaggcttc gcaggtataa tctcaagctt 8340 aatcctgcaa aatgtgtatt tggagtactg tcaggagagc ttttggggtt tataggtagt 8400 cgacgaggta tcgagttaga tcctttaaaa ataaaagcca ttcatgaact gccacctcca 8460 aagaataaaa ctgaggttat gagctttcta ggaaggttaa actacatcag tagattcatt 8520 gctcaactca caacaacttg cgagcccatt tttaagttgt taaaaaagaa tgccacagtc 8580 gagtggaccg aagaatgtcg agaggctttt gaaaggatta aaaattactt attgaatccc 8640 cctgtgttgg ttcctcccga gccaggcaga ccgttgatat tatatatgtc agtactggat 8700 aattcttttg gatgtgtatt gggtcagcat gatggcactg ggaagaaaga gcatgccatt 8760 tattacctca gcaagaaatt taccgtttat gaatcgaagt acacccttct cgaaagaacg 8820 tgttgtgccc taacttgggt agcacagaag ttgaagcact atctttcatc ttatactact 8880 tatctcattt ctcgtatgga tccgttaaaa tatatttttc aaaagcccat gcccacgggc 8940 aggcttgcga aatggcaaat attactcaca gagtttgaca ttatctatgt gacgcggact 9000 gcaatgaagg ctcaagcctt ggcagatcat ttggcagaga accctattga tgatgaatat 9060 gaaccactta agacctactt tccagacgaa gaggtatcat gtatcgatga agttattcat 9120 aataaggatc aaggatggaa gttgttcttt gacggtgctg ctaacaagaa gggagttggg 9180 atatgactag ttcttatgtc tgaatcaggg gaatatttcc ctataacagc ccaacttaga 9240 ttctattgta ccaataatat gtcagagtat gaggcttgta tcttgggttt gaggttagct 9300 gctgacatgg gcatccaaaa gttgctagtg ctaggagact cagacttact ggtccatcaa 9360 atccaaggag aatgggagac tcgtgaccca aagctcatac catatcaaca ttgtttacaa 9420 gatctttgtc aacagtttgt gtcaataaag tttagacaca ttcctagagt tcataatgag 9480 attgttgatg cattggcaac tttatcttcg atgcttcaac atcctgacga agctcatatc 9540 gaccctttgt acatacagat tcgtgatcag aatgcttatt gcaacttggt ggaggaagaa 9600 tttgacggta aaccttggtt ccatgatatt aaaacatatc ttcagtccgg agaatgtcct 9660 actaatgcca ctagtaatca aaaaagaact attcggcgac tagatagcgg ttttttctta 9720 agcggaggca tattgtacaa gaaaacacct gatttgggtc ttctaagatg tgtaaatgct 9780 aaagaggctt caacaatcat gattgaagta cactcaggaa tttgtggacc tcacatgaat 9840 ggatatgttc tggcaaagaa gatacttcga gcaggttatt attggctcac catggagcgg 9900 gattctatac ggtttgttcg taaatgtcat aaatgtcaaa tacacggtga tttgatacat 9960 tctcctccct ccgagttaca tgcgatgtct gctctatggc ctttcgtgga tggggaatgg 10020 atgtgattgg accaatagaa ccaaaagcat cgaatggtca taggttcatc ctggtggcca 10080 ttgagtactt tacaaagtgg gtggaagcag taactttcaa gtcagtgacc aagaaggtcg 10140 tggtggattt cattcatttc aacatcatct gtcgatttgg tattccaaag gcaattgtta 10200 ccgataatgc tgtaaatctc aacagtcact taatgcaaga ggtatgccgt caatttaaga 10260 ttgaacatcg aaattcgact ccttatcgcc caaaagaaaa tggggctgta gaagctgcca 10320 acaaaaatat taaaagatac ttcgtatatg ggactgaggc agttttacct gcagaggttg 10380 agattccatc cctgcggatt gttgtagagg ctggaattga tgacgatgag tgggttagaa 10440 catgcttgaa gcaattaagt ttgattgatg agaagcgaat gacatcagta tgccatggac 10500 aattgtacca gaaaagaatg gcacaagcat acaacaaaaa ggtgcgtccc agacgtttcg 10560 aagagggtca attagtgttg aggcgtattc tgccacacca ggctgaagtc aaaggcaaat 10620 tttctccaaa ttggaaagga ccattcattg taaagaaggt attatccaat ggtgctcttt 10680 acttagcaga tatagaaggc aaaatgacag aaatggtcat caatgctgat gctgtgaaga 10740 gatattatat atgatgtgat ttttcggttt tagaaaccct tatgtttgga cttgacattt 10800 caaaggttga tgtaatggaa attcttggtt ctgtgtctaa gtattaattc atatgttgtc 10860 acccttgttg agagctaatt tacttccttg gttcttctgc tttcttggct cttccaaaaa 10920 aaaaaaaatt aataataaaa taaaataaaa aatcaatcat tatgaactac gtttgacctg 10980 attcttgttt cgataagata cgtaggcaac cctattatgg ggttcggtct aaccaaataa 11040 aaaatccaaa atttcatatt tgtaaaaaac taggggcaaa agtcattttt ttttattatt 11100 tttttttcct atcccaaagc taaagtcaat cccattattt aaagtcgtat ttgagccttc 11160 accttgtcat ttctttctaa ccttgtataa aagttgtgtt tcaatcaaag aaagaccttt 11220 ggatcaatct ttgaaatgtc aagagtaagt atgttaaggg tacaaatgat gaaaccatga 11280 gagagtctta ttagtgaaaa cactaattgg gcatcataag acgaatgtga gttgagagaa 11340 acaaaaatga gagagtctta ttggtgaaaa ccctaactcg gcatcataag ccgaaagtaa 11400 gttgtgaaaa taagaaaaaa taaaataaaa gaatgagaga gttttattgg tgaaaaccct 11460 aattgggcat cataaggcga atgtgagttg agagaaataa aatgagagag ttttattggt 11520 gaaaacccta acgggcatca tgagacgaat gagagttgaa ggattcaaag tgaaagagtt 11580 ttagtgaaaa aaaaaaactc tcgtggacat cataaggcga ataagggttc gaaattagtt 11640 atgactccgt caaatagttg gaactccaca tcaagattag atgatcaata atggtcgatg 11700 aatagattgg atggacaaat cgggtaatca attcaaattg catgtcatga tcagtagagt 11760 cggctacctc actcagataa gtttttcttt ctttctcttt ctaaaagaga gtcttcatcg 11820 aatcattttc tgctattctc gtgtagtata tatctttctt tcacttttca tcgctttgtt 11880 tcatatgtcc ttgagtcaag tttatgtcaa gaaagtaaga aaggatttca agaattgtta 11940 ccaattctaa atttgtacaa tgcaaagcat caggccaatg agttattatc tgtcggcaag 12000 ttttggattc agaagaagtc catgatttga tgaagggtaa acaatgagtg tcatgacata 12060 aaggcatata ttggatttaa gtccctcaaa atgagcaaat ttgggtgaaa atacaatcaa 12120 tcaataacga gcactgggtg tttggaaaaa gtaaagcacg atgagtactg gagcaatcct 12180 cgtcaaaagg cagaaccaca aaccaaccac catattttta aactcacaaa ttttctttgt 12240 tgaagcaggg gcacaagtta tttcgagatc aaagatccaa aaacctagat gttcaattta 12300 gtctatgaag agctaaatgg caacattaca cacgaattat agtccatatt gggtaagtgt 12360 ttgtttgtct tattagtcta tggaacatag tgtagcaagg accctcctga ataatgggac 12420 gtagtgtagc aaggaccctc ctgaataatg ggacatagtg tagcaaggac cctcatgaat 12480 aatgggacgt agtatagcaa ggaccctcct gaataatggg atgtagtgta gcaaggaccc 12540 tcctgaataa tgggacgtag tgtagcaagg accctcctga ataatgggac gtagtgtagc 12600 aaggaccctc atgaataatg ggacgtagta tagcaaggac ccttatgaat aatgggacgt 12660 agtatagcaa ggaccctcct gaataatagg acgtagtata gcaaggaccc tcctgaataa 12720 tgggacgtag tatagcaagg accctcttga ataatgggac gtagtatata acaaggacca 12780 tcatgaacaa tggaacgtag tatagcaagg accctcctga ataatgagac gtagtatagc 12840 aaggaccctc ctgaataatg ggacgtagtg tagcaaggac cctcttgaat aatgggacgt 12900 agtatagcaa ggaccctcat gaataatggg acgtagtata gcaaggaccc ttatgaataa 12960 tgggacgtag tatagcaagg acccttctgg ataataggac tagactaaca taattctgtt 13020 taatcggttc atcatgaaga atggagttgg tgtaaacacg cataagccct ctaaagagta 13080 catcgcgaca aagctcgaat cgttcaaagt ctcgatttaa agctaagcac catcctttat 13140 atctctcaca aatttttctt atattaaact agggcaaaat tttgtgttat tagttttgtt 13200 tgttttaatt tcaggaatct agtgatagaa tggggtcaat ccacatttcc agctcaggat 13260 cttggatgga aaaaagtgta attttcaaga tcaatttcga ttgaagaagc aacagctcat 13320 tctaaaaaaa aaaacacaat caataaccaa gtaccagtaa aaggaaccta cttggagaaa 13380 gacgtttacc tttgaactca tttgagatga aaatcaatat ctcataactc aagaagcgcg 13440 aagactcaag tcatggttca agagaagcta catagatagg gtcgtgtact tgtatttcca 13500 ttaaattttt cgtcttttat attcatgtaa caataggagt cgcgaactag agcctcaagg 13560 ggacctcact tgacttccaa ctcatcattt catctccttg aactacacgt gacctgattc 13620 tcttataacc cgggatatgt aggatgtcca aaactaggac tcagtcgcat atttttcttt 13680 ttggataaga gttcgatcaa aacttgtcac gttgtctact tctttgtcta aaaactcttt 13740 gtgtttccag tcaaagaggg gcaaact 13767 // ID GYPSHAN_I_MT repbase; DNA; EDCOT; 5383 BP. XX AC . XX DT 22-JAN-2007 (Rel. 12.01, Created) DT 22-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, GYPSHAN_MT, from Medicago DE truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; ORF; Interspersed; repeat; GYPSHAN_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5383 RA Shankar R. and Jurka J.; RT "GYPSHAN_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 28-28 (2007). XX DR [1] (Consensus) XX CC The element exists in moderate copy number having complete length CC and intact LTRs. It has intact domains for gag, CCHC motif and RT CC polymerase with arrangement resembling Gypsy-like. The LTRs are CC identical to MEGY_LTR_MT (~90%). XX FH Key Location/Qualifiers FT CDS join(2483..2554,2558..2800,2804..2875,2879..4279, FT 4283..4384) FT /product="GYRAV_I_MT_2p" FT /translation="MSRTLARPVLTLARPCQTMPSKTSNSRMLARPVLSLA FT RPCPTTGKDKPPLSSSSSIILHHKLLSPFTLLSKTSITIEFQNLHISPKTS FT PFHKISSPNQPQSPFPSPINQKQLSSIPTKYHQIRSPHSPTKPTNSSPIHP FT TQLLPLTQTPTPSPNQPFPPKTFPKTLPSPKTQKVNQGSGLMASRKGGASS FT SGGPQSKKKTQAKNHGIIFKDTKQRERYKILLSKPLHPCRYPDPYTLSVLG FT LRDNVFSLLGNLGWVDMLRPMKGFENFTYEFLSSIEFTKDKVNFDNPDHRV FT SFRLLNMDYEMSLENFCLEMDFANAGFIHDSWNPNLKSENYDPALFWKRIT FT GLRQYNPRNNKASNIHNPVLRYLQRVMACTIWGRKEVGTTRTDELFMLWAM FT LSNNPVNTCFYLLDYLSSIGARPDNRAEIVVGGIITFITRKFGVGEEDGIN FT PIEGNNRLNIETLVAMNFIKIHPPMTYALQLRIPLLFLLPNPSRTNPEVEE FT NLLYVGDGLQVHEEHHQGDEEGAHMHHEEEPHDHNDNNERWAWMQTEVQRI FT STEQQRQGVELSGLRNDVLQGNRISKENNQMLRNMMQHFNLQGPPYGPQKC FT ELSSSSFSPYLFTLYLTLLPLLPFYSSFILNH" FT CDS join(135..158,162..560,564..842,846..1358, FT 1362..2315,2355..2585,2589..2705,2715..3029, FT 3033..3110,3114..3200) FT /product="GYRAV_I_MT_1p" FT /translation="MRRSKGLGFIPEIERFLHKKKREAQNNTAMAERTLKE FT YATPSTEEPQAIIVYPTVAGNNFEIKPALLNLVQQNQFSGSPTEDPNLHIS FT SFLRLSGTIKENQEAVRLHLFPFSLRDRASAWFHSLEVSSITSWDDMRRAF FT LAFFPPSKTAKLRDQITRFNQKDGESLYEAWERFKEMLRLCPHHGLEKWLI FT VHTFYNGLSYTTKMSVDAAAGGALMNKNYTEAYALIEDMAQNHYWTNERTV FT TTPTPSKKEAGIYEVSEYNHLAAKVEALTQKIEKLNVNDVTPSSASPPCEI FT CGISSHIGVDCQLGSAANIEQLNYAQYNQGTRPNQNFYKNPQGSYGQAAPP FT GYTNNQRVAQKSSLEILLKNCMMNQNKNLQELKNQTGFLNDSLSKLNTKVD FT SIATHTKMLETISQVAQQVAASSQTPGVFPGQPETNPKAHVNAIFLGGSKL FT EETITKAKSVKRESVRCLGKNGVIKSEKPLDKNKALTPLRLTKLNLEAQFT FT KFFNIIRKICIKIPYAEALSRMPLYAKFLKEIFSKKKAIDHNETIALTRDN FT SAIVKKPPTKLRDPGSFAIPCMIGNETLNRAWCDLGASVSLLPLPLFTRLG FT LGKLKPTETTLKLADCSDIQPVGYVEDIPVKIEGIDIPTDFMVLDIDEDNA FT CPIILGRPFLATAGAIVDIQNGRIVFQVSDELIGFELKNYMKGPALYSCNM FT IKGHNVKERLLAPSTQYDLFDPFRSASWEATHVFNCFRFVCFCCLNYFVGN FT CPKVIQENEKNFEAPCPEPWHGPCSHWHGRARPCHPKPAETPECWHGPCVW FT HGRARLQVRINLPFHLLLPSFSTTNFSLHLHFSQKPPNFKTSISPPKPHHF FT TKFLHPINHNPHFHHNPSIKNNFPPSLPNIIKFVAPIHLPKNPQILHQFTQ FT PNSYHLLKPQPHHPTNLFHQKHFPKPYLHPKHKRSTKVQDWHLGKVAQALP FT EDHNQRRKRKPKIMASSRTPSKGKGIKFFSLNLCILVDIQILIL" XX SQ Sequence 5383 BP; 1656 A; 1187 C; 1005 G; 1535 T; 0 other; gtttttggcg ccgctaccgg ggagtaaact aatttgatta actctttctt tgtgattaga 60 actctcttct cttcttcttt tcttctactt ctttcttttg tattaccact aacttcttgg 120 gttctaggtt tcttatgcga agaagtaaag gtctcggata atttattcct gagatcgaaa 180 ggtttttgca taagaaaaag agagaggcac aaaataatac tgctatggct gaacgcactc 240 tcaaagagta tgctactcct tcaacggagg agccacaagc tattatcgtg tacccaacgg 300 ttgcgggtaa taacttcgaa atcaagcctg cactactcaa tttagtgcaa cagaatcagt 360 tttctggatc acccactgag gatccaaatc tccatatttc ttccttcctt agacttagtg 420 gcaccataaa agagaaccaa gaagccgtaa gacttcatct ctttcccttt tccttaaggg 480 atagagctag cgcttggttc cattccctag aagtcagttc cattacttca tgggacgata 540 tgaggcgagc attcctcgcc tgatttttcc ccccatctaa aactgctaag ctcagagacc 600 aaatcacacg tttcaatcaa aaagatgggg aatctctcta tgaggcgtgg gagcgtttca 660 aggaaatgct tagactttgt ccccaccatg gcctagagaa gtggcttata gtccacacgt 720 tttataatgg cttgtcttat accactaaga tgtctgttga tgcagctgca ggtggagctc 780 taatgaacaa aaactacacg gaggcttatg ctttgattga agacatggct cagaatcact 840 actaatggac caacgagaga accgtcacca ctcctactcc ctctaagaaa gaggcaggta 900 tatatgaagt ctctgaatat aaccaccttg ctgctaaggt tgaggcatta acccaaaaga 960 ttgaaaaact taatgttaat gatgttacac cttcctctgc atcccctcct tgtgaaatct 1020 gtggtatatc cagtcacata ggtgttgatt gtcagttagg tagtgctgcc aatattgagc 1080 aactgaatta cgctcaatat aaccaaggaa cgaggccaaa tcaaaatttt tacaaaaatc 1140 ctcaaggttc ctatggacaa gcagcaccac ctggctacac aaacaaccag agagtggctc 1200 agaaatctag tctggaaatt ctgttaaaaa actgcatgat gaaccaaaat aaaaatcttc 1260 aagaattgaa aaaccaaaca ggatttctga acgactctct ctccaaactc aataccaagg 1320 ttgattctat cgccacacac accaaaatgc ttgagaccta aatctcccaa gtggcccaac 1380 aagtggccgc ctcttctcaa acaccaggag tctttcctgg tcaacctgaa actaacccca 1440 aagcccatgt caacgctatt tttctaggag gtagtaagct agaagagact attactaaag 1500 ccaaaagtgt caagagggag agtgttaggt gtttaggtaa gaatggtgtg ataaaaagtg 1560 agaaaccgct tgataagaac aaagccctta caccattaag gcttactaag ctcaacttgg 1620 aggctcaatt cactaaattc tttaacataa ttcgaaagat ttgcattaaa atcccctatg 1680 ctgaagcttt gtctcgtatg cctctatacg ccaagttttt aaaagaaatt ttttcaaaga 1740 aaaaggctat cgatcataat gaaacaatag ctttgacaag ggacaatagt gcaatcgtca 1800 agaagccacc tacaaagctt agagatccag gaagttttgc catcccttgt atgataggga 1860 atgaaacctt aaacagagcc tggtgtgact taggagctag tgttagtctg ttgcccttac 1920 ccctctttac aaggctgggg ttgggcaagc taaagcctac cgaaacaaca ttgaaattag 1980 ccgattgttc tgatatccaa cctgtcggat atgtcgagga catccccgtt aaaatagaag 2040 ggatagacat cccaactgat ttcatggtgc ttgacataga tgaggacaat gcgtgcccta 2100 taatcttagg acgacccttt ctcgccactg cgggtgctat agtagatatt caaaacggta 2160 ggattgtttt tcaagtgagt gatgagttga taggatttga gttgaagaat tatatgaaag 2220 gtcccgccct ctattcttgt aatatgatta aaggtcataa tgtgaaagaa cgcttattag 2280 caccatctac acaatatgac ctctttgatc ctttctaagg atactttctt ataacgtcaa 2340 gctaatgact ataaagaagc gcttcgtggg aggcaaccca cgtatttaac tgctttcggt 2400 ttgtttgttt ttgttgttta aattattttg taggtaattg tccgaaggtg attcaagaaa 2460 acgagaaaaa ttttgaggcc ccatgtccag aaccttggca cggcccgtgc tcacactggc 2520 acggccgtgc cagaccatgc catccaaaac cagctgaaac tccagaatgt tggcacggcc 2580 cgtgctaagt ttggcacggc cgtgcccgac tacaggtaag gataaacctc ccctttcatc 2640 ttcttcttcc atcattctcc accacaaact tctctctcca tttacacttc tctcaaaaac 2700 ctccataacc atagaatttc aaaacctcca tatctccccc aaaacctcac catttcacaa 2760 aatttcttca cccaatcaac cacaatcccc atttccatca taacccatca atcaaaaaca 2820 actttcctcc atccctacca aatatcatca aattcgtagc ccccattcac ctacctaaaa 2880 acccacaaat tcttcaccaa ttcacccaac ccaactccta ccacttactc aaaccccaac 2940 cccatcaccc aaccaacctt ttccaccaaa aacatttccc aaaaccctac cttcacccaa 3000 aacacaaaag gtcaaccaag gttcaggatt aatggcatct aggaaaggtg gcgcaagctc 3060 ttccggagga ccacaatcaa agaagaaaac gcaagccaaa aatcatggca taatcttcaa 3120 ggacaccaag caaagggaaa ggtataaaat tcttctctct aaacctttgc atccttgtcg 3180 atatccagat ccttatactt tgagtgtgct aggactaagg gataatgtgt ttagcttact 3240 aggaaatctg ggatgggttg atatgcttag acctatgaaa ggtttcgaaa atttcactta 3300 tgaattctta agttctattg aatttacgaa ggataaagtg aattttgaca accccgacca 3360 tagagtctct ttccgacttt tgaatatgga ttatgagatg tctctcgaaa atttctgttt 3420 agagatggac ttcgcaaatg cggggttcat ccatgactct tggaatccaa atttaaagtc 3480 ggaaaactat gaccccgctc tcttttggaa acgcattacc gggttaaggc aatataatcc 3540 tcgcaacaac aaggctagta acattcataa cccagtactt cgatacctcc agagagtcat 3600 ggcttgtacc atttggggta gaaaagaggt aggaacaact aggacggatg aactttttat 3660 gctttgggca atgcttagta acaatcccgt taatacttgt ttctacctac ttgattacct 3720 ttcctccata ggagctagac ctgataatag agctgagata gtagtcggtg gtatcattac 3780 cttcatcact aggaaatttg gagtgggtga ggaagatggg ataaatccaa ttgagggcaa 3840 caataggctt aatattgaaa cccttgttgc tatgaacttc attaagattc acccacccat 3900 gacttatgca cttcaacttc gcatacctct tttatttcta cttcctaacc catctcggac 3960 taaccccgag gtggaggaaa atttgttgta tgttggtgat ggattacagg tacatgaaga 4020 gcatcatcaa ggtgacgaag aaggtgccca catgcaccat gaggaggagc cccatgacca 4080 taacgacaac aatgaacgat gggcatggat gcaaaccgag gtacaaagga taagcaccga 4140 gcaacaaagg caaggtgttg aattatccgg gctaagaaat gatgtcctac agggcaaccg 4200 catatccaaa gaaaataacc aaatgcttcg gaacatgatg caacacttca acctccaagg 4260 ccctccctat ggacctcaat aaaaatgtga gctttcctct tcctcttttt caccttatct 4320 cttcactctc tatctcactc ttcttcctct ccttcccttt tattcttctt ttatcttgaa 4380 tcattgagga caatgcttct cctaagtgtg gggggagcct aataaagtgt ctttagtcgt 4440 agtgttttca aactcccttg aactttattc ttctgttttg ttttattgta aaaggcatga 4500 ataagcagct tgtttttatt gttttattat gacataattt tttgttgtct cttcaatggt 4560 cgtttcttgt acatgaaagt gatttcttgt gttataagta ttcttgctat acccacatca 4620 agttttattg tgaaattaat tctccaatga gaaaaacacc tagttgcaat ccttgagtaa 4680 gtgtatgaat aggtatttta aggaacacgt tctaacttta atggtaacct ggacccttaa 4740 aaatcttcag agtaaaagca gtataagttt atgtgggaat aattctaatg tgatgaaatg 4800 tgtaaaccga aatggggcgg aaggatatca ccacacgtgg aggaaaggat accctctcac 4860 taacttccta aatgtggtga cgacttctca aataaattgt gcttaaatta aaccctctaa 4920 aaaaaggaac ttcctaagtg aagtaaacaa gttgtagcac tacttagggt gatcatagaa 4980 acttggagga aaggataccc cctcacggac ttccaatgtg aaatgatagc ccctaggcat 5040 ctacaagccc ccaaatgtat aaattcatca agtctatctt aactctccca cttctcttat 5100 atgaaatgaa gaaaagattt ttcttggtca ttttagtgtt aaagttagaa cctgttcctc 5160 ataatatcta tcttatacag gagcaagaaa agggttggac taaatttgtt gtcgggttga 5220 ataagtttac aaggaatgct tgaagttgtg attagtgtac attgaaatga aacctcgagg 5280 gagacataag cttattattt aaagtgtcat atattaatcc ttttgttgct gacatgtcta 5340 tgccttttgc ttgaggacaa gcaaagattc aagtgtgggg gag 5383 // ID RAM12_LTR repbase; DNA; EDCOT; 2093 BP. XX AC . XX DT 06-DEC-2006 (Rel. 11.12, Created) DT 14-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Long terminal repeat sequence of LTR retroposon RAM12, from DE Medicago truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW repeat; internal region; RAM12_LTR. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2093 RA Shankar R. and Jurka J.; RT "RAM12: LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 640-640 (2006). XX DR [1] (Consensus) XX SQ Sequence 2093 BP; 603 A; 251 C; 483 G; 730 T; 26 other; tgtgtgattt atgtggtgtg twgtattttw ttatataatt tattttaata taattagaat 60 aatatgagaa ataggrttat tttaggaggt tagggagtta attagaaatt aatagtaatt 120 argggrggtt taatgaaata agggragtta cactttgagg gagtaaggaa agaaaaaggc 180 agaaaaactg ttttacgtra aaacaagttt tgggagagaa aagctaaggc aaggagagaa 240 gaccaagaga gaagaactag agaatcgatt gctgtgcttt ctttgtcttt gcaattctaa 300 ggtaagggtg agactatctt tcaataatca taatctataa tttctgaaaa ttgatctaat 360 tgaatagttt tggaaaataa tangaaaatt agggtttgat gatgattctg aaggaatggg 420 taawgatgat gttagttttc tttgaattta atgttaagaa tgaawactta atccatgttg 480 ttgctgyaat ccattaattg attgaattta ggatgaattg tatgaattga tgaatatttg 540 tatgatggta gaatgattct gtaattgttg ttgttgatgg ttgaattgtg tttctttatg 600 atgcctagtt gtatatagga cctgtaaaca tctrttggaa aacattttgg gtgatcaggg 660 gattaaaatg gagtttttgg agtgaggagt ggtctgaaac cgtaggtttt gcactgccca 720 gacgaatggt cgcttaagcg aagcatccgt cgcttaagcg agcattcaag caagctgccc 780 agaatgcgat ttttgcccgt tcgcttaagc gaaccgtgag cgaactggta agcgaaaatt 840 aagtttgatt ctgccaagaa ttcgctcaag cgaatggtaa gcgaccctgt gagcgaaaaa 900 ccattttgat tctgtccaaa gttcgctcaa gcgaaccgtg agcgacccgt aagcgaactg 960 aacccagagc ctactgtaag ctggtcgctt aagcgaacta gccgtcgctt aagcgaagtg 1020 raccttagtc agccttttct gaattttgct tcgtgcacta ggrgatcctt ttgtgtactt 1080 ctaaagtgtt tctttcagct tgtataaccy ttrtataggt atcaaatcct acttaaaaca 1140 taatgataaa tggtttggtt gatttctatg aatttttgag ggtgttgaaa tgtktgatat 1200 taattraatg aacatgttgc attgagaggg tgatgagtca tataaatata tatgtkatag 1260 ttgagttgta tgtagatata cacaagtggg gtcagttgca taagcataaa agygggagag 1320 cttcggctct ggaacgcctt gtcgttcaaa gcggtggaac actatgttgt tcaaagcggt 1380 gttgagcggt gaggacttat gtcctgataa agaatgcttt aaccattcga ttagcggtga 1440 gggcttcggc cctgaattat ggtaccacat gcatatttgc atttattgag gagtcttaga 1500 tggagttgtc rtgtcattgc atgagttgca tgttgttgaa tgtgattgct attatgaatg 1560 actgttgttg ataataaata attatgctta ttgaataatc tttgatatta tagggtgtta 1620 gattccaatt gatgaattta ttattatttt tattgattga gaatctcacc ccttctgctt 1680 gaaaatgttg cccttcctat gggtaacttg caggtgatcc tgagtagtag gtggtggctc 1740 aaagtgtcta gggctctgat acgtacggga tgggatttta ttgttttatt tcattcctat 1800 gtatcaaatt ttggataatg acgatgtagc cctatggttg tttgaattat tntggttgag 1860 gcttttatgc caagatattt tttggagatt taaatagttg ttgatgttgc tatgaaaata 1920 ttccgctgca arttwaatga trattttatt tggatgttta ataaatagat ttttatatat 1980 attctattta agaaatttta aaaatgaagt gtgacatgcc cgtttggrtt ttatgactct 2040 gatgtatgtt tattattatt taattaaatt attttgggaa acggggtgtt aca 2093 // ID Gypsy-1_Mad-I repbase; DNA; EDCOT; 8307 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-1_Mad_; KW Gypsy-1_Mad-LTR; Gypsy-1_Mad-I. XX NM Gypsy-1_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-8307 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1732-1732 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [4076-4543] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 800..2665 FT /product="Gypsy-1_Mad-I_1p" FT /translation="MAPPPRPEPCHPRRSRHQGHGPSPMSLQAQRAAQLPP FT EQPTPWPSLLRRAAHSLASSPPWPSLAEQPTPVAQPAPAEQPTLVAQPAPP FT SSPLSWPSLLPTPVAQSAPVAFQAAQIDPRLVQPSRLQISGPTIEPGAFSP FT HFSADLTFPNSNLAPGVYHTSTAQGDAFLPSYSNPNGEQHLSRQVIELTSA FT LAQQTTLVNQLLQRTEMQRAPDEVSRSRTRADKEPLQQRPGKQPLDQPRTE FT RSGSVHSRLGPRDSVYSRLSARRSVHSRLGPRTSIHSRLGSHSDSQHEQPS FT RRSVHSRLSPQGASSTSHRSRQHDGRREAVTQSGSSSTGSLRRTRSPARNA FT PHAPHPRHRRAKHMEEQPRPASHGWGQPRAPLPQQRQIQEEVERLLTKRLR FT NFQRNEVTDEALRRNMTNISRSPFTDEIEQAEPPREFSMPHFTSFKGDEDP FT ERHLKHYRSAMILYRNNDDLMCKIFATTLQGEAQDWFYTLPPQSIRSFDEL FT SLVFTKEYSSYRSIKKKSDHLFNVKKNPKESLRDYVKRFKAEKARIVGCND FT SIARAAFQKGLPADHPLFGKLIMKEDLTLADSFALAEKHALWDEARQCTFK FT DLKKYPTSPPYYPNRKQRMTYSHV" XX SQ Sequence 8307 BP; 2285 A; 2469 C; 1850 G; 1702 T; 1 other; aaacctatct catctcctca tatcccaaaa cctatttcat tccataatcc tcacccattt 60 tcccttttaa tcataaggta tatcattcca taacctccaa aacattcctt ttaaattgtg 120 ttaattggct aattaatgga tttattacct aattaatcca ttaattgcca attaaatcac 180 caaattacac ccaaaaaaca cccaaaaggc cggccacctt ttctccaaag gggaccggcc 240 atgctctata tattgaaccc cattttctct aaaaacctag ttccaacact cttgctaaaa 300 ctcccaaaaa ctctctaaac acttttctct ctaaattcta actttggcat cggaggttct 360 tcggccaaag ccccccattc atcgtgggcg cgtgaggctc ttggccttga ccaaaggtgt 420 taattgtttt gtaggtgcaa ttttgtccaa gatcaaggag gaagaaattt gcatccacaa 480 attggtgctt tcattgagag ttgagtccca cactcgtaga agactctcgc atcaaaggtt 540 tttctatttt cttgtccatt tgtagatttt tcgtacgttc ttattattag aattttttat 600 ttgcaaagat tctttgataa aacgtaaaag agaagtacaa tggctagaaa tttagaaaat 660 tccacaagtg aaaattccaa tattcaagag atgggaccgc ggcgatccac gaggctaaat 720 gtgacaataa gtggagcggc accaccacca cgagtctcca ccatgggaac caccgcggtg 780 gccacccgcg gcgaggtcca tggcgccacc accacggccc gagccgtgcc atccaaggcg 840 ctcacggcac caaggccacg gcccaagccc aatgtcactc caagcccaac gcgcagccca 900 actgccaccc gagcagccca ctccgtggcc cagcctgctc cgccgagcag cccactctct 960 ggccagcagc ccaccgtggc ccagccttgc cgagcagccc actcccgtgg cccagcctgc 1020 tcccgccgag cagcccactc tcgtggccca gcctgctccg ccgagcagcc cactctcgtg 1080 gcccagcctg ctccccactc ccgtggccca gtctgctccc gtggccttcc aagcagccca 1140 aatcgatcca agattagttc aaccgtcccg gctccaaatt tccggaccga cgatcgaacc 1200 gggagcattt tcaccacatt tttctgcgga tttgacattt cccaactcaa atctcgcgcc 1260 cggagtctac cacacttcca ctgctcaagg agacgcattc cttccaagct attccaaccc 1320 aaatggagaa caacacttgt ctcgacaagt catagagttg acgagcgccc tcgcacagca 1380 gacgaccttg gtgaaccagc tcttgcagcg caccgagatg caacgtgccc cagacgaggt 1440 gtcccgaagt aggacaaggg cagacaaaga acctctccag cagcgtcccg gcaagcagcc 1500 actcgaccag ccacgaaccg agcgttcggg cagtgtacac tcccgattgg gcccccgaga 1560 tagcgtatac tcccgtctta gcgcgcggag gagcgtgcac tctcgactag gcccacggac 1620 gagcatacat tcacggttgg ggtcacactc cgatagtcaa catgagcaac cttccaggcg 1680 aagtgttcat tcgcggctaa gcccgcaagg agcatcatcc acctcacatc ggagtaggca 1740 gcacgacgga cggagagaag cagtcactca atccggctca agttcaaccg gcagcctgcg 1800 aagaactcgc tcgcctgcta ggaacgcacc acacgcaccg catccgcggc atagacgagc 1860 caaacacatg gaagagcagc ctagaccagc aagtcacggc tgggggcagc cgagagctcc 1920 gctaccccaa caaaggcaaa ttcaggaaga agtagagaga ctcttgacca agcgattgcg 1980 caatttccaa cgcaacgagg tcaccgacga ggcactacga cggaacatga ccaacataag 2040 caggtcaccc ttcacggacg agatcgagca ggcagagcct ccacgcgagt tcagcatgcc 2100 acatttcaca tctttcaaag gggatgaaga cccggagaga cacttaaagc actaccgaag 2160 cgcaatgatc ctctatcgaa acaacgatga tctcatgtgc aagatattcg ccaccactct 2220 acaaggcgag gcgcaagatt ggttctacac cctgccgcca caatccatcc ggagtttcga 2280 cgaactttct ttggttttca ccaaagaata ttcatcctat cgctcgatca aaaagaagtc 2340 cgaccatttg ttcaacgtca agaagaaccc aaaggagtcg cttcgcgact atgtgaagag 2400 gttcaaagca gagaaggcaa ggatagtcgg atgcaacgac tcgatagcta gagcagcctt 2460 ccaaaaagga cttccagcag accacccgct attcggaaaa ttgatcatga aagaagatct 2520 aactctggca gactctttcg ctctggcaga gaagcatgca ctttgggacg aggctcgcca 2580 atgcacattc aaggacttga agaagtaccc gacatcacct ccctactatc caaaccggaa 2640 gcagcggatg acttattcgc atgtttgacg gtatctaaag cagcaataag ctctaccatc 2700 atgcgagaag agctgggggc ccgactacct gtattccaca gttcaaaagc tctcctcgat 2760 gctatcagaa attcaaaagc taactttggc gatagttgtt gcaacccgga agctcaagtt 2820 ttaccttcaa acgcatgcag tcatcctcat gacgcactat tccgcccaat ccagacgcgc 2880 gacgataaag gcgtaagacc ctggcggatg caaagttttc tgacgaacgc aacaactcgg 2940 cccaaaagac acgccaaggg cagacgaaca ctggaaggac acactcgaaa gcaagttttg 3000 tcctcgtcgc cccaaaagat tctacataga gcaacatgta ccggcagttg agcaccactt 3060 cctgctacgt gtcacacggc cctagccgac ccttgctcca taattcaact ctagagtggt 3120 ccaataccag cagttgagca tctcctgctg cgtgtaacat ggccccagct ccacggctcc 3180 ctaccacgca ttcatgacgc aacagagcgg cccaacgacg ccccggaggt agccgagcac 3240 gccctagccg cgcctgctcc acccgatgga gacttctggc atttgcatgt ccacggcgca 3300 tccaactaca aaggttcaag agcaggcgta gtccttgtca ccccagacgg ttcgatgccc 3360 gagcaggcga tcactctagg cttcaaagca tccaacaacg aagcagagta cgagacccta 3420 ctagcaggcc tccgaatggc aaaagacttg gcggtgaaaa agctcgcaat tcattctgat 3480 tcccagctaa tcactagcca gactgcttga ggcgtttcag acttacaccc tcactcaagt 3540 tccacaggca gacaacgctc acgtggacgc actagccggc ctaggctccg ccctcgacca 3600 ccaactcaaa cgctctattc cggtggagta tctagacgag ccaagcatag aggcgaagcc 3660 agcagccgag gtgtcacagg ttagtacaac tccaaactga caagattcca tcgtagacta 3720 cctggtcaat ggcacattcc ccacgaaaag attggagtct aggaagctcc aaatcaaggc 3780 agcacgctac tacatgtgga acgacattct catccgaaaa tcctacaccg gaccacatct 3840 ccgctgccta gcgcctcccg atgacttgaa ggttctaagc tcaatccacg aaggcgtttg 3900 tggaaatcac tccggaggtc gatccttagc acagaaggct cttaacgcag gctactactg 3960 gcctaccatg caccaagatg ctaaggagtt agtacaaaag tacgaccgtt gccaacgcta 4020 caagccggta ccagcactgc ctgccagcga gctacacccg cagacgagtc cttagccgtt 4080 catgcagtgg gcaatcaacc tggtaggacc tatgccgcct gctactgggg gcagaggcat 4140 gatgatcgtg gcaaccgact acttcaccaa atgggtagaa gcagagccca agacgaccac 4200 gactcagacg gacatagagc acttcatatg gaggaacatc atttgccgat ttggcatccc 4260 tcagtccatc gtcaccgaca acggcccgca attcgtgggc caagatgtgg cgaagttctt 4320 ccaaaagtat ggcatcaagc agcacatgtc catgccaaga tatcctcaag gcagtaggcg 4380 ggccgaagca tccaacaaga tgatcctcga ctgcctcaag aaatccctca ccaacaagaa 4440 gggaaaatgg ccagacgaac tccccggatg tctatgggca tatcgcacca ccaaaagacg 4500 agcaaccggt gagactcatt tctctttggc atttggctca gaagcaatca ttcatcccaa 4560 tgtcatcaag ccaagtatca ccgctctact actaagcatt gagcagaaca gtaaggagat 4620 ggccacaagc ttagatctgg cagaggagaa gcgcgagcag accatcacct gcatcgcagc 4680 ctaccagcaa cagctcattt ccagctacaa caaaagggcc aagatccggc agttccagcc 4740 cgaagatcta gtcctaagaa aagccttcat cactgcccgc agagaaggct ccaaaaagat 4800 ggatcccatc tgggaaggtc cgtacaagat cagcagagta ggcggcaaga gtaattacac 4860 cctcgccacc atgaaacgat aaaaagatcg aaaagcagtg gagcgcctac aatctgagga 4920 agtaccatgt gtgacctccc gctacatcaa agcccgaaga ctcaagcagc tcgacgggca 4980 ccacctcaca agccgaggac tatccagttg ttatgcagtt cctaccttac agctaagttc 5040 tcgttcgttt cactcgtttt tcaatgagga attcagaagt aatcacaact tggctcggct 5100 gcatgcttac aacaactgat cactcatgca cttcaaaaga agaccgcgcc cttcttaggg 5160 actcatcgca ggaattgcgc cccccgaggg accaaccatg ctctccagtg cgagagggta 5220 aactaattgc tctccagtgc gagagggtaa accaattccc cgacacccac atgggtcagc 5280 tctccaagac gggaggataa actctacact ccgaatatcc agacgtggat gagcctggct 5340 gccctagtat aactagatgc acgatggctt gcgccgggat tcctagaagt agccacaatg 5400 gtctttttca aggcttagct aactgaagga ttttgggtct cttggcctaa tccgcgggga 5460 accgggccct agagacggag ggggcacatt acgcagtacg ccctacagac ggctgccctg 5520 gaaccctaaa gctgctaccg agtgcactaa ggtagcctac ggtttccgga agactgccta 5580 cggcttgccc ttcgagcagt aaaaccacgc tagacttata caaccgcaca ttcttgtgaa 5640 aggttaaaca agctagcgtg catatacgaa gctttatcca ctgccgacat gctacgtagt 5700 cgataagctt cacctctgcc aagcgcagaa caacctacac caagtcctaa agtgttgtga 5760 tacttgctac gcaacctacg gaattggaga aagccaaggt taacagccta gtggttacgc 5820 ggacttgtct gcttctgtaa gtaaggcatc cggctgccaa ccctatggct aacaactttg 5880 caaagttcta caccaacacc tacggctgca taggctacgc gggcctgtct gcttatagaa 5940 aagtagcacg cctgccactg gtctataaag tctaaaggtt agggcatgaa caaaagaagt 6000 gaagatgaag aaaagcgaag gaagcatgtt tataaacaac tagcaaaggc cgaaggagtt 6060 caagcaaaac aagagctaca aggaaaaaca aagaaaatcc taaaggctac ctagaagact 6120 acacttcagc agcttggaca tcccacgact actcggtcgc cacaccttca gcagccgcga 6180 cgctcttagc agcggcatca tccagcgctt cacccccggc tgccccagcc tgggcaccaa 6240 cttctccaac tacttcacca atggaagcct caaaagtaaa agcaagcaag tcttccggag 6300 aaatagagaa ggtctcgaaa cctcgagccc atcattctca cccttcagct gctcatcctc 6360 ctcgagcaga ccaacacgga cgcgctgcag ctcatccact tccttcttca gactttcgtt 6420 gatcttcagt acaccttgaa gttccaacac ttggggttca agcctatcga cgattctctt 6480 gaagtggatc acttgattat aagcagcaat caactcttca tcctttgcat aagcagcgaa 6540 acgaagctca gaaactgcaa actcaagatc ttgaatctga ggtatgtaac atccaatctc 6600 cttctctgca ctttcatact taacttggat cgcgtcaagc ctagtcttca agtcaacaat 6660 mtcttggcga gcggtctcaa gctgcagaga agtgggggca gaaatattag accccttcaa 6720 agcaacgagc tcagaatcca acctcttgat ctcctcggcc gaggaataag cttcagctgc 6780 catagtcttc gccacctcct tggcagcctt gctatatctg catcatagca agcagagcag 6840 tcttctatat tgggtcgtat gcttcgcaaa ggaacttggg caaacaaacc tttctaaacg 6900 ccatcaacaa acttggcaca agcgtccatg tcttcaagca gatctggttt caagagcaca 6960 cagatctcag cagcctcccc agaagcaggc ttagtggatt tctcacagct gcccacgcga 7020 gcagtctcct ccttcccagc aggcgaatca gtctcagcag cagagggagt gggccttagc 7080 gccactttag cagcagagtc caccttatcg ctcttcataa tagcaagcct ctccaaaggt 7140 gaaccagact tagctcccaa cggacgtctt ggtacagact tcggcactgg gggcatgaca 7200 agacctctac gctgagcaat cctatcagca atcgtacaag ccattctcga catggcaggc 7260 gccacatgct cagatctagc agcctcattt ttcttcccat tggaagaagt catgtcaatc 7320 acaggcctct cggcagcagg cggaccctca cgagcagcgg aggaagtctt cagtttttct 7380 caaccggcat ctcttgagca ggcggggaag atctcttctt tccaccttca ttcatagtag 7440 gctccacgac agcgttcaga cgagccaatg catccgcctt gatcctcttt acctcctctc 7500 tcgggagcag cccacctttc tcccggcgaa gagaactaag cagccaacgc cattcacggt 7560 actcagcagg ggagctcaac ccatactggc ttttccctca tttttttctc accagcaggc 7620 aggaggcctg catgcccagc attccagcag cccatgaggc ccgcgacctc ctcatttctc 7680 tcaatcgccg gcctggcccg cgtcaggtcc aagagcccaa aggacatgag ccatgcggct 7740 cgcctagcac tgcgccccag cgcctcaatc tgcggcccca gccgcgcaag ctgcccttgg 7800 ctctagccaa gccgagcggc ccaagcagtg gtccctgcca caacacctcc tcggcccatg 7860 ccgagccgac tcctggcccc tgccagccga cgtgccgcac caccccgacg gctgccccgc 7920 gacagcacta tccaagaaga agacaaggaa aattaaattt ttcttacctc ggtgcggcgc 7980 ggagaagacg aagaaagcaa cgaaagacgg tcatttgcac gggcaagatg tagaagattg 8040 ctagaggagg gggaacaaat atcctctaag ctctctctct tgtagggtag aataaattgc 8100 tctccaaagt tgatttaata acccacttaa ggtggactta aataggcttt gagagaaatt 8160 tatttccctt tcctagaagg atctaatttc caattaaaga gggaatctac atcaaaatag 8220 gaagcaatcc tatgtttcct aaagcaagaa gatctctaca cctgctgccc tttcctgcga 8280 gcagcccaac aggtgtgggg gcatttg 8307 // ID Copia-61_VV-LTR repbase; DNA; EDCOT; 302 BP. XX AC chr14; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-61_VV_; KW Copia-61_VV-I; Copia-61_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-302 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr14; Positions 2120204 2120505. XX SQ Sequence 302 BP; 70 A; 35 C; 73 G; 124 T; 0 other; tgttgaagac tgattcaaag tggctgttgg tatattccta ttcttatggt tgagttagtc 60 aaataaggag cttgttgcta aaatcgagtt agtgggtgta gtgggtcaag tgttagtggt 120 gtagtggggc agattgtgtc ctctttgttt ttttttataa atagacatgt ttgctgtagt 180 ggaaaaatga ctgcaataaa atatccagaa gcattttctt tggtctggtg aagctctgtt 240 ttttagagtt aaagagctct atttttttcc ttgctattgt tttgtcttgt ttttgtccaa 300 ca 302 // ID Copia-67_VV-LTR repbase; DNA; EDCOT; 228 BP. XX AC chr17; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-67_VV_; KW Copia-67_VV-I; Copia-67_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-228 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr17; Positions 10721883 10721656. XX SQ Sequence 228 BP; 66 A; 40 C; 38 G; 84 T; 0 other; tgataagcca agaacagagg aaaacagagg agttggttct gatgtcatga gatgaagccc 60 acttgttgtt agatttattg ttattgagtt gttatttttt accaactgtc attacaacct 120 gtctccatct attttgaaca ctatatatat attaaatctc tctctcttgt aactttaaca 180 aaagagagca gagttttcag cttcagcttt tctatctgcc attgttca 228 // ID Copia-91_Mad-LTR repbase; DNA; EDCOT; 428 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-91_Mad_; KW Copia-91_Mad-LTR; Copia-91_Mad-I. XX NM Copia-91_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-428 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1721-1721 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 428 BP; 126 A; 77 C; 94 G; 131 T; 0 other; tgtaagttct atttgagagc aaacactttg tgatttgtac aaagactttt gggacgataa 60 ggagattagc attaacacat gtggtagact tataaggagt tgtattactt aggtatacaa 120 gtcagaaaca ttcttagata aactagaact cttctagctg atattatgca taagtgatct 180 acggtgataa ggttaatctt tgatagggtt tacttaatgg gaggactcct aatcgaagac 240 catcgcatat agtatataac tgaggtccct gcgctctcac taaataccgc aagtttacag 300 aaatctcaag ccccattgag cgagccttgc ttccggcagt gcagagtcgc agaagagcct 360 cagttcttta ccctatttct gagacgatgt cttcctcagg ttagtggtta ggttggtaat 420 atgagtca 428 // ID Copia-5_SL-I repbase; DNA; EDCOT; 4382 BP. XX AC AC243358; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the tomato genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-5_SL_; KW Copia-5_SL-LTR; Copia-5_SL-I. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-4382 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the tomato genome."; RL Direct Submission to RU (22-JAN-2011). XX DR Genome; AC243358; Positions 96545 100926. XX CC Positions [1719-2216] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 783..2363 FT /product="Copia-5_SL-I_1p" FT /translation="MEPATALTASKNYMGGRCGGRHGSRGGYDRNSRSRGR FT GGRQGSPPPYDGPQHGSNNSLHSFGSGGQSSSSGGQGTNERDRLTCEIYQK FT IGHTAVHCWFRYEESRNSYNRVNYASQAGPSSEWLLDTRVNIHVTSDLAKL FT NAPNPYYGSNGITVGNGKSLNISHTGTGTIKTPTAIFHLGNLTHVPSIKTN FT LLSVHQFTKDNNCSLLFTSNDFQILDNTTKRVIFQGSCEHGLYVLPGTSSS FT AHPVSESVPVAPVALSAYGHSLLWHSRLGHPFTQIINSLMSQLGFSSIHVN FT NCDSCSIAKSHKLSFSLFEKRTTAPFQLIHSNLWSPTAVPSFAGFRYYICF FT VDDFTKYTWLYPLKHKSQAYTTFVTFEKMIKTQFNSHVKLFRSDNEKEYVN FT NIFGQFLQSLGIIHQTSCPYTPEQNGVAERKHLHLIETVVTLLHQSLPISF FT WVEALATANYLINRIPSHTLSNKSPYQLLYLELPNYTILRVFGCLAYPWLR FT PHINHKLQPRSHPCNFLGYHPTSKGYRCLHP" XX SQ Sequence 4382 BP; 1143 A; 1235 C; 808 G; 1196 T; 0 other; tggtatcaag agccagaaaa cctagatctt cttttctcta gttttttttc tctttagggc 60 accgatcgtt ccctctcttc tcttgggcgg cgacagccat gacaaccgag gtggatcctc 120 tcgattaact tccttctggc gttaaactcc ttctcaggca tcttcatgcc ctgattcctg 180 aaaaattatc agacataaat taccctacat ggaaaatcac cgttcttaca gccattgagg 240 ccaattacct tctcaaatac atcgatggaa gcacagaacc gccgccggca gtcatcaccg 300 ccacggacaa atcagaaaaa accaatccgg tccatgccgc ctggaaagcc gtggatggcc 360 agatccgatc atgtttgatt gcggtcatct ctcccacggt tcagaaacat gtccgatcct 420 acacaactgc ttcagccttg tggacggccc tcgcaacacg ctatgcatca atttcccact 480 ctcataattt tcaattgtgt gatcgtctcc acacaattac caaagacacg aaaattatgg 540 aggagtattt agacgaggtc tccactatca tcacagccct cgacaccgtg aatgaaatca 600 ttcccgaaaa agatctcatc atgtgcgtcg ttcgggggct cccatcagct tactcctcca 660 ttaaacaggc ggttcgcatc agtccaacgc ccgttgacct tgctactctc tcctcgtggc 720 taaaaagtga agaaatcaac gtagatctgg agagcaaact tcttctctga gaaactgctg 780 ttatggagcc ggccaccgcc ctcaccgcaa gcaagaacta tatggggggg cgttgtggcg 840 gccgacatgg gagtcgcggc ggctacgaca gaaacagcag aagccgcggg cgcggcggtc 900 ggcaaggaag tcctccgccg tacgacggtc cgcaacacgg cagcaacaac agcctgcact 960 ctttcggcag cggcgggcag tcatcttcca gcggcgggca gggcactaac gagcgggatc 1020 gtctaacttg tgaaatctat cagaaaatag gacacaccgc tgttcattgc tggtttcggt 1080 atgaggagag ccgaaatagt tataaccgag tcaattatgc atctcaagcc ggcccctcct 1140 ctgaatggct gttggatacc agggtcaaca tacacgttac ctctgatcta gccaagctta 1200 acgctccaaa tccatattat ggctccaatg gtattactgt tggcaacggt aagtccctta 1260 atatttctca cactggcacg ggtaccatta aaacccccac cgctatcttt cacctaggta 1320 accttaccca cgtcccttct attaaaacca atctcctttc agttcaccaa ttcacaaaag 1380 acaataattg ctcactcttg ttcacctcta atgattttca gatcctagac aatactacca 1440 agagagtgat ttttcagggc tcctgtgagc atggtctgta cgttcttcct ggcacaagtt 1500 catctgccca cccagtttca gaaagcgttc ctgtggctcc ggtggctctt tcggcttatg 1560 gccacagtct gttgtggcac agtcgtctgg gtcacccgtt tactcaaata ataaattctt 1620 taatgtctca attaggtttt tcttccattc atgtaaacaa ttgtgactcc tgttcaattg 1680 ctaaatctca taaattatct tttagtttat ttgagaagcg tacaactgca ccttttcaac 1740 ttattcattc taacctatgg agtcctactg ctgttccttc atttgctggt tttcgctatt 1800 atatttgttt tgtggatgat tttacaaaat acacttggtt gtacccacta aaacataaat 1860 cacaggcata caccaccttt gtcacttttg aaaaaatgat caaaacacaa ttcaattctc 1920 atgttaaact ttttcggagt gacaatgaaa aggaatatgt aaataacatc tttggccagt 1980 ttctgcaatc cctgggaatt atacatcaaa cctcctgtcc atacactccc gaacagaatg 2040 gggtggctga gcgtaagcat ctccatctca ttgaaacggt ggttactctt ctacatcaat 2100 ctctccctat ctccttttgg gtagaagctc tagccaccgc aaactacctc attaacagaa 2160 ttcccagtca caccctctcc aacaaatcac cctatcaact cctttaccta gaacttccca 2220 attataccat cctccgcgtc tttgggtgtc ttgcctaccc ttggctacgc cctcatatta 2280 atcacaaatt acaaccccga tcccatcctt gtaatttttt gggctaccat cctacctcca 2340 agggttatcg ctgtcttcac ccataaactc ataaagtcta catatctcgt catgtcaaat 2400 ttgtcgaaaa tgagtttccc tacgagtcta tttcctcctc cacaaataca tcattcattg 2460 gcgtccttcc cctttttcca acatactcac agggtccctc atcaccttcc cccacacctc 2520 cacccactac ccaatcaccc ctcatcaccc cttcgaccgt cacccacaat acacccgcaa 2580 ccaccaccca cactcacaac caacccaaac caccccatac ccacaacatt tccagcccga 2640 tccattttgg gtccttcccg gccacccccg aatcaccacc gcccgtaccc ccccccccca 2700 atactcatcc catgttaacc cgtggcaaag tcggtatctt taaacccaaa aacattcagg 2760 ctaccatact accaaataca cccattccac atagtgaacc aacaacctac tctgttgcct 2820 caaaaaatgc ttattggcgt catgctatgg atgacgagtt taaggctttg actgatcaga 2880 aaacatgggt tcttgtacct aagccccatg ggcggcaccc agtgggcttt aaatgggtgt 2940 acaaaattaa acacaatgca gatggcagta tttccaggta caaggctcgt ttggttgcta 3000 aaggctacaa tcaggagtat gggcttgatt actccgatat attcagtcct attattcggc 3060 aggaaaccat tcacctggta ctgtcactcg ccgtgcgcaa caattggctc atcaatcagt 3120 tggatgtttc caatgctttt tttcatggca tgctttatga aactatctac atgacataac 3180 cagcgggcta tgttgatccc cgcttccctc aacatgtttg caaactccag aagtctctgt 3240 atgggctcaa gcaagccccc cgtgcttggt acacacatct gaaaacgttc tttcagggac 3300 tcggcttcac gtgttgcgta cacgacatga gtctgtttac tcgacattca gcactcggta 3360 cagtcattct tcttgtctat gtagatgata tcattattac aggctctact gcagctctca 3420 ttcaggatgt cactcgagct atgcatacta ccttcaaaat gaaggacctc ggccagttac 3480 attattttct gggaatggag gtttctcgga caggcagcgg cttgtttctt catcagtcaa 3540 actatgctcg agatctgttg cagaaagcta cactggaaaa atgcaccagt caacaaacac 3600 cgatggcagt ctcttcatct acgaatggag ccgacacccc ctttgcccat atcacccact 3660 tccgtagcct aattggggct ctacagtatc tggccattac ccgtcctaac atccagtgtg 3720 ctgtcaaccg agttgctcag cacatgcatc aaccaagtga acatgattac cattgtctaa 3780 aatgcattct caggtacatt tttggcactc ttggtcgtgg tttactcatt cgacccgggg 3840 atttggagct tcggaggttc tcagattcag attgggtgaa caataaaaat gacagaaaat 3900 ctacatcggg gtttctcctt ttttttgggg ccgaacctga tctcctggtg tacaaaaaaa 3960 taacccaagg tctctcggtc ctcgactgaa gctaaatacc gcgtccttgc ttttcccgct 4020 gctgagacca tgtgggtcac atatattctt cgcaaactcc gcgtcactca cactcttcct 4080 gctctctatt gtgacaaaaa atcaaccatc tgtgtggcca agaattccgt cctactcacc 4140 agaatgaaga atgttgatac cgattgtctc tttgttcgcg atgaagttca ggccggcacc 4200 atgactgtgc agtatgtacc cactgaacaa caaccggctg atattctcac caagcctctc 4260 ccgagccgac agcacgatta cctcagttcc aagcttccgt tcgcttccgt tcagctcagc 4320 ttgagggggg gataataaca gatagtattt aataaatagt attaaataat attagtatat 4380 ac 4382 // ID Copia-68_VV-I repbase; DNA; EDCOT; 4143 BP. XX AC chr18; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-68_VV_; KW Copia-68_VV-LTR; Copia-68_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4143 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr18; Positions 24282524 24286666. XX CC 'CTTAC' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 79..4143 FT /product="Copia-68_VV-I_1p" FT /translation="MGDLQVIGGIKKLNNQNYNTWSTCMMSYMQGQDLWEV FT VNGSEITQPEVEDANGILRKWKIKAGKAMFALKTTIEEDVLEHIRDAKTPY FT EAWNTFTKLFSKKNDTRLQLLESELFSVAQRDLTIAQYFHKVKTLCREISE FT LDLEAPIGETKMKRIIIHGLRPEFRGFVAAIQGWQNQPSLVEFENLLAGQE FT ALAKQMGGVSLKGEEEALYAHKGGWNSKQHTVRRTKKNEDKAKCSQGERSA FT RVEGDSKNPGTIKKFEGKCYNCGKKGHMAKDCWSKKGLVESNAATSKSEDE FT WDTQALFAAIGESAFIATTSEQIDYEKDWIIDSGCSNHMTGDKEKLQDLSE FT YKGRHMVVTANNSKLPIAHIGNTVVSSQYNTNDVSLQNVYHVPGMKKNLLS FT VAQLTSSGHSVLFGPQDVKVYHDLEVMEEPVIKGRRLESVYVMSAETAYVD FT KTRKNETADLWHMRLSHISYSKLTMMMKKSMLKGLPQLEVRKYTICAGCQY FT GKAHQLPYEESKWKAKGPLELIHSDVFGPVKQASLSGMKYMVTFIDDFSRY FT VWVYFMKEKSETFSKFKEFKEMTEAEVDKRIRCLRTDNEGEYTSDEFFYFL FT RECRVRDQFTCANTPQQNGVAERKNRHLAEICRSMLHAKNVPGRFWAEAMK FT TAAFVINRLPQQRLNFSSPFEKLWNIKPTVSYFRVFGCVCYVFVPNHLRSK FT MDKKAVRCVLVGYDSQRKGWRCCDPTTGKCYTSRNVVFDESSSWWSSEKEI FT LLDSNVFKDELQSARIQLSLGEAENAVDGDIGDDKTQSPWQTGVHGQPSEE FT GEPSETEAPIPLRRSARTKKPNPKYANVAIVEDANAKEPETFAEAFQNSDW FT SKAMKEEIAALKRNQTWELVPKPRDVEPISCKWVYKIKRRTDGSIERHKAR FT LVARGFSQQYGLDYDETFSPVVKLTTVRVLLALAANKDWDLWQMDVKNAFL FT HGELDREIYMNQPMGFQSQGHPEYVCKLRKALYGLKQAPRAWYGKIAEFLT FT QSGYSVTPADSSLFVKANGGKLAIVLVYVDDLIITGDDVEEIFRTKENLSV FT RFEMKELGQLKHFLGLEVDRTNEGIFLCQQKYAKDLLKKFGMLECKPISTP FT MEPNAKMCEHEGKDLKDATMYRQLVGSLLYLTLTKPDISYAVGVMSRYMQN FT PKKPHLEAVRRILRHVKGTIDYGLLYKKSEDCKLVGYCDADYAGDHDTRKS FT TTGYVFMLGSGAISWCSKRQPTVSLSTTEAEYRAAAMATQESMWLIRLMND FT LHQLVDYAVPLYCDNQSAVRLAENPVFHARTKHVEVHYHFIREKVLKEEVE FT LNQIKSEDQVADLFTKGLSGSKFESFCHQLGMVKILEADVEGE" XX SQ Sequence 4143 BP; 1372 A; 713 C; 1015 G; 1043 T; 0 other; tttggtatca gagccaggtt gaagaggcat ttcagagagt gtttgagagt caaacacgtg 60 aggaaaagag agagtgaaat gggtgatctt caagtcattg gcggaataaa aaagctcaac 120 aaccaaaatt acaatacttg gtcaacatgc atgatgtcat acatgcaagg ccaagacttg 180 tgggaggttg tgaatggaag cgaaattact caaccggagg ttgaggatgc gaatggtata 240 ctgcgaaaat ggaagataaa agcgggcaaa gcgatgtttg ctttgaagac aacgatcgaa 300 gaagatgtgc tagagcatat tcgagatgcc aaaacccctt acgaggcttg gaatacgttc 360 accaagctgt tctcaaagaa gaatgacaca aggctccaac ttctagagag cgagttgttt 420 tcggtagcac agcgtgactt gacaatcgct caatactttc acaaggtgaa gacgttatgc 480 cgggaaattt ctgagttgga tctagaagcc ccaatcggtg aaaccaagat gaagagaata 540 atcattcatg gtttgagacc agaatttaga ggctttgttg ctgctataca gggatggcaa 600 aatcaaccat cacttgttga gtttgagaat ttgcttgctg gtcaagaagc cttggctaaa 660 caaatgggag gagtttcact caagggtgaa gaggaagcgc tttatgccca caaaggcggg 720 tggaattcca agcagcacac cgtcagaaga actaaaaaga atgaggacaa ggcaaagtgt 780 agtcaaggtg aaaggagcgc tcgtgttgag ggagattcga agaatcctgg caccataaaa 840 aaatttgaag ggaagtgcta caattgcgga aagaagggtc acatggcaaa agattgttgg 900 tcgaaaaaag ggcttgtgga aagtaatgct gctacttcca aaagcgaaga tgagtgggac 960 actcaggcac tttttgctgc aataggagaa tcagctttta tagcaacaac gtctgaacaa 1020 attgattatg agaaggattg gatcattgac tcaggctgct caaatcatat gacgggtgat 1080 aaagaaaagc tacaggattt gtcagagtac aagggaagac atatggtagt cacagcgaac 1140 aattcaaaac taccaatagc tcacattggt aatacggtag tctcttccca atataatact 1200 aatgatgtgt cgcttcaaaa tgtctatcac gtcccaggta tgaagaaaaa tcttctctcg 1260 gtagcacaat taacgtcttc aggccattct gttctatttg gccctcaaga tgtgaaagtt 1320 tatcatgacc ttgaggttat ggaagagccg gtgataaagg gacggagact agagtcagtc 1380 tatgtgatgt ctgcagaaac cgcatatgta gacaagacca gaaagaacga gacagctgat 1440 ttatggcata tgcgattaag tcacattagt tattccaaac taactatgat gatgaaaaag 1500 tcaatgctga agggacttcc acaacttgaa gtgagaaaat atacaatctg cgcaggatgt 1560 caatacggca aagcgcatca gttgccgtat gaagagtcaa aatggaaagc aaaggggcca 1620 ttagagctaa ttcactctga tgtgtttgga cctgttaagc aagcctctct tagtgggatg 1680 aaatacatgg tgacctttat tgatgatttt tccaggtacg tgtgggtgta ctttatgaaa 1740 gaaaaatctg aaactttctc aaagtttaaa gaattcaagg aaatgacgga agcagaggtt 1800 gataaaagaa tccgttgttt gcgtactgac aatgaaggag agtatacctc agatgagttt 1860 ttttacttcc tccgagaatg ccgagtacgc gatcagttca catgtgccaa cactccgcag 1920 caaaacggcg tagcagaaag aaagaatagg cacctagcag aaatctgtag aagtatgctt 1980 catgcaaaga atgttccagg acggttttgg gcagaagcaa tgaagactgc agctttcgta 2040 atcaataggc ttcctcaaca aaggttaaat ttttcatcac cctttgaaaa attgtggaac 2100 ataaagccta cagttagtta tttccgagtt ttcggatgtg tttgctatgt ctttgtacct 2160 aatcatctac gcagcaagat ggacaagaag gctgttaggt gtgtcttagt aggatacgat 2220 agtcaacgaa aaggatggag atgctgcgat cctacaactg gaaagtgtta cacatcccgg 2280 aatgtggtgt ttgatgaatc atcttcatgg tggtcctcag aaaaggaaat attactagat 2340 tcaaatgttt ttaaggatga gttgcaatct gctcgaatcc aacttagctt aggtgaagct 2400 gaaaatgcag tcgatggtga tatcggagat gacaaaactc aaagtccttg gcaaactggt 2460 gtgcatggac aaccaagcga agaaggtgag cctagtgaaa cagaagcacc aattccactt 2520 agaagatcag caagaaccaa gaagccaaat cccaaatatg ccaatgttgc catagtagaa 2580 gatgcaaatg caaaagaacc agagacattt gcagaagcat ttcagaattc agactggagt 2640 aaagctatga aagaagaaat tgcagcatta aaacgaaatc agacttggga gcttgtgcca 2700 aaaccaagag atgtagagcc tatttcctgc aaatgggttt ataagataaa acgtcgcaca 2760 gatggatcaa tagaaaggca caaggctcgt ttggtagctc gaggattctc tcaacaatat 2820 ggactagact atgatgaaac gtttagtcca gttgtaaaac ttacaactgt acgagtctta 2880 cttgcacttg cagctaacaa agattgggac ttgtggcaga tggatgtgaa gaatgcattc 2940 ttgcatggag agttggatcg agagatctat atgaatcaac cgatgggctt tcagagtcaa 3000 ggtcatcctg aatatgtatg taagctgcgg aaggcactct acggattgaa acaagcaccc 3060 agagcatggt atggtaagat tgctgaattt ctaactcaaa gtgggtattc agtaacacct 3120 gcagattcta gcttgtttgt caaagctaat ggaggaaagt tagctatcgt acttgtatac 3180 gtagatgatc taatcatcac tggagatgat gttgaagaaa ttttccgaac aaaggagaac 3240 ttgtcagttc gtttcgagat gaaagaactt ggacaactta agcactttct tgggctagag 3300 gtggatcgta caaacgaagg gatatttctc tgtcaacaaa aatatgccaa agatttgttg 3360 aaaaagttcg ggatgctcga atgtaagccg atctcaacac caatggaacc aaatgccaag 3420 atgtgtgaac acgaaggcaa agacttgaaa gatgcaacaa tgtatcgaca attggtgggt 3480 agtttgcttt acttaacttt aactaaaccc gatatctctt atgcagttgg tgtgatgagt 3540 cgatacatgc aaaatccaaa gaagcctcat ttggaagcag ttcgacgaat tttgagacat 3600 gtgaagggta caattgatta tggtctgttg tataagaaaa gtgaagattg caagttagtt 3660 ggctactgtg atgctgatta tgcaggagat cacgacaccc gcaaatcaac taccggatat 3720 gtgtttatgc ttggatcagg agcaatttct tggtgtagca agagacaacc gacagtatct 3780 ctgtcaacaa cggaggcaga gtaccgagca gcagcaatgg caactcaaga aagtatgtgg 3840 cttatacggc tgatgaatga tctacatcaa ctagtggact atgcagttcc attgtactgt 3900 gacaaccaat cagcagttcg tttggcagag aatccagtct ttcatgcaag aacaaaacat 3960 gtggaagtgc attatcattt tattagggaa aaggtcctga aagaagaggt tgagctgaat 4020 cagattaagt cagaagacca agttgcagac ttattcacaa aaggtttgag tggcagcaag 4080 tttgaaagct tttgtcatca gctcggtatg gtaaagattt tggaagctga tgttgaggga 4140 gag 4143 // ID SIRE1_LTR repbase; DNA; EDCOT; 999 BP. XX AC AY205610; XX DT 09-JUL-2004 (Rel. 9.06, Created) DT 01-FEB-2007 (Rel. 12.03, Last updated, Version 2) XX DE Glycine max cultivar Williams 82 SIRE1-8 retroelement: long DE terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; SIRE1; KW SIRE1_LTR. XX NM SIRE1_LTR. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RA Laten M.H., Havecker R.E., Farmer M.L. and Voytas F.D.; RT "SIRE1, an Endogenous Retrovirus Family from Glycine max, Is RT Highly Homogeneous and Evolutionarily Young."; RL Mol. Biol. Evol 20(8), 1222-1230 (2003). XX RN [2] RA Laten M.H., Havecker R.E. and Voytas F.D.; RT "SIRE1_LTR."; RL Direct Submission to Genbank (20-DEC-2002)Zoology and Genetics, RL Iowa State University, 2278 Molecular Biology Bldg, Ames, IA RL 50011, USA. XX DR Genbank; AY205610; Positions 8311 9309. XX SQ Sequence 999 BP; 301 A; 158 C; 232 G; 308 T; 0 other; tgttagtgct tagctttact gagttttaaa agattggcta aaattttgtt aaaacataag 60 cacttagaca atgaaggaaa gctggagttg ctgcacatga tgtctaacat tatgtcaagg 120 aatcagatcg ggttgcacaa tgcacaaggc aagataaaat gtcaaatgaa gaattgaagc 180 tgcaggatcc acgatgtcgg atacaatgtg caggacatcc tgcccgaaaa tactggacac 240 ataaatctgt tatatcttta acagattaat gtgcagtcag caacagatta ggcgatctat 300 ctttaggaac gaattaaaag aaaattaaag ttcgaattac aaacttgaat agttcgttca 360 gggattaaag attaaagata aaaactaaaa gatcaaactt tatctttgag atctttaagt 420 gcagattttc aggagaatga tagatcttat ccagcgcaag ttgttgcagc ccagatacgc 480 acactgctat ataaacatga aggctgcacg agttttctac caagtccgag attgaagagt 540 tattttgtga gttttgggac ttgagtgttt tgtgagccac cttgatgtta ccctaacatc 600 aagtgttgga cctgagtgtg tagagttgat ctctattgtt cagagagcaa tctctggtgt 660 gtctttgatt tatttgtaaa cacgggagag tgattgagag ggagtgagag gggttctcat 720 atctaagagt ggctcttagg tagaggttgc atgggtagtg gttaggtgag aaggttgtaa 780 acagtggctg ttagatcttc gaactaacac tattttagtg gatttcctcc ctggcttggt 840 agcccccaga tgtaggtgac gttgcaccaa actgggttaa caattctctt gtgttattta 900 cttgtttaat ctgttcatac tgtcaaatat aatctgcatg ttctgaagcg tgatgtcgtg 960 acatccggta cgacatctgt cattggtatc agaatttca 999 // ID Gypsy7-PTR_LTR repbase; DNA; EDCOT; 432 BP. XX AC scaffold_629; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy7-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-432 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-432 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 339-339 (2007). XX DR Genome; scaffold_629; Positions 938 507. XX SQ Sequence 432 BP; 96 A; 83 C; 77 G; 176 T; 0 other; tggtggggac actagaccca caccacaaac tacacgagta tatggacgga gacgacgtag 60 gatgacccag cctgtcacgc tttggttggg agactaagcc catttgggct catttcattg 120 ttattttatt tatttagccc atttgggctc atttcattgt tattttattt atttagccca 180 tttgggccta ctcattgtta ttttattatt tatgttaaac agtttgattt gatgggccga 240 gcccaatagc ggaatgtttt agggtttact atttatatgt tcttctgtca ttttgagaga 300 cagttttgat gattaatgaa aattgcagac tttgcatatc tccaatcccc tttcttctct 360 tcttcagctt ctttcttttc taaagcttct ttctgttctt gctttaattt tattatttat 420 tgttccgcat ca 432 // ID Gypsy-21_VV-I repbase; DNA; EDCOT; 5037 BP. XX AC chr10; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-21_VV_; KW Gypsy-21_VV-LTR; Gypsy-21_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5037 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr10; Positions 565587 560551. XX CC 'ATACA' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 307..2394 FT /product="Gypsy-21_VV-I_1p" FT /translation="MENQGENQQTQQGPNICNSHMSRSMREYMHPQRIGMG FT SCIVLPNEPIVIKTHLVPLLPQFHGVENENPYTHIKDFEEVCHTFQEGTAS FT IELMRLKLFPFTSKDKAKLWFNSLRPQSIRSWLELQTTFLKKFFPIHRTSG FT LKRQITNFVTLDNEKFYTCWERYMEVINACPHHGFDTWMLVSYFYEGMSPT FT MKQLLETMCGGDFMSKSPDEAFEFLNYVAEISRSWDEPHERDLHKSKSQSN FT SKGRMYMLNEDVDLQAKIVALTKRLEELEAKGFHEVNAIYDNPIYMEQCSS FT YQSIEHEVSDCPTIPTMGERLVESHLNMSWNCEQEQFSSRQHSQSQQFMED FT SPQQVSLVEQAIVNLSKILGNFIGDQKNINTQVNQMIDHVETSFNQKFDSL FT QTNLTQKIDNMQLVISKLTSMHTVQEKGKFSSQPQQNPSGVHEIGETSESS FT IEKDEVKAVITLRGGKQVDQPMPKPKENKRGEQKENVKEQEKGKEVNDDNR FT SKEDEIVKEEVKKKDMLLAPPFPMALQSKKVVNNAPEIFEVLKQVKVNIPL FT LDMIRQVPTYAKFLKDLCTIKRGMHLKKKALLTEQVSAIIQCKTPIKYKDP FT GCPTISVKIGNTFVKRVLLNLGACVNLLPYSIYKQLGLGELKSTSITLSLA FT DRSVKFPRGIIEDVLIQIDNFYYLVDFVVLDTEQGTSGLNHVPIILG" XX SQ Sequence 5037 BP; 1602 A; 765 C; 1027 G; 1643 T; 0 other; aaaatggcgc cgttgccggg gatggtgcca aggtgattga ggcattttct ttggtgagga 60 ttagcccttg tgatccacat cacaagattg gtgaagttct ctttaccgat tctccatgtt 120 ttttaattat ttttttattc cattttttat cttttatttt tctattttgt tctttttgtt 180 ttggtttgat ttttcctagc ttgttttgta ggctctccat tgcatgctag aataaaactc 240 aagggagaga ttgaaaagga cttatattgc taatcatttt tggtttgtga tccaattgtt 300 gaggaaatgg aaaatcaagg ggaaaatcaa caaactcaac aaggaccaaa catttgcaat 360 tctcacatgt ctagatcaat gagagaatat atgcatcctc aaaggatagg catgggatca 420 tgtatagttc ttcctaatga gcctattgtg ataaaaactc acttggtacc ccttctacct 480 caatttcatg gagtggagaa tgagaatcct tatactcaca taaaggattt tgaagaagtt 540 tgtcatactt ttcaagaagg gactgcatcc atagagctta tgagattgaa gctttttcca 600 ttcacatcga aggataaggc taagttgtgg ttcaactcat tgaggcccca aagcataagg 660 tcatggttgg aactacaaac aaccttcttg aagaaatttt ttcccataca tcgcacaagt 720 ggcttgaaga ggcaaattac caactttgtg acattggaca atgaaaaatt ttatacttgt 780 tgggaaagat atatggaagt aatcaatgct tgtcctcatc atggttttga cacatggatg 840 ttggtgagtt acttctatga gggcatgtcg ccaactatga agcaattgct agaaaccatg 900 tgtggaggtg actttatgag caaaagtccc gatgaagctt ttgaattttt gaattatgtg 960 gctgaaatat caaggtcatg ggatgaacca catgaaaggg atttacacaa gtctaagtct 1020 caaagcaatt caaaagggag aatgtatatg ttgaatgaag atgttgatct acaagctaaa 1080 atagtagctt tgacaaaaag gctagaggaa cttgaagcta agggatttca tgaggtgaat 1140 gcaatatatg ataatccaat ttacatggaa caatgttcta gttatcaatc tatagaacat 1200 gaagtgagtg attgtcctac aataccaacc atgggggaaa gacttgttga gagtcatctg 1260 aacatgtcat ggaattgtga acaagagcaa ttttcttcaa ggcaacactc acaaagccaa 1320 caattcatgg aagactctcc acaacaagtt tctttagttg agcaagctat tgtaaacttg 1380 agtaaaattt tgggaaattt tattggtgat caaaagaata tcaatactca agtaaaccaa 1440 atgatagatc atgtggagac atctttcaat cagaaatttg atagcttgca aaccaatctc 1500 acacaaaaga ttgataatat gcaacttgtt atttctaaac tcacaagcat gcatacggtg 1560 caagaaaaag gaaaattctc ttcacaaccc caacaaaatc caagtggagt ccatgaaatt 1620 ggagagacaa gtgaaagttc tattgagaag gatgaagtca aagcagtcat taccttaaga 1680 ggtggtaagc aagttgatca acctatgcca aaaccaaaag agaataaaag aggggaacaa 1740 aaggaaaatg tgaaagaaca agaaaaagga aaagaggtga atgatgataa tagatcaaag 1800 gaagatgaga ttgttaaaga agaggttaag aagaaagata tgctcttagc tccacctttt 1860 cccatggctc ttcaatccaa gaaagtggta aataatgctc cagaaatttt tgaagttctc 1920 aagcaagtca aagttaatat accactcctt gacatgataa gacaagttcc aacctatgcc 1980 aagtttctta aggatttgtg taccataaag agagggatgc atttgaaaaa gaaagcttta 2040 ttgactgaac aagttagtgc aatcatccaa tgcaagactc caatcaagta taaggatccg 2100 ggatgtccaa ctatctcagt gaagattggc aacacttttg tgaaaagagt acttttaaac 2160 ttgggtgcat gtgtgaatct tcttccttac tcgatatata agcaattggg gcttggagaa 2220 ctaaagtcta cttccatcac actttcattg gcggatagat cggttaagtt tccaagagga 2280 attattgaag atgtgttgat ccaaatcgat aacttctatt atctggttga ttttgtggtg 2340 cttgatacgg aacaaggaac tagtggactc aaccatgttc ctattatact tggctgacct 2400 ttccttgcca cagcaaatgc attgattaat tgtcaaagtg gagtgatgca acttaccttt 2460 ggtaacagga caattgagct gaacattttt cattcatata agaagcatgg taccaaagag 2520 gatgaggaac ttaaggaggc ttatttgatt gaattgccta tggaagagct agtgaaagaa 2580 aaggttgaag ataatttttc aaaacttggt gaagtaattt ccaatgaacg gattgaagtt 2640 tggaggatca atgaagaaat tcaacctttg aagttaatga aatggtcttt cagtttcaag 2700 aaagtgaaaa ccatgaagca tggtatgaaa aataatccaa agaccatgaa aaagaaactc 2760 aaggaatggc atgaccaact tatacaaaag aacaagttca aagaaggcta tttcaagcca 2820 catatttttc cgggaaagct taagtaccaa ggagttggtc cattcattgt ttgcaagcca 2880 tatccaaatt gagtattgat gcaaatgtta atgggcttag tcatgtcaat ggctagctag 2940 cccaatggct tctcatttct ttagtctcct ttgaattttg atttttttat tttattttga 3000 ttttttttag tttccattaa ataaattcat ctcaattctt tgatttgtgt tttgaaggac 3060 tttccggatg gatggaatgc atgaagcaaa ggaaaaatga gtttttatgg tccatcacca 3120 tttttgcaca gtcatgccaa aacagcacag tcatgccaag gggaatcatg ccaaaacaga 3180 ggagttttca tgccaaaaca ggggagtttt catacctttg gaaatgtgca aaatgagttt 3240 ctatcacaat ttgcatagtc atgcgaaatt ttcgcatgac tgtgcaaaaa ctgaaaatga 3300 tagttgcaaa aatgaaccct tttgagcatt tcgcatcagc atgcgaattt ttgcatgact 3360 atgtgaaatt ttgttgaagg ttataataag atagaacttt cttgactaat tcgcatgtac 3420 atgcaaattt ccgcatgatt gtgccaagtt ctttcaaaag aagaaagtgg ttgcaacaca 3480 cttcaccttc ttgtctagtt tgcacacttg tgtgaaattt tcaaaaactc catgataatc 3540 tttaacttat cattgaaatc atgttttctt tggacattgt catcatctat accttgattt 3600 tactccatac attgtgtttc taacatagtt tttttttggt ttttaataga tttgttttca 3660 tattttcttc tcttatgtca tttatatccg acaattctca tttgtggtct tatttttgtt 3720 ttagctattg aagctgaaat tcatgagaga ttgaggtatc ttcccttcct ttctttgtat 3780 attttcatta cacattgagg acaatgtaca agttaggttg gggggagggt taaaaatgaa 3840 gagaaggaaa tatgttatta gttttattag tttttctata attttttttt ttcataaatc 3900 acatttgtga cttatttggt gagatttttt tttagatgac tatagcattt gtgattgata 3960 aatgagcaaa cctaacttgg aaaaagttga tttagaatac tagcttattt gcttgatctt 4020 agaagattgg ttatgtgaat taaagttgat ttgactttga agtcttcact ttccaaaggg 4080 tcatttctat ttgagtcttg acacatactg tgcactttag accccggata taagatgaaa 4140 aactattcta accttaagac ttggacttaa ttgtcttgta acattgatta ctcttgaatt 4200 gagttgagac accttaaaaa gaggccaata tggccaattg aaaaaaaaaa agttgatgaa 4260 taaaaaggtt gagttatgct tgccttgaaa cctgagcaag gtccgagggg tatatggccc 4320 aaaggtcttt aaagcctggt gccctaagcc attttggttg ggagccaccg acctcaatgc 4380 ttgttacatg ggtggatagg tggagtatga gctcaattgt aggtgctaag gtattggatc 4440 ctaatttgag gagtccgggg tgaagtctga gaagttagtg gctggttaaa tagtcctata 4500 aacttggtgc cctatgcctt atggttggga gtcatcgatg aatccccgct acatggacca 4560 tatacttgga gataccttta gcattgcact cctacaataa gtcctttgaa aaaaaaaata 4620 ataaaataaa gataggtgcg ttcttgacct atgagagagt gatttttgtt gtttgagata 4680 atttgagtta ggctgggggg gaggattagt tttgagtact atattcggga gttagcttaa 4740 ttacactcaa gacttgtttg gaaagattgt ttgggaaatg aaaatggata tgtttttgat 4800 accttgactt ccatgatatt ctttctatta gagatagtaa ataagttggg attttgttga 4860 tacctatgga tagtagggtg tgcttgttta tcaaccattt atgctatgga aatttcaaag 4920 attttttttt ttcaaatgat tttcttatgt gacttatgat ttcttttgtt tggtattatt 4980 tttgttttct tttgttatac cattgctaag ggactagcat gtgttggttg gggggaa 5037 // ID Copia-93_PTr-LTR repbase; DNA; EDCOT; 453 BP. XX AC . XX DT 23-DEC-2009 (Rel. 15.02, Created) DT 23-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Copia-type LTR retrotransposon: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Copia-93_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-453 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 171-171 (2010). XX DR [1] (Consensus) XX CC >93% identity to consensus. 5-bp TSD. XX SQ Sequence 453 BP; 117 A; 104 C; 119 G; 113 T; 0 other; tgttaggata ttgccatttg tggcaatacc ccaccactaa gcaagtggtt gctccattag 60 tgccacaatt ggtggcatgg tttaaggctt tatcgacccc tccatgttga cgaagatggg 120 agctcaccat gcttgcctat aaaagaggca gttatttgag agcaaagcga agagagtgaa 180 gagagttgtg agagaacgtg agggagtaga gagaaagaga gagctgcaat ggcagcagcc 240 tgctgccatt gcagcagctg tgagagcgag tggagtgatc ctcctcctcc atgtatttta 300 tcctttctct atctctaata aaatgactct ctcccgtgga tgtaggcggt tttgccgaac 360 cacgtaaaat attgtgtcag tgtgctttac cctcctatga gcaactatca gtacaccccc 420 ggtccgcgca tgggggagcc ggaatcccca aca 453 // ID Copia-3_TC-LTR repbase; DNA; EDCOT; 386 BP. XX AC CACC01000721; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-3_TC_; KW Copia-3_TC-I; Copia-3_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-386 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01000721; Positions 1232 1617. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 386 BP; 128 A; 71 C; 71 G; 116 T; 0 other; tgagctcaca cttgaaggat caaggaattg aagaactgaa taagtggctt cactgaacag 60 agtgatcagg ttaaagaaga aagccacagg aaaaagaccc cagacgcacc gtttcaataa 120 taatggggta agaagaaaag aaggaggcct gtacgcagcg tttcaataag agtcaaaagc 180 ttcagaacta caccgtttta tgtacaattt attttcaaaa tttagttagt gtaatgatta 240 gttagttaag catttaatag cttagtcttc tttcagctta aggttaaact tctgcatata 300 aactttgtaa agattttttc cctatctggt aatgagaata tcccattctc tcatcatcct 360 ccgtcgctct ctcatctttt ctgaca 386 // ID Copia8-PTR_LTR repbase; DNA; EDCOT; 272 BP. XX AC scaffold_156; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia8-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-272 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-272 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 293-293 (2007). XX DR Genome; scaffold_156; Positions 321897 322168. XX SQ Sequence 272 BP; 94 A; 50 C; 40 G; 88 T; 0 other; tttattagga cagctcatgg aaaaccagat ccaccagact cctagccgag aatcatgtat 60 attaatgcag aaagataatg cagcaacatt acaggaaaac aattgcaaat cattctatat 120 ttaacttact gtaatttctc tgtaactcct tacatttagc atacattgtg tataaatcta 180 tgctcaacaa cagtaataaa gtgtggaaaa tttctgttga agaactctgc tatatctctc 240 tctgttataa tttgctttat ggtatcagag ca 272 // ID Copia-91_PTr-LTR repbase; DNA; EDCOT; 1697 BP. XX AC . XX DT 17-DEC-2009 (Rel. 15.02, Created) DT 17-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Copia-type LTR retrotransposon: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Copia-91_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1697 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 167-167 (2010). XX DR [1] (Consensus) XX CC ~87% identity to consensus. 5-bp TSDs. 89% similar to CC Copia-55_PTr-LTR. XX SQ Sequence 1697 BP; 585 A; 227 C; 309 G; 576 T; 0 other; tgttagtgaa tatgccttgt agtcaatcgg ttggttacac gtgacactga ttttattcat 60 gtaaaacata tttattatta ataaagactt tctttatctt taatattcat ttatatttat 120 taatgaatct aatatttgat taatgaatct agagtaaaga taaagttcat gggacaaaaa 180 tattttgcaa agaaaattat aaagttgtta taattatgag attcctattg catcaaagca 240 ttgtttctaa atgttcctgg tcaatgctct attaagactg gacattaatt agagttgttg 300 agactaatac atattatgtt ctttctttta tgaaaggaag cagttgttct cataaactga 360 ggtatgaggg atacctagaa ctaatatgta ggtgcttgtc agatgacatg tacactgaac 420 tgacccgtat gagaattcca tatggagaga tcacttgtgt ctatggaaag gctcacgtga 480 tagttgtgta agtgatcttt agacttgaga tcactaagtt atcttatata gagagtgtta 540 tgctttgatc ctgactacac gttgtcctaa tcaagggtaa caaatgggta gatattgggt 600 ataacatgaa ctatatgaag gtatttgagt aatcaagaga ggattcatca ccctaggtga 660 attagaaaaa atatttcatt tgttctcaaa tagtattgat tgtgaaatcc ttgcgcaagg 720 tggaatgaga tttgaaaaga gtttcaaatc ttattcaaag aatcaatgac tatagtgttg 780 agaacaaaca tgatttgaca aagcagacac acttcatgct ataatgtcta aatcagaaca 840 ttcttgatga agggataata attacactga gaaactggtc actaaaaggt taagtcaaac 900 cacttatgac tttcctaata tttgggggat catgacaggt tgctagacat tgtacttgat 960 cttcaaatat aaatcaatca attattgaat tgataataaa ttaaattgtt taatttattt 1020 aatcttattt tatttaggat tatgatttat atttgggcca acttattagg gaacctaatg 1080 ggtcacacac ataagaacca ttggtcagaa attaaaatgg gatgattaat caagtgtgac 1140 ttgattgtaa ataagtttta gaaattgagg actagaatgt aattaataca ggggattaca 1200 attctagacc tagaaaaaat caagtaggga cttgattgaa taaatttcta aaattatcct 1260 aaaataatat atgtgatatt attcaagggg caaattgata ttttatcatt tatagggttt 1320 ttaggttttt ctataaatag aatgttatgc cttttatttt ttatgaaaat atgagaatag 1380 tacagtacaa aaacacctaa aagaaaagag ctagcactct aaggcataac aatctctctc 1440 tcctaaaagg gtttaggaga tttctcactg gtggttcgtg tggattaccg ttagaggccg 1500 gacacttgga tgacttgtgg tttgcgacaa cccagccttg aagcaattat tcaaagccaa 1560 aaagaacatc tgatcttcag gtaatcttcg tataaaccct aaacaactct agatctgtct 1620 aacaggatcc ttgggactcc taaaaaattt taaatttatt gtttccgttg tgtgtatgtg 1680 tttcgggaaa cccaaca 1697 // ID COPIA1-I_LC repbase; DNA; EDCOT; 2511 BP. XX AC . XX DT 24-MAR-2005 (Rel. 10.02, Created) DT 29-MAR-2005 (Rel. 10.02, Last updated, Version 1) XX DE L. corniculatus copia-like LTR retrotransposon - internal DE consensus sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; 5 bp TSDs; KW COPIA1-I_LC; copia-like retrotransposon. XX OS Lotus corniculatus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RP 1-2511 RA Gentles A. and Jurka J.; RT "COPIA1_LC: L. corniculatus copia-type LTR retrotransposon."; RL Repbase Reports 5(2), 29-29 (2005). XX DR [1] (Consensus) XX SQ Sequence 2511 BP; 831 A; 444 C; 511 G; 686 T; 39 other; attggtatca gagcgcaagt tctgattacc acacttaaca gtgttcagta gatccgggcc 60 agtgtgaaaa actcatggat tccaccacta ctacaagcaa atatcaatac agtgcaagac 120 cacctatctt tgatggtcag agatttgatt tctggaaaga yagaatcaaa agcttctttc 180 ttggctttga tcctgatcty tgggattttg ttgttgatgg ctacacccct cctgttgatg 240 aacatggtgt aaagatccca agggagaaga tgagtgaaga tcaaaagaag gagttcagag 300 atcatcaccg atcaagagct attctgcaaa gtgccatttc atatgaagaa tatgagaaaa 360 ttactgatcg tgattccgcc aagggcatct ttgaatcctt gaagatgtct catgaaggaa 420 acaagaaagt gaaagarwca aaggcgttgt ctytgatcma gmagtatgaa tccttccaaa 480 tggaacctga cgaatccatt gaggatatgt tttccagatt tcagttgcty gtagctggaa 540 taagacctct caacaaaagc tacactacaa aagatcatgt cataagggtc atyagaagtc 600 ttcctgaaag ctggatgcct ttagtgactt caatagagct tacaagagat gttgagcata 660 tgagtttaga agaactcatc agcatactga artgtcatga actraagcgy gctgaacatc 720 aagatcwgar gaagaagtct atagccttga aatccaaatc tgaaaaggct aaggctctcc 780 aagctgaagc agaagaatct gaagaagcat cagaagattc tgatgaagat gagctgactc 840 tgatatccag aaagctcaac tgcatctgga agcacaggca gagcaaatac aaaggctcat 900 caaaggacaa aaagtcaaag aagcatttca aracaaagaa ragtctgatg gtgacttttg 960 atgaatcaga gtcagaggat gttgactctg atggtgaagt tcaaggactc atggctattg 1020 tcaaagacaa aggagcagag tcaaaggatg ctgttgactc tgactcagaa tcagaaggag 1080 atccagactc tgacgatgaa aatgaggtat tygmttcttt ctcaacytct gaacttaaas 1140 atgctttgtc tgawattatg gataartata actctytctt gactaagcat aaaargttga 1200 aaaagaattt ctctgctgcy tctraaactt cttctgaaca tgagaaaatc atatctgatt 1260 tgaaaaatga taaccatgct ttagttaatt ctaactctgt gcttaagaat caaattgcta 1320 agttagaaga agttattgcc tgygatgcct ctgatagtaa gmatgaatct aagtatgaaa 1380 aatcttttca aagattcctg gctaaaagcg tagayagaag cttaatggct tcaatgatct 1440 atggcgtaag cagaaatgga atayatggca ttggttattc taaaccaatt agaaatgagc 1500 cctctgtgct aaagctaaat cttgtatgat gctttgttcc ctctgtacca tattgcctga 1560 ccttacctkc tgaagttgct amaycwyctc ttaaraaagg aactttctct atgtcaaaat 1620 atcatgctma aattccttta tattatcctg ttgaaagacc caaagttgtc agaacttctg 1680 ggctaactaa caagaaagga cccagaaagt gggtacctag ggataagatt atatatgttg 1740 cagatatctt caataggtcc atcgaaactc caaccatgga acctggacag tggatgcagg 1800 caacacatga cgggagaaag gcatatgtcc caagatccaa aacttgaacc tgaaggtgaa 1860 gttaatcttg gaggcatcag tagagtaaga tttggtcaag tcaaagctag ctgaaaaagc 1920 ttgcagagat gagcatgacc gtttcagaaa gaaacaaaga ctcagaactt gwcaaaccag 1980 aagcaacaac atcagaagat gctactacaa cttctgactt gcgtcatcag aagaagagta 2040 ggttcatagc ttctcattct gaagtatctg aagatgaaat tttgtccaga atggagatgt 2100 caccagaacc acacttctgc tctcatmaga agatatacta atcagcagcc aagtatccct 2160 tggtattcct tctgaggggg agtatttcgt cttatgctct tactattttt tttccacctt 2220 cattcttttt gcttatgaca aaaaggggga gaacttatag tatcttgaca actcctatat 2280 tatttagctc agaatctaga tattactaac gttgatatta agtattagat tcagggggag 2340 cttagctcag aatcaagcac gagtcttgga ttcagaagga gcaagataaa ctatacacat 2400 caggataagt tttaactctg ataccttata ctctgagtgt attcagttta tttgtttaga 2460 gttgttcatc aaaatacatg gttttgtcat catcaaaaag ggggagattg t 2511 // ID CMREP repbase; DNA; EDCOT; 393 BP. XX AC X13059; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 11-NOV-1996 (Rel. 1.1, Last updated, Version 1) XX DE Curcurbita maxima repetitive sequence. XX KW CMREP; Repetitive sequence. XX OS Cucurbita maxima OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Cucurbitales; Cucurbitaceae; Cucurbiteae; OC Cucurbita. XX RN [1] RP 1-393 RA Siegel A.; RT "CMREP."; RL Direct Submission to Genbank (26-SEP-1988)Siegel A., Dept of RL Biological Sciences, Wayne State University, Detroit, MI 48202, RL USA.. XX RN [2] RP 1-393 RA Kelly J.R. and Siegel A.; RT "Direct submission."; RL Unpublished. XX DR GenBank; X13059; Positions 1610 2002. XX SQ Sequence 393 BP; 87 A; 108 C; 119 G; 79 T; 0 other; ggtcggttga aaagtcatga aacttgattt atagacccat gagaatgtcc cattcacgaa 60 tcaatcgagt tcccggaaaa aaacattgta aaactcgaga tattcgaccg tatgacgcct 120 cggaaaatcg tgtctgggcc tggcagacca aaaatgcctc aaaatgtact atataggggg 180 gtgactagtc tgcatgggct ggccacgggg gctcccccta tatcctccgc cacccccacg 240 ccccaagcac tatgcgccgc acatgggcat atgcttgggt cgtcgaggtg gtggtcgagg 300 tcgagggcgg ttgacggcgg tggtgcggtg gcggaacgcg cacggtgggg cagtgtccga 360 acgttcccgc gctgtggcca gccccgccct gcc 393 // ID Copia11-PTR_I repbase; DNA; EDCOT; 4182 BP. XX AC scaffold_1749; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia11-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4182 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4182 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 194-194 (2007). XX DR Genome; scaffold_1749; Positions 4874 693. XX CC Positions [1533-2066] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 528..4166 FT /product="Copia11-PTR_I_1p" FT /translation="MDDDDLIICILRGLGSEFDPIVAALNARDMFPPLEGV FT IGKLRDFEIRLQGTRTSQSSVAFYTNKNRFHARSQGSHNARGRSGGYQKMH FT FQQRSKDVRSSRSIDNSSGAKLSSFTRGSRNSSRGRGGITCFRCGGPNHKA FT DGCFASDEEAEQYKAFAAIHIGDTTEDTWYPDTGANQHMTPNSNEVQGIHP FT YSGTDTVMVGNGNGLSITGIGQTTLPTTTLQLHNVLVVPDIKGKLLSVSQF FT TRDNNCYFLFYPWGFLLKDMKTNQVILKGPMTNGLYPINLQQLSKPSLSFL FT ANKVPGSLWHARLGHPHSQILSRLCLPSLNKMTAFCESCMLGKSSKLPFHS FT RQTYANSFLHTLHTDVWGPASVSSYDGFRFYLLIVDEYSRYIWLFPMARKS FT DVATIFPAFLQQMAKQFPNSVKIIQSDGGGEFVNTVLQTHFAANGIIHRLS FT CPGTPEQNGLAERRHRHIVETSLTLLAHASVPVKYWTAAFNTAVFLINRLP FT SSVLDHMSPHELAFGSSPNYDFLRVFGCSCYPLLSPFGRTKLEYKSICCVF FT LGYSANHKGYCCLEPHSGRLYISRHVRFNEQHFPFKNVTASHSSRSQLFQL FT QALPTSLQNTALQHSPTSSQSAGMAAVEVVPTQLMEAIHSSVHLSPTPPPS FT ALHSSSPASAPPSIPQRTHQMVTRTQTGNLKPKVFLSSRYHIPVCFLADLA FT AQPPEPTSYRQALQNPQWKQAMQAEMDALHANNTWTLVPRKPDMNVVSSKW FT VFKVKTKSNGTLDRYKARLVARGFTQLPGLDYDETFSPVVKASTIRLILTI FT GLSQGWTIRQLDVNNAFLHGDLQERVYLAQPPGHEDPALPQHVCLLHKALY FT GLKQAPRAWYMKFSNYIQSMGFLQCPYDQSLFYQRQGSDILLLLIYVDDIL FT ITGSSPSQISAFISHLSSVFSMKDLGDIHYFLGLQIARDATTITVTQTRYL FT VSLLQKFSLAGAKPVATPLASGTLLTATEGALLSDPTFYRQLVGSLQYLTL FT TRPDISYSVHRVCQYMHAPREPHLIAVKRIFRYLKGTLTLGLHLVHTPLIA FT LHGFCDADWAGCHDDRRSTSGFAIYMGNNLLSWGAKKQATVSRSTAEAEYR FT ALASTTAELMWFMNLLQSIGYCLPPPKLYCDNISAVTMAKNPVFHHRTKHI FT EIDVHFVRERVASGDLLLEHVAGPDQIADIFTKSLCSAKFVPNRDKLFIGS FT LPP" XX SQ Sequence 4182 BP; 1060 A; 1003 C; 813 G; 1306 T; 0 other; tggtatcaga gcttgcaatg gaatctctca ccacctcaat cttgtctcca gccgctgctc 60 tttctctaga ttttacacct tccaaaactc gcttacctga tatttccact aagctagcct 120 caaataatta tcttctatgg aaagcgcaag ttgttccaat cttaagagga catggtcttc 180 ttggatatgt gacagatgga gttccttgtc cagaattaac cattgttgat gctgatggtg 240 catcgcaacc caatccagct acagcaactt ggctgcgtat tgatcaattg gtccttggat 300 ggatcaacag ttctctgtca gacggtcctc tctcccaagt catcaacagt gagtctagtc 360 atgatgcttg gactgtattg gagactcttt atggaagtca tacccgagac cgtattcagt 420 aaataaaggg agagttgcaa actctcacca aaggcatctt ttctttagaa gattatctgc 480 acagagccaa gtcgttggcc ttgtctcttc gtggtgcagg caaaccaatg gatgatgatg 540 accttattat ttgtatcctg cgtgggctag gatctgagtt tgatcctatt gttgcagcac 600 tcaatgctcg tgacatgttt cctcctttag aaggggttat tggcaagctt cgtgactttg 660 aaatcagact tcaaggtaca agaacgtctc aatccagtgt tgctttctat actaataaaa 720 atcgtttcca tgcaagatct caaggtagtc ataatgctcg tggtcgttct ggcggttatc 780 aaaagatgca tttccagcaa cgcagcaaag atgtgcgttc ctctcgttct attgacaatt 840 cttctggagc caagttgtcc tcctttaccc gtggaagccg caattctagt cgtggacgag 900 gtggcattac atgttttcga tgtggcggtc caaaccacaa agcagatggt tgtttcgcct 960 cagatgaaga agcagaacaa tacaaggctt ttgctgccat tcacattgga gacactacag 1020 aggacacctg gtatcctgac actggtgcaa accagcacat gacccctaat tccaatgagg 1080 tgcaaggtat tcatccctat tctggtactg atactgttat ggttggcaat ggtaatggtt 1140 tatctataac tggtattgga caaactactt tgccgactac tactctgcag ctccataatg 1200 ttctagttgt tcctgatatc aaaggaaaat tattgtctgt gtctcagttt acaagagata 1260 ataactgtta ttttctcttt tatccatggg gatttcttct caaggacatg aagacaaatc 1320 aagtgattct taaaggtccc atgacgaatg gtctatatcc tatcaatctg cagcaactct 1380 caaagccttc actcagtttt ctagcaaata aagttccagg cagtctgtgg cacgctcgcc 1440 ttggtcaccc tcactctcaa attcttagca gattatgttt accatcttta aataaaatga 1500 cagcgttttg tgaaagttgt atgctgggaa agtcttcaaa gttgcctttt cattctcgtc 1560 aaacatatgc aaattctttt ctgcatacat tacatactga tgtttggggg cctgcatcag 1620 tctcctctta tgatggtttt cgattttatt tactcattgt tgatgaatat tcacgttata 1680 tatggctttt ccctatggct cgaaaatctg atgttgccac gattttccct gcattccttc 1740 aacaaatggc aaaacaattc cctaactctg tgaaaattat tcagagtgat ggtggtggtg 1800 aatttgttaa cacagtattg cagactcatt ttgcagctaa tggtataatt catagacttt 1860 catgtccagg gacacctgaa caaaatggtt tggctgaacg aagacatcga catattgtcg 1920 agacaagttt aactctacta gcacatgctt ctgtcccagt caaatactgg acagcagcct 1980 tcaacactgc tgtcttccta atcaatcgtc tgccatcttc agttcttgat cacatgtctc 2040 ctcatgagct tgcttttggt tcttcaccca actatgactt tctacgggtc tttggttgct 2100 cctgctatcc attgctttca ccttttggtc ggaccaaact ggaatacaaa tcaatatgct 2160 gtgtattcct tggatattca gccaaccata agggatattg ttgccttgaa ccacattcag 2220 gccgcctcta tattagcaga catgtcagat ttaatgagca acattttcca ttcaagaatg 2280 ttacagcctc tcattcctct cgtagtcaac tttttcaact acaagcactt cccacatctc 2340 ttcagaatac tgctctacaa cactcaccta ctagttccca gtctgctgga atggctgctg 2400 tagaggttgt gccaacacaa ctgatggaag ccatccactc ttcagtacat ctgtctccca 2460 ctccaccgcc atcagcattg cactcttcat cacctgcgtc tgctcctccc agtattccac 2520 aacgtactca tcaaatggtc acccgcactc aaacagggaa tcttaaacca aaagtcttcc 2580 tttcttctag atatcatata cctgtttgtt ttcttgctga ccttgcagct cagccaccag 2640 agccaacttc ataccgacag gcacttcaaa atcctcaatg gaagcaggct atgcaagctg 2700 aaatggatgc tcttcatgcc aataacacat ggactttggt tcctcgaaaa ccagatatga 2760 atgtcgtaag cagtaagtgg gtctttaaag ttaaaacaaa gtccaatggc acacttgaca 2820 ggtataaggc taggcttgtg gccagaggct ttacacaact tccagggctg gactatgatg 2880 aaacctttag ccccgttgtc aaggcaagta ctattcggct cattctcaca atcggtttat 2940 ctcagggctg gaccattaga cagttagatg tcaacaatgc ctttcttcat ggtgatttac 3000 aagaacgtgt gtacttggct caaccgcctg gtcatgagga tcctgctctt ccacagcatg 3060 tctgtcttct ccataaagca ttgtatggct taaaacaagc accgcgtgct tggtatatga 3120 aattcagcaa ctacatccaa tcgatgggtt ttctccaatg tccctatgat cagtccttgt 3180 tttatcaacg gcagggttca gatatccttc ttttattaat ttatgttgat gatatactta 3240 ttactgggag ctctccttca caaatctctg catttatatc tcatctctcc tctgtgttta 3300 gcatgaagga tctcggtgat attcattact ttcttggtct tcaaattgct agggatgcca 3360 ccactatcac tgtaactcag acacggtacc tagtgtccct tctgcagaaa ttcagtctcg 3420 ctggtgctaa accagttgcc actccccttg cctcaggaac cttattgaca gccactgagg 3480 gtgccctgtt atctgatcca actttttatc gccagcttgt tggatccttg caatatctta 3540 ctctcacaag acctgacatc tcctattctg ttcatcgtgt ttgtcaatac atgcatgcac 3600 ctagggagcc tcatcttatt gctgtgaaga gaatatttcg atatttgaaa ggcaccctca 3660 ctcttggtct tcaccttgtt cacactcctt taattgctct tcatggcttc tgtgatgcag 3720 actgggccgg ctgccatgat gatcggcggt ccacatctgg ttttgctata tatatgggca 3780 acaatctgtt atcctggggt gccaagaagc aggccacggt atctcgttcc acggcagagg 3840 cagaatatcg tgccttagca tccactacag ccgaactcat gtggtttatg aatttgctac 3900 agagtattgg ctattgtctt ccacctccaa agttgtactg tgacaatatc agtgctgtga 3960 ctatggccaa gaatccagtt tttcatcatc ggacaaagca tattgaaatt gatgtccatt 4020 tcgtccgaga acgggttgct agtggagacc ttttgttaga acatgttgct ggtcctgatc 4080 aaattgcaga tatcttcact aaatcgctct gctctgccaa gtttgttccc aatcgtgaca 4140 agctcttcat tggttcactc ccaccttgag cttgaggggg ga 4182 // ID Gypsy-47_Mad-LTR repbase; DNA; EDCOT; 510 BP. XX AC . XX DT 27-OCT-2010 (Rel. 15.11, Created) DT 27-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-47_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-510 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1992-1992 (2010). XX DR [2] (Consensus) XX SQ Sequence 510 BP; 153 A; 104 C; 152 G; 101 T; 0 other; tgtgggagga taaaatccgg tttcgactca tgggccaatc caagtcaccc aaggatggtg 60 ttatgcaagg taaaccgtaa ggaaagccca cgaggaacaa gcaggcgcac gtgtccaggt 120 aaccgcctcc actacggagg atcaccgagg aagtgggaaa ggaagatatg acgtggtgct 180 tgttcccgaa gcatgcagtc atattacgga ggaccactaa ggaagtggga aggagagaga 240 gatcgtggta cttgttctcc aggcatgcaa tcctataaat atggagtgga gccaaagaac 300 aagggtacgt gaggagaacc cgagagaatc cagagaatag aaaccaatcg actgacttga 360 gcgtcggagt atcttttgca ggtacccgcc cgggcaagct gcggaggaag attattttgg 420 gacatctcga agaaggattc ggcgaacgtg aggattgcgg tcaacaaatc tgtggaggta 480 tttcttcttg taggaaatct cactccaaca 510 // ID MUDSOLD1 repbase; DNA; EDCOT; 630 BP. XX AC . XX DT 25-OCT-2006 (Rel. 11.1, Created) DT 26-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Solanum demissum. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW MUDSOLD1. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-630 RA Shankar R. and Jurka J.; RT "MUDSOLD1: A putative non-autonomous DNA transposon from Solanum RT demissum."; RL Repbase Reports 6(10), 498-498 (2006). XX DR [1] (Consensus) XX CC This is a putative non-autonomous DNA transposon sequence from CC Solanum demissum, two regions of which have characteristic of CC MUTSOLD1. Orientations of these two regions are different. It is CC flanked by 14 bp long terminal inverted repeats and 5 bp long TSD CC (GGAAA). XX SQ Sequence 630 BP; 218 A; 109 C; 97 G; 200 T; 6 other; tagagaraag gcccaaaata gtcccttatc tttgggttaa gactcaaagt catccttgag 60 ttttcacatg gagcaytaat agtccctcat gtttgcaata ttggtgcact tttggtcctc 120 ccccaaactt ttgcctattt tttaacattg attttgttca taaaawtgtc ccatcgtcaa 180 tttatatatt tagtagaaat aataactcta tgtgagagaa ggtgagaaga agaacacctt 240 gttctgttcg gtataaatat tactgcagct aaactaagaa catttaaaca tatgacattg 300 caaggaaaga aaaaattgta ctattgcatg aaatcgtcgt gatgaacctc tcgattttac 360 ctgcaatact atttctacta aacaaaacaa ggtgtttttc ttctcacaat ctctcacatt 420 atttctacta aatatataaa atgacgatta aacattccat acataaatta tgaataaaat 480 caatgttaaa aaataggcaa aaktttgrag gaggaccaaa agtgcactaa tattgcaaac 540 atgaggaact attartgctc catgtgaaaa ctcaaggatg actttgagtc ttaacccaaa 600 gatgagggac tattttgggc cttttctcta 630 // ID SHACOP19_I_MT repbase; DNA; EDCOT; 4186 BP. XX AC AC151523; XX DT 26-JAN-2007 (Rel. 12.01, Created) DT 26-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP19_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; terminal; repeat; ORF; SHACOP19_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4186 RA Shankar R. and Jurka J.; RT "SHACOP19_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 65-65 (2007). XX DR EMBL/GenBank/DDBJ; AC151523; Positions 46298 50483. XX CC The internal region contains intact domains for gag-pol CC polyprotein with arrangement of domains like in Copia-type LTR CC retroposons. The LTRs of this element are identical to RAM14_MT. XX FH Key Location/Qualifiers FT CDS join(68..892,896..2026) FT /product="SHACOP19_I_MT_1p" FT /translation="MAATTNPTKTSLLIHASITLKLSRASHRAWKRQATSL FT LSGIQVIGHIDGTTPSQSPTIVTAGVSTPNPQYTNWFTIDQLIINLLISSM FT TEADSISFASYDTAKTLWDAIEAQYANTSRSHVMSIKNQIQHCTKGEKSIT FT DYLFSVKSLADELTIIDRKISDDDLTLYVLNGLGSEYRDIAASIRTRERPF FT TFEELHSHLLAHDEYIRRESQVEIQVPTANFAQRNSKNDGILPSPAYGRGN FT SSLHTRGSNHGRGYGQSRKSRGFNPRGNRPPPRCYCSAIGHIARYCPEISK FT FSNPPTAQYASASSTTPNWVFDTGASHHVANSLNNMHIHSEYDGPEEVQIG FT DGTGLKISHVGSTTLPTQNTIFNLKNILCVPHAKHNLISISKFCKSNNVYV FT EFHSSFFLCVKDQVTGAVLMRGPSNGDLYIYNPNFSSPTALSTVTSTVSLW FT HARFGHPSPRVLTQMLSNCGLSRNFNKKSLHCNSCSINKSHKLPFSISSIQ FT TFSPFELIFSDVWGPSPITSINGYRYYLVFVDHFTRYTWIYPLKNKTDVAI FT IFPQFHSKIENFFSHKVKSIYTDGGTEYFKLKPYFNTHGISHYISPPYTPE FT HIGIAERKHRHIVETALTLLSHSSVPQTFWCYAFQMAVHLINHAHSSMSQQ FT MSS" FT CDS join(1326..1610,1614..1703,1707..1898,1905..1982, FT 1986..3125) FT /product="SHACOP19_I_MT_2p" FT /translation="MVIYTSTTQISHHLLPYQLSLQLYPSGMLDLVIHPLE FT SLHKCCQIVACLGILTRNLCIVIPALLIKVINFLFLYLQYKLSLHLNSFSL FT MFGDHPLRPLMVTGIILSLLTISLATRGFIHLKTKLMLSYFLNFILKLKTF FT SPTKSNLFTLMVELNTLNSSHISIHMEYPITLAHLILLNTLALLNANTAIK FT LLSHFSLTLLYLKHSGVMLFKWQFTLIMPTPQCHNKCPHEILFGSKPNYLN FT LRVFGSLCYPWLRPYSKHKLSNRSMPCVFLGPSNQHHAYQCYHIPTKKLYL FT SRHVVFHESISPFTSTVCDSTNPSPPLSTNNQNISMSRHPLIFSQLHPTIP FT PHNPPPTIPQNSTTSIITPPVTSNLPHTPTSSTSSTNQSSPRTSIDSPLQM FT DSPASVQPVPLRPVTRAMNNIHKPNPKYLLTTKHPLPITIEPTCLTQEIKT FT SEWRDAMSNEFNALIQQQTWDLVPRPSNKNLIGCKWVYRVKRKANGDIERY FT KARLVAKGFHQRPGLDYTQTFSPVVKPITVRLVVSLALQHNWPLRQLDVNN FT AFLHGSLTEEVYMQQPPVLSIQISLTMFVALESQYTASKKHHGHGIKL" XX SQ Sequence 4186 BP; 1234 A; 1091 C; 619 G; 1242 T; 0 other; attctctata atggtatcag acttagcctt agcctaacag catctcacga tccatacctc 60 cttcactatg gcagccacca caaacccaac aaaaacaagt cttcttattc atgcttccat 120 cactcttaag ctttctcgag ccagtcatcg tgcctggaaa cgtcaggcta cctctcttct 180 ctctggtatc caagtcattg gccatattga tggaaccaca ccttctcaaa gtcccaccat 240 tgttactgct ggtgtctcaa ccccaaatcc acaatacaca aattggttca ctattgatca 300 actcatcatc aatcttctta tctcctctat gacagaagca gacagtatat catttgcctc 360 ctatgacact gctaaaacct tgtgggatgc cattgaagcc caatatgcaa acacctctcg 420 atctcatgta atgtcaatca aaaatcaaat tcagcattgt accaaaggtg aaaaatccat 480 cactgattat ctcttttctg tcaaaagtct cgctgatgag ttaactatca ttgacagaaa 540 aatttctgat gatgatctca ccctctatgt gctcaatggt cttggttcgg aatatcgtga 600 tattgctgcc tcaatccgga ctcgtgagcg tcccttcacc tttgaagagc ttcatagtca 660 cctactagct catgatgaat atattcgtcg tgaatctcaa gtggaaatcc aggttccaac 720 agcaaacttt gctcaaagaa actcaaagaa tgatggtata ttaccatcac cagcatatgg 780 tcgtggtaac tcctccctcc acacaagagg ttccaatcat ggtcgtggtt atggccagtc 840 acgcaagtct cgaggcttca accctcgtgg aaatagacca cctccacgtt gctaatattg 900 ttcagctata ggacacattg cacgttactg cccagaaatt tctaaattca gcaatcctcc 960 aacagctcag tatgcatctg cttcctccac cactcctaac tgggtgtttg acactggagc 1020 tagccatcat gttgccaaca gcctgaacaa tatgcacatc cattcagaat atgatggtcc 1080 cgaggaagtt caaattggtg atggtacagg tttaaaaatt tctcatgttg gctctaccac 1140 actccccaca caaaatacta ttttcaatct caaaaatatt ctctgtgttc ctcatgcaaa 1200 acacaatcta atttctatct ctaagttttg caaatctaac aatgtttatg ttgaatttca 1260 ttcttctttt tttttgtgtg tgaaggatca ggtaacgggg gcggtattga tgcgaggtcc 1320 aagtaatggt gatctataca tctacaaccc aaatttctca tcacctactg ccttatcaac 1380 tgtcacttca actgtatccc tctggcatgc tagatttggt catccatccc ctagagtcct 1440 tacacaaatg ttgtcaaatt gtggcctgtc taggaatttt aacaagaaat ctttgcattg 1500 taattcctgc tctattaata aaagtcataa acttcctttt tctatatctt caatacaaac 1560 tttctctcca tttgaactca ttttctctga tgtttgggga ccatccccta taacgtccat 1620 taatggttac aggtattatc ttgtctttgt tgaccatttc actcgctaca cgtggattta 1680 tccacttaaa aacaaaactg atgtagctat catatttcct caatttcatt ctaaaattga 1740 aaactttttc tcccacaaag tcaaatctat ttacactgat ggtggaactg aatactttaa 1800 actcaagcca tatttcaata cacatggaat atcccattac attagcccac cttatactcc 1860 tgaacacatt ggcattgctg aacgcaaaca ccgccatata gtagaaactg ctctcacact 1920 tctctctcac tcttctgtac ctcaaacatt ctggtgttat gcttttcaaa tggcagttca 1980 cctaattaat catgcccact cctcaatgtc acaacaaatg tcctcatgaa atcctttttg 2040 gttccaaacc caattatctc aatcttcgtg tttttgggag tctttgttat ccttggttac 2100 gtccttactc taaacataag ctatcgaata gaagtatgcc ttgtgtattt ctaggtcctt 2160 ctaatcagca tcatgcctat caatgttatc acattcccac caaaaaactt tacctttcaa 2220 gacatgttgt cttccacgag tcaatttccc cgttcacctc aaccgtatgt gactctacaa 2280 atccatctcc accattatcc actaacaatc aaaacatctc catgtctcgc catccactaa 2340 tattttcaca acttcacccc actatccctc ctcataatcc tccaccaacc attcctcaaa 2400 attctaccac atccataatc actccccctg taacttcaaa tcttccacat acacctacct 2460 catctacatc ctcgacaaat caatcttccc cccgaacctc catagactca ccattacaga 2520 tggactctcc tgcatcagta caacctgtgc ctcttcgccc agtgacaaga gcaatgaaca 2580 acattcataa accgaatcct aagtatcttc tcaccaccaa gcatcctctt cctatcacaa 2640 ttgagccaac atgtctgacc caggaaatta aaacaagtga atggagagat gctatgagca 2700 atgagtttaa tgctttaatc caacaacaaa catgggatct ggtacctcga ccatctaata 2760 aaaatctcat tgggtgcaaa tgggtttatc gagtcaaaag gaaagcaaat ggtgatattg 2820 agagatacaa agccagatta gtggcgaaag gcttccacca acgacctgga cttgactaca 2880 cacaaacatt cagcccagtg gttaagccca tcacagtacg gttggtcgtt tccttagccc 2940 tacaacacaa ttggccatta cgtcaactag acgtaaacaa tgctttctta catggttctc 3000 taactgaaga agtttacatg caacaacctc cagttttatc catccagata agcctcacca 3060 tgtttgttgc cttagaaagt caatatacgg cctcaaagaa gcaccacggg catggtatca 3120 aactctaagt aagtttcttt gtgactatgg gtttgctaat tccaaatctg attcatctct 3180 gtttgtcttt cgtaaacaag gcatggtact atacacatta gtgtacgtag atgatataat 3240 tatcacaggg aattccactg ctaaagtgaa tgagtgtatc agcaaacttg cttcttcctt 3300 ctccatcaaa gatctaggtt cattgcacta cttccttggt gttgaagtca ttccaacctc 3360 cacatgccta ttcctttccc aacataagta tatagctgat cttcttgaaa ggacaaaaat 3420 gacagatgcc aaggctgtac tcactccact ctccacttcc attgccctaa caaaagatga 3480 tagttcgcca aatactgatg ctacctttta tcgtagtacc ataggcagcc tccaatattt 3540 gtccatgaca cggcctgaca ttgctttccc tgtcaataaa cttgctcagt ttatgcaaaa 3600 accaacaact actcatctta caacactaaa gagaattctt cgctatctca aaggaactat 3660 ttttcatggt ctccttcttc agaaaccagc cacgtcttca ctcatagcat acagtgatgc 3720 tgattgggcc ggaaataagg atgattacac ctcaacatct gctcatcttg tctactttgg 3780 atctaatctc atctcctgga aatcatccaa acaaagagca gtagcaagat cctctacaga 3840 agcagagtat agagcattag ccaacactgc agctgaaata tcttggataa actcccttct 3900 caatgaatta ggagtatcat cttcctcaac accaattatc ctttgtgaca atctcagtgc 3960 cacatatctt actcaaaatc cggtatatca cactcgcatg aaacacatct ccattgacat 4020 tcattttgtc cgtgatctag tccaacaagg gaaactcaaa attcagcatg tcagcactac 4080 tgatcaatta gcagattgtc tcacaaaacc tctctcaaaa ggtcgacatc attatctacg 4140 aaacaagatt ggagtttctg acggcactcc aaccttgcgg ggggcg 4186 // ID MtPH-A6-4-Ia repbase; DNA; EDCOT; 4699 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 12-MAY-2011 (Rel. 16.05, Last updated, Version 2) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-A6-4-Ia. XX NM MtPH-A6-4-Ia. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4699 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC An autonomous element representing subfamily A6-4 of CC PIF/Harbinger transposons from Medicago truncatula, carrying 17 CC bp-long TIRs. Most elements belonging to this subfamily carry a CC 60 bp imperfect tandem repeat containing 2 to 35 core motifs. XX FH Key Location/Qualifiers FT CDS join(699..1437,1521..1996) FT /product="MtPH-A6-4-Ia_1p" FT /note="DDE-transposase." FT /translation="MARQTIMELIRWRARLRMTLVHVICLVVCYYRIKIHS FT QSRIVDRSLTLEKDRVRNKIMNIVVTSEGRKIIRMSPKAFLDLCSILQQEG FT GLLPTQRVTVEEQVAKTLYLLTHNVRNREIQFWFRRSGETTSRHFHRVLRS FT IIEIGRTYLKQPDGSRIPIEILGNHRFYPYFKDCVGAIDCTHVRVKVPLAE FT ASRYRGRKSFPTQNVLVACSFDLKFTYVLPGWEGTASDSRILKHALQRRNG FT LKIPRGKFYILDAGFMLRKGLITPFRSTRYHLKEFSARNPPRTAQELFNLR FT HSSLRNVVERAFGIVKKRFPIISSGAEATYGINTQNYIILACCILHNFLMG FT VDPDEDLIAEVDEEIANQSASQTGHGHIEVDEDEENSDLGQNFRNSILGAM FT WTNYLSYHSR*" XX SQ Sequence 4699 BP; 1444 A; 678 C; 906 G; 1671 T; 0 other; ggctttgttt gggagttggg ttttggaggg gaagggaggg aaaggaaagg cttgtgagtg 60 ctaaaccctt gtttgtgagt tttaaaaaaa taagggaaag gttttggggg gttttgaagg 120 ggttaattta tccaatttta gagttccccc aatttggggg gttttggagg gttaaagata 180 cgaattgacc atattaccct tacaataata caaaattcca attttagccc taacctaatt 240 tcatctcatt ctaacgattc atttcactgt aactgtgcac gctctctctt ctcccgacgg 300 cgacgtgaat ggcgatctca acctgaacgg cggcgaacgg cggcgagcgg cggagaagga 360 agttgaacaa cacagtttcc ttcatctctc tcgatcctct ttcttctggt atcaatctca 420 aactatcttc cattcttttc caatttcttt tccttttgct attcattcat gaattgattt 480 atgttttgtt gtttgattca caatttgatt tatgtttttg tgtttgattc acaatttgat 540 ttctgttttg ctatttgatt ttttagagtg aatcacatct actcaatgga tactgtataa 600 tcactattat tatgatttca ctattattat aaataaatgt tgcttgtttc acaaaaatgt 660 attatttttt gttggattca gtttaaatgg atcatgaaat ggctcgtcaa acaattatgg 720 aattgattag atggagagca agacttcgaa tgacacttgt tcatgtcata tgtcttgtag 780 tttgttacta taggattaaa atccattctc aaagtaggat agttgatcgt agtttgactc 840 ttgagaagga tagagtacgc aataagataa tgaatatagt tgttactagt gaaggtcgga 900 agataataag aatgagtcct aaggcgtttt tggacttatg ctctatatta caacaagagg 960 gtggtcttct accaacacaa agggtaaccg tagaggaaca agttgctaaa actctttacc 1020 ttctaacaca caatgttaga aatagagaga ttcaattctg gttccgacgc tctggcgaaa 1080 ctactagtcg tcattttcat cgggtgctcc gatcaataat tgagataggg cgtacctatc 1140 tcaaacaacc agatggatca cgcattccga tagaaattct tggaaatcat cgattttacc 1200 cctactttaa agactgcgtt ggagcaattg attgtacaca tgttcgtgta aaagtaccat 1260 tggctgaagc ttcaaggtat cgtggtagga aaagttttcc tacacaaaat gtgttggtcg 1320 catgttcttt tgatcttaag ttcacttatg ttttgcctgg atgggagggt actgcttctg 1380 attctaggat attaaaacat gcactacaga gaagaaatgg tctcaaaata cctagaggta 1440 gttaaaactt attgttatca ttttcccttt ttttccgctt ctttttctta tatatgttgg 1500 taataattat ttgcttttag gtaagtttta tattcttgat gctggattca tgttgagaaa 1560 ggggctaatt acaccgttta gatcaacacg ttatcatttg aaagaattct cagccagaaa 1620 tccccctaga acagctcaag agttattcaa ccttcgacat tcatcgttgc gtaatgttgt 1680 tgaaagggct tttggaattg tgaagaaaag atttcctatc atttcaagtg gcgctgaagc 1740 aacttatgga atcaatactc aaaattatat tatccttgca tgttgcattt tgcataattt 1800 cttgatgggg gtagatcctg atgaagactt gattgctgag gtagacgaag aaatcgccaa 1860 tcaaagtgca tctcaaactg gtcatggcca tatagaagta gatgaggatg aagaaaattc 1920 agatttaggt caaaatttta gaaattctat acttggtgcc atgtggacca attacctatc 1980 atatcatagt agatgataat gatttactta gctattattc agtgtgtatg tttccaaata 2040 gctattgcca aaaatattgg aaacttgttt gttcaaaata ttctataatt tgtagcttta 2100 agtggaagaa tgtgtgttgt tattgtttct aaatattgga aacttgtttg agtaacttgg 2160 atattgatgt tcctgatata ttgaataaac atactatttg ttgcaactgt tattccaaga 2220 gtcaccaaag aaaggtatac atgagttcat ctcaaattta tctataaatt tatatgatga 2280 ttttataata tgatatcttt tcttctaata taacagaatc atgtctacct ctaaaagaga 2340 gacatggaca acagagatga acaatgctct tattgatgcg tttgttcatc aagtaagtgc 2400 gggaaacaaa caaggtggga cctttacatc aatagcatac accaatataa caaaggagat 2460 gtccgaaaag tttcaaagac cttttgacaa ggaaaaggtg aaagatagat ggaaattggt 2520 gaaaagaaat tttactaaat gtcatgacat tttcaatggc atgagcggtt ttgcttggaa 2580 atcagacaca catatgtggg atgctttacc tgaagtttgg aaaacattaa tcgaggtaca 2640 tacttataac ttacattaat tgagttgttg ggtttgcttg cttatatata tggcctgaac 2700 ctatgtcagc atgtgcactt atttgaattt tttttgatag gcaaaacctg aagctgcaca 2760 atggatgaac aaaccttttg ccaattatga caaattggtt attgcttgtg gagatgaaag 2820 ggccactgga ggaaaggtta tgaatgatga agatattcgc caaaatcatc ccctcaatcg 2880 tgagtcagaa tccattggta ctagtgacca ggtgacacta gagagtttgc aagagggcgg 2940 caatgagcag gatgtcactt ctcctgaggt ccaaattccc ccagaaccta gagccaaaag 3000 atctagaaag tcccgagatg aagatgaagt tgaagggata aaagctgccc ttttgaacgt 3060 tgctgatgct tttagagaga gtactgcatc tcatgataag tattttaaag acagcattgc 3120 agcttatgag aaagctaatt taaaacttcc aatttcagaa gaagaagttt ttaaacttct 3180 tgaggaattg caagtggata gtcatatgat cattcgggca tattcttatc ttctagagtt 3240 tcctgagaag gttagagctt tacttggact tccaaaacac ttgcggaaga gttttctatt 3300 agaatcgatg gttggtcaag gttactcgtc aaggtaattt acccattttc tcatcaagtc 3360 aatgttatat cttggcattg gtgtatgagt aggttgaaga ttgcagcttg tttattttat 3420 tgatagtgtt tgtctatcac atattagaac ccacctatca tcatgctact gatggttgtt 3480 tcatctctac atattgtttt ggtctctaat gaggatcttg aagtcctaga ttatgacatt 3540 agtatagaat tttgtaatct tgtattggga tttagttact agcatatttg acacatttgt 3600 catttttatg tcatgtattg atataacagg atatgttgca ttttcatttt taaatgtctt 3660 atttacaagt aagatatttg tcaaaaactt tctctaattt atttgaaaat aaataagttg 3720 ttttgaataa gcggtttttg aaaaagatgt cgtaataatc tgttttgaat aagctgtttt 3780 tttaaaagag gttgtaataa gttgttttgc ataaataagc tgttttgaat aagctgtttt 3840 gaataagctg ttttttttaa aagaggttgt aataagctgt tttgcataaa taagctgttt 3900 ttttaaaaga ggttgtaata agctgttttg cataaataag ctgttttgaa taagctgttt 3960 tttgaaaaga tgccgtaata atctgttttg cataaataag ttgttttgaa taagctattt 4020 ttttaaaaaa agaggttgta ataagatgtt ttgcataaat aagctgtttt tgaaaatgag 4080 gtcgtaataa gctattttgc agaaataagc tgtttataat aagttgtttt tgaaaatgat 4140 gtcgtaataa gctgttttgt ataaataagt tgttttgaat aagcggtttt tgaataagcg 4200 gtttttgaaa aagatgtcgt aataagttgt tttgcataaa gaagctgttt ttgaaaaaag 4260 agatcgtaat aagttgtttt gaataagttg tttttttttt tttataaaaa aaaaaaaaga 4320 tcgtaataat ttgtttttca tgagataagc tattttttaa aatgagactg taataagttg 4380 ttttgtataa ataagttgtt ttttataaag tgattgtaat aagttttttt ttattctata 4440 tataatttgt tttttatgag ataagctctt ttgaataaat tagaagataa attacaaagt 4500 ataacataat gtattaattt taagagaaaa aagggtaaaa ttgtcaaatt ataacataag 4560 cccttcatct cctttccttg ttggtgtctt aactcccaaa caaggggaag gttttcctcc 4620 tttctccctt ccttcccttt ccttcccttc ccctccttag cctttccttt ccttcccctt 4680 aaaactcgca aacaaagcc 4699 // ID Gypsy-76_PTr-LTR repbase; DNA; EDCOT; 1185 BP. XX AC . XX DT 23-DEC-2009 (Rel. 15.02, Created) DT 23-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-76_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1185 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 186-186 (2010). XX DR [1] (Consensus) XX CC >87% identity to consensus. XX SQ Sequence 1185 BP; 318 A; 194 C; 250 G; 423 T; 0 other; tgatacgatc caagaaaggg ttgaacaagg aaattcggat tctagcgtaa ttgtgtctac 60 tgtccagttt tacggcaaca atcataattc tcaatccgac cgttggatca ggctaaaaat 120 ttacccagag tttcccggaa tattgttcta tgttggggta aaatttcagg tcaatcggag 180 ttcgggaagg ccttgcgata taggtcagaa caggttgtac gaattttgtt atttacttcc 240 ttttgacttg tggacttcct atttggcaag gatccttttc ctacaaggat gtgacagctt 300 gttttgggaa tttcctagtt ctacaaggat ctttaatggg ctgcaacata attttcaagt 360 gtggcaagga ttcattaatg tttcaaaatc cttttcttac aaggattcct tattcatcct 420 agctacacag attggttagc ttattttggg gagtttccta atcctacaag gaaggttaaa 480 ggaaggcaac aagggtttcc atgttttgag aggattcttt aaagctacaa ttaattatcc 540 tagacaaaca aggaaactaa aggggaggca acttcaacaa tcaatttcct agcttatttt 600 ggatatctaa aggtggcaac aaagacccta gtgtttctag gatgagaatt tcgttcatga 660 cattatttaa actaggaaaa ttatctatct taggttattt tgtttaatta ggtgcaacaa 720 ctttagttta tgtgtcagat ttgttatttt tattattttc ttcatgtttg ggcttagtta 780 acatactttg ggtttattgt aagtgggtaa atattagccc acaagttttg ggtccattag 840 ggttactagt tgaactatta tataaggttt tgtaagctga aattttcagc agccatggat 900 ttatgaaata aacttgtgtt ttgcgtgatg caacacgttt tctttgctgg gacaaagaac 960 aaatttgact tatcaaggta taactgacct tgtggcgtct tccttatact tctcgttcac 1020 gaattggtat tcgttaggtg ggggtttctt attccaatag tgttggtgcc ttgagacagg 1080 ttttcattgt gtcacactcc tatcaaacct gatttcttgg ctttccggga gttgtatcat 1140 ctttgttgtg ggttgcttga ccacgtgatc aagaggtccg catca 1185 // ID TOPIE1_LE_LTR repbase; DNA; EDCOT; 1065 BP. XX AC AF220603; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 25-JUL-2007 (Rel. 12.08, Last updated, Version 2) XX DE Lycopersicon esculentum retrotransposon TOPIE1_LE_LTR, long DE terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Long terminal repeat; KW retrotransposon; TOPIE1_LE_LTR. XX NM TOPIE1_LE_LTR. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-1065 RA Lavelle T.D., Oldroyd E.G., Dalhbeck D., Staskawicz J.B. RA and Michelmore W.R.; RT "Direct submission."; RL Direct Submission to Genbank (04-JAN-2000). XX DR Genbank; AF220603; Positions 53616 54680. XX SQ Sequence 1065 BP; 383 A; 132 C; 228 G; 322 T; 0 other; ttggaattta tgcagttttg atgattgaca aagaaagaag aaacacgtca gtcaacatgg 60 tacaaaggtg cactgtcacg agctgttgaa ttcgagaaag cttctaaaat gaataaagac 120 aaaagtgcag aaataaaaga atggataatg ttaacttcgt cagaaacccc acggaaataa 180 acatctgatg aattgaagag aaagaattga tgagtttgat ttgaagaagg agactaaaga 240 gacaaacaat tttaattgaa gaaaaagtct cacttaaaat agaactcttc aagttactgc 300 tgaattgaag tgttagagtt cgactacaat acaaaagaat caacgaatgt aatttgaaga 360 agaagtctaa aaaagttaga agtttaaatt aaagaaggag tcttacttga agtaaaactc 420 taagtcaaga gagtacaagt caataaggag tttgaagtga acaataactc tatgataaat 480 gtgcttaaat agaagcgaag tcgttcagaa tacttgtgca cttactgagt aaaaaagcga 540 ttgagaaatt cacttcgtaa gtgctaccag cgaactgaag gaacacatcg aagaatctaa 600 tcctttacag agtttatgtg ttaggagttt ttctttgtga atgagtcttg atgtaatctt 660 agttcagtga gttataaact gaactaggag tattgtctta gggttgtgat aattcgaagt 720 gttaggaaca cataccttgg gaggtttgtg ttgaaggtta gaattagagt tagttcctag 780 gattacaaga gttgtaattc aaattcataa cttgaagtta aggtaggttg caaagtttgt 840 aatctatctt ttgtggaggc tcgtaattga tttagtgaag ttggagttaa atcttgtaag 900 ggtacaggtc gtggttttta caccttttga gctaggtctt tccacgtaaa aataatgtgc 960 ttttacttac tatcttaact gctttgctgg aacacattag tcaacctgtt tcacacttag 1020 gtggaaagtt aaaatcagta aattattagg tcgtgtagaa tatca 1065 // ID Gypsy-42_Mad-LTR repbase; DNA; EDCOT; 1168 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-42_Mad-LTR. XX NM Gypsy-42_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1168 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1779-1779 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 1168 BP; 288 A; 286 C; 292 G; 302 T; 0 other; tgtttgggcc caaaataata ttattgggcc gagcttaggt ttgtgctcgg cccaatgctc 60 ttccggaaat attatgggcc gtccagctgt cataagccgc caatcaggtc ggccgagtcc 120 tgttgcgaga aggattgatt tggataaggg cgaagaagtc gagtcctggt acaacaaggg 180 ggtttcagag ttgaaggcgc tgggaattag ggagtgaatc tggttcatta tagagcttgg 240 ttcagaaacc tattggaact aggattggcc gaatcctaat cagattaggt tagggagttc 300 tagtccgagt atatctctgg ttcggccagg agtaggttcg ctgctataaa taagaaggga 360 gtgcatcatt caaggcccct ccaattcaac acacaaactg ccctgcgcaa actctcgctc 420 tacgcgaaac ctctcaacaa ccttgagatt tttattttct ttttccgcca acacatcttc 480 agtttggata aacagcactg tgaaggcaac cggtgacatc ttcagtttgg ataaacaaca 540 ctgttgccgt agaatcagcc gaccgcggag caccttcagt ttggataaac agcactgcgt 600 cgaggccgac tggttatcta tccaagtctc ggtcaagaag gattttcgag tccttattgg 660 cagaggtcat ctcattagcc ttctcggcga agtgaggtgt tacagattac tgggctcggc 720 gcattgaacg ccgagttgtt ttatgattgg atattcacaa gtaagtttta gagttcggca 780 ttctgacggc cgaaccacat tcaccatcaa gacatacatc tcttttgagt acttgtgtcc 840 gtatagtttg gtgccagttc ggcgtgctta tactcttacg aatataatca ccgtgaccga 900 acccggcgcc gacgatccgt gaacttcgca agactagcag ccttgtcttc aggctctaga 960 acccgaaggc cgagacgtgt tccttcctcg gccgcagtcg caagatcgag aagtcagcag 1020 cgcgctcaac gcaacatcaa cacattttac tccccggccg agctcggccg acgagttggc 1080 acgccccgca cacaaccgaa tgacgtagtt agcttattaa ttactcggcc tgcgcgccac 1140 gtaggcttgg tagtttttag ggtcaaca 1168 // ID Gypsy-2_Mad-I repbase; DNA; EDCOT; 4953 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-2_Mad_; KW Gypsy-2_Mad-LTR; Gypsy-2_Mad-I. XX NM Gypsy-2_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4953 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1734-1734 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [3811-4308] - Integrase core CC LTRs are 92% similar to each other. XX FH Key Location/Qualifiers FT CDS join(79..3216,3220..4905) FT /product="Gypsy-2_Mad-I_1p" FT /translation="MPPRREPRSPAENNFPDFGQFGEAIANAIQSSLRPTP FT RNTLDIVSRLKINDFFGNEGSEKSEIWFDHVEKTFRVMHRQGNLPLERWVE FT TATWFFRLGAESWWDHERKSLSDEDAINWDVFKRLFQTRFVPPEYLDSKKN FT EFTDLRQGKMSATEYHRRFTDLSRYCPETAANPREMLRLFKRGTCKKWRTI FT ATSTPCATYQEFFEVLLRIEDSENAPDDEDEDVGRNAQRYSNRGQSSLGPR FT RAQNFKRSGNSSGSSSGGSNSGTPQRGGRSTGGSRFQNQGNSSSSGVQFCR FT RCNTRHYGECKRGSRGCFTCGQTGHMAYNCPQNQKNQPANLPPAVPLQQLP FT APGNRQQIGHGGAFHYQGGVAPNQGGPYQYTPEVPYYQGGYQQTQGGYPQF FT QGDYTPYQGGGAQMYTGGQYQNLDVASSSGGSGRQANPPQQGRGNQGRGNQ FT TQANRGRGGRQQVQGRVNNITLQDAQANPDLIMGTLNVLGHFAKVLIDSGA FT THSVISHKFAQTTQPHPTSLDYELEFSMPRGEICYVSWEYQGCPILVEDVV FT MSANLVPLDIVDFDVILGMDWLHYNRARLDCYEKVVTFHRPGMPTVTFVGE FT RGGLKHGVITAMRARRLLSKGCQGYLAHVVLAEETTASVEDVGVVRHFPDV FT FPEELPGLPPDREVEFTIDLLPGTNPISLTPYRMAPAELRELKTQLQELVD FT KGFIQPSTSPWGAPVLFVRKKDGTLRLCIDYRQLNRVTIKNRYPLPRIDDL FT FDQLKGACVFSKIDLRSGYYQLKIRSDDVPKTAFRTRYGHYEFLVMPFGLT FT NAPAAFMNLMNRVFHPYLDRFVIVFIDDILVYSKNETDHARHLRLVLKTLR FT ANRLYAKFSKCQFWLDQVSFLGHVVSAQGVLVDPQKVAAVENWEQPRTVTE FT VRSFLGLAGYYRRFVKDFSTIALPLTKLTRKDVPFVWSSECEQSFQQLKYL FT LTHAPVLALPDDGGNFEIYSDASLNGLGCVLMQHDKVIAYASRQLKPHEKN FT YPTHDLELAAIIFALKIWRHYLYGEKCKIFTDHKSLKYIFQPNLNLRQRRW FT VELLSDYDCTIEYHPGRANSVADALSRKSHGQLNALYASRIPLLTDLRSTG FT VALKEGRRGALIASFQVRPVLLDRVLEAQRNDTESQELIQAVSDGKKKDLW FT IRDPDGMLMQGDRMYVPNVEELKRDILDEAHISAYAMHPGSTKMYHTIRHF FT YYWPGMKREIAEYVSRCAICQQVKAERKKPFGLLQPLPIPQWKWEDITMDF FT VYKLPRTRNGYDGIWVVVDRLTKSAHFIPVRENYSLSQLAERFISEVVRYH FT GVPVSIISDRDPRFTSKFWVAFQEALGSRLLYSTAYHPQTDGQSERTIQTL FT EDMLRSSVLQFGDAWHKRLPLIEFAYNNSFHSSIGMAPFEALYGKPCRTPL FT CWSEVGERVLVGPEIVDETTQNIQVIKANLKAAQDRQKSIADRHSTDRVYK FT VGDWVFLKLSPWKGVVRFGKKGKLSPRYIGPYQIVERVGEVAYRLALPPEL FT ARVHNVFHVSMLRRYVSDPSHVIPPQPLEINPDLTYDEVPVTILDWKDKVL FT RNKTVRMVKVLWRNHSVEEATWETEERMRDMYPRLFYGFDL" XX SQ Sequence 4953 BP; 1270 A; 1021 C; 1308 G; 1353 T; 1 other; gcttggtatc agagcatagg tttagacagt cctgcacttc ctagtgtgtt ttaactcttg 60 ttttcttatg tcagaaccat gccacctcgt agagagccac gttctccagc tgagaataac 120 tttccggact ttgggcagtt tggtgaggct attgccaatg ctattcagtc ttcactccgt 180 cctaccccga ggaatactct ggatattgta tctcgcctga agattaatga tttctttggt 240 aatgagggat cggagaagtc agagatatgg ttcgatcatg tggagaagac ttttcgagtt 300 atgcataggc agggtaatct tcccctagag agatgggtcg agacagcgac ctggttcttt 360 cgattgggag cagaatcttg gtgggatcat gagaggaaat cattatctga tgaggatgct 420 ataaattggg atgttttcaa gcggttattt cagaccagat ttgttcctcc ggagtatttg 480 gatagtaaga agaatgagtt cacagacctg aggcagggca agatgtcagc cactgagtat 540 catcgaaggt tcacagactt atctcgttat tgccccgaga ctgctgctaa tccccgggag 600 atgcttcgtt tgtttaagag gggaacttgc aagaaatggc gtactatagc aacctctact 660 ccctgtgcta cttaccagga attcttcgag gtcttgcttc ggattgaaga ttcggagaat 720 gctcctgacg atgaggatga ggatgttggc aggaatgccc agaggtacag taacaggggg 780 caatcatcac ttggcccgag aagggctcag aattttaaaa ggagtggaaa cagctctgga 840 tcgtcgagcg ggggttctaa ctccggtaca cctcagagag gaggcagatc cactggtggt 900 tctcgttttc agaatcaagg aaactccagc agttcaggtg ttcagttttg tcgcaggtgt 960 aacacccgtc actatggcga gtgtaagaga ggaagcagag gatgtttcac ttgcggacag 1020 acagggcata tggcctataa ttgtcctcag aatcagaaga atcagcctgc taatctacca 1080 cctgcagtcc ccctacagca gcttccagca cctggtaacc gtcagcagat aggccacggt 1140 ggagctttcc actaccaagg gggcgtagcc ccgaatcagg gaggaccata ccagtataca 1200 cctgaggttc cctactatca gggaggctat cagcagactc agggaggtta tccacagttc 1260 cagggagact atacgccgta tcaaggcggt ggagcacaga tgtatactgg agggcagtat 1320 cagaacctag acgtagcgtc tagcagtgga ggttcaggca gacaggcaaa tccaccccag 1380 cagggccgag gtaatcaggg tcgaggtaat cagactcaag caaacagggg tcgtggaggc 1440 aggcagcaag ttcagggaag agttaacaac atcacccttc aggatgctca ggctaatccg 1500 gacttgatca tgggtacgtt gaatgttcta ggccattttg ctaaagtttt aattgattct 1560 ggtgctacac attcagttat ttcccataag tttgctcaaa cgactcaacc acatcctact 1620 tcactcgact acgagttgga gttctcgatg cctaggggtg aaatctgtta tgttagttgg 1680 gaatatcaag gatgtcccat ccttgtcgaa gatgtagtca tgtcggctaa tcttgttcct 1740 ttggatatcg ttgattttga cgttatctta ggcatggatt ggttacacta caatcgtgcc 1800 aggttggact gttatgagaa ggttgttact tttcaccgac cgggcatgcc tactgtcacg 1860 tttgtcggtg aacgtggtgg tctaaagcac ggagttatca ctgccatgag ggcgagacga 1920 ctgttgagta aaggttgtca aggttactta gctcatgttg tgctagcgga ggagactact 1980 gcatctgtgg aagacgtcgg agtagttagg cactttcccg atgtttttcc cgaggaatta 2040 cctggcttac ccccagatcg tgaagtggag ttcaccatcg atctacttcc aggtactaat 2100 cctatttccc ttacacctta ccgtatggct cctgcagagt taagggaact taaaactcag 2160 ttgcaagagt tggttgataa gggtttcatt cagccaagca cttccccgtg gggagctcca 2220 gttctgtttg taaggaagaa agatggaact ttgaggttat gcatcgatta caggcagttg 2280 aatcgggtga cgattaaaaa ccgttatccg ttacctcgta ttgatgacct ctttgaccag 2340 cttaaaggtg cttgtgtgtt ctcgaagatt gacctgaggt ctggttacta ccaattgaag 2400 atcagaagcg acgacgttcc gaagacagct ttcagaactc gatatggtca ttacgagttt 2460 ctagtgatgc catttggatt gactaatgca ccagcagctt tcatgaacct gatgaatcga 2520 gtatttcatc catacctcga caggttcgtc attgttttca tagatgacat tttggtgtat 2580 tcgaagaatg aaactgatca tgccaggcat ctgcgtttgg ttctaaagac gctaagggca 2640 aatcggttgt atgctaagtt cagcaaatgt cagttttggc tggatcaagt gtcattctta 2700 gggcacgtgg tatcagctca gggtgtgctt gtggatcctc agaaagtagc agctgtggag 2760 aattgggaac aacctcggac agttacggaa gttcgaagct ttcttggtct tgctggttat 2820 tatcgacgct tcgtgaaaga cttttcaacc atagcactac ctctgacaaa attgactaga 2880 aaagacgttc cttttgtgtg gagtagtgag tgtgagcaga gtttccagca gttgaagtac 2940 cttctcactc atgcacctgt cttagcactt cccgatgatg gtgggaactt cgagatctac 3000 agtgatgcgt ctctgaatgg tcttggttgt gtgttaatgc agcatgataa agtgattgct 3060 tatgcatcgc ggcagttaaa gccccatgag aagaactatc ctactcatga tctcgagttg 3120 gcagcgatca tctttgcttt gaaaatctgg aggcactatc tttatgggga aaagtgtaag 3180 atcttcactg atcataagag ccttaagtac atcttcamtc agccaaacct caatctccgg 3240 cagcggaggt gggtagagtt gctcagtgat tatgactgca ccattgagta tcacccaggt 3300 cgtgccaatt cggtagctga tgctcttagt aggaagtctc atggccaact taatgctctt 3360 tatgctagtc gcattcctct tttgactgac ctaagatcca ctggagtagc attgaaagag 3420 ggtcgtcggg gggccctaat tgccagtttt caggtcagac cggttctgtt ggatcgtgtt 3480 ctcgaagccc agaggaacga tacagaatct caggaattga tacaggcagt gtcagacggg 3540 aaaaagaagg acctctggat tagagatcct gacggcatgc ttatgcaagg tgatcggatg 3600 tatgtaccga atgttgagga actaaagaga gacatattgg atgaagcgca tatttctgct 3660 tatgcgatgc atccagggag caccaagatg tatcatacca tccgacactt ctattattgg 3720 ccaggtatga aaagagaaat tgcagagtat gttagtcgtt gtgcaatttg ccagcaggtt 3780 aaggcagaaa ggaaaaagcc gtttggattg ctacaaccac tcccgatacc tcagtggaaa 3840 tgggaagata ttacgatgga tttcgtgtac aagttacctc gtacgcgaaa tggttacgat 3900 ggtatctggg tggtagttga tcgacttacc aagtcagcgc acttcatacc cgttcgtgag 3960 aattactcgt tgagtcagtt ggccgaacgg ttcatctctg aagtggttag gtaccacgga 4020 gttccagtta gtatcatttc tgaccgggat ccccgattta cttcgaagtt ctgggtagct 4080 tttcaggaag ctttgggatc gagattactc tacagcaccg cctatcatcc tcaaactgat 4140 gggcagtcag agagaactat ccagactttg gaagatatgt tgagatcgtc agttctacag 4200 tttggagacg cttggcacaa gcgcttaccg ttgatagagt tcgcgtacaa caacagcttc 4260 cattctagta ttggtatggc accatttgaa gcgttgtatg ggaaaccatg tcgtactcca 4320 ctttgttggt ccgaggtcgg tgaacgagtt ttggtgggcc ctgagatcgt ggatgagacg 4380 acacagaaca ttcaggtgat aaaggctaac ctgaaagcgg cccaggatcg gcagaagagt 4440 atcgccgaca gacattctac cgacagagtt tataaggttg gtgattgggt attcttgaag 4500 ttatcgccgt ggaaaggtgt tgtgcgattc ggaaagaaag ggaaactcag ccctaggtac 4560 atcggaccgt accagatcgt tgaacgagtt ggtgaagttg cttatcgact tgctttgcca 4620 ccagagttgg cgagagtgca caatgtgttt catgtatcga tgctacggag gtacgtctct 4680 gatccgtcac acgtgatccc tcctcagcca ctggagatca atccagattt gacctatgat 4740 gaggttccag tgactatcct tgattggaag gataaggttc ttaggaacaa gaccgtgcgg 4800 atggtgaagg ttttgtggag gaaccactca gtggaggaag ccacttggga gacagaagag 4860 cgtatgcgag atatgtatcc acgtctgttt tatggctttg atttgtagtc agtattgaaa 4920 tttcggggac gaaattttta taagggggta gat 4953 // ID CAGYPSY1 repbase; DNA; EDCOT; 476 BP. XX AC AF121444; XX DT 30-MAY-2000 (Rel. 5.04, Created) DT 30-MAY-2000 (Rel. 5.04, Last updated, Version 1) XX DE Capsicum annuum retrotransposon gypsy-like retrovirus, a partial DE sequence. XX KW Gypsy; LTR Retrotransposon; Transposable Element; B54 pseudogene; KW CAGYPSY1; Gypsy superfamily; Retrovirus. XX OS Capsicum annuum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Capsiceae; OC Capsicum. XX RN [1] RP 1-476 RA Pflieger S., Lefebvre V., Caranta C., Blattes A., Goffinet B. RA and Palloix A.; RT "Disease resistance gene analogs as candidates for QTLs involved RT in pepper-pathogen interactions."; RL Genome 42(6), 1100-1110 (1999). XX RN [2] RP 1-476 RA Pflieger S., Lefebvre V., Caranta C., Blattes A., Goffinet B. RA and Palloix A.; RT "CAGYPSY1."; RL Direct Submission to Genbank (21-JAN-1999)Genetique et RL Amelioration des Fruits et Legumes, INRA, Domaine St-Maurice, RL Montfavet 84143, France. XX DR GenBank; AF121444; Positions 1 476. XX SQ Sequence 476 BP; 155 A; 110 C; 79 G; 132 T; 0 other; gccaccagtg ggcaacacct aaacagactc ccaaaaggaa aattgatttt ggaataaacc 60 ttcttcctaa cactcaaccc atctctattc tgccaaatag aatggctcca acagagctta 120 aagaattaaa agaatagttg aaagacctcc tagataaggg attcatcagg cccagtatct 180 ccccatgggg tgaactattt ctattcatgt gtaagaaata tggttctctc agaatgtgta 240 ttgactaccg tcagttgaac aaagtcacca ttaagaacaa gtacccactt cctagaatcg 300 atgacttatt tgaccaactt tagggggcta gctacttttc taagatagac ctcagatcag 360 gctatcatca accctgagtc agagaatgtg acaatttaaa aatagctttc agaactcggt 420 atggttactt aaaattccta ttcatgtcat ttggttttac caatcccacc catccc 476 // ID Harbinger0_MT repbase; DNA; EDCOT; 57 BP. XX AC . XX DT 15-NOV-2006 (Rel. 11.11, Created) DT 01-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative non autonomous DNA transposon with TIRs only, from DE Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW non-autonomous; Inverted repeat; Interspersed element; KW Harbinger0_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-57 RA Shankar R. and Jurka J.; RT "Harbinger0_MT: A multicopy non-autonomous DNA transposon from RT Barrel Medic."; RL Repbase Reports 6(11), 568-568 (2006). XX DR [1] (Consensus) XX CC This sequence resembles Harbinger type DNA retroposon. It CC completely lacks the transposase domain and has only TIRs. Exists CC in multiple copies in the genome. XX SQ Sequence 57 BP; 9 A; 15 C; 20 G; 13 T; 0 other; cccgaacccg tcggggacgg ggatgggatt caatttctca tccccgttgg gtatggg 57 // ID INMU1 repbase; DNA; EDCOT; 612 BP. XX AC AB041765; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Ipomoea nil Mu-like DNA transposon INMU1. XX KW DNA transposon; Transposable Element; INMU1; Mu-like. XX OS Ipomoea nil OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea. XX RN [1] RP 1-612 RA Hoshino A., Johzuka-Hisatomi Y. and Iida S.; RT "Gene duplication and mobile genetic elements in the morning RT glories."; RL Gene 265(1-2), 1-10 (2001). XX DR Genbank; AB041765; Positions 1 612. XX SQ Sequence 612 BP; 190 A; 96 C; 125 G; 201 T; 0 other; gagttaatac ccaaaatagt ccatcgacta tgtcgtaatt accaatttgg tcctcgacta 60 tcattcttac ccaattaagt cctcaactat acaagtttta cccaatttag tcctttgtca 120 atttgactgt ttgttgactg tcaaaagtgg aaataaagtt gtaattttac aagttttctc 180 cttcctccgc atttagcagc gctaaaccat gtagcaataa gcttcggttg ggttctaaac 240 ctgtcagtat cgaagtagtg gttgtgcatc ggatagccca tgaatttgat tttcaacgat 300 tttttgacga tcgaaatctg atcggagtgt attgctacat ggtttggcgc tgctaaatgg 360 agaggatgga gaaatcttgt aaaattataa ttttatcccg acttttgaca gtcaacaaac 420 agtcaaatta atacagagga ctaaattggg taagaattgt atagttgagg actaaattgg 480 gtgagaattg tatagttgaa gacttaattg agtaaaagtt acatagttga ggacttaatt 540 gggtaagaat ggtagttgag gaccaaattg gtaattatca catagtcgag agaccatttt 600 aggtattaac tc 612 // ID STSAT_SL repbase; DNA; EDCOT; 309 BP. XX AC . XX DT 11-MAY-2005 (Rel. 10.05, Created) DT 03-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE S. latifolia subtelomeric satellite DNA, a consensus. XX KW Satellite; Simple Repeat; STSAT_SL. XX OS Silene latifolia OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC Caryophyllales; Caryophyllaceae; Silene. XX RN [1] RA Garrido-Ramos M.A., de la Herran R., Ruiz Rejon M. RA and Ruiz Rejon C.; RT "A subtelomeric satellite DNA family isolated from the genome of RT the dioecious plant Silene latifolia."; RL Genome 42(3), 442-446 (1999). XX RN [2] RP 1-309 RA Gentles A. and Jurka J.; RT "Subtelomeric satellite DNA from S. latifolia."; RL Direct Submission to Repbase Update (11-MAY-2005). XX DR [2] (Consensus) XX SQ Sequence 309 BP; 65 A; 80 C; 61 G; 94 T; 9 other; ctcatttcag gamtcaacct gttcgatttc agcctcaaat aacgagyttt aacacatttt 60 tcacgataat ccgagtttcg gcgaatgctg gtttgtggca caccggcacc cccaaatgtc 120 ttccgttggt gctcaaactt tkcgtkgccg ctttatctga cccgkggaac tttctatgtg 180 atttccgaag wattttktyc ggaccccgga atcccgaaaa accgtgtatt atacacttca 240 atttcagycg ttcggaaggt cgtaccggac ctgtttcttt ttctcgctgt ttgcaatcac 300 gcgtccgag 309 // ID Gypsy7-PTR_I repbase; DNA; EDCOT; 6062 BP. XX AC scaffold_629; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy7-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-6062 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-6062 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 338-338 (2007). XX DR Genome; scaffold_629; Positions 7000 939. XX CC Positions [3340-3876] - Reverse transcriptase CC Positions [4891-5373] - Integrase core CC 'ACTAC' target site duplication CC LTRs are 88% similar to each other. XX FH Key Location/Qualifiers FT CDS 2863..5532 FT /product="Gypsy7-PTR_I_1p" FT /translation="MDVGHAILGRPWLYDLDVTIFGRSNSCSFTFQGKKIQ FT LIGLPPRSNDNSQKKSKVKDGGLNIISPREFDKEICEESVVFAVVAKEIVE FT DFLEEPPEEVIEVLREFLDVFPSELPNVLPPMRDVQHAIDFFPGATLPNLP FT HYRMNPSEHAELQRQVCELLQNGFIRESLSPCAVHALLTPKKDGSWRMCVD FT SRAINRITIKYRFPIPRLDDMLDMMAGAQIFSKIDLKSGYHQIRIRPGDEW FT KTTFKTKDGLYEWLVMPFGLSNAPSTFMRVMTQVLRPFMGKLLVIYFDDIL FT IYSKTKEEHFDHLIQVCTILRKASLFVNVKKCSFFTDQVVFLGFIVSWKGV FT SADSQKVQAIVDWPEPKTIHEVCSFHGLSTFYRRFIKGFSTIMSPITDCLK FT QGEFKWSKGANRAFEEVKKKMTEAPVMRLPDFTKVFEVECDASGVGTGGVL FT SQERHPVAYFSEKLNEAKQKYSTYDKEFYAVVQALRYWRHYLLPQEFVLYS FT DHEALCYLNSQKKLNHRHGHWVEYLQAYSFVLKHKSGIENKAADALSRRVT FT LLSVMSVEVTGFERLKEEYESCSEFGEIYLTLKDENHRAINGYHLQDGYLF FT RDNKLCIPKTSVRDFLIWEIHAGGLSGHFGRNKTIEEVERQFFWFSLKRDV FT AKLVGQCRTCQLAKHRKQNTGLYTPLPVPTCPWQDVSMDFVFGLSRTAKKH FT DSIFVVVDRFFKMTHFIPCIKSTDASKVAKLYFDEIVKLYGLPQTIVSDRD FT VRFTSYFWKTLCHMVGTKLKFSIAYHPQTDGQTEVVNRSLGNLLRCLVSDH FT NRNWDLILPTTHFAYNSSINRSIGMSPFEVVHGYKPRKPLDLFPMSLHARV FT SESAESFARRIQDLHIEITKQIQASNAQYKLQADLHR" XX SQ Sequence 6062 BP; 1793 A; 1181 C; 1282 G; 1806 T; 0 other; aatttggtat cagagcatgg cttttaattg ttcttacaat taaacgatcc acaggtttat 60 gtttaaccct agattgatct aaaaaaaaaa gaaaagaaaa aaaaaagcat actgttctga 120 ttacaaaaaa aaaaactgtt catcggcact gttcatcgtc gatcctcaac agcggcgcct 180 caagcaatca caacggcaga cccaccacca agaagacctg cacatcagtc ccacaaaaca 240 atcagccatt ctacatcaac gccgatcaca gccaacgatc acagccaacg gtcacaagtc 300 cacgtcgatt tactgccttc aacaacccgc agcgccgccg ccacaacagt tctttgtctt 360 cggtccaaat ttgctaacca tcagcgccat cagttgcacc ccagcagcag caccagccgc 420 aacgccacca ttcacagtgc cctcaccttc agcagcgaca acgaatcaac aggcccccgt 480 ccagcagcga caccacagac accaccgcct cttccctcgc accaccgggc ccaagcaaag 540 tcacgaagcc ctgttttgtg cgctgtcgcc gacagtagcg gcaacagttc acagaagcta 600 gggaagcaag aaaacagaag ctgcaaacat aattaaccta gccacgtcag caccacgcca 660 gagcatccgt ggcatctgcc acggcgccag ttcttccatg tcagcgcccc ccgccacatc 720 atctatctca tcagcatatc ctgccatgtc agctgccacg taatccttca ctgccacatc 780 atacggccag aattttatcc attaaaaatc atcattcctg gtatgttttt acacttgtta 840 accaatgttt agcattaata ttattttttt gtgcttgccc ataactaaat tacatagctc 900 gcctttacat tgaattacct taattttgag cttgtttagc attgaagatc tgatcctctt 960 aattaattgt ggagcttggt taaattagtg ggaaaactga aacattgtgt ttggattact 1020 tgtgtgtatt tagaggactt acattgcttg tttgcgcatt ttcctggttt aatctgtcat 1080 tacttagtct ccaagataaa aaaaaattta aaaaaaaatt atttttcttt atttttattt 1140 ttattttatt tttttatttt ttttattagc tataatttta ttttgtgttt ttacttgcaa 1200 gtgttatttt gtgatctcag tctcaggatt agtttttgca tgcatttacg tagtggtcgt 1260 ctagtacaca atctagaagt catagctacc atggactcgt actctagtaa tgttcttaga 1320 gatattcaag aacaattaca acttatgcga acggaaatga gcaacatgtc caatcaaatg 1380 aacaaccttt ctgggaggat ggagtccata gaaactttgc aaataagaca gtctagtgag 1440 agtgagcatt ctagtgacaa ccataggaat cctcaaagac cagttcctcg taggaaccgc 1500 caccataacc aataccaggg tcacaatgac tttgatgacc ttcatgatag tgagcgttcc 1560 aatgattacc gtcaaagacc agttcatcct aggaaccgtc aatacaacca tcaatcaggg 1620 ccatcatgac tatgatgacc ctgacgagcg agtcatgagg catatcaagg tagaagcccc 1680 aacttttgag ggtcaacttg acccgtggat ttttgataga tggatccatg acatggatca 1740 attctttggc tggtataatc tatttgagaa tagaatggta agatttgcaa agatgaaact 1800 tagtggaacc gctcagctct attggaaaag tagaagagtc tttgattagg agaggtcaac 1860 cccctattac tgactgggtt gaaatgaaga ctaagttaga agaaaagtac ttgcctcgtt 1920 cttatagagg aaatcttttg gaccagtgga ataacttgag gcaaggaggc aagtctgcca 1980 atgaatatgt gacacaattt gatgagtata ggatgaggtg tgcagttagg gaggatgaag 2040 tgatgaccct aagtagattt tgaaaaggct taaacgatga ccttagaaga gaggttgtgc 2100 tttgggggtg ttttcaccct tgatgaagct tataccctag tataaaatta tgacttggtc 2160 acaaaaagcc agtggacaag acatcaggac actcgtaata ccccttctag atctcaacct 2220 ggtagtaata actccatatt aggtgcccta cctcataaac ccaatccttt gattttccag 2280 atacctagag aagacaaggg taagagtatt tttcatgaag cacctaaaac ttcaagaatt 2340 caatgtttta agtgtcaggg ttttggtcat atctcctcta gcttccctaa taaggctttg 2400 ctcatcaagg ggcaagagga tatggatgaa gaagataatt atgatgataa gatatatgaa 2460 cccaatcccg atgattttca agatctaaat gatgaggatg atgagtctaa cttgctagga 2520 tgtgtttagg tctatatcca ctcaaatcaa gacaaccagg ttaggtgtgg ttagatgtgc 2580 attaacacaa cctaaaggaa ctgaggattg gagaaggact gctatttttt acacttacat 2640 taaatgtgga gataaagggt gtaagatcat catagacaat gatagttgta tcaatgcagt 2700 ttcctcgggt agtgtatccc gcttggctta aagtctgttc cacaccctaa accctacaat 2760 gtgtcttggg ttaatgatac atctatagcg gtcaaagaga gatgtccttt tcccattaag 2820 attttttact ataatgatga aatttggtgt gatgtcattc ccatggatgt aggacatgcc 2880 attttgggta ggccttggtt atatgatttg gacgttacaa tctttggacg atcaaattct 2940 tgttcattca cttttcaagg taaaaaaatc caacttattg gattaccccc aaggtctaat 3000 gataatagtc agaagaagag taaagtgaaa gatggagggc ttaacataat aagtcctagg 3060 gagtttgata aggagatttg tgaggagtct gttgtgtttg ctgtagtggc taaggagatt 3120 gtagaagact ttttagagga gccacctgaa gaggtaatag aagtgttgag agaatttcta 3180 gatgtttttc cttctgaact acctaatgtt ttacccccta tgcgtgatgt tcaacacgcc 3240 atagattttt tccctggggc tacattacca aacttgcctc actataggat gaacccgagt 3300 gaacatgctg aattgcaaag gcaagtatgt gagttgttac aaaatggatt tatacgagaa 3360 agtttgagcc cttgtgcagt acatgcactg ttaacaccca agaaagatgg atcatggaga 3420 atgtgtgtcg acagtcgagc catcaataga attacaatca agtatcgttt tccaattcct 3480 cgattggatg acatgctaga tatgatggca ggagcccaga tcttctctaa gattgacttg 3540 aagagtggat atcatcagat taggatccgt ccgggagatg agtggaaaac aacatttaag 3600 actaaggatg gtttatatga atggctagtc atgccttttg gcctttccaa tgcaccaagc 3660 acttttatga gagtaatgac acaagtgctt cggccattta tgggaaagtt attggtgata 3720 tactttgatg atattcttat ttatagcaaa accaaggaag agcatttcga tcatcttatt 3780 caagtttgta ccatcctaag aaaggcaagt ttgtttgtaa atgtcaaaaa gtgttccttc 3840 tttacagatc aagtggtctt tttagggttt atagtgtcat ggaaaggagt ctctgctgac 3900 tcccagaaag tccaagcgat agtagattgg cctgaaccta agactattca tgaggtttgt 3960 agttttcatg ggctttcgac tttctatcgt cgttttatta agggatttag caccatcatg 4020 tcgcctatta cagattgttt gaaacaaggt gagtttaagt ggagtaaagg agctaatagg 4080 gcatttgagg aggttaagaa gaaaatgacg gaggccccag taatgcggct acctgatttt 4140 actaaagtgt ttgaagtaga atgtgatgct tcgggagtcg gtacaggtgg agtacttagt 4200 caggaacgtc accctgtagc ctactttagt gagaagctta atgaggcaaa acaaaaatac 4260 tcaacttatg ataaggagtt ttatgcggtg gttcaggctt tgcgttattg gcgccattac 4320 ttgctaccac aagagtttgt tctttactcc gaccatgaag ccctctgcta tcttaactcc 4380 caaaagaagc ttaatcatag gcatggtcat tgggttgaat atttgcaagc atactcattt 4440 gttttgaaac ataaatctgg aatagagaat aaggctgcag atgctttgag tcgtcgggta 4500 acgctgttat ccgtaatgag tgttgaagtc acaggatttg agagacttaa agaggagtat 4560 gaatcttgct cagaatttgg agaaatatac ttgacattga aggatgagaa tcaccgtgct 4620 ataaatggtt atcacctcca agatggatac ttatttcggg ataataagct ttgtatcccg 4680 aaaacatccg tgcgtgattt tttgatatgg gagattcatg ctggaggtct ctcaggacat 4740 tttggaagga ataaaaccat cgaagaagtg gaacggcagt ttttttggtt tagtttgaaa 4800 agagatgtcg ctaaattggt aggtcaatgt cgaacttgcc aactagctaa gcatagaaaa 4860 caaaatactg gtctttacac cccattgccc gttcctactt gcccttggca agatgtgagc 4920 atggattttg tgtttgggct ttcacgtact gcaaagaaac atgattctat ttttgtggtt 4980 gtcgaccgct tctttaagat gacccatttt attccttgta ttaagagcac agatgcttcc 5040 aaagttgcaa aactctattt tgatgagatt gtcaagttgt atggtcttcc ccaaactata 5100 gtttcggata gggatgttag attcacaagt tatttctgga aaaccctttg tcatatggtg 5160 ggaaccaaat tgaagttttc tattgcttac cacccccaaa ctgatggtca aactgaggtg 5220 gttaacagga gtttgggcaa ccttttaagg tgtctagtga gtgatcataa tcggaattgg 5280 gatctgattc ttcctacgac ccattttgcc tataatagct ctatcaatag gtcaataggc 5340 atgagtccct ttgaagttgt acatggttac aagcctagga aacctttaga cctttttccc 5400 atgtcccttc atgctagagt gtctgagtca gccgagtctt ttgcacgtag aattcaggat 5460 ttgcatattg agatcactaa acagattcaa gcaagtaatg cgcaatataa acttcaagct 5520 gatttacata gatgacataa tgagtttaat gtgggagact atgttatgat acggattaga 5580 cccaagtggt ttccttcggg agctaatcga aaattacatg cacgtagtgc tggacctttc 5640 aaagtgctac aacgggttgg tccaaatgct tatgttcttg atttaccaca tgattttggc 5700 attagcttta catttaatat tgaggatcta gttgcatacc acaaaccact tcctattcca 5760 gatgatccat ttgagatacc acttaactcc ccttctgatg atcctattga aacctctatc 5820 cctttcacct tgacatcagc acaaaaggat aatattgatg ctattctgga tgaacaagtt 5880 gtttttaaca ggaatggtga ggttcaacgg tttctagttc gttgggtggg tcgacctgac 5940 tcagattgca cttggattac tagagatact ttgcagcagc ttgacccaga tctttgggag 6000 tactatcaga gtcggccagt actacactcg acggggtcga gtttctctaa cctcgggaga 6060 gt 6062 // ID VLINE5_VV repbase; DNA; EDCOT; 6355 BP. XX AC . XX DT 13-SEP-2007 (Rel. 12.09, Created) DT 13-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE Non-LTR retrotransposon from grapevine. XX KW L1; Non-LTR Retrotransposon; Transposable Element; VLINE5_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6355 RA Obukhanych T. and Jurka J.; RT "VLINE5_VV."; RL Repbase Reports 7(9), 1004-1004 (2007). XX DR [1] (Consensus) XX CC This is a non-LTR retrotransposon from Vitis vinifera. CC Individual copies are ~87% similar to their consensus. XX FH Key Location/Qualifiers FT CDS 1233..2372 FT /product="VLINE5_VV_1p" FT /translation="MDQSXLKAGPVMKSKKAHSGEGPHCGKDFGLFSLISE FT EQAHLDGPXDRXLSCNXSKVLKVVGDDGSKEALPKNISXSFXASRSHHSPS FT RKLGSSRARSLPLSSVFENLLSPLPGSVVANREFRFQEXKLSSKAEIFLGR FT EXQSFPLKEAARLSNLQGPIEEAKGASSPFVLSLGDGPXGAEVRDGSXHRG FT CHIQVQSSTPLSXXKGXFLEGAFEVSSSPFSPVVSLQSHSXSVPSXTLPFR FT SFYCLVSTSTNPSRVNKLLSGSFRVCSSPKGVVSPVVKPSQELEGXSFLRL FT SQTNPSGASSPMRCLSRESGPAQLEDFHIEGISPSKMASIKSVLGTLNVKI FT VKYNKNGVQSAKSNGCSVEKVYSRRKNKTSSGAPSXL" FT CDS 2251..4794 FT /product="VLINE5_VV_2p" FT /translation="MSKLSNTIRMEFSRPKAMAAQWKRCIPEGRTKPLLAP FT LAFFSFLGPLVSSGFFSVFMKIISWNTRGLGSIKKRRVVKDFLCLENPDVV FT LLQETKRESCDRRFVGSVWKVRNKQWAVLPASGALGGVVIFWDALRFKCLE FT VVLGSFSVTVKLESEEEGSFWLSSVYGPSSSHFRKDFWLELQDLSGLTFPK FT WCVGGDFNVIRRISEKLGGSRLTPSMRDFDDLIRECELIDPPLRNASFTWS FT NLQENPICKRLDRFLFSSEWEQDFPQCIQEALPRLTSDHCPIVLDTNPFKW FT GPTPFRFENMWLIHSDFKDILGCWWNECRFEGWEGHKFMKKLQFVKSKLKE FT WNKVSFGDLKEKKKNILLDIVGLDEKEQEGNFSSKLAARRTLRKGELEEVL FT LKEEVFWRQKSRVKWIKEGDCNSKFFHRVANGRRNRKFIKSLVSEDGVILD FT NIESISEEIKHHFGKLFSKPLGGSWRIEGLDWSPISAESVEWLDRPFSEEE FT IHNVVLHLNKEKAPGPDGFTIAFYQECWETIKDDLLRVFLEFHNNGIINQS FT TNATFIALVPKKSQTSRISNYRPISLVTSLYKIIAKVLSGRLRKVLQDTIF FT LTQGAFVEGRQILDVVLIANELVDEKRRSREEGVVFKIDFEKAYDHVDWDF FT LDHVLERKGFSSRWRSWMRGCLSSATFAILVNGNAKGWVKAYKGLRQGDPL FT SPFLFTIVADVLSRLIVRAEERGLFEGFLVGRNRTRVSHLQFADDTIFFSR FT ASFEELHSLKLILLVFGRLSGLRINLNKSTLSGINISQDQTARLASLLDCA FT VSDWPLSYLGLPLGGNPNSISFWDPVLDRVSRRLDGWKKGLFVLRR" XX SQ Sequence 6355 BP; 1617 A; 1029 C; 1671 G; 1983 T; 55 other; gttacggaga aggttcaagg gcagctttyt cggtggcttt tgaagagagg aaatcgtwtg 60 gattttrgaa cagttgaaga aggctgtgga gttgtcagaa tcttggggtt tcatttaaag 120 ttcaggggta gatcgagaac acatttggtg gaaatttgtt tcaatagcag aggaagattc 180 attagaattt cggagttcgt tacaaacaga aaaactwctt ctctgattgt tcttgaaggt 240 gtcaaaggta gaggatggga agccctaagg aagtcgatmt tctttgtgtc ggagagccct 300 tttcgttctg tcaytagaac agaggaggtg gaagcaaagg tgaaraacaa agtggggttg 360 gtagggtggt ctgggayagg tcttatgcaa gagtggttga cgaggagggt ccaaggaaat 420 gagctctctt accagttgga aagtgggcta gggctgtgat ttgtgaaggc caagttttgg 480 ttcaagattg gggtgttrta ggtaaggctc ttgcragaat gatgggggtg aggggaatga 540 tttccataaa ccctttttca gctttcaaag gtgtcttctt cgtggattca gttgaaagag 600 cggagtggct tcaggcgcaa ggaaggytgg tttcgagagg agtggttttt aggttgcgga 660 aatggtcgcc aagagaaaat acagtggttc ttggaaaatt caggagggtt ggatagagtt 720 gcggggtctc ccattccatc tatggaatga aaaccagtta cggttcataa tgaagaattg 780 ggggaaggtg acagaggtgg atcgagatac tttaaagctt attgatttat caaaggttaa 840 agtgaaggtg gaaatgaatc caaatgtggt gttgccggcg ctgttggagg tgatagatgg 900 tgcctgggtt tttacagttg cagtctcagt catcggaggg gaagaagaag atgtacagag 960 aaagctcgag ttaactcgct gcagaagcga gtyggcttca atgggagatg gcgtggtgya 1020 gggcccttca yaggctttga ggacacgtgg yaaggctarg atagttttgg ggaacaactg 1080 ccacccactt tctctggtct caaacattat ttcaaattca aatgggcttg twaagcaggg 1140 gattgtttta aaggaraagg aggcctgyay aggargagaa tcaggcccat ttgagaagga 1200 aagcccaggc ctttccaaag gttwcytrgg taatggacca aagyyaattg aaggcaggcc 1260 cagtgatgaa gtcaaagaag gcccactccg gagaaggccc acattgtggt aaagactttg 1320 ggctgttttc tctcatctct gaagagcaag cccatttgga tggccctara gatagaagmc 1380 tragytgcaa tgyttccaaa gtgctgaagg ttgtggggga cgatgggtct aaggaagctc 1440 tcccaaagaa catcagtycc tctttctrtg cgtcgagatc ccaccayagt ccaagcagga 1500 agttgggtag tagtcgkgcg agaagcttgc ctctgtcgtc ygtttttgag aatctgctaa 1560 gtcccttgcc tgggagtgtt gtagcgaaca gagaatttcg ttttcaagag wggaagcttt 1620 cctcgaaggc tgagattttt ttgggaagag agawccagag ctttcctcta aaggaggcag 1680 caaggctrtc aaatcttcaa gggccgatcg aggaggctaa gggagcttcg agcccttttg 1740 tgttgagctt gggggatggt ccagawgggg ctgaggtcag agatgggtct yaacaccgcg 1800 ggtgtcacat ccaggtacag tcttctactc cactttccwt ggytaaaggc yggtttttag 1860 agggggcttt ygaggtgtct tcttctcctt tctcccctgt tgtttctctt cartcccata 1920 gtckttctgt gccttcttyg accctccctt ttaggtcttt ctattgtctt gtctctacrt 1980 caactaatcc ttcaagggtt aacaagttac tttctggttc wtttagggtt tgttccagtc 2040 ccaaaggtgt ggtgtcccca gtagtcaagc ccagccaaga gttagagggc rtttcttttc 2100 tcaggttatc acaaaccaac cctagtggag cttcttcccc aatgaggtgt ttgtctcggg 2160 agtcaggtcc tgctcagttg gaggatttcc atattgaagg catctctcct tcaaaaatgg 2220 cttccattaa gtcggttttg ggtactttga atgtcaaaat tgtcaaatac aataagaatg 2280 gagttcagtc ggccaaaagc aatggctgct cagtggaaaa ggtgtattcc agaaggaaga 2340 acaaaacctc ttctggcgcc cctagcyttc tttagttttc tgggtccttt ggtgtcttcg 2400 gggttttttt cagtttttat gaaaattatt agttggaata ctagaggtct tggttccatt 2460 aagaaaagaa gggtagtgaa ggattttctt tgtcttgaaa atccagatgt tgtcctgttg 2520 caagaaacaa agagggagtc ttgtgatagg aggtttgtgg gtagtgtgtg gaaggttaga 2580 aacaaacagt gggcagttct tccagctagc ggggctttgg gaggagtggt aatcttttgg 2640 gatgctttga ggtttaagtg cttggaggtt gttttaggat ctttctctgt aacagtcaag 2700 ttggagtcag aggaagaagg gtcgttctgg ctttcttcgg tctatggtcc tagttcgtca 2760 cactttagaa aggatttttg gttggagctt caagatcttt caggcttaac ttttccaaaa 2820 tggtgtgttg gtggggattt taatgtcata agaagaattt cagaaaagtt aggaggttcc 2880 aggttaaccc caagcatgag ggattttgat gatcttataa gagaatgtga attaattgat 2940 ccgcctctga ggaatgcgtc cttcacttgg tctaatttgc aagaaaaccc tatttgcaaa 3000 aggttggata gattcttatt ttctagtgaa tgggagcaag atttccctca atgcatccaa 3060 gaagctctcc ccagattgac ttcggatcat tgtccaattg tgttagatac caatcctttt 3120 aagtgggggc caacaccttt tagatttgaa aacatgtggy tgattcattc agatttcaag 3180 gatattttag gttgttggtg gaatgagtgt cggtttgaag ggtgggaagg tcacaaattc 3240 atgaaaaagc tacagtttgt caagtcaaaa ttgaaagagt ggaataaggt gtcttttgga 3300 gacttaaaag aaaaaaagaa aaatattctt ttggacatag tgggtttgga tgagaaggaa 3360 caagaaggga atttttcttc taaactagca gcaaggagga cgttaaggaa aggggagttg 3420 gaagaggtgt tgctaaagga agaggtgttt tggaggcaga aatctagagt caaatggata 3480 aaagaagggg attgtaattc taaatttttt catagggtgg ccaatggtag gaggaatagg 3540 aagttcatta aatccttggt gtcagaagat ggggtaatct tagataacat tgaaagcatt 3600 tcagaggaga ttaagcacca ttttgggaag ttattttcca agcctttagg tggttcttgg 3660 aggattgaag gtttggattg gtctcctatt tcagcagaga gtgtcgagtg gttggatcgc 3720 cctttttcgg aagaggagat tcacaatgtt gtgttgcatt taaataagga aaaggcccct 3780 ggtccagatg gtttcacaat tgctttttat caagagtgtt gggagacgat taaggatgat 3840 cttttaagag tgttcttaga gtttcacaat aatgggataa ttaatcaaag cacaaatgct 3900 accttcattg ctctagtgcc aaaaaagagt caaacaagta ggatctcaaa ttatagaccc 3960 atcagtttgg ttactagttt gtacaaaatc atagccaagg ttctatcagg gcggttgcgt 4020 aaagtcctcc aagacaccat ctttttaact caaggtgctt ttgttgaggg gagacagatt 4080 ttggatgttg tcttgattgc taatgagttg gtggatgaga aaaggagatc aagagaggaa 4140 ggggtagtct tcaaaattga ttttgaaaag gcctatgatc atgttgattg ggattttttg 4200 gaccatgtac ttgaaagaaa agggtttagt tcaagatgga ggtcttggat gaggggatgt 4260 ttatcttcgg cgacttttgc aatcttagtg aatggaaatg ctaaggggtg ggttaaggca 4320 tacaaaggcc taagacaagg agatcccctt tccccttttc tcttcaccat tgtggctgat 4380 gttttaagca gattgattgt gagagcggag gagagaggtt tatttgaggg gtttctagtg 4440 ggtagaaata ggaccagggt gtctcattta caatttgcgg atgacaccat ctttttttct 4500 agagcatcct ttgaagagtt gcattctctt aagctaattt tgttggtgtt tgggcgttta 4560 tcagggctaa ggattaatct aaataagagc actctctctg gaatcaacat tagtcaagac 4620 caaactgcca ggttggcttc tttgcttgat tgtgcagtct ctgattggcc tttatcgtat 4680 ttgggtctcc ctttaggggg gaacccaaat tcgatttcct tttgggatcc agtgctggat 4740 agagtctcta ggaggttgga tggatggaaa aaaggccttt ttgtccttag gaggtagaat 4800 caccctaatt cagtcttgtt tgtcacacat cccaagctat tttctttctc ttttcaagat 4860 tccaacttca atagctttga ggattgagaa attacaaaga gattttcttt ggtcaggttc 4920 tggggagggt aaaagggatc atttggtcag ttgggacata gtctgtaagc ctaaggagtt 4980 tggtgggtta gggtttggga aaatttctct gaggaaccaa gctttattag ggaagtggct 5040 ttggaggtac cctaaggaaa gttctgccct ttggcatcag gttatcttga gtatctatgg 5100 gacacatcct aatggatggg acgccaacaa tataattaga tggtcacatc gttgcccttg 5160 gaagggccat tgccattgca cattttctcc aagttttttc tacacacact cgttttgtgg 5220 taggtgatgg gaccagaatt cgtttttggg aagatctatg gtggggggac caaccttttt 5280 gtttacaatt tccaagactt ttcagagtca ccactactaa aactcgtcct atttcagcta 5340 ttttgggtaa taacacttct ttgtcttggg atctaatctt tagacgcaat ctaactgatg 5400 aggagattgt ggatcttgaa agactaatgt ccttactttc ccttgttcat ttgactcctt 5460 ctgttctaaa tgcgaaagct tggattccgt cctcttcagg agttttctca gttaaatcat 5520 ttttttcagc cttatccaat ttctcaaatt ctattccttt ctacccagct aattttttgt 5580 ggaaatcaaa agtcccttct aaggtcaggg cctttgcttg gttagtggca cataagaagg 5640 taaataccaa tgacatgcta cagttgagaa gacctttcaa agcccttagc cctgattggt 5700 gcatcctttg taggaggagt agagagacaa ttgatcatct cttcttgcat tgtccgatta 5760 ctttgggatt gtggcatagg attttttcac aggctgggat ggagtgggtt cagccaagca 5820 gtatttgtga tatgatggtg atctccttca agtgttttgg gaattctatt agaggcaaga 5880 ctctttggag gatcgcgtgt ctctctttgt tgtggattgt gtggagagag aggaatgcta 5940 ggattttcga ggacacttgg aagacgccgg agatgatgtg ggatcagctt catttttatg 6000 tttctttttg ggcttactgt acaaacattt ttaaacccta tcctttgagt gtaattcagc 6060 ttagttggct tcagttatcr atttgtacac cttagggttg ggtttatagg gtcaggattg 6120 ttttacttgt ataggccttt tgttcctttt gtatagccct ccttggttag tggaggttta 6180 cttagttctt tcgatcaagc ggccttttgt acctcttgta tagccttcct tggttagtgg 6240 aggtttactt agttcttttg atcaggtttg tacttcatgg ggaggatttc tcatccttct 6300 catgtttctt ttctcwttta atacatttgt tttgtttttg ataaaaaaaa aaaaa 6355 // ID Gypsy10-PTR_I repbase; DNA; EDCOT; 3345 BP. XX AC scaffold_156; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy10-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3345 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-3345 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 298-298 (2007). XX DR Genome; scaffold_156; Positions 228423 225079. XX CC Positions [2441-2923] - Integrase core CC 'ATTTG' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 656..3343 FT /product="Gypsy10-PTR_I_1p" FT /translation="MIWAKQLLQVEGLDLPIQIKELLEEFKDVFPDELPKG FT LPPIRGIEHQIDLVPGASLPNRPAYRCNPEEAKEIQRQVGELLEKGYVRES FT LSPCSVPTLLVPKKDGTMRMCMDSRAINKITVKYRFPIPRLDDLLDELHGA FT ALFSKVDLMSGYHQIRMKEGDEWKTPFKTKQGLYEWMVMPFGLSNAPSTFM FT RLMNHVLRKYIGLFVVVYFDDILVYSKTFDDHMKHLRVVFETLRDSKLYGK FT LTKCYFCKESVVFLGYIISSRGVKVDEEKIEAIRDWPKPASIAYVRSFHGL FT ASFYRRFVKDFSSIVAPMTECLKNGNDFRWSEDAQKAFELIKEKLCTAPVL FT ALPDFAKTFKIECDASGVGIGAVLLQEKRPIAFFSEKLNGARLNYSIYDKE FT FYALIRALEVWQHYLLPKEFVIHTDHESLKYLKGQSKLNRRHAKWVEFMES FT FPYVIKYKKGQVNVVADALSRRFALISMLNARLMGFEQVKEQYANDSYFAN FT VVVECAKGACDGFFMHEGYLIKMGRMCIPSGLLRELLVREAHGGGLSGHFG FT EKKTYELLKEHFFWPSMLRDVHKVIERCAICKKAKGKENAYGLYMPLPIPE FT QPWMDVSMDFVLGLPRTQRGKDSIMVVVDRFSKMSHFIPCNKTDDAVHVAD FT LFFQEVVRLHGVPKSIVSDRDTKFLSHFWKTLWRKLGTKLLFSMACHPQTD FT GQTEVVNRTLSSLLRAVIHKNLKSWDTCLPIVEFAYNRSVHGATKFSPFEV FT VYGFNPCVPIDLIHIPIDERTSMDGIRKAELMKKLHEQVRLHIEEKTIKYA FT KQANKGRKMVRFEPGDLVWIHISKGRFPSKRKSKLMPRADGPFRIIEKVND FT NAYKVDLPGNYNVSATFNVKDLTPYLDDDDDSDLRTNHFQPGA" XX SQ Sequence 3345 BP; 977 A; 518 C; 845 G; 1005 T; 0 other; tctggtatca gagcatcagt tgcgatctaa ggcaggagcc aaaaacagaa gaaaggcttg 60 ctggaattga ggttgataaa cttaattatg gctggagatt tgttggttgt gcaacgggtt 120 ctgaatgcac aaattgtcgt tagtgatgag caacgcgaga acatctttca tactcgatgt 180 cagattcgag ataaggtgtg tgggatgatc attgacaatg aaagttgcac taatgttgcg 240 tcaactacct tggtggagaa attgggttta actacccttc cacatcccag gccgtacagt 300 ttgcgatggc tgaatgagaa tggggagatt cgggtgacaa agcaagttcg tgtacctttt 360 tccattaaaa cctatcatga tgaggttttg tgtgacgttg cgccgatgtt agctagccat 420 ttgttgctgg gtcgtccatg gcagtttgat aaggatgtga cctacaatgg acgaaagaac 480 acttattctt ttatgctgaa tggaaagaag gtgaacttgt taccattgag ttctcaacag 540 gttagagagg atcagatacg aagccaacaa aaggaggtga aatcatgtaa agggctgttg 600 ttagccaaaa aaaggagaca tcaaacaagc attagcttca gcaggggctg ttttcatgat 660 ctgggcaaag caattactac aagtagaagg attggactta ccaatacaga ttaaagaatt 720 gcttgaagaa tttaaagatg tgtttccaga tgaattacct aaagggttac cacctattcg 780 tggaattgag catcaaattg atttggtgcc gggagcttca cttcctaaca gaccagcata 840 cagatgtaat ccagaggaag caaaagagat tcaaaggcag gttggtgagc tcttagagaa 900 gggctatgtg cgagaatcac ttagtccatg ttccgtacct actttgcttg taccgaagaa 960 agatggtacc atgaggatgt gtatggacag ccgcgctatc aacaaaataa cagttaagta 1020 tcgatttcct atacccagac ttgatgattt gcttgatgag ttgcatgggg ctgcattgtt 1080 ttctaaagtc gatttgatga gtggttatca ccaaattaga atgaaagaag gagatgaatg 1140 gaaaacacca tttaaaacta aacaggggtt atatgaatgg atggtaatgc cgtttgggtt 1200 atctaatgcg cctagtacat ttatgaggct tatgaatcat gttttgagga agtatattgg 1260 gctgtttgtt gtagtatatt ttgatgatat cctggtgtat agcaagacct ttgatgatca 1320 tatgaagcat cttagagttg tgtttgaaac tttgcgagat tctaagttgt atgggaaact 1380 cacaaagtgt tacttctgta aagaaagtgt cgtgtttctt gggtatatta tctctagcag 1440 gggagttaag gttgatgagg agaaaattga ggcaattcgg gactggccaa aacctgctag 1500 tatcgcttat gtgaggagtt tccatggttt agcttctttc tacaggcgat ttgtgaaaga 1560 cttcagctct attgttgctc ctatgacaga atgcttgaaa aatgggaacg actttagatg 1620 gagtgaagat gcgcagaaag catttgagct aattaaggag aagttatgta ctgctccagt 1680 tttagcactt ccagactttg ctaaaacatt caaaatagag tgcgatgctt ccggagttgg 1740 aattggggct gtcttgctgc aagaaaagag gccgattgca ttctttagtg aaaagttaaa 1800 tggagcacgt ttgaactact ctatttatga caaggagttc tatgctttga ttcgggctct 1860 agaggtatgg cagcactact tgttgcctaa agaatttgtt atacatactg atcatgaatc 1920 cttgaagtat cttaaggggc aaagcaagct gaatcgcaga catgctaaat gggtggagtt 1980 tatggagtca tttccttatg tcataaagta caagaaaggg caagttaatg tggttgctga 2040 tgctctttct aggaggtttg cactgatctc tatgttgaat gcaaggctga tgggttttga 2100 acaagtgaag gaacagtatg ctaatgattc ctactttgct aatgtggttg tcgaatgtgc 2160 aaagggagct tgtgatgggt tctttatgca tgaaggttac ttgatcaaaa tgggcagaat 2220 gtgtattcct tcaggattgt tacgggagtt gcttgtgcga gaggctcatg gtggtggtct 2280 tagtggtcat tttggggaga agaagactta tgagctgctg aaagaacatt tcttttggcc 2340 tagcatgtta cgggatgtgc acaaggtgat tgagagatgt gctatttgca agaaagctaa 2400 gggtaaagag aatgcatatg gactgtatat gccattgcct attccagagc aaccatggat 2460 ggatgttagc atggactttg tacttgggtt accaagaaca cagcgtggaa aagattcaat 2520 aatggtcgtg gttgatcgat tctccaaaat gtctcatttc attccttgca acaaaactga 2580 cgatgcagta catgttgctg atttgttctt tcaagaggtt gttcgtttgc atggagttcc 2640 taaaagcatt gtctctgatc gtgatacaaa gttcttaagc cacttttgga agactctttg 2700 gaggaagctt ggaacgaagt tacttttcag tatggcatgt catccacaaa ctgatggaca 2760 aactgaggtg gtaaaccgaa ctttatcttc tttgttacga gctgttatac ataagaattt 2820 gaagagttgg gatacttgtt tgcctattgt ggagtttgca tataatcgta gtgtgcatgg 2880 ggctacaaaa ttttcaccat ttgaggttgt gtatggcttt aatccttgtg ttcctattga 2940 tcttattcat attccaattg atgagaggac atctatggat ggaattagaa aggcagaatt 3000 gatgaagaaa ctacatgagc aggttcgatt acatattgag gagaaaacga taaagtatgc 3060 taaacaagct aacaaggggc ggaaaatggt taggtttgaa cctggagatc ttgtttggat 3120 tcatattagc aagggcagat tcccaagcaa acgtaagtcc aagttgatgc caagagctga 3180 tggtccattt cggattatag agaaggtgaa tgacaatgcg tataaggtag atcttcctgg 3240 taattacaac gtatcagcta cttttaatgt gaaagacttg actccatact tggatgacga 3300 tgacgattct gatttgagga caaatcattt tcaacccggg gctga 3345 // ID TE-1_Mad repbase; DNA; EDCOT; 2915 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative transposons from the apple genome. XX KW Transposable Element; Nonautonomous; TE-1_Mad. XX NM TE-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2915 RA Kojima K.K. and Jurka J.; RT "Putative transposons from the apple genome."; RL Repbase Reports 10(10), 1826-1826 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~88% identical to the consensus. No TIRs. No TSDs. XX SQ Sequence 2915 BP; 763 A; 624 C; 622 G; 888 T; 18 other; attgtttttg tagatgtcga acttaatatc aaaccggcgg gcagctagta gggtcagtca 60 gacaccttct ccaggaggta gtgctgctgc cacctccaca cctgatatgg gcacgacggg 120 tgtccctccg gtcacgcctt tggggccaac ggtgtctacg gctcctgcgt catcgacttc 180 ttcggtgacg catcctgtac taagcgcccg gcggactcat cgacggcccc ggagttctga 240 ggaggctcag cagtctggtg aggcttcctc tgtccatgga gaggggtccc agacaggtaa 300 gcttgctctg tccattgata agcttgcttc tggtttcatt tgttggtcgt tgtgaaaatc 360 gaacttttaa attatttcca ggtcgtatgt gaaatctgtt ggtggatgac aaaagaagat 420 ccccaatctt ctttagaaaa agttggttga taaattcttt ggttacactc ttaaaaagtt 480 atctttctta ttcttttatt ttctcattgg tgaaaatctt cagtagtcaa tgtatgtttt 540 caagttacga atacggtgat gttaaaattt gtcaanaatg aatgatcttt taatttacgc 600 agagaataac atgcatgcta gctagttant ttgaattgtg atttcgacct atattaatga 660 ttgttaagta gcactgagtg aagtcatatc aacaagttgt aaattttgtt ttaacgtccc 720 caattggtat aaactgtttg aattgttggg tggatgtgtt gtttttgttg ttatattgtc 780 tgcaggtttt aggaaatgtt atagttttag gggaggttct gccgaatttt cggtagaaaa 840 tagaattcgt ctaatgttta ctttgtttat ttggtaggtc aaaaaaaaaa accaggggcc 900 cttgcagact nctnaagacg tcacagacca ctcgcaccac gaccgagaag atcaccatta 960 cgtgggatcc tcgacatcgt gcggctgcaa caaaggagca gcacagtgcg ttggccaccg 1020 acgttggctc ggttatcagg aaccattgcc ccctcatgtg ggagtcatgg agagctgtcc 1080 cacangaagt caaggacgcc gttcttcatg aattatcggt aagtattttc aacctcaaat 1140 actaaatttt tattaaagta tacaaagatt ataaatttta actactattt atttgttgag 1200 ttttgcagca tcactatgag ctctccaacc tcgatgccaa tcaaatgcag tacatcaacg 1260 acctttgctc cggtaggttc actcaatgga agagcgacct ccacaagcat tatgagctat 1320 atgacggtcc ggaggtcgct ctagaagttg ggtgccctat agagttggtg gaccgtcggg 1380 atgaatggga gtggctctgc ggccattttc aagacgagaa atacctngta cgtataatat 1440 atatttcaat aatatattaa taaaaaattt acaattttaa ataaaatttt catttttttc 1500 attcatttgt tataaatatc taaactaata cgttttttta attcaacaga aaaaagtgaa 1560 ggcaaactcg atcaatcggt cgaagaagaa acttcttcac cgatccggct cacgacgctt 1620 ctcttatagg ttggaggagc gacgtaaggt aaccgtatat ttattttaag ttttcaatct 1680 ttttactctt tattacacaa ttggtaatct atgttaacac tttttaaatt ttttcagggg 1740 ggtcaaagtt tcctgaaatt gacatgttca aggaggtgta cgttcggccc ggggatgagc 1800 tgacggagca gcttcatgta agttatttca attttttaat attcaattag tattaatatt 1860 aattacatgt atattcaaat taatttgttt ntttttttca tttttctagt ccaccatggt 1920 ggagaagggc cagaccgttc tggaggaggt ggcttcccag cttcccctag agaccccgat 1980 cgaggaggtg tttccccctg aggatgctgg ntttcagatc atgacggaca cactcgatca 2040 gaccctcggt cgtcggcgtg ggaatgttca ccgggggctt gggaaagccc gccttcggga 2100 cccgtctgcc tcatcctcca ggcagagaac ngaagaggtc gaaacgctga catctgaagt 2160 ggcgggcctg aaggagcaga ttgcggccca aaacaatttg atgaaccaaa ttcgtcgcgc 2220 acttcaaatc tctggcattc aattccccga cgttgaacca cctccagaaa cgacctccca 2280 gccccccgcc gcagcagcta cgacctccca gccccccgnc gcagcagcna caccaccagc 2340 cggcgattgc gacgtcgacg actacntntt ttagttttgt tttaaattgt tttcgaattt 2400 aaaaatactt tttttccatt gtatgtacat ttncaataat tttttaattc aatattcttc 2460 tttacatttt ctatttttaa tttcattaaa ttnatttaca aaaactaatt taaaaataaa 2520 aaaaaaaaat aaataataaa ttatttaaaa ataaataata aataatttta aaatcttact 2580 gcgacggcct ctatatccgt cgcgcaagag tttgtgggtc gaacctatgt ccgtcgcgca 2640 agagtttgtg ggtcgaaccc acgtccgtcg cgcaagagtt tgggggtcga accccagttt 2700 cgtcgctcgg tacgcgcaac gaccaccant tccgtcgcgc aatcttcatt tcgcgcgacg 2760 aagaactttc ctccgtcgcg caatgcctga cgtcacgagc tttgcgcgac ggantttgcg 2820 cgacgctctc ttcgccgccc aatgtttccg gcgacggttt ttncctttgc gcgacggttt 2880 ccccttcgtc gcccaagaag ttattcctag tagtg 2915 // ID Gypsy19-VV_I repbase; DNA; EDCOT; 9526 BP. XX AC . XX DT 11-SEP-2007 (Rel. 12.09, Created) DT 11-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW internal portion; Gypsy19-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9526 RA Obukhanych T. and Jurka J.; RT "Gypsy19-VV."; RL Repbase Reports 7(9), 794-794 (2007). XX DR [1] (Consensus) XX CC This is an internal portion of Gypsy19-VV LTR retrotransposon. CC Individual copies are about 92% similar to their consensus. LTRs CC of this retrotransposon, deposited as Gypsy19-VV_LTR, are 97% CC identical to each other with small indel mutations. Target site CC duplications are 5 bp-long. XX FH Key Location/Qualifiers FT CDS 248..5749 FT /product="Gypsy19-VV_I_1p" FT /translation="MPYWIRDSEGRLVKIXTPHETELELCVNVMEATPEDQ FT HSQHAQEENFNAYRSMRDRMHPPRMSAPSCIVPPTEQLVIRPHIVPLLPTF FT HGMESENPYAHIKEFEEVCNTFQEGGASIDLMRLKLFPFTLKDKAKVWLNS FT LRPRSIRTWTDLQAEFLKKFFPTHRTNGLKRQISNFSAKENEKFYECWERY FT MEAINACPHHGFDTWLLVSYFYDGMSSSMKQLLETMCGGDFMSKNPEEAMD FT FLSYVAEVSRGWDEPNAREVGRMKSQPNAPNAKAGMYTLNEDIDMKAKVAA FT MARRLEELEMKKIREVQAISETPVQAMSCSICQSFEHLVEECPTIPAVREM FT FGDQANVIGQFKPNNNASYGNTYNSNWRNHPNFSWKPRAPQYTQPGQAPPQ FT ASNLEQAIVNLSKVVGDFVGDQKSINAQLSQRIDSVESTLNKXMDGMQNDL FT SQKIDNLQYSISRLTNLNTVQEKGKFPSQPHQNPKGIHEVEAQEGESSQVR FT EVKAVITLRSGKEVDLPTSKPEHEPESEAEKEKREEIKGKRKGNSAKKEDL FT ESTVNEEPERTINQEDMMKKHTPPPFPQALHGKKGINNASEILEVLRQVKV FT NIPLLDMIKQVPTYAKFLKDLCTIKRGLNVNKKAFLTEQVSAIIQCKSPVK FT YKDPGCPTISVMIGETCVEKALLDLGASVNLLPYSVYKQLGLGELKPTSIT FT LSLADRSVKIPRGMIEDVLVQVDKFYYPVDFVVLDTDPIAKGTNXVPIILG FT RPFLATSNAIINCRNGVMQLTFGNMTLELNIFYLCKKQFHPEEEEGPEEVC FT MIDNLVEEHCDQKMLEDLNESLGDLDEGLPEPSDLLATLPPWKRREEILPL FT FNGEETQEAVKEEPPKLILKPLPTELKYAYLEENKQSPVVISSSLTTTQED FT CLLEVLRRCKKAIGWQISDLKGINPLVCTHHIYMEEEAKPVRQPQRRLNPH FT MQEVVRAEVLKLLQAGIIYPISDSPWVSPTQVVPKKSGITVVQNDKGEEVS FT TRLTSGWRVCIDYRKLNVVTRKDHFPLPFIDQVLERVSGHPFYCFLDGYSG FT YFQIEIDVEDQEKTTFTCPFGTYAYRRMPFGLCNAPATFQRCMLSIFSDMV FT ERIMEVFMDDITIYGSTFDECLVNLEAVLNRCIEKDLVLNWEKCHFMVHQG FT IVLGHIISKQGIEVDKAKVELIVKLPSPTTVKGVRQFLGHAGFYRRFIKDF FT SKLARPLCELLVKDAKFVWDDRCQRSFEELKLFLTTAPIVRAPNWQLPFEV FT MCDASDFAIGAVLGQREDGKPYVIYYASKTLNEAQRNYTTTEKELLAVVFA FT LDKFRAYLVGSFIVVFTDHSALKYLLTKQDAKARLIRWILLLQEFNLQIKD FT KKGVENVVADHLSRLAIAHNSHSLPINDDFPEESLMLIEVAPWYAHIANYL FT VTGEVPSEWKAQDKKHFFAKIHAYYWEEPFLFKYCADQIIRKCVPEQEQQG FT ILSHCHESACGGHFASQKTAMKVLQSGFCWPSLFKDAHTMCRSCDRCQRLG FT KLTRRNMMPLNPILIVDLFYVWGIDFMGPFPMSFGYSYILVGVDYVSKWVE FT AIPCKRNDHRVVLKFLKENIFSRFGVPKAIISDGGTHFCNKSFETLLAKYG FT VKHKVATPYHPQTSGQVELANREIKNILMKVVNTSRRDWSVKLHDSLWAYR FT TXYKTILGMSPYRLVYGKACHLPVEVEYKAWWAIKKLNMDLSRAGMKRFLD FT LNEMEELRNDAYNNSNIAKQRLKRWHDQLVSRKEFQKGQRVLLYDSKLHIF FT PGKLKSRWIGPFTIQQVYSNGVVELLNSNSTGSFKVNGHRLKPFVEPFSRD FT KEEIILLEPHQA" XX SQ Sequence 9526 BP; 2708 A; 2024 C; 2125 G; 2660 T; 9 other; aatggcgtcg ttgccgggga tggtgccact tcacagtgat atgatctttt cagaacactt 60 gtgatcttca tcacaagttt ggtgattttt cttttctttt actaactctt tttatttgtt 120 tttattttag tttatctttt atttagtttt tagttaacct taattttttt tttctttcta 180 gaattgtttt tcttttgttt tgtttttttt ttttttttgt ttttgtttca gttattgcta 240 gttgtgcatg ccctattgga tacgagacag tgagggaaga cttgtgaaaa tcraaactcc 300 tcacgaaaca gagttggaat tgtgtgtgaa cgtcatggaa gctacacctg aagatcagca 360 tagtcaacat gctcaagagg agaatttcaa cgcataccga tccatgaggg accgcatgca 420 tccacctcgt atgagtgcac cgtcatgtat agtgccacct acagagcagc tagtgatccg 480 accacatatt gtgccacttc tacctacttt ccatgggatg gaaagtgaga atccctacgc 540 gcatatcaag gaatttgagg aggtttgtaa tactttccaa gaaggaggag cttcaatcga 600 cttgatgagg ctcaagctat ttcctttcac tttaaaggat aaggccaagg tctggcttaa 660 ttctttaagg ccaaggagta tccgaacttg gactgatttg caagctgaat ttctcaagaa 720 atttttcccg actcatagga ccaatggctt gaaaaggcaa atttcaaact tctcagctaa 780 agagaatgag aaattctatg agtgttggga gagatacatg gaagctatca atgcttgtcc 840 tcaccatggc tttgatacat ggctattggt gagctatttt tacgacggta tgtcttcctc 900 aatgaagcaa ctcttagaaa cgatgtgcgg aggagacttc atgagtaaga atccggagga 960 agccatggat ttcttgagtt atgtggctga agtttcaaga ggatgggatg agccgaatgc 1020 cagagaagtg ggaagaatga agtctcaacc taatgctcct aatgctaagg ctgggatgta 1080 tactttgaay gaagacatcg atatgaaagc aaaagttgca gctatggcaa gaagattgga 1140 ggagctagaa atgaagaaga tacgagaagt gcaggccatt tctgaaacac cagtgcaagc 1200 tatgtcgtgt tccatttgtc aatcttttga gcacttggtg gaggagtgtc ctacgattcc 1260 agctgtgaga gaaatgtttg gggatcaagc aaatgttatt ggacaattta agcccaataa 1320 caatgcttca tatggcaaca cctacaattc aaattggagg aaccatccga atttctcttg 1380 gaagccaagg gcacctcagt acacgcaacc tggccaagca cctccgcaag cctcgaatct 1440 tgaacaagcc attgtgaatc ttagcaaggt cgtgggagac tttgttggag accagaaatc 1500 catcaatgct cagctcagtc aaagaattga cagtgtagag agtacattga acaaaakgat 1560 ggatgggatg caaaatgatc tatctcagaa gatagataat ctccagtact caatctcaag 1620 gctcaccaat ctcaacacag tgcaagagaa aggaaaattt ccttctcaac ctcatcagaa 1680 tcccaagggt atccatgaag tggaggctca ggagggagaa tcttcacagg tgagggaagt 1740 caaagcagtg atcactctaa ggagtggtaa agaggttgat ctgcctacat ccaagccaga 1800 gcatgaacca gagagtgaag cagagaaaga gaagagggag gaaatcaaag gaaagagaaa 1860 agggaacagt gcaaagaagg aggaccttga atctactgtg aatgaagaac cggagaggac 1920 catcaaccag gaagatatga tgaagaaaca cacgcctcca cctttccccc aagctttgca 1980 tggaaaaaag ggaatcaata atgcatcaga aattcttgaa gtgttgaggc aagtgaaagt 2040 taacatccct ttgctagaca tgatcaaaca agttccgact tatgcaaaat tcctgaagga 2100 cttatgcact ataaaaagag ggttgaatgt gaataagaaa gccttcttaa ctgagcaagt 2160 aagtgccatt atacagtgca agtctccagt gaaatacaaa gatccgggtt gtcctaccat 2220 ctcagtgatg attggagaga cgtgtgtgga gaaagctttg ttggacttgg gggcaagtgt 2280 gaatttgcta ccctactctg tctacaagca attgggactt ggagagttga agccaacatc 2340 aatcactcta tctctagcag atagatctgt gaaaattcca agaggcatga ttgaagatgt 2400 cctagttcaa gttgacaaat tctactaccc agtggatttt gttgttcttg atacggaccc 2460 gattgccaaa ggaactaact rtgttcctat catacttgga agaccattcc tagctacatc 2520 aaatgctatc atcaattgta ggaatggagt catgcaactt acatttggca acatgacgtt 2580 agagctcaac atcttctatt tgtgcaagaa acaattccat ccggaagaag aagaaggacc 2640 agaagaggtg tgcatgattg acaacttagt ggaggagcat tgtgatcaga aaatgctcga 2700 agatttgaac gagagtcttg gggatcttga tgaagggtta cctgaaccct cagatttgct 2760 tgctactctg cccccttgga agaggaggga agaaattctc cctttattca atggggagga 2820 gacacaagaa gctgttaagg aggagccccc aaagcttatt ctgaagccat tacccacgga 2880 gttgaagtat gcatacctgg aagaaaacaa gcagagccct gttgttattt cttcatctct 2940 taccactact caggaggatt gtctacttga agtcctcagg agatgtaaga aggcgatagg 3000 gtggcaaatt tctgatctga aagggatcaa ccctttagtc tgtacccatc atatatacat 3060 ggaagaagaa gctaagccag ttcgtcaacc ccagagaagg ttgaaccctc acatgcaaga 3120 ggtggtgcga gctgaagtgc ttaagctact tcaggccggt attatctacc ccatatcaga 3180 tagcccatgg gtgagtccta cgcaagtcgt gccaaagaaa tcagggatca cagtggtgca 3240 aaatgataag ggagaagaag tttctacacg cctcacttca ggttggaggg tgtgtattga 3300 ttatagaaag ttgaatgttg taacaaggaa ggaccacttc ccgttgccgt ttattgatca 3360 agtgcttgag agggtctctg gccatccatt ctactgtttc ttggatggct actccgggta 3420 ttttcaaata gaaattgatg ttgaagacca ggagaagacc actttcacat gtccattcgg 3480 aacctacgca tacagaagaa tgcctttcgg cttatgcaat gcaccagcaa cattccaaag 3540 atgcatgtta agcattttca gtgatatggt ggagcgtatt atggaagtct ttatggacga 3600 tatcaccata tatggaagta cgtttgacga atgcttagtc aacttggaag ctgttctgaa 3660 ccgatgcatt gagaaagact tggtgcttaa ctgggagaaa tgtcatttca tggtacacca 3720 agggattgtc cttgggcata ttatctcaaa gcaaggcatt gaagtggaca aagcaaaggt 3780 tgaacttatt gtcaagttgc catcgccaac aactgtcaaa ggagtaaggc aattccttgg 3840 ccatgctggg ttctatagga ggtttatcaa agatttctct aaacttgcaa gacctctttg 3900 tgaactattg gtaaaggatg ctaaattcgt atgggatgat cgatgtcaac ggagttttga 3960 agaactgaag ctatttctga caaccgctcc aatagtgaga gctcccaact ggcaattgcc 4020 ctttgaagtg atgtgcgatg ccagtgactt tgctatagga gctgttcttg ggcaaagaga 4080 agatggaaag ccctatgtga tctactatgc gagcaaaacg ttgaatgaag cgcaaagaaa 4140 ctacacaacc acagagaaag aattgttggc tgtagttttt gccttagaca aattccgcgc 4200 ttacttggtg gggtctttca ttgtggtttt cactgaccac tcggccttga aatatctgct 4260 gactaagcag gatgcaaaag cgaggctgat tagatggatt ctcttgcttc aagagttcaa 4320 tcttcagatc aaagacaaga aaggagtgga gaatgtggta gccgaccatc tgtcaaggct 4380 agccatcgca cataattccc atagtttgcc aattaatgat gattttccag aggagtcact 4440 catgttgata gaagtcgctc cttggtatgc tcatattgct aactatctag ttaccggaga 4500 agttccaagt gagtggaaag cacaagataa gaagcacttc tttgcaaaaa ttcatgccta 4560 ctattgggaa gagccatttc tattcaaata ttgtgcggat caaataatac ggaagtgcgt 4620 ccctgaacaa gagcaacagg ggatcctcag tcattgccac gaaagcgcat gtggaggcca 4680 ctttgcttct cagaagacag ctatgaaggt attgcaatcg ggtttttgct ggccatcact 4740 tttcaaagat gcccacacca tgtgcaggag ctgtgataga tgccagaggc ttgggaaatt 4800 aacacgtagg aacatgatgc ctttgaaccc cattttaata gttgatcttt tttatgtctg 4860 gggcattgac ttcatgggac cttttcctat gtcctttggc tactcctaca tcttggtggg 4920 agtagattat gtttctaaat gggttgaagc gatcccgtgc aaacgcaatg atcacagagt 4980 tgttctcaaa tttctcaaag agaacatctt ctctagattt ggagtaccca aggccataat 5040 cagtgatggg ggtactcatt tttgtaacaa gtcgttcgaa actctcttag ccaagtacgg 5100 ggtgaagcat aaggtagcta caccttacca ccctcagact tctgggcaag ttgagttagc 5160 aaatcgggag atcaaaaaca tactgatgaa ggtggtgaat acgagcagaa gagattggtc 5220 tgttaagctt catgattcac tatgggctta cagaacarct tacaagacca ttcttggaat 5280 gtctccttat cgcctagtct atggcaaagc gtgccatctc cccgtggaag tggaatacaa 5340 agcttggtgg gcaatcaaga agctcaacat ggatttgagc agagccggca tgaagaggtt 5400 cttagacctt aatgagatgg aggaactgag aaatgacgcc tacaataatt caaacattgc 5460 aaaacaaaga ttgaagaggt ggcatgatca gttagtctcc cgcaaagaat tccagaaggg 5520 acaaagagtc ttgctgtatg actctaagct ccacatcttc ccgggaaagt tgaagtcaag 5580 gtggataggt ccttttacta tccaacaagt gtattcaaat ggagtagtgg aactactcaa 5640 ttccaacagc accgggagtt tcaaagtcaa tggccatcgt ctcaagccat tcgtggagcc 5700 tttttctcga gacaaggagg aaatcatcct ccttgagcca catcaagctt aacaagacaa 5760 atggttagat ggacttagtc tgtcggaaga cattaagtcc ataatttttt tttgttttaa 5820 tgttgattta aagttttatt gatttagtac ttgttttaaa ttgtaatttc ttgctttaat 5880 tttattttgt tgtgatttaa tttaattttt gatgatcaat tgcaggtgga ttccaaaaca 5940 gatgggaaaa agctttaaaa atttttctgg caaagtcaga aaaacagagc atttcgcaca 6000 ccttgcgaaa atttcgcaag gcttgcgaaa atcccaaaaa tcaatttgca aggggtgcga 6060 aaatttcgca acaccctgcg aaaatttcgc aaagcctgcg aaaaatttcg caaacccagc 6120 tttgccttgc gaaattgctt tgttttgcra aaatcccttg cgaaaacctr tgcgaaatta 6180 gaaagggtgt gcgaacccat ttcgcaagcc cctaaaatcc atttsgcaag cctgtgcgaa 6240 ttccaaaagc ccgtgcgaaa accaaaggtc acttaaaagc ctatttaaag acctccaagc 6300 cctgttttca tttcgcacac cccatctgct cattgcgaaa agccctccat caccttgcga 6360 cgcccaagct tccatcggtt ttctctccat tggacgcccc gcggccaacc atttgaagag 6420 gcgacctaca cctctcactc catttcrgac atggcgcgca ttagaggagg ccataccgac 6480 ccttcattat ctcgcgagcc gaggccaaga gcctcctctc ctcaggattc aacatctcag 6540 gcccctgagg ccccgaccat tccatcttct gagggtggag tgccctctaa ccctcctcag 6600 cgccgatatg cgacacggag accaccgact tctccacccc ctgagccatc agtacgtcgc 6660 attccaccta agagagccag gacctcaggc cctggagagt cgtctaggca ttcacagcct 6720 gatcctcagg cccctaccga ttctcagcgt ccttccggca tttcaccgga agccatcatc 6780 aagaggccta tggtcaccgc gccgcccatt gagggcaatt cagattgtag agccagacca 6840 tttcattctg agctttattt tgaccttgag gccatgcgac agcagccgga gcttcgggat 6900 tcatttggac tgctccagag gtaccatctc gagcgcctta tgactcccag ggagttcttc 6960 taccccagag tggcaatgga cttctatcag tccatgacta ctcagggcgc ccagagtcct 7020 accgccattc atttcagcat tgatgggcgc cagggtatcc ttgaggctag acacattgct 7080 gaggctctcc atattccata cgagccagtg gatccagcac atttccggga gtggtcccct 7140 atatctcagc gggacatggt ccgcatccta tccaggggga cttctggaga ttcattcctt 7200 ctacgtaagg agcttccatc tgggatgctc ctagtagatg tgttgttgcg gtccaacatt 7260 tttcctcttc agcatctagt gcagaggcga ggagccatcc tggacgcttt attcaggata 7320 tctgagggct tctattttgg gccacatcac ttgattatgg ccgctctcct ccactttgag 7380 gagaaggttc acaggaagaa gctacagaga gccgacacta ttccactatt gtttccgagg 7440 ctgctctgtc acatattgga gcatatgggc tatcctactg agccccacct tgagcgccgc 7500 caccattgtc gagagcattt cactctcgac aaatggacac agttggcagg ttattcagca 7560 cctctaggag ccccacccag gccagcacct ccagtgccac cacaggctga gcaggcacag 7620 caggatgagc ttcccacaga gtctgtacca cctgcccctg ctgcaccacc tatgcctgag 7680 gccacttcta ctgctcctcc taccactcct cctgttccac cagttgcacc ttctacatcg 7740 gaggcctcca tcaccatttc tgccacagag tttcgtgcca tggtacattt gttccagaca 7800 ctgaccacta cacacaatgc tttattccgg cagatggccg acatacgtgc tcagcaggac 7860 cagcatactg ctatccttcg tcagattcag cagcatctgg gacttctgcc accacctcag 7920 actgacattc ctggaccatc agagcccata gctccagctg aggagaccac cagagccgat 7980 gtcccgctcc aggccactca cgaggcagcc atagagccat catctccacc agagaccccc 8040 gctacttgat catttcttta ttttgtattt acttattata ttagtagaca taattacttg 8100 ttttgatatt ttatattctg ggattggatg tattacatga tcatatctca cattgtactt 8160 tctcagagta atatatacac atcatttttg tttatacttg gcattttttc tatttccttt 8220 actcattaat cttttgtttt ttgaatcatg tggtttctcc tatacgactc agactccatg 8280 tcactcagga ggtaccactt cctcccttta tttacaatcg ctcttgccac attgagggca 8340 atgttgatct tggttggggg gagagttaag gaaggaagtt ttgttaataa tgctaggtta 8400 ttttgttaat ttagtacttt ttgcttaatt ttaaaagttt ttactctact ctccatgatt 8460 attaaggaaa aattctcaaa atgaaatggg agaaattgaa ttcttacctt tttacttgaa 8520 tattagagtt tgtattatgc ttattgaggt tgatgaatta ttgaaactcc tattgaattc 8580 aaccttattt cttccacttt aatcttacca cacactgtgc acattaggtt ccgtttataa 8640 gatgaaaaac tatctcaccc cctgaactta ggaaaattta gacttggtac ctttgacctc 8700 gttttaatag tgttgggaca ccttataaaa ggccaatgag cctttgaaaa aaaaaaaaaa 8760 gaaagaacaa agtgttacac ttgctttgaa acccgagcaa ggtccgaggg gtatatggtg 8820 aaaatcttta aaacccggtg ccctaagcct ttattggttg ggagtcaccg acctcaatgc 8880 tcgttacaag ggtgaatagg tggagtttaa catattgtag gtgcttgggt attaaatttc 8940 aatctcaaaa gtccggggta aaatctgagg agttagtggt cgaaagatcc ttaaagcttg 9000 atgccctaaa ccttgattgg ttgggagtca tcgatggatc cccgttacat ggacacttta 9060 gaaaacaata cctttagcat tgcacaccta caatgaaaaa aaattgtgaa ataaaagagg 9120 tgcgttctta gcctattgga ggttggtcag tttgctaaag tttgagaaag aactaggttg 9180 gggggagaga ttagttcagc atactatatt cggaaactaa taagcttaac acatagattt 9240 ttgtggaaga gtaatgattg agcctatgag agtggaaatc cttttaatac ttaaatttgc 9300 ataatgccta ctctttatga attgtgatca ggcaagatat ttgataaact cttgttgaag 9360 gttgagtttt gcttctttaa tgttccatga gagagtatgc tctacatcat gccacttgaa 9420 aattttttgg agtgatcagc atgattttgt aaattatttt actgtctatt tttttttttt 9480 ctctccttca ttgctaaggg actagcaata tgtcggttgg ggggag 9526 // ID Harbinger-3N1_VV repbase; DNA; EDCOT; 280 BP. XX AC . XX DT 05-FEB-2009 (Rel. 14.03, Created) DT 05-FEB-2009 (Rel. 14.03, Last updated, Version 1) XX DE Harbinger-1N1_VV, non-autonomous DNA transposon - a consensus DE sequence. XX KW Harbinger; DNA transposon; Transposable Element; PIF; TIR; MITE; KW mPifvine-3.1; Harbinger-3N1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-280 RA Benjak A., Boue S., Forneck A. and Casacuberta J.M.; RT "Recent amplification and impact of MITEs on the genome of RT grapevine (Vitis vinifera L.). submitted."; RL Repbase Reports 9(3), 707-707 (2009). XX DR [1] (Consensus) XX CC Harbinger-3N1_VV (mPifvine-3.1 in [1]) is a non-autonomous DNA CC transposon of the MITE type. It is a deletion derivate of the CC autonomous Harbinger-3_VV. Individual copies are >90% identical CC to the consensus sequence. TIRs are 18 bp-long and flanked by 3 CC bp-long TSDs. There are approximately 1300 highly conserved CC copies present in the genome. XX SQ Sequence 280 BP; 105 A; 30 C; 30 G; 110 T; 5 other; ggtggtgttt gtttttttgg ctttttgctg aaaaccattt agttttagaa tttaggttgt 60 ttgtttttbt actttttcat gacttattat aaacttttta ctaaatagaa aaagccaaaa 120 atatgtrgct ttttctaaat agaaaaaata acanahtggt ttttttttac tttttaatac 180 ttaatagaaa taaaaatact acaaaaacaa acaacctaat atttaatact attaaghatt 240 aaggttctat ttagaattaa gtaaaaaaac aaacaccacc 280 // ID Copia27-PTR_I repbase; DNA; EDCOT; 4224 BP. XX AC LG_XIX; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia27-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4224 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4224 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 228-228 (2007). XX DR Genome; LG_XIX; Positions 1014128 1018351. XX CC Positions [1504-2034] - Integrase core CC 'CCGAC' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 55..4185 FT /product="Copia27-PTR_I_1p" FT /translation="MQQQRNMTPEGNFVQPAIPRFDGHYDHWSMLMENFLR FT SKEYWGLIENGYVETESGIEQTEMQRKRIDELKLKDMKVKNYLFQAIDRTI FT LETILVKDTSKQIWESMKKKYEGSARVKRSHLQALRREFETLEMKAGEGVS FT EYFSRVLTVANKMRIYGERMTDVTVVEKILRSLSEKFNYIVCSIEESKDID FT QLSIDELQSSLIVHEQKFQRHTGEEQALKITNSEDRFNARRRGRGAAYRGR FT GRGRSSQFYNNKATVECFKCHKLGHFQYECPSWDKEANYAELGEEEEMLLM FT SYVDMNHTRREDVWFLDSGCSNHMCGDKSLFHVINENFRQKVKLGNNTRMD FT VLGKGNVKLKVNGLTHVVSDVFFVPDLKTNLLSIGQLQDKGLTILIQHGYM FT NIYHPEKGLIIHTEMTANRMFVLLTNSLHQKPACLYNSTPDLAHLWHCRYG FT HLSYKGLRTLQAKNMVHWIPQFKIPSTVCATCMIGKQHRDPIPKHNNWRAT FT EKLQLIHADLCGPISPISNSKKRYIICFIDDFTRKAWTYFLVEKSEALHMF FT KRFKNYVEKEIGGYIKCLRTDRGGEFTSFEFNEYCIEHGIKRQLTAAYTPQ FT QNGVAERKNRTTMNMVRCMLTERRIPKNLWPEAVNWTIYVLNRSPTLAVQN FT HTPEEAWSGIKPSVEHFRIFGCMAHVHIPNVRRTKLDAKSIPCVLLGLSEE FT SKAYRLYDPVEKKIVISRDVVFDEEKSWDWDQSYNEQLVADLECGDEGVTG FT TSMNEEDIPEELEHGADSNEDLIASFQPGENRGESSSLHENLLGSPQSRPQ FT LGENSRASPGYYGGSSQHGENRGESSVFHERRVRGPPRWIRDYVTGELSEE FT EDANVNLILFTSTDLVQFEDAVKYEHWRTAMDIEIKAIERNNTWELTDLPA FT GAKTIGVKWIYKTKLKEDGEVDKFKARLVAKGYVQQQGIDYTEVFAPVARM FT DTVRMIVALAAHKGWILYQLDVKSAFLHGELNEEVYVEQPKGYENKQNPQQ FT VYKLKKALYGLKQAPRAWFSRIEAHFINEGFEKCYSEHTLFIKTDREGNIL FT IVSLYVDDLIFTGNNELMFAEFKTSMLREFDMTDLGRMRFFLGIEVLQRPE FT GIYICQRKYASEVLKRFKMENSNSVHNPIAPGCKLYNDENGACVDETLFKQ FT MVGCLMYLTATRPDLMFAVCLISRYMAKPTKLHLLAAKRILRYLRGTTELG FT IFYKKGGREGLIGYTDSDYAGDLEDRKSTSGYAFMMGSGAVAWSSRKQPIV FT TLSTTEAEFVAAAACASQAVWMQRILEKLSLKESKGTTIFCDNSSTIKLSK FT NPVLHGRSKHIDVRFHFLRDLTREGAVELVYCGTQEQLADIMTKPLPLAAF FT QKFRNQLGVCEIPE" XX SQ Sequence 4224 BP; 1428 A; 706 C; 988 G; 1102 T; 0 other; ttgtggtatc agagcctttc tacttaaatc aaagcagcag tctttgagtc tcctatgcag 60 cagcaaagaa atatgacacc ggaaggaaat tttgtacagc cagccattcc tcgttttgat 120 ggccattatg accactggag catgttgatg gagaatttct tacgctctaa ggaatattgg 180 gggttgatag aaaatggcta tgttgagact gaaagtggca tagagcagac agaaatgcaa 240 cgaaagagga ttgatgagtt aaagctgaaa gacatgaagg tgaaaaatta tctttttcaa 300 gctatagatc gaacgatatt ggaaaccatc cttgtaaagg atacttccaa acaaatctgg 360 gaatcaatga aaaagaagta tgaaggaagt gcaagagtca aaagatcaca tctgcaagct 420 ctccgcagag agtttgaaac cttagagatg aaagctggtg aaggagtctc tgagtatttc 480 tccagagtgc tgacagttgc taacaaaatg agaatatatg gagagcgaat gactgatgtt 540 acagtggtgg agaaaattct cagatcattg agtgaaaagt ttaattatat tgtttgttca 600 attgaagaat ccaaagatat tgatcaactc tcaattgatg aactccagag ttccttgatt 660 gtccatgagc agaaatttca gcgtcacaca ggagaagaac aagcactcaa gatcaccaat 720 tctgaagata gattcaatgc cagaaggcga gggagaggtg ctgcatacag aggcagaggc 780 agagggagaa gcagtcagtt ctacaacaac aaagcaacag tggagtgttt taagtgccat 840 aagcttggac actttcaata tgagtgtcca agctgggata aagaagctaa ttacgctgaa 900 ctaggagaag aagaagaaat gttactcatg tcatatgtgg atatgaatca tactcgaagg 960 gaagatgtct ggtttttaga ctctgggtgc agtaaccaca tgtgtggtga caagagccta 1020 ttccatgtga taaatgagaa cttcagacag aaggtaaagc tgggaaataa cacacgaatg 1080 gatgtgttgg gaaaaggcaa cgtgaaattg aaagtaaatg gtcttacaca tgttgttagt 1140 gacgtattct ttgttcctga tttgaagact aatcttctca gcattggtca acttcaagac 1200 aaagggttga caatcctaat tcaacatgga tatatgaaca tctatcatcc ggagaaaggg 1260 cttattatac atactgaaat gacagcaaat agaatgtttg tgctattaac aaattcacta 1320 catcagaaac cagcctgcct ctataactca acaccagatt tagcacattt gtggcactgt 1380 cgatatggac atttgagcta caaaggattg aggactcttc aagcaaagaa catggtgcat 1440 tggatacctc agttcaagat tccatccaca gtatgcgcta cctgcatgat tgggaagcag 1500 cacagagatc ccattccaaa gcacaacaat tggagagcca cagagaagct tcagctcatc 1560 catgcagatc tctgcggacc gatatctcct atttctaaca gcaaaaagag gtatattata 1620 tgctttattg atgactttac tagaaaagca tggacttatt tcttagtaga gaaatctgaa 1680 gcattacata tgttcaaacg ttttaagaat tatgttgaaa aagaaatagg gggctatata 1740 aaatgcttaa gaacagaccg aggaggggaa ttcacatcct ttgaattcaa tgagtattgc 1800 attgagcatg gtatcaaacg gcagttgaca gcagcatata ctccacagca gaatggagtg 1860 gctgaaagaa aaaacagaac aacaatgaat atggttcgtt gcatgctaac tgaaaggaga 1920 attcccaaga atctctggcc agaggcagta aattggacaa tatatgttct caatcgaagt 1980 cctactttgg cagttcaaaa tcacacacct gaagaagctt ggagtggcat caaaccttca 2040 gttgaacact tcaggatctt tggatgcatg gctcatgtac atattcctaa tgtacgaagg 2100 acaaagctcg atgccaaaag cattccttgt gtgctactag gactcagtga agaatctaag 2160 gcttacagac tttatgatcc agttgagaag aagattgtaa tcagcaggga tgtggtattt 2220 gatgaagaaa aatcttggga ctgggaccaa agctataatg aacaattggt ggctgaccta 2280 gagtgtggag atgaaggtgt tactggaaca tccatgaatg aggaagacat tcctgaagaa 2340 ctagaacatg gagcagattc aaatgaagac ttaattgcta gttttcagcc tggtgagaat 2400 cggggagaat catcaagttt acatgaaaat cttcttggca gtcctcaatc taggcctcaa 2460 cttggtgaga atagcagggc atcgccaggt tattatggtg gcagttctca acatggtgag 2520 aacaggggag aatcatcagt ttttcatgaa agaagagtta gaggacctcc aaggtggata 2580 agagattatg taactgggga actttcagag gaagaagatg caaatgttaa cttgatttta 2640 tttacttcaa cagatctagt acagtttgaa gacgcagtaa aatatgaaca ttggaggaca 2700 gcaatggata ttgaaatcaa ggccatagaa aggaacaaca cctgggaact tactgatctg 2760 ccagcagggg caaagacaat tggagtaaaa tggatttata agaccaaact aaaagaggat 2820 ggagaagtag acaagttcaa ggcaagattg gtggctaaag ggtatgtgca gcaacaaggg 2880 atagactata cagaagtatt tgcaccggtt gcaagaatgg atacggtgag aatgattgtg 2940 gccctagcag ctcacaaagg atggatatta tatcagcttg atgtcaaatc tgctttcctg 3000 catggagaac ttaatgaaga agtctacgta gaacagccaa aaggttatga gaacaagcag 3060 aatccacagc aggtatacaa actgaaaaaa gctctttatg gactgaaaca agctccaaga 3120 gcttggttca gccgtattga agcacatttt ataaatgaag ggtttgagaa gtgttatagt 3180 gagcatactt tgttcattaa aactgacagg gaaggtaata ttcttattgt cagtttatat 3240 gtagatgatt taatatttac tggcaataat gaattgatgt ttgctgagtt taagacatca 3300 atgttgaggg agtttgacat gactgatcta ggaagaatgc gtttctttct tggcattgaa 3360 gttctacaga gacctgaagg catttacatt tgccaacgaa aatatgcttc agaggtatta 3420 aagagattta agatggaaaa cagcaactca gtccataatc ctattgcccc gggatgtaaa 3480 ctttacaatg atgagaatgg agcttgcgtt gatgaaactt tatttaaaca aatggtgggc 3540 tgtctcatgt atttaacagc tacaagacca gatttaatgt ttgcagtttg tttaattagc 3600 agatatatgg ctaaaccgac taagttacac ttattggctg ccaagagaat tctgcgctac 3660 ttaagaggaa ctactgaact tgggatcttc tacaagaagg gagggcgtga aggattaatt 3720 ggatacactg acagtgacta tgcaggtgat ctagaagaca ggaaaagcac atctgggtat 3780 gccttcatga tgggatctgg agctgttgcc tggtcttcaa gaaaacagcc tatagtcaca 3840 ctttcaacca ctgaagcaga attcgtggct gcagctgctt gtgcttcgca agctgtttgg 3900 atgcaaagaa tacttgagaa actaagtctg aaggaaagca agggcactac aattttctgt 3960 gataacagtt ccacaattaa gttgtccaaa aaccctgtgt tacatggtcg cagcaagcac 4020 attgatgtgc gattccattt tcttcgtgat cttacacgag aaggagcagt tgaattagtc 4080 tactgtggaa cacaagaaca gctggcagat ataatgacaa aacctctccc attagctgca 4140 ttccagaagt ttagaaatca gttgggagtc tgtgaaattc ctgaataaac tagtaacagc 4200 tgggaactag tttaagggag ggaa 4224 // ID Gypsy-41_Mad-I repbase; DNA; EDCOT; 6608 BP. XX AC . XX DT 18-OCT-2010 (Rel. 15.1, Created) DT 18-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-41_Mad-I. XX NM Gypsy-41_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6608 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1776-1776 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS join(712..1416,1284..2171) FT /product="Gypsy-41_Mad-I_1p" FT /translation="MGREVKRNDRITNPVKKDNPARLGRKWYVVGKNGQPA FT KQMGASMVRRVQRQHKAYMNSLKTPATSEASKNQKLEKTSSGGSSQLRWRS FT KKEVERANSKTEGEGNHVPQSLHPGKYRILRRAQEDMIMVPTPGWKTEPIC FT FGTVSPERKPPSLSLVDPFGEVPKQTPYSGMNQQEGAPEPLLPADAMAWLD FT EFMDQIGSKKEDCQSLAIFISTWRMCYPPCLVPNLISPPLWKVIMVHGPDW FT EQERRLPEPSNFHINMAYVLSAMFGAEPDQPATMEGDYVTTEPMMAHVSVE FT VAEEGESGKAESSEASKDGPLRIYTDKMVFSRPNISLANHLKPIYVTAHLE FT GVPFKRILIDGGAAVNVLPAKQMKKMGRGTEDLIPTDLTVSSFSGAITKTH FT GILPLEVDLGSKQIMLAFFVVDCTSTYGALLGRDWIHQSLAIPSTLHQQVA FT VYHEAGTEGPGFWEMVEAESRPFLPTANVAEASFYNPNVGILKCSGADENG FT RPTKVTAQKLLEQGMLLTREEWDRPCIVPTPLHHQ" FT CDS join(2171..2917,2890..4389,4302..5879) FT /product="Gypsy-41_Mad-I_2p" FT /translation="MTEQKRKDQVMAVRSLIKRLLVYGKGRRQERELLDKE FT EQEWQVGASTSQDESREESCGEELERAIQMAECIYDLDGPDDLPESPELVE FT FLCAEPDKPPPEVQDPLEVIDLGTEEDPRPIQISGLLETDDRAKIICLLQE FT FKDCFAWHYTEMPGLDSTLVEHRMPIKEGYKPVKQAPRRMSKEIEEKVKEE FT IERLVKAGFIRPAKYVEWLANIVPVLKAITKAVRCCVDYRNINGATPKDEY FT PMPMAIYPVSHAHGDLSIDAVAKHKVLSFMDGNAGYNQIKMAPEDIHKTAF FT RCPGHVGAYEYLVMPFGLKNAGATYQRAMNAIFHDLIGQNMEVYIDDIVVK FT SKTEEQHLIDLRQALTRMRIHKLKMNPKKCAFGVRAGNFLGFLVHQRGVEV FT DKNKSRAIMESPSPTNKVQLQRLLGKINFLRRFIANLAGKIQPLTPLLRLK FT DKENFEWGPPHQKAFDSIKAYLTSPPVLVPPQRGKPLKLYISASEKSIGSL FT LAQNNEGGKEQAVYYLSRILTEVETRYSPVERLCLALYFTASKLRHYMLPC FT HVHIIAKTDVIKYMLSKPMLTGRIGKWILALSEFSFQYVPQRAVKGQAIAD FT FLAEHQESQDEIINIPGTLEVTSVWIPPGKGISGKEEWVQQEIRRVTGLWI FT TPWKLYFDGSYTQKASGAGIVIINPQGVYHYYSFLLDYQGNTNNRAEYEAL FT IIGLEILMDLGAVEVEVFGDSELVINQLNGEFKCRHITMAGITWRPRNCFR FT VGNKPAKWGVQVQTYHHGGYYLAATQLLSYWDSEISVNHVPRGSNLAANEM FT AQLASGVPIQERKYGVDVEIQRRNLPSILERGFSLDVMVLETEIEDWRSPI FT IHHLKDPSSPTSKKNRQQATKYVLWAKNLLRKTPDGLLLKCLGQEESMRVM FT AEVHEGVCGAHQAGTKMRWLLRRYGYFWPDMEKDCKSYARGCEECQRHGPL FT QHVPSVPLNPVVKPWPFRGWAMDFIGQIYPASSKGHTFIIVATDYFTKWVE FT ASAVKSITSAAVKNFIETKILHRFGVPETIVTDRGPSFISKEVEEFASKYK FT IKMIQSSPYYPQSNGQAEASNKILVNIIKRMVIDSPEKWHEKLGNTLWAYR FT TSKRAGTGTTPYALTFGQDAVLPMEINVSSVRIQNQFGLHSEEYIEAMCQG FT IEDLDVARIEALNQIQEGKKAVARAYNKKVKMKSFKEGDLVWKTVLPLGAQ FT LRGFGKWSPTWEGPFIVSRVLDKGGYYLADLEGNWQKHPINVKFLKKYCPT FT LWDVRDCYIEEDAR" XX SQ Sequence 6608 BP; 2069 A; 1309 C; 1741 G; 1489 T; 0 other; tagttttggc acgcccggtg ggatcctttg atcaaaagaa atatgtcaaa agtaccagaa 60 gatttgcaaa ctaccttgtt gcaaatgttg caaagattgg agaacgcctc cgcaggctcc 120 agaagggaag cagacctggt tataagacca actattccta tatctttacc tcaacttggg 180 gaaaaagatg atagggaaaa agagagactt aaaaccagcc agccagaaga agcggtggtg 240 gacaaacatg cagatccctt ctcagaggcc cctgtaaata tgatcagtat ggcatgggcc 300 gagaagggga aagaaaaggt cacaagggac agaagaagga agactggctg acaaacccac 360 aaaaggggtg atcaaattgc ccgaacatcc aaaagcagcc ataatcaaag ggatggttct 420 gtgcagtaag tgccaatgcg agtgtgagct cgaaataccg ccagcaggag tcctcattga 480 tcatgaactg atcaggagga aggaagaaga gaaagaaaag aggcccacga gaaggctagg 540 cggactgcag gaagggatac ttcccgaagt gtttttcagc ggttaggagg cgattcccaa 600 cccagagctt tatcagaagt atttcgaaac catgaagctt ctgaggaggc agaagataag 660 gaggccaaaa agccaaaaga gaggggtgta gggcatcctc aatatggcca tatgggaaga 720 gaagtcaaga ggaatgatag gataacaaat cctgtcaaaa aagataatcc tgcccgcctc 780 gggcgaaaat ggtacgtggt cgggaagaat ggacagcccg ccaaacaaat gggagcctcc 840 atggtcagaa gggttcagag gcagcacaaa gcctacatga attccttgaa gacccccgcg 900 acgtctgaag cctccaagaa tcaaaagttg gagaaaacgt catctggggg gagtagtcag 960 ctccgctgga ggagtaagaa agaggtggaa agggctaata gcaagacaga aggcgaagga 1020 aaccatgtgc cacaaagcct acaccctggg aagtatagga tcttgaggag agctcaagaa 1080 gatatgatca tggtgccaac tcccggatgg aagacagagc ctatttgctt tggaactgtt 1140 tcgcctgaaa gaaaaccacc ttctctatca ttggtggatc ctttcggtga agttccaaag 1200 caaacaccat attcgggcat gaatcaacag gagggggcac cagaaccact acttccagca 1260 gatgcgatgg cctggttgga tgagttcatg gaccagattg ggagcaagaa agaagattgc 1320 cagagcctag caattttcat atcaacatgg cgtatgtgct atccgccatg tttggtgccg 1380 aacctgatca gcccgccact atggaaggtg attatgtgac aactgagcca atgatggccc 1440 atgtcagtgt ggaggtagct gaagaaggag agtcgggaaa agctgaatca tctgaagcat 1500 ccaaggatgg tcctttaagg atctatacag acaaaatggt gttcagccgc ccgaacattt 1560 cgcttgccaa tcatctgaag cccatatatg ttacagctca tttggagggg gtgcccttca 1620 aaaggatttt gattgatgga ggagcagctg ttaatgtatt accagccaag caaatgaaga 1680 agatggggag aggcacagag gatcttattc ccacagacct cacggtttct agcttctcgg 1740 gcgctatcac caagactcat gggatattgc ctttagaagt ggatttgggg tctaaacaga 1800 tcatgctggc gttctttgtg gtggactgca cttccaccta tggagcctta ctcggaagag 1860 attggatcca ccaaagtctc gccataccct ccactctaca tcaacaagtg gctgtttatc 1920 atgaggcagg cacagaagga ccaggctttt gggagatggt agaggccgaa tcacggccat 1980 ttctccccac agccaatgtt gcggaagcaa gtttctacaa tcccaacgta ggaatcttga 2040 aatgttcagg agcagatgag aacggccgcc ctaccaaggt gacggcccaa aagcttttag 2100 aacaaggaat gctccttact agagaggagt gggatagacc ttgtatcgtc ccaacacccc 2160 tacaccatca atgacagaac aaaagaggaa agatcaggta atggcagtca ggtccctgat 2220 taaaagactg ttggtgtatg ggaaaggaag aaggcaagaa agggagctct tagacaaaga 2280 agagcaggaa tggcaggtag gagcttcaac cagccaggat gaaagcaggg aggaatcttg 2340 cggagaagaa ttggaaaggg ccattcaaat ggccgagtgc atatatgacc tagatgggcc 2400 agacgacttg cccgagagcc cggagttagt cgaatttttg tgtgcagaac ctgataagcc 2460 accaccagaa gtccaggatc ctttggaagt tattgatcta gggacagagg aggatccaag 2520 accaatacaa atcagtggtt tattggagac tgatgatcgg gcaaagatta tctgtctttt 2580 gcaagaattc aaagattgtt ttgcttggca ttatactgag atgccaggtt tagattcaac 2640 cttggtggaa cacagaatgc ccatcaagga gggatataaa cctgttaagc aagcaccacg 2700 aaggatgtca aaggagatag aagaaaaggt caaagaagag attgaaaggc tagtaaaagc 2760 tggatttatc agaccagcca aatatgtgga gtggttagcc aacattgtac ccgttttaaa 2820 agccataaca aaagcagtac gatgttgtgt tgattacaga aatattaatg gcgctacacc 2880 aaaagatgag tatcccatgc ccatggcgat ctatccatag atgcagtagc aaaacacaaa 2940 gtcttatctt ttatggatgg aaatgccggg tataatcaga taaagatggc cccggaagat 3000 atacataaaa cagcttttag gtgtcccggg catgtggggg catatgaata tctggtcatg 3060 ccattcgggc tcaagaatgc tggtgcaacc taccaaaggg caatgaatgc catctttcat 3120 gatctgattg gccagaacat ggaggtgtac atcgatgaca tcgtggtgaa atccaagaca 3180 gaagagcagc atctgataga cctcaggcaa gcattgacaa ggatgaggat ccacaaattg 3240 aagatgaatc caaagaagtg cgcgtttgga gtaagagcgg gcaacttctt gggattcctg 3300 gttcatcaaa gaggtgtaga agtggacaag aacaaatctc gggcaataat ggagtcacct 3360 tcacccacca acaaagtgca acttcagagg ctgctgggca aaattaattt cttaaggaga 3420 ttcattgcca atttagcggg caagatccag ccgctgactc ctttgctaag actgaaggat 3480 aaagagaatt tcgagtgggg accaccacac caaaaggctt ttgacagcat caaagcctat 3540 ttgacttctc caccagtgtt ggtaccacct caaaggggaa aacccttaaa gctatatatc 3600 tctgcttcag agaaatcaat cgggagtttg ctagctcaaa acaatgaagg cgggaaagag 3660 caggcagtgt actacctcag tagaattctg accgaggtag aaacaagata ttccccagta 3720 gagagattgt gcctagctct gtattttact gccagtaagc tgaggcatta catgttacct 3780 tgtcacgtgc acatcatcgc caagacagat gtgataaagt acatgttgtc aaagccaatg 3840 ctaacaggaa ggattgggaa gtggattcta gcattatcag agttcagctt tcagtatgta 3900 ccccaaaggg cagtcaaagg ccaagcaatt gctgacttct tggcggagca tcaagagtct 3960 caagatgaga taatcaatat cccgggaacc ctggaagtta ctagtgtttg gatcccgcca 4020 ggcaaaggta tctcgggcaa agaagagtgg gtccagcaag agataagaag agtgactggt 4080 ctctggatta ctccttggaa gctgtatttt gatggttctt acactcagaa ggcttcagga 4140 gctgggattg tgattataaa ccctcaaggg gtttatcatt attactcatt tctcctagat 4200 taccaaggga acaccaataa tcgggcagag tatgaggcct taataattgg tttggaaatc 4260 ttgatggatc tgggggcagt ggaggtagag gtgtttggtg attcagagtt ggtaataaac 4320 cagctaaatg gggagttcaa gtgcagacat atcaccatgg cgggtattac ttggcggcca 4380 cgcaattgct gagttactgg gattctgaga tatcagttaa tcatgttccc aggggatcca 4440 acctagcggc caacgagatg gcgcaactag cctcaggagt gccaatacag gaaagaaaat 4500 atggggtaga tgtcgagatt caaagaagaa accttccttc tatcctagaa aggggattca 4560 gtctggatgt aatggttcta gaaaccgaga tagaagattg gaggtcgcct atcattcatc 4620 atttgaagga tccctcttca cccacaagca agaagaatag acagcaagca accaagtatg 4680 tcttatgggc gaagaacctg ctaaggaaaa ctccagacgg gttactattg aaatgcttag 4740 gccaagagga atccatgaga gtgatggccg aagtacatga aggagtatgt ggagcacatc 4800 aggctggaac gaagatgagg tggttgctta ggaggtatgg gtatttctgg cccgacatgg 4860 aaaaagattg caagtcctat gcccgaggct gtgaagaatg tcaaaggcac ggacctctcc 4920 aacatgtgcc ctcagtacct ttaaatccag tggtcaagcc ttggcccttc agaggatggg 4980 caatggactt catcgggcag atttatccag cttctagcaa ggggcatact ttcataattg 5040 tggcaacgga ttacttcacc aaatgggtgg aagcctcggc cgtaaaatcc ataacctcag 5100 ctgcagtcaa gaattttatt gagaccaaga ttctgcacag atttggggtg cccgaaacta 5160 tagtgacgga tcgtgggcca tcttttattt caaaagaagt tgaagagttt gcaagcaaat 5220 acaaaataaa gatgatccag tccagtcctt actaccctca gtcaaatggc caggcagaag 5280 ccagcaacaa gattttggta aacattatca aaagaatggt gatagatagt ccggaaaagt 5340 ggcatgaaaa gctggggaat actttgtggg catacagaac ttccaagagg gcaggaacag 5400 ggacaactcc ttatgcttta actttcgggc aagatgcagt gcttcccatg gagatcaatg 5460 taagttctgt cagaattcaa aatcagtttg ggttacacag tgaagagtac atcgaagcca 5520 tgtgtcaagg gattgaagac ttagatgtag cccgaattga agccttgaac cagattcagg 5580 aaggaaagaa agctgttgcc cgagcttata acaaaaaggt gaagatgaag tctttcaagg 5640 aaggagattt agtatggaag acagtcctcc ctctaggagc tcagcttagg ggctttggaa 5700 aatggagccc gacatgggaa ggtcctttca ttgttagtcg agtattagac aaaggaggat 5760 actacttggc ggacctcgaa ggaaattggc agaaacatcc cattaatgtt aaattcttaa 5820 aaaagtattg tcctacatta tgggatgtta gagattgtta tattgaagag gatgcaaggt 5880 aaagcaggct tcgggatgcc aaagtgcagt gtttgttcat caaccattca agaagacaga 5940 aagacaaaag ttgctaaaat aatgtttatt tcatttcgac aaattggtga aatttacaac 6000 agattcaact ccgatgtgct acgttcgatt ccttctggat gcagtggtgt ctccagctgg 6060 ttttccgatg tcttcatgga tagaacccga tcaggtgatc gggttgtgcg gccaagatga 6120 gcctggtaga ggatcctcag tcagaaccat caccatgtat gatggtgaag cccgacttat 6180 cacggcaacg agcaggaagg caagccttcg tgaggaaacc gcctgaccaa gggtgttggg 6240 gatagcgggg tgtttgacca aaggtgttgg agatagtagt tatctgatga aaaccctttt 6300 tctcacgaaa agggagtttt aggaaacccc acttgaatcc tgaggaaccc atttcccagt 6360 tttgggaaga aaactaagga ggcagaaacg ctcgagggga tgaaggatga ggttgaagat 6420 gatttgagcc ggaatttata ggaacatcag aggatagctc aaaggtcgtg ggaagagcaa 6480 gagacgcgag attgcattaa tcccgtccag aagacacaag ttccgagagc aagggtacac 6540 acgcatgcgg ctattcaatc aatattggcg cctggaattc cagcctgaat attaattgaa 6600 gggggcac 6608 // ID Copia-27_Mad-LTR repbase; DNA; EDCOT; 247 BP. XX AC ACYM01133169; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-27_Mad-I; KW Copia-27_Mad-LTR; Copia-27_Mad_. XX NM Copia-27_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-247 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1374-1374 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01133169; Positions 437 191. XX SQ Sequence 247 BP; 53 A; 46 C; 47 G; 101 T; 0 other; tgttaggatc ctagttattg ggtttatatc ctttatggta ttttatctta tctctgtagt 60 agttggtttc atccaacggt agtgagggtg gagatgtgtt ccaatcttag aactccttat 120 ctagggttgt atttaagcct cctttcacca tttgggaagg gcatgaaaga aaaagactta 180 ttattttatt tcttactttc cttgcatttt cctttccttc tccattcctc tggaatgggt 240 cctacca 247 // ID Copia43-PTR_I repbase; DNA; EDCOT; 9691 BP. XX AC LG_I; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia43-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-9691 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-9691 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 264-264 (2007). XX DR Genome; LG_I; Positions 10466812 10457122. XX CC Positions [5471-5965] - Integrase core CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS join(3944..6478,6482..7516) FT /product="Copia43-PTR_I_1p" FT /translation="MQMKPFLLGQGVYSFVDGTSPCPPSHLISTTTSLPSV FT NPSYLLWTQQDHLIMSALLSSLSIKVLHLVVDCKTSQEIWTTLETALASPS FT NSRIMQLHSAFQDLRQHDDSASTYLQKAKALFDELAATGRPISMAEFNLYV FT FRGLHSDFKDLVTSLSTKADPISYTDLHSHLLTHEFLHKASLHLAVTAPLL FT PTPSQQPFAFFGQRQFGSSTGRRGRFRGGWRQSNCSYNRGNHGYSSDSQII FT SYGYGSGLKFGQQQNRFSSGSGQQFGQQGNRLGGYNRTAKCQLCYDYGHTA FT QQCSQLATHNLQANANLAFNNAPITAPVTWFPDTGANHHVTPDLASMTSSE FT PYCGNDHLHVGDGKGLTISNIAHSKIRSPKRTFTLSNILHVPHIKKPLLSV FT QKFCLENNVFFEFHPFLFYVKDLMTKEVLLSGRSRDGLYILSASSAMSLPQ FT VFSSTCVSTSTDVWHRRLGHPSPRILNFLVSTKQVSCTSKQFNFNCLACPL FT GKSSRLTLKTTGHQTQAPLDLIFSDVWGPSPMFSSDGFRYFVIFVDAHTKF FT IWFYPLVVKSDVFAIFHQFQALVERQFSLKIKSVQTDWGGEYRKLNTYFKT FT IGIQHRVICPHTHEQNGMVERRHRHIVETGLTLLGQCKAPLKYWSYAFESS FT VYLINRMPTAVFNHKTPFECLLKSTPDYAFLRTFGCLCFPFLRPYNAHKLD FT FRSSPCVSLGYSNSHLGYRCLDLSSNRIYLTRHACFHEIVFPLDKTEQIVD FT SPIQPPAATLEPIPSSYPNTHPTPPAHNTSLWAPLSLPAYHCHDHSSGTGS FT DLSFSLAGSTTVSPVVPTSSEQSVEVTPAGSPVSSPIRLPRSEIMTVSPVV FT SPSRFVSVLSSSSPGSSSISSLGLNLCVDLSQFSLQQATTSESATPPPAAR FT THSMVLRPRVSKTANFSVSPASRVVSLPQQEPLSFKDANRYLIWHNAMTEE FT IKALHGNHTWSLVPLHPSMNVVGSRWVYKIKRHADGRVDRYKARLVARGFT FT HQEGIDYLETFSPVVKPTMVRLVITIAVTHGWKIHQLDVHNAFLNGILQEE FT VYMAQPPGFVDPTLLSHVCRLHKSLYGLKQAPRAWYNRLSEFLISIGFQAS FT KVDTSLFILSFGGAMIYLLVYVDDILLTGSDSALLQRLITLLSSEFKLQDL FT GSAHFFLGIEVKSTSMGLLLSQHKYTLDIIQ" XX SQ Sequence 9691 BP; 2678 A; 2077 C; 1697 G; 3239 T; 0 other; agtgattctg tatgcccaat ccatacagag gtatgtaaga taatcacgtc tattgcaaag 60 ttatcatggc taattcaata cctataaatg taagcaaggt actcacatcc attctaataa 120 taatataatt aatttgatac atagaaatgc acatagtgta ctcatgttcg tttaaacatt 180 atcctaacta acttgatcca tatcattgta cgcaagatac acatgttcat tcaaacatta 240 tgataattaa ttggatccat accaatgcat gcaagatact cttattcatt caattaatat 300 catcacaagt ttatacatat caatgtatgc aacatactcg tatccattcc aattatatca 360 gaaccagttg atacacatca atgtacgcaa ggtactcata ttcattccaa tatttatcaa 420 agcaataaaa caataaattc taatatttat caataagttt acacatattg aaaagataag 480 gtgcgatgca cctatttgtt tccccaaccg acctagtccc ttcaattacc gatgacccta 540 ctccaggtat ctcttctgtt taagaatcaa gagatacaat gaataccctc ttataatttt 600 atcacaatgt gcattcttat actattgcaa tctcattcac atgaattcat tgccatcttt 660 taatttcatt tttcgattat tttccttcaa ctacatcatt acactcctta tgtatgtttt 720 tattggagag cattgtttac catcttatta ataagtcaag ttatagactt cggttttaag 780 tgtggcttga ctcggaaagg taagacacgg ttccacaact ctattgaaga atagaaagcc 840 ctgttctgcc cttaagaccc ttgaaattat ccgttatata tagcactcaa cacaatatgt 900 cctgtacgag acagtttgac ccgtcttcca ttttcagtcg ttatctagag ttctataact 960 ccaaattaag cgcggtcagt ttttttaaaa agataacatc catacctata acatttatta 1020 aaaaaaatat attaaattta tcatttgggt gccctgacct tagctgaagt tgggtgacca 1080 aactgttcag tcccaataca tggattggac aaccaatatc tcacttttcc tactattaac 1140 ttgtttttac attaatatcc taagttttat atatgtcatc atcacttatt catgtttcta 1200 ctaccaattt agcctatcca acttctttag aatccatatt tgtcacaagg tcctttttat 1260 aagtggcttg tctctatttc tcattccttg cccccataat ctagtcctca ctttttcatt 1320 aagtcatgca tttaacacca acacatgtac gtcatgtcta ccattttatt ttccttgcca 1380 ataatctagc tgaacatgcc taaggaaaga cactaagcat tttcttcaat ttaaatcata 1440 attagcttgc ttttgatggt taaacacaaa tcaagccacc acactttcca tttattttat 1500 tcttactaac ttaatttaaa caaaagtttc agcaaggtta aagtctccaa acccccctgt 1560 catagccatt tgcatgcaca atacattttg catgcaaatg gaaaaatgcc attaacaaca 1620 atgagttgaa cctgtttcag ccaagcccag atgactaggt ctggcccaac ccaaaaaaaa 1680 agagagaaag gttgttgagc cgccagtcga cctaacccga ccaagtcggg tggacctatt 1740 tcattcgagc ccagatgact gagctgggtc taatccaata tatatttcat aataaaataa 1800 aataatatta aaatatatat ttttttaaaa aagagaaact ttcaagaatt ccaatgggca 1860 tttgaaaaat atatgtgggc ctctcgcatg tttttccaac tatattgtat aatatcaggc 1920 tttagactta cattataaaa tacccggttt tctctgaaat gtttctttat aaacaaattt 1980 gaaaattaaa aaaaaattca aattaatttt ctctttccaa aaaaatacaa aaaaaaaaaa 2040 ctattttgtc tttgtgcata cggccaaatc ctaaaagttt ttcatgcata ttttctaaag 2100 agagataaaa atcatattta tcatgattta aaatatacaa aatggatatc ataaccggtt 2160 tatgattatc tattagggtt tgatcaaaat acaaaatatc ccattataat tagtttgtca 2220 ttcggatcga ttgctatgac ttagctatct ccaagaaata aataaatttg gcctttagaa 2280 ttgtcaagat ttaacccgat aaggtagaga cttcctcatg aagggagatc tacattgaac 2340 cttaaacaag accaatgaac aaaaatgcga cttagaataa caatcaaata acaatgcagc 2400 ttaccttagg gagggtgtgc taggcgtgat acgtcttccc cttgcacaac caatccctta 2460 cccggactct cgcagaccat taggttttct aacaaccata atactaggtt gcgactcctg 2520 aatcttataa tcataatttt atgattaaat ccaaaacccc tttccaacac actttggaga 2580 catatctgcc aatcgacgcc gtgcacgcca caagaatggg cttcctgtgt tttctgtttc 2640 tttttctcca acctggcgag gcattgtttt gactttctcc acaagagaaa gcatagccat 2700 tcgacttaat tcaagcattg ggttcaaggt aggtgatgac actaacgttt ggtcttggat 2760 cgattcttgg ctaggtactc cagctcctct tcataattta tttcctagac tatttaatct 2820 ttctctgcag caattagttg gccatacaaa tgtgtatagc ccgattgata attcggttag 2880 cttgacttgg aggaggaatc tgaggtctca tgagctttgt atgcgggaaa ttttaattgc 2940 agcggtggag cgtggtttag ttttttctgg aggtgaagat agtgaggcat gtaaatttga 3000 tatttccaac acttattcag tgttgcaaat ttctagatag cctgtctgct tcaggggctc 3060 cttctttttt tgttttgctt tggaaaggtt ttgcacctcc tcaaattgat gtgttcatat 3120 ggctcctgct taatgctagt ctcaacgcta ggggtttttt agctgagagg gggattgtta 3180 attatgagga tgctcgtttt cctttttatt gtgaggagat ttggactagt aataatctat 3240 ttcatcattg tactatttcg tggaattttt agggtagatt catgcattgg ttctggtgtt 3300 taagttgtct atctagggac cctaaacaaa atcttcaaga atggtacagg tcgatgagag 3360 gcaattttca gtgttaggat attattcttc tatgcaaaga cttttattga tctatctagt 3420 tattatggaa agagtcctat atatatgtaa ataccttgta taggaataag tatcatgtat 3480 agtacattcc acccttgtat tatacacaac cctaaaggat caaggaaggg ttgctgtgat 3540 tcgcgtccaa tacattatac attaattcaa tctctttaca aaactcaact tggtatcaga 3600 gcagcaacaa aatcttcctt cacgcttctg gattattgtt cggtcgtctc ctctagaccg 3660 ttgcactcct ctgcttccat cttcattcag cccttcattc agcccttcct ccctcacctg 3720 tctgtctgcc tctccctctc tcttgacaat ggacaaccaa gaacttcaac atggtgctgg 3780 tgttgcacca atctctcaat cctctttagc ggctgctact gccagcatag ttcctatgaa 3840 ctcttctcta gatatcatga acaggtctgc catcattcct ctttctaata tgcagcaggt 3900 aatctcctta tgactctcca ataccaactt cttgtattgg aggatgcaga tgaaaccgtt 3960 tctcttgggc caaggtgtgt actcctttgt tgatggcact tcaccatgtc ctccctctca 4020 tcttatatct actaccacat ccttaccatc ggtcaatcct tcatatttat tatggacaca 4080 acaagatcac ctaatcatga gtgctctttt atcctcgctc tccataaaag ttctgcacct 4140 agttgtggat tgtaaaactt ctcaagaaat ctggacaacg ctggaaactg cccttgcttc 4200 cccttcaaac tcacggatta tgcagctcca cagtgcattc caagatttac gacagcacga 4260 tgactctgcc agcacttatt tgcagaaggc taaggccttg tttgatgaac ttgcagctac 4320 tggcagacca atctccatgg ccgaatttaa tttatatgtg tttcgggggt tacacagtga 4380 ttttaaggat ctggtaacca gcctgtccac taaggctgat cccatctctt acacagacct 4440 ccatagccat ctcctcacac atgaatttct ccataaggct tcactccatc ttgctgtaac 4500 agctcctctg ttaccaactc catcacagca gccatttgca ttttttgggc agcgtcagtt 4560 tggttccagt actggaagaa ggggccggtt tcgtgggggt tggagacaga gtaattgtag 4620 ctacaatcgt gggaatcatg gctatagttc agactcgcaa ataatcagtt atggttatgg 4680 ttcaggtctg aaatttggac aacagcaaaa ccgtttttca tctggctctg gtcagcagtt 4740 tgggcaacaa ggaaaccgat tgggaggcta taacagaact gcgaagtgtc agctgtgtta 4800 tgactatgga cataccgccc agcagtgctc tcaattggct actcataatc tacaagctaa 4860 tgccaattta gcatttaata atgctcctat aactgctcct gttacttggt ttcctgatac 4920 aggtgcaaat catcatgtga caccggacct tgcgagtatg acgagctcag aaccttattg 4980 tggtaatgat catttacatg ttggcgatgg taagggcctc actatttcta atattgctca 5040 ctctaaaatt cgttcaccca aacgcacatt taccttatcc aatattttac atgtgcctca 5100 cattaaaaaa cctctacttt ctgttcaaaa gttttgtctt gagaataatg tgttttttga 5160 atttcatcca tttttatttt atgttaagga cctcatgaca aaggaggtgc ttctttccgg 5220 tcggagtaga gatggtctat atattttatc tgcatcgtct gcaatgtcgt tgcctcaagt 5280 cttctcatct acatgtgtct ctacttctac tgatgtctgg catcgtcggc ttggacatcc 5340 tagtccacgc attctgaatt ttctagtgtc aactaaacag gtgtcctgta cgtcaaaaca 5400 atttaatttt aattgtctag catgcccttt gggaaaatct tctcgtctga ctttaaaaac 5460 tacgggtcat caaactcaag ctcctcttga tctaattttt agtgatgttt ggggtccttc 5520 ccctatgttt tcgtccgatg gttttcgcta ttttgttatt tttgtggatg cccataccaa 5580 atttatctgg ttttatcctt tggttgtaaa atctgatgtg tttgctatat ttcatcaatt 5640 tcaagcactc gttgaacgcc aattttcttt aaaaattaag tctgttcaaa cagattgggg 5700 tggtgaatat cgcaaactca atacatattt caaaaccatt ggtattcagc atcgtgttat 5760 ttgtccgcat actcatgaac aaaatggaat ggttgaacgt cgtcatcgac atattgttga 5820 aactgggctc actcttcttg gccaatgtaa agctccccta aaatactgga gttatgcttt 5880 tgaaagttca gtatatttga ttaatcgcat gcccactgct gtttttaatc ataaaacacc 5940 atttgaatgt cttttaaaat caactcctga ttatgctttc ctccgcactt tcgggtgtct 6000 ttgctttcca tttcttcgtc catacaatgc tcataagtta gattttcgct catccccttg 6060 tgtctctcta ggatatagca attctcattt aggatatcga tgtcttgatt tgtcatcaaa 6120 ccgtatttat cttactcgtc atgcttgttt tcatgaaatt gttttccctc ttgacaaaac 6180 tgaacagatt gtagattcac ccatacaacc tcctgctgct actttagagc ccatcccatc 6240 atcctatcca aacactcacc cgacaccccc tgcacataac acaagccttt gggcaccctt 6300 atcattacct gcatatcact gtcatgatca ttcctcaggt acaggttcag acttgtcgtt 6360 ctctcttgct ggttcaacta ccgtctcccc tgttgttccc accagcagtg aacaaagtgt 6420 ggaggtcacc cctgctggtt cccctgtcag ctcccctatt cgtctcccca ggagtgaata 6480 gattatgact gtctcacctg ttgtttcccc ttctcggttt gtctctgtat tgagctcttc 6540 atcaccaggt tcttcatcta tttcctctct tggacttaat ttatgtgttg atttgtctca 6600 attctccctt cagcaagcca cgactagtga gtctgccact ccccctcctg ctgcccgcac 6660 ccactccatg gtacttcgcc cacgtgtatc caagacagca aattttagtg tctcccctgc 6720 ctcccgggta gtttctctac ctcaacagga accactttct ttcaaagatg ccaaccggta 6780 cttgatttgg cataatgcta tgacagagga aatcaaggca cttcatggta atcacacttg 6840 gtcactggtg cccttacatc catccatgaa tgtggtaggc agtaggtggg tttataagat 6900 taagcggcac gccgatggtc gagttgacag atataaagca cggttggttg cccgcggttt 6960 cacgcatcaa gaggggattg attacttgga gacatttagt ccagtggtta agcctaccat 7020 ggttagactt gtgatcacga ttgctgtcac acatggttgg aaaattcatc agttagatgt 7080 ccataatgcc ttcctgaatg gcattcttca ggaagaagtg tacatggcac aaccacctgg 7140 ctttgttgat cctacacttc tatctcatgt gtgtcgtctt cataaatcct tgtatggttt 7200 gaaacaagca cctcgagcat ggtacaatcg gttaagtgag tttctcatct ccattggatt 7260 tcaggcatcc aaggttgata cttcgctgtt tattctctct ttcggtggtg caatgatcta 7320 tctgcttgtg tatgttgatg atattctatt aactgggagt gactcggcct tacttcaacg 7380 actgattact ttgttgagtt cagagtttaa gcttcaggac ttagggtcgg ctcacttctt 7440 cctaggaata gaagttaaat cgacttctat gggtctctta ctcagtcaac acaagtacac 7500 actagacatt atccaatgaa taggtatgac ttcttgcaaa ccagttgata ctccgttgtc 7560 tccctcgtct aaattgggat ctgtgcctgg tactcttcac tctaccccaa cacggtatag 7620 acagattgtt ggtgctctac agtaccttac tttcactaga cctgatattt gttatgcagt 7680 aaacaaggtg tgtcagttta tgcatgctcc tactgaggac cattgggcgg cagttaaacg 7740 catcttacat taccttcagg ctacagccac ctatggtctg catattactc gggactcctc 7800 cttgtctctt catggcttta ctgatgctga ctgggctggc agtattgatg atcgaaaatc 7860 cacaggtggt tatcttgtgt accttggttc cactcctatt tcctggaaat ctgggaaaca 7920 acgcacttgc tagatcctct acagaagctg aatacaaagc cttagctgat ggtactgctg 7980 aaatcttgtg gattcgctct ttgttgtcag aactacgact tccgtcttca cccagcacta 8040 cgttatggtg tgataattta ggggccactt tcctgtatgc taatccagtg tttcacgcac 8100 gtactaaaca tgttgaagtt gattatcact tcgttcgtga tcgcgttgct aagaaagaaa 8160 ttcaggtacg attcatctct tccaaggatc aactagctga tgttcttacc aagcctctcc 8220 ctctagtttc gtttgttttc tttcgatcca agcttcaggt ggagtctcca ccttcagctt 8280 gacggggcat attatggaaa gagttctata tatatgtaaa taccttgtat aggaataatt 8340 atcatgtata gtacattcca cccttctatt acacacaacc ctaaaggtat aaatatcaag 8400 gaagggctgc tgtgattcgc gtccaataca ttatacatta attcaatctc tttacaaaac 8460 tcaactctag ttagttcgca atcgagttat cttcgagtcc aaggtctata attgggatgt 8520 gattttttat cttacctttc aatgtttggc cttttggttg aaattctcag tcagaaactt 8580 tagttacaca ggttctgatc agactagaag tcttgaatgt atcttgaact agactaatta 8640 gtttgatttt tctccttctt ttagatactt atgttgtaag tttttattcc ttcggtcact 8700 atcttcttaa tggtgctctt ttaatttaat tctactcgat tactataaag aaataaatta 8760 aagatacacc tatatatttt atacagctcc tatttataat cctcgtatat ggagcaatgc 8820 atggtagcag aattacaggt ttcctactga caacctttca actaaaaaaa aaaagggtct 8880 ataagcatct tgcaaatgtt cggaaatctc aataatgaag tacaatgaca ataattacgt 8940 gaacttgagg cactatactg tggtgtgatt tgtattctgt gtttaatcgt gcctagataa 9000 tgggggatag tatgataaaa atggtaatct aataacgcta attgttaagg aattcgttgg 9060 aggcttgaag aggatgcttg aattccgata gaagcaaaac gcagtttctt tctcctaatc 9120 aagttgaagt tttcgcgcgg ataaactttc ttggaaaata aattccagac agctgtaaaa 9180 ttgaattcca gggtgatgac tagttgatgg cttcaaagcc aaatgaattc caggctgatg 9240 actagttgat cgcttcaaag catttcttgc acgatttaga gatggttgtc agtttgggat 9300 tgaagaaagg tcatcttaga gattgatcgt aattggttac tctcctaggc ttttggttaa 9360 agatcatgta ttgtgcttga cttggctgat tcagcgtaag gaaatgaaaa ttgtttcatg 9420 caaaatttct agcacgtgat tggtaatgtt tttttgtagc tcggaatatc cttcatgtct 9480 gaatgcgaaa ggtcaacata tcatttaaaa actcttcttg ggctggaaac ccgtcaactt 9540 tcgcttggct tcattgccat cagacaagaa aattaaagtc gttgaaaatt cttatgttga 9600 cgatccggta gctgaatttt ctcagcaagc ttcaagtaca attgctaggc ttcacagtgc 9660 aattagagca cggaatctta agtttggagc t 9691 // ID Copia4-PTR_LTR repbase; DNA; EDCOT; 485 BP. XX AC LG_XI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia4-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-485 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-485 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 257-257 (2007). XX DR Genome; LG_XI; Positions 7936217 7936701. XX SQ Sequence 485 BP; 154 A; 79 C; 78 G; 174 T; 0 other; tgttgaccgt ttctgataga gtcattataa acgactctct aactctcgtt cacatttatt 60 aactctcgtt cacatttatg aactattaaa gtggtccact ttaaaggttg taacctttat 120 atttatgagc tcttaaagtg gtttacttta aggatgtaac attcacattt atgagctctt 180 aaagtggttc acttgtaact acccatgata taataaatat gtgagacata gccattaaag 240 cttgatggaa gctttggcta taaataatgt tatttgatcc ccatactcac ttactcaatt 300 cccttaagtt ttacaccatc tatatagagt gagtagagtt tggaagtgcc aaatatatat 360 aaaagagagc agcaaatacg tgaggaacat caatagctgg aggtattgtt tcattgttat 420 taagacttac gattctgtta taaacatatt tattccgcat catagaatcg ttagttaagt 480 tttca 485 // ID LTR-10_Mad repbase; DNA; EDCOT; 3330 BP. XX AC . XX DT 27-OCT-2010 (Rel. 15.11, Created) DT 27-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; LTR-10_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-3330 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 2001-2001 (2010). XX DR [2] (Consensus) XX SQ Sequence 3330 BP; 805 A; 486 C; 813 G; 1223 T; 3 other; tgtgaaatcc cgttcctgga tttcactgtt ataatctacg tatttgtatt attgagattt 60 tatattattt ttcgagaatt tattttaatt tgtttgaatt aagattttaa ttaaattagt 120 tacgaagttt gaagtttgga gattaattat ttaaaatccg tggacctttc gaggtcacaa 180 tttatatcgt tgaatagatt tcgagatcac gaacgtatag gcgaaagccg cttgcgagtt 240 cgagttttaa cggtatagtt acggatattt gaagttgtgt tactaatcta tatattttaa 300 tttattttaa aactcccaca tagtgggaga gggaccaggg asaaatggga aataaaaggg 360 aacggacaga aaaaaaaaaa aaaaggggga ggagggtctg attttgaccc ctttttgggc 420 attttcgacc mttttgaccc ataaacttga cccgctcata tcttcttcat ccgagctccg 480 ttttgggtga tcttggtgtc catggaaagc tcttgaagag ccctacgacc ctgtggtgtt 540 agatttccca ttttctgatc cacttttcca gttcgaggca gcaaagtccc gtgggttttc 600 cggcgattgt gtcatttttc cggtgattcc ggcaaccatt tccttcgagt gaggtatgaa 660 acttcatcta ctcttcataa tctccaagtt ggtatgcttg gtttgtgctt tcgtattcgt 720 tttagagttg ggtgtttaaa accctagaaa cccggttttc cccgatgaat ttggatggtt 780 tccggttaga atttgttgtt ggcctagttg tgaataatgt ttcccttgtt gagatcttca 840 ttcttgtaaa atatgagaat ttttggaaaa agtcggattt tccgatgtgt ggcattcgat 900 ttatgaaatg ttgttggttg agtatattta gataggtcca ccacttggat attctaacag 960 ttgacgatac tttaaattct tatatttata tcatttgtga atatggcttg gtgttataaa 1020 tgtgatttct attgaaatgt gattttatat atttagccgt agacatatgc ttattagcat 1080 gatttggctt gtgtactgat gatggttgtg atatatgtga gtttaattat ccttttagta 1140 atgtgaatga tgagtatgat tattttcatg acaatgtgat cctagaatcc tattagaggt 1200 atgttgtagc acttatatgc ttgggtgaca tattagtggt gacctcgaga agttgatggt 1260 gtaggcgact acgttgtaac tcataggggt tgagatgtgg ataagttgag gtgttgagtt 1320 tactgcacca tgtagtagtt gtacattgat ggtcctgctt ggtatatccg cattggggga 1380 ccatacgcat tctaggagtg atcatgcttg gtatatccgc attgggtgat cactacctac 1440 ctgattattt tgaccctgct tggttaatcc gcattggggg gtcattagtg gtcctgcttg 1500 gttaatccgc attgggggac catactatat atggatcgcg cttggttaac ccgcgttggg 1560 taatccttat ggccatgtat gcttaggagt gatcatgctt ggttaatccg cattgggtga 1620 tcacttccta atagttgtag gggtgactct gcttggttaa tccgcattgg ggggtcactg 1680 cctacttggt tactttctta agggtggctc tgcttggtta atctgctttg ggggggggcc 1740 acttcttgtt tggttactta tgtgggcttc agttgaattg cgtccctcta gccctagttt 1800 taatgtacat atgaatgatg gtttttgaga atcttgatgg tttgaatggg ataagtcgtt 1860 ggatgtctgg gtgacttctt cggagttgtt agagacttga ttatgttttc atatttacga 1920 acttatattt gaggttataa actatgatca atggtctttc tttttataga ttatctcata 1980 cttgtaattt ggttccgttg agtggtccgg aacccagtgt tgttggattc cgttgagtgg 2040 ttcggaatcc ttgcttttgc tcatttccat aaggttatct tagaatccta gattcgagtg 2100 aatgagaatt acgcacaatg gatcttgtgc atacaaatta gaattatcat gttattatcc 2160 ataactcaag tagggaatta tgtagagttc tttaattaaa ctcgtgaaat gatgtgctat 2220 ctcactgatt gattaacgta attaaatatt aatattgtgc ttcgtgattc cctgatatgt 2280 tacaagctat ggatagagat ataatgttgg aagcatagtg attggtatga tgtagtgaaa 2340 tgtgatttga cttgtgwatt ggaaatggtt gtgtcatgtg attgaaatgc ctattgaatt 2400 gcttgggaga tgtgagatct agtaatggac cgataaccca ttgtgatggg gatttgttgc 2460 tcgatattag ttcgttttgt tgagtcttcg tgaattgagt aacttgaatc ctgtcttgtt 2520 ccttcgagcc gtagttatgc ttcttggact tccgttcggt tctgttgaat ggttcggaac 2580 taagttctgt ttggattccg ttgagtgatg gtccggaatc ccttatactc tgcgattccg 2640 ttgagtgatg gtccggaatc gtatcctggt ttggattccg ttgagtgatg gtccggaatc 2700 gtatcattga cttgttagtt ccttggattg atatcaactt ctgagatgta ggcttcggcc 2760 aaaatgtgtc gctctagccc tgcattttgg tatatgatgt gttgttgatt gatgtgattg 2820 tggaataatg ttggttgtga tttttgtcat tataattaga ctcgttgact attttggcta 2880 gagaatagca tggtgatccg ttgattgttc tttgagatgt tgcatattat gaaatggaga 2940 atcatgtgaa atgtagtgat ttatatgaag gatgaagtgg aaaatatatg tgtgggcata 3000 gcatacctgc gtgcatgaca agatgatagt tgtgtatggc ttatggttga tgcgtagtgt 3060 ggtaccctat gttttttttc actataagta ttttacgaaa agattaaagt ttgacgaacg 3120 ttgaactacg aatggcttga tccctattga gggtacgtag gcagtctaac gaagaggtta 3180 gatgcagcca taaattgtac gaaaaatgct atgaaatttg aatcttgatt tatgctttgt 3240 acatatcccg gaggcggggt atgttagatg tacgggtatt ggtgacgtca cgtgtcgatt 3300 ctggacgtat gttgggatcg gggcgtgaca 3330 // ID Copia-49_VV-I repbase; DNA; EDCOT; 5279 BP. XX AC chr19; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-49_VV_; KW Copia-49_VV-LTR; Copia-49_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5279 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr19; Positions 11013322 11018600. XX CC Positions [2719-3051] - Integrase core CC LTRs are 92% similar to each other. XX FH Key Location/Qualifiers FT CDS 3993..5036 FT /product="Copia-49_VV-I_3p" FT /translation="MKFDRIITQNGFKENTVDRCIYLRVSGSSYIFLVLYV FT DILLALNDSDLLIETKHMLSTHFDMKDLGEASYVLGINILRDKANGVIKLS FT QRTYIEKILKRFNMHNCSSARAPIVKNDKFSKAQCPQNDAERKEMRTIPYS FT SLVSSLMYAQVCTRPNIAFVVGMLGRYLSNPGSQHWKAAEKVLRHFQGTKD FT LMLTYQRTNILDVVGFCDADFPGYIDDKKSTTGYIFVMAGGAVSWKSVKET FT LTTSSTMEAEYVACYEACCHAIWMRNFISVLGVVDSISRPLKLFCNNSATV FT AFSKNTRSTSRSKHIDLKFYFVKEKVIESLIDIEHMSTKGMLADPLTKGLP FT HNCVS" FT CDS join(1903..2715,2719..3639) FT /product="Copia-49_VV-I_1p" FT /translation="MIETNIVDVHANSWWLDTGATIHVTNSLQEMTNKRRS FT SKHEECVYMGDGSKVKVEFFGMIKLRLTIESFLLLHNVAYIPSLRRNLISV FT SILDRQGCTFHFGGGKVDVFSYSVLIGNVVLFGNLYSLSLHHGPLCDSSSV FT NSVVGCKHARMNLSSSMLWHKCLGHISRQRLERLVRDGVLSNLDFSDFKTC FT VVCLKGKMTAKTRKEKIDKCGSTLDLIHTDTCRPLTPTALGGYKYFITFID FT DFSRYGYVELIHEKSDSLNVFKAFKAKVELLGKPIKAVKSDRGGEYYGRYD FT EIGRNPGPFAKFLLECDIDARYTMADTPQQNGVVEKRNCTLLDMVRCMLSN FT SSLPEFIWGEALRITTYILNQVPSKSVPKTPYELWSGKKPSLNHFHVWGCK FT AEVRPYNPQSKKLDPKTISGFFVGYDIGSRGYRFYCSSHTTRIIESKKLVY FT FEDEVNVDPNFVPREIPFGEEHVIITFLTSHVPDADVPIVQQPTTNQGEHD FT DQVEPGIPVDGTVVDGILLRRSQRVRRLTISDDYMIYLQDHEYDGYDAFDP FT VTYQEAIHYPQFTSWKEAMDGIWSNCHMVVN" XX SQ Sequence 5279 BP; 1579 A; 735 C; 1144 G; 1821 T; 0 other; attggtatca gagctataca tggatgacat ttgagttgca tatttgggtt attttgggtt 60 tcccattttc tagtttggaa gccacttttt ggagctcatt taacgggatt taaaaaatta 120 gggcttattt tggttcttat ttttatgcgt tttttgtgta atttttgggt ttagattaaa 180 ggattgatgt ttaaggatgg aaacctaagt gtttttgtcg gaaaatgcac aaaattttgg 240 atgatttttt ttttcttttc cagaaaaacc aagtcgtgtt tagtccgatg gagaagatga 300 acaatgcatg atgatgtcat catgacatca taaaaataaa taaaaataaa aaataaaaaa 360 actttttttt tggttgtctt gctattcttg gaattattat gcatttgtta aatttggttt 420 tattgggaca attaatatta ttattattat tgttctttat ggtataattt tttatcttat 480 gccaataatg ttgtcctagg cctttttttt gttaaagttt taaatttatt atggcaataa 540 agaacacttg tgtgattgcc tatcgcaatt ccaagtgtgt caagttgtgc aaattaaata 600 tttgagttta tcatgaaaat agtgaacata tatgtggttg cctatcgtga tcctatatgt 660 gtcaaattgt ctttgttgag atattttatc tcctactttt ggttgcttta ttattgtgat 720 tgctaaggtc cataacagta ttgtaattat cttgttgatg attataatac ttggtaggat 780 gcttagattg gtgaaggaaa ttaattatat tttataaacc gtactaattt tcttttttcc 840 ttttccgtaa taaaattagt gcatcttggt tgtgatattt aattagttgt ccttactact 900 atggaatttc aaaattccaa gctattgcta aattgagaaa ttttggaaac tagcaaataa 960 catgatattg tagtaacatg catattgttt aatttttcta ttttccagct attagcaatc 1020 ctggaattac tctgcaatta tttgccatca agcctcttac tggaaataac tttgaggaat 1080 ggtatgagtc tttcaatgtg catatgactt tacacaattt ggacttggct ttgagagttg 1140 atgagccaag taagcccact aatgtgaact ctgctaatga aagatccttt tatgagatat 1200 aggagcactc cgataggagt tgtttgatgg tgatgaagta tactatggat aaatctatta 1260 aagaatgtgt gccaaagacg caaatggcca aagacttttt ggaatatgta aaggccaatt 1320 ataccaagat tgataaggca aaaatgacaa cttatttgaa gcttctcata accactatgt 1380 atgatggagt aagtggggtt agagattaca tcatcaatct aaagcactac ttcaacaagg 1440 caaatgagat gaaagtggag ttgagtgaga aattcttgaa atagttgata cttgagtctc 1500 ttcctacttc ctttgatacg atgaagttga cttataatgc cttaaaggaa taatggactt 1560 tggaggagtt gatgtccatt gtggtgcaac atgaagtctc actaaagaaa aatgagactc 1620 actctcttgc tcttgttact gaccaagtga gcaatatgaa gaaaaaaagc tccacataag 1680 aattttggag gctctaaaca attcaagagg aaaaggaatt cgagtcaagg aatctctaat 1740 gcatttgctt cttctaatgc tacaaagaat gagagattca aggggaagtg caacttttgc 1800 cacaagattg gccacaagca ggttgattgc ttcaagttta aaaattgggt agagaagaaa 1860 aagaaatgtg aaattgtggt tgtggttaat ttgaatgcaa acatgattga gactaatatt 1920 gttgatgttc atgccaattc ttggtggtta gatactggtg ccactattca cgtcactaat 1980 tctttgcagg agatgacaaa caaaaggagg tcgtcaaagc atgaagaatg tgtgtatatg 2040 ggtgatggaa gcaaagtgaa agtagaattt tttggcatga taaagctaag attgaccata 2100 gaaagttttc tgttgttaca caatgttgct tacataccct cacttaggag gaatctgatt 2160 tctgtatcta ttttagatag acaaggttgc actttccact ttggaggagg aaaagttgat 2220 gtatttagct actcagttct aattggcaat gttgttttgt ttggcaatct ttatagtctc 2280 agtttgcatc atggtccttt atgtgattca tcttctgtta attctgttgt tggttgcaaa 2340 catgctagaa tgaatttgag ttcttccatg ttgtggcata aatgcctagg tcatatttct 2400 aggcaaagac tagagagatt ggttagagat ggtgtgcttt ctaatcttga tttctcagac 2460 ttcaagactt gtgttgtttg cttaaagggg aagatgacag ctaagaccag aaaagagaag 2520 attgataagt gtggaagtac tttagacttg atccacacag atacatgtcg tcctttgaca 2580 ccaactgctt tagggggtta taaatatttc atcactttta ttgatgattt ctctagatat 2640 ggttatgttg aactaattca tgagaaatct gactccctaa atgtgtttaa ggcctttaag 2700 gctaaggtgg aattgtagtt gggaaagccc attaaagctg tgaagtctga tagaggtggt 2760 gagtattatg ggagatatga tgagattgga cggaatcctg gaccattcgc taagtttcta 2820 ttggaatgcg acattgatgc tagatataca atggcagaca ctcctcaaca gaatggggtt 2880 gtagaaaaga ggaattgcac attgttggat atggtaaggt gcatgttgtc taattcctcc 2940 ttaccagaat ttatatgggg tgaagcctta aggattacga catatatttt gaatcaagtg 3000 cctagtaagt ctgtgcctaa gacaccttat gagctatggt cagggaagaa accgagtctt 3060 aaccattttc atgtttgggg atgtaaggct gaggttaggc catataaccc acagtcaaag 3120 aaacttgatc ctaaaaccat tagtggtttc tttgttggtt atgacattgg atcaaggggt 3180 tatagatttt attgttcatc tcataccacc aggatcattg agtcaaaaaa acttgtatac 3240 tttgaagatg aagttaatgt tgatcccaat tttgtgcctc gtgagatacc ttttggagaa 3300 gagcatgtta taattacttt tcttacatct catgttccag atgcggatgt tcctattgtc 3360 caacaaccga ccactaatca aggagagcat gatgatcaag tggaacctgg cattcctgtt 3420 gatggtactg ttgttgatgg gattcttttg agaagatcac agagggttcg taggctaact 3480 atttcagatg attacatgat ttatttgcag gaccatgagt atgatggtta tgatgctttt 3540 gatccagtca cttatcaaga agcaattcat tatcctcaat tcacttcttg gaaagaagcc 3600 atggatggaa tttggtcgaa ttgccacatg gttgtaaact agttggatgc aagtgggtcc 3660 ttaagaccaa acgtgattct agcgggcaaa tagagagata taaaactaga cttgtggtta 3720 aaggttatag tcaaagagaa ggaattgatt ttaaagaaac cttctcactt gtgtcgagca 3780 aggactcttt tagagtgatt atggccatag tagctcattt tgatttgaag ctacatcaaa 3840 tggatgtcaa gacagctttc ttgaatggtg atctggatga ggacgtttat gtggagcaac 3900 ctactggttt tgctgaagtt ggaaagaaaa atttagttta caagctcaat aagtcaattt 3960 atggtcttaa ataggcttcg aggtagtggt atatgaagtt tgataggatt atcactcaaa 4020 atggttttaa agagaataca gttgatagat gcatatattt gagggtcagt gggagtagtt 4080 acatatttct tgttttatat gttgatatac tactcgcatt aaatgattct gacttgttga 4140 ttgagacaaa gcatatgttg tcaacccatt ttgacatgaa agatcttggt gaggcttctt 4200 atgttttggg cataaatatt cttcgtgata aggctaatgg ggtgattaaa ttgtctcaaa 4260 gaacctatat tgagaaaata ttgaagaggt tcaatatgca caactgtagt tctgctagag 4320 cgccaattgt gaagaatgat aagttttcaa aggcccaatg tcctcaaaat gatgctgaga 4380 gaaaggaaat gagaaccatt ccttattcat ctttggttag cagccttatg tatgctcaag 4440 tatgtacacg ccctaatatt gcttttgttg tgggcatgtt gggaaggtac ttgagcaatc 4500 ctgggagtca acattggaaa gctgctgaga aggtccttag gcattttcaa ggaactaagg 4560 atttaatgtt gacatatcag cgcaccaaca tacttgatgt agttgggttt tgtgatgctg 4620 attttcctgg ctacatagat gataagaaat ccactacggg ttatattttt gtgatggcag 4680 gaggagctgt atcttggaaa agtgtcaagg agacacttac aacatcctca actatggagg 4740 cagagtatgt ggcatgttat gaggcttgtt gtcatgctat atggatgcgg aattttattt 4800 cagttttggg agttgttgac tccatttcta gaccgttgaa attattttgt aataattccg 4860 caactgttgc tttctctaag aacactagga gtacttctcg ctccaaacat attgatttaa 4920 agttctattt tgttaaggag aaagtgatag agtctcttat tgatattgag cacatgtcaa 4980 caaaaggtat gttggcggat ccactaacaa aaggcttacc ccataattgt gtttcatgaa 5040 catgtatctc aaatggggtt gttgcgagcc taggttgcat taagttagtg ggagccattt 5100 ttggtattgt aatattatgc tattgttgga aggattgcta ttattgtata tttccctatg 5160 aatcaagcaa tgaagcatgt atgattgctt ttgattattt gttttgatga gattctatgc 5220 attgatttat gattatgtat atgttgtgat gtttgattat gtagtccaag tgggagaat 5279 // ID Copia-1_CP-I repbase; DNA; EDCOT; 4017 BP. XX AC ABIM01005961; XX DT 10-MAR-2010 (Rel. 15.04, Created) DT 10-MAR-2010 (Rel. 15.04, Last updated, Version -1) XX DE LTR retrotransposon from papaya: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-4_CP_; KW Copia-1_CP-LTR; Copia-1_CP-I. XX OS Carica papaya OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Caricaceae; Carica. XX RN [1] RP 1-4017 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from papaya."; RL Repbase Reports 10(4), 573-573 (2010). XX DR Genome; ABIM01005961; Positions 1905 5921. XX CC Positions [1570-2064] - Integrase core CC 'CCTTG' target site duplication CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS 427..2064 FT /product="Copia-1_CP-I_1p" FT /translation="MQENESVRDYASKLSDIVNKMRLLGEDFPESRVVEHI FT LISLPPKFESKISALEELADIDKISSTELINKLQSQEQRVNMHARVPIEGA FT LFSSQTKATPSNQYQGRRNGGNQTGNQSSRKQKKYPPCNICSLTNHLESEC FT CYKGKKTVQCNFCKRLGHKEKFCRQKQKLEAAQSKQELQHVNVTEISSEQN FT NTILVASSELTVEDNSLWVVDSGCTSHMCKNEAMFVLLDKSVTGQVRLGNG FT MLETIKGKDNIAIETKKGRKLITDVNFIPTLSQNLLSVNQMTDRSYSVGFN FT DNCCRIYDPEDHLIAFIQKKNQVYSLKLREVIERASVASVTEGEIWHRRLG FT HFHAAGLQQLQKGGLTKDFPNIAVTETVCDACQMGKLARNSFPSQADWRAK FT EKLALIHFDICGPMTESFMSGCRYFGLFIDDFSKMIWVCFLQNKAQIFGEF FT KKFKVIAEKESSSVLRCLRTDNGLEFNSSQFNDFCYENGIKRKLTTPYSPQ FT QNGVSERKNRTIMEMARSMLADKHLPKALWAEAVNTVVFLLNMLPTKAVK" XX SQ Sequence 4017 BP; 1360 A; 740 C; 930 G; 987 T; 0 other; agtggtatca gagccaggtt ctcctacgtc tcaggtgaat caaaaatttc tcaaacccga 60 tggctacctc aggaactacc cctgctccgc agttcaacgg agaaaattac catgtgtggg 120 caataaagat gcgagctcac ctcaaagctc tgggtttatg ggatgttatt atagacgata 180 gtgaaccaac cccactacaa gaaactgcta cattgaacca gattaaaaga cacgaggaag 240 agaaggccaa gaaaccaaaa gcaattgcct gcctcttctc agcggtttcg gacagggttt 300 tctctaggat tatgactatg aatcacccaa ggaagcgtgg gagaaactga aggaagagtt 360 gatggaggag acagaagcaa gaagatcaaa ctactgaggc taaaaaatga atttgcatta 420 ctcagaatgc aagaaaatga gtctgttagg gactatgcct ccaaactctc ggatattgtg 480 aataaaatga gattgttggg ggaggacttt cctgaatcaa gggtggtaga acacattctt 540 ataagcttac caccaaaatt tgagtctaaa atctcagcct tggaggaact tgcagatatt 600 gataagattt cttcaactga actaatcaat aagctgcaat cacaggagca acgtgtcaac 660 atgcatgctc gtgtacctat tgaaggagcc ttattctcgt ctcaaactaa agctacccct 720 tcaaatcagt atcaaggcag aaggaatgga ggaaatcaaa ctggaaacca aagttccaga 780 aaacagaaga agtatcctcc ttgcaacatc tgctccctca caaatcattt agagagtgaa 840 tgctgttata agggaaagaa aactgtccaa tgcaacttct gcaaaagact tggccataag 900 gagaagttct gtaggcaaaa acaaaagctg gaagctgcac aatctaagca agagttgcaa 960 catgtaaatg tcactgagat atccagtgag caaaataata caattcttgt tgcttcaagt 1020 gaattgacag tggaagacaa cagcctctgg gttgttgata gtggttgcac ttctcacatg 1080 tgcaagaatg aagccatgtt tgtgttactt gacaaatcag taacaggcca agtaagactt 1140 ggaaatggca tgctggaaac cattaagggc aaagacaaca ttgctattga aaccaagaaa 1200 ggcagaaaac ttatcactga tgtaaatttt attcctaccc tctcacagaa tcttcttagt 1260 gtgaatcaga tgactgatcg aagctactcg gttggattca atgataactg ctgcaggata 1320 tatgatcctg aggatcactt gattgctttc atccaaaaga agaatcaagt ctactccttg 1380 aaactcagag aagtaattga gagagccagt gttgcctccg taactgaagg tgagatttgg 1440 cacaggcgcc ttgggcattt tcatgcggct gggctacaac aactacaaaa gggaggtcta 1500 accaaggact tcccaaatat tgcagtcact gagacagtat gtgatgcatg tcagatgggg 1560 aaattggcaa ggaattcatt tccttcgcaa gcagattgga gagcaaaaga gaagttggca 1620 cttatccatt ttgacatttg tggtccaatg acagaaagtt tcatgagtgg ttgcaggtat 1680 tttggcttgt tcatagatga tttttccaag atgatttggg tttgtttcct gcagaataaa 1740 gctcaaattt ttggtgaatt caaaaagttc aaggttattg cagagaagga aagtagcagt 1800 gtactgaggt gcctaaggac agataatggg cttgaattca attccagcca attcaatgat 1860 ttctgttatg agaatgggat caaaaggaag ctcacgacac catattctcc tcaacaaaat 1920 ggtgtctcgg agaggaagaa cagaaccatt atggaaatgg caagaagcat gcttgctgac 1980 aagcacctgc ctaaagcctt gtgggctgag gcagtgaaca ctgttgtgtt cctgctcaac 2040 atgctgccta caaaggctgt aaagtagatg acaccggtag aggcctggag tggcatcaaa 2100 ccatcaacta agtatctaaa ggtgtttaga tcaatgtgct actgccatgt ctcggatgac 2160 aggagatcca agctaaaaat gaaggccgag ttgtgagtat ttttggaata cagtactgaa 2220 gcaaaagcat acagaattct aaacctgaaa accaacaagc ttatgattcg aagaaatgta 2280 acggtggatg aaaacagcta ctggaattgg gagaaacaga aagtcaaacg agactatgtt 2340 acatttgaag aatgaaagaa atcaatgaca gtatcaaacc caactcagag tgatgaagaa 2400 gatgaagaat gtgaagcaaa agggagaata aaattgaaaa tctagctaac atctatgaaa 2460 ggtgcagttt tgcctcaaaa gaacctttct ctgttgagga agcacttcag cagtaagagt 2520 ggagacttgc tataaaagag gaaatcagga tgattgacaa aaacaatatt tggtctctgg 2580 taaaattaag tacaaacaaa aaaccaattg gagtaaagtg ggtgttcaaa gtaaaactca 2640 atccggacgg gacaacaaat aagcacaagg cacggcttgt ggcaaaggga tactcccagc 2700 ttccaggaat cgactacaca gaaacctttg ctcctgtggc cagatatgaa acaattagac 2760 tcattctggc catggcagct gagtttggtt ggagtgtgat gcacttggat gtgaaatcgg 2820 cttttttgaa tggcaagctg aatgaagaaa tttatgttga gcagccaccg gggttcattc 2880 aacctggaaa ggagattcac gtctatcttc ttcacaaggc cctatacggc ctcaaacagg 2940 ctccacgagc ctgatatgat aagttaaata catacttact tcactgtggg tttgagagaa 3000 gcatgacaaa aaacacactg tatgtgaata gagaagaaga ccgacttatc actgcagtat 3060 atcttgatgg tatactggtg acagacaaca acaaaaggaa aatgatagag ttcaagctga 3120 aattggaaaa ggaatttgag atgtctgatc ttggggaagc tacctacttt ctgggaatgg 3180 agattcatca aagcagcttg ggtatttttc tttcacaagg caagtatgcc aaagaaattc 3240 taaataaatt caacatgaat cactgtaaat cattatctac accactggtg tccaacctga 3300 aattgtcaaa ggacgagaaa ggtagcaaag tcgaagaggg aaattacaga agtctgattg 3360 ggagccttct gtatctcaca gctaccagac cagacatttt gtttgcagtg agtttacttt 3420 caaggtacat ggcttcaccg agggaatcac acttacaagc tgccaaacat gtgttgaggt 3480 acttgaaagg aacctagaat tttggtgttc aattcaaagc aagagttgag ggtggattag 3540 tcggctacag tgacagtgat tgagcaggaa gcgtaaaaga tgcacgcagc acaactgggt 3600 acttgttcaa aataggctcc ggtgtttttt catgggcatc taagaaacag gatactgtgg 3660 ctcaatccac agctgaggct gagtatgtag ccgcagctac agcaactaac caagcaattt 3720 gattgaggaa ggtgttcaac gatttaaagc tggacaaaca aacacctaca gtgttgtatg 3780 tagacaacaa gtctgcaatt gccattgcaa aaaatcctgt aatgcacgag agaactaaac 3840 acatcaacgt taagtatcat gctatacgtg aggctgagag gaatcaagaa ataaagctga 3900 tacattgctc caccgatgat cagcttgcgg acattctaac caaggccctg tctaaagcta 3960 aatttgagga tttgcggaaa aaggtgggga ttggtgaaaa aattcattaa gggggag 4017 // ID hAT-2_SD repbase; DNA; EDCOT; 4068 BP. XX AC AC149301; XX DT 17-OCT-2006 (Rel. 11.1, Created) DT 17-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE hAT DNA transposon from Solanum demissum. XX KW hAT; DNA transposon; Transposable Element; hAT-2_SD. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-4068 RA Jurka J. and Kohany O.; RT "hAT-2_SD hAT transposon from Solanum demissum."; RL Repbase Reports 6(10), 492-492 (2006). XX DR EMBL/GenBank/DDBJ; AC149301; Positions 1 4068. XX CC 21-bp TIRs. XX FH Key Location/Qualifiers FT CDS 1456..3288 FT /product="hAT-2_SD_1p" FT /translation="MVQTQLNPSNVSGSSIQRSYSREKDLEELAKMIVVMG FT LPFSFAENPGFIHYIQIVYNPHFKGFTRNTIKKAIFDYQAQHFQYLRCLFY FT YNNCKIAITSDMGRSVNGNDYFTITAHWIDENWTLQKRILGYKCCEMHKTG FT SYIAQTIIDVLQNYGICDKISSVTLDNASNNSNAVEILKPSLCPIYIDGFH FT IRCAAHIYNLIVRDGIAIYDDGCTKVETACHFIFKCQIKSRRRDFENRCRE FT FNLPPRKIPKLVCTRWNSLFEMLEVAYEYRKPLQMVWNAHNSNMTYRLDNN FT DWNDIKELIEFLKVFYLTTKKISALYYPTICSVLPNICAISTKFYKFKNKP FT RFEQSVKKMIEKFKKYFIPIPQIYLTACLLNPHYKDEGASRMVDKIYFNLG FT IDSEDDETPSCQDVKDSIKIEARKLYDLYNSNIRNVVHNEEPQSSRSRYNN FT EDDIDDMIDCIIELSHNDRNDFDAYINQNTEPTTIDLLEWWSNRGKGFPKL FT QPVARDVLAIQASSVASEGAFSAARFQIGEHRYSLAADSLEISVLFRDWIN FT GERRSYGRPPLPTKFENDIDEIMLDFSDDGIDAMEELANQPILEHVTREML FT NDLKKDFLGSMNY" XX SQ Sequence 4068 BP; 1339 A; 602 C; 661 G; 1466 T; 0 other; taagggtggc aacggaaccg ggaggtaccg gttccggtcc gttaccggtt ccgtctcggt 60 tccggatagt gccggttaga tccggatttg ttccggtccg ggaggggtaa cgggacggaa 120 atcgggattt actggtccgt cccggtccgg ttagtcccgg ttccgtcccg gtccagtccg 180 gttcagaact tttttatttt ttattttttt aatctgaaaa tttgaaaaat agccgttgag 240 agccgttggg caacgggttt tgggccccac caacggctct ttcaccccat aaccccccat 300 ttacacctcc ctacccccaa acttttttta ataccccaaa cttcttaaaa ctacattttc 360 aacctttttt tttaaactat aaatacccct aatctttcat tctttttcac tcacaaaaat 420 atcttataat ctctctactc tctagtctct ctactctcta aattctctta ttctcgactt 480 ctcgttaaaa ttacgaattt gatctttgga aattggagct tcaaaattca actttcaatt 540 ttcgccttcc ggtcatacac gtctactttt ttaagtagac gtttggtaca ttcgttccaa 600 ctcacttttc atttagttat ttatttgttt acatttaatt atttattttg tgagtaatta 660 atctctagtc tctacttatt tagttgttta tttgtttaaa actttgctaa tcattttcgt 720 attatatata atttactcac tttttataat ttgaatatgg attttggaaa aaacattatt 780 gaaaagggta aaacaaccat agttaattcg ttcactaatt tatctagctc aaaatccaag 840 aaaaataaaa aaaccgatag tacttctcaa tctaaaacta aaaaaacttc tcaattaaga 900 ataaatacgg atgattatac gcatgttgat gaaactgttt ttaatattga tagtaatagt 960 ggattagatc cttatcatga acatttacaa agaagatttg gtaattttga agaggaatta 1020 cctgaagatg atgaacatga tgatgttaat gcttatgttg atagttttga taataatgtt 1080 gatgaatatg atgatgatga aactgagcca ccatcggcta ctagtcccac tcccaatccc 1140 tcttccccgg ctcccgctcc ctttcgttgt cctgctccca ctccccccgt gcatcctagg 1200 actaaggtag aacgcgctaa aaaatcagtt gtgtggcaat ttatgactca gaatgaagat 1260 aaaacacaag ctatttgtaa taaatgtaaa catagaatga atcataaaac tgtaggaaaa 1320 cagggtggga tgagacattt gagtaatcat ttaatgtcat gttgtaaaaa tgaatttttt 1380 gcatgctaaa gctgtagccg aagctaaaaa aatggtacca cccttcctga aaatgtatga 1440 gtagatgact ctaatatggt ccaaacacaa ttaaatcctt ctaatgtttc tggttctagt 1500 atacaacggt catatagtag agaaaaagat cttgaagaat tagctaaaat gattgttgtt 1560 atgggtttgc catttagttt tgctgaaaat cccggtttta ttcattatat tcaaattgtg 1620 tataatccac attttaaagg ttttactaga aatacaatta aaaaggctat ctttgattat 1680 caagctcaac attttcaata tcttcgttgt ttattttatt ataacaattg taaaatagct 1740 attacttctg atatgggccg tagtgtaaat ggtaatgatt atttcacaat tactgcgcat 1800 tggattgatg aaaattggac tttgcaaaaa agaattttag gttataaatg ttgtgaaatg 1860 cataaaaccg gtagttatat agctcaaaca attatagatg ttttgcaaaa ctatggaatt 1920 tgtgataaaa taagtagtgt cacattagat aatgcttcta ataatagtaa tgctgttgaa 1980 atactaaaac cgtctctttg ccctatttat attgatggtt ttcatattag gtgtgctgca 2040 cacatatata atttgattgt tagagatggt atagcaatat atgatgatgg ttgcacaaaa 2100 gttgaaactg catgtcattt tatttttaaa tgtcaaatta agtctagacg tagagatttt 2160 gaaaatcgtt gtcgtgaatt taatcttcca cctagaaaaa ttccaaaatt agtgtgtact 2220 agatggaatt ctttatttga aatgcttgaa gttgcttatg aatataggaa acctttacaa 2280 atggtttgga atgctcataa ttcaaatatg acatatagac ttgataataa tgattggaat 2340 gacataaaag aacttataga attcttaaaa gttttttatt taactacaaa aaaaatatct 2400 gcactttatt atccaactat ttgctctgtt ttacctaata tttgtgctat ttctactaaa 2460 ttttataaat tcaaaaataa accaagattt gaacaatctg ttaagaaaat gattgaaaaa 2520 tttaaaaaat attttattcc tattcctcaa atttatttaa ctgcttgttt gttaaaccca 2580 cattacaaag atgaaggtgc atcacgaatg gttgataaaa tatattttaa tttgggtatt 2640 gatagtgaag atgatgaaac acctagttgt caagatgtta aagatagtat aaaaattgaa 2700 gctagaaaat tgtacgactt gtataattct aatataagga atgtagtaca taacgaagag 2760 cctcaaagtt ctaggagtag atataataat gaagatgata ttgatgatat gatagattgt 2820 attattgaac tttctcataa tgatagaaat gattttgatg catatattaa tcaaaataca 2880 gaacctacta ctattgatct tctagaatgg tggagcaatc gcggcaaagg atttccaaaa 2940 ctacaaccgg ttgctcgaga tgtgttagct attcaagcat cttcagtagc ttcggaaggc 3000 gcttttagtg cagcaagatt tcaaattgga gagcatagat attcattagc agcagatagc 3060 ttggagatat ccgtactatt tagagattgg attaatggcg agagaaggag ttatggtcgt 3120 ccacctctac cgaccaaatt tgaaaatgac attgatgaaa taatgctaga ttttagtgat 3180 gacggcattg atgcaatgga agaactagct aatcaaccaa ttctagagca tgttactaga 3240 gaaatgttaa atgatttaaa aaaagatttc cttggtagca tgaactatta aatttaaatg 3300 tctattagta tgagtataat aattcgaggt ctaattcaaa cagaaccctt cctagaaggt 3360 ggctgtgtag attagatttt ttaatactct actaatattt tgtaactcaa cttgtactat 3420 ttaattaata ttaataaaag tataggctat tcgccttaat ttttttttat tattgtcttc 3480 aaaagttcaa atttaacttt taaagtgtga aatttaaact tttatagttt taaattttca 3540 aacttttaaa gtgtgaaatt taaactttta tagttttaaa gtttgaattt aaattttcaa 3600 acttttaaaa tttaaagtgt gaaatttaaa tttttatagt tttatagttt taaagtttat 3660 aatttaaatt taaattttca aacttttaaa gtgtgaaatt taaacttttt atagttttaa 3720 agtttgaaat ttgaatttaa attttcaaac ttttaaaggg tgaaatttaa acttttatag 3780 ttttaaagtt tgaatttaaa ttgtgaaatt taaattttta tacttttaaa agtttgaaag 3840 tttgtattta aaactttaaa agtataaatt tttaagtgta atattcctaa ttttgtaatt 3900 ttaataaaaa aatataattt ataatggttg gacccggttt ccggtctggt ccggtccgtt 3960 accggtccgg gacgggtaca cgtatttttt tccagaatta ccggttccgg ttcggttccg 4020 gaacgtcccg gtccggtagt tccgttaccg gttccgttgc ctccctta 4068 // ID Copia12-VV_I repbase; DNA; EDCOT; 1917 BP. XX AC AM468287; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia12-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1917 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-1917 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 720-720 (2007). XX DR Genbank; AM468287; Positions 22289 20373. XX CC Positions [1660-1875] - Integrase core CC 'GTTTC' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 79..1917 FT /product="Copia12-VV_I_1p" FT /translation="MEESSLTVAPSILDGDNYETWAVRMTVHLQALDVWEA FT VEENYEVPPLGANPTVAQMKLHKERRTRKAKAKACLFAAVSPSIFIKIMKI FT DSTAEIWEYLKEEYKGDERIKNMQVMNLIREFEMKKMRESDAVKDYAAQLL FT SIADKVRLLGKEFSNEKIVQKILVTLPEKYEATISSLENSKDLSTISLTEL FT LHSLEAVEQRRLMRQGDTAEGAFQARMQKNAGHKNGKMNNNKPCSNNQKNG FT VFPPCPHCKKTNHSPQKCWWRPDVKCNKCGKQGHVERICKNQQQEETSAAV FT DYCQEEQLFAATCFANKSTSKSWLVDSGCTNHMTNNQDLFRELDRTIISKV FT RIGNGEYIPVKGKGTVAIESQTGLKLIYDVLFVPDIDQNLLSVGQLVEKEF FT KVYFEDKNCIIKDAEGKEVFNIKMKGKSFALNLLEDKHTAILQQDSTTMFW FT NRRVEHFHHDDVLYMKKNQIAEGLPDLEKDLPICATCQYGKQTKLPFPKKI FT SWRATQKLQLVHTDVGGSQKMPSLKLNANNVHQLTAPYNPQQNGVVERKNR FT TILKMTRCLLHEKYLPKKFWAKIASRTVYFLNILPTKVLKKQTPFEVWFEC FT LRARLGVCIYEVKEE" XX SQ Sequence 1917 BP; 694 A; 319 C; 416 G; 488 T; 0 other; aagtggtatc agagccatag ttatcttgag gggccagtga ggtgagtgaa cccaaacacc 60 ttctaaaatc atttagcaat ggaagagtca agtctcacag ttgcaccatc aattcttgat 120 ggagacaatt atgaaacttg ggctgttaga atgacagttc atctacaagc acttgatgtt 180 tgggaagcag tggaagaaaa ttatgaagtt cctcccctag gagccaatcc aactgtggct 240 caaatgaagt tgcataaaga aagaaggaca agaaaggcta aagcgaaagc ttgcttgttt 300 gctgcagttt caccatcaat tttcatcaaa atcatgaaaa ttgattcaac tgcagaaatt 360 tgggagtatc tcaaggagga atacaaagga gatgaaagaa tcaagaacat gcaggtgatg 420 aacttgattc gagaatttga aatgaagaaa atgagggagt ctgatgctgt taaagactat 480 gctgcacaac ttctttccat agcagacaaa gttaggctgc ttggaaaaga attttccaat 540 gagaagattg ttcaaaagat attggttaca cttcctgaga aatatgaagc tacaatttcc 600 tctttggaga attcaaaaga tctgtcaact attagcttga cagaattatt acattccttg 660 gaggctgtgg aacaaagaag actcatgaga caaggagata ctgcagaagg agcatttcaa 720 gcaagaatgc agaaaaatgc aggccataaa aatggaaaga tgaacaacaa caagccatgc 780 agcaacaacc agaaaaatgg agtttttcca ccttgtcctc attgcaagaa gacaaatcat 840 tctccacaaa aatgttggtg gagaccagat gtgaaatgca acaagtgtgg taaacaagga 900 catgtggaga ggatttgcaa aaatcaacaa caggaagaaa ctagtgcagc agttgactat 960 tgccaggagg agcaattgtt tgcagctacg tgttttgcta ataaaagcac ctctaaaagc 1020 tggcttgtgg atagtggttg tacaaaccac atgacaaata atcaagatct ctttagagaa 1080 cttgatagaa caattatttc caaagtcaga attggaaatg gtgagtatat tccagtgaag 1140 ggcaaaggaa cggttgctat cgaaagccaa acaggtttga aactcattta tgatgttttg 1200 tttgtgcctg acattgacca aaacttactc agtgttggac agctcgttga gaaagaattt 1260 aaagtttatt ttgaagataa gaattgcatt atcaaggatg ctgaaggcaa agaggtgttc 1320 aacataaaaa tgaagggcaa gagttttgcc ttgaatttac tggaagataa gcatactgct 1380 attttacaac aagatagcac aacaatgttt tggaacagaa gggtcgagca ctttcatcat 1440 gatgatgtgc tctacatgaa gaaaaatcaa atagctgaag gacttcctga cttagaaaaa 1500 gatcttccta tatgtgctac ttgtcaatat gggaagcaaa ctaaacttcc ctttccaaag 1560 aaaatatcct ggagagcaac ccaaaaactg caactggtgc atactgatgt aggtggatct 1620 caaaagatgc catccttgaa attgaatgca aacaatgttc accagctcac tgcaccatat 1680 aatccacaac aaaatggagt cgtggagagg aaaaatagaa caattttgaa gatgacaaga 1740 tgccttctac atgaaaaata tctacctaaa aaattttggg ctaaaattgc aagtagaaca 1800 gtatattttc tgaacatatt gccaacaaaa gtgttaaaga agcagacccc tttcgaagtt 1860 tggtttgagt gtctacgtgc aagacttgga gtttgcatct acgaagtcaa ggaggag 1917 // ID Copia-77_Mad-I repbase; DNA; EDCOT; 6327 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-77_Mad_; KW Copia-77_Mad-LTR; Copia-77_Mad-I. XX NM Copia-77_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6327 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1692-1692 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [3221-3712] - Integrase core CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS 2015..5674 FT /product="Copia-77_Mad-I_1p" FT /translation="MEDKLIPLYEEYDSAKEIMDVLEKKYGPKSQTYIQLL FT LEKYNGTKMEETDSMVDHITKMEVMAKDLANAGHPVSDKMQVSVLLGSLPN FT SWENVVTSMTYGQVELTMDTLPAMLAIEEVRKNYRKKETGQGRANLLIAED FT SQKNKQHMHKPHSSNKRPNFKKFGHRKQNKFKGKESACYNCGETGHYRYKC FT PKRRKNNKNPKELILTVSEALIAEDQGQWWIDSGATRHVCKDKSCFINFKE FT KALGEHRLYMGNNTYVDVLGEGDCKINNSKSTIVLKNVLFAPNIRRNLVSV FT SVLEKKGFETRFMNGAVTIGKKGYIYVRGIRVDDMYSVCINKSISSEYAFV FT STVQNLSYLWHLRLGHINKNKMIRMSKNGMLPQVNAHDFDTCESCIKGKMT FT RKSFSQHWTSTNLLEIVHTDLCGPMRTKTHRGMKYFVTFIDDYSRYGHVYF FT LQHKNEALDKFKEFKAEVENQLGRSIKTLNSDRGGEFEAFDDFCKENGIRH FT NYTMPYTPQQNGIAERRNRTLMDMMRSMMSYADLPLHFLGEALATAAYILN FT KVHTKAKPLTPYELWHGRKPDLSNLKVWGCKAHVLIPKPLRNKLQAKTLEC FT KFIGYPDNSIGYRFYHPEKGLIESRDATFIETTDLVNPIQELESLEEENSP FT TDDQDFHLDLDLSHDHDIDNDQVGDVNMGDHNNVDHDTHMDDDHDIIMEDI FT NSGRNDQISGSKRKREPSRRLKDHFVFNLEEVDHSVGDPDPRNYKEAMDSF FT ESEQWQQAMNEELDSIKKNEVWELVDLPNGRKPIGCKWVLRKKYKSDGTLD FT KFKARLVAKGYTQKPGIDFVDTYSPVAKFTSIRILMAIVARMDLELHQLDV FT KTAFLNGDLKEDIYMIQPEGYHVKGHENKVYKLRKSLYGLKQSSRQWYLKF FT HQAIMEMGYKINPLDHCVYSWKCQDNFCMLSLYVDDILLAGNSIDMIEKTK FT SYLGSKFEMKDMGEASYVLGIKITRDRDAKTLYLDQQNYLDKIFKRFNMQD FT CKPVSTPVCKGMMLSKNMCPVQKQDIIDMQNVPYAQAVGSLMYAMTSTRPD FT ICHAVGLVSRYQSNPGKQHWMAVKRIIRYLKGTQGMKLCFGLNDLDLVCYC FT DADFAGDLDDRKSTSGNIVLFGGTAVSWLSKKQGCVAKSTMEAEYISCSTA FT VSTAVWAKRFIDNLNIGIPKEHVNVFCDNKSAIFLIKSGANSSKGKHIDVK FT YHYVQDIVEK" XX SQ Sequence 6327 BP; 2116 A; 1080 C; 1332 G; 1792 T; 7 other; atttccatca ttggcctcag agccaggttt tcatgaatca aaacaatttg cccagttttc 60 atccgaggac gtctcgaact acatttgaga cttcctcttc gtcaagtaac gaatccaaca 120 acgttcttac taagtttcaa cttgagaaga aattagggaa gaggacgttg gtggataagg 180 aaaatattca accgattttg atcgaaagtt cgaaatcgkc atctgagaat tttcctgcag 240 aacccaaaac tcacaaaaat acccaatcat tcgaaatccc atcctacaac ccgtttgaac 300 ctaggcctga attaacccaa caattcgaac tatattcccc tacaccattt cattcgacag 360 agaacaaaat tctctgaaat tgaaccattt cagcgttcaa attcactaag ttcatccccc 420 tacmattatc agaattcgga aaggttttac agtcctatta ggacctcaga aaacccattt 480 cagtcgggat tkttggctgc aaaaaccgaa tctgcacaag aacttgaaac ctacaggccc 540 agtgcccaga tccctttcct amatttggtc accaagccca agggatttac ctgcaccatc 600 gagtctgatt cgaagtcgtt ctctgactgc tcaaatatcg cgccctggcc tccgccgtgg 660 actcgccgca cccgccggcg tggtcgtgct ctcccaccgt ggtcgcgtcc atccagccgc 720 ggtctcgtcc tctcgtggta atacacaaca ccgacgacac cgatttcctc caagaaaaat 780 tgtctctgcc gttcgtgatt acccgccggg ttgcgggacg aagaagagag aagaaacttt 840 tttcccagag aaagtgtttg gaaataaaga aggagaagat tacttaaaaa agggatcttt 900 ttcggggaga aaggtgattc acaagagtcc aggtcaagga aaaactcctc cattgcattc 960 gagattcatg tgaaaggcat cacgtgttga aagacaaagg gaatttgttt tggttcwgag 1020 cactctgaca gtgcacgtga aagatcaggg gtttcacgtg gagaagcaac caawgatagc 1080 agattttttg gtccatcaca aagtcaaatc gacaggtcct ttgaagtggg ctcctcctct 1140 aggcaaaatt cgggacagct gcaattggag ccatttccta ctcatttggg tgttacgatc 1200 gaaccaaatt caggttttat taatcccgtt taccctaata atttcactca tagagttgat 1260 ttgtggaata ctttgaataa tagtcacaaa gatcaaaagt ggaagcaagg gtttaatttt 1320 cggaattcta gagtcaaagt gcttaattat ttggatcaac ataatacccg ttacggtttt 1380 atatatcctg atttggcaca aagagaaatt tcgactgcaa gaaatttaag ggggccaaga 1440 ccactgagaa ttgaaagaga atccagtaga cgagaagaga ctgcttttgt gcacgaaaat 1500 agaggaagaa ttgatcacac ctggccaagt agacaagcaa gaaatccacg agccttctat 1560 cgacgtgatc gcctgaacaa gtactcgtct ttcactgatt ggacaaagcc tctgtgagtg 1620 tgtgcggtat ctgctactaa aaataaataa gtctctatct ttattttatt ttttttttta 1680 gtctttaatt tattaagaac atttagtatt tgtggcttgt aataattaaa agtacactag 1740 tagtatttgt atttgtattt aagtttgtat taagtattgt gtttgttttg taattttctg 1800 agctatggca actaaatctt ccaaatccga agtttttaaa atagagaggt tgaataacgt 1860 taattatcga atatggaaga gaakgatcac ttatctttta acccatgaca agactttgta 1920 cactatcaag gacgagagac cccttgggcc ctctcgagtt tataataaat gggtggaaga 1980 taatgagttg gctaaggcca caatcctcaa ttacatggaa gataaattaa tacctctcta 2040 tgaagaatat gattcggcca aagaaatcat ggatgtactt gaaaagaagt atggccctaa 2100 atctcaaaca tacattcagt tattgcttga gaaatacaat gggacaaaaa tggaggaaac 2160 tgattctatg gtcgatcata ttactaaaat ggaagtaatg gcaaaagact tagccaatgc 2220 tggccatcca gtttctgata aaatgcaagt tagtgttctt cttggtagcc tcccaaattc 2280 ttgggaaaat gtagttactt ccatgactta tggtcaagtt gaattaacga tggatacatt 2340 gcctgcaatg ttggctattg aagaagttcg taaaaattat aggaaaaagg aaactggaca 2400 aggcagagcc aacctcctca tagcggaaga ttctcagaaa aacaagcaac acatgcacaa 2460 gccacatagt agtaacaagc gcccgaactt caaaaagttt ggacaccgca agcagaacaa 2520 gtttaaagga aaggagagtg catgttacaa ttgtggagag actggtcatt ataggtataa 2580 gtgcccaaaa cgacgcaaga acaacaaaaa tcctaaagaa ctgattttga ctgtctccga 2640 agcactcatt gctgaagatc aaggacaatg gtggatagac tcaggagcaa ctcgtcatgt 2700 atgcaaggac aaaagttgct tcatcaattt caaggagaaa gcactaggag aacatcgtct 2760 ctacatgggc aacaatactt atgtcgatgt tttgggtgaa ggagattgca agatcaacaa 2820 tagtaaatct accattgtgc ttaaaaatgt tctgtttgca ccaaatataa ggaggaatct 2880 tgtctctgtc tctgtcctag aaaagaaagg ttttgagaca aggttcatga atggtgctgt 2940 cactattggg aaaaagggtt atatttatgt aaggggaata agagtcgatg atatgtactc 3000 agtttgtatt aataaaagta tttcttccga gtatgccttt gtctctactg ttcaaaattt 3060 gtcatattta tggcatttac gtttaggtca cataaataaa aataaaatga tacgcatgag 3120 taaaaatgga atgttgcctc aagtaaatgc acatgatttt gatacatgtg aatcatgtat 3180 taaaggaaaa atgactagaa aatcattttc tcagcattgg acttctacaa atttacttga 3240 gatagtgcat acagatttat gtggaccaat gagaactaaa acccatagag gaatgaaata 3300 ttttgtgact ttcatcgatg attattcccg ttatggacat gtctacttct tgcagcataa 3360 aaatgaagcc ttagacaaat ttaaagagtt taaggcagaa gtagagaacc aattgggaag 3420 atccataaag acccttaata gtgatagagg tggagaattt gaagcctttg atgatttctg 3480 caaagagaat ggtataaggc ataattatac tatgccttat acaccgcaac aaaatggtat 3540 cgcagaaaga agaaatcgaa ctctaatgga tatgatgcga tctatgatgt cttatgctga 3600 cttacctcta cattttttgg gtgaagcttt ggctactgca gcatatatat tgaataaagt 3660 tcatacaaag gcaaagccac tgactccata tgaattatgg catgggcgaa aacccgattt 3720 atcaaactta aaagtttggg gttgtaaagc gcatgtcctc attccaaagc cattaagaaa 3780 taaattacaa gcaaagactt tggaatgtaa attcatagga tatcctgata atagtatcgg 3840 atataggttt tatcatcctg agaaaggatt gatcgaaagt agagatgcta cttttattga 3900 aactactgat ttggttaatc caatacaaga attggaatct ttggaagaag aaaattctcc 3960 tacggatgat caagatttcc atcttgattt agacttgtct catgatcatg acattgacaa 4020 tgatcaagtg ggagacgtaa acatgggtga tcataacaat gtcgatcatg acacacacat 4080 ggatgatgat catgatatta tcatggaaga tataaatagt gggagaaatg atcaaatcag 4140 tgggagtaaa agaaaaaggg aaccatctag aagattgaaa gatcactttg ttttcaatct 4200 tgaggaggta gatcattcag tgggagatcc agacccaagg aattataaag aagcaatgga 4260 tagttttgag tctgaacaat ggcaacaagc aatgaatgaa gaactagatt ccataaagaa 4320 aaatgaagtt tgggaattgg ttgatctacc taatggaaga aagcccatcg gttgtaagtg 4380 ggtacttcgt aagaagtaca aatcagatgg taccctggat aagtttaagg ctcgacttgt 4440 agctaagggt tatactcaga aacccggtat agattttgtg gacacttact ctccagttgc 4500 gaagtttaca tccattcgta ttcttatggc aattgttgct agaatggatt tagaacttca 4560 tcagttagat gtcaaaacag cattcttgaa tggagatttg aaggaagaca tctatatgat 4620 tcaacccgaa ggatatcatg tcaaaggaca tgaaaacaaa gtctataaat taagaaagtc 4680 gttgtacggc cttaaacaat catcaagaca atggtattta aagttccacc aagccattat 4740 ggaaatgggc tacaaaataa atccattgga tcattgtgtt tactcttgga agtgccaaga 4800 taatttctgt atgttgtcac tatatgtaga tgacatctta cttgcaggta actctataga 4860 tatgattgaa aagactaagt catatctggg atccaaattt gaaatgaaag atatgggaga 4920 agcatcttat gttctaggaa ttaaaattac tagggataga gatgccaaaa cgctctattt 4980 ggatcaacaa aattatctgg ataaaatatt taaaagattt aatatgcaag attgcaagcc 5040 agttagtaca cctgtttgta aaggaatgat gctttccaaa aatatgtgtc cggtacagaa 5100 gcaagacatc attgatatgc aaaatgttcc gtatgcccaa gcagttggaa gtttgatgta 5160 tgctatgacc agcacaagac ctgacatatg tcatgcagtt ggattggtaa gtagatatca 5220 atccaacccc ggaaagcaac attggatggc agtaaagaga attattagat atctaaaagg 5280 cacccaaggt atgaaacttt gtttcggatt aaatgatctg gatttagttt gttattgcga 5340 tgcagatttc gcaggcgact tggatgacag aaagtcaaca agtggtaaca ttgtcttgtt 5400 tggtggaacg gctgtttctt ggttaagtaa gaaacaaggc tgtgttgcaa agtctaccat 5460 ggaagcagaa tatatatctt gtagcacagc ggtaagtact gcagtatggg ctaaacgatt 5520 tatcgataat ttaaatatag gtatacctaa ggagcacgtc aatgtgtttt gtgataataa 5580 gtccgccatc tttctgataa agagtggagc aaatagttcc aaaggaaaac acattgatgt 5640 taaatatcac tatgtacaag atatagtgga gaaatgagag gtagaggtcg actacatacc 5700 ctccgaagag atggtggccg atccgatgac caagggattg tctctggaaa aattcagaga 5760 gcatgtgact acaatgggtt tgcaaaacat ctagatgtgt tgtagtgtga gacgtgcggc 5820 gggcatcgtt gtatggtttt agggacgcct gaaacatgga caagtagatg cgactctatc 5880 tggttcttta gtacttggtc ggttaaagat agagggcact agcgaggtaa ccaggttata 5940 ataaatcgtc ttgaaagtaa aatccgtaat aagcttcaag aaataattta tataacactg 6000 tggcgtatag tgcggggcta agtcatcatt tgtaaccggg tatggattgt ttttcctagt 6060 tacttggata tgatgccatt ttactaaaga gtaaaatgtt atcagattaa gtggaatggt 6120 gcgcaccagg taaagaagcc acatatctga tgttacattc aatttgttta tgagtaatac 6180 tcttgagaaa caaatcagaa taggaaacca tttatgtcat cataatcaag tgggagatgt 6240 tggaatatga ttatgataac atggttttca caatatgtgt aatcatgtgt gaaggtacac 6300 cataacattg gtgtactaat atacata 6327 // ID GYPSY3-LTR_MT repbase; DNA; EDCOT; 2088 BP. XX AC . XX DT 14-SEP-2005 (Rel. 10.09, Created) DT 14-SEP-2005 (Rel. 10.09, Last updated, Version 1) XX DE Gypsy-like LTR retrotransposon from Medicago - LTR consensus. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; gag-pol; reverse transcriptase; GYPSY3-I_MT; KW GYPSY3-LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2088 RA Gentles A. and Jurka J.; RT "Gypsy element from Medicago truncatula."; RL Repbase Reports 5(9), 249-249 (2005). XX DR [1] (Consensus) XX CC LTR element corresponding to GYPSY3-I_MT. XX SQ Sequence 2088 BP; 719 A; 465 C; 308 G; 588 T; 8 other; tgtcataccc caaattttga cctaaggtcc cactgacaca cgtctccgaa ctcggaccag 60 actcgcattt cagtgaaaaa ttcggcaggg aggtattttg aaatacctca taaaattccg 120 aatcgggccc tcttctctca gtctttaatt atttatttcc atcttttaat ttagaactct 180 aattttaatt ttagtccaag attagattaa atttctttta ttcatttttc ttttttagac 240 attatccttt tattattatt tatttttttt ccttttaatt aaaatcccaa aattgtccaa 300 aataagtcca aaaatagtcc gagttcaaga tctcaatcct tatacacgtt ctgttccttt 360 tccatcccaa tccaaaatcc agttcatgcc tcatctgaaa caaatccagt aaaaaacaga 420 cgcatttcct tttttctcct ccacaagcca ctgattttgt gctcatcagt aacaaattct 480 agcctcaaac tcactctata aatagagacc tgcacaacaa agaaaaacac aacaaaaacg 540 cagcagaaca agaaaaacag agaagccaca cacaacagaa tacgggaaca agagaagcca 600 cacacgcggc atcacaacaa cggcagaacc gcaacaacaa caacggcaga accgcaacaa 660 caacaacggc aacgcacama cacccacacg cggcaacaca acacggcaga accgcaacaa 720 caacaacggc agaaccgcaa cacaagcacg cacacacaca actcaacgtg aacacasaac 780 acggcaacgc acacacaaca ggaaatcgca aaccaacacc ataacaaaac cggatccaca 840 aaaaaacaaa aaggtataaa tttctttctt ttttagatct agacgtttgg gtaaaggttt 900 tgggaatttt aggkttagaa gtgaacagag ggagagaagt agaagagaaa gagcgaaaaa 960 aattaaaaaa aatggagctt tttgggctcc ggcgcggygg cgcmgccgcg atggctcgcc 1020 ggccaccgcg ccggaattcc cccatcccct ycgccggaga agaagagagm tagagagaga 1080 acagagaaga agagagagaa cggtgaggaa gagagagaaa gaaaaggaaa aatgaaagaa 1140 ttagggttca acaaccctta tatayccccc aaacgggtca acccatgacc catgacccac 1200 gacccggttc gtttccttaa gcccaattct tttttttctg ctttctgcac acccctgttt 1260 actactgcac cccaccttgt gtttggacct tttttatttt tttccttatt ccttttcgta 1320 tttatttatt tttcttagca ttttaattct tattgcagac cttagaatgt aaataggctt 1380 tttatgtaat agtcatagat tttatatttc taacttaggg tagccgcgct tttattcttt 1440 atgctccgtt agtttatata tttattcaaa aatcacaaaa acatgcaaat aaccaaaaat 1500 cacaaaaaca ttttcataaa taaaccttga tcctaaatca agtgatcgtc tttattttat 1560 ttttttcata aatcaaatat caatcaattt aattctactt tgagttattt ttttttaata 1620 aaaaacacaa acaaattctt atttgccact tggcttttat ttttaaaacc ttttttcaaa 1680 actaataaaa aacacaaaac caatcaaacg ttgttttcta ccccgaacta cgaggttttg 1740 atccttcacg ggtacgtagg cagaggacac tcgtccttcc aaacaataaa aaatgtgtag 1800 ataattaggt ctttatcttt ttcactttaa ttctttcttt tcaaaagcaa gcaagttata 1860 gcacattgaa ttaaataaaa tcaagaggtt cccgtagagt actacggaca tagagggtgc 1920 taataccttc cctttatgta actaaccccc gaaccctaaa tcttttcaaa taggggtagt 1980 ttgaactttt ttcccctttt tcttaataaa attaaatgtt cagtcgtgaa ataattagtg 2040 agtcaaaagc taatcaaata gccttgatct ccaaaaaatg acgcgaca 2088 // ID Gypsy-34_Mad-LTR repbase; DNA; EDCOT; 1467 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-34_Mad-LTR. XX NM Gypsy-34_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1467 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1763-1763 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 1467 BP; 400 A; 221 C; 289 G; 557 T; 0 other; tgatgagtga attttatatt atatatttaa ccctattctt agtatatttt ggttaatatt 60 ttggaagaat tttgatactt tgaattgtat tttcaatata ggactttcga cttcctctgg 120 agcaaaacgt ggtcaaatgg acgaattttg gagtaattcc agttggagga cgttcgtgag 180 tcacttagct tgatcgtatc aaaatttggg atttttccac caagcggtta ttttctggcg 240 ataaaataaa ggagcgatgc gcggtgctgg aataatgacg tttctgggct taaattgcgt 300 ttttggagcc caagatgacc tcggatggtt tcgtggcctt ctggagatgt gttcggaacg 360 tccttatctt taaaacaagc tatcttgggc cggatttgga ggagatctga ggctaaaacg 420 tggctggaca agtacttggc agattctcct agtttaatta gggttttatt ttctaagata 480 ttttattatt tttcttagtt tcctagttgg aataagagac ctatgtctta gggtttgtgg 540 agggctgagc aaatatattg ctttggccgt ctacagtttt tcgctacgct tattattatt 600 caacttcaga gacaaagaac ttggctaggg ttcttggaga ttttctactt taaggtgttt 660 tcattccttt tcttcttaat aatattttct atgatttcaa ttatgaatat gcgtaactaa 720 ttccttttgc tagggcgaag ccttgagcct tagcatgaat atgtaatttt tatttaattg 780 cttatgattg attgcatgca cactttgaat tattgatcac tgttttaaac tatctaatta 840 tcttgatgac tggccaccat taggatgttt agacaagtaa ttggatgcaa ttcggtcgga 900 atatcaccgg aggattgagt attgcttctt gtgattgata attgtaattt catctaaggc 960 gaatatcacg ttcttagggg ttgcatggtt cttcaaaagg ttttcataaa acttaatgag 1020 tcttgcatgt tcatatttga tctgaatatc acagacggat tgcatgttag atatacgttc 1080 ttgcttgaat atcacgagga gaatatatat taggaaaacc taaccttcaa agtggcatgt 1140 gtaaatcgta agtaattggt agaaattcat aggattgcta ggtgatggtg gaaccctagt 1200 gcctttataa attggtattt aaaactcttt tcttcgatta ttttagtttt tgtttaaaat 1260 tcgtttttaa tattacccat tctcaaactc tcttttctca agttttaatt ctaagtattt 1320 aattaggaat tgtttctaca caaattatcc aaatagtcct tgaggagaac gaccttgcat 1380 gagcatctat actacaatat ccttgtattc ttgcaagtat ttcatgtgat tttgacccta 1440 tttgcataga cgttaaaaat cctatca 1467 // ID Copia-93_Mad-LTR repbase; DNA; EDCOT; 177 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-93_Mad_; KW Copia-93_Mad-LTR; Copia-93_Mad-I. XX NM Copia-93_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-177 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1725-1725 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 177 BP; 54 A; 19 C; 32 G; 72 T; 0 other; tgttagaaag tcaatgtaac tagataggaa tgttttattt aattgatttg taattgatac 60 tttctgttat cgtattccta gtttctaggt cttcttgttg tacaaggaaa ggtattgtat 120 atatattgag cattctatca atgaaaggaa tgattctggc taaatacagt tttcaca 177 // ID COP14_I_MT repbase; DNA; EDCOT; 3961 BP. XX AC . XX DT 02-JAN-2007 (Rel. 12.01, Created) DT 02-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of COP14_MT LTR retroposon from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR; retroposon; internal region; Interspersed; repeat; ORF; KW COP14_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3961 RA Shankar R. and Jurka J.; RT "COP14_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 9-9 (2007). XX DR [1] (Consensus) XX CC The internal region is flanked on both sides by LTRs and has CC domain for reverse transcriptase. XX FH Key Location/Qualifiers FT CDS join(1374..2507,2643..3950) FT /product="COP14_I_MT_1p" FT /translation="MENGIVHQSTCVNSPQQNGIAERKNRHLLEVARALLF FT STKVPKYLWGEAVLTAAHLINRMPSRVLNLKTPLETFLKFFPIASVAANLP FT LKIFGSTAFVHEHKQIGKLEPRAIKCIFVGYSPTQKGYKCFDLNSKRLLVT FT MDVTFFENKPFFESNHLQGGKSNEDSSYFFEDLILSENMFMSHSSRPSVPI FT ENAPDNVNESTPSMSEDVTESGATNQNSNNDSLEPKDNQELIQMSLHEHPY FT NETERKFGEVEGTWKGVIYGRKNHDKVVEDLIPQHSHESEPRENQLTKTNK FT GKGKISPDFHDPILDVPIAHMKPVRACTKHPMSRFVSNSNLSSSFSAFTSH FT LSCIEIPKNVQAALNVPKWKEAVFEEMRTLEKNNTGMDYSETFAPVAKLNT FT IRILLSLAANLDWPLHQLDVKNAFLNGELEEEVYMDGPPGFEEKFGSKVCK FT LKKSLYGLKQSPRAWFEKFTKSVKKQGYTQGESDHTLFVKYTPGGKITILI FT VYVDDIVLTGDDVTEMERLKRNLAAEIEIKDLGSLKYFLGMEIARSKKGIS FT VSQRKYVLDLLQETGMSGCRPADTPMDPNLKLWEKGDTPVDSGRYQRLVGK FT LIYLAHTRPDIAFPVSVVSQFMHAPYEEHLDAVYRILRYLKAALGKGLFFG FT KTNDRDVAIFTDADWAGSITDRKSTSGYCTYVWGNLVTWRSKKQGVVARSS FT AEAEFRAMAQGICEGLWIHRVLKELKMTVELPLKLYCDNKAAISIAHNPVQ FT HDRTKHIEIDRHFIKEKLDSGILCLPFVPSNQQTADILTKSLARTSFEHLI FT SKLGMIDIYAPT" XX SQ Sequence 3961 BP; 1262 A; 694 C; 780 G; 1225 T; 0 other; atggtatcag agcccccaat ttttttgggg ctttgcttcc gcataaaccc tagccaccat 60 cattacattt tttttcttta ctgggttttc agatccagcg tcagtactgt tcataccgcg 120 tgtactgttc acactattca tctcagcggc actgttcata cgcggttact gttcactcgt 180 cactattcat tggaaaaaaa ataaattcaa acttagtagt ttgcagtatt tgagtcggat 240 caaagagtga aaattaaggg gatgaataaa tcaaagaccc gaagagagaa ggcgcggcaa 300 agggtgatga tgggtaagac aatttttaac tcgtcaaccg aaggtcttgc actccaagat 360 acttctcatc aagggcagca gtcttcctca aactcacttc catccaccaa tgaacaactg 420 tacaatattc ttgagtctca aactacttcc cgtatgtttt ctttcggttc cattgccgaa 480 aaagataatt ttttagagtc agcccttctt agtgtcaaac caagtcgtac ttggattgtt 540 gattcaggtg ctaccgatca tatgacagga gagtctagta tgttttcttc atatagtcct 600 tgtgcaggta atttaaaaat taagattgcc gatggttctc tttcagccgt ggcaggaaaa 660 ggttctgtca ttatttctcc attattaact cttccaagat gttttacatg tcccaaattt 720 gtcgtataac ctattgtctg tcagtaaatt aatccaggat aaaaggtgtc aaactcattt 780 ttttgatact cattgtttga ttcaggattc aatctcgggg aagatgattg gcaatgctaa 840 gctgaacgga ggactctact accttgaaga taaacttgaa actggacatc aacttggaca 900 aataagttct ttctctgaat ccttttttgt ttcaaataat aaggatgatg ttatgttgtg 960 gcatttaaga ttgggccacc caagtttcaa atatttaaaa actgtatttc gaaaattgtt 1020 tgttggcaag gatttttctt cttttcaatg tgaaatttgt gaacttgcaa aacatcacag 1080 aagttctttt cctgcccaaa catataaacc ttcaaaacct ttttctatta ttcatagtga 1140 tgtttggggg cctaatatga ttaattcttt atccaacaaa agatggttta tcacctttac 1200 taatgatcat actagacttt gttgggtata tttattaaaa gaaaaatcag aggtaggaca 1260 aattgtcaag aattttattt aattagtgca gactcagttt aattccacta tacaagtttt 1320 cagaactgac aatggaactg aatattttaa cacagtttta ggaaactttt tttatggaaa 1380 atgggatagt tcatcaaagt acatgtgtta actcacccca acaaaatgga atagcggaga 1440 ggaaaaatag gcaccttctt gaagtggcta gagccttact tttttccact aaagttccaa 1500 aatacttatg gggtgaggct gttttaactg ctgcacattt aataaatcgt atgccatctc 1560 gtgttttaaa ccttaagact cctctcgaaa cttttttaaa attctttcca attgcctctg 1620 ttgcagccaa tttgcctcta aaaatattcg gatccactgc atttgtccat gaacacaaac 1680 aaataggcaa acttgaacct cgcgctatta aatgtatctt tgttggatat tcccccactc 1740 aaaaaggata taaatgtttt gatctcaatt ctaaacggct attggtaact atggatgtta 1800 ctttttttga aaataaacct ttttttgaga gcaatcatct tcaagggggg aaatcaaatg 1860 aagattcatc ttattttttt gaggatttaa ttctttccga aaatatgttt atgtcacata 1920 gttctaggcc atctgtacct atagaaaatg ccccagataa tgtaaatgaa tctactcctt 1980 ccatgagtga ggatgtcaca gaatcagggg caacaaacca aaattctaat aatgactctt 2040 tggaacctaa agataatcaa gaattgattc aaatgtcact acatgaacat ccttataatg 2100 aaacagaaag aaagtttgga gaagttgaag gaacttggaa aggagtaatt tatggaagaa 2160 agaaccatga taaggtagta gaagacttga ttcctcagca tagtcatgaa tctgaaccga 2220 gggagaatca acttacaaaa acaaacaaag gtaaaggtaa aatttctcct gattttcatg 2280 atcctattct tgatgttcca atagctcata tgaaaccagt tagagcttgc accaagcacc 2340 ccatgtctag gttcgtatca aattcaaatt tatcctcctc tttttctgca tttacctctc 2400 atttgtcttg tatagaaatt ccaaagaatg tacaggcagc tctaaatgtt ccaaagtgga 2460 aggaagctgt gtttgaggag atgagaactc ttgaaaagaa taacacttga aatgttatga 2520 ctttaccagt tggaaagaga actgtgggtt gtaagtgggt gtttaccgta aaatacaact 2580 ctgacggttc agtagaaaga tataaggcaa ggctggttgc taaaggattt actcaaacat 2640 aaggcatgga ctattcagaa acttttgctc ctgttgcaaa gttgaacact attaggatcc 2700 tcttatctct tgctgcgaat ttggattggc ctctacatca attagatgta aaaaatgcat 2760 ttcttaatgg tgaactagaa gaagaagtgt acatggatgg tcctccaggc tttgaagaaa 2820 aatttgggtc aaaggtgtgc aaattgaaaa aatctcttta tggtttaaag cagtctccaa 2880 gagcttggtt tgaaaagttt actaaatcag taaagaaaca aggatacact caaggggaat 2940 cagatcacac tttattcgta aagtacactc ctggtgggaa aattactatt ctaattgttt 3000 atgttgatga tatagttctt accggagatg atgtgacaga aatggagaga ctaaagagaa 3060 acctcgcagc agagattgaa atcaaagact tgggatctct aaagtacttt cttggcatgg 3120 aaatagctag atcaaagaaa ggaatatcag tgtcgcaacg gaagtatgtt cttgatctct 3180 tacaagaaac gggtatgagt ggatgtagac ctgctgatac tcccatggat ccaaatttga 3240 aactttggga aaaaggggac acacctgtcg actcaggaag ataccaaagg ttagttggga 3300 aattgattta cttggcacat acaaggcctg acattgcttt ccccgttagt gttgttagtc 3360 aatttatgca tgccccttat gaagaacacc ttgatgccgt ctatagaatt ctgagatatt 3420 tgaaggctgc cctcggaaaa ggcctattct ttggcaaaac caatgataga gatgtggcta 3480 tttttactga tgctgattgg gcaggatcca ttacagatag aaagtcgact tcaggttatt 3540 gtacctatgt gtggggaaac ttggtaacat ggagaagtaa gaagcaaggt gtagttgcta 3600 gaagcagtgc agaggctgag tttagagcaa tggcccaagg aatttgtgag ggtctttgga 3660 ttcatcgagt tctaaaggag ctaaagatga cagtagaact tccattgaaa ttatattgtg 3720 acaacaaggc cgcaataagt atagctcata atccagttca acatgatcga acaaagcata 3780 ttgaaatcga tcgtcacttt ataaaagaga aattagattc tggaatactc tgtctacctt 3840 ttgtgccttc aaatcagcaa acagctgata ttttgaccaa gagcttagca aggacaagtt 3900 ttgagcatct cataagcaag ttgggcatga ttgatatcta tgcaccaact tgaggggggg 3960 t 3961 // ID DNA9-3B_Mad repbase; DNA; EDCOT; 964 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-3_Mad; KW DNA9-3B_Mad. XX NM DNA9-3B_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-964 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1483-1483 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~96% identical to the consensus. AT-rich 9-bp TSDs. The consensus CC is ~78% identical to DNA9-3_Mad. XX SQ Sequence 964 BP; 316 A; 129 C; 81 G; 438 T; 0 other; ggagaaatta ggttctcatc cttcattttg ctactccatt gattaaaatc ctattccttt 60 tcaatttttg atcaaggtcc ttgggtatta ataacatcat taattatttc aataataaaa 120 tattttttta tttctaaata tattcattta atgttaaaaa tgttacaatt agtatattta 180 tatttatgac taaatttttt atcatatatt tttagtttta gtttgtaccc atttttaatt 240 tgtaattctt ttttaacttg taccaatttt cttttcagtt ttaatttgta cccatatatt 300 aatttctttt tgtgcccata ttttttaaag tttatttgta tttgtaccca tatatttttt 360 ttatttgtac tttttatttt gctaaatgta cccatgctaa ttatatgtac ccattcatgt 420 aaaacttttt aatcttaaaa tgtactcatt cttaaatata ccaatttgtt atatgtaaaa 480 tgtacccttt tttttatata aaatctattc aatttttttc taatccattt ttaaacttat 540 atgggtacat tcttttttct ttgattttaa aatgtatcca tgtcaagttt aatcgaagaa 600 atttactaat gttattaagc ctaatatctt tttttttttg ttgtgatttt gaagaatgta 660 cccatgtttt gatacaataa attttttggt taattttgat gaatgtaccc atgtttatat 720 aacacacaca cacacaatag tatatttata ttttaatatt tttaatccca caaattatgg 780 tttttttatt taaaatctca tttatataaa caactaaaat ttctaatttt taatttaaaa 840 aatatagtaa cgtacataga aataaattat cacattaatt tcagggacct cgatcaaaaa 900 ttaaaaacca acaaggtttc aatcaaagaa tattcataac taaggaccgc atccaaagtc 960 tccc 964 // ID TDK1D repbase; DNA; EDCOT; 243 BP. XX AC AB060978; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Diospyros kaki TY1/copia-type retrotransposon TDK1D, DNA for DE reverse transcriptase, partial cds. XX KW Copia; LTR Retrotransposon; Transposable Element; retrotransposon; KW TDK1D; Ty1/COPIA superfamily; reverse transcriptase. XX OS Diospyros kaki OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; Ericales; Ebenaceae; Diospyros. XX RN [1] RP 1-243 RA Nakatsuka A., Iwami N., Matsumoto S., Itamura H. RA and Yamagishi M.; RT "Ty1-copia group retrotransposons in persimmon (Diospyros kaki RT Thunb.)."; RL Genes Genet. Syst 77(2), 131-136 (2002). XX DR Genbank; AB060978; Positions 1 243. XX SQ Sequence 243 BP; 70 A; 40 C; 54 G; 79 T; 0 other; gcttttctca atggagatct ggaggaggag gtttatatga aacaacctga aggattcccc 60 tctagtgatg gtgagcattt ggtttgcaag ctcaagaaat ccatatacgg tctaaaacaa 120 gcgtcccgtc aatggtattt taaattccat gaggtaattt cttcattcgg atttgttgaa 180 aaccccatgg atcaatgtat ataccaaaag gtcagtggga gtaagatttg ttttcttgtt 240 tta 243 // ID Gypsy13-PTR_I repbase; DNA; EDCOT; 12152 BP. XX AC scaffold_132; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy13-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-12152 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-12152 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 304-304 (2007). XX DR Genome; scaffold_132; Positions 399454 411605. XX CC Positions [8773-9252] - Integrase core CC 'TCCAT' target site duplication CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS 2711..5659 FT /product="Gypsy13-PTR_I_3p" FT /translation="MHLFHFAFIFIHSFIITHMHTPGQNIGPQRVYNTRLR FT ARKMEDEERAYREAHFQEELDSLKVSVACLTSLLEQALRNTSSEGPSTRPA FT IFPANQPEEIIGEQAQEPRHNPAFVQSTTPVPTPAVAYAFANESHKTKPFD FT DINQDKMAALEARIRAIKEVDLYNPVRAAKICLVPNVVVPKKFQVPEFIKY FT TGTQCPITHLKSYCNKMAEVVHDDKLLMHFFQDSLSEATLSWYMRLDNTRI FT HTWKDLVDAFIKQYKYNMDIALDRTSLSNLEKGDKESIREYAERWRDLAAQ FT VHPPLLEKEMVALFANTLKAPYYEHVMGSSAQQFTDAVAVAERIEQGVKSG FT RISAPMEKKGFGVKKREIDHVESSYKSKKGQFQIYNTPSLSSQITNTNFNF FT PIPTKKPEPQNHQVKNQAESFPKKNYQRTQEQLPPLPLPLNKMYQRLLSIR FT QVAPVPLAPLQPPYPSWNKPDLTCVYHAGVAGHNIHTCNAFKRKLLQLIKV FT GWITFEEAPNVNMNPLPNHASGSGSVNMLEIEHSKILKVPMDKIYQMMVDA FT RYKEGSEKCCEHHNIEGHVISQCEGFHQKVIQMMSRGLLRIEKATGEEVSM FT MEAPNKEVCRVQFVTGKPPKLVLSKPVVAHKGNYNALPHDYGCSFKSTQHL FT PVFQVEIRGLTRSGRCFTPEELEKQRKAKGKEGVDVTEEINKPVTEEETNE FT FLKLMKHSEYSVVEQLKKTPARISLLSLILSSEPYRKALQKVLNEAYVPHD FT INQEAMEHLVGRIQASNYVYFTEDELGPDGTGHNKPLYITVRCKDILIGKV FT LINNGSALNVLPRHMLKEMPIDESHMKPSTLMARAYDGSPRQIIGTLEVEL FT YVGPQMFLITLQVMDIHPSYNILLGRPWIHAAGAVASSLHQCLKYIMNGIL FT ITVKAEETVSMIKNIAIPFIEVEDCRDGDIHAFEIVNMEWVPEGAVLRKPK FT IHEAAKMAARCFLKNGAPFQYLKLAQSS" FT CDS 6095..7012 FT /product="Gypsy13-PTR_I_4p" FT /translation="MLTEQFCFNEIMHFLVSNVSSSFYPFTSHTYMSTPCT FT FRNPESSIDSQNHCTKNNWPNFDNMVAMGDEEWEEEDIKEFTRLVENSEKS FT WEPASEKLEVINLGNEQEKKELKIGTLVTTEERNKLVSLLREYADVFTWTY FT ADMPGLDTDIVVHKIPLIEGSKPVKQKTRRMRPDMLLKVKAEIQKQWDARF FT LDVVQYPQWVANVVVVPKKDGKIWVCVDYRDLNKASPKDDVPLPHIDILVD FT NAARNATYSFMDGFSGYNQIRMVEEDKEKTTFVTPWGTFCYKVMPFGLKNV FT GATYQRQWLPYSMI" FT CDS 7500..8522 FT /product="Gypsy13-PTR_I_5p" FT /translation="MGCVLGQHDESGRKEQAIYYLNKKFNDCESRYTTIER FT LCCALVWSAKRLRQYMLYYTTWLISKLDPLKYICEKLYLSSRIARWQVLLT FT EYDIVFMTRKAVKGSVIADHLADHAMKNYEPLNFDLPDEDVIVIENRGGES FT DTWTLYFDGVVNVSGNGAGAVVISPENKQYPVSARLLFECTNNTAEYEACI FT IGLEVALELKAKKLEVFGDSLLIIYQVKGEWQTKNEKLKLYQNYLLRLANE FT FEEIKFTHISRDKNQFADALTTLASMTQVDIRSKIQPIDIEVRSFQAHCCL FT IEESPDGKPWYNDIEVSPTSRIPLRDFQDRLKDFEENDHEFLLRWRNFI" FT CDS 8677..9645 FT /product="Gypsy13-PTR_I_1p" FT /translation="MERDCIDYVRKCHKCQIYGDRINAAPTPMFNMISPWP FT FDMWGLDVIGPINPKASNGHRFILVAIDYFTKWVEANSYAHVTQKVVKRFI FT EKDLVCRYGLPARLVTDNAQNFNGKLIDKLCTKWKIKHLNSSPYRPKMNGA FT VEAANKNLKKIIQKMVVTYKDWHEMLSYALHAYRTIIRTFTKATPYSLVYG FT MEAVMPLEVEIPSLRILKDAELDESDWARLRFEQLNLIDERRLAAVCHHQL FT YQSRIAKAYNKKVKPRVFKEGDLVLKKISLASGEDQTKWAPNYEGPYVVKK FT ALSGGALILTNMDGNDLPRPVNLDVVKKYYA" XX SQ Sequence 12152 BP; 4067 A; 2320 C; 2565 G; 3200 T; 0 other; ggatggggac tccactgggg acgccttctt gtctggtcag actaagcttt gcttgtttga 60 ttgctagcct ttttgttggt ctttaatttt agcttgcatt ttactgtttt agcatgcatt 120 ttaattttgc gaataaaccc aattctaagt ttggtgggga gtaacggtct gcctcatgac 180 tttcagtcgg ggttcagatt cgtgaaacat ccaactatga gctgagtgtt tactcggtga 240 tggcggtcac acagtgcccc aaccatccct tgtaaacccc tatactgcct tcacgaaagg 300 ttgtcactgg gtagttcata gacctcttga gaccagttag aaaacatatc cctcatataa 360 taagctagaa cttgtttaaa ctctgcagga ttcttgagct aagaccatga cttccattac 420 cttttcagaa tacggggaaa gatttgagat gatgcaatta gtcgaagggg attgctcaag 480 aaccaaggtt gaagaattac cacacataac caaagtgcac tgcttcatag acagcataaa 540 gaagttggcc ccaattctgg gatatataga tgagaatctg tttgagaaaa agtatggaag 600 aatcgctcat ctagtaagaa ttcctgtcca gatttcagca gtcaaagcct tgatgcattt 660 ctgggatccg agctacaggt gtttcacctt cagggatgtt gatatgaccc ttactcttga 720 agagtatgcc cagatcttga gtttcccgaa tgacccttac aaagtgtact tcaggcaaag 780 aattgagagt acagctgcag cagttgcaaa acttctacat ttggaccaag ttgatcgata 840 catgacatcc aatggagggt tcaaatggaa aatgatcgag agtaaattga agacggataa 900 agaaaaaggg aagttaggtg aagaaagata tcagataatt gctttcgcca tctttgggct 960 gtttctgttt ccttcggaag ccgctggaat tattatcatt gaagctacta acgctttcct 1020 tgaatttgaa cagacaaaga ataaccctac ttcagccatc ttagctgaaa ccttcctatc 1080 tctaaatcat tgcagactgc atgggaaagg ggcgatgcga tgctgtattc ctctcttatt 1140 catgtggcct cttgagttgg tgctgactaa agaatggagt gatttggatg aaaaggcatg 1200 ggtaaggaaa taccaagtac ttccccaaag taattttaga tggagagctc cttgggtaag 1260 cggttcatct tacctcatgg gttgtggcga caaagcatag gttctattga ttggcttaac 1320 tggatatatc agttactcac cctcattggt ggccagacag tttggaggag tacaatacat 1380 gccaagaact cgggagttag ccgagtacac cggtctgttt aaagaagcta gctctttgga 1440 tatgttagat gccatcagaa atgactggaa gcagcctgtt ttggtctata aggaagagca 1500 tgaaaaggag ttctcagtta gccctgcata ttcaatatgg aggagtggca gctcatttaa 1560 gatacttcaa gaggcaaaag agcaaagaag agcccaagat aagccatctg tgacattgga 1620 gctcaaaaga aaaagggtca acaatgagga agatctccaa aaagaattgg ataagctgag 1680 gattgagctc agcaatagca aaaatcatca gaaattcctg gagaaccaac ttttgaaaga 1740 agaagagata aaggcttctc tagatcaaca attgaaggaa aaatatgagc aaatgacgag 1800 ttggtaaaca agcatgtaat ggtggagtag gaattggtga ctctaaaaag ggcctcagaa 1860 agtaaaaagt ctgctaacaa agagacaata acttctctga agaaagaaaa ggaccaatat 1920 caactaaaat gggaagctga aaaaaagaag aacagattag ccgatctcac cattgaagaa 1980 gaaagaagct taagaactcg atatcgggta caggctgaag atgagagaga agcaaggagg 2040 atagctgagt caggcatgaa ggaatacctg gacaaaataa atggtatgag aaaccgagtt 2100 tctgatatac aagccgagct tgagtcccga gaggaagaag caaagaagat gcaagaacag 2160 tttgaggaat ggcaagacta tatcagcagc ctcgatgtac agctaaacac taagacaacc 2220 gagcttgata tagagaagga ggaattgcaa agggccagaa aacagattca acaattggaa 2280 aagatggttc aaatcttgga gaaaaacaat gaatcattag ccgttagtaa tggaacactg 2340 cttcaagata acaccttgtt ccattacaag attgaacaaa ctgacaggct aattgacatg 2400 gtggctcgaa aggcaaatga gctacgagtg aaggcttcca agattggcaa cagccgtcat 2460 agatatgaag agtatttgaa tgaagtttcc tctttcatca ggaatgtagc caatagagga 2520 ataacatttg aataaagaca ctttgtatga accatctgta taggcctaag cctacttttg 2580 aacttttgta atgtgtatgg aattcaatca atcaaaggac ttggtgtaaa acctcattga 2640 gtatatcaga cttcagattc tacttgtatt tgacaaagga agtcatggat taactcttta 2700 atccatatac atgcatcttt ttcattttgc attcatattc atacattcat tcattataac 2760 acacatgcat acgccaggtc aaaatatagg tcctcaaaga gtctacaaca cccgacttcg 2820 agcaaggaag atggaagacg aagagcgtgc ttaccgtgaa gctcatttcc aagaagagtt 2880 ggattctctg aaggttagtg tggcttgcct caccagctta ctcgagcaag cactaaggaa 2940 tacctctagt gaaggccctt ccactagacc agccattttc ccagcaaatc aacctgaaga 3000 aataatagga gaacaagcac aggagccccg acacaatcca gcatttgtgc agtcaacaac 3060 accagtacca acacctgcag tcgcatatgc atttgctaat gagtctcaca aaaccaagcc 3120 atttgatgac attaatcaag acaagatggc agcattagag gccaggatta gggccattaa 3180 agaagtagac ttatataacc cagtacgagc cgcaaaaata tgtctagtcc ctaatgtggt 3240 ggtaccaaag aaatttcaag ttcctgaatt tatcaaatat accggaactc aatgccctat 3300 tacccatctc aaatcttatt gcaataaaat ggcagaagta gtacacgatg ataagctact 3360 gatgcacttc ttccaagaca gcttgagtga agcaacattg agctggtata tgaggttgga 3420 taataccagg attcatacat ggaaggatct cgtagatgct ttcatcaagc aatacaaata 3480 caacatggat attgctctgg atagaaccag tctatctaat ctggagaaag gagacaaaga 3540 gagtataagg gagtatgccg agagatggag agatttggca gcacaggtac acccccctct 3600 cctagaaaag gaaatggttg ctctgtttgc taacacacta aaagcgccat actacgaaca 3660 cgtgatgggt agttcggctc aacaattcac tgatgctgtg gcagtagcag aacgaataga 3720 gcaaggggta aagagcggga gaatctctgc acccatggaa aaaaagggtt ttggagtaaa 3780 aaagagggag attgatcatg tcgaaagtag ctataaaagc aagaaaggcc aatttcaaat 3840 atataacact ccatcccttt catcccaaat taccaatacc aatttcaact tcccgatccc 3900 aaccaaaaaa cctgaacccc aaaaccacca agtaaaaaac caagctgaaa gtttccccaa 3960 aaagaactac caaagaaccc aagaacaatt gcctccattg ccattacccc tgaataaaat 4020 gtaccaaagg ctactaagta tcagacaagt agcccccgta cctttggcac ccctacaacc 4080 gccttaccct agctggaata agccagatct tacctgcgta taccatgccg gtgtagctgg 4140 gcataacatc catacttgca acgccttcaa gagaaagctt ctgcaattga tcaaggtagg 4200 atggataaca tttgaagaag cccctaatgt gaatatgaac cctttaccca atcatgcttc 4260 aggtagtggg tctgtaaaca tgttagaaat agaacactca aaaatcttga aggtgccaat 4320 ggataagatc taccaaatga tggtagatgc aaggtacaaa gaaggtagcg agaagtgctg 4380 tgaacatcat aatatagaag gccatgtgat tagccaatgt gagggctttc accaaaaagt 4440 gatacagatg atgagtcgtg gattgctacg aatcgagaaa gcaacaggtg aggaggtgtc 4500 catgatggaa gcaccaaata aagaggtatg tcgagtacaa tttgttacgg gaaaaccacc 4560 caaactagtc ttatccaaac cagtagtggc acataaaggg aattacaatg ccttacctca 4620 tgactatggg tgttccttta aaagcactca gcatctgcct gtttttcaag tagaaattag 4680 aggattaacc cgtagcggta gatgtttcac tccagaagaa ttggaaaaac aaagaaaagc 4740 taagggtaaa gagggggttg acgtgaccga ggaaataaac aaacctgtta cggaagagga 4800 aaccaatgaa ttcttgaagt tgatgaaaca cagtgaatat agtgttgttg aacagcttaa 4860 gaaaactcca gcaagaatat cattgttgtc tttaattcta agctctgagc catataggaa 4920 ggccctacag aaggtattga atgaggcata cgttcctcat gacatcaatc aagaagctat 4980 ggaacatttg gtgggaagaa tccaagcctc gaattatgta tacttcactg aagatgaatt 5040 gggtcctgat ggtaccgggc ataacaagcc actatacatt acagtgcggt gtaaggatat 5100 tctaatcgga aaggtactca tcaataacgg ttctgcactg aacgtcctac caaggcatat 5160 gttgaaagaa atgcctatcg atgagtcaca tatgaaacct agcacattga tggcgagagc 5220 atatgatggt tcgccaagac agataattgg gaccttagaa gtggagctat atgtagggcc 5280 gcagatgttc ctgataacat tacaagtaat ggacattcac ccatcttaca acatattatt 5340 agggaggccg tggattcatg cagctggagc agtggcttct tcactacacc agtgtttaaa 5400 atatattatg aatggaatat tgataactgt caaagctgaa gagacagttt ccatgataaa 5460 aaatatagcc atacccttca ttgaagtgga agattgtaga gatggggata ttcatgcatt 5520 tgaaattgtg aatatggaat gggttcctga aggtgcagtg ctgagaaagc ccaaaatcca 5580 tgaagcggca aaaatggctg ccagatgctt tctgaagaat ggggctcctt tccaatatct 5640 aaaactggcc caatcaagct aaagagtgta gatcaaagat ttgggcttgg atataagccc 5700 aagaaagatg actacaaacg agttgcccag attagaaagg aggcaagaat gacaaggatt 5760 gaaggaagag agccagaaga agaggaattt gtcgtcccat cgctccaagt atctttccca 5820 agggctacag aagtgattag atccggcata gtagatctcc acatcagtac cctagagagc 5880 caagaaggaa aacatataga ggaagcggat ctagaagtga aggatgaagt tctaccacag 5940 ctttccattc acaccattga cgaacccctt gcaagatttt ttatgcgaag attggctgaa 6000 ggagaggtgt accagaattg gaagatggag attgctccta ttgtgtttaa aaagtaattg 6060 atcttgttta gctcatgata ccacaagatt ttctatgtta accgagcaat tttgttttaa 6120 tgagatcatg cattttcttg tgtccaatgt gtcttcatcc ttttatcctt tcacaagtca 6180 cacttacatg agcacacctt gcactttcag gaatcctgaa agttccatcg attcacaaaa 6240 ccactgcact aagaataatt ggccaaactt tgataatatg gttgcaatgg gcgatgaaga 6300 atgggaggaa gaagatataa aagaatttac taggttggta gaaaactccg agaagtcctg 6360 ggaacctgct agtgagaaac tagaagtcat caacttggga aatgagcaag aaaagaagga 6420 actaaagatt ggcacccttg ttacaactga agaaagaaat aaactagtct ctcttttacg 6480 tgaatatgca gatgttttta cctggactta tgcagatatg cccggtctag atactgacat 6540 agtagtacat aaaattccct taatagaagg aagcaaacca gttaagcaga aaaccaggcg 6600 aatgcgccca gacatgttgc tcaaggtaaa ggctgagatt caaaaacagt gggatgcaag 6660 gtttctagat gtggtccaat atcctcaatg ggtagctaat gtggttgtag tcccaaaaaa 6720 ggatggcaag atctgggtgt gtgtggacta tagagatttg aataaagcga gcccaaaaga 6780 tgatgttcct ttacctcaca tagacatttt agttgataat gctgcaagaa atgctacgta 6840 ttctttcatg gatggattct ctggctataa ccagataaga atggtggaag aagacaaaga 6900 gaagaccacc tttgtcacac cgtgggggac attctgctat aaagtaatgc cattcggatt 6960 gaagaatgtc ggagccacat atcaaaggca atggttaccc tattccatga tatgatgcac 7020 cgagaagtgg aggtttatgt ggatgacata cttgcgaaat caaagaagga agaagatcat 7080 gtgcaagtat taagaagact atttgaaagg ctgcaaaaat tccaattaaa gttgaaccct 7140 gcaaaatgct tattcggggt aaaaacagga aaattgctgg gcttcatagt aagtgatcaa 7200 ggaatagaag ttgatcctga taaagccaaa gctattcagg agatgcctgc acctaagaca 7260 taaaaggaag taagaagttt ccttgggcgc ctaaattaca tagctcggtt tatatctcag 7320 ctaacagtga cctgtgagct aattttttgc ttgctcagga agaaaaatcc tggagtatgg 7380 gacaattact gtcaggaagc ctttgataaa ataaagaggt acttgcaaaa tccaccgctg 7440 ctagacctcc aacactaggg cgacctttga tcttgtattt gacagtaaca gaaacaacta 7500 tgggctgtgt actgggacaa catgatgagt caggaaggaa agagcaagct atttactact 7560 tgaataaaaa attcaatgac tgtgagtcaa gatacacaac aattgaaagg ttgtgttgtg 7620 ccttggtttg gagtgcgaaa agactcaggc agtatatgtt gtactacaca acctggttga 7680 tttcaaaatt agatccgctc aagtatatat gtgaaaaact ttacctgtca agtagaatag 7740 caaggtggca agtgttgttg acagaatatg acattgtctt tatgacaaga aaagctgtaa 7800 aaggaagcgt aatcgccgat catcttgcag atcatgctat gaaaaactat gagcctctaa 7860 actttgacct cccagatgaa gatgtgatag taatcgagaa tagaggcggg gaaagcgata 7920 cgtggaccct ttactttgat ggtgtagtaa atgtatcagg aaatggggca ggtgcggtag 7980 taatttcccc agaaaataag cagtatcctg tttcagcaag gttactgttt gaatgtacca 8040 ataatacggc cgagtatgaa gcctgcatta ttggcttgga agtggcttta gaacttaaag 8100 ccaagaagct tgaggtcttc ggggattcct tactaatcat ctaccaagtc aaaggtgagt 8160 ggcaaaccaa gaatgagaaa ttgaagctgt atcaaaatta tctcttgagg ttagccaatg 8220 aatttgagga gatcaaattc actcatataa gtagagataa gaatcagttt gctgatgccc 8280 tgacaacctt agcttcaatg acacaagtcg atatcagaag caagatccag ccaatagata 8340 tcgaagtcag aagcttccaa gcccattgtt gcttaattga agaatctcca gatgggaaac 8400 catggtataa tgacatcgaa gtttctccaa catcgagaat acccttaagg gatttccaag 8460 acagattaaa agactttgag gagaatgacc atgaattttt acttagatgg agaaatttta 8520 tataaaaggt catttgatgg taccctactc aggtgtctga atgaaaatga gattgaacaa 8580 acattaaaag aagtccatga ggggatttgt gctacacatg ctaatgggca tacaatggca 8640 aagtaaatac aaaggtcagg atatttctgg ttgatcatgg agagagattg tatagactat 8700 gtgagaaaat gccataagtg tcagatatat ggtgatagaa taaatgcagc tccaacacct 8760 atgttcaata tgatctcacc ttggcctttt gatatgtggg gtttggatgt tatagggcca 8820 atcaacccta aagcgagcaa tggacataga tttattctgg tggccatcga ctatttcacc 8880 aaatgggtag aagccaattc ttacgcccat gtaacacaga aagtagtcaa gagattcatt 8940 gaaaaggatt tggtttgtcg ttatggtttg ccagcaagat tggtaactga taacgctcag 9000 aatttcaatg ggaagctgat tgacaaacta tgcaccaagt ggaagattaa acaccttaat 9060 tcttcccctt atagaccaaa gatgaatggg gcagtggaag cagccaataa gaatctcaag 9120 aagatcatcc aaaaaatggt ggtcacctac aaggattggc atgagatgct ctcatacgca 9180 cttcatgcgt accgcaccat aattagaact tttacaaagg caaccccata ttctttagtg 9240 tatggaatgg aggcagttat gcccttagaa gtagaaatcc catcactgcg gatcttgaag 9300 gatgcagaac tggacgaatc agattgggcg aggttaagat ttgagcagct aaacttgatt 9360 gatgaaagaa gactagcagc tgtttgtcat caccagttat accaaagcag gatagcaaag 9420 gcttacaaca agaaggtcaa accaagggtg tttaaggagg gggatttggt gttaaagaag 9480 atctcactag catcaggaga agatcaaact aagtgggcac caaactacga agggccatat 9540 gtggtgaaaa aggctttatc tggaggggcc ttaattctga ctaatatgga tggaaatgat 9600 ctacctagac ctgtaaactt agatgttgta aagaagtatt atgcttgatg tattttcctt 9660 tatcattcaa taaaattgaa gtttggccaa gatttcttta gtgtgcttcc cctaaaaaaa 9720 ctatgcatga tctcaagttt tcacaaggat ttttgggaaa tcaaagtttt aataaaaaaa 9780 tcaaattggt gtttgttcga acaaacaagt tctgaaaatt caagttatat cttaacacct 9840 atcaaaacct gaaaaacaac ccaaatgcca tgaaatgact tcaaagctga gttttggctg 9900 catgaataat gagaaaccat ttcgcatatt tgcatcagag aaagcaaagc ttgtcgattc 9960 tgaatgtata catttgaaat gaagaaaggc catctttgat catcctttca caaattctaa 10020 aaaacccttg cagtcccttg ttgagcctaa tgcatttttc ttgaaaaata accttgacta 10080 ggatcacacc ctatactagg gggcaagtgc aaaaaatcct tgataattaa aagtgtccaa 10140 acaatcctgg gggcataaaa aatcctcaat gataaaagtg cccaaacaac acaagggggg 10200 gcatgaaaga aaatccttaa tgatcaaaag tgcccaaaca aagttggggg gcatgaaaga 10260 gttccaaaag atttgagtgt gccacaaaaa tcactaatat agtgatactt aaaaccaaaa 10320 aaagaaaaag cctaacattg gagggcaccg tggaccattt tgcaaatcaa ttccaaggtc 10380 tagaaataca tggacaaaaa aaaaaaaact tgagatataa gcattagtga tccttagtct 10440 taaagtccat taaacacctt ttgagccaat agatatcctt tttcttcata gccaagagcc 10500 aaagcctaca ttacatgctt aatcaagccc tttctgatca aaggcaagca atctggatcg 10560 gcagacaatg ctttcctgtg caaaacaagt cattattcat acaatcaaaa tgaatgcttt 10620 gaaaactagt tctttgaaac cttcagactg gatcttaaat cctttttaac caacaaaaca 10680 tcacttcaca ttttcaccaa aaacaacatt tatgcaaacc tatccatgag aattgcttga 10740 atttttcaga acaagtttgt tttaaacaaa catcaaaatg attttttttc aagaataact 10800 ttgaaattcc aaaagttcat tgtaaaaaca actccttgta aataaccaaa tctcatttca 10860 cataaccttg tccctaaaga aaaccccaaa caaacacttg cggcatgatc aaatgaaggg 10920 caatccagca aaacacatag ggttggctcc atgattccct ttctaagaaa ataagagaca 10980 tggtgcagag atgacaattc ttcagataaa gatttatggg caaagaagta tgctcatgtt 11040 atacccttcc tagaggttaa gatcacaaga tgtggctcga gtaagcaaga gtatgaaagc 11100 catcaaagct tactattaga gactcaaact tttgagaaaa ggaaaactcc atgaagaaaa 11160 ggggggccta tatttctcag gtaagtatac atgcatattg atcatgatgc attactttca 11220 tccttgacag atcagtgtct caccatcacc tctttttgag cgggctgttg agtcctcatc 11280 atttagatag tgtactttct agccctatct tccttctctt tgagtgcgcc cttgagccat 11340 caaacatccc agctggtgca ccttacaacc ctacctcttt ttgagtgtgc ctttgagccc 11400 tcacatcttg ggtagtgtgt tttctaaccc tacctctttc cgagtgcgcc tttgggccat 11460 cacctcacgg gtagtgcgtt ttctaaccct gcctcatttc gagtgcgcct ttgagctctc 11520 atcccttagg tagtgtgttt tctaacccta cctccttccg aatgtgcttt tcagccctcg 11580 ctccccttca agtcatatct cttttcaaac gctcatatga gctcccgtct cttgaataat 11640 gtgcctttga gtcctatcat gtcattcctt caagacattt catttttttc acatgggtag 11700 gtcacccatc acaatcagac ctctttaaaa actcttttca tcttccattt gggccggttg 11760 cccattacaa tgaaaccact ttgaaaaatc ttcgcatttc tcaccacttt gaaaaatctt 11820 cgtatttttc accattttaa aaaatctctg aaaaatcctt gcgttttcca cccgggtagg 11880 ttgcccatta caataagacc atctcaattt tcttttttaa ttttctctgg gtaggtcacc 11940 catgacaatt cgaccacttc aaaatctttg aattttcaaa agaaaaatct tccagttttt 12000 actttgagtg cgctttctag ccctcaaaat gattcatcat ttctcaatat gatgagtcca 12060 tcatctttca ttcttctttt tttttacaac gcttactacc taaagtctct tacgagactt 12120 tctatcgtaa gcattgtaaa gaggagggca ac 12152 // ID Gypsy-40_Mad-LTR repbase; DNA; EDCOT; 983 BP. XX AC . XX DT 15-OCT-2010 (Rel. 15.1, Created) DT 15-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-40_Mad-LTR. XX NM Gypsy-40_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-983 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1775-1775 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 983 BP; 286 A; 207 C; 192 G; 298 T; 0 other; tgtttgcact caaaatatac ccatttttac ttatttgggc aatttgggta aaatatggca 60 tttggaggat taatatgcaa gaaagctaac ttggaaagat atttggctgc aagtggaggg 120 gtttgacact ataatattgt ttctcccatt tgtttgggtg gtggaggttt gtcaagcctt 180 tgtttaatca agatacatgc atgcattgca agtggatggg aaggcacatg cagctttcgg 240 gcaagaacat gtgaaagaag ccaacttgct tcttttaatt gttagtttat tacaagtggg 300 aaaacatgtg ctgaaagcat gtggtggaga tgcaagttcc ccttttaata ttatttctcc 360 atgcaagttg gcaagtgaaa tgcaagctaa gcaatgaata caagctgccc aagcttcttt 420 cgggcaggta caagacctca gcagggggtt tcctccagac ctctatataa aggagcagat 480 gcacaaggat tatggacact caacaaacaa acaagcaaaa actctgctca aaccagctca 540 tcagcttcct tgtagacatt tatttttagc caagcatcct ttgctttctt gtttattagc 600 tctgctgctc acttgtagta tcgatctcat ttgtagcttt tatgtacaac tcatttccag 660 tcatataaat tacaagcaat ctgcaatatt agtcactttc ctctgtcatt tatatttcca 720 agcaaccttg tcatttacat attgttctat ctctccatat aagtaaagtc cttattttta 780 aggcaaacaa agaaccttaa tttgagcaac tcccactcaa atggcacaat ctcttgattt 840 gaagtcaaaa ggcgcaacct caatcattca aatcccgtct actagcggca tctagtagtg 900 gcacgcccgc acccaccaat ctcgtatgtg aagtaaatcc ccggcttgcc cgcaaggccc 960 atggcggatt tagggagcga aca 983 // ID TONT2-I_PV repbase; DNA; EDCOT; 4670 BP. XX AC AY341443; XX DT 04-JUL-2005 (Rel. 10.07, Created) DT 01-AUG-2005 (Rel. 10.07, Last updated, Version 1) XX DE Copia-like retrotransposon from common bean (internal portion). XX KW Copia; LTR Retrotransposon; Transposable Element; TONT2-I_PV. XX OS Phaseolus vulgaris OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Phaseolus. XX RN [1] RP 1-4670 RA Jurka J.; RT "Copia-like LTR-retrotransposon from common bean."; RL Repbase Reports 5(7), 192-192 (2005). XX DR Genbank; AY341443; Positions 6612 11281. XX CC LTRs are 99% identical. ORF first identified by automatic CC screening in Genbank annotation. XX FH Key Location/Qualifiers FT CDS 160..1701 FT /product="TONT2-I_PV_1p" FT /translation="MAENPNNNDNTAPETSNVVSATQTIFAKLFPDVSKIE FT VFTGQNFRRWQERVSTLLDMYGVAHALTTAKPDSTTAAKQVDDWIHANKVC FT RHTLLSVLSNDLFDVYASYKNAKDIWDSLILKYTAEDIVRQRFVIAKYYRW FT EMIKGKDIKIQINEYHKLIEDIKTESIKLPDEFVSELLIEKLPQSWTDYKQ FT QLKHRQKQMSLSDLITHIIIEDTNRKECAAAKAKALSAKANVIEDKPAPKR FT YEKKFDHKKKPNNKFSRPSGTNPTFKKKGNCFVCGKPGHHAPQCRHRAKND FT YPPKANLAEGEDTIVAVVSQVNLVTNVSKWVVDSGATRHICANRNVFTSYT FT SVGDGEEQVYLGDSRTTPVLGKGKVLLKLTSGKTLALNDVLHVPSIRVNLV FT SVALLSKVGVKVSFESDKIVITKNNVFVGKGYCDQGLFVLNISEIMNESTS FT SAYIVDSYDIWHARLGHVNSSYVIKLQRLGLINMHDKESSKCDVCVESKIT FT KKTCHSVENSWFNSYRPC" FT CDS 1718..4075 FT /product="TONT2-I_PV_2p" FT /translation="MSRGGKNYFVTFIDDFSRYTKVYLIKHKDEAFDMFLT FT YKAEVENQLNKKIKRIRSDRGGEYVLFNDYCVKEGIIHEVTPPYSPESNGV FT AERKNRTLKEMMNAMLISSNAPDNLWGESLLTACFLQNRIPHRKTGKTPYE FT LWKGYQPNLKYLRVWGSLAKVMLPDPKKRKIGSKTSDCMFLGYAEHSAAYR FT FLVLNSDIIERNTIVETKNAEFFEHIFPLKSSGTSEQPIDSVSDTLSEDVR FT RSKRQRKETSFGNDFYTYLVENDPISFVEATSAPDAKHWDKAIKTELESIK FT KNNTWTLVDLPKGAKPIGCKWIFKKKYHPDGSIEKYKARLVAKGFTQKHNI FT DYFDTFAPVTRISSIRVLLALASIHKLVIHQMDVKTTFLNGELEEEIYMTQ FT PEGCVVLGQKEKVCKLLKSLYGLKQAPKQWHEKLDNVLLCEGFSTNDADKC FT VYSRSENGEYVIICLYVDDMLIFGTCNDIVFKTKLFLGSKFEMKDMGEASV FT ILGVKIIRKGDSILLSQEKYTEKLLKKFGYYDFKSVSTPYDANSKLKKNRG FT ESISQTQYAQIIGSLLHLMSFSRPDIAYAVGRLSRCTQCPSQDHWEALARL FT MKYLRGTMDYAIEYSGFPAVLEGYSDANWISDSDETKSTSGYVFTLGGGAV FT TWRSARQTIIARSTMESEFVALEMAGSEAEWLKNFLANIPLGMKPTPSVSM FT HCDCQSAIAIAKNKSYNGKNRHIQLRHNLVKQLLKSGTISIDYVKSERDLA FT DPLTKPLGRKMILETSRGMGLKPLANKQEMETQPL" XX SQ Sequence 4670 BP; 1562 A; 789 C; 968 G; 1351 T; 0 other; cgtgggtctg atcctcggaa attaccggga agttcctgtt gtatcctggg ggatttgcgg 60 aatacaccgc ggataagtcc ttacggacag tgattactca cgcctcggga aacctttttg 120 ttcgttttaa agcctatatt actacaatcg taaggactta tggctgaaaa tccgaacaac 180 aacgacaaca ctgctccgga aacatcgaat gttgtttccg caacgcaaac catttttgcg 240 aaactttttc cggacgtctc caaaattgaa gtcttcaccg gtcagaactt ccgacgttgg 300 caagaacgcg tgtccaccct attggacatg tacggagttg ctcatgcact tacaactgcc 360 aaacccgact caaccacggc tgcgaaacaa gttgacgact ggatccatgc gaataaggta 420 tgccgtcaca ctttactcag tgtgttatct aacgatctgt tcgatgttta tgcttcttat 480 aagaatgcga aagatatttg ggattctctt atcctcaaat atactgctga agacatcgtc 540 agacaaaggt tcgtaattgc aaaatactac cgctgggaga tgatcaaagg caaagacatc 600 aaaatccaaa taaacgaata tcacaagctg attgaagata tcaaaactga aagcataaaa 660 ttgccagatg aattcgtgtc tgaactcttg atcgaaaagc ttccgcagtc ttggacggat 720 tacaaacaac aactgaagca cagacagaaa cagatgtctc tatcagattt gatcacccac 780 atcatcattg aagacacaaa caggaaggag tgcgctgctg caaaggccaa agctttgtct 840 gccaaagcaa acgtgataga agacaaacca gctccaaaaa ggtacgagaa aaaatttgat 900 cacaaaaaga aacctaataa caaattctct cgtcccagtg gaactaaccc cactttcaag 960 aaaaagggta attgctttgt ctgtggaaag ccaggccatc atgcacctca gtgcagacat 1020 agggctaaaa acgactatcc tcctaaggca aatctagccg aaggggaaga tactattgtg 1080 gcagtcgttt cacaagtaaa ccttgtgaca aatgtgagca aatgggtggt agactctggg 1140 gctaccagac acatctgtgc aaacagaaat gtgttcacct cctacacaag tgtgggggat 1200 ggagaagaac aagtatatct cggtgactcc aggacaactc ctgtcctagg aaaaggaaaa 1260 gttcttctga agctcacatc tggtaaaact ctagctttga atgatgtgct acatgtacca 1320 tcaattagag ttaatttggt ctctgtggca ttactaagca aagttggggt taaagtgtca 1380 tttgaatctg ataagattgt tataacaaaa aacaatgttt ttgtgggaaa gggatattgt 1440 gatcaaggcc tttttgtatt aaacatttct gaaattatga atgaatctac atcttctgct 1500 tatattgttg actcgtatga tatatggcat gctagattag gacatgtgaa ttcttcgtat 1560 gttataaaat tgcaacgact aggattaatc aacatgcatg acaaagaaag tagtaaatgt 1620 gatgtatgcg tagaatctaa aataacgaag aaaacatgtc actctgtaga aaattcttgg 1680 tttaattcat accgaccttg ctgatttaaa acaaaccatg tctagaggtg gtaaaaatta 1740 ttttgtaacc tttatagatg atttttctag atacaccaaa gtgtatttaa ttaaacataa 1800 ggatgaagct tttgacatgt ttttaactta caaagcggaa gtagaaaatc aacttaataa 1860 gaaaattaag agaattagat cagatagagg tggtgaatat gttttattta atgactattg 1920 tgtaaaagaa ggtattattc atgaagtaac cccaccatat tcacctgagt ctaatggagt 1980 agctgaaagg aaaaatagga ctcttaaaga aatgatgaat gccatgctta ttagttctaa 2040 tgctcctgat aacttatggg gtgaatctct gcttactgcg tgttttttac aaaataggat 2100 accacatagg aaaactggta aaacacccta tgaattgtgg aaaggttatc aacctaattt 2160 gaaataccta agagtgtggg ggagtttagc taaagtgatg ttacctgatc ctaagaaaag 2220 gaaaataggc tctaaaacat ctgattgtat gttcttagga tatgcagaac atagtgctgc 2280 ctataggttt ctggttctta atagtgacat aattgaacgc aacactatag tagagacaaa 2340 aaacgctgag ttctttgaac acatctttcc gctaaagagt agtggtacat ctgaacaacc 2400 tatagatagt gttagtgata ccttgagtga ggatgttaga agaagtaaaa gacagagaaa 2460 ggaaacatct tttggaaatg acttttatac ttatctagtt gagaatgatc caataagttt 2520 tgtagaagct actagtgctc ctgatgctaa acattgggat aaggccatta aaacagagct 2580 tgaatcaatt aagaaaaata atacgtggac cttagtagat ctgcctaaag gagcaaaacc 2640 cattggttgt aagtggatct ttaagaagaa gtatcatcct gatggatcca tagagaaata 2700 taaggcaaga ttagttgcta aagggtttac tcaaaaacat aacatagatt actttgatac 2760 ttttgcacct gttactagga tttcctctat tcgtgtattg ctagccttag catctatcca 2820 taagttagta attcaccaaa tggatgttaa aacaactttt ctgaatggtg aattagaaga 2880 ggaaatttat atgactcaac ctgaaggttg tgtagtccta ggtcaaaagg aaaaagtatg 2940 caaactttta aaatctttgt atggtttgaa acaagcacca aaacaatggc atgaaaaact 3000 tgataatgtt ttactttgtg aaggtttttc taccaatgat gctgataaat gtgtgtattc 3060 tagatctgag aatggtgaat atgtcattat atgtttgtat gtggatgaca tgctaatttt 3120 tggtacatgc aatgatatag tttttaaaac aaaattattt cttggatcta agtttgagat 3180 gaaagacatg ggtgaagcaa gtgtgattct aggagttaaa atcataagga agggagatag 3240 tatattacta tcccaagaaa aatacactga gaaacttcta aagaagtttg gttactatga 3300 ctttaagtca gtgagtaccc cttatgatgc taactctaaa ttaaagaaga acagaggaga 3360 atctatttct caaactcagt atgcccagat aattgggagc ttattgcatt taatgagctt 3420 ttctagacca gatattgctt atgcagtagg tagattgagt agatgcactc aatgtcctag 3480 tcaggatcat tgggaagcac ttgcgagact catgaaatac ttgagaggta caatggatta 3540 tgccattgaa tatagtggat ttcccgctgt gctagaaggg tacagtgatg ctaactggat 3600 ctctgattca gatgagacaa aatccactag tggttatgta tttacacttg ggggtggtgc 3660 agttacatgg agatcagcca gacaaactat tattgcaaga tcaacaatgg aatctgagtt 3720 tgttgctcta gaaatggctg gtagtgaagc tgagtggttg aaaaacttct tagcaaacat 3780 tcctttagga atgaaaccaa ccccatctgt atcaatgcat tgtgattgcc aatcggcaat 3840 agccatagct aaaaataaga gctataatgg aaagaataga catatacaat taagacacaa 3900 tttggtgaaa cagctgttaa agagtggaac gatttctatt gactatgtca agtcagaacg 3960 ggatttggca gatcctctga caaaacccct agggagaaaa atgattttag aaacatcgag 4020 gggaatggga cttaagccac ttgcaaacaa acaagagatg gaaacccaac ctttgtgatt 4080 ggagatccca tgaataaggt tcatatgggt aaaaacaagt cacttgttag ttctgttagc 4140 actaatattg attttaaatc aagtttgtcc attcctatgg tgtgtgtgaa agtgctagat 4200 actacattat cgagaggata acctttgtgg ttaaaattca gaagtaagag agttttaacg 4260 atttacaaag ttctaatgat tttcatatcc cttatgggtg gtgtatgatt tgtagcatac 4320 acttgatgaa atcacctata taagtgtcaa gtggggccgc ttgcatgaga tcttggcaag 4380 atctctagag cactcatgaa taccgggcac gcgcatggcc tagtagcgca acacagcgat 4440 aacagcaagt aatgtggggg tgtattgtga ctgataaacc tctaacacat actaagtgtc 4500 ttggttcata tagcttgcta taccaactac actatgtgtt acgttcatca atctaagact 4560 ggttcatata gcttgctata ccagatctga tgcattacat tttagatgaa cccagaatat 4620 tcttttcttt ctctatctct atgttttatc ttttgcaata tgtgggggat 4670 // ID HAT-N9_Mad repbase; DNA; EDCOT; 989 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; HAT-N9_Mad. XX NM HAT-N9_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-989 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1631-1631 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~97% identical to the consensus. 8-bp TSDs. Both termini show CC similarity to those of HAT-7_Mad. XX SQ Sequence 989 BP; 358 A; 196 C; 143 G; 292 T; 0 other; taggggtggg ttcaaaaaac cgaaaaccga aaaaaaccga aaaccaaacc gaaccgaaac 60 cgaaaaaacc gaaccgaacg aaaaaaccga accgaattga aaaaaccgaa ccgaaccgaa 120 ttcttttggt tcggttcggt tttagtgatc tagaaaccga accaaaccga accgaaccga 180 attaattaaa ttaatttttt tatttaatta tttgttttgg gtattatttt ctaaacccaa 240 tttgtaagtt aaaatgtgct aaacccaatg tgttgccaaa ctttaagctc aaaatattaa 300 aaaaaggcct ataaaaactc taaaccctaa cctattattt ctcccccata taaggttccg 360 gaaccaaacc tcttcccgaa gtacctacat ccatctccat agcactgtct acttctgcgc 420 cagctttctt ttccaaatct actctcatat aacatgtaac ataatccata aacatttatt 480 tcgggtagat tacttgggta atttgtgatg gaaaagaatc caacacacac taaataaatc 540 cacccacgca ttacctttac taatcaagtt gtcaacatgc agttacaagc aaacaacact 600 gatctttgaa caacatcata caatttaact tttctaagtc atttgtacga tttttgtgtg 660 atttttgtgt tgtgaggttg ttagtttgga ctttgaaaga cttgattgat gattttagtt 720 caactttaaa tgtttatttt cattgtcttt gattctagtt agaatgttta tgttatgatt 780 gtgttggata tgttaaaatt taaaatttca atgtttttca ttttttgaaa aaaaataaaa 840 acaaaaaacc gaaaccggaa accgaaccgg aaaaaaccga accgaaaaaa accgaaaaaa 900 aaatcgaacc gaaccgaacc gaaccgaaat ttcggtttgg tttcggtttt ggcaaaaaac 960 cgaaccgatt taaaccgaac ccaccccta 989 // ID hAT-N4_Mad repbase; DNA; EDCOT; 911 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW hAT-N4_Mad. XX NM hAT-N4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-911 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1639-1639 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >97% identical to the consensus. TSD is 8-bp long. XX SQ Sequence 911 BP; 298 A; 132 C; 147 G; 334 T; 0 other; cagggccggc ccaggcccag tgcaggaggg gcgaccgtcc agggcccaaa aaaattaggg 60 gcaccaaaat tattagggcg gtatatttat atatgttttt ataagagtat aaatttataa 120 aatttggttc aaagacacag aaatttaact agaagtggtg gtttgtcatt tgaaaataat 180 aaggaggtct tgggttcaaa acaccatgtg tgcttattta ctttcctttt tttacaaatt 240 tctttttata agagtataaa tttagaaaat ttggttaaag gatcaagaag tttaattaga 300 aacaatgatt tttgttgttt aaaattaaca agaggtccta agttcgaaat gctatgtgca 360 tgtttattct tttcaatttt tacaaatttt tgtttggttg ttaatttatt tttagttact 420 atctagtagc tatgtgggtt gttattttta aatattcgtt ttaattcaag tctaatcttc 480 aacaaagaat aatacgtaga ccaaatttgc aaattatatg acgtgtcatc aaaatgttta 540 atttagtgcc cattcattaa taatacatat caattaaaga ctcgaaaaca tcattatttt 600 ttagtcccat attgacaagg ttagtaaata agaaaaaaac acctcacgat ttattcaaaa 660 acacattcaa agttcagatg gaaaacaaaa ctcatcatct atctacttgt aagcccgaag 720 tttttttgtt tccctctctc aatacaaaat aaattagtct ttctgtgttt ctaaattatt 780 gagtttgaag tgtttttcta agtataattt tttcgatgtc ttatgtgtga aaataaataa 840 ttttcttaca tgaagttagg gcactttttt ttacgtcgcc ccgggcctca aaaatctctg 900 gaccggccct g 911 // ID DNA-9-2N_Mad repbase; DNA; EDCOT; 686 BP. XX AC . XX DT 07-OCT-2010 (Rel. 15.1, Created) DT 07-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; KW DNA-9-2N_Mad. XX NM DNA-9-2N_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-686 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1463-1463 (2010). XX RN [2] RP 1-686 RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [2] (Consensus) XX CC TSD is 9-bp long. TIRs (Pos. 5-45 and 642-682) are 79% identical. XX SQ Sequence 686 BP; 229 A; 146 C; 139 G; 172 T; 0 other; gggtaatttt atttagaccc aacaatactc tttctacacc cagctacaaa aaacttttta 60 tgtaattcct atattacccc ttatacaaaa taaaataaga aactgaaaat taaatatctt 120 tctacaccca ttcaaccgag atagaaccca catacatcgc caccactcaa ccaccacttc 180 agacctccct ccctcttcct tctcctgcat atagaagtag ttaggcggga ttgctaaatc 240 agccatcgcc ttcaacaacc cgacccaata caaaatccat ttgactccat tttggacttc 300 tgcaacaagt cgcttacgga gtcgacgatg ccgcttagtt ttgcctatta acagcaaggc 360 cctatcacgc gcaatagaag aaaaatggaa agattcactg gacgtttggt ggagtagcca 420 ccgcaaagaa ttggtgggtg tgggagaggt gggggaacac accgagaata tcagggaaaa 480 aaaacagtcg ggagggagac agacccaaca aatacaggga ggagacgcca gaaggcgaga 540 gaacagtcgg gaaatgggtt tgatgagttt ttctttttcc agtttattta tgtttataat 600 ttatgagggt aaactagaga gtttaggtaa caaaatatta aagttgggtt tagagagagg 660 aaaactgggt ccaaataaaa tttctc 686 // ID SHACOP6_LTR_MT repbase; DNA; EDCOT; 278 BP. XX AC AC131248; XX DT 15-JAN-2007 (Rel. 12.01, Created) DT 15-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of LTR retroposon, SHACOP6_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; SHACOP6_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-278 RA Shankar R. and Jurka J.; RT "SHACOP6_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 77-77 (2007). XX DR EMBL/GenBank/DDBJ; AC131248; Positions 106378 106655. XX SQ Sequence 278 BP; 84 A; 52 C; 33 G; 109 T; 0 other; tgttaagaat catgatccta cctaataact ccctgattct cttttggttg actgattaag 60 tttaatgtct atacttaatt attgccttgt atagctcctg ctaattacat cagtacttga 120 ctctctctta gttgactgat ttaatttaat gtccatattt aattgttgct ttatatagtc 180 tgtgctaata agcacattat cattcccaca tgtataaagg ataacatctg tatactccat 240 agaatcaata acaacagaag caattatctt cttttaca 278 // ID Copia-53_VV-LTR repbase; DNA; EDCOT; 623 BP. XX AC chr2; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-53_VV_; KW Copia-53_VV-I; Copia-53_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-623 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr2; Positions 6580904 6580282. XX SQ Sequence 623 BP; 157 A; 93 C; 110 G; 263 T; 0 other; tgtaggaaaa gtgtaaataa tttctatttt tatttttggg aattatttta atttatttta 60 tttcattcta tgaatcttat atttttggga agtgtcctat tgagaattat tttatatttt 120 attatatttt attttattct attagtgtta tattttttgg aagagtccta ttgggattgt 180 gcaagtggag tttcattcct tttataagta gaatcacctt ccactttgtg tcatattcta 240 attataagta gatttctttt gggactatgt tagtggccta taaaagcagg tcacccctat 300 ctcatatcag tcccaatttt tttccagaga actatttaga gagttttcag ggaatatttt 360 catacatcta tttggaggaa tttattcaac ctagctgtac acatctcgct tttagagtgc 420 acccaaggcg agatttggct attgaatcct ggaggtagac cactggtacc ctagtgcacc 480 gagtttgtct tcgaggaagg tggatctatt tcaaggacaa tgtttgtcac gcctcagccg 540 ataagttttt ctttttaatt attttgttct ttgtttgtgg tttttgggct agttttttgt 600 ttccataccc ttaaaatcca aca 623 // ID BRENSPM1 repbase; DNA; EDCOT; 2112 BP. XX AC AB022082; XX DT 13-APR-2000 (Rel. 5.04, Created) DT 30-MAY-2000 (Rel. 5.04, Last updated, Version 2) XX DE BRENSPM1 is a En/Spm-like transposase. XX KW EnSpm; DNA transposon; Transposable Element; BRENSPM1; KW En/Spm superfamily; transposase. XX OS Brassica rapa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-2112 RA Suzuki G.; RT "Direct submission."; RL Direct Submission to EMBL/GenBank/DDBJ (06-JAN-1999). Go Suzuki, RL Tohoku University, Laboratory of Plant Breeding and Genetics; 1-1 RL Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, RL Japan (E-mail:gsuzuki@cc.osaka-kyoiku.ac.jp, Tel:81-22-717-8652, RL Fax:81-22-717-8654). XX DR GenBank; AB022082; Positions 1 2112. XX SQ Sequence 2112 BP; 644 A; 375 C; 516 G; 577 T; 0 other; atggctggct ctgggactat ttacgagttg cggaattgga tgtatatgca tagagatgct 60 aacgggagag tgacgaaaga ataccttgcg gggctggaga catttatgca ccaagcagat 120 tcaacaccgc tcgcccaaga aagtggtaag atgttctgtc cttgtcggaa atgcaacaat 180 tcgaaattgg caaaccgtga aaatgtttgg aagcatttaa taaatagagg tttcacgcca 240 aattactata tctggtttca acatggggaa ggttataatt atgatcagaa tgaagctagt 300 agtagtaata gcaattttca ggaagaaccg gttaatcatc atttgcataa tgaacatagt 360 taccatcagg aggagatggt agattatgat agggttcatg atatggtagc tgatgcattc 420 gtagctcatg atgaagatga agaacctaat atagatgcaa aaaagtttta cggaatgtta 480 aacgcggcga atcaaccact ttacagtggt tgtagagaag gtctctctaa attgtcgttg 540 gctgctagaa tgatgaatat taaaactgat cacaatctac ctgaaagttg catgaacgaa 600 tgggcggact tgtttaaaga gtatttgccg gaagacaatg tgtctgctga ttcttattat 660 gagattcaga aattagttta tagtcttggg ttgccttcgg agatgataga tgtctgcatc 720 gacaactgca tgatctattg gggagatgat gagaagctcg aagcatgtcg attctgcaag 780 aagccacgat tcaagccgca aggacgggga cttaataggg taccgtacca aaggatgtgg 840 tacctaccaa ttacagacag attgaaaaga ttgtatcaat cagagcagac tgctgcaaat 900 atgagatggc atgccgagca tactcagacg gatggtgaga tgactcatcc atcagatgca 960 agagcctgga aacatttcaa caaagtacat ccggattttg ctagcaatag ccggaatgtg 1020 tatctcggat tatgcacaga tggatttaat ccgttcggaa tgtcagggag acaatattca 1080 ttgtggccag tctttcttac gccatacaac ctgccaccgg agatgtgcat gcaacgggag 1140 ttgctattct tgacgatatt gatacctggt ccgaaccatc caaaaaggtc cctggatgtt 1200 ttcctacaac cactgataaa agagttgaag gatttgtggt caacaggggt gaggacgtat 1260 gattgttcaa cgaagacgaa ttttacgatg cgagctatgc ttttgtggac cataagtgac 1320 tttcctgcat atgggatgtt gtctggatgg actacacatg ggagattagc ttgtccatat 1380 tgtaatggaa cgacagatgc gtttcaactg aagaatggta ggaagacaag ttggtttgat 1440 tgtcatcgtc gatttcttcc cattggccat ccttaccgaa gaaacaagaa tttgtttagg 1500 cacaaaaggg ttgtgagaga cacttctcca ccatatctaa ctggagaaca aattgaagca 1560 caaatcgact actacggagc taacgaaaca gttcgttggg gtggtaattg gcatgtccct 1620 cgtaatatgc ctgattctta cggtgttcat cacaactggc acaagaagag tatattttgg 1680 gagttgccat gttggaagga tcttcttctg cgccacaacc tcgatgtgat gcatatagag 1740 aagaatttct ttgagaacat catgaataca atattgaatg tcccagggaa gacaaaagac 1800 aacataaaat cgaggttgga cttgccggat atttgctcaa gaagcgagtt acatattaaa 1860 agcaatggac aagttcccgt tccgatattc agactgtctt cagaaaaaaa gtcggtgttg 1920 ttcaactggg tggcatcaga agtgaagttt cccgatgggt atgtttcaaa tctctctaga 1980 tgtgttgaaa agggtcaaaa gttctctggg atgaagagtc atgattgtca tgtctttatg 2040 caacgactac tgccctttgc atttgcggag ctacttccaa caaacgtaca tgaagcactt 2100 gcaggttcgt ag 2112 // ID Copia44-PTR_I repbase; DNA; EDCOT; 4384 BP. XX AC scaffold_1239; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia44-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4384 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4384 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 266-266 (2007). XX DR Genome; scaffold_1239; Positions 5436 9819. XX CC Positions [1663-2163] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 79..4374 FT /product="Copia44-PTR_I_1p" FT /translation="MTTESPSPIIHVQTENSGFNAGIILTETNYDTWSQII FT EMQIAGREKLDYIIGDSPQPDAKDPYYSKWYAENQKIKGWLLTSMTPEIMK FT RYLRLRTAREIWSALAKAFYDGSDETQIFALNQRAFSIRQSSRSLPTYYGE FT LVEIFQELDYRDKVKMRDPEDIIMYKAAVDKLRIHIFLNGLDAEFEQVRGE FT ILRMDPSLDLECTYAYIRREANRRILLTSDLTTSDYVAMLARRNTPPVRHS FT GSMVTSRSFDIGNKQASSSRYCTHCGDTGHSKSRCYDLIGYPEWWDPSKAP FT KRKGKTSPATSSVSTAIAEMSSPNTNATTLHISSESPGKPFDKPTPIGSCA FT WIIDSGSTDHMSFDTSSVSKLKPSEKYVVSTANGTQATVVGKGSFSLNKLN FT LNSVLIVPSLNFNLISVSQITTSLNCVVIFWPDHCVFKDIKTRKTIGCGTK FT KGRLYYLDLTSSSSSALAQSLSVTSSTSTSNIWLWHKRFGHVSFGYLKHLF FT PELFLNTSPPLFKCETCELAKSHRVPFHPSLNKSPLPFTLIHSDVWGPAKV FT PTLNGSRWFVSFIDDHSRMTWVCLMKTKQAVCSLFKQFYSMVATQYKTSIQ FT VLRTDNGGEFVNHEMKQFLQCQGIIHQTTCPYSPQQNGVAERKNRHLLEMV FT RATLFEANMPLHYWGESLTTASYIINRIPSRSLDFHTPFDTLNHSLSSPLI FT PNLPPKVFGCIAFVHIPKHTRHKLQPCALRCVFVGYGLHQKGYRCFHPPTQ FT KLYVTMDVKFHEHQMYFPATETTNQGEESFNIQSLSHQTENISHSLPEPET FT PEQEPVEPEHMDAVIEPTTLELQPCDQPNIAEATVPQQQSSPLDASIPHES FT PLTDESQVNLEPPLRILPNRITRGIPRVSYEPVRTSTPKYPLNNYVSYHRL FT SKACESFANQLSTVHVPNSVQEAIKDPRWKNAMNEEMKSLQRNATWEVIDL FT PAGKKPVGCRWIFSVKYKADGDIERFKARLVAKGYSQTYGIDYAETFAPVA FT KINTVRILLSLAANFDWPLHQFDVKNAFLHGNLQEEVYMELPPGCQLQVEG FT SKQVCKLRKSLYGLKQSPRAWFGRFTNSMKAFGYQQSSSDHTLFIKHKEGK FT LTILIIYVDDMIVTGNDSVEKESLQTYLSREFEMKDLGPLKYFLGIEVLRS FT RHGILLSQRKYTIDLLNEVGMLACKPSDTPAAENVKLSAHSNQIPANKEQY FT QRLVGRLMYLTHTRPDLAYSLSVVSRYMHSPSEEHMKAVMRILQYLKSSPG FT KGIMFTKGDTLNIEGYTDADWAGSIDDRRSTAGYLTFVGGNLVTWRSKKQG FT VVARSSAEAEYRGMAKGVCELLWIKNLLQELKISSTFPMKLYCDNKAACDI FT AHNPVQHDRTKHVEIDRHFIKEQLEAKIIAVPHVRSQDQLADILTKAVSSK FT AFHQVLDKLGMKNIHAPT" XX SQ Sequence 4384 BP; 1378 A; 911 C; 842 G; 1253 T; 0 other; ttactgaatt ctatatggta tcagagcagg ttttctaaaa tccctgcaaa tccactgaat 60 caaatcaccc tcaatacaat gactactgaa tcaccctctc ctattataca tgtccaaact 120 gaaaactcag gtttcaatgc tggtataata ctcaccgaaa ccaattatga cacctggtcc 180 caaatcatcg aaatgcagat tgctggtcgt gaaaaactgg attatattat tggcgactca 240 cctcaacctg atgcaaaaga cccctattac tccaagtggt atgctgaaaa tcaaaaaatt 300 aaaggctggt tactcacatc aatgacccca gagattatga agaggtatct tcgcctacgt 360 actgctcgtg aaatttggag tgctcttgct aaagcattct atgatggatc ggatgaaaca 420 caaatctttg ctctcaatca gcgtgccttc tctattcgtc aatccagtcg ttctcttcct 480 acatattatg gtgagctagt tgaaatattt caagaacttg attaccgtga caaagttaaa 540 atgagggacc ctgaagatat tattatgtat aaagcagcag ttgacaaatt aaggatacat 600 atcttcttaa atggccttga tgctgaattt gagcaagtgc gaggagaaat acttcgcatg 660 gatccaagct tggatcttga gtgcacatat gcatatattc gccgtgaagc aaatcgtcga 720 atccttctaa ctagtgacct gactacttct gattatgtgg ccatgttagc tcgtcgaaac 780 acaccacctg tccgacactc tggttccatg gtgacatctc gcagctttga cattggaaac 840 aaacaggcta gctcatctag atactgtacc cattgtggag acactggaca cagtaaaagc 900 cgctgctatg acttgattgg atatcctgaa tggtgggatc cttccaaggc tccaaaacgt 960 aaaggcaaga cttcacctgc aacatcatct gtctctaccg ccatagctga aatgtcatca 1020 cctaatacta atgctacaac attacatatt tcctcagaat caccaggtaa gccgtttgat 1080 aaacctacac ctattggatc ttgtgcatgg attattgatt ctggatcaac tgatcatatg 1140 tcctttgata cttcttctgt ctctaaattg aaaccatctg aaaaatatgt tgtgtctaca 1200 gcaaatggaa ctcaagccac agttgttgga aaaggttcat tttctttaaa taagctaaat 1260 ttgaactctg ttcttatagt tccttccctt aattttaact tgatatctgt ctcacaaatt 1320 acaacttctt tgaattgtgt cgtgattttt tggcctgatc attgtgtttt taaggacatc 1380 aagacaagga agacgattgg ttgtggtact aaaaagggga ggctctatta tcttgatctc 1440 acatcatcta gctcaagtgc attggctcaa tcattatcag ttaccagttc aacatctacg 1500 tctaatattt ggttgtggca caaacgattt ggacatgttt catttggata tttaaagcat 1560 ttgtttcctg aattattttt aaacacatct ccaccattgt ttaaatgtga aacatgtgaa 1620 ttggcaaaga gccaccgtgt tccttttcac ccaagtttga ataaaagtcc tttgccattt 1680 acacttatac actctgatgt ttggggacct gcaaaagttc caactctgaa tggatcacgt 1740 tggtttgtct cattcataga tgatcatagt cggatgactt gggtatgtct gatgaaaacc 1800 aaacaggctg tgtgctcact ttttaagcag ttttattcaa tggttgctac ccagtataaa 1860 acttcaattc aggtcctgcg cactgataat ggtggggagt ttgtcaatca tgagatgaag 1920 caattcttac agtgtcaggg cataatccat caaactacat gcccttattc cccccaacag 1980 aatggggttg cagaaagaaa aaacagacat ctcctggaaa tggttcgagc cacactattt 2040 gaagccaata tgccccttca ttactggggt gagtcactta caactgcatc atatataata 2100 aaccgtatcc catcccgcag cttagacttc catacaccat ttgatacatt aaaccatagt 2160 ttgtcctcac cactcatacc aaacctgccc ccaaaagtct ttggctgcat tgcttttgta 2220 cacataccaa aacatacccg ccataaactt caaccatgtg ctcttcgatg tgtctttgtt 2280 ggatatggtc ttcatcagaa aggatatcgg tgtttccatc cacccactca aaaattgtat 2340 gtcacaatgg atgtaaaatt ccatgagcac cagatgtact ttcctgcaac agagactaca 2400 aatcaggggg aggaaagttt taacatacag tctcttagcc atcaaactga gaacataagt 2460 cactctttac ctgaacctga aacaccagaa caggaaccag tagaaccaga acatatggat 2520 gcagtaattg agccaacaac acttgagctt caaccatgtg atcaacctaa tatagctgaa 2580 gcaactgtac cacaacaaca atcatctcca cttgatgctt ctattcctca tgagtcacca 2640 ttaactgatg aatcacaggt aaaccttgaa cctccactcc gcatacttcc taaccgtatc 2700 acaagaggaa ttcctagagt tagctatgaa cctgttcgta cttctacccc taaataccca 2760 ctaaataatt atgtatctta ccataggcta tcaaaggcat gtgaatcatt tgcaaatcaa 2820 ttgtctactg tacatgttcc taatagtgtg caggaagcta tcaaggatcc taggtggaaa 2880 aatgcaatga atgaagaaat gaaatctctc caaagaaatg caacatggga ggtgatcgac 2940 ttacctgctg gaaaaaaacc tgtgggatgt cgatggattt tttcagtcaa atacaaagct 3000 gatggtgata ttgagaggtt taaagcacgg cttgtggcca aggggtacag tcaaacgtat 3060 gggattgatt atgcagaaac gtttgcacca gtggctaaaa taaacacagt ccgtattctc 3120 ttgtcattag ctgcaaattt tgactggcca ctacatcaat ttgatgtaaa gaatgcattc 3180 ctgcacggga atctccaaga agaagtatac atggagctgc ctccaggatg tcagttacag 3240 gttgaaggaa gcaaacaagt ttgtaaactg cgaaaatcat tgtatggatt aaagcaatca 3300 ccaagagctt ggttcggcag atttacaaac tcaatgaagg catttggata tcaacagagt 3360 agttctgacc acaccctatt cataaagcat aaggaaggga agctcacaat attgattata 3420 tatgttgacg atatgattgt gacaggaaat gactctgttg aaaaggaatc cctgcaaact 3480 tatctctctc gagaatttga aatgaaagat cttggacctt taaagtactt tctgggaatt 3540 gaggtattga gatctagaca tggtatactc ttgtcacaac ggaaatacac aattgatttg 3600 cttaatgaag ttggcatgtt agcctgcaaa ccaagtgaca cacctgctgc tgaaaatgtc 3660 aagttgagtg cacactcaaa tcagattcct gcaaataaag aacaatatca gaggctggta 3720 ggacgattga tgtatcttac acatactaga cccgacttag catactcact tagtgttgtt 3780 agcaggtata tgcactctcc aagtgaagaa catatgaagg cagtaatgcg tattttacaa 3840 tatttaaagt cttctccagg taaaggaatt atgttcacta aaggagacac tttgaatatt 3900 gaaggctata ccgatgcaga ttgggcaggc tcaattgatg atagacgttc cactgcagga 3960 tacttgacat ttgttggggg aaatctggtt acatggcgaa gcaaaaaaca gggagttgtc 4020 gctagatcta gtgcggaagc agagtacaga ggtatggcta aaggtgtatg tgagctgcta 4080 tggattaaaa atttgttaca ggaactcaag atttcatcaa catttcctat gaagttatac 4140 tgtgataaca aggctgcatg tgacatagct cacaatcctg ttcagcatga ccgaacaaag 4200 catgtagaga ttgacagaca ctttattaaa gaacaactgg aagcgaagat aattgccgtt 4260 cctcatgttc gatctcaaga tcaactggct gatattctca ccaaggcagt atcaagtaaa 4320 gcctttcacc aagtattgga caagttaggc atgaaaaata tccatgcacc aacttgaggg 4380 ggag 4384 // ID Copia-1_CP-LTR repbase; DNA; EDCOT; 375 BP. XX AC ABIM01005961; XX DT 10-MAR-2010 (Rel. 15.04, Created) DT 10-MAR-2010 (Rel. 15.04, Last updated, Version -1) XX DE LTR retrotransposon from papaya: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-4_CP_; KW Copia-1_CP-I; Copia-1_CP-LTR. XX OS Carica papaya OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Caricaceae; Carica. XX RN [1] RP 1-375 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from papaya."; RL Repbase Reports 10(4), 574-574 (2010). XX DR Genome; ABIM01005961; Positions 1530 1904. XX SQ Sequence 375 BP; 120 A; 71 C; 55 G; 129 T; 0 other; tgttaaaatt aatgattttt tctgttaagt ttaaattcaa aaaaaaaaaa aaaagaaatc 60 caccgtgaag ttgtatcaca ataggatacg taaatttcat gcgatgtgta tgcataattt 120 tcggacgatc tgatttgatc gtttggttga tgtaatcagt ttaaatttat atttctatat 180 atatatataa gctgaaataa aacaaagaga tcaactcctt ctctcccgaa aaaggcactc 240 ctcttcaaaa tagcaaaaca gaggcagttg catgagtttg ctctgttttg ctgccctctc 300 tctctcctca actttctctc tctaagtttg ttcaatcaca gagcctccct tgaagctttt 360 cgctttcgat caaca 375 // ID POPCOP2_I repbase; DNA; EDCOT; 6774 BP. XX AC . XX DT 09-APR-2007 (Rel. 12.04, Created) DT 03-MAY-2007 (Rel. 12.04, Last updated, Version 1) XX DE Copia-type LTR retrotransposon - internal sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; internal portion; POPCOP2_I. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-6774 RA Jurka J.; RT "POPCOP2: Copia-type LTR-retrotransposon from black cottonwood."; RL Repbase Reports 7(4), 151-151 (2007). XX DR [1] (Consensus) XX CC LTRs are ~97% identical. XX FH Key Location/Qualifiers FT CDS join(1570..2511,2465..5077,5017..5601) FT /product="POPCOP2_I_1p" FT /translation="MAASKSIIADLNHGDKLSEKNYDVWHRKIEYLLEEQE FT MLETITQPMAEPEQGNTAQHRLDMEAYQTYKRKDRVARILMLSSMRNDIML FT RFERHRSAQSVWDAVKIQYGGTSTTRLRQLTLKFDGYKKRQNQTMRQHLTV FT MSNMISELRGVGHEMTDEQQVQAVIRSLPSNWEHMRVNLTHNDNIKTFDDV FT ARHVELEEDRLHAEKPINEAFISETKMRGAYGSKYKKGKAKGPKYGKRGIE FT ASSSGHKRKRGKRGGKKDKNMNCFNCGKPGHFARNCTEPKVMFNHNHPSNL FT YVSSCLMLAESVPFLDYRLRSNCLLNLFPFWTIDSGATDHIARDRTTFVEF FT RRIPKGSRYIYMGNNASAAVLGIGTCKLDLRGGRTLYLHDVLYAPEVRRNL FT VSVLALLQLGFNIAFVGCCVKIHLDNIFYGSGFVLNGFMVLDTVNVSINYD FT ASIYVVQNSSTINDSNIITWHARLGHIGQDRLHRLARAGLLGSLTKEELPV FT CEHCLAGKATRLPFGKAKRASSPLQLIHSDICGPMNVRARHGGNYFITFID FT DFTRFGHVYLISHKSEALDCFIRYTNLVENKLSTKIKALRTDRGREYLSEQ FT FKNFCDEKGIARQLTIPYTPQQNGVAERRNRTLFDMVRSMMAQANLPISFW FT GDALLTAAYILNRVPSKSVSSTPYELWNGVKPNLGYFHPWGCATYIHNTSH FT EYGKLGPRGKKCIFIRYSEHSKGFVFIGEKANGRVTEIESRDVVFLEKVFP FT KTGEVEKDFQLYEMENLDYGATSHSVEDLDETFNPPRNSGSDILSIPTLME FT QDHEQSQPRRSIREPIPRRRFEIEGEAFMIAPQDDEEPKTFSHALSGPKAR FT EWIKAMEEEMESMKINQVWDLVDLPSGRRSIGNKWVLKIKRKADGSIERYK FT ARLVAKGYTQEEGIDYEDTFSPVVRITSVRLILAIVAHMDLELYQMDVRTA FT FLNGELNEEIYMDQPLGFETKGQERKVCKLKRSIYGLKQASRQWNVKFHQA FT ILKDGFTMMEEDHCVYLKCSNNSFIILSLYVDDILIAGNNKEMIDTTKKWL FT SSNFEMKDMGEASYVLGVKIIRDRAKRLLGLTQETYIKKMLERYHMQDCKP FT MDTFVDKSLSLSCDMCPKTLEEKEKMSRVPYASAVGSLMYAMMCTRPDICY FT AVGLVSRYQSNPGQKHWMTVKRFYDIPISIKPWSETLDDSQKILRYLKGTS FT NYMLCYQGKKDLRLIGFSDADWGGDVDQSKSTSGCAFLLNDSAILWRSKKQ FT SCIALSTMEAEYVACSAATQDAVWLKNFLYHLKIVKSASDPVTIYCDNTAA FT IAVAKDPKYHGKTKHIKMRYHYIREAITEQDVILKHISTNSMVADPLTKPI FT ARDAFVRHVRSLGLCRM" XX SQ Sequence 6774 BP; 2233 A; 1042 C; 1371 G; 2127 T; 1 other; ttggtatcag agccatggtt tttaatattg tttttatgca gtatatctat tattacatga 60 acgatagatg taaattttgt gttaaaagaa tacttccatt gagaattttg aatttacaaa 120 attttatgaa gtaatttagt tatgaatttg tcttttctat aattaattag aaaagacttt 180 ctgcaaaata aatggtagtt gtataattct attatcaatt catgtgtgaa ttgatgatgg 240 aaatggagat taraaactat catttccatt tccaattgac tacaattgca gtagtcaatt 300 ggactttgac agttaataga taaaaaaaaa ataaccacct gaaagaacac atattttaaa 360 agatgtgtaa ctgccattcg gcagttaata ttttcatttc caattgacta caatcccagt 420 agtcaattgg aaactgccat ttggcagttg ttagagaaaa aaaaaaaaag aaagaaggaa 480 aaccgaatga acacatcttt taaaagatgt gtacatatat taactgccat tcggcagtta 540 atatatatta ataatgatta atatatatta atattaagaa taatattaag acaattaata 600 ttttttttgt taatataaat tgtcaaattg tggtgccaat ttatttattg ttaaaataaa 660 ttgcttaatt tccatatttg ttttttaaca tatatgatga tacatgcttt aattaaatat 720 taagtataat atttatgtgc tttttggaat attttgttgt agtggatagg caacaacaaa 780 ttgatcaaca ttggtaccat ttattgggtt atgcctttaa tcctgttcac aaaattcaag 840 agcacattga ttatatgtat cattggatga gtagactagc tatgagtggt gtttacgaat 900 tctacatgga acatcaaatg ttaatcgttc tcaattctct gcctgaggaa tggatgtcgg 960 tgcgactatc gttggaatat aggctggaat ccttagattt caacaatctc gcagatgaaa 1020 tgctgcttga gagggaacgt cagtatgccg aaaagggtat acgacgcact ggaagaagca 1080 caggtcgttt ggatgctgct gctaaattca ttccatggtt tgagcagaat gaacttggag 1140 gagatgactt tgatgaagtg gatgacgtaa ttggagaccc tacttatgtg cctacaatat 1200 aaaataattc tgaaatttat tattcttaat attgtatttt ttttaaagat gattggttgt 1260 ttaattgtga actgaatatt ttatgtaatt taagttttaa ttacattata tgcatatata 1320 tatgataata tctgcaacct gattagtggg agttgttagt tgaaactaat aactataatt 1380 ttgcactcat ttaaatttcc aataataatt agaccataca aatagaaatt gattaagtgt 1440 ttaacattct tttcatttct attgtatgtg ttagattatt atttgtttaa tttagaatgg 1500 agtggcaaaa tatgtcaatt aaattgtact agatactaat atttgtaatt gctgtcaata 1560 acgcttaata tggctgcatc taagagtatt attgctgatt tgaaccatgg agacaaacta 1620 agtgaaaaga attacgatgt ttggcatcgt aagattgagt atctcctgga agagcaagaa 1680 atgctggaaa caatcacaca accgatggct gaacctgagc aaggaaacac tgctcagcac 1740 aggcttgata tggaagcata tcaaacctat aaacgcaagg atcgtgtagc tcgcattttg 1800 atgttgagca gcatgagaaa tgatataatg ctgcgttttg aaaggcatcg ttcagctcaa 1860 tctgtttggg acgcagtaaa gattcagtat ggaggaacct ccactactag acttcgtcag 1920 ttaaccctca aattcgatgg ttataagaag cgccaaaatc aaacgatgag gcagcatctt 1980 acagtcatgt ctaacatgat cagtgaatta aggggtgttg ggcatgagat gactgatgaa 2040 caacaagtcc aagcagttat ccgctctttg ccaagcaatt gggaacacat gcgtgttaac 2100 cttacccaca atgacaacat caagacattt gatgatgttg ctcgtcatgt cgagcttgaa 2160 gaagatcgac ttcacgctga gaagcctata aacgaggctt ttatatctga gactaagatg 2220 cgtggagcat atggctctaa atataaaaag ggtaaggcta aaggtcccaa atatggcaag 2280 agaggaatag aagcaagtag tagtggacat aagcgcaagc gtgggaaacg cggcggtaag 2340 aaagacaaga atatgaattg tttcaattgt ggtaaacctg gtcactttgc tcgtaattgc 2400 actgagccaa aggtaatgtt taaccacaat catccctcta acttatacgt tagcagttgt 2460 ttaatgcttg ctgaatctgt tccctttttg gactatagac tcaggagcaa ctgaccacat 2520 agcaagggat cgaacaacct ttgtggaatt ccgtcgaatt ccaaagggaa gtagatacat 2580 atacatgggg aataatgctt ccgctgctgt gcttgggatc ggtacctgca aactggattt 2640 gcggggcggt cgcacacttt atcttcatga tgtactctac gctccagaag ttcgacgaaa 2700 tcttgtgtct gttcttgctt tactccaatt gggctttaat attgcgtttg ttggttgttg 2760 tgtaaaaata catctggata atatttttta tggttctggt tttgtattaa atggttttat 2820 ggtgttagac accgttaatg tatctattaa ttatgatgct tcaatttatg ttgttcaaaa 2880 ttccagcact attaatgata gtaatatcat aacttggcat gctagattag gacacattgg 2940 gcaagatcga ttacatagat tagcaagagc tggtctttta ggatcactta ccaaagagga 3000 attgcccgtt tgtgagcatt gccttgctgg aaaagcaact agattaccat ttggcaaagc 3060 taaaagagct agtagtccat tacagcttat tcattcagac atttgtggcc caatgaatgt 3120 gagagcaaga catggaggaa attatttcat cacatttata gatgatttta cacggtttgg 3180 tcatgtttat ttgatctcac ataagtctga agcattggat tgcttcattc gatacaccaa 3240 tttggtggag aataaactaa gtaccaagat caaagcttta agaactgatc gaggacgtga 3300 atatctgtct gaacaattta aaaatttttg tgatgaaaaa ggtatagcta gacaactaac 3360 tattccttat actccacaac aaaatggtgt agcagaaagg aggaatagaa ccctatttga 3420 catggttagg tcaatgatgg cgcaagctaa cttaccaatt tccttttggg gagatgcatt 3480 gttaactgct gcttacatac ttaatcgtgt gccctctaaa tctgtctcat ccaccccata 3540 tgaactatgg aatggtgtca aacctaatct aggttatttc catccatggg ggtgtgcaac 3600 ttatattcac aatacttctc atgaatatgg gaaacttggt cctaggggga agaagtgtat 3660 ctttatacga tattctgaac attccaaagg atttgtattt attggtgaaa aagctaatgg 3720 aagagtgaca gagattgaat cgcgtgatgt tgtattctta gaaaaggttt ttccaaagac 3780 aggtgaggtt gaaaaagatt ttcaattata tgaaatggaa aatctagatt atggcgcaac 3840 aagccattca gtagaggact tagatgaaac ttttaatcct cctagaaata gtgggagtga 3900 tattttatct attcctactc tcatggagca agatcatgag caatctcaac ctcgaagaag 3960 cattcgtgaa ccaattcctc gtcgtcgatt tgagattgag ggggaagcgt tcatgattgc 4020 tccacaagat gatgaagagc ctaaaacatt cagtcatgct ctatctggtc ctaaagcaag 4080 agaatggatt aaagctatgg aagaagaaat ggagtcgatg aaaattaatc aagtctggga 4140 cttggttgat ttaccgtcag gacgaagatc cattggaaat aaatgggttc ttaaaattaa 4200 acgtaaggcg gatgggtcaa tagaacgtta taaggctcga ctagtagcga aaggctacac 4260 tcaagaagag ggaattgatt atgaagatac attctcacca gttgtgagga ttacttcagt 4320 tcgccttatt ttagctatag tcgcacatat ggacctagag ttataccaaa tggatgttag 4380 aactgcgttt ctcaatggag aactaaatga ggagatctat atggatcaac ctttaggatt 4440 cgagactaaa ggacaagagc gcaaagtttg caagcttaaa agatccatat atggtcttaa 4500 gcaagcctct agacaatgga acgtcaagtt tcatcaagct atccttaagg atggttttac 4560 aatgatggaa gaagatcatt gcgtgtattt aaaatgttct aacaatagtt ttataatatt 4620 gtccttatat gttgacgaca ttttaatagc tggaaataac aaagagatga ttgatactac 4680 taaaaagtgg ttatcatcaa actttgaaat gaaagacatg ggtgaggcca gctatgttct 4740 tggtgtgaaa atcataagag atcgcgctaa aaggcttttg ggtttaactc aagagactta 4800 catcaaaaag atgttagagc gctatcacat gcaagattgc aaaccaatgg acacctttgt 4860 tgataaaagt ttgagcctaa gctgtgatat gtgtcccaag actctagaag aaaaggagaa 4920 aatgtccaga gtaccttatg ccagtgctgt cggtagtttg atgtatgcaa tgatgtgcac 4980 acgtcccgat atatgttatg ccgttggatt ggttagccga tatcaatcaa accctggtca 5040 gaaacactgg atgacagtca aaagattcta cgatatctga aaggaacttc aaattacatg 5100 ctatgttacc aaggaaagaa agatttacga ttgattggtt tctctgatgc tgattgggga 5160 ggagatgtcg accaatccaa atcaacttca ggatgtgctt tcttgcttaa tgatagtgca 5220 atactatgga ggagcaagaa acaatcctgc atagccttat ctaccatgga ggctgagtat 5280 gtagcttgtt ccgcagcaac acaagatgct gtttggttaa aaaatttcct gtatcatttg 5340 aaaattgtca aatcagcatc agacccagtg acaatttact gtgataacac tgctgcaata 5400 gctgtggcca aagatccaaa ataccatgga aagaccaaac acatcaagat gagatatcac 5460 tacattagag aagcaattac tgaacaagat gtgatcctaa aacacatttc tacaaattct 5520 atggttgcag atccactcac aaaaccaata gcaagggatg catttgttag acatgtgaga 5580 tcccttggcc tatgtagaat gtaattagta atataattag ttttaaggat catacgaaag 5640 cttacagtga ttgagtaatg aataaatgcc attagaatat cattttattc attatttgtt 5700 tcatgaatat attgtgagta tcgtatagta caatttgtta tagtatgtcg atagacttag 5760 attggctcac tcacatgagt aatcacctct agcacttgta aggtgagtag agatgagact 5820 atttgagttt taatgctcaa taagcgactt gggcgcagtg aaagcaattt taactcaaaa 5880 tgattattaa aaagtcacct tgactaggac caagatgagg ttcttaaata aaagaatcga 5940 catgaatgaa ttcccgccat tcatgtgtct attatgattg aagccgagta tgaaattatt 6000 catctgccac taatgaaaaa tgagcaaata agaatttctg atttgaagtc tatgttttta 6060 gcaacaaaac taagactcgt atagtgtatt tcctctaaca aggagagcaa cgacatacac 6120 tctttgtctt aagaaaagaa aagagtaagc tccactataa catgtatttc atactacatg 6180 tgctagcgac cattacagga ataaagaatg gatccctgct tctttattat gtgagtcctg 6240 aagatcatat ctaagatctc aaaatcttac cctttgtgac ttttgactat atcatgaggt 6300 gatgtattaa tgatcgctac tttaggagta tatcctatgg tcatggaatg attcgactta 6360 aaggaatact cttaggaaag cgagttaatt cagatttgat tgatatgaga gcgaaagaaa 6420 aagtaatttt agttctacac ctgttacttg tattcaccgg ccgggatcat atcacttgaa 6480 tagatttgat atgatttaga atacttgtaa ttgtaaggat ggattgagta tgaaattctt 6540 gagggattga attatattca gtcatgtgta actaaaaatg cttggggtat attagtacac 6600 tttaaggaat aattaattat gaggttgatg tctcctatat ggcctgtatt aggtttatat 6660 attggagctc ctttcactgt gtgcttcagg tccgttcgtc aagtatgaaa ttcttgtgca 6720 agtttgaagt ataatgtatt agagagattc agtccttcat gggtgagtga gaga 6774 // ID TAM11 repbase; DNA; EDCOT; 982 BP. XX AC AY077455; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Antirrhinum majus DNA transposon TAM11. XX KW DNA transposon; Transposable Element; TAM11. XX OS Antirrhinum majus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Lamiales; Plantaginaceae; Antirrhineae; OC Antirrhinum. XX RN [1] RP 1-982 RA Galego L. and Almeida J.; RT "Role of DIVARICATA in the control of dorsoventral asymmetry in RT Antirrhinum flowers."; RL Genes Dev 16(7), 880-891 (2002). XX DR Genbank; AY077455; Positions 1 982. XX CC 53bp terminal inverted repeats. XX SQ Sequence 982 BP; 338 A; 158 C; 170 G; 316 T; 0 other; ggaaaatact taggtggact aggtcccaaa agtatcctat ggaccttgtg gtcttgttaa 60 ctcttgtcat tttattaaat gaaaaacagc aagaaaatgt tttccctctc ttccccaccc 120 tctctggccc tccctgtaag ctgtacccca aataaaaaaa ggaaaacctc ctgcagattg 180 tgagaagaac attctcctca ctcttctcat cgtgcaagaa accaaagaag aatggtctaa 240 aaaatattgt tgggtttcaa aattgctggt tttgaagatt cgtcaagatg ggtaaaaaaa 300 ctaaccagaa aaacatttat tatgataaca agttaattcc attgattact ttgaaaaaaa 360 ttgtaatgca aataaagttg aagagtatat gacaaataat aactgtatat atgtaaaatt 420 taagcaaagt atatgcaata atttatgatg aagtgggttt cttatattag catagtctca 480 attcttcttc atccattaac aagattcacc acttcttcat caaaatattc caaagaaaac 540 atcgaaatcg aacgtggttt ttcacttttt ttccaaggac tgaacctggt tctctctggt 600 tttacattct ctgaatttct ttagccttcg agaaaagata gagagagaaa aaaaaaaaaa 660 aaaaggaaag aaacaatgta tcgtcttttg atgttgggtt atttctactc tcttatttgc 720 acagatgcaa gaatcttgac aactttcttt caattagttt ttgagaaagc tttttcttta 780 tggttacaaa aagttaacat tggcgagttt atggagcagt gaaatggctg agttttcctt 840 tttggggtac aagaggggcg gagtggaaga aagaggaaag acaattttat ttttattttt 900 taatttaata aattgcaaga atgaataacg accacaaggt ccataggata gtttgtggac 960 ctagtcccac taagtatttt cc 982 // ID HARB-3_Mad repbase; DNA; EDCOT; 3809 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; HARB-3_Mad. XX NM HARB-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3809 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1499-1499 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is ~32-bp long. XX FH Key Location/Qualifiers FT CDS 566..1915 FT /product="HARB-3_Mad_1p" FT /translation="MGDRRRRSRAMEMAQYQARLDIEDSELINAEAELVNS FT FMQYEHHGESSHRGSVTGRSFVQRDREECHDQMMKDYFIERPRFPAHDFRR FT RFRMRRELFEGILNAVVNHDHYFARKIDVVGRQSLSPHQKLTSAFRMLANG FT CSADSTDEYCRLAESTAIENLKRFCQAIQAIYGATYLRKPTREDLKRLLRK FT ADKRGFPGMIGSLDCMHWEWKNCPTGWAGQFKGRHNKPTIVLEAVASYDTW FT IWHAFFGSPGSNNDINVLWSSPLFDEVVNGWAPEFRYKVNGNRYELGYYLT FT DGIYPSWSTFVKSFSHPDSAKKKLFSQRQESYRKDVERAFGILQARWAIVR FT GPARFWQPEDLHSIMMTCIILHNMIVEDEYIEIEEDSDEDVDDDQPTHARA FT IARDVEYLAPTTYETRHDRVTLGEYMRRLNRIQAPQIHDTLRKDLVEHVWR FT REGER" FT CDS join(3204..2860,2831..2247) FT /product="HARB-3_Mad_2p" FT /translation="MAREHVRGRNWTFEEDVSLCLAWVSVSEDGAVGTNQN FT KKVLWDKIIAKFQENCNGGGRDGGGVYDRWKTINKACTLWKGSLERAMVGM FT PSGRSAIEIVSFFLDILFVMYIILFCNGDKAMEIYKTRVTPKNQVFKLQHA FT WDVLKDCPRWATDADQQWGRLFQREAAPRNEGDEGVDEMTPSPSLARPPGR FT DKQKEAKRKGKSQDSTSGDFATGIAKLHETHSARQEEAARMRLQMKEISDR FT EENRFEIEFMMKDLSKYTPERKKFLRDKQKEIMRKSASRSMFQDDESSEPY FT IPTFQRSPSPSEDGGYDC" XX SQ Sequence 3809 BP; 1109 A; 792 C; 755 G; 1150 T; 3 other; gaccatctcc aacccttggg ctaaaagcca aattttttag cccggaaaat ttggctttta 60 gcccagaaac atcttttctg ctccaaccct tctggcctaa aattttagcc cgggattatt 120 aaagaatgaa cttaggctaa tttttttctt aaatcaattt tttaaataaa taaatatgta 180 gactatcgta aattaatttt atgaacattt taatctaaaa aaatttaaat tccgataaat 240 attgaaaaat cactaaattt ttcacaaagc aagctttcaa ctttcaccaa ccttcatctt 300 tcaccaaccg ttcggctcca aactttcaac tttcacaaca caaactttca accgttcaac 360 accaaatttt taactttcac caaccgttca acaccaaact ttcaactttc accaaccgtt 420 cactttcatc aatcatcctc tatataaaca catgtccaat attagttgat cacacaacct 480 ttcaaccttc aatcatcctc tatattcacc aatctttcaa ctttcaaaga gtttttgttt 540 cctaaaaatc ctcaatatct catcaatggg tgatagaaga aggcgtagca gggcaatgga 600 gatggcacaa taccaagcaa ggcttgacat tgaggattca gaactgatca acgccgaagc 660 tgaacttgta aactcgttta tgcaatatga gcaccatggc gaatctagcc atcgtggttc 720 tgtcacgggg cgttcattcg tgcagcgtga tagagaagag tgtcatgacc aaatgatgaa 780 agattatttc attgagcggc cgagatttcc tgctcatgat tttcggaggc ggtttcggat 840 gaggagagag ctttttgaag gcatcttgaa cgcagttgtc aatcatgacc actactttgc 900 aaggaagata gatgtcgtag gccgacaaag tctatcacct catcagaagc tcacatctgc 960 atttcgaatg ctagctaatg ggtgctctgc tgactcaact gacgaatatt gccgacttgc 1020 ggagagtact gctattgaga acctgaagcg cttctgtcaa gcaattcaag ccatctatgg 1080 agccacatac ctccgcaagc caactcgtga agacttgaaa aggcttctac gcaaggcaga 1140 caaaagaggc ttccctggca tgataggaag tctcgattgt atgcattggg agtggaagaa 1200 ttgtcctact ggttgggctg gccaattcaa gggccgtcat aacaagccaa ccatcgtgct 1260 ggaggctgtg gcatcttacg acacatggat ttggcatgca ttcttcggct ctcccggatc 1320 aaacaacgat atcaacgttc tttggtcttc tcctctgttc gatgaggttg tgaatggatg 1380 ggcaccagaa tttcgataca aggtaaatgg taataggtat gagctaggtt actacctaac 1440 tgatggtatt tatcctagtt ggtctacctt tgtcaaaagt ttttctcatc ccgatagtgc 1500 aaagaagaaa ttattttcgc agaggcaaga gtcttacagg aaggatgtgg agagagcgtt 1560 cgggatctta caagctcgat gggccattgt tagagggcct gcacgatttt ggcaacccga 1620 agacctccat tcaatcatga tgacgtgcat aattttgcac aatatgattg tggaagatga 1680 gtacatcgaa attgaagaag attcagacga agatgtggat gatgaccaac caacacatgc 1740 gagagctatt gcaagagatg ttgaatatct cgctccaacc acatatgaga cccgacatga 1800 tagggtcacc ttgggtgagt atatgagacg tttaaataga attcaagctc ctcaaattca 1860 tgacacactc cgcaaggatt tggttgagca tgtgtggcgc cgagaaggtg aacgttgatg 1920 atgttggttg agcatttatg taataatttt aagtgtacta tgttgttatt tttagtaata 1980 aatttaagtt gcaaatattt tgtctactac gttggataat ttattgaatg gaggttgaat 2040 tattgaaggc atctattcta catcaaagtg tggaataata agtacaataa ttattgaaga 2100 catctagatt aaatagaaac aataattaat aagacataaa tttaataaag tacataaacc 2160 acataataaa caacataaac ttaatacaaa cgacaattaa taaacttaat taataaagca 2220 cataattcat acactacata aacttaacaa tcatatccac catcttcact tggtgatgga 2280 cttcgttgaa atgttgggat atagggttca gaggattcat catcttgaaa catactcctt 2340 gaggcagact ttcgcataat ttccttttgc ttatcacgta agaacttctt cctctctgga 2400 gtgtatttgc tgaggtcctt catcatgaat tcaatttcaa acctattttc ctccctatcc 2460 gagatttcct tcatttgcaa acgcattcgg gccgcttctt cttggcgagc gctatgagtt 2520 tcgtgcaatt ttgcaattcc ggtagcaaag tctccactcg tcgaatcttg ggacttccct 2580 tttctctttg cttccttttg cttatctctt cccgggggcc ttgctaaaga aggagatggg 2640 gtcatttcat cgacaccttc atcaccttca tttctcggtg cggcttcacg ttgaaataat 2700 cttccccatt gttggtctgc atcggttgcc caccttggac aatccttgag gacgtcccaa 2760 gcatgttgca acttaaaaac ttgatttttt ggtgttactc ttgtcttgta aatttccatt 2820 gctttgtcac cctatgcaaa aaatacataa aaataattag ttgcaaaata atattatgta 2880 catgacaaat aaaatatcaa gaaaaaaact cacaatttct atggcgctcc ttccactagg 2940 catgccaacc atggctctct ccaagcttcc cttccataaa gtgcatgctt tgttgatagt 3000 cttccaccga tcataaacac caccaccgtc ccgcccgccg ccgttgcagt tttcttgaaa 3060 ctttgcaatg attttatccc acaaaacctt tttattttga tttgtgccaa ctgcaccatc 3120 ttcgctaaca gaaacccatg ccaagcataa agaaacatct tcctcaaagg tccaattacg 3180 acctctaaca tgctctcttg ccatgttgaa caatttggaa atggaaagaa atggtagaaa 3240 gataaattgg aagaattgta ggagaaaatt gagttttgtg tggatgtttg aacaaataca 3300 taggtattta tagagttttt gggtaaattt tgtgttaaat aaatttattt aattatttta 3360 gccgttggat ttaaatttgg gccgttagat cttttttttt accgttagat ttgaktatat 3420 tcaatctcaa ccgttggatt caatgtattt taaaataaca tattttttaa aaatgaaatt 3480 tgaatctgga ccgttggatc aaccaacggt ccttaaatgc tggccgtccg attctgaaaa 3540 gagccgttgg gctcgggtga gtggccgaca aggccctgaa gctgggcccc ctccctgtcg 3600 ggmtccgatt gcaagcgggc cgcgtggggc gcgtgcgcga gtgaacgggc cgagastggc 3660 ccaaaagcgg gcgagtccac gcggcttggg ggggaatttg gcccaacttt agcattcccc 3720 ttttagccca atattttagc ttgggttggg gggtgtttgg ggggaatttg ggctaaaatt 3780 tggcttttag cccagggttg gagttggtc 3809 // ID COP16_I_MT repbase; DNA; EDCOT; 4547 BP. XX AC . XX DT 08-JAN-2007 (Rel. 12.01, Created) DT 08-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of COP16_MT LTR retroposon from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; COP16_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4547 RA Shankar R. and Jurka J.; RT "COP16_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 11-11 (2007). XX DR [1] (Consensus) XX CC The internal region has two possible ORFs. It has domains for gag CC and pol. Flanked on both termini by LTRs. XX FH Key Location/Qualifiers FT CDS join(730..1590,1594..1950) FT /product="COP16_I_MT_1p" FT /translation="MFAVSNNNAKKKFVGAVLKPADKPFKNPNRPMNKNFN FT RNKTRNNPRPQIQQPPKNDVAPPFNCYNCGQAGHIPRKCRNRTNRPAQAHM FT ATAVAPDEPYVAMITEINMIAGSDGWWVDTGASRHVCYDRDMFKIYTACDD FT QKVLLGDSHSTNVAGIGDIELKFTSGKILILKDVLHTPKIRKNLVSGFLLN FT KAGFTQSIGADLYTITKNGIFVGKGYATDGMFKLNIDMNKISSSAYMLCDF FT NIWHSRLCHVNKRIISNMSGLGLIPKICLNDFEKCQFCSQAKINKEHKSVT FT RITEPFELIHSDLCELDGNLTRNGKRYFITFIDDCSDYTHVYLMRNKNEAL FT EIFKQYVKEIENQFNIRIKRFRSDRGTEYGSHTFNEYYKELGIIHETTAPY FT SPEMNGKAERKK" FT CDS join(1847..1924,1928..2884,2888..4039,4043..4156) FT /product="COP16_I_MT_2p" FT /translation="MDHIHSMSIIKNSELFMKQLLLILLKTVKRKEKNRTF FT TELVVATMLNSGAAPHWWGEILLTVCYVLNRVPKTKNKISPYEILKKRQPN FT LSYFRTWGCLAYVRKPDPKRVKLASRAYECVFIGYALNSKAYRFYDLKSKT FT IIESNDVDFYENKFPFKSGDSGGNSGGTDNSVLDQPSEIITSNENIERDVI FT EPRRGKRARIAKEYGPEYVAYTIEEDPSSIKEALSSIDADLWQEAINDEMD FT SLMSNETWHLTDLPPGCKTIGCKWILKKKLKPDGSIDKYKARLVAKGFRQR FT ENVDFFDTYSPVTRITSIRVLISLAAIHNLRVHQMDVKTAFLNGEVEEEIY FT MDPEGFVIHGQENKVCKLDRSLYGLKQAPKQWHVKFVNLMIENEFKVNESD FT KCIYSKYENNTCTIICLYVDDLLIFGSNLNAIKDVKSLLCHNFDMKDLGEA FT DVILGIKITRTDNGISLNQSHYVEKILRKYNYFNCKPASTPCDPSVKLFKN FT TGDSVRQIEYASIIGSLRYATDCTRPDIGYAVGLLCKFTSRPSMEHWQAIE FT RVMRYLKKTMTLGLHYQRYHAVLEGYSDVDWNTLSDDSKATSGYIFSIAGG FT AVSWKSKKQTILAQSTMESEMIALAAASEEASWLRCLLSEIPLWERPLPAV FT LIHCDSTATIAKIENRYYNGKRRQIRRKHITIREYLSNGTVRVDFVRTNEN FT LADPLTKGLNREKVANASSRMGLMPIDHKWKPDLNDWRSQELGSMGNNKSQ FT VIEHAMRTHDPAVTEG" XX SQ Sequence 4547 BP; 1550 A; 792 C; 964 G; 1241 T; 0 other; aagacgtttc gaatacgata cgatgagttc tgaaaaaaat taccgcggtt tcagctgatg 60 actttaacaa accgtttctg tttacgggta gccacttcaa acgttggcag caaaagatgc 120 tgttcttttt gaccactaaa aaggttgcct acgttttgaa tgaagctatg cctgtagcac 180 cttcgagttc gactcctgct ggagcgaata ataacggtaa ggtagcagac cctactgctg 240 ctgagaaagc tgaacttgag aaagctgacc cagataaaca gctagccata gatattgctc 300 tatggaagga aaatgactac ctctgtaaga attatattct taatagactc acagaccctc 360 tgtatgatta ttatagacgc tgtgatactg ctaaacaatt atgggaaaca cttcagaaga 420 agtatgatac tgaagaggct ggtgttaaaa aatacgctgt aagccgctat ctgaatttca 480 aaatgagtga tgataaatcc gttgaggcac aatcacatga gctgcaacaa attgctcacg 540 agatcatagc tgaagggatg gcacttcccg aacagttcca aatagctgtg attattgata 600 agctgcctca ctgcctggaa ggacttcaag agtcttctta gacacaaaac taaggagttc 660 tctcttgaaa gtctgattac tcgctttcgt attgaagaag aagtgagaaa gcaggaccag 720 aatgaagaga tgtttgctgt ttctaacaac aacgctaaaa agaaatttgt aggtgctgtt 780 ctgaagcctg ctgacaaacc atttaagaat ccgaaccgcc ctatgaataa gaatttcaac 840 aggaataaga ctaggaacaa tccaagaccc cagattcaac agccaccaaa gaatgatgtt 900 gctccacctt tcaactgtta caattgtggg caagcaggtc atataccacg caagtgcaga 960 aacagaacca accgaccagc acaggctcac atggctactg ctgttgcacc tgatgagccc 1020 tatgtggcta tgattactga gataaatatg attgcaggtt ctgatggctg gtgggtggac 1080 actggtgctt ctcgccatgt ctgctatgat agagatatgt ttaaaatata tactgcttgt 1140 gatgatcaga aggtgttgtt gggagactcc cattccacta atgttgctgg aatcggagat 1200 atagagctga agttcacatc tggaaagatt ctgatactga aggatgtgct gcacactcct 1260 aaaattagga agaatttagt ttcaggtttt cttttgaata aggctgggtt tactcaaagt 1320 ataggggctg atttgtacac catcactaag aatggtattt ttgttgggaa agggtacgcc 1380 actgatggca tgtttaagtt gaacattgat atgaataaaa tttcttcttc tgcttatatg 1440 ttgtgtgatt ttaatatttg gcattctaga ctctgtcacg ttaacaaaag aattatttca 1500 aatatgagcg gtttaggatt aattcctaaa atatgtttaa acgattttga aaaatgtcaa 1560 ttttgtagtc aagcaaaaat aaataaagaa taacataaat cagtaaccag aataactgaa 1620 ccttttgaat taattcattc tgatttatgc gaattagatg gaaacttgac tagaaatgga 1680 aaaagatatt tcatcacttt tatagatgac tgctcggatt acacacatgt gtatttaatg 1740 agaaataaaa atgaagcgct tgaaatattt aaacagtatg taaaagaaat tgaaaatcaa 1800 ttcaatatta gaatcaagcg ttttagaagt gacagaggta ctgaatatgg atcacataca 1860 ttcaatgagt attataaaga actcggaatt attcatgaaa caactgctcc ttattctcct 1920 gaaatgaacg gtaaagcgga aagaaaaaaa tagaacgttt accgaattag tagttgcaac 1980 aatgcttaat tctggagcag cgcctcattg gtggggagaa attttattga ctgtttgcta 2040 tgtgctaaac agagtaccca aaacaaagaa caaaatttct ccatatgaaa ttttgaagaa 2100 aagacagcca aacttgtctt attttagaac atggggatgt ctagcctatg taagaaaacc 2160 agaccccaaa agagtcaaac tagcaagtag agcctatgaa tgtgtattca ttggttatgc 2220 cttaaatagt aaagcctata ggttttacga cctgaaatct aaaacgatca tagaatcaaa 2280 tgatgttgac ttctatgaaa ataaatttcc ctttaagtca ggagacagtg ggggtaatag 2340 tgggggcacc gataactcag ttcttgatca accttctgaa atcataacaa gcaatgaaaa 2400 catcgaaaga gatgttatag aacctcgtag aggtaagaga gcaagaattg ctaaagaata 2460 tggccccgaa tatgtggcgt atactataga ggaggatcca tcaagcatca aggaagctct 2520 gtcttcaatt gacgctgatt tatggcaaga agctataaat gatgaaatgg attctctaat 2580 gtccaacgaa acctggcacc taactgactt gcctcctgga tgcaagacta taggttgtaa 2640 atggatcttg aaaaagaaac taaaacctga tgggtcaatc gacaaataca aggcacgcct 2700 tgtagccaaa ggttttagac aaagagaaaa tgtagatttc ttcgacacat attcgcctgt 2760 aactagaatc acgtccatta gggtactaat ctctttggcg gccatccaca atttgagagt 2820 acaccaaatg gatgtaaaaa ctgctttttt aaacggtgaa gtagaagaag aaatctacat 2880 ggactgacct gaaggtttcg taatccatgg acaagagaac aaagtttgta agttagacag 2940 atctttgtat ggtctaaaac aagcaccgaa acaatggcat gtgaaattcg taaatcttat 3000 gattgagaat gagtttaagg tgaatgaaag cgacaagtgt atttattcca agtacgaaaa 3060 taacacttgc acgatcatat gtctatacgt agacgactta ctcatatttg gttcaaacct 3120 taatgccatt aaagatgtga aatcattgtt gtgccacaac tttgatatga aagacctagg 3180 agaagcagat gtaattcttg gaatcaagat tactagaact gataatggaa tttccttgaa 3240 tcaatctcac tacgttgaga agatcttaag gaaatataat tacttcaatt gtaaacctgc 3300 gagcacacct tgtgacccaa gtgtgaagct atttaagaac actggagata gtgttagaca 3360 aattgaatat gcgagcatca ttggcagtct cagatatgcc actgattgta ctagacccga 3420 catcggctac gccgtgggac tattatgcaa gtttacgagc aggccaagca tggagcattg 3480 gcaagctatc gaaagagtca tgagatactt gaagaagacc atgactctag gactgcatta 3540 tcaaagatat catgcagtgc ttgaaggata cagtgacgta gattggaaca ccttatcaga 3600 tgattccaaa gcgaccagtg gctatatatt tagcattgct ggaggagctg tttcctggaa 3660 atccaagaaa cagaccattc tggctcagtc cacaatggaa tctgagatga tagcactagc 3720 tgctgctagt gaagaagcaa gttggctaag atgcttgcta tctgaaatcc ctttatggga 3780 gagaccgtta ccagctgtgt taattcattg tgatagtacc gcgactatcg caaagattga 3840 gaatcgttat tacaatggta agagacgaca gataagacga aaacacatca cgataagaga 3900 atatctttcg aacggaacgg taagagtaga tttcgtacga acaaatgaaa acttagctga 3960 tcctttgacg aaaggactaa acagagagaa agtcgcaaat gcatccagta ggatgggact 4020 aatgcctatt gatcataagt gatggaaacc cgacctaaat gactggagat cccaagaact 4080 aggttcaatg ggtaataaca aatcacaagt gatagaacat gctatgagaa cgcatgatcc 4140 tgcagtgacc gaaggttgag ataatataaa ctcttaatga gatctatact tcttatggag 4200 tgaagtacat agctacagga gtacttctga tagactcacc tatacgtatg tagaactgag 4260 gccggttctt atggaatttt gaggcagaat tcttagagca ttcgttaaaa ctgggataga 4320 cgtgcaaggc cattaacgca cgggcttttt agaaaacacc taagaaaagg ttgtgtgtgg 4380 gtcctatgtc tgagatagag ttcaatcctg taagcaactc ttgttaatcg gaatactact 4440 cactatgcaa aggttcaagt tgttggcgac acctttgttt actagcaatc tttaagaaac 4500 gtttaaaaca taactttcga aaccaatttt gaattcaagt gggggat 4547 // ID Gypsy-10_Mad-I repbase; DNA; EDCOT; 8755 BP. XX AC ACYM01129446; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-10_Mad-I; KW Gypsy-10_Mad-LTR; Gypsy-10_Mad_. XX NM Gypsy-10_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-8755 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1333-1333 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01129446; Positions 9174 420. XX CC Positions [5991-6494] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 1509..3932 FT /product="Gypsy-10_Mad-I_1p" FT /translation="MQGRRSLQFELIHIDQELESTLREQRRQQVFQEPAMG FT EVNNGRDNPPPLPPPQPRLMRDYTKPTEYNAPSCIVLAPIAQRFEIRPQIF FT QLLPIFLGKEEENPYHHIKAFFKLCSTFTFTNVTEEQIRLRLFPFSLRDKA FT SSWLDSLPEASIDTWTELSKKFLSKFFPARRTNALINEIMSFRQQEGEQFH FT ESWERYKDLFLQCPHHGFNTWQKVHYFYKGLNSQCRSLVDSTVGGTLMDKT FT PEDAIHAFETICENSEHWDFPTKDSRVPTASSTKRGGIYEVDTRTGLEAQV FT AALTKLLTPLVSKIATQPCSLCASIAHDMEHCPANPNLEGMHEVKAFSGRP FT RNDPYSNNYNPGWREHPNFSWRDSQNSMGSSTSTKQYQQPYQAPPIQQQDP FT SIKDMLSQLLKKTDRYEHEVVSLRQSQTVLEKAQSNFETQLGQIATTLNKL FT ERAQGQFPSQTETNPGNQKHVQAVTTLRSGKTIGNNVESSKINKEEDEGVS FT AHIRQQLDKKSRSSIKSKSNETTSDKANKSDCPTQFSSTAEILGALPFPQR FT ARQAKKEKYMGDILEQFRKVQINIPFLDAIKQIPSYAKFLKELCTNKRRYE FT EHEEVKLSDTVSAILQRKLPPKLQDPGSFTVPCVIGERKFEKALLDLGASV FT NLMPYSVYEHLKLGELKHISISLQFADRSVKYPRGIVEDVLVCVDQFILPA FT DFIILDMEEAEIPGRDLPLILGRPFMATAGTKIDVKSGLLTMTVQGITVEF FT QVFEALKKPMDLYDCFRVEVVDPIIKKTFIESSISDPLEVCISQHGMSFEK FT ATIIEA" FT CDS 5220..6950 FT /product="Gypsy-10_Mad-I_2p" FT /translation="MCDASDYAIGAVLGQRVNKLPHVIYYASRTLTGAQLN FT YTTTEKELLAVVFALEKFRSYLVGSKVIIFSDHAALRYLLTKKDAKPRLLR FT WILLMQEFDIDIRDKKGAENVVADHLSRLVHGRDDIPINESFPDEQLFSIA FT EIPWYADIVNYLARKFIPADWDKQQRKRFFSKIRHFYWDDPYLFKHCPDQI FT IRRCVHQSEIQSILTFCHSYACGGHFGAKKTALKVLQSGFYWPTLFKDAHH FT FAMTCDRCQRTGNLSSRSQMPLQNILEVELFDVWGIDFMGPFPTSHGYLYI FT IVAVEYVSKWVEAIPTRTNDHKVVLSFLKEHIFTRFGTPRALISDGGSHFI FT NKPFEALMKQYNITHKVATPYHPQTSGQVEVSNREIKHILEKTVSQNRKDW FT ALKVSDACWAYRTAFKTPIGMSPFRLVFGKACHLPVELEHRAFWALKKLNF FT DINQAGPLRKFQLNELDELRNDAYENAKIYKEKTKLAHDKILLPKHFEPHQ FT KVLLFNSRLRLFPGKLRSRWSGPFLVIQVFPHGAVEIQDMQTGSIFKVNGH FT RLKPYLENAETVLSQTKTIEVAYLDDSPFI" XX SQ Sequence 8755 BP; 2599 A; 1558 C; 1769 G; 2782 T; 47 other; gtcgaagccc aaagcccaag atagaaaacg ttggagatga ttttagtcct atttcaaatg 60 ggtctggagt aatttacttg ggaaacttac ctgccacatc atcaattatc caatamaaat 120 gaggaaaaga ttaaaaaaag acctaaggat gctaggattt tgacgaatct ataagggaga 180 gattgtagga agcaaaggsg gttckctgkk gagggattct ckgcgtgttt ttggaggagc 240 agcagccgct ttccattttt ktcckaagtt tttcatgttc ttaatacttt taattatgtt 300 ttcttatttt atgagtaact aaactctttt tctagggtta ggatgatgcc ctagcatgaa 360 trtctatggt ttttaatgtt attcattgga tttctagttt cttttagatg aatgcttaat 420 cactgtttga actgttactg tttgtttgag ttctttgatt gatcacctta ggactttgca 480 tctagtaaga ttggaagatg aatttgaggc tgaactagca atataattca attagcttct 540 tgtggttaag tgtggtaaat tacattattg cttgacaaag aataatggtt tgcttggttc 600 ccttgttttc tagagcgtaa agagtcctac ttgttaaatt tatgccttaa ccaggataga 660 ctgcatgtta ggatatacga cctctgcctg aactaggaga gaatcattca cttaaggaaa 720 actatggtct aatgtgyctg acaaggactt agatacgaga attatcatct aaagaattga 780 aagatccatt gaatgcattg aaacctaaat tagattgctt gtggttgatt ccgaatccct 840 agacttttca tcacttgcct taaaacacaa cattttcttt tctttgattt cagtttttac 900 ttaaggttct gtttttgttc atttataaaa tcatcacaac aaattcttta catccttgat 960 tgatttatta attaagatcg agtctagttc gttgtttggg gttgygtgtc attaatatta 1020 ttagatttgg tttagtttat caaattggag atttaattag aatcctcgtg ggaacgatac 1080 ttggacttgc aacacgctat attacgacta tcttgtgcac ttgcaagttt acaccaagtt 1140 tttggcgccg ttgccgggga ctctaattga gtcccccaat ttgatatttt atttcatatc 1200 taataagtag ttattgtaga ttattcaatt tgattttgtt ttgttctcta gtttcgagta 1260 agagtcataa ctattaagat aagtaaaagt aattttcgtc actgttttat ttcagtttct 1320 gtatcactgt ttcgacacag ttttggacta aactattcga ttttttacca ggcatattgt 1380 atatcgttgg aaagccccag aagtctagtt ttcaacccaa caaacagatc aatgattgga 1440 tttttgagct gcaagaaatt tacaaaatac tgagcagtgg tcaaacaagg agcacagtct 1500 ggtcgtatat gcaaggtaga cgttcgttgc aatttgagtt gattcatata gaccaagaac 1560 ttgagagtac tttaagagaa cagcggaggc agcaagtgtt tcaagaacca gccatggggg 1620 aagtcaataa tggtagagat aatcctccac cattgccacc accacaacca aggctcatgc 1680 gtgattatac aaagccaacg gagtacaacg caccgtcatg cattgttttg gctccaattg 1740 cgcagcgatt tgagattcgt ccacaaatct ttcagttgct gcctatattt cttgggaagg 1800 aggaagaaaa tccataccat catatcaagg cgtttttcaa gctatgttcc acattcacat 1860 tcaccaatgt tactgaagag caaattcgac ttcggttatt cccattctct ttgagggata 1920 aagcaagcag ttggttggat tctcttcccg aagcatctat cgacacatgg acagaattat 1980 ccaagaagtt tttgtccaag ttcttccccg ctcgaagaac caatgctctg atcaatgaaa 2040 tcatgagctt tcggcaacaa gaaggtgaac agtttcatga aagttgggag cgatataagg 2100 acttgtttct kcaatgtcct catcatggtt tcaacacttg gcaaaaggtt cattattttt 2160 acaaaggttt gaactctcaa tgtaggagtt tggttgattc aacagttggt ggaaccttga 2220 tggacaaaac tccagaagat gccattcatg cctttgaaac tatatgtgaa aattctgagc 2280 attgggattt tcctacaaaa gattcgagag ttccaactgc atcgtcaaca aaaagaggag 2340 gcatttatga agttgataca aggacgggtt tagaggcaca agtagcagct ctcacgaagc 2400 ttctcacacc actagtaagc aagatagcca cgcagccatg tagcttatgt gcaagcatcg 2460 cccatgacat ggaacattgt ccagcaaatc ctaatctaga aggcatgcat gaggtcaaag 2520 catttagtgg gaggccccgg aatgatccat attctaataa ttataacccg ggatggagag 2580 aacatccgaa tttttcttgg agagattcac aaaatagcat gggatcatcc acttcaacaa 2640 agcaatatca gcagccttat caagctcctc caattcaaca acaagacccg tctatcaagg 2700 atatgttatc tcaactctta aagaaaactg atcggtatga acatgaagtt gtgtcgctta 2760 gacaaagtca gactgtgttg gaaaaggctc aatctaattt tgagactcag ttgggacaga 2820 tagctactac cttaaacaag ctggagcgag cacaagggca atttccaagc caaactgaaa 2880 caaatcctgg gaatcaaaag catgttcaag ctgtcaccac tttgaggagt ggaaagacga 2940 ttggtaataa tgtggaaagt tcaaaaatta ataaggaaga agatgaaggg gtcagcgcac 3000 atatcaggca gcagcttgac aagaagtcta gaagttctat aaagtctaag agcaatgaaa 3060 cgacctctga caaagcaaac aaatctgatt gtccgactca attttcttct actgcagaaa 3120 ttcttggcgc tctacctttt ccgcagcgtg caagacaagc taaaaaagaa aagtacatgg 3180 gagatatttt agagcaattt agaaaggtgc aaattaatat tccttttctt gatgccatca 3240 aacaaattcc atcatatgcg aagtttttga aggaactttg tactaataag agacggtatg 3300 aagaacatga ggaggtgaag ttatcagaca cggttagtgc gattcttcaa agaaaattgc 3360 caccaaaact tcaagatcct ggtagcttta cagtcccatg tgtcattgga gaaagaaaat 3420 tcgaaaaagc tttgcttgac ttgggagcaa gtgtgaattt gatgccctat tctgtttatg 3480 aacacctcaa attaggtgaa ctaaagcaca tatccatttc tctacaattc gctgatcgtt 3540 ccgtgaaata tccaagaggg attgttgaag atgtacttgt gtgtgttgat caatttattc 3600 ttcctgctga ctttatcatt ttggacatgg aagaagctga aattcctggt cgtgacttgc 3660 ctctcatcct tggcagacct ttcatggcta ctgcaggtac gaagattgat gttaaatcrg 3720 gattattaac tatgactgtg caaggtatta ctgtagaatt tcaggtcttc gaagcattga 3780 agaagcccat ggatctttat gactgctttc gtgttgaggt wgtggatcca attatwaaaa 3840 aaacattcat tgaatcaagc atctcagatc ctctggaagt ttgtatctct caacatggga 3900 tgagttttga aaaggctacc atcattgaag cagamcgaga tctcaatgyc gtaacgtcct 3960 actctcttag akgscagccc aaatttgaag csttgccact ctcacaagcc aaaattgtac 4020 catccattat acaacctcca aagcttgaat tgaagcctct tccagagact ttaaagtatg 4080 catatttggg tgattcagag actcttcctg tgattatagc tgctgatctt aaccaaacag 4140 aagaggaaaa gttgatgcaa rtgttgaggg agcataaaac agcattggga tggagtattr 4200 cagacataaa aggaattagt ccytcaattt gcatgcatcg gatatatctt gaggaymagt 4260 cmaagccttc tagagaggca cagmgacgtc taaatccaca tatgcaagaa gtggttcggg 4320 cagaagttct taaattactg aatgtcggca ttatttatcc tatatctrac agcaaatggg 4380 taagtccact gcaggttgta ccamagagat ctggaattac agttgtcaag aatgaaaata 4440 atgagcttat accccagagg actgtcacrg gytggagaat gtgtacagat tayagaaaga 4500 tcaataattc aactcgaaaa katcattttc cactcccttt ccttgatctc atgcttgaga 4560 gacttgcagg ccatagttat tattgttttc ttgatggcta ttccrgatat aatcaaattc 4620 cyatagctcc ggargatcaa gaaaagacta ctttcacatg tccatttgga acttttgcct 4680 atcgacgaat gccttttggg ttatgtaatg ctcccgcaac attccaaaga tgcatgatga 4740 gcattttctc aracwtggtg gaaagrtgta tcgaagtgtt crtggatgat ttttccgtgt 4800 ttgggtcatc gtttgatcaa tgtcttcatc atctttcatt ggtgctcyaa cggtgtcarg 4860 aaaccaactt grttttaaat tgggaaaaat gtcagtttat ggtgaaaagt ggtattgttc 4920 ttggtcatgt aatttyagct gacggaattg aagttgataa agctaaggtg gagctgattt 4980 cgaagcttcc tcctcccact tctgtaaaag aagttcgatc ctttctcggg catgcaggtt 5040 tttatcgccg attcattaaa gatttctcta aaatcaccaa gccactttgt gatctgcttg 5100 ctaaagattc tgtgtttaat ttaaatggtg agtgcttaca agcctttgag accctcaaga 5160 aagaattaac acaagcccca atcataaaag ctccggagtg gtttcttcct tttgaaatca 5220 tgtgtgacgc ctctgattat gcaataggtg ctgtgttagg gcagcgagtt aacaaacttc 5280 ctcatgttat atattatgct agccgaactc tcactggtgc tcaattaaat tacacgacaa 5340 cggagaaaga attgcttgct gtggtgtttg ctttggagaa gtttagaagt tatttggttg 5400 gttcaaaagt gattatattt tctgatcatg cagctctccg atatttatta accaagaagg 5460 atgcaaagcc cagacttcta agatggattc tacttatgca agagtttgat attgatatta 5520 gagataaaaa aggggctgaa aacgttgtgg cggatcacct ttccagattg gtacatggca 5580 gggatgatat tcctatcaat gaatctttcc cagatgagca attattttcc attgcagaaa 5640 tcccctggta cgcagacata gtgaactatt tggcacgaaa gttcattcca gcagattggg 5700 acaagcaaca aaggaagcgt tttttttcta agatacgaca cttttattgg gatgacccat 5760 atcttttcaa gcactgtcct gatcagatta ttcgacgttg tgttcatcaa agtgaaatcc 5820 aaagtatttt gacattttgt cattcgtatg cttgtggagg ccactttggt gcaaaaaaga 5880 cagctttgaa ggttttgcaa agtggttttt attggcctac tttatttaag gatgcacatc 5940 actttgcgat gacgtgcgac agatgtcaac gcactgggaa tttatcatct agatcacaga 6000 tgcctttgca aaatatcctg gaggttgaat tgttcgacgt ttggggtatc gatttcatgg 6060 gtccattccc tacatctcat gggtatcttt acatcattgt ggctgtggaa tatgtttcta 6120 aatgggtgga ggcgatacca acaaggacca atgatcataa agtcgtgttg agtttcttaa 6180 aggaacacat tttcactcgg tttgggacac cacgtgctct cattagtgat ggtggatctc 6240 actttatcaa taagccattt gaagctctta tgaagcaata taacatcact cacaaggttg 6300 ctactcccta ccatccgcag actagtggac aagttgaagt ttctaatagg gagatcaaac 6360 acattctaga gaaaacggtg agtcaaaatc gaaaagattg ggcattgaaa gtgagtgatg 6420 catgctgggc atataggaca gctttcaaga ctcccattgg catgtcccct tttcgacttg 6480 tctttgggaa ggcatgtcat cttccggtgg aactggaaca tcgagcattc tgggcattaa 6540 agaagttgaa tttcgacatc aaccaagcag gacctttgcg aaagtttcaa ttaaatgagt 6600 tggatgaatt gaggaatgac gcttacgaga atgctaagat ttataaagaa aaaacaaagc 6660 ttgctcatga taagatttta cttcccaagc attttgagcc acatcaaaag gtgttattgt 6720 tcaactcaag gcttcgattg tttcccggga agctgcgttc tagatggtct ggtccttttc 6780 tggttattca ggtatttcca catggggcag tagagattca agacatgcaa actggttcca 6840 tattcaaggt gaatgggcat cgtcttaaac catatttaga gaatgcggaa actgtgctat 6900 cgcagacaaa aactattgag gtggcatacc tcgatgattc tccattcatt tgaaggtcgt 6960 tgagtccggc tgaagacttt aaatttagcg cttcttggga ggcaacccaa gcatttgatg 7020 caagaagatg gagttggtat gtgcggcaag tytgacttta gcgaccactt aaccagggga 7080 gtcctaaact ttactcttta tttttcatct tatttttatt ccgttctact tttccttatt 7140 cgtttaactc attgcatgcc ttgtttttca tttcacattg aggacaatgt gttattcaag 7200 tttgggggag agatctcatt ttgatagttt ttcagttagt tgttttgtgt cataaaacgt 7260 aggctctctg ttttagtaaa ttctggaaca atctgttgct gattctgagt tttggtccgc 7320 gttgtgttct ttaatttttc gttctgaatc caaccatata aagaacgttg aattctacca 7380 agtagtttgc aagatatatg taaaaaaatg aacagaggtc agaaattggt tattgcagag 7440 catgaagtct tcgttttcaa gtcttgactg ttagtttttg ttagttgtcc tgttctgtct 7500 ttgttagttg tcctgttttc attagtgtct aaaaaaaaaa aaatatatat atatatatat 7560 atattatttt ttgctcttct ctcaatcttg ttggttagtc ctttccaaat ccaatgataa 7620 taactcggtt gccacttaaa tatggttcta agaaattgat aagcattgtt tgtgttcttt 7680 gtttgattct ttggttagct atgctttata agatcattct ttacaccttt ctcatgcact 7740 tagccaaggt taatgcaatt gtttgcttgc ttagagaatt atatgcagat taagtactca 7800 ttaagatctc aacgaacact agaacttgct tcaatatctc tcgaggcgaa atcctaaatc 7860 atgcaatatt ggggagatga ttttggccat ttttggaccg tttgagcctt tatataccca 7920 acctcttatg ttatgttatc cttagttagc cccttgaagc caaacactta actttttctt 7980 tcattaccca cattaatcct tacccattta acctgtatta gccatacctt atagcttgag 8040 atgaatacca agatgatgaa gacagcgata aaggttgagt gtacatcaaa gatgtggcgt 8100 gtaccgaggt accatgtgtt atattactat tcagttaaaa aaaaaaaaaa aaaaaaaaaa 8160 aaagaaaaaa gaaaaaaaaa gaaagaaaga aagaaataaa aagtttgaaa gtgttccatt 8220 cctaacatga gtcctggacg cyaagaatta tatttcaaaa gcggctcgac cgaaatacat 8280 atgaagaagt cttggtatat ctcagrttct agttttttcc taccctttct ttcatagcca 8340 ataacctagc ctaacgttac aacctttgta aagtccattt gatctttggt gttgcactga 8400 tttacattag tggagagacg atatgaagag caagcctatg gggttcgata cattcattat 8460 tcagagatca ctcataatca cacttatgtg catataccta tccgagttgc aagtgttgtg 8520 ttaattattg gctagtctta tacgtaccgg aagaatggtt gtgtaaggtg ttgttaactt 8580 ttgaatcatg tatagaatcc ttacaatgtt tctctattct ttgaactata tttttccatg 8640 caatctttga ggaatatatt tggaaagtct aactgcattg tgttttgttt aaatttaatt 8700 ttgagtcttt gttgtgtttg cttgaggaca agcaaagtct aagtttgggg gtatt 8755 // ID Gypsy10-VV_LTR repbase; DNA; EDCOT; 325 BP. XX AC AM469898; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy10-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-325 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-325 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 736-736 (2007). XX DR Genbank; AM469898; Positions 2240 1916. XX SQ Sequence 325 BP; 80 A; 56 C; 65 G; 124 T; 0 other; tgatatgtgc atacacgtgc cagtagtggc aacaagatgg aaagtgatag tgggcctagt 60 ggcaagatgg aagacttggt ctaatttgtt tgttcagtca ttaattgttg agtcggttat 120 tgaataagtc ttggtagtag agtgggtgct attctgttgc ctattctgca acatttcctt 180 tttttcaact ttgttgttat tttctcttcc atgtatggct atacatatag cgtgaatgaa 240 ttgaataaag taagtagctt tatcaccaac agttccctct ttgtcttatt cttttctgcc 300 cttaactcca aattccttca tatca 325 // ID HAT-4N2_Mad repbase; DNA; EDCOT; 1856 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-4_Mad; HAT-4N1_Mad; HAT-4N2_Mad. XX NM HAT-4N2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1856 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1614-1614 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >94% identical to consensus. 8-bp TSDs. The 3' terminal 348 bp is CC ~96% identical to that of HAT-4N1_Mad. XX SQ Sequence 1856 BP; 518 A; 317 C; 382 G; 639 T; 0 other; caaggtatga aatgccgata ttatcggcga tatttcgccg ataatatcgg ttttttgagt 60 taccgatatt ttaatactta tccactgagt tttcgtcaaa atatcgcgat attatcgata 120 atatcgacaa tatcgcgata ttaccgataa tatcgcgata ttttggagat gtgcgaatcg 180 gagaagaacg ccggagcttc tacagctccg gccgactgta aaagagcacc ctagactccg 240 atctaggtat caaaatgaaa tacaagacga gaggaatgtt tttataactt ccgtttgccg 300 tgaaacggtc ggaggtgttc ggaaagttcg tcgacaccca cggcctcgcc ggagatgggt 360 gtgcctattc ccgagccgat ttcgtcccaa aaaccttgca aaaacacgag atagaactta 420 aatttcacat ctaagcttca atctagaaca gaatgaggta aacccgaagc ttacctaacc 480 ggagaaattc aagaaactcg ccggagggtt cctgcgtcgc cgagttgcag agacgagaag 540 gagagggaga aagacgaggt tgctgatgac gatgggtgtc ttcctcaagc aggtgcgatg 600 gtgtgcgtgt gtgtatgtgg gtctcggtgc agagagaaag gagagagatg agagtttcga 660 gagagagacg gcgccgacga gagctatttg tttttttttt tttttttatc ttaaagagag 720 agaggtctga gagaaatggg aagagagggc cgagtgaaat gaaaggaggt ccttgaatta 780 ttgagagata tctctgagag aggcctagga tttctaaaag gtaatcagaa atgggaaaaa 840 tggggcacat cttagccttt attttggaat cctaagaagt tcaccacatg gatgcatgac 900 atgtgtgcat gccatgtctg ttgaatggga aaagtctgac acggaaagac aaagagccgt 960 ttggggctct gggctcgagg caagacagaa agtgctaggg tttttttttt tgaaatgaac 1020 ataagctgct aaattcgcat atattatagt tgttgctaaa gattgacacc agtgtggact 1080 tggacgtgtt ggtcaacatg tcctcacaat ccccaagttc tccagttcga acccttgcgc 1140 ccatcaaatt tttctttctt tttgatgcgc ttttcccatg gctctaggtc ttgatttcga 1200 atccaggtga gccctttcct ttttcttttt ttttcttttt gttttattat ttgtttattt 1260 taatttattt gtttctttta tgtttttcct ttcttttagt ttctttgtct taggcgttcg 1320 tttttattaa agtaggacgt aaaatcaatt atctcaaaat tatgtgtttt taaattttgg 1380 acttgtttgt tggatacttt ttttgcattt tatcattctt ttattatgaa aatatgctaa 1440 aatatcactt atgtttttgt gaaaatatgc taaaatattt atatatatgg ttttgttttg 1500 aattcttttt gtactaattc attatatata aatgattatg gtgtgtttaa acttctttca 1560 ttaattacta catattttct atactcacaa tgtttgccag ctcgctatat aatcaactta 1620 aatcagttaa atccatcatg caatgcattt ccttccaatt ttttgtgata aactaataga 1680 taattgacta aataaacatc ctgcaaagtt tcaataaaaa tttccaagtt tttcttacaa 1740 tttccgtggt ttccatatta tttttatcga tatcgataat atcccgatat ttccatcgat 1800 atttccgtgt ttttggacta ccgatatttc cgatatcatc gatattttat accttg 1856 // ID IBGYPSY1_I repbase; DNA; EDCOT; 6813 BP. XX AC AC073166; XX DT 09-AUG-2005 (Rel. 10.08, Created) DT 30-AUG-2005 (Rel. 10.08, Last updated, Version 1) XX DE Gypsy-like LTR-retrotransposon from sweet potato (internal DE portion). XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; IBGYPSY1_LTR; internal portion; IBGYPSY1_I. XX OS Ipomoea batatas OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea. XX RN [1] RP 1-6813 RA Jurka J.; RT "IBGYPSY1: A Gypsy-type LTR-retrotransposon from sweet potato."; RL Repbase Reports 5(8), 199-199 (2005). XX DR Genbank; AC073166; Positions 65475 72287. XX CC LTRs differ by 1 bp deletion (possibly a sequencing mistake). ORF CC appears to be intact, indicating a recent insertion. XX FH Key Location/Qualifiers FT CDS 906..4466 FT /product="IBGYPSY1_I_1p" FT /translation="MSSMASTSEQGSIIAQMEKMMTMMKDLSDRLQNIENQ FT RVRVENEGVQNHEGGNQEERRGREITRYNSLPRMLPRRFVEERVDNNLSSL FT RMEMPTFNGDDEPEVFLNWVDEVEDIFGLHNFGEEKKFKTAIASLKDFAKL FT WWKQLSRRRLEDQDEPIETWGELKREMRRKFVPSNFYRDMRRKLQELKQGS FT KSVREFYKEMERLKARANIQEDDETTIARILEGFNRDIRRELRNQEFDDVD FT KLVRVASKVEDELRSERGSKPSLSSQWDQPRRATNNSYQSRTQKEYSRPSH FT TQEEKKNNQREKEKFQEGSKQKVSTVTCYRCQGRGHYARECPNTKKILTTG FT KDEREYMSANESDDEELEPIGERQKDDHSEEEVQEDDALHFNCVVHKALST FT LVVLDQEEQRENIFYGKCKIPGATCSFIIDGGSCTNVISEDVVNAMKIPTI FT QHPQPYKLQWLNDDGELKVHKQALISISIGKYQDDVLCDVIPMHACHILLG FT RPWQYDRDTLHHGKTNKYTIHKGGKKYTLTPLAPKEVYNLQVQSKKLREEL FT AQKAKEAMKETTSGKQNTIAHEKKQRKEGMKKDTTQSSHNLLMTKREVEQA FT LRRGEGVFLLYPIDFCLNVIKSEIIPSDVSALLSEFADVFPEELPKGLPPI FT RGIEHQIDLIPGASLPNRPAYRTNPDEAKEIQRQVDELLQAGFIQESLSPC FT AVPVLLVPKKDGTWRMCVDCRAINNITVKYRYPIPRLDDMLDELHGAKIFS FT KIDLRRGYHQIRMQKGDEWKTAFKTKNGLYEWLVMPFGLTNAPSTFMRLMN FT HVLRNFIGKFVVVYFDDILIYSKDPQKHIIHLKEVFLVLRREQLYANLEKC FT YFGVESVVFLGFIVSSKGIEVDETKIQAIRDWPTPKTATKVRSFHGLASFY FT RRFVKDFSTIAAPLNELVKKDVKFEWGPKQEQAFQTLKEKLCSAQVLSLPN FT FDKTFEIECDASGIGIGAVLMQEGHPIAYFSEKLSGPALNYSTYDKELYAL FT VRTLETWEHYLWFKEFVIHSDHEALKHLRGQGKLSKRHAKWLEFIEAFPYV FT IKYKQGKENRVADALSRRYALLSSLQAKLLGFEFLKELYSNDVDFAEKYKA FT CSTTPIGKYYLLDGYLFKENRLCVPNCSLREMFIKEAHSGGLMGHFGVTKT FT YEVLHGHFFWPKLRRDVELFVIVVKNDV" FT CDS 6029..6811 FT /product="IBGYPSY1_I_2p" FT /translation="MAHFIGCHKTNDASHIADLFFKEVVRLHGIPRTIVSD FT RDAKFLSHFWRILWGKLGTKLLYSTACHPQTDGQTEVVNRTLTQLLRVVIR FT KNLKSWEESLPYVEFAYNRAIHSTTNMSPFEVAYGFNPLTPLDLIPLHVND FT KECVDAAKKAQGIREFHSKVRAQIEKKNEQYAQKANKGRKAIIFKPGDWVW FT IHYSKNRFPNQRKSKLMPRGDGPFQVLERINDNAYKLDLRGEHSVSSTFNV FT ADLAPFDFSDSGTNLFQEGE" XX SQ Sequence 6813 BP; 2291 A; 1165 C; 1340 G; 2017 T; 0 other; gtttggtatc agagccaagt tcattttttt ttccttctta ttctatcatt cctatcttta 60 atttcctttt tttttctctc tcttattcca ttatttctat ctgtaatttc atatttactg 120 ttgttctatt tctttttccc ttatatccgt tacgttcttg ctttattcta ttattgctat 180 cttaaagttc atatttactc ttccttgcta ctttaaattt catatctact attgtgtcta 240 ttttttttta ttcatttccg tacttttact ctttatattc atagctttga tttggtgacc 300 ttataaaggt tagataccat caagcttctt ttaatctatt ctactattgt atttataatt 360 tagttgaagt ttactttatt ggaggtttgt taaaaaacaa aagaaaaaaa aaaaacaaaa 420 caaaacaaaa aaagagcaaa aaaaaaagaa aaaaaaaaca aacaaaaaaa aaggtggata 480 aggttggttt gatttttagt ttgaattgtt aaatttatat ctaagcatta cttgaaatta 540 attgtgcttt gtttcttttt atcacatata cttcttctac tttctttgtt tcctacaaaa 600 aaaaaaaaaa aaaaacacct gtgtcagttt caaacacact ctgtgtcagt ttctacatca 660 ctctatacat actatttcct acctttcgtg cttactggac tcaaactcta caagtgtttg 720 gtttgttgtt tgtggtggat acaacccttg tgaattttaa gctttgttaa ggaccaagag 780 gaaaagaact agtacttgag aaaaaaaaaa gtcaaaaaaa aaagagtgaa tgaactgtga 840 gtgattaaat atttcctttt gattactacc ttcttatttt tgcatttttt tttttactta 900 aaagaatgtc aagtatggct agtactagtg aacaaggtag tattattgcc caaatggaga 960 aaatgatgac catgatgaaa gatcttagtg ataggctaca aaacatagaa aatcaaagag 1020 tgagagttga aaatgaggga gtacaaaatc atgagggagg aaatcaagaa gagaggaggg 1080 gtagagaaat aacaagatat aatagtttac ctcgcatgct ccctagaaga tttgtggaag 1140 aaagggtaga taataatctt agctctttaa gaatggaaat gcctactttt aatggggatg 1200 atgaacccga agttttctta aattgggtag atgaagtgga ggatattttt gggcttcata 1260 actttgggga agaaaagaag tttaaaacag ccatagcatc cctaaaagat tttgctaaat 1320 tgtggtggaa acaacttagt cgtaggcgtc tagaagacca agatgaacct atagagacat 1380 ggggagagct taagagggag atgagaagga agtttgtgcc tagtaatttt tatcgtgata 1440 tgcgcagaaa attacaagaa ctcaaacaag gcagcaagtc cgttcgtgag ttctacaagg 1500 agatggagag attgaaggca cgagcaaata tccaggagga tgacgagacc accatagccc 1560 gtatccttga aggattcaac cgtgatattc gaagagagct ccgcaaccaa gaatttgatg 1620 acgtggacaa attggttcga gttgcttcga aggtagaaga tgagctgaga tccgaaaggg 1680 gaagcaaacc atctctgtct tctcaatggg atcaaccaag gagggctacc aataactcct 1740 atcagtcaag gacacaaaag gagtactctc gaccatccca cacccaggag gagaagaaaa 1800 ataaccaaag ggagaaagag aagtttcaag agggctcaaa gcaaaaggtt agtactgtga 1860 catgttacag gtgtcaaggc cgaggacatt atgctcgaga atgccccaac accaaaaaaa 1920 ttctcaccac cggcaaagat gagcgagaat acatgtccgc aaatgaatct gatgacgaag 1980 agttggagcc tatcggagaa agacaaaaag atgaccattc tgaagaagaa gtgcaagaag 2040 atgatgctct acatttcaac tgtgttgtcc acaaagcctt gagcactcta gttgtcctag 2100 atcaagaaga acaacgagag aacatcttct atggaaaatg caagattccc ggtgctacat 2160 gcagtttcat cattgatggg gggagttgta ccaatgtgat cagcgaggat gtagttaatg 2220 caatgaaaat accaacaatc caacatcctc aaccctataa gctacaatgg cttaatgatg 2280 atggtgaact caaggtacac aaacaagccc tcatttctat ttccattgga aaatatcaag 2340 atgatgtgtt atgtgatgtc atcccaatgc atgcttgtca catcttgctt ggtcggccat 2400 ggcaatatga ccgagacacc ttacaccatg gtaagacaaa caagtacacc attcataaag 2460 gaggtaagaa gtatactttg actccactag caccaaaaga agtgtacaac ctacaggtgc 2520 aatcaaaaaa attgagagaa gaacttgccc aaaaggcaaa agaggccatg aaggaaacca 2580 ctagtggaaa acaaaatacc atagctcatg agaaaaagca aagaaaggaa gggatgaaga 2640 aggacactac gcaatcatct cataatttgc tcatgacaaa gagagaagtg gagcaagcct 2700 taagaagggg agagggagtt ttcttacttt acccgattga tttttgttta aatgttatta 2760 aaagtgaaat tatcccttct gatgtttctg ctttgctttc tgaatttgca gatgtctttc 2820 ctgaagagtt accaaagggg ttacctccaa ttcgtgggat tgagcatcaa attgatctca 2880 tacctggagc aagtttgcct aatagaccgg catatcgcac caatcctgac gaggccaagg 2940 agattcaacg acaagttgat gagttgttac aagctggatt catccaagaa agcctcagtc 3000 catgtgctgt acccgtacta cttgtaccaa agaaagatgg cacgtggcgg atgtgtgttg 3060 attgtcgcgc catcaataac atcacggtaa agtatcgcta tcctattcct aggttagatg 3120 atatgcttga tgaattgcat ggggctaaaa ttttcagtaa aatagatcta agaagaggtt 3180 atcatcaaat tagaatgcaa aagggagatg aatggaaaac tgccttcaag actaaaaatg 3240 gtctctatga atggttagtt atgccgtttg gattaacaaa tgcccctagc accttcatga 3300 gattgatgaa ccatgttctt aggaatttta ttggaaaatt tgttgttgtg tattttgatg 3360 atattctcat ttacagcaaa gaccctcaaa agcatataat acatcttaaa gaagtctttc 3420 ttgttttaag aagagaacaa ttgtatgcta accttgagaa atgctatttt ggtgtggaaa 3480 gtgttgtttt tcttggtttt atagtaagtt ctaaaggcat tgaagtggat gagaccaaga 3540 tacaagcaat tcgagattgg ccaacaccaa aaacagcaac taaagtccgt agtttccatg 3600 gtcttgccag tttctatcgg agatttgtca aggacttcag tacaattgca gccccgttga 3660 atgaacttgt gaaaaaagat gttaaatttg aatggggccc taaacaagaa caagcctttc 3720 aaaccctcaa ggaaaaattg tgttctgctc aggtactttc gttaccaaac tttgataaaa 3780 cttttgagat tgagtgtgat gcatctggga taggtattgg agctgttctt atgcaagaag 3840 gacatcctat tgcctacttt agtgagaaat taagtggtcc tgcacttaat tactctacat 3900 atgataagga gttatatgca cttgtaagaa ctcttgagac ttgggagcat tacctatggt 3960 ttaaagagtt tgtcatacac tccgatcatg aggcactcaa acaccttagg gggcaaggta 4020 agttaagcaa gagacatgcg aaatggcttg agtttattga agcatttccg tatgttatca 4080 agtataaaca aggtaaagaa aaccgagtgg ctgatgcttt atctcgaagg tatgctctac 4140 tttcctcatt acaagccaaa ttacttggtt ttgaatttct caaagaattg tatagtaatg 4200 atgttgattt tgcagaaaaa tataaggcat gttctacaac tccaattggc aaatattatc 4260 tacttgatgg atatttgttc aaagaaaata gattgtgtgt gccaaattgt tctttaagag 4320 aaatgttcat taaggaagcc catagtggtg gattaatggg acacttcggt gtgactaaaa 4380 cttatgaagt cctacatgga cacttctttt ggcccaagtt aagaagggat gtggaattgt 4440 ttgtgattgt tgtcaaaaat gatgtatagt tcgggtttag tattgtcgtt ccgcaaggga 4500 ttggcgctat ggcacgtact tgtgtgatta tttattttag gagcttttta acccattaat 4560 gagaatccaa gcacaaacat aaatagaaaa ttactaacaa cctacaaaca taaaaagtaa 4620 agaaaaggat ttaagttagg aattattact atcaagatgc tatatattct tatggattag 4680 ggagaacaat aatcatggat caagagggcg tacactttaa agaattcaag atccttccga 4740 aacttgaatt agagcaaggg ttgccccact cccgtgacgt atcaaccaca aacccttgaa 4800 gaacaaaagg tacaaaagcc ccccaattcg tctcctactc ccgtagtgag atatttggat 4860 tgtacaaagg tggcttgagt ttttacccaa ctcccgttgt agcaaaactc tccaattact 4920 tgccaataaa aatagctagt aattattaac aagatacaaa catacctcat tgtacaagct 4980 tatgattcaa gattatagtt cttcccctta tgaaattatt agcaaggtag catcaggata 5040 aataataaat tcctacctca aacccaaact aaactaaata aacataaaat gcataaatta 5100 aaagaggaag aaaataaatt gcataaggaa aataaaataa cattacataa aaataaaaag 5160 aagaaaattc gaaagagaag aaaagaaagg aaaaggaagg tttgctctac attctacatc 5220 ttggcaagct tgtttctaat ttgggagaag agaggggtat ttataggatg aggaagggat 5280 taaataaata atatgtgtac agtagatggt cacatgggat gcttagcctt gctggtttgg 5340 tcaaaaaggc aaagaatttc cgccacctta tggtccatag ttcgaatcct ccagctggca 5400 tcatttgcat cttttgtata tacaataggc gtctgtttct gcacaatagg cgtctgtttc 5460 tggccaaaaa gagacgccta ttgtctgttc cagaatttct gccactttaa gctccacttt 5520 tgatgcaata ttccaccttt tgagattgtc ttcttcctta gccaccccca atttcaggaa 5580 atatgtttgt cttccaccac caatgccact ttgaattatt tctttaccca ttttataatc 5640 accacaaaga taattaggta ttagaataat aacaatgaga ttaatactac ctaaaattat 5700 gctcaataat atttcctact tcatatttca tcaaattgca attatttatc ccaaagagga 5760 aaatatgaac ataaatgtga tgattagtga cataaaaata agcttaagca tggggtaaaa 5820 atataatcaa atatgcactt atcagtttgt tagcaaatgt gttacttgca aacaagctaa 5880 atcacgatct ctcccacaag ggttatacac accattaatt gttcctaagg aaccctggac 5940 tgatttatct atggatttta tagtagggtt acctagaagt agaaggggcc atgactcaat 6000 ctatgttgtt gttgatcgat ttagtaaaat ggctcatttt attggttgtc acaaaactaa 6060 tgatgcctct catattgcag atttattctt caaagaggta gtgcgtttac atgggattcc 6120 acgcaccatt gtgtccgatc gagatgccaa gtttctaagt catttttggc gaatactttg 6180 gggaaagctt ggtacaaaac ttttgtactc tactgcttgt catccacaga cagatggcca 6240 aaccgaagtt gtgaatagaa ctctaacaca acttctaagg gtagtcatta gaaaaaacct 6300 caagtcttgg gaagaaagct taccatatgt ggagtttgct tataaccgag ctatacattc 6360 cactacaaat atgtcaccat ttgaggttgc ttatggtttt aatccattaa cccccttaga 6420 tttgattccc ttacatgtga atgataagga atgtgtggat gctgctaaga aagctcaagg 6480 gattcgtgaa tttcattcca aggttcgagc tcaaattgaa aagaaaaatg agcaatacgc 6540 tcaaaaggcc aacaagggac gcaaggcaat aatttttaaa cccggagatt gggtttggat 6600 ccactacagc aaaaacagat ttccaaacca acgcaagtcc aagttgatgc ctcgaggaga 6660 tggacctttc caagtgcttg aaagaatcaa tgacaatgca tacaaattag atcttcgagg 6720 tgagcatagt gtttcttcta catttaatgt tgctgattta gctccttttg atttttcaga 6780 ttcggggacg aatctttttc aagaagggga gga 6813 // ID Copia13-PTR_LTR repbase; DNA; EDCOT; 345 BP. XX AC scaffold_3625; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia13-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-345 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-345 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 199-199 (2007). XX DR Genome; scaffold_3625; Positions 862 1206. XX SQ Sequence 345 BP; 110 A; 55 C; 47 G; 133 T; 0 other; tgtaaagata tcaacgatcc taatgatgcc aagtgtcaga agattagcaa ctaatgttgt 60 tacaatgttg ttagtagttt tgttacaaaa ggagattctg ttagcattta tattgtgtgt 120 aaaaggaaga atattcttcg tatagtatct tccaatacta catatataaa ctgagtatga 180 gtaatgaaaa cattaagcaa aagcaaataa taaaacagtg ctataattcg tcttctgctt 240 ctctatgcat aacagattca ttcattctct gttcttcgtt cttttcactt tctgcttctt 300 ttcttcattt ctatttcatt tctatataaa cattactgtc tatca 345 // ID Copia34-PTR_I repbase; DNA; EDCOT; 4595 BP. XX AC scaffold_342; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia34-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4595 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4595 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 244-244 (2007). XX DR Genome; scaffold_342; Positions 49196 53790. XX CC Positions [1829-2323] - Integrase core CC 'AGGTT' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS join(80..3373,3377..4585) FT /product="Copia34-PTR_I_1p" FT /translation="MTNNETSSNLEAHTDFSRGNLSNPYFTHHSDHPGLVL FT ISKPLNGDNYSTWKRAMTLALNSKNKLSFVNGSIKAPSEETDPEGYAAWSR FT CNDMVHSWIINTLNPEISDSVIYYSTAHEVWEDLHDRFSQSNAPRMFEIQR FT DIACFRQEQLSVSVYYTKLKGLWDELASYNDSLHGAQQDQQRLMQFLMGLN FT ESYSAVRGQVLLMNPLPSVRQAYSFVSQEEKQRLLSSAHTINDSVNSAAMA FT VQSNNSKFNDKGERSYHSFRSQDRLTDNFSGGRRFEQDRRRFGPRRGRPHC FT SHCGEPGHWVQTCYELHGYPAGHPKAKHNSARRFNHNNKSAANHVSESFAK FT ENGKSVVGISETQLKQLLSLLNDKGAESSSQAHAATTVTKPGLPKIASRSW FT IIDSGATDHISSSSQSFFQRDNNCSLPPVLLPSGETANIVAKGSLPLNSTY FT YLHDVLCVPTFKVDLMSVSRLTRGLNCSVTFFPYWCILQDLATRRMIGLGK FT QRDGLYYLVAIATKKSMVQPSQPLHRPACNLTISSTDLWHKRLGHISPHRL FT SFIAQQFLNFSVQSSHVCPICPLAKQSRLPFNSSVISSIKPFEIIHCDIWG FT RYRHPSISGAYYFLTIVDDYTRFTWIFLMRHKTEAQSLIKRFFSYVLTQFE FT SPIKIFRSDNGGEFISLRSFFQDKGVIFQHSCVYTPQQNGVVERKHRHILQ FT VARALKFQAQLPTQFWGECALTAVHIINRLPSSVLSFKTPFELLYSKPPSF FT SHIRVFGCLAYAINVHPSHKFDFRSMPSIFIGYPTGQKAYKLFDLSSKKIF FT TSRDVRFHEHIFPYASAKPGFVQHPSPIEFGPIPLLTHATTSLYSSLQTSP FT PVTAPAPSCSPPFASSNPHPSSPQPPPILRTYTRRPRPSDPIPPAENTPPP FT EPAPPEPSWPSENPPPPEPAPLRRSSRHTAPPAKLNDFVCSNVSSNQSATL FT LPGPSKGTRYPMANFVSYHRYTPAYHAFVAQLSTIPEPKSYAEAVVHPEWQ FT QAMRSELDALQANGTWSLTSLPSGKTPIGCRWVYKIKHHSDGSVERYKARL FT VAQGFTQMAGVDYHDTFSPTAKIISVRCLFALTAAHGWPLHMDVHNAFLHG FT DLAEEIYMSLPPGLRRQGEDHLVCRLHKSLYGLKQASRQWFAKFSEAMHSA FT GFIQSRADYSLFTRKQGMSFTVLLIYVDDILITGNDLVNIAATKQFLHKHF FT HIKDLGDLKYFLGIEVSTSKNGIFISQRKYALEVIEDAGLSGAAPINTPME FT RGLKLSDKSTLLKDTNRYRRLVGRLIYLTVSRPDITYAVHVLSRFMQQPRK FT LHMEAALRVVRYLKGAPGRGLFFSSKSDLKLRAYCDSDWAGCPLTRRSTTG FT YCVFLGPSLISWRSKRQKTVSLSSAEAEYRAMTGACCELTWLRCLLKDLGI FT SHRESALLYCDNKAALHIAANPVFHERTRHIEMDCHYIRDKIQDGSITTKH FT VDSAHQLADVLTKPLGKEIFVPMVSKLGVQDIHSPT" XX SQ Sequence 4595 BP; 1223 A; 1129 C; 869 G; 1374 T; 0 other; tggtatcaga gctggcttag aatcctaatc cattactgca attaaatctc tcgcctagca 60 tctctcttct tcagctacca tgaccaacaa tgaaacgtca tcaaacctag aagctcatac 120 agatttttca agagggaatc tgtcaaatcc ctatttcact caccattcag atcatccagg 180 tttggttttg atttccaaac ccttgaatgg agacaactat tctacttgga aaagggctat 240 gaccctggcc ttgaattcta aaaacaagct aagttttgtt aatggctcaa tcaaagcccc 300 ttcagaagaa actgatcctg aaggatatgc ggcttggtct cgatgcaatg atatggtcca 360 ttcatggatt attaacactc tcaatccaga gatttcagat agcgtgatat actactctac 420 cgcccatgaa gtttgggaag accttcatga ccgattttct caaagcaatg caccccgtat 480 gtttgaaatt cagcgagata tcgcttgttt taggcaggaa caactttctg tttcggtgta 540 ttacacaaaa ttgaagggac tgtgggatga acttgcttcc tacaatgatt cactacatgg 600 ggcgcagcaa gatcaacaaa gattaatgca atttctgatg ggtttgaatg agtcttacag 660 tgctgttcgt ggacaagttc tcttgatgaa tccccttcct tcagttcggc aagcttattc 720 ctttgtctct caagaagaaa agcaacgcct tttgagttca gcacacacca tcaatgattc 780 cgttaacagt gcagccatgg cggttcaaag caacaacagt aagtttaatg acaaaggtga 840 gcgttcctac cattctttta gatcgcaaga cagattgaca gataatttca gtggaggacg 900 cagatttgaa caggacagac gccggtttgg acctagacga ggacggcctc attgttccca 960 ctgtggagaa ccgggacatt gggtccaaac ctgttatgag ctccatgggt atccagcagg 1020 gcaccccaag gcaaagcaca attcagccag acgcttcaac cataacaaca aatctgcagc 1080 aaaccatgtg tcagaaagtt ttgctaaaga aaatggcaag tctgttgttg gaatttcaga 1140 gacccaattg aagcagctct tatctcttct taatgacaaa ggcgccgaat ccagttctca 1200 agcacatgct gcaactactg taaccaaacc aggtttgcct aaaattgctt cccgcagttg 1260 gattattgat agcggggcaa cggatcatat ttcttcatca tctcaatcat tttttcaacg 1320 agataacaat tgctcattgc ctcctgtatt actgcctagc ggggaaacag ctaatattgt 1380 tgcaaaggga tcattacctc tgaattccac ttattatttg catgacgtgc tttgtgtacc 1440 cacattcaaa gttgacttga tgtcagtcag tcgtttgaca agaggtttga attgttcggt 1500 aacctttttc ccttattggt gtattttgca ggatctggct acgaggagga tgattggttt 1560 gggtaaacaa cgtgacggac tatactactt ggtggcaata gcaacgaaga aatctatggt 1620 tcaaccttcc caaccattac atcgaccagc ctgcaacctc accatctcat ccactgatct 1680 ctggcataaa cgcttaggcc atatctcacc tcatcgttta agtttcattg cccaacaatt 1740 tttaaatttt tctgttcaat ccagtcatgt ttgtcctatt tgtcctttgg ctaagcaaag 1800 tcgcttgcct ttcaattcta gtgtcatttc ctctataaaa ccttttgaaa taattcattg 1860 tgacatttgg ggtcgttatc gacacccttc catttctggt gcttattatt ttcttactat 1920 cgttgatgat tatacacgtt tcacatggat atttttgatg cgacacaaaa ctgaagctca 1980 atctcttata aaacgctttt tcagttatgt tctcacacaa tttgaatctc ctattaaaat 2040 tttccgaagt gataatggtg gtgaatttat atcacttcgt tccttttttc aagataaggg 2100 tgtaattttt cagcattcct gtgtttacac acctcaacaa aatggggttg tggaacgcaa 2160 acatcgtcac atcttacaag tagctcgagc tttgaaattt caagctcaac tcccaaccca 2220 attttgggga gagtgtgctc ttactgctgt ccacatcatc aatcgactcc cttcctcagt 2280 gctctccttc aaaactccat ttgaacttct ctattcaaaa ccgccttctt tttctcatat 2340 ccgggttttt ggttgcttag cttatgctat caatgtacat ccttctcaca aatttgactt 2400 tcgctcaatg ccctcaattt ttattggtta tcctaccggt caaaaggcat ataaattatt 2460 tgatttatct tccaaaaaaa ttttcactag tcgcgatgtg cgctttcatg aacatatttt 2520 tccttatgca tctgccaaac ccggttttgt tcaacatcct tcacccattg aatttggtcc 2580 tattcctctt ctaactcatg ccacgacttc tctttattcc agtctacaaa cttctcctcc 2640 tgttacagca cctgcacctt cctgttcacc gccatttgcc tcctcaaatc cccacccctc 2700 atcaccccag cctccaccca tcctccgcac ctatacacgt cgccctcggc cttctgaccc 2760 aattccccca gctgaaaata caccaccacc cgaacccgcc ccacctgaac ccagttggcc 2820 ttctgaaaat ccaccaccac ccgagcccgc cccacttcgt cgctccagtc gccatactgc 2880 tccaccagcc aagctcaacg actttgtctg ctccaatgtt tcctccaacc aatcagccac 2940 cttactgcca ggtccatcca aaggtacgcg atatcccatg gccaactttg tttcatatca 3000 tcgttatact cctgcatatc acgcatttgt tgctcagctc agcaccatcc cagagcctaa 3060 gtcttatgca gaggctgttg ttcatcctga atggcagcag gccatgcgct ccgaactgga 3120 tgctctccaa gccaatggca cttggtctct cacctccctg ccgtcaggca agacaccaat 3180 tggctgcaga tgggtctaca aaattaaaca ccattcagat ggttctgtcg agcggtacaa 3240 agctcgttta gtcgcccaag gtttcactca aatggcagga gtcgactatc atgatacatt 3300 ttctcctact gccaaaataa tctctgtccg ttgtttattt gccttaactg cagctcatgg 3360 ctggcccctg cactagatgg acgtccacaa tgctttcctt cacggagact tagctgagga 3420 gatatatatg tctctgccac caggtcttcg gcgccaaggg gaggatcatc tagtttgtcg 3480 cctccacaag tccctttacg gtttaaaaca ggcatcccgc cagtggtttg ccaaattttc 3540 cgaagctatg cattctgctg gttttataca atcaagagca gattattctc tattcaccag 3600 gaagcagggt atgtccttta ctgttctctt gatatacgtt gatgatatct tgatcactgg 3660 aaatgatctg gttaacattg ctgcaactaa acaattcctg cataaacatt ttcatatcaa 3720 agatcttggt gatttaaaat actttcttgg aattgaggtg tctacttcaa agaatggaat 3780 tttcatttca caacgtaaat atgcactgga agtcattgag gatgcaggtt tgtcaggtgc 3840 tgctcctatt aatactccta tggaacgggg cttgaaatta tcagacaaga gcaccctgct 3900 caaggataca aaccggtata gaagattggt gggtcggtta atttatttga ctgtatcaag 3960 gccagacata acgtatgctg tacatgtctt gagtagattt atgcagcagc cccgaaaact 4020 tcatatggag gcagctcttc gagttgttcg atatctaaaa ggtgcacctg gccgaggctt 4080 atttttctct tcgaagagtg atttaaaatt gagagcttat tgtgactcag attgggcagg 4140 ctgtccactc actaggagat ctacaacagg ctattgtgtt tttcttggac cttcactgat 4200 atcctggagg tcgaagcgcc agaaaacagt ttcgctttct tctgctgaag cagaataccg 4260 agcaatgaca ggagcctgct gtgagttaac atggttgcga tgtctactga aagacttggg 4320 aatttcacac cgtgaatctg ccttactata ttgtgacaat aaagctgcat tacacattgc 4380 agccaatcca gtgtttcatg agagaactag gcacattgaa atggattgtc actacatccg 4440 agacaagatt caagatggtt ccattactac aaaacatgtc gactctgcac atcaactagc 4500 agatgtcttg actaagcccc tgggaaaaga gatctttgtt cctatggtta gcaagttagg 4560 agtgcaggat atccactctc caacttgagg gggag 4595 // ID Copia-44_VV-I repbase; DNA; EDCOT; 4517 BP. XX AC chr11; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-44_VV_; KW Copia-44_VV-LTR; Copia-44_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4517 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr11; Positions 12490321 12494837. XX CC 'CAAAT' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS join(646..2514,2518..3753) FT /product="Copia-44_VV-I_1p" FT /translation="MVEESNGGTNKANAVSKANHPRGKNNNKRNSGNYMSP FT KKNQEQFKGKKGPCFVCGKPGHYARECRYRKDLKGAVVNAIDEEIIATLSD FT VCVVQGKVQGWWYDTYATVHVTYDKSLFKTFEDAKGDQEVQMGNEGRSKVL FT DKGIVEVVFTSGKEVTLINVLYVPDMNKKLVSEDLLGKPGIKAVFESDKLI FT LSKSGNFVGKGYSYDGMIKLCTNDNIIKMASTSAYMCDSNSLFLWHNRLAH FT VGLSTIKRIVKCGLIACDTKKFEKCEICVKSKMIKKPFHSVERSSNLLDLI FT HSDICELNGMLTRGGNRYFLTFIDDCSRFTYVFLLKNKSETFNAFKVYKAE FT VENQLGKNIKVLRSDRGGEYFSSEFNSFCEEYGIIHECTAAPYTPQHNGIA FT ERKNRTFLKMVNAMLLHAKLNFNLWGEALLTACHILNRIPRKKNEISPYEL FT WKERKPNIGYFKVWGCLAYCKKTDPNKTKLGPRAIKCAFVGYASNSKAYRL FT LDLESNVIIESREVEFFENLLSDSNSQVPTSVGESLEETPSKVVEQPIVPR FT KSQRARKEKVLGSDEIDSQRISFYLVEGNREDIIRKIPIVLQIEEDPKTYK FT EAMASRDVAFWKEAINDEMDSIMSNTWELVNLPPRSKPIGCKWVFRRKYHT FT DGMIQTFKARLVVKGFKQREGIDYFDTYAPVARTTSIRILFALASIHNLFV FT HQMDVKTTFLNGDLNEEVYMEQPEGFVLLGNENKVCKLVKSLYGLKQAPKQ FT WHEKFDHAILSDGFRHNNVDKCLYSKTCDDYMVIVCLYVDDMLILSDDMKG FT IIETKRFLSSTFKMKDLGEVDTILGIKMKRNSEGYALNQTHYIDKVVSKFS FT HLKIKDANTPFDSSIKLEKNDGRSVTQLEYASAIGSLMYDAQCTRADISFA FT VSKLSRFTSNPKVEHWKAIGRVLGYLKNTKELSLQYSKFPAILEGYSDASW FT ISSVGDNLSTTGWVFTLGGGAVSWGSKKQTCISHSTMEAEFIALAAIGKET FT EWLRDLMMDIPFTAIMCQQCRYIVTVKPL" XX SQ Sequence 4517 BP; 1501 A; 676 C; 1024 G; 1316 T; 0 other; atcaaagact ctaagtttca atggaaggag agactatcaa gattatgaac caagaccttg 60 tgaggttgaa tcgttttgat ggttccaact tcactaggtg gcaagacaag gtgagattcc 120 ttctcacaac tctcaagatt ttctacatcc ttgatcctac cttggcacca ttactggaac 180 caaaggaaaa tgacacacct caagtggtgg cggcggcaag gaagaagagg aaggaggatg 240 agctcatatg taagggtcat attttgaatg ccttatccga taggctatat gatctctaca 300 ccaacaccaa ttccgtgagg gagatttggg aggctcttga aaacaagtac aaagctgagg 360 aagaagatac caaaaagttt cttatttctc aatacataga tttcaaattt tttgatgaaa 420 agcctctctt accacaaatt catgagttgc aagtaattgt gaataagttg aaagttctca 480 aaattgaact tccggaggcc ttccaagttg gtgctattgt ggctaaatta ccatcaagtt 540 ggaaaggtta ccggaagagg attctccaca agagtgaaga ttactccttg gaagagattc 600 aaaaacatct tcgcattgag gaagaatcga gatcaagaga caaaaatggt ggaagagtcc 660 aatggtggga ctaacaaagc caatgcggtt tcaaaggcca atcatcctag aggtaaaaat 720 aacaacaaaa ggaattccgg aaattatatg agccccaaga aaaatcaaga gcaatttaag 780 ggcaagaaag gtccttgttt tgtgtgtgga aaaccagggc attatgctag ggagtgtagg 840 taccgaaagg acctaaaagg ggctgtggtg aatgcaattg atgaggagat cattgcaaca 900 ctaagcgatg tgtgtgttgt ccaaggaaag gtgcaaggat ggtggtatga tacttatgcc 960 acggttcatg ttacctatga caaatctctt ttcaagacct ttgaagatgc aaagggagat 1020 caagaggttc aaatgggcaa tgaaggaaga tccaaggtgc ttgacaaggg cattgttgaa 1080 gttgttttta cctccggcaa agaggttacc cttataaatg tattgtatgt ccccgatatg 1140 aataaaaaat tggttagtga ggatttgctt ggcaaaccgg gtatcaaagc ggtgtttgaa 1200 tccgataagc taattttatc caaatcgggg aactttgtgg gaaaggggta ttcttatgat 1260 gggatgatca aactttgtac caatgacaat atcattaaaa tggcttctac ttccgcttat 1320 atgtgtgatt caaattcttt atttttgtgg cataataggc ttgcacatgt tggtttaagc 1380 actattaaaa gaattgtgaa atgtggtttg attgcttgtg ataccaagaa atttgaaaag 1440 tgtgaaatat gtgttaaatc aaagatgatt aaaaagcctt ttcatagtgt tgagagatca 1500 tctaatttgc ttgatttaat acatagtgat atttgtgaac ttaatggcat gttaacaaga 1560 ggtggaaata ggtattttct tacattcata gatgattgtt ctagatttac ctatgtgttt 1620 ttgttgaaaa acaaaagtga aactttcaat gcctttaaag tttacaaagc cgaagttgaa 1680 aatcaactag gaaaaaatat taaggtgctt agaagtgata gaggtggtga atatttctct 1740 agtgaattca attctttttg tgaagaatat ggcataatac atgagtgcac cgcagcaccc 1800 tatacacctc aacacaatgg catagcggag agaaagaata gaacattctt gaaaatggtg 1860 aatgctatgt tattgcatgc taaattgaat ttcaatttgt ggggtgaagc tttgttgact 1920 gcttgccata ttttgaatag aattcctagg aagaaaaatg agatatctcc atatgagtta 1980 tggaaagaaa ggaagcctaa tataggttac ttcaaagtgt gggggtgtct tgcttattgc 2040 aagaaaacgg atccaaataa aacaaaattg ggtccaagag ccattaagtg tgcatttgta 2100 ggctatgcct caaatagcaa agcttatagg ctattagact tggagtctaa tgtgataatt 2160 gaatcaagag aggtagagtt ctttgagaat ttgttgagtg atagcaattc tcaagtacct 2220 actagtgttg gagagtctct agaggagaca ccttcaaagg ttgttgagca acccattgtg 2280 cctcggaaaa gccaaagagc tagaaaagag aaagtgttgg gatcggatga gattgactct 2340 caaagaattt ccttttactt agtagaagga aatagagaag atattataag aaaaattcct 2400 atagtacttc aaatagagga ggatcccaaa acatacaaag aagctatggc ttctagagat 2460 gttgcctttt ggaaagaggc tatcaatgat gaaatggatt caattatgtc caactaaaca 2520 tgggaattgg taaaccttcc accaagatct aaaccaatag ggtgcaagtg ggtatttcga 2580 aggaaatatc acaccgatgg catgattcaa acctttaagg ctagattagt agttaagggg 2640 tttaaacaaa gagaaggtat tgattatttt gatacctatg caccagtggc tagaacaaca 2700 tcgattagga tattgtttgc tttggcatca attcataatc tatttgttca tcaaatggat 2760 gtcaaaacga cattcttgaa tggggatctc aatgaggagg tctacatgga acaaccggaa 2820 ggttttgttc tactggggaa tgaaaacaaa gtgtgtaagc ttgtcaaatc attatatggt 2880 ttaaaacaag ctcccaaaca atggcacgaa aaatttgatc atgctattct ttcggatgga 2940 tttagacaca acaatgtgga caagtgctta tattctaaga cttgtgatga ctatatggtc 3000 atagtgtgtc tatatgtgga tgacatgtta atcttgagtg atgatatgaa aggaataata 3060 gaaacgaaaa ggtttctatc ctcaaccttc aagatgaaag atcttggaga agttgatact 3120 atattgggta tcaaaatgaa aagaaatagt gagggttatg ctttgaacca aacccactat 3180 attgataaag tagttagcaa atttagtcat ctcaagatta aagatgctaa tactccattt 3240 gattcaagta taaaacttga aaagaatgat ggtagatcgg tgactcaact tgagtatgca 3300 agtgcaattg gaagtcttat gtatgatgct cagtgtacta gggctgacat ttcatttgca 3360 gttagtaaac taagtaggtt tactagcaat ccaaaagtgg aacattggaa agctattggt 3420 agagttcttg gttacctaaa gaataccaaa gaactaagcc tccaatattc aaagtttcct 3480 gctatccttg aagggtattc agatgcaagc tggatatcga gtgtgggaga taatttatct 3540 actacaggtt gggtgtttac acttggtggt ggggctgtct cttggggatc caagaaacag 3600 acttgtatat cacactcaac catggaggca gagtttatag ctctagctgc aattggaaaa 3660 gaaactgagt ggcttaggga tctcatgatg gacatccctt ttactgcaat aatgtgtcaa 3720 cagtgtcgat acattgtgac agtcaagcca ctctagctcg tgcgtacagt ggagtgtaca 3780 atgggaagtc tagacatata agcattagac acgagtatgt gagacaattg attcaatatg 3840 gaatcatctc aatctcattt gtgaggtcaa gtggaaactt gacagatcct tttactaaac 3900 ctcttacaag agatttagta aggataacat ctagagggat gggactaaaa ctccttaaat 3960 aaaattcacc aatgatggta acccaactta atactacgaa atgactagtc ttaagttcaa 4020 tgggtaaaaa caagtcattg ataagtgagt tgtggcagca ttagaacatg tgagttccat 4080 ctgtgatgat taatgctggt tgttaccgtt ggagggttaa gcttaaagct tttaatgaaa 4140 ttcagtctat gtgtgacaag catcttaaag gtaacaagga tgctggaaga atttcaccta 4200 tgtgaactta ggggtggtgc cgcctctcat gagattggag tttctttcaa gaaagttcat 4260 gaatggattg agcacatggc cataaaagtg ctaagcaaga aaataatggg cactcgtgtg 4320 gttagtggaa gtgtgtgtgt tgttaccggt ttcgttacaa ggaataacta gttcaatgct 4380 ataagcaacc tgggatttca acggagcttt gtgacaatta cactaaggta aaattcaaat 4440 cgaaagatat tttattttat gcattttcac tgttaaggtt ataagggttg atgtttattt 4500 ttaaccaagt gggggat 4517 // ID Gypsy-72_PTr-LTR repbase; DNA; EDCOT; 3663 BP. XX AC . XX DT 15-DEC-2009 (Rel. 15.02, Created) DT 15-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-72_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3663 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 180-180 (2010). XX DR [1] (Consensus) XX CC >90% identity to consensus. XX SQ Sequence 3663 BP; 1222 A; 525 C; 844 G; 1071 T; 1 other; tgtaaacccc ggggaaaaat aaaggttgct tagattgcaa actaactaca tgagaaataa 60 aagtgaagaa attcatgcat atggttaaat aaaaacggga attcagaaat ttttggatat 120 aagtttctgg acgaaatatt tcgagacatt ataaatcaac ccgaaaatgt tgagggttgg 180 attaaattaa agaaaataaa ctaaactaaa agttgtgggg tgaaattata agaaatgaaa 240 agaggtataa cttaattata agaagaaaaa aaagtggggg cctaaatgca aataagaaaa 300 attatagagc ataaatactc ctcttctcac caaaaaatct gcagcaatcg taaggaaaga 360 aaagagggag tttttgtatc cattcttgca aaatcaagag agaaacacca aaatttcaag 420 aacccatcca agattaaggg tttatagatg gaataaacac ttgtgggcaa gggattaaca 480 agaaaattga acaagaagag aagatggagg gccggctgtc attagataag aaaggaggga 540 gttgaaaatc ttcaactggt tgaagatcaa aaccttaatt cgtaccgggt aaggtgttct 600 aaacatgatc ttataagtca tttcaaattc gataatgaat tgatgccttg atgtgaatta 660 tagattaggg ttcttagact tgaattgggg gaaaagtatt tgttgttaaa attaagttaa 720 ttcatgtgtg gtatgtgatt ggggacgtga aaccatgata atttacccag aaaatgtagt 780 ttgtgaaagt tatgtgtgaa gggaaggggg gtgacgaatc tggacagact cgtctcctga 840 ctttcggtaa gatttcggat aggaggatga gggaattaga accgggttcc tcctagaaat 900 tgtagtttcg gatgttagct aactaaggaa attggtctcg ctcgatttgg agcttagaac 960 tccagttatg ggttaaactg agactgggtc atgacagtcc gtgggcagta agtccgatgt 1020 ttgttgatga gcaattttga ctatcttaga ggcagaactg ggttctcctt tcaagaactt 1080 gtagcctcat gtcttagctt tccaacgaga ctaatctcgc ttgaatcgga gttctataac 1140 tccagatata gttaaaaatc tgaggagagg tcagacagta acagttcaaa aacgagacag 1200 taacagttgg acagtaacag tccaatgcga atacaggagg ttcaaatgca ataatagttc 1260 cgagtaaaag tcagacagta acagttgaga cagtaacagt ccaaatgttt gttgatgagc 1320 aattttgact atcttagagg cagaactggg ttctccttat tcaagaactt gtagcctcat 1380 gtcttagctt tccaacgaga ctaatctcgc ttgaatcgga gttctataac tccagatata 1440 gttaaaaatc tgaggagagg tcagacagta acagttcaaa aacgagacag taacagtcca 1500 aatgtttgtt gatgagcaat tttgactatc ttagaggcag aactgggttc tccttccttc 1560 agagaacttg tagcctcatg tcttagcttt ccaacgagac taatctcgct tgaatcggag 1620 ttctataact ccagatatag ttaaaaatct gaggagaggt cagacagtaa cagttcaaaa 1680 acgagacagt aacagttgga cagtaacagt ccaaatgttt gttgatgagc aattttgact 1740 atcttagagg cagaactggg ttctccttca ttcagagaac ttgtagcctc atgtcttagc 1800 tttccaacga gactaatctc gcttgaatcg gagttctata actccagata tagttaaaaa 1860 tctgaggaga ggtcagacag taacagttca aaaacgagac agtaacagta accaaatgtt 1920 tgttgatgag caattttgac tatcttagag gcagaactgg gttctcctta ttcagagaac 1980 ttgtagcctc atgtcttagc tttccaacga gactaatctc gcttgaatcg gagttctata 2040 actccagata tagttaaaaa tctgaggaga ggtcagacag taacagttca aaaacgagac 2100 agtaacagtt ggacagtaac agtccaaatg tttgttgatg agcaattttg actgtcttag 2160 aggcagaact gggttctcct tattcagaga acttgtagcc tcatgtctta gctttccaac 2220 gagactaatc tcgcttgaat cggagttcta taactccaga tatagttaaa aatctgagga 2280 gaggtcagac agtaacagtt caaaaacgag acagtaacag ttggacagta acagtccaaa 2340 tataaagaaa ggaatgataa ctgtggttgg acaaagaacg acaatattaa tgggtgaaat 2400 gagaaaaacg taaaatatta agaaatgact gaaagaaaga cttattggtt gttgatatgg 2460 ttattataaa acatatcctt gagtgaggaa aatttatgag ataaacctgt gatttgcagg 2520 agggaccaca ggcgtggtgc aacagcagca gcaggggagc acgagtagag cttctattgc 2580 aggtaggtga ttcgcaccta tactttctag ttaaattcca tgatttaata tgttattgat 2640 gtgagatgtg aattaccgaa cgttggatat taggagaaat gaggaaagtt tgcgtaatga 2700 tgccgatatt ttggatagta ttctgaatgt atgtgtattc aaggtgaacg gttgttgtgt 2760 gaattgccaa gtgatgaaat tatcgttgac aaaggaaata tgagaagtgt gatttggggc 2820 gtgaactagc atacatttag tgtatgttag gatcccgggt aaggggatca ccttgcatcg 2880 actcctacgg ggtgatgatg ataacagtga aattggtatc ggtaatgtgt taagcgaaaa 2940 taatcatggg tggtcttatg aggtcttgaa tggaggttga taatggaaga gggaacggtt 3000 tttagtagtt gaakgaggaa gagtttccaa tgaaaaccag aagggagaag tgaacaaaat 3060 atgaatgcat gtttgccttt ttgaaattgt tggatattcg tattgctata ttattgtgat 3120 attcatattt caataatatg tattttgttt tcaggatcat cgcatgcacg acaggagtag 3180 attctagctt aggttcactt tttgtaattt aggttctagg gagtataccc ttgtattttg 3240 gtaatattac aacgtttgta taactcaatt tgtataattg atgtttaaac ttgaatggat 3300 gaatttaact ctgtagttcg tataaccatg ttccatgtat gcgtgtttat atctttatcc 3360 atccataatg ataattgttg tacaatgtat atcataaaca ttgtggttga tatgaatgat 3420 gatgtttgtg ggattgagac ccaggatgat tgggttgaat tgagttagga gatgcggtat 3480 attagaagtg taaacaggtc gtatgtcgat aacttgggac ctcccggtat aggggagact 3540 ccgtcgaaat ttcggtagac tttaatacaa acaccatgaa tagatatata aaaaaataat 3600 taatcactct gtttatcagt taacatgaga tcgttgcttt atcccggata tggggatgtt 3660 aca 3663 // ID HAT1_MT repbase; DNA; EDCOT; 4589 BP. XX AC AC144516; XX DT 03-JAN-2007 (Rel. 12.01, Created) DT 03-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE hAT-type element. XX KW hAT; DNA transposon; Transposable Element; HAT1_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4589 RA Jurka J.; RT "HAT1_MT: hAT-type element from barrel medic."; RL Repbase Reports 7(1), 29-29 (2007). XX DR EMBL/GenBank/DDBJ; AC144516; Positions 19118 23706. XX CC This is a relatively new sequence with up to 98% identity with CC other copies. CC The copy number is low. XX FH Key Location/Qualifiers FT CDS 1186..2961 FT /product="HAT1_MT_1p" FT /translation="MLQELQSVCASNMRDNDIDSSGSHENMCVDGEIESQA FT REIPLVPPIDQNAQEVSSDPKDKKRKGKAKAKDKSKGKALTSDVWLYLVKV FT GIVDGVEKCRCKACHKLLTCESGSGTSHLKRHVRSCSKTIKNHDVGEMMID FT VEGKLRKKKFDPMANREFLARIMITHGAPFNMVEWKVFREYQKFLNDDCVF FT VSRNTIAKEILNVYRDEKQKLKSQLAQIRGRVCLTSDCWTACSNEGYISLT FT AHYVNVNWKLESKILAFAHMEPPHSGRDLALKVLEMLDDWGIEKKIFSITL FT DNASANNSMANFLKEHLSLSNSLLLDGEFFHIRCSAHILNLIVQDGLKVVS FT DALHKIRQSVAYVRVTEGRTLLFSECVRIVGDIDTTIGLRLDCVTRWNSTY FT IMLQSALVYRRAFYSLSLRDSNFKCCPTSEEWRRAEIMCEILKPFFTITNL FT ISGSSYPTSNLYFGEIWKIECLIRSYLTSEDLLIQKMAENMKVKFDKYWSD FT YNVVLAVGAVLDPTKKFNFLKFAYEKLDPLTSEEKLKKVKMTLGKLFSEYI FT KNGIPSNLSSSQVQPSYGGGTRITSSSYDVSSYIFSLFYSFINYL" XX SQ Sequence 4589 BP; 1322 A; 774 C; 961 G; 1532 T; 0 other; taaagctgtc aaaatgggcc gggccgtaag ggccggcccg aaagcccgaa taaaatgtag 60 ggtttgggcc gaataattgg agcccgaaat ttgaataggg ctttttagcc cggcccgtaa 120 aagcccttgg cccgttaggg ctagcccgtc cgggctccgg gctgcccgaa agcccgcaca 180 aaatacaaca gttttttttt ttttttttgt ggtatgtgct gtgtgtgagt gtgagtcagc 240 cagcccgccc caatttggaa atccgacccg gcccggccca agtgaattga aaagagaaca 300 attgaacaaa ccctaattca ctcaacactc tcctctctct cactcactct ctcttacgta 360 ccgtacggtg ccgccgctcc tccatttctc tcaagtctca acactctcct ctcactctct 420 ctttgttacg gccgccgctc catttctctc taatctcagc tcaacactct cctctcactc 480 tcctcgccgc tccatttcac actctcctct cactctcatt tttacggccg ccggcgccgc 540 tccatttctc tctaatctca gccctcaggt caggtcggag gtcgcacaag ctcaccatca 600 ggtctcactt ctcagccctc aggtcgcatc gcagccatca ggtcggaggt cgcatctcgt 660 ctcaatctga ggtcgcatca ggtcagagct caccatcctt tcttcgtttt attggttttg 720 ttagtttctt tgtttcttcg ttttttgcag tttctgcgat cctcatcatt ttcttaattt 780 ctaattcagg ctcagcaggc agcagctatt gtttctaatt caggcttaac agctccattt 840 ctaattcagg cttaacagct ccatttctaa ttcaggttcg tatttctttt gttattgaag 900 tgaactgtgt gaagtataat atacttggct aaaattgaag taacagcaac atcgtgtcgt 960 gttacaatta caatgtattt cttttcttaa tcttcatcga tgaagttatt acaatgtatg 1020 taaattgaag tataacatta atagctgctg aaatataata tacttatgta atcatattta 1080 atgaactgat atagagtagt tattctatat gtaatcttta atgattgaat ttctggttta 1140 gaagtcgtta ttctacattt aattaggctt ataatttggc atataatgtt gcaggaatta 1200 caatctgttt gtgcttcaaa tatgagggat aatgatattg atagtagtgg aagtcatgaa 1260 aatatgtgcg ttgatgggga aattgagagc caagctcggg aaattccatt ggtaccacca 1320 attgatcaaa atgcacaaga agtgtcttct gatccaaagg ataagaagcg taagggcaag 1380 gctaaggcta aggacaagag caagggtaaa gccctaacat ctgatgtgtg gctatatctt 1440 gtgaaagttg gtattgtaga tggagtagag aaatgtagat gcaaggcgtg tcacaaatta 1500 ttaacttgtg aatcaggaag cggaactagt catttaaagc gtcatgtacg tagttgtagc 1560 aagactataa aaaatcatga tgtgggtgaa atgatgattg atgttgaagg aaaattgaga 1620 aagaaaaagt ttgaccctat ggctaatcga gaatttttag ctagaatcat gattacacat 1680 ggtgcaccat ttaatatggt tgagtggaag gtgtttagag aataccagaa gtttttgaat 1740 gatgattgtg ttttcgttag tagaaataca atagccaaag agattttgaa tgtttatcgt 1800 gatgagaaac aaaagctgaa atcacagtta gctcaaattc gagggagagt ttgcttgact 1860 tctgattgtt ggacggcatg cagcaatgaa ggttatattt ctttaactgc tcattatgtt 1920 aatgtgaatt ggaagttaga aagtaagatt ttagcatttg ctcacatgga acccccacat 1980 agtgggcgag atttagcttt gaaggtttta gaaatgttag atgattgggg cattgaaaag 2040 aaaatttttt ccatcacttt agataatgct tctgcaaaca atagtatggc taactttttg 2100 aaagagcatc taagtttatc aaatagtttg ttgcttgatg gagaattttt ccatataaga 2160 tgctcagctc acatcttgaa cctcattgtt caagatggac tgaaggtagt tagtgatgct 2220 ttgcataaga ttagacaaag tgtggcttat gtgagggtaa cagaaggtag aacactactt 2280 ttttccgaat gtgttagaat tgttggtgac attgatacaa ccataggatt gagattagat 2340 tgtgttaccc gatggaattc cacttatata atgctacaga gtgcgcttgt ttatcgtcgt 2400 gcattttata gcttaagttt acgggattca aattttaagt gttgtcctac aagtgaggag 2460 tggagaaggg ctgaaataat gtgtgagatt ttgaagccat ttttcactat tacaaacttg 2520 atatctggct cttcatatcc tacatcaaat ctgtactttg gtgaaatatg gaagattgag 2580 tgcctcataa gatcttatct gacaagtgaa gatcttttaa ttcaaaaaat ggctgaaaat 2640 atgaaggtga aatttgataa gtattggagt gactataatg ttgttttggc agttggggct 2700 gttcttgatc caaccaaaaa gtttaacttt ttgaaatttg cttatgaaaa acttgacccg 2760 ctcacaagtg aggagaagtt gaaaaaagtt aagatgactt tggggaagct tttttccgag 2820 tacatcaaga atggaattcc ttctaatcta agctcttcac aagtccagcc tagctatggt 2880 ggaggaactc gaattacatc atcttcatat gatgtaagtt catacatttt ttctttattt 2940 tattctttta ttaattattt gtaacttggt taggttggat gatttgtagg aatttgaaga 3000 atatgaaagc caatcaagta acaacaccgg aaaatcagaa cttgatactt atttagatga 3060 gttgcggatg cctctatctc aagaatttga tgtcttagct ttttggaagg aaagaagtcg 3120 tagaagtcca aatcttgcaa ggatggcttg cgatatattg agtattccaa taacaacggt 3180 ggcatcagaa tctgcgttta gtattggcgc ccgagttgtg aataggtata gaagttcaat 3240 gaaagatgat tctgttcagg ctctcttgtg cgcacgtagc tggttacatg gttttgaagg 3300 tattagttct atcattttta caattgtttt atagtttata ttattgtcaa tagctggtta 3360 caattgtttt atggtttttt tttaaaacat ttgcaacatg gtttctgcaa aattgtattc 3420 agttcccctt actggtttga tagaatgcta attatgtttg attcctttgc attttttcca 3480 tgttctggtg tttgaaaaaa ctataggttg ataagttcta gaatagtctc gtgaatttat 3540 tgcttcttag ttccttatca atttctgctt tggttttctg tttggtgtgc aagatattgt 3600 ctctaaatta ttgaagatgt tggtgaaaga ttagtatgca atattcttgg agtttcatga 3660 ttgatttttg ttcaatattt aacaatcaaa tttctcacag aattgattta tttttagtta 3720 gtatgctaga ttaggtagtt agtaatagta tgcaatattc tcacagaatt aatttatttt 3780 tagttatcaa tactgaagtg attttttaat ctctatattt aacaatcaaa tttcgtaatt 3840 tgtagaatta tatgatgaca acaatgatgt tcaagaagat gaaactcatg gaagtggaca 3900 agcatcaaat agtaccgtgg atgttgtgaa ccttgaagaa gattaagtga ctgactttgt 3960 tgggagtgac tttttggatt aaaacttttg ttatgttatt gttattactt attctggata 4020 attagtaatt tgaatttaga atcttcattc tggataatta gcttgatgga agcctatttt 4080 gtcatcctag ttgaaggatt gaacaataga tacttctact gttttacatg atgcctgtct 4140 ctgttaatta catacagttt tggattttag ggtacattaa ccaacatgag ttggcatgga 4200 gaaaatgaaa caccagcccg gtaatatcaa gcttacctcc aggaaaaatg gaaaatgaac 4260 ataaacttgt gtataagtat atttaagtta ttataattta tgttcaatca ttaaagaatg 4320 ggaagaaaaa gaaaaaaaaa cagatacggg cccgggctgg cccgttagcc cggtatattt 4380 atgtatttcg tacttaaaag aatggaaaag ggaaggaaaa aaatacgggc cagggctggc 4440 ccgttagccc gggagcccgt atagggccgg gctcgggcct gtttttagca gcccatattc 4500 aaaccgggct ttttagcccg gcccttaaaa gcccttggcc cggccgggcc gggcctaaac 4560 gggccgggcc gcccgttttg acagctcta 4589 // ID Gypsy-13_Mad-LTR repbase; DNA; EDCOT; 336 BP. XX AC ACYM01012269; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-13_Mad-I; KW Gypsy-13_Mad-LTR; Gypsy-13_Mad_. XX NM Gypsy-13_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-336 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1416-1416 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01012269; Positions 341 6. XX SQ Sequence 336 BP; 123 A; 63 C; 51 G; 99 T; 0 other; tgtagacatc gaaattttgg taaataaatg ttgaccgata aatcaaagtt tcaacgctca 60 tgtattacac aaattttaca cgtagcgtgt gtctaaacaa aaaaatcgaa ataagttgga 120 aaagtcatca aacaggacat gtgtcaacgc ccggcagaaa tgatttattt catctgatta 180 tttaatccca aaaatcaagt tttggaattc tataaataga agccaatttc attcatttgg 240 aaggaattga tattacacct tgaagctctg aaactccgaa gctctcaagc atccaattcc 300 caaagaatca agaaagcctt cttcgttctt cattca 336 // ID DNA9-2_Mad repbase; DNA; EDCOT; 477 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-2_Mad. XX NM DNA9-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-477 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1482-1482 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >88% identical to the consensus. 9-bp TSDs. XX SQ Sequence 477 BP; 130 A; 97 C; 105 G; 145 T; 0 other; gagaaaattg tagcaatggt ccctcaactt taacccaatt ggagcaatgg tccctcaact 60 aaaaattcat gaccattggt cccttaactc atcaaaacgt gcagctatgg tcattttcgt 120 caactccgtc agaattccgt caaaatgagt catgttggaa ggaccattgc tacaattggg 180 ttaaagttga gggacatgct ccaattgggt taaagttgag ggaccatttc tccaattggg 240 ttaaagttga gggaccattg ctacaatttt tctcatttgg ttttccatat ttgccccttg 300 attcagcctc acgtgcgtgg cacgtgactc attttgacgg aagttctaac ggagttgacg 360 aaaatgacca tagctgcacg ttttgatgag ttaagggacc aatggtcatg aatttttagt 420 tgagggacca ttactccaat tgggttaaag ttgagggacc attgctacaa tttcctc 477 // ID Murbi_MT repbase; DNA; EDCOT; 524 BP. XX AC . XX DT 30-NOV-2006 (Rel. 11.11, Created) DT 04-JAN-2007 (Rel. 11.11, Last updated, Version 2) XX DE A non-autonomous DNA transposon from Medicago truncatula. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; repeat; KW Interspersed; Murbi_MT. XX NM Murbi_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-524 RA Shankar R. and Jurka J.; RT "Murbi_MT: A harbinger type putative non-autonomous DNA RT transposon from Barrel Medic."; RL Repbase Reports 6(11), 582-582 (2006). XX DR [1] (Consensus) XX CC The sequence is very well conserved in the Medicago genome as CC well as exists in multiple copies. XX SQ Sequence 524 BP; 147 A; 106 C; 130 G; 141 T; 0 other; gggttgggaa taggccaggc cggcctacag gggcctatgg cctggcctgt ttaagcctgg 60 cctggcctgg cctgtttatt aaaaaggcta ggcttaggct ttttaaaaag cctatttaag 120 taaataggcc aggcttaggc tatcaaaaaa gcctatgaag cctaataggc cggcctgttt 180 atgcatgtta ggcttcatag tggacttttt aaataggctt taaagcttta tagtgaaata 240 ggcttttaag gccttatagt agtgatagac aagtcttaca ctgaaatagg ctttgaggcc 300 tattaagcct atttaaaagt agataaaatg gaatgtttag tgactttaat agtaagtagg 360 cctgtaaata ggctttcagg ccaggccaga cttttaaata ggccaggcca ggccaaaaaa 420 ataggcctat gaaaggccat aggccaggct caggcctgca aattttttcg taggccaggc 480 tcaggcctat caaagcctgg cctggcctgg cctattccca accc 524 // ID DNA8-8B_Mad repbase; DNA; EDCOT; 1146 BP. XX AC . XX DT 18-OCT-2010 (Rel. 15.1, Created) DT 18-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA8-8B_Mad. XX NM DNA8-8B_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1146 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1479-1479 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC The termini are similar to those of DNA8-8_Mad. XX SQ Sequence 1146 BP; 301 A; 277 C; 357 G; 211 T; 0 other; taggggtggg cacgggccgg gccgggccca aatttgaagg gaccggaccg gacccgcttt 60 aaaatggaac ggggcggggc ggggcgggta ttgaaatttc tgaagttgga accggacata 120 acccggcctg tttgaaacgg gcggttcggg ccgggtccac gggtccaacg gaagggaacg 180 acgtcgttgt ctatcttcct ccgatgcgaa acctagatgc ccagcgacaa ccttcaccgt 240 cgcgccgttc agcatcgtca cgtctccggc gaacaccact cgaatctgtg actgatgcat 300 gtcggtctga gtatattacg agtgtgcaaa taccactcag atccatgaca aagagcttta 360 tttgcacaga acactcggat ccatgacaga tccgagagaa atgagggacg tgtagagagt 420 gagactgtga aagagtgaga gaaaggggtg agagagaaat gagagtattg aattccaacg 480 atgttggcga tgacgaagcc gagtatgaag gtgtccgagg aagaagagag agactgcgag 540 tcttggtcct gggaagaaag agcggcaaag tcatctgcgt ctcgggaaga aagagcggca 600 aagtcatctg cgaagccaag ggtgtctatg tccaacggga atacgagaga aacgtgaatg 660 tcgtgagaaa tcacctcttg ctgcagagcc tcggccaagc cacggagccc gaacttgctg 720 gcggagtagg ccgtgtagcc gtagattccg acttggccgg cctgggatga catcagcgcg 780 atcgagctcc ggaatgagag ttgcagagat ggggggagaa gaaacagaga agaggaatga 840 gggagaaggg agaaggttcg agagattggg tgtgtgttct cgagagtgag agaaccatca 900 cggggaggga caaaaagaag tgggcctggg acagtaacag tacccaacac agggtatttt 960 tgcaaacggg ccggtccggg tacccgtttt tctatacttt tggaaccggc ccgaacctaa 1020 aatttcaaag acccgccccg ccccgccccg tttctctttt ttaaaattag gacccgcccc 1080 gtacccgccc cgaaccgcta atacccgccc ctacccgcgg atccaggacc cgtttgccca 1140 ccccta 1146 // ID VIHAT2 repbase; DNA; EDCOT; 4577 BP. XX AC . XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE hAT-type DNA transposon from Vitis vinifera. XX KW hAT; DNA transposon; Transposable Element; VIHAT2. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4577 RA Obukhanych T. and Jurka J.; RT "VIHAT2."; RL Repbase Reports 7(8), 765-765 (2007). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 1508..3322 FT /product="VIHAT2_1p" FT /translation="MESNLTPSSGQDSTTNSQSTRSKTDPAWEHVSEERYA FT NGRKALICLYCKKITKGGGIHRMKQHLAGVKGDIGPCKSVPPDVRFRMENS FT LQEFVNSKKATQEAYECRNPYGPNVSQFEGDMAEGEEEVQEMQSPMAANSG FT KRKKSTVDKYFAPRNTQGAQPSMRSVLAGKEAIWRADMAVGRFFYDACIPI FT NAVNSFYFKPMLDAISAIGPGYKGPNYHQLRVNLLKDAKKEVQLLVDSYRA FT IWAKVGCTIMGDGWTDNRQRTLINFLVYCPEGISFVKSVDASDIVKDATNL FT FQLFDEVIEWVGPLNVVHIVTDNAANYVAAGRLISQKHKHINWSPCAAHCL FT NLIFKDIGKMDHVAELVRRASKVTIFVYNHVALLSWLRKREGWTEILRPGA FT TRFATTFIALKSLHDHKHDLQALVTSKFFVDSRYSKDYKSKVAVSIILDNR FT FWNDCLIVVNLMSPLMRLLRIVDCDERPSMGYVYEGMYRVRLGIKKLFNYN FT ERLYKPYTEIIKQRWDQQLKKSIHSAAYWLNPCFQYDQENFCNKPNVIGGV FT MDVIDQKVLKGKLETMNEMKLFRDRLGSFGRELAYSSREVLQPGKILFSFI FT SMFILFY" XX SQ Sequence 4577 BP; 1400 A; 781 C; 929 G; 1462 T; 5 other; caatgtttta aaaaccggac cggaccggcc ggtccgaccg ycggtcgatc accgttccgg 60 tccggtccgg tcatttggac cggatgggga tcgaaccggg gtyggaccgc ttgaaccggc 120 ggtccaaccg gtgraccgga cgaaccggcc ggttcaattg attttaattt tttttaaaaa 180 aaaaacaaca tcaaaacgac gtcgttttga tgcttctggc atcaaaatga cgccgttttg 240 gagtcctatt taacaaaatg aaaatctcca ggctgcgccg ctgcaacctc caaactccaa 300 cccttcctcc tccgcccgcc gtcgacgcgt cccagccgcg acaccaaggg tccaagacag 360 atcccgccga cggcctgcga cacccacaca ggtcccgccg gcggcccacg acacgcacac 420 tggtagcttc ccccctctcc tccgccagcc gtcaacgcat ccttgccacg acaccaagag 480 agatcccgct gacggcctgc gacacccaca caagtcccac cggcggccca cgacacgcac 540 actggtagct ccccccctct cctccgcccg tcgtcgacgc atccctgccg cgacaccaag 600 agagatcccg ccgacggcct gcgacactca cacaggtccc gccggcggcc cacgacaccc 660 acacaggtat cgcctgcgtt ggaaagctcc ccccctctcc cagctggtag cccgccccgg 720 cgttggagtt tgcccagtga gtagttgttt tctaggtttt ctttgttatg ctatacaagt 780 tcattaagat taatatatta ttaataataa taattcaagg tgatgatgct aattgctaag 840 ataagtrgtt ggattatgtg tttcctttaa atttatttat ttatttattt attgtttaaa 900 gtaaatatac aatgaggtaa atgtggaagg aagccatcat gccttttggt ttaattaatt 960 gcctattcat gaggaattct tcagtaactt aaagcaatat tgatttagtt tataatatga 1020 tggaatgcat argatgcttt aataattctt attttaaaaa tgaccttacc tttgatgaag 1080 aagtggtaaa ataatggtat aatgatatca tacattaatt atatacgagt gattatgaag 1140 attgatccct tttggaccac atgtatgttg acgcatgcca tagagaaaat gtgaaagcat 1200 gcattgaaaa agaagcaaaa tttacaagat atttgtggaa aaattctcca aacatgcttg 1260 tttagatatt tgtggagttt gcccatcaat atatctctac aaaattactt tagaatttag 1320 ataaatttat aattggatca aaacatgctt gttataatga ccattattcc tttagataaa 1380 tttacccatt gatatgtgat tgttataaat tgttgatgac ttgattataa atcattaaat 1440 tgttgatgac ttccattctc tacgttaatg tgagattttt gtttctaatt tgatagagaa 1500 ataaaaaatg gaatcaaact tgactccatc ctctggtcaa gattcaacta ccaattctca 1560 atcaactaga agtaagaccg atcctgcatg ggagcatgtt tctgaagaaa gatatgcaaa 1620 tggaaggaaa gctcttattt gtttgtattg taaaaagatt acaaaaggtg ggggtattca 1680 tagaatgaaa caacatcttg ctggagtgaa aggagatatt ggtccatgta aatcggttcc 1740 tcctgatgta agatttcgaa tggaaaattc tttgcaagag tttgtgaatt ctaagaaagc 1800 aacccaagaa gcatatgaat gtagaaatcc ttatggtcct aatgtgtcac aatttgaagg 1860 ggatatggca gaaggtgaag aagaggttca agaaatgcaa agtcctatgg cagctaatag 1920 tggaaaaagg aaaaaatcaa cagtggataa gtattttgca ccaagaaata ctcaaggagc 1980 tcaaccttcc atgaggagtg tactagctgg gaaagaagct atttggagag cggatatggc 2040 ggttgggaga ttcttttatg atgcatgcat tcctattaat gcagtgaatt ccttctactt 2100 caagccaatg ttggatgcta tatctgcaat tggtcctgga tataagggtc caaattacca 2160 tcaactacgg gttaatcttt taaaggatgc caagaaggaa gttcagttac ttgtggactc 2220 ttatcgtgca atttgggcaa aagttgggtg tacaataatg ggtgatggtt ggacagataa 2280 tagacaaaga acactcatca acttccttgt gtattgtcct gaaggaatat cgtttgtgaa 2340 atccgttgat gcttcggaca ttgtcaagga tgcaactaat ttgtttcagt tatttgatga 2400 ggtgattgaa tgggttggtc cactcaatgt agttcatata gtcactgata atgcagcaaa 2460 ttatgtggcc gcggggagat tgatttctca gaagcataaa cacattaatt ggtcaccttg 2520 tgcagctcat tgtcttaatt tgatctttaa ggatattggt aagatggacc atgttgctga 2580 acttgtaaga cgtgcatcaa aggtgacaat ttttgtttat aatcatgttg ctttgttaag 2640 ttggttgaga aaaagagaag gatggacaga gattttgcga cctggtgcaa ctcgctttgc 2700 tactacattc attgcactca agagtcttca tgatcataaa catgacttgc aagctttggt 2760 gactagtaag ttttttgtgg actctagata ttcaaaggat tataaaagca aagttgcagt 2820 ttccatcatc ttggataata gattttggaa tgattgtttg attgttgtga atcttatgtc 2880 tccactaatg cgcttattgc gtattgttga ttgtgatgag aggccttcga tgggatatgt 2940 gtatgaaggc atgtataggg ttcgtttggg catcaagaaa ttgtttaact acaacgaaag 3000 actatacaag ccttatacag agatcataaa gcaacgttgg gatcaacaac taaagaaaag 3060 cattcattca gcagcttatt ggttgaatcc atgtttccaa tatgatcagg aaaacttttg 3120 taataagcca aatgttattg gaggtgtcat ggatgttatt gatcagaaag ttctgaaagg 3180 caagcttgaa acaatgaatg aaatgaagtt atttcgtgat cgattgggaa gttttggaag 3240 agaacttgct tattcttcac gtgaagtact tcaacctggt aaaatattat tttcatttat 3300 tagtatgttt attctttttt attagttacc tacttactat ttaatatttt aaacttgcta 3360 atgtgtttta ttttttttct tatttttaat gtgaaatggt aactagatga atggtggagg 3420 ctacatggat acagtgcacc acatttgcaa aagttagcca ttctaatatt gagccaaacc 3480 gcatcgtctt ctggatgtga gaggaattgg agtgtctttg aacgtataca taccaaaaga 3540 aggaatagat tggaacatca aaggcttaat gatcttgtat acgttcatta caatttgcgc 3600 ctaaaaaatc ggtataaatg atttcttagt tgttttgaat ttaaattctt ctattcacaa 3660 ttatgaataa ttatatgttt ttctttttta ggttctataa caagaaaaga atctatgatc 3720 ccattgacta tgcatgcatt gatgagaccg atttttgggt agttgatgac gatcaaccag 3780 cagagttaga tgttgaagaa ttggaaaatc ttctatatga agaagggtca attccaataa 3840 atgaagtgga aggttcaagt tctcacattg gttagtaaaa tatttaaact tataaaagtt 3900 caataattat attttttttc ttcaaaaatg atttcttgtt gatatatatt caatattttt 3960 gtagatgatg aggatggtgg tgacgtggct atagaagggc ttgatgtgga gaactttggt 4020 tttccaaatg ctcatgttca atctccatat tccaatttcc aaaatgaatg aagacatgaa 4080 ttttatattt attagtatgc aaaaaacttc atgaatattc aaacattgac atgttatatt 4140 tttattttga gtaattattt aagtgttgtg gacctatggt tgacatttgt attatctatt 4200 atggacaatg tgttaagtta acaactcttt gataatttgg ttattatagg atagtaatgg 4260 tttgattatt tgataaatat tgagtttatt gacattatga atgtataaca tcttatattg 4320 tgttatagat atcatatatg ataattgatg acttctacag gtaaaaaatt ttgtgacaaa 4380 actcaacaaa caaagtagat gctgtcaaaa tttacataga atttattaat tttttaattt 4440 tttataatat ataaaataat aaaatatata tttatgacgt caccggttcg atagacggtt 4500 cgaccgccgg tccgaccggt gaaccgtgaa ccggtaactt ttccggttca atgaccggtc 4560 cggttctgaa aacattg 4577 // ID COPN_MT_LTR repbase; DNA; EDCOT; 1263 BP. XX AC AC137995; XX DT 12-DEC-2006 (Rel. 11.12, Created) DT 12-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Putative Copia-type non-autonomous element - long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW COPN_MT_LTR. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1263 RA Jurka J.; RT "COPN_MT: putative non-autonomous Copia-type element from barrel RT medic."; RL Repbase Reports 6(12), 616-616 (2006). XX DR EMBL/GenBank/DDBJ; AC137995; Positions 80407 81669. XX CC 99% identity between LTRs. XX SQ Sequence 1263 BP; 399 A; 196 C; 228 G; 440 T; 0 other; tgttggaaca tgtgtggaaa ttgagttaaa cagactaaac acaaattccc atgttgggta 60 gaactagtgt tgtgtgaatt gaaacagtgg aagtctcaca tcgaatggaa cacacacatt 120 agtagtgttt atatagtagg ggtgtacctc taagaggtac atagttatgt gaacgaagta 180 agcactgaga aaaaaaaaat atactgatat atattttatt atttggaaat gataaattaa 240 ataattaatt taatcattat tagaaagtgt tttcttagtc cccaagtttt gctaaaataa 300 tttggaacgc aatctagaat attttggaac acaatctgaa atatttggga aggcaatcta 360 atatatttta gtacatgatc taaaatatat tttgatactc agtaatatat ttatgtattg 420 aataatatat ttttgtactc aatatgatat attttgagac tcaatttgag atatttttgt 480 actagatcta atatgagaat tacttgctcc caaagtttct cacttattag ttgtgaactt 540 tctctataaa tagagagctc acacagtgca ttccacacac cgaaattcac agttgatgct 600 tcctgtgttt ttcctctctt ctccctcctt cgacttgtgt tgacaagttc ttctcctttt 660 tctactcctt tctgtccctt cggaattaag agtaatctta agaccatagt cccttttcgg 720 tttaatgtcc cttcggaatt aagaatggtc ttaacagcat agtcccttcg ataattcatt 780 ctcttcggaa taaataatgt tttaagatca tagtcccttt tcgatataat aagaatgatc 840 ttaaacatat atattcttct tcaactcatg gagaagttag atgttagaat ggtcgtagca 900 ccatatttga gtggttgaaa tgcctattga tatttggaga agttaaaaat tagaatggtg 960 gtaacaccat atttgagtgg tctcaacatc ataattgagt ggttacaata ccatattggt 1020 ttcagtatta aaagattggt cttagtacca tattgaaggt gtaattctcg aacggttttc 1080 tacagtgcag tagttaatcg aacagttgta gctgggcttg ttttatcctg gaggcggcgt 1140 ggttgatagt ctgccttgca caattttggg cagtgccatg aaacgtctta aagagagcga 1200 cctggtcgtg actcaaccta ataacaactt cggtagataa tagaatttgg aaatccaaaa 1260 aca 1263 // ID EnSpm-4_VV repbase; DNA; EDCOT; 9693 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE EnSpm-4_VV, an autonomous DNA transposon - a consensus sequence. XX KW EnSpm; DNA transposon; Transposable Element; CACTA; TIR; KW Cactavine-4; EnSpm-4_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9693 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 756-756 (2008). XX DR [1] (Consensus) XX CC EnSpm-4_VV (Cactavine-4 in [1]) is an autonomous element. Its CC individual copies are >90% identical to the consensus sequence. CC It is questionable whether individual copies contain an intact CC ORF due to premature stop codons and/or frameshifts. EnSpm-4_VV CC contains short TIRs which are flanked by 3 bp-long TSDs. CC Downstream of the TPase gene (region 5393-8718) is another ORF CC encoding for a ULP1-like protein similar to CAN78020.1. Although CC ULP1 (Peptidase C48) -like proteins are usually found in Mutator CC elements, our study shows that such proteins are common in CACTA CC elements as well. This feature is not restricted only to Vitis as CC similar examples were found in rice [1]. XX FH Key Location/Qualifiers FT CDS join(1408..3875,3963..4068,4148..4792) FT /product="EnSpm-4_VV_Transposase" FT /translation="MENRDWMSKDRRSVEYDEGVENFINFALAHSTNHTSI FT KCPCLRCGNLLCQTPQVIREHLFFNGIDLSYRVWYWHGEKGPSGGFSNVSQ FT QRYDKCEYNDVADTIDMVNAAQVNCMNDPQVFGRLLEDAEKPLYPGCMKYT FT KLSALVKLYNLKARYGWSDKGFSELLQLLGDMLPLNNEMPLSMYEAKKTFS FT ALGMEYQKIHACPNDCILYRNQYKDAIACPTCGKSRWKINNEGGKIKKGVP FT AKVLWYFPPIPRFKRMFQSSETAKHLMWHAKDKECDGKLRHPSDSSAWKLV FT DHMWPDFASEPRNLRLALSTDGINPHKSMSSRHSCWPVILVIYNLPPWLCM FT KRKFMMLSLLISGPRQPGKNIDVYLSPLVDDLKTLWEKGVETYDAHLXEVF FT TLKAILLWTINDFPAYGNLAGCTVKGYYACPICGEGTYSKRLKHGRKNSYM FT GHRRFLPRNHPYRRQKKAFNGEQDFRIPPKILSGEEILEKVDLIPISWGKM FT KIKSLESDVNTNCWKKKSIFFELEYWKYLHVRHNLDVMHIEKNVCESIIGT FT LFNIPGKTKDGLNARLDLVEMGLRSELFPRVDLKKTYLPPACFSLSRNEKK FT LVCQTLSNLKVPEGYCSNFRNLVSLEELKLFGLKSHDYHALMQQLLPVALR FT SVLPKHVRYTISRLCIFFNKLCTKVVDVPKLNEVHNELVVTLCLLEKYFPP FT SFFDIMLHLTVHLIREVRLCGPVYFRWMYPFERYMKVLKGYVRNHNRPEGC FT IAECYLAEEAVEFCTEYLSGTHAIGIPKSNNYDNKFGRPITGGRSTNIDHK FT SWLQAHHYVLENTTIVQPYIEEHMNWLKSQYPRQSKRQIWLQEEHMRCFTY FT WLKGKVEEAIHNGQDIPNTLRWLAHGPTHQVVKYPGYIINGCRYHTKERDM FT TCVTQNSGVSILAGTMQIASSKDKNPVFGELCFYGVINEIWDLDYNMFRIP FT IFKCDWVDNKNGIKVDELGFTLVDFSKIGHKSDPFILASQAKQVFYVEDQL FT DPKWSIVLSIPPKDFNNMEGLDDFTDNCMEHHPFISSMPEVESFDVMDESE FT AIYMREDCEGIWIENN" XX SQ Sequence 9693 BP; 3266 A; 1414 C; 1679 G; 3320 T; 14 other; cactactaca aaaataattt atggtgtcac tatttatggt gtcactttta aaataatgac 60 accatagggt ttataattaa taaaggtgac acatcatatw aaaaatcttc aattgaggta 120 gttagatgat attagtttta tatttatagt gtcatttttc gggaagtgac atcatataaa 180 ataatttttt tttaagtatt ataacttaat gagcccactt gagcccactt ttagaattaa 240 taatgaggaa taatatataa aaagcccatt gtttccatat kdcacccaca attagaagta 300 ataatgatgg ataatatata aaaatcccat tgtttccata tttcaccwac aatchaaaaa 360 atctcaatat ataaacccta tatataataa aaatcataat cttcttctac cttttctctc 420 amccatagty aacacgttca caatcgacat tcttcacttt gtggactccc aggtaaccca 480 aaatctctta gatctatcat ttttttcttt taattaatgt cattatatta attgtttcaa 540 catctttgta ttatgttttt tgtgaattgt gttttcttga gttgtgggga agaaaaactt 600 aggtttaatc ttctagcata gaagaaaaaa ctgtagatta attgattttt taatctaaac 660 caaacacatg atcaagtcct taaaaaaaaa agtgaaaaac adgaaaaaak gaatgatttt 720 taataagtat ttattktgag catgtaatat atattaatac acatgttcat acttgaaatg 780 ttacattttt ttggattatt agtttaattt aatggagatg aatatttagt ggaaaagtta 840 caatgtatta ttgaaaatat gacttgatag ttgattatgt atatgtgtca tttcttagta 900 taaaaaaaat atttaaatct gtatcatttt acattgataa tatattgttc ttgtaacagg 960 ttcaaatagt aagtaagtca ttatcaaaga agttattgaa agtataagtg tatgtttatt 1020 tatagcatgc tcttatatat atcaattgta aggaagataa aattaccttg taaaggtaat 1080 taaatnttta tataattgaa aagttttttt ctatatatta tgtttttgaa gcttgtttaa 1140 tgaaacatat tcaagttatt tgacayactt ttcacaaagt tttgaagcat aatactgatg 1200 tatattattt cacaaacttt tgacaactat tttgtgtact aatgcatatt aagttttgtt 1260 cttgcctatt taagttacat ttagttattt aaatatatcc aatattatgt tgaaaaaaga 1320 tgtacttaat taaatttttt tgttcttaat attaacaagt tttgcagttc tcttgtatag 1380 gatatatatt ccattatttt aattgaaatg gaaaatcgag attggatgtc aaaagataga 1440 aggtcagttg agtatgatga aggagttgaa aactttatca atttcgcatt agcacattca 1500 accaaccata cctctataaa atgcccatgc ttacgttgtg gaaatctgtt atgtcaaact 1560 cctcaagtca ttagagagca tttgttcttt aatggaatag atctcagtta tcgagtatgg 1620 tattggcatg gagaaaaggg tcccagtgga ggattttcaa atgtctcaca acaacgttat 1680 gacaaatgcg agtataatga tgttgctgat acaatagata tggttaatgc tgcacaagtt 1740 aattgtatga atgatcccca agtgtttgga aggttacttg aagatgcaga aaaaccttta 1800 tatcctggat gcatgaaata cacaaagttg tcagcattgg taaaacttta caacttaaaa 1860 gcacgttatg gttggtctga caaaggattc tcagaattgc ttcagttgct tggagatatg 1920 ttgccattga ataatgagat gccgytgtcc atgtatgaag ctaaaaagac tttcagtgct 1980 cttggtatgg aatatcaaaa aattcatgca tgtcctaatg attgtatttt gtatagaaac 2040 cagtataagg atgctattgc atgcccaact tgtggaaagt caaggtggaa gataaacaat 2100 gaggggggga agattaagaa gggggttcct gcaaaggttt tgtggtattt cccaccaatc 2160 cctagattca aaaggatgtt ccaatcctca gaaaccgcta aacatcttat gtggcatgcc 2220 aaggataaag aatgtgatgg taaactacgc cacccatcag actcctcagc gtggaaacta 2280 gttgaccata tgtggcctga ttttgcttct gaaccgcgaa accttagact agcactctca 2340 acagatggta taaatcctca taagtctatg agcagtagac atagttgttg gcctgttata 2400 ttggtcatat acaaccttcc tccttggttg tgcatgaaaa ggaagtttat gatgctatca 2460 ttattgatct caggaccacg acaacctggt aaaaatatag atgtttactt gagtccattg 2520 gtggatgacc ttaaaacttt gtgggaaaaa ggagttgaga cttatgatgc acacttgcrt 2580 gaggttttta ctttaaaggc catcctttta tggacaatca atgattttcc tgcatatgga 2640 aacttagctg gttgcactgt gaaaggatat tatgcatgtc caatatgtgg agaaggaaca 2700 tattccaaaa gattaaagca tggtaggaaa aactcgtata tgggtcaccg acgatttctt 2760 ccacgtaacc atccctatcg gagacaaaag aaggcattca atggtgaaca agattttagg 2820 attcctccta aaattttgag tggggaagaa atacttgaaa aagttgatct cattcctatt 2880 tcttggggaa aaatgaagat aaaatctctt gaatctgatg tgaacacaaa ttgttggaaa 2940 aaaaagtcca tattttttga gttagaatat tggaaatatc ttcatgtccg tcacaacttg 3000 gatgttatgc acatcgaaaa gaatgtctgt gagagtatta ttggtacttt gtttaacatc 3060 ccagggaaaa caaaggatgg acttaatgct cgacttgacc tagttgaaat gggtttaagg 3120 tctgaacttt tcccaagagt tgacttgaaa aagacctacc ttccccctgc atgtttttca 3180 ctatccagaa atgagaaaaa attagtttgt caaacgttgt ctaatttgaa ggtccctgag 3240 gggtattgct caaattttag aaatcttgtc tccttagagg aattgaagtt gtttggtcta 3300 aaatctcatg actaccatgc acttatgcaa caactgttgc cagtggcatt acgttctgtt 3360 ttgccaaagc atgtgagata tactatatca agattgtgta tcttcttcaa taaattatgt 3420 acaaaagtgg ttgatgtgcc aaaattgaat gaagtacata atgagttagt ggtcacgttg 3480 tgcttacttg aaaagtattt tccaccttca ttttttgata ttatgcttca tctaacagtg 3540 catttgataa gggaggtgcg actatgtggt ccagtttact ttaggtggat gtacccattt 3600 gagaggtata tgaaagttct taaaggatat gttcgcaatc ataatcggcc tgaaggatgc 3660 attgctgagt gctatttagc agaggaagct gtcgaatttt gtactgaata tttatcaggg 3720 actcatgcaa ttggaattcc aaaaagtaac aattatgaca acaaatttgg tagacctata 3780 actggtggtc gttctaccaa cattgatcat aaatcgtggt tacaagcaca tcattatgtg 3840 ttagagaata caactattgt ccaaccatac attgagtaag aaaaatatac ctttattttt 3900 ttataatttc ataacataat gatgaaatcc taagtttgca ttccttgtct ataacgttat 3960 agggaacaca tgaattggtt gaagtctcaa taccctcgac aatctaagag acaaatttgg 4020 ttgcaagaag aacatatgcg ttgttttaca tattggctta aaggaaaggt aatctcttag 4080 ttttcagaaa ttattttaat atgttgaaaa caccacaagt ttccaattat gttttgatta 4140 cacacaggtt gaagaggcta tccataacgg gcaagatatt cccaacacgc ttaggtggtt 4200 agcacatggc cctactcacc aggtggtcaa atatcctgga tacatcatta atgggtgtcg 4260 ttaccatact aaggaacgcg atatgacatg cgtcacccaa aatagtggtg ttagcatttt 4320 agcagggact atgcaaattg ccagttctaa ggataagaac ccagtttttg gtgaactttg 4380 cttttatggg gtcattaatg agatatggga tcttgattac aacatgttca gaattccaat 4440 tttcaagtgt gattgggttg acaacaagaa tggtataaaa gtggatgaac tcgggttcac 4500 attagttgac ttctccaaaa ttggtcacaa atcggatcca tttattttag catcacaagc 4560 caagcaagtc ttctatgttg aagaccaact tgatcccaaa tggtcaatag ttctctcaat 4620 tcctccaaaa gatttcaaca acatggaagg actggatgac ttcaccgata attgcatgga 4680 acatcacccc tttataagtt caatgccaga agttgaatca tttgatgtta tggatgaatc 4740 agaggcaata tacatgagag aagactgtga gggcatatgg attgaaaata attaaataat 4800 atattgtacc cttgacatga gatataataa ggcatttcac ttattagttt tcatgagttg 4860 cacattagct tagcttctat atattgctca tgatatatat atatatatat atagatatat 4920 atatagatat atatatatat atatatatat attgatcatc ctaaatttct ttcatgcatc 4980 ataaacatat gttattcaaa ggtaccactt caatcttcat ttaactatct tttttgttgt 5040 ccatggaact agatttatat tattttttat tatcatgttt tgattttatg ctcacataac 5100 ttgaaactct cattcctaaa tttctttttc attaaaacta taaataataa ttgaaactat 5160 atatgcacta atttatttta ttattatcct cacaaataaa ttcttcatta ttgataagaa 5220 atcaaaaaac aagacaaact ttgaaagaaa atttcaaaaa ctatatttgt gaatgaccaa 5280 tttaattata ggaaatatat gcaaggatat actaatcttg cttttgagtc attttacagg 5340 tttgttggtg aagtactagt ttgcacattt acttgatatc ttccacacaa atatggatcc 5400 agaagaagag gaaatgccaa aagtaaagca tagaggtagt acattgaaac cagagattgc 5460 aaaaaatcga agtaaaggga taaagctcaa gattgaatac aatagccttg gtagtcacat 5520 tggggaaaat tcagttgaac taagtagtta tcttggtaca ataactagaa cccatgtgcc 5580 aataattgtt gagagttgga ggaaagtccc taaagagact aaggagaagt tatgggattt 5640 gatcacggta agtctatcta tagctttcat atataattat tgtatacatt cattaacatg 5700 agctaacatg ggttgctatt ttgtagacaa gctttaatgt gaatcaaaat tccaagagga 5760 attgtttcct actaatgggc atcaggtttc gaacctttaa gtacaagttg acaaagaaat 5820 atatattgcc tttcaagaat gacccagaaa agctgaaaaa gccacctcct atctacccat 5880 tcatacaaga ggatcattgg agacagtttg ttaaagatag actttctgaa cattttaatg 5940 ttaagcatta tttttaatac atcttcaatt tttacattta catagtttca ccatgtacta 6000 attttgtgtc tatatttttt aggaatatcg caaggttcag aaatcgagaa gagataaaca 6060 catttacaat cattatcttg gaagaaaagg atatgcacgt tttgagcagg atatagtaag 6120 ttatcaatat cggtaaaaaa aatggagtat atattttgtt tataggaaaa tgattccaat 6180 ttttaaatgt catttattaa cttgatcata ttgaactaat gagttttatt gttaaaattt 6240 ttatagctac aagcagaagg gggtattggt agggttgata gaagtgtttt atggaagaaa 6300 gcacgtgaga agaaaggaaa gtttaataag attacagagc cagtgattaa catgatagta 6360 agttagcata tttatgcctt ttagagccta tagtgttagt atgtctatgt gactatggtt 6420 tgtgatgata tcgttaggtg ttaataggca agaggcttaa tgctatcatt tttatgagta 6480 gttatgttat acaccaattt gtctattatc ctttgtatta aaacaattca ttttctagct 6540 accttgaatt ggttgtcttt gattgatatg taaatcatct tcatcaaatt attactaata 6600 tatgttttgt tgtaggatga attactagaa aatgctaagg agactggact acctccacct 6660 ggtccaaatg acatattagg tcaggcattg ggtaagcctg atcatccagg acgtgtggta 6720 ggtcaagacc gtttggttag gcctagctca tactttcatc aaccatctga tgacatgaaa 6780 aaaatcaaag aagaaatatg ggaaatggta cgaaaagaga tggaagatgc tgcaacaaga 6840 caagttatgt ctccccccac accccattct gatatgggta gtaataacat gagacaacaa 6900 cttgttttac aaccagttgt agcagaaaaa ccaatgttta aaatgataga agagccccaa 6960 ccaccagaac caccactgaa acacaaggta tgcatttact tactaataat acaagattaa 7020 tataagtgat ataaagccta tgtaaatgat attatttgtt gtattgaagg taattaaatg 7080 taaattagca gtggaaagaa aaggaaatgt tgttgcaact ggtacactaa tagaagaaaa 7140 aggatcgaat aggttggttg taataaatgt tgcacacaag ccagatgcta gactcccatt 7200 tccaaatcca tatgagatta tcaatgttgg ggatgctatt ggctttgagc ttgactggcc 7260 aacaagcctt gtcatacttg aaactgaaca tcctcaggta tgtcatttta tgcctatagt 7320 aaatttgatt gtaacttggt attttattgt ttaggagtat atatatctaa cattccttcc 7380 tttttcatag gtgttggata aaggaaagaa gaagatagtg aagacaccaa ttattcgaaa 7440 atctaagcct caaaatcatt cggtcattaa aaattttcag aaatttgtgg atggttgtct 7500 tggtaatgac aagacatacc caatacagct ccccatttca ctatttggtg tcgaatttca 7560 aacatatata tctagagagg attgtgaata cattatttca tctttagagg tgtcatcaaa 7620 ctgcatctcc ttctatttat ggtgtgcacc ttttattttc atttgttttt atttttttta 7680 atatgagttg cccatgttga acgaaattgg atatgactaa tgataatttt cttttggtgt 7740 tttgatacaa taataggcac atgcatgatc aactacatat tgccaaaaag gaatcacaat 7800 ttatatttgt taatcctttt acaatatcac gagcaggcct tagtactcct caaacagaga 7860 aaagagcaca attgttgtca aaacgcttaa tggagtgcca agatgctaaa tatgttttca 7920 taccttacaa ccccgagtaa gtgacaaata ttatacttta atttgaggtt ttatgattga 7980 tttatatttc taattagatg ctacttttgt ttttaatgtt ttagctttca ttgggtcttg 8040 gtagtgattg agccaaggaa aatgatagtc cactatcttg accctatgca tcacaaacca 8100 tgtgaggact taaaggatat cgtaaacatg taagttcttc ctattatttt tcatagtatt 8160 attttttttt tttaaaaaaa atacattcat ctcaaacaca ttttttatta ttatttatat 8220 atatgttaaa acatataaca tttacctatt ttaaaaatgt acccattgaa cttatttaca 8280 tagggctctt cgaatatctg caaagaaaac atctaagagg gagccatctt ggcaactagt 8340 gcaggtgaca tccaaaaaat tttctttaca cattagctta tgcatttgca ccatttatat 8400 atatgagtac taatgttatt ttataattga tcgattagtg tccaagacaa gaaggagggt 8460 tcgaatgtgg ctactttgtt atgagattca taaaagagat aattttttat cctacaatta 8520 ttgcttcaaa ggtattacaa atttaatgaa ttgtacatag ttttaggctt ccaaatgtta 8580 tgcattttaa tgttattttc ttatttgatt tcagtttggt gataaaaaaa aacatattct 8640 caagtagaat tcgatgaaat tagaggagaa tgggctactt ttgtgctaca actaatcatg 8700 aatcatgttg atgcatcatg atcaccatgc atggtgagtc ctttagctac tacatgaatt 8760 tttccatagg tatctttgaa taatgtttct atttgaaaaa aaaaaaagaa aaaaaaatag 8820 ttcttagatt tgttcattta tgataacatc gatccatgtt tattttcttc aataaaaatc 8880 tataaaactc attaaactat gaaatgcagg tatacacttt tgggatggtg gaatggagaa 8940 taaaaagaaa gaagaaggca acaagatttt gggtttttaa atgcaactct tatgtcatac 9000 gttgtaggac ataaatgtta ctttaattag tactgagaaa tttagatttt tagatgagac 9060 ttttatgtca ttttatagtt agccggtttt atgcttatga aatggaggta tacatgaatc 9120 ttgggatctt taacatttct aaatcatgtt ttggtatgta ttcactcttc tttttttttt 9180 tagttttgat gggtttgata tgttggatgt actatctttt tgtgaacatt tgatatacaa 9240 atattattag atgatcaatg tattatgagt tattccagaa acattacaga aaaatgagtt 9300 aaatataata tgattgttat atttatggac aaaatataaa caggttaatc ttacttatta 9360 attcataagc attacaaaaa tctataacta aaagcaatca tatcttccac aataatttac 9420 aatgatgtga caccattact caaaggtgat gcatttaata tgacatcata actcaaagat 9480 gatgcattta atgcgacacc ctatcatcac tagaaatata tggtgtcact tccgaatggg 9540 tcaccattta tctactttgg tgtcacttcc aaatacgtca ccaattggta ccctctatgg 9600 tgtcagtgga gaaggtgacg ctatgttgta gtgacaccct atgtttatgg tgactcgtta 9660 taaatgtcac catatatctt tttccttgta gtg 9693 // ID Copia-53_VV-I repbase; DNA; EDCOT; 4441 BP. XX AC chr2; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-53_VV_; KW Copia-53_VV-LTR; Copia-53_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4441 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr2; Positions 6585345 6580905. XX CC Positions [1456-1962] - Integrase core CC 'CCACA' target site duplication CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS join(523..2112,2116..3579) FT /product="Copia-53_VV-I_1p" FT /translation="MKHKRKQMSLEDVIIHIRIEEQNRNRDNIDKARELSS FT KGNVVEEKSKPKNNSSRKQNSRTKPNASNKVQNSSIKKRGNCFVCGKFGHH FT AAQCCHKKRIEKTSSKANLAETEVIIVVISFEVRMVTNMKEWVVDSGATRH FT IYGNRSAFTSYTTVKEGEKQVFMGNSRFTPVIGKGKVLFKLTSGKVFALCD FT ALHVPDIHWNLVLVSLLGKAGVRILFEYDKIVLTKNDAFVGNGYCNQGLFM FT LNVYDIINNNTSSSAYIVDSCDILHGRLGHVNFSYMKKMVELSLIPKLSLE FT NHGKCESCVESKTTKKSCKSVERESDLLSLIHNDLRDIKNTMTRGGKRFYI FT TFIDDYSRYTRVYLLRNKYEARNAFIKYKNEMENQLSKKIKRLRTDRGGEY FT ESNPFNSFCEDHGIIHETTPSYSPESNGIAERKNRTLKEMMNAMLVSSGAP FT LNFWGEAILSACHIQNRIPYKKTGKTPYELWKGYAPNIAYLKVWGCLAKVL FT LLEPKKQKLSPKTFDAMFIGYVENSVAHRFLVTKENNLVDVNTIIETKNAD FT FFENIFPMKLNGEQQVQKTNRDKYIEPSEFEPRRSKRNRKETNLGDGFYTF FT LIDEDPRSYKETITFPNAPFWKEAINSEIESIMYNHTWELVDLPHGAKTIG FT CKWIFKRKLKQDGSIEKYKARLVAKGFKQRNDVDYFDTFAPMTRIASIRVL FT IALASIHNLVIHQMDVKTAFLNGDLEKEIYMDQPEGCVVSRKEKNVCKLVK FT SLYGLKQAPKQWHNKFDHVLVTNGYSINDADKCIYNKHENNTCVVICLYID FT DMLISGTNLEVVCETKKFLGSKFDMKDLGEAEVILGIKITRTPNGLKLSQE FT HYVEKILRKFEHFDCKPVSTPYDPNSQLKKNREHSIAQIEYAQIIGSLMYL FT MNCTRPDIAYVIGRLSRYTQSPNQDHWTVVRRVLKYLRGTINYGLCFSGFP FT SVLEGFSDANWISDSDEMKSTSGYVFILGGSVVSWKSTKQTCITRSTMDAK FT FIALEKASSEAE" XX SQ Sequence 4441 BP; 1522 A; 696 C; 913 G; 1310 T; 0 other; atcttgaaat aaatccaaat ggaagcttcc ctagttcaca cccgtcctga cacctctaaa 60 attgatccct tcaatgggac attctttaag agatgacagg aaagggtttt ctctgtaatt 120 gatgtggtga cttgggacat attttgacta acccaaaacc agaatatggt tttcatctgt 180 taccaacctg ggaaactgga aataaacaag ttaggcatgc tattctgagt accatttcta 240 atgaactttt tgatatttat tgtaaattta aagttgcaaa agaaatttgg gatgcaataa 300 acaaaaaaat atattttgga aaatgcggga actcagaaat atgtcatagg gaattttaga 360 aatttccaaa tgtctgagga tagagatgta tcatcttaaa tccatgatta ccacttgttg 420 attaatgact tagctattga agacattaaa ttacccgaac cttttgtggc tagttattta 480 gtagagactc ttctagagtc ttggaaagac tataaaaaca acatgaaaca taaaaggaaa 540 caaatgtctc tagaggatgt cataatccat attaggattg aggaacaaaa tcgaaatagg 600 gacaatattg ataaagccag ggaattgtct tctaaaggta atgtggtaga agaaaaatct 660 aaacccaaaa acaatagttc caggaaacaa aactctagga caaagcccaa tgcatcaaac 720 aaagtccaaa actcatctat taaaaaacgg ggtaattgct ttgtttgtgg caagtttgga 780 caccatgcag ctcaatgttg ccacaagaag agaattgaga agactagttc aaaggcaaat 840 ctggcagaga cagaggtgat catagtagta atctcctttg aggtgaggat ggtcaccaat 900 atgaaggaat gggtggtaga ctctggggct actaggcaca tctatgggaa tagaagtgca 960 tttacttcct ataccactgt aaaggaagga gagaaacaag tgttcatggg taattctaga 1020 tttactccag tgattggcaa agggaaagtt ctcttcaagc taacctctgg aaaagtgttt 1080 gccctctgtg atgctcttca tgtgccagat atccattgga acttggtgtt agtatctctg 1140 cttggaaaag caggagtgag gatcttgttt gaatatgata aaatagtttt aaccaagaat 1200 gatgcatttg tgggaaatgg ctattgtaat caaggtttat ttatgttgaa tgtttatgat 1260 attatcaata ataatacatc ttcttctgct tacatagttg attcttgtga tattttgcat 1320 ggtagactag gacatgtgaa cttttcatat atgaagaaaa tggttgaatt gagtttaatc 1380 cctaaactgt ccttagaaaa ccatggaaaa tgtgaatctt gtgtagaatc taaaaccaca 1440 aagaaatctt gcaaatcagt tgaaagagaa tcagatctac taagtttaat acacaatgac 1500 ttaagagaca taaaaaatac aatgactaga ggtggtaaac gattctacat aactttcata 1560 gatgactact caaggtatac aagggtatat cttttgagaa acaaatatga agcaagaaat 1620 gctttcatca agtacaaaaa tgaaatggaa aatcaactaa gtaagaaaat taaaaggctt 1680 agaactgata ggggaggaga gtatgagtcc aaccccttta attccttttg tgaagatcat 1740 gggatcattc atgaaactac cccttcttat tcccctgagt ctaatggaat agcagaaagg 1800 aaaaatagga ccttaaaaga aatgatgaat gcaatgttgg taagttcagg agcacccttg 1860 aacttttggg gggaagctat cctatccgca tgtcatattc aaaatagaat accttacaag 1920 aaaactggta aaactcctta tgagttgtgg aagggttatg cacctaatat agcatacttg 1980 aaagtgtggg ggtgtttagc taaagttctt ctccttgaac ctaaaaaaca aaaattaagt 2040 cctaaaacct ttgatgcaat gttcattggc tatgttgaga atagtgtggc acataggttt 2100 cttgttacca agtaagaaaa caatcttgta gatgtcaata ctataataga aacaaagaat 2160 gcagatttct ttgaaaacat ctttcctatg aaactaaatg gtgaacaaca agttcagaaa 2220 acaaatagag acaagtatat tgaaccttct gaatttgaac ctagaaggag taaaagaaat 2280 aggaaagaaa caaaccttgg agatggtttc tacactttcc taatagatga agaccctaga 2340 tcctataaag aaactataac ttttcctaat gcaccatttt ggaaggaggc cattaacagt 2400 gaaatcgaat caataatgta taaccataca tgggagttag tagatttacc tcatggtgca 2460 aagaccattg gttgtaagtg gatctttaaa agaaagttaa aacaagatgg gtccatagag 2520 aaatataaag ctcgtttagt tgccaaaggc tttaaacaaa ggaatgatgt agactacttt 2580 gacacctttg cccctatgac tagaatagca tcaattagag tattgattgc tttagcttcc 2640 attcataatt tggtgataca ccaaatggat gtcaagaccg cattcttgaa tggggatttg 2700 gaaaaggaaa tttatatgga tcaacctgag ggttgtgtag tttcaaggaa ggagaaaaat 2760 gtgtgtaagt tggttaaatc attatatggg ttaaaacaag ctcccaaaca atggcacaac 2820 aagtttgatc atgtgttagt aactaatgga tattccatta atgatgctga taagtgtatc 2880 tacaacaagc atgagaataa cacatgtgta gtcatctgcc tttatattga tgacatgttg 2940 atctctggaa ctaacctaga ggttgtgtgt gagaccaaga aattcctagg ttctaagttt 3000 gatatgaaag acctaggaga ggcagaggtg attctaggaa ttaaaataac tagaacacct 3060 aatgggctta aactttctca agagcactat gttgaaaaaa tcttaaggaa gtttgaacac 3120 tttgattgta aaccagtgtc aactccttat gatcccaact cacaactgaa gaaaaataga 3180 gaacatagta ttgctcaaat agagtatgct cagatcatag ggagcctaat gtatttaatg 3240 aattgtacca gacctgacat tgcttatgta ataggtagat tgagtcggta cacccaaagt 3300 cctaatcagg accattggac tgttgttcgt agagtcctta agtatttgag ggggaccatt 3360 aactatggtt tgtgctttag tggatttcca agtgtccttg aaggatttag tgatgcaaat 3420 tggatctctg attcagatga gatgaaatcc actagtggat atgttttcat ccttggtggg 3480 agtgtagttt cttggaagtc taccaagcaa acttgcatta ctcggtctac tatggatgct 3540 aagtttattg ccttagaaaa ggcaagttct gaggctgagt gacttagaaa ccttttagca 3600 gatatccctt tatggacgag actagtcccg tctatgtcta tgcattgtga tagccaaatt 3660 gcaattgcta aggctaagag taaaatattt aatggtaaga acaggcatat atgcctaaga 3720 cacaatattg tgcggcagtt gcttgaaaca tgggttatat tcctagaatt tgtgaggtca 3780 gagttgaatt tggccaatcc tttggccaaa ccactaaata agaaactagt ggaagaaaca 3840 tcgaggggga tgaggcttat gcctattaca gaagtcaaga gtggtggtaa cccaacatat 3900 tagagtggaa attccatgaa ataggttcat atgggtaata acaaatcatt tgttgacttg 3960 aggtgctcta ttaactctaa ttgtatgaga gtccatccct atgctgtaga tagaacgtat 4020 tctgcattga ctaaggttga ctatttgctc ttaatgaata ccatattcct tatggatggt 4080 atgtttaaat gtaaaacata cttgatggat tcacctatat gagagtggag gtggggccgc 4140 ttcctaggaa aacttaggca ggttttctgg agctctcatg aatatccagg caaggcgcat 4200 gacctatttg tgccaacccg ttttgtacag ctcgtagtgt agttgagaaa ccaatgtgga 4260 taaaaatccc ttgagttaca tcaagaaaca ctggttcata gaaatttatt tttcaccatg 4320 tttcgtgatt caacacttat ttgtcctaag actggttcat agcctttgag caccaatact 4380 aatgcattgg attctttttt cctccaaaaa aaaaaaaata cgtttacact ttgtggggga 4440 t 4441 // ID TST1_I repbase; DNA; EDCOT; 4493 BP. XX AC X52387; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 08-AUG-2007 (Rel. 12.07, Last updated, Version 2) XX DE Potato DNA for copia-like transposable element. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Copia-like element; TST1; TST1_I; TST1_LTR; retrotransposon; KW unidentified reading frame; internal portion. XX NM TST1. XX OS Solanum tuberosum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-4493 RA Brisson N.; RT "TST1."; RL Direct Submission to Genbank (02-APR-1990)Brisson N., Universite RL de Montreal, Departement de Biochemie, P.O.Box 6128, Station A, RL Montreal, Quebec, H3C 3J7, Canada.. XX RN [2] RP 1-4493 RA Camirand A. and Brisson N.; RT "The complete nucleotide sequence of Tst1 retrotransposon of RT potato."; RL Nucleic Acids Res 18, 4929-4929 (1991). XX RN [3] RP 1-4493 RA Camirand A., St-Pierre B., Marineau C. and Brisson N.; RT "Occurrence of a copia-like transposable element in one of the RT introns of the potato starch phosphorylase gene."; RL Mol. Gen. Genet 224, 33-39 (1990). XX DR GenBank; X52387; Positions 286 4775. XX SQ Sequence 4493 BP; 1438 A; 779 C; 958 G; 1318 T; 0 other; tggtatcaga gcggaccatt tcccctaata tcatatggat aaaacagcct ttcacagaga 60 cgatctttct gaaacatcaa caggaacgtc ctgcaaaaaa tctgatgaca caaggaggca 120 atgcttctca catgcccttc cagttaactt ctcatcgatt aaatgggaag aactatctgg 180 aatgggcaca gtccgtaaag cttgcaatcg atggccgtgg aaagctggga catctgaccg 240 gagagacaaa gaagccggga gttggagaga tcagagaatt cactcgtgat tgcttggtta 300 ataaattcta tggaactagt cataggtaaa tcttatctct ttttgcccac tgccaaggat 360 gcatgggaag ccgttaggga gtcatattct gatttagaaa atgcctctca aattttggag 420 ttaaaaattg aactatggca agctaagcag ggtgagaatg aagtcactac ttattataat 480 gaaatggtgt ccttgtggca ggagttagac cagtgttaca atgatgaatg ggagtgttct 540 atggatagtg tgaaagccaa aaaaaaggaa gaaaatgaga gagtttacct ttttttagca 600 agattaaacc gagagtttga caaggtcagg tcgcgaatcc taggaaaaaa tcctctgccc 660 cttcgtgaaa ctttttctga aattaggaca gaggaaactg ggaggaaagt tatgttaaaa 720 cctgatttaa atgttgaact aaaacctgtt atagactctt cagctcttgt aacagtgaag 780 aatgaagagg acaaaaagaa aaagccattg tgtgatcatt gcaaaaaata ttggcacacc 840 cgtgaaacgt gttggaagat tcatgggaaa ccactaaact ggaagaacaa gggagttgat 900 gatcatggct ttcaatctca aaatggtcag gccctccaaa caacttattt tgatcagggg 960 caacaacctt ctccagaaac gtctctattt acaagggaac aattggaaat tctgcacaaa 1020 ctccttcaat ctccacaatt tcgtgcaaat gcaccaaaat cttctaatcc ttcttgttct 1080 tttgctgaaa ctgtatcatc tgtatcgtct gcttttctta gtgtcaattc caaccaaata 1140 gattcttgga tcatagattc aagagctagt gaccacatga ctgggagttt ccgttttttc 1200 tctacttaca ctccttgtgc agggaacagt aaaatcaaga tagctgatgg ttccttctct 1260 gcaattgctg gaaaaggaac tattaaactt atcaccatct cttgtacttc atgatactct 1320 tcatgttcca aagctctctt gtaatctagt ttctttccgt aaattaaccc gttctcttaa 1380 ttgtcgtgtt attttttatt ccgatttgtg tgaatttcag gaaaaggtct cggggaagat 1440 gattggcagt gctagagaat caggaggtct ttattttctt gacaacggga acaactcact 1500 acagctgaat cctatttttt taaactctac ttttgttttg aataaagtca tgctttggca 1560 ctatgggctt ggacatccaa gtttttatta tttaagacat ttgttacctc agttatttag 1620 aaataaaaat ccatccttat tccaatgtga attttgtgaa atggctaagc atcatgtaga 1680 tacttctttt ccttctcaaa gatatcaggc ttcaaaacct tttacaatga ttcatagtga 1740 tgtttgggga ccgtctagaa tttcaacaat gtttggaaaa cggtggtttg taacttttat 1800 tgacgatcat actagattga gttgggtttt tttattgaag ggcaaatctg aggttaaaaa 1860 tgtgtttgag actttccatg tcatggtgga aacacagttc aatgagaaaa tcaagatttt 1920 tcggagtgac aatggccgtg aattttttaa tgaacaatta ggaagttttt tcagaaaaac 1980 tggggtagta caccaaagct cttgtccaga tacacctcaa caaaatggta tcgccgaaag 2040 aaagaataga catcttttag aggcaacgag agctttaatg tttactagta aagttccaca 2100 acacctttgg ggagaggctc tcttgactgc cacttacctt attaatagaa tgccatctcg 2160 ccctcttgaa tttaagacac cttttaaagt tttcagagaa agttttccta gttctaggtt 2220 aactacagat ctacctctga gagtttttgg ttgtacaaca tttgttcatg ttcataatcg 2280 tagtaaactt gaaccgcggg ctaagaagtg tatttttgta gggtatgccc caagtcaaaa 2340 gggatataag tgttatgatc cacatgctag gaagataatt gtcacaatgg acctaacttt 2400 ctttgagtcg caactctatt ttactactca tcttcagggg gagtatcatt taggtgaaga 2460 ttcatttttt gtgatattga ggaaactaga tatcaagcaa atgaggagcc taatattaca 2520 aataaatact gatgtgagag atgtagggga agatataaat aagtgtgatc caagagatga 2580 taaggaccaa agtgacttaa tgataaaaac tcagaaattc aaacctgaac ctgtagcgcc 2640 ttcaaatgac aaaaataaaa atgggaatag agaacaaaaa acagaaatgc aggtgtattc 2700 gagaaggaac cgaactcaag aaaaaaggac cgaagattct caacactgcc aaaaatcagt 2760 cccacaagac cttactgtaa ttcaaggtac tcttccaact gattctattt ctaattcctt 2820 agatctagat ctacctattg cgaaacgcaa aggtgttaga aatacttcta aatatcctat 2880 ttctatgttt gtgtcctaca aaaagttgtc tcctagttat tcagccttta cttcacaact 2940 ctctagtgtg gagattccaa caaatgtgca ggatgctcta caagttcccg agtggaagga 3000 ggctattttg gaggaattgc gagctcttga aaaaaatgag acatgggagt tagtggattt 3060 acccgaggga aagaaaccag tgggttgtaa atgggtgttc accaccaaat tcaaatcaga 3120 cggatccttg gaaaggtata aggcccacct agtagttaag gatcacacag acatatcgat 3180 gcatgactat ctcgagacgt ttgctccagt agctaagcta aactcaatta gagttctgtt 3240 gacaatcgca gtaaatctcg actggtctct ttagcaattg gatatgaaga atgttttctt 3300 gaacgggcac ctagaggaag aagtctatat ggatccccca ccaggttttg aagggaagta 3360 caagtcaaaa atatgcaggc ttagaagatc tctttatggt ctaaaacaat ctccaagggc 3420 ttggttcgaa aggtttactc aatttgtgaa aaggcaaggg tatgtgcaag gacaagcaga 3480 tcacacaatg tttactcgac attcactaga aggaaaaaca accgttctta tagtgtatgt 3540 tgacgatatc atcctcacag gagatgatgt ggttgagata aaaaatctaa aggaacgtct 3600 tgcctcagaa tttgagataa aggacttagg cccgctaaag tactttcttg gcatggaggt 3660 tgcacgatcg aagaaaggaa ttatagtgtc acaaaggaag tatgttcttg atctgttaaa 3720 agaaacagga atgagtggtt gtagaccaac tgaaactcca attgatccaa atctgaagtt 3780 tgtaaaggaa ggaaaattga ttgataaggg tcaatatcag agattggtag gcaagttgat 3840 ttacttgtca catactagac ctgatatttc ctttgctgtg agcctagtca ttcagttcat 3900 gcattatcca cgagaagaac accaagaagc tgtgtatcga atcctaaggt atctaaagag 3960 ttcacctggg aaagggttgt tcttcaagaa gaatgagcaa agaagtcttg aggcttatac 4020 ggatgcagat tgggctggtt catctattga taggaggtct acatctggat attgtacatt 4080 tgtttgggga aatttggtga catggagaag taagaagcaa aatgtggtgg ctcgaagtag 4140 tgctgaggct gagtatcgat ccatggctct cggaatttgt gaaatattgt ggctcaagag 4200 atttttggaa gaactaagaa gacctgtgag ttttccaatg aagttgtatt gtgacaataa 4260 ggctgccata agcattgctc ataatccagt tcaacatgat agaacaaagc atgttgaagt 4320 gacagacaca tcattaaaaa gaagattgaa gatggaagtg tgtgcattcc ttttgttcca 4380 acaacagaac aagttgcaaa tattttcaca aaaggtcttt tcagaactac ttttgagtcc 4440 tttgttagca agttaggcat gtttgctatt tacatgccga cttgaggggg agt 4493 // ID RT_VF repbase; DNA; EDCOT; 231 BP. XX AC . XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Vicia faba Ty1/copia-type retrotransposon RT_VF, reverse DE transcriptase gene - a consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; RT_VF; KW retrotransposon; Ty1/COPIA superfamily; reverse transcriptase. XX OS Vicia faba OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Vicia. XX RN [1] RA Pearce R.S., Harrison G., Li D., Heslop-Harrison J., Kumar A. RA and Flavell J.A.; RT "The Ty1-copia group retrotransposons in Vicia species: copy RT number, sequence heterogeneity and chromosomal localization."; RL Mol. Gen. Genet 250(3), 305-315 (1996). XX RN [2] RP 1-231 RA Jurka J. and Drazkiewicz A.; RT "RT_VF: a Ty1/copia-type retrotransposon, RT gene from Vicia RT faba."; RL Direct Submission to Repbase Update (18-SEP-2002). XX DR [2] (Consensus) XX SQ Sequence 231 BP; 93 A; 31 C; 45 G; 62 T; 0 other; ggaacttgaa gaagaaatat atatggagct accagctggt tatgaaaaaa aaggaaaaga 60 aaaccaggtt tgcaaattga aaaagtctct atatggtctg aaacaagcac ctagagaatg 120 gtatgagaga ttaacctcgg ttatgattaa acatggctac aaacagacca acatcagatc 180 actcattatt tgttaaaaag tttgaggaaa atgatttcat cattttgtta t 231 // ID Gypsy8-VV_I repbase; DNA; EDCOT; 4436 BP. XX AC . XX DT 10-SEP-2007 (Rel. 12.09, Created) DT 10-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW internal portion; Gypsy8-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4436 RA Obukhanych T. and Jurka J.; RT "Gypsy8-VV."; RL Repbase Reports 7(9), 832-832 (2007). XX DR [1] (Consensus) XX CC This is a internal portion of Gypsy8-VV LTR retrotransposon from CC Vitis vinifera. Its individual elements are 82% similar to their CC consensus. LTRs of this retrotransposon, deposited as CC Gypsy8-VV_LTR, are 96% similar to each other. Target site CC duplications are 5 bp-long. XX FH Key Location/Qualifiers FT CDS join(941..1561,1565..3088) FT /product="Gypsy8-VV_I_1p" FT /translation="MPRTATTVVGRELHSKDKEDDVDEEIEEQPAIKEQTE FT PEISLHALTGWSTPKTMRITAKIGPHEVVVLIDSGSTHNFISERVAEMLHL FT PVVPTKPFTVKVANGEPLKCQGRFENVQVILQGIPFSFTLYSLPLTGLDMV FT LGVQWLEQLGTVVCDWKKLTMEFQWENQTHKLQGIDXQPIQAASLKAVSKE FT IRQGNSMFAICLQSAIKSTTXYSSRHAAIVXRIRGHFSRAKSSLPPAREID FT HHITLKEGTEPINVRPYRYAYFQKAEIEKQVHDMLKLGLIRPSTSPFSSPV FT LLVKKKDGTWRFCTDYRALNAVTIKDRFPIPTVDDMLDELYGATYFTKLDL FT RAGYHQVRVHPPDIPKTAFRTHNGHYEYLVMPFGLCNAPSTFQAIMNSIFR FT PYLRKFVLVFFDDILIYSPNWNMHXEHVKQAFEILRQHQFFVKISKCAFGQ FT QELEYLGHIVTPQGVKVDXGKIKAMLNWPRPTNISELRGFLGLTGYYRKFV FT RNYGIIARPLTNLFKKGQFGWTEEAETAFQALKQAMTSTPTLAMPNFNEPF FT IIESDASGDGIGAVLTQQGKPIAFMSRALGVTKQSWSIYAKEMLAIVQAIR FT TWRPYLLGRKFYIQTDQRSLKYFLEQRIATPEQQEWVAKLLGYDYEITYKP FT GRENSAADALSRVVSSPSLNAFFVPQATLWDEIKKEANEHPYMDKIDKLAN FT WPRKILEHLTHGEMG" XX SQ Sequence 4436 BP; 1414 A; 904 C; 951 G; 1143 T; 24 other; ttggtatcag agccaggtta cactgatggc aaccaacaaa gaaagaatyg agcatttgga 60 ggctgggcta ggaggacttc aagacrgaat gagtcgaatg gagctgggta tgactgacaa 120 gctgcatcaa ctggaggaaa ctatcaacag gctatctgaa gttttgcttt ccaacaaaga 180 aggatccagt agcaacacca atgatcgtaa tggtcgtgtc cgcaacaata gagacaactc 240 taaggaaaaa atggaagggg gacaacaaat gttctcwtcc aagttggcaa agcttgaatt 300 tccaaggtat tctggagatg atccaacaga atggttcaac cgtgtggacc aattctttga 360 atatcaaggc actccagaag cmcaaaaggt gtctttagct tcatttcatt tggaaggtga 420 agctaatcaa tggtggcagt ggttkcgcag ggcctaccat gaagaaggga aagaagtggc 480 gtgggcagat tttgaagagg aactctgggc tcgttttgga cctacagagt gtgaagattt 540 tgatgaggct ttatcaagga taagacagat gggatcattg cgtgactacc aaagggaatt 600 tgaaaggtta gggaatcgag ttcaaggatg gacacaaaag gctttggttg gaacgtttat 660 gggtggtctt aagtcggaaa tagccgatgg cattcggatg ttcaagccca aatcattgaa 720 agaagccatc agtttggcaa gaatgagaga tgatcagcta actcgacata agaagattca 780 cacgaccttt gcaacccaac tgcccgcagc ctractcttc tactcaaatg aaatccaagc 840 caacaccaac catgaaacga ctcacttggg aagaaatgca gaaaaggcga gctcaaggcc 900 tatgtttcaa ttgtgatgac aaattcaccg caggtcacaa atgccaagga ccgcaactac 960 tgttgttgga agggaactcc attccaagga taaggaagat gatgtagatg aggagatcga 1020 agaacagccc gctatcaagg aacaaactga acccgaaatt tcactccatg ctctaactgg 1080 atggtcaacc cccaaaacca tgcggatcac ggctaaaatt ggaccccatg aggtggttgt 1140 cctaattgat agtggatcaa ctcacaactt tattagtgag agagtagccg aaatgttgca 1200 cttaccagtg gtgccaacca aaccattcac tgtcaaagtg gctaatggag aaccactaaa 1260 gtgccaaggg aggtttgaga acgtgcaagt catattgcag ggtattcctt tttcttttac 1320 tctttattct ttaccactaa cwgggttgga catggtgtta ggagttcaat ggcttgaaca 1380 attgggtaca gtggtttgtg attggaagaa actgacaatg gagtttcagt gggaaaacca 1440 gacacataaa ctacaaggaa ttgataamca acccattcaa gctgcatcat tgaaagctgt 1500 ttcaaaagaa atacgacaag gaaattctat gtttgcaatc tgcctacaat cagccatcaa 1560 atgaagtaca acaagstatt catctagaca tgcagcaatt gttncaagaa ttcgaggaca 1620 tttttcaaga gccaaatcaa gcctaccacc agcaagagag attgaccacc acattactct 1680 caaagaagga accgagccca ttaatgtgcg gccctacagg tatgcctatt ttcaaaaagc 1740 tgaaattgaa aaacaagttc atgacatgtt aaaattgggg cttataagac caagcactag 1800 tccattttca tctcctgttt tattggtaaa aaagaaagat ggaacttggc gtttttgtac 1860 tgactataga gcacttaatg ccgtaaccat caaagatcga tttccaattc caacagttga 1920 tgatatgcta gatgagctct atggggcaac ttattttact aaacttgatc tccgagctgg 1980 ataccatcag gtacgggtac atccaccaga tattcctaaa actgctttcc gtactcacaa 2040 tggtcattac gaatatttgg ttatgccttt tggcttatgt aatgcacctt ctacctttca 2100 agctattatg aattctatat ttcgaccata tcttcgaaaa tttgtgttag ttttttttga 2160 tgatatttta atttatagcc ccaattggaa catgcatwtt gaacatgtta aacaagcttt 2220 tgaaatatta aggcaacacc aattctttgt taaaattagc aagtgtgcat tcggccagca 2280 agaattggag tatttgggtc atattgtgac tccacaaggc gtaaaggtgg atsaaggaaa 2340 aattaaagct atgctaaatt ggccaagacc tactaatatt tctgaattrc gtgggttctt 2400 aggcctaaca ggttattata ggaagtttgt tcgtaattat ggcattatag ctcggccwct 2460 caccaatctc ttcaaaaaag gacaattcgg atggacagag gaagccgaaa ctgccttcca 2520 agctctcaaa caggccatga cttcyacccc tacacttgct atgcctaatt ttaatgaacc 2580 ttttatcatt gaatctgatg cttcaggaga tggaattgga gcagttctaa ctcaacaagg 2640 aaaaccaata gccttcatga gtcgagcctt gggagtgact aagcaatcat ggtccatcta 2700 tgccaaagaa atgctggcca ttgttcaagc catwcgaact tggcgacctt atttgttagg 2760 ccgaaaattc tatatccaaa ctgatcaacg aagcctcaaa tattttctag agcaacgaat 2820 agcaactccg gagcaacaag aatgggtggc aaaattgctg gggtatgact atgaaatcac 2880 ttacaaaccg ggacgggaga actcagcagc tgatgctcta tcaagagtgg taagcagtcc 2940 tagtcttaat gctttttttg ttccacaagc tactttatgg gatgaaatca aaaaagargc 3000 taacgaacat ccatacatgg acaaaattga caaattggca aattggccac ggaaaatcct 3060 ggagcacctt acacatggcg aaatgggcta gtatgctata aaaagcgagt ggtgattcct 3120 ccaaactctc cgataatcaa gccaaattat tgcaagaatt ccatgattca ccaatkgggg 3180 gccattcagg ggtgttacgg acatacaaaa ggttggcaca acaattctat tggccatcaa 3240 tgcataaagt agtgcaagac tatgtcacgt catgtgatgt atgccaaaaa attaaagctg 3300 aaactttagc tccagctgga cttcttcaac cattgcccat tccatgccaa gtatgggatg 3360 acatcaccat ggattttatt gaggggctac caacttccaa tggcaagaac acaatccttg 3420 tggtggtcga tcgcctgagt aaatcagctc atttttttgc tttawctcat cctttcactg 3480 caaaaatggt agctgaaaaa tttgttgagg gagttgtcaa gcttcacggc atgcccaaat 3540 caatcattag tgatcgggat ccaatcttca tcagccaatt ttggcaagaa ttcttcaaga 3600 tgtcgggcac caaactgaaa atgagttctg cctaccaccc gcaaacggat ggccaatctg 3660 aagtcgtcaa ccgatgtgtc gaacaatatc ttcgctgttt tgttcatcaa cagccacgaa 3720 aatggagctt ctttcttcca tgggcagaat tttggtacaa cacaacttac cacacctcaa 3780 cagggatgac accttttcaa gctctgtatg ggcgtctacc accaaccatt ccacactatc 3840 tagatgggca catctccagt tcatgaagtg gaccaaactc tcgtatccmg agatgcaata 3900 ttacgccaac tcaagatcaa tttacatgct gcaatcaatc gaatgaaaca ggtggcagac 3960 tcaaaaagaa gagatattga gttccaagta ggcgatatgg tcttccttaa gctacatccw 4020 tatcgccagc aaacggtctt tagaagagct tatcaaaaat tagccagtcg attttatggc 4080 ccttatcaaa ttgaagaaaa aattggaaag gtagcataca aattaaagct cccagaagga 4140 tcccaaattc accccgtttt ccatgtttca ctgcttaaac gaagaaattg ggggagccta 4200 acaatacyac ggttgagttg ccaycttact gatgatgaag gagaaattat cctggaacct 4260 gaagctattt tggatacacg ctgggttaag aaaggatcac gtattgttga agaaagcctg 4320 gtgcaatgga aacaacttcc actagaagat gctacgtggg aggatacaaa aatgctgcag 4380 gataagttca ttaatctgaa ccttgaggac aaggttccac tgcaagasgg gggtat 4436 // ID HELMET repbase; DNA; EDCOT; 7018 BP. XX AC AC148291; XX DT 18-DEC-2006 (Rel. 11.12, Created) DT 09-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE A helitron sequence form Medicago truncatula. XX KW Helitron; DNA transposon; Transposable Element; Nonautonomous; KW transposon; Interspersed; repeat; HELMET. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-7018 RA Jurka J. and Shankar R.; RT "HELMET: A helitron sequence from barrel medic."; RL Direct Submission to Repbase Update (18-DEC-2006). XX DR EMBL/GenBank/DDBJ; AC148291; Positions 74268 81285. XX CC The 5' terminal end of the sequence seems to be truncated. XX FH Key Location/Qualifiers FT CDS 3777..4994 FT /product="HELMET_1p" FT /translation="MFTVIYTIEFQKCGLPHAHILVFLKPTYRCKKPKDLD FT KIISAEIPNKDTDGELFNIVTTLMIHGPCGDQNTRSPSMLNNKCSKHFPMK FT FVDQTVIDKDGYPVYKRRDNGVYVKKGECFADNRFVVPYNKTLLLKYKAHI FT NVEWCNQIRSIKYLFKYVNKGHDRVTANFYGNGCENSLDEIKMYYDCRYLS FT ACEAAWRIFSFDINYREPSVERLNYHLENEHSVLYEENDDIEQVIERSHRK FT TTKFLAWMKANEKYPEARNLTYNQFPTQFVWKEKDHEWTPRRCGFSIGRVH FT FAPPGSGERFYLRTLLNYIKGPTSFNDMKTVDDVKYNTFKEACFAMGLLDD FT DKEFIDAIIEASLWGTGIYLRRLFVALMVTDQFARPEVVWNSTNENLIDDI FT LHKQRRLLGAPG" FT CDS 5448..6083 FT /product="HELMET_2p" FT /translation="MLQSFGKSLSDFPPMPKADASLVPDVESRLIHDEMSY FT NRPVLAAQHDRMMSTMTLEQRNVYDKIMTRVKEDKSGLFFLYGYGGTGKTF FT IWRALCAALRSDGGIVLACASSGIAALLIPDGRTAHSRFGIPFTIDECSMC FT GVTPNTPLASLLIKAKLIIWDEAPMMHKHCFEALTQLGKSMMSTYLLLSRP FT TCLFQVQVILLHLSLIALTQIC" XX SQ Sequence 7018 BP; 2185 A; 1223 C; 1169 G; 2441 T; 0 other; taacaatgat tttctaactt cgctcctcct aaaacctatc taattgattt ccataaacca 60 tatctcctaa ctcccctcca aactctcacc aatatatttt aatcctttct cctaaaccga 120 aatctctttc taaaaccata cctttctctt aagtcgaaat ttcttaatca acatggcttc 180 cagaaacatt cagactttgc tgtcaaacta ctgcctcatg gtaaccatat cttcatttca 240 ctctggttta tactaaatat atagactttt gctcttattc cttgctgttg taaagtataa 300 atcattcttt ccatcccttt taatcttttg taggtccgtt ggtgaaaaac cctatttccg 360 atcttgacaa agcaatcaac aagctgagac tgaaatacag atcatatatc gttgaatatg 420 acattgatgc tgtatgtgtt ttttgcaaaa tatacctatt cttaattatt tgcattctat 480 tttatcaact tttgtgatgt ttttgtttgt tattttttta gggtgcagta tgcttgccaa 540 acatgtttgg cggtgatttt ggagatcaaa ttgggcgcta tgcaatattg actgatccac 600 ttttattctt taacttcttt tattcctttt ccgcttagtt gatataagtt acatggattt 660 ctaattttgc agattctact ttacaccggc aatgttccgc aaatgcttga tacactcaag 720 acaactgtga atattatcga cgattgcgct aacttatggg tgtgtgagct aacttttgca 780 acttttcctt atgaacactt caagatagga tggcgttgga ataggtttgt ggaagctcgc 840 aggctccgtg aaggtgtgag atcagagggg gtgctccgat ggttgggtca catgatacca 900 tctaccttga tgttatttac aattagtcca tgtttagata aattgtgcaa cacctttcca 960 ctttgaattt taagttttag tttcttagag ttttggaagc atctattttt ttgtctttga 1020 atttagcaaa tgtcccttga atttcagaaa taatttagtc ttgcttgctt tagtttttga 1080 tttatatatt tgtgtttgtg ctgctcaaac tatatttagt agcattgctg tgttattgaa 1140 gcattttagt agcatagctt ttagtaacat tattagtaac aattactacc ttttggtgac 1200 acttttagta acattattac ttacaattac taatcctaat ctctaaaata tgttttgggt 1260 ggaatcaaac taaaatccta atcctaattt ctctcattca agtaattaag aaatttcatc 1320 cacatctcta aagtaacttt ttggtggaaa caaactaatt aaaatcctta tttctctcat 1380 tcaaataatt acgggatttc atccacatct ctaagatatg ttttgggtgg aaacaaacta 1440 aaaatcctaa ttcctctcat tcaagtaact actaaagatt tcatccacgt ctctaaaata 1500 ttttttaagt ggaaacaaac taaaatccta atcctaattt ctctcattca agtaaccaag 1560 agatttcatc cacatctcta aagtaacttt ttggcggaaa caaactaaaa tccttattta 1620 tctcactcca ataagtaggg gatttcatcc acatctctaa aatatgtttt gggtggaaac 1680 aaactaaatt cctaatccta atttctctca ttcaagtaac taagagattt catccacatc 1740 tctaaagtaa ctttttggtg caaacaaact aaaatcctta tttctctcat tcaaataatt 1800 aggggatttc atccacatct ctaaaatatg ttttgggtgg aaataaacta aaaatcctaa 1860 ttcctctcaa gtaactacta aagatttcat ccacatctct aaaatatgtt ttgggtgaaa 1920 acaaattaaa atcctaatcc taatttctct catgtaacta agagatttca tccacatctc 1980 taaactaact ttttggtgga aacaaactaa aatccttatt tctctcattc aaataagtag 2040 gggatttcat ccacatctct aaaatatatt ttgggtggaa acaaactaaa aatcctaatt 2100 cttctcattc aagtatctaa gagatttcat ccacatctct aaagtaactt tttggtggaa 2160 acaaactaaa atccttattt ctctcattca aataagtagg ggatttcatc cacatctcta 2220 aaatatgttt tgggtggaaa caaactaaaa aacataattc ctctcattca agtaactact 2280 acacatttaa tccacatcta tgttttggcg agtcaactat ggtaattctt aagtcaaaaa 2340 aaaatgcccc atcaaaaata ttaatttcat tttatacata ttaatcttta tccaaaaatg 2400 ttgagcataa ttttattcca cttcaactag atccctttgt tctgcgcccc ttccctattt 2460 acatgtcaat tcttaagtaa aacaaagtgc cccatcaaca atattaattt cattttattc 2520 atattaatct ttatcctaaa atgttggcca cttcctaatt ttgttccact tttttgtgct 2580 tatcctgata actaatactc tttattgcta aaccgacata tcctactaac acgtattgca 2640 cctttttcct tcaagttgct ctgtcagcta tatttgctta tctatggaaa ctttttccag 2700 tccacctaaa taaatttatt cattggcata agtattattt caaaaattta ttatcattgt 2760 cttttatcag cgcttcgacc tctaaaagta caaaatttat ttttcgatct acctccgaaa 2820 gatgttaata tttttctgaa tgttaaaaaa gcaatagata tagagattta gatccatatt 2880 gtgcttttat gaatgttact tcaaaattaa ctcgtggtaa ttgtggagtg caagcctaac 2940 atgcacccct ccaaagtcac tctatccatg acgaggttta ccttaatttt gtagagacta 3000 ttgatgtttc tgctaaatat tttttctttc tttcttttct tcggtgactt gacatctttt 3060 cctttttaag tagacagaat gcttgacatg tcttttatta tgaaatctgt tatacaaatt 3120 gtctttgatc tatagtctaa gtcgtgcttg agttgtcaaa gatgaaaatg taaatttgat 3180 caatattcaa tgtttatagt ttcttatgtt aggacatctg taatatggga ggatggttgt 3240 tgtgcaaata attcattcct ttagcctgac aagagcgaag taaatttaca ttgaatagag 3300 gaaagtggta aataatatct aaaattaaaa tgacagattt tggagatcac ctaaatagta 3360 aaaaatatat aataatacaa atacacaaac tgatgttttt cattttacag atactttaca 3420 ataatcatat acaaactgat ctaaagcaaa tggtgaacaa aaatactaaa taggtggaag 3480 ttttataggt ggaagttgta tcgctatttt gtccttatat tatatataaa acacgatgca 3540 aacacttgaa tatatttcaa ttggttccat tcagcacatt gatgaaatag gatgttaatc 3600 catgtcgtgt ttttagcgta tccaacgtaa atataatgtt tgtaagaggt cttttatact 3660 caatatttta tagttagctt atatcgatct tccacgaagt taaatgacat ttgtacaatc 3720 ctttcttttt ttggattaat ttaccatgaa gttagcttat atcgattttc catgttatgt 3780 ttacagttat atatactatt gaatttcaaa aatgtggact accgcatgca cacatactgg 3840 tgtttttgaa gccaacttat cggtgcaaga aacctaagga tcttgataag attatatcag 3900 cagagattcc aaacaaagat acagatgggg agttatttaa tattgtgact acgctcatga 3960 ttcacggccc atgtggtgac caaaacacaa gatcgcctag catgctaaat aataaatgta 4020 gcaagcactt tccaatgaaa tttgttgatc aaactgtgat cgataaagat ggttatccag 4080 tttacaagag aagggacaat ggagtttatg taaaaaaagg agagtgcttt gcagataata 4140 ggtttgttgt gccgtataat aaaacactcc tcttgaagta caaagcccat atcaatgtag 4200 agtggtgcaa ccaaattcgg tcaatcaagt accttttcaa atatgtaaac aaaggacatg 4260 atcgcgtcac cgcaaacttt tacggtaatg gatgtgaaaa tagtttggat gagataaaga 4320 tgtattatga ttgtcggtat ttgtccgcat gtgaagcggc ctggagaata ttctcttttg 4380 acataaatta tagagaacct tcggtggaac gcttaaatta tcatttggaa aatgagcatt 4440 cagttttgta cgaagaaaac gacgacattg aacaagtcat tgagagatcg catagaaaaa 4500 ctacaaagtt tttggcttgg atgaaagcaa atgaaaagta tccagaagct agaaatttga 4560 cttacaatca attcccgacc cagttcgtgt ggaaggaaaa agaccacgaa tggactccta 4620 gacggtgtgg tttttcgata gggcgggtcc attttgctcc gcctggttcc ggcgaaaggt 4680 tttacctaag aactctcttg aattacatca aaggtcctac atctttcaat gacatgaaga 4740 cggtcgatga tgtcaaatat aatactttca aggaagcctg cttcgctatg gggttactcg 4800 atgatgacaa ggagtttata gacgcgataa ttgaagccag tctttggggc actggtattt 4860 atttacgtag actattcgta gcactgatgg tgacagatca atttgccaga ccagaggtcg 4920 tgtggaattc tacaaacgaa aatttaattg atgacatact ccacaaacaa aggcggcttc 4980 ttggagctcc aggataattt tagtgcatat ttattttttg taattacata tgaattatat 5040 tggttccttc tttttttttc aaataattat ccatttctca ccttacatgt gtatgtattt 5100 aaaccaatat aaatacggtt gtttcttcag attacatgca atgacattcg tgtatctaat 5160 tttggttcca tgtttgtgcc aaatatttgt tatactcata gtttgcttat attatgaagg 5220 aaaaactatt tacatcacag aaatttattt gttcaagttt aaaaaaaaaa aaataacatg 5280 catcgacacg tctgtttatt atgagaaatg acatgaacat tgttgttttt acatggatat 5340 tttcaattta caagtcacgc tgatttttaa caaaccttat ttgtttccca aatttacggt 5400 tgactcatga gcagttgaag gcgtatgcgt tggccgaact agaaacgatg ttgcaaagtt 5460 ttggaaagag tttgtctgat tttcctccaa tgccaaaggc ggatgcatct ttagtaccgg 5520 atgtcgagag taggttgatt cacgatgaga tgagttataa taggcctgta ctagctgctc 5580 aacatgaccg gatgatgtca accatgactt tagagcaacg taatgtatat gataaaataa 5640 tgacaagagt taaggaagac aaatctgggt tgttcttcct gtatggttat ggtggtactg 5700 ggaaaacatt tatttggagg gctttatgtg ctgctttgag gtctgatggt gggattgttt 5760 tggcatgtgc atcaagtggg attgctgcct tgcttatacc cgatggaaga actgcacatt 5820 caagattcgg tatccctttt acaatagacg aatgctctat gtgtggagtt acaccaaata 5880 caccgttggc atcgctgctg atcaaggcta aacttatcat atgggatgaa gcgccaatga 5940 tgcacaagca ttgtttcgaa gcacttaccc aattggggaa atcaatgatg tcgacatatc 6000 tgttgttatc ccgtccgact tgcttattcc aagttcaggt aatcctgttg catctatcgt 6060 tgatagcact tacccaaatt tgttaggaaa cattggtaaa gcaaaatatt ggcgccaaag 6120 aataccattg ttgaacaggt taatgattat gtgttcaact tgattcctgg tgaagaaaaa 6180 atctatttga gttatgatac accttatcat aaaaacatag atggtgacgc cgtagatgac 6240 atccacactc ctgaattcct caacaccatt gtggcgtccg gatttccaaa tcatcggttg 6300 cgactgaaag taggagcacc tgtcatgtta ctcaggaaca tggatcaaag tttgggctta 6360 tgtaatggta cgagattgat cattacaaag atgggaaaat tcgtgctcga agaacgggta 6420 atatctggtt ctaatatcgt tgagaagatg tttattccaa ggttatcgct aacaccatct 6480 gataatagaa ttcctatcaa atttaaacga aggcagtttc tgatatttgt ctcatttgca 6540 atgactatta acaagagtta gggtcagtcg ctagaacatg ttggtgtcta cctaccgtct 6600 cctatttttt cacatggaca gttgtacgtc gcaatatcac gggttacttc gaggggtggt 6660 ttaaaaatat tgattgctga cgacgacggc gatgatatcg atgttgcatc aaatgtggtc 6720 tacagagaag ttttccgtaa tgtgtaggac ttttttgtgt actgttcatt ttcttactta 6780 ttgaaactat ttgcatgtca acgaacttca atttcccttt caaaattata tgttatttta 6840 aagtaacagg aactacgtac tagaattatg gaacaataac aaagtctttg atattgacat 6900 tttgctttga ttcacgacaa tttttagatt cacgcgaact acagtgtctt attttttcag 6960 tgaatattat attttttaaa tgacacgtgt gttagcacgg gtcaatggtc tagtaaat 7018 // ID Copia-48_VV-LTR repbase; DNA; EDCOT; 597 BP. XX AC chr19; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-48_VV_; KW Copia-48_VV-I; Copia-48_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-597 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr19; Positions 4825762 4825166. XX SQ Sequence 597 BP; 143 A; 99 C; 112 G; 243 T; 0 other; tgttgggttt cccttatttg tgggactctt aaatttacta aatatggttt ttctattttt 60 ggccaacacc ttggttagca catgactctt ggcatattca agattggttt gaagtcttca 120 aagaaagaaa aaaaaactac aagtcttttg tcttttcctt tggtttatta tcttggtcgg 180 caagaagact tttgggatac ctttttggtt caaacaaaac aaaaagaaaa ttcagccttc 240 ttcttctcaa tttttttggt gctacacaat cagcaagttt gttcttcaag tgggtaacgt 300 tccttcactt gatatttggg gtttcttgcg gtttgttctt agagatttgg tttacttttg 360 tgaggtattt tcctcttgta atttacacct tggtgtgttt gtaaggctta tgccttttgg 420 ccactttgta aactcttttg gtgatagtgg aagaaactga cctaccagtt gtcgtggacg 480 tacctcaagt tatttaaggg aaccacgtaa atcttgtgtg ctcatttatt ttctgttatt 540 ctatttatat tacttccatt gatttacact tgtgggaaag cctagttttt ttcaaca 597 // ID Copia-7_TC-LTR repbase; DNA; EDCOT; 266 BP. XX AC CACC01015606; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-7_TC_; KW Copia-7_TC-I; Copia-7_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-266 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01015606; Positions 3283 3018. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 266 BP; 53 A; 44 C; 46 G; 123 T; 0 other; tgttttgtgg ccatgaaagc cactactctg atgcagtttt cttttttatg tatgtgaagt 60 tcatggacag tagttatttt ttagtttgta ggtttgcacc atgaactgac agttaagttc 120 agttttaatt ttttttttct cttcttcatg tattaatgct atgttgaagt tacgaatgaa 180 gttgtctgtt agccttcttt cttctgcgga caacttttat tttttctgct tgctcttgct 240 ctctgttttc ttatcaagtt ccaaca 266 // ID Copia-34_Mad-I repbase; DNA; EDCOT; 5338 BP. XX AC ACYM01063166; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-34_Mad-I; KW Copia-34_Mad-LTR; Copia-34_Mad_. XX NM Copia-34_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5338 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1304-1304 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01063166; Positions 259 5596. XX CC Positions [2702-2965] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 558..2000 FT /product="Copia-34_Mad-I_2p" FT /translation="MNNPTVKVENLLGMLTIKLKDDNFAKWAFQFKAVLMG FT YKLFGHFDSTDVCPSKFVLSTDLGVTKEITKAYVDWESTDMALISLLLATL FT SDEAMEYVLGCKNAHEAWVNLVDRVASVSKSRVNHLKTELHTIQKGTDSID FT KYLLRLKNIREQLSAAGEYVSDNDVIIAGLDGRPKDYAIIRTIILAKESSI FT TLKKFRAQLLGAEKEIDGEINMLSQSLSTLYVKGTGTHPGSSMVNGSSSNP FT QNHTHIPASTGGVLSQVPYPLSSQFQPNMQSSQFYSTQQPPDIFYTPAPYG FT FGFFENSGSYSDTRNQSSNSGFRSFNGSNSKGQHNYRSNNGYKGKSFHSGG FT YRQNSNNNGWSGNTDTRMNVVIECQICNKRGHTSANCFHRNNNNSTSGFVI FT ECQICGKMGHVALNCHHQSNYSYQSQSPPFSITALNAQQSSQFMPTDSWIV FT DSGASHHMTADVNALAQLLHMKEMRQLLLVMVLVYQ" FT CDS 2753..4282 FT /product="Copia-34_Mad-I_1p" FT /translation="MLSCPYTPQQNGIAERKHWHIIETSITLLTNVALPLE FT FWYIACAHSVFLINRMSCKSLSMVSPYTLLYKKLPNLKFLKTFGTAVFPWL FT RPYNSNKLQTRSTLCVFLGYSSGYKGVICYDLVSKKCIISRHVIHNEMMFP FT GKQRLQHQVNAPVVDQKATHSPILVHVPVTQTSSTHEVNQIHSENDRIASS FT SVDQSETSSSSSGHSQSQSTSGHTLSTTSDTTLLLPVLSPDQLQVILPLSL FT NSYPSGIEHTTTSTHVHQSSGIQTRLQTGALSRKNYAAYSATFPEIAYLEV FT MDDFSSGFSFLVDITNIEEPKNFKTASVKAEWQRAMQDEFDAIKAQGTWCL FT VPPPVDRSIVGNKWVYKIKKNPDGSISRYKARLVAQRYSQEQGLDYSETFS FT PMVRHTTVRMILALAVQFVWSLRQLDIKNAFLHGELEEEVYMKQPQGFVDS FT QHPNYVCKLIKSLYGLKQAPRAWNSKFTIYLPTLGFVTSLSDTSFLLKKIM FT GMLFSSCYMLMTSL" XX SQ Sequence 5338 BP; 1580 A; 951 C; 1057 G; 1750 T; 0 other; tggtatcatc gccggatagg ttcgtcgccg caccgatgaa ttttccgttg ctctggaaga 60 ttgaagacgc tttgttgtct gcaatttcga aggtctcgat tacggaaggc tgttgaagtt 120 gggtgtgtcc ttcgatcgtt gaaattgatt caagtgacat ctttctttcg gtgggttgaa 180 gctattttga tcatgggtat tggtttttta agagtcttga agaaagtttt tggtgtaaaa 240 tttgagaaat ttgatgattg actgtatagt cgaatgttca taaggttttg atgaagaaat 300 aattgtgaag ttagagtatt tgagaaagtg ttattctttc ttgctcattt tggaaagtgt 360 caacctttca tggtaaaaag tttcagtctc ttcgacaagt gttattcttt cttgttaatt 420 ttggaaagta tcaatctttc ttagtaaaga gtttcagtct cttcgaagtc ttgcagtttg 480 tttcaattgc aaagagtgtc aatctcttcc ttttcattac atatctggag ttttgtgtat 540 ctgtgatcta agtcaagatg aataatccga ctgttaaagt agaaaatttg ttggggatgc 600 ttactataaa attgaaggat gataattttg ccaaatgggc atttcagttt aaagctgtgt 660 tgatgggtta taaattgttt ggtcatttcg atagcactga tgtgtgtcca tcaaagtttg 720 tgttgtctac tgatcttgga gttaccaagg aaattactaa agcgtatgtt gattgggagt 780 caactgatat ggctttgata agtcttttgc ttgcaacgtt atctgatgaa gcaatggagt 840 atgttctcgg atgcaagaat gctcatgagg cttgggtgaa tcttgtagat agggttgctt 900 ctgtatcaaa atcaagagtg aatcatctaa agactgagtt gcatactata caaaagggaa 960 ctgactcgat tgataagtat ctgctgagat tgaaaaacat tagagagcag ttgagtgctg 1020 caggggagta tgtctcagac aatgatgtta tcattgccgg attggatggg cgaccaaaag 1080 actatgcaat aatcagaact attattcttg ctaaagagtc atcaattact ctcaaaaagt 1140 tcagagcaca acttcttggt gctgaaaagg aaattgatgg tgaaattaat atgttgtctc 1200 aaagtttgtc aaccttatat gtgaaaggga ctggtactca tcctggatct tcaatggtca 1260 atggttcttc ttctaatcca cagaatcata ctcacatccc tgcttctacc ggtggtgttt 1320 tatcacaggt tccttatcca ttgtcatcac agtttcagcc taatatgcag tcctctcagt 1380 tttattctac acaacaacca cctgatatat tttatactcc tgcaccatac ggttttggtt 1440 tcttcgaaaa ttctggttct tattcagata caagaaatca aagctcaaat tctggtttca 1500 gatctttcaa tggctctaat tctaagggtc aacacaatta ccggtccaat aatggataca 1560 aggggaagag ttttcattct ggaggatata ggcagaactc aaataacaat ggttggtcgg 1620 gaaacacaga cacaaggatg aatgtagtga ttgaatgtca aatctgcaac aaacgaggtc 1680 atacatcagc aaattgtttt cacaggaaca acaacaattc aacttctggt tttgtgattg 1740 aatgtcaaat ttgtggaaag atgggtcatg ttgctcttaa ttgtcatcac caaagcaact 1800 actcctatca aagtcaatcc cctccgtttt ccataactgc gttgaatgca caacagtcat 1860 cccagtttat gcctactgat tcatggatag tggattctgg tgcttctcat cacatgacag 1920 ctgatgttaa tgccttagca cagttgctcc atatgaagga aatgagacaa ttactattgg 1980 taatggttct agtatatcaa taaaaaacac tggttctacc actcttcata caaaggacaa 2040 atccttatta cttactcatg ttttacatgt tccaaagatt gctcgaagtt tgttgtctgt 2100 taaacaaata tgtgctgata ataacagttg gtttatttgt gatgagtcca atttcttttt 2160 acaggacaag aagacaaagg aggtcctgta tcacggaaag agtaggccta aggagttgtt 2220 tcagattcca gtttttcata gtgctaaagg tgtgcagtct acatttccca ctacaacagc 2280 tttgcttggt caattagtga agtcaaatat gtggcatcaa agattgggtc accctacaaa 2340 tgaagtactt tcttgtatgt taatacagtg tagtatatca tataaaccag atgataagca 2400 cagtatttgt acatcgtgta ttcagggcaa aatgtctaga ttgccatttc atgtaagaac 2460 tgaaaaatgt ttgtctccat ttgataagat tcactctgat gtttggggac cgtttcctat 2520 aaagtctgta gatggctata ggcattatgt actgtttact gatgaatata caagatacac 2580 ttaggtactt ccaatgtgca ataaatctga tgtcttctct atttttgtaa agttttatca 2640 gtttgtatta acccagtatg gagtgtcagt catgtgttta caaactgatg ggggaggata 2700 gtacgttagt aatgctttta caaagttctt agatgataaa gggattgctc agatgctgtc 2760 atgtccatat acccctcagc aaaatggaat tgctgagaga aaacactggc atatcattga 2820 aacttcaatt acattactca ctaatgttgc tctaccattg gagttttggt atattgcttg 2880 tgcacactca gtatttctta tcaatcgaat gtcatgcaag tctctatcta tggtttctcc 2940 ctatactctg ctatacaaga aacttcctaa cttaaaattc ttgaaaacat ttggaactgc 3000 tgtgtttcct tggcttaggc cttataattc taataagctt caaacaagat caacattgtg 3060 tgtctttctc gggtactctt caggatacaa aggtgtaata tgttatgatc tagtgtccaa 3120 gaaatgcatt atttctcgac atgtcataca caatgagatg atgttccctg gtaaacaaag 3180 gttacaacac caagtcaatg ctccagtggt tgatcaaaag gctacacatt ctcccatttt 3240 agttcatgtc cctgttactc agacttctag tactcatgaa gttaatcaga tacacagtga 3300 gaatgataga attgcatctt cttcagttga tcaatctgag acgtcaagtt caagctcagg 3360 gcattctcaa agtcaaagta catcgggcca tactctttcc acgacaagtg atacaactct 3420 tttgcttcct gtcttgagtc cagaccaact ccaggtaata cttccactct ctttaaattc 3480 atatccatca ggtatagaac atacaaccac atctactcat gtgcatcaaa gttctggaat 3540 tcaaacaagg ctacaaacag gtgcactttc aagaaagaac tatgcagcat attcagcaac 3600 ttttcctgag attgcttatt tggaggttat ggatgatttt tccagtgggt tttcattctt 3660 agtggatatc actaatatag aggagcctaa aaattttaaa actgctagtg ttaaggctga 3720 atggcaaaga gccatgcaag atgagttcga tgctataaag gcacaaggaa cttggtgttt 3780 agttcctcct ccagttgaca gaagtattgt tggaaacaaa tgggtataca aaattaagaa 3840 gaaccctgat ggatcaattt ctaggtataa ggctcgacta gttgcacaac ggtatagcca 3900 agagcaaggt ttggactatt ctgaaacgtt tagtccgatg gtgagacata ccactgtcag 3960 aatgatttta gctttagcag tacaatttgt ttggagttta aggcaactag acattaaaaa 4020 tgccttctta catggagagt tagaagagga agtctatatg aagcagcccc aagggtttgt 4080 tgattcacaa catccaaact atgtttgcaa gttaataaag tcactttatg gcttgaaaca 4140 agccccacga gcttggaatt caaagtttac tatctaccta cctactttgg ggtttgttac 4200 atccttatcc gatacaagtt ttttgttaaa gaagatcatg gggatgttat tctcctcctg 4260 ttatatgttg atgacatcat tgtgaccggt tccaatgctt caaagattca atcagtgatt 4320 aaaagccttg ctgcagtatt tgatcttaaa gatatgggaa aacttaccta ttttcttggt 4380 cttcatatcc agtataatca agatgggttt atattcatta atcagtctaa atatgctcga 4440 gatttgttga aaaaggctgg tatggaacat tgtaaaccta catctacacc ctctaaacct 4500 catactcagt tgcttgaatc tgaaggcata ctaatgacag atcctactct ttatcgaagc 4560 ttggtgggtg ctttacagta cttaacattt tctagacctg atatagcata ctcagtgaat 4620 atggtatgtc agtttatgga cactccaaca gattcacact ttcatttggt caagagaatt 4680 ctgaggtatt tgcaaggtat tctcacttat ggtttgaaat atacaaaggg tgaagatata 4740 tttatagctg cctattcaga ttcagactgg gcagcatata tcaatactag gagatcaata 4800 acccggtatg tggtatactt atgatctaat cctatctcat ggcagtccaa aaagcaatcc 4860 actgtctcac gcagctcaac agaggcagaa tataaggcaa tagctctgtg tgtagctgat 4920 gtttgttgga ttagatcagt gctcagagat atgcatcagt gtcttccctc acctcctcat 4980 ctttactgtg acaacttgtc agcacttgct atatgttcga atcttgtttt tcattctaag 5040 atcaaacatc tcgacactga ctatcacttt atgagggaga aagtacaaaa aggtgatctg 5100 cgtgttcaat acattcccac agaagagcaa gttgttgatg tcctaactaa aggattacat 5160 agccctgttt ttgtgaagca ttgtcacaac ttgagcttag gatcacaatc tgcaatctcc 5220 aatattacag tttcgagttg attcacttac acaatagcat tacagggttg tgtttttgta 5280 gattcaaact ttgctaagtt gtaccctagc acaatttgag ggggggagta ttagccat 5338 // ID Copia17-PTR_LTR repbase; DNA; EDCOT; 252 BP. XX AC LG_X; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia17-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-252 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-252 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 207-207 (2007). XX DR Genome; LG_X; Positions 4558415 4558164. XX SQ Sequence 252 BP; 77 A; 38 C; 44 G; 93 T; 0 other; tgtggaaatc agtctcaaaa tcagttagga tcttagagaa atcttagtat atatggttta 60 ggaaagagaa tctggtatta actatccaga ttctctagat tattgctttc tagtttagtg 120 gaggatactt tcctatctag tatttatttc ttgttttgag ggtcagtagg ttagcctctc 180 ttccctattt attgtacaaa catactgcta gtaatatcaa gaaaagagaa agacttctct 240 caaaattctt ca 252 // ID MTCOPIA1_I repbase; DNA; EDCOT; 4442 BP. XX AC CT963078; XX DT 29-DEC-2006 (Rel. 11.12, Created) DT 05-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE Copia-type LTR-retrotransposon - internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW internal portion; MTCOPIA1_I. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4442 RA Jurka J.; RT "MTCOPIA1: Copia-type LTR-retrotransposon from barrel medic."; RL Repbase Reports 6(12), 630-630 (2006). XX DR EMBL/GenBank/DDBJ; CT963078; Positions 1 4442. XX CC This is a very young element, LTRs are identical. XX FH Key Location/Qualifiers FT CDS join(72..2585,2589..3206,3210..4439) FT /product="MTCOPIA1_I_1p" FT /translation="MVRGNTAANGGANGGTMIPPPLDPSQQPGNVYYVHSS FT DGPSSVTVTPVLNNSNYHYWARSMRRALGGKNKFDFVDGSIPVLMEFDPSF FT KAWNRCNMLVHSWIMNSVEDSIAQSIVFLENAMDVWNELKERFSQGDYIRI FT SELQCEIFGLKQDSRSVSEFFTALKVLWEELEAYLPTPVCACPHRCTCNTG FT VLNAKHQHEITRSIRFLTGLNDQFDLVRSQILLMNPLPTLNKIFSMVLQHE FT RQFRVSIPVDESKILINSVNKFQGRGRGNGSTSGGAKRSCSFCGRSNHTVD FT TCYKKHGFPPNYGKNFATANNSSLEMHEEREDLDDSKSCKGSDSFSMTKEQ FT YEHLVNLLQTQQSSSSKVNHVTNHVTSGISTLSYALNHCSFGSWIVDSGAS FT DHICSSIKAFDSYQSIKPVHIKLPNGNITIAKISGTVQFSSGLVAKNVLYV FT ADFKLNLLSVPKLCVDDDCIVTFDNDKCLIQERRNLKMTGLADLIEGLYFL FT TTQASPSTKPQSVIASINSQSSSFLPQEALWHFRLGHLSNHRMISLKQSFP FT CIKIDDNSVCDICHYSRHKKVPFHLSVNKANKCYEMFHFDIWGPVSIPSIH FT GHKYFITALDDHSRFTWIILCKSKSEVQKHVQNFIIMIENQFGCHVKTIRT FT DNGPEFLMSEFYSSKGIEHQTSCVETPQQNGRVERKHQHILNVARALLFQS FT KLPKQFWSYSVLHAVYIINRIPTPLLQNKSPYFLRFGNNCDFNDFKVFGCL FT CYASTLHNHRTKFDSRAKKSLFLGYKQGVKGAILFDLNTKIIFVSRHVTYH FT EHILPYSNSNQPFQWQYHSNQPISSAIEPVTNLNTNNESTVTKPINPEDSE FT SEISSNIELDDHIQPHSQTLPEPDSLSLRKSTRPIQKPTYLPDYVCNLSKE FT SDNSSSSGILYPITHYHSLNSLSPSHQKFALAVTNAAEPTSYNEASKQECW FT VKAMESELDALKHNKTWIFVDSPPNIKPIGSKWVYKIKHKADGSIERYKAR FT LVAKGYNQVEGIDFFDTFSPVAKITTVRTLLALASINSHLHQLDVNNAFLH FT GDLSEDVYMTIPQGVVNTKPNQVCKLLKSLYGLKQASRKWYEKLTSFLISQ FT GYKQSASDHSLFTLHSDSMFTALLVYVDDVILAGNSMDEINKIKVTLDAEF FT KIKDLGQLKYFLGIEVAHSKLGISICQRKYCLDLLHDTGLLGSKPVSTPLD FT PSIKLHQDTSKAFDDIFSYRRLVGKLLYLTTTRPDIAFVTQQLSQFLSAPT FT ITHYEAACRVVKYLKGTPDQGLLFRRDSILQILGFTDADWAGCPDTRRSTS FT GYCFFLGSSLISWRAKKQHTVSRSSSEAEYRALSFASCELQWLLYLLKDLG FT VSCIKSPVLYCDNQSAIHIAGNPVFHERTKHLEIDCHFVRERLQQGLFKLL FT PIKSQSQLADFFTKPLPLKNFHSFISKLNMLDLYHAKLEG" XX SQ Sequence 4442 BP; 1341 A; 864 C; 766 G; 1471 T; 0 other; tggtatcaga gctcttttga gctctgctgc gcatcgttct tgcttcgctt cttcttcttc 60 tttgttttac gatggttcgt ggaaacaccg ccgctaacgg tggtgcaaat ggaggaacca 120 tgattcctcc acctcttgat ccttcgcaac aacctggtaa cgtgtattac gttcattctt 180 ctgatggtcc ttcctccgtc actgttactc cggtattgaa caactcaaac tatcactatt 240 gggcgcgttc aatgagaaga gctttaggag gaaagaacaa gtttgatttt gtggatggat 300 caattccagt tcttatggaa tttgatccaa gtttcaaagc atggaatcgt tgcaacatgc 360 ttgtacattc atggatcatg aattctgttg aagattctat tgcacagagt attgtgtttc 420 ttgagaacgc catggatgtt tggaatgaac tcaaggaacg gttttctcaa ggtgattaca 480 ttcgaatttc tgaattgcaa tgcgaaatct ttggattaaa gcaagattcg cgttcagttt 540 ctgagttttt cactgctttg aaggttctat gggaagaact tgaagcatat cttcctactc 600 cggtttgtgc ttgtccccat cgttgtacgt gtaatactgg tgtgcttaat gctaagcatc 660 agcatgagat tacacgctct attagattcc ttactggtct caatgatcaa tttgatcttg 720 tacgttctca aatcttgttg atgaaccctt taccaactct caacaagatt ttttcaatgg 780 tattacagca tgaaagacaa tttagagttt ctattcctgt tgatgagtca aaaatcctta 840 tcaattcagt gaataagttt caagggcgag gacgtggcaa tggaagtact tctggtggtg 900 caaagcgttc ttgttccttt tgtggacgaa gcaatcatac tgttgatact tgttataaga 960 aacatggttt tcctccaaat tatggtaaga attttgctac tgctaacaat tcctcccttg 1020 agatgcatga agaaagggag gatcttgatg attcaaaaag ctgcaaagga agtgattctt 1080 ttagcatgac aaaagagcaa tatgaacatc ttgttaatct tcttcaaact caacaaagtt 1140 cttctagcaa ggtgaaccat gtcactaatc atgtgacatc aggtatatcc acactttcat 1200 atgctctgaa tcactgcagt tttggttcat ggatagttga ttcaggagca agtgatcata 1260 tatgctcatc tattaaagct tttgattcct atcaatctat taaacctgtc catattaagt 1320 taccaaatgg taacataact atagcaaaaa tctctggcac agtgcaattc tcttcaggac 1380 ttgttgccaa aaatgtgtta tatgttgcag acttcaaatt aaatcttttg tctgtaccca 1440 aactatgtgt tgatgatgat tgcatagtaa cttttgataa tgataaatgt ttaatacagg 1500 aaaggaggaa cttgaagatg actggtttgg ctgatttgat agagggattg tatttcctga 1560 ccactcaagc ttccccatcc accaaacctc aatctgtcat agcttctatc aactctcaaa 1620 gttcttcttt tctacctcaa gaagccttat ggcattttag attgggtcat ttgtccaatc 1680 atagaatgat tagcttaaaa cagtcttttc cttgtattaa gattgatgac aattcagttt 1740 gtgatatatg tcattactct agacataaga aagttccttt tcatctcagt gtaaataaag 1800 caaacaaatg ctatgaaatg tttcattttg atatatgggg tcctgtttcc attccttcta 1860 ttcatggtca taaatatttc attactgctc ttgatgatca cagtcgtttt acctggatca 1920 tcctatgtaa atcaaaatct gaagttcaaa aacatgttca aaatttcatt atcatgatag 1980 aaaatcagtt tggttgtcat gttaaaacta ttaggacaga taatggtcct gaatttctta 2040 tgtcagaatt ctattcttct aaaggcattg agcatcaaac aagttgtgtt gagactcccc 2100 aacaaaatgg gagagtagaa agaaaacatc aacacatctt gaatgtagct agagctttac 2160 ttttccaatc aaaattacct aaacagttct ggtcttattc agttttgcat gcagtttaca 2220 taataaatag aattcctact cctctgctgc aaaacaaatc cccttatttt ctcagatttg 2280 gtaataattg tgatttcaat gatttcaaag tctttggttg cctttgttat gcctctacct 2340 tacataatca tagaacaaaa tttgattcta gagccaaaaa gtctcttttc ttaggataca 2400 agcaaggtgt taaaggagca attctttttg atcttaacac caaaatcatt tttgtgtcca 2460 gacatgtaac ctatcatgaa catattcttc cttactctaa ttcaaatcaa ccttttcaat 2520 ggcagtacca ttcaaatcaa cctatatctt ctgccattga acctgtcacc aatctcaaca 2580 ctaattaaaa tgaatccact gtaaccaaac ccattaaccc tgaagattct gaatctgaga 2640 tatcttccaa cattgaactt gatgatcaca ttcaaccaca ttcacaaact ttacctgaac 2700 cagattcttt atctcttaga aaatcaacca gacctataca aaaaccaacc tatctgccag 2760 attatgtatg caatctctct aaagaatcag acaattcatc atcttcaggt atactttatc 2820 ctattactca ttatcattca ctcaatagtt tatccccttc acatcagaag tttgctctag 2880 ctgttactaa tgctgctgaa cctacaagtt acaatgaagc aagcaagcaa gagtgttggg 2940 ttaaggctat ggaatctgaa cttgatgctt tgaaacacaa taaaacttgg atttttgtgg 3000 attcaccacc caatatcaaa cctattggta gtaaatgggt gtataaaatc aaacataagg 3060 cagatgggag catagagagg tacaaggcca gactggtggc taaaggttat aatcaagttg 3120 aaggtattga tttttttgac actttttcac cagtagccaa aattactact gtcagaactc 3180 tccttgcctt agcatcaatc aactcatagc acctacacca attagatgtg aacaatgctt 3240 ttctccatgg agacttatct gaagacgttt acatgactat tcctcaaggt gttgtcaaca 3300 caaaaccaaa tcaagtgtgt aaattgttga agtctcttta tggtttaaag caagccagca 3360 gaaaatggta tgaaaaattg actagtttct taatcagtca aggttacaaa cagtctgctt 3420 ctgatcattc cctcttcact cttcattcag attctatgtt cactgccctt cttgtgtatg 3480 tggatgatgt cattttagca gggaattcaa tggatgagat caataaaatc aaggttaccc 3540 ttgatgcaga atttaaaatc aaggatcttg gtcaacttaa atatttcctt ggcatagagg 3600 tggcacattc taaacttgga attagtatat gccaaagaaa atattgtctt gatcttcttc 3660 atgatacagg cttacttggt tcaaagccag tttcaacacc acttgatcca tctataaaac 3720 tacaccaaga cacttcaaaa gcttttgatg atatttttag ctatagaaga cttgtgggaa 3780 aactcttgta tctcaccaca accagaccag acatagcctt tgtaactcaa caactaagtc 3840 aatttctgtc agctccaacc attactcatt atgaagcagc ttgcagagtt gtcaagtatc 3900 tcaaaggtac ccctgatcaa ggtttattat tcagaagaga ttcaatttta cagattcttg 3960 gttttacaga tgcagattgg gctggatgtc ctgatactag aagatccact tctggttatt 4020 gtttcttcct tggatcttca ctcatttcat ggagagctaa gaaacagcat acagtttcta 4080 gaagttcatc tgaagctgaa tacagagcac tttcctttgc tagttgtgaa ttacaatggc 4140 ttctatattt gttgaaagat ttgggagtgt catgcatcaa gtcacctgta ttgtactgtg 4200 ataatcagag tgcaatacat attgctggga atcctgtgtt tcatgagaga acaaaacact 4260 tggagataga ttgccatttt gttagagaaa gattacagca gggtcttttc aagttgcttc 4320 ctatcaagtc tcaatcacaa cttgcagatt tctttactaa gcctttgcca cttaaaaact 4380 ttcattcttt catttccaag ctcaacatgt tggacttata ccatgctaag cttgagggag 4440 gg 4442 // ID Copia-1_Mad-I repbase; DNA; EDCOT; 4232 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-1_Mad_; KW Copia-1_Mad-LTR; Copia-1_Mad-I. XX NM Copia-1_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4232 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1648-1648 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1382-1882] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 728..4222 FT /product="Copia-1_Mad-I_1p" FT /translation="MAVWTCDSANTGNDGKALKVSASVTNNTWIIDSGATE FT HMTCDSRQVQTLKPSTKTVVSVANGNPAPVIGEGTVSLSDTLSLDTVLVVP FT SLDYNLLSVAQITVVLHCLVIFWPSFCVFKDIRTRKTIGYGIRKGKLYYLE FT LTSNSSRMLTQALAVEGNPGDRNKASEVWLWHRRLGHASFGYLRRLFPSLF FT VKHDVSSFKCGVCELAKSHRASFPSSLNKSSVPFMIIHSDVWGPSKTATFG FT GAHWFVTFIDDCTRMTWVCLMKSKGEVTSLFQQFYKMVQVQYKSQIQVLRS FT DNGGEYVNSELRAFLDHHGIVHQTTCPYTPQQNGVAERKNRQLLEVVRASL FT LEARLPLSYWGEALTSAAYLINRVPSRSVDFQTPLQALSSHVDAPAVPNLP FT PHVFGCVAFVHLHKQQRSKLEPRALRCVFVGYASRQKGYRCYHPPTNKLFV FT TMDVAFHENDMYFANPESSLQGENQKEVQTLDYTIPDIDRVNDLDLSGDVL FT EISGDHSHENNDVNELELSGNVLETSGDHSHGNNVENLERDESTSPDNSLP FT DSSLPVSSPPDSPVSPATSQSILSPNNHNQSSSIPDAPPPRRLPDRVNRGI FT PKLTYEADPKCKTRYPVSKPNPESNVLYPLSNYVSTSHLSESNKSFVHQLS FT TVSIPNSVQEALTDPRWQVAMNEELKSLKKNATWEITDLPAGKKPVGCKWV FT YTVKYKADGTVDRFKARLVAKGYTQKYGIDYTDTFAPVAKINTVRVLLSLA FT ANLNWPLQQFDVKNAFLHGDLTEEIYMDLPPGCNAPDKYKRKVCRLKKSLY FT GLKQSPRAWFGRFTKSMRAFGYRQSNSDHTLFLKRQNGKLTALIVYVDDMV FT VTGNDPEERAALQRYLSTEFEMKDLGSLKYFLGIEVSRSSSGIFLSQRKYI FT IDLLHETGMSACQPVATPLEEGLKLSVDPNQVPVDKGRYQRLVGRLMYLAH FT TRPDLAYALSVVSQYMHDPGEQHMNAVMRILRYLKGSPGKGILFKRNNHFS FT VEGYTDADWAGSIDDRRSTSGYFTFVGGNLVTWRSKKQNVVARSSAEAEYR FT GMALGICEILWLKLLLSDLGIQHDQPMKLFCDNKAARDIAHNPVQHDRTKH FT VEVDRFFIKEKLEGKIIEVPAIRTEDQLADILTKAVSSHKFSSFLHKLGMS FT DIYAPT" XX SQ Sequence 4232 BP; 1178 A; 850 C; 979 G; 1224 T; 1 other; ttctcttctt ggcaccagag cctaggttga aaaaaaaaag gaaaaaaaaa cccatagccg 60 cgatagcacc gttgcgctca gccatktgtg gtgcgccgcc tcgaccagcg agcgactgcc 120 gtcgttgctg ccccatctga attcgaaacg aacagcgagc gacgccgtcg ttgctgaccc 180 gaatccatcg aaccgcaact ctcgtcgttc accaagacca actgcatctg cttctgattt 240 gatccgaagc cgcgaaaaat tgcacagact gcaacccgac gaattgtgtt gctgcgccgt 300 acccgactcg aggtccgcga cccacgagcc tgctctcatc cgacttgctg atctgaccag 360 tccgccacag cactgttgca cccctgtctc gcacctcgaa ctgcaatctg tccttgctgc 420 tgttgtcctt gttgaagtct tgcacatcca ctgctgctgt ttcgaagtgg aagaaaggaa 480 aaagaaaagg aaaaaaaaaa agaaaaaggg aaaaaggaaa agattggtgg tgttaaaaaa 540 aaaaaaatgg ttatttgatt aaggcccaca cggcaaggaa agaaaaattg tttttttttt 600 ttatagatcg ttattgtttt tgttgggcta tccttcttgt tggcccgtgc aattcttggg 660 ctcggtttgc ttggaaattt gggctttatc aatcaccgag tgacgtattg attgaagtcg 720 cttgggaatg gcagtctgga cttgtgattc tgctaataca ggtaacgatg gtaaggcttt 780 aaaggtttct gcctctgtta cgaataatac atggataatt gattctggtg ctactgaaca 840 tatgacttgt gattctagac aggtacaaac cctaaaacca tccaccaaaa ctgtcgtcag 900 tgtcgccaat ggtaatcctg cccccgttat cggggaagga accgtctccc tttcagatac 960 ccttagtctt gataccgtac ttgttgttcc ttctcttgac tataatttat tatctgttgc 1020 tcaaataact gtcgtcctgc attgtcttgt gattttttgg ccttcttttt gtgtttttaa 1080 ggacattcgg actcgcaaga cgattggtta tggtattagg aaggggaagc tctactactt 1140 ggagctgaca tcaaacagtt ctcgaatgtt gactcaagct cttgcagtgg aaggaaatcc 1200 gggggatagg aataaagctt cggaggtttg gttgtggcat cgtcgacttg gacatgcttc 1260 tttcggctat ctacggaggt tgtttcctag cctatttgtt aagcatgatg tttctagctt 1320 taaatgtggt gtttgtgaac tagctaaaag tcatcgtgct tcgtttccat ccagtttgaa 1380 taaaagttct gttccattta tgataattca ttctgatgtt tggggtccat ctaaaactgc 1440 tacatttggt ggtgctcatt ggttcgttac ttttattgat gactgcacac gtatgacttg 1500 ggtttgtttg atgaaatcca aaggtgaagt tacttctttg tttcagcagt tttacaaaat 1560 ggtacaagta caatataagt cacaaataca ggttctcagg agtgataatg gtggcgaata 1620 tgttaactct gaacttcgtg cctttcttga tcatcatggg attgttcatc aaactacatg 1680 tccatatact ccacaacaaa atggggttgc cgaacgcaag aaccgtcagc ttctggaggt 1740 tgttcgtgct tctttactcg aggctcgtct cccgttatcc tattggggag aagctctcac 1800 ctcagctgcg tatctcatta atcgtgttcc atcccgatcg gttgattttc agacacccct 1860 tcaggcactt tcttcacatg ttgatgctcc tgcagtccct aatcttccac ctcatgtgtt 1920 tggttgtgtg gccttcgttc atcttcataa acaacagcga agtaagcttg aacctcgagc 1980 cttacgatgt gtgtttgtgg ggtatgcatc aaggcagaaa ggataccgtt gttatcaccc 2040 accgacgaat aagttgtttg tcactatgga tgttgcgttt catgagaatg atatgtactt 2100 tgccaatccc gagtcttcac ttcaggggga gaatcagaaa gaagttcaaa ctcttgatta 2160 tactattcca gatatagata gagtgaatga tttggattta agtggtgatg tcttggaaat 2220 aagtggtgat cattcacacg aaaataatga tgtgaatgaa ttggaattaa gtggtaatgt 2280 cttggagaca agtggtgatc attcacatgg aaacaatgtt gaaaaccttg aaagggacga 2340 gtcgacatcg ccagataact cactgcctga tagctcactg ccagtttcct caccaccgga 2400 cagccctgtg tcgccagcta cctcacagtc gatcttgagt cccaataacc ataatcaatc 2460 gtcttcgatc ccggatgcac caccaccacg tcgtctccct gatcgcgtca accgaggtat 2520 tcctaaactt acttatgaag ccgaccctaa atgcaaaact aggtatccgg tgagtaagcc 2580 caaccctgag tctaatgtgt tatacccgtt aagtaattat gtgtctacca gtcacctgtc 2640 agaatcaaat aagtcgtttg tgcatcaatt atctactgta tctattccta acagtgtgca 2700 ggaggcttta actgatccac gttggcaagt agcaatgaat gaagagttga agtctttgaa 2760 gaagaatgct acctgggaga tcacagattt gccagctggc aagaaacctg tgggatgcaa 2820 atgggtctat actgtgaaat acaaagcaga tgggacggtg gatcgtttca aggcaagact 2880 ggtagcaaaa ggatacactc aaaaatatgg aatcgactac acagatacat ttgcacctgt 2940 agccaagatc aacacagttc gtgttttgtt gtccttggct gcaaatctta attggccctt 3000 acaacagttc gatgtgaaga acgccttctt gcatggagac ttgacagaag agatttatat 3060 ggatcttcca ccgggatgta atgctccaga taaatacaaa agaaaagtgt gcaggttgaa 3120 gaaatccttg tatggcttga agcagtcccc tcgagcatgg ttcggaagat tcacaaaatc 3180 tatgagagca tttggttaca gacaaagtaa ctctgatcat actttgttcc tgaaaagaca 3240 gaatgggaag cttactgcac ttattgtgta tgtagacgat atggtggtaa caggtaatga 3300 tccggaagaa cgtgcggcct tgcaaagata cctgtctaca gaatttgaaa tgaaggacct 3360 tggatccctg aaatattttt tagggattga ggtgtcgaga agcagttctg gaattttctt 3420 gtctcagagg aagtatatta ttgatttgtt gcacgaaact ggcatgtcag cttgtcagcc 3480 agtagctaca ccattagaag aaggattgaa gcttagtgtt gatcctaatc aagtaccagt 3540 tgacaaagga agataccaaa ggttagtagg ccgtttgatg tatttggcac acacaagacc 3600 ggaccttgct tatgccttga gtgtagtgag tcaatacatg catgatcctg gagaacaaca 3660 tatgaatgcc gtgatgagaa tattgcgata tttgaaggga agtccgggca aaggaatttt 3720 gtttaagagg aataatcact ttagtgttga aggttatact gatgcagact gggcaggttc 3780 cattgatgat agacgctcaa catcaggtta ctttacgttt gttgggggta acttggttac 3840 atggagaagt aagaaacaga atgtggttgc ccgttccagt gcagaagcag aatacagagg 3900 tatggctttg gggatttgtg aaattttgtg gcttaagctt ctgttaagcg atttgggtat 3960 acaacatgat cagcccatga aattattttg tgataataaa gctgctcgtg acattgcaca 4020 taatccggta caacatgata gaacaaagca tgttgaagtt gatcggttct tcatcaaaga 4080 aaaattggaa gggaaaataa ttgaagtacc ggcgataaga acagaagatc agttggcaga 4140 tatcctcaca aaagctgttt cgagtcacaa gttttcaagt ttcttacaca agttgggcat 4200 gagcgacata tatgcaccaa cttgaggggg ag 4232 // ID Copia15-VV_I repbase; DNA; EDCOT; 5415 BP. XX AC AM451502; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia15-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5415 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-5415 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 708-708 (2007). XX DR Genbank; AM451502; Positions 22737 28151. XX CC Positions [2417-2911] - Integrase core CC 'GTGT' target site duplication CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS 1379..3292 FT /product="Copia15-VV_I_1p" FT /translation="MMLSETFQVAAIIEKLPPAWKDFKNYLKHKRKEMSIE FT DLIIRLRIEEDNRRSEKKGAHTLNEAKANFVEHGQSSKAKTNNNKGKGSKL FT GPKGGISKKPKFQGKCFNCGKQGHKSVDCRLPKKNKPKEANVIDDITKNVS FT DIDLTAVVSEVNLVGSNPKEWWIDTGATRHVCSDKKMFSTFEPIENGEKVF FT MGNSATSEIKGQGKVILKMTSGKELTLTNVLYVPEIRKNLVSGSLLNNHGF FT RLVFESNKFVLSKSGMYVGKGYMSDGMWKLNVMTIIKSNMNKASTSTYMLE FT SSNLWHGRLGHVNYDTLRRLINLNHIPTFQINSNHKCETCVEAKLTRSSFQ FT SVERNTEPLDLIHSDICDLKFVQTRGGNKYFITFVDDSTKYCYVYLLKSKD FT EAIEKFVLYKNEVENQLNKKIKVLRSDRGGEYESPFVDICAQHGIIHETTA FT PYSPQSNGVAERKNRTLKEMMNAMLISSSLPQNMWGEAILTANYLLNKVPK FT KKAEKTPYELWKGRKPSYTYLRMWGCLAKVAVPPPKKVKIGPKTIDCIFIG FT YAHNSNAYRFLVYESNIPDIHKNTIMESRNASFFEDVFPCKSKEEPSSSKR FT MLETINENSQDQNEEVEVEPRRSKRVRTEKSFGPDFLTFM" FT CDS 3347..4300 FT /product="Copia15-VV_I_2p" FT /translation="MWKEAIKSEIDSILQNHTWELVDLPPGCKPLSSKWIF FT KRKMKVDGSIDKYKARLVIKGYRQTEGLDYFDTYSPVTRINSIRMVLAIAA FT LRNLEIHQMDVKTAFLNGDLDEEIYMEQPEGFSAPGQEKKVCKLVKSLYGL FT KQAPKQWHEKFDNVMLSHGFKINECDKCVYVKDTEHGYVIVCLYVDDMLIV FT GSDDKMITSTKNMLNSRFDMKDMGLADVILGIKIKRTSDELILSQSHYVDK FT ILGKFDKDNSGVARTPVDVTLHLSKNKGESVSQVEYSRVIGSLMYLMSCTR FT PDIAYAVSKLSRYTSNPGAKHWQGKL" XX SQ Sequence 5415 BP; 1914 A; 826 C; 1127 G; 1517 T; 31 other; gtgtggttgt ctaacattct taaaacagat tttttcaaag gaaaaccagt ggattggtga 60 aaaggaaama aagttatcag aaagaagaag aagaagaaga agaagaaaaa aaaaaaaacc 120 cstgswwgtk wwkacgaaaa aaaaaaaaaa attaaattac aatttgtaat tggaaaaata 180 aataaataaa taatcttgtt gtttaagttt tccgggaaaa caaacaaaca atttggtttg 240 ttgttttcgk tttcggraaa aaaaaaaatt ttcgaaagaa aaaaaaaaaa aaataagttt 300 gttgaaattg ggtttatctg aagaaaaaaa aaaaaaaaat atctggaaaa ttttwttttt 360 tcaaatttgt gtttttttta gaagagaaaa aaaaaaaaaa aaacaaccat ttgttacaaa 420 aagaagtttc gaactcttaa cctgarccct ttttctcatg ctcaactcag tawgacacca 480 ttggactrtg actcatkttt tttttattat tattatggga aaaaatacct tcttataaag 540 tttgtaccaa gtcttttgaa aatttggaaa ttatgataca ragaagttct gtctaaggta 600 attggaattt aagcgggacc atttgtgacc cctccaattt cctgggaact gaatattctg 660 tctaaggaag ctagtcctgg tctgggtcat tataccccac tagtctttcc tgggaatact 720 ctgtaaagtg attttcagtt tttttgaagt tttttttttt tggaaaaaaa aaraaaaagg 780 raaaaagaaa aagaaaaaaa gaaaaaagrg aaaaagaaat tgacacattt tcttggatgt 840 ttcagaaaaa atgacaactg aatccgataa cgttgttgta actgaattag ccccagtggc 900 aacccctact gtggcccaag tgccagcgat gcctactgct gtaccaatct ytgtctcacc 960 aggagaaaaa ccagagaagt tcagtggact aaattttaaa aggtggcaac aaaagatgtt 1020 attctatttg accacgttga atcttgcaag attcttgact gaggatgctc ctaagctcaa 1080 agaagacgag cacgatatcc aagtcatcag tgctatarat gcttggaaac attctgactt 1140 cttgtgtaga aattatgtca tgaatggttt agctgattcg ttgtacaatg tttattctga 1200 caagaaaaca gctaaggagc tatgrgaatc tctagaccgg aaatataaaa ctgaggatgc 1260 cggggctaag aaatttgttg tgggtcgctt cctcgactat aagatgrtag attccaagac 1320 tgtggtaagt caagtccaag aacttcaagt aatcttgcat gagatacatg ctgagggaat 1380 gatgttgagt gaaactttcc aagtagcagc tattattgag aaactacccc ctgcttggaa 1440 agattttaag aattacctca agcacaaaag aaaggaaatg agcatcgagg atctaattat 1500 tagacttcgc attgaagaag ataatagaag atctgaaaag aaaggggcgc acactctaaa 1560 tgaggccaag gctaactttg tggaacatgg tcaaagttcc aaggcaaaga cgaacaacaa 1620 caaagggaaa ggatctaagt tgggacctaa aggagggatc tcaaagaagc cgaaatttca 1680 agggaaatgc ttcaattgtg gtaagcaagg tcacaagtct gttgattgta gactgcccaa 1740 aaagaataaa cctaaggaag ctaatgtgat tgacgacatc actaaaaatg tttctgacat 1800 tgacctcaca gcagtagtct ctgaggtgaa cttggtgggt tctaacccaa aggaatggtg 1860 gattgatact ggtgctactc gccatgtatg ctctgataag aaaatgttct ccacttttga 1920 accaattgag aatggggaaa aagtgttcat ggggaactct gccacctctg agatcaaggg 1980 tcaaggtaaa gtaatcttga agatgacttc tgggaaagag ttgactctga ccaatgtttt 2040 atatgtaccg gaaattcgca agaacttggt gtctggttca ttgctgaata atcatggatt 2100 tcggttggtc tttgagtcaa acaaatttgt tttgtccaag agtggaatgt atgttgggaa 2160 agggtatatg agtgatggaa tgtggaaact caatgtaatg actattatta agtcaaatat 2220 gaataaagct agtacttcta cttacatgct tgagtcttct aatctatggc atggtagatt 2280 aggacatgtt aattatgata cattacgtag attaattaac ttaaatcata taccaacatt 2340 ccaaattaat tccaaccata aatgtgaaac ttgtgttgag gcaaaactaa caaggtcatc 2400 ttttcaaagt gttgaaagaa acactgaacc ccttgatttg atccatagtg atatctgtga 2460 tttgaaattt gtacaaacaa gaggtggtaa taaatatttt attacttttg ttgacgatag 2520 caccaaatac tgttatgtgt atttactaaa aagcaaggat gaagctatag agaaatttgt 2580 tctctataaa aacgaagttg agaatcaact caacaagaaa attaaggtac taagaagtga 2640 tcgaggtggt gagtatgaat cgccatttgt tgacatttgt gctcaacatg ggattataca 2700 cgaaacaaca gcaccttatt cgcctcaatc caatggagtg gctgagcgaa agaatcgtac 2760 cttaaaggaa atgatgaatg caatgttaat aagttctagt ttgccacaaa acatgtgggg 2820 agaagccatt ttaactgcta attacctttt gaataaggta cccaaaaaga aagcagaaaa 2880 gactccatat gagttatgga aaggaagaaa gccatcctac acatacttac gaatgtgggg 2940 atgtcttgct aaagtggcag ttcctccacc taaaaaggtg aaaataggac ctaagactat 3000 tgattgcatt ttcattggct atgcacataa tagtaatgct tatcggtttc ttgtttatga 3060 atcaaatatc ccagatattc ataagaacac gataatggaa tcaaggaatg catcattctt 3120 tgaagatgta tttccatgta aatccaaaga agagccaagt tcatcaaaaa gaatgcttga 3180 gactattaat gaaaatagtc aggatcaaaa tgaagaagtt gaggtagaac ctagacgtag 3240 caaaagggta aggacagaaa agtcttttgg tccagatttt ctaactttta tgyttgaagg 3300 cgaacctcaa acttttaaag aggcagtgaa ctctayagaa ggtcttatgt ggaaagaggc 3360 cattaagagt gaaattgatt cyatattgca aaaccatact tgggaactag tggatcttcc 3420 accaggttgt aaacctttaa gttccaagtg gattttcaag agaaagatga aagtagatgg 3480 atcaattgac aagtataaag caagacttgt aatcaaaggc tacagacaaa ctgaaggcct 3540 agattatttt gacacatatt ctcctgtgac gagaataaat tccataagga tggtacttgc 3600 aattgctgca ttgagaaatc ttgaaataca tcaaatggat gtaaaaacag cctttctaaa 3660 tggagattta gatgaagaaa tctatatgga gcaacctgag ggtttttcag ctccaggaca 3720 agaaaagaaa gtttgtaaac tggtgaaatc tttgtatggc ttaaaacaag caccgaaaca 3780 atggcatgaa aaatttgaca atgttatgct gtcacatggc ttcaaaatca atgaatgtga 3840 caagtgtgtt tatgtcaagg atacagaaca tggatatgtc attgtatgtt tgtatgtaga 3900 tgacatgctt attgttggta gtgatgataa gatgatcaca tctacaaaga acatgttgaa 3960 ttcaaggttt gacatgaaag acatgggact tgctgatgtt atattgggaa taaaaatcaa 4020 aagaacatca gatgaactca tattaagtca gtcacattat gtagacaaaa ttcttggaaa 4080 gtttgataaa gataattctg gagttgctag aacaccggtg gatgtaactc tacatttgtc 4140 caagaataaa ggtgagagtg tttctcaagt agaatactct agagtaatag gcagtctaat 4200 gtacttaatg agttgtacaa gaccagacat agcctatgcg gttagtaaac tgagtagata 4260 tacgagtaat cccggagcca agcattggca agggaaatta taagagtact aaagtactta 4320 cggtttactc gtgattatgg gctgcactat acgagatatc ctgctgtact tgaaggatat 4380 agtgatgcga attggatatc taatgttaaa gactcaaaat cccatagtgg ttatgtgttt 4440 acactaggag gtgcagcagt gtcgtggaaa tcctcaaaac aaacggttat tgccagatcc 4500 acaatggaat ctgaatttat agcactagat aaatgtgggg aagaggctga atggttacgc 4560 cacttcctag aggatattcc aaggtggtca aagcctgtgc ctccaatttg catacattgt 4620 gatagtcaat ctgcaattgg tagagcacag agtaatatgt ataatggtaa gtctagacac 4680 attcgtcgta gacacaatac cattagacaa ctactctcaa ctggggttat ctctgtggac 4740 tatgtgaaat ccaaagataa cattgcggat ccactaacca aagggttaaa tagagagtta 4800 gttgaaaagt catcaagggg aatgggacta aagcccataa aagaataagt caatacagtg 4860 gatacccaac ctagttgact ggagatcccg agatctaggt tcaaaaggga caactaaact 4920 gtaaagactt tgttaaatca ctgtggggat cttccctagt ccattcctat gataaaatag 4980 tgatgcccgt aagaggaaag ggtaagctat gctwttaatg atccttatgc ttcrgaaatc 5040 cgaacagagt aatgcgggtt actcgtgakt aagagatcac ctatgtaaga gtgaagtggg 5100 gccgcttcta agggaattga atagggcaca attcttatta aactcttaca gaaccaggcg 5160 tatgttcatg gccaaaatga acataaaagt gagaactgaa atttgttagg aagattcctg 5220 tgtgagatat gtcatcatct acataaatgg cagaacagtt caaggacatc gtgtctactg 5280 tttagctagt agagtaaaca tatttctaca agggaaggtt caaagggtaa cacctacctc 5340 tcctatgcag gtttcaaccg ttgtactcta tcacaaagtt catcgtgtct taatttcttt 5400 catktgggga attgt 5415 // ID Copia-61_Mad-LTR repbase; DNA; EDCOT; 519 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-61_Mad_; KW Copia-61_Mad-LTR; Copia-61_Mad-I. XX NM Copia-61_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-519 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1661-1661 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 519 BP; 136 A; 82 C; 122 G; 179 T; 0 other; tgtagtcaaa gtccaaatct ttgggctact tttgtggtca aaattgttgg atggcatgct 60 acatgtggga aaccaaaatt ggatgcactt atgcctaatt ctttttgact tgatgttagg 120 cctttggcca ttgatgtctt tgagaagctt ttctttggct ataaaaggag agcaaggtgc 180 agcccataag catggagaag tagagaagaa caaggaagag agaaaaatag caagaagcca 240 tttggcatag agaagaattt tctcaaattg tcttgctttg tatttttggt tttctcttcc 300 tattgtaagt gtgagagctt ggggttattt gggtctttgg gaaattgagt gataaacact 360 attgtatgtt ctcattgatt atagtggaat actccgtcgt ctccaaactg gatgtaggca 420 ttgccgaacc agtataaatc ttggtgttct tgttggtgtt ggttttattc tgttctgtct 480 tactattcac ttacagtcga atgccgcttc cgcacaaca 519 // ID Copia6-VV_I repbase; DNA; EDCOT; 4524 BP. XX AC AM431515; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia6-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4524 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4524 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 745-745 (2007). XX DR Genbank; AM431515; Positions 9011 4488. XX CC Positions [1989-2270] - Integrase core CC 'GGGGT' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 78..1985 FT /product="Copia6-VV_I_1p" FT /translation="MADIDPHSGEHSGESSILPSVLSELTARMTEALSKAP FT TSIPATDSAIAPIGIKLDGTNYALWSQVVEMYVAGKDKLGYINDDLPQPLT FT TDPSFRRWRTENATVKGWLIGSMDPSLIGNFIRFPTAKQVWDAIATTYFDG FT SDATQVYELRRRVARLRQGSGSLEKYYNDLQGLWREIDFRRPNPMQCPADI FT QHFNNMLQEDRVYTFLDGLDDKLDNIRSDVLQLKPFPTVEQAYAHVRREAV FT RQAVMTANNGEEAAGAVMASRSLKQGLSTAVNSLSLNGKFSKSNGPSNDMK FT CSHCGNSKHTRDTCFKLHGYPDWWHELQAKRQRDGNGKDGGASKNAANGTG FT KAAIASAESQLSLIPTTTVDLDTGMSFLGTNITESYDGWILDSGATDHMTY FT DASDFSERSSPRRTSIANANGDISLVKWAGTVMISPALSLTNTLFVPSLSH FT KLLLVSQVTKELNCIVLIYPTFCLLQDILTKEIIGRGTKKGGLYYMEDFSI FT GQANHTRSSSDRNKANILLWHRRLGHPSFGYLKLVFPALFSGLSNLDFKCE FT TCILAKSHRVSYPLSFNKSQMPFELIHSDVWGPSPKSTISGVQWFVIFVDD FT CTRMTWLYLMKNKDEVFSVFCSFHEMVKTQYSATIRIL" XX SQ Sequence 4524 BP; 1316 A; 930 C; 995 G; 1264 T; 19 other; tggtatcaga gcagaattcg atcctctacc ctctggtcaa ccaaatttct taaaaacaga 60 gcccaaactc ttttcacatg gcagatatag atcctcactc gggtgagcac tcaggtgaat 120 cttcaatctt gccatctgta ctgtctgaac taacggcaag gatgacagaa gctttgagta 180 aagctccgac gtccattcca gccaccgact cagcaattgc cccgattggc atcaaactgg 240 atggcacgaa ttacgccctc tggtcacaag tcgtagagat gtatgtcgca ggcaaggata 300 aactcggcta catcaacgac gaccttcctc aaccattaac aaccgaccct tccttccgta 360 ggtggcggac tgagaatgca actgtgaaag gatggctgat tggttcgatg gatccatccc 420 ttattggcaa cttcattcgg tttccaacgg ccaagcaagt ttgggatgca attgcaacca 480 cttactttga tggaagtgat gcaacccaag tttatgaact ccggcgacga gtggcgcgac 540 tcaggcaggg tagtggctct ctagaaaaat actacaatga tctccaaggt ctatggcggg 600 agattgattt ccgtcgtccc aatccaatgc aatgtccagc agatatccaa cattttaaca 660 atatgctgca ggaggatcgg gtatatactt ttcttgatgg tttggatgat aaacttgata 720 atattagaag tgatgtgttg cagcttaagc catttcccac agtggaacag gcatatgccc 780 atgttcgtag agaagctgtg cgtcaagcgg tgatgacagc caataatgga gaagaggcgg 840 ctggagcagt gatggcttca cgaagcctca aacaagggct ctccactgca gtcaactctc 900 tgtcattgaa tggaaaattt tctaagtcaa atggcccatc taatgacatg aaatgctctc 960 attgtggaaa ttcgaagcat actcgagaca catgcttcaa actacatggc tacccagatt 1020 ggtggcatga attacaagcc aagaggcagc gagatgggaa tgggaaagat ggtggagcta 1080 gcaaaaatgc agctaatggc acgggcaagg ccgcgatagc ctcggctgag tcccaattgt 1140 cacttattcc gacaacaaca gttgatttgg atacaggtat gagttttctc gggaccaata 1200 tcactgaatc atatgatggt tggattcttg attcaggggc gacagaccac atgacgtatg 1260 atgcaagtga tttttctgaa cgatcctctc ctcgacgtac tagcattgct aatgctaatg 1320 gggacatctc tttagtaaaa tgggctggta cagtgatgat atcaccagct ctctccttaa 1380 ccaataccct ttttgtaccc tcattgtctc ataaattatt gttagtgagc caagtcacga 1440 aggagttaaa ttgtattgtt ctaatttatc caaccttttg tcttcttcag gatattctca 1500 ccaaggagat aattgggcgt ggtactaaaa agggggggct ctactatatg gaagatttta 1560 gcatcggtca agctaaccat acgagaagct ctagtgatcg aaataaggcg aacattttgt 1620 tatggcatcg tcggttagga catccttcat ttggatattt gaaacttgta tttcctgctt 1680 tattttcggg tttgtcgaat ttggatttta aatgcgagac atgcatctta gctaaaagtc 1740 atcgtgttag ttaccctttg agttttaata agagtcaaat gccttttgaa ttgattcact 1800 ctgatgtgtg gggtccatct cccaaatcca ctatatctgg ggttcaatgg tttgtgattt 1860 ttgtggatga ttgcactcgt atgacatggt tgtatctaat gaagaataag gatgaagttt 1920 tctctgtttt ttgctcattt catgagatgg ttaaaactca gtattctgct acaattcgca 1980 tactttgatc cgacaatggt ggagagtata tgcatcgtga cttcaaaaat tatttcagtc 2040 accatggctt gattcatgaa actacctgtc ctcaaacacc acaacaaaac ggaattgccg 2100 aaaggaaaaa tcggcatatt ttagagactg ctcgggctat tcttcttggt gctcatgtac 2160 ctaatcattt ttggactgat gctgtcacta cagcagttca ccttattaat cggatgcctt 2220 ctagggttct taagttcaag actcctctcc aggccctatc caccgtcatc tctctaccta 2280 ctgccttaat gctttcgcct cgagtatttg gctgtgttgc cttcgttcat ttacacaaga 2340 atcaacgcac taaacttgat ccctgcgcag tccggtgtct ttttttgggg tatggcctac 2400 atcaaaaggg atatcgctgt tatgatccat ctaatcatcg catctatgtg acgatggatg 2460 tcaccttctt ggaatcagag actttctact cttcgaccac atccacttct actcttcagg 2520 gggcgcctca aaataaagag ttgaattggc tgaggtttga ttgggagctt gttgtttcta 2580 tatccaatac agaacttgat gttgagcctg ttgtttctgt atccaataca aaacctgatg 2640 ttgatgttga cacagaacct agtgttctac cattagtaat tgaagagcaa cagccacagc 2700 agtcgatagt accccctcct cccacagtat ccaaagaccc atctcctgag aatattcctg 2760 aggtaagttc cctgaacact ctgagtacac ctgtgttaac taatgatgct catrtgggct 2820 atgagttacc atacaggcat aatcgaggca agccaccaga tagatactct cctaacatag 2880 aagaccggag gttgaaatac ccgattgcca actatgtatc cacaaagaca cttcctgaac 2940 ctctaaagac tttcgcagat gcaytctcct cgtgtcaggt tcctacaagt gttgaagaag 3000 caatgaaaga cccgaggtrg gtcyaggcta tgaaggagga gatggaggca ctattgaaaa 3060 ataagacctg gattyttgtc aatctaccta aaggacagaa aacagtgggg tgcaagtggg 3120 tgttttctat caaatacaag gtagatggaa caattgagcg ttacaaggcg agacttgtag 3180 caaagggatt cacgcagaca tacrgagtyg actatcagga aacattctca cccgttgcca 3240 aactaaatac ggtgagagta ttgttgtcac ttgcagcaaa yctggattgg cccctgcatc 3300 agttcgatgt aaagaatgcg tttttacatg gtgatctaga agaagatata tatatggaca 3360 ttccctcagg atatgtagcc aacacagaag gcaacattgt ttgcaaatta caaagaactc 3420 tatacgggtt gaaacaatca cctcgagctt ggtttgggag attcagtacg rcaatgaaaa 3480 agtatggatt ccagcaaagt aactctgatc acactttgtt cctaaagcat agacagggca 3540 aactgactgc tctgatagtc tatgtagatg atatgatcat cacaggagac gattcagagg 3600 agatagcgag acttcaagag cagttggcat ytgagtttga aatgaagaac ctaggaggac 3660 taaaatactt tttgggaatt gaagttgcta gatcaaagcg aggtatattc ctgtctcaga 3720 gaaaatatat tttagaccta ttaacaragg ttggattact tgattgtaag cctacagaaa 3780 ctccaataat tccgaatcac aaacttggag aatatcccaa tcaagtacca ayagacaaag 3840 gaaggtatca aagactggta ggcaagctta tttatctttc tcacacacgg ccggatattg 3900 cttatgcagt aagtgtggta agccagttta tgcattgtcc aagtgaarat catatgagtg 3960 ccgttatgca gattttgaga tatttgaagt cctcyccyrg aaagggactt akgttctcca 4020 aaaatgatca cctaagagta gaaggatata cagacrcaga ttgggcaggg aacattatgg 4080 ataggaaatc cacctcaggc tacttcactt ttgttggagg aaacttggtt acttggagaa 4140 gcaaaaaaca gaaggtggtc gmtctatcca gtgcggaagc tgagtttcgt ggaatggcta 4200 aagggctatg tgagttattg tggcttagga gacttctaat ggagattggt tttgcccctg 4260 actccgagat gaagttgttt tgtgataata aagcagcaat tgacatctct cataatccta 4320 ttcaacatga tcggactaag cacgtagaag tagatcgaca ctttattaaa caaaatcttg 4380 atgcaaagat tatccaattc ccttttgtga aatcccaaga ccaactggcc gatattctta 4440 caaaagctgt gagcagtaaa atattccatc actcactaga caagttggga cttattgata 4500 tttacgtacc aacttgaggg ggag 4524 // ID BoSB6B repbase; DNA; EDCOT; 285 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB6B. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-285 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 285 BP; 76 A; 56 C; 81 G; 72 T; 0 other; gtggaagccc ccttggtcca gtggtttgac caagggttca ttaatgcttc tacaccagga 60 ggtctgggtt tcaattcccg gagaaggcgg aattatgcga attaaaggag aaaaggctta 120 caagagatct gcagcatggc gcaaggagta ccgtcaagcg tggatcccat agggcggctc 180 aggtgatgca gtcaggcgtg aatcctcata aggcaggtag aattgtcggc tgtagaatcg 240 tctgtaatat ttctcatagt tgtaatagca taattatcca gcgtt 285 // ID MuDR-N2_Mad repbase; DNA; EDCOT; 1293 BP. XX AC . XX DT 21-OCT-2010 (Rel. 15.1, Created) DT 21-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW MuDR-N2_Mad. XX NM MuDR-N2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1293 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1512-1512 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is ~400-bp long. XX SQ Sequence 1293 BP; 469 A; 224 C; 193 G; 407 T; 0 other; gagtaaactg tcgatttgcc ccctaaactt tcacctagtt ttcgatttcc cccctgaact 60 tttcgattgg aaaattaagg actcaaacta atttttttag ccaatttgcc ccctaccgtt 120 agtttttcaa acattccatc catatttctg ttaagtgaga ccatgtgcac aacatgtgag 180 ggtagttaag tcatttcact cttaaaaatg attaaaaaac tgaaaataaa tttaagaaaa 240 aaaaactttc cctctatttt ttccctctaa ttcctatcct caattttatt tttcactcat 300 tcctatgcat gagaaatgac atatggtgtt attgtcttca aaagtatcta agttagtctt 360 tttcttgaag catgtactgc catttttatt ttctttaaca aattaataat ttgacaaatg 420 ctcatggtgt tattgtctcc aaagcagtgc attaatataa gcatgttacg tgttgtgctt 480 cattttagag acattaagac tttactagta gaagagttag aagagttata aaaatagttt 540 ccagcagtta acatgtccgc catctagtaa aaactacaac aagtcaaaga aaaaaactac 600 tccaatcacc agcatcaaaa ctccaaagat cggctaactg cactaatcct aactattcct 660 ccaattttct agcaatagta tccaaccaaa tcacaaaaaa aaaaaaaaaa gcatatcata 720 cccacgcagt tccacaaagc tttgcttgcc tcctcaaagt acaatgtttt caaataataa 780 attaattact ataaaagaga agaaagtgca caactcaacc tagaatcaaa tgatggatat 840 ttcaactgca ttcttgcaca tttaacacca tgagcatttg tcaaattatt aatttgttag 900 agaaaataaa aatggtagta catgcttcaa gaaaaagact aacttagata cttttgaaga 960 caataacacc gtatgtcatt tctcatgcat aggaatgagt gaaaaataaa attgaggata 1020 ggaattagag ggaaaaaata gagggaattt ttttaaaaaa aaatttattt tcagtttttt 1080 aatcattttt aagagtgaaa tgacttaact accctcacat gttgtgcaca tggtctcact 1140 taacagaaat atggatggaa tgtttgaaaa actaacggta gggggcaaat tggctaaaaa 1200 aattagtttg agtccttaat tttccaatcg aaaagttcag gggggaaatc gaaagttagg 1260 tgaaagttta gggggcaaat cgacagttta ctc 1293 // ID Copia29-VV_I repbase; DNA; EDCOT; 4902 BP. XX AC . XX DT 13-SEP-2007 (Rel. 12.09, Created) DT 13-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW internal portion; Copia29-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4902 RA Obukhanych T. and Jurka J.; RT "Copia29-VV."; RL Repbase Reports 7(9), 790-790 (2007). XX DR [1] (Consensus) XX CC This is an internal portion of Copia29-VV LTR retrotransposon CC from Vitis vinifera. Individual copies are ~90% similar to their CC consensus. LTRs, deposited as Copia29-VV_LTR, are 94% similar to CC each other. Target site duplications are 5-bp long and some CC contain point mutations. XX FH Key Location/Qualifiers FT CDS 1192..2340 FT /product="Copia29-VV_I_1p" FT /translation="MSLMKISLPLNKNLFYSDKEHYEKLKTLLNQLDTXAE FT IPTAKTASCSFVQTGNIKALSASKDCLSSIWIIDSGATNHMTSHSNFFSNY FT TILSSRPKVKVADGTFSSIIGQGIASITPSLTLQNVLHVPNLSCNLLSVSK FT ITKDLNCFVTFTPSHCVFQDQIMGRMIGHGERKGGLYYLNTHWKIGDSIPQ FT ALITTNNPSKVDQIWLWHKWLGHPPFFILEKMFPTLFGKTKSHDFHCEVCE FT LAKHHXVPFPIRNKKETSPFSLIHTDVWGPSRIPNISGSRWFVTFIDDCTX FT TTWVYLLKSKSEVNSIFPIFHKFVCTQFGTKIHTLRLDNGXEYFNHNLVTY FT LQNEGIVHQSSCVDTPQQNGVAERKKIDISWKLLGLYFFK" XX SQ Sequence 4902 BP; 1593 A; 991 C; 918 G; 1387 T; 13 other; tggtatcaga gccagaagtt tgactctgcc aagatccata gagccttcat tgctcggtca 60 catacaacct tcattgttgt agcttgttcc ctctttttaa ccagccttta ttgttggttc 120 cttagttccc attataattc cctcaaggtc atctcttgtt tactccgaaa aaaaaaaaaa 180 aaaaaaaaaa aaaaaacyag aaaccttgtt gttttttccc taaaatgttt gaaactagtg 240 aaaatacacc atcctctcaa acaaccctac ccttcaatcc ctcctctaca ctccaaacct 300 taccaccttt atctacccat cataatgaca gccctacact ccaaatcacc actcaaaaac 360 tcaatggcca gaatttccta caatggtccc aatcagccaa acttttcatt aaaagtaaag 420 ggaagatggg ctatatcatg ggtgccaaat cagaacttga ctccaatgat ccacgatatg 480 aattatggga tgaggaaaat tccatggtca tgtcttggct actacactcc atgcagyygg 540 agattagcca aacatacttg tttctctcca ccgccaaaga gatttgggat gccatcagtc 600 aaacttattc caagattgga ataacaacac aagtatatga gttgaagtgc caaattcatg 660 ctacaaagca aggaagttgg tctgtcactg aatattacaa taaattgcga agcctatggc 720 tggaattaga tcattaccag cacatagaaa tggtagttgc tgaagacact actagattga 780 agaagataat ggagcaagag agagtatttg aattcttggc tggtcttaat cctgaattag 840 accaagtaag agtacaaata ttggggaaag aacctcttcc atccatccgg gaggtttatg 900 cctatgtgat tggagaagaa agtcatcgag ttgtgatgct aggaggctat actccagaaa 960 attcagcact agctactgct ggaaatttca agtcgatggg atccaaagta gaaggaagaa 1020 aaccagatga taaagattca ctttggtgta attattgtca caaaccaaga catacacgtg 1080 aatcttgctg gaaactccat ggcaagcctc agttaggaag taaaggggga agcaatagag 1140 gaggaaaacc tgtcacaaga tctggacagg cgcatcaagc tgccaccatt gatgtctctc 1200 atgaaaatat ccctaccact gaacaagaac ctattttact cagacaagga gcattatgaa 1260 aagctgaaaa cacttctcaa ccagcttgac acacrtgctg aaattcccac tgcaaaaacc 1320 gcctcatgct ctttcgtcca aacaggtaat atcaaagctt taagtgcctc caaggattgt 1380 ttatcgagca tttggatcat tgattctggt gctactaacc atatgaccag tcactccaat 1440 tttttttcca attatacaat actttcaagt aggccaaaag traaggttgc tgatggcact 1500 ttttcttcca taattggtca aggcatagcc tccatcactc cttctttgac cttgcaaaat 1560 gtgttacatg ttccaaactt gtcttgtaat ctcttgtctg ttagtaaaat cactaaagat 1620 ttgaattgct ttgtaacatt taccccttcc cattgtgttt ttcaggacca aataatgggg 1680 aggatgattg ggcatggtga gaggaaaggt ggactctact acctcaatac acattggaag 1740 attggtgatt ctatcccaca agctcttatt accaccaaca atccctcaaa agttgatcaa 1800 atatggctat ggcacaaatg gttgggacac ccacctttct tcatcttgga aaaaatgttt 1860 cccacattgt ttggcaaaac taaatcccat gattttcatt gtgaggtttg tgagcttgca 1920 aaacaccatc rtgtgccttt tccaataaga aataaaaaag aaacatctcc ttttagttta 1980 atacatactg atgtttgggg accctctaga attccaaaca tttcgggttc tagatggttt 2040 gttaccttca ttgatgactg cactygtacc acttgggttt atctcctaaa atccaaatcg 2100 gaagttaatt ccattttccc aatattccac aaattcgttt gtacccaatt tggcaccaaa 2160 atccatacct taaggttaga taatgggarg gaatacttca accataatct tgtcacctat 2220 ctccaaaatg aaggtattgt gcatcaatct tcatgtgtag ataccccaca acaaaatggg 2280 gtagcagaga gaaaaaaaat agacatctct tggaagttgc taggtcttta ctttttcaaa 2340 tgaatgttcc aaaaacatat tagggggaag ccattttgac tgctacattt ttaataaatc 2400 gaatgccttc tcaagtcata gactttaaat cccctattga tgtactttca aagtcttttc 2460 ctaactttaa gggtattgga acacttcctc caaaaatatt tgggtgtgta tctttcattc 2520 acattcccaa acaatctaga gacaaacttg acccaagagc tcttaggtgt gtcttccttg 2580 gatattcttc caatcaaaaa ggatataagt gctaccatcc acccacaaaa aggtcatata 2640 tcaccatgga tgttaccttc tttgagagtc aaccatattt cacacacact tatcttyaag 2700 gggagattgg aggaatggaa gataagctgt cagaaatttt tcctaggaat ggtgagaatg 2760 gtgggggtgt ccttccacaa ccggttaatg tgccaaatgt ctctacctca aacacatcaa 2820 gttcccctac tgtccaagat gtttcagccc cagaattttc agattttgca tcaatactcc 2880 ctattgtcca agatgtttca gccccagaat tttcagattc tgcaccaaca ctccctgttg 2940 ttccaaatgt tccagccttg gattcatcta atgaatcagc tagtgaacat aagaaattcc 3000 agcaaactcc caatgaagag ctaattgtag aaaatttgcc cactgaaatt ccagccaatg 3060 aacttgagat tcagctcaaa gaaagggaac acatgctgcc agcaaacacc tctaaactaa 3120 aagtgtattc gaggaaggga aaatctacaa catcctctca tatcccatca tccaaccttg 3180 aatcaggtaa tgaaaatact cattctagtg tctataatga tttgtattgg cccattgcat 3240 tgaggaaagg cactagaaaa tgcactcagc attcctattt caaattttac ctcattacat 3300 cgtttatcat ctacataccg agcctttatt acccaaatgt cttctgttga aattccaaac 3360 acaatccaag aggcacttag agatgagaat tgraggaaag caattaatga ggagatgcaa 3420 gccttggaaa aaaatgagac ttgggatata gttgagcttc ccaaagggaa gaaaacagta 3480 ggttgtaagt ggattttcac aattaaatac aaggctgatg agacaataga aaggtataag 3540 gctagattgg tagctaaggg attcacccaa acttatggca ttgactacca agagaccttt 3600 gcaccagtgg caaaaatgaa cactattcgt attctattgt ctttagctgc taatcttgat 3660 tggcctttgc agcaatttga tgtgaagaat gctttcttac atggcgactt agaagaagag 3720 gtatacatgg acactccacc ggggtttggt gacaaggctt ggaagaacaa agtctacaag 3780 cttaagaagt ctctttatgg acttaaacaa tctccaagag catggtttgg gagatttaca 3840 aaatcaatga taagaatgaa ctaccatcaa agccaaggag accacacatt gtttatcaaa 3900 cataactcct ctggtaagtt gactgccttg atagtttatg tggatgacat tattgttact 3960 ggaaatgatg agggggaaat tcaaagacta aaaacttatt tgtctaatga atttgagatc 4020 aaggatctaa ggagtctaaa atatttcctc gggattgaag tggcacgttc aaaaggggga 4080 atatttattt cccaacaaaa atatatcctc gatttgctaa gggagacagg gatgctagga 4140 tgcaaaccag tagagactcc gattgagcaa aatcataaat tatgaggaaa aatagaggat 4200 gatatggtag accgtggcct ctatcaaaga ttggtgggga aatttaattt atttatctca 4260 cactcgacca gacattgcat atgttgtagg tgtggtaagc caattcatgc attcaccaca 4320 tgaatctcac atggaggcaa tatatagaat cctatgttac ctaaagtcta caccaggcaa 4380 gggaatctta tttcagaaga taggaaatat ggaattggaa gcttayagtg atgctgattg 4440 ggctggatca attgtcgata gaaggttaac ttctggatat tgtaccttct tgggaggaaa 4500 tctagttact trgagaagta aaaagcaacc aatggtggct agatctagcg cagaagctga 4560 gtttagggtc atggctcaag ggatttgtga actactctag ataaagatca ttcttactga 4620 ccttggcatc actttgaaag gacccatgag gttatattgt gataaccaag ctgctataaa 4680 tatarcccat aaccccgttc atcatgatcg aaccaagcat gtggagatag atcgacattt 4740 catcaaagaa aaacttgata atgggctgat ttgcactctg tatgtcccct cttctaaaca 4800 gttggcagat atactaacaa agggcctacc aagttcaaca tttttataca atcttagaca 4860 agctaggaat gcaaaatatt tttgcaccaa cttgaggggg ag 4902 // ID SHACOP2_I_MT repbase; DNA; EDCOT; 4491 BP. XX AC . XX DT 11-JAN-2007 (Rel. 12.01, Created) DT 11-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of a LTR retroposon, SHACOP2_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; ORF; SHACOP2_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4491 RA Shankar R. and Jurka J.; RT "SHACOP2_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 71-71 (2007). XX DR [1] (Consensus) XX CC The internal region has 2 ORFs with domains for gag, integrase CC and RT polymerase. The intact element exists in very low copy CC number. XX FH Key Location/Qualifiers FT CDS 31..2046 FT /product="SHACOP2_I_MT_1p" FT /translation="MVSQPPSLPPETPIPTAIPINSIPLDSFLEDNDSDRS FT KFAFALKISEKLTEKNFLLWRQQVAPYINAHNLDGFIVAPIVPPCFLNAQD FT RATGTLNPAFRKWRLTDQMLLSWLQYTLSSAILARFIGCSHAYELWDKLVA FT YFHKQMRAKARQLSVELRSTSLANLTVQDYLLRIRDLVDNLASIGDPVPVN FT QHLDVILEGLPQDFSPVISVVESKFDVIDVDEVESLLLAHETRLDKFKKKV FT LEDVASINLTSSSASQASSPSESSQSQASVNVTTGSDHSTFNPNFTPNFGS FT NRGRGGRSGRGRGRGGRLSNVQCQVCFRFGHPASTCWHRFNQQFQPQIPPN FT FQGFQGFNNAPIDPYHLASPSMMPYGAPYGGYNQHSLGYGSFNNWPRPSAQ FT QRPPSVQFSQPSAMMINAPSTSGSSTWFPDSAASFHVTGDAINIQEQSFFE FT GPDQLFVGNGQGVPIHSYGSSVFPSPLKPHKTLSLNKLLNVPDITKNLLSV FT SQFAKDNTVFFEFHADYCVVKSQDTKEVLLRGSVGPDGLYTFPSLSMDTAK FT CSSPSVFFTSPDSTINTIFPSCNNQMPSKSHNLWHQRLGHPNNHTLKLVLQ FT HCNISTINKEKDISTFCNACCIGKAHRLHSPTSHTIYTHPLQLVFSDLWGP FT SPTVSSLGYHYYITFVDAFSRFT" FT CDS join(2426..3010,3014..3607) FT /product="SHACOP2_I_MT_2p" FT /translation="MLDYHFLKVFGCSCFPLLRPYNSHKFDFRSHECLFLG FT YSTTHKGYKCMSPSGRIFISKDVLFNESKFPYLSLFQNYTYDPLHPIQDVS FT LSSLPIHPSDLPSNFHNQSTSSSPTSQMASPSPPNSLVPTTTSATNIEPQS FT FTASQHSTHTTAPLPVNSHPMQTRSKSGIVLPRLNPNIFLTYTEPKNVKQA FT LLDPKRAAMQDEFDALQKNSTWSLVPLPPNRKAIGCTWVFRVKENSDGTLN FT KFKARLVAKGFHQVQGFDFTETFSPVIKPITIRLILTLALSYKWPIQQLDV FT NNAFLNGILEEEVYMQQPPGFEHSDSTLVCKLHKALYGLKQAPRQWFERLT FT TALIQFGFQASKCDPSLFTYAKQKQVVYLLVYVDDIIMTGSSFFIGFCFS" XX SQ Sequence 4491 BP; 1147 A; 1070 C; 763 G; 1511 T; 0 other; ggtatcagat tagcctctag atccatggtg tctcaaccac cgtctctgcc accggagaca 60 cctattccga cggcgattcc gatcaattct ataccgctcg actcgtttct tgaagataat 120 gactcggatc gttccaaatt tgccttcgca ctcaagatct ctgagaaatt gacggaaaag 180 aattttctgc tatggcgtca acaggttgca ccgtacatca atgctcacaa ccttgacggt 240 ttcatcgttg cgccgattgt tcctccttgt tttctcaatg cgcaagatcg cgctactggt 300 acgctcaatc ctgcttttcg caaatggcgt ttaactgatc agatgctctt atcgtggctt 360 caatacactc tttccagtgc aattttggct cggttcattg gttgctctca tgcgtatgaa 420 ctttgggata aacttgtggc atattttcac aaacagatgc gtgcgaaggc gcgtcaactt 480 agtgttgaac tgcgttctac ttctcttgca aatcttacgg tacaggatta tcttcttcgt 540 attcgtgatc ttgttgataa tctagcctct ataggagatc cagttcctgt taatcaacat 600 ttggatgtga ttttagaagg tttaccgcaa gattttagtc ctgttatatc tgtagtggaa 660 agcaaatttg atgttattga cgttgacgaa gttgagtctc ttcttcttgc tcatgaaaca 720 cgtcttgata aattcaagaa aaaggttctt gaagatgtgg cttctatcaa ccttacttca 780 tcttctgcat ctcaggcttc atctccctct gaatcctctc agtcacaagc ctctgttaat 840 gttactactg gttcagatca ctccaccttc aaccctaatt ttactcccaa ttttggttca 900 aatcgtggta gaggaggtag atctggcaga ggtcgtggta gaggaggcag actttctaat 960 gtccagtgcc aagtctgttt taggtttgga catccagctt ctacatgctg gcacaggttt 1020 aaccaacagt ttcagccaca aattccacct aatttccaag gttttcaggg attcaataat 1080 gctcctattg atccttatca tcttgcatct cctagtatga tgccttatgg tgctccttat 1140 ggtggataca atcagcactc tctgggatat ggctctttca acaactggcc tcgtccttct 1200 gctcaacaaa ggcctccctc tgtgcagttc tctcaaccaa gtgccatgat gattaatgct 1260 ccatctacaa gtggatcttc cacttggttt cctgactctg ctgcctcttt tcatgtgact 1320 ggtgatgcta taaacattca ggagcagtcc ttttttgaag gtcctgacca actcttcgta 1380 ggaaatggtc aaggtgtgcc aatacattct tatggttcca gtgtttttcc ctcacccctt 1440 aaaccacata aaaccttaag ccttaataaa ttacttaatg taccagacat taccaaaaac 1500 cttctcagtg tcagtcagtt tgctaaagat aatactgtat tttttgaatt tcatgctgac 1560 tattgtgttg ttaaatctca ggacactaaa gaagttctcc ttcgtggcag tgttggtcct 1620 gatggtcttt acacctttcc cagtctctcc atggacactg ctaagtgctc atccccttct 1680 gttttcttta cttctcctga ttccactatt aataccatat ttccttcttg taataatcag 1740 atgccatcta aatctcacaa tttgtggcat caaagactag gacaccctaa taatcatact 1800 cttaaacttg ttttacaaca ttgtaatatt tccacaatca ataaagaaaa agatatttcc 1860 actttttgca atgcttgttg tataggtaaa gctcacaggt tacattcacc cacttcacac 1920 actatataca ctcaccctct tcaacttgtg tttagtgatt tatggggtcc ttcaccaact 1980 gtttcctctc ttggttacca ctattatata acctttgttg atgctttttc tagattcacc 2040 tgatttattt gcttaaaaac aagtctgatg ctcttactgt tttcatgcaa tttaaatcta 2100 tggttgaact tcagctaggt cattccatta aatctattca aactgattgg gggggggggg 2160 tgaattcaga tcttttactc aatatcttac tggtttagga atcactcaca gactcatttg 2220 tcctcacact caccatcaaa atggtgtcat agaaagaaaa catagacata ttgtggattt 2280 gggtctaact cttcttagcc atgcttccct tcctttgact tattgggatc atgcttttct 2340 agctgttgtt taccttacaa acagactacc tactgcctct ttacagtttc aaattccttt 2400 tcaaactctg tttcacaaaa tgcttgacta tcatttttta aaagtgtttg gctgctcttg 2460 ctttcctttg ttaaggccct ataattcaca caagtttgac tttaggtctc atgaatgtct 2520 ttttttggga tattccacca ctcacaaagg gtataagtgc atgtctccta gtggtcgtat 2580 ctttatatcc aaggatgttc tctttaatga gtctaaattt ccttatcttt cattatttca 2640 aaattacacc tatgatcctc ttcaccctat ccaagatgtc tctctgtcct ctttacccat 2700 acatccttct gaccttcctt ctaactttca taatcaatcc acctcatctt ctcctacctc 2760 tcaaatggcc tcccccagcc ctcctaattc tcttgtccct actactacat cagcaactaa 2820 cattgaacct caatcattta cagcttccca acactctaca catactactg cccctttacc 2880 tgttaattct caccctatgc aaactcgttc taagtctggt attgtcctcc ctcgtcttaa 2940 ccccaacatt tttctcacct acactgaacc taagaatgtt aagcaggcct tacttgatcc 3000 taagtgacgt gctgcaatgc aggatgaatt tgacgcactg cagaaaaaca gcacatggtc 3060 cctggtgcct ttgcctccca ataggaaagc cattgggtgt acatgggtat ttagagtcaa 3120 agaaaactct gatggtactc taaataagtt caaagctcgt ctggttgcta aaggatttca 3180 tcaagtgcaa ggctttgatt tcactgaaac tttctcacct gtgatcaaac ccatcactat 3240 tagactcata cttactcttg ccttatcata caagtggcct atccagcaat tggacgttaa 3300 caatgccttt ctcaatggta ttcttgaaga agaagtttac atgcagcaac ctccaggttt 3360 tgaacattct gattctacat tagtgtgcaa actccataag gctctttatg gtcttaaaca 3420 agcacccagg cagtggtttg aaaggttaac tactgctctc attcagtttg gctttcaggc 3480 tagtaaatgt gatccctctt tgtttaccta tgccaagcag aaacaagttg tttatctact 3540 tgtttatgta gatgacataa ttatgactgg tagttctttc ttcattggtt tctgctttag 3600 ttaagcaact tgattcagtg tttagcctta agcaacttgg tctgttggaa tattttcttg 3660 gcattgaagt gaagcatctt cccaacaatt ctcttttgct cactcaaagt aaatacatta 3720 atgatttact agccaaaaca catatgcttg agtgcaactc catcaatact cctatggtgt 3780 ccagttgtaa attgtctaaa attggatcag acaccttctc agatccctct cttacagatc 3840 tgttgttggc tctctgcaat atgcaactat taccaggcct gagatagctt actctgtgaa 3900 taaggtatgc caattcatgt ccaaccctct tgaatcccac tgggttgctg tcaagagaat 3960 tctcagatac ttaaaaggaa tcttcacctt tggacttgag ttgcatcctg ctccaattca 4020 caaacctctc tcacttcatg ttttttgtga tgctgactag gctgctgatc cagatgacag 4080 aagatccact tttggtgctg caattttctt tggtcccaat ctcatttcat ggtggtccaa 4140 gaagcagcct gttgtggcca gatcaagtac agaagctgaa tacagggctt tggcacaagc 4200 tacagctgat gctctctggg tccagacatt gttacaggag ctcactgttc cctttaacaa 4260 tctcaccgtt tactgtgata atcccatttt acacaccaga acaaagcata tggagataga 4320 cctctttttt gtcagggaaa agatcattgc caagcaactc tccatagttc atattcctgg 4380 tactgatcag tgggcagata ttctcaccaa acctgtctcc acttcaaagt ttcttttaat 4440 gagatccaaa ctcaatgtga tttcacaccc cactgagttt gaggggggag t 4491 // ID COPIA_PO repbase; DNA; EDCOT; 276 BP. XX AC M94485; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 25-MAR-1997 (Rel. 2.02, Last updated, Version 2) XX DE Platanus occidentalis copia-like retrotransposon reverse DE transcriptase gene, partial cds. XX KW Copia; LTR Retrotransposon; Transposable Element; COPIA_PO; KW POCOPIA; Copia-like element; retrotransposon; KW reverse transcriptase. XX OS Platanus occidentalis OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; Proteales; OC Platanaceae; Platanus. XX RN [1] RP 1-276 RA Voytas F.D., Cummings P.M., Konieczny A., Ausubel M.F. RA and Rodermel R.S.; RT "Copia-like retrotransposons are ubiquitous among plants."; RL Proc. Natl. Acad. Sci. U.S.A 89(15), 7124-7128 (1992). XX DR GenBank; M94485; Positions 1 276. XX SQ Sequence 276 BP; 74 A; 37 C; 71 G; 94 T; 0 other; tgtgaagaca gcgtttctgc atggtgaact agatgaacag atttatatgc atcagcctaa 60 ggggtttatg atccagggaa aggaggacca tgtttgttta ttaaagaaat ctttgtatgg 120 tttgaaacaa tctcctaggc aatggtataa gaggtttgac acctttatgg ttggaaatga 180 ctactgtagg agtaagtttg acagttgtgt ctatcacagg aagcttttgg atggttcttt 240 tgtttatttg ttgctctacg tggatgacat ggatcc 276 // ID DNA3-1_Mad repbase; DNA; EDCOT; 429 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA3-1_Mad. XX NM DNA3-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-429 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1465-1465 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >97% identical to the consensus. 3-bp TSDs are usually TWA. XX SQ Sequence 429 BP; 146 A; 57 C; 75 G; 150 T; 1 other; ggggggtgta ttcaattggg attttgaggg attttaattc ttttaatgaa tctaggggta 60 ttcaatcagg attttaagtg attctctgaa attcwaggtg tattcaatta gaattttaag 120 atagtttatt aaaatcctta gaaatccggg tgtattcaat taggatttta aagaagttta 180 taacattcca ggtgtattca attagaaatt gattttaaag aatttgagaa agttgaggaa 240 ttagagggaa ttggagagat ttcgtagtgt attttaagca tccacaaatc tcacctcttc 300 ccatgagatt tcgagggaat tgaatcaaaa ttttatatgg aatctctaca aatcaattaa 360 actccataaa aatccatgga tttataaatc cattaaaatc tctcacattc tcaattgaat 420 acacccccc 429 // ID MtPH-M-1-Ia repbase; DNA; EDCOT; 5140 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 13-MAY-2008 (Rel. 13.05, Last updated, Version 1) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-M-1-Ia. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5140 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC (MtMaster) CC An autonomous element representing subfamily M-1 of PIF/Harbinger CC transposons from Medicago truncatula, carrying 14 bp-long TIRs. CC orf1 and TPase transcripts were identified in the M. truncatula CC EST database. XX SQ Sequence 5140 BP; 1595 A; 757 C; 944 G; 1844 T; 0 other; gtgcatgttt ggtaaagctt cttcacgcct caaacccacg ttttcttctc caaacgcgag 60 ttcggcggtt cctatgatgt ttggatgaat tcaaacgcga ttctgtagat tgtacggcaa 120 gtgctcaaac gcggtttggg atgacgctac aaatctgagc ttctgcggca gatcaaaatc 180 acttttcaac ctttaatttc tcaaggtaca agtacttacc taattacccc taaattcaag 240 ccttcaattt ttctttctcc tagttttctt ccttttcatt acttcacatc acttcaacct 300 taaattttct gctacttggg aagattttgc aaatccaagc tttcaatttt cttcagattt 360 tcctctattt tttcagattt tgtggttaat ctcattactc atggtagatg tgttggttgg 420 gtgaatttat tcattcatct ttcccctata tatgatgctt atgagctact tgtgagaatc 480 atttcattgt tctgccaagg cctaaaggta aatacatatt cataaaaaaa aattgctttg 540 ttttcttgct tcaaaactgt taatttctat ctctatttgc tctagttgtt ataaatttta 600 ccttaatttt ttcatcctgt atcaatgcat tgtatgtgtt tgataaatag tctcaaagaa 660 gaaaacaatt ttcttattga tatgtttatg atgactgttc tattattatt gacatgttta 720 tgtttttttt tctctcctgt tgttctgttt tgagcaatga gtgtattgtt tttgtttaaa 780 gttacttggt gtgagtttaa attaattgaa cttgaatgaa ataatgtaag aaaagcaact 840 tacaacttca agccattgtt gtattactaa tttttatgta ttttcattgt tagataaacc 900 ttttccaacc tttacaaaaa agagttacat ttagcacaaa gtaacagaac ttcttttagt 960 atttttgttt tgttttctgc tatcattttc atatgcacaa aacaaggata ttggtgtcag 1020 tttgatcaag ttccttatgt atagtttgtt tcattttttt atcatacttt tgtgtatata 1080 gtattatgga ctcacttaag aggaaagttt ctgctaaccc cccatcaact aacaatgagg 1140 gtcaaagttc caaagctagt tggagggata ttaaagccac tgagtacttt gtgaaggcat 1200 gtttggatca agttaccaag ggtcaacgaa atggtacttg ttttaccaag aaaggatggc 1260 aaggtattgt ttcccaattt catgaacaaa gtggactgaa ttatgacaag gtacaattga 1320 agaataggta tgatagcttg agaaaggaat ggaaagtatg gtataacttg tttggaaaag 1380 ttacaggatt aggatggaat tttgagaaga acaccgttga tgcatccgat gagtggtggg 1440 agaagaaaga attggtatgt gaatcacaaa tattttgttt aggatacttt tatgtttata 1500 tttaccatag ttttatatgt taggttatga atatgcagga aaatcctcaa tatgcaaagt 1560 ttagagacaa gggacttcca tttgctcacc aactaaccac acttttcaag gatgtagtgg 1620 ctaatggaga gcatgcttgg gcaccatcaa gtggtgtatt acctaatgag aacttgggta 1680 atgatgatat tgatgttggc ttggatgatg cagaaggttc gggtgatagt gaagatgcaa 1740 gcattggagc agcaactggt tttggaaata ttaacttgaa tacatcacaa ggagctgtta 1800 gtcaaagtag tggacaaaag agaaagagag ttattggggc tgaacagaaa ggaaagaaaa 1860 aagctactcc ttcaacgtca atagctgagg ctgttaatgt tattgcggag acttgcaagt 1920 cgcggaatga ggctataagt aatgcatcta ttggtgaggt gatggctgag attcaaacca 1980 tggaggcagt tacttctgat ttagagtttc atacaatgtg ttgtaaccta atgatgttta 2040 agccagctag ggagatgttt gtatcactgc ggggttttga ggaaagaagg ttgatttggc 2100 tcaaatttgc atcattcaac cctactctat tcatgaggcc gtgatttgga aaaaaaattg 2160 gctcaagaat tggcttagtg atgcgtcttg gacttagctt atgcttttgg acttagttta 2220 tgtatttggt ttcttagttt atgtatttgg ttgcttagtt tgtgtttaga tctttattat 2280 atcgcactat gtgtgaggat tttcctttat aaattccgta ttaagaactc aagtagtatg 2340 gtgatataaa acctatgtat tatgccttgt gaatttgaat gaagtgaatt tgttacatgg 2400 ttgcctctgt tattttttat atgtcttatg acttattggt tatattatta aatggtaatg 2460 gaaactattg tgtctggcag gcaagtgtgt actagtttgt gctaagctgc aaaaggatgt 2520 actttatgta gatgtgttga agattgagac tacaacaaaa ttatcatctg tgtcaggtaa 2580 taaattctat gtatctgtta tgcctaaaag ttccatagtt taaattgttg attctgcttg 2640 gaattagttg gtacctatga atcatatcct aatttacata gtgattgacc tttagacatc 2700 ttatgcctca tttcttttaa gaatgttgag tgcatgtttg cttccacgtt gccgtggagt 2760 tgaatgtgcg gttggtaaac tctacaagac atagcattta tccagtttta cagtatacca 2820 aacacacttt gagttcgtcg aagctcagtg agaaacaaaa ccagtagtaa tgtatcatat 2880 ggatttttga cgatatcact tttatgccct tgctagaagt ttgaagattc ctttgaattg 2940 ttaaaccaga atcataacat tctgttcagc tttgctagtg ctataattaa ttcatatttt 3000 gatgtttaaa acacagtgta gtgccaatgg tactttattc tagaatttca ttttacctgt 3060 agtctaataa catgattatg taaagtagtg gatttttgtt agagttgctg caaacattgt 3120 gctgtaagtg tgaagataca tgcttatttg aaacatatac atcactaacc aaattacaaa 3180 caagatagtt atgggctcaa gggtatacaa tgcacatgta ttttggtgca tgtattatac 3240 tgacagatgg gatacaatgg atggtagtgt ttatatattg tgatttattt gctttacttc 3300 acaatggatg gtgtgtttat atattgtcat ttacacacat gtccacttta ttaaaatgaa 3360 cttttggaag gaacaattgg aacacaatac acaagaagaa gaagatgatg atacatttga 3420 agaatcctat attttggctg cactacttgg tgagtatgca acaaaatatt tatgcaaaga 3480 gccatgtaga actagtgagc tcacaggtca tgcatgggtt caagaaatat tgcaagggaa 3540 tcccactcgt tgttatgaga tgtttcgaat ggaaaaacat atttttcata aactttgcca 3600 tgaattggtg gaacatgatt taaagtcttc taaacatatg ggggttgaag aaatggttgc 3660 aatgtttttg gtcgttgtag gccacggtgt cggtaataga atgattcaag aaagatttca 3720 acattcgggt gagactgtaa gtagacattt tcatcgtgta cttcatgcat gccttaagtt 3780 gtccttcaaa tatattaaac ccgaagatcc tatgttttgt gaatgtcatg ccaaaattaa 3840 aaatgatcaa cgttattggc ctttttttaa gaatgctata ggagtaattg atggtacaca 3900 tgtgtcatgt gtagttagtg ctagtgagca accaaggttt attggaagaa aaggatatcc 3960 aacacaaaat attatggctg tatgtgattg gaatatgtgt ttcacttttg tattagctgg 4020 ttgggaaggc actgcccatg atgcccgtgt ttttgacaaa gctcttacta ctgctaacct 4080 taactttccg catcctcctc aaggtatgtt atacattgcc ttactatata tgattaattt 4140 gttatatcaa taattaattt attttcatat tttaataatt aatttatttt taggtaagta 4200 ttatttggta gattctggtt atccaacacc aatagggtac attggtccat atagatgtga 4260 acgttatcat cttcctgaat ttagacgttc aagtgggttc gaaaatcata atgaagtatt 4320 caattactat cactcaagtt taagatgcac aattgaaaga acttttgggg tatggaagaa 4380 tagatttgca attctacgta gcatgcctaa gttcaaatat gagacacaag ttcatatagt 4440 tgtcgcaaca atggcaatac acaactttat tagaaggagt gctgaaatgg atgttgattt 4500 taatctttat gaagatgaaa atacagtcat tcaccatgat gatgatcata gatcaactaa 4560 cttgaatcaa tcccaaagtt ttaatgtagc ttcttcttca gagatggatc atgctcgaaa 4620 ctcaatccgc gatcaaatta tagcgtataa gctaaataat taaaaatgta ataattttca 4680 atattatatt gcacttgaac ttatattatc tattatctat ctatttgtaa tatattttag 4740 tttacaattg tgtaactttc tcatttgttt tacatctttt tatgtttata ttattttatt 4800 aaaaatcacc caattgataa aaaattatat tagaaataac ataaattaat atttttttaa 4860 aattaatttt ggaaccaata aaattcatgt atgataaatt gaaataattt tttaatgaga 4920 atgagtttta aatacaatta aaaggatagt ttagtcatta cacattcaaa atcaattttg 4980 attcaaacta tccaaacaac atcaactcac atgaatcact tttaataaag tgtatccaaa 5040 cataatcaat tcacattcaa ctcactttta accaaaatca attctctcaa aattaattct 5100 atcaaaatca attctccccg ccgccatacc aaacacacac 5140 // ID Copia-31-I_VV repbase; DNA; EDCOT; 4028 BP. XX AC CU459240; XX DT 01-SEP-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-31_VV, LTR retrotransposon Ty1-copia like, internal portion DE from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Edel-B05; KW Copia-31-LTR_VV; Copia-31-I_VV; Copia-31_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4028 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL; CU459240; Positions 3626632 3630659. XX CC Size = 4774 bp CC LTR = 373 bp CC LTR are 100 % similar to each other. CC Direct flanking repeats =ggagc CC UTL size = 39 bp CC gagpol putative polyprotein size = 1298 aa. XX FH Key Location/Qualifiers FT CDS 40..3933 FT /product="Copia-31_VV_1p" FT /translation="MAEEAGKASGIEKFDGTDFAYWRMQIEDYLYGRKLHL FT PLLGTKPESMKAEEWALLDRQVLGVIRLTLSRSVAHNVVKEKTTTDLMKAL FT SGMYEKPSANNKVHLMKKLFNLKMAENASVAQHLNEFNTITNQLSSVEIDF FT DDEIRALIVLASLPNSWEAMRMAVSNSTGKEKLKYNDIRDLILAEEIRRRD FT AGETSGSGSALNLETRGRGNNRNSNQGRSNSRNSNRNRSKSRSGQQVQCWN FT CGKTGHFKRQCKSPKKKNEDDSANAVTEEVQDALLLAVDSPLDDWVLDSGA FT SFHTTPHREIIQNYVAGDFGKVYLADGSALDVVGLGDVRISLPNGSVWLLE FT KVRHIPDLRRNLISVGQLDDEGHAILFVGGTWKVTKGARVLARGKKTGTLY FT MTSCPRDTIAVADASTDTSLWHRRLGHMSEKGMKMLLSKGKLPELKSIDFD FT MCESCILGKQKKVSFLKTGRTPKAEKLELVHTDLWGPSPVASLGGSRYYIT FT FIDDSSRKVWVYFLKNKSDVFVTFKKWKAMVETETGLKVKCLRSDNGGEYI FT DGGFSEYCAAQGIRMEKTIPGTPQQNGVAERMNRTLNERARSMRLHAGLPK FT TFWADAVSTAAYLINRGPSVSMEFRLPEEVWSGKEVKFSHLKVFGCVSYVH FT IDSDARSKLDAKSKICFFIGYGDEKFGYRFWDEQNRKIIRSRNVIFNEQIM FT YKDRSTVTSDVTELDQKKSEFVNLDELTESTVQKGGEEDKENVNSQVDLST FT PIVEVRRSSRNTRPPQRYSPVLNYLLLTDGGEPECYDEALQDENSSKWELA FT MKDEMDSLLGNQTWQLTELPVGKKALHNKWVYRIKNEHDGSKRYKARLVVK FT GFQQKEGIDYTEIFSPVVKMSTIRLVLGMVAAENLHLEQLDVKTAFLHGDL FT EEDLYMIQPEGFIVQGQENLVCKLRKSLYGLKQAPRQWYKKFDNFMHRIGF FT KRCEADHCCYFKSFDNSYIILLLYVDDMLIAGSDIEKINNLKKQLSKQFAM FT KDLGAAKQILGMRIIRDKANGTLKLSQSEYVKKVLSRFNMNEAKPVSTPLG FT SHFKLSKEQSPKTEEEMDHMSKVPYASAIGSLMYAMVCTRPDIAHAVGVVS FT RFMSRPGKQHWEAVKWILRYLKGSLDTCLCFTGASLKLQGYVDADFAGDID FT SRKSTTGFVFTLGGTAISWTSNLQKIVTLSTTEAEYVAATEAGKEMIWLHG FT FLDELGKKQEMGILHSDSQSAIFLAKNSAFHSKSKHIQTKYHFIRYLVEDK FT LVILEKICGSKNPADMLTKGVTIEKLKLCAASIGLLA" XX SQ Sequence 4028 BP; 1257 A; 614 C; 1045 G; 1112 T; 0 other; actggtatca gagcctaggg ttaggtttga gtgggagcaa tggcagagga agcaggaaag 60 gcgtctggaa tagaaaagtt tgatggcaca gactttgcgt attggaggat gcagattgaa 120 gattatctct atgggaggaa attgcatctg cctcttttgg ggacaaaacc tgagagtatg 180 aaggctgagg aatgggcgct tcttgacaga caggttctag gagttattag gttaactctg 240 tctaggtctg ttgcacacaa tgttgtaaag gagaagacca caacagattt gatgaaggct 300 ttgtccggta tgtatgaaaa gccgtccgca aacaataagg tgcatctgat gaaaaaattg 360 ttcaatttga agatggcaga gaatgcatca gtagcacaac atctgaatga atttaataca 420 atcacaaatc aattgtcgtc tgtagaaatt gattttgatg atgagattcg tgctctgatt 480 gtcttggctt ctttgccaaa cagttgggag gcaatgagga tggcagtaag caattctaca 540 ggaaaggaaa agctcaagta caatgatata cgagatttaa ttctggctga ggagattcgc 600 cgaagagatg caggtgaaac ctcaggatct ggttctgccc taaaccttga gacaagaggc 660 agaggtaata acagaaattc aaatcagggt agatcaaatt ccagaaattc taatcggaac 720 agaagcaaat ctagatcagg ccaacaagta caatgttgga attgtgggaa aacaggtcac 780 tttaaaaggc aatgcaaaag ccctaagaag aagaatgaag atgattctgc taatgctgta 840 acagaagagg tacaggatgc attacttctt gcagtagaca gtccacttga tgattgggtt 900 ttggattcag gagcttcgtt tcataccact ccacaccgag aaatcataca gaattatgtt 960 gcaggtgatt ttggtaaggt atatttggct gatggttcag ccttggatgt tgtgggtctg 1020 ggagatgtcc ggatatcgtt gcccaatggg tctgtttggt tactggagaa ggttcgacat 1080 attcctgacc tgaggaggaa tctgatttct gttggacaac ttgatgatga aggacatgca 1140 atactatttg ttggtggtac ttggaaggtt acaaagggag ctagggtatt ggctcgtgga 1200 aagaagactg gcactctgta tatgacctca tgtccaagag acacaattgc agttgctgat 1260 gcaagtactg atacaagcct atggcaccgt agacttggtc acatgagtga gaaagggatg 1320 aagatgttgc tgtcaaaagg aaaactacca gaattgaagt ccattgattt tgacatgtgt 1380 gaaagttgca tcttaggaaa gcaaaaaaag gtgagcttct tgaaaactgg caggacaccg 1440 aaggctgaaa aattggaact agtacacact gatttgtggg ggccttctcc ggttgcatcc 1500 ctaggaggtt caaggtacta catcaccttt attgatgact caagtagaaa ggtatgggtt 1560 tattttctga aaaataaatc tgatgtattt gtaactttta agaagtggaa ggccatggtt 1620 gagacagaaa caggtttgaa agtaaaatgt ttgaggtcag ataatggagg agagtacata 1680 gatggaggat tcagtgagta ttgtgctgca cagggaatta ggatggagaa gaccattcct 1740 gggacaccac aacagaatgg tgtggctgag cgcatgaata gaactctcaa tgagcgtgct 1800 agaagtatga ggttgcatgc tggactacca aaaacttttt gggctgatgc tgttagcact 1860 gcagcttacc tgataaaccg aggaccatca gtttccatgg agttcagact tcctgaggag 1920 gtttggagcg gtaaagaggt gaagttttca catttaaaag tttttggttg tgtttcttat 1980 gttcatattg attctgatgc tcgtagtaaa cttgatgcaa agtcaaaaat atgttttttc 2040 attggctatg gtgatgagaa atttggctat aggttttggg atgaacaaaa caggaaaatc 2100 atcagaagta gaaatgtgat atttaatgaa cagattatgt acaaggatag gtcaactgta 2160 acgtcagatg ttacagagtt agatcaaaag aaatctgagt ttgtcaactt agatgaattg 2220 actgaaagta ctgtccaaaa agggggtgaa gaagataagg agaatgtaaa ttcacaggta 2280 gatctgagta cacctatagt tgaagttcgc agatcttcta ggaacactag acctccgcag 2340 cgttattcac ctgttttaaa ttatctcctg ttgactgatg gtggtgagcc agagtgttat 2400 gatgaagcct tgcaagatga gaattcaagc aagtgggagt tagccatgaa ggatgagatg 2460 gattccctgt tggggaatca gacatggcaa ctgactgaat tgccagtagg aaagaaggct 2520 ttgcacaaca agtgggtata cagaataaag aatgagcatg atggtagcaa acgttacaag 2580 gccagattag ttgttaaagg gttccagcag aaggagggca ttgactacac agagatattt 2640 tctccagttg tgaagatgtc aacaattaga cttgtacttg gaatggtggc cgcagaaaac 2700 ttacatcttg agcagttaga tgtgaagaca gcattccttc atggtgactt ggaggaagac 2760 ctttacatga ttcaaccaga agggttcatt gttcagggac aagagaatct agtctgcaaa 2820 ctgagaaaga gcttgtatgg ccttaaacaa gctcctagac agtggtacaa gaagtttgac 2880 aattttatgc atagaattgg gttcaagaga tgtgaagctg atcactgttg ctattttaag 2940 tcctttgaca attcttatat catattacta ttgtatgtgg atgatatgct tattgcaggg 3000 tctgacattg agaagattaa taatctgaag aagcaattgt ccaaacagtt tgcaatgaag 3060 gatttgggag ctgcaaagca aatccttggt atgagaatca ttagagacaa ggctaatggt 3120 acattgaagc tttcacagtc agagtatgtg aagaaagttc tcagcaggtt caacatgaat 3180 gaagctaaac cagtgagcac acccttgggt agtcatttca aactaagcaa agaacagtca 3240 ccaaaaacag aagaagaaat ggaccatatg agcaaggtgc cctatgcctc agctattggc 3300 agcttgatgt atgctatggt gtgtacaaga ccagacattg cacatgcagt gggagttgtg 3360 agcagattca tgagtaggcc tggaaagcag cattgggagg cagtcaagtg gattttaaga 3420 tatctgaagg gttcattaga tacatgtctt tgcttcacag gtgcaagttt gaaactgcag 3480 ggttatgtag atgctgattt tgctggtgat attgatagta gaaaaagtac tactgggttt 3540 gtttttactc taggtggtac agctatatca tggacttcaa atctacagaa gattgttact 3600 ttgtctacta cagaagctga gtatgttgca gcaactgaag ctggaaagga gatgatttgg 3660 ctacatggtt tcttagatga attgggtaag aagcaggaga tgggcattct acacagtgat 3720 agtcagagtg caatttttct tgccaaaaat tcggcttttc attcaaagtc aaaacatata 3780 caaacaaaat accactttat ccgttatctt gttgaggata aactggtaat acttgagaag 3840 atttgtggat ctaagaaccc tgcagacatg ttgactaagg gtgtcactat tgagaagttg 3900 aagctgtgcg cagcttcaat tggtcttcta gcttgaggac aggaggatga gttgtaggga 3960 tgagggatcg tttcttggag gatagcggtt tgatgttggt gattggacta gtctccaagt 4020 gggagatt 4028 // ID Copia-59_VV-LTR repbase; DNA; EDCOT; 1194 BP. XX AC chr13; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-59_VV_; KW Copia-59_VV-I; Copia-59_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1194 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr13; Positions 23518268 23519461. XX SQ Sequence 1194 BP; 396 A; 134 C; 215 G; 449 T; 0 other; tgatagagat atactattaa ccatgcataa gcgtgaattt aatagtatgt tattatgatg 60 tcattctata aacaattatt tctttgtatt taattggaga tttgcattag ataaattaat 120 ctttcggcat aatttaataa taattgtgtt agtatatttt atatataact aactggacca 180 agtagagaat ggatgttttg tactgactgt taaaacatat tctctaggac attagaaata 240 agatttatgt ttttaatcat gatttaatta atatgagcaa atataaaatg tcttgtgttt 300 tgattcatta aagagtgagt ttcatttatt ggagcgataa gactcgatga gttggacaaa 360 gacgctttat gtttgcgatg tattaaataa tgattgaatc cacatctcgg tataaagatt 420 gatgatgcac tttaagtaag cttataaggt ttcatagtgt aaaccctgca ggtggatttt 480 tatccgacac atgaattaag ttaagcgaca atcttgaaga tctattgtta ctcaaataaa 540 ttgtcagtaa tttgtttgat gtaaatagca tctgtaatct taacgtggga aacataaatt 600 attatgtaat ggaattgtaa gattaataag gagttcaatc atgaattttt agtggtataa 660 tttgtgatta attataatga gaatatactg gtcttgtatg aattcttatt ataattagta 720 gccttgttaa ttttattcct atggtccctg ctgtgcctta attgtttgga ctatacatga 780 attatgtgtt ttaaataaat gatagattag tttttaatta aattttattt aattaaaaat 840 agataatcta atttatttaa aatgagcatt ttaagggaaa gagagtcacg cttatatcgg 900 tttttctgga agcaaattat acgcttaaga gtttctaaga aagcggtctt cttcccatcg 960 aagagaggta tattagaaac agaaaagaga gtgacaaaac cctagcgatt gttttttttt 1020 tgcccactca gaaatcatag tccggaaatt gataaggtaa acaacagaag attgtaggag 1080 attgtgggcg ttttcagtag agaaaaaggt tagtctttta catatggttt tggcttgcct 1140 ccatgcttgt ttcatcatga tttgtttccg ctgcgtaaat catggtttct atca 1194 // ID DNA-9-1BN_Mad repbase; DNA; EDCOT; 712 BP. XX AC . XX DT 07-OCT-2010 (Rel. 15.1, Created) DT 07-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA-9-1N_Mad; KW DNA-9-1BN_Mad. XX NM DNA-9-1BN_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-712 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1461-1461 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TSD is 9-bp long. Imperfect TIR is ~90-bp long (81% identity). XX SQ Sequence 712 BP; 275 A; 104 C; 136 G; 197 T; 0 other; gagtaatgct attcttacca caattttata ccacatttct ttaccatctt aggtggcaga 60 tgagttggac aagctacatc atttaatttc aattttctta ttaattaaaa cacttaaata 120 aggaaaattg cagacttcaa gatctccctc tggcgttagt aacttaattg ggtatgaacc 180 ctaatccgat agacaaattt gattttgact cctaattcgc atgaaagcta ataggcgtta 240 cttaatgaaa taatcagatg aaatccttct tttaaaccac aaaaaaaaaa aaaaaaatca 300 cgagatgaac aaccatggag taccaatgaa gattggagac agaaatactt gaaggggaat 360 gaggattggg gctacggggc atgagtctgg agatagaaat caatggtgat tgtggtatac 420 gagtaaattc tataaagctt gaccataatc atggaaatca acagaaatca ataaaaaaac 480 tggcgtgaaa aaagaaaggg gaaggaagaa gaagcagaat ggaaagggga aggaagaagg 540 agactcctcg tataccacaa tcatcattta attaacaatc tttttattaa ttattgatta 600 acattttgaa attaaatgct aattaattta gatgatgtgg ctgtccacat cagatgccac 660 ctaaggtggt atacaattgt ggtacaaaaa catggtaaga ataacattat tg 712 // ID Gypsy21-PTR_I repbase; DNA; EDCOT; 13180 BP. XX AC LG_XIV; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy21-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-13180 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-13180 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 322-322 (2007). XX DR Genome; LG_XIV; Positions 14288357 14275178. XX CC Positions [8960-9445] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 4800..6143 FT /product="Gypsy21-PTR_I_3p" FT /translation="MEVNKPISEDESNEFLKLMKHSEYSVVDQLKKTPARI FT SLMSLILSSELHRKALQKVLNEAYVPQDITQDTMEHLVGRIQASNYLYFTE FT DELDPEGTGHNKPLYITVKYKGCLIDKVLMDNGSALNVLPRHILDEMPIDA FT TYMRPSTMTARAYDGSPRQVIGTIDIKLFVGPQMFLITLQVMDIHPSYSML FT LGRPWIPASKAVTSSLHQCLKYIINGTLVKVKAEETLSMIRNVSVPYIEAE FT DCKDGNLHAFEIVNIEWIPENTVLRRPIISDTARMIAKCFFKHGLPFQNAP FT ITGNLKRVNMMKINAADKRFGLGFKPKKDDHKRAVRIKRERRLARMEGRKP FT EEEDIVIPPIHVSFPKSAYVMKPENMMEVLGQELVVMDINNVDEGKGKGWN FT CNDEPKTTKEDELLPQLTIHSLEEALTNAFVRKLLVDEVFQNWEIEEAPVI FT FKK" FT CDS 8321..9838 FT /product="Gypsy21-PTR_I_2p" FT /translation="MLIICQVKGEWQTKKEKLIPYQQYLSKLAEGFNEIDF FT THMGRDKNQFADALATLASMAKTDYGIRVQPICIEIKNFPTHCCSIEGEVD FT ENPWFYDIKRFIQYQEYPLGASKADMKTLRRLAMEFYLDGEILYKRSSNGT FT LLRCLDEIEAKVALQEIHEGICATHASGHMMARQMQRSGYFWMTMEKDCID FT YVRKCHKCQVYSDKINAPPAPLFNMTSPWPFAMWGIDVIGPINPKASNRHQ FT FILVAIAYFTKWVEASSYAHVTQKVVKCFIEKDLICWYGSPKKIVTDNAQN FT FNGKIIKELCVKWKIKHSNSSPYRPKMNGVVEATNKNIKKIIQKMVVTYKD FT WHEMLPFALHAYRTAIRTSTGATPYSLVFGMEAVMPLEVEIPSLRVLIESE FT PEEAEWAKVRYEQLNMISEKRLAVICHHQLYQRRMAKAYDRKVRPREFKEG FT DLVLRKILPLQSEDQSKWAPNYEGLYVVKKAFSRGALLLTRMDGDDLSRPV FT NSDSVKKYYV" XX SQ Sequence 13180 BP; 4456 A; 2216 C; 2699 G; 3809 T; 0 other; gaatggcgac tccgctgggg aattagggtt gagccaattg cttgtgtttg cttttcattt 60 gttctttctt attgctattt attttttggg catttatttt tttgcattat ttattttatg 120 taatatctac tgtaattctt ttcaattttc cagattgcca catgcatgca tgcttattta 180 tttgtgtatt cacacacttc actgtgaacc cataaaagct ctggacccga gctcatcctt 240 tttaagatta gaaaagaaag attcaggtgg caagtgtgac ttatgtccac tgatgctcat 300 ttgaactttc gtttagattg taactcaccc tatacaacta gtattatgga gtctttctct 360 catactcatg ttgtttaagg ttaagaggcc gattactcca tgggtaattc aggcaatcta 420 agaaccaaaa aatatcttta agattagact aaactgagcc aaatcttatg agttagatcc 480 tatcaattag gatatacctt ttaggacaca aaaaaatgtt aatgcattaa catacatgtt 540 catatacatt tcatattctc attaaatctc catcgatcct tataggaagt gtgagatgga 600 aaaacccatt actattgagg aatttttgac cagatcagaa ttgaaccaac atgatgaagg 660 ggattgtttg ccatcagaat ttgagtctca gttacttgcc agagcatgtt aaattagatg 720 acagaccact tggtacagga caattgctag attgctggga aaagttatca tttcatgatc 780 aaatcaattt tcagaaacaa tatggggatc tatcacattt actgaaaatt agggtccagc 840 atgcttgttt tcaagccatg atagggttct gggacctaga atatcggtgc ttcacttttg 900 ataccgtgga tatgactcct attatggagg agtatgcact ttctaatttt gcttggatta 960 cccagataga ctgtcaacga gcaaaatcac atgcaactaa acgaggaaat agccagggtt 1020 ggttttggaa tgaactagaa gccatattca agaggagatt acatgatgaa agcaatgaaa 1080 tttgattgag aattttggcc ataggcatat atggtttggt tcttttccca tctgctgagg 1140 aaatgatcaa ttttgaggct gtcaatgtat ttaaaaatgt ggtgaccctt aaaattaacc 1200 ctgctacaac aatattggca gaaactttct catccttgaa ttattgtaga aaagctggaa 1260 ggggtcgttt aagatgttgc ttgcagctgt tgtttgtctg gaccatgagt catatgatta 1320 aggggaagat ttcaggtttg gttggtaccc catggcatct ttattctaag ctggagaatt 1380 ttgctgaaaa acatttgcat gaagtaggaa gaaccacatg ggaatcaatg tttctaagtc 1440 taagtaaatc tcaatttcat tggagaagtc gatactctta cttcaaatct tatttggcat 1500 actgtggtga gtacccatgg gtcccgttga caggagcccg ctgctgtatt agttattgtc 1560 ctaacatggt tttacgacag tttggatttg agcagtttat tccaaggatt accgaactgg 1620 caacatttta tgaagatttc aagacctcaa agaaattatt ggagtcagta aagaaggtat 1680 ggaagcatcc tggtagggtt acttctgcta agagagtaga aggaaaaaca actaaaggat 1740 atccaatatg gcaaaggaag aaagggaaag gttacaaagt tcctcctttt gaagggccac 1800 ccaggtcttt gattcagtct gctgaagaca tacacgaaga agtccgcgcc caacaagaat 1860 cttacaacct aagtttgaat gctgaagtgg aagagttagg ggctaaaaaa agaaagttag 1920 aaagttagaa tctaatctaa taaaacagga aaagaatgac ttgtcagctc agctacaaca 1980 tcaacaactt gagttccagc aattacaaga aaaatatgta cttttggcag aagataagag 2040 gaagcaagat gccagcatga aaagatgggt tagaagagca tcaaaagctg aggaaatgat 2100 attaaagttg gaagagacaa ataaatcact tcaggaacaa tgtcaaaatc aagatacaat 2160 cattgccaat ttagatgagc aggtggacca tttgctttct attgagcaaa ccttatcatc 2220 agaaaaagaa aatgcaaaaa aagaagcaga atgttgggct tctgaagcta tgcgctatca 2280 tgtacaagca tatgatgcca aaaattatgc tttaggatta aagaggcata gcccaacaaa 2340 tagcagatgg tgagccaatg actagaaatg aattccatcg gttttttggg ttgatcagag 2400 atggaattaa tgagatctca gcatatgacg gtccaaggct ttggaaagat tgacttgttg 2460 tgattttaat attgtaaatt aatgaaagat aatttcatca tcttttcatc atgagaaatg 2520 cttctgattt atggcatcaa atttctcccc taaatcggtt caagttcttg taggtttgga 2580 gtcctcagtg agaactttct taagagaatc tgatctggtc tgttcctcgt cataagttat 2640 aggaaaaaca aataacaagc atgcataaaa catatggcat tttgcatcca tttgtgcatt 2700 tcattcattt tacttgcatt cattcaggtt gaaatatagg tcccccaaaa gaccataaaa 2760 ttcattacac tcgactacga aggaagataa tggagaacga agaaagagca catctagagg 2820 ctcattatca aagggagttg aagagcatga aaagcgatat cacacgactt acaagtctac 2880 tcgagcaggc cttagtatcc aagtctgggg aggatacctc tactcagccg gcaattgcaa 2940 ctccatctgt atctatgcca gcagctcctt ttgtattcac gtctcaaaat ttaggggcaa 3000 acccctcttc atttgaacaa cggttcacta cccatgttcc accaacacaa gtgccggtta 3060 ctgtaaactt gacaaccgat gacccatata ggatgaaatt ctctaaacat gttgattatg 3120 ataaattgac tgctctggaa gaaagattga gggcagtcga aggggcagac ttatatgatc 3180 ctgttcatgc tgcagagatg tgtttagttc caaatgtagc tgtacccaaa gaatttaggg 3240 taccagaatt catcaagtat actggaactg aatgcctagt cactcatttt aaatcttatt 3300 gcaataagat ggcagaagta gtgaatgatg agaaacttct catccatttc tttcaagaca 3360 gtctttctgg atcggcacta agctggtagg tatacaaggc tagataatac aaagatcaga 3420 aagtgaaaag atttggtaaa agcttttgtg gagcagtata aattcaacat gaaggtagcc 3480 ccagacaggt caagcttgtt agtcatggag aagggcaaca aagagactgt aagagaatac 3540 gctttgagat ggcgtgaaaa agcatctcat gtgcaaccct ctttgttaga aaaagaaatg 3600 gtcactctgt tttccaacac ttttaaatct ccttactttg aacacctagt gggtagttca 3660 gctcaacatt tctatgatgc tcgtaaatat cgctaagagg atagaacaag caataagaat 3720 ggggggaatg ttagagccta ctgagaagaa aggctttact gggaaaaaga aggattctga 3780 ggtgaacaac ttggaaggag tgtattaggg taagaaaaaa aaattaccat cattataact 3840 tccaaatacc tacccaacaa gttgcaagtg taaacttcac taaatatttc cctaccaacc 3900 aacaaaacca accaaatgac caacaaagta accagattgt taatcctcca agaaggaatt 3960 ttcaaagaac ccaaaaacga ttgccaccat taccacttcc cttgggagaa atgtattcaa 4020 agttgttgag tattgggcaa gtggcccctg ttcccttaac cccactgcaa cctctatatc 4080 caaattggta taagccggat ctgacatgtg agtatcatgc tggcattgct gggcataaca 4140 ttgaaagcta taatgcattt aaaaacaagc ttctgcaatt gataaaagct ggatggataa 4200 cttttgatga tgcaccgaat gtgaattcca accctttacc caatcatgct gcaagtagtg 4260 gaggggtaaa tgttgtagga gtagagggta agaaggaaag agttttgaag gtttccatgg 4320 aaagactgta tggtatgctg gtatagtctg gatatttacc tgagtttgaa ccagtgatga 4380 atgaaaataa ttactgtaag tttcatggcg aggtgggaca tcacattgat gattgtcaag 4440 aatttcacca ggaagtgaaa aggatgctga cttttggcat gataaggata gagagtgaag 4500 aagagagtag tgaagttggg atgataggcc gtcaggggaa aaaaatggag gtttgtagac 4560 tccaaccaac tgtgggtggt ccaccaaaac taatcctgac caagcctgta tgcacaaata 4620 gtggaagtta tggcacaatg ccttataatt atgggtattc tttcaacatt aagaatccta 4680 ctcctatctt ccatactgaa attggcggtt tgactcgaag tggtcgttgt tttacaccag 4740 aagaattaga gaggtagagg aaagctaaag gaaaagaaat agttgatgct tttaaaggta 4800 tggaagtgaa caaacctata agtgaagatg agtctaatga atttctgaag ttgatgaagc 4860 atagtgagta tagtgtggta gatcagttga agaaaactcc tgctagaatc tctttaatgt 4920 cacttatctt gagttctgag ttacaccgta aagcattgca aaaggtgttg aatgaagcat 4980 atgtgccaca ggatattact caggatacaa tggaacactt ggtgggaaga attcaagcct 5040 ctaattactt atacttcact gaagatgagc tagacccgga agggactggg cataacaagc 5100 ctttgtacat caccgtgaaa tataagggct gtctgatcga caaagtgctt atggataatg 5160 gttcagcttt gaatgtgcta ccaaggcata tactagatga gatgccaatt gatgctactt 5220 atatgaggcc aagcactatg acagctagag catatgatgg ttcccctaga caggtaatag 5280 ggaccattga cattaaattg tttgtagggc ctcagatgtt tttgataacc ctacaagtga 5340 tggatatcca tccttcatat agcatgttat taggaaggcc atggataccc gcctctaagg 5400 ctgtgacatc atctctacac caatgtctga agtacattat caatggtact ctagtgaaag 5460 ttaaggcaga agaaaccttg tccatgataa ggaatgtgtc ggtcccttat attgaagcag 5520 aagattgcaa agatggaaat ctccatgcct tcgagattgt gaacattgaa tggataccag 5580 agaatacggt gttgagaaga ccaattattt ctgatactgc cagaatgata gctaagtgtt 5640 tttttaaaca tgggctacca ttccagaatg ctccaattac tggaaatctt aagagagtca 5700 acatgatgaa aattaatgct gctgataaga ggtttgggct tggctttaag cctaagaaag 5760 atgatcacaa gagagctgtt aggattaagc gagaaagaag gttggctaga atggaaggaa 5820 gaaagccaga agaagaagat attgtaatcc caccaatcca tgtttctttc ccaaagtcag 5880 catatgtaat gaaacctgaa aacatgatgg aagtcttggg acaggaactt gttgtcatgg 5940 atatcaacaa tgtagatgaa ggtaaaggaa aaggctggaa ttgtaatgat gagccaaaaa 6000 caacaaaaga agatgaactg ttacctcagt taaccatcca ctctctagaa gaggctctaa 6060 ccaacgcctt tgtacgaaag cttttggttg atgaagtatt ccagaattgg gagattgaag 6120 aagccccagt tattttcaag aagtaatgat taagcatcta cttatattcg cttttatgtg 6180 ctttgtgtgc tttgctttgt attttgcttt gtgtttttgt acctagttgg aaattttggc 6240 tcaagatgtc aacataaggt ctttcataat tattgagcca acttttaaaa tattattgag 6300 atcatgcatt ttcttcaaca tttgttatct tattttgctt tgtttggcta caagatatgc 6360 atttacacta aaaacacctt ccgttttcag gaattctgaa agtgaatcct ccataaatcc 6420 acaaacatat tgcattgaaa atgaatggcc aaactttgat aaggatgtga ttgcaatgga 6480 tgaagaggaa tggaataaaa atgatatgaa agagtttact agacaaatag aatagtctga 6540 gcatgcttgg aaacctacaa aagaagaatt agaggtgata actgtaggca ccgagcaaga 6600 taaaagagag ttaaagattg gaactctgat tactacagaa gaaagatgta gtttaaccac 6660 actactataa gagtatatgg atgtgtttgc ctggtcttat gcagatatgc ctagtttaga 6720 cattgatgtt gtagtacaca aagtgccttt gatagaagga tgtaaacctg ttaagcagaa 6780 attgagaaga actcacccgg atattctatc aaggtcaagg tagagataga gaagcagtgg 6840 catgccggtt ttctagaagt tattaaatac cctcaatggg tatctaacat agtggtagtc 6900 ccaaaaaagg atgacaaaat cagagtatgt gtagacttca gggatctaaa caaagctagt 6960 cccaaggatg attttccttt gcctcacata gacgttctgg tggacaatgc tgctaagagt 7020 tcaacttatt ccttcatgga cggattctcc gggtataacc agattaaaat ggctgaagaa 7080 gagaaagaga agaccacttt tgtcacacca tggggaacat tttgctacaa agtgatgcca 7140 ttcgggttaa agaatgctgg agccacatat caaagggcaa tggtgacact tttccatgat 7200 atgatacata aagagattga agtgtatgtg gatgatatga ttgccaagtc taaaaatgaa 7260 gaagatcatg ttcaggttct aagaaaatta tttgatagac taaggaagta tcagttgaag 7320 ctgaatcctg caaaatgctc atttggggtg aagttcggaa agttgctagg atttgtgata 7380 agcaataaag gaatagaggt cgatcctgat aaagtgaaag caattcaggc tatgacagtt 7440 cctaaaaccg aaaaagaagt aagaggcttc ttaggacgtt taaactacat cgctcgattc 7500 atatctcaat taataacaac atgtgagcca attttccgat tacttcgaaa aaagaatcct 7560 ggtacatggg acaaagattg tcaagaggct tttgacaaaa taaagcaata cttacagaat 7620 ccacctttgt tagtgccacc tgtgcctgga agacctttga tcttgtattt gatagtaacc 7680 gaggcagcaa tgggttgtgt gttgggacaa catgatgagt ctggaagaaa ggagcaagcc 7740 atctattatc tgagtaagaa gtttaccgat tgtgaatcca gatacaccat gactgaaaag 7800 ctatgttgtg cccttgtgtg gagtacgaag cgtcttcgac aatatatgtt gtattatacc 7860 acctggttga tctcaaaaat ggatccgctt aaatacatct ttgagaaacc ttacttgtca 7920 agctgaatag caaggtagca agtaatgttg gcagagtatg acattgtata caagacaaga 7980 acatctgtaa agggaagtgt aattgctgat catttagcag ataatgctat caaagattat 8040 gagcctttga aatttgactt tccagatgag gatgtgttga tagtagaaga agacaaagag 8100 aagaatgatt ggtggattat gtattttgat ggggcagtga atgtatctgg caatggagca 8160 ggggctgtga taatctcatc ctaataagaa gcactatccc atctcaatca agctataatt 8220 tgaatgtact aacaatactg ttgaatatga ggcttgtatc cttggtttag aagctgcttt 8280 agagattaag ataaagaagc ttgatatcta tggggattca atgttaataa tctgtcaagt 8340 gaaaggcgaa tggcagacca aaaaagaaaa attgatacca tatcaacaat atctctcaaa 8400 actggctgag ggctttaatg agatagattt tacccatatg ggaagagaca aaaaccagtt 8460 tgctgatgct ttggcaacct tagcttctat ggccaaaact gattacggaa tcagggtaca 8520 accaatctgc attgagatta aaaattttcc aactcattgt tgttcaattg aaggagaagt 8580 agatgagaac ccatggtttt atgacatcaa gcgatttatc caatatcaag agtatccctt 8640 gggggcatct aaagcagata tgaagacctt gagacggtta gccatggaat tttacctgga 8700 tggagaaatt ctatataaaa gatcatccaa tggaacttta ttaagatgtc tagatgaaat 8760 cgaagctaag gtagcattgc aagaaattca tgaaggaatt tgtgcaactc atgcaagtgg 8820 gcatatgatg gctagacaaa tgcaacgatc tgggtacttc tggatgacca tggagaaaga 8880 ttgcatcgat tatgtcagaa aatgccataa atgtcaggtg tatagtgata agataaatgc 8940 acctccagct cctctgttta atatgacatc accatggcca tttgcaatgt ggggaataga 9000 tgtgattggg ccaatcaacc caaaggccag caataggcat caatttatct tagtagccat 9060 tgcttacttc acaaagtggg tggaggccag ctcttatgct catgtaactc aaaaggtggt 9120 caagtgtttc attgagaaag atttgatttg ttggtacggt tcacctaaga agatagtgac 9180 tgataacgcc caaaatttta atggaaaaat aatcaaagaa ttgtgtgtga agtggaaaat 9240 taaacattca aactcgtctc cttacagacc aaagatgaat ggtgttgtcg aagctacaaa 9300 caagaatatc aagaagatta tccagaagat ggtagtcact tataaggatt ggcatgagat 9360 gcttcccttt gctctgcatg catatcgcac agcaataagg acatctactg gagctacacc 9420 ttactcatta gtatttggga tggaggcggt gatgcctttg gaagtagaaa ttccatcttt 9480 gagagtacta atagaatctg aaccagaaga agctgaatgg gctaaagtga gatatgagca 9540 gctaaacatg ataagtgaga agaggttggc tgtaatttgt catcaccagt tataccaaag 9600 aaggatggcc aaagcatatg accggaaagt ccgaccaagg gaattcaaag aaggggatct 9660 tgtactaaga aaaatcttac cattacaaag tgaagaccaa agcaagtggg caccaaacta 9720 tgaaggcctt tatgtagtga agaaagcatt ctccagaggg gctctgttat taactaggat 9780 ggatggagat gatttatcta ggcctgtgaa ctctgattct gtgaaaaagt attatgtatg 9840 atgtgtttca tccaatcaaa atcaattaaa tgaagttttg gtcaggaaat tctctttgca 9900 tatacctcac caaaaaaccc atgcatgatc tcaatggctc aacaatttga tctttcaaac 9960 ttttttacag gagaacccat tcttcttaaa tgaggtttta aaagaaatga ttttgtttgt 10020 gatttcaatg aaataaatca atgatttgtt taggataatg ttcagagcaa ttcctttgaa 10080 agagatgacc aaacaagtca aaaacatgca attggaacaa ctatcactca aattatgtct 10140 tggatttaca ttttatcaac atgaataatg gttggtagta tattagttgt catggactcg 10200 aaaaacatgg tatcttgcaa atccaaagca ttacactgga tgtggacaaa gtttattggt 10260 tttaactgat cttacttgaa atgaggaaag gccatctttg atattccttt cactttcttt 10320 aaaattatcc tttgccgtcc ccatttgagc tgagtctatt ttaagttttt tttctttctt 10380 tcataaggac cttaactaag atcacatcct acaccagggg gcaaaaagag agaaatgatt 10440 atggaaatcg tcttgaaagc atgtgtgagc ttataaagtc tgtcgccaag gaattcaaca 10500 aaattccaaa taactgagaa aatgctcaac aaatatgaga gtacaaaaga caaaaaatcc 10560 taatttggaa tatgtagtat cattttttgg ttgtcaagat agcaaaagaa aaggtgaaga 10620 taagataaca gtgatctata gtttttaaac ccttaaacac tcttttgagc ttatgaaata 10680 ctctttcttc tatagccttg agccataaaa tacattacgt gcctttaaag tcctttctaa 10740 tcaagtaagc aacctggatc aataaacgac gttctcaaaa tataagagac ttttccataa 10800 agagtcatgg cgtagcaaat aattactcgt tattattcat gctgttaaaa ggagtgtttc 10860 taaaaataaa aggcaaattg tttcttttct ctcaaaatac attcaagcaa tcgcttgaac 10920 actttgaaaa tcaaagcaga aggtcatctc atcacttacc ttcatctgag cttactttta 10980 ctaagagatt tgacataaag ccctaaagtt gcctgaacat tgttataaac agacattgag 11040 agttttagtt ttcaagaaca aaacagatct tttgtaaaat catttttgaa agaaggtttt 11100 ctttgtaaga aaaatgaata tatgacacac tacgaggcac tattagaaaa tcaaagattc 11160 taatgacaac aagagcaaag gaggaaatga aatgaggcaa ttaattctcc caggggggca 11220 gagaagcagt taccagatcc ctaatggcac aaagaaattt gcttccctag tggaaaatac 11280 acatgataaa actgtagact tcttccagca tgaggactga aatagtatga tttgcagtat 11340 ctacgaaagg agattattga ctctcacaat atgattagtt agacaacaag ataactgata 11400 catcgtcagt aagcgaaatg tatatgaaaa tcccaggtga agcgggataa tcctcatata 11460 ttgaccatat gaattggtta aagaatcctc aataatggga atattgcaaa cagaacaatg 11520 tcgtgccaag gagaagttaa tgctctcagt gaagtaacca atagagaaag gtgcagtaac 11580 tgttgggaaa ctcaaacaaa gtttatctta gaaaaatgag caacatgggt cggcttaagt 11640 agatttgaag gatgcgtgaa tcaaaatagg tcactaaaaa tcaagatcct caaacaagat 11700 gaatggggga tttatatttc aaaaacaggt aagatgcatt gcatatcatc taatttcatg 11760 agcattgcat atttgttttg cagatatttc acgaaacaaa attcccattg ggatccaaca 11820 agactcagat gaattgaagt tcttttaaat cacatcaaat atggcaagtc cacaaaagca 11880 aaattcataa atgaagacaa gaaagatgga tttttattca tggaaaaaag tgtacaagta 11940 taaatgttaa acagtgcgag gacgatcagg gatattttca tcttgatgat caatcatgcc 12000 tcgaaattcc tcaaattgtt tatgcatacg ctccatctct tcctcgaact cgaggtgtcg 12060 tgtgttaaca tagtccctcc aaaagtcaac acgtgtattt agctcttggt ttctcctctc 12120 caagttgttt ctgtgacgtc tctcatcaca gagtctattc cttaaattct cgatctgatg 12180 atggagatca ggaacctgag tattcaactc aagtcttctg gcatgaagac gctctgcaac 12240 gctcaccaaa gacgaagtag ctctaatact gagagcaagt gactgattca ctgcttcaat 12300 attgatcctg gctgccagca ttatttcatc acgaggaagg atcatgtctc tagccacggc 12360 tacaacagta tctttattgt ccattacagt atcctctatt gtaactggat gaccattcac 12420 ttcaaaggta gtacgccaaa ctacagactc caccgcagga acaaggtttg ggttagcatt 12480 ggaagaagag gaagacatgg ttaaagcttc aaaagttgag aactttgaaa gtattgaaaa 12540 tacaagaagt tgatgatgtc tttcaccaaa tactgcgtga tttataagga ttttactcct 12600 accattattt tgaatagaag atcgaatctc agtcgtacat ataagacttt cttgagaagc 12660 tttcatcatc tgtgagatcg atttacaaat cagatctcaa ccgtagatat aagactttct 12720 tgagaagctt tcatcatctc tgagatcgat ttacaaatca gatctcaatc atacaagtat 12780 gaattccttt agaagttttc atcaaccctg aagctcatgg tgaaatccct ttcatgtatt 12840 tcacaagact aatgctgaaa tcacttttat gtatttcata aaaatcaatg ttgaaatcac 12900 ttttatgtat ttcaaaaaaa tccatgttga aatcactttc atgtatttca caaacaggtt 12960 ggtcacctgg aaaataagac caatgctgaa atcactttca tgtatttcac aaaactaatc 13020 tgaaatcact ttcatgtatt tcacaaaact aatctgaaat cactttcatg tatttcacaa 13080 aatcaatttt gaaatcactt tcatatattt cacaaaacca ttgctgaaat cactttcaga 13140 tatttcacaa aatcaatatt gaaaacgtca atattttaga 13180 // ID Gypsy-2_TC-LTR repbase; DNA; EDCOT; 664 BP. XX AC CACC01024994; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-2_TC_; KW Gypsy-2_TC-I; Gypsy-2_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-664 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01024994; Positions 29 692. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 664 BP; 221 A; 72 C; 155 G; 216 T; 0 other; tgaaattttt ggaaaaagat tcaactacaa agctaccaag gtgagtagga aattagaatt 60 tgatatttaa gtgttgagaa tagctagtga tgagacttgg gaatgttttg cagttgaggt 120 tgtttattca ttttaaagtg attaggatgg tgcaaataat agccatttaa tagtagttgg 180 aaactagtta ggaatgacta gtagaaccca atttagaaaa tagctttgga atagtaataa 240 tgccaagttg ggttgatggt gatgttgttg tgtgtgatag gttccaacga aaccctacac 300 ctctattcgg agcattagtc aaagctagag cccaccaaaa catcaataaa gactggtgag 360 tgaacttgca tttcaaaatt tctttggaaa atgtaatgta tttgaatgaa catttgaatg 420 attttatcca acttttcttt aaaaatatgt gccagggaac aagcccttga tgaaatgttt 480 caatactgtg aaaaatgtga aatgtttaaa aggatgaatc catgtgcttc tatattatgt 540 tggtaggtat atatatgaat atatgttttg tattgatgaa taatgttgtg tgatgatgtt 600 gaagtgtgcg agtagggagt gcacacatga tgatgataga gtgtgcgagt agggagtgca 660 caca 664 // ID SHALINE18_MT repbase; DNA; EDCOT; 3585 BP. XX AC . XX DT 23-JAN-2007 (Rel. 12.01, Created) DT 23-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A LINE element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW retroposon; Poly-A tail; ORF; Interspersed; repeat; SHALINE18_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3585 RA Shankar R. and Jurka J.; RT "SHALINE18_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 95-95 (2007). XX DR [1] (Consensus) XX CC The element has 5' end truncated heavily. It lacks the first ORF CC while the second ORF is present with intact domain for reverse CC transcriptase. The sequence is present in multiple copies in the CC genome. XX FH Key Location/Qualifiers FT CDS join(214..246,310..324,334..1710,1714..1761) FT /product="SHALINE18_1p" FT /translation="MVYEGISFSLLNKPPIQPIRKEIEKCRKKLERVRTQV FT CSSNINYFNTLRQRLDKLLVKDDVFWKQRAKTHWYRDGDLNTKFFHAAATS FT RRTVNKITHLEDANDVKCTSVDGMKXIAKDYFLDLFQHQDGDRVRVINAVP FT XSISTEDNDXLTRPFSVDEFKEAAFSMXADKCPGPDGFNPGFFQNFWNXCG FT KEIFEAACYWLDNGAFPPYLNSTNITLIPKGDTQTSMKDWRPIALCNVLYK FT IVAKVLANRLKVVLDKCISXNQSAFVPGRSILDNAMAAIEIVHYMQCKTKG FT KEGDVALKLDISKAYDRIDWDYLRSIMVKMGFSSKWSNWIMMCVETVDYSV FT LVNGXKVGPIIPGRGLRQGDPLSPYLFIICAEGLSSLIRXAEGSGNISGAK FT ICKNAPIISHLLFADDCFLFFRAKSGQAQGMKNILAIYENASGQAINFQKS FT EIFCSRNVPDDAVKASIATNLWSSTSFGYRIPWSTFYDWQKSYINF" XX SQ Sequence 3585 BP; 1123 A; 540 C; 768 G; 1133 T; 21 other; gtgtctactt gttaccaata gttaataaag ataatttggt aaaataatca ttctctttct 60 tttaatcatt acatttctta atatgtgtgt aaagacctaa aacgacactc attttgaaat 120 ggagagtagt agataagctc ataaattggc tttattttat taaataaaaa ttggcttggt 180 aacaaaaggg gtaaatttgt cacaaaaaag gtaatggtat acgagggaat tagttttagt 240 ttgttataat atatatttgc tttggtttgt tacaacacaa ggtatttgcg taaaaaacga 300 aaatcataaa acaaacctcc aatataagta taacaaccaa taaggaaaga aattgaaaag 360 tgcaggaaga aacttgaaag agttcgaact caggtgtgtt cctcaaatat caattatttt 420 aatactctga gacaaaggct cgacaaattg cttgttaaag atgatgtktt ttggaaacaa 480 cgggcgaaga cacactggta tcgagatgga gatcttaata ccaagttttt ccacgctgca 540 gcaacctcaa ggcgaacagt taataaaatt acccatctcg aggatgcaaa tgatgttaag 600 tgtacctctg tagatggtat gaaaratatt gctaaggatt attttcttga tttgtttcaa 660 caccaggatg gagatcgtgt cagagtcatt aatgcagttc ctmcktctat ctcaaccgaa 720 gataatgatw tgctcactcg accgttttca gttgatgaat ttaaagaggc tgctttctct 780 atgmaagcag ataagtgtcc aggaccagat ggctttaatc caggtttctt tcaaaatttt 840 tggaataytt gtggtaaaga aatttttgag gcagcatgtt attggctaga taatggtgct 900 ttccctccat atttaaattc taccaacatt actcttattc cgaaaggaga tactcagaca 960 tcgatgaaag attggagacc tattgctttg tgtaatgtgc tttacaagat agtggctaaa 1020 gtgcttgcta acaggttaaa ggtagtgctc gataaatgta tatctgawaa tcagtctgct 1080 tttgtcccag gacgatctat tttagataat gctatggctg ctattgagat agttcactat 1140 atgcaatgca agactaaagg taaggaagga gatgttgctc ttaagttaga cattagtaaa 1200 gcttatgaca gaatagattg ggattatctg agaagcataa tggttaagat gggtttttct 1260 tcgaaatggt caaattggat tatgatgtgt gttgagacgg ttgattactc tgttytggty 1320 aatggtgawa aagttggtcc tattattcca ggtcgtggcc tcaggcaagg kgatcctcta 1380 tcaccttatt tgtttatcat ttgtgctgaa gggctttcat cacttattcg traagcagaa 1440 ggaagcggta atattagtgg tgctaagatt tgtaaaaatg caccaattat ttcccatctt 1500 ctgtttgcag atgattgttt tctcttcttt agagctaaaa gtggtcaagc tcagggtatg 1560 aaaaatattt tagcaattta tgaaaatgct tctggtcaag ctattaattt ccagaagtca 1620 gaaatttttt gtagcaggaa tgttccagat gatgcagtca aagcttctat cgctacaaat 1680 ctttggagtt caacaagttt tgggtacagg taaatacctt ggtctacctt ctatgattgg 1740 cagaagtcat acatcaactt ttaaatttat taaggataga gtgtggaaga aaattaactc 1800 ttggagcagc aaatgcttgt cacaagctgg aagagaaatt ctaatcaaat ctgtcttgca 1860 atcgattcct tcatacatca tgagtatttt cgctatccct aaatccatta ttgttgagat 1920 agaaaaaatg cttaattcat tctggtgggg tcacaacaaa agaaacacta aaggaatcca 1980 ctggatgtct tgggaaaggc tcagcattca gaaaaaggaa ggaggtatgg gttttaaaaa 2040 tcttcgcgct tttaatgwgg ctatgcttgg aaagccagga tggaagttgg tttcttctcc 2100 acacaacatt gtcactagat tgttcaaagc aaaatatttt ccsmaatgtg attttttgga 2160 ctctaagatt ggtcacaatc caagttatgt ttggcgcagt atttgggggg ctaaaagagt 2220 tgttagagaa ggatacaagt ggagtatagg ttcaggaact gatatttcag tttgggatca 2280 gcggtggcta gtagatggtg gtgttctaca gaagccagaa agtgtgccag aagaattcaa 2340 agagcttact gttgcagatc ttttcatacc tcaaactcag ttttggaatg ttggtttatt 2400 aaggaacctt gttagcaacg aagatactaa tcgcatcctt aatactccaa tctttgaacc 2460 taatcagtac acgataaaag agtttggaag ttagaaacaa atggtatcta ttctgttaaa 2520 agtgcatatc gtatcagtct cagtcaacat gtggatttga gtactcaccg ttgtgatgga 2580 aattgggwwc tcatttggaa tcttaaagta cctcctaagg tgaagaattt tctatggcga 2640 gcttgccgaa attgctcttc caacaagagt tcgacttcaa gacagagggg ttaattgtac 2700 aaaaacttgt gctttatgcg agaatgagga tgaagatagt atgcatttat ttttttattg 2760 tactaagagc aggcagtgtt ggcagcaatt agggttgtgg agcacagttc agcaaaaggc 2820 tcaattatta atctcagctt tgsggtcacc atgtttgaaa tcctgcagga gctagattcg 2880 agtcaacgag tcatttgggc ttgtgttatg tggtctattt ggaaacagag aaataatagt 2940 atctggagga atgaagtcat gactactgca gcagttcgtg acagaggcct taatcttcta 3000 acgggttggc aaaacgcgca aaatagccgt aatcatagcg ratgtacagc aacaacgtat 3060 tgacgacaca gtttggagaa agccagatga aggtcggttc aaatgtaatg ttgatgctgc 3120 tttcttcaaa gaaagtaacc gggttggcat aggaatatgc attagagatg ataacgggag 3180 tttggtgtta gccaaaactg attggttaac kccactctta gatgtacata tgggagaagc 3240 tattggtctt ttatatgcta gcagatgggt taaagagctg aatttagata atatggattt 3300 tgagcttgac tctaagaggg tagtagatag ttttcatagc actagaaatg atgtatctga 3360 tttaggagct atcattaaag attgtaggac tactttctca tcttttttca caaactctaa 3420 ggtagagttt attaggagac aagcaaatga ggttgctcat agtcttgcta gggcggccac 3480 attttatgct agtttccact atttcactgt attacctgat tgtattcaag atattcttat 3540 taatgaaatg cgataatttt ctttctgtca aaaaaaaaaa aaaaa 3585 // ID Copia-46_Mad-LTR repbase; DNA; EDCOT; 262 BP. XX AC ACYM01031533; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-46_Mad-I; KW Copia-46_Mad-LTR; Copia-46_Mad_. XX NM Copia-46_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-262 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1396-1396 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01031533; Positions 12086 11825. XX SQ Sequence 262 BP; 80 A; 49 C; 35 G; 98 T; 0 other; tgtaaggagt agtcaatcta agggatattc tcttgacatg tatcataaga ttaggcaatt 60 agttaagggt ttgttatatc tgttagctta gtctgtaagt taccttagtt acacatatat 120 atactacaat taaatgtact gagtaatgag taaaaagatt aatacaaaca agattacttc 180 tctctctcta aattctctct ttctctctct ccctgtctct gcattcatct tctctactac 240 aacagatcat tcttgcttaa ca 262 // ID Gypsy-26_VV-I repbase; DNA; EDCOT; 14102 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-26_VV_; KW Gypsy-26_VV-LTR; Gypsy-26_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-14102 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 13433649 13419548. XX CC Positions [5620-6075] - Reverse transcriptase CC Positions [7878-8138] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 6393..7610 FT /product="Gypsy-26_VV-I_4p" FT /translation="MLAQLDDSGKDRAIYYLSKRMLDYETRYVTIERYCLA FT LVWVTRRLRHYMTEYSVHLISRLDPLKYLFDRPTLVGRLMRWLVLLTEFDI FT HYVTQKSIRGSIVADHLASLPVSDARAIDDDFPDEDVAAVTSLSGWCMYFD FT GAANHSGYGIGVLLISPHGDHIPRSVRLAFTNRHPATNNIVEYEACILGLE FT TALELGIRQMEVFGDSNLVLRQIQGEWKTRDAKLRPYHAYLELLVARFENL FT RYTHLPRAQNQFADALATLASMIDIPADATVRPLLIESRSAPAYCCLIDDM FT EIDDGLPWYHDIYHFLRLGVYPEAATAKDRRALRQLATRFVICGETLYRRS FT LDGILLLCLDRASADRVMREVHAGVCGPHMGGHMLARKIMRTGYFWLTMET FT DCCQFVQRCPEC" FT CDS join(2647..4110,4114..5550) FT /product="Gypsy-26_VV-I_1p" FT /translation="MPQTLVLPSYATQGIERPAVSYTPTGQPCYAAQFTPR FT PAPLYPGPRAQQTSAPFASRTQRQFSQIGMPLSQALRKLIETGLLTALTPR FT PLPQPIPAQFRMDLHCAYHQGPGHETDRCTALRHAIQDLIDQGLVHLGQPS FT VTTNPLPTHTTHAVPPPAGGIHFLDFDETDDHVHMLSWDDPDPEPIMPAGI FT YETSGVTLEPQMLAPFRLVPEAASVQAATSEPLTFTRYSVQAPYILIPDVE FT EVQAPHSDDPQTLDVQYILRGGRVVRQPPPAAARPVEGTFASQEEVRAEDD FT GILRQLQSTQARISIWSLLASSSTHRDALTRALSQIRVDTTTTPEGLIHMM FT TAGRATCIVFSDDDLPPEGSDHTRPLYISVGCSGRRVPSVLLDNGSALNVC FT PLAIAIALGYGPSDFGPSTQTVRAYDSTRREVMGTLEIELLIGPATFVAIF FT QLLRIPTSFNLLLGRPWIHRAGAIPSSLHQKVKFIHDSQIVVVSVGDMFIA FT AEPVLEISHTDDDLFLTGFTFDEVQTVEIEDFCRDFVAMSFDRHGSTVVLD FT IMRSMSYLPGMGLGRRQHGPSEFIAIPDHDVPFGLGFIPTEADYLYMARLR FT KERVRARLTHTPFYYPLRPYTRSLADYFARASEPHAPSDGIVGGLSTTQEA FT ELQRLVQQLRLRDGSPSPSTSVLIAPSSPDRTSLMTLCFPDEIDEHETLAE FT VGDVVDGAAPHDEYINEMLALSLSQIEETIQPGLASSFDLFGVFIIELAEE FT SLTAPALESIEDLIPFDDLTDSHVGIVEGASDFVDPPLSFDVLSGFVSRSD FT YVSDVSSMDLSIFEYLPVSCDIDLSAPSSPTSQIFYIDDEIAQHDSDDDSS FT SVSDSNPVDQRVSPAVGDIEIVDFGTADQPRELRIGSDLSTDERDSLIQLL FT RAYLDVFAWSYEDMPGLDPSIVQHRLPLLPHARPVKQKLRRLHPRWSLQVK FT EEIQKQLSVGFL" XX SQ Sequence 14102 BP; 3030 A; 3252 C; 3405 G; 4415 T; 0 other; aaatggcgac tccactgggg atcattagag ggtcaagctt gaacttagga tgtagcaaat 60 gtggcttttg atgagtcgat tagtggatac tcacttcttg attgcacaat gagggttctc 120 gagttttcac ctgggacatt gacatgattg atcgtattag tcgattatct tgattgggga 180 ttttgacaca gtgattttct ttgtgcttca ttgatatatt ttgtttgaga tatttgacat 240 gttgattacg atgattgatt cgtattgata gaggattctg agatagctat tttctctgtg 300 cttgattgcc atgttcgttt gaggtattga catgctgatt gtattgattg cctatcttat 360 ttcgcttagt atagtgattt tgatttgcca tgattattct gaccgccttg catgtatgga 420 ttcgttgttg gtttgattcg acatgtcgat tctctggctt gcatattatc ttgatcgtct 480 tttgagcatg atgttcatat cgctattcat cttgatagtt gtagcttttt gtgtggacat 540 gagtgatata tcctgtactc tgctttactg tatgatgcat gactgtcctc cctctgtatg 600 attgcatgtt gcttgtctat gtgggtctca cttctatccc cctacctcca actcttttgg 660 tgtcggtcat tcctttcatc tcggttctca ctattgcaag tgtgagacct tctgtgtgct 720 tgctctttga ccgagccaga gattaggagt agggtctagc gacgggctat atcgatgtac 780 gggagcattc tggaggagag cgacactttg atgtcaattg gagtccgatc attgaagacc 840 tgtatagccc ggagctaggt ttcatggata tttgtgtggc cagtgtgttt catatcctac 900 tttagcttct tagggtttcg gatgcaccca caccatcact gtgcacgcta gtagactatt 960 gagtgttgag agtttgagag gtttcaccat aggaaacccc ctgggatgcg aggtagtgca 1020 tgtgtggagg tgatgaccat cttgcatgga agcgccccgt ctcttcggag gcgtgcagag 1080 ggttgcgtac cgccggaggg tatgatcgct tctactaggg atattttaaa gtccaccctt 1140 atccatttag agccaccttg accttgtagg ttgagccgta gatcattcga ttaggattcc 1200 ctccctacac gtgggtgcat ctgagggctt tccgtgcctc tgtagccgca gttttggatc 1260 cgattttccc tctgtttagt ctccagttga gagtgcactg agatcatgac gagtttgagt 1320 acggtcggac cgctcatctt cacttggatg ctttgcttgt tcctgttcag attatctttt 1380 cttctataca ttccccgagc catatcctta ttcctttctt cgtgctttgt aggatcggac 1440 ctttgttcct tgtcttgata tacctttgtg gatcagagca gaggaggagt actttcagga 1500 tcaggatttt tactctcagt ctgggtatag tttcgtggat cagagtagag ggcagattag 1560 ttcgggtttc agatacacca gatatggatc agcaggttgt cacggttgat cagttcacga 1620 ccgccatggc ttctatctag gaggctttgg ctagcctcag gcaggagatc ggtggtcaat 1680 agggtagacc accagcagtt caggatgaga cgccgtatga ctcacatcca cctccaccac 1740 ccctacccgt tccttcagtg catcaggcat caccatatgt attacacggg cactcagaga 1800 tcgctccacc cgtagtcacc caggcccctg tcgctgatga cacgcatgcg cgcatggacc 1860 gcatcgagca gtgtatgagg cagatgagag tgtcagatgg atcagttgtt tgggacgatt 1920 ttgggggtat gccggtagcc agtttgccgg ctaagttcag gatgccagat attgagaggt 1980 acactggtat cggttgtcca cgcatccatc tccgactgta cagcaccgtg atgagggctc 2040 atggactgga cgagcctcag atgatcactc ttttccccct atctctgagt ggggcggctc 2100 agcgctggtt tgcgtctctg gagtcctcga gacgccgtac atgggatgac ttggcccagg 2160 agttcctacg acagttttcg tttaacactg ttatagacgt atcgaggaga gagctcgagg 2220 ctctgaggca gaggacagag gagtccgttt cttctttcat ttcccgctgg cgcgggaaga 2280 tagctgagat agtggataga ccatcagaga gagaccagat tcagatggtt ttgaggagtc 2340 tacagccgag gatcgccaga catgtagtcg gggtcccgtt cacagatttt gggtctctgg 2400 ttatggcttt atatgatgtc gaggacggca tcacaagagg tttatgggca gattcttccc 2460 ctagtgatgt taaggggaag aaaccattca taggaccgag accgacagag gttggcgcta 2520 tcagttcatc cagtcagagg ccttttagac accatcagcc gcccacagtt ttctgagcct 2580 cattcttctt atgcatctca tcagtacagg ccacgggcac ctcgtccagc ttacgatcaa 2640 acacacatgc cacagacatt ggttttacct tcttatgcca ctcagggcat tgagagaccc 2700 gcggtctcct acacacccac tggacagcca tgctacgctg cacagttcac tccgaggccc 2760 gcacctttat accctgggcc tcgagctcag cagacctctg ctccgtttgc ttcgaggacg 2820 cagagacagt tttcacagat aggcatgccg ttgagccagg ctcttcggaa gcttatagag 2880 accggtttgt tgactgctct cacccctcgg ccactacctc agcctattcc agctcagttt 2940 aggatggatt tacactgtgc ttatcatcaa ggacctggac atgagaccga tcgatgcacc 3000 gctctgaggc acgctattca ggatctgata gaccagggtt tggtacactt gggccagccg 3060 agtgtgacca caaacccgtt gccgacccac accacacatg cagttcctcc accagccggt 3120 ggtattcatt tcttggactt cgatgagact gatgatcatg tccatatgtt gagttgggat 3180 gatccagacc cagagcctat catgccagct gggatttacg agacgagtgg ggtgactcta 3240 gagccacaga tgcttgctcc attccgacta gttcctgagg cagcatctgt acaggcggcc 3300 acttctgagc ctctgacatt cacacgctat agcgttcagg cgccgtacat tctgatccca 3360 gatgttgagg aggttcaggc tccacacagt gatgatcctc agactctgga cgttcagtat 3420 atcctccggg gagggagagt agtgagacag ccacctcccg cggcagctag gccagttgag 3480 ggtacatttg cttcccagga ggaggtcaga gcagaggatg acgggatttt gaggcagttg 3540 cagagcactc aggctcgtat ttctatctgg agccttttag cgtcctctag tactcatcga 3600 gatgcactga ctcgagcttt gagccagatc agagttgata ccacgaccac tcccgaggga 3660 ctcattcata tgatgacggc tggtagagcc acttgtattg tcttttccga tgatgacttg 3720 ccaccggagg gctcagacca cactcgcccg ctctacatat ctgttggctg ttcaggccgt 3780 cgagtcccat ctgtcctctt ggacaatggc tcggccctga acgtatgtcc tcttgccatt 3840 gccatcgccc ttggatacgg tccttctgat tttggtccct ctactcagac cgttcgcgca 3900 tatgacagta ctcggaggga ggtcatgggt acattagaga tcgagttgct gatcggtccg 3960 gccacttttg tcgctatatt ccagcttttg aggattccta catcctttaa cctgcttttg 4020 ggccgaccat ggatccaccg agccggggcc attccttctt cccttcatca gaaggtgaag 4080 tttattcacg atagtcagat cgtcgtggtg tagtctgtgg gagatatgtt cattgctgcc 4140 gagcctgtgc tcgagattag tcacactgat gacgatcttt ttctgactgg attcaccttc 4200 gatgaggtgc agactgtgga gatagaggat ttctgccggg attttgtggc tatgtccttt 4260 gatcggcatg ggagcacagt ggtgctcgat attatgcgga gcatgtccta tctacccggc 4320 atggggttgg gtcgacgtca gcatggaccg agcgagttca tagccatccc tgatcacgac 4380 gtaccgttcg gactcgggtt catccccact gaggctgatt atctctacat ggcgcgtttg 4440 cgcaaggaga gagtgagggc tcgactgacc cacacaccct tctactatcc tcttcgccca 4500 tacaccagga gcttagcaga ttactttgcg agggcatcgg agccgcacgc accatctgat 4560 gggatcgtcg gaggacttag caccacccag gaggccgagc ttcagcgcct tgtccagcag 4620 ttacgattga gagatggatc ccctagtcct tcgacttctg tgttgattgc tccttcttct 4680 ccggatcgca cgagccttat gacgctttgt tttcctgatg agatcgatga gcatgagacc 4740 cttgctgagg tcggggacgt agtggacgga gctgccccac atgacgagta catcaacgag 4800 atgctcgccc tgagcctgag ccagattgag gagactattc agcctggact tgcttcatca 4860 tttgatctct tcggggtatt catcattgag cttgccgagg agagcctgac tgcccctgct 4920 ctggagtcta ttgaggacct tatacctttt gatgatttga ctgatagcca tgttggcatt 4980 gttgagggag cgtccgactt tgtggaccca cctctttcat ttgacgttct gtcggggttc 5040 gtctcccgtt ctgactatgt ttccgatgtt tcatctatgg atttgagcat ttttgagtat 5100 ttgcctgtct cttgtgatat tgatttatct gcaccatctt cacccacatc acagattttt 5160 tatattgatg atgagattgc acagcatgac tcagatgatg actcatcttc tgtttccgat 5220 tcgaatcccg ttgatcagag ggtttcacct gctgtaggag acatagagat tgttgatttt 5280 ggcactgcag atcagcctag ggagttgagg atcgggtcag atctatctac agatgagagg 5340 gacagcctca tccagttgct cagagcatat ttggacgtct ttgcatggtc ctatgaggac 5400 atgccaggcc ttgatccatc tattgtccag catcgtttgc cacttctacc ccatgccaga 5460 ccggttaagc agaagttgag acgattgcac cctcgttgga gcttgcaggt gaaagaggag 5520 attcagaagc aactcagtgt gggatttcta taagtggtca agtacccgga gtggctggcc 5580 aatgtcatcc ctgttcccaa aaaggatggc aaggtgagag tctgtgttga tttccgagat 5640 ctcaacaagg ccagtcctaa ggatgatttt cctctcccac acatcgacat gttagttgac 5700 agtacagcag gtcactcgat gttgtccttt atggacggat tttccgggta cagtcaaatc 5760 ttgatggctc cagaggacat ggagaagacg tccttcatta ccgagtgggg tacttattgc 5820 tatagagtca tgccattcgg attgaagaac gcaggagcca catatcagag agcagcgacc 5880 accctattcc atgacatgat gcatcgggat gtcgaggttt atgtagacga catgatagta 5940 aaatcccgag gtagatcaga tcacttagca gccttggaga ggttctttga gaggattaga 6000 cagttcagat tgagactgaa tcccaagaag tgcactttcg gagtgacttc tgggaaactc 6060 ttgggataca tggtcagtga gcgaggcata gaggtagatc cggacaagat tagagccatc 6120 cttgacatgc ctgcaccgag gaccgagagg gaggtcagag gcttcctggg cagacttcag 6180 tacatcagca gattcattgc cagattgaca gacatttgtg agcccatttt ccgactcttg 6240 aggaagagtc aacctactgt ttgggataat cagtgtcaac gcgcatttga gaggatccga 6300 gagtattgtt atctcctcca gttttggctc cgcctacacc aggccgtcct ttactcctat 6360 acttatcagt ctcagatttg gctttgggat gcatgttggc tcagctcgat gattcgggca 6420 aggatcgagc catttattat ttgagtaaga ggatgttaga ttacgagacg agatacgtca 6480 cgattgagcg ctactgcttg gcattggttt gggtcactcg ccgattgaga cattacatga 6540 ccgagtattc agtgcatttg atatcccgtc tagatcctct gaaatatttg tttgacagac 6600 ccaccctagt tggtcgcctc atgagatggc tggtacttct gactgagttt gacattcatt 6660 atgtcactca gaagtccatc agagggagca ttgtcgcaga tcacttagcc tcattaccag 6720 tttctgatgc tagagctatt gacgatgatt ttccagacga ggatgtcgca gctgtgacta 6780 gtctgtcggg ttggtgcatg tactttgatg gtgcagccaa ccattctgga tacgggatag 6840 gcgttttgtt gatatcccct catggtgatc acattcccag atctgttcgt ttggcattca 6900 cgaatcgaca tcctgccacg aacaacatcg ttgagtatga ggcttgtatc ctgggattgg 6960 agacggctct cgagcttggg attagacaga tggaggtgtt tggtgactcc aatctggtat 7020 tgagacagat tcagggcgag tggaagacta gagacgcgaa gcttaggcct tatcatgcat 7080 atttggagct actggtcgcg agatttgaga atttgagata tacacatctg cctagagcgc 7140 agaaccagtt tgctgatgct ttagctactc tagcttccat gatcgacatt cccgctgatg 7200 ccactgttcg cccattgttg atcgagtcga gatctgctcc tgcgtactgt tgtttgattg 7260 atgatatgga gatagacgat ggtttgccct ggtatcatga catatatcac tttttaagac 7320 tcggcgtata tcctgaggcc gccacggcca aggataggag ggcattgaga cagttggcca 7380 cccgattcgt gatttgtggc gagacgctat atagacgatc acttgatggg atactgctat 7440 tatgtttgga tcgcgcttct gccgatagag tgatgcgaga ggttcatgcg ggagtctgcg 7500 gaccacatat gggagggcat atgttggccc gtaagatcat gaggaccggc tatttctggt 7560 tgactatgga gacggattgt tgccagttcg tccagagatg tcctgagtgt tagatacacg 7620 gagatctcat tcacgtgccg ccctccgagt tgcatgcact gacttcacca tggccatttt 7680 ctgtgtgggg catcgacatc atcgggaaga tttcgccgaa atcttccagt ggtcatgagt 7740 ttatccttgt tgctattgat tacttcacca agtgggtgga ggccgcctcg tatgcgagat 7800 tgacatcatc tggagttgcc agtttcatta gatcgcacat catttgtcgc tatggagtca 7860 ctcacgagct tatttaagac agaggggtgc attttagagc agaggttgac accttggtgc 7920 agagatatgg catccggcat catagatcga ctgcgtacag gccgcagacg aatggggcag 7980 tagaggccgc gaataagaat attaagagga tattgcggaa gatggttgag acttctcggg 8040 attggtccga gaagcttcct ttcgcactat gggcttacag gacttctttt cgcacctcta 8100 caggagccac accatactca ttggtatatg gcatggaggc agtgctaccc gttgagattg 8160 agatgggatc attgagagta gcattagagc aacagattcc cgagacagat tgggctcagg 8220 ctcggtttga tcagctcaat ctcctggatg agaggagatt gagagcagca gaccacgttc 8280 gtgcatatca ggggaagatg gcccgtgctt tcaaaaagcg ggtcaagcct agaccactgc 8340 atgtaggtga cttagttttg agagtcatca gaggattgat cagagatcct agagggaagt 8400 tcagacctag ttggagcgga ccttatttca tcagggagtt gactccagag ggcgctgcat 8460 ggctgatgga tttagatgga aaccagttct cagagccgac caatgtggat tagctaaaga 8520 ggtactacgt ttgagtccat ggttgcagga tgggtggcca tcatttcggt tagctatatc 8580 cctttatccc gtttctgata tatatagtcc attgctagcc catttgagcc ttgcacgcgc 8640 atcatagcct tcatttctta tagccttgct cacattttca caccgggatt ggggcccttt 8700 agtgtatgca tgcattgttt gagagtttca tgagccttgg acctaggggc acgttcttct 8760 cattatctgt gctcgccact acatcactgc atttcatctc atctcactgt tcgtgttatt 8820 catcatattt tctttatctt atctactgtt cgtttcacgt catcttcttt caccccgagg 8880 ggtgatcctc ctcatttcat cacatggagg gtagtcatgt catttccact atctatccca 8940 cggacactga tccagggatc ctcagtttga gaaggtcacc tcatctcatt agattgagtt 9000 tgtgatatat tgatatttga gggcatgttt attcattttt gatcccatct ttgggtcttc 9060 tttgtatgcg ttcagatcat gtacaattca tttatatgtt gtaaaaaaaa aaaaaaagaa 9120 aaaaagaaaa ataaataaat aaataaataa ataaataaaa ataaaaataa ataaaaaaaa 9180 tggaaaaaga aataaaaacc aggtgtgtat tgtcatccat cactgagtgt atgtattgat 9240 attcgagggt cacttgatcg agtatgtttg ttggcgggag ttcgtatgtg agcttcccgg 9300 gatcccccag gctttgtatt cactttgttg catgttttgt gagcgagatg agtgactttc 9360 tcttaggagc tctgggttat tgtccgttcc atcattatgt tcgtagttga tgtgacttca 9420 ctccatgtct gatctgagtt gatcatcact ccttttgatg ttattcgctt cattatcatc 9480 gtcctcgttt tcgcttctga ttcatcattc tcacttcacc tcttattctt ttcttaccac 9540 gacccatctc gggtttgata ttcccttcgt atcaccatta catatctcat tatcagtttg 9600 atttgcttca cttgtttcct cattgacact atgttcacat taggcaccat tgggtccatg 9660 gctcacggga tttactatac ttgttgcatt tcatacatga gggcatgggt tttgatcatc 9720 gggtatttga gcttagtttc ccttcgtttc tatcacccta tcaccctagc ctacattacg 9780 tcccgtgtct taagaccacc ctgaggccat gggatcggat atcgtcttct acagcttcta 9840 tgtggacagg tgtttgagat ttggttgaca tttagatatt tgtcatgcat cttcttctgg 9900 gagacgcttc tccgatgttt agatccgttt cgaccatgtt tggattacca ggatcacgtg 9960 tttgatgatg gatgattcga tgttacctgt ttttcctgat ttgtcgcaca tcagatgcca 10020 tactggggca tattccgttt cggaggatct ttatggatct tcgcagaggt cacatgttcg 10080 aggatagatg attccatgct atctgatctc cgacctatcc tacatttcga tgccatacag 10140 gggcatattt ccgttcggat gagatttaca gatcatgagg gagtcgcgtg cttatcctta 10200 tttacgagat gtatgcaggg atgatgacat attcgctatc ctcgcgatga ttccttagtg 10260 gaacctatcg agagccatct agccagttgc aggcatagat gatttgaact catctgattt 10320 ttcgacatgt tacatttccg atgccacact ggggcatatt ccccatcttg atagagattt 10380 atagatcccc actggtttac atgatcatcc acggttatga gatacacgcc aggttgatga 10440 ttgatttcat tttgtcctga tactccgagg agcctctctt gactcgttca gccagattca 10500 tactctttga tatagtcgtg attcctggat ggggttatgt cgagtgcttg gatccccaag 10560 tcattatttc agtgcggtac acatcaggtc ttttatgcat ccccatggtg ttattctcgg 10620 gtcatcaggg cagatcgggt acatctgatg ccatactggg gcatatttcc ctcatttagc 10680 catggaggcg atcgttctct cacatgtccg tcgcagtttc catcactcgg ccgagatata 10740 ttgtattcac ctcactgacc gttgttcctg agctcttcat tgacatgagc tcttagtggt 10800 gcgtcgttcg agactcgtag agcccctttt agccagttct agcagtttga gatttgcagc 10860 ggcatgccac actggggcat atttccccca cattgtttcc ttgcagtctg gcgttcagag 10920 ccgccgttca ttcacggttt acgacattca gagtcatcat gtcacatttt tcagtttggc 10980 gttcagagcc atttctcagt ttgacgttca gagtcatcat catcacttct cagtttcggc 11040 gttcagagcc atcatcggtt ttcagatcga cattcagagt cacatcctag gtttcggcgt 11100 tcagagtcgt tatcacttct tagtttgacg tccagagtca tcatcatcac ttctcagttt 11160 cggcgttcag agctatcatc ggttttcaga tcgacattca gagtcacatc ctcggtttcg 11220 gcgttccaga gccatcatca ctacttctct cagtttcggc gttcagagtc gttatcactt 11280 ctcagtttga cgttcagagt catcatcatc actacttctc ttagtttcgg tgttcagagc 11340 cgtcatcggt tttcagatcg acgttcagag tcgcgttctc ggtttcggcg ttcagagtcg 11400 ttatcacttc tcagcttcgg cgttcagagc catcatcact acttctctta gtttcggcat 11460 ttagagccat catcgatttt cagatcgaca ttcagagtca catcctcggt ttcggcgttc 11520 agagtcgtta tcacttctta gtttgacgtt cagagtcatc atcatcactt ctcagttccg 11580 gcgttcagag ccatcatcgg tttttagatc gacattcaga gttgcatcct cggtttcggc 11640 gttcagagtc gttatcactt ctcaatttga cgttcagagt catcatcatc acttctcagt 11700 ttcggtgttc agagccatca ttatcacttc tcagtttctg cgttcagagc catcattgcg 11760 ttctcagttc gacgttcaga gtcatcatca tcgcttctca gttttgacgt tcagagtcat 11820 catcatcact tctcagtttc ggcgttcaga gtcgtcatcg attttcagat cgacattcag 11880 agtcgcatcc tcggtttcgg cgttcagagt cgttatcact tctcagtttg acatgagtca 11940 tcatcatcac ttcctagttt cggcgttcag agccatcatc ggttctcaga tcgacgttca 12000 gagtcgcgtt ctcggtttcg gcgttcagag tcgctatcac ttctcagctt cggtgttcag 12060 agccatcatc actacttctc ttagtttcgg cgttcagagc cgtcatcgat tttcagatcg 12120 acattcagag tcccctcctc ggtttcggcg ttcagagtcg ttatcacttc tcagtttgac 12180 gttcagagtc atcatcatca cttctcagct tcggcattca gagccatcat cgattttcag 12240 atcgacattc aaagtcgcat cctcggtttc agcgttcaga gtcgttatca cttctcagtt 12300 tgacgttcag agtcatcatc atcacctctc agtttcggcg ttcagagcta tcatcggttt 12360 tcagatcgac attcagagtc gcatcctcga tttcgacgtt cagagtcgtt atcacttctc 12420 agtttgacgt tcagagtcat catcatcact ttttagtttc gacgtccaga tccattaccg 12480 tcatcttgtt taggcttcca gagccaccac cgtcatcttg tttaggcttc cagagccatt 12540 gctatcatct tgtttaggct tccagagtca ttatcgtcat cttgtttagg cttccagagc 12600 caccaccgtc atcttgttta ggcttccaga gccattgata tcatcttgtt taggcttcca 12660 gagtcattat catcatcttg cttaggcttc cagagccatt accgtcatct tgtttaggct 12720 tccagagcca ttaccatcat cttgcttagg cttccagagt catttccgtc atcttgttta 12780 gacttctaga gtcattacct tcattttgtt taggcttcca gagccattac tatcatcttg 12840 tttaggcttt cagagccatt accgtcatct tgttcaggct tccagagcca ttactgtcgt 12900 cttgtttagg cttccagagc tgttattttc tagttttagt ttttagagtt agtttttgtt 12960 ggcttccaga gctgttattt tctagtttag ttttcagagt tagttttttt gttggcttct 13020 agagctgttg ttttctagtt tagtttttag agctagtttt ttttggtttg ctttcagagc 13080 tgttattttc tagtttagct tttagagtta gttttttttt gtggcttcca gagctgttgt 13140 tttctagttt agtttttttg gttggcttct agagctgttg ttttctagtt tagtttttag 13200 agttagtttt tggtttgctt ctagagctat tattttctca gtttagcatt tagagttagc 13260 tttttttggt ttagcttgca gagctttatt ttcttatttt ctagtttagc gtttaaagtc 13320 agtcttgtca tgcagagtca cagctcctag cattcctatt cactggcatt gcgtgtctca 13380 ccttcattgg atttgcactt attctcgttc tccacacttc gttaccctgt gcttatcgtg 13440 tattcatcat gtagtccaca tagggctgtc tcctttagac gcattctcgt ccgtactcca 13500 gggtggttcg accgttactc atctttgaca tcgatcttcg agtcattttt ggagacgttt 13560 tagagggagc ctggatcctt agtgtggccg cagaggcatt ttgtgacatc tttttttttt 13620 taggattaga gcctttatgt tagtctggca gcctgagcga attcgtgttt tgctgatgtc 13680 cctatggggg tctccttggt tcttcggtag agttcacttc attgcactca ctattcacac 13740 ttacctttca cttcagtgtt catattcttt acactcgtga actctaccga agaagggcat 13800 atttgtagac ccccatttgg ggttcacttt ctgcagctaa ctttggacag atgtcgcaat 13860 ctcaaggaac cacgtgtcac ctcgtaattg gcttttagtg aatcaagtag tggagttgaa 13920 ggagccaatg aatggttgac acctgggggg atcttcagag aggagtgcgt ttctgttgag 13980 gtagcaggcc agctgcagct agagggaggg tgccttggct gccgttggaa gggatttttg 14040 agtatggggt atcttttctg ttagagaggc tgcagagttt ttttttgggg gagaggagct 14100 tt 14102 // ID Copia-19_Mad-LTR repbase; DNA; EDCOT; 374 BP. XX AC ACYM01079582; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-19_Mad_; KW Copia-19_Mad-LTR; Copia-19_Mad-I. XX NM Copia-19_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-374 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1365-1365 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01079582; Positions 14018 13645. XX SQ Sequence 374 BP; 106 A; 50 C; 72 G; 146 T; 0 other; tgttgaatta taagtgtttg agctgaaaat gaattagaat aaaactttga tttaattggt 60 gtactcactt atgcaaagaa tgctaagtgt attgtttttt tttttttatg tgtaaaaggc 120 cttgagagcc atgtggactt agattttagt tattagttag atgaatggtt gagatccttt 180 gatctgatga attgatccag ctcagctttt gttagctgta atattcccta ctgcacgttt 240 tgtgtgtaga ggtgagtgag aaaatattaa tacaattatg ggtttctctg tgacttacag 300 agagagcagt attcctcctt cagtcttttc ttcttcttta gaacttcata ccaaaacatc 360 agtttacatt aaca 374 // ID TreLTRRT2-LTR repbase; DNA; EDCOT; 1055 BP. XX AC . XX DT 03-DEC-2010 (Rel. 15.12, Created) DT 20-DEC-2010 (Rel. 15.12, Last updated, Version 2) XX DE Gypsy-type LTR retrotransposon: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; TreLTRRT2-LTR. XX NM TreLTRRT2-LTR. XX OS Trifolium repens OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Trifolium. XX RN [1] RP 1-1055 RA Hand M.L., Cogan N.O.I., Sawbridge T.I., Spangenberg G.C. RA and Forster J.W.; RT "Comparision of homoeolocus organisation in paired BAC clones RT from white clover (Trifolium repens L.) and microcolinearity with RT model legume species."; RL BMC Plant Biology 10, 94-94 (2010). XX RN [2] RP 1-1055 RA Laten H.M., Hand M.L., Cogan N.O.I. and Forster J.W.; RT "LTR retrotransposons in white clover, Trifolium repens L."; RL Repbase Reports 10(12), 2177-2177 (2010). XX RN [3] RP 1-1055 RA Jurka J.; RT "Classification as Gypsy."; RL Direct Submission to Repbase Update (20-DEC-2010). XX DR [2] (Consensus) XX CC Composite of LTR region of two independent LTR retrotransposon CC insertions that are 97.1% identical at the DNA level, including CC LTRs and 98.4% identical excluding LTRs. LTRs from each element CC are 99.9% and 100% identical, respectively. Related to Ram4 from CC M. truncatula. LTRs flanked by 5 bp target site duplications. XX SQ Sequence 1055 BP; 312 A; 153 C; 165 G; 361 T; 64 other; tgttagcctg tattttcgac aggcattaaw gaattggart gagatgatga aatctcattt 60 aatgtatatt attgcytttt aatattctct tggaaactga ttctggcaat aaayyaagag 120 araatcaagg yatttgacat yaaagaytkt yratgtgcaa agttgcttgt caaakcctrr 180 arwyctgtcg aattcgacag raygtktgtt gtytgaataa gcttgtcgag ttcgacagag 240 rwattryttr tktaarmgyr tmttttcgac aytrwywkrw ratkgtcgaa awytatatat 300 atatgyayat atatgtaygt gtgtatgttt gtttgtctaa cgtactgtgc agaacgaaag 360 aagcgtactc tggacttagc raaatattca aaagwgagag taacgtttgr agggttcgcc 420 aggtgtcmaa grgaattcaa attgtcaaga cacgtggagc atagttagrc rwattgtagk 480 tttatagcag ttatgttagt ttgtctataa atacaagttt ctsatagrag aaacgggtcc 540 acaawtcaat acacatgcaa attcctaaaa tattcagagt acccatgtca acgagcgaaa 600 tgaatgacag gaacatgtac gaatctgtgt accatccttt gtaaacattt tacatttgtt 660 aaatgcaatt tacattctgc aagtcttgat tacttgtttg tcatttaagt tttatgcaat 720 ttaaagcttt ctgcaacttt atcattctgc aactttatca ttctgcaatt tattttcatt 780 gcattgyctt tactrtttca aaagtytttc tttaaacttt atttgcaatt catttacaag 840 ttttctgyaa atttaacttt gaagcatttt accttttaaa caaaccattt gactgcgtca 900 aatgctttta cttttattca aattgtccga tttaacccaa agatatgaat atgttttcat 960 catcttccac acaatccata tgtcccgaga tttactagtt gatctctctt gtaataatta 1020 aactagcggt tgtttactaa aaatcggggt aaaca 1055 // ID Copia28-PTR_LTR repbase; DNA; EDCOT; 257 BP. XX AC scaffold_857; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia28-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-257 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-257 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 231-231 (2007). XX DR Genome; scaffold_857; Positions 6411 6155. XX SQ Sequence 257 BP; 65 A; 35 C; 43 G; 114 T; 0 other; tgttagactt agtcttaata attttaataa gtgtcctagt tattaggaca atgttgttag 60 catttgatat tctgttttag ttttacctat tcttaagcaa ggatccacat cttcagggtg 120 ttgaagacgt gaacttattt ttagctgttt ctgttgtttc ttgttctggc tatttaagcc 180 ttagtctcat ttgatcaatt tattgtatta ttctaagcat cctgtgtgaa agagtaatat 240 acatcagttt tttatca 257 // ID RAM4_I repbase; DNA; EDCOT; 12800 BP. XX AC AC138014; XX DT 08-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE Internal region of LTR retroposon RAM4, from Medicago truncatula. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR retroposon; internal region; Interspersed Repeats; KW internal portion; RAM4_I. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-12800 RA Shankar R. and Jurka J.; RT "RAM4: LTR retroposon from Barrel Medic."; RL Repbase Reports 6(11), 592-592 (2006). XX DR EMBL/GenBank/DDBJ; AC138014; Positions 100766 113565. XX CC The internal region codes for a protein very similar to viral CC proteins having conserved domains for RT polymerase and RNAseH. XX FH Key Location/Qualifiers FT CDS 3737..6178 FT /product="RAM4_I_1p" FT /translation="MALSLRLPNMLPHLWGGAQEIEIMSSTNMWEKITAYL FT AEKEPQTAREAESSKSGSIEKPKDGLIDVEVEDQKLDCIYDDEPLGFEEDP FT MGSTTKMKAQDPLEEIDLGDGTVKKPTYVSAKILEKFRCQIAELLKEYKDC FT FAWDYNEMPGLKREVVELKLPIRQNKKPVKQIPRRFAPQILPKIKEEIDRL FT LKCGFIRPARYVDWLANVVPVKKKNGIIRVCIDFRDLNLATPKDEYPMPVA FT EMLVDSVAGFDYLSMLDGYSGYNQIFIAEEDIAKTAFRCPGALGCYEWIVM FT PFGLKNAGATYQRAMNLMFHDFIENFMQVYIDDIVVKSSSEERHLEHLRQS FT FERMRQYGLKMNPLKCAFGVCAGDFLGFVVHKKGIEINQNKTKAIIETKAP FT STKKELQSLLGKINFLRRFISNLSGRTQAFSPLLRLKKDDVFKWEPEHQKA FT FDEIKSYLVNPPVLSPLLKGKRMKLYIATSDGTIGSMLAQEDEYGAEKAIY FT YLSRVLNDAETRYHPSEKLYLCLFFSCTKLKHYIKPFDVYVYSHFDIIKHM FT LSKPILHSRVGKWALALTEYSLTYQSLKAVKGQIVADFIVDHSMSEVLTTE FT IDNHPWCLYFDGSSHKNGTGIGIVLISPKHHKFEHMFRISRFCSNNEAEYE FT ALITGLEIALELGARCIEIKGDSELVLKQMTKEYRCVKESLVTYHAIASRL FT LKQFNHVGIRHIPRMENQDANDLAQKASGYKMSKEQMQEPIEIRNRRNSIE FT CFSGKSLTPKLGGTRASQASLNGTDSIEIFVINDLNENDWRKPIVDYLENP FT NGTTPRKMNIGP" XX SQ Sequence 12800 BP; 4131 A; 2457 C; 2824 G; 3388 T; 0 other; gtaaacaaat tggcacgccc agtgggacct tttgtgtttt aactttgaaa ttatttgttt 60 ttgaattcaa aacttttatt tggtctgtac ggtgcatgcg tttaaggaat aagaaaatac 120 ttcctgaaat gacgcgccct cctgtagttt ctggtacgac ggcagccaat attgcttcta 180 cttcaggaac agcgaccaat caatcaatcc ccgcagggtc tactttactt ggccgaaata 240 accctacagg tcatgtatta gaacccgtcg aggccgtact tgaagaaaat gtaacttcac 300 aaacatcgca agccaatacg tcgaatacta tggctaataa ttcttcaagg aatatcccag 360 tggctacgac agccgcccac acgacccaat ccgcgggaaa tatgttttct caaagtgttc 420 tcaatttggg aaacaatgga agagggtcat atggtatccc aacatcctcg acccaaactt 480 cacacactac cacaatcacg cctccctttt ctaaccaagg ggagaatata gcgtttggta 540 gatctccaca agggtttgtc ccatttggtt cgcctcaaca atcgttgacc aacgcttcga 600 cgaatgcgtt aaggcaaacc atggcggaaa ctaaccacga tatggttaat atggtaacac 660 aacaagtggc gacagttatt agccctttga tcaaagatac gaatagcagt taccaagccc 720 tttcacaaca tatggggcgg atagcagatt ttctgggagc accccaagca cgcgctacgc 780 cggctacgcg aaattcgaat gcgaatgcca ggccaagaga ggcgtcagtc gaagaacaga 840 ctaatcaagt gctcgaaaac caggcgcaaa acgaacagcc tgaaattcca gaagaacccg 900 ttaggatccc agtagtggta aataggaacc aaaatgctga ccaagtggtt atgcaggccc 960 gtcgaaataa ttatggaggc cataataaca tagccgatat agtcgaaact ttgatggcct 1020 aaaatggttt caacactgga attcatcgtc caaatttcgt ttccgcgtta gccgatttcg 1080 ttttagaaac ggagatgcca agaaaccata agattccaaa atttaccaag tttgctgggg 1140 aaacaaatga atccactgtt gaacatattg ctcgatatat tatggaggcc ggagatctgg 1200 caaacaatga gaatttgaaa ttgaaatatt tcccaagttc tctgacgaag aacgcattca 1260 catggttcac aacattacct ccacattcca tagtcacttg gaatcaattg gagaaagcgt 1320 tccatgagca gttttacatg ggccagtcga aaatcagttt gaaagaactg gccagtgtta 1380 gacgaaaaac gcatgagtcg atagatgatt acctgaacag atttcgactc ctcaaagccc 1440 gatgtttcac cgccgtgcca gaacacaaat tggtcgaaat ggctgcgggt ggtttagatt 1500 attccgtccg aaagaaattg gatacacaat accttaggga catggcacaa ttagcagata 1560 gagtccgcca agtggaaaga ctcaaggctg aaaaggccag gacaaataga ttccctaaga 1620 aagaaaaagt tggttacatc gaaactgggg atagtgagcc agaattcgat tggggtttcg 1680 attccgttga ggacagcgaa ataaatctcg cggagttaaa agaagggccg ccttacactt 1740 gcaaattgtt aaggccatca aacggaaaaa acgtagaaga gcccaaaaat tataaatatc 1800 cctcaaaaac ttatacgttt gatgtatcta aaagcgaaga aatatttgat cttttagttg 1860 ctgatggcat aattttagtg ccagataata tgaaaattcc tcctcttgac cagaggaaga 1920 aaagaggttt ttgtaaattt catggttttt tgggccataa cttatcccgt tgtactcgtt 1980 tcagggattc tgtgcagaaa gctctcgatg aaggaaggct aaagcagcaa gcaagcctga 2040 tgtcgattct tccaaaaagg ccgaatccat gtacgctgaa gtagtgggta taaacatggt 2100 ggacgtagca acaccaaatg atggtagact atcatcaagg gaggctgtac ctgatgacat 2160 caaaatggtt actgaaggcc atgttcaaaa tactagcctg gtcactgagg atcaattcca 2220 aaagaatgtt gaaaaggcat atcccaaagc tgaagaagat ctaattgatt ttctgaattg 2280 ttgcaaaatt tcaaacacca acgctatgct ttgcccaaga agtagcgcgg tcttcgataa 2340 agaggccgct aaagccatag agggtaccca gccacaagca aagtggaaag ggaagaagaa 2400 ggataaccgc cctagataca atttcaacaa aaggggtgct ccatataaag accatgccac 2460 cggaaatact caaaaaagga attgggggaa aactttcaat ccacctgcaa attctcccac 2520 caacacttgg gttttttcag gaggaagaaa atctggttac tctgcccctc caactaaatg 2580 ggtaaagaga aaagtacccg ctcctcgagt tgaggcgcca agatcgccta ccaggtatcc 2640 ctataataat aattacaggc gacaacagcc aatgacgcga actcaatggc gtaggtatca 2700 acgccagaaa aagccacagc ctcacaagat accaccaaca ttgataagat ggaggacaag 2760 cagaaagctg tgtttgagat ggttaagaag ccagcaacag agcgaatttc gcccccattg 2820 tcgattctga tgaaagatca tccaaaagaa gatgaggaaa tgacttcgaa tttcacagaa 2880 tctgacccaa gtcttgacat agtttgtaat gtggtttcca ttttgcctgt ggaatatgat 2940 gtccagtcag aaattaatga agccgaaagt gattttgtcg atgagatggc aactcacaaa 3000 ccactgtgct attatgtcat gaataatgac tgtgtggaag aacaacatgc ggttttcgag 3060 aagccagata tttcgatgaa atcgcatctt aagcctttat ttattcaggc caagataaat 3120 ggcgtggggg taaataaagt actggtagat ggtggagcca ccgtcaatct gctgcctcaa 3180 tctttcctgg ggagaatagg actctatgat tctgacttga agcctcacaa tgtcatactc 3240 acaaactatg aaggcacttc gggaaattct ttgggcgcca ttgaacttga attaatggta 3300 ggcagcacca aaagaatacc gactttcatg gtggtccctt tgaaagcaaa cttcaatgta 3360 ctgttgggta gggaatggat acatggtgtg ggtgcagttc cctctacggt gcatcaaagg 3420 attgccatat ggaaagaaga tgggctcgtt gaaaatgttg aagctgatca aagttacttc 3480 ttggctgaag taaacaccat caccaagaat aatttcgata aacagctggc gcatatagcc 3540 ccagtcgtat ctccagggct caaacagata gcttcgaaca atgaaatgta ctcgatgaag 3600 ttacaaccag aagcagggtt cgtatgggag aaagatttca gagaccatga ttttgtaatg 3660 gtcaatcaac aagaagctca gttggatgac gagggtctgt tggtgactag agcccaagca 3720 tacaaaaagg ctactgatgg ccttgtccct aaggcttccg aatatgttac cccacctctg 3780 ggggggagcg caggaaattg aaattatgtc cagtaccaat atgtgggaga aaatcacggc 3840 ctacttggcc gagaaagaac cacaaacggc cagagaggcc gaatcttcga aatcaggaag 3900 cattgaaaaa ccaaaagatg gcttgataga cgtggaggtc gaagaccaga aactagattg 3960 catttatgac gatgagccac taggtttcga agaagatcct atgggttcca ccacgaagat 4020 gaaggcacaa gatcccctcg aagaaatcga tttgggtgat ggaacagtta aaaaacctac 4080 ttatgtaagt gccaaaatcc ttgaaaaatt tagatgtcaa attgcagagc tattgaaaga 4140 atacaaagat tgctttgcgt gggattacaa cgaaatgcca ggtttaaaaa gagaagtggt 4200 ggaattaaaa ctaccaattc gacaaaacaa aaagccggtc aaacagattc cgcgtaggtt 4260 cgctccacaa atcttaccaa agatcaaaga agaaatagat cgattgttga aatgcggctt 4320 catcaggccg gcaaggtatg tggattggct agcaaatgta gttccagtta aaaagaagaa 4380 tggaatcata agggtatgca tagattttag agatttgaat cttgctaccc ctaaagacga 4440 atacccaatg cccgtagcag aaatgctagt agattcagtg gcgggtttcg attatttgag 4500 tatgcttgac ggatactctg gttataatca aatctttatt gcagaagaag atatcgctaa 4560 gaccgcattt cgatgcccag gggcgttagg atgttatgag tggatagtaa tgccattcgg 4620 tctaaagaac gctggtgcta cgtaccagag ggcgatgaat ttaatgttcc atgatttcat 4680 agagaatttt atgcaagtct acatagatga cattgtagtg aaatcttctt cggaagaaag 4740 acacttggaa catttacgcc aatcattcga aaggatgagg caatatggat tgaaaatgaa 4800 tccattaaaa tgcgcatttg gggtttgtgc aggtgatttt ttagggttcg ttgtgcacaa 4860 aaaaggaatc gagatcaacc agaacaaaac caaagcaata atcgagacta aagctccctc 4920 tacgaagaaa gaattacagt ctctattggg aaaaatcaac tttctccgaa gatttatatc 4980 aaatctaagt ggcaggacac aagctttctc accactactt cgattgaaga aagatgatgt 5040 tttcaaatgg gaacctgagc accaaaaagc cttcgatgaa atcaagtctt atttggtgaa 5100 tcctccggtc ctttctcctt tgttgaaagg gaaacgaatg aagttatata tagcaacgtc 5160 agatggcacc attggaagca tgttagcaca agaggatgaa tatggcgcag aaaaggccat 5220 ttattattta agtcgagtac ttaatgatgc tgaaacaaga taccatccta gtgaaaagct 5280 ttatttgtgt ttattcttct catgtacaaa actgaagcat tatataaagc cttttgacgt 5340 ttatgtgtat tctcattttg atatcattaa acatatgttg tcgaaaccaa ttttacatag 5400 ccgagtcggg aaatgggctt tggcattgac agaatattca ttaacttatc aatcattaaa 5460 agctgtcaaa ggccagattg tggccgattt cattgtagat cattcgatga gcgaggtttt 5520 gacaactgaa atcgacaacc atccatggtg tttatatttc gatggttcta gccataagaa 5580 tggtactggc atagggatag tcttaatatc gcctaaacac cacaaattcg aacatatgtt 5640 tcgaatcagt cggttttgct ctaacaacga agccgaatat gaagccctaa ttacaggtct 5700 agaaattgca ctcgaactgg gggcaagatg catcgagatc aagggagatt ccgaacttgt 5760 cctcaaacag atgactaaag aatataggtg cgtcaaagag agtttggtta cttatcatgc 5820 aatagctagc agattactaa agcaatttaa tcatgtgggc attcggcata tacctcgaat 5880 ggagaaccaa gatgcaaatg atctagcgca aaaggcttct ggatacaaaa tgtccaaaga 5940 acagatgcag gagccaatag aaattagaaa caggcgaaat tcgatagagt gtttttctgg 6000 caaatcgtta acgccaaaac ttggggggac cagagcaagc caagcttcct taaacggtac 6060 ggattctatc gaaatttttg tcattaacga tttaaatgaa aatgattggc gcaagcccat 6120 agtagattat ctggaaaatc caaatggaac cacccctcga aagatgaata tagggccctg 6180 agttatgtga taatgggtac tgagctattc aaaaagactt cagaaggagt tttattgaaa 6240 tgcctaggag aaacagacgc gtatctggct gtttccaata ctcatgatgg agcatgcgga 6300 acacaccagg caggccacaa gatgaaatgg ctcttgtttc gacaaggctt atattggcca 6360 actatgctca aagattgcat agaattcgcg aaaggatgcc agggatgcca gaaatatgct 6420 ggaattcaac gcgttccagc aagtgaactc catgcaataa taaaaccttg gccattcaga 6480 ggatgggctt tagatgtgat aggggagatt aaacccactt catcgaaagg atacaaatat 6540 atcttagtgg ggatagatta ttttacaaaa tggatagaag cgattccctt aaaagatgtt 6600 actcaagagg aagttataag ctttatccaa aaattcatca tctataggtt tggtattcca 6660 gaaaccataa ccacagacca aggatcaata ttcactggtc gaaaaatggt gaaatgtgcc 6720 gaagatacag gttttaaatt gctaacttcg acacatacta tgcacaagca aatggtcaag 6780 ttgaagcagc aaacaaaaat atcatcgcca ttattaaacg gaaaataaag gcaaagccca 6840 agaattggcc tgaaatatta ggcgaagctt tatgggcgtg tcgaacttct cccaaagaat 6900 cgacaaatac tacacctttc agatcgacat ttggtcatga tgctgtgcta ccagtagaga 6960 ttctgttgca atcagtcaga attcaaagac aatgtgaaat accagttaat cattattggg 7020 acatggtcat agatgaattg accgatctcg atgaagaaag attaacagcg ttagaagtcc 7080 tagcgagaca aaaagaaagg gtagcaaaag catataataa gaaggtgaag tcgaagtttt 7140 ttgcccaagg tgatttagta tggaaagtca tattacccat ggacaaaaaa gatagagcat 7200 tgggaaaatg gtctcccgga tgggaaggac catggcaaat attaagggtt ttttcaaata 7260 acgcgtatga gatcgaagag ttgaacgacg atcgaaggat tttgcgaata aatggaaaat 7320 acttgaagaa gtataaacca acattgcaag aaattaaaat catacaagag taattcgaaa 7380 ataaacataa acatagcatt tcattaaagc caactaatgg gcggtttaca caaagtttca 7440 aaataagctc taaaagagcg caaaagtaaa ccattacaaa agaaatgcta taagaaagaa 7500 aatggctttt cgatggaaaa ccctacgcaa gttggccaaa gctaaagaga tcgaggaacc 7560 atcgaacttc gctatccaga cgacacctga gacagaagcg ctggagatca tattgctcgt 7620 cctcagcagg gtgataacct cgatagttac gtctcaatcc atccccgtga cagttgtgcc 7680 agttattaca aaatcgacgg cgaaccaact gaggaggcag taatcttttg taccagcctg 7740 aaacgaagcg gaaacgggtg tccccgcctg ttatctctct gcgatagcgc gcaacgtttt 7800 ttgtctccaa aagagaccag aaatcatgaa aaagtctagc ggaatcaagt ctgacaccgt 7860 taagcgccct cagcagtaca tcgaagtaca gggcggtcac agagccagcg tccatagcat 7920 tctgcaacaa gccttggacg gtaggaatgc agggctcagg gtctagcatg aactgggtac 7980 acctcagaat gcagaacatg tgatgtccat gctcccataa acgaagctgg aaatccaact 8040 taggatgaga aggcttcaaa tcggtgagta gcttgataca atccccacca aatgctcttg 8100 aaaatgtagg gtctctacaa agagcagcaa tccgtttgtt ctgcctttgg aagtagaaaa 8160 gatcagacat gctttctttg gccactctgg cagcaatgtc aataagcaga tcatcgctta 8220 aactgcttat atgatccatg aaattttctt tttgttttgt gtttgcaaag aagtgtttga 8280 taaaacacaa agaaagataa gtgagaaatg aagagacaaa accaaaggac tctatttata 8340 agaggagtgg gaagttgaaa gcggtttttt catctttgaa atggacggtt cttgtcttga 8400 tcatcatgga tcatcaaagg acatgtggca atagatttac ggtttgattg ccaaatcttg 8460 ggaaggaagt agttgtaaaa aactttttgt ttcatcttcc ctaaaaagaa tctcataatt 8520 agatttttat agggtttacg gttccctagg cgaactaatc ctactaaaag ttatgagagg 8580 acttttcggt ttctcatcat gatgaatgcc ttgagatttg ttccaacaaa attttattga 8640 agaaaataag gaacttctca ataaaaattg tgccaataaa aaaaacggtt gctagaccgt 8700 tacaaagtta atgcaagtac aatgagaaac aaaataaact aaactcccat aatggtttcg 8760 atacaagatg attacatttg gaaaccagaa gtaagccggt gtaattgttg tttgaagcca 8820 tcgagtttgt cttcgagtgc tttgccctgg gcagtaagaa gcaatatttc ctgttgagaa 8880 gacttcgatt ctttgatctt cttgatagca atctgggcct catacttcat tacaccttct 8940 ttggccaaga gttgggtttt ttgaccctcc agctgttcga ttttagcttt atattgagca 9000 atcgacgaat caatgtcagc tacttgggat tgaatgaggg gagtttcttg tcgaaaggct 9060 tccagtttgg acttgaaggc agcaacctca tccaacagct gatcatatcg aagagtctgc 9120 tcctttagct tggactcacc atcctttctt tgaagacatc cttgctttat gctatctaac 9180 aaaggattta aggcttcaaa aagctactgg aaattgagac tcgagggaag agctatgagt 9240 ttgtggaaca atgcttgtat ttcggaaata gcattttcat cttgctctat aacttcgaat 9300 aaatcagccc tcaacacttt gctccggaat tccgcaaaga gaccttcggt cgaagcgtga 9360 gagggatcct caatcgacac attggaagat ctcccagtac tcctggacat aagaaggtca 9420 ctggccaaaa gatcgaaagc atccaaaggg ttagattcct caagttgact taggttcgtt 9480 gggaccaaag ttggatccaa agatgggtca gcattgcgtt gatcatccaa ggtgtgtgtt 9540 agtggcgaat tttcaactac cagattttct ttgggagtag caataaactg atcaatgtcg 9600 agatccactc ccatgtcact atcctcctct agcccttcat cttgatgatc actcgagtca 9660 accaccacat gattaggtga agtgatctcc aaatcaggtg ttaggatact ggtttcgaca 9720 ccttcatcct cttcagcaat aggcgaagct tcggcttgac caacctgagc atgttgggga 9780 atgtcggttt gcatggcctg caaaataaaa cgctattgta agaggcatat ttcgaaactc 9840 atgaaaagaa aaggcaaaga gattcttttt gaaaaatacc ttcgaagtgt tgtcaccaac 9900 gcaagaatga gcactggtag gatttgaatc tttgcgagtt ttcatcttct tgggactagg 9960 ttgacccaga gtttcttcta ttacaatcat ctcgagagcc ggagagtcat gtttcctctt 10020 cctacgagtc tcctttggtt gaatgggctc agagacagca gttctttcga tggcagcatg 10080 ggaaacttcg acctacagag gaacataagg tttagaaaat cccttacggc gagtgtaaga 10140 ttaaagttat tcgatggaat aactcacttc atcttcgaca atatgggctt gtttgccttt 10200 ggaagatttg tcggacttct tctttttgtc cgccttcgaa gattttttct tctgagcagt 10260 cttatcagac ttcgatctag acgtccttcg agaattgtct tcctccaggt cttccacatc 10320 tcctgaagac aaaggaattg ctgctagcca tgaacacaaa acagataagt atcctctctt 10380 attcaagtat aatagattcg aaattgggat attttttttc taggaaaaaa gaaaaaatcg 10440 aaaaggttca ttacctaatc ccatttcgga caaaattcga atataaggat catttaagtg 10500 cagatgccat ctatatgtat ataggttatg tttggttgca gttaccctgt ctttttccct 10560 ctttacaaat ctttgtttca ttcccatcaa gctatcacaa aacaaccatt tgggataggg 10620 tggcctaaag gccaaggcca acgggctagt tggcaaaact gggaacttaa ttctaaagtg 10680 aagtgcaaaa agatatttac taggggtaaa gggtggaaaa gacatcgaag gaattctgtc 10740 atgaatttta tcatttaaag ttttggccgc ataatgaact gtcctcttta gatggagagg 10800 atcatataca gtttgaaaga aattttgaaa agcttgaatt tctcgaatat gcgtaccttt 10860 gtttttcttc gattttttct gcacagtatg aaaagcaaga atcagttcag gaagtagaga 10920 atcaggatct acgcgatcgg attggtgctt aaaatagcac tgccaccatc gatagaacac 10980 ttcagtgcat gcataagatg aagtaaacag tttgggttca aaaatcagct tttgccgttg 11040 agcttgacgc agaatagacc tccaggcatg ctctataagg ggttgtctca aatcatctaa 11100 acacttatgc aacgaatttg gcttgatttg aactaagcca aactgtcgag ccacatgatt 11160 gggttgatag ctgtacacac cataggggct tccagcggtc actcgactgg ataaaaaggt 11220 gggggtaagg taagcctccc agatgacatt tatatccacc tcttcttcag tagaatccga 11280 tgggaatttt gaagtaaacc acgaaggccc acgagatctg gtagtaaaag gagccatcga 11340 aggagtaaag gaaatgcagc ttaagaaggc gttgaaagcc actgcaaata aatctggaga 11400 gctcctgttc ccgtattgga gcatggctag acctaaacct tcgatagatc tgttgtcata 11460 ggctttcgag agagcagggg gcaagtgaac tgccagcttt gttctgaaag tggccaaaag 11520 ccacagttga aataaccaga cagggccagg aatgataaga ctgctaccag ctcgaaaatt 11580 ctttatgctg gataccgcat ggttcaaact ttcatataaa gatcctaaga tgagtttact 11640 taggcatatg tctcgccctt cgtgcaactg aatagctaaa gtggtaaatt ttttggggat 11700 ttgaatcgat ctcgagcaga atatatacat ggatagccaa taagtcaaga aggctatgtg 11760 ctcctgatcc gacactgtag tgctagaagt gtcgtaatga tcaatgatga agttaccata 11820 agcaggtctc gaaaaatcaa aagatgtttc cgaagaatga gtatcaggat cgaaaatttg 11880 gcctatgggt ttcaggccaa ctaaaccagc aacatctagt aacgtaggag tcagcatccc 11940 acattttaag tgaaggctat tggttgaagg attccagaag tgaagagcag caattatcat 12000 ttcattatga tatttcggtc cttggcgaga taattgaatg agatcgaaga tgcccatttc 12060 tttccaaaat ggacctttga ttttctctaa tttctccaac cattcaagat atttttcgtt 12120 gttttctatt ttgggttcag tcctaaattt ggatttcaga aaacttaggt catatggacc 12180 tttggagaaa ataagaggcg aatgtgtttc gttgcaagga aaaacggggg ctagtttttt 12240 ctgatcgtcg gagtcatccg gcaaaggccc taggtatgca tgcgatgagt ttgagcatgg 12300 aataattacc tgggatttcc agattctgtc tttagcttct ttgacgtctg gttcttccat 12360 aaactgagta tttatggaaa gattggcatt tgtttcttgt tgcttcattg attgagaaga 12420 agaaccttct atgcgcacca taaaaattca aaaattttgg ttcgttgaga tgaacagtat 12480 tttggatcgt aaggtagaag aaggggatgg tgaaaagagt aaaagtaact aaaaggagca 12540 aagtaagagc aaaagtatga ctcgcagtca tatataactt ttgatactgg acagatgtca 12600 atcatcgcgt ggagcagttg tttttgatga ttccaaatgg cggtatggcc cactaagtct 12660 ttatgatgac ggttctacac ttttttgata tcccatttcc aaaagaatga tgtcatgcta 12720 aggaattaca tgttttcttc agaaacgtca agtttctcct gaaaatcgaa gaagagaaag 12780 ttcgaacata acgtttctgg 12800 // ID TDC1 repbase; DNA; EDCOT; 5251 BP. XX AC AB001569; XX DT 28-AUG-1998 (Rel. 3.07, Created) DT 06-AUG-2007 (Rel. 12.09, Last updated, Version 3) XX DE DNA transposon TDC1. XX KW EnSpm; DNA transposon; Transposable Element; TDC1. XX NM TDC1. XX OS Daucus carota OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; campanulids; Apiales; Apiaceae; Apioideae; Scandiceae; OC Daucinae; Daucus. XX RN [1] RP 1-5251 RA Ozeki Y., Davies E. and Takeda J.; RT "Somatic variation during long-term subculturing of plant cells RT caused by insertion of a transposable element in a phenylalanine RT ammonia-lyase (PAL) gene."; RL Mol Gen Genet 254(4), 407-416 (1997). XX DR GenBank; AB001569; Positions 5254 10504. XX SQ Sequence 5251 BP; 1662 A; 838 C; 1046 G; 1705 T; 0 other; cactacaaga aaacgcgaat ctgccaacca aatttaccaa cggaatcgtt ttggttgcag 60 tttcccaacg gaatgctgac tgattagtag gcaggccacg gtcaaacact caacaacgga 120 ataccaaccg ttccccaacc aataattaac aacggaagat tccgttggga aatgttggcg 180 ccaaaatcac ccgctgctcg gcaatgacag aattacttac gaattgccaa cgaaaatttt 240 agcaacggaa taccaacgga gtttttacgg attaccaacg gatattctgt tggtaatgtg 300 gtagtacatt cgtcattaat tcatttggta attccgttgc taatcggtca gtaaatgggg 360 gtgactttta caaaatagag gcgttggtaa ttcgttggta ttttagatcg gtcacctttt 420 cttaccgttg ggaatcggtt ggtaaaatag atcggtcaac tcgatatccg ttggtaaacc 480 gttggtatct tgaacatatt taatacattg gcagacagtt ggtactatta ttcagtcact 540 ttttcatccg ttggcaatcg gttggtaaac tagatcggtc agctcaactt ccgttggtaa 600 accgtcggta aagatcaacg gtcatttttc cgttggtaat ccgtcagtat ccaaaacata 660 ttaaataata tattggcaga cagatgataa tttaactcag tcaccttttt aaccgttggc 720 aatcggttgg taaaggagat cggtcaactc gatatccgtt ggtaaaccgt tggtaaggta 780 cagctgtcat attttccgtt ggtaatccgt cagtattcaa acatattaaa aagattgaca 840 gacagtttct tctttctttc tacgttttct aaacttatat cctctcattt tctctcctca 900 tagcaactga aaatagctaa aatcatctca atttttccca tttggatcga agctatttac 960 aagaaggtta gttattcttc atgtacattc taatatttat tcgttattat aatataaatt 1020 atttatgttg ataatctttt agtgttgtga agaattaaaa caatattcat gtttgatagt 1080 attttataaa aaatttataa ttgaccatgt atatatgtgt tgataatgtg atagtctaat 1140 tagtggttaa ttagatataa tttttagcaa ttatgcacta cattatgtgt aataagattt 1200 aacaaataca taaatctaaa catgatgttt gaaaacaata tagttctagt tatattaaca 1260 tgtgttagtt attgatttgg aagaatcatt tatattgact tgatatattt cactaaataa 1320 attttagtta aaatattgtt gttactgaat ttttatgtag gtggtcttga aacatgaata 1380 ataaccgatc ttggatgtac gaaaggacgg atgagagtgg tttcttgaat tctctattta 1440 tttctggagt ggaagaattc atgaatcatg ttatatctca gccaacgtct atgaatggta 1500 cgagtataca atgtccgtgc acaaagtgta agaatcggaa attttggaat tcagatatcg 1560 tgaagctaca tttgttgaag aatggatttg tgagagatta ttatatatgg agtcgacacg 1620 gagagtcata catttttaat gggaacgaag accaatcttc agcaaactat tcaaatgttg 1680 cacgtggcac agatgggaac aatttaatgt acaatatggt gattgatgca ggcggtccta 1740 gttttgatcc acatcgttca gaagagatgc cgaacgcaga agcacaaaat atatacaaca 1800 tgctaaattc ttcggaacga gagctatatg atggttgtga aacatcacag ttggctgcca 1860 tggctcaaat gttgagtctg aaatctgatc atcactggtc ggaggcatgc tatgatcaga 1920 catcacaatt catcaaaggc atcttgccta aagataatac atttctcgat agtttctatg 1980 gaacaaagaa acatatggaa ggactgggcc taccttccat tcatatcgat tgttgtgtta 2040 atgggtgcat gatatattgg aacgaagaca ttgacatgga gtcatgcaaa ttttgttcta 2100 aaccgagata taagatcaga gttaacagat ctacaagaga gagaaagaaa gtggctgttc 2160 aaaggatgat atattttcca ttggccccga gattacaaag gttatatgcc tcaccgacga 2220 ctgcagctca tatgagatgg catgctgatc attacaaaga agatggtgta atgcatcatt 2280 gttcagattc aggggagtgg aggcaatttg atagagcaca tccattattt tcctcggagg 2340 tcagaaatgt gagacttgga ctttctgctg acggatttca gccatttggt agttcaggca 2400 agcaatattc ttcttggcca attatagtga ctccatataa tttacccccc tggatgtgtt 2460 caaaagaaga gtacatgttt ctatccatac ttgtgcctgg cccgaggaat ccaaagcaga 2520 agatagatgt ttttcttcag ccattgattt ccgagttaaa aatgttatgg gaggttggtg 2580 ttgagacatg ggatacttcc ttaaagcaga attttcaaat gcgagctgca ttgatgtgga 2640 ctataagtga ttttcctgct tattcaatgt tatcaggatg gaaaactgct ggtcatttag 2700 cttgtcctca ttgtgctcat gaacatgatg cttataatct caaacatgga ggaaagccaa 2760 catggttcga taatcatcgg aagtttttgc ctgcaaatca tccatttcga aagaataaaa 2820 actggtttac caaggggaag gtcgtgtctg aatttcctcc acctattcgg acaggtgaag 2880 atgtcttaca agaaattgag tcacttggtt tcctccacct attccaactt ttgtagtgat 2940 gctcggaaaa aatgggaagc tggtgaagtg gacaatagag tagccatgca tgtatggcta 3000 ccttgggttg agttttggaa aactccagat ttccagacta aatcaaaaac tcaaaagaaa 3060 aatcgtcgtg gtgggacgga ccactaccct ccaactcaca caggtggttc agcatcctta 3120 agaactcatg ctgctgtcct ggtaagagct tgaacttaac taatctaatt tattttgtta 3180 ttctttattg attgtttggt tttggtttaa tgctttttat tgtaatgact attatatgga 3240 cagcctgtga tagaggataa tcgactaaga taattttgtt tgaaattcat atgatttaat 3300 tattctgaat gaagtaatat accatgcggt tttgaaatcc attgaggctc tggttcttcc 3360 ttgagtacat gtttatctat tttgcactaa ttatctttgc gcgttcgtca gaaagaatga 3420 ttagcctgaa tttatcaaac atttccgctg caaatagata aacactgagc tattaggaat 3480 aatcaagttt aatactacta tattacagaa catgtaattg tttgttgtgc taggctgtgg 3540 tgcacgggca aatgtataaa tgccaattat actatttaca acttgttgaa agcagcttga 3600 tagtgatttt ggcaggataa caaatgagat tcacttggcc tttagaatct tagaattttt 3660 attgtcaaat gattattatg aacattttgt tttaattttt atatggaata acattgtaga 3720 gaacctttaa aagatcgcac tcctgttgtt gcagtgtact taaattaata tatggatatc 3780 tgaaaaatat gaacagaaaa ctggcagata atagttttct ggtgaagtaa tatatactgt 3840 aatgagcttt gttgctggct tggcttggaa tttacctgtg atcagaaatg caggacatac 3900 tagtatgtgt ttttttaact tgtaaattaa atttaatttc aggcggagac taatggtaaa 3960 gatccaactc cggccgatgt gtatttgctt acacatacta agaaacgtga caaaaagacc 4020 tttgttacta agaaagcgga agcagtatat gtaagtagta ttccgaaata ttgcaattgc 4080 gagtgctgta ggagttttaa tatttttatt gtcgttattg ttgcacaaaa attaattggt 4140 atgatgtgtt ttcgttattt tacagaataa ggttattgaa attcgtgagg aacgctctaa 4200 acctattgaa ggttctgatg aacctcagat tgttgatgaa gacgaaatat tcttggaggc 4260 agttggaggg ctggacaaaa gaaatagaat atatggcttg ggttctttgc aaagcgtcat 4320 atatgggcca gaaagcaaga gcagtacatc cacttcccgt tacagtggct ctaacttcaa 4380 taaagaatat gagctaatgc aggttgagct ccaagaaatg aaggaacagg taaaggagtt 4440 acaggagacg agagataagg aacttgaaga tatgagaaac caaatggaag agatgaagag 4500 ccaacttgct ttggtattta aaaatcagaa cacaagttag gcaagttcat cagtacaaaa 4560 gacaatagca agctcctgct tttatatatt ctgctatata ttttgtacca acttaatgaa 4620 tggtatttgt gaatatttgg atacttgtga tcaggtactt tatttctaat caaagttagt 4680 ctttcttttg attctacaag tatttgttaa taatataatg tagtgtataa tgtagtatta 4740 gctaaaaaaa ctatatgtat ccaaaaaaag ttattgctta attttcccaa tcatttcact 4800 aataaaaaat gtattataaa atattaattt ttaacattcc ctacgaattt gcaaccaaat 4860 ataaaagcaa aacatgtaaa tttttccgtt ggtaaattac caagttacca accaaaagat 4920 ggttgctagt tgtggttgca atattagcaa cagagtagaa tccgttggca atctgttggc 4980 aaattaccaa cggaaattct gttggcaaat tagcaaccga aaatccgttg gcatattggg 5040 catctcagca aagtcaacac accaattttc cgttgataat ccgttgcaaa agtaccaacg 5100 gaaagtatat ttccgttggt aatagtttac caaccatgat tttactaaca gtttattccg 5160 ttggtaattc cgttggtacc tcgttttagc aacgggaatt tgtgtttacc aacggaaaat 5220 tccgttggga atctcgcgtt ttcttgtagt g 5251 // ID TGM1_GM repbase; DNA; EDCOT; 3550 BP. XX AC K02837; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 25-MAR-1997 (Rel. 2.02, Last updated, Version 2) XX DE Soybean seed transposable element Tgm1. XX KW GMTGM1; TGM1_GM; Tgm1 transposon; transposon. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-3550 RA Rhodes R.P. and Vodkin O.L.; RT "Highly structured sequence homology between an insertion element RT and the gene in which it resides."; RL Proc. Natl. Acad. Sci. U.S.A 82(2), 493-497 (1985). XX DR GenBank; K02837; Positions 4 3553. XX SQ Sequence 3550 BP; 1316 A; 489 C; 429 G; 1316 T; 0 other; cactattaga aaatatgttt tttacatcgg ttatttatga ctttcaacat cgatttttga 60 accgatgttg aaagtaccga tgttgatagt attatcgtta acatcggttt ttgaaaaatc 120 gaaaaaccga tgttaacgta aaattaccaa cattggttat ataaataatc gatgttgcta 180 atatgaatta cacccagaaa atgtatatta atgttgaaag ttaacatcga tttttacaaa 240 aaaccgatgt taacgaatgt gttacttaac atcgattttc tgtaaaaatc gatattaacc 300 cacgttaaca tcggtttttt ataaaaatcg atgttaacga atgtgttatt attgacagtt 360 aacatcggtt ttttcaaaaa actgatttta acgaatgtgt tactattgac agttaacatc 420 ggttgttata aaaaactgat gttaatcaag ttaacatcgg tttttcaaaa aaccgatgtt 480 aacggatgtg ttattattga catttaacat cggtttttat aaaaaactga tattaacgaa 540 tgtgttacga ttgacagtta acatcggttt ttcaaaaaac cgatgttaac gaatgtgtta 600 ttattgacag ttaacatcgg tttttataaa aaatcgatgt taacggatgt gttactattg 660 atagttaaca tcggttttta taaaaaaccg atgttaacga atgtgttact attgacagtt 720 aacatcaatt ttaataaatt aaatattaaa tagaaaaaaa gattttcttt ctaaccaatt 780 aatatttatt ttttcacaaa ggtcaattaa tatttaatta attcgacatt aacttttaga 840 aggcgttagt ataaaaaaaa gcttttaaga aaccgaaatt aaatgtgaat acatatggag 900 aaaccgaaaa gattttctct caatctttct ctaatttcca cctacaaccc aacatacggt 960 atatgttcat acttttcctt agctaaatga ataaagttag tattaaggaa ttaaaacaac 1020 aatggcttca taccacattc atcagaaatg agcatataaa ttcaacaatg tttattcgtc 1080 tttgaaatcg tgaatagaag tctcattttt ctaattcctc ttctagaacc atctttaaaa 1140 ttttgagtat attttttttt actaatctct ttttaaatta atccttgaaa atctgaacat 1200 acttctcatt ctaatagctc tatcccgaac actcgcgtaa actccaacaa caacatctta 1260 acactcacat tccatggaag agaatcaaag tttacaagaa aactaaaaca tccaaaaaaa 1320 gcccttttac agtttcggat aatgtatgac tgattttgaa gttgctaaac taaatcctca 1380 caagtagcta gtgtgttcaa caattgaata agagcaaaac aagaaaaaca aaaacaaagc 1440 cattgcaatg cttacccgat tgaagaccat gaaaccaagg tcaatatcaa ccccctcgtc 1500 actttctcct gcttatacat tttatcattc ataaacagaa gaataataat acatagttta 1560 atagcaacat aaaaactgcc caaaaaaacg gcataaaaac tttacgcaaa aaataaaatc 1620 aaatgtaatc acatgagatt acctggtttg tgctgaacgt gcaagtgaag ggtaacaaag 1680 gaaggtgagt gagtgagtga gagtggggaa ggaaacaaaa caaaagagtg agagtctttg 1740 tcacttcacg gaactcaact ccagagaaga aatcggtttc aactatcact ttgagtccgt 1800 attatacctc cacttttttt taaaagaaaa gaaaacaatc ttatacctct ctttataaag 1860 cgttgcttcc tactagtagt tggttaaatt cttgtaaagt cattagtaat ttttttatct 1920 gaaaaaatta ctttattcca agagtctatc tttatttatt ttttaataat aaattaaaaa 1980 ttctaagggg aaggaatgat atttctgttt ccaaattctt taatgagcaa tcacgtcatt 2040 ctgctgtcta gaccaaattc tttaatgagc aatcacttta tccttttaaa ttttatagtt 2100 tttaattttt tattaccatt tttagaaaaa cttatataat tttttatttg atatcagttt 2160 tgtaaaaaaa gtcacatacc ttaactaaaa gatcccacaa atcactattt tctttaaagt 2220 agaaaatcct ttctcaattt acgttttaag cttcatttta tgttaggctg acattgaatt 2280 ggtgctcata gaatattaat taaaaaattt taaaaaaatt attatataaa tcacaagaga 2340 ttataaatac ttatcagtat aattttattg aatactacta ccagtataat ttttatttaa 2400 ttttattata aatacttatc aatcagttgt ttttaagtgt attttcggtt tagcatctcc 2460 taatgtgaaa tccacgattg cagtgaaact gttaactgat tttattttat ttttaatttt 2520 taaccaattg acgtgatatt ttatgttctt taacgttttt ttctaaaatg tatcttttta 2580 acggcatgta tttaatatta tgcaagaatc atatcttaaa ttaattttta gaattttttt 2640 ataaataaca atgattttat atttattctg aaatatgtcc attaaaataa attattttat 2700 cggtcaaaga gatctgacta aacaattatt ttttttttgt cttttcttgg ttgaatagtt 2760 attatatatt tttatgttta atttttacga ataaaaaaaa ttaatcaatc cgaccctaca 2820 cttacttgga ttgtagtcac acactacatt tggacatttg cagtagatcg atctttgaca 2880 aaaaaaaagt tacgcaagat tttaatatct ataaagaaac catataattt ttttatatca 2940 ttcattagtt aaaatttatt attactacaa tttttaggat aactaacatg aaaaaacaat 3000 tgtacataat aatttattat taaatattag tgtaaaaaat taaattatta acatacacta 3060 tttactcttt tttttagtag catccactat ttactcttaa cacaatgcat ttggtaataa 3120 ccaaaatatt aaatttcacc tccatttgta tgttggtcat ttaagcagtg aagaaaaaac 3180 tttgcttaat caaatgacaa aaaatatggc gaagtctgat caaattttgt tgattaaata 3240 ataataaaat taaatttacg aaattcattt taaaaattta gtttaatttt taaatgttta 3300 ccttttgaat ttataattgt ttcttaatta ttatattttt ttaattaaaa tataattaat 3360 aacgcaatat attatttttt taaaatatat aaaaattaaa aaaaaagttt atattaacat 3420 cggttttttg gaaaaccgat gttaagaatg atactttatt tacaaatatg tcaccgcgtt 3480 taacttaaca tcggttttgt acaaaaccga tgttaataag ccgatgttaa aactactttt 3540 tgtaatagtg 3550 // ID MuDr5_MT repbase; DNA; EDCOT; 280 BP. XX AC . XX DT 14-NOV-2006 (Rel. 11.11, Created) DT 01-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE Sequence of a putative non-autonomous DNA transposon from DE Medicago truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW Inverted repeats; Interspersed repeat; MuDr5_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-280 RA Shankar R. and Jurka J.; RT "MuDr5_MT: A putative DNA transposon from Barrel Medic."; RL Repbase Reports 6(11), 577-577 (2006). XX DR [1] (Consensus) XX CC The sequence is self-complementary with 9 bp target site CC duplication. XX SQ Sequence 280 BP; 87 A; 46 C; 50 G; 95 T; 2 other; gggttaatag tgtttttcac ccctgtaata tatgtcattt tcggttttcg cccctataaa 60 attttcggtt tgatttgcac cctcgtaaaa tttttatttt ccggaaaaca cccttaatag 120 gccattcaga attttttttm agaaawtttg gtttaatggc ctattaaggg tgttttccgg 180 aaaataaaaa ttttacgagg gtgcaaatca aaccgaaaat tttatagggg cgaaaaccgg 240 aaatgacata tattacaggg gtgaaaaaca ctattaaccc 280 // ID Copia-42_Mad-I repbase; DNA; EDCOT; 5464 BP. XX AC ACYM01024266; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-42_Mad-I; KW Copia-42_Mad-LTR; Copia-42_Mad_. XX NM Copia-42_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5464 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1312-1312 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01024266; Positions 5900 11363. XX CC Positions [2568-2882] - Integrase core CC 'CATA' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 663..1709 FT /product="Copia-42_Mad-I_1p" FT /translation="MTVPVFKVEGVLGMITIRLREDNFAKWAFQFQSVLRG FT YKLFGHFDGSNPCPPKFVINFDTGVTNEITVAYLEWEATDMALLSLLLVTL FT FDEAMKYVIGCRTAYEAWINLVDRFASVSKSRLNHLKTELHTIQKWSDTID FT KYLLRLKHIRDQLSAACEVVSDNDIMIVGLAGLPKEYGVIHTVILARESTL FT TLKEFRALLLGAEREIEGELNVITQNLSALYVQGSSSSSNSGSSSSALGSN FT PQSHDHIPAVTAGTITVVPYSSTSSSNADQQSYYHLPESYGYGFNAHSGGQ FT NAPRSHSLNGQFTPQGNQYRGGHDYRGGNSYRNNNGFRGRGYINSGNTSHS FT YLGGSR" FT CDS 4428..5453 FT /product="Copia-42_Mad-I_4p" FT /translation="MDGGDLVILLLYVDDIILTGSNPVKIQVVIDDLAGVF FT DLKDMGRLSYFLGLHIHYKDDGSLFITQTKYAKDLLKKASMDSCKPTSTPS FT KPHAQVLAGEGRLLSEPSQYRSIVGALQYLTFTRPDISHSVNLVCQFMTQP FT TDMHMLLVKRILRYIQGTVDYGLHYTQNKHFDITAFSNSVWAADITTRRSI FT TGFVVYLGDNPISWQSKKQSTVSRSSTEAEYKALAHCAADIFWIRSVFKDL FT HQYISDPPSLYCDNLSALALSLNPVFHSKIKHLDTDYHFVREKVQKGDLTV FT HYIPTYEQVVDVFTKGLHSPIFLTHCIRLGLGIMTVTNSASAAHLRLRGK" FT CDS join(1806..2882,2886..4190) FT /product="Copia-42_Mad-I_2p" FT /translation="MNTNVPVTGFVVECQIYGKRGHSALDCYQRGNYAYQG FT QPPSSSLSAMNAQRTSTFVPQDAWVVDSGASHHITSDINALSQVTPFEGSE FT RINIGNGTGLPIKHIGSTILQTPTHSLTLNKVLHVPDITRSLLSVKQLCAN FT NKSWFIYDESEFFVQDKKTKEIVFQGKSRPDELFQIPVVTSSRGFQFITRN FT PEAYLGKAVKNSIWHKRLGHPTHDIVDIMLKQSKILVRTDDTHSACISCII FT GKMSRTPFPLRTDKCTFPFEKIHTDIWGLSPIRSLEGYRYYVIFVDEYTRF FT VWIFPMSNKSDMFMIFVKFYKFIFNQFGVSIKTLQTDGGGEYTSKSFTSFL FT ADKGIVQLVSCPYTPQNGVAERKHRHIVETAITLLTDAGLPSELWYFACAH FT AVLLINKMPCKSLSFSSPYLSLYKKAPDLLFLKVFGSAIFPWLRPYNVHKL FT QPRSELCVFLGYTQGYKGYICYHMPTKKIIISRHVHFDEFLFPAHMINNTK FT TGVPQRHKDHQDSTLIPVIVPIPLSRSQQCATHAGSQSSWVQTATNLSSPT FT SNENMVAFDSSAVQHSQSERQSGESGSTELALQGSGPSHTLLSIQDTTHLL FT HVMDLAQLQVILTSTSSSIDHNSVITGTNSNRIQTRLQTGAISRKSYVGYL FT ASLPQLSSLQLEELYTDDQSSAISEQFSGGFSFLADITDNEEPKTFKSAST FT KPEWQRAMQEEFDALKTQGTWLLVPPPSNRSMIGSKWVYKVKKNPDGTVSR FT YKARLVAQGYTQEQVLDYSETFSPVVRHTTVRIILALVAQFGW" XX SQ Sequence 5464 BP; 1594 A; 928 C; 1124 G; 1818 T; 0 other; catatgttaa tatggtatca tcgccggtat ttggctagct gccgtagtcg gttctgaagg 60 gtcttccgct gtgttcgtcc cgaagggtat tccgctgtgt tcctccttga tgcatcttga 120 tcggttggag tgtcagtgtt tgttgcagga gtttagagta ctgggttttg tgatttgttg 180 atggattgtg tcgtatcagg tgatattatt caattttttc atctgggttg ttctataaat 240 tttgttgaat gatggttggg tatttgcaat acgattagat tgagattctg ttttgtttcc 300 tttgatttga gaattctgct gtggtttctc ttgattttgt ggtagaagtt tgatatgggt 360 atgctgcaat agttgattga agtgctggaa ttatagtttt aagaaagtgt cattctttct 420 tgtttgccag gaagtgtcat tctttctgcg tccaagattt gtttacaaga aagtgtcaat 480 ctttctgtgt ttgagagttg tttgccagaa agtgtcattc tttttgtgtc caagatttgt 540 ttgcgagaaa gtgtcaatct ttctgaattc gagatttttc tgcatagaat gtcattctct 600 atagagtgtg tttctgttca tcatatagtt ttgtgatttg tggaagtgtc aatctttcaa 660 tcatgactgt tcctgtattc aaagttgaag gtgtgttggg tatgattacc attaggctca 720 gggaagataa ttttgcaaaa tgggcatttc agtttcagtc tgtcctacga gggtataaat 780 tgttcggtca ctttgatggt tcaaatccat gtccaccaaa gtttgttata aattttgata 840 ctggagtcac taatgagatt acagtggcat atcttgaatg ggaagcaact gatatggcat 900 tattgagttt gttacttgtt actttgtttg atgaagccat gaagtatgtg attgggtgta 960 gaacagcata tgaagcctgg attaatcttg tagatcgatt tgcttctgtt tctaaatcaa 1020 gacttaatca tctgaaaacc gaattacata caattcaaaa atggtccgat acaattgata 1080 aatatttgtt aagactcaaa catattaggg atcaacttag tgctgcatgt gaagtggtct 1140 cggataatga tattatgatt gttggtcttg ctggattgcc aaaggagtat ggggttattc 1200 atactgttat tttggccagg gaatctacac ttacgttgaa agaatttcga gcattgttgc 1260 ttggtgctga gagagaaatt gagggagaat tgaatgtaat tactcagaat ctgtctgcct 1320 tatatgttca agggtccagt tctagttcaa attcaggttc tagttcatct gcattaggat 1380 caaatcctca aagtcatgat catattcctg ctgtaactgc tggtactatc actgttgtgc 1440 catatagttc aacttcatca tctaatgcag atcaacaatc atactatcat cttccagagt 1500 cttatggata tggttttaat gctcattctg gtggccagaa tgcaccaagg tcacattctt 1560 taaatggtca atttacacct caaggcaatc agtatagagg aggacatgat tacagaggag 1620 gaaatagtta cagaaataac aatggctttc gaggaagggg atacattaac tcagggaaca 1680 catctcattc ctatttaggt ggttcaaggt agtttggctc tggaaatgtt gatactagag 1740 ctactgttgt gattgaatgt tagatatgta ataaacgagg acacactgca gttaattgtt 1800 ttcacatgaa taccaatgtt ccagtcactg gttttgtagt tgagtgtcag atttatggca 1860 agagaggtca ctctgcactg gattgttatc aaaggggaaa ttatgcttat caaggtcagc 1920 ctccatcctc atcattgtct gcaatgaatg cccaacggac ttcaacattt gttcctcaag 1980 atgcttgggt tgttgattca ggagcatctc atcatataac ttctgatatc aatgctttat 2040 ctcaagtaac accatttgaa gggtccgaga ggatcaatat tgggaatggt acaggtttac 2100 caattaaaca tattggttca actatacttc agacaccaac acactctcta actcttaata 2160 aagttctaca tgtgcctgat attactagaa gtttactttc tgtgaaacag ttgtgtgcta 2220 acaataaaag ctggtttata tatgatgaat ctgaattttt tgtgcaggac aagaagacaa 2280 aggagatagt gtttcaagga aagagtaggc ctgatgagtt attccagatc cctgtagtta 2340 caagttcaag aggttttcag tttattacca ggaatccaga agcttatttg ggaaaagcag 2400 tgaagaatag catttggcat aaaaggctcg ggcatccaac acatgatata gtagatataa 2460 tgttgaagca gtcaaaaatt ttagttcgaa cagatgacac acatagtgct tgtatttcct 2520 gtattatagg caagatgtct aggactccat ttccactgag aacagataaa tgtacttttc 2580 cgtttgaaaa aatacacact gatatctggg ggctgtctcc tataagatct ctagagggat 2640 ataggtacta tgtaatattt gttgatgaat acacaagatt tgtatggatc tttcctatga 2700 gtaataaatc tgatatgttt atgatatttg tcaagttcta caagtttatt tttaatcagt 2760 ttggtgtatc aatcaagact ttacaaacag atggaggggg tgaatataca agcaaaagtt 2820 ttacttcgtt tcttgctgat aaaggtattg tgcagttagt ttcatgtcct tatactccac 2880 aatagaatgg agttgcagaa agaaaacata gacacattgt agagactgca attactcttc 2940 tcactgatgc tggtttacct tctgagttgt ggtattttgc gtgtgcacat gcagtgttgt 3000 taatcaacaa aatgccttgc aaaagcttat catttagttc tccttacttg agtttgtata 3060 agaaagcacc tgatttactg tttcttaagg tgtttggttc agctattttt ccatggctga 3120 gaccatataa tgtgcataaa ttacaaccaa ggtcagagtt atgtgtgttt ttgggttata 3180 cacaagggta taaaggctat atttgttatc atatgccaac caagaagatc attatctcca 3240 ggcatgtgca ttttgatgaa ttcttatttc ctgctcacat gatcaataat actaagactg 3300 gagttccaca gagacataag gatcatcaag attcaacact tattcctgtt attgtaccta 3360 ttcctttgtc cagaagtcag caatgtgcaa cacatgccgg ttcacagagt tcatgggttc 3420 agactgcaac caacctatct tctccaacaa gtaatgagaa tatggtagcg tttgactcta 3480 gtgcagtaca acacagtcaa tctgagagac aatctggaga gagtggatca actgagttag 3540 cattacaggg atctgggcca tcacatactc ttttatctat ccaagacact actcatttgc 3600 ttcatgtcat ggatcttgca caattacagg taatcctcac atctacctct tcttctatag 3660 atcataattc tgttatcaca ggcacaaatt ccaatcgtat tcagaccaga ttacaaactg 3720 gtgcgatttc tagaaagagc tatgtgggat atcttgcttc attaccccag ttgtcttcct 3780 tacaacttga agagttatat actgatgatc aatctagtgc aatcagtgag caattttctg 3840 ggggattttc attcttggct gatatcacag ataatgaaga acctaaaaca tttaaaagtg 3900 catcaaccaa accagaatgg cagcgtgcaa tgcaagagga atttgatgca ttgaaaactc 3960 aaggcacttg gttgttggtt ccaccaccat caaatcgatc catgattggc agtaaatggg 4020 tgtacaaggt gaagaaaaat ccagatggta ctgtctcgag atacaaagct cggttggtag 4080 cacaaggtta cactcaagaa caagttttag attattccga gacatttagt cctgtagtaa 4140 gacatactac agtaaggata atcttagctt tggttgctca atttggttgg taattaaggc 4200 aactcgacgt taagaatgca tttcttcatg gagagtttga ggaagaggta tatatgaaat 4260 agccacaagg ttttgtggat cctacatgcc caaatcatgt atgcagatta gtcaaaacac 4320 tctatggcct aaaacaggct cctagagctt ggaactctaa attcacaagc tatcttccag 4380 ctcttggttt caaatcatct ctttcagaca ctagtctctt tgtaaaaatg gatggtggtg 4440 atcttgtcat tctattgctt tatgttgatg acataattct tactggatca aatccagtaa 4500 aaatacaagt tgtgattgat gatcttgctg gtgtgtttga tctcaaagat atggggaggt 4560 tatcatattt tttggggttg catatacatt ataaagatga tggatctttg tttataactc 4620 agactaagta tgctaaagat ttattgaaga aagcaagtat ggacagttgt aaacctactt 4680 caacaccatc aaaacctcat gctcaggtcc ttgcaggaga aggaaggttg ttatctgaac 4740 ctagtcagta tagaagcata gttggggcac tacagtacct aacttttact cgacctgata 4800 tctctcattc cgtgaacttg gtttgtcaat tcatgacaca accaactgat atgcatatgt 4860 tgttagtcaa aagaattttg agatatatac aagggactgt cgattatggt cttcactata 4920 cacaaaacaa gcattttgat atcactgcct tttcaaactc agtttgggca gcagatatta 4980 caaccagacg atcgattaca ggttttgttg tatatcttgg agacaatcct atctcatggc 5040 aatccaagaa gcagtctact gtgtctcgaa gttctacaga agccgaatat aaagcattgg 5100 ctcactgtgc agctgatatc ttctggattc gatcagtatt caaagatctg catcagtata 5160 tatcagatcc accttcttta tattgtgaca acttatccgc tttggcattg agtttaaatc 5220 ctgtttttca ctccaaaata aaacatctgg atactgatta tcatttcgta cgagaaaagg 5280 ttcaaaaagg tgatcttaca gttcattaca ttcctactta tgaacaagtg gtagatgttt 5340 tcactaaagg gctacatagt ccgatctttc tcacacattg tataaggctt ggattaggga 5400 taatgactgt aacaaactca gcttcagcag ctcatcttcg tttgaggggg aagtaataac 5460 cata 5464 // ID Copia-63_VV-I repbase; DNA; EDCOT; 4243 BP. XX AC chr15; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-63_VV_; KW Copia-63_VV-LTR; Copia-63_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4243 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr15; Positions 19157233 19152991. XX CC Positions [1620-2117] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1008..2288,2292..4241) FT /product="Copia-63_VV-I_1p" FT /translation="MVAHSNAEQEEETWFADSGANQHITANLEHLTLQQPY FT TGQENVAVGNGQGLSIAHTGTTIFHTPEAKLNLKRVLHCPQASANLLSINQ FT FRLDNNCLFILTGTHYFVKDIQTGATLLEGRSEGGLYPIQLRSMSINKSHA FT LSVVVGIKAPVSVWHSRLGHASLPIVSQLLNKHSLPVEGLVNKMHFCEPCQ FT LGKGKQLPFKPSTCVSSFPLQLIHTDVWSCSTKSLSGCKYYVIFIDDFSRF FT SWLYPLQNKSDVYACFVKFKTLVENQFSCKIKQLQSDGGGEYMSNQFQLFL FT SSNGIQHRRTCPHTPQQNGVAERKHRHVVEMGLSLLAQSLLPTKFWVDAFL FT TSIFLINRLPTSTLDNQTPNLKLFGKHPDYTSLRTFGCACFPLLRPYATHK FT LMFRSKRCIFLGYSSHQNGYRCLDPVTQKVLISHVVFNENTFLAKDGLQSS FT ELLPVVSSQGTPLPSPSFSLSTSNLQHSSPIISDSPDSPLESLPIPTSPHI FT STLPSPIPGPAPTLSIPEFSSSSNHSHHPMTTRSQTGNLKPRTFSDFKLYS FT TQYPLQALSSTVTPLAPTSYRQAALLLDWCVAMREEYDALLANETWKLCPR FT PVDHNVVGNKWVYKVKQTSTGEVDRFKARLVALGFAQEEGIDFTETFSPVI FT KPSTVRVLLTLSIQFDWEIRQLDVSNAFLHGILLKDVYMEQPKGFVNSDFP FT DYVCKLNKSLYGLKQAPRAWFMRLSQTLLEFGFLSSPVDASLFVYHKGHIH FT LFILIYIDDILVTGTYPSLIQSLIQKLQTEFKMKDLGPLGYFLGIQASRDS FT SGLHLRQSKYIGDLLHRTKMAGAKPASSPCTTGLKLSTHVGEPLTASQITE FT YRQTVGALQYCTLTRPDIAFSVNQLCQHMHCPNSVHWTAAKCVLRYLKGTI FT DLGLWYTKGEQTLQAFCDSDWAGNPDDQRSTIGYGVFFGSCLISWTAKKQY FT VVARSSTEAEYRTLAITTAELYWIRMLLKELHISLPTAPTIWCDNSGALAL FT ASNPVFHARTKHIEVDFHFIREKVANRDISLQFIGSYDQPADIFTKGLSLA FT RFCLLRDKLMVVSLPISLRG" XX SQ Sequence 4243 BP; 1134 A; 986 C; 742 G; 1381 T; 0 other; tggtatcaga gcaattggca tacgcctaat ttcaatcgat cctttccttc tcaactatgg 60 ccttctcttc ttccgcttcc tccaatgtta tctttgctcc tccaaacatt ggtcatctgg 120 tgtcaatcaa gctgagtgac acaaactacc ttatatggtc atctcagatt gtgctagtac 180 tgaaaagtca tgacttgatg ggcttcgtgg atggttttga gccgtgtcca tcaaaatctc 240 ttgatggttc tcttaatcca gcatatattc tctggaataa gaaagatcag tgtgtgttaa 300 gttggatcaa tgccactttg tctgacaagg tgctagcttc tgtttatggc atcacatctg 360 ctcgagaggt gtggagttct ctagcaaaca agtttgcctc tcaatccaga acccgtgtac 420 accacctaaa gcgaaagttg tagactcttc atcaagggtc aatgaagtgc actgattttc 480 ttgaaaaagc aaagttggtg tctgatgaat tagctgcagt tggtaagcca cttaaggatg 540 atgacttaat gtcttatatt gtgagtggac tcaacccatc ctttaatccc tttataacct 600 ctctgtcctt tgccactaga gacaagaatg tttcttttga agactttcaa gccgagctct 660 tgtcatatga actgttattg gaaaaccaga atattgctat accacctgag acaaataatt 720 ttgctttctt cattcccaaa tctaaccaac agcagtacaa tcgcaaaccc aaaaacccaa 780 gtaaaccata ttcacgtcct tcattttcac aaaatcctcg tcctcgatat tcaccacaac 840 cctctggttt accttcctca cctcagccaa atcagaagca gcactcattt tccactccta 900 aggcaccttg tcaaatctgt ggaaagctaa gtcataaggc attagattgc tttcatagaa 960 tggattatgc atatcagggt cgtcatccac caacctagtt agctgctatg gtggcacata 1020 gcaatgctga gcaagaggaa gagacatggt ttgctgatag tggagctaat cagcacatta 1080 ctgccaatct ggagcatctt actctgcaac aaccatacac aggacaagaa aatgtagctg 1140 ttggtaatgg ccaaggttta agtattgcac atactggtac tactattttt catactcctg 1200 aagctaaatt aaacctcaaa cgtgtcctcc attgtcctca agcttctgcc aatttgcttt 1260 ccataaatca attccgtctt gataataatt gcctctttat tctaactggt actcattatt 1320 ttgtcaagga catacaaacg ggggcgacac tactggaagg caggagtgaa gggggtctct 1380 atccaatcca gttgcggtca atgtctatca ataaatcaca tgctttgtca gtcgttgtag 1440 gaattaaagc accagtttca gtttggcatt ctagattagg acatgcatct cttcccattg 1500 tgtctcagtt attaaataaa cactccttac ctgttgaagg attagtgaat aaaatgcatt 1560 tttgtgaacc ttgccaactt ggcaaaggta agcaacttcc tttcaaacct tctacttgtg 1620 tttcttcctt tcctttgcaa ttaattcata ctgatgtatg gtcttgttct accaaatctc 1680 tcagtggatg taagtattat gttatattca ttgatgattt ttcacgattc tcatggcttt 1740 atcctctcca aaataaatct gatgtatatg cttgctttgt taaattcaaa acactagttg 1800 aaaaccaatt ttcttgcaaa attaagcaat tacaatcgga tggaggtgga gaatacatgt 1860 ccaaccaatt tcaattgttt ctttcctcta atggaatcca acatcgccgc acttgtcctc 1920 atacacccca acaaaatggg gttgctgagc gtaaacaccg tcatgtggtg gaaatgggac 1980 tgtctctatt agctcagtca cttttgccca ctaaattctg ggttgatgcc tttttaacat 2040 ccatttttct catcaataga ctgccaacat ctactcttga taaccaaaca ccaaatctta 2100 aattatttgg caaacatcct gattatacct ccttgcgcac ctttggttgt gcctgttttc 2160 cattgttgcg accatatgca actcacaaat taatgttcag atccaaacgt tgcatatttc 2220 taggttatag ttcccatcaa aatggatata gatgcttgga tcctgtcact caaaaagttc 2280 taatctcatg acatgttgtg tttaatgaga atacatttct tgctaaggat ggattgcagt 2340 cttctgaact tcttccagtg gtctcctctc aaggtacgcc tttaccttct ccttcatttt 2400 ctttatctac ttctaattta cagcattcct ctccaatcat ttcagattca cctgattctc 2460 ctctagaatc tttacctatc cccacttctc ctcatatctc cactctacct tctcccatac 2520 ctggtccagc tcctaccctt tctatacctg aattttcctc ttcttccaat cactctcatc 2580 accccatgac aactcgctcc caaacaggaa acctcaaacc tcgcacattt tcagatttta 2640 aactctattc cacccaatat cctctccaag cattatccag tactgtgact ccccttgcac 2700 caacctctta ccgacaagct gctttattac ttgactggtg tgttgctatg agagaggaat 2760 atgatgcttt attggctaat gagacatgga agctatgtcc tagacctgtt gatcataatg 2820 tggtgggaaa taagtgggtg tataaagtta aacaaacatc cacaggtgag gttgacagat 2880 tcaaagcaag attagtggct ttgggatttg ctcaagaaga aggtattgac tttactgaga 2940 cttttagtcc agtaattaag ccttctactg tacgggttct tcttacactt tctattcaat 3000 ttgattggga aatcagacag cttgatgtat ctaacgcttt tcttcatggg atcttgctaa 3060 aggatgtata tatggagcaa cctaaggggt ttgttaattc agattttcca gattatgttt 3120 gcaaactgaa caagtcactt tatggcctca aacaagcacc tcgtgcttgg tttatgcgtc 3180 tatctcaaac tctacttgaa ttcggtttcc tatcctcacc agtggatgcc tccttatttg 3240 tctatcataa gggccatatt catctattta tcctcatcta catagatgat atccttgtta 3300 caggtacata tccttctctc attcagtctc taatccaaaa gctacagacc gagttcaaga 3360 tgaaagacct tggtccttta ggctattttc tcggcatcca agcaagtcgt gactcttctg 3420 gcctacatct tcgacaatcc aagtacatcg gggatcttct tcatcgtacc aagatggctg 3480 gggccaaacc tgcttcctct ccttgtacca caggccttaa attatccact catgttggtg 3540 agccactcac agcttctcaa attacagaat atcgacaaac tgtgggagct cttcaatatt 3600 gcaccttgac tagacctgat atagcatttt ctgtcaacca actatgtcaa catatgcact 3660 gtcctaattc tgttcattgg acagcagcaa aatgtgtctt acgttactta aaaggcacca 3720 ttgatctggg attatggtac actaagggcg agcaaactct tcaagccttt tgtgattcag 3780 attgggctgg taatcccgat gatcaaagat caactattgg gtatggcgtt ttctttggct 3840 cttgcttaat ctcatggact gccaagaaac aatatgtggt agctcgttct agcactgaag 3900 ccgaatatag gacattagct attactactg ctgagctgta ttggattcgt atgctcctca 3960 aagaacttca tatttctttg cccacagctc ctactatttg gtgtgataac agtggcgctc 4020 ttgctcttgc ttctaatcct gtgtttcatg cccgcaccaa acatattgaa gttgattttc 4080 acttcatccg cgagaaagtt gctaatcgag atatttccct tcagttcatt ggttcttatg 4140 atcagcctgc tgatatcttt acaaagggac taagtttagc tcgtttttgt ctgcttcgtg 4200 acaagctaat ggtggtttct ctccccatta gcttgagggg gga 4243 // ID Ogre-SD1_LTR repbase; DNA; EDCOT; 2277 BP. XX AC AC146506; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 10-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-SD1; Ogre-SD1_LTR. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-2277 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC146506; Positions 59796 57520. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). XX SQ Sequence 2277 BP; 946 A; 294 C; 294 G; 743 T; 0 other; tgtagacacg tatttttgac cgaacttaaa attttacacc atttttagag ctgaaatatt 60 tttataaata taaattaaat attttgactt ttctcttatt ttattaagtt tattttaaaa 120 gatttgaaaa caacaaaaat agaatccttt ttttaaggta agttttattt tcaattgttt 180 aaaaagaaat aaaagattac aaaaaatcta tattattttt gaaattaagt ttttataaat 240 aagctagtat tatttaattg attttatata tatagctagt tgactttttc ttagattttt 300 attaatttta aataattagt tgatatgtta ttataattct tttaagagta aagtaaaact 360 aaaactaaaa aataataaaa aaaaaaacta aataatctaa ctaaccatac accccccaca 420 ctcccacttt cccacaattc tctacactcc ctcacgttct cctcaactaa atccactcca 480 atacccacta aactactact acaatctgca aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa 540 acctatccta tatatatagg acacacaacg tacacatggg gggactccta tatacatcac 600 catcataaag catcatcagt tatacggaat aacagtgcac aaaaaaaaaa gaagcaatac 660 actttaagtc agaaagattt tttcgtggat tcaagttcgt ggctccttaa agttaattat 720 aattaacttt ggaaatcagt agattgtagc ggtttctttt gttggaatta agttttacga 780 aaaggtaatt ctaattcctt atatagttca atgaaataat tgttctgaat ttgattatga 840 tgttatgaag tcctaaaaat tacatgtatt gttatatgcc actattttat gacgcatgtc 900 atatcgttga ttgcatgaat tgctactgtt ttaatttgtt catcgaatta tttttacacc 960 tgactttaat ttaatcaact aatttgatcc aaagatggtt gttgtttact cctagtttta 1020 ttccaacatg tttatgtaca tttatttgat ggtacaaatt gacaacttcg tttataactt 1080 taatttaatt acatgtaaat tggttagaga ttctgtatta gttatcattt ggagtttctg 1140 gattttaata aataaataat attgccatac ttatggagac aattaattat tagaataatt 1200 ttattgtatc cgaaatatta aaaatggagg agataaacat tagttcattt gagtgagtca 1260 ttaattcatc aacgtgagat agttctttta ttagtaattt cacacaatca tcatttggtg 1320 aaggaatatt attatatcac tacgtatatc aattttctct caattagttt aaaggggaaa 1380 aaaattaatt aaaaataata tatagaatta aaaaataaaa cgtgagcaga gaaaaatgaa 1440 gataaaaaaa aaagaagagg aatagatcat taaaaagaaa gtaagaataa aataaataaa 1500 catttaaaac aaaaacagaa gaaacaaaag atgaaaagtg ataaaaagcc aaaaaaataa 1560 aaataaagaa aaggtaaaaa aggggaaaac aaaacttagc caaaaaatta tttaaataaa 1620 aaaagaagag aaacattttg ttagacaaaa acaaaaaaat aacggtaaga agaagaagaa 1680 acagaatgtt ttaaaaaaat aaataaataa ataacgtgca aaaaaaaaat atagaataaa 1740 agataaaaga aatttccaag aaattggtct taacctcttt tatattttct tttcctaaaa 1800 ttaatcctaa atcccataga agtttatctc ctattataat tcaaatatct attctcacta 1860 aaatgataat actaaaattt ctcggatttt caaagaaaaa tttaaataag acagttacaa 1920 taaatcaaag agggtgggat ataggtaaat gtatagctaa taagtagtat atccaaaagc 1980 taagtcaggc caagatataa gtcaatgaag cgactgtgct agaaccacag gactcgaggg 2040 gtgccttata ccttcccctt ggtcaataga atttcttatc cagatttcta gttcgtagac 2100 cattaaaaat tagagtcaac ttccttttga ttaggggtaa aaattaggtg acttggaaca 2160 ccaaaactca attccaagtg gcgactctga aataaaataa tccattttcg aaacatcact 2220 ttaattggag aaactctatg ttcaaacatt tcgtttggga aaaatagggg tgtgaca 2277 // ID L1-3_Mad repbase; DNA; EDCOT; 6384 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-3_Mad. XX NM L1-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6384 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1807-1807 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 375..1700 FT /product="L1-3_Mad_1p" FT /translation="VNLLVSMDKSPVALCPWGFLDFSATSSKLNTATGQLS FT GQLPKARTFAAIVTNGVESSVNLSQLPSPTVRGDVTYVKISEDLYQEQLRS FT CRTNLIGRLLLKKGTMPMKTELLKSALASLWKLHNSWKLVPLGKGYFDLHF FT SSEEDMRRVWGGGTCTLQFGLFRLSQWQPDFKPGDVLPQTHAQVWIKIYGL FT SQEYWHPRILMEIARGVGTPLQLDHATREKLYGYYARILVDVDLSADLPST FT IMVEREQHGFSVDIIYENLPPTCGHCGVIGHNTNKCRHLKGNHSDGMHPDV FT EAHRRGRSPTRQVYRPKPSAKTVSPSGDTIHMERSPSVEIIHNKRSTGLNN FT DMGAPLCSSLEQRHAEQVNDFANQILMTVVNNELSVLADKVIDSSTDPHGH FT LETISDRQLLEVQPTNIINDSPSCNLNDTLSEEMRDVPTEEINIDQQC" FT CDS 1899..6038 FT /product="L1-3_Mad_2p" FT /translation="MKLVYWNIRGIGNSDTRTELSNVCHSHHPDLVCISEP FT MVTFDSIPSAYWNSLGLSLLTVNNRGDLLPNIWVLYSTDYCSPTVISSSGQ FT QVTFQTSFEGVLSQFTIVYAATTSTLRRVLWCDLLNIRSNTTMPWMAIGDF FT NAILGAHEQMGGHLPARTSCEDFRSTTELCDFTHMDTTGAFYTWTNGWSVR FT GYMERRLDRSLCDTRWLQSWPYTSCSALPRVVSDHNCLVFSASAIRLGGPR FT PFRFQSMWTLHSEFSGLVAKCWQSTVVYGCPMFVMLEKLKALKRCLRVWNS FT NVFGDVHRNVTFAKERLHNIQNSISSDGNSQEKFNEEVVAKTAVLDALQMQ FT EAFWHDRARVKWLTEGDRNTAFFHAYARGRHSSSRIVTLLDGDNVLSSHTA FT IVDHVVNFYQSLYNSSFTPTGIEDVCGVIPPMVSEEENLSLSCLPSADEIR FT SVVFSMDPSSAPGPDGFPGSFYQSCWDIVGLDVIAFVQDFFKRGWLYPNAN FT CNFVVLIPKVEGVATIAQYRPIALANFLFKIIPKILADRLGPIATRIISPQ FT QTTFLKGRRISDCIGLVSEGFNFMDKKAFGGNVGIKVDIAKAFDTLNWDFL FT LHVLSSFGFSSIFVDWVRVLLQSARLSILVNGTPHGFFSCSRGVRQGDPLS FT PLLFCLAEEALSRGLSSLFSTGRITSISAPRGCCPPTHVLYADDLFIFCRG FT NVRSLRSLRNFLDKYGCASGQLVNASKSTFYLGSSSVHRKAHVSRHLGFRL FT GVVPFTYLGVPIFRGKPKRIHFQALVDKAKARLSGWKGKLLSMAGRFQLVQ FT SVYQSLFLHSFSVYQLPSCVLKHLSACARNFIWSGDLSSRKLVTVDWSMVC FT GPKKEGGLGLRDLASLNLTALLSFGWDALQSYSLWGSFARQRFPLSPYRNQ FT NIYLRSSVWHGLKRALPILNNNSRWIIGDGRSVSFWFDKWLDEPIISPSLS FT SVISPKVLPRVSDVIEAQSWSLPDYFSNLFPSIVQQILRLPLPLNVKDDKL FT IWEPSPTGKFSFSSGYHLIRRRHSDCAWAKVIWQHFIPPRLSILAWRLFHD FT KLPTEDALQRRGISLASICCLCHNSEESTAHLFFGCRISRQLWRWLACQFG FT TSLPLPDSLVAFWDVYVRKPFSKQLHNLWIFAGLSTISAIWKARNKFIFEG FT RPIYFHRLCMSINSAIVHGGKFIPGYSQGFDTRIISSLGIQPIPRKAPTIL FT PVLWSPPWFPWVKLNTDGLSKGNPGPAACGGVFRNCHGRFLGGFCQRIGHC FT NSFFAELSAIIIGIEFAYQRGWHCLWLESDSSSVISALQSSDFDPPWPLHT FT QWSICLDRIRKMTFYASHIYREGNLVADNFANMGLSSPSLTWHDSPPMAVR FT AALFSDYVGLPGYRFSN" XX SQ Sequence 6384 BP; 1426 A; 1260 C; 1380 G; 2317 T; 1 other; gcacgtgctc gtgtccctag ggtttgacgg tgttctgtcg gcgtcgtccc aggcggcgtc 60 gtcccggcgc cgttgttgaa tcttccacat cgccatccgt tggtcttggt tcgttatttc 120 gctgcgctgg ttactcttcg gtgttgaaga ttggctgctg tttgcgaact gcgataaccc 180 gcaattgggg tttttaatct aaagcaattc ttagggtctt gctgcaccta tactgcacca 240 acagactctg cttttgaagg attttcaaca attggttgca cctacacact tttcaacagg 300 ttgaactatc taattttata tttaattttt tttttttttt ttatattatt attttggaat 360 gcattttgtt ctaggttaat ctcttggttt ccatggacaa gtcacccgtt gccttatgcc 420 catggggatt tcttgacttc tctgctactt cttccaaatt gaatactgcc actggtcaat 480 tatccggaca acttccaaaa gcacggacct ttgctgccat tgtcacaaat ggtgtggaaa 540 gttcagttaa tttaagtcaa cttccctctc ctactgttcg gggagatgtg acttatgtca 600 aaatcagtga ggacctttat caagaacaat tacgttcatg tcgaacaaac ctcattggta 660 ggcttttgtt aaaaaaagga acgatgccga tgaagactga gcttctcaag agtgctttgg 720 cttctttatg gaagcttcac aattcatgga aactggtacc tcttggcaag ggmtattttg 780 atcttcactt ttccagcgaa gaagatatga gaagagtgtg gggtggtgga acctgtacac 840 ttcaatttgg tctttttagg ttgtctcaat ggcaaccaga tttcaaacct ggtgatgtcc 900 ttccccaaac acatgctcag gtatggatca aaatatatgg cctaagtcaa gagtattggc 960 accctcgcat tcttatggaa attgctcgtg gggtgggtac cccactccag ttggatcatg 1020 ctacacgtga aaagttatat ggttattatg ctagaattct ggtcgatgtg gatctttctg 1080 ctgatttgcc ttcgactatt atggttgagc gggaacaaca tggtttttct gttgatatta 1140 tttatgagaa tttgccacca acctgtggac attgtggtgt aattggccat aatacaaaca 1200 aatgccggca tttaaagggt aatcattccg atgggatgca tccggatgtt gaggcgcatc 1260 gtcgcggacg atcaccaact cgtcaagttt atcgtccaaa accgtcggct aagactgttt 1320 ctccttcagg tgatactata cacatggaac gttccccttc agttgaaatt attcacaata 1380 agcgttctac tggacttaat aatgatatgg gggccccact ttgtagctct cttgagcaac 1440 gccatgctga acaagtcaac gattttgcga atcaaatact aatgactgtt gtgaataatg 1500 agctaagtgt gttggctgac aaggtcattg attcatcaac agatcctcat ggtcacttag 1560 agacaatttc agatagacag cttctagagg tacaaccaac caatattatt aatgattccc 1620 cttcttgcaa cttgaatgat actctttcag aggagatgag agatgtgcct acggaagaaa 1680 ttaatatcga ccagcaatgt tgatgttgat gtcccacctg gttttggttt gaggaaagag 1740 atcaatgttg tggatgcagg gaaggattca aatgacttta ctctagttct tagtaaatcc 1800 cagcagaaga aacaaaagaa aaaccaaaaa gttgatgcat gtaggcaaga agaaccctat 1860 gttacaaggg caggaagaca agttatttct acctccaaat gaagctagtt tattggaata 1920 ttcgcggtat tggtaattct gatacacgta cggagctttc taatgtttgc cactctcatc 1980 atcctgactt ggtttgcatc tctgaaccta tggttacttt tgattctatt ccttctgctt 2040 attggaattc attaggtctc tctttactta ctgtcaataa caggggtgat ttattgccta 2100 atatttgggt tttgtattct acggactatt gttctcctac tgtgatttct tcttcagggc 2160 aacaagttac ttttcagact tcttttgagg gtgttctttc tcagtttact attgtttatg 2220 cggctactac ctcgactctt cgtcgtgttt tatggtgtga cctcttaaat atccgttcta 2280 atactacaat gccgtggatg gcaattggtg actttaatgc tatccttgga gcgcatgagc 2340 aaatgggtgg tcacttgcct gctcgaactt catgtgagga ctttcgcagt actactgagc 2400 tttgtgactt tactcatatg gatactactg gtgcttttta cacttggact aatggttgga 2460 gtgtccgtgg ttacatggag aggcgtcttg accgctctct ttgtgacaca cgttggttac 2520 agtcttggcc ttatactagt tgttcagctt tacccagggt cgtttctgat cataattgtc 2580 tagttttctc ggcttctgct attcgtcttg gaggtccgcg accttttcgg tttcagtcca 2640 tgtggacttt acattcagaa ttttctggtt tggttgctaa gtgttggcaa tcaactgttg 2700 tctatgggtg tcccatgttt gttatgttgg aaaagcttaa ggcccttaag cgctgtcttc 2760 gagtttggaa ctctaatgtt tttggcgatg tccatagaaa tgtcactttt gctaaggaaa 2820 gacttcataa tatccaaaat agtatttctt ctgatgggaa ttcgcaagag aagtttaatg 2880 aggaagttgt ggctaagacg gctgtcctcg atgctcttca gatgcaagaa gctttttggc 2940 atgaccgtgc tcgagttaaa tggctcactg agggtgatcg taataccgct tttttccatg 3000 cttatgctcg aggtaggcat tcttcctcca ggattgtaac tcttttagat ggtgataatg 3060 tactctcttc acatactgct attgttgatc atgtggtaaa cttttatcag tctttatata 3120 attcttcgtt caccccaact ggaattgagg atgtttgtgg tgtaatacca cctatggtta 3180 gtgaagagga aaatctttct ctttcttgtt taccttcagc agatgaaatt agaagtgttg 3240 tcttttctat ggatccctcg agtgctccgg gacctgatgg ttttcctggt tccttttatc 3300 agtcatgctg ggatattgtt ggtttagatg tgattgcttt tgtacaagat ttttttaagc 3360 gtggatggct ttatcccaat gccaattgca attttgtggt gcttatccct aaagtagaag 3420 gtgttgccac gattgctcag tatcggccca ttgctcttgc taactttctg ttcaaaatta 3480 tccccaagat tcttgctgat cggctcggcc caattgccac tcgcattatt tctcctcaac 3540 aaacgacatt tttgaaaggt agacgtattt ctgattgcat tgggctagtt tcagaagggt 3600 tcaattttat ggacaaaaag gcttttggtg gtaacgtagg cataaaagtc gacatcgcta 3660 aagcttttga tactttgaac tgggattttc ttctccatgt gctttctagt tttggctttt 3720 ctagtatctt tgtggattgg gtgcgtgttt tattacagtc agctcgcctt tcaattctgg 3780 taaatggcac accgcatggg tttttctctt gctcccgagg ggtacgtcag ggtgaccctc 3840 tttctccact tcttttttgt ctagcagagg aagctttgag tagaggttta tcttcgcttt 3900 tctctactgg aaggattact tctatttcag ctccgcgagg ttgttgccct cctactcatg 3960 tgttatatgc tgatgatctt ttcatttttt gtcgtgggaa tgttcgatct cttcgttctc 4020 ttcgaaattt cttggataag tatggttgtg catcggggca acttgttaat gcatctaaga 4080 gtacttttta tctcggctct tcctcagtcc atcgtaaagc tcatgtttct aggcatcttg 4140 gctttcgttt gggtgttgtt cctttcactt atcttggggt acccattttt cgtggtaagc 4200 caaagagaat tcactttcaa gctttggtag acaaggctaa agctcgcctc tcgggttgga 4260 aaggtaaact tctctcaatg gctggacgat ttcaattggt gcagtctgtt tatcaaagct 4320 tatttctcca tagcttctca gtttatcaat tgccatcttg cgttttaaag catctttctg 4380 cttgcgcaag gaattttatt tggtcagggg atttatcttc ccgaaaattg gtaacagttg 4440 attggagtat ggtgtgtgga cctaaaaaag aaggtgggct tggtcttcgt gatttagctt 4500 ctttgaattt gacggctttg cttagttttg gatgggatgc tttacaatcc tactctctgt 4560 ggggttcttt tgctcgtcag cgttttcctc tttcgcctta cagaaatcaa aatatctatt 4620 tacggtcttc tgtgtggcat ggtttgaagc gtgctttgcc tattttgaat aataatagtc 4680 gttggattat tggtgatggg aggtcagttt ccttttggtt tgacaaatgg ttggatgagc 4740 ctattattag cccttcttta tcttcggtca tttcacctaa ggttcttcct cgggtttcag 4800 atgttattga agcacaaagt tggtctttgc cagattattt ttcaaattta ttcccttcaa 4860 ttgtgcaaca gattttacgt ctacctttgc ctttaaatgt taaggatgac aaattgattt 4920 gggagccctc acccactggg aagttttctt tttcttctgg ttatcacctt attcgaagga 4980 gacatagtga ttgtgcttgg gctaaggtta tctggcaaca ttttattccg ccacgactat 5040 ctattttggc ttggaggctt tttcatgata aacttcctac agaagatgcg ctacaacgac 5100 gtggtatttc tttggcatcc atttgttgtt tatgtcataa ttctgaagaa tctactgctc 5160 atcttttctt tggatgtcgg atatctaggc aactttggag gtggttagca tgtcaatttg 5220 gtacatcttt acctcttcca gattctttgg ttgctttttg ggatgtatat gttcgtaagc 5280 cattttccaa acaattgcac aatctatgga tttttgcggg tctttctact atttcagcta 5340 tttggaaggc tcgaaataaa tttatttttg agggtcgtcc aatctatttt catcgtcttt 5400 gcatgtctat caattcggcg attgttcatg gtgggaagtt tattcctggt tattctcagg 5460 gttttgacac tcggatcatt tcttctttgg ggatccaacc tatccctcgc aaggcaccta 5520 ctattcttcc tgtcctttgg tctcctcctt ggtttccttg ggttaagctt aatacagatg 5580 gtttgtctaa aggaaatccc ggtcctgctg catgtggagg agttttcagg aattgccatg 5640 gtcgttttct cggaggtttc tgtcaacgga ttggtcattg caactctttt tttgcagagt 5700 tatcagcaat tattattggt attgagtttg cttatcagcg gggttggcac tgtctttggt 5760 tggaaagtga tagttctagt gttatttctg ctcttcaatc atctgatttt gatcctcctt 5820 ggcctcttca tacgcaatgg tctatttgtt tggatcgcat tcggaaaatg actttctacg 5880 catctcacat atatcgcgaa ggaaatcttg ttgcggacaa ttttgctaac atgggcttgt 5940 cttctccatc tttaacatgg catgattctc ctccgatggc ggttcgtgct gctctgtttt 6000 ctgactatgt tggcttgcct ggttaccgct tctcaaatta atgtgcatgt cggcatccag 6060 gtttgtctca ctttcctttt tttctcctaa ctttatggtg ttgtttgact tgttttgcag 6120 gtttagacct tcatgtttgg ttctagaggg gttaggtttc atgtcccccc ctcttttctt 6180 tgtatcattc tcgttttttg tttctagaag ggtaaggttt atgtcccccc ttctttctag 6240 tgtattcctt tttgttgtct ctgttttttg gaggggtaag gtttatgtcc ccccctgact 6300 aggtgtaact tgttttttcg ttatcaataa aattaccctc gtaccgtcga ggttttccaa 6360 aaaaaaaaaa aaaaaaaaaa aaaa 6384 // ID Copia-73_Mad-I repbase; DNA; EDCOT; 3227 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-73_Mad_; KW Copia-73_Mad-LTR; Copia-73_Mad-I. XX NM Copia-73_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3227 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1684-1684 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1706-2206] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 125..2938 FT /product="Copia-73_Mad-I_1p" FT /translation="MGDLQVVGGIKKLNNKNYNTWATCMESYLQGQDLWDV FT VGGNEVTQPEEDTSGTLRKWKIKAGKAMFALKTTVEDDMLEHIRKAKTPKE FT AWDTFATLFSKRNDTRLQLLENELLSVAQRDMTIAQYFHKVKSICREISEL FT DPSAAIVESRIKRIIIHGLRPEYRGFVAAVQGWPTQPSLVEFENLLADQEA FT LAKQMGGVSLRGEEEALYTKSKGSFKQRAGGGSKRNGDKEKGHQGGGSSRP FT GGAPKYHGNRGQSQNNKRFEGKCYNCGKKGHMAKDCWFKKPAESNVASSEK FT KSEDDWDAVASLALEEEWDAEASVAMEKQESALTAASPESIDYQNDWIVDS FT GCSNHMTGDEKKLQSLTEYKGGRLVVTANDSRLPIAHIGKTVIEPRYNTNH FT VPLQDVYHVPGMKKNLLSVPQLTSLGNYVLFGPRDVKVYRHLKILGTPTME FT GRRLQSVYVMSAETAYVDKTRKNETADLWHMRLGHVSYHKLNVMMKKSMLK FT GLPQLDVRTDTVCAGCQYGKAHQLPYEESKFKAKEPLELVHSDVFGPVKQP FT SISGMRYMVTFIDDFSRYVWVFFMKEKSETFSKFKEFKETVEGEVGKKICC FT IRTDNGGEYTSNEFSQYLRECRIRHQFTCANTPQQNGVAERKNRHLAEICR FT SMLHAKNVPGRFWAEAMRTAAHVINRLPQPRLEFVSPFEKLWDMKPTVSYF FT RVFGCVCYVFVPSHLRSKFDKKAIRCIFVGYDSQRKGWKCCDPTTGRCYTS FT RDVVFDEASSWWSSEKEALPDSREIEDKLQQKMGEQTVRIQSRPDESEDSL FT DGDGVEQAVPQNPWQAGVYQQPEEDRPSEVEVSTPQSQLRRSTRIRKPNPK FT YANAAIEEEAVEPEWLKVGRRGHCSRAKSSLESSAKAKRCETHIMQMGVQE FT KAPSSTQHGGKNELVLRGSVEDQHQPNWSLKNKV" XX SQ Sequence 3227 BP; 1024 A; 608 C; 866 G; 729 T; 0 other; attggtatca gagcggtacg atcagggacc gtctctagtg aagctttcga gaatcgtgag 60 aagtttagta cttcgcaaga ttgttggcta atcttgttcg gcttatcgaa gttctgccga 120 cacgatggga gatcttcaag ttgttggagg aatcaagaag ttgaacaaca aaaattacaa 180 cacatgggcg acatgcatgg agtcttacct acaaggccaa gatctttggg atgtcgtcgg 240 cggtaatgaa gttacacagc cggaagaaga caccagtggc actttgcgga agtggaagat 300 caaggcaggt aaggccatgt tcgccttaaa aaccacagtt gaagatgaca tgttggagca 360 catacggaaa gccaaaacac caaaagaagc gtgggacacc ttcgccacac tcttttcaaa 420 gaggaacgat acaagactgc agcttctcga gaacgagctg ttatcggtgg cccaacggga 480 catgacgatt gcccaatatt tccacaaggt aaagtctatt tgccgtgaaa tttctgagtt 540 agatcctagt gctgccattg tagaatccag gataaaaaga ataattatcc atggattgag 600 acccgaatat cgaggcttcg ttgccgctgt acaaggatgg ccgacccaac catcacttgt 660 tgagtttgag aatttgcttg ccgatcaaga agctttggca aagcaaatgg gaggggtctc 720 gttaagaggt gaggaggaag cgctctacac caaaagtaaa ggcagcttta agcagcgtgc 780 tggtggtgga tctaaaagaa atggtgacaa ggagaaaggt catcaaggag gagggagttc 840 tcggccaggg ggagctccga agtatcacgg caaccgtggt cagtcccaga ataataaaag 900 gtttgagggc aaatgttaca attgtggaaa gaagggccac atggcgaagg attgctggtt 960 caaaaagccc gcagagagta acgtcgccag ctcagagaag aaaagtgaag atgattggga 1020 cgccgtagcg tctctagccc tggaggaaga atgggacgct gaagcatccg ttgctatgga 1080 gaagcaagag tcagctctca cagcagcaag tccggagtcg attgactacc agaatgattg 1140 gatcgtggat tcaggctgct caaaccacat gacaggtgat gagaaaaagt tacaaagtct 1200 gactgagtac aaaggaggcc gcttggtggt gacggccaac gactcgaggc taccgattgc 1260 tcacatcggt aagacagtaa ttgagccccg atacaacact aaccatgtgc cgcttcaaga 1320 tgtctaccat gttccaggta tgaagaaaaa tctgctttca gtgccgcaac tgacgtcatt 1380 aggaaattat gtcttgtttg gtccacgaga tgtgaaggtg tatcgacacc tcaagatctt 1440 agggacgcca acaatggagg gacggcgatt gcagtcagtc tatgtaatgt cagcagaaac 1500 tgcatacgta gacaagacaa ggaagaatga gacagcagat ttatggcaca tgagattggg 1560 tcacgttagc tatcacaagc taaatgtgat gatgaagaag tcaatgctta aggggctacc 1620 tcagcttgac gtgagaacag acacggtttg tgcaggatgc cagtatggta aagcacatca 1680 actaccatac gaagagtcga agtttaaagc gaaagaaccg ttggagttgg ttcattccga 1740 tgtgttcggg cccgtcaagc aaccatcgat aagtgggatg cggtacatgg tgacgttcat 1800 tgatgacttc tccaggtatg tgtgggtttt ctttatgaaa gaaaaatctg aaacattttc 1860 aaaatttaaa gagtttaagg agacagttga aggagaagtg ggaaagaaga tctgttgcat 1920 acgcacggat aatggaggag aatatacctc gaatgagttt tcccagtatc tacgagaatg 1980 tagaatacgt caccagttca catgtgctaa cacgccacaa cagaatggcg tagcggaaag 2040 aaagaaccga catcttgcag agatatgtcg aagtatgctc catgccaaga atgtaccagg 2100 aaggttttgg gccgaagcta tgagaactgc agctcatgtg atcaacaggc ttcctcaacc 2160 aaggttagaa tttgtctcac cctttgagaa actatgggat atgaaaccta cagttagtta 2220 ctttcgagta tttggctgtg tgtgctacgt atttgttcca agtcatttac gtagcaagtt 2280 tgacaagaag gcaatccgat gtatctttgt gggatacgac agccaaagaa aagggtggaa 2340 atgttgtgat cctacgactg gaaggtgtta cacatcacga gatgtggtgt ttgatgaagc 2400 atcttcttgg tggtcctcag aaaaagaggc gttgcctgat tcgagagaga ttgaagataa 2460 gctgcagcag aagatggggg agcaaactgt tcgaatccaa tcgagaccag atgagtctga 2520 ggattcactt gatggtgatg gtgttgagca agcagtacct caaaaccctt ggcaagctgg 2580 cgtatatcaa caaccagaag aagatagacc tagtgaagtg gaagtatcaa ctccacaatc 2640 acaactaagg aggtcaacaa gaatccggaa gccaaatcct aaatacgcca acgcagccat 2700 agaagaagaa gcagttgaac ctgagtggct caaagttggg agaagaggtc actgcagtag 2760 agctaaatca agcttggaat ctagtgccaa agcgaagaga tgtgaaaccc atatcatgca 2820 aatgggtgtg caagaaaaag ctccgtcgtc aactcagcat ggaggaaaga atgagctggt 2880 gttgaggggg agtgttgaag atcaacacca gcccaattgg agtctaaaga ataaagtcta 2940 gcctatgatg aagagccaaa ggaaaaagca tgtcatgcta gaaattctag cataagtatg 3000 tcggtggggt gcatgcatat taacaagcta gaaaggtcta gctattgtaa catatgtgag 3060 gttataagca aagcccatgt cggtgggctg tttgtagaaa agtctagaac aatgctagat 3120 gaaatgagcc attccaccga cttagtaagt cggttcagca agcctataaa tatgtatatg 3180 gtgtaagtaa gcgtaacgaa gaagtgatca aagcaaccaa gtgagag 3227 // ID Copia-40_VV-LTR repbase; DNA; EDCOT; 889 BP. XX AC chr10; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-40_VV_; KW Copia-40_VV-I; Copia-40_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-889 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr10; Positions 7189868 7188980. XX SQ Sequence 889 BP; 230 A; 136 C; 213 G; 310 T; 0 other; tgggttgggt tatttccttc ttgtggagga aagcccaaag cccaaacatt taaggcttct 60 taggccttaa tgtataaaag ggaagaagaa actgttttct cttcttcttc atctttgcag 120 ccctaggagg agagtaagaa gaaaaaagga agagaaagtt agtgagaaaa aagaaaaaga 180 gccactgatt tttgaagtta gagagaagaa aaacgctgat tttttttctt ctctttactg 240 tccagatttc atcaaatgac cgatcccgct tcgtgtgtgg tccgatcgac ctgaaatttg 300 aaggagagat tttcaactca ttgatctcta atctgaacgg tggagatcgg atttggagtt 360 ccggaaggtt gttgtttcag tccgtgaaca atgcatcttt gttgttgaat ttcttctcac 420 ccgggcagtt atgatcttca gctttgatcg agattaatcc gtggtctgat cgagatgatt 480 tttggttagc acgttcttaa ctcattgatc ttcattttga acggtggaga ttggatttgg 540 agtttggaac agtggtgatt tgtgtccggg aacagtgact ctgttttggt gagatctctc 600 cattgtttta tgcaagttgt tttgtatttg ccaagactaa ttgtcttgag atatgactga 660 tgtaaacctc tagtttcatc tagagagaat tgtgtaaccc attgattata ttagtggagg 720 gtttaagtgg cctaagggtc ccgtggtttt tacttctcac atttgggaag gttttccacg 780 ctaaaaattg ttggtgttca tattcttgtt gcattgggtg aattgttgtt actctattaa 840 attgattcat agtaggttct cacaagaggg gataaaattt ggttgtgca 889 // ID Copia2-PTR_I repbase; DNA; EDCOT; 4523 BP. XX AC LG_V; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia2-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4523 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4523 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 212-212 (2007). XX DR Genome; LG_V; Positions 13739202 13743724. XX CC Positions [1872-2390] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 141..1265 FT /product="Copia2-PTR_I_1p" FT /translation="MYDHLEGNASTAHNDPFNTTTVNLSDDSSNCYYLHPF FT DNPGALLVSEIFTCENYIAWSRSMTIALTVKNKIAFIDGSLPQPITNNQTL FT RVAWLRSNNLVLSWLMNSIAKDIRSSLLYFTTAFEIWEELRVRYLRSDGPR FT VFSLEKSLSSISQNSKTVTDYFSEFKALWDEYISYRPIPNYKYGNLDSCSC FT NILKLLTDRQQSDYVMKFLVGLHDSFSAVRSQLLLQTPLPSMGKVFSLLLQ FT EESQRTLTNMVGIPIDSQAMVAEQHHNPIPSQVQHMLHVLLNKKENLRQLA FT PTMDIQATLLINAFRSLDILLDGRGQKGKDLLLHHMQIEIIKDYLLHIILL FT FLINIKTLPTSFSLKSKYRIYLPLQIAFPTQS" FT CDS 1893..4523 FT /product="Copia2-PTR_I_2p" FT /translation="MHTSIQAFQLIHIDIWGSFSVTSYSGHQLFLTIVDDY FT SRFSWLFLMKSKSETRGLLSNFLIYVHTQFNTSIKTIRTDNGQEFNMPTFY FT QDHGIIHQTTCVETPEQNGRVERKHQHLLNVARSLMFQTKLPLTYWTDCIL FT TSTHIINRTSSLILQNQTPYQILFNKPPTYNYFRVFGCLCFANTLTHNRGK FT FQPRATKCIFLGYPPHIKGYKVLDLTTCKTFVSRNVIFHESIFPSIPNTVH FT TPLVFPDFPQVFDSFPCKSSQPTPSYSIPPATLPLQTSAPPTSTLIQNDIS FT QLRRSARTTHQPHYLQQYYCGTMAQIPSADPISPNCSIPGKPHSLFYFLST FT SQLSLQHRAFTSSISLVFEPTTYKQASSIPHWQKAMTNEIIALEQNQTWDL FT VLLPHNKSAIGCKLVYKVKFQADGKVERYKARQVAKGYTQQEGIDFFDTYS FT PVAKMTTVRVFLTIAAVNNWHLHQLDVDNAFLHGDLHEKVYMQLPPGYSTP FT HDPRVCKLKKSIYGLKQASRQWFSKLSTSLLLFGFLQAKSDSSLFIRKTTN FT SFITVLIYVDDVIITSNTFTKINQVKQFLRTTFPIKDLGKLKYFIGIEVAR FT SAKGIVLCQRKYALDILADSGFSGARPVSFPMGTTLKLSANDASPPLIDPA FT SYRRLIGRLLYLTITRPDLSYAIQTLSQFMANPHTMHLQAAERVLRYLKAT FT SGQGLFLKADSTFHLKAYSDSDWGGCIDTRRSVTGYLVFLGDSLISWKSKK FT QPTVSRSSAEAEYQALATTSCEVQWLVYLLKDFHINHSKPALLYTDNKPAS FT EIASNLVHHERTKHIQLDCHLIREKLQDGLLTIIHIPSRFQLADALTKPLG FT CLTLHPILSKIGMVNIHSHLEGGY" XX SQ Sequence 4523 BP; 1364 A; 1096 C; 687 G; 1376 T; 0 other; tggtatcaga gcataattgc tgagaattca agttttttgt tcttcctttc ttctctcttc 60 aaaactctcc tttatcaatc aacagaaaag attcaagttc ttttcttcat catcttcttg 120 atcccttcac agacttcaaa atgtatgatc atcttgaagg aaatgcttct acagcacaca 180 atgatccatt caacaccacc actgtgaatc tatctgatga ttcttccaac tgctactacc 240 tgcacccttt tgataaccct ggtgcacttc tggtttctga aatcttcacc tgtgaaaatt 300 acattgcatg gagtagatcc atgacaattg ccttaacagt gaaaaacaag attgctttca 360 ttgatggttc tttacctcag ccaatcacca acaatcaaac gcttcgtgtg gcatggctac 420 gatcaaataa tctggttctg tcatggctga tgaattctat tgctaaagat attcgcagca 480 gccttcttta cttcacaaca gccttcgaaa tttgggaaga attgagggta agatacctga 540 gaagtgatgg accacgagtc ttcagtttgg agaaatcttt aagttctatt tctcaaaact 600 caaaaactgt tacagattat ttcagtgaat tcaaagccct atgggatgaa tacattagct 660 atcgtccaat accaaactac aaatatggaa atcttgattc atgctcttgc aacattctaa 720 agcttctaac agatcgacaa caatcagatt atgtgatgaa atttctggta ggactccatg 780 attccttctc tgcagtcaga agccaattgc tcctccaaac tcctttacca tctatgggaa 840 aagtattttc tttgcttcta caagaagaaa gccagagaac cctgacgaat atggtaggga 900 ttcccattga ctcacaggct atggttgctg aacaacatca caatccaatt cccagtcagg 960 ttcaacatat gttacacgtt ttgctaaaca aaaaggaaaa tctgaggcaa cttgctccca 1020 ctatggatat ccaggccacc ttgttgataa atgctttcag atcattggat atcctcctgg 1080 atggaagggg ccaaaaggga aaagatttgc tgctacacca catgcaaata gaaattatca 1140 aagactacct actgcacata atactgttgt ttctgatcaa catcaagaca ctcccaacat 1200 cgttttctct caagagcaaa tacagaatct acttaccctt gcaaatagca tttccaactc 1260 aaagctaaac aacactgcca aggaagtatc tgtatcgggt atatcctttt catgtcatac 1320 caattcttca cctcagaaca ggtttacttg gattcttgat acaggagcaa cagatcacat 1380 gatctgtagc cccattcttt tcgaatccat tgttctgcct caaactcaaa accaagttca 1440 tctaccaaat ggccaaaagg tgcccattgc tttttcaggg acgttaaatt ctctcctgat 1500 atcaccttac acaatgctct ttacgttcca tctttcaata ttaatcttat ttctgtttca 1560 aaattaactg ctgataacac tattggcttg ttttttcttc acacaaaatg tattttgcag 1620 gatctaagca aatagaggac gattgggctt gctgaaactg aatctggtct ataccatctt 1680 cacaaacctc ctgatcaatc tacagaccag ttagaccatt aataaaatct tgtattgttg 1740 ccactgatct ttggcattta cgttaaggcc acattcctac ttccaaaatc aatcttctaa 1800 acaaaataaa tccttcagta acttccacag gtaaatccat ttgtgacatt tgccccttag 1860 ctaagcaaaa acgactcccc tttcccttct atatgcatac atctatacag gcttttcaat 1920 taattcacat tgacatttgg ggatccttct ctgttacttc atactctggt catcagctct 1980 ttcttacaat tgtcgatgat tacagtagat tctcttggtt gttcttaatg aaatccaagt 2040 ctgaaactag aggtcttcta agcaactttc taatctatgt tcatactcaa ttcaacacca 2100 gcattaagac tatccgcaca gacaatggac aagagttcaa tatgcctact ttttaccaag 2160 accatgggat aattcatcaa acaacctgtg ttgaaacacc tgaacaaaat ggaagggttg 2220 aaaggaaaca tcaacatcta ctaaatgtag ctagatctct catgtttcaa accaaactcc 2280 ccttaactta ctggaccgat tgcatcctca catccactca cataatcaac cgcacttctt 2340 cactcattct acaaaatcag acaccatatc agattctatt caacaaacca cccacttata 2400 attactttag ggtgttcggt tgcttatgct ttgccaacac actcacacac aacagaggaa 2460 aatttcaacc acgagccacc aaatgtattt ttctaggcta tcctccacac attaaagggt 2520 ataaagtgct tgacttaaca acatgcaaaa cctttgtgtc tcgcaatgtt atttttcatg 2580 aatccatatt cccatctata ccgaacacag ttcacacacc ccttgtgttt ccagattttc 2640 cccaggtttt tgattctttc ccttgcaagt catcccagcc aactccaagt tattctattc 2700 ctcctgcaac attaccttta caaacttctg ctccaccaac ttctacctta attcaaaatg 2760 atatttccca actcagaagg tctgcacgaa ctacacatca acctcattac ttacaacagt 2820 attattgtgg cactatggct cagattcctt cagcagaccc tatctctccc aattgctcca 2880 ttcctggtaa gccacactca ctcttctatt tcttatctac ttcccaatta tctttacaac 2940 accgagcttt cacttcttct atttccttag tttttgaacc aacgacttac aaacaagcca 3000 gctctattcc tcattggcaa aaggctatga ctaatgaaat tatcgctctt gaacaaaacc 3060 aaacttggga tttagtactt ctgcctcata acaaatctgc cattggatgt aagttggtat 3120 acaaagttaa atttcaagca gatggcaagg tggaacgcta caaagccaga caggtagcta 3180 agggatacac acaacaagag ggaattgatt tctttgacac ttattcccct gtggccaaaa 3240 tgacaacagt tagagttttt ctcaccattg cggctgtcaa caattggcat ttacatcaac 3300 ttgatgtaga caatgctttc ttacatggtg acttacatga gaaagtatat atgcagttgc 3360 cccctggtta ctccactccc catgatcctc gcgtttgcaa actcaaaaag agcatctatg 3420 gcctgaaaca agcttccaga caatggtttt ccaagttgtc tacttctcta ttactttttg 3480 gatttctaca agcaaaatca gattctagcc tcttcatcag aaaaactacc aactccttca 3540 tcacagtatt aatctatgtt gatgatgtta tcatcacttc caatactttt acaaaaatca 3600 accaagttaa acagttcctt cgaacgactt tccctataaa agatttggga aaattgaagt 3660 actttatagg cattgaggtc gctcgatctg caaaaggcat tgttctttgc cagagaaagt 3720 atgccttaga tatcctagcc gatagtggat tttctggagc tagaccagta agctttccta 3780 tgggaaccac actgaaactc agtgccaatg atgctagccc tcctctgatc gaccctgcct 3840 cttatcgtcg attaattggt agacttctct acctcacaat cactcgccca gacttgtcat 3900 atgccatcca aactctcagc caattcatgg ccaatcccca tacaatgcat ctgcaagctg 3960 cagaaagagt tcttcgatat cttaaagcaa catcaggtca aggattattt ctcaaagctg 4020 attctacctt ccatttaaaa gcttattctg acagtgattg gggaggttgc attgatacta 4080 gacgaagtgt cactggatac ttggtgtttc ttggagattc tctcatctcc tggaaatcca 4140 agaaacaacc aactgtcagt cgatcgtcag cagaagcaga atatcaagca ttggcaacta 4200 catcatgtga agttcaatgg ctggtttatt tgttaaaaga cttccatata aaccactcca 4260 agccagccct gctgtatact gacaacaaac ctgcttcaga aattgcttct aatctggttc 4320 atcatgaacg cactaaacat atacaacttg actgtcacct tatacgtgaa aaattgcagg 4380 atggattgct taccatcatt catatcccgt ctagatttca gctagctgac gcactcacca 4440 aacccctagg ttgtctcaca cttcatccta tccttagcaa gataggaatg gttaatatcc 4500 attctcatct tgagggggga tat 4523 // ID MTIS112A repbase; DNA; EDCOT; 3914 BP. XX AC AC119415; XX DT 05-JAN-2007 (Rel. 12.01, Created) DT 05-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Harbinger-type DNA transposon. XX KW Harbinger; DNA transposon; Transposable Element; MTIS112A. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3914 RA Jurka J.; RT "MTIS112A: Harbinger-type DNA transposon from barrel medic."; RL Repbase Reports 7(1), 39-39 (2007). XX DR EMBL/GenBank/DDBJ; AC119415; Positions 131260 135173. XX CC Present in low-copy number in Medicago. XX FH Key Location/Qualifiers FT CDS 2229..3506 FT /product="MTIS112A_2p" FT /translation="MDPFDLEAYFQKRDAEDTYMVNRFIQRRKQIEEGSGS FT RSRKYFNRDHAAANQRLIDDYFADAPTYDDAMFRRRYRMQKHVFLRIVGDL FT SSSDNYFTQRIDAANKEGISPLAKCTTTMRMLAYGVAADAVDEYIKIGSST FT ALECLLRFCKGIIRLYEEVYLRAPTQDDLQRILHVSEMRGFPGMIGSIDCM FT HWEWKNCPKAWEGQFTRGDKGTTTVILEAVASHDLWIWHAFFGCPGTLNDI FT NVLDRSPVFDDVEQGKAPRVNYFVNQRPYNMTYYLADGIYPSYPTFVKSIR FT LPQSEPDKLFAKHQEGCRKDIERAFGVLQARFKIIREPARLWDIGDLGIIM FT RSCIILHNMIVEDERDTYAQRWTDFEQPGGSGSSTSQPYSTEVLPAFANHV FT RGRSELRDPDVHHELQADLVKHIWTKFGMYRD" FT CDS join(502..1059,1063..1620) FT /product="MTIS112A_1p" FT /translation="MDPNNNHFNTQNFSNYPYNYENPNIYPNPNQFYNQRP FT QNIHQNVPNFGFSPNFNQSSSVPNFHPYYGSMMRYPSQTPPFNGYMPMGNE FT NFPSVDANQYPEFSTQITSGGMAVADEVTPEDSTPKSKRSKEPAWNTQQNL FT VLISAWIKYGTSSVVGRNQRGETYWGKIAEYCNEYCSFDSPRDLVACNRFN FT YMSKIINKWIGAYESAKRMQGSGWSEDDVLTKAQELFAGGKNIQFTLNEEW FT HALRDQPRYGSQMGGNVGSGSSGSKRSHEDSVGSSARPMGREAAKKKGKMK FT SKGETLEKVEKEWVQFKELKEQEIEQLKELNLVKQQKNKLLQEKTQAKKMK FT MYLKLRDEEHLDDRKKELLEKLERELFEN" XX SQ Sequence 3914 BP; 1258 A; 652 C; 820 G; 1184 T; 0 other; agaccatctc caatggccaa tttaatgaga cattcaacac caatttcccc tccaatggtg 60 tgtttaaagt gtgttgaatg gtggaagaga agagagagaa ggtgaaccga ttcaacacaa 120 ttgaaccctg ccaggccgga cacgtggcga cgcggaattg gcccaaaacg ggcgcgtgcg 180 ttacacgcgc agacaaggcg cgtgacgcgt cagacgtgcg gagagagaat gacttttttg 240 gatagataat gacacgtggc gcgttttaat tggctgtccg gattcttatc attttaataa 300 tttgacctca attatttcgt tgtaaattaa ttttaaaaaa aaaaaaatta ccaaaattca 360 tgattttttt tcctctataa atagagactt ggatcatttg atttggacac agaaaaaaaa 420 accaagtttt tcactatctt catcttatta ttatctttct attagcaaac taagtgaagt 480 tttaatctta ttttttgtga aatggatccc aataataacc atttcaacac ccaaaatttt 540 tctaattacc catataacta cgaaaatccc aacatttatc caaatccaaa tcaattttat 600 aaccaacgtc ctcaaaacat acatcaaaac gtacctaatt ttggtttttc accaaatttc 660 aaccagtcat cctctgttcc aaactttcat ccatattatg gatctatgat gagatatcca 720 tctcaaacac ccccgtttaa tggttatatg ccaatgggga atgaaaattt tcctagtgtt 780 gatgcaaacc aatatcctga attttcaaca caaataactt ctggtggcat ggcagttgct 840 gatgaagtca ctccagaaga ttcaactcct aagagcaaga gaagtaagga accagcatgg 900 aacactcaac aaaatttggt tctaattagt gcatggatta aatatggaac aagcagtgtt 960 gtcgggagaa accagagagg agaaacatat tggggtaaaa ttgctgagta ttgtaatgag 1020 tattgctcat tcgattctcc ccgcgatcta gttgcctgct gaaaccgttt taattatatg 1080 agcaaaataa taaataaatg gattggtgct tatgaaagcg ctaagcgtat gcaaggaagc 1140 ggttggtcgg aagatgatgt tttgacaaaa gcgcaggaat tatttgcagg tgggaagaat 1200 attcaattta ctttgaatga agaatggcac gctctccgtg atcaaccacg ttatggtagt 1260 cagatgggag gaaatgttgg gtcagggagt agtggatcta agagatctca cgaggactct 1320 gtaggatcta gtgctcgtcc aatgggtagg gaggcagcta aaaaaaaagg taaaatgaaa 1380 agcaagggcg agacattgga gaaggtggaa aaggaatggg ttcaattcaa agaattaaaa 1440 gagcaagaga ttgaacaatt gaaagagtta aatttggtga aacaacagaa aaacaagttg 1500 ctgcaagaaa agactcaagc taaaaaaatg aaaatgtatc taaagttaag ggacgaagag 1560 catctcgatg accggaagaa ggagctgttg gagaagttgg agcgtgagct gtttgaaaat 1620 taattttaat caaatatttg tttgtattca gtcaacatta tcagtgttgt ctagtcccga 1680 ctgtttgctt taatatttgt cagtgttgtc tagtccgtag tgtttgcttt aataattatc 1740 agagtgttgt ctagtcctca ctgtttgctt taataattat cagtgttgtc tagtcccgac 1800 tgtttgcttt aatatttgtc agtgttgtct agtccgtagt gtttgcttta ataattatca 1860 gagtgttgtc tagtcctcac tgtttgcttt aataattatc ggtgttgtct agtcccgact 1920 gtttgcttta atatttgtca gtgttgtcta gtccgtagtg tttgctttaa taattatcag 1980 agtgttgtct agtccccgtg acttatttgc tttaataatt atgtccactg tgtgcccatt 2040 atttcaccta ctataactta tttcaaatcc gtcagtgtcc accacacaat gtacttatat 2100 atagggactc atatctactt tcaatttcac aagtctcatt aaaatctact tccaatttca 2160 caaatctcat tcatatctac tttcaatttc acaaatctca ttcatatctt cttccaaaaa 2220 acctatcaat ggatcctttt gatttggaag cctacttcca aaaacgtgat gctgaagaca 2280 cgtatatggt caaccgattt attcagcgtc gaaaacaaat agaggaaggt agtggatctc 2340 gtagtagaaa atatttcaat agagatcatg cagctgcaaa ccaaagacta attgatgact 2400 actttgccga tgcacctaca tacgacgatg caatgtttcg tcgtcggtat cggatgcaaa 2460 aacatgtttt ccttcgaatc gttggagatc tttcaagtag tgataactac ttcacccaac 2520 gaattgatgc agccaataaa gaaggtatat caccgttagc aaaatgtacc acaacaatgc 2580 gaatgttagc atatggtgtg gcagcagatg cggtcgatga atacatcaaa ataggaagta 2640 gtacagcatt ggaatgctta cttagattct gcaaaggaat catacgactc tatgaggaag 2700 tgtatttgag agcaccaacc caagatgacc tgcaaagaat attgcatgtt agtgaaatgc 2760 gggggttccc agggatgatc ggcagtattg actgcatgca ctgggagtgg aaaaattgtc 2820 ctaaagcatg ggaaggtcaa tttaccaggg gggataaggg aaccaccaca gttattctag 2880 aagcagttgc atctcatgat ctatggatct ggcatgcctt ttttggatgt ccgggaacgt 2940 tgaacgatat aaacgttcta gaccggtcac cagtgtttga tgatgtggaa cagggaaagg 3000 ctccgagggt gaattacttt gtgaatcaac gtccctataa tatgacatac tatctagctg 3060 atggtatcta cccttcgtat ccaactttcg tcaaatcaat tagacttcct caaagtgaac 3120 ctgataagtt atttgcaaaa catcaagagg gatgtcggaa agacatcgaa cgtgcttttg 3180 gagtgcttca agctcgattt aaaatcatcc gtgaaccagc tcgcttgtgg gacataggcg 3240 atttgggtat catcatgagg tcatgcatca tattacataa tatgattgtt gaggatgaac 3300 gagatacata tgctcaacgt tggactgatt ttgagcaacc tgggggaagt ggatcaagta 3360 catcgcaacc atactcgacc gaggtgttac cagcttttgc aaatcatgtg cgtggtagat 3420 ccgagttgcg tgatccagat gttcatcacg aattgcaagc agatctagtg aaacacatat 3480 ggacaaagtt tggaatgtat cgtgattgaa gatgatttgt atcgtactaa ataaattact 3540 tgtgtgtttt atgcttagtt tgttgtattg cattttaagt tatttgtgtg ccgcgtgctt 3600 agtttgttgt acttgaattt gaaattaaga aaataaaaat aaattatttt acaaaatttt 3660 ttcttccaaa aatactaaaa aataaatagt taattgtatt attttaattt aattataatc 3720 gataatttta tgtaattata aaaacaaaaa ttaaataaga ataaaaaata aaaaatggtg 3780 gggtagagtg ttgaatgaaa aaccattgga gagggtaaaa gttgaatgag tgttgaataa 3840 gagagagaaa atgatgtgga gtgttgggaa ttgaaaaagt ggtgttgaat ggtgaaaacc 3900 attggggatg gtct 3914 // ID Copia-56_Mad-I repbase; DNA; EDCOT; 4510 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-56_Mad_; KW Copia-56_Mad-LTR; Copia-56_Mad-I. XX NM Copia-56_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4510 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1650-1650 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1867-2364] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 268..4497 FT /product="Copia-56_Mad-I_1p" FT /translation="MSLTIFHGREQFTLALGGRSKLGYVNGAIPMPETTSP FT EYDAWLCKDQLVMSWLLNSMDRKIAEIFSYAESSMTLWKNLKEMYGNQNNA FT ARVFQLKKDIAGLQQEGKPFVQHLGKLTTMWNELNVYRPHTIDAAVLTKRA FT EEDKIFQLLASLSPEFEDLRSHILMNPDLPSFSSVCATIQREEVRRKVMTL FT DIKANIPEARAYFSNQKLGEERGYKGKKTGLKCSHCDAGGHSRDRCWILHP FT ELKPKFPRDNKGVSKGSYNPSYKANHVATTSSEGALKFTTNPAALINEFAM FT FLHKKQGLGDSEGPLNQCDNNQTALLGQFAGFLAGNEGVVQRDIPGILHSF FT STALNIGNVHDYWIIDSGATDHMTNKSTNLHKFEKFSIPSQVSVANGKNAM FT VVGKGKIHLISSDVESEALYVPSFPFQLLSVGKITNSLNCLAIFSPKNVIF FT QDVVTKKTIGEGFFLNGLYYLSKHIQVPKVFQVTSSLAQEQQLWHQRLAHP FT SEKVLSTLFPNMCKVTSPCDVCHFSKFTRLPFTSSLSRASNPFEIVHSDVW FT GPILESFDGYKYFVTFVDDFTRITWLYLLKFKSEVMEVFQDFHRLVATQFA FT SKIHILRSDNGTEYMSHNMSHYLSTHGILHQTSCVGTPQQNGVAERKNRDL FT LEKTRALMFHMNVPKKFWSQGVLTAAYLINRLPSKVLNFKSPYEVLKNRKI FT NFSHLRVFGCTCFVHIQAQNRDKLDPRAAKCVFLGYSSTQKGYKCYNSTTR FT KMVVSRDVKFEEHVPYFSQSLDYSRQGEHLMDLFPFPYPNGEDATCTPSDH FT VPDDVNLHSVEHLEDETPSSSEIHTAPSSDPSNHDVVQIPVVQSPTVRRNP FT ARERKLPSKLHDYVTYTARYPVTDVIDYSKVSSSFATFLSAINEAREPQSF FT QEANLHSEWRNAMAEELQALHENNTWTIVKLPKGKKAVGSRWVYKTKFHSD FT GTIERNKARLVARGFTQTYGVDYKETFAPVAKMNTVRVLLSVAINNAWPLF FT QMDVKNAFLHGELEEEVYMKLPPGHPQSNNPEMVCKLHKSIYGLKQSPRAW FT YAKLSHVLERVGFCRSIADSSLFVRSSSVGKLVVLIYVDDLIVTGDNMSEI FT NALKQYLNNKFAIKDLGTLKYFLGIEMAHSHKGFFLNQRKYVMDLLHEAKM FT TDCKPARTPLDSNLKLKTHGDPIPNLSYYQRMVGKLIYLTITRPDISYAVS FT IVSQFMHSPSMDHLKIVHRVLRYLKGSVGRGILMRNNSHTRISGYTDADWA FT GNSLDRKSTTGFCTFVGGNLVTWKSKKQSVVARSSAEAEYRAMASTACELI FT WLKSLLLALGFPHQQPMSLHCDNQAAMHIASNPVFHERTKHIEVDCHYVRN FT QVQSKVIDTHYTRSHDQLADIFTKGLTSANFQRLLFKLGSINPFDPA" XX SQ Sequence 4510 BP; 1312 A; 943 C; 924 G; 1330 T; 1 other; gcacatatat attagctatc tcttgtactt ggtttctcat aatgaatata acattcgcaa 60 aattcaatat ggtatcagag cagtgaccct aaccggcctg tctctgtggt gttctcttga 120 gagatttgtg agcttcttct tgtccttcaa tcatggctga agaaagctca gtaaatttgg 180 aaggagacgg ctttcatgct actccaccat caccacactc agatattgat atcaacccaa 240 atcaacgtct tagttctgtc ttgctaaatg agtttaacta tcttccatgg gagagagcag 300 tttactcttg ctctgggagg acgatcaaag cttggttatg ttaatggtgc tattccaatg 360 cctgagacta cctcaccgga gtacgatgct tggctatgca aagaccagtt ggtcatgtcg 420 tggctactca attccatgga tcgtaagatt gcagaaattt ttagctatgc tgaatcctcc 480 atgactcttt ggaaaaatct caaggaaatg tatggaaatc agaacaatgc ggctcgagtg 540 tttcagttaa agaaggacat tgctggtttg caacaggaag gaaagccatt tgtgcaacat 600 cttggaaagc tgaccactat gtggaacgag ctgaatgtgt atcgaccaca caccatcgac 660 gctgctgtgc taactaagag agccgaggaa gacaaaatat tccaactcct agcaagcctg 720 agtcctgaat tcgaagatct tcgaagccat atcctcatga atcccgacct gccttctttt 780 tcaagtgtgt gtgccacaat tcaaagagaa gaggttcgaa ggaaagtcat gaccttggac 840 ataaaggcaa atataccaga agctagggct tacttctcta accaaaaact tggtgaggag 900 agaggctaca aaggaaagaa aactggctta aaatgtagcc attgtgatgc tggtgggcac 960 tcaagagatc gatgctggat tcttcatcca gagttaaaac caaagtttcc tagggataac 1020 aaaggtgtct cgaaaggctc gtacaaccct tcttacaagg caaatcatgt tgccacaact 1080 tcttctgagg gagcactgaa gttcaccact aatccagccg cactgatcaa cgagtttgct 1140 atgtttcttc acaagaaaca aggtcttgga gatagtgaag gaccactaaa tcagtgtgac 1200 aacaatcaaa ctgcactact aggacagttt gctggcttcc tggctggaaa tgaaggcgtg 1260 gtacaaaggg acatcccagg tatcttacac tccttctcaa ctgctctcaa cattggtaat 1320 gtgcatgatt attggattat agattctgga gccactgatc atatgactaa caagtctaca 1380 aacttgcata aatttgaaaa attttctatt ccatctcaag tgtcagttgc caatggaaaa 1440 aatgctatgg ttgtgggaaa aggaaaaata catttgatct caagtgatgt cgagtctgag 1500 gctctttatg ttccctcatt cccttttcaa cttttatctg ttggcaagat cacaaactca 1560 ttaaattgtc ttgccatttt ctctccmaaa aatgtgatct ttcaggatgt agtcaccaag 1620 aagacgattg gtgaaggatt tttcttaaat ggtctctact atctttccaa gcatattcaa 1680 gttcccaagg tttttcaagt cacttcaagc ttagctcaag aacaacaact ttggcaccaa 1740 cgtctagcac atccttctga aaaagttcta tccaccttgt tcccaaacat gtgcaaagtt 1800 acaagtcctt gtgatgtttg tcatttttct aagtttacta gattaccatt tacttcctct 1860 ttgtctaggg ctagtaatcc ttttgaaatc gtgcattccg atgtttgggg accaattcta 1920 gagtcttttg atggatacaa atattttgta acttttgtgg atgatttcac aaggattact 1980 tggttgtatc ttttgaaatt taaaagtgaa gtgatggaag tttttcaaga ttttcataga 2040 cttgtggcca cccaatttgc ttcaaaaatt catattttac gatcagataa tggcacagaa 2100 tatatgtctc ataacatgtc acactacttg agcacgcatg gtatattaca ccaaacaagc 2160 tgtgttggaa cacctcaaca aaatggggtg gccgagagga agaatagaga tctacttgag 2220 aagactagag ctcttatgtt tcacatgaat gtgcctaaga agttttggtc tcaaggagtt 2280 cttactgcgg catatctcat caatagattg cctagtaaag tgttgaattt taaatcacct 2340 tatgaggtct tgaaaaatag aaagatcaac ttttcccatt tgagagtctt tgggtgtaca 2400 tgctttgttc acattcaagc tcaaaatcgt gacaagctag acccaagggc tgccaaatgt 2460 gtctttctag gttattcatc tacccaaaaa ggttacaagt gctataattc aacaactaga 2520 aaaatggttg tttcaaggga tgttaaattt gaagaacacg ttccttactt ctcacaatca 2580 ctggattact ctagacaggg ggagcatttg atggacttat ttccttttcc atatccaaac 2640 ggagaagatg caacatgcac tcctagtgat catgtgccgg atgatgttaa tcttcactcg 2700 gtggaacatc ttgaagatga aaccccttcc tcatcggaga ttcacactgc accctccagt 2760 gatccttcca accatgacgt tgttcaaata cctgtagttc aatctcctac agttcgtcgc 2820 aatcctgcac gagagaggaa acttccatcc aagttgcatg attatgtgac ctacactgcc 2880 aggtatcccg tgactgatgt tattgattat agcaaagtct catcttcttt tgctacattc 2940 ctaagtgcca ttaatgaagc tcgagaacct caaagttttc aagaagccaa tcttcacagt 3000 gagtggagaa atgctatggc agaggagctt caagccctcc atgaaaataa cacatggact 3060 atagtgaaac ttccaaaagg aaagaaggca gtggggagtc gttgggtgta caaaactaag 3120 tttcattcag atggcacaat cgaaaggaat aaggctcgct tggttgctcg aggttttaca 3180 caaacctatg gcgtcgatta taaagagaca tttgctccgg tggcaaaaat gaacactgtt 3240 agagtattgt tgtcggttgc aattaacaat gcatggcctc tctttcaaat ggatgttaaa 3300 aatgctttcc tgcatggtga acttgaagaa gaggtttaca tgaagctacc cccaggtcat 3360 cctcaatcaa acaatccaga aatggtgtgc aaactccata aatccattta tggtctcaag 3420 caaagtccac gtgcatggta tgccaagctc agtcatgttc tggaaagggt tggtttttgt 3480 cgaagtattg cggattcttc cctatttgtt cgttccagct cagtgggtaa actagttgtg 3540 ctcatttatg ttgatgatct aattgtgaca ggtgataata tgtcagagat taatgctctt 3600 aaacagtatc tcaacaacaa gtttgctatc aaggatcttg gcactctcaa atactttctg 3660 ggcatcgaga tggcacactc tcacaagggt ttcttcctca accaacgcaa gtatgtcatg 3720 gatcttcttc acgaagcaaa aatgacagat tgcaagcctg ctcgtacccc cttggatagc 3780 aacttgaagc taaaaactca cggtgatcca attcccaatt taagttacta tcaaagaatg 3840 gttggcaaac tcatttatct gactatcaca cgtcctgata tatcatatgc cgtcagcatt 3900 gttagccagt ttatgcactc tccaagcatg gatcatttga agattgttca tcgtgtgcta 3960 cgttatctta agggttccgt tggtagagga attcttatgc gcaacaatag tcacactcgg 4020 atctcaggct ataccgatgc tgactgggcg ggcaattctc tcgatcgcaa gtctaccact 4080 gggttttgta cgtttgtggg aggcaaccta gttacctgga aaagcaagaa acaaagtgtt 4140 gttgcacgct ctagtgcaga ggcagagtat cgtgctatgg cgtcgactgc ttgtgaactt 4200 atttggctca aaagccttct gttggcttta ggttttcctc atcaacaacc catgtcccta 4260 cactgtgata atcaggccgc gatgcacatt gcatcgaatc ctgtattcca tgagcgaact 4320 aaacatattg aagttgattg tcactacgtc agaaatcaag ttcagtccaa ggtgatcgat 4380 actcactaca cgcgcagtca tgatcaactt gcggatattt tcacaaaagg attaacctct 4440 gctaattttc agcgtctttt gttcaagctt ggatcaatta atccctttga tccagcttga 4500 gggggagtat 4510 // ID NTERV1I repbase; DNA; EDCOT; 250 BP. XX AC . XX DT 30-NOV-2000 (Rel. 5.1, Created) DT 30-NOV-2000 (Rel. 5.1, Last updated, Version 1) XX DE NTERV1I is an internal portion of the NTERV1 endogenous DE retrovirus - a partial consensus sequence. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW endogenous retrovirus; Gypsy superfamily; NTERV1; NTERV1I; NTLTR1; KW internal portion. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RP 1-250 RA Jakowitsch J., van der Winden J., Matzke J.A. and Matzke A.M.; RT "NTERV1I."; RL Direct Submission to Repbase Update (NOV-2000). XX RN [2] RA Kapitonov V.V. and Jurka J.; RT "NTERV1I."; RL Direct Submission to Repbase Update (NOV-2000). XX DR [2] (Consensus) XX CC This retrovirus has been identified [2] based on a sequence data CC deposited by [1]. CC NTERV1I is a 3'-end of an internal portion of the NTERV1 CC endogenous CC retrovirus [2]. Long terminal repeat from NTERV1 is deposited in CC Repbase Update as NTLTR1. PBS (primer-binding site) of NTERV1 is CC identical to PBS in the RETROSORT1 Gypsy-like retrovirus from the CC Sorghum bicolor genome; putatively it binds tRNA-Lys [2]. CC NTERV1 PBS: TTGGCGCCCACCGTGGGGC. XX SQ Sequence 250 BP; 75 A; 50 C; 62 G; 63 T; 0 other; agaaagtgaa agtaaagttt gaattaatga gaaatgggtc tatttattgg attcacggcg 60 acggttcaaa ggcactagtg gccgaccgcc aactgacact cattaatgac ttggggaact 120 gtaccgacgg gacatttcgg tcactttcgt cgcttacgtc acgaggatga cgtcatgaca 180 ggtcgaggta gaaaatcgaa ggctcaattc attttcttgt cattacactc caaaaaacga 240 ggggactatc 250 // ID Copia-24_Mad-I repbase; DNA; EDCOT; 5008 BP. XX AC ACYM01122703; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-24_Mad-I; KW Copia-24_Mad-LTR; Copia-24_Mad_. XX NM Copia-24_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5008 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1298-1298 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01122703; Positions 1665 6672. XX CC Positions [2056-2556] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 1651..3285 FT /product="Copia-24_Mad-I_1p" FT /translation="MCCMFLIYHNTYYPYINSARITNVDSYMMIFPFGSRT FT KSQGKSYSRDCVKLAITPILFKSPQNTLPASSILHACYLTKPITISLWHQR FT LGHPSNTVTSAMLQHTKASAFTDTCQTICTPCLKGKFIKLPFSFPANKSVT FT PLEMIHSDVWGPAHVLSFEGYRYYASFIDECARYTWIFPLRNKAEVFQIFV FT KFHAFLSTQFSVHIKTFQSDGGGEYTSHQFQHFLASKGILYQKSCLYTPEQ FT NGLAERKHRHILETAITLLQRATLPSKFWFFACSTTIYLINRMPYISLKMQ FT SPYKLLIGKPPTFTHLKVFGCACYPLLKPYNSSKLQPKTTTCTFLGYVDNY FT KGFLYLDGITNKVYISRHVLFDETQFPYSTTPFAVPQLIQPTSESSLPLSV FT PSIPSVSLHNQVTLPISHLHSSLSRVSESMCLISSSATDSLTTSTASEFLE FT TQSSSVSESIQTPLLHHSTTRLLSSPTESSHHEFTQFPIHDDPDFQQDQLI FT VDLPIHMNLHPMQTRSKSGIVKRKVYSASVAINSPQLEPKTLKVTAKIP" XX SQ Sequence 5008 BP; 1566 A; 996 C; 853 G; 1593 T; 0 other; tggtgtcatc accgtaggtg aatccaaagc ttccgcatac tatttgatac atatatttct 60 ttctctcaac cctctgattt gttgattctg tgagttttct aggttcatca aaatcccagt 120 tctcaagata ctcgactcct aaacagttgc ccaccaactg ttcgataaaa gttcgaagtg 180 aagaaatttc ttgctgttac aacaatgggt accgcaactc aattgcaaat tgttcaatcg 240 cccattacaa gtctcatctc tactgtgtca tcttctgtta cagtcaaatt ggatgactca 300 aactatcttg tatggagttt tcatatcaat cttctgctag atagtcatgg aattcttgat 360 ggatccaagt aatgtcctct acgatttctt gatgaggcga atcttgaagg agttgaaaca 420 aatgcctatc aggtttggaa aatgcacgat cttgctctta tgcagctttt catagctata 480 ttgtcatcta ctgcgatttc ttgtgttttt ggcagtacta attctcatgc aatgtggaca 540 aatctcaaag aacggttctc tacagttaca aaggctacaa ttttttcaga tgaagacaga 600 gcttcaaacc atacaaaaag ggtttgattc aatatctgtc tatttacaaa aaatcaaata 660 tgccagagac tatcttgttg cagccgatgt tctatttgac gatgatgata taatcatcct 720 tgctcttgtc tgctgattat aatacatttc aatgtgttat tagaggaaga gaaactggga 780 tttccttgaa agaatttcga tcatagcttc ttactgaaga agctataatt ggacaatctt 840 gtgagtcttc tgtgtctttt ggaactgcaa tggttgcatg cactcagtct aaaaaaggaa 900 aaattcttac tcttgatcac agttcatctc agtcccaggg atttgacata gggtcttcga 960 gccaaggtta cagtctcaat agaggatcta cttttaatgg atataactct ggacaagggt 1020 catcttctca atatgactct ggaaatttta atggcaatta tggcaattca ttttcttcta 1080 ggggatacaa agggacaaac tatagaagaa aaggaagagg tgggtttcag tataacaatg 1140 gtctcaggtt tcactctcca tcatacaatt ctagtcctgg aattcttgga gctccaaaag 1200 tttttcaaca cacctgccct gatcatccaa ctaagattcc tacttgccaa atctacaaca 1260 aaaaaggtca tgtggctgca gattgttttc aaaggcacaa tataccaatt gctggacatg 1320 aagcagctat tcaatgtcaa atatgttgga agtttgggca ctctgctact tagtgctatg 1380 acaaaaacaa ctttgcatac caaggaagac caccctcagt taatctcact gtgatgcaag 1440 caagtcacaa tccttctaca ccacttaaac atttctaggt tgcgaatact ggtgccacat 1500 ctcatatgac ttcagagctt gcaaatcttg atttggctac tcaatatcaa ggcatatata 1560 caataaccac tgcgagtggt gcaggtttga caatttctag tattggtaca tctacactgc 1620 aagctcctag tcatactttt acattgaaaa atgtgttgca tgttcctaat ctatcacaac 1680 acttattatc catatatcaa ctctgcaagg ataacaaatg tagattcata tatgatgata 1740 tttccttttg ggtccagaac aaaatcacag ggaaaatcct attcaaggga ctgtgtaaag 1800 ctggctatta cccccattct gtttaaatct ccacagaata cactacctgc atcatccata 1860 ttacatgcat gctatctaac caaaccaatt actataagct tatggcatca acgattaggg 1920 catccctcaa atacagtcac ttctgcaatg ttgcaacaca ccaaagcttc tgcattcaca 1980 gatacttgtc agacgatttg tactccttgt ttgaaaggaa aatttataaa attgcctttt 2040 tcttttcctg caaataagtc tgtaacccca ttagagatga ttcatagtga tgtatgggga 2100 cctgcccatg tgttgtcttt tgaagggtat aggtactatg ctagttttat tgatgaatgt 2160 gctcgataca catggatttt tccattaaga aataaagcag aagtatttca aatatttgtt 2220 aagtttcatg cattcttaag tacccaattt tctgtccata ttaaaacctt ccaaagcgat 2280 ggtggtggtg aatatacaag tcatcaattt caacactttc tagcatccaa gggcattttg 2340 tatcaaaaat cttgcctata cactccagag caaaatggat tggcagaaag gaaacatagg 2400 cacattctgg aaactgccat cacattattg caaagagcta cacttccatc caagttttgg 2460 ttttttgctt gttcaacaac catttatttg ataaacagaa tgccttatat ttctttaaaa 2520 atgcaatccc cttacaagtt gttaattggt aaacctccaa cttttacaca tctcaaagta 2580 tttggatgtg cttgctatcc tttattaaaa ccttataaca gttcaaaact acaacccaaa 2640 acaacaactt gtacattttt gggatatgta gacaactaca aaggttttct ctatttagat 2700 gggatcacaa acaaggttta tatttctaga catgttcttt ttgatgaaac acagtttcca 2760 tattcaacca caccatttgc tgtacctcag ttgatccaac caacatccga gtcatcacta 2820 cctttatctg taccatccat accatcagtt tcattgcata atcaagtcac attaccaata 2880 tctcatctgc attcatcttt atctagggtt tcagagtcca tgtgtctaat ctcatctagt 2940 gccacagatt ccttgactac atctacagcc tcagagttct tggaaacaca atcaagtagt 3000 gtttcagagt ctattcaaac acccttacta catcattcaa ctacacggtt actttcttca 3060 cccacagaat ctagccacca tgaatttaca cagttcccta tccatgatga tcctgatttc 3120 caacaagacc aactaattgt tgatcttccc attcatatga atctgcatcc aatgcaaacg 3180 aggtcaaaga gtggcattgt caaaagaaag gtttattctg catcagtggc tatcaattca 3240 ccacaactag aaccaaaaac attgaaagta actgcaaaaa taccataatg gcagtctgca 3300 atgcaagagg aaattactgc tctacaatct caacaaatat ggtctcttat tcctttccca 3360 ccacataaaa atcttgttgg ctgtaagtgg gtgtacagaa tcaaatggaa tgcaaatggt 3420 tcgatatcca gatataaagc acgacttgtt gcaaagggtt acagccaaga gaagggcatt 3480 gattatggtg aaatgttcag tctggtggtt aaaccaacaa ccattagatt gattctaaca 3540 ttggcagcac aatttaaatg gactcttaga caactggatg ttaaaaatgc attcttgcat 3600 ggtttactac aagaagaggt gtatatggaa catccttaag gttttcaaag ttctagtcat 3660 cactcaaata atgtatgcaa gcttcaaaaa tccctatata tcttaaacaa gctactcaag 3720 cttggaatta gtggttcaca agttttctgc caggattggg atttcaactg tctcaagcag 3780 atccttcttt atttgttaaa cacacatcac agggcacagt tgttatattg ctctatgttg 3840 atgatgtgat tctcacaggc agtgatcctc agttggttta tgatgttatt gcagatctca 3900 caaaggaatt ttacatgaag gatttgggag ttttgaacta cttcttagga ctacaaattc 3960 aatatacttc taatggctta tttgtctctc aatcaaaata tacaaaggag ttaattgaaa 4020 aagttgatct tcaagattgc aaaccttatg ctactccttg tcttccctat cacagattgc 4080 taaaagatga tgggagacct tatcacaatc ctgactagta tcgaagtatt gttagagcac 4140 tacaatatct aacgtttact cgacctgata tagcattttc agttaatcaa gcttgtcagt 4200 ttatgcacaa tcctatggaa tcacatgtta ttgcagtaaa aagaataatt aggtatctca 4260 aaggcacttc ggagtatggt attcgatttc aatcaggacc aatctatcta caataatata 4320 atgatgcaga ttgggctgga aatcctaatg atagaaggtc tacatctggt ttcattgtgt 4380 ttcttggttc caatctaatt tcgtgggctt tgaataagca acatactatt tctaggtcct 4440 taacataagc tgaatataga gctcttgcca tcactgcagc tgagcttgcc ttgataggat 4500 aattatttta tgatcttcac attccattac aattgcctcc catgattcat tgtgacaatg 4560 tttctgctat cgctctatcc acaaatccag tgtttcatgc taagtccaaa catattgaaa 4620 tcgattacca ttttgtgaga gaacgagtaa caagaggaga tcttcagatt caacatgttt 4680 cttcatctga tcaatctgct aacatattga ctaaatggct gtctacacca ttgtttcaat 4740 tgcattgtgg caatctcatg cgtagctcct acaagcgtga gattgagggg ggatgtaaga 4800 gtagtgaagt gaagaaaacc aacatccgag tgacagataa atctaaggaa aactaatgaa 4860 aagggcttga aaactttgag ttttaatgat aaggacaaaa taaagggtaa agtgaatagt 4920 accaggattg actttttagt gtaaaaatgt ggtttttctt taaagtgaac agtaccgggt 4980 gtttttcgtt aaagttccca taaatcta 5008 // ID Copia37-PTR_I repbase; DNA; EDCOT; 4388 BP. XX AC LG_XV; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia37-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4388 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4388 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 250-250 (2007). XX DR Genome; LG_XV; Positions 7979330 7974943. XX CC Positions [1719-2219] - Integrase core CC 'GTCGA' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 228..4355 FT /product="Copia37-PTR_I_1p" FT /translation="MATDKYVQATIPQFDGHYDHWAMRMENLLRSKEYWDL FT IETGVSSAVEDGAGAVPTEAQKQLQIKDLKVKNYLFQSIDRTIMETILDKR FT SAKSIWDSMRQKYQGSTRVKRAQLQALRREFEVLQMKEGEKVDEYFARTLT FT IVNKMRVHGETMEQVTIIEKILRSMTFRFDYVVCSVEESNDLSQLTIDELQ FT SSLLVHEQRLNRHFQNDEQALNVSYEGGRSRGGRNAFRGRGRGRGRHGFNK FT ALVECYKCHKLGHFQYECPSWEKGAHYAEINEEEMLLMAYTAHDSSNSTWC FT QTAPTNSKETMWFLDSGCSNHMTGDKKWFSHLDETFRQFVKLGNDTKMAVM FT GKGNIKLRINGTSQLIGDVFYLPELRNNLLSIGQLQERNLAILMEHGECKI FT YHHKRGLIMSTQMSANRMFILLAERETQMQTQVLIPTCFKTTSESPADLWH FT RRYGHLHFKGLSILSRKQMVKGLPHLHESSTVCTVCMTGKQHREFIPRKSM FT WRATQKLQLIHADICGPITPESSSHKRYILTFTDDYSRKLWTYFLNLKSEA FT LAMFKKFKCLVEKESANVICCLRTDRGGEFTSSDFNEYCSSNGIVRQLTAA FT YTPQQNGVAERKNRTIMNMVRCILAEKLVPKIFWPEAVNWAVHLLNRCPTF FT AVKDMTPEEAWSGFKPSVEYFKVFGCIGHVHIYDKHRQKLDDKSHRCIFLG FT LSQESKAYRMYDPVSAKIIVSRDVVFEEDKQWDWSTIETENQTLTWGDNAE FT TEWQHADHPAREHDNVEAEQLVDNNDELNVQPAFEGDDNAEEEPQSDSNTT FT GDSSGVADANSPGIISSSSEDISSPAQGRVRRIPAYLQDYVTGDGLSDSDE FT ESNFMLLTASNDPILFEEAAKHPKWREAMDLEINSIEKNGTWELTTLPYGA FT KRIGVKWVFKTKLNENGKVDKFKARLVAKGFSQKFGIDYTEVFAPVARWDT FT IRMILALAACRGWDVYQLDVKSAFLHGELNEAVFIEQPQGYEVKGAEYKVY FT RLKKALYGLKQAPRAWYNKLESYFIKEGFERCPSEHTLFTKKMEGKCLLVS FT VYVDDLIFTGNNVEMFERFKNSMKQEFDMSDLGRMKYFLGVEVVQHRGGIF FT INQRKYANEVLERFGMRNCNPVKNPIIPGFKLAKDEGGVSVDATTYKQMVG FT SLMYLTATRPDLAFVVSLVSRFMERPTELHQQAVKRVLRYIKGTTELGISY FT QKGGEEKLAAYTDSNYAGDTEDRKSTSGYAFLLSSGAVAWSSKKQPVVTLS FT TTEAEFIAAAACACQSIWMRRILDELGFERSKCTDIFCDNSSTIKLSKNPV FT MHGRSKHIDVRFHFLRDLTMDGIVKLEFCGSKDQLADIMTKPLTLEVFTRL FT RELLGVCTTPILN" XX SQ Sequence 4388 BP; 1426 A; 766 C; 1043 G; 1152 T; 1 other; tttggtatca gagcctcaac acagagagag tttggttgag tgttctgttt ggaattgcaa 60 ttcctaaaca caagagtgag tgacacgaga gcaagagtca atcacttggc aactggtgag 120 tgaaacacga gagcaagagt gagtgaaaca cgagagtgag tgaaacacga gagcaagagt 180 ggatcacttt gtgagaatta ttcttttgtg agaacgagaa ggctgagatg gctacagata 240 aatatgttca agcaaccatt cctcagtttg atggtcacta tgaccactgg gctatgcgta 300 tggagaatct tcttcgttca aaggagtact gggatctaat agaaacagga gtttcttcag 360 cagtagaaga tggagctgga gctgtgccaa ccgaggctca aaaacaactt caaatcaaag 420 atttaaaagt aaagaactat ctgtttcagt ccattgatcg cactatcatg gagactatcc 480 ttgataaaag aagtgctaag agcatatggg attctatgag gcagaaatat cagggatcaa 540 cacgagtcaa aagggctcaa ctgcaagctt taagaagaga atttgaggtg ctgcagatga 600 aggaagggga gaaagtggat gaatattttg ctcgaacatt aacgattgtg aataagatga 660 gggttcatgg tgagacaatg gagcaggtga ccatcattga gaaaattcta agatcaatga 720 cttttcgatt tgactatgtg gtatgttcag tagaggagtc taatgattta agccaactta 780 ctatagatga attgcaaagc agtttacttg ttcatgaaca aagattgaat cgtcattttc 840 aaaatgatga acaagcactg aatgtttcat atgaaggagg aaggagtcgc ggtggtcgaa 900 atgcgtttcg gggtcgtgga agaggtagag gcagacatgg atttaacaaa gcacttgtgg 960 agtgctacaa gtgtcacaag ctaggacact ttcaatatga atgtcctagc tgggaaaagg 1020 gcgctcatta tgctgaaata aatgaagaag aaatgttgct gatggcttac acagcacatg 1080 atagctcaaa cagcacctgg tgtcaaacag cgcctaccaa ctcaaaagaa acaatgtggt 1140 ttcttgattc gggctgcagc aatcatatga caggagataa gaagtggttc agtcatctgg 1200 atgaaacctt tcggcaattt gtgaagcttg gcaatgacac caaaatggct gtgatgggga 1260 aaggaaacat caagcttcgg attaatggca caagtcagct gattggtgat gtattttact 1320 tacctgagct aagaaataat cttcttagta ttggtcagct tcaagaacgc aacttggcta 1380 ttctaatgga acatggtgaa tgcaaaattt atcatcataa acgagggtta attatgagta 1440 ctcaaatgtc tgctaatcgg atgtttatcc ttctggctga acgagaaaca cagatgcaaa 1500 ctcaagtcct cattcctaca tgcttcaaga ctacatctga aagtccagct gatctatggc 1560 accgtagata tgggcatcta catttcaaag gcttgagtat cttgtcccgt aagcaaatgg 1620 tgaaaggcct gcctcatctc catgagtcct ctactgtctg cacagtatgt atgacaggga 1680 agcagcatcg agaattcatc cccagaaaga gtatgtggag agctacacaa aaattgcaac 1740 tcattcatgc tgacatctgt ggtcccatta cacccgagtc cagcagtcat aagaggtata 1800 tactcacatt tacagatgat tatagcagaa aactgtggac ttattttctg aatcttaaat 1860 ccgaagcact tgccatgttc aaaaagttca agtgtctagt agaaaaagaa tctgcaaatg 1920 ttatatgctg tcttcgaact gatcgggggg gggagtttac ttcgtctgat ttcaatgaat 1980 actgcagctc taatggtatt gttagacaac tcacagcagc ctatacccct cagcaaaatg 2040 gggttgcaga gcgaaaaaac cgaactatta tgaatatggt gcgttgtata ttagcagaaa 2100 agctggtacc aaaaatattt tggccagaag ctgtcaactg ggcagttcat ctgctcaacc 2160 gttgtcctac atttgcagtt aaagacatga caccagagga agcttggtct gggttcaagc 2220 catcagtaga atacttcaaa gtgttcggtt gcattggtca tgttcatatt tatgataagc 2280 accggcaaaa acttgatgat aaaagccatc ggtgtatctt cttggggttg agtcaggaat 2340 ctaaagctta tagaatgtat gatccagtgt ctgcaaaaat cattgtgagc agagatgtgg 2400 tgtttgaaga agataagcaa tgggattgga gtacgataga aactgaaaat caaactctta 2460 cgtggggtga caatgcagaa acagaatggc agcatgcgga tcatccagca cgagaacatg 2520 acaatgtaga agcagaacag ttggttgaca acaatgatga acttaatgtg caaccagcat 2580 ttgaaggaga tgataatgca gaagaagagc cacagagtga cagcaatact actggtgaca 2640 gttctggagt tgctgatgca aattctcctg gaattatttc ttcatccagc gaagacattt 2700 ccagtccagc tcaagggaga gttagacgga taccagctta cttgcaagat tatgtaactg 2760 gtgacggctt atctgactca gatgaagaaa gtaacttcat gttgctcaca gcctccaatg 2820 atcccatctt gtttgaagaa gctgccaagc acccgaagtg gagagaagca atggatttgg 2880 aaattaattc tattgagaag aatggaacgt gggagctgac tacacttcca tatggagcca 2940 aacggattgg agtaaaatgg gtcttcaaga ccaagctcaa tgagaatggg aaagtagata 3000 aattcaaagc aaggcttgtc gcaaagggtt tctcacagaa atttggaatt gactacactg 3060 aagtctttgc accggtagct cgatgggata ctattcgaat gatactagct cttgctgctt 3120 gtagaggttg ggatgtgtat cagctcgatg tgaaaagtgc tttcttacat ggagagctca 3180 acgaagccgt ttttattgaa caaccacaag gctatgaagt aaaaggagca gaatacaagg 3240 tttatagact caagaaagct ctatatggac tcaagcaagc tcctcgagct tggtacaaca 3300 aactggagtc ctatttcatt aaagaaggtt ttgaaagatg tccgagtgaa cataccttgt 3360 ttacaaagaa aatggaaggg aaatgtcttc ttgtaagtgt ntacgttgac gatcttattt 3420 ttacaggaaa taatgtagaa atgttcgaaa ggttcaagaa ctctatgaaa caagagtttg 3480 acatgtctga tcttgggaga atgaaatatt ttcttggcgt ggaagtagta caacatagag 3540 gagggatctt catcaatcaa aggaaatatg ctaatgaggt gcttgaaaga tttggcatga 3600 gaaactgcaa tcctgtcaaa aatccaatta taccaggttt caaacttgca aaagacgaag 3660 gtggggtaag tgttgatgcc acaacatata agcagatggt gggtagcctc atgtacttga 3720 ctgccaccag accagactta gcatttgtgg taagtttggt cagcagattc atggaacgac 3780 caactgagtt acatcaacaa gctgtaaaga gagttcttcg ttacatcaaa ggaacaactg 3840 agctgggaat ctcttatcaa aaaggaggag aagagaagtt ggcagcctat acggacagca 3900 actatgcagg agatactgaa gaccggaaaa gcacatcagg atatgcattc ttactcagtt 3960 caggtgctgt cgcatggtct tcaaagaaac aaccagtagt tactctttcc actactgaag 4020 ccgagttcat agctgctgcc gcttgcgcat gtcaaagtat atggatgcga agaattcttg 4080 atgaacttgg ttttgaacga agcaagtgca ctgatatatt ctgtgataac agctctacta 4140 tcaaattatc aaaaaatcct gttatgcacg gaagaagcaa gcacattgat gtcagattcc 4200 attttcttcg tgacttaaca atggatggaa ttgttaagtt agagttttgt ggttccaaag 4260 atcagttggc agatattatg actaagcctt tgacgcttga agtattcaca agactgagag 4320 aactacttgg agtttgcaca acaccaattt taaactgacg aaattgcaag tcagtttaag 4380 ggagagtt 4388 // ID DNA9-19_Mad repbase; DNA; EDCOT; 1029 BP. XX AC . XX DT 27-OCT-2010 (Rel. 15.11, Created) DT 27-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-19_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1029 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1859-1859 (2010). XX DR [2] (Consensus) XX CC TSD is 9-bp. The whole length forms perfect hairpin structure. XX SQ Sequence 1029 BP; 293 A; 218 C; 217 G; 301 T; 0 other; ggctaaatag ccaaaatggt ccctgagatt tgcataactc atcactttgg tccctaacat 60 ttcaaatcga taaaagtggt ccctgagatt gtccaccatc catcattttg gtccttccgt 120 taaaaactcc gttaagtgtc ccggagctct tggccggaag tttgggcaat tttcaaagct 180 tcgtaactca atcgtttctt aaccaaattc gacccataat atatcaaaat gaagatagga 240 aagtgtagaa taagattata cctatttgga agcccaatgg ctgccggaga tggccggaaa 300 atagcctcaa agttgactgg tccgagggaa aactggaaaa ctcgccggaa actgggtaaa 360 ctttaaacgt tcataacttc ttcaatactc aacgaaatca agtgattcaa aaacgaaaat 420 catacttctc gacgagacga agagaatggt acctttttga tggctaactc gccgtggttt 480 ggccggaaaa cggctcgaaa gtggctgtct tggtctcgag ttagccactt tcgagccgtt 540 ttccggccaa accacggcga tttagccatc taaaaaggta ccattctctt cgtctcatcg 600 agaagtatga ttttcgtttt tgaatcactt gatttcgttg agtattgaag aagttatgaa 660 cgtttaaagt ttacccagtt tccggcgagt tttccagttt tccctcggac cagtcaactt 720 tgaggctatt ttccggccat ctccggcagc cattgggctt ccaaataggt ataatcttat 780 tctacacttt cctatcttca ttttgatata ttatgggtcg aatttggtta agaaacgatt 840 gagttacgaa gctttgaaaa ttgcccaaac ttccggccaa gagctccggg acacttaacg 900 gagtttttaa cggaatgacc aaaatgatgg atggtggaca atctcaggga ccacttttat 960 cgatttgaaa tgttagggac caaagtgatg agttatgcaa atctcaggga ccattttggc 1020 tatttagcc 1029 // ID SHALINE10_MT repbase; DNA; EDCOT; 5420 BP. XX AC . XX DT 02-JAN-2007 (Rel. 12.01, Created) DT 06-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE A LINE element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Interspersed; KW repeat; retroposon; non-LTR; Poly-A tail; ORF; SHALINE10_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5420 RA Shankar R. and Jurka J.; RT "SHALINE10_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 88-88 (2007). XX DR [1] (Consensus) XX CC The sequence has 2 ORFs. First one has domain for zinc finger CC CCHC type while second ORF has domain for LINE reverse CC transcriptase. 5' is incomplete but very close to start. 3' is CC well conserved. In general the element is present in Medicago CC genome in very few long copies. XX FH Key Location/Qualifiers FT CDS 1..894 FT /product="SHALINE10_MT_1p" FT /translation="MEGRKLKRSTDEEDEAIPVEADEMCNDDESFSRTLVG FT KLWTENPYNTRAFKQTMLQAWRSRNPVEIQDLNKNLFLFKFSSKKEADLVC FT KNGPWSFDRNLLILNRISGNEQPSELAMNTASFWVRVYDLPLKLRSEAMAK FT KLGNILGKFDEVDMKEVNRMGKFLRIKASMDLTKPLKRGSMLHFQGKDIWV FT FFKYESLPNFCFICGRIGHQMRDCEDMAGHDQEGYSEIEEKEQAFGPWLRA FT SPLPKITYELNKESSSSACSKNLFPSHSNNKGQNSGTETEKEDEVEQQESQ FT THHNGA" FT CDS join(1275..1994,1998..4484) FT /product="SHALINE10_MT_2p" FT /translation="MKILSWNCRGLGNPRAVRALLRLTRIENPQIVFLMET FT RLKANEVESVRNKFGFKYGLTVDCRGAGRERAGGLALLWMEHMNISIKSYS FT LNHIHGICDDEEGGEAWDLTGIYGHPEEQNKKKTWNLIESLGRQISGRWIC FT YGDFNDIXDSEEKKGGNIRSLSQLSLGRQVVAECSLIDLGFDGYPFTWSNG FT REEGENIQCRLDRGFGNEAFINRFSPIKVIHLPRFGSDHAAILFCLEYINR FT NRRRKRPFRFEESWTKEXRCEALIRQSWNSTTSSCTEKIEAIKHLEGEFDD FT HNMGKLKKEISRLEKRMNNQSLWSGNDEDLCXLKRIEKEHEELLKLEETMW FT RQRSRAVWLKDGDKNTKFFHGKASQRRKVNDIKKIKDEDGVWWKGEENVEK FT VLINYFADLFSSSNPSDIDETCEVVKGKLSEEHKNWCETVYTQEXVKEAIK FT QMHPLKAPGPDGLPALFFQKYWHIVGRDVQDLALNILNEDKEPDEINKTFI FT VLIPKGKNPSSPKDFRPISLCNVVMKIVTKTIANRLKHILPDVIDEEQSAF FT VQGRLITDNALIAMECFHWLKKKKKGKKGMMALKLDMSKAYDRIEWTFVQQ FT ILXSMGFPEKMVELILRCISTVSYQILINGQPSXSFYPERGFRQGDPLSPY FT LFILCADVLSGLIHKEAXYKKIHGIQVARTAPKISHLFFADDSLLFARANS FT EEASKILNVLXTYQKASGQMVNLDKSEASFSRNVHKEEKNMICNKMGVKAV FT ESHSRYLGLPVLFGRSKKVVFSFVIDRVWKKLKGWKEKFLSRAGKETLIKA FT VAQAIPNYIMSCYKIPEGCCNDIESMLAKFWWGSNXDXRKIHWMSWERLSK FT AKVKGGMGFRGFSDFNKALLGKHCWRLXTGXHSLLERVFKSRYYPSGNFLE FT AKVGYQPSYAWRSIXSARDVIEKGGRWKIGNGKSVRIWNDNWLPDXRTLEA FT KSAVFTLQDDAXVXELIDXDTKQWNRELILSSFNRYVAXKIVSIPLSLRLP FT EDKMVWNWEKDGEYSVRSAYHLLCDEKSKNPTGTIKSAKRQTVEGNLECXY FT PQQDQKFHVEAC" XX SQ Sequence 5420 BP; 1689 A; 909 C; 1306 G; 1446 T; 70 other; atggagggtc gaaaactgaa acggagcacc gacgaagagg atgaagccat tccggtggag 60 gccgatgaga tgtgtaatga tgatgagagt ttttcccgca cccttgttgg aaaactctgg 120 actgagaacc cctataacac cagagcattc aaacaaacca tgctacaagc ttggagatcg 180 aggaacccag ttgagattca agacctcaat aaaaaccttt tccttttcaa gttctcatca 240 aagaaggaag cggatctggt ttgtaaaaac ggcccatgga gctttgacag aaacctcctg 300 atcctaaaca gaatctcagg taatgaacaa ccatctgagc ttgctatgaa cacagcgtct 360 ttctgggtta gagtttatga tcttcctctg aagctgagat cagaagctat ggcaaaaaag 420 ctgggaaaca ttctgggcaa gtttgatgaa gtggatatga aagaggtgaa caggatggga 480 aagttcctcc gaattaaagc ttctatggat ctcacaaagc ctcttaaaag gggatcaatg 540 ctgcactttc aaggtaaaga tatttgggtt tttttcaagt atgaaagttt accaaatttc 600 tgcttcatct gtgggagaat agggcatcaa atgagggatt gtgaagatat ggctggacac 660 gatcaggaag ggtacagtga aatcgaagag aaggagcaag cttttggacc atggctgagg 720 gcatctcctc ttccaaagat tacatacgaa ctgaacaaag agtcaagctc tagtgcgtgt 780 agtaagaatt tgtttccttc gcacagtaac aacaagggcc aaaactcagg aactgaaacg 840 gagaaggagg atgaagttga acagcaggag agccagaccc accacaacgg cgcctaaaaa 900 gaccaaccaa atgttgctgc tagttcaggc gccttagtgc ctatggtgca aaatgaagtt 960 gaaggagtgg ctgaatcttt aggtgcggta accatctttc aaactccaaa agttcaaact 1020 gttgaacaaa caccaaaaga ggggaaaggc aggaagtggg ttagacaaaa gagtggcaag 1080 acaaagaaga accagtctgt caagaaggtt atcaaagagc tagggaagcg ggcacttgtt 1140 gatgtggtag tcactgaagc aaaatttgag actgtttggg gatcagataa gagacaaaaa 1200 ggggatgctg agatggagga acctattgaa tcaacaggaa cggtggtgtt ggatgaccaa 1260 caccgccagt cacaatgaaa atcttaagtt ggaactgtcg ggggttgggg aaccctcggg 1320 cagttcgagc cttgttaagg ctcacccgta ttgaaaatcc ccaaattgtc ttcttgatgg 1380 agactagatt aaaagctaat gaagttgaaa gtgtccggaa taaatttggt ttcaaatayg 1440 gtctgactgt tgattgtaga ggagctggcc gagaaagagc agggggtctc gccctcttgt 1500 ggatggagca tatgaacatt tccattaaat catattctct gaaccatata catggaatat 1560 gtgatgatga ggaaggtgga gaagcttggg atctgactgg aatctatggg catcctgagg 1620 aacaaaataa gaagaaaaca tggaatttaa ttgaatcttt ggggaggcag atttctggaa 1680 ggtggatatg ctatggtgac ttcaatgata ttttsgactc agaagaaaag aaaggaggaa 1740 atatcagaag cctatctcaa ctgtcgttgg gaagacaagt ggttgctgaa tgtagcctaa 1800 ttgatttggg ttttgatggt tatccgttta catggtcaaa tggtagagaa gagggggaga 1860 acatacaatg taggctagat agaggttttg gaaatgaagc ttttatcaac cgattctccc 1920 caataaaagt cattcacttg cctagatttg gctctgatca tgcagccatc cttttttgct 1980 tggagtacat taactaaaga aataggagaa ggaaaagacc ttttcggttt gaagagagct 2040 ggacaaagga akcaagatgt gaagctctga ttcgacaatc atggaacagt accaccagtt 2100 cctgcacaga gaagattgaa gccatcaaac atctggaggg tgagtttgat gatcataaca 2160 tgggcaaact aaagaaggag atatcaaggc tagaaaagag gatgaataac caatctttgt 2220 ggtctggaaa cgatgaggac ctgtgtmgcc ttaaaagaat tgaaaaggaa catgaggagc 2280 tgttaaagct ggaagaaact atgtggagac aaagaagcag agctgtttgg ctaaaagacg 2340 gggataagaa tactaagttt tttcatggta aagctagcca aagaaggaag gtgaacgata 2400 taaaraagat caaagatgaa gatggggttt ggtggaaagg agaagaaaat gttgaaaaag 2460 tgctcatcaa ttatttcgct gatttgttct cttcttcaaa tccgtctgat atcgatgaga 2520 cttgtgaggt ggtgaaaggg aaactctccg aagaacacaa gaattggtgt gaaacggttt 2580 acacccagga ggakgtcaaa gaagctatta aacaaatgca ccccctcaaa gcccccggtc 2640 cggatggtct cccagctctt ttcttccaaa agtattggca cattgttggt agggatgttc 2700 aagacttagc actcaatatc ctgaatgagg ataaagaacc cgatgagatc aacaaaacct 2760 ttattgtcct tattcccaaa ggcaagaatc catcatctcc aaaagatttc aggcccatta 2820 gtctgtgcaa tgtggtaatg aaaattgtca caaagactat tgcmaataga ttgaagcaca 2880 ttcttcctga tgttattgat gaggagcaaa gtgcttttgt ccaaggtagg ttgatyacwg 2940 ataatgccct tattgcyatg gaatgtttcc actggttgaa aaagaagaag aaagggaaga 3000 aagggatgat ggctcttaaa cttgatatgt caaaggctta tgacagaatt gagtggactt 3060 ttgtgcagca gatycttaww tctatggggt ttcctgagaa gatggtggag cttatcttga 3120 gatgtatctc tactgtttct taccaaattc ttatcaatgg ccaacctagc amctcctttt 3180 atcctgaaag gggtttccga caaggggacc cactctcacc ctatcttttt attttgtgtg 3240 ctgatgttct ttcaggtctt attcacaagg aagcctmata taaaaagatt catggaattc 3300 aagtagcaag gacagcsccm aaaatatctc atctgttctt tgcagatgac agcctcctct 3360 ttgctagagc aaattcagag gaagcatcga agattctcaa cgttcttrct acttaccaaa 3420 aagcttccgg tcaaatggtg aacttggaca agtctgaagc ctcatttagc cgaaatgtgc 3480 ataaagaaga gaaaaatatg atctgtaaca agatgggagt aaaggctgtg gagtctcatt 3540 ctagatacct tggtcttcct gttctttttg gaagatctaa gaaggtwgtt ttctcctttg 3600 tcatagatag ggtgtggaag aagctgaaag gatggaaaga gaagttttta tctagagctg 3660 ggaaagagac tctcatcaaa gcagtggccc aagccatccc aaattatatt atgagttgct 3720 acaaaatwcc agagggatgc tgtaatgata ttgaatccat gttagcaaaa ttttggtggg 3780 gatcaaacra ggacsagagg aagattcatt ggatgagttg ggagagacta tccaaagcaa 3840 aagtgaaagg tgggatgggn ttccgaggtt tcagtgattt taacaaagca cttcttggra 3900 aacattgttg gagacttntr acaggggakc attccctytt ggaaagggtt ttcaagagta 3960 gatactatcc aagtggtaac ttcttggagg ctaaggtagg ataccaaccg agctatgctt 4020 ggagaagcat catkagtgct agagatgtga ttgaaaaagg aggtagatgg aagattggta 4080 atggcaaaag tgtyagaatt tggaatgaca attggctgcc agatmtgaga actttagaag 4140 caaagagygc agtctttact ctacaggatg atgcttktgt tkcagagctt attgatgwag 4200 ayaccaaaca gtggaatagg gaactgattt tatctagttt taayaggtat gtagctmaga 4260 aaattgtaag tattcctctw tccttgaggc ttccagaaga taaaatggtt tggaattggg 4320 aaaaagatgg tgaatactcc gtgcggtcag cttaccatct cctctgtgat gaaaagtcca 4380 agaatccaac cgggaccatc aaatccgcaa agagacaaac tgtggaagga aatttggaat 4440 gctyctatcc ccaacaagat caaaaatttc atgtggaggc ttgctaagaa catcctacca 4500 actagatcaa atctgcaaaa aaaaggtatt attcttgaca ctttatgccc tctctgtcat 4560 tctgaasatg aatcctcaca ccatctctty atgaastgta atatgctgaa gctwtctctg 4620 tttgcttctc accttggttc ccatattcca actgatgttg acttacatga ttggatgcta 4680 aaatggttaa cttgccaaga acctataggt gcccaactgt tttgtactat tctttggaaa 4740 ttttggtmtg cwagaaatca agctgtgttc aaagggagtc ctctagaccc ctctctatta 4800 gctgatgatg ctatgtattt tgttcatgag tttaatgaag ckaatcctag aagaggcaga 4860 aggacggttc aggaatgtkc casataccca ggaactgycc actgattttt ctgtgtttgt 4920 tgatgctggc tgttttgctg atggcccaac tggttggggg ctgaatttga aaaaccggag 4980 gggggatact tgcttaagca agtgcaagan ggatgacatt gatgttgatc ctctrttggc 5040 tgaggctttg ggtgtgagat gggctctcca agtggctaag gatcaaggaa taamctcaat 5100 cgccatttat tcagatgctg cyaatgtwgt saattgtatc aatrggaagt caawctttgc 5160 arcaatagat atggttrttc aagattgtag agwtcttatg tctagtttgt aaaatgtttg 5220 tgttrtttnt gttagtagag accaaaactt tgatgctcat aatttggcct ctttggcaaa 5280 artagtgggt aatagaactt ggctaagggt agtycctaat agtttatttt cttctgcaat 5340 gctaamtctt ttccaattgt acygttatag ctgtttycca gcyagtttct aatgaaagtt 5400 gkttcatttc aaaaaaaaaa 5420 // ID TLP2 repbase; DNA; EDCOT; 306 BP. XX AC . XX DT 20-OCT-2006 (Rel. 11.1, Created) DT 24-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE Putative non-autonomous DNA transposon - a consensus. XX KW DNA transposon; Transposable Element; TLP2. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-306 RA Shankar R. and Jurka J.; RT "TLP2: A subfamily of TLP family of non-autonomous transposons."; RL Repbase Reports 6(10), 509-509 (2006). XX DR [1] (Consensus) XX SQ Sequence 306 BP; 106 A; 45 C; 53 G; 100 T; 2 other; aatatgcata atacataaac atgtcyttta acttggcctc atttgacatt tatgtccttc 60 aattttgggt gtgcacaagt agacacttaa acttgtataa agttgaacaa gtagacacat 120 gagtcctacg tgacataata cacgyaggac aatatattgg atgcaaatta tcatgtaaga 180 tgtcatgtag gacatgtgtg tctatttgtt caactttata caagtttaag tgtctatttg 240 tgcacaccca aaattgaaga acataaatgt aaattgaggc caagttaaag gacatattta 300 tgtatt 306 // ID Copia-55_Mad-I repbase; DNA; EDCOT; 5020 BP. XX AC ACYM01042437; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-55_Mad-I; KW Copia-55_Mad-LTR; Copia-55_Mad_. XX NM Copia-55_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5020 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1325-1325 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01042437; Positions 28339 33358. XX CC Positions [2251-2754] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 2143..3672 FT /product="Copia-55_Mad-I_1p" FT /translation="MLKHSNISCTTDDNSSICSHCISGKMSRLPFLDKIDK FT VDIPFYKIHSDVWGPSPTISLEGYRYYVSFIDEATRFVWIFPLINKAAVFG FT SFLKFCAYVDNQFHARIKILQTDGGGEFMSNVFKTYLDNNGILHHISCPSY FT TPQQNGLAERKHRHLIETAITLLSVAKLPQRFWFYAVAHAVFLINRMPCKI FT LKMDSPFSKLFGQQPELGSLRVFGSAIYPYLRPYNIHKLQPRSTQCVFLGY FT SSGYKGALCYNIVTGKVIISRHVLYDENCFPYKDLEPIKSSIQSQSPDIQS FT SRPIIVTLPSPASIPHTESSHQFNSPGVHHSSTSTSATVSSHRLSSSSQDS FT GSNATNSSNATLSNSTPTLPVLQSSQLQVVLPSLASPIAIPSQSDSLPQGI FT QTRLKTGTISRQDYSALTANFPEVQSLTLSENSPFSGGFTFVADIVDASEP FT TTFKQASQIPQWQVAMQEEFDALQTQGTWVLVPSSSGKNVIGSKWVYKIKR FT NSDGTISRYKARLV" XX SQ Sequence 5020 BP; 1343 A; 929 C; 1013 G; 1691 T; 44 other; tgaaggttaa gatggtatca cgagcttaga atcgcttgcg ctcttggtgc tgggttaatt 60 ttccgctgct caattgaatt ttgatggtga tttcgttccc ttttcctctg ttatttggtg 120 cgatatagct gtacagtttt gcagttcttg atgtttgtga tttttttttt tgaaattgat 180 gaatgtttga aggccgatgc cgtaccgtaa atcattacta ttttgttgat tgttgagatg 240 ttccgaggcc gatgccaaga atgaagtgtt gttatgattt tcttgattct ttgatgaagg 300 ccgatgccat gtatttgatt cttgaagatt tatagattgt tatagtttgg aaattgattt 360 gttggtggtt tcttcattag tgctctggtt ttttgggcga aatttggcta ctttttcatc 420 tgggtttttc ttgttgtggt gcaattttct ctgggtatag gttgatatca tgttttgatc 480 ttttgggaaa atcttcctgc tagtaatcat gtcgacttct gtaaagattg agagtttgtt 540 gggaatgctc actattaagc tcaatgatga aaactttatc aaatggagtt ttcaattttg 600 ttctgtgctt cgtggatacg atcttcttga tcatttcacg ggtgaatcag tttgtcctcc 660 caagtttgtt cttattcctg atcttggtgt tacgaacgaa attagtatta cttataaaga 720 atgggttaag aaagatatgg cattgcttag tcttttaatt gctacactaa gtgatgatgc 780 gattgagcat gtagtgggat gtaagacttc atatgaggcc tggacagctt tgcaagatcg 840 ctatatgtct gtttctaaag ctagtgtgaa ccatttgaaa gctgaattac acactatgca 900 gaagggtggt gattctattg ataaatactt gctgagatta aagggtatta aggatcaact 960 acaagcagct ggtgaaaagg tttgtgataa tgatcttata atcgctgctc ttactggttt 1020 acctcctgac tatgatatca gtcgaatggt aatggtccta ttgctggaaa tggtttttca 1080 tccaattcta ataatggtgg taatcaaggg cagagatatt ttggtactag ctctaactca 1140 tacaggccta aaggaaatgg gggttataag cagaggttca atggatctaa cagaggtaat 1200 tcttggcaat cctggtcagg aaacacttcg aatagatttg atgcgattcc agagtgtcaa 1260 atttgctcca gaaaaggtca tgttgcggtt acatgtttgt acataaacga taatggacag 1320 ccaatacaag agtgtcaaat ttgtggtaag aaagggcata ttgctctcaa ttgcaggcat 1380 agaagtaact atgcatatca aggcactcca cctccagctt ctttatctgc caattatgcc 1440 aatcaagggt ttcatcctca gaatccatct tatgtttcat tatttcccac tgcatcacag 1500 tatatctctc caagcaattt ccctcaattt actcagtatt caactcagaa tcctgcagtt 1560 ccatattcat ttcaaatcat gcctaagggt aatttgcctt ctcctcaacc tttctttcca 1620 gcaatgacag ctcagaattc taatgagtct gcaggaggtg actcgtggat tgtagacaca 1680 ggagcatctc atcacatgag tcctgatgta actgtcctaa ctcgagctgc tccctatgaa 1740 ggcactgaga agattgttgt aggcaatggt gaaggtctgg acgttaaaca cattggtcat 1800 ggcactttgc aaactcaatc tcatatgtta catctcaaaa acatactaca tgtccctatg 1860 ttaactgtta acttactttc tgtcaagaag ctttgtgccr ataatcacag ttggtttatt 1920 tgtgatgaat cacagttttt tgtrcaggac aaggcaacag gggtgcttct acatcacgga 1980 aagagtagca ataatgaact attcaagatt ccagtccatg tttttccaac agtgatgasc 2040 tcaggtgcta tttctcmagc ttctgrtttc ttgggacatg cagtmaaatc atctttgtgg 2100 catcagagat tgggtcatcc atccaatgac attttagcta ctatgcttaa gcattctaat 2160 atttcttgta ctactgatga taattctagt atctgttcac attgtataag tgggaaaatg 2220 agcagattac ctttcttaga caagatagat aaagttgata tcccatttta caaaattcat 2280 agtgatgttt ggggaccatc tcctactatt tctctggaag gctatagata ctatgtgtcc 2340 tttatagatg aagccactag gtttgtatgg atattcccgt taataaataa agctgcagtt 2400 tttggttcat ttctcaaatt ttgtgcgtat gttgacaatc agtttcatgc tagaattaag 2460 attttacaaa ctgatggtgg tggtgagttt atgagcaatg tgtttaagac ttatctggat 2520 aataatggaa tattgcatca tatatcttgt ccctcctata cacctcagca gaatggattg 2580 gccgaaagga aacatcggca tctcattgaa acagcaatta ctcttttatc tgttgctaag 2640 cttccacaaa ggttttggtt ttatgcggtt gcacatgctg tctttctcat caatcgaatg 2700 ccatgtaaga tactcaagat ggactctccg tttagtaagt tgtttggtca gcaacctgag 2760 ttgggatcat tgagagtatt tggatctgcc atttatcctt acttgaggcc ctataatatt 2820 cataagttac aacctaggtc cacacaatgt gtatttctag gttattcttc cggatataag 2880 ggtgctcttt gctataatat agtgactggc aaggtgatta tttcaaggca tgtattatat 2940 gatgaaaatt gttttcctta taaggattta gagcctatca agagttctat tcagtctcag 3000 tctcctgata tacagagttc aaggcctata attgttacac tgccttctcc agcatctata 3060 cctcacactg aatcttcaca tcagttcaat agtcctggag tgcatcactc atctacatca 3120 acctcagcta ctgttagttc tcacaggtta tcatcatcat ctcaggactc tggatccaat 3180 gctacaaata gttcaaatgc tactctttcc aattctaccc caacgttgcc tgtcctccaa 3240 tccagccagc ttcaggttgt tttaccaagt cttgcttctc caattgcaat tccttcacaa 3300 tctgattctc taccacaggg cattcaaact agattgaaaa ctggtacaat ttcaagacag 3360 gattattccg ctctcactgc caattttcct gaagtgcagt ccttaacttt aagtgaaaat 3420 agtccttttt ctggagggtt tacatttgtt gcagatattg ttgatgcttc agaacctaca 3480 acatttaaac aagcttctca gattcctcaa tggcaggttg ccatgcaaga agaatttgac 3540 gcactacaaa ctcaaggtac ttgggttctt gtcccttctt cttctggtaa aaatgttata 3600 ggcagtaagt gggtctataa aattaaaagg aattctgatg gtacaatatc tcgatacaag 3660 gctaggcttg ttrctcaagg ctttagtcaa cagaaaggtt tggactacac agagactttt 3720 agtccagtgg ttagrcacac cactgtgcgm ttgatcttag ctttagctgc aacacataaa 3780 tgggatctta ggcagctgga tgtaaaaaat gcattccttc acggcgactt gcaagaggag 3840 gtttatatga aacarcctag aggttttgtg catcctgatt accctacaca tgtttgtaag 3900 ttrgtmaagt ctttatatgg scttaaacaa gcccctyggg cttggaatra taaattcacc 3960 agttacttgc aagcmgtggg gtttcaarca tcactytcag attccagttt gtttgtrmag 4020 aagagtggtg atgatgtggt cattcttttg ttgtatgttg atgatataat catcacakga 4080 tctagctcta cactggttca atctgtgata gacactttrg gtgcartytt tgatctcaaa 4140 gacatgggma aattggccta ttttttggga cttyaagtgg aatacaagay taatggtgat 4200 atatttgtta accaagcmaa gtatgttaag gatcttmtac ataaggytgg gatggatgat 4260 tgcaagcctt gtgcaacacc ttgcaaacct cacaatcaag ttcttactac tgagggtact 4320 cttctttctk atccaacaca ctatagaagt ttggttggar cattgcaata tctaaccttc 4380 actaggccmg atattgcatt tgctgttaay actgtttgtc aatatatgaa ctcaccaaca 4440 ratgttcatt ttggtatggt taaacgtatt ttacgatttc tgcaagggac tctccgttgt 4500 ggtcttamat atacatcagg gacttccatg gcattgtctg cattcagtga ttcaractgg 4560 gmtgcygatc tsaacactyg acggtctatc acaggatatg ttgtttattt gggggaaaat 4620 ccgatatctt ggcaatcaaa gaagcaagct tctgtttcaa ggagttctac cgaggcagag 4680 tatagggcty ttgcacatac arctgctgat atagcatgga tcaggctcat tcttcgagat 4740 gtccaccagt tcctgtcttc acctccctta attcattgtg ataatcagtc ggccatagca 4800 cttagcttga atccagttca gcrttctcgg atcaaacatt tggaaactga cttccatttt 4860 gttcgagaga gggtatagaa gggtgacttg gtgattcaat atgtttcaac aaaagatcag 4920 gttgctgatg ttctcacgaa aggtcttcat ggtcctgatt tccttcacca ttgtttcaat 4980 cttaagcttg cctatcccag ctaagattga gggggggtat 5020 // ID Copia-90_Mad-I repbase; DNA; EDCOT; 5811 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-90_Mad-I. XX NM Copia-90_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5811 RA Kojima K.K. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1718-1718 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~95% identical to consensus. XX FH Key Location/Qualifiers FT CDS 831..1883 FT /product="Copia-90_Mad-I_1p" FT /translation="MANLAKLDFAALDITGKNYLTWVLDTKIHLEAANLGD FT TIKEESSSSSQDRAKAMIFIRRHLDEALKSEYLTVEDPLALWNALRSRYNH FT QTTVILPRARYDWTHLRIQDFKSVAEYNSALFRITSQMKLCGDTITEEMLL FT EKTFSTFHASNMVLQQQYRARGFTEYNQLISVLLVAEQNNELLMKNHNSRP FT TGSAPFPEVNVASLERNTISSRGNNYKRGRGHKQGRWKGKGKNHGVQFHNQ FT VPRHNPGPSFKNANRQKGKAHVNTPRNHEGGCHRCGGNGHWARTCRTPKHL FT VELYQASFKEKGVEINFLDQAXPMETPDPVTNLSGQLNTTHLDATDFINER FT GNEVYGSD" FT CDS 1971..5597 FT /product="Copia-90_Mad-I_2p" FT /translation="MNKLLFLYSEXMDKNYGYSQNKXNGGDFCLADSATTH FT SILRDRKYFSNLVLAKVKVTTISGQSDVIEGSGKAQIMLPNGTILSIKNAL FT YATRSIRNLLSFKDIRLNGYHXETKSVENVEYLCITSNDTQKRILEKLHGL FT SSGLYCTYIKTVEAYTVMNQKFIDSKVYMLWHDRLGHPGSTMMRRIITNSN FT GHPLLSRHIDVSNDNPCKACSQGKLVIRPSQLKVDDESPSFLQRIQGDICG FT PIQPPCGPFRYFMVLVDASTRWSHVCLLSTRNVAFARLLAQIIKLRAQFPD FT HPIKSIRLDNAGEFTSQTFDDYCMALGIDVEHPVPHVHTQNGLAEAFIKRL FT QLIARTLLMKTKLPVSTWGHAILHAASLVRLRPIANHQYSSIQLVFGHQPN FT ISHLRVFGCAVYVPIAPPQRTKMGPQRRLGIYVGFDSPSIIRYLEPLTGDV FT FTARFADCHFDETVFPSLGGEKTVPEERQELTWVVPTLSHFDPXSTQCENE FT VKRIVHLQGIANQMPDAFNDASKVTQSHIPAANAPARIDVPVGQNKVAAND FT SSSARLKRGRPPGSKDSAPRKRKMRAQLNPNDIIQEKELNDKSTIRDSVLP FT EKENVLDETHVPEETEVHESKEISINYACTNELWDRNEIIIDDMFAFAIAT FT EIILSDDIEPRSVDECRQRQDWPKWKDAIQAELNSLERRSVFGPVVQTPPG FT VNPVGYKWVFTRKRNEKNEIARYKARLVAQGFSQRPGVDYEETYSPVMDAI FT TFRYLISLVISEKLDMRLMDVITAYLYGELDTDIYMKVPEGLKLPEATNKP FT RGMFSIKLRRSLYGLKQSGRMWYNRLSEYLIKEGYANNVICPCVFIKKSNT FT GFAIVAVYVDDMNLVGTPEELNKTAEYLKSEFEMKDLGKTKYCLGLQIEHC FT VSGILVHQSAYIEKILKRFGMDKAYPLSTPMVVRSLDIKKDPFRPKEDDEL FT VLGPEVPYLSAIGALLYLAQCTRPDIAFSVNLLARYSSAPTIRHWKGVKDV FT LRYLRGTTDMGLFYSDKPTNEQILVGYADAGFLSDPHKARSQNGYVFTNGD FT TAISWRSTKQTLVATSSNHSEIIALHEASRECSWLRSMIHHIRNSCGLPSK FT TDTPTVIHEDNAACVAQMKEGFIKGDKTKHISPRFFSAHELQKAKVIEVRQ FT IRSNENLADLFTKSLPKCTFQKLVQGIGLRRLTDLKNAESGGDTIQGEHP" XX SQ Sequence 5811 BP; 1748 A; 1190 C; 1204 G; 1656 T; 13 other; cgttatcagc acgactctct aatcatttct catttccctt caccgaaaga aaaaaaaatg 60 tttcctctaa ggtttttact gttcttcttc ttcctctgcc tcaattgctg ggtataccct 120 cgcgaagaac tgtttgcacc atgtttactt ctagttctcc aactaacagt cacttatatc 180 tttgatttct tgtttggtgt agatattgac tactaaccca ctgattattt atgcaatcca 240 agatngtgcg gtnctatcgc ctatcttgga ctgcagatct aattttactg caaattttaa 300 gtggagcggt ataatcgccc gccctatcct gcatatttaa attttcccgt tatttaattt 360 tatcgcaatt ttaggtggtg tggaataatc acccaccctg ctttgcatat ttaattttat 420 cgcaatttta ggtggtgcgg tataatcgtc caccctgctt tgcatattta aattttatcg 480 caattttagg tggtgcggta taatcgtcca ccctgctttg catatttaaa ttttatcgca 540 attttaggtg gtgcggtata atcgtccacc ttgctctaca tatttaaatt ttcctgctgt 600 ttaaagtagt gcggaataat cgcccatcct atacttgttt cgatgagaat ggtgcggtac 660 aattgccctt ctcattaatc gtgtaaatct cgagcctgaa gtttcgagta cttatcattt 720 tggcctgaag atcaaaaatt tgtaagaacc agaagttcta acaatatatt cctccagnac 780 acatattatt gcaagttctt acacacctca tttttctttc agaaaagaaa atggcaaact 840 tggcaaagct tgattttgct gccctggaca ttactggaaa gaattacctt acatgggtac 900 tggataccaa gatccatctg gaagcagcga atcttggaga taccatcaag gaagagagca 960 gctcatcctc tcaagatcgg gcaaaggcca tgatttttat tcgtcgccat cttgatgagg 1020 cactaaagag cgagtactta acggttgaag atccgttagc cctttggaat gccttgagaa 1080 gcagatacaa tcaccagaca acggtgattc ttccaagagc tcgctatgac tggactcacc 1140 taaggatcca ggatttcaag tcagtggctg agtacaattc ggcgttgttc agaattacct 1200 ctcagatgaa gctctgtggg gatactatca ctgaggagat gttattggaa aagactttca 1260 gcacattcca cgcctctaac atggtactgc aacagcagta tagagcgcga ggcttcactg 1320 aatacaacca gctgatatct gtgctcctgg tagctgaaca gaacaatgag ctcctgatga 1380 aaaaccataa ttcccgacct actggatcag caccgttccc agaagtgaat gttgcttccc 1440 ttgaaaggaa taccatatcc tcccgtggca ataattacaa acgaggacgt ggccacaagc 1500 aaggccggtg gaaagggaaa ggcaagaacc atggtgtcca gtttcacaac caggttccaa 1560 ggcataatcc aggcccgagc tttaaaaatg caaatcgcca gaaaggaaaa gctcatgtga 1620 acactcctag aaatcatgaa ggaggttgcc ataggtgtgg tggcaacgga cattgggcgc 1680 gtacttgtcg caccccaaag catctggtgg aactgtatca agcctccttc aaggagaagg 1740 gtgtcgagat caatttcctc gaccaggctn aaccaatgga aacccctgat ccagtgacca 1800 atttatcagg acagttaaac acaacccacc tggatgctac agactttatt aatgaaagag 1860 ggaatgaagt ttatgggtcc gattgaatta tttatgttta atgtactcnt gttatttgta 1920 cctgtggttt aatgctcgca ttttcaattc aataaaagta gtattccagt atgaataaac 1980 tgctttttct ttactcagag ancatggata aaaattatgg ttattctcaa aacaaganca 2040 atggcggaga cttttgtctt gcagatagcg caaccacgca ttcaatactt cgagatcgaa 2100 agtatttctc gaatttggta cttgcaaaag taaaggtaac aacaatatca gggcaatcag 2160 atgtaattga aggctcagga aaagcccaga ttatgttacc aaatggaaca atattgtcca 2220 taaagaatgc attatatgct actcggtcca ttcgaaattt gttgagtttt aaagacatac 2280 gtctaaatgg ataccacntt gaaacgaaaa gtgtagaaaa tgtggaatat ttatgcatta 2340 cctccaatga tacccagaag cgtatattgg agaagttgca tggtttatcg agtggattgt 2400 attgtacata cataaagaca gttgaggcat atactgtcat gaaccagaag ttcattgatt 2460 caaaggttta catgctttgg catgaccgtc taggtcatcc aggatctacc atgatgcgta 2520 gaatcattac caactctaat ggacatccat tactgagcag acacattgat gtctcgaatg 2580 ataacccttg caaggcttgt tcccaaggga agttggtaat tagaccatca caactaaagg 2640 ttgatgatga atccccatca tttttgcaaa gaattcaagg ggatatttgt ggacctattc 2700 aaccaccttg tggaccattt cgatatttta tggttttggt tgatgcatct acccgatggt 2760 cacatgtttg cctattgtct actcgaaatg tagcttttgc gagacttctt gctcagataa 2820 ttaagttgcg agcacagttc ccagatcatc ccattaagtc cattcgactt gataacgctg 2880 gtgaatttac gtctcaaacc tttgatgatt actgtatggc actgggcatt gatgttgaac 2940 accctgttcc tcatgtccat actcaaaatg gtttagcaga ggcatttatc aagcggcttc 3000 aattaatagc ccgcactctg ctcatgaaaa cgaaattgcc agtctctaca tggggacatg 3060 ccatattaca tgctgcatca ttggttagat tgagacccat agccaaccac caatactcat 3120 caatacaact cgtgtttgga catcagccaa atatttcaca tttacgagtt tttggttgtg 3180 ctgtttatgt gcctattgca ccgccacaac gaactaaaat gggacctcag cgcagactgg 3240 gaatttatgt gggttttgat tcaccatcta tcattagata tttggaacct ttgactggtg 3300 atgtgtttac agctcgtttt gctgattgtc attttgatga gacagttttc ccgtcgttag 3360 ggggagaaaa gaccgttcca gaagaacgac aagagctaac atgggttgtt cccaccttat 3420 ctcattttga tccangaagc actcaatgtg aaaacgaagt gaaaaggatc gttcatcttc 3480 aaggtattgc taatcaaatg ccagatgcat ttaatgatgc ttcgaaagtg acacagtcac 3540 atataccggc tgcaaacgca cctgcaagaa ttgatgtccc tgttggacaa aataaagtgg 3600 cagcgaatga ttcatccagt gcacgcctga agcgtggtag acccccaggt tcaaaagatt 3660 cagcccctcg aaagagaaag atgagggcnc aattgaaccc aaatgatatc attcaagaaa 3720 aggaattgaa tgataaatcc acaattcgtg actctgtact tccagaaaaa gaaaatgtcc 3780 ttgatgagac acatgtccct gaagagacag aagtacatga aagcaaagaa atatccataa 3840 attatgcatg tactaatgaa ttgtgggatc gaaatgaaat aatcatcgac gacatgtttg 3900 catttgcaat agccactgaa attatattaa gtgatgatat tgagccccgc tctgttgatg 3960 aatgcagaca gagacaagat tggcctaagt ggaaagatgc aatccaggca gaattaaatt 4020 ccttggaaag acgaagtgtt tttggaccag tagtccaaac cccgcctggt gtgaaccccg 4080 taggttacaa atgggtattc acaaggaaac gcaacgagaa aaacgagatt gcaagatata 4140 aagcacgact cgttgcacaa ggtttttcac aaagacctgg agttgattat gaagagacat 4200 actctcctgt aatggacgca attacgttcc gttacttaat aagtttggtg atttcagaaa 4260 aacttgacat gcgacttatg gatgtcatca ccgcgtatct atatggagaa ttagatactg 4320 acatatatat gaaagtccca gaaggactta agttgcctga agcaactaac aaaccacggg 4380 gtatgttctc aatcaaatta aggcgatcac tatatgggct gaaacaatct gggcgaatgt 4440 ggtataatcg tctcagtgag tatttgatta aagaaggata tgccaacaat gtcatctgcc 4500 cttgtgtgtt cattaagaaa tcaaatactg gatttgctat agtggcagta tacgtcgatg 4560 atatgaacct agttggaacc cctgaagagc tcaacaaaac tgctgaatat ctgaaaagcg 4620 aatttgaaat gaaagacctt gggaaaacca aatattgtct cggcctgcag atcgagcatt 4680 gtgttagtgg aattttggtc catcaatcag cttacattga aaaaatactg aagcgatttg 4740 gcatggacaa ggcttatcca cttagcaccc caatggtcgt tcgttctttg gacattaaga 4800 aagatccatt ccgtccaaaa gaagatgatg aactggtcct tggtccagaa gtaccatatt 4860 tgagcgcaat aggtgcttta ttgtatttag cacaatgtac tagaccagat atagcttttt 4920 cagttaactt gttagccagg tacagctctg ctccaacaat tcgtcattgg aagggagtca 4980 aagatgttct acgatacctt cgtgggacaa cagatatggg tctcttctac tcagacaagc 5040 ccacaaatga acagatcctt gttggatacg cagatgctgg ttttctctcc gatccgcata 5100 aagcccgctc acaaaatgga tatgtgttca ctaatggaga tactgcaatt tcatggcgat 5160 caacgaagca aacgctagtt gcnacatctt ccaatcactc ggaaataatt gctttacatg 5220 aagcaagtcg tgaatgttct tggttaagat caatgatcca tcacatccgg aattcatgtg 5280 gtctaccttc aaagacagac actccaactg tcatccatga agataatgca gcctgtgtcg 5340 cccagatgaa ggaaggattc atcaaaggtg ataagactaa acacatatct ccaagatttt 5400 tcagcgcaca tgagcttcag aaggctaaag ttattgaagt cagacaaatc cgttccaatg 5460 aaaatttagc agacttgttc accaaatctc taccaaagtg cacatttcag aagttggtgc 5520 agggaatcgg attacgtcgg cttacagatt tgaagaatgc ggaatcaggg ggagatacaa 5580 ttcaggggga gcatccatga tacatgcatg ttgtactctt tttccttcgc ttaggatttt 5640 tcccactggg tttttcctat caaggtttta acgaggcaac ntaagcatgc tcaacaccat 5700 ccgggtaaag ttgtactctt tttccttcgc tatggttttt tcccacnggg tttttccaag 5760 caaggtttta atgaggcaac tgatgttgat atgtgggcat ccaaggggga g 5811 // ID Copia-95_Mad-I repbase; DNA; EDCOT; 2059 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Copia-95_Mad-I. XX NM Copia-95_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2059 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1728-1728 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 2059 BP; 415 A; 379 C; 494 G; 770 T; 1 other; tggtatcaga gccaccaagg ctcacgccat ggatcttggt ggtcgattcc tcttctcatt 60 atttctatct ttcttcatta ctttcttttg ttttcgctta tttgattagt tttatgttta 120 gctttggtct ggattttttt tttccgccga gggttgtgtt tgttctgggg tttttcctcg 180 gggcttcgat gaactggcga gaccatcacg gcaccactac ttgaccttca catggaagac 240 gtcgatcttc tcccttcagc acgccgttct ttagagctga gattttggcg gggagcaaaa 300 tcgaagttca cccatgattc tgcgtaatct ctaccaaaaa gaagctatgg ttgtcagtat 360 atggtgacca attcgcctgg gttttcatga agatctacat agtttcagaa attggggata 420 tgaaattcaa aagaaattag ggatctgtga gagatttcgg cttgaacaga gtgtcggtca 480 aaatctggat cgccaaaaga tcatggtgcc gagattcatc ttctttctgc tatgcaaatc 540 tcgattcggt ggtgattatt tctgtttttc atctgggaat ttctctctgc gttgctgatt 600 ggaaagtggg atcttggact ctgtcaggtt tactacctct tcgatcttga ttcttccgct 660 gttatcgtct tcaagggttg ttgcagaggt gcacagttgg aacgacggag tggcagtctt 720 cgtgaattgc tgttggatgt ctccgaaatc agagtgttgg attcttctgg gtttcctggg 780 ttttcaagat tcaagttctc aggttttgtt ttcgattact ggttttcttt ccagcatatc 840 aactgtttgt gataatgtct cggtgagaat tttctgggtt tcgtgttcat tggttttctg 900 cgattgttct ggttgcgtat tcttgttggg ttgatcgttc ttgggaaagt cgtgtagccg 960 ccttgttgac gacagccttg ccgtcgagtc actcgatctt ggcggaagac gacgatgcat 1020 gagactctgt gtgactgaga gcagagtttg ctttctttgc actgttgatt atctacttct 1080 tcattcatct tggtggtgtt ttcagagcag ttttctgaat tcgattttct gtgattttga 1140 tccgtgctct gttttctggt atggcagaac gtttagacta tgtgcagcct aagtgtttga 1200 cgaattgccc atattttctt catctgggtt cttttctcga atttgatttg ggattttggt 1260 tatgtgttct tctgaattgg taaatgattc tggtatatgg gttgtgcgat agatcatcga 1320 agtgttgata gcagtcattt ggaattgttt ggtgatctgc aacgcttatt tcttgaagct 1380 gtggtctttg atgtactttc gaggtttaat tgaagtgaag ctgtggtctt gatgtgttga 1440 tctctgcaag tattagtttt cttgtcgatt taaagaagaa agtgtcattc tttctatgaa 1500 tcttggagtt tcattctcct aagttgcagt atgatttgga gtttcattct cctmagttgc 1560 agtatgattt gtgttcatgg agtgtcagtc tccttatttg gtatttttta gtagaagtgt 1620 gagatttgtg ttgtgctttg gagtgtcatt ctccttggct gatttggttt cttggagtgt 1680 cattctcctt ggtagattta gtttcttgga gtgtcattct ccgtggtagt ttagtttctt 1740 gggagtgtca ttctccttgg tagatttagt ttcttggcag tgtcaactat ggcttctcag 1800 ttcacagtcg aaaatttgtt gggtatgttc agaccaagac cacgaagcac agctctttct 1860 cccgcaacca tcatgtactt tggaacatcc tgtgccatca cagaaccacc accaataaat 1920 gagaaatagc caacatggca gaattgatga acgacaacag cccctgcata catcttggtc 1980 ttgcagttcc agatcagttt cagcgttcta gctcgttcaa ccttcacttg gctacaccaa 2040 gttcagtttg aggggggag 2059 // ID Copia-31_Mad-I repbase; DNA; EDCOT; 4447 BP. XX AC ACYM01069187; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-31_Mad_; KW Copia-31_Mad-LTR; Copia-31_Mad-I. XX NM Copia-31_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4447 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1379-1379 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01069187; Positions 12879 17325. XX CC Positions [1704-2063] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 339..2063 FT /product="Copia-31_Mad-I_2p" FT /translation="MEPLQQLGQDMATRVHVKRNFRECSRQMWLDLQERFS FT YVNIVQLFHVENEIHDCIQGNMSVSSYFTKLKSLWDERDVLCLILACNCGT FT KKEITSYVETQKTMKFLMALNDSCAIVRSNTLLLNPLPTVNKAYALVIRHE FT RHAEVSNRKNIQPEAVVFAVKNPSREPDTYDNGTQCGKCNKTNHTTKNCPA FT HLKCTFCGWKGHTFEFCRKRRADVETESNCSFSSKGNQVTTYAKMDKPSFP FT FSQEDCKQILQMLNRNKSSFVNQVGNSSTHEELSGKAFSFIHNGTKNIWIL FT DSGVTDHIFCNPNLLTNSKPIENYIVELPNGSFAKVTHIGQIVLFPNLILD FT NVLCVPPFRLNLISINKLAYDSLYVTIFLKHFCVIQDLHLGKMIGMGIERE FT GLYYLDPPKIRICNTVHTVSPNLWHQCLGHPSHKVSLLFPFFHNKSCVTNN FT FLICPLDKQTRSPFPSSSISSKSTFELLHIDIWGGYKVASLSGAKYFLTIV FT DDHTRTTWVYLMKHKFDTKDLLVKLIHMVETQFNTKVKIIRSDNGPELKLE FT IFYAFKGIIHQSSCVNTPQQNGVAKRKH" XX SQ Sequence 4447 BP; 1335 A; 1011 C; 791 G; 1310 T; 0 other; tcatactatt gttctttagt tggtaccaga gcactgatat gggaaaacac acaacacaaa 60 cttaacccta gctgacaagg catgggtgac aagttagaat caaagtcaac cacttcaggc 120 atgacttccc actcacaatg ggaaaatccc aaccatccac ttttccttca tcacttaaac 180 caacctggtg caattcttgt accacagcca ttgatggaag ataattatag tacatgggtt 240 cagtccatga gcatggcctt aattgtcaag aacaaacttg gacttgttaa tggaacaatc 300 aaggaaccga gttcaaacaa tcctgaggag ttacaataat ggaaccgctg caacaacttg 360 gtcaagacat ggctactagg gtccatgtca aaagaaattt cagggaatgt tctcgacaaa 420 tgtggcttga cttgcaagag agattttcat atgtaaatat tgttcagcta ttccatgtag 480 agaatgaaat ccatgattgc atacaaggta acatgagtgt aagttcttat ttcacaaaac 540 ttaaaagctt gtgggatgaa cgcgatgtct tgtgtttaat cctagcatgc aattgtggaa 600 caaagaaaga aatcacatca tatgttgaaa ctcagaaaac aatgaagttc cttatggcac 660 tgaatgactc atgtgctatt gttcgaagca atactcttct tctcaaccca cttcccacag 720 tgaataaggc ttatgcatta gtcattcgac atgaacgaca tgcagaagtc tccaacagga 780 agaacattca accagaagct gttgtttttg cggtgaaaaa ccccagccga gaacctgata 840 catacgacaa tgggactcaa tgtggtaagt gtaacaaaac taaccatacc accaagaact 900 gtcctgcaca tctcaagtgc actttttgtg ggtggaaagg tcataccttc gagttctgtc 960 gaaagagaag agccgatgtt gagaccgagt caaattgttc attttcttca aagggaaatc 1020 aagtcacaac atatgcaaag atggacaagc ccagttttcc attttcccag gaggattgca 1080 agcaaatcct tcaaatgctc aacaggaaca agtcatcatt tgtcaatcaa gttggtaatt 1140 cttctactca tgaagaactt tcaggtaaag ccttctcttt catacataat ggcacgaaaa 1200 acatatggat cctggacagt ggtgttacgg accacatttt ttgtaacccc aatcttctta 1260 caaattcaaa acctattgaa aactacattg ttgaactacc aaatgggtca tttgccaaag 1320 tcactcatat tggacaaata gtgctctttc ccaatctcat ccttgataat gtcttgtgtg 1380 tgccaccttt taggttgaat ttgatatcca tcaataaact agcctacgat tccctatatg 1440 tcacaatttt tctaaaacat ttttgtgtca tacaggacct acacttgggg aagatgattg 1500 ggatgggaat tgaacgggag gggctctact acctcgatcc accaaagata agaatatgca 1560 acactgttca caccgtgtct ccaaatcttt ggcaccaatg tcttggacat ccatctcata 1620 aagtgtcttt gttatttccc ttttttcata ataagtcttg tgttaccaac aattttttaa 1680 tttgtccttt ggataaacaa acaagatcac catttccttc cagttccatt tctagtaaat 1740 caacttttga attacttcat attgatatct ggggtggtta taaagttgct tccctttcag 1800 gtgccaaata tttccttact attgtcgatg atcatactag gaccacatgg gtctatttga 1860 tgaagcataa atttgacaca aaagatctct tagtcaaatt gatccatatg gttgaaactc 1920 aattcaatac taaggtcaaa ataattagaa gtgacaatgg tcctgaattg aaacttgaga 1980 ttttttatgc tttcaaaggg attattcacc agtctagttg tgtcaacaca ccacaacaaa 2040 atggtgtcgc taaacgcaag cattgacatt tgctcaatgt agctagggcg ttactttttc 2100 aagcctttct gccaaaacat ttttgggggg gatgccatac ttgcttcagc ttacctcatc 2160 aattgtacac caactccact tctccaaggt aaaacacctt acgaaaaatt atttcataaa 2220 gaacctacct attaccattt aagagttttt ggccgtttgt gttttgcctc tacacatgca 2280 cacatacctt ttaaatttga cccctgtgca acacgttgtg tttttcttgg atatctttat 2340 ggacaaaagg gttatcgact gtttgatccc actctgaaga aagtctttgt ttcacgagat 2400 gttgtgttct tggaggacca atttccctat caaaataatt aaacttccgc tgcccaacac 2460 catatcttgc cacctaccca tttcactgct accgtcccat atggcctcct ttaatgagtc 2520 cccaacttta gctgacacat caggggacat ccctcctgat ttttcccctc aacttgctga 2580 ttctactcca ccacttaata cacctacccc accctcatca aacacacacc attcccctac 2640 tttgactctt atttcaccac cctctatcct agacccctca tcacctactt cagcacttcc 2700 ccacccccct tcatcgcagc acgcgtccca ccaaaccttc tacctttttg caggattttc 2760 acttaaaagc aactctcctc tcccgcgttg ttcttaactc ttccacgagc atggttcaat 2820 cgtcaggtac gtctcattct ctctcccgtt atttatcata tgaccacctc tctcataaac 2880 acaaaacctt caccactaat ctcaccctta tcaaggaacc cactagtttt tcacaggctg 2940 tttaggactc caaatggcgt gatgccatgc aacatgagat tgcagcatcc aggcaaatca 3000 tacctggact cttgtgccct taccatctca caaacgtccc attggttgca aatgggtgta 3060 caaagtgaat ctcaaaccta atgggagtgt cgagcgctat taagctcgac ttgttgcgaa 3120 aggttacagt caaatagagg ggattgatta tcgggaaact ttttctcctg ttgccaagct 3180 caccactgtt cgtgtccttc tgagcgttgc tgcacccgtg gttggcatct ttaccaactc 3240 gacgtgaaca atgcattctt gaatggtgat ttgtacaaag atgtctatat gaccttgcct 3300 tctgcgttcg gacgaaaggg ggagactcgt gtatgcaaac taaacaaatc actttatggt 3360 ttaaaacagg cttcaagaca atggtttatc aagctatcca atgccctcaa agtcgctggt 3420 ttccatcaat tatggtctga ttactcattg ttcgttcgaa gtcatcaagg tagttttatg 3480 gcgttactag tctacgttga tgatgtaata tttgcaggaa ataacctaca agagattgaa 3540 gagactaaac gctttctttc ccaacatttc aaactaaagg atttgggaca actcaaatat 3600 ttcctgggaa tagaagttgc aagatcaagc aagggaatta ctttatgtca acgcaagtat 3660 gcgttggaaa tattagacga tgctggtttc cttggatcaa agccttcacc gtttcctatg 3720 gaacaaaatt tttccctcac gcaaacaaat gggacactgt tgagtaatcc atcttcacat 3780 agatggctcg tgggtaggtt aatttattta acaattacaa gaccggacct aacctatgtg 3840 gttcatgtgt tgagtcaatt catggataaa ccacgacaac cacaccttga agcagcacat 3900 aaagtcctta aatacattaa acaggctcct ggacagggaa tttttctacc tactacaggt 3960 tcattgcaat tacaagcttt ttgtgacgct gactgggctc gatgtaaaga cacaagaaga 4020 ctggttattg tatctttctt ggacaagcac ctatctcttt gaagacaaag aaacaaagca 4080 ctgtatctcg ttctagtgta gaggcagaat atcgctccat ggccattacc tgttgtgaag 4140 tcatgtggct caagaatatt ttgaaggact tgcgagtgaa tcatgcataa cctattacat 4200 tattctgtga caatcaagcc atcatgcatt tttcttcaaa ctcagtattt catgaacgaa 4260 tgaaacatat agaaatagac tgtcacctag tacgcgagaa aattcaagga gggatggtgc 4320 gaacaaccta tatacgaata gaaaatcaac tagcagattt attcaccaag ccactgagtt 4380 caacacagtt tgagacctta cttggcaagt tgggtgtcat caacatacac tccaacttga 4440 aggggag 4447 // ID Copia-87_Mad-LTR repbase; DNA; EDCOT; 139 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-87_Mad_; KW Copia-87_Mad-LTR; Copia-87_Mad-I. XX NM Copia-87_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-139 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1713-1713 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 139 BP; 49 A; 13 C; 25 G; 52 T; 0 other; tgtaaataca ctatcaaggg ataatactta gaggttaagg aaagttgtta tttgttatga 60 gttagttagt ctacacaggt gtatatatac ttcagattgt aatcttattc gattgagtaa 120 aatgaaaata tatttctca 139 // ID GYVIT1_I repbase; DNA; EDCOT; 9808 BP. XX AC AM427137; XX DT 25-APR-2007 (Rel. 12.04, Created) DT 15-AUG-2007 (Rel. 12.09, Last updated, Version 2) XX DE Gypsy-type LTR retrotransposon - internal sequence. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; GYVIT1_LTR; internal portion; GYVIT1_I. XX NM GYVIT1_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9808 RA Jurka J.; RT "GYVIT1: Gypsy-type element from Vitis vinifera."; RL Repbase Reports 7(4), 142-142 (2007). XX RN [2] RP 1-9808 RA Obukhanych T., Kohany O. and Jurka J.; RT "Update of a more complete sequence from difference locus."; RL Direct Submission to Repbase Update (15-AUG-2007). XX DR EMBL/GenBank/DDBJ; AM427137; Positions 17607 27414. XX CC LTRs are 96% identical to each other and show no similarity to CC other CC Gypsy LTRs known to date. XX FH Key Location/Qualifiers FT CDS 262..1863 FT /product="GYVIT1_I_1p" FT /translation="MPKWIRDSGGRLVKCDTPQKGEFEVILNIMEAAPEDQ FT HSHQGRQDNLNEFRSMRDRMHPPRMSAPSCIVPPTEQLVIRPYLVPLLPTF FT HGMESENPYAHIKEFEDVCNTFQEGGASIDLMRLKLFPFTLKDKAKIWLNS FT LRPRSIRSWTDLQAEFLKKFFPTHRTNGLKRQISNFSAKENEKFYECWERY FT MEAINACPHHGFDTWLLVSYFYDGMSSSMKQLLETMCGGDFMSKNPEEAMD FT FLSYVADVSRGWDEPTKGEVGKMKSQLNAYNAKAGMYNLKEDDDMKAKLAA FT MTRRLEELELKRMHEVQAVAEAPVQVKLCPNCQSFEHLVEECPAISAEREM FT YRDQANVVGQFRPNNNALYGNTYNSSWRNHPNFSWKARATQYQQPDPPSQQ FT SSSIEQIIANLSKVVGDFVGKQEATNARVDQRMDRVDQRMDRMESMLNKRM FT DGMQNDMNQKFDNIQYSISRLTNLNTLQEKGRFPSQPNQNPKGVHEVESLE FT GESSQVKDVKALITLRSGKKIEQPTPKPHVEKEEEIKK" FT CDS 2009..2908 FT /product="GYVIT1_I_2p" FT /translation="MGKRGVRNAAEILEVLRQVKVNIPLLDMIKQVPTYAK FT FLKDLCTIKRGLTVNKKAFLTEQVSAILQCKSPLKYKDPGSPTISVMIGGK FT VVEKALLDLGASVNLLPYSVYKQLGLGELKPTAITLSLADRSVKIPRGVIE FT DVLVQVDNFYYPVDFVVLDTXPTVKEANLVPIILGRPFLATSNAIINCRNG FT LMQLTFGNMTLDLNIFYMSKKQITPEEEEGPEELCIIDTLVEEHCNQHMQD FT KLXESLVDIEEGFSESPIGLATLQSWXKIEGILPLFNEEXEAAVEKEIPKL FT NLNSAFTC" FT CDS 4832..5878 FT /product="GYVIT1_I_3p" FT /translation="MEHLLAPRDFFYPRVVTDFYQTMTTKEVRNPTLIHFI FT IDGRHGILGARHIAEALQIPFEPTQFDNFKAWTNPTELEMVRTLTRGAANR FT SHLLRGELPPVMFLIDAFLRHNIYPLQHWTQRRGVLLEALYKMSEGFFFGP FT HHLIMAALLYFEEKVHKKKLQRADCIPLLFPRLLCQVLEHLGYPSEPQQER FT KRICREPFTLDKWNNMTAYKIDQPGQPQPAARRASPRHPPXGITLATPAIP FT RASPXAPAPSQPSTSAEPRMAIPISEYRELCRALETLTASQSNLAQELAAI FT KACQEQMLASQAQQAAILRQLQVHFDLPQAVEPSTEDSTRATLSAFRVSXS FT RARSXS" XX SQ Sequence 9808 BP; 3012 A; 1833 C; 2127 G; 2797 T; 39 other; aatggcgycg ttgccgggga atgagtgtca agttcattgt gataccattt ttgagcactt 60 gccgctgatt ttcatcaaca agttggtaaa gtttctttcg ctttactaat tttcattctt 120 tctttgttga ttcataatct aagtttatct ttttaaaatt tagtctagtt taattttgtt 180 gttgtagccc tgtttctctt gttgtcctct gtttttattt aagttgcagg tagatactag 240 ttgtgtatgc ccaagtggat asgagacatt ggaggtaggc ttgttaagtg tgatacacct 300 cagagaggag aattggaagt aatcttgaac atcatggagg ctgcacctga agatcagcat 360 agtcaccaag gtcgtcaaga caatctcaat gaattcagat caatgaggga ccgtatgcat 420 ccacctcgta tgagtgcacc atcatgtata gtgcccccta cagagcagct agtgatcaga 480 ccatatcttg ttcyacttct accaactttc catgggatgg aaagtgagaa tccgtatgca 540 cacatcaagg aatttgaaga tgtttgtaat acattccaag agggaggagc ttcaattgat 600 ttgatgaggc ttaagttatt tcctttcact ttaaaggata aggccaaaat ttggcttaat 660 tctttaaggc caaggagtat ccgctcttgg actgatttac aagctgagtt ccttaagaaa 720 ttttttccta ctcatagaac aaatggcttg aaaaggcaaa tttcaaattt ctcagctaaa 780 gagaatgaga aattctatga gtgttgggaa agatacatgg aagctataaa tgcttgtcct 840 caccatggct ttgatacttg gctattggtg agctattttt atgatggtat gtcatcctca 900 atgaagcaac tcctcgagac aatgtgtgga ggagatttca tgagcaaaaa tccagaggaa 960 gctatggatt tcttgagcta tgtagctgat gtttcaaggg gatgggatga accaactaaa 1020 ggagaagtgg gaaagatgaa gtctcagttg aatgcttaca atgcaaaggc tgggatgtat 1080 aatttgaaag aagatgatga catgaaagca aagttggcag ctatgacaag aagattggag 1140 gagttggagc tgaaaagaat gcatgaagtg caagctgttg ctgaagcacc agtgcaagtg 1200 aagttgtgtc ccaattgtca atcatttgaa catttggtga aggagtgccc tgcaatttca 1260 gctgaaaggg aaatgtatag agatcaagca aatgttgttg gacaatttag gcccaataac 1320 aatgctcctt atggaaatac ctacaattca agttggagga atcatccaaa tttctcatgg 1380 aaggccagag caactcaata ccaacagccg gatccaccat ctcarcaatc ttcaagtatt 1440 gaacaaataa tagccaatct cagcaaggta gtgggagatt ttgtgggaaa gcaagaagcc 1500 accaatgctc gagttgatca aagaatggat agaatggaga gtgtgttgaa caaaagaatg 1560 gatggaatgc aaaatgatat gaaccaaaag tttgataaca tccaatattc aatttcaagg 1620 cttacaaatt tgaatacact gcaagaaaaa ggaagatttc cttctcaacc tcaccaaaat 1680 cccaaaggtg tccatgaagt ggaaagccat gagggagaat catcacaggt gaaagatgtg 1740 aaagctttga tcactctaag gagtggtaag aaaattgagc agccaacacc caagccacat 1800 gttgaaaaag aagaagagat aaagaaaggg aaggaaatgg aagataaaga gaatgagatc 1860 agtgaagaga agaaggactc tgattcaata atgaaagcaa ttccagagaa agagcttctg 1920 aaggaagaaa tgctgaagaa atcaactttt ccaccttttc ctcaagcatt acatgggaaa 1980 aagggggtta gaaatgcagt tgaaattctt gaagtcttga gacaagtgaa agttaatatt 2040 ccactgttgg atatgatcaa acaagttcca acatatgcaa aattcttaaa ggacttatgt 2100 actatcaaaa gagggttgac tataaacaag aaagccttct tgactgagca agtaagtgca 2160 atcttacaat gcaagtctcc tttgaagtac aaagaccctg gaagtcctac catttcagtc 2220 atgattggag gaaaggtagt ggagaaagcc ttgctagact tgggagcaag tgtgaatttg 2280 cttccatact ctgtctacaa gcaactaggg cttggagagt tgaagccaac agcaatcact 2340 ttatctttgg sagatagatc agtgaaaatt ccaagaggag taattgagga tgtattggtt 2400 caagtagata atttctacta tcctrtagat tttgttgttc ttgatactga tccaactgta 2460 aaggaagcta atttagttcc tatcatcctt ggaaggccat ttcttgcaac ttcaaatgca 2520 atcatcaact gtagaaatgg gcttatgcaa ctcacttttg gtaacatgac actggatcta 2580 aatattttct atatgtctaa aaagcaaatc actccggaag aagaagaagg tccagaagag 2640 ctatgtatta ttgatacttt ggtggaggag cactgtaatc aacatatgca agataagttg 2700 aatgaaaatc ttgaggatat traggaaggt ttttctgaat ctcctattgg gcttgctact 2760 ctacaaagtt ggagaaagat agaaggaatt ctacctctgt tcaatgaaga agaggaggca 2820 gctgttgaaa aagaaattcc aaaactcaat ctgaagcctt tacytgtgga gctgaaatat 2880 acatatcttg aagcaaataa tcaatgtcct gttgtgatat cctcatctct gaccagtcat 2940 caagaggatg gtttaatgga agttctcagg aggtgtaaga aggcaatagg atggcaaata 3000 tctgatttga aaggcattag tcctttagtt tgtactcatc atatatatat ggaggaggaa 3060 gcaaagccaa ttcgtcaatt tcaaagaagg ttgaatcctc atctacaaga ggtggtgcga 3120 gctgaggtgc tgaagctact tcaagcagga atcatttacc ctatatctga tagcccttgg 3180 gtgagtccta ctcaagtggt accaaagaag tcagggatca cagtgattca aaatgaaaaa 3240 ggggaagaaa ttactacacg cctcacttca ggttggaggg tgtgtattga ttatagaaag 3300 ctgaatgctg tcaccaggaa ggatcatttt ccattgccat ttattgacca agtgctggag 3360 agagtctctg gacatccatt ctattgtttc ttagatgggt attcagggta ttttcatatt 3420 gaaattgatt tggcagatca ggaaaagacc acttttacat gtccatttgg aacatttgct 3480 tatagaagaa tgccttttgg tttatgcaat gcacctgcta catttcaaag atgtatgttg 3540 agtattttca gtgatatggt ggagagaatt atggaggttt tcatggatga catcactgta 3600 tatggaggta catttgagga atgcttggtt aatttggaag cagttcttca tagatgcatt 3660 gaaaaagatt tggtgctgaa ttgggaaaaa tgccatttta tggttcgtca aggaattgtc 3720 cttggccata tcatctctga aaaaggcatt gaagttgata aagcaaaagt ggagcttatt 3780 gccaaattac catmtccaac aactgtgaaa ggagtaagac agttccttgg ccatgcaggg 3840 ttctatagaa ggtttataaa aggtttttca agtctttcaa aacctctttg tgagctgtta 3900 gctaaggata ctaagtttat atgggatgaa aggtgtcagc atagctttga tcaactgaag 3960 aagtttctaa taacaactcc aatagtgaga gcccctaact ggcaattacc ttttgaactg 4020 atgtgtgatg ccagtgactt tgctatagga gctgtgcttg gccaaagaga agatgggaag 4080 ccctatgtga tttactatgc aagtaaaaca ctaaacgaag ctcagaggaa ctayacaact 4140 acagagaaag aattgttagc tgtggtattt gctttggata aatttcgagc ttatttagtg 4200 gggtctttca tcattgtctt tactgaccat tcagccttga agtatttatt gacaaaacaa 4260 gatgcaaaag caaggttgat tagatggatt cttttgttac aagaattcga tcttcaaatc 4320 aaagataaga aaggagtgga gaatgtagta gctgaccact tgtcaaggtt agttatagca 4380 cataattccc atcccttgcc tatcaatgat gattttcctg aagaatcact catgttccta 4440 gtgaaaactc cttggtatgc tcatattgct aattatttag taackggtga aattccaagt 4500 gagtggaatg cataggacag gaagcacttc tttgccaaaa ttcattctta ttattgggaa 4560 gagccctttc tctttaagta ttrtgcagat cagattatta ggaaatgtgt ccctgaagat 4620 gagcagcaag ggattctatc tcattgtcat gagaatgcat gtggaggcca ctttgcctct 4680 cagaaaacaa ccatgaaggt attgcaatca gggtttactt ggccctctct tttcaaagat 4740 gcccacatca tgtgtaggag ttgtgataga tgccaaaggc ttggaaagct aacaaaaaga 4800 aatcaaatgc ctatgaaccc cattctaata gttgagttat ttgatgtatg gggcattgac 4860 ttcatgggac ctttcccaat gtcttttggt aattcttaca ttttggtagg ggtagattat 4920 gtttctaaat gggttgaggc aatcccctgt aagcaaaatg atcacaggat ggttctcaag 4980 tttcttaaag agaacatttt ctcaagattt ggggtgccca aggccataat cagtgatgga 5040 ggtgctcatt tttgcaacaa accttttgaa gctctgttat ccaagtatgg agtgaagcat 5100 aaggtggcca caccttatca tcctcagact tctggccaag ttgagctagc taacagggaa 5160 ataaagaaca tattgatgaa agtggtgaat tccaacagaa aagattggtc tattaggctt 5220 catgattcat tgtgggcata tagaacagct tataagacta ttctagggat gtctccctat 5280 cgtcttgtct atggcaaagc atgccatctc cctgtggaag ttgaatacaa ggcttggtgg 5340 gcaataaaaa agctgaacat ggatttgatc aaggccggag aaaagagatt tctagacctt 5400 aatgagatgg aggaattaag aaataatgct tatatcaatt ccaaagttgc aaaacaragg 5460 atgaagaagt ggcatgatca acttatctcc aacaaggaat ttcaggaagg gcaaaaagtt 5520 ttgatgtatg acacaagact ccatatcttt cctgggaagc tcaaatcaag gtggattggt 5580 ccatttgtta ttcaccgagt atattccaat ggagtggtgg acttattgaa ttccaatggc 5640 aaagacagct ttagagtcaa tggatatcgt cttaagccgt tcatggagtc atttaaatca 5700 gaaaakgagg caatcaacct ccttgaacct caaaaagcct aagtgaaaag ggtttgctgg 5760 acgtggtctt aaccacaatc caaaattttt gtaaattttg taaaatttca agttgtttcc 5820 atacttttga tcttagtttt tgatcttaaa ttatgttttt aggtatgttt taatcgtttt 5880 aaatgatccc aggtggaaga aatttcaagg agattgaaaa gaaaaaaatc gggccgaaat 5940 tggagccgaa acagagcaaa aacaggggaa aagtcaacag agctctgcga aatmmrttcg 6000 cagagagaag gaaactcctg cgaagtgagg cgttcrtyct tgttgccaac cwcattccgc 6060 agcactgtac aagtctctgc tkgacgtgta tttawycgca attgcgaaag tggttttggc 6120 acacgagtgc cactttgcag tacagtagca cccatmcttc gcagctgcga aactcattgc 6180 gaaykatgtw gaaaagcgtg attkawtcgc accaaaagat cccattccgc agggcatttc 6240 wwkgcaattg cgaaagtggt tttggcacac gagtgccact tcgcagcaca gtgacatcaa 6300 tttcgcagct gcgaaactca gctctgcgaa gtttcgctgc gaaaatggca agttgctgcg 6360 aaattggcgt tttgttgcga aacttaaact gacccctgag cttctgtttt tcctagttta 6420 taccggtcaa aagtgctgcg aaaagggttt caaaaatcag agcaccattc tcgcagcccc 6480 ttcgtcttca tttcgccaag ccacgccgtc cgtttctcca tggtaaagcg tcttctcygt 6540 ttagcagtcg ccgaccaaag atcgatattc caaaatggca cgaacgcgag gggcaaagtc 6600 ttcatcccct tcgaaccgca aaaggagtct gcaaaaggag ccaagtccag gttctgttcc 6660 agaacctgct ccaaagcctt cgccgtcgag accaaatcct ccttcagtga agccggcgcc 6720 accaaagccr ccggcaaggt gatatttaac aaggtcaggc ggtcagccat tgaagaagaa 6780 aaccagggtt gagagctcta aaccaattga tttgactgag caatcccctg agaaatcccc 6840 aaagctaaca ccggttcaat ctccggtatc ttcaccaaat ccttcaccgg tacaaattcc 6900 agagccgtca ccggttccct cgccaattcc ctcaccagaa gcaactccaa ttccattgcc 6960 ggtaccatct ccggcacccc aagaaaaagc tcaggagcct caagcgccaa ttccagagcc 7020 ccaaattgca gctgaagcac ctctggaaga agtgatccga aggccaatgc tgccccagcc 7080 cccaatcgaa ggaaacttgg attgtcgaac tcgggcattc cattctgagc tttgcttcga 7140 tttaacagca ttcagagtga ggccagagct tgcccaatcc ttccagctgc tgaggagata 7200 tcatatggag catctgctag ctccaaggga ttttttctat ccccgggtag tcacggactt 7260 ctaccagacc atgacaacca aagaagtaag aaatccaact ctgatccatt tcataattga 7320 tggaagacat ggaattttgg gagcaagaca tattgttgaa gccctgcaaa ttccttttga 7380 gccaacccaa ttygacaatt ttaaagcttg ggcaaatcct actgagttag agatggttcg 7440 caccctaact agaggagctg caaatcgatc gcatttgctg aggggggagc tacctccagt 7500 tatgtttttg attgatgctt ttttgaggca taatatatat cccctgcagc attggaccca 7560 aagaagggga gttctcctgg aagctctgta caagatgtca gaaggattct tctttgggcc 7620 tcatcatctg atcatggcag cccttctata ctttgaggaa aaggttcaca agaagaagct 7680 tcaaagagca gattrcattc cactcctctt cccacgrctg ctatgccaag ttttggagca 7740 tctcggatac ccctctgagc ctcagcagga aagaaagaga atatgccatg agccatttac 7800 ccttgataaa tggaataata tgacggccta caaagttgat cagcctgggc agcctcagcc 7860 agcagcaagg agagcctccc caagacatgc acctgaaagg tataacactt gctactcctg 7920 ccatccctcg agcttcacca gctgcacctg ctccatcaca gccatccaca tcagttgagc 7980 cgaggatggc catccctata tccgaatatc gagagctgtg ccgagcattg gagactctta 8040 cagcttccca gagcaatctt gctcaggagt tggcagctat caaagcatgc caggagcaga 8100 tgttagcctc tcaggctcaa caagctgcca tcctaaggca gcttcaagtc catttcgatc 8160 tgccacaagc tgtagagccc tccactgaga ctccaccaga gccacactct cagccttcaa 8220 agtctcatcc tccagagcca gaagccccag ctgatccacc tactgaggag gcagatcctt 8280 ctgcctagca ctatcacccc actcatcaga cattatatat atttgctatt tatgttttta 8340 tgcttgtttt gttttagttg aaaagaaatc ccagtatttt ggtatattta tgggattcct 8400 tgtgttactt gtccttagca ttgtaatcaa atgaacagaa agtaatacaa gttgaatttt 8460 tcttattaaa agttagcatt aagttctcct tatttctttt tctcacatat tctatttttt 8520 ttgaaacatg tggttttccc caatcaatat tcgaatttga tatcagcatg gaggtaccac 8580 ttcctccctt ttattacaat cactcaaatc acattgagga caatgctcag ttcggttggg 8640 gggtatgagg aaggaagtag tctaaacctt tttggtattg caattatatt ggttaattag 8700 ttgtaaattt tactttttac tcttgttact ctattctcca tgaattttga rgaaaaattt 8760 tcaaattaaa ccaagagaaa ttgaactgtt gtttttcact tgacttagag tatggattat 8820 gcttactaaa gtggtttaat tgttgaaact tctactgaaa ttgaattaag ttcttccact 8880 ttaagctatc cacacactgt gcacattagt ttccgattat aagatgraaa gctatttccc 8940 tcttgactta ggataatttt gagacttggt atatttgacc tcatttgata aaaattgaaa 9000 caccctgcca aaaggccaat gagcctttga aataaagaaa gttgtttgct tgccttgaaa 9060 cccgagcaag gtctgagggg tatatggtga aagcctttaa agcctggtgc cctaagcctt 9120 aattggttgg gagtcaccga cctcaatgct cgttacaagg gtgaataggt agagttagca 9180 tatggtagat gcttgggtat tagaaactca ttcttaaaag tccggggaaa aatccgagga 9240 gttagtggtt gaaagatcct taaaacttgg tgccctaaac cttaattggt tgggagtcat 9300 cgatggaccc ccattacatg gacaagtcag aaagagtacc ccataaagct accttaaaaa 9360 aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaagatga tgaaagtgtg ttattttctt 9420 attgattttg gtcaggttgc taaagtgttg aaaagagata ggttgggggg gagactagtt 9480 tagcatatta ttctcggaag ctaaggaacc aatacacata gatttttgtg gaagattgaa 9540 gtttagttct ttaaaagggg aaatgatttt aaaacttcag tttacataat gcactccctt 9600 gattgacagt gtttagcata ggtgttatga ctcttgttga gatttgggtt tgtatttctt 9660 taatgattca tgtgagaagt aaatcatcat gccacttgag aattgatttt gtttagcatg 9720 atgttgtaaa ttttagatta gttgctattt attttcattt ttctctcctt tattgctaag 9780 ggactagcaa tatgtcggtt ggggggag 9808 // ID HAT-12_Mad repbase; DNA; EDCOT; 3669 BP. XX AC . XX DT 03-NOV-2010 (Rel. 15.11, Created) DT 03-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-12_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-3669 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1901-1901 (2010). XX DR [2] (Consensus) XX CC TSD is 8-bp long. TIR is not obvious. XX FH Key Location/Qualifiers FT CDS 1185..3536 FT /product="HAT-12_Mad_1p" FT /translation="MERFFKKISVPPSPVIEKNNDTRGXDSAEFILSNLPS FT DPGKRIRILDYNPNIRDQVRRAYVLAGPQQPKTHNFPYKKYGDTQRRFNPA FT WFDDFPTWLEYSVEKDAAFCLCCYLFKPNIGEQAGGDFFVGEGFSNWKKKE FT RLLTHIGGVNSAHNQAWSNFEALRSQKQHIQSFFSKTHDEARIQYRARLNA FT SIDCCRFLLRQGLAFRGNDESEHSSNHGNFLELLQFLADHNEDVKAVTLKN FT APENHKLTSPDIQKDIVNACATETIKAIIEDVGTSLFSILIDESRDVSTKE FT QMAIVLRYVDKNGHVVERFIGIEHVTSTAALSLKETIDEVFSRHKLSMSRL FT RGQGYDGASNMQGEFNGLKALIMKESGCAYYIHCFAHQLQLALVAVAKKNI FT QIESLFSIVTILVNVVGASSKRCDLLREKQSIAVIEALNSGEFTSGKGKNQ FT ETTLKRAGETRWGSHFGTLVSIMTMFSSILDVLEVIADDGVSSQQRCEANN FT LLDSMQSFDFVFNLHLMKDILGITNELSQALQRKDQDIVNAMKLVGVCKQR FT LEIMRKSGWDSLLSEVSEFCLKHDIDVPNMDDMFLSRRRGQRKAQAVTNMH FT HYCVGIFYVVLDWQLQELNNRFNETNTELLLCLACLCPADSFSAFDSQKLL FT RLAQFYPKDFSMNELVILKIQLETYIVDMRSSIEFSGLKEIGDLAKKMVQC FT KKHKVYSLVYLLVTLALTLPVATATVERAFSAMKILKNRLRNRMGDQWMND FT NMVIFIEREIFDGIGNDVVMQRFQNMKTRRGIL" XX SQ Sequence 3669 BP; 1094 A; 609 C; 764 G; 1200 T; 2 other; caagggcgga gctaccatgg gcctaggggg cggatgcccc cactgagatt tttctgatgc 60 tggcatgctc atctgtttct gcagcagcaa agcccccact gcgattttga gcagcagcaa 120 agcccccact acaattttct ggttcctccg atctgggtct ttctaaacca ggccaaaggc 180 aagacgaacc tctgcagagg cctggtctga tttttttttt aaatgtaaac gaaacggcgt 240 cgtttcgtat atgtttaaaa aaaacaaaaa aaagttatgt tatagtatta gtgggggacc 300 gcttgtcccc acggtccaga ctcccattcc ttctttcttt tcctcccttt gttttcgttg 360 ccctttgcgt cagagagcag cttggtgctg ctctgtttgt cttccccaaa gtccaaacca 420 acaccttgaa agttgctctc ctgtccaggt gctctctgga gcaaagttgc tcttcccagc 480 catgccagca gccagccatt ctctagtctc tagccgacaa tatatatata tatatttagg 540 taaatttttt aattcctaaa tctataatcc ctaaccctaa ttaattattt aagacgaatt 600 tttgtttaat tggtatagaa atatagaatc atatggatat ggtcatgcac taatatggat 660 ggttattgac ttattgatta ttgatatgat gaattctatg attattgatg aatgaaatta 720 tgaaattacg aattctatga atatgggtat acatttattc atatgattag ttgaattaaa 780 tgtttatttg ttgaataatt tgtatgctta ttggtattgg ttaattgaat tgttgccttg 840 gttggatatg ggttagttat taggcattta ttttattttt tggtcaagaa ggcacatgta 900 ttatttatat ggataacgtt gtcaacatct ccaagaaaac tcaattctac ggcttaacag 960 tctaaaaaca aatccatttt tcagaaatgg aatcataatc atcccctttc gaaacccaaa 1020 aaagaagaag aaatggatta gttattatta ggcatattag tatagtatac tctaggatta 1080 agagtctaag aattttattg agatttttat tctataaatt ctacaaatta cgtatgaacc 1140 ttatatgtta ttggtatatg actgactttg caggctgaaa catcatggag aggtttttca 1200 aaaaaatatc agtgccgcca tccccagtta ttgagaaaaa taatgatact cggggacawg 1260 atagtgcaga atttatttta tcaaatcttc catcagatcc tggtaagmga attcgaattt 1320 tggattacaa tcctaatatt cgagatcaag tacgaagagc gtatgtgcta gctggtcctc 1380 aacaacctaa aacccataat tttccttaca agaaatatgg agacacgcaa agacgattca 1440 accctgcttg gtttgatgat tttcctactt ggttggaata tagtgtagaa aaagatgctg 1500 ccttttgtct gtgttgctac ctttttaaac caaacattgg agaacaagca ggtggtgatt 1560 tctttgttgg cgaaggattt tctaactgga agaagaaaga aagacttcta actcatattg 1620 gaggcgtcaa tagtgcacac aatcaagcgt ggagtaattt tgaagcttta aggagtcaaa 1680 agcaacatat ccagtctttt ttctctaaaa ctcatgatga agctcgaatt caatatagag 1740 ctcggttgaa tgcatcaatc gattgttgtc gatttctttt gagacaaggg cttgcatttc 1800 gtggtaatga tgaatctgaa cattcaagca accatggaaa ctttcttgag cttctacagt 1860 ttcttgccga ccacaatgag gatgtgaaag ccgttacttt gaaaaatgct ccggagaatc 1920 acaaattgac atcaccagat attcaaaaag acattgtaaa tgcttgtgca actgagacga 1980 tcaaggctat tattgaagac gttggcactt cgttgttctc tattttgatt gatgaatctc 2040 gcgacgtatc aacgaaggaa caaatggcta ttgtattgcg ttatgtggac aagaatgggc 2100 atgtcgttga gcgttttatt ggcattgagc atgttactag tactgctgct ctctcactca 2160 aggaaaccat tgatgaggta ttttctaggc ataaattgag catgtctagg ttgcgtgggc 2220 aaggttacga tggggccagc aatatgcaag gtgagttcaa tggtcttaaa gctcttatta 2280 tgaaagaaag tggttgtgcc tattatattc attgctttgc acatcaactt caattagctc 2340 ttgtagctgt ggcaaagaag aacatccaaa ttgagtctct ttttagtata gttactattt 2400 tggtaaatgt tgttggagct tcatcgaagc gttgtgatct tcttcgggag aagcaatcta 2460 ttgcagttat tgaagcacta aacagtggtg agtttacaag tgggaaaggc aaaaatcaag 2520 aaactacttt gaaacgtgct ggagaaacac gttggggttc acactttggt actttagtaa 2580 gtataatgac tatgttttca tccatacttg atgtacttga agtaatagca gatgatggag 2640 taagctctca acaaagatgt gaagcgaata atttattgga ttccatgcaa tcatttgatt 2700 ttgtgtttaa tctacacttg atgaaagata tactaggaat aaccaatgaa ttgtcacaag 2760 cattgcaaag gaaggatcag gatattgtaa atgccatgaa gttggttgga gtttgtaagc 2820 aaaggttgga gataatgagg aaaagtggtt gggattcttt acttagtgaa gtctcagaat 2880 tttgtcttaa acatgatatt gatgtgccta atatggatga tatgtttctt tctcgaaggc 2940 gagggcaacg aaaagcacaa gcagtcacaa atatgcatca ttattgtgtt gggatatttt 3000 atgttgtttt ggattggcag cttcaagaac taaataatcg tttcaatgag accaacactg 3060 agttacttct ttgtttggca tgtttatgtc cagccgactc cttctctgct tttgatagcc 3120 aaaagctatt gcgtcttgcc cagttttatc ctaaagactt ctctatgaat gagctggtga 3180 tacttaagat tcaacttgag acttacattg tggatatgcg gtctagcatt gagttttcag 3240 gtttaaaaga gattggagat cttgcaaaaa aaatggttca atgcaagaaa cacaaggtgt 3300 attcgctggt ttacttgctt gtgacattag cactaactct tccagttgct actgcaaccg 3360 ttgaaagagc attttcggcc atgaaaattc tgaagaatcg attgagaaat cggatgggag 3420 atcaatggat gaatgacaac atggttattt ttatagagag agagatattt gatggtattg 3480 gtaatgatgt tgtcatgcaa cgctttcaga acatgaaaac gcgtcgaggg atattgtaag 3540 ggactgttgt atgaaaaact ttatggatta atatataagt attgtgttta gtaaattctt 3600 gagcttttta attatgactt tgttgtttga ggatgccccc attcacacaa atctctggct 3660 tcgtccctg 3669 // ID Copia24-PTR_I repbase; DNA; EDCOT; 4674 BP. XX AC LG_XVIII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia24-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4674 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4674 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 222-222 (2007). XX DR Genome; LG_XVIII; Positions 5893986 5898659. XX CC Positions [2063-2563] - Integrase core CC 'CTTAG' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 737..3811 FT /product="Copia24-PTR_I_1p" FT /translation="MTTKFDYVVCSIEESNNLAEMTIDELQSSLLVHEQRM FT RGHKEEEQVLKVMSEAREDARFGGRGRNRGGFRGNFRGRGRSWGRQSFNKA FT IIECFRCHKLGHFSYECPGYEKKANYAELECEEEMLLLSHVEIHDFTELHE FT EIMMTEVNAEEEMVLTKELNAEEMVRPEELNAELHDFAELHEEKVLTLTEE FT LNAELHDVAELHEEKVLTYLNEEEMVLTEWHEEDEMVLTELNAEEEMVLMS FT HVELHNSTREEVWFLDSGCSNHMSGNKLWFTELDEKFRHSVKLGNNSRMAA FT MGKGYVKLKVAGAIQRIDEVYYIPELRNNLLSIGQIQEKGLAILIKGNTCK FT LFHPTKGLIMEIAMTVNRMFIMLATIPPKESVAFFQTSEESEAQLWHSRFA FT HLNFKGLRMLYYNKMVNGLPLLKAPTKVCADCLSGKQHRDNISKKSHWKAT FT HKLQLVHSDICGAVNPESNSGKRYLITFIDDFSRKCWVYFISEKSYAFNMF FT KKFKNLVEKEAGSLVECLRTDRDGEFTSKEFNEYCSMNGIKRQLTTTYTPQ FT QNGVAERKNLTIMNLVRSILAEKHIPREFWLEDVNWCIHTLNRSPVAAIKE FT VTPEEAWSGVKPSVGYFRVFGCIGHVHVPNERRTKLDSRSMKCILLGVSEE FT TKGYRMFNPLTKKLIISRDVIFEENATWNWAADNTSNTLSRGDNNDSIHEE FT ELEEDEEQIGDDVAADTSEQIGDDVAAETSAADVAEPEAEEENENLPQAGV FT RNRRAPQWMEDYVMGANIAEEEETQNMVLYTTAGDPHTYEEAKKNQQWRAA FT MDNEIAAIERNDTWELTVLPNNSRKIGVKWIYKTKLNEKGEVDKYKARLVA FT KGYAQQHGIDYTEVFAPVARWDTIRMVLAIAAQRKWKVYQLDVKSAFLHGK FT LDEDVYVEQPLGYEKKGEEHKVLKLKKALYGLKQAPMAWFSRIETYFVKEG FT FARCPSEHTLFVKIEEDKKILIVCIYVDDLVFTGSDEGMFADFKASMKREF FT DMTEFRQNEVFSWSRSCAE" XX SQ Sequence 4674 BP; 1720 A; 693 C; 1145 G; 1116 T; 0 other; attggtatca gagcctttta tcaagagaga agagtgaaag aacacgagaa agagaagagt 60 gacacacgag aggagtgtga gcaattagtg agaaagagaa gagtgaaaca cgagaggagt 120 gtgagcaatc agtagcaagg agtgtgtggg tagagtaaaa aaaaaaaaaa aaggggagtg 180 aaacgagtga aacacagaga ggagaggagc gaaatcaaag tgaaatcaaa gacaaattca 240 tggcagaggg aaattttgtc caacctgcaa ttcccagatt tgatggtcac tatgatcact 300 gggcaatgtt aatggaaaat ctgctacgat ccaaagatta ctggagctta atagagagtg 360 gaattcctgc aagcacaact ggagctgaag cagaactcac agaggtccag cagaaacaca 420 tggaggagat gagattgaaa gatttaaaag tgaaaaatta tctttttcaa tccattgatc 480 gaactatcat ggaaacaatc ctgaatagag attctgcaaa agggatatgg gattcaatgc 540 cccagaaata tcaagggtcc actaaggtga aaagagcaca actacaagca ctgcgaagag 600 aatttgagct acttggaatg aaggatggtg agagtgttga tgagtacttt ggaagaactc 660 ttaccattgc caacaaaatg aaaacacacg gtgaaagaat ggagcagatt gttattattg 720 agaaaatttg aggtctatga caacaaagtt tgactatgtc gtatgctcca ttgaagaatc 780 aaataatctt gctgaaatga ctattgatga acttcaaagt agtttacttg tacatgaaca 840 aaggatgagg gggcacaaag aggaagagca agttcttaag gtcatgtctg aagcaagaga 900 agatgctcga tttggaggaa ggggcagaaa ccgtggagga ttcagaggca atttcagagg 960 cagaggcagg agctggggaa gacaatcttt caataaagct attattgaat gttttagatg 1020 tcataaacta gggcattttt cttatgaatg tcctggttat gaaaaaaaag ctaactatgc 1080 agaattggag tgtgaagaag aaatgttatt gttgtcacat gtggaaattc atgatttcac 1140 agaattacat gaagaaatca tgatgacaga agtgaatgca gaagaagaaa tggtgctaac 1200 aaaggaattg aatgcagaag aaatggtgcg gccagaggaa ttaaatgcag aacttcatga 1260 ttttgcagaa ttacatgaag aaaaggtgct gacgctgaca gaggaattga atgcagaact 1320 tcatgatgtt gcagaattac atgaagaaaa ggtgctgaca tatttaaatg aagaagaaat 1380 ggtgctgaca gaatggcatg aagaagacga aatggtgctg acagaattga atgcagaaga 1440 agaaatggtg ctgatgtcac atgtggaact tcataactca actagagaag aggtatggtt 1500 tttggattca ggttgcagca atcatatgag tgggaataaa ctatggttta cagaattaga 1560 tgaaaaattt agacattcgg tcaagcttgg caataattca agaatggcag caatgggcaa 1620 ggggtatgta aaattgaaag tagctggtgc aatacaaaga attgatgaag tttattacat 1680 tccagagctg agaaacaatt tactcagtat agggcaaata caggagaaag gtttagcaat 1740 actgattaaa ggtaatacat gcaagctatt tcatccaact aaaggcctca tcatggagat 1800 agctatgaca gtcaacagaa tgttcataat gcttgcaact atacctccaa aagaatcggt 1860 ggctttcttt caaaccagtg aagaaagtga agcacaacta tggcatagca ggtttgctca 1920 tctcaacttc aaaggattaa ggatgttgta ttataacaag atggttaacg ggctgccact 1980 acttaaagct cctaccaaag tatgtgcaga ttgtttaagt ggcaagcaac acagagacaa 2040 catttcaaag aaaagccact ggaaagcaac acacaaacta cagctcgtcc actctgacat 2100 ttgtggagcc gtgaatccag aatccaacag tggcaagagg tacctaatca ctttcattga 2160 tgactttagt agaaagtgtt gggtttattt catttcagaa aaatcatatg ctttcaatat 2220 gttcaaaaaa ttcaagaatc tagtcgaaaa agaagctggt tccttggtgg aatgtttacg 2280 cacggataga gatggtgaat ttacttcgaa agaatttaat gagtactgca gtatgaatgg 2340 gatcaagaga caattaacga ccacgtatac tcctcaacaa aacggtgttg ctgagaggaa 2400 gaatctgaca ataatgaatc tagttagaag catattggct gaaaaacaca ttcccagaga 2460 attctggcta gaagatgtaa attggtgtat acatacacta aatagaagtc ctgttgcagc 2520 aataaaagaa gtcacccctg aagaagcatg gagtggagtc aagccttcag taggatattt 2580 tcgagtattt ggctgcattg gccatgtaca tgtacccaat gagagaagaa caaagctgga 2640 ttcaaggagc atgaaatgca tactgttggg agtcagtgaa gaaaccaagg gctacagaat 2700 gtttaatcct ctcacaaaga agttgataat cagccgagat gtcatatttg aagaaaatgc 2760 aacctggaac tgggcagcag acaacacaag caacacacta agccggggag acaacaatga 2820 cagtatacat gaagaagaac tagaagaaga tgaggagcag attggagatg atgttgcggc 2880 agatactagt gagcagattg gagatgatgt tgcggcagaa actagtgcag cagatgttgc 2940 agaacctgaa gcagaagaag aaaatgaaaa tttgccgcaa gcaggtgtta gaaatcgaag 3000 agcaccacag tggatggagg attatgttat gggagcaaac atagctgaag aagaagaaac 3060 acaaaatatg gtgttataca ctactgcagg agatccacac acctacgaag aagctaaaaa 3120 aaatcaacaa tggagagcag ccatggacaa tgaaattgct gcaatagaaa ggaatgacac 3180 atgggaatta actgtgctgc cgaataattc aaggaagatt ggggtaaaat ggatatacaa 3240 gacaaagctc aacgaaaaag gtgaagttga taaatacaag gccagacttg tagcaaaagg 3300 atatgcacag caacatggaa ttgactacac cgaggtattc gcaccagtag caagatggga 3360 cacaattcgg atggttctag caatagcagc acaaagaaaa tggaaggtgt accaactgga 3420 tgtaaagagt gctttccttc atggaaaatt agacgaagat gtatacgtag agcaacctct 3480 cggctatgag aaaaagggag aagaacacaa agtcctcaaa ttgaagaaag cattatatgg 3540 tttgaaacaa gcaccaatgg catggtttag caggattgaa acatactttg tgaaggaagg 3600 ttttgctcga tgtccaagcg agcatactct gtttgttaaa attgaagaag acaagaaaat 3660 tctgatagta tgcatatacg tagatgattt ggtgttcact ggaagtgatg aagggatgtt 3720 tgctgatttc aaagcctcaa tgaaacgaga gtttgatatg acggagttta ggcaaaatga 3780 agttttttct tggagtagaa gttgtgcaga atgatgaagg aatttattta agccaaagaa 3840 aatatgcact agaagtacta gagagatttg gcttagaaaa ggcaaattcc gttcgcaatc 3900 caatgatacc aggtatgaag ctgatgagaa atgaagatgg cgagcaagtg gatgtaactc 3960 aatacaaaca aatggttgga agtctcatgt atttatcagt aaccaggcca gatctcatgt 4020 ttgggattgg tttgatcagt agatacatgg agaaacctac aactttacat atgcatgcta 4080 ttaagagaat tctgagatat gtgaagggat ctgtaaactt gggcattcat tataaaagaa 4140 aagctgcagg tgacgaaaga ttaatggcct actctgacag tgattatgct ggggatcaag 4200 atgactgtag aagtacttcg ggatatgttt tcatgttaag tgaaggagca gtagcttgga 4260 gctccaagaa acaaccagta gtctctttat caactactga ggcagaattt atatcggcag 4320 ctcattgtgc gtgccaagcg gtatggatga gaagagtact tgaaaggata gattgcaagc 4380 aaggaacaca tactatcata cactgtgata atatgtcttc aattaaatta gcaaagaatc 4440 caattatgca tggcaggagc aagcatatag atgttagatt tcattttcta cgtgagctgt 4500 gcaaagaagg agtaattgag ctgaaacact acaacacgca agatcaaatt gctgatatca 4560 tgacaaaggc tttgaagatg gatacatttg agaaactaag aggtttgctg ggtgtctgtg 4620 aggtaccaac cgaataaact gctagttaac aactatgcag tttaagggag ggat 4674 // ID TVF5_VF repbase; DNA; EDCOT; 239 BP. XX AC AJ243103; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Vicia faba Ty1/copia-type retrotransposon TVF5_VF, partial RNase DE H gene for Ribonuclease H and 3'LTR. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; KW retrotransposon; TVF5_VF; Ty1/COPIA superfamily; Ribonuclease H. XX OS Vicia faba OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Vicia. XX RN [1] RP 1-239 RA Pearce R.S., Stuart-Rogers C., Knox M., Kumar A., Ellis H.T. RA and Flavell J.A.; RT "Rapid isolation of plant Ty1-copia group retrotransposon LTR RT sequences for molecular marker studies."; RL Plant J 19(6), 711-717 (1999). XX DR Genbank; AJ243103; Positions 1 239. XX CC gene 1..87 CC /gene="RNase H" CC /product="Ribonuclease H" CC misc_feature 76..81 CC /gene="RNase H" CC /note="Polypurine tract (PPT)" CC LTR 83..>239. XX SQ Sequence 239 BP; 70 A; 37 C; 47 G; 85 T; 0 other; gctgacattt ttatcaaggc acttgatgca aatcaatttg aaaacttgag gggcaagttg 60 ggtatttgcc aacatgagga attgtagcaa ttaattttgc ttaaaacaag ggttgaagga 120 gttatttttg ttaagtctat tttgattggg ttaatcatat gttttcccca attctttcaa 180 aaattattaa gaaggttgga atagacactc atttgcctcc ttccactctc gctcaggat 239 // ID Copia1_I_MT repbase; DNA; EDCOT; 1417 BP. XX AC . XX DT 24-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE Internal region of LTR retroposon, Copia1_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW internal region; LTR; retroposon; Interspersed Region; KW Copia1_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1417 RA Shankar R. and Jurka J.; RT "Copia1_MT: LTR retroposon from Barrel Medic."; RL Repbase Reports 6(11), 557-557 (2006). XX DR [1] (Consensus) XX CC The ORF shows presence of an integrase domain. XX FH Key Location/Qualifiers FT CDS 47..883 FT /product="Copia1_I_MT_1p" FT /translation="MGSKWDIEKFTGLNDFGLWKVKMQAVLIQQKCEKALK FT GEGGLPDTMSQEEKTEMVDKARSAIVLCLGDKVLRDVAKEPTAASIWSKLE FT SLYMTKSLAHRQFLKQQLYSFKMVESKTVMEQLAEFNKILDDLENIEVQLE FT DEDKAILLLCALPRSFESFKDTMLYGKEGTVTLEEVQAALRTKELTKSKDL FT RADENSEGLSVSKGNGGGRGSRGSSKSGNKDKYKCFKCHKLGHFKRDCPEE FT DDSSAQVVSEEYGDAGALMVSCWEEGEGEGSHLGIDSL" XX SQ Sequence 1417 BP; 388 A; 214 C; 471 G; 344 T; 0 other; ggcgcccacc gtggggcaac ggtagtgatt tggtttagtg tgtaccatgg gttcaaagtg 60 ggatattgag aagttcaccg ggctcaacga ttttgggttg tggaaggtga agatgcaagc 120 ggtgttgatt caacaaaagt gtgagaaagc tttgaagggt gaaggtggtt tgccggacac 180 catgtcacaa gaggagaaga ccgagatggt ggacaaggcg aggagtgcca ttgtcttgtg 240 cctcggggac aaagttttga gggatgtcgc gaaggaacca accgcggcat cgatatggtc 300 taagttggaa tcgttgtata tgaccaagtc gttggctcat aggcaattcc ttaagcaaca 360 actctactca ttcaagatgg tggagtcaaa gaccgtgatg gagcaattgg cggagttcaa 420 caagatcctc gacgatttgg agaacattga ggtgcaactt gaggacgaag acaaggctat 480 actcttgttg tgcgcactac cgaggtcatt tgaatccttt aaggatacca tgctctatgg 540 caaagaaggc actgtcacct tggaagaagt tcaagcggct ttaagaacca aggagttgac 600 caagtccaag gacttgagag cggatgaaaa cagtgaaggc cttagtgtgt caaaaggaaa 660 tggtggaggt agaggcagcc ggggaagctc aaagagcgga aacaaggata agtataagtg 720 ctttaagtgt cacaagttgg gacacttcaa gagggattgt ccggaggaag atgatagctc 780 cgcgcaagtt gtgtccgagg agtatggaga tgcgggtgct ttgatggtga gttgttggga 840 ggaaggtgaa ggtgagggtt ctcaccttgg tattgattcc ttgtagatgg tgtggttcgt 900 ctggagagac gttaaacact caacgtcagc ctggagaggc ggtggtgaga atactcatgg 960 ttagtctgga gaggcggtgt taacaatact cgtgatcaac ctttgaggtg gagtggcaag 1020 gcggaagcat agtggaagta ctcatttgga agttgaggta gagaaagctc aacttgaggt 1080 ggagttggtg actccgggaa tggtacggct atggaggctt tgggagttta tgctctagtt 1140 gtgagcatgt gaattcttca tgaggacgga tggtattccg gggtttgaag aatgtatggg 1200 gtggcttgtg tgattaccta aaagaccaag ggtgatcgga tgcaaggtga tcttcgagga 1260 ggcgggagac gttccgtggt tgaagatggt ttggtgaaaa atgaagactt gtggagcaac 1320 ttggtgtaga gttggatgca agggaaaaga aaagggagat tggtggttga tggttaaagt 1380 ggcatcatca ccaaattaga agtcaaggtg gagaaat 1417 // ID Copia52-PTR_I repbase; DNA; EDCOT; 4656 BP. XX AC LG_VII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia52-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4656 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4656 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 284-284 (2007). XX DR Genome; LG_VII; Positions 11315726 11320381. XX CC Positions [1854-2348] - Integrase core CC 'ACTAT' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 132..4646 FT /product="Copia52-PTR_I_1p" FT /translation="MDLTKANLSNPFFTHHSDHPGLILISKPLNGDNYSTW FT KRAMTLALNSKNKLGFVNGSIRAPSEDNDPEEHAAWSRCNDMVHSWIINTL FT NPEISDSVIYYSTAYEVWEDLHERFSQSNAPRIFEIQRDIACLRQEQLSVS FT TYYTKLKGLWDELASYNDTVHGTQQEQQKLMQFLMGLNESYSAIRGQILLM FT NPLPSVRQAYSSISQEEKQRLLSSMHTGGDSSGSAAMAVRNSNNRSTEHLS FT AGFGRSERFNNSYGPQGFRSQEKPAGNFSGGRRFQQDGRRPTFGRGRPYCT FT HCEEAGHWVQTCYQLHGYPAGHPKIKYGSGSKRFNNNKHIANHVSTAENEQ FT PVIGISQDQLKQLLSLLDNKTEGSSPHANAVTKPGLSKVTSRNWIIDSGAT FT DHISSKLFTEKHTKCSLPPVLMPSGQKADIVAKGSLPINSVYYLHNVLCVP FT TFKVDLLSVSRLTRDLNCSIIFFPYWCLLQDLATRRMIGLGKQHNGLYYLV FT ALATKQHTSKQTPTINQPTCNLITSSTNLWHNRLGHTSPSCLRFIAQNFLN FT FSIQSNNTCHVCPLAKQSRLPFHSSVISSTKPFALIHCDIWGPYRHPSISG FT ARFFLTIVDDFSRFTWIFLMRHKSETQSILKNFFRYVFTQFEAHIKIFRSD FT NGGEFISLRTFFHNNGVIFQRSCVYTPQQNGVVKRKHRHILQVARALRFQA FT HLSTQFWGECALTATHIINRLPSPVLSFKTPFELLFSKPPSFSHLRVFGCL FT AYATNVRITHKFAPRSIPSIFLGYPPGQKAYKLFDLSNEKIFTSRDVIFHE FT NIFPYAFTQPTPSSPPYNPGPIPLIHTDTTTFPFPPSSSPQPPLPTQIPLS FT TTHSSPPPTTLRTYTRRPKPINLDTHPTDCSNTPSTIISAQTPPSTTSPSL FT EPGSIAPTPLSLEISPPITPAPTPLRRSSRHIGPPVKLRDYVCSHVFSGQS FT PSSPPGLNQGTRYPLSNYVSYHRYTSPHHSFIAQISHTMEPKSYSEAAAHP FT EWQAAMLSELQALQQNGTWSLTSLPQGKTLIGCRWVYKVKHRSDGSVERYK FT ARLVAKGFTQLEGIDYQDTFSPTAKIVSVRCLLALAAARGWTLHQLDVHNA FT FLHGELSEEIYMSPPPGLLRQGEEDLVCHLHKSLYGLKQASRQWFAKFSEA FT ICSAGFKQSQADHSLFTRQRDKSFTALLIYVDDILITGNDLDSIAMTKKFL FT HSHFHLKDLGPLKYFLGIEFSASKNGIFISQRKYALEIIEDAGLLGAAPID FT TPMERGLKLSDKSDLLKDPGRFRRLVGRLIYLTVSRPDITYAVHVLSRFMH FT QPRKLHMEAALRVVRYLKGAPGQGLFFPSHTDYKLRAYSDSDWAGCPLTRR FT STTGYCVFLGPSLISWRSKRQKTVSLSSAEAEYRAMTGACCELTWLRCLLR FT DLGLLHHEPALLHCDNKAALHIAANPVFHERTRHIEMDCHYIRDKIQDGSV FT ITRHVHSEHQLADIFTKPLGKDVFIPMIHKLGVQDIHSPT" XX SQ Sequence 4656 BP; 1269 A; 1214 C; 826 G; 1347 T; 0 other; tggtatcaga gctggactaa ttatctccat caaaattttc atcaattctc tgtttcgttc 60 ctccttccac atcagtcttt atcttctctg tttccatcct ttaaacctag aaaccacaaa 120 accttcagag catggatctt acaaaagcaa atctctcaaa ccccttcttt actcatcatt 180 cagatcatcc tggactgatt ttaatctcaa agcccttaaa tggagataac tactctacgt 240 ggaaaagagc aatgacattg gctttaaact ccaaaaacaa attgggcttt gtcaatggct 300 cgataagagc tccctcagaa gacaatgatc ctgaagaaca tgcagcctgg tcccggtgca 360 acgacatggt tcactcttgg attattaaca cccttaatcc agaaatatca gatagtgtga 420 tatattattc aactgcttat gaagtttggg aagaccttca tgaacgattt tctcaaagca 480 acgcgcctcg catctttgaa attcagcgcg acattgcttg ccttcgacaa gagcagctct 540 cagtttctac ctattacaca aaattgaagg ggttgtggga tgaactagcc tcctacaacg 600 acactgtaca tggaacgcag caagaacaac aaaaattgat gcagtttttg atgggattaa 660 acgaatctta cagtgccatt cgcggtcaaa tcctcttaat gaatcctctt ccttcagtgc 720 ggcaagcata ttcctccatc tcacaagaag aaaaacagcg cctcctaagc tcaatgcata 780 caggaggtga ttccagtggt agtgctgcca tggcagtccg taatagcaac aatcgatcaa 840 ctgaacatct cagtgcagga tttgggagat cagagcgctt caacaactca tatgggccac 900 aaggattcag atcacaagag aaaccagcag ggaatttcag tggaggacga cgatttcaac 960 aggatggacg acgcccaacc tttggcagag ggcgtcctta ttgtacacac tgtgaagaag 1020 cgggtcattg ggtgcaaaca tgctatcaat tacatgggta tccagcgggt catccaaaga 1080 taaaatatgg gtcaggatca aagcgtttca ataacaataa acacatagct aatcatgtgt 1140 ccacagccga aaatgagcaa ccagttatcg gtatttcaca ggatcaatta aaacagctct 1200 tgtcactcct agacaataaa actgaaggtt ctagtcctca tgcgaatgcc gtaactaaac 1260 caggtttgtc taaagttact tcccgcaatt ggatcatcga tagcggcgca acagatcata 1320 tctcttctaa attattcact gagaagcaca ccaaatgttc attaccaccg gtactaatgc 1380 ccagtggaca aaaggctgac attgtggcaa agggatcttt acccattaat tctgtctatt 1440 atttacataa tgtgttgtgt gtccctacat tcaaagtaga cttgttatct gtcagtcgct 1500 tgacaagaga ccttaattgc tcaataatct tctttcctta ttggtgtcta ttgcaggatc 1560 tggctacgag gaggatgatt ggtttgggta aacaacataa cggactatac tatttggtgg 1620 ctctggcaac gaagcaacat acatctaaac aaacccccac catcaatcaa ccaacctgca 1680 atctcatcac ctcatctacc aacctttggc ataatcgctt aggccataca tcaccttctt 1740 gtttacgctt cattgctcaa aattttttaa atttttccat tcagtccaat aatacttgcc 1800 atgtatgtcc tttggcaaaa cagagtcgtc tacctttcca ttctagtgta atttcttcta 1860 caaaaccttt tgcattaatt cattgtgaca tttggggtcc ttatcgacac ccttccattt 1920 ctggtgctcg tttttttctc actattgttg atgacttctc acgtttcaca tggattttct 1980 taatgcgaca taaaagtgag acgcaatcaa ttctaaaaaa ttttttccgt tacgttttca 2040 ctcaatttga agctcatatt aaaatttttc gaagtgacaa cgggggagaa tttatatcac 2100 ttcgcacctt ttttcacaat aatggtgtca ttttccaacg ttcttgtgtt tacacacctc 2160 aacaaaatgg ggttgtgaaa cgcaaacatc gtcacattct acaagtagct cgagctttaa 2220 gatttcaagc tcacctctcc acccaatttt ggggggaatg tgcccttact gctactcaca 2280 tcatcaatcg cctcccatct cctgtcctct ccttcaaaac cccttttgaa cttctctttt 2340 ccaaaccacc ttccttttct catcttcgtg tcttcggttg tttggcttat gctaccaatg 2400 tccgcattac tcataaattt gctcctcgtt ccatcccttc tatttttctt gggtatcctc 2460 ccggtcaaaa agcttataaa ttgtttgatt tatcaaacga aaaaattttt actagccgcg 2520 atgtcatatt tcatgaaaac atttttcctt atgcatttac ccaacccact ccttcctccc 2580 caccttacaa tcctggaccc attcccctaa tccataccga caccaccacc tttccctttc 2640 caccatcctc ttcaccacaa ccacccctac ctacccaaat tcccctttcc accacacact 2700 cttccccacc tcccaccact ctacgcacct acacacgccg ccccaaaccc attaaccttg 2760 acactcatcc cactgattgc tccaacacac cttccaccat catttcggct caaacaccac 2820 cctccactac ttcaccctct ttggaaccag gttccattgc gccaaccccc ctctctttag 2880 aaatcagccc accaatcaca cctgcaccca ccccgcttcg ccgatccagc cgccatattg 2940 gccccccggt caagcttcgt gactatgtct gctcccatgt tttctccggc caatcaccct 3000 cctccccacc aggtctgaac caaggtactc gctatccatt atccaattat gtttcctatc 3060 acagatatac atctccacat cattcattta ttgctcaaat tagccatacc atggaaccta 3120 aatcctattc agaagcagct gctcatcctg agtggcaggc cgccatgctc tctgaactac 3180 aagctcttca gcagaatggt acttggtcac tcacttctct tccacagggc aaaactttga 3240 ttggctgtcg ctgggtctac aaagtcaagc accgatctga tggctctgtg gaaagataca 3300 aagcccgttt ggtggctaag ggtttcaccc aacttgaggg aatcgactat caggacactt 3360 tctccccaac tgccaaaatt gtttctgtcc gttgcttgct tgctctggcc gcagctcgtg 3420 gttggaccct ccatcaattg gatgttcaca acgcgtttct ccacggtgaa ttatcagagg 3480 agatttatat gtctccgccg ccagggcttc ttcgacaggg ggaggaagac ttggtatgcc 3540 atcttcataa gtccttatac gggctgaagc aagcatcacg ccaatggttc gccaagttct 3600 ctgaagccat ttgctctgct ggattcaaac aatctcaagc cgaccactct ttattcacca 3660 gacaacgaga taagtccttc actgcccttt taatatatgt tgatgatatt ttgattactg 3720 gaaatgatct cgacagtatc gctatgacaa agaaatttct gcatagccat ttccacctta 3780 aagatcttgg ccccttaaaa tacttccttg gtatagagtt ctcagcttct aagaacggca 3840 ttttcatttc tcaacgtaaa tatgcattgg aaattattga ggatgcagga ttgttgggtg 3900 cagcccctat tgatacacct atggaacgtg gcttaaaatt atcagacaag agcgacttgc 3960 tcaaagatcc gggtcgtttt agaagattgg ttggtagatt gatttatttg actgtttcaa 4020 gaccagatat cacttatgct gtgcatgttc tgagcagatt tatgcaccaa ccccggaagc 4080 ttcatatgga agctgctctt cgggttgttc gatatctgaa aggggcacct ggtcaagggt 4140 tattctttcc ttcacacact gattacaaat taagagccta ttcagactca gattgggcag 4200 gttgcccact gactcggagg tctaccacgg gttattgtgt gttccttgga ccctcgttga 4260 tatcctggag atcaaaacga cagaaaacag tctcactctc ctctgcagag gcagagtatc 4320 gtgcaatgac aggagcatgt tgtgagttga catggctccg atgtctgttg agggatttag 4380 gccttttaca tcatgaacct gctttgctac attgtgataa caaggctgca ttacacattg 4440 cagccaaccc agtctttcat gagcgcaccc gacatattga gatggactgt cactatatca 4500 gggacaaaat tcaagatggc tcagtgataa caagacatgt tcattctgaa catcaattgg 4560 cagacatctt caccaaaccc ttaggaaaag atgtcttcat tcctatgatt cacaagttgg 4620 gagtgcagga catccactct ccaacttgag ggggag 4656 // ID Gypsy-5_Mad-I repbase; DNA; EDCOT; 4958 BP. XX AC ACYM01109377; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-5_Mad-I; KW Gypsy-5_Mad-LTR; Gypsy-5_Mad_. XX NM Gypsy-5_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4958 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1328-1328 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01109377; Positions 6142 1185. XX CC Positions [3729-4211] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(933..1841,1845..2747) FT /product="Gypsy-5_Mad-I_1p" FT /translation="MSRFIHGLRDDIKREVRRFRPYTLEDAYCHALEAETF FT LRPQRRYTGTPGYPATSAPNRSNPSSKYGITGPPAPTVPATEKGPALSTAT FT HLECYRCHAKGHIASRCPHRTLNISSNTEDPRVDEYVEPLEPIYDPDLDNC FT CEEEALQQLSVMRCIYSASTPPPPDSWKRTSIFQTYVPCGTTRCQLVIDGG FT STLNVISKAAVDRLHLQAEPHPHPFQVGWVDKTRLPVTERCLVPLQLGPCH FT EKLYCDILPMSVAHVLLGRPWLYDRNVKSCGRENTYTFQHEGKNITLKPSN FT PAIKPIKEVQPLPLNGKASEHRLSILSPVDFTHELQDTGVVFALLLKPVSK FT CTPTPFAEPIRQLLTEFSDVIPEDLPDELPPAREIQHAIDLVPGSQLPNLP FT HYRMNPPERAELNRQIQGLLAKGFIRHSLSPCAVPVLLTPKKDGSWRMCVD FT SRAINKITVKYRFPIPRLEDMLDDLAGSQWFSKIDLRSGYHQIRIREGDEW FT KTAFKTPDGLYEWLVMPFGMSNAPSTFMRVMTHVLRPYIGKFLVVYFDDIL FT VYSHSREEHLKHLHSLFFTLRAEKLYANLPKCSFLQPQVLFLGFNISAAGV FT STDPTK" XX SQ Sequence 4958 BP; 1202 A; 1242 C; 1041 G; 1448 T; 25 other; atttggtaat cagrgcctac aatccctttc rttggcgttt gatccctgcc atggcacccc 60 aaaccgtggc caaccttgca garcaatgtc atacgttcca aaacaaagtc acggacgata 120 tcgcgrgcat agaaacccaa ctctctaaac tcagcactga cctcaaagaa gagttggtac 180 aggctcacgc ccatcgttca acgacggacc ttgccatcac taaacttcaa aactccgttc 240 agttacttat caaccacttt cgggttgaac acgctgcaac ttcgtcttcc tccacagtga 300 tcccaagctc gtctacgcca ccaccaacaa gtggcctttt gcccactcca ccggtggatc 360 ctaaattaaa ggcagtgtcc tacggaatgc cgcttagctc caytgggtct atgccgccac 420 tccattatac tcaacacaca ataggtcctc ctccagtgac tcctcaggct ctaaacctcc 480 cacccgctcc acatgatcag taccctcctc cmcctcgcca gtttgacaac gagatcatcc 540 gccacatcaa acctatcgct cctacttttg atggtcgtgg ggatcctacg atgtttcttg 600 attggatcca agccctggaa gattattttg cttggtatga tttgacggat gcttataaac 660 tacgcattgg taagatgaca ttacagggag ccgctagaca atattggaat tccgtggagg 720 agcaactata ccaactggga caacagcctg tgactctttg ggacgagatg aaattcaagc 780 ttcgcraaca atatcttcct acattttatc gccatcaatt gtatgatcag ttatggaccc 840 tttcacaagg aagttttacc gttacagaat tccacgctcg ttttattgaa cacaaaatac 900 gtgcggggct tcgtgaagaa cccgacatca ccatgtctcg ttttattcat ggtcttcggg 960 acgatatcaa gcgtgaagtc cgtcggttcc gtccgtatac kttggaagat gcatattgcc 1020 atgcattgga agctgaaacc tttttgcggc cacaacgtag gtacaccggg actcccgggt 1080 atcctgccac ttctgctcca aaccgcagta atccaagctc caaatatggc atcactggtc 1140 cacctgctcc cacggtacct gccacagaga agggaccagc cctatccacg gctactcacc 1200 tcgaatgcta tcgttgccat gctaagggcc acatcgcctc ccgttgcccc cacagaactt 1260 taaatattag ctccaacact gaggaccctc gtgtggacga gtatgtggag ccccttgaac 1320 ctatttatga tcccgacctt gataattgtt gtgaggaaga agcattgcaa caactgagtg 1380 ttatgcgttg tatttattca gcatctacac ctccacctcc tgattcatgg aaacgcacaa 1440 gtatcttcca gacttatgtc ccttgcggta ccactcgatg ccagctagtt attgatgggg 1500 gaagtacgct gaatgttatt tctaaagctg ccgtcgatcg tcttcacctt caggccgaac 1560 cacatcccca tccttttcaa gtcggctggg tagataaaac taggttacct gttactgaaa 1620 gatgtcttgt tcctcttcaa ttgggtccct gtcacgagaa actttattgt gatatcctac 1680 ctatgagtgt tgcacatgtg ctactaggcc ggccttggct ttatgaccgt aacgtcaaaa 1740 gttgcggccg agagaacacc tatactttcc aacatgaagg gaaaaacata acactcaagc 1800 cttccaaccc agccatyaaa ccaattaagg aggttcaacc gayactgccc ttaaacggga 1860 aggcttcgga gcatcgttta agtatcttat cacctgtaga ttttacacat gaactacaag 1920 acacgggtgt ggtctttgct ctcttgctta aaccggtctc caaatgtacc cccactccat 1980 ttgccgaacc catacggcag ctactcacgg aattctctga tgttatacct gaggacttac 2040 cagatgaact acctccagca cgagagattc agcatgccat cgaccttgtt cctggttcac 2100 aacttcctaa ccttccccat tatcgtatga acccacctga gcgagcggaa ttaaatcgac 2160 aaatccaggg gttgctggct aagggtttta ttcgtcatag tttaagtcct tgtgctgttc 2220 cagttctcct tacaccaaaa aaagatggct cctggcgaat gtgtgtggat agtcgcgcca 2280 taaataaaat tacagttaag tatcgtttcc caataccgcg acttgaggat atgttggatg 2340 atttggctgg ttcccaatgg ttttctaaga tagatcttcg cagtggttac catcaaatcc 2400 gaattcgtga aggagatgag tggaaaaccg cgtttaaaac ccctgatggt ttatatgagt 2460 ggcttgttat gccctttggc atgtccaatg cacctagcac gtttatgagg gtgatgactc 2520 atgtgttacg gccctatatt ggcaaatttc tggtggttta ttttgatgac atccttgtat 2580 acagccactc tcgagaagaa catctcaaac atcttcactc gctcttcttt acattacgag 2640 cggaaaaact gtatgctaac ttacccaaat gttcgtttct tcaaccgcaa gttctatttt 2700 tggggttcaa tatttctgca gctggggtta gcaccgatcc cactaaaktg gaggctatta 2760 ctcgttggcc aacacctacg acattaacag aggcacgcag ctttcatggt ctcgcctytt 2820 tttatcgccg attyattccc gggttcagta ctattatggc accaataact gattgcatga 2880 aacaakgagc gtttctttgg acccctgcag ctgccacgrc ctttacaatt ttgaagcaaa 2940 agatgagtca agcacctgtt cttcgacatc ctgatttgac taaagtcttt gaagtggcat 3000 gcgacgcttc cggagtcgga attggtggcg tgcttagcca agaaggacat ccagtagcct 3060 actttagtga gaaacttaat gcagcaaagc aacgttattc tacttatgac aaggagtttt 3120 atgctgtggt acaggccctt cggtattggc aakattacct attgccaaac gaatttgtgc 3180 tatattccga tcatcaagct ttgaaatatc tccactctca acgcaccatc agcagtcgac 3240 atgtcaagtg gtccgaatat ctacagatct ttacgtttgt tttacgacac cgtccaggca 3300 ttgacaataa ggcagctgat gcccttagtc gcgtggctac tattttgcac acaatgacag 3360 ttgaggtcac tgggtttgat cgtattaagg ccgagtattc gtcgtgtcca gattttggaa 3420 ttattttcca tgaagtttcc aacggtaacc gtcgtgagta tgtggacttt attacaaggg 3480 atgggttctt gtttcggaaa acccaattat gcattcctcg tacttctcyt cgtgaattcc 3540 ttatttggga actacatggt ggtggtttgg ctggacattt tggtaaagat aaaaccattg 3600 ccttgatgga agaycgtttc tattggccgt cgttaaaacg tgatgttgct cggctcctct 3660 cccaatgccg cacatgccag ctagctaaag ctcgcaaacg taacacaggt ctgtataccc 3720 ctctaccaat ccctcatgct ccttggaagg atattagtat ggattttgtg cttggtttac 3780 ctaagactag tcgcggccat gactctatct ttgtcgtagt tgatcgcttt tctaaaatgg 3840 cgcattttct accttgtgcc aaaaataccg atgcttctca tgtggccaaa ttatttttta 3900 aggaagtagt tcgtttgcat ggcctccctg tctctattgt ttctgatcgt gatgtcaaat 3960 ttgttagtta tttttggaaa accttgtgga agcttttsgg gactactttg aagttttcct 4020 ccgctttcca tccccaaacg gatggacaaa cggaggtggt taatcgcagt cttggaaatt 4080 tacttcgctg tttagttggg gataagcctg gtaattggga tctcttgttg cctgtggctg 4140 agtttgctta taacaactca gttaatcgaa gcaccggtaa aagtcctttt gaggttgttc 4200 aygggttttc tccccgatca cctgtggatc tagttgctct tcctatggct gcccgcgcct 4260 ccractctgc tacgtcgttt gctgaacata ttagacaact gcatgatgac gtccgtcggc 4320 aaatagccat gcacaccgac agttatcaac tggccgccaa tgctcatcgt cgtcaccarg 4380 agtttcasca cggggatttt gttatggtgc ggatctgtcc tgagcgtttt cctaagcaat 4440 cttttaaaaa gcttcatgct crttcgatgg gtccttatcg tgtccttagg aagcttgggt 4500 ccaatgctta cttgattgag ttacctgcca cgatgcagat cagtcccatt tttaatgtct 4560 ctgacttatc tccttatcgg ggaacctttt ctccacctct gtcgatggat gttgctcaga 4620 gttccattcc tcctatggca ccacgacttc cgtccactat ttctgcccct acagagcaga 4680 ttgctgacgt tttggatcat gaagttgtga cttcgtctac tggaggatcr acccgttatc 4740 tggttcgttg ggtgggaaag cctgctactg aggatacttg gattacagaa gctgaatttc 4800 gcgagttgga ttccagtctt ttgcaccatt atcaggatgc tcttcaggat cttgatttgg 4860 cagcatcccg tcctcctatc atccatactt acaaacgtcg tcgttgtcct taatattggc 4920 ttactcgcct gtgtcgagtt cttttcagta ggggagaa 4958 // ID GYPSHAN3_I_MT repbase; DNA; EDCOT; 4645 BP. XX AC AC150244; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE The internal region sequence of a LTR retroposon from Medicago DE truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW ORF; internal region; Interspersed; terminal; repeat; KW GYPSHAN3_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4645 RA Shankar R. and Jurka J.; RT "GYPSHAN3_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 24-24 (2007). XX DR EMBL/GenBank/DDBJ; AC150244; Positions 14502 19146. XX CC The internal region has intact domains for gag, protease, reverse CC transcriptase and integrase in a single ORF. The positioning of CC domains is Gypsy-like. Present in the Medicago genome in high but CC disrupted and incomplete copy numbers. XX FH Key Location/Qualifiers FT CDS join(555..4241,4245..4643) FT /product="GYPSHAN3_I_MT_1p" FT /translation="MRCYLERYGGHGEGDVYEQLTELRQRGSVDDYIAEFE FT HLTAQIPRLPDKQFLGYFLHGLKEEIRGKVRSLAVMGDLNRSKVLQVARVV FT ERETKGDSGMSYHRQTKSGHGSNRGGIQGSNRGNSTDWVMVKGNKEHGSAG FT GSKGTGFGPKGEKQAQYDKKKSGPRDRSFTHLSYNELMERKQKGLCFKCGG FT PFHPMHQCPDKQLRVLVLEEDEEGEPEGKLLAVEVDDEEEGDGEMCMMEFF FT HLGHSRPQSIKLMGVIKEVPVVVLVDSGATHNFISQQLVHKMNWAVVDTPC FT MSIKLGDGSYSKTKGTCEGLEVDVGDVHLEIDAQLFDLGGVDMVLGIEWLR FT TLGDMIVNWNKQTMSFWHNKKWVTVKGMDTQGGAIATLQSIICKSRRRSTG FT WWTYEDKCKEDGSIHTLASEQSRELELLLENYGGVFQEPTGLPPKRKKEHV FT ITLKEGEGAVNVRPYRYPHHHKNEIEKQVREMLQAGIIRHSTSSFSSPVIL FT VKEKDNSWRMCIDYRALNKATVPDKFPIPVIEELLDELHGARFYSKLDLKS FT GYHQVRVKEEDIHKTAFRTHEDHYEYLVMPFGLMNAPSTFQSLMNDVFRLL FT LRKFVLVFFDDILVYSQDWKTHMEHVEEVLRIMQTHGLVANKKKCYFGQET FT VEYLGHLISKEGVAVDPSKVVSVTRWPIPKNVKGVRGFLGLTDYYRKFIKD FT YGKIAKPLTELTKKDAFMWNEKTQDAFDQLKRRLTTSPVLALPDFNKEFVI FT ECDASGGGIGAILMQDRKPVAYYSKALGVRNLTKSAYEKELMAVVLAIQHW FT RPYLLGRRFVVSTDQKSLKQLLQQRVVTAEQQNWAAKLLGYDFEIIYKPGK FT LNKGADALSRVREDGELCQGITSVQWKDEKLLREELSRDSQLQKIIGDLQR FT DASSRPGYMLKQGVLLYEGRLVVSSKSVMIPTLLAEFHSTPQGGHSGFYRT FT YRRLAANVYWVGMKNTVQEYVRSCDTCQRQKYLASSPGGLLQPLPVPDRIW FT EDLSMDFIMGLPKSKGYEAVLVVVDRLSKYSHFILLKHPYTAKVIADVFIR FT EVVRLHGIPLSIVSDRDPIFMSNFWKELFKLQGTKLKMSIAYHPETDGQTE FT VVNRCLETYLRCFIADQPKNWASWIPWAEYWFNTSYHAATGHTPFEMVYGR FT PPPVITRWVQGETRVEAVQRELLDRDEALKQLREQLLRAQVRMKQIADKKR FT CDRSFEVGEWVFVKLRAHRQSVVSRIHAKLAARYHRPYPVEARVGAVAYKL FT KLPEGSRVHSVFHVSLLKKAVGNYHEEENLPDLEEDKGVVIEPETVLTRRT FT IQVQGEKIDQVLVHWMGQKVEEATWEDTLIIRSQFPNFYLEDKAMLSGGS" XX SQ Sequence 4645 BP; 1434 A; 753 C; 1312 G; 1146 T; 0 other; atttggtccg acctaccgga ttaaaacgtt ggagaatcag tgaatgccac cgaagaagtt 60 aacactcaag agtatggaag caaaagttgc atctctagag gaagaaatca tgggagtgaa 120 ggtcacactg gccgcaatgg agaaaactca aacagcgctc cttgcgttgc ttgagaagaa 180 tctggggaag acggtacgaa cagagaacga gagtgtggtt gacggaggaa gctcggagaa 240 gaacgctggc gaaggtacgg cgaagaacac cggcgaagct tcggcgaaaa catccgggaa 300 atccggatcg agcaaactcc aaggtgaggc gttggtcgaa ttccgacatt cagtgaagag 360 ggttgaactt ccgatgttcg acggtgaaga tccagctggg tggatatcta gagcagaggt 420 gtattttcgc gttcaggata cgatcccgga ggttaaggtg aatctggctc agttgtgtat 480 ggagggacca accatccatt tcttcaattc gctcctcaac gaaaacgaag aactgacatg 540 ggaaagtttg aaggatgcgt tgttacttag aacgatatgg cggacacggc gaaggcgatg 600 tgtatgaaca attgacggag ctccggcaaa gagggagtgt ggatgattat attgctgagt 660 ttgaacatct cactgctcag atacctagat taccagataa acaatttctg ggttactttc 720 tccatgggct gaaggaggaa attcgaggga aggtcaggag tttggcggtg atgggagatc 780 tgaatcgttc caaggtgttg caggtggcca gggttgtgga gagagagacg aagggcgatt 840 cgggtatgag ttaccataga caaacaaaat caggccatgg gtcaaaccgt ggaggaatcc 900 agggatccaa tagagggaac agtactgact gggtgatggt gaagggtaac aaggaacatg 960 ggtcagctgg aggatcaaaa ggaaccgggt ttgggcccaa aggtgagaag caagcccaat 1020 atgacaagaa aaaaagtggg cctcgagacc gtagttttac tcacttgtct tacaatgagc 1080 ttatggaaag gaagcagaaa gggttatgtt tcaaatgtgg gggacctttc catccaatgc 1140 atcaatgtcc agataagcaa ctaagggtat tggtattaga ggaggatgaa gaaggagagc 1200 cagaagggaa gttgttggca gtagaggtag atgacgagga agaaggtgat ggggaaatgt 1260 gcatgatgga attttttcac ctgggtcact ctagaccaca atccattaag ctgatggggg 1320 tgataaaaga ggtgccagta gtagtattgg tggatagcgg agcaacccac aacttcatct 1380 cacaacaatt ggtccataaa atgaattggg cagtggttga tacaccgtgt atgagtatca 1440 agctaggcga tgggtcttac tctaagacca agggaacatg tgaaggatta gaagtagatg 1500 tgggagatgt gcacttggaa attgatgcgc agttgtttga tttaggggga gtagacatgg 1560 tgttagggat tgaatggctt cgtacacttg gagacatgat tgtaaattgg aacaaacaaa 1620 ctatgagttt ctggcacaac aaaaaatggg tcacagtgaa ggggatggat acacaaggag 1680 gtgcgatagc aactttacaa agtatcattt gtaagtccag acggaggagc actggttggt 1740 ggacgtatga agacaagtgt aaagaggatg gtagtatcca caccttggca agtgagcagt 1800 caagggagct ggaattattg ttagaaaatt atggtggagt ttttcaagaa cctacagggc 1860 tgccacctaa gagaaagaaa gagcatgtga tcaccttgaa ggagggggaa ggggcagtta 1920 atgtgaggcc ctataggtac cctcaccacc acaagaatga aattgaaaag caagtaaggg 1980 aaatgttaca ggcgggaatt atacggcaca gcacaagttc tttttctagt cctgtcattt 2040 tggtcaagga aaaggataat tcttggagga tgtgtattga ttatagagca cttaacaagg 2100 caactgtacc tgataagttt ccaataccgg tgattgaaga attacttgat gaactgcacg 2160 gagctagatt ttattccaaa ttggacctaa aatctggtta ccatcaagta agggtcaagg 2220 aagaggatat tcataaaacc gctttccgaa cacatgaaga ccactatgag tacctggtga 2280 tgccatttgg gttgatgaat gctccatcta cattccagag cctgatgaat gacgtgttca 2340 gactattatt gaggaagttt gtgcttgtat tttttgatga tatattggtt tacagtcaag 2400 actggaaaac acatatggag cacgtggaag aggtgctgag aattatgcaa acacatggtc 2460 tggtggccaa caagaagaaa tgttattttg ggcaggagac ggtggaatat ttggggcatt 2520 tgatttcaaa ggaaggtgtg gcagtggatc ccagcaaggt ggtgagcgtt accagatggc 2580 caataccaaa aaatgtaaag ggagtaagag gttttttggg tttgacagat tactatagga 2640 agtttatcaa agattatggt aaaattgcca agcctttgac agaacttacc aagaaagatg 2700 cgtttatgtg gaatgaaaag acacaagatg cttttgatca gttaaaaagg cgtcttacta 2760 catctccagt tttggctctt ccggatttta acaaggaatt tgttatagaa tgtgatgcgt 2820 caggtggagg aattggagca atactcatgc aggacaggaa accagtagct tactacagta 2880 aggcgttggg cgttaggaac cttaccaagt ctgcttatga aaaagagttg atggctgtag 2940 tgctggccat tcaacattgg aggccgtatc tgttggggag gaggtttgtg gtgtctaccg 3000 atcagaaaag cctcaaacaa ctactgcaac agagggtagt tacagcagaa caacaaaact 3060 gggctgctaa gctacttggg tatgatttcg aaatcattta taaacctggg aaacttaaca 3120 agggagcaga tgcgctttca cgggtaaggg aagatgggga gttatgtcag ggaattacta 3180 gtgtgcaatg gaaggatgag aagctgttgc gggaagagtt gtcacgggat tcccaattgc 3240 agaagataat tggtgatctg cagagagatg caagctccag accaggatat atgctcaaac 3300 aaggagtgtt actatatgag gggagactgg tagtgtccag taagtctgta atgattccta 3360 ctttactagc agaatttcat tctactcctc aaggaggaca ttctggcttc tacaggactt 3420 accggagatt ggctgccaat gtatattggg ttggtatgaa gaacacggta caagagtatg 3480 taaggagttg tgatacatgt caaaggcaga aatacttggc tagttcacca ggaggattat 3540 tgcaaccgct tcctgtgcct gatcgtattt gggaagactt atccatggat tttatcatgg 3600 ggttacctaa atcaaaaggg tatgaagcgg tgttagtagt ggtggataga ctgtcaaagt 3660 actctcattt catcttactt aaacatccgt acacagctaa agtaattgca gatgtgttta 3720 ttagagaggt tgtcaggctg catggaattc cgttatccat agtcagtgac agggatccca 3780 tttttatgag caatttttgg aaagagttgt ttaaattgca aggaacaaaa ttgaaaatga 3840 gtattgctta ccaccctgag acggatgggc aaacagaggt ggtgaatcga tgtctggaga 3900 cttatttgag atgctttata gctgatcagc caaaaaactg ggccagttgg ataccatggg 3960 cagagtattg gtttaatact agttaccatg ctgctactgg tcacacacca tttgagatgg 4020 tgtatgggag acctccaccg gtcattacac gttgggtaca aggggaaacc agagtagagg 4080 ccgtacaaag agagttgttg gatagagatg aggccttaaa gcaattaagg gagcagctac 4140 ttagggccca agttaggatg aagcagatag cagacaagaa aaggtgtgat aggagttttg 4200 aagtaggaga atgggtgttt gtaaagttga gggcccatag ataacaatca gtagtgtcca 4260 ggattcatgc taagttggca gcaagatacc acagaccata cccggtggaa gcacgtgttg 4320 gagcagtagc ctataagttg aagctaccgg agggttcacg tgttcattca gtttttcatg 4380 tctcactgtt gaaaaaagct gtaggaaatt atcacgagga ggaaaaccta ccggatttgg 4440 aagaagataa gggggtggtt attgaacctg aaactgtact aacccgtagg acaatacaag 4500 tacagggcga aaagattgat caagtgcttg tacattggat gggacaaaag gttgaagagg 4560 ctacatggga ggacactttg atcataagaa gtcagttccc aaatttctac cttgaggaca 4620 aggcaatgct ttctggtggg agtat 4645 // ID Gypsy-46_Mad-I repbase; DNA; EDCOT; 15231 BP. XX AC . XX DT 26-OCT-2010 (Rel. 15.11, Created) DT 26-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-46_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-15231 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1989-1989 (2010). XX DR [2] (Consensus) XX CC ~94% identical to the consensus. XX FH Key Location/Qualifiers FT CDS 68..4936 FT /product="Gypsy-46_Mad-I_1p" FT /translation="MASKKAQVVLAANARNKNVITVGGVTSGVITRSKARA FT LSAASSTPASTPPKEQEHLRHEPVITLASLKAPRKESPRKYSGFMLSDADS FT SGNSAMQVMTTGATSIDEQLAHMNEAIARLTRIVEEKDQQIAALVNQLDVK FT PDVKIEQGDGSVKKENDEDEEPPVEKIDVKPEPGQAEALMGSLSIQQLQEM FT ITSTIKAQYEGSSHTSSFYSKPYSKKIDALKMPRGYQPPKFMQFDGKGNPK FT QHVAHFVETCNNAGTEGDYLAKQFVRSLKGNAFEWYTDLEPESINSWEQLE FT REFLNRFYSTRRTVSMLELTSTKQWRDEPVVDYINRWRNLSLDCKDRLSEI FT SSIEMCVQGMQWGLHYILQGIKPRTFEELATRAHDMELSIAHHGKKEPITD FT FKKDKVFSPNVDKTGKKPPKEAFTVSTAPVKTASAPIKISSKTKAKEIKKS FT EPPRTQERYKSTLRELEQKVYPFPDSDMDAMLDDLLEKKVIELPECKRPEE FT MNRINDPKYCKYHRIVSHPVGKCFVLKELIMKLAQQGRIELDLEDTAATHT FT TTIAFGSFDPVPLQAAPDHSYQCSSYTIPSAQPSPGANEQDAHADDEEGWT FT LVTYKKTRKPKPQAIRQKVEQVRKHRRRNSRKPKRNVKVDKPTYAGEPMEQ FT EPRIPVSLHEYFPNDFFQQCTIAACHMVEVEIEEPSKGKDITTEGEKTLTL FT EEGLPTHFSIEEALRLPKKMRIALAAVLESPNDHEVQESKNEGFKLRPHEY FT ATCCAIEDTIHFTDEDLLLGSKPHNRPLFVSGYVREHKVNRMLVDGGSAIN FT IMPKSTMTTIGIKADELSLSRLLIQGFNQGGQKAMGMIRVEMTIGELKSST FT IFHVIDARTSYGLLLGRPWIHANGVVPSTLHQCLKFYREGVKVIYGDTKPF FT TEAESHFADAKFYMDEDMVLEALPKEIKSTGKATPKKQEWQAMPKKQEEEA FT MSSSSKNDDELAKPATTKGSRTPSNVLNTPVFRYIPMSRRKNGQSPFETEA FT SKADAQRYMDNVKLLKTNAVLPLTQLSNAKVARLPQGFVKALPKRAEPSFL FT PTKRTEEGFDPNAYKLMSKAGYDFASSSNPGKKVSNTVNNKERDLTETQKK FT LKKHGYGVNNNKAGLGFTPNAPVKISSKAKNASTQHISVSIEQDREEPKST FT PRTPVFDRMNRSRPRTSALDHIGGQNRTSVFKRLNRPTSRSSIFERLSKPN FT KQSNTASSPPRQSALERLEDNMKFSGNRETTSKEEKLDRLAEKGDIRSSIP FT SRMKRQAILEVDANGPLIVRRRTIIHTGQSAYQQTQEDDTKEEVQDVFHIT FT IQEGKEDETPEEDVTAAPPQLEDGGQATVDDLKELNLGTKEEQKPIFVSAL FT LRADEIEEYYQLLSEYKDVFAWTYKEMPGLDPVIAVHHLAVKPGTRPIKQT FT QRRYRSELIPQIEAEIDKLIEAGFIREVQYPKWISNIVIVLKKSGQIRVCV FT DFRDLNDACPKDDFPLPIIEIMVDATTGHEALSFMDGSSGYNQIRMALEDE FT ELTAFRTPKGIYCYKVMPFGLKNAGATYQRAMQKIFNDMLHKNVECYVDDV FT VVKTKKRSDHLKDLRVVFERLRKYNLKMNPLKCAFGVTSGKFLGFIVKHRG FT IEVDQ" FT CDS join(5327..6262,6266..7375) FT /product="Gypsy-46_Mad-I_2p" FT /translation="MCLALVFAIQKLRHYMHAYTIHLVAKADPVKYVMSKP FT VLTGRLAKWALLLNQYEIIYVPAKAVKGQALADFLADHPIPADWKISDDLP FT DEEVFYIDIFPTWTMFFDGSARADGAGAGVVFMSPQRHILPYSFQLSELCS FT NNVAEYQALIIGLQMAINMGITALEIFGDSKLIINQLLTEYEVRKDDLIPY FT FRLATQLLQEFETVTLEHVPRKENQMADALANLASSMTLGEDEAADVPVCQ FT RWVIPLVTEMLLDDTNVISVLPVDVEEWRQPLIDYLEHGKLPDDPRHRSEI FT RRRAPRFLYYKETLYRRSFEVLLRCLGEEEVNQAMEEAHSGVCGAHQSGPK FT LHFQLKRMGYYWPSMVKDCLEHAKRCQACQFHANFIHQPPEPLHPTAASWP FT FDAWGLDVVGPITPKSSAGEAYILAATDYFSKWAEAIPLREVKKETVVRFI FT KEHIIHRYGVPRYIITDNGKQFSNRLVDELCEKYKFKQHKSSMYHAPANGL FT AEAFNKTLCNLLKKVIGRTKRDWHERISEALWAYRTTHRTPTQATPYSLVY FT GVEAVLPLESQIPSLRMAIQEGLTDEENAKLRLQELEALDERRLEAQQHLE FT CYQARLSKAFNKKVRPRSFQTGDLVLALRRPIITTHKTKSKFTSKWDGPYV FT IQEVYTNGAYLIMAEDGLKIGPINGRFLKRYYP" FT CDS join(10699..8525,8521..7664) FT /product="Gypsy-46_Mad-I_3p" FT /translation="MVFFKCFRNNTITILAKEGDSQDEGTTLKLYPPLTGP FT KALAFLVKDNSMHIKSWSSEVSWEVVDAVQPNTKKKACTLRVLILNHSHHA FT RDHHPASFKLLGDHIRSGAMAWNGTLSTTGEAVFDEFYWEWLEDVLSRSKD FT VLTKVGLYHAVYASLFSYDRHPSVLRAFFEHWCSATNTLHTAQGEMSISLW FT DLHRIGGLPIHGKFYDEVVPSAEELSLCNSRGLPASCRYLFWAYHKLFQDA FT QGKSGVRISSWIRFWYWEAMRYKKSSKKSCRNKTTRPKGDSDPSGVIGSTR FT RRSSDELRAFEDLGIVSEHVDESYLAAFLACWLCKFVFPTGDVNLVRPGVF FT KIASKMAAGESFSLAIPVLANIYNGLSIVSNSASTEDRAAVLPYHYVYGWL FT GEYFGTHFSLTTLDKSRPSSSTAAKMGPLMTKYSGVLSAKSLDDLQARALF FT ESCEDLRMDPLARVGSVRRGIVDNSHLRSSDLSYLISLRSGFVSLRQEDRC FT IVQPYSPHRFSRQFGFVQNLPGKLKEKNQSASLQAVYMHWESCTRACTNAV FT ITLPAKDEFKSNPVTRVYARWWSKVYYKNLGMASGTNSSHSGNDMSREGCH FT VVPMQVVALDCTSAAPLQDRPVALAPQRPCLSPRHPDASEEAGDEVDSHED FT GFILQQRQQVSNKRPLEDAQVDSDVNFRHKKKEVFRPPLLDDRVPFERDVC FT TSFSLVISYAFIILAFVSNIFLCLLVGPSCSFDLATADVYSYTEMLFAGEL FT PTDREIGDPPGAELVPNPPNFPSLPCVGEGMQEPVMRPTPLPASSEISLRG FT PNLSGTEQVIHRISLGAAMDIKSHIEERISKCPLEDLTLLNEDLSKLVSVI FT DNLNVDSSSLKIKIAELMAASTEYSSLRAISLEKLSPDVRAHQLATINSSL FT AQVQSSQQAASGDYQVTETSLTSVQVRLDALAREREQLVIEASQLESVLAE FT QGTTLSQYQEEISRLEREKCMTMELPILSPTEAETLKTLEGLLEDRLRSFG FT DIVFK" FT CDS join(14390..13956,13093..12353,12126..11551) FT /product="Gypsy-46_Mad-I_4p" FT /translation="MQFCREGCPAIMICSSSSCCILLCLFLSPSRSGAQPF FT AFKWSFRASLFSHSSMLGSFSVKSQHHINCFEVFAEEIRDPSTVEDEHSRA FT TLGKQPGKGSGQSVPDRTFNFRFRLIASFLLVLQARARAKERIGEKHDMRY FT LCFRPRRGVNRIQHAHFEDCPPLKIVFAVFLRFYSLQPFSFTIFLEMANPS FT NICLDLSLSSDTGAPRQGNIWRPSFSSSNGPLTVEDSVMRDAATATVVARN FT LITPRDNRILSRRSDELAVRESQALSVQCANSVSNMGQRLLVRTRQVESLT FT AEVAALNQEIRQLKRENRELHVLANSYSTSMKRKLDQLLDSEGRIQSDHRR FT FVDVFQRHLLPSSSGVRPSIEAPNNPSPVPPSSRVPPSTKASSTEASHKMV FT PDAHYSFTLFFFFFRRKTFFLSIIMSPPPFSLFFFRWCLMHTILSPFLFFR FT RKTFFLSIILSPPPFSLFFFFDLLTVACTFFCVYIIIFSQCTIPSPLILVF FT FPRHGWSFAQFAQSRTCVLNSHRISFASPGTVIYIWDCSFACTLITQLQPL FT RCLLPCIATTPLSSNPALLLLLGESLEYIYIYRKLLL" XX SQ Sequence 15231 BP; 4865 A; 3754 C; 3353 G; 3259 T; 0 other; aatttggcac gcccggtggg accatctcta cctctcatct ctatctttga atccgcaaaa 60 agcacaaatg gcatcaaaga aggctcaagt tgttctcgca gccaatgcaa ggaacaagaa 120 cgttatcacc gtaggcggtg tcacttcggg cgtcataact cgaagcaagg caagagctct 180 ttctgccgca tcttccaccc ctgcatcaac tccgccgaag gaacaagagc acctgaggca 240 tgaacctgtg atcaccctgg cttcgctaaa ggcgccaagg aaggaaagcc caaggaagta 300 ctctggtttc atgctttccg atgccgactc aagcggcaac tcagccatgc aagtcatgac 360 tactggagcg acttcaatcg atgagcagct ggctcatatg aatgaagcaa tcgcaaggct 420 aacacggatt gtggaagaaa aagaccagca aatcgccgca ctcgtcaacc aactagatgt 480 aaagcccgac gtgaaaatcg agcaagggga tggttcagta aagaaggaaa acgacgagga 540 tgaagagcct ccggtggaga aaatcgatgt gaagccggag ccaggccaag cagaggcact 600 catgggatct ctttctatcc aacaactgca agagatgatc accagcacca tcaaggcgca 660 gtacgaaggg agctcacata cctcatcatt ctactcaaag ccctactcca agaagattga 720 tgccctaaag atgccaaggg gttatcaacc accaaagttc atgcagtttg atggaaaagg 780 aaacccgaag caacatgtcg cacatttcgt cgaaacctgc aacaatgcag ggacggaagg 840 agattacctc gccaagcagt ttgtgcgctc gttaaaagga aacgcctttg agtggtacac 900 agacctggag cccgaatcca tcaacagctg ggaacagttg gaaagggaat tcctcaaccg 960 cttctacagc acccgccgca ccgtgagcat gctagagctg acaagcacga agcaatggag 1020 ggatgagcca gtcgtggact acatcaaccg atggcgcaat ctgagcctcg actgcaagga 1080 caggctctcg gagatctctt cgattgagat gtgcgtccaa ggcatgcaat gggggttaca 1140 ctatatcctt caaggcatca aaccacggac atttgaagag ttagccaccc gtgcccacga 1200 catggagcta agtattgccc atcacgggaa gaaagagccg atcaccgact tcaagaagga 1260 taaggtgttc tccccaaatg tagacaagac tgggaagaaa ccccccaagg aagcgttcac 1320 cgtcagcact gcgcccgtca agaccgcctc cgcgcctatc aagatctcct ccaaaaccaa 1380 agcaaaggag ataaagaaaa gtgagcctcc tcgcacccaa gaaaggtaca aaagcacctt 1440 gagggaattg gagcagaagg tatacccttt tcctgactca gacatggatg caatgttaga 1500 cgacttgcta gaaaagaagg taatcgagct acccgaatgc aagcggcctg aagaaatgaa 1560 tcgcataaac gatcctaaat actgcaagta ccatcgaatc gtgagccatc ctgtgggtaa 1620 atgcttcgtc ctcaaagagc tcatcatgaa gctagcacaa caagggcgaa tcgagctcga 1680 cctcgaagac acggccgcga cacatactac tacaattgca tttggatctt tcgatcccgt 1740 gcctctccaa gcagcacctg accattccta tcaatgctca agttacacga taccttctgc 1800 gcaaccatcg ccgggggcaa acgaacaaga tgcacatgcc gatgatgaag aaggatggac 1860 attggtgacc tacaaaaaaa caaggaaacc aaaaccacaa gccataagac aaaaggtgga 1920 acaagtgaga aagcaccgtc gccgcaacag taggaagccc aaaagaaacg taaaagttga 1980 taagccaacg tatgctgggg aacctatgga gcaagagcca cgcattcctg tctcattgca 2040 cgagtacttc ccgaatgact tcttccaaca gtgcactatc gctgcatgcc acatggtcga 2100 agtagaaata gaagaacctt caaaaggcaa agatatcacc actgagggag aaaaaactct 2160 cacgctcgaa gaaggtctgc caacacactt tagcattgag gaagcgctac gattaccaaa 2220 gaagatgcga atagcattag cagcggtctt ggaaagtccc aatgaccacg aagtgcaaga 2280 aagcaagaac gaaggcttca agcttcggcc acatgaatat gccacatgct gtgccatcga 2340 ggacacaatc catttcaccg acgaagactt gctgctagga tccaagcctc acaaccgtcc 2400 tctcttcgtc tctgggtacg taagggagca caaagtcaac cgcatgcttg tggatggtgg 2460 atcagccata aacatcatgc caaagtcaac aatgactaca atcggcatca aggcggatga 2520 actgtcctta agtcgtctac taatccaagg ttttaatcaa ggaggacaaa aagcgatggg 2580 catgatccga gtggagatga ctattggtga actcaagtca agcacgatat tccacgtgat 2640 tgatgcaaga acttcctacg gcttgctctt aggaaggcct tggatccatg caaatggagt 2700 agtaccgtcc acccttcacc aatgcttgaa attctaccga gaaggagtga aggtgatcta 2760 tggcgacacc aaaccattca ccgaagccga atcacatttc gcagacgcca agttctacat 2820 ggatgaagac atggtgctcg aagctcttcc aaaagagatc aaatccacgg gtaaagcaac 2880 acctaaaaag caggagtggc aagccatgcc caagaagcaa gaagaagaag ccatgtcgtc 2940 ttcaagcaag aacgatgatg agcttgctaa acctgcaaca accaaaggga gtaggacgcc 3000 ctcaaatgta ctaaacacac ccgttttccg atacatcccg atgtcaagaa gaaagaatgg 3060 tcaatcccca ttcgaaaccg aagcaagcaa agccgatgca caacggtaca tggataatgt 3120 aaagttgctc aagacgaatg cagttctacc tctgacacag ctaagcaacg ctaaggttgc 3180 aagattacca caaggcttcg taaaagctct accaaagagg gcggaaccaa gttttctccc 3240 aaccaagagg accgaagaag gttttgatcc gaacgcctac aaactcatgt caaaagctgg 3300 gtacgacttc gcttcttctt cgaatcctgg aaaaaaggtt tcaaacaccg tcaacaataa 3360 agaacgtgac ctcaccgaga ctcaaaagaa gttgaagaag catggttacg gagttaacaa 3420 caacaaagct ggacttggct tcacaccaaa tgcacccgtg aagatttcaa gcaaagcgaa 3480 aaatgctagc actcaacaca tcagcgtgag cattgaacaa gatcgagagg agcctaaatc 3540 cacccctcga acgccagtct tcgataggat gaatcgttca agacccagaa cgtcagccct 3600 tgatcacatt ggtggtcaaa accgaacctc cgtcttcaag aggcttaaca ggccaacatc 3660 ccgaagctct atttttgaaa ggttgtcaaa acctaataag caaagcaaca cggctagctc 3720 tcctcctcgt cagtcagctt tggaaagact tgaagacaac atgaagtttt ctggaaatag 3780 ggaaacaacg tcaaaggaag aaaagctcga caggctagca gaaaaaggcg atattcgaag 3840 ctcaattcct tcaaggatga agcgtcaagc aatcttggag gttgacgcaa atggaccact 3900 gatagtaaga aggcgcacca tcatccatac tggacaatct gcataccaac aaacccaaga 3960 ggacgacact aaagaggaag tccaagatgt cttccacatc acgatccaag aaggcaaaga 4020 agacgagacc cctgaagaag atgtcactgc tgcaccacca caacttgagg atggggggca 4080 agccacggtt gacgatctca aggagctcaa cttgggcaca aaagaggagc aaaaacctat 4140 ctttgtaagt gcactgctaa gagcagacga gatagaggag tactaccaac tgctatcaga 4200 gtacaaagac gtctttgcct ggacttacaa agaaatgccc ggccttgacc ctgtcatcgc 4260 tgtgcatcat cttgcagtca agcctggaac acgaccaata aagcaaactc aaaggcgcta 4320 tcgatccgag ctcattccac aaatcgaggc agagattgac aagctaatcg aagcaggatt 4380 cattcgagag gtgcaatacc ccaagtggat ctccaacatc gtcatcgtcc ttaagaaatc 4440 tggacaaata cgtgtttgcg tagacttccg ggacctcaac gacgcttgtc cgaaggacga 4500 cttccccttg ccaatcatcg aaatcatggt ggacgcaacc actggccacg aggcactgtc 4560 attcatggac ggctcttctg gatacaatca aattcgtatg gctctcgaag acgaggaact 4620 aacagcattc cgcactccaa aaggtatcta ctgttacaag gtgatgccct ttggtctaaa 4680 gaacgctgga gctacatatc aacgcgcaat gcagaaaatc ttcaatgaca tgctacacaa 4740 gaacgtagaa tgttatgtgg acgatgtggt ggtcaaaaca aagaaaagat cagatcactt 4800 gaaggatttg cgagtagtgt tcgaaaggct gcgaaaatac aacctcaaga tgaacccgtt 4860 aaaatgtgcg tttggcgtca cctccggaaa gttcctcggc ttcattgtca agcaccgtgg 4920 tattgaagtg gaccaataaa aaatcaaggc cattcaaagc atgcctgagc caagaaacct 4980 gcacgagctg aaaagtctac aaggacggct agccttcatc agacgcttca tctctaacct 5040 tgcagggcgt tgtcaaccgt tcagccgact catgaagaag gatgttccgt ttgtatggga 5100 cgaagcatgc cacaatgctt ttgaaagcat aaaaaagtat ttgtcaagtc cacctgtctt 5160 gggggcgcct gtgcccggga aaccactcat attgtacatc gccgctcagg aaagttcagt 5220 tggagcactc ttggcgcaag agaatgaatc ccagaaagaa tgagcgcttt actacctcag 5280 ccgaaccctc accggcgccg agttgaacta ctccccaata gaaaagatgt gccttgcctt 5340 ggtgttcgcc atccagaaac tcaggcatta catgcatgct tacaccatcc acttggttgc 5400 aaaagctgac ccggtcaaat acgtcatgtc caaacccgtc ttgacagggc gactcgctaa 5460 atgggcgctg cttcttaacc aatatgagat catctacgtc ccagctaaag ccgtaaaggg 5520 acaagcgctg gcagactttc ttgccgatca cccaatccca gctgattgga aaatctcaga 5580 cgacttgcct gacgaggaag tgttctacat cgacatcttc ccgacatgga cgatgttctt 5640 cgacggatct gcacgagcag acggagcagg ggcaggagta gtattcatgt cgccacaaag 5700 gcatatatta ccttattcct ttcaactaag cgaattatgc tccaacaacg tcgctgagta 5760 ccaagcactg atcatcggac tccaaatggc gatcaatatg ggaatcacag cccttgagat 5820 atttggcgac tccaagctca taatcaatca actcttaact gaatatgagg tgaggaaaga 5880 tgatctcatc ccatacttcc ggctggcaac tcaactgcta caagagtttg agactgtgac 5940 actagagcat gtgccaagaa aagaaaatca aatggcagac gctcttgcca acctagcctc 6000 aagcatgaca ttaggagaag acgaagctgc agacgtgcca gtctgccaaa gatgggtgat 6060 ccccctcgtc actgaaatgc tactagatga tacaaatgtc atctcagtac ttccagtcga 6120 tgttgaagag tggagacaac cgctgatcga ttacttagag catggaaaac ttccagatga 6180 tcctagacac cgctccgaaa tacgtcgacg agcacctcgc ttcctctatt acaaagaaac 6240 actctaccga cgctctttcg aatgagtact tctgagatgc ctaggtgagg aagaagttaa 6300 tcaagccatg gaagaagcac actcaggcgt atgcggggcg catcaatctg gaccaaagct 6360 acatttccag ctcaaaagaa tgggttacta ctggccaagc atggtgaagg actgcctgga 6420 acatgccaaa aggtgccaag cctgccaatt ccacgccaac ttcatacacc aaccacctga 6480 gccattacac cctacagctg cttcatggcc attcgatgca tggggattgg acgtcgtagg 6540 accaattact ccgaagtcat ctgcaggaga agcttacatc ctagctgcaa cagattactt 6600 ctccaagtgg gctgaagcca tacccctaag ggaagtaaag aaggaaactg tcgtccgttt 6660 catcaaggag cacatcatcc accgatatgg ggtgcctcgc tacatcatca ctgacaacgg 6720 aaagcaattc tccaaccgac tcgtggatga gctctgtgag aaatacaagt tcaagcagca 6780 caagtcttcc atgtatcatg ccccggccaa cggtcttgca gaagcattca acaaaacatt 6840 gtgcaatctc ttaaagaagg tgatcggccg aacaaagaga gactggcatg aaagaataag 6900 cgaagcactt tgggcatatc ggacgacaca taggactcct acccaagcta cgccttattc 6960 tcttgtatat ggcgtggaag ctgttctacc gctcgaaagt caaatcccct cactgagaat 7020 ggctatacaa gaaggcttga ctgatgaaga gaatgcaaag ttgcgccttc aagagttgga 7080 agcactcgac gaaagaaggc tcgaagctca acaacacttg gaatgctacc aagcacggct 7140 atccaaggca ttcaacaaga aggtccgccc aaggtctttc caaactggag atctcgtcct 7200 cgcattgcgt aggcctatca tcacaactca caagacgaaa agcaagttca catcaaagtg 7260 ggatggacca tacgtaatac aagaggtcta caccaacggc gcctacttaa tcatggcaga 7320 agacggcttg aagattggcc ctatcaatgg aagattcttg aagcgctact acccctaaaa 7380 ggcgacaacc aaagctcctg gcccgcaaga gcataaactg tgtacggcaa aatcatcata 7440 aaaaaaaatg catttgaact acgttatgac ttgatccctc ctcaacagag ggtacgtagg 7500 caacttgaaa cgtcaaaact tcaagtacag tcacaccatc taaaaaaaaa acactttgaa 7560 gaatgaagag caaattcaag aatgtaaata ctttatttct ttgaaagaag gagtcggctc 7620 caaaagcctt attacaaaaa aaaaaaaaaa acagaagata ctacttgaaa actatgtccc 7680 caaaactacg aagacgatct tcaagcaagc cttccaaagt cttcaaagtc tctgcctcgg 7740 tgggagacaa gatgggcaac tccatagtca tgcatttctc tcgttctagg cgtgaaatct 7800 cctcctggta ctgagaaagt gtagttccct gctccgcgag aacactttca agttgcgatg 7860 cttcgattac caactgctct cgctctctcg ccaacgcatc tagacgcacc tggacagaag 7920 ttaaagaagt ctctgtaact tgataatctc ccgaagcagc ttgctgagaa gactggactt 7980 gagccagtga cgagtttatt gttgctagct gatgagctct aacatctgga ctcaacttct 8040 ccaaggaaat agcacgcaag gaagaatact cagtcgaggc ggccataagt tcggcaatct 8100 tgatcttcaa ggatgaagag tcaacgttaa ggttgtcaat cacagaaaca agcttcgaca 8160 aatcctcatt gagcaacgta aggtcttcca acgggcactt agaaatcctc tcctctatat 8220 ggctcttgat atccattgcc gcaccaagac tgatgcgatg gatgacttgc tcagtaccgc 8280 taaggttcgg ccctctcaaa gagatctcag agctagctgg caaaggtgtt ggacgcatga 8340 cgggttcttg cataccttca cctacacatg gcaaacttgg gaagttcggc ggatttggaa 8400 caagctctgc accaggcgga tccccgatct ccctgtctgt aggtagttcg cccgcaaata 8460 gcatctccgt ataggaataa acatctgcag ttgccaaatc aaaagaacaa gaaggcccaa 8520 cctaaagaag acaaagaaag atgttagaaa cgaaagccaa aatgatgaaa gcataagaaa 8580 tcacgagaga aaatgaagta catacatctc tctcaaatgg cacacggtca tcgagtagag 8640 gaggtctaaa cacttctttc ttcttatgac gaaaattgac atcgctgtca acctgagcat 8700 cctcaagtgg tcgcttgttt gaaacttgtt gacgctgttg caaaataaat ccatcttcgt 8760 gcgagtcaac ttcatctccc gcctcttcag aagcatccgg atgtcgagga gacaagcatg 8820 ggcgttgagg agctaaagct acaggtctat cttgtaaggg agccgcactg gtgcaatcaa 8880 gagctaccac ttgcatagga accacatgac agccctctct cgacatatca ttgcccgagt 8940 gagaagaatt ggtaccactt gccatcccca agttcttata atataccttt gaccaccaac 9000 gagcataaac acgggtcact ggattactct tgaactcgtc cttggctggc agcgtgataa 9060 cagcatttgt acatgcacgg gtacaagact cccaatgcat atacacggct tgcaaggatg 9120 ctgattggtt cttttccttc agcttgcctg gcaagttttg gacaaaacca aattgcctgc 9180 tgaaacggtg gggactatat ggctgaacaa tgcatcggtc ttcttgccgc aaagaaacaa 9240 accccgaacg aagacttata agataagaca agtctgacga gcggagatgc gaattgtcta 9300 cgatgcctcg ccgcaccgag ccaactctcg ctaaggggtc catcctcaaa tcttcacaac 9360 tttcaaatag cgctcgtgcc tgcaaatcat caaggctctt cgcggagagc acgccagaat 9420 acttcgtcat caaaggcccc atcttggctg cagtcgatga agaaggcctt gacttgtcta 9480 gagtcgtcaa agaaaagtga gtgccaaaat attcacccaa ccaaccatac acatagtggt 9540 aaggaagcac cgcagcacga tcttcagtgc ttgccgagtt cgaaacaatg ctcaagccat 9600 tgtaaatgtt ggctaaaacc ggaatagcaa ggctaaaaga ctcacctgca gccatcttgc 9660 tagcaatttt gaaaactcca ggacgaacta agttgacgtc gcctgtcggg aaaacaaact 9720 tacaaagcca acaagctaag aaagcagcta ggtaagactc atccacatgc tctgatacta 9780 tgccaagatc ctcaaacgct ctcaactcgt cagaagagcg gcgcctggtt gagccaataa 9840 caccggacgg gtctgagtct ccctttggcc tagtggtctt gttacgacaa cttttcttcg 9900 aagacttctt atacctcatg gcctcccagt accaaaatcg gatccatgag gaaatcctca 9960 cgcctgattt accttgagca tcctggaaaa gcttgtgata cgcccaaaac aaatagcggc 10020 aactcgcagg caatcctcgg ctattgcaaa gagaaagttc ctccgcgctg ggaacgacct 10080 cgtcataaaa cttaccatgg atcggcaagc ctcctatcct gtgaagatcc cacagtgaaa 10140 ttgacatctc cccttgcgcc gtgtgaagtg tgttggtcgc tgaacaccaa tgctcaaaga 10200 acgcccgaag gacggaagga tgacgatcat aactaaacaa agatgcgtac acagcgtggt 10260 aaaggcccac tttagtaagc acatctttag atcggcttaa gacatcttca agccactccc 10320 aataaaactc atcaaagacg gcttctccag tagtcgacag ggtaccattc caagccatgg 10380 ctccgctgcg aatgtgatca ccaagaagct taaacgaggc cggatgatgg tcacgagcat 10440 ggtgcgaatg attcaaaata agaaccctca atgtgcacgc ctttttcttc gtatttggtt 10500 gaacagcgtc taccacctcc caagatactt cagaagacca cgacttaata tgcatggaat 10560 tgtctttcac gagaaaagca agcgccttag gaccagttag tggcgggtaa agcttcaacg 10620 ttgttccctc atcttgtgaa tcgccttcct tcgcaagaat ggtgatggtg ttgttcctaa 10680 aacatttgaa aaataccatg accgcaaatc agccacaaaa cttgagcagc acgacaaaga 10740 tggcagctac aggatggtcc ttcaaggcac gctacagtgg caaaggaaac caaaatgcta 10800 cgcaatcgca ctacgcaaac ccgcagcgat tacgcaagca gtttcttgca ccgcatgtcg 10860 acgtcaccac caagaaagaa ctgtgaccaa aaggcattac gcagcgaagc cccgctgcag 10920 gctcttgcac agcaccacac ggcagcgcgc caccgaggga aaactgtggt caaaaggcac 10980 tacacagcga aacctcgttg cagtctcttg cacaagcacg gcacccacga cctgctacca 11040 cggctctaaa agcttcgcga agatcctggc gtcaagctct gccttctcaa gattaaagat 11100 tcctgacatt acaaacaaag aaatccatca gtggggacac acacattgtg cgtaaaaaaa 11160 aaaaaaacat tatattatgt taatatatat atatatatat agacatatgt gtgcacggtt 11220 tggtgatggg acaagtgcac ggaatggaga tggtcaaacg ggacgatcaa cttccataca 11280 tatatatata tatatatata tatatatatg gcttgaaaag acgcaaatgg tgatggtgat 11340 gggacaaata tatatataca tatatgcatg gctcaaaaga tggaaatggt atgcacggct 11400 caaaagacat atatatatat atatacacac acatgtgact caccaagtaa aagcagcatg 11460 aaggaattgc agagggcaaa gcacattata ttacatatat atatgtatgc acggtgataa 11520 agcaaactac aacagcgata aagcaaacta caacagcagc tttctgtata tatatatata 11580 ctcaagtgac tcaccaagta aaagcagcag cgcaggattg ctggacaatg gtgtagtggc 11640 gatgcaaggc agcaagcaac gcagtggctg aagctgtgta atgagtgtac aagcaaagga 11700 gcagtcccat atatatataa cggtccccgg agaagcaaat gaaatgcggt ggctattcaa 11760 aacgcaggtc cgtgactgtg caaactgtgc aaacgaccac ccgtgcctgg gaaagaaaac 11820 caaaatgaga ggtgatggga tggtgcactg tgaaaatatg attatgtaca cacaaaagaa 11880 agtgcaagct actgttagca agtcaaaaaa aaaaaaaagt gaaaagggtg gtggagacag 11940 aatgattgaa aggaagaaag ttttccgtct aaaaaaaaga aagggtgaaa gaatagtgtg 12000 catcaggcac catctaaaaa aaaaaagtga aaagggtggt ggagacataa tgattgaaag 12060 gaagaaagtt ttccgtctaa aaaaaaaaaa aaaaagggtg aaagaatagt gtgcatcagg 12120 caccatctaa aaaaaaaaaa agtgaaaagg gagggtggtg gagacataat gattaaaaga 12180 aagaaagcca tctaaaaaaa ggaagtaaca catcttagtc agatatacgt tttatttgta 12240 tttagcacaa catactgaat aaaataaagc atgtccattg atatctctaa gaaattacaa 12300 gtgcgtaaaa aaaaaaaaaa aaaaaaaaaa gagggagcct tcacaaatgt cacttatgtg 12360 aagcctcagt acttgaagcc ttagtactcg gcggaaccct agaagaggga ggcactggag 12420 atggattatt cggagcctca atacttggtc gaactccaga tgacgaaggc aaaaggtgcc 12480 tctggaatac atccacaaac ctccgatggt cactttgaat ccgaccttcg gagtccagca 12540 gctgatcaag cttcctcttc atgctcgtcg aataactatt tgcaagcaca tgcaactctc 12600 tattctcgcg cttgagctgt ctgatctctt gattaagagc tgccacctcg gctgtcaatg 12660 attcaacttg gcgagttcga acaagtaagc gttggcccat gttggaaaca gagttcgcac 12720 actggacact gagagcctgg gactctcgaa cagctaactc atcggaccgt cgtgaaagta 12780 tcctattatc tctaggagtg atgaggttcc tagctacaac cgtagccgtt gctgcatccc 12840 tcatcacaga gtcttcaact gtaagagggc cattagaaga tgagaaggac gggcgccata 12900 tattaccctg acgcggtgca cctgtgtcac tgctgagact caaatctaag caaatgttag 12960 acgggttagc catttccaaa aagatggtaa aagaaaaggg ttggagtgag taaaatctca 13020 gaaatacagc aaagacaatt ttcaaaggcg ggcaatcttc aaagtgtgca tgttgaatac 13080 gattgacacc tctttaaaaa gaagaggcaa cacaaccact tgttcaaaaa aaaaaaaaat 13140 cgaagagaca ccactcttcg aatttcaaaa cccggatttt cctgcgtaaa gtccgtcaac 13200 acttttcaga cgcagtctca gctttcggct atcacgtgca actttgccag agatcactga 13260 caaagttgaa aacgtgtgga gtccatcatt cccacctacc cgacttttgg ccgacaaagc 13320 atgggtgaca aggccacatc caccctgcca cttgctgttg ggagctcacc atataattcg 13380 acctccatcc tctatagcaa ggcacacatc cagcctgact cttcttcctt gccgaatgca 13440 tctgcaacca aaactcagtt ttcttcctcc ctgaaaatac aaacgcctga ctcttcttcc 13500 ttgccaagaa tacatctgca actaaaacct ctcaacatac tcagttttct tcctccctgg 13560 aaacgcctct tcaaccaagt cacaccagag caaaggtatc tcatatcact ggggttgaga 13620 gcaagagtat ctcatagcat gctttctccc tatccttttc tttgtcctcg ttcttcactg 13680 cgaagacaag gataaagaaa gcaatatgtc ggaacctcca ctcaagctcc tggtaaggaa 13740 ccgactgcct ggaacctttc cctgattgct cacctagcac tgctctcgaa gtacccattg 13800 tttcaacatc ttatgcttcc agagaagata ccacatctgc ctggagaaca gaagaggcaa 13860 gtgaaaatga tgcatcgaag catgtggaga caagcgcaac aaatacatgt gctgatcatc 13920 cgctacttct tcaaaagcaa aagtatctca tatcatcggg gtcgaaagca aaggtatctc 13980 atatcatgct tttcccctat cctttccttt gcccttgctc ttgcctgcag aacaaggaga 14040 aaggaagcaa tcagtcggaa cctgaaatta aacgtccgat caggaactga ttgcccggaa 14100 cctttgcctg gttgcttacc tagcgttgct ctcgagtgct catcttcaac tgttgacggg 14160 tctcgaattt cctcagcaaa tacttcaaaa cagttgatat ggtgttggct ctttacactg 14220 aagctgccaa gcatggatga gtggctgaaa agtgatgctc tgaaggacca tttaaaggca 14280 aagggttgcg caccacttcg gctaggcgaa agaaacaagc agagaagaat gcagcacgat 14340 gagctggaac aaatcattat ggcaggacac ccttctcggc agaactgcat aatccagacg 14400 gaggggtcta agtcaaatcc aagcctgcca tcgttgctat aatcaaagag ctcgagaagc 14460 ttcaacaacc tttcgctggc actgtcgccg aagagcaaag tctcgataat ccttaaagat 14520 caagtcacca actggaagaa gagcccatca atcttgaaga tcataccgtt gaccaaactg 14580 ctcagggttc atatgaaaat gctgcgaact tccttgatct ttcaaagcaa attctttgca 14640 tgtcctgaaa ctgctcgtgg tcatgtttaa gttcgagatc aagcctcaac ggcccttaaa 14700 gaaatcacaa gtccgattca agatcaagtg tccaccaccc ttgaatcaaa tccagttcaa 14760 gattaagtct gtggaaagtc ccttggagga aaccagaaaa ccctccagcc cagttcaaga 14820 tcaagtgtcc accacccttg aatcaaaccc agttcaagat taagcctgtg gaaagtcaac 14880 aattggagga aaccagaaaa ccctccaacc cagttcaaga tcaaagctgt ggaaagtcaa 14940 caagcgcaac aaaatacgtg ccgattcatc cattaccaaa gccaaagatc atctaccaca 15000 tgaagctcct tgtggtccaa tttcacctcc aagatcaagc ctcaacggcc cttgaagaaa 15060 tttcaaacaa aattcaagat caagccccaa cggcccttga agaaattacc agcccagttc 15120 aagatcaagc ctcaacggcc cttggatcga catctacagt aagggacttc aaaacgcatc 15180 ttctacacgt gacaagcaca tgtatacgac gcgccttgaa gtgggggcat t 15231 // ID GYPSY2-LTR_MT repbase; DNA; EDCOT; 1619 BP. XX AC . XX DT 31-JUL-2005 (Rel. 10.07, Created) DT 21-JAN-2007 (Rel. 12.02, Last updated, Version 2) XX DE LTR consensus of M. truncatula gypsy element. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; GYPSY2-LTR_MT. XX NM GYPSY2-LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1619 RA Gentles A. and Jurka J.; RT "Gypsy-like retroelement from Medicago truncatula."; RL Repbase Reports 5(7), 176-176 (2005). XX DR [1] (Consensus) XX CC Internal sequence is GYPSY2-I_MT. XX SQ Sequence 1619 BP; 511 A; 291 C; 171 G; 644 T; 2 other; tgtcataccc caatttttga cctaaggtcc cactgacaca tgtcacttaa ctctgatcga 60 tctctgactt ttcagtaaaa aaattcggca gggaggtatt ttaaaatacc tcattttttt 120 gattccgagt cggaccctct tttctctttt ttattttatt tccatctttt attaatttta 180 attttaagat aagttacttt ttttatattt aataattttt aatttccatc ttttaatttt 240 atttttcttt acataattta gtttaatttg tttttatttt tatttcgtat tagatttatt 300 ttatttttat tttatttctt tttaattaat tagtgtccaa aaaaacaaag tgtcaatagg 360 tccaaaaata aaatgcccaa ggtctaaaaa aaaattcaaa tcaaagtgtc aactttaaca 420 ttcctttttc aaaattcaca taattgtcca tcatttccat taaaccaatt ttcctttttt 480 catcaaactc ctgacctata aatagagccc tcattccaca caatttcaca caccaaaagt 540 tctcttgagt agtcaaagaa cttttctctc ttctccctct ttagcttgtg ttgacgagct 600 attcttttct tctccctctt ttttctgtcc cttcggaata agtcccttcg gaaaagtccc 660 ttcagtaatt tttgcccctt cggttgtcaa tttcttttat tttcttgcat tttatttctt 720 tttagcattt ttgcattttt ttaatttcta tttagcattt taattattgt tatttatttt 780 ccagcaatta gaatgtattt aggtccaatg taaatataaa tgagaaaagt gtgtgggtat 840 ttgtttgtgt cattttattt ctttaccgcc ttagatatat ccaaaaatgc aaaaaaatta 900 gattagggat tttgtggtga tccaacgtca ctacaaaaat ccacgcgctt ttatttttat 960 tgctccgtta gtttaatttt tatttaatat tccaaaaaaa caacaaaaaa catgcaaata 1020 atcaaaatca caaaaatatt ttcataaata aaccttgatc caaatcaagt gaccgcattt 1080 ttattttctt ttcttaatca aacttcaatc aatttaattt tactttaagt ctcttttttt 1140 aatattaaaa aacacaaaca aatacttatt tgccacttgg cttttcattt taaaaccttt 1200 ttcaaaacta ataaaaaaca caaaaaccaa tcaaacgtca ttttctaccc cgaactacga 1260 ggttttgatc cctcacgggt acgtaggcag aggacaatcg tcctttcaaa tcaataaaaa 1320 atgtagataa ttaggtcttt atttttttca ctttaattct aayttctttt tmaaaataag 1380 caagcaagtt atagcacatt aattaaataa aatcaagagg ttctcgtaga gtactacgaa 1440 catatagggt gctaatacct tccctttatg taactaaccc ccgaacccta aatcttttca 1500 aaatggggta gtttgaactt tttccccttt ttcttaaaaa attaaatgtt cagtcgtgaa 1560 ataaattagt gagtcaaaag ctaatcaaat agccttgatc tccgaaaaat gacgcgaca 1619 // ID Copia-60_VV-I repbase; DNA; EDCOT; 4059 BP. XX AC chr14; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-60_VV_; KW Copia-60_VV-LTR; Copia-60_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4059 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr14; Positions 10835211 10839269. XX CC Positions [1483-2013] - Integrase core CC 'ATAAT' target site duplication CC LTRs are 90% similar to each other. XX FH Key Location/Qualifiers FT CDS 1411..3345 FT /product="Copia-60_VV-I_1p" FT /translation="MVNGLPQFKASKTVCTDCMVETQHRNPIPKKSTWRAS FT SKLQLIHADICGHITPISNNKKRYLISFINDFSRKAWIYFLVEKSEALVIF FT KQYKSCVEKETGSYIKCLRTDRGSEFTSQDFNEFCKENGIKRQLTTAYTPQ FT QNGVAERKNRTIMNMVRSMLSEKKLPKTFWPEAVNWIVHILNRSPTLAVKN FT MTPEEAWGGVKPSVEHFRVFGCISHVHVPDIKRTKLEDKSFTCVLLGVSEE FT SKAYRLYDPITKKIVINRDVVFEEDKSWDWDKSYKEHVVAMLEWGDNEENV FT ATNNEGEVESEDGSSAEEVGVVSPNRVDEESSPSSNEEKVRRPPVWMRDYE FT TSEGLSEEEDETTLALFASGDPFYFEEAVKSAKWRAAMDSEIKSIEKNDTW FT VLTDLPAGAKKIGVKWIYKTKLNEYGEVDKYKSRLVAKGYMQQHGVDYTEV FT FASVARMDIVRMIIALVAKRNWTIYQLDMKSAFLHGELSEEVFVEQPRGYE FT QKDNPHKVYKLKKALYGLKQASQAWFSRIEAHFVNEGFERCHSEHTLFIKT FT SKGGKILILSLYVDDLIFIGNDESMFYEFKSSMMHEFDMTDLGKMRYFLGI FT EVLQKTYGIYISQKKYALDVLKRFGMEESNFVHSSIVTGFRRKWSQG" XX SQ Sequence 4059 BP; 1356 A; 597 C; 971 G; 1135 T; 0 other; ttctggtatc agagccaggt tcaaagcagc agcttttgta atttgcagca gcaagagaga 60 tgacaattga agggaatttt gtgcaacctg ctattcctcg atttgatggt cattacgatc 120 attggagcat gttgatggaa aaaattttaa gatctaagga gtactagagt cttgtggaga 180 ctggttatgt tgagccagaa agcggagcag tattgacaga ggcgcaacag aagaagcttg 240 atgagatgaa gttgaaagac ttgaaggtga aaaattattt atttcaagct atcgatcgaa 300 tgattctaga aaccatccta caaaagaaca catccaaaca gatatgggat tccatgaaga 360 agaagtatga gggcaatgaa agggtgaaac gatccattct tcaagctctt cgcaaagagt 420 ttgaaactct tgagatgaaa tttggtgaaa gtgtctctaa ctatttctca agagtaatgt 480 atgtatccaa taagatgaga gttcatggtg aacaaatgag agatgttaca ataatagaaa 540 aaaatacttc gatcattgag tgacaaattc aattatattg tttggtcaat tgaagagtca 600 aaggacattg atctcctatc aattgatgaa ctgcaaagtt ccttaattgg tcacgagcag 660 aagttccata ggcacaaagg agaagagcag gcactcaagg taattcatga agaaagtgta 720 ggaggacgag gtcatggtcg cggatcctct cgaggaagag gcagaggtag aggacgccaa 780 tccttcaaca aagatactgt agaatgctac aagtgtcaca aacttggaca ctttcaatat 840 gagtgcccaa gttgggacaa agaggctaat tttattgagc ttggagaaga agaagcgatg 900 ttgttgatgt cctatgttga gataaatgaa gcaaaaaagg aggatgtttg gtttttagat 960 tctagttgca gtaatcatat gtgtggagat aaaactctct tctacgactt caatgaacgc 1020 ttcaggcaga tggtgaagct aggaaacaac tcaaaaatga cagtgatggg taagggtaat 1080 gtaaggttga aagtgaatgg attcaatcat gtagtcactg aggtttttta tgtgcctgag 1140 ttgaaaaaca atttactgag cattgggcag ctgcaggaga aaggtttagc gattcttatt 1200 caacataaca agtgtaaaat ctatcatcct gagaaaggct tgatcattca agtagagatg 1260 tttgccaata gaatgtttat tttattggtt gcgccacaac taaagaaacc aacttgcttt 1320 cacacaacta cagaagactt atcacatctc tggcattgct gatatggaca cttgagtcac 1380 aaaggattga ggactcttca aaacagcaag atggtgaatg gactaccaca attcaaagct 1440 tcaaaaaccg tatgcactga ttgcatggtt gaaacgcaac atagaaatcc aattccaaag 1500 aagagcactt ggagagcttc ttcgaaactt cagctcattc atgctgacat atgtggccat 1560 atcacaccga tctcaaacaa caaaaagagg tatctaatta gcttcattaa tgattttagt 1620 cgaaaggcat ggatttactt tttagttgaa aaatctgaag ctttagttat ctttaaacaa 1680 tataaaagtt gtgttgagaa agaaacaggt tcctatatta agtgtttgcg tactgatcga 1740 gggagtgagt tcacttcaca agactttaat gaattttgta aagaaaatgg catcaagagg 1800 cagttgacaa cagcttacac tccacaacag aacggagttg cagagaggaa aaatcgaacc 1860 atcatgaaca tggttcgaag tatgctttca gagaaaaagc ttccaaagac tttttggcca 1920 gaagctgtga attggatagt acatattcta aaccgaagtc ctactctagc agtgaagaac 1980 atgactccgg aggaagcttg gggtggagtc aagccttcag ttgaacattt tcgagtgttt 2040 ggttgtatct cacatgttca tgtacctgat atcaagagaa ccaagttgga agataaaagt 2100 tttacttgtg tgttgttggg agttagtgaa gagtctaaag cttataggct ttatgatcca 2160 ataaccaaga agattgtaat caacagggat gtagttttcg aagaggacaa gtcttgggat 2220 tgggataaga gctataaaga acatgtggta gctatgttgg aatggggaga taatgaagaa 2280 aatgttgcta caaataatga aggtgaggtt gagagtgaag atggaagtag tgcagaagag 2340 gttggggttg tttctccaaa tcgagtagat gaagagagtt cacctagttc caatgaagag 2400 aaagttagaa ggccaccagt ttggatgaga gattatgaaa cgagtgaggg tttgtctgaa 2460 gaagaagatg agactactct agcattgttt gcatctggag atccctttta ttttgaagaa 2520 gctgtgaaaa gtgcaaagtg gagagctgct atggattctg aaataaaatc catagaaaag 2580 aatgatactt gggtgctaac agacttacct gcaggtgcaa agaagattgg tgtcaagtgg 2640 atttacaaaa caaagcttaa tgagtatgga gaggtagaca agtacaagtc acgccttgta 2700 gcaaaaggct atatgcaaca acatggggtt gattacacag aggtttttgc atcggtggca 2760 agaatggata tagttcgaat gattattgct cttgtagcta aaagaaattg gacaatttac 2820 caactagata tgaaatcagc ctttctccat ggagagctaa gtgaagaggt gtttgttgag 2880 caaccaagag gctatgagca aaaggacaat ccgcacaagg tgtacaaact gaagaaagcc 2940 ttatacggac tcaaacaagc ttcacaagct tggtttagtc gtatagaagc acactttgtg 3000 aatgaaggct ttgagaggtg ccacagtgag cataccttgt tcatcaaaac aagcaaagga 3060 ggtaaaattt taattttgag tttgtatgtt gatgacctca tttttattgg aaatgatgaa 3120 tcaatgtttt atgagttcaa gagttctatg atgcatgagt tcgatatgac tgatttggga 3180 aagatgaggt attttcttgg aattgaagtg ttgcagaaga cttatggcat ttacatcagt 3240 caaaagaaat atgccttaga tgtgttgaaa agatttggga tggaggagag caattttgtc 3300 catagttcga ttgttacagg ttttagacga aaatggagtc aaggttgatg caacattctt 3360 caagcaaatg gtagggaatc tcatgtatct aacagcaact cgacctgact tgatgtttgt 3420 agtgagttta attagtagat acatggtgca accaactgag cttcacttat agagtgtaaa 3480 gagggtgtta agatatttga gaggcacaac aaatcttggg atcttctaca agaagggaga 3540 gaatgataaa ttggttgcct ttactgatag tgactatgtc ggtgatttgg aggataggaa 3600 aaacacaccg gggtatgtat tcatgttgag tttcggagct gtgtcttggt cctctagaaa 3660 gtagcctatt gtttcactct ccacaattaa agctaaattc atagttgaat catcctatgc 3720 atgtcaagct atttggatga ggagaatctt ggagaagctc agtcatacac aaggtaattg 3780 tactactgtg ttttgtgaca atagttcaac aattaaatta tcaaagaatc caatgatgca 3840 tggacgaagc aaacacatag atgtttgctt tcattttcta cgtgatctta ctaaagaagg 3900 agtaatggaa ttagttcatt gtggtacaca agatcagatt gcagacgtga tgactaagcc 3960 tctcaagctt gacatgtttc tgaagctaag agagttgatg ggtgttcgtg aagttccaga 4020 tgtaaactaa ttactgttag cagttagttt aagggaggg 4059 // ID MtPH-M-3-Ia repbase; DNA; EDCOT; 4048 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 13-MAY-2008 (Rel. 13.05, Last updated, Version 1) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-M-3-Ia. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4048 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC An autonomous element representing subfamily M-3 of PIF/Harbinger CC transposons from Medicago truncatula, carrying 14 bp-long TIRs. XX SQ Sequence 4048 BP; 1323 A; 596 C; 722 G; 1407 T; 0 other; gagcctgttt ggttcagctt ttcaccacta agacgtgatt ctacaaccct caaaagtgaa 60 aagctgaatt ttcaatggtg tttggtttgg cttttaagaa ttgattctat cctccaaaag 120 caattatcca tgaagctaca aatcctaact tttggctttt gtagaatcaa ttctacatta 180 aactattatc aattccataa ctaccctctt aattatcatc aatttttatc accctttctc 240 caaccatatt tgtttttctc tacctggaac cttaaattca ttcgctccac tgtctacttt 300 tctctagcta gaactcaacc acccttcaca aatttaatct aaaaatttat tgctattagg 360 ttatataaca acaccacctc ctgctagcaa atatctactc aagagaacaa caaaaaggaa 420 aaattctgct caaaagataa caatcaacaa caaggtaatt tggcattttt gagtgatttt 480 tactttgatt tgcttacttg tttgtattaa atttaacctt ttttctttgc tgcaatgctt 540 ataaaatttg tttggttgca tagtataaca tctcttatga atttctacaa acaaaaaata 600 ttgcattata tgtgtttgat aaaatgtctc ttagagctta aagtgatttt ttatgaaaat 660 tatgcagtta gtaacttaaa tatttatgct aaagtgtttg aatgtaattt taaacactag 720 tttaaaatga acacttgtta tgtaaaattt atatattcat gccatgatgt aaaatttata 780 caataaaaag aaagaatact tgttatgcat ctatagaggt agtgttggct cattttatct 840 tttatttttc ctatcatact ttgtgtacat agcattatgg ctaaacaaaa gaaagtttat 900 gcggattggt cggatcttaa agtgaatgaa atattcatcc aaacatgttt ggatcaagtt 960 gtcaagaatg aacgcgttag cactagcttt actaagaaag ggtggaaaaa cattgtttgc 1020 caatttcatg aatcaaccgg gagagattat gacaagattc aattgaagaa taggtatgat 1080 gccttgaaaa aggaatggag agtatagttt aacctatttg gaaaagttac cggaatgggg 1140 tgggataatg agaggaatac ctttgatgca ccagatgagt ggtgggagaa caaacaattg 1200 gtatgtgaaa aaacaaatat gttgcttagt aatacttaga tttatattta gcatgttaat 1260 tacatgatga tggttatgaa atgcaggaaa atcctctcta tggaaaattt agagagaaag 1320 gacttccatt tgctaatcaa ctaatcacac tttttaagga tgtggtggct aacgggagca 1380 tgcttgggca ccttcaagtg gcatattgcc caacgaggac tgtggtactg atgttggtca 1440 agacgtaaat aatattgact tggatgtggg agaaggatca ggtgatagtg aagatgtgag 1500 tattggagca actggagaat ttgcaaatat taatttgaat atttcacaag gagcttctag 1560 ccaaattagt ggacaaaaga gaaagagagc tggtggtgtt gataagaaaa ccaagaaaaa 1620 gacaactccc gcattggcaa tagctgaagc tatgaaagag attgctgaga catgtaagac 1680 gagaaatgat gttttaacta atgcatctat tggtgatgtg atggctgagc tccatagcat 1740 ggatgaaatt acaagtgatg tagacttgtt cgcaaaatgt tgtcaactaa tgatgttcaa 1800 gccagctagg gagatgtttg tttcctttca aggctttaag gatagaaggt tgaaatggct 1860 taagtatgca acagataacc ctatgtcatt tatgaagatg taactgtttc ggactctctt 1920 aagtatcagg acttatctta tattaggagt aagcttaagt tttaggagtt atcttatatt 1980 aggagtaagc ttaagtatga atctgctata aatattagga gtaagtttaa gtattaggag 2040 tgatcttata ttaggagtta tctttaatga tgtggatcct tttagaactt gcactgtaac 2100 atataatgta acatgtaata tgtcttttga aatttgaatg aagtggatcc tattatgtat 2160 ttttctatca tgttttttgc tatagttttg tgtacatatg aatatgccct atacttatga 2220 atttgctata attctgctgt acataaatat tatagaactt acctactgtg cagccataaa 2280 acatgtatat agttttcttc atgttttcta ctatggtctt ttccatcctt tctccatgtt 2340 ttttactata gttttttaat aacattattt tacaataggt gaaggtagac atgaacgatt 2400 ggaatgagca atcagaccac attagagatc aagatgaaga agatgatgac attttccaac 2460 aagctatttt agtgtctgca ctagttggtg agtatgcaat aaaccattta tgcaaagaac 2520 cttgtagaac tagtgagcta acaggtcatt cttgggttca agaaatattg caaggtaatc 2580 cgactcgttg ttatgagatg tttcgaatgg aaaaacatgt atttaatcta ttgtgcacta 2640 aattagttaa gcttggttta aagtcatcta atcgaacgac ggttgaagaa atggttgcaa 2700 tgtttttagt tgttgttggc cacggggtag gtaatagaat gattcaagaa aggtttcaac 2760 actcgggtga gactgttagt agatattttc atcgagtact tcatgtcgtc cttaagttgt 2820 ctatcaaata tattaaaccc gaagatccta cgtttcatga ttgtcattcc aaaataaaaa 2880 atgatcaacg atactggccc ttttttaaga atgctatagg agcaattgat ggtacacatg 2940 tgtcatgcgt agttagtggc agtgagcaaa caaggtttat tggaagaaag ggatatccta 3000 cacaaaatgt aatggccgta tgtgattgga atatgtgttt cacttttgta tttgctggtt 3060 gggaaggtac tgctcatgat gctcgtgttt ttgaccaagc tttaacaaat gcaaatctta 3120 attttccaca ccctccgcca ggtttgttat ttaatattac tccaaatgat ttgttatatt 3180 taacttaagt ttaaatattt ttttctttct ttctaggtaa gtattatttg gtagattctg 3240 gctatccaac accaataggg tacattggtc catacagaca tgaacggtat catcttcctg 3300 aatttaggcg ttctaacggg tttgcaaatc ataatgaagt atttaattat tatcactcaa 3360 gtttaaggtg cacaatagaa agaacttttg gggtatggaa gaacagattt gcaatcctac 3420 gtcgcatgcc taactttaaa tttgagacac aagttcaaat agttgtcgca acaatggcta 3480 tacacaactt tatccgaagg aagccagaaa ttgatattga ttttaatgtt tatgaagatg 3540 aaagcacgat cattcaccat gatgatagct catctaactt ggatcaatcc catgttttaa 3600 atgtagtttc gtcgtcagag atggatcgcg ttcgaaacat aatccgcaat gaaattattg 3660 agcacaggca aaataattag tattgttttt taaattatta tatcaatatt ttagtactat 3720 aatacacttt aaattagttt tgtaataata ttagtacttt gttgcaattt aaattctatt 3780 atctatttgt aatttttatt ttcatgctat tagtattgta ataacttata ttttaactat 3840 attgcactta attatcctaa tttagtaatt tctatttagc tatgtccatt ttagtaatta 3900 tacattcaaa agcaattttg ataaaactat ccaaacaaca ttcagtttgt ttaatcgatt 3960 ctgcattatt gtatccaaac ataaatcaat tctctcataa tcaattctgt cagaatcaat 4020 tctatctaaa gctaaaccaa acacacac 4048 // ID ALFARE1_LTR repbase; DNA; EDCOT; 1358 BP. XX AC . XX DT 25-MAY-2005 (Rel. 10.05, Created) DT 06-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE M. sativa (alfalfa) putative LTR retrotransposon, LTR consensus. XX KW LTR Retrotransposon; Transposable Element; LTR sequence; KW ALFARE1_LTR. XX OS Medicago sativa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1358 RA Gentles A. and Jurka J.; RT "M. sativa putative retrotransposon ALFARE1."; RL Repbase Reports 5(5), 99-99 (2005). XX DR [1] (Consensus) XX CC LTR corresponding to internal sequence ALFARE1_I. The complete CC element is flanked by 5 bp TSDs. XX SQ Sequence 1358 BP; 432 A; 236 C; 267 G; 418 T; 5 other; tgataagtgc tagaaagttg taatttaagt gatatatttt aggcactttt gttacttgtt 60 ttgcaagtta ttaagggaaa agccgagaaa taagtgatta ttgccctttt acgctttatc 120 tatcttactt cacccatttg tgcaggattc gaactcaaga catcaagcaa agagaagaaa 180 atggagaaaa gtacaaaaag gcagaaaaag gagatcactc gcctccaact cgccatggca 240 agcacaaagg cgagcaattc cagaatgcaa caaagatcac acgccaccaa ctcgcaatgg 300 cgagtagaag gcgagcttac tcgccatggc gagtggaagg actcgcgagg cgagtaaagg 360 cggtttagcc tctcaatgct gacgtggcac aaacccaatg gggaagaaac ttcaactcgc 420 catggcgaat gaagtagctc gcgaggcgag ttaaggcaga ctcagaattc tataaatagc 480 ccactcaacc atttcagana tatatagttt tttacatagt tttttactta gtttttctct 540 gagtttttca cttgtaatat ttctagagag agagataggg cttgtgcttt atagagtgag 600 agtgatagag agtggattct tcatcctttg ttgagacatc acaagttgta atgaatcttg 660 cttcttcaat tcattcttgc aaggcttcca tgacaatgag tagctaaatc tcctttgttg 720 ggattagagg tacttgatca tagcttaaca tgtaatcktt tgatctataa atatatggtt 780 ctagcatttg atttgatatt gaggttattc ttgcacttta atctttatct ttgatttaat 840 tgtgattgag aaatactttt gaatctaggt ttagaataac catctatcaa aacatagktt 900 ctagacatgg aatcgatgtt ttgataatca ccttgtgtat ccaaacctaa agctttctta 960 tcattcaata gattgagaaa tcatcgattg aacgataaga tcgactcttg aatcattcaa 1020 tagtttgaga catcgacgat tgaatgatac aattgatttc acaatattgt ttggacacga 1080 atggtgttgt cgagggatac gtgataatat caaagaaaag ctagaatcca tgtatgatca 1140 ttaggttacg tgcgacgctc gatcaaggaa ctctaatcct aacaagtttt acgccctatt 1200 aatctcaatt ttatcatttg caattsagtt actaaaacaa acaaycaact atcgttttaa 1260 cttggaatga tatttggtgt cgaacggtcc gcgatatcgc actagtccct gaggagacga 1320 tataaatact tacaattgtt tgatgcaaaa atactaca 1358 // ID DEM1_LTR repbase; DNA; EDCOT; 2773 BP. XX AC AJ291492; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 15.11, Last updated, Version 2) XX DE Malus domestica retrotransposon DEM1_LTR, long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Long terminal repeat; KW retrotransposon; DEM1_LTR. XX NM DEM1_LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2773 RA Yao J., Dong Y. and Morris A.B.; RT "Parthenocarpic apple fruit production conferred by transposon RT insertion mutations in a MADS-box transcription factor."; RL Proc. Natl. Acad. Sci. U.S.A 98(3), 1306-1311 (2001). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genbank; AJ291492; Positions 1 2773. XX SQ Sequence 2773 BP; 804 A; 467 C; 641 G; 861 T; 0 other; tgtcacagcc cgttccaaat tattatattc gtggctgtga atgaacgaaa ttgcccttaa 60 gaaatactaa atttgtgaag ctcaggttgc taattatcta ggttcctaag tttgaaaata 120 aaatggaatt taataaggat ggaacttaga tttttaggtt aaaatgttaa agtttggtgt 180 ttggagattg gaataaggac cacgtgggat ccccacatcc ctcaaaaccc tcctcatttc 240 ccgttcactg tctttctctc tcctccttca cgatttctca ctctctctgt ctctctcctt 300 cgaactcaca cggaccacca ccaaaaccac cctaaatcta taccaacgtc aagtttgaga 360 ccaccattgg aatcctgagg acttcacgat cacgttggta tccatttcag gtaagtttta 420 cttcggaaaa cctagattct aaactcccca tgaaagtgta ctgttcatga gctttgaatt 480 ggttgatttt taggacaatc caagctcata gtgagcttag tgaggtccca aggaagctcg 540 gagtgcttcg ttggaagttt ttggacgtaa gaacacggag atcgacaagt tcaaaatttg 600 gccggagctt tcgaggcgtt ttccggcgaa tctccggcga gttaggagtt gaggtaggta 660 ttcaatctct tcgtctcgtc aagtactaca actttccttt ttgtttcact caatttcgtt 720 gagtattgaa gaagttatac tcatttgaaa aatacccagt ttccggcgac ctccgaggct 780 ttcgaggcag tttccggcca aaccacggcg aactaggtgt tgtgcaaggt accattctct 840 ttgtctcttc aagggctaca actttcgttt ttgaatcact tgatttcgtt gagaaatgac 900 aaagttatgg caatttgaaa aactgttcag aaaacggccg ccggaaaaac cagtccggcg 960 acccaaggaa gaagaaggtg ctacagtaaa aataaaaaat aaaaataaaa ttattttaaa 1020 aatatgtcga cgtccgtgac gtcgagtaga tcactgtggt atattcatat acctaaattg 1080 aacaccgtat gagaaagtta ttgaagattg ttggttaggt gttcaaataa cgttttatag 1140 ttttcacatt taggtgaaaa tgtgaattga tgatccgacc gttggatcat caccaaactt 1200 tgatacgtta tagtacgtaa tatttgagga ttattggaac ttacggattg ggaatccgag 1260 ttacggatct tccggaattg gaattgtaag tccataatat aaaatgttaa ccgtcactta 1320 gttttggaaa ttgacggaga tccgaccgtt ggatggtaat gaaattttag gatgttgtcc 1380 tagagatata ttgtggacct ctggaagtta tggatttaaa atctgagtgg cagatcttcc 1440 ggatcgaact acgtagtgac gtattttata taagttatat attctatcga tatgaattct 1500 gaggttggaa ttgattattg ttttaggcgc cgatcgtcat ggcgccttgg cgtattgtgc 1560 tagggagttg tagggcgaac tccaggtgag tgggcagttt tgttttccgt atatatatat 1620 atatatatat acttaacgtt ttcccagaaa ttgaaaatgc atgaaattat gtttaaaatg 1680 aaatgcatat gagttatgtg gaaaaacggg aagtgaaata ccatgcatag aattgatatg 1740 aaaagtatat agaaatgtga gttgaaatgc catgcatgaa ttaatatatg atgcatatgt 1800 atgaattggt gcggtggacg cacatgtaag aattgattta tgatgcatat gtatgaattg 1860 gtgcggtgga cgcacaggta agaattgatt tatgatgcat atgtatgaaa tggtgcggtg 1920 gacgcacaga tgagtattta attactgtta tgatgatgat gatatatatt gagctcaaat 1980 cctgcaccgt ggtttagtgc ttatagtatt caccgcatcg cacgctcgcc ttggatccaa 2040 gtagatgcta gtcgtacagt ccacgcggag tgggtacgac agaccagtcg cgagagtgtt 2100 agtgagattc cgactggtgg gtgaccttag attatgtgca cagatgattt atgagaagca 2160 ctagagcgta acttgtgtgc agaaggccgg acgggtcaca gaggtgactc cggtagagtg 2220 ataatgatag attttgagct ctaggttcaa ccgtataggg ctattagagg gcctacggtt 2280 gattactttc ttgcacttga tatgattatg ttgatgcatt cataccttat tactgttgag 2340 atgatgtggc atggcataat taatatgaga aatgttgaga tgacatggca tggcatgatt 2400 gataaagaga taatgttgag atagtaaaaa tgaagttttg agaatatata tgtatattta 2460 tattttacat ttctgaaaag tatacaggtt ttacggagag gggttacaac gttttgagaa 2520 atgtttggat ttggaaaaga attgttttac tgacccactc aattttggtt ttgcgcccct 2580 ccaggttcag gaatcacaaa ggtgtggtga ctacgaggaa ttcgacggtg ttctgacaga 2640 ttggacaaaa ttaggactca ccctcgggtg tatcaactta taaattgtat aattaaagct 2700 tccgtactgt gcaaatggtt acgtcactct cacgtgacgg ccagcatgcc ctccttcggg 2760 acggggtgtg tca 2773 // ID HARB-4_Mad repbase; DNA; EDCOT; 6263 BP. XX AC . XX DT 22-OCT-2010 (Rel. 15.11, Created) DT 22-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; HARB-4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-6263 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1864-1864 (2010). XX DR [2] (Consensus) XX CC TIR is 13-bp long. XX FH Key Location/Qualifiers FT CDS join(3063..3575,3517..3906,3965..4441,4627..5070, FT 5099..5632) FT /product="HARB-4_Mad_1p" FT /translation="MDRRKLLLILLLEMSYLETICICTILVVMMLRGKQRH FT VERPTLTNRSLIRREISLCYLNGIIGNTDTECVNELRMDRRTFGILCDLLR FT QDGRVKTDGLVSVEEQVCMTLQILAHHTKNRSVGGRFYRSGETISRYFNSV FT LQGILRLQGILLKVPQPVPIDSTDPRWRCFKVKSPSLCLLILQILGGDVLR FT YDENFFSFSLSFNSSFPLYKLTKTFLFFIFKNCLGALDGTHIDVHVPEIDK FT PRYRTRKGRVATNVLGVCSGDMQFIYVFPGWEGSASDSRVLHDAISRPNGF FT KVPAGKTITGLFFFSLGCYYLVDGGYTNGEGFLAPYRGIPYHLSEWEGRTP FT SNKEEYFNMKHSKARNVIERCFGLLKGRWSILRSPSFYPIRTQGRIITACC FT LLHNLIRQEMSVDPMENLPIIEDGQNTEEGEYVGSVQTSDQWTAMRNDMAQ FT EMYNEWRAIRNQQPNNIFCLGMDNENILNATQEPKGRRRKWEAFEEEVLLG FT VLEDFVARKQRCDTGAFKQGTLVEIAKAVNVLCPHSNIKANPHIESKLKKW FT KKTYSMVVDMINTSGFAWNDVKKCVEVDSDDAWQTYVQVHILFYLCISYIL FT AAIFVTHAKFRNKEADGWRSKPFPLFDRFAYIFGKDRATGNVAETPAQMVE FT EQSHDHVGESDIGGENFVSSMNQQSQQSTPSENSQRKRKRAVGSSSDGTEA FT IISGLKDFYVESGKRMQMVTEALVQGTADHTDIANELEAMGLSPMDQIDAL FT SLILDKPKNVGVFRAIKPELKKVFVQRLLSDNASG" XX SQ Sequence 6263 BP; 1735 A; 948 C; 1357 G; 2223 T; 0 other; gggtgtgttt gtttgggctc actaagtttc actggactgg actggactat agtccagtgt 60 ttgtttcgca cgggaattaa gtttaatggg attagccggt actcgctccg actaacccct 120 tcgctaaaag ttcttagcga gaaccccaat tctcacggga ttgctaagcc cttctttgag 180 agcgttgctc gttcctcatt cttggtcgtc tttctcgtcg gtcctcctcc tcgctgatcc 240 tcctcgctcg tcctactccc tcgtcctgct cgtcctcatc tggtaaattc caaatccgac 300 gacctatttc tatgattttg ttttgtagat tgtgaaatta ttattgggtt ctgatcgatt 360 ttgttgtttt gggttcaaaa tctatgacat tattaatggg ttctgattga ttcctcgtat 420 aatcctttta tttatgatat accttcttat aatttgaaga aatcaaaatc agttatgatt 480 tcaatgttcg atcttttgat ctaccattat tttccatata ttaagtgaat tctctagccc 540 ccttgcctat ttggacagtc tagtttgaga tgatatagta gttgatagct gtgagtgcat 600 cagtcatttt taatgtccac tgggattgca gttttgttgt agctttgtat aatcgtgata 660 caatatgatg cttttaccat tgccattgca ttagtttcat ctggtcccat agggtcacag 720 ggttaactta gttgttcggt tgatgtttgc gagaaaatgg tgttatcctt gttgttcaga 780 aataattttg aattttgatt agaaagattg tcaatttttg tggataattt tagttttttt 840 tcttcaattt tatggttttg agcacagtat cagcatccct tcctttcacc atatagtatg 900 tacttgtggc acaagagaag taccaagtat cgtgtaggtc cttaccgatg cttgttctct 960 caacgaacac aactatatat atatatatat atatatttgg tggtgaggat ttacttctat 1020 gaggtatttc gttatctaat ttcttcaaag tggtggtgtt actaggtttg ccagatcctc 1080 agggatgcag ccactagtta caacatgatt atagttttct attaagtaga atcatcattt 1140 ctaggtgtag cgcctttttg agctttgatt gtgaaagagg aaattttcct ctgtaacttg 1200 ttagaaatag tctagttgtg attgtgacta tgtattgtat ctaacacttg tggcttttac 1260 ttgttcgttc acacctcatt ttgttatttt attgtgttgg attggcggtc cattttttac 1320 tggtaccatg catgtagagg cttccttatt ggtaatgtaa gtaggaattg gtatgctatg 1380 ttgaggttgg agctcttgtc ttgtttcgtt atgtgtctaa aattcgtgag tgagtgtgag 1440 atgagtgagt gggtgtgaaa tggttggcca ttcatgtctg atcttggttt tcaacacctc 1500 taggcatttg aactcagatt tctgtcttta agtatatgca ttcttcagat gcttacttaa 1560 aaccaactta gtgaaaatga ttcaatgtta acggttgatc tcattttctt ttaaacagtt 1620 tgattcgaat ttgatttaaa gaggaaacag cgcttttgag catttcgtct cttgacttcc 1680 taaggttaat tgtttcttgt tatcagacat actagaaagg tcgacatata aaagataaat 1740 acaataaagg ttaacaacta tttagaaact ttccctatat tggacaatct cagtgttgac 1800 ttgttgtgaa gtgacctaga acaagccaat gatcggtact cttgtgttcg catagggtaa 1860 gcttttgttt gtgccttttg atcttgttag gaaatagaaa ggaattataa atatgcaaat 1920 taaaaaggaa tagattctat tgaataagtt tacaactaaa tgaatccaaa gcctttgctc 1980 taaaaatatt gtgctattgt tgagacccct gctgattcta ttgatggagt ttcggttaca 2040 tattttcaca taaagcaata tacttaagac taggacaaca tgaagttttg catctttgtt 2100 tattgagttt acttcttttg atatagttgc cttgtttcat gcttacttct tttgtctaaa 2160 gcttaattat gatgtccagt ggaagtgtta agttttctgg gcatgtgctt tcaccttcta 2220 tgtatgtaac agggactttt gttggtatac atggaaatga gactcattag cattcctgaa 2280 ttttgtgaga cgggagttgt tgttgtgtta aacttgggga atcttgaatg ccgtacactc 2340 agtgtgtgtg tatgcagtat gtgtgcagtg tgtgtgtgtg cagtgtgtgt gtgtatgcag 2400 tgtgtgtgtg tgtgcagtga gtgtgagtgt gtgcagtgtg tgtgtgtgtg tgcagtgagt 2460 gtgtgtatgc agtgtggtgt agtgtgtgtg tgagtgtgtg tagtgtgtgt gtagtttgca 2520 cagtgtgtgc agtgtgtgtg tgtgtgtact tggtttataa ccatgatatt acaatgtgaa 2580 tgttttgtat tgtgtggggt tgatgctgaa ttgcaatttt ttgtggttgt tggttgcaga 2640 gaagaggagc ataaacggaa ggctaaggct aaggctactg cattacaggt gtcctttaat 2700 ttccctcttc acatgcaatg cctagcaatg atagcaatcc tcatactagt gttcttagac 2760 acatgtttat agatgtataa gagtagaaca ttttgaatat gatgcctcgg gttaatgaaa 2820 cttttttttt tcaacgccac ctgtatattt gttgcctcgg gttaatgaaa tttttttttt 2880 tcaacgccac ctgtatattt gttgcctcgg gttaatgaaa cttttttttt tcaacgccac 2940 ctgtatattt gttgcctcgg gttaatgata actttttttt tttcaacgcc acctgtatat 3000 ttgttgcctc gggttaatga tttagttaat ttgttttttg tttttttttt gtttggatag 3060 atatggatcg aaggaagctt ttattgatct tattgttaga gatgtcttat ttggagacaa 3120 tttgtatttg tacgattctt gtggtgatga tgctacgtgg caaacagaga catgttgaac 3180 gacccacatt gactaaccgt tcacttatta gacgagagat tagtttgtgt tatctgaatg 3240 gtataatagg gaatactgat actgaatgtg tcaacgaatt gagaatggat agaaggactt 3300 ttggcatatt atgcgactta cttcgtcaag atgggagggt aaaaactgat ggtttggtgt 3360 ctgtagagga acaggtgtgt atgactttac aaatattagc acatcatact aagaatcgta 3420 gtgttggcgg tagattttat aggtcgggag agactataag taggtatttc aatagcgtat 3480 tgcaaggaat tttgcgatta caaggtatcc tactaaaagt cccccagcct gtgcctattg 3540 attctacaga tcctaggtgg cgatgtttta aggtatgatg agaatttttt ttcattttcc 3600 ctaagcttta actcttcatt ccctttgtat aaattaacaa aaactttttt attttttatt 3660 tttaagaatt gcttgggagc attggatgga acacacattg atgtgcatgt acctgaaatt 3720 gacaaaccaa gataccgaac aagaaagggt cgagtcgcaa ctaatgtgtt aggtgtgtgt 3780 tcaggagata tgcagttcat atatgtgttt ccggggtggg agggttccgc atcagactct 3840 agagtgctac atgatgcaat tagtaggcct aatggtttta aggtaccagc gggtaagact 3900 attacttagt ctcaactttg taagttaggt ttagttctgt ttgtcaacta caaaacacta 3960 ataaggtctg tttttttttt cattaggttg ttattacctt gtagatggtg gttatacaaa 4020 tggtgaagga ttccttgcac cctatagagg aataccttat catttatctg aatgggaggg 4080 acgaacacct tctaataagg aagaatattt taacatgaag cattctaagg caaggaatgt 4140 aattgaacgc tgttttggct tgctaaaagg aaggtggtcg atactaagga gtccatcttt 4200 ctatccgata aggacacaag gtcgaataat taccgcttgt tgcctactac acaatcttat 4260 taggcaagag atgtctgtag atccaatgga gaatttgcca ataatagaag atggacaaaa 4320 tacagaagaa ggtgaatatg ttggtagtgt tcaaacatcg gaccagtgga ctgcaatgag 4380 gaatgatatg gctcaggaaa tgtataatga gtggagagca attaggaacc agcaaccgaa 4440 ctagctatat gtgttaatga taacatttta ttttagtatt cctttttatc atgcatttgt 4500 tagatattag cacaatgatt ggatggtatg caaattaatt ggatattatg caagttgatt 4560 ggatattatg caagttgatt ggatattatg caaattgatt atttgtatgg tattttcctt 4620 cattaaaata ttttttgttt aggtatggat aacgaaaata ttttgaatgc tactcaagag 4680 ccaaaaggaa gaaggcgtaa atgggaagca tttgaggaag aagtattact aggagttctt 4740 gaggattttg ttgctcggaa gcaacggtgt gacaccggtg ctttcaaaca aggtactttg 4800 gttgaaatag caaaagctgt caatgtttta tgtcctcatt caaatataaa ggcaaatcca 4860 catattgagt ccaagttgaa gaaatggaaa aaaacatata gtatggtcgt tgacatgata 4920 aacacaagtg gatttgcatg gaatgatgtc aaaaagtgcg ttgaagttga cagtgatgac 4980 gcatggcaaa cttatgtgca ggttcatatc ctattttatt tatgcattag ttatattctt 5040 gctgctatat ttgttacgca tgctaaattt tagttttgct atgttgatat aatcttagag 5100 aaataaagaa gccgatggat ggagaagcaa accttttcca ctgtttgata gatttgcata 5160 tatatttgga aaagatcggg ctacgggtaa tgtagccgaa acccctgctc aaatggtgga 5220 ggaacaaagt catgatcatg ttggtgaaag tgatattgga ggtgaaaatt ttgtttcttc 5280 aatgaaccaa caaagccaac aaagcacccc atctgaaaat agccaaagaa agaggaaaag 5340 agctgtggga agttcaagtg atggaaccga ggcaattatc agtggactga aagattttta 5400 tgttgaaagt gggaagagga tgcaaatggt aactgaagct ttagttcaag gtactgcaga 5460 tcatactgac atagctaatg aacttgaagc aatgggtctc tctcctatgg atcaaattga 5520 tgcattgtct cttattttgg ataaaccaaa aaatgtggga gtgttcaggg caatcaaacc 5580 ggaactcaag aaagtgttcg tccaaaggct tttaagcgac aacgcaagcg gatgaggatt 5640 ttggctaatg ttaacatgga tgtattttat taacgttaac atggatgtat tttattaatc 5700 atacaatctt atgttatgac ttataactta gctttgcact agtattttgg cttatgttaa 5760 ctagccattt tgtaaattat ggagatctat tttggctaat gttaactaat gttaactagg 5820 attttctaaa ttatggagat tcttatgtac ttgtatttgt tgaagttgca tgtattggcc 5880 actattattt ttcttctgtt gggtgataga gtttaaacca agctacattt gcaaattaaa 5940 cccaattcta ttagcaggta atagaaacaa aacaattgtc aatttttttt aagattcata 6000 atatacatgg caaaaatatg ctccaattaa cccatatcat gagatttgta gcattactct 6060 attacacaat ggcaaaaatt tgtagtccta gtctaagcaa acacaaatct ggtgaacagt 6120 actgtttttc ttatcctgct tcttagtccg agactgcacc aaacgcttca ctaagttagt 6180 ccagcttagt ccagtctaag ccagtccagc ttagtcccgg cagctagtcc agtccgagac 6240 agtccggcgc aacaaacgca ccc 6263 // ID SHACOP7_LTR_MT repbase; DNA; EDCOT; 240 BP. XX AC CT573421; XX DT 15-JAN-2007 (Rel. 12.01, Created) DT 15-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of LTR retroposon, SHACOP7_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed repeat; terminal; SHACOP7_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-240 RA Shankar R. and Jurka J.; RT "SHACOP7_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 79-79 (2007). XX DR EMBL/GenBank/DDBJ; CT573421; Positions 29415 29654. XX SQ Sequence 240 BP; 74 A; 34 C; 26 G; 106 T; 0 other; tattaccatt tatcactctt catatttaac tatagttatt ccttgtattt aactttagtt 60 agtctcttag tctttcacta gtttagaata taaatagtta gtggaaactg taattgtttt 120 ggctagctag cttctttacc attgtatata agttgttcta ttgtattgtc ctttatatac 180 ataaaaaaca aaattgatta atgaaatcag tttatttaaa ttacctctct gttaatacca 240 // ID TNA1_NA repbase; DNA; EDCOT; 1863 BP. XX AC Z35426; XX DT 04-MAR-1998 (Rel. 3.02, Created) DT 20-SEP-2007 (Rel. 12.1, Last updated, Version 2) XX DE Nicotiana alata retrotransposon Tna1-2 integrase motif. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Tna1-2; KW integrase motif; NATPINTR; TNA1_NA. XX NM TNA1_NA. XX OS Nicotiana alata OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RP 1-1863 RA Royo J., Nass N., Matton P.D., Okamoto S., Clarke E.A. RA and Newbigin E.; RT "A retrotransposon-like sequence linked to the S-locus of RT Nicotiana alata is expressed in styles in response to touch."; RL Mol. Gen. Genet 250(2), 180-188 (1996). XX RN [2] RP 1-1863 RA Royo J.; RT "TNA1_NA."; RL Direct Submission to Genbank (22-JUL-1994)JOAQUIN ROYO, PCBRC RL SCHOOL OF BOTANY, UNIVERSITY OF MELBOURNE, PARKVILLE, VICTORIA, RL 3052, AUSTRALIA. XX DR GenBank; Z35426; Positions 1 1863. XX CC Partial sequence, possibly LTR. XX SQ Sequence 1863 BP; 523 A; 365 C; 430 G; 545 T; 0 other; tgttatatta cggcggttcc aaataactgc cacaaaatat aattaaaaat gacgttttac 60 cggccgccgg attaaatttt ttttatagcg gcgattattt cgtattgtgg cggttacaaa 120 acgccacaat attttaacta ttagtataag aattgtaatc gattcaatgt gaattgtact 180 gcatacgtgg gcccatttca ttaaatcagt atatagctat ttgtctatta tacccttgac 240 caacaccatt tacttaattt tccctttagg ggtaaacagg taattaaatt attttctttc 300 aagtatttgg ttgaaagaga ctggcccagc gtaaagttga tcaattttaa aatatattca 360 ttgaataaaa tttagtattc ccccttacgt tttttagtct ccctccagaa tttccccaat 420 ttctttaatt tccctccata aatctcgtat atcccccagt tcctttcccc cgattcattc 480 caggtattca gtgaacccag gctctacaaa tatgtaccgc gatctcaggg aaatctattg 540 atggggtggt atgaagaagg gcgtggcgga cttcgtctct aagtgtccga attgccagca 600 agtgaaggcc gagcatcagc ggcccagtgg gttgactcag cttatagaga taccaacgtg 660 aaagtgggaa atgatcaata tggacttctt gacaggacta cctcacactc aatacaagtt 720 cgactcaatt tgggtaatag tagaccgact caccaaatca gctcactttt tgccagtcaa 780 gtcgaccgat actacagaac aatatgcttg attgtatatc aaggagatag tgaggcttca 840 tggtacgccg ctttccatta tttcggatca aggagcttag ttcacagcta acttctggag 900 gaaatttcag caaggtttgg gtacctatgt gaatctcagt acggctttcc atccgcagac 960 cgatggtcaa gcagagcgga ctattcagac gctcgaggat atgttgcggg catgcgtctt 1020 gaatttcaag ggtaattggg ataatcacct gccccttata gagtttgctt ataacaacat 1080 ctttcatgct agcatccaaa ttgccccatt tgaagcattg tacggaagaa ggtgtaggtc 1140 cccgatcggg tggttcgagg caggtgaagc agaactgata gggccagatc tcgtgcacca 1200 ggccatggag aaggtaagag tcattcagga gaggataaag actgctcaga gtcgccagaa 1260 atcctatgcg gacgtgcgtc gaagagaatt ggaatttcaa ataggtgatt gggtgttctt 1320 gagggtgtct cctatgaagg ggatcatgcg ctttgggaag aagggaaact aagtcctagg 1380 tatgtcgggc cttatcagat tattcaaagg atcggtcaag ttgcgtatag gttggagttg 1440 ccccctgaga tgtccttagt gcacccggtg ttccatgtgt ccatgttgag gaaagtagtt 1500 ggagatccgt ccgccatcgt gccagctgaa gacatcaagg ttactgaaga attatcatat 1560 gaggagattt ttagctatta tagatatgca agtccgtaag ttgcgaaata aggagattgc 1620 ttcagttaaa gtgttgtggc gaaatcaaca agtcgaagag gccacgtggg aagaggaaga 1680 cgagatgaaa agaaaatacc cccatttgtt tgaagaagtc tagaagtgat cgtctgaatt 1740 cttgtcccta agtgatttaa tgtcgtgtcc cgtttgatgt tagaacaccc ccatcctagg 1800 tgctttacta ttgtaattct tccaagttgt gccgaaaatt gatgtgttgt gattatttga 1860 aca 1863 // ID Copia-33-LTR_VV repbase; DNA; EDCOT; 297 BP. XX AC CU469250; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-33_VV, LTR retrotransposon Ty1-copia like, long terminal DE repeat from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Gentil-B05; KW Copia-33-LTR_VV; Copia-33-I_VV; Copia-33_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-297 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL; CU469250; Positions 207547 207843. XX CC LTR = 297 bp CC LTR are 99.7 % similar to each other. CC Direct flanking repeats = gttgt. XX SQ Sequence 297 BP; 98 A; 31 C; 50 G; 118 T; 0 other; tgttgagata ttaagaatgc tttccgtata tcattctttc cttatattat ttagtgttga 60 gatattagga atgtttaaat attaggaaag ttgagatatt aagaatattg agatattagg 120 aatattgaga tattaggaaa gttgagatat taggatatta gttgttattt ccttatatca 180 ttctttcctt gtatcattcc ttcccatttt tagaatggtg attaccctct atatattctc 240 tgtacatgaa cgaatgaaag aatgaatgga aaagactacc atttatcaat ttgaaga 297 // ID ShaMUDRAV2_MT repbase; DNA; EDCOT; 367 BP. XX AC . XX DT 22-JAN-2007 (Rel. 12.01, Created) DT 22-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW Interspersed; repeat; transposon; DNA; TSD; TIR; ShaMUDRAV2_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-367 RA Shankar R. and Jurka J.; RT "ShaMUDRAV2_MT: A putative non-autonomous DNA transposon from RT barrel medic."; RL Repbase Reports 7(1), 103-103 (2007). XX DR [1] (Consensus) XX CC The sequence is composed of terminal inverted repeats lacking any CC transposase domain. It has characteristics of MuDr type of DNA CC transposon as well as 9 bp TSDs. This element is present in the CC genome in very low copy number. XX SQ Sequence 367 BP; 130 A; 66 C; 39 G; 132 T; 0 other; ggctaaattg tatttttggt cccttaacta tttaattagt atcgctttgg tcccttgatt 60 aaaatttgat ttattttagt atcttaactt tctatccgtt acacatttgg tcatttccgt 120 tagttttatt caaaaatgtt atggtttctc atcttcttcc cctcttcttc atcttcatat 180 caccttcatc taccttcaac aacaaaaacc tccgaaaaat tccagaagaa aatgaaaaaa 240 ctctaacgtt tttaaattaa aactaacgga aaggaccaaa ttaaaatacc aaaataaatc 300 aaattttaat taagggatca aagcaatact aattaaatag ttaagggatc aaaaatgcaa 360 tttagtc 367 // ID Copia-1_TC-LTR repbase; DNA; EDCOT; 390 BP. XX AC CACC01007196; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-1_TC_; KW Copia-1_TC-I; Copia-1_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-390 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01007196; Positions 13448 13837. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 390 BP; 96 A; 63 C; 75 G; 156 T; 0 other; tgttgagagt ggttcctgtc tcagcattga agttgttcac agtgtcaaca gtggagcttt 60 acttattgtt tatgtttatt ttatagttaa tgcttaaaag ttggttgtgg tgcttgacca 120 catttcatgt agtgggtggt tatcccattc taggtaccag acttagaatg tgcagatcat 180 ggcactagat tttcagtttt tcgttgttgg ttttccttga cttaagttgc agttttttaa 240 gtaatgtatg gcaagacaag tctgtgtgta agtgtgagaa aatatcttct ctaatgtcca 300 gcacctggtt ttcttgatat ctctggtctt ccttctcaaa aaaactctct ttactctatt 360 ttaatcatca taaaaataca tttcttaaca 390 // ID SHACOP_LTR_MT repbase; DNA; EDCOT; 596 BP. XX AC . XX DT 10-JAN-2007 (Rel. 12.01, Created) DT 10-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of LTR retroposon, SHACOP_MT, from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; SHACOP_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-596 RA Shankar R. and Jurka J.; RT "SHACOP_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 85-85 (2007). XX DR [1] (Consensus) XX SQ Sequence 596 BP; 187 A; 97 C; 126 G; 186 T; 0 other; tgttggtgaa cattgtgtaa ggacccacat gcacgtggga taaccagcca aagcaatttg 60 ctgaagcaaa ttgtcacaca aagtctcatg catttattat aggttgcatt tttctttcaa 120 atagtaagcc tatggtatag ctcggtgcag aagcatagct tgctaagttt gaaagcatga 180 cattcataca caggtttcac acttttgtta gatgactttg gtgtgaaagg attgcatagc 240 tttgcaactt tcacggttca ctacatctat aaatagaggt gcatttgaag gaagaagcat 300 cagaagcaaa aacacaacaa caacacaagt gagtgaatta catcaataga gagtaagaga 360 aaaactcagt gtgagaattt tagagaaaat tcttgggtgt aattgggttg tgggtagtga 420 gagtttgtga gtgtttgtaa acacatatat ttcccttttt attaaagaga tctgcagcag 480 tccggagagt aggcattatt ggccaaactt cgttaacaat tttgtgtctt attattccgc 540 atttatttca cttccactta atctgactat gggaaattgt gcctagtttc ctaaca 596 // ID DNA9-8_Mad repbase; DNA; EDCOT; 398 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-8_Mad. XX NM DNA9-8_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-398 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1489-1489 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 128-bp long. TSD is 9-bp long. XX SQ Sequence 398 BP; 135 A; 64 C; 77 G; 122 T; 0 other; ggaaatcttt aaggaaaggg atccccattt ttttataaaa atggggatta gttgtggggt 60 ccacattaca tcgaacttta acgatccgaa ccgtctattt ttcaagttgc acctcataga 120 tcatccttac aaaatattag ccaaatcgga aatgtttaag acatctaatt gggttcaaag 180 aaatgaacga atactttgtt atataagaaa caatgaaatt ttatcttgat aattaaatag 240 gcaaatggtt tcggattaaa ttgaattttt gcaaggatga tctatgaatc gagacttaca 300 aaatagacgg ttcggatcgt tgaagttcga tgtggagtga gccccacacc taatccccat 360 tttttgaaaa aaatggggat ccctttgcat aaagggcc 398 // ID Copia-3_SL-I repbase; DNA; EDCOT; 3741 BP. XX AC AC209587; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the tomato genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-3_SL_; KW Copia-3_SL-LTR; Copia-3_SL-I. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-3741 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the tomato genome."; RL Direct Submission to RU (22-JAN-2011). XX DR Genome; AC209587; Positions 132070 135810. XX CC Positions [669-1172] - Integrase core CC 'ATAAC' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 60..2015 FT /product="Copia-3_SL-I_1p" FT /translation="MSNGDVCLLDSATTHTILKEKKYFSNLVMKMAYVNTI FT SGSTKLIEGSGRATLLLPGGTILSIDNALYCSKSQRNLLSFKVIRQNGYHV FT EIANEGKVEYLYITTINVEKKIVHEKLPAFSSGLYYTSISTVESHAVVNKR FT FTNFNDFIIWHDRLGHPGFNMMRKIIENSHGHTLKSPNILQSKEFSCAACS FT QGKLIIKPSTVKVGIESPAFLERIQGDICGPIQPACGPFKYYMVLIDASTR FT WSHVCLLSTRNMAFARLLAQIIRLKAQFPDYTIKTIRLDNAGEFTSQAFND FT YCMSTGITVEHPVAHVHTQNGLAESLIKRLQLIVKPLLMRTKLSVSMWGHA FT ILHAATLVRIRPTNYHEFSPLQLTFGQEPNISHLRVFGCAVYVPIAPPQRT FT KMGPQRRLGIYVGYESPSIIKYLEPMTGDLFKARFADCHFDESVYPTLGRE FT HKSLGKEIDWNSSSLSHLDPRTNQCEQEVQRIIYLQNIANQLPDTFTNLSR FT ITKSHIPAVNAPVRVDIPTGQIVKANESRPHLKRGRPIGSKDKNPLKRKGI FT NDQDDHGLKEISQDETQVITHDDEEVRTSENNEISMNYVSTRKLWNQNNVV FT IDNIFAYNVAIEIMQQDEDFEPKSVHECRQRNDWPKWKDAIQAELASLEKR FT EVF" XX SQ Sequence 3741 BP; 1242 A; 641 C; 751 G; 1107 T; 0 other; cgttatcagc acgaagttgc tacttgcaaa gaaatcccca gttgtcagtt ggattcaaga 60 tgagtaatgg agatgtatgc cttcttgata gtgctacaac gcatacaata ttaaaagaaa 120 agaaatactt ttctaatttg gttatgaaaa tggcatatgt caacacaata tcaggtagta 180 caaaattaat tgagggctct ggaagagcga ccttattact acctggaggg acaatattaa 240 gcattgataa tgcattatat tgtagtaagt ctcaaagaaa cttattaagt ttcaaagtta 300 ttcgccaaaa tggctatcat gttgagatag ctaatgaagg aaaggttgaa tacctttaca 360 ttactacaat taatgttgag aagaaaattg tgcatgaaaa attacctgca ttttcttctg 420 ggttgtacta tacaagtata agtacagttg aatcacatgc cgtagtaaac aaaaggttta 480 ctaattttaa tgattttatc atttggcatg accggttggg ccatcctgga tttaatatga 540 tgcgcaaaat cattgagaat tcacatggac acaccttaaa gagcccaaat atccttcaat 600 caaaggaatt ctcttgtgct gcttgttctc aaggaaagtt gatcattaaa ccatcaacag 660 ttaaggttgg aattgaatcc cctgcgtttc tggaacgtat acagggtgat atatgtggac 720 caattcaacc tgcatgtgga ccctttaaat attatatggt cttgatagat gcttctacaa 780 gatggtcaca tgtgtgttta ttatcaactc gcaacatggc ttttgcgaga ttgttggctc 840 aaataataag attgaaagca caatttccag actatacaat aaagacaatc cgtctagata 900 atgctggtga gtttacatct caggcattta atgattattg tatgtctact ggtataactg 960 ttgaacatcc agttgcgcat gttcacactc aaaacggtct agcagaatca ttgattaaac 1020 gtctgcaatt gatagttaaa ccattactaa tgagaacaaa gttatctgtg tctatgtggg 1080 ggcatgctat tttgcatgca gcaacacttg tgcgcataag gccaaccaat tatcatgaat 1140 tctccccatt acaattgact tttggtcaag agccaaacat ttcccatctt agagtttttg 1200 gatgtgcagt gtatgtccca attgctccac cacaacgcac aaagatgggg ccgcaaagaa 1260 ggttggggat atatgttggg tatgaatctc cttcaatcat aaaatatttg gagcctatga 1320 ctggagattt atttaaggca agatttgctg attgtcattt tgatgaatca gtatacccaa 1380 cattagggag agaacataag tcattgggaa aagagataga ttggaattca tcatctctat 1440 ctcatctgga tcctcgaaca aaccaatgtg agcaagaagt tcaaagaata atttatttgc 1500 agaacattgc aaatcagcta ccagatacat ttacgaatct ttcaaggatt actaaatcgc 1560 atattccagc tgttaatgct ccagttcgag ttgatatccc gacgggacaa attgttaagg 1620 caaatgagtc tagaccacat ttgaagcgtg gtagaccaat tggttccaag gataaaaatc 1680 ctctaaagag aaaaggaata aatgatcaag atgatcatgg gttgaaagaa atttctcaag 1740 atgagaccca agtcataaca catgatgatg aggaggttcg aacttctgaa aataatgaaa 1800 tttcaatgaa ttatgtctcg acgagaaagt tgtggaacca aaataatgtt gtgattgaca 1860 acatatttgc ctataatgtt gctattgaaa taatgcaaca agatgaagat tttgagccaa 1920 aatctgttca cgaatgtaga cagagaaatg attggccaaa atggaaggat gcaattcaag 1980 ctgaattggc ttcactagaa aaacgtgaag ttttttgacc aataatccga acacctgaag 2040 gtatcaagcc agtggggtac aaataggttt ttgtatgaaa aagaaatgag aaaggtgaag 2100 tcatgagata taagtcccga ctcgttgctc aaggtttttc tcaaagacct ggcattgatt 2160 atatggagac atattctcta gtggtagatg caatcacctt tagatatctc ataaatctgg 2220 cagttcatga aaaacttgaa atgcgtctaa tggacgttgt cacagcctat ctatatggct 2280 cattggacca caacattttc atgaaaattc ctgaagcatt taaagtgcct gaaacataca 2340 aagattcaag agaaacttgt tcaataaagc ttcagaaatc tctgtatgga ctgaaacaat 2400 caggaaggat gtggtacaat cgtttgagtg aatatttgtt aaagaaaggg tacaaaaatg 2460 acccgatttg tccctgcatt ttcattaaac ggttggggtc tgaatttgta ataatagctg 2520 tgtatgttga tgatttgaac atcattggaa ctcgtaaaga gcttttagaa gctgttgagt 2580 ttctgaaaag agaatttgaa atgaaagatc tcggcaagac aaaattttgt cttggtctac 2640 agattgagaa tttgtcaaat ggaatacttg ttcatcaatc aacgtacaca gaaaagatac 2700 taaagcgttt ttacatggat aactcacatc cattgagtac tccaatggtg gtaagatctc 2760 ttgacatcaa tacagatcca tttcgacctc aagagaatga tgaatagctt cttggtgatg 2820 aaactcctta tcttagtgcg atcggggcac taatgtacct tgctaacaat actcgaccag 2880 atatctgttt tgcagtaagt ctactggcaa gattcagttc ctccccaaca aaaagacatt 2940 ggaatggtgt taaacacata cttcgatatc ttcgagggac catggacatg ggtttattct 3000 attccaatga atccaaatca gaactgattg gttacgcaga tgcagggtat ttatcagatc 3060 cgcataaagc tcgatcacaa acaggctatt tgtttacatg tggagacacg gcaatatctt 3120 ggcgatcaat gaagcaaaca ttggtagcca cttcttcaaa tcatgcaaaa ataatagcca 3180 tccatgaagc aagtcgagag tgcgtctggt tgagatgaat gacccatcat attcagaaaa 3240 tgtgtggttt ttctttgaaa aagaatatac caaccacaat gtacgaagat aatgctgcat 3300 gtatagctca attgaaagga ggatacatca aaggagaccg gacaaagcat atctcaccaa 3360 agttcttttt cacgcatgat cttcaacaaa atggtgagat agaagttcaa caaattcgtt 3420 caagtgataa tcttgctgat ttattcacta aggcattgcc aacatcaaca tttgagaagt 3480 tgagatacaa gattggaatg cgccgtctcc gagatatcaa gtaaagtttt catcaggggg 3540 agcgaaatac gcgttgtact cttttcctta actatggttt tgtcccaagt taggttttcc 3600 tggtaaggtt tttaatgagg caacattcaa agcgtattat gaaatatgtg tactcttttt 3660 ccttcactag gctttttccc actgggtttt tcctagtaag gttttaacga ggcacataat 3720 ctatggacat ccaaggggga g 3741 // ID PSAT6 repbase; DNA; EDCOT; 607 BP. XX AC AF155746; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Pisum sativum dispersed repetitive DNA, PSAT6. XX KW SAT; Satellite; Simple Repeat; PSAT6; Repetitive sequence; KW dispersed. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-607 RA Neumann P., Nouzova M. and Macas J.; RT "Molecular and cytogenetic analysis of repetitive DNA in pea RT (pisum sativum L.)."; RL Genome 44(4), 716-728 (2001). XX DR Genbank; AF155746; Positions 1 607. XX SQ Sequence 607 BP; 159 A; 97 C; 184 G; 167 T; 0 other; tcgagtcgta attattctgt tcccttgtac ggtataggtg ttgtgtgacc ctatcagtac 60 tcattgtttt agtttgtttg ggttttcaga atagagatgg ctggaagagg tagagatgat 120 gctgcgattg ctgaggctct gggtatgcta gctggagtac ttggaggaaa cccgaatgtt 180 gtgggaatgg gagctgctcg tcaactgagt gagttccaga agaacaatcc tccaatgttc 240 aagggagcat acgatccaga tggtgctcag aagtggttga aggagataga gagaatcttc 300 cgagtaactg agtgtgccga taaccagaag gtcaggttcg gtacgcatat gctgtcagaa 360 gaagctgatg attggtgggt tgctacccgc actgagttgg aatctgctgg gaatactgag 420 atcacttggg ctgtgttcag agagagattt ctgaggaagt actttccaga ggatgtcaga 480 ggaaagaaag agatagagtt tttggaattg aagcagggca atcggtctgt gactgagtat 540 gctgcgaagt tcacagagct gtcaaagtat tacactccct ataatgaggc tgctggagaa 600 ttttcga 607 // ID Gypsy22-VV_LTR repbase; DNA; EDCOT; 1537 BP. XX AC . XX DT 24-SEP-2007 (Rel. 12.09, Created) DT 15-SEP-2008 (Rel. 13.1, Last updated, Version 2) XX DE LTR retrotransposon from plants: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy22-ZM; KW Gypsy22-VV; Gypsy22-VV_I; Gypsy22-VV_LTR. XX NM Gypsy22-ZM_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1537 RA Kohany O. and Jurka J.; RT "LTR retrotransposon from maize."; RL Repbase Reports 7(9), 956-956 (2007). XX DR [1] (Consensus) XX CC Originally annotated as maize sequences by mistake. XX SQ Sequence 1537 BP; 479 A; 144 C; 294 G; 612 T; 8 other; tgaaaraata taatttataa ataaaagtaa gtaaattttt tggtattata attakattaa 60 tgrtaartat aagttaataa atagaataaa atttaattag tgaaataaat tgtaatttaa 120 ttaaattatg ttgtgtccca agaaataaat tgaaaataaa atttaagttt tatatgaatt 180 agaaatttat taaattttct aaaataggaa tagattaaat tatctttcat aattaaaaaa 240 tattaatttg aatayttaaa attttaggat trtcaaacyt ataattttag ataaatagta 300 ataattattt ctcttatatt ttgttaggtg aagagtagat tttcaggatt atttttctcc 360 aaagtttttg aggacttctt ttgaggtaag ggaaattaat gcagttattt tttttttaga 420 aacaaatttt tatatacatc atttggaaat gttttgagtt attatttgtt ttatgcatgg 480 atcaaatatg ttttgcatga aaagtatgtt agaaccttat attttgttta taacacagaa 540 atgtggagat attatgtttt gcaaatttga ataattgaaa taagtgtttg actctggttt 600 gtttggccct tgtcaacggg atataatagt tgacttttga ctttttggcc cttgtcaacg 660 ggatataata gttgaccttt acatttcttg gtggggaatg taattgattt ggaccccagc 720 ctctaggggt ttggttagag gttactagta ctagtagtgt ttggttccgt ccaccttaaa 780 ggaacaattt gaggctagcc acccatttga aaagtcccac ctaactgggc accatttgat 840 gtttgatgac cagagtaaat aaataatttg aatgttttga ttgaatttga tatgaaaatg 900 tttgaattag aaatgaaagt gtacagttaa aagttttgaa tgtattggca aaaytaactc 960 aaaggtttat gaaaataatt aattataata tctcctattt tgcaagtgaa attgaaatat 1020 ttgatccatg gattgcatta atgttcctta ttgggctttg agctcattcc catttgttga 1080 taatttttca ggtaccctta gttcgggtga ggagtgatgg ctaggttgag gaatggtcat 1140 cattaggatt tgacttagga ttttatgttt ggattttgtt agcttataag tttatgttca 1200 tttggatcat ttggtatttg gaagctattt ggatattgaa ctttcaaatt tttttatgat 1260 agtttgaagt tgagatttgg agattatgaa aatttgttag cacttgaatt gtttgagttt 1320 gcaatctatt tggataatgg attttggttg atggatgctt agttttaaag ttaagtttga 1380 ggattttaga attttgttcc gctactctaa acaggtattt ggtaattggt tacttccagt 1440 tacaatatga ttgtttgggt caggttacac tttaagcctt cgggtttgag gtgtgaaatg 1500 accgtcacgc ccttggagtg ggtcttgggg cgtgaca 1537 // ID MuDR-4_VV repbase; DNA; EDCOT; 7205 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-4_VV, an autonomous DNA transposon - a consensus sequence. XX KW MuDR; DNA transposon; Transposable Element; mutator; TIR; KW Mutavine-4; MuDR-4_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-7205 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 764-764 (2008). XX DR [1] (Consensus) XX CC MuDR-4_VV (Mutavine-4 in [1]) consensus is a virtual autonomous CC element. Its individual copies are >90% identical to the CC consensus sequence but do not contain an intact ORF due to stop CC codons and/or frameshifts. MuDR-4_VV contains 140-144 bp-long CC TIRs which are 96% identical to each other, flanked by 9 bp-long CC TSDs. MuDR-4_VV has an intronless transposase gene. Downstream of CC the transposase is a putative gene in a reverse orientation CC virtually encoding for a ULP1-like protein similar to CAN65286.1 CC (region 5952-4866). XX FH Key Location/Qualifiers FT CDS 1159..3603 FT /product="MuDR-4_VV_Transposase" FT /note="Intronless MUDRA transposase." FT /translation="MLLYEGEWVRDGNVFYFEGSKGKGIEIPKTISYKELL FT GVVHHILKLDPTNCFLSMKYVFNANIPTSPIQLTDDGDVKFFIGLNCTNGK FT LPVPLCITVEKRIDNHNQKSICNSYFECHMSSEIDKELNGDSMLMHKSRHI FT HCDSVETLTVDGENGPRFQNESLEGYKVHDWNMNETAINEEDYRMNTNPTS FT DKQVTQIGSFRTGSAQSAEILTMIDTNDGFIHDNPTIIEDVANERQNMMQQ FT PIVSGISDDHLEEHQIYSSKKELQRKLYMMALKRKFEFKTTKSTTKLLLVE FT CFDKECKWRVRATKLGISNMFQIMKFYSTHTCRLDMMSRDNRHASSWLIGE FT SIRETYQGVGCEFRPKDIVADIRKQYGVQISYDKAWRAKELALGSIRGSPE FT ESYNTLPSYCYVLEQKNPGTITDIVTDCDNQFKYFFMSIGASLVGFHTSIR FT PVVAVDGTFLKAKYLGTLFIAACKDGNNQIYPLAFGIGDSENDASWEWFLQ FT KLHDALGHIDDLFVISDRHGSIEKAVHKVFPHARHGVCTYHVGQNLKTKFK FT NPAIHKLFHDAAHAYRVSEFNFIFGQLEMIDPRAARYLMDIGVDRWARSYS FT TGKRYNIMTTGIVESLNAVLKNARDLPVLQLVEELRNLLQKWFVTRQQQAM FT SMSTELTMWADGELRSRYNMSATYLVEPINSKECNVNYAGISAQVNLDTRS FT CTCRQFDLDHIPCAHAIAACRFYNISCYTLCSKYFTTKALLSSYSECIYPT FT GNEIDWVVPNHIRDKVVLPPKTRRPTGRPRKVRIPSGGEGKRTSRCSRCGQ FT YGHNRKTCKRPIP" XX SQ Sequence 7205 BP; 2430 A; 1079 C; 1173 G; 2469 T; 54 other; gggaaaactg atcaaaaggg acaaaaatcc ctcaatatta taaaactaac ccccactttt 60 aatagcctcc aaaatgaccc gatctagaca aaaatacccc tcagctacat caactctttt 120 ttccctccca ttctaatttt atttccctcc attcacctct ttttattatt tcttccactt 180 tctccttttt tttcattttc tcctgttatt ccatttctct cttttcagtg catttcttca 240 agtctcacac agtttctctt cagatttctt caacttaaag cgctttaagt tgtggttgga 300 taaacagtgt acgtttattt ttatttttcc atgttttttt ctttcatgtt ttatttattg 360 aatattttca aacatttaat gagatgtagt aaatatttaa ataagtttga aattgttgta 420 atttttttta atatcattta cagccatgaa aaaatggatt aaaagaagga aacaatcaac 480 ttaaaaagtg taatgtggag aaacattgtc tatatggaaa aatcaaatga tggtaagtaa 540 taaaacttat ggaattttat gatggttttg gtattatttg catatttgtt ctttatatag 600 atgtaaatat gtgttaatag ggttttgata taatatataa agttatcttt tttagttata 660 tatcaaaacc ttacggatat taagttgaac ttgacgtaag ttaagattgt atatagttat 720 tttatagtaa cattatatta ttgttatttt atttaattat actcaatttg agttgaatca 780 tttgcaaatt acccttgaca ttaaatgaat tacaacataa ccaatctttt agtaaataaa 840 tatattttta ttgtttaaaa tagtttagag ttacaatgtc tgaatttatt taataactat 900 atacattgta tttctatagc attattggta ttatttgagg tagtaaagat gattaataat 960 gttatttatt tgttgtttat taaaaaaawa aatatgtgta atkaaataat atgtatttaa 1020 taatgaatga gttttttaaa attaatacct acttattggt gctaatgcta tgatgtaact 1080 aaaaaatatt ctaatattgt ttgttgatgc cactaattga attattttgt tatttyagtg 1140 gttgatgaag taggaataat gcttttatat gaaggagaat gggtacgaga tggaaatgtt 1200 ttctatttcg aaggaagtaa aggtaaaggc attgagatcc cgaaaactat atcatataaa 1260 gagttattag gggttgtcca tcatattctg aagctagatc caacaaattg ttttctttca 1320 atgaagtatg tattcaatgc caacataccc acaagtccta tacaactaac tgatgatggg 1380 gatgtgaaat tctttattgg tttaaattgt acaaatggta agctgcctgt tccattgtgc 1440 atcacagttg aaaagagaat tgataatcac aatcagaaat caatttgcaa ttcttatttc 1500 gaatgtcata tgtcttctga gattgataaa gaattgaatg gggactcaat gttgatgcat 1560 aaaagtagac acattcattg tgattcagtt gaaactctta ctgttgatgg tgaaaatgga 1620 ccaagatttc aaaatgagtc acttgaaggg tataaagttc atgattggaa catgaatgag 1680 actgcaatta atgaggagga ttataggatg aatactaacc ctactagtga taagcaagtg 1740 acccaaattg gctcattcag aactggttca gctcagagtg cagaaatctt gaccatgatt 1800 gatacaaatg atggtttcat acatgacaat cccactataa tcgaagatgt agcaaatgaa 1860 agacaaaaca tgatgcaaca acctatagtt agtggaatta gtgatgacca tctagaagag 1920 caccaaatat actcaagtaa gaaagaatta caaaggaagt tgtatatgat ggctctgaaa 1980 aggaagtttg agttcaaaac aactaaatcc actactaagt tattgcttgt tgaatgtttt 2040 gataaagaat gcaagtggcg agttcgtgct accaagttgg ggatttccaa tatgtttcaa 2100 ataatgaaat tctattcaac acacacttgt cggttagata tgatgtctcg tgacaatcga 2160 catgcaagta gttggttgat tggtgagagt ataagagaaa catatcaagg ggttggttgt 2220 gaatttcgac caaaagacat tgtagcagac attcgaaagc agtatggcgt tcaaatcagt 2280 tatgataagg cgtggagagc caaagaactt gctctaggtt ctattagggg atcacctgag 2340 gagtcttata acactttacc atcctattgc tatgttttag agcaaaaaaa tcctggtacc 2400 attactgata tagttactga ttgtgataat caattcaaat acttttttat gtcgattggt 2460 gcatctcttg ttgggtttca cacatcaata aggcctgtgg ttgcagttga tgggacattt 2520 ttgaaagcaa agtacttagg gactttattt attgcagcgt gtaaagatgg caacaatcag 2580 atataccctt tagcctttgg gattggtgat tcagaaaatg atgcctcatg ggagtggttt 2640 ttacaaaaac tgcatgatgc acttggacac attgatgatt tgtttgtgat atcagatcga 2700 catggtagca ttgagaaagc agtacataaa gtatttcccc atgcgaggca tggtgtctgc 2760 acttatcacg ttggacaaaa tttgaagaca aagttcaaga atcctgcaat tcataagttg 2820 ttccatgatg ctgcccatgc ttatcgtgtt tcagagttta attttatatt tgggcaacta 2880 gagatgattg acccaagagc agcaagatat ttgatggata taggagttga tcgatgggca 2940 cgttcatatt ctaccggaaa aagatataat atcatgacga cagggatcgt tgaaagcctt 3000 aatgctgtgt tgaaaaatgc tagagatctt ccggttttgc aattggttga agaattgaga 3060 aacttacttc aaaaatggtt tgtgactcgt caacaacaag caatgtcaat gtcaactgaa 3120 cttaccatgt gggctgatgg agaacttcgt tcaaggtata atatgtcagc aacatatcta 3180 gtggaaccta tcaactccaa ggagtgtaat gttaactatg ctggcattag tgctcaagtg 3240 aatttagaca ctcgttcatg cacatgtcga caatttgatc ttgatcatat tccatgtgca 3300 catgctattg ctgcttgtag attttacaac atttcatgtt acactttgtg ctccaagtat 3360 tttactacta aagcattgtt atcttcatat tcagagtgta tttatccaac tggaaatgaa 3420 atagattggg tagtacctaa tcatattcgt gacaaagttg tgttaccacc taaaacgaga 3480 cgcccaacag gaagaccaag gaaagtaaga attccttctg gtggagaggg caagcgcaca 3540 tctcgttgta gtcgatgtgg tcaatatggg cataatcgga aaacatgcaa acgaccaatc 3600 ccttgatatc atgatagctt trgcactcta tgaacttaca tggaatgaaa attgtaatag 3660 tgagcttttt tgtttttttt ggtacccatg tgaacggaaa tgtaagttac ttttttgtat 3720 aaggtgatag gataagcaca tagatgaata ttgtaataat gatcccctwt ttttttgcat 3780 acccatagaa atggagatat ttgttacttt tgtacatata tgttatgatg agttatgtat 3840 aaagtatgaa tgaaaattac aygtttattm tcaaactatg gactcaactg ttctcacgtt 3900 tattgataag gaacttgaya atagttaagt tcaggttttg tytgaagact rtagacttaa 3960 ctaccttcaa gtttgtacat aaaacaactt gacaatggtt aagttcaggt tttgtctaaa 4020 gaccgttgac ttaamtgcct tcaagttggt acataaaaca acttgacaat agttaagttc 4080 aagttttgtc taaagaycgt tgacttaact gccttcaagt tggtacataa aacaayttga 4140 caatagttaa gttcaggttt tgtctaaaga ctgtggactt aactaycttc aagtttatac 4200 ataaaacaac ttgacaatag ttaagttcag gttttgttta aagactgtga acttaactac 4260 cttcaagttt gtacataaaa caacttgaca atagttaagt tcaggttttg tctgaagact 4320 gtgaacttaa ctaccttcaa gtttattcat aaaacaactt gacaatagtt aagttcaggt 4380 tttgtctkaa gactgtggac ttaactacct tcaagtttgt tcataaaata acttgacaat 4440 agttaagttc aagttaaaat ggcaaactgt agacacawct tcctatgagt ctatagaaga 4500 tcaacttgat acctgttaag tcyagattaa atatgttatt ctggaataga tttcgactta 4560 atatctgtca agtttgttca cagttaactt gawagtagtt aagttcaggt gttctattaa 4620 gactgtgrac ttaactacst tcaagtttgt acacataaca acttgamaac attcaagttt 4680 agtttaaaag gtcaattgta tacataacta ttgaacaaca ttcatcaaaa tatccaagta 4740 gatatatcaa cctgtccaac tacatttatc aaaatgtcta actacatata tgaagctatc 4800 caattacata taacaaacca tccaactaca ttatcaaaat gtgaaatatc aacatgaatt 4860 cattacatag gcaagtattt catataaaat aactctgctg ccatcttttc ccraaacyag 4920 tccattcgag cacttgttaa tgacttcaat ggatggttgt gcattaagta ttcaacatat 4980 ttgataacaa acatgccaca atcaccactg catggtacac arataatcaa tgttagggct 5040 attattaagg attaagtgta taagttatga aagtaaattr aagatcactt actcattttc 5100 ctgttgagga atatcttgca rccgttcaat ttyccattcm trgtagttaa cttttgtgtc 5160 accatgaaac ccataatatg ctattgcatt caatatatgc ggcaacaatt tggctaatgg 5220 tttaatggca acttgcaatc ttgcattatt attgatgccc atcaatragt catatacata 5280 tataatcctt cgatraaggt ggacaactcc taataccyaa tgactagccc gaacattkat 5340 ggggacatac acaatgtcaa catcaggcca tttgacagaa taaagargct gcaaaccatt 5400 ggcataatca ataagaatgt cattctctgg taatttgaat tggttccatt tcttgccatg 5460 cttaatccat cttcaaattt ttttttytwt attttttttc tttttctttt cctctcctaa 5520 agaaagaaaa actttctcca actcatyatt acgcaccttg ttttctcctt taaagtatgt 5580 gycccttatt cgtaatgatt ttttatcaca ttttgtaata tgaccaaaac ycaagcccgt 5640 aatcaatgca aactcttctt tackaaatmt taagcccttt gactttaata aaatccatat 5700 ttcattgtct tttttggttt cacattgayg taacaacaat tgatgaacaa tttgggytga 5760 aaatctaagt tyggraagga gtaaaaaatg accaaaayat gawtttctaa acatctccaa 5820 ttgtggttca atcaatttct tcttaatatt ttcaatggcw accaagtgag acaaacatgc 5880 aatttttcca ggaaagtact cctctttagg tattttagat ataaaagata ggagaggagg 5940 aggaatgtca atctgcaaga taataacaaa ttrtaaaaat atcaatataa attgagcaaa 6000 attatattac caaacttatc caactatgtt aaatccatca tttcrtatta cttcttaaca 6060 tagactttat tttcctatta tttaaggatg tcatgtcaaa tgctaatatt ctaaagatat 6120 tattttacta atgcaattga agctattata ttttactaag ttgcaactac aaaamattgg 6180 agacattatt ctagtgttta ttgaaatttg aaacaaaacc aaaccatttt gaaattgcca 6240 cctattgaca atgaacttga tagcagttaa gttcagtttt ttcttaacat atatatttaa 6300 atcaaaattc taaatatttg gataaaataa tttcataaaa attatattca aatacattat 6360 aaattcataa caaataactt cattacacaa aatttcaaaa ccttttgatg gtaaacttga 6420 tagtagttaa gtttagtttt ttctaattat tcaaatattg ctttaaacct tggactataa 6480 cctcactgag aaaattttca acaattagat tatcaattca tgaaaaataa attcataaaa 6540 aaaaggataa tcgattaaaa atgataaaat taaaaaaaaa aaaaaaaaca aaatttcaag 6600 tagaaaatta atgcttactg aatcggttga tttcttctca ttttctgatg acgataacga 6660 ggtttcaaaa cctggctttc tttcacttct tttttttccc aaaattttat acctcttctg 6720 tttttcatca ccgaattttt ttcttcctcc attttcatga actaaatcaa cacacaatat 6780 tagaaagatg aaaaataggg tttgattgaa aaaaaaaaaa tgaaccaaaa taagacactt 6840 agggwttctt ctcakttcat ggatgaagat tcatatgtac agttcgaaaa actaaaatca 6900 aagartggaa acaatgaaac ttactttctg ttttttcttt gtgttgtgtt gtctttttgt 6960 tctcttgcaa taaacggaaa aatccttcgt gatttctttc tcgcaggtta acagatggaa 7020 taaatgggtt tgcagggtaa ggaagagaca caacataagg gaaaattgga gttggaggga 7080 aaatgagctt aaaagatagc tgagggggta tttttgtcag aattgggtca tttttgagac 7140 ttaaataagt gaggggttag ttttgcaata ttgagggatt tttgtccctt ttaatcgatt 7200 atccc 7205 // ID Copia-55_PTr-I repbase; DNA; EDCOT; 4509 BP. XX AC . XX DT 08-DEC-2009 (Rel. 15.02, Created) DT 18-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Copia-type LTR retrotransposon: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed repeat; internal portion; Copia-55_PTr-I; KW Copia-55_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4509 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 163-163 (2010). XX DR [1] (Consensus) XX SQ Sequence 4509 BP; 1526 A; 608 C; 864 G; 1511 T; 0 other; gtggtatcag agccttcgtt agacaattag ggttgttgat tgcatgtttt aattgttatt 60 ggtgttaatt gtgaattaat tttatgtgca aaattatttt tccaaaaatt attttttctc 120 tcatgatttt taaataaaaa aaaatctttc tactgtttcg gccagatctc ttgaatctgg 180 tggaatctag tgaaatttta gaaacaaaaa ggtggctgtc atgggcgcca ctgctgccag 240 tgttgcagga ggcggcatcc catggtggcg tggtaggcct tgctatggag ttgcgcagcg 300 cgagcgctgc cctcacgcta ctggctggca gcggcaacat tggctgccgc tgctagggcc 360 gccaacggtg ggcagagtcc cactaccagc agaagcagaa gaagaagaag ggtatagtta 420 catgtttacc cctataccct ttttagggtt tttaagaggt aaaattatga tttaaccctg 480 caacttatgt ctaattacat ataggtattt taggctgaaa ttatgatttt accctccata 540 tataaataat aattttatat taaaattgaa accctaaatt aaattaatta agaattaatt 600 ttcctaatag gattaggaat gaattaaatt gtttaattca ttttttagtt ttatgatatc 660 ctaatgggat taggatttat ttaattaaat aatatttaaa aaatggtttt tctaaaataa 720 gagagttttt aagcagaaaa ttttatttaa ttgatcctaa aatagtttag gatattaata 780 agaattttaa tgtgattaat tttcttatta aattttgaaa aatgtttttc aggaatttat 840 gttaaataaa atttattttg tttgggaaat tatcaaattg gatttgattg aatatttcta 900 agtgttagaa atattatttt aaattgcaca taaagccaat aattagaatt gaagcatgca 960 atatatttta ttatgcatat taaaatgttt ttatgcatga tggatgatta tggacattaa 1020 agaccaatgt gattgtgttt ttatttatgg ttgaatggtt gtaatttatt aaatagggct 1080 tgtgtgtcct gtcttatctc tatttttctt ctgggttgta aattcttttc tcatctaatt 1140 cccctcgaat gtaactcgag gtttcttaat taattatgta aatgttatgt aatttagaaa 1200 tgtaggaatt tagatagaaa attatttgta atccaagacg aagaaagaaa tggcgatgaa 1260 ggctacaatc aaggtgcttg caaggactta tgaagatttg caacagctac ctaggatttg 1320 accatctaat tcccttcaat ggctcgaggg aattagctta gatatgtcca taatcatcca 1380 attagaatga catgctaggg gtgtatgttt atatataaat tgttatgtat gattgttatg 1440 ccatgttatg aatgagacct aattaattaa taaatccctc attaatatat taagtacatg 1500 ttgagaacat gatgttgcct tccaatttta tatgcataaa accagagttc tattcatgga 1560 taacttgttg agccactcaa ggttaccgtt aatcgaatat gtttaatgct ataaaattag 1620 gtcctactta actaacctat atgatttgga tgagtcactt atgatcatat aaggttagag 1680 gcatgagtta ggcgaaacat atatgatatg tttagacaaa gagttgtcac ctaactgatc 1740 taggagtcac atagagatgt gattgataaa ctatgttatc tacctaattt aatttatttt 1800 gatttgttga gtcactcaag gtcagataaa ttaaatagga tcctagccca ctaggaaaat 1860 ctaagcgaga tttcctgaat taatagggag ggctattaat ttgcaagaaa atagtgggag 1920 accaaattag gattaaagac cttatctaaa tttagaattt aaatatgtat gcatgaaact 1980 aatactcttt atctttacat aaataggttg gtagatcaaa atgagtagta acatatccct 2040 acaaagcata cttgatgcta acaaattgac tggaccaaat ttcttggatt ggcacgaaat 2100 gtgagaattg ttctcaagca agaaaaaagg ttgtatgttc ttgaaaatcc aattccaaat 2160 gcccctgtga ggatgctgaa gaagaagtta ggaatgaaca tcaacgtcat gttgatgatg 2220 atgaacaggc tgcatgtgtg atgttagcca gtatgtcacc tgaacttcaa aggcaacatg 2280 agaatatgga tgcccatact atgattatgc atctcaaaga gttgtttgat gaggccagta 2340 ggactgagag gtatgagacc tctaaggaat tgttccgctg caagatgata gagggttctt 2400 cagtgaacac ccatgttttg aaaatgattg gctatattga gaaattaggc caattgggtt 2460 ttgtcatgga ccatgagtta agtgttgact tggtcttgca gtcattaccc caaagctttt 2520 cacaattcat tatgaactat cacatgaaca agttggatag tacattgtta aaattgctta 2580 atatgcttaa gactgctgaa gggaccctta agaaggaaaa aggccttgtt gcttaatgag 2640 ctttcttagt atgtttataa ttgaaaacta tcttactact ttgcattgta gtttttggta 2700 ttggataccg aatgtggttt tcacatttgc aattgcatgc aggaactaaa gaaaatagaa 2760 gattagttga aggcaaagtg gacctacgac tcagtaatga agcaagggtt gttgcattag 2820 ttgtaggaac tagttatttt gttttgttaa tgggctgata ctagaacttt ataattgtta 2880 ttttgttcca gtattttaag acattgtttc cattttattt agtattaaat ggatttaaat 2940 ttattattga ggacaaatat tgttctttta taataatgat gtttttatgg atctggtaat 3000 tatatgaatg gtttgtatat acctgaattt aaaatgccca ggttcaatat aaactgcaat 3060 aaaattgaaa tacatattgg aataagtatt aagaaacttc gattggatcg aggtggttaa 3120 tatttgacca aatatttcaa ggattatcta aaagagaatg agattctcta cacctcttag 3180 aacactacat ctagatgaaa tatatttctt aaggctaaaa cattggatgt ttagcctgaa 3240 ccttaagaaa cacaaaatct ctataaattt ggtaggacat gtcatgcatc aatgagataa 3300 ggacctctca tggaagctgt gaatgacatg ttgctcataa ttgatgagcc taccaattac 3360 ttggaagtaa tatatgatat ttattccaag aaatgacttg aagctatgga cttcatgtac 3420 taaccaagtt tggaacttgg ttgatccacc tgaagggata aaacccaatg gatctaagtg 3480 ggtctttaag agaaagacta acatgaaaga caatgtacaa atgtacaatg caagctttaa 3540 ggagtaggaa tatccaattt tgatggtata atcaacagat ttgatttcat aaaaaatatg 3600 gataaacctt gtgtttacaa aaggttagtg ggagtggtgt cgttttccta atattatatg 3660 tagatgacat attattgtta agaaacgaca tatctttact ttaatcagta aagttttggt 3720 tgtccaagaa tttctccata aagaaattgg gagaagcaac ctatatattg gatataaaga 3780 tctatagaga tagatctaaa aggttgctta gattgtccca atccatgtat atagactaga 3840 tgctaaaata gcttagcatg gaagaatcta agattggatt cttatctatt ttgcatagaa 3900 tacctccctc caaagacatg tgttctaaga cacagattga gagagatatg atggaaatgg 3960 tatcctatac ttggctatag gatccatcaa tggagaagat aaactagaag ttcaaaattg 4020 tttgaattaa aatttttcaa tgaaatgttg gaaaaatagt aaataccagt caatatatat 4080 tttactctaa atggtagtgc tctgagttgg aagagttcca aacaagagag caaaattgat 4140 tctacaactg aataagagta cacctccatg tttgaggaaa caaaaaggtt gtttggatca 4200 agaagttcat caatgaacta ggttggttcc tagcattgtt gatccagttg ccctgtactg 4260 tgataacaat ggagtcattg cataagcaaa ggaaccaagg tctcatcaat gatccaaaca 4320 agtacttaaa aaattccatt tgatttgata aatcaatgaa atgaaagatg taaagataga 4380 gtgagtaccc accaaagaga atctagaaga tcctcttact aagtcactat ccatgcagaa 4440 gcattaatgc tacatagagc aatatgatat tagatacatg agcgattggc tttagtgcaa 4500 gtgagagat 4509 // ID DNA-3-3_PTr repbase; DNA; EDCOT; 826 BP. XX AC . XX DT 15-DEC-2009 (Rel. 15.02, Created) DT 15-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Non-autonomous DNA transposon - consensus. XX KW DNA transposon; Transposable Element; Nonautonomous; TSD 3-bp; KW DNA-3-3_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-826 RA Kojima K. and Jurka J.; RT "Non-autonomous DNA transposons from black cottonwood."; RL Repbase Reports 10(2), 194-194 (2010). XX DR [1] (Consensus) XX CC TSD is 3-bp long, TIR is not detectable. XX SQ Sequence 826 BP; 296 A; 142 C; 110 G; 272 T; 6 other; ttaagagccc gtttggctac gcgttagagg ttgcgttttn tcaaaaacgc acgaagcaaa 60 cgtttggtta acaaaaaaaa gcgatttact gtgcatggtc ccacaataaa ttgcgtgcga 120 aacgcaggna gatgaaaagc agaaaaatgc tgctttcttg cgcggctctc aattcgaacg 180 ntgatacact gttcactgaa cagtgtagca tgatccactg ttcagtgaac agtgcaagan 240 nactgcactg ttcactgaac agtggagcac gtgaacagtg caaaattgca ctgttcacgt 300 gaattttttt ttttcagcgt gttaattttt ttaacatttt tttttaaaaa aaactagttt 360 aaagtgaatt aaaactagta taaagtgaat taaattcact cgcactgtaa tatcaatttt 420 atacctgata atattttatc tacgctcaaa aaattatgaa aactgtagtt cttatcggat 480 gaattttgta cgtaatggaa ttataaatag tttaatggaa taataaaaag tattttttat 540 aaagtatttt ttatttcatg atgtaatagg agtaattaat tctacaatat ttaaatttaa 600 aaccatcaat attaatatat attttttaaa ttattttata acctcaattt caaaagcatt 660 cttaaccaaa cacattaaac tactttttct tcaacctcaa tttcaancac agttttaacc 720 aaacacctat tttttcaaac caacctcaac taaaagtact ttttataaaa caactttttt 780 caaaccacaa ccacaacagc taccgcaata ccaaacacac tctaag 826 // ID Copia-36_Mad-LTR repbase; DNA; EDCOT; 116 BP. XX AC ACYM01002754; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-36_Mad-I; KW Copia-36_Mad-LTR; Copia-36_Mad_. XX NM Copia-36_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-116 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1386-1386 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01002754; Positions 11792 11907. XX SQ Sequence 116 BP; 37 A; 26 C; 13 G; 40 T; 0 other; tgtactcgca atcctacaag aaaaaggatt tcactaagct tgttaatagg acttctccat 60 tcaaaagatt tatacttctc ggctcttaat gttcaattca tactcatact cttaca 116 // ID HAT-3N1_Mad repbase; DNA; EDCOT; 413 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-3N1_Mad. XX NM HAT-3N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-413 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1610-1610 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~80% identical to the consensus. XX SQ Sequence 413 BP; 103 A; 101 C; 96 G; 113 T; 0 other; caagcagggg cggatgtaca ttgggaccaa ggtggtccca ggaccactcg gagtccgaaa 60 aatatacatg tgaaggtctt ctgaggaccc tccgaatgtt tggtatgggt cccttttgtg 120 cccaccaagt gtttgatgta atgtctgcta ggcatatctc gacaggttgc gtcgacaaca 180 ctcgacaaat tctctcgata tcactcatca gattgcttcg gcatatgtcg atatctgttg 240 acatgtgcgc aacatggttt ggctgacgac aacaagccca ccaagtgttc gacgaaatgc 300 ctcagtgaat aaactgaaat tttttttttg cgcgcttcgc gctctgtttc tatctaaaaa 360 acttggactt taacactggg acccccaagg ttcgaatcct gaatccgcca ctg 413 // ID Copia-9_Mad-LTR repbase; DNA; EDCOT; 315 BP. XX AC ACYM01100325; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-9_Mad-I; KW Copia-9_Mad-LTR; Copia-9_Mad_. XX NM Copia-9_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-315 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1351-1351 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01100325; Positions 4818 5132. XX SQ Sequence 315 BP; 111 A; 37 C; 56 G; 111 T; 0 other; tgtaagaatg atgaagttaa agagactatc aatggttaaa acaaaatcca tgtgtcaaaa 60 gattaaatca gttgataaac atatagttag ttagttggaa tctggagagg ttagatattt 120 ggttagaaga agttagttga gataaggtgg ttatgaatta cttgcttcct aagtcatata 180 gctaaacaca tatataagtg aggattgtaa ctcatagaga ttttaatgaa gaaagcttat 240 atctgatata catttctatc tcttttatct ctctgttcaa ttggttttac ttctctcagt 300 aaacctatct taaca 315 // ID Copia21-VV_I repbase; DNA; EDCOT; 4382 BP. XX AC AM479441; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia21-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4382 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4382 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 701-701 (2007). XX DR Genbank; AM479441; Positions 9634 5253. XX CC Positions [1580-1912] - Integrase core CC 'AATT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 2807..4327 FT /product="Copia21-VV_I_1p" FT /translation="MSSELTALMRHGTWDLIPPPINCHPVGCKWVFRVKRK FT VDGSVDKFKARLVAKGYNQQPGVDYNETFSPVVKPATIRTMLSIAIMNGWP FT LKQMDVNNAFLHGNLTETVYMMQPPGFKDLSRPDYVCRLRKAIYGLKQGPR FT AWYSALKTALLALGFQNSKADSSLFVYHHDSIVCYFLVYVDDLVITGNDKK FT FVAHVVTKLGDQFSLKDMGSLHYFLGVEVIPTTAVVFLSQHKYARDILENT FT HMAGAKDVSTPLSTTQSLHLVDGMNAINNTEYRRVIGNLQYLSLTRPDISF FT AVNKLSQFMHKPIVTHWTATKRLLRYLKKTIFHGLHLKSAAAPCLTTYTDA FT DWAGNIDDRTSTSAYITFLGYNPISWSSKKQRAVARSTTKAEYRALANGAS FT ETMWLLALLQELGFSLKLPHSLLCDNLGATHLSFNPIQHSRMKHIQIDLHF FT VCDQVQKGALKVSYVHTQDQLADLLTKPLSREHTECLRAKIGLADGSSILR FT GHIKESDTRQE" XX SQ Sequence 4382 BP; 1225 A; 1086 C; 749 G; 1302 T; 20 other; gattatttac tttactatat ggtatcagag catctctcca acgagaattt gatcctaatg 60 tcttccccaa cacagcctac cttcgaaatc ccccttgttg tttttaacat cacaactcag 120 atcaatgaga aactcacacc ttcctttttt ccccaatgga gagctcagtt tgaggctttc 180 ctaattggct atgatctaat ggactacgtt actggcgaat cccgttgccc tccctctgat 240 ggcaccccac catctatagc caagaaacac cactgggtta ggcaagataa attaattctt 300 agtgccatcc ttgacctcta ctttcccaac cattacctct cttattgcca caacaaaaac 360 ctcctatgat gcctataaaa aattatccac catgtatgca agtaaatcgc gtataagggc 420 catgcaactc aaggaagaac tcaccttgat tcagcgtgga aaccgcccaa ttctggagta 480 ccttcatgtc gttaaaggca tggctgatga gattgcactc atsgaccacc caatctccga 540 cgacgacatc actctctacg tcctcaacgg gttaggaccc gaattcygtg agattgctgc 600 ccctattcgg gcaagagaaa aatcccttgc ctttgaggag cttcatgacc tccttatagg 660 gcatgaaaat tacctgcgca ggatggaggc tgctacccag cagctcgkgg ccgctrcaaa 720 tttcacaagc cgacgctytg gcttttctgc mtctcagcaa caraaagctt ctcayaaggg 780 aaatgggtct ccccgttcac aaggccagta tcggttttcc agctcaaatg gcccatttcg 840 tgacccacgc cgttccaaca atcagggtcg gttcaactct aatcagagac gctatcagcc 900 caaatgccag tactatgatc aaatgggcca cacggccaag gcctaccctc aattaaattc 960 ttctgaaatg actgttaatt gtgcaggaac ttctgatggt caagaaaata aatggttaat 1020 tgactctgca gcctctcaca atatcacggg agatataaaa aatttatcaa ttcactctga 1080 gtatgatggc actgatgaag tccttcttgg tgatggtaca ggtttagtgg ttacgcatat 1140 tggttcttta gcattaccca cacccaaaaa aatctttcat ttacatgata ctttatgcgt 1200 tcccaatatt cacaaaaatc tcatttcagt tcatcatttc accaagtaaa atgatgtttt 1260 tcttgaattt caccattttt ttttccttgt gaaggcacga tccacggggg tgatactact 1320 aagaggtgca tgtgagaatg gcgtctacat ttttcccaac tccatggtgg ctccttctac 1380 tcccaaaatg gttgcttatg tgcatgaacg gacttcaatc gatggatggc acaagcgtct 1440 tggacaccca tcgattaaag ttgttcaaaa tcttgttaat cttttttctc ttcctytgac 1500 aacaaataaa ttaccattgt catgtccttc ctgttcaatc aataaagcac atcaacaacc 1560 atttggctct acaagttttc aaagtcattc tccccttgaa attatttaca gtgatgtttg 1620 gggtcccrcg caygttaccg gtttaaatgg tgaacgttat tatcttattt ttgtggatca 1680 ttacaccaaa tatatatggt tttacccaat gtccacaaaa tctcttgttt ctacactctt 1740 tccacagttt aaattacttg ttgaaacaag attcaagtgt tccataaaaa gcttgtactt 1800 ggacaatggt ggcgaatttt tgagttttaa aaaatatttg tccgatcatg gcataagcca 1860 ctacaccacc gccccccata ccccccaaca aaatggtgtt tccgaaagac gttagcgtca 1920 tcttgtcgaa acgggtctca ccttgcttca cgatgcttct ttatctcttt cttattggcc 1980 ccatgccttt caaacaacca cttatctcat aaatcgccaa ccaacccctc tttttaaaca 2040 caagtctcca tctgaggttc tttttggtca acgaccaaat tatctcaaat tgagaaaatt 2100 tggttgttta tgctaccctc tcacaaggcc atacaatacc cataaattac aaccaaaatc 2160 aatcccttgc atttttctcg gctattccca aacacagaac gcctataaat gtatggatcc 2220 attaatgaat cggttgtata tctcacaaca tgtgactttt gatgaattgc agagcccatt 2280 cctttcaaaa accaagcacg ggccatctgc cgaaacccac ttattttcct ctactcctca 2340 ccttttcctt cagcagaacy cgtgccctaa tttcctctcc cctcctcctt ccattcctgt 2400 gcctccatct cgtcccgatc gctcctcgca gccaccacyg agctcggaac ctgcagctgc 2460 cattcctgsa ccacctccag gtatatcccc ctctatctyt ccttmttttc attgtgaatc 2520 gcatgacaat acctgtgata tgaatctgaa cwtmgatgct ggtatacata tgactattct 2580 gcatgcttct ctttcaaatt cacttgcatc tagtttaatt cctgattcac aatctcytgt 2640 acacactgaa cccacttccc accgaaccca ttccatgact actagatcta tgaacaacat 2700 ctttaaacct aagcaattac acactgtgtc taagcactat cttccattac ctctagaacc 2760 aacatgcgtg actcaagctg tatctcaccc tgaatggcrt gaagccatgt ctagtgaatt 2820 gactgctctc atgcgacatg gtacttggga tttaattcct cctcccatca attgtcatcc 2880 agtgggttgt aaatgggtgt ttagagtcaa aaggaaagta gatggctcag ttgataaatt 2940 taaagcccgg cttgttgcca agggctataa tcagcaacct ggtgttgatt ataacgaaac 3000 ctttagtcct gtggttaaac cagccaccat aaggacaatg ttgagcattg caatcatgaa 3060 tgggtggcct ttgaaacaaa tggacgtaaa caatgctttt ttacatggaa atctgactga 3120 aactgtgtac atgatgcaac ctccgggttt caaagatttg tctcgacctg attatgtgtg 3180 ccggctcagg aaagcaattt atggtctcaa acaaggccca agggcctggt attcagcatt 3240 aaaaactgct cttctagcac tcgggttcca aaattctaaa gctgattcct ctctttttgt 3300 ttatcaccat gattccattg tctgctattt ccttgtttat gttgatgatt tagtcattac 3360 aggtaatgac aagaagtttg tagctcatgt tgttaccaaa cttggtgacc aattttcctt 3420 gaaagatatg ggttcccttc attacttcct tggagtggaa gttataccaa ctactgcagt 3480 tgtatttctc tcccaacata agtatgctcg tgacatcttg gagaatacac acatggctgg 3540 tgcaaaggat gtctctaccc cgctgtcaac aactcaatcc cttcacttgg tagatggcat 3600 gaatgctata aacaacacag agtataggcg tgttattggc aacttacaat acctttctct 3660 tactcggcct gacatttctt ttgctgttaa taagctctct caatttatgc acaagccaat 3720 agtcactcat tggactgcca ctaagagact tcttcgatat ctcaagaaga caatctttca 3780 cggtcttcac ctcaagtcag ctgcagcacc atgcttaaca acctacactg atgcagattg 3840 ggctggaaac attgatgatc gaacatccac atcagcttac attacatttc taggctacaa 3900 tcccatctca tggagttcaa aaaaacaacg agctgttgct cgttccacca caaaagcaga 3960 atatcgagcg ctagccaatg gtgcatcaga aacaatgtgg ttacttgccc ttcttcaaga 4020 attgggtttt tcattaaagc tgccacattc tcttctatgt gataatcttg gagcaactca 4080 tctcagcttc aatccgatcc aacattcaag aatgaaacat attcaaattg atcttcattt 4140 tgtgtgtgat caagttcaga aaggtgcact taaagtgagt tatgttcata ctcaagatca 4200 attggctgat ctactaacta agccactatc ccgggaacac acagaatgtc taagagccaa 4260 aattggtctt gccgatggaa gctcaatttt gcgggggcat attaaggaaa gtgacacaag 4320 acaagaataa gatttaaatc tggaagtgat ttgtagcaat catcaagccc caacaacaaa 4380 tc 4382 // ID Copia23-VV_LTR repbase; DNA; EDCOT; 162 BP. XX AC AM484507; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia23-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-162 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-162 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 689-689 (2007). XX DR Genbank; AM484507; Positions 9137 9298. XX SQ Sequence 162 BP; 46 A; 27 C; 24 G; 65 T; 0 other; tgttgaatat aatgtatgta tagtatacta tctttccttg ttaatatagg tcacatgtat 60 ggtagttagg actcctagcc ttgtatatat atatctctca attgtaagta gagattacaa 120 tgaatgaata aggtttttct cctctctctc tctctctcaa ca 162 // ID Copia-11_TC-I repbase; DNA; EDCOT; 4114 BP. XX AC CACC01006392; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-11_TC_; KW Copia-11_TC-LTR; Copia-11_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-4114 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01006392; Positions 26379 30492. XX CC Positions [1640-2140] - Integrase core CC 'AATAC' target site duplication CC LTRs are 97% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS join(1244..2953,2957..4114) FT /product="Copia-11_TC-I_1p" FT /translation="MKSISNVMFVPEVAQNLLSVRQLIEDGYILLFKTNAC FT TILDASGKELFSVEMRNKCFSVDWMKVKHKAYQCLSTNSEIWHRRLGQVNY FT RSLMHMISNNLVEGLPSLTQTDRICSTCQYGKQCRVSFPKSRNWRAKQKLQ FT LVHSDVEGPMKTLSLNGSLYYLIFVDDYTRYSWIFFMKHKYDVFNLFTKFV FT AAVENESGSNLMILRTDNGGEFNSTEFKEFLARKGIKHKLMVAYNPQQNGV FT CEHKNRTVMEMTRCLLFEKDLPKEFWAEAANVAVYLLNVLPTKALNVKCPY FT EAWHGTKPSVAHLKVFGCICYAKIPDGKRTKLDPKSQLAIHLGCSNLSKGY FT RLYDLKTKKVFVSRDVRFDEDLKWNWKTTAVEKSKSNNTTGDVNEGLKWNL FT EIATDENNADGDENLFDDEESVDENDESLAVRGTRPLQEIYGRCIMAVIEP FT NEVSKALKDEKWKEAMDAEMQMIARNRTWYLVDRPQGPKVSGVKWIFKTKL FT NPDGSVNKLKARLVVKGYSQVQGVDFEETFAPVARYDTIRVLTALAVKENW FT SIWHMDVKSAFLNGVISEDIYVEPEGYVVQGKEDKVCKLVKALYGLKQAPR FT AWYDRIDSYMREKGFIRSNNEATLYVKKSGNAVKLIVSLYVDDLLITGPDD FT EFLKEFKAQMKFEFDMTDLGKMSYFLGLEFQQLEGQICLYQSKYAEDLLKK FT FKMNFCKPAPTPLTMGWKLSKDDGEIKTDARLYRSIIGCLLYLSATRPDIM FT FATSLLSRFMQEPSEMHMKAAKRILRYIRGTTTFGLKFVKQDSNHLQGHCD FT SDWAGSVDDSKSTTGYCFSFGSAIFSWNSRKQEVVAHSSAEAEYIAASSAT FT NHVLWLRKLLDDLGFRQFIGTVLWVDNMSAISIAKNPVQHARTKHIRVKFH FT SIREAVKNDEVVIKHCSTNDQVADIFTKSLNKDKYYYLRSKLGICEINSKE FT V" XX SQ Sequence 4114 BP; 1357 A; 654 C; 950 G; 1153 T; 0 other; tggtatcaga gcatttcatg tgttcttaag ggacctatga aagcaatttt ttttttttag 60 aatacttaat cttgctgtct catatcttcc attagaatac ttaacctatg gcttccacca 120 gtttcaatgt tgtagctcca ccagtgttta acggagataa ctacccaatt tgggcagtga 180 agatgaaagc ttatctccgt gtatttgacc tctgggaagt tgtggaggtg ggtggagatc 240 ctccagttca aaggcatgcc aatcctacaa tggcacaatt gaagcagcat agtgaagagg 300 ttgctaagag atacaaggcc ctttcatgta tccactctgc tatatctgac tccatattca 360 ctaggattat ggcttgcgag aatcctaaag atgcttggga caagttgcaa gaggaattcc 420 atggaagtga taggactcga cagatgcaag ttcttaattt gttgagggaa tttgaagttt 480 taaaaaagaa agacaatgag actattagga gtattctgat aaagtaataa aagttgtgaa 540 tcaactgagg ctacttgggg aagaccttcc agataaaagg attgtgaata agtcctagta 600 agcctaccgg ataagtttga agctaagata tcctcacttg aagagtccaa ggatatctca 660 cgccttactg tcacagagct tgttaatgct ctccaagcac aagaacaaag acgagctctt 720 aggcaagaaa acacggtaga aggagccttc ataactcgaa caaaggagaa atggagtgac 780 aacaacagaa agaatgattc agagaagaga gacaaggaca ggacatctgg agatggaaaa 840 caaggcaagc cgagagctaa gtatcctgtt tgttctcatt gcaaaaagag aacacatctt 900 gaaaaatatt gttgatatcg tccaaatgtt aaatgcaggt catgccatca attaggacat 960 gtggagagag tttgcaaatc gaagggaaac agacctaagg agaaggctac tgttgcagaa 1020 catcaggaaa tagttgatga atttttattc atggtaagga aatctgaagt ttcaaacaag 1080 aagcacacat ggctgattga tagcgcttgt tcgaatcata tgatcgggaa ggaagaaaat 1140 tttattacct tggacgagtt ataaatctca ggttgagatt ggaaatggac ttaatttgca 1200 gattcaaggg ataggaacag ttgcggtgca tacacttgca ggtatgaaat caatttccaa 1260 tgtaatgttt gtacctgaag ttgctcaaaa tctacttagt gtgaggcaat tgattgagga 1320 tggatatatt ttgttgttta aaaccaatgc ttgcactatc cttgatgcct caggcaagga 1380 acttttctct gttgaaatga gaaataagtg tttctctgta gattggatga aggttaagca 1440 taaagcttac caatgcttgt ccactaattc tgaaatttgg caccgtagat tggggcaagt 1500 aaattaccgg tctttaatgc atatgatatc caacaacttg gttgaaggac tccctagttt 1560 gactcaaaca gatagaatct gtagcacttg tcaatatggt aagcaatgcc gagtctcttt 1620 tccaaaatct agaaattgga gagcaaaaca aaagcttcaa ttagtgcact cagatgtgga 1680 aggtcctatg aagactctat cattgaatgg gagtttatat tatctgattt ttgtagatga 1740 ttatacaagg tacagttgga ttttttttat gaaacacaag tatgatgtgt tcaatttgtt 1800 taccaagttt gttgcagcag tggaaaatga gtctgggagc aatttaatga ttcttaggac 1860 agataatgga ggagaattca actcaaccga gtttaaagag tttctcgctc gaaaaggaat 1920 caaacacaag ttgatggttg cctataaccc tcaacaaaat ggagtttgtg agcataaaaa 1980 taggacagtg atggagatga cacgctgttt gttatttgag aaagatttgc caaaggaatt 2040 ttgggctgag gctgctaatg ttgctgtgta tttactaaat gttctcccaa caaaagcttt 2100 aaatgttaaa tgcccctatg aagcttggca tggtacaaaa ccatcagtag cgcacctcaa 2160 agtttttggg tgcatttgtt atgccaaaat tcctgatggt aagagaacaa aactcgatcc 2220 taagtctcaa ttggcaattc acttgggctg cagcaatctg tcaaagggat atcgattgta 2280 tgatctgaaa actaagaagg tttttgtaag ccgtgatgtg agattcgacg aagacttgaa 2340 gtggaattgg aaaactactg ctgttgagaa atcaaagtca aataatacca ctggtgatgt 2400 gaatgaaggt ttgaagtgga atttggaaat agctactgat gagaataatg ctgatggtga 2460 tgagaatcta tttgatgatg aggaaagtgt ggatgagaat gatgaaagct tggctgttcg 2520 aggaacaaga ccactccaag aaatttatgg tagatgcatt atggcagtaa ttgaaccaaa 2580 tgaagtttca aaagctttaa aagatgagaa atggaaagaa gcaatggatg ctgaaatgca 2640 aatgatagca aggaacagga cctggtactt agtagataga cctcaagggc caaaggtaag 2700 tggtgttaaa tggatattta aaaccaagct gaatccagat gggtctgtta acaaattaaa 2760 ggccagatta gttgtaaaag gatattcaca agttcaagga gtggactttg aagagacctt 2820 tgcaccggtg gctcgatatg acaccattcg agtcttaaca gcacttgcag tcaaagaaaa 2880 ttggtccatt tggcatatgg atgtgaaatc ggctttcttg aatggggtta tatcagagga 2940 catttatgtt gaataacctg aaggttatgt ggtacaggga aaagaagaca aggtgtgcaa 3000 gcttgtcaaa gctctctatg gactcaagca agccccaaga gcatggtatg accgaattga 3060 cagctacatg cgagaaaaag gatttattcg cagcaacaat gaagctacac tctatgttaa 3120 gaaatctggt aatgccgtga aactgattgt atcattgtat gttgatgatt tgttaataac 3180 agggcctgat gatgagtttc taaaagaatt taaagctcaa atgaagtttg aatttgatat 3240 gaccgactta ggaaagatgt cttacttcct aggcctggag tttcagcaat tggaaggtca 3300 aatttgtctc tatcaaagta aatatgctga ggatttactt aaaaaattca agatgaactt 3360 ttgtaaacca gctccaacgc cactaactat gggttggaaa ctcagcaaag atgatggtga 3420 gattaaaact gatgctcgac tctatagaag tataatagga tgtcttctat acttgtcagc 3480 taccaggcct gatattatgt ttgccacaag tctcctatct cgatttatgc aggaaccatc 3540 agaaatgcat atgaaagctg caaaaagaat cttgaggtac atcagaggca caacaacatt 3600 tgggcttaag tttgtgaaac aggacagtaa tcatctgcaa ggccattgtg acagtgattg 3660 ggctgggagt gtggacgatt caaagagcac cactggctat tgtttctcat ttggaagtgc 3720 aatcttctcc tggaactcaa ggaaacagga ggtggtagct cattcttctg ctgaggcaga 3780 atatatagca gcatcttctg caactaatca tgtgttatgg ctcaggaaat tgcttgatga 3840 tctgggtttt aggcaattta ttggcactgt cttatgggtg gataacatgt ctgcaatttc 3900 gatagcaaag aacccagtgc agcatgcaag aactaaacat attcgagtga agtttcactc 3960 aatcagagag gctgtgaaga atgatgaagt tgtaatcaag cactgcagca ccaatgatca 4020 agttgctgat atatttacaa aaagcttgaa caaagataag tattattatc tcaggagcaa 4080 gcttggaata tgcgagataa attccaagga ggtg 4114 // ID Copia18A-VV_I repbase; DNA; EDCOT; 3607 BP. XX AC CU459284; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 08-SEP-2008 (Rel. 13.1, Last updated, Version 1) XX DE LTR retrotransposon Ty1-copia like, internal portion from Vitis DE vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Kastel-B06; KW Copia18-VV; Copia18-VV_LTR; Copia18A-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-3607 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL/GenBank/DDBJ; CU459284; Positions 574289 577895. XX CC Size = 4086 bp CC LTR = 249-231bp CC LTR are 89.2 % similar to each other. CC Direct flanking repeats = gtaaa. XX FH Key Location/Qualifiers FT CDS 1056..2699 FT /product="Copia18A-VV_1p" FT /note="Incomplete putative gagpol polyprotein." FT /translation="ILSPYFQSQGILHDSLCVNTPQQNGVAERKNGHLLNT FT TRALLFQGNVPKSYWGEVVLIATYMINRIPSRVLDNKSPVEILKSFYPHFR FT TSNGLTPRVFGCTAFVHVHSQHRDKLDPRAIKCVFLGYSSTQKGYKCYNPL FT ARKFYIFADVTFTENKPFFHKSSLQGEISMMEDSPYVSFEPLDLPHVSTHG FT DEEPVSSSVPASVTHNFPQFPKVYSREKAIPEQKQVQESNSDLGNEITVRS FT DPPLHTQPGETSTNSTDNLDLDLPIVRSDPPLHTQPGETSIDSTDNLDLDF FT PIAVRKGTRECTNRPLYPLSHYVSLKHLSPAHKNFIVSLNTTIIPNTVSEA FT LTKREWKDAMREEMSALEKNKTWEIVERPKGKNIVDCKWIFTLKYKANGSL FT ERHKARLVAKGYTQTYGVDYQETFAPVAKMNTVRILLSLAAHYNWQLLQYD FT VKNAFLHGDLDEEIYMNIPPGFEENTGNKVCKLKKALYGLKQSPRAWFGRF FT AKVMKESRYKQSQGDHTLFIKHSATGGVTALLGYVDDIIVTGNDEREKHEV FT K" XX SQ Sequence 3607 BP; 1116 A; 737 C; 712 G; 1042 T; 0 other; tggtattaga gttgtaggtt tttaagacct gggcatcatt ctggccttca tcgccatttt 60 tctggccttc atagctggat tttttttatt cacatgttct tttaccagcc ttcattgctg 120 ttgatttttt tgttttgcga tctgccttaa ttccaagaga ttaggttttt tcgtggaaga 180 tgttggaaaa ttcaggtaca ccttcattct ctttttgcat aaatgcttta cacagagttt 240 atgatgactc ttggataata gactctggtg ccacagacca tatgacctcc aaatctcaac 300 ttttcaatac ctatacccca agcccaagta acaagaaaat tgtagtggct aatggctctt 360 tagttaccgt tgcaggtttc gaagacatat acatcacacc tacccttatt cttaaaaatg 420 tcctccatgt accaaaattg tcggccaacc ttgtttccat tcaaaagctt acccatgatc 480 ttaaatgtta tgctattttt ttcccttctt attgtgttct tcaagaacaa ggctcgggga 540 ggaggattgg acttgctaag gaaatgagcg gtctttacca ccttgaatca tcttagaaaa 600 ctagtaataa tttgtcgttg tctcttctca gttcctcaaa taaagatacc atttggttgt 660 atcacctatg tcagggtcat ccatctttta gggttttaaa ggtcatgttt cctcatttgt 720 tccaaggatt agatatttct gagtttcatt gcgaaacttg tgaattggca aaacatactc 780 gtgtatcttt tcctattagc aataaaagaa gttctcatcc ttttcatttg attcatagtg 840 acatatgggg tccttcgact atacctaatg tttctggggc tcgttggttt gtatccttaa 900 ttgatgactg cactcaggtt acatggatct ttcttcttaa acaaaaatct gatgttagca 960 ttgttatacc taatttccac tcaatggttc aaaaccaatt tggggttaaa ataaaaagct 1020 ttaggacaga caatgctaga gattacttca actagatttt gtcaccctat tttcaatcac 1080 agggcattct ccatgactca ttatgtgtta acacacccca acaaaatggg gtagccgaga 1140 ggaaaaatgg gcatttactc aatacaaccc gagccttact ctttcaaggg aatgttccta 1200 agtcctattg gggggaagtt gttcttattg ccacatacat gataaataga attccctcac 1260 gagtattaga caacaaaagc cccgtcgaga tacttaagag tttctatcca cacttcagaa 1320 cctcaaatgg gctcactcct agggtatttg gatgcactgc atttgttcat gtccacagcc 1380 aacatagaga caagctagac ccccgagcca taaaatgtgt cttccttggt tactcatcca 1440 ctcaaaaagg atacaagtgt tacaatcctt tagctagaaa attttacatc tttgcagatg 1500 tcaccttcac agaaaataaa ccttttttcc acaagtcctc tcttcagggg gagatttcaa 1560 tgatggaaga tagtccttat gtgtcctttg aacctcttga tcttcctcat gtctcaaccc 1620 atggtgatga agaacctgtg tcatcctctg ttccagccag tgtcactcac aattttccac 1680 agtttcctaa ggtgtattca agggaaaagg ccattccaga acaaaagcag gtccaagaat 1740 ccaactcaga ccttgggaat gaaatcacgg taagatcaga cccaccttta catacacaac 1800 ctggtgaaac ttccactaac tcaacagaca acctagacct agaccttccc attgtaagat 1860 cagacccacc tttacataca caacctggtg aaacttccat tgactcaaca gacaacctag 1920 acctagactt tcccattgct gtcagaaaag gcaccagaga atgcactaac cgaccacttt 1980 atccactatc acactatgtg tctcttaaac acctatcacc agcccacaag aattttattg 2040 tgagtctaaa caccactatc attcctaaca ctgtttctga ggcattgaca aaaagggaat 2100 ggaaggatgc tatgagagag gagatgagtg cattagaaaa gaataaaaca tgggagattg 2160 ttgaacgacc gaaagggaaa aacattgttg attgcaagtg gattttcaca ctgaaatata 2220 aggctaatgg atctctagag agacataaag caagattggt agccaaaggg tacactcaaa 2280 cttatggagt tgattatcag gagacttttg ctccagttgc aaaaatgaat actgtaagaa 2340 tcctgttgtc actggctgcc cactacaatt ggcaactcct acagtatgat gttaagaatg 2400 catttcttca tggtgattta gatgaagaga tttacatgaa catcccacca ggatttgagg 2460 aaaacacagg taacaaggtg tgcaagctga agaaggccct ctatgggcta aaacaatctc 2520 ccagggcttg gtttgggaga tttgcaaaag tcatgaaaga gtctaggtac aaacaaagcc 2580 aaggtgacca cactctcttc attaagcact cggctacagg gggagtaact gctcttctag 2640 gctatgttga cgacatcata gtgactggaa atgatgagag agaaaagcat gaagtgaagt 2700 agagattagc aacagagttt gagataaaag aactagggaa actgaagtac ttcctcagta 2760 ttgaggtgac aaattccaca caagggatct tcatctctca acaaaagtat gtgactgatt 2820 tattggtaga aacagggaag attgggtgta aaccagtctc taccccaatg gatccaaacc 2880 acaagttggg agaagctaaa gaggaaccaa tggtggataa aagaatgtac cagaggctgg 2940 ttggtagact catatacctt gctcacactc ggccagacat cgcctactcg gtgagcgtga 3000 ttagtcaatt catgcatgat ccaagagaac ctcatcttca agctgtttac agggtgctac 3060 attacttgaa aggcaacccc aggaaaggaa ttatgttcaa gaagaacaat actcttgctc 3120 tagaagcata caccgatgct aactatgcag gttccctagt ggatcgaaga tcaactacag 3180 ggtattgtac ttttcttgga ggaaatctgg taacatggag aagtaaaaag cagaatgtgg 3240 tagcaaggtc gtctatagaa tcaaagttta gggccattgc tcaagggttg tgtgaactac 3300 tttggctgaa gattattcta gatgatttga gaatcaagtg ggatggtcct atgaagctgt 3360 attgtgacaa caagtcagct atcaatattg ctcataaccc tatacaacac gataggacaa 3420 aacatattga gattgataga catttcatca aagaaaaatt ggagaaagga gtagtgtgta 3480 tgtcctatgt tccatcagaa catcaattag ctgatattct aacaaaaggg ctgaacagtt 3540 caatgtttaa agatcttgta ttcaagctgg gaatggaaga catctattcc tcagcttaag 3600 ggggagt 3607 // ID Copia6-PTR_LTR repbase; DNA; EDCOT; 141 BP. XX AC LG_I; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia6-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-141 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-141 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 289-289 (2007). XX DR Genome; LG_I; Positions 14950891 14951031. XX SQ Sequence 141 BP; 48 A; 26 C; 19 G; 48 T; 0 other; tgtaaatgct taaataggaa atttacctta ctatatttag cttcctagat ttcctctttg 60 taattactat gtacagcaca acagcactac ttttcctata tataatgaaa gcctagtcga 120 aaggttgagg caattcaaac a 141 // ID Copia19-VV_I repbase; DNA; EDCOT; 4405 BP. XX AC AM447619; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia19-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4405 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4405 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 685-685 (2007). XX DR Genbank; AM447619; Positions 1964 6368. XX CC Positions [1887-2051] - Integrase core CC 'GACTA' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 2290..4089 FT /product="Copia19-VV_I_1p" FT /translation="MPSLQQLTFSIDYQLQFSIVRLPMNSCLNHHLHFLFL FT KTFGCACYPYLQPYKNHKLEYQSTQCTFIGYSLSHKGYLCLHPSGKVYISR FT SVIFDEKTFPYSSLPMNDSSPTPHTSSTSFSIPLLQTMSQTSSPPSMCPTA FT SRPVSPFILSPPISVPSLHPMTTRSKVGTIKPKLLPDHITYLSTSVSPSDQ FT LPTTVSQALKNPNWHTTMVEEYQALVRNNTWTLVPFHPSMNVIDSKWIFRV FT KYNSDGTIQRYKARLVAKGFQQYAGVEFTDTFSPVIKASTIRVVFTLAITY FT NWEIRQIDFNNAFLNGEITETVYLSQPAGFVSTSHPQHVCKLQKALYGLKQ FT APRVWFHKLREALHTWGFISSTSDTSLFIYKHNGNFLLLLVYVDDLLITGN FT NVPLVQTLIQDLQNRFALKDLGLVKDFLGFEALRTTTGLHLTQSKYTTDLL FT IKTKMHSAKPVPTPMSAALKLHAASGPAFSDPTLYRSTIGALQYLTYTRPD FT IAFAVNKLSQYLQQPTELHWTACKRVLRYLKGIVHRGLHFTPASSLHLQVY FT TDADWASSIDDRRSTTGYCVFLGTNLFTWSSRKQPVVARSSTKAEYRALAH FT AS" XX SQ Sequence 4405 BP; 1263 A; 1051 C; 754 G; 1328 T; 9 other; tagtattaga gctccattga cacacgtcca aaatggttac tgatcacatc gattcctttg 60 caccagagat gtcctcacga ggactccaat ctccggcaag aaactcgtcg gaagtttcct 120 caattcttac gggacaaatt tcttctacgc ttcatccgat ctcggtgaag ctagacagga 180 acaattacac aatatggcga tctcaggtat taccatcagc tagagcacat cgactggatc 240 aaattctcat tggtaagcta ccaaaacctc caagattctc tcaatcaaca tcagttaatt 300 catctcaacc tacatcyaat ccagaatatg atcagtgggt gattttagat maattcttgt 360 tgagttggat tcttgcttcc atatctgaag ccatgtatgg tcatgtggtt aattgtcaaa 420 catcagccga agtatggagt gttcttgaaa aactttttgt ctcggattac aaaagcaaga 480 actcttcaac tacggttcat gctacaatca ttaaagaaag gtgctctaag cataaatgat 540 tatgtgctga aaatgagaaa catagcagat atgactctct gcctctggaa aacctgtacc 600 agatgaagat ttaattcttt acatcttagg tggattagga ccagaatttg aaacaattgt 660 tgtgaatatt acgtctagat ctgaggcaat atctctacaa gaggtccatt atctgctgca 720 aagtcatgaa attcgtcttg agcaactttc agcagcatct gttattgatg ttccaccagc 780 agcacatatt acagttggag gtgttcaaaa ctctaacact aataatggac agttcagagg 840 ctcaagcagc aagaattttc gtcctagaaa tgtacgtaat ccacaaactt caagaattgt 900 ttgtcaattg tgtggaaaaa tgggacatac tgctatgaag tgcttccacc gttttgatgt 960 gtacttccaa tctccaccac gtgcacaaaa tcaacagttt tcatctcttc atcaaccaca 1020 acaacctcaa cttcggccac ctccactgca tcagcctcaa tattattcca cagggccact 1080 ggtaccatca cgtccaattc agaattcaca ccaacaactt gattcaacaa gcacttctcc 1140 tcatgcctat attgttgctc cagatcttga ttcaaacact tcatggtttg ttgacagtgg 1200 tgctactcac cacatgacca ctgattccaa tactcttaat gtctctgatc actactgtgg 1260 cayaggtaat gttgtggtag gcaatggaca aacactagat atatctatct agtgttggtc 1320 atacttcttt tccttcacat aaatcttcca agtcattgca tcttgccaat gtacttcatg 1380 tacctcagat cactaaaaat cttatcagtg tagctaaatt cactcaagat aatgatgtta 1440 ttcttgagtt tgactctcat tgctgttttg ttaaggacaa gaagtccaga gagatattac 1500 tccaaggcaa ccttaaggaa ggcctatatc agctggatat ctccaaggtc tcatctaacc 1560 gacagtttgc aggtttcttt gaagatacaa atgtgtttct acctcatcta gctactactc 1620 cgtctactgt caacaaacaa tcagctgctg catctgttgg atatagcctg caagtaaata 1680 aaattgagtc tacaaggtgt gtagaagaca acaacacggg tgttggacac ttgtggcatc 1740 aaagattggg tcatccatgc aacaaaattg tgtctctagt acttgacaga ttgggcatta 1800 aatccaagct ccaaaatgaa ctcarttttt gtactgcttg tcctttaggc aaggcaaaac 1860 agtttccact ccctaccact attaataaaa cacaagttcc atttgaacta gttttttcgg 1920 atgtgtgggg acctgcacat acaacttcat gtgatgggta caaatattac attgcatttg 1980 tagatgcttt tacaaactat acttggattt atcccatgca acaaaagtcc caagcaacat 2040 caattgtctt atagttcata gcattggtag atcgacaatt tcccaccaaa cttaagtgtc 2100 tacaaacaga ctgggatgga gagtttcatc cccttcaatc tcttctgcag aagaaaggca 2160 tcctcttccg tcatccttgt cctcatgttc atcaacaaaa tgggaaggtg gagcgaaagc 2220 rtagaagcat tgtagaaatt ggattgactt tgttggctaa gtctcaattg ccacttactt 2280 tctggtggca tgccttctct acagcaactt accttctcaa tagactacca actccagttc 2340 tccattgtaa gactccctat gaactcttgt ttaaatcatc acctgcattt tttattcttg 2400 aagacctttg gttgtgcttg ctatccgtat ctccaacctt acaaaaacca taaactagaa 2460 tatcagtcaa ctcaatgcac atttattgga tatagtctct cccataaagg atacctatgt 2520 ttgcatcctt ccgggaaagt ttacatttca agaagtgtta tttttgatga aaaaacattt 2580 ccctactcat ctctaccaat gaatgattcc agccctactc cacacacttc ctccacatct 2640 ttctctatac cccttttaca aaccatgtca cagacctctt ctcctccttc catgtgtcca 2700 actgcatcaa gaccagtgtc cccttttata ctctcacctc ctatttcagt tccttccctt 2760 catcccatga ctactcgttc aaaggtgggt acaatcaaac ccaaactact cccagaccac 2820 atcacatacc tgtctacttc cgtttcaccc tcagaccaac ttcctaccac tgttagtcaa 2880 gcgttgaaaa atcccaactg gcacacaact atggttgaag aatatcaagc cttagtccga 2940 aacaatactt ggaccttggt tccctttcat ccatccatga atgtgataga tagcaaatgg 3000 atttttcgtg tcaaatataa ttctgatggt accatccaac gctacaaggc cagactagta 3060 gccaaaggat ttcaacaata tgcaggtgtg gaatttactg atactttcag tccagtgatc 3120 aaagcctcta ctattcgagt tgtatttaca ttggctataa catataattg ggaaattcga 3180 caaattgatt tcaacaatgc attcctcaat ggagagatta cagagactgt ttatctttcc 3240 caaccagctg gatttgttag cacatctcat ccccaacatg tttgtaagct acagaaagca 3300 ctatatggcc ttaaacaggc accacgtgtc tggttccaca agctcaggga agctcttcat 3360 acctggggct tcatctcctc cacgtcagat acgtccctgt tcatctacaa gcacaatggc 3420 aattttcttt tgttgctggt ctatgttgat gatctactaa ttacaggcaa caatgttcca 3480 cttgttcaaa ctcttattca ggatcttcag aacaggtttg cactaaaaga cctgggtctt 3540 gtgaaagact ttcttggatt tgaagctctt cgcacaacaa ctggtcttca tcttacacag 3600 tcaaaataca cgactgatct cctcattaag accaaaatgc attcagctaa accagttcct 3660 actcccatga gtgcagccct caaacttcat gcagcctcgg gtcctgcatt ttctgatccc 3720 acactttata gaagcaccat tggtgctctc caatatttaa cttacacaag accggacata 3780 gcgtttgctg taaacaaact cagtcaatac ttgcagcaac ctactgagct ccattggaca 3840 gcatgtaaaa gagtattacg atatctcaag ggcatagttc atcgtggact gcacttcact 3900 ccagcttcat ctttgcatct tcaagtatac accgacgcag attgggcaag ttcaattgat 3960 gatcgtcgct ctacaactgg ctactgtgtg tttcttggca ccaatctttt cacatggagc 4020 tcccgtaaac agcctgtggt tgcaagatcc tcaaccaaag cagagtatcg cgccctcgct 4080 catgcatcaa ytgaagtagc atggctacgt tctctttttt cagaacttgg aatttctctt 4140 gtcaacacac ctgtcatatg gtgtgacaat caaggtgctg gtgccttagc tgctaatccg 4200 gtatttcatt cccgaacgaa gcatattgaa gtagatgtcc rttatgttcg tgagcaggtg 4260 ctagataaaa aactagtggt atcttatgtt ccttctgtag aacaartggc tgacttattc 4320 actaagccct tgtctattcc taggtttcaa tatctgctta ccaagctcaa ccttgytgtt 4380 tctctaggtt gtgcttgagg ggggg 4405 // ID DNA3-9_Mad repbase; DNA; EDCOT; 2569 BP. XX AC . XX DT 21-OCT-2010 (Rel. 15.1, Created) DT 21-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous Harbinger family DNA transposon from apple. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW DNA3-9_Mad. XX NM DNA3-9_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2569 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1473-1473 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Termini are similar to those of DNA3-4_Mad. XX SQ Sequence 2569 BP; 887 A; 486 C; 526 G; 670 T; 0 other; gggtgcgttt gttgcaccgg actgtctcgg actggactag cttcagggac taagctggac 60 tggcttagac tagactaagc tggactaact tagtgaagcg tttggtgcag tgtcggacta 120 aaaagcagga taatgaaaac agtactgtca tcaatttggt gtttgctcag actaggacta 180 cattattgtt ctattttaat ttctttttta ttaaagatat tattaaaatt aataatattg 240 gatgagagtg agactcaata aaaatacaaa aacgaaaata catgattaaa gagtagcatt 300 attccaaaca tcaatataac aaagtgttct cccaacaatc gacagggttc aggatgcttt 360 tcttaattat tcacctttgg tttaaagttg tagattaaag ttaaaggtgt tggtaaatac 420 ttgtatttga gtagaacgaa aattgatgtc taacaagttc aattttttac tcaattgtga 480 aataattact tggaattgct cttgtatgta taagccaatt tcagtccata ccgtgaaaat 540 tgcattcaat cccaagacca caatgatgcg aggcacaatg acaaatggat agctgcgcat 600 tgatcattgc tacatttgga ttcctagcac gtaaattggc ttgctccaac tagtttgaag 660 aaaactagta acaatatgca aaaggaagag atcatgaaca atttatgcat tccatttgta 720 tattaaacta agcaattaaa atgtcttccc tcacaacgga gcaagtcagt tagtcaattc 780 catgtgcact agtgctaatc caatgaaagg aaaaacaaat gagagaggga aaggtcacca 840 atttaatcaa actgttggat gttccaacta gaacaaatga aagatcccaa tactacatta 900 acacagtaca cagcagagca aggtaaactg cataattgta cattctacaa ttttttacaa 960 taactctgga aaataactaa ctgcctcaat catccgagct atatttactc aattcaagaa 1020 ctgcaacaga agcgcagcaa aacaactctt tatccttcaa gaggagacag cttccaactc 1080 aattccattt tagatcaagt atgctaaatt gtggctaggg cgggatgctc acactgtagg 1140 caacaccagg agtccacatg tacaaacgag aacttcctgt gcaaaaaata ggacgagtgc 1200 acgtaggatc ccaaactgtt gcacgaataa gatatttctg caccaagata gcaacgagtt 1260 caagatggcg tatgtgacat gtcccatatc caaagaatgc ttggcatgct atcagaacca 1320 tatcaactac aatagccaaa ctcatagcta agatagcttt ccttgtacaa aaaagaatgt 1380 gaaacagtag tgctgcaatt catcattttt cttttcaaac aaaaatcttc acggtctgag 1440 ttactccaca aaattgatcc caaaatactt gaccattgaa gaccaaacgc caaaacacac 1500 caatttcctc cacatatgga gaccaacatc acaaccccaa acattccatc ttggctacat 1560 tcaaaagaat tttcagattc attcatacaa ggaaaacaaa taaagaccaa aagtttaaca 1620 caataagcag attgatacca tagatttgtg atgtttccac gtgacaaaaa cctgaacaag 1680 tatgattgca caatactcaa ataacttatt caaggacctt caattgacca gtgatatact 1740 gtggtctgag taacttattt aaggacttta attggggtta tccacttcta gaaaggtaag 1800 gcgctggtga tggattatgg tcaaaatcaa accatagcct ctttcaaaag tgacgacaag 1860 gaaactaagt agcaaaaaca aagcaaaaat cacaaatcaa gccaagtaat tgaccataaa 1920 ttaataaatt aatccaaatt aacgtaattt tatcaaaccc attaacacaa acctgattaa 1980 caagctggtg gggctggaga agggggacgg tgttggagct gcgggtcaag gctttgctgc 2040 cctttttaga gttgcatcac gagtttgaaa ttgaacaaaa aaaaatacag gaaatgaaat 2100 aaattaacct acacaactcc tcgacggtat tgaatcgagg acggcgagtg cgagatcttc 2160 ctcggaggtg gatcggagga cggctagagt tggacagaca acggtaagag cgggatcttc 2220 ctcagttcga aattctgggt tcagggtgag gagagaggga gaaagtggtg gtgggctggt 2280 ggtatggtct cgctggagtt ggcgagttgt ggtgtgatgg tggctgtcgg tgctcaagag 2340 aacagagagc aagagagata agagcacgat gaggacggag tagacgaggt cttagcaatc 2400 ccatgggtat cggggggtct ggccaagaac tcctagcgaa ggagtttgtc cgtgcgagtc 2460 cctcttagtc tcattaaaga taatcctagt acaaaacaaa cactggattg gactaattgt 2520 tagtccagtc tagtccagta ccacttagtg agggcaaaca aacgccccc 2569 // ID Gypsy-17_Mad-I repbase; DNA; EDCOT; 4863 BP. XX AC ACYM01052055; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-17_Mad-I; KW Gypsy-17_Mad-LTR; Gypsy-17_Mad_. XX NM Gypsy-17_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4863 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1339-1339 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01052055; Positions 1785 6647. XX CC Positions [2205-2630] - Reverse transcriptase CC Positions [3762-4250] - Integrase core CC 'GGAGG' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1533..3449,3453..4613) FT /product="Gypsy-17_Mad-I_2p" FT /translation="MRLQGSILNTPVQVFIDSGADQSFLNPQVAARLGLHT FT DSSRCEPVMVAISRYFRTKSVAPQVSVLIQGYAFCGDFHLLAVADYDMVLG FT IDWLETLGLIGWNFLLKVMEFTINGTNYRLVGSSTPPPSLCATLAALDARF FT GVPPQIVAQLSSVPPGSLPSSPLPVILQALFLRYSNLFEPPTTLPPYRAFD FT HQIPLLPGTGPVNVRPYRYGHAQKAELERQVADMLSTGIIQPSFSPFSSPA FT LLVAKAEGDWRFCVDYRVLNSVTIKDCFLIPVIDELLAELHGAAIFSKLDL FT RSGYHQIRMHQADIPKTAFHTHEGHYKFTVMPFGLTNAPATFQALMNSILK FT PLLRKSVIVFFDDILVFSDTLAHHVAHLATVFELLHTHQLKLKPSKCLFGQ FT RSIAYLGHVISLEGVSVDSSKISAIMEWPSPANIRDLRGFLGFAGYYCKFV FT RNFGLLAKPLTDLLRKYSFQWSLAADQVFGALKVAMMSTSVLALPDFTKSF FT TIECDASDSGIGAVLSQENHPIEFLSKPLALKHHALSVYDKEMLAVVFAVQ FT KWRPYLLGQHFKILTDHQTLKYFLDQRITTPAQQKWLLKLLGYNYTLEYKP FT GSSNAVADALSRRPEVLALMGLSRPLFDCIMDIQADYASDPASSILKDLQV FT NPTSHALFKLQGDLLYYKQGVFMAASSPWRSRLLAEFHSSPSAGHSGFLRT FT YKRLTRNFHWPRLKKDVKKFVASCDTCQRINYETIKPPGLLQPLAIPKQIW FT TNIAMDFVEGLPSVHDRNAILVVVDRLSKYGHFIPIKHPYSAPKIAEVFIK FT EIFRLYGMLASIVSDRDPIFISEFWTAFFKQQHTNLCKSSAYHPQSDGQTE FT VLNRTLKHFLRSFVSDKPRDWIQWLPWAEWWYNTTFQSAINMTPFQAVYGY FT PPPTVSSYLPGSSPVHSVYIALGDRDALLKQLREHLQLAQHRMRQYADKQR FT SEHTFTVGDWVFLKLQPYRQTSVSKTHCLILAPRYYGPFKVIAWVGQVAYT FT LDFPPQSRIHPTFHVSLLKP" XX SQ Sequence 4863 BP; 1093 A; 1397 C; 1030 G; 1342 T; 1 other; tttggtatcc agagcccagg cggcttccat gggcaagagc aaggcgtcgg tcacggtggc 60 taacgtttcc gactcggaac tcgacataga gtttcagcaa caacaaatca tctcgcaact 120 ccatgagttc catgagatag tcacgctgat gaatgtccgc caagatgatc tgcagcacca 180 tctcactgat ctgcagcaca cgcttcccga gatgacggtc gaccgagccc ggcaagagaa 240 atttcaacag acagtcctta aggaacttcg tactctcaaa accccaccct cttcccaaaa 300 caggtttcag attcccatcg ggtccattcc catttcccta ggctcctctc cttttgcggc 360 cgtccccacc cctcttcccc aaccaacctg gggttctcca cactcccaaa ccctccatcc 420 aaaccacctc gcgcggtccc acttagccgc gggtccttcc ttcttacctc acacttcttc 480 aactctcctt agtcattccc ccaactctcg tctcataccc ccacactccg gcgactcaat 540 cttgcatccg ttagactttg cccactttcc ccccattcac tacccccatc ccacaccaca 600 ccacaccagg gcccccattt caccacatcc ttacccaacc tttccccctc aatggcggga 660 ccaaaacagt taaagattga gctcccttgc ttctttggtg aagacccgta tggatggtta 720 tccatggctg aagaatttct ggattaccat gaaattgagg attgtcgccg cgtcacagtc 780 gggagattgc atctgggggg tgacgtcgcc cattggcaac gatggttcaa gcaacgattt 840 cctcttgcct cttgggctac attcaccacg caactgctgc aacgctttgg accggctgac 900 gctttgaatt tccacatggc tctctcccac atcactcaaa cggagttggt cgagacctat 960 gtcggccagt ttatccggct ttcatgttgt actccaaatt ggtctgatga gcagctctta 1020 ggggcgtttt tgggtggact caaagaggac ttgcaggatg acgtggtagc ccaacggcct 1080 acgtcccttg cccgggctat tgaactcgct cgtatttatg aacataaaaa tgggcgccgt 1140 tcgtcgactc gcagtgggtt ttcccatcca tctcccaatc tctctaaacc tcacccactg 1200 acaccagcac ctctaacagt tttccctcat cctccacgyc ccactctacc tgcccctacc 1260 caaccacctt ctaaaccagt tcttcgactc acccaagcgg agatgtggac acgcagggaa 1320 caagggctct attttaattg tgatgaccag tttcggccgg gccatcgttg tcgacaatcc 1380 catattctac tcctccttgc gaaggatgat tttactgacc cattccaaga ggtgcaccaa 1440 tcccaccgct agagccggtt ttggtggagc agcctgacca ccctattgca ctccatgcca 1500 tttcggccac gaagcgctct cgcgggcggg cgatgcgttt gcaagggtct attctcaaca 1560 ccccggttca ggtgtttatt gattccgggg cggatcaaag ttttcttaac cctcaagtag 1620 ctgccagatt gggccttcac acagattctt cccgttgtga accggtcatg gtagcaatca 1680 gtcgttactt tcgtacgaag agtgtcgctc cccaagtctc agtactgatt caaggctatg 1740 cattctgcgg ggactttcac ctcctcgccg tcgccgacta cgacatggtt ttggggattg 1800 attggttaga aaccttgggc cttattggtt ggaacttcct cctcaaggtc atggaattca 1860 cgataaatgg aacaaactat cgtctcgtgg gatcttccac acctcctcca agtttatgcg 1920 ccactttggc ggcattagac gcccgttttg gcgttccccc tcagattgtg gctcaactat 1980 ccagtgttcc tcctggttcc ctgccttctt ctccactacc ggtaatactc caagcactgt 2040 ttttacgata ctcgaaccta tttgagccac ccaccacctt gccaccctat agggcatttg 2100 accatcaaat ccctctcctt ccaggcaccg gacctgtgaa tgtgcgccct taccgctatg 2160 gtcatgccca gaaagcggaa cttgaacggc aggtggctga catgttatcc accggtatca 2220 ttcaaccgag ttttagccct ttctcttcac ctgcactgtt ggtagctaag gctgagggcg 2280 attggcgttt ttgtgtcgac tacagagtct tgaattcggt caccatcaaa gattgcttcc 2340 ttattccggt tattgatgaa ttattagccg aacttcacgg cgctgccatc ttttccaaac 2400 tggacttgcg ttcgggatat caccaaatac ggatgcacca ggccgatata cctaaaacag 2460 ctttccatac ccatgaaggt cactacaagt tcacggtcat gccttttggc cttaccaacg 2520 ccccagccac atttcaggca ttgatgaatt caattttgaa gcccttgttg cggaaatcgg 2580 tcatcgtctt ttttgacgat atattggtct tcagtgacac gctggcacac catgttgctc 2640 acttggctac tgtctttgag cttctccaca cccaccaact gaaattgaag ccttcaaaat 2700 gtctttttgg ccaacgttct attgcttatt tagggcatgt tatttcttta gagggtgtat 2760 cagtggattc ctccaaaatt tctgccatta tggagtggcc gtctcctgcc aacattagag 2820 accttcgagg gtttttgggt ttcgccggtt actattgtaa attcgttcgg aactttgggt 2880 tgctagcaaa gccactcact gacttgctcc gtaaatatag tttccagtgg tctcttgcgg 2940 cggatcaggt ttttggggct ctcaaagtag ccatgatgtc tacgtcggtt ctcgctcttc 3000 cggatttcac caaatccttt accattgagt gtgatgcttc ggatagcgga attggagcgg 3060 tcttatcgca ggagaaccac cctattgagt ttcttagtaa gccattggct ctgaaacatc 3120 atgctctttc ggtatatgac aaagaaatgt tggcagtggt ctttgcagta caaaaatgga 3180 ggccttattt gcttggccag cacttcaaaa tacttacaga ccaccaaact ctgaagtatt 3240 ttctggatca acgcattaca actcccgctc agcaaaaatg gttgttgaaa ttacttggct 3300 acaattatac cctggagtat aagcctggat cctcgaatgc agtcgcggat gccctttctc 3360 gtcggccgga ggtcctggcc ttaatgggtt tgtctcggcc cctgtttgac tgtatcatgg 3420 acatacaagc tgactatgct tcggacccgt aggcttcctc cattctgaag gatttgcaag 3480 tcaatcccac aagccatgcc ttgtttaaac tacaagggga tcttctttat tataaacaag 3540 gtgtgtttat ggcagcctca tccccttggc gttctcgcct cctggcggaa tttcactctt 3600 ctccttcagc gggtcattcg ggcttcctcc gcacatataa aagactgaca cgcaacttcc 3660 actggccaag gcttaaaaag gacgtgaaaa agtttgttgc ttcatgtgac acttgccagc 3720 gtatcaatta tgagaccatc aagcctccgg ggctgttgca acctctagct attcccaaac 3780 agatttggac gaacattgcg atggattttg tcgaaggcct tccttcggtc catgacagga 3840 atgcaatctt ggtggtagtg gataggttgt caaaatacgg ccattttatc cccatcaaac 3900 atccctattc cgctcctaaa attgcagagg tgttcattaa ggaaatcttc cgtctctatg 3960 gaatgctggc ttctatagtc agcgatcggg atccgatctt catcagcgaa ttttggactg 4020 ccttctttaa gcagcagcat accaaccttt gcaaaagctc tgcctatcac cctcaatccg 4080 atgggcaaac ggaggtgctc aatcgcaccc ttaaacactt cttgcgcagc tttgtgagcg 4140 acaaaccaag ggactggatt cagtggcttc cgtgggcaga gtggtggtat aataccacct 4200 tccaatctgc catcaacatg actccattcc aggctgtgta tggatatcct ccacctaccg 4260 tgtcttctta cctccctggt tcctctccgg tgcacagcgt ctacatagca ctcggtgatc 4320 gcgatgcact gctcaaacag ttgcgggagc atttgcaact tgcacaacat cgcatgcgcc 4380 aatacgccga taaacaacgc tctgagcaca ccttcactgt gggtgattgg gttttcctga 4440 aacttcaacc ttatcgccaa acttcagtgt ccaagactca ttgcctcata ttggctcccc 4500 gttactatgg ccccttcaaa gtgattgcat gggttggtca ggttgcctac acattagact 4560 ttccacctca gtctcgcatt caccctacct ttcatgtttc tttgttgaaa ccatagcttg 4620 ggaaccatat ggtagcttct ccaactctgc caccattctc tactacaggt accttcctgt 4680 ggacccctga gaaaattctt caacgcgggc tattcaagct agggaaccgt ggagtcactc 4740 gttggttaat ccagtggaaa ggacttccag agcatgacgc cacttaggag gatgctgatt 4800 ccatcctcac ccgttttcca tcctttacag cctgaggaca tgctgtttca gggaagggtg 4860 cca 4863 // ID hAT-7_VV repbase; DNA; EDCOT; 4003 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE hAT-7_VV, an autonomous DNA transposon - a consensus sequence. XX KW hAT; DNA transposon; Transposable Element; TIR; Hatvine-7; KW hAT-7_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4003 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 776-776 (2008). XX DR [1] (Consensus) XX CC hAT-7_VV (Hatvine-7 in [1]) consensus is an autonomous element. CC Its individual copies are >90% identical to the consensus CC sequence. hAT-7_VV contains 17 bp-long TIRs which are flanked by CC 8 bp-long TSDs. XX FH Key Location/Qualifiers FT CDS join(1090..2922,3028..3358,3448..3605) FT /product="hAT-7_VV_Transposase" FT /note="hAT transposase; pfam05699:hAT family FT dimerisation domain." FT /translation="MSSSDSKNSRKDFVWKYVIEVSGEQYLRCKFCNQRCT FT GGVNRLKHHLAGTHHGMKPCNKVSEDARLECKEALANFKDQKTKRNELLQE FT IGMGPTSMHESALSKTIGTLGSGSGSGSGRSGSGEPIPRGPMDKFTTSQPR FT QSTLNSKWKQEERKEVCRKIGRFMYSKGLPFNTVNDPYWFPMIDAVANFGP FT GFKPPSMHELRTWILKEEVNDLSIIMEDHKKAWKQYGCSIMSDGWTDGKSR FT CLINFLVNSPAGTWFMKSIDASDTIKNGELMFKYLDEVVEEIGEENVVQVI FT TDNASNYVNAGMRLMEKRSRLWWTPCAAHCIDLMLEDIGKLNVHATTLSRA FT RQVVKFIYGHTWVLSLMRTFTKNHELIRPAITRFATAFLTLQSLYKQKQAL FT IAMFSSEKWCSSTWAKKVEGVKTRSTVLFDPNFWPHVAFCIKTTVPLVSVL FT REVDSEERPAMGYIYELMDSAKEKIAFNCRGMERKYGPIWRKIDARWTPQL FT HRPLHAAGYYLNPQLRYGDKFSNVDEVRKGLFECMDRMLDYQERLKADIQL FT DSYDQAMGEFGSRIAIDSRTLRSPTSWWMRFGGSTPELQKFAIRVLSLTCS FT ASGCERNWSTFESIHTKKKRNRLEHQRLNALVYVRYNTRLRERSLQRKQNV FT DPILVEEIDSDDEWIAEKEDPLLPLDLCWLQDNELFNVDAIRVVSSNSQET FT QASSDHMVSSHSYKRKHNEVPSTSGGKGKEKELNLTPIDEDEDLDEMGIHD FT SGHFPTIDTLDEDDDDLGEEDLS" XX SQ Sequence 4003 BP; 1222 A; 631 C; 809 G; 1334 T; 7 other; caatgttttt aaaggcgttt gtgggggcgc cttgaggcga ggcgcagcga aaacgcgttg 60 aggcgttaaa aataaaacga aacacctgaa aggcgtacgc cttttccggt gaggcgtgat 120 tgaggcgcgc tttgatcgcg cctttcacgc tccaagaaga aggcgtacgc ttcgtcggat 180 ctgatgtggc aatgaacaga gatttaaaaa aaaaaaccct aagtaaatcc ctaaaacccc 240 agtccccgac tgaaagcaaa cagaaattgg gagacaaact ccaaaacgaa accctacctc 300 ttccgactca agcggagacg gagtgctcac ccttcggcgg cgaccaatcg cagcgcatct 360 tctccggcgg cgaccaatcg cagagcatct tctccggcgg caatccctct cgttcatctc 420 caggtatgtt gcgaactccc thtcttcgtc ttccatggtt tctccctctt cgtttcatct 480 ctctcatctt tctctccgca dtccacaccg gcgcgtcggc tcttcatcca attttttdtt 540 tttttttttt atcaaatcag atgtgctgta tatctattta agttttaaac ccttttttct 600 ctctctcaca gcatttaaat tctctcacag gctcacagcc cacacttccg gtccacactt 660 ttctctctct cccagtaggt ttttcatctt tttttttttt tttttttttt ttaaattatc 720 aaatcagatg tgccttttgt ttaataagat ttttttttga agttttttta tatdtttdct 780 tatagtatca ataaacaaat ataattaaaa ttattataaa agataattat ttgtgaattt 840 tgaatttttt atttctggtt taattttaat tttcacctca attttcttta tttcattatt 900 aaattccaat taaaatttat gtgtataatt tttaaahtcc tttaaaaaaa attggttttt 960 ttaaatttaa accaattaaa ttttgtattt catttttaaa ttcctttcaa ttatgctttg 1020 ttattatttt ttagtcaatt atattgttat atggaaattt gaatattatt attggtgatt 1080 ttttttagaa tgagttcctc cgattcgaaa aattcaagaa aagattttgt gtggaagtat 1140 gtgattgaag tttctggrga gcaatattta agatgtaaat tttgcaatca aagatgtacg 1200 ggaggggtga atagactaaa gcatcactta gccggaactc atcatggtat gaaaccatgc 1260 aacaaagtta gtgaagatgc tagattggaa tgcaaagagg cattggccaa ttttaaggat 1320 caaaaaacga agagaaatga attgctccaa gaaattggta tgggtccaac ttcaatgcat 1380 gagagtgcct tgtctaaaac aatagggaca ttagggagtg ggagtgggag tgggagtggg 1440 agaagtggga gtggggaacc tattcctagg ggacccatgg ataaatttac cacttcacaa 1500 cctagacaaa gtactttgaa ttcaaagtgg aagcaagaag aaaggaagga agtgtgtaga 1560 aaaattggta ggtttatgta ttcaaaaggt ctcccattca acactgtgaa tgatccttat 1620 tggtttccta tgatagatgc tgttgcaaac tttgggcccg ggtttaagcc tccatctatg 1680 cacgaattga ggacatggat tcttaaagaa gaggtgaatg acctaagtat cattatggaa 1740 gatcacaaaa aagcttggaa acaatatgga tgttcaatta tgtcagatgg ttggacagat 1800 ggaaaaagta ggtgtcttat caattttttg gtgaatagtc ctgctggcac ttggtttatg 1860 aaatcaattg atgcttctga tacaataaaa aatggggaat tgatgttcaa atatcttgat 1920 gaggtggttg aagaaattgg agaggagaat gttgtgcaag tcatcactga taatgcctct 1980 aattatgtga atgctggaat gaggcttatg gaaaaaagga gtagattgtg gtggactcct 2040 tgtgctgctc attgcattga tttgatgttg gaggatattg gaaagctaaa tgttcatgct 2100 actacacttt ctcgagctag gcaagttgtg aagtttatat atgggcatac ttgggttctt 2160 agcttgatga gaacatttac aaaaaatcat gaacttattc gtccagcaat tacacggttt 2220 gctactgcat ttcttactct ccaaagtctt tataagcaaa agcaagctct tatagcaatg 2280 ttctcctcag aaaaatggtg ttcaagcaca tgggctaaaa aggtagaagg tgtgaaaact 2340 cgaagtacag tgttgtttga tccaaatttt tggcctcatg ttgctttttg cataaagacc 2400 actgttccat tagttagtgt cttgagagag gttgattcag aggaaagacc agccatgggt 2460 tatatttatg agttgatgga ttcagctaag gagaagattg catttaattg tcggggcatg 2520 gagagaaaat atggcccaat ttggagaaaa attgatgcaa gatggactcc gcaacttcat 2580 cgacctttac atgcagcagg ctattatctt aatcctcaat tgcggtatgg agataagttc 2640 tctaatgttg atgaggtgag gaagggatta tttgaatgca tggataggat gttggattat 2700 caagaacgtt taaaagctga cattcagttg gactcatatg accaagcaat gggtgaattt 2760 gggagtcgta ttgcaattga ttctcgaaca ttaagaagtc ctacaagttg gtggatgcgt 2820 tttgggggtt caacaccgga gttgcaaaag tttgctattc gagtccttag ccttacttgt 2880 agtgcttcgg gatgtgaaag aaattggagc acatttgaat cggtaatact tctatttttg 2940 taaattttta tacatatatt tctatttcaa tgttagagaa ctttatttca ttttaacaca 3000 taaaattgtt tcttttatta tttgtagatc catacaaaaa aaaaaagaaa tagacttgaa 3060 catcaaaggt tgaatgctct agtgtatgta aggtacaaca ctagattgag agagcgaagt 3120 ctacaaagga aacaaaatgt tgatccaatc ttggtagagg agattgattc cgatgatgaa 3180 tggattgcgg agaaagaaga tcccctcctc ccccttgatc tttgttggct tcaagataat 3240 gaattattca atgttgatgc cattagagtt gtgtcatcca actcccaaga gacgcaagca 3300 tcatcggatc atatggtttc ttcacattcc tacaaaagga aacataatga agtaccaagt 3360 aagtactcaa aaattgaaat cataaatttg attaaattta ataaaaaaaa cttttaatat 3420 ttacacataa ttaatacttt atgctaggta caagtggagg caaaggcaaa gagaaggaat 3480 tgaatttgac accaattgat gaagatgaag atttagatga aatggggata catgatagtg 3540 gacattttcc tactattgat acattggatg aggatgatga tgaccttgga gaggaggatt 3600 taagttgaaa caatttactc tagttgttat ttcatgactt agttatggat tttttgtaaa 3660 agtttagaac tattattatg gttgactcta ttttctattt catgacttag ttatggcttt 3720 ttgttaaagt ttgaaactat tagtatagtt gaatctataa tctattttat gaatttgtta 3780 tggtttttgt gaaagtaggg aactagtatg tctttttttt tatgattcta atgaattgtt 3840 ttcatgtttt tatttatgct attttatttt atatatttta aaatattaat taattatata 3900 atgtgaggct caaaaagctt acgcctcaac gcctcggagg cttacgcctc gcctcacgaa 3960 cacaaaaacg cctcacctta cgctttcgcc tttaaaaact ttg 4003 // ID Copia-4_CP-I repbase; DNA; EDCOT; 3938 BP. XX AC ABIM01012539; XX DT 10-MAR-2010 (Rel. 15.04, Created) DT 10-MAR-2010 (Rel. 15.04, Last updated, Version -1) XX DE LTR retrotransposon from papaya: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-4_CP_; KW Copia-4_CP-LTR; Copia-4_CP-I. XX OS Carica papaya OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Caricaceae; Carica. XX RN [1] RP 1-3938 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from papaya."; RL Repbase Reports 10(4), 579-579 (2010). XX DR Genome; ABIM01012539; Positions 6728 2791. XX CC Positions [1502-2032] - Integrase core CC 'CATAC' target site duplication CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1487..2461,2465..3415) FT /product="Copia-4_CP-I_1p" FT /translation="MGKLARNYFPSQADWRAKDKLALIHSDICGPMTENSM FT SGCRYFGLFIDDFSRMIWVCFLQNKSQIFGEFKKFKAIVEKKSGSVLKCLK FT TDHGLEFNSSQFNDFCYENGIKRQLTAPYSPQQNGVSERKNRTIVEMARSM FT LADKHLPKALWAEAVNAAVFLLNMLPTKAVNQMTPAEAWSGIKPSTKYLKV FT FGFVCYYHISDDRRSKLEMKAELGVFLGYSTEAKAYKVLNLKTNKLMIRRN FT VTVDENSYWNWEKLKVERDCVTVQEGKKSMTVSNPTQSDEQDEEDEEGEAK FT GKIKLKSLADIYERCSFASKEPSSVEEALQQQERLAMEEEIRMIDKNNTWS FT LVKLSTNKKLIGVKWVFKVKLNPDATTNKHKVRLVAKGYSQLPGINYTETF FT ALVAKYETIILILAMAAQFGWSVMHLDVKSAFLNGKLNEEIYVEQPPGFIQ FT LGKESHIYLHHKALYGLKQAPRAWYDKLNTYLLHCGFERSMTENTLYVNKD FT EDRLITAVYVDDILVIRSNKRKMEKEFEMSDLGEATYFLGMEIQQSNLGIF FT LSQGKYAKEILNKFNMNHCKSVSTPLVSNLKLSKDEKGSKVEEGNYKSLIG FT SLLYLTAIRPDILFAVSLLSRYMASSRESHLQAAKHVLRYLKGI" XX SQ Sequence 3938 BP; 1329 A; 729 C; 917 G; 963 T; 0 other; agtggtatca gagctgttat cttaagggac ctgtaaatta atatatcctc aaaaatccaa 60 tgacatccac tggaacaaca cccccctcca cacttcaatg gagaaaacta ccatgtatgg 120 gcaatcaaaa tgagagctca tctgaaagcc ttaagtctgt gggatgttat actggatgac 180 agtaatcctc ttccaccagg ggacactacc actataaact aaattagaag gcacgaggaa 240 gataaagcca agaaaccaaa ggcaattgct tgccttttct cagccgtttc ggatagggta 300 ttttcaagga ttatgaactt cgaatcacca aaggctgctt gggaaaaact taaggaagag 360 ttcgatggga gagtcagaaa caggaaggta aaaatcctga gactgaagag tgagtttgca 420 ttactcagaa tgcaagaaaa tgaatcagtg aaggactatg catccaaatt cttatcagct 480 tgccccccaa attcgagtct aaaatttcag ccttggggag cctgcagaca ttgagaatat 540 ctcctcggct gagctgataa acaagcttca atccagtgag caacaggtaa atatgcatgt 600 tcgacaacat actgagggag ccttaatttc aactcagaac aaaggcagct cttcaacaca 660 gaatcaagga agaaggagtg aatggaatca aactggaaac caaaatccca gtaaacaaaa 720 gaaatattct gagtgcagta tctgttcttt gacaaatcat tctgaaaatg agtgctggta 780 caagggaaag aaaaccgttc ggtgcaattt ttgcaaaagg cttggtcaca aggaaagatt 840 ctgtaaacag aaacagaagc aggaaggatc acgaccaaag caggaacaac tgcaagccaa 900 tatcaccaag gtgtcctgtg agccaagtga cacaattctc gttgcactaa gtaggctgcc 960 agtggaggat gatactctct gggtggtaga cagtggatgc acctcccaca tgtgcaagga 1020 tgatggctta ttcgtatcac ttgacagaat aatcacaggc caggtccgac ttggaaatgg 1080 tatgctggaa accatcaagg gcaaaggcaa cacagccatt gaaaccaagg aaggtaggaa 1140 acttatcact gatataaatt ttgttcctac catctcacag aatcttctca gtgtgaatca 1200 gattactaat tgaggctact cggttggatt caaggataac tactacagga tatatgatcc 1260 taaggatcgt ttgattgctt ctatccaaaa gaagaatcaa gtctactctt tgaaactcag 1320 agaagtagtt gagaaggcca gtgttgcctc tgtaactgaa ggtgagattt ggcacaggcg 1380 ccttgggcat tttcatgcgg ttgggctaca acaactgcag aagggaggtc taaccaatga 1440 cttcctaaat attacagtta ctgagacagt atgtggtgca tgtcagatgg gaaaattggc 1500 aaggaattat tttccttcgc aagcagattg gagagcaaaa gataagctgg cacttattca 1560 ttcggacatt tgtggtccaa tgacagaaaa ctccatgagt ggttgtaggt attttggctt 1620 gttcatagat gatttttcca ggatgatttg ggtttgtttc ctgcagaata aatctcaaat 1680 ttttggtgaa ttcaagaagt tcaaggctat tgtagagaag aaaagtggca gtgtactgaa 1740 gtgcctaaag acagatcatg ggcttgaatt caattccagc caattcaatg atttctgtta 1800 tgagaatgga atcaaaaggc agctcacggc accatactct cctcaacaaa atggtgtctc 1860 ggagaggaag aacagaacca ttgtggaaat ggcaagaagc atgcttgctg acaaacacct 1920 gcctaaagcc ttgtgggctg aggcagtgaa cgctgctgtg ttcctgctca atatgctgcc 1980 tacaaaggct gtaaaccaga tgacaccggc ggaggcctgg agtggcatta aaccatcaac 2040 taagtatcta aaggtgtttg gattcgtgtg ctattaccat atctcggatg acaggagatc 2100 caagctagaa atgaaggctg agttgggagt atttttggga tacagtactg aagcaaaagc 2160 atataaagtt ctaaacctaa aaaccaacaa gcttatgatt cgaagaaatg taacggtgga 2220 tgaaaatagc tactggaatt gggagaagct gaaagtcgaa agagactgtg tcacagttca 2280 agaaggaaag aaatcaatga cggtatcaaa cccaactcag agtgatgaac aagatgaaga 2340 agatgaagaa ggtgaagcaa aagggaaaat aaaattgaaa agtctagctg acatctatga 2400 aaggtgcagc tttgcctcaa aagaaccttc ctctgttgag gaagcacttc agcagcaaga 2460 gtgaagactt gccatggaag aggaaataag gatgattgac aaaaacaata cttggtctct 2520 ggtaaaatta agtacaaata aaaaactaat tggagtaaag tgggtgttca aagtgaaact 2580 caatccggac gcgacaacaa acaagcacaa ggtacggctt gtggcaaagg gatactccca 2640 gcttccagga atcaactaca cagaaacctt tgctcttgtg gccaaatatg aaacaattat 2700 actcattctg gccatggcag ctcagtttgg ttggagtgtg atgcacttgg atgtgaaatc 2760 ggccttcttg aatggtaaac tgaatgaaga aatttatgtt gagcagccac cggggtttat 2820 tcaacttgga aaggagagtc acatctatct tcatcataag gccctatacg gcctcaaaca 2880 ggctccacga gcctggtatg ataagttaaa tacatactta cttcactgtg ggtttgagag 2940 aagcatgaca gaaaacacac tgtatgtgaa taaagatgaa gaccgactta tcactgcagt 3000 atatgttgat gatatattag tgatacgcag caacaaaagg aaaatggaaa aagaatttga 3060 gatgtctgat cttggggaag ctacctactt cctgggaatg gagattcaac aaagcaactt 3120 gggtattttt ctttcacaag gcaagtatgc caaagaaatt ctaaataaat tcaacatgaa 3180 tcactgtaaa tcagtatcta caccactggt gtccaaccta aaattgtcaa aggacgaaaa 3240 aggtagcaaa gttgaagaag ggaactacaa aagtctgatt gggagccttc tgtatctcac 3300 agctatcaga ccagatattt tgtttgcagt gagtttactt tcaaggtaca tggcttcatc 3360 gagggaatca cacttacaag ctgccaaaca tgtgctgagg tacttgaaag gaatctgaaa 3420 ttttggtgct caattcaaag caagagctga gggtggatta gttggctaca gtgacggtga 3480 ctgggcataa agtgtagaag atgcacgtag cacaactggg tacttgttca aactaggctc 3540 cggtgttttt tcatggacat ctaacaaaca ggatactctc gctcagtcta cagctgaggc 3600 tgagtatgta gccgcagcta cagcaactaa ccaagcaatt tggttgagga aggtgttcaa 3660 cgatcttaag ctggacaaac aaacacctac agtgttgtat gtagacaaca agtctgcaat 3720 tgccattgcg aaaaatccag taatgcacga gagaactaaa cacatcaacg ttaagtatca 3780 tgttatacgt gaggctgaaa ggaatcaaga aataaagctg atacattgct ccactgatga 3840 tcagcttgcg gacattctaa ccaagcctct gtctaaagct aaatttgagg atttgcggga 3900 aaaggtgggg attggtaaaa aaagtcatta agggggag 3938 // ID MuDR-N1_Mad repbase; DNA; EDCOT; 544 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW MuDR-N1_Mad. XX NM MuDR-N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-544 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1511-1511 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >89% identical to the consensus. 9-bp TSDs. XX SQ Sequence 544 BP; 187 A; 102 C; 91 G; 164 T; 0 other; gggtaaactg cggtttgacc ccctaaacta ttaccctagt tgaaattgac cccctgaact 60 atttttttgg taaattaacc ccctgaacta tttaaaatca gccaattaac cccttgccgt 120 tagattccgt ccactattcc gtcaaattca agggcaaatt agtcttttta tcatcaattc 180 ttacttgtca gttataacca ccaataaaat aatgacacgt ggacacggaa taattcaaaa 240 acttatagca taataagaaa cataaagaaa ccaaacgttt acataacgga ccatttcaca 300 ttgtcattac acattattat gtgtccacat gtcataattt tattggtggt tataagtgac 360 atgtaagaat tgatgataaa aagactaatt tgcccttgaa tttgacagaa tagtggacgg 420 aatctaacga caaggggtta attggcttat ttcaaatagt tcaggggtta atttaccaaa 480 aaaaagttca gggggtcaat ttcaactgga gtaatagttc agggggtcaa acggcaattt 540 accc 544 // ID DNA9-3D_Mad repbase; DNA; EDCOT; 707 BP. XX AC . XX DT 26-OCT-2010 (Rel. 15.11, Created) DT 26-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE Tansposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-3D_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-707 RA Bao W. and Jurka J.; RT "Transposons from the apple genome."; RL Repbase Reports 10(11), 2028-2028 (2010). XX DR [2] (Consensus) XX SQ Sequence 707 BP; 231 A; 95 C; 59 G; 322 T; 0 other; ggagtaatta ggttttcatc cttattttta ctactctatt gattaaaacc ttattacttt 60 tcaatttttg atcaaggtcc tttgtattaa taatatcatt aattatttca ataataaaat 120 attttttatt tctaaatata ttcatttaat attaaaaatg ttacaattag tatatttata 180 tttatggcta aattttttat catatatttt tatttttagt ttgtacccat ttttaatttg 240 caaccctttt ttaatttgta ccaattttcc tttcagtttt aatttgtacc catatattaa 300 tttctttttg tgcccatatt ttttaaagtt ttatttgtat tgtacccata tttttttatt 360 tatttgtacc catttttatt tttgctaaat gtacccattt tgaagaatgt acccatgttt 420 tgatacaata attttttggt tattttttat gaatgtaccc atgtttacac acacacacac 480 aatagtatat ttatatttta atatttttaa tcccacaaat tatggttttt tatttaaaat 540 ctcattacta taaacaacta taaattttaa tttttaattt aaaaaatata gtaacgtaca 600 tagaaataaa ttatcaatta atttcaggga cttggatcaa aaattgaaaa ccaacaaggt 660 ttcagtcaaa gactattcat aactagggac cgcatccaaa gtctccc 707 // ID NTLTR1 repbase; DNA; EDCOT; 644 BP. XX AC . XX DT 30-NOV-2000 (Rel. 5.1, Created) DT 30-NOV-2000 (Rel. 5.1, Last updated, Version 1) XX DE NTLTR1 is a long terminal repeat from endogenous retrovirus DE NTERV1 - a consensus sequence. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW endogenous retrovirus; Gypsy superfamily; NTERV1; NTERV1I; NTLTR1; KW TMLS; Long terminal repeat. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RP 1-644 RA Jakowitsch J., van der Winden J., Matzke J.A. and Matzke A.M.; RT "NTLTR1."; RL Direct Submission to Repbase Update (NOV-2000). XX RN [2] RA Kapitonov V.V. and Jurka J.; RT "NTLTR1."; RL Direct Submission to Repbase Update (NOV-2000). XX DR [1] (Consensus) XX CC NTLTR1 is a long terminal repeat from the NTERV1 endogenous CC retrovirus [2]. It has been reported originally by [1] as MITE- CC like transposon. Solo copies of NTLTR1 are flanked by 5-bp CC target site duplications [1]. XX SQ Sequence 644 BP; 203 A; 115 C; 128 G; 198 T; 0 other; tgtatacggt taaaatcggg cccacccgat tttactattt gaccgagacc aggaggttgc 60 atcgaaggtc ggccctgtaa tggatcagac caatgcacga ggataaggta ccgagttcag 120 aattcgaggt acctgtcgag atcgaggcca gtagcgatcg agaccaaatg agacagacat 180 cgagcaagat cgaagatagc ataataacag aaaggcgaga tatccgtgac tggtcgagga 240 tcatggcgta aatctcggaa cggatcaaat caggaacggt taattagcta atcatgagat 300 ttccttctgt aattagaatt ataccataag tagaattcct ctactatata aaggggagtt 360 ctaatcattt gtaagaaaca ttgttcacag atataaaagc aatataattc tctttctcgt 420 ttatactatt tgttcatcag cttgttatat tttaattgtt cttgcatcaa ccagttcgag 480 ggtatccaaa ctcgagggct gagttccatt ctaacactgg tttgctttac tttatagtta 540 tttctattat taatcttcat atttatcaat tggtattaag tgaaatcacg tgtccttaaa 600 accacattat aagtttaatt gttatccaat tttaagggta aaca 644 // ID Tvv1_I repbase; DNA; EDCOT; 5033 BP. XX AC . XX DT 31-AUG-2007 (Rel. 12.09, Created) DT 04-NOV-2009 (Rel. 14.12, Last updated, Version 2) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW internal portion; Copia25-VV_I; Tvv1_I. XX NM Copia25-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5033 RA Pelsy F. and Merdinoglu D.; RT "Complete sequence of Tvv1, a family of Ty 1 copia-like RT retrotransposons of Vitis vinifera L., reconstituted by RT chromosome walking."; RL Theor Appl Genet 105(4), 614-621 (2002). XX RN [2] RP 1-5033 RA Obukhanych T. and Jurka J.; RT "Copia25-VV."; RL Repbase Reports 7(9), 782-782 (2007). XX DR [2] (Consensus) XX CC This is an internal portion of the Copia25-VV LTR retrotransposon CC family. Individual elements are on average 95% similar to CC consensus. Long terminal repeat (LTR) sequence of this CC transposon is deposited as Copia25-VV_LTR. Target site CC duplications (TSDs) are 5bp-long. CC This sequence was originally published as Tvv1 (see ref. 2). XX FH Key Location/Qualifiers FT CDS 878..5023 FT /product="Tvv1_I_1p" FT /translation="MEENKNSVADIVPIVSKITEHKLNGSNYIEWSKTIKI FT YLRSVAKDDHLTEEPPNDNTRKLWMQDDARLFLQMKNSINSDIVGLLSHCE FT FVKELMDYLDFLYSGKGNVSRMYDVWNAFHCPEKGAKSLTAYFMDFKKVYE FT ELNALMPFSPDVRVQQAQREQMVVMSFLSGLPSEFETAKSQILSGSDIGSL FT QEVFSRVLRTENVSSSQHTNVLVAKGGNAENARRVNNRGGNRAFENRGNDS FT STIVCFYCHEAGHTKKNCRKLQNRNRRIQTANVATSDTATFSDSSDKIVTM FT TAEEFAKYSQYQDALKASTPVSALAESGKTCLVSSSNKWIIDSGATDHMTG FT NHKTFSTFRTHSAPPVTVADGSTYEIKGSGTVKPTSSITLSSVLNLPNLAF FT NLISVSKLTKNLNCSVSFFPDHCVFQDLMTKRTFGKGHVSDGLYILDEWVP FT RPVACVSTASPVEAHCRLGHPSLPVLKKLCPQFDTLPSLDCESCHFAKHHR FT SSLGPRINKRAESLFELVHSDVWGPCPVTSQTGFRYFVTFVDDFSRMTWIY FT FMKNRSEVFSHFCAFSAEIKTQYDVSVKILRSDNGKEYVSNSFQNYMSHNG FT ILHQTSCVDTPSQNGVAERKNRHLLETARALMFQMKVPKQFWADAVSTACF FT LINRMPTVVLKGDIPYKVIHPQKSLFPLEPRIFGCTCYVRDTRPFVTKLDP FT KALQCVFLGYSRLQKGYRCFSPDLNKYLVSTDVVFSEDTSFFSSPTSSASE FT EEDEEWLVYQVVNSRPTVGQSSVVDSDASLAHLGPVVNIPPAPVKPPIVQV FT YSRRPVTTDTCPAPAPSSSDPSSDLDLPISLRKGKRHCKSIYSIANFVSYD FT HLSSSSSVLVASIDSISVPKTVTEALNHPGWKNAMLEEICALEDNHTWKLV FT DLPQGKKVVGCKWVFAVKVNPDGSVARLKARLVARGYAQTYGVDYSDTFSP FT VAKLNSVRLFISIAASQQWMIHQLDIKNAFLHGDLEEEVYLEQPPGFVAQG FT EYGKVCCLKKALYGLKQSPRAWFGKFSKEIQAFGMNKSEKDHSVFYKKSAA FT GIILLVVYVDDIVITGNDHAGISDLKTFMHSKFHTKDLGELKYFLGIEVSR FT SKKGMFLSQRKYVLDLLKETGKIEAKPCTTPMVPNVQLMPDDGDPFYNPER FT YRRVVGKLNYLTVTRPDIAYAVSVVSQFTSAPTIKHWAALEQILCYLKKAP FT GLGILYSSQGHTRIECFSDADWAGSKFDRRSTTGYCVFFGGNLVAWKSKKQ FT SVVSRSSAESEYRAMAQATCEIIWIHQLLCEVGMKCTMPAKLWCDNQAALH FT IAANPVYHERTKHIEVDCHFIREKIEENLVSTGYVKTGEQLGDIFTKALNG FT TRVEYFCNKLGMINIYAPA" XX SQ Sequence 5033 BP; 1326 A; 1047 C; 1131 G; 1527 T; 2 other; tggtatcaga gccacgtttg gttcaaggga attttctggg ttttgggttt tgttcctaac 60 aatctggaac agtaacctgt tacgtgtcac tgccttctkt ttggtctgga ttgcgtcacc 120 gccgacccag ggaggagcgc attcttgttt ccggagcgtg ggagtgcttg aggccgccgt 180 ttcttcaccc atttgacktt ccgacgtttc ccatctctcg atctgacttt ccgacgtttc 240 tcatccggtg ttcgatcaac tgtcgaggga tcgcaaagat tcatcgacga ctgcggaatc 300 gctgtcgcta gtccggcgaa ccttgcccct cgattcacct tcctgagacg ccttcttctc 360 agatcccgcc accctctcac gccttctctt cgccccgttc tccgtcaacg cggtcttcac 420 ctcggccgga accctaagcc cccccaccga aaactcagca cggcgccttt cctcatcggc 480 agcaccgtgt tcgcgctcaa atccacgcca gaaaacaaac cgtcgccgtc gtccgagatc 540 attgaaagcc ccggcttcca ctcttctcgg gcccgacaca cctctgtctc cggcttgtgc 600 tgccgagctc cagcgccgga gccgatccag ttgaactgct ccacttagaa accggaccga 660 tctgagtttc ttcgcccacc ttggtcgcca cgactcacga ctttcagggt gagaaagaga 720 gggagtcaag ggtttgacgc acgcttttga cccttttgac gctttttgac accttgtaag 780 agaggtactt gtctctttct ttcttcttgc tgtggtgaat tgcaatttct ggtctgggct 840 gggtgtaaaa ttactttgga gattgaattt tattgtcatg gaagagaata agaattctgt 900 tgctgatata gtgcctattg tgtcaaaaat aactgaacac aaattaaatg ggtctaatta 960 tattgaatgg agcaagacta tcaaaattta tttgagaagt gttgctaaag atgaccactt 1020 gactgaggaa cctcctaatg ataacactag aaaactttgg atgcaagatg atgcacggtt 1080 atttctgcag atgaaaaact ctattaatag tgatattgtt ggtctgctga gtcattgtga 1140 atttgttaaa gagctaatgg attatcttga ttttctgtac tctggaaaag gaaatgtatc 1200 tcggatgtat gatgtatgga atgccttcca ttgtcctgag aagggagcta aatccctcac 1260 tgcatatttt atggacttca agaaggtata tgaggaattg aatgcactta tgcctttcag 1320 tccggatgtt agagtacaac aggctcaacg ggaacagatg gttgttatga gtttcttatc 1380 cggtctccca tctgagtttg agactgcaaa atctcagatt ctttctggtt ctgacattgg 1440 ttcccttcag gaagttttca gtagagttct acgaactgag aatgtctcat cttctcagca 1500 caccaatgtt cttgttgcaa aaggaggaaa tgcagaaaat gcaagaaggg tgaataacag 1560 gggcggaaac agggcatttg aaaatcgtgg caatgattca agtacaattg tgtgttttta 1620 ctgccatgag gctggccata ccaagaagaa ctgcaggaaa ttgcaaaatc gaaatcggag 1680 aattcaaact gccaatgttg ctacatctga tactgctaca ttttcagact cctcagacaa 1740 gatcgtcaca atgacagcag aagagtttgc taaatattca cagtatcaag acgcactgaa 1800 agcatctact cctgttagtg ctctggcaga gtcaggtaaa acatgtcttg tctcctcctc 1860 aaacaaatgg ataattgatt caggtgccac agatcatatg acaggtaatc ataaaacttt 1920 ctctaccttc agaacacatt ctgctcctcc tgttactgtt gctgatggtt ctacctatga 1980 gattaaaggg tctgggactg tgaaaccaac atcttctatt acgttatctt ctgtgttaaa 2040 cttaccaaat ttggccttta acctaatctc tgtcagtaaa cttaccaaaa atctgaattg 2100 tagtgtctca tttttccctg atcattgtgt gtttcaggat cttatgacga aacggacatt 2160 tggtaaagga catgtatctg atgggctcta tattcttgac gagtgggtac ctcgaccagt 2220 tgcgtgtgtc agtactgcct ctcctgttga agctcattgt cggttaggac atccttctct 2280 accggtgttg aagaaattat gtcctcagtt tgatacttta ccttcattag attgtgagtc 2340 gtgtcatttt gcgaagcatc atcgtagttc tttaggccca aggattaata aacgggctga 2400 gtctttgttt gagttagtac attctgatgt ttggggtccg tgtcctgtta cttctcaaac 2460 tgggtttcga tattttgtta cctttgtgga tgatttttct cgaatgactt ggatttattt 2520 tatgaagaat cgttcagaag tattttctca tttttgtgca ttctctgctg agattaaaac 2580 ccaatatgat gtgtctgtga aaatattaag aagcgataat ggaaaagaat atgtgtctaa 2640 ctcatttcag aattacatga gtcacaatgg gattcttcat caaacatctt gtgttgatac 2700 tccttctcaa aatggggttg ctgaaagaaa aaacaggcat ttacttgaga cggctcgtgc 2760 cctcatgttc cagatgaagg ttccgaaaca gttttgggct gatgcagttt ccacagcttg 2820 ctttctgatc aaccgtatgc ccactgtagt gcttaaaggt gatattccgt acaaagtaat 2880 acatccacag aaatcacttt ttccacttga accaagaatt tttggatgta catgctatgt 2940 tagagataca aggccttttg ttactaaact tgatcctaag gcgttacagt gtgttttctt 3000 ggggtactca agactgcaaa agggctatag atgtttctcg cctgatctca ataagtatct 3060 agtatcaacg gatgttgtgt tttcagaaga cacatccttt ttctcttcac ccacaagttc 3120 tgcaagtgag gaggaggatg aagaatggct tgtgtatcaa gtggttaatt caagaccaac 3180 tgttgggcaa tcaagtgtgg ttgattctga tgcatctctt gctcatttgg gtcctgttgt 3240 taatattcct cctgctccag tcaaaccacc aattgttcag gtgtactctc ggcgcccagt 3300 gacaacagat acatgtcctg caccagctcc ttcgtcatct gatccttcca gtgatctcga 3360 ccttcctatt agccttcgaa aaggtaaacg acactgcaaa tctatctatt ccattgctaa 3420 ctttgtgtct tatgatcacc tgtcatcttc ctcaagtgtc cttgtagcct ctatagattc 3480 tatttcagta cctaaaactg ttacagaggc cctgaatcat cctggttgga agaatgcaat 3540 gcttgaagaa atctgtgcat tggaggataa tcatacatgg aaacttgttg atttgcctca 3600 aggaaagaaa gttgttggct gcaagtgggt ctttgcggta aaagttaatc ctgatggctc 3660 tgtggcacga ctgaaagcca ggcttgtagc tagaggatat gctcagacat atggagtaga 3720 ctattctgat actttctctc cagttgccaa actcaattca gttcgactat ttatttctat 3780 tgctgcttcc caacagtgga tgatacatca gttagacatc aagaatgctt ttcttcatgg 3840 tgatctagag gaagaggtct atctggagca acctcctggg tttgttgctc agggggagta 3900 tgggaaggtt tgttgtctga aaaaagctct ctatggattg aagcagagtc cccgtgcttg 3960 gtttggaaaa ttcagtaagg agattcaagc atttggcatg aacaagagcg agaaagatca 4020 ctccgttttc tacaagaaat cagctgctgg tatcatactt cttgtggtct atgtcgatga 4080 tatagttatt acaggaaatg atcatgcagg aatctctgat cttaagacat tcatgcattc 4140 caagtttcat acaaaggact tgggtgaact gaagtatttc ctgggaatag aagtatcaag 4200 gagcaagaaa gggatgttct tatcacagag gaagtatgtg cttgatctgc ttaaagagac 4260 cggtaagata gaagcaaagc catgtactac cccgatggtt cctaatgtac aacttatgcc 4320 agatgatgga gatcccttct acaaccctga aaggtatcgg agagtggttg ggaagctgaa 4380 ttatctcacc gtgacgcgac cagatattgc atatgcagta agtgttgtta gtcagttcac 4440 atctgcgcct acaataaagc attgggcggc tttagagcag attttgtgct atctaaagaa 4500 ggctcctggt ctaggcatac tatatagtag tcagggacac actcgcattg agtgtttttc 4560 tgatgcggat tgggcaggtt ctaagtttga tagaagatcc actacaggtt attgtgtgtt 4620 ctttggcggg aatctagtgg cttggaaaag taagaagcag agtgttgtat cccgttcgag 4680 tgcagaatct gagtataggg ccatggcaca ggctacttgt gaaatcatat ggatacatca 4740 actcttatgt gaagtgggaa tgaagtgcac aatgccagca aagctttggt gtgacaatca 4800 agccgctctt catattgctg cgaacccagt ctatcatgaa agaaccaaac acattgaggt 4860 cgattgtcac ttcattcgtg aaaagattga ggaaaatcta gtctctactg gctatgtgaa 4920 gactggagag caacttgggg atatttttac aaaagctcta aatggaactc gagttgagta 4980 cttttgtaac aagctgggca tgatcaacat ctatgctcca gcttgagggg gag 5033 // ID Gypsy-33_Mad-LTR repbase; DNA; EDCOT; 355 BP. XX AC . XX DT 08-OCT-2010 (Rel. 15.1, Created) DT 08-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-33_Mad-LTR. XX NM Gypsy-33_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-355 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1761-1761 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 355 BP; 96 A; 89 C; 68 G; 102 T; 0 other; tgtttatacc atatttaggg cctccgtatt tagatctcgt acaaatactc gggggactta 60 aatgtaatta tgtgataaag gaaggggcaa atatgtaata agtgaggagt ccttattcta 120 taaaaggacc cctcaccctc acaattaggg gaggccaatt cctaggccct ctcaccccct 180 ctcaaagctc tcactctcag agctctctcc ctcacccctc agataaatac aatatcagtg 240 tggacgtagc ccaaaccttg gggtgaacca cgatacatct tgtgttattt acatttcttg 300 cagattcacg gtcggattta cgttgttcca agacctccgg ttttgtgcat caaca 355 // ID Gypsy4-VV_LTR repbase; DNA; EDCOT; 1802 BP. XX AC AM438099; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy4-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1802 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-1802 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 693-693 (2007). XX DR Genbank; AM438099; Positions 14167 12366. XX SQ Sequence 1802 BP; 548 A; 319 C; 359 G; 576 T; 0 other; tgattactac tcaaaaaggg ctatttgata gcttgtaatt aactctttta aacatttttg 60 agtaatagtt attacctttt aactcaatta gcatattaag taccttttca atcatttcta 120 atcaaattgt gtatgttttg gtgcttttga tagtaatttg atcaccaaag caatccaaga 180 ttaaggagag ctctatggaa tccatggaaa agcaattgga agctcattta catgaagaac 240 ctaagctttg gagctttata gtcattttcc ataagcaaat catgaatgca aggatgaaag 300 caaagagaga aatctaacat gaagaatcca agaggacatc aactgtttga aacttttgga 360 gtactttatg aattccattt gatgcatact atatgccgtt tcgaagcttg ggaagtcagt 420 aatccaatgc tttaaacggt tcacaaatca gagttgaaat gaagaagtta gagccattgg 480 aagctgatca caccaagctg aaggccaatt tcgcaggctg cgaaattagc ctttggctgc 540 gaaataattt cgcagccatc ttgtacgtct gcgaaatttc gctaccattt tgtgcgcctg 600 caaaattctc ctgagtgctt ccagatattt gcgaccgaca ttttttgata ttttgcttca 660 gatatttgat gtctaaatcc caattttctc cttgtaatcc accaattata ggattcctta 720 gttgttaagc aagaacaaaa gggtgaataa cctcatatat attgttttgt aattttcatt 780 acagtgacat ctcgggagct tgttatcaga gaatctactt ttttgtatag tttgaaagga 840 agtaaaatac agagctttgc tctaccttac ctactcaata tgattgtatt tttcattact 900 agccaaacaa gctttgagga tgtttcctca gagaatgggt ggctaggttt tttgtctctt 960 ggaggtaagg tagccgggta aggtgccgaa tgtaagaatt gagagttttg ttgtttcaac 1020 tgttaatgaa gagaaagtgt aacccgttta tggtttctat gtttttagtt aacttaaaac 1080 gccttcaatt cacctgggcc aacacttggt aatgcaagtg atctccgtcc attgagatgc 1140 actagtttac ctcttgtgag cctttgggag gtgacttgaa ggtaggattt tctagaattg 1200 ccaacacttg gtaaactttt ggactctaag gagacatcca ttagttatct cttgcgagct 1260 tgagaaggga agtccaaggt taatgatcac cttgaatggc aaatgctagg tgagaggcac 1320 gggccattgc aagatgcatc agtgagaggg aattagtgct gaaattcata aaagggaaac 1380 atctgtacaa caccggttgg agaatgaact atatgttaac tctccaatgc gaggaaaaga 1440 accaaagtga tcggaactct gtttttgcat gaggagcctg accccagtga tcctaaaact 1500 ccaagagacg ctttttcttt ataagtaatt cccattactt tctttttagt tagcttgaaa 1560 ccaaaccttt ttcaaccaaa gtttatgttt tcttttgaat ctaaccttga aatgaaaagg 1620 caccaattca actttgaatt ggtatcagtt gtaaattgaa aacccttccc agtgaacgat 1680 cctagagcta ctatgctatg ctagctgagg ctatcctagt acatggtgta ataggttata 1740 aattttgttg attactccca tatgaggacc aaaatcaagg tacaccaact gggcacgaat 1800 ca 1802 // ID Copia-41_VV-LTR repbase; DNA; EDCOT; 269 BP. XX AC chr10; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-41_VV_; KW Copia-41_VV-I; Copia-41_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-269 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr10; Positions 5083007 5083275. XX SQ Sequence 269 BP; 83 A; 27 C; 50 G; 109 T; 0 other; tggaaatatg ggattatgat ttgtaattaa atgccaagat tagagggatt gtgttagaat 60 actttctatt tttatggatg agagaatctc ttcttgtgtt aggatacttt ttatttttat 120 ggataagaga atctctccta attagttatt gtttccttag agatagtgat tgtgcatatt 180 atatggctta gattaggaat cccacttgta tatatatagg tcactttgta ttcagttttg 240 acacagaaaa aaaaagaata ttttcttca 269 // ID Copia1-PTR_I repbase; DNA; EDCOT; 9484 BP. XX AC LG_XI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia1-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-9484 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-9484 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 190-190 (2007). XX DR Genome; LG_XI; Positions 13092348 13101831. XX CC Positions [6729-7229] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 6111..9482 FT /product="Copia1-PTR_I_1p" FT /translation="MAENFTTSSSPTADVANTNWCLDSGATHHMTTNATSL FT PDVHPYTGTDTIVVGNGNQLAITHIGNTQLTGLHKSLNLNEVLYVPAIRKN FT LISIRRFCCDNDCYFKMDANGFSVKDNKTEKVLLTGSSFDGLYHIQTSPSI FT ARQIACYGKRTTQDVWHARLGHPSHSVFTTLLNKYNLPLDGAIVSNKNCHI FT CPLGKSCRLPFEDRQSHAQFPLALLHLDLWGPAPISSNFGYRYYFSIVDDN FT TRFTWLYPLAKKSDVLTTFVHFKKLVENRFSSHIKQLQVDGGGEFTSKLFL FT TFLRDHGISHQISCPYTPQQNGVVERKHRHIVAMGLCLLAQSRLPHSFWVE FT AFSTAVFLINRLPTPKLDHISPYEKLLQRTPDYAFLKSFGCACFPHMVPYN FT RHKLSFKSVPCVFIGYDDHYKGYRCLDPISSRIYISRHVIFDEASFPYPQL FT QSTSVAQSTPTVHLDIGPDLYSQETNNSTNPTHSAPIILDSPLVTTSASPQ FT PSPTPPLSPSPIVVVPSPVSQSSHPLQTSSTNPTSVTHTTTPSPMSTPPPS FT PIDPSLLPNSPATPNPPKKFKSLKTIIPFGPEPKPLYSHTTPHPLPQALSA FT ACSDPMSLEPTSFTQASKYSHWQATMQDEYDALMQNHTWSLVPASSHMNIV FT GCKWVFKVKRKADGSVDRYKARLVAKGFNQQEGFDYAETFSPVVKPATIRT FT ILSLAVSCNWSLQQLDVRNAFLNGYLEETVYMKQPPGFHDSSRPQDVCQLH FT KALYGLKQAPRAWFQRLSAFLLAQGFAHSQSDASLFIHRSSSSTIYVLVYV FT DDIIVTGSDLQHIHRFLDQLCSTFDSRRLGELNFFLGMEITRFTDHLFLSQ FT TRYAVDLLKRFNMTDCKPCPTPLPFDTRLSYLDGDPLSDPSTYRSMVGGLQ FT YLTLSRPDISFAVNQVCQFMHNPRSSHLQVVKRILRYIKGTVEQGLVFHQS FT DDFTLRSFSDADWAGSVDDRRSTTGACIFFGPNLLTWTAKKQSTVSRSSTE FT AEYRALAHTAAEICWFGFLFRELGIPLQTAPCIYVDNLSAIHMAANPIFHA FT RTRHIEIDYHFVRELVARKSLHTFYVPSSHQLADIFTKGLSRDRFSFLKSK FT LNLRVAPLRLRGGKEN" XX SQ Sequence 9484 BP; 2678 A; 2048 C; 1893 G; 2865 T; 0 other; tcagagctct ttggagctaa ccctcaaaat atcaatccta cccaaaccaa tggccaacac 60 acccaaatct ggagaatcaa gtaatcttga tatgtcaaaa ctgatttctg aaatgtcaaa 120 actttcctct cctccactct catcccattc cttgcccacc tccttcaata tctgaaaaca 180 agataaaaga atgctgggaa gaataataac agaagtttta ttccaaaaat taattactgc 240 agagtttaca atgagaatat atatacaaat acgtagctag aaagtaggag ctgcaagtga 300 ttgagtccaa ctcaatcagt tcatctacac aactcaattc cagaggataa tcttcaatag 360 tggatcaaca tcagcagtaa gtagataatc ttcaacagtg aatcaacatt agcagcagat 420 taactttatc tgttgaagat caacttctac ttatcttttc aacactcccc ttcaagttgg 480 agcatgaata ttgagaatgt tcaacttgcc tgataatttc ttgaaattgt ctccccctaa 540 tgccttggtg aatatatctg ctagttgaag ataggaggga acgaatttcg taacaatttg 600 acctgcttga atcttttctc tcacaacatg gcaatcaatt tctatatgct ttgtgcgttc 660 atgatagacc ggatttgcag caatatgaag tgctgcttga ttgtcacaga ataaagtgat 720 tggttttaag ggcacctgta gatctttaaa taagcatcga agccaggtga gttcacatgt 780 tgcggcagcc atagacctgt actcagcttc ggcagatgac ctggagactg ttttctgttt 840 tcttgtcttc cacgagatga gagaatctcc aagaaataca cagtaaccag atgtagatct 900 tcttgtcata ggacaatttg cccaattggc atcacagtaa gctcttagtt gcagagagct 960 gctggaagag aataacaagc cgttacctgg gttgttcttt aagtatctta ttacacgaag 1020 agcagcatcc caatgaggtt ttctcggtgc atgcataaat tggcttaaga tgttgacaga 1080 atacatgata tctggtctag taattgtaag atagattaat cgccctacca atcttctgta 1140 gtgtgaagca tcattcaata tctcaccttg gtcattagtg agcctcagat tttgttccat 1200 aggaaaatca acgggtttag ctccaagaaa tccaacatcg tcaataattt ccagtgtgta 1260 ttttcgctga gatataacta ttccagcctt tgatcttgcc acttccagtc cgagaaaata 1320 cttcagatta ccaagatctt ttatgtggaa ttgtttttga agaaacaact tgatatcttg 1380 aatagcactg tcattgttcc cagtaatgat tatatcatct acgtagataa gaacaatggt 1440 tagagtagaa cctttttctt gcacaaagag agaatgatct gagtgtgatt gagagaaccc 1500 agccgtttta atggcttctg agaatttagc aaaccagttt ctaggcgctt gtttgagtcc 1560 atacaaggac ttatgaagcc gacatacaac cttctcccct tgtcggcaaa gtcctggtgg 1620 tggagtcata taaacttcct catgtaaatc accatggagg aaggcattat taacgtccat 1680 ctggaagagt ggccaattac ggactgctgc caaggcaaga agacagcgaa ctgtagttaa 1740 ctttgcaact ggtgcaaaag tttcatgata gtccaagcct tcttgttgat tgaagccctt 1800 ggctactaac cgtgctttat accgttccac agtccatcag atttgtattt gattctgaaa 1860 acccatttgc tgcctatggg acgacaatgt gatggtaatg aaactagaga ccatgttttc 1920 tgattttcaa gtgcagtgag ctcagttctc attgcttcac accacctagg atcactgagt 1980 gcctgctcat atgttgttgg ttcaagagtg ctagtaatgt tgttaataaa tatctgatga 2040 gaaggagata aggactggta ggaaataaag cttgataatg gatattgagt acctaactgt 2100 gaagaggctg acttggttgt ggatgcagag agctgtgaca taccaacttg accacaatga 2160 aaatcacgga gcagaacaga ggtttgtcgt ggccgatcac tgcgactagg attggatgat 2220 ggtgatgatg gtgatgatgg agagtctgta gaggcagagg aagataatgg agtggtagga 2280 gtctcggttg gtgagggaga aaaaattaat ggttgtggaa ttgggctgtc attaggatca 2340 ggaagtatgg tgggcagaga tggttgttga gaggaatcga cagaagtggg ttttatgaaa 2400 ggaaatgtct tttcatgaaa aacaacatct cgactagtga aaaactgtcg agtggtaaga 2460 tcataaacac gatatgcttt ttgattagga gggtatccaa caaaaataca tcgacgagct 2520 cgtggtgaaa atttggtcaa tggttgtaag ttggtggcat aacagagaca accaaaagca 2580 cgaagatgtg tatatatggg tggttttcca tataggagtt catatggtga cttgtgattc 2640 aaaactgggg tgggaagacg atttatgaga taggtggcag tgagcaagct ctctccctaa 2700 aattgtaatg gtaaatttgc ttggaatctc aaggcacgac caacattgag tagatgtctg 2760 tgttttcgtt ctacaacacc attttgttga ggtgtgtaag aacatgaatt ttggagtaaa 2820 atgccatgag tggaaaggaa tggctttaag gagataaatt ccagcccatt atcatttcat 2880 atatttttaa cttgacagtt aaattgagtg tggacaaaag tgatgaatga ttttaacaac 2940 ccttgtgttt cagatttgaa tttcataaga aaaatccaag taaaacgagt gtagtcatcc 3000 acaatagtta aaaaataatg tgcaccagag tgtgtttcaa tcttttgtgg accccaaata 3060 tcacagtgta taagctcaaa aaatttagta ctttgaatag aacttatggg aaaggataac 3120 ctggtttgtt ttgccaaagg acaaacttca catgaatgtt gcgaatcata aacaaaagat 3180 ggaattaatt ttgacagaaa ctgagagggt aattttgatg gatgtcctaa tctgttatgc 3240 caaacagctc ctgatggaaa agagacttga tatgattttg ttgaagatga atgtgattct 3300 gattgtggca taaggtagta tagtccctta ctctgcttcc ccaggccaat catcctcttc 3360 gtagctaggt cctgcaatat acagaaagtg ggaaaaaaat gaacagaaca attaagagca 3420 gatgtgagtt ggctgactga aagcagattc acatggaatg agggtgcaca aagaacatca 3480 tggacatgta ggcttttggt aacatgtgca gagccagcac ttgtaatttt tgcgtaggaa 3540 ccattcggca aggtgacttg agagaacata ggaaaagtgg ctttatcaat aactgaagtg 3600 gctatatggt tagtggcacc actgtcaatg atccattgta aagcctcaga attttgagtc 3660 gtgaaagatg agcaaaaagg agtggtatta cctgtataat ttgtagatac agtggatttt 3720 tcgcttgaaa gaaagctttg atttgtgaaa attcttcagg agtgaattga agaggctgat 3780 cagaggtttg aacagacttg atgttggtgt gaaatgattc aattcctgtt tggtttgcag 3840 cagctttttg agctcgattg cgaggctgca cattcttgcc atgaagtgcg tggtcggtgg 3900 gaaatccaat caaataaaaa catctctcca ctgtatgtgt agttccatca cagtaggtgc 3960 aatgaagtcg tttgtttgat ccttacatag ttgatgagcc agacatccaa tttcgagaga 4020 aatctcgtcg ttgtgaagta gaacctgatc tttttacatt catggcatga acctgttcag 4080 taactttgtg ctcaactagt cctctttgct tttcttcctc acacaagagt gaatatgctt 4140 tcttaacagt tggtaaaggt tgcatgagca tgatttgccc tctaatggct gaatagtttt 4200 catttaatcc cataagaaac tgacgtctca tcttttcttc actgtttgac agttgtttca 4260 ttccaccaca tgtgcactga atggctggac tggtcatttt caattcatcc cataacgttt 4320 ttatcttggt gtaatatgtg aagatggaat cctgattttg ctgcaattct actatggaac 4380 gctgaacttg ataatgatga gaaaaattac cttgtgagaa tcgttcttgt agatccaacc 4440 agatttcaga aagggtttca atatagagaa cactattggc aagctcttgg tttaaggagt 4500 taagaatcca agagagaacc atatcattgc atcgttgcca taacatgtat ttaggatcag 4560 attctcctgg tataagtatg gttccattga tgaatcccaa cttgtttttg gcgttgagac 4620 ttattagcat ggaacgtctc cacattgcat aattggttcc atcaagaact tttggaacaa 4680 gagtcatgct tggatgatct gatgtatgaa taaaaaaagg atcagaagga tcaatggttg 4740 aaagggacat gttctaaagg gtagtgtttt ggttaatact ggttgaatca gtattgtcct 4800 ccattggagg ttttgcggaa gcttggttaa tatgtttaag gtttcatgtg ctctgatacc 4860 atgaaaacaa gaaaaaagaa tgctgggaag aataataaca aaagttttat tccaaaaatt 4920 aattactgca aagtttacaa tgagaatata tatacaaata cgtagctaga aagtaggagc 4980 tgcaagtgat tgagtccaac tcaatcagtt catctacaca acctcaattc cagaggataa 5040 tcttcaatag tggatcaaca tcagcagcaa gtagataatc ttcaacagtg aatcaacatt 5100 agcagcaaat taactttatc tgttgaagat taacttctac ttatcttttc aacaatatct 5160 catccttgtt cactgtcccc atggatcgca ccaactacct gagtttgaaa tcccaatttg 5220 aagatatact ggagatgcat ggctttacag tagtcatcaa aaacaacaca gaaccaccta 5280 aagtgcaaga agatggttct gtgcaccgag aattagcaaa agctaaattg gtcctgagtt 5340 ggatcaaagc aacttcctcc tcttccatca aaacacttct catcccatgt accactgctc 5400 atcaagcctg gaccatgctg gccaagcgtc tttcacctct tgctagcacc cgtgtacgaa 5460 tccttcgaga ccaaattcgc actctccgga aggacagcag caccacagtg gttgattatc 5520 tcaattatgc caaatcactc tttgattctc tcatacaatc tggtgcaacc atggacgatg 5580 atgaattaat cagttatgtt ttggatggac ttggtcttga atataaagag ctagccacaa 5640 cacttcacct gcatcccgat attgactttg atcaattcta tgatttagct ctaagagaag 5700 agcatttaca gaaacgcatg tctcttacca tgacttcagg agttgctatg gctgctgatc 5760 gtatgcccaa agaacgtccc ttcaattcac acatgcccaa tcataatcac ggatttggaa 5820 gaggacacgg tcgtggcagg aattggaatc aagggcgtgg atcaaggcga acagggcatt 5880 gagagccggc tcaaggggct tggtttccag accgcaactc tcagccacgt gacccttaat 5940 ctgttgtcct cacctcttct cctgctactc tctctgatgg gcgccctcct ttacttccaa 6000 cacctcaagg cagattctca aatacccaac gcagtgaagt catttgtttt cggtgtgata 6060 agtaggggca tatagctcgt ttttgtcctg accgtcggcc tcatgcatac atggcagaaa 6120 actttaccac ctcttcttct cctacagctg atgtggcaaa taccaattgg tgtcttgatt 6180 caggtgctac tcaccatatg acaaccaacg caacctctct ccccgatgtt catccttata 6240 caggtacaga tacaattgtt gttggaaacg gcaaccaatt agcaataact catattggca 6300 atacacaatt gaccgggttg cataaatcat taaatcttaa tgaagttttg tatgtgcctg 6360 ctattcgcaa aaacttgatc tctatccgtc gtttttgctg tgataatgat tgttacttta 6420 agatggatgc taatgggttt tctgtgaagg acaacaaaac ggagaaggta ctccttactg 6480 gcagtagttt cgatggcctt tatcacatcc agacatcccc ttctattgct cgtcaaattg 6540 cttgttatgg aaagcgtaca acacaagatg tatggcatgc cagactcgga cacccatctc 6600 attcagtttt tactacattg ttgaataagt acaacttacc acttgatggt gcaattgtct 6660 ccaataaaaa ctgtcatatc tgtccgttgg gaaaatcttg tcgcttacct tttgaagaca 6720 gacaatctca tgctcaattt ccattagcac ttttacatct tgatttatgg ggtcctgcac 6780 caatctcctc aaattttggc tatcgttatt atttttccat tgtcgatgat aatactcgat 6840 ttacttggtt atatccattg gctaagaaat cagatgttct tactacattt gttcacttca 6900 aaaagttggt ggaaaatcgg tttagctctc acattaaaca actgcaggtt gatggtggag 6960 gtgaatttac cagcaaatta tttctgacat ttttacgtga tcatggaata tctcatcaga 7020 tctcatgtcc gtacactcct caacaaaatg gagtggtgga aaggaaacat cgacatattg 7080 ttgcaatggg actctgttta ttggcccagt cccgcttgcc ccacagcttt tgggttgaag 7140 ccttctctac tgcggttttt ctgattaatc gcctaccaac tcctaagctt gatcacatat 7200 ctccttatga gaaattactt caacggacac cggattatgc atttctcaaa agttttggat 7260 gtgcctgctt tcctcatatg gtcccataca acaggcataa attatccttc aaatctgttc 7320 catgtgtatt tattggctat gatgatcatt acaaaggcta tcgctgtctt gatcctattt 7380 caagtcggat ttatatatct cggcatgtga tttttgatga ggcaagcttc ccctacccac 7440 aacttcaatc tacatcagtt gcccaatcca cacccacggt tcaccttgat attgggcccg 7500 atttgtactc tcaagaaact aacaattcta caaatccaac ccactctgcc cccattatcc 7560 ttgactcccc attggtcact acttctgcca gcccacaacc ttcccccaca ccacctctct 7620 cccctagtcc aatagtagtc gttccttccc ctgtctccca atccagccat cctctacaaa 7680 ccagctctac aaaccccacg tctgtcaccc acaccacaac cccctcaccc atgtcaacgc 7740 ctcctccttc ccctattgac ccatctctcc tccctaactc tcctgctaca ccaaaccctc 7800 ctaaaaaatt taagagtctc aagaccatca tcccatttgg tcctgaacca aaacccctct 7860 actctcacac cactccgcac cctttacccc aggctctctc tgccgcttgc tctgatccca 7920 tgtcccttga acccacaagt ttcacccagg cctccaaata cagtcactgg caagctacca 7980 tgcaggatga atatgatgcc cttatgcaga atcacacatg gtctctggtt cctgcctcct 8040 ctcacatgaa cattgttggc tgcaaatggg tattcaaagt aaaacggaaa gctgatggct 8100 ccgttgatcg ctacaaggct cgccttgttg ccaaaggctt caatcaacag gaaggatttg 8160 attatgcaga gaccttcagc ccggtagtta aaccggccac cattcgcact atcttgtctc 8220 tagctgtgtc ctgtaactgg tctcttcaac aacttgatgt tcggaatgcg ttcttgaatg 8280 gctacttgga agaaacagtt tacatgaaac agccccctgg ctttcatgat tcctcacgtc 8340 ctcaggatgt atgtcagctc cataaggctc tttatggcct taagcaggct cctagagctt 8400 ggttccaacg tctcagtgca tttctccttg ctcagggatt tgcccatagt caatctgatg 8460 catcgctctt cattcatcgt tcctcttcca gcacaatcta tgttcttgtt tatgtggatg 8520 atatcattgt caccgggtct gacctccaac atatccatag gtttcttgat caattgtgct 8580 ccacctttga cagtcgccga ttgggtgagc tcaacttttt ccttggcatg gaaattacac 8640 ggttcactga tcatttattc ctctctcaaa ctagatatgc agttgattta ttgaaacggt 8700 tcaatatgac tgattgtaaa ccatgtccta caccgttacc gtttgacact cgactatctt 8760 atttggatgg cgatcccttg tctgatccct ctacctatcg cagcatggtg ggtggcctcc 8820 aatatctcac tctctcgcga cctgatattt cctttgctgt caatcaagtg tgtcagttca 8880 tgcacaaccc tcgttcttcc catcttcagg ttgtcaaacg cattcttcgg tatattaagg 8940 gtacagttga gcaaggcctt gtgtttcacc agtccgatga cttcacttta cgcagcttct 9000 ctgatgctga ttgggctggc tctgttgatg atcgacgatc taccactggt gcttgtatat 9060 ttttcggccc taatcttctc acatggactg ccaagaaaca atctactgtt tctcgttcta 9120 gcactgaagc tgaatatcgt gcccttgccc acacggccgc tgaaatctgc tggtttggat 9180 tcttatttcg cgaacttggt atccctcttc agactgctcc ttgcatctat gtcgataatc 9240 tctctgctat ccacatggct gccaatccaa tttttcatgc tcgcactcgg catattgaga 9300 ttgactatca ctttgttcgc gaattagttg ctcgaaaatc tctccatacc ttctatgttc 9360 cctcctctca tcagcttgct gacatattca ccaaaggcct gagtcgtgat cgattctctt 9420 ttcttaagtc caagctcaat cttcgcgttg ctccgttacg cttgaggggg ggtaaagaga 9480 atat 9484 // ID COP4_I_MT repbase; DNA; EDCOT; 4325 BP. XX AC . XX DT 22-DEC-2006 (Rel. 11.12, Created) DT 22-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Internal region sequence of COP4_MT LTR retroposon from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW internal region; LTR; retroposon; COP4_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4325 RA Shankar R. and Jurka J.; RT "COP4_MT: A copia type LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 609-609 (2006). XX DR [1] (Consensus) XX CC The internal region is very well conserved but the LTRs are not CC well conserved and vary a lot across the genome. XX FH Key Location/Qualifiers FT CDS join(2470..2592,2854..3342,3430..3960) FT /product="COP4_I_MT_1p" FT /translation="MFCSMSTDFHMRNYLPVISLPLLHQFIFHHFSHHYHL FT NILYACISPPHCIHPNNIHTMATRGKRGIVQQRIQPTLLLTHLEPTSYKQA FT MKHQIWLQAMTLEYDTLLKNNTWTLVSLPHNRKVVGCKWMFRVKQNPDGSI FT NKYKARLVAKGFHQMPGFDYKATFSPVVKPVTVMTVLTLAVTNKWCIQQLD FT VNNAFLNGYLRKRTNHLYCTFILVYVDDIIITGSSKSPLQQLVQKLNSEFS FT LKDLGQLDYFLGIEVHHSDTGSLHLSQTKYIHDLLVKENMSQANGIASPMA FT SSTKLSKYGSNHVSDPTFFRSIVGGLEYATITRPEISYSVNKVCQFLFAPL FT EDHWKAVKRILRYLQGTIHHGLLISPASLLNLCNHRIL" XX SQ Sequence 4325 BP; 1174 A; 1002 C; 792 G; 1357 T; 0 other; caattctaaa atggtatcat gagcttctcg atcctaaacc atggcctctg cttcgtcttc 60 tcctattccc tcaaatgttc aacgtatcac tccagcagct tcgaaaactt tcaaacaagt 120 cgtatcggtc aagctcgacg atacgaacta cctttaatgg aagcagcagg ttgaaggagt 180 tctcgtggaa caaaaatggt gcgttatgtc gtttcgccgc aaattccacc agttttcctc 240 tctgatgctg cgcgcgaggc cggtgaagaa aatccggcgt tcaccgattg ggaggagcaa 300 gactcgttgc tgtgtacgtg gattctctcc accgtcttgc ctccctgctt gcgcggtttg 360 ttcggttgcg ccactcgcat gaggtatggg atatgattca cacttactgt tatactcaaa 420 tgcgtactcg ttcgcgacaa cttcgttctg agttgcgcac tattaccaag ggaacgtgtt 480 ctattactga attcatagct cgtgttcgga cattttctga atccttgatt caattggaga 540 tccggtttct caccgtcacc tcattgaact tgttcttgag gccttaccag aagaatacaa 600 cgccatagtt gctaatgtga acagtcaggt tgacctggat gaactggaat ctcagctttt 660 gacacaagaa tcacgcaatg aaaaatttaa gaaagcctta attggagata ttgcagtgaa 720 tgtgactcag gcacctactt cagaatggca atcttctggt tcatattttg accagcagaa 780 taattttaat cctaatgcaa atgatgcttc tcagttttaa ccctaatttt ggtaatagag 840 gtggttttag aggaagagga tctcgtggtg gccgcttcag aggcagggga ggccgttatg 900 gtagaggagg ctctgttcaa tgctagatat gttcaaggtt ggacatgatg ccactattgc 960 tatcacaggc tatctgttcc acgatatgag ggatatggca cctatggttc atttgctggc 1020 tatggaggtt ctggaaatgg atggatggaa actatggacc tcctcctaat tttggacaag 1080 gtcctggatc ttcaacacaa tatggtaatc tcaggccccc accaccacaa gcttacttaa 1140 ctggtactga tccattcaac tctcttcaca acagttggta ccctgattct ggtgcaacac 1200 accatgtcac atctgatgcc accaacttca tggatgctgt gtccctatca ggttctgacc 1260 aagtacatgt tggtaatggt caaggtctgt gtacaaattc tgttggctca ttaagtttca 1320 cctcaccctt ttctccccat acaactctta aacttcataa tttacttcat gtgccctcta 1380 ttactaagaa tcttgtcagt gtcagtcaat tcactaaaga taacaatgta ttctttgaat 1440 ttcatcctaa cacttgcttt gtaaaatctc aggatacttc taaagttctt cttaaaggtc 1500 acattggtgt tgatggcttg taccagtttg atagtcctcc tgtgtctcaa agctcctcaa 1560 ctctgcttca agtcaagttt caactccaaa tgttaatgat gcttctctta ctctagcttt 1620 cctaactagt ttcaatgtaa taatcttgga agtacttata ctaatcagta gtagtagtaa 1680 catttaaatc tattgtttct tctctgtcta tgtacaaagt ctggcacaat aggcttggcc 1740 accctcatcg tgaggttctt aggaatgtaa tgaaattgtg ttatcaaaat cttcaaataa 1800 aagtgtcaca gatttttatt ctgcctgttg tttgggaaaa tctcatagat taccctctgt 1860 tgcttctaat acttcttata acaaaccttt tgagcttgta ttttgtgatt tgtggggtcc 1920 tgcatcaatt gagtctcatg tggtttctcc tatttcctaa catgtgttga tgcctattct 1980 agatacactt ggatttttcc acttaaactt aagtctcaaa ctcttactat gttcaaaaat 2040 ttcaaaagta tggtggaact gcaatacaat tatcctataa aatcagttca aactgatggg 2100 ggtggagaat tcaaacccct cactcagttc ctcactggcc tcattgtgga aaggaaacac 2160 aggcatatag tagagactgg tctcacactg ttagctcctg tgctaatgcc tttttgacag 2220 caacctatct caccaatagg ttaccctcac ctactcttga caacaaatca ccctatttta 2280 tgttgcatct tcagttccct gattacaagt tcttcaagag ttttggttgc tcttgtttcc 2340 cttttaccag atcctacaat tataacaaac ttgaattcag atccaaggag tgcaaatttc 2400 tggggtattc tccttctcat aaagggtaca agtgtcttga ttctacagga aggctttaca 2460 tctccaaaga tgttttgttc aatgagcaca gatttccata tgaggaatta tttacctgtc 2520 atcagccttc cactacttca ccagttcatc tttcaccact tttcccatca ttaccacctc 2580 aacatcctct actgatgatt catctctacc ttcatcttta ccttctggtt ctactcccac 2640 atcacactca tccactactc acactactca ctctaacact atcactagtg ctcatttatc 2700 acctcatcac actacatcca ttacttctca tcatgcttct catgataaca atctcatttt 2760 taatcctaca ccaattacca ctatttcacc ctcctcttct ggtgtttctt caccttagtc 2820 acacagcaac aacactgtca gtcagcataa tgagcctgca tctctcctcc tcattgtatt 2880 catcccaata atattcacac tatggccact agaggcaaac gtggaattgt tcaacagaga 2940 attcaaccta cactacttct aactcatctt gagcctacaa gttacaagca agctatgaaa 3000 catcagattt ggcttcaagc catgacactt gaatatgata cattattgaa gaacaatact 3060 tggactcttg tctctcttcc ccacaacagg aaggttgtgg gttgcaagtg gatgttcaga 3120 gtgaagcaga accctgatgg gagcataaac aaatacaaag caaggctggt ggcaaagggg 3180 ttccaccaaa tgccaggctt tgactacaag gcaacctttt caccagttgt caaaccagta 3240 actgtcatga ctgtattgac tttagcagtg acaaacaagt ggtgtattca acaacttgat 3300 gtcaataatg cctttttaaa tggttatttg aggaagcgta catgactcaa ccccctggtt 3360 ttgaagcaac tgattacaag gccctatatg ggttaaagca agctcccagg gcatggtttg 3420 agagattgaa atcatcttta ttgcaccttc attttagttt atgtggatga tattatcatc 3480 actggcagct ctaaatcccc gcttcagcaa cttgttcaga agctaaattc agagttctct 3540 ctcaaagatt tgggtcaact tgactatttc ttagggattg aggtgcacca ttctgacact 3600 ggctccctgc acctatctca aaccaaatat atacatgact tactggtcaa ggaaaatatg 3660 tctcaagcca atggcattgc ttcccccatg gcttccagca caaagctgtc aaaatatggg 3720 tcaaatcatg tatctgatcc aacattcttc agatcaatag tgggaggact ggaatatgcc 3780 actataacca gacctgaaat ctcttactct gttaacaagg tttgtcagtt tttatttgca 3840 cctctagagg atcattggaa agcagtaaag aggatcctca ggtatttgca aggcactatt 3900 catcatggtc tgctaatcag tcctgcatct ttactgaacc tttgcaatca caggattctg 3960 tgatgctgac tgggcatctg atccagatga tagaagaagc acttcaggtg cctgtatttt 4020 cttaggtccc aacctcatct cttggtgggc taagaaacaa actcttgttg ctaggtcaag 4080 tgcagaggct gagtacagaa gtctagctta agcttctgct gaaatcttac aggaactaca 4140 tgtacccatt aaagtgcctc aaatttactg tgacaattta agtgctgtat ccctggctca 4200 taatccagtc cttcactcca ggatcaaaca catggagctg gatatttttt gttcgggaaa 4260 aggttatcaa caggagtcta cttgtgtctc atgttccagc acattctcaa tgggcagata 4320 ttctc 4325 // ID SPLN3_SO repbase; DNA; EDCOT; 411 BP. XX AC AB016137; AB016137.1; GI:4126545; VERSION; XX DT 08-JUL-2003 (Rel. 8.06, Created) DT 08-JUL-2003 (Rel. 8.06, Last updated, Version 1) XX DE Spinacia oleracea LINE retrotransposon DNA, endonuclease region DE of SPLN3. XX KW Non-LTR Retrotransposon; Transposable Element; SPLN3_SO. XX OS Spinacia oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC Caryophyllales; Amaranthaceae; Spinacia. XX RN [1] RA Noma K., Ohtsubo E. and Ohtsubo H.; RT "Non-LTR retrotransposons (LINEs) as ubiquitous components of RT plant genomes."; RL Mol. Gen. Genet 261(1), 71-79 (1999). XX RN [2] RP 1-411 RA Noma K., Ohtsubo E. and Ohtsubo H.; RT "Direct Submission to GenBank."; RL Direct Submission to Genbank (09-JUL-1998)Kenichi Noma, The RL University of Tokyo, Institute of Molecular and Cellular RL Biosciences; Yayoi, 1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan RL (E-mail:aa77116@hongo.ecc.u-tokyo.ac.jp, Tel:81-3-5684-3269, RL Fax:81-3-5684-3269). XX DR Genbank; AB016137; Positions 1 411. XX SQ Sequence 411 BP; 118 A; 89 C; 85 G; 119 T; 0 other; ctggaatgtg cgaggtctaa ataggagagc aatacagatc gaggtgagga gattcattca 60 tacccacaat attaaactgg ttagccttct tgaaaccaag gttaaagcat ctaaattagg 120 tgacttatac cttggggtgt gcccagggtg gaacttcaca actaatatca gttgttccac 180 ttccagtagg attgttttag catgggatcc taactctttt acactgaaca ttttgtcaat 240 gagcagtcaa ctcattcact gcttcataac tccaagaagc acaggtgtgg ggttttttgg 300 taccttcatc tatggcatga atactaagga ggatagagtg cctttatgta actctctcac 360 tcagatttca gacaactgta cccaaccatg gctcctcccc ggaaacttca a 411 // ID SORE1_GM repbase; DNA; EDCOT; 431 BP. XX AC AB033271; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-JUL-2004 (Rel. 9.06, Last updated, Version 2) XX DE Glycine max gypsy-type retrotransposon SORE1_GM, partial DE sequence. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy superfamily; retrotransposon; SORE1_GM; partial sequence; KW reverse transcriptase. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-431 RA Kumekawa N., Ohtsubo E. and Ohtsubo H.; RT "Identification and phylogenetic analysis of gypsy-type RT retrotransposons in the plant kingdom."; RL Genes Genet. Syst 74(6), 299-307 (1999). XX DR Genbank; AB033271; Positions 1 431. XX SQ Sequence 431 BP; 123 A; 79 C; 112 G; 117 T; 0 other; agaggatgtg tgtggactat cgagatctaa accgagccag tccaaaggat aattttcctt 60 taccgcacat cgacattctc atggctaaca tggccagttt tgccctattc tctttcatgg 120 atggattttc gggttataat cagataaaga tggcaccaga ggatatggaa aagacaactt 180 tcattactct atggggaacc ttctgctata aggtgatgtc gtttgggctg aagaattttg 240 gggcaaccta ccatcgggcc atggtggcat tattccagga catgatgcac aaggagatcg 300 aggcctatgt ggatgaaatg atcgcgaaat caagaatgga ggaggaacac ctagtcaatt 360 tgcaaaattt gtttgggcaa ctacgtaaat acaggttgag actgaatccc aggaagtgtg 420 tgttcgggtt g 431 // ID Gypsy24-PTR_LTR repbase; DNA; EDCOT; 334 BP. XX AC LG_II; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy24-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-334 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-334 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 329-329 (2007). XX DR Genome; LG_II; Positions 21462985 21462652. XX SQ Sequence 334 BP; 115 A; 78 C; 41 G; 100 T; 0 other; tgatacaaga agattcagct taagaaagta aaggagggaa aagccgttac caacaaatta 60 gaattctgtt acaacaacac acaccgtttc atttacatgc attactcacg cttgtctttt 120 aatacgcacc gtttcaataa tgtaaacaga atacacgaga attcaactca tttccataat 180 gcctatatta agaggcagtt gtaacaaaca atctacacgt gaaaatagca agaatacaat 240 tctgttctct tctctcagat tctcaattct tcccttagct tctcattctg tgaattctct 300 tcacccgtta cacattcatc aaacaccttc atca 334 // ID Gypsy-25_Mad-LTR repbase; DNA; EDCOT; 241 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-25_Mad_; KW Gypsy-25_Mad-LTR; Gypsy-25_Mad-I. XX NM Gypsy-25_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-241 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1745-1745 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 241 BP; 70 A; 26 C; 57 G; 88 T; 0 other; tggttgttgt atgacaactg agatggtgcc aagtgtcatc atattagtga ataagattgt 60 attagctgta aaagttgtta gttggttgta ataggaaaag attgttgtgg ctagttgcta 120 tatagcagga attgtaagat acaaaggata tgtgataaaa atagtattgt cttcttcttg 180 ttcatattct ctctcgactt ctatggcagc ttaagagtca aggttgattt agggtctatc 240 a 241 // ID Copia-3_Mad-LTR repbase; DNA; EDCOT; 282 BP. XX AC ACYM01009006; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-3_Mad-I; KW Copia-3_Mad-LTR; Copia-3_Mad_. XX NM Copia-3_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-282 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1343-1343 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01009006; Positions 1323 1604. XX SQ Sequence 282 BP; 86 A; 40 C; 45 G; 104 T; 7 other; tgttaggagt actaagatcc aatggttatg aaatggacaa gtgtcaaatg agtatgaagt 60 tagttgagtt ggttatgttg tgacttagag tgtaagctac caaagggata ttataaatag 120 cttgaaacaa atcattgtaa ctaataagaa aagaatakta carttgaata actgatttyt 180 ctctctaaac tctaattctt ctacttctct ctctgtcttt ctttcttcat tctttcttgt 240 atmtgtataa tcytcttcyt caagaacctw tgatggttta ca 282 // ID Copia-44_Mad-LTR repbase; DNA; EDCOT; 238 BP. XX AC ACYM01035308; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-44_Mad-I; KW Copia-44_Mad-LTR; Copia-44_Mad_. XX NM Copia-44_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-238 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1394-1394 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01035308; Positions 3542 3305. XX SQ Sequence 238 BP; 62 A; 29 C; 48 G; 99 T; 0 other; tgttagagta taaggtttgt aggttgtttg taaagtgtaa cacttggtag tgtattagtg 60 gatatggttt agggtagtta ttgtgggtgt aaatataaat agtgaagagt cttgtattgt 120 taactattat taaaaagatc aggaattcta agatatgatt ctctctctct ctctctctaa 180 attccctcga gtactttctc tctctagttc ttgattgttc ttctcagtat tgttaaca 238 // ID Copia-97_Mad-LTR repbase; DNA; EDCOT; 621 BP. XX AC . XX DT 28-OCT-2010 (Rel. 15.11, Created) DT 28-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Copia-97_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-621 RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-621 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1980-1980 (2010). XX DR [2] (Consensus) XX SQ Sequence 621 BP; 166 A; 82 C; 154 G; 219 T; 0 other; tgttggagta tgtggccaag tggccaactt ttggctataa acaattcaaa agaaaaaaga 60 caaataatat gtccttcctt gttttgggga ggaaaacatg atgatgtttt cttcttttgt 120 ggctttttgt taaccataat tattgaggtt tgtttcgggt agaagagaag aaaagaagag 180 ctcatttttt tagagagaga gctgaagaga gaaggagagc tgcagagaga aggagagttg 240 cagagagccc aaaaggaaga agaagctgct gcttcatttg gttagtaatc atccaccaaa 300 gtagttgttg ttgtaatagc tttgagctat atgtatagag aagaaattat tcattatatt 360 tctttctcta tttgtttctt tggtgtgtga gagctattgg gtgtattggg ttatttgggt 420 tgtgagattg ccaacacttt gtaaactccc atttggttga tagtggatta ttgggtgagc 480 tcctactgct ccgaggacgt actccagtta cactgactgt tgaggaacct cgttaaaatc 540 ttggtgttct tttatatttt gttcttgcat tttcatttga taaatttcct gtgggttagc 600 ttgagttggt tccaacgggt t 621 // ID LCCOPIA1_LTR repbase; DNA; EDCOT; 255 BP. XX AC . XX DT 14-JUN-2005 (Rel. 10.06, Created) DT 15-APR-2011 (Rel. 16.04, Last updated, Version 2) XX DE L. corniculatus copia-like retrotransposon LTR consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; LTR-retrotransposon; integrase; gag-pol; KW LCCOPIA1_LTR. XX NM LCCOPIA1_LTR. XX OS Lotus corniculatus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RP 1-255 RA Gentles A. and Jurka J.; RT "L. corniculatus copia-like retrotransposon LCCOPIA1."; RL Repbase Reports 5(6), 151-151 (2005). XX DR [1] (Consensus) XX CC LTR corresponding to LCCOPIA1_I. XX SQ Sequence 255 BP; 82 A; 35 C; 44 G; 94 T; 0 other; tgtcaaagga attgattgac taatcaattg aataacagtt actgaccaga ttaattgctg 60 tatataattg tagttgacca agcctgtaat taggattaat tgttgattag ctgttacaga 120 tcagggaaat tattcccata attaggagag atattatttc catatttgta atatgttatc 180 agtataaagt tagctctatg ctgtgtactc agcatcaaga cagtattttc attccatatt 240 ttcctgagtt tgaca 255 // ID HARB-2N1_Mad repbase; DNA; EDCOT; 811 BP. XX AC . XX DT 25-OCT-2010 (Rel. 15.11, Created) DT 25-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE Harbinger DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW HARB-2N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-811 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1861-1861 (2010). XX DR [2] (Consensus) XX CC TIR is 11-bp long. XX SQ Sequence 811 BP; 168 A; 250 C; 147 G; 235 T; 11 other; gagcaactcc agcgttgcaa aggcccccta gggcaactca ctattgaatc cacccagtga 60 acagtaactg cctttaatga acagtaactg ccttttgcat ctccacccct aaattgaata 120 gccatggcaa taggtaataa aatattagta ttttttcctc acccaatcca tcagacatcc 180 ccatcaccct ttcccttttt cccctcattt gaccggttct tcctctctct ctctctctct 240 ctcttttctt tctatctctc tcttcctttt tctttctttc tctccctctt ttccagctca 300 ctctcgtgag ctctcttcct ccttcctctt caaaccttca acaaatcaag ctcaaaaata 360 atatttttgg aatccctgga actcaaggaa cccaaccatg gccttgcatg cggcatcggt 420 gcatggtgcg aggtcctacc attgaagccg agagcttgag ctctcaatct cgaacccagg 480 tgatgtttct atcactatct tgtgttcttg agctttaaat cctgttgtgt tgcaattctt 540 gtggtttaat tcgagggctt aattccctgc atgcatccca ttctttttcc agattccgac 600 aaaggaaaac ggacgaattc gagccgggtc accctgaggt cagccacaca tcacacaacc 660 ctcaggctct cgggcsacsg attcscgcct ggcctctccm ccgggccccc ccccgagccc 720 cattgcccgc atgggctgga gccagttgct ggggctattg ggwkakkgga atcgccggtc 780 catcgggcta awggkcacgs tggagttgct c 811 // ID Copia-37_VV-I repbase; DNA; EDCOT; 3982 BP. XX AC chr1; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-37_VV_; KW Copia-37_VV-LTR; Copia-37_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-3982 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr1; Positions 267896 263915. XX CC 'TCCAT' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 710..2848 FT /product="Copia-37_VV-I_1p" FT /translation="MRQGSSVEGAFQAKTQTNEGNTRRRKNKKNNNKPSNN FT NNQKAGTYPPCPHCKKTNHPQQKCWWRPDVKCNKCGRQGHIERICRTQQQQ FT GETNVAVEQYQEEQLFSATCFANGNTSESWLVDSGCTNHMTYDQDLFRDID FT RTAISKVRIGNGEYIPVKGKGTVAIESLTGLKLISDVLFVPDIDQNLLSVG FT QLVEKGFKVCFEDKNCIIKDAEDREVFNIKMKGKSFALNMLEDEQIVAAQH FT ENNTMLWHKRLGHFHHNAVFYMKKNQIVEGLPDLEEELPICATCQYGKQTR FT LPFPQKAAWKSTQKLQLVHTDVSQYGKQTRLPFPQLKGSKYYIAFIDDFTR FT FCWIYFLTYKSEVADVFLRYKAMVENQSEYIIKVIRSDNGTEYTSEKFNEF FT CEDADIDHQLTAPYTPQQNGVVERKNRTIMEMTRCLLHEKELPKSFWAEAA FT NTAVFLLNKLPTKALQKQTSFEAWFGYKPMLMNLKTFGCLCFSYVPQVKRD FT KLDKKSEPGIFIGYSSTSKAYKIYLPQNNKIVVSRDVKFLETEKWSWDEQN FT QQYIDEDVDELPVKGFRALFDIYQRCNIVVLEPAGFVEAAENKRWRVAMQE FT ELNMIDKNNTWELVDRPSHKKPIGVKWVYRTKLNSDGSINKHKARLVVKGY FT AQMFGVDFLETFAPVARLDTIRMLLALAAQRKWKIYQLDVKSAFLNGYLEE FT EIFVEQPEGFAIK" XX SQ Sequence 3982 BP; 1388 A; 642 C; 886 G; 1066 T; 0 other; gtttggtatc agagcatttt tgtcttgagg gaccagtgag gtgtgtgagc ctaaacaccg 60 tataccaaac ctgtatctga aaaccttctg aaaaccttgc agaaatggaa gaagcaagct 120 tcacagcagc accaccagtc ttcaatggag aaaattacca aacttgggct gtcaggatga 180 ctgttcatct acaggctctt gatgtctggg aagcaataga ggaagattat gaaatttctc 240 cacttggagc caatccaact gtggcacaga tgaaaaacca taagaagaaa aagacgagga 300 aggctaaggc caaggcttgc ttattttctg cagtctcacc attaattctc accagaatca 360 tgcaacttga atctgctgca gaaatctgga agcatctacg ggaagaatat caaggcaatg 420 aaagagtcag aaatatgcag gtgatgaatc tgattcgaga atttgaaatg gtgaggatga 480 aggagtctca aaccataaaa gattatgcag aacaacttct taccatagca aacaaggtga 540 ggttgctagg taaagagttt tctgatgaaa gagttgttca aaaatttttg tcacacttcc 600 tgaaaaatat gaagctacaa tttcttcttt ggaaaacaca aaagatttgt caagtatcac 660 cttggcagaa ctactaaatg ctttacaagc tttggaacaa agaagactca tgaggcaagg 720 aagttctgta gaaggagctt ttcaagcaaa gacacagacc aatgaaggca acacaagaag 780 gaggaagaac aaaaagaaca acaataagcc aagcaacaac aacaatcaaa aagctggaac 840 ctatccaccc tgtcctcatt gcaagaaaac aaatcatcct caacaaaaat gttggtggag 900 accagatgtg aaatgcaaca aatgtggtag acagggacac atagaaagga tctgtagaac 960 tcaacagcag cagggagaaa ccaatgtagc agttgaacaa taccaggagg agcaactatt 1020 ttcagcaaca tgttttgcaa acggaaacac ctctgaaagc tggctcgtgg acagtggttg 1080 cacaaaccac atgacatatg atcaagatct ctttagggat attgatagga cagctatttc 1140 caaagtcaga attggaaatg gtgagtatat tccagtaaaa ggtaaaggaa cagtagctat 1200 tgaaagccta acaggtttaa agctcatttc tgatgttttg tttgtgcctg acattgacca 1260 aaatctgcta agtgttggac agcttgttga gaaagggttt aaagtttgtt ttgaagacaa 1320 aaattgcata atcaaggatg ctgaagatag agaggtgttc aacataaaaa tgaaaggcaa 1380 aagttttgcc ttgaatatgt tagaagatga gcaaattgtt gctgcacaac atgagaacaa 1440 tacaatgctt tggcataaaa gattagggca tttccaccac aatgccgtgt tttacatgaa 1500 gaagaatcag attgtagaag gactccctga tttggaagaa gaacttccta tatgtgcaac 1560 ctgtcaatat gggaagcaaa caagacttcc ttttcctcaa aaagcagcat ggaaatcaac 1620 acagaaacta caattggttc acacagatgt tagtcaatat gggaagcaaa caagacttcc 1680 ttttcctcaa ttgaaaggga gtaagtacta tattgcattt attgatgact tcacaagatt 1740 ttgttggatt tattttctca cttacaaatc tgaggttgct gatgtgtttt tgagatataa 1800 agccatggtt gaaaatcaaa gtgaatacat aatcaaggtt ataaggtcgg ataatggtac 1860 agaatatact tcagaaaaat tcaacgaatt ttgtgaagat gcagacatag atcaccagct 1920 cactgcacca tacaccccac aacaaaatgg ggtggtggaa agaaaaaata gaacaataat 1980 ggagatgaca agatgtcttt tgcatgagaa agagctgcca aaaagtttct gggctgaagc 2040 tgcaaataca gcagtatttt tgctaaataa actaccaaca aaagcattgc agaaacagac 2100 atcttttgag gcctggtttg gttataagcc tatgctaatg aatttaaaga cctttggttg 2160 cttgtgtttc tcttatgttc ctcaggtgaa aagagacaag ttagataaaa agtcagaacc 2220 aggaattttc attggataca gcagcacctc aaaagcttac aaaatctact tgccacaaaa 2280 taataaaatt gtggtaagta gagatgttaa gtttttggaa acggagaaat ggagctggga 2340 tgagcagaat cagcaatata ttgatgaaga tgttgatgaa cttccagtta aaggtttcag 2400 ggcacttttt gatatttatc aaaggtgtaa tatagttgtt cttgaacctg cagggtttgt 2460 tgaagctgct gaaaataaaa gatggagggt tgcaatgcag gaggagctaa atatgattga 2520 taagaacaac acttgggagc tagtagatag accttcacac aaaaaaccta ttggggttaa 2580 gtgggtttat agaaccaaac tcaactctga tggttctata aacaaacata aagcaaggct 2640 ggttgtcaaa gggtatgcac aaatgtttgg tgttgacttt ttggaaacct ttgcaccagt 2700 agctcgtttg gatacaatca ggatgttgtt ggctcttgca gctcaaagaa aatggaagat 2760 ttatcaacta gatgtgaagt cagcattttt gaatggctac ctggaggaag agatttttgt 2820 tgaacaacca gaaggttttg ctatcaaatg aaaagaagaa aaagtatacc ttcttaagaa 2880 ggccttgtat gggttaagac aagcctctag agcctggtac agcaggattg acactcacct 2940 gctaacttta ggctttcaca agagcttgag tgaatttaca ctctacatta agaagattga 3000 agaagatata ttaattgttt ctctatatgt tgatgatttg cttgtaacag gaagtaatgc 3060 agggtttgtg aacaaattca aggctgaaat ggagtaggtc tttgaaatga cagacctagg 3120 tgagatgtct tacttcttgg gaatggaagt acaccagaag cagaatgaga ttttcatctg 3180 ccaacaaaaa tatgccaaag aaattctgaa gaaattcaaa atggaggaat gcaaatctac 3240 atctacccct atgaaccaga aagagaagtt ctgtaaggag gacggtgctg aaaaggtaga 3300 tgaaggactt tatcgaagca tgattggatg cttaatgtac ttgactgcaa caagacccga 3360 tataatgcat gctgtaagtc tactttcgag atacatgcat tgtgctagtg aaattcattt 3420 ccaggcagca aagcgtgtga taagatatgt taaaggcact gtggattatg gcattaagtt 3480 cagttaagtt caaagtttca attttcatgg attttctgat agtgattggg ctggttgtgt 3540 tgacgatatg agaagtactt caggctattg ttttagcttt ggttctggtg ttttttcatg 3600 gagttcaagg aagcaagaag tcgtggctca atccacagct gaggcagagt atattgctgc 3660 tgctgcagct gtaaatcaag ccttatggct tagaaagttg ctgacagatt tggatatgaa 3720 gcaagaagtg agtacaaagg tgtttgtaga caaccaggcc actatatcta ttgcaaatga 3780 tccagttttt catggtaaaa caaagcactt caagattaaa ttgtattttc tgagggaagt 3840 acagaaagaa ggagatatac aactagtcta ctgcaataca gaaagtcaga atgcagatat 3900 tctgactaaa gctcttccta aaataagatt tgagtttcta cgagaaagac ttggagtttg 3960 cagctcctaa gtcaaggagg ag 3982 // ID COPMET_I repbase; DNA; EDCOT; 7285 BP. XX AC AC161863; XX DT 09-NOV-2006 (Rel. 11.11, Created) DT 09-APR-2007 (Rel. 12.05, Last updated, Version 2) XX DE Internal region of COPMET retroposon, from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed repeat; LTR retroposon; Medicago; GYPMET; KW internal portion; COPMET_I. XX NM GYPMET_I. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-7285 RA Shankar R. and Jurka J.; RT "COPMET: LTR retroposon from Medicago truncatula."; RL Repbase Reports 6(11), 559-559 (2006). XX DR EMBL/GenBank/DDBJ; AC161863; Positions 65555 72839. XX CC The internal region sequence resembles Copia type. XX FH Key Location/Qualifiers FT CDS 1739..2992 FT /product="COPMET_I_1p" FT /translation="SSAFKTFCLEIKTQLGKTIKVLRSDNAKEYFSTQFNS FT FLISHGITHQSSCPHTPQQNGVAERKHLHLVDAARTLLINAHAPLKFWGDA FT VLNCMPSSVLDNEIPHSLLFPKDPLYSVPLRVFGSACFVHDLSPGRDKLSP FT RAVKCVFWGYSRVQKGYRCYCPSTHRFYVYADVTFFEDTPFFTTPSTSDST FT SHSTSQVLPIPLFEPFVPTQRLPQSLTRPGFRRYGATYERRHVTIPESAPT FT DFDNIVQETTPTISDDSSSILILSPNVDPPDPIIDLPIALRKDNRSTSNPH FT PIYNFLSYHRLSPLHHAFVSAISTVSIPKTVKEALSHLGWRQAMIDEMNTL FT ESSSTWKLVPIPHGKSKVGCRWVFAIKVGPDGHVDRLIARLVAKGYTQIYN FT SCKNGICSCFLINGFYEPLAFVST" XX SQ Sequence 7285 BP; 2061 A; 1401 C; 1455 G; 2368 T; 0 other; aaagcctacc gacactattg tatcacactt tttattatta actaaatttt gaaattaaat 60 gttgattatt ctctatttat tatggttgat ttagtttcct tattttgttt tcatgagatt 120 ctctcgtgta tattgttgga aattccgcct taattgcggt ccgcccctag tcgcctaaat 180 tgtgaccttt ggttagcctt aattgcagcc tccaacacct tcattgtgtt ggctttgagg 240 gggtggaatt agtcccacat tgggtagata ctactcttga taagagttta taaagaggag 300 gcactcctca ccttacaagc cggttttgta aggatgagtt aggccccaaa tttcaacata 360 tataacttgc atacatcatt gtgaattatt caagttattc attctaaatt attcagattg 420 gtaccagagc tctctggtca ggtaccttcc actgttttgg tttagggttt cagccggcga 480 cccagtgttt agattggtac cagagctctc tggtcaggta ccttccgctg ttttggttta 540 gggtttcagc cggcgaccca gtgttgtttt taaacacagt cagagtgact gccaccggtg 600 acacgcgcca taccattgtg accgggacac tccgatctgc cttcattaga agtttctccg 660 tcataaggtt ccgcatgcgc cgccacgcga cgcctccgta tacggcgcgt gtgtgtcacg 720 tgccgccctc tgaacgcctg tttgcggcgg cgcttgtttc agtagactcg ttttttgttc 780 ctgattctgt tgggacacct tccagctttt gggtctcacg tttgaggcgc gtttcagtga 840 ttttttgctt cagctgtgtc tgttcttgag gttcttttcc tcttgctgca actgttcaga 900 aggtcttttt cattcattgt gcatatctgc acatttatca gtattgttga actgaacggt 960 ttacggtttg ctttttccgt tgtttgtatt tgatggctgc ccaaaaggtt tcaacttcgg 1020 ttacattggc tcatttcagt aattctacaa tctgcttatc tcattctatg ggatcacgga 1080 ttttagattc gggtgcttct gatcatgtag ttggtaatcc gtcacttatt tatgatttgt 1140 cacctcctaa aatatctcac aacattactc ttgctaatgg ttctaaggca caagttactg 1200 gtattaagct tcacccctgc catctctacc cttgcattat gtgttatttg tacctggctg 1260 ccctttcaat ttgatttcaa tcagtaggct tactcgttct ctcaattgtt ttataacatt 1320 tacatctctc tttataaaag accaaagtac aggaaatcaa attggagcag gctctgaatg 1380 acaaggtctc tgttaccttg aatcaccttc accaactgta tgcaatgttt atgcatctcc 1440 agatatcatt catcatcgtt tgggtcatcc aagtctagat aagttaaaag tgttggttcc 1500 ataactctca catttaaagt ctcttgattg tgagtcgtgt caacttggca aacatgttcg 1560 gacatctttt catagcagtg tcaataaaag atctaagcat gccttcgata ttgtgcattt 1620 tgatatttgg ggtcctagtc gcatgccttc taatttagga tacaggtatt atgttacttt 1680 catcgatgat ttctcgcgat gtacttggat aaccttattg aaggatagtt cagaatagtc 1740 tagtgcattt aagacttttt gtttagagat aaagactcag ttggggaaaa caatcaaagt 1800 tttgagaagt gacaatgcca aagaatactt ttctacacaa tttaactcct ttttgatttc 1860 tcatggtatc acacatcagt ctagttgtcc acacacaccg caacaaaatg gtgtcgctga 1920 gcggaaacat cttcatctag tagatgcagc tcgaacctta ttgatcaatg ctcatgcacc 1980 tttaaaattt tggggtgacg cggttctcaa ctgcatgcca tcatcggtct tggataatga 2040 gattcctcat tctctcttgt ttcctaagga ccccttgtat tctgtcccac ttcgagtttt 2100 tggctctgct tgttttgttc atgatctttc tcctggtcgt gataaattgt ctccacgggc 2160 tgtcaagtgt gtgttttggg ggtactccag agttcaaaaa gggtaccggt gttattgtcc 2220 atctacacat cgtttttatg tttatgcaga tgttactttc tttgaggata cacctttctt 2280 taccacacca agtacatcag attctacttc tcattctact tctcaggtgc taccaattcc 2340 tctatttgaa ccatttgttc ctactcagag acttccacag tcactgactc gtcctgggtt 2400 tcgtcgctat ggtgctactt atgaacgtcg gcatgtcaca attccagaaa gtgctcctac 2460 agattttgac aatattgtcc aagagactac ccctactatt tctgatgatt caagttctat 2520 tctaatcctt tcacccaatg ttgatccacc tgatcctata attgacttac ctattgctct 2580 tcgtaaagat aatcggtcta cttctaatcc tcatcctatt tataattttt tgagttatca 2640 tcgtctgtct ccattgcatc atgcttttgt gtctgctata tctactgtct ctattcctaa 2700 gaccgtcaag gaagcattat ctcatctagg atggaggcaa gcaatgattg atgaaatgaa 2760 tacattggag tctagtagta catggaagct tgttccaatt ccacatggga aatctaaagt 2820 tggttgtcga tgggtctttg ctattaaagt aggccctgat ggacatgtgg atcgtttgat 2880 agcccgatta gtagcaaaag gatacactca aatttataac agttgcaaaa atggcatttg 2940 ttcgtgtttt cttatcaatg gcttctatga accattggcc tttgtatcaa cttgatatta 3000 aaaagctttc ttgcatggtg acttggaaga ggagatttat atggagcaac cgcctggctt 3060 tattgctcag gggagtacga tcttgttttc aagttacaaa aatcattgta tggtctaaaa 3120 caatcacctc gagcttggtt tggaaaattc agcaaggtta ttcaatagtt tggcatgatt 3180 cgtagtgaaa cagatcattc tgtattcttt aaacgttcat ctttgaaccc agtcatttat 3240 cttgtagtat atgtagatga cattgttatc actggcaatg atcaagaagg cattaaagac 3300 ctaaagcaac gtttattcag ccactttcaa acaaaagatt taggtcgatt gtgttatttt 3360 cttgggattg aagtagcttg gtcccaagta ggcattgtta tttctcagag aaaatacgtt 3420 ttcgatatct tggaagaaac atggatgctt aattgtaaac cagatgatac tcatgtggac 3480 cccaatgtga agcttttacg gaaccaagga gatttgtatc ctaacccaag aagatacagg 3540 aggtaagttg ggaggctaaa ttatctcaat atgactagag catatatttc gtttgttttt 3600 agtgttgagt caatttttta tctcaccttg tgatagccat tggaatgctg tggttcggat 3660 cttgcggtat attaaagggt cgcctgaaaa aggacttgtt tattcagaca gaggccatac 3720 caatattgtt ggatattcag atgcaaattg ggcaggtgat gtgaatgata gaagatccac 3780 ttcgttattg tgttctaatg ggaggaaact taatttcatg gaaaagtaaa aagcaaactg 3840 ttgttgcaag gtcaagtaca gaggcggagt atcgtgctat ggcacttgct acttgtgaac 3900 tttaagtgtg ataatcagtc ggagttgtat cttacgtcaa atccaatttt tcatgagagg 3960 acaaaacaca gaagttgatt gtcgatttat cagagagaag ataatttccg gcatcattaa 4020 aacctcttca gtgagctcca atgattagct agccgatatc tttaccaaac ctctacgggg 4080 acctcagatt gattacatat gtaacaagct ggatgtatat gctccagctt gagggggagt 4140 gttgattatt ctctatttat tatggttgat ttagtttcct tattttgttt tcatgagaga 4200 ttctctcttg tatataagct tgcatacatc attgtgaatt attcaagtta ttcattctaa 4260 attattcaaa ttaaagagtc ccacatcgaa cgagagatgg cctcacaaag tgtttatagg 4320 tgggggcaat cctcacctca caagccggtt ttgtggagtt gtgttaggcc caaccacgat 4380 ttcaaagatg gtatcagagc ctcttcatca agatccattg ggccacctgc tgtcaggttt 4440 ccgctatcgg gccacccatc attcatttcc acgctctaga tgttcagtcc tgggcgtgag 4500 aaggtgtttt aaagagtctc acatcggaca ggaaatggcc tgacaaagtg tttataagtg 4560 gggacaatcc tcacatcaca agccggtttt gtggggttgt gttaggccca accacgattt 4620 ctaagattaa acaatcacac gaatacttaa tataaagaaa caagaccagg tcaataaata 4680 tatcataaat ggtacctgaa tagatagtca agaacaaata tttccacaat cctgcaaccc 4740 aactctgtga caatgctttc ataatcctct tcagtaggtg tgtttacctt cataggttta 4800 taccctatac caacaacgat attaattagg gatggaacat caccaaccaa cccaaaccta 4860 tttttctcaa ttctgacaaa cttagccgta gtattgtcag catttattga ttgataacca 4920 ttgtataata tctccattag caaaggagat gtcacagcac catctacaaa gaagtgcttc 4980 accaaggctt ccataattac atcttgtttt tcccaaaaca tttggtcctt tgaaatttgg 5040 ccactttctt ctatgaaagt acagaatctg caaatattga aaaatcatat tagttaatta 5100 gcaaacaaaa aatttgaggg agtgtgacga ccgttttttt tttgttgaat aacaaaacat 5160 gggtttcaaa atttcatttc tcataaatta agagtataac atttaaattc acaacattta 5220 tacaacatag actcctacaa aagcatcaaa tacaaactta gactcctgca acgtttgtac 5280 aacatttgta ctgttgaaac tgatttactt agctatatca gtcataggat ttgttcctat 5340 catgtagtaa attattccta tttgttaggg agtgctaatg gaattgactt agtgtttcca 5400 caattcacat ttaagttagt gtagtcattt tatttagttg ttttcatctc ttcgtaaggc 5460 tatattaaag ccacctcttt tgcacttgaa taataaggct atattaaagc cgcctctttt 5520 gcacttgaag aatagtgata aattcccttc tgttttactc tgacatgtac atcatgatat 5580 gcacataaaa aataaaaaaa cacttagatt ttcttatatc taatatttag cttgccaaca 5640 tatattctta aaacttacaa gttgaaatcc attaggaaaa tcataactta atcacacaat 5700 tcgtcatttt ctaggtccca tgactacata cttataaact tcatctgaat aacactgcac 5760 aagttcacta ggatcaataa aattagtaag agctcaagga taaccatcta atagtaagat 5820 cacgcacaat ttgatatgcc ctgggaagaa ccattgacac atgtgtataa gagaaggggt 5880 aaaatgggaa gcaaagaaga aaaaggggaa catgtaaaac cgttagtgaa tgggagcaaa 5940 aggaatgatg agctgttgat ttgagtaact aaatgggcac tcacagaatt tacaattcac 6000 ctttcttgtt cctccttcaa tagaaacaac atattgccat gttgaagccg ttacaaaagg 6060 ttgtgtgaaa aacagagtta aggaaggaaa attcgaaaaa agagttatgg gttatggagg 6120 agaaaacaaa aacgggttta ggtgagggaa gagagtgaac gacggcgaga actttgccgg 6180 aaaagggaac acggccgtcg ttcgtgaaac agtggcatgg ccgtcgttct tggttaaggt 6240 tgtttcaaaa caccgtggag ggagaaaggc aacgacaccg gccgtttcga agctgagaat 6300 ggatgaatga agaaagggaa cacggtggcc gtttttggtt agggtttttt tcgtgaaggt 6360 gggatgggaa gagaaagaat gaaaaaacca ggtcataact atatataggg aaccaggttt 6420 ttaatttgga cccaacccgg ttcgtaaagc ccaatttcaa ttttgccagc cgaactcatt 6480 tttcattacg ttccttcctg tacaggaact cgatcctaac cacaaaacac acaaaattga 6540 cccagaacaa gtacggagca cgccggtgag gctgtggcat gtaggatcgt ccgatcctac 6600 gacccggcac tcatttttta ctaccttgtt tgtgtcaatt atttggtatt cagagatcaa 6660 cctggggaga gaatgctgat ctgtttggtt tatacacaca tgaggtgaaa agggaaggag 6720 cagggttgga ggtgttaaga gagtatgttg atctgtttcg agaggtatca gaattgcctg 6780 agtatgttaa tctgtttcga gaggtatcag aattgcctcc acgcaacccg tatgatcatg 6840 ctattgaaat caaggaggcg actcgaattc ccaacatccg accctacaga taccggcaca 6900 gtcagaagga agcaattgat gcttttgcta cagacatgtt aatatcagga ctcgtcaggc 6960 ccacggtaag tcgatatgct agccctttaa ttcatgttaa gaaaagacat ggtagttggt 7020 ggttttgtac tgattatagg gctcttaata agattactac aaataaattt ccaattctgg 7080 tgattgatga gttgtgggga gcggtaaaat ttttaagatt ggatttgaaa ttagggtatc 7140 atcagattca aacgaaagag ggtgatattc acaagactga attttgaact catgaaggac 7200 attctgaata tctcgtaatg caccgcccac gtttcaagct ttgatgaatg atatttttaa 7260 gcctttccaa agaatatttt ttttg 7285 // ID Copia17-VV_I repbase; DNA; EDCOT; 6266 BP. XX AC AM481163; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia17-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6266 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-6266 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 683-683 (2007). XX DR Genbank; AM481163; Positions 915 7180. XX CC Positions [3318-3836] - Integrase core CC 'ACCAC' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 4429..5973 FT /product="Copia17-VV_I_1p" FT /translation="MNCKESELWYNAMKDEMSSMKCNDVWDLVELPNGAKT FT IGCKWVFKTKKDSLGNIKRYKARLVAKGFTQKEGIDYTETFSPVSKKDSLR FT IILALVAHFDLELQQMDVKTAFLNGELEEEVYMKQPEGFPSSDGEQLVCKL FT KKSIYGLKQASRQWYLKFHNIISSFSFVENVMDQCIYLKVSGSKICFLVLY FT VDDILLATNDKGLLHEVKQFLSKNFDMKDMGEASYVIGIKIHRDRFKGILG FT LSQETYINKVLERFRMKNCSPSVSPIVKGDRFNLNQCPKNDLEREQMKNIP FT YASAVGSLMYAQVCTRPDIAFAVGMLGRYQSNPGIDHWKAAKKVMRYLQGT FT KDYKLMYRRTSNLEVVGYSDSDFAGCVDSRKSTSGYIFILVGGAISWRSIK FT QTMTATSTMEAEFISCFEATSHGVWLKSFISGLRVMDSISRPLSIYCDNSA FT AVFMAKNNKSGSRSKHIDIKYLAIRERVKEKKVVIENISTELMIVDPLTKG FT MPPLKFKDHVVNMGLSSLM" XX SQ Sequence 6266 BP; 2008 A; 999 C; 1303 G; 1938 T; 18 other; tttggtatca gagccatgaa aaccttgcct ttgccttggt atctattttg caccagaatt 60 gtttagttaa tgtttccttt tctggttata aaatacaatc atacagtatg cttgatagga 120 atatccgttt tatgatctct caatgactac ttaaaaaaat taaaataccc atgcttgccg 180 acaccacaaa tgatggatca ttgctactgc cactgtagta tatttttaat aaagtcggct 240 ctggatggtg agcctccacc caatctatga gccatagctt tacttgaaag aacccatttg 300 ccaaacttgg agatcgactt ctccaattat ctccaatgat agccgttgtc cggcgacttt 360 ccgacagaaa tcctgcatca tttccgaagt gggtttgcct ccggtacacc catttccaaa 420 ggtgaccatg ataagggcta aggaagcaat ctggtgggtg tttaagaggc cattgtgact 480 gtgagtcatg caaagctttc ccggagcgct gccaggctgc tttgcggctg aagcatggtg 540 ytgcctgtga ggagaggcgc agtctatctg gtgcattcag tctccaccgt cattgcctca 600 gttcagccat ggtcggactt ggactagcgg cggtggattt ggtgccggaa aaagcggcag 660 cagtggcgtt catccactag tgatgcaggc tgcttgaaag gcactgcgtg gggctgttct 720 tgcatgtgtt gcaggcggct ccatagctag ctgataatgg tgcaatccat gtgggtggcg 780 gcgagtacat ggctactggt gatgaagtag tccacggggt ggcggaaaat taggatgatg 840 ggttttggtt gcagttgata acaataaaaa aaaaaactag agagagattg ggttctgcta 900 agtttttgga ccttggtata agtgactttt gggcctatga agcttattac atgacagtgg 960 cccattttta ctgaattaag gggctttaag tgttgggcta tgggttaatt gttaaaattg 1020 ggtcaattta agtacttatg gcccggttta aattattttt gattgggctt gtaactgatt 1080 gtgaaatttg ggccaattta ggcaattatg acmtgtttga aataatttta ttgggtttag 1140 gcacccattc ataatttgaa accttttaaa ttattctaaa ttatatgtga tttttataca 1200 tgcaaattaa attatttatt ttaatttata tgtttgtatg tgtaaaaata tagcctaaat 1260 ttagttagat atattaaaat tatatcatat agtatgcatg caattgttgc ctaaatttag 1320 ttagatatat taaaattata tcatatagta tgcatgcaat tgttgcctaa aatttagtta 1380 gatatattaa aattatatca tatagtttta atgtctagtg aatccatatg attttttaaa 1440 taattaagga atagccacag catccttaat tatataaaaa attatatatt aataaggatc 1500 acattatgga cattaattgt aattaactat ataaatatga tgtttttacc cccacagggt 1560 tttcattgtg tttatataat taattaggat aaaatattaa aattawtttt ttcctaattt 1620 acccacagga gttaggaaga attaatttaa taagtttatc ataaagatta tagacagaaa 1680 atatcaaact atattcataa taaatttcat gatttaataa aatagtttga taaagtctat 1740 cataaagata atgaatctta ttgaattaaa gatttagccc acaggcaatt tttaataaaa 1800 ttagattcaa ttttaagcat gttctacatt ggtaaagcat gaatttatat taaagcctca 1860 aatttttaat aagcttgtaa tccttttgtg cagttttacc tagcatatct gatattcgtt 1920 gtgaggttcc cgaacttaga ggagataact ttamgatatg gaaggagaga attcttcttc 1980 aattagggtg catggacata gattatgcta taaggaaaga tgaaccacat aagatcattg 2040 ataccagcac acctgaagaa atattattgt acgaacgcta ggagaaatct aattgcctta 2100 gcgtgatgta cattaagaca aaaatcagtg ctggtatacg tggttcaatc gagcaacatg 2160 agaatgtccg tgaattgcta aaggytattg acgagcaatt cgtcacttya gataaagcct 2220 tggcaagcac cctaattatg aagttcacat ccctgaagct caccggtata araggtgtgc 2280 gtgaacatat catggagatg agggacattg tggctcaatt gaagaaaccc gaggtagaaa 2340 tgtctgaatc tttcttggtg cactttatcc tyaacactct tccacctcag tatggacctt 2400 tcaaaatctc ttacaacaca cataaggata agtggtctat caatgaatcg atgaccatgt 2460 gtgttcaaga ggaaggaagg ttattgatgg aacagggaga aagtgccatg ctggtgacgc 2520 aaaggaaakg aaagaaagga aaatctcaag ctagtcagaa aggaaagcaa caaattcctc 2580 ccaaatctga cattaagaaa gacgaaaagt gttttttctr taaaaagaaa ggacacgtga 2640 agaagaaatg tctgaaattt caraattggc ttgagaagaa aggtaaccyt acctcatttg 2700 tttgctatga atctaatatg gttaatgtaa acaccaacac atggtggatt gattctggat 2760 ctataatcca catttcaaat tccttgcagg gtatgcaaaa cctaaggaag ccagtgacaa 2820 gtgagcaatt catcttatcc rgaaacaaga tgggctcgca tgtggaagca atagggatrt 2880 gttatttaac tttaaatagt ggttttrttt tagaattgca aaagaccttt tatgtaccaa 2940 gtttmtcacg aaacttgatt ttagtttcta gacttgtacc gtttggatat tcctttcatt 3000 tttcataaac atctttcagt ttgatttata aatctgaatg tgttgggaat ggtatcttgt 3060 ctgatggtct ttattgtata ttcttacaaa atgataccgc tcataattca ttacatgtcc 3120 aaactggcat taagagatgt gttgtaaaag aggattcctc tacattgtgg catcggagat 3180 taggtcatat ctccatagat agaatcaaaa gattggtgaa tgatggggta cttagtactc 3240 tagattttac tgactttgag acttgtgtgg actgcattaa gggtaagcag accaataagt 3300 caaagagagg tgctactagg agttccacca tactagagat catacatact gatatatgta 3360 gtcttgacat ggactctcat ggtcagaaat acttcatctc tttcatagat gatttctcac 3420 gatacatgca tctctacata cttcataata aaaatgaagc tttagatgcc tttaaagtct 3480 tcaaggcaga agtagagaaa caatatggta aacaaattaa gattgtgaga tcagatagag 3540 gtggagaata ttatggtaga tacttggaag atggacaatc acctgggcca tttgcgaagt 3600 ttcttcaaga gcatgggatt gttgcccaat acaccatgcc tggttcttca gaccaaaatg 3660 gtgtagcaga aagaagaaac cgaactttat tggacatggt gaggagtatg cttagcaact 3720 caaaacttcc taaattcttg tggactgaag cacttacgac agcagtgtat atattaaacc 3780 aagttccaac caaggctgtc ccaaagacgc catttgagtt attgaaaggt tggaaaccga 3840 gtttgcgaca tatgcgcgtt tggggatgct cgtctgaagt gagaatttat aatccacaag 3900 agaagaaact ggacccaagg actattagtg ggtatttcat tggatatgct gaaaagtcta 3960 aggggtacag attttattgt ccatctcaca gcactaggat tgtggaatcg agaaaatgct 4020 aaatttcttg aatatgactt ggtcagtgga agcgatcaat ttagaaacat agtttctgat 4080 attgatcata cagagtctca accttccact tcaagtgata gattgtttat tgttcataac 4140 acccctcaag tacaatcggg tgtagaacga acaatcactg aagttcaacc agtcgttgaa 4200 gttccacaag ctgttgacaa cattccaata gatcaagttg atcaggagtt tcctgatact 4260 yytggacaac aagttgaacc tcatacttcc ttagaagata ttggtgcaac cttaagaagg 4320 tctactcgaa ctaagaggtc agcaattcct aatgattatg tagtgtattt acaggaatgt 4380 gactacaata taggagccga aaatgatccc aaatcatttt cacaagccat gaattgcaaa 4440 gaatcagaat tgtggtacaa tgccatgaag gatgagatga gttccatgaa gtgcaacgat 4500 gtttgggacc ttgttgagtt gcctaatggt gcaaaaacca ttggttgtaa atgggttttt 4560 aagacaaaga aagactcatt aggcaacatt aagagataca aggccagact tgttgcaaag 4620 gggttcactc agaaagaagg aatcgattac acggaaacct tttctcctgt atctaagaaa 4680 gattccttgc gcattatatt ggcattagta gcccactttg atttagaatt gcaacaaatg 4740 gatgtgaaaa cagcatttct taatggagag ctagaggagg aggtttacat gaaacaacct 4800 gaaggattcc cctctagtga tggtgagcaa ttggtttgta agcttaagaa atccatatac 4860 ggtttgaagc aagcatcccg ccaatggtat ttaaaattcc ataacataat ttcttcattc 4920 agttttgttg aaaatgttat ggatcaatgc atatacctta aggtcagtgg gagtaaaatt 4980 tgttttcttg ttttatacgt ggatgacatc ttacttgcaa ccaatgataa gggtttactt 5040 catgaggtga aacaattcct ctctaaaaat ttcgacatga aggatatggg tgaggcatct 5100 tatgtcattg gcattaagat ccatagagac agatttaaag gtatcttagg tttgtctcaa 5160 gaaacctata tcaataaagt tttagagaga tttcggatga agaattgttc acctagtgtt 5220 tctcctatag tgaagggtga taggttcaat ctaaaccaat gcccgaaaaa cgatcttgag 5280 agggaacaaa tgaaaaacat tccatatgct tctgcagtcg gaagtttgat gtatgctcag 5340 gtctgcacaa ggcctgacat tgcatttgct gttggaatgt taggacgata tcagagtaac 5400 ccaggtatag accactggaa agctgcaaag aaagtgatga gatatcttca aggaaccaaa 5460 gattacaagc ttatgtatag acgaacaagc aatttagagg tagttggcta ctcagattca 5520 gactttgctg gctgtgttga ttcacgtaaa tcaacatctg gatacatttt tatattggtc 5580 ggtggagcta tatcttggag gagcattaag cagaccatga ctgctacttc tactatggaa 5640 gctgagttca tatcttgttt tgaggctact tcacatggtg tatggcttaa gagtttcatt 5700 tctgggctta gagttatgga ttcaatatct aggccattga gtatatattg cgacaattca 5760 gctgcagtct ttatggcaaa gaacaataaa agtggaagtc gaagcaagca catcgacatt 5820 aagtatctag ccataagaga acgtgttaaa gaaaaaaaag tggttattga gaacattagc 5880 actgaattga tgattgttga tcctttaact aagggcatgc caccattgaa attcaaggat 5940 catgtagtga acatgggact tagttccctt atgtagtttc tactgtacaa actcttatta 6000 tgatgttttc tcatattgat gcgcattttt tatttaattt tgagaaaatt caacttcatt 6060 ggaccaagaa tgaacatagg gtttattcat taagtaatat tgccacataa agtataatgt 6120 taagaaatga gtacactgca atacatggaa ggtaacactc gttaaataga ggacttatcg 6180 ccatgattca tgtatttgtt acttaatggg ataattgatg gactaaatta ggacattagg 6240 ttaaaggtgt ggaccaagtg ggagaa 6266 // ID Copia30-PTR_I repbase; DNA; EDCOT; 4406 BP. XX AC scaffold_225; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia30-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4406 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4406 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 236-236 (2007). XX DR Genome; scaffold_225; Positions 13712 18117. XX CC Positions [1604-2101] - Integrase core CC 'GCAT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 80..4405 FT /product="Copia30-PTR_I_1p" FT /translation="MTSSDSTTLPLFSSPQKIQSNSQPVSQRLEGHNYLPW FT SVQFQVFLRSHDLNGMIDGSEEPPTRTLPDHSSNPAYAIWFKKDNCVLSWL FT LASISEKLVSTVFNLKTSKQVWDSLQARFSSTSRSRIALLKRQLQTLVQGN FT RPCSAFLEDAKQLADQLAAAGKPVDDQDFITFLIGGLRPNFTPFITSYNFA FT CRDKDLSLDDFQSELLSFETLLEASTTVQTHNFAFAAKTSHYPKRKPAIIP FT AKFQPTSALPPSRGTSRIQPHSDRVPSYDRPQCQICDKYGHAALDCFQRFN FT FSFQGRRPPSELAAMAAEANTTFEQHTWYADSGANAHITANAADLTTLQPY FT NGMDTVQVGNGSGLMIHNTGSSLLNTSHNSFRLNNVLYCPQAASNLLSINQ FT FCLDNNCYFILTGTTFFVKENKTRRLLLQGLVENGLYPINGNKNCNKQFRC FT FTSKLGTKATRDQWHKRLGHPSNSTLNYLSSFLPIKDSPRKSSVCSSCQLG FT KAKKLPFSDSQRQSARPLALIHTDVWISPVTSVGGCRYYVLFIDDFSRFTW FT MYPMRFKSDVFSIFQQYKILVENLFSCTIQQLQSDNGGEYLSTEFQNFLAD FT HGIFHRLTCPYTSPQNGIAERKHRHIQEMGLTLLAQACLPNCYWVDAFFTS FT VYLINRLPTKVLNNITPYFVLHKTMPRYSDLRTFGCACYPYLRPYEKHKLA FT FRSKQCIFLGYSSQQKGYRCLDFATGRVFISRHVVFDEDTFPYLDKSHSST FT TSASNQSSGTTLSSNIVPLISHAPHFNFTPPVVITNSSATERLTYTESPPL FT QPSAIATPITTPSDPSFCPVIPPVLPSLILPSSPNQTPIPTPSDPSLCPVI FT PPVLPSPILPSFPNHVSSTDPGSSPTMSPVLPKQMVTRSQTGCLKPKEFPG FT FKTFYSTRHPLQAFSSIVIESEPTCFTKAVSNPHWKAAMGCEFDALLANNT FT WSLCPRPSHTHVVRNKWVYKLKRHPDGSIDRYKARLVAKGFEQIPGIDYFD FT TFSPVVKPTTIRLILSLAVSFKWNIRQLDVSNAFLHGILDEVVYMEQPKGY FT EDHTFPDHVCYLHKSIYGLKQAPRAWFTRLSQQLIDFGFSESKMDYSLFTY FT NSDTLRVFVLVYVDDIIITGSDSQAVRYFIDQLQNVFPIKDLGELSFFLGV FT EAIRNQAGLHLRQTKYITDLLNSTYMLGARPLRCPSSSGSKLSSTAGELLE FT NPTEYRRVVGALQYCTITRPDISYSVNQLCQFMHSPCTLHWIAVKRVLRYL FT KGTIEFGLLYTPGTIAMHAYCDSDWAGNPDDRRSTTGYGVFLGSNLISWCS FT KKQSVVSRSSTEAEYRSMAQTAAELYWLRMLLQELQITLSAAPSLWCDNVS FT AIALASNPVFHSRTKHIEIDYHFVREKVVNHDIQIQHISTQDQIADVFTKS FT HTANRFCFLRDKLCVCLLPHSLRGGIRA" XX SQ Sequence 4406 BP; 1213 A; 1022 C; 749 G; 1422 T; 0 other; gagcaaaaat aggttaacac ctaatttgcc acagcttccg cacattaaac acaaatccac 60 tctttcacta ttctcaacca tgacttcatc cgattccaca acacttcccc tgttctcttc 120 accccaaaag attcaatcca attcacaacc agtcagccaa agacttgaag gacataatta 180 cctgccatgg agtgttcaat ttcaagtttt tcttcgtagt catgatctaa atggtatgat 240 tgatggttct gaagagccgc caaccagaac tcttccagat cattcttcta atccagccta 300 cgcaatttgg ttcaaaaagg ataattgtgt tctcagctgg ctactagctt ccatttctga 360 gaagttagtt tctactgtct ttaatttaaa gacttccaaa caagtttggg actctcttca 420 ggcaagattc tcgtctacct caagatcccg cattgctctt cttaagagac aacttcagac 480 tcttgttcaa ggcaatcgtc catgttctgc atttcttgaa gatgctaaac agttagctga 540 ccaacttgct gctgcaggca aacctgtaga tgatcaagac ttcattacat ttttaattgg 600 aggacttcgt cccaacttta ctccctttat cacgtcctat aattttgctt gcagagataa 660 ggatctgtct ttggatgatt ttcaatctga acttctgagt tttgaaacat tacttgaagc 720 ttccactaca gtccaaactc ataattttgc ctttgctgca aaaacatccc attatccaaa 780 aaggaaacct gcaattattc ctgccaaatt ccaaccaact tctgcattac caccatctcg 840 aggcacttcc agaattcagc ctcatagtga tcgtgttcct tcatatgaca gaccacaatg 900 tcaaatctgt gacaaatatg gtcatgctgc gttggattgt tttcagcggt ttaatttttc 960 atttcaaggc agacgacctc cttctgaatt ggcagcaatg gctgctgaag ccaatactac 1020 ttttgagcaa catacttggt atgctgatag tggggctaac gctcacatta ctgctaatgc 1080 cgcagattta acaactctgc agccttataa tggtatggat actgtccaag tcgggaatgg 1140 ttcaggtttg atgattcata acactggttc ctccttgtta aatacatcac ataattcctt 1200 tcgtttgaat aatgtcctgt attgtcctca agctgcatct aatctgttgt ccattaatca 1260 attctgccta gacaataatt gctacttcat acttactgga actacttttt ttgtcaagga 1320 aaacaagacc agacgactgc tgctccaagg actggttgag aatggccttt atccaatcaa 1380 tgggaataag aattgcaaca agcaatttcg atgttttact tctaaattag ggacaaaagc 1440 cactagggat caatggcata aacgccttgg tcatccttcc aattccactt taaactattt 1500 atcttctttc ctgccaataa aagattcacc taggaaatcc agtgtttgct cttcctgcca 1560 gttagggaaa gctaaaaagc taccttttag tgattctcaa agacagtcgg ctagaccttt 1620 agccttgatt cacactgatg tctggatatc tcctgttact tcagtagggg gatgtcgata 1680 ttacgtttta ttcattgatg attttagtcg ctttacatgg atgtatccta tgcgtttcaa 1740 aagtgatgtc ttttccatat ttcaacaata taaaattctt gttgaaaatc tattctcctg 1800 tacaattcaa caactacaat ctgataatgg tggagaatac ttatcaacag aatttcaaaa 1860 ttttttagct gaccatggaa tatttcatcg cttgacatgt ccctatacat ccccacaaaa 1920 tgggattgct gaacgtaaac atcgccatat tcaagaaatg ggattgacct tattagcaca 1980 agcctgtctt ccaaactgtt attgggtaga tgccttcttc acttcagtat acctgatcaa 2040 tcgtttacca accaaagttc ttaataatat aacaccttac tttgtactcc acaaaactat 2100 gcctcgctac tctgatctgc gcacatttgg ttgtgcatgc tatccttatc tcagaccata 2160 tgaaaaacat aagttagctt ttagaagcaa gcaatgtatt ttcttagggt attcaagtca 2220 acaaaaaggt tatcgatgtt tagattttgc tacaggtagg gtgtttattt ccaggcatgt 2280 tgtttttgat gaagatactt tcccttactt ggataaaagt cactcttcta ccacttctgc 2340 gagcaaccag tcttcaggta ctactctttc ttccaatata gttcctttaa tttctcatgc 2400 accacatttc aattttactc ctccagttgt cattacaaac tcttctgcta ctgaacgtct 2460 tacttacact gaaagtccac ccttgcaacc ttctgcaatt gcaactccaa ttactacacc 2520 ttctgatcct agtttctgtc ctgtcatacc cccagtactg ccttccctaa tactgccttc 2580 ttccccaaat caaactccaa ttcctacacc ttctgatcct agtttatgtc ctgtcatacc 2640 cccagtactg ccttccccaa tactgccttc tttcccaaat catgtgtcgt caactgatcc 2700 tggttcctct cctacaatgt cccctgtact gcctaaacag atggttacca gatcccaaac 2760 aggatgtctt aagcctaaag agttccctgg ttttaaaacc ttttattcta cccgacatcc 2820 tctacaagct ttctccagta tagtcattga atctgaacct acttgtttca ccaaggcagt 2880 atccaatcca cattggaaag cagcaatggg atgtgaattt gatgcgttac tagcaaataa 2940 cacatggtct ctctgtcctc gaccttcaca tacacatgtt gtcaggaata aatgggtgta 3000 taagctaaag agacatcctg atggtagcat tgatcgctac aaagcaagac ttgtagctaa 3060 ggggtttgaa caaattcctg gtattgatta ctttgatact ttttcacctg tagtaaagcc 3120 tactaccatc agattaattc tctctcttgc agtctcgttt aaatggaata ttaggcaatt 3180 ggatgtttcc aatgcctttc tgcatgggat tctcgatgaa gttgtataca tggaacagcc 3240 caaaggttat gaggatcaca cctttcctga tcatgtatgc tatctacaca agtctattta 3300 tggtctcaaa caagctcctc gagcttggtt tactcgtctc tcacagcagc tgattgactt 3360 tggcttttca gagtccaaga tggactattc attgtttaca tacaattctg acactttacg 3420 tgtttttgtg ttagtatacg ttgatgacat aataatcaca ggttctgaca gtcaagcagt 3480 tcgttatttt attgatcaac tacagaatgt gtttccaatt aaagacttgg gtgaattaag 3540 cttctttctc ggtgttgaag caattaggaa tcaagctggt ttacatttgc gacagacgaa 3600 atatatcact gatttgctca acagtaccta tatgcttggt gcaaggcctc ttcgttgtcc 3660 atcatcttct ggctccaaac tctcatctac tgctggtgaa ctgttagaaa atccaaccga 3720 atatcgacga gttgtagggg ctcttcaata ctgcacaatc acaagaccag atatttccta 3780 ctcagtaaac caattatgtc agtttatgca ctctccgtgt acacttcact ggatagctgt 3840 taagcgtgtc ttacgctatc ttaaaggtac tatcgagttt ggtcttcttt acactccagg 3900 aacaatcgca atgcatgcct actgtgactc tgattgggca ggcaatcctg atgataggcg 3960 gagcaccact ggttatggtg tgtttcttgg ctctaacctt atctcttggt gcagcaaaaa 4020 gcagagtgtt gtctctcgat ctagcactga agctgaatat agaagcatgg ctcaaacagc 4080 tgctgaattg tactggcttc gcatgcttct tcaagaattg caaatcacgt tgtctgctgc 4140 tccaagctta tggtgtgaca atgtcagtgc tattgcatta gcttctaatc ctgtttttca 4200 ttcacgcacg aaacacatcg aaattgacta ccatttcgtc agggagaagg tggttaatca 4260 tgatattcaa attcagcata tctccacaca agaccaaatt gccgatgtct ttacaaaaag 4320 ccatactgca aatcgatttt gctttctcag agacaaactg tgtgtctgtc ttcttcccca 4380 cagtttgagg gggggtatta gagcat 4406 // ID Copia-2_Mad-I repbase; DNA; EDCOT; 4811 BP. XX AC ACYM01105711; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-2_Mad-I; KW Copia-2_Mad-LTR; Copia-2_Mad_. XX NM Copia-2_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4811 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1282-1282 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01105711; Positions 6354 1544. XX CC Positions [2088-2588] - Integrase core CC 'AAAGG' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 2553..4811 FT /product="Copia-2_Mad-I_1p" FT /translation="MKSPYQLLYGHLPHIGHFKIFGCACFPLLKPYNTSKL FT QPKTATCVFLGYAGDYKGFLCLNLIQNKMYISRHVLFDESTFPYEKFSVSV FT QSSPLVVSSPSFHPSPSLPCITLTNQVTPSLHTHASSSHPTTSMHSASSTP FT KSLPASSASDSLAASSASDSLETLTSVPHMHTSLPPSVDIPGTMPTQSPIH FT VDPDFQPDHLNVVLSLPLNVHPMVTRSKNGIVKPKAFSASIGSPSPVSEPK FT TFKAASKVVEWQTAMQEEIDALHSQKTWSLVPLPCDKNLVRCKWVYRIKKN FT ANGTVARYKARLVAKGYNQEEGVDYGETFSPVVKPTTIRLILALASQFHWH FT LRQLDVKNAFLHGVLQEDVYMEQPPGFLSNQYPSNYVCKLHKSLYGLKQAP FT RAWNDRFTSFLPALGFQSSHADPSLFVQSSPQGIVVLLLYVDDVILTGSSS FT QLIAQVIKALTAEFEMKDLGDLHYFLGLQISPTAEGLFVSQSKYISELVAK FT VDLQACKPCATPCLPYHRLLKDDGKPYHSPDQYRSIVGALQYLTFTRPDIA FT FSVNQACQFMHNPMESHVIAVKQIIRYLKGTPDYGIHFKPGPLSLLSYSDA FT DWAGDPNDRRSTSGFIVFLGSNPISWSSKKQHTVSRSSTEAEYRALAITAA FT ELSWIRQLLCDLHIPLSHAPLIHCDNLSAIALSTNPVFHAKSKHIEIDYHF FT VRERVTRGDLHVHHVSSAGQFADIFTKGLSAPLFQHHCGNLMLSSLKHEIE FT GG" XX SQ Sequence 4811 BP; 1250 A; 1144 C; 875 G; 1534 T; 8 other; tggtatcatc gccgatccga ctggcgcttc cgcatctcaa tcaaagcttt catttcttct 60 ctctatcctc tagtttgcaa actattctgt gataaaacaa aatattggcg ttgttcggat 120 attacagagc ctccagaact tcgtcttcgc cttctgccta tcaactgttt gttaaaaggt 180 ctcagtgaat tccttgtatc ccaactcaaa aatggttact gctgatcagc tacggattgt 240 tcagtctcca atcaccggtc ttatctctac catttctacg tcagttacag tcaagcttga 300 tgattccaac tacttaacct ggagttttca gattaaactt ctctttgaaa gtcatggtat 360 tctgggtttt gttgatggat cacgaaaatg tcctccaaga tttgatacgg atgctacaac 420 tgaagggatt gaaaccgatg attatcttgt atggaagatg catgattgtg ctcttatgca 480 attaatcatt gccaccttgt ctacaactgc aatgtcctgt attattggga gtaacagttc 540 tcatgaaatg tggggttaat cttgctgagc gattctcggt agtcacaaaa gcaacaatct 600 ttcagatgaa aactgagctc caaaacattc aaaaagggtc tgactctgtc tctgtgtatt 660 tgcaaaagat caaagatgcg agagatcatc ttgctgctgc aggagtaatt tttgatgatg 720 atgatatcat cattcttgcc ctgaaaggtc ttcctgcaga atttaacacc tttaggtgtg 780 ttataagagg cagagaaact ggcatttctc taaaagactt caggtctcaa ctgttagctg 840 aagaaactac aattggtcaa tcttttgagt cttctccatc ctttagtgct gcaatggttg 900 ctagtgctac cactgacaaa gggaaagctc tcgttcttga tcaagattct tctcattctg 960 ctgagtttgg atctagttct ggcatcaatg atcaatcata caagaacaat ggtggtggtt 1020 tccgttcccc tagttataat tctggtgggc agtattatac caatgggagt ccatctagca 1080 attttggcag tacttctcag ggttcttatc actatggcgg gtacaagggt aacaacttca 1140 gaggcaaagg acgaggcagg tcatatcagt ctggttcccg aacttataat ccttttccaa 1200 atccaagtcc ttgaactctt ggtgccccaa gaccatttca gtctcattgt cccgatcatc 1260 cctctgacat accaacttgt caaatatgca acaaaaaagg gcatgttgca gctgactgtt 1320 ttcagcgcca tagtacaccg gtctcagctt ctcattctcc gattcaatgc caaatttgct 1380 ggaagtttgg tcattccgct attcaatgct atcatcgagg gaattttgct tatcaaggaa 1440 ggccaccaac cccacatctc tctgccatgc atgttcaaca ccatccatct gctcctgatg 1500 atcaattctg ggttgcagac acaggggcaa catctcacat gacctctgac ctagctaact 1560 tggagttggc acgaccatat caaggcaatg acacgattac cactgccagt ggtgcaggtt 1620 tacctatttc tcacataggc tcttccaaat tgcatacatc ctctcatact cttgtgttac 1680 agaatgtttt tcatgttccc aagctatctc agcctttact ctccatttat caactttgta 1740 aggataatcg atgccgattt atatgtgatg atgtttcttt ttgggttcag gacaaattca 1800 cagggaaaat tcttctcaag gggctgtgta gggctggtta ttatcctata ccttttcaca 1860 tttctccgaa gctgccatct gcatcatctt cgtttcacaa atgctttctt gcacaaccag 1920 ttagtacaag tctatggcat cgacggctag gacacccctc taatgcaatc acttctgcca 1980 tactacatca acatcaactc tctgcatctt aagcctcttg taaaacagtt tgtacaccat 2040 gtctagaagg gaaatttacc aagttacctt tttcttttcc cacaaataaa tttgtacatc 2100 ccctagcaat cattcatagt gatgtatggg gccctgctcc tatcttgtca tatgaagggt 2160 ttagatacta tgtaacctty atagacgaat gtacacgatt tacatggatt tttcctttga 2220 aatwtaaatc agaagtgttt rctacatttg tcaagtttca tgcatttgtg tgtactcaat 2280 tttctgccaa agttaaaatt ttacaaagtg atggtggagg agagtatatt agctctcmgt 2340 ttcaacattt tctcaccacc aatggtatcc ttcatcacaa atcatgccca cacactcctg 2400 arcagaatgg attagctgaa cgwaaacata ggcacattgt agaaactgcc cttactctcc 2460 ttcaaactgc taagttacct aatctcttct ggtttcatgc ttgtgcmact gcagtctatc 2520 tmatcaatcg cttgccctgt gtcattcttc acatgaaatc tccttatcaa ctgttatatg 2580 gtcatcttcc acacattggt catttcaaaa tttttggttg tgcatgtttt cctctattga 2640 aaccatataa cacttccaaa ttacaaccca aaacagctac ttgtgtgttt ctgggctatg 2700 caggcgatta taaaggtttt ctatgtttaa atcttattca aaacaaaatg tacatatcta 2760 gacatgtgct ttttgatgaa tccacctttc catatgaaaa gttctctgtt tctgtccaat 2820 cctcaccttt ggtagtatca tctccatcat ttcatccttc tccgtcatta ccatgcatta 2880 cattgactaa tcaagtcaca ccatcacttc atactcatgc atcctcatct catcctacaa 2940 cttcaatgca ttcagcatct agtactccaa aatccttgcc tgcatctagt gcctcagatt 3000 ccttggctgc atctagtgcc tcagattcat tggaaacact tacatctgtc ccacatatgc 3060 atacttctct tcctccaagt gttgacatcc caggtaccat gcctacacag tcccccatcc 3120 atgtggatcc tgatttccaa cccgatcatc ttaatgttgt tctctcatta ccactgaatg 3180 tgcaccctat ggtcacacgt tccaagaatg gtattgtcaa accgaaggct ttctctgcta 3240 gcattggctc tccgtctcct gtctccgagc caaagacatt caaagctgct tctaaagttg 3300 tcgaatggca aactgcaatg caggaagaga tcgatgccct tcattctcaa aaaacatggt 3360 ccctagttcc tcttccatgt gacaagaact tggttagatg taaatgggta tatagaatca 3420 agaagaatgc caatggcact gtggcaagat ataaagcccg gcttgtagcc aaagggtaca 3480 accaagagga gggtgttgac tacggtgaaa cattcagtcc ggtggttaaa cctacaacca 3540 ttcgtcttat tcttgccttg gcatcacagt tccactggca cctccggcaa cttgatgtca 3600 aaaatgcctt cttacatggc gttttacagg aagatgtgta catggaacaa cctccaggat 3660 ttctcagcaa ccagtatcca tctaattatg tctgtaagct tcacaagtcc ctctacgggt 3720 taaaacaggc tccaagagca tggaatgata gatttacaag ttttctccct gccttgggat 3780 ttcagtcttc acatgccgat ccatcgttat ttgttcaatc ctctccacaa ggcattgttg 3840 tcttactgct ttatgtggat gatgttattt taactggcag ttcctctcag ttaatagctc 3900 aagtcatcaa agctcttact gctgaatttg aaatgaagga tttaggtgat ctccattatt 3960 tcttggggct gcaaattagt cccactgcag agggtttatt tgtttctcaa tctaaataca 4020 tcagtgagtt agttgccaag gtggatttac aggcttgtaa accttgtgct actccctgtt 4080 taccatatca tcggctctta aaggatgatg gcaagccata tcacagtcct gatcaataca 4140 gaagtatagt gggagctctt caatatctca catttacgag gcctgacata gccttctccg 4200 tgaatcaagc ctgccagttc atgcataatc ctatggagtc ccatgtcatt gcagtcaaac 4260 agatcatccg ctatctcaag ggtacaccag attatgggat acattttaaa cctggtcccc 4320 tctcccttct atcctatagt gatgccgact gggctgggga tccaaatgac cgccgttcca 4380 cctctggctt tattgttttt cttggatcca atcctatttc ctggtcctca aagaagcagc 4440 atacggtctc tcggtcatcc acagaggctg agtatagggc tcttgctatc acagctgctg 4500 aactctcttg gattcgacaa ttgctttgtg atttacatat tcctctctct cacgccccgt 4560 tgattcactg tgataacctt tcggccattg ctctttccac gaatcctgtc tttcatgcga 4620 agtctaaaca cattgagatt gattatcatt ttgttcgtga aagggtgaca cgaggagatc 4680 ttcatgttca tcatgtttct tctgctggtc agtttgctga tattttcaca aagggtttat 4740 ctgcaccctt gtttcaacat cactgtggca atctcatgct cagttcccta aagcatgaga 4800 ttgagggggg a 4811 // ID ENSPM_CA repbase; DNA; EDCOT; 1112 BP. XX AC AJ406381; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Cicer arietinum En/Spm-like DNA transposon ENSPM_CA, partial DE sequence. XX KW EnSpm; DNA transposon; Transposable Element; ENSPM_CA; KW En/Spm-like; partial sequence. XX OS Cicer arietinum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; OC Cicer. XX RN [1] RP 1-1112 RA Staginnus C., Huettel B., Desel C., Schmidt T. and Kahl G.; RT "A PCR-based assay to detect En/Spm-like transposon sequences in RT plants."; RL Chromosome Res 9(7), 591-605 (2001). XX DR Genbank; AJ406381; Positions 1 1112. XX SQ Sequence 1112 BP; 365 A; 191 C; 215 G; 341 T; 0 other; ttttaggaaa aggaaagatg agacagtgtt gcccccacaa aggttgacaa atgaagaaat 60 atgggaaaaa gtcaagcatt taccaagcat aattggacct ccatatgata atttgtcggg 120 gtatggagtt tttcacaatt ggacaaaaaa aacccatctt ttgggagtta ccgtattgga 180 aaacaaatct tctcccacat aatctagatg tcatgcatat tgagagaaat gtgtttctca 240 atatattgta tataataatg gacaccaagg gcaagacgaa tgacactttt aatgctagac 300 tggacttggc agatatttgt ttacggaaag atttagagct acaagatggt ggagggggga 360 agctaaaaaa tccgaaagaa aattacacac taaaacaaca acaaagatta tttgtgtgca 420 agtggataaa aaaactaaag ttaccaaatg ggtatgcctc taccttatct aaatgtgttg 480 atatgcgaga aacaaaatta tttggaatga aaagtcatga tttccacgtg ttcttgcaat 540 gcttgccccc aattgcattt aaagctctac caaaacctat ttggaacaca cttacagagt 600 ttagtcaatt ctttcgagag cttacttcac ctttactaaa agaggataat atacgtgtaa 660 tggagcaaaa tattccaatc attttgtgta agcttgaaca aatatttccc cctagtttct 720 ttgactctat ggagcatctt ccaattcatt tgtcgtttga agctagggtt ggtggtcctg 780 tgcaataccg atggatgtat ccttttgaaa ggttgggtca tctatcaatg tttttaatta 840 attaccatgc aatacttatt gtattaattt cttcaaatac ttttattagg tttcttcatg 900 ccttaaaaga caaagtcacc aacacaactg ctgttgaggg atctatttgt gaaggatact 960 tagtggagga gacctctaca tttgcatcgt actattatcc acccgatgtt ccatgtagga 1020 ggacaagaga gcaacgaaat gatgatgcag gtgaaggttc ttttgttgca caacccctat 1080 ctatattaat tatcccggat gtccttctgg aa 1112 // ID hAT-N5_Mad repbase; DNA; EDCOT; 1684 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW hAT-N5_Mad. XX NM hAT-N5_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1684 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1640-1640 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >95% identical to the consensus. The consensus can be incomplete, CC but encodes a part of transposase. XX FH Key Location/Qualifiers FT CDS 2..835 FT /product="hAT-N5_Mad_1p" FT /note="a part of transposase." FT /translation="KWLESDHVEVKLMATKMSIKFEKYWHKIHGAMAIAAI FT LDPRFKMKLIEYYFSLIYKENAPSEIEKVFDLAVKLVKEYELKHRPGLRSS FT ESSSSTDFPSQSCDFRVGDPLTSYDQFVMDSTIGNEQSDLDLYLGEKVLPR FT TQDFDILSWWKTNGIKYPILHQIARDILAIPVSTVASESSFSTGGRIISPH FT RSRLHSSTVEALMCSRDWLWGQMRGTYCKISYKLCICSKIYYFSLILIFTI FT EPDSNSTRVEDSSFGDDTDVNVVKTNLYFCFLLWSYW" XX SQ Sequence 1684 BP; 522 A; 233 C; 346 G; 583 T; 0 other; taagtggctt gagtctgacc atgttgaagt taagttaatg gcaacaaaga tgtcaatcaa 60 gtttgaaaag tattggcata aaattcatgg tgctatggca attgcagcta ttctggatcc 120 aaggttcaag atgaaattga tcgagtatta tttttctctt atttataaag agaatgctcc 180 atcggaaatt gagaaagtct ttgacttggc tgttaagttg gtcaaagagt atgaattgaa 240 gcatagacct gggcttcggt cttctgaatc ttcttcttcg actgattttc catcacagtc 300 atgtgatttc agagttggtg atcctttaac atcttatgac cagtttgtta tggattctac 360 catcggtaat gaacaatctg acttagacct atatttgggg gagaaagtct tgcctaggac 420 tcaagatttt gatatattgt cgtggtggaa gacaaatggg attaaatatc ctattttgca 480 tcagatagct cgagatattt tggctattcc tgtatctaca gtagcttcag agtcttcatt 540 tagtactggt ggtaggatta ttagtccaca ccgtagccga cttcattcaa gcacagtgga 600 agcactcatg tgttctcgag actggttgtg gggtcagatg cgaggtactt actgtaaaat 660 ttcatataaa ttatgtatat gttcaaaaat ttactatttt agcctaattt taatttttac 720 tattgaacca gattcaaact ctactcgtgt tgaagattct tcattcggtg atgatactga 780 tgtgaatgtg gtaaaaacta atctttattt ttgtttttta ctttggagtt attggtgata 840 ctcattcaat ttatgcatac taattcaatt atacatttct tttgtaggcc tcttttggtg 900 acaacgagtc gatgatactt tgtgattgaa cgtgttcgaa acacagattt caattagatg 960 aaattatatg aaataataga gggttaactc agttttgtga tgaattagat gaaatttggt 1020 tggtttcgta cggttgtttt ttgttatcgg aaacacagat ttatgagctg ttgctaaagg 1080 gtctgttgct ttaaaaatca ttcgggaatt cagaaataaa aaagctctac ttttactctt 1140 cctttaggct caattttctc aggttcctga acttccataa tttattggtt gctatacaga 1200 ataaaaaaaa ttgattggtt gctatacaga aaaatatcgt tcgtaaacta ttatttcaat 1260 tattggaatt atacgaggac ttaaatgatt aaaataggga aatgtatgct aaaatgtact 1320 tataacggtg tttaattgtc agaaaataaa aattatgaca aatttttctt ttgtaatttt 1380 caaattgtta aaaaaaataa tgtagacggg cgaaaaaaaa gggtaaatgg gtaaaaaaag 1440 gataaacggg cgaaaaaatg ggtaaacggg taaatggtta tggttatggt taaatgggta 1500 aatggttatg ggtaaatggg tacacggtta tgggtatgga taaccgttta taaacggtta 1560 tggttatggg tataaccatt tatgtaatta cccaacgggt aaacggttat gcgggtatga 1620 acataaacgg ttatgggtaa aataaccgcg gttacccgcc cgccataacc attgcccatc 1680 ccta 1684 // ID Copia-75_Mad-I repbase; DNA; EDCOT; 4998 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-75_Mad_; KW Copia-75_Mad-LTR; Copia-75_Mad-I. XX NM Copia-75_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4998 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1688-1688 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [2202-2702] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 366..4967 FT /product="Copia-75_Mad-I_1p" FT /translation="MVTAAQLQIVQSPITNLIPNVSVSVTVKLDDTNYLVW FT HYQMRLLLESHGIFGFVDGTRRCPTRFVEDLDVEGVESDEYQIWKMHDRAL FT MQLLIATLSTPAMSCVIGCSNSHEIWTNLKDRFSTITKASIFQLKTELQNI FT KKGSENVSQYLQRIKDVRDHLSAAGVSFDDDDIVILALKGLPLEYNTFRTV FT IRGRENVISLKDFRAQLLAEETTVEHAPVHESFTTAMTAQHTLSKGKALVL FT DDGSSNSLTTQYHTGSSSGGSSNSGGPYPSGGTYHSGNNTNNSGGYRGQHF FT RGRARGRHPFGNNFRFSGPNNSPGILGPARPHVSTCPEHNNDIPVCQICNK FT RGHIAVDCFQRHSSTIVTSSPVQCQICCKFGHSAMQCYHRANFSFQGRPPP FT SSITAMQANYQPSAPQEQFWVADTGATSHMTSDLSNLTFAAPFTGTDTITT FT ASGAGLQISHTGSSVLHTPKSVFQLKTVLHVPKLSQHLLSIYQLCKDNKCR FT FICDEFCFWIQDKITGKVLLQGLCRAGLYPIPLYIPSSILKQASPTPHLHK FT QQHCYLGQQVTTSLWHNRLGHPSNTVVSQMLQQSQVPFSVDRSKHVCVSCL FT QGKFTKLPFSFPANKSVKPLEIIHSDVWGPSPTLSIEGFKYYVLFIDECTR FT FTWIFPLMNKTEVFHTFVQFHSFIQTQFSTAIKVFQSDGGGEYIGTPFKQF FT LLDKGIVHHKSCPYTPEQNGLAERKHRHIIETALTLLQTAHLPSQFWFHAC FT AISVYLINRMPCQTLFRQSPYACLFQKSPVLTHLKVFGCSCFPMLRQYNTS FT KFQSKTAQCIFLGYAGQYKGYICFNPLTKKFYVSRHVIFDEHTYPYLTLIS FT QSHATQSPSLSSSHVIPPSVTLQNVVGSHTSSSSSTSLHLAPRAPESSSMI FT SSASESLASPTTAPELSNPSPTNPMPLPTPSTYPDMSPSPLMAPLSATQSP FT IPVDPDFQQESLSVVLPVPSVSFHPMQTRSKSGISKRKAFSASVTSSVVQL FT TEPSSYKTASKIPEWQVAMQDEIHALEAQQTWTLVPLPVGKNLVGCKWVYR FT LKKNPNGSIARYKARLVAKGYSQEEGIDYTETFSPVVKPTTVRLILALAAQ FT FNWSLKQLDVRNAFLHGDLLEEVYMSQPPGFVSSSHPSNYVCKLQKSLYGL FT KQAPRAWNEKFTSFLPGLGFNASLSDPSLFVKKHPTGIVILLLYVDDIILT FT GSSSSLISEVVSALTQAFDMKDLGNLHYFLGLQITYKSTGLFVSQTKYIQD FT LLAKVDMQDAKSCATPCLPYHRLSKTEGTLYHSPEQYRSIVGALQYLTFTR FT PDIAFAVNQCCQFMHNPLDIHVVAVKRILRYLSGTLDFGIHFNSGPLHLQA FT YSDADWAGDPNDRRSTSGYVVYLGNTPISWASKKQHTVSRSSTEAEYRALA FT ITAAEVSWIRKLLCDLHVPLYDAPVLFCDNISAIALSSNPVFHSRVKHIEI FT DYHFVRERVIRGDLAVQHVSSKEQFADILTKGLSISLFQDHCSNLMLGSHK FT HEIEGGCKGIKTQDQSNG" XX SQ Sequence 4998 BP; 1294 A; 1127 C; 948 G; 1628 T; 1 other; tggtatcctc gccgggtcgg cacgtctcga tcctgatcag gtgttgcttc tgctgtgttg 60 cttctgctgt gttgcttctg ctatcttcga ttctctcttc tcacttcatt ctctgtgttg 120 atggtatgaa ttcttctctc gtgaatcttt atttgtctgg cgaagtatga tctgcaattc 180 agttgtgttt cttgcacgca aactgtttga tgatatgtgt gaatgactct ttctctctga 240 atctcccaat tcttctcaac actttctgac tattactctg gcaaagtgaa gtgtgtgtaa 300 ttacgaaccc tagattctca atctcttcca gttttcttca atttttctcc aagaatttcg 360 acggtatggt gactgctgca caattacaga tagttcagtc tccaattaca aacctgattc 420 ctaatgtttc ggtttctgta acggtgaaac tagatgatac aaattacttg gtttggcatt 480 atcaaatgcg gttgcttctt gaaagtcatg gaatttttgg atttgtggat ggaacacgtc 540 gatgtccaac tcgttttgtt gaagatttag atgttgaagg tgttgaatct gatgagtacc 600 aaatctggaa aatgcatgac agagctctta tgcagctcct tattgccact ctctccactc 660 ctgcaatgtc gtgtgtcatt ggttgctcca attctcatga aatttggaca aatctgaagg 720 acagattctc tacgatcact aaagccagca tttttcaact caagactgag ttgcagaata 780 tcaagaaagg ctcagagaat gtttctcagt acttacagag gattaaagat gtccgagatc 840 atctctccgc tgctggagtt tcatttgatg atgatgatat tgtcatcctt gccttgaagg 900 ggctacctct tgagtataac acctttcgta cagttataag gggtcgagag aatgttatat 960 ctctcaagga ctttcgagct cagttacttg ctgaagaaac aactgttgag catgctccag 1020 ttcatgaatc atttactact gctatgacag cacaacatac tttgtccaaa ggaaaggcct 1080 tggtacttga tgacgggtct tctaattctc taactactca gtatcatact ggtagttcat 1140 ctggaggttc ttccaattct ggaggacctt atccttctgg tggcacctat cattccggta 1200 acaataccaa taattctggt ggctatagag gtcaacattt cagagggcga gcaagaggca 1260 ggcatccatt tggtaataat ttcagattct ctggtcctaa taatagtcct ggcattctag 1320 gccctgcgag accacatgtc tctacctgtc ccgagcacaa caatgatatc cctgtgtgtc 1380 agatttgcaa caaacgtggt catattgcgg ttgactgctt ccagcgacat tcttctacta 1440 ttgttacctc atcaccagtg caatgtcaga tctgttgcaa gtttggtcac tctgcaatgc 1500 agtgttatca tcgtgccaat ttctcatttc aaggaagacc tccaccatcc tccattactg 1560 caatgcaagc taactatcag ccatctgctc ctcaagaaca attttgggta gctgacactg 1620 gtgctacatc acacatgacg tctgatctgt ccaacctcac ttttgccgct ccattcactg 1680 gcactgacac aattaccact gcaagtggtg caggtttgca aatctcccat actggttctt 1740 cggttttgca tactccaaaa tctgtctttc aattaaagac tgtattgcat gttccgaaac 1800 tgtctcaaca tttgttgtct atctatcaac tgtgcaaaga caataaatgt cggtttattt 1860 gtgatgagtt ttgtttctgg attcaggaca agatcacagg gaaggttctt cttcagggac 1920 tgtgtagagc tggtctatat cccattccat tatacatacc atcatccatt ctcaaacaag 1980 catcaccgac acctcactta cacaaacagc aacattgtta ccttggtcaa caagtgacca 2040 caagcttgtg gcacaacaga ttaggacatc cctcaaacac tgttgtttct caaatgttgc 2100 aacaatctca agtcccattt tctgtggatc gttctaaaca tgtttgtgta tcctgtttgc 2160 aaggaaagtt tactaaactt cctttttcat ttcctgcaaa taaaagcgta aaacccttag 2220 aaatcataca cagtgatgtg tggggaccat cacctacttt gtccattgag ggttttaaat 2280 actatgtact tttcattgat gaatgtacca ggtttacctg gatatttcct ttaatgaata 2340 aaactgaggt gtttcatacc tttgtgcagt ttcattcttt tatacaaact caattttcaa 2400 ctgcaattaa ggtttttcaa agtgatggtg gtggtgagta catcggtacc cctttcaaac 2460 agtttttact agataaaggc attgtgcatc ataaatcttg tccttataca cctgagcaaa 2520 atggccttgc cgagagaaag cataggcaca ttatagaaac tgctctcact cttcttcaaa 2580 cagctcattt gccttcacaa ttttggttcc atgcctgtgc catttctgtt tatttaataa 2640 atagaatgcc atgtcaaact ttgtttaggc aatctcccta tgcttgtttg tttcagaaat 2700 caccagtgtt gacacattta aaggtctttg gatgtagttg ttttcccatg ttgagacagt 2760 acaatacttc taagtttcag tccaaaactg cacagtgcat atttttggga tatgctggcc 2820 aatataaagg atatatctgt tttaatcccc ttaccaaaaa attttatgtg tcgagacacg 2880 tgatctttga tgaacacact tatccctatt tgactctcat ttctcaatct catgctacac 2940 agtcaccatc actgtcttcc tcacatgtta taccaccatc agtcacactt caaaatgttg 3000 ttggatcaca cacmtcttca tcatcatcta catcattaca tttagcccct cgagctccag 3060 agtcttcttc tatgatctct agtgcttcag agtctttggc atctcccact acagctccag 3120 agttatcgaa tccttcaccc accaatccta tgcctttgcc tacaccttct acttacccag 3180 atatgtcacc ctcacccttg atggctcctc tctcagctac acagtccccg atccctgttg 3240 atcctgattt tcagcaagaa agtctcagtg tcgtactgcc agtaccttct gtcagttttc 3300 atccaatgca aacaaggtcc aagagtggga tttctaagag aaaagctttc tcagcttctg 3360 tcacctcatc agtcgtgcaa cttacagaac catcttcgta taaaacagct agtaaaatcc 3420 ctgaatggca ggttgccatg caagatgaga ttcatgcttt ggaagcccaa cagacttgga 3480 cacttgtacc tctcccagtt ggcaagaact tggttggttg taagtgggtg tacaggctta 3540 agaagaatcc aaatgggtct atagcgaggt ataaagctcg ccttgtagct aaaggctaca 3600 gtcaagagga aggcatagat tatactgaga cttttagtcc cgtagtcaag ccaaccactg 3660 tcaggttaat tctagcactt gcagctcagt ttaattggag tttaaaacaa ttggatgttc 3720 gaaatgcatt tttacatggt gatctccttg aagaagttta tatgagtcaa cctccggggt 3780 ttgtgagctc ttctcatcct tccaattatg tgtgcaaact tcaaaaatcc ttgtatggcc 3840 ttaaacaggc ccccagggca tggaatgaga aatttacgag tttcttaccg ggtttaggct 3900 ttaatgcctc tctttccgat ccttctttgt ttgttaagaa gcaccctact ggtattgtga 3960 ttttattact ctatgtggat gatatcatcc taactggcag cagttcttct cttatttctg 4020 aggtcgtttc agccttgaca caagcattcg atatgaagga tttgggtaac ttacattact 4080 tcttaggttt gcagattact tacaagagca caggcttgtt tgtttctcaa accaagtata 4140 ttcaggatct tctagccaag gtggatatgc aagatgccaa atcatgtgct acaccctgtc 4200 tcccttatca caggttatcc aagaccgaag gcacattgta tcatagtccc gaacaatatc 4260 gcagtattgt tggcgcactg caatatttga cctttaccag gccagatatt gcatttgcag 4320 tcaatcaatg ctgtcaattt atgcacaatc ctctggatat tcatgtagtt gcagtgaaac 4380 ggattttacg atatctcagt ggcactcttg acttcggtat tcatttcaat tctggaccac 4440 tacatcttca agcttatagt gatgcggatt gggccgggga tcctaatgat cgacggtcaa 4500 cgtctggcta tgttgtttat cttggtaaca ctcctatttc ttgggcttcc aagaaacaac 4560 acacggtgtc gagatcctct actgaggccg aatacagagc acttgccatt actgctgcag 4620 aggtctcttg gatacggaag cttctatgtg accttcatgt tcctttatat gatgctcccg 4680 tcttgttctg tgataatatt tcagccatag cattgtcctc taatccagtc tttcattccc 4740 gagtaaagca tattgagata gactaccatt ttgtccggga gcgtgttatc cgaggtgatc 4800 tagctgtgca acatgtctct tccaaggagc aatttgctga cattcttact aaaggcttgt 4860 ctatttcttt gtttcaagat cattgttcca atctcatgct tggttctcat aagcatgaga 4920 ttgagggggg atgtaaaggt ataaaaacac aggatcaatc caatggctga tgtgctacca 4980 tgtgtcaata gattaagc 4998 // ID Gypsy-24_VV-I repbase; DNA; EDCOT; 4633 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-24_VV_; KW Gypsy-24_VV-LTR; Gypsy-24_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4633 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 13169178 13164546. XX CC Positions [1720-2208] - Reverse transcriptase CC Positions [3525-4019] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 24..1319 FT /product="Gypsy-24_VV-I_2p" FT /translation="MASNKERIEQLEAGIGSIHDNVSRIEMGMADKFQQLE FT TTLHRVMETVSISREEVVGSTGGRRRDSHHSGRAENSTPMFQSKFAKLEFP FT RFAAGDPTMWLTKVKQFFDYQETPGTQKVQYAAYHLEDEANEWWQATKRAY FT AEEEAEITWEVFEEELWARFGPTECEDFDEALSKIKQVRTFQDYQREFERL FT VNKVQGWTQKALVGTFMGGLHPSIADGIRMFRPKSLKEAISLARMKDEQLQ FT RQRRTQPNTPQIQRNTQQNSKGSLTTKRLSWEEIRKKRSLGLCFSCDERYT FT LGHKCRQPQLLLMEGELGWESSEMEEPLVEQEPEISLYALVGWSESRTMRI FT YAQIGQHQLVALIDSGSTHNFISEKMATMLQLPVGPTRPFPVRVANGTPMQ FT CQWKYETVCVSLGGVFFFLNSFRFTTNQSGFSVGSTMA" FT CDS 1363..2925 FT /product="Gypsy-24_VV-I_1p" FT /translation="MEFEWRSQNCVLQGLRTTPIQPVDFQCLSKEARQGHA FT LFAIYATEEGNSTPVQQELKELIEAFDDIFQAPSQLPPQRDIEHQITLKEG FT TDPINVRPYRYAYFQKDEIERQVSDMLNSGLIRPSSSPFSSPVLLVKKKDG FT SWRFCTDYRALNAATIKDRFPIPTVEDMLDELHGAAYFTKLDLTAGYHQVR FT IHPPDIYKTAFRTHNGHYEYLVMPFGLCNAPSTFQALMNSVFRPFLHKFVL FT VFFDDILVYSSSWQEHLQHVKTIFKLLRQHQLFVKFKKCEFGKHELEYLGH FT IISADGVKVDQSKIQAMLDWPRPTTVTELRAFLGLTGYYRKFVHNYGIIAR FT ALTNLLKKGKFQWDEAAKKAFENLKAAMTTTPTLALPDFSSPFVIQTDASG FT DGIGAVLSQNGRPIAFMSRALGVSKQSLSTYAREMLAIIVAIQTWRPYLLG FT RRFTIQTDQRSLKYLLKQRILTPEQQKWMSKLVGYDYEIVYKPGKTNQAVD FT ALSRNMTSPCLNVFFVPQVQVWDEI" XX SQ Sequence 4633 BP; 1284 A; 1109 C; 1079 G; 1161 T; 0 other; tttggtatca gagccaatca acaatggctt ccaacaagga aagaattgag caattagagg 60 ctggaattgg ctcaatccac gacaatgtca gccgcattga gatgggtatg gccgataagt 120 tccaacaact ggaaaccaca ctacaccgcg tgatggaaac tgtctcaatc tccagggagg 180 aagtcgtcgg atctaccgga gggcggcgcc gcgacagcca tcactcggga agggcagaaa 240 acagtacacc catgtttcaa tccaaatttg ccaaactaga attcccacga tttgcagcag 300 gggatccaac tatgtggctt accaaagtca aacaattctt tgattaccaa gaaacacctg 360 gaacacaaaa ggtgcagtac gctgcctacc acttggagga tgaagctaat gagtggtggc 420 aagccaccaa gcgggcttat gcagaggagg aggccgagat aacctgggaa gtctttgagg 480 aggaattgtg ggcccgcttt ggacctactg agtgtgaaga ctttgatgag gccctatcta 540 agatcaaaca ggtcaggact ttccaagact accagcggga atttgagagg cttgtcaaca 600 aggttcaggg atggactcaa aaggctttgg tgggcacgtt tatgggtggg ttacatccgt 660 ccattgctga tggaatacga atgtttcgac ctaaatcact aaaagaagcc attagcctag 720 ctcgcatgaa ggatgaacag ctacaacgcc aaaggcgaac ccaacccaac actccccaga 780 tacaaagaaa cacacaacag aattcaaagg gatcactgac aaccaagcga ctcagttggg 840 aggaaatacg caagaagcga agtcttggcc tttgtttcag ttgtgatgag cgctacaccc 900 ttggacataa atgccgccag ccgcagctac tcctcatgga aggcgagttg gggtgggaat 960 ccagtgaaat ggaagaacct ttggtggaac aagaacctga aatctccctc tatgctttgg 1020 tgggttggag tgaaagccga accatgcgga tttatgcgca aattgggcaa catcagcttg 1080 tggcgttgat agatagtggt tctactcata actttatcag tgagaaaatg gccaccatgt 1140 tacagcttcc ggttggtccc acccggcctt ttccggtacg cgtcgccaac ggaacaccaa 1200 tgcagtgcca atggaaatac gagacagtat gtgtatcact cgggggagtt ttttttttcc 1260 ttaactcttt tcgctttacc actaaccagt ctggatttag tgttgggagt acaatggctt 1320 gagttgttag gttcggtggt ttgcgattgg agaaatctca ccatggaatt tgagtggagg 1380 agccaaaatt gtgtgttgca gggactcagg acaacaccca tccaacctgt agattttcaa 1440 tgcctctcta aggaagctcg ccaaggacat gctctatttg ccatatatgc tacagaagag 1500 ggcaattcaa cgcctgtaca gcaagaactc aaagaattaa tcgaggcatt cgatgatatt 1560 tttcaggcac cctcacagct gcctcctcaa cgagatattg agcaccaaat cactctgaaa 1620 gagggcaccg acccaatcaa cgtccgaccc tatcgctatg cctacttcca gaaggacgag 1680 attgagcggc aagtgagtga catgttgaat tcggggttga ttcgccccag ttccagtcca 1740 ttctcttcac cagtgctctt ggtaaaaaag aaagacggat cctggcggtt ctgcacagat 1800 tatagagcct tgaacgcggc aacaataaaa gacagatttc caattcctac agtagaagac 1860 atgctggatg aacttcatgg agctgcctat tttactaaac tcgatctcac tgccggttac 1920 catcaagtgc gaattcatcc acctgacatt tacaagacgg cattcagaac acacaacgga 1980 cactatgaat atttagtgat gccgtttggg ctatgcaacg ccccgtccac atttcaagcc 2040 ttgatgaact cagtcttccg accttttctt cataagtttg tgctggtatt ttttgacgat 2100 atactggttt acagctcgtc ttggcaggag cacctacaac atgtgaagac aatatttaag 2160 ctgctgcggc aacaccaact ctttgtcaaa tttaaaaaat gcgagtttgg gaaacacgag 2220 ctcgaatact taggccatat catctctgct gacggtgtga aagtagacca atcgaagatc 2280 caagcaatgt tggattggcc acgaccgaca acagtcaccg agctccgggc attcttagga 2340 cttactggat attaccgtaa gttcgttcac aattatggca ttatagctcg tgcactcact 2400 aatctcctta aaaaaggaaa atttcagtgg gatgaagctg caaagaaagc attcgagaat 2460 cttaaggcgg ccatgaccac tactcctaca ctggccttac ccgacttcag ttcgccattt 2520 gtcattcaaa ccgacgcttc gggtgatgga attggtgctg tcttatctca gaatgggcgc 2580 ccaatcgcat tcatgagccg tgccctggga gtttccaaac aatccttgtc aacctatgct 2640 cgtgagatgt tggcaatcat tgtggcgata caaacttgga gaccttacct ccttggcagg 2700 aggttcacca ttcaaactga ccagcggagc ttgaaatacc tcttgaaaca acgaattcta 2760 actcctgagc agcagaaatg gatgtccaag ttggtgggct acgattatga gatcgtatac 2820 aaaccgggga aaaccaacca agcagttgat gcactttccc ggaacatgac cagtccatgt 2880 ttaaatgttt tttttgttcc tcaggtacaa gtttgggatg agatttgacg tgaagcaaac 2940 tctaacccat acatgcaacg tattgggcag ctagccacaa aacaaccaag acaaccttac 3000 caatggcgca atggactggt ctgctacaac aattgcattg tggtgccacc aggttcgcct 3060 ctaattcacc gtctcctgcg tgaatttcat gacactccaa taggtggaca ctctgggatc 3120 ttgcggacct ataaacgact ctcccagcaa ttttattggc cctctatgcg ccgttcagtc 3180 catcagtacg tggcggcttg cgatgtgtgc caaaaagcca aagcagaaac tatgtctccg 3240 gcaggtctct tatagccctt acccattcct tgtcaagttt gggatgatat cacaatggac 3300 ttcatcgacg gcctacctcg atcggatggg aagacttagc ctacctcgat cggatgggaa 3360 gacttcaatc atggttgttg ttgataggct aagtaagtcc gctcatttca tcgcaatagc 3420 tcacccttac actgccaaaa cccttgctaa caagtttgtg gaaggggtgg tcaagttgca 3480 tggtatgcca cgctaaagca gaaactatgt ctccggtagg tctcttacag cccttaccca 3540 ttccttgtca agtttgggat gatatcacaa tggacttcat cgatggccta cctcgatcag 3600 atgggaagac ttcaatcatg gttgttgttg ataggctaag taagtccgct catttcatcg 3660 caatagctca cccttacact gccaaaaccc ttgctaacaa gtttgtggaa ggggtggtca 3720 agttgcatgg tatgccacgc tctattatta gcgaccgaga tcctgtgttt attagtaatt 3780 tttggcaaga gtttctcaaa ttgtcaggca ccaagctacg catgacatcc gcctatcatc 3840 cccaaagcga cggccaaacc gagatcgtga atcgttgcat tgaacaatac cttcgctgtt 3900 ttgtgcacca caagcctcgt cattggaatt ctcttcttcc atgggccgaa tattggtaca 3960 ataccaccta ccattcctct attggaatga ctccattcca agccctgtat ggccgtcctc 4020 cgccagccat tcctagttat gaaattggct catgccccat cgaagagctt gatgatcaga 4080 tgacagcacg ggatgagctg cttcaggaac ttaaggcgca tttacatgca gcaaataatc 4140 gcatgaagta agcagctgat aaaaaacggc gtgaagtcaa ttttgaggtt ggcgattgga 4200 tctatctttg cctacagcct tatcggcaac agtcggtctt ccgccgaact tcacacaaat 4260 tatccaatcg ttattacggg ccttaccaga ttgaagagcg cattggaccg gtagcttata 4320 aattgaagct ctcgccagga tctcggatac acccggtgtt ccatgtgtcg ttgcttaaga 4380 aaaaaatagg ggaggttgct attgccaatg acgaacttcc accactgaca gaagaaggcg 4440 tgattcgctt acaaccacga aaggtgttgt ctactagatg ggttaataag ggctcaacct 4500 ccgcttccga gagtttggta ttgtgggaag gcttaccaga aaaagaagcc acttgggaag 4560 actcccagca gctcctgcgc agctttccta atctgaacct tgaggacaag gttctcattg 4620 agagggggag tat 4633 // ID Copia-2_SL-I repbase; DNA; EDCOT; 4071 BP. XX AC AC243710; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the tomato genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-2_SL_; KW Copia-2_SL-LTR; Copia-2_SL-I. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-4071 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the tomato genome."; RL Direct Submission to RU (22-JAN-2011). XX DR Genome; AC243710; Positions 104285 108355. XX CC Positions [1415-1942] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 50..3970 FT /product="Copia-2_SL-I_1p" FT /translation="MSALNVKIDKFTGRNSFSLWQIKMRALLKQQGFWAPL FT SKDKNAVVTPEMAILEEKAHSTIMLCLADDVITEVSDEETAAGLWLKLESL FT YMTKSLTNKLLLKQRLFGLRMAEGTQLREHLEQLNTLLLELRNIDVKIEDE FT DAALILLVSLPMSFENFVQSFIVGKDTVSLEEVRSALHSRELRHKANGTST FT DIQPSGLFTSSRKGRKNGGKKNKPMSKGAKPDDVCNYCKEKGHWKFDCPKK FT KKQSEKQSVSAAVAEEDTNSEEDIALVADEHTHHSDVWVLDSGASYHICPR FT REWFTTYEQVDGGSISMANSSVCKVVGTGSIKIRTHDGSFCTLNEVRHVPL FT MTKNLISLSLLDSKGFSWSGKDGVLRVWKGSNLILKGVMRGTLYFLQGSTV FT TGSAHVASSEFHQKDMTKLWHIRLGHMGERGMQILSKEDLLAGHKVKSLEF FT CEHCVFGKLHRNKFPKAIHRTKGTLDYIHSDCWGSCRVESLGGCRFFVSII FT DDYSRMTWVYMMKHKSEAFQKFKEWKILMENQTGKKIKRLRTDNGLEFCWS FT EFDQFCKDEGIARHRTVRNTPQQNGVAERMNQTLLERARCMLSNAGLDRRF FT WAEAVSTACYLINRGPHTGIQCKTPMEMWSGKAADYSNLKAFGCTAYYHVS FT EGKLEPRAKKGVFVGYGDGVKGFRIWSPAEKRVIMSRNVVFDESPLLRTIV FT KPTTTSETGSLDKQVEFQVIQNESDLKEPEEEDQEPQTETDIPESMPSDIH FT QSIAQDRPRRVGVRPPTRYGFEDMVGYALQVAEEVDTSEPSTYKEAILSSD FT SEKWFAAMGDEMESLHKNQTWDLVIQPSGRKIITCKWVFKKKEGISPAEGV FT KYKARVVARGFNQREGVDYNEIFSPVVRHTSIRVLLAIVAHQNLELEQLDV FT KTAFLHGELEEEIYMTQPDGFQVPGKENHVCKLKKSLYGLKQSPRQWYKRF FT DSYMVKLGYTRSSYDCCVYYNRLNDDSFIYLVLYVDDMLIAAKKKYDIQKL FT KGLLSAEFEMKDLGAARKILGMEIIRDRERRKLFLSQRSYIQKVLARFGMS FT SSKPIDTPSAANIHLTAMFAPQSEEEKEYMSRVPYASAVGSLMYAMVCTRP FT DLAHAVSVVSRFMGQPGREHWQAVKRIFRYLRGTSDVGLIYGGDTQCLVTG FT YSDSDYAGDVDTRRSMTGYVFTLGGSVVSWKATLQPTVTLSTTEAEYMALT FT EAAKEGIWLKGLVSDLGLHHDQATVYCDSLSAICLAKDQVHHERTKHIDVR FT YHFLRSEKRIKVKKVGTADNPADMFTKPVPQSKFQHCLDLLNIRSC" XX SQ Sequence 4071 BP; 1184 A; 721 C; 1106 G; 1060 T; 0 other; aattggtatc agagcctctc ggttaatcgg tgttcttgga gaattcgaga tgtctgcttt 60 gaacgtgaaa atcgacaaat tcacagggag gaacagtttc agtttatggc agatcaagat 120 gcgggccttg ttgaaacagc aaggcttctg ggcgccgttg tcgaaagaca agaacgccgt 180 cgttactcct gagatggcga ttctggagga aaaggcgcac tcgacgatca tgctgtgtct 240 cgcggatgac gtcatcacgg aggtctcgga tgaagagact gctgctggtc tgtggttgaa 300 gctggagagt ttgtacatga caaaatctct aaccaacaag ctgcttctga aacaacgtct 360 attcggttta cgaatggctg aaggtacaca actcagggaa cacttagagc aattgaatac 420 tttgttatta gaattgcgta atatcgatgt gaagatcgag gatgaagatg ctgccctgat 480 tctgttagta tctctcccaa tgtcgtttga gaattttgtt caatcgttca ttgttgggaa 540 agatactgtg tcactggaag aagtcagatc agcccttcat agcagggaat tacggcataa 600 ggctaacggc acaagtacgg acatacagcc ttccggtctg ttcaccagta gcagaaaggg 660 aaggaaaaac ggcggaaaga aaaataagcc gatgtcgaag ggtgcaaagc cggatgatgt 720 ttgtaattac tgcaaggaga agggacattg gaaatttgat tgtccgaaga agaagaagca 780 atcggaaaaa caatcagtgt ctgctgctgt tgctgaagaa gacaccaatt ctgaagaaga 840 tattgcccta gttgcggatg agcacactca tcattcagat gtgtgggttc ttgattctgg 900 ggcatcctat cacatctgtc ctaggagaga gtggttcacg acttatgagc aggtagacgg 960 aggcagcatc tcgatggcca acagttctgt ctgcaaggtg gttgggacag gctcgatcaa 1020 gataaggaca catgacggta gcttctgcac attgaacgag gtcaggcacg ttccattgat 1080 gacgaaaaat ctgatatctc tcagtctttt ggacagcaag ggattcagct ggtcgggaaa 1140 agatggagtc ttgcgggtct ggaagggttc aaatttgatt ctgaaaggtg tcatgcgtgg 1200 tactttgtat tttctacaag gttccacggt tacaggttca gcccatgttg catcgtcaga 1260 atttcaccag aaggatatga ctaagttatg gcacataaga cttggtcata tgggtgaaag 1320 agggatgcaa attctgtcaa aggaggattt acttgctggt cataaggtta agagcctaga 1380 gttttgtgaa cattgtgttt ttggaaaact acatcgcaac aagtttccaa aggccattca 1440 tagaacaaaa ggcacacttg attatatcca ttctgattgc tggggttcat gccgtgttga 1500 gtctttggga ggctgcagat tttttgtgtc cattattgat gactactcaa ggatgacttg 1560 ggtgtacatg atgaagcata aaagtgaagc cttccagaag ttcaaggagt ggaaaatttt 1620 gatggaaaat caaacaggga agaagatcaa gaggttgcga actgataatg ggctggaatt 1680 ctgttggtct gaatttgatc aattctgtaa ggatgaaggg attgctcgac atcgcacagt 1740 cagaaataca ccacagcaga acggtgtagc tgagcggatg aatcaaacac ttctggagag 1800 agcaaggtgc atgctctcta atgctgggct agatagaaga ttctgggcag aagcggttag 1860 tacagcttgc tacttgatta accgcggacc acatacaggt atacagtgca agacacctat 1920 ggagatgtgg tctggaaaag ctgctgatta ttcaaatctg aaagcttttg gttgtacggc 1980 ttactatcac gtcagtgaag gtaagttaga accaagagct aaaaagggag tatttgtggg 2040 ctacggagat ggagtgaaag gtttcagaat ctggtctcca gcagaaaaga gggttattat 2100 gagcaggaac gttgtctttg atgaaagtcc tctgcttaga accattgtga agcctacaac 2160 tacgtcagaa actgggagtc ttgacaaaca ggtggagttt caagtcattc agaacgagag 2220 cgatttaaag gaacctgaag aggaggatca agagccacag actgaaactg atattccaga 2280 atctatgcca tcagatatcc atcagagtat agctcaagat cggccaagga gggttggagt 2340 tcggccacct acgaggtatg gttttgagga catggtgggt tatgcactgc aggttgctga 2400 agaggtagat acatctgagc cgtctactta caaagaagcc attttaagtt ctgattctga 2460 aaaatggttt gccgctatgg gagatgagat ggagtcccta cacaagaatc agacatggga 2520 tctggtcata cagccttcgg ggagaaagat tattacttgc aaatgggttt tcaagaagaa 2580 ggaagggata tcaccagcag aaggagtcaa gtataaagcc agggttgttg ccagaggttt 2640 caaccaaaga gagggagtgg actataatga gatcttctca ccagtggtca gacatacttc 2700 catccgagtg ttactagcga tagttgcaca tcagaatctg gagcttgaac aacttgatgt 2760 gaagacagcg tttctacatg gagagttgga ggaagagata tacatgactc agccggatgg 2820 tttccaagtt ccagggaagg aaaatcacgt ctgcaagttg aagaagtcct tatatggact 2880 taagcagtct ccaaggcagt ggtataaaag gtttgacagc tatatggtga agttgggcta 2940 tactcggagc tcatatgatt gttgtgtcta ctacaatagg ctcaatgatg attcattcat 3000 ctatctggtg ctttatgtag atgatatgtt gatagctgca aagaagaagt atgacattca 3060 gaagctgaag ggtttactta gtgctgagtt tgagatgaag gatctgggag ccgctcggaa 3120 gattttaggg atggagatca ttagagacag agagagaagg aaacttttct tgtcacagag 3180 aagctacatt cagaaggtct tggcgaggtt tggcatgtct tcatctaagc ccattgatac 3240 ccccagtgct gccaatatcc atctcactgc catgttcgct ccacagtcag aagaagagaa 3300 ggagtatatg tcacgagtcc cttatgccag tgccgtagga agtttgatgt atgctatggt 3360 ctgtacaagg ccagatttag cacatgcagt cagtgtagtg agcagattca tgggacaacc 3420 agggagagaa cattggcagg ctgtgaagag aattttccgg taccttagag gtacatctga 3480 cgttggtctc atttatggag gtgatactca gtgcttggtt actggctatt ctgattcaga 3540 ctatgctgga gatgttgaca caagaagatc gatgactggc tatgtgttta cccttggagg 3600 atctgtcgtc agttggaagg caactttgca acctacagtg actttgtcta ctacggaagc 3660 ggagtacatg gccttgacag aggctgcaaa agaagggatt tggttgaaag ggctggttag 3720 tgatcttggt ctgcatcatg atcaggctac ggtgtattgt gacagtttga gcgcaatttg 3780 tctagccaag gatcaagtcc atcatgagag aaccaagcat attgacgtaa ggtatcattt 3840 tctaagaagt gagaagagaa tcaaggtgaa gaaagtagga actgctgata atcctgctga 3900 tatgttcaca aagccggttc cacagagcaa gtttcaacac tgtttggact tgctcaacat 3960 cagaagctgt taattgccct gcggggcaac tctgaggaag agggggaggc ttggcactat 4020 catagtgcgt ctgaagaatc tgttcggaga attcaagtca aggtggagat t 4071 // ID Gypsy-36_Mad-LTR repbase; DNA; EDCOT; 958 BP. XX AC . XX DT 13-OCT-2010 (Rel. 15.1, Created) DT 13-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-36_Mad-LTR. XX NM Gypsy-36_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-958 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1767-1767 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 958 BP; 300 A; 255 C; 158 G; 245 T; 0 other; tgtagacatc gaaatttcgg taaataaatg ttgaccgata aatcaaagtg tcaacgctca 60 tgtattacat aaattttaca cgtagcgtgt gactcaacga aaattgaaat gagttggaaa 120 agtcatcaaa taggacacgt gtcaacacct ggcagaaacg acttatttca tctgggatat 180 tatattcaaa attaggcctt ggaaaattct ataaatacaa gcccatttca ttcatttgag 240 ggggaattca tattacacct tgaagctctg aagctctgaa actccgaagc tctcaagcat 300 ccaggttccc gaagaatcaa gaaagccttc ttcgttcttc gttcatcgtt cttccaagat 360 caagccccaa cggccctttg gatcaacaat catccaccaa ttcaagatca agccccgacg 420 gcccttgaag aaagcgttct tcgttcttcg ttcatcgttc atcatccgtt catccaagat 480 caagccccaa cggccctttg gatcaacaac gtcgacaaat ccacacatcc aaccgttctt 540 caagatcaag ccccaacggc ccttgaagat ccgttcatca ccgttcttca agatcaagcc 600 caaaagccct tgaagatccg ttcatcaccg ttcttcaaga tcaagcccaa aagcccttga 660 agatccgttc atcactgttc ttcaaagatc aagcccaaaa gcccccttga agatccgctc 720 aaatccacct tcaaagatca agcccacggc cctttgaaga aacttccaac agttcatcca 780 agatcaagcc tcgacggccc ttggatcaac gaaacatcca caaatcaaca ccttacggag 840 atcgaatcag aggatcaaaa tagagagaga ttgtaaccca aaatcatcaa atacaaatat 900 ttgtttgtgc acgtcgttgt tcttgtctct ttcgtttcag gaattttccg tgttcaca 958 // ID GYPOT1_I repbase; DNA; EDCOT; 5099 BP. XX AC . XX DT 24-OCT-2006 (Rel. 11.1, Created) DT 02-NOV-2006 (Rel. 11.1, Last updated, Version 1) XX DE Internal sequence of GYPOT LTR, from Populus trichocarpa: DE internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW internal portion; GYPOT1_I. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-5099 RA Jurka J. and Shankar R.; RT "GYPOT1: Gypsy-type element from black cottonwood."; RL Repbase Reports 6(10), 488-488 (2006). XX DR [1] (Consensus) XX CC The sequence from black cottonwood (Populus trichocarpa) genomic CC DNA is the internal region of the transposon flanked by GYPOT CC LTRs. XX FH Key Location/Qualifiers FT CDS join(223..2670,2666..5098) FT /product="GYPOT1_I_1p" FT /translation="MPRNRRIADTVRVEDDQDDVPIGRLRTARQRRRRGAP FT VPQHVEEVPPPVEEEPQEIEEEDIVNETGVGVADPEPVTEFQQLSQVVRTW FT IEFSMERDRRRDRDVPSTSHTVQGVNVPLNDFMKLAPPIFTGMDSSEDPQR FT FLDDIWRRCEALGCTDHRAVSLASFRLEGDVAISWFESRKRARPVEAQWTW FT KEFSSMFLDRFLPQSVRDARLYEFERLSQGSMTVDEYDLKFTQLSRYAEHL FT LPTEEWRVKRFIRGLKSSMYKVMVSQVFPSYSLAVDSARLIEARELEDMTA FT GQSKRPREEGQSFRQQGLSAGLSRGRSGRQGSWVQRGFRQRPSVSGSGGQS FT GSSGTQSLVQTAPRSSFITPSDSSSCQHCGGSHTSAECYRRTGACFSCGQM FT GHKIRECPRRQLSASGLSASVQHPIQAPSTSQSVAHGSRGFGGRGQRGRGA FT GDRGQIQQGQGHARVFALTQQDAQASNTVVSGILPVCSFEAKVLFDTGATH FT SFVSSYFAMRLDRQPTLLKSPISVSTPLDELILVKYVYLDCEIEIGDKIFM FT EDLNVLDMVDFDVILGMDWLAKHRASVNYWGKKIIFDLDEEVGLVFQGDKI FT GSPSIMLSAISRKMARKGVQCYLAYIVDVEKEVPQLDQVPIVREFIDVFPD FT DLPGLPPYREIEFCIDLVPGTEPISMAPYRMAPAELRELKEQLQDLLDKKF FT IRPSVSPWGAPVLFVKKKDRSLRLCIDYRQLNRVTVRNRYPLPRIDDLFDQ FT LQGAQFFSKIDLRSGYHQLRIRETDILKTAFRTRYGHYEFLVMSFGLTNAP FT AAFMDLMNSVWLVYFIDRFVIVFIDDILVYSRSREEHEQHLRMVLQTLREH FT QLYGKFSKSEFWLESVAFLGHVVSRNGIEVDPQKIEAVKQWLRPTSATEIR FT SFLGLAGYYRRFVENFSRISAPLTKLTQKNVKFQWSEACEKSFLELKERLT FT TAPVLAVPSGSGGYTVYCDTSRVGLGCVLMQHGKVIAYASRQLKKHEQNYP FT THDLEMAAVIFALKIWRHYLYGETCEIFTDHKSLKYIFQQRDLNLRQRRWM FT ELLKDYDCTIHYHPGKANVVADALSRKSSGSLAHIQEVRRPLIRELHELVD FT EGVRFDLSEAGAMIAYFQVKSDLFDKIKAAQKKDDSLLRIRNEVEQGKAAG FT FVIGDDDVLRYKDRLCVPDVDDLRRELMVEAHQTVYTMHPGSTKMYKDLKV FT CYWWNRMKVDVADFVSRCLTCQRVKGEHQKPPGLLQPLLIPEWKWERITMD FT FVTGLPRSQEGYDSIWVIVDRLTKSAHFLPVKITYGYAKLAELFISEIVRL FT HGVPISIVSDRGPQFTSRFWVKFQEAMGTKVQLSTAFHPQTDGQSERTIQI FT LEDMLRACVMDFGVGWSKFLPLVEFAYNNSYQASIEMAPYEALYGRKCRSP FT VCWFEVGEKRLMGPEFIQITSEKIEVIRQKLQTTQSRQKSYADKKRRDLEF FT SVGDCVFLKVSPTKGVFRFRKKGKLSPRFIGPYEILERVGAVAYRLALPPN FT LSAIHPVFHVSMLRKYMSDPSHVLEVYPIELRDDMVYEVQPEAIVDRQVRK FT LRSKDIASVKVKWKGHSREEATWELEDKMREEYPHLFDNLGKYSIFSLKFR FT GRNFYKVGR" XX SQ Sequence 5099 BP; 1402 A; 790 C; 1410 G; 1497 T; 0 other; aacttggtat cagagcttta ggttaaagaa acaataatat aattaatttc ataataagtg 60 gagcattagg atccgtgttg tcttgtttgt tgtctttgaa attctgaatt ctcattaagc 120 atgtcttctt ccttgtgata gatatgcttt cctataattc tgtggtaatt atcatgctat 180 tgttctagca tgacttgagt gctctcattt ttattttagg aaatgccgag gaatagacga 240 atagctgata ctgttagagt agaggatgat caggatgatg tccctattgg gcggttgaga 300 actgcaaggc aaagaaggag gcgcggtgca cccgtgcctc aacatgttga ggaggtacct 360 ccaccagtgg aggaagagcc tcaggagata gaagaagaag atattgttaa tgaaacaggt 420 gtgggggtag ctgatcctga acctgttaca gagtttcagc aacttagtca ggttgtgcgg 480 acctggatag agttttctat ggagagagat agaaggaggg atagagatgt accctcgaca 540 tcccacactg ttcagggagt taatgtgccg ttgaatgact tcatgaagtt ggcacctcct 600 atttttactg ggatggatag ttcagaggat cctcagaggt tcctagatga tatttggcga 660 cggtgtgaag ctttgggatg tacagaccac cgagctgtga gtttggcatc gttcaggttg 720 gaaggagatg tggcaatctc ttggtttgag tctaggaaaa gagcaagacc agtagaggct 780 cagtggacat ggaaggagtt tagctccatg ttcttagaca ggtttctccc tcagagcgtc 840 agggatgctc gactttatga gtttgagagg ctatctcagg ggagcatgac agtggatgag 900 tatgatctga agtttactca gctgtctagg tatgcagaac atcttctacc cactgaggag 960 tggagggtaa agaggtttat tagaggactc aaatcctcta tgtataaggt gatggtgtca 1020 caggtgtttc catcatactc tttagctgtt gatagcgcca gattgataga ggcgcgagaa 1080 ttggaggata tgactgcagg ccagtctaag aggcctagag aagagggtca gtcttttagg 1140 caacagggat taagtgcagg tctgtctagg ggacgaagtg gccgtcaggg ctcatgggtt 1200 cagagggggt ttagacagag accgtcagtt agtggctcag gcggtcagag tggcagtagt 1260 ggtactcaga gtttagttca gactgcacct cgtagttcat ttattacacc tagtgatagt 1320 tcttcatgtc agcactgtgg aggaagtcat actagtgcag agtgctacag aaggaccggg 1380 gcttgtttta gttgtggcca gatgggtcat aagatcagag agtgcccgag gagacagttg 1440 tcagcttcgg ggttatctgc ttcagtccag catcctattc aggcaccatc gacgagccag 1500 tctgtggctc atgggagtag aggttttggt ggccgtggtc agagaggccg gggtgcaggt 1560 gatagaggtc aaatacagca gggtcagggg catgctagag tttttgcctt gactcagcag 1620 gatgctcagg catccaacac agttgtttca ggtattcttc ctgtttgctc ttttgaagca 1680 aaagtgttgt ttgatacggg tgcaactcat tcatttgtgt cctcatattt tgccatgagg 1740 ttagatagac aaccaacttt gttaaaatcc ccaatttcag tctccactcc cttagatgaa 1800 ttaatattag tgaagtatgt gtatctggat tgtgaaatag agattggaga taagattttt 1860 atggaagact taaatgtctt agatatggtt gattttgatg tgattttggg aatggattgg 1920 ttggcaaagc atagggcttc agtaaattat tggggtaaga aaataatatt tgatctagat 1980 gaagaagttg ggttggtatt tcaaggagat aagattgggt ctccatcaat tatgttgtcg 2040 gctatctcga ggaaaatggc cagaaaagga gtacagtgct acctagcata tatagtggat 2100 gtagagaaag aagttcctca attagaccaa gtccctatag ttagggagtt tattgatgtc 2160 tttcccgatg acttacctgg attgcctcca tatagggaaa tcgagttttg tattgatttg 2220 gttccgggta ccgaaccaat atcaatggca ccatatagaa tggcgccagc agaattgagg 2280 gagctaaagg agcaactgca ggatttgttg gataaaaagt tcatccgacc aagtgtgtcc 2340 ccttggggag ccccagtgtt gtttgtgaag aagaaagata ggtcattgag gttatgtata 2400 gattataggc aactgaatcg ggtgactgtt cgaaatagat acccactccc tcgcattgat 2460 gatttgtttg accagttgca gggagctcaa ttcttttcta agatcgatct tcgatctggg 2520 tatcatcagt tgaggattag ggagacagac attttgaaga cagcttttag aactcggtat 2580 ggtcattatg agttcttagt gatgtctttt gggttgacga atgcaccagc agcttttatg 2640 gatttgatga atagtgtttg gctagtttat tgatcgattt gtaatagttt ttattgatga 2700 tattttggtg tattcgaggt ctagagagga gcatgagcag cacttgagaa tggtgcttca 2760 aactctgcga gaacatcagt tgtatggcaa gttctcaaag agtgagtttt ggttggagag 2820 tgtagcattt cttgggcatg tagtgtcaag gaatgggatt gaggttgatc ctcaaaagat 2880 tgaagcagtt aagcagtggc ttagacctac ttcagcgaca gagattagaa gtttcttagg 2940 tttggccggc tattatcgga ggtttgtgga gaacttttct cggatttctg caccattgac 3000 taagttaacg cagaaaaatg ttaagtttca gtggtctgaa gcttgtgaga aaagtttctt 3060 agagttgaaa gagagattga ctacagcgcc tgttctagca gtaccatcag gttctggtgg 3120 ttacacagtg tattgtgata cttcgagagt ggggttagga tgtgttctaa tgcagcatgg 3180 caaggttatt gcctatgctt cacggcagct gaagaagcat gaacagaact atcctacaca 3240 tgatttagag atggcggctg taatttttgc cttgaagatt tggaggcact acttgtatgg 3300 tgaaacttgt gagatcttca cagatcacaa gagtttgaaa tacatctttc agcagaggga 3360 tctaaacctg aggcagagga gatggatgga actgctgaag gattatgatt gtaccataca 3420 ttaccacccg ggtaaggcaa atgtagttgc cgatgctttg agtagaaaat catcagggag 3480 cttagctcat attcaggagg tacgaagacc tctgattagg gagctgcatg agttggtgga 3540 tgaaggagtc agatttgatc ttagtgaagc tggagcaatg attgcttatt ttcaggttaa 3600 gtcagatttg tttgataaga taaaagcagc tcagaagaaa gatgattcac tactcaggat 3660 tagaaatgag gttgagcagg gtaaggctgc aggttttgtg ataggtgatg atgatgtgct 3720 gagatataag gataggcttt gtgtacctga tgtagatgat ctgaggagag aattgatggt 3780 agaggcacat cagacagttt acacaatgca tccaggttcc accaagatgt ataaagacct 3840 taaggtgtgt tattggtgga ataggatgaa ggttgatgta gcagactttg tttctaggtg 3900 tttgacctgt cagagggtaa agggtgaaca ccagaaacct cctggattgt tgcaaccatt 3960 gttgattcca gaatggaagt gggaaaggat cacaatggac tttgtgacag gattgcctag 4020 gagtcaggag ggttatgatt caatatgggt gattgttgac aggttgacaa aatcagccca 4080 ttttctgcca gttaagatta cttatggata tgcaaagttg gcggaattat ttattagtga 4140 gattgtacgg ttgcatggag tgccaatctc gatagtgtct gatagaggtc cacagtttac 4200 atcgcggttt tgggtgaaat tccaagaagc tatgggtact aaagtgcagt tgagtacagc 4260 ttttcaccct cagacagatg gtcagtctga gaggactatt cagatcttgg aggatatgtt 4320 gagggcttgt gtcatggatt ttggagttgg ttggagtaag ttcctaccat tagtggaatt 4380 tgcttacaac aacagttatc aggctagcat agagatggca ccttatgagg ctttgtatgg 4440 tcggaagtgt agatcaccgg tttgttggtt tgaggttggt gagaagaggc taatgggacc 4500 ggagtttatt cagattacct cagagaagat agaggtaatt agacagaagc ttcaaacaac 4560 tcagagtaga caaaagagtt acgcagataa aaaaaggcgt gacttagagt tttcagtggg 4620 tgattgtgtg ttcttaaaag tatcaccgac aaaaggagta ttcaggttta ggaagaaagg 4680 caagttgagt cctcgattca ttggaccgta tgagattctg gagagagttg gggcagttgc 4740 ttataggtta gcattaccac caaacttgtc cgctattcat ccggtatttc atgtttccat 4800 gctaaggaag tatatgtcag atccatcgca tgtattagag gtttatccca ttgaattgag 4860 ggatgatatg gtttatgagg tgcaaccaga agctatagtc gaccgacaag tgaggaagct 4920 taggtcaaag gatatagctt cagtaaaagt gaaatggaaa ggtcattcac gtgaggaagc 4980 gacatgggag ctcgaggata agatgcgtga ggagtatcct catcttttcg ataatctcgg 5040 taagtattca atcttttctc ttaagtttcg aggacgaaac ttttataagg tggggagat 5099 // ID Copia1-VV_I repbase; DNA; EDCOT; 4471 BP. XX AC . XX DT 13-AUG-2007 (Rel. 12.08, Created) DT 31-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW internal portion; Copia1-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4471 RA Obukhanych T. and Jurka J.; RT "Copia1-VV - LTR retrotransposon from grapevine."; RL Repbase Reports 7(8), 665-665 (2007). XX DR [1] (Consensus) XX SQ Sequence 4471 BP; 1399 A; 872 C; 911 G; 1253 T; 36 other; tggtatcaga gccgtgtttg ctctaaaacc ctaatcagtc catggatgcc caaagaggaa 60 acaaccatga aagagtgtcg gagatacact cctcaatggg ccccgtcggt gcattcgaca 120 actccccact ccaacttacc attgaaaaat tgaatggtaa gaattacaga gagtgggcgc 180 aagcaatcaa gctcgttatt gacggaaagg gaaagttagg gcttcttacc ggcgagactc 240 ggcgaccacc tccaaccgat gtagcagcat cccagaaatg gcggtccgaa aactccttta 300 tcacytcatg sttgattaac tccatgaagc cagccattgg aaagacttac atgttcctcc 360 caacggcaaa ggatgtgtgg gatgcgatac gggaaacgta ttccgatgtc gagaatgctt 420 cccaaatctt tgaaatcaag acgcagcttt ggcagatgaa gcaaggagat cgggaagtca 480 cggaatacta caccgagatg ctgggtttgt ggcaagatct cgatctcagc trcgaagakg 540 agtgggagtg cacgagtgay agtgtgcgct tcaagaagaa gatggagaat gagagggtct 600 tcgagttcct agcggggcta aaccgcaagc ttgatgacgt caggagtagg gttctcagtc 660 gacagccgtt gccctccatc cgagaagtct tctctgaggt gcggcgagag gaaagcagaa 720 ggagagtgat gttggatctc tcatttgggc ctgaggcttc agccctttta acccatgggc 780 ctcatgggcc tcatgctgct gctggacgtg ggccttatgc ggacctagtg ggcctcatgc 840 tgctggatct agtgggccaa gcccaagaca gtccaagagg acttattgtg agcattgtaa 900 gaagttrggc cacactaaag acacttgctg gactttacat ggcaagcccg cagattggaa 960 gcccagacaa cctaataaag cccatagtca tcaggcctcc accgaaaccc aggcagacaa 1020 aacacccaca gaaatttgtc agtcaacttc tagtgtgggg tttaattccg accagcttgc 1080 gaaattatat ragctttttt ctaatttcca agcctctggt cagtcttcta ccactttatc 1140 ctttggttct ttggcccaaa aaggtaatta tctcacagya cttagcatca tgtctcagat 1200 tactccttgg attattgact ctggtgcatc tgatcatatg actgatgctc atcatttatt 1260 ttctacatay tctccctgtg ccggtaatta aaaagtaaaa attgcagatg gtactttatc 1320 accagttgct ggcaaaggga gtattcgtat ttctgagtct attactctca ataatgtcct 1380 acatgttcct aatttgtctt gcaatttgct gtctattagt aaattaacca aagatyctaa 1440 ttgctcagct aaattcttac catctcattg tgattttcag gacctatcat cggggaagac 1500 gattggcagt gctaaggaac gtgagggtct atatttcttt gatgaaactg atttgcttgg 1560 acagagtcct cctactgttt gtaattctrt ttctgttcct aaggatagtg aaattatgtt 1620 atggcattat aggttaggtc atccaagttt tcagtattta aaacatttat ttccttcact 1680 attttcaaat aaaacttcat tttattttca gtgtgaaatt tgtgaattag ccaaacatca 1740 tcgtgcgtct tttcctaaat ctaagtataa accatccaaa ccatttactc taattcatag 1800 tgatgtatgg ggaccctcac gtacccctaa taggacccat aaaaaatggt ttattacttt 1860 tattgatgat catactcgcc tatgttgggt atatttgttg actgataaaa ctgaggttcg 1920 atcagtyttc awaaactttc actctatggt acaaactcaa tttcacacaa aaattcaaat 1980 ttttcgtagt gataatggta atgagtattt caataaatcc ttgagcactt atcttcaaga 2040 aaatggtatt rtacatcaaa gttcttgtaa tgacactcct caacaaaatg gggttgcwga 2100 aagaaaaaat aaacatattc ttgaagttgc tcgtgcttta ctttttacaa ctaagatgcc 2160 cacatatttt tggggtgamk ccattctkac agccacatat cttattaatc gaatgcctag 2220 tagggtctta tattttgtca cacccctcca gawattccaa aagttttttc ctcattctag 2280 acttgatgca catcttccac ttarartctt tgggtgcact gtgtttgtcc acattcatgg 2340 acmtaagcgg aacaaayttg atcccagagc tmtwaaatgt gtctttcttg gctactcttc 2400 cacacaaaaa ggatacaaat gctatgaccc aatttcaaaa aagctatatg ttaccatgga 2460 tgtcacattt ttttagcata ctccctacta ctcatcttca gggggagtcc atgagtgaaa 2520 ctagaccacc cttaaccttt gactatcttg atgttgctat gtttgaatcc actctgtgcc 2580 ttatatctac cccttcgcct aatacagaag gacacttaaa ctcaggggga gatacagaat 2640 tacagacaaa tagggaaaca cttgtctact caaggaggcc aaaatcgaag ttcaatgaga 2700 cactcatctc cgaagcacta aaagagtcag aacctaggtg atagttccaa cccctctgga 2760 gtatgactcc aattctaatc agttaacaga tgacttagat rtcccattgc tcttaggaaa 2820 caacctcgtt catgtactaa acatcctatg tctaactttg tgtcttataa aaatctttct 2880 ccaaattttc gtgcttttac aactcacctt kctagaatcg agattcctaa aaatattcaa 2940 gaagctttar agattccaga atggaaggag gctgttattg aagaaatgag ggcacttgaa 3000 aaaaataaga catgggaagt gatggatttg ccaagaggaa agaaaacagt gggctgcaaa 3060 tgggtattca caatgaaata taagtcagat ggcacactag aaagatataa agctcgaytg 3120 gtggcaaaag grttcactca gacctatggc attgactata tagagacatt tgcaccagta 3180 gcaaagctaa atactataag agttctctta tcamttgcag caaatctcga ttggcctcta 3240 caacaattag atgtgaagaa tgcttttctg aatggagatt tggaagaaga agtgtatatg 3300 atgcttccac cagggttctg taatgaagaa tttggatcaa aggtatgcaa attgaagaaa 3360 tctttatatg gtctcaaaca atcaccaaga gcatggtttg ataaatttac tcagttggtt 3420 aaaaaccaag gatacaawca gggacaaact gatcatacta tgttcatcaa acactccaat 3480 gatggaaaga taaccatttt aattgtgtat gtggatgaca tcattctcac tggagatgac 3540 ataggagaaa tggaaaggtt gaagaaggtc ttagccacag aatttgagat caaagatttg 3600 ggttcattaa ggtattttct tggaatggag gttgctcgat caaagaaagg aattgttgtc 3660 tcacaaagaa agtatgttct tgatctcctg aaagaaactg gaatgagtgg atgcaagcca 3720 atagataccc ctatcratcc aaatcgaaac ttagagatgg aaagcgacgg aaatcttgtg 3780 gatacagctc aatatcaaag attagtaggt aaactgatct acttatctca cactcgaccw 3840 gacattgcat ttgccgtgag catggtaagt caattcatgc actcaccaaa tgaaaaacat 3900 cttgaagcag tatataaaat cctaagatac ttaaagagta ctccagggaa aggactattc 3960 ttcaagaaga gtgataataa gaaagtagag gtctacacag atgcagattg ggcaggatca 4020 acagatgaya gaagatctac atcaggttac tgtacctatg tttggggtaa tttagtcaca 4080 tggagaagta agaagcaaag tgtagtagca agaagcagtg tcgaagctga attcagagca 4140 atggcacatg gaatgtgtga aatattatgg ttgaagaaag tactagaaga attaagcatt 4200 acaataaagc tgcctattaa actgtattgt gacaacaaag ctgccattag cattgcacat 4260 aatccagtgc aacatgacag aaccaaacat attgagattg atagacactt cataaaggaa 4320 aaaattgaga aagggattat ttgcatgcca tttgttccta caacgcaaca aatagctgat 4380 attttcacca aaggattgyt caaatcaaac tttgaagttc ttattagcaa gttgggcatg 4440 attgatatct atgctccaac ttgaggggga g 4471 // ID Gypsy19-PTR_I repbase; DNA; EDCOT; 4390 BP. XX AC LG_XIX; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy19-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4390 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4390 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 316-316 (2007). XX DR Genome; LG_XIX; Positions 4225644 4230033. XX CC Positions [3300-3770] - Integrase core CC 'GTTAG' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 3369..4388 FT /product="Gypsy19-PTR_I_3p" FT /translation="MVVVDRLSKSANFLPLKHPFTAKSVAEKFVEGVIKLH FT GMPRSIVSDRDPFFASHFWQEFFKMSGIKLQLSSAYHPQTDGQTEVVNRCI FT EQYLRCFVHQWPKKWSLYLPWAENWYNTTYHISTGMTPFQALYGRLQPTIP FT SYNEGLLPVHKVDQQLQDRDELLQQLKINLARSINRMKQITDKKRRDVSFD FT VGDLVLLKLHPYRQHTVFKREYQKLASRFYGPYEILEKIGPVAYKLRLPAE FT SRIHPIFHVSLLKQYNTNSEVHNHSIEIPSFNADGEVLLIPQAMLDHRWIK FT QGAQIVEDSLVHWKYLTVEEATWVSTKQLLELFPDVNLGDKVARDGGG" FT CDS join(573..1535,1539..3296) FT /product="Gypsy19-PTR_I_1p" FT /translation="MDAKGSCRYIYGGLKTEISDGIRMFKPQTLKEAISLA FT RMKDDQLSRQRRFSRPAPSPPMRSTISPPSFNRDAPTVPATPIRRLTWEEM FT QRRRAQNLCFNCNDQFTAGHKCREPRILMLEGYDGTNTLLCDNEGEDQPLQ FT EIVETITEPEITLYALTRWAAPKTMCITTRIGSSDVIALIDNGSTHNFISE FT RLANALRIPVVPTASFTVRVANGEKLKCQGRFEEVGVDLQGTHFSLTLYSL FT PLTGLDLVLGIQWLEMLGSVVCNWKQLTMEFQWKNQLRQLRGMGDEGIQIA FT SITKLTKAIHQNPAIFAICLQISTAEPHITTHPDMEAILHEFADILKEPAG FT LPPTRGVDHCISLKDGTKPINVRPYRYAYYQKEEIEKQVQEMLNSSLIKPS FT TSPFSSPVLLVKKKDGTWRFCIDYRALNATTVKDRFPIPTVDDMLDELYGA FT SYFTKLDLQAGYHQVRVNPMDIPKTAFRTHNGHYEYLVMPFGLCNALSTFQ FT AIMNSIFQPHLQKFILVFFDDILVYSPTWDMHLMHVRQTFEILQQHQFFVK FT ASKCVFGQQELEYLGHIITNHGVKIDENKISAMVAWPRPTNISELRGFLGL FT TGYYRKFVKNYSIVARALNNLLKKGQFGWNEEVETAFLTLKQAMTTTPTLA FT MPNFKDVLTVEVDASGDGIGAILTQQGKPIAFMSKALGVAKKSWSTYPKEM FT LAILEAIRLWRPYLLGRKFYIQTDQRSLNFLLEQRITTPEQQKWVAKLLGY FT DYEITCRPGRENVAADALSRKQGSHVLQHLLVSQVTLWEEIKQAVKTDLYI FT QSMSQIAADQLHSHFVWRNGLLRYKERVIIPADPTLRAKLLHEMHDTKVGG FT HSGVLCTYKKLGQQFYWPGMRKSVQEYIKNCVVCQKTKLDTLAPVGLLQPL FT PIP" XX SQ Sequence 4390 BP; 1314 A; 934 C; 975 G; 1167 T; 0 other; ttggtatcag agcttgtaga agatcttatg ggcactaata aggaacgcat tgagcagtta 60 gaagatgggc tgcaccgaat ggagcagggc atggctgata ggttgcaaca tctggaggac 120 acgcttaacc gactttctga tgtattgctt gcaaatcaag agccttcaaa ccagggcaac 180 caacaacgtg aaggtcaaga tgggggacga ctaattgtct catccaagat aacacgactt 240 gagtttccta gattttcagg agatgatccc actgagtggt ttaatcgtgt gaatcagttt 300 tttgcatttc aaaataatcc agaacttcag aaggtcgccc tggcttctta ccacttggaa 360 gcggatgcca accagtggtg gcaatgggtt caccggttga atgaagaaga aggacgagtt 420 ttatcatgga caaactttga agacgaactt tgggcgcgtt ttggtccttc agaatgtgag 480 gattttgatg aggccctttc aagaataagg caaggaggtt cactaagata ttaccaacgc 540 gaatttgagc gcctaggcaa ccgagtacgc ggatggacgc aaagggctct tgtaggtaca 600 tttatggtgg cttaaaaact gaaatttcag atggaatacg catgtttaag ccacaaacgt 660 tgaaagaggc catcagtcta gcccgaatga aggatgatca acttagcaga cagaggaggt 720 tcagcagacc agcaccatca ccaccaatga gatctacgat ttcccctcct agtttcaatc 780 gagatgcccc aacggttcct gccactccta ttcggcgcct cacttgggag gaaatgcaga 840 gaagacgagc tcagaattta tgttttaatt gcaatgatca atttactgca ggacataaat 900 gtcgcgagcc tcgcatctta atgttggaag ggtacgatgg cactaacact ctgttatgtg 960 ataatgaagg tgaagaccaa ccacttcagg agattgttga gacaatcacc gaaccagaaa 1020 ttacactata tgcgttgaca agatgggctg cacccaagac catgtgcatc actacaagga 1080 tagggtcaag tgatgtcatc gcactaatcg acaatggctc aacccataac tttattagtg 1140 aaagattggc caatgcatta cgaataccag tggtgcctac cgcatccttt acagtgcggg 1200 ttgcaaatgg cgaaaaattg aaatgccagg gacgttttga agaggtcgga gtggacctgc 1260 aaggcaccca tttttcatta actctttatt ctcttccact tacagggttg gatctagtgc 1320 tgggcatcca atggttagaa atgctaggtt ctgtggtttg caactggaaa cagttaacca 1380 tggaatttca gtggaaaaac caactcaggc agttacgtgg aatgggcgat gaaggcatac 1440 aaattgcgtc tatcactaaa ttaaccaaag caattcacca gaaccctgcc atttttgcaa 1500 tatgtctaca gatcagtact gcggagccac acatctagac aactcatcct gatatggagg 1560 ccattttgca tgagtttgca gatattctaa aggaaccagc aggtctacca cctaccagag 1620 gggttgatca ctgcatttct ctcaaagacg gcaccaaacc tattaatgtt aggccttatc 1680 gttatgcata ttatcaaaag gaagaaattg agaagcaagt tcaagaaatg ttgaattcca 1740 gccttatcaa accaagtacc agtccttttt catcacctgt actgttggta aagaaaaaag 1800 atggaacatg gcgtttttgc atagattaca gggccctcaa tgctacaacc gtgaaggacc 1860 gcttccctat tcctacagtt gatgatatgt tagacgagct ctatggtgct tcatatttca 1920 ccaagcttga tcttcaagcc ggatatcatc aggtacgggt taatcctatg gatattccaa 1980 aaactgcttt ccgcactcac aatgggcact atgaatattt ggttatgccc tttgggttgt 2040 gtaatgcact ctcaacattt caagctatca tgaattcaat atttcaacct catcttcaaa 2100 aatttatatt ggttttcttc gatgatatat tagtctatag tcctacgtgg gacatgcatt 2160 taatgcatgt aaggcagact tttgaaatct tacagcaaca tcaattcttt gtcaaggcta 2220 gtaaatgtgt ttttggtcaa caagagctag agtacttagg gcacataatc accaatcatg 2280 gcgtgaagat agatgaaaat aaaatttcag caatggtggc atggccacga cctactaata 2340 tttcagagct tcgtgggttt ttagggttaa caggttatta caggaagttt gtcaaaaatt 2400 atagcattgt ggcgcgggct ctcaacaatc tccttaaaaa gggccaattt gggtggaatg 2460 aggaagttga aactgccttc ctcacactca aacaagcaat gacaacgaca ccaacgttag 2520 caatgcccaa tttcaaagat gtcttaactg tagaagtcga tgcctcaggt gatggtattg 2580 gcgccatatt aacccagcaa ggcaaaccaa ttgcatttat gagtaaagca ctcggagtgg 2640 caaagaaatc ttggtctact tatcctaaag agatgctggc cattcttgaa gctatacgat 2700 tgtggcgtcc atatctatta ggccgcaagt tctatattca gacggatcaa cgcagtctaa 2760 attttttgct agagcaacgt atcaccacac cagagcagca aaaatgggta gccaaactct 2820 tgggctatga ctatgagatc acatgccggc ctggacgaga aaatgttgca gccgatgctc 2880 tctctcgtaa acaaggtagt catgttcttc aacatctttt ggtttctcag gttactttgt 2940 gggaagaaat taaacaggcg gtaaagacag atttatatat acaatcaatg agtcagatag 3000 ccgcggatca gttacacagc cactttgtat ggcgaaatgg tttgcttcgt tacaaggaac 3060 gggtcatcat tcctgccgac cctactctac gtgcaaagct gctgcacgaa atgcatgata 3120 ccaaagttgg tggccactct ggggttctgt gcacatacaa gaaattgggg caacaattct 3180 attggccagg aatgcgtaaa tcggtccaag aatatatcaa gaattgtgtg gtatgccaga 3240 aaaccaaatt agatacattg gcacccgtag gtctcctcca accattgccc atcccttgac 3300 aggtgtggga ggacattaca cttgatttca tcgagcgttt acccgcttct cagggccagg 3360 ataccatcat ggttgttgtc gataggctca gcaaatcagc taatttcctg cccttaaaac 3420 atccttttac agctaaaagt gttgcagaga aatttgtgga aggtgttatt aagctacatg 3480 gcatgccaag gtccatagtc agcgatcggg atccattttt tgcaagccat ttctggcagg 3540 agttctttaa gatgtcaggt ataaaattgc agctcagctc cgcgtatcat ccgcaaacgg 3600 atggccaaac tgaggttgtc aatcgatgca ttgaacagta tttgcgatgt tttgttcatc 3660 aatggccaaa aaaatggagc ctctacttac catgggcaga aaattggtat aatactacat 3720 accacatctc aaccggaatg actccttttc aggcactata tggtcggctt caaccaacta 3780 ttccatccta caatgaaggt ttattgccgg tgcataaagt ggatcagcag ttgcaagacc 3840 gagatgagtt acttcagcag ctcaaaataa acttggcacg ctcgattaat aggatgaaac 3900 aaatcacaga taaaaagaga agagatgtct catttgatgt tggtgattta gtccttctga 3960 aactccatcc atatcgacag catacggttt ttaagcgaga ataccagaaa cttgccagtc 4020 gcttctatgg accctatgaa attctagaga aaattggacc cgtcgcttac aaactccgtt 4080 taccagcaga gtcacgcatt catccaatat tccatgtctc tctgcttaaa cagtacaaca 4140 ccaactccga ggttcacaac cacagcatag agataccgtc cttcaatgca gatggggaag 4200 ttctgctgat accacaagct atgcttgatc atcgctggat aaaacaaggc gcccaaattg 4260 tcgaagatag tttagttcac tggaaatatt taaccgtcga ggaggcgaca tgggtatcta 4320 ccaaacagct actggaacta tttccagatg tcaaccttgg ggacaaggtt gcacgtgatg 4380 ggggaggtat 4390 // ID BvL1-2 repbase; DNA; EDCOT; 6934 BP. XX AC FM993987; XX DT 03-AUG-2009 (Rel. 14.07, Created) DT 03-AUG-2009 (Rel. 14.07, Last updated, Version 1) XX DE BvL1-2, LINE-type retrotransposon. XX KW L1; Non-LTR Retrotransposon; Transposable Element; BvL1-2. XX OS Beta vulgaris OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC Caryophyllales; Amaranthaceae; Beta. XX RN [1] RP 1-6934 RA Wenke T., Horn A. and Schmidt T.; RT "The genomic organization and diversity of a non-LTR RT retrotransposon (LINE) family in Beta vulgaris."; RL Direct Submission to EMBL (28-JAN-2009). XX DR EMBL/GenBank/DDBJ; FM993987; Positions 1 6934. XX SQ Sequence 6934 BP; 1876 A; 1348 C; 1365 G; 2345 T; 0 other; ataggcacca tcgaaattta acataggtcc ttatgttaga aaaacaataa aatattatgt 60 atatatagga tactgttagg aaacaggatg ttgtagtttg attaatgtag aacagaaaat 120 cagtgaaata ataaaggtga gaaaactata aagatgaaca aacaaagaac acaaggattt 180 aaaaaaaaaa gatgagagag aaagctctag aaagagaaac tctagaaccc aaagaaaacc 240 tagctggcga ttccacttct ccaaacccta aaatcttccc caaatcaatt gaatttcttc 300 tccacttaat tctcttccaa ttttccttct ctgcaactcg aaaagttact gtattctacc 360 ttctcctctc taatcaatgc catagaccct cagtagggag tagggtggca gtttgcttaa 420 gttccccaaa tcaattgaaa gtctattatt taggctaccc attagcgaaa tcattacaga 480 tttctcattt ctctccaaat aatgttaaat gtgtagcgct ttgttctgat tttgtccaaa 540 gaacttccca aaatcaattt aagtggatta agggtttcgt atttttctca tttaagtaca 600 agccagctgg attttttagg gttgaatcat ttgttgcatt tatggcgagt gtgagtttac 660 tctgcaagct ttgcggcttt tcttcaaaga gtgtgcagta agttggtaga gttgtgctat 720 taatcctctt tttgtggttt tctttgtcca actatgcgtg gattggaact ttcttcttgt 780 tcttccctgc tccaacattg aatgcgatgg aatttatcat tcctttggcg tatttgagta 840 aagtggtgag cctcttttgt tttcaagtcc ataatcccta taaaagggat acccaggtga 900 tgttctctta tatcccgaac tccttctctt ctctctttag aacttgtttg ctagtgctta 960 aattttctat tattctattg tctgttatga tgggtagtca ttctaacttc aaagatgttt 1020 tattatcaaa ccctaaccct aatgtggaac ttgctgcttc tggttttcca ttaggggacc 1080 ctcctactaa tttatccctc caaaatgacc ctccccatcc cccttctttt cttgaggctg 1140 tagtgttaga ctctctgcct caagtgcaga aagatataga agagctttcg aaatcttgcc 1200 tttttggtaa aatgctctca gccccattgg acttgcgcac cattatcgca aggacgaagg 1260 ctgattggaa aattataaat ggtgaggtgg attatttgca aatgggcaat ggctggattc 1320 tgttgaggtt tgctaatcct caggatctct ctctcatctg gagtgagaga ccttggcata 1380 tacaaggtga tttgtttgtt ctttctccct ggaaaccttt ttttgatcct tacttggaag 1440 aaataaaatg ggtggatttg tgggtaagaa tccctagact tcctactgaa cttctgaatt 1500 ttgattcaat agctaacttg ttagcctcta atgacattgg tgctctcatt aagattgacc 1560 aacgttctct gttgcataat aagattcgtt ttgcacgagc ctgtgttagg gtggatattc 1620 agggcccctt gcttgagttt gctgaggtca gtagagtggg tgatcttgtg catggctatg 1680 ttatttggta tgaggacttc tcctcaggtt gctccttctg tggtgagtca gaacatgcta 1740 ttgaggtttg tcccctttta aactccccta aaaaagaaat tactcataaa actgctaaag 1800 acaccctaaa cagaacatct ctctcatgca tgcaattgct aaggctactg ggcaagcttg 1860 tcatgtaacc acagccgagc cagcaaatgt ggttcatgtg aagcctaagt acctatcaaa 1920 acctcctgtt gctaagtccc tttctaaaaa gtttatgtct gatggttttg ctggtggttt 1980 gttgcccact ccctctggga aaggggttgt tattaaagaa aatactaact ctgctaagaa 2040 agtttctgaa gtctctcatg ttgtccaagg taaaggtaaa ggtaagctca tggtttctca 2100 tactttttgt tctgaggatt cctctgatga tgaagctggg tatcttatcc ctcaagtctc 2160 tccttctcct gctctgcctt ctgggaagat tgtaggtgac actggggggg tccctgtctg 2220 tcacccttct cctgtccagg tttattgtgc ctctgatttg tttgatgaaa atcagtactt 2280 agcccttact tcttctaaag tgcctgctgt taatcaattc tgttataatg aggaagagga 2340 tgcaactttt tgcattgatg atcaggatga tctctctcct aatgagaaca aatctttagc 2400 tgaaaactcc tttcactcta ttaactccag cagctctatt gtaaggcaga ttgaaagaat 2460 gggtgttgat gcttcccacc cagtggagct ctcttccccc tctggctctg caaagagaag 2520 gatggtagac aaagaggatg aagatgatgc atcttcagct ctgaagagga aaaggaacta 2580 atctctgatg acaaaatcta tggtagccat gtttccacct tattttgtta ttaaataatg 2640 tcagtttcat gttggaatat tcgaggttgt gctagaaaaa atgctttggt agacactagg 2700 gacttttgtt tgcataacaa tgttaagatc ctaatgcttt gtgaagtaaa atcacaatct 2760 cccccctccc aagctatgat cacccaatgt gggtttctga attttgatgt tattccaact 2820 ataggatact ctggtggatt atggattatg tggaagcaat gttttattaa cccttttgat 2880 cttactatta tttttaaagc tgaaagattt atttcctgtc ttgtatctct cacggcactt 2940 caaaaagaat atgtgattat atttgtctat gctccggcca aacaagaatt taaacatgag 3000 ttttggtgtg acctattcaa tatgcacttt ctttatctct cccctttgtc attatgggag 3060 attttaatga gattgcttgt ttagaagata aaagtggggg tgctcctatt tcttcctcca 3120 gatttaatat tatgaataat atattttctc aactcccatg ttcagaaatc ccattttcag 3180 gacaaagatt tacttggcgc aaaaaaaggg caggagataa caatatttac gaaagattag 3240 atcgaggatt agcttctccc ttgtggattt ctttatttcc ttctgctaat attcttcacg 3300 ctgtatttac ttcttcggat cattgccaaa ttgtacttaa ttatcttccc tcgtcatctg 3360 ctaaagcccc tcccttcagg tttgaaaaaa tgtggtgtgc aagaaaagac tatgataccc 3420 ttgtaaagaa aacgtggtgt gttcagtttg atggctccca tatgtttagg ttagtaaaaa 3480 aatgcaaact cttaaaagaa aaatctaaag aatggaataa gtttcagttt ggaaatgttt 3540 ttcgccagtt aagacaagtg gattctaagc tgaaaacgct tcaacaagaa attcttgcta 3600 atcccctaaa tgtagatttg ctcaaaaagc aagacttatt tcttaaaaag cgctcttctc 3660 ttttagcttt tagtagtgag tattggaagc gaaaaaagta aaactatgaa cttaacttta 3720 ggagatacca attcatctta ttaccatact catgctacta ttcgaaaaaa caggaaccaa 3780 attcgtaggt tggtattatt aaatggtgac caaatcacca atccaaatgc aattgcccag 3840 aagttaaccg atgcttttgt tcatcgattt aaatcagatg acaaagtgtc atttgatagt 3900 aatcttgatt ttgctcttct ggatccaata atttcgcttc aagataacaa ttttttaact 3960 tcaacagtat taggtgaaga aattaaaaat gctgtttttg atctggcccc agataagtaa 4020 cctggcccgg atggattccc tccttttttc tttcaaaagt actggacttt gtttggaaat 4080 agtgttataa gagcggtcca agcattcttc cattctggaa atatcctaaa agaaataaat 4140 catactttcc tagctctaat cccaaaaatt gataatcctt ctactgcaaa tcattttcgc 4200 cctattagtc tctgttcaat aatttataaa atcatttcca aagttattac ctctcgttta 4260 aagacagtgt taggagaaat cattcatcct ctccagggtg cttttgttcc ggaccgtctc 4320 attcaagaca atattttgat tgctcatgaa gtttttcagg cctttcggtc taagactggg 4380 cctaatggct ggatagctat taagttggac atggaaaaag cgtatgatcg attagagtgg 4440 agttacattt tcatgaccct tgagaaactg gggttttcgc ctatttggat tggatggatt 4500 aaggagtgta tctcttcctc ttctttttcc gttctagtca atggggtgcc tggtgaaaaa 4560 ttcttccctt cccgtggtat tcgtcaaggg gatcctatct ccccttacct atttatttta 4620 tgtgcggaac ttcttgcaag attactttct tctgcggcta atagccccac gaaatcggta 4680 ggaatgccag taggtaaaac tggtattcgt gttccttttt tgacatttgc ggacgataca 4740 atgattattg ccaaagctaa taattatagt tgtttagtca ttcgacagat tttagataaa 4800 tatttttcca tgtcaggata aatggtgaac taccataaat cggcgttcca atgtacgggt 4860 aatgtttctg ctaatgaaaa acaagatttt gctaacatat tgggaatgac agaatctaac 4920 tctttgggtg actatttggg atgtcccatt atcacttcca aggttacgaa agaaactttt 4980 actccagttc ttaataaaac cataaaccaa cttcccaaat ggaaagctaa ttctctctct 5040 caggctggtc gttcggtcct tattcagtcc aatcttgctt caaagtccaa ttattacgag 5100 atgcaaagtt ttcgccttcc taagtatatc ttggagaatc ttgataaaac gtataggaat 5160 ttcttttgga acaaggacca tttaaataaa gcccccaatc tgattggttg ggatagaatt 5220 tgtaagccaa aaacagcagg aggcttaggt ttccgttctg cggaagtctc taataatgcc 5280 ctccaaatga agctgttgtg gagaataatc aaagatgata ataatatttg ggttcgtctt 5340 gttacaaagc gttttattaa gaattcaaat ctcttttata ttaaagtttc caagtctgcc 5400 tcgttggcaa tggcgaaatc ttcttaaatt aagagacacg ttcaagaaag ggttacgttg 5460 gcatcttggg gatggtaaaa gtattagatt ttggtcggat aattgggttt tccaataccc 5520 acttagtgct attattgttc ctactcctgg gacggagacc tatttggttg atcattgtat 5580 tttagactca ggaaggtgga acacccagat tttgctctct ttggtccctc ctcatattgt 5640 agcacaaatc atttctatct atatcccttc tgaatctcag ccggactccc ttgtttgggg 5700 ccttacggct gatggtgagt actctgtcaa gactggggct ctgcttgctc aaggtattct 5760 ccctgcttct gcggaaaaag tcgagtatgg gtggatttgg gggctccata tccctcctaa 5820 aattaaaaac ttcctgtgga aggcgtgtaa tgatggtctt cctatgaaat ctcggttaga 5880 aaaaagccat atcttcctcc ctcaacaatg tgttttttgt aattatgcaa gtgagtctat 5940 tggtcacctt tgttttcagt gcccttttac tagtgatgtt tttcatcacc ttaatgccag 6000 ctttcactgg cctattcctc gtgtctgtct tcaatctttg aatctttcct gcttccggtc 6060 ggctttggaa gcctgccata gtgtctcttc gaaaggagaa atagttaaat tctcctttgt 6120 atggtggttt gtctggtatt ttaggaacaa gcttattttt aataatgaag tggtctcttc 6180 taggcgggct accttcatta ttagctctta tgttttgacc tgggataagg ctcttgcggg 6240 tgatcatatt ggcagcttca ttcctgaggg acatagcaaa gttggtggtt ctcagcggtc 6300 cgggcctgct ttggactggt ccccgcctga tccaggtcac ttcaagctaa attttgatgg 6360 ttcgaaactt tccaatggca gttctgcttt agtgctttgt tattcgaaac tcggatgggg 6420 aagtcttgat tgctggtggt atatcgttag gctgccacac taccattctc caggaggaag 6480 cttggggaat gaaagagggc attgtggcgg ctctctctct taatatttct aaccttacca 6540 ttgagggtga taacttggcg gtggttaacg ctgtcagaaa gatatggaaa gttccttggg 6600 aaattcgtaa cattgtgact gatatacatg ctaatatagc tcgttttgat tcttttcagg 6660 tccagcactg ttttcgcgaa gccaacagat tagccgactt catggctcat cggggccata 6720 ccttccagaa tcttcattat tgtactccgc cctatgattt tgatttttct ctttgcatcc 6780 gcaaggatgt tttagcgtgg cctcctcatt gaggagctat cctaagtttt gtttccttat 6840 caaaaaaaaa aaaaaagaac acaaggattt acgtggttca gtcaaatttg acctacgtcc 6900 acaggtgggg gattagagct tcttcactat attg 6934 // ID Gypsy11-PTR_I repbase; DNA; EDCOT; 4519 BP. XX AC LG_XII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy11-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4519 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4519 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 300-300 (2007). XX DR Genome; LG_XII; Positions 4354160 4349642. XX CC Positions [3410-3904] - Integrase core CC 'GAATT' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS join(578..3088,3092..4519) FT /product="Gypsy11-PTR_I_1p" FT /translation="MLHRFGPTDYEDPSKALTRLRQSTTVSTYQMEFEKLS FT QRIDGLPENYLVGCFIAGLRDEIRLDVKVKQPSTLLDAIGVARLVEERIQL FT QKRFTPVLRTAGVLPQPKNNTSTLVDLLGPPPITSSSQKSQGGFTRITSQE FT ARDRRAKGLCFYCDEKFVRGHRCQRPQLFMIEDTSIGDELNFEEGVDDLPD FT MEPIPEISFHSISGANHPQTIRVISRLKNQDIIVLIDGGSTHNFLDQSVVS FT RLGLSVLRDKTFRVMVANREMIECNGQCLSLTVMIQGCTIQADFYVLPVAA FT CQAVLGEQWLETLGPIKTDYRELTMSFQQDGITRIFQGLRQSPHRILRDKE FT LVNIEGLGFFLQIAAVEVNETTTYHPNDLSQLLTEFQPIFEAPTKLPPERP FT QDHRIPLQPHQGPISVRPYRYPHYQKGKIEKMVKEFLESGLIRPSVSPFSS FT LVLLVKKADESWRFYIDYRALNQITIKDKYPIPVIDELLDELHNTRYFSKL FT DLRSGYHQIRVKEEDILKTAFRTHDGHYEFIVMPFGLTNAPATFQGLMNDL FT FRPHLRKFVLVFFDDILVYNHNWGDHLSHLHTVLTILSTNKLFVKQSKCRF FT GVMQVDYLGHLISHEGVQVDPVKTRAVNEWPTPTTIKGVRGFLGLAGYYRK FT FVSGFGGIAAPLTRLLTKEGFHWSAEATTTFNRLKQALVSPPTLRLPDFTQ FT TFIVESDACGVGIGAILIQEDHPIAFYSEALKGSALTLSTYEKEMLAIVKA FT IRKWHTYLLGKPFIVRTDQRSLKYLLEQRITTPSQARWLPKIMGYDYTIQY FT KKGKENQGADALSRVTECSCAAISMPVADWWAILQEVSQDPFYAQLDNPTS FT PLHHKLYFQRDGVWYKKGRVYLSPSSSLLPAILKEHHSSPTGGHFGYHKSL FT SRLKKSFNWPGLRSAVKDFIKHCEVCQRCKYDNTKPAGLLQPLPIPLQVWT FT DIFMDFVEGLPVSKGFTVIMVVMDRLSKYAHFVPLKHPFTASSVAKAFIDH FT IIRLHGMPKSIVSDRDKIFVISFWKTLFQLHGTNLTMSSSYHPQTDGQTEV FT VNRTLEQYLRCFTSAQPNKWIEWVSWAEYSYNTSVHTATKLSPFEVVYGVP FT PPSLLSYVPGTTKIQVVDDLLRSRSELLCELRLNLNVARDRMKMQADQSRK FT DVVFNVGDYVYLKLQPYRQNSVNFRRSLKQSPQFFGPYRVLARVGSVAYRL FT ELPVGSLIHDVFHVSLLKKHVGTLAPASPVLPPISKDSTLLPQPEAILDKR FT IIQKGRYSPRKELLVKWVGAPVEDATWENQWRFSRSYPEFILEDKDFSGRK FT E" XX SQ Sequence 4519 BP; 1297 A; 1089 C; 1005 G; 1128 T; 0 other; attggtatca gagcctggtt tgatcatgga gacgcgaact aaaacaaata cgaaatttcg 60 aaacgaggtg aatgaaactc tagctcgtca cgaagcgggg atcgatcaag ccaataacaa 120 catcacccaa gccaatcaca gcatcgatca aatgaatgca accctgctaa tggtggtggc 180 tgagttacag gccttttgtc atgcacaaaa ttccacggaa agagaggtaa gcccattttt 240 ccaagccgaa acatcgaccc atcaaaattc caacccacca gattttaacc catccaccca 300 acctgttatt cagaaccctt cacaaacaga cacttttcat tccacccaaa tagctgatcg 360 gaattacaca cagctcaagt tgtccttccc aagattcaat gggttagacc caacgggatg 420 gctatataaa gctgagcagt attttgaatt caaaaatgtc catcaccaac ataaggtgca 480 gctagcttcc tttcacttgg aagaagatgc tctccaatgg caccgttggt tgagtaaatt 540 ccggggacat ctcacttggg cataattctc ccaagctatg ctacaccgtt tcgggccaac 600 cgactacgaa gacccttcaa aagccctcac tcgcctgaga caatctacca ctgtcagcac 660 ctaccagatg gagtttgaga aactgtccca acgcattgat ggattaccag aaaattattt 720 ggttgggtgt ttcatcgcag gcttgcgaga tgaaatacgg ctggatgtca aggttaaaca 780 gccaagcaca ctattggacg cgattggagt ggcaaggttg gtagaggagc gaatccagct 840 gcagaaaaga tttactccag ttcttcgaac agccggggtc ctaccacaac cgaaaaacaa 900 caccagtact ttagtcgacc tcctaggacc accacccatc acaagctcaa gtcagaagtc 960 acaaggaggt tttacaagaa ttaccagtca ggaagccagg gatcggcgag caaaaggctt 1020 atgcttctac tgtgatgaaa aatttgtccg aggacaccgg tgccaacgac ctcaactttt 1080 catgatcgag gatacttcta ttggagatga attaaatttc gaagaaggcg tagacgatct 1140 tccagacatg gaaccaatcc cggaaatttc attccattca atttcaggag ctaatcaccc 1200 tcaaaccatc cgcgtgatta gtagactaaa aaaccaagat attattgtct tgattgatgg 1260 ggggagcacg cacaacttcc tcgatcagtc tgtggtgtcc agattaggac tgtcggtgtt 1320 gcgggataaa accttccggg taatggtagc taaccgtgag atgattgagt gtaacggaca 1380 gtgtttgagc ctcacagtga tgattcaagg gtgcaccata caagcagatt tctatgtgct 1440 tccagtggct gcatgccagg cagtattagg ggagcaatgg ttagagaccc tggggcctat 1500 taaaacagac tacagggaac tgacaatgag cttccaacaa gatggaatca ccagaatatt 1560 tcaggggctg aggcagtccc cgcacagaat cttacgtgac aaagagctgg tcaatataga 1620 ggggttggga ttttttttac agattgctgc cgtggaagta aatgagacaa ccacatatca 1680 tcctaatgat ctttcacaac tactgacaga attccaacca atcttcgagg ctccaacaaa 1740 actaccaccc gaacggccac aagatcatcg cataccgtta caaccacacc aaggccctat 1800 tagtgttcgg ccctaccggt acccacatta tcaaaaaggc aaaatcgaga agatggtaaa 1860 agaatttctg gagtctggcc tcattcgacc cagtgttagc ccattttcat cactagtgtt 1920 gctggtcaaa aaggcggatg agagttggcg cttctacata gattatagag ccctgaatca 1980 gatcacaatc aaagataagt atcctattcc ggttatagat gaattgctag atgaattgca 2040 taacacccga tatttttcga agcttgattt gcgttcaggg taccaccaaa tcagagtcaa 2100 agaggaagat atactgaaaa cggcattccg gacacatgat gggcactatg aatttatagt 2160 aatgccattc ggtctcacca acgcccctgc caccttccaa ggtctcatga acgatttatt 2220 caggcctcat ctgcggaaat ttgtgctggt gttcttcgac gatatattgg tgtacaacca 2280 caattggggg gatcatctct ctcatctcca tacggtactc acgatcctgt ccacaaataa 2340 actatttgtt aagcaatcca aatgccgttt tggagtcatg caggtagact atttggggca 2400 tctgatttca catgaagggg tgcaagtgga tccggtaaag acaagggctg tgaatgaatg 2460 gccaactccc accacaataa agggcgtaag aggattcctt gggctagcgg gttactaccg 2520 caagttcgta agtggattcg ggggaatcgc cgcccctctc acccgattgc tgacaaagga 2580 gggtttccat tggagtgctg aagcaactac aacctttaat cggctaaaac aagcactagt 2640 gtctcctccg accttgcgac taccagactt cacacaaact ttcattgttg aaagtgacgc 2700 gtgtggggta ggaatcggcg ccatcctaat acaagaagat cacccaattg ctttttatag 2760 tgaggctctc aaaggttcag cactcaccct gtctacatat gagaaggaaa tgttagccat 2820 cgtgaaagct atccgcaagt ggcacacata tctcttgggc aaaccattca ttgttcgaac 2880 ggaccagcgg agcctgaaat atttattaga acagaggatt acgacaccct ctcaagcacg 2940 ttggctgccc aagatcatgg ggtatgacta cacgatccaa tacaagaagg gcaaggagaa 3000 tcaaggagcg gatgcattgt caagggtgac agaatgtagt tgcgcggcca tttcaatgcc 3060 cgtagctgac tggtgggcta ttctgcaata agaagtatcc caagatccct tttatgctca 3120 gttggacaat ccaacttcac ctctgcatca caagctttat tttcaacgtg atggagtttg 3180 gtacaagaag ggacgtgtgt acctgagtcc ttcatcttcc ttactacctg ctattctgaa 3240 ggaacatcat tcctctccta ccggggggca ttttggctac cataagtctc tcagtcgcct 3300 caagaaaagc ttcaactggc cggggttacg atcggctgtt aaagacttta ttaagcactg 3360 tgaggtatgc caacgatgca agtatgacaa caccaaacca gccggcttgc tccaaccttt 3420 acccattccc ctacaggtat ggactgacat tttcatggat tttgtggagg gattaccagt 3480 ttccaaaggt tttactgtca ttatggtggt tatggaccgc ttgtccaaat acgcccattt 3540 cgtgccatta aaacacccat ttacagcatc ctcagttgct aaagccttca ttgatcacat 3600 tattcgcctt cacggaatgc caaaatccat tgtgagtgat agggacaaga ttttcgtgat 3660 ttcgttctgg aaaactctat tccaattgca tgggaccaac ttgacgatga gttccagtta 3720 ccatccacag accgacggtc aaacagaggt ggttaatcgc acactggaac agtacctccg 3780 ttgcttcacc agtgcacagc ccaacaaatg gatagagtgg gtttcttggg ccgagtacag 3840 ttacaacacc tccgtgcata ccgccaccaa actatcaccg tttgaggttg tttacggtgt 3900 gcctcctcct tcactgctct cgtatgtgcc agggactaca aaaattcaag ttgtcgatga 3960 cctcctccgc agtaggtctg aactgttatg cgagttacgt ctcaatctga atgtcgcacg 4020 agacagaatg aagatgcagg cagatcaaag tcgtaaagat gtagtattca atgtcgggga 4080 ttatgtctac ttaaagcttc aaccataccg ccagaactca gtcaattttc ggcggtcctt 4140 aaaacaatcc ccacagtttt ttggacccta tcgagtgttg gctagggtgg gctctgttgc 4200 ctatcggttg gaattaccag ttggatcttt aatccacgat gtgtttcacg ttagcctttt 4260 aaaaaaacat gtgggcactt tggccccggc ctccccagtt cttcctccta tttcaaaaga 4320 ttctacactg cttccccaac cagaggccat actggacaaa cgcatcatcc aaaagggacg 4380 gtatagccca cgcaaggaac tgctagtcaa atgggtgggg gccccagtcg aagacgcaac 4440 atgggaaaat caatggcgtt tctcccgatc atatccggag tttatccttg aggacaagga 4500 tttttcgggt aggaaagaa 4519 // ID Copia46-PTR_LTR repbase; DNA; EDCOT; 479 BP. XX AC scaffold_218; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia46-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-479 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-479 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 271-271 (2007). XX DR Genome; scaffold_218; Positions 142818 143296. XX SQ Sequence 479 BP; 129 A; 81 C; 106 G; 163 T; 0 other; tggtgtaaag tcacttaatt aaatccacat aattggtgga gttgttggca taattggtgg 60 agtatgagtg gagatgagtt gttggcataa tttgtgccat aatttatggc ctttgtctcc 120 tcactcttgc ctataaatag gcaaggcctc caagcttatt ttgcacacca agatagagag 180 aaagaagaga gagtgaacag agagtaatcc cacaaagttg tgagttattt gtgaaagagt 240 aactgaggtg ttttctccta gtaatagaga gatttcagtt gttctcctat tagtaaagag 300 aggttgtaat tcccacatta cttagtaaaa tccttctata cttgcccgtg gacgtagcca 360 aattgggtga actacgtaaa tttttgtgtc tcttttctca tcccttacct tttatcttgt 420 tgggtttgca tgccaatttc ctaacagtgg tatcagagcc tcctggttgg tgttttcaa 479 // ID SHALINE9_MT repbase; DNA; EDCOT; 2968 BP. XX AC . XX DT 01-JAN-2007 (Rel. 12.01, Created) DT 21-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A LINE element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed; repeat; Poly-A tail; SHALINE9_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2968 RA Shankar R. and Jurka J.; RT "SHALINE9: A LINE element from barrel medic."; RL Repbase Reports 7(1), 99-99 (2007). XX DR [1] (Consensus) XX CC The 5' of the element seems to be truncated while the 3' end is CC very well conserved and exists in multiple copies. The sequence CC is present with domains for RT polymerase as well as RNAse. XX FH Key Location/Qualifiers FT CDS join(37..402,406..450,469..492,496..693,697..1269, FT 1273..1314,1318..1398,1402..1473) FT /product="SHALINE9_1p" FT /translation="MNKKKGKNGYILFKIDFEKAYDRVDWNFLRITLRDFG FT FPTSIITLIMKCITSFTLSLKWNNEKLESFNPQRGLRQGDPMSPYLFVFCM FT EKLSMLILEKVQSNEWHPIKIFNNGLAISHLFFLMIAFCSLKLNPLKLERV FT FVMLLGKLILKKSKFMSSANISRKKVNKFSSIIHFTHYTQLAQYLGFPMLS FT ARIKNVDFAYIMDRVNSILDGKTKLFSRAGRVTLAQSMVYSLPTYSMQNLW FT IPEGVCNQIYASIRQFTSGRKHSHWVNWKMITQPKSRGRLEIRTDRASNIS FT IMGKHVWDLLHNPDKLWVNFLSSKYLHGISILVATNYQGSSCVWKAITKTV FT EVLKFGFKTRIGREDVSLWYDKWLEDDYLCNLVTYVHISETNLRLKDIYHT FT TAGISLISLRYLSIFNSKFKVSSISLPKTSRFGLIPHQVCTLLKVVISGHQ FT TLFILQVRLSRKHDIGFGNSTF" FT CDS join(644..727,731..862,878..1033,1037..1099, FT 1103..1219,1229..1378,1382..1552,1556..1801, FT 1820..1993,1997..2371,2375..2572,2576..2629) FT /product="SHALINE9_MT_2p" FT /translation="MLTLLISWIESIAYWMVERQNSLVEQGGHWPNLWSIL FT FLPTLCRIYGFLKGCVTKYMHLSDNLLPEGSIVIGLHNLSLEGVLKFGQIV FT LQIYLLWANMFGICFIIRISFGSTFFLLNIFMVSLFWQQIIRVLLVFGRLS FT PRQLKFNSVSRLELEEKMFLFGMTNGWRMIIFVILSLMSTLVKLIRTFTTR FT LLEFLSSHNSDTSQYSTPNSKYLNRLVFPRHQDLDSFPIRYVLCKWLSVVD FT IKLSLFCRLDSAGNMTLDLETQPSRESETYLFCWLCMVTFQRMHLVLVDIP FT YIHHARDVDLVLSHFFTPFGVFHLSLAIWDALLFNKDTNFNSQDFNWWLKH FT HSLDPNGNIFIITCWVLWKAQNHKVFNGNDLSHIYSLHSYVVVYLSNDATQ FT KPIRQVKWIPHLDNIIKVNVDGSSLSNPGRSGFGGLIKSNGDWLLGFYRFC FT GITSCLAAKLYVIFHGLRIAYDAGHKNIILESDFRMALDLIMSDVQSHHPH FT APLISQIVQLQHRDCIVNFHHTLRQGNACADWLAKHDASSSYALKSWIFLP FT SSTASFPSECSWSCSFEIVVWFCFYHFFLIKKKKIIIVSLVCYNLKAKKNY FT IFSFNQNQNFLKKNVVHNFQTLAEKERKDENVSVHLLTSTYL" XX SQ Sequence 2968 BP; 869 A; 491 C; 557 G; 1051 T; 0 other; gataatgtta ttatcgcata ggaaatagtt catagcatga ataagaagaa agggaaaaac 60 ggttatattt tgttcaaaat tgattttgaa aaagcttatg atagagtaga ttggaatttt 120 cttcgcatta ctttacgtga ttttggtttc cctacttcca ttattactct tattatgaag 180 tgtataacct ctttcacttt atctttgaag tggaacaacg aaaaactaga gagttttaat 240 cctcaaagag gcttaaggca aggggatcct atgtctcctt atctatttgt cttttgcatg 300 gaaaaacttt ctatgttaat tctggagaag gttcaatcta atgaatggca tccgatcaaa 360 atctttaata atggtctagc tatttcacat ttattttttt tgtagatgat tgccttttgt 420 tcactcaagc taaatcctct caagctagaa tagtgaaaca ggtgttagag agtttttgtc 480 atgcttctgg gttgaaagtt aatattaaaa aaatctaaat tcatgtcttc tgctaatatc 540 tctagaaaaa aagtgaataa attttcttct atcattcatt ttactcatta tactcaatta 600 gcgcagtacc ttgggttccc tatgttatcg gctaggataa aaaatgttga ctttgcttat 660 atcatggatc gagtcaatag catattggat ggttgaaaga caaaactctt tagtcgagca 720 gggagggtaa cattggccca atctatggtc tattctcttc ctacctactc tatgcagaat 780 ttatggattc ctgaaggggt gtgtaaccaa atatatgcat ctatcagaca atttacttcc 840 ggaaggaagc atagtcattg ggtgaattgg aagatgatta cacaacctaa gtctagaggg 900 cgtcttgaaa ttcggacaga tcgtgcttca aatatatcta ttatgggcaa acatgtttgg 960 gatttgcttc ataatccgga taagctttgg gtcaactttc tttcttctaa atatcttcat 1020 ggtatctcta ttttagtggc aacaaattat cagggttctt cttgtgtttg gaaggctatc 1080 accaagacag ttgaagtttt gaaattcggt ttcaagacta gaattggaag agaagatgtt 1140 tctctttggt atgacaaatg gttggaggat gattatcttt gtaatcttgt cacttatgtc 1200 cacattagtg aaactaattt gagactgaag gacatttacc acacgactgc tggaatttct 1260 ctcatctcat aactcagata cctctcaata ttcaactcca aattcaaagt atcttaatcg 1320 attagtcttc ccaagacatc aagatttgga ctcattcccc atcaggtatg tactctgtta 1380 aaagtggtta tcagtggttg acatcaaact ctctttattt tgcaggttag actcagcagg 1440 aaacatgaca ttggatttgg aaactcaacc ttctagagaa tctgaaacat atttattttg 1500 ttggctatgc atggtaacct tccaacgaat gcatttagtg ctagtagata tttaacctta 1560 tattcatcat gcaagagatg tggatctagt attgagtcac tttttcacac cttttggagt 1620 tttccatctc tcattggcga tctgggatgc cttgttgttc aacaaagata caaatttcaa 1680 ttctcaagat ttcaattggt ggttgaaaca tcattccctt gatcctaatg gtaatatctt 1740 cattattaca tgttgggtct tatggaaggc acaaaatcat aaggttttca atggaaatga 1800 ttaggtaaat tgggtttgac ttagccatat ttattctctt cattcatatg tggtggtgta 1860 cctttctaat gatgcaactc agaagcccat tagacaagtt aaatggattc ctcatttgga 1920 taatatcatc aaagttaatg ttgacggtag ttctctttct aatcctggga gatcaggttt 1980 tggaggtctt atttgaaaaa gtaatggtga ttggttgctg ggtttttata gattttgtgg 2040 tattacttct tgcttggcgg ccaaattgta tgtcattttt catggccttc gtattgcgta 2100 tgatgcgggt cacaagaaca ttattcttga atcagatttt aggatggctc ttgatttaat 2160 catgtcggat gtccaatctc atcatcccca tgctcctcta attagtcaga ttgtccaact 2220 gcaacatcga gattgcattg ttaattttca tcataccctc cgtcaaggta acgcgtgtgc 2280 ggattggctt gctaagcatg atgcttcttc ttcgtatgct ctaaagtctt ggattttttt 2340 gccctcctca actgcgtcat tcccttctga atgatgctct tggagttgct cgtttgagat 2400 tgtagtttgg ttttgttttt atcatttctt cttgataaaa aaaaaaaaga taatcatagt 2460 tagtttagtt tgttataact tgaaagcaaa aaaaaattat atttttagtt ttaatcaaaa 2520 tcaaaatttc ttaaaaaaaa acgtcgttca taattttcaa acgttagcgg aataaaaaga 2580 gcggaaagat gagaatgtga gtgtccatct tttaactagt acttatttat aaataaggtc 2640 atgttgaact tgaaaaagaa attctacaac aactaacaca tcacgctttc cacttaagtt 2700 tgggccacgc agggcaagtc ctaggccata gactaggggt gcgacggcct aggcccttgt 2760 cggtaggggc ttaatttttg tttacggagg gggtgtatat agaaatattt ttttatgggg 2820 ggatatatat aataaatttc acataaaggc cctaaacatt gacattatga agggcttgac 2880 ttaagtctgt tcatattttt ggcgcaattt gttatatgta tttccgtaca gcacaaagat 2940 ttctttatac actctcccta taaaaaaa 2968 // ID SHACOP17_I_MT repbase; DNA; EDCOT; 4131 BP. XX AC AC127428; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP17_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW ORF; aspartyl protease; Interspersed; repeat; SHACOP17_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4131 RA Shankar R. and Jurka J.; RT "SHACOP17_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 61-61 (2007). XX DR EMBL/GenBank/DDBJ; AC127428; Positions 43416 47546. XX CC The internal region has intact domains for gag, pol, aspartyl CC protease and integrase. XX FH Key Location/Qualifiers FT CDS 104..2386 FT /product="SHACOP17_I_MT_1p" FT /translation="MKNLLISQKLHKALVGKEQKPVSMKDEDWEELDLEAR FT AAIILCLERDVAFLVNEEATTAGVWSKLEKTFMTKTLTNRIYLKSKLYTCK FT MEEGTSIRDYVNKFDRIISDLKDIDVKIDEEDQALILLLSLPESYENLVQT FT LMLVGDTLTMDETRTSLLADDLRKVATSGMSSSGREHREQAQGLFATRGRT FT NERGQGRGRKSRSKSRAPAERTCFKCGELGHFKANYPNKRVLFQNKQANNG FT NNSKGKQQDLSKASYVSNDEDDCFSVSERDHDISGKWMLDSGASHHMCPNR FT KWFATYQSIDGGTVLMGNNHACKIMGYGTIQIKMHDGALRTLMNVRHVPNL FT RKNLISLGVLEENGCKIVMEDGILKVVRGSLVVMKGVRHRNLYPLIGKTVT FT GDLAVGIIGSKDQTECTRIWHMRLGHMSEKGLSLLGEKGLLKNMKKPCMEF FT CEHCVYGKAHRLKFSTRKHKSRGLLDYVHTDVWGPASVTSKGGSRYFVTYV FT DDYSRYAWIYFLKHKNKVFDIFKCWKAMVENRTGRKLKTLRSDNGTKYTDG FT AFKRFCDQEGIVRHWTVRGTPQQNGVAERLNRTLLEKARCMRSNSRLDREW FT WAESVATAGYVVNRSPHSSLGGDTPYKVWSGEYADYDKLKIFGCMSYYHVK FT DNKLDNRAKKAIFLGYAKGVKGYRLWCLEDSKFVISRDVTFDEKSMVPNYG FT DVQVSNQRVDIESKDQPDSSHDQVEHPSVTQDDEEDELDNEVQQGKYTCIA FT TAAAGIFGYH" FT CDS 2265..4055 FT /product="SHACOP17_I_MT_2p" FT /translation="MIRWNILVSLKMMRRMNLIMRFNKENTHVLQQQLQES FT LDTTRPKTNYKTVQKLGSDKPLRHYGQVNLVEYALSVEDDEPVTFKQAIKD FT KDKESWLVAMEEEMQSLHKNKTWEVVPLPVGKSAIGCKWVYKRKEDHTKSC FT GTRYKARLVAKGFAQKEGVDYNEIFSPVVKHTSIRVLLSLVAHGDLELEQL FT DVKTAFLHGDLDEEIYMYQPEGYKVEGKESQVCRLRKSLYGLKQSPRQWYK FT RFDSFMIKQGFSRSSYDSCVYIQKLHGGDYIYLLLYVDDMLIASKGKVEID FT KLKSKLGKEFETKNLGAAKKILGMEISRERTNRKLFLSQKGYLERVVERFG FT MKGSKSVVTPLAPHFRLSGNQSPTTAEDKENMKNVPYASAVGSLMYAMVCT FT RLDILQAVSVVSRFMANPGKAHWEAVKWILRYLNGTINTGLCFGGDTCQIS FT GFVDSDYAGDLDRRRSTTGYVFKIHGAPVSWRSMLQSTVALSTTEAEYMAV FT AEAVKEALWLRGLLGDLGVTQERVSLMCDSQSAIHLAKNQVHHARTKHIDV FT RYHFVRDVIEEGRISLAKVHTDENSADMLTKVVSGGKFQHCLDLLNILTC" XX SQ Sequence 4131 BP; 1330 A; 621 C; 1044 G; 1136 T; 0 other; tcagaagcca aaaatggctt cttctagtgg atcggtcaag gtcggcaaat atgaaataga 60 gaagttcaat gggaaaaatg atttttccta ttggaggatg tagatgaaaa atctgcttat 120 atcacaaaag ttgcataagg cgttagtggg aaaagaacaa aaacctgtga gtatgaagga 180 tgaggattgg gaagagttag atcttgaagc acgggcagcc ataatcttat gccttgagag 240 ggatgttgca tttttggtta atgaagaagc aactactgct ggcgtatggt caaagttaga 300 gaaaactttc atgacgaaaa ctctgacaaa tcgaatctat ttgaaatcca aattgtatac 360 atgcaagatg gaggaaggca cctcaatccg ggattatgtc aacaagtttg ataggattat 420 atcagacttg aaggatatag atgtgaagat tgatgaagaa gaccaagcac tcatattatt 480 gctttcatta ccagagtctt acgaaaatct agtacaaaca ttgatgcttg tgggtgatac 540 tctaaccatg gatgagacta gaacatcact tttagcggat gatcttcgaa aggttgctac 600 aagcgggatg tctagcagtg gaagagaaca tagggaacaa gctcaaggat tgtttgctac 660 tagagggagg accaatgaaa gaggacaagg caggggaagg aagtctagat caaaatctag 720 agctcctgcg gaaagaacat gttttaaatg tggtgagctt ggacatttta aagcaaatta 780 tccaaataag agggtattat ttcagaataa gcaggccaac aacggcaaca actctaaagg 840 caaacaacaa gatttgtcaa aggcgagtta tgtatctaat gacgaggatg attgtttctc 900 tgtctcagag agagaccatg atatttcagg taagtggatg cttgattcag gagcctcaca 960 ccatatgtgc ccaaatagga agtggtttgc tacctaccaa agtatagatg gtggaactgt 1020 tttaatgggg aacaaccatg cctgtaaaat tatggggtat ggtacaatac aaatcaagat 1080 gcatgatgga gcgttaagaa ctctgatgaa tgtgagacat gttccaaatt tgcggaaaaa 1140 ccttatttct cttggcgttc tagaggaaaa tggttgcaaa atagttatgg aagatggaat 1200 tttaaaagtt gtacgtggtt cgttggttgt gatgaaggga gttcgacaca gaaatcttta 1260 tcctcttata ggtaaaaccg ttacaggaga cttggcagtt ggaatcattg gaagtaaaga 1320 tcaaacagaa tgcacaagga tatggcacat gcgccttggg catatgtcag aaaagggtct 1380 atcattactt ggtgagaaag gtttgctgaa gaacatgaaa aagccatgca tggaattttg 1440 tgaacattgt gtgtatggaa aagcacatcg cttgaagttt tctacaagaa aacacaaaag 1500 cagaggattg ttagactacg tgcatactga tgtttggggt ccggcttcgg ttacttctaa 1560 gggtggttcc aggtactttg ttacatatgt tgatgattat tcgaggtatg cttggattta 1620 ttttcttaag cataagaata aggtatttga tattttcaag tgttggaaag caatggttga 1680 gaacagaacg ggtagaaagc tgaaaactct gcgatcagat aatggtacaa agtatacaga 1740 tggagctttc aagaggtttt gtgaccagga aggcattgtt agacactgga cggtaagagg 1800 cacaccacaa cagaatggag tcgcggaaag actgaaccgt acacttcttg agaaagcaag 1860 gtgtatgcgc tctaattcta ggttagatcg agaatggtgg gcagagtcgg ttgctacagc 1920 tggttatgta gtaaacagat ccccacattc tagtttaggt ggagacacac cctacaaggt 1980 gtggtcaggt gaatatgcgg actatgacaa actcaaaatt ttcggatgca tgtcatatta 2040 tcacgtcaag gataacaaac ttgataatag agccaagaaa gctatttttt taggatatgc 2100 aaaaggggtc aaaggctatc gtctttggtg tctagaagat tctaaatttg tgattagcag 2160 ggatgttacc tttgatgaga aatctatggt gcctaactat ggtgatgttc aagtatcaaa 2220 tcaaagagtt gacatagaat ctaaagacca accagattct agtcatgatc aggtggaaca 2280 tcctagtgtc actcaagatg atgaggagga tgaacttgat aatgaggttc aacaaggaaa 2340 atacacatgt attgcaacag cagctgcagg aatctttgga taccactagg ccaaagacaa 2400 attataaaac agttcagaag ttggggtcag acaaacctct aaggcattat gggcaggtaa 2460 acttggtgga atatgcactc tcggttgaag atgatgagcc ggtcaccttc aaacaagcta 2520 tcaaagacaa ggataaagag agctggttgg ttgcaatgga agaagagatg caatctcttc 2580 acaagaacaa gacatgggag gtagtcccat tacctgtagg aaagtctgct attggttgca 2640 aatgggtgta taaaagaaaa gaagatcata ctaagtcgtg tggtacaaga tataaggcta 2700 gactagtggc taaagggttt gcacaaaagg aaggagtcga ttacaatgag atattttctc 2760 cggtggtgaa acatacttct atccgagtgc tattaagttt agtagctcat ggtgatcttg 2820 agctggaaca actagatgtg aagacagcct tcttgcatgg agacttagac gaggaaatat 2880 atatgtatca acctgagggt tacaaggttg agggtaaaga gagtcaggta tgtcgcttga 2940 gaaaatcact ttacgggttg aaacaatctc ctagacagtg gtacaagcga tttgactctt 3000 ttatgataaa acaaggtttc tctagaagta gttatgatag ttgtgtctat attcagaagc 3060 ttcatggagg tgattatatc tatctattat tgtatgtcga tgacatgctt attgcttcaa 3120 aaggcaaggt ggagatagat aagctgaagt ctaaacttgg taaagagttt gagacgaaga 3180 atttgggcgc tgcaaagaaa atactgggta tggagattag tagagagagg acaaaccgga 3240 aactgttctt gagtcaaaaa ggctatttag agcgggttgt tgaaaggttt ggaatgaaag 3300 gttctaagtc ggtggttact ccattagctc cacattttag actttctggt aatcagtctc 3360 ccactacagc agaagataag gaaaacatga aaaatgtacc ttatgctagt gcagttggca 3420 gtttgatgta tgctatggtg tgtacacgtc tagacatttt acaagcggta agtgttgtta 3480 gtagattcat ggcaaatcca ggaaaggcac actgggaagc agtgaaatgg attttgaggt 3540 acttaaatgg taccattaac actggtttgt gttttggtgg agatacatgt caaataagtg 3600 gctttgttga ttcggattat gctggtgatc tagatagacg acggtctact actggttatg 3660 tgttcaaaat acacggtgct ccagtaagtt ggcgatcaat gttacaatct acagtggcac 3720 tatctactac ggaggctgaa tatatggccg tagcagaagc cgtaaaggaa gcattgtggc 3780 tgagaggtct tctaggtgat ttgggtgtta cgcaagaacg tgtgagtctg atgtgtgata 3840 gtcaaagtgc gattcacttg gctaagaatc aggttcatca tgctcggacc aagcatatcg 3900 atgtaaggta tcattttgta cgggatgtga tagaggaagg tcgtatttct cttgcgaagg 3960 tacatactga tgagaactca gctgacatgt taaccaaggt tgtgtcaggt gggaagttcc 4020 aacattgtct ggacttgctc aatattctaa catgttgatt catgtggagg cataataaga 4080 cgcaatttgt tcgtccaaaa tttgaagttt cttttcaaat tttgaacgag g 4131 // ID Gypsy-12_Mad-I repbase; DNA; EDCOT; 12162 BP. XX AC ACYM01056235; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-12_Mad-I; KW Gypsy-12_Mad-LTR; Gypsy-12_Mad_. XX NM Gypsy-12_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-12162 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1335-1335 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01056235; Positions 41760 29599. XX CC Positions [6642-7073] - Integrase core CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS 4244..6118 FT /product="Gypsy-12_Mad-I_1p" FT /translation="MADDLRPLFISALLPHIMKVELCHLLDEFKECFAWSY FT HKMPGLDRSLVEHELHIKASCKPFHQPPRRFSTEVQLGIKDELVRLLKAGF FT IRTARYVEWLANIIPVLKKNGALRICIDFRNLNLTTPKDEYPMPISDLLID FT AAAHHEILSFMDGHAGYNQIFIAEADVYKTAFRCPRALGTYEWVVMPFGLK FT KARATYQRAMNTIFHDLIGTIVEVYIDNVVIKSARRQTHLDDLRQAFLCMR FT RHNLKMNLAKCAFGVSVGNFLGFLVHHRGIEVDDNKARTIINALPSTTKKQ FT LQSLLGKINFLRRFIANSAGKMKAFSTLLKLKDSDTFEWHAEHQEAFTQIK FT VSLTTPPVLVPPRQGQPLKLYISTVEESIGCLLAQDNDVGREHAIFYLSWN FT LNPPEINYSAVEKLCLTLFFAVSKLRHYMLPSVTQVIVQTDVISYMLTRPI FT VKGRIGKWTMALSEFSLQYVPQKAVKGQALADFLAHHPSPYEFGGNNIDIG FT LIQTRDNYWTMYFDGSSTSVSVGVGIVIQSPTHNHWYFSLKLDFDCINNQA FT EYEALVIGLSVLHDLRATRVLVLGDSELVINQLNGTFRWMICTLAPYHMVA FT SYLIESFDRITFKHISPVHNTDADELA" XX SQ Sequence 12162 BP; 3528 A; 2674 C; 2828 G; 3132 T; 0 other; ttttggctca cctagtggga cccagtgcta agattacgaa gttcatgacc atcgaaacac 60 gatcaataaa aaagaaaacg accatgggaa aatcaacaac cgatttgtcg gttcaaagtc 120 ctggacaaga ggtgtcacat gggcgaaatc ctatcgtcgt tgtgacccct gaggctacaa 180 gtatgacaca ccaagaaaag gaagtgtgcc tcggtggcta gcctcgaaat acagaaatac 240 ccaaccgaac tgcaggcgtt ttcattgaag gaatagtgaa ggactgcgat gaagacggtg 300 gtgaaggctc tgatcctccg actaggtcgt ttcttcgaag atgacttgac gagcaatctc 360 gacaagagga atagacagtg ggccataaaa tgaattgttt gcttgaagtg atacaaagca 420 attgagagac ccaaacccga tttctcgaac taatagttag taaagttttc gaagagaaac 480 ctgttgatca agctcgacaa cttccactta aaggtaattc cttacaggcc gaagtggtgt 540 ctactcggcc caagacaatt gacctagaaa aaaagggagg ttcaagtagt aggacagatg 600 aatccgacca gagagtggaa gcaacacccg tcgatatgat cgaggtccag cggatgatta 660 attcggccat gaaaaaaggg ccaaagtttc ctaaattcat ccatccgtat ccagcttatg 720 tagaaaggtt caaatatcct aaaggtttca aaattccaga ttttagcctt ttcgctggag 780 aatcgtcctt atcctcttta gaacatgtgg ctcgtttcac cgcacaatcc ggagatgtta 840 atagtgactt tcacaagctg cagctgttca atttttcgtt gatcggctca gcattttcct 900 ggtatatcaa actcccacct aattctgtcc aaagctggga ggagttggtc gagaaatttc 960 acgagcagtt ttatcggcca gggatggaaa tgtcagtttc ttcattcgcg aggatggctt 1020 aagcatctga tgagtcacca atggattatc ttaccagatt taaatcggcc aggaattggt 1080 gccgagtacc tctccccgaa gttgaatttg ttaggcttgc tttaaatgac ctcgacgtag 1140 aatacaaaaa gaaattctta ggggtaaact ttcgggatat gtatgaacta gcccagcatg 1200 tcgagcaata tgattatttg ctccaagaag agaagatctc gaaatcccca tcctgaagga 1260 cgatttacaa aaatcccacg gtcagttacg catcgaccga atgcgaggag tcttaatacg 1320 tcagcgtgga tgcggctgag atagtaatag ataaaccata catttgctag gcattgactc 1380 aaattaattc caaggatgtc aaaacccgtt cggccactga agaaatagcg aaaaacatca 1440 aaagtttaca cttttgatat cacaaaggac gaagtaattt tgtatcaact gttatcagca 1500 aagatcatca aacttcggcc tgggcataac attcccaagg ccgaagagcc taaaggaaag 1560 acatattgca aatatcataa ctcgaccaag catgccacaa ataattgtgt catatttcgt 1620 gatgatgtcc agagttggat tgacaaaggc aagctaaagt ttcctgaaaa atgcatgaca 1680 gttgatacag atccattccc ttcggcaaca gttggcatgg tagacgcccg tttgcccgag 1740 agcaaaggga aagagaaggt caggtttgcc ccaatacaac acatcctaaa gaaaggttcc 1800 cagtctcaac tcaagatcga cctattttcc aatacgccac ctaccgagct ctcaggaccg 1860 gccatagttg aatccatgtc aaactccagc aaagaagaaa atggcgggcc gatagttttg 1920 tgcagcaatt gtaaggcacg cgttttatta atagagccca aggagaaact gcctcagacg 1980 cagacgccga cgtcacaata acaatcggcg atcacggtga caccttcaaa ggaacatagt 2040 gaaggccagc gccagaaagt gttctagagg ctcggcccta agaaacagac ggatggccct 2100 acctcggtta gacggtgcct taatttcgac gcaccgtttt ataataagga ttattatttg 2160 tgtaattcca gtagctcaat cttataagca aatccaaaaa ctttcaagcc gcctgaacca 2220 cgtgaccaac gttggtacaa ctacaattct cccaccggca tgtataccgc actttccaaa 2280 tctcagaaac gtcgacgtca gcgtatagat tgcttggctc aacggcaagt ggcccagcct 2340 gtttcggcca ctaaatggca gccgaaagag acggcaggga gcggagatga ccagccaacc 2400 tcaataatca tggttgagtt acaagggcag aaggaaacca attgtgactt ataaactact 2460 atcgaagagt ccgagaagca catcaaactc ctcattcggc ccggagaaat gaaggcctgc 2520 ttcgagcaat ttaagaaaga ggccgaaagc caattgcccc tgttaccttt gaaagaaccg 2580 ctaatcagag ttcggtggaa tttgcacctc ccattccttg gtgaatcttt ggagtacatg 2640 aaagagtttc acaagaaata ttctaccaac gacttgtatc gtttgcccaa ggcatgccaa 2700 taagctcttg acctggcatt aacttgcccc gatgctgagc agatcatcca aaaaactact 2760 gatccagcga tgaaagctag attccagcac attcgagagg ctagggttct tggcttcgag 2820 gtcgacccat acacagacat tgacatagcc gaactctttt ttttctcgaa gaccttcaac 2880 acctttgata tcacttcgaa gtctttttgg tcgtatcctt attcggttta acggccaatg 2940 agaaagatcg ggtggcacgt ctcgacgcct acctagatac aaggaatgcc cagatcgcct 3000 atgaggaacg agctcgtaag atgcggcagg agcaaagtca gacactagat gcatgcaagc 3060 ccgacgacga caatcaaaag gacacagagt cggattatat ggcacaagcg taagagtatg 3120 ttgagacaca caataatcag gccaagaatg ctctaacaca cgatgctata gtcctcacca 3180 acccggaaga tgacgatcag gatctaatgg gccattcagt ccttgaaaat atggaaatca 3240 acatggtcca ttttctactt gctgaattcc agctgactac acaccaacca agctcattgg 3300 atggcgatgt ggttgccaag gaagcaacac aagttgattt cgtcactacc actgaagatg 3360 agtcagcaaa cggcgatgat aaacttaaaa cagccttggg catcttgttt ccccattctt 3420 cctcggctaa tcttcagcat ttaaaaccgt tgtatgtcac ggcccatatt gaaggctacc 3480 caatctccaa aattttcgtc gattgtggag caacgatcaa tatcatgcct gtatccgtca 3540 tgaaagcatt aagacgatcc aacgacgaac tcattccttc aggaataacc atgagcagct 3600 ttgtcggtga caagtctcaa accaaaggag tactccctct agaggtcaac attgcaggtc 3660 gcaatcacat gaccgcattt tttatcgtcg actccaagac cgaatataat gctttgctcg 3720 gtagggattg gattcatcaa acgaattgca ttccttcttc tttataccaa gttctcattt 3780 tttgggatgg taaattggtt atggtccacc tagccgatat tcagccgttt gaaaccaaca 3840 tgattcaggc ctgctattat gatgatcacg tcggctatat taccctacag ggttttaatg 3900 aagatggacg gctgactcgg atctcagtcc agaaaaccat cgaggtaggc gccgagactg 3960 tccatcagga ttcggcaaga ctcggtttgg ccaacttgat cccaactact gatgattgat 4020 gacaaagatg agaggtatca ggccgcggtt tcatccataa tggaacgcct gctggcccat 4080 tggtatgtta tttccagaca cccacattcg ggcatcaact taatcgaatt cttggccgaa 4140 taacggccta gtattatcgt tcgacagagt tcaggccgca ccggtcgaac tcgaagacaa 4200 tcgaccccaa gttaagaacc cttcagagaa aataaatgtc ggaatggctg atgaccttcg 4260 accattattt attagtgcat tgttacccca tatcatgaaa gtcgaactct gtcacttact 4320 tgacgagttt aaagaatgtt tcgcttggag ttatcacaag atgccgggtc ttgatcggtc 4380 cttggtggaa catgaattac acatcaaagc tagttgtaag ccttttcacc agcctcctcg 4440 ccgtttctcg accgaagtac aactcggcat aaaggacgaa ctagttcgac ttttaaaagc 4500 tgggtttatt cggactgccc gatacgtcga gtggttggct aatatcatcc cggtattaaa 4560 gaaaaatggt gccctgcgta tctgcattga ttttcgtaat ctgaacttga caacgcccaa 4620 agacgagtac ccgatgccaa tatccgattt gttaattgac gctgcagcac atcatgagat 4680 tctatccttc atggatgggc atgccggtta taaccagatt ttcatcgccg aggcggatgt 4740 ctacaagact gcctttcggt gtcccagagc actcggcaca tacgagtggg ttgtcatgcc 4800 cttcggtctc aagaaagcca gggctacata ccaacgagct atgaacacta ttttccatga 4860 tttaatcggt accatcgtcg aagtttatat tgataatgtg gtcatcaaat cagcacgacg 4920 acagacgcat ctagatgacc tacgtcaggc attcttgtgc atgcgccggc ataatctgaa 4980 gatgaatctc gccaaatgtg ctttcggcgt atcagttggg aattttttgg gcttcctcgt 5040 ccatcatcgt gggattgagg tggacgacaa caaggctcgt acaattatta atgctctacc 5100 gtcgacgacc aaaaaacaat tacaatcgtt gcttggcaag atcaactttc tccgacgatt 5160 cattgctaac tcggccggga aaatgaaagc cttttccacg cttttgaaac tcaaggactc 5220 cgacaccttc gaatggcatg ccgagcatca agaggcattc acgcagatta aagtctctct 5280 aacgactcca cccgtccttg tcccaccacg acagggtcaa cctcttaagc tatatatctc 5340 gacggttgaa gaatccattg gttgccttct cgcccaggat aatgacgtcg ggcgagaaca 5400 tgccattttt taccttagct ggaatctcaa cccaccagag attaattact cagccgtcga 5460 gaagctctgc ctgactttat tttttgctgt gtcaaaacta agacattaca tgctcccgtc 5520 agtcactcag gtcatcgtcc agaccgatgt catcagttac atgctcactc ggccaattgt 5580 aaagggccga attggcaaat ggacgatggc cctttctgaa ttcagcttac aatatgtacc 5640 ccagaaggct gtcaaaggtc aagccctagc cgattttttg gctcaccacc cttccccgta 5700 cgaattcggg ggtaataaca ttgacatcgg cctgatacaa acacgggata attactggac 5760 gatgtacttt gatgggtcca gtacgtcagt ctcggttggg gttgggatcg ttattcaatc 5820 ccccactcat aatcattggt atttctctct caagctcgat tttgattgta taaataatca 5880 ggccgaatat gaagcccttg ttatcggcct cagcgtattg cacgatttac gagcaactcg 5940 tgtacttgtg cttggtgact ccgaacttgt cattaatcaa cttaacggga cttttcgttg 6000 gatgatttgt actctagcgc cttaccacat ggttgccagc tatttgatcg aatccttcga 6060 cagaataact ttcaaacata tttcacccgt tcataacact gacgccgatg aactagctta 6120 aataacctcc ggagcccaac ttatgggtgg caaattaggc cgagaaatac ctgtgttatg 6180 acaagtacat tcggccatga ttaatcatca agttatccaa caagattgcg tgacccgtac 6240 acgagccatg tccttgtcgt cgttgttaga acgtaaagac tttgtcgagg tttgtgccgt 6300 cgaagcatta ccaaatgatt ggagaatgac aattatgcaa tatattgata accccaatga 6360 aaaacacgac cggcagacaa gggctcatgc cataaattac gtgttatacc agaatgagct 6420 gtatcgcaaa ggtaaggatg ggttactgtt gttgtgcctc ggcccgcaaa aagctgccca 6480 agcaatggca gaagtacacg aaggaatttg tggagcccac caatctggac gaaaaatacg 6540 ttggctactt caacggcacg gttatttctg gtcgagtatt ctgaaggatt gcattgagta 6600 cgcaaaaagt tatgtacagt gtcaaatcca tgagccggta catagagtgc cggccaaatc 6660 attacattcg atcaccaaat catggtcgtt ccgaggaaca tgcgtggata cttgttgtaa 6720 tggactactt caccaaatgg gtcgaagcca agtcatatgc cgagctaacg tcaaaggaag 6780 tttgtagttt tgttgaagaa aacattgtga ctagattcgg cgtgccagaa acaatcataa 6840 cagataatgg tatggttttt acatccgaca gatttaagga ctatatggca aatctaaaga 6900 ttcaactcga gcaatctacg ccatactacc cacaggcgaa tagacaggcc gaagcaagta 6960 ataaggttct tattagtatt cttgaaaaga tgataaaaga aagtccaggc gtgtggcatt 7020 taaggataaa tgaagcatta tgggctcatc gaacctctcc gcgaatagcc atctgaacga 7080 ctccatacgc gttgacttat ggacatgacg caatgttgtc tgtcgagcta agtgtaaact 7140 cgttgcgaat aattgagcaa agtagtcagc gccgagtaca atcaagccat gagacaaaag 7200 ctagaagatt tggaatacgt tcgacttgat gtttataatt tattagtggc tcaaaggaaa 7260 atcaccgagc gtgcatataa tcagcgagtt agataaaaaa catttggcga aggagaatcg 7320 gtttggcaaa tcgtactacc tgtaggaatt aaagacccca ggttcggcaa gtggtcgcag 7380 aattgggaag ggctattcat tattcataaa gtcctcggta aaggggcata ccggcttaga 7440 gatcgaaccg gtgttattca taagttgcca atcaatggaa agttcttaaa gaaatactac 7500 ctagtcacat gggagatgca agaataaaag ctcatttcat atcatcgata atcagtttac 7560 aataaaaatt ctagggtgat aaaggaagaa gagttccaag aagggtcttc agttccaacc 7620 acctcacctt gcccattatg acctcagctt gtcggttctt cttgtctatc ttcaactgct 7680 cgactcactt cacgttcgtc gcatattcag ttaagcaagt tttgccgccc gactcaaagt 7740 cccttgcaag ctcagaagca atggacgacc ttcattttgc tagttcggcc atttgacggt 7800 caaggttggc cagggcctct tttttcacct ttaaagcgtc gatcttcaga cgaagagtgt 7860 ctcaaacggc tgttgcaact tttaagtcat cgtcagcccg aagagcgttg tcgaaaatac 7920 tgaaggattc ccgggttcgt tccaaggcgg acgatgcctg aatgatagct ttggtgctaa 7980 attgaccatt agctctgagg tcgtttaggc atgcacctaa cgaatcaaga cctttgagct 8040 cgaggacttg tgaagctaag agagacaaaa cttcttgcaa ctgagtaaga gcagctgatt 8100 cggcaggttc agttgtagtt gccgaaggac tagccgctcc agaagtgctt aatagaagag 8160 catcaaactc gacttcccat gaaggctgca catgaaaaca gtttaagcgc aaggaaattc 8220 acaaaggaat atagcaagaa ggtttttgtt ttaaacctgc cgagaggaga cttcggccat 8280 gtcttcgggt tcattgctcg aacctaaaga actcaatagc cgagcccaat gtttcaaact 8340 gcttcttaat tcacgcggcc gatgaaggtt atctacgttc gatggccact gaggtggcca 8400 ggaaatatag ataacacctt tcggcgcata aaattttcgg tgaaatgaat aactgggcac 8460 ctgacattta atattttctc gattcagaca tgttataaca aattgacaat agaaagtaat 8520 caagccttac aaaagtcgag gtcacttctt aagaagggat gtcgaggtct tggtcctgag 8580 ggtgaattag agtttctgac gtcatttcag gctcgacgat aagcctcttt ccgcaatcag 8640 ccacatgaag atcaacctga tcggccacct caactacggg ggaaagatca acggaaagag 8700 tttgggttgg tcgagagcga cttgccaacg gagtttcgtc actttcatca tcctaaaata 8760 aaaagtgtta ataatttttg ttacttaata aacaaaggga tttgacggca taatcgtacc 8820 tcttttaaga tgatcgccga atgctttgga ttcttagaaa gatcattccc aatcaaaggg 8880 tccgtctccc ccagaacggg tattcatgtt gaccctggag ctgcaagcaa gtcaactgat 8940 aggacaacaa ccggctcaac cacgacctca gggacctcat gtattggttg aggttgggtt 9000 tccgggctgg ccgaagatgg ccgattatcc gccgaagcct gagcagcggg atcaggagga 9060 gatgcattgg gagcagttgt cctagtggtg tggctggaga taacatcaat ctcccgtgcc 9120 ctttttttcg ccaatttctt gatgcgtttt gggggacggg gagtttcacc tgctgtctcg 9180 gcatccaggc gaagccgttt gctcggtagg ttttgtgcag cggttttggt cttcttggag 9240 aaaggggcca attttttctt gaccactgcc gggacgacca cgtcctcttg tttcagtacc 9300 cgattgccta agaaagcgaa gtttcgttag tgaaatcact caaatatttg aagaataaag 9360 gtagaaacaa gggtatacct tggggcacct ctttaggtta agggatggag ggtttcttgg 9420 gccggtcacc aaaaattttg ttgactactt cttcgaccga agtgccaaaa aagttgtgag 9480 tatattgttc ccaccagtcg tcgaagatat tagtgccgag tgattcagga gaatttggtc 9540 gaagacgaaa tttcctacat cgttcctgaa attctttctc ggcatctcca cactcccttt 9600 ctgaagaacc agatatgcac cctcgggtca gaagggagcg agaagaaagt aaaggcaatg 9660 ggcaaccttg gaggtaaccg agctactgag cggcaaagtg agggtgataa acttcccaac 9720 ttgttcgatg agcatcacaa ccaaggggaa agtcacgagt taacacgaat gacacccatt 9780 tttgacgaaa agccgcttcc tcgctgtcac tccaagtgga tgtgggaagt ctgatggagt 9840 gaagatattt ttcggctcgg tgagggggca ctggtcaaga ggccaattga aggccgagca 9900 ctacagtaga ctggaggtcg gagacttctg gccgaagcgt ggagaaataa acctgcagcc 9960 agagttggaa cacccagaga ggtcaattct ggtacgggtc gatcttgttg agggtcgtct 10020 ttaccaagca atgaagaagg ttggcaagga tggcggggct gagcgctaaa gagtggccac 10080 tagccagggc ttccaccaat gacatgttct caaccaagca tttattcgac ttggtacaac 10140 aaatgaattt gttataccag taaaacagga agggctcgtg ttcccccttc cgaagactcg 10200 cctctcctca accggtaaaa tggaggataa gggtgttgta gttcaaaaaa ttcttgtaca 10260 atttttgaac atcagttttt aaaggctctt gacgttcctg acataatgtc tcaatgtcct 10320 gatcgttaaa caacgccttg aggtcaaggt tggaggggca ttcaataagg gtggcgtcga 10380 ccaggatgcc agaaggagaa gtcccaatga tagccgagat gttgaggatg gtaggagtca 10440 tatgaccgaa tggaaggacc atggtgctgg tggccgaaca gcagaggcta atagctacca 10500 tgaagtgctc tttatccatt gtaatctcca tggtcgagaa cttgatagca tcgtaaatac 10560 caagagtttt ccactcttta ccgaagaatc tttccatttg aacgacccaa gccacccaat 10620 tcgcattggg cgaaggccag gatccttggg attttgtctg gcaccacttc gaccaatcga 10680 atccttacag caaacctacc aaacaatatt ttttgaacag gttggtgatg gatgacgaca 10740 ccgtatcctt gaagagtggg ccccgaactt ggtgagtagt gtttgactca ccctcgaaac 10800 gcagagtctt gatagcgtgc tgatcgatga aatcttgcac ttgttacact tagatgagag 10860 ttttgagcca aaggaggcca ttgaggaaag gttagaaatt tctgagatga aagtttcaga 10920 atccctggtt tttgaaagtt ttaaaaatag aacggcaaga aaatttcaaa ggtttgggat 10980 agcgtaaggt acgaatggaa gagacccagg catttataga catttgggaa cagaagtcta 11040 aacggttgac tttcaaaatc aagggtagaa tcaagcggga gagatacaaa tcattgtaca 11100 tgctcagaaa atcaaggcga aaggatcaag gtttcatgga ttgaggacac atgatggcgt 11160 gttacggcgg atttaatgca agagagacgt ttcggcggtc acatgttttt gaggatcata 11220 atttaaggct gctagggtaa ccagggggtt gacacgtggc aggacgattt ggaaatcaag 11280 atcgtgggat tacgtctcat aagtgcgcat agtggcagtt ctcgagagtt ggtttcactt 11340 tttcaaggtc gaggctcgaa ctaaggagta taggtcgacg acctcaaaag cgagggggca 11400 atgtttgggc ccaaaaattt tgttttgggc cgagtttaga tctttttcgg cctagtgttg 11460 gataggccaa gtttagattc tttctcagcc cagaagttgt gtacatgtgt cattgggaga 11520 tattcagccc atgggccgtg cgatcgaagt tggccatatc atatcagaaa ttgggaatgt 11580 ggacaaatcc tattatgaga aagagttttg acgagatcag gatgctgaga ttgaatacgg 11640 tttgataacg agttatgttc aaagtcctag taggaatagg attggccgag ataaagttgg 11700 atcatgagaa ggagttctaa ttcgggagtg attgagattc aatacaggtt agctgctata 11760 aatagggagc gaagacatcg aaacaagccc tccaattcaa catacaaatt gccctgcgca 11820 ttctctcgct ctacgcgaat cctctcaaca accttgagat tttttttgtt ttcctttttt 11880 caccgacgca acttcagttt ggataaatag cactgtgaag gcaaccagcg aacatcttca 11940 gtttggataa acagcactgt tgccgtagaa ttagctgacc gtggagcatc tttagtttga 12000 ataaacagca ctgcgacagg gccgactggt tacctatcaa agtctcggtc gaggaggatt 12060 tttgaatcct tatcggcaga ggtcatctcg tcagccttct cggcgaagcg aggtgttaca 12120 agttattata ctcggcacat tgaacgccga gtcgtttatg at 12162 // ID SHALINE11_MT repbase; DNA; EDCOT; 3705 BP. XX AC . XX DT 05-JAN-2007 (Rel. 12.01, Created) DT 21-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A LINE element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW non-LTR; retroposon; Interspersed; ORF; Poly-A; SHALINE11_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3705 RA Shankar R. and Jurka J.; RT "SHALINE11_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 89-89 (2007). XX DR [1] (Consensus) XX CC The 5' end is truncated while the 3' is well conserved. The CC sequence has domain for non-LTR reverse transcriptase. XX FH Key Location/Qualifiers FT CDS 998..2905 FT /product="SHALINE11_MT_2p" FT /translation="MLSEDDNRGLIAPFTLEEIEKVVKDSDGNKSPGPDGF FT NFAFIKEFWHLIKHEVRIMFDQFHANEVLPRSFLSYFVTLIPKVNNPFTLK FT EFRPISLLGCLYKLLAKVLAGSLSKVMNSIISTSQSAFVKGRNLVDRVLVI FT NEVVDFAKRANRECLILKVDFEKAYDSVEWSFLEYMLKRVGFCPKWVAWMK FT ACVFGGNMSILVNGTPTATEEICIQRGLKQGDPLAPFLFLLVAEGFSGLMR FT NAVNSNSFEGFDFRNNGFVVSHLQYADDTLCIGEASVENLWTLKALLRGFE FT MVSGLKVNFVKSCLIGVNVGREFMEAACNFMNCREGSLPFKYLGLPVGANP FT RSLSTWEPLLDCLKKRLNSWGNKYVSLGGRVVLLNAVLNAIPIFYLSFLKM FT PVKVWKKVVRIQREFLWGGVNGGKKVCWVKWSTVCQPRAKGGLGVRDIRLV FT NFSLLAKWRWRLVQPDQALWKEVLICKYGNRIICLLXPGDNVWPSFASRWW FT LDLMSLEGAVGTNWFNREVVRKVGNGENTRFWLDRWVGNEPLCVTFPRLFS FT ISSQKEAMVGEVWVDGVGGGDWNFMWRRNLFVWEEGLFLNLIEELEGWEKV FT ELVDSWWWKLEEEGIFIGDLILCXAXEFVNAAGIFGEY" FT CDS join(7..399,403..420,424..501,497..511,505..597, FT 601..660,664..732) FT /product="SHALINE11_MT_1p" FT /translation="MIVSSFNVRGLGGGLKKNKIKELIRNHGVDFMAIQET FT KLENVSPELCYNLWGSDNCNWAFLPSEGNSGGILSLWNKSSSKLIFSFSGE FT GFVGVCLEWGPLATRCFLVNIYSKCDLVSKRRLWDNLVELKGGVTVFGLWE FT ILIRCVLVTREGGFKRWNLAIVGRGDETLDSLMIFLIRLSWKIKIRLEGSL FT RGFILMGWPVELIESWCRRIGSWCGVPHLGFYLETFPIIARCYSSQVIVIG FT P" XX SQ Sequence 3705 BP; 864 A; 445 C; 1117 G; 1264 T; 15 other; tgatcaatga ttgtgtcatc ctttaatgtt agggggttgg gaggtggttt gaagaagaat 60 aagattaagg agttgatccg aaatcatggg gtggatttta tggcaattca agaaacaaag 120 ttggagaatg tctctccgga gttgtgttat aatctttggg ggagtgataa ttgtaattgg 180 gcttttcttc cttcagaagg aaatagtgga ggtattttat ctttgtggaa taagtctagc 240 tctaaactta ttttctcgtt tagtggtgaa ggttttgtgg gtgtgtgttt ggagtggggt 300 ccgttggcga ctagatgttt tttggtcaat atttattcaa aatgtgatct tgtctctaaa 360 aggcgtttat gggataactt ggtggagttg aaggggggtt aggtgacggt gtttggtcta 420 tgatgggaga ttttaattcg gtgcgtgctc gtgacgagag aaggggggtt caagaggtgg 480 aacctagcta tcgtagggag atgagactct ttaatgattt ttttgataag gttgagttgg 540 aagataaaaa tacgcttgga aggaagttta cgtggtttca ttctaatggg gtggccatga 600 gtagaattga tagagtcttg gtgtcggagg attgggagtt ggtgtggggt tccccatctt 660 taggggttct acctagagac gtttccgatc attgcccgtt gttactcaag tcaggtgatt 720 gtgattgggc cctaaacctt tccgttttaa taattattgg atccttaatc gcaagctcaa 780 aaaggtggtg gaggagaatt ggagggatgt gaactccaag tttttccata aaagtgttaa 840 attgagatca aatagtaact caattagagc tcttcaagtg gatggaggtt gggtgcaaac 900 tccggaagag attagagggg ccgtggtgga gtattttgga aagcaagtgg caactactca 960 ctgggaaaga ccaaagttag atggggtggc ttttgatatg ctttcggaag atgataatag 1020 gggcttaatt gctcctttta cgttggagga gattgagaag gtggtcaaag atagtgatgg 1080 taataaaagc ccgggtccgg atggatttaa ttttgctttt attaaagaat tttggcacct 1140 tatcaagcat gaagtgagaa ttatgtttga ccaattccat gcgaatgagg tgttgcctag 1200 gagttttttg tcttattttg ttactttaat ccctaaggta aacaatcctt tcactttgaa 1260 ggagtttcgt cctatttccc tcttagggtg cctttacaaa cttcttgcta aggtgttggc 1320 aggtagtttg tcaaaggtta tgaattctat tatttcaact tctcaatcgg cttttgttaa 1380 agggaggaat ttagtggatc gggtgttggt gattaatgag gtggttgatt ttgcgaaaag 1440 ggcaaaccga gaatgcttga ttcttaaggt agattttgaa aaggcctatg actcggttga 1500 gtggagtttt ttggagtata tgcttaagag ggtgggtttt tgtccaaagt gggtagcttg 1560 gatgaaggca tgtgtttttg gtggtaatat gtcaattctt gttaatggca caccgacggc 1620 gacagaggag atttgtatcc aaagagggct aaagcaaggg gatccgttag ctcctttctt 1680 attccttttg gtggcggaag gatttagtgg cttaatgagg aatgctgtga attcaaattc 1740 ttttgaaggt tttgatttta ggaataatgg ctttgtggta tctcaccttc aatatgccga 1800 tgacactctt tgtattgggg aggcgtccgt ggagaatctt tggactctaa aggcattgct 1860 wagaggtttt gagatggtgt cggggttgaa ggttaatttt gttaagagtt gtttgattgg 1920 agtgaatgtt ggtagggagt ttatggaggc ggcgtgcaat tttatgaatt gtagggaagg 1980 ttctcttccg tttaaatact tgggtttacc ggtrggggca aatccgagaa gtttgtcgac 2040 ttgggagccg ttgttggatt gtttgaagaa aaggcttaat tcttggggta ataagtatgt 2100 gagccttgga ggtagagttg tccttcttaa tgcggtgttg aatgctatcc caatttttta 2160 tctttctttt ttgaagatgc cggtgaaggt gtggaagaag gtggtgagaa ttcaaagaga 2220 attcctttgg ggaggtgtga acggtggtaa gaaagtgtgt tgggttaaat ggtcgacggt 2280 ttgtcaacct cgtgcaaagg ggggtttggg ggttagagat ataaggttgg taaattttag 2340 tcttttggct aagtggaggt ggaggttggt gcaaccggat caagcgttgt ggaaggaggt 2400 ccttatttgt aaatatggga accgtattat ttgtctcttg katccggggg ataatgtttg 2460 gccgtcattt gcctctaggt ggtggttaga tttgatgtct ttggaaggtg cggtggggac 2520 aaattggttc aatagggagg tggtgaggaa ggtggggaat ggggagaata ctaggttttg 2580 gctagaccgg tgggtgggaa atgagcctct ttgtgttaca ttcccgagac ttttctctat 2640 ttctagtcaa aaagaagcka tggtggggga ggtttgggtg gatggagttg gtgggggaga 2700 ttggaatttt atgtggagga gaaatctktt tgtgtgggaa gagggtttat ttcttaatct 2760 tatagaggag ttggagggtt gggagaaggt ggagttggtt gattcttggt ggtggaagtt 2820 ggaggaggaa gggattttta tcggtgacct catcttatgt trtgcttgwg aatttgttaa 2880 tgccgcwgga atctttggag aatactaaga aagtggtgtt tgatttggtt tggaagagtc 2940 cggcaccgtc caaagtggtg gctttttctt ggaaattgct ccttgatcgt atcccaacaa 3000 aagataacct tttgaaacgg cgtattttag caccggaggc ttcggttagk tgtgtgtttt 3060 gtgatcaagt gggtgaaacg gcgactcatc tttttcttca ttgtgagttg gccttcaaag 3120 tttggtcaag ggtgkgtggt tggttrggga ttaatttcat tactcctcaa wctttgtttc 3180 aacattttga gtgttggaat ggggagatyg ggaggcgaaa gyttcgaaaa ggttattgga 3240 tgatttggca tgcggtgatt tggatgattt ggaaagcgag gaatgatagg attttcaata 3300 atcttgtgaa ggatgttggt gaaattgtgg atgacattaa ggtgatctct tggaattggg 3360 cgaattcaag acttaagagt cctccttgcc tcttttacga gtggtgttgg aaccccaagg 3420 aatgcctttt gmgataggtg gggtagtttt agaggtgtcc gggacttttg gtgttggtgg 3480 ttgctggttt ttggttgtgt ttttcggctt ctgtttatcc gcagtagcag tttttggcgt 3540 ctggtgtttt tctgttttta ggtagtgttg gttggttgct gctgtgtttt ggttacaacc 3600 cttagcagct gcttttttct gttttggttc tttggccatc gccttgtaat tgtactgctt 3660 gtataatttg gtgtttaata atataagctg tttaaaaaaa aaaaa 3705 // ID Gypsy-37_Mad-I repbase; DNA; EDCOT; 1637 BP. XX AC . XX DT 13-OCT-2010 (Rel. 15.1, Created) DT 13-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-37_Mad-I. XX NM Gypsy-37_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1637 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1768-1768 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 1637 BP; 465 A; 284 C; 315 G; 573 T; 0 other; aaatggcgcc gttgccgggg actgcgctta aacaactttg taattccttt tagttttgct 60 tactaactta atttattttg ttttcagttg tatgtctttc aatccattca agcagcccat 120 tgatttagag cagctacaaa gtgtgtggta ttgaattttt agtctttttg agtcatgatt 180 agagctattt gcaattaaat aatgggaatg tacatgttta acttagtctt gcaatcataa 240 ctttggctat gctttgaaag ttgttgtatc tgctatataa taccactgct ctcagttcta 300 agaatacttg tgaaaagtta ctagttcaag ccttagaaga aggatagtgg agactgcctt 360 ttgtgaaatt ttgtgcctat ttgcttcttt tagagggatt aaactgtttc tactcctcct 420 atccttttct ttcaaattca tttcaaatga tctcattatt catttttgat tgaatactaa 480 gagttattct cttttgtgga tacttgtgct tattatcacc catgaatgaa ctcattgaga 540 cgatgttagg ctgtgcatgt tttaactagt aaatggccta attccctacc tttgttgtgt 600 gagacattac ccattttgaa gccaaacaca gccatatctt tcatcaccca cactaaactc 660 tacccatttt cccccataat agccattccc tatagcttgg ggaataccaa agtgatgaag 720 acaaatataa tgctcgagct ttaagctaag aaagtggcgt gtaccgaggt aacatgggct 780 ggaattgcaa aaaaagaaaa aaaaaaaaaa agaagaagaa gatgcaattt ctaaatccat 840 gggtcctgga cgccgagaac aagtaaagaa gatcaattca agaggaaagc atgctggttt 900 tgcaaggaag acactttggt atatctcaag ttctagtatt ccttatccat cctttcatag 960 cccctaccat aaaaacctta cattacaacc ttatgaaaga cctagctgat ctttgaggat 1020 gtattcatgg atgttagtaa gtatgtgtgt tatcctattc ttagtatttg attcctttca 1080 tgagatctgt ccagaaagtt cttttgtttc taattgaatt atgtgtgaga atatcttgct 1140 ttccattaca taacctcact cacatatact tgttgagagc aagccctagg aatcaagtga 1200 aagagtgaat ctgtgagatt agagttgaga cgaatcttat cttccttgct tgagcttgta 1260 acttagtaac aggttgaatt tgggctagag cacctcacta acatgcagat ttgattgctg 1320 gaaaggtaaa gtcaaagtta ggaatgtaag gcatagttga gctttgattc ttattatctt 1380 gtttcaaaag tgctctaatc gttgttttgt aggttgtttc ggacgtttat gggtaccgtc 1440 actgttaaac ccttaggaga cacaactcct cctactaggg atgcctagag gtttaaaggc 1500 ttgatgcata agctgaatgc attcgtctca ccaacggaat tggtcttaga ttaacttatg 1560 tttgtctttt gtgttgtttt tgtttctttt agttttggtt tgctcgagga ctagcaaaat 1620 ctaagtttgg gggtatt 1637 // ID VHARB-N1_VV repbase; DNA; EDCOT; 327 BP. XX AC . XX DT 30-AUG-2007 (Rel. 12.08, Created) DT 30-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE Non-autonomous DNA transposon from Vitis vinifera. XX KW DNA transposon; Transposable Element; Nonautonomous; VHARB-N1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-327 RA Obukhanych T. and Jurka J.; RT "VHARB-N1_VV."; RL Repbase Reports 7(8), 763-763 (2007). XX DR [1] (Consensus) XX CC This is a putative non-autonomous DNA transposon family (possibly CC derived from Harbinger). The consensus sequence forms an CC imperfect palindrome, surrounded by 3 bp-long target site CC duplications. XX SQ Sequence 327 BP; 117 A; 46 C; 35 G; 129 T; 0 other; ggctatgttt ggttcccgga aagtacaaag gaaagaaaaa aaatgttaag gaaaatgatt 60 ttctcatgtt tggttgtcct atgaaaaata tcaaagaaaa tcaaatataa ttaaaactaa 120 ttaaaaactt atgtattttt aaattattta atctttatat tgatgagtta aaataaataa 180 aatgagtttg aagtaacaaa taaaaataat ttatcaactt ttaatctatt tttttatttt 240 ccttcacttt ttctttcctt ctacttttcc tttgtatttt ctttccctcg cattttccct 300 caaattttcc gggaaccaaa catagcc 327 // ID Gypsy23-PTR_LTR repbase; DNA; EDCOT; 285 BP. XX AC LG_XVI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy23-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-285 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-285 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 327-327 (2007). XX DR Genome; LG_XVI; Positions 13225657 13225373. XX SQ Sequence 285 BP; 71 A; 45 C; 48 G; 121 T; 0 other; tgatgtagga catgaggaag ttaatactgt tagttagttt atttgttaga tcgcagtcct 60 tttaggattc tacttttatt tttatctgtc gttagtgttg gaaacaaatc aaacttgttt 120 gatattagtt tccccttcct tttaggattc tattttctgt tttcgtttct ttaaaagcac 180 caagtcagga aggttgtaga cattattatt tttcatcaat aaacttgttc tttgaacaca 240 actattctct cgtggattcg agattattta gcttccgcta cgtca 285 // ID HAT-10_Mad repbase; DNA; EDCOT; 6710 BP. XX AC . XX DT 20-OCT-2010 (Rel. 15.1, Created) DT 20-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-10_Mad. XX NM HAT-10_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6710 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1626-1626 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 11-bp long. XX FH Key Location/Qualifiers FT CDS 3409..5058 FT /product="HAT-10_Mad_1p" FT /translation="MDARDSDSVTDEESVEIIMGTERDLGSESIDNTNSSS FT TKKKARTINLGKRKLRSPVWNTFTKLDTIFEDSKRRAQCKACKKVMIDDSH FT HGTGNMKRHLNTCPAKNNVELFMSASELCSQKFDPLVFRGLLVEAIIKHNL FT PFNFVEHEGIKALFAYVCPDIKLPCRNTIKACVLRMFKTEKQALHNLLGSV FT EGRICLTSDLWSSQCTDGYLALTAHFVDKDWKLNKRIISFCHMPXPHTGVA FT LCEKISALVTEWGIEKKLFSITLDNASSNICFVNILRNQLNIRGLLLMNGD FT FFHVRCCAHILNLIVQDGLKEIDSSVVKIRECIKYVKGSEARKLKFQECVK FT QVGILDSKRGLRQDVPTRWNSTYLMLDSAIFYRYAFINLGLSDSNFESCXS FT SEEWDKVVKISKFLGYFYDVTCLFSGTKYPTSNLFFPKVFVIQLQIKAAID FT DCDSFMNKMGDYMHIKFQKYWSDYSLIMSIAIILDPRYKLHFVDWAYTKLH FT GVNSMEYXNVHGTLIALFNVYSEISAHLNFSNIPMNSMSNHQTEGEGDALF FT EVT" XX SQ Sequence 6710 BP; 2032 A; 1010 C; 1224 G; 2440 T; 4 other; tagacttggc agtttctgac acgacacgaa aataacgggt ttcgggtcaa cacgataact 60 tatcgggtcg ggtgacccgt taagaacccg ttattaacgg gttcttaacg ggtacggggt 120 acacgtgggt gacccgtttc gacccgttaa gaaaaaaatt aatttgataa ttttaaagtt 180 taattactaa aagatttatt ataaaataca atagccatat taatatatac aatatattct 240 atattaaata tatagttttg tattattatt ctatataagt tataaaaaaa agttttagtc 300 attatttatt tttaggggct tttagatcta ggtccaaaaa tatagatgat ttttaggagt 360 gagtccagtt atataattac atgtttttat ttcttttata ctcattttat atttttttaa 420 aatattaaaa atcaattaaa atcttctaat atgaagcatt tttcaactcc aaaaaatcta 480 attaatatct tataacagaa aaaactaata tactaacata aattatctac aaaacattct 540 accttaactc aagcaacaaa tatatgaata tatattatac ctgtaagtga gatatgaaac 600 ctaactaaaa agtaggaaaa acataatata cctacaagcg aagcaagaca cattaatctg 660 taacacgtta attataaaga agaatttgtc atatagatac ataaaaataa ttaacctgtg 720 atataggttg attataaaaa ttaaaaataa aatctataaa tgaggtttaa agagggagga 780 agaacaagaa ataacaaaat aataataata ataataatca aagagataat taggaagaaa 840 tttgattttt ataataaatc ttattattga atagataatt attgataata aaataattaa 900 atttaaagaa ttggacttat tttaataaat tggactattc ctactattgg ctaaaaaaat 960 tggacttata tcaagtttcc ccttattttt attatgagag ttctttatta tcattactaa 1020 tttactagga taataaattt tacttaacag ttaacatgtt cttgtccaaa attaaaataa 1080 actagtatag tatttgtata ggcaagaact aagaagacat acatacaata caagtatgaa 1140 aaatgtgaaa gaatatataa acacttgcga ttcatcatta ttcctctacg agtagataat 1200 ggttacactt tatcgtttag atttttaaaa tcctcccaaa ccctcatgaa taatgttttt 1260 tatttgaagg caaaattaat aaaattaata ataattattg tagaagtgta aaaaatgtaa 1320 aaaaaatatc caatcactca taatgacaag ctttacaact ttcatgaagg ggtcagcttc 1380 gaaatccaac actataatcc ataaaccttc aatttatatt taaccgtcga ttatcattta 1440 cgctttattc ttgttactga atttcatttt ttaaattttc tttttttaaa acatgatcat 1500 ctggtggatg taagaagatg aacggttcag atctttgata tcacgtttcg atatttacgg 1560 ttaattgaaa tatgagtcga tgtcatatag tttgtagaaa ctttataaac atcaagcaat 1620 attttcacta atcgtaaaac tctgaacata atatcaacga tccaaaccgt tcatcttctt 1680 gcatcctcta atagatcatg ttttcaaaaa agaaaatctg aaaaaacaaa atttgatgag 1740 aaaaataaag cgtaaatgta aacaataatc aacggttaaa ttttgatcta tgatttatat 1800 gattatagtg gcgaatttcg aagttaagtt cttcacgaaa gttgtaaagc ttgttattac 1860 gagcgtttat atattttttc tatatttttt atacttctac attaattaaa aaactattaa 1920 agactttact taaataacag ccgttagatc aatgagatta aatctgtacc gttggattct 1980 atttcaatta tattattaca atttttttgg acaaaaaaac ccctcatatt ttccattgtt 2040 ttccatatga gtcctgactg atttgatcaa aacaaaaaaa ccccactgcc tagccctaaa 2100 ttctttctgt ctattctctc cccactcccg gccgtaaccc tctctcccaa cccgcccgcg 2160 gcgccgtttg ttcttcctag cccctctctc ccgccgtctt tcttccaaaa ttccgacagc 2220 cacgatcttc tcgtcttcca ttcatacgag gtacgacatc ttcctatgta ataatgtaag 2280 tatttctccc tcttcttcaa cctttctctc tcttcactct ttctacgctc atagttccca 2340 tttctgacca cgaacgattg acacagcttc ttgcgttgga ttcctctctt cctcttgttg 2400 atctcgtcag tgttacattg tccaggtaag aaattcgctg tcatcatcta ttgttgtttt 2460 tttttatgaa tcgggattgg acaccagttt tgatatgcgt tcatgttcga ttacacttgg 2520 tacaattttg attgttttgc tcccatttga cactcaccca tgttacaact cccattcgac 2580 gcttttgctg atctgtgtgt gtatctcaat ttttttttta aattgatgct tttaatgact 2640 ttacgaaaaa taattttatg cttgaaaatt tggaatgagt tgttttttat gattattagc 2700 agtgattttc acatgcactt tgttttctcc ttttatactc attttttggg cttcttgata 2760 tctaaatgct agagaataca agcgagtgca aagaagaaaa taaaaagttc gaaatgtgtg 2820 tgtgtgtgct gtctgtgtgt gtgcgcgctg tgtgtgtgtg tgtgtgtatg tgctgtgtgt 2880 gtgtgttgta tgtgctgtgt gtgtgtgtgt gtatgtgctc tgttgtgtgt gctgtgtgtg 2940 tgtgtatgtg ttgtgtgtgt gtgctattag tgcctgacag acccgcagcc atgcataaaa 3000 ccaaggcaaa gaagctgtgt tgtgtgtgtg cactgtgtgt gtgctattag tgctgtttgt 3060 gtgtgttgtc tgtgcgtgtg tgtatgtgct ctgtgtgtgt gtgttgtgtg tgtgctatta 3120 gtgcttgtgt gtgtgtgtgt gtgtgtgtgt gttctctcat cggattctac attatcaaga 3180 ctgtgtgtgt gcgcgctgtc tgtgtgtgtg tgtgtgctct gtgtgtgtgt atgtgcgctg 3240 tgtgtgctgt gtatgtgcgc tatgtgtgtg ctgtgtatgt gcgctgtgtg tgtgctgtgt 3300 atatgcgctg tgtatgtgtt gtgtgtgtgc tgtgtgtgct gtctctcatc agatcctact 3360 agtttaaaaa gctattaatt aatttatacc tattttgatt cagaagcaat ggatgctaga 3420 gattcagatt cagtaaccga tgaggagtcc gtggagatta taatgggaac agaacgagat 3480 cttggaagtg aaagtataga caatacaaat tcgagttcta caaagaaaaa ggctagaaca 3540 atcaatttag gtaagcgaaa acttcgatct cctgtttgga acactttcac taaattggat 3600 actatttttg aagatagtaa aagacgtgct caatgcaaag cttgtaagaa ggtaatgata 3660 gatgatagtc atcatgggac aggaaatatg aaaagacatt tgaatacatg ccctgcaaag 3720 aataatgttg aattgtttat gtcggcatct gaattgtgtt cccaaaagtt tgatcctctg 3780 gtattccgtg gcttattagt agaggcaatc atcaagcata atcttccttt taattttgtt 3840 gaacatgagg gaatcaaggc tttgtttgca tatgtatgtc ctgatattaa gctaccatgt 3900 cgaaatacta tcaaagcttg tgtgttgagg atgttcaaaa ctgaaaaaca agcattgcat 3960 aatttgttag gctcggttga aggtagaatt tgtttgacat cagacttatg gtcatctcag 4020 tgcactgatg ggtatcttgc acttactgct cactttgtag acaaggattg gaaattgaat 4080 aaaagaatta taagtttttg tcacatgcct cmtccgcata ctggtgttgc attatgtgag 4140 aaaataagtg cgttggtaac tgagtggggg attgagaaga agttattttc tattactttg 4200 gataatgctt cttcaaatat ttgttttgtt aacattttga ggaatcaatt aaatattaga 4260 ggtcttctct tgatgaatgg tgacttcttt catgtgcgtt gttgtgctca tattttgaat 4320 ttgatagtcc aagatggact taaagaaatt gattcttcgg tggtaaaaat tcgtgaatgc 4380 atcaagtatg taaagggttc tgaggctagg aaactaaagt ttcaagaatg tgttaagcaa 4440 gtagggatat tggatagtaa aagaggtttg agacaagatg tccctactag atggaactca 4500 acctatctta tgctagatag tgccattttc tatcgatatg cttttattaa tttagggttg 4560 agtgattcaa attttgaaag ttgtcmttct tctgaagagt gggataaagt ggtgaagatt 4620 tcgaagtttt tggggtactt ttatgatgtt acatgcttat tctctgggac aaagtacccc 4680 acatcaaatt tattcttccc taaagtgttc gtaattcagc ttcaaattaa ggcagccatt 4740 gatgattgtg atagtttcat gaataagatg ggggattata tgcacataaa gtttcagaag 4800 tattggtcag actacagttt gattatgtca attgcaatca tcttggatcc tcgttataag 4860 ctacattttg tggattgggc ttacacaaag cttcatggcg tgaattctat ggaatatwaa 4920 aatgttcatg gcacattgat tgctctcttt aatgtgtact cggaaatatc tgctcatctt 4980 aatttttcaa atattccaat gaactcaatg tctaatcatc aaacagaagg tgaaggagat 5040 gctctctttg aggtaacata aagtttgtat tttccttttt atacatagta ctttaaaatt 5100 attaatatta tatttgaaat tgggttatgc ataattttta tgatgtttct gttttttttt 5160 tttaattttt atgatgtagg attttgataa taattacaat ggtccaaact cagttgaaaa 5220 aggtgaatta cagaagtatt tggatgataa aagactagat agaagacaag atatagatgt 5280 tctttcttgg tggcaaatgg agckttttca ttatccaata ctttctcagt tagcacgaga 5340 tgtgctaaca attcctattt caactgttgc ttcagaatct gcttttaata ttgggggtaa 5400 agtgctagat caatatcgta ctttattgtt gccagacacg gttcaagctt tgctgtgtac 5460 acgagattgg ctttttggaa aaggaggtag tatatcgttt ttataatata aaactattgt 5520 ttatttcttt tcataattat ttttagtacc cataatttga atggtttaca tacaatgttt 5580 gatttttcta tgtttagttt atgcggaaga gagtgctaat gtggaaagcc tcaatgaaaa 5640 catcttcaat ataactcttg aagataatat atcaagccaa aattccaata ctttttccca 5700 tggtgattga ggaaaattga agggtttgat tggaagaaaa tgtgcaagat gttctaatgt 5760 tccaatgtcc ttaattttgc aaatcttttg aacatttgat attttgtaat gttctaatgt 5820 ttttttttat tatgctctta ttttggatat gtaaatatat acttaaaacg aaaaatgctt 5880 ttttatgttt tggttttgga tgtgacaata tggtatgtat tatctatcgt tatagaccat 5940 accaacaaat aatatgacta tttggaagca ggggtatggg tgtgaattaa attggtgtac 6000 acatattggc tctagcagac tctagaaagt ctaggttatg tccattgtgt atggcatcac 6060 actcgcaata aggtgggcaa tgggatccct tgcataatca tatagtctca tatgatctcc 6120 tttattgtca gtgcctatag gcatggcaat cgtatatata tcctcctgtc aattgcacca 6180 atcaaataac tgggccacat gcattccttt gacagtagat aatttatgct cttattttta 6240 ttgtcgcgcc tttttttctt tcattcactt attgcttcct aaaccctttt tttccgcaca 6300 aagcttccta cgccatagaa ctcaccatca ttgctatggt gctttggtaa ttctgatggc 6360 acatagcaag agtagtcttc gtcggtggcc tgcaatacca ttcttgcacg gttagaagat 6420 tgatttgtgt tttggttcta atcaagcaat tatgggttca agtttcaacc tttttttcac 6480 tcaaaaaaag tattatgttt tttatttaat tatttattgg tttaaattat attttcctta 6540 acgggtaacg ggtcgggtca tattacccgt taatattatc gggtcgattt cgggtcgggt 6600 cattttaccc gtttatttta acgggtgtta cacgacacga cccgttaaga tatcgggtat 6660 gacacgaaaa cgacacgaac acgggaaaca cgacacgaat gccaagtcta 6710 // ID hAT-10_VV repbase; DNA; EDCOT; 5599 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE hAT-10_VV, an autonomous DNA transposon - a consensus sequence. XX KW hAT; DNA transposon; Transposable Element; TIR; Hatvine-10; KW hAT-10_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5599 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 777-777 (2008). XX DR [1] (Consensus) XX CC hAT-10_VV (Hatvine-10 in [1]) consensus is an autonomous element. CC Its individual copies are >90% identical to the consensus CC sequence. hAT-10_VV contains 11 bp-long TIRs which are flanked by CC 8 bp-long TSDs. The 5' and 3' TIRs have a conserved mismatch. XX FH Key Location/Qualifiers FT CDS join(1896..3519,3605..3735,3820..3895,3995..5268) FT /product="hAT-10_VV_Transposase" FT /note="hAT transposase; pfam05699:hAT family FT dimerisation domain." FT /translation="MASKHDIGWEHAEPVGGSRRTTKCKYCGKVIHGGITR FT LKQHIAHISGQVEGCPRVPVEVSHSVRQHMSNTSKEKAQLKKKKERLLNSL FT NRENFYEIDEGDSDDEIEEVAMADFERRQMKQAMKESRRIFEEGGQEHQKG FT GSSSQPSNARIKRGLTRSFSVREGASIPPKGIDPYMFPSKQKSIKSLFSTE FT GVKKVGKAISKFFLFNAIPFNAADSGPYYQSMIDTIAEAGPGIKGPTGYQI FT GNTYLEEEVQELEVYITTLKAKWPIYGCTIMCDGWSSRTRKPIINFMIYCD FT RSMIYHSSVDTTNIPKTADYIFSLMDKVVEEVGEENVVQVVTDNEASFKAA FT GMLLMEKRKHLFWSPCAAHCIDLMLEDIGSMKQIKETLDQAKMITGFIYNS FT LKVVNLMKVFTKDRDLLRPGITRFATEFISLESLIRYEADLKRMCTTNEWR FT EFNKDRSRKSLRDKVSNLILTDRFWKKAGEVQTIMEPLVKVLKLVDQDKKP FT TLSIIYEAMDRAKLAIKASVKQWEKYWEVIDRRWEGQLHRHLHAAAYFLNP FT MFQYSKHFSNHPEIKVGLKEVIKRLEPDLDRQAKAINEVKLFVDGQGEFGS FT ALTKKAINQSLPAEWWNNYGDEGPHLQKIAVKILSQTCSSSGCERNWSTWS FT LIHTKLRNRLAMKKLHKLVYVHYNMRLRVKNLMQERSNEDLYNPIDLNHIF FT NDDDILDEWIREGEEPILSSDNLDWLDKGLPTNEEGRETVHEDDGATNRRV FT SRRTSNATQERDVDSRRKGKASRTISSSSSSDDGDNRGSRRGGGTSGGNRG FT VGGTSEGTGGDGSTGGGYVSQVDPGMSWAQGGENYYATQDTDHGYRPGIWE FT QRKHLERLTTFPSDDDYSSGHDYHRSNYHRIDEHLQNLGIGSRPYFRGVDD FT RSYHNFRDRDSSSSTFSRNDFNRFPMMHPEGYSNTGTRASDSYGYDQSSSS FT SSIAYRGFGYYQSGVDPEQPSKPYFPDYGSSSQSSHPTYSSYEQLFQPYPH FT YGNCHPNLYARRRTDDDDDFEPPRHSTWN" XX SQ Sequence 5599 BP; 1938 A; 781 C; 1073 G; 1798 T; 9 other; cagggttcaa aaatcggcca agtcgtatcc gcctcgaagt ggaccgcgac gagtccgata 60 ccagttacct agactcggcc tgaatcggtt ggactcggat gagtcgatcg aaattccgag 120 ttaactcggt caactcgggg aaaaaattca atagattctc tgcaaaaagc cccacaacaa 180 atcttgattt tttcagagaa atcagagatt cctctgcaaa agaaaaccta tgaaacctat 240 gaaaattaaa aaaaaaaccc gtgaagattt gacaaacctg tgagtccgtg accctttcaa 300 aagcctttaa aaagaggctc ggttgaagaa atccaccatt gccggagtct ataatcttca 360 tctttggtgc ggtgcttggt ggaaggtagt agattgtgcc acgagaggct gcgtcttcgt 420 ggtctgggga agaagacaga gggctgcatc aatgcatcag agcatcttcg tggtgttgtt 480 gtgttgggga agaagaagaa gagggtaaaa cgtcttcgtg gtgttgttgt gtaggggcta 540 ttgctgtttt ggggaagaag aagaaacaga gggcaggggg ttagggcagc ctgggcagga 600 ggtttgagtc gtttgaccga taagtaacaa attcatatag acttatattg aataatttaa 660 ttcaatcata gaataggtta gaattttatt acttgattta atatgattta gttctgcaaa 720 tcttaatgga agtcaagtgt tcctaattta tatgatatat tattcctttt caatttaata 780 tatgtaatct ctatatataa ttgaatattg ttgatatata taatttgtta ttcattttca 840 aatattgttg ccatatatct tataaactaa ataagatata attaataatt ttaaattatt 900 tcatgaattt tttaattttt aaaaataatt ttgaaattta aaaaccaatc taattaatta 960 catataaaat aaattttatt ttttataata ttatgttgat aattcaattc taaatgagta 1020 catrgaatga aaattttgac tcatttttaa aaagttaaac tttattaatt attcaattta 1080 aataaaatat tatgaaaaat tattagttta aatatttatt attaattttt aacccaaaaa 1140 atgataaaga tgttaatatt tttatrtttc taacatatgy taaaatagta ttttttttta 1200 taaaaataaa ataaaatwaa cctgtgattt tattataata tcatatatat aatatgttat 1260 tccttttcaa attaatatat atactctcta tatatggttt aatattgttg ctatatataa 1320 tatattattt cttttcaaat attgttccta tatgtcttat aaactaaata agacataatt 1380 aataatttta agattrtttc atgaatttta aaatttttaa aaatataatg tacaagaaat 1440 tgtcttgaat actttaaaaa tatcactcaa wtttctatta gtataaataa atttasatta 1500 tattagtgac aaaaaatttc cctattactc aattacatta atactatatt gcaaaattaa 1560 attactatac aaaattaatc attattgaaa tttttttctt caaataatca taaatgattt 1620 aataatacgg aatgaagggt atgcatttac atggtcaatt acattgattt taatttaaaa 1680 aacatataaa taagtggaaa acaaaagatg atgaacttag gtgagatcrt gtttattgtt 1740 tttttartac aatttatttt tatatggcaa caatatgaaa catataagtg agtggaaaat 1800 tgaatattat aattcttata taaatgtgtt tatatatatt caatttgaaa agtaaattgt 1860 tttcctttta tacatggtta ggttaaaatt tcaaaatggc ttcaaaacat gatattggtt 1920 gggagcatgc agaacctgtt ggtggtagta gaagaaccac aaagtgtaaa tattgtggga 1980 aagttataca tggcggtata acaagattaa agcaacacat cgcacatata tctggacaag 2040 tggaaggatg tccacgtgta ccggtagaag tgtcacatag tgttagacaa catatgtcta 2100 atacttcaaa agaaaaagca cagttaaaga aaaaaaaaga acgacttttg aattccttaa 2160 atagagaaaa tttctatgaa attgatgagg gtgattctga tgatgaaatt gaggaagttg 2220 ctatggctga ttttgaaaga agacaaatga aacaagcaat gaaagaaagt cgtcgaattt 2280 ttgaagaagg tggacaagag catcagaagg gtggtagttc ctcacaacct tctaatgcta 2340 ggattaagcg cggactgaca cgtagcttca gtgtaagaga aggagctagc atacctccaa 2400 aaggaattga tccctacatg ttcccatcaa agcagaaatc aataaaaagc ttgttttcta 2460 ctgaaggcgt gaagaaagtg ggtaaagcta tttctaaatt ctttctcttt aatgcaatac 2520 cctttaatgc agctgacagt gggccttact atcaatcaat gattgatacc atagcagaag 2580 caggtccagg catcaagggt cccacgggat accaaattgg aaatacatat ttggaagagg 2640 aggtgcaaga gcttgaggta tacataacaa cattgaaggc taaatggcct atatatgggt 2700 gcacaatcat gtgtgatggt tggagttcta ggactagaaa gcctatcatc aatttcatga 2760 tttattgtga tagaagtatg atataccatt cttcagttga cactaccaac atacctaaga 2820 cagcagacta catcttttcc cttatggata aagttgtaga ggaggttggg gaggaaaatg 2880 ttgttcaagt agtcactgat aatgaggcaa gttttaaagc agccggtatg ttgttgatgg 2940 agaagcggaa gcatttgttt tggtctcctt gtgcagccca ctgtattgat ttaatgcttg 3000 aagatattgg aagcatgaag cagattaagg agacattaga tcaagctaag atgatcacag 3060 gatttattta taatagcttg aaagtagtga atttgatgaa agtgttcacc aaggatagag 3120 atctgttaag gccaggaata acccgttttg ccactgaatt catttcactt gagagtctta 3180 tacgttatga ggctgatttg aagagaatgt gcacaacaaa tgagtggcgt gaattcaata 3240 aagataggag cagaaaaagt ctaagagata aggtatccaa ccttatctta actgatcgat 3300 tttggaagaa ggcaggggaa gttcaaacca tcatggaacc tctcgtcaaa gtattgaaat 3360 tggttgatca agataaaaag cccacactat caatcattta tgaagcaatg gatagagcta 3420 aattggctat caaggcatcg gtcaagcaat gggaaaagta ttgggaagtc attgatagaa 3480 ggtgggaagg tcaattgcac agacatttgc atgctgcagg taataaaaaa attctttata 3540 tattttttat tatttttttc aagtacaaat tattataaac tgatcattat ttaacttatg 3600 gcagcatatt ttttaaatcc aatgttccaa tattcaaagc atttctccaa ccatccggaa 3660 attaaagttg gattaaagga ggttatcaag agattagagc cagatttgga tagacaagca 3720 aaagctatta acgaggtata ataatagttt gtgaccttta tataatgcat tttgtatatg 3780 taatgtgcat taacaaaaaa aaaaatgtta atgatgtagg tgaaattatt tgttgacggc 3840 caaggagaat ttggaagtgc acttacaaag aaagcaataa atcaatctct tccaggtact 3900 caatacattt acgtctatta caaataagaa attatcatca ttttttgtta aatatatcat 3960 agtgattaat aagtatgcat tttctttatt atagctgaat ggtggaacaa ctatggcgac 4020 gaaggtccac atctacaaaa gattgctgtt aaaattttaa gccaaacttg ttcttcatca 4080 ggttgtgaaa gaaattggag cacatggtca ttgattcaca caaagttgcg caaccgtttg 4140 gcaatgaaaa agttgcataa gttagtttat gtgcactaca atatgcgact tcgagttaag 4200 aatttgatgc aagagcgaag caatgaagat ttatacaatc caattgatct gaatcatatc 4260 tttaatgatg atgatatatt agatgagtgg atacgagaag gagaggagcc tattttatca 4320 tctgataatt tggattggtt ggataaaggt cttcccacta atgaagaagg tagagaaaca 4380 gttcatgaag atgatggtgc cacaaatcgt agagttagta ggcgtacaag taatgctaca 4440 caagaaagag atgttgattc ccgtcgtaaa ggtaaggctt ctagaacaat ttcttcaagt 4500 tctagtagtg atgatggtga caataggggc agtaggcggg gtggtggcac tagtgggggc 4560 aatagaggag ttggtggcac tagtgagggt actggaggag atggtagcac tgggggcggt 4620 tatgttagtc aagtagatcc tggcatgtca tgggcacaag gaggtgaaaa ttactatgcc 4680 acacaagata cagatcatgg atatcgacca gggatatggg aacaacgaaa gcatttggaa 4740 agactaacta catttcccag cgatgatgat tattctagtg ggcatgatta tcatagatca 4800 aattatcacc gtattgatga gcacttacaa aatttgggta taggatcaag gccgtatttc 4860 agaggggtag atgatagatc atatcacaac tttagagacc gtgatagctc ttccagtact 4920 tttagtagaa atgattttaa tcgatttcca atgatgcatc cagagggata ttcaaatact 4980 ggaacacgag ctagtgactc atatggatat gatcaatctt ctagtagcag tagcattgct 5040 tatcgaggtt ttggatacta tcaatctggt gttgatcccg aacagccttc gaaaccatat 5100 tttcctgatt atggatcatc aagccaatca tctcacccaa catattcgag ttatgaacaa 5160 ctctttcaac catatcctca ctacgggaat tgccacccca atttgtatgc tcgtcgtagg 5220 actgatgatg atgatgattt tgaaccccct cgtcattcaa catggaattg attattgtat 5280 tgtatgtgtt gttcgtaaaa atgttattat atttgaaata aaataacttt ctttttatta 5340 gcattatcat aaataacttt gagcatatac ttttataact atttaaataa tgttaaatgt 5400 gagacaattt tattttttta atttttttag cttatttaat tgtatatatt tttctgatga 5460 tttacataat atttttatat ttttttgaat tttctaatta gcttatttta cgtatcaccc 5520 gataccaggc cgatacaccg agaccgatac gcctcgagac cctccgagtc agtgaccgat 5580 accgcgactt tgaaccatg 5599 // ID TS repbase; DNA; EDCOT; 161 BP. XX AC D17453; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 11-NOV-1996 (Rel. 1.1, Last updated, Version 1) XX DE Tobacco DNA, short interspersed repetitive element, TS family. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; TS; KW TS family; short interspersed repetitive element; KW tRNA-related region. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RP 1-161 RA Yoshioka Y., Matsumoto S., Kojima S., Ohshima K., Okada N. RA and Machida Y.; RT "Molecular characterization of a short interspersed repetitive RT element from tobacco that exhibits sequence homology to specific RT tRNAs."; RL Proc. Natl. Acad. Sci. U.S.A 90(14), 6562-6566 (1993). XX DR GenBank; D17453; Positions 40 200. XX SQ Sequence 161 BP; 37 A; 37 C; 52 G; 35 T; 0 other; agaggttgtg agttcgagtc actccaagag caaggtgggg agtttcttgg agggagggag 60 ccgagggtct atcggaaaca gcctctctac cccatggcag gggtaaggta tgcgtacaca 120 ctatcctccc cagaccccac tagtgggatt atactgggtt g 161 // ID LTR-16_Mad repbase; DNA; EDCOT; 3189 BP. XX AC . XX DT 04-NOV-2010 (Rel. 15.11, Created) DT 04-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE Putative LTR-retrotransposon from the apple genome: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR-16_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-3189 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 2006-2006 (2010). XX DR [2] (Consensus) XX SQ Sequence 3189 BP; 863 A; 451 C; 763 G; 1111 T; 1 other; tgtgaaatcc cgttcctgga tttcactgtt ataatctacg tatttgtatt attgagattt 60 tatattattt ttcgagaatt tatttaattt attgaattta gatttcaatt aaattagtta 120 ccaagagtga agtttggaaa ttaattattt aaaatccgtt gacctttcga ggtcacaagt 180 aacgtttttg aatagatctc gagaccacga acgcataggc gaaagccgtt tgcgagtccg 240 gattataacg gtatagttat ggacatttga aatcatttac taaactatag tttttaatta 300 attaaaatcc cactttgtgg gaaagaggcc caatcatgta agatttaagg tggaccaatc 360 agaaaagaaa aaggaagggg actttgaggg tagcacagga ggaaggaaag aaaaaggggg 420 cggaagaaaa aaaagaaaag aaaaggggga ctcagaggac agcacgggag gaagaaaagg 480 aaagggggga agaagaaaaa aaaagggagg agagaaggaa aaagggagtt gcgaaagaga 540 aggggaaaag aacgttcttc cacgttcttc ctggctttgc gagggaagaa aaagaaacag 600 ggaggaggtg gctcttccat agctgttgga agaaaatcct tctttcttca ggcaaaaatc 660 ggagagagag gagttagaga acgtgattgt gaaggaagga ttcagagatt taaagggtaa 720 attccttgtt acttcattat cttgattttc gaatttaact ttcttaagtt gaattgaaac 780 tgccatgata tatttggagt tcttagttct atttagggtt ttctatcatt caatgaacta 840 gtctaaacat gaattagagt tgggtatttc ggattgggtg tgtagatcaa atttcttgat 900 caagggtttg gttcaaaagg tcaatttctt gttaattttg agtcatgtta gttttggatg 960 ttgtatacat gacttctgga ctacctggaa gtattttggg atttgttata tgaattggaa 1020 gtgggctgtt acgtaagctg cagaaaattg atttctttgc aaagaaaact caagtttcga 1080 gtagccttct ttggctctta atttctaggc ctttatgtgc tcctttggag aaaatttttg 1140 tgtgttgaaa gtacatatgt tcatggtcgt aacccaattg ttttcactca gttccgttga 1200 gttttggttg atcaaaacct tatttaaact tgggtcgcga gctgccaaac agcagcagaa 1260 aactgggtkt ccagtttcaa gactccgttt ttcttttggc ataacttcca atttagagct 1320 ccgttttcta caaactttgt atgcttttaa agtacagaac acaagcttca aaacccatat 1380 aatattacat gatttggttt agttttgaat gttccaaagg gagcctaaac ttggtccaat 1440 ggtgctgttt tctgcagatt ttgtggagaa gcagagtact gtttttgcca cacctagttt 1500 ctttccagat tcctttctaa tcttctttac tactaattga gtgatggtat taatatcatt 1560 tgtggatatg acatggtttt ataaatgtgt tttctattaa atgtgattct tttataattg 1620 gccatcgatc tatttttatt aaatgtgatt tggttcatgg atgggtatta tttgtggaaa 1680 agtgattcga attgcatatt gaaatgtgaa ttatatatat atgccataga cccatgttaa 1740 ttaaatgtga attctattga agtgttattt tatttttggt cattgatcta ttttcattaa 1800 gtatgatttg acttgtgcat tggaaatatg gtttgtattg tatgattgga ttgatgtgat 1860 gaaatgcgag ggctagtagt ggaccattaa ccattgttat ggggtttgtt gccttcgaaa 1920 catgtttcaa ccctcgtgtc attattcatc ctcgtttcgt tgagtctttg taccttgagt 1980 aacttgatcc atgtcttgtt tcattgattg gtgttacaca ttctactccg cgattccgtt 2040 gagtgatggt ccggaatcgt atcctggttt ggattccgtt gagtgatggt ccggaatccc 2100 ttctactccg cgattccgtt gagtgatggt ccggaatcgt atctgattcg ttggcggaat 2160 cccttctact ccgcgattcc gttgagtgat ggtccggaat cccttctact ccgcgattcc 2220 gttgagtgat gttccggaat cgtatctaac ttgggtttca tttagtggtg gttatgcatt 2280 gtgctccgcg attccgttga gtgatggtcc ggaatcgtat ccacttggat tccgttaaga 2340 gctggtctcg gaatccctca tacttcgtga ttccgttgag agatggtccg ggatcgtgtt 2400 caccttgggt tttattgagt ttggatcgag atagcttcag agatgtaggc ttcggccgaa 2460 ctgtgtcgct ctagccctac ttttcatggt gttgtatgag attatgatta tgagctgttg 2520 tgatttgttc cagacgaacc gttggatgtc tgggtgactc cttcggagtt gttagagttc 2580 cttggttaaa tttgtgaaat gatatgttac tgcattcatt gattaaacaa ttaaatgcta 2640 agatcatgta tctttgattc atgattaatt aattgatgtg attgtggaat gacgttgggt 2700 atgattgaga ttattatgat tagagtaatt gattaatgtg acttgagaat aacattgtgc 2760 ttcgttggtt ctttgatatg ttacatacta tgatttgcgg tattatgtga aacagagtga 2820 tttatatgat ggatgaattg gaaagtatct gtgtgagaat gggttacatg cgtgtatgaa 2880 agatgataat tgttgttgac gtaaggttga tgtgtaatat ggtgccttat gattttctgt 2940 tagaagtatt ttacggaaag attagagttg acgattgtgg aactacgaat ggcttgatcc 3000 ctattgaggg tacgtaggca gtctaacgag gaggttagat gcagccataa agtatacgaa 3060 aaattattat gcaatttgga tcttgagtta tgctttgtac atatcccgga ggcggggtat 3120 gttagatata cgggtatttg gtgacgtcac gtgtcgatcc tggacgtatg tcgggatcgg 3180 ggcgtgaca 3189 // ID Copia-68_Mad-LTR repbase; DNA; EDCOT; 388 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-68_Mad_; KW Copia-68_Mad-LTR; Copia-68_Mad-I. XX NM Copia-68_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-388 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1675-1675 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 388 BP; 94 A; 65 C; 82 G; 147 T; 0 other; tgttagtgtg taaattgtga tctgatgtgg tagttgtatt tctagcttat attgctagga 60 tgtttagcta aattggttgt atgctttctt atctaagtct cttagttctt aagtaagtga 120 gtgtacatgt gtcttcatct catagggtgt aagatggatg gctaggatta cttggatgta 180 attttgaata ctgccaaaag attggaagtg taactgttaa gtgtagagag atgttcctct 240 ctcactgggg agcaatcaaa cagtgcgtgt gtgaagaatt gcagagtcat attctctgct 300 ctcattcatt ccctctctct cactctagtc attgcagcat atcctccatt gttgtactac 360 attttcttct aattctaaca tggcctca 388 // ID TLC1_I repbase; DNA; EDCOT; 4107 BP. XX AC AF279585; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Lycopersicon chilense Ty1/copia-type retrotransposon TLC1_I, DE internal region. XX KW Copia; LTR Retrotransposon; Transposable Element; TLC1_I; KW Ty1/COPIA superfamily; internal region; internal portion. XX OS Solanum chilense OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-4107 RA Ruiz-Lara S., Bratti S., Yanez M., Verdugo I. and Gonzalez E.; RT "Expresion Especifica de Retrotransposones LTRs en Lycopersicon RT chilense Inducidas por Heridas y Congelamiento."; RL Biol. Res. 32, R146 (1999). XX DR Genbank; AF279585; Positions 580 4686. XX SQ Sequence 4107 BP; 1388 A; 720 C; 972 G; 1027 T; 0 other; attggtatca gagcacaggt tctgctcatt tacagaaata ttttttgcag cttattgtac 60 tatactcaaa taaaaaatgt ctggagtaaa gtacgaggta gcaaaattca acggagataa 120 gccggttttc tcaatgtggc agagaaggat gaaagacttg ctcatccaac agggtctgca 180 caaggcacta ggcggcaaat ccaaaaagcc cgaatccatg aaacttgagg attgggaaga 240 attggatgaa aaggctgcta gtgcaatcag attgcactta acagatgatg tggttaataa 300 catcgtcgat gaagagagtg catgtggcat ttggacaaag ttggaaaatc tatacatgtc 360 caaaacgctg acaaataaat tgtacctaaa gaaacagtta tacaccctac atatggatga 420 aggtacaaat tttttgtctc atttaaatgt acttaatgga ctaatcacgc agcttgcaaa 480 cctcggagta aagatcgagg aagaagataa acggatcgtg ctcctaaact cgttgccatc 540 ttcctacgat actttatcaa caaccatttt acatggtaag gactctattc agttgaagga 600 tgtcacatca gcccttttgc tcaatgagaa gatgagaaag aagcctgaaa atcacggaca 660 ggtcttcatc acggaaagta gaggcagaag ttaccaaagg agctcaagca actatggtag 720 atccggagct cgtggaaagt ccaaggtccg atcaaaatca aaggccagaa attgctacaa 780 ttgcgatcaa ccaggacact tcaaaagaga ttgtccaaat ccaaaaaggg gcaaagggga 840 aagcagtggc cagaagaatg acgacaacac agcagccatg gtgcaaaata atgacgatgt 900 tgttctcctc ataaatgagg aagaagaatg catgcacttg gcaggtacag agtcggaatg 960 ggtggtcgac acagcagcat cttatcatgc cacaccggta agagatcttt tttgcagata 1020 tgtagccggt gattatggca atgtgaaaat gggtaataca agttactcaa agattgcggg 1080 gatcggagac atttgcttca aaacaaatgt tggatgcaca ttggtgttga aagatgtgcg 1140 ccacgtacct gatttgcgga tgaacttgat ctcgggaatt gctttggacc aagatggata 1200 cgagaactac tttgcaaatc aaaaatggag actcaccaaa ggggcattgg tgattgcaaa 1260 aggagttgct cgtggcacgt tatacaggac aaatgcagaa atatgccaag gtgaattaaa 1320 tgcggctcac gaagaaaatt ctgcagattt atggcacaaa agaatgggtc atacgagcga 1380 gaaaggattg caaattcttt ccaaaaagtc actcatctct tttaccaaag gtacaacgat 1440 aaaaccctgt aactactggc tatttggtaa acaacataga gtctcatttc agacatcatc 1500 tgaaagaaag tcgaatatac ttgatttggt atattctgat gtttgtggtc caatggagat 1560 tgaatcgatg ggaggtaaca aatactttgt tacctttatt gatgacgctt ctcgaaaatt 1620 gtgggtttat atcttcagag ccaaagatca ggtgtttcaa gtatttcaaa agtttcatgc 1680 tttggtagaa agagagacag gtcgaaagcg aaaacgactc cgaaccgaca atggaggtga 1740 gtacacttca agagaatttg aagagtactg ttcaaaccat ggaatcagac atgaaaagac 1800 agttcctgga accccacaac acaatggtgt agccgagaga atgaatcgca ccattgtgga 1860 gaaggtgaga agcatgctca gaatggctaa attacccaag acattctggg gtgaagcagt 1920 tcggacagcg tgttatctta tcaatcggag tccatcagtt ccgttggagt ttgacattcc 1980 ggagagagtt tggaccaaca aagagatgtc ttactcgcac ctgaaggtgt tcggttgcaa 2040 agcttttgca catgtaccga aggagcaaag aaccaagctg gatgataaat cagttccttg 2100 catattcatc ggatatggag atgaagagtt cgggtacaga ctatgggatc ttgtgaagaa 2160 gaaggtcatc agaagtagag atgtaatctt tcgagaaagt gaagttggta ctgctgctga 2220 tctatccgag aaggccaaga aaaagaatgg tataatccct aatcttgtta ccattccttc 2280 ttcttctaac catcccacaa gtgcagaaag tacgatcgac gaagttgtcg agcaggaaga 2340 gcaacccgat gagattgttg agcaggggga gcaacttggt gataataccg agcaaatgga 2400 gtacccagaa gaagaacaat ctcaacctct gaggagatca gaaagacaaa gggtagaatc 2460 aaccaaatac ccttcctcag agtatgtcct tatcaagtat gaaggggagc cagaaaatct 2520 taaggaggtg ttgtcccatc cagaaaagag ccaatggatg aaagccatgc acgaagagat 2580 gggatctcta cagaaaaatg gcacatacca gctggttgaa cttccaaaag gaaaaagacc 2640 actcaagtgc aagtgggtct ttaaactcaa gaaagatgga aatggcaagt tggtcaggta 2700 caaagctcga ttggttgtta aaggcttcga acaaaagaaa ggtattgatt ttgacgaaat 2760 tttttcgcct gttgtcaaaa tgacttctat tcgaactatt ttgagcatag cagctagtct 2820 agatcttgaa gtggagcaat tggacgtgaa aactgcattc cttcacggag atttggaaga 2880 agagatttat atggagcaag gagagggatt tgaagtatct ggaaagaaac acatggtgtg 2940 caaattgaat aagagtcttt atgggttgaa acaggcccca aggcaatggt acaaaaagtt 3000 tgactctttc atgaaaagtc aaacatacag aaacacctat tctcatccat gtgtatactt 3060 caaaagattt tctgacaaaa attttattat tttgttgttg tatacggatt acatgttaat 3120 tgtaggaaaa gacaaagagc ttattgcaaa gttgaggaaa gatttctcca agtcatttga 3180 catgaaagac ttgggcccag caaaacaaat tctagggatg aagattgctc gagaagaaca 3240 aaaaaaattg gggctatctc acgagaagta cattgaacgt gtactagaac gcttcaacat 3300 gaagagtgct aaacctatta gcacgcctct tgtgagttat ttgaagttga ccaaacagat 3360 gtttcctaca aaaaaaaaag gagagaaagg ggacatggct aaagttcctt attcttcagc 3420 agtggggagt tttatgtatg ctatggtgtg tactagacct aacattgttg cagtttgtgt 3480 tgtcagcaga tttcttgaaa ttcctggaaa agaacacttg gaggcagtca agtggatact 3540 caggtaccta agacgtacta caagagacta cttctgtttt gaaggatctg atccaatctc 3600 gaagggctat acaaatgttg atatggaagg tgacctcgac aacagaaaat ccactacttg 3660 ttatttgttt acattttcag ggggagatat atcatggcag tcaaagttgc aaaaatatgt 3720 cgcactctct acaactgagg caaagtatat tgcaggtaca gaagtttgca aggagatgct 3780 atggctcaaa cgatttcttc aagaacatgg attgcatcag aaggagtatg tcgtctattg 3840 tgaaagtcaa agtgcaatgg accttagcaa gaaagccatg tatcatgcaa cgacgaagca 3900 tattgacatg agatatcact ggattcgtga aatggtagat gacggttctc tgcaggtcgt 3960 gaagatccct acaagtgaaa accctgcaga tatggtgacc aaggttgtac aaaacgagaa 4020 gttcgagcta tggaaagaac ttgtcggcat gcactcaaaa tagaaacctg gagctaccta 4080 tttcagttaa tggtcaagag gggagat 4107 // ID MUDRAVI2 repbase; DNA; EDCOT; 10808 BP. XX AC . XX DT 12-SEP-2007 (Rel. 12.09, Created) DT 03-DEC-2010 (Rel. 16.01, Last updated, Version 2) XX DE DNA transposon from grapevine. XX KW MuDR; DNA transposon; Transposable Element; MUDRAVI2. XX NM MUDRAVI2. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-10808 RA Obukhanych T. and Jurka J.; RT "MUDRAVI2."; RL Repbase Reports 7(9), 982-982 (2007). XX DR [1] (Consensus) XX CC This is a MuDR-type DNA transposon from Vitis vinifera. Copies CC are 92% similar to their consensus. Terminal inverted repeats CC are ~190 bp-long. XX FH Key Location/Qualifiers FT CDS 3528..6152 FT /product="MUDRAVI2_1p" FT /translation="MSESIVPVICFCKGKMLRTETDVKYIGDXAVIVPLDV FT PVSSTYEHLLSMIYSRTGIDKKQFQLVLNCRYPLKRENRFQPCPIWDDNSL FT SQMLKLVNTFGMDEIELYIEQVPVQPRVRGQLLGNFTQLLLGQNDNVEEFE FT YGCGPSSAPVAMTYECRADEDEDEKECESQEGDDQSERAEDVQHDGDGVFE FT FIDEENNNVNVVSSFLALHEAMESEQGRYVSVDGEGCDMSNNPDPEDPIEF FT SPVQYHSAPSLQFENVENIGNAVSSDWTPWGNTNIGNSGGEFMVGQVFNSK FT ADLQHAAKLYSISAHQEYVVVSSTTKLLVLRCKKAKQSQCPWKLRAMVVKG FT TTSFAINKYNGPHKCVNPCLNRDHQQLDSNLIAAHIQGMIKAQFTLSVAAI FT QASIVEKFGYQISYKKASKAKLKALTNLFGDFYKSYAELPHFFIALEQANP FT GCVVISKTFPGIMENTEIFQRVFWTFHPSIEGFKHCRPVLSIDGTHLYGKY FT KGTLMIAMGCDGNNQLFPLAFALTEGENIDSWGWFLTCIRTRVTHRRGLCV FT ISDRHPGIMAAMSDVHLGWSEPYAYHRVCMRHLASNFMTRFKDKILKNLMC FT RAALATKIEKFNKHMNTIGRINAAAQQWLEAIPFEKWALSHDGGRRYGIMT FT TNMSEVFNSVLKGARSLPITALVQLTFFRLNSYFVVRREQGANRLASNEEY FT TPYVDAKIKANVVKAGSHEIVLYDHIQGQFHVKTNKGTKSSSTRGRTYRIN FT LQEYACTCGKTLIYGFPCSHILAACHFRSVDFRPLVQHYYSTQSYYNTWAP FT LFHPIFNVYEWPPYDGPIIVPSESMKRASSGRPKSSRLHNEMDVREGKTSI FT TCGLCKQSGHNRRSCQNSNRID" XX SQ Sequence 10808 BP; 3452 A; 1680 C; 1771 G; 3861 T; 44 other; gagctttgac ccaaaagcta cctttaaaaa aaaaatccat aaagtacmcc catttttaaa 60 ataatgccca atctaatgtg tctgcgccac gtagattgcc acgtcataaa accgtagttg 120 gtaactacgg ttttattttt tttttaactt gtttaaaacc gtagttggtg actacggctt 180 tactttcctt ttaccttttc ccctttccca ttaggttttt cattttccca cctttcccag 240 ttacctttct tccttttagg gtttcgtcct ttagggtttc atccttcctt tgcatccttg 300 gctcaaattc aaagtttgga agtcattgtc aggtaagatt tatgagtttt tctgtttatc 360 gtaaatttta attttttttg taaatccgtt tggttttcat gttgttgttg ttatagctgt 420 gtttgggttc tatttggtga agatgtgttt gatatttttt gtttttattt tgactgtgag 480 cttatctgaa agaaaaaagg kttttttggt aagaaaacgg atatggaatg ggggccgcat 540 ggattttttt ttgttaaaga tccaaaaatg gaggggacca ctgtaaaaaa ttccaaaaaa 600 gcggtggttt ttgttatagg aatagaaaaa ataggagtac tccacttttc aagggttaga 660 tttatcttaa gagatttctt attcctcaca attgggcatc ttcgtgaacc tagtgatgaa 720 aaggatgtga aggcttgaat tttgaagagt cctcagaacc tgacacccca taggagattt 780 aatcttactg taaatttcgg atacttgaaa ataaaaaagg agaatattta tcctaaataa 840 ccaaaaataa aattaagaat taatctgtat tttctctaag taggatctac tgatgaatat 900 ttgggttgaa ttcaaccttc cttaatagag agctagacyt ttccacaaca taaaaaattc 960 attttggtgt caattaaata ctcaaattat atatatatat tttccaataa aacacttcct 1020 aaacaaagct tctatttttt tttctttttt aatgaaaacc aattcctatt tccacaattt 1080 tattcactaa tttataataa ttttgcttaa acatgcctaa cmatgtaaac aacagcagtg 1140 tattcccaaa attaagactt atttatttta tttattatac atttaatttt gtgcatagat 1200 atattgtaat gttattaaac atagtacatg ataaataagg taaataacct ttttcccatt 1260 tacttatctc ttattagact ggaatttttt agattcaaca attttatact tcaacwttta 1320 aaatatggta attaaataac ccttcttacc attaaatagt ttagacaatg agcgacaaat 1380 ctataaccag atgttttctc tcaagtcctt ttttttataa ytatcttatg tcttactctt 1440 gtccctttga ttattagggg tcacaatctc tcaacctctc cttccattaa gttaattaat 1500 tgttactttt tttattcatt aaagaagtct tagttttcca actatgaaat gattaaataa 1560 gaacccagca atgtcttttt gtttgtgctc ttaagttaat atgtgtttgt gttggattgt 1620 ttggtgccaa gtgacttgac cccaatatag aaataagaaa aaaaaatata tataattttt 1680 ttgaaaaaaa ctcttatgat ataataaaaa aatggttctc gtrtttataa tatcattaat 1740 gatttaagat aaaaaaaaat tgatttataa aacaattaat tgattctttg atatttaaga 1800 aagtaatcca aaaatcttat ttttatatat atatatattt tgtagagaaa tatagattta 1860 tcttatattt tttaaaaatt attttaattt ttttttaaat ttaagagagt atttttttta 1920 tatcttaatt tttttcttaa aataatattt attatgattt tctattttac aaaaagaagg 1980 aaatatgtcc aaatgtgtac ctaagtaatg ccttttcaac gactctttga taagtttact 2040 acacrtgttg aattatttcc atgatgggac ttttgagaaa tttaaaaccc atatgtatsa 2100 atgcaatgaa cttgtttgtt tttgtgggtc aaagttagtt gtagtgtgaa agytgyaagm 2160 gatgaaaagg atttttgtat gaacatgaca tgatatgagt gttggtatga aattcttata 2220 tggtactctt attttgcttt aaagcagtca tttgacttta attaatttat ttatattttc 2280 aactttctta aaagataagg rttaatttca ttcgttttyt tagaagtttt ggttaagcac 2340 tttccttatt grtttaaaat ttgatcaaat atctccctta tttttctcat ttgttatttt 2400 cagtcacctt atctcttatt aaaaaataga ttatttttag ttacctctcc tcctatttaa 2460 tgaaatttca atcaatgagg ataaagtgta tttagcmaaa tcttgggggg atgtgagtgt 2520 taaccttgaa agataattak attattttka ttttgtctag tgtatgttta taaaaawatt 2580 targaataag aaacaaagra taaatatagk acaaaarwat aawaatcaaa aygaagttct 2640 cawtaaaata tttttgttyt atgyaaattk tttaattaaa wattmtatag attttsctty 2700 taytttttgt attcaaatst kmatatagaw yatgagatca aacccactta aaattkgtyt 2760 tataaaaaat caaacaaata taaattaaaa ttaatattca atagatttat aaattaaaat 2820 taaatttaat attaatttat aaatgatttt ttccctatat ttaaaattaa tattaaatag 2880 atttataaaa tgtttatttg tttgcatttt taatattcaa ataatgttta tatatatata 2940 tatatatata tatatatata tatatatata tatattatat ttaatgattt ttttttataa 3000 ttgtgtattt gatattttat taatatattt ttctgtggtg ggttactttt atttgatttt 3060 gagtttttaa tttttttttt taattttatt tttaatcaaa tatcaagtga ttcatgrata 3120 ataacataat tatttaaatt atatattatt taatacttga taatattcaa ttttatttta 3180 atatatgata ttttattaaa aaaaatttgg tggattattt tttatttaat tttaagatta 3240 ttgtaattgt ttaactcaaa atttattgat ttataaccca ctatctaagt tttaaattaa 3300 aattctataa aacatttatc tatgattata tttgtatcat agataactat ttaaataaaa 3360 aaaatttatt attattaagt gatttatatt tttccctcct aatgtgtaag aaggtgtttt 3420 attatataat tgtgtattca catgttaaaa gattatatgc aatttctctt gctattattt 3480 tcattaatta ttaaaccatt tgatattgta ttttttgtag gtaaatcatg tctgaatcta 3540 ttgttcctgt gatttgcttt tgtaaaggaa aaatgttgag gacagaaaca gatgtaaagt 3600 atattgggga tsaagctgta attgtgcctt tggatgtgcc tgttagttca acctatgaac 3660 acttgttatc tatgatatac tcgagaactg gcattgacaa aaaacaattt caattagtcc 3720 tcaactgtag gtatccttta aaaagggaaa ataggttcca accttgtcca atatgggatg 3780 ataatagttt atctcaaatg ttgaaattgg ttaacacatt tggaatggac gaaattgaat 3840 tgtatattga acaagtgcca gtacaaccac gggtgagagg gcaattattg ggtaacttca 3900 cacaattatt actcggacaa aatgataatg ttgaggaatt tgagtatggt tgtggaccta 3960 gtagtgcccc agttgcaatg acttatgagt gtagagcaga tgaagatgaa gatgaaaaag 4020 aatgtgaatc ccaagaaggt gatgatcaaa gtgagagagc agaagatgtt caacatgatg 4080 gcgatggggt gttcgaattt attgatgagg aaaacaataa tgttaatgtt gtttcatctt 4140 tcttagctct tcacgaagca atggaaagtg aacaagggag atatgtctct gtggatgggg 4200 aaggttgtga tatgtcaaat aacccagatc ctgaggaccc aatagagttt tcccctgttc 4260 agtatcactc ggcaccatca ttgcagtttg aaaatgtaga aaacattggt aatgccgttt 4320 caagtgactg gaccccatgg gggaacacta atattggaaa ctcaggtgga gagttcatgg 4380 ttggccaagt ttttaattca aaagcagatt tacaacatgc tgcgaagttg tactctatta 4440 gtgcacacca agagtacgtt gttgtttcgt caactacaaa gttgttagtc ttaagatgca 4500 agaaggctaa gcaatctcaa tgtccatgga aactccgtgc tatggttgta aaaggtacaa 4560 cttcatttgc aatcaataaa tacaatggtc cgcacaaatg tgtaaatcct tgcttgaatc 4620 gggaccatca acaattagat tccaacttga ttgctgctca tatccaagga atgattaagg 4680 cacaattcac attgtcagtg gctgctattc aagcaagtat tgtggagaaa ttcggatacc 4740 aaatatcata caagaaggca tctaaagcga agcttaaagc tcttacaaac ttatttggtg 4800 atttttataa gtcatatgca gagctgccac attttttcat tgccttagag caggcaaatc 4860 caggatgtgt tgtaatttca aaaacatttc ctggtattat ggagaataca gagatatttc 4920 agcgagtttt ttggacattt catccatcta ttgaaggatt caagcattgt cggcctgtac 4980 tcagtattga tggtacacat ttgtatggga agtataaagg cactttaatg attgctatgg 5040 gttgtgatgg aaataatcag ttattcccat tggcttttgc cctaacagag ggtgagaata 5100 ttgatagttg gggatggttt ttgacatgta ttagaaccag agtaactcat aggaggggac 5160 tttgtgttat atcagatcga catccaggca ttatggctgc aatgagcgat gttcatcttg 5220 gttggtctga gccatacgca tatcataggg tttgtatgcg tcatcttgcc agtaatttta 5280 tgactcgatt caaggataaa atattgaaaa atctgatgtg cagagcagcc ttagcaacca 5340 agattgaaaa attcaataaa catatgaaca caattgggag gattaatgca gccgcacaac 5400 aatggttgga agcaatccct tttgagaaat gggcgctctc tcatgacgga ggtcgaaggt 5460 atggcatcat gactacaaac atgtcggagg tgttcaatag tgtgcttaaa ggggctcgta 5520 gcttacccat aactgctttg gttcaattga cattttttcg gctaaatagt tactttgttg 5580 tgagaaggga acaaggtgct aatcgacttg cttcaaatga ggaatacact ccatatgtcg 5640 atgctaagat taaggcaaat gtggttaagg cgggatctca tgagattgtt ttatatgatc 5700 acatccaagg acaattccat gtgaagacta ataagggtac taagagtagc tcaactcgtg 5760 gtcgaacata tcgcatcaac ttacaggagt atgcatgcac atgtggtaaa acactcatat 5820 atggattccc atgtagccat attctagcag catgtcattt tcgttcagtt gattttagac 5880 cacttgttca acactactac agtacacaat cgtactataa tacttgggca cccttgttcc 5940 atcccatttt caatgtatat gagtggcctc cttatgatgg tccgattatc gtgccttctg 6000 agtcgatgaa acgtgcatca agtggacgac ctaaatcaag tcgtttgcat aatgaaatgg 6060 atgttagaga gggcaagact tctattacat gtgggttatg caaacaaagt ggccacaatc 6120 gtcgttcttg tcaaaacagt aatagaattg attagaccat gtgatgtatg catgtaattt 6180 tcttggatat tgtgatgtaa gctactatga tactaccttt atgcaattat tggctttggt 6240 ttgattataa atattgatgt tatttgcata atcaggttat ttgtatttgg aataatgtcc 6300 atattatagg ggaaactttg tcaaaatttt gaaattttct attaaaaatg ttaacaaaat 6360 gctcaattgt atttgtatct ctaattttaa tttagactag tatgacttgt ttattggtca 6420 taaatgaatt gatgtactta aatttatcaa attgatatat acttaatata gggaaaactc 6480 cataaatttt taaaactttt ccattagaaa tatttttttt tttaaaacaa taagtattgt 6540 ttatttatct tcacaatttt gttacagata tggagtatag aggacatagt tctgatccag 6600 atccattaga tacgtctgtt ttggttctac aggatagaca caggtctcat ttagttgact 6660 ctggccaggt atgtatatga aaacacataa tatctcttta aataatggaa aaaatttgca 6720 gtttattatc taaatgattt atttgtattt ttacagcttg cttcagtctt gacttgtcga 6780 caacatatat ctaggtttat gcgggagtgg gagatggatc ctcgtcttcg accttatatt 6840 attcgatctg gattttatgg tgtataccgt attggacaca ttacactaga ttggggattg 6900 atcactagtc tagttgagag atggcgtcct gagacacaca catttcactt acctgttggg 6960 gagatgacca ttactttaca ggatgttgct gtcatattag gacttcgtat tcatgggctt 7020 cccatcactg gcacatgtga catagattgg tcactgctat gttatgaact tttaggagtg 7080 actcccccta catctgagat taaaggatca gcgatatcga cacgatggct atgtcaccag 7140 ttctctcatc caccagttga tttagatgat gccacattag agcggtatgc acgagctttc 7200 atattaggac tcataggttc aacgctattt acagacaaga agggtaccca catccatatg 7260 tgttatctcc cactacttag agacttgact cagacatcta tgtatagttg gggcagtgca 7320 gtattagcac acctatatag ggagttgtgt cgagcgagtt tggatggtgc caccgatatt 7380 gctggatgtg tcacactatt acaggtataa ttaattattc acattagatt aaaatttcta 7440 gttgcttcaa gtttataatt taagtaaaat tttaatgtta catttttttc cagttgtggt 7500 cttgggagag actccacgtg ggtcgacccg attttggtcg accaccagcc cctccagcag 7560 cccagcattt agagcatgat gcagccgatg atttaccagc tgagcagtta gaccagggat 7620 tacaggatga ggcattgtta cacgagggtt taccagctga tccgttagga tgtaggtgga 7680 gagtaccttt atcatgggct caaaacccat cacgtgtgtt gacattttat cgagaccaat 7740 tagatgcaca gacccatgac caggtacata taagatgtaa tgtgctattg ttaaccatat 7800 aaaccttaac tcagtattaa tgtcaaatgt tgattttaac aggttttatg ggagccttac 7860 atgggagact tagttgccca tcttccggcg atatctctag cagaccagga gatttggcgg 7920 acgatgtcac ctcttatttg ctttgacatt gtcgagtggc atcgaccgga gcgagtgctg 7980 cgacagtttg gcctccaaca agggatacct ccatcttgtt ccatagagct agacctccat 8040 tccgtggata ggcgaggacg acataagtat gattggggag cattccatgc acagtatatt 8100 accttatggg gtagtcgtga ggagcgtatt gcgacggcac cacctatggt gggtgttatg 8160 cagtttcatg atccatatat ggagtggtac cgacgtatta cacgacgttt gatcacaccc 8220 cctctccata gagatcagat gaggtatcat agtacagcag cagctactca gttattggta 8280 agatttttta atttataaat ggtttattaa attataatta attaaaaatc atttttgttt 8340 gtttaacttt ttttattttt ttttatttta tttagatcac tggtatggtt gagattgcta 8400 gtcgatctgc tgggcctact tcaggtgcat taggcgacat tcatcggatt gctattgata 8460 ttttgcatgt tattggagag gagcatcgca tacattcact ccgtcagtcg cctacatcat 8520 catacccatc catgagccca cctgtgtcag ccactacagt taggatgcag cctattcgag 8580 gccgagggag aggtagtaga cgagatgatg ggcgagctgg tcgacagcct cgacgatcta 8640 tgcatccacc tgagaccatg ttagcaccat ccacatcatc taccccattt gcacctgagg 8700 cttccacact tcccccttca cccctaccat caccttcacc tagaccttct cccttagagc 8760 atgtcgtatc agataccact ctaccatcac ctgtatttcc taccacagag gccactatac 8820 ctgatgtcac tataccagag actaccccac tatctactaa tctaccatca cctctacctt 8880 ctctcgagga gaccactaca ccacatgtca cctcaccatc atcacttata tctcctctcc 8940 tcgagcccac tatatcagat gttattgcac cagctaccat tacagcagat gtcattcttc 9000 catctcctat atcacctctt ctagatgcta ccatatcaga tatcactgta cctgagatcg 9060 ccccaccatc taccacttta ccatcaccta cacctcttcc catagagact accatgcatc 9120 atacccttac acatgttaca cagttagatg tatgtccacc taggagacgt cgtggtccac 9180 gtagacgtcg agtcttgcct ccatcagctc catctcaacc tatacatact gagacatggc 9240 agattgcaca gatagattcc acaaagatgt ctctttatca taggcgtccg cagagaaaga 9300 ggaagacccc atcatgtggc actcattgag gactgttttt tagtttttgt gtttattttc 9360 atttgcatta tattgttaac tttttttttt tattatgaac aaattattat atatttaaat 9420 gaaaatatga taaattttaa acttaaattg aacttatata tatatatata tatatatata 9480 tatatatata ccacttacat atagcaatct gacaatctaa aaaattggtt ttaggtttaa 9540 atttaaacta attatattta taactaatta gttacaacaa cactatattg atatagaaaa 9600 aataatgcat taaaaaaaat ttacaatcta aacctccaat caaaataatt tttaaaaaat 9660 tgaacattca catgatttaa aatttgaact taaaaaattg gttttaggtt taaatttaaa 9720 gttatgatca ccaactacta ttttgactat ttaaaaaaaa aaatcaaaaa tcatgattac 9780 caattacagt tttgtgatgt gaatacccac atgaataaga cacacatcac attgaaaatt 9840 attttgagaa taaaattatt ttatgaattt tttgttttaa agaaatcatt tttgcccaaa 9900 actcccatta gtacccaata agaaacattt ttcttattct caatgaattt acaaaaatat 9960 tccaaaagca ttttcatcta tttaccaaaa caattaaact aaatagtgaa ttgattggaa 10020 aaacaaaggt attttctttc tacaattcta tattttaaga agtggaaaaa caaattcttt 10080 taggttggca ttttaagttt aacattttaa gcctttccat tccattttga tcccattttg 10140 aaaggagaaa aatggaaaaa aaaaaattat ttttgttgta tttaagtaat tttccaatta 10200 tttacccact tgaagtcata ttatattttg tacaaatgca taattggctt taatttttgc 10260 acaaagttac aaaataatat aatattcttc attatgaggg tataaaatag tatatttata 10320 actaattata tttatattga gtatagtgcc aaatatttta ataaaattat caaaatatat 10380 ttttatatca aattaaagac atcaattatt taatttcata tattactatt ctttaaataa 10440 tgagatcaat taaagttaaa tatttttatt acaccactca catattttta atcaatataa 10500 aatcaaaata atataatatt tttatttaaa aaaattaaag ttaaatatat atatatatat 10560 atatatatat ataattaaag ttaaagccgt agttggtgac tacggctttg actattttta 10620 aaaatagtca aagtcgtagt caccaactac ggttttaaat ttttaaaaaa taaaaccgta 10680 gttaccaact acggttttat gacatggcaa tctacgtggc gcaaacacat tagattggac 10740 attattttga aaatgggggt actttatgga tttttttttt ttaaatgtag tattttgggt 10800 caaagctc 10808 // ID LINE1I_MT repbase; DNA; EDCOT; 3534 BP. XX AC AC165446; XX DT 19-JAN-2007 (Rel. 12.01, Created) DT 19-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LINE1-type non-LTR retrotransposon. XX KW L1; Non-LTR Retrotransposon; Transposable Element; LINE1I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3534 RA Jurka J.; RT "LINE1I_MT: L1-type element from barrel medic."; RL Repbase Reports 7(1), 34-34 (2007). XX DR EMBL/GenBank/DDBJ; AC165446; Positions 82389 85922. XX CC It may be 5'-truncated. XX FH Key Location/Qualifiers FT CDS 75..1628 FT /product="LINE1I_MT_1p" FT /translation="MKLVCWNVRGCNKPFKQKEIKNFLLKNKFDMCILVET FT RVKANKFNKISSMIFKRWPVLNNYDSAANGRIWVSWNPNVLDVKPIASSAQ FT AIHCEVVNLTSSECFNFVAVYAFNTLEQRKELWNFIAHTSAQNSRNLLIGG FT DFNNVLLVDDRRNGNPVTQHEIQDFSDCLLHNRLSEVRTIGDYYTWCNNQT FT SGDRIYSKIDRFIANTSWLQKFTNAVDEVLPKGASDHCPISMDMSCPASPK FT NTPFRFINDLTDHHLFPALIQEKWGPNLHTNLLTNIWFKLKALKKDLKELN FT STHFQGIAKKVEDARTALVDVQRQLSSDPMNLDLIEAEKVCLSSLEKWSTI FT EEKIWMQKSRANWIQLGDSNTKFFHAYAKERRCQNNIKFLITEDDTRIDKH FT NLIKEEIRGFYLKLMGSSVDSLPMVDKNIVKRGPMLSQHQQDLLCSEFTAV FT EVKNALFSMDSSKAPGIDGYNVHFFKCSWNIIGDSVIDAILDFFKTGFMPK FT IINCTYVTLLPKEVNVTSLVVQ" FT CDS 2764..3399 FT /product="LINE1I_MT_3p" FT /translation="MDVPAQASWVIKKVFGAAKTISSVDGSIFQQANFSIK FT RMYNALRGDFAKVGWRKMICNNPAPPKCLFVTWLIIHARLPTCDRMLKVGI FT QCDQVCILCTKENETHSHLFFSCDYADAVWKGVMRWMNMTVNTSNWHSILQ FT YIQSHCNSNNGMHQAHIMVLSVTLYMIWKERNDRKFQNCYRSVQQLLNQIK FT MDAYIRGLQFKKVQTLMIRVRG" FT CDS 1751..2257 FT /product="LINE1I_MT_2p" FT /translation="SHELVKSYSRKGISPRCMVKIDLQKAYDSVEWPFIKH FT LMLELGFPYKFVNWVMACLTTASYTFNVNGDLTRPFAAKKGLRQGDPISPY FT LFVICMEYLNRCLIQLRKNAAFRFHPRCKRLNLIHVCFADDLLLFSRGDVD FT SVSQLLACLVLLLALKQIRLRAQFIWEVYP" XX SQ Sequence 3534 BP; 1053 A; 530 C; 751 G; 1200 T; 0 other; actaatgatg aactgcatgt atgtgaagct tctacttctg aaaggggcgg ggaccctatc 60 ccctttggtt tgatatgaaa ctagtgtgtt ggaatgtgag gggttgtaac aagcccttca 120 agcaaaaaga aatcaaaaac tttttgctta aaaataagtt tgatatgtgt attttagtag 180 aaactagagt taaagctaac aagtttaata aaatttctag tatgattttt aagaggtggc 240 cagtgcttaa taattatgat agtgccgcta atggtagaat ttgggtctct tggaatccaa 300 atgtattgga tgtcaagcct attgcttcta gtgctcaagc cattcattgt gaagtggtta 360 atctaacttc aagtgagtgt ttcaattttg tagctgtgta tgcttttaat accttggaac 420 aaaggaagga gctttggaat tttattgctc atactagtgc tcaaaactct agaaatttgt 480 taataggtgg tgactttaat aatgtgttgt tggttgatga taggcgtaat ggtaatccag 540 tgactcaaca tgagattcaa gatttttccg attgtctgct gcataatagg ctatcagaag 600 tgagaacaat cggagattat tatacttggt gtaataacca aactagtgga gatagaatat 660 attctaagat agatagattt attgctaata ctagttggct gcaaaagttc accaatgcag 720 tggacgaagt gcttcctaaa ggagcatctg atcactgtcc tatatctatg gatatgtctt 780 gtcctgcttc tcctaagaat actcctttta gatttattaa tgatttgact gaccatcatc 840 tttttcctgc cttgatacaa gagaaatggg gtccgaattt gcatactaat ctcttgacta 900 atatatggtt caagttgaaa gccttgaaaa aagatctaaa agagttaaat tctacacatt 960 ttcaaggtat tgccaaaaaa gttgaagatg ctagaactgc tttagttgac gtccaaaggc 1020 agcttagttc agatccgatg aatcttgatc tcattgaagc tgaaaaagtt tgtttgtcct 1080 ctcttgaaaa gtggagtact atagaggaga agatatggat gcagaagtct agagctaatt 1140 ggattcagct tggggactcg aacactaaat ttttccatgc ctatgcaaag gaaagaagat 1200 gtcagaataa tattaagttc ctcataacag aagatgacac cagaattgac aagcataacc 1260 tcatcaagga ggagattaga gggttctatt taaaattgat gggtagttcc gttgattcat 1320 tacctatggt ggacaaaaat attgttaaaa gaggtcctat gttatctcag caccaacaag 1380 acttgttgtg ctccgagttc acagctgtgg aagtcaaaaa tgcgttattc tccatggact 1440 cttctaaagc tccaggtatt gatggttaca atgttcattt ctttaaatgc tcttggaaca 1500 ttattggtga tagtgtcatt gatgctatat tagatttctt taagactgga ttcatgccta 1560 aaattattaa ctgtacttat gtgactttac tccccaaaga agttaatgtt acatcgcttg 1620 ttgttcagtg atatataaga ttatttctaa aattttaaca agcagaatgc aaggagtctt 1680 aaatagtgtt gtaagtgaaa atcaatctgc ttttgtcaaa ggtagggtga tttttgacaa 1740 tattatttaa agccatgaac tagtcaaaag ttatagcagg aaagggattt ctccgaggtg 1800 catggtgaaa attgatcttc aaaaggctta tgattcggtt gaatggccgt ttataaaaca 1860 tttaatgctt gagttgggtt ttccctacaa atttgtaaat tgggtgatgg cttgtcttac 1920 tactgcttca tatacattca atgttaatgg ggatttgact agaccttttg ctgccaagaa 1980 gggtcttaga caaggagacc ctatctctcc atatctattt gtgatatgta tggaatatct 2040 taacagatgc cttatacaac ttaggaaaaa tgctgctttc cggttccacc ctagatgtaa 2100 aaggttgaac ttaattcatg tatgttttgc tgatgatttg ctgctttttt ctagaggtga 2160 tgtggattct gtctcacagc ttttagcttg tttagtgctg cttctggcct taaagcaaat 2220 caggctaaga gctcaattta tttgggaggt gtatccatga gcggtcaaga tgctattgtc 2280 actaagttta acctcgttaa aggtgagctt ccttttcggt accttggggt ccccttgtca 2340 tccaaaaaat tatctgttat tcagtgtcaa cctttggtga agaggatcat ttgtagaatc 2400 gaaaattggc attctaagtt gttatcgtat gctggtaggt tacaacttat caaatcagtc 2460 ttgtttggtg ttcaaactta ttggagtcag gtttttgtgc ttcctcagaa ggtgctaaaa 2520 cttattcaaa cagcttgtag ggtttttctc tggactggaa aatttggcac ttccaaaaga 2580 gcacttattg cttgggagcg tatatgtctt cctaagacag ctggtgggtg gaatgtaatt 2640 gatttgaaag tttgaaacca agctgcaatt tgtaaacttc tttggaattt ggccaataag 2700 aaggatgttt tatgggtgaa atgggttcat gaatattaca ctaaggggag gaatgtgcta 2760 ctcatggatg tgcctgcaca agcttcatgg gtaataaaaa aagtctttgg tgcagcaaag 2820 actatttcaa gtgttgatgg cagtattttt caacaagcta atttctctat taagagaatg 2880 tataatgctt taagaggtga ctttgcaaag gttggttgga ggaaaatgat atgtaataat 2940 ccagcccctc caaaatgtct gtttgttact tggttgatta ttcatgctag attgccaact 3000 tgtgatagga tgcttaaagt aggtatccaa tgtgaccaag tttgcatttt gtgtacaaag 3060 gagaatgaaa ctcattctca cctctttttt tcttgtgatt atgctgatgc tgtttggaaa 3120 ggtgttatga gatggatgaa tatgacggtc aatactagca attggcattc tattttgcaa 3180 tatattcagt ctcattgtaa cagtaacaat ggtatgcatc aagctcatat aatggtgttg 3240 agtgtgaccc tgtatatgat ctggaaggag aggaatgata gaaaatttca gaattgttac 3300 cgatctgttc aacaactcct taaccaaatc aaaatggatg cttacattag aggattgcaa 3360 ttcaagaagg tgcaaactct gatgattcgg gtgcgaggct aatggttctt tttgtttgtt 3420 tgagcttagc tcttgtttct tggttttagt gttttctgat tccatgtagt ttgtaataac 3480 tgttttggtt aatgaaagat atctctattt accaaaataa aaaaataaaa aaat 3534 // ID Copia-25_Mad-LTR repbase; DNA; EDCOT; 374 BP. XX AC ACYM01078046; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-25_Mad_; KW Copia-25_Mad-LTR; Copia-25_Mad-I. XX NM Copia-25_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-374 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1372-1372 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01078046; Positions 5272 4899. XX SQ Sequence 374 BP; 119 A; 56 C; 67 G; 127 T; 5 other; tgttagtgtt taastgtttt agcttaaata aatcaatcca ttttacttgt tttaattaga 60 gcccttggat tacattccaa atggatgctc tagatttaag tgagagttaa tgatatagag 120 tgacaactgt agytatctca taagatagat gaaatgaatg gttgtgatgt attctttctg 180 ttatgagaga gagwgtgtaa tgatgctttg tactagtgag tgctatcggt aacattcccg 240 attagcaaag aagaagaaat ggaagttgtt gttcactcat ctctgtgaat actycctgca 300 acctttcgtk ttcctttcct ccagaaatct cataaaaaca cattgaatca cagcataaaa 360 tacataatct aaca 374 // ID GYPSHAN2_I_MT repbase; DNA; EDCOT; 4372 BP. XX AC AC158209; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, GYPSHAN2_MT, from Medicago DE truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW ORF; Internal; Interspersed; repeat; terminal; GYPSHAN2_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4372 RA Shankar R. and Jurka J.; RT "GYPSHAN2_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 22-22 (2007). XX DR EMBL/GenBank/DDBJ; AC158209; Positions 42858 47229. XX CC The internal region contains intact domains of gag-pol CC polyprotein with Gypsy-type arrangement of domains and their CC similarity. XX FH Key Location/Qualifiers FT CDS 2316..4370 FT /product="GYPSHAN2_I_MT_2p" FT /translation="MVEWPQPRSVKHLRGFLGLTGFYRKFIRHYATIAAPL FT TELLKKDAFLWNDSAQQAFDSLKLAMTAAPVLALPNFTEPFILETDASGSG FT MGAVLIQNNHPICFFSKQFCPRMLNASTYVRELCAITSAVKKWRTYLLGSK FT FVIHTDQRSIRELMTQVIQTPEQQFYLAKLLGYSYEIMYKPGAQNRVADAL FT SRIHCFAITVPHWDFLDKLKEQYTTDEELKKWVEDIINKPSTNPGFQVHDG FT LLFLHGKLFIPSSSSLKLVLLEEFHSSPLGGHSGIAKTYGRLRENVTWFGM FT KKDVEKFVQQCHICQVMKSPTHAPFGLLQPLPIPERVWEDISLDFIVGLPS FT FQNNTVILVVVDRLSKSAHFGMLPTGFTATKVADLFAQMVCKLHGMPKSIV FT SDRDPIFLSQFWKGLFKASGTKLRMSTAYHPQSDGQTENVNKTLQQYLRCF FT VHDQPKQWGKFLHWAEWHYNTSTHSSTGFSPFQIVYGRPPPALPEYITGSS FT PVQALDTDLTQREQILAVLKKKLLKAQATMKEFADKKRIPHKFVVGDYVFV FT KLRPYKQHSVAGKRIQKLSNRFFGPFKITKAVGEVAFELELPPTSKIHSVF FT HVSKLKPCHGHSPGSLSLPDNIVDNHPLLQPLTVLDWKHEAHDVEPYVLIQ FT WESSFPEDSTWEPYSAIAQQYPEFHLEDKVTLEGPG" FT CDS join(458..496,500..2344) FT /product="GYPSHAN2_I_MT_1p" FT /translation="MSNYYCQCLPDPINPSQPDYWSSSQFYLSCFVSGLKP FT EIRREVQAFQPMTLTQAISLAKLQEEKILDRSNSSKPRYNYPISSASSPTP FT QPTNSFRPTLSVTPPKTPTTPIKRLSPAELQARREKNLCYNCDEKFTPGHR FT CRRQFHLLIVQTDQPETTEEITHISTNESDSSIDPEIVPETEPAQISLHAL FT MGHSIPQTLRVTSHIQKKPIHTLIDSGSTHNFLQDRIATQLGLKLQPAEQF FT QVLVGNGEELQCISMCSNVQLMLGPHEFFIDLFVLPLRGAELVLGVQWLKT FT LGPIVTDYTQLTMSFIRNGHHILLSGEPKPTHAEASLHQLQRLITTDAIDT FT VYQLQEISSTTNPTSTTHTDDRINTLLKQYSPLFATPHTLPPPRQIDHQIP FT LTDNNQIVNVRPYRYPQFQKREIEAQIRDMLANGIIQHSSSAFSSPVLLVR FT KKDGSWRFCVDYRALNALTVKDRFPIPAIDELLDELHGTRWFSKLDLRSGY FT HQIRMAPQDTHKTAFRTHQGHYEFLVMPFGLSNAPSTFQSSMNRILQPYLR FT QFVIVFFDDILIYSPTLEDHRHHLEVVFNCLLENQFCLKYSKCAFAQNSII FT YLGHVVSDSGVGPDPEKNQCYGRMASTTLS" XX SQ Sequence 4372 BP; 1269 A; 1168 C; 778 G; 1157 T; 0 other; actggtgcct ttcatttgtt accatgacct cccctcccag agatgagctc ctccaccgca 60 ttcttctaag ccaacaacaa ttccaagaac aaattaccac tctcaccact gaagtgaacc 120 aatggcgaaa tcggtttgga ccacctggat ttacacccac cggccccgat ataacagcac 180 cttcaaccac caccatgaaa ctcgatatac caaggttcga cggaacaaac gcaccaggct 240 ggatcttcaa gatcaaacaa ttttttgatt ttcatcaaac cccagaggag cagcgcctcc 300 gtatagcttc attttacatg gagggagaag ctttgacatg gttccagtgg atgcactcca 360 actctcaact cctatcttgg tctggatttc ttctggcttt ggagtccaga tttgctccgt 420 cactctacca agacccccaa ggtgaacttt ttaaattatg tcaaactact actgtcaatg 480 cttaccagac ccaatttgaa accctagcca accggattat tggtcttcct cccaatttta 540 cctcagctgt tttgtttctg gactcaaacc tgagatccgg agagaggtac aagcatttca 600 acctatgact ttgacacaag ccataagcct cgccaaatta caggaagaaa agatcctaga 660 tcgatctaat tcatccaaac ccagatacaa ttatcccatc agttctgctt cctctccaac 720 accacaacca acaaactctt ttcgtcccac tctatctgtc actccaccca aaacccctac 780 cacaccaatc aaacgattgt ctccggctga gcttcaagct cgtcgtgaaa agaacctatg 840 ctacaactgc gacgagaaat tcacaccggg tcaccgttgc cgtcgacaat tccacctcct 900 catcgtccaa acagaccaac ccgaaaccac tgaagaaatt actcatatat ccacaaatga 960 atcagattcg tcaatcgacc cggaaattgt acccgaaacc gaacccgccc aaataagcct 1020 acatgcctta atgggccatt ctattccaca aacccttcgt gtgacaagcc atattcaaaa 1080 aaaacctatt cacacactca ttgacagtgg tagcacccac aatttccttc aagaccgcat 1140 tgccacacaa ttgggtctca aattgcaacc agccgaacag tttcaagtct tggtgggcaa 1200 tggtgaagag ctacaatgca tatcaatgtg ttccaatgtt cagctgatgc taggccccca 1260 cgaattcttc attgatttat ttgttcttcc tctacgtggg gcggagctcg tgcttggggt 1320 tcaatggctg aaaaccctag gtccaatcgt cacggattac acacaactca ccatgagttt 1380 catcagaaat ggccatcaca tattactctc tggcgaacca aagccaactc atgctgaggc 1440 ttctcttcac caactccaac gattgataac tacagatgct atagatacag tatatcaact 1500 ccaggagatt tcttccacta caaaccccac atcaacaaca cacactgatg accgtatcaa 1560 cacccttctc aaacaatact caccactttt cgcaacaccc cacacccttc ccccaccacg 1620 acagattgac catcagatcc ctctcaccga caataatcaa attgtcaatg ttcgtcctta 1680 tcgctaccct caattccaaa agagagaaat tgaagctcaa atccgtgaca tgttggcaaa 1740 tggtattatc caacacagtt ctagtgcatt ctcttcaccc gtgctgcttg tccgaaagaa 1800 agacggatct tggcgattct gtgttgatta tagagctctt aacgctctaa cagtgaaaga 1860 ccgctttccg ataccagcaa ttgatgaatt attggatgag ttacacggta cccgttggtt 1920 ctccaaactt gaccttcgtt ccggctacca tcagattcga atggcacccc aagatactca 1980 caagactgcc tttcgtaccc accaaggcca ttatgagttc cttgtcatgc cattcggcct 2040 atccaatgca ccttccacct tccaatcttc aatgaatagg atcctacaac cgtatcttcg 2100 gcagttcgta attgttttct tcgacgatat cctgatttac agcccaacac tagaagacca 2160 tcgtcatcat ttggaggttg tattcaattg tcttctagag aatcagttct gcctcaagta 2220 ctccaaatgc gcatttgctc aaaattccat tatatacttg gggcatgtgg tatccgactc 2280 aggcgtagga cctgatcccg aaaaaaatca gtgctatggt agaatggcct caaccacgct 2340 cagttaagca ccttagaggg ttccttggtt taacgggatt ttaccgcaaa ttcatccgcc 2400 actacgccac tattgcagca cctctaaccg aattactgaa gaaggatgcg tttctttgga 2460 acgattctgc tcaacaagct tttgactcat taaagctagc aatgacggca gcgcctgttc 2520 ttgctcttcc caattttacc gaacctttca tcttagaaac agacgcatct ggatcaggca 2580 tgggtgcagt tctaattcaa aacaatcatc caatctgttt cttcagtaag caattttgtc 2640 ctagaatgct gaatgcctcc acctatgtga gagagctgtg tgctattaca tccgctgtaa 2700 aaaaatggcg tacttacctt ttgggcagca aattcgtcat acacacggat caaagaagca 2760 tcagggagct tatgactcag gttatccaaa caccggaaca acaattctac ttggcaaaat 2820 tgttagggta ctcttatgag atcatgtaca aaccaggagc acaaaacaga gttgctgatg 2880 ctttgtctcg cattcattgt tttgcaatta cagtaccaca ctgggatttc cttgacaaat 2940 tgaaggaaca atatacaact gatgaagaat taaagaaatg ggtcgaagat atcatcaaca 3000 aaccatccac aaatccagga tttcaagttc atgatgggct actgtttctc cacggtaaac 3060 tattcattcc ctcctcttcg tccctaaaat tggtgttgtt agaggaattt cattcatcac 3120 ccttaggagg acatagtggc attgcaaaaa cttatggccg tttaagagaa aatgtcactt 3180 ggtttggaat gaaaaaagat gtggaaaaat ttgtccaaca gtgtcacatt tgtcaagtta 3240 tgaagtcacc aacacatgct ccttttgggt tactccaacc tctgccaata ccggaacgcg 3300 tatgggaaga catctccctc gatttcatcg tggggctccc ttccttccaa aataacacag 3360 tcatcttagt cgttgttgat cgcctctcca aatcagcaca ttttggcatg ttacccactg 3420 gcttcacagc tactaaagtt gctgacctct ttgcacaaat ggtctgtaaa ctacacggta 3480 tgcccaagag tatagtatcc gacagagacc caatcttttt gagccaattt tggaaagggc 3540 tattcaaagc aagtggcacc aagcttagaa tgtcaacagc ctatcatcct caaagtgacg 3600 gacaaacaga aaacgtcaac aaaacactcc aacaatatct tagatgcttt gttcatgatc 3660 agccaaagca atggggtaag ttcctacatt gggctgaatg gcactataat acatctaccc 3720 attcctcgac tggtttttct ccattccaga ttgtctatgg cagaccacct ccggcgctac 3780 ctgaatacat caccggctct agcccagtcc aagctttaga cactgacctt actcagcgtg 3840 aacaaatcct tgctgtcctc aagaagaaac tcctaaaagc tcaagccaca atgaaagagt 3900 ttgctgacaa gaagcgcatt ccccataaat ttgttgttgg tgattatgta tttgtcaaat 3960 tgcggcccta caagcaacac tcagtggctg gcaaacgcat tcaaaagctg tctaataggt 4020 tctttggccc tttcaagata accaaggccg tcggagaagt tgcttttgag ctagaacttc 4080 caccaacaag caaaatccac tcagtttttc atgtatccaa actcaaacct tgtcacggac 4140 attctccagg ttccttgtca ctgcctgaca atattgtgga taaccaccca ttacttcagc 4200 ctttaacagt gctggactgg aaacatgaag cgcatgatgt cgaaccttat gtgttgattc 4260 aatgggaaag ctcatttccg gaagactcta cttgggaacc ttactctgcc attgcacaac 4320 agtaccctga attccacctt gaggacaagg tgactttgga aggtccgggg ga 4372 // ID Copia26-VV_LTR repbase; DNA; EDCOT; 185 BP. XX AC . XX DT 05-SEP-2007 (Rel. 12.09, Created) DT 01-OCT-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia26-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-185 RA Obukhanych T. and Jurka J.; RT "Copia26-VV."; RL Repbase Reports 7(9), 785-785 (2007). XX DR [1] (Consensus) XX CC This is the 5' LTR sequence of Copia26-VV LTR retrotransposon. 5' CC and 3' LTRs are 99% identical. XX SQ Sequence 185 BP; 51 A; 32 C; 23 G; 79 T; 0 other; tgttagaaaa tatgagaatt tatcggatta tgggaacttg tggatgatca tccatattga 60 tgtatatctc tttgtgactc cctataaaag ggagatacct ctaatgaaaa tctattttat 120 tctcttccta cattctaatt tctctttctt gttttcttct cctttcactt tataatttta 180 caaca 185 // ID MtPH-A6-2-Ia repbase; DNA; EDCOT; 4218 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 13-MAY-2008 (Rel. 13.05, Last updated, Version 1) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-A6-2-Ia. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4218 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC An autonomous element representing subfamily A6-2 of CC PIF/Harbinger transposons from Medicago truncatula, carrying 15 CC bp-long TIRs. XX SQ Sequence 4218 BP; 1287 A; 655 C; 798 G; 1478 T; 0 other; ggctatgttt ggattgatgg gttgtagtgg aatggaatgg aatgagatgg tatataataa 60 aattccattg tttggattga tggggatgta cgtggaatgg aatggaatgc aatggaacca 120 attccattct ataccactca atccttcaat ttctcattcc ccccaatttg ggaggtatcc 180 aatggaatga aatttgtgtc ttgaaatttt actattctac cctcctttta tttgcctctt 240 cctctactca atcacaattt tcaacacgtt cttttctcta tttctactga ctgcatttca 300 ctttcatctt ctttgtactg ctgactgctc ttcttcttct cctgtcttct catttctacg 360 attttgcttc acaaggtacc tcatttctac cccatttatt ttttcaccgt atgcttctat 420 gcatgtttag ttatgtgtat caaattttat ttgtcacgtg atcttttcat ttttattatg 480 tgtatcataa catcaatcct ttgtgagcca tttattttgt gaactagcgt caaaattttc 540 atttatttta ggtgatcgtg ataaatttat acacttgctc tgtttgggta tcctatgatt 600 ttgtcatttt tggtagtgtg gagtatctct atgtagatag ttgatgaatg taaaatagag 660 ggtgtgttct ttttatttgt ttattctagt ttcttatata tggcatatgc atgtcatttg 720 attttttttc ctggaactga gattatgtct atatgctagt tgtataaagt aaccatcatt 780 agaacagtga agacttgtga gattttgtct atatatgatt ttttttgctt agttatttgt 840 ggtactgggt ttttgtctat atatgattct ttgctttgtt atttgtggta ctgagttttt 900 gtctatatgt gattttcttt tcttttcttt ttttgctttg ttatagatga ttaatgaaga 960 catgagaaca aaacatttga aattgcttca aatgatgatt gttcaagtat ccatcattat 1020 agttctaata tttcgcctaa aaaacaagtc tagatctcaa ataccctcta gaatcataga 1080 gcatagagag aaagttagga acgaactaat gaaacatata ataggtagtg accgatgtta 1140 tgatataatt cgtatgagtc ccaaagcttt cgtaaacttg tgcaccttat tacgagatca 1200 cggtgggctt acacatacac gaagagcatc tatcgaggaa caagtagcca aatttcttca 1260 cacagtcgga cataacgtca gaaatcgtgt gttgtccttc ttctttagac gctcaggtga 1320 aacaattagt cgtcattttc atagagtatt agatgctttg atagaattgg aagacaaatt 1380 tttgaaacaa cctgatggaa cacaagtgcc tccaaagata cgtaacaaca ataggttcta 1440 cccatatttc aaggtaagaa taagtttgtc ttacacttcg ataagttatg ttatacactt 1500 ttaatgggat aattgaatgc caggattgta tcggagcaat tgactgtaca catatacgtg 1560 tcaaagttcc aacagaactt gcacctagat accgtggtag aaaagattac cctacacaaa 1620 atgtactcgc tgcgtgcaca tttggcttga aatttacata tgtcttggtt ggatgggaag 1680 gaacagcatc agactcaaga atagtaaaga gtgctttgac acgtcggtat cctcttaaag 1740 tcccgcaagg taacgaaaaa atacaaaagc tttttataag tatgtagctt atccaaacta 1800 atagactcat tattttctat aggaaaatat tatcttgctg atgcggggtt tcctttaaag 1860 gcatgtctca tcacacctta taggggagaa cgttaccact tacaagaata ttctagaaat 1920 ccacctcgaa accctcgcaa gttgttcaac aatcgacatt catcgttaag aatgtctatt 1980 gaatgtgcat ttggagtgtt gaagaagata tttccaattc tgcaaacttc aactgaaccc 2040 acatttgaaa ttaaaactca aaataaaatc attgttgatt gttgcatctt acacaattat 2100 ttgatgactg aagaccctaa ccagaatcta atagacgagg tgcgtcacga gctcacaaat 2160 gaaagcggtt tgcaagaggg acatcaagct caaagagaaa acaatgatga taccgctaga 2220 ggagagctag ttagagctga tgttactggt tcaatgtgga tagcttacta aaaaagtgtt 2280 tgaaggcctc tctttcaaat atggagtgtt cttaggctat ttaggctagt ttattggtgt 2340 ttgttttgat gttttgggct tatgttttga agcttaacgt gttgccattt gtttgagtat 2400 gaaaactgac actttgttga tactaatgtg aacttgggga atctgtttgc aatctgaatc 2460 ttaattttta gtgcttggaa tcttcatatt tcaacttgtg cttgagtttg taatttgtgc 2520 ttgaattatt atatatgtcg tttgtttttt ttaatattag atatggaaga aagtgcaaag 2580 aggccaagga aatgcaaagg tcctgatact tgtaattgga ctttagctat ggatgaggta 2640 ttgattgatg catatttgca tcaacatact ctgggaaata aaaatggtaa cagtctgaca 2700 tcatttgcaa tggatagtat ttttcaagag ctgaaaactc actttccaga caagccaatt 2760 actaaagaca agattaaaga tcacatgaaa aatatcaaag caaagttcaa tccttgttat 2820 gatgttttca agaatggtct gagtgggttt gcatggaatg cagagacaaa tatgtggatt 2880 gctgaagatg aagtctggga aagtctaatt aaggtattat ttacttcaac tgaagtattt 2940 tttttttatc aagtgtacat gataagtttt tttttttttt tatgtaacac tttgtttaat 3000 ttacgaaatt gtagacaaaa ctcgtagctg ctgagtggaa aaataagcct attatgtttt 3060 atgataaact agcaactctt tttgggaaag atcgagcaac aggagatgat gaagatacag 3120 gatttgaaat gagagcaaaa aaagctgcta gtgctaaaaa aaattacggt ccaaccattg 3180 aggatataga ccatttggtt gaaaccaatg aagttacttt ggagggattt gaagttgatg 3240 aagaatttga tcccaatggt tctcctaaaa gaccttctat taggaagcct caagatgtac 3300 catcatctag gaataagaaa cgtgcaagaa aggtggatga agatgagaca agcatgagcg 3360 aaattgctaa gacttttaag aaaatggctg agatgtttga actgaacact gcagagttgg 3420 tcaaacagaa taagagttct agtgctgaag atgtttgggc taacttggtc gagattggtg 3480 ttgaagaagc ttccttgcct tgtgtctaca tgcaccttgt tcaacatcca gaagcattga 3540 aagcttttaa tggaattcca gttgataagc gtaaggaaat gttaccttac attgtgccga 3600 actatccttg aagaagagta ttatgatctg cagtgaaccc atgctttact tattttgtta 3660 ttaacagcta atgttggttg aaaagaaact cttttgtttg ttagcttttt gagaggttta 3720 aaaagccatt tttgtagaag caagaaaagc ttgttttggt gggaaaaaaa aaaaaaaaaa 3780 gacaagcact gttattttgt tctgtttggg ttctaacatt actcatgcaa gtacatgtta 3840 attatcaact attgcgtttt gacaggataa tgtttcttgt ctatgatgtt ttctttatta 3900 gtctatgatg tttcttagtc tatgattttt ctcgttacat tcagtcagtg atattagcca 3960 ttgtttgata catatatgaa taaataatca taatatggaa cttattttat aagggtaaaa 4020 atggaaaaaa aatattgtaa cttattttat tccatccatt atctaaacaa tggagtggga 4080 accttgttct attaaattgt aaaatatcca aacaatggaa tggaatccat attccattcc 4140 gttccgttcc gttccattcc attccgctca tttaaatacc gttccgttcc actctcttcc 4200 atcaatccaa acagagcc 4218 // ID SINE-1_Mad repbase; DNA; EDCOT; 180 BP. XX AC . XX DT 21-SEP-2010 (Rel. 15.11, Created) DT 21-SEP-2010 (Rel. 15.11, Last updated, Version 1) XX DE SINE element: consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; SINE-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-180 RA Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 2017-2017 (2010). XX DR [2] (Consensus) XX CC ~94% identical to consensus. XX SQ Sequence 180 BP; 56 A; 41 C; 33 G; 50 T; 0 other; gccacttagt actacggtct agtggtattc ctcttcactt gtaagtgaga ggtcttaggt 60 tcgattctcg ccaaaggcga atttgaacca cattattgct agcccattgt gaggctaagc 120 ccaccccctc ccccttagtg tagataatat cgtttgttca aaaaaaaaaa aaaaaaaaaa 180 // ID Gypsy-44_Mad-LTR repbase; DNA; EDCOT; 1782 BP. XX AC . XX DT 22-OCT-2010 (Rel. 15.1, Created) DT 22-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-44_Mad-LTR. XX NM Gypsy-44_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1782 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1783-1783 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 1782 BP; 500 A; 365 C; 303 G; 614 T; 0 other; tgataggagc atatttatgc gacttagtta gcttgtttct tggcatttac ttagttaatt 60 cctagttatt ttagtacttt aagctatttt cgtgtgtttg taggttcaaa taacaaagtt 120 ggcaacaaag tgctatttgg agcattttgg agcatttttg ggccaagatt ggatagtgca 180 agcatggaga catgaggatg gacgtttttg aagatttgaa ggctagaaat cagcatgtgt 240 gtgtgcaagt gtgttgacct acaactacca aacatccatc cactacaccc attacatcca 300 ctcattacca aacacccacc cactacaccc attacatcca ctcattacca aacatccacc 360 cactacaccc attacatcca ctcattacca caacactcac ccactacacc cattacatcc 420 actcattaca actccataca ctcctctccc tagcctataa atacatccac cattcaccat 480 aacggagggg agaaaaagat ccatccaaag acactacatt cacatctcac aactccatac 540 acttacactt tcattccttg gccgggagaa cacaatccac ccatccaccc ttcaccataa 600 ctcacctata tccatccacc accataattt accactcatc catcaaacca caccttgtgc 660 cgcaacaaag agaagaagga ggacccttgg acgtgcttgc cattcaagtt ggattgttgg 720 agcgttttta ggtgttttca ttcttttgtt ttcaatgtct aaatttgttt atctttgctt 780 tgtgagtatg aggaactaaa ccccccttag ctagggggga attcgaaacc atgttcatgc 840 ttgcaatatg atttgattac cttcagttgt gatttcataa gttgtgaatt caatttgttt 900 aactgcttga ttgataactt attcgtgtat gtttattaag agtgcacact tagtttgcat 960 gcatgaatat gatgctagag tataagggag tttcacctaa tagttacaaa cttatattca 1020 caagtagtgg aggtcgctta taaacgatcg cgttaaataa attcttggca ggagtttcat 1080 gctcatcata gtaacgaatg cctcgtcaat acttatagtt ttcataatgc ttaatgatct 1140 ttgattgtat ctttattgtg ctgttcacgt aaagaacttt tgaagaatgc ttgaattgtt 1200 gtatgcgttt tcccatccaa ttcaataact taaggagaac ttgaaggtta atttaagcgg 1260 acttaattaa cctggggtgt tgagtttcat gattgatcga aagaacaact ggaaattggt 1320 ttatgtgcaa gtatgtcatg tgtggagaag aacctcctag ctagccttcc atccattcaa 1380 tttactcaaa ttcgtgcaga tttcattagt tctttaattt acttgttttg ttttcaaatt 1440 cgtcaaaacc aaaaccccct ttactttaaa gtgttttatt agtcaaaatc tgttttgatt 1500 tgtgttttta ggtgtcccaa aagtgtgtta gagtccaaat ctgcccagtt tgtgttttta 1560 ggcagatttg agcgttttta gcttgttttg agtcctttga gtttgtttta agttctttga 1620 gtctagttta gtgtttttaa ctttgtttat atgtttttaa gtcagtttag aggttttagc 1680 aagccctcct aatccccggt ttagaacgat ccctacttgc atttatacta caatttgaca 1740 acaagagggt ttaatttgtg tgttaagtta attttcgcat ca 1782 // ID HARB-1N1_Mad repbase; DNA; EDCOT; 833 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW HARB-1N1_Mad. XX NM HARB-1N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-833 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1494-1494 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~89% identical to consensus. The consensus shows similarity to CC HARB-1_Mad. XX SQ Sequence 833 BP; 232 A; 191 C; 171 G; 239 T; 0 other; ggccatctcc aaccgaaggc tggccagatg gctcgtttta gccctctggc cctccaagaa 60 attaatattt taatgaacag tgcatggcca tatttcttac catctccaac cgagggccaa 120 agggtcatag ggctcgtttt agccctgtca caaaaaacca tctccaaccg agggccaaag 180 ggccataggg ccaaacataa ttattattta aatttaaaaa ctacaacaac ttaaattaaa 240 tgactttcgt cagtaattgg ccttgtctac ttgcttaaat tgtgttaaat taatttttaa 300 tttaagtgtc aattactagt acaacttagt ttgagatgtt acatgtataa atgcacattt 360 accatctcta ataggaagct tatatttggg gcacccatta tatttgtccc acatcgggag 420 agaattgagc aagcaaaagc ttgcatgtgt ggcacccatt atatttgtcc cacatcggct 480 gtgggagagg tttgagcaat caaacatgct tataaaagca acatccccac atagaaccaa 540 tcacctttct gggccttaat taaatattct ttttaaattt ttggcccaaa aaaaaaaaaa 600 actgtaaaaa aaataaaaaa taacggctag ctgacgtcag ctagccgttg agattcaaat 660 tttttagccc ggcccggggc cggctggctg gctcatttgg gccgccggtt ggccctttgg 720 cccttttttg tccagtgggg cccacgagcc ctttggcctg gccctcggtt ggagacggtt 780 ttagggctat tttcgaccct ctggccctct ggacccttcg gttggagatg gcc 833 // ID Gypsy2-VV_LTR repbase; DNA; EDCOT; 1695 BP. XX AC . XX DT 04-SEP-2007 (Rel. 12.09, Created) DT 01-OCT-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy2-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1695 RA Obukhanych T. and Jurka J.; RT "Gypsy2-VV."; RL Repbase Reports 7(9), 797-797 (2007). XX DR [1] (Consensus) XX CC This is LTR sequence of Gypsy2-VV LTR retrotransposon. LTRs are CC 95% identical to each other. 5' LTR sequence is deposited. XX SQ Sequence 1695 BP; 383 A; 430 C; 541 G; 330 T; 11 other; tgtcagcccc ttagmccctt gacttaacca tggaggaata ggcctcatgg gtaggccttg 60 cacccatgag agcctaggat gaaagcargg aaakcctgga ggtttggtgg ttcaaactct 120 aggagcyawg tgaggagacc acgggygagc cagacacgca ccgcggcgag ccaggcgcgc 180 accgtgggcg agccagacgc gcaccgcgcg cgcaccacgg gcgagccaga cgcgcaccgc 240 gcgcgcaccr cgggcgagcc agacgcgcac cgcgcgcgyg cgcaccgcgg gcgagccaga 300 cgcgcaccgy gcgcgagcaa acgcgcrcca ggcgcgcacc gcgggcgagc cagacatgca 360 ccgcgtgcgc accagatggg catcgcgcgc gcacctgact taggtggtgc agatgaaggt 420 tgagggactt ggaattttaa tttataatta ttttattatt ccattatgtc tcctcagaca 480 tattgatgtc tcctccagaa acaatgaaaa cggcccgtat tgctctttaa ggggggaggt 540 aggggggtga ctcaaaggag ggagccacca agggaagcct tgaccgcacc aagggggcac 600 catggcacgg ccttgggcgt gccttaggac acacgacggg actcgagcac gcacacatgg 660 gctccacgac atgtgtggtg tgcaccccgt ggccgcaacg gcacggggcc tggtgcggcc 720 taccccctcc ccgcgcaggc acgagggcgc ctaagccttg tgcggtgagc cagctgatga 780 aaccatgggc gcaatgccat ggtctgatgg caccaacagc tgactcgcac caagatgcct 840 acgcacagca caggggcgca atgccttgtg caccaagagg gatcagccat gggcgcaatg 900 ccatggctcg ttgctgtgaa gggaagcaag caacaagccc aagccatggg cacctagaca 960 tggcatgggc tcacacatca gtgtggggaa ggcacactga tgcaccagac gcttggtcag 1020 ctggttggtg cacgctgcct ggctcagagg gccttgatca aagacatgct gatgggcacc 1080 cggtcacaag aggcacctta cggggaagga gtcggcttgt tagggggact ctccagcagc 1140 ttggcgagca agacctgagg agatggcagt gcarctagct agtggcagct agctcagtga 1200 ccaagtcaag ccgtcatttg acctgcagtt ggctgaggga tgatggctgg tgcaagtggg 1260 tggcatgtgc aggccactat ctgggtggtg ggtggttatg caaggcagtt gagggcggtt 1320 ctggccagtt gcataaccac caagttggct ccaagatttg aattaggaaa ttcaaatttg 1380 taactgcagg ttgagtcttt taaatagggc tcctgcagcc ttgaaacaga gagagagaga 1440 gtttggggaa agggttcctt ctcgtatgcc ttgggtgtga gcattgtact ctggttcagg 1500 aaacaatttt gtatcttgta agagtgatta atacaagttg ggaaaggatt cctgtaacct 1560 cgtgtgtccc tgttgctttg ttgtttgctg ttctactctg tttttctaaa cgctgggaag 1620 ggaaggttgg ctaaggaagg gtccttagca ccgcgcactc gtgaaaaatt tagtgtgata 1680 ttcaggggtg tgaca 1695 // ID DNA9-18_Mad repbase; DNA; EDCOT; 1168 BP. XX AC . XX DT 27-OCT-2010 (Rel. 15.11, Created) DT 27-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-18_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1168 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1858-1858 (2010). XX DR [2] (Consensus) XX CC TSD is 9-bp long. Imperfect internal TIR is 50-bp long: Pos 25-75 CC and 1143-1094. XX SQ Sequence 1168 BP; 486 A; 170 C; 138 G; 374 T; 0 other; gggaaaatta gaatgcccta catattttct atagttgtta gattaaacat tcatcccttt 60 taaagatttg attaaggtgc ttcaatcaat tgccacctca ataattttct atttatttaa 120 tttccatgtc attaatttaa atgcatttat atagaggcat aaggtagctt agcaactaat 180 tgcctataat ataggaattt aatttcctca atccccttct gcgcattaaa tgacattttt 240 ttaataaaat aaaataaaaa attaattaac taattcctca tttccttatt atcagtattt 300 aaaaaaaata ctctttctat taaaattgta tcaataaaaa gtcttcaata catatttttt 360 ttcatgtata gatatataaa aaatatactt aaaacttatg gtacatttga gaacaaaagt 420 atcgactttt ggtacgttta gatttcaaat gtaccgagaa accaaatgta ccaaaaattc 480 aaatgtacca taaaaccaaa tgtacccatt gttatgtaac ctttttggta cgtttagatt 540 tcaaatatac agagaaacca aatgtaccaa aatttcaaat gtaccataaa accaaatgtg 600 cccattgtca ggtaatcctg ttggtacgtt tagattccta ttgtaccaaa agaccaaatg 660 aacaaaaaat ctcaaatgta ccacaaaacc aaatgtctct atcagataac ccttttggta 720 catttacatt ccaaatgtac caagaaatac aaaaaatcaa atccactata aaactaaatg 780 tgtccatatt ataggtaact agacgtagct atataatcaa acaaatcttt actatgtgtt 840 gggtcttcta aataataaaa tttgacaatt tttttttata aatattctac tatattcaca 900 aaaaaaaagt aaatattata acaaacaatt aaaaaaatgc atagagatgg ataataaatg 960 cataaatata gggataatag gaaaagaaaa aaaaaaaaac gaaatgccca ggagatggat 1020 aataaatgca taaatatagg gataataggg ataataggaa ctgaaattaa taaccaaaat 1080 tttaggaaaa tgtttgatca aattttcaaa aggagtgtat gtttagtcta aaaaattaaa 1140 aaacgaggcg cctatatcaa aatgcccc 1168 // ID Gypsy-28_Mad-I repbase; DNA; EDCOT; 5517 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-28_Mad_; KW Gypsy-28_Mad-LTR; Gypsy-28_Mad-I. XX NM Gypsy-28_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5517 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1750-1750 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1-282] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 3333..5516 FT /product="Gypsy-28_Mad-I_1p" FT /translation="MSSSIDFWMFSVRIMPPRRDPRRAAEPNFPDITQLGA FT AMAQAFQANIRPPQRTPVETMYNLKLETFEGNEGYEGAEKWLDRIEQTFQV FT MQSQGNLPANRWVETTTWFLGREPAAWWINQSRHMAPERAAEWEVFKENFM FT KRFVPPEYIDRKKQEFTSLKQRNMSAHEYYRKFTDLSRYDSDLAGNQAEML FT RRFKLGSKKKYRTFANALPCADYHEYFEILVRMEDSDNLPDSEDEEDKGNG FT QKKNEKGKGVSIPGPRQTQNFKKSGMSSSSSSGGFSATGPRRGGGRFGNGP FT RFSGQRGFGGTGSSGPPLCRRCNFRHHGECRRSSGACFTCGQTGHRATYCP FT QNQQRPQQPVMPTPAPTQQNFNSGSYGQGGRGGAYHYQGDAAPYAPGQYHY FT SQDPYFQSGYSQDQGGYTSYPSMPASGSQWYQGGQPQQSGVAASSAGSFRP FT PAQAGQGRTHQGRGNQSGRGRGGRQPAQGRVNHISLQDAQNHPDLIMGTLN FT VLGHFARVLIDCGATHSVISHTFAQMTQPHPSPLGFDLEFAMPRGDKCYVD FT SFYSGCPVMVDNVIMPANLIPLDIVDFDVILGADWLHYNRAHIDCYGKSVT FT FLRPGLPEVTFVGERSGVRHGVISAIRAKKLLSKGCQGYLAHVVLNDVDSG FT SVEEVGVVRHYPDVFPDDLPGLPPDRDVEFSIDLLPGTNPISLAPYRMAPA FT ELRELKIQLQELIDKGFIQPSSSPWGAP" XX SQ Sequence 5517 BP; 1438 A; 1033 C; 1412 G; 1631 T; 3 other; gtgaatatta tttctgatcg agatccaaga tttacttcta agttttggat agcttttcaa 60 gaagctttgg gtactagatt gctttacagt acagcttatc atccacagac agatggtcag 120 tcagagagaa ctattcagac actcgaggat atgttgagat cctctgtgat gcaatttggt 180 gattcttggc atgatcgttt ggatttgatg gagtttgcct acaataatag ttttcattcg 240 agtattggaa tgtctccatt tgaagcactt tatggtaaag cttgccgtac gccattatgt 300 tggtcagagg tcggtgaaag aatacttgag ggcccagaga ttgtggatga gactactcag 360 aatattcagg taattaagtc taacctgaaa gtggcccagg atagacaaaa gagcctagcg 420 gatcgacata ccacggacag aatgtataat gtgggcgact atgtttttct gaaattatcg 480 ccttggagag gtgtggttcg ctttgggaag aaaggaaagc taagtcccag gtacattgga 540 ccttatgaga tcactgagag gattggtgaa gttgcttaca ggttggagct acctccagag 600 ttgtctaagg tacataatgt gttccatgtc tcgatgcttc ggcattatgt ttcagatcct 660 tcacatgtga ttcctcctca accattggaa attaatccgg acttgacgta cgatgaggaa 720 ccagtgacta tactggattg gaaagataag actttgagga ataagaccgt gagcttggta 780 aaagtattgt ggaggaacca ttcagcggaa gaagctactt gggagacaga agaacggatg 840 agagatatgt atccgaggtt attctatgag ttttgatgtt ctggttggtg actggaattt 900 cggggacgaa attctataag gaggggagat tgtcacagcc cgtcccagaa ttactaaata 960 ccgaggacgt gaaattactg aaacgccctt aaacgggatt aaggtgcgta aatttggtat 1020 ttgttttaca ctaagatcct aaactagggt tagaattata ttagtatgtg ttaatttatt 1080 tgtgtttgga cttagggtgg ggccctaccc cctaaatcct tccccaaaac ccgtgtgtct 1140 cttctctctt ctccctgtca ctctctctct ctctcttcct tctcagaaac actctctctc 1200 tctcttactc tcgaactctc tcaagctctc ggacaaacac caagaacaat cacaatcctg 1260 caccaacgtc cgatctaaga tcaccaccgc gctcctgagg acctcacgag cacggggata 1320 ccggtttcag gtaagttcca tttcsagaac cctagtttta aaacaccccg tgtaatggca 1380 ctgttcacga acttaatttt ggttgtgttt taggctaaac caagatcacc acgagtctta 1440 ggaagtccca aggaggctcg gagtgcctcg tttgaacaaa atggacgtcg ggatcgtcgg 1500 gttcgagttt ggccgaaatt gaggaatttt ggaaggtatg atcttgttgt ttttaggcct 1560 taaaaccctt ccaacgtgat agtacatgtt aaatgcttca ttttggtata aaattcgaag 1620 aaattggttg aaaaacgaag gagaatagtg gatttgaaaw ttttccagaa accggcgaac 1680 agtcgccggc gaccggcgac tcgccggaga agacagggaa tcttccgtca agtttgacgg 1740 aatattccga cgccgttagt taactttaac ggaaaccgtt agtttttaac ggaatattct 1800 aggatttgac ggaatattcc ctaacgccgt tcactgtagc cgtcagtgtg catggcacgt 1860 ggccgcgcgt gggccgcgcg taggtccgtg ccacgtcagg cgcgtggggg cgcgtgaggc 1920 ctccaaaaat tattttaaaa atatggggat gatcctgagg ttgtgtaggt cactgtggta 1980 tattcatata cccaatttga gcatcgtatg aagaattaat tacctagttt ggtttaggtg 2040 cgttaaatgt gcgttaaatg attgttttaa gttatttcac ttctaggtgg aacttttaac 2100 gaggacgagc acatccaggg gcgtcaaggg ggttacgacc cggcgacata ccagtgagtg 2160 ggcattgctt tctatatata tacctatata ctcgatttcc ccagaaatca aatttaaatg 2220 aaaagtatat tgaaatgaaa tgaaatatga tgtgattgcc atgcatagaa tgttatggat 2280 attatgaact gtcgtatgat gcatatatgt atgatggtgc tgtggacgca caggtaagta 2340 tttaattact gttatgwtga tgatgatgat atattgagct catatcctgc accatggttt 2400 agtgcttata gtattcaccg catcgcacgc tcgccttgga tccaagtaga tgctggtcgt 2460 acagtccacg cggagtgggt acgacgggcc agtcgtagag cgttagtgag attatgactg 2520 gtgggtgacc ttaggttatt gtatacagat gattgatgag agaagcacta gagcgaatat 2580 taccatgagt cgttcagact acattaggtg gttccgactt atgtgcagaa ggccggacag 2640 gtcacgcgga gtgactccgg cagagagtga gattgataga tgttgagctc taggttcaat 2700 cgttcagggc tattagaggg cctccgattg attatttctt ttacctgatt atattatgtt 2760 aatgcattca tactaaactg ttgaaattgg catggtacat tctttattga atctgttata 2820 agattgatga tcgagacggt tgagatatat atgctatata ctatttttct gggaaagtat 2880 acaggttttc caaaaagggg ttataaatgt ggatttatga aatgatttgg aaaagcttta 2940 ttttcgccca ctcacgtttt ctgtttttcg cccctccagg ttctagttga tagttgaggc 3000 gttggtggcc tacgaggact gcttcggcgt tctgacagac taaataaatg taggattcac 3060 ccgagggtgt tgtaaaatag ttatgttcct acttgactgc acctagacgc ttatgctctg 3120 tttatgtgtg tttagtacac tcttatgcac atagaatgct aggttgtaaa taactgcaat 3180 tagtggtttt cgttgactcg tattttatta ttaaatcgtt tccgcttgcg ttatggttac 3240 gtcacgctca cgtgacggcc agcacgtcct agtcttcggg ttagggtgtg tcagtttggt 3300 atcagagcat aggttgcagt cctgtataac taatgagttc ttctattgat ttttggatgt 3360 tttctgtcag aattatgccg cctcgtagag atcctcgccg tgctgctgag cctaatttcc 3420 ccgatataac tcagttaggg gcagcaatgg ctcaagcttt tcaggctaat atccgtcctc 3480 ctcagagaac gcccgtagag acgatgtata atctgaaatt ggaaaccttt gagggaaatg 3540 aaggttatga aggggcagaa aagtggttgg atcggattga gcagaccttt caagtgatgc 3600 aaagtcaggg aaacctgcca gctaatagat gggtggagac caccacctgg tttttgggcc 3660 gtgagccagc tgcgtggtgg ataaatcagt cgaggcacat ggcacctgaa agggcagccg 3720 aatgggaggt atttaaggaa aattttatga agagatttgt tcctccggaa tatatagatc 3780 gcaagaaaca ggaattcacc agtctgaagc agagaaatat gtctgcacat gagtactaca 3840 ggaagtttac tgatttatcc cgttatgatt ctgatttagc gggtaatcaa gcagaaatgc 3900 ttcgtcgttt caagctagga tctaagaaga agtacagaac gtttgccaat gcacttccct 3960 gtgccgatta tcatgagtat tttgagattc tggtccggat ggaagactct gataatcttc 4020 cggacagtga ggatgaagag gataagggta atggtcagaa gaaaaatgag aaaggtaaag 4080 gtgtttccat tccaggacct cgtcagacgc agaatttcaa gaaaagtgga atgagttcga 4140 gttcttccag tggtggattt agtgccacag gtccgaggag aggaggtggt aggtttggta 4200 atggacctag attttctggt cagagaggct ttggtggtac tggtagttcg ggtcctccgt 4260 tatgtcgccg ttgtaatttc cgacatcatg gggaatgtag gagaagcagt ggtgcatgct 4320 ttacatgtgg tcagacagga catagagcta cgtattgtcc ccagaatcag cagaggcccc 4380 agcagcctgt tatgccaaca ccagcaccga ctcaacagaa ctttaattca ggcagttatg 4440 gccagggtgg tcgtggtggt gcttatcact atcagggtga tgctgctcct tatgctccgg 4500 gacagtatca ctattcccag gatccttatt ttcagagtgg atattctcag gatcagggag 4560 gttatacttc atatccgtct atgccagcta gcggatctca gtggtatcag gggggtcagc 4620 cccaacagag cggagttgct gctagtagtg cagggtcgtt taggccgcct gcccaggcag 4680 gtcaaggacg tactcatcag ggacgaggta accagagtgg cagaggtcgt ggaggacgac 4740 agccagctca gggacgtgtt aaccacatat cgctgcaaga tgctcagaac catccagact 4800 tgattatggg tacgttgaat gttcttggtc attttgctag agtcttgatt gattgtggtg 4860 ctacacactc tgtgatttct catacatttg ctcaaatgac gcaacctcat ccttcacctc 4920 tagggtttga tttagagttt gctatgccta gaggggataa atgttatgtt gatagttttt 4980 actctgggtg tccagtgatg gtagataatg tcattatgcc tgctaatctt atcccgttag 5040 acatcgtgga ttttgatgtg attttagggg cggattggtt gcattataat cgcgcccata 5100 tagattgtta cgggaaatca gttacttttc ttcgtcctgg actacccgag gttacttttg 5160 tgggtgaaag aagtggggtg aggcatggtg ttatttccgc cataagggcg aagaagttgt 5220 tatccaaggg ttgtcaggga tacttggcac atgtggtttt gaatgatgtt gattccggta 5280 gtgtggagga agtcggagta gtcagacact atcctgatgt atttccagat gatttgcctg 5340 ggttgcctcc agatagagat gtggagtttt cgattgattt gcttccaggt acgaacccta 5400 tctctttggc tccttataga atggcaccag cggaattaag agagttgaaa attcaattgc 5460 aagagttaat tgataaaggt ttcattcagc ctagttcttc accttgggga gctccgg 5517 // ID TST1_LTR repbase; DNA; EDCOT; 285 BP. XX AC X52387; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 11-NOV-1996 (Rel. 12.07, Last updated, Version 1) XX DE Potato DNA for copia-like transposable element. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Copia-like element; TST1; TST1_I; TST1_LTR; retrotransposon; KW unidentified reading frame. XX OS Solanum tuberosum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-285 RA Brisson N.; RT "TST1."; RL Direct Submission to Genbank (02-APR-1990)Brisson N., Universite RL de Montreal, Departement de Biochemie, P.O.Box 6128, Station A, RL Montreal, Quebec, H3C 3J7, Canada.. XX RN [2] RP 1-285 RA Camirand A. and Brisson N.; RT "The complete nucleotide sequence of Tst1 retrotransposon of RT potato."; RL Nucleic Acids Res 18, 4929-4929 (1991). XX RN [3] RP 1-285 RA Camirand A., St-Pierre B., Marineau C. and Brisson N.; RT "Occurrence of a copia-like transposable element in one of the RT introns of the potato starch phosphorylase gene."; RL Mol. Gen. Genet 224, 33-39 (1990). XX DR GenBank; X52387; Positions 1 285. XX SQ Sequence 285 BP; 94 A; 42 C; 48 G; 101 T; 0 other; tgttgaatga gtaggcagat ttagtcataa ctgctccacc attgagctgc cagatttgat 60 tataactgct ccacaaataa agctggcaga tttgattaga atctgctcct gtaaatatgg 120 gattagaata tattattcta ggaaaatagt ttagaggaaa tcctttaatt caaggatttc 180 ctaagaatta gggattgatt agtttatttg gtctttactt gttctcttat aaatactgta 240 caaacacatc gaataaaatt acattttgca gtatctaaac tttca 285 // ID Gypsy-25_PTr-LTR repbase; DNA; EDCOT; 3399 BP. XX AC . XX DT 08-DEC-2009 (Rel. 15.02, Created) DT 08-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-25_PTr-I; Gypsy-25_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3399 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 173-173 (2010). XX DR [1] (Consensus) XX SQ Sequence 3399 BP; 1138 A; 503 C; 766 G; 992 T; 0 other; tgtaaatccc gagaaaaacc aaggctggat taaattaaag aaaataaact aaactaaaaa 60 gaagtggggg caagaacgaa tacacttaaa gaaaatgggg cctaaatgca aataagaata 120 attatagagc ataaatactc ctattctcac caaaaacaga tctgcagcta tcgtaaagaa 180 agaaaagagg gagtttttat atctattttt acaaatcaag agagaaacac caaaatttca 240 agaacccatc ccagattgag ggttataggt aaaataaacc ctggtgggaa agggattaac 300 aagaaaaaat tgaacaagaa gagaagaggg gagggtcggc tgtcattaga aagaaaagga 360 gggatcgaag ccttgattcg caccgggtaa gatattctaa acctggtctt atgagtcatt 420 tcaagtcgat tatgaattga tgcctggatg ttaatttata tattgagttc ttagacttga 480 attgaggaaa aagtaagagt tgttaaagta aagaacttca tgtgttgtgt gtaaatggaa 540 aggttgatga atctggacag tttcgtctct tgaccttcaa agagattttg ggtaggagaa 600 tgaaggaatt aggatcaagt tccttcatag aaattgtagt tttggatgtt tactaactaa 660 tgaaattggt cttgctcaat ttggagtcat agaactccag ttatgggtca ccaaccgaga 720 ctgggtcatg acagacccta tagggtagta ggtctggttc attgatgagc aattttgact 780 atcttagagg cagaactggg ttctcctcaa aacatagaac ttgtagcctc atgtcttacc 840 tttccaacgc cataaatttc gcttgaatcg gagttctata actccagata tagttaaaaa 900 tctgaggaga ggtcagacag taacagttca aaaacggaca gtaacagttg gacagtaaca 960 gtccaagtgt ttgttgatga gcgattttga ctatcttaga ggcagaactg ggttctcctc 1020 aaacatagaa cttgtagcct catgtcttac tttccaacgc acaaatttcg cttgaatcgg 1080 agttctataa ctccagatat agttaaaaat ctgaggagag gtcagacagt aacagttcaa 1140 aaatggacag taacagttgg acagtaacag tccaagtgtt tgttgatgag cgattttgac 1200 tatcttagag gcagaactgg gttctcaaaa atggacagta acagttggac agtaacagtc 1260 caagtgtttg ttaatgagcg attttgacta tcttagaggc agaactgggt tcttctcaaa 1320 acatagaact tgtagcctca tgtcttacct ttccaacgcc acaaatttcg cttgaatcgg 1380 agttctataa ctccagatat agttaaaaat ctgaggagag gtcagacagt aacagttcaa 1440 aaacggacag taacagttgg acagtaacag tccaagtgtt tgttgatgag cgattttgac 1500 tatcttagag gcagaactgg gttcttctca aaacatagaa cttgtagcct catgtcttac 1560 ctttccaacg ccacaaattt cgcttgaatc ggagttctat aactccagat atagttaaaa 1620 atctgaggag aggtcagaca gtaacagttc aaaaatggac agtaacagtt ggacagtaac 1680 agtccaagtg tttgttgatg agcgattttg actatcttag aggcagaact gggttcttct 1740 caaaacatag aacttgtagc ctcatgtctt acctttccaa cgccacaaat ttcgcttgaa 1800 tcggagttct ataactccag atatagttaa aaatctgagg agaggtcaga cagtaacagt 1860 tcaaaaacga ggcagtaaca gttggacagt gacagtccaa atataaagaa aggaatgata 1920 actaggattg gacaaagaac gacagtaata atgagtgaaa tgagaaaaac ataaagtact 1980 aagaaatgac tgaaagaaag acttattggt tgttgatatg gttattataa aacatatcct 2040 tgagtgagga aaatttatga gataaacctg tgatttgcag gagggaccac aggcgtggtg 2100 caacagcagc agcaggggag cacgagtaga gcttctattg caggtaggtg attcacacct 2160 atgctttcta gttaaattcc atgatttaat atattattga tgtgaaatgt gaattactga 2220 atgtatgtgt attcaaggtg aaaagttgtt atgtgaattg ccaagtgatg aaattatcac 2280 tgacaaagga aatatgagaa gtgtgatttg aggcataaac tagcatacat tgagtgtatg 2340 ttaggatccc gggtaagggg atcaccatgt attggctagc atacatttag tgtatgttag 2400 gatcccgggt aaggggatcg tcacgaatgg actagcatac atttagtgta tgttaggatc 2460 ccgggtaagg ggatctccac gtattggcta gcatacattc agtgtatgtt aggatcccgg 2520 gtaaggggat caccatgtat tggccagcat acatttagtg tatgttagga tcccgggtaa 2580 agggatcgcc ttacatcgac tcctatgggg tggtgatgac gataccagtg aaattggtat 2640 cggtaatgtg ataagcaaaa gtaatcacgt tgatcttata aggtctggaa tgaaggttga 2700 tagtggcaga gggaacggtt attaatagtt tgaataagga agagatttta ataaaaaaac 2760 tagaagggag aagtaaatga aatatgaatg catgttaccc tgttgaaatt gttagatatt 2820 cgtattgtta tatttattgt gatattcacc ttgcaataat atgtattttg tttcaggatc 2880 atcgcatgca cgacaggagt agatcctagc ttatgttccc ttcttgaaat ctaggttcta 2940 gggagtatac ccttgtattt tgtaaacatg aaaatgtttg tataacttaa tttgtataat 3000 aaatgtttaa acttgattgg atgaatttaa cgctgtagtt catataacca tatttcatgt 3060 ctatgtattt atatttattt aaattatcca tccataatga tatttttgtt atataatgca 3120 tatcataaat attatggttg ataggtgtga gtataattgt ggaattgaaa cccaggatga 3180 ttgggtcggg aattaagtta tgagatgcga actgttagaa gtgtaaacag gttacatgtc 3240 ggtaacttgg gaccttccgg tatagggggg actccgtcga aattccggta gatgttaata 3300 cgaagaccat gaatatatat atataaaaaa aaaattaact actctgtttt tctattgaca 3360 tgagattgtt gttttatccc agaaatgggg gatgttaca 3399 // ID Copia-51_VV-I repbase; DNA; EDCOT; 4365 BP. XX AC chr2; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-51_VV_; KW Copia-51_VV-LTR; Copia-51_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4365 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr2; Positions 9760394 9764758. XX CC Positions [1743-2267] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 1512..4346 FT /product="Copia-51_VV-I_1p" FT /translation="MIGKGSRKGQLYQLDFDSFVADKAFVAASRIPTSNIL FT SLWHSRLGHPSFSRLKGLQSILDFDSSFDLTPCNVCPLAKQRCPPYISLNK FT RCSSTFDLLHLDIWGPFSVGSVEGYKFFLTIVDDYSRVTWVYMLKNKSEVQ FT KYIPDFFAFVKKQFGKEVKAIRSDNAPELFLSNFYHSLGVIHYRSCVETPQ FT QNSVVERKHQHILNVARALLFQSSLPVCYWSDCILTAVYLINRTPSPFLNN FT KTPFEILHDKLPDYSHLQVFGCLCYVSTLKANRTKFSPRAKAAVFLGYPFG FT FKGYKLLDIETRSISISRNVIFHEEIFPFSKTNPCSSPDISSDLFHDRVLP FT CIAADNDQSSSVLPRVVSQPPLQVAPSSRPTRVSKQPSYLKDYHCSLINSV FT AHVETHSTSHPIQHFLSYDKLSPSYKIFSLSVSIISKPSSFAKAAEIPEWR FT AAMDCELEALEENKTWSIVSLPVGKHPVGCKWVYKIKHKADGTIERYKARL FT VAKGYTQREGIDYVDTFSPVAKLVTVKLLLAIAAIKGWHLSQMDVNNAFLH FT GDLNEEVYMKLPPGYNRKGESLPSNAVCLLHKSLYGLKQASRQWFSKFSTA FT IMGLGFSQSPSDHSLFIKNVDGLFIALLVYVDDVIIASNNQGAIADLKSEL FT NKLFKLKDLGDVKYFLGLEIAKSSTGICVSQRKYVLDLLSDFGYLGCKVAS FT TPMEANVKLSMDEGVNLPDVSLYRRLLGKLLYLTLTRPDISYAVGRLSQFI FT SRPKLPHLHAAQRILRYLKGNPSMGLFFPSNSELRLMAYTNSDWARCPDSR FT RSVTGFCVFLGNSLVSWKSKKQHIVSRSSAEAEYRAMANTSCEITWLLALL FT KDFGIDHSAPALLFCDNQSALHIAENPVFHERTKHIEIDCHLVRDKVQSGV FT LKPLFVSTEHQLANVLTKALHPSSFKLLIGKMGLKNIFSPS" XX SQ Sequence 4365 BP; 1129 A; 797 C; 842 G; 1597 T; 0 other; tggtattaga gcgatccatt tagggtttca aatccctaat ttctattttt tttcttctct 60 ttctctgttc tttgttctcg atcgtgttca tggcgaaagg tggatctggt aatggtaatc 120 gcggtggcca ggtgaattct gagattgttg ttgttgaaga ttcgagtagt ccctattttc 180 ttcataatgg agatcatcca gggctcaatc ttgtttcaaa tcttttgact ggagcgaatt 240 atcatacctg gcgtagagcg atgctgatgg ctctcacagc gaagaacaaa gttggttttg 300 tggatggtac gatttctaaa cctatgtctc atgatttgat ttacggtgct tggaatagat 360 gtaacattat gatttcttca tggatcataa atgctgtttc aagagaaatt gtagatagtc 420 ttttatattt ggattctgct tatgatattt ggagagattt gaatgataga tttaatcagg 480 gtaatggacc tcgaattttt caaattaaga agcaattatc tgctcttaat caaggttcat 540 tggatgtcaa ttcatatttc actaaattga agattctttg ggatgaattg agggagtttc 600 aacctgttcc agtatgtcat tgtggtggat tgagagtttg gacagattat taacataggg 660 agtatgtttt acaatttctt atgggtttaa atgactctta tgctcagatt agaggacaaa 720 ttttgatgat ggatccctta cctgctatta ataaagtgtt ttctctggtt attcaagaag 780 aacgtcacag gattgttggt tattcttatt ctggttctca caattctgat cctatgacat 840 ttggctctaa ttctaatgca ccaacaggaa gttcaagtgg ctctaaaact agaagggata 900 gaattacttg ttcttattgt ggtttccaag gtcatatcaa agataaatgc tataaacttg 960 ttgggtatcc accgggatgg aaattaaaaa ataaaggccc taattcaagc tcaatggcta 1020 acaattcaga agtccttgag tctttgaatg caggttcttc tgaatccact gtttcttccc 1080 tcactaccat gcagtgtcaa caattgattc aactcttaac caaccaatta agctctactt 1140 cttcagcttc cacagagaat tcttcaacag gaccatcagt gtctaatttt gctggtaata 1200 aagttaaaat ccaaaataaa ggttggatta ttgatagtgg ggccacccat catgtttgca 1260 atgacatttc tctatttgat tcttctattg ttgttcaaaa tgtccgagtt actttaccta 1320 ctggtattac tgtccctatt gatagagttg gttcggtcat tctttcgaag gatgtcaagc 1380 ttctaaatgt gttgtttgtg cctactttca gatataatct actttctgtg agtgcattta 1440 cagacacttt atctctttca atggttttta ctcctgatgc ttgcattatt caggaaccat 1500 cttgaggcaa gatgattggg aagggtagca ggaaaggtca gttatatcag ctagattttg 1560 acagttttgt tgctgataaa gcttttgttg cagcttctcg gattcctact tctaatattc 1620 tttctttgtg gcattctaga cttggacatc cttcttttag tcgtttaaaa ggtctacaat 1680 ctatattgga ttttgattca tcctttgatc ttactccctg caatgtatgt cctttagcta 1740 agcagcgttg tccgccttac atttctctta ataaaagatg ttcttccact tttgatcttt 1800 tgcatctaga tatatgggga cctttttctg ttggcagtgt tgaaggctac aaatttttct 1860 tgactatagt tgatgattat agtcgagtaa cttgggttta tatgttgaag aataaatctg 1920 aagttcaaaa atatattcca gatttctttg cttttgtaaa gaagcagttt ggtaaggaag 1980 ttaaggccat aagatcagat aatgctccag aattatttct ttccaatttc tatcattctc 2040 ttggtgtcat acactatcgt tcttgtgttg aaactcctca acagaattct gtggtagaaa 2100 ggaaacacca gcatattcta aatgtggccc gtgctcttct ttttcagtcc agccttcctg 2160 tctgttactg gagtgactgt atactcactg cagtatactt aatcaataga acaccaagtc 2220 cttttctaaa caataagact ccttttgaaa tcctacatga taagctgcct gattatagtc 2280 atttgcaggt ctttggttgc ttgtgttatg tttctacttt gaaagctaac aggacaaaat 2340 tctcacctcg agccaaagca gccgtttttc ttggttatcc ctttggtttt aaaggataca 2400 aattattgga tatagagaca cgttccatat ctatctctag aaatgttatt tttcatgaag 2460 agatctttcc tttttcaaag acaaatccct gttcttctcc tgatatttct tctgatttgt 2520 ttcatgatcg agttcttcct tgtattgctg ctgataatga tcaatcttcc tcagttcttc 2580 ctcgtgttgt ttcacagcca cctcttcaag ttgctccttc ttcacgacca acaagagtct 2640 ccaaacaacc ttcatatttg aaagattatc actgctcttt aatcaactct gttgctcatg 2700 ttgaaactca ctccacttct catcccatac aacatttttt gagttatgat aagctctctc 2760 cttcttacaa aattttttct ctctcagttt ccattatttc aaaacccagc tcttttgcaa 2820 aggctgctga aataccagaa tggagggctg ccatggattg tgaattagag gctcttgagg 2880 aaaataagac ctggtccatt gttagtttac ctgttggtaa gcaccccgtt ggctgtaaat 2940 gggtgtacaa aattaaacat aaggctgatg gtaccataga acggtataaa gctcgtttag 3000 tggccaaagg gtatactcaa cgtgaaggca ttgattatgt tgatactttt tcaccagtgg 3060 caaaactagt gactgttaaa ttgcttttgg ctattgctgc tattaaaggt tggcatttgt 3120 cacaaatgga tgtgaacaat gctttccttc atggagactt gaatgaggaa gtgtatatga 3180 agttacctcc tggttataat agaaaagggg agtctttgcc ttcgaatgct gtttgtttgc 3240 ttcataaatc cttatatggt ctcaaacaag cctcaagaca gtggttttct aagttttcta 3300 ctgccattat gggcttggga tttagtcaat ctccttccga tcattctctt ttcatcaaaa 3360 atgttgatgg cttgttcatt gctcttcttg tttatgttga tgatgtgatt atagctagta 3420 ataatcaagg ggccattgct gatttgaaat ctgagttgaa taaactcttc aaactgaagg 3480 atttgggtga tgtcaagtat ttccttggtc ttgaaattgc taaatcctct actggaatct 3540 gtgtttctca gcgaaaatat gttcttgatt tgctttctga tttcgggtat ttaggttgca 3600 aagttgctag tacacctatg gaagctaatg tcaagttatc catggatgag ggggttaatc 3660 ttcctgatgt tagcttgtat cgtaggctac ttgggaagct gttatatttg acattaacac 3720 gacctgacat ttcttatgct gtaggtcgac ttagtcagtt catttctcgt cctaaattgc 3780 cccatttaca tgctgctcaa agaatccttc gttaccttaa aggtaatcct agcatgggtt 3840 tgttctttcc tagtaattca gagcttcgtt tgatggctta tactaattca gattgggctc 3900 gttgtcctga ttcgagaaga tctgttactg gtttttgtgt tttcttgggg aattctttgg 3960 tgtcatggaa atccaagaaa caacacattg tttctcgctc ttctgctgaa gctgagtatc 4020 gtgctatggc caatacttct tgtgagatta cttggcttct tgctcttctc aaggactttg 4080 gtatagatca ttctgctcct gctcttcttt tttgtgacaa tcagtctgct ttacatatag 4140 ctgaaaatcc cgtgtttcat gaacgcacaa aacacattga gattgattgt catcttgttc 4200 gagacaaggt tcaaagtggg gttctcaagc ctctatttgt ttctacagaa caccagttag 4260 caaatgtttt gacaaaagcc cttcatcctt cttcttttaa gcttcttatt ggcaagatgg 4320 gtctaaagaa catctttagt ccatcttgag ggggagtatt aggat 4365 // ID Gypsy17-VV_LTR repbase; DNA; EDCOT; 1744 BP. XX AC AM437405; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy17-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1744 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-1744 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 715-715 (2007). XX DR Genbank; AM437405; Positions 6043 7786. XX SQ Sequence 1744 BP; 494 A; 349 C; 336 G; 565 T; 0 other; tgattactac tcaaaaagta ctatttcata gcttgtaatt aactctttta aacacttttg 60 agtagtagtt atcacctttt aacccaatta acatattaag gacccttgca atcaattcta 120 atcaaattgt gttaagtttt ggtgttttga tagctttttg atcaccaaag caatccgaga 180 ttaaggagag ttctttggaa tccataagca aatccagaat ataaggagta tgggatcctg 240 cttattccac ccggacagga atcatagctc attccacccg ggtaggaatt acatccggca 300 gccgccatta catccggctg cagccactac acctggctgc cgccattact tccagcgccg 360 ccactttcca cccggatgta tcacatctgg aattctgacg ccggatggga gaggagagcg 420 tttcaacttc ctcggtcaca catatccgga tccgcttata gcgcttacct ggagagtttc 480 gcagccattt tgcacagtgc tgcgatgttc tcctgaagct tcccgatatg tgcgaccgac 540 attttgagat attttgagat attttgtttt agatattttg ctttaaatat ttgttgtcta 600 aatccccaaa ctctccttgt aacccaccaa ttataggatt ccttatttat taagtttgga 660 aaaaggatga ataaccttgt agatattatt attgtaattt tcatataaat atctctcggg 720 agcctgttct cgggaggacg aaacttttgt ataattttca aaggaagaaa aatacagagc 780 tttgctctgc ttttaccttc tcattttgat tgtattttct tactagccaa acaagctctg 840 aggatgtttc ctcagagaat gagtggctag acttttagtt ccttggagtt aaggttgtcg 900 ggaaaagttc taagtgcaag aattagtagc tttgtggttt cagccattaa tgaagagaaa 960 gtgtgatcct ttaatgattt ctatgttttt agttaactta aaacgccttt aaatcacctg 1020 ggccaacact tgataaggca agtgatctcc atccattaag atgcactagt ttatctcttg 1080 cgagcctttg ggaggtggtt tgaaggtagg attttctaga atagccaaca cttggtaagc 1140 ttttggactc cacggagaca tccattagtt atctcttgcg agcttttgac aggtaatcca 1200 aggttaaaga tcaccttgaa tggcaaatgc taggtgagag gcacgagcca ttgcaagttg 1260 catcagtgag agggaattag atctgaaatc catttaaagg atacatctat ataacaccgg 1320 ttagagaatt gactatatgt taattctcta atgcgaggaa atgaaccgag tgaccggagc 1380 tctatttttg catgaggaac ctcccctgtg aacctaaacc tccaatgaat gtttttcttc 1440 ataagtaatt tccattactt cctttgccgt tagcttaaac ctaaaccttt ttcaatcaaa 1500 gtttgtgttt tatttcttaa gctaaccttg aaatgaaaag gcaccaattc atctttgaat 1560 tggtatcatt tatgaattga aaacccttcc cagtgaacga tcctagagcc actatgctat 1620 agtagctttg tctttgctac cgtagttcat ggtgtaatag gttataaatt ttgttgatta 1680 cttcctcaat caaggagcac cagctagaca tgaatcagct gatacaccaa ttgggcacga 1740 atca 1744 // ID Copia-12_Mad-LTR repbase; DNA; EDCOT; 243 BP. XX AC ACYM01088783; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-12_Mad_; KW Copia-12_Mad-LTR; Copia-12_Mad-I. XX NM Copia-12_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-243 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1356-1356 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01088783; Positions 8503 8261. XX SQ Sequence 243 BP; 69 A; 40 C; 43 G; 91 T; 0 other; tgtaaatgcc aagtggcaag agttgatgta gaccattaga tcaaagattg gttagagaaa 60 tattgaccgt tggatgtgag tagttaggag attacttagc tgttaagaat tcttttttgt 120 ataaatagtt agctggctca ctttctgatg taatcaacat tctctctcta gaaatatata 180 caagattctt catttgtttc tctctctcaa aatctctctg catttccttg atttctgtca 240 cca 243 // ID Copia-87_Mad-I repbase; DNA; EDCOT; 4399 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-87_Mad_; KW Copia-87_Mad-LTR; Copia-87_Mad-I. XX NM Copia-87_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4399 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1712-1712 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1803-2297] - Integrase core CC 'ATAT' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(135..1967,1971..3674) FT /product="Copia-87_Mad-I_1p" FT /translation="MAPAVSSSTASDSPILPPSEASNPNSSNSTSITIQNI FT GSMVPIKLTTTNYLTWSALFAPIFRRYNLTGLIDGSSPAPPQFLTDSSGNR FT SLNPAYVAWFENDQNILIWLNSTLSESLIPYTVGVSSARELWAKLESRLAA FT ASHSHIHELRSRLRSLTKGDLTAAQYLQRTEEIADALASAGAPVEDSELIS FT VILHGLPPEFDSFVDAIQFRLGSTTMDELHGLLLSKEIQLTNRKQSPPVSS FT FQAYNTSTGLLPLPVPSISHGYVAQQSFSSHNQNRGLDRNFTRGNHNSRGN FT FRQNNNPRFSTFNRGNNQRSNRGPRSNFSSNRKLSCQICRQFDHEACDCPH FT RMDPHYNGKSSQTALVANTSNSSSPWIVDSGATSHMTNNYATLQNPEVYTG FT PEQVYIGDGKGLPITHTGSSSITTSHSNFALKNVLFVPDLKHNLLSANQFL FT IDNQCSMHLYPSHFTVKDLSSGRMRFKGPVQHGFYPFYPSSHTGAKHTALT FT ATPKASRTLWHGRLGHPSVKILNKLASQSCISVFQHKTSSFCSACALGKCS FT RLPFVSTTCTTTKPLELIHTDVWGPSPIASQDGFRYYVIFVDDFTRYCWFY FT PLRYKSDVLSVFMYKSLVENTLCTKIITLRSDSGGEYMSTLFSTFLAQHGI FT QHQLSCPHTPEQNGCAERKHRHLVETARTLFAASKVPHLYWVDVFAAAIYL FT INRLPTLSRPSPWESLFKTLPCYGTLRVFGCLCFPWLKPYTSSKLDAKSKP FT CVFLGYSLNHKGYKCLDPVTGRLYISRHVLFDESKFPFSDLSSSSPSSPLQ FT PASPSSAIPSSLTFTSLTPSSPSSPFSGPSSSPPPTAPPPSSPPSGPSSSP FT PPPAPPPPSPPPSSSINTHPMQTRSKSGIYKPKAFTATNHPLPSHLSLDYI FT PTTYLQASKHPHWRQAMQEEFNALLHTQTWSLVPYHSSQNIVGCKWVFRIK FT RKPDGSIDRYKARLVAKGFHQQEGLDYTETFSPVAKPVTIRLLLTLAAQFD FT WFLHQLDVSNAFLHGTLSESVFMQQPPGFADSTKPHHVCQLHKSLYGLKQA FT PRAWYDKLHAALASLGFVGSQSDHSLFVKKDKSLVFVLVYVDDILVTGPSS FT VDCQHVITQLSNLFPIKDLGPLHYFLGLEVKRSSTGIFLSQTKYILDLLNK FT AKMVGAKPCNTPLSTSKIDH" XX SQ Sequence 4399 BP; 984 A; 1238 C; 780 G; 1394 T; 3 other; atatggtatc actcgccctc gtctgacgac ctctctcttc gatcccaaat cttcccgctt 60 ctctgctact ccgatcttga tctccgatct tgcttgatct tctccgcttg atcctcttct 120 ctgcatctct gatcatggct cccgccgtct cttcctctac ggcatcggat tctccaattc 180 ttccaccgtc ggaagcttca aaccctaatt cctcgaattc tacctcaatt accatacaga 240 acattggatc tatggttccg atcaagctta ccactaccaa ttacctgaca tggagtgctc 300 tctttgctcc aatttttcgt cgatacaatc tcaccggttt gattgatggt tcttcgccgg 360 cgccgcctca atttctcacc gactcctccg gaaatcgcag tcttaatccg gcgtatgttg 420 cttggtttga gaatgatcag aacattctca tctggctcaa ttcgactctc tcggaatccc 480 taattcctta tactgttgga gtttcctcgg ctcgagaact atgggccaaa ttggagtctc 540 gtcttgctgc tgcctcgcat tctcacatcc acgaacttag atctcgcctt cgcagtctca 600 ccaaaggaga tctcacagcc gctcaatatc ttcaacgcac tgaggagatt gctgatgctc 660 ttgctagtgc tggtgctcca gttgaagatt cagagctgat ttctgtcatt ctacatggct 720 tacctcctga atttgactcg tttgtggatg ccattcagtt tcgtcttggt tcaactacca 780 tggatgaact ccatggtttg cttcttagca aagagatcca actgaccaat cgcaagcaaa 840 gtccaccggt gtcttccttt caggcctaca acacctccac tggtcttctt cctctgcctg 900 ttccttctat ctctcacggc tatgttgctc agcagtcgtt ctcttctcac aatcaaaacc 960 gtggactgga tcgcaacttt actcgaggca accacaattc tcgtggcaat ttcaggcaga 1020 acaacaatcc gcgattctcc actttcaatc gaggcaacaa tcagcgttcc aatcgaggcc 1080 ctcggtccaa tttttcatcc aacaggaaac tttcttgtca aatatgtcgt caatttgacc 1140 atgaggcttg tgactgtcct catcgcatgg accctcacta taatggcaag tcatcccaaa 1200 ctgcgttggt tgccaacacc tccaactcct cctctccatg gattgtcgac tctggagcca 1260 cttctcatat gaccaacaac tatgccactc tccagaatcc tgaagtctac acagggcctg 1320 aacaagtgta tatcggtgat ggcaaaggtt tgcctatcac tcacactggc tcttcttcca 1380 ttaccacttc acatagtaat tttgcactca aaaatgtttt atttgtgcct gatctgaagc 1440 ataatctcct ctctgcaaat caatttctta ttgataatca atgctctatg catctttatc 1500 cctctcactt tactgtgaag gatctttctt cggggaggat gcgttttaaa ggtcctgttc 1560 agcatggctt ctatccattt tatccttcat ctcacactgg tgccaagcat acagctctta 1620 ctgctactcc gaaagcttcc cggactctgt ggcatggacg gttgggccat ccttcagtca 1680 agattttaaa taagctcgct tctcaatctt gtatctctgt gttccaacat aagacctctt 1740 ctttttgctc agcctgtgca ttaggaaagt gttctagatt gccatttgta tccactacat 1800 gtactaccac gaaaccgtta gaactcattc atacagatgt ttggggaccc tcacctatag 1860 cttctcagga tggtttccgg tactatgtca tatttgtgga tgattttact cgatactgtt 1920 ggttctaccc tctgagatac aaatctgatg tactatcagt cttcatgmaa tataaatctt 1980 tggttgaaaa tactctgtgc accaaaatta ttaccttgag atctgattct ggtggtgaat 2040 acatgagtac tcttttctct actttcttgg cacaacatgg catccagcat cagttatctt 2100 gtcctcacac acccgagcaa aatgggtgtg ctgaacgcaa acacaggcat cttgtggaaa 2160 ctgcccggac tctttttgca gcatctaaag ttcctcactt atattgggtt gatgtttttg 2220 cagctgcaat ctatctcatc aacaggttac ctactctatc tcggccctca ccttgggagt 2280 ctcttttcaa gacattgcct tgttatggta cactcagagt ttttggttgc ctctgctttc 2340 cgtggttaaa gccgtatact tcttctaagt tggatgctaa gagcaagccc tgtgttttct 2400 tgggctacag tctcaatcat aaggggtaca aatgccttga tccagttaca ggacgccttt 2460 acatctcccg gcatgttctc tttgatgaaa gtaagtttcc attttctgat ctttcttctt 2520 cctctccttc ttccccatta caacctgcaa gtccatcctc tgctattcca tcttccttaa 2580 cctttacatc ccttactcct tcctcaccct catctccttt ctctggccca tcctcctccc 2640 ctcctcccac tgcaccaccg ccatcctcac caccctctgg accatcctcc tcccctcctc 2700 ctcctgcacc accaccgcca tccccaccac cctcttcctc cataaacact caccctatgc 2760 aaacccgctc taagtccggc atttacaaac ctaaagcttt tactgccaca aatcatcctc 2820 ttccctctca tttgtctctg gattatattc ctacaaccta tctccaagcc tctaaacacc 2880 ctcattggcg ccaagcaatg caggaggaat tcaatgctct tcttcatact caaacatggt 2940 ccctggttcc atatcattct tcacagaaca tagttggctg caaatgggtg tttcgcatca 3000 aacgaaaacc cgatggctcc atcgatcgct acaaggctcg gttggttgcc aagggctttc 3060 accaacagga aggtctcgat tacactgaaa cgtttagccc tgtggctaaa cctgtgacaa 3120 ttcgcctctt actcaccctt gctgctcaat ttgattggtt tctgcaccaa cttgatgtca 3180 gtaatgcatt cttacatggc actctttctg aatctgtgtt tatgcaacaa ccacccggct 3240 ttgcagactc taccaagccc catcatgtgt gccagcttca taaatcgtta tatggtctga 3300 aacaagctcc ccgagcttgg tatgataaac tacatgctgc ccttgcttct cttggctttg 3360 ttggttctca aagtgaccac tctctgtttg tcaaaaagga caaatccttg gtctttgttc 3420 ttgtgtatgt ggacgatatt ttggttactg ggccctcttc tgttgattgt caacatgtga 3480 tcacacagct cagcaatttg tttcctatta aggatcttgg tcctttacac tattttcttg 3540 gtctcgaggt caagcgctct tctactggca ttttcctatc ccaaactaaa tatattctgg 3600 atttgcttaa caaagccaaa atggttggtg caaaaccctg caacacacca ctgagcacct 3660 ccaagattga tcatgmttct cctcttcttg acaatgcttc tgagtacagg tccttggtgg 3720 gtgctcttca atatctaacc tggacaaggc cggatcttag tttcgctgtc aaccttgtat 3780 gccagttcat gcacactccc aaagtctctc acttccaagc tgtcaagcgt atcctccggt 3840 atcttaaggg caccattgat cacggtctct ggttctcgaa gtgctcctct gttccatctc 3900 tcaaggcctt ttccgatgct gactgggctg gttgtgagtt agataggaga tccactggtg 3960 gttactgcat ttttctgggt aattctctca ttagttggag cgctaaaaag caacccactg 4020 ttgctcgttc ctctaccgag gcagagtatc gctcccttgc aaacactgct tctgagatca 4080 cttggatttg tcaattactc gctgacattg gctattgtct gccttgttct cctcaacttt 4140 ggtgtgataa cgtmtctgct atatcccttg ccaagaatcc tgtttttcat gctcggacca 4200 agcatgtcga gcttgattat cattacatcc gtgaaaaagt agttgccaag cacatctccc 4260 ttcactacat ctgctcccaa gaccaagtgg ctgatatctg tacaaaatcc ttagctgcag 4320 cacgattttt gtttctcagg gacaaacttc aacttcgggt cccccagttt cgtttgaggg 4380 gggatattaa gggtaatat 4399 // ID LycEPRV_LTR repbase; DNA; EDCOT; 185 BP. XX AC AC171732; XX DT 16-MAR-2006 (Rel. 11.03, Created) DT 14-DEC-2010 (Rel. 16.01, Last updated, Version 2) XX DE Long terminal repeat of an endogenous caulimovirus from DE Lycopersicon esculentum. XX KW Caulimoviridae; Integrated Virus; LycEPRV_LTR. XX NM LycEPRV_LTR. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-185 RA Jurka J.; RT "LycEPRV: Long terminal repeat."; RL Repbase Reports 6(3), 160-160 (2006). XX DR EMBL/GenBank/DDBJ; AC171732; Positions 85944 86128. XX CC LTRs are ~97% identical. No LTRs have been reported previously CC for this retrovirus. XX SQ Sequence 185 BP; 48 A; 42 C; 29 G; 66 T; 0 other; tgctttgttt tcttgtgtcg gccgaataaa gagaggccat gtgtaaagta tgtgtcggcc 60 acttttagcc aaaagtttgt aaattttgtg tataaataga ggagctttcc tcataaataa 120 aacacacctt catccttaca tctctcatct ttctgaatat tctctttacg cttccatccc 180 ctcca 185 // ID BPCOPIA1 repbase; DNA; EDCOT; 247 BP. XX AC AJ249707; XX DT 30-MAY-2000 (Rel. 5.04, Created) DT 30-MAY-2000 (Rel. 5.04, Last updated, Version 1) XX DE BPCOPIA1 is a copia-like LTR retrotransposon, a partial pol gene DE for reverse transcriptase. XX KW Copia; LTR Retrotransposon; Transposable Element; BPCOPIA1; RT; KW endogenous retrovirus; pol. XX OS Beta procumbens OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC Caryophyllales; Amaranthaceae; Beta. XX RN [1] RP 1-247 RA Desel C., Jung C. and Schmidt T.; RT "Physical mapping of multiple single-copy DNA sequences on sugar RT beet (Beta vulgaris L.) chromosomes by multi-color fluorescence RT in situ hybridization."; RL Unpublished. XX RN [2] RP 1-247 RA Desel C.; RT "BPCOPIA1."; RL Direct Submission to Genbank (22-SEP-1999)Desel C., Institute of RL Crop Science and Plant Breeding, Christian-Albrechts-University RL of Kiel, Olshausenstr.40, D-24118 Kiel, GERMANY. XX DR GenBank; AJ249707; Positions 1 247. XX SQ Sequence 247 BP; 68 A; 60 C; 62 G; 57 T; 0 other; actgcgtttt tgcacggccg gacatgccct ctttagtttc cttgacgcca acgcgggata 60 tcatcaaatc cgcatggctg aagaagacag cgtccatacg gccttcatct caagccacgg 120 gatccatgcc tataagatga tgcccttcgg gctacgaaat gcaggggcaa actatcaaat 180 gttagtgaac aagatgtttg agaaacagct gggccggaat atagaggtat acgtcgacga 240 catgtta 247 // ID SHACOP18_LTR_MT repbase; DNA; EDCOT; 286 BP. XX AC AC147006; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of a LTR retroposon from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW terminal; Interspersed; repeat; SHACOP18_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-286 RA Shankar R. and Jurka J.; RT "SHACOP18_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 64-64 (2007). XX DR EMBL/GenBank/DDBJ; AC147006; Positions 61167 61452. XX SQ Sequence 286 BP; 71 A; 45 C; 43 G; 127 T; 0 other; tgttaattat tgcttttgga ctgcattacg tggctgattt atctttattc cctattgttt 60 cagtttttta ttttagtcaa taagtggtac ctacacttta ggagaaagca gttgttgtta 120 tcccacgatc ctagtttagt ggtgatgtag ttgtgttctg ttttgttttg tgaaacacta 180 ttaagtgtat tgttttagtg aaattaataa atcaatttcc cattccattt caacgtattc 240 ttccctgtct atcatattat ttttcattta taccatataa ccaaca 286 // ID Copia36-PTR_I repbase; DNA; EDCOT; 3986 BP. XX AC scaffold_3831; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia36-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3986 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-3986 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 248-248 (2007). XX DR Genome; scaffold_3831; Positions 4525 540. XX CC Positions [1563-2063] - Integrase core CC 'CAGCA' target site duplication CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS join(36..1433,1437..3158) FT /product="Copia36-PTR_I_1p" FT /translation="MDNEASFSHISSPISNGENYQLWAVRMETYLEALDIW FT EAVEEYYEIPPLPTNPTMTQIKSHKERKTKKSKAKACLLAAVSTTVFTRIM FT SLKSAKDVWDYLKEEYAGDERIRGMQSLNLIIEFELQRMKESETIKEYSEK FT LLGIVNKVRLLGTDFTDCRIVEKILVTVPERYEASITTLENTKDLSKINLA FT ELINALQAQEQRRLMRLDHVTEGALQAKYHDSKSHFRKNQVSSNSNTSARK FT FQNKGKFLKRNFPPCQHCNKTGHAPFKCWKRPDAKCSKCNQMGHEAIICRT FT IIQKQDVDAQVANQDDEDQMFVASCFSVQTTSDHWLIDSGCTNHMTPDRSL FT FRTLQSTEVAKVRIGNGACIAVKGKGTIAITTKSGTKTISEVLYVPEIDQN FT LLSVGQLIEKRMKVVFENYFCYVFDAAGQLILQAKMKGKSFSFLPFEEEYS FT AFQTKLTDMEVWHKRLGHCHQRMISMKKHDSVRGVPQFTDFPSNCSACQFG FT KQSRKPFQKSTWRSTQKLQLIHTDVDGPLSTPSIKGSRYYILFIDDFSRMC FT WIFFMKYKSEVAGIFFKFKKNVENISNYRIQVIRSDNGKEYTSSEFNLYCE FT EVGIDHQLTAPYTPEQNGVGERRNRYIMEMVRCMLHDKNLPKDFWAEAAST FT AVFLQNRLPTKLLDEKTPFEAWYNYKPSLRFLKVFGSLCFVHIPQIKRDKL FT DKKAAPGIFVGYSGASKAYKVYHPQTQKMVVTRDVHFQEEDQWDWGQSQMN FT NQPHEEEQWDWGHSQRNQQPADPLLDETFNDPPTRGTRSLEDVYQRSNVAL FT CEPEGYEEAKQSPEWQKAMQEKISMIEKNCTWELVDRPPGKNIIGVKWILR FT TKLNADSTINKHKARLVVKGYAQIYGVDYSYTFAPVARMDTIRLLLVVAAQ FT KNWKVFQLDVKSAFLNGILQEEIYVEQLAGFEIQGKEDKVYLLKKALYRLK FT QAPRAWYGRIDDYLTGAGFQKSLSEATLYVKSINNDVIIISLYVDDLLVTW FT SNTEQVEHFKLNMMEVFEMTDLGLMSFFLGMEIL" XX SQ Sequence 3986 BP; 1342 A; 714 C; 886 G; 1044 T; 0 other; attggtatca gagctgattt cttaaaggac ctgtgatgga taatgaagca agtttttctc 60 acatttcttc tccaatctcc aatggagaaa attatcaact ttgggcagta aggatggaaa 120 cctacttaga agcacttgat atttgggagg ctgtcgaaga gtattatgaa attccaccac 180 tgccaactaa tcctaccatg actcagatca agagtcacaa ggagagaaaa accaaaaaat 240 ccaaagcaaa ggcatgtcta cttgctgctg tctcaacaac agttttcaca aggatcatgt 300 ccctaaaatc tgccaaagat gtatgggatt atctgaagga ggagtatgca ggagatgaaa 360 ggatacgtgg aatgcaaagc ctcaacctca taatagagtt tgagctgcag aggatgaagg 420 agtctgagac catcaaagag tactcagaaa aattgcttgg aattgtcaac aaggtgagat 480 tgctgggcac agactttact gattgcagaa ttgtggagaa aatccttgtt acggtgcctg 540 aaagatatga ggcatctata actaccttgg agaacaccaa ggatctgtcc aagatcaatt 600 tggcagaatt gataaatgct ttgcaggctc aagaacaaag gagactgatg aggctggatc 660 atgttacaga aggagcatta caagcaaagt atcatgattc taagagtcat ttcaggaaaa 720 atcaggtttc aagcaatagt aacactagtg ctcgtaaatt ccagaacaaa ggaaaatttc 780 tcaaaagaaa ttttccaccc tgtcaacact gcaacaagac gggacatgca cctttcaagt 840 gctggaaaag gcctgatgca aaatgcagca aatgtaatca aatgggacat gaggcaatca 900 tctgtaggac aataattcag aaacaagatg ttgatgcaca agtggccaat caagatgatg 960 aagatcaaat gttcgtagct tcatgttttt cagtccaaac cacctcagat cactggctga 1020 tagacagtgg gtgtacgaat cacatgaccc ctgacagaag cctctttcga accttgcaat 1080 ctactgaagt tgcaaaggtc agaattggga acggtgcttg catagctgta aaaggaaagg 1140 ggacaattgc catcaccaca aagtcaggta caaaaaccat ttctgaagtt ttatatgtac 1200 ctgaaataga tcaaaatcta ttaagtgtgg ggcaattgat tgagaaaagg atgaaggttg 1260 tcttcgaaaa ttatttttgc tatgtctttg atgctgctgg acaattaatt ttgcaagcta 1320 agatgaaagg aaagagtttt tcattcctac catttgagga ggagtattca gcttttcaaa 1380 caaagctgac tgatatggaa gtgtggcata aaagacttgg ccactgccat caatagagga 1440 tgataagcat gaagaaacat gactctgtaa gaggagtgcc tcaattcact gactttccat 1500 caaattgcag tgcatgtcaa tttggtaaac aaagcaggaa gccattccag aaatcaactt 1560 ggagatctac acagaaactc caattgattc acactgatgt tgatggtcca ctcagcacac 1620 cttcaatcaa aggtagtcga tactatattc tttttattga tgacttttct aggatgtgct 1680 ggattttctt catgaaatac aaatcagaag ttgctgggat ttttttcaaa ttcaagaaga 1740 atgtggaaaa cataagcaat tacagaattc aggtcattag gtctgataat ggcaaggagt 1800 atacctcatc agagttcaat ctctattgtg aggaagttgg catcgatcat caactcactg 1860 cgccttacac accagagcag aacggtgttg gtgaaagaag gaatcgatac atcatggaga 1920 tggtgagatg catgttacat gacaagaact taccaaagga tttttgggca gaagcagcca 1980 gcactgcagt ttttcttcag aacagactgc ccacaaaatt gcttgacgag aagacacctt 2040 ttgaagcttg gtataattac aaaccttcat taagatttct taaagtcttt ggcagcctgt 2100 gttttgttca tattccacag atcaaaaggg acaagctgga caagaaggct gcaccaggaa 2160 tctttgttgg ctatagtggt gcatctaaag cttacaaggt ttaccatcct caaacacaaa 2220 aaatggttgt taccagggat gtccactttc aagaagaaga tcagtgggac tggggacaat 2280 cacaaatgaa taatcagcct catgaagaag agcaatggga ctggggacac tcacaaagaa 2340 accaacagcc tgcagatcca ttgctagatg aaacatttaa tgatccacca acaagaggca 2400 ctcggtcact tgaggatgtc tatcaaagga gcaatgtagc cctctgtgaa ccagaaggct 2460 atgaagaagc taaacaaagt ccagaatggc agaaagcaat gcaggagaag atatcaatga 2520 ttgagaagaa ttgcacatgg gaacttgttg acagaccacc tggaaaaaac atcattggcg 2580 tgaagtggat attaaggact aaactgaatg ctgacagcac catcaacaag cataaagcta 2640 ggctggtggt caaggggtat gcacaaatct atggtgttga ttattcatat acttttgcac 2700 ctgtagcgag aatggacacc attagacttt tacttgttgt tgctgctcaa aagaactgga 2760 aagtgttcca gttagatgtc aaatctgcct tcctcaatgg catattgcaa gaagaaattt 2820 acgttgagca gcttgctggt tttgaaattc aagggaagga agacaaagtg tatttactga 2880 aaaaagctct ctatagatta aagcaagcac ctagggcatg gtatggtcgg attgatgatt 2940 atttgacagg tgctggcttt caaaagagct tgtctgaagc aactctttat gtgaagagca 3000 tcaacaatga tgtgattata atttcactct atgttgatga tctcttggtg acatggagca 3060 acacagagca ggttgaacat ttcaagctga atatgatgga agtttttgag atgactgatc 3120 tcggtctaat gagcttcttc ctgggaatgg aaatcctata gggcaaggat gaaatcttca 3180 tttgtcaaaa gaagtattca atggaaattt tgaagaaatt ccatatggaa agttgcaagc 3240 caacaactac cccaatgaac caaaaggaca aattcagcaa agaagatggc actgccaagg 3300 tggatgaaga gaaattcaga agcttgattg ggtgtttgct gtatttaaca gcaactagac 3360 ccgatatact tcatgcaaca agtttactat ctcggtttat gcattgtccg agtgaaattc 3420 acatgagagc tgccaaaaga atcctaaggt acatcaaagg gacctgcagc tatggagtca 3480 aatttcagaa gtgtcaggaa ttaaaactac atggattttc tgacagtgat tggggaggat 3540 ccattgatga catgaagagc acctctggtt tttgtttcaa cctagggtca gctatatttt 3600 catggtcatc caagaagcaa gacacggtgg ctcaatctac agcagaggca gaattcattg 3660 ctgctacagc agctgtaaac caagctcttt ggcttcagaa attgctacgt gatttacata 3720 tggaaggaga ggaagcaact gaaatttcag ttgacaatca agcagctata gcaatctcac 3780 ataatcctgt gtttcatggg aaaacaaaac actttaacat caagctttat tttttacgtg 3840 aggtgcagaa aaatggtgat gtcaggttga tatattgcaa gtctgaagaa caattagcgg 3900 atttgtttac taaaccactt ccagtaaaca ggtttgaatt tttaagacaa aagattggag 3960 tttacagctc ctaaagtaag gaggag 3986 // ID SHALINE7_MT repbase; DNA; EDCOT; 5627 BP. XX AC . XX DT 28-DEC-2006 (Rel. 11.12, Created) DT 05-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE A LINE sequence from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; LINE; KW Interspersed; repeat; retroposon; Poly-A tail; SHALINE7_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5627 RA Shankar R. and Jurka J.; RT "SHALINE7_MT: A LINE element from barrel medic."; RL Repbase Reports 6(12), 643-643 (2006). XX DR [1] (Consensus) XX CC The LINE element has two ORFs and seems to be an autonomous CC element. It has intact domains of exo-endo-phosphatase, reverse CC transcriptase and RNAseH. The sequence looks relatively younger. XX FH Key Location/Qualifiers FT CDS 1377..2369 FT /product="SHALINE6_MT_1p" FT /translation="MKCIFWNIRGLANSPSRLALKNLILQHKPDFIFISEP FT WILFEHFPRHWFNRLHFKLFALNNRNHLDSNLWCFCLNHLNPILFSTDDQQ FT ISFSIQEYNVIYCISAIYASNSYIKRRLLWQTLEINQTQYNIPWCFIGDFN FT TILGSHEHRGAYRPARAPMNDFLAWSDTNNLFHIPTRGVQFTWSNGRRGRR FT FTERRLDRAICNQEWLDLCSSLYVSTLTKLKSDHFPLLMEFETVTTPFASQ FT FKFLKMWSLHPDCRDLIQQSWNTNVVGCPMFILNQKLKYLKHKLKIWNKNV FT FGDVNILVKEAEQKLISFKLKLTSMVLLMLFLINKKMHK" FT CDS join(2531..5080,5084..5524) FT /product="SHALINE6_MT_2p" FT /translation="MITEPDQISNHITNHFQNIFSTNFSVQDLQVDDLIDG FT VIPNLITDDMNQLLTMLPTHQEIHKAVWSLNKDSAPGPDGFGAIFYQTYWD FT IVKKDVINAVLEFFTKDWILPNFNSNTIVLIPKVHDALSVTQYRPIAIANF FT KFKIISKILADRLAPIMKNIISTQQRGFIQGRNIRDCICVASEAINQLHNK FT SFAGNLAFKVDISKAFDTLEWKFLLKVLSSFGFNDKFCSWINTILNSATLS FT IYVNGKLNGYFNCKRGVRQGDPLSPLLFCIAEDVLSRNISKLVDQGKLELI FT KGTRSVKVPSHSLYADDIMIFCKGKLSSINALMDLFNSYALASGQVINPSK FT STVYYGSISNARLEQITNLIGFNKGSLPFSYLGVPIFKGKPKKSHLQPIAD FT KIKSKLSAWKASLLSIAGRVTLVKAVIQSMMMHTISMYSWPNSLLKDVEAW FT IRNFIWSGDVSKRKLVTVSWKKVCKPFSEGGLGLRSLYTLNEATNLKMCWD FT LKNSSEDWAILLRSKVLRGRKVISHHIFSSIWSSVKSEINNINDNCSWIIG FT NGENINFWLDTWVEKSIASFLNFPDIVHSTLTTRVSDYIHNSLWHIPQSIL FT DSYPILSQLVMQITLPRDPKDDKLVWKTSSTGDLSLKEAFLFKYGTGQNIS FT WAKDXWSPDIPPSKSLMTWRLMHNKLPTDDNLALRGCNLPSMCSSCQAYEE FT TSFHLFFECPFASKMWSWLASLLNMPLIFNSXMDIWTILENSWTPQCKVVI FT QACIINFLNIIWFRRNNIRFQDKTVDWRTAINLIISKVSLSGNLTTKTAAA FT NMLEFTILKACKVNIKPPRASMIKEVIWAPPMHSWVKVNTDGASIKNPRAA FT AGGIFRNSEGVCLGGFSQFLGNANALYAELIAAMNAIEIAALMGFSNVWLE FT SDSQLVIFAFKSKSVVPWSLRNRWENCIQSTHRMRFCASHIYREGNICADR FT LANFGLSLSSSELFWFDNIPDFVRGEYNRNRLGMPNFRYVTF" XX SQ Sequence 5627 BP; 1734 A; 1030 C; 1070 G; 1786 T; 7 other; caaaaaaacc acccaaaaat ctacccaact cagatctttt gcacaagccc taaccaacat 60 atgtgataca ccatcaagcc agctcccaaa acccacaatc aagggtgaca aattctcaat 120 ttcaattcct gatgatgagt atgatttggg tatggaggcc tgcaagaaca acttgcatgc 180 tcgaatcatt tggccgaaag gtacagctcc tttaactgtt gttgctctaa aagaaaagtt 240 gaaacctgtt tggaaaaatc tagctccttg gggtgtcacc tctattggaa aagggtacta 300 tgagtttgtc ttctcatctt tgaagatgca agaagagtgc gatcagttgg gtcatggatg 360 ttaaatcctg ggttattgaa actatttcca tggagtaaag actttagtcc taacctacaa 420 acaaatactt ctgcacaagt ttggcttaag attcatggat tagcacagga gtactggagg 480 aaaagaatca tctttgcaat tgctagtagt gtgggcactc ccatttgtgt cgacgctgta 540 acaagcaaac cggcaattga aagaacgttt ggtcattttg cgagagtttt gatcgatatt 600 gatttgagta aagagctgag atacgaggtt cttgttgaac gtaagggata tgcattcttt 660 gtggagttgg aatatgaaaa tgtgcctgaa ttctgtgctt attgcagggc tgtaggacat 720 catgtaaatg tttgcagagc cggtaataga aatgttcaca ccaggaaaat aataaagcga 780 gccagctgag aaaattcagg acaaaggtaa ggcttggtga aacagaatgt tgtttggact 840 gcgaaagata cacctgttat tgacctagac atagagaatt ctagtaagca aatacagcag 900 gatgctgata aggacgaagg gatgaaagaa ggaacacaaa agactcaaca acatgaaata 960 gatgcaagga atttaactcc cctgttgctg ctctgaaccg taatgaagag ttccctgctg 1020 atggtcaaga aagtgaagca agcactcaag aatctgaatt cgtaaacgcc acacagctga 1080 acaatgatgc caatgagcat gattaagtcg gagcaagact catctgcaag ggtacgaaac 1140 aatatgcatt ttctgaatca atcatgggcc aatgtagtga atgattaagc aacaagaagc 1200 agattctaag acaaatgagg cagacataag cgcaaattca aaatgaacaa caacattgct 1260 gctcaggttt carytagtca ctacaaaaag aaataagaag aatggtcaaa aagccaacaa 1320 ctcaaaggca gtgcttcgta ccttaccaga tctaaggttc caactaaacc tttcaaatga 1380 agtgcatatt ctggaatatc aggggtttag ctaactcccc gtcaaggtta gctctcaaaa 1440 atttaatttt acaacataag cctgatttta tctttatttc tgaaccctgg atcttatttg 1500 aacatttccc aagacactgg tttaacagac tgcacttcaa actttttgcc ctaaataata 1560 ggaatcactt agactccaat ctttggtgct tttgcctaaa tcacttaaac cctatccttt 1620 tttctaccga tgatcaacaa atatcctttt caattcaaga atacaacgta atctactgta 1680 tatccgctat atatgcttca aacagttaca taaaaaggag acttttatgg caaacccttg 1740 aaattaacca aacacaatat aatattccct ggtgctttat cggggacttc aataccattt 1800 taggatccca tgaacataga ggtgcctatc gtcctgcaag ggcccctatg aatgattttc 1860 ttgcatggtc agatactaat aatctctttc acattcccac tagaggagtg cagtttacct 1920 ggtccaatgg taggagaggt cgaaggttca cagaaagaag gttagataga gcaatatgta 1980 atcaagaatg gttagatttg tgttcttcat tatatgtttc taccttaact aaactgaagt 2040 cagatcactt tcctttgttg atggagtttg aaactgtgac aacaccattt gcttcccaat 2100 ttaaatttct caaaatgtgg agccttcacc cagattgtag agaccttatt caacaaagtt 2160 ggaatactaa tgtagtaggg tgccctatgt ttattcttaa tcaaaagctg aagtacctca 2220 aacacaaact taaaatttgg aacaagaatg tctttggcga tgttaacatt cttgttaaag 2280 aagctgagca aaagttaatt tcattcaagc tcaaattgac atcaatggtg cttctgatgc 2340 tcttcttgat caacaaaaaa atgcacaaat agctttagag tatgctttgg agaaagaaga 2400 agccttttgg agagaaaaat ccaaaatttc gtggcactct caaggggaca gaaacacaaa 2460 atatttccac agactagcca aaatcaaaaa cacctctaaa cttatcactt ccattctgga 2520 tggggagaac atgattactg agccggatca aatctcaaat catattacaa atcactttca 2580 aaatattttt tcaactaact tttctgtgca ggatttgcag gttgatgatt taattgatgg 2640 agtaattcct aatctaataa ctgatgacat gaatcagttg ctcactatgc ttcctactca 2700 tcaagaaatc cataaggctg tttggtcttt gaacaaggat agtgcccctg gtcctgatgg 2760 gtttggtgca attttttatc aaacttattg ggatattgtc aaaaaggatg ttataaatgc 2820 agtattagaa ttttttacaa aagattggat tcttccaaat ttcaattcta acaccattgt 2880 tcttattcca aaagtccatg atgcattgtc agtgactcaa tataggccaa tagctattgc 2940 taatttcaaa ttcaagatta tttccaaaat tctagcagat aggttagctc ccatcatgaa 3000 gaatatcatc tctacacagc aaagaggttt tattcaagga agaaacatca gagattgtat 3060 ttgcgttgct tcagaagcta tcaatcaact tcacaacaag tcttttgcag gaaacttggc 3120 tttcaaggta gatatttcta aagcttttga cactttagaa tggaagttcc ttctcaaagt 3180 cttaagcagt tttggtttta atgataaatt ttgctcttgg attaatacaa ttcttaactc 3240 tgccactcta tctatttatg ttaatggtaa actgaatggt tattttaatt gcaagagagg 3300 ggtgagacaa ggtgaccctc tatctcctct tcttttttgc attgctgagg atgttttaag 3360 caggaacatt tctaaacttg tggatcaagg caagcttgag ctcatcaaag gtactagaag 3420 tgtcaaggtt ccttctcact ctctttatgc agatgacata atgatatttt gtaaaggaaa 3480 attatcttca attaatgctc tcatggatct gttcaattct tatgctctgg cttctggcca 3540 agttatcaat ccctccaagt ctactgttta ttatggttct atttctaatg ccaggctaga 3600 gcaaataact aatcttatag gttttaataa aggttctctt cctttttctt accttggagt 3660 tccaattttt aaagggaaac caaaaaaatc tcatttgcag cctattgctg ataagattaa 3720 gtctaagctt tctgcttgga aagcctctct tctatctatt gcaggtagag tcactcttgt 3780 gaaagctgtg attcaaagta tgatgatgca cacaatctct atgtactctt ggcccaattc 3840 cttgttaaaa gatgtagaag cttggatcag aaattttatt tggagtggtg atgtatctaa 3900 aaggaagctg gttactgttt cttggaagaa agtgtgtaaa cctttttcag aaggtggctt 3960 gggtttgagg tctttgtata ctctgaacga agcaactaat ttgaagatgt gctgggatct 4020 taaaaattct agtgaagatt gggcaattct ccttagaagc aaggttttra ggggcaggaa 4080 agtaatctct caccatattt tctcttctat ttggagcagt gttaaatcag aaatcaacaa 4140 catcaatgac aattgcagct ggatcatagg taatggagaa aatattaatt tttggcttga 4200 tacctgggtg gagaaatcta ttgcttcttt tcttaatttt ccagatattg ttcatagcac 4260 tctaacaact agggtctccg attacattca taattctctc tggcatatcc ctcaatctat 4320 cttggattct taccccattc tgagtcaact tgtcatgcaa attactcttc ctagggatcc 4380 gaaagatgat aaacttgttt ggaaaactag ttcaacgggt gatctatctc tcaaggaagc 4440 ttttctattc aagtatggta ctggtcaaaa tatttcttgg gccaaggatw tttggagtcc 4500 ggatatccca ccttcaaaat ctttgatgac ttggagactc atgcacaaca agctccctac 4560 cgatgataat cttgctctta gaggttgtaa cctaccctca atgtgttcat cctgtcaggc 4620 ttatgaggaa acctcttttc atttattctt tgaatgccct tttgcttcwa aaatgtggtc 4680 ttggctagca tctcttctca atatgccgtt gatcttcaat tctycgatgg atatttggac 4740 tatcttagaa aatagctgga ctcctcaatg caaagtagta attcaagctt gcatcatcaa 4800 ttttttaaac atcatctggt ttaggaggaa caacattcga tttcaagata agacggttga 4860 ttggagaaca gccattaact tgattatttc caaagtctct ttatctggga accttaccac 4920 taaaactgct gctgctaata tgttagaatt cacaatttta aaagcttgca aagttaacat 4980 caagcctcct agggcttcta tgatcaaaga agtcatttgg gctcctccta tgcattcttg 5040 ggttaaggtg aacacagacg grgcatctat caagaatcct tgaagagcag cagctggtgg 5100 aatttttaga aactctgagg gtgtttgttt aggtggattc tctcaatttc ttggtaatgc 5160 taatgctctt tatgctgaac taattgcagc aatgaatgct attgaaattg ctgccttgat 5220 gggattctcc aatgtttggt tagagtcaga ttctcagtta gtgatttttg ctttcaaatc 5280 caaatctgtt gttccttgga gtttaagaaa taggtgggaa aattgtattc agtctaccca 5340 taggatgaga ttctgtgctt ctcatattta cagggaagga aatatttgtg cggacagact 5400 tgctaatttt ggtttgtctt tatcttcttc agagttgttt tggtttgata acatacctga 5460 ctttgttagg ggggagtaca ataggaatag gttgggtatg cccaacttta ggtatgtcac 5520 cttttgaaaa ggttttggtt tagtccccct tttctctttt gtacttcttt tctctttaat 5580 gaaatgatta gatgctcttt gcatcttttc taaaaaaaaa aaaaaaa 5627 // ID Copia-88_Mad-I repbase; DNA; EDCOT; 5190 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-88_Mad_; KW Copia-88_Mad-LTR; Copia-88_Mad-I. XX NM Copia-88_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5190 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1714-1714 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [2406-2933] - Integrase core CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS 478..1677 FT /product="Copia-88_Mad-I_1p" FT /translation="MAESNVRIENLLGMLTVKLQDDNFVKWSYQFSSVLRG FT YDLFDFFTGEAPCPPKYVIDTESGVTNEINAAYKDWVKKDLALLSLLIATL FT SDDAMEHVIGCKTSYEAWKCLQERFASVSMVRVNQLKTELHTAQKGGDSVD FT KFLMRLKGIRDQLVSAGEKVTDNDFIIAVLSGLPADFEMIKTVILARDSPM FT SIKDFRAQLLVAEGSIESRMHSLSSSMSAMVVQGEGLVYKAFKGMNMVRVP FT ILRGLRLVSAMINSVTTFREEMVLMISLVVIFREEMVFQELEMVMVVEVFS FT LHREEILIIESLEVGITIPGFHQGLITEMGIMVTLEVVRVLQDMNMQVMVS FT PQLIHLLAMAILSPIGMGIPTLSTRYHLNVRYVREGDTLHQTATIELRVEV FT HSLLVL" FT CDS 1785..3458 FT /product="Copia-88_Mad-I_3p" FT /translation="MTAQANVTQTEGSGVGFTAEENWILDSGATHHMTANL FT NHLNHVIPYTGDGTITIGNGTGLEVTHIGSTSIPISKQSLMLRNVLCVPKI FT TVNLLSVKKLCRDNGCWFICDDVVFFIQDKATRKILYTGTSDDGELFSIPV FT NVFAKSFAAKLEHCAGFVGKKIQVSRWHKRLGHPSEEVLAVMLKKFNNSVK FT VDSCESICSSCMSGKMRRQSFPVRQNTATCLFEKVHTDVWGPSPKVSVQGY FT RYYVSFVDEYSRFLWIFPMNNKSEVFSVFVKFRAFIQTQFSASLKCLQSDG FT GGEYTSRTFVDFLDTKGIKHMISCPYTPQQNGLAERKHRHVVETAVTLMTE FT AKLPAQFWFHACSHAAFLINRMPCRILHMKSPYQVLIGQEPDVQNLKIFGS FT AVYPFMRPYNANKLEPRTTQCVFLGYMMGYKGVVCYNIGSGKLILSRHVVH FT DEEIFPYRNIQVSKIQQSSSSSSQNSRPIAIQLPRDTITPSPVHQDRGSAQ FT AIEVISHSQGSDPVASGNSDMVVSQSSESAVVSILIIRFHLLTIISQVHRF FT KVTNFSSNCIT" FT CDS 3493..4881 FT /product="Copia-88_Mad-I_2p" FT /translation="MVTRLKSGAIQRKNYAALTATFPELNTLQITNDDPFV FT GGFSFISEIADSLEPTCFRQAASISHWQHAMQEEYDSLRIQGTWNLVPAPD FT HRSIIGSKWVYKVKRNPDGTVSRYKARLVAQGFSQEHGVDYSDTFSPVVRH FT TTVRLILALAAMNKWELKQLDVKNAFLHGELQEEVYMKQPQGFVDSSHPNY FT VCKLLKSLYGLKQAPRAWNSKFTSYLVTMGFTASVSDTSLFIKTDNNDIII FT LLLYVDDIILTGSCVTKVQLVVQELSSVFDLKDLGKLTYFLGLQIQYKPNG FT DIFVNQSKYIKDLLHKAGMDSCKPANTPCKPHNQMMMTEGELLSDPSSYRS FT IVGSLQYLTFTRPDIAFAVNTVCQHMHSPTEVHFGAVKRILRYLHGTMQRG FT IVYSSQSQMHLTAFSDSDWAADLNTRRSVTGYIVFLGEILFRGNRRNKLQC FT PEVLRKLNTKPLLIQLLM" XX SQ Sequence 5190 BP; 1528 A; 859 C; 1147 G; 1655 T; 1 other; tggtatcatc gccgtgtacg ttccttcgtg gctatcgtct tccgctcatg gtggttgttg 60 ccggagatct ttcttggtga cagtctcgaa ttcgtgaagt ttaatcagtg ttgtgcgttc 120 agtcggaggc ttggtgtttc ttgaaagtac agtatgtttt ctgcactcta tctgtttgtg 180 aaaatgtctc aaggttattt cttctgggtt tgttgatttt tttgtgcgaa agaaaacaag 240 gccgatgcca tctttctgca atcttgattt gagatataag gccgaagcca ttatctcggt 300 gtaaatgttg tttcctccat aaggccgatt gccggagtgt agttcttgtg caattctgtt 360 ctctttcttc attaaaggcc gattgccgaa gagaggtgta tttcttgatt tctgtggtta 420 tatatcttgt tgtttgaaat cttgggttgt acttttgata atctttagtg tgtgaagatg 480 gctgaatcta atgttagaat tgagaatttg ttagggatgt tgacagtaaa gctgcaagat 540 gataattttg tgaaatggag ttatcaattt tcatctgtgt tgagggggta tgatttgttt 600 gacttcttta ctggagaagc accatgtcca cctaagtatg tgattgatac agaatctggg 660 gtcacaaatg aaattaatgc tgcttacaaa gattgggtga aaaaggatct agctttgtta 720 agtttgctaa ttgcaactct ttcggatgat gctatggaac atgtgattgg gtgtaaaaca 780 tcttatgaag cttggaaatg tttgcaagaa agatttgcct ctgtctcaat ggttcgtgtg 840 aatcaactta aaactgaatt gcatactgct cagaaaggtg gtgattcggt tgataaattc 900 ttaatgagac taaaggggat aagggatcaa ttagtatctg caggagaaaa ggttactgat 960 aatgatttca tcattgctgt tctttctggt ttgcctgctg actttgagat gattaagaca 1020 gtcatattgg caagagattc tcctatgtct atcaaagatt ttcgagcaca attgcttgta 1080 gcagaaggca gtattgaatc tagaatgcat tctttatcta gttctatgtc tgctatggtt 1140 gttcaaggtg aaggattggt ttacaaggct ttcaagggta tgaacatggt gagagttcca 1200 attctcagag gtctcaggtt agtctcagca atgataaatt cggtaacaac tttcagagag 1260 gaaatggttt taatgatcag tttggtagta attttcaggg aggaaatggt ttttcaggaa 1320 ttggaaatgg taatggtagt agaggttttc agtcttcaca gagaggaaat tttaataata 1380 gaaagtttgg aggtgggaat cacaattcca ggttttcatc agggtttaat aacagaaatg 1440 ggaataatgg ttactctgga agtggtaaga gtgttgcagg atatgaatat gcaagtaatg 1500 gtttcacctc aactaattca tctgctggcc atggcaattc taagtccaat tggaatggga 1560 ataccaactc taagtactcg gtatcacctg aatgtcagat atgttcgaga aggggacaca 1620 ctgcaccaaa ctgctactat agagctgaga gtggaggttc acagtcttct ggttctgtaa 1680 tctgtcagat atgtggaaag agggggcaca tagctcttga atgctttcac aggaacaact 1740 ttgcatatca gggaaatcct ccaccaccac catcgattgc agctatgaca gctcaagcca 1800 acgtcactca aactgaagga tctggtgttg gttttactgc tgaagaaaac tggatattgg 1860 attcaggtgc aactcatcac atgactgcaa atttaaatca tcttaatcat gttattcctt 1920 atactggtga tggaactatt acaattggga atggtacagg attggaagta acacatattg 1980 gttccacaag cattcctatt tctaaacaat ctttgatgtt aagaaatgtg ctttgtgtac 2040 ctaaaatcac tgtgaattta ctttctgtta agaagttatg cagagataat ggatgttggt 2100 ttatatgtga tgatgttgtc ttcttcatac aggacaaggc aacaaggaag atactgtaca 2160 cagggacaag tgatgatggg gagctgtttt caattccagt caatgtcttt gcaaagtctt 2220 ttgctgcaaa gttggagcac tgtgctggtt ttgttggaaa gaagattcaa gtgtcaaggt 2280 ggcataagcg gttaggacat ccatcagagg aggtgcttgc tgtaatgctg aagaagttta 2340 ataatagtgt caaagtagat agttgtgagt ccatatgttc ttcttgtatg agtggtaaaa 2400 tgagaagaca gtcgtttcca gtaagacaaa atactgctac atgtttgttt gagaaagttc 2460 acactgatgt atgggggcca tctccaaagg tgtctgtaca gggttataga tactatgtga 2520 gctttgtaga tgaatattca cgatttttgt ggatttttcc aatgaataac aagtctgaag 2580 tgttttccgt atttgttaag ttccgtgctt ttatacaaac tcaattcagt gcttcactta 2640 agtgtttaca atctgatgga gggggagagt atacaagtag aacgtttgtt gattttttgg 2700 atacaaaggg tataaaacac atgatttcgt gtccttatac ccctcagcaa aatggacttg 2760 ctgagaggaa acacagacat gtggttgaga ctgcagtgac actcatgaca gaagcaaagt 2820 taccagctca attttggttt catgcctgtt cacatgctgc atttctaata aacagaatgc 2880 catgtagaat attgcatatg aaatcaccat atcaggtgtt aattggacaa gaacctgatg 2940 ttcaaaatct gaagattttt gggtctgcag tgtatccatt catgaggcct tataatgcaa 3000 ataaacttga accaagaaca actcaatgtg tatttctggg atatatgatg ggatataagg 3060 gagtagtatg ttataacatt ggttcaggga aattaattct ttctagacat gttgtacatg 3120 atgaagagat atttccttat cggaatatac aagtgtcaaa gatacaacag tctagttctt 3180 catcttccca gaattcaagg cctattgcga ttcaattacc aagggatacg attactccat 3240 ctccagtgca tcaagataga ggatctgcac aagctataga agtcatttca cattctcaag 3300 gctcagatcc agtagcttca ggaaattctg atatggtagt gtctcaatct tcagagtctg 3360 cagtagtcag cattctgata atcaggtttc atcttctcac catcatttct caagtccaca 3420 gattcaaggt taccaatttc tcaagcaatt gtatcacatg atattcaagc acagaatggt 3480 aatgaacatt caatggtgac aaggttgaag tctggtgcta tccaaaggaa aaattatgca 3540 gccttaactg caacatttcc agagttaaac actttgcaga taacaaatga tgatcctttt 3600 gtgggaggtt tctcttttat ttcagagatt gcagattcat tagaacctac atgctttaga 3660 caagcagcat ctatttcaca ttggcaacat gcaatgcaag aggagtatga ttcacttcga 3720 attcaaggta cttggaattt agtacctgca ccagatcaca gatcaataat aggaagcaaa 3780 tgggtgtata aggtgaaaag aaatcctgat ggtactgtat caaggtataa agcaagacta 3840 gttgctcaag ggttttctca agagcatggt gtagattatt cagatacttt tagtccagtt 3900 gtgagacata caactgtaag actcattctt gctttggctg caatgaataa atgggaattg 3960 aaacaacttg acgtcaagaa tgcatttctg catggtgagt tacaagaaga agtttatatg 4020 aaacagccac aagggtttgt tgattcaagt catcccaatt atgtatgcaa actcctcaag 4080 tcactatatg gactcaaaca agccccaagg gcttggaatt caaaatttac aagctacttg 4140 gtgacaatgg ggtttactgc atcagtatct gataccagtt tgttcatcaa aactgataac 4200 aatgatatca tcatactatt gctctatgtt gatgatataa tattgactgg atcatgtgtg 4260 actaaagtac aactcgtagt tcaagaactc tcttctgtgt ttgacttgaa ggatttgggg 4320 aagctgacat atttccttgg tttacagatt caatataaac caaatggaga catttttgta 4380 aatcagtcga aatacataaa ggatttactt cataaggcag gtatggattc ttgcaagcct 4440 gctaatacac catgtaaacc acataatcaa atgatgatga cagaaggaga gttactttca 4500 gatcctagtt cgtacagaag cattgttggt tccttgcagt atcttacgtt tactagaccg 4560 gatattgcgt ttgctgtgaa tacagtttgt caacacatgc attcaccaac tgaagttcat 4620 tttggtgctg taaaaaggat tcttcgatac cttcatggta cgatgcaacg tggcatagtc 4680 tattcttcac aatcacagat gcatctcacg gctttctctg attctgattg ggctgcggat 4740 cttaatacca gaagatcagt gactggatat attgtttttc ttggagaaat cctatttcgt 4800 ggcaatcgaa gaaacaaact tcagtgtcca gaagttctac ggaagctgaa tacaaagccc 4860 ttgctcatac agctgctgat gtagcttggg ttagacacat tttgagggat ttgaagtgtg 4920 ttttacttca accacctgtt attaattgtg ataacatgtc agctattgca ttaagttcga 4980 atccagtgtt tcactcaaga atcaaacact tggataccga ttatcatttt gtaagggaga 5040 gggtacaaaa aggagatctt gccgtggcmt atgttcctac tgatgagcaa actgccgatg 5100 ttctaacaaa gggtcttcac agtcctgcat ttatcagaca ttgctacaat ctgaagcttg 5160 gcaccccaag cttagattga ggggggatgt 5190 // ID Copia-5_Mad-I repbase; DNA; EDCOT; 4456 BP. XX AC ACYM01007529; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-5_Mad-I; KW Copia-5_Mad-LTR; Copia-5_Mad_. XX NM Copia-5_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4456 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1285-1285 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01007529; Positions 8230 3775. XX CC Positions [1891-2181] - Integrase core CC 'TTTAT' target site duplication CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 206..2050 FT /product="Copia-5_Mad-I_1p" FT /translation="MHFIDGSSECPPPFLKDDAGQLTTTVNPDYEDWIQKD FT QLVLSWINGFLGLQALSATARHQSARDVWAALQHRYASHNQSRIIQLRTDY FT LDRINSLADSLALAGSPITDIDLVSVIMFNVGPKFENTVAVAQARETPVSY FT VDLEALLFSTELRLADPTHAVDHSIQAMAASRNRDSSRGGGRSFSGRNDGR FT STRGGGSYRGNSNASWNSNRGERNGGFYRGTPNASGNSNRGQQAPGLLGLA FT PNQHHASSSSTFGESRIKCQICGGLGHPAIDCFNRMNLAYERRIPSKRLTA FT MVAQAPQSDKPWLLDSGANSHITNDLGKLILTREYRGNDSVGGVLGGPGLP FT ISHIGNSTLSSNNLTFKLQDVLHCPNASTSIVSAYQFMKDNGCFITLFLDY FT FFVQDSVTAKILFWGKNRDGVFPIHSSSKDFHGHVAMLGVRVGSNIWHSRL FT GHPSSQVFQFLFSRNKLPSSGKISMNNFFCHSCPLGKSIKLPFSPSLSVTS FT HPLELIHSDVWNASNLSISGYKYYVLFVDNYSRYSWIFPMRLKSEVYSIFV FT SFKTMVENQFSTKIKMFQSDGGVNILVLNLNFFLLNMGFIIVFLVLTIPSK FT MVWRSVSIATLSTLGSP" FT CDS 2625..4355 FT /product="Copia-5_Mad-I_2p" FT /translation="MPTSSITTQPAPPVHSSPTVPQQPTPAPLHVYHRKNS FT RPPASEPVPPTSSRHPPVPATSSVREMNAHSMVTRSKSAGLKSNSKYAHFA FT DASVSPNVFFEPTCFSQANKFPEWRQAMADEFNALQRAGTWVLVPRTCSMN FT ILPNKWVFRIKRNFDGSIQRFKARLVANGFHQQPGLDYGETFSPVVNHSTI FT RLILALSVQFRWPVRQLDVQNAFLHGFLSEDVYMRQPSGFVDSQFPDHVCK FT LQRSLYGLKQAPRAWFQCFSSHLEDLGFTPSQADTSLFIYLLGSIRIYLLI FT YVNDILITGNDLSHITQLIADLGRRFSMKDLGPAHYFLGMEIVRTSDGLSL FT SQHKYVQDLLSRTKMAAAKPVHTPAVSGRRLSLQDGDPLPDPMEYRSVVGT FT LQYLTLTRPDIAFPVNQVCQFMHQPTSQHWLAVKRILRYLVGTPSHGLTYK FT PGSILLTAYSDADYAGDPDDRRSTGGYCIYLGSNLVSWSSKKQGGVSRSST FT EAEYRQLAYTAAAISWFRKLFHDLRLPLYCPKVHCDNISAISLASNPVFHA FT RTRHVEVDYHYVREKVVRNELKVLYLSTHD" XX SQ Sequence 4456 BP; 1001 A; 1174 C; 811 G; 1465 T; 5 other; tggtataaca gagcccttga ctaatcgtcc aatttttttt tctcttctct actgtctcct 60 aatkkctgcc actaccaaga ctccctcttc cgctgaacct tccaccttcc ccaatgtttc 120 ccatgtcatc actatcaaac ttgataccac caactaccct ctctggcttg ctcagattgt 180 accggttatc aaaagtcgcc gtctgatgca ctttattgat ggttcttcag aatgtcctcc 240 cccttttctt aaggatgatg ctggccaact taccaccact gtcaatcctg attatgagga 300 ttggattcag aaagatcagt tagtcctttc ttggatcaat gggtttcttg gcctccaggc 360 tctttctgca actgctcgcc accaatctgc tcgtgatgtc tgggctgctt tgcagcaccg 420 atatgcttcc cacaatcaga gtcgcatcat tcaacttcgt actgactacc tggatcgcat 480 caactctctt gctgatagtc tggcgctcgc tggttcgccg atcactgata ttgatcttgt 540 ttctgtgatc atgtttaatg ttggacccaa gttcgaaaac accgttgctg ttgcccaagc 600 tcgtgaaact ccagtgtctt atgttgattt ggaagccctt ctcttctcta ccgagcttcg 660 cctcgctgat ccaactcatg ctgttgatca ctctattcaa gctatggcgg cttctcgcaa 720 tcgcgattcc tctcgcgggg gtggtcggtc cttctctggt cgcaacgatg gccgctccac 780 tcgtgggggt ggttcctatc gaggcaactc taatgcctct tggaattcta accgtggtga 840 acgtaatggt ggcttctatc gaggcactcc taatgcctct ggaaattcta atcgtggtca 900 gcaagctcca ggtcttttag gcctagcccc aaatcagcat catgcatcct cttcttccac 960 ctttggtgag tcccgcatca agtgtcaaat ttgtggtggt cttgggcatc ctgcaattga 1020 ttgtttcaac cgtatgaatc tggcgtatga aaggcgtatt ccatctaagc gtctcacggc 1080 tatggtggct caagctcctc aatctgacaa accttggctt ctcgattccg gtgctaattc 1140 tcacatcacc aatgacttgg gcaaactcat tcttactcga gaatatcgtg gcaatgattc 1200 tgttggcggt gtgcttggtg gaccaggttt gcccattagc cacatcggta actcaacctt 1260 atcatcaaat aacctcactt ttaaactgca agatgtcctc cactgcccta atgcttcaac 1320 ttccattgtc tctgcatatc aatttatgaa agataatggt tgcttcatta ccttatttct 1380 tgattatttc tttgtacagg attcggtgac ggcgaagatc cttttttggg gcaagaatag 1440 ggatggtgtt tttccaattc actcctcatc aaaagatttt catggtcatg tagcaatgct 1500 aggtgttcgt gttggtagca atatttggca ttctcgtctt ggtcatccct cgtctcaagt 1560 ttttcaattt ttattttcta gaaataaatt gccttcttct ggcaaaatct ctatgaataa 1620 ttttttttgt cattcatgcc ctttgggcaa aagtattaaa cttccttttt ctccatcctt 1680 gtctgttaca tctcatcctc ttgaactcat tcattctgat gtgtggaatg cttcaaattt 1740 atccattagt ggttataaat attatgtttt atttgttgac aattattctc gttattcttg 1800 gatttttcca atgcgcttaa aatctgaagt ttactccatc tttgtttcgt ttaagactat 1860 ggttgagaat caattttcta ctaaaattaa aatgtttcaa tcagatgggg gggtgaatat 1920 actagtactc aatttaaatt tttttttact caacatggga ttcatcatcg tctttcttgt 1980 cctcaccatc ccgagcaaaa tggtttggcg gagcgtaagc atcgccacat tgtcgacact 2040 gggctcacct tgatggccca agcgtcgatg cctcctgctt attgggccga ggccatgcac 2100 actgcggtat acttaataaa ccgtcttcct tccaagattt tagattatga tactcctttt 2160 caaaaactgt ttggcaaaga acccaattat acctttttaa aaacatttgg ttgtgcatgt 2220 tttccatact tgcgtcccta taataataat aaactacgtt atcgttctac caaatgtgtg 2280 ttcttagggt actctttgaa ttatcaaggg tatagatgct tagatatttc aaccaaccga 2340 atttttttct cacgccatgt tcttttttat gagttaaatt ttccattttc tgagttatcc 2400 tctactcttg cctcccacaa gacatcttcg tccccggatc ccgcgcttga aattattggg 2460 cccctcccca cacacacatc ctagcacacs tcmccccttg ctaaacctat tacccagatg 2520 ccaacatctt cccmaccccc ccaagcggtg cacctcacca ccacccaacc ggtgcaatcc 2580 aacatcatac atcctacccc accctaccta ttccccccgc ctcgatgccc acctcatcca 2640 ttaccactca acctgcacct cctgttcact catcccctac tgtcccgcaa caacctacac 2700 ctgccccctt acacgtttat caccgtaaaa attctcgccc tccagcctct gaacctgttc 2760 cgccaacttc ttcaagacac ccacctgtcc ccgccacgtc ttcggtaaga gagatgaatg 2820 ctcattctat ggtgactcgg agtaaatctg ctggtcttaa gtcaaattca aaatatgctc 2880 attttgcgga tgcttctgta tctcctaatg ttttctttga gcctacttgt ttcagtcaag 2940 caaataaatt tcctgagtgg cgtcaagcaa tggcagatga attcaatgct cttcaacgag 3000 ctggcacttg ggttcttgtt ccccgtactt gttcaatgaa cattttgcca aataaatggg 3060 tcttccgtat caagaggaac tttgatggct ctatccaacg attcaaagcc cgccttgttg 3120 ccaatgggtt ccatcagcaa cctggactcg actatggcga aactttcagc cccgtggtca 3180 accattccac cattcgtctc atccttgctc tttctgttca gtttcgatgg cctgttcgtc 3240 agcttgatgt tcaaaatgca tttctacatg gttttttatc tgaagacgtc tatatgcgcc 3300 agccaagtgg ttttgtggat tctcaattcc ctgatcatgt ttgtaaactt cagcggtctc 3360 tctatggtct taaacaagcc cctcgggcat ggtttcaatg tttctcttct cacttggagg 3420 atttgggttt cactccatcc caggccgaca catctctttt catttatctt cttggatcca 3480 tacggattta tttgcttatc tatgtcaatg atattttgat cacaggaaat gacttgtctc 3540 acattacaca gttgattgcc gacttaggtc gtcgattctc tatgaaggat ttaggccccg 3600 ctcattattt tcttggcatg gagattgttc gaacctcgga tggcttatct ctttctcaac 3660 ataaatatgt gcaggatctt ctatcacgta cgaaaatggc agcagctaaa cctgttcata 3720 cccccgctgt cagcggtcga agactcagcc ttcaagatgg cgaccctctt ccggatccca 3780 tggaatacag aagtgttgtc ggtactctcc aatatctcac tctcacacgt cctgacattg 3840 cgtttccagt caatcaagtc tgccaattta tgcatcaacc tacctctcaa cattggttag 3900 ctgtcaaacg tatcctacga tatctagttg gtactccctc tcacggtctt acatacaaac 3960 ctggctccat tcttctcact gcctattctg atgccgacta tgccggtgat cctgatgacc 4020 gacgttccac tggtggatat tgcatttatc ttggttctaa ccttgtctct tggagctcta 4080 agaaacaggg tggtgtttct cgttctagta ctgaagcgga gtaccgccaa cttgcctaca 4140 ctgcagctgc gatatcctgg tttcgtaagc tttttcatga tcttcgactt cccctgtact 4200 gtccaaaagt ccattgtgat aacattagcg caatatcttt agcctccaat cctgtatttc 4260 atgcccgcac tcgtcatgtt gaggtagatt atcactatgt tcgtgaaaag gttgttcgga 4320 acgagctgaa agttctttat ctttcgacac atgattagat tgctgacatc ttcaccaaag 4380 gtctgtccgt tactcgcttt cgctatcttt tgtccaagct tccagtgctc tttcgccccg 4440 tcagcttgcg ggggtg 4456 // ID Copia-55_VV-I repbase; DNA; EDCOT; 4587 BP. XX AC chr6; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-55_VV_; KW Copia-55_VV-LTR; Copia-55_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4587 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr6; Positions 19927412 19922826. XX CC Positions [1854-2354] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 897..2951 FT /product="Copia-55_VV-I_1p" FT /translation="MISGADTPLGAVMASKGIKGSHHQMPPKPGALSLSSG FT KSNSSFKTKPPSDGMKCTHCGNTKHTRDTCFKLHGYPDWWNDLQARKKREI FT IANDNHTGRAVVVTCDASLSLIPQAESSHDSGTSSKVFHISTHKDDEDWIL FT DSGATDHMTFDSKDFSNTTQPRRSCVANANGVTYPVTGAGTVTLSSSLSLS FT NTLLVPSLSNRLMSVSQVTSDLNCVVLMYSTFCLLQDILTKEIIGRGTKRG FT GLYYVDAFSSGRANHMHHKVGNKERQIWLWHHRLGHPSFGYLKHLLPGLFS FT KATHLDFKCDTCILAKSHRASYPMSMNKSMIPFYLIHSDVWGPSLVTTSSG FT HRWFVIFVDDCTRMTWLYLLKHKDEVFSIFQSFHAMVQTQFSARIKILRSD FT NGGEYVNQQFQTYFNNHGILHETSCSQTPQQNGIAERKNRHILETARALLI FT NAHVPNRYWSDAVTTVVYLLNRMPTKVLQFQTPLKVFSYHVSLPTVLMIPP FT RIFGCVAFVHLHKNQRTKLDPCAVRCLFLGYGVQKKGYRCYDPIAKRTYIT FT MDVTFLESEFFFSPISNSPLHGEIYGEERNWSDVEVLEVGDNPTHPNDDND FT LVEHDPVPEPLRTEAKPVPESSEDAEYDVFPHSLVPNDPPTENIPEVSSPT FT TPLQTNAIDTSAGYVLPFRHNRGKPPNRYSPDIEER" FT CDS 3417..4577 FT /product="Copia-55_VV-I_2p" FT /translation="MDIPPGYTATSEAKIACRLQRALYGLKQSPRAWFGRL FT SSAMRKYGFQQSNSDHTLFLKHRLGKITALIVYVDDMIITGDDVEEISRLQ FT DQLSTEFEMKNLGGLKYFLGIEVARSRQGIFLSQRKYILDLLAKVGLLECK FT PADIPIVQNHKLGEYVDQVPADKQRYQRLVGKLIYLSHTRPDIAYAVSVVS FT QFMHRPSEDHMDTVMRILRYLKSSPGKGLMFSKNGHLKVAGYTDADWAGNI FT TDKKSTAGYFTFVGGNLVTWRSKKQKVVALSSAEAEFRGMVKGICELIWLK FT KLLAEIGIAPSSEMNLFCDNTAAIAISHNPVQHDRTKHVEVDRNFIKQNLE FT EKIIQLPFVKSEDQLADVLTKAVSARNFYNSLDKLGIKDIYAPT" XX SQ Sequence 4587 BP; 1350 A; 991 C; 979 G; 1267 T; 0 other; tgactgtgac cggaaaaaaa ctccggaaga cccacctggt atcatcttca tcttcctggt 60 cagtttccag cgctgcttcc ctctgattcc tgctacctca cagtgctcca gccggttatc 120 cgttaatata caacaaatct tgtcaaacca gaaccgacaa actccatggc ggaatctaaa 180 gacataacac aacctctcat tccccagacc gattccatcc ttagcgatct aactacaaga 240 atgaccgagg tcctgactag agcccagacc tcccctcaac ctctgctgct gattcgtcaa 300 ctactccgat tggtatcaag ttggaaggat ccaactatgc cttatggtcc caggttgtcg 360 agatgtatat ctctggcaag gacaagctgg gatatatcaa tggagattct cctcagcctc 420 cagaaaccga tccttcattc aggagatggc gcaccgaaaa cgccattgtc aagggatggt 480 tgatcaattc aatggaccct tccttgattg ccaattttat ccgattccca actgcaaaac 540 aggtttggga ttctgctgct ataacctatt ttgatgggac agacacgtct caagtctatg 600 atctccgacg tcgggttact catatgaagc aggcgagtgg atccattgaa aaatactaca 660 acgaccttta agggttgtgg cgagaaatcg attttcatcg tcctaacccg atggagtgtg 720 ctattgacat acagaaatac aattccgttc tataggaaga tcgagtttat actttccttg 780 atggactaga tgacagattg gataaaattc ggagtgatgt tctacaaatt aaaccattcc 840 ctacggtgga acaggcctat gcatttgtcc gtagggaaga ggtcaggcag accgtgatga 900 tctcgggtgc agatactcct ctaggagcag ttatggcttc caaagggatc aagggcagcc 960 atcaccagat gccaccgaaa cctggagctc tctccctaag cagcgggaaa tccaactcct 1020 cattcaaaac taaaccacca tctgacggca tgaagtgtac ccattgcggc aacaccaaac 1080 acacccgtga cacctgcttc aaactacatg gatatccaga ttggtggaat gaccttcaag 1140 cacggaaaaa acgggaaatc attgctaatg ataaccacac tgggagagct gttgtggtta 1200 cctgtgatgc ttcgttatcc ctcattcctc aagccgaatc ttcacatgat tcaggtactt 1260 cgagtaaggt ttttcatatc tctactcaca aggatgatga ggactggatt ctcgactctg 1320 gggctacaga ccacatgaca tttgattcaa aggatttctc taatacaact cagccgagac 1380 ggagctgtgt tgcaaatgct aatggggtca cctatccagt tacaggggct ggaacagtga 1440 ctttatcttc ttccctttca ttatctaata cattacttgt accatctctt tcaaatagac 1500 tgatgtctgt aagccaagtt acttcagatc ttaattgtgt ggtattgatg tattctactt 1560 tttgccttct tcaggatatt ctcaccaagg agataattgg gcgtggtact aagagagggg 1620 ggttatacta cgtggatgcc ttcagttcgg gaagagcaaa tcacatgcac cacaaggttg 1680 gtaacaagga gaggcagatt tggttatggc atcatcgact tgggcatcca tcatttgggt 1740 atttgaagca cttactacct gggttatttt caaaggcaac acatttagat tttaaatgtg 1800 atacttgtat cttagccaaa agtcataggg cttcttatcc catgagcatg aataaaagta 1860 tgattccttt ttatttaata cattccgatg tttggggacc ttcactagta actacgtctt 1920 ctggtcatcg ttggtttgta atatttgttg atgattgcac acgaatgaca tggctttacc 1980 tcttaaaaca caaagatgag gtattttcta tttttcaatc atttcatgcc atggttcaga 2040 cacaattctc tgcaagaatt aagatccttc gttctgacaa tggaggggaa tatgttaatc 2100 aacaattcca gacatacttc aacaaccatg gtattctcca tgaaacctca tgttcacaaa 2160 ccccacaaca gaatggtatt gctgaaagga aaaataggca tatcttagaa actgcccgtg 2220 ctctattgat caatgcacat gtgccgaata gatattggag tgatgctgtt accacagtcg 2280 tgtatctact gaaccgtatg cccaccaaag tcttacaatt tcagactcca ctaaaggtgt 2340 tttcttatca tgtctcctta ccgactgttt tgatgattcc tccccgaatt tttggttgtg 2400 ttgcttttgt tcacctccat aaaaatcaac gaactaagtt ggacccatgt gctgtccggt 2460 gtttattctt ggggtatgga gtacaaaaaa agggatacag atgctacgat cccattgcta 2520 aaagaaccta cattaccatg gatgtcacct tccttgaatc tgaatttttc ttttcaccga 2580 tatccaattc ccctcttcat ggggagatct atggtgaaga acggaattgg tctgatgttg 2640 aagtgttaga agttggtgac aatccaacac atccgaatga tgacaacgac ttggttgaac 2700 atgatcccgt acctgaacct ctgagaactg aagctaaacc agtacctgaa tcatcggaag 2760 atgcagaata tgatgtattc cctcactctt tagtacccaa cgaccctcct actgagaata 2820 ttcctgaggt aagctctcct accacacctt tacaaactaa tgctatagat acatctgcgg 2880 gttatgttct acctttcaga cacaatcgag gcaagcctcc aaatcgatac tccccagaca 2940 tagaagaacg atgatccaag tatccaatag ctaatcatgt gtctacacaa agattatctg 3000 aacctctcag agcttttgca catacactct cctcatgtca gattccgagt agggttgaag 3060 aagctttctc ggatccgaaa tgggcttaag ctataaaaga agaattggag gcgttgcaga 3120 aaaataatac atgggttttg agtgtgttgc cggaagggag gaagacagtg gggtgcaagt 3180 ggattttctc tattaaatat aaagcagatg ggtcgattga tcgatacaag gcgaggttgg 3240 tagcaaaggg atatacacag aaacatggta tagattatca ggaaactttc tcacctgtag 3300 caaaactaaa aactgttaga gttctgttat ctcttgcagc aaacttagat tggccattgc 3360 accaacttga cgtaaaaaat gccttcctcc atggtgatct tgaagaggat atttacatgg 3420 atattccacc aggctacact gctacatcag aggcaaagat cgcatgtagg ttacaacgag 3480 cattgtatgg actaaagcaa tcacctcgag catggtttgg caggttgagt tcggcaatga 3540 ggaaatatgg atttcaacaa agcaactctg accacactct cttcctaaaa catcgattgg 3600 gaaaaataac agccctcata gtctatgtag acgacatgat aattacaggg gatgatgtag 3660 aagaaatatc caggcttcaa gatcaattgt caactgagtt tgagatgaag aacttaggag 3720 ggcttaaata ttttttgggc attgaagtgg caaggtcaag acaaggcata tttctttccc 3780 aaaggaaata tatactagac ttgctggcaa aagtgggatt actagagtgt aagcctgctg 3840 atattccaat tgtccaaaat cataaacttg gagaatatgt agaccaggta ccagcggaca 3900 aacagagata tcaacggtta gtgggtaaac tcatctattt atctcatact cggccagaca 3960 ttgcttatgc tgtgagtgta gtgagtcaat tcatgcaccg gccgagtgaa gaccatatgg 4020 atactgtaat gcgaatcctt cggtatttga agtcctctcc tgggaaaggg cttatgttct 4080 caaagaatgg tcatttgaag gttgctggct atacagatgc ggactgggca gggaacatca 4140 cagataagaa atccactgct gggtacttta cttttgtggg aggcaaccta gttacatgga 4200 ggagcaaaaa acagaaagta gttgccctgt ctagtgctga agctgaattt cggggaatgg 4260 tcaagggaat atgtgagctc atttggctga aaaagctgct agctgagatc ggtattgctc 4320 ctagttccga aatgaacttg ttctgtgata acacagcggc cattgctatc tcccacaatc 4380 cggttcaaca tgatcgcact aagcacgttg aggtggatcg gaacttcatc aaacaaaacc 4440 ttgaagaaaa gattattcag cttccatttg tcaaatcaga agaccagttg gctgatgtac 4500 tcaccaaagc agtgtctgca aggaatttct acaactcact tgacaagttg ggcataaaag 4560 atatctatgc accaacttga gggggag 4587 // ID VLINE4_VV repbase; DNA; EDCOT; 5997 BP. XX AC . XX DT 29-AUG-2007 (Rel. 12.08, Created) DT 29-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE Non-LTR retrotransposon from Vitis vinifera. XX KW L1; Non-LTR Retrotransposon; Transposable Element; VLINE4_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5997 RA Obukhanych T. and Jurka J.; RT "VLINE4_VV."; RL Repbase Reports 7(8), 769-769 (2007). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 2964..4295 FT /product="VLINE4_VV_1p" FT /translation="MWLLSDGFKELVREWWTGYSVAGSNSHCLAEKLKALK FT RDLRRWNKEVFGNVSARKSEAFSRIQLWDSKESVNPLSFEEAEARMGDLEE FT YKKCVLMEETFWRQKSREIWLKEGDKNTKFFHKMANARARRNFLSKVKING FT VTLTDEEDIKAGVCRAYRTLLSETEDWRPRIGDLQFRVLGTERSRSLEEPF FT SEKEVFEALCSLSGDKAPGPDGFTMAFWQFSWDFTKAEIMAFFGDFFRLGT FT FQRSLNSTFLVLIPKKGGAEELKDFRPISLVGSLYKLLAKVLANRLKLAVG FT EVVSEYQHAFIQDRQILDVALIANEAVDSRLKDNIPGLLLKLDIEKAFDHV FT NWDCLLSVMSKMGFGQRWINWISWCISTANFSILINGTPSDFFRSTRGLRQ FT GDPLSPYLFLLVMEVLSQLLFRARSGGFIEGFKVGSSSGVGKGSAPSSVC" XX SQ Sequence 5997 BP; 1434 A; 1003 C; 1779 G; 1766 T; 15 other; atggctgtgg tttctcccgg cggaaagtgt tggtttggag tggattcgaa gaccttcgag 60 atttcagtcg acgaggccaa ggggaaagtg ttaggaacag tttgcgaaag gagtcccaac 120 ttttcttctt ggattcgttt cagcggtaag ggcttgtcct tccttttgga aggagctgag 180 acctgctgct ttctcaaagt gggggagcgt ttcaaaaaag cttgggtgga ggggggaaga 240 agatatcagt tggaattgcg ctctaacaaa gcaggtcggt ttttgttttg cacggcctgg 300 gatgtagaag gtaagaaatt ctcattggct ttccccgaag gcaggggagt ggttggaggt 360 tggcaacttt tggctgggaa attaagaagc ctgggtttct ccttagctca aaggggtgas 420 gagcactcag cctctccttc aagagggagg ggtcttaatg gggccagtgt tgggaagaag 480 gacctacttc cagagacaga tctttctggt tctactgaaa ttcggaatgt tgtgtggtta 540 gaaacagaaa aggaggtgat tgatagtaac aaggaagttt tgaggaggag cttggtgggg 600 agatgggggg gttccgatca gccccctttc ctcgactccc ttaagtcttg ggcgcagtcc 660 agttggatgt tgagaggaaa tcttcgcttg gctctgttag gaggcccgtt tatactcttt 720 gagtttgaag atgtcgttga agctgagagg gtgttgcact caggggtcaa gtggtttaaa 780 ggtaaatgtc ttctcttgga ttggtggaaa ccttctgttg gttgtctcat agaggacagg 840 aagagccgag aagtgtgggt aagaattttg gggctccctt tgcatctttg ggggatgagt 900 tttttcaaga gcttagggga tgcctgtggc cgctttgtga gtgttgacga ggatacgatg 960 gaacgccgga acttgcagtg ggccagaatc ctcgtcggag taagatggtg gaatttcccg 1020 agctctttgc agctagtaac aggttctacc tgtttcgcgg tccagttatg gtgggagact 1080 gctccttgga tcagtgaagt gcagccttct tggtgttgya ggggaagaag gggtaaggtt 1140 gagggtgagg ttgggtcacg cgccttcctg agagttgcag aagtttgctc tgggaaagag 1200 gttggccagg tgtcgacggt tgacccgctg ccctctgcwa aagagggaga ggactttgct 1260 cctttcctga caggaacrgc tgcaggtact gataggaaag graagctcag tggtgcgggg 1320 gtttgggggc tyagttgggc tcagagttag aggcccctac ttctgattct tgggctttgg 1380 gctctacttt tggtggaagc ctcaaaaggc tttccttagg taaggcccag ttggaagtgg 1440 gtcgggcctg tttttcaaaa ggtggggaga cttttctctc ttcccctaga ggccatcttc 1500 acgctcggag ccctagactc cttccctcgg cgatgggtcc ttcgcaaggc cttgttcatt 1560 gtgcatcttt cccgacgggt ccttcgcaag gcgttgatcc ctgcgcgtct cttccaatgg 1620 ctccgaaggc gatcgcgaag cctctwgccg acgtcgctct cttagaagaa gttctcagat 1680 tccaaaaagg tacgctttct tcgtctcgtt cttcttgggg ggaagggcct tcttcttctt 1740 ctactccttt ctgggtgycg aattcttctt ctttgggcga agattgtaga gggacatcgc 1800 tgtgtttaaa gcgttgggga gratcccctg agtgggaaga gggtgtgctg gaggtaaggg 1860 ccgacgttgt aaaggggcct ctatctatgg ttctgcaaga tggrtcagag gtggttttcc 1920 ctgagaatgc ttcctctgaa gaggatccgc cttccgacaa ggagctctcc aatttcaaag 1980 atttcagtag atttttggga atgccggttg aggggtgtga agaaaaaatt gttttgttgt 2040 taaagaagtt gaagaagatg actggtgggg ggaccctttg taaaaagaga aagaagaaag 2100 cggtgtccgc atcacgctct gaaagggaac ttaagagatt ggattgttcg gttagctatg 2160 gagagcctgc gaatagaagg agtggcagga acaaatggga attgatccct gtggattgat 2220 gaagattaaa atcctctctt ggaatgttag agggctcaac gacagggaga aaaggaggat 2280 gattaaktca gtagttagag cccagaaggc agatttagtt tgttttttag aaacaaaggt 2340 gcaagagatg tcgttaaagg tggtgaaaag cttgggtgtt ggaaggttta tggactgggg 2400 tgcagttgat gctaggggtg cctcaggagg cattctgatt ttttgggaca atagggtttt 2460 ggaactcttg gagctggagc gtggtggttt caccatttca ggtcgcttta ggaatgtgga 2520 agatggcttt gtttgggtgt tcactggtgt ctatggacca gtcttttcga gggaaaaaaa 2580 ggagttttgg gaagaattgg gtgctatcaa aggcctgtgg gatgatccct ggtgtgttgg 2640 gggggatttc aattccatta gatttccagg ggaaaggagg aatgggctca atctgacagc 2700 agagatgaga aggttctctg aggtcattga ggagttgaga tctaaaggat ctgccctctt 2760 ccggtggtca gttcacgtgg tatggtggtc ttaattctca agcagcttca aggttggatc 2820 gctttctagt ctccaacgag tgggaggatc atttttcggg tgtctttcaa tgtgctctcc 2880 ctagaattgt ctctgatcat tgtcccattt ttttggaggg tggaggggtt aaaaaaggca 2940 agactccttt ccgctttgag aatatgtggc ttttgtcgga tgggttcaaa gagctagtaa 3000 gagagtggtg gactgggtac tcggttgcag ggtctaacag ccactgcctt gctgaaaagt 3060 tgaaagctct taaaagggat ctaagaagat ggaataaaga agtttttggt aatgtctctg 3120 ctagaaaatc agaggccttt tctcgaattc aattatggga ttcaaaggag agtgttaatc 3180 ccctgtcttt tgaggaagca gaggctcgaa tgggggattt ggaggagtac aagaagtgtg 3240 ttttaatgga agaaactttc tggaggcaaa aatctaggga aatctggtta aaggagggag 3300 ataagaatac caaatttttt cataagatgg ccaatgccag ggcgagaagg aactttttat 3360 ccaaggtgaa aattaatggg gtcactctta ctgatgagga agatatcaag gctggggtgt 3420 gtagggctta taggactttg ttatcggaaa ctgaggattg gagaccgaga attggggatt 3480 tacagtttcg tgttttgggg acagaaaggt ccagaagttt agaggagcct ttttcagaaa 3540 aagaagtgtt tgaagccctg tgcagcctct ctggagataa agcgcctggt ccagatggct 3600 tcaccatggc attttggcaa ttttcctggg attttaccaa agctgagatt atggcctttt 3660 ttggtgactt tttccgcctt ggcactttcc agaggagtct aaactccact tttctcgttt 3720 tgattccaaa aaaggggggt gcggaagagt tgaaagactt cagaccaata agtttggttg 3780 ggagccttta caaattactc gccaaagtct tggcaaatag gctgaaacta gctgttgggg 3840 aggtggtttc agagtaccag catgccttca ttcaggatag gcagattttg gatgttgcgc 3900 tcattgcaaa tgaggctgta gactccaggt tgaaggataa tatccctggt ctccttctaa 3960 aattggacat tgagaaggcg tttgatcatg tcaattggga ttgccttctk tcagttatgt 4020 ccaagatggg gtttgggcag aggtggatta attggatcag ttggtgcatc tccacagcta 4080 acttctcaat tttaattaat ggaacccctt cagacttttt tcgcagcact aggggcttga 4140 gacaaggtga tccgttatcc ccttatctct tcttattagt catggaggtt ctcagccagc 4200 tgctcttcag agccagaagt gggggcttca ttgaggggtt taaggtggga agcagtagtg 4260 gagtaggaaa gggatctgct ccatcttctg tttgctgacg acaccctttt attttgcaag 4320 gccaatagtg agcagttgag atacttgagt tgggtgttct tatggtttga ggcgatttct 4380 gggttaaaag tgaayaggga taaaagtgag gttatccctg taggaagggt tgattctttg 4440 gagaatatcg tttcggtgtt ggggtgtaga attgggaagc ttcccacttc ttatttgggt 4500 cttcccttgg gtgccccttt caaatcttca agggtgtggg acgtagtgga agagagattc 4560 agaaaatgtt tgtccttgtg gaagagacaa tatctttcta aagggggaga cttaccttga 4620 taaaaagcac cctttcaagt ctcccaattt acttaatgtc tctctttgtc attccgcgga 4680 aggtgtgtgc aagacttgaa aagatccaaa gagacttctt gtggggcggt ggtgcyttag 4740 agaaaaagcc gcacttggtg aattggagtg cggtttgtgc tgatatgaga cagggaggct 4800 taggtattcg cagtcttgtg gccctaaaca aagctttgct tgggaagtgg agttggaaat 4860 ttgctgtaga gagggattct ttgtggaaac aagtcatcat agacaaattt ggggtagagg 4920 aaggaggttg gtgttcgaga gaagtgaggg gagcctatgg tgtgggagtg tggaaagcca 4980 ttagaaaaga ttgggaaagc attcgctcta gatcccgctt tatagtaggg aatgggagga 5040 aggtcaaatt ttggaaggat ttgtggtgtg aggaccaaac tttgaaagat gctttcccta 5100 acttattcmg attggcggtc aacaaggatg agtgggtgtt tgatgcttgg gaggagggcg 5160 gagaggtggg tagttggaat cctttgtttt caagacactt taatgattgg gaaatggaag 5220 aggtggaggg cttgctccga aaactacatc ctttggtttt gaatagagat gtggaggatg 5280 ttttgagttg gaagaatagc aagaatgact ccttttctgt tagatctctc taccgctccc 5340 tcacaagtgc ctctagtgaa ccttttcctt ggagtattat ttggagatct tgggctccca 5400 tgagggttag cttttttgct tgggaagcgt cttggaacag aattttgacc attgatcagc 5460 tcaaaagaag gggttggaat atgccaaata ggtgttactt gtgtaaagtg gaagaggaaa 5520 ccagtgacca cttgatcctt ttttgtaaga aggctacaat gttatggagc ttgcttttct 5580 ccctttttga tgtgcagtgg gtcctgcatt cctcaatcaa aaggaatttg ataggttggc 5640 atggtgcttt tgtgagtaag agaaaggaaa aggcttggag ggctgccccc ctttgtttaa 5700 tgtggacctt atggaaggaa agaaatgaaa gagtgttcaa tgacactgaa cgatccgacc 5760 aagctttaaa actttctttt ttgtacactt ttgtgaattg gggtagggtg tatttagagg 5820 atcattcttt gtccttgatt gattttatag agtggctttt gtctagatag gagaaaggtt 5880 tttctttctt tttgcctagc ttcttgggcg ttgcttgtat acttcgtgtg tactcttttc 5940 gccttttcta ggcttttcta atacaatctc ttatttacct atcaaaaaaa aaaaaaa 5997 // ID ALIEN1_CA repbase; DNA; EDCOT; 271 BP. XX AC X87869; XX DT 04-MAR-1998 (Rel. 3.02, Created) DT 04-MAR-1998 (Rel. 3.02, Last updated, Version 1) XX DE C.annuum Alien DNA transposable element. XX KW Transposable Element; ALIEN1_CA; Alien-1; CATRANELE; KW Inverted repeat. XX OS Capsicum annuum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Capsiceae; OC Capsicum. XX RN [1] RP 1-271 RA Pozueta-Romero J., Houlne G. and Schantz R.; RT "Nonautonomous inverted repeat Alien transposable elements are RT associated with genes of both monocotyledonous and dicotyledonous RT plants."; RL Gene 171(2), 147-153 (1996). XX RN [2] RP 1-271 RA Pozueta-Romero J.; RT "ALIEN1_CA."; RL Direct Submission to Genbank (09-JUN-1995)J. Pozueta-Romero, RL Institut de Biologie Moleculaire du CNRS, 12, rue du Gl Zimmer, RL F-67000 STRASBOURG, FRANCE. XX DR GenBank; X87869; Positions 1 271. XX SQ Sequence 271 BP; 83 A; 49 C; 36 G; 103 T; 0 other; taggggttgt ttggtagagt gtattgaata atacaacaca tggattaatt aatgtgtatt 60 gttaatacct tgtttggtat cttttttagc ctatgtataa ctaatacttg cattatttat 120 acactctatt atgtattgag gtgtgtatta gtaatacaca ccattttcaa tgtattagta 180 atacaaagct gtcccctgaa tacattccat ctttattact ctcctccatt ttccagaaat 240 aacgtcaata cactctacca aacaacccct a 271 // ID DTPH4 repbase; DNA; EDCOT; 757 BP. XX AC Y07722; XX DT 17-NOV-2004 (Rel. 9.1, Created) DT 17-NOV-2004 (Rel. 9.1, Last updated, Version 1) XX DE P.hybrida dTph4 transposable element. XX KW Transposable Element; DTPH4. XX OS Petunia x hybrida OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Petunioideae; Petunia. XX RN [1] RA Alfenito R.M., Souer E., Goodman D.C., Buell R., Mol J., Koes R. RA and Walbot V.; RT "Functional complementation of anthocyanin sequestration in the RT vacuole by widely divergent glutathione S-transferases."; RL Plant Cell 10(7), 1135-1149 (1998). XX DR Genbank; Y07722; Positions 1 757. XX CC Sequence includes 12 bp terminal inverted repeat. XX SQ Sequence 757 BP; 212 A; 175 C; 112 G; 258 T; 0 other; caggggcgga gccacctggt ggcaaggggt tcaattgaac ccccttcgcc ggaaatttgc 60 gcgttttgct tgtttaaagt ttaccaaata tccgtaatat ctaagtcttg aacccccttc 120 agacatgaaa aaacactggc gcagatggca agggggttca agattatgcg gatggtccct 180 tgttcgagtc ctggtgatag cagttttcca tttttcagag agaaagtgaa tacttttcac 240 caataatttc catctatttt cccattctat cattgtggtc cctggtcccg ctaactcttc 300 tcaatgcgtg cttctatttc ctagaactag aaaggaccaa acccccacat aagctcattt 360 ctctccaatt ttgttacctt tacccctttt tctctcactt taatttttcc ttttaagtaa 420 ttaccataat taggaaagct atcacctata ttatatgtat tagtaataaa caaatgtaaa 480 tcgtgctcaa tcctaccata attaatgatt aatatctcaa aatcccctga ataatctaaa 540 ctttctaaaa ctatattttt tcacccatct tattccctcc attttaaaat ggtgtggcac 600 aatgggtccc aagcgagttt cggataatga tattgttagg cttaatcatt aaatattgtc 660 ttttaaaaaa ctatgcacca ctttattaga aaattttact gttcatctat ttcaaatcct 720 gaaccccctt tctgaaatat ctcctgctcc gcccctg 757 // ID Copia-9_TC-LTR repbase; DNA; EDCOT; 328 BP. XX AC CACC01005488; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-9_TC_; KW Copia-9_TC-I; Copia-9_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-328 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01005488; Positions 12975 13302. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 328 BP; 105 A; 55 C; 54 G; 114 T; 0 other; tggagaattt gcttaattgg agttagaagt tagaagacca aagccttaag aagtcagagg 60 atcgaatgcc aaatgccaga gtatatccaa ggcttagtaa caagagccat gcgcaagtca 120 tgtgactatt taatataaat atttttttta ctattttacc attcaactgt aaagtaatta 180 tgtagttagc ctagtcatta gtcagttact tgaaacaaac tattataaat agtttactgg 240 tgatattttc ttcctttaac gaagaatgaa agaacttctt cttcaccatc gttttgctct 300 ctctgcactt gttctcttga tttcaaca 328 // ID COPIA2-LTR_MT repbase; DNA; EDCOT; 1424 BP. XX AC . XX DT 23-MAY-2005 (Rel. 10.05, Created) DT 23-MAY-2005 (Rel. 10.05, Last updated, Version 1) XX DE M. truncatula LTR sequence - a consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW copia-type; COPIA2-LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1424 RA Gentles A. and Jurka J.; RT "M. truncatula LTR consensus."; RL Repbase Reports 5(5), 102-102 (2005). XX DR [1] (Consensus) XX CC At least 15 copies in the M. truncatula genome, flanked by 5 bp CC target site duplications. The corresponding internal sequence is CC not yet identified. XX SQ Sequence 1424 BP; 474 A; 273 C; 221 G; 456 T; 0 other; tgaaggtaaa tcgacataaa cagaataagc agcggaataa aatttcgatt tactttcctt 60 ggatcattac gaattggaac ttgaaccagt gattcgattg ttaccttaga acgattagtc 120 tgaaaacgat cggtggaatc tgcgaaccgg aatcacgatc acagccaagc aaacagcaga 180 gcctctatca agtccacacg aacagtgctc ctccaaaacc tcggtgctag ccaagaagac 240 ggaagtcaga gaactagggt ttctgcaaaa gaacgtaacc gcaaactatt gcactagggt 300 tctatttata gaactcctta tgtgctttgc aagtcagaac tcgtttttga cttcactaag 360 cccaataacg agtttagtaa attttgctaa ataattagca ttatttacta agcgcaccct 420 ttatataagt cgtacttata tatatctctt ttgactgttc tttgtgtgtg accctttagg 480 ttctagtcac gttggcaata atattaaatc taatatttaa tattataaac aatgagcggt 540 atctagcaac acatcattgc tacccaagtg acaagaatgt caagtgatct gacgaaacct 600 ttcatgataa tacttatgtg tataattact cctttgtctc aatatcttta ttgatcccaa 660 ggcatagata ttgtcaccct tgtatagatc aatgtttata tttcttgatt ccgaaatata 720 ctatataacg aataagtcca atatctcata ttgacttagt tcggcatggc catgcatatt 780 tacagtcata tttcatcaag aggcctaaag atatatctcc tgtttatgag gagggacaaa 840 tcccatctag gacactcatg cccctcagca tgattcatca agtacccatc aaccaacgtt 900 atggttatcc ttttacagac aacgttagaa tggcaacaaa gcacttgagt ccacatctag 960 agatcatagt ggtttcaggt ctaagagcga tatacattat tatcattgtg agaatatctt 1020 atgacaattt cataacttac tatgtagtat tctcacagtg ggtcaatcca atataaatat 1080 tactcctaat atttatatct atgtatagac ttgatatctc atatctatga cccatgagat 1140 gcggtcatca gtctacatac ataatagtct cgacgcttta ttattatcct ttattcatat 1200 taaagctttg actacggata catttaagaa tagcgttcta taagataatg taatctcatg 1260 attaagtcac acttaatata ttattacacg aactatctat tctaaggact ttattaacat 1320 tatctaaata taataaagag tgccatatat tattcaataa taaaagtcat gatacataag 1380 ataggtttaa cataaactat tggcctctag ggcttacacc aaca 1424 // ID MARINER2_MT repbase; DNA; EDCOT; 2134 BP. XX AC . XX DT 04-FEB-2007 (Rel. 12.02, Created) DT 04-FEB-2007 (Rel. 12.02, Last updated, Version 1) XX DE DNA transposon. XX KW Mariner/Tc1; DNA transposon; Transposable Element; MARINER2_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2134 RA Jurka J.; RT "MARINER2_MT: Mariner-type DNA transposon from barrel medic."; RL Repbase Reports 7(2), 123-123 (2007). XX DR [1] (Consensus) XX CC This is a small family (~40 copies), over 98% identical to CC consensus. XX FH Key Location/Qualifiers FT CDS 321..1925 FT /product="MARINER2_MT_1p" FT /translation="MNVLKVFKPYLTHEMASHLKGVAKSTMSDQIRKELCE FT YKRDNPASTQKDLQRWLEGKFQLKVSQGTISNTLKRSNDYLSAEIEKGRAE FT IKRHKPAKYPDMEKVVYEWFLQHQERVNITGELILQKARDTMKLLYPHDDS FT DFNFSTGWLGKFKHRHGIKSFRRFGESGSVDVQDMEQKLVSIREKIDQFPM FT KDVFNMDETGLFYRLQADHSLATKQLEGRKQDKERLTVVICCNEDGSEKIP FT LWIIGKYAKPRCFKNVNMNSLDCQYRANKKAWMTSVLFDEYVRSFDQMMHG FT RRVLLVVDNCPAHPRNIEGLRNVELFFLPPNMTSKIQPCDAGIIRAFKMHY FT RRRFYRKILEGYEVGQSDPGKINVLDAINLAIPAWTIDVRKETIANCFRHC FT KIRSASDVVGNLDESTFDEETQDLQTMINQCGYRNKMDIDNLMNYPGENEA FT CSEVQSLEDIVRTIIENNAEDDDEDDTVSLEPVTRKEALMASNTLHNFMIQ FT YKNTTPQLLDAIRKVRDELQTDLNFKGKQTTIESYFNKV" XX SQ Sequence 2134 BP; 752 A; 324 C; 431 G; 627 T; 0 other; tacagtagaa actctataaa ttaataatgt cgggaccgga gaaatttatt aatttagaga 60 gttattaatt tatcgataaa ttaataatta ttaatttaaa gagtttttaa gtaattatac 120 tgtacatacc aaacaaaaag gcaaattagt ctatgtctct tagaattacg ttgcaccaaa 180 tcttgggact caatgtaaat taataaatat tgtattcata tccattggaa atatgacttt 240 tgacttttga agtgtatagt aaatgtaaac aagtggaatg ttcaatgtat tcttaagcaa 300 gtttggcata tataaattac atgaatgtgt taaaagtatt caaaccatat ctcactcacg 360 agatggcttc tcatctaaaa ggtgttgcaa aatcaactat gtcagatcaa atacgtaagg 420 agttgtgcga gtacaagaga gataatcctg caagcacaca aaaagacttg cagagatggc 480 ttgagggaaa atttcagttg aaagttagtc aaggaacaat atcaaacaca cttaagcggt 540 caaatgacta tctctctgct gaaatagaaa agggaagagc ggagatcaaa agacacaaac 600 cagcaaaata tcctgacatg gagaaggttg tttatgagtg gtttctacag catcaagaac 660 gtgtgaatat cacaggagaa ttaattttgc agaaggcaag agatacaatg aaactcttgt 720 accctcatga tgattcagat tttaacttct ctacaggatg gcttgggaaa ttcaagcacc 780 gacatggcat aaagtcattt cgtcgttttg gcgagagtgg gtctgttgat gtacaagaca 840 tggagcagaa attggtatcg attcgagaga aaattgatca gttccctatg aaagatgttt 900 tcaatatgga tgaaactggg ttgttttata ggctacaagc tgatcattca ctggcaacaa 960 aacaacttga aggaagaaaa caagataaag aaaggctgac ggtagttatt tgttgcaatg 1020 aagatggctc tgaaaaaatc cctctatgga ttattgggaa atatgcaaag cctcgttgct 1080 tcaagaatgt caacatgaat agcttggatt gtcagtatcg agctaacaaa aaagcatgga 1140 tgactagtgt gctttttgat gaatatgttc gttcatttga ccaaatgatg catggtagaa 1200 gagttctact tgtggtggat aattgtccag cacatccaag aaatattgaa gggctaagaa 1260 acgttgagtt gttcttcttg ccacccaaca tgacatcaaa gattcaacct tgcgatgctg 1320 ggataataag agctttcaag atgcattacc gtagaaggtt ttaccgcaaa atattggaag 1380 gttatgaggt gggacaatct gatccaggga agataaatgt ccttgatgct atcaatttgg 1440 caatcccagc ttggacgata gatgttcgaa aagaaacaat agcgaattgc ttccgacact 1500 gtaaaattcg ttcagctagt gacgttgtag gaaatttgga tgaatccact tttgatgaag 1560 aaactcaaga cctccagact atgatcaatc aatgtggcta tcgtaataag atggatatcg 1620 acaatctaat gaactaccca ggtgaaaatg aagcatgttc ggaggttcag agtttagaag 1680 atattgtgcg tactatcatt gagaacaatg cagaggatga cgacgaagat gatacggtgt 1740 ctttggagcc tgttacgcga aaggaagcac ttatggcgtc gaacactctt cacaacttta 1800 tgatacaata caaaaataca acacctcagc tattggatgc aataagaaaa gttagagatg 1860 agctccaaac agacttgaac tttaaaggaa aacaaacaac tattgaatca tatttcaaca 1920 aagtgtaata tatttttttt cagtttctat gaattattaa tttatgattt tcttgggacc 1980 gaaaattata aagggatctc ccaaaaaatt attatcttat tattttatcg aattattcaa 2040 ttttttacac tggcccaagt cgggaccgga caaatttatt attttagaga gtttattaat 2100 ttaccgagta ttaatttaaa gagtttctac tgta 2134 // ID Copia-46_VV-LTR repbase; DNA; EDCOT; 1605 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-46_VV_; KW Copia-46_VV-I; Copia-46_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1605 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 12371025 12372629. XX SQ Sequence 1605 BP; 562 A; 175 C; 254 G; 614 T; 0 other; tgttggaata tgtgcccata aacaaatgag atgtttttta ttttgttgat tattaatatt 60 tttttaagga atatgtgccc atgttataga tgctttataa atatcgaaaa ccctagatta 120 tttaattgta actttaaata ttgtatataa gtgttatata caggaggata atatttaaag 180 taaaataatc taatatgttc gtaattaaaa attaaagttg ggatctttaa tttaaaatta 240 ctagcgcggt tcattacatt ctgaatgaaa tgatcttatc cggattgtta ataatgagat 300 tattggaatg aaagcgcttc atataatttg attatatagg actggaacac gattaattat 360 gaatctctga taaattccgt tataatatag agcattcaat attaatcaat gatggtcata 420 tatgcattga tcttaattct gagtaattaa tagactccta tttattgtat tgtatttttt 480 gacataccgg gtaatgacac aaatacatag tgtcaaattc ttggtgtatt ggaagtataa 540 taaaataaat agtcgggaat attaatatac aagatgaaat ccattccttc gttaagaagt 600 cagatggacg gttcccataa gtattggttc gagccttgaa tgataagagc gctcaattta 660 tgattagacc ataaatatat tattcattag agaaccaatg gcacttaagg agaaagatat 720 aattaaagag gttaacagaa aaacctagct ttaattatga acagtttatg gaggattgac 780 tcatatgtag tgactatatc aatgggcaat tcaaatcatt tgaatatatt taattttata 840 attttaagag tgcaattcca aatttttagt ggagtaattt ttggaattaa taatttgatt 900 ttttaattaa gttgttaatt aattgtcaaa attattggag cttaaaatta taatgtccat 960 agttcctctc aacggctcca ttaaaattat atgaacattt ttttttatgt tgggttgatt 1020 ttattagttt ggaattttga attctaaatt aatttcacac aatcttgatt tgatttattt 1080 attttataat ttgattattt aaaatatttt ttgatacaat gtggtgaaga ccacacttac 1140 ttgtattccc taagaaacac tttttaagtg gggatcatgg ggagagatat tctctccctg 1200 gtttttcaaa attcaaaatt caaaatatgt tagttatttt ttcttggttg tattaaaaaa 1260 aaaaaaagtt ttttttctca atgagaaggg ggatgagaat gcaagttttc aatagattaa 1320 gttgtgtgat aaaaacccaa aaaataaaaa aacgcctact cgttttgagt tcatcataat 1380 ttggagaacg taagagaaag atccatggtg ctttagagga tttggaattc taagatcttt 1440 ttgacggagt tcaaatttat cagcctaatc gcaaggtaca attctaaatt acctatattt 1500 gttatttcat taaattaata caagtattga tcattgagaa aaaattttga gaaaattttt 1560 ctggtttctg ttttttcttt tatttatctg gtttcaaaac caaca 1605 // ID Copia-6_TC-I repbase; DNA; EDCOT; 4035 BP. XX AC CACC01004662; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-6_TC_; KW Copia-6_TC-LTR; Copia-6_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-4035 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01004662; Positions 8548 12582. XX CC Positions [1591-2121] - Integrase core CC LTRs are 92% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS 421..2511 FT /product="Copia-6_TC-I_1p" FT /translation="MLRIEDSENIREFSRKMMGLVNQLRLLGKEVTEERLV FT SKMLMSLLEKYETKVSSLEDSKDLAQITFKELVHALEGLEQKRAFKQKSAS FT NFALVAKAKNVKMRGNGLKDSSIDKKNKGRKSGDTQQGDQKREFPPCKHCK FT KTSHTEKYYWFRPNVKCRACNQQGHVEKICKNWAEAPEKAAVVEHTDGDAD FT KVLFMATIDENSSNVTAGENSRRSNVWLLDSACSHHLTSNKSLFSTLDKSF FT KSKVKIGDGNYLDILGVGTVDIETTSGRTSISTVHYVHTADHNLLSVGQLA FT NEHYRILFKGDSCIVFDSQGKELIIVSMKNNCYPLNLANAAHLALYNELDV FT SEVWHQRIGHVNYNTLTLMSFRNLVKRLPVILKPNKICQTCQFGKQTRKSF FT PIESRWKATKKLELVHTDLRGPMKTASLNGSRYYIIFIDDYSKFCWIFFLK FT QKSEALSYFKKFKVVAENFSRQSVRTLRTDNGKEYTSTEFEQYLESCGIQH FT QLTIPYSPQQNGKAEKMNKTLAEMGRCLLYQIKLLGVVWVEAVNTANYLLN FT GVYIRALDSKTPYEMWFDHKLDVSHLKIFGCICYATISDVKRTKFDPKSVA FT AVLVGYSEVSTGYRLFDPELKNIFVSRDVIFDEGQSWNWPNSGAGQVDFTK FT TANVDAQRTVVDDDSDLEDESKAIRCTRSLADIYSICNITVTEPATFK" XX SQ Sequence 4035 BP; 1318 A; 573 C; 949 G; 1195 T; 0 other; attggtatca gagctctcag tgatcttaag ggcttaggat ttgatcagtt tttgtaaata 60 tgagctatgg attcaatgca tcagctccat caaagttcac cggagagaac tattcattct 120 ggagtgtgaa aatggaggct tatctcagag ccttcatgtt gtgggaagca gtggagactg 180 atgaggaacc agtgcaaagg agagctaatc cgatgatagc tcagatcaag caatttgagg 240 aagacaaagc caaaaggtac aaagctctgt cttgccttca ctcagcttta tttgatgaaa 300 gttttgctca ggttatgcat ttgaaatctc ttaagcaagt ttgggattat ttgagaggag 360 ttttttggga gtgaaagaac taggcagatt caagcattta atcttactca gaaatttgaa 420 atgttaagaa tagaggacag tgaaaacata agagaatttt ctagaaagat gatgggatta 480 gtgaaccaat tgaggctact agggaaggag gttacagaag agagactggt aagcaaaatg 540 ttaatgagtt tacttgagaa atatgagact aaggtgtcct cattagaaga ttccaaggat 600 ctagctcaga ttacttttaa ggagttagtt catgctttgg aaggtctgga acaaaaaagg 660 gctttcaaac aaaagagtgc atcaaatttt gccttagtag ctaaagctaa aaatgtgaaa 720 atgagaggta atggcttgaa ggacagttca attgataaga aaaacaaagg aaggaagagt 780 ggagatactc aacaggggga tcagaagagg gaatttccac catgcaagca ttgtaagaag 840 actagtcata ctgaaaaata ttactggttc aggcccaatg ttaaatgcag ggcttgcaat 900 caacagggtc atgtggaaaa gatatgtaaa aattgggctg aagcacctga gaaagctgct 960 gttgtagagc atacagatgg agatgctgat aaagttctct ttatggctac aattgatgaa 1020 aattcaagca atgtaacagc tggtgagaat tcaagaagat ctaatgtttg gcttttggac 1080 agtgcttgct cccatcactt gacaagtaat aaatctcttt tctctaccct tgacaaaagc 1140 tttaagtcaa aggttaagat aggagatgga aattatctgg atattttagg agtaggaact 1200 gttgacattg aaactacttc aggcagaaca agtatatcta ctgtgcacta tgttcatact 1260 gctgatcata atctgttgag tgtgggacaa ttagctaatg agcattaccg tattttgttt 1320 aagggtgata gttgtatagt ttttgattct cagggtaaag aattgattat agtgtctatg 1380 aaaaacaatt gctatcctct gaatttggct aatgctgctc acttagcttt atataatgaa 1440 cttgatgtgt ctgaagtatg gcatcaaagg attggccatg ttaattacaa tactttgact 1500 ctgatgtctt tcagaaactt ggtgaaaaga ttgcctgtta ttttaaaacc gaataagata 1560 tgtcagactt gtcagtttgg taaacaaaca agaaaatcat ttcctataga aagtagatgg 1620 aaggctacca agaagttgga attggtacat actgatttgc gtggtcccat gaagactgct 1680 tcacttaatg gaagcagata ctacatcatc tttattgatg attattcaaa gttttgctgg 1740 atattcttct tgaagcagaa gtctgaagct ttgagttatt tcaagaaatt caaagttgtt 1800 gctgaaaatt tttcaagaca aagtgtaaga accttgagga ctgataatgg taaggagtat 1860 acatctactg aatttgagca atatctggag tcctgtggaa tacaacatca gttaactatt 1920 ccatatagtc ctcagcagaa tgggaaagct gaaaaaatga ataaaacctt ggcagagatg 1980 gggaggtgct tgttgtacca gataaagttg ctaggggtag tttgggtaga agctgtgaat 2040 acagctaact atcttttaaa cggagtttat ataagagctc tggatagcaa aacaccttat 2100 gaaatgtggt ttgatcataa actagatgtt tcccatttaa aaatatttgg ctgcatttgc 2160 tatgctacga tatcagatgt taagaggact aagtttgatc caaaatctgt ggcagcagtt 2220 ctggttggct acagtgaagt ctccacaggc tatcgattgt ttgatcctga attaaaaaat 2280 atttttgtaa gtagggatgt gatatttgat gaagggcaaa gttggaattg gcctaatagt 2340 ggtgctggac aggttgattt caccaaaaca gctaatgtag atgctcaacg gactgtagtt 2400 gatgatgatt ctgatctgga ggatgaaagt aaagcaatta gatgtacaag aagcttagct 2460 gacatttata gcatatgcaa tattacagta actgaaccag caactttcaa gtaagcttag 2520 cttgataaca attggaagtc agctatggat gctgaaaatg gaaatgatat ccaagaatag 2580 gacatggact cttgttgaca gaccagttga caaaaacatc atagaagtga agtggattta 2640 cagaaccaaa tttaatccag atggttttat aaataagtat aaggctcggt tggtggtcaa 2700 agggtatgct caagtttatg gggttgacta catggaaaca tatgctccag tagccagaca 2760 tgacactata aggatgtttg ctgccttgtc atccagggaa ggatggacaa tttatcatct 2820 ggatgtcaaa tcggccttcc ttaatggcat tcttactgaa gacatttata ttgagcagct 2880 tgaaggttat gtgcagcagg ggtctgagat gaaggtatgc aagcttatta aggcactgta 2940 tggcttgaaa caggctccaa gagcctggta caccagaatt gatgaatact tcaagaatta 3000 ggggtttatg aggagcatca atgaatccac tttgtatgcg aagcatgagc ataatactgt 3060 ggaacttata gtagcattat atgtggatga tcttttggtt actagaccag aaaacaagta 3120 tgtgtctgaa ttaaaatctt gaatgaagga agaatttgat atgactgact tgggagttat 3180 gacttatttt cttggcatgg aagtgaggca aactactggt aaagtcatac ttgatcaagg 3240 taaatatgct caggatttat taaagaagtt taatatgagc atgtgcaagg cagtaaatac 3300 tccattgtgc attggtgcta aatttagtgt agcagatggt gctgagaatt ctaatggaca 3360 gttatataga agcattattg gttctttact ctatttggca gctaccaagc tagatataat 3420 gtttgcaaca agcttgctgc caaggttcat gcaaaatcct tcagaagtac accttgctgc 3480 agctaaaagg attctaagat atgttagagg gactgtgaat tatggactgg tgtacatgaa 3540 gtaggagagt agtcagctga taggtttttc tgatagtgac tgggcaggtt cattggatga 3600 ttctaagagc acatgaggtt tttgtttctc atttggaagt gttgtgtttg cttggagttc 3660 caagaaacag ccaatggtag ctcaatcaac agcagaagca gaatacatgg catgtgcagc 3720 tgctaccaat catgctttat ggttgaggaa gctattagat gagctagggt ttaagcaaga 3780 aaaaagaaca ctgattaatg ttgacaactt gtcagcaatt gctatatcga agaatcctgt 3840 tcaacatggg agaactaagc acattagagt taagtaccat gctcttagaa aagttgtaaa 3900 agagggagag attgaattga ttcattgctc aacaagtgat cagcttgctg atatattcac 3960 taagagtttg ggaagagaga gatttgaatg tttgagacaa tgtcttggtg ttcatcagat 4020 tatgaattaa ggggt 4035 // ID Copia-83_Mad-LTR repbase; DNA; EDCOT; 178 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-83_Mad_; KW Copia-83_Mad-LTR; Copia-83_Mad-I. XX NM Copia-83_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-178 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1705-1705 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 178 BP; 58 A; 23 C; 23 G; 74 T; 0 other; tgtaaatagt agtttattgt cccacattgg tgaagtacat atgtaatacc aattgtaact 60 cctatatata ctccactttg gagattaatg aatatataag aaattcccaa atattatcat 120 atattttttg gtatttacca tgtttagttt aatattggta tttaccatgt ttagttca 178 // ID Copia-79_Mad-LTR repbase; DNA; EDCOT; 201 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-79_Mad_; KW Copia-79_Mad-LTR; Copia-79_Mad-I. XX NM Copia-79_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-201 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1697-1697 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 201 BP; 69 A; 21 C; 35 G; 76 T; 0 other; tggaaagtca atgagatttt accttataag gattgattta gaagagaaat tgatttgtaa 60 tttatatgta attgatacat tagttagttt cctttgttgt atagcaagat tgtaggacgt 120 cagttgtata aattaagttc atcaaatcaa tggaaaatat cctggcagaa tatttttcca 180 taccaatttt atatggtacc a 201 // ID Gypsy-15_Mad-LTR repbase; DNA; EDCOT; 277 BP. XX AC ACYM01037991; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-15_Mad-I; KW Gypsy-15_Mad-LTR; Gypsy-15_Mad_. XX NM Gypsy-15_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-277 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1419-1419 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01037991; Positions 24127 23851. XX SQ Sequence 277 BP; 78 A; 44 C; 53 G; 102 T; 0 other; tgttatgatc acaagtatta ggaatagacc aaaatgtaat aagtaagata gttgggggtt 60 ctttttctat ttgtagttct ttaagggagt ttgtttacaa gtttcatgtt gtattgggct 120 actatataac catatgttct ctctattgga aaggcagaaa aagaattaat acaatttaca 180 gaaaacaatt ctgttgcttc ttctctcttc ttccaccgcc atttctgatc ttgcaagcag 240 gtttaggttt gagcctctcc ggatattggt gctaaca 277 // ID Copia-60_Mad-LTR repbase; DNA; EDCOT; 268 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-60_Mad_; KW Copia-60_Mad-LTR; Copia-60_Mad-I. XX NM Copia-60_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-268 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1659-1659 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 268 BP; 73 A; 57 C; 43 G; 94 T; 1 other; tgttgcagtc mtatttagaa taggaatgtg attgtgtaaa tcctagtgta tctagggata 60 tcttgtatat tccctttagt agttaatttc ctattaagag ttgtaatcct attagggtaa 120 ggatttaacc tatcctacta ctataaataa aggcacaatg gggtgataca acacacacct 180 cacaattaaa tctctctctt ttctctcttg ttgccgccgg cctctccctc tctattccct 240 tagtacagtt cagtcaaata ggcctaca 268 // ID HAT-N12_Mad repbase; DNA; EDCOT; 1215 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-N12_Mad. XX NM HAT-N12_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1215 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1634-1634 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 1215 BP; 342 A; 306 C; 213 G; 352 T; 2 other; taggggtggg ttcaaaaaac cgaaaaccga aaaaaaccga aaaccaaacc gaaccgaagc 60 cgaaaaaaaa ccgaaccgaa actgccaaac cgaaccgaac cgaatctggc cggttcggtt 120 tcggtttttg aggtccggaa accgaaccgg accgaaccga accgaaaaaa aaaatataaa 180 tactaaaaaa acatgttggc gtcggggttt gaaccccttc cctgcaggtt ggggttagtc 240 gctgcaagcc aacttgactg taggctttga gttgttataa ttgtaccagt aagttattta 300 taggtttctt gtatttaatg ctttataaaa tttcttaact ttacaaaccc tagccgtctc 360 actcccattt cccatttccc atttcagatc tcaaacactc tctctccccc gcttcccctc 420 tctgcctttg cttcctcagc cctctctctc tctctctctc tctctctctc cttcctctct 480 tcctccaaat cactctctct ccagtcttct catgtcctcc tcgcggattc cttcttccaa 540 accatgattt tccctcgccc ctttcgaatc ggaaccccct ccaaattgga agattctaat 600 ccgggttttc cgatctctca caggtaattt tcgaatcaaa ackaatatga tttataattt 660 tatattgtga tttactgaat taaaatgggt ttttctttta ttatttgttg ggattttgta 720 taatcttgcc aatttggcaa cagatgcgta ggtgttgcca tggctggcga gaggtttggg 780 actaaaaacg aacccccgag gtaaaaatct ctcctggttg gctgctattt agttctattg 840 ggtttatttt catggaaaaa tcaaagaatt aacgcatgcg tgtggttttc tctgcgagag 900 ctctcagatc cacaacaaga aakgcgcacc aacacctaat aatgtcagat ccatggcaga 960 tttgttccag tcagatttgc gatttgttca gttcattcat ttgctccaga cacccaataa 1020 gtttctgcat cttcagtgct gcaatcaatc gttgcagatt tgttccagat taaaaaaaaa 1080 agtcatggaa aaaaccgaac cggaccgaaa ccgaaccgaa aaaaccgaaa aaaattgaac 1140 cgaaccgaac cgaaatttcg gttcggtttc ggttttggct aaaaaccgaa ccgtttcaaa 1200 ccgaacccag cccta 1215 // ID Gypsy-21_Mad-LTR repbase; DNA; EDCOT; 446 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-21_Mad_; KW Gypsy-21_Mad-LTR; Gypsy-21_Mad-I. XX NM Gypsy-21_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-446 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1737-1737 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 446 BP; 128 A; 77 C; 96 G; 145 T; 0 other; tgtagaacaa atggcggaat ggatcgagga ggagatggaa cgtcggaaga caaaagggcg 60 caatcataaa aggggtgtta atttcccata aaagtggctt gagccacttt tcgcagaaac 120 gtgttaaaat aattctccca caaaagtggc ttgagccatc ttttgcagaa agtcatcaag 180 acagcagcct actaataaat ggagtctttt ggggtttcaa gggctttatt atatgtcagt 240 tattttcatt ttaatttcct aagtcttttg agttttccaa gaggttgtaa aaggcttatt 300 taagccatgg ctttgtaatc atttggacat ctttttatca attaatcaaa ttatcctttg 360 ggatttctat caactggtgg actccagtaa actttgttct acaagggatt acgctggtaa 420 ccctttcatt gcttcgtgct gcgtca 446 // ID LTR-2_MX-LTR repbase; DNA; EDCOT; 659 BP. XX AC . XX DT 28-SEP-2010 (Rel. 16.02, Created) DT 28-SEP-2010 (Rel. 16.02, Last updated, Version 1) XX DE solo LTR from the apple genome, consensus. XX KW LTR Retrotransposon; Transposable Element; LTR-2_MX-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-659 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 11(2), 827-827 (2011). XX DR [1] (Consensus) XX CC Solo-LTR. XX SQ Sequence 659 BP; 140 A; 167 C; 215 G; 137 T; 0 other; tgtaacatcc cacatcgccc aggggagtgg atcctgtaag ccttatatgt atattcccat 60 ctctacctag cacgaggcct tttgggagct cactggcttc gggttccatc ggaactccga 120 agttaagcga gttcgcgcga gagcaatccc atgatgggtg acccactggg aagttctcgt 180 gtgagttccc agaaacaaaa ccgtgagggc gtggtcgggg cccaaagcgg acaatatcgt 240 gctacggtgg agtcgagccc gggatgtggt gggggcccgg gccgggatgt gacaatttgg 300 tatcagagcc aatccctggc cggaagtgtg ccgacgagga cgtcgggccc ctaagggggg 360 tggattgtaa catcccacat cgcccagggg agtggatcct gtaagcctta tatgtatatt 420 cccatctcta cctagcacga ggccttttgg gagctcactg gcttcgggtt ccatcggaac 480 tccgaagtta agcgagttcg cgcgagagca atcccatgat gggtgaccca ctgggaagtt 540 ctcgtgtgag ttcccagaaa caaaaccgtg agggcgtggt cggggcccaa agcggacaat 600 atcgtgctac ggtggagtcg agcccgggat gtggtggggg cccgggccgg gatgtgaca 659 // ID COP_LTR_MT repbase; DNA; EDCOT; 186 BP. XX AC AC133572; XX DT 13-DEC-2006 (Rel. 11.12, Created) DT 13-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Long terminal sequence of LTR retroposon, COP_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; COP_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-186 RA Shankar R. and Jurka J.; RT "COP_MT: LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 618-618 (2006). XX DR EMBL/GenBank/DDBJ; AC133572; Positions 58102 58287. XX CC The LTR sequence flanks both termini of an internal region. XX SQ Sequence 186 BP; 65 A; 26 C; 22 G; 73 T; 0 other; tgatagaata aaatattcat gccattaagc cttaggatat ttgtaattat ttgtaattaa 60 atttatttat gtttgtcatt attcccaagt ttgaccaaca tattatgatt gtataaatgt 120 acccttattg atatgagaat gcaacacagt acattacata ttttcaaaga atactcacgt 180 ctttca 186 // ID Gypsy-28_VV-I repbase; DNA; EDCOT; 6431 BP. XX AC chr20; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-28_VV_; KW Gypsy-28_VV-LTR; Gypsy-28_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6431 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr20; Positions 12633829 12627399. XX CC Positions [5299-5619] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 2281..4170 FT /product="Gypsy-28_VV-I_1p" FT /translation="MIKTTQDVTKMVWMQFELFLSNYFPEAVRRQKRAEFI FT HLIQRNMTVTEYAAKFTQLSRYAPNVVADEQMRAEQFQEGLRLNIRAQVAP FT FMLRTYSEVVERALVIEREMEKAQRLRSKNSRFGGSEKREQDFKRLKMTHP FT QQQPRKQEQYNGATDSAKGPRRCYECGEVGHLRRECPKFQRLAFQPSQRQF FT QQMNPQIQGRQPQGEGNFRQGKPGGKPEQAQQGRFYAIGSQNAESNALVEG FT MLLYFSTWAHVLFDPGATHSFISASFASMLDIEFVPLHCSLCVETPMGGKV FT ETKWVCHACVLYIGGLEVTMDLVLLDISSFDVIVGMDWLARHHAVLDCYLK FT KVTFQTSSGSYMSFYGDRRLTFIPLIRNLDDKWSRKNGRHYFLFNLKGEGK FT KMTTIDCIPMVCEFSDVFPKEFPCLPPHREMDFSIELYPGTDPISIAPYRM FT APVELKELNIQLQELQTKGFIRPSTSPWGAPVLFVKKKDGSLRLCVDYRKL FT NRVTVKNKYPLPRIDDLFDQLCGACYFSKIDLRFGYHQLRVRETDIPKTAF FT RTRYGHYEFVVMSFGLTNAPAAFMDMMNRIYWPYLDHFVVVFVDDILIYSK FT SKEEHGHHLHMALQTLRENQLYAKLEKCDFWL" XX SQ Sequence 6431 BP; 1993 A; 936 C; 1492 G; 2010 T; 0 other; attaattaaa gattaaagta ttttattaat ggtaagatca gcataaatct ttgtttaatt 60 tggtttgatt gaaaaataga ttagtaaaca tgtgatgaat tgggttattt ggacacttgg 120 gatttgttaa taggttgggc tttaagaaaa tcaaaagaat tagtgtttgg taattaatta 180 gggaaattaa tatgcattgt aaatattgtt taattcaatt taaaatttga tctgaaaaca 240 tgtaggatat agattagaga atgtgagaat taaaaatttg caacaataaa ctatataaat 300 tttcatggtt aggaagccta aattatgttg tttcatttca gttcctcgta ataggcaaag 360 atcgcctact tagaagaaac acaaaaagga agtcggtgta aggtagggaa ttttatgcta 420 ttctatggtg tatctgattt ctttccttga attatttgtt ggaattttat gttattttta 480 tgatttcata aaatctttta aagtgtcatt gcatctcggt ttattgcatg gaaatgttac 540 catgatgttg gaacgtatat tggtatgaag attcgtggtt ttgtgttgtc gaaatggttt 600 atggtgtgat tgcattgcaa gaaggatatg gaattatcac agatcatatt cagagaattt 660 attggtggcg aagtgcttat gtgatctaca ggccttatca tttgatatat tgtttatgtg 720 ggaccgtggg tccttgggtg aaagtcccta aagccctcga ggaagacact ccgatgtggg 780 tgtatggggt tggtcctgcc cctgggtttt agtccctaaa gacacggggt tggtcctgcc 840 cttgggtatg agtcccaaaa gacacggggt atgacttgcc cttaggtgat gtcccaaaat 900 agtcattatt atattgatcg agtgtcttgt ggagcattga tatctactgt gtagattgtt 960 gggagtcagc aaattatcag ttgtgaaagg atggatgggg aaaagcaatg atgaaaccaa 1020 caaacacatg catacatgtt tgacatgatt acacatttgt taatggttat gaaatgttta 1080 tcatgcatgt tattaaacgt ttaattcaag gtttttgagg gtatacttag gatggttata 1140 aactttccta ctgagttgtg aactcaccct attccttcca cctatagatg caggtcagaa 1200 gacctatgca ggaaagaatg cttgagcaat gctttactgt gattggatgt tgtttgctca 1260 tattgaaagt cttttgaggc catgcctttt gtatcaagac tacacttttt gttggaatga 1320 tgtaatgtat atatttgtta gatacacttg tagtatgggc tacccatagt aaacaatggg 1380 gtttggtata tgtaaattaa tgttgtataa gtttcttttg tgaaacaaaa catattttgt 1440 taactcaata gtcacaatgt ttattacagg atgtactctt tataacaggt tttccatatc 1500 ctctttttga acaaattcaa gtaggaactc aacatttaaa tttttgagag catttatact 1560 gtatttgagt atcaattctt tagttgaaga ataaataata ataatcataa aaaaaaattt 1620 ggggtgtgac agcttggtat cagagcataa gggattagat ccctattgtg gacaataggt 1680 ggggagccca atagaagcac tagagtcatt attattgtga cattgtttta ttgtgtatta 1740 tatattgata ttaagtgaag gcttaaagga tggatgtcag gtttatgttt ttattgtgtt 1800 gatgacattc cttgttgtat tgaatatgcc tagctataat aattgagatc atgttgcctc 1860 tttgagtggt ttgattgtat tggttaaggg tgcttgattt tatgaataac ccttataagg 1920 tgatgtattg ataataataa tccttgtata cctttctaag agaaaatgcc tagaggaagg 1980 gacagattaa ccacaaggcc taaacggaca actagatcat ctccaatatc tcatggtgat 2040 gtaactgagg gaagacctat aatacatcca gttgctagtt cagaatgcca gaatgtgagc 2100 ttgatttggg aatttaaagc attgaatcct ccaagctttc ggggtggccc taattttctt 2160 gaagctgaga attggatgaa agaaataaag aaaatactgg atgtaatggc aatgcccgag 2220 gaaaggagag tttctttagc ttccttcatg ttgagggatg aagcagacaa ctagtgggat 2280 atgatcaaga ctactcagga tgtaactaaa atggtttgga tgcaatttga gctattttta 2340 tctaattact ttccagaggc cgttagaaga caaaagagag ctgaatttat acatttgatt 2400 caaaggaaca tgacagtgac tgaatatgca gcaaaattta cacaactatc tagatatgct 2460 ccgaatgtgg ttgcagatga acaaatgcga gctgaacaat tccaagaggg gttgagattg 2520 aacattagag cacaggttgc tcctttcatg cttcgtactt acagtgaggt tgtggaaagg 2580 gctcttgtta tagaaaggga aatggagaaa gctcaaaggt tgagaagcaa aaattctagg 2640 tttggtggtt cagaaaaacg agaacaggat ttcaagcgcc tgaaaatgac tcatccccaa 2700 caacaaccta gaaaacaaga gcagtataat ggggctacag attcagctaa gggaccaagg 2760 agatgttatg aatgtggtga ggtgggacat ctaaggagag agtgcccaaa atttcaacga 2820 cttgcattcc agccatctca acgacagttt cagcagatga acccacaaat tcaaggaagg 2880 caacctcaag gggaaggaaa ctttagacaa gggaagcctg gagggaagcc agagcaagca 2940 caacaaggga gattttatgc aatagggtca caaaatgcag agtcaaatgc cttggtggaa 3000 ggtatgctct tatattttag cacttgggca catgttttat ttgatccagg agctacccac 3060 tcttttattt ctgcatcatt tgcctccatg ctagacatag aatttgttcc cctacattgt 3120 tcattatgtg ttgagactcc tatgggtggt aaggtggaaa ccaagtgggt atgtcatgct 3180 tgtgtacttt atattggggg tcttgaagtt acaatggatc tggttcttct tgatatttca 3240 tcgtttgatg taattgtggg gatggattgg cttgcccgac atcatgctgt gttagattgt 3300 tatttgaaga aagtaacatt ccaaacctct tctggttcat atatgagttt ctatggtgat 3360 agacggctta catttattcc tctaattcga aacctggatg acaagtggtc aagaaagaat 3420 ggcagacact attttctttt taatctgaag ggagaaggca aaaagatgac aactatagat 3480 tgtattccaa tggtttgtga attttctgat gtttttccta aagaatttcc atgtttacct 3540 cctcatagag agatggattt ttctattgaa ttgtatccag gtacagatcc aatatcaata 3600 gctccatata ggatggctcc agttgaactt aaggaattga acattcagtt gcaggagttg 3660 caaactaaag ggtttattcg gcctagtacc tcaccttggg gtgctccagt attgtttgta 3720 aagaagaagg atggatcctt gcggttatgt gtggattaca gaaaattgaa cagagttact 3780 gtgaaaaaca aatatccgct acctcggatt gatgacttat ttgaccagtt atgtggggct 3840 tgctattttt caaagattga tttaagattt ggttatcatc agttgagggt acgagaaaca 3900 gatattccaa agactgcatt tcgtacaagg tatgggcatt atgaatttgt ggtcatgtcg 3960 tttgggttaa ctaatgctcc agctgcattc atggatatga tgaatcgtat ctattggcct 4020 tatttggatc attttgtggt ggtatttgtg gatgatattt tgatatattc taagagtaaa 4080 gaagagcacg gtcaccattt gcatatggca cttcaaacac ttagagaaaa ccagttatat 4140 gccaaattgg agaaatgtga cttttggctg taagaaattc aatttttggg gcacatggtt 4200 tctcaagagg gtatctcagt ggatccaaca aaagtggaag ctgtgacaaa gtgggaaaga 4260 cccaagaatg tttttgaagt acgtagtttt cttgggctag ctgggtacta cagaaggttt 4320 gttgaaaact tttctcgaat tgcttgccca atgactagat tgacacgcaa gggagtgaac 4380 tttgattgga atgataggtg tgaagaatcc ttacaagagc taaaaaggag actgttaaac 4440 agcgccagtg ctaattactc ctattagtgg cgaaagatat acagtttatt atgatgcttc 4500 aaaaaatggc ttgggatgtg ttttgatgca aagaggaaga gtggttgctt atgcttctag 4560 gcaattgaag aaccatgagt agaactatcc tacacatgat cttgaactcg cagcaatagt 4620 ctttgcttta aagttatgga gacattactt atatggtgaa aattttgaag tgttttcaga 4680 tcacaaaagt ttgaagtata ttttctctca aaaagatctg aatgcaaggc aaaggagatg 4740 gatggaaacc cttaaagatt ttcactttac tttgcagtat catacaggaa aagctaatgt 4800 ggttgctgat gccctaagta gaaaggctca atgtgtgtta tctgggttgg tggtttatga 4860 gtggaaaatg tatgattaca tcagtgaatt caatccttgc tttgatgtac atgattctgg 4920 tgcatgtttt gtactttggt agctcaacca acaatattgc agaaggttat tgaagctcaa 4980 aggaaagata aaaagttaga gtgcatgcgc tctcaaatca tggcgggtga tgcagtagaa 5040 ggttagaaca tacattctaa tggtgggatt catttcttga ataaactttg ggttcctaat 5100 gatgctcagg tgaaggagga ggtaatgaag gaagctcatc atactcgatt cacagtacac 5160 cctagagaaa ctaaaatgta ccatgatttg aagcgtcaat attggtggca gggtatgaag 5220 cgggatatat ctcaattcgt ttccaagtgt ttaacatgtc aacaagtgaa agttgaacat 5280 cagaaaccag cagggttgtt acaaccacta cctatagcag aatggaagtg ggatcatgtg 5340 acgatggact ttgtgacagg gttgccaaga actctccaaa gtaaggataa tgtatgggtg 5400 atagttgata gattaacgaa attagcacat ttcttaccaa tgagaatcac tgattcagtt 5460 attgtgttga gtaaattgta tgtgaaagaa attgtgaggt tgcacaaggt accactctct 5520 attgtttcag atagggatcc tagatttaca tcacagtttt ggcagtcctt acaaaaagcc 5580 ttgggaactc aaatcaaatt gagttcggca tttcatcctt aaactgatgg gcaatcagag 5640 agagttattc agattttaga agatatgtta cgagcatgtg tgatggattt aaaaggaaat 5700 tgggtggaac atttaccttt gattgaattt gcgtacaata acagcttcca aagcagtatt 5760 ggaatggcac catatgaagc actgtatggg aggccttgta gatctcctat gtgttggatg 5820 gaatctggtg aagctagtct gattgggcca gaattggtgc aagagactac tgacaagatt 5880 cgagtaatac gtgataggtt attggcagca caaagtagac agaaaagtta tgccgatcac 5940 agaaggagac ccctagaatt tcagatagga gatcacgtgt ttttacgtgt aacaccaagg 6000 aaaggcgtat ttcgatttgg aaaaagggga aagcttgctc caagatatgt tgggcccttt 6060 gaaatccttc aaaagattgg agaggtagca tacaaattag ccttaccgcc acaactatca 6120 ggtatacatg atgtgttcca tgtttccatg ttgcggaagt atgagcctga taccacacat 6180 gtactagatt ggcaagattt gaatttgcaa gaagatgtaa cgtatgagga agggccgaga 6240 cagattttag ataaaaaaga gaaggtactc cgaaccaaaa ccatacctct agtgaaagtg 6300 tcatgggatc atcatggagt ggaaggagct acatgggagt tggaatcaga tatgagaaac 6360 aagtacccgg aactctttac aggttcgctt ttgtaaattt cgaggacgaa atttttgtta 6420 gggggagagg a 6431 // ID Copia8-VV_I repbase; DNA; EDCOT; 4165 BP. XX AC AM467700; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia8-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4165 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4165 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 733-733 (2007). XX DR Genbank; AM467700; Positions 3105 7269. XX CC Positions [1525-1887] - Integrase core CC 'AGCTC' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 97..1374 FT /product="Copia8-VV_I_1p" FT /translation="MSSTSEGQFAQPAIPCFNGHYDHWSMLMENFLRSKEY FT WSLVETGYDEPQANAAMTKAQQKRLDEMKLKDLKVKNYMFQAIDRTILETI FT LQKNTSKQIWDSMKKKYEENARVKRSILQTLRRDFETLEMKSGECITDYFS FT RVMSVSNKMRFHGEQIREVTIVEKILRSLTDNFNYIVCSIEESKDTDTLTI FT NELQISLIVHEQKFHKKPVEEQALKVTTDERIGAGGHGRNGYRGRGRGRGR FT QAFNRATVECYRCHQLGHFQYNCPTWNKEANYAELEEHEDVLLMAYVEEHE FT AMRNDVWFLDFGCSNHMCGDARMFSELDESFRQQVKLGNNSKITVKGRGNV FT RLQLNGFNYVLTVVFYVPELKNNLLSIGQLQEKGLAIMIHDGLCKIYHPNK FT GLIIQTAMSTNRMFTLLANKQEKNEVCFQASA" FT CDS 1906..4077 FT /product="Copia8-VV_I_2p" FT /translation="MNMVRLMLSEKKIPKTFWPEAVNWTMYVLNRSPIVAV FT KNVTPEEAWSGVKPTVEHFRVFECVAHVHVPDAKRTKLDNKSLECVLLGFS FT DESKGYKLYDPVAKNVVTSRDIVFEENRQWEWDTSYEEQVLVDLEWGDDDK FT NDTEDNEGDENLEAASEGNEEAEGNENQAAANDAGDATATDASDAPAEGSD FT AMERKVRRAPIWMEDYISGKGLSEGEIELNMALVASTDPINYEEVVMSSKW FT RLAMDSEINSIEKNQTWKLTDLPTGAKTIGVKWIYKTKLNELGEVDKYKAR FT LVAKGYSQQQGVDFTKIYAPVARMDTVRMIVALTAQRGWTIYQLDVKSAFL FT NGELNEDVYVDQPKGYEKKGSEHKVYKLHKALYGLKQAPRAWFSRIEAYFI FT SEGFQKCPNEQTLFTKRSSAGKILIVSIYMDNLIYTSNDEDMISGFKNSMM FT KVFDMTDLGRMRFFLGIEVLQKSNGIFICQMRYATEVLKRFGMFDSKPVSS FT PIVPGFKMSRDDDGVAVNMTNFKQMVGSLMYLTATRPDIMFNVSLISRYMA FT KPTELHLQVTKRILRYLKGTTNYGILYKKGREEELLVFTDSDYAGDIDDRK FT STSGYVFLLSSGVISWLSKKQPIVTLLTTKVEFVAATACACQAIWMKRVLK FT KLSHEQKGCTTIMCDNSSTIKLSRNQVMHGRSKHIDVRFHFLRDLTKDGVV FT ELIHCGTQEQVADLMTKPLKLEAF" XX SQ Sequence 4165 BP; 1406 A; 664 C; 1009 G; 1086 T; 0 other; attggtatca gagccagcac ttggattgag agagggggaa gtcgcaatct ttctgacttg 60 cacacacagg agagtttaaa cacgagagtt tgagagatgt cgagtacaag cgaaggtcaa 120 ttcgcccaac cagccattcc gtgttttaat ggtcattacg accattggag tatgcttatg 180 gagaacttct taaggtcgaa agaatactgg agtttggtag agacgggata tgatgaaccg 240 caagcaaatg cagctatgac aaaagcacag caaaagaggc tcgatgagat gaaactcaag 300 gatttgaagg tcaagaatta tatgtttcag gcaatagaca gaacaattct tgagactatc 360 ctacagaaga atacgtcgaa acaaatctgg gattcaatga agaagaagta cgaagagaat 420 gctagagtaa agcgttcaat ccttcaaact ctaaggaggg atttcgagac tctcgaaatg 480 aaatcaggtg aatgtattac tgattatttt agtagagtta tgtcagtaag taacaaaatg 540 agatttcatg gggagcaaat tcgtgaagtc accattgttg agaaaatcct taggtccttg 600 acagacaact tcaactatat tgtttgttct atcgaggaat ctaaggatac tgacacactc 660 accatcaatg aattacaaat ttccttgatt gtgcatgagc aaaagtttca caaaaaacca 720 gtggaggaac aagctctaaa ggtgaccaca gatgagagaa ttggcgcagg aggacatggc 780 agaaacggtt atagaggaag gggacgaggc agagggcgtc aagccttcaa tagagccaca 840 gtggaatgct accgctgtca tcaactgggg cattttcagt acaattgccc tacatggaac 900 aaagaagcga actatgctga gttggaagag catgaggatg tattgttgat ggcttatgta 960 gaagaacatg aagcaatgcg taatgatgta tggtttttag acttcggctg ctcaaatcat 1020 atgtgtggag atgctaggat gtttagtgaa ttagatgaga gtttcaggca gcaagtaaaa 1080 ctcgggaata actccaaaat aacagtgaaa ggaagaggaa atgtcagatt gcagttaaac 1140 ggtttcaatt atgtcttgac agtagtcttc tacgtgccgg agttgaagaa taatcttctg 1200 agtatcggac aactacagga gaaaggatta gctattatga ttcatgatgg attgtgtaag 1260 atctatcacc caaataaagg cttaattatt caaactgcta tgtcaacaaa tagaatgttc 1320 accctgctag ccaacaaaca agagaagaat gaggtatgtt ttcaggcaag tgcataagaa 1380 ctctatcact tatggcatcg cagatatggt catttaagtc ataaaggtct caatatctta 1440 caaaccaaga atatggtaca tggactgcct catcttcttc ctactacatt ggtgtgcact 1500 gattgtttga acgggaagca acaccgagac cccattccca agaagagtgc atggagggca 1560 accaaaaagc tgcaacttat acatgcaaat atctgtggtc ccgtgactcc cacatcaaat 1620 ggcaaaaaga ggtatgcctt atgctttatt gatgatttta gtagaaaaac atgggtttac 1680 ttcttagttg aaaaatcaaa agctttgaat tcatttaaat gctttaagag acttgttgag 1740 aaggaaacag ggatgtatat caagtgttta cgcactgata gaggaggtga gttcaactta 1800 gaggagttca atgaattttg tagacaatgt ggtatcaaaa ggcagcttac cattgcatac 1860 accccacaac agaatggagt tgccgagtga aagaaccaga cagtgatgaa tatggttcgt 1920 ttaatgctct cagaaaagaa gatcccaaaa accttctggc ctgaggcagt gaattggacc 1980 atgtatgtgc taaacagaag tcctatagtg gcagtcaaga atgtcacccc tgaagaagca 2040 tggtctggtg tgaaacccac agttgaacat tttagagtct tcgagtgtgt ggcacatgtt 2100 cacgtgccag atgccaaaag aactaagctc gataacaaga gccttgaatg tgtgcttttg 2160 ggatttagtg atgagtcaaa aggctacaaa ctatatgatc cagtagccaa aaatgtggtg 2220 acaagcagag atatagtatt tgaggaaaat agacagtggg agtgggacac tagctatgag 2280 gaacaagtct tagtagatct tgagtggggt gatgatgaca agaatgacac agaagataat 2340 gaaggcgatg agaatcttga agctgctagt gaaggaaatg aagaagctga aggaaatgaa 2400 aatcaagcag ctgcgaatga tgcaggtgat gcaactgcga ctgatgcaag tgatgcacct 2460 gcagaagggt ctgatgctat ggaaagaaaa gtcagacgtg ctcctatttg gatggaagat 2520 tacatcagtg gtaagggact atcagaggga gaaattgagc ttaatatggc ccttgtagct 2580 tctacagatc caatcaacta tgaagaggta gtgatgagtt caaaatggag attggcaatg 2640 gattcggaga ttaattccat tgaaaaaaat cagacctgga aacttactga cttgccaact 2700 ggtgccaaaa ccattggagt gaaatggatt tataaaacga agttgaacga acttggagaa 2760 gtagataagt acaaggctcg gttggtagcc aaagggtact ctcaacaaca aggggtagac 2820 ttcactaaaa tttatgctcc agtagctcgt atggatacag tgaggatgat agtggctctt 2880 acagcacaaa gaggatggac gatttaccag ttggatgtaa aatcagcatt cctcaatggt 2940 gaactcaatg aagacgtgta tgtggatcaa ccaaaaggtt atgaaaaaaa ggggagtgaa 3000 cataaggtgt ataaattaca taaagctttg tacggtctaa aacaagctcc aagggcttgg 3060 tttagtcgca ttgaagctta tttcattagt gaaggcttcc aaaagtgccc gaatgagcag 3120 actttattca ccaagaggag cagtgcaggt aaaatcttga tagtaagtat ttatatggat 3180 aatctgattt acactagtaa tgatgaggat atgatttctg gttttaagaa ttctatgatg 3240 aaagtatttg acatgactga tttgggaaga atgagattct tccttggcat tgaggtacta 3300 caaaaatcaa atggcatttt catttgtcaa atgaggtatg ctactgaagt gttgaaacgt 3360 tttgggatgt ttgacagcaa acctgtaagc agtccaattg tgccaggttt caaaatgagc 3420 agagatgatg atggagttgc agtaaatatg acgaatttca aacaaatggt gggaagtttg 3480 atgtacctca cagcaactcg tccagatata atgttcaatg tcagtttaat cagcaggtac 3540 atggctaaac ctactgaact tcacttacaa gttaccaaaa ggattttgag atacttaaag 3600 ggcactacaa actatgggat tttgtataag aagggaaggg aagaagaact gcttgttttc 3660 acggatagtg actatgcagg tgatatagac gatcgtaaaa gcacgtctgg ttatgtattt 3720 cttttaagct caggtgtcat ttcatggtta tccaaaaaac aacccatagt tacattgtta 3780 accactaagg tagaattcgt ggctgctact gcgtgtgcct gccaggcaat atggatgaag 3840 agagtattga agaagttgag tcatgaacag aagggttgca ctactatcat gtgtgacaat 3900 agttcaacga tcaagctttc aagaaatcaa gttatgcacg gaaggagcaa acacattgat 3960 gtgcgatttc atttcttgag agaccttaca aaagatggtg ttgttgaatt aattcattgt 4020 ggaactcagg aacaggtggc tgatttaatg acaaagccac taaaattaga agcattttag 4080 aaactcagga cgatgatggg agtgtgtgaa cctgggatac tgatataaac taattgcagt 4140 ctacagatta gttcaaggga gggta 4165 // ID RAGYPSY3_LTR_MT repbase; DNA; EDCOT; 3310 BP. XX AC AC144592; XX DT 07-NOV-2006 (Rel. 11.11, Created) DT 01-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A long terminal repeat sequence from Medicago truncatula. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW RAGYPSY3_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3310 RA Shankar R. and Jurka J.; RT "RAGYPSY3_LTR_MT: LTR sequence from Medicago truncatula."; RL Repbase Reports 6(11), 587-587 (2006). XX DR EMBL/GenBank/DDBJ; AC144592; Positions 103519 106828. XX CC A long terminal repeat showing characteristic of Gypsy-like LTR, CC from Medicago truncatula. The internal region shares >90% CC identity to Gypsy-like internal region with conserved RT CC polymerase, RNAseH and integrase domains. XX SQ Sequence 3310 BP; 1003 A; 682 C; 528 G; 1097 T; 0 other; tgttataccc tgtttttgga cctaaaaata ctgggcccaa tttcatttca aactttgtca 60 attatcaaat ttcaactgca cagttcaaat tgtctctgcc tcgcagtatt ttcaatcaca 120 attttaccta tgtttttctt gcataaaacc tttcgaaatg tctttacttg tcttgtaagt 180 cattcaaaag tgtctctgaa tcattacatt gctttttcta cagtttattt caaaatttgc 240 aaaaagtcgt acagaagggt attttggtca tttcctgcag tgggacccat tttcatcctt 300 gtgactgtct ctgagtcttt tcagattgat ttttaacatt tcatcagtaa accttgttaa 360 attcatttca aacttgcatc tgagtcagtg tcaagtcaat ttgaatctgt ttaggtcatt 420 tttagcccta ggggcatttt ggtcatttca cacaaaattt tggcatagag aggttacttt 480 gaagtacctc atttaagcca ttggttcgtt ttagtctgtt ttgtcaattt tatttttgtt 540 tcgctttacg tttggtcaaa ttacattttt tactcagttt tatttttaat tgcattttgg 600 tccctcaatt gaggtcccaa aattgcattt tttgtccaaa aagtttttaa tttcatttca 660 gtccttattt tctttttttt cagtccagtc cctatttctt ttaaaattgc aaacaggtcc 720 ttcaagtcaa aaattacagg gcagcgtctc ttttttttcc aatgccacat gtcagctttc 780 taatggtcca atcactcaca catgtcagct ataaatactg ttcacagtgc cacatggatg 840 agatccactc attacaatac acatcaccaa aaaaaacaaa ttcccatttt ctctctcttt 900 tctgttagat caaagcagaa aattcctcaa gaacacaaag aaccctaact gaaattcatc 960 atcaattctc agagattcgt gtacgaatct tcatcatcga attgattcca ccgcaataca 1020 aggtgcgaat tcctcaccgg aagtgaagaa ctcaagcacc gatcacggta gaggcagaag 1080 gaggaaaacc gaatctgcac agagaaaggg gaagaagaca gaaccaaaga aacagcaagc 1140 aaaagagcaa aacgcgcacg caagcaaaca cacgcgcaag ccagcaagca agcaagcaaa 1200 acgcgcacgc aagcaagcac gcgcgcaagc cagcaagcaa gcaagcaagc acgcgaagca 1260 caagcagcaa gagccgtaac agaaaacaag aagaggtaag catcctcttc gttcgtatct 1320 cttccttttt ccaccgttcc tttacaaaaa tttcatcaag attcaaactc agatctactc 1380 cgattcaagc ttttttcgaa aaatctaagt tcggattcga gaagtatata aaaaaggata 1440 tctaaaaatg tgaaaatttc tcgaatcgga gcattttgat tttccggcac ggtggcgccg 1500 ccgccatccg ccgtgccgga acggaggagc tggccggaga agatgaccgg aaagttagag 1560 agaaggagga gcttctctct ctaaaagaga gaagaaagag aaagaggagt aacaaatgag 1620 aaaaaaccgg atttcacata tatatataga gatttaaacc ggtccggttt attttcggtt 1680 ttactctctc attctcagcc ttcagatcaa tctaacgctt cctgtgcttc caggctttct 1740 gattttggtt tgggcctatt attttcaatt tttgcttttt tttgctattt gcaccatgtt 1800 tctttgctgt ttgaacctct gcatgcttaa attttctcta aaaaatctcc aaaaattatc 1860 acatatttct tgataaattt tcatgccttt ttgatgcttc tcaatggttt taaaatgata 1920 aaagagagta tgtgatattt cttggttaat tagagcgctt aggcataatt ttgtgcattt 1980 tagtagtata ttcctcatga aaacgttggc atgcgatatg agttcttaag atgcaatttt 2040 tgtgatgaat tatcactggt tatgggtgca agttgctgct tgtgtatagt gtttttttac 2100 ttccctcttt gctttgcaat taacatgcac ttttactagt taatgaagtg ccaaaatatt 2160 gtgaaagtgt gctataaatt ctagcataaa atgtgtccta ttttccctca tttcgacacc 2220 aaacaagacc tctaaaattt gtcataatga aggaattagg ggtcatgcat gtactagaat 2280 tctataacca ctttcatgca cattttgtca ctttattagt ctcttttatg tcttttctct 2340 taatattttt gtgcactcct tttactctat gctttatttt actaactatt tcatctcatg 2400 tgccatacat ttcatagcat ttcactacct cctccacctt ctctagctta gcatttattt 2460 ttacaagttt taattcattt agaggtgtaa tttgttatca ttggtttgta gcttggcaaa 2520 ggggccatag aatgtattta ggcaattttt gtaatatgga ctatggacac tatgacgcac 2580 cgacacgcac acactcaccc tagatgtatg cttaggattg tatgcataga tgtatggcta 2640 ggattgcatg attagatgaa cgcttagttt cgaacactta gataaaaatc aacttttttc 2700 taaaacatgc aaataacact tgaaaacctt tttgaaaata aaatggagtc aaaactcctt 2760 atttccccct ttattttctt aagtaaaatc ttcaataaat cttaatcctc cttggacttt 2820 atttttgcaa aatgactaat tccacctcac actttccaaa tcttatgccc ttgaggcctc 2880 tcatctcctt tcttcaaaat ctcttttcaa acttaaaatc aaccaacaaa aacaaaaacc 2940 atttttgaga gtgaactacg aacggttttg atcccttaaa agggtacgta ggcaatgagt 3000 caaaactcat ccaagccgaa gtaaaaatca aattctactt cttctcacct ccattcttaa 3060 ctaatcacac cttctttttt acaaataagc aataaaaata aagcgtagaa atcaatttag 3120 gagaacggtt cttatggaat accataatcg ctccgggtgc ctaacacctt cccgtagcga 3180 aaacgacccc cgaatctaga actttttaag ggtttttctc cttttaccct tcccaagaaa 3240 aaagagagat atcaacagtc aaaaggttca agtccaatta atggcttggc acccaaaaac 3300 catgataaca 3310 // ID L1-4_PTr repbase; DNA; EDCOT; 4696 BP. XX AC . XX DT 18-DEC-2009 (Rel. 15.02, Created) DT 18-DEC-2009 (Rel. 15.02, Last updated, Version 2) XX DE L1-type element - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-4_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4696 RA Kojima K. and Jurka J.; RT "L1 elements from black cottonwood."; RL Repbase Reports 10(2), 160-160 (2010). XX DR [1] (Consensus) XX CC The consensus is not complete at its 5' end. XX FH Key Location/Qualifiers FT CDS 430..753 FT /product="L1-4_PTr_1p" FT /translation="MKQKTVGTGKQISKLNNKAKAPIRVRDNRSYLEAVRS FT GSQVHQASDNATPRPHNFISFNTTDEEILWLRNSLIGKISQGVDYAQIRHG FT LIQLGICFSAVRFLGVPRQX" FT CDS 895..4518 FT /product="L1-4_PTr_2p" FT /note="This protein includes endonuclease and FT reverse transcriptase domains." FT /translation="MNILSWNSCGLGMMRKRRRITKLITEYKIDICFLLET FT KLANCSIGFVSRIWNENHVSWFSNDAQGSKGGLLAMWKNTNFEVSNIEYGH FT GWIGLYGKHVHSDFHCFVIGIYAPCNYQDRQXLWDDLILLKHAFEVPWIIA FT GDFNETLSQKDRNSGICHPAGSNSFSRFLQSCELTEYPLAEGYFTWFRGGS FT KSKLDRMFANSSCHLHFPSLSLRRLPREFSDHCPLILSSFLQDHGWRPFRF FT LDCWTQYPNFKHIIENFWNDACSLHPGRFKFLKKLNHIAVRLRQWNKLEFG FT NQEAALQRTLSAINILEEKCEEEGITDQEQEHLDFLLKDRWVRNNHIESIW FT RQKSRQMWCKLGDRNNRFFHLIANFRKAKSSILKIHHNGNTFDSQQGIKQA FT AVDYFSELYDSPSERKPQLNPLGFKCLSKESSEWLEQEITMEEVKRSVWGC FT DGSKCPGPDGFNFKFYRLAWDFIAQDILDIVLSFFRTGRLPKGINTTYVTL FT LPKTVXPIEFKDFRPISMIHGIYKIIAKILASRLKTVMQDIISINQSAFIA FT DRNIIDGFMIANELVSDLKKRKAAGLIFKIDFHKAFDSVSWDYLDDIMGYM FT GFGRKWRSMIYECLSSSKLSVLINGSPSKEFSVRRGLRQGDPISPFLFDIA FT AEGLSVLFQRASXGNILKGLQFASGIFLSHLQYADDTLIFIPADIDQLVQV FT KRILRWFALSSGLHINFHKSSIIGINVDDHLCLRLATSIFCRSDSLPSKYL FT GMPLGANPSRISTWKPVIEKFRKRLHMWKGRLLSMAGRLCLIKSVLNSLPI FT YFMSVFKMPKGVGRLLSSIQRRFLWCGCTKQRSFCKIQWRLVMRDKKQGGL FT GVGSLISKNRALLLKWIWRLSSPGTSLWKMIISSMYNPAYENGIPIFYNQP FT SKIWKDIMSIVQTDVHHVFTNHCKFMVGNGSLTSFWLDNWIGDYPLKTAFP FT RLYLLSSSKSALVADMGRWSNGIWLWSLQWRRPLFHFEQEQLSLLSSLLES FT KPMFCHKMDKKIWTLNSDGLFSVKSCSKMMDQLLYGGAKPFQSSVWIKLTP FT PKVQLFLWLLVQDKVTTRDFLFQHDYLTLQESRCAFCNKSLESSSHLFIHC FT HFTWNIWMKLLSNRGFCSVFPKSVDDMCYQWSSMVKGKQQNLSWQLLFSCV FT VWNLWLHRNDVIFNDAAPNLQICFSMVRQSIALWLRLDSNSLELNIENV" XX SQ Sequence 4696 BP; 1348 A; 1011 C; 956 G; 1370 T; 11 other; gagagagatg ggggaaaggs tctctttcaa aaaacccagc caccgttcca gacaaacata 60 attccttctc acaaacacag aaaacaacct gatcttccat acaagccata ttacccccag 120 cctcagctac catccatcac cttaaacact cagamtttaa caaactaccg tggttttcac 180 ctacaatgtt actttgaaaa cttcccaagt tgggtcgatt accataagct caaagaccgt 240 ttcagaaaac agggcaaagt tattaagttt gtttctcgga aaacaaatca agcaggaaag 300 cattttggct tcgtcaccat cctctcgaat ctgtcagaca aaactctgct agaatgttta 360 aatgacatat ggtttgattc ctacaaactg agagttaatg tggctaagca cagaagaaaa 420 gatgaagtga tgaaacagaa aacagtggga acagggaaac aaatatccaa gctcaacaac 480 aaagccaagg cccccatccg tgtaagagac aaccgaagct atcttgaggc agtaagatca 540 gggagtcaag tgcatcaagc gtcggataat gccacaccac gtcctcataa cttcatctct 600 ttcaacacta cagatgagga aattctatgg ttaagaaata gtcttatagg caagatatct 660 cagggagtag attatgcaca aatcagacat ggattaattc agctaggcat ctgcttctct 720 gctgtccgtt tcctgggggt tcccaggcaa wcataagctt tgatggtgag aaatctatgc 780 aacaagccat gcagaaaggt atggaatgct kgaagctcta ctttgatgaa gttsgcccgt 840 ggacggaaga agatgtgata gagagtcgtc tagcatggat cttttaattc tgtcatgaat 900 attctttctt ggaattcctg tggcttgggc atgatgagga aacgaagaag aatcacgaaa 960 ttaataacag aatataagat tgatatatgt ttcctgctgg aaactaagct agctaattgt 1020 tccattggct ttgtatctcg tatttggaat gaaaatcatg tgagttggtt tagtaatgat 1080 gctcagggat caaaaggagg tctgcttgct atgtggaaaa acactaactt tgaagtctct 1140 aatattgaat atggtcatgg ttggatcggt ttatatggta aacatgttca cagtgatttt 1200 cattgctttg ttattggcat ctatgctcct tgtaactatc aggacagaca amaactttgg 1260 gatgatctca ttcttcttaa gcacgctttt gaagttccct ggataatagc aggagatttt 1320 aatgaaacac tctctcagaa agacagaaac agtggaatct gtcatcctgc aggctcaaat 1380 tcttttagca gatttctgca gtcttgtgag ctcactgaat accctttagc agaaggttat 1440 tttacctggt tcagaggagg gtccaagagc aaactggacc gtatgttcgc aaactcatcc 1500 tgccatcttc acttccccag tttatctctt cgwcgacttc caagagagtt ctcggatcat 1560 tgccctttaa ttctatctag cttcttgcag gaccatggat ggcgtccttt tcgtttcttg 1620 gactgttgga ctcagtaccc aaatttcaag cacatcattg aaaacttctg gaatgatgca 1680 tgctcccttc accctggccg ctttaaattt ctcaaaaagc tcaatcatat tgcagtcaga 1740 ttgaggcaat ggaataagct cgaatttgga aatcaagaag ctgcccttca acgaaccctt 1800 tcagctatca acatactaga ggaaaaatgt gaagaagaag gtataaccga ccaagagcag 1860 gagcatttag actttctgtt gaaagaccgc tgggttcgca acaaccacat tgaatctatt 1920 tggaggcaga aatcaagaca gatgtggtgc aaattgggtg acagaaataa caggtttttt 1980 cacttgattg ccaatttcag gaaggctaaa tcatctatcc twaaaatcca ccataatggc 2040 aacacttttg attctcagca gggtattaag caggctgctg tggattattt ctctgagctg 2100 tatgactccc cctctgaaag aaaaccgcag ttaaatcctt tgggtttcaa atgcctctct 2160 aaagaatcct ctgaatggct ggagcaggaa atcacaatgg aagaagtgaa gcgcagtgta 2220 tggggttgtg atgggtcaaa atgtcctgga ccagatggtt tcaacttcaa attctacaga 2280 ttagcatggg attttattgc tcaagacatc ctcgatatag tcttaagctt cttcagaaca 2340 ggaaggctac ccaaaggaat caatacaacc tacgtaactc tcctccccaa gacagtagam 2400 cccatagagt ttaaagattt tcggcccatc agcatgattc atggtatcta caagatcatt 2460 gccaaaatcc ttgcatccag actgaagact gttatgcaag atatcattag cattaaccaa 2520 tcagcgttta tagcagaccg caacattata gatggcttta tgattgcaaa tgagctggtg 2580 agtgatctaa aaaagcgaaa agcggcaggt ctgattttca agattgattt ccataaagcc 2640 ttcgactcag tctcttggga ttacctagat gatatcatgg gttatatggg gtttggcaga 2700 aaatggagaa gcatgattta tgaatgtctt tcttcatcaa aactctcggt cctcatcaat 2760 ggatctcctt caaaagaatt ctctgttcgg cgaggattgc gtcaaggaga cccgatttcc 2820 ccttttctgt ttgacatagc tgctgagggc ctctcggtcc tctttcaaag ggcatctagk 2880 gggaacattc tcaaagggct gcagttcgca tcaggaattt tcctcagcca cctgcaatat 2940 gcagatgaca cgctaatatt catcccggca gatattgatc agttagttca agtcaaaaga 3000 attctgagat ggtttgctct gagttcaggc cttcacataa acttccataa aagctccatt 3060 attggtatca atgtcgacga tcacttgtgc ttgcgcttgg ctacgtctat tttttgcaga 3120 tcagactccc tcccaagcaa atatctcggc atgccactag gagccaatcc atctcgtatc 3180 tccacatgga agccagtgat agagaagttt cgtaaaaggc ttcatatgtg gaaagggaga 3240 ttattaagca tggctggacg tctttgtctc attaaaagtg tccttaattc cctgcctata 3300 tattttatgt ctgtattcaa gatgccgaaa ggggtaggca ggcttctttc atccatccaa 3360 agacgtttct tgtggtgtgg atgtaccaag cagagatctt tctgcaagat ccaatggaga 3420 ctagtgatgc gcgataagaa acaaggaggc ctcggtgtag gctcccttat atcgaaaaac 3480 agagccctgc tgctaaaatg gatttggaga ctctcttccc caggtacaag tttatggaaa 3540 atgattatct cttcgatgta caatccagct tatgagaatg ggatcccaat tttctacaac 3600 caaccctcca agatctggaa ggatattatg tccattgttc aaaccgacgt tcaccacgtc 3660 ttcacgaatc attgcaaatt catggtgggg aatggcagtt taacatcctt ttggctagac 3720 aactggattg gtgactaccc tctcaaaaca gccttcccta ggctatatct tttgtcttcc 3780 tctaaatctg ctttggtggc tgacatgggt agatggagca atggaatctg gctctggtcc 3840 ctgcaatggc gcagacctct atttcatttt gaacaagaac aactatcact tttatcatcc 3900 ttgctggaat ccaagccwat gttctgccac aagatggata agaaaatctg gaccctcaac 3960 agcgatggcc tcttcagtgt aaaatcttgc tccaaaatga tggaccagct gctctacggt 4020 ggtgccaaac cattccaatc ttctgtttgg ataaaactaa ccccaccaaa agtgcaactt 4080 ttcctttggc tccttgtcca agacaaagta accacaagag attttctatt tcagcatgac 4140 tacctcaccc ttcaggagtc aagatgcgct ttctgcaata aaagcttgga atcttcaagt 4200 cacctcttca ttcactgcca cttcacttgg aatatatgga tgaaactgct ttctaatcgg 4260 ggcttttgca gtgtttttcc aaaatctgtt gatgatatgt gctaccaatg gtcttccatg 4320 gttaaaggca agcagcagaa tctctcatgg cagcttcttt tctcatgcgt tgtttggaat 4380 ctttggctcc accggaatga cgttattttt aatgacgctg cccctaacct ccaaatctgt 4440 ttctccatgg tgcgccaaag tattgcttta tggctgaggc ttgattccaa ctctttggag 4500 cttaatatag agaatgttta gtagggagga gttggtttct tatgtttttt ttgttccccc 4560 ttttgttgct ctcccctgtt tcatgcaaca gcttttgtgc tttcctttcc tctgcttgtt 4620 catctgatgt aagttaggct attatctttg tagccttttt cttaataaaa ctttcgacta 4680 ttaccaaaaa aaaaaa 4696 // ID SHALINE2_MT repbase; DNA; EDCOT; 7617 BP. XX AC . XX DT 19-DEC-2006 (Rel. 11.12, Created) DT 21-JAN-2007 (Rel. 11.12, Last updated, Version 2) XX DE A LINE from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW retroposon; LINE; repeat; Interspersed; SHALINE2_MT. XX NM SHALINE2_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-7617 RA Shankar R. and Jurka J.; RT "SHALINE2_MT: A LINE element from barrel medic."; RL Direct Submission to Repbase Update (19-DEC-2006). XX DR [1] (Consensus) XX CC The sequence contains 2 ORFs. One products of this sequence is CC ethylene insensitive protein while another one is RT polymerase. XX FH Key Location/Qualifiers FT CDS 1565..2272 FT /product="SHALINE2_MT_1p" FT /translation="PPCKSYVSFVAADYGFHNNAGNYSGRGEVDSDLMDIY FT NSGIQLNKNTNVMSTMIPTSGVNHNVHHQIYHASAQLEKNNMSTMIPNHGI FT NQSMHRQIYTGSVQQNKNTIMSTMVPTPSVNLHPQVYTSSVHQQQKRNTMM FT NTSMMSNSMPVMNMVATPGFNQNMQHQMDQNFYAQQGGANSYYHCKVRDAE FT VANVPMQANVSTTSFDPTFEHLKAFNSQFDVDAYNNSVASSSYNWN" FT CDS 5051..6994 FT /product="SHALINE2_MT_2p" FT /translation="MKNILSLYEAASGQAISLPKSEIYCSRNVTDPLKHTI FT TNICSRNVPDPLKHTITNILGVQAVLGTGKYLGLPSMIGRDRNSTFSYIKD FT RVWQKINSWSSKCLSKAGREVMIKSVLQAIPSYVMSIFQLPTTLINSIEKM FT MNSFWWGHGRTTQRGIHWMSWEKLSMPKIHGGMGFKDLTAFNLAMLGKQGW FT KFLTEPDSLVSRIFKARYFPSGTYLTANLGHNPSYVWRSILRARFIVCGGA FT RWSIGSGASIPILNEPWLSNGECIDGDITGAHFVQNFTVNSLMNLYXKSWN FT EQVVRQVFSXDIADKILHTPLIAQVQEDRLIWKAERHGRYSVRSAYRLCVX FT ELIDSSYLWRPGYWSGIWNLKVPPKVKNLVWRMCRGXLPTRVRLLDKGVQC FT PTNCVSCASNHEDLAHVFFDCPFAIQVWNRTGLWGAIQHAMSSTTSAADAI FT FYLLETLSIELNQRLASXIWSLWKHRNLKVWDDVTETSATVVERARNMFDD FT WQLANAPTVIVPSPQHQVQQPIDEGISAAILYPCGSSASAISSGWQHLCLV FT GISVTLMPLSFLTSTVPXLVFVFEILKVRLFWPRLLVSYPCIYSVDVGEAL FT GLHSALQDKLPFDEKLMKIGCQLAYVFNLCFKIGETTLHLFFYSPLAIKL" XX SQ Sequence 7617 BP; 2164 A; 1289 C; 1514 G; 2622 T; 28 other; ggaattacaa caacaaatta tgaaaagttg aatggtgaac caattacact tcactcgctg 60 aatgaactat ccgacaccat attaggttca cttctctcat cattagtgcc gcattgtcac 120 ccaccacaac ggagttttcc attggaaaaa ggcattcctc caccatggtg gccaacaggg 180 aaagaatcat ggaggaatga gatgagattt tgtgaagaac ctggcctacc cccttataga 240 aagccgcata atctaaagaa ggtttggaag gtttatgttt tggcagcggt tattaaacat 300 atgtctccta atgttcataa tattaggaac atagtcagac aatcaaggag tttacaagat 360 aaactcacta tgaaggaaac atctatttgg ggtgcaatta ttgatcatga agaaacaatt 420 gcaagaaaaa tacatcctga atttttctca agttttgatt ctcgtgttga aggaagtaat 480 tatttgcatg ttgaggcaaa tgatgttgat gttgtggaag gtggtgagca caatctagca 540 aaacgaaaat tatcaccatc atcttcacca tcatcatcgt cctcatcgtc atatgagggt 600 actaacaaga gaaaacgtaa acttggcaag aaaattggta ctcatcataa ctcttttctt 660 aacactcatc aacatgctac acctcttgac caacatgaat tccagaagga gaggaatgtg 720 agaaacaatc atcatgttac cagtacacat attggaagca gcagtaacat caacaacaac 780 aaccaattcc aaatggttgg agttgaagtg tcaactactc atcaaaatgt tgcacctctt 840 gcccaacgtg tgcaacctgc ggtacctgtt gcaaatcaga tcattcatca tacaggtaat 900 cattattatt atccaaactt attttcttct actttgttag tcaaaaactt ttttttgcca 960 tttgatgtat gacttgaatc tttgacttat tttcagtcta gtaaattata tgttagctta 1020 taggtttgcg aagttgcttg tttcaaactt aaaatagtat ttttatttaa ctaggaaaat 1080 gttagcttat aggtctcaat tttggacatc attcttaaaa cttattagtg acttaactga 1140 tcatcttaca ataatgtagc atcatataag ttattatatt acaattcata ataagatttg 1200 actcatgctt tagaaaatag gccttatcat tcacaatatg attatggtta ggggcgaatc 1260 ccttcacatc aatggggtag catctacccc aaaagaaaaa taaatctggc tatagttttg 1320 aatgtagata tttatttata ttacttggct actttaaaca atttagttta gtgtcaatta 1380 taaataaatt tgatttttaa aaattcatag agttcaactt ctatacataa tatttgttag 1440 attttatttt cttcgttgta gtttcattaa atataactaa aaattaatgt aaatttattt 1500 tacttattaa ttaggttcac tatattaact tttaaaatat atattttttt ttctatgtat 1560 ttgacctcct tgtaaaagtt atgttagctt tgtcgccgct gattatggat ttcataacaa 1620 tgcaggcaat tactcaggaa gaggagaagt ggattctgat ttgatggaca tatataattc 1680 aggcattcag ctgaataaaa acaccaacgt catgagtacg atgattccaa cttctggtgt 1740 taatcataac gtgcaccatc aaatctacca tgcaagtgct caactggaga agaacaacat 1800 gagtactatg attccaaatc acggtatcaa tcaaagcatg catcgtcaaa tctacactgg 1860 aagtgttcaa cagaacaaga acaccatcat gagtactatg gttccaactc ctagtgtaaa 1920 cttgcatcct caggtctaca cttcaagtgt tcatcaacaa cagaagagaa acaccatgat 1980 gaatacctca atgatgagta attcaatgcc agttatgaac atggttgcca ctcccggatt 2040 taaccaaaac atgcagcatc aaatggatca aaatttctat gcgcaacaag ggggtgcaaa 2100 tagctattat cattgcaaag tgcgtgatgc tgaagtagct aatgttccaa tgcaagcaaa 2160 tgtctcaaca acaagctttg atccaacttt tgagcatttg aaggcattca attcccaatt 2220 tgatgttgat gcttacaaca actctgtggc atcatcaagt tataattgga attaataatt 2280 aaggtaaaat catgaattac tttttaaaaa gtttcaccaa tttttctcaa atagccccct 2340 cttctggtta aagagagtga aactaataat tggtaattta tgattttact tgtaggtcat 2400 tggaaaagga agctttgtgt ttgttatgtg ttcttttgtt aagtttgtgt tattttcttt 2460 aattagtctg cacaaggtgt cgcttcgaga tgcctagcta catagtattt ttttttaagg 2520 aagctacata gtattattaa gcatatttat gaacaatgaa tttgagtgtg gccattatat 2580 gaaggcaggt gtgttgtgtt tatgctcatc atatgaaatg cagacaatta ttttagggtt 2640 tgtgtctttg catatatttt ttttaactgt catgttattt atttttcctt agtcatttac 2700 tttttaacct attttaccgt tgaaagtaaa atcattctct cctattttac tattcttcaa 2760 tcaatgaaga agggatatta taaataaaaa ataataaaga agggaatgga agctaaacat 2820 aacattataa agacgggttt gtgtttgttt ctgccttcct tcttgccgtg agaggatatt 2880 ctctcctatt ttgctattca atcaattgta attacaagta acggttggta ttaatggtgc 2940 acatgctttt ttcttgtctt ccttgtttca ttacttttcg tattgcatca catatatatt 3000 attgaaggat tgatagtggt tcttaatact attacttact gttgcttttg atgccacggg 3060 ttcagccatt atggtgatag aggtttttgg aatttttggg aatgaattag gtgttgttag 3120 tggaatattg gaattaagtc taatcttgcc aaggtaaatc agtcttatag ggtggaattg 3180 ccaggtttag gtagctcgag cgcaattcct gacctaaaat acctagctcg acacttcaat 3240 ccggacctcc tcttcttaag tgagacatta gtccaccgaa ataaaattga agatttacgt 3300 tatttgcttg gttttgatgc ttgtttttat gtagaccgca ccggcagagg agggggtctt 3360 gctttatttt ggcacaattc tttaaattgt cagctttttg atttttctaa taatcatatc 3420 actgttgaga ttattgatta tgttcttggt acttggagac ttaccgaata ttatggttat 3480 cctaatggag gtcgtagaac tgctgcttgg aattttctcc gacaactttc taatcaattt 3540 gcaagtcctt ggtgtatttt tggtgatttt aatgatattt tggatgcaag tgaraaaaga 3600 ggtcgcaact ctagaccccc atggctgaty aatggctttc gacaagctgt gcttgattca 3660 ggtttgtctg atgttcagat tgaaggctat ccctttactt ggtttaaaag tctaggtacg 3720 ccacgtgcgg tagaggaaag gttagattgt gctcttgcta ataatttgtg gtttaattta 3780 tttycgratg cttatgtaga aactcttgtg gcaccagctt ctgatcatta tcctattctt 3840 ttaaatcgta ctcctatgcc tcggcctcat ctcaataaac gccattttcg ttatgaaaat 3900 gcgtggcayt ttgaaccggg gtttaaggaa atggttacta attcttggca ggtatattct 3960 agcaatcgtc ttattccaaa gttgttctct tgtgcggaag atatgttyat ttggagtaaa 4020 tmtcattgyc aaaaattaaa aagagacatt gaagactgtc gtaaacaatt gaaaaatact 4080 cggctcaact cttcaggtga ggawtaggtc cgcatgtatg agytaacgaa acgcatgcag 4140 cgtttattat ctcaagatga tgcttattgg cgtcaacgtg caaagaccca ttggtataag 4200 gatggagaca aaaataccaa attttttcat gcttccgcta cggctagaaa gaaggtaaat 4260 cgtattattt ctcttgatga tgatgctggt aataaaatta ctgatgagca gggtttacac 4320 gatgtcgcaa gaaattattt tgtgaatatt tttcaaaagc aaggaagtga tttatctcct 4380 gttattgatg ttattaacta gtctatttct gcttttgata atgagaaact camggcwccy 4440 ttcaccaagg ccgagtttcg tgctgctatg ttttccatgc acccggataa atgtccaggt 4500 cctgatggtt tcaatcyggg tttttaccaa catttttgga atttgtgtag tgatgatatt 4560 tttaaagaat gttgtggttg gtcaattatg gataatgcta tggttgcaat ygaggttatt 4620 catttcatga aaactaagac gaggggcgag gacagatatg ttgctcttaa actagatatt 4680 agtaaggctt atgatcgtat ggattgggat tacttgagag ccgttatgat taaaatgggg 4740 ttcaatgttc tttggattcg ttttcataaa atgctctttg gattcattgg atgagtatgt 4800 gtgtagagtc agtggattat tctgttcttg ttaatagtga aaaggttggc cctattattc 4860 cggggcgcgg cattcgacaa ggggatcctc tttccccgta tttgtttatt atttgtgcag 4920 aaggtctatc ttctcttatt agagatgccg agrcgagagg tgttattaca ggtaccaaaa 4980 tttgtcgagg ggcgccctct gtttctcatc ttttcttttc ttcaaagctg acgagagtca 5040 agcacatgtt atgaagaata ttctctcctt atatgaagca gcgtctggtc aagccatcag 5100 tttgccaaag tctgaaattt attgtagtcg taatgttact gatcccctaa agcatacaat 5160 cactaatatc tgtagtcgta atgttcccga tcccctgaag catacaatca ctaatattct 5220 tggggttcag gctgttttgg gaacaggtaa atacttgggt ttaccttcta tgataggtag 5280 agaccgcaat tcaacttttt cttatatcaa ggatcgtgtt tggcagaaaa taaattcttg 5340 gagtagtaag tgtctatcta aagcagggcg tgaggttatg ataaaatctg tcttgcaggc 5400 tattccgtca tatgtcatga gtatttttca gctaccgact actttaatta actccattga 5460 gaagatgatg aattctttct ggtggggtca tggtagaact acacaacgag gtattcattg 5520 gatgagttgg gagaagctgt caatgcctaa gattcatgga ggaatgggtt tcaaggacct 5580 cactgctttt aatttggcta tgctaggtaa gcaggggtgg aaatttctta cagaacctga 5640 ctctcttgtc tctcgtattt ttaaagctcg atattttccc tctggtacct atctcacggc 5700 caaccttggt cataatccga gctatgtttg gcgtagtatt ctgcgcgcta gatttattgt 5760 ttgtggtggt gctcgatgga gtattggttc aggtgcgtct attcctattc tgaatgaacc 5820 gtggttgtct aatggggagt gtattgatgg tgatattaca ggtgctcatt ttgttcaaaa 5880 ttttactgtt aatagtttga tgaatttata tgrtaagagt tggaatgaac aggtagttcg 5940 acaggtgttt agtgwtgata tagcagacaa aattcttcat acgccactta ttgctcaggt 6000 acaagaggat agacttattt ggaaagcgga aagacatggt cgttattctg ttcgtagtgc 6060 ttacaggtta tgtgtgaamg aacttattga ttcttcttat ctttggcgtc cgggttattg 6120 gtctggtatt tggaatctma aagttccycc gaaggttaag aatttagtkt ggcgtatgtg 6180 tcggggctkc ttaccgactc gwgttcgtct gcttgataaa ggagtccaat gtccaactaa 6240 ttgtgttagt tgtgcctcga atcatgagga ccttgctcat gtattttttg attgtccttt 6300 tgctatccag gtttggaata ggacaggyct ttggggtgct attcaacatg ccatgtcatc 6360 tactacttca gctgctgatg ctatttttta tttgctggaa actttgtcta ttgaacttaa 6420 ccaacggttg gcatctayaa tttggagtct atggaagcac cgtaatctta aagtttggga 6480 tgatgttaca gaaacaagtg ccacggttgt tgagcgtgct agraacatgt ttgatgattg 6540 gcaactggct aatgctccca ctgtaattgt tccatctcct caacatcaag tgcaacaacc 6600 tattgacgag gggatttcgg ccgcaatttt gtatccatgt ggtagttcgg catctgcaat 6660 atcctctggc tggcagcacc tctgtctggt aggtataagt gtaacattga tgccgctttc 6720 ttttctcacc tcaaccgtac cagyattggt atttgtgttc gagattctga aggtacgttt 6780 gttctggcca agactgctag ttagttaccc atgtatttat tcggttgatg ttggtgaagc 6840 tttgggattg cactctgctt tgcaggacaa attacctttt gatgagaagt tgatgaaaat 6900 aggctgccaa ctagcatatg tcttcaatct ttgcttcaaa ataggtgaaa ccactcttca 6960 cctcttcttc tatagccctc tagctattaa gctttgatta ctttggaact atggaggatg 7020 tttggaattt atgtgaggtc ttggtctcct taatgaaaaa ttgtcattat tgcagctttg 7080 gttaacctta ttaacactat ttggtttgtg agaaatgaag ctagacttaa taacaaagta 7140 atcacttgta ggtcagttat ttcttctata attactaata catctgttac tggtaatcac 7200 acacacaaag cttccaataa ctctattaca ggcttctcaa ttctcaaaag tttcaaggtt 7260 gacattcacc attctaatgt tccttccatt atagaagtct tgtggtctcc tccactacct 7320 gacaggacaa aatgtaacac agatggagca tctgttggta accctggtcc ctcctcttgt 7380 gggggtagtt ttagagataa cgaaggtaac tgtttagggg tgtttttccg aacccttgcg 7440 atttttcaat tcttatctgg cataactatg tggggctatg agagccattg aagtggctgc 7500 tcataatcac tggtttaatc tttggttaga gacaaattct atgttagttt tgcaggcttt 7560 taaaaattca aaccttgttc catggcaaat tagaaataga tggaacaatg ttcatat 7617 // ID GYPSY3-I_MT repbase; DNA; EDCOT; 11760 BP. XX AC . XX DT 14-SEP-2005 (Rel. 10.09, Created) DT 14-SEP-2005 (Rel. 10.09, Last updated, Version 1) XX DE Gypsy-like LTR retrotransposon from Medicago - internal DE consensus. XX KW Gypsy; LTR Retrotransposon; Transposable Element; gag-pol; KW reverse transcriptase; GYPSY3-I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-11760 RA Gentles A. and Jurka J.; RT "Gypsy element from Medicago truncatula."; RL Repbase Reports 5(9), 248-248 (2005). XX DR [1] (Consensus) XX CC This Gypsy-like element has large ORFs, with several nearly CC complete copies in the M. truncatula genome. It shares regions of CC similarity with GYSPY2-I_MT, but is a distinct full-length CC element. XX FH Key Location/Qualifiers FT CDS 2565..6008 FT /product="GYPSY3-I_MT_1p" FT /translation="MDYLEQENRVLREEMTAMQTRMDEMAELIKTMAEXQT FT QAQAQIQAQAQALAQAQTQAQAXTEAQARSQAPPPPPPVRTQAEASSSWTL FT CADTPTQSAPQRSXPWFPPFTAGEIFRPITCEAQMPTHQYTAQVPLPAMRV FT TPATMTYSAPVIHTIPQTEXPIFHSGNXEAYXEVSDLREKYDELRRDMKAL FT XEKGKFGKTAYDLCLVPSVQVPHKFKIPDFEKYKGSSXPEEHLKMYVRRMP FT AYAQDDQILIYYFQESLTGPASKWYTNLDKTRVQTFRDLCEAFVEQYSYNV FT DMTPDRSDLQAMTQGDKXTFKEXAQRWRDTAAQVSPRIEEKEMTKLFLKTX FT NHFXYKKMVGSTPKSFAEMVGMGVQLEEGVREGRLVKNTTPASGTKKTGNH FT FPRKKEQEVGMVTHGXPQQTYPAYQHIAAITPTSHPFQQTNNHPQIPQYPQ FT XPQYPQIPQYPQFPQNPSPQNXQQQNXQQQXFQQQPYQQYPYQQYPQQNFQ FT QQPYQQRPQQPRPPRMPINPIPVTYAELLPGLLKKNLVQTRTAPPIPEKLP FT SWYRLDQTCDFHEGGRGHNIETCYAFKSXVQRLINDGKITFTDSAPNVQTN FT PLPNHGAATVNMIEDCQKTRPILNVQHIRTPLVPLHAKLCKVDLFEHDHDL FT CEICLMNSGGCQKVRNDIQGLLDRGELVVERKCDDVCVITPEGPLEVFXDS FT RKSTITPLVICLPGPLPYASEKAIPYKYNATMIEEGREVPIPPLSSVDNIV FT EDSRVLRNGRVVPIVFPKKIDATINKEXRTKDAGXAKEVDQPNGAGTSAEF FT DEILKLIKKSEYKVVDQLMQTPSKISIMSLLLNSEAHKDALMKVLEQAFVD FT YDVTVGQFGGIVGXITACNNLSFSDEELPAEGRNXNRALHISVNCKTDALS FT NVLVDTGSSLXVLSKTTYTXLAYQGAPLRRSGVMVKAFDGSRKDVLGEVXL FT PITVGPXVFQVNFQVMDIQASYSCXLGRPWIHEAGAVTSTLHQKXKFVKNG FT KLVTVNGEEALLVSHLSSFSFIGADDVEGTPFQGFTIEDKNTKRNEASISS FT LKDAQKVIQAGGSTSWGKLIELPENKHREGLGFFPSTGLSTAKXGTFHSSG FT FIHAIIEDDPESVPRGFITPGVSSHNWVAVDVPFVAHLSK" FT CDS 6272..9742 FT /product="GYPSY3-I_MT_2p" FT /translation="MCRLEIDEPVEQHNPMISPNFEFPVYXAEEEENEEIP FT DEISRLLEQERKTIQPYGDELEVINLGTKEDKKEIKVGASLETSVKKQVIE FT LLKEYVDVFAWSYXDMPGLDTDIVVXHLPLXPXCPPVKQKLRRTRPDMALK FT IKEXVQKQIDAGFLXTSNYPQWLANIVPVPKKDGKVRMCVDYRDLNKASPK FT DDFPLPHIDVLVDSTAKSKVFSFMDGFSGYNQIKMAPEDREKTSFITPWGT FT FCYKVMPFGLINAGATYQRGMTTLFHDMIHKEIEVYVDXMIVKSITEEDHV FT KYLQKMFQRLRKYKLRLNPNKCTFGVRSGKLLGFIVSQKGIEVDPDKVKAI FT REMPAPRTEKEVRGFLGRLNYISRFISHMTATCGPIFKLLRKEQGIVWTED FT CQKAFDSIKKYLLEPPILIPPVEGRPLIMYLTVLENSMGCVLGQQDETGRK FT EHAIYYLSKKFTECESRYSMLEKTCCALAWAAKRLRHYMINHTTWLVSKMD FT PIKYIFEKPALTGRIARWQMLLSEYDIEYRSQKAIKGSILADHXAHQPLED FT YRPIKXDFPDEEIMYLKMKDCDEPLFGEGPDPDSVWGLIFDGAVNVYGNGI FT GAVLLTPKGXHIPFTARLRFDCTNNIAEYEACIMGIEEAIDLRIKNIEIYG FT DSALVINQIKGKWETLHAGLIPYRDYARRLLTFFNKVELHHXPRDENQMAD FT ALATLSSMIKVNHHNDVPLISVKFLDRPAYVFAAEAVFDDKPWFHDIKVFL FT QTREYPPGASNKDKKTLRRLSSNFFLNGDILYKRNFDTVLLRCVDKYEADL FT LIHEIHEGSFGIHPNGHTMAKKILRAGYYWMTMESDCYKHTRKCHKCQIYA FT DKIHMPPTTLNXLSSPWPFSMWGIDMIGRIEPKASNGHRFIXVAIDYFTKW FT VEAASYANVTXQVVVKFIKNHIICRYGIPNRIITDNGTNLNNKMMKELCDD FT FKIEHHNSSPYRPQMNGAVEAANKNIKRIVQKMVVTYKDWHEMLPFALHGY FT RTSVRTSTGATPFSLVYGMEAVLPVEVEIPSLRVLMEADLSEAEWVQNRYD FT QLNLIEEKRMTALCHGQLYQKRMXQAFDKKVRPREXKEGDLVLKKIFSFQP FT DSRGKWAPNYEGPYVVKXAFSGGAMTLQTMDGEELPRPVNTDAVKKYFV" XX SQ Sequence 11760 BP; 3684 A; 2555 C; 2309 G; 3039 T; 173 other; gaaatggcga cttcactggg gacnnacccc tnaagagggt tgagcctaac ttggctttat 60 ttaattcttt gtgctataac ttgcttaaaa caaaaanaaa aaaaataaag atggaaataa 120 attgtatata tcttttatct tctcttttct ctctttcttc ntttcttntt aaatatgagt 180 ggtgagataa agccctacac ccgggcttga gagaaacata agataggacg gtggtataac 240 caaagtgcct ttccgagagt caagtctcgt gtttaggttc atgtggtaca accccactca 300 atggaggnat cttgaaagta atntatgttg gcatgaatag tcgtgttggc attatatttt 360 caagtgaccg tcgaagttga ggacctttag ttacccttaa cccatcttag cctttttagg 420 acgtagtgcg gtggctaatc aagagtagtc ttgaattagt tgatacgcga tactacactc 480 aaangaaact ttcctacgna tnttattgga tcaagagtag tcttgtaacc tgataacatt 540 cggaggtngt tnatgacttt gggaactngn tagaacccgt gatacaggta caaatgaaac 600 catagtcctt accaaatggg ggttattacc tttaaactcc aacatgatga gcntaaccta 660 cgcataatca tgcatacatg cattcattca taattttatc tttttttcat caaaaaatat 720 cgaagggctt atacttgttt ttgtaaatat cataggcatg gaaagaagaa atactaggaa 780 gtttacattc aggaaattgg atctagagaa nttaaagaag cttgcatttg aagtaactag 840 cttggagaan ttttgtgatc gtcatgggaa nttgcttggt ntcctctgga caaatatcga 900 gaaggggtgc ttggagacct tggtccagtt ctatgaccct gcttaccact gtttcacctt 960 tcccgactac cagcttatgc ctaccctcga agaatactct cacttaattg gcctacccgt 1020 acttgataag gtacctttta cnggnttaga accntttccc aaagccgcca ctattgcaaa 1080 tgccctccat ctcaaaacct ccctcataaa agaaaaactn accctaaaag ggaatctccc 1140 aagcttacct actaaatttc tttaccaaca agcctccgan ttntccaaaa caaacaatgt 1200 tgaggccttt tactctatcc tagctttact catctatggc ctagtattgt tcccaaatat 1260 tgataactat gttgacatcc atgccatnca aattttcctc acaaagaacc cagtccccac 1320 attgttagct gatatatatc attccattca cgatcgaacc caagtaggtc gtggagctat 1380 ccttggttgc gcacccttac tatacaaatg gtttacctct cacttacctc agacccactc 1440 ctttcaagcc aacccagaaa atctctcctg gcccaaaaga atcatgtccc ttaccccatc 1500 cgacataacc tggtaccgtg ccacttgtaa cttcacgaac atcattgtca gttgtggaga 1560 atactcaaat gtaccccttc tcggtacgca aggaggaatc agctacaatc ctatccttgc 1620 caaacgtcag ttcggatgnc caatggaagc taagccagat aacatctacn tacagggtga 1680 attctacttc aaccatgaag atccctcaaa caaaagaggg agatttgtcc aagcatggca 1740 tgccattcgc acactcaata gaagccaatt ggcgaggaga tcagactctt tacaggggtc 1800 ttacactcaa tgggtcatca atagagcttc cnatctggtc ttaccatatc atttgccnag 1860 gtacctatct tcaacaaccc cagcnccggc tttacccttg gcccccgcaa ctgtggagga 1920 atgtcaagag aagttggccc natcggaatg tgtgggtgct acttggaana ggaagtatga 1980 tgaagctatg ctcaagatgg aaactatgag tggtgagata gagcaacnag agcatgaggt 2040 tcacaagntg agacgacaaa tagtaaaaaa gaatgttcag atccgagctc agagcacaag 2100 gctatcacaa tttatcagcg caggggagcg ttgggagttc ttcaaagang cacattcaga 2160 ttctgatgaa tagtctactt caaagagctt gagagttccc agtttttctt ttatttttgt 2220 ttttagcttt aagattagat atttatctta ttttattttt tgcaaagtct atcccttggc 2280 ttcgttgttt agaaagggaa ttatctnnta gtatgnnaat tattcaaatg gaactctcaa 2340 ctatgatatt tacaaaaata ctttcataag tccttcgata aaaaaatana nntntatttt 2400 tgcataaaca tcatgcatca tcctgcattt catagtctca aatcaaagtc tcacacaaan 2460 ttccttttcc aganaaaagg gtcaactcgt ttcatanggt ggccccacgt atcatctaca 2520 agtcaacccg tactcactac actcgagcaa acgtaaagaa gaagatggat tatcttgagc 2580 aggaaaatcg ggtacttcgt gaagaaatga cagccatgca gactaggatg gacgagatgg 2640 ctgaattaat aaaaacaatg gcngaanctc agactcaagc tcaagcacag attcaagcac 2700 aagcgcaagc attggcacaa gcncaaactc aagctcaggc cntaacagaa gcgcaggccc 2760 gatcacaagc acctccaccc cctcctcctg tcagaactca ggccgaggca tcttcttctt 2820 ggacactatg tgctgacact ccaacgcagt ccgctccgca acgttccncg ccttggtttc 2880 cacctttcac tgctggggag atatttcgtc ctatcacttg tgaagctcag atgcccactc 2940 accagtacac ggctcaagta cccctacctg ccatgagggt cactccagcc accatgacct 3000 actcagcacc tgtgatacat acaattccgc aaactgaaga ncctatcttt cattcaggga 3060 atgnagaggc ttacgangaa gtaagcgacc tacgagaaaa gtatgatgaa ctacgccgag 3120 acatgaaagc tctccntgaa aaagggaaat ttgggaagac tgcgtacgat ctctgtttgg 3180 taccnagtgt gcaggtacct cacaaattca agattccaga tttcgagaaa tacaaaggga 3240 gttcttgncc tgaggaacat ctaaaaatgt atgtgagaag gatgcctgcg tatgcccaag 3300 atgatcagat tcttatttac tacttccaag aaagcttgac cggccctgct tcaaagtggt 3360 acacaaacct agacaaaaca agggttcaaa ctttccgtga cctttgtgaa gcttttgtgg 3420 aacagtacag ttacaatgta gacatgactc cggaccgaag tgatctccaa gccatgactc 3480 agggngataa aganacgttc aaagagtang cccaacggtg gagagacacc gctgcccaag 3540 tcagcccacg nattgaggag aaagagatga ccaagctctt cctaaaaact ntnaatcatt 3600 tttantacaa aaagatggtc gggagtacac caaagagctt cgcngagatg gttggtatgg 3660 gagtacagtt agaagaagga gtccgagaag gacgcttagt aaagaataca actcctgcca 3720 gtgggaccaa gaagaccggg aaccatttcc cgaggaagaa agaacaagaa gtcggtatgg 3780 tgactcatgg anggcctcaa caaacttatc cagcctatca acacattgct gccatcacac 3840 ccacctctca cccttttcaa caaacaaata accatcctca aataccacaa tatcctcaaa 3900 tnccacaata tcctcaaata ccacaatatc ctcaattccc acaaaatcct tcaccacaaa 3960 atncncaaca acaaaatntc caacaacaaa anttccaaca acaaccatac caacaatacc 4020 cataccaaca ataccctcaa caaaatttcc aacaacaacc ttatcaacaa cgcccacaac 4080 aacctcgacc accaagaatg ccgattaacc caataccagt cacctatgca gaattacttc 4140 ccggcttact caagaaaaac cttgtccaaa ctagaacagc tcctcctatc ccagaaaaac 4200 taccatcttg gtatagactt gaccaaactt gtgacttcca tgaagggggc cgtggccata 4260 acattgaaac ttgttatgcc tttaaaagcn cagtncagag gttgatcaat gatggaaaaa 4320 taactttcac agactcggcg ccaaatgttc aaacaaaccc attgccgaat catggtgccg 4380 caacagtcaa catgatcgaa gattgtcaaa agactcgtcc cattctgaat gttcaacata 4440 tcagaacacc nttggtcccn ttacatgcca agttatgcaa agtcgacctn tttgagcatg 4500 atcatgatct ctgtgaaata tgccttatga actccggagg atgtcagaaa gtaagaaatg 4560 atattcaagg gcttctagac cgaggagagc ttgtggtcga aaggaagtgt gatgatgtgt 4620 gtgtaataac tcccgaagga cctttggagg tattttanga cagtcgaaag tcaactatca 4680 cccctctggt gatctgctta ccgggtccac tgccatatgc ttctgaaaaa gccattccat 4740 acaaatacaa tgccaccatg attgaagagg gtcgtgaggt tccaataccg cctttgtcta 4800 gtgtggataa tattgttgaa gacagtagag ttctgagaaa tgggcgcgtt gttcccatag 4860 tgttcccaaa gaagattgat gctacaataa acaaggagnt tcggactaaa gatgctggtn 4920 tcgccaaaga agtggatcaa cccaatgggg ctggtacaag tgcagagttt gatgagattc 4980 tcaagttaat aaagaagagc gagtacaagg ttgttgacca actgatgcag actccatcca 5040 aaatatccat aatgtcttta ttactaaatt ctgaggccca taaagatgca ttaatgaagg 5100 tnttagaaca agcttttgtg gattatgatg taacggtggg tcagtttggc ggaatagtng 5160 ggaanatcac tgcatgcaac aacttgagtt tcagtgatga agagctccca gcagaaggaa 5220 ggaaccanaa tcgggcgctg catatatctg tgaactgtaa aaccgatgct ttgtcaaatg 5280 tgctggtnga tactggatca tctttgaang tnttgtccaa aacaacttat acccanctcg 5340 cttaccaagg cgcacctttg agacgaagtg gggtaatggt gaaagctttt gatggctcga 5400 ggaaggatgt cctnggagag gtgnttctac ctatcacagt tgggccacan gttttccaag 5460 ttaattttca agtcatggac attcaagctt cgtatagttg cntactgggt cgaccctgga 5520 ttcacgaggc aggggctgtc acatccacgc tgcatcaaaa gntgaagttt gtgaagaatg 5580 ggaagctagt aactgtaaac ggtgaagagg ctttattggt gagtcatttg tcatctttct 5640 ctttcattgg ggcagacgat gtcgaaggga caccttttca agggtttact atagaagata 5700 agaataccaa gaggaatgaa gcctctatct cntctctnaa agatgctcag aaggtcatac 5760 aagcaggagg gtccacaagc tggggaaagc tgatagagct tccagaaaac aagcaccgag 5820 aaggtttggg tttcttccca tctactggtt tgtccacagc naagaanggc actttccaca 5880 gttcgggctt tatccatgca atcattgaag atgatcctga aagtgtgcca cgaggtttta 5940 taacgccagg agtatccagc cacaattggg ttgcngtaga tgttcctttt gttgctcact 6000 tgtccaagta atgcatttgt ctagtttatg cttttctttt caaaaaaaaa aacaaacaaa 6060 aatcctttcg ccccgcccca agcgaaagtg aacttatcta gggcttttta tttcaagaaa 6120 ttatcatcaa taaaataaaa atgtcgtttt ttttcccgat gttttgtctc attttctttt 6180 atgcttttct gaaaagtggt aatacaaaaa acccaacatg aattttcaaa aaaatctgca 6240 tgtatcttnt ttctaaaaaa tcatccatca catgtgcaga ttagaaatcg acgaacccgt 6300 tgaacaacat aaccctatga tctctcccaa ctttgagttc cctgtgtatg angcggagga 6360 agaagagaat gaagagatcc ctgacgaaat ctctcgacta ctcgaacaag agaggaagac 6420 cattcagcct tatggggacg aactagaagt gattaacttg ggcaccaaag aagacaagaa 6480 agaaatcaag gttggggcat cgctcgaaac aagtgttaaa aagcaagtga tagagctcct 6540 caaagaatat gttgatgtgt ttgcctggtc ctaccnagat atgccgggtc tagacactga 6600 tattgtggta cancacctac ctttgaancc tgantgtccg ccagtcaaac aaaaattgag 6660 aagaacacgt cctgacatgg ctctcaaaat caaagaagan gtacagaaac agatcgacgc 6720 tggtttcctc ntcacatcaa attaccccca atggttagct aacatagtgc ctgttccaaa 6780 gaaagatggt aaggtcagaa tgtgtgttga ctaccgtgat ttaaacaaag ctagcccgaa 6840 agacgacttt cctttacctc atattgacgt gttggttgac agtactgcaa agtctaaagt 6900 cttctcattc atggatggat tctccggtta taatcaaatc aagatggcac ccgaagatag 6960 agagaaaacn tcatttatta caccttgggg cactttctgt tacaaagtaa tgccgttcgg 7020 tttaatcaat gcaggagcta cttatcagag gggtatgact actctnttcc acgatatgat 7080 acataaagag attgaggtct atgtggatga natgatagtc aagtcgatta ctgaagaaga 7140 ccatgtcaag tatctacaga agatgttcca gcgcctgagg aagtacaaac ttcgtctaaa 7200 tcccaacaaa tgcacttttg gtgtcagatc cggaaagctt ctaggnttca ttgtcagcca 7260 gaaaggcatc gaagtagatc cngacaaagt caaagccatc agagagatgc ctgctccgag 7320 aacagaaaaa gaagtaaggg gttttcttgg acgactaaat tacatctccc ggttcatttc 7380 tcatatgact gcaacttgtg ggccgatatt caaactactc cgcaaagaac aaggtattgt 7440 gtggaccgaa gattgccaga aggcttttga cagcataaag aagtacttgc tagaaccacc 7500 gattctcatc cctccagttg aaggaagacc tttgatcatg tacctaacng tgttagaaaa 7560 ttccatgggt tgtgtgctcg gacaacaaga tgaaaccgga agaaaagagc acgccattta 7620 ttatttaagc aagaagttta ctgaatgtga atctcgctac tccatgctcg agaagacntg 7680 ttgtgctcta gcctgggctg ccaaacgcct ccgtcattat atgattaatc acactacttg 7740 gctggtatct aaaatggatc caatcaagta catatttgag aagcccgctt tgacaggaag 7800 gattgcacgg tggcagatgc tactatctga atatgatatc gagtaccgtt cccagaaggc 7860 aattaaaggc agtattcttg ctgatcactt ngctcaccaa ccacttgaag actatcgacc 7920 tatcaagttn gactttcctg atgaagagat tatgtatcta aagatgaaag attgtgacga 7980 gccactattc ggagaaggtc ctgatccaga ttcagtgtgg ggtttgatat ttgatggggc 8040 tgtcaatgta tacggcaacg gcataggngc agtactcctt actcctaagg gtnctcacat 8100 ccctttcaca gcaagactcc ggtttgactg cacaaacaac atcgctgaat atgaagcctg 8160 catcatgggt attgaagaag ccattgatct nagaatcaag aacatcgaaa tatatggaga 8220 ttcagctctt gtaatcaacc agatcaaagg aaaatgggaa actcttcacg caggactaat 8280 accttatcga gactatgcaa gacgtttatt gaccttcttc aacaaagtgg aattacatca 8340 tatncctcgg gatgagaatc agatggcnga tgccttggct actttgtctt caatgatcaa 8400 ggtgaatcat cacaatgacg tgccactaat cagtgtcaaa ttccttgata gacccgctta 8460 tgtgtttgcc gctgaagcag ttttcgacga taaaccntgg tttcatgata ttaaagtgtt 8520 tctncaaact cgagagtatc ctcctggagc atccaacaaa gataagaaga ctctcagaag 8580 attatctagt aatttcttcc tgaatgggga tatcttgtac aaaagaaact ttgacacggt 8640 cttgctcaga tgtgtagaca aatatgaagc tgatttattg atacatgaaa tacacgaagg 8700 atccttcgga attcatccta atgggcacac aatggctaaa aagatattgc gagcaggcta 8760 ctactggatg acaatggaat cagattgcta caagcatacc agaaagtgtc acaagtgtca 8820 gatatacgcc gacaagattc atatgccgcc nactacactc aatttncttt cctctccgtg 8880 gcctttctct atgtggggca ttgacatgat cggaaggatt gagcccaaag cttcnaatgg 8940 acaccgtttc atcntagtgg ctattgacta cttcactaag tgggttgagg ccgcatcnta 9000 tgccaatgtg accaancaag tngtggtcaa atttatcaag aatcatatca tttgtcgcta 9060 tggcatcccc aaccggatca tcaccgacaa cggaacaaat ctaaacaaca agatgatgaa 9120 agaattgtgt gatgatttca agatcgagca ccataactct tcaccttaca gacctcaaat 9180 gaatggtgct gtcgaagctg caaataagaa tataaagagg attgtccaga agatggtggt 9240 gacttataaa gattggcatg aaatgcttcc ctttgcatta catggatatc gtacttctgt 9300 acgcacatca acaggggcaa cncctttctc cctggtatat ggcatggagg cagtacttcc 9360 tgtagaagtc gaaattccat cattgagagt cctaatggag gctgacttat cagaagctga 9420 atgggttcag aatagatacg accagttgaa tctaattgaa gaaaagcgca tgacagccct 9480 atgtcacgga cagttatatc aaaaaaggat gaancaggct tttgacaaga aagttcgtcc 9540 ccgtgagttn aaagaaggtg atctngtgct caaaaagatt ttctctttcc aaccagactc 9600 ccgaggcaag tgggctccta attatgaagg nccgtatgtt gttaaaanag ccttctcagg 9660 tggtgccatg actctacaaa ccatggacgg tgaagaactt ccacgacctg tgaacacaga 9720 tgcagtcaag aaatactttg tctaaaaatt tttnaaagaa cagctcggta agtcgaaaac 9780 ccgaaaaggg cgacttaggc aaaaatgagc gtctcggtgg actgaaaacc cgaaaagggc 9840 ggtccaggca aaaattagag acaataaaca gagatcatta tcctgataga gtgaaaaccc 9900 gaaagggcag tctatgcaaa aattaaggat ttaaaaaaaa aaaaaaaaaa aaaaaaaaaa 9960 aaaaaaaaan agacaaagta actgcatcca gtcgaacaca gatacacttg gggcatacct 10020 gatatcaaag antattcgag ccncaagata acgggatttc aaagttgtta gagaangata 10080 gggttatgaa gttcaacgta cctttccatt ttaaaattac catttctttt caaactttgt 10140 aaanaactcc atgaagtcat gccattggca tagcgtcatt cgatnaataa actttgagcc 10200 tttagcctct ctgtttgaaa tttcccattt gttttgtttc nnganttttt cctcttttat 10260 tgatgataat attttgaaat agatttctaa aanaggntta tataataaaa agcataaaca 10320 aaatagatac ancttggcac tcgggagtaa nanaggcata tatcaactca agagaggtta 10380 gatcctgcta aaagcgtggc tcgacactaa ggaaantctc tgaataaaca aatacaaaaa 10440 taatacaaaa agctcgctaa gttgaaaacc tgaaaaggcn acttaggcaa cagagagcgt 10500 cccggtggac tgaaaacccg aaagggcggt ccaggcaaaa attaggggca aaacaaaaaa 10560 atattcccgg tggactgaaa acccgaaagg gcggtccagg caaaaattag ggatttttca 10620 ataaaacaaa aggnatgact gctgaancat accaatggaa ggacactctg tgccggttta 10680 caaatggcga cttcttccag acttctttca tcgacaatgg gctcaccccc caggaggcat 10740 cggtggctac cnagtgccag gttcttacac catcaacggc tcgatttgct cacaataata 10800 tcatctccaa ggaaggttgc cgaatgtttg taatgcaatg tcggtccgac tcccatctta 10860 cctgtcttgt ctcagttcat cgattcacgt gtcatgtaca ttcatatatc catacattca 10920 tacaatcatg cattcancaa tattttcaca taatcatacg tttacgcgta cacgacatat 10980 gcataacatc aattcacaca taattgcatc agtcaaagct taccattgtg tcaagccgca 11040 agtttctacg aatgagcgtc ttccatttca aatgtcaatc tcaatttcaa attcaaaagt 11100 gtcatccccg gcgtaaagcc gtgctagtta tgtcactaat caatgtcaat ttcaaatttc 11160 aaaggtgtca tgcccggcga aaaaccgtgc taagtcatgt cactaatcaa tgccaatttc 11220 aattttagtt tcgaagtgac atccccggca gaaggccgta ctagtcatgn cgctagttga 11280 tctcgatgtc aacttcaaac tccaggtatc atccccagca tagctgttct agagatgtca 11340 ccnatccaaa cttttcaagc naccnagttc caacnaacga anagcntntg tntttatttn 11400 nagnaaccag ttccaacnaa cgaacaactn ntgtttnaag cgaccgattc caacaaacga 11460 atagcctatg ccaatgtttc ttaccttccg agcaactagt tccaacaaac gaacaactca 11520 tgtcaatctt ttatctttat gcccagcgac cgattccaac aaacgaatag cctatgccaa 11580 tgtcttttac cttccgagca actagttcca acaaacgaac aactcatgtc aatcttttat 11640 ctttatgctc agcgaccagt tccaaccaac gaacagcctg taacaagtgg ccaatttcaa 11700 ccaacaaata gcttgtatcc ttctattttt cattttcaaa accaagtcca caaatggaca 11760 // ID COPIA3-I_LC repbase; DNA; EDCOT; 7511 BP. XX AC . XX DT 09-SEP-2005 (Rel. 10.09, Created) DT 15-APR-2011 (Rel. 16.04, Last updated, Version 2) XX DE Copia-like retroelement from Lotus corniculatus - consensus of DE internal region. XX KW Copia; LTR Retrotransposon; Transposable Element; gag-pol; KW COPIA3-I_LC. XX NM COPIA3-I_LC. XX OS Lotus corniculatus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RP 1-7511 RA Gentles A. and Jurka J.; RT "L. corniculatus copia-like element."; RL Repbase Reports 5(9), 238-238 (2005). XX DR [1] (Consensus) XX CC Similar to the SIRE1 element from Glycine max. Target site CC duplications could not be determined. XX FH Key Location/Qualifiers FT CDS 66..4910 FT /product="COPIA3-I_LC_1p" FT /translation="MDNKEGGSVNRPPILDGTNYDYWKVRMTAFLKSIDNK FT TWKAIVKGWKHPTKAEVEGTSTTVVEKPEEEWTSVEDEAALGNSKALNAIF FT NGVDKNMFRLINTCTVAKDAWEILKTAHEGTTRVRMSRLQMLTTQFENLMM FT TEEETISEFHMRVRDLSNASFALGEPMSDEKLVRKILRSLPQKFAMKVTAI FT EEAQDIENMKVDELIGSLQTFELKLSGKSEKKNKSIAFVSNTDEGDDEDCE FT GENLSEALAMLAKKFNRALRKIDKRTRPNVQDMKFDNKPKFSNSQRKTKEE FT ERSGQNKGVQCHECEGYGHIRSECATYLKKQKKGMMVTWSDEDTEDEEEIS FT ANKVNAFSGTIYESETSDEDISDEELAETYKLLHNKWEEACKLVREKQSEI FT EQLVSQNERLKELSTKLKEDLEEWQSKFNNADVMEKANLXLINAGLQEEVA FT TLTRKLEATHKSVRMLNSGSDMLDEILKETSKQGGSLKGIGFDYRTXNKED FT QKGSKKFVSAAKQTEFKKPRNYQLSDPLPRHVPQHVKPQLKLDKTVPWKCH FT YCGKNGHIKPYCYRLYGYPQMHDKKPXQMRKXWKPKGEVRCQVAYTSFRAS FT SKEDWYFDSGCSKHMTGNKSFLQDIRSHSTNYVTFGDGAKGKIKGVGKLVS FT TESPNLNNVLLVNGLTANLISISQLCDQGYDVKFNKIECVVTTDDERVVMR FT GVRSKDNCYMWTSEEKAHVSRCLLTKEDEVNVWHQRLGHLNYRSMQKXIAD FT EAIRGLPNLSLGEGKLCGECQIGKQTKVSHKMLQHQTTTKVLELLHMDLMG FT PMQVESLGGKRYVFVCVDDFSRYTWVEFMREKSETFEIFKNLCLRLQNEKD FT CVIVRIRSDHGREFENSKFLEFCGTEGISHEFSAPITPQQNGIVERKNRTL FT QESARVMLHAKKIPHQFWAEAMSTACYIHNRVTIRAGTSSTQYELWKGRKP FT SVKYFHIFGSKCYILADRDPKRKLDPRSDEGIFMGYSMNSKAYRVFNSRTR FT TMMESVNVTVDDEPSKKEEAVLNEDDDGADVPADAPATALDNESETSADEK FT EDKDITSNKAPSIRVQKNHPQENIIGNLQEGVTTRSRSIIAHSCFISKIEP FT KNVNEALTDEYWINAMQEELEQFRRNEVWELVPRPEEVNIIGTKWIFKNKS FT DETGTVTRNKARLVAQGYTQIEGVDFDETFAPVARLESIRLLLGVACLLKF FT RLYQMDVKSAFLNGYLSEEVYVEQPKGFTDPHHPDHVYKLRKALYGLKQAP FT RAWYERLTEFLVSNGYCKGGIDKTLFVKNDKGKLMIAQIYVDDIVFGGMSN FT SMVEHFVRQMKSEFEMSLVGELNYFLGLQVKQMEDSMFISQSKYAKGLVKK FT FGLEKAGHKRTPAATHIKXSKDEQGEDVDQSLYRSMIGSLLYLTASRPDIT FT FAVGVCARYQAAPKASHLLQVKRIIKYINGTSDYGILYTHDTNSSLVGFCD FT ADWAGSADDRKSTSGGCFFLGNNLISWFSKKQNCVSLSTAEAEYIAAGSSC FT TQLMWMKQMLKEYDVEQDVMTLYCDNLSAINISKNPIQHSRTKHIDIRHHF FT IRDLVEDKIVNLEHVTTDKQLADIFTKPLDAITFEKLRGNLGIXLFDA" FT CDS 5347..7014 FT /product="COPIA3-I_LC_2p" FT /translation="MFLLEDVTDEEEINDEDSPVKSPPDVVPDVETSXSXE FT SSXQENPGKDSTSHEDSGNATQPDXSVSSSSKDADPKNGNSEXTNSEEPXQ FT APXXVQXISDDASDDVPLTXSFXDSVAARMKXKRRVSXPEVTPTPXKXSKS FT SPXTYKSRQASVKXKGKQKXDKTPXEKKKRKXPVDVEDSESDVEXXVQDIR FT XSEKKKXSGKRIPQNVPXVPIDRVSFHLEEXVQKWKFVCKRRMAKEREVGX FT DVLECXDVIALIEKAGLMKTIQNVGRCYERLVREFLVNLSVDVGRPDSXEF FT RKVYVRAECVVFSPAVINQALGRSAIXFXDEEVSMDVVAKELSAGYVKKWP FT SKKLLSTGNLSVKYAILNRIXAVNWVPTQHTSGVSATLAKLIYRIGKSIXF FT DFGTFVFEQTLKHADTCAVKLPVSFPSLLTEIILKQHPQILRADDVAMSCG FT VPITLDQRLFMXPHVLDIALPTSXTSAXPVTESGTQAIIAELQEVSKALQX FT TIRVXTARKLKVDALLLKLQEEERQEGDKVKRRKDLXXVQRKVQKXXXXSP FT VLKTSLFCF" XX SQ Sequence 7511 BP; 2277 A; 1211 C; 1788 G; 2048 T; 187 other; attggcatca gagcaggcac cctgttctgg ttgggtgagc tccagggagt ttkattcaag 60 ttctcatgga taacaaggag ggaggatcag tcaataggcc acccattctg gatggtacta 120 actatgacta ctggaaggtt cgcatgacag cctttctcaa atcaattgac aacaagactt 180 ggaaagctat tgtcaagggt tggaagcacc ccactaaggc tgaggttgaa ggcacctcta 240 ctactgttgt ggaaaaacct gaagaagaat ggaccagtgt tgaagatgaa gctgctcttg 300 gaaattcaaa ggctctaaat gctatcttta atggagttga caagaatatg tttaggctga 360 tcaatacgtg tactgtggca aaggatgctt gggaaattct gaaaactgca catgaaggaa 420 ctactcgagt aaggatgtca agacttcaga tgcttactac tcaatttgaa aatttgatga 480 tgactgaaga agagactatt tcagaattcc acatgcgtgt ccgtgacttg tctaatgctt 540 catttgcttt gggagaacct atgtcagatg agaagcttgt aaggaagatc ttgagatctc 600 ttcctcagaa gtttgctatg aaagtcactg caattgagga ggctcaagac attgagaaca 660 tgaaggttga tgaacttatt ggctctttgc agacatttga gttgaaactg agtggaaaat 720 ctgagaagaa gaataagagt attgcttttg tgtctaacac tgatgaaggt gatgatgaag 780 actgtgaggg tgaaaatctt tctgaggctc tggccatgct agcaaaaaaa ttcaacagag 840 cattgagaaa gattgacaaa agaaccaggc ctaatgtcca ggacatgaag ttcgataaca 900 aacccaagtt ttctaattca cagaggaaga ccaaagaaga agaaagatct ggtcagaata 960 aaggagtgca gtgtcatgaa tgtgaaggat atggtcacat caggtctgaa tgtgccacct 1020 atctaaagaa gcagaagaaa ggtatgatgg taacttggtc agatgaagac actgaagatg 1080 aggaggagat atctgcaaac aaagtcaatg ctttctctgg aactatctat gagtctgaga 1140 caagtgatga ggacatctca gatgaggaac tggctgagac ttacaagctg ctacacaaca 1200 agtgggaaga agcatgtaaa cttgtgagag aaaagcaaag tgagatagaa caacttgtyt 1260 ctcagaatga aaggctgaaa gagctcagca caaagctgaa ggaagatctg gaggaatggc 1320 aaagtaagtt taataatgct gatgttatgg aaaaggctaa cctartgttg attaatgcag 1380 gacttcaaga ggaagtggca actctgacaa gaaagcttga agctactcac aaatctgtta 1440 gaatgttgaa cagtggttct gatatgcttg atgaaattct gaaagaaact agcaagcaag 1500 gagggagttt gaagggaatt ggctttgact acagaacarc aaacaaagaa gatcagaaag 1560 gatcaaagaa atttgtgtct gctgcaaaac aaactgaatt caagaagccc agaaattatc 1620 agttgtcaga tccattgcct cgacatgtac ctcagcatgt gaaaccccag cttaagcttg 1680 acaaaactgt accttggaag tgtcactact gtggtaagaa tggtcatata aagccctact 1740 gttacaggtt atatggctat cctcagatgc acgataaaaa gcctrttcag atgaggaags 1800 aatggaagcc caagggtgaa gtcagatgtc aggtagccta cacatcyttc agagcatcat 1860 caaaggaaga ttggtatttt gatagtggct gctcaaagca catgacagga aacaagagct 1920 tcttgcaaga catcagaagt cactccacca actatgttac ttttggagat ggagctaaag 1980 gaaagatcaa gggagtagga aagcttgtta gcacagaatc tcctaacttg aacaatgtgt 2040 tacttgtaaa tggyttaact gccaacctaa tcagcataag tcaactgtgt gatcaagggt 2100 atgatgtgaa gttcaataag atagaatgtg ttgtgaccac tgatgatgag agagttgtga 2160 tgagaggagt cagatcaaaa gacaactgtt acatgtggac atcagaagaa aaagctcatg 2220 tttccagatg tttgttaact aaagaagatg aggtgaatgt atggcatcaa agactaggac 2280 atctcaacta caggagcatg caaaagrtta twgctgatga agcaataagg ggattgccca 2340 atttgagctt gggagaagga aagctatgtg gagaatgtca gattggtaag caaaccaagg 2400 tgtcacacaa gatgctccag catcagacca cgacraaggt tctggaattg cttcacatgg 2460 atctcatggg tcccatgcag gttgaaagct tgggaggaaa aaggtatgtg tttgtctgtg 2520 tagatgattt ttcaaggtat acatgggttg aatttatgag agaaaaatca gagacttttg 2580 aaatattcaa gaatctatgt ttgagacttc agaatgagaa ggactgtgtg attgtaagaa 2640 tcagaagtga tcatggaaga gagtttgaga attcaaaatt cttggagttc tgtggaacag 2700 aaggtattag ccatgaattt tctgccccca tcactccaca gcagaatgga attgttgaaa 2760 ggaaaaatag aactctccag gaatcagcta gagtaatgtt acatgctaag aagattccac 2820 accagttctg ggctgaagct atgagtactg cctgttacat acataataga gtcaccatca 2880 gggcagggac atcctctaca cagtatgagc tatggaaagg tagaaagccg tctgtaaaat 2940 actttcacat atttggaagt aaatgttata ttcttgcaga tcgtgatcct aagaggaagc 3000 ttgatcctag aagtgatgaa ggaattttca tggggtattc tatgaacagc aaagcttata 3060 gagtttttaa ctctcgcaca aggaccatga tggaatctgt gaatgtgact gtggatgatg 3120 aaccaagcaa gaaggaagaa gcagttytga atgaagatga tgatggtgct gatgttccag 3180 ccgatgctcc agcaaccgcc ctcgacaatg agtcagaaac aagtgctgat gaaaaggaag 3240 acaaagatat cacatcaaac aaagctccat caatcagggt tcagaagaat catcctcaag 3300 aaaacattat tggtaatctt caagaagggg tgactaccag atccagaagt attattgctc 3360 acagttgttt catctctaag atagaaccca agaatgtcaa tgaagctctc actgatgaat 3420 actggataaa tgctatgcaa gaagagctag agcagttcag gagaaatgaa gtgtgggagt 3480 tagtgcctag acctgaagaa gtaaacatca ttggcaccaa gtggatcttc aagaacaaat 3540 cagatgaaac tggaacagtc acaaggaata aagcaaggct agttgctcaa ggatatactc 3600 agatagaagg agttgatttt gatgagacct ttgctccagt agctagactg gaatctataa 3660 gactcttgtt aggtgttgct tgtcttttga agttcagact ttatcagatg gatgtgaaga 3720 gtgcttttct gaatggctat ttgagtgaag aagtttatgt tgaacaacct aaaggattta 3780 cagatccaca tcatccagat catgtgtaca agttgaggaa ggccttgtat ggkttgaagc 3840 aagcacctag ggcttggtat gaaaggttaa ctgagtttct tgtaagcaat ggttactgca 3900 agggtggaat tgataaaact ctgtttgtga agaatgacaa aggtaagctc atgatagcac 3960 agatttatgt ggatgacatt gtttttggag gaatgtcgaa ctcaatggtg gagcatttcg 4020 tccgacaaat gaaatctgaa tttgagatga gcttagttgg tgaattgaat tattttctag 4080 gactacaagt caaacaaatg gaggattcta tgttcatatc acagagtaag tatgctaaag 4140 gcttagtcaa gaagtttggc cttgaaaagg ctggtcacaa gagaactcct gctgctacac 4200 acatcaaamt gtccaaggat gagcaaggag aagatgttga tcaaagtctc tatagaagca 4260 tgattggaag cttgttgtat ctyactgcta gcagaccaga tatcaccttt gcagttggtg 4320 tatgtgcaag atatcaagca gctcctaagg cwagtcatct gctacaagtc aagagaatta 4380 tcaagtacat caatggcacr agtgactatg gtattctcta tactcatgat acaaattctt 4440 ctttagttgg wttytgtgat gcagattggg caggtagtgc agatgataga aagagcacat 4500 ctggtggatg tttcttcyta gggaataatt tgatttcatg gtttagcaag aagcagaayt 4560 gtgtctcatt gtctacagct gaagcagagt atattgcagc mggaagtagt tgtactcaac 4620 tcatgtggat gaagcaaatg ttgaargagt atgatgttga rcaggatgtc atgacattgt 4680 actgcgacaa tctcagtgca atcaatattt ccaagaatcc catacagcat agcaggacca 4740 agcayattga yattagacat catttyatta gagacttggt ggaggataaa attgtcaayt 4800 tggagcatgt tacaactgac aagcaattgg ctgatatttt cacaaaaccc cttgatgcaa 4860 tcacttttga aaaattaaga ggaaatctag ggatttkcct ttttgatgca tagcaattag 4920 cgtgycmcaw tgtgtyaacg gctagtttat ttttgwtcat cattaactgc cgttgtgaca 4980 tcagcagaga gaagrttact tcatggttcr ctyatcctat aactacctyc aacggkcaaa 5040 ttgtgttytc tcaaccgctt gtgcatctat cttyttcwag actyatyaty kytcatytkm 5100 aakttktnct catygttctg trctctgttt gtrtttactc tcgwttcatc atgtctcaaa 5160 gytcaggaar gaakgawtmt gtcaaggcwa agattgarag aactgcwaaa ggagtcaart 5220 gyatgggttt gaagagtgrt tcttctcaac catcttctgt gtccaagaaa gcytcyraga 5280 agaagmrrwc aagaaaccca acrwgwaagr yctacawrtc mmaggtymag aacarcraag 5340 ccmcaaatgt tcctccttga ggatgttact gaygaagagg aaatcaatga tgaagattct 5400 cctgtgaaat cgcctcctga tgttgtgccy gatgttgaga catctgkgtc tmaggaaagt 5460 tctgmtcaag aaaatcctgg aaaggattcc acttctcatg aagattcagg caatgctacc 5520 cagcctgatr tctctgtgtc rtcctcttca aaggatgctg atccaaagaa tggyaaytct 5580 gaggrtacca attctgaaga gccaawccag gctccarccy ctgttcagra catctctgat 5640 gatgcttctg atgatgttcc tctgactgmg tcctttsctg atagtgttgc tgcsaggatg 5700 aararraaaa gaagggtytc twctcctgaa gtcactccta ctccaycaaa garatccaar 5760 tcytcwcctr taacctacaa gtcymgacar gckagtgtga agrgtaaggg aaagcaaaag 5820 gawgacaaga ctcccastga gaagaagaar aggaagaytc cagttgaygt tgaagactct 5880 gagtcagatg ttgaagycgr tgtycaggac attcgayctt ctgagaaaaa gaartwttct 5940 ggtaagcgta ttcctcaraa tgttcctgyt gttcctattg atagagtgtc tttycactta 6000 gaagagartg ttcagaagtg gaagtttgtt tgcaagagaa gaatggccaa ggaaagggaa 6060 gttggyyctg atgttcttga rtgtarrgat gttattgcac ttattgagaa agcaggtctg 6120 atgaagacta ttcagaatgt tggtaggtgc tatgagaggc ttgtgagaga gttcttggta 6180 aatctctctg ttgatgtggg acgtcctgat agtgmagaat tcaggaaagt ctatgtgaga 6240 gctgaatgtg ttgtgttctc acctgctgtg atcaatcaag cacttggcag aagtgctatt 6300 gmctttgytg atgaagaagt gtccatggat gttgtggcca aggaacttag cgctggttat 6360 gtgaagaagt ggcctagcaa gaagytgctc tcyactggaa atctgagtgt gaagtatgct 6420 atycttaaca ggattgrtgc tgtgaattgg gttcctactc agcatacttc tggagtttct 6480 gcaacgcttg ccaaattaat ctatcggata ggcaagtcta ttgawtttga ttttggaact 6540 tttgtgtttg agcagacatt gaagcatgct gatacttgtg ctgtgaagct gcctgtttcg 6600 tttccatcac ttcttactga gatyattctg aagcarcatc ctcagattct cagggctgat 6660 gatgtggcta tgtcttgtgg tgttccaatc actttggatc aacgtttgtt tatggancca 6720 catgttctag acattgcctt rccaactagc araacatctg ctyctcctgt gactgaatct 6780 ggcactcagg ccatmattgc tgaattacag gaagtctcca aggctttgca gkagacaatc 6840 agggtgasca ctgccaggaa gctcaargtt gatgcgttgc twctcaagtt acaagaagaa 6900 gaacgtcaag aaggtgacaa agtgaagagg aggaaggatc tgawgaragt gcagaggaaa 6960 gtgcagaagr gtcngrrgar ragtccagtt ctgaagacta gtttgttttg tttttgattt 7020 ttcgtgcacc ctttgcaaat ttgtgctaaa aagggggagt agtttgaagt ttcaggaggt 7080 tyaraagttg gttctgttta gatktttcat gttctgttca gatgttcgca gatcagaaga 7140 tgttttagtt cagaagatgt tttttgcttc tgtttctact gtgcwrtgtg tgttytgata 7200 gtgttagctc tggtcaagac gatggctatg tttgtttytg aaatgtttct tctgrtkakc 7260 agtacttctg atggtagtat ttctgatacg atgatgttca aactgcattt tgatgttatc 7320 atgtgctaag gctgattgta cctctggttg tgtgtttgtg ctgctaaagt gttttgttyc 7380 gactatgcat agtgggttgt gtrgatgcgt tgtttgaggg ggagytytga ctaaggggga 7440 gagttttttc tctaggtttt wtcytctytg wttgtgagtt gttttagaca aaatttgaca 7500 aagggggaga t 7511 // ID Copia-15_Mad-I repbase; DNA; EDCOT; 4429 BP. XX AC ACYM01118580; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-15_Mad-I; KW Copia-15_Mad-LTR; Copia-15_Mad_. XX NM Copia-15_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4429 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1291-1291 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01118580; Positions 10728 6300. XX CC Positions [1944-2234] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 89..1999 FT /product="Copia-15_Mad-I_1p" FT /translation="MGEPIPKASTDTQNPMETITDVSNPFILHPSDQPGNI FT LVSKTLQGDNYNTWSRAMRISLSAKNKLGMVDGTIDPPSETDKQFASWQRC FT NDMVLAWILNSVHDDIASSVSYYTTATDVWADLRDRFSQGNDSRIYQIKRE FT IVEHRQEQQSISVYYTKLKALWDELASYNETPTCTCGGLKKINDRDEKERV FT MQFLMGLNDSYAAVRGQILLMQPLPDTRRAYSLVLQQEKQVEVSLNRNNIN FT LHAMNITRNRDTAAPKGNTLQCSYCDQKYHTVDRCFYLYGFPPGHKYHGKS FT VKPPNKRKPAANQVTVETETTKGVDSRHKATSSDGPKFTTEEYNQLMAMLK FT KSNVDGNPQHFANATGTITPSSDLSEKTLYWIIDSGATDHVSPSPHLLDKK FT SLSMLDSVQLPNGGHALIDSIGSIQVTPHMKLDGVLHVPNFRVYLLSVSKL FT TEALRCIVIFFPDFCVIQDMDTRRTIGLGKRYNGLYYLAPEQNLRLAHHIS FT HNSTLWHQRLGHPSTGPLQTLTKQVPSIVFDSSHTCDICPLAKQTRLSFPS FT SFISSKAPFDLIHCDIWGPHRVNSHSGARYFLTIVDDYSRYTWIHLMRFKS FT ETQGLLRSFIAWVQTQFNCMIKALRADNGGEFTSLRSFF" XX SQ Sequence 4429 BP; 1201 A; 1140 C; 857 G; 1218 T; 13 other; acatggtatc agagcaccgt ttctggtgac tctgaatacc cacacagctt ccgcaaatct 60 taacaaacac aacatcacct aaaccaccat gggcgaacca atacctaagg cgtccactga 120 cacccaaaac cctatggaga caatcacaga tgtctcgaac ccttttattc tacatccctc 180 agatcaacct gggaatatct tggtctccaa aacacttcaa ggagacaact acaatacctg 240 gagtcgtgct atgcgaatca gcttgagcgc gaaaaataaa cttggcatgg ttgatggcac 300 catcgaccct ccatcagaga ctgacaaaca atttgcatca tggcaaagat gcaatgatat 360 ggttcttgcc tggattctca actcagttca cgatgacatt gcgagcagtg tttcttatta 420 cacgacagca accgatgttt gggctgacct gcgagatcgt ttctcacaag gaaacgactc 480 acgcatttat caaatcaaga gagagatcgt tgaacacaga caggaacaac aatcgatctc 540 ggtttactac acgaaactga aagcgttgtg ggatgaactg gcatcctaca atgaaactcc 600 gacttgtacc tgtgggggat tgaagaagat aaatgatcga gatgagaaag aaagggtgat 660 gcagttcctg atgggtttaa acgactctta tgcagcagta cgtggacaga tactattgat 720 gcagccacta ccagacactc ggagggcata ttcccttgtt ctccaacaag agaagcaagt 780 agaggtatct ctaaatcgta acaatataaa tctgcatgct atgaatataa cccgtaacag 840 ggacactgct gcaccgaaag gaaacaccct tcaatgctca tattgtgatc aaaagtacca 900 caccgtggat cgatgctttt acttgtatgg tttcccgcct ggccataagt atcatggcaa 960 atcagtcaag ccaccaaaca aaagaaaacc tgcggcaaac caagtaacgg tggagaccga 1020 gaccaccaag ggtgtagact cacgacacaa ggcaacgtcc agtgacggtc cgaagttcac 1080 cacagaagaa tataatcaac ttatggcaat gctcaagaag agcaacgttg atggtaatcc 1140 gcagcatttt gcaaatgcaa caggtacaat cacaccttct tctgacttgt cagagaaaac 1200 tttatattgg atcattgata gtggggcaac agaccatgta tctccttctc ctcatttgct 1260 agacaagaag tcattatcca tgctggattc tgttcaatta ccgaatggag gacatgcctt 1320 gatagactcg attggttcta tacaagttac tccacacatg aaacttgatg gagtgctcca 1380 tgtgcccaac tttcgagttt acttattatc tgttagcaaa cttactgaag cattacgatg 1440 catagtgatt ttcttccctg atttctgtgt gatacaggac atggatacga ggaggacgat 1500 tggcctgggc aagcgatata atgggcttta ctacttggcg ccagaacaaa accttcgcct 1560 tgctcaccac attagccaca actccaccct ctggcaccaa cgattagggc acccttctac 1620 cggtcctctg caaactttaa ccaaacaagt tccatcaata gtttttgatt ccagtcatac 1680 atgcgacatt tgtcctcttg ctaaacaaac ccggttatct tttccgtcca gttttatttc 1740 ttctaaagca ccttttgatt tgatacattg tgatatttgg ggacctcatc gagtcaattc 1800 ccattcgggg gctcggtatt ttttaacgat tgttgatgat tattctcgct atacttggat 1860 acatctcatg cgttttaaat ccgaaacaca agggttatta cgttctttta ttgcttgggt 1920 ccaaacacaa tttaattgca tgattaaagc acttagggct gataatggtg gtgaatttac 1980 ctctttacgt tcgttttttt gataacaagg gtatcatatt ccaaacttct tgtccgtcca 2040 caccacaaca aaacggggtt gttgaacgga aacaccgtca tctactaaat gttggtcgag 2100 ctctacggtt tcaagcccat ttaccacaaa ccttttgggg ggaaagcata caaacagcat 2160 gttatttaat taatcgttta cctacacctc ttcttagtca taaaacacct tatgagcttt 2220 tgcattgtca aactcccgtt ttttcgcatc tccgggtttt cggttgttta tgttatgcta 2280 ccaaccttca tcctcaccat aagtttgatc aacgtgctaa aagatgtgtt tttgttgggt 2340 acccattagg tcagaagggt tatcgtgttt atgaccttac cacacacaaa aawttttcca 2400 ctcgtgacgt gaycttccat gaaaccacgt tccctttctc cactyaacca cttgaccatc 2460 accctgatac acctgtccta cctatcccca ccgactccct atctcatcct aatcccccac 2520 cgccaccgac tgcacctcct tcccccacay cgaccgacac ttttttatcc acaccaacgg 2580 aaactgctcc tcccatagaa ccttctcctc ccacaccgac cgaacctcac ttagtccctc 2640 caccactccc taccccacmt gccccacctg cccctcgcca atctggccgc gcccttaagc 2700 cctctgtcag gctgcaggga taccatttat atcatgtgca atcccttgct cccagcgcca 2760 cgtcctcctc catgtcaggt actcgctatc ctttaaatca ctatgtatct tatgctcatc 2820 tttcaccatc acatcgctct tttgcttgtg ctatttcgac tcttgtcgaa cccactacat 2880 ttgcacaggc taacggtgat cctcaatggc gtgctgccat ggactctgag cttctggctc 2940 ttgaacaaaa caacacatgg actctcacta ccttacctcc tggtcatcgc gcaatcggtt 3000 gccgatgggt ctacaagatc aagtacaact ctgacggtac cgtcgagcgt tataaagctc 3060 gtcttrtggc caaaggcttt actyaacgcg aaggtattga ttacaaggaa acttttgctc 3120 ctgttgccaa actcatcacc gtccgttrtt tgttagccgt tgcttctgtt cgtcattggt 3180 ccttacatca aatggatgtc cayaatgcct tycttcatgg tgacctttct gaggaagttt 3240 atatgcagct gcctcctgga cttcatcggc agggggagca taatgtatgc cgactcaaca 3300 agtcccttta tggccttaag caagcctctc gcagctggtt ccataaattt tccactgcca 3360 taggtcaagc tggctaccag caatcaatgg ctgactactc cctattcact aaggtgcgtg 3420 gaaattcgtt tacagccrtc ttgctttatg ttgacgacat gattatcaca ggcaacgatg 3480 aggctgccat ccatgacctc aagcaatttc ttcaatctca ttttcgcatt aaggaccttg 3540 gacacttaaa gtatttcctt ggtgtggagg tggctcgatc ttctcaagga atcgccatct 3600 cacaacgtaa atatgcgctt gacattattg atgaagccgg cttacttggt gcaaagcctg 3660 caaagttccc aatggaagaa aacttgagat tatctccaac ggaagggcaa cttctccata 3720 atgcctcaca atacaggagg cttgttggga aacttattta tctcacaatc actaggccag 3780 agatttcata ctcggtccat atactcagcc aatttatgca acaaccaagg aagcctcatc 3840 tagacgcagt gcatcgtctt ctacgatact tgaagggatc acctggacaa gggcttmttt 3900 ttccttcaaa tgggagttta acgttgaaag gatattgcga cgccgattgg gctcgctgtt 3960 cacttacgag aagatctgtc acakgctatt gtatatttct tggaggtgca ctagtgtctt 4020 ggaaaaccaa gaaacaatct accgtttcga gatcctcagc tgaagcggag tatcgtgcca 4080 tggcttcagc tacatgtgag cttacgtgga tgaagtactt attgactgat ctacaaattg 4140 atcacaaggg tccagcaaag ctgcactgcg acaaccaagc tgcactccac atagctgcca 4200 atccagtttt tcacgaacgc accaaacaca tagagattga ctgtcatgtt gttcgtgaac 4260 gactacgttc tggggttatt tcgacaacct atgtacctac tggacagcag cttgccgata 4320 tattcaccaa gccacttgga cagtcagcat tccgttctct acttggcaag atgggtgttc 4380 ttgacattca cactccacct tgagggggag tattaagcga cgatatcgt 4429 // ID COP20_I_MT repbase; DNA; EDCOT; 4168 BP. XX AC . XX DT 11-JAN-2007 (Rel. 12.01, Created) DT 21-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of COP20_MT LTR retroposon from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; terminal repeat; ORF; COP20_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4168 RA Shankar R. and Jurka J.; RT "COP20_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 15-15 (2007). XX DR [1] (Consensus) XX CC The internal region has domains for gag-pol polyprotein and CC integrase in typical Copia type arrangement. XX FH Key Location/Qualifiers FT CDS join(106..216,220..1131,1135..3768) FT /product="COP20_I_MT_1p" FT /translation="MSNNNFNIVWSGPKLNSELDFNYWEFMMTTHLKAHNI FT SYVESGLQQGADELARRRDQLALSQILQGIDYSIFGKIANVKTSKEAWDIL FT KLSHKGVEKAQKSKLQSLRREYERYEMSSSETVDQYFTRVINLVNKMRVYG FT EDIQDSKVVEKILRTMPMKYDHVVTMILESHDTDTLSVAELQGSIESHVNR FT ILEKTEKVKEEALKSQVNLNNVAESSQMGEARARDNFNNGGRGNFRGRGRG FT SFRGRGRGNFNQWRDNNYNNFNPSHQGKGGNNFGSNNRGRGRGCYNQERTN FT NGCFNCGKYGHKAADCRYKHQANMAENSYQHFGESSQNQHSLFLASNTLEE FT ENIWYLDTGCSNHMCGKKELFSSLDETVKSTVKFGNNSNIPIEGKGQIAIR FT LKDGSQNFIGDVFYAPGLHHNLLSMGQLSEKDYNMQIHKGYCTLIDGNGRF FT ITKVKMSPNRLFPLRIQHDQFPCLSSIIPNNDWLWHMRFGHFHFSGLNYLS FT RKEYVSGLPVVKIPSGVCETCQMGKKHRESFPTGKSWRAKKLLEIVHSDLC FT SVEIPTPGGCRYFITFIDDFSRKAWVYFLKQKSEAVDSFKTFKAFVEKQSG FT CLIKALRTDRGQEYLVGTDFFEQHGIQHQLTTRYTPQQNGVAERKNRTIMD FT MVRCMLKAKQMAKEFWAEAVATAVYILNRCPTKSVQEKTPEEAWSGRRPSI FT RHLRVFGCIAYAHVPDQIRKKLDDKGKRCIFIGYCSNSKAYKFYNLETKKV FT IISRDVTFDEGGMWNWSSKSQKEPIVTPNDYEEEDEHVDTTPDEPDEPETS FT NREKRNRRLPARLQDCVLGTDNDPSDEEIINFALFADCEPVTFEEASRDEN FT WIKAMDEEINAIEKNKTWELTELPPDKKPIGVKWVYKTKYKPSGEIDRYKA FT RLVAKGYKQKPGIDYFEVFAPVARLDTIRMLISLSAQNNWKIHQMDVKSAF FT LNGTLEEEVYVEQPAGYVVRGKEDKVYRLKKALYGLKQAPRAWYKKIDSYF FT IQNGFQRCPFEHTLYIKFIDPGDVLIVCLYVDDLIFTGNNSKMIAEFREAM FT ISYFEMTDLGLMSYFLGIEVIQQKDGIFISQKKYASDILKKFKMEHSKPIS FT TPVEEKLKLTRESDGKRVDSTHYKSLIGSLRYLTATRPDIVYGVGLLSRYM FT EDPCVSHLQGAKRILRYIKGTLTEGIFYGNNSDVKLVGYTDSDWAGDTETR FT KSTSGTHFI" XX SQ Sequence 4168 BP; 1435 A; 653 C; 965 G; 1115 T; 0 other; caggttaggt cctgcaagtg tcagtgtcaa aaatagtcta agtgtgtgag gaacaaaaga 60 gttctcattg tgtcgaaatt attgtaagca tattctgaga aagatatgtc aaacaataat 120 ttcaatatcg tttggtccgg tcctaaattg aattctgaat tagatttcaa ttattgggaa 180 tttatgatga caacacatct taaagctcac aacatctgaa gctatgtgga gtctggtttg 240 caacaaggag ctgatgaact tgctcgtaga agggaccagc tggcactatc acaaattctt 300 caaggaatag attactcaat tttcggcaaa atagcaaatg tgaagacttc gaaagaagcg 360 tgggacatat tgaagttgtc acataaagga gtagagaaag ctcagaaatc aaagctgcag 420 tctctgcgta gagaatacga aaggtatgaa atgtccagtt ctgaaacagt ggatcaatat 480 tttactcgtg ttataaatct tgtcaacaaa atgagagtgt atggagaaga tattcaagat 540 agcaaggtgg tggagaaaat tctacgcacc atgccgatga aatatgatca tgtggtgact 600 atgatattgg agtcccatga tactgatacc ttgtcggtag cagagttgca gggaagcatt 660 gaaagccatg tcaaccgaat attggagaag actgaaaaag taaaggagga agccttgaag 720 agccaggtga acctcaacaa cgttgctgaa tccagtcaga tgggtgaagc cagagctcgt 780 gacaatttca acaatggagg aagaggaaat ttcagaggaa gaggtcgagg aagctttaga 840 ggaagaggac gtggcaactt caaccaatgg agagacaaca attacaacaa tttcaatcca 900 tcccatcaag gaaaaggtgg aaacaatttt ggttccaata accgtggcag aggaagaggt 960 tgttacaacc aagagagaac aaataatggt tgttttaatt gtggaaagta tgggcacaaa 1020 gcagctgact gcagatataa acatcaagca aatatggcag agaattcata tcaacatttt 1080 ggtgagtctt ctcaaaatca acatagttta tttttagcaa gcaatacact ttaagaagaa 1140 gaaaatattt ggtatttgga caccgggtgt agtaatcaca tgtgtgggaa aaaagaatta 1200 ttttcttctc tggacgaaac ggtaaaatct accgtgaagt ttggaaataa ttcaaatatt 1260 ccaattgagg ggaaaggcca aattgctatc agattgaaag atggatcgca aaattttatt 1320 ggtgatgttt tctatgctcc cggtcttcat cacaatctct taagcatggg acagctgtct 1380 gagaaagatt acaacatgca gattcacaaa ggctattgca cgttgattga tggaaatggg 1440 agattcatca caaaggtaaa aatgtctcct aaccgcctat tccctctaag aattcaacat 1500 gatcaatttc cttgcttgag ttcaataatt ccaaataatg attggttgtg gcacatgaga 1560 tttggtcact ttcatttttc tggattgaat tatctgtcac gaaaagaata tgtttctggt 1620 ttgcctgttg tgaaaattcc aagtggtgta tgcgagacat gtcaaatggg aaagaagcat 1680 agagaatcat ttccaaccgg aaagtcttgg agagcaaaga aactcttgga gatcgttcat 1740 tcagatttgt gctcggttga aataccaaca cctggtggat gcaggtattt tattactttc 1800 attgatgatt ttagcagaaa ggcatgggta tattttctga agcagaaatc agaagctgtt 1860 gattccttca agacattcaa agcgttcgta gaaaaacaaa gtggttgtct aatcaaagca 1920 ctaagaacag acagaggcca agaatacctc gtcggcacag atttctttga gcaacatgga 1980 atccaacatc aattgacaac aagatatact cctcaacaaa atggagtagc tgaaaggaag 2040 aacagaacaa tcatggatat ggtgagatgt atgctgaaag ccaaacaaat ggcaaaggaa 2100 ttttgggcag aagcagttgc tactgcagtt tatattttga acagatgtcc aacaaaaagt 2160 gttcaagaga agactcccga agaagcatgg agtggaagga ggccctcaat caggcacctc 2220 agagtttttg gatgtattgc ttatgctcat gtaccagatc aaataagaaa gaagttagat 2280 gataaaggca agagatgtat ttttattggc tactgctcaa attcaaaggc ctataagttt 2340 tacaatctag agaccaagaa ggtgatcatc agtagagatg tgacatttga tgaaggaggg 2400 atgtggaatt ggtcatcaaa gtcacaaaag gagccaattg taactccaaa tgattatgaa 2460 gaggaagatg agcatgtaga tacaacacct gatgagcctg atgagcctga aacatcgaac 2520 agagaaaaaa ggaatcgaag attaccagct cggctacaag actgtgtttt gggtaccgac 2580 aatgacccat ctgatgaaga gatcattaac tttgctttgt ttgcagattg tgagccagtt 2640 acttttgaag aagcctcgcg tgatgaaaat tggataaaag ctatggatga agaaatcaat 2700 gcaattgaga agaataaaac atgggagctg actgaattac caccagacaa gaagccaata 2760 ggagtgaagt gggtgtacaa gacaaagtac aaacccagtg gtgagattga tcgctataaa 2820 gcgaggctgg tggctaaagg ctacaaacaa aaaccaggta ttgattattt tgaagtattt 2880 gctcctgttg caagattaga tacaattcgc atgcttattt cactctcagc tcaaaataac 2940 tggaaaatac atcaaatgga tgttaagtct gcatttctta atggtacttt ggaagaagag 3000 gtgtatgttg agcagcctgc aggatatgtg gttagaggaa aggaggataa agtatataga 3060 ttgaagaaag cattgtatgg cttgaagcag gcgccaagag catggtacaa aaagattgat 3120 tcttatttta ttcaaaacgg ctttcaaaga tgtccattcg agcacacact ctacatcaaa 3180 ttcattgatc ctggagatgt tcttattgtg tgcctctatg tcgatgattt gatattcacc 3240 ggtaacaatt caaagatgat cgctgaattc agggaggcta tgataagtta ttttgaaatg 3300 acagatttgg gcttgatgtc ctattttctc ggcattgagg tcattcaaca gaaggatgga 3360 atctttatct ctcagaagaa gtatgcaagt gatattttga agaaattcaa gatggagcat 3420 tcaaagccaa tttccacgcc ggttgaagaa aagttgaagc tgacaagaga aagcgatggt 3480 aaaagggtag actcaactca ttacaaaagt ttgattggaa gtttgagata tttgactgca 3540 acaaggccag atatagtata tggagttggt ttacttagca gatacatgga ggatccgtgt 3600 gttagtcatt tgcaaggagc caagaggatt cttcgttata ttaaaggtac tctgaccgaa 3660 ggaatttttt atggtaataa tagtgatgtg aagcttgttg gatatacaga tagtgattgg 3720 gcaggagata cagaaacaag aaaaagcacg tcaggtacgc atttcatcta ggaaccggtg 3780 caatatcatg gtcttcgaag aaacaacctg tggttgctct ttcaacagca gaagcagaat 3840 atatagcagc aaccagttgt gctactcaaa cagtgtggct gagaagaatt ttagaagtga 3900 tgcatcatga gcagaacact cctacaaaga tatattgtga taacaagtca gcaattgcat 3960 tgagcaaaaa tccagttttt catggacggt ccaagcatat tgacatccgg tttcacaaga 4020 tacgagagtt aattgctgag aaagaagtgg tgatcgagta ttgtcccact gaagagcaaa 4080 ttgcagatat ttttacaaag ccattgaaga ttgagtcatt ttacaaattg aagaaaatgc 4140 ttggaatgat gaaagcttga tttaaggg 4168 // ID HAT-7N1_Mad repbase; DNA; EDCOT; 1035 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-7_Mad; HAT-7N1_Mad; HAT-7N2_Mad. XX NM HAT-7N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1035 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1618-1618 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~93% identical to the consensus. 8-bp TSDs. Both termini are ~96% CC identical to HAT-7_Mad. XX SQ Sequence 1035 BP; 328 A; 183 C; 190 G; 334 T; 0 other; taggggtggg cacttggaac cgaaacacga atcgaatcga accgcaccga acggtttggt 60 tttgcggttt tgaaacggtt tcggtttcga aaccgaaccg cggcaaagaa aacggtttgg 120 tttcggtttt gggttttcaa aaccgcaccg aaaccgaaac cgaaaccaaa cgcaccatat 180 aataaaatta ataaataaat gttatatttt aaacttttaa ttagttcaac taggttacta 240 gactatcatt atcatctagt tttgaatctt taatatggga cgagatgaaa catgttctct 300 gacctttttt ttgtcggttg gggaaccctt atagacaagc tgttacattt tctaaatatg 360 tgtttattgg gttgggaatc atacaagttt catcatggag actacactaa ctcaaacaaa 420 tatttactgg atatgtgatt caaataagca actcactttg agcctaaata aacaaatatt 480 tactggatat gtttatttct gttgtaagca ctgagcaatg acaatgagca tcggtcatat 540 tgaatttgag ggggctggaa taacaaaata acattagcac tttctttctt cgtttgttta 600 tttctgtttt gttgttctct agtagattat ggcattgaat tattttgttc tgttctattt 660 tggagcactg gtggattatg gcattgaatt caacatgcca atctgacaaa aaaaaaaact 720 cattaatatt atggcattga aattcaaagt taggacatta ctttagtaag tattaatatt 780 aatcaaagtt aggacataag accgtcttaa ttaatatatg aggaaaataa gaccgtctta 840 tgcataaata agtgtatatt ttaaattgta cattttttct caaaaaccaa accgaaaccg 900 tttgaaaccg caccgaaccg aaccaaacgg tttggtttca tttcggtttt ggcttcaaaa 960 ccgcaccgca aaaagtttcg gtttcggttg tggtttcact cgaaaccgca ccgaaccgca 1020 ccgcgcccac cccta 1035 // ID Copia-3_Mad-I repbase; DNA; EDCOT; 4771 BP. XX AC ACYM01009006; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-3_Mad-I; KW Copia-3_Mad-LTR; Copia-3_Mad_. XX NM Copia-3_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4771 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1283-1283 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01009006; Positions 1605 6375. XX CC Positions [2081-2548] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS join(2906..3451,3455..4771) FT /product="Copia-3_Mad-I_1p" FT /translation="MNSSSNNVMPNTVPIPISEGSTTHPGTVSISDTESPG FT CSQSIATSPTQPLSSILPVVPEFQPDQLQVVLSIPPVNLHPMQTRSKSGII FT KKIALLAAVHDNGGVDWTQVEPATYKSALKTPVWYEAMKEEIAALHSQGTW FT SLVPLPKHKNLVGSKWVFKIKKNANGSIGRYKARLVAQGFNQEGIDYGETF FT SPVVKPTTVWLVLALSAHFGWSLRQLDVKNAFLHGILHEEVYLAQPPGFVD FT IHHEDYVCRLHKSLYGLKQAPRAWNERFTSFLPSLGFTSTYTDPSLFVKLV FT DSSVVILLLYVDDIIITGSATTAITEVIQSLAKEIDIKDLGPLHYFLGIQI FT LQKKDGLFLSQDKYVTDLLTKSEMLLSKPCATPCLPYNRLLKDDGKPFNNP FT ALYRSLVGALHYLTFTRPDIAFAVHQVCQFMQHPMDSHFMAVKRILRYLRA FT TQGCGIHYVKGSLDITAYSDADWAGDPNDRRSTTGMVVFLGSNPISWSSKK FT QNTVSRSSTEAEYRALSTTAAELDWINQLLAFLHIPVIEKPVLFCDNLSAI FT ALTLNPVQHQRTKHIEVDVHFVRERVATQQLQVHFVSSTEQFADILTKGLS FT APLFQTHCANLRLKFSAPELEGG" XX SQ Sequence 4771 BP; 1269 A; 999 C; 892 G; 1564 T; 47 other; tggtatcatc gcccgaacaa gcgtaaaacg cttgccggtt ttgtcgatct tggtttcgat 60 tgcttccgct actgtgattg cttttctttt gctttggttt tctggaatat tgggttattg 120 ttgatcgtgt ttctgatata ttggggtgtt ttctgcaaat cttcgtctgg ttcttcactc 180 gttaaagggt gcataccaac tgtttgtgat ttgrtgtcag tcaagattct ttggaatttc 240 tctacaattt gcaacaatgg taacagcagc tcagttayag atcttacagt ctccgattac 300 ttcgttgatt tcrtctgttt ccagttcggt yamtgtgaaa ttggacsaga craactattt 360 rgcttggcat tttcagatgc agctccttct tgaaggccat agcatcattg gttttgttga 420 tggttcaatg ccgtgtcctg ctcaattcag tcaagattcc tctgctactt ctryagtttt 480 gtctrgtgat tcgtctacam grattccttc tgatgactac aytatatgga agatgcatga 540 taaggcatta atgcaattga tcactgcgmc tctatctcct gctgcagttt cttgtgtcat 600 tggaagtact agctccaaak aattgtggac wcgtcttaaa gatcaatttt ctacagtcac 660 aagaacgagt attttccaac tcaaatccga acttcagaca ataaagaagg gtactgattc 720 tgtcacatta tatttgcaga aaattaagga agcaagagat ttgttgtctg ctgctggtgt 780 attcttykat gatgatgaca ttgtgattct tacactaaat ggtttgcctg ctgaattcaa 840 taccatamgg tctgtgatca grggtcggga gagtgtgata tcactgaaag atcttcgatc 900 tcaattactt gctgaagaaa ctttgcttga aaattgttct cattcacctg tgttgtctgc 960 attaatggct yaaagtaatg gtttaccttc caagaatcag tctttttctk ggaattatkg 1020 taacaataac catgctagtc ckaattcgac tgcatacaag tctttcaata ataccaaagg 1080 caggaatcgg ttcactccta acttcaatcc camgtatggc aattacaaga attttcattc 1140 ragtcctgct cctggaatcc tyggtamttc accaccaaga tcaaacaatt atggatttct 1200 gtctcaacct tgtcaaatct gtgggaaaca caatcatwtg gcatcaacwt rtcrttttcg 1260 taatacaaac tctgtacagg gttgtcaaat ttgtggaaag aacaaccatt ttgcggatac 1320 ttgcagattt cgcaactctg gtgctccttc tggttgtact atatgtggaa atcaatatca 1380 cagtgcagac acatgytttc aaaagaattc taawcctcaa ctcaatgctc tacatgctgc 1440 aacamctagt ggtccatatt ctccattcac agtgmcagtg ccatctgcac catcccagca 1500 acaagtatgg cttactgatt ctggtgccaa taatcacatg acctcagatt tgagtaatct 1560 ctccttggca actccatatc catcacatga gacaattcar acagcgaatg gtgaaggttt 1620 agcaatatct catattggtt ctacacttct cagamcttca aarcagccta ttaaacttac 1680 ttcagttctt tatgtaccma aattgtctca aaatctgttg tctgtgcata ggatttgtct 1740 ggataataat tgttggttga tttttgatgy gttttctttt tggattcagg acaaagccac 1800 agggaggata ctttacaaag ggctgtgtaa caatggattg taccccatca tytcttcaac 1860 atctcctgca gcaagcttca saggacatcc tgcagccttt ctgggaaagc aagttcctca 1920 cagtatttgg cataagagat taggtcaccc ttcaaattca atagtttctc aggttcttac 1980 atcgtcaaat gttttmtgtg ttaytgatac aaacccatct ytgtgtcaga cctgtttaga 2040 gggcaaattt agcaaattgc cattttcttc ttccctagtc aagtctgtca aaccttttga 2100 tattgttcat agtgatgtgt gggggcctgc tccgtgtatt tcttttgacg gtttcaaata 2160 ctatgtcact ctcattgatc attgtacaaa atattcctgg atttttccta tctgcaataa 2220 aagtgatgtt tttggaatct ttagggcctt ttacaatttt attctcaatc agtttcaagt 2280 ctccattaaa actcttcaaa gtgatggtag tggtgagtat gttagtaagg catttcaaac 2340 attcttatct gataaaggca tccatcatca agtgtcttgt cctcatacac ccgaacaaaa 2400 tggcattgcc gaaaggaaac acagacacat cattgaaaca tttatcactt tgttacaaac 2460 tgcatctcta ccatccctgt tttggtccgt tgcttgtcaa acttcagtgt acttaatcaa 2520 caggatgcca tctccttctt tacacaacta gtctccattc caattgctgt ataattcaaa 2580 acctgagatc caacatctga aagtttttgg ctgttcttgt tatccttggt taaaacctta 2640 caccaacact aaactagacc ctagaacaac caaatgtgta tttttggggt atgcatctaa 2700 gtataaaggg tatatctgct atgatgtgac taaaaacaaa atctatatat ctagacatgt 2760 catttttgat gagacagagt ttccttatcg gtttcttcac actacacatc actctacttc 2820 ttcaacactg ccatcagtcc ttcaaacccc aagtccagtt ccagatcaca ataatgttct 2880 tgtgttccca caccatgact atcatatgaa ttcctcatca aataatgtca tgccaaatac 2940 tgtacctatt ccaatctcag aagggtctac tacccatcca gggacagttt caatctcaga 3000 tacagaatct ccaggttgca gtcaatccat tgctacatca ccaacacagc ccttgtcttc 3060 catactccct gtggtacctg aattccaacc tgaccaattg caagtggttc tctccatacc 3120 tcctgttaac ctccacccca tgcagacaag atctaaaagt ggtattatta agaagattgc 3180 tcttcttgcg gctgttcatg acaatggagg tgttgactgg actcaagtgg aacctgccac 3240 ttataaatct gctttaaaga ctccagtatg gtatgaggct atgaaagagg agattgctgc 3300 attacactct cagggtacat ggtctttggt tcctctacca aaacataaga atttagttgg 3360 ttccaaatgg gtgtttaaga taaaaaagaa tgctaatggg tccattggga ggtataaggc 3420 acgactggtc gctcaaggct ttaatcaaga ataagggatt gactatgggg aaacctttag 3480 tccggttgtt aaaccaacaa cagtgtggtt agtcttagct ttatcagcac actttggttg 3540 gtcattgcga cagttggatg tgaaaaatgc gttccttcat ggtattttgc atgaagaggt 3600 gtacttggcc caaccacctg gttttgttga tattcatcat gaggactatg tttgcagatt 3660 acataagtct ttatacggat tgaaacaggc acctagagcc tggaatgaga gatttacctc 3720 ctttctacca tctttggggt tcacatctac ttatactgat ccttctttgt ttgtgaaact 3780 ggttgacagt tctgtggtca ttttacttct gtatgtggat gacattatta ttactggcag 3840 tgcaactaca gcaattactg aggttattca gtcacttgct aaggaaattg atattaaaga 3900 tttgggtcct ttacattatt ttctagggat tcaaatcttg caaaagaagg atggcctgtt 3960 tctttctcaa gataagtatg ttacagattt gttaactaag tctgaaatgc tgctgtctaa 4020 accatgtgcc actccctgtt tgccatataa ccgattgctc aaagatgatg ggaaaccttt 4080 taataatccg gctctttata gaagtttagt tggagcttta cactacttga catttactcg 4140 acctgacatc gcttttgcag tacatcaggt ttgtcagttt atgcagcacc ctatggactc 4200 tcatttcatg gcagttaaac ggatccttcg gtacttaaga gctactcaag gttgtggtat 4260 tcattatgtc aagggttccc tggatattac tgcatatagt gatgcagact gggctggcga 4320 tcctaatgat cgccggtcca ccactggaat ggttgtattt ttgggctcta atcctatttc 4380 gtggtcatcc aagaagcaaa atactgtctc tcgttcctcc acagaagctg aatatcgggc 4440 tctatccact acagctgctg aacttgattg gatcaaccaa ttgttggctt ttctgcatat 4500 tccagttata gaaaagccgg tcctcttttg tgacaattta tctgctatag cactgacttt 4560 aaatccagtt caacatcagc gaacgaaaca catagaggtt gatgtgcatt ttgttcgtga 4620 gagggtcgca acacagcaat tgcaggttca ttttgtgtct tcaaccgagc agtttgctga 4680 catactgaca aaaggcttgt ctgctcctct ctttcagact cattgtgcca atctcaggct 4740 caaattctct gcccctgagc ttgagggggg a 4771 // ID Copia-21_Mad-I repbase; DNA; EDCOT; 5391 BP. XX AC ACYM01138139; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-21_Mad-I; KW Copia-21_Mad-LTR; Copia-21_Mad_. XX NM Copia-21_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5391 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1295-1295 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01138139; Positions 30534 35924. XX CC Positions [2168-2695] - Integrase core CC 'ACCGC' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS join(767..3382,3386..4816) FT /product="Copia-21_Mad-I_1p" FT /translation="MKTLNLVNIPILTGGGNYKKWRREMSLLLTLNEFDIA FT IENPKPVVNDQSTRAEKADHLNAIEKKFQESEKAEMSQYMSLLTTYKMEGT FT CSIRDHIMKMSDAAERLNAMDINIGEKQLVFMILQALPSKYSQLKISYNTQ FT DKNWDVGQLIAQCVQEETCQKQERGKEVEDINFVQTINDKKQFNNRGFSGS FT GKSSKPFKNSNKFSNSAKVVDSPRKSIKFKAKPKDVSKLKCFWCKTKGHLK FT VNCEIFKDYVKSKEREQVLVCIESNLCEVPVDSWWFDTGCSVHITNSLNGF FT QKQKEVGNAIYNVFVGEGTKVAVESVGIVKLVLCFGFVLELKDVLYVPKMR FT RNLISASKIVKDRFSFLGDDECLKIFKKNCHNTILGTALLSDNLWNLNCPV FT KALNHTIFSISAKRMIGQDTSYILWHKRLGHISKERLIKLSKTELIPKLDL FT STTTECVDCLKGKMTNFRKTDAKRSQGLLEIIHTDICGHFPVKTICGNKYF FT INFIDDFSRLGYTFLISEKADALKCFIIYKTKVEKQLGKVIKIVRSDRGGE FT YFGRYTELGQQKGPFALYLEHNGIIAQYTTPGTPQQNGVSEKRNRTLIGMV FT RSMMTRSKLPGFLWGEALKTANYIMNRVPSKSVPSTPFELWHGRAPNFDYF FT HVWGCKSEARFYNPDERKLDPKTQSCYFIGYPEKSKGFRFYVPQGHTRIQE FT THNAVFLEDEDVSHLSRENFIFEEMNADGGDHVTMDYNQVPLFPNQSSTAI FT EDISADLGVPDDNSVGVDYTTQAATIPFAEIRASVSVPSPDEIRRSTKARK FT TTAINDYVYLQETEFDIGDIDDPLSYTQAIESPQAVLWNNAMKDELDSMFK FT NQVWTLVESNSEIRPIGCKVYKTKRDANGRIERYKARLVAKGFTQREGIDY FT NDTFSPVSSKDSMRVIMSLAAYFDLELHQMDVKTAFLNGDLQEDIYMKQPV FT GFVERGKENLVCKLNKSIYGLKQASRQWYLKFDQIVSAQGFVENKLDDCTY FT IKFSGSKFIFLVLYVDDILLASSCSHLLQSTKRMLSDNFEMKDLGEAHYVL FT GIEIVRDRKMRLIGLSQKGYIERMLEKFHMESCNSGQVLVNKGDKFSKIQC FT PRSDLEVKKMQAKPYASLIGSLMYATICTRPDIAFIVGMLGRFQENPGEAH FT WVAAKKVLRYLQRTKTHMLVYGRTNSLELMGYTDSDLAGDVDDRKSTGGYI FT FILNGGAVSWKSAKQTVIATSTMEVEFVACFEGMKQAAWLKNFLTDLKIVN FT SVQKPVKMFCDNNSAVFFAKNNKRTSASRLMDVKFLKVREQVKKRVIEVQH FT ISTTMMIADPLTKALSIGEFKKHVSSMGVLEGFDQWE" XX SQ Sequence 5391 BP; 1739 A; 795 C; 1162 G; 1695 T; 0 other; tgtggtatca gagccttaga ttcatgttct taaattcaat cgataaaatt ggttgaatcc 60 aaataaaaaa ataataataa attaaaaaaa aaattcggtc ttcagacttc gaaacaggtt 120 ctggtggtta aaactaggaa aaggagaaac ggtgcgtttt gattaaaata tgatgtttaa 180 tatttgaccg ttaagaacta aaaacaaaaa tcctatcttc ttttccggat tgggaataca 240 aatcgacatc tttcgatttc gattttgggg tttgaaaatc tgggcaatat gaattgttgt 300 tgagtattca cgatttatgt taattgcttc cgctactggg tgttgatact catagaacaa 360 acgggtatgt cttctgaaca ttggattgaa atttgttttg attatgttct tcagcatgat 420 tcgaatagtg agcataaaaa tatgcttatt tatgctgatt agtcctatgt ttatgcgttt 480 tctctaactg tctatggaaa ggagttcttc atattagaac ctctgcagac atcacttgtt 540 ttatacagaa agttttatga agaattgttc atttgagaca aatcagctaa aactgtgttc 600 ttaaaatctt ttattctata tgtgcttatc aattcttcat tgttaagatt atatatatgg 660 ataaaagttt tttgatgata tgatgtgcaa aagactgtga gatgaaatct ggaaccctaa 720 acgttcttct gtgatttcat tatgttcttc agtgtctgca atatcaatga agactctgaa 780 tttggttaac atcccaattc ttactggtgg gggaaattat aagaagtgga gaagggaaat 840 gagtttgctg ttgactctaa atgagtttga tatagcaatc gagaatccca agccagtagt 900 taatgatcag agcacaagag ctgaaaaggc agatcatctt aatgctatag aaaagaaatt 960 tcaagaatct gaaaaagctg aaatgagtca gtacatgtct ttattaacta cttacaagat 1020 ggagggtaca tgctctataa gggatcacat aatgaagatg tcagatgctg cagaaagact 1080 caatgcaatg gacataaaca taggtgaaaa gcagttagta ttcatgattc ttcaagcact 1140 tcccagtaaa tatagtcagt tgaagatctc ctacaatact caagacaaaa actgggatgt 1200 tggtcagttg atagcacaat gtgtgcaaga agaaacttgt caaaaacaag aaagaggcaa 1260 agaagttgag gacatcaact ttgtgcaaac tataaatgac aagaagcagt tcaacaacag 1320 aggcttttct ggttctggta agagttctaa gccctttaag aattctaata agttcagtaa 1380 ttctgctaaa gtagttgact cccctagaaa atctatcaag tttaaggcta aacctaaaga 1440 tgtgtctaaa ctaaaatgtt tttggtgcaa aactaagggc catttaaaag ttaattgtga 1500 aattttcaaa gattatgtaa agagcaaaga aagggaacaa gtacttgtct gtattgaatc 1560 aaatctttgt gaagtacctg ttgattcttg gtggtttgat accggatgct cagtgcatat 1620 aactaattct ttaaatggtt ttcaaaaaca aaaggaagtt ggaaatgcta tatataatgt 1680 ttttgttggg gaaggaacta aagttgcagt agagtcagtt gggatagtaa aattagtctt 1740 atgttttggt tttgttttag agttgaaaga tgtgctatat gtgcctaaga tgagaaggaa 1800 cttaatttct gcctctaaaa ttgtaaaaga tcgtttttcc tttcttggtg atgatgagtg 1860 cctaaaaatt ttcaagaaaa actgtcataa cactatttta gggactgccc ttttgtctga 1920 taatttatgg aatcttaatt gccctgttaa ggccctcaat cacacgattt tcagcattag 1980 tgctaagaga atgataggcc aggacacttc atacatttta tggcacaaaa gactaggaca 2040 catctctaaa gaaagattaa ttaagctgtc aaaaactgaa ttgattccaa aattagatct 2100 ttctactaca actgaatgtg ttgactgcct aaagggtaag atgactaact ttcgaaaaac 2160 agatgccaaa aggagtcagg gattacttga aatcatacac actgatatct gtggtcattt 2220 tccagttaag acaatatgtg gaaacaagta tttcattaat ttcatagatg atttttcaag 2280 gctgggatat acctttctta ttagtgagaa agctgatgcc cttaagtgtt ttataattta 2340 caaaactaag gttgaaaaac aattaggcaa ggttattaaa attgttagat cagatagggg 2400 aggtgaatac tttggcaggt acactgaatt agggcagcaa aagggaccgt ttgcacttta 2460 tttggagcac aatggaatta tagctcaata tacaacacca gggacacctc agcaaaatgg 2520 tgtttcagaa aagaggaatc ggactctcat tggtatggtt agaagcatga tgacaagatc 2580 caaattacct ggtttcttgt ggggggaagc tttgaaaact gcaaattaca ttatgaatag 2640 agttcccagc aaatccgttc cctcgacacc atttgagcta tggcatggga gggcacctaa 2700 ttttgattac tttcatgttt ggggctgtaa atctgaagca agattctata atcctgatga 2760 aagaaagttg gatcccaaaa ctcaatcttg ctatttcatt ggctatcctg aaaaatcaaa 2820 aggattcaga ttctatgttc ctcaaggaca cactcggatt caagagacac acaatgcagt 2880 tttcctggaa gatgaagatg tctctcattt gtcaagggaa aatttcatat ttgaagagat 2940 gaatgcagat ggtggggacc atgtgacaat ggattataat caggtcccat tgtttcccaa 3000 tcaatcatcc actgccattg aagatataag tgcagatttg ggagttcctg atgacaactc 3060 tgtaggagtt gattacacaa cacaagctgc aacaattcct tttgcagaaa tacgtgcatc 3120 agttagtgtt ccatctccag atgaaatcag aagatctaca aaagctcgga aaaccacggc 3180 aatcaatgac tatgtgtact tgcaagagac tgagttcgat atcggtgaca ttgatgatcc 3240 tctttcatat actcaggcaa ttgaaagtcc tcaagcagtt ctttggaaca atgcaatgaa 3300 ggatgagtta gattcaatgt tcaagaacca ggtttggaca ttggtggaat caaactctga 3360 aattaggcca ataggctgca agtaggtata taaaactaaa agggatgcta atggaagaat 3420 tgaacgatat aaagcaaggt tggttgctaa ggggtttact caaagagaag gaatcgacta 3480 caatgatact ttctctccgg tttcctctaa agattccatg cgagttataa tgtctttagc 3540 tgcctacttc gatcttgaat tacatcaaat ggatgtcaaa acagcttttc tcaatggaga 3600 cctccaagag gatatctaca tgaaacaacc tgttggattt gttgaaaggg ggaaggagaa 3660 tttggtatgc aagctcaata agtcaatata cggcttgaaa caggcatcaa ggcagtggta 3720 cctaaagttt gatcaaattg tctctgcaca aggttttgta gaaaacaaac tagatgattg 3780 tacatacatt aagttctcag gttccaagtt cattttctta gtgctttatg ttgatgacat 3840 tctccttgct agttcatgtt ctcatttgct tcaaagtact aagagaatgc taagtgacaa 3900 ctttgagatg aaagatcttg gagaagcaca ttatgtactg ggaatagaga ttgttcgaga 3960 taggaaaatg aggctcattg gtttatcaca aaaggggtat attgaaagaa tgctggagaa 4020 atttcatatg gaaagttgca atagtggtca ggttctagtc aataaaggtg acaagttttc 4080 gaagattcaa tgtccaagat ctgatttgga ggtgaagaaa atgcaagcta agccttatgc 4140 ctcattgatt ggaagtctca tgtatgcaac tatctgtaca aggcctgata ttgctttcat 4200 agttggtatg ctgggacgat ttcaagaaaa tcctggagaa gcacattggg tggcagccaa 4260 gaaggtcctg cgatacttac agagaaccaa aactcacatg ttagtatatg gcagaaccaa 4320 ttctttggag cttatggggt atacagactc ggatttagct ggtgatgtgg atgacagaaa 4380 gtccacaggg ggttatatct tcatactcaa tggaggggca gtttcgtgga aaagtgcaaa 4440 gcaaactgtt atagctacat caactatgga agttgagttt gtagcctgtt ttgaaggcat 4500 gaaacaggca gcatggttga agaatttttt gacagacttg aagattgtga attcggttca 4560 aaaaccggta aagatgttct gtgataacaa ctcggctgtg ttttttgcta agaataacaa 4620 aaggacttca gcatctagat tgatggatgt gaagtttctt aaggtcagag aacaagtcaa 4680 gaaaagagtt attgaagtac agcatattag caccactatg atgattgctg atcctttgac 4740 taaggcactg tcgattggag aattcaagaa acatgtttct tcaatgggag tactagaggg 4800 ttttgatcag tgggagtgat cacgagtgtg ttaggggctt gggattgcaa aagtatatat 4860 gtttcaagaa ctgtaagtgc aattctgaca agctgaggat aattatgttt taacttgctt 4920 tagctagttt gttgagtttg tttgtgtttt aataagtgtc tttgtctgct actcgatgct 4980 ttggctttca aagtgttgaa gtacagatac tcgactgagt tagaattcag tttcattagt 5040 aactttggaa gaacagtttg tctgttttaa agtttgtggt taatgatctt atatatagtc 5100 aattactatg ttgcttttct gtgaagatta atgtgtgttg tgatcttttg aaaagtggga 5160 gcataatgtt tgacggttta tattagtcat gagtcatatt tgcaaattgg atatatgtga 5220 gccttgaatt aatactacaa tttggttgtg gtctgagatt cttggtttct atgttttgag 5280 atgtaatggg acagtggtca tgatggttaa atcttagatg aggttatgtg atcacttctt 5340 atgtttggtg acggctatgt ttgatctttg tctcctgttc aagtgggaga a 5391 // ID Copia15-PTR_LTR repbase; DNA; EDCOT; 251 BP. XX AC scaffold_320; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia15-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-251 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-251 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 203-203 (2007). XX DR Genome; scaffold_320; Positions 34898 35148. XX SQ Sequence 251 BP; 64 A; 45 C; 46 G; 96 T; 0 other; tgaatcatca cctccccacg tcactaaaga gaaggatggc atggttacct gaattctgtt 60 actctgttac ttattatttg ttgcttctgt aatgagctgt acataaaggg taatgttgac 120 attgcatggg ataagttagt tagaatattc tttgcttgct gtatataatt ggacgagctg 180 catcattcaa tagacatgag gaatttctct ctgcaattct gttttcctct atttcacatt 240 cttttgtttc a 251 // ID GYLES1_I repbase; DNA; EDCOT; 4631 BP. XX AC AF119040; XX DT 02-SEP-2005 (Rel. 10.08, Created) DT 02-SEP-2005 (Rel. 10.08, Last updated, Version 1) XX DE GYLES1: Gypsy-type LTR retrotransposon from tomato (internal DE portion). XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; GYLES1_LTR; internal portion; GYLES1_I. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-4631 RA Parniske M., Wulff B.B., Bonnema G., Thomas C.M., Jones D.A. RA and Jones J.D.; RT "Homologues of the Cf-9 disease resistance gene (Hcr9s) are RT present at multiple loci on the short arm of tomato chromosome RT 1."; RL Mol Plant Microbe Interact 12(2), 93-102 (1999). XX RN [2] RP 1-4631 RA Parniske M. and Jones J.D.; RT "Recombination between diverged clusters of the tomato Cf-9 plant RT disease resistance gene family."; RL Proc Natl Acad Sci U S A 96(10), 5850-5855 (1999). XX DR EMBL/GenBank/DDBJ; AF119040; Positions 18275 13645. XX CC LTRs differ by 2 base substitutions. XX FH Key Location/Qualifiers FT CDS 26..4630 FT /product="GYLES1_I_1p" FT /translation="MVKNAELWELARKIESFVGFTEDVLADPTFVDLFTQI FT IELRVDAEKVQGEIGGYRQNVDNHITEILDFRATTTQKLEGLQKENENLRA FT ELVVLCRAVATLSSTRVESSKVKIPDPKAFSGARSAKELENFIWDMEQYFT FT AARVPDADKLNITTMYLSGDAKLWWRTRNADDVSAGRPRIDTWDKLIKEMR FT DQFLPSNASWLARDKLKRLRQTGSVREYIKEFTSVMLDIQNMSDEDKLHNF FT ISGMQGWAQNELRRQNVKDLPGAIAAADSLVDFRTTRPSTDVPSTSKNKKK FT NEKKGEWRKDSRKENANDKGKAQMKDGKDRPKSKDGNSKGCWTCGGPHLAK FT SCPNREKVNALLAGNVNQREEDEEIVAAMANPLGLSFNHIMGINNVREISS FT TSNPHASLIHIEMKVKEQCVMAMVDTGATHTFVDVKIATKLGLKLSKSPSY FT VKTVNAKAQAIVGMAYSVSMSTGNWVGKHNLMVMPLGDFEIILGIDFLRKY FT QFVPFPHLDGVMVMSGSDAGFLKGVHPFGNINKVAKKKDKEMLLSAMSIDK FT GLKKGDETILAALVEIKPDVKMEVPDCVAELLKQYADVMPPELPKKLPPRR FT DIDHKIELLPGTVAPAQAPYRMAPKELVELRKQLNELLDAGLIQPSKAPYG FT APVLFQKKQDGTMRMCVDYRALNKATIKNKYSVPLVQDLMDRLSKACWFTK FT LDLRAGYWQVRIAEGDEPKTTCVTRYGSYEFLVMPFGLTNAPATFCNLMNN FT VLFDYLDDFVVVYLDDIVIYSRTLEEHVNHLSLVLSQLRKYTLYVKMEKCE FT FAQQEIKFLGHLVSKNQVRMDPKKVQAIVDWQAPRHVKDLRSFLGLANYYR FT KFIAGYSKKAASLTDLLKKDAKWVWSEQCEKAFQNLKNAIASEPILKLPDF FT ELPFEVHTDASDKAIGGVLVQEGHPVAFESRKLNDAEQRYSTHEKEMVAVV FT HCLQVWRVYLLGTRFVVRTDNVANTFFKTQKKLSPKQARWQEFLAEYDFMW FT EHKPGKHNQVADALSRKEVFVAVYSISKLETDFYDRIRLCAANDSLYVKWM FT GQVQDGTMRRYWIEDDLLYFKGGRIVVPNQGGLRKDLMKEAYDSAWAGHPG FT VERMLALLSRVYFWPKMEDDIEAYVKTCHVCQVDKTERKKEAGLLQPLPIP FT ERPWLSVSMDFISGFPKVDGKASIMVVVDRFSKYSVFIAAPELCSSEVAAE FT LFYKHVIKYFGVPADIVSDRDTRFTGRFWTALFNMMGTELKFSTANHPQTD FT GQTERINHLLEEYLRHYVTASQRNWVELLDTAQFCYNLHKSSATEMSPFEI FT VLGKQPMTPLDVAKSKNQGKCPAAYRVARDRLEMLSEAQDSLRKAQQRMKK FT YADQHRRSVEFSVGDKVLLKLTPQIWKQIVSKTRHRGLIPKYDGPFEVVKR FT VGEVAYRLKLPERLKIHPTFHVSFLKPYFADEDDPDRNRSKRAPPSVPTQY FT DAEIEKILDHRVLGTSKKNTKTEFLVHWKGKSAADAVWEKAKDLWQFDAQI FT DDYLKTVSMRTSSSSGAGG" XX SQ Sequence 4631 BP; 1429 A; 779 C; 1174 G; 1249 T; 0 other; attggtatca gagcaaggtt aaacaatggt gaaaaacgca gaactatggg agttggcacg 60 aaaaattgaa tccttcgtcg ggtttactga agacgttctg gcagacccta cgtttgtgga 120 tttattcaca caaatcattg agttgagagt ggacgctgag aaagttcagg gagaaattgg 180 tggatatcga caaaatgttg ataatcacat cactgaaatc ttggactttc gtgctacaac 240 tacacagaaa ctagagggac tgcagaagga aaatgagaac cttcgtgcag aactcgtcgt 300 tttgtgtcgg gctgtggcta cgttgagttc gactcgtgtt gaatcatcta aggttaagat 360 tccagaccct aaagccttca gtggcgcaag gagtgctaaa gaacttgaaa acttcatatg 420 ggacatggaa cagtacttta ccgctgcaag ggtgccggac gccgataagt taaacattac 480 cacaatgtac ttgtcgggtg atgcgaaact ttggtggagg actcgtaatg cagatgacgt 540 aagtgctggt cgtcctagaa ttgatacatg ggataagctt ataaaagaaa tgcgcgatca 600 atttcttcct agcaatgcat cttggcttgc aagggataaa ttgaaaaggt taaggcagac 660 gggttcagtg agggaatata taaaagaatt tacctctgtg atgttagaca tacaaaatat 720 gtctgatgag gataaacttc acaatttcat ttcgggcatg caaggctggg ctcaaaacga 780 actacgaagg cagaatgtta aagatctgcc tggggcaatt gctgctgctg attcgttggt 840 agatttccgg acgactcgtc cttcgacaga tgtcccttct acttcgaaaa ataagaaaaa 900 gaatgaaaag aaaggggaat ggagaaagga tagtcgtaaa gagaatgcaa acgataaagg 960 aaaggcacaa atgaaggatg ggaaagacag acccaagagt aaagatggaa actctaaagg 1020 ctgttggact tgtggtggtc ctcatttggc caaatcttgt ccaaaccggg aaaaagtgaa 1080 tgctttgctt gctggtaatg tgaatcaaag ggaggaggat gaagaaattg tggctgcaat 1140 ggcaaaccca ttgggattat ccttcaatca cattatgggg atcaataatg ttagagagat 1200 ctctagcact tcgaatcctc atgcttcctt aattcatata gaaatgaaag tgaaggaaca 1260 atgtgtgatg gcaatggttg atacaggggc cacacacacg tttgtagatg tgaagattgc 1320 tacaaaattg gggctgaagt tgtctaaaag cccttcctac gtaaagacag tcaatgctaa 1380 ggcacaagcc attgtgggca tggcttatag tgtgtctatg tcgactggaa attgggtggg 1440 aaaacataat ttgatggtga tgccgcttgg agactttgaa attatacttg ggattgattt 1500 cctaagaaaa taccagtttg ttccgtttcc tcacttagat ggagtgatgg taatgagtgg 1560 aagtgatgct ggttttctga agggtgttca tccgtttgga aacattaata aagttgcgaa 1620 gaagaaagac aaggaaatgt tgttgtctgc tatgtcgatt gacaaagggc taaagaaggg 1680 tgatgaaact atacttgctg ccttggtcga aattaaacct gatgtgaaga tggaagtgcc 1740 tgattgtgtt gctgaattac ttaaacagta tgctgatgtt atgccacctg aattaccaaa 1800 gaaattacca ccaaggaggg atattgatca caagattgag ttgctgcctg gtacggttgc 1860 ccctgcacag gctccttatc gtatggctcc taaagaattg gttgaactac gcaaacaatt 1920 gaatgaattg ctagatgctg gattgattca gccgtctaag gctccatatg gcgcccctgt 1980 tctatttcaa aagaaacagg atggaacaat gagaatgtgt gtagactacc gggcgctgaa 2040 taaggcaact ataaagaaca aatattcggt tccattggtg caagatttaa tggacaggtt 2100 aagcaaggca tgctggttca caaaacttga tttgagggca ggctattggc aagttaggat 2160 agcagagggt gatgaaccaa aaacaacatg tgtaactaga tatggttcct atgaattcct 2220 tgtaatgccg ttcgggctga ctaatgcccc ggcaacattc tgcaatttaa tgaacaatgt 2280 actgtttgac tatcttgatg acttcgttgt tgtttactta gatgatattg ttatatatag 2340 tcgaacgttg gaagaacatg ttaatcacct aagtctggtt ctgtctcaat tgagaaaata 2400 cacactttat gtcaagatgg aaaagtgtga atttgctcaa caagagataa aattcttggg 2460 gcatcttgtt agtaaaaacc aagttcgaat ggatcctaag aaagtgcagg ccattgttga 2520 ttggcaggca cctcgtcatg tgaaggattt gaggtcgttt cttggcttgg ctaactatta 2580 tcgaaagttt attgctggtt actcaaagaa ggcagcgtct ttgacagatc tgttgaagaa 2640 agatgcaaaa tgggtttggt ccgaacagtg tgaaaaagca tttcaaaatt taaagaatgc 2700 tattgcatca gaacctatac tcaaattgcc tgattttgag ttaccgtttg aagtacacac 2760 tgatgcgtca gacaaggcga ttggtggcgt attagtgcag gaaggtcatc cagtagcctt 2820 cgaaagtaga aagttgaatg atgctgaaca aagatactca acacatgaga aagaaatggt 2880 tgcggtggta cactgtttgc aggtttggag agtctatctc ttaggcactc gatttgtggt 2940 aagaactgat aatgtagcaa atacattctt caaaacacag aaaaagttga gtcctaaaca 3000 agcacggtgg caagaattcc tggcagaata tgatttcatg tgggaacata aaccaggaaa 3060 acacaaccag gttgctgatg cgctgagtag gaaagaagtg tttgttgcag tatattcaat 3120 ttcaaaactg gaaactgatt tctatgatag aatcaggttg tgtgctgcaa atgattcgtt 3180 atatgtcaaa tggatgggtc aggtgcagga cggcacaatg agacggtatt ggatcgagga 3240 cgatctgctc tattttaaag gggggagaat cgttgtgcca aatcagggcg ggttgcgcaa 3300 agacttgatg aaagaagcgt atgactccgc ttgggctgga catccaggcg ttgaaaggat 3360 gttagcctta ctgtctcgtg tgtatttttg gccgaaaatg gaagacgata tagaagcgta 3420 cgttaagact tgtcatgttt gtcaagttga caagacagaa cgtaaaaagg aagcagggtt 3480 gctgcaacct ttgcctattc ctgaaaggcc atggctatcg gtaagcatgg atttcatttc 3540 tggattccct aaagtagatg gcaaagcatc tatcatggtg gtagttgaca ggttttcaaa 3600 atattctgtt tttattgctg ctcctgagtt atgctcatct gaagttgctg ctgagttatt 3660 ctataaacat gtgattaaat actttggtgt tccggctgac attgtgagtg atagagacac 3720 aaggttcacg ggtagatttt ggacagcatt gttcaatatg atgggaactg aattaaaatt 3780 ttctactgca aatcacccac aaacagatgg acagacggaa agaattaatc atttgttgga 3840 agagtacttg aggcactatg tgactgcaag tcaacggaat tgggtggaat tgttagacac 3900 tgcgcagttt tgctataatc tgcacaagtc gtctgcaaca gaaatgagtc cttttgaaat 3960 cgtcttaggt aaacagccta tgacgccatt agatgttgct aaatctaaaa atcagggaaa 4020 gtgtccagca gcatacagag ttgcaaggga cagacttgaa atgttatctg aggcacaaga 4080 tagcttgcgc aaggctcagc agcgcatgaa gaagtatgct gaccagcatc gtcgctcagt 4140 tgagttcagt gtgggggaca aggtgttgct gaaacttacc ccacaaatct ggaaacagat 4200 tgtaagtaag accagacatc ggggtttgat acctaagtat gatggtccat tcgaagtggt 4260 aaaacgagtg ggcgaagttg cttataggtt gaagctgcca gaaaggttga aaattcaccc 4320 caccttccat gtgagtttct tgaaacctta ctttgcagat gaagatgatc cggacaggaa 4380 cagatcaaag agggctcctc catcagtacc tacacagtat gatgctgaaa ttgagaagat 4440 ccttgatcac cgggttttgg gcacaagtaa gaagaatact aagactgagt tcttggtcca 4500 ttggaaaggc aagagtgcag cagatgctgt ttgggagaaa gcaaaagacc tatggcagtt 4560 tgatgctcaa atcgatgact atctcaaaac agtctcgatg aggacatcga gttcaagtgg 4620 tgcgggtggt c 4631 // ID LINE1A2_MT repbase; DNA; EDCOT; 2947 BP. XX AC . XX DT 15-NOV-2006 (Rel. 11.11, Created) DT 01-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A LINE sequence from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW LINE; Interspersed repeat; non-LTR retroposon; LINE1A2_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2947 RA Shankar R. and Jurka J.; RT "LINE1A2_MT: A 5' truncated LINE from Barrel Medic."; RL Repbase Reports 6(11), 572-572 (2006). XX DR [1] (Consensus) XX CC Contains an ORF coding for Reverse transcriptase like protein. 5' CC end seems truncated. XX FH Key Location/Qualifiers FT CDS 2..2824 FT /product="LINE1A2_MT_1p" FT /translation="EWHVTHSKDLSRKIKSLKERQSELDGKGESEDLSAAE FT IEELHVVSSDIHSLSRVNTSIAWQQSRVHWFREGDANSKFFHSVLLGHRRR FT NRLHSIVVDGAVIEGVLDVRAAVFSHFSNHFKRCGSERIALDGLTFQTLSY FT AEGGGLTKPFSLEEVKEAVWDCDSYKSPGPDGVNFGFFKDFWGFLKDDIMQ FT FMVEFHRNGKLTKGINSTFIALIPKIDHPRNLNDXRPISLVGSXYKXLAKV FT LANRLRQVIGSVVASESQSAFVKNRQILDGILIANEVVDEASRLKKELLLF FT KVDFEKAYDSVDWRYLDAVMEKMNFPILWRKWINECVATATASVLVNGSLT FT DEFPLERGLRQGDPLSPFFFLLAAEGFNVIMKAVVARSIFEGYKVGAPDSV FT PVTHLQFADDTLILGVKSWANVRAMRAILLLFEEMSGLKVNFHKSMLVGVN FT VSDSWLSEAASVLNCRVGRMSFMYLGLPIGGDPRRLIFWEPLLRRIKSRLS FT GWNSRFLSFGGRLVLLKSVLSSLPVYALSFFKAPSGIISSIESIFYNFFWG FT GCEDSRKISWVNWNSIYSRREDGGLGVRRLREFNLALLGKWCWRLLVERSS FT LWYRVLVARYGEEDGRLTVGGRRGSAWWHAIXNIGDGVLGVGGGWFXEXMS FT RMVGDGTDTLFWHDMWLGEVPFRVRFRRLYDLAIDKSCTVANMFSSGWDVG FT GAGWRWRRRLLAWEEEMLGECAVLLHNVSLQVDVKDTWRWLLDHSAGYTVR FT SAYHLLTSQAIPHVEGAAALVWHKHIPLKVYIFVWRLFRNRLPTKDNLVHR FT GILSDAEASCVLGCGAVETSQHLFISCDFYGSFWSLVRAWLGVSGLDPCIV FT FDHFIQFTHLAGGLRARHSFMQLIWLFCVWVIWKERNQRLFNNIGSSIVQL FT LDKVKLHSLWWLKANHAIFAFSYHVWWSRPLHCLGLG" XX SQ Sequence 2947 BP; 630 A; 411 C; 845 G; 1055 T; 6 other; ggagtggcat gttacacatt ccaaggattt gtcgaggaaa attaaatctt taaaggaaag 60 gcaatcagag ttggatggga aaggggagtc ggaggatttg tcggctgctg aaattgaaga 120 gttgcacgtt gtctcatctg atattcactc tttgtctcgg gttaatacta gtattgcttg 180 gcaacaatca cgggtgcact ggtttcgaga aggggatgca aattccaagt tctttcattc 240 cgtgctttta ggccatcgtc gtcgtaatcg cttgcactcc attgttgttg atggggcggt 300 gattgaaggg gttcttgacg ttcgggcggc ggtgttctct catttttcga atcattttaa 360 aagatgtggg tcagagagaa tcgctctgga cggtttgact tttcaaactc tgagttatgc 420 agagggtgga ggtcttacta agcctttttc tttagaagag gtgaaggagg ctgtgtggga 480 ttgtgacagt tataaaagtc caggtccgga tggtgtgaat tttggtttct ttaaagactt 540 ttggggtttt ttgaaggatg acattatgca gtttatggta gaattccatc gaaatgggaa 600 gctgactaaa ggtataaatt ctacttttat cgcgcttatt ccaaaaatag atcatcctcg 660 gaatttaaat gactwtcgcc ctatttcgct ggttggcagt atstataagr ttttagcgaa 720 ggttcttgct aatagactac ggcaagtgat tggttcagtt gtggcttctg agtctcagtc 780 ggcttttgtt aaaaatcggc agattttaga tgggatttta attgccaatg aggtggttga 840 tgaagcctcc agattgaaaa aggaattact tttatttaag gttgattttg aaaaagctta 900 cgattcggtt gactggaggt atttggatgc tgttatggag aaaatgaatt tccctattct 960 ctggagaaaa tggattaacg aatgtgttgc gactgcaaca gcttcagtgt tagttaatgg 1020 tagtctaact gatgagtttc ctttagaaag ggggctacgt caaggtgatc ctctttcacc 1080 tttttttttt ctgttagctg ccgaggggtt taatgttatt atgaaggctg tggtggccag 1140 aagcatcttt gagggttata aggttggggc gcctgattcg gtgccggtga ctcatcttca 1200 atttgctgat gatactttga tcctaggagt taaaagttgg gcgaatgtcc gggctatgcg 1260 ggctattttg cttttgtttg aggagatgtc tggtctgaaa gttaattttc ataagagtat 1320 gttggttggt gtaaatgttt ctgattcgtg gttgtctgag gcagcctctg tcctgaattg 1380 tcgagtgggt agaatgtcgt ttatgtattt ggggctgcct attggtgggg atcctcgtcg 1440 attgattttt tgggaacctc ttttgcgtcg tattaaatcg agattgtcgg gttggaatag 1500 tcggttttta tcttttggtg gccgtctggt tcttctaaag tctgtcttgt cctctctacc 1560 tgtttatgct ctttccttct tcaaggctcc gtcaggtata atttcttcta ttgaatctat 1620 tttttataat tttttttggg ggggatgtga ggattctagg aaaatttcgt gggttaattg 1680 gaactctatt tattctcgga gggaggatgg aggtttgggg gtgaggaggt tgcgggagtt 1740 taatttagcg ttgttgggta aatggtgttg gcggttgttg gttgagagga gtagtttatg 1800 gtatagggtg ttggtggcga ggtatggtga ggaggatggg aggttgacgg ttgggggtag 1860 gagaggttct gcttggtggc acgcgattgy gaatattggg gatggggttt tgggtgttgg 1920 tggtgggtgg ttttwggaaa kaatgtctcg tatggtaggg gatgggactg atactttatt 1980 ttggcatgat atgtggttgg gtgaggtgcc ttttcgtgtt cgctttaggc gcctttatga 2040 tctggcgatt gataagtcat gcacggtggc taacatgttc tctagtgggt gggatgtggg 2100 gggagcgggt tggagatgga ggcggagatt gttggcgtgg gaggaggaga tgctggggga 2160 gtgtgctgtt ttacttcata atgtttcttt gcaggttgat gttaaagaca cttggagatg 2220 gctgctggat cactctgcag gttatacagt tagaagcgct tatcacttgt tgacttctca 2280 ggctatccct catgtcgaag gtgcagctgc gttggtttgg cataaacaca ttccgcttaa 2340 ggtctatatt tttgtttggc ggctgtttcg gaatcgcttg ccgacaaagg ataatctggt 2400 tcatcgtgga atcctttcag atgctgaagc tagttgtgtg ttaggttgtg gagctgtgga 2460 gacttctcag catttattta tttcttgtga tttttatggt tcattttggt ctcttgttcg 2520 ggcttggcta ggtgtctctg gacttgatcc ctgtattgtt ttcgatcatt ttattcaatt 2580 tactcattta gcaggtggtt tgcgagcaag acactctttt atgcagctta tttggttgtt 2640 ttgcgtgtgg gttatttgga aggaaagaaa tcaaaggttg tttaataata taggtagttc 2700 cattgttcag ttgttggata aggttaagtt gcattctttg tggtggttaa aagctaacca 2760 tgcaattttt gcttttagtt atcatgtgtg gtggtcaaga ccgttgcatt gtttgggtct 2820 tggctaattt ttgattgact ttgtatatct gtaatttttt gaggatccct tggtacacct 2880 tgtgctaggg aagcccctga cttgttaata taagttccat ttttgattgt tcaaaaaaaa 2940 aaaaaaa 2947 // ID MEGY-LTR_MT repbase; DNA; EDCOT; 1279 BP. XX AC AC146683; XX DT 09-JUN-2005 (Rel. 10.05, Created) DT 29-MAR-2007 (Rel. 12.04, Last updated, Version 2) XX DE Medicago truncatula LTR retrotransposon MEGY-1 (LTR). XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Long terminal repeat; Metaviridae; KW MEGY-LTR_MT. XX NM MEGY-LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1279 RA Neumann P., Pozarkova D., Koblizkova A. and Macas J.; RT "PIGY, a new plant envelope-class LTR retrotransposon."; RL Mol Genet Genomics 273(1), 43-53 (2005). XX RN [2] RP 1-1279 RA Lin S., Dixon R., May G., Sumner L., Gonzales B., Cook D., Kim D. RA and Roe B.A.; RG Department Of Chemistry And Biochemistry, The University Of RG Oklahoma, 620RL Parrington Oval, Room 208, Norman, OK 73019, USA; RT "MEGY-1 LTR retrotransposon."; RL Direct Submission to EMBL/GenBank/DDBJ (12-DEC-2003). XX RN [3] RP 1-1279 RA Toth G.; RT "Medicago truncatula LTR retrotransposon MEGY-1."; RL Direct Submission to Genbank (09-JUN-2005). XX DR Genbank; AC146683; Positions 124339 125617. XX CC Long terminal repeat of Ty3/Gypsy-like retrotransposon MEGY-1. CC 5bp CC target site duplications. XX SQ Sequence 1279 BP; 388 A; 223 C; 227 G; 441 T; 0 other; tgatgagtca tttatatgtt attttaatat gctttttagt ttagttttaa ttagatttta 60 tataatttta tattagtatt atttcctttt taggatagtt tactttaaaa tgcaatttat 120 tatatttcag ggaagaatat tggatggaga gagtcttgga gcaaaagaaa gggatttgga 180 gcagattgga cacaaaaata tgaagattgg gaaacaaaat atatctccca caagtcagaa 240 gtttggcacg gcccgtgctg gccttggcac ggccgtgcca ccctccagat gccttttgct 300 gcttttgctt tgactccaag ctattctatt ttggcgcaca atctaccgag gaatattcta 360 ggaatatact tgcttagatt ttaagtcaat tgtgtactat aaatagagta gctagccatc 420 actaaagatt catctttact tggaatacaa taagtgacaa ttgcttttct aaataaagtt 480 cttttccttt cctttatttt cctgtctttt actttcatgc tttctctctt ctcccccatg 540 tctacgatga acatgagtga gtagacttct tcttgtcttg ggattgttgg ataagtctaa 600 atgacataat cctaatcaaa ccaagcccta agccttaatc ttatgtaacc ctagtttctt 660 atctgaattc accgtcttaa catggattaa ccattatcaa actgtggaaa cgaaagtgga 720 gggtttgata attgttcgtc cattattcca aatatcaatt cataaaacga aagtggagct 780 ttgatattcg aacaagtgaa ttcagacaag gattgcaaag tcagcgaaat aggctttgca 840 atctttgaga catatagttt cgatcttcaa gggaactaat aacaatcaag tcagcgaaat 900 aggcttggtt gttagaggaa ccaaaatcca atagtaatca agtcagcgaa ataggcttgg 960 ttgctagagg aacttaagag aaactgtctt gagaaattag gtctaacata acattgtctt 1020 gagaaattag gtctaacata acattataag cttatggttt tggtttgaga gggacttgtt 1080 atttagatga aaccaacgat ccaaggctct tttattatat tgctttttaa cagtttaaaa 1140 acccccaact tacaattctc ttctctcttc taatcacctc taaagattaa ttaagttgaa 1200 ctactccctg tcggaacgat actcttttat actacttcgg taagaccgtg cacttgcggt 1260 ttgcggtttt atctcatca 1279 // ID TE-2_Mad repbase; DNA; EDCOT; 175 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative transposons from the apple genome. XX KW Transposable Element; Nonautonomous; TE-2_Mad. XX NM TE-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-175 RA Kojima K.K. and Jurka J.; RT "Putative transposons from the apple genome."; RL Repbase Reports 10(10), 1827-1827 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~93% identical to the consensus. 4-8 bp TSDs. No TIRs. XX SQ Sequence 175 BP; 56 A; 35 C; 31 G; 53 T; 0 other; atgagagatt tttcagtgtg accgtcacac gaggcggtac accacgtgtc tctatgtaaa 60 tggttggata tgtgtgttaa aaggttaata acttaaaaat taaaattttc caccacttac 120 ataaaaacac gtggtgtacc atccgtgttc ccgtcacaac taaaaatttc tccat 175 // ID Copia32-PTR_I repbase; DNA; EDCOT; 4502 BP. XX AC scaffold_516; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia32-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4502 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4502 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 240-240 (2007). XX DR Genome; scaffold_516; Positions 40697 36196. XX CC Positions [2026-2283] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 89..2332 FT /product="Copia32-PTR_I_2p" FT /translation="MAANDIDFLSSGDSSSAPSTLGSPLFLHHSDHPGLLL FT VSKRLNGDNYNSWHRAMKISLSAKNKTGFITGKIKEPHEASNPEEHALWQR FT CNDMVLSWILNSLEPELADSVLSCNTPYAIWEDLRERFSLGNAPRIFQVQR FT DIYKIEQGQMSVAAYYTKLKGLWDELVSFNSETCTCGAQNDRTKLIQFLMG FT LNESYSGARGQILLMNPLPSVRQAYASVVQEEKQRELGSAVTIPSNTAAMV FT VRGNYNMSKGRHNNQVHGNQSNNSRNKEPFQCTYCGDMYHRKATCYKLIGY FT PPGHPKSKEKAPHQRQGYDRHNSHSASGNPSANQVDFSPTFQELQVSLPNL FT TEDQYVQILSALTTKPVTPQANVVADSTFKHTSGLLPVAHNRWILDSGATH FT HITSSPTLLKHVNKNQSLAPVSLPSGDVAKITVTGSIQFNNSFQLNNVLCV FT PSFKVDLMSVGKTTDDLHCSVMFFPSWCILQDLATRTMIGVGKRRDDLYYL FT VALASTPPSTRFVCNLIISSNLWHRRLGHLSSNRLQFLADNSLKFNFDSSH FT KCEVCPLAKQTRQPFPSSSISTSKCFSLIHCDIWGRYKTPSISGAFYFLTI FT VDDFSRFTWVFLMCNKSETQTLLRQFFHYVHTQFNTKVQKLRSDNGAKFLS FT LNFFFLRKGFFFNTLVYIHLSKMVSLSANIDTSLKLLALYVFNLIYPLLSG FT KNVFLQPSILLIAFLLCCFIKKHHLRFFTTNFLIILACEFLDVLLLQP" FT CDS 2299..3579 FT /product="Copia32-PTR_I_1p" FT /translation="MRVFGCVAFATIVNPSSKCSPRAIKCIFLGYPIGQKA FT YKLYDIATQKIFTNRDVVFLEDTFYHPPQVNPPAHNPPALSIPLPIVSDSY FT SHLPPSSVIIDPFDPPISSSPAPTDSIPSLPEPPSSTPLTPPIAQQTPVQP FT DDPVFPEPTLVIPDQPLRRSQRPREANVRLKDYVCSQVILPPHQLFSASSA FT PTPGTKYPLCHFIFYNRYSPSHLCYIANVSRDEEPLSYELAMTDPKWQEAM FT NSELKALIDNQTWSLVPFPPGKRPISCKWVYRIKRKADGSVERYKARLVAR FT GFTQTAGIDYHDTFSPTAKMVTVRCLLAIAASLNWPLHQLDVNNAFLNGDL FT LEEIYMSPPPGLRRQGENIVCRLHKSLYGLKQASRQWFSKFTEAVLAAVFL FT VKSRLFLVHQKRRHMSYYPIDLCGCYFDNREQH" XX SQ Sequence 4502 BP; 1176 A; 1050 C; 822 G; 1454 T; 0 other; ggctacaacc taaccctatt ttttcttctt cttcaacgca tctgtttgtt gcgtctctgc 60 cttgccttct ttttttctct tataaatcat ggctgctaat gatattgatt tcttgagttc 120 tggcgattca tcctctgctc ccagcaccct tggttctcca ttattcctcc accactcaga 180 tcaccctggt ttgcttcttg tttcaaaacg attgaatggt gacaactata attcttggca 240 ccgtgccatg aaaatttctc taagtgccaa gaataagaca ggttttatta ctggcaaaat 300 caaagaaccc catgaggctt caaatcctga agaacatgcc ctttggcagc gctgcaacga 360 tatggtgctt tcatggatcc taaattctct tgaaccagag ttagccgatt ctgttctttc 420 atgcaacact ccttatgcca tctgggaaga tcttcgtgaa agattttctt tagggaatgc 480 tccccgtatt tttcaggttc agcgcgacat ctacaagatt gagcaaggtc agatgtcagt 540 tgcagcatat tacacaaaat tgaagggttt atgggacgag cttgtatcct ttaattcaga 600 aacatgtacc tgtggtgcgc aaaatgatcg aaccaaactt atacagtttc tcatgggact 660 caacgagtca tattcaggtg caagaggtca gattttactg atgaaccctt taccatcggt 720 tcgtcaagct tatgcctctg ttgtgcagga agaaaaacaa cgagagttgg ggtctgctgt 780 caccatacca tcaaatacag cagccatggt tgtgcgtggc aattacaaca tgtctaaggg 840 tcggcacaat aatcaagttc atgggaatca atcaaataat tcacgtaata aagagccttt 900 tcagtgcact tactgtggtg atatgtatca caggaaagca acctgttaca aactaattgg 960 ctaccctcct ggtcatccaa aaagtaaaga aaaggcacca caccagcgcc aaggctatga 1020 caggcataac tcacactctg catctggtaa cccctctgca aatcaagtgg attttagtcc 1080 cacttttcag gaactccagg tctctctgcc caacttaact gaggatcaat atgttcagat 1140 actcagtgcc ttgaccacca agcctgtcac tccacaggct aatgttgttg ctgactcaac 1200 cttcaaacat acatcaggtt tattaccggt tgctcacaat cgctggatac ttgacagtgg 1260 ggcaacccat catattactt cttctcccac gttattaaag catgtcaaca agaatcaatc 1320 gttggcacct gtttccttac ctagtggaga cgtggctaaa attactgtga ctggctcaat 1380 tcaatttaac aattcttttc aattgaataa tgtcctctgt gtaccaagct ttaaagttga 1440 tcttatgtct gttggtaaga caaccgatga tttacattgc tcagtgatgt tttttccatc 1500 ttggtgtatt ttgcaggact tggctacgag gacgatgatt ggtgtgggta agcgacgtga 1560 tgacctgtat taccttgtgg cgttggcttc aactcctcct tctacccgtt ttgtttgcaa 1620 tttgattatc tcatccaatc tttggcatcg ccgattgggt cacctttctt caaatcgttt 1680 acaattttta gctgataatt cgcttaaatt taattttgat tccagtcata aatgtgaggt 1740 ttgtccgttg gcaaaacaaa ctcgtcaacc ttttccttcc agttcaattt caacttcgaa 1800 gtgtttttct cttattcatt gtgatatttg gggtcgttat aaaacccctt ctatttctgg 1860 tgctttttat ttcttgacca ttgtggatga tttttcccgt tttacatggg tttttttaat 1920 gtgtaacaag agtgagacac aaactctact tcgtcagttt tttcattatg ttcacactca 1980 attcaataca aaagttcaaa aactccgttc tgataatggg gctaaatttc tttcattaaa 2040 tttttttttc ttgaggaagg ggttcttttt caatactctt gtgtatatac acctcagcaa 2100 aatggtgtcg ttgagcgcaa acatagacac atccttgaaa ctgctcgcgc tctacgtttt 2160 caatctcatt tacccattac tttctgggaa gaatgtattc ttacagccgt ccatattatt 2220 aatcgccttc ctactctgtt gcttcataaa aaaacaccat ttgagattct ttacaacaaa 2280 cttcctgatt attctcgcat gcgagttttt ggatgtgttg cttttgcaac catagtcaat 2340 ccatcctcaa aatgttctcc ccgtgccata aaatgcattt ttcttggtta ccctatagga 2400 caaaaagctt acaaacttta cgatattgct actcagaaaa ttttcactaa tcgggatgtg 2460 gtatttcttg aggacacctt ttatcatcca ccacaagtca atcctcccgc acacaatcca 2520 ccagccttgt ctattcctct tcctattgtg tctgattctt attcccatct tcctccctca 2580 tcagtcatca tcgacccctt tgatcccccc atatcctctt cacctgcacc aaccgactca 2640 ataccttctc ttcctgagcc accttcctct actccattaa ctccaccaat tgcacagcaa 2700 acccctgttc agccggatga ccctgtcttt cctgaaccta ctctggttat tcctgatcag 2760 ccacttcgtc gttctcaacg ccctcgagaa gccaacgtcc gcctcaagga ttatgtttgc 2820 tcgcaggtga ttctgcctcc acaccaattg ttctcggcct cgtctgcacc tacaccaggt 2880 acgaagtatc ctctctgtca ttttattttt tataatcggt attctccatc acatctctgt 2940 tatattgcca atgttagtcg tgatgaggaa cctctttcat atgaacttgc tatgactgat 3000 cctaagtggc aggaagctat gaattctgag cttaaagctc tcattgacaa tcagacatgg 3060 agccttgttc cttttccccc tggcaaacgc ccgatcagtt gtaaatgggt gtatcgcatc 3120 aaacgcaagg ctgacgggtc tgttgagcgc tataaagctc gcctggtagc tcggggtttc 3180 acacaaactg ctggaattga ttatcatgat actttttccc ccactgcaaa aatggtcaca 3240 gtccgctgcc tccttgctat tgctgccagt ctgaactggc ctttacatca gctagacgtt 3300 aacaatgctt tcttaaatgg tgatttattg gaagaaatat atatgtctcc tcctcctggt 3360 cttcggcgac agggggagaa cattgtgtgt cgccttcaca agtcactata cggtcttaag 3420 caagcgtctc gacagtggtt ctctaagttc acagaagctg ttcttgctgc tgttttttta 3480 gtcaaaagcc gactattcct tgttcatcaa aagagacggc acatgtctta ctatcctatt 3540 gatctttgtg gatgttattt tgataaccgg gaacaacatt gaatccatca aaggtttaaa 3600 gcagttcctt catactcgtt tccgcatcaa agaccttggt gataagaaat tcttcttagg 3660 cattgaaata gcccgttcca agaaaggcat ttacatttcc cagcgcaaat atgctttgga 3720 aattatcaaa gacagtggat acttgggtgc caaaccagtt gagtttccta tggaagaatg 3780 cagactttca aatacaggag aattgctcaa agatccttgt atataccaac gtctagttgg 3840 tcgattaatt tacttaacca tcactagacc tgatatcaca tattcagttc acattcttag 3900 ccgattcatg catgaaccac gtcaacctca catggctgct gctcttcgag ttgttcgtta 3960 tttaaaatca gctcctggtc aaggtttgct tcttcattca aataactcat tacacttaag 4020 ggcattttgt gactctgatt gggcgggttg tcctgtcaat cgccgctcca ccactgggta 4080 ttgtgtattc cttggaaatt ctttaatttc atggagaacc aaaaggcaaa agacagtttc 4140 cttatcaagt gcggaagctg aatacagagc aatggcaggt acatgtagtg agcttacttg 4200 gttaagacat ttattagcag atttacatat gccagtttca gatcctgtta ctcttcattg 4260 tgataatcaa gctgccttat acattgcaaa aaatcctgtg tttcatgaga gaactaggca 4320 tattgaaatg gattgccact ttattcggga caaaatttta cgaggtgaaa ttgctactcg 4380 atacgtaatt tcttcacaac aattagcgga tgtgtttaca aaagctttgg gaaaagagaa 4440 gttcaaacaa ctcatgtgca agttgggagt tattgatatt cactctccaa cttgaggggg 4500 ag 4502 // ID RTE1_MT repbase; DNA; EDCOT; 3155 BP. XX AC . XX DT 02-JAN-2007 (Rel. 12.01, Created) DT 02-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE RTE-type element - consensus. XX KW RTE; Non-LTR Retrotransposon; Transposable Element; RTE1_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3155 RA Jurka J.; RT "RTE1_MT: RTE-type family from barrel medic."; RL Repbase Reports 7(1), 50-50 (2007). XX DR [1] (Consensus) XX CC The youngest elements are 98% identical to consensus. XX FH Key Location/Qualifiers FT CDS 883..3057 FT /product="RTE1_MT_1p" FT /translation="MFSCRFFLIRKSDRKICLDCKVIPGESLTTQHRVMVM FT DVRVKRRAKRRSQNGAPRIKWWHLKGEKLRIFQHKILEGGFRQPHGSANDM FT WERMAHEIKKVAKETLGESRGFGPRGKESWWWNDSVQSKVRIKRDCFKDWS FT RCKNVETWDKYKIARKEAKKAVSEARTQAFEGLYQSLGTKEGEKSIYKLAK FT GRERKTRDLDQVKCIKDEEGRVLVQERDIKGRWKKYFHNLFNEGYEILPDS FT NRLDIGEEDRNYNYYRRIQEHEVREALKRMSSGKAVGPDNIPIEVWKSLGD FT RGIVWLTNLFNEIMRTKKMSDEWRRSTLIPIYKNKGDIQNCANYRGIKLMS FT HTMKLWERVIERRLRKETRVTDNQFGFMPGRSTMEAIYLLRRVMERYRTDK FT KDLHLVFIDLEKAYDRVPREILWKALEKKGVRIAYIRAIKDMYEGASTSVR FT TQDGTTEDFPITIGLHQGSTLSPYLFTLVLDVLTEHIQELAPRCMLFADDV FT VLVGESREEVNGRLETWRQALEAYGFRLSRSKTEYMECNFSGRRSRSTLEV FT KVGDHIIPQVTRFKYLGSFVQNDGEIEADVSHRIQAGWLKWRRASGVLCDK FT KVPLKLKGKFYRTAVRPALLYGTECWAVKSQHENQVSVAEMRMLRWMSGKT FT RHDRIRNDTIRERVGVAPIVEKLVENRLRWFGHVERRPVDAVVRRVDQMEE FT SQVKRGRGRPRKTIRETIRKGFRGQ" XX SQ Sequence 3155 BP; 1024 A; 430 C; 921 G; 780 T; 0 other; taatcctgcc aaggccggtc ccaagcccgg ataaaaggag ggttgtgtta ggcctcgaca 60 gccaaagtaa aactttgtcg aatctctatg acatggacca aatgcaaaat agcgtgaatg 120 ctaggtcgtt gcccggaagc aacgcgttgt atggctcgag tacagtgtca aatgagcaag 180 agccgctgca tcaccacctg gatgtagtga aaattaagca agggttcccg catcttcgtg 240 aacgggtgcg ggtaaagaag ctagttcatg agaataggat tcgttttgga acttgaaata 300 taggtacact tacaggaaaa tctatggaag tagtagacac aatgactagg aggaagatca 360 atttcatgtg cctacaagaa actaagcggg tggggaaaaa ggcgaaagaa ttagatagtt 420 caggatttaa gctttggtat actggtgaag ttagatcgag aaatggggta ggcatctttg 480 tggataagga gtggaagaaa gatattgtag atgttaaaag gataggagat cggattatag 540 ccctaaagat tgtagtggaa caagacacct ttaatgtaat tagcgcttat gcacctcagg 600 tagggttaga agcacacctt aaagtgaagt tttgggagga gctagaaggc ttaattcagg 660 atatcccgtt aggagaaaga tttttctagg aggggattta aatgggcatg tagggagtgt 720 ttcgagaggt ttcgagggtt tgcatggggg gtatggtctc ggggagatta atgcggaggg 780 taaatccatc ttagatgttt catcggcttt tgatcttact atagctaata cttgtttcag 840 gaaaagagag gagcatctta tcactttcaa gagtggggtc tcatgttctc atgtagattt 900 tttcttatta ggaaatccga caggaagatt tgtttggact gtaaagtcat acctggagag 960 agcttaacta cccaacatag agtgatggtg atggatgtaa gggtaaagag gagggctaag 1020 agaagaagtc aaaatggggc tccgcgaatc aagtggtggc atttaaaggg tgaaaaacta 1080 aggatattcc aacacaagat attagaggga ggcttcaggc aaccacatgg aagtgcaaat 1140 gatatgtggg agaggatggc acatgagatt aaaaaggtag caaaagagac gttgggagaa 1200 tctcgaggtt ttggacctag gggtaaagaa tcttggtggt ggaatgacag tgttcagagt 1260 aaagttcgga tcaaaagaga ttgttttaaa gattggtcta ggtgtaaaaa tgtcgaaact 1320 tgggataaat ataagatagc taggaaagag gctaagaagg cggtgagcga agcgagaact 1380 caagcttttg aaggattata ccaatcttta ggtaccaagg agggagagaa atctatatat 1440 aagcttgcta agggacgaga aagaaagaca agagatttgg accaagtaaa gtgtattaag 1500 gatgaagagg gtagagtttt ggttcaggaa agagatatta agggtagatg gaagaagtat 1560 tttcacaacc tatttaatga aggatatgag atcttaccag actctaacag gttagacatc 1620 ggagaggagg accgaaacta taattattat cgtcggattc aagagcacga ggttagagaa 1680 gcgttgaaaa ggatgagtag tggcaaggca gttgggccgg acaacatacc tatcgaagtg 1740 tggaagagtc ttggcgatag agggattgtg tggctcacaa acctttttaa cgagattatg 1800 aggacgaaga aaatgtcgga cgagtggaga agaagcactt taattccaat ctataagaac 1860 aagggggata tacaaaattg cgcgaattat aggggaatta agctaatgag tcataccatg 1920 aagttatggg aaagggtgat cgaaagaaga ctaagaaagg agactcgagt tacggataac 1980 caatttggtt ttatgcctgg gaggtcgact atggaagcaa tctacttact tcgacgcgtg 2040 atggagcgat atcggacgga taaaaaagac ttgcacttag ttttcattga tttggaaaag 2100 gcgtatgata gagtaccgag agagattttg tggaaagccc tggagaagaa aggggttagg 2160 attgcctata ttagggctat caaggatatg tatgagggag cttcgactag tgtgaggacg 2220 caggatggga ctaccgaaga ttttcccata acaataggat tgcaccaagg gtcaacccta 2280 agtccttatc tttttacttt agttttggat gtattgacgg aacacatcca agagttagca 2340 ccgagatgta tgctttttgc agatgatgta gtcttggtgg gtgagtcgag ggaggaagtg 2400 aacgggaggc tagagacctg gaggcaagcc ttagaagcgt atggattccg cttgagtaga 2460 agcaagacgg agtatatgga atgtaacttc agcggaagga gaagtaggtc taccttggag 2520 gtgaaagttg gagatcatat cataccccaa gttacacggt ttaaatatct tgggtccttc 2580 gtacaaaatg acggagaaat agaagcagat gtaagccatc gtattcaagc tgggtggttg 2640 aaatggagaa gagcctcagg tgttttgtgc gataagaaag taccacttaa gttgaaagga 2700 aagttctatc ggacagcagt cagaccggcg ttgttgtatg gtacggagtg ttgggcggtt 2760 aagagtcaac atgagaatca agtaagtgta gcagagatga ggatgttgcg ttggatgagt 2820 ggtaagacta gacatgatag gattaggaat gacaccatta gagagagagt gggggtagca 2880 cctatagtag aaaagttggt agaaaatagg cttagatggt ttgggcatgt agagagaaga 2940 cccgtagatg ccgtggtaag aagagtagat caaatggagg agagtcaagt taaaagaggt 3000 agaggaagac ctaggaaaac tattagagaa accattagaa aaggatttag aggtcaatga 3060 gttggatcca aatttggtgt atgatagaac actatggcgt catttgatcc atgtagccga 3120 ccccacttag tgggataagg cttggttgtt gttgt 3155 // ID DNA9-12_Mad repbase; DNA; EDCOT; 214 BP. XX AC . XX DT 21-OCT-2010 (Rel. 15.1, Created) DT 21-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-12_Mad. XX NM DNA9-12_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-214 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1493-1493 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 84-bp long. TSD is 9-bp long. XX SQ Sequence 214 BP; 51 A; 46 C; 51 G; 66 T; 0 other; ggaaaaggat cctcgccgga tccttttcct ggggatccta gggatcccgt gatcgtgacc 60 gttcatcgta catcgtgcgg tcagttttcg ttaggtacta tttatattta attttaaatt 120 ttaaattttg aaatgatttc tgaccgcacg atgtacgatg aacggtcacg atcacgggat 180 ccctaggaaa aggatccggc gaggatcctt ttcc 214 // ID Copia-69_VV-LTR repbase; DNA; EDCOT; 226 BP. XX AC chr18; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-69_VV_; KW Copia-69_VV-I; Copia-69_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-226 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr18; Positions 16221406 16221631. XX SQ Sequence 226 BP; 67 A; 37 C; 32 G; 90 T; 0 other; tgttcagttg ttggcattcc agattccaat ccttgaagac ttagtctttg ttgaagatta 60 gctcaagttt gttatgactt tgtttgtttt aaatttcaaa aacagctgta acagcctaaa 120 taaatatgca ggaaagataa tttgttattt ttcttgtata aatatctcat ctcaaatgga 180 ataaaatcat cagcttctct ctatcatatc tgtagccttt tcttca 226 // ID Copia-5_TC-I repbase; DNA; EDCOT; 4062 BP. XX AC CACC01013735; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-5_TC_; KW Copia-5_TC-LTR; Copia-5_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-4062 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01013735; Positions 10029 14090. XX CC Positions [1618-1959] - Integrase core CC 'TTATA' target site duplication CC LTRs are 94% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS 373..1959 FT /product="Copia-5_TC-I_1p" FT /translation="MECETAKAAWTKLQEEYVGTSRTRHMQAQNLRRHFDM FT MRMKESKSVKEYIDQILKLTNQIKLFGEELKEVRVAKKILNSVPGKFEPTI FT ASLLQSKNLIDISIIEIVSALQATELRISTRDEALGEKAFLAKGKGKAKAE FT AFAKKNYKDKDKKTAQSGQSSNKKNKFKPCSFYKKRIHTDDYCWFRPDAKC FT KICSQSGHTNKVCRNRTIEDKPAQTIESLELAEEVLFMAQSDSESDCGNCE FT WLLDSGSSRHIAFSEAVFIDLDKNHRSRVRIGNGGYLQAYGIGKVRIPSST FT RHKYISDVLFIPSFAQNILSIGQLLENHYVLLFEDKACRIYNPSGAYLMTI FT PMRNRCFPIKPKHICLQVEEQSVSLIDLWHRRLGHCNYKTLEQVSNSGMLD FT KLPKLSNNALICSVCQLGKISRKPFPLSSTNRTRSKLELIHSDIGGPLSEE FT SLNGNKFYLLFIDDMTRWSWIFFMKFKLKVFTLFKNFKTRVGLETGHKIKT FT LRTDNGGEYTSNEFTQFLNQQGIAHQFTAPYTP" FT CDS 2572..4062 FT /product="Copia-5_TC-I_2p" FT /translation="MQKELQMIQKNGTWSLVDRPVDRNIIGAKWIFKKKLN FT ADGSLNRCKARLVAKGYSQLPGVDYGETFAPVARYNTIRLLLGLAAALKWN FT VYHLDIKSAFLNGILEEEIYIDQPKGFELLSRENKVYKLHKTLYRLKQAPR FT RWYSRINDHLIHRGFVKSQNEAILYTLESGNKFLLIVSLYVDDLLVTRNCE FT QALQNFKSQMQAEFEMSNLGLMRYFLGLEVHHLRTGIWLSQQNCISKVLKK FT FQMSDCKSVSTPSIANKKICADSGNQLEDPSTYRRLIRCLLYIYASRPDIQ FT FSVAFLSRFMQAPTNQHMIAAKRILRYLKKTEFYGIHYTKIVDFALCGYTD FT SDFAGSSEDAKSTSGYLFIVGNGPFSWNSHKQFKVAQSSAESEYVAAIEAT FT NQALWLRKLLVDIKFEQKFPTDLFIDNKSAIAIAKNPVWHGKTKRINVKYH FT AIRNTVEKNEINVQYCPSELQLADILTKPLQKSRFEALRTKLNLSIASVKG FT E" XX SQ Sequence 4062 BP; 1363 A; 691 C; 802 G; 1206 T; 0 other; tggtatcaga gttcctctcg attcttgtaa gaccttagat aaccttcttc aatactcttg 60 tgttcttagt ggttctcctt taacctcttg tctcaagaat taattccctg ttataatgac 120 aactccaaac ataactcatc agcctccacc agttttcaat ggctctaatt atggtgttta 180 ggctgtgaaa atgaagactt acttgaaagg ttataaccta taaaatgcag tagaacaaga 240 tgttgaacca caaacaccaa gggagaatgc tcttgctgct caagttaagc aatatgaaga 300 ggaagttgca aagaagttta gagctctttc attcattcag tctgttgtct ctacggatat 360 ttcagtagaa tcatggagtg tgaaactgcc aaggcagctt ggacaaagct acaggaagaa 420 tatgttggca cttctagaac aaggcatatg caggcacaga acttaagaag gcattttgac 480 atgatgcgaa tgaaagagag taagtctgta aaagaatata tagaccagat tcttaagctt 540 actaaccaga taaagttgtt tggtgaagag cttaaagaag ttagagtagc taagaagatt 600 ctcaacagtg taccaggaaa gtttgaacct acaatagctt ccctgctaca atcaaagaac 660 ctcattgaca tttcaattat agaaattgtc agtgccttgc aagctacaga actgaggata 720 tcaacaagag atgaagctct tggggagaaa gcctttcttg ctaaaggcaa aggtaaagca 780 aaagctgagg cttttgccaa gaaaaattac aaagacaaag acaagaagac tgctcaatct 840 ggtcaatctt caaacaagaa aaacaagttc aagccatgtt ccttctataa gaaaagaatt 900 catactgatg actactgttg gtttaggcca gatgcaaagt gcaagatatg tagtcaatca 960 ggacacacta ataaagtgtg cagaaataga acaattgaag ataaacctgc acagacaatt 1020 gaaagcttag aattagctga agaagttttg tttatggctc agtcagattc tgaaagtgat 1080 tgtggtaact gtgaatggct tcttgatagt ggcagctcac ggcatattgc attctctgaa 1140 gctgtgttta ttgatcttga taagaaccat cgatcaagag tcagaatagg gaatggtggt 1200 tacctacaag catatggtat agggaaggtt cgaattccaa gctcaactag acacaagtac 1260 atatctgatg ttttgtttat accttctttt gcacaaaaca ttctgagtat tggacaattg 1320 ttagaaaatc attatgttct gttgttcgaa gataaagctt gcagaattta taacccctca 1380 ggtgcatatc tgatgactat accaatgaga aatagatgtt ttcctattaa acctaagcat 1440 atatgcttgc aagttgaaga acaatctgtt tcattgattg atctgtggca tagaagactt 1500 ggtcactgca attacaagac cttggaacaa gttagcaact caggtatgct tgataagctt 1560 ccaaaattat ctaataatgc tttaatatgc agtgtatgtc aacttggtaa gatttcaagg 1620 aaaccttttc ctttgagcag taccaacaga accaggtcaa agcttgaact tatccactct 1680 gatattggtg gacctctaag tgaggaatca ctaaatggca ataagtttta tcttctattt 1740 attgatgata tgaccagatg gagttggatt ttctttatga aattcaagtt aaaagtcttt 1800 actttgttca aaaacttcaa aaccagagtt ggacttgaaa ctggtcacaa aatcaaaacc 1860 ttgaggactg ataatggtgg tgaatatacc tccaatgaat tcactcagtt tctcaatcag 1920 caagggatag ctcatcaatt tactgctcca tacactcctt agcagaatgg agtcagtgaa 1980 aggaaaaaca ggacagtcat ggacatgagc agatgtctat tatatcagaa aaggatgcct 2040 caaaagtttt gaacaaaagc agtaaagact actgtatatt tgcagaattt gttgccaacc 2100 catgccttga ataatcaaat ccattttgaa gcatggtatg gtttcatgcc ctcagttgcc 2160 catttgaaag tctttgggtg tgtatgttat atgcacatac cagatatctt gagaaacaaa 2220 ttgagtgaaa aagctgaatc aggagtattt gttggctata gtactcaagg taaggcatat 2280 agaatttatt tgccaagcaa aaataaagtt attgtgagtc gagatgtagt gtttgatgaa 2340 gcttccagct agaactggaa tgaacctcaa ccaccactat catttccaag acagcatgtt 2400 caaagttttg cttctgatgc ttaacttgaa attcaagaag acgagagtat aaatgatctg 2460 ccagttaggg gaaccagatc tcttgaagac atctatcaaa atagcttggt gactattgaa 2520 gaacctagct gctatattga agcttgtaag gatcctgttt agtttaaagc tatgcagaaa 2580 gaacttcaaa tgatccaaaa aaatggcact tggtctttgg ttgacagacc tgtagataga 2640 aatattattg gtgccaaatg gatattcaag aagaaattaa atgctgatgg ttccctcaac 2700 agatgcaaag ctcggttagt agccaagggc tacagtcagc tacctggtgt tgattatgga 2760 gaaacgtttg ctccagtagc tagatataac acaatcagat tattgttagg tctggctgct 2820 gcacttaagt ggaatgtcta tcatttagac ataaaatctg catttctcaa tggcatctta 2880 gaagaggaaa tttatattga ccaacctaaa gggtttgaac tcttgtcaag agaaaacaag 2940 gtatataagc tccacaagac cttatataga ttgaagcaag caccaaggag atggtacagc 3000 agaatcaatg accacttgat tcatcgaggc tttgttaaaa gtcagaatga agccatattg 3060 tatactcttg aatcaggtaa caaatttcta ttgatagtgt cattgtatgt ggatgatttg 3120 ttagttacta gaaattgtga acaagctttg cagaatttta aatcccaaat gcaagcagaa 3180 tttgaaatgt caaacttagg acttatgaga tattttcttg gacttgaagt tcatcatttg 3240 agaactggta tttggttgtc tcagcaaaat tgtatctcca aggttctcaa gaaatttcag 3300 atgtcagatt gcaagtctgt gtcaactcct tctattgcaa acaaaaagat ttgtgcagac 3360 tctggtaacc aacttgaaga cccttctaca tatagaagat taattaggtg tctgctttat 3420 atctatgctt caagaccaga tatacaattc tcagtggcat ttctctctcg atttatgcaa 3480 gcaccaacta atcagcatat gattgctgcc aagagaattc tgagatattt gaagaaaaca 3540 gaattttatg ggattcatta taccaagata gtagactttg cattatgtgg atatactgat 3600 tctgattttg caggaagcag tgaagatgca aagagcacat caggttattt gtttatagtt 3660 ggtaatggtc ctttctcttg gaattcacat aaacaattta aagtagctca atcttcagca 3720 gaatctgaat atgttgctgc tattgaagct acaaatcaag ctctttggct aaggaagttg 3780 cttgtggaca tcaaatttga acaaaagttt cctacagatt tgtttattga caataagtct 3840 gccattgcta ttgctaaaaa tcctgtttgg catggcaaga ctaagcgcat aaatgtgaaa 3900 tatcatgcca tcagaaatac agtagaaaag aatgagataa atgttcaata ctgcccttca 3960 gagttacaac tagctgatat tctaaccaag cctcttcaaa agtcaagatt tgaagctctc 4020 agaactaaac taaatctctc cattgcaagt gtcaaggggg ag 4062 // ID L1_CA repbase; DNA; EDCOT; 597 BP. XX AC . XX DT 02-AUG-2005 (Rel. 10.07, Created) DT 02-AUG-2005 (Rel. 10.07, Last updated, Version 1) XX DE Portion of L1 reverse transcriptase from C. arietinum - DE consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; LINE-1; L1_CA. XX OS Cicer arietinum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; OC Cicer. XX RN [1] RP 1-597 RA Stagginus C.; RT "Thesis (2001) Department of Plant Molecular Biology, University RT of Frankfurt."; RL Unpublished. XX RN [2] RP 1-597 RA Gentles A. and Jurka J.; RT "Fragment of L1 reverse transcriptase from C. arietinum."; RL Direct Submission to Repbase Update (02-AUG-2005). XX DR [2] (Consensus) XX SQ Sequence 597 BP; 181 A; 96 C; 121 G; 198 T; 1 other; gggatcctgg tcctgatggc ttgaacccaa tattttattt ttattttttt gtctttgtgt 60 ggtagtgaaa attttcaata atattgtgtt tggcttttaa ttggtgtatt tcctagtaca 120 ccaaacatta ccaatatagc tctgatccca aaaggcgacg aacagaagac tgtgaaagat 180 tggcggccta tagctctttg taatatgatt tataagattg tgacaaaggt tcttgcaaac 240 atattaaaac atgttctgca taaatgtgta tctaataatc aataagcttt tgtgcttaat 300 aggtccatac ttgacaatgc aatgacaaca cttgaaattg ttcatcacat gaaaaccaag 360 actcgtagta gagttggcga cgtcgcattg aaattggata tcaacaaaac ttatgactgc 420 attgattaga gttaccttcg agaggtgctg gtttggattt tgcaaatcag tgggtgaatt 480 ggattatact ttgtgtcgag tcagtagagt acaatatcat agtgaataat gattgtgttg 540 gtcctattac cccatgaaga ggcctctaac aaggagaccc attatsgccg aattcca 597 // ID Copia-79_Mad-I repbase; DNA; EDCOT; 3569 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-79_Mad_; KW Copia-79_Mad-LTR; Copia-79_Mad-I. XX NM Copia-79_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3569 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1696-1696 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [787-1281] - Integrase core CC 'TGTGT' target site duplication CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 112..1719 FT /product="Copia-79_Mad-I_1p" FT /translation="MKARLMLLIQFFLITPIFLVVFLKARRPAPRLSKLVP FT DLRWIIDSGATDHIVSTPNLLNRKVMKPSMPPVLLPSGESAPITSTGTLSL FT NSYLYLRDVLCVPTFQVNLMSVSRLTEGLQCSVTFFPRWCILQDLATRTTI FT GLGKERNGLYYLVALASNKAPSIPRPTCHLAISAADLWHRRLGHISSSRLQ FT FLAKSSLDCPSQFNGVCDACHLAKQTRLPFPISSISTSRPFSLIHCDIWGP FT HKIPTMSGAHYFFTIVDDYSRFTWVSLMHHKHETQGLLKSFFSMVRTQFNT FT NIQNIRVDNGGEFVSLKDFFLEQGTIYQHTCVYTPQQNGVVERKHRHILEV FT ARALRFQAHLPLPFWGECIYTAVYLINRLPTLLLSKKTPFEKLYNKFPSYS FT HMKVFGCLAFATTVGPTTKFDPRAKKCVFLGYPRGQKAYKLYDLSTEKIFT FT SRDVVFHENVYPFQGQDHSTTKSIIPTPEPILDLTSQPQELHDSSTTTPQN FT PQEPDTSLTPPHDLTIVPSQPQEPHDSSGGTTTSTQPPRT" FT CDS 2078..3556 FT /product="Copia-79_Mad-I_2p" FT /translation="MQSEIDALESTNTWTFTTLPPGKQPIGCKWVYKIKHR FT SDGSIERYKARLVAKGFTQTEGIDYHDTFSPTAKMTTVRCLLALAAARNWS FT LNQLDVNNAFLHGDLHEEIYMSPPPGFQRQGENLVCRLNKSLYGLKQASRQ FT WFAKFTEAVHAAGYVQSKADYSLFTRKCGKSFTALLIYVDDILITGNDEKA FT ISSLKQFLHTRFRIKDLGDLKFFLGIEVSRSKKGICISQRKYALDILKDAG FT LQGTRPVNFPMEQNLKLSDSGEILNDPSRYRRLVGRLIYLTITRPDITYTV FT HVLSRFMHEPRKPHLDAALRLLRYIKTTPGQGLYFSAENNLKLRAYSDSDW FT GGCRLTRRSTTGYCVFMGNSLISWRSKRQKTVSLSSAEAEYRAMAGTSCEL FT TWLRYLLHDLQLPHYEPVTLFCDNKAALHIAANPVFHERTRHIEMDCHFIR FT DKIQEGSIVTSHVRSAQQPADVFTKALGEVAFTGILRKLGVLDIHSPT" XX SQ Sequence 3569 BP; 922 A; 909 C; 676 G; 1059 T; 3 other; gagcaggtta attcctagct ctttgcttcc gccattgatc tcctagctta gaatattgcg 60 agtttctttg agttgtcctc ttcacaatgg gcagcaatca agacatcaaa gatgaaagca 120 agactaatgc ttctcatcca gtttttcttg atcactccaa tatttcttgt agtcttccta 180 aaggcccgcc ggcccgcgcc ccgtctgtca aagttagtgc ctgatcttcg ttggattatt 240 gatagtgggg caacggacca catcgtctca acccctaact tactaaacag gaaagttatg 300 aagccttcta tgccaccagt gcttcttccc agtggagaga gtgcacccat cacttcaacg 360 gggactctat ctcttaactc ttacctctat ttacgagatg tcttatgtgt gcctaccttt 420 caagttaatc ttatgtctgt gagtcggctt acagaaggat tacaatgttc agtgactttt 480 tttcctcgtt ggtgtatttt gcaggacttg gctacgagga cgacgattgg tttgggtaaa 540 gaacgtaatg gactttacta tctcgtggca ttggcgtcta acaaagcacc ttccatccct 600 cgcccaacct gtcacctagc tatttctgct gctgatttgt ggcaccgtcg tttaggacac 660 atctcttcat cccgtttgca gtttttagcc aagtcatcgt tagattgtcc ttcacaattc 720 aatggtgtgt gtgatgcttg ccatttggct aaacagactc gccttccttt tcccattagt 780 tcaatctcaa cttcaagacc attttccctt attcattgtg acatttgggg tcctcataaa 840 attcctacca tgtctggggc acactatttt tttactatag tggatgatta ttcccgtttc 900 acttgggttt ccctaatgca ccataaacat gaaacacaag gcctactcaa atcttttttt 960 tctatggtcc gtacccagtt taatactaat atccaaaaca tccgtgtgga taatggggga 1020 gagtttgttt cgttgaaaga ttttttccta gaacaaggga ccatttacca acatacatgt 1080 gtctatactc cccaacaaaa tggggtagtc gagcgcaaac atcgccatat ccttgaagtg 1140 gccmgggctt tgcgatttca agcacatctt cctcttcctt tttgggggga gtgtatctac 1200 acagcggttt acttgattaa ccgtttacct actttgcttc tttcaaagaa aacccccttc 1260 gaaaagctgt ataataaatt cccctcttat agccacatga aggtttttgg gtgtcttgcc 1320 tttgccacta ctgttggacc tactaccaaa tttgacccta gggccaagaa gtgtgttttt 1380 ctcggttacc cacgtgggca aaaggcctac aagctttatg atttgtctac cgaaaaaatc 1440 tttacaagtc gtgacgttgt gtttcacgaa aatgtttacc cttttcaagg tcaagatcac 1500 agcaccacca aatctatcat tcccactcct gaaccaatcc ttgatttgac tagtcaacca 1560 caagaacttc atgactcatc aacaaccact ccacaaaacc cccaagaacc tgacacctca 1620 ctcacaccac ctcatgactt aaccattgtc cctagtcaac cacaagaacc tcatgactca 1680 tccggcggaa caaccacgtc cacacaaccc ccaagaacct gaccgccggg accttattsa 1740 cagccwcctc atcgacccaa ctttgacttc tcccgcgtca ccaccacaac atgccccctc 1800 aactccacca ccacaaccta ttcgccagtc aacacgtctt cgaggtcctc ctacctacct 1860 caaggatttt gtctgcaacc aggccgcatc gcggggaccc aaacaatcgt tgtcttcgtc 1920 ttcaagtctc acaccaggta cacgttatcc gctttgtaat ttcctttcat accatcgata 1980 ttcacccaaa catttggcct ttattagcca aatcagtcgc gctgtggaac cccgttcttt 2040 tgcagaggct aaatctgatc cccgatggca gcaagccatg caatctgaaa ttgatgcctt 2100 ggaatccact aatacatgga cctttaccac tctccctccc gggaagcaac ccattggctg 2160 caaatgggtc tacaaaatca agcatcgttc tgatggctct attgaaaggt ataaggctcg 2220 tcttgttgcc aaaggtttca cccaaaccga aggcattgat taccatgata cattttctcc 2280 tactgcaaaa atgactactg ttcgttgctt gcttgctctt gctgctgcac gtaattggtc 2340 acttaatcag ctcgatgtca ataacgcatt ccttcatggt gatcttcatg aagagattta 2400 catgtctcct ccacctggtt ttcagcgaca gggggagaac ctagtgtgtc gccttaacaa 2460 atcattgtat ggcctcaagc aagcctctcg ccaatggttt gcaaagttca cggaagctgt 2520 tcacgctgct ggttatgttc agtctaaagc ggactactct ctcttcactc gtaaatgtgg 2580 aaagtctttt actgcccttc tgatttatgt tgacgacata ttaatcacag gtaatgatga 2640 aaaagctatc tcttccctca aacagtttct tcacactagg tttcgtatca aagaccttgg 2700 ggatttgaaa ttctttctgg ggattgaagt ctctcgttca aagaaaggca tatgtatttc 2760 acaaaggaaa tatgctctgg atatactcaa agatgctggc ttgcagggta cacgacctgt 2820 caattttcca atggagcaaa acctcaagct ctcagattct ggcgaaatac tcaatgatcc 2880 atctcgatac cgaaggttag taggacgctt aatatatcta accatcactc gacctgatat 2940 cacctacaca gttcacgttc tcagtaggtt catgcatgaa cctcgcaaac cacatcttga 3000 tgcagctctc aggctcttac ggtacatcaa gactactcca ggtcaaggct tgtacttttc 3060 agcagaaaat aatctaaaat tgagagctta tagtgactct gattggggag gttgtcgact 3120 cactcggaga tccactactg ggtactgcgt ttttatggga aattcattaa tatcttggcg 3180 gtccaaaaga caaaagacgg tttcactttc ttcagccgaa gctgaatatc gagccatggc 3240 agggactagt tgtgaactca catggttgcg gtacctttta catgatttgc aactacctca 3300 ttatgaacct gtgacgcttt tctgtgacaa caaagcagca ttacacatcg ctgctaatcc 3360 ggtttttcat gagagaactc gacacatcga gatggattgc cattttatta gagacaagat 3420 tcaagaaggt tcaattgtga ctagtcatgt tcgttctgca caacagccag ctgatgtgtt 3480 taccaaggct ttgggggaag ttgcttttac tggaattttg cgcaagttag gagttcttga 3540 cattcactct ccaacttgag ggggagtgt 3569 // ID Gypsy-38_Mad-I repbase; DNA; EDCOT; 11367 BP. XX AC . XX DT 14-OCT-2010 (Rel. 15.1, Created) DT 14-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-38_Mad-I. XX NM Gypsy-38_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-11367 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1770-1770 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 4937..6274 FT /product="Gypsy-38_Mad-I_2p" FT /translation="MLEQAITLSFKASNNEAEYEALLAGLRLAKDLAVKKL FT AIYSDSQLITNQTSGEYAAKHPRMARYLEKVREQLATFQAYTLTQVPRAEN FT AHADALASLGSALDHQLRRSIPVEYLEKPSIDEEPAVEVAQINTTPSWQDP FT IIDYIVNGTLPADRLESRKLQMKAARYYMWNGMLVRRSFSGPHLRCLSPPD FT DLKILSSIHEGVCGNHSGGRSLAQKALNAGYYWPTMHQDAKEYVQRCDSCQ FT RFKPVPALPASELHPQTSPWPFMQWAIDLVGPMPPATGGRGMMIVATDYFT FT KWVEAEPMTTTTQTDIERFIWKNIICRFGIPTPSSPTMVRSSWAKTWRSSS FT KNMASSSTCPRPGIRRATGRPRRPTRPSSTASRSPSQTRRASGQTSSPVFY FT GHIAPPRDEQPVKLHSPWRMALRRSFLPTSWCQASALYCRISSRTRRRWPQ FT T" FT CDS join(154..1260,1101..3233) FT /product="Gypsy-38_Mad-I_1p" FT /translation="MVGNSETTTNGTPYVQGFGPESGDEDIAPRRRSSRLN FT ATAGGAPPPRSRATTTTAVTQQPRQGHQATTPFHRRCPCSAAPTKPWAGGP FT GPFPSPWAGGPKLGSCHSRPRAGGPAHCSSRPAAQQPKPEPRAGSCCQPGS FT PTGPSPSHPASRPRCGSPTAMQAQGEQASVQRAPRPAPTTRPAAQSNPRPP FT PAIQILTTGPAIDSGLFSPHFSAGMPALGSSFVPAVHYTSTTHGDAHYPDS FT SNPNGEHHLPQQVANLTSALAQQTTLVNQLLERIEMQRAPDEVSRSRTRAE FT ERDSFQRRPGKEPLSPPRTVRSGSVHSRLGPRGNVFSRLDAQRSVHSRLGS FT RVSVHSRLGPHSDEHSDIPGEASTRGCALSFGPSGKRLLPPRCAEKRSFPT FT RLTSQCAFEVGSTLRRALRHSRRSVHTRLGPQGDPPARHRSRQPHDGQRRA FT REQSSSSSTGSPRQARRRAAQNEPRAPRPRHRRAGHAEEQHGPAGQHRGQL FT EAPLPHQAQIQEEVQRLVAEQLRGFQRIDTTDDALRRDVANLSRSPFTDEI FT EQTEPPRKFSPPHFTLFKGDEDPDRHLMHYRSAMTLYANNDALMCKIFATT FT LQGEAQDWFHTLPPRSIRNFSELSLVFTKEYSSYRSIKKKSDHLFNMKNDP FT NESLRTYVKRFKAEKAKIVGCDDSIACSAFRKGLPADHPLFGELIMGENLT FT LADSYALAEKHSLWDEAKRSQKPPEQPRKDAEPTQKKASDKPLNNKNKPGS FT RRRDRSPAKGGTTPKTYTKFSVPINQILRDLKDKPWFKLPPPMRGDTSKMD FT QTKYCAFHRGPGHTTNDCTTWMKYLEQLVKEGKCDQYVDRPAARPRREADA FT EPPAKTIRINGIFAESEHLGATNNSKKRKIQQARSVFQVQAIDVVPGPIVG FT FTEQDAEGVDFPHDDALVISVQLAHAIVDRIMVDNGSSVNILQLSVIQKMG FT LESTIKRKAEVLTGFNGLTSTAIGTITLDVTSPPIVSSQTFMIVSDPSPHN FT GILGRPWLVKIGAVTSIEYQKIRFRIPGGAVGEIKGDQAMSRRCTVQVLKE FT SKKKSFAPAVAAEVQKDDSTSAK" FT CDS join(10451..9846,9383..8100) FT /product="Gypsy-38_Mad-I_3p" FT /translation="MSSSDRKSDEYPPPLYRQGGSSGKVGYFKAAHVKINS FT DELFRDFLEAYKHAIPSGVRVKRVKDDSGHEPCGEGATARKRAIKFHPYYF FT VLGFTFPMPRLFQEVICSMKCAPAQCSPNAVRAMVGFSNLSRFFDLGLTIN FT EFWYFFEIGHKEGVGQLRSRHRLLDASCKGDHEWARDTLEVSGEWESDSSP FT ELRVPTTFISGKNLLLRRWPHPLLRDLIAQRKGSVVPPVSGFVSKRPSGAK FT SGSASERLAAMKSGKVDSAAKVAPGPVPPSAVTDSSAEKGKSARTGSCERS FT TESEAGEFPEVCALLKADLLEDVDACAKFVDSVGKVVIRSDSFAKRPAYSR FT RSSLIATMHKTLILAAESMRVDQDAVKCAKEAEVALVAQLRSAAEKIEKLE FT SELAVLKGSDVSAPTSLQLEIAHQEVAHLKAKLSATQAMLEAAEKEVSRVS FT PVVEDLERVNSELRSACFAKDEELIFMHAEVSRLKEVASKLESKEVDLQGA FT LSASENLKKELDELQGAHTGLVEENVQLKNEKAGHEVALASCQADFYKLGY FT VDHLQGRPSDYEFSEKDFETFSISPVDLLDFSFEAAFGGAAEGQAVQAGAA FT EDELMEALAARSGAAAEGVAVEGPVVAQAANE" XX SQ Sequence 11367 BP; 3066 A; 3432 C; 2815 G; 2052 T; 2 other; aattggtgct ttcattgaga gctgattcaa atactcgaag aagcctcttg catttggttt 60 cttgaatttt ctgttacgtt gaatttctca cacgtcgtat caattaattt ttcctagaaa 120 agtttcttga tcaatccctg gagaaaggat acaatggtag gaaattcaga aaccacgacg 180 aacggaaccc cgtacgtaca aggatttgga ccggagagtg gagacgagga catagcccca 240 cgacggmgat cctcaaggct caacgcgacg gcaggaggag ccccaccgcc gcggagccgc 300 gccaccacca ccaccgccgt gacccagcag ccacggcaag gccaccaggc cacgacacca 360 ttccaccgcc gctgcccttg cagcgccgca cccaccaaac cctgggcagg aggcccaggt 420 ccatttccaa gcccatgggc aggaggccca aaacttggca gctgccacag caggcccagg 480 gcaggaggcc cagcccactg cagcagcagg cctgctgcac agcagcccaa gcccgagccc 540 agagccggca gctgctgcca gccaggcagc ccaacgggcc caagcccaag ccacccagcc 600 agcaggccac gatgtggcag cccaacggcc atgcaggccc aaggcgagca agcgtcggtc 660 cagcgcgccc cgcgacccgc tccgacgacc cggcccgcgg cccaatccaa tccaaggcca 720 cctccggcga tccagattct gaccaccggt cccgcgatcg actcagggtt attttcaccc 780 cacttttctg caggaatgcc cgctttgggc tcaagctttg tacctgcagt ccactacact 840 tccaccacac atggagacgc ccattatcca gactcttcca atccaaatgg cgagcaccac 900 ctgccccagc aggtcgccaa tttgacgagc gccctcgcgc agcagaccac cttggtgaac 960 cagctcctcg agcgcatcga gatgcagcgc gccccagacg aggtgtcccg aagcaggaca 1020 agggcggaag aacgtgactc attccagcga cgtcccggca aagagccgct cagcccgcca 1080 cgaaccgtgc gttcgggtag tgtgcactct cgtttgggcc ctcggggaaa cgtcttctcc 1140 cgcctagatg cgcagagaag cgttcattcc cgactcggct cacgagtcag tgtgcattcg 1200 aggttgggtc cacactccga cgagcactca gacattccag gcgaagcgtc cacacgaggc 1260 taggcccaca aggagatcct cctgcgaggc accggagtag gcagccgcat gacggacaga 1320 ggagagcacg agagcagtcc agctcaagtt ccactggcag cccccgccaa gcgcgacggc 1380 gagcagcaca gaatgaacca cgtgcaccgc gaccgcggca cagacgagca ggacatgccg 1440 aagagcaaca tggaccagca ggtcaacacc gggggcagct ggaggctccg ctgccccacc 1500 aggcgcaaat ccaggaggaa gtacaaaggc tcgtagcaga gcagctgcgc ggattccagc 1560 gcattgacac taccgacgat gcccttcgta gagacgtggc caacctgagc aggtcaccat 1620 ttacagacga gatcgagcag acggagccac cgcggaagtt cagcccgcca catttcacct 1680 tgttcaaagg agatgaagat ccggacaggc acttgatgca ctaccgaagc gccatgaccc 1740 tctacgccaa caatgacgct ctcatgtgca aaatctttgc cacgacgctc caaggcgagg 1800 cgcaagactg gttccacacc ctgccgccac gttcaatccg gaacttcagc gaactttcct 1860 tggttttcac taaggaatat tcgtcctacc gctcgatcaa gaagaagtct gaccacctct 1920 tcaacatgaa gaatgacccg aatgagtcac tccgcacata cgtcaagagg ttcaaggcgg 1980 agaaggcgaa gatcgtcgga tgcgatgaca gcattgcatg ctcagccttc cgaaaggggc 2040 tcccagcaga tcacccactt ttcggagaat tgatcatggg cgagaacttg accctggcag 2100 actcttatgc tttggcagaa aagcactccc tctgggatga ggcaaagcgc tcccagaagc 2160 cgcctgagca gccgcgcaaa gacgcagagc cgactcagaa gaaggcgagc gataaaccgc 2220 tcaataacaa aaacaagcca ggaagcagac gcagggaccg atccccagca aagggaggca 2280 cgacgcccaa gacgtacacc aagttctcag tcccgatcaa ccagatcctt cgcgacctca 2340 aggacaagcc gtggttcaag ctgccgccac ccatgagggg ggacacctcc aagatggacc 2400 agacaaagta ctgcgcattc cacagaggtc ctgggcacac aaccaacgac tgcaccacat 2460 ggatgaagta ccttgagcag ctcgtgaagg aaggcaagtg cgaccagtat gtcgacagac 2520 cagctgcccg gccaaggcga gaagcagatg ccgaaccccc agccaagaca atccgaatca 2580 acggaatctt tgccgaatcc gagcatctgg gggccaccaa caattccaag aagaggaaga 2640 tccagcaggc gagatcggtc tttcaggttc aagccataga tgttgtacct ggaccaatcg 2700 tcggcttcac cgagcaggac gctgagggag tagactttcc ccacgacgac gccttggtga 2760 tttctgttca actggcccac gccatcgttg acagaattat ggtggacaac ggcagctcag 2820 tcaacatcct acaactgtca gtcatccaga agatgggcct ggaaagcacg atcaaacgca 2880 aagcagaggt cttgaccgga ttcaacggac ttacctcaac tgccattggc actatcacgc 2940 tcgacgtaac cagcccaccg attgtctcat cgcagacctt catgatcgtc agcgacccat 3000 ctccccataa tgggatattg ggccgacctt ggctagtgaa gattggagct gtgacctcga 3060 tcgagtatca gaagatccga tttcgcatcc cgggaggagc agtcggagag atcaaaggcg 3120 accaggccat gtctcggcga tgcactgtac aagttctcaa ggagtcgaag aagaagtctt 3180 tcgccccagc agtagcagct gaagtgcaga aagacgattc tacctccgcc aaatagcaat 3240 tacagcaggc aggtcaagaa gatggcgtca aggtcgacaa tgccctggca gatgaatcag 3300 gatggaaacc cgaagaagac gccgaaacat cattcttgac ccccaccagc cggagaagac 3360 ggctaggatt ggctcacgtc tgagcccgac ggagaaggaa gaactcacgg ttttccttag 3420 ggaaaatcgt gacgttttcg catggtcacc ctctgacatg cccggtattg atccagcgat 3480 agcttgccac aagctgcacg tcgaccccgc tgccaaacct gtgatccaga aaaggcgaca 3540 tttcacaccc gagcgagtag cgattattga ggcggagatc gacaagttac tggaggccgg 3600 attcattgag gaagtggcgc actcagcatg gctggccaac gtcgtgctag tgatgaaaaa 3660 aagaagggca aatggagagt atgcgtggat tacaccgacc tcaacaaggc atgccctaaa 3720 gacaactacc cggttccccg aatcgacctg ctcgttgact caacatccgg gaaccagctg 3780 ctcagcttct tggaccatac tcaggctaca atcagattgc catgcacgag cctgacaagg 3840 agaaaaccgc attcgtgatc gagcgaggca catactgcta caaggtcatg ccctttggcc 3900 tcaagaacgc aggagcaacc taccaacgac tcgtaaacac gatgttcaag aagcagatca 3960 gagtaccatg gaagtctaca tcgacgacat catggtgaaa ggcaagcagc ggtcagacca 4020 cattgcaact tggcagagac ttttgacatc tccgagagta caaatgaagc tcaacccagc 4080 caagtgcact tttggcgtct cctcaggccg attcttaggg taccttgtaa cccaacgagg 4140 aatcgaggct catccaaggc agatcagagc gatcctggac atgaagtctc ccacaactct 4200 gaaggagatc caaagtctga ccggacgagc agctgcactc aatcgtttcc tctcgcgatc 4260 caccgaccga tgcaagccct tcttcaaggc aatcaagaag gcgcagaagg acaaatggga 4320 cgacgagtgc gagaaagcat ttcaggacct gaagcagtac ctgacatcac ctccactact 4380 atccaagccg gaagcagcgg agaacctata catctatctg gcggtatcag aagtagcaat 4440 gagctctgcc ctcatacgag aagagttggg ggcccaactg cctgtattct atacatccaa 4500 agctctcctc gatgcggaaa ccagataccc gaagattgaa aagctaattt tggcgctagt 4560 tgttgcagct cggaagctca gacctacttt caagggcatc cggtcatcgt catgacccaa 4620 tacccactgc gatcagtttt gcatagtcca gacgcttctc aacgagtgat gaagtgggcg 4680 ttggaacttg gccaatacgg cttagcatac caacccgcac gacgataaag gcccaggcat 4740 tggcggactt cgtagcagaa ttcaccccaa gcctgaagac gcagcaactc agcccaaaag 4800 cgccccagag gcagccgagc acgccgtagc cgcaccagcc ccacctgcag gagatttttg 4860 gcgtttgcac gtcgacggat catccaacta ccaaggatcg ggggcaggcc tagttctcac 4920 taccccggac ggttcgatgc tcgagcaggc gatcactcta agcttcaagg cgtcaaacaa 4980 cgaagcagag tatgaagccc tactagcagg tctccgattg gcgaaagacc tagcggtgaa 5040 gaagctcgcg atctattccg attcccagct gatcaccaac caaacctcag gggagtacgc 5100 agcaaagcat ccaaggatgg cccgatacct cgagaaggta cgagagcagc tagcgacgtt 5160 ccaggcgtac acactcactc aggttccacg agcagaaaat gcccacgcag acgcactagc 5220 aagcctaggc tctgccttag accatcagct caggcgctcc atcccagtcg agtacttgga 5280 aaagccaagc atagatgagg aaccagcagt cgaggtggcg cagatcaaca caactccgag 5340 ttggcaagat cccatcatcg actacatagt caatggaacg ctccccgcag acagactgga 5400 gtccaggaag ctccagatga aggcagcacg ctactacatg tggaacggca tgctcgttcg 5460 aagatccttc tcaggaccac atctccgctg cctatcgcct cccgacgacc tgaagattct 5520 tagctcaatc cacgaaggcg tctgtggaaa ccactctgga ggccgctccc tggcgcaaaa 5580 agctcttaac gctggctact actggccaac catgcatcaa gacgccaagg agtatgtaca 5640 aaggtgcgac agctgccagc gcttcaagcc cgtgcccgca ctacctgcca gcgaactcca 5700 cccgcagacg agcccttggc cattcatgca gtgggcgatt gacctggtag gaccaatgcc 5760 gcctgccact gggggcagag gcatgatgat cgtagcaacc gactacttca caaaatgggt 5820 cgaagccgaa cccatgacta caactaccca gacggacata gagcgcttca tatggaagaa 5880 catcatctgc cgcttcggca tccccactcc atcgtcaccg acaatggtcc gcagttcgtg 5940 ggcaaagact tggcgaagtt cttcgaaaaa tatggcatca agcagcacat gtccacgccc 6000 cggtatccgc agggcaacgg gcaggccgag gcgtccaaca agaccatcct cgactgcctc 6060 aagaagtccc tctcagacaa gaagggcaag tggccagacg agctccccgg tgttctatgg 6120 gcatatcgca ccaccaagag atgagcaacc ggtgaaactc cattctccct ggcgtatggc 6180 tctgaggcga tcattcctcc caacgtcatg gtgccaagca tcagcactgt actgccgaat 6240 ttcgagcaga acgagaagga gatggccaca aacttagacc tggcagagga agagcgcgag 6300 aaggttatca cccgcattgc ggcctatcag cagcagctcc tctccagcta caacaagagg 6360 gcaaagatcc ggcagttcca gccaggagac ttagtcctca gaaaagcctt catcaccgcc 6420 cgacgggaag gctccaaaaa gatggctccc atctgggaag gtccgtacaa aatcagccga 6480 gtaggcggaa agggcagcta caccctcacc actatgagcg acaaagaaat cgacaagcag 6540 tggaatgcct acaacctgag aaagtactac gtgtgacctc ccaccattcc ttggaccctg 6600 ttcaagacaa ataaagttcg aagactcaag cagctcgacg aacaagacct cgcatgccga 6660 ggattatcag ttgttatgcc attactgcct acaagcaaag ttaataaatt tctctatttt 6720 caatgaagat tgaaggaatt attcacaagc ctgggccgaa tgcataaaca aactgaccac 6780 ccctgtgaca agcagaagac gccctctgcc ttgcagacat ggcgtgtgct ctccaatagg 6840 agagggtaaa ctaatccgga atatccagac gtggatgggt ggtacgactg ctcagtttcc 6900 cctgaatgca gcgactacct gagccggacg actcccagaa ttggccacga tagtccttcc 6960 cctggaatag acttagccga ctgaaggatt caattccgcg ggatcccggg tctctaaccg 7020 gaagagacgc taagtgcagg atccctgccc atgaaagaat tcgcgtgact agatggtccg 7080 tcctcgacgt gcaagtcttc atgaacgtag cttggtttta aagtgttgca atactagtta 7140 agcgacctgc ggaatcaagt tacaactcgg aaggatatgg cctctgaggc gcgatttcgc 7200 ctacacctta cgcctaaaac gcctccgaga gccagggacg acgcctgaag tggtcacgcg 7260 ggtcgtctgc ttctgtaagt aagacgcccg gccgacgacc caacggctgg cagcccaagg 7320 caatccgtaa gccgagactt acacctgcta tgactacgcg gactcgtctg cttatttaaa 7380 agcagcgctt ccggccgacg gtctacggtt taagttttgc tgggataaag ccgaggtacg 7440 actatagcag ctacgcggac ctcctctgct ttctacgaga agcatgagtc cggccgacgg 7500 ctctataagt taaaaatttc gcaacatgcc ccgggagggc caaggctcaa gaagccacta 7560 aagccgagaa aagctcaaga agccactaaa gccgaagtac aactatagca gctacgcgga 7620 ctcctctgct ttctacgaga agcacgtgtc cggccgccgg ctctataagt taaaaatttc 7680 gcaacacgcc ccgggagggc caaagctcat gaagccacta aagccgagat tcacaactat 7740 agtagctacg cgaactcgcc tgcttcctac ggaggcaacg agttcggccg ccggctctat 7800 aagttagaaa tctcgcattt tttcctcttg caggtaaagc tctagaagcc ccgaagccga 7860 aactaaaacc taagtgacga cgtgggatcg actgcttcat tgaagcagct cacccagccg 7920 cccgtcctac ggtaaagttt tgcaaaagac atggcgaaat agaaggatga agcaaagcaa 7980 ggaaagctgt ttattaaatt tctagcaaat tgataaaccg gctcgaaggc caacaaagtt 8040 caaataaagc agaacaaaaa ggaaaagaag aaaattccta agtctaagca aaaagactac 8100 tcattggcag cctgcgcaac cactggtccc tcgactgcca cgccttcagc agccgcaccg 8160 ctcctagcag ccaaagcttc catcagctca tcctcagccg cccctgcctg gactgcctga 8220 ccctcagctg ctccaccaaa ggcagcctca aacgagaaat caagcagatc aactggagaa 8280 atggagaaag tctcgaagtc cttctcggaa aactcataat ccgacggcct gccctgaaga 8340 tggtctacat agccaagctt gtagaaatcg gcctgacaag aagcaagcgc cacttcgtga 8400 ccagctttct cattcttcag ctgcacattc tcctcaacaa gcccagtgtg agcaccctgc 8460 agctcatcca gttccttttt caggttctcg ctagcagaca gcgcaccttg cagatccact 8520 tccttggact caagcttact ggcaacctcc ttgagacgag acacttcagc atgcatgaag 8580 ataagctcct cgtccttggc aaaacaagca gatcgtagct ccgaattgac acgctcaagg 8640 tcctcgacca ccggagaaac acgactgact tccttctctg cagcttccaa catcgcctga 8700 gtcgcactaa gcttagcctt caaatgggcg acctcctgat gagcgatctc cagctgcaaa 8760 gaagtggggg cagagacatc agaccccttc aaaacggcga gttcagattc gagcttctcg 8820 atcttttcag cagccgagcg aagctgagcc accaacgcca cttcggcctc cttagcacac 8880 ttgacagcat cctgatcaac gcgcatagac tcagctgcca ggatcaaagt cttatgcatt 8940 gtagcaatca gggaggacct cctcgagtag gcaggacgct tcgcaaaaga gtctgagcgg 9000 atgacaactt tcccaacact gtcaacaaac ttggcgcatg catcgacgtc ctcaagcagg 9060 tcagccttca gcagcgcaca aacctcggga aactctccag cctcagactc ggtggatctc 9120 tcacaactgc ccgtgcgagc agatttcccc ttctcagcag acgagtcagt cacggcagaa 9180 ggaggaacag gcccaggcgc caccttagca gcagaatcca ccttcccgct cttcatagcg 9240 gcgagcctct cagaagccga accagactta gctcccgacg gacgcttcga cacaaacccg 9300 gacaccgggg gcaccaccga acccttccgc tgggcaatca agtctctcag caatggatgt 9360 ggccaccttc ggagcagcag gtttcacagg ctcaggctca acggtcttct tcgccccctt 9420 gggggaagtt agatcaatga caagcttctc ggcagcagac gagcccccac gagcagcaga 9480 agaagtcatt ggcttcttct cggccgaagg ctcacaagca ggtgaggaag atctcttctt 9540 tccaccctca ttggcagcag gctctacagc agcgatcgga cgagccaacg cctcatcctt 9600 tatccgcttt atctcttcct tcggaggcag gccacctttc tcccgacgaa gagggctgag 9660 cagccagcgc cactcacggt actcagcagg aatgcccaag gcgatgtgca ctttcttcat 9720 atctgccgaa gtccttggag ttgagccaaa ctccgaatct acacaaagta agaaagacga 9780 tcaataaact gaagtcatgg agcagctcaa caaaaattca agcaggacaa gaatgaagca 9840 gttcacttac cactgataaa ggtagtcggg acacgcagct caggagaaga gtcagactcc 9900 cactctccac tcacctccaa ggtgtctctc gcccactcat gatcaccttt gcaagaagca 9960 tcaagcagcc tatggcgaga cctcagctgc cccacacctt ccttgtggcc gatctcaaag 10020 aagtaccaga actcatttat ggtcaagcca agatcaaaga acctgctcaa gttcgagaac 10080 cccaccatcg cacgaactgc atttggggag cactgagcag gcgcgcattt catggagcag 10140 atcacctcct ggaaaagacg cggcatggga aaagtaaatc ccaacacgaa gtaatacgga 10200 tggaatttga tagccctctt cctagcagtg gcaccctcgc cgcacggttc atggccgcta 10260 tcatccttca cccgcttgac gcgaacccct gacggaatcg catgcttgta cgcctcaaga 10320 aaatcccgaa acagctcgtc ggaattgatc ttgacatgtg cagccttgaa gtagcccacc 10380 ttgccggaag aaccaccttg acggtacaaa ggtggaggat attcgtcact tttgcgatcg 10440 gaggaagaca tctcaaagtc tctgcaaaaa gtacgaagaa aaatatttag aaggcagctc 10500 gcgagaagag aaaaaaaaaa aaaaaggacc gcagagccca gcgccccaca gccctcacat 10560 tctctctcgg cccgagccca agcggagccc agcggcaagc caggccccac ggcccgaccc 10620 ggctctccct ctctcgccag cacggcccaa cgcgggggga ggcccacgcc tctctccctc 10680 tctccttcgc gcgccagcgc accaagcggc ccagcctctc ggcccaggcc accaaggccg 10740 agagccggcc cacgccggtc tctcccctct ctcacctcac gcctgcatgg gcccgtgccc 10800 agcagccctg aaggcccggc ccaagcggcc tccccgcgcc ccagcgcacc agtcacctcg 10860 gcccgagccg agccgccacc tggcccacgc cagccgaccc ccgtgccgca ccaccacaca 10920 gcagccccgt ggcatccttg ccacgtgttt cacacccccg ccgagccaat ttttcaagtc 10980 ccaagactcc caaaaaatca agaagaagaa aattcaaatt tttcttacct tggtgcggca 11040 cggagaagaa gaacaacaac gagagacgac tctttgcaag ggcaagagaa gaagaamgct 11100 aggggagggg gaagaaaaat ttcctctggc ttctctcttc cttgttggaa tgatgattgt 11160 tctccaaatt tatttaatcc cctgcttaag gcagaattaa ataggtattg ggggcaattg 11220 gtttcctttt cctagaagaa gtctatctcc aaatcaagaa agaagatcaa gttcaaattg 11280 ggaaacaact ctacaagccc aagcagcttg ggatttctac acctactgcc cttttcctgc 11340 gtgcagccca gtaggtgtgg gggcatt 11367 // ID DNA9-15_Mad repbase; DNA; EDCOT; 1245 BP. XX AC . XX DT 25-OCT-2010 (Rel. 15.11, Created) DT 25-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-15_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1245 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1855-1855 (2010). XX DR [2] (Consensus) XX CC Terminus are distantly similar to those of DNA9-13_Mad. TIRs are CC not obvious. TSD is 9-bp long. XX SQ Sequence 1245 BP; 447 A; 238 C; 188 G; 372 T; 0 other; tagaaaactt cattttaatc cctaaataag attaacattt caaaaatacc gtattgaaga 60 ttaaaaacta aaaatagtcc tttgactcat gtccacgtca gattatatag tccatgtcat 120 atttaattat ttttttacaa atttgttata attttagttt acctatattg cccttcggta 180 tagataaatg cctaaatgac agtaccaaat ggaggggact taattggtcg taccgaatga 240 aggggaccta attggtcata ccgaatggag aggatctaaa catacacaac gtacctaact 300 gcccattcca aacctaaagg accgtaaaaa aaattacaaa aatatatgat ggcattgcac 360 agccagcaaa atctttaggc catatcctca ttcccttccc aactaagatg cacaatacac 420 tatttttcaa tgagctttca tccctctgct tcacatcata ttctacttgc cattttgcaa 480 tgttttcaat ctcatttatc ctttacgctg tctcaaatgc tttcattttt ttaatagtcc 540 tacactctat aaattaaaaa tgagtcaaag tataaacgaa aggaactgat ttgtatgtag 600 agaaaagtac cgtaacggaa accatttagt gtacctaact gaccgtaccg aatgaagagg 660 acctaactga ccgtacctaa tggagggaac ctaattgacc gtaccgaatg aaacaagcac 720 caacatatac aaaatctcca caaaaggtct ttcaacaaac acatggtgtg cattgtaaaa 780 atcaattctt gctaaaacaa tgaaacttat cggaccaaaa catgcacacc atacgaaaca 840 agctatacaa gtatcacccc gtgtgtgttg attatgacag ctaaacacat attccacacc 900 atatatagct tatgattatg acaaaagaac aacatgtttg tgagaggaga cagcatgttg 960 gaaaatttga aaattttcat tgattacagc tttaatacca gatgaaacgc gctctctctc 1020 taaatctctc tctaatgttg actgttacaa atataagagc aaaaatgttg acgttacagt 1080 actaacattt aagtggcagg catgtaaata gtggtaaaaa ttgtggtatt tgtatagatg 1140 acatgtcatg gtgcattgaa ataaaggatc atttttaaat actgaaaacc tcttaggttt 1200 tattctaaaa attatctttg ataaggacta atctctaaga gcccc 1245 // ID Copia33-PTR_LTR repbase; DNA; EDCOT; 322 BP. XX AC scaffold_117; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia33-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-322 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-322 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 243-243 (2007). XX DR Genome; scaffold_117; Positions 915734 915413. XX SQ Sequence 322 BP; 108 A; 53 C; 53 G; 108 T; 0 other; tgtaaagatg tcaatgatca agatcatgcc acatgtcaag tgaatacagg atgaggaagt 60 taaaatactg ttaggcagtt aaagtcgtta atattgttag gcagttagaa aagctgttaa 120 agttgttaaa cattgaagaa ggaagctagt ttacgtctac agcttctgct ataaatacat 180 cttcaataat gtaaaagtgt taaggtgaaa acagtgaata tattcatctt cttccttcaa 240 ttgtcaacta cttcttctgc cttcttcatt tctctctaga attccttcat tcaaaactgc 300 tatctttata aacatgagtc ca 322 // ID Gret1_LTR repbase; DNA; EDCOT; 824 BP. XX AC AB111100; XX DT 27-MAR-2007 (Rel. 12.03, Created) DT 27-MAR-2007 (Rel. 12.03, Last updated, Version 1) XX DE Vitis vinifera gypsy-type retrotransposon Gret1 - long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gret1_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-824 RA Kobayashi S., Goto-Yamamoto N. and Hirochika H.; RT "Retrotransposon-induced mutations in grape skin color."; RL Science 304(5673), (2004). XX DR EMBL/GenBank/DDBJ; AB111100; Positions 4672 5495. XX CC LTRs differ by 4 bp substitutions. XX SQ Sequence 824 BP; 235 A; 231 C; 175 G; 183 T; 0 other; tgtagggacc cctccctctg ggaaacacgt ggcacgcacc tcacagtgac acgcagcacg 60 tgttatcagc cggaccatca tcatccggat tcccttaagg atacgcatga tgatggttct 120 cctatccgga ccgcctcaag gaaaagcaca tgacgtttca gcttcttctg tccaaggaag 180 agcaaacgac gctgacagag catagacatc cggacaacct tcataatgta tctgctccac 240 tatacaatcc ggatagtcag catgtgacca tccggattta atcgtccgga tcatcaatta 300 aagtaaagca agtcttacac gctatcacga caaccagcca tggcccacgt cccatcatct 360 gcagagtgaa aggacgggtc gaggtgacaa caagtcactt cccacgatca ttctacatga 420 tcatttccca cgatatctag acagcagcat cacctaccac ggtttctgac agccgccagt 480 agggtggcga tgaccatgct gcctccgaat gtcatcatga caaacataaa atatctcctc 540 gccattaatg agaggaacag tacccctgaa gctgtatata tatgccttcg cacgaagaag 600 aaggggatcc tcctggtaac ttcttaatac ctggtaaaag gccaactgat ttatattcct 660 ctctctgacc atggctaaca aaaccatcgg aggatgcgtc cggacaccct gtccggatgc 720 cttcttgcag gaatgacgac tggatcaaaa acctttatga gttgagatca cgcgtccatc 780 catctggtta ctacgtggac cgccaaagac gcgaggtaac aaca 824 // ID Ogre-VP1_I repbase; DNA; EDCOT; 12174 BP. XX AC AY936172; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 13-APR-2007 (Rel. 12.03, Last updated, Version 2) XX DE LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; gag-pol; Ty3/gypsy-like; LTRs; intron; KW plant retrotransposon; Ogre superfamily; Ogre-VP1; Ogre-VP1_I; KW internal portion. XX NM Ogre-VP1_I. XX OS Vicia pannonica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Vicia. XX RN [1] RP 1-12174 RA Neumann P., Koblizkova A., Navratilova A. and Macas J.; RT "Significant expansion of Vicia pannonica genome size mediated by RT amplification of a single type of giant retroelement."; RL Genetics 173(2), 1047-1056 (2006). XX RN [2] RP 1-12174 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AY936172; Positions 19102 6929. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). CC In Vicia pannonica, Ogre elements occur at very high copy CC numbers (100,000/1C), making up about 38% of the genome. CC Additional annotation: 7058..7374: putative intron; CC 10327: frameshift mutation (insertion of 1 bp). XX FH Key Location/Qualifiers FT CDS 890..2416 FT /product="Ogre-VP1_ORF1" FT /translation="MDLGRRNTKRYDFRIPEVGGLQELASLVKKPVDFRKR FT YGKLLSILNTSVNIGLLKTFIQFYDPVYHCFTFPDYLLVPTLDEYANLLGI FT QVTDGVPFNGLEAIPKSRLIATITHLEKSEIDNNLTVKGNTLGLESDFLMK FT KAFKFAKSGNSEAFEAILALLIYGLVLFPNIKGFVDVSAIRIFLIGNPVPT FT LLGDIYFSVHLRNRQGGGVIVCCAPLFYKWIISHLPKSPIFKENPNGWNWS FT RRLMSLTHNDIHWYTLIYDGLETIESCGEFSNIPLIGTQGGISYNPILARR FT QLGLPHQKPVGLTVESYFYQEGIDPHGLKARMVRAWHHIQRREGGRARNCV FT ALELYTSWVEQRARDLQMPYAYEAPSLPAIPDWPDVPVETMEEYQETLSYI FT AQEKDLWEDKFHKTVSENRKLKKQVEEHDQMLYFQDDWLMEKDEKIRRKDA FT AIRKYLKERREMFNGSTSTTPDLDWKSEVNKLEAEKAEMKAYYEKEIMKHK FT RHKSVDCSSNEDA" FT CDS join(2741..7057,7375..10326,10328..10837) FT /product="Ogre-VP1_ORF2+3" FT /note="gag-pol." FT /translation="MEDFEQENNELRGTITTLQGEVERLASLVDALMVEQT FT RSSAPQNQPTVIAEVTPDPDNAAAASKPLFTMPEGYPWGMPFHFGASSQPN FT LPKVQTTRIEVPASQNPVFTPRRRGTSVPTSQPIMTFSNPVVHTTSDQVYH FT DSGDDAIPFGCMEELKEQFKEMQREIKVLRGEDIYGKNAYDLCLVPNVKVP FT VKFKVPDFEKYKGNSCPQSHLVMYARKMSTYNDNHQLLIHCFQDSLTGAAL FT RWYMGLDSTSIRTFDDLSKAFLRQYKYNISMAPDRDQLRAMAQKEKETFKE FT YAQRWREIAAQINQPMEDKEMTKIFLNTLSSFYYERMVASAPNDFTEMVNM FT GMRLEDGVRMGRLTKESGSSSGTKKYGTAFPKKKEQDVGMISQGNPRGNQR FT QHVAAIAPASNPAPNVRITPQIQQNQQPQQQAQPFNNNQNRAPRILQFDPI FT PISYTELYPALIRENAIQTKAPPPVPAKLPWWYKADVSCPFHQGAPGHDLE FT HCIALKSEVQKLVRANILSFKDSAPNVQANPLPNHGGNTVNMVYGCPGEFR FT IFDINWSKANLVEFHITCCRGNSNFRPHLYQRCPNGCRNSIRGCAIIRRDL FT QRLLDEDVIRIYRPRNQGHIDLGNVNSICECTDLYQIFDINLSNENLVQIH FT TAFCAMIGVTQHDYVSCEICHNNPRGCSNVRKDLQSLLDDDVIQVYKNRNE FT HNVNMLGSHPHELVSDINSVTPEVNVITPCFNMPKRIDMTYKPRKAVAPLV FT ICLPGPIPYKSDKAVPYKYSATMMKDGQEIPLPTLPSTVNIAEISRVTRSG FT RVYTPLPPKVPVVRQNPLATPASNPAVIPIGNPNPNCDVGQSSGTNVNPDF FT EEILKLIKKSEYKIVDQLMQTPSKISILSLLLNSEAHREALMKVLDQAFVD FT HDVTVNQFDGIVSNITACNSLCFYDEELPKEGKDHNFALHISMNCQSDSLS FT NVLVDTGSSLNVMPKTTLDRLSYKGAPLKFSGVVVKAFDGSRKSVIGEVDL FT PMTIGPHTFLITFQVMDIQAAYSCLLGRPWIHEARAVTSTLHQKLKFIIEG FT KLITISGEQALLVNHLSTFSFIDADDMEGTQFQGLTLEDESTKKDRASISS FT YQDAVRVVNTGTTAGWGQVINPVNNGTKTGLGFSSIPPKSSKKDETLRPIQ FT ETFCSGGFLDQVPQEVNLLSKEISSEKEHSDSEEEWKTYLDDSGYISQEEL FT FTPFGTLSEKFADMFQIRDKEVPPIPDEIWDTLGQPSGKFDYKVKYTAPES FT SKIAIEDIQPTGWGYPYETSEQLEVYTDSQLPHPFEITNGDLRFNAITQIE FT EPEFIYPQINAIFGDNWESNLEEDLESVSDNDFLSLDDLETPLENPKSVSK FT HASRSTSRPVEKAEEDRHSSTKGKTSKSSSSKSAQSSVNVITKDDSKQVMP FT EFIIHNGVRHYWTAVEVKNVVHRSKLVVNKSIESNNRTPSPNFAFPVFETE FT EDEEEDIPDEISRLLKQEERMIQPHEEPLELINLGSEENRKEVNIGALLDA FT DVKSQLIDLLKEYVDVFAWSYQDMPGLDTNIVKHHLPLRPECPPVKQKLRR FT THPDMADKIKKEVQKQLDAGFLLTSEYPQWLANIVPVPKKDGKVRMCVDYR FT DLNKACPKDDFPLPHIDTLVDNTAKFNVFSFMDGFSGYNQIKMAPEDREKT FT SFITPWGTFCYQVMPFGLKNAGATYQRAMTTLFHDMMHKEIEVYVDDMIAK FT SSTEEEHLEYLLKLFQRLRKYQLRLNPNKCTFGVRSGKLLGFIVSQRGIEV FT DPDKVKAIQEMPAPKTEKQVRGFLGRLNYISRFISQMTATCGPIFKLLRKN FT QGVVWTEDCQKAFDSIKEYLQEPPILVPPIEGRPLIMYLTVLEESMGCVLG FT QHDETGKKEHAIYYLSKKFTDCESRYSMLEKTCCALVWASKRLRQYLINHT FT TWLISKMDPIKYVFEKPALTGRIARWQMLLSEYDIEYHAQKAVKGSILADH FT LAHQPIDEHQSLKFDFPDEDVMYLKMKDCDEPLPEEGPDPESRWGLVFDGA FT VNAFGNGIGAVIITPQGTHIPFTARLLFECTNNIAEYEACIMGLEEAIDLR FT IKILDVYGDSALVINQIKDTYETNHLGLIPYRDYARRLLTFFNKVELHHIP FT RDQNRMADALATLSSMIKVNHWNDTPSVGIMRLERPAYVFTAEVVIDDKPW FT FHDIKRFLQTQEYPLGASRKDKKTLRRLSGKFFLNGDVLYKRNYDMVLLRC FT VDRHEADLLIHEVHEGSFGTHSNGHAMSKKILRAGYYWLTMEADCCKHVKR FT CHKCQIYSDKIHVPPTLLNVLSSPWPFSMWGIDMIGEIKPKASNGHRFILV FT AIDYFTKWVEAASYANVTRQVVARFIKNNLICRYGISSKIITDNGSNLNNN FT LMRELCEEFKIVHHNSSPYRPKMNGAVEAANKNIKKIVQKMVITYKDWHEM FT LPFALHGYRTSVRTSTGATPFSLVYGMEAVLPVEVEIPSMRVIMETKLSEA FT EWCQNRYDQLNLIEEKRMTALCHGQLYQTRMKQAFDKKVRPRVFKEGDLVL FT KKILSFQPDVRGKWSPNYEGPYVVKRAFSGGALTLTTMDGDELTHNINADA FT VKKYFV" XX SQ Sequence 12174 BP; 3774 A; 2577 C; 2463 G; 3360 T; 0 other; gaaaaatggc gacttcactg gggactttat tgtttctaaa aagaggatta ggcttatttg 60 tttatctact tggctttttt acgctttctc ttctgaatat aaactgcttg tttggttctg 120 agacatagtc acgcctgaca ttgtgactcg ttttgatgga taaaatccta gacccaagga 180 ttaagaaaca ttttaagatt aggagtttgg tcttaactac ttgtgggggg ttcagtcctc 240 ataaggaaag tctgagatca agcacttcag tggaggtctc ctaaggggta atttttgttc 300 aagcttgttc aattgcgcga acataaatta tttccattag gcctgcgaag ctgagggact 360 ttttagaaca taagggtgat ggtttctcgg tgaaatccac tctttaaccc atctttggcc 420 ttttgttagg gtggtgcaga gacttttaaa gttgtcatgc gagaccgcac ccagccgagt 480 ttttcctgag aataatatta tcgcacaagt tcaattgtgt aaagactata ttatgcgatg 540 gaagaatgta gactctgtgg taccagtaga acatgctcta caggttttta cccctagaac 600 ttaaacaacg gttactgtcc ttttgacctc atgctcgtga tgttgaagaa atgaacccat 660 cttgtttgaa acccatgttt tattgtatgt actcgttccc cacctctgac ctcatgctcg 720 tgacgtcgtt ttgttgaacc gccctcgcgt gaaattttgc ttggagtcgt tatgctgtcc 780 gcgtaacctt gcattcataa gcatacataa aacatactta aaatctttct cctaaaaatt 840 tcaaggaatt tagaaaattt tctttgcgaa ctgtccatag gttaggatca tggatctggg 900 aagaagaaac accaagcgat acgactttag gatacctgaa gtaggagggc tacaagagct 960 agcatctttg gtaaagaaac ctgttgactt tagaaagcgc tatggaaagc tcttgtctat 1020 tcttaacacc agtgtcaaca taggacttct taagactttt atacagtttt acgatcctgt 1080 ctaccactgt tttacctttc ctgattatct gttggtacca actttggacg aatacgccaa 1140 tcttttgggt attcaagtga cagatggggt acctttcaat ggtttggaag ccatcccgaa 1200 atctcgtctc attgcaacca tcactcattt agaaaagtct gaaatagaca acaacctaac 1260 cgtaaaagga aataccttag gtttagagtc agactttttg atgaaaaaag cttttaagtt 1320 tgccaagtct ggtaattcgg aagcctttga ggctattttg gctttactca tctatggatt 1380 ggttttgttt cccaacatca aaggatttgt tgacgtctca gccataagga tctttttgat 1440 tggaaacccc gttcccactt tgctaggaga tatctatttc tccgttcatc ttaggaaccg 1500 tcaaggcggt ggagtcatcg tatgttgtgc acctctgttt tacaaatgga ttatctccca 1560 cttacctaag tctcctatct tcaaggaaaa cccaaatggt tggaattggt ctcgaagact 1620 catgtcctta acccacaatg acatccattg gtatactctg atttacgatg gcttggaaac 1680 cattgaaagc tgtggagagt tctctaacat acccctcatt ggaacccaag gaggtatcag 1740 ctacaatcca atcttggcaa gacgtcaact tggacttcct catcaaaaac ccgttggtct 1800 tacagtagaa agttactttt accaagaagg gattgatcct catggattaa aagctaggat 1860 ggtaagagcc tggcaccaca tccaaagaag agaagggggt agagcaagaa attgtgtagc 1920 tttggagctc tacacttctt gggtagaaca aagagcaagg gatctgcaaa tgccttacgc 1980 ttacgaagca ccctctttac cagcaatacc agattggcct gatgtccccg ttgagactat 2040 ggaggaatat caagaaactt tatcctatat tgctcaagaa aaggatcttt gggaggataa 2100 gtttcacaag accgtttctg aaaacaggaa gttaaagaaa caggtagagg agcatgatca 2160 gatgctttac ttccaagatg actggctcat ggaaaaggat gagaaaattc gtcgaaagga 2220 tgctgccatc agaaaatacc ttaaggaaag aagggagatg ttcaatggat caaccagtac 2280 tactcccgac cttgattgga aaagtgaggt taacaaactc gaggctgaga aagccgagat 2340 gaaagcctac tacgagaaag aaatcatgaa gcacaagcgt cacaagtctg ttgattgctc 2400 gtcaaatgaa gatgcttagt ttagcatagt ttagttttta tcgctttcat ggtgtaagag 2460 ctactatcaa ccgttgtaac tttatttcag tattaataaa gtttggaatt tttattccat 2520 ttgtttgcaa gaatcttttc tttaggaaat tccttgaaat ttttcttaac tattaaaaca 2580 ttgcaacatt aaaacatact tcatctccgc tttccgccat agctaagtct aatctttgga 2640 attttctcca tagattttca agctgtctca tctcaaagtt tctcgatcgc gttcgcaatc 2700 tactcataga tacgacacta gagcaaagag aaggaaagca atggaagact ttgaacaaga 2760 aaacaacgag cttcgtggta caattaccac acttcaagga gaagtggaaa gactcgccag 2820 tttagtggac gctctgatgg tcgaacaaac tcgatcatcc gctcctcaaa atcaaccaac 2880 agtgattgcc gaagtcactc cagatccgga taatgctgct gcagccagca aaccgctctt 2940 cactatgccc gaaggatacc cttggggcat gccatttcac tttggtgcaa gctctcaacc 3000 caatctaccc aaggttcaaa caaccaggat tgaggttccc gcttcccaaa acccagtgtt 3060 cactccgaga cgtagaggaa catctgtgcc aacttctcag ccaatcatga ctttttcaaa 3120 tccagtagtt catactacga gtgatcaagt ctatcatgat tcgggtgacg acgcaattcc 3180 gtttggttgt atggaagaac tcaaagagca gttcaaagaa atgcaacgag aaatcaaagt 3240 tcttcgtgga gaagatatat atgggaagaa cgcgtacgac ttatgtctag ttcccaacgt 3300 gaaggtacct gttaagttca aagtccccga ctttgagaaa tacaagggta attcatgtcc 3360 acaaagccat ttggtgatgt atgctagaaa gatgtctacg tacaatgaca atcatcaact 3420 gctcattcac tgcttccaag atagtttaac tggtgccgct ctgaggtggt acatgggttt 3480 ggatagcacc agcattcgta ctttcgacga tttaagcaag gcctttcttc gtcagtacaa 3540 gtataacata agcatggctc ctgatcgaga ccaactccga gccatggctc aaaaggaaaa 3600 ggaaactttc aaggagtacg cccaacgatg gagggaaatt gctgcccaaa ttaatcaacc 3660 gatggaggat aaagagatga ctaagatctt tcttaacact ctcagttcat tctactacga 3720 gcgaatggtt gctagcgctc caaacgattt taccgaaatg gtaaatatgg ggatgcgtct 3780 agaggatgga gtccgaatgg gacgtctaac aaaagaaagt ggatcttcaa gtgggactaa 3840 aaagtatgga actgcttttc ccaagaagaa agaacaagat gttggcatga tatcccaagg 3900 taacccaaga gggaatcaac gacaacatgt ggctgctatt gcaccagcat ctaatcccgc 3960 accgaacgtg aggattactc cacaaattca acagaatcaa cagcctcagc agcaggctca 4020 gccattcaat aacaatcaga atcgtgcgcc aaggatttta cagtttgatc caatcccgat 4080 ctcatacact gaattatatc ctgccttgat tagggaaaat gctattcaaa cgaaagcacc 4140 gccgcccgtt cctgcaaagc taccatggtg gtacaaagcg gacgtatctt gtccttttca 4200 tcaaggggca cctggccacg atctcgaaca ttgcatagcc ttgaaatctg aagttcagaa 4260 gttagtaaga gctaacattc tctcgttcaa ggactcggct ccgaacgtac aagcaaatcc 4320 attaccgaat catggaggaa ataccgtaaa catggtatat ggatgtcctg gagaattcag 4380 gatcttcgac ataaattggt caaaagcaaa tttggtggag tttcatatta cttgttgcag 4440 aggcaatagt aatttcagac cacatcttta tcagcgctgt cctaatggtt gtaggaacag 4500 tattcgtgga tgtgccatca taagaagaga tctccaacga ttgttggatg aagatgttat 4560 tcgaatctat cgaccgagga atcaaggtca tattgaccta ggcaacgtca actcaatttg 4620 tgaatgtact gacctctacc agatctttga tatcaactta tcaaatgaaa acttggtaca 4680 aattcacact gctttttgcg caatgatagg cgtcactcag catgactatg tctcctgtga 4740 aatctgtcac aacaatcctc gaggatgctc taatgtcaga aaagacctcc aatcgttatt 4800 agacgatgat gtcattcaag tttacaaaaa cagaaatgag cataatgtta acatgttggg 4860 tagtcatccg catgagcttg tctcagatat caactcggtg actcccgaag ttaatgttat 4920 cactccctgt tttaacatgc ccaagcgcat agacatgaca tacaaaccaa gaaaagcagt 4980 tgctcctttg gtcatttgtc tacctggacc aattccttat aagtcagata aggcagttcc 5040 ttacaaatac agtgcgacta tgatgaagga tgggcaagaa attcccttac cgactcttcc 5100 atctacagtt aacattgccg aaatcagtcg tgtaactaga agtggacgcg tgtatacacc 5160 gttgccacca aaagtgcccg ttgttaggca aaatcctttg gctacgccag cttcaaatcc 5220 tgcagtgatt cctattggaa atccgaatcc caactgcgac gttggacagt ccagtggaac 5280 caatgtcaac cctgactttg aggaaatctt gaagttaatc aagaaaagtg aatacaaaat 5340 tgtggaccag ttaatgcaaa ctccgtccaa gatctccata ctttctctgc ttctaaactc 5400 tgaagctcac cgagaggctt taatgaaagt tttggatcaa gcttttgtag atcacgacgt 5460 aactgtcaac cagtttgatg ggatagtatc caacataaca gcttgtaaca gtctatgttt 5520 ctatgatgag gaactcccta aagagggaaa ggatcataac tttgctcttc atatctctat 5580 gaattgccaa tcagactcct tatccaatgt gttggtagac acaggatctt cactcaatgt 5640 gatgccaaag acaactcttg accgtctgtc atacaaaggg gctcctttga aattcagtgg 5700 agtggtcgtc aaagcctttg atggatcacg taaatcagtt ataggagaag ttgaccttcc 5760 aatgactatt ggtccgcata ctttcctaat caccttccag gttatggaca ttcaagctgc 5820 ctacagctgt ttgttaggtc gaccatggat tcacgaagca agagcagtaa catctactct 5880 tcaccaaaag ctgaaattca taatagaggg aaagctgata accataagcg gagaacaagc 5940 cctattggtc aatcacttat ccacgttctc tttcatcgat gccgatgata tggagggaac 6000 tcagttccaa ggacttacat tagaagatga atctacaaag aaagatagag cctctatctc 6060 ttcttatcaa gatgcagtac gagtagttaa cactggtact actgccggtt ggggtcaggt 6120 cattaatcct gtcaacaatg gaaccaaaac aggattggga ttttcctcaa tacctccaaa 6180 atcaagcaaa aaggatgaaa cacttcgtcc gatccaggaa acattctgta gtggtggatt 6240 ccttgatcag gttccccaag aagttaatct cctcagcaag gagatttctt ctgaaaaaga 6300 acattctgat tccgaagaag aatggaaaac ctacctcgac gattctggat atatatctca 6360 agaagaactg tttacaccat ttggtactct ctcagagaag ttcgcagata tgttccaaat 6420 ccgagacaaa gaagttccac ctatccccga tgaaatttgg gataccttgg gacaaccaag 6480 cggcaagttt gattacaagg tcaaatacac tgcccctgaa agttcaaaga tcgcaatcga 6540 agacatccag ccaactggat ggggataccc ctatgaaaca tcagaacagc tagaagttta 6600 cactgactct cagctacctc atccatttga gattacaaat ggagatcttc gcttcaacgc 6660 aataactcag attgaggagc cagaattcat ttatcctcag ataaatgcaa tctttggaga 6720 caattgggaa agcaatctag aagaggactt ggaaagtgtc tccgacaatg actttcttag 6780 tctcgacgac ttagaaacac ctcttgagaa tcccaaatct gtgagcaaac atgcctcacg 6840 atctacttct cgacctgttg agaaagcaga ggaagaccgt cacagcagta ccaaggggaa 6900 gactagtaag tcaagctctt caaaatctgc tcagtcgtca gtcaacgtta tcactaagga 6960 tgattccaag caagtcatgc ctgagttcat cattcacaat ggagttcgtc actattggac 7020 agctgttgaa gtcaagaatg ttgttcatcg ctcaaagtaa tgatctcgct tttgttttga 7080 cctctcgcct agcccgaggc agagtgtttg ttttataggg tttgctttta atttccctca 7140 ttgtctcgcc caaggcaata gagttttgtg tttagggccc tgtttcaaat gtgaatcata 7200 aataaaacgt cattttgaat tccttatatc atgtgttttt atttttctgc ttttttctgg 7260 aaatggtaat cctaaaaaaa aaaaaaacaa ataaaaacaa aacacttttt agcaatctgc 7320 acgcaatatt tcattggtca gtttctaaaa taaaacataa atcatacgtg cagattagtt 7380 gtcaataaat ccattgaaag caataatcgt acgccctctc ccaactttgc gtttcctgtg 7440 tttgaaaccg aagaggatga agaagaggat attccagatg aaatttcccg actgcttaag 7500 caagaggaaa gaatgattca gcctcatgaa gaacctctgg agttgatcaa cttgggttca 7560 gaggagaaca gaaaggaagt gaacattgga gcacttcttg atgctgacgt caagagccaa 7620 ttgattgatc ttctcaaaga atacgtcgat gtgtttgctt ggtcctacca agacatgcca 7680 gggttggata ccaacatcgt caaacatcat ttgcctctaa ggccagaatg tccgccagtt 7740 aagcagaagt tgagaaggac tcaccctgat atggctgaca aaatcaaaaa ggaagttcaa 7800 aagcagctcg acgctggttt tctccttact tctgaatacc cgcaatggct agccaacatt 7860 gtacctgttc caaagaaaga tggaaaggtc agaatgtgtg ttgactaccg tgacttaaac 7920 aaggcatgtc caaaggacga ttttccttta ccgcacattg acacgctggt tgataacacc 7980 gcaaagttca atgtattctc ctttatggac ggtttctccg gttataatca gatcaagatg 8040 gctcctgagg acagggagaa gacatctttt atcacaccat ggggcacctt ttgctaccaa 8100 gtaatgccat ttggattaaa gaacgcaggc gcgacttacc aaagagcaat gactactctc 8160 tttcatgaca tgatgcataa agagatcgaa gtgtatgtgg acgacatgat cgccaagtcc 8220 agcactgaag aagaacattt agaatacctt ttgaagttgt ttcaacgctt aaggaaatat 8280 caactacgct tgaatcctaa caagtgcacc tttggggtga gatcaggaaa actcctagga 8340 ttcattgtca gtcaaagagg tattgaagta gatcctgaca aagtcaaggc tattcaagaa 8400 atgcctgcac caaaaacaga aaagcaagta agaggatttc ttggacgatt gaactacatc 8460 tccagattca tctctcaaat gactgctact tgtgggccga tcttcaaact tctccgcaag 8520 aatcaagggg ttgtatggac agaagactgc cagaaagcgt tcgacagtat caaagaatat 8580 ctgcaagaac caccaatttt ggtccctccg atcgaaggac gaccattaat catgtacctt 8640 accgtgttag aagaatccat gggctgtgtg ctgggacagc acgacgaaac cggtaagaag 8700 gagcatgcaa tctattactt gagtaagaaa ttcacagact gtgagtctcg ttactccatg 8760 ctcgagaaaa cttgttgtgc attggtttgg gcatctaaac gtctccgcca atatctaatc 8820 aaccacacta cttggttgat ctccaaaatg gatccaatca agtatgtatt tgaaaagcct 8880 gccttaacag gaaggattgc ccgatggcag atgctgttat ccgaatacga cattgagtat 8940 cacgctcaaa aagctgtcaa aggaagcatt ctcgccgatc atttggcaca tcaaccaatt 9000 gatgaacatc aatctctcaa gtttgacttt ccagacgagg atgtcatgta cttaaaaatg 9060 aaagattgtg atgaaccatt acccgaagaa ggtcctgatc ctgaatcaag atggggccta 9120 gtcttcgatg gagcagttaa cgcttttgga aacggaattg gggcagtcat tatcactcct 9180 caaggaaccc atattccatt cacagccaga ttactcttcg aatgtactaa caacatcgca 9240 gagtacgaag cttgtatcat gggactcgaa gaagccattg acttaaggat caaaatcctt 9300 gatgtatatg gagattcagc tcttgtgatc aatcagatca aagacacgta tgaaactaac 9360 caccttggtt tgattccata cagagattat gcaagacgtc tgttgacttt cttcaacaaa 9420 gttgaattgc atcacatccc tcgagatcag aatcgaatgg cagacgcctt ggccacttta 9480 tcttccatga tcaaagttaa ccattggaat gatacgccga gtgtcggcat tatgcgcctt 9540 gaaaggccag cttatgtgtt tacagccgaa gtagtcatcg atgataaacc gtggttccac 9600 gacatcaaac gcttccttca aactcaagag tacccgcttg gggcatctcg caaagataag 9660 aaaactctaa ggagactttc tggcaagttc ttcctaaacg gagatgtact ttacaaacga 9720 aactacgaca tggttttgct cagatgcgtg gatagacacg aagcagatct gttaattcat 9780 gaagtacatg aagggtcctt tggaactcat tcaaacgggc atgcaatgtc caagaaaata 9840 ctaagagcag gatactattg gctgacaatg gaagctgatt gctgcaaaca cgtcaagaga 9900 tgtcacaaat gtcagattta ctcagacaag atccatgtgc caccgactct actcaacgta 9960 ctctcttctc cttggccttt ctctatgtgg ggcattgaca tgattggaga aatcaaaccg 10020 aaagcttcaa atggtcatcg tttcatcttg gtagcgattg attatttcac caaatgggtc 10080 gaagcagcat cttacgccaa cgtcacacga caagtggttg caaggtttat caaaaacaac 10140 ctcatctgcc gatacggtat ttcaagtaag atcattacag ataatggatc taacttgaac 10200 aacaacctga tgagggaact gtgtgaggaa ttcaagattg tgcatcacaa ctcttctcct 10260 tacagaccaa aaatgaacgg cgctgttgag gccgccaaca agaacattaa gaagatcgtc 10320 cagaaaaatg gtcatcactt acaaagactg gcatgagatg ttacctttcg ctttgcatgg 10380 ataccgtacc tcagtacgta catcaacagg ggcaacccct ttctccttag tttatggcat 10440 ggaagctgtg ctccccgtag aagttgagat tccctcaatg agagtcatca tggaaactaa 10500 gttatctgag gctgaatggt gtcaaaacag atacgatcag ttgaacttga tcgaagaaaa 10560 acgtatgact gctctctgtc atggacagtt atatcaaacg agaatgaagc aagcatttga 10620 caaaaaggtt cgacctcgag tattcaaaga aggtgacctt gtgcttaaaa agattctgtc 10680 ttttcaacca gacgttaggg gcaaatggtc tcctaattac gaaggaccgt atgttgttaa 10740 gagagctttc tcaggcggtg ctctgactct tacaactatg gatggtgatg aactcactca 10800 caacatcaat gctgatgcag tcaagaaata ctttgtctaa acaagacaaa agaacggctc 10860 ggtaagttga aaacccgaaa agggcgactt aggcaaaaat gagcgtctcg gtggactgaa 10920 aaacctgaaa aggcggtcca ggcaaaaata agagacaata aacagaacaa tattatcctg 10980 gtagattgaa aacctgaaag ggcaatctag gcaaaagtta aggatttatg acaaagtaac 11040 tgcattagtc cgagcttcat cacctgaaga atctccaacg agaaatcttc gaacaaatca 11100 tcgtccaagc aacaaacaca gttggaattc aaagttgtta gggagaatac gattatcgct 11160 ttcagtgtag tcttttccac ttaattacca tttccaaact tttgtaaata ttctatggaa 11220 tcacgctttt ggctgattac catcctataa ataaacttga gctttgtgcc atttatttgc 11280 aattcttaat ttattctgct tttgcaaaat gacgttttgt tcttgataat cattttttga 11340 aacaaaaaaa aaactttttc aaaatgaatt tactttttca aaataaaagc gacacttttc 11400 tttgagcaat gaacgccgaa ggaaacaaca acagctttct cagcgaacgt tcaaatctga 11460 aggatgaaca tatgactgat cttgctctct tcctcgaaag agacttcgac ggtattcttt 11520 tcctcaaaga aaatttgtga ccaagcgtca ccaacaaaaa gaaaatgatt tttttcttcc 11580 ccagagaagt ctgaaacatt caactctgaa tcaactaatg agtgttgcct acacttcatt 11640 aacagacgct tccctcagtg aagtcaaagg ggataaacca gaagcctcat tatccgagca 11700 aaacatccct gttgcatttt gcagtaagag ttaattggac atttttctct tctgttttca 11760 tttgttattc acaaagctga ataatcaatt cctcctaaac attaccttgt tataattatc 11820 actcggctga taattggtaa aagttctagg atcctctctt tatcatcaca aggctgataa 11880 acgataaaga aatcaccatc accttatcac taggctgata acgggataag atatctcatg 11940 atcacctaaa acattgtcac caggctgaca gtatgttgag acatccttac aatttctcct 12000 cggttgtgtt acctctaggt acctctgggc agaaattttt ctcacatcaa cgtgacccgc 12060 atttttggta tcttaggtcc aaaattcgcg tattctgata tttaaatctc tttcttccta 12120 taaagatttt caatctttat ttatcaggtt aaagaaattt aaataggggc atct 12174 // ID BoSB15 repbase; DNA; EDCOT; 206 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB15. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-206 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 206 BP; 40 A; 56 C; 61 G; 49 T; 0 other; aactgggcgc ttgtggcctg gtggtaaagg gttcatgact gtgagttccg ccacctaggt 60 tcgagtcccg accaccgtcg attaaaatgg ggtgaaaaag gcggccctcc tggatgcctt 120 cggctgactc cccggctcat ctccggtgga cggtcattag gcgctagtcg ggtctctttc 180 gaggacatcc gaataccaga atcatt 206 // ID DNA8-3_Mad repbase; DNA; EDCOT; 1063 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA8-3_Mad. XX NM DNA8-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1063 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1476-1476 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~87% identical to the consensus. 8-bp TSDs. XX SQ Sequence 1063 BP; 359 A; 226 C; 172 G; 306 T; 0 other; tagggttttt gtcacaaatg gtccctgaaa ttgacccacc ccatcaaggt ggtccctgaa 60 attgaaaatc aatcaatgta gtccctgaaa atgagtgtcg caaatcaatg tggtcattcc 120 gtcacaattc cgttaaaaat tatgttaagt gctgacgtgg cacttaaatg ggtcccacaa 180 atttattaaa atattatttt gtgaattaaa aagatttaaa tattaaaaaa caatttttag 240 tttttataat taaaaacttg aaacataaaa aataagaaaa aggagatgat tgaacactgt 300 tcatcatctt cttcccctcc caacctccca ctacagcccc caccccacac ccccctccca 360 ctctctgggt agagtgccgc cgtcggaact gtggccgggt tcccgggtca gttgaaagat 420 cctggccgca cacatggtgg ccattggatt ttcccacccc gttcctccac cttcgtgtgg 480 cgaaccttcg acggcctcct agccggtttc gccgtcatag aaacgggtac cggaacaatc 540 ccatggacaa agttcaagaa tctcaggaaa ttttcaagaa cctagaaatc taacccattt 600 tcttcacaaa aaatctaact caaaaatctg cccggaacca ataatctcag aaaatttcaa 660 gaacccagat gaaaaaacac taaatcaagc taaaaacgag gaaatttcaa gaaattaaga 720 acaagaaatg tcaagaattt aaaacataaa aactttaaaa aaatttattc tcacgggaag 780 aagatgatga acagtgttca atcatcttct ttttttttat tatttaaata tatatttttt 840 atatttaaat atttttaatt cacaaaataa tattttatta aatttgtggg acccatttaa 900 gtgccacgtc agcacttaac ataattttta acggaattgt gacggaatga ccacattgat 960 ttgcgacact cattttcagg gactacattg attgattttc aatttcaggg accaccttga 1020 tggggtgggt caatttcagg gaccatttgt gacaaaaacc cta 1063 // ID HELMET2 repbase; DNA; EDCOT; 7483 BP. XX AC AC125481; XX DT 04-JAN-2007 (Rel. 12.01, Created) DT 19-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Helitron-type element. XX KW Helitron; DNA transposon; Transposable Element; HELMET2. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-7483 RA Jurka J. and Shankar R.; RT "HELMET2: Helitron-type sequence from barrel medic."; RL Repbase Reports 7(1), 32-32 (2007). XX DR EMBL/GenBank/DDBJ; AC125481; Positions 89408 96890. XX CC Putative autonomous. XX FH Key Location/Qualifiers FT CDS 2371..2871 FT /product="HELMET2_1p" FT /translation="IAYRMQDRVVDYGNVVNSRRSVDCYTMIESQRLRYIR FT KNQKTIRCGILNGLHEAMDMGETDASNVGQKIVLQPSFAGGRHYMFNNCQD FT AMSICKKYGYPDLFVTIACNTNWREIQDFLKERNLKASDRPDIVCRVFKMK FT LDKLMDDFEKEECLAKLMQVYTVILVVF" FT CDS 3543..4007 FT /product="HELMET2_2p" FT /translation="LCGMPRQRHVPCGGARPFSPCMDRGRCTKYYRKNYKG FT TTTIDEGYPRYKRRDFGIHVDKQRVLLDNRYVVPYNPHLLIRYGGHVNVEC FT CNKSNSIKYLFKYVNKVPDKALMQLSVDGDNRDKSKPVDEIKQYYDCRYVS FT PCEAVWRIFAFDIHHK" FT CDS 5690..6334 FT /product="HELMET2_3p" FT /translation="LIIWDEAPMMHRWCFEAVDRSLRDIMSKNDPLNALKP FT FGGMTIVLGGDFRQILHVVRGGTTPDIVDASVNSSKIWAYCNVLRLTVNMR FT LGASSVPAEQEEIANFCKWILSIRDGNNASGDNGEMKVEIPEDLLISNTTN FT PLMSLMDFVYPDLNDNLGDQLFFQERGILAPTLDSVEHVNEFMMSLIPSEE FT KEYLTSDSIFRSGENSDVQSEWFTP" XX SQ Sequence 7483 BP; 2528 A; 1092 C; 1279 G; 2584 T; 0 other; ttgttatgct tttttgtttt cgttattatt ctatttaaat ttatggatgg tttataaatg 60 aatactatag ttatttttat ttttttttac ttttgtggtt cctatgcaaa cagggtattg 120 aatcaagaaa tcacgaacaa gcacaaaaaa taagaatatg gagatattat tttatagatg 180 aaaccgatta tatgatggtt gagttcaaga caacatattc ttcacacgag ggcctagggg 240 aaaaaaagat gacattatga caaactttga gattccaaag aaattagtcg ttcttagaaa 300 agaatctaga taaaattttt actatgatga gtcactattt tatgtctctt atacaaagaa 360 ggattgtgta gttttttggt atgatttata tgtaatcgga ctgaaaaatg gaacaaagga 420 gtattatatt gatgaaatta gttaataaat tacttatcat tttaatgctt tttactatta 480 gttcataatt gagtttatca ttttctgcat atttaaagtc agtttagtcg aaatcaaaaa 540 taaacatcat gcacacacac tatcaaatgg caacacccaa gtttcaccag caatctcatg 600 tcctcttttc ttcggtaaat tgtatattcg tttataattt gttatgattt tatttcaata 660 atttctttaa aaaattattt ttcattatgt agttgacaaa gaaagctatg accagttgtt 720 tattggacgg taatcaatag caatattttt ttgttgttga gggaagtaat aatcttgatt 780 aacatattta atttatccat cgcaacacca tatatgttgt aatgtaaatg gtaattaata 840 aaaatatata ttaattgagt aatatagtta cagctcattt agtcattttc acaaagagta 900 gatagaactc tttttttcga gaaaaattta agaatgtcat gaaataaacc tttgaccaaa 960 taattaagga gtttattttt tcatgtttat aaatcatgaa aattctagac attattattt 1020 tttaattaag acaaatatcc ctaaggatca acaatatttt ggatgtaatt aatttgatac 1080 aaacttttta aataagtgat tgcattgtaa tatttgaaat aaacgttgca atattttgaa 1140 tgaaattaat ttggtgcaaa cgttctaaat aggctatcta ttttttcttt gtttcacgac 1200 atttgattcc aacgactttg gtatgcttat agtaaaggat cgtgacttcc gcatgaatac 1260 gatataaaaa attgttagta attaagtacc tttaaataag cataaaaaaa attatatttt 1320 gtcctttcaa aaattaaaca catagtttaa ttgtcttaat tataaatcat ttgttgaaac 1380 tttgaaatgc tccaatcagg gctatcttaa agaagaaact cacagagttc tttaaatcat 1440 ttgagaatat aaagcaagtt ttatgttttc ccttagctcg ccttagtgtt gttaatggat 1500 tctacaacca aactttgatc attcacaata attaaagata caattatgtc ttgataataa 1560 taaaaaatgt ataattactt cattaaaaat aataagtaaa aaagaggaca ttgagataga 1620 gattaaattt tcaaattaat ttttttgaac ttaaaggttt ttttttctta gcaactaatt 1680 gggtctcagt ttttatacga atctaaattt gtcttgactt aaaattcaaa tctaccctca 1740 atcactacat taacccataa atataaattt tacggtataa tatttttaat agaaattata 1800 ttaccaatta accatccatt attgtattta tagcaaaaac aatgacaatc aaatgatttc 1860 aatacagaga tatacatatg tcaacatgta ttgaaaaata aataaggatg caaactttct 1920 tgcctttcta atttgaaacc ttaactatta gttcctttat ttgcattctc acatatttca 1980 tctattgcag accaaagttt gtgctttttt ttcttcatac atatatgact cacttatcac 2040 gtatcaaaat attctcctaa atcatcaatc ataaaaaagt ttaatagaca tgcattttgt 2100 caactgagca taacacattc atgtttttct atgattagtt ttcaccaaag atcaaaagtg 2160 aaggaattta aaataataca aaaaatttaa atattttttt tatatttaat ataaaaaaag 2220 taagaaaata acaaaatatt tcatcataac gtttggagtt ctgagggagt ctacaatttg 2280 ttggatcatc atatttgggt tagagaaacc caacatcttc attgaaaaca cttaagacat 2340 acggaaatga attgcatcat acgcgaatag attgcatata gaatgcaaga cagggtcgtt 2400 gattatggca atgttgttaa ctcgaggaga tctgttgatt gctatactat gattgaatca 2460 caacggttga ggtacattag aaaaaatcaa aagaccataa ggtgcggcat tctgaatggt 2520 ttgcacgagg caatggatat gggtgaaact gatgcgtcta atgttggaca aaagatagtg 2580 ttacagccgt cctttgcggg tggcagacat tacatgttta ataattgtca ggatgcaatg 2640 tcaatttgta agaaatatgg atatcccgat ctgttcgtaa caatcgcgtg caatacaaac 2700 tggcgagaaa ttcaagattt tcttaaagaa cgaaacttaa aggcatctga tagacctgat 2760 attgtttgtc gagtgttcaa aatgaagttg gataaattga tggatgattt tgagaaagaa 2820 gaatgtttgg caaagttgat gcaggtatac actgtaatat tagtagtatt ttaggcttaa 2880 atatgcaatc cgtcccaata attttgacac gtttttattt tcgtccttat aaaaaaaaaa 2940 ttaaaaacat ccctgtaaaa aaaaatgttt taaaaaggtc cctggcccca cttttttgtt 3000 gacatgggat ggctttggcc acgtggcagt tgctgactgt gcgacttttg ccacgtggcc 3060 ctgacggggc agtccacgtc atttttttaa aaaaaatttg aaaaaaaatt aaaaaatcat 3120 aaaaaaattc caataatttt ttctaaatat gaagaaaaaa attgaaaatt agttttttta 3180 aaatttagaa ataaatttaa gaaaaataaa attgaaaatt atataatctc aaaatttata 3240 acttttgaaa atataattta attttcagaa ttaaaaaaaa ctgaattttc gaaaatttaa 3300 ttttcagttt ttttaaattt tttaaaaatg aattttcaga attttgaaaa aaatattttt 3360 ttaattaaaa atcaaaaatt caattttttg atttttttaa tttaaaaaaa aatgaatttt 3420 cagaattttg aagaaaaaaa aataattaaa aatcgaaaaa ttttaatttt cagttttttt 3480 tccgattttt caatttaaaa aatgaatttt tagaattttg aaaaaaaata aacaaaaatt 3540 aattatgtgg catgccacgt cagcgccacg tgccatgtgg tggtgcccgt cccttctcgc 3600 cttgcatgga caggggcaga tgtacgaaat attatcggaa gaattataaa ggaactacga 3660 cgattgacga gggttatccg aggtacaaac gtcgtgattt tgggatacat gttgacaagc 3720 agagggtcct attggataat cgatatgtcg tcccatacaa tccacatctt ctcattagat 3780 acggaggtca tgtaaatgtg gaatgttgta acaaatccaa ctctatcaag taccttttca 3840 aatacgtgaa caaagtccct gataaggcat tgatgcagtt gtctgttgac ggtgacaatc 3900 gtgataagtc caagccggtt gatgaaataa agcagtatta cgattgtcgt tatgtttcac 3960 cttgcgaggc tgtttggagg atatttgctt ttgatataca ccataaatag cctcatgttc 4020 tcaaactatt gtttcacttg cataatgaac aaggaaacat agaccatgtt tctcgcatgg 4080 tttgaagcaa atcgtcagta tgtaggcggt tgcgatctaa catatgctga atttccaaca 4140 agatttactt atgagaagaa ggacaaacag tggcagccac gtaaactagg atatcaaatt 4200 ggaatgcttc attacacgcc gcctggtata tgggagttgt actacatgag gatactattg 4260 accgttaaga agggttgcat gagatataga tgcataaaaa cgattaatgg acatacctat 4320 gacacgttcc aggaagcacg ctctgcttta ggattacttg atgacgacag agagtttata 4380 gatggtatca cggaaaatgg tgagttacgt tcgggccatc aattgcgttg gttgtttgtg 4440 catctcttaa ccactaggac aatgacgagc cctgatatag tatgagatgc ggcatggcag 4500 ttactgtccg atgatatctt atttgatcgt aggaagcatc tgaatattct gggtaatgtt 4560 tattgtactt attacgaaat ctatgcacca ttttttgttt tgtttacgat ctaatttttg 4620 catttttttt ttctgtctaa aaaggcacat tttagaaaat tggttaacat agttttgttc 4680 aaagtattgt atgcctatct caataaatat atttatctat ttaagtagtg ataataaaca 4740 aatacaatat tctttcaaaa aaaaaaaaaa caaatacact gttaatttga ttatacacta 4800 ttaaataaat atatttatct actgtcaacg ccacaaaact gtcatatata gctttccact 4860 atgtatatct tgattaattt gttcacattt tctgttttca cgttatctag attagtgagc 4920 attcatgaca tcattttgta gcagttccta tatctattta ttttcgcttt aaataaataa 4980 tggcttggga aatcctttac aaataagctt atttttttag tttgagttaa gctgaaagaa 5040 gctttttcga ttaagaattg agtcgtgact ttaatatcat tttttctgtt gcattgcata 5100 tattctctta ctatcgtttt tctttaggtg tgttcatatt aatttcgtga ctttacattt 5160 aatatgtaga tatgcgtatc ggtggcgatg acttgaagaa catgtgtttg attgaaattg 5220 aaatactgct tcaggaaaac cgacgtcgct tactgacttc aaatctatgc ccaggccaaa 5280 cgcggcagac atgccaactt tcacaaacaa gctaatcatt gatgagctaa attacaacaa 5340 agttgaactg gaaaagacac acgctgatat gttactgatg ctgactgatg aacaaagatg 5400 tgtgcatgac aagatcatgg agtctgttgg ttctgacgac agtggtttct tttttttata 5460 tggttacggt ggtactggaa aaacctttat atggaaaaga ttgtcggcta ctgttagatc 5520 gaatgggtta attgtattga atgttgcatc caaccgtata gcggctcttc tattaccagg 5580 tggaagaacc gcgcactcca cgccgacagt ccctattgag attaatgagg catcatcgct 5640 tacgatggaa aaggatagtc ctagggcaga cctggtgcgt gctgcatagt tgataatttg 5700 ggatgaggct ccgatgatgc accgatggtg ttttgaggca gttgaccgat cattgcgtga 5760 tatcatgtcc aagaatgatc ccctaaacgc acttaaacct tttggtggaa tgacaatagt 5820 tttaggtggt gattttaggc agatattgca tgttgtccga ggaggaacga cgccggatat 5880 tgttgatgcc tcggtcaatt cgtcaaagat atgggcttat tgtaatgtgt tgaggcttac 5940 tgttaatatg agattgggtg catcttcggt acctgcagag caggaagaaa ttgctaattt 6000 ttgcaagtgg atactctcaa ttagagacgg caacaatgct tcgggtgaca atggtgaaat 6060 gaaggtagaa attcctgaag atttgctgat atcaaacaca acaaatccgt tgatgtcact 6120 tatggacttt gtgtatcccg atctgaatga taaccttggt gaccaactat ttttccaaga 6180 aaggggaata ctcgcaccaa cgcttgattc agttgagcat gttaacgaat ttatgatgtc 6240 gctgattcca agtgaagaga aagagtattt aacctctgat tctattttta gatcgggtga 6300 aaattctgat gtccaaagcg agtggttcac accataattt cttaatggta ttaagagctc 6360 tggaaatcca aatcacaggt tgaaactaaa ggtgagatgt ccagttaatg gcactaggct 6420 gacagttaca catctaggga agagcacgat agctgctatc gtaattacag gaaaaagggc 6480 aggtactagg gtattcattc ccaggatgaa tcttattccg agtgatccag gactaccctt 6540 caaattcagg cgcgggcaat ttccattgac gctttgtttt gcaatgacaa taaataaaag 6600 ccagggtcaa tctttatctc gagtgggggt ttatcttcct aagcctgtgt tcacacatgg 6660 acaactttat gtcgctgtct ctcgagtaac ttcaagaaaa ggtctgaagc tgctcatcct 6720 ggatgaagat aataatgttt gtaaggagac cacaaatgtt gtgtatcgtg aagtttttca 6780 aaaagtatga tcattggtta tgttttagaa ttgttgttgc tataatttat aaaactaaag 6840 ttgcctattg tttggaagtc gttttatttt taatttcttt gtaaggcgta ctggtcatta 6900 tagacatgca atttctatat aagcagatcc ttctgtcatt gactattaat tcatgcactt 6960 ttcaggttta acaatccgtg aaaccttttt ttttttacat cgttgttacc ctaaaataca 7020 atatttacat tagaccattt gttttgtaaa aattaaaaac aaataacaat cggcgtttct 7080 gtagcccaaa ctatatttat acacacccgt aaaaaattaa acgtttgcat ttaccgacta 7140 tgtgtatgca tgtgacaatg actattatat aaaaaaaata catatttttt agtttttatg 7200 attaataaaa tacattttgt caacaaatat tattacacag tacgtcggcg tatttttgaa 7260 agaaaattac atatgctaag tttaacaata agtgcatctt atactacaaa taattagtac 7320 aagtataata atccaaatat ttttatcgtt atatgcaatg tttagatatt tcaaaatata 7380 tacaaaatta gatgatattt ttttcatatc gaatttaaaa tctatacatt tgatcaaaaa 7440 agttttttat ttccccgtgc tggcacaggt cactatacta gta 7483 // ID SHACOP14_I_MT repbase; DNA; EDCOT; 5408 BP. XX AC AC169177; XX DT 24-JAN-2007 (Rel. 12.01, Created) DT 24-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of a copia-type LTR retroposon, SHACOP14_MT, from DE Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Internal; ORF; Interspersed; terminal; repeat; SHACOP14_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5408 RA Shankar R. and Jurka J.; RT "SHACOP14_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 55-55 (2007). XX DR EMBL/GenBank/DDBJ; AC169177; Positions 109014 114421. XX CC The element has internal region having domains for gag-pol CC polyprotein with proteinase, CCHC zinc finger motif and CC integrase. XX FH Key Location/Qualifiers FT CDS join(64..1047,1051..1758,1765..1791,1795..1812, FT 1816..1854,1873..1887) FT /product="SHACOP14_I_MT_2p" FT /translation="MEKVGGFVNRPPLLYETNYDYWKSRMSAYLKSVDSKT FT WKAVLRGWEHPVVLDKDDNKTTDLKPEEEWTAPEDELALANSKALNALFNG FT VDKNMFRLIKKCDVAKDAWDILRTTHEGTSKVKSSRIQLLTTKFESLKMQE FT DETIQDYYMNVLDIANSFDSLGEKLSDEKLVRKILRSPKRFYMKVTAIEEA FT QEVSNMQVEELIGSLQNYELVVDNRTEKKGKGIAFTTSTADDVGKDEDAEE FT DKLTEDMAMLGRQFNRVMKQVNNKFRGNGRNFRFNTDRQQGNPKYDRGDEK FT NSQYKGVQCHECEGYGHIRTECATFLKKQKNGMIVASDDEGTDGDVDSDAA FT RHVTAMTGRVEPSYDSADEELICEEVILPKCDQEGTNAVSAKFTSGHEATI FT NQLLQERSKHLSKITELNNEVILLKSQLDHVLKQVKMMTTGTEVLDRMLNS FT QIVGKPNGIGFTHEHLKKEHHSNSHSQALEHYQKNRNKKPVKKIMFVTSSS FT KVSVPDKMLEHSVELSISESVKESSTLRCDFCNRPGHKKSFCFDLPGIPKQ FT YQPRSALKKEWIPKCVFWLFPSHDWSELSGKCNLCKKLCYIWGWCDWRLS" FT CDS join(2124..2162,2166..2342,2349..2426,2430..2519, FT 2613..2720,2724..2756,2760..2933,2937..3242, FT 3246..4517,4521..4772) FT /product="SHACOP14_I_MT_1p" FT /translation="MKKLNCGTKNWDMICKGLRRPYLMMQSEGYPSWTSLK FT EVFVENVRLVNRYGCLIQGWNIKVPLRLLNFFILIDKCKWPVLVERGMFWW FT LLMTSQDSLGTSLEKSQILLNLSRNFAFNFKGRRIEALSGHPNRMVWWKGK FT TELYKNLLGSCFMLNIFPTISGLKLIQLVMFTTESLELVLQLLCMNYGRKE FT NLLLNTSTFLEASATFLLIKTTEKRWILRVMKEFFWDIFNNKTVVMESINV FT VIDDGVKEEISEVVPDVEADLETSTQENVVPETEVEPEATSVVAEVDQAEA FT NKGPSIRVQKNHPQDLIIGDPNQGIRTRRSNEVVSNSCFVSKFPKNVKEAL FT TDEFWIEAMQEELNQFKRSEVWELVPRPNDINVIGTKWIYKNKSDENGIIT FT RNKARLVAQGYTQVERLDFDETFAPVARLESIRLLLGVACILKFKLFQMDV FT KSAFLNGYLHEEVFVEQPKGFIDPNFPDHVYKLKKALYGLKQAPRAWYERL FT TEFLINQGYKKGGTDKTLFVKKEHGGVMIAQIYVDDIVFGGMSNQMVQHFV FT QQMQSEFEMSLVGELTYFLGLQIRQMEDTIFISQSKYAKNIVRKFGLDNAS FT HKRTPTATHLKLSKDENGVAVDQSLYRSMIGSLLYLTASRPDITFAVGVCA FT RYQAEPKMSHLAQVKRILKYVNGTTDYGVLYSHSNNSQLIGYCDADWAGSA FT DDRKSTSGGCFFLGNNLVSWFSKKQNSVSLSTAEAEYIAAESSCSQLVWMK FT QMLEEYDVQSVLTLYCDNLSAINISKNPIQHSRTKHIDIRHHFIRDLVEDK FT VVTLEHVATEEQLADIFTKALDVKQFENLRSKLGVCLHKEQ" XX SQ Sequence 5408 BP; 1785 A; 871 C; 1231 G; 1521 T; 0 other; ggcatcagag caggcaccct gcctgttatt gggtgagatc tagaggagtt ctattctggc 60 aatatggaga aagtaggagg attcgttaac agaccacctc tgttatatga aaccaactac 120 gactattgga agtctcgcat gagtgcttac ctaaagtctg ttgacagcaa gacctggaaa 180 gccgtgttga gaggttggga acatcctgtt gttcttgaca aggatgacaa caaaacaacg 240 gatctgaaac cagaagagga atggactgct cctgaagatg aattggctct tgcaaattcg 300 aaggcgttaa atgctctctt taatggggta gacaagaaca tgttccgact catcaaaaag 360 tgtgatgttg ccaaagatgc ttgggacatc ctcaggacaa ctcatgaagg aacttctaag 420 gtaaagagct caagaatcca gctcttaaca accaaatttg aaagtctgaa aatgcaagag 480 gatgagacta ttcaagacta ctacatgaat gttttagaca ttgcaaattc atttgattcc 540 cttggggaaa agctgtcaga tgagaaattg gtaagaaaga ttctcagatc tccaaagaga 600 ttttacatga aggtaacagc cattgaagaa gcacaggagg tatccaatat gcaagtggaa 660 gaactcatag gttctcttca gaactatgag cttgttgttg acaacagaac tgagaagaaa 720 ggaaaaggca ttgctttcac aacaagcaca gctgatgatg ttggaaagga tgaagatgca 780 gaagaagaca agctaacaga agatatggcc atgcttggta gacaattcaa cagagttatg 840 aaacaagtca acaacaaatt cagaggaaat gggcggaact tcagattcaa caccgacagg 900 caacaaggga atccaaaata tgacagaggt gatgaaaaga atagtcagta caaaggagta 960 caatgccatg aatgtgaagg ttatgggcat atcagaactg aatgtgcaac ctttctcaag 1020 aaacaaaaga atgggatgat tgtggcttga tctgatgatg aaggtacaga tggagatgtt 1080 gatagtgatg cggctagaca tgtcactgcc atgactggaa gagtggagcc atcttatgat 1140 tctgctgatg aagagcttat ctgtgaagaa gttattcttc caaaatgtga tcaagaagga 1200 actaatgctg tttctgccaa attcacttca gggcatgaag caactattaa tcaactctta 1260 caagaaagaa gtaagcatct gtccaagatt actgaactga acaatgaggt aattcttctt 1320 aagtcccaac ttgaccatgt tcttaaacaa gttaagatga tgactactgg aactgaagta 1380 ctagatagga tgttaaatag tcaaattgta gggaaaccta atgggatagg attcactcat 1440 gaacacctaa agaaagaaca tcatagcaat agtcattccc aggccctaga acattatcag 1500 aagaatagaa ataaaaaacc tgtgaagaaa ataatgtttg taacctcctc tagtaaagta 1560 tcagtaccag ataagatgtt agaacattca gtagaacttt ctatctctga gtcagtgaaa 1620 gaatcttcca ccttgagatg tgatttctgt aacagaccag gacataaaaa atccttctgt 1680 tttgatttac ctggtatacc taagcaatat caacctaggt ctgctttgaa gaaagaatgg 1740 atacctaagt gtgtattttg atagtggttg ttcccgtcac atgactggag ttgagagctt 1800 tctggaaaat gttagaactt atgcaaaaag ctgtgttaca tttggggatg gtgctaaagg 1860 aaaaattgtt gagattggag acttagttag agaagggtct cctaggctga gtaatgtctt 1920 gttggtaaat ggtctaactg caaatttgat cagcatcagt caattgtgtg atcaagggct 1980 aagtgtaaat ttcagtaaaa ctgaatgtca ggtcttggat ggaaagggaa aattgagcat 2040 gatggggact agatcaaagg acaactgcta cttgtggatg tctcaagaaa aggctcattt 2100 gtcttcttgt ctgataagca aagatgaaga agttaaactg tggcaccaaa aattgggaca 2160 tgtgaatatg caaggggtta agaaggccat atctcatgat gcaatcagag ggttacccaa 2220 gctggacatc actgaaagaa gtatttgtgg agaatgtcag attggtaaac agatacgggt 2280 gtctcatcca aggttggaac atcaaggtac ctctaagact cttgaacttc ttcatattga 2340 tttaatgaga caaatgcaag tggccagtat tggtggaaag aggtatgttc tggtggttgt 2400 tgatgacttc tcaagattca cttgggtgaa cttcattaga gaaaagtcag atacttttga 2460 atctttcaag gaactttgca ttcaacttca aagggagaag aatagaggca ttgtcaggat 2520 aagaagtgat catgggactg agtttgagaa ttccagattc catgaattct gtgcaaagga 2580 aggaatcaga catgagttct catcccctat aacaccccaa cagaatggtg tggtggaaag 2640 gaaaaacaga actctacaag aatctgctag ggtcatgctt catgctaaac atcttcccta 2700 ccatttctgg gctgaagcta tgaatacagc ttgtcatgtt cacaacagag tcactttgag 2760 aactggtact acaactactc tgtatgaact atggaaggaa agaaaactta ctgttaaata 2820 cttccacatt tttggaagca agtgctacat tcttgctgat aaagactaca gaaaaaagat 2880 ggatcctaag agtgatgaag gaatttttct gggatatttt caacaacaaa acttaagtgg 2940 tcatggaatc cattaatgtg gtaattgatg atggtgtcaa agaagaaatc tctgaagttg 3000 ttcctgatgt tgaagctgat cttgaaacat caactcaaga aaatgttgta ccagagactg 3060 aagttgaacc tgaagctact tctgtagttg ctgaggtaga tcaggctgaa gcaaataagg 3120 gaccctcaat ccgagtacag aaaaatcatc ctcaagatct gattattgga gatccaaatc 3180 aaggaatcag aacaagaaga tctaatgaag ttgtttccaa ctcctgtttt gtttccaagt 3240 tttaacctaa gaatgtaaaa gaagctctca ctgatgaatt ctggattgaa gccatgcaag 3300 aagagctcaa tcagttcaag aggagtgaag tatgggaatt ggtgcctagg ccaaatgaca 3360 taaatgtcat tggcacaaaa tggatatata agaacaagtc tgatgagaat gggatcatca 3420 caagaaacaa ggcaagactg gtggcccaag gttatacaca ggtggaacgg ctagactttg 3480 atgaaacatt tgctcctgtt gccaggttgg aatccataag actgcttttg ggggtagctt 3540 gtattctgaa attcaagctt tttcagatgg atgttaaaag tgccttccta aatggctatc 3600 tgcatgaaga agtgtttgtt gaacaaccta aaggtttcat tgatccaaac tttccagatc 3660 atgtctacaa actcaagaag gccttatatg gtttaaaaca agctcccaga gcttggtatg 3720 agagactcac agaatttctg atcaatcaag gatacaagaa aggtggtaca gacaagacct 3780 tgtttgttaa gaaggaacat ggaggagtca tgatagcaca aatatatgtt gatgatattg 3840 tgtttggagg aatgtcgaac caaatggttc aacattttgt tcaacaaatg caatctgaat 3900 ttgaaatgag tctggtagga gaattgacct attttcttgg cttacagata agacagatgg 3960 aggacactat tttcatctct caaagcaagt atgctaagaa tattgtgagg aaatttggac 4020 tggataatgc cagtcataaa agaactccaa cagccactca tctaaagctg tcaaaggatg 4080 aaaatggcgt agctgttgat caaagtctat acaggagtat gataggaagt ctactttatc 4140 ttacagcaag cagacctgat ataacttttg ctgtgggagt ttgtgcaaga tatcaagcag 4200 agcccaaaat gagccatctg gctcaagtca aaagaattct gaaatatgtc aatggcacca 4260 cagactatgg tgttctgtat tctcatagta acaactctca attgattggt tattgtgatg 4320 cagattgggc aggtagtgca gatgacagaa aaagcacatc aggaggatgt ttctttcttg 4380 gaaacaatct ggtgtcctgg tttagcaaga agcaaaactc tgtgtctctc tcaacagcag 4440 aagctgaata tattgctgca gaaagtagct gttctcagtt ggtgtggatg aagcaaatgt 4500 tggaagaata tgatgtataa caaagtgttc taacattgta ctgtgataat cttagtgcaa 4560 tcaacatctc caaaaatcct attcagcaca gcagaacaaa gcatattgac atccgacatc 4620 acttcatcag ggatctggtt gaagataagg ttgtaactct agagcatgta gccactgaag 4680 aacaattggc tgacattttc accaaagctt tagatgtcaa acaatttgag aatctaagga 4740 gcaagttggg tgtttgcttg cataaggagc agtaagtggt tcactactgg gttactgggt 4800 atggcatatt ttctagctaa aaagggggag taataaagtg gtcataccta tgtaatatcc 4860 agctgtaagg acagatgcca gcagaagcta caaaccttgg atgcacatgt tcagggggag 4920 taaggctatt taagtaatca ctcaatgatt atttaattga gggggagtga ttatgttctg 4980 cagttgctgt gtatgaaaat ttattttttc cattatgtgt ggatgctttt acgaatgtct 5040 gaacatcagt atattctgca tgttctatca ggaaattatt tttcctgtat atccgctgct 5100 gcaattctct ggttttctat ttggtatctt attctctcat ctactggatt catatggtgt 5160 tttgtttttg aaaaattatg agagtagatt cagagatcat aatataattc tgaagtcttg 5220 aagattgtga tgtgattgaa gttttatatg tatggtacct cttagttttc caagagctgt 5280 gtattttctt catggatgtt ttatttgtgt ttttgatgat tgaagaaaat tgtgcatgtg 5340 cttatctctc cggtttgatt agattggcat gaagttgttt tagccaaaaa tttgccaaag 5400 ggggagat 5408 // ID Gypsy22-PTR_LTR repbase; DNA; EDCOT; 155 BP. XX AC LG_V; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy22-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-155 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-155 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 325-325 (2007). XX DR Genome; LG_V; Positions 5838983 5839137. XX SQ Sequence 155 BP; 49 A; 23 C; 27 G; 56 T; 0 other; tgctgaaagt tgttatggtt tagttattta tatgtatgaa gaagaataaa aaggatagca 60 ttatttttat ccaaacaata ttgtggtaac ttctcaccct aagagaatcc tagcatttct 120 gcaattgtgt atcactcttg actgggacct tatca 155 // ID Copia-49_Mad-I repbase; DNA; EDCOT; 4382 BP. XX AC ACYM01035317; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-49_Mad-I; KW Copia-49_Mad-LTR; Copia-49_Mad_. XX NM Copia-49_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4382 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1319-1319 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01035317; Positions 3338 7719. XX CC Positions [1796-2152] - Integrase core CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS 332..2260 FT /product="Copia-49_Mad-I_1p" FT /translation="MSLLLNTMEKHVAEIFSYSNSAHDLWKALQDMYGNQN FT NYARVFQLKKDIASAQQEGKAFVQHLGSLKAMWNELDVYLPHTTDPTILLK FT RAEEDKIYQLLGSLSSEYEDLRSHILMSQDLPTFNNVCATIQREEARKKVM FT NVDHNPRLTETRAYASKYKNSEAKVYKGRNTHLKCKYCNGVGHEEDKCWEL FT HPELKPKFSKDGRMIPRSSQQFQPHFKAQLANAHAPTISQGSMEFTANPLS FT LINEFAAYLQSKGHGGGSHGQGNEEGSHTAMLGQFAGFLAGNEKVPKGEAS FT GILKAFTTALLTSTEIDCWIIDSGATDHMTNKVTNLHHFKKISSPSHVSVA FT NGKNVLVLGKGEINLLSQKTPSTALYVPTFPFQLLSIGKITNTLNCRAIFS FT PNKVMFQDVLTMKMIGEGVFINGLYYLCKNACFTQALQAQSKSIDENQLWH FT RRLAHPSELVLSKLFPNFCNPYPTCDTCQFSKFTRLPLGNSMSRTSKPFEM FT IHTDVWGPATESMEGFKYFVLFVDDFSRTSFLYLMKSKSEVPTIFKDFHMH FT VKTQFQSNIKVLRSDNGTEFLSNNMLQYISSQGIIHQTSCVGTPQQNGVAE FT RKNRDLLEKNSCSHDSHARSKEILVVCHPYCHLSHQSTSKSCARV" XX SQ Sequence 4382 BP; 1337 A; 913 C; 895 G; 1214 T; 23 other; gagcaggttc atttgtaacc tgtctctgcc attcttgctg ctgcaatttt ttctttcttt 60 caaagtctaa gtcatgactg aagaaagttc tgtgaatcat gatgaggaaa cccggcacaa 120 tctctctcta aacttctcag acgttgaggt taacaycaat caacgtttgt gttcagttct 180 cttgaacgag ttcaattatc ttccttggtc ccgagctgtt tcactagctc tcggaggcaa 240 agggaagtta gggtttgtaa atggaagcgt ggaagctcca gacagttctt cctctacata 300 caatgcatgg ctctgcaaag atcaacttgt catgtccttg ctgctcaaca ccatggagaa 360 acatgttgct gaaattttta gctactccaa ttccgcacat gatctttgga aagctttgca 420 ggatatgtat ggaaatcaaa acaactatgc acgggtcttc caattaaaga aggacattgc 480 cagtgctcaa caagaaggga aagcatttgt tcaacacctt gggagcctca aagccatgtg 540 gaatgagttg gatgtatatc tccctcatac cacagatcct accattctcc taaaacgagc 600 tgaggaagac aaaatttatc agctgttagg gagtttgagc tctgagtayg aggacctaag 660 gagtcacatc ttgatgagtc aagacctgcc taccttcaac aatgtttgtg caactatcca 720 acgagaagaa gcaaggaaga aggttatgaa tgttgatcac aatcctagat taacagagac 780 tcgggcatat gcatcaaagt acaagaactc agaagccaag gtatacaagg gaagaaacac 840 acatctaaaa tgcaaatatt gcaatggtgt tggtcatgag gaagacaagt gttgggaact 900 ccatcctgaa ctcaagccta agttcagcaa agatggaagg atgataccaa ggtcctcaca 960 acaatttcaa cctcatttca aggcacaact tgctaatgct cacgctccta ctatctcaca 1020 aggatccatg gagttcactg ccaatccatt gtcattgatc aatgaatttg cagcttacct 1080 acaaagtaag gggcacggag gaggctcaca tggtcaaggc aatgaagagg gtagtcacac 1140 agctatgttg ggacaatttg ccggatttct tgctggaaat gagaaagttc caaagggaga 1200 agcatcaggt atactcaaag cctttactac tgccctatta actagtactg aaattgattg 1260 ttggataatt gattcaggcg ccacagatca tatgacaaac aaagttacaa atttacatca 1320 ttttaaaaaa atttcaagcc cctcacatgt gtctgttgca aatggaaaaa atgtcttagt 1380 tttgggaaaa ggagaaataa acttactctc tcaaaaaaca ccttccactg ccctctatgt 1440 accaaccttt cccttccaac ttttgtcaat tggaaagatc accaacacct taaactgccg 1500 tgctattttc tcaccaaata aagtaatgtt tcaggatgtt ctcaccatga agatgattgg 1560 tgaaggggtc ttcataaatg gactttacta cctgtgcaag aatgcatgtt tcactcaggc 1620 tcttcaagct caatcgaagt ccatagatga aaaccaactt tggcatagga gattagctca 1680 cccttctgaa cttgtcttgt caaaactgtt tccaaatttt tgtaacccct atcctacttg 1740 tgatacttgt caattttcta agtttactag gctacctttg ggtaattcaa tgtctaggac 1800 aagtaaacct tttgaaatga tacacactga tgtatgggga cctgcaactg aatcaatgga 1860 aggttttaaa tattttgttc tatttgttga tgatttctct cgaacaagtt ttctatatct 1920 tatgaaatca aaaagtgaag tccctaccat tttcaaagac tttcacatgc atgttaaaac 1980 rcaatttcaa tcaaacatta aggttttaag gtcagataat ggcactgaat ttctatccaa 2040 caacatgctt caatacataa gttctcaggg tatcatacat caaaccagct gtgtggggac 2100 tccccaacaa aatggagtag ccgagaggaa aaatagagat ctcttggaaa aaaactcgtg 2160 ctctcatgat tcacatgcac gttccaaaga aattttggtc gtttgccatc cttactgcca 2220 cttatctcat caatcgactt ccaagtcgtg tgctagggtt taaatctccc tatgaagttc 2280 tcaaggggag gaaaatagat ttgacacatc tcaaggtgtt tggttgtgtg tgttttgttc 2340 acatccaaac cttgaaccgt gacaaactag atgccagggc aaccaagtgt gtgtttatgg 2400 gatactcrac cactcaaaag ggatacaagt gmttcaatcc agtcactaag aagtgcacag 2460 tttcaagaga tgtgaagttc gaagaagact atccctattt tacaagtcag ggggaggatt 2520 tagttgacat gttcccactc cctcaaaact ttaattatcc gatgttggaa aagagatcag 2580 tcattgtaag tccagattgt gaagaagttc aaactgacca aattactgcc agtgagagtg 2640 aagacgagcy ctactctgat ycttctccgc cctctacaga rtctcaggtg attaaaagaa 2700 awcctcctcg aatcagaaaa cctccagcta ggttgcagga ctatgttaca tatgcctcac 2760 gacatccaat caatgaatgt atcagcttta gtaagttctc aacatctcat gctrcatttc 2820 tcagtgaaat tgataagcac tatgaaccaa gaagctttca agaagcktct cttctcccac 2880 aatggaacca agccatgaaa gaagagattc gtgcactgga agagaattgy acctggagyc 2940 tagttcaact accacyagga aaaaaggctg ttggaagtcg ttggatttac aagactaaat 3000 tcaaagytga tggatctatc gagagacaca aggctagact tgttgctcga ggtttcaccc 3060 aaacctttgg tgtagattat aaggaaacat tcgcaccggt ggccaagatg aactcagtca 3120 gggttttact gtcagttgya atcaattgtg gatggtcact ctaccaaatg gacgtgaaka 3180 atgctttcct tcacggcgag ctgcaggaag aagtgtatat gcaacctcct ccaggctatg 3240 atggtattaa aggcaacatg gtttgtaaat tgcacaaggc aatatacgga ttgaaacaat 3300 caccaagagc ttggtatgcc aagctcagtt ctgttctgga aaaggctgga ttcatgcgaa 3360 gtaatgctga ttcttcgtta tttgtaagaa ctggcaycag ggggaagttg gtggtcctcg 3420 tctatgttra tgatcttatc atcactggag ataataccgt ggagattgag gcactaaaac 3480 tctcactaca tcaagctttc gctatcaaag atttggggag gttaaartat tttttgggga 3540 tcgaaatggc aacatcttca aaaggactgt ttctacatca acgraaatat gtattggacc 3600 tccttcaaga agcaaaatgc ttgactgcaa gcctgctatc actcccgttg attgtaaact 3660 raagctcagc atagatggag aagccatgca tgatgtaagc tactatcaac gattagtagg 3720 caagctcata tacctcacta tcactcgtcc agatatcaca tatgcagtga gcttggctag 3780 tcagttcatg cactctccca ctgttgatca ccttaacytt gttaagagaa tccttcgtta 3840 tcttaagggt tcaattgggc aaggaattac aatgcataac aatcaatcca ctgtcattag 3900 tggctacaca gatgcagact gggcaggtaa tgcaattgat aggaaatcaa tcacaggcta 3960 ttgtacattt gttggtggaa atcttgtcac atggaagagt aagaagcaac aggtaattgc 4020 tcgttccagc gcagaggctg agtatcgagc catggcagcc actgcatgtg aactcatttg 4080 gcttaaaggg cttctttcag acttagggtt tcctagttct actcctatga tgcttatgtg 4140 tgataatcag gcagccatgc acattgctgc caatcctgtg ttccatgaaa gaaccaaaca 4200 tattgaagtg gattgtcatt tcatcagagc tcaagttcaa acgcaaatca tccggaccat 4260 gttcacacga agccatgatc aactagcaga tctttttaca aaggcactag catcatctca 4320 gtttcatcgg ttattgggca agcttggctc agtgaatccc ctcgatccag cttgaggggg 4380 ag 4382 // ID Copia14-PTR_I repbase; DNA; EDCOT; 4099 BP. XX AC LG_XI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia14-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4099 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4099 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 200-200 (2007). XX DR Genome; LG_XI; Positions 12518071 12522169. XX CC Positions [1688-2215] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 905..4099 FT /product="Copia14-PTR_I_1p" FT /translation="MRGKEKKEHFPACKYCQKTNHLEAWCWLKNAQCRNCK FT QFGHIQRFCKNKTEAEQQAQVADCSEVKEDLLFMVTIQDMCNSAEPKDSSW FT LIDSGCTNHMTADLSLFKDLDKSYLSKVRIGNGDFMKVEGKGAIAVETLSG FT TKILKNVLYVPKINQNLVSVGQLIESGYSIVFNDGVCDIKDKNGVLLLSAK FT MMNRSFNVNWKEVCLSANTYENNESVLWHKRLGHFNYTTLKRMADQQMTHG FT LPDIQEQQIICEACQLGKQTRTVFPDNAYRAVSKLQLVHTDVCGPMHNESL FT NGSKYFLLFIDDFSRYCWVYFLKSKADVFAEFVKFKAAVELETGNKLKILR FT SDNGGEYTSRQFEAYLAKEGIKHQLTIPYTPQQNGVSERRNRTLMEMARCL FT LYEKKLPLNFWAEAVNTASYLINRMASRVLTDKTPYELWYGFKPSIDHLKV FT FGSICYVMKPEVGRRKLDQKADIGIFIGYSTTSKAYKIYDLNFNKVVVARN FT VKVVENATWDWKNSSGEGSKQIQQTEWDAAENIDDQPVKGTRSLSDIYSRC FT NVAEAEPVDVEEAMNSQVWIAAMKEELAMIDKNQTWMLVDRPTHKKVIGVK FT WIFKTKLNADGKINKHKARLVVKGYSQEAGIDFTETFAPVSRHETMKLLLA FT LAAQNGWYIFQLDVKSAFLNGVLNEEIYVEQPAGFEKSNSTNKVYLLKKAL FT YGLKQAPRAWYSRLDNHLLSLGFNRSMNEVTLYVKHADGHKLIVSVYVDDL FT LITGDKEQLVEEFKTNMKDMFEMNELGLLTYFLGMEVTKSDQGYFLCQKRF FT SLKILDNFAMSKCKPVSTPMIQGQKLMKEDGSPKADGKVYRSLIGSLLYLT FT ATRPDIQFAVNYLSRFMQEPSQNHFVAAKRVLRYLRGTAGFGIHFVKSSSI FT NLVGFSDSDWGGSDEGMMSTSGYCFAVGKSVFCWNSKKQSVVAHSTAEAEY FT IAAYVAAKQLIWLRKMLSDLDCNQQNPTTLFCDNTSAIAISKNSVFHDRTK FT HMKIKYHAIRQFQQEGELELCYCTSEDQLADFFTKPLAKTRFEDLRARIGM FT TSFGTKEE" XX SQ Sequence 4099 BP; 1432 A; 624 C; 920 G; 1123 T; 0 other; attggtatca gagcatcctt aggatctttg aagggctttc ttgtgagtga gaaacatgag 60 agtacagaga ggataaatca aagtttttac tttgagggtt ggtgagtgaa aaacacgaga 120 gaataaagtg agtttttttt taatggattc tgcaagtttt tcaccaaaaa caccattgtt 180 tacgggacag aattttggtg tgtgggctgt aaaaatggaa acctatctca aagctcttga 240 tttatgggag atagtggaaa gtgataggca acctactcct ttaggtaaca atcccacaat 300 tgcacagatg aagttcttta atgaagaaaa ggcaaagaga ttcaaagctc tttcttgtct 360 tcatagtgct gtaagtgaag acatcttcac aaggatcatg gcatgcaaat ctgccaagga 420 aacatgggat aaattaaaag cagagttcca tggtgatgag aagtcaagaa ggatgcagat 480 tctgaatctg agaagacaat tcgaaggtct gaagatgaaa gaaaatgaga gcatcaaaga 540 tttctcttct caaatttcaa aacttgtgaa tcaagtaaga cttttgggag aagattttcc 600 agactctaga attgtagaga aagtcctggt gagtctgcca gaaaattttg aacataaaat 660 ctgttcttta gaagattcta aagatttttc tgaaatgagc ttgtaagaac tggtaaatgc 720 attgcaagct gtggagcaaa ggcaagcata tagacaagaa ggatcaagtg aaggagctct 780 agtagcagtt tacaaggata agagtcgggc taagaacatt ttcagaaata atcaagaagg 840 aaaaagagaa aaagggagaa gctggaaatc tgctaactgg caacagaaca tcaataacag 900 cttcatgagg gggaaagaga agaaagagca ttttcctgct tgcaaatact gtcagaaaac 960 taatcatctt gaagcatggt gttggctcaa gaatgctcaa tgccgaaact gcaagcaatt 1020 tgggcacatc caaagatttt gcaaaaataa aacagaagct gaacaacaag ctcaagtagc 1080 cgattgttca gaagtcaaag aagatctttt attcatggtc acaattcagg acatgtgtaa 1140 ttcagcagag ccaaaggact catcatggct cattgatagc ggctgcacta accatatgac 1200 agcagactta agcttattca aagacttgga taaaagctac ctatctaaag tcagaattgg 1260 caatggagac tttatgaagg ttgaaggaaa aggagcaatt gcagtagaaa cactgtcagg 1320 tacaaaaatt cttaaaaatg ttctttatgt gcctaagatt aaccaaaatc tagttagtgt 1380 gggtcaattg attgaatctg gctattcaat agtctttaat gatggagtgt gtgacattaa 1440 agataaaaat ggagtacttt tactttctgc aaaaatgatg aaccgaagct ttaatgttaa 1500 ctggaaggaa gtatgtttga gtgccaatac ctatgagaac aatgaatctg ttctttggca 1560 caaaaggttg ggacacttca actatacaac tctaaaaaga atggctgacc agcagatgac 1620 tcacgggtta ccagatattc aagaacagca aattatttgt gaagcttgtc agctgggaaa 1680 acaaaccaga actgtgtttc ctgacaatgc atatagggca gtgtcaaaac tccagcttgt 1740 acacacagat gtgtgtggac ctatgcacaa tgaatcatta aatggttcaa agtattttct 1800 tctatttatt gatgatttta gtaggtactg ctgggtttac tttctaaaat ccaaagctga 1860 tgtgtttgct gagtttgtta agttcaaggc agcagttgaa ctagaaacag gaaacaaatt 1920 gaagatattg agatctgaca atggaggaga gtatacctct cgacaatttg aagcatacct 1980 tgctaaagaa gggattaaac accagctgac tattccctac acaccacagc agaatggtgt 2040 aagtgaaaga agaaaccgaa cattgatgga gatggcaaga tgtttgctat atgagaagaa 2100 gctgccattg aatttctggg cagaagcagt aaacacagca tcatatctta taaaccgaat 2160 ggcttcaaga gttttaacag ataaaactcc ttatgaactc tggtatggtt ttaaacctag 2220 tattgatcat ttaaaggtgt ttggtagtat ttgttatgtt atgaaacctg aagttggaag 2280 aagaaaactt gatcaaaagg ctgatatagg gatctttata ggctatagta caacatctaa 2340 ggcttataaa atttatgatc tgaattttaa caaagttgtg gttgctagaa atgtcaaagt 2400 tgtagaaaat gctacttggg attggaaaaa ttcatcaggt gaaggatcaa aacagataca 2460 acaaactgag tgggatgctg cagagaatat tgatgatcaa ccagtaaagg gaacaagatc 2520 tctatcagat atctatagca ggtgcaatgt agctgaggca gaacctgtag atgttgaaga 2580 agctatgaat tctcaagttt ggatagcagc aatgaaggag gagcttgcaa tgatagacaa 2640 aaatcaaaca tggatgctag ttgacagacc aactcataag aaggtaattg gagtgaaatg 2700 gattttcaaa acgaaattaa atgcagatgg taagatcaac aagcataaag ccagacttgt 2760 agtgaaagga tattcacaag aggcagggat cgacttcaca gaaacttttg ctccagtttc 2820 cagacatgaa acaatgaagc tcctgcttgc tctagcagca caaaacggtt ggtatatatt 2880 tcaattggat gttaaatctg catttttgaa tggtgtgcta aatgaagaga tttatgttga 2940 gcaacctgct ggttttgaaa aatcaaattc aacaaacaaa gtttatttac tgaagaaggc 3000 attgtatgga ttgaaacaag ctcctagagc ttggtatagc aggttggata atcatctttt 3060 aagcctggga tttaacagga gcatgaatga ggtaacttta tatgtgaagc atgctgatgg 3120 acataaactc attgtatcag tttatgttga tgatttacta atcacagggg acaaggagca 3180 gcttgtagag gaattcaaaa ccaatatgaa agacatgttt gagatgaatg aacttggttt 3240 gttgacatat tttttaggaa tggaagtaac taagtctgat caaggttact ttctttgtca 3300 aaaacgtttt tccttgaaaa tactggacaa ttttgcaatg agcaaatgca agccagtaag 3360 cacacctatg atacaggggc agaagctaat gaaagaagat ggatctccaa aagctgatgg 3420 gaaagtttat aggagtctaa ttgggagttt gctatattta acagccacac gtcctgacat 3480 tcaatttgct gtgaattatc tttccaggtt catgcaagag ccaagtcaaa accactttgt 3540 ggcagctaag agagtattaa gatatttgag agggactgca ggttttggca tacattttgt 3600 gaagtccagc tcaatcaatc ttgttggatt ttcagacagt gactggggag gaagtgatga 3660 aggaatgatg agtacttcag gctactgttt tgctgtggga aagagtgtgt tttgctggaa 3720 ttcaaagaaa caatcggtgg tggctcattc tacagcagag gctgaatata tagctgctta 3780 tgtagcagca aaacaactta tatggctgag gaagatgcta agtgacttag attgcaatca 3840 acaaaatccc acaacattgt tttgtgacaa cacatcagct atagccattt ctaaaaattc 3900 tgtttttcat gatagaacca agcacatgaa aatcaaatat catgcaatca ggcagtttca 3960 gcaagaagga gaactggaac tatgctactg cacttctgaa gatcaactag cagatttttt 4020 caccaaaccg ttggctaaaa ccaggtttga agatctgagg gcaagaattg gaatgactag 4080 ctttggaacc aaggaggag 4099 // ID Copia-23_Mad-I repbase; DNA; EDCOT; 5336 BP. XX AC ACYM01124502; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-23_Mad-I; KW Copia-23_Mad-LTR; Copia-23_Mad_. XX NM Copia-23_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5336 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1297-1297 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01124502; Positions 10927 5592. XX CC Positions [2259-2786] - Integrase core CC 'CTGAA' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 2856..4436 FT /product="Copia-23_Mad-I_2p" FT /translation="MSCRFIGYSEKSKGFKFYCHHGPSRIMETHNAKFVEE FT PEELSALAITSQLVEFKELRNDDTILLDQQEITLGFRISPPQMLSTPPETQ FT NEAPISFTEEGTSNNAAETNDTNEEIYEQPMNITTAGNKSPLEVPAAENVR FT RSQRARKTVMLPDFVYLNEAEYSLGDEDNPATYHQAITSIRAPLWHQAMTE FT KIDSMNTNQVWSLVPKPAGLTKTVGCKWVFKTKRDSQGNVEKHKARLVAKG FT FTQREGINYNETFSLVSTKDSMRVILTLTAHFDLELHQMDVKTAFLNRDLE FT EDICMHQPPGFVERGKESMIYKLNKSIYGLKQAFRQWNKKFDQVMAAFGFH FT ENKMDECVYLKIIGSKVVFLVLYVDDILIASSDITLLQSTKQMLSNSFDMK FT DLGEAKFVLGIEIVRDRSKKALGLSQRLYIDRITKRFNMENCSSGELSIGK FT GNKFSNDQSPKNDLEKDSMKAKPYASLMGSLMYAQLCTRLDLAFTVSVLGR FT FQSNLGAAYWTAAKKVLRYLKKTRDYMLVYS" XX SQ Sequence 5336 BP; 1779 A; 860 C; 1090 G; 1607 T; 0 other; tgtggtatca gagccactca acatggctag ggttcatact agaacttact ctattgaata 60 ttaactttaa ggtcttgatc gttccgctgc aaacttttcg tcatatccga taaaagtttc 120 aaatttctta tcaatgtcga tgcatgcata cattcattaa aacttggtta tatacatgtg 180 tgtgtgtata tatatatata tatatctata tatacatttt atatcagaat gatgtgtttg 240 ttcaagtttt accaggaaaa gattctctaa caatgacaaa tatgactact cgaagaaact 300 aaagaaaaag tgcaagatta tagggttcat gttatcaaaa tgataacatg tgaacaacta 360 aaacaagaaa acaataccta ttctgctcaa aagtgtttag tttattgttt tgacttgtga 420 atcaaatata tggagatagt gactcattta agaatgattg aataataatt tgctcaaaag 480 tgtttattat tcaaatcaat tagatgattc aatgtatact ggaactgtga gattgacaag 540 attacattat tcatctgctc aaaagtgttg aaaaacatgt aaattgacct tgtatcttat 600 cttccaacta tacaaaatta atatgaacaa catctgtcca aagatgttgc tgtgttctta 660 tgcttattgt tgaaatgaga aaatagtaag taaaaatttt ctcgctaaat gttaagatgc 720 tgagtgagat ttctaataca aagaattttt cgtttatgtc catcaacagc tccgcatatg 780 acctctctta acttcagcaa cattgaaact cttattggtt ccaacttcaa gaagtggaag 840 gaggatgttg agatagtttt gggactgatg gatctcgacc tagcgttaag agaagacaaa 900 cctgcaacct tgactgataa aagcacaact gaggagaaac tgaactttga caagtgggag 960 aggcctaata gaatgtcact gatgattatg aagaaaacca tgacacaacc tgtcaaatga 1020 gggattccaa aacttgacaa tgccaaggcg tttctagcta ctgttggaga aaagtttatg 1080 gaatcagaaa aggctgagac aggtacactt ctcacacagc ttacctctat gaaatttgat 1140 ggcactggga gtgtgagaga acacattctt agaatggttg atctttcctt gaagctgaaa 1200 gacttagagg tacctgtgac tgatcaattt ttggtacata tggctctaaa ctcattacct 1260 gctaagtatg gtcagcttaa ggtgtcgtac aatacgcaaa aagacaagtg ggggataaat 1320 gagttgattt caatgtgtgt tcaagaggag gatcgactta aaactgacaa gactggtgaa 1380 gtaaatctgg tgcaaatgga gaaaggatcc aaactcctca gtgctggttc atcgttttct 1440 gttggtaaga agaagaagaa tataatttct tattctttta aaaatgctaa cacctctaaa 1500 ggctctttca aatttaaacc catgaacact gaaatagaaa agacaaatga gtgctatttt 1560 tgcaaagaat caggttattt gagaaagaac tgcattggtt tcaaaaactg gcttacaaag 1620 aaagggaaaa taacaaatgt ttttgtctgt gttaagtcca atttgattta tattcctcct 1680 aaaagttggt ggtttgatac tggatgttcc attgacataa ctaactcctt ggaaggcttc 1740 tcgaaaacaa aggaagtaaa caatgaagtc tacaatgtct atgttgggaa tgggagtaaa 1800 gttgttgtcg agcctattgg cagtgttaaa ttagtcatgt catcaggttt tattttagag 1860 ttgaatctag tgctttatgt accttcaatg agaagaagtt taatttctgc atccaaatta 1920 gttcagttag gcatttcttt tgttggggat gataaaggtt tttcgaatca aataatatga 1980 attccttgct tggtatcgct tatttacaaa ctgatatgtg gcaaatggaa tgttcatatg 2040 tccatgaatg ttttcacgtt caaggtattg gttctaaaag gttgctcact ttagaaaaat 2100 cctctatgct ttggcacaag aggttagggc acatttcgaa agaaagaatt atcaccttat 2160 gcaaacaaaa cttgttacct caattggatt ttaatgattt tcaaacatgc acagattgtt 2220 ttaaaggaaa actcaccaac acaagaaaat tgggttcaac ttgcagtcaa catctacttg 2280 aaatcattca tactgacatt tgtggacctt tcccaaacaa aaccatatgt ggaaagtcct 2340 atttcatcac tttcattgat gacttttcac attttgcctt tgtttactta atttctgaaa 2400 aatctgaagc tttagattgt tttaagattt ttaggttaga ggttgaaaaa caattggaaa 2460 aacatattaa aatagtaaga tctaatagag gtggtgagta ttttggcagg tatactgaag 2520 ctggacagca caaaggccat tttgctacat accttcaaga caatggcata gttgctcaat 2580 acaccactcc agggactcca caacaaaacg gggtggcaga aaggaggaac aggacttcaa 2640 aagacatgat tcggtcaatg tttgcacagg caaagctacc tatattccta tgggggaaag 2700 ctttgaaaac tgccaactac atcatcaaca taattccaag caagtcagtg acagtagtgc 2760 cttttgaagc ctggactgga agaagaccaa gttttaatca ctttcacagt agtgcctttt 2820 gaagcctgga ctggaaaaag cttgatccac gaacaatgag ttgcaggttt attggttatt 2880 cagaaaagtc aaaggggttt aaattttact gtcatcatgg tccatctcga ataatggaaa 2940 ctcacaatgc aaagtttgta gaagaacctg aggagttaag tgcgcttgcc attacttcac 3000 agttggttga gtttaaggaa ctgagaaatg atgacactat cttgcttgat caacaagaaa 3060 taacattagg gtttaggatt tccccaccac agatgttatc tactccacct gaaacacaaa 3120 atgaagcacc aatctcattc acggaagagg gaacttcaaa taatgctgct gaaactaacg 3180 acacaaatga agagatttat gagcagccaa tgaatatcac tactgcagga aataaatcac 3240 cacttgaagt accagctgct gaaaatgtta gaagatccca aagagctagg aaaacagtta 3300 tgcttccaga ttttgtctac ttaaatgaag cagaatatag tctcggcgat gaagataatc 3360 ctgcaacgta tcaccaagcc attactagca taagggcacc actttggcac caagcaatga 3420 ctgaaaagat tgactcaatg aacacaaacc aagtttggag ccttgtacct aaacctgcag 3480 gtctcacaaa gacagtaggt tgtaaatggg tctttaagac caaaagagac tcccagggca 3540 atgttgagaa acataaggca agattagtgg ccaaaggttt cactcaaaga gaagggatca 3600 attacaatga aaccttctcc ctcgtgtcca caaaggattc tatgcgagtg atcctaaccc 3660 taaccgctca ttttgaccta gaacttcacc aaatggatgt taagactgca tttctcaatc 3720 gcgatcttga agaagacatt tgtatgcacc agccaccagg atttgttgaa agagggaagg 3780 aatcaatgat ctataaactg aacaaatcca tttatggatt gaaacaagcc tttcggcaat 3840 ggaacaagaa gtttgatcaa gttatggctg catttggctt tcatgaaaac aagatggatg 3900 agtgtgtgta tctaaagata attggttcta aagtggtgtt tttagtacta tacgttgatg 3960 atatcttgat tgctagttca gatataactc ttctacaatc aaccaaacaa atgttatcta 4020 atagctttga catgaaagat ttgggagaag ccaaatttgt tttaggaatc gagattgtta 4080 gagacagaag caagaaagct cttggccttt ctcaacgatt gtacattgat agaataacca 4140 agagatttaa tatggaaaat tgctccagtg gtgaattatc gattggaaag ggaaacaagt 4200 tcagcaatga tcaaagtccg aagaacgatt tagaaaaaga tagcatgaaa gccaaacctt 4260 atgcatcact tatgggcagt ttgatgtatg ctcaactatg cacgagactg gacttagcat 4320 ttacagtgag tgtactagga agatttcaat caaatcttgg ggcagcttat tggactgcag 4380 ccaagaaagt gttgcgatat ttgaaaaaga ccagagatta tatgcttgtc tacagttagg 4440 ttgacgagtt ggaattagtg gcatacacat attcaaattt tgcagggtgt gtagatgata 4500 gaaggtccac caatggatac ttattcttac ttgctggtgg tgcgattttg tggaaaagtg 4560 ccaagcaaaa gtcaattgca tcatcgacaa tggaagctga attcattggt tgttacacag 4620 caaccaagca agcagtgtgg ttgagaaata tgataaaagg gttgcaagtt gtggacagaa 4680 ttgacagacc attgaagtta ttttgtgata ataaggcagc tgtgttattc tcgaagaaca 4740 acaagaggtc attggcaaat agattgatgg acacgaaata cttaaaggtg agggatgaag 4800 ttaagaaagg gactattgat attcaacata taggcacgac ttttatggtg gcagatccca 4860 tgactaaagc tttatcagtg ggagtgttca aaagccatgt tttcaatatg ggtgttaaag 4920 agacttttga attaattaat gagtgggagt aaacactcga ttaactgtga taatcatgtt 4980 tgaatatggt tggttttgtc agtactctca ttattttgat tcaatcagca gctagtatga 5040 tttgaagttt tcattcatat tttatcttaa cagctaatgt gcttatattg tgaatcattg 5100 ttttggttaa tgattcttgt tatcatgact ttgctggtga tattgtactt caagttaaat 5160 gtgtctgtaa gcatggaatg caaagtacag accgacttgt tatttgcttt ccttggttcg 5220 acattcaact tttagtgtca cgttgtcaag aaaggttggt tgcaaatttt gaaggctcag 5280 tgatcaccgt gagtccttgt gagtggggat ttctcattga cattcaagtg ggagaa 5336 // ID COP16_LTR_MT repbase; DNA; EDCOT; 562 BP. XX AC . XX DT 08-JAN-2007 (Rel. 12.01, Created) DT 08-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE The LTR sequence of COP16_MT LTR retroposon from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; COP16_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-562 RA Shankar R. and Jurka J.; RT "COP16_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 12-12 (2007). XX DR [1] (Consensus) XX SQ Sequence 562 BP; 155 A; 105 C; 118 G; 184 T; 0 other; tgttggaaca ctagtgtata atggaaaaaa acttggagta tactagtgag tttgtggagc 60 ctttggaatg taaacacaag gatggaaaaa ttagtgtaaa gtgtgaattg aaaattctat 120 gtcccacatc gggtagatca cactctagta gaaattctcc ttataaattg agagctcggg 180 aatagtattc ttcactccaa aactgagaat cgaatactct tctctggttt tctcttctct 240 cttccgcggt ttgtgttgac gaaccgttct ttctttcctc attctttggt ttatcgagtg 300 gtctacatac catattagag tggttttttg aaacttttcg aaaaccatat tgaggtgtta 360 ttctcgagcg atttctggca gtgcagcctt taatcgtaca gttagaatct gggctgtttt 420 atcctggaga cggcgcggtt gctagtctac cttgcacaac ttaggtagtg ccgtgaaacg 480 tcttaaagaa agcgacctga tcgtgactca cccggtaata gtttcaaagc tctgtcgtaa 540 ttttcaaatt acaaaaacaa ca 562 // ID HAT-2N1_Mad repbase; DNA; EDCOT; 1092 BP. XX AC . XX DT 22-OCT-2010 (Rel. 15.11, Created) DT 22-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-2N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1092 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1899-1899 (2010). XX DR [2] (Consensus) XX CC TIR is 12-bp long. XX SQ Sequence 1092 BP; 323 A; 211 C; 167 G; 391 T; 0 other; cagtggcgaa gctacatagg ggcgaggggt ggccgttgcc cctccgctcg ccggaaaaca 60 agcccaggag cgcctctttg gttcggtcgg aaactggaaa gtatggtggc tttctggcgt 120 ttgttgctgt gcagcgcccc tgcgcgctgc aggatttgct tttatataaa aaaattatta 180 actaaaacga cacagtttta cagcttcatt aaaaaacaat aataaaatat tgtgtggacc 240 cctggttccc attagccatc acccctttca atttcccatc tctcactcac acactttacc 300 aaacacaaca aatcccgcaa ttcctagctt ccatttcaat caccacccgt cacgccatcc 360 ttcccaattt tatgtaaatt ttttattttc taaatttata tattatttca aaccctaatt 420 aattattcaa tacaattttt tctttaatta gtatagaatc atatgataat acattaatat 480 ggttattgat tattgattat taattgaatt attgaaaatg tatcattatt catattgatt 540 agttgaatta tttttttttt aataattcta tgattattgg tattgattaa ttgaattgtt 600 gttgattagt tattagtcat atcatataag agttaagatt ttttttccat ataagttagt 660 aataaatact ataaaaaagt ttctccttca aatattccgg gtagttcaca acagtgagct 720 gagttggatg aattattggc taatcttcct caacttggac atgacgtcaa atgttcttac 780 acctaattat cgcgaagcaa ttcatagaca ctcttcaaaa tgattattgt caacctaaag 840 accacatcat tgccaagaaa agctagcaac aatcgatgtt ttattacggt cgggatcaat 900 ggttaaatga taacatgatt gtttacattg agatacatgt atttgctttt attgacaata 960 atctattatg cacgttttca tgacatgaaa cctcgtcagc aacaattgta atttggttgt 1020 tgcccttttt ttttttaact ttgcactttt taagttcgcc cctcccatcg gcaattcctg 1080 gcttcgccac tg 1092 // ID Gypsy-21_VV-LTR repbase; DNA; EDCOT; 1596 BP. XX AC chr10; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-21_VV_; KW Gypsy-21_VV-I; Gypsy-21_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1596 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr10; Positions 560550 558955. XX SQ Sequence 1596 BP; 533 A; 251 C; 275 G; 537 T; 0 other; tgattactac tcaaaaagag catattttag ataataattc tcatgagttt cacatctttt 60 gagtagtaat tatacctaaa acactcaatt agcatgttgt tgcccttgca agagttacta 120 acaagtttta tgaagttttg gagtcatttt aaggtataat tttgataaat tggtgacaaa 180 agagattaat caaattgaag aaaacaaata aagttgatga tgatccaaat gcataatgaa 240 agaagcaatg caatcagttt ggattgggat ttggagctta attgaaggtg gtggagatgg 300 attgaacatg aagaaatgag agaaattgca aagaggagcc gaaatagcat gattttcaat 360 ttcgcatgac catgcgaaat tttcacacaa tcatgcgaaa ttttcgcaca atcatgcgaa 420 atgaaataga aaggttgtgg ctgcagcaca tagggaaatt atgaaaaagt gatttcgcat 480 gaccatgcga aattttcgca caatcatgcg aaatgctcca gaagaacgaa attgaagctg 540 atggatcctc cacttcgcac catcatgcga gattgctagg ggctcgtgcg aaaatgcatt 600 ctttccagat tccttgatga agaagcatcc gaaagacctc taaaatgttg ctgagtgtcc 660 tttttacctt ggcctataaa tagaaacggg atttactcat ttaaaaacct tacttttgat 720 tcattttcta attgtagaac ttttcatact tcttctctct atataattct ccactttcct 780 tcagtttctc ttattttctc ggtagccaaa catgccttgt gagatcaaat ctccaagcat 840 gagtgactaa atctcgtttt tctcggagga gggaggatct agaggcaaga tctatggtga 900 attagagaat tgagcttgaa ttgctaaggt aatttgatcc aattgattga ttaattgaaa 960 tttggggatt tttctcttca aattgtcttg gatgattact acaatgcaag ttaggtagat 1020 tcatcaaatt cttaatgcta gatttgatga aattgaatag ttgcattgtg tgaatcattg 1080 gaagataatt taagatgaat tgaatatatg attcaaattg atctcttgga ttagattacc 1140 taatttgaag agaaattata tctagatcta aagctaaatc aaaaatcggt ttagatgaaa 1200 atttaggttt tcaatctaac ttgatgaaaa ttagatctta acatctattc accatggaaa 1260 ttgctctcta gaaaatcctt actccgagaa tctcacatct tattaatttt cttctctttt 1320 acacttcatt ttcaattcaa tttgaataca ttgctatctt gagattttat catgcaattt 1380 caagtaaatt tcatttgatc accatcattc cttatcatct cgttcaagtc ttaattaccg 1440 agaataatcc atccttgtgg acgataccta aaaaccacta tactacagta gtttgtacta 1500 aaaccacttt ttgattgggt acaaattgtt atataatagt gaattaggtt ataaattttg 1560 ttttgatcca ataaacgaca aaaatccaag cgatca 1596 // ID HAT-8_Mad repbase; DNA; EDCOT; 4667 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-8_Mad. XX NM HAT-8_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4667 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1624-1624 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~92% identical to consensus. XX FH Key Location/Qualifiers FT CDS 1733..3700 FT /product="HAT-8_Mad_1p" FT /note="transposase." FT /translation="MAECKHCKLLVPAHPITHGTTGILKHLRKCPGSSLFE FT NVDPNQPTLTQARMGGPVVTHTFNKKRLDRRCVRWIIIAEMPFRVVDQEDF FT RDFIRDLNPKYKLPNRHKVAAAVLELYVEEKAKIKSVIEGLRVSITTDTWT FT SIQMINYMVITAHFLDTNWGLHKRILNFVQVTSHKGDDIGRCLEVCLNDWG FT IDKVFSITVDNASANDTAIAYMKRRLKSNGTLLLDGAHLHMRCACHILNLI FT VKDGMTELSCEIDAIRNCVKFIHSSPARLESFREYCVLLRFDRMSSIPFDV FT VTRWNATYEMLNSAFKFKEVFSKMAFECDSFIAYFKEEVSKEVDGVTTKAK FT RVGPPEVDDWERSVSFAHFLKKFYDATLTLSATLTPTSHLILSTVIALQVE FT IEEQILNASNATLQSVATSMKLKFDKYWGDIEKVNPILFVAQALDPRYKFD FT MLETNLEELGYGWDKIREEKVRVKGYVTELYNAYKEGVVLSSSSSSSTSSS FT ATSNVEQRSSVVLDDVGGVMVDIDVASRMAKKIQRKRAEAQQNEIANEVDM FT YFNDPHQSLTYEGFNLLDWWKGNCGQYPTLSKVAKDVLALPSSTVASENAF FT SLGGRVVDPFRASLTPKTVEALVCTSDWLRGKEFCFYKEPTLDEFRFYEEL FT ERLERSK" XX SQ Sequence 4667 BP; 1317 A; 822 C; 1053 G; 1461 T; 14 other; tagggctgga aaaaaatccc aaaaatccca aaccaaaccm aaaaaatccc gatcccaaac 60 caaaattccc gaagttttcg ggatgtcatc ccgaaccaaa ccgaawtttt cggtatggga 120 ttcggtattg catctccatt tttcggtatt cccataccga accgaaaaat atatatatat 180 atatattatt ttttaattat aagagaatta tttcaaccgt tgattatttt ggatttaatc 240 tgtgccgttg atttgttttt aggtcagatc caaatggtac tctttccgtt catttgtttc 300 ctttcctsca tccatcgaag tgatctgact gtctaccacc accggccctc gtctctcatc 360 tagaagtgat ctgactgtct accaccaccg gcctaccacc acacagccac cgcgctctct 420 ctctctgtcc gctctgcctc caaatatttc gctcactttc gctcmcgctc tctctctctc 480 tagaagtcga aaaatacatt caccagtaag cgctctctct atctccatat ctctgascta 540 actctggtta kcaacatttc taggtttttg aaatttttgc ataattacaa tttgccccgc 600 gatcctggta attttattcc akctcwgtgc cttgttcgaa ttcttatttt tgagctttat 660 tttggctgtt tggtcctcca gctctggttc tccgatcatg catttactta gatttgtaat 720 ttttgttttg tttggggtta tcatttttgg attttttgta ttttatgtat atgtttggat 780 tttggttgat tttattgtgc actgtgaaaa taggattgtt acttagaaat tgtatggaca 840 ggaagaaaag ctgagattcc acattttcta agcacccaga tggggttttt ctcatatttt 900 ttaaatttga gatgtgatcc tggggctcga tctagaacta gwagtatcca attgatgtat 960 gttttacwgc tgttggatat taatcactta stttctgatg cagggtgttg atccaagtat 1020 tcgagctgaa gtgtggccgt ttcttcttgg aktgtaagta ttttcatatc tatgcgattg 1080 ctttaatgct tcaagttttg cawgtgttgt atgaaaatta gttagtatat gattttcaaa 1140 ttttcaccct gaacctacac tacgtacata tttgctctcc taatttagaa acaagttgga 1200 ttttatttgc tttctagttc aaatacacga tatatgctca gatttttgaa tgctcagatt 1260 tttctatgct caaattattg attggaattt ggatatatgc tgaactgtgg ttgtgatata 1320 tattgatgtg cattgttatt ttatttgtta ggtaggatgg acgggtctag tagccaatct 1380 agtacacata tggtctcggt attaggaaaa cgaaaacaaa cccaacctag tggtaccctt 1440 caactaggca ctccctcacc tcaagattat ttgcataatg attattatgt agattcttgg 1500 gatgatgatc cggatacgga ggaggatatt gcattagaac aaatagaaga agagggggaa 1560 gaggggggga agagggaagg aagaggggga agaggaggaa gaggaagtag aagtagtgag 1620 acaatgggag ggtcctcctc cgaaaaaggg caataggaga aagggtccaa gtccggcgtg 1680 gaatgatgct aagagggtaa cgatcaccga taataatggg gagaaatctt tcatggccga 1740 atgcaagcat tgcaaactct tagtaccggc acaccctata actcatggga caacgggaat 1800 tcttaagcat ttgaggaaat gcccgggttc tagtctcttt gagaatgtgg atccgaacca 1860 acctacattg acacaggcga ggatgggagg tccggttgtc actcacactt tcaataaaaa 1920 gagacttgat aggagatgtg tgaggtggat tataatagcg gagatgcctt ttagggtggt 1980 tgatcaagag gactttcgag attttattcg tgacttgaat ccaaagtaca aacttcctaa 2040 taggcataag gtggcggcgg cggttttgga gttgtatgtt gaagagaagg caaaaataaa 2100 aagtgtgatt gaggggttga gagtgagtat tacaaccgac acttggacct cgattcaaat 2160 gataaactac atggtcatca cggcccattt tttggacact aattgggggt tgcataagag 2220 gatcctaaac tttgtccaag ttacttctca caagggtgat gatattggaa gatgtctaga 2280 ggtttgcttg aatgattggg gcatagacaa ggtgtttagc attaccgttg acaatgctag 2340 tgcaaatgac accgctattg catacatgaa aagaagactc aagtcaaatg gtactctttt 2400 acttgacggg gctcacttgc acatgaggtg cgcttgtcac atcctcaatt tgatagttaa 2460 ggatggaatg acggagctta gttgtgagat tgatgccata agaaattgtg tgaagtttat 2520 acactcatcc ccggcaaggt tggagtcttt tagggaatat tgtgtcttgt tgagatttga 2580 taggatgtca agtatccctt ttgatgttgt cacaaggtgg aatgccacgt atgaaatgct 2640 taatagtgct ttcaagttta aagaagtgtt ctctaagatg gcctttgagt gtgactcttt 2700 tattgcttac tttaaagagg aggtctcgaa agaggttgat ggggtgacaa caaaggccaa 2760 gcgggtgggt cctccggagg tggatgattg ggaaaggtcg gtgagttttg ctcactttct 2820 caaaaagttt tatgatgcca ccttgacatt gagtgcaacc cttactccaa cgtcacactt 2880 aatacttagc acggtgattg ccttgcaagt ggagatagaa gaacaaattt taaacgcctc 2940 taatgccact ttgcaaagtg tggctacctc aatgaagctc aagtttgaca aatattgggg 3000 tgacattgaa aaggtgaatc ctattctctt tgtagcccaa gcactcgacc cgaggtacaa 3060 atttgatatg ttggagacaa atctagaaga gctcggctat ggatgggaca aaataaggga 3120 ggagaaagta agggttaaag gctatgtaac cgagttgtat aatgcatata aggagggagt 3180 ggtccttagt agtagtagta gtagtagtac tagtagtagt gctacctcaa atgtggagca 3240 aagatcaagt gttgtactag atgatgtggg gggtgtgatg gtagatattg atgttgcttc 3300 aaggatggca aagaagatcc aacgaaagag agcggaggca caacaaaatg agatagccaa 3360 tgaagtggat atgtacttca atgatccaca tcaaagccta acatatgagg gtttcaatct 3420 tttggattgg tggaaaggaa attgtggtca atatccaact cttagtaaag ttgctaagga 3480 tgtattggcc cttcctagta gcaccgttgc tagtgagaat gcctttagtc ttggtgggag 3540 agttgttgat ccttttagag cttccttaac acctaaaacg gttgaggctt tagtgtgtac 3600 tagtgattgg cttagaggaa aggaattttg tttctacaag gagcctacac ttgacgaatt 3660 ccgtttctac gaggagcttg aacgcttaga aagaagtaag taaacaattt aatttcctct 3720 tttattttct tagtatttat tatctattag actataattc aatgtaaatg atttgtggtt 3780 tattgtttta ggcacggcta atttgggagg tgaggagaat acaacacaag aaaatgaaat 3840 gccacctcca cctcctcgac cacctcaagt tcaagttcaa caacgtcaaa atcaatcact 3900 acctccacga ccacgaccac ccattgtaag gggaagggct caaccatcaa catcaagggg 3960 aagagtacaa gtaccaacaa gaagggagca accacaagca tcaacaagat caaggggccg 4020 aaggggccga agaggccaac aatcttcata aactttaagc tttgtttttt tgcttttggt 4080 ttgtaactta attattgaaa ctttggcttg taactaattt ttttgctttt gggtttgtta 4140 ctttatttat tttaaaacct tggcttgtaa ctaatttttt tgcttttgga tttgttactt 4200 aatttatttt tattgcatgc atgtgtagta gaaattgaat aggcatatgc tattgtgcac 4260 agattggcga attgctttga atagatttgt gcacagattt gacakgttta ccactattgc 4320 gcatgctcgg ctgctcattt aatcatagca gcagttgccc aaattttttt ttgttgaatc 4380 aagttaagcc catatggtat gggctgttaa atttcagtgg gcatgcccaa tatgtcagat 4440 tttgccaatg gaccaatatt agctttttgt ccaaaagccc aaaagcccaa aaccattttg 4500 ggattcccga tttgtcccga aatcccgaaa ctatttcggg attcccgaaa attgggattc 4560 ccgaaaattt ggtttgggat cggtattgaa attgggattc ccgaaaattt cggtttggga 4620 atcgggacaa gggtttcggt atgggatccc ataccgaacc accccta 4667 // ID Helitron1_VV repbase; DNA; EDCOT; 4943 BP. XX AC AM479827; XX DT 27-AUG-2007 (Rel. 12.08, Created) DT 27-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE DNA transposon from Vitis vinifera. XX KW Helitron; DNA transposon; Transposable Element; Helitron1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4943 RA Obukhanych T. and Jurka J.; RT "Helitron1_VV."; RL Repbase Reports 7(8), 676-676 (2007). XX DR EMBL/GenBank/DDBJ; AM479827; Positions 6198 1256. XX CC incomplete copy. XX SQ Sequence 4943 BP; 1728 A; 769 C; 855 G; 1585 T; 6 other; caagaacaag ctccaaaacg taattatgta acgagaaggt atgctaggtt aacaaatgaa 60 caaagggaaa agcatgtaca acatgtgatg caaaattaaa aaaaaaccgt gaaactatca 120 cttgcagttc ctcaatgcgt gaaaatatag gtgtcccaat cacaactttt ggaaacgaag 180 aatatccatc tatagagcaa tttgaaagtg tgttatatta gtggaaaaaa tgttggattt 240 ttatatgcac ttgtgctttt tcgccataaa cctaacaaca gtgttttaat aggtaaggta 300 cgaaaccaca ttgtttactc accattacat gaattgagta caacacattc ttgtccattt 360 tgtggtgcaa aacgattgca acatgaacct tctacctttt gttgctacaa tggcaaagta 420 gttctttcta tacctcaaat tccagaagat ttgtatattt tatatacttc tcacaagtga 480 agaagctgta gaatttcgac ggcatattcg agcttataat aatattttct cctttacatc 540 atttgggtta aattagacaa agagcttgca agctccaaaa aaaaggagtt tacacttttt 600 gagctcaagg tcagatatac catcaacttc tagctctaca agcatatcac aactctcttg 660 ccttcttcca attatacttc tatgacattg ataatgaaat ccagaataga ttatgcatac 720 tataagatgt gtcccttaat gagacaattg ttcaaaattt gatgaatata ctactacaaa 780 atccatatgg tcaatttttc cacatactag agcgtgctcc attagatgtt tatgaaatcc 840 gaattaaaag tgaaatttca ttggataaaa gggtttacaa ttctccatca gttgatcaag 900 tggccgccat atggattgaa gggaataatt ctaatctagc tcacgaacgt gatattatag 960 ttcatgccca atccggtgac aaacataaag ttaaacacta ctatggttgt tatgatcctt 1020 tacaataccc tctattgttt cttaaataag atgttggatg acatcaaaat attctgaaag 1080 agatctattg aactatagta atgacaatgc acatayattc aaagatttga gtatacaaaa 1140 tttttcatca gctaaagatg ttctacattg agaacaacaa ggtagcactt taaatctcat 1200 tttatttaga taaacccaag aatctatcta atagaaacta accttcaact tattcatttt 1260 ccttatagat cttattcatg gagggaggag aaaagtgtct tatcaacaat attattgcta 1320 aagttgtaaa ttatagatga tggctcaatt ttattacttt ctggtagact tttgcaacaa 1380 tatgtagtcg acatgtatat caagcttaag acaacatggt tggactacta tagaaggcaa 1440 caataaaaaa ttagagtaga gttgtactaa tgcatcrttg atagagtgct agctagaaat 1500 agtagggcaa gtcaagttgg gaaaatgatc gtgctaccta catcatttgt aggaggcctt 1560 acagacacgc gtcgtagata tttagatgct atgtctttgg tccaatagtt tggaaagcta 1620 gaccctttta taacaatgac atgcaaccca amgtagaagg aaattcaaaa tgaatcgaat 1680 gaaaaccaaa taccacaagg tagacctgat taatgtttgt gtgttttcct agcaaagata 1740 caggagttaa aggagaaatt gtttaaaaaa catatatttg gaaatgttgc agcacatttt 1800 caygtaataa agttctagaa aagaggtttg cctctatgta catatattga taatcttaaa 1860 gccagaatat aagattctca ctctcgacca atatgaacga tttattattg ctgaaatccc 1920 aaatcctata agatatccar gtttacayga caaggttgtt aagcatatga tgcatggccc 1980 ttatggacct ttaaggatta ataattcatg catgcgtgat gggaagtaca aaaataggta 2040 ccctcatttg ttctgttcga attcgtatcc aacccataga agaagatatg acaaatgaca 2100 agtatttgtg tgtaatgctg ctttggataa ttgttgggtt gtcccctaca atccctatct 2160 tttaaaaaga tataactatc atattaatgt caacatctat tctagcatta aagcaattaa 2220 atatctttac aaatacatat acaaagagca tgacaaagta gttgttcaca ttgctgaaag 2280 aaatgatggc attatagttg atgaaatgaa ggagttttaa gatactcaat gggtttcaac 2340 aaaagaagct gtatggagaa tttttgagtt tgagctaaac gagattcatc cagcagtcat 2400 caatttgcaa ctacatcttc ctaataagca atcaatttgc tattgggaaa accaaaattt 2460 ggaacatgtg atttatttta gtctcgcatt aaggactatg ctcacaaaat ttttcacttt 2520 atgctctcaa gatgatgaag caagaaattt tttgtataaa gaatttccag agcattatgt 2580 gtggaataag taaagtaaat cctcgactaa aagaaaggct agagaagtta ttggtcaagt 2640 aaatgtagct aatccatcga aagatgagaa atattatcta agacttttac ttaatcacgt 2700 tagaggaccc aaatcttttg aaaatttatt aagttacaat ggtcatcaat atctatcatt 2760 taaggaggct gcccaaaaaa gaggtctgtt ggaatcagat gactccattt ccaaatgttt 2820 tcatgaaatt gaaacatttc aaatgccatt agcaatgaaa gatctttttt caacaatctt 2880 ggtgtatagt caaccaactg atgtaagaaa attgcagaat actcattttg aagcaatatc 2940 ggaggatttt tgcacccttg attcacaatc aattgaatct caaatgttga acacattgaa 3000 aagtgtaaac tttttcctta aaagcatggg gaaaagttgt gctaattatg acttacccat 3060 gctggatttg agtttacctg atttactaat cattcattgt agataaattt atgatgaaat 3120 tgagataaat attatttcta aagatttgaa tgcatcaatg agattaaatt caaaacaaca 3180 acatgcttat tcaactatcc ttgatcaagt aagttttggt ttgggtagtc tttttcattg 3240 atgacccagg aagggcagga aaaacatatt tgtatcgagc attgttggcg gcggttggat 3300 taagaagaat gattgctatt gcaacaacaa ctttaagcgt agcttcctcc attatgcctg 3360 gtagccaaac attgcattca agatttaaaa taccaattaa tcttgatgaa tcaagtttat 3420 gtaacatgat taaacaaagc ggcagtatag agctcctaaa aaaggcaagt ttaatagtat 3480 gggatgaagc acccatggca gctcattggg ctattgaagt ggttgataga attttaaggg 3540 acattatgga taaccaattg gtgttttggg gaaatgttat tgtatttgga agagatttta 3600 gacaagtact ccccatggtt cctcatgtta caaaggcaga aactatgaat gaaagtttag 3660 tcatgtcata tctttggcct aaaatggaaa aattaaggtt gattagaaac atgagagctc 3720 agttagatac cacatttagt gattttctac tatgggttgg agatggtgat gagagctcaa 3780 aatcaggata tgataaatat acttgatcac atgttagttc aatataaaaa tggtgacgac 3840 cttaaagagt gtttgattaa tacaattttt ccctcattgt agagagaatg caagctcgtc 3900 agaatatatc aaggaatgcg ctattcttac aacaacaaac gaatttgttg atatgatgaa 3960 tgaaaagtta attgctatgt tcctaggtga atctaaagca tattatagtt ttgactgagt 4020 agttgatgac acttaacaag tttatcaaga agatttctta aatacattaa caccaagtgg 4080 tctgccctca cattaattgg tgttgaagac aaaatgtccc ataatgcgac taaggaattt 4140 agatccatca aatggacttt gtaatggaac aagaatggtt aatttgcaaa ggttttgagg 4200 caaatgtcat acatgtagaa attacaatgg gacaaaatgc tggaaggcaa gttctaatcc 4260 taagaatacc tatgtctcca gtagaaaatg aaggctaccc tttccatttc aagcatgctc 4320 aaatattaat atagattcga ctttgttttg caatgactat taacaaagca caaggccaaa 4380 caataccttt tgttggggtg tccttacctc aaaatgtctt ctcacatgga caattatatg 4440 ttgctttgtt gcatggaact tctttctcaa caacaaaagt gtttatcaaa gaaactgacc 4500 acaaaagtac aagaaggact tacacaaaaa atgtggtcta tacaaaagct tcagctttgt 4560 gtaggtattg aaactatgga tctgtttagc tttgtgcttt acaatttttc aaaatgatat 4620 ttctaatata cgtatcatat tattctattc taattttact aactttccaa ttttgattat 4680 tttttccttt tttttttaat gcagtatcca attatgaagc aaataatgaa ggttttatcg 4740 ctataagcac acttcaacct ttcaataggg attggactat taaggcatgt gtacttcaat 4800 gtacatggat ccatacaggc gtacaaaaat tctaaaggct tgagcaaaat atggaagata 4860 atattcatgg atggtcaagt tagctaagct atgtatcaaa ctactttatt attttaactt 4920 tttttttatt attataattt tac 4943 // ID Copia-18_Mad-I repbase; DNA; EDCOT; 4304 BP. XX AC ACYM01115884; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-18_Mad-I; KW Copia-18_Mad-LTR; Copia-18_Mad_. XX NM Copia-18_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4304 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1293-1293 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01115884; Positions 6993 2690. XX CC Positions [1795-2295] - Integrase core CC 'TCCGA' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 538..3990 FT /product="Copia-18_Mad-I_1p" FT /translation="MNDVESLDDYLARFFEIVNNLKSLGEDVTEKRIVQKL FT LMSLSRRYKSIVSIIEETRDLDTIRIEEVLASVKVYDKREDLHDERDKYTG FT TERAFNNLKVGGNGNGTGNFKGSQYKSNPKFGQYKKGKNWGQNSSWNNGSG FT GGWNNKFAAHNKQTSGSQGNVKPLCQVCDKYHFGICRYKGKPKCGRCSRFG FT HLTKDCDNGKQVANCAKEEDLVTGTMFYACHASSIASSKSMWFVDSACSNH FT MTSQESLLINLDKSVTCKVKMGTGDLVQATGKGTLVVETRRGKRYINEVLL FT VPGLDENLLSVGQMMEHGYYVLFGGNMAVIFDDSNLENVVAKVVMTGNRCF FT PLSFESVNAVARKASIEEESRIWHKRLGHLNFNSLKRMQREGLVLGLPALS FT EMKEVCESCVSGKMHIEPFDKEKVWRASQPLELVYTDVCGPMQNESVGGNK FT YFIAFIDDFSRMCWVYFLRNKSDVFNVFKKFKAFVELQSGFKLKKLRSDRG FT GEYTSHEFLNFCSNIGMERQLTVAYSPQQNGVAERRNRTICEMARSMMAEK FT NIPVVFWAEAVGTAVYLQNRCPTISVKSKTPFEAFTGRKPGVKHLRVFGSI FT CYSHIPSNLRQKLDDKASKGIFMGYGSCEKGYRIYNLQTKKIILSRSVIFD FT ESKSWNWESKQEETVFMPLSFENENPEITETERFIHETQSCDSPNLTQLVS FT CDEHVTGSNSGSTSQGSTPSNTPVKLRSLEDIYARCHMTIIEPETYHEAIE FT DNAWKEAMNAEIETIEKNGTWELVERPADKPVIGVKWVFKTKLNLDGSVQK FT HKARLVAKGYAQKPGIDYNETFAPVARLDTIRTLIALAAQKGWKLFQLDVK FT SAFLNGVLEEEVYTEQPEGFEVRNASHKVYKLKKALYGLKQAPRAWYSEID FT TYLTSCNFKRSISEATLYTRTDDEGNMIIVSIYVDDIVYTGGSNTLLSEFK FT RDMMQKYEMTDLGLLHHFLGMGVLQTERGVFIHQSKYAKSLLAKFGMEDCK FT SVTIPLPTGEKLKKIDGSELTDEGLFRQIVGSLLYLTATRPDIMYAASLLS FT RFMHGPTKKHMGIAKRVLRYIQGTLSYGIEFTRDKEVVLIGFCDSDWAGSE FT DDSRSTSGYAFSFGSGVFSWASVKQNTVALSTAEAEYVSAAGA" XX SQ Sequence 4304 BP; 1440 A; 664 C; 1047 G; 1145 T; 8 other; tggtatcaga gctccgggtc tgatttcgaa gaagggaagt gattctgtga agatacaaat 60 ccagaaaggg ttaaaggtgg tacctttata accatttgtg ctgtgctacc tgagaagatg 120 gtcggatcaa gctcctccgg tggtgattta cgaacaccac aatttaatgg gtcaaactat 180 gatttttggg ccattaaawt ggaaaccatt ctcatagcct atgatctatg ggatgtggtt 240 gaagctggtc ttgttgaaca acaagccccc gcagaagatg tctctgagga agatgaagaa 300 agcgagtctg agcaccttcc agttgaagga ccggttgtct caaaggaggt gaagatcaag 360 aatgccaagg ctctgagtct tattcaagga gccataactg atgaactttt tcccagaatc 420 cgaaatgaga aaacggcaaa gggtgcctgg gaaattctga ggagagaatt cagaggagat 480 aaaaaggtaa gagctgtgaa actacaagcc attagagctg attttgaata tttaagaatg 540 aatgatgttg aatctctgga tgattacttg gctcggtttt ttgagatagt aaacaacttg 600 aaatctctag gagaagatgt aacagaaaaa aggattgttc aaaagctgtt gatgagtcta 660 agtagaaggt acaagtccat agtgtcgatt attgaagaaa ccagagattt agatactatt 720 aggattgaag aagttctagc ctcagtgaaa gtttatgaca agagggaaga cctgcatgat 780 gaaagagaca aatatacagg tactgagagg gctttcaata atcttaaagt tggaggaaat 840 ggaaatggca ctggaaattt taaagggtct cagtataaat caaacccaaa gtttggtcag 900 tataagaagg gaaagaactg gggtcagaat agcagctgga ataatggcag tggtggtggc 960 tggaacaaca agtttgctgc acacaacaaa caaaccagtg gcagtcaagg aaatgtgaaa 1020 ccactatgcc aagtatgtga caaatatcat tttggtatat gcagatataa aggaaaaccc 1080 aagtgtggca ggtgcagtcg atttggtcat ctaactaagg actgtgataa tggtaaacaa 1140 gttgcaaatt gtgcaaagga agaagatctg gtcacaggaa caatgttcta tgcttgtcat 1200 gcaagttcaa ttgcatcaag taagtctatg tggtttgtgg acagtgcttg cagtaatcac 1260 atgacttccc aagagtcctt attaatcaat cttgataagt cagtgacctg caaagtaaaa 1320 atgggtactg gtgatcttgt tcaagccaca ggaaaaggga cacttgtagt tgagacaaga 1380 agagggaaaa gatacataaa tgaagtgctg ctagttccag gattagatga aaacctgtta 1440 agtgttggtc aaatgatgga acacggttat tatgttctat ttggcggtaa catggctgtg 1500 atatttgatg atagcaatct tgaaaatgtg gtagcaaagg tggttatgac agggaataga 1560 tgctttccat tgtcctttga atctgtaaat gcagtagcta gaaaagcttc aattgaagaa 1620 gagtcaagga tctggcataa aaggcttggt cacttgaact ttaacagtct gaaaaggatg 1680 cagagagaag gattggtgct tgggttgcct gcattatctg agatgaagga agtttgtgaa 1740 agttgtgttt ctggaaagat gcatatagaa ccattcgata aagagaaagt gtggagagct 1800 agtcaaccat tagaactggt atacactgat gtttgtggac caatgcagaa tgaatctgtt 1860 ggtggcaaca aatatttcat agcattcata gatgacttct caagaatgtg ttgggtgtat 1920 tttctaagga acaaatctga tgtgttcaat gtgtttaaga aatttaaagc ctttgttgag 1980 ctacaaagtg gtttcaaact taagaagctg agaagtgaca gaggaggtga atatacctcc 2040 cacgaattct tgaatttctg ttctaatatt ggaatggaga gacaattaac agtggcatac 2100 tctcctcagc aaaatggagt tgctgagaga agaaatagaa ctatttgtga aatggccaga 2160 tcaatgatgg ctgagaagaa cattcctgta gttttttggg ctgaagcagt tggaactgca 2220 gtatacttgc agaataggtg tcctacaatc tcagtgaaga gtaaaacacc atttgaagct 2280 ttcacaggaa gaaaaccagg tgtaaaacat ttgagagtgt ttggaagtat ttgttacagc 2340 cacattccat caaacctgag acagaaacta gatgataaag caagcaaggg aatatttatg 2400 gggtatggca gctgtgagaa aggttacagg atctataatc ttcaaactaa gaagatcata 2460 ctctcaagaa gtgttatatt tgatgagagc aaatcatgga attgggaaag caagcaagaa 2520 gaaactgttt tcatgccact cagttttgaa aatgaaaatc cagagataac tgaaacagaa 2580 aggttcattc atgaaactca aagctgtgac tccccaaatc tcactcaatt agtgtcttgt 2640 gatgaacatg tcactggaag taacagtggc agtaccagtc aaggttcaac accaagtaat 2700 acacctgtaa agctgagaag cttggaagac atttatgcaa gatgtcatat gaccattatt 2760 gagcctgaaa cctaccatga agctattgaa gacaatgcat ggaaggaagc aatgaatgct 2820 gagattgaaa ctattgagaa aaatggaact tgggagctgg tggaaagacc tgcagacaag 2880 cctgtcatag gagtcaaatg ggtgttcaaa accaaactaa atctagatgg atcagttcaa 2940 aaacacaagg ctaggcttgt ggcaaaaggg tatgctcaga aacctggtat tgactacaat 3000 gaaacctttg ctccagtggc aaggttagat acaatccgaa ctttaattgc acttgcagca 3060 caaaagggtt ggaagttgtt ccaattagat gttaaatcag ccttcttgaa tggagtactt 3120 gaggaggagg tttacactga gcaaccagag ggttttgaag tcagaaatgc aagtcacaag 3180 gtctataagt taaagaaggc tctctatggt ttgaagcagg ctcctagagc ctggtacagt 3240 gagattgaca cttatctcac aagctgcaat ttcaaaagaa gcattagtga ggctacctta 3300 tatactagaa ctgatgatga aggaaatatg atcatagtct ctatatatgt tgatgatata 3360 gtatacactg gaggtagcaa tacactactc agtgagttta aaagagacat gatgcagaaa 3420 tatgagatga ctgacttagg actcttacat cacttcttgg gaatgggagt tctacaaact 3480 gaaagagggg tctttattca tcaaagtaag tatgcaaagt ccttacttgc aaagtttggc 3540 atggaggatt gtaagtctgt gacaattccc ctacctactg gtgagaaact gaagaaaatt 3600 gatggaagtg agctgactga tgaaggttta tttaggcaga ttgttggcag tttgttatat 3660 ttaactgcaa ccaggcctga tataatgtat gctgccagtt tgctatcaag attcatgcat 3720 ggtcccacga aaaaacacat gggaatagct aaaagagttc tcagatacat tcaaggcact 3780 ctcagctatg gtattgaatt cacaagggac aaggaggttg ttttgattgg tttttgtgac 3840 tcagattggg ctggaagtga agatgacagt agaagcacat ctggatatgc atttagcttt 3900 ggaagtggtg ttttttcatg ggcctcagtc aagcaaaaca cagttgcatt gtcaacggca 3960 gaagctgaat atgtctcagc agctggagca ayagctcaag ccatytggct aagatttgtg 4020 ttggatgatt ttggtgaatt gcaagctgat gcaacaccat tgttytgtga taacatgtcw 4080 gcaatatcaa tggtcaaraa tccagtcttt caycagagaa ccagacacat aaacaggaaa 4140 tatcatttta ttcgagaagc attgyagcaa ggatccattg atgtgaagta ttgcagaagt 4200 gaagagcagt tggcagacat atttactaaa gccttgccca aagatcgatt caattatctg 4260 agaatgaagt taggagtgaa gccagtaagc agcttaggag aggc 4304 // ID Copia-83_Mad-I repbase; DNA; EDCOT; 3651 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-83_Mad_; KW Copia-83_Mad-LTR; Copia-83_Mad-I. XX NM Copia-83_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3651 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1704-1704 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [889-1386] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 274..3111 FT /product="Copia-83_Mad-I_1p" FT /translation="MAQYNHSVVMHLGGTNKWIIDTGATDHVTSDPRVFDE FT LCDYVRDPYITSANGALSPVKGEGTISLTPTLSLVRALLVPDVKCNLLSVG FT KLLDTLYCSAHFYPTYCYFQDIQTQKIIGYGKRIGGLYILTMEDTVVSGSN FT NHQVLSAKVDNRHQIWLWHRRLGHPSFSYMKHLFPSLFRTCSDSEFKCETC FT VMAKSHRASFPVSDSKATLPFDLIHSDVWGPAKVTSNGFRWFVTFIDDCTR FT VTWVFLMKNKSDVPLLLQEFCTMVSTQFQTKVKVFRSDNGGEYVNHTLACF FT FRDHGIIHQTTTPFTPQQNGVSERKNRQIMEVARSLMLDKCVPNHLWGHAV FT LAAVYLINRVPSRVLDFQTPFDVLQKHVSLVSVSKLPPKVFGCIAYVHVYS FT HQRSKLDACALRCVFIGYANNQKGYKCYHPPTQKTYITMDVTFHEEVSYFV FT KPSSDSPLQGERGSEVQIRRDGMDDVLQAELGTEPIMLRDTDQSATDSDRS FT PAADMSDELPSDDRLPAADMSNELPDDGSSSDDSSNSLVQDGGIHEVNSDD FT SSTYQLPPRANRGKPKVQYEPDMHAKAKYPINNYVSTHRLSKPYASYICQL FT SSVSIPTKLQDALSDPKWVNAMKVEMEALEKNSTWDLVPLPNGKKAVGCRW FT VFTIKHKADGSIDRYKARLVAKGYTQTYGVDYQETFAPVAKLNTVRVLLSL FT AANQDWPLLQFDVKNAFLHGDLKEEVYMDLPPGIGTSPGKGVVCRLRKALY FT GLKQSPRAWFGRFTSSMKKFGYIQSHSDHTLFLKRQNGKLTALIIYVDDMI FT VTGDDQKEIQRLQKYLATEFEMKELGELKYFLGIEVARSKHGIFLSQRKYV FT LDLLAETGMLDCKPVDTPIEQNHRLGLFPDQVPTHKERYQRLVGRLIYLSH FT TRPDIAYAVSVVSQFMHSPSEAHMDAVTRILRYLKMAPGRGL" XX SQ Sequence 3651 BP; 952 A; 630 C; 860 G; 1208 T; 1 other; atatggcatc agagcagttc gctcttggtg acctgtgtgc tttaaatttt gtgcccacat 60 ttttcgtgat ttcctccgtg tgaaaaaaaa aaaaaagtgt cgtgctacag tgccgtgaac 120 agtggtcttc tacagtgcgt gaacagtgat tgctacagtg ccgtgaatag tatttgctac 180 agtgccgtga acagtgattg ctacagtact ctggtaaatt gttttcattc cgctgcgtat 240 cttttgtgcc tttattgttc gtgattttgt tcaatggctc aatataatca tagtgttgtt 300 atgcatcttg gtggaacaaa taaatggata attgatactg gggccactga tcatgtgacg 360 agtgacccta gagtgtttga tgagttatgt gattatgttc gtgatccgta tattactagt 420 gcaaatggag cactttcccc tgtgaagggt gaaggcacta tctctttgac tccaacctta 480 tcactggtcc gtgctttact tgttcctgat gttaagtgca atcttttgtc ggtaggaaaa 540 cttcttgata ctttatattg ttctgctcac ttctatccta cgtattgtta ttttcaagat 600 attcaaactc agaagataat tggttatggt aaaaggatag ggggtttgta catcttgact 660 atggaggata ctgttgtttc cggttcaaat aatcatcaag ttttaagtgc taaagtggat 720 aacagacatc aaatttggtt gtggcatcga cgattgggac atccatcatt cagttatatg 780 aagcatctat ttccttcttt gtttcgcact tgtagtgatt cagagttcaa gtgtgaaaca 840 tgtgtcatgg ctaagagtca tcgtgcttcc tttcctgtaa gtgattctaa agctacttta 900 ccatttgatt tgatacattc tgatgtgtgg ggtcctgcaa aagttacttc taatggattc 960 cgttggtttg ttacttttat tgatgattgt actcgggtaa cttgggtgtt cttgatgaaa 1020 aataagagtg atgttccgtt acttcttcaa gaattttgta caatggtatc tactcagttt 1080 cagaccaaag ttaaggtctt caggtctgat aacggaggag aatatgtgaa tcacactttg 1140 gcatgttttt tccgtgatca tggtattatt caccagacga ctactccgtt tacaccccaa 1200 caaaatggtg tgtccgaacg gaagaatcgt caaataatgg aggttgctcg ctccttgatg 1260 ttggataaat gtgttcctaa tcatttgtgg ggtcatgctg ttttggctgc tgtgtatttg 1320 atcaatcgtg ttccaagtag ggttcttgat tttcagacac cgtttgatgt gctacaaaaa 1380 catgtttctc ttgtttctgt atcaaagctt cctccgaaag tgtttgggtg tattgcgtat 1440 gtgcatgtct actctcatca gcggagtaaa cttgatgcat gtgctctccg gtgtgtcttt 1500 attgggtatg ctaacaatca aaaaggctat aagtgttatc atcctccgac tcaaaaaact 1560 tatattacca tggatgtcac cttccatgag gaagtttcgt attttgtgaa gccctcttcc 1620 gactctccac ttcaggggga gagggggagt gaagtgcaga ttcgaagaga tggtatggat 1680 gatgtgttac aggcagagtt gggaacagaa cctattatgt tgcgtgatac tgatcagtcg 1740 gctacagata gtgatcggtc gcctgctgct gatatgtctg acgaattacc ttctgatgat 1800 cggttgcctg ctgctgatat gtctaacgag ttgcctgatg atggttcgtc cagtgatgat 1860 tcttctaaca gtttggtaca agatggtggc atacatgagg taaattctga cgattcttct 1920 acttatcagt tgcctccacg agctaatcgt ggaaaaccta aagtacaata tgagcctgat 1980 atgcatgcca aagccaaata tcctatcaac aattatgtgt ctactcatcg tttgtccaaa 2040 ccatatgcat cttacatatg tcagctatct agtgtatcaa ttccaacaaa attgcaagat 2100 gctttgtctg accctaagtg ggttaatgcc atgaaagttg agatggaagc tttggaaaag 2160 aattctactt gggatttggt tcctttacca aacgggaaga aagccgttgg atgtagatgg 2220 gtgtttacta ttaagcacaa agcagatggt tctattgacc ggtataaagc cagattagtt 2280 gctaagggtt atactcaaac ctatggggtg gactatcagg agacctttgc tcctgttgcc 2340 aaacttaata ctgtgcgtgt tcttctgtcc ttagcagcaa accaggattg gcctctgttg 2400 cagtttgatg ttaagaatgc tttccttcat ggtgatctta aggaggaagt gtatatggat 2460 ctcccacctg gtattggaac atctcctgga aaaggtgttg tatgcaggtt acgaaaggcc 2520 ttgtatggtt tgaaacaatc tcctagagcg tggtttggga ggtttacaag ttcaatgaag 2580 aagtttgggt atatccagag tcattcagat catactttgt ttctaaagcg acaaaatggt 2640 aagctaactg cattgattat ttatgttgat gacatgatag tgactggtga tgatcagaag 2700 gagatacaac gccttcaaaa gtacctagct actgagtttg agatgaaaga attgggtgaa 2760 ttgaagtatt ttcttggaat cgaggttgca cgatccaagc atggtatttt tctgtctcaa 2820 cggaagtatg ttcttgattt gttagctgaa acaggtatgt tagattgcaa acctgttgat 2880 actccgattg agcagaatca tcgtctgggc ttatttccag atcaagttcc tactcataag 2940 gaacggtatc agaggcttgt ggggagatta atttatttgt ctcacactcg ccctgacatt 3000 gcttatgcag ttagtgtggt aagtcagttt atgcactcac ctagtgaagc tcatatggat 3060 gcagtaaccc gtattttgag gtacttgaag atggctcctg gcagaggcct gkttttctcc 3120 aagaatggtc atttgaatgt cgaagggtat acagatgcag attgggcagg ttctatcact 3180 gatcggcgat ctacatctgg atactttacg tttgtgggtg gtaatttagt tacttggaga 3240 agcaagaaac aaaaagtggt ggctaggtca agtgcagaag ctgagtttcg tggtatgtct 3300 catggtgtat gtgagttgtt gtggttgaaa aaattgttga gagatcttgg gtttaaaccc 3360 aaaggtgcta tgaaacttca ttgtgataac aaggctgcta ttgagattgc tcataatcca 3420 gtgcaacatg atcgaacaaa acatgtggag attgatcgac atttcattaa ggaaaaattg 3480 gatgctggaa ttattatgtt tccgtttgtg agatctgaag atcaacttgc tgatgctctt 3540 actaaggctg tgtctaatag tgtgttttcc aactcgcttg acaagttggg catgcgtgac 3600 atctttgcac caacttgagg gggagtgttg cgagttatat attagttaaa g 3651 // ID MINISIP2 repbase; DNA; EDCOT; 962 BP. XX AC AB000397; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Ipomoea purpurea minisatellite DNA MINISIP2. XX KW MSAT; Satellite; Simple Repeat; MINISIP2; Repetitive sequence; KW minisatellite; tandem repeat. XX OS Ipomoea purpurea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea. XX RN [1] RP 1-962 RA Hisatomi Y., Hanada K. and Iida S.; RT "The retrotransposon RTip1 is integrated into a novel type of RT minisatellite MiniSip1, in the genome of the common morning glory RT and carries another new type of minisatellite, MiniSip2."; RL Theor. Appl. Genet 95, 1049-1056 (1997). XX DR Genbank; AB000397; Positions 1 962. XX SQ Sequence 962 BP; 317 A; 221 C; 271 G; 153 T; 0 other; agggactcgg tgagagaaag ttaggaaaca agggcccaga cccttagtcg tttccgtgaa 60 aaagccaaaa gcagtcgcct cgactgaggg actcggcaag tatatataga aacaacgggg 120 cactgaccct aaaccgtttc tgagagcaga aaaaacctaa agggtcgcct cgactgaggg 180 actcggcgag agaaagttag gaaacaaggg cccagaccct tagtcgtttc cgtgaaaaag 240 ccaaaaggag tcgcctcgac tgagggactc ggcaagtata tatagaaaca acggggcact 300 gaccctaaac cgtttctgag aacagaaaaa gcctaaaggg tcgcctcgac tgagggactc 360 ggcgagagaa agttaggaaa caagggccca gacccttagt catttcagtg aaaaagccaa 420 aaggagtcgc ctcgactgag ggacttggca agtatatata gaaacaacgg ggcactgacc 480 ctaaaccatt tctgagaaca aaaagagcct aaagggtcgc ctcgactgag ggactcggcg 540 agagaaagtt aggaaacaag ggctcagacc cttagtcatt tccgtgaaaa agccaaaagg 600 agtcgcctcg actgagggac tcggcaagta tacatagaaa caacggggca ctgaccctaa 660 accgtttctg agaacagaaa aagcctaaag ggtcgcctcg actgagggac tcggcgagag 720 aaagttagga aacaagggcc cagaccctta gtcgtttccg tgaaaaagcc aaaaggagtc 780 gcctcgactg agggactcgg cgagagaaag ttaggaaaca agggcccaga cccttagtcg 840 tttccaagag aaaaagcaga aaggagtcgc ctcgactgag ggactcggcg agaaagagct 900 ggagacaagg cccagaccct tagtcgtttc tcggagtaag cataaaagag tcgcctcgac 960 tg 962 // ID Gypsy-31_Mad-I repbase; DNA; EDCOT; 4222 BP. XX AC . XX DT 08-OCT-2010 (Rel. 15.1, Created) DT 08-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-31_Mad-I. XX NM Gypsy-31_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4222 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1756-1756 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 4222 BP; 1249 A; 630 C; 1048 G; 1294 T; 1 other; gttggtatca gagcctaggt tgcaattctg gacatcttga gaatttccta gtgtcttctg 60 tcagaactat accgcctcgt agcgagccac gtagttcgga tgagcctaat ttccctgata 120 tagtagtttg gggggaaact attgccattg tgattcagtc tattatctaa aggaaccttt 180 tgagactggt tataagttaa atttgaatca ctttagggaa atgaagaacc taagggagca 240 gatcgatggc ttaatcattt gggaaaagac gtttcggatt atgcaaagtc aagggaatct 300 tcctcccgac aggtgggtcg agatgactac ctagtttctg agtgttgaat ctgcattctg 360 atggagatag gaatgttatc cgatgttatc ggaagaacag ctgtttggaa gtcgtttaaa 420 gaattgttta aggaaaagtt cattcctccg gcatattatt atagagagtt tacagacttg 480 ccttgtttcc attcggatgt tgttgctaat ccggtcgagg tgttatgtcg tttttggctg 540 gataataaga agaagtggcg ttctttggcg accactattc attgtacttt ttaccaggag 600 tttacgagat gttgttgagc attgaggact ctgagaacat gatcagcgag agtaaagagg 660 aataagaaaa gaatgagaat cagaagaaag acgataaagt taaagatccg tcatatcaaa 720 gacctcggaa gactcagagc ttcaaaagaa gtgaaactag agctaatttt cccagctgag 780 gttttagtgc cactggtcag aggcgaagtg atagatttac tagtgatccc agatttcaga 840 gacaaggtga ctctggtaga ggaaatgtat ctttgtaccg taggtacaat attaggcact 900 ttggagagtg tgggaagttg tgaatgtgtt catgtggtta gatgagacat agaggtatga 960 attgtcccta ggatcagttg ttacccagca gtcttccttg acatattact tggaaaattg 1020 atgagtaagt cgtacaggtc actataggtg actccgactt atgtgctaac atggatggtc 1080 gagctgtaga ctcagccgta caggtcattc tagctgactc cggctgatat aattcttatt 1140 attgacgatg ttgccaaagg aagtagtgaa tgagcacgat cgaggcgtat atatgtattt 1200 tccctgtgag gagtaaaatg ataatattgc acccttaaga attgttgctt acttatcgag 1260 acgacagtga gttatcgtta ttgcgggctg cagaccgtaa tacccataac ttatttgttg 1320 gattcgttaa gcaagtaaac aggtaggtca ttctatgtcg gttatgacta ttcagggtgt 1380 ccagtgatgg tggaagaagt agttatgcca gcgaatcgta tcccgttaga cattgtggat 1440 ttcgatgtga ttttaagcac agattggtta cattataatc gtgccaatat ggattgctac 1500 gggaaatcag ttactttcca ttgtcttgga ttatcagagg ttacttttgt gattgagcaa 1560 agtggagtga ggcatgccgt tatttctgtt gtgagagcaa agagattgtt atcaaaaggt 1620 tgccaaggat acctagctca tgtggtgttg caggatcgta ctcctagtat tgtggatgac 1680 gtacgagtgg tagacatttt cctaatgtgt ttccggaatg atttacatgg attgccacca 1740 gacagagatg tggtgttcac tattgaattg tctccaagta cagactttat gctatagatt 1800 ggttcctaca gagttaaagg aattgaaaat tcagtcacag gaattggttg ataaaggttt 1860 cagtcaacct agtacgttac tttggaaaac cccagctttg tttataagga agaaagacgg 1920 gaccttaaga atatgtatgg atattaggta attgaatcgg gtaacgagta agaaccgtta 1980 tccattgccg cgcattgatg attgtttgat cagcttagag gtgcctatgt gttttcaagg 2040 aaagagttga ggtctggtat actcttaagt gaaagtaaag catactagtc attttgagtt 2100 ggtgttaaaa tgtttgaggg aacatcggtt gtatgctaag tttagcaaat gtcaattttg 2160 gacgaatcaa gtggcatttt tgggacatgt gatatctaca caaggtattc aagtagatcc 2220 tcaatgagtg acaactgggg agaattggga acaacctcga accgtcactg aggtactgag 2280 ttttcttggt ctagcaggct actatagacg tttgtaaagg atttttcagt cattgctttg 2340 ccattgacgg gatcgactag aaaagaggtt aggtttgagt ggatgaaaat tgtgaacaaa 2400 gtttcagcaa ctgaagcatt atctcactca tacacctgtt ttagcactcc cagatgataa 2460 aggtaattat gaggtctaca gtgatgcatc cttgaatggg ttaggatgtg tgttgatgca 2520 acatggtaga gtgattgcta cacttcacga caattgaaac ctcatgagat gaattaccct 2580 actcatgatt tagaattagc aactatcatc tttgctttga agatttggag acattgtctt 2640 tatgggaaga aaagtgcaag atttttacga atcaaaagag tatccaatat ctgtttattc 2700 agaggtatct taatcttagg caacgaaggt ggattgwgtt gcttagtgat tatgattgca 2760 cgaccagggt gatcgtgcaa atgttgtggc caatgctttt agtaggaaga ccccagcgag 2820 aattaatgct tggtacgatt gccatgttca tcttcttgtg gatttgagat ctactggagt 2880 aaagttggga atggaagatc gaaaagaaaa cgtacttgct aattttcaag ttaggcctat 2940 ttggtaggtc gtactcgaga ctcaagcgtt tgacgaagaa attcaagaat ttatttaaag 3000 caaggaataa cgggaaaaag aaagacctca gagttagaga atcagatggc aagcttatgc 3060 aagagaacaa ggtgtttata cctaatgtta tggaattaaa ggaagcaatt ttggaatttg 3120 cgtactgttc aacttataca atgcatcctg gaggtactaa gatgtattat accattcgat 3180 cattttacta ttggtcaggt atgaaaagag aaatgtttgt atatataaat agatgtaaca 3240 tctgtcagca ggttaaaacg gaaagaaaga agtcttttgg attgatgtag ttacttcccg 3300 ttccacagcg gaaatgagaa aatattaata tagattatgt gtgcaagttt cctcgttcac 3360 gagatggtta tgatgaaatt gaggtgataa ttgattggct tactaaatca gcgcagtatt 3420 cttcaatgaa agagcagtaa cctttccaga agtgcaacag ttatttatct gtcttatgga 3480 aaagagattt gggcttacgg atctgttgaa cttcttgggt atgttggtcc tttcagtttg 3540 ttccctagag caacgccata aggccgtgga aagctgtgtc ttgtgtttcg aaattgttag 3600 aattgtggac ggatggtatt caaggccctg agttagtgga ggagactact cggaatattc 3660 aagtaattaa gtctaacctg gaagtgagcc aggatcggct gaagagctta gcagacaaac 3720 atgccactga ccggacgtgt aatgcaggag attggatgtt tttgaaatta tcaccttgga 3780 aaggtgcggt tcgggtcgaa atggaagaca agttaaatcc taagtacatc aggccgtctt 3840 tgactattga aggaatcggt gaaatacttt caagtttgag taccttcggg attggataag 3900 gtgtatagtg tagttcatgt tttgatgctt cgttacaaag tagcagattc gtcgtgtatg 3960 attccggttc agcccttaga gattaatccg gatttgactt ataatgagga acccatgatt 4020 attttggaat agaaagagga agtcctgaga aataaaacag tgtacttggt aaaagtttta 4080 tggaggaatc attcagcaga agaaactact tgggagacaa aagatcgaat gagagggatg 4140 tgttccaggt tgttttatgg atatcgatgg attgtaaaga ttgtgtaaat ttcgaggacg 4200 aaatttttta aggtgggtag at 4222 // ID Copia46-PTR_I repbase; DNA; EDCOT; 4244 BP. XX AC scaffold_218; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia46-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4244 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4244 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 270-270 (2007). XX DR Genome; scaffold_218; Positions 143297 147540. XX CC Positions [1682-2164] - Integrase core CC 'CCAA' target site duplication CC LTRs are 90% similar to each other. XX FH Key Location/Qualifiers FT CDS 1508..4051 FT /product="Copia46-PTR_I_1p" FT /translation="MMWQQKLGHMSEKGLKILSNQKLLPRLTKVTLPFCEH FT CVTSKHHKLKFGTSTTKSKCILDLIHSDVWQAPVVSLGGARYFVSFIDDFS FT RRCWVYPIRRKADVLTIFKTFKARVELEYEKKIKCLRTDNGGEYTSDEFDN FT FCQHEGIKRQFTTAYTPQQNGVAERMNKTLLERTRAMLKAAGLGKPFWVEA FT VNTARYVINRSPSTAIELKTPMEMWIGKPADYSRLYIFGSLVYVMYNTQEV FT SKLNSKSRKCVFLGYADGVKGYRLWDPTAHKVVINRDIIFAEDKMQMEENN FT SILKKTTEVQMENTQNHTSSEVAPEHEEQEQIESETPEVRWLTRERRPPAW FT HLKYVTESNIAYCLLIEDGEPSTFHETIKSTYVSIWMTAMQEEIEALHKNN FT TWDLVPLPQGRKAIGNKWVYKIKRDGNDQVERYRARLVVKGYAQKEGIDFN FT EIFSPVIRLTTIRVVLAMCAIFDLHLEQLDVKTAFFHGELEEEIYMLQPEG FT FAETGKENLVCKLNKSLYGLKQASRCWYKRFDSFIISHGYNRLSSDHCTYY FT KRFEEDDVFIILLLYVDDMLVIGPNKDRVQELKAQLAREFDMKDLGPANKI FT LVMQIHRDRSKRKIWLSQKNCLKKILRRFNMQDCKSISTPLPINFKLSSSM FT SPNNEAERMEISRVPYALVVGSLMFAMICTRPDIAQVVGAASRYMANPGRE FT HWNTIKRILRYIKGTSDAALCYGGSELTVRGYVDSDFAGDLEKRKSTTGFV FT FIIAGGAVSWVSKLQTIVALSITEAEYMAATQACKEAIWMKKLMEELGHKQ FT EKILLYCDSQSALHIARNPAFHSRTKHIDVQYHFVHEVVEDGSVDF" XX SQ Sequence 4244 BP; 1444 A; 708 C; 983 G; 1109 T; 0 other; tacacaaagg ttattcgtgt atatagttat tattcacgtc tacgacacta ttcacctata 60 cgacactatt catccataca gtactgttca catacattac tgttggcgta taaagaaagt 120 cagtgcggtg attaaataca gtctaggaag ttctgtctga ggagattggg ttttaagcgg 180 gaccgtttgt gacccctcca atctttcctg ggaacttact tagtaaagta ttattcacac 240 gatactattt ctttatacat tacagaccag tgaaaacggt gatagctgaa tagatcacgg 300 tgaataaaat ggcaataaag tacgagattg agaggttcaa tgggagcaat ttctcactgt 360 ggaaaatgag aatcaaggca attttaagga aagacaattg cttgacagca attggagatc 420 gacccgcgga gatcactgat aatgcaaaat ggaatgagat ggatggcaat gctattgcta 480 tcatacattt agcattagct gatgaagtat tatcaagtgt ggcggagaat aaaacaactc 540 aggagatatg gtagactcta acaaagctat acgagtccaa gtctttgcac aataagattt 600 tcttaaagcg gagactttat acccttcgaa tggcagaaac cacggcgatg actgaccaca 660 tcaacacaat aagaactcta ttttcacaac tcactacgtt gggtcaacaa atagaggaag 720 atgaacgtgc agagcttcta cttcaaagtc ttcctgattc atatgatcag ctcattatca 780 acttgaccaa taatatcctc tcaaactatt tagtctttga tgatgttgca gtcgttatct 840 tggaagaaga aaataggcgc aaaaacaaag gagatagaaa tagttcaaac caagtagagg 900 cattgttggt gtcaagagga agatcaacgg agcgtggctc tagtgggagt caaaggtagg 960 ggaggtccaa atcaagaagt aagaagactg tgaaatgcta caattgtggc agaaaatggc 1020 acttcaaaag ggattgttgg tttaaaaagg gtatggagaa tactgcagag tcattaaaac 1080 ctcaaggatg tgttgcaagc acctcagaag atggagaggt tttatatagt gaagcagcga 1140 caatctctac agatagagaa gagctcactg aggtctggct aatggattca ggagcaacat 1200 gacatatgac tcctaatcga gattggtggc actggcacca tcaaattgaa gatgtatgat 1260 ggcttaattc gtactattac aggagtgcga catgtgaaag acttaaagaa gaatcttttg 1320 tccgtaggac aatttaatag tcttggctgt aaaatccgaa cagacaatgg aataatgaaa 1380 attgtcaaag gagcgctggt ggttttaaag ggaagaaaga tagttgcaaa tatgtttgta 1440 ttaataggag acacatcatg aggcagaagc gtcaatcaca tcagccattc ctgcagaaga 1500 gaagacgatg atgtggcagc aaaaactagg ccacatgtca gagaaaggtt tgaaaattct 1560 ctctaatcag aagttactcc ctaggcttac aaaggttact ttaccctttt gtgagcactg 1620 tgttacaagt aaacatcaca agttgaagtt tggcacatca acaactaaga gcaaatgcat 1680 cttagacctg attcactctg atgtttggca agcaccggtt gtatccttgg gaggagcaag 1740 atactttgta tcatttatag atgacttctc caggagatgc tgggtgtatc caattagaag 1800 gaaggcagat gtgcttacaa tctttaaaac ttttaaagcg cgggtagaac ttgaatatga 1860 aaagaagatc aagtgtttga ggactgacaa tggaggagaa tataccagtg atgaatttga 1920 taacttttgt caacatgaag gtatcaaaag gcagttcaca acggcataca ctccacaaca 1980 aaatggagtg gcagagcgga tgaacaaaac tctattagaa agaacaagag caatgttgaa 2040 agctgcaggt ctaggaaagc cattctgggt agaagcagtc aataccgccc gttatgtgat 2100 aaaccgatct ccatcaactg caattgagct gaagacaccg atggagatgt ggattggaaa 2160 accagctgat tattctcgat tgtatatatt tggaagtctt gtgtacgtga tgtacaatac 2220 tcaagaagtc agcaagctga attcaaaatc cagaaaatgt gtattcttgg gatatgctga 2280 tggagtgaag gggtatcgcc tgtgggatcc cactgcccac aaggtagtca taaacagaga 2340 tatcatattt gcagaagata aaatgcaaat ggaagaaaat aatagcattt taaagaagac 2400 tacagaagtc cagatggaaa atactcagaa tcatacttct tctgaagttg caccagagca 2460 tgaagaacaa gaacaaatag agtctgaaac tcctgaagtt cgatggttga ctcgtgaaag 2520 aagaccaccg gcttggcact taaaatatgt taccgagagc aatattgcat actgtcttct 2580 aatagaggat ggagagccat caactttcca tgagactatt aaaagcacat atgtatctat 2640 atggatgaca gcaatgcaag aggagattga agctctgcac aagaataaca cttgggatct 2700 tgttccgcta ccacaaggaa gaaaggccat tggcaacaaa tgggtttaca agataaagcg 2760 tgatggcaat gatcaagtgg agcggtaccg tgcaagattg gtggtgaaag gatatgctca 2820 gaaagaagga atagacttca atgagatatt ttctccagtg atacgactta ctacaatcag 2880 agtagtcttg gcgatgtgtg ctatatttga tcttcactta gagcagttag atgtgaaaac 2940 tgcatttttt catggagaac ttgaagaaga aatttatatg ctccaaccag agggttttgc 3000 tgaaacaggc aaggagaact tggtttgcaa gttgaacaaa tctctatacg gtctcaaaca 3060 ggcgtcgagg tgttggtaca agagatttga ttccttcata attagccatg ggtacaacag 3120 acttagttca gaccattgta cgtattacaa gaggtttgaa gaagatgatg ttttcatcat 3180 tttgttgttg tacgtggatg acatgttggt aataggcccc aacaaagatc gagtccaaga 3240 attaaaggca cagttggcta gggagtttga tatgaaggac ttgggaccag caaacaagat 3300 tctagtgatg caaattcacc gagatagaag taagaggaag atttggcttt ctcagaagaa 3360 ttgtttgaag aaaatcttgc gacgcttcaa catgcaagat tgtaagtcaa tttccacccc 3420 acttcctatt aacttcaaat tatcctcaag tatgtctcct aacaatgaag cagagaggat 3480 ggagatatct cgagtaccgt atgcattagt agtgggaagt ttaatgtttg ccatgatatg 3540 tacaagacca gacattgcac aagtagtggg agcagctagt cgatacatgg caaatcctgg 3600 tagagagcat tggaatacta ttaagaggat cttgagatac atcaagggta cctcagatgc 3660 tgcattatgt tatggaggat cagaacttac tgtcagaggt tatgttgatt cggattttgc 3720 tggtgacctt gagaaaagaa aatccactac aggctttgtg ttcataattg caggaggagc 3780 tgtgagctgg gtctctaaac ttcagactat tgtagcgtta tccataacag aagcggagta 3840 tatggcagct acacaagctt gtaaagaagc aatatggatg aagaaactta tggaggagct 3900 cgggcacaaa caagagaaga ttcttttgta ttgtgatagt cagagtgcct tgcatattgc 3960 aagaaatcca gcgtttcatt caagaacaaa acatatagat gttcaatatc actttgttca 4020 cgaagtggtg gaagatggaa gtgtggattt ttagaaggtt caaacaaaag aaaacccagc 4080 aaatgctttg accaaatcag tcaacactga taagtatata tggtgcagat cctcttatgg 4140 cctagcagaa acgtaagcag catgaagatg gtaagcatag aaaggataga agaatcacaa 4200 atgatcaagt gtgaagactt gattaaatca tcaaagtctt caag 4244 // ID Copia-93_PTr-I repbase; DNA; EDCOT; 2902 BP. XX AC . XX DT 23-DEC-2009 (Rel. 15.02, Created) DT 23-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Copia-type LTR retrotransposon: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Copia-93_PTr-I. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2902 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 170-170 (2010). XX DR [1] (Consensus) XX CC >90% identity to consensus. XX SQ Sequence 2902 BP; 842 A; 576 C; 850 G; 634 T; 0 other; attggtatca gagcacatgg tttaaagggg tgtttgattt ttgctcaaaa atgaaagttg 60 tcaaaattgt gttttgacca taccactgtg tagaggagga agagacgaag ccactggtga 120 aaacggcgtc aaaatcggac gtcggacatg gccgcactct ccatcactct ccggcaaggc 180 gtctgcccac gcgcgcagac gcgccccacg cgtcttcttc gcccggatgg gctgacccga 240 cccgaatacc agttgacccg acccacgtgg ctgacccgga tatggatgac gtcagcatga 300 cataattgtg atgtcagcat gcacagtagg catgccaggg atgacatcag catgatgtaa 360 gtgtgacgtc agcatgcaca gtaggcatgc catgtcagca gccacgtcat cgaccagtca 420 gcagacacgt cagcacagtg ggacccacct gccacgtcac cagccgcgag ccgagccgag 480 ttgagccgag ccgagagccg agccgagccg cgagccgagg gacaggatcc agtgtagctg 540 atcctacgtg caaccggatc tgagattgaa tctgggccgt tcatcaggcc agaattgttt 600 tgatcaaatc ttagccgtct gaaatgcgat ttggacgatt tcagacttgt ttccagctaa 660 tttgatcgtt ccggatgcaa tggtacggtc cgatcgttga gatttgagac caaaaatggc 720 ggtggtgaat taacaaaaga gattgcccga tcaggaggca tctgaaggtc atcatggtgg 780 tcgatggaga tgaagaagaa gaaggcgcac atgtttaccc aattacatgt gctgaactgc 840 taagtgggga gaattttaat tgccttgagg gaaggcaaaa ttgggacact ctggacaccc 900 gatcatgtgg acaatttgag gtgtagagtg gaaattgatg aagaccaatc ttgacgaatc 960 taagaactgg tagtctcgcc agatgttgag aaatcatgta ttaaaccagt atattccaga 1020 tcacttgtaa aggaaagccg caacaaagct agcaaatggt tgtatatacg gaaagacagt 1080 acgatggata gatatggcct aagaagttct gtctaggaga ttgggtttta agcgggacca 1140 gtgtgacccc tccaatcttt cctgggaact tgcttagtgg aaggattatc catacggtac 1200 tattttcgta tatatagcag tttgtaatga aacggttgaa gactagcagg atgacggcac 1260 aagggaacag ttgggttccg tatgatcaag gatctgatgg agtggtgatt tctccaaaga 1320 agttagattc ggtgactgtg atttctcgag gggagaattg atgaagaccc tgataatgga 1380 agagaaatac agcaagggga taaagattgg caccctattt tgacttggac aggtgttgtg 1440 acaggatgag ctgctgtcaa acataagcaa ggaataggga gaaatctgga gaacagaaat 1500 tgcacgaggg cacacggaga ttgtgcagga gtacccgtag gatccaacga ggtactgtaa 1560 tgagacaaca ggtgcaagga gaagaagtgt tcccagatga agctcagagc agagactgtt 1620 aaagtttgta caacaggaag tctcttgtgc tcttgatgaa gacaacaggc gaagaccttt 1680 ccaatgcatg caaggatgga aagagagctg ttgcagaggc acctaattga gggggtgcaa 1740 acgcctgtga taaaaggcaa ccgcctatga tgaaaggcga agacaccaaa gagagttggt 1800 gtaggtggag ctgtcaagca gaaaggcaca gaagctccaa acatagaaat cgaggtggag 1860 gattgcgagg agtataccgc aactttctct ttctatgtag tcagtggcag taatctctcc 1920 catagtgcac atggtggtag agaattttgg agccactttg aagcatctca gctgaaggag 1980 gatgcgaccg ccccatgaca acgggcgaag acaccttaga gaaggtgtga gggccatgat 2040 aggagcccag atcagaccgc cccatgacaa cgggcgaaga caccttagag aaggtgtgag 2100 ggccgtgata ggagccccag ttcagaccgc cgcatgacga cgagcggaga cacctaagga 2160 gaaggtgtgt gggccacgat atgagcccag ttcagaacaa ccccagagcc aatgtgatgg 2220 ctagatacga gtggacaggt gtatagccaa tgaagtggct atgatgagta tggagacaaa 2280 tgcaggattg actttcatgg atattgcccc catgctaaag atcaatgagc tagaagacat 2340 ttgccttgga caataagtgt gtgacttgtg gagcattaag acgcggctgc tatgaagaag 2400 cagaagggca tgcgcaggtt ccgggaacga gttgactctt gtcaaggtgg tgagctcggt 2460 aatggcattg taatactcag agtatgaaga cagatatgga tcaaccttta atgggctgcc 2520 cccatggtta aaggtggaga gctacctgga ctcttacgac taagagcgag agactcacgg 2580 agaagtaagg cgtggttcct agggtggaac agagggcagg cgcaactcct ggatgagtag 2640 actcttggaa gagtggtgag cttgtgatca cattgagata ctcaatgact gtcgcacttg 2700 gaaatattcg tttgaggggg tgttgtaagc cttggtgtaa ggcttgaaaa atcattccgg 2760 accgagcatg gttgatacgc tcgaagggga atgttgtgtt gaagacgctc tcagaatggt 2820 aagcttggaa gagctgcaga atgcaagctt gtgctgaaga agcaagagga caattgccca 2880 cacgaatggc aaagggggtg at 2902 // ID Gypsy6-VV_LTR repbase; DNA; EDCOT; 1959 BP. XX AC AM424945; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy6-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1959 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-1959 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 695-695 (2007). XX DR Genbank; AM424945; Positions 2797 4755. XX SQ Sequence 1959 BP; 583 A; 357 C; 382 G; 634 T; 3 other; tggttactac tcaaaatgtg ctatttcata gcttgtaatt aactctttta aacacttttg 60 agtagtagtt attgcctttt aacccaatta acatattaag gacctttgca agcacttcta 120 atcaatatgt gttaaatttt ggtgttttga tagctttttg atcaccaaag caatccgaga 180 ttgaggagag ttatgtggaa tctttggcaa agcaaattga agctcagaaa crtgaagaac 240 taaagctttg aagtmctttg cttccatgag taaatccgga atgtaaggag aagaarcaaa 300 gagaaatctg ttaggaagca tattcttgat gatagtcatg tcaaccactt ttggagcact 360 ttccgaagtc cattttctac atgctatatg ttgtttcgaa gctcaggaag tgaaaaatcc 420 aatgcttcaa acggtgcata atttggagtt gaaatgaagg agttacaacc attgtaagcc 480 tatcactcca agctgaagga agaattttgc acagtgctgc gaaatcaccc ttttgttgcg 540 aaatgatttc gcagcctttt tgcacagtgc tgtggaattc ctcctaaagt ttcccgatat 600 atatgacacg ttggaagccg aacaccacaa gctgaaagat cacttcgcag cgttgcgaaa 660 tgagccggtt gctgcgaagt gatttcgcag tccttcttgt gcctctgcga aatctcgcag 720 acatcatttt cacttgcgaa atgatcctta gtgcgtcccg atatttgcta ccgacattgg 780 gagatatttt tcatcagatt tttgttgtct aaatcccaaa attctccttg aaagccacca 840 attataagat tccttagttt ttaagttagt aaaaagagta aatatccatg taataattag 900 tttttgtttt tgttgatata aatagctctt gagagcgtgt tctcagagaa gaaccttttt 960 tttgtaaaag tttgaaagta agtaaaattc aggacctttg ttttgcctta ccttctcact 1020 ttgtatcatt tattttttct aagttatgca ctctctgagg aagtttccct agagaatgag 1080 taactaaacc tttagttcct tggagctaag gttgtcggga aaggttccaa gtgcaaaaat 1140 gtagagcttt gtggtttcag ccatgaatga agaggaagag aaatccttta gtgatttcta 1200 tgtttttagt taacttaaaa caccttagag tcacctgggc caacacttgg taaggcaagt 1260 gatctccaac catagagatg cactagttta ccccttgcga gcctctacga ggtgacttga 1320 aggtaggatt ttctagaatt gccaacactt ggtaagcttt tggactccaa ggagacatcc 1380 attagttatc tcttgcgagc ttaagaaggg aagtccaagg ttaaagattc accttgaatg 1440 gttaaggctt agtgagaggc tcgaaccgtt gcaagttgca tcagtgagag aattaaagct 1500 gaaatctaat taaatgatat atctgtacaa caccggttag agaattgact atatgttaat 1560 tctctctcac gaggaaatga accaactaac ctgagctatg tcttttgcat gaggaacctc 1620 ccctgtgaac caaaatctct aaggaatgtt ttcttcataa gtaatttcca ttacttgttt 1680 tgccattagc ttaaatctaa atctttttaa accaaagttt gtgttttatt tcttgagcta 1740 accttgaaat gaaaaagcac caattcactt tgaattggta tcatttgtaa tttggaaacc 1800 cttcctagtg aacgatccta gagccgctat actatagtag ctttttcttt gctaccctag 1860 tatatggtgt aataggttat aaattttgtt gattactccc tcgatcaagg agcaccagct 1920 ggacatgaat cagttgagac accaagtggg cacaaatca 1959 // ID Copia16-VV_I repbase; DNA; EDCOT; 5582 BP. XX AC AM460200; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia16-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5582 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-5582 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 696-696 (2007). XX DR Genbank; AM460200; Positions 17580 23161. XX CC Positions [2811-3137] - Integrase core CC 'CTTG' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 2937..4661 FT /product="Copia16-VV_I_1p" FT /translation="MPGTPQQNGVAERRNRTLMDMVRSMLSNSSLPISLWM FT EALKTAIYLLNRVPTKTVPKTPFKMWTGRKPSLRHLHVWGCPAEARIYNSH FT EKKLDFKTISGYFIGYPMKSKGYRFYCPNHSTKIVETGNARFIENDEIRGS FT DQLQKTNIQEVRVQVPLPITSKEIVVPTIVESFGNVEQQINDQSLSNEIIT FT NEPIMEGPQQSTLRSQRERRPAISDDYVVYLQESDYNIGTSKDSVSFSQAI FT SCSDSDKWIDAMNDELKSMDQNKVWELVELPERYKTVGCKWVFKTKRDSKG FT NIERHKARLVAKGFTQKGGIDYKETFSPVSKKDSLRIIMALVAHFDLELHQ FT MDVKTAFLNGNLEENVYMDQPEGFSIKGKEQMVCKLNKSIYGLKQASRQWY FT LKFNDTITSFGFKENIVDRCIYLKVSGSKFIFLILYVRYILLASSDLGLLH FT TTKKFLSENFEMKDMGEATYVIGIEIFRDRSRGLLGLSQNQYIETILERFS FT MKNCSASVAPIQKGDKFSLMQCPQNEWEHKQMERIPYASVVGSLMYAQTCT FT RPDISFAVGMLADTKVILEWIIGKLQRK" XX SQ Sequence 5582 BP; 1810 A; 834 C; 1097 G; 1837 T; 4 other; cttgggtcca tttgagaatt agtttcaaat ctcttcatat cctaaaataa tagtagacat 60 atagatgaag ttatgcagca accatcttct agtagacata aaaaaaaatt cagccaaaat 120 aaagccagag atagaaacta ctaggattta gaaattctgt ggctcttctt catgatgccg 180 aataaagatc tgcaaatcac attaaaggag tggcagaaaa atacccgtaa aatataagac 240 aaattaaatt tttatttatt taatttattt acattattta taacatatta tccagtgact 300 aactaattcc tagataagtg ggtttttatt tttctgggta attcatatat gatgctattt 360 ccatgagaat ttctagtgat attgttggct actttaattt attaaacaaa tcacatattt 420 ttcgtgcatt tttttttcca cgtgatgcta catgctacat gcctatcttt tagtaaattg 480 ataattatag aacacagtgc acggaatgtg tatcatttac aaatctgatt catgtctaga 540 ttttataagt gacatttctt gtattgatat gttataattt ttttctatag tttatatgaa 600 catgaaattg tcacttatat gaaactgttt agatgataat gtgatgtgat tgatgataaa 660 ttgttttgca aagtgattat ttcaactcga aatcctattt tatgaaatag tttggtgatc 720 accaaagtga accaactaga aagtcatagg ttttaagttg tattttggat cttaatacta 780 atatcccaca tattaagaaa atagctttgc aaatttttga atagatatta atatgtatct 840 ttgatcatga gaatattttg gcttggccca aaggtgcacc atttttcttg tgattaacat 900 attgaggtaa aataattaat atgtaccctt aattgagagt tggaatcgga tacccaaagg 960 taacggacct atcggattat ggatacatta ttaattattt ttgataggtg aaagggaatc 1020 accataatag tcaaaagttt aattttgtat gttgtaattt tcatccaaag atatgttaca 1080 atagtactat ttattattta ttatttaact caaagcatta atgtgtgagc atatatttaa 1140 ttgcagtttc agttcctatt tcgcttcatt ctcacgcttc atctgttcca atccttaatg 1200 gaacaaattt ctcagactag tctgagcaag tccagtttca cctaggtgta ttggatcttg 1260 atttggcact tcggactgag aaaccgcctg ctattactga ggaaagtagt gcggaagaaa 1320 aaacttttaa gttattcttg ggaaagattg aacagattga gcattatgtt tatgcgaatg 1380 agtatagcaa acaacattaa gtcaacactt cctraacatg acactgctaa ggaatttttt 1440 aagactgtgg aaraacgttt tcgttcagct gacaagtctc ttgctgggac attaatggct 1500 gaacttacca ccatgaagtt tgatggtact cgtgggatgc atgagcacat ccttgagatg 1560 tcaaatctag ctgctaaact aaaggctctt gggatgaatg tgaatgagtc ttttcttgtt 1620 caatttattt tgaactcctt acctcttcaa tatrggccat ttcaaattca ttacaacact 1680 attaaggaca agtggaatgt aaatgaattg gccaatatgc ttgttcaaga agagacaaga 1740 cttaagcaac aaggacatca ttcaattcac cttataagta aaggagctag taagaagtgg 1800 aagaaaccta agaagggcaa aatggcagaa ccacctaaga tcaatgggcc aactcaaaga 1860 atagaggttc atgaaagggg acaaaacagt atcaagtgtc gtttctgtaa gaagcttggg 1920 catgttcaga gagattgcca caaacgtaag gtatggtttg agaagaaagg taagccttta 1980 gcttacgtat gtttcgaatc aaatcttact gaagttcctt ctaatacttg gtggattgac 2040 tcaggttcca ctgttcatgt ttctaattcg atgtagggct tccttataat ccagacttta 2100 aaccaaaatg aaagttccat agttgtggga aatggagtca aagttccagt ggttgctacc 2160 aggacatttc gtttatttct agacactgat tgttatctag atttgtttca gactctttat 2220 gttccttcta tttcttgtaa tttggtttct atgtctaaac ttgaccttga aggttattca 2280 ttttcatttc gtaatagaag attcagtttg tttaaaaatt cttcttttgt tggttccgga 2340 agtttatgtg atggtttgta taaactgaat cttaataatc gttttgctga aagccttcta 2400 accctgcatc ataatgtcgg aactaaacgt aacctgatca atgaaagttc ttcttacttg 2460 tggcacaaac gtttgggtca tatatccaaa gaaagaatga agagattagt gaaagatggg 2520 attttgcata acctagattt tactgatctc gatgtgtgtg tggattgtat taagggaaaa 2580 caaaccaaac atacaaagaa gggtgctaca agaagtggag aacttcttga aatcatccat 2640 atagacattt gtgggccgtt tgactcacca tcttttggta aagaaaaata ttttatcact 2700 ttcattgatg atttttcacg ttattgttat atctatttat tgcatgaaaa atctcaagta 2760 atggatgccc tagaggtgta cattgttgag gttgaaaagc aattagataa aaaaaagtga 2820 caattatcag atcagataga ggtggtgaat attatggtag aaatgatgga ttgggtcaat 2880 gccctggccc atttgctaaa ctcctagaaa agcatggtat atgtgcacaa tacactatgc 2940 caggtacgcc tcagcaaaat ggagtggctg aaaggcgtaa tcgtacattg atggatatgg 3000 ttaggagtat gttaagtaat tcctctttac ccatttcatt atggatggaa gcccttaaga 3060 ccgctattta tttattgaat agggttccaa ctaaaacagt tccaaagact ccttttaaaa 3120 tgtggacagg aaggaaacca agtttaaggc acttgcacgt ttggggttgc ccagcggagg 3180 ctaggattta taattcacat gaaaagaaat tggatttcaa aaccattagt ggttacttta 3240 ttggctatcc aatgaaatcc aaagggtata ggttttattg tcctaatcat agtacgaaaa 3300 ttgttgaaac gggtaatgcc agattcattg agaatgatga aatccgtggg agtgatcaat 3360 tacaaaaaac aaatattcaa gaagttaggg tgcaagtccc actacccata acttctaaag 3420 aaattgttgt tcctacaatt gtagaatcat ttggcaatgt tgaacaacaa attaatgatc 3480 agtcactctc caatgagatt atcactaatg aaccaattat ggaaggacca caacaatcaa 3540 cattaaggtc tcaaagagaa cgtagacctg ctatttctga tgattatgtg gtttatttac 3600 aagaatctga ttataatatt gggacaagta aagactcggt ttcattttca caagccatta 3660 gctgtagtga ttctgataaa tggattgatg ccatgaatga tgagttgaaa tcaatggatc 3720 aaaataaagt ctgggaactt gtcgaattgc ctgaaagata taaaacagtt ggttgtaaat 3780 gggtctttaa gaccaaacgc gactcaaaag gcaatatcga acgacataaa gccagacttg 3840 tggccaaagg tttcactcag aaagggggta ttgattataa ggagaccttc tctcctgtat 3900 ccaagaaaga ctcacttaga atcattatgg ctttagttgc tcattttgat ttagagttac 3960 accaaatgga tgtgaaaact gcttttctta atgggaattt agaagaaaat gtttatatgg 4020 atcaacctga aggtttctcc ataaagggaa aagaacagat ggtttgcaaa ttaaataagt 4080 caatatatgg acttaaacaa gcttctagac aatggtatct taaattcaat gatactatta 4140 cttccttcgg atttaaggaa aacatcgttg atcggtgtat atacctgaag gttagtggga 4200 gcaagtttat atttctaatt ttatatgttc gttatatttt gcttgccagt agtgatcttg 4260 gtttattgca cacaaccaag aaattcctct ctgagaattt tgaaatgaaa gatatgggtg 4320 aggcaactta tgtgattgga atagaaatat tccgtgatcg ctcacgtggt ttgttggggt 4380 tgtctcaaaa ccaatatatt gaaacaatct tagagagatt tagtatgaag aactgttcag 4440 ctagtgtagc cccaattcag aaaggggata aatttagtct catgcaatgt ccacaaaatg 4500 aatgggaaca taaacagatg gaaagaattc cttatgcttc tgtcgtagga agtttgatgt 4560 atgcacaaac ttgcaccagg ccagacatca gttttgcagt tggtatgttg gcagatacca 4620 aagtaatcct ggaatggatc attggaaagc tgcaaagaaa gtgataaggt acttgagggg 4680 aacaaaagat yacatgctta cttttaagag gtctgataat ttggaggtga ttggctacac 4740 aaattcagac tttgctggat gtgttgatag tagaaaatca acttttggtt atgtatatct 4800 attggctggg gcagcaattt catggaaaag tgctaaacaa actatcattg ctgcatccac 4860 aatggaagct gaatttgtgg catgctttga ggccacgatt catggtttat ggctgcgaaa 4920 ttttatctca gggcttgcta ttgtcgacac tattgagaag tcgttgaaga tttattgtga 4980 taattctgca gctgtatttt tctccaagaa cgacaaatac tctaatggtg ctaaacacat 5040 ggagttaaag tattttgccg ttaaggagga agttcagaaa caacgtgtgt ttatattaat 5100 actgagctca tggttgcaga tccactaact aaagggttac caccaaagac atttaaagaa 5160 catgttaaaa gaatgggtct tgattgtaac ccttgatgcc tattatgttt ggattgcaaa 5220 tgtttgttta tgttattaga cattttgaga tctcattaat catgttttcc attttgtacg 5280 tacatctatg agattggata aatgataaca ggaagtcttt tacaaagaca tttttttgtt 5340 ggaccaattt tggatacttc tcatttatga accatggttg attggattgc tagtgttgta 5400 gtacatggaa gggactatgt tgccttatta atgtacaacc gccatgactc atactagtga 5460 ttcatttgac catagtattt atgatgacca atttgagtta gaaatggatt agttttttat 5520 gcgcataatg ttgacttcat tggggctaaa ataaagttag tcatatggga taagtgggag 5580 aa 5582 // ID Copia-62_Mad-I repbase; DNA; EDCOT; 4631 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-62_Mad_; KW Copia-62_Mad-LTR; Copia-62_Mad-I. XX NM Copia-62_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4631 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1662-1662 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1866-2366] - Integrase core CC 'TGTAG' target site duplication CC LTRs are 92% similar to each other. XX FH Key Location/Qualifiers FT CDS 67..1854 FT /product="Copia-62_Mad-I_1p" FT /translation="MENLPPLHGGNNPILTDSTPTLNTTTLTDPTMNPTLP FT IPQVVTQIVHHDSSTASIGIKLNGANYGVWSQIVEMFVAGKDKLGYLFGSN FT PQPPIDDPAFTKWRTENAIVKGWLINSMEPNLIGYFLRLPTAKEVWDAVAR FT TYYDGSDISQVYDLTCKASRMRQDGRPVETYYSDLQSLWQEIDYRRPNPMK FT CGTDIEIFNKIVQTDRVYTLLAGLDEMFDKIRSDILRTEPLPSVEQTFAYV FT RREGMRQAVMNTGGQLPSGAAMVARPATRAVAPPRPRAPDKSPAPSPGLQP FT QATAPSPAQGSLFAARTASRPTTGPRPPRPKPPVPAGGCTYCGSEKHGRDN FT CFQLHGYPDWWEPLKLQKQRERDEQANLATSMSQLSLISQDDPPPVSSSSD FT MPPESSGNCGYAFNMNSDDTPSGWIIDSGATDHMTYDPTDLACDTVPLRRN FT ITNANGVTSPVTGAGTVRLTPTLSLPHTLLVPSLKHKLMSPGQATEQLNCC FT VLMYPKFCLIQDILTKEIIGRGTKRGISILWMMSVQDGSISPKEPLITSGV FT RYGYGITVWVIHLSVICSICFRIYLLVVRFQTLNVTLAYLPRVTVFLIR" FT CDS 1764..2846 FT /product="Copia-62_Mad-I_3p" FT /translation="MFPDLFVGCSVSDFKCDTCILAKSHRVSYPLNSNKSV FT IPFGLVHSDVWGPSPITTSSGIRWFVTFIDDCTRMTWLYLLKHKSDVFLAF FT KTFHTMVQTQFSTKIRILRSDNGGEYVNNDFSHYLTNHGILHETTCPQTPQ FT QNGVAERKNRHLLETARSLLIGAHVPRSSWDVALQTATYLINRLPSKVLDF FT LTPLQVLATFVHLPSVLVLPPRVFGCVAFVHLHKNQRTKLDPCALRCIFMG FT YGLHQKGYRCYHPPSRRMYVTMDVTFSESEMYYPSASSNPPPQGETRHDEK FT DWTMGATADLPLPLAEPIAAALPAQPTAAAVLPTEPTAGTAVPSSPTATVL FT PLVNFETSTDTTPPRLQI" FT CDS 3137..4621 FT /product="Copia-62_Mad-I_2p" FT /translation="MEEEMDALQKNQTWDLVPLPRGKKRVGCRWVYTIKYK FT ADGSVERYKARLVAKGYTQTYGVDYTETFAPVAKINTVRVLLSLAANLDWP FT LQQFDVKNAFLHGNLKEEVYMDIPPGYASVSQPGVVCKLNKALYGLKQSPR FT AWFGRFRTAMRKYGFRQSNSDHTLFLKRRMGKLTALIIYVDDMIVTGDDKE FT EISRLKDYLATEFEMKDLGGLKYFLGIEVARSKQGIFLSQRKYVLDLLAET FT GMLDCKPADTPIVQNHHLAVHPDQVPTNRDRYQRLVGRLIYLSHTRPDIAY FT AVSVVSQFMHSPSDTHMGAVERILRYLKSSPGRGIMFSKNDHCRIEGYTDA FT DWAGNVTDRRSTSGYFTFVGGNLVTWRSKKQKVVALSSAEAEYRGMAKGVC FT ELLWLRRLLGELGCPSKSASDLFCDNKAAIDISHNPIQHDRTKHVEVDRHF FT IKEKLDGNIIQFPFVKSEDQLADILTKAVASQAFYNSLVKLGMNDIYAPT" XX SQ Sequence 4631 BP; 1196 A; 1097 C; 1060 G; 1276 T; 2 other; tggtatcaga gcagagatcc taggatttct gctctgcccg ttccctcaag caaactcggc 60 cctcccatgg agaacctacc accactccac ggtggaaaca accccatcct aaccgattct 120 actcctacac taaacactac aaccctaacc gaccctacca tgaatcctac cctacctata 180 ccgcaagttg ttacacagat tgtccatcat gattcgtcta ctgcttcgat tggcatcaaa 240 ctcaatggtg ccaattatgg agtttggtct caaattgttg agatgtttgt tgctggaaaa 300 gacaagttgg gctacttgtt tgggagtaat ccccaaccac ctatcgacga tccggccttc 360 accaaatggc gtacggagaa cgctattgtg aagggttggc tcatcaactc tatggaaccc 420 aatttgattg ggtactttct tcgactaccg acggcaaagg aagtgtggga cgcagttgct 480 cgcacgtatt atgacggctc cgatatatct caagtctatg atcttacctg caaggcctct 540 cgcatgaggc aagatggacg accggtggag acatactata gtgatcttca atctttgtgg 600 caggagattg attatcgtcg acccaatccg atgaagtgcg gtactgatat tgaaattttt 660 aataaaattg ttcaaacgga tcgtgtgtac actttgcttg caggattgga tgagatgttt 720 gataaaattc gtagtgatat tctacgaact gagccccttc cttccgtcga acaaactttt 780 gcctatgttc gccgggaggg aatgcgacaa gctgtgatga ataccggagg acagctgcca 840 agtggggcag ccatggtggc tcggcctgcc acacgagccg tagctccacc tcgtccccgc 900 gcccccgata agtcacctgc accgagccca ggactgcaac cccaggctac tgccccgagc 960 ccagcacagg gctcactctt tgctgctagg acggcctcac ggcccaccac gggtccccgc 1020 cctcctcgtc ctaaaccacc cgtcccggct ggtggttgta cttactgcgg tagtgagaag 1080 catggccgtg ataattgctt ccaattgcat ggctatcctg actggtggga accgttgaag 1140 cttcagaaac aacgggaacg agacgagcaa gccaatctcg ccacctccat gtcccaatta 1200 tctttgatat ctcaagatga tcctcctcct gtttcgagtt cttccgacat gcctccggag 1260 tcctcaggta actgtggtta tgcttttaat atgaatagtg atgatactcc gtccggatgg 1320 atcattgact ccggtgccac agaccatatg acttatgacc ccactgattt agcttgtgat 1380 actgttccac ttcgacgtaa tattactaat gctaatggwg tcacctcacc ggtaactggc 1440 gctggcaccg tgcgcctcac gcccaccctc tctttgcctc atacattact tgtaccttca 1500 ctaaagcata aattgatgtc tcctggccaa gctactgagc aattgaactg ttgtgtgcta 1560 atgtatccaa agttttgtct tatwcaggat attctcacga aggagataat tggtcgtggt 1620 actaagaggg ggatctctat tttgtggatg atgtcagtac aggacgggtc aatctcgccc 1680 aaggagccgt tgatcacaag cggcgtcaga tatggttatg gcatcaccgt ttgggtcatc 1740 catctttcag ttatttgcag catatgtttc cggatttatt tgttggttgt tcggtttcag 1800 actttaaatg tgacacttgc atacttgcca agagtcaccg tgtttcttat ccgctgaatt 1860 ctaataaaag tgttattcct tttggtcttg ttcattcgga tgtttgggga ccatctccga 1920 ttactacttc atctggtatt cggtggtttg taacgttcat agatgattgc acacggatga 1980 catggttata ccttcttaag cataaaagtg atgtgttttt ggcttttaag accttccaca 2040 ccatggttca gacacagttt tctactaaaa tccggatttt gcgttctgat aatggtggtg 2100 aatatgttaa taatgatttt tcacattatt taactaatca cggaattctt cacgaaacta 2160 cttgtcctca gactcctcaa cagaatgggg tggctgagcg caaaaatcgc catctcttag 2220 aaacggctcg ctcactcttg attggggcgc atgttccccg ctcttcttgg gatgttgctc 2280 ttcagaccgc cacttatctt atcaaccgcc tgccatccaa agtcctggat tttcttacac 2340 ccttacaagt ccttgctacc ttcgtgcatc taccgtcggt tttggtactc ccacctcggg 2400 tttttggatg tgttgcattt gttcatcttc ataaaaatca acggacgaaa cttgacccgt 2460 gtgctctccg ttgtattttt atggggtacg gactccatca gaaagggtac cgttgctacc 2520 accctccttc ccgtcgaatg tatgttacta tggatgttac tttttccgag tctgagatgt 2580 attacccttc ggcttcttcc aaccctcctc ctcaggggga gacacggcat gacgagaagg 2640 attggaccat gggtgctacc gctgatcttc cgctgccact agccgagcct atagcggctg 2700 cgctgccagc ccagccaaca gcagccgcag tgctgcccac agaaccaacg gcaggcacgg 2760 cagtgccgtc ctcacccacg gcaacagtgc tgccacttgt caactttgag acttctactg 2820 atactactcc ccctcgtctc caaatatagt accaccagat gaccatactc ctgagaatat 2880 tcctgaggta agctctacta tccctgttga tgtatccgat gttccgaatt atcagttacc 2940 tttcaggcac aaccggggaa agccacccaa tcgatattca ccggaaacaa cgaaaggctc 3000 taaatacccc attgccaact atgtgtcatc acataaatta tcagaacccg gcaaagcttt 3060 tgtacaacaa atatccaatg atagcacacc aagttcattg aaggaggcac tatctgacga 3120 tcgatggacc aaggcaatgg aggaagaaat ggatgcactc cagaaaaatc aaacatggga 3180 tttagttccg ctaccccgag gaaagaagag agttgggtgt cgatgggtgt acaccatcaa 3240 gtacaaagct gatgggtccg ttgaacgata caaagcacga ttggtggcca agggatacac 3300 tcagacgtat ggtgttgatt atacagagac atttgccccg gtagcaaaga ttaatacggt 3360 aagagtgttg ctttcattgg cggccaactt agattggcca ttacagcaat ttgatgtgaa 3420 aaatgctttc ttacatggta atcttaaaga agaagtgtat atggatattc cacctggtta 3480 tgcatcggtt tcacaacccg gagtggtgtg caagttgaat aaagcattgt atgggttgaa 3540 acaatcacct cgagcatggt ttggtaggtt ccggacggct atgaggaagt atgggttcag 3600 gcagagcaat tccgatcata cacttttctt gaaacgtcga atggggaaat tgacggcact 3660 tattatttat gtggatgata tgattgttac gggtgatgac aaagaggaaa tctcaaggct 3720 gaaagattac ctagcaaccg agttcgagat gaaagatctt ggtggattga aatatttctt 3780 ggggatagaa gtagctcgat ctaaacaggg tatatttcta tctcaaagaa aatatgttct 3840 agacttgtta gctgaaaccg gaatgcttga ttgtaaaccg gctgacaccc ccatagtcca 3900 aaatcaccat cttgccgtgc accctgatca agttcccact aacagagatc gttatcaaag 3960 gttagttggg aggttaattt atttatctca caccaggcct gatattgcat atgcagtaag 4020 tgttgttagt caatttatgc attctccgag tgatacacat atgggtgcgg ttgaacgcat 4080 cctacgatac ctaaagtcct ccccgggtag aggcatcatg ttttccaaga atgatcattg 4140 ccggatagaa ggttacaccg atgcagattg ggcagggaac gttactgatc gacggtccac 4200 atctggttac tttacatttg tgggaggaaa tttagtgact tggcggagta agaaacagaa 4260 agtggttgct ttatcaagtg cagaggcgga atacaggggt atggcaaaag gagtatgtga 4320 actattatgg cttcggaggt tacttggtga actcgggtgt ccttcaaagt cggcctcgga 4380 tttgttttgt gataataaag cagctattga tatctcacac aacccaatcc agcatgatcg 4440 cacgaaacat gtggaagttg acagacactt cattaaggag aagttggatg ggaatattat 4500 tcaattcccg ttcgtaaagt cagaggatca attggcggac atcttaacta aagctgttgc 4560 aagtcaagcg ttctacaact ctctcgtcaa gttgggcatg aacgacattt atgcaccaac 4620 ttgaggggga g 4631 // ID MuDr6_MT repbase; DNA; EDCOT; 863 BP. XX AC . XX DT 28-NOV-2006 (Rel. 11.11, Created) DT 01-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon, from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW MuDr6_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-863 RA Shankar R. and Jurka J.; RT "MuDr6_MT: A MuDr type non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 578-578 (2006). XX DR [1] (Consensus) XX CC The sequence lacks the transposase domain. On the both termini, CC it is flanked by 9 bp TSD (TATTTTAAC). XX SQ Sequence 863 BP; 289 A; 126 C; 109 G; 339 T; 0 other; gggttaattg ttcaaattga ccctgtaata tactttatgt ttgaaaaatg acccaataaa 60 atacaaaaca tatattctag cattgtaact tgaatttctt cttatttaat tttgaccacc 120 ctataatata cgtgtagtct aaaaatgtga cctacatgtt gaattttttc actatttttt 180 tcatacatgt ttagcacgtt aaaatatagc tttacacaaa aaattaaatt tcttcgacca 240 gggataaatt aattatgaat ttttattccc tcataattat gaatttctta aacaatttat 300 aattaatttg tatctcgttt aaaaattaca aaatttcatt gtgaaggttt cttatcatgt 360 tctagtcatg cctacaaaat tagggaacta aatttgactt gtgagtatac gcttacgcgg 420 aacaaaattt caattttgca cgtttcagtt gaaaaatcaa aataaattta aacgacttcg 480 aaatgctatg aaactttaca tatccttttt atgtattttt atagatgtct ctgcaaataa 540 tgagctcaaa attcgattta tagatcgaga tttccgttgt tttgtttttt gagcttttga 600 cactttaaaa attcataatt aatttgtcgt ttgtcgaaaa tttataattt ttttgtgtaa 660 agccatattt taacgttctt aactcgcctc taggaaatca tgaaaaaatt caatctctcg 720 gttgcttttt tggacttcgc gtatattaca gggttataaa taataaaaat ctcgaattac 780 atggtcagaa tacatgttat ttaattacag ggtcaatttt cagacttcac gtatattacg 840 tggtcaattt caattaataa ccc 863 // ID Copia-8_TC-I repbase; DNA; EDCOT; 4784 BP. XX AC CACC01018230; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-8_TC_; KW Copia-8_TC-LTR; Copia-8_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-4784 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01018230; Positions 6749 11532. XX CC Positions [2241-2540] - Integrase core CC LTRs are 97% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS 3254..4462 FT /product="Copia-8_TC-I_1p" FT /translation="MSAELKALQDSETWSIVPRPLNSHVIGCKWVYKVKLN FT ADGQIERYKARLVAKGYNQIAGFDYKETFSPVSKQTTVRVFFAITAAFNWH FT LTQLDVNNAFLNGDLKEEVYMDIPPGYEIQGEYPENVKLVCKLHKSLYGLK FT QASREWNAKIKSFIIQYGFIQSNADHSLFTMKTNNGEFIALLLYVDDIVVG FT SSSKQAADDVKLFLSSHFKLKDLGTVKYFLGLEIARSPEGISISQRKYTLD FT LLEEHGLLGAKPVSTPIDYNQKLVKAQDEEKLINSTNYRQLVGKLLYLTFS FT RLDIAYAVQVLSQFMDKPSLEHMNVAHRVLKYLKGSLGQGILMKSESNLMI FT VGYCDSDWAGCPNSRKSVTGYNMFIGNSLVTWKSKKQSVVSRSSAEAEYRA FT MASTSCEII" FT CDS join(798..2237,2241..3254) FT /product="Copia-8_TC-I_2p" FT /translation="MVFRFLNGLNDSFSAIRSQIIMMDPIPTLDKVYSLVQ FT REETQRSLLIQGQAVFESSAMMTVVETRKKGTRKDISCDHYGKKGHIKDKC FT YKLITFLGDFKFTKSKPNFRKAKTVANNATSIHEGPESDGCKIEQLDEGIG FT TGSMSQLLTIKQQISKLMELLNENNISSNYGKTSTQITQQGSYSLVNSAFA FT GITSSHLCFHTSNNLPPNLKNVNVQMIKQNHWIIYSGATDHICYSLDSFES FT AKTVNNCYVELPNDRKATVSHIRTVKLSPTLTLENVLHVPSFKFNLLSVGK FT LTQNKKTYVLFTDMHCIVQDVISQTVIGVARAYTGLYLMQEKHVEKDTSMS FT GFDKLKFPFISSVNGCNSADRCFDLWHFRLGHVPLEKINVIQKQFPTIKCS FT NDLLCEICSLAKQKKLPFLIHIQSTKIPFELIHVDIWGPYETPTLSNQRYF FT LTVIDDYTCFTWIFLMRCKSDVLSVIPTFNNYVKKFEHSIKCIKSDNGLEF FT RLKDFFDKTGIVHQLSCVETPQQNGVVERKHQHILVVAKALLFQSSLPIHF FT WGDAVMTAVHIINRVPTRLLKNKSPFELLYKRQPSYEHWRVFGSLCFVSTL FT SQHKKKLDQRATKCIFLGYPNNTKGYRVYDLNANRIIISRNIVFHEGTFPF FT QSKQHTTWPEPFCQTLGMHTKYSPQIDSDLPNFHFQDYKPAETYSSEPNTS FT AQTPLTSQINDFEPNSLDTVNMLTATNNENVTSNNEHDPMKIYQLEEAQDI FT NMLLNIWMLIILTCLQNLTMSLLTQSPNSYPQRTCHLHTKHSLHLCHTHLN FT LPLIIKLLVILIREMP" XX SQ Sequence 4784 BP; 1608 A; 891 C; 862 G; 1423 T; 0 other; tggtatcata gcaggtcata atccagctgg aaattagctt ttttctacag taatggtgga 60 cctcacatca tcggttgggt attctctatc ctctttggct gtttttattt ctttaccatg 120 aatttattcc tagtcttctg ctgctatatc atctatcaga ttcatttaat ctgtcatctg 180 gtcatttttt ttagttgatt aactatggct gaatcaaccc atgctaatac acgaaacaac 240 tctcaaacca ctcaaatcac tcagatctcc ccaatagtag accctcaatc ttcctttttc 300 ctgcatcaca ctgatagccc aagctcaata gttataaatc ctaaacttaa cagtagcaac 360 tatctagcat ggagcaggtc ttttctactt gcaatgtcca ttaggaacaa agtaggcttc 420 ctcaatggta caatacctaa acctcaaatt acagaccctc tctttttatc atggacccga 480 tgtaacaacc tattggtggc ctagttactt gactcaatat cttagccaat agcctcaacc 540 atattcttca tggacatagc atctgaaata tggctacttt aaaataaaac tttgcacaat 600 ctgatgatac cagggtgtgc aatcttcagt atacattagg aaatatcagt caagggagta 660 ggacagttga ttcatatttc attgagctca aggggatttg ggaggagctg aggagttata 720 ggccattgcc tcactgcaaa tgtggaaact gcaattctgg ttgctttaag gcatattcgg 780 accaatacca aaaggacatg gtctttagat ttttgaatgg attgaatgat tctttttctg 840 ctatcagatc acagatcata atgatggatc ctattccaac tctagacaaa gtttatagtc 900 tggtacaaag agaggaaaca cagagaagtc tgctcattca aggtcaagca gtttttgaat 960 cctctgcaat gatgactgtt gttgaaacaa ggaagaaagg tactaggaaa gatatcagct 1020 gtgaccatta tggaaagaag ggacatatta aggataagtg ctacaaactt atcacgtttc 1080 ttggagattt caaattcacc aagtcaaaac caaacttcag gaaggcaaaa acagtggcaa 1140 acaatgcaac aagtatacat gaaggaccag aatctgatgg ctgcaagatt gaacagttgg 1200 atgagggaat tgggactggc tctatgtcac agttgttaac cataaagcaa caaataagta 1260 aattgatgga gctcttaaat gagaataaca taagcagcaa ttatggtaag accagcacac 1320 aaatcactca gcaaggaagt tattcacttg ttaattcagc ttttgcaggt ataacttcaa 1380 gccatctttg ctttcatact tcaaataatt tacctcctaa ccttaaaaat gtgaatgttc 1440 aaatgataaa acaaaaccat tggattattt attctggtgc tactgatcat atatgctata 1500 gtctggatag ttttgaatct gctaaaacag tgaataattg ctatgttgaa ctaccaaatg 1560 atagaaaagc cactgtttct cacataagaa cagtaaagtt gtctcccact ttgaccttag 1620 agaatgtcct acatgtacca agtttcaagt ttaaccttct atctgtaggt aagcttaccc 1680 aaaataagaa aacctatgtt ctctttactg atatgcactg tattgtccag gatgtgatct 1740 ctcagacagt gattggggtt gctagggcat acacaggact atacttgatg caagaaaagc 1800 atgttgaaaa agatacttca atgtcaggtt ttgacaaact caaatttcct tttatttctt 1860 ctgttaatgg ttgtaattca gcagacagat gttttgatct ctggcatttt aggcttggac 1920 atgtgccttt agagaagata aatgtcattc aaaaacaatt tcctactatt aaatgttcaa 1980 atgatttact ttgtgaaatt tgctcattag ctaagcaaaa gaaactgcca ttcctaattc 2040 atatccaaag cacaaaaatt ccatttgaac taattcatgt tgacatctgg ggtccctatg 2100 agactcccac tttatctaat caaagatatt ttttgactgt aattgatgac tacacatgtt 2160 ttacttggat ttttctcatg aggtgtaagt cagatgtttt atcagtgata ccaacattta 2220 ataattatgt gaaaaaatag tttgaacact caataaaatg catcaagtct gataatggat 2280 tagaatttag actaaaagat ttttttgaca aaacaggcat agttcatcaa ctttcatgtg 2340 ttgagacccc tcaacaaaat ggggttgttg agcggaagca tcaacatatt ttggttgtag 2400 caaaggcctt actgtttcaa tctagtctgc ctattcactt ctggggtgat gctgtaatga 2460 cagcagtgca tatcattaat agagtgccaa caaggttact caagaacaaa tccccatttg 2520 aattgttata taagagacaa ccttcatatg agcattggag agtgtttggt agcctatgtt 2580 ttgtatctac tttatcacag cacaaaaaga aattagacca aagagccaca aaatgcattt 2640 ttttaggcta tccaaacaac acaaaaggtt atagggtata tgatctcaat gcaaacagaa 2700 tcataatttc aaggaatatt gtttttcatg aaggaacatt tccttttcag tcaaaacagc 2760 acactacatg gcctgaacca ttttgtcaaa cacttggtat gcataccaaa tattcacctc 2820 aaattgactc agacttacca aattttcatt tccaagatta caaacctgct gaaacatata 2880 gttctgaacc taatacaagt gctcaaacac cattaacatc acagataaat gactttgagc 2940 caaattcact tgatacagtt aatatgctta ctgcaactaa caatgaaaat gtaaccagca 3000 acaatgaaca tgatccaatg aaaatttacc agttagaaga agcacaagac ataaacatgc 3060 tcctaaacat atggatgctt atcatcttaa catgccttca aaatctcaca atgtcactgc 3120 tcacccaatc accaaattcc tatccacaaa gaacctgtca cctgcataca aaacattcac 3180 tacatctctg tcacacacat ttgaaccttc cacttatcat caagctgcta gttattctca 3240 ttagagagat gccatgagtg ctgaattgaa agctttacaa gacagtgaaa catggagcat 3300 agtaccaaga cctctaaatt ctcatgtaat tgggtgcaag tgggtgtaca aagtgaagtt 3360 gaatgcagat ggacaaattg aaagatataa agctcgcttg gttgcaaaag ggtataatca 3420 aattgcaggt tttgactaca aagagacttt cagtcctgta tctaagcaaa caacagtaag 3480 agtattcttt gccataacag cagctttcaa ttggcatcta acacagttgg atgtgaacaa 3540 tgcattcttg aatggagatt taaaggagga ggtgtacatg gacataccac caggatatga 3600 gatccaaggg gagtatccag agaatgtgaa attggtctgc aaacttcata agtcactata 3660 tggcttaaag caagcatcta gggagtggaa tgccaaaatc aagtctttta ttatacaata 3720 tggttttatt cagtccaatg cagatcactc actgtttact atgaagacaa acaatggtga 3780 gttcattgca ctcttattgt atgtagatga catagtagta gggagttctt caaaacaagc 3840 tgcagatgat gtgaaattgt tcctaagttc acattttaag ctcaaggatt taggaacagt 3900 caaatatttt ctcgggttag aaatagcaag atctcctgaa ggtatctcca tatcacaaag 3960 aaaatacact ttggatctct tagaagaaca tgggttgtta ggtgcaaaac cagtctccac 4020 tcccattgat tataatcaga agttagtcaa ggctcaagat gaagagaagc ttatcaattc 4080 aacaaactac agacaattag ttgggaaatt actgtacctc acattcagca gactagacat 4140 agcatatgca gttcaagtat tgtcacagtt tatggacaag cctagtcttg aacatatgaa 4200 tgtagctcac agggtgctaa aatatctgaa ggggtcactt ggccaaggta tcctaatgaa 4260 gtcagaatca aatttaatga ttgtgggata ctgtgacagt gattgggcag gttgtcctaa 4320 ttctaggaag tcagtcacag gatacaatat gttcattgga aattctttag tgacatggaa 4380 atctaagaaa caatcagtgg tgtctcgaag ctcagcagaa gctgagtaca gagcaatggc 4440 atcaactagt tgtgaaatta tctagttgaa acatctttta gtagactttg gaattgagca 4500 taaagttgca gtggtactct attcagatag tcagtcagcc attcacataa gcaagaaccc 4560 ggtcttccat gagaggacta aacatataga gatggattgc cacttcatta gggagaaagt 4620 gattgaaggt acaatcaaac cagtatatat ttcaattgat ttgcaactag ctgatctatt 4680 cactaaagcc ttacaaccaa ggcaatttca caatcttttg aacaagatga atgttcacaa 4740 cattcacata tcatcttgag ggggagtatt agacaacata gcat 4784 // ID Copia-4_SL-LTR repbase; DNA; EDCOT; 714 BP. XX AC AC243415; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the tomato genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-4_SL_; KW Copia-4_SL-I; Copia-4_SL-LTR. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-714 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the tomato genome."; RL Direct Submission to RU (22-JAN-2011). XX DR Genome; AC243415; Positions 39073 39786. XX SQ Sequence 714 BP; 159 A; 112 C; 172 G; 271 T; 0 other; tgttaagggt ccagcccatt gatgggtggc ccatatattt tgggctttgt tgacttcttc 60 tagaagtctt gggcagctga tattggggct ggggtttttt gttttggaag agaaaaaaga 120 aatagagaga gggttttgag agagaaaagg gttgctggtt tttctagaca gcgagacaaa 180 atttcatatt tcaagagatc cgaccgttgg atcgttctga aattttcaca gctggttcac 240 aacacatagc aatacatctt gaccgttcag atcgtcaatc ggagttcttg atcgtctgtt 300 atcgcagctg gcgtaaccta catttttttg gtgatatttc tcaatttctc ttctcttttg 360 tgttggctct tatgtatgtt gttgttggtg ggctgtgaca tccttgtaga ctgatttggg 420 tgtttttacc ctcaatttgc ataataagag aagaagaagg gtggactcct tcaagtcccg 480 tggtttttat ccttcatacc gaaggggttt tccacgtata aatcttgtgt gtcacttgcg 540 tatttataat tcatatttgc ttgtgattca attgatgtgt tgctgatttg agcttggtta 600 atatagtagt gaatttcttt tggtaaattg gtgaagtata tttggttgat tgtcttgaag 660 tcgatccttg taggtgttgt atcctacttg tgttgttttg tgactcccct caca 714 // ID Copia18-PTR_I repbase; DNA; EDCOT; 4171 BP. XX AC LG_III; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia18-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4171 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4171 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 208-208 (2007). XX DR Genome; LG_III; Positions 15255762 15259932. XX CC Positions [1499-2029] - Integrase core CC 'GTGCT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 902..3658 FT /product="Copia18-PTR_I_1p" FT /translation="MLLMAYVEKHQARREDAWFLDSGCSNHMCGYKAMFSD FT LNLEFRHSVKLGNNTRMNVMGKGSVKILLTGINHVIAEVYYVPDLRNNLLS FT IGQLQERGLDILFKGGTCKIFHPKRGLIIQTTISINRMFILLPDSQSSSQE FT QADQCFHTGTQNLCHLWHQRYGHLSYKGLRTLSYRNMVRGLPQLSTSNVTC FT TDCLKGKQHRDPIPKKSTWRASQKLELIHADICGPITPTSNSNKRYILLFT FT DDYSRKTWVYFLVEKSEAFSSFKSFKSMAEKQTGLFVKCLRTDRGGEFISN FT EFNEFCKHNGIKRQMTTAYTPQQNGIAERKNRTVMNMVRSMLSDKNIPKTF FT WAEAVNWAVYVLNRCPTLAVRDVTPEEAWSEMKPSVDHFRVFGCIAHVHVP FT EERRTKLDNRSITCVLLGVSEESKGYRLFDPVAKKIIVSRDVIFEEEKLWK FT WGESCDQQSVENLDWGDEDEERARENRNRGDGIDDAEQPGGNNCREGCREG FT DEEACDTGVETINYREGDERVRDSEIMQLEERSSRQLRGRQPPTWMGDYVS FT GEGLYEDETNMALEVSTDPSVYEEAVKSTDWRMAMNSEIESIEKNKTWTLT FT ELPAGTKKIGVKWVYKTKYDENGKIDKYKARLVAKGYSQKYGVDYTKVFAP FT VARMDTVRMIIALAAHKNWMISQLDVKSAFLHGELSEDVYVEQPRGNEKKG FT SEHLVYKLHKALYGLKQAPRAWFSRIEAHFIGEGFQRCESEQTLFTRRTQE FT GRIIIVSIYVNDLIFTGNDEVMLSDFKNSMVREFDMTDLGKMRFFLGIEVL FT QKSDGIYICQRKYALEVLRRFGMMESNSVGSPIVPGFKISINEDGNIVDET FT YYKQLVGSLMYLTATRPDMMFVICLISRYMTRPMEIHLQAAKRALRYLKGT FT VNYGIHYKRGGKESC" XX SQ Sequence 4171 BP; 1409 A; 644 C; 1034 G; 1084 T; 0 other; aattggtatc agagcctcca ctaggcctga aattcaaagc agcagacttt gaaatccttt 60 gcagcagcat agcaagatga ctacagaggg aagttttgtc cagccaacta ttccaagatt 120 caatggtcat tatgaccatt ggagcatgtt aatggaaaat ttccttcgat ccaaggaaat 180 gtgggaactg gtggagattg gatatactga ggcaagtgga tcaatgcaaa ctgatggaca 240 acaaaagaag aacgatgaga tgaagctgaa agatttgaaa gtaaaaaatt atctctttca 300 ggcaattgat cgaacagttc ttgatactat tctcaagaaa gatactgcca aaaatatatg 360 ggatgcaatg aagaagaaat tcgaaggaaa tgcaagggtt aagagatctc accttcaagc 420 tctccgcaga gagtttgaaa cacttgaaat gaggtctggt gaaggagtga cagagtattt 480 ctctagagtc atgacagtgg ccaataaaat gagaatttat ggagaagaca tgcaggatgt 540 taaagtagtg gagaagattt tacgttcgtt gactgagaaa ttcaactatg ttgtatgttc 600 tattgaagag tcaaaggaca ttgatgctct cactgttgat gaattacaga gttcattaat 660 cgtccatgag cagaaatttg tgagacataa gagtgaggaa caagctctga aggtaacata 720 tgaaggaggt agaggtcgtg gtcgaatttc ctatcgagga agaggaagag gcagaggacg 780 aacagacttc aataaagcaa caattcaatg ttacagatgt cattgacttg gacatttcca 840 atatgaatgt cccactgtga acaaagaatc actttatgca gagcttgatg aggaggagga 900 aatgcttttg atggcttatg tggagaaaca tcaagccaga agagaagatg catggtttct 960 tgattcagga tgttctaacc acatgtgtgg ttataaagcc atgttcagtg atctcaactt 1020 agaatttcga cattctgtga agttggggaa taacacaagg atgaatgtaa tgggtaaagg 1080 aagtgtgaag atactgctga ctggaatcaa tcatgttatt gctgaagtat attatgtccc 1140 cgatttgaga aataacctcc tgagcatagg ccagttgcaa gaaagagggt tagatatctt 1200 attcaaaggt ggaacctgca agatattcca tccaaaaagg ggattaataa ttcaaaccac 1260 cataagcata aatcggatgt tcattttgtt gcctgattcc caatcttctt ctcaagaaca 1320 agctgatcaa tgcttccaca caggaacaca aaatttgtgc catctttggc atcaaaggta 1380 tggacatttg agttacaaag gcttaagaac tctatcatac aggaacatgg tgcgtggtct 1440 tcctcaacta tcaacctcaa atgtcacctg cactgattgc ttaaaaggga agcaacaccg 1500 tgatcccatt ccaaagaaaa gcacctggag agcatctcag aaactggaac tcattcatgc 1560 tgatatctgt gggccgatca cccctacatc caacagcaac aagaggtata ttctgctatt 1620 tacagatgac tatagtagga aaacctgggt atattttctg gtagagaagt cagaggcctt 1680 cagttcattt aaaagcttta agtccatggc tgaaaaacaa acaggtttgt ttgttaaatg 1740 tcttcgcact gacagaggag gagaattcat ttccaatgaa ttcaacgaat tttgcaaaca 1800 caatgggatt aagaggcaga tgacaactgc ctataccccg caacaaaacg gtatagcgga 1860 gaggaagaac agaaccgtaa tgaacatggt tcgatccatg ttatctgaca aaaacattcc 1920 caaaaccttc tgggcagagg ctgtaaactg ggctgtttat gttcttaaca ggtgccccac 1980 gttggcagta agggatgtta caccagagga agcttggagt gagatgaaac cctcggtaga 2040 tcattttagg gtttttggtt gcatagcaca cgttcatgtt ccagaagaga gaagaacaaa 2100 gcttgacaac agaagcatta cttgcgtatt attgggggtt agtgaggagt caaaaggtta 2160 cagactcttt gatcctgttg caaagaaaat tatcgtgagt agagacgtaa tttttgaaga 2220 agaaaagttg tggaaatggg gtgagagctg tgaccaacaa tcagtggaaa atttagactg 2280 gggtgatgag gatgaagaaa gggcgaggga aaatagaaac agaggagatg gtattgatga 2340 tgcagaacaa cctggtggaa ataattgcag agaaggttgc agagagggtg atgaagaagc 2400 ctgtgatacg ggagttgaaa caattaatta cagagagggt gacgagagag tgagggacag 2460 tgaaatcatg caacttgaag aaagaagctc aagacaatta cgtggtaggc agcctcccac 2520 gtggatggga gattatgtca gtggtgaagg gctgtatgag gatgaaacaa atatggcact 2580 tgaggtgtca acagatccct cggtttatga agaagctgtg aagagtacag attggaggat 2640 ggctatgaac agtgaaattg aatctattga gaagaataaa acgtggacac tcactgaatt 2700 accagcggga acaaaaaaaa taggggtgaa gtgggtttat aaaaccaaat acgatgagaa 2760 tgggaaaatc gataaataca aggctcggtt ggtggcaaaa gggtattctc aaaaatatgg 2820 tgtagattat acaaaagtgt ttgccccagt agcaagaatg gatacagtac gaatgattat 2880 cgccttggct gcgcacaaaa attggatgat ttctcagctg gatgtcaaat cggctttcct 2940 tcatggcgag ttaagtgaag atgtttatgt agagcaacca agaggaaatg aaaagaaagg 3000 gagcgagcat ctggtttaca aactgcacaa agcactgtat ggtttgaaac aagctccacg 3060 agcttggttt agtcgaattg aagcacattt cattggcgaa ggatttcaga gatgcgaaag 3120 tgagcagacc ttatttacaa gaagaaccca agaaggaaga atcatcattg tgagtatcta 3180 tgtgaatgac ttaatcttta ctggaaatga tgaggtaatg ttatctgatt ttaaaaactc 3240 tatggtaagg gagtttgata tgactgactt gggaaaaatg aggtttttcc ttggaattga 3300 ggtgttacaa aagtctgatg gcatttatat atgtcaaagg aagtatgctt tggaggtttt 3360 gagaagattt ggtatgatgg aaagtaattc ggtaggaagt ccaatagttc caggattcaa 3420 gataagcata aatgaagatg gaaatattgt tgatgaaacc tactacaaac agttagtggg 3480 tagcttaatg tatcttactg ctacaagacc cgacatgatg ttcgttattt gcctcataag 3540 tagatacatg acgagaccta tggagattca tctacaagca gctaagagag ctcttcgata 3600 tctaaaagga actgtgaact atgggattca ttataaaagg ggggggaagg agagttgtta 3660 gcattcacgg atagtgatta tgctggcgat atggaagaca ggaaaagcac atctggtaat 3720 gtttttctga tgggttcaag tgctgtctca tggtgttcga agaaacagcc tattgtgact 3780 ttgtcaacaa cggaagctga attcgtggca gcagcagtat gtgcctgtca aggagtatgg 3840 atgaagagaa ttttaaagga actgggacac tcagatgaag gttgtacaac cataatgtgc 3900 gacaatagtt caactattaa gttgtctaaa aatcccgtaa tgcatggtcg cagtaagcat 3960 attgatgtga ggtttcattt cttaagaaac cttactaagg agggtacagt tgagttaatt 4020 cattgtggga gtcaggatca aatcgcagat ataatgacca agccattaaa gcttgaagtg 4080 tttcaaaagc ttcggaagtt actgggagta tgtgaaatac taccataata taaactaact 4140 gcttcataag catttagttt aagggatgga a 4171 // ID hAT-5_PTr repbase; DNA; EDCOT; 4104 BP. XX AC . XX DT 18-DEC-2009 (Rel. 15.02, Created) DT 18-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE hAT-type DNA transposon - consensus. XX KW hAT; DNA transposon; Transposable Element; hAT-5_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4104 RA Kojima K. and Jurka J.; RT "DNA transposons from black cottonwood."; RL Repbase Reports 10(2), 115-115 (2010). XX DR [1] (Consensus) XX CC ~92% identity to consensus. 8-bp TSDs. XX FH Key Location/Qualifiers FT CDS 1130..3046 FT /product="hAT-5_PTr_1p" FT /translation="MSSHDGSTPSSDPSTAQSSQPSISMSSGSRGRTDLAW FT GHCREAPELSVGCKKTKLVCLYCAKVFAGGGINRFKQHLAGAKGEVEQCRK FT CPPDVRHQMLLNLKGNAETKKRVREMQADFNPFNAQQREHEEMMIRQLEDD FT DDGDDEEDDEDVNTKKHMLPPKVAKKKKIQSTSTVKQSTTSYGKQKKSATL FT GTYFMPRTTPGAQKSLQNCWQRKEAVERCDLALAKWMIDACVPFNAVNSVY FT YQHAIDAVTAMGPGYKGPNLHAIRGYYLAKAVDEVKIYVETYREIWKKTGC FT TLMADGWTDQKRRTLINFLVYCPKGTVFLKTVDVSDVSKTARLLYQLFREV FT VLYVGVENIVHMVTDNAANYVAAGKLLMEEFPSIFWSPCAAHCINLILQDI FT GKLQSVCCVVEHASGITKYIYNHCYPLYLMRKFTGGKEILRPAPTRFATNF FT IALQSILAHKDELRAMVTSREWVSSAYAKDSKGKKFVESVLDSLFWEECAI FT IVRMSEPLVRVLRMVDGDDRPSMGYLYDAIHHAKEEMMRRFQKRKARVKPF FT IDIINNRWDGQFYRNLYAAAFWLNPRFQYDANIMDKHMSTISGLLDVLEKY FT AHGNLPLQSKITSEMKLFRNAEHDFGRASAINNRTLMPPGI" XX SQ Sequence 4104 BP; 1203 A; 625 C; 897 G; 1378 T; 1 other; cagtgtttta aaacccggac cggcccggcg ggccgacccg ggcctgggac cggtccgggt 60 ggaggcaaaa acccgctcgg gagttggccc ggtgaaaccc ggtcgacccg gcgggtcgac 120 ccgggacccg ggccacccgg tctatttttt ttatactgat gacgttaaac gacgtcgttt 180 tggcctttgt taaaaggcca aaacgacgaa gaacaatgaa gcagaattga gcattcgatt 240 acagatagag caaacctaat taacaaaaaa tctttcaaac tttcaatcga tgagctgagg 300 agcagaggag agcagaagac gatcttgatc attgttgttt cactgcgaaa aaggttagtt 360 tcttgtttct gttcacgaat cttcttcttt cactctctct tttctttatt cttggccgtg 420 ttgaacttgc agttctggag catcattttg ctgttccctc gtcgacccat ctcttccctg 480 ttgatccagt ctcgttgatt cagtcgcagc ccagtcatct caacctcagg tatgtttctc 540 tgttctttct tttctgcagc gtaataactt cctctgctat taggaagtgt tgaaaatgga 600 tgaggaaact agaatggttc ggtgcatttg cttttggaac tgttatagcc atagtttgaa 660 ctattttgtc aagaacttta gccagagatt gaaattgttg taagtttttg ttatggttag 720 aatattttgg ctggtgattg ttggtgtgtt tgttcgttct gcttttgctt catgaatgaa 780 gcaaactgtg atggataatg taattgacta tggatgatga ttgctaaatc tgttttctgc 840 taaatcatga attgctatga ttttgttttt tgtttttcct ttggcgacaa tgtgtgatta 900 aatatggatg ggtcctcctc ctcttgaatt cgccttttct tgtttaaacg ggaggaatat 960 tagttgtgta ctaatagcat gaaagaattg gaattttatc ggtatcattg cctctccttt 1020 tccggtatat ttaatacaaa ttctccaatt gtataattta attaatggat tgcaaagtga 1080 tttggcttga aattatattc cctcttataa attatgtcag gtccttaaaa tgtcttcaca 1140 tgatggtagt actccaagta gtgatccttc aacggcccaa tcatctcaac cttcaatttc 1200 catgtcaagt ggtagtagag gaagaacaga tttggcatgg ggtcattgta gagaagctcc 1260 tgaacttagt gttggatgta aaaaaactaa attagtwtgt ttatattgtg ctaaagtatt 1320 tgcgggtggt ggcattaatc gatttaagca acatttagct ggagctaaag gagaagttga 1380 acaatgtcgc aaatgtcctc ctgatgttcg acatcaaatg cttttgaatc ttaaaggaaa 1440 tgctgaaaca aaaaaaagag ttagagaaat gcaagcagat ttcaatccat ttaatgcaca 1500 acaaagggag catgaagaga tgatgattag gcaattagaa gatgatgatg atggtgatga 1560 tgaggaggat gatgaggatg tcaatactaa aaaacatatg ttaccaccga aggttgcaaa 1620 aaagaaaaag attcaaagca ccagcactgt aaaacaatcg actacaagtt atggaaagca 1680 gaagaaatct gcaacattag ggacatattt catgccgaga acaactcctg gtgctcaaaa 1740 gtctcttcag aattgttggc aaaggaagga agcagttgaa cggtgtgatc ttgctttagc 1800 gaagtggatg attgatgcat gtgtgccatt taatgctgtt aactctgtgt attatcagca 1860 tgccatagat gctgtaacag ccatgggtcc tggttataaa ggaccaaact tgcatgctat 1920 tcgtggttat tacttggcaa aagcggttga tgaagtcaag atttatgttg agacttatcg 1980 agagatttgg aagaagactg gttgcacatt aatggctgat ggatggacag atcagaagag 2040 gaggacttta attaacttct tagtatattg tcctaaagga acagtttttt tgaaaaccgt 2100 ggatgtatca gatgtctcaa agactgctag attgttgtat cagttgttta gagaggttgt 2160 tttgtatgtt ggggtagaaa acattgtgca tatggtgact gataatgctg caaattatgt 2220 tgctgctggc aagttattga tggaagaatt tccttcaata ttttggtctc cttgtgctgc 2280 tcattgcatc aacctcatac tccaggacat tggtaaattg cagtcagttt gttgtgttgt 2340 tgagcatgct tctggtatca caaagtacat ttataatcat tgttatccat tgtatttgat 2400 gaggaagttc actggaggaa aagaaatact tcgtccagct cctactcgtt ttgctaccaa 2460 tttcattgca ttgcaaagca ttttagctca taaagatgag ttgagagcta tggtgacatc 2520 tagggaatgg gtctcatctg cttatgctaa agatagcaaa ggaaaaaagt ttgttgagag 2580 tgtgctagac tctctgtttt gggaagaatg tgcaataatt gtgcgaatga gtgagccttt 2640 agttcgagtt ctacgaatgg ttgatggtga tgatagacct tcgatgggat atttgtatga 2700 tgctattcat catgcaaaag aagaaatgat gaggagattt caaaagagaa aggctagagt 2760 gaaacctttc atagacatta tcaataatcg gtgggatgga caattttata gaaatcttta 2820 tgcagcggca ttttggttga atcctcgatt tcaatatgat gcaaatataa tggataaaca 2880 tatgagcacc atttctggac ttctagatgt tcttgagaag tatgcacatg gaaatctacc 2940 attgcaaagt aagattacaa gtgagatgaa gttgtttagg aatgctgaac atgactttgg 3000 tcgagcgtcc gcaataaata atcgcaccct tatgcctcca ggtatataat ttttatattt 3060 aaaaatatta tttgacatag tctcctttta cttattattt ttttgtatag atgaatggtg 3120 gatgacatat ggaaccagcg ctccaaatct acaacagttg gctatacgag tgttaagtca 3180 aacttgtagt tcttcgggat gtgagagaaa ttggagtatg tttgaacata ttcattccaa 3240 gaagagaaat agattggagc accaaaggct taatgacctt gtttacgtcc actgcaatct 3300 aagattgaaa caaaagtatt tttcttttct ctaattcctt aaatattatt ttatcttgtt 3360 tagtagcatt attaatactt atattgtgtt taccttcact tttaatatat aggaattatt 3420 ggaaaggacg aaattatgat ccaattaatg ttgagacaat ttgtgacatt gaaaattggg 3480 tagtagaaga tgacccgtca atcttgacaa ctgaagaagc agagagtttt caccaagctc 3540 tatcaactat gaccatacaa gatactttag atgatggtaa ttaatgattg attatttagt 3600 gataaatatt atttaaaata aagttttgtt taacacataa tatttatttg ttaattgtgt 3660 ttgaaatgta gatgtcataa atgttaatga tattgaagat gattgtgacg atgaagtttc 3720 aaaggagcat gctgatgatt tattaggtgt tgacgagatt ggctcaattc catcgacatt 3780 tgatccaaat tttgctccta tggacacaga agaacttaat gtgttcattc aacaaaagtg 3840 aatgtgttgt tgatttagaa tttatgttgt tggatgtttt gttttaaata ttttagaatt 3900 tatatttggt ttgtgttttg gatattgaat taaatttatg ttgttggttt aaaatttaaa 3960 tttggtttat gtaagtgttg cattgtaact agttatgtgt ttttttttat aggttttttt 4020 tttgggttga cccgggtcaa cccatctgac ccgtgacccg atcacttgac cgggtcgatg 4080 accgggtcgg gtttcaaaac tatg 4104 // ID Copia-56_VV-LTR repbase; DNA; EDCOT; 239 BP. XX AC chr6; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-56_VV_; KW Copia-56_VV-I; Copia-56_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-239 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr6; Positions 3223830 3223592. XX SQ Sequence 239 BP; 74 A; 25 C; 37 G; 103 T; 0 other; tgttgaagat taggataatt agtttttgtt tctaataaat tcaaattaag atttgaatta 60 gtttgttagg ggagtcagtc tgttagttgt tcctattttt ttgcatttga tatttttatg 120 taatctggta gcttaggata gacttttacc ataaccactt tggatataaa tacctattgt 180 aacttctatt aatttaagga aaaagaaaga taagtttttc ttcttctcaa aaactttca 239 // ID TONT1_LE_LTR repbase; DNA; EDCOT; 1004 BP. XX AC AF220603; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Lycopersicon esculentum retrotransposon TONT1_LE_LTR, long DE terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Long terminal repeat; KW TONT1_LE_LTR; retrotransposon. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-1004 RA Lavelle T.D., Oldroyd E.G., Dalhbeck D., Staskawicz J.B. RA and Michelmore W.R.; RT "Direct submission."; RL Direct Submission to Genbank (04-JAN-2000). XX DR Genbank; AF220603; Positions 30045 31048. XX SQ Sequence 1004 BP; 312 A; 154 C; 176 G; 362 T; 0 other; tgttgggtat gtaacaagaa ttgatgggaa atagagggaa ggagaggaat ttgaaaggtt 60 tagaacttga aaggttggga acttgaaaag tcctctaatg ctttattgaa aaaggcaata 120 gtctctcatc ggtaatggaa aggaaaatag gagagtttaa ataaataaac actcctatta 180 gttgttaaaa gggttggaaa gagggaaccc ctcgcgccgt cgtcgtcgct cgcttcggct 240 ttggcaaatc gagagataat tttttggaca aaatttattt taattattta ttaattaatt 300 ttaaatggcc aaaaattatt ttcaataaat tagttgataa cagaatttaa ccgaaatgtt 360 ttcaactttt tagttaaccc gacccgactc ggatccgctc gagtgaccca ttttaaattc 420 cgttatattc aaaatttccc gccatgactg ttctgaaagg ttgcaacttt caggaacagt 480 caatatcatt tgaaagtttg caacctttca ttaatggtcg tgttaattct gaaagggttg 540 caacctttta gaatatattc ttcttgccta taaataccat tcagtcttca gaatatttcc 600 tacgaatttt ttttttctga tcttcctttt tcttaaaaac atatatttct tcgtgtactt 660 tcctgctgtg gattgattcg ctgacagtag agtttttggt atctatactc tactgattaa 720 aatcatttta cccagggagg ttgtattcca aatcaaacct tggatactag aggggaataa 780 tttccttaag gggacactgt gaattcagtg gacttgattt tcttcctaaa ttttcaataa 840 gagtattcca gattctggta cgtttttaca aattaaatta ttttttacaa ataaatttct 900 gttcatctta tttactggtt ataaaaaaaa tctcagttac tttgtgtttc tgaatgattt 960 attagaacca gtaatttctg attttataac acagattgga aaca 1004 // ID Gypsy-10_Mad-LTR repbase; DNA; EDCOT; 417 BP. XX AC ACYM01129446; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-10_Mad-I; KW Gypsy-10_Mad-LTR; Gypsy-10_Mad_. XX NM Gypsy-10_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-417 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1413-1413 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01129446; Positions 419 3. XX SQ Sequence 417 BP; 120 A; 57 C; 91 G; 147 T; 2 other; tgatacgacc aatattgcat acattttaat gcccyttagt ttagattttt gttatgtttt 60 tgagtgaatt tagtttgttt catttagttt tatgtttttc ttagatttga agagtgaaga 120 tgaagaaaga agaaaaatga gcattttggc rattgaagtg agttatgtgc cctggaagca 180 gaagctgttt gtgcagatca gccaacttga cggaataaac tgtacttcct caaaatgaac 240 cagctgttga gccttatacc attggaaaga tatggatgtt agctttcaga ggaattttac 300 ggactgtgat ttcgagtttc ctagacgatg ttatgaaagt ttttgtacaa gacgtcggtc 360 agccaagtct acgcggaaat tgcaaaatct gttgggtttt tttcaagtca taattca 417 // ID Copia-75_Mad-LTR repbase; DNA; EDCOT; 199 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-75_Mad_; KW Copia-75_Mad-LTR; Copia-75_Mad-I. XX NM Copia-75_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-199 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1689-1689 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 199 BP; 58 A; 33 C; 33 G; 75 T; 0 other; tgatatgttt gttaagtttg ttatgagcta gcttagtctg taaggaaagt gaagtgtata 60 tatagcaata gtttgtaatg attcagtgtg aaagaaaaca atatataaca gaagaagaat 120 tctctctctc tctctctctc tctctctctc tctcagtgtg aaacctccat tgtttaagct 180 taaagctttt cttcttaca 199 // ID BoSB11 repbase; DNA; EDCOT; 170 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 13-JUN-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB11. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-170 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 170 BP; 27 A; 45 C; 57 G; 41 T; 0 other; acccaaggtg cgttgggcta gtggtttagt gcttggagta ggttccattg cacccctagt 60 tcgattccca tggggagggg tgctttacgc catgttatcg gtatcagcgc cggccggccc 120 cgggcctggg gtgggattaa ggccgaaggc ccgaacccat cctggtttac 170 // ID VIHAT2-N1_VV repbase; DNA; EDCOT; 774 BP. XX AC . XX DT 05-FEB-2009 (Rel. 14.03, Created) DT 05-FEB-2009 (Rel. 14.03, Last updated, Version 1) XX DE VIHAT2-N1_VV, non-autonomous DNA transposon - a consensus DE sequence. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; TIR; KW MITE; mHatvine-2.1; VIHAT2-N1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-774 RA Benjak A., Boue S., Forneck A. and Casacuberta J.M.; RT "Recent amplification and impact of MITEs on the genome of RT grapevine (Vitis vinifera L.). submitted."; RL Repbase Reports 9(3), 712-712 (2009). XX DR [1] (Consensus) XX CC VIHAT2-N1_VV (mHatvine-2.1 in [1]) is a non-autonomous DNA CC transposon which is a deletion derivate of the autonomous VIHAT2. CC Individual copies are >90% identical to the consensus sequence. CC TIRs are 23 bp-long and flanked by 8 bp-long TSDs. There are CC approximately 22 highly conserved copies present in the genome CC which could place this family in the group of MITEs. XX SQ Sequence 774 BP; 235 A; 122 C; 145 G; 270 T; 2 other; catggtttta aaaaccggac cggaccggcc ggtccgaccg gttggaccgc caaccggtca 60 tcgttccggt tcggtccggt cattagaccg gatggagacc gaaccgggat tggaccgctt 120 gaaccggcgg tccaaccggt gaaccggacg aaccggccgg ttctgaggga aaaaaaccgg 180 ttcaaattat tttaattttt ttttttggtt ttccaaatgc tcattttcaa tctccatatt 240 ccaatttcca aaataaatga agacatgaat tttatattta ttagtatgca aaaatcttca 300 tgaatattca aacattgaca tgttatgttt ttattttgag taattattta agtgttgtgg 360 acctatggtt gacatttgta ttatttgtta tggacaatgt gttaagttaa caactctttg 420 ataatttggt tattatagga tagtaatggt ttgattattt gataaatatt gagtttattg 480 acattatgaa tgtataacat cttatattgt gttataaata tcatatatga taattgatga 540 cttctacagg taaaaaattt tgtgacaaaa ctcaagttac tcaataaaca aagtagatgc 600 trtcaaaatt tacatagaat ttattaattt tttaattttt tatattatat aaaataataa 660 aatatatatt tatgacgtca ccggttygat agcggttcga ccggcggtcc gaccagtgaa 720 ccgtgaaccg gtaacttttc cggttcaatg accggtccgg tttttaaaac attg 774 // ID METMAR1 repbase; DNA; EDCOT; 278 BP. XX AC . XX DT 12-JUN-2006 (Rel. 11.06, Created) DT 12-JUN-2006 (Rel. 11.06, Last updated, Version 1) XX DE Putative non-autonomous mariner from Medicago truncatula - DE consensus. XX KW Mariner/Tc1; DNA transposon; Transposable Element; Nonautonomous; KW METMAR1. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-278 RA Jurka J.; RT "METMAR1: Putative non-autonomous DNA transposon from barrel RT medic."; RL Repbase Reports 6(6), 350-350 (2006). XX DR [1] (Consensus) XX CC On average 93% identical to consensus. Relatively abundant. XX SQ Sequence 278 BP; 101 A; 46 C; 32 G; 99 T; 0 other; tactacctcc gttccttttt aattgtcact ttttgacatt ttacacaaac caagacaatc 60 aataattgtt actacttttg atacaataat ttatactttt actataatga ccttattcat 120 ttaatatctc atttcatata tttctctctc cgcaataaat aactaagggt aatattggta 180 aaacaacatt taatgttgca ttgaactttg aaagtgacag ttaaatagga acaaaaattt 240 tctccaaaag tgacacttaa aaaggaacgg agggagta 278 // ID Copia-64_VV-I repbase; DNA; EDCOT; 4043 BP. XX AC chr15; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-64_VV_; KW Copia-64_VV-LTR; Copia-64_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4043 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr15; Positions 13490325 13486283. XX CC Positions [1404-1919] - Integrase core CC 'CTATC' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 27..3959 FT /product="Copia-64_VV-I_1p" FT /translation="MGTAKFDVEKFTGKNDFGLWRLKMRALLVQQGLQDAL FT LGEKNLPSTMQEKQKIELLEKAHSAIILSLGDTVLREVAKAKSVAEVWLKL FT ESLYMTKSLANRLHKKIKLYTFKMTPGMSIEDHLDHFNKIILDLENIDITI FT SDEDKAILLLTSLDASYTNMKDAIMYGRDSLTFDEVQSILHARELQKQEES FT KEESGEGLNIRGRSEKREKKGKNSKSRSKSKTKKFKCFICHKEGHFKKDCP FT DRRQNTVKKTVNEGDAAVILDGYDSAEVLNVAEVDSSKEWILDSGCSFHMC FT PIKAWFEDFKEADGGYVLLGNNKHCKILGTGTVRIKHYDGIERVLEDVRYI FT PELKRNLISLGMLDKSGYTFKSEPNSLRVARCSLTVMKGTIKNGLYTLIGQ FT TVTGKVSTVLKEDVGTTKLWHQRLGHISHRGLQELEKQGVLGNYKLTDLPF FT CEHCVFGKATRVKFAKAIHETQNQLDYIHSDLWGPSRVPSIGGARYFLTLI FT DDYSRKVWIYFLKNKSETFLKFKEWKILVETQTSRKVKKLRTDNGLEFLSN FT DFNSLCQKEGIARHRTVRYTPQQNGLAERMNRTILERVRCMLSSSGLSKVF FT WAEAAETAVHLINRSPSSALQFKTPQEKWTGKAADYQHLKVFGCTAYVHTK FT TDKLEPRAVKCIFLGYPKGVKGYKLWIETQGKGKCIISRDVTFNEQDMSKQ FT TPAKDVEGLDQLQFEVEHETLQPEKSKETSSKTTQEEIVHERQNEPTQGLE FT SYNLVRDRQKRQVKPPKRYGQAEMTAFALSVAEEIVDMEPKTYQEAINSNE FT ADQWVKAIQEEMDSLRKNETWELVTKPKDRKVVGSKWVFKRKQGTLGNEAP FT RYKARLVAKGFSQKEGVDYNEIFSPVVKHSSIRLLLAFVAHEDLELDQLDV FT KIAFLHGELDELIYMQPPEGFGEGIKDGQVCLLKKSLYGLKQSPRQWYKRF FT DKYMLDIGFNRSSHDGCVYFKLTEDSMVYLLLYVDDMLVACKEKRHLEQVK FT EMLKAEFEMKDLGSAKRILGMEIERDRSKRVLRLSQNSYISKVLSRFEMNN FT VKTVSTPLGQHFRLSITQAPETHEEKRFMERIPYASMVGSVMYTMVCSRPD FT LAYAVSMISRYMSCPGKPHWQAVKWLFQYLAGTRSLGLVYGGNSQLETQLQ FT GFVDADYAGNIDTRKSLTGYVFTVFGGAVSWKANLQSVVALSTTEAEYMAM FT TEAVKEAIWLKGITEELAMYRGKVVVYCDNQSAIHLAKNQSFHERSKHIDV FT RLHFVRDIIAAGEIGVGKVHTKDNPSDMLTKSLNVTKFKHCLNLINMGDC" XX SQ Sequence 4043 BP; 1356 A; 656 C; 1005 G; 1026 T; 0 other; attggtatca gagcctttgg gttataatgg ggactgcaaa gtttgatgta gaaaagttta 60 cgggcaaaaa tgatttcggg ttatggagac taaagatgag ggcattgctg gttcaacaag 120 ggctccaaga tgccctactt ggagagaaaa acctacccag taccatgcaa gaaaaacaaa 180 aaatagagct gttggagaaa gctcacagtg ctatcattct ttctttaggt gatactgtgt 240 tgagagaggt ggccaaagca aagtctgtag ctgaggtgtg gctcaagctt gagagcctat 300 acatgaccaa gtcattagca aaccgattac ataagaagat caagttatat actttcaaga 360 tgaccccagg tatgtcaatt gaagatcatc ttgatcactt caataagata atcttggatt 420 tggaaaatat tgatatcaca atatcagacg aagataaagc aattctatta ctgacttctt 480 tagatgcatc atacactaac atgaaagatg ccataatgta tgggagagac agcctgacct 540 ttgatgaggt gcagtccatt ttgcatgcta gagaattaca gaaacaagaa gaatccaagg 600 aggagtcggg tgagggttta aacatcaggg gcagatctga aaaacgagaa aagaagggca 660 agaattcaaa gtccagatca aaatccaaga ccaagaagtt caagtgtttt atctgtcaca 720 aggaagggca cttcaagaaa gattgcccgg ataggagaca aaacacagtc aagaaaaccg 780 tgaatgaagg tgatgctgct gtgattttgg atggatatga cagtgctgag gtgctgaatg 840 tggcagaggt ggactcgagt aaggagtgga tacttgattc agggtgctct tttcacatgt 900 gtcctatcaa agcttggttt gaagacttta aagaagctga tggaggttat gttctgctag 960 gcaacaataa acattgcaag attctaggta ctggtactgt caggatcaag cactatgatg 1020 gcattgaaag agttcttgaa gatgttaggt atatacccga gttaaaaagg aaccttatct 1080 cacttggaat gttggacaag tcaggatata cattcaagtc agaacctaac tctttgagag 1140 ttgctagatg ttcacttact gtcatgaaag ggacaataaa aaatgggttg tacactctta 1200 taggccaaac tgtgacaggg aaagtttcta ctgtgctgaa ggaggatgtg gggacaacca 1260 agctatggca tcagaggctt ggtcacatca gccacagggg actacaagag ctggagaagc 1320 aaggagtgtt gggaaactac aagctaacag atttgccctt ttgtgaacat tgtgtgtttg 1380 gcaaggctac aagggtgaag tttgccaaag caatacatga aacacaaaac cagctggact 1440 acatacactc tgacttgtgg ggaccatcac gggtaccatc aataggtgga gcaaggtact 1500 tcttaactct tattgatgat tactctagga aagtgtggat ttattttctt aaaaataaaa 1560 gtgagacctt cctaaagttc aaagagtgga aaattctggt tgaaactcag acaagcagaa 1620 aagtgaagaa gttgagaacg gataatgggc ttgaattcct atcaaatgat tttaattcat 1680 tgtgtcaaaa ggaaggcata gctagacata gaactgtcag atatacacct caacaaaatg 1740 gcctagctga gcgcatgaat aggaccattt tggagagggt gagatgcatg ctgtcaagtt 1800 cagggttgtc aaaggttttt tgggctgagg ctgcagaaac agctgtccat ttgatcaaca 1860 ggagcccatc atcagcatta caattcaaaa cccctcaaga aaagtggact gggaaagctg 1920 cagattatca acatctcaaa gtttttggat gcacagctta tgtacacacc aaaacagata 1980 agttagaacc acgggctgta aagtgtattt tcttggggta tccgaaagga gttaaaggtt 2040 acaagttgtg gatagaaaca caaggcaaag ggaagtgtat aattagcaga gatgtaactt 2100 ttaatgagca agatatgtca aaacaaactc cagccaaaga tgtggaaggg ttagatcagt 2160 tacagtttga ggtggagcat gagactttgc aacctgaaaa gtctaaagag acttcatcaa 2220 agacaactca agaagaaatt gtacatgaaa gacaaaatga accaactcaa gggctggaat 2280 cctataatct ggtaagagac aggcagaaaa gacaagtcaa acctcccaag agatatggcc 2340 aagctgaaat gacagcattt gcattgagtg tagctgaaga aatagtggat atggaaccaa 2400 aaacatacca agaagccatc aatagcaatg aggctgatca gtgggtaaaa gctatacaag 2460 aggagatgga ttccttaagg aaaaatgaga cttgggaatt agtcactaaa cccaaggacc 2520 gaaaggtagt aggctccaag tgggttttca aaagaaagca agggacacta gggaatgagg 2580 ctccaaggta caaggcacgg ctggtggcta aggggttttc acaaaaggag ggagttgact 2640 acaatgagat attctctcct gtagtcaaac acagctcaat ccgattgctg ttggcttttg 2700 tagctcatga agacttggag ctggatcaac tagatgtgaa gatagcattc ttgcatggag 2760 agcttgatga gctgatttat atgcaaccac ctgaaggctt tggggaagga atcaaggatg 2820 gtcaggtatg tttacttaag aaatctcttt atggtctaaa gcaatcacct aggcaatggt 2880 ataagagatt tgataagtac atgctggata ttggattcaa tcggagcagc catgatggat 2940 gtgtatattt taagctaact gaagacagca tggtatatct tttactatat gtagatgaca 3000 tgctggtggc atgtaaggag aaaagacact tggagcaagt caaagagatg cttaaggctg 3060 aatttgaaat gaaagatctt ggttcagcca agaggatttt gggaatggag atagaaagag 3120 acaggagcaa gagggtactt aggctttctc aaaattcata catctcaaag gtactaagca 3180 gatttgagat gaataatgta aagacagtga gtactcctct aggacaacat tttagacttt 3240 ccataacaca agcacctgag actcatgaag agaaaaggtt tatggaaagg ataccttatg 3300 ctagcatggt gggtagtgtg atgtacacta tggtgtgttc tcggcctgat cttgcatatg 3360 cggttagcat gataagtaga tacatgagct gccctggaaa gccacattgg caagcagtaa 3420 agtggctttt tcaatactta gctggtacta gaagcttggg cctggtttat ggaggtaata 3480 gtcaattgga aactcagcta caagggtttg tagatgctga ttatgctgga aacattgaca 3540 ccagaaagtc tcttactgga tatgtattca cagtgtttgg aggagcagtg agttggaagg 3600 ccaaccttca atcagtggta gctctttcaa ccactgaagc tgaatacatg gcaatgacag 3660 aggctgtgaa ggaggcaatt tggctgaagg gtattacaga agaattggct atgtacagag 3720 gtaaagttgt tgtatattgt gataaccaaa gtgcaatcca tttagccaag aatcaatcct 3780 tccacgaaag gtccaaacac attgatgtaa gattgcactt tgtgagagat atcattgctg 3840 caggagagat tggagtagga aaagttcata ctaaagacaa tccatccgac atgttgacta 3900 agtctctaaa tgtgactaag ttcaaacact gtttgaattt gatcaacatg ggagattgct 3960 gaagacttcc cattagggaa ggtactgaga cctgaaggta gttcagacac ttgtcaactt 4020 aataggttgt caaggtggag ttt 4043 // ID HAT-8C_Mad repbase; DNA; EDCOT; 4866 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-8C_Mad. XX NM HAT-8C_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4866 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1622-1622 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >86% identical to consensus. XX FH Key Location/Qualifiers FT CDS 1623..3923 FT /product="HAT-8C_Mad_1p" FT /note="transposase." FT /translation="MDGSGSGSGSQSQSTSTPRISVLVKRKPQYIRTQEYY FT EDYCDDDPDMDADIGLEEIDEEIEEEEGEEDSVELDRRQMPSVATLASRVG FT QRKKSNRTKGPSPAWNDATKVXVTDEFGITTVMAECNHCKMQVPAESSRHG FT TKGILNHLKKCPDSSLYEAPDSKQPLLSQGVMGGQVVAHTFNQKRLDMKCV FT KWIIKAEMPFRAVDQEDFRDWIHDLNPKYKLPNRHKVAAAVLELYFTEKEK FT IKRVVDGLRVSITTDTWTSIQNINYMVVTAHFLDNDWALHKRILNFVQITS FT HKGDDIGRCLEVCLNNWGIDKVFSITVDNASANDTAIAYMKRRLKSNGTLL FT LDGAHLHMRCACHILNLIVKDGMTELSREIEGIRNCVKFIHSSPARLETFR FT EYCVLMRFDRMSNIPFDVVTRWNATYEMLNSAFKFKQVFSRMADECNTFIS FT YFQEEVSKEINGVTTKVKRVGPPVVEDWERAVSFAHFLKKFYDATLTLSAT FT LTPTSNLILGTVMALQVEIEEKICXSSNATLQSVATSMKLKFDKYWGDIEK FT VNPILFIAQALDPRYKFEMLEASLEELRYSCDAILDVKTTIKKNLTDLFKA FT YKEGEVSSSSSSVTVDQRPSVVVDDSSGLEDDDVATRMQRKIQQKRAAAQQ FT NEISNEVDMYFNDPHQSLTYEGFNILDWWKVNSGIYPTLSRVAKDIFALPS FT STVASENAFSLGGRVVDPFRASLTPRTVEALVCTSDWLRGNEMSFYKEPTI FT DDLMFYKELEELEKGK" XX SQ Sequence 4866 BP; 1350 A; 923 C; 1118 G; 1467 T; 8 other; taggggtgga atttttttcc cgaaaatccc gaaccgtccc gatcccgtcc cgaaattagc 60 ccgaaaaatt cccgaaccga atttcccgaa acattcggta cccgaaaccg atcccgaccc 120 gaaagtttcg gtttgggatt cggccacagc tttgaaagct ttcgggaatc ccgaaccgaa 180 ccgaataata tatatatata tttatttatt tttaattttt aattagaaat tacttgaacc 240 gttggatttg ttaaaatcta atccaaccgt ccattgagtt aggtcattcg tttgttaggt 300 tggtatcaga ctctctcagt cgctctcgct ctctcacctc actggctcac tcacacacac 360 tctcactctc acagtcactc actctcacag tccccccgct ccactcctcc gtcgaatcca 420 cgccgctcct catcgtccat cactccattg actcacgccg ctccactcct ccgtccccag 480 ttaaaggaat ccatgccggt cctcgtcgtc cattgactca cgccgcttct ccgtggactg 540 acgcttctcc gtcgacactc acacgctcga atccgacacc aatcgagtcc caaaatccag 600 gttagtaggc ctagaagctt tcccagttgc atgcaacgct tcgtctctgt gcctcgagag 660 gtgagaaatt tcctcactga ttagcacaac ggagctcgat tgtcgagagg gagggtgggg 720 gtttgcggcg gagggtcgga gaatgggata agagcaattt cgtgcagtcc tgatctgttt 780 gcttttcttc gtccacggga tctgtggcga gctttacgga ccatcattgc cagttctcca 840 gctaactcct tccgacttca agcccaaggt aaatgttgaa actttaccag taactgggtg 900 taacctcttc agattcttta gttttttgca ttaaatctat tggaatttgt caccgtttgg 960 attgaaaagc acttgcggct tcattatttc gaacacgttt tactcattca tatggatgtt 1020 aagttttaat ttgtttttgc tttctccggt mcatttttca tttggatgcc ctgccatttt 1080 tcatttttca atccagcaaa tattttcatt tttgcatgcc ctgctatttg kcagcaaata 1140 tctttctctt tgcatgccct gcaacgattg tgaagacttg gttagtgtgt gtgatactta 1200 attttggcaa tttgattttg tattcaggtc agattttaaa gcagctatca gagataacta 1260 gcagggaggt tctaacttct aagtttaaac aagagctcaa taacaaacag gtcagatttt 1320 gcactctgtc aatatatgta atgtgatata tataatgtgg tatatatgtg cactctctgt 1380 caatatatgt aatgtgatat atataatgtg gtatacatct gccatctstg tcagtatata 1440 taatttgatg tatatgcgcg ctctgtcaat atattgtatg tactgaatgt gtttacgtat 1500 ctgcgatctg agtttatata cgtggaatgg tcaatttatg gatcagttaa catgctttaa 1560 tctcatatga atattatata tatgctgaac tgtgttgtga tatattattg tgcattgtca 1620 ggatggacgg gtctggtagt ggtagtggta gccaatcaca atctactagt acacctagga 1680 tctcggtttt agtaaaacga aagccacagt acattcgaac tcaagaatac tatgaagatt 1740 attgtgatga tgatccggat atggatgctg atatagggtt agaagaaata gatgaagaaa 1800 tagaggaaga agaaggtgag gaggatagtg ttgaattgga caggcggcag atgccttcgg 1860 tggccacatt agcaagtagg gtgggtcaac ggaaaaaaag taataggact aaggggccaa 1920 gtccggcttg gaatgatgcc actaaggtaa awgtgaccga tgaatttgga attacaacgg 1980 ttatggcgga gtgcaatcat tgcaaaatgc aagtgccggc ggagtcctct agacatggga 2040 cgaaaggtat tcttaatcat ttgaagaaat gcccggattc tagtctctac gaggctccgg 2100 attcgaaaca accattgttg tcacaagggg tgatgggggg tcaagttgtc gctcacactt 2160 tcaatcaaaa aagacttgat atgaaatgtg tgaagtggat aataaaagcg gagatgcctt 2220 ttagggcggt tgatcaagag gactttagag attggatcca tgacttgaat ccaaagtaca 2280 agcttccaaa taggcacaag gtggcggcgg cggttttaga attgtatttt acagagaagg 2340 aaaaaatcaa gagggtggtt gatggtttga gggtgagtat cactaccgat acttggacct 2400 caatccaaaa tattaattac atggtggtga cggcacattt tttggataat gattgggctt 2460 tgcataagag gatcctaaat tttgttcaaa ttacgtctca caagggtgat gatattggga 2520 ggtgtctaga ggtatgcttg aataattggg gcatagacaa ggtatttagc attaccgttg 2580 acaatgctag tgccaatgac accgccattg catacatgaa gagaagactc aagtccaatg 2640 gtactctttt acttgacggg gctcacttgc acatgaggtg tgcttgtcac atcctcaatt 2700 tgatagttaa agatggaatg acggagctta gtcgtgagat tgaagggata aggaattgtg 2760 tcaagttcat acactcatcc cccgcgaggt tggagacttt tagggagtat tgcgtcttga 2820 tgagatttga taggatgtcg aatattcctt ttgatgttgt cacaaggtgg aatgccacct 2880 atgaaatgct caatagtgcc ttcaaattta agcaagtgtt ctcaaggatg gcggatgagt 2940 gcaacacttt catctcttac tttcaagagg aggtatctaa agagattaat ggggtcacaa 3000 ccaaggtgaa acgggtgggt cctccggtgg tggaagattg ggagagggcg gtgagttttg 3060 ctcactttct taaaaagttt tatgatgcca ccttgacact tagtgcaacc ctgacwccaa 3120 cttcaaactt aatacttggc acggtgatgg cattgcaagt ggagatagaa gaaaagattt 3180 gcamttcctc taatgccact ttgcaaagtg tggcaacttc catgaagctt aagtttgaca 3240 agtattgggg ggacattgaa aaggttaacc ctatactctt tatagcccaa gcactcgacc 3300 cgaggtacaa gtttgaaatg ttggaggcaa gcctagagga actccgctat tcatgtgatg 3360 caatcttgga tgtgaagacg actattaaaa aaaacttgac agatttgttt aaggcgtata 3420 aggagggaga ggtttctagt agtagtagta gtgttaccgt ggatcaaagg ccaagtgttg 3480 tggtagatga ttcttcgggg ttggaagatg atgatgttgc tacaagaatg caaaggaaga 3540 tccaacaaaa aagagcagcg gcccaacaaa atgagatatc caatgaagtg gatatgtatt 3600 tcaatgatcc tcaccaaagc ttaacttatg agggtttcaa tattttggat tggtggaaag 3660 tcaattctgg aatatatcca actcttagta gggttgccaa ggacattttt gctcttccta 3720 gtagcaccgt tgctagtgag aatgctttta gtcttggtgg gagagttgta gatcctttta 3780 gagcttccct aacaccgaga acggttgagg ctctggtgtg tacaagtgat tggctaaggg 3840 ggaatgaaat gtctttctac aaggagccta cgattgacga tcttatgttc tacaaggaac 3900 ttgaagagtt ggagaagggt aagtgaagta tttgatttca tgttttcatt ttcttagttt 3960 taaaatttat gcattcacta tctaaatata ttttgcgttt tattgttttt atcgttttag 4020 agttgcctaa tatgggaggt gaggagaatc ccacacaagg tgaaatgcca cctcctccac 4080 cacctcaagt tcaacgccgc ccatcattac ctccacgacc acccatttca agagcatcta 4140 atccaacaca aaggagggtt caattatcaa caagaggaag gggtccacca ccaccatcaa 4200 caccaacgtc aacgggtcat tcatcaacaa ggggaagagg ccgaaggggc taaaggaaat 4260 gaactacgtt tataaactat gttttgcttt tggtttgtaa tttaatctaa attcattcgg 4320 aagtttggtt tgtaaaattt aacttatttc attttggttg catgcacttt taattaacta 4380 gttcgttaga cgtttataaa cttaagctta acttgttagt tgtatgcttt cttggtatga 4440 aaattgaaac aggtgtggta ttgtgaatct gtgatattgt gatgaaattg aaacaagtgg 4500 gctgcctgtg cttgtgcggg cagtggctgg ttgcaattgc caattgtaac cttctttttt 4560 tttttttatg aaaaaagggt gggcttaccc tttaaatggt gggcttactc tttaaaagcc 4620 caacattttg ggcttcaaat tgtaaaaags ttaaaattgt aaaaagttat aaaagcccaa 4680 cattttgggc ttcaaggccc aatcccgaag tttcccgaaa atcccgaaac actttcggga 4740 atcccgaatt tcgggattcc aatagttttg gttcggtttc gggatataaa atccmatccc 4800 gaaatgtttt ggtttgggaa tcgggttcgg ggtttcggtt cgggatcccg acccgaacca 4860 gcccta 4866 // ID PSAT19 repbase; DNA; EDCOT; 659 BP. XX AC AF155749; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-JUL-2004 (Rel. 9.06, Last updated, Version 2) XX DE Pisum sativum dispersed repetitive DNA, PSAT19. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy retrovirus-like; PSAT19; Repetitive sequence. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-659 RA Neumann P., Nouzova M. and Macas J.; RT "Molecular and cytogenetic analysis of repetitive DNA in pea RT (pisum sativum L.)."; RL Genome 44(4), 716-728 (2001). XX DR Genbank; AF155749; Positions 1 659. XX SQ Sequence 659 BP; 197 A; 116 C; 166 G; 180 T; 0 other; tcgaagcaga agaagatgat gttgaaggga ttcctaataa gattacccga cttcttgagc 60 acgaagagaa gatcattcag ccgcaccttg agaatctgga aacagtcaac ttggggtctg 120 aagattgtgt tcggatagtg aagattgggg cactccttga agagtctgtt aagaaggggt 180 tgatcagttt gctacgagaa tattccgata tctttgcttg gtcgtatgaa gacatgccgg 240 gtctagatac agatattgtg caacatttcc tgcctttgaa gcctgagtgc gtgcctgtga 300 agcagaagct cagaagaact catccagata tggcagtgaa gatcaaagag gaggttcaga 360 agcaaattga tgcggggttt ctggtgactt ccacatatcc tcaatgggtg gccaatattg 420 tgcctgtgcc taagaaagac ggaaaagtcc gtatgtgtgt tgattataga gatttgaata 480 aagctagtcc gaaagatgat tttcctctac cacacactga tatgttggta gataatacag 540 ctaaattcaa agttttctcg tttatggacg gattttccgg atataatcaa attaagatgg 600 cacccgagga tatggagaag acaacattca tcacaccttg gggaacattc tgttatcga 659 // ID COPN_MT_I repbase; DNA; EDCOT; 3491 BP. XX AC AC137995; XX DT 12-DEC-2006 (Rel. 11.12, Created) DT 12-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Putative non-autonomous Copia-type element - internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW internal portion; COPN_MT_I. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3491 RA Jurka J.; RT "COPN_MT: putative non-autonomous Copia-type element from barrel RT medic."; RL Repbase Reports 6(12), 615-615 (2006). XX DR EMBL/GenBank/DDBJ; AC137995; Positions 81670 85160. XX SQ Sequence 3491 BP; 1226 A; 499 C; 684 G; 1082 T; 0 other; acaattttaa gacgtttcga tctgctatgt ctatcgaaga agttacttat tgaggttgaa 60 ttgtccctaa acaaattaag aataaatcaa gctatagaat tacatctttt gatgaagtgc 120 ttgttgttta aaacaacaac attaatattc accgaagaag caatgtttat cttacttaac 180 atgagaagcc acgcttgcta tatttcattc ggcatggctt gtttcctttg atattaagta 240 agaacatgac ttctgaagtc gttaaagaac ttttatgcaa ttacataaaa gtatgaaatc 300 aaagttggat atgactttat ccctgctatt gcaaagtcaa catttgcaga gaacttttta 360 ttggttacta tggatggtaa tgtataattg atttcttatg caattagtgt ggatggattc 420 ggttgttacc ttagtgaatt gctctcggaa taaccatcgg aaaaaatgcg caaattcctt 480 aatatgtgcc cacggttaat cggttaaagg aacaagcgtg attttagttc ggaagggagt 540 attagttact ctaaaaataa gaaagaatct gaatttcaga tttctattga ataaaactgg 600 gttgactcag acttaaagag agacttgtgt gtcatacact cttgtcggaa aaggacttca 660 ctttgatgac atgttcaaaa ttaaaattct ccttctattt tattagttgt gtgattttaa 720 tatttgacat atcaaaattg atcacgaact catgtttaat tttaaatttg agtaacttgg 780 atttaattcc aacgttatat gattaaacaa ttttatattt tgcagtcaag atatatgaac 840 caaatgttca tataaacaag tgtttagaga atttgaatgt gcatacttga tagcacataa 900 attagaaatg ataaaataat cttttatcat acttatcgat gactgtgaat tttggaaaat 960 aaaattgatg cgcttgatat gttcaatttc tataaattga aatttatgtt ggatagagta 1020 cccaagtcta agaacaaaaa ttctaattaa gaaatttttg aagaaaagac aatccaactt 1080 gtcttatttt ttgaacttgg gattgtctgg actatattta gattctggac cccaagagag 1140 ttgaactcac tagtagagcc tatgaatgta tattcattgg gtatgctata aatagcaaaa 1200 catataggct ttatgaccta aatgttaaag tgattataga attaaaagac gccgatttct 1260 atgtaaatat ttacccctcg aaactaaaga atagtggggg cactagtggg agcacgacat 1320 tagtgggggc aaaataaatt cccttctaaa aattaagaac tagtgggggc actatatctg 1380 atcacattcg tgtaatcaga aatagttatg aaaacatcgt accagatgtt atagaacctc 1440 gaggaggtag gaaagctaga atagctaaag agtatgaact cggtttatac attggaagaa 1500 tatccattaa gccttaaaga agttatatcc ttattggatg ctgaattatg gcaagaagca 1560 ataaacgatg aaatggattt tctagagtct aacaaaacaa gacagttggt tgacttgtct 1620 catagttgca aactaatcgg ttgtttttgg attttaggaa aaagaactaa aacctgatgg 1680 tacggttgat gaatacaagg ctatccttgt agtcaaaggt tttagacaga gaaaaatata 1740 gtcttcttcg acacttattc accagtcact agaatcatat ccataagagt actagtccct 1800 ttagccgcca ttcataactc gataatactc caaatggatg tgaaagttgc cttctttatg 1860 gtgaactaga agaagaagtc tatattaaac aacctgaagg ttttgtgatt catggactag 1920 aaaacaagtt ctgtaagtta gataattctt tgtgaggtct aaaataaact cttaaggaat 1980 gacatgaaaa agttgacatt ctaatgctat cgaatgagta taaagtgaat gaaagtgaca 2040 aataatattt acacgatcat atgtctctat gaagacaact tgctcatatt tggtttaaaa 2100 atttatgtta tgaattatat gaaatcattg tttatcaata acattgataa gaaagaccta 2160 gacaaagttg aagtaattct tgatttcaag attactagat cagaaaagag aatttttctg 2220 atgaatctca caaagttgag aatatcttaa ggaatgtaat tatttgacta taaacttgca 2280 agtataaaac ctttcaagaa cacttgagat ggtacgccat tgaatgtatt agactcgacg 2340 ttggccacgt cgtgagattt ttgttcaagt ttattagtag acggataaga agcattgaca 2400 tgctattgaa agagtcatga ggtgccttaa gaagattatg actctaggat tacattatga 2460 gaagtatcct attgtacttg aatggtacaa gatacaaatg agaagtatca tattgtacat 2520 gagtggtaca agataaaaaa ttgaacatcc ttcagatgag tctcaaagcg accagtgact 2580 gcccattgag catcacttga ggagttattt gttgaaacaa atgatattat ggaatgaatc 2640 tgagatgaga acactagaga aaactagtga agaagcaagt tgataagatg cttgctagtt 2700 aagaaccctc agtgggtgaa accgttgtcc gaagtgttaa tttattgtga tagtctgcag 2760 ctattacaaa attgagaatc gttaccacaa tggtgagaga cgataattaa ggcacgaaca 2820 cagaatgatt agagagctct aaaagaaacg gttaaagtat atcgtgcacg tattgataaa 2880 gaattagtca atcctttgac gaaaggaatt actagaaaga aagtcctaaa cccatccaac 2940 aggatgggac taatgcccaa aggtcacaag tgatggtaac ccgacctaca tgattggaga 3000 tcccaagaaa taggttcaat gggtgataac aagtcatgag tgatagaaca tgctatgaga 3060 aaagtaagaa agcatgattc ctgcagtgac agaaggatga gataatagaa actcttaatg 3120 agatctatac tctatgtgga gtggagtacc tagctacagg agtactcttg atagactcac 3180 ctatacgaat gtggaactta agccgattcc tatggtattc ggggcaaaat acctagagcg 3240 ttcattaaaa ccgggataga cgtgcaaggc cataaaaagc acgggttttt agaatacacc 3300 ttatgaaaag gtttgtgtgt gggttctatg tctgagatag agttcaatgc tgtaagcaac 3360 tcttgttaat cagaatttta ctcgctatgc agaggttcaa gttgtaggcg acacctttgt 3420 ttactagcaa atcttatgga gacgtctttg acgttatttt tgaaaccatt ttttaaattc 3480 aagtggggga t 3491 // ID Copia-86_Mad-LTR repbase; DNA; EDCOT; 177 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-86_Mad_; KW Copia-86_Mad-LTR; Copia-86_Mad-I. XX NM Copia-86_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-177 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1711-1711 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 177 BP; 54 A; 24 C; 34 G; 65 T; 0 other; tggtgttgga tgactagtga aattaggcta gtcaactttc ttgttcaaag ttaggcaagt 60 taggttagtc aagcaagata ggtaagttag gcaaaattag gcttatgatc tttttcttcc 120 ctatatatat gtttcatctt gtaattgttt catcaagcaa atatacatcg aaattca 177 // ID EnSpm-8N_VV repbase; DNA; EDCOT; 3671 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE EnSpm-8N_VV, DNA transposon - a consensus sequence (partial). XX KW EnSpm; DNA transposon; Transposable Element; nonautonomous; CACTA; KW Cactavine-8; EnSpm-8N_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-3671 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 759-759 (2008). XX DR [1] (Consensus) XX CC EnSpm-8N_VV (Cactavine-8 in [1]) is a DNA transposon family which CC has few deleted copies in the genome. We were able to recover the CC putative transposase gene by multiple alignments of sequences. We CC could not identify TIRs or TSDs and we therefore report here only CC the coding region. XX FH Key Location/Qualifiers FT CDS join(1..2204,2293..2598,2666..2780) FT /product="EnSpm-8N_VV_Transposase" FT /note="Tnp2 family transposase (pfam 02992). Most FT likely partial." FT /translation="MNMQLVLKHFFKLQKLMWIKMESPCKHCQNAFWKSIY FT DIETHLYKYGIATTYQRWIFHGEKVCVDYNERKDMSGPNRLDHHETFTVND FT DVDDDDEMIELLSDVCGPIPNRDATSETTNVETKHFDELLGEAGKKLFTGS FT KLSSLTFIVKLMHLKVLNHWSNKSFDMLLELSSETFPEGTNLPSCTYDAKK FT MLRDLGLGREKIHACKFDCALFWKENEFLDKCPICDEDRYKINDGKGKKSI FT PHKTLRFFPLKPRLQRLFMSRHTASDMRWHKEKRVDDGVLRHPADAEAWKL FT FDRMYPSFSSESQNVRLGLSSDGFNPFGNMSHSYRMWPVILVPYNLPPWKC FT MKEPFLMMSLLIPGPHSPGKEIDLYLRPLIDELKELWHDGIETYDVSIGQH FT FKMHAAILWTINDFPAYGMLSGWSTKGYMACPVCNVDTSSQSLRSKICYMG FT HRRYMPTNHPWHKSRLHDGKLEMNPAPQSFSGDDILEQLENVDHVILGKNP FT NKKDKKRKRIPSELNWTKRSIFFELEYWSKLSIRHILDVMHIEKNVCDNVM FT GTLLNIEGKTKDTYKARLDLQDMNIRKELHLVLHGNKYLKPHACYTLTSME FT RREFCAFLKSIKFPDGYAANISKRVNIEDGKILGLKSHDCHVLLQRLLPIG FT IRKFLRKDISTTLTELSCFFQKLCAKSLRIQDLEILEHDIVLILCKLERIF FT PLAFFDIMVHLLVHLPHEAKLAGPVGLRWMYPIERILSTYKSYVRNKAYPE FT GSIVEAYIVNESLTFCSQYLLGIETKFNRPDRNVDDLNDQSNEFSVFSQRA FT RPFGSYQQLEFSRAEIEKAHWYILNNCQELQSYLCVLTKVCTTSEHMEQLE FT KETNDNLFQRQKQLFPKWFANR" XX SQ Sequence 3671 BP; 1250 A; 511 C; 738 G; 1172 T; 0 other; atgaatatgc aactggtgtt aaaacatttc ttcaagttgc aaaaactcat gtggatcaaa 60 atggaaagtc catgtaaaca ttgtcagaat gcattttgga aatccatata tgacattgaa 120 acccacttat ataaatacgg aatagccaca acatatcaaa gatggatttt tcatggagaa 180 aaagtttgtg ttgattacaa tgaaagaaag gatatgagtg gtcctaatag gttagatcat 240 catgaaactt ttactgttaa tgatgatgtt gacgacgatg atgaaatgat tgaacttttg 300 agtgatgttt gtggcccaat accaaataga gatgctacat ctgagacaac taatgtagag 360 accaagcatt ttgatgagtt gttaggtgaa gccggaaaaa agttgtttac tgggtctaaa 420 ttgtcatctt tgactttcat tgttaaattg atgcatctaa aggttcttaa ccattggagt 480 aataaatcat ttgatatgtt acttgaattg tcaagtgaga catttcctga aggtacaaat 540 cttccatcat gtacgtatga tgctaagaag atgttacggg atttgggttt agggagggaa 600 aaaattcatg cttgcaagtt tgattgtgca ctgttttgga aagaaaatga atttttagat 660 aaatgtccta tatgtgatga ggatcgatat aagattaatg atggtaaggg caagaaatcc 720 atcccacata aaaccttgcg attttttcct cttaaaccaa ggttacaaag actatttatg 780 tcaaggcata cagcaagtga tatgaggtgg cataaagaaa agcgagtaga tgatggtgtg 840 ctaaggcatc cggctgatgc tgaagcatgg aagttgtttg atagaatgta cccctctttt 900 agtagtgaat cacaaaatgt gaggttaggt ctttcatcag atggttttaa tccatttggt 960 aacatgagtc actcatatag gatgtggcct gttatactag tgccatataa cttgcctccc 1020 tggaaatgca tgaaagaacc gttcttaatg atgtcacttt tgattccggg tccacattct 1080 cctggaaaag aaattgatct ttacttacgc ccattaattg atgaactcaa agagttatgg 1140 catgatggca tagagactta tgatgtctct attggtcaac attttaaaat gcacgcagca 1200 attttatgga caataaatga ttttcctgcg tatggcatgt tatccggttg gagtaccaaa 1260 ggttacatgg cttgccctgt ttgcaatgtt gacacatcat ctcaatcatt gagaagcaaa 1320 atatgttata tgggtcatcg tcgttatatg ccgactaatc atccttggca taaaagtaga 1380 ttgcatgatg gtaagttgga aatgaatcca gcaccccaaa gtttttctgg tgatgacata 1440 ttggagcaat tagaaaatgt tgatcatgtt attttgggta agaatccaaa caaaaaagat 1500 aagaaaagga agcgaatacc tagtgaatta aattggacca agagaagtat attttttgaa 1560 ttggaatatt ggtcaaaatt aagtataaga catattcttg atgttatgca tattgagaaa 1620 aatgtatgtg acaatgtgat ggggacacta ttgaatattg aagggaagac aaaggacaca 1680 tataaagctc gattagattt acaagacatg aacataagaa aggagttgca tttagtgtta 1740 catggtaaca aatacttgaa gcctcatgca tgctacacat taacatcaat ggaaagaaga 1800 gaattttgtg cttttttgaa atcaatcaag tttcctgatg gatatgccgc aaatatttca 1860 aagcgtgtga acatagaaga tggaaagata ttaggtctca aaagtcatga ttgccatgtg 1920 ttgctccaac gacttctccc aattggaatc cgtaaatttc taaggaagga tattagtaca 1980 acacttacag aactctcatg ttttttccaa aagttatgtg caaaatcatt gaggatacaa 2040 gatttggaaa tattagaaca tgatattgtg ttgattcttt gtaagcttga gaggatcttt 2100 ccacttgctt tttttgatat tatggtacat ttacttgtgc atttaccaca tgaggcaaaa 2160 cttgctggac ctgttggact tagatggatg tatcctattg aaaggtaata tttataaact 2220 ttatattcaa ttttaaaaat taatttcttt aacaatttga acaatgtttc aatgaccttt 2280 gtttttattc aggattttat cgacttataa gagttatgta agaaataagg cttacccaga 2340 aggttcaata gtagaggctt atattgtgaa tgagtcatta acattttgtt ctcaatatct 2400 tcttggaatt gagactaaat ttaatcgacc agatcgaaat gttgatgatt tgaatgatca 2460 gtcaaatgag ttttctgttt tttctcaaag agctcgccca tttggaagtt accagcagct 2520 tgagttctct cgtgcagaaa tagagaaagc tcattggtat atcttgaaca actgtcaaga 2580 actacaatcg tatttatggt aagacataaa attatttttg caaccattta taattattta 2640 tgactcaata gctaatgtaa tgcagtgtac taacaaaagt ttgtacaact agtgaacaca 2700 tggagcagtt ggaaaaggaa accaatgata atttatttca aaggcaaaaa caattattcc 2760 caaagtggtt tgcgaatcgt gtatgtatat ctaatgacat tttttctctt aaacaaattt 2820 aattagaatg atattattaa ttacatatct tctcaattat gcagatgaaa atattacgcc 2880 atcaaggatc accagaagct actgatgagt tgtattcatt agcctctgga cctgatcgta 2940 gagtatcttt atatcatagt tgtgtggtaa atggaattcg atttcacact aaagatcgag 3000 atgatcgaca cacaactcaa aatagtggtg ttcttgtatt gggtgaccat tatgaggata 3060 tgattgattt ctatggtgtg ttgctgaatg ttgttgtgtt agattatatc ttcaacaacc 3120 aagttgttct attcaagtgt gaatggtttg atactgatcc caataaaaag agattgcaag 3180 atgatggtgt ccttaggtgc attaatgtgg ataataagtg gtatgaagaa gatccttatg 3240 ttcttgcaag ccaagcacaa caaatctttt acgtaaatga tccaaagtta ggatcaagtt 3300 ggaaagtggt gcaaaaagta cttcatagac acatatttga tgtcccagag caaactacaa 3360 caaatgatag tgaaaatgat aatgaagatc caacaataga agaagcatat caagaaaatg 3420 attcaactga tattgtttgg tcagtaaacc aagattgtaa tgttctacaa tatcaaaggg 3480 cagatggtga tccaagctat attgatattg aaaatgtggc tgatcatggg agaagatttg 3540 aaaatgatga tttaactgct ttcataaatg accaagatga agaagatgaa acacttgtag 3600 actattgtag tgaggataat gaaaatagtg atgaagaaga tcatgatagt gatagtgata 3660 gtgatagtta g 3671 // ID Gypsy-1_LJ-LTR repbase; DNA; EDCOT; 393 BP. XX AC BABK01000660; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the Lotus japonicus genome: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-1_LJ_; KW Gypsy-1_LJ-I; Gypsy-1_LJ-LTR. XX OS Lotus japonicus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RA Sato S., Nakamura Y., Kaneko T., Asamizu E., Kato T., Nakao M., RA Sasamoto S., Watanabe A., Ono A., Kawashima K. et al.; RT "Genome structure of the legume, Lotus japonicus."; RL DNA Res 15(4), 227-239 (2008). XX RN [2] RP 1-393 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the Lotus japonicus genome."; RL Direct Submission to Repbase Update (02-FEB-2011). XX DR Genome; BABK01000660; Positions 200 592. XX SQ Sequence 393 BP; 116 A; 63 C; 98 G; 116 T; 0 other; tgttagagca gctagtcgtg cagggccttt ggtgcaagat ggcgtagggc ccaaagagtg 60 gaaggtttat tctagaaggg gaaaagggaa tctccaggtg gataactaat tccctaactt 120 tcaggaagag agagagccaa tgattgtaat aggactttac tataagaagg tagttagagg 180 agggtcgagg ggtatcttat tttcatagct gtgtaaggaa atggatagga agcaataagc 240 ttcctattag gagctgagct cttgtcagat ttagggaacc attccccttc tctgtaattt 300 accaagtata attcaataag caatcatttc agtttcagtt catttacctc tattctgtgt 360 ttgagaccat tgttaggaaa tcgattccta aca 393 // ID LTR-2_Mad repbase; DNA; EDCOT; 2029 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR-2_Mad. XX NM LTR-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2029 RA Kojima K.K. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1785-1785 (2010). XX RN [2] RP 1-2029 RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~97% identical to consensus. 5-bp TSDs. XX SQ Sequence 2029 BP; 545 A; 403 C; 344 G; 737 T; 0 other; tgataggagc atatttatgc gactgagtta gcttgttctc atgcatttat gttgttattt 60 cttagttaat tatgtatttt aagctatttt cgtgtgtttg taggtccata ggccttataa 120 agcaataaga tgcattttgg tgcattttgg agcagttttg ggcttggaat gaatagcaca 180 tgcatggagc aaggtggatg gacgaaattg aagactaaag aggctaggaa tgtgttaaag 240 agaaagaaga attaatgtaa aaaggacaaa gagctcagcc acaaaggggt gtcactccac 300 cattcacctt tccatcattg ccgtgcacca ccattgcact ccctttggat tcctatgccg 360 tgcatcatca tccatgttcc ctccattgac tcatttgttg catcattcca cttcctttcc 420 tttgtctacc atgtgcacaa tatcctttca cctccttgca ctcattgatt caccacttac 480 tcacctttcc acccatgcca tgcataatca cccttgtccc ctccatcatt tcagatttca 540 tgcatcatta cattgaatca ttgcactcaa ttgctacacc attccttgtt ccctccatca 600 tttcagattt catgcatcat tacattgaat cattgcactc aattgctaca ccattccttg 660 ttccctccat catttcagat ttcatgcatc attgcactca attgctacac cactccatgt 720 tcccctccat tgccatgcac ttcctctata aaaggaagtg tgtgtaacat aaattgagtt 780 catacttggt tagatcattc actcccattt caacacaacc ttcatccaaa cacatccatt 840 catcttcaca tccattcctc catacaaaca aaccttcaaa cactcaccaa caccttgtgc 900 cgtagcaaag gaagggaagg aaagtgcttg gacgtgcttg ctgtccaact tggatcgttg 960 gagcgtttag gtgttttctt tcttttgttt ctaatgttta aattcatttc ctttcgtttt 1020 gttgtaaata tgagtggcta aacccctctt ggctaggggt gatttcaaag ccatgattat 1080 gtgtgcaata taatttgata aattccagtt atgaactctt gaatcgtgaa tgcaattggc 1140 ttaactattt gattgataac ttatttgtat ttgttaatta agggtcgaca cttaattggc 1200 atgcataaat ccgttgctag aatataagga agtttcacat aatcgttaca aacttatatt 1260 cacatgtagt gaaggtcgct tataaacgat cgcgttaagt tcaattccta gcatgagtga 1320 catgatgtca tagttgcaag tgctttgtca atgcttatga ttttcattaa acgtaatgat 1380 ctttgattgt atctctatta tgatgtcatg tagggaactt ttgaagaatg ttttgggttg 1440 tcgaatgatg tcatccaatc caataaaaca aggaaaatct gagagttaac tagtgatgtc 1500 acggttaatt tggagcattg tcgttcataa ttcaatgaag tagtaactgg aaatcgagtt 1560 atttgcatac atgtcatgtg tggagaaaaa gcctctagct atcccatcca tcatcttatt 1620 tctcaaattt gttttacaat ctgtctagtt tttcatactt gtttgtttgt ttcaacttcg 1680 tccaaaactc aatccccctt tactttagtg tgtctaatta gttagaatct gttttaattt 1740 gtgtttttaa atgttttgat tcaagtaaaa gtcaattttc gtccaaagtc attcctagtg 1800 tctagtttaa gtttatttag ttgttttaag ctgttttgag tattttaagt ttgctttgag 1860 tcttgtgagt cttgttaagt gtttttaagt ttagttttat gtttttgagt cagtttagag 1920 gttattagca agccctccta atccccggtc cagaacgatc cctacttata cttatactac 1980 aattgtcaaa agagggttaa atttgtgtgt taagttaatt ttcgcatca 2029 // ID TY3_CA repbase; DNA; EDCOT; 855 BP. XX AC AF457586; AF457586.1; GI:22770457; VERSION; XX DT 08-JUL-2003 (Rel. 8.06, Created) DT 08-JUL-2003 (Rel. 8.06, Last updated, Version 1) XX DE Cicer arietinum Ty-3/gypsy-like retrotransposon-like sequence and DE CaSat2 satellite-like microsatellite sequence. XX KW Gypsy; LTR Retrotransposon; Transposable Element; TY3_CA. XX OS Cicer arietinum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; OC Cicer. XX RN [1] RP 1-855 RA Benko-Iseppon M.A., Winter P., Huettel B., Kahl G., Stagginus C. RA and Muehlbauer F.; RT "Fine Mapping of Fusarium Resistance in Chickpea (Cicer arietinum RT L.) using DAF (DNA Amplification Fingerprinting)."; RL Theor. Appl. Genet0-0 (2003)In press. XX RN [2] RP 1-855 RA Benko-Iseppon M.A., Winter P., Huettel B., Kahl G., Stagginus C. RA and Muehlbauer F.; RT "Direct Submission to GenBank."; RL Direct Submission to Genbank (12-DEC-2001)Genetics, UFPE, RL Universidade Federal de Pernambuco, UFPE/CCB/Genetica, Av. Prof. RL Moraes Rego, s/no, Recife, Pernambuco 50732-970, Brazil. XX DR Genbank; AF457586; Positions 1 855. XX SQ Sequence 855 BP; 320 A; 175 C; 143 G; 217 T; 0 other; gaacctacgg aggacgaaaa tgaactaaac gttaatccca tgtcacaaac gtacttattg 60 gatgcataag attggttaaa acccctaaat ggattagact aaaccttgag aggacgaaaa 120 tgacttaaat tttaatccaa tgataaaaac gcacttattg gatgcacaag atcggttaaa 180 aaccctaaat agactacaat aagcctaagg aggacgaaaa tgacctaaat gttaatccaa 240 tgtcacaaac acacttattg gatgcacaag atgggttaaa aatccaaaat gaactataat 300 aagcctaagg aagacgaaaa tgacctatta gaggcataag tttggtttaa aatcccaaaa 360 ggactaaaat aattcaaaga ataaggggga atgacctcca tgggtgatcc aatgaatcaa 420 acgcccttgt tggatatatg taacaccccg tttttcaaag cgaggggatt tttttttttt 480 tttttaggga agtcaccaaa atcgaacaaa ggaataaatc ggtaaatgct tttggatcaa 540 taattgagtc attataattt actatcagcg gaaaagtctc tccaatacaa atccaggaac 600 atttctccat aatcgccaaa tggtacatgg gtccccttca atgataaaat aaaagtgata 660 atatttgcat aagtacagtt ttccaaaact aaaatggtcc aaaccaaaaa gaaggacccc 720 tagtccgtat acatcatcct aatctgatca tcctaccaaa aactatacac cctgagtaat 780 ctccacgcgc cccgtgagat cctcctatca caaccgcagt caagcattac catctccatc 840 cctgtccgta ggttc 855 // ID VHARB-N2_VV repbase; DNA; EDCOT; 6789 BP. XX AC . XX DT 31-AUG-2007 (Rel. 12.08, Created) DT 31-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE Harbinger-type transposable element from Vitis vinifera. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW VHARB-N2_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6789 RA Jurka J.; RT "VHARB-N2_VV: Harbinger-type putative non-autonomous element from RT common grapevine."; RL Repbase Reports 7(8), 764-764 (2007). XX DR [1] (Consensus) XX CC Despite its length this sequence appears to be non-autonomous. CC Individual copies are up to 98% identical to this consensus. XX SQ Sequence 6789 BP; 2138 A; 1042 C; 1182 G; 2425 T; 2 other; ggctatgttt ggttcccgga aaatgctaag gaaaggaaaa aaaatacaaa ggaaaatgat 60 tttttttagt ttggatgaca tggaaaatac aatggaaaaa aaatatgaag gaaaatatta 120 aagaaaatat tgtaatattt tcctcactat tttccttaaa aaataatgtg gaaaatataa 180 gagaaaaaga gcagggaaaa gaggaggaaa attttgtcgg ctcttgttca ccgaagcttc 240 atctctaact tcctcttcgt cagtggctat ggcttctcaa cgtcgtcgac cctttcaacg 300 gccaccacta tcactccgac caccttcgag tgcctctgaa aacctaccaa tttcaggcac 360 ccgagttccc attgatgaag tgcgttcttc aaatcaagtt cccatggatg acggatccat 420 gtcttcaagt caggtatgaa ttgaactctt ttctcttaac ctcacatcat ctctgtgttt 480 gatgttggtt taattttatg atctctttcc ctcattcagc cttttccata caactgacta 540 gaaattaggg tttaaggttt ccaatgggaa tttcgagttt gtttggattg atatttgctt 600 ttttttttcc ccttcaaatg agggtttgaa ttcgatttga gttatttctt agggctttat 660 ggaccaatga tttcaggttt cagaatgggg attttgaata ttattagggt tttgattctc 720 tttattgtta attgcaactt tgaatgttaa tatgaagaaa tgataattgt aattttgcat 780 gtgttgttgt tattagcctt ccgataagat tgaaaatgtt tattacttat ttattgtcag 840 taatatatga ttttccggga aacacgaggt tgaattggga attcaaaagg cgtaaggata 900 gggttggact aattctcatg aacttctcat ctattgtggg atagaaattg ctggacttgg 960 attatacact gccattagct catgaagtcg taaggggtag acgtacacaa cccaagcatg 1020 ttctctggtg gaggtttggg acctttcact tgattgaaaa ataaataaat aaattcatta 1080 tgctccatat ttttagttgc gaaagttcaa ggagactata gcttgtgatt tttttccttc 1140 tcagatgtct tgatctttat gaattgtgtt aatttatctt tattctattt acttgatatt 1200 gctaacttta catatgtatt tgattgtact aagcataaaa atggcattta cttgcttaat 1260 tcttttatat ctattgttag gaaattattg tccttcttaa ataaccaagt ctggtcttaa 1320 gccactggtt tagggtgagg gacaatgttg tttagacacc cgaaaaccaa ttagacaaca 1380 ggcagaagta ggagaacagg aactacaatg aagaaagaac ttatgtattt tctatgttaa 1440 tttctttact ttggggaagt tccaatgcag cagcatctag ctagcagata aaatggcaaa 1500 aattcatgat gacatccaag acgattttac aagaactaat ataagaacta atataagcaa 1560 gagcaacatt gtcagtttgg tttgaactca tgtgaactcc tattcatgat ggcacctcaa 1620 cttctatacg tatagttagt ggtttcaagt catttgtaaa gcaccatgaa taacatgaac 1680 atactactga aataatgaaa gtttgatatt ctktttaaac aacttgataa gttcaccctt 1740 ttctttggtc tctggaattg taatacgtca cacatcaaga ataatctaag cttcatttta 1800 taaaaaacat gcttttaaag cttaaattta ataatccata ttcaactacc cccctcaaca 1860 tgcaaatccc attcttatgt aaatatagga ggcctgcagc accttgagga ttctgtcctc 1920 aatcctagga attttcttta agcaactttt gggcaacttc tacattcttg atggattaaa 1980 tgtagctcac aaagccacac acgtattcac tctaagccta gcccattaag tacaattttt 2040 aaaaactgtt caacattaag taaaaaggtc caattaattc agtgtcttga ttcatagaac 2100 caggtagttt tgtctccttg ttccaacatt atatagcaga gccatgttgc aattaacatc 2160 aagaaaataa ctagtgggca gaaacatccc ttaattttca tgcaatattt tcctcgaaat 2220 tttcatagct agaaatcata atacttcaat tcctcttact ttacctaatg actttactaa 2280 atcattcctc ttactttgct atcatgtaga cttataatga agagtggcaa agacttagaa 2340 gatgggctgc aacttgtgta gctatgtatg ctgcatatgc ggcaattctt gtttcagttt 2400 atcatcgctc aaactatttg gagagatcaa tctctaatga aggagattat gaacgacatg 2460 ctttgatgga aagacttaca ctaatggata atgaagattg ttataatcaa ctacgtatgg 2520 gaaaggatgc attcgcaaga ctagtaaaca ttcttcgggg aacaggtcgt cttagaaata 2580 atgcacatag taatgtagaa gaacaagttg ccaaattcct tcacattgtt ggtcataatt 2640 taaggaatag aactatgaaa ttttatttca agcgttctag tgaaactgtt agtcgtcact 2700 ttcatcaagt tcttagagct ataatatctt tagatgatgt cttcttaaag cagcctgatg 2760 gattaaagtg ccctcaagaa atcaaggaca ataccaaatt ttggccctac tttaaggtaa 2820 acttacttat ctaataaaca tcattagaat attatttata tttcaaaata aactaataat 2880 tttgtttctt tataggattg cataggggcg attgatgggt cacattttcg tgtaaaagtg 2940 tcaaatgatg ttgtacaaag gtatcgaggg cgaaagtact atccaacaca aaatgtttta 3000 gcagcatgtt cctttgactt gaagttcaca tatgttttac ctggttggga aggatctgcg 3060 tcagactcga gaatcctaga taatgcatta atgagagatt ttgataaatt gattgttcca 3120 caaggtgatt attggtgatt agataataac ataatttatt agctcaagtg actattacta 3180 ataacaaaga tcctttgtct atgcttctta ggtaaatatt atttggctga tgcgggtttt 3240 cagctaaaaa ctggatttct taccccatat agaagcactc gttaccattt aaaagagtat 3300 agtgttcatc aaccagaaaa tgctcgagag gttttcaacc ttcgacactc gtccttgaga 3360 aatgcaattg aaagagcatt tggtgttttg aagaaaaggt ttccaataat agctagtggg 3420 acggagccac attaccctgt tgacacacaa tctgatatta tactagcatg ttgtatcctc 3480 cataactatc tcatgggtgt tgatccagat gaaagattaa tagcagaggt cgatagagag 3540 ctttttagcg aagaagcgga gtttgaatca atggtcttga gtttagctga aaaatgcaag 3600 gaaggagaaa tcttaaggga gaaaatagcc atggatatgt ggaaagatta caatagaaac 3660 cgttgatgag tccttttatt ttatggttct tttcttgtat agttttttgt gtttcatatt 3720 aagtacgatg attgtattta gaactataac tcctctagtt aaaatcacac tttgaatgag 3780 ttacaatgaa gttattatta tatctcctcc tcttgacttt tcattttaaa catatatata 3840 tatatatgta ttattatttc agatggaaca tagtgaaggc tttgaagtac acaaaagtgt 3900 aagtgaaaaa agaaacttga cttggattga tgaaatggac aactttttgg ttgatcgatt 3960 aatggagcaa atgcataaag ggcaaaagat aggaggagtc ttcaccaaga cagcttatgc 4020 aatagttgct cgagaaattg gggaaaattt tgaattgagt tgtaactctg agcacataaa 4080 aaatagaatg aaaactttaa aaaaaaaact tttatgctgc tcaagaagtt ttacaaaatg 4140 gtagtggatt tggtttcaat gaatcaactc aaatgatcga agctaccacg gaagtatgga 4200 ctacttacac taaggtgagt taattattat ttttgagtta ttagaaataa aatttttgca 4260 tgtaatgtag agttataaat ttctaataga cattatcaca attgaactcg agttttgtta 4320 atatttgttt tttctgatgt taaaaggcac acccaggagc atctcagctc agatacaaac 4380 ctattagaaa ttatgataag ttgtccattc ttcttggaaa agatcgagca acaggaagtc 4440 ttgctgcagg tgcaaaagaa agacaacttc gttgggccca ggaacaaaat ttggatgaca 4500 caattccatt aggatcatca caacatggga tcagagatga aacatttgct tatgttgaaa 4560 atgaagcaac aactgagaca tctttctcat ctgcagatgc atctgtttct gcaccaaagt 4620 caaacaaaga aacaaaaaag cgaaaagcaa aatatgctga cattgtaagt gaagaattaa 4680 ggtcaattag agttggaatg gatgcagttg ttgcggctct tgatagaagc aaccttcaaa 4740 attatacaga agagcaattg tttgaagaga ttgctaagat tggaggcatg agtgatgtat 4800 ctcatatgaa agcatatcaa gctcttaccg gtgatgtgag tgcagctcga gccttccttg 4860 cttgtccaat tgataggcgt aagctttggt tgtcagttaa atttggacct actttttttt 4920 atgcctaatt tgagatggag attattttta tttttagttt tacttttgtt ttggggctat 4980 acgtgaagtt ttgatatcaa aactcatgga tgatagttga ctattagaaa ttgatctatt 5040 atatttttag acttatgaag acttttttta ttcatctata ttttcaaaca gctactttta 5100 ccttagtttt gatacttttt ttggtttgag aattgagaac ttggttgaga ttctgattca 5160 ttttactttt ccagctcagc atccatgtgg tttctttgcg tttcagataa agtttttgct 5220 tcttagtatt tggaatattc aggaatcttt cggtatttgg atagagaatg ccttttaatt 5280 aaactgttat ataactgaat tgttgaatat gatcaatatg cattgtattg tcaggaatgc 5340 tgataattgt ttccttcttc gtacagtcat tttgaataag cattacagcc tttttctggg 5400 aagagaccca gaatcatgct ttgcttttga agtagttttt tgttctcctt tgattctcct 5460 ttacatcatg gaatgagatg tcaaagtgac atggggtagg aagcttcata tcacctgttc 5520 ctgttctttt agggccttct ctatattttc ttttyttctt ttttcttttt ttttcttctt 5580 tttccttttg ttgttgttgt tgttgttccg tgatgtcctt gagaaatccc tcgtttgttg 5640 gatcatattt gaaggaaacc tgaagcttat tcagaattgt gatgtcttgt atggaatcag 5700 gtagaggtaa ggccgaattg gtcaaacaat tttcaaaact gtggtaatct tgcaaagatt 5760 ttatatatat aacctagata tcatggaatc tttgaaccag gtttaactac attcctgttt 5820 gactcagtac tggtttaatt gcaattttct atacctcgac tggccattca ataaaagaca 5880 atggaaaatg atacttttta gaacatttct gaggtttttc ttcttcaaaa attggtatac 5940 accacaacca tccactgagt gctgatattg attatttacc ctacgttttt gaaaaatttc 6000 acgaaaattg caaagaaaaa ataaaattaa tatattattt ttatttactt tttctttcat 6060 atcttttatg attaaccaac gtgaaaaaaa atcattttat ttgtattgct ttgtcctttc 6120 cttattattt aacatagctt catatcatgt taatttgtaa gaagagtgtg aataatttgt 6180 tgctagattt aggagcggga aaatgattta gcagatgtaa aatgggcctc agctcttaat 6240 tttgaatttt atattttata tagtagtttt ttatttttac attatatgaa catattttat 6300 ttctaaattt tgattccgaa aatccttttg aattttttaa gagcttttta ttagctataa 6360 atgtttcctt gaaaataaaa aatagttatt actcgtatat tttatttgta ttacatgaag 6420 aaaattttat acataaattt tataattatt aataaaaaaa ataatagcaa agacttttta 6480 tgagcaatgt tttatgtcga aatattcacg tttttcaaca gtttttttat tggattaatt 6540 tattattatt caacaaattg ataaccattt aagacaaatt gttgatttta ttttccttcc 6600 atttttcctt acttttttat ttgtggttaa ccaaacaaaa gaaaatgaat tctttttttt 6660 ttcccttgaa ttttccatgg ataaccaaac aagtgaaaaa aattatattc ctttccttac 6720 ctttttcttt ccttccattt ttcctctcaa ttttctttct ctcgcatttt ccgggaacca 6780 aacagagcc 6789 // ID Copia-51_VV-LTR repbase; DNA; EDCOT; 228 BP. XX AC chr2; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-51_VV_; KW Copia-51_VV-I; Copia-51_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-228 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr2; Positions 9760166 9760393. XX SQ Sequence 228 BP; 44 A; 31 C; 39 G; 114 T; 0 other; tgattgtatt agttgttttt tactagaagg gtagttttgt cattatttgt agctgagcta 60 tttttgagtt gttttgttta gtttgtttcc gcttttctcg ttcagtttgt tgagccattt 120 tactctgtta tataatagag cagccttgta ttttctgggg aatcaatgaa gagaattctt 180 ttcatctttt ctctcaattc ttctttcttt agatttcttt ttctaaca 228 // ID Copia-89_Mad-LTR repbase; DNA; EDCOT; 525 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-89_Mad_; KW Copia-89_Mad-LTR; Copia-89_Mad-I. XX NM Copia-89_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-525 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1717-1717 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 525 BP; 148 A; 92 C; 126 G; 159 T; 0 other; tgttgaatta taagtatatg agctgaaaag tttagaataa gttttgatgt taattggtgt 60 atgcacttat gcagaatgag ccaagtgtga gggtctagtt atgtaaaaag gccatgagtg 120 ccatgtgttg attgatccta gaaattagct agatgtgtgg ctgagatcaa atgcggtgtt 180 gtgtggtccc aagttaagga ccttcagtta tgtaaagcac gtgagtgctc atttctgaaa 240 tgagagaata ttcctctgtg aaatttttgc agagagaaga acaagaaacc attcgctttc 300 tccatccttc gttcatcgtt gttctctgtc atctccatct tctcaaaact cacattgaaa 360 tcaagttaca ctaacatggc ctcagagcca ggttggatca attgaatctg ggcgtgaatc 420 tgtgaagcca tctgagctaa atcgaagctc tcttgaagct ccgtgaaggt tgtcgattca 480 gatcaaaaca tgtctggatc tggaggctcg gaggtgagga ctcca 525 // ID L1-1_Mad repbase; DNA; EDCOT; 6675 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-1_Mad. XX NM L1-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6675 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1805-1805 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 1..2112 FT /product="L1-1_Mad_1p" FT /translation="MHRKELGEGRRKGWERGDWEKRERVLPSSRLSGRNVR FT YKHLARDFKVEQKVFILEVEDKSLGERICLTERTRFRGFQISFDLGCASWL FT SVQIKTAITASARSFFRLYRGLNYQFWVESFNNKNGIFLVLSKSENQGLVR FT KIIVPKGVNFFGWRKMEELLSEILRGGKKGGVASGTLFQSKRLARREAPEP FT PRIHSCVVPQLSYKDAALGGIKATNLVPNAIAGEKIWIEKSRTKSDKSPEA FT FNWGSVIVCERQVVHQPWREVEDSLLNIMGRKASLVPFQCNKALFVCKNEE FT EAAQIAQIGVLSMIGFPEVVLSGWWESIKPSERKVVSYGGWIALEGLPPHL FT WTSDFFHEIGDACGGLVEIDRKTADFEFLLEAKIRIKQNNTGFIPEFVEVA FT DGDFVVRVKIRQLSPARRPKASVAEYGESRHLKMSRRPLKAELKTQKANGI FT LPPAMAISNPGNQSCPSVESRACFQIGEFKCPITMGSGRKQGVLSGEKLTD FT GGRSKELEVYVREKQGVLSGEQKLSEGGSNSPSGKFVRVEEGLISNGGDYF FT NLSKGLSSTVGGISNCLEKEFYIHEEVASGFXTHQGVFNINFEGKVGCGPI FT KAYDGQSQVDCGSTSDQKIFNVFVGGKDGSGPHKVCNGHIQIGAFLGYPQR FT PITLEFFGLNPRAHHGNEVMVMPNFQSVDLFTSRWHQKGAPLGPREGNRSH FT YNLQ" FT CDS join(2554..2865,2855..6517) FT /product="L1-1_Mad_2p" FT /translation="MISATEEEGTLRDXRQDLEVVEQNQTKENDDNNXVLK FT YSRRKRSGRVSDKWEATGRSSEFLSNMKISLLPLKKSLFLGKSSGVRVGRG FT EKRKSKRGLINLNEDNMKIISWNIRGLGSRRKXVLLKDYFRRARADIIILQ FT ETKTATIDRKLVASVWGSRFKEWVFAPARGSSGGIVVMWNTKHISVVESLV FT GVFSVSIKIRESNGLEWWLSGVYGPCKYRERQDFWEELAGLYGLCGPRWCV FT GGDFNVVRFENEKSNGGRSTASMRIFNQFIQDSELIDPDLLNAQFTWSNFR FT EETVCRRLDRFLFSGGWEESFPHARQKALARVTSDHCPIELDTNKVTWGPG FT PFRFENSWLQHPDFRNNLKEWWLSAIVEGWEGYKFSSKLKIIKKKLQSWSK FT EVFGDTERNLKEAHAKLEEIDFKEGREGLDPDSKRKREETRFLVEDLAWKE FT EVKWRQRSKVEWAKDGDGNTRFFHKVASGRRKRNFIERLEAEDGRMVEGVE FT EIENEIIHFFKSLYSSNEEECWGLDGINWCPINATEAAWLERPFEEAEVKK FT AVFDCGNDKSPGPDGFSLQMFQSCWDILKADILKVLEEFFENGIINAVTNE FT TYICLIPKKADSVNLRDYRPISLVTSLYKVVAKVLATRLKNVMGSTISPSQ FT GAFVKDRQILDAVLVANEVVEEVRQKKEEGLVLKIDFEKAYDHVDWRFLEE FT VLLRKGFGYRWRKWVLGCISTANFSVLINGRPRGKFKASRGLRQGDPLSPF FT LFTLVVDVLSRLIEKAQENHLIXGLRVGQDNVEISHLQFADDTIFFLAGHE FT EAWNNLLHLLQIFGKVSGLKINKAKCSLVGINSDGEKITRLASSWGCEVGS FT WPMKYLGLPLGGKPKSIKFWDPVVEKVELRLQGWKKAFLSRGGRLTLIQAV FT LGSLPIYYMSLFKAPRGVIGRLEKLMKGFLWEGVEEGKKFHLVKWEKVCKS FT KEEGGLGLGNLRNRNAALLAKWLWRFPRESNSLWHRVIKSKYGLVANGWDA FT NCPSRGSSRCPWTDISAGYPPFLHSCNFEVGNGERLRFWEDGWLEGGPLKE FT QFPRLFSLSRTKNQSISNLVASSLQPVSWNLEFRRNLRESEIEEVAGLLQK FT VESVRLCHSREDRRRWNLEGSGQFTCKSYNSFLCNNDVVQQFPPFAQIWKA FT KVPPKVKILVWLVALGKVNTCDQVQRRMPFACFSPHWCTLCKSGEESVNHV FT FLHCPYSIQLWWKLLKEAGARWVTPKGCFELLSTKFEGLGKGRKAKTLWGS FT LLMALFWNIWLERNKRVFEDYKGVGVEXLWDRVKHWAALWASVSVEFRDYN FT FSSIFRDLLAAVI" XX SQ Sequence 6675 BP; 1890 A; 1168 C; 1872 G; 1734 T; 11 other; atgcatcgaa aggagttggg agaggggcga cgcaagggat gggagagggg cgattgggag 60 aaacgggaaa gggtccttcc aagctctcgg ttgtcaggaa ggaatgtgag atacaagcat 120 ctagccagag atttcaaagt agagcaaaag gttttcatcc tagaagtgga agacaagtcc 180 ttgggtgaaa ggatatgttt aactgagagg actagattca gagggtttca gatttctttt 240 gacttgggct gtgcctcttg gctcagtgtt cagattaaaa cggcgatcac agcaagtgct 300 cggagctttt tcagactgta taggggtctt aactaccagt tttgggtgga aagcttcaac 360 aacaagaatg ggatcttcct tgttctgtcc aaatcagaaa atcaggggct tgtaaggaag 420 attatcgttc ccaaaggagt caatttcttc gggtggagga aaatggagga gttattgtcc 480 gaaatcttgc gaggaggaaa gaaagggggg gttgcctctg gtaccctttt tcagtcaaaa 540 aggcttgcga ggagggaggc acccgagccc ccgaggatcc attcgtgtgt ggttcctcag 600 ttgtcatata aagatgcagc tctcggaggc ataaaggcaa caaacctggt gccgaatgca 660 atcgcaggtg agaaaatttg gattgagaag agtcggacca agagtgacaa atccccggaa 720 gcctttaact ggggaagtgt aattgtctgt gagagacaag tggtgcatca gccttggaga 780 gaggtggagg actcacttct aaatatcatg ggaaggaaag caagccttgt gcccttccaa 840 tgcaataagg ctttgtttgt ttgtaagaat gaggaggaag cagcacagat tgcccaaatt 900 ggcgtccttt ccatgattgg attccccgaa gtggtgctgt ccggatggtg ggaaagcatc 960 aaaccaagcg agaggaaggt ggtcagttat ggaggatgga ttgctctgga aggattaccg 1020 ccgcatctgt ggacaagcga tttctttcat gagatcggcg acgcttgcgg tggtttggta 1080 gaaattgacc ggaaaacagc tgattttgaa ttcttgcttg aagctaagat aagaatcaaa 1140 caaaacaata ctggctttat tccagagttt gtggaagtgg cagatggaga ttttgtcgtc 1200 agggtaaaaa ttagacaact ttcgccagca aggagaccta aggcttcggt agccgagtac 1260 ggagaatctc gtcatctgaa gatgtcacgt cgtcctttga aggccgaact gaagacacag 1320 aaggcgaacg gaatactgcc tccggcaatg gcgatttcta atccgggaaa tcaatcttgt 1380 ccctcagtcg agtcacgtgc gtgctttcag attggggagt ttaaatgtcc catcaccatg 1440 ggctctggca gaaagcaagg tgtgttgtcg ggagaaaagc tgacagacgg tgggcggagt 1500 aaggaattgg aagtttacgt ccgggaaaag caaggtgtct tatcaggtga acaaaagttg 1560 tcagaaggag ggagcaactc cccaagcgga aagtttgtcc gggtggaaga aggattgatt 1620 tcaaacggtg gggattattt taatctgtca aaaggattgt cttcaacagt gggtgggatt 1680 tctaattgtc tggaaaagga attttatatt catgaagagg ttgcaagtgg gttttmcaca 1740 catcaggggg tttttaatat taattttgag gggaaggtgg gttgcggccc aatcaaagct 1800 tatgacggac agtcccaagt ggattgtggg tctaccagtg atcagaagat tttcaatgtt 1860 tttgttgggg gaaaggacgg gtctggccca cacaaagtct gtaacggaca tatccaaatt 1920 ggggcatttc ttgggtatcc ccagagaccc ataacgttag aattctttgg gctaaatcct 1980 cgggcccatc acggaaacga agttatggtg atgccaaatt ttcagtctgt ggatctgttc 2040 acgtccagat ggcatcagaa aggagcacct ctcggcccac gagaagggaa tcgaagccac 2100 tataatttgc agtaatctga aatttattgc gaaattcgga gacttagcca atgtascgaa 2160 aaggtttaaa cttgtttatc caaaagagtt cggatcgcgg ctgaacctca atgaggaaga 2220 tacgccaaag aaaatcggtg cttctaatct tctatcccta gatgacgatt cggatcagga 2280 cgaagagatg gaggagttat tgggtcwcaa tcctctttgt gtaacatcag tcgcagagag 2340 gatggaaccg gtcatcggca atatttcctc aacaaacttt tttccaactg tggatttcga 2400 ttacctgccg ctgctgagga agatgattgg tctcaggttt ctgaatcwga agttgagctc 2460 ggggattcgt cccaagatga aaaggctaat ttcgatccaa ttgacagtgg tgaaggtata 2520 ctgcagaatc tattctccga tggagacaag gaaatgattt cggcaactga agaggagggt 2580 accctacggg atwacagaca agatcttgag gtagtcgaac aaaatcaaac caaggaaaat 2640 gacgacaaca acaasgtgct taaatatagc aggaggaaaa ggtccggccg agtctctgac 2700 aaatgggagg ctactggacg atctagcgaa tttttgtcaa acatgaagat ttcgttgctg 2760 ccactaaaaa aatccttatt cctcggtaaa agctcagggg tgcgggtggg aagaggagag 2820 aaaaggaaga gcaaaagggg tttgataaat ttaaatgaag ataattagct ggaatattag 2880 aggtttgggt agcagaagga aaakggtgct tttgaaggac tacttccgcc gagcacgggc 2940 tgatatcatc attttacaag aaacaaaaac ggccacaatt gatagaaagc tagtggcaag 3000 tgtgtgggga agcagattta aagaatgggt tttcgcccct gctcgaggaa gttctggggg 3060 catagttgta atgtggaaca ctaaacatat ctcagtagtc gagtctctag taggagtgtt 3120 ctcagtttcc atcaaaatta gagagtcgaa cggtttggaa tggtggctct caggggtcta 3180 tggcccttgc aaatataggg agagacaaga tttctgggaa gaactagctg gcctttatgg 3240 tctttgcggt ccaagatggt gtgtgggggg agattttaat gtggtgaggt tcgaaaacga 3300 gaagtcaaat gggggaaggt ccactgcaag tatgaggatt tttaaccagt ttatccagga 3360 ctccgaactc attgacccag atctgctcaa cgctcagttc acttggtcta attttcgaga 3420 agaaacagtt tgccgaagat tagacagatt cttattctct ggtggttggg aggagtcgtt 3480 tccacatgca aggcaaaagg ctctggcaag ggtaacctct gatcattgcc caatcgaatt 3540 agataccaac aaggtgacgt gggggccagg cccttttagg ttcgagaatt catggctaca 3600 acatccagac tttagaaaca atctcaaaga gtggtggctt tctgcgatag tcgaaggttg 3660 ggaggggtac aaattttcca gtaagttaaa aattattaaa aagaagttgc aatcttggag 3720 caaggaggtc ttcggagaca ctgagagaaa tcttaaggaa gcccatgcca aattagagga 3780 aattgacttt aaagaaggaa gggaaggtct agacccggac tcaaaaagaa agagggaaga 3840 gacccgcttc ctagtggaag acctggcttg gaaggaagaa gtaaagtgga ggcagagaag 3900 caaagtggag tgggccaaag acggggatgg caacactaga tttttccata aggtagcaag 3960 tgggagaagg aagagaaatt ttatagagag attggaagcg gaagatggta gaatggtaga 4020 aggggtagag gagattgaaa acgaaatcat tcattttttc aagtctctgt acagtagcaa 4080 cgaagaggag tgctgggggc tggatggtat taattggtgt ccaattaatg ccaccgaggc 4140 agcttggctt gaacggccgt tcgaggaagc cgaagtcaaa aaagccgttt tcgattgcgg 4200 gaatgataag tcccctggcc cggatggctt ctctttgcaa atgttccaaa gttgttggga 4260 tattttgaag gcggatatct tgaaggtgtt ggaagagttc ttcgaaaatg ggattataaa 4320 cgcagtaaca aatgaaactt atatctgcct aatcccgaaa aaggcagatt ctgtgaactt 4380 gagggactat aggcctataa gcttagttac cagtctttac aaggtagtgg cgaaagtcct 4440 tgctacaaga ctaaagaatg tcatgggcag tacaatttcc ccatctcaag gagcttttgt 4500 taaagacaga caaattctgg acgctgtcct cgtagcaaac gaggtggtcg aagaggtgag 4560 gcagaagaag gaggagggtt tggttcttaa gatcgatttc gaaaaagctt atgaccacgt 4620 cgattggaga ttcttggaag aagtattact gagaaaggga ttcgggtata gatggagaaa 4680 atgggtgctt ggttgcataa gcacggctaa tttctcagtt ttgatcaatg ggagacctag 4740 gggaaaattc aaagcttcaa gaggactgag acaaggtgac cctctgtctc cgttcttgtt 4800 caccctagtg gtagacgtgc tgagcagatt gattgagaag gctcaagaga atcatttgat 4860 cmaagggctg cgtgttgggc aagataacgt ggagatttct catcttcaat ttgcggatga 4920 caccatcttt ttcttggcag ggcatgagga ggcttggaac aatttattac atttgctgca 4980 aatttttggc aaggtttcag gtttgaagat taacaaagca aagtgttcct tggtgggaat 5040 taattctgat ggtgagaaaa ttacaaggct agcaagttct tggggctgtg aggtgggcag 5100 ttggccaatg aaatacctgg gtcttcccct cggaggtaag ccaaaatcta ttaagttctg 5160 ggacccggtg gtagagaagg tggaattgag acttcagggt tggaagaaag cttttttatc 5220 tagaggcgga agattaacat tgatccaagc tgtcctggga tccttgccca tatactacat 5280 gtccctgttc aaagccccac gcggggtcat tgggagactg gaaaagctaa tgaaagggtt 5340 cctttgggaa ggggttgagg aaggaaagaa gtttcacttg gtcaagtggg agaaagtgtg 5400 taaaagcaag gaggaaggtg gccttggtct gggaaatttg agaaatcgga atgccgcctt 5460 attagccaag tggctgtgga gattcccgcg cgaatcaaac tctctttggc atagggtgat 5520 aaagagcaag tacggtctgg tggcaaatgg ttgggatgct aattgtccga gtcgaggctc 5580 gagcaggtgt ccctggacag acatctcggc tggttaccct ccctttcttc actcatgcaa 5640 cttcgaggtt ggtaacggag agaggctgag attctgggag gacggttggt tggagggcgg 5700 wccgttgaag gagcaattcc ctagattatt ttctttatca aggacaaaaa accaaagtat 5760 ttccaatttg gtggcttctt ctttacagcc ggtcagttgg aatttagagt ttaggagaaa 5820 cctaagagag tcggagattg aagaggtggc tggtttactg cagaaggtgg agtccgtacg 5880 gctgtgccat tctagagaag acaggagaag atggaattta gaaggctctg gccagttcac 5940 ttgcaaatcc tataactctt tcctttgcaa caatgatgtt gtgcaacaat ttcccccttt 6000 cgctcagata tggaaagcaa aagtgcctcc aaaagtcaaa atccttgtgt ggctagtggc 6060 gctcgggaag gttaatactt gtgatcaagt ccaaagacga atgccttttg cttgcttctc 6120 cccccattgg tgcactttgt gcaaatctgg ggaggaaagc gtcaaccatg ttttcctcca 6180 ttgtccgtat agcattcaac tctggtggaa attgctcaag gaagccggag caagatgggt 6240 caccccaaag ggttgttttg agcttctaag cactaagttc gaaggcctag ggaaagggag 6300 gaaagccaaa actttgtggg gatctctgtt gatggccctc ttctggaaca tttggttgga 6360 gcgtaataaa agagtctttg aggattacaa gggagtgggg gtkgaggasc tttgggatag 6420 agtaaaacac tgggcagccc tttgggcttc ggtttcagtg gagtttagag attacaattt 6480 ctcttctatt tttagggatt tgttagcagc cgttatttga tttggtctag cttttcctct 6540 gttcttagtt tctttagggg tccttgctag ttctcttcta gctccaggtg gatatctttt 6600 ccacgtggtt tattttttct cttttgtaat tctttcgttt tataaaattc tttcgtttct 6660 tttcaaaaaa aaaaa 6675 // ID TABARE repbase; DNA; EDCOT; 7981 BP. XX AC . XX DT 16-MAR-2006 (Rel. 11.03, Created) DT 14-DEC-2010 (Rel. 16.01, Last updated, Version 2) XX DE Nicotiana tabacum pararetrovirus-like sequence, ORF1, ORF2, ORF3, DE ORF4. XX KW Caulimoviridae; Integrated Virus; TABARE. XX NM TABARE. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RP 1-7981 RA Jakowitsch J., Mette M.F., van der Winden J., Matzke M.A. RA and Matzke A.J.; RT "Integrated pararetroviral sequences define a unique class of RT dispersed repetitive DNA in plants."; RL Proc Natl Acad Sci U S A 96(23), 13241-13246 (1999). XX DR [1] (Consensus) XX CC Integrated caulimovirus. XX FH Key Location/Qualifiers FT CDS 267..2060 FT /product="TABARE_1p" FT /note="putative coat protein." FT /translation="MNKEEFALEEKTYENPEGLKITIIFSNLGRRYKKIGN FT NLNLMLEKETVKLEDSLTAMVRITKENEEIDRKREIKEIQQQAKEKIQQIE FT EVKNTKITELEKELEMLKQMYANKLKEKEKRKEEEEELKLTNEIERFKLQL FT EEVQESPSKISINEINDQSDKDTELGENYSETSETYTELIEKTEKIKINPE FT INTGDMNEDKPSISGIKNPKQLNPTYYRVSYDAYDRNKTLWDKRLNKKWAP FT RQITEQYNFLDLDCVADINKTIQLWIGYISKQLIDNKITITETPGYIERTL FT IGTVKLWLQNLSSESLDTLRSNKKLDGTTTTTVTDILNKYEIAIRNEFSSM FT TTEVEEQNKEKITNRNLMTKLAICNMCYIDEYTCAFRDYYYKGTYSPDESK FT EIRKLYFTKLPEPFSSKIIKSWNEAGLADTLGVRIKFLQNWFIELCEKYKE FT NMKMEKILVKNLACCKSRIAPQFGCTDKYYKKEGKKKKFKSKYSKYKYRKP FT RRRYYVKNYKHKKPYRKKKKLTECTCYNCGKLGHLAKDCKLPKNPKKKQIT FT EILIDNDKYTQVEYVDYELSSEDSIYEISENEFSENEINKDIEESDEENYD FT " FT CDS 2044..3318 FT /product="TABARE_2p" FT /note="putative movement protein." FT /translation="MKKIMTEKDIQIIQQEEHQDEQSSEQKIIFDANIFEQ FT IKGKELDLSIDKILEVPTIKNWFKRQKEEYYVVSQREHIIDCKYIKGKAQI FT PILNKRLLNKEIQDIKAKNPIKYVHLGGTEILIKACFREGIDTPIEIYLAD FT DRIVQPIEKSIISAVRGNLIYQKFKFIVSANYSVAVDDKNIDKSLVLYWKM FT SGIELAPGSKIFTARCKNLYVLTTKHKITAKNKINKIKIENPFERIVSVID FT NNDYSYTEIDMDEDLEIVKERLSTSKRINNEMPETSSRSTSRSTSKRINYT FT TPQKLIEQKIEEINPHHYYITGIMDQRKYLILINTGQEENYVIRELIPEQE FT IVTIEQQNSELPKALRKNEETTEKELIIGGIPILINFKIYQGDKNITLGIK FT WLEKVKPYKLEDRQLTISYENKKIIIKRTLI" FT CDS 3321..5228 FT /product="TABARE_3p" FT /note="putative polyprotein (aspartic proteinase FT reverse transcriptase, ribonuclease H)." FT /translation="MPKIYILSKIIVEGYYNRYYTPMVDTGAEANMCRHNC FT LPESKWEKLKTPIVVTGFNNEGSMITYKARNIKIQIWDKILTIEEIYSYEF FT TNKDILLGMPFLDKLYPHIITKTHWWFTTPCKQKLGAKRVNNKVRKTTPWI FT KGSEKITQKLENVIQSNHNIEIIIFSINKIKPLQDKLELLYNDNPLQGWEK FT HQTKIKIELIDENSIITQKPLKYNFNDLTEFKMHIKELLDNNYIQESNSKH FT TSPAFIVNKHSEQKRGKSRMVIDYRNLNAKTKTYNYPIPNKILKIRQIQGY FT NYFSKFDCKSGFYHLKLEDESKKLTAFTVPQGFYEWNVLPFGYKNAPGRYQ FT HFMDNYFNQLENCIIYIDDILLYSRTENEHIKLLEKFIHIVEISGISLSKK FT KAEVMKNQIEFLGIQIDKNGIKMQTHVVQKIINLNETLDTKKKLQSFLGLV FT NQVREYIPKLAENLKPLQKKLKKDIEYHFDEKDKIHIQKIKNMCKKLPKLY FT FPDEKKQFTYIVETDSSDHSYGGVLKYKYDNEKIEHHCRYYSGSYTEPQLK FT WEINRKELFGLYKCLLAFEPYIVYNKFIVRTDNTQVKWWITRKVQDSVTTK FT EIRRLVLNIQNFTFTIEVIRTDKNVIADYLSRQRYPNR" FT CDS 5185..6390 FT /product="TABARE_4p" FT /note="putative translation transactivator/ FT inclusion body protein." FT /translation="MLLQTTYQDKGTQTDESQESKDIFTILTTLSLQMESM FT GKRLQQLESQQHDYKNAELSQSEDSKLPEVEGDVGKLQKTHNTVALYTAAG FT TSKQVSKKPHINVNLNTVFDKPFTSKKPREAIVIAPQTSTYANSLHHNKKV FT YNHITQTYIENIYKIQTFLNLNPRSTTTTDPTQDYVTQKLQGYNRLIAQPK FT TKANLVKTCYNYGLLSTVYTHDGEEIIGIPELYKAFVTFKRITKGNLFFIK FT FYTAPAEILYDEIKPIIQVIKIGLTRDMIIPEEIEKQPEIQKMEIPSFYAN FT KRIIGIATIIQELANNYLQGNAIWSYYSRDQLMIYANSKELRQGDMDEVQK FT WILSLLKPEMQPTTRALKKEFISNELLTRYCKLVGHKYPDHICSKCNGDDN FT YVPEVQLE" XX SQ Sequence 7981 BP; 3814 A; 1023 C; 1189 G; 1955 T; 0 other; tggtatcaga gctatgacaa ataaacatat actttaagaa acaaaaccat ggaaaggaac 60 actgacatta atagtacaaa cccgcaaaac agtgaaacaa tcaaaataac taagaaatcg 120 cagaaaatta ggaagaaact aaagaaacta tatatagaat atgaatactt aagtatcaca 180 aaaataaaca aagctaggct gtccaaatta atcgatataa tatctaaaac agaatataaa 240 tatatttgtt atctaaagga taaaagatga ataaagaaga attcgcatta gaagagaaaa 300 catatgagaa tccagaagga ttaaaaataa caataatatt ttctaactta ggaagaagat 360 ataaaaaaat aggaaataac ctaaacttaa tgttagaaaa agaaactgta aaactagagg 420 atagtttaac cgccatggtt agaataacaa aagaaaacga agaaatagat agaaaacgag 480 agattaaaga aatacaacag caagctaaag aaaaaataca acagatagag gaagtaaaaa 540 acactaaaat aacagaatta gaaaaagaat tagagatgct aaaacagatg tatgcaaata 600 aactaaaaga aaaggaaaaa cgtaaagaag aagaagaaga actaaaacta acaaatgaga 660 tagaaagatt caaattacag ttagaagaag tacaggagag tccatcaaaa ataagtataa 720 acgaaataaa tgaccaaagt gataaagaca cagaactagg agaaaactat tcagaaacaa 780 gtgaaacata cacagaactt atagaaaaaa cagaaaagat aaaaataaac ccagaaataa 840 atacaggaga tatgaacgaa gataaaccaa gcatatcagg aataaaaaat ccaaaacaat 900 taaacccaac ctattacaga gtaagttatg atgcatatga cagaaacaaa acattatggg 960 ataaaaggtt aaataagaaa tgggcaccaa gacagataac tgaacaatat aattttttag 1020 atctagattg tgtagcagat ataaataaaa caatacaatt atggatagga tatatctcaa 1080 aacaactaat agataataaa ataacaataa cggaaacacc aggatatata gaaagaacat 1140 taataggaac tgtaaaatta tggttacaaa atttatcaag tgaaagctta gacacattaa 1200 ggagtaataa aaaacttgac ggtacaacta caacaacagt tacagatata ttaaataaat 1260 atgaaatagc aataagaaat gaatttagta gtatgacaac agaagtagaa gaacaaaata 1320 aagaaaaaat tacaaataga aatttaatga caaaattagc aatatgtaat atgtgttata 1380 tagatgaata tacttgtgca tttagagact attattataa aggaacatat agtccagatg 1440 aaagtaaaga gataagaaaa ttatatttta caaaattacc agaacccttt agctcaaaaa 1500 taataaaaag ttggaacgaa gcaggactag cagatacatt aggagtaagg ataaaatttc 1560 tacaaaactg gtttatagaa ttatgtgaaa aatataaaga aaacatgaaa atggaaaaaa 1620 tattagtaaa aaatttggca tgttgcaaaa gtagaatagc accccaattt ggctgcacag 1680 ataaatatta caaaaaagaa ggaaagaaaa agaaatttaa atcaaaatat tcaaagtata 1740 aatataggaa accaagaaga agatattatg taaaaaatta taaacataaa aaaccatata 1800 ggaaaaagaa aaaactaaca gaatgtactt gctataattg tggaaagcta ggacacttag 1860 ccaaagattg taaattacca aaaaacccaa agaagaaaca aattaccgaa atattgatag 1920 ataatgataa atatacacaa gtagaatatg tagattatga attaagcagt gaagacagca 1980 tatatgagat atcagaaaac gagttctctg aaaatgaaat aaacaaggat atagaagagt 2040 cagatgaaga aaattatgac tgaaaaagat atacaaatta tacaacaaga agaacaccaa 2100 gatgaacaat cttcagaaca aaaaataata tttgacgcta atatatttga acaaataaaa 2160 ggaaaagaat tggatctaag tatagacaaa atattagaag taccaacaat aaagaattgg 2220 tttaaaagac aaaaagaaga atactatgta gtaagccaaa gagaacatat aatagattgt 2280 aaatacatca aaggtaaagc acaaatacca attttaaata aaagactact aaataaagaa 2340 atacaagata taaaagcaaa aaatccaata aaatatgtac acttaggagg aacggagatc 2400 ctaataaaag catgttttag ggaaggaata gataccccta tagaaatata cttggcagat 2460 gataggattg tacaacctat agaaaagagt ataataagtg ctgtaagagg taacttaata 2520 taccaaaaat ttaaatttat agtaagtgct aactattcag tagcagtaga tgataaaaat 2580 atagataaat cattagtatt atactggaaa atgtctggaa tagaattagc accaggaagt 2640 aaaatattca cagcaagatg taaaaatcta tatgtcttaa caacaaaaca taagataaca 2700 gctaaaaata aaataaataa aataaaaata gaaaatccat tcgaaagaat agtatcagtt 2760 atagacaaca atgattacag ttatacagaa atagacatgg atgaagattt agaaatagta 2820 aaagaaagat taagcacatc aaaacgaata aataatgaaa tgccagaaac atcatcaaga 2880 agtacatcaa gaagtacatc aaaaagaata aattatacca ctccacaaaa attaatagaa 2940 caaaaaatag aagaaataaa cccacatcat tattatataa caggaataat ggaccaaaga 3000 aaatatttaa tactaataaa tacagggcag gaagagaatt atgttataag agaactaata 3060 ccagaacaag agatagtaac aatagaacaa caaaattcag aactaccaaa agcgttaaga 3120 aaaaacgaag aaacaactga aaaagaatta attattggag gaataccaat attaataaat 3180 tttaaaatat atcaaggaga taaaaatatt acactaggga taaaatggtt agaaaaagtc 3240 aaaccatata aattagaaga taggcaatta acaataagtt atgaaaataa gaaaataata 3300 ataaaaagaa ctttgatata atgccaaaga tatacatact ttccaaaata atagtagaag 3360 gatattataa tagatattat acacctatgg tggatacagg agcagaagct aatatgtgta 3420 gacataattg tttaccagaa agtaaatggg aaaagctaaa aacccccata gtagtaacag 3480 gatttaataa tgaaggaagt atgataacat ataaagcaag aaatataaaa atacaaatat 3540 gggataaaat attaaccata gaagaaatat atagttacga attcacaaat aaagatatat 3600 tattaggaat gccattttta gataaattat acccacatat tataacaaaa acacattggt 3660 ggtttactac cccgtgtaaa caaaaattag gagcaaaaag agtaaataat aaagtaagaa 3720 aaacaacacc ctggattaaa ggaagtgaaa agattaccca aaaattagaa aatgtaatac 3780 aaagtaacca taatatagag ataatcattt tctcaataaa taagataaaa ccactacaag 3840 ataaactaga attactatat aatgataatc cactccaagg atgggaaaaa catcaaacaa 3900 aaataaagat tgaactaata gatgaaaata gcataataac acaaaaacct ttaaaataca 3960 attttaatga tttaacagaa tttaaaatgc atataaaaga attattagat aataactaca 4020 tacaagaaag taatagtaaa catactagcc cagcatttat agtaaataag catagtgaac 4080 aaaaaagagg aaaaagccgt atggttatag attatagaaa cttaaatgca aaaacaaaaa 4140 catataatta tccgatacca aataaaatac taaaaattag acaaatacaa ggatataact 4200 attttagtaa atttgactgt aaatcaggat tttaccattt aaaactagaa gatgaatcta 4260 aaaagttaac agcattcaca gtaccacaag gattttacga atggaacgta ttaccttttg 4320 gatataaaaa tgcaccaggt aggtatcaac attttatgga taattacttc aaccaattag 4380 aaaattgtat aatatatata gatgatatat tgctatattc tagaacagag aacgaacata 4440 taaaactact agaaaaattc atacacattg tagaaatatc aggaataagt ttaagtaaaa 4500 agaaagcaga agtaatgaaa aatcaaatag aatttttagg tatacaaata gataaaaacg 4560 gaataaaaat gcaaacccat gtagtacaaa aaataattaa cttgaatgaa acacttgata 4620 caaaaaagaa gttacaatca tttttaggat tggttaacca agtaagagaa tatattccta 4680 aattagcaga aaacttaaaa ccattacaga aaaaattaaa aaaggacata gaatatcatt 4740 ttgacgaaaa agataaaata catatacaga agataaaaaa tatgtgtaaa aaattaccaa 4800 aactatattt tccagatgaa aagaaacaat ttacatatat tgtagaaact gattctagtg 4860 atcacagcta cggaggagtt ctaaaatata aatatgataa tgaaaaaatt gaacaccatt 4920 gtagatatta ttccggatca tacacggaac cacaattaaa atgggaaata aataggaaag 4980 aactatttgg attatataaa tgtttgttag catttgagcc atatattgtt tataacaaat 5040 ttatagtaag aacagataat acacaagtaa aatggtggat aactcggaaa gtacaggatt 5100 cagtaactac aaaggaaata aggagacttg tattaaatat acaaaatttt acatttacaa 5160 ttgaagtaat acgaactgac aagaatgtta ttgcagacta cctatcaaga caaaggtacc 5220 caaacagatg aaagccaaga atcaaaagac atatttacaa tccttactac tctatcctta 5280 cagatggaga gtatgggaaa aagattacaa cagctagaaa gtcagcagca tgactataaa 5340 aatgcggagc taagtcaatc ggaagactct aaacttccag aggtagaagg agacgttggg 5400 aaactccaaa aaacccataa cacagttgct ttatatacag ctgcaggtac aagcaaacaa 5460 gttagcaaaa agccacatat caatgtaaac ctaaataccg tatttgataa gccatttaca 5520 tcaaaaaagc caagagaagc aatagttata gccccacaaa cttcaaccta tgctaatagc 5580 ctacaccaca acaaaaaggt atataaccat attactcaaa catatattga gaatatatat 5640 aaaatccaga catttctgaa cctaaaccct agatcaacta ctactacaga tccaacacaa 5700 gattatgtaa cccaaaaact acagggatat aataggctta tagcccagcc aaaaacaaaa 5760 gcaaacctag taaaaacatg ttacaactac ggactactta gcacagtata tacccatgac 5820 ggagaagaaa taattggaat accagagcta tacaaagcat ttgtcacctt caagagaatt 5880 acaaaaggca acctattctt catcaaattc tatacagcac cagcggaaat actatatgat 5940 gaaataaaac ccataataca ggtgataaag ataggactaa cacgagatat gataataccg 6000 gaagagatag agaaacaacc ggagatacag aaaatggaga taccaagttt ctatgccaat 6060 aaaagaataa ttggtatagc aactattatt caagaactag ctaacaatta tctacaagga 6120 aatgctatct ggagctacta ttccagagac cagttgatga tatatgccaa ctcaaaggaa 6180 ctacgacaag gagatatgga tgaagtccag aaatggattt tatcattatt aaagccagaa 6240 atgcaaccaa ctaccagagc attgaaaaaa gaatttattt caaacgagtt attaacaaga 6300 tactgcaaac tagtaggaca caaatatcca gaccacatat gttcaaagtg caacggagat 6360 gataactatg taccagaagt ccaactagaa tgaaggtatc aacaagaaga caaaagaaga 6420 agacagctac tggaaacata taatgtaaag taaatagtac tagtcacatt catgaacagt 6480 aaaggtcgtt catgaatagt aagagtcatg taaaaaagtc gtaaagtaaa tagtatatgt 6540 cataatcatg aacagtaaag gtcgttcatg aatagtaaga gtcatgtaaa aaagtcgtaa 6600 agtaaatagt acgagtcata atcatgaaca gtaaaggtcg ttcatgaata gtaggagtca 6660 tttgtaaaca gtaagagtcg ttttaatttt ctttatatag aatgtaaatc tgaggaagga 6720 ggacatcctc agacatcctc atcctcacct tctctctctt atcttctctc aataaaatat 6780 ctgattatat acaaacttct gaaagctatg gagcattcaa acgagttaca aaaccaggta 6840 agtttattta taatcatgtt taactaaact cttatattcc ttataatctc ttgaatatca 6900 taattgttta tcatgttata gtactgttat aaagaacatc ttgagaaagt ttgcctgtct 6960 aataatgctg agagtagtta agcccagact atgccatcct aaagtggaaa ccagtaggca 7020 aggaagccgt ttaggggagt acacagagtt gaggcgctgt tagggtaaat gattgaagca 7080 tgaaaaacat ggtagtgacc agaaaagatt gttcagtata acttattaaa atatgataaa 7140 ctctatgata aacaaagagg ttagagggaa tatgtttagt aaacacatga taaggataaa 7200 tagtaaatct gaatgaacaa ccacacgtat ttattagaag aaaatattga ctacaaaata 7260 cttatgttat atatctttaa gagacttaat aacgatgtta aaagaaaaat ttacgatatt 7320 ttagttactt ttgaaataat atatgtaatg gaacaagcat ttacagaact aattgtatca 7380 catgaaatag atatattaga tctatatgaa ctagatttat attcagacta atgatcacat 7440 atcaagttaa taaaatcttt ttataaatga aacataacac ttttcattat ataagattct 7500 ataataccca gaaatggaaa cttcttaaaa acctcagtaa cataaataga aaaatagatt 7560 gtgttaaata caatattaaa acctgcaaag atattattag atataataga ttacgtaata 7620 aagctttatt aactatagaa aatgaaattg aattttatga agataaactt gaaagttatc 7680 aacacagaaa agaaataact ctgagaaata tagaaaccat ggatatatgt atcaacaggt 7740 atacatctca gtattaatat gaacaaatca aaaattgata gttacaaata ttttaagtac 7800 tggttagaaa ttctaaaaca tataaatatg tcaaaaataa tattagaaaa aaatatagaa 7860 gaatatcaaa aaactaaaga tattaaatac ttagaataca cacttgaaaa tataaaagaa 7920 atttccaaca taaaaaagat cctatgaaaa ataagatgaa ctcaaacaac cacccccaaa 7980 t 7981 // ID RASH_MT repbase; DNA; EDCOT; 881 BP. XX AC . XX DT 29-NOV-2006 (Rel. 11.11, Created) DT 04-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE Putative non-autonomous DNA transposon from Medicago truncatula. XX KW DNA transposon; Transposable Element; Nonautonomous; KW non-autonomous; Inverted repeats; Interspersed Repeats; RASH_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-881 RA Shankar R. and Jurka J.; RT "RASH_MT A putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 601-601 (2006). XX DR [1] (Consensus) XX CC The sequence is present in genome in high copy number and exists CC well conserved. It has 3 bp TSD (ATT). XX SQ Sequence 881 BP; 311 A; 117 C; 147 G; 306 T; 0 other; gagtaaatag tcaatttccc ccctgaaatt gtaagtttca tcaattaccc ccctgaaatt 60 aacaaaactt caattacccc cctgaaattt cacaacgtta gtcaatttac cccctccgtc 120 aaatttttct gttagtgaac atgacgtttt gcaaataccc cccctgaagt tttgcactta 180 tgtgcaaaat gccccccaaa cttaaaaatt tatattattt ttttcttaaa aacaaacaat 240 taatagttaa atattaaaac taactattaa ttttggaatt tgggaaaact acatgcatat 300 atacatcaaa ataggctcca aaatggggaa aaatatgtat tttttaaagt gacaataatg 360 ggatgatttg tggattaata ttgggggttg tgtagtttaa atggtttgag caaattgttg 420 aaggagttgg aggagttaaa agactaagat ggtgaaggag aaaatataaa tttaaatctg 480 attattaatt tgtttataaa cctctaaaaa taataatttg tctattagaa ataaccatta 540 ttgtcacttt aaaaatacac atttttccct attttgatgt atatatgtat gtagtttttc 600 caaactccaa aattaatagt tagctttaat atttaactat taattgtttg tttttaagaa 660 aaaaataata taaattttta agtttggggg gcattttgca cataagtgca aaacttcagg 720 ggggtatttg caaaacgtca tgttcactaa cagaaaaatt tgacggaggg ggtaaattga 780 ctaacgttgt gaaatttcag gggggtaatt gaagttttgt taatttcagg ggggtaattg 840 atgaaactta caatttcagg ggggaaattg actatttact c 881 // ID Gypsy14-VV_LTR repbase; DNA; EDCOT; 1958 BP. XX AC AM472713; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy14-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1958 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-1958 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 729-729 (2007). XX DR Genbank; AM472713; Positions 35892 37849. XX SQ Sequence 1958 BP; 582 A; 364 C; 382 G; 627 T; 3 other; tgattactac tcaaaaagtg ctctttgata gcttgtaata aactctttta aatacttttg 60 agtwttattt attgcctttt aacccaatta acatgttaag gacccttgca atcaattcta 120 atcaaattat attaagtttt ggtgttttga tagcctatgg atcaccaaag caatccgaga 180 ttgaggagag ttatatggaa tcttgggcaa agcaattgga agctcagaaa catgaagaac 240 cgaagctttg aagtcctttg ccataagtaa atccagaatg caaggagaat aagtaaagag 300 aatctgccat gaagcatatt cttgatgaca gtcgtgtcag ccacttttgg agcactttct 360 aaagtccaat tgatgcatgc tatatgtcat ttcaaagctc aggaagtcaa caatccaatg 420 cttcaaacgg tgcgcaattt ggagttgaaa cgaagaagtt acagccactg caagtcaatc 480 actctaagct gaagaaagca ttttgcaaaa gtgttgcaaa atcacccttt tgttgcgaag 540 tgatttcgcg gcctttttgt acagtgtggt ggatttcctc ctgaagttgc ccgatatatg 600 cgacaagttg gaagttgaga acctcaagat gaaagccaac ttcgcaaccc tgcgagaata 660 accttttgct gcgaagtgat ttcgcagccc tttttgtatg tctacgaaat ctcgcagaca 720 tcattttctc ttacgaaatg atccttagtg cgtcccgata tttgctaccg acattgggag 780 atattttcca tcagattttt gttgtctaaa tcccaaaatt ctccttgtaa gccaccaatt 840 acaagattcc ttagctttta agttagtaaa aagagtaaat atccatgtaa taattagttt 900 tgtgttatgt tcatatataa acctctcgag agcctgttct ggaagaggag accttttgta 960 aagttttgga aaatcaagta aagtttaggt cctttgtttt gccttacctt ttcactttgt 1020 attttttatt tcttactaag ttatgyactc tctaaggaat tttccctaga gaatgagtaa 1080 ctaaaccttt agttccttgg agctaaggtt gccggggaag gttccaattg caagaatgca 1140 aagctttgtg gtttcatcca tgaatgaaga ggaagtgaaa tcctttagtg atttctatgt 1200 ttttagttaa cttaaaacac cttagagtcg cctaggccaa cacttggtaa gacaagtgat 1260 ctccaaccat gaagatgcac tagtttaccc cttgcgagcc tctgggaggt gacttgtagg 1320 taggattttt tggaattgcc aacacttggt aagcttttgg actccaagga gacatccatt 1380 agttatctct tgcgagcttg agaagggaag tgcaaggtta aagatcacct tgaatggtta 1440 aggcttagtg agaggtttga accattgcaa gttgcatcag tgagagaatt aaagctgaaa 1500 tctaattaaa ggatgtatct gtacaacacc ggttagagaa ttcactatat gttgattctc 1560 tcacacgagg aaatgaacca actgacctga gctatgtctt ttgcatgagg aaccctcccc 1620 agtgaacctg accctccaag gaatgttttt cttcctaagt aatttccatc acttgttttg 1680 tagtcatttt aaatctaaag ctttaccaat caaagttttt tttttatttc gtgagctaac 1740 cttgaaatga aaaaagtact aattcacttt gaattggtat catttgtaat ttggaaaccc 1800 ttcccagtga acgatcctag agccgctata ctatagtagt tttttctttg ctaccctagt 1860 atatggtgta ataggttata aattttgttr attactccct caaacaagga gcaccagctg 1920 gacatgaatc agctgagaca ccaattgggc acgaatca 1958 // ID RAGYPSY2_I_MT repbase; DNA; EDCOT; 6666 BP. XX AC AC148525; XX DT 07-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE Internal region of RAGYPSY2. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW RAGYPSY2_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-6666 RA Shankar R. and Jurka J.; RT "RAGYPSY2: LTR retroposon from Medicago truncatula."; RL Repbase Reports 6(11), 585-585 (2006). XX DR EMBL/GenBank/DDBJ; AC148525; Positions 82653 89318. XX CC Internal region of RAGYPSY2 retroposon. The internal region is CC present with patched DNA making it self-complementary in some CC regions. XX FH Key Location/Qualifiers FT CDS 1045..1938 FT /product="RAGYPSY2_I_MT_1p" FT /translation="MSSSKFGSHMQTLVQTGKMDRLEQEVHELRGEVTTLR FT AEVEKLTSLVSSLMATKDPPLVQQRPQLLCQPTCMKRPRQQGSQSLIPQNQ FT VRKASQCDPIPVKYADLLPILLKKNLVQTLPPPQMPNPLPPWYRPDLNCVF FT HQGAPGHDTEQCYPLKEEVQKLIENNVWSFDDPDIKVLLQQQHMSSHSIAT FT LRSITNVVQDPGYQSQFQQYQQQPRQRASGQPQFDSIPMKYAVLFPDLLRR FT KLVQTRPPPRMPEKLPTGYRPDLSCVFHQGAPGHDIERCFAFRNEVQKLIQ FT DKVLRF" XX SQ Sequence 6666 BP; 1802 A; 1312 C; 1355 G; 2197 T; 0 other; gaaatggcga cttcactggg gacttaaatt ctacgcgggt taaacccacc ttactttatt 60 tattttgtgc tgtactattt gcttatgctt tgtaaatatt ttgcttacat accttgttac 120 atgagtggtg agataagtcc tacacccggg cttgagtgaa acataagata ggacggagta 180 cgatcatagt gccataccag gagcggtcct gcgatatgtg tacacatgat gtaactccac 240 tcaacgtagg tctttcaaaa gtaataatat gtcgtcatga gcagtcgtga ttggcgttat 300 tatttttgaa gtccgctaaa cgttgaggac ctttagatca cccttaacac atcttggcct 360 tttttaggac gtagtgcggt ggctaaacca agagcagtct tgactttggt cgacacgcga 420 tactacactc aaactagact tacttatgga tgttattgga ctaggagcgg tcctatacac 480 cgatatgttc ataagggaag ttgtaatttg ggaacttggt agaacccgtg atacaggtac 540 aatttgaaac catagtcctt accaaatgat gttgttaccc ttgactccaa cattgtggaa 600 cttaaacatc ctcatgtatt caatgtactt tattataacc atgcatacat gcatttattc 660 ataaatatat ttttccatca aaaattgaag gacttagaca agttttttgc aaacattatg 720 gatatggacc ttgtaagaat gaacaccaag agatacaact tcaaaaaatc ttaactaagc 780 tttagctttt gttaagaact ttttccttgg tttcgatttt accttttgaa aaaagaacct 840 tttgcaatat cttcacaatt ttcaaatgaa accatgtttc tctaccatgt ttaaaaatta 900 actttgataa gtccttcaaa aaaaaaaaaa attttacatt tttgcataaa tatatcattc 960 atcatctttg cattcatatt tctagtctgt atctcatatt ttgtttctac cagcaaaagg 1020 tcaatccatc cgtaaagtcg ttcaatgtct tcatccaagt tcggctcgca tatgcagaca 1080 ctcgtgcaaa caggaaaaat ggatcgactt gagcaagagg tccacgagct tcgtggagag 1140 gtaacaacac ttcgggctga ggtagagaag ttaactagcc tagtatcttc attgatggct 1200 acaaaggatc caccgcttgt tcagcaaagg cctcagctac tatgtcagcc aacatgcatg 1260 aaacggcctc gacaacaggg ttctcagtcg cttattcctc aaaatcaggt ccgaaaagca 1320 tctcagtgtg acccaattcc ggtgaaatat gcggatttgc ttcccatttt gcttaagaag 1380 aaccttgttc aaaccctgcc acctcctcag atgccgaatc cgctgccacc ttggtatcgc 1440 cctgacctca actgtgtatt ccatcaaggg gcgccaggtc atgacactga gcagtgctat 1500 cctttgaagg aagaagttca gaagttgatt gaaaataatg tctggtcctt cgatgaccct 1560 gatataaaag tgttacttca acaacaacat atgtcttctc actctattgc cactcttagg 1620 tccatcacca atgttgttca agatccgggc tatcaatccc aatttcagca atatcaacaa 1680 caacctcgac aacgagcttc gggacaacca caatttgatt cgatccccat gaaatatgca 1740 gtgttgtttc ccgatttgct taggaggaaa cttgtccaga ccagaccgcc tcctcgtatg 1800 cctgagaaat tgccaactgg gtataggccc gacctctctt gtgtcttcca tcaaggggca 1860 cctggtcatg atattgagcg ctgttttgct tttaggaatg aagttcagaa gttgatccaa 1920 gataaggtct tacgcttcta agattgaacg cagacatgca agttaatccg ctatcggatc 1980 ttgaagccta atgttgatac atggaatgtt tagctacaat tgggtctttg ctgatgttta 2040 tttctactac tcatttgttc aattagtatg tttgtttgtt gctttatgtt tttcaaaaaa 2100 caaataaaaa aaatccttcc gtcccacccg aggcgagagt gaatttgttt agggcttttt 2160 gctttatgta ttttcatcat taatgaaagg tcgtcttgat cccgacctcg tttttatttt 2220 gtgctttttc tggaaaaatg gtaatacaaa aaaccaaaaa aaatctttcc ctttaatcat 2280 tttcacatat ctgcataatc ataatgttta tatcaataat caactcatgc attaataaac 2340 ccgttgaaca cttaaacctt gtactctttc tcgactttga gttccttgta tctggggctg 2400 aagaagagga tgatgaagaa gtttccactg aggtttctcg catattgggg catcttggcc 2460 gtcgtagctg caaatatgaa gaaagaatgt ccagaagagg actttcatgt acaaagattg 2520 gcacgagatg ctaccatctg ccttgcaggg atattgtact tcatgcacat ttcaacaggg 2580 gcaacccccc cgccatccct cagtattcaa tgtaaaggca ctgtgccaca tgaaggtcaa 2640 agtcctgtca atggaagttc caaagaaagc caagattgat tgaacttaaa agtgttattg 2700 ccgggtgcca tggacagtca tatcaagagg ataaagcaag tattcgacaa agaaggctcg 2760 tccccgtgaa tgtcaagaaa gtggctttgt gcttaaaaat atgttaccca attctagggg 2820 caaatggatg ccaaattaca aagaatggtg gtaaacttgt atgtcctgta aataccgatg 2880 cagtcaagaa atactttgtt aaaatgaaaa ggctcgataa gtcgcaaacc tgaaaaagcg 2940 gcttaggcaa aaaagagcat ctcgatggac tgaaaacccg aaagggcggt ccatgcaaaa 3000 gttagagaca tttataaaaa aatgattatc ctgataggtt gaaacccgca agggcaatct 3060 atgcaaaagt taaggatcat gacaaagtaa ctgcatctgg tcggacatga ctcacttggg 3120 gcatttcagc tgtcaaaaga cctccggctc attgcaaggt aactgcacca aatcatatat 3180 gattcatctg gggtatctta gctgttaaag ggtttccgat ctgaagcgtc tgcaaatcaa 3240 agactcagaa cagtggaatt caaagtcggt agaggaaaca atagttattg tgttcaatgt 3300 accttttcca tataattacc attttccaaa ctctttttaa aatctgtgga gccacacctt 3360 tggcaggcca ccgctccatt tacattaatt tgagcctgtg cccatttatt tgaaattctc 3420 atttattctg tttgcaaatt tttcttctat ttttgatgtt aatacctaaa gcaaaaaaaa 3480 aaaatctttt aaaaactttt ttcatgtctt ctgaaaagca taaacaatag gtacatcttc 3540 tttgaactta tgggtaggtg aaacatacat caacatccgt ctcaagtaca gttaaactct 3600 acaaggtaag catgaccaaa agttgtgaga tgacctctgt caaaaaatat atatatacaa 3660 aaaaaaaaaa aaaaagctcg ctaagtcgaa aacctgaaag ggcggcttaa gcaaaaaatg 3720 agcatcctgg tggactgaaa acccgatagg gcggtccagg caaaaattag ggggcataca 3780 aaaaaagaat atattctcgg tggattgaaa acccgaaagg gcggtccagg caaaagttag 3840 ggactaaaaa aaaaaaaaaa attgaaatga aaaagacaga ggcatcaccg ctcaagtggg 3900 tcgtttggaa gaatcacttt gtactgattt acaaatgaca acttctgcca agtggttaga 3960 tgaaatggcg tcttctacca taatgattta aatgttggca acttctgtct gtgctttgat 4020 tgatgacgat ttctgctggt ggtttgaaga aatggcgact tctgccataa tgattgattg 4080 atgggtttca tcccgagaaa tggcgacttt tgcctatgtt ttgattgaag gcaactcatg 4140 ccaatggttt gtttaaatgg cgacttctgc ctatgttttg attaagggca acatctgcca 4200 gaatggttga ttgatgggtt tcaccccgag aaatggcgac ttttgcctat gctttgattg 4260 atggcaactc atgccaatgg tttgtttaaa tggcgacttc tgcctgtgct ttgattgatg 4320 acaacttctg ccaggtttat gatcggtggg ctttatcccc aaggaatgat tactccacca 4380 tcaatggtct gtttattggg tcgtatccca tcaaagttat gcctaatggg atgttacctc 4440 tttagtagcc tgattatgga gtttgttacc tcttcagagg tatggttata aggtgtgacc 4500 ctgccgttgg ttttgattag tgggcagtta cctcttcagt ggttaaatca acgttcttgt 4560 tacctcttca gtggtatggt tataaggggt gaccccgccg ttggttttgt ttagtgggca 4620 gttacctctt cagtggttga gtaaatggtt tgttaccttt gttacctctt cgacggtata 4680 attgatgggc cgttcccctt tagcggtatg attcatgggc agttacccct tcagtggttg 4740 aatcaagttt tgctatctct tcagtggtat ggttataagg cgtgccccct accgtttggt 4800 ttgaacatgg gtttttaccc cgtaagttgg tttggacatg ggtcgtatcc catcagtagt 4860 ttgaatatgg attttacccc atcagttggg tgactgttgg ttcgtatccc catcagcagt 4920 ttgattattg ggttgtatcc ctatcattgg tttgattatt gggttgtatc cctatcatta 4980 gtttgattat tggtttgttc tcctatcagg ggtttgattt tgagctttac cccactaatg 5040 ttttgtttgg acggatttac cccgtcagtg tttgactcac ctcctgtatt ggtatccccg 5100 ttgaagattc tcgagtgttt gtgctgcgat gccgggctac ttccttttag gacctgtcca 5160 aatcttgtct caacagtctt ccgttgtact gtcatatgtg tctcgtacat gttcattcat 5220 tcatgcatac atagcatgca tacaaatatc attcatgcat ggttgcatta ttacctagtg 5280 tcttattcca gtgtacctcg taaaagtgtc atacccaatg tgtctgattc aggaatgtta 5340 ccaattgagt ttatttcaag gggcaggtcc catccaatag tctttgtatc aatatatttc 5400 ggctccctag taccttatgt gagctatcct tgtaccgaaa gcatgtgcct tttatctatg 5460 ttggtcgtta cccgagttga ggtaactgac ggtatttcct tttggtatgt tggtcgttat 5520 ccgagttgag gtaactgaca gtatttcttt ttgtatgttg gtcgttaccc gagttgaggt 5580 aattgaccgt atttcctttt tgtatcttgg tcgttatccg agttgaggta actgacggta 5640 tttccttttt ctatgttggt cgttatccgt gatgaggtaa ctgacggtat ttcgtatctc 5700 cctttttgac ggtatttcct tttcttatgt tggtcgttat ccgtgttgag ataattgaca 5760 gtatcttctc tttcgtattt tggtcgttac ccgtgttgag gtaattgacg gtatttcctt 5820 ccatatgttg gtctttaccc gagtaaaggt aattgacagt atttcccttt cgtatgttgg 5880 tcgttacccg tgttgaggta actggcggta tttccttcca tatgttggtc tttactccaa 5940 taaaggtaat tgacagtatt tccctttcgt atgttggtcg ttacccgtgt tgaggtaact 6000 gacggtattt ccttccatat gttggtcttt actccaataa aggtaattga cagtatttcc 6060 tttttaaatg ttggtcgtta cccgtgttga ggtaactaac ggtatttcct ttttctatgt 6120 tggtcgttac ccgtgatgag gtaattgacg gtatttcctt ctgtatgttg gtctttaccc 6180 cagtaaaggt aattgacagt attttctttt cgtatgttgg tcgttaccca gtaaaggtaa 6240 ttgacggtat ttcctttcgt acgttggttt ttaccccagt aaaggtaatt gacggtattt 6300 cgtttcgtat gtgggtcgtt acccctgtaa aggtaactga cggtttttcc tttcctatgt 6360 tgctcgttac cccagtaaag gtaatagaca gtatttcatt tcgtatgttc gtctttaccg 6420 cagtaacggt aataaaataa tatttcctcc ctagtgatat ctatcagttt tttccccagt 6480 caatgtattt ttgtcgtcct tgcattcata cttgcatcgc agacattcat accagtatat 6540 tcataagcat tgcattctca gcatttcaac tggtcaaaaa ttggtgtact tagtatttaa 6600 gtctcttcga cccgttgatt taaaattttc atttttttaa atctccgtga cggagaaact 6660 taaata 6666 // ID Copia39-PTR_I repbase; DNA; EDCOT; 3491 BP. XX AC LG_II; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia39-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3491 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-3491 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 254-254 (2007). XX DR Genome; LG_II; Positions 17680310 17683800. XX CC Positions [917-1417] - Integrase core CC 'AAAAC' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 1046..3481 FT /product="Copia39-PTR_I_1p" FT /translation="MRNRLELFSIFSAFCAEIKTQFNVSVRILRSDNAKEY FT FSKPFNSYMSQNGILHQSSCVDTPPQNGVAECKNRHLLEVARALLFQMNVP FT KQFWADAVSTACFLINRMPSSVLAGATPHSILFPSHSLFPVEPRIFGCTCF FT IRDVRPGMSKLDPKSLKCVFLGYSRLQKGYRCYSPELGRYLVSSDISFFET FT TPFFPISKIYNCEGENDDILVYNITTTINHASSNDPVPIKPVITQVYSRRP FT PPDNSRPPPAPTSTDPSLDLPIAVCKGKRQCTHPISSFASCIHLSPSLRCF FT IAYLDSVPVPKTLVEALSHPGWRVAMEEEMRALDDNGTWELVDLPARKQTI FT GCKWVYVVKVNPDGAVARLKSRLVAKGYAQTYGVDYSDTFSPVAKLASVRL FT FMSIAATNDWPLHQLDIKNAFLHGDLKEEVYMEQPPGFVAQGECSKVCRLR FT KSLYGLKQSPRAWFGRFSEVIQEFGMKKSKCDHSVFYQQSEVGLILLVVYA FT DDIVITGSDSKGISTLKSFLQAKFQTKDLGMLRYFLGIEVTKCKKGIFLSQ FT RKYILDLLTETGKLGAKPCSAPMVTNTQLTTEDGEPFADPEMYRRLVGKLN FT YLTVTRPDIAYPVSIVSQFMASPRTTHWAALEQILCYLKGVPGRGIWYRNH FT GHTHIECFSDADWAGSKIDRRSTTGYCVFVGGNLVSWKSKKQNVVSHSSAE FT SEYRAMAQSTCELVWIQQLLNEIGLGSSLSMKLWCDNQAALHIASNPVFHE FT RTKHIEIDCHFIREKIQQNLISTSHVKTTEQLGDIFTKALSGPRIEYICNK FT LGMINIYAPA" XX SQ Sequence 3491 BP; 942 A; 651 C; 707 G; 1191 T; 0 other; tggtatcaga gccatagaat tctcttttct tttagcgtgg cccaattgag tcccaatttt 60 tttttctcta ctgttggttg tcctgctttg agtgcagtaa tggcagaggg taggaacaca 120 gaagtgcaaa ctgtgatttc tgatgttgtt cctatgacaa caaaaatcac agagcacaaa 180 ctgaataata ccaattattt gaattggagc aaaacagtgc gagtgtatct tcgtagtatt 240 gataaagatg atcaccttgt tgatgatcca ccatctgatg ctgcagcaaa gaaggcatgg 300 ttgagagatg atgccagaat tttcctgcag attcgaaatt ctattgatac tgaagtgatt 360 ggtctagtta atcactgtga atttgttaaa gatctcctgg attatttggc ttttttatat 420 tctggcaaag gaaatatctc tcgtatatat gatgtgtgta aggagtttta tcgcccacag 480 aagcaagaca ggtctctcac tgaatatttt atggatttta aacgggtata cgaggagctg 540 aattctcttc ttcacttcaa tttactctct gttagtcaaa tcactaaagc tctcaattgt 600 tgtgtcttat ttttctctga cctttgttta tttcaggatc ttatgacggg gaagattatt 660 ggtagaggac gtgaatctgg tggtctttat gtgcttgaaa ctactatccc aaaaatacca 720 aatccgaaag tgccaaaact tgttgcttgt tccagtacta tgacacctct ccaacttcac 780 tatcggttag ggcatccttc gttacccatt ttaaaaaaaa ttatttcctc atttccaaaa 840 gttatctcat ttaaattgtg agtcttgtca atttgccaaa catcatcgct cttcatatgt 900 accaagagtt aataaacggg ctgcgtcccc ctttgagtta atacattctg atgtttgggg 960 tccttgtcca gtactttcta agtctagatt tcgatatttt gtcactttta ttgatgacta 1020 ttctcgtgtc acttggttat atttaatgag aaacaggtta gaattattct ctatatttag 1080 tgccttttgt gctgaaataa aaactcaatt taatgtttct gtgcgcattt tacgaagtga 1140 taatgcaaaa gagtattttt ccaagccttt caattcctat atgtcacaaa atggaattct 1200 tcatcagtct tcatgtgttg acaccccacc tcaaaatggt gttgcagaat gtaaaaatag 1260 acatttacta gaagttgcta gagccctcct ttttcaaatg aatgtcccta aacagttttg 1320 ggcagatgca gtttcgactg cttgtttttt aattaatcgt atgccctcat ctgttttggc 1380 tggtgctact cctcattcta ttttgtttcc ttctcattcc ttatttccag ttgaaccacg 1440 catttttggt tgtacttgtt ttattcgtga tgttcggcct ggcatgtcta aactagatcc 1500 taagtctctg aagtgtgtct ttttagggta ttctcgtcta cagaaagggt atcgatgtta 1560 ctctcctgag ttgggtcgtt atttggtgtc ttctgatatt tcattttttg aaaccactcc 1620 attctttccc atatcgaaaa tttataattg tgagggggag aatgatgata ttctagtgta 1680 caatatcacc actactatta accatgcttc ctcaaatgac ccagttccca taaaaccagt 1740 catcacccaa gtgtattctc gacgtcctcc accagacaac tcacgtcctc caccagctcc 1800 tacgtctaca gatcctagtc tcgatcttcc tattgctgtt tgtaaaggta aaagacaatg 1860 tactcatcct atctcatcgt ttgcttcttg tatacatttg tctccttctt tgcgttgctt 1920 tattgcttat ttagactctg tacctgttcc caaaacttta gttgaggctt tgtctcatcc 1980 tggttggcga gttgctatgg aagaagagat gagagcttta gacgataatg gcacttggga 2040 actcgtagac ttaccagcaa gaaaacaaac tattggttgt aaatgggtgt atgttgtcaa 2100 ggtcaatcct gatggggctg tggctcgtct taaatctcgt cttgttgcca aaggatatgc 2160 tcaaacatat ggagtagatt attctgatac cttctctcca gtggctaaac ttgcatctgt 2220 tcgtttattt atgtctattg ctgctactaa tgattggcct ttacaccagt tagatatcaa 2280 gaatgcattt cttcacggtg atctgaagga agaagtgtat atggagcaac cacctgggtt 2340 tgttgctcag ggggagtgta gtaaggtttg tcgacttcga aagtccttgt atgggttaaa 2400 acagagtcca cgtgcttggt ttgggcgatt cagtgaggtt attcaagaat ttggtatgaa 2460 gaagagtaag tgtgatcatt cggtattcta ccaacaatct gaagttggcc ttatcttgtt 2520 ggttgtgtat gctgacgata ttgttatcac tggtagtgac agtaaaggca tctcaactct 2580 taagtctttt cttcaagcaa aattccaaac taaagatttg gggatgctaa ggtatttttt 2640 aggtattgaa gttacaaagt gtaagaaggg tatctttcta tctcaaagaa agtatattct 2700 tgatcttttg acagaaactg gaaagttggg tgccaaacct tgtagtgcac caatggtcac 2760 caacacacaa cttacaacag aagatggtga gccgtttgca gatcctgaga tgtatcgtcg 2820 attagttggc aagttaaatt atctaacggt gactcgtcct gacattgcat atcctgttag 2880 cattgtgagc caattcatgg cttccccacg aaccacccat tgggcagcct tggaacagat 2940 tttgtgttat cttaaaggag ttccagggcg tggtatatgg tatagaaatc atggtcatac 3000 tcatattgaa tgtttctcag atgcagattg ggcaggttct aaaattgata gaagatctac 3060 tacaggttat tgtgtttttg ttgggggaaa cttggtgtca tggaaaagta agaagcaaaa 3120 tgtagtctct cattccagcg ctgaatcaga atatagagcc atggcacaat ccacgtgtga 3180 acttgtatgg atacagcaat tgctcaatga gattggtctt ggtagttcac tatctatgaa 3240 gttatggtgt gacaatcaag ctgctcttca cattgcatca aatccagttt ttcatgaaag 3300 gactaagcat attgaaattg attgtcactt catccgtgag aaaattcagc aaaatttgat 3360 ctctactagt catgtcaaaa ctacagagca gttgggtgat atcttcacta aagctttgag 3420 tggtcctagg attgaatata tctgtaacaa gctgggcatg attaacatat atgctccagc 3480 ttgaggggga a 3491 // ID SINE-5_Mad repbase; DNA; EDCOT; 165 BP. XX AC . XX DT 08-OCT-2010 (Rel. 15.1, Created) DT 08-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE SINEs from the apple genome. XX KW SINE2/tRNA; SINE; Non-LTR Retrotransposon; Transposable Element; KW SINE-5_Mad. XX NM SINE-5_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-165 RA Bao W. and Jurka J.; RT "SINEs from the apple genome."; RL Repbase Reports 10(10), 1837-1837 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~2000-3000 copies in the apple genome. ~99% identical to the CC consensus. TSD is 15-20-bp long. It is derived from tRNA, the CC 5'-end show similarity to A and B Box of tRNA. XX SQ Sequence 165 BP; 32 A; 45 C; 52 G; 36 T; 0 other; agaggtcgca cttggtgcga tggcaagtgc cttcgcccat gagcggtagg tctcgggttc 60 gagacttggg agcagcctct ccataaatgg gggtaaggct agccgacatt cacctctccc 120 agaccctgcg taaagcggga gccttgtgca ctgggtacga ccttt 165 // ID SHANSINE_MT repbase; DNA; EDCOT; 139 BP. XX AC . XX DT 17-JAN-2007 (Rel. 12.01, Created) DT 17-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A SINE element from Medicago truncatula. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Nonautonomous; retroposon; Interspersed repeat; SHANSINE_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-139 RA Shankar R. and Jurka J.; RT "SHANSINE_MT: A SINE from barrel medic."; RL Repbase Reports 7(1), 107-107 (2007). XX DR [1] (Consensus) XX CC The SINE element is present in Medicago genome in moderate copy CC number of about 50. The copies present are well conserved, mainly CC in the central region. XX SQ Sequence 139 BP; 38 A; 31 C; 20 G; 49 T; 1 other; aaaacatctt gtatgcagtg gcggagccac attcaactga ggggatgcac ctgcaccccc 60 tgaaatttta aaatttgcac tactattcta ttatattttt attttgaayc ccctgaaatt 120 tttattttgc acctcctat 139 // ID LTR-2_Mad-LTR repbase; DNA; EDCOT; 248 BP. XX AC . XX DT 26-OCT-2010 (Rel. 15.11, Created) DT 26-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome, consensus. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR-2_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-248 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 2000-2000 (2010). XX DR [2] (Consensus) XX SQ Sequence 248 BP; 53 A; 30 C; 54 G; 111 T; 0 other; tgttggaaaa tattagtatt ttggtttatt ttaatgtttg gttttctggg cttagcccgt 60 tagagttagg ttttgttaga gattagggtt agttcactat aaatagggtg ctttgttatt 120 cagtttgaga acaagttagt cacaatgtag cctcttaggg ttttgtagcc gtttcggcat 180 tctcgtttgt ttaataatat tcttattatt ttgttagtct tgttcgttgc gcactctgat 240 attcaact 248 // ID Gypsy-28_PTr-I repbase; DNA; EDCOT; 5649 BP. XX AC . XX DT 09-DEC-2009 (Rel. 15.02, Created) DT 09-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: internal DE portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; internal portion; Gypsy-28_PTr-I; KW Gypsy-28_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-5649 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 175-175 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 1266..4304 FT /product="Gypsy-28_PTr-I_1p" FT /translation="MSENNESATQNADVAFQLRAIGQQLELLSRTYKDLKD FT EVNSIKQQNSGADRRGNTVRMAVRNVRSDFEEFVDENADAGEDDYDFASAG FT QGIRSGPNRARRNVNFRGMGTYEDMDGDLDTIKLKIPNFQGKNDPEAYLEW FT EKKVDWIFDCHSYSEQKKVKLVIIEFTEYALIWWDQIVISRRRNGERPVQT FT WGEMKVLMRRRFVPNHYYRDLYLKLQGLNQGYKTVDEYHKEMEIAMIRANV FT VEDREATMARFLNGLNRDIANVVELQHYVELEDMVHMATKVERQLRKGHAR FT PAFNSGSSSSWKPNLKREGTVRPRSFVPSRTEPPKAKVDVPTDAKGKSETQ FT PKRTRDVKCFRCQGHGHYASECPNKRIMMIRDNGDMESESDRSDCEGMPPL FT EDSDGDELALPVGESLVIRRTLQVQVKEDEINQQRENIFHTRCYVQSKVCG FT LIIDSGSCVNVCSTTLVSKLNLCTVKHAKPYRLQWLNDSGEVKVTKQVVVP FT FSIGKYVDEVLCDVVPMQASHILLGRPWQYDRKAIHDGVKNRYTIVKDGKT FT ITLVPLTPKQVYDDQIKLKSEHEAMGRENQGEEQGERRPSDSARTQTTTTH FT SATHPNTNKYSANTPNKSNHSTTTQKHPNLAESGGKTRGVKKVSKGDENCV FT EKLKKQPNFYAREGEVRSAFFTNKPMILLVYKEAYFNTNDLDHIVPSVAIA FT LLQEFDDVFPDDTPSGLPPLRGIEHQIDFVPGASIPNRPAYRSNPEETKEL FT QRQVDELMEKGYIRESMSPCAVPVLLVPKKDGTWRMCVDCRAINNITVKYR FT HPIPRLDDMLDELHGSCIFSKIDLKSGYHQIRMKEGDEWKTTFKTKHGLYE FT WLVMPFGLTNAPSTFMRLMNHVLRAFIGKFVVVYFDDILIYSKNLTEHLDH FT LRNVLSVLRSEKLYANLKKCAFCMEKIVFLGYVVTAQGIEMDEEKVKAIRD FT WPTPKSVSEVRSFHGLASFYRRFVKDFSTIAAPLNEVVKKSVGFGEGAFWL FT YLTLKMD" FT CDS 4595..5647 FT /product="Gypsy-28_PTr-I_2p" FT /translation="MGHFGVAKTLDVLHEHFYWPKMKRDVQRICEQCIACR FT KAKSRVQPHGLYTPLPVPTEPWVDISMDFVLGLPRSKKGRDSIFVVVDRFS FT KMAHFIACNKTDDASHIADLFFREIVRLHGIPKSIVSDRDVKFLSYFWKTL FT WGKLGTKLLFSTTCHPQTDGQTEVVNRTLSQLLRAVIQKNLKSWEECLPFV FT EFAYNRTVHSTTGFSPFEIVYGFNPLTPMDLIPLPFEERVSLDGEKKAKMV FT RQLHEGVRLQIEKKNRLYASKANKGRKLVVFQPGDWVWVHMRKERFPNQRK FT SKLQPRGDGPFQVLERINDNAYKIDLPGEYGVSATFNVADLTLFDTDFDSR FT SNPFEERG" XX SQ Sequence 5649 BP; 1693 A; 903 C; 1348 G; 1705 T; 0 other; gttggtatca gagctaggct ccgaaacaag gtcatatcct tctgttattt tcgttttttt 60 tgtgttcctt taagtttttc agtgtttgcg tccatcttct tgttcttcgt gtctgcgtca 120 tctaagcaaa aaaaaaaggt tatatttcat cttgttactg tctctaatca tatcagtata 180 ttaaaaagaa agagagatag ggattagttg aaatttgaag gatcattcaa tttttgccgc 240 agaaacacaa ctcttggtga accataagca aaccacctcg gaatcaatta cttcatttgg 300 ggtgagatcg ctaaattctt attctgatat tttgcttgag gtttaatggt tcgcaaacac 360 atgtgaacca taagaaacca cctcagaatc aattgaaact tcatattcag tctattgggg 420 gtgagatcgc atcatatgtc aaatttgggc ttattctgat attgtttgct tgaggtttta 480 attcgaggtc aattctgccg cagaaacact actctttgtg aaccataagc aaaacacctt 540 agaataaatt gaaacttcat attctgtgta ttggggatga gatcgcacca tatattaaat 600 ttgggcttat tttgatatcg gcttctggag gttttaattg ggggttcaat tctgccgcaa 660 actgatcata caaggggttt gggtacctag acataaaaga acgacctata aattgatttt 720 tgttgttttt ttagtattat aatactaaat attgaatttg aggtcatttc gagatcgttt 780 ggtctgggtt tcaattctgt tacgtaaaaa ttgcgtaaca ggttagattt gcgtcaagtt 840 tcaaaacgtg atccttactg tttagttttg tccaaatctt tttgtttcta ttatatttgg 900 gttatctagg agtcaagtaa ctgttttcgc taatattcgc ttctgtttta tttcgtgtct 960 tcgtttcgtc cacaattcgt acgaatttgc attgctactc gcaaaatcat aatcgtagtt 1020 ttgttttgct ttgttttcag tatatttatt gattcttgag tctgaaaatt ataattagag 1080 tgcgctgcga aggctactga ctttgatttg ttgatttcag ttcctaaaga accaaaagaa 1140 agcaagttgt gaggtaaaag gcgtagtgag cttattagag tgaaaagcct tgattttttt 1200 gtgtgataca cgagaggtgt gaggatatat tttgtgctac taaccaaatt ttgcagattc 1260 aaagaatgtc tgaaaacaac gaatcagcga cacaaaacgc tgacgtagct ttccaattgc 1320 gagccatagg ccagcaactt gagctgttgt ctagaacgta caaggatctg aaagatgagg 1380 tgaattcaat aaagcaacag aatagtgggg ctgatcgccg aggaaatacg gtccgtatgg 1440 ccgtacggaa tgtcagatct gattttgaag agtttgttga cgaaaacgca gatgcgggtg 1500 aagatgacta tgattttgca tctgctggcc aaggaatcag gtctggaccg aacagggcta 1560 ggaggaatgt gaatttccgt ggcatgggca cttatgaaga tatggatggg gacttggaca 1620 ccattaaact gaaaattcct aactttcaag gtaaaaacga tcccgaggct tatttggagt 1680 gggagaaaaa ggtagattgg atttttgatt gccatagcta ttctgaacaa aagaaggtga 1740 aattggtgat aattgagttt acggagtatg cattgatttg gtgggatcaa attgtaatca 1800 gtaggaggag gaatggggag cgacccgttc agacttgggg ggagatgaaa gtcttaatga 1860 ggagacgatt tgtgccaaac cactattaca gagacttata tctgaagctc caaggtctga 1920 atcaaggtta taagacagta gatgaatatc acaaagagat ggagatagca atgattcggg 1980 ccaatgttgt tgaggataga gaagccacca tggctagatt tcttaatggg ttgaatcggg 2040 acattgccaa tgtggttgag ctacagcact atgtggagct agaggacatg gttcacatgg 2100 ctacgaaggt ggagagacaa cttcggaagg gacatgctcg gccagcgttt aattcgggct 2160 cttcatcatc ttggaagccg aatctaaaga gagagggtac tgtccggcca agatcctttg 2220 ttccttctag aactgaacca ccaaaggcta aagttgatgt ccctactgat gccaaaggta 2280 aatctgaaac tcaacctaaa cgtacccgtg atgttaaatg tttcaggtgt cagggacatg 2340 gacattatgc ttcagagtgt ccaaacaaga gaatcatgat gattagagat aatggtgata 2400 tggaatctga aagtgacaga tctgattgtg aaggcatgcc accattggag gatagtgatg 2460 gggatgagtt agcattaccg gttggggagt ccttggttat aagacgaaca cttcaggttc 2520 aggtaaagga agatgaaatt aatcaacaaa gggagaacat cttccatacg cgttgttatg 2580 tacaaagcaa ggtgtgtggt ttaattatag atagtggaag ctgtgttaat gtttgtagta 2640 ccacccttgt tagtaaactg aatttgtgta ctgttaagca tgctaaacca tatagattgc 2700 aatggctgaa tgatagtggt gaagtgaaag tgactaaaca ggttgtggtt ccattttcga 2760 ttgggaaata tgttgatgaa gttctgtgcg acgtggtacc aatgcaagca agtcacatct 2820 tgttggggag accatggcaa tatgatagga aggcaattca tgatggggtt aaaaataggt 2880 ataccattgt aaaagatggt aaaaccatca ctcttgtacc tcttacaccc aaacaggtgt 2940 atgatgatca aataaagcta aaaagtgagc atgaggcgat ggggagagaa aatcaaggtg 3000 aggaacaagg ggagagaaga ccatcagatt cggctagaac ccaaaccact acaacccatt 3060 cggccaccca tccaaacaca aacaaatatt cagccaacac tccaaacaaa tcaaaccatt 3120 cgaccacaac tcaaaaacac ccaaatctgg ccgagagtgg aggtaagaca agaggagtga 3180 agaaagtcag taagggtgat gagaattgtg tggaaaaact aaagaaacaa cccaattttt 3240 atgctagaga gggtgaggtc agatctgcat ttttcactaa caagccaatg attttacttg 3300 tgtacaaaga ggcttacttt aatactaatg atcttgatca tattgtgcct agtgttgcta 3360 ttgctttgtt gcaggagttt gatgatgtgt tccccgacga tactcctagc ggattaccac 3420 cattgagggg gatagagcat cagattgatt tcgtacccgg agcttcaatt cctaaccgac 3480 cagcctatag aagcaatccc gaggagacga aggagcttca aaggcaagtt gatgagctga 3540 tggaaaaggg ctacattcgt gagagtatga gcccgtgtgc tgtacccgtg ctacttgtgc 3600 ctaagaagga tggaacatgg aggatgtgtg ttgattgccg agccatcaac aacataacgg 3660 taaagtatag acaccccatt cctaggcttg atgacatgtt agatgagtta catggatcct 3720 gtattttctc taaaattgac ttgaaaagtg ggtaccatca aattaggatg aaagaaggtg 3780 atgagtggaa aacaacattt aagactaagc atggtttgta tgaatggtta gtaatgccgt 3840 ttggacttac aaatgcacct agtacgttta tgcgtttaat gaatcatgtg ttgcgtgcat 3900 tcataggtaa gtttgtggtt gtgtattttg atgacattct gatctatagc aagaacttaa 3960 ctgagcatct tgatcatttg cgtaatgtac ttagtgtgtt gcgtagtgag aaattgtatg 4020 ctaatcttaa aaagtgtgcc ttttgcatgg agaaaattgt gtttcttggc tatgttgtaa 4080 ctgcacaggg tatcgagatg gatgaggaga aagttaaggc catccgggat tggcctacac 4140 ccaaatcggt aagtgaggta aggagttttc atgggttagc tagtttttat aggcgttttg 4200 tgaaagattt cagtacaata gctgcaccct tgaatgaagt tgttaaaaag tcagttgggt 4260 ttggggaggg ggcgttttgg ctttacctga ctttaaagat ggattagtga gaagttaagt 4320 ggagcgactt gaactatccc acttacacaa agagttccat aacatttaaa agagggttga 4380 attcattgaa acttttcctt acgtaatcaa gtataagcaa ggcaaagaga ctctgatgtc 4440 ttttacactg aatactaatt gaatatgtga agcattataa tggacattcg gcttttggta 4500 agtttttttg gttttgttca aagagaatag attgtgtgtt cctgctagtt ctttgcgtga 4560 attgcttgtt cgtgaagcac atgggggtgg tttaatgggt cactttgggg ttgcgaaaac 4620 cttggatgta ttgcatgagc atttctattg gccaaagatg aaaagagatg tgcaacgaat 4680 ttgtgaacag tgcattgctt gtagaaaggc aaaatctaga gtacaaccgc atggactata 4740 tacaccatta cctgtgccta ctgaaccttg ggtagatatc tctatggact ttgttttagg 4800 tttacctagg tcaaagaaag gtagagactc tatttttgtt gtggttgata ggttttctaa 4860 aatggcgcat ttcattgcat gcaataaaac ggatgatgca tctcatatcg cagacttgtt 4920 ctttagggag attgtacgtt tgcatggcat tcctaagagt atagtgtcag atcgtgatgt 4980 taagttcctt agctactttt ggaagacctt atggggaaag ttgggaacta aactcttatt 5040 ttcgacaaca tgtcatcctc aaacagatgg acaaactgag gtagtgaata gaacattatc 5100 ccaacttttg cgtgctgtaa ttcaaaagaa tttaaaaagt tgggaagaat gtttgccttt 5160 tgttgagttt gcttataata gaactgtgca ttcgaccact ggtttttctc cttttgaaat 5220 tgtttatggt tttaatccac taactcctat ggacttaatt cctttgcctt ttgaagaaag 5280 ggtaagttta gatggtgaaa agaaggcaaa gatggtgaga caactccatg agggagttcg 5340 actgcaaata gagaaaaaga acagacttta cgcttctaaa gcaaataagg gacgtaaact 5400 agttgttttc caacccggtg attgggtttg ggtgcacatg cgtaaggaac gatttcctaa 5460 ccaaaggaaa tcaaaattac agcctcgtgg tgatggtcca tttcaggttt tagagagaat 5520 caatgacaac gcatacaaaa ttgaccttcc aggtgagtat ggtgttagtg ctacctttaa 5580 tgttgctgat cttacgttgt ttgacacaga ttttgattcg aggtcgaatc ctttcgagga 5640 gagagggga 5649 // ID VLINE3_VV repbase; DNA; EDCOT; 6128 BP. XX AC . XX DT 22-AUG-2007 (Rel. 12.08, Created) DT 22-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE Non-LTR retrotransposon from Vitis vinifera. XX KW L1; Non-LTR Retrotransposon; Transposable Element; VLINE3_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6128 RA Obukhanych T. and Jurka J.; RT "VLINE3_VV."; RL Repbase Reports 7(8), 768-768 (2007). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 2360..4060 FT /product="VLINE3_VV_1p" FT /translation="MKLRLLSWNVRGANDSSKRKVIKAMIRSQRVDLFCIQ FT ETKIQSMSEGVVRSLGSGRFLDWGAMGAHGSAGGILICWDKRTLEVLEMEV FT GQFSISCRLRNVEDGIVWIFTGVYGPFSREEREILWEELGAIRGIWDDPWC FT LGGDFNVTLSQRERSSQGRLTGAMRRFAQVVDELELLDLPLQGGVFSWSGG FT RNNQSWARLDRFLVTQNWLDHFSGVVQSRLPRPTSDHFPILLKGGGLRRGP FT SPFRFENMWLKVDGFKDLLRGWWQGSGGRGRASFRLATKMKVLKEKIKDWN FT RDVFGRLEVNKNSALQQVEFWDGVESERSLSEGETELKKEAKETFKKWVLL FT EETHWRQVSRELWLKEGDKNTGFFHRMANAHRRNNSLDRIKINGVWLAEEQ FT EVREGIVNAFQQLLSEEPGWRADIEGLHLQSLNLSEAEVLELPFTEEEIHS FT ALMEMNGDKAPGPDGFTVAFWQSCWDFVKEEIVDLFKEFFDQKSFAKSLNT FT TFLVLIPKKGGAEDLGDFRPISLLGGLYKLLAKVLANRLKKVLDKVVSVDQ FT NAFVRGRQILDASLIANEVS" FT CDS 4149..5870 FT /product="VLINE3_VV_2p" FT /translation="MKVLHKMGFGSRWMEWIWWCISTAKFSVLVNGVPAGF FT FSNSKGLRQGDPLSPYLFVLGMEVLSALIRRAVDGGFISGCSLRGRGGMEM FT NVSHLLFADDTIIFCEARKEHLTSLSWILAWFEAASGLRINLAKSELIPVG FT EVEDIEEMAVELGCRVGSLPTVYLGLPLGAHHKALSMWDGVEERMRRRLAL FT WKRQYMSKGGRITLIKSTLASIPIYQLSLFRMPKLVAKRLEKLQRDFLWGG FT GSLERKIHLINWEVVCTQKEKGGLGIRKIDLLNKALLGKWIWRFAFEKEIL FT WKKVIGVKYGQEGFGWRTNEARGTFGVGVWKEILKEANWCWDNIEFKVGKG FT TKVKFWTDQWCGNEALSQNFPQLFALAVHRNATVNEVWDSSLGQGGWNIRF FT SRDSNDWELDVIGELFHMLRDFRISSEEDSVLWKGGGHGSFRIRDAYKLLA FT APNAIAFPKKSIWVDKVPTKVAFFAWEATWEKILTLDRLQKRGWQLPNRCF FT LCGCEEENVNHILLHCIVVRVLWEIVLALFGAHWVFPETVKEVLFSWRGPF FT VGKKRKKIWNSIPLCIFWTVWKEREID" XX SQ Sequence 6128 BP; 1536 A; 981 C; 2002 G; 1599 T; 10 other; atggaggaga gagagagaga gagggttaga gagagagaga gagagagaga gagagcgacg 60 gaggagwgcg agggtttcyg agtgcgaccg agartgtaga gggcgatgtc ctcgcggggc 120 ctcggaaaag cttcaggaag ggtagcttcg gagtggagtc gaagtcgttt gaggtcgagg 180 tggaggagaa gaaaggcaaa ctgcaagcta cgattgtgga gaggaaaaga gggatctcct 240 cgtggattag gctgggaccg gagagccttg ggctatttct cgattgtctg gttctttgca 300 ttaaggacat gagaactgga aaatgggtaa gaaagtggaa ggaaaatggg agggcttatt 360 ctctggtgcg agatcaaaac aaaggggggt gtttcctccg gttaggtgtt gtggatctgg 420 agaacaaaag gtttagcatc tttatcccca aaggaagagg agcaaagggt ggttgggttt 480 caatggtgga gacgctacgg cgcttgggtt ttgctaatgg aggaaaggaa agccagaaag 540 aagaagagat gctgttgaag ccaagtatgg tgaaaacctt tgcggaagtg gtcaaaatgc 600 cgaggggtaa agatagagca gcaatcaggg tggaggtcag aaagaaggag ctaagccgaa 660 acttaaacaa attggctcac tgtgtggttg ggatttggaa ccctagctca gcgagggggg 720 atgacctaag aagttggggg acccatttgg caaaaatttg gagtctgaag ggcaacctag 780 ggttagcaaa actggagagg ggcaaggtat tgctggaatt tgagctcttg gcagaagcag 840 agaaagccct aaaacttgga agcatctcgg ttggggggat ctttcttcgc ctggagaaat 900 ggaggcctga gacgggatgt ctgatggaag gggagaaaag gagtgaggct tgggtgcgaa 960 ttgtgggctt acccgtctcc ttatgggatc gggacattct gagaaggata ggggaggagt 1020 gtgggggttt tctcgcagtc gactcccaaa cggagaagct ggaggaattg cagtgggccc 1080 ggattttggt gaagcttaac ggcgaggagc ttcccaatgt ggtggaggtt tgggttgaag 1140 agttgtgcta ctcgttaacc ctctggtggg aggtcaggcc agtaatgaga gcggcgacgg 1200 caggaaagag agggaagaaa gtcgcaacag gaggcgaggt tgggggtgag gcttgtgcac 1260 gcgcgggcaa gcgcgtgctg gaggcgragg acggttcgag gctcgaggcc ctgctgctgc 1320 ctgccgatgg gacgcggggg cagtcaagcg ggtcggggca acctatggat cctgttcgga 1380 gctttgaygg gtcgtcgggt gggccccaag gaggtcgggt gggcctcctt tgctgggcct 1440 agcagagccc ccttggagct ctaaggaatc tgggcccatt gggcttgctc cyttctcgga 1500 cttctctttt gaaaatgggt cgtctctttt tgggctgtcg tctaggaagg attctgggtg 1560 ggccaagact ttggagcctc ttgtggtgcc tgggctggac agccgaggcc cgtctatgcc 1620 cttagctgag gwtagagccc agttggggga ggcccgtccc tccatggtaa ctggcccaag 1680 ccttatgagg ggtccagacg ctggtatttc tcctttctgg gtgaaggatg gcctgcggag 1740 gccttctgag gaggagctac agtccgagga gagatcgaag actgactgtg ccttattgga 1800 ggaagctgcg aggtatggaa acgcccctat cccttttgga ttgttggttt ctggttctct 1860 tttttctccc tcttctwttt ctggtcggac tccattgggg gagtattacg acttttctgg 1920 ggctggtttg gagataaccc agggggaaac accgtgtcgc attgtgcaat ggcacggggt 1980 ctacagagca ggagacagtc actcgctggg agttgatgga ggttaataat ggcagtattg 2040 aagaaagtag agaggagttg tgcttagttc gtactatgcc acaagaagtt agaggatggg 2100 aggaggtaag ttgggaggaa agtgatctgg ctaggttcag caagtttttg gggttttcga 2160 cagagggatt ggagaaagat attttggagt ttctggtcaa aatcagaaag aggagggaaa 2220 gagttcatag caaaactctt ctggagaaat cgaaatttga aagggaattg aaaagacttg 2280 aatgctccat caattatgag ggggggaaga agcagaagtg tggtatgcaa ggaagagggt 2340 gccagattat ggaagtccaa tgaagttaag gctgttgagc tggaatgtgc gtggagctaa 2400 cgatagctct aaaagaaagg tgattaaggc catgattaga agtcagaggg tggacttgtt 2460 ttgtatccag gagacaaaaa ttcagtcaat gtcagagggt gtggtgagga gtttgggctc 2520 tgggaggttt cttgattggg gtgccatggg tgctcatgga tctgcgggag ggattttgat 2580 atgttgggat aaaaggaccc tggaggtgct tgagatggag gtggggcagt tctcaatttc 2640 ctgtaggctt aggaatgtag aagatgggat tgtttggatt ttcacaggag tgtacgggcc 2700 gttttctaga gaggaaaggg agattctgtg ggaggagcta ggggcaataa ggggcatctg 2760 ggatgacccc tggtgtttag ggggcgactt caatgtcacc ctctcccaaa gggaaaggag 2820 cagtcaggga aggctaactg gtgcaatgag aagatttgct caggttgttg atgagctaga 2880 gctcctagat cttcctctgc aagggggtgt gttttcctgg agtgggggta ggaacaatca 2940 atcttgggct agactggatc gattcctagt gacccagaac tggcttgatc attttagtgg 3000 ggttgtccaa agtaggttgc ccagacccac ttcagatcac tttcccatct tgctgaaggg 3060 tggtgggtta agacggggcc cttccccgtt taggtttgaa aacatgtggc tcaaagttga 3120 tgggtttaag gatcttcttc ggggttggtg gcaggggtcg ggggggagag ggagggccag 3180 ttttagattg gctactaaga tgaaggtgtt gaaggaaaaa atcaaagatt ggaataggga 3240 tgtgtttgga aggctggaag ttaataaaaa ctcagctctc caacaagtcg aattctggga 3300 tggggtggaa agtgaaagga gcctgtcaga aggtgaaacg gagctgaaaa aagaagctaa 3360 ggaaaccttt aaaaagtggg tgctattgga agaaacccat tggagacaag tgtcaaggga 3420 gttgtggctt aaggaagggg ataagaacac aggcttcttt caccggatgg ccaatgccca 3480 ccgaagaaat aactccttgg atagaattaa gatcaatggg gtgtggttgg ctgaggagca 3540 ggaggtgagg gaggggattg tgaatgcttt tcagcaactg ctctcagaag agccaggctg 3600 gagagctgat attgaggggc tgcaccttca aagtctaaac ctcagtgaag ctgaagtctt 3660 ggagctgccc ttcactgagg aagaaatcca ctctgctctg atggaaatga atggagataa 3720 ggctccaggc ccggatgggt tcacagtggc cttttggcaa tcttgttggg actttgtgaa 3780 ggaggagatt gtggatctgt ttaaggagtt ttttgatcaa aaatcttttg ccaaaagtct 3840 caatactacc ttcctggtcc tcattccaaa gaaaggtggg gctgaggacc ttggggattt 3900 ccggcccatc agccttttag ggggattgta caagcttttg gccaaggtgc tggccaatag 3960 gctgaagaag gttttagata aggtggtttc tgtggatcaa aatgcttttg tgaggggaag 4020 acagattttg gatgcctcgc tcatagctaa tgaggtgagt tgacttttgg cataaacgta 4080 aagagaaagg gttgatttgt aaactggata ttgaaaaagc ctatgatagc attaattgga 4140 atttcctcat gaaggtcttg cacaagatgg gctttgggtc tcgttggatg gagtggattt 4200 ggtggtgcat ttcaactgca aaattttctg ttctggtcaa tggggtgcca gcaggtttct 4260 tctccaattc caaggggctg cgtcaaggag atcccctttc tccttacctt tttgtcttgg 4320 gtatggaagt gctaagtgca cttataagaa gggctgttga tgggggattc atttcaggtt 4380 gtagtcttcg agggagaggg ggratggaga tgaatgtgtc tcatttgctc tttgctgatg 4440 acacaatcat tttctgcgaa gcaaggaaag agcatctaac ctctctaagc tggattttgg 4500 cttggtttga ggcggcttct ggtctaagaa taaacctagc taaaagcgaa ttaattccgg 4560 ttggggaggt tgaagacatt gaggaaatgg cagtggagtt agggtgtaga gtggggtctc 4620 ttcctactgt ttatttgggg ctgccccttg gagcccatca caaggccttg tctatgtggg 4680 atggggtgga agaaagaatg aggagaagat tagccctttg gaaaagacaa tatatgtcta 4740 agggcgggag aattaccctc attaagagta cattggccag catacctatt taccaattgt 4800 ccctctttcg aatgcccaag ttagtagcaa aaaggcttga aaaattacaa agagactttc 4860 tttggggagg gggaagcttg gaaaggaaaa tccacttaat caattgggag gtggtgtgca 4920 ctcaaaagga gaaggggggt ctaggcattc ggaagattga tctcttgaac aaggccttgt 4980 tgggcaaatg gatttggaga tttgcctttg aaaaggaaat cctttggaag aaggtgatcg 5040 gggtgaagta tggccaagag ggttttggtt ggagractaa tgaagctcgc ggaacgtttg 5100 gagtgggggt ttggaaggag attttgaagg aggcaaattg gtgttgggat aacatagagt 5160 tcaaggtggg aaaggggact aaggtcaagt tctggactga tcagtggtgt ggtaatgagg 5220 cgctgtccca aaattttccc cagttatttg ccttggcggt ccataggaac gcaacggtca 5280 atgaagtgtg ggattcaagc cttggtcaag gaggttggaa tatcagattt tctagagatt 5340 ctaatgattg ggagctggat gtaataggag agttgtttca tatgctgagg gacttcagga 5400 tttcttcaga agaggactca gtgttatgga aaggaggggg tcatggttct tttcggatta 5460 gggatgctta taagctgctg gctgctccta atgccatcgc cttcccgaaa aagagcattt 5520 gggtggataa ggttccaacc aaagttgctt tttttgcttg ggaggccacg tgggagaaga 5580 tcctcacttt ggataggctt caaaaacggg ggtggcagct tcctaatcgt tgttttttgt 5640 gtggttgtga agaggaaaat gtaaatcaca ttcttttaca ctgtatagtg gtcagggtcc 5700 tctgggagat cgtccttgcc ttgtttgggg ctcattgggt gttcccagag acagtcaaag 5760 aggtgttatt tagttggagg ggcccttttg tggggaaaaa gaggaaaaag atttggaatt 5820 ccatcccgtt gtgtattttt tggacggtat ggaaggaaag agaaatagat tagcttttag 5880 ggggggttct ttagctatac agaaactcaa aaattctttt gtatgtaatt tgtggagttg 5940 ggctagggtg tatatgggag aggagtcctc ttcgctttta ggctttttgg agtggctagc 6000 ggctccttaa gggctggtga ggttgtttgt tcttgtgttt tttgttttta ggctgctatg 6060 tatactccct gtatgctttg tggctttttg ccctttaata tatttgtgct catttatcaa 6120 aaaaaaaa 6128 // ID Gypsy-43_Mad-I repbase; DNA; EDCOT; 11612 BP. XX AC . XX DT 21-OCT-2010 (Rel. 15.1, Created) DT 21-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-43_Mad-I. XX NM Gypsy-43_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-11612 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1780-1780 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 44..3985 FT /product="Gypsy-43_Mad-I_1p" FT /translation="MPIETRSVKKKTTMGKSTADLPNQSMGQSVPQAQNPL FT SAVTPESTSATRREREVNLGGQLRGLEIPNRNTCVLNEGIVEECDEDGGEG FT SDPPTRSFLRKRLDEQSRSVEQTFSRGIDKLHDAILSSNDRQTRLLEMLVS FT QVGGSRPFDLRQHCLPGNNPVPIVPAEPIPAPLKPINLEKGGGSNSRSDGT FT DQRVEATPVDMTEVQRMIDSAMKKGPKFPKFIHPYPAYVETFGYPKGFKIP FT DFSLFAGESSLSSLEHVARFTAQCGDVNSDFHKLRLFNFSLTGSAFAWYIN FT LPPNSVQNWEELVEKFHEQFYRPGMEMSVSSLARMAQASDESPMDYLTRFK FT SARNWCRVPLPEVEFVRLALNGLDVEYKKKFLGANFRDMYELAQHVEQYDY FT LLREEKTSKTPTRGTIYKNPTVNYASTEDECVSVDAAEIVIDKPYVCKALT FT QVDSREAKSRSATEGTSKPSKVYTFDITKADAIFDQLLSARIIKLRPGHNI FT PKAEELKGKVYCKYHNSSKHTTNNCVVFRDNVQSWIDNGKLKFPEKRMSVD FT TDPFPTATVNMVDAYLPKDKGKGKAEVVETQRPRNQNVRPRFMADFRSNKP FT PTALTGPAIVKPMTDYSADEDSGTAVLCRKCRAKVDSEPEEKPSSQPVAAT FT RQKVANEGQHHGVFGRLGPKVRMEETPPVRRRLDFDASFYDDDYYKRNSSS FT SESSRSQKTFKPPEPRDQRWYTYHSSKGVYTALSKSQKRRHQRIDCMARRQ FT AAQETSAPKWRPKDTVATDEERPPPXIMTELAQGKRLVDQDVETMFEEADK FT RIKLLIRPGEMKARLEHFRQEAESKLSPLAIQEPLVKIRRNLHPPFLGESL FT EYMREFHKKHSANDLYGLPKACQDTIDLVLTCPDAERIIQKTSDPGLKARF FT QHIREARVLGFEVDPYTDIDAADLPFSLEDLQYLRYHFEVFSAVSLFGLTT FT DEIARIARLDAYLDTRDARLHYQEQVQVLTPSTLSISTLPEAVTQNQQVAE FT AAPPGDVVEEGTEESRCPTLTTTESVVADQPNEEGLDQMGPSVLDNMEISM FT VHVLPADFQSSTAQPNFLDGDVVAEEPGHVDFVSIAEGESTTKDDSLKAAL FT AELFPRSSSAKLHHLKPLYVTAHIEGYPVSKVFVDCGATVNIMPLNIMKAL FT RRSNDELIPSGITMSSFVGDKSQTKGVLPLTVNIAGRTHMTAFFVVDSKTE FT YNALLGRDWIHQTSCIPSSLYQVLVFWDGKSVTVHPADSQPFEANMIQARY FT YDDHVGYITLQGFNEDGRPTRISVQKAIEVGAETVHQDSARLGLANFLPES FT DV" FT CDS 3828..7553 FT /product="Gypsy-43_Mad-I_2p" FT /translation="MTTTSAILRCKASMKTDGRLGFPFRKLSRLAPRLSTR FT IRRDSDWPTFSPNPMSDTDRXXRRAAVSSTMERLLAHWYTISRQPNSGVNL FT VEFLAEGDXGPALSFDKVRAAPAELEDHRPQVKDPLEEINVGTADDPRPLF FT VSALLPQQMKDELRALLTEFKDCFAWSYHEMPGLDRALVEHELRIKPGFKP FT FRQPPRRFSTEVQLSVKDELVRLLKAGFIRTARYVEWLANIVPVLKKSGAL FT RICTDFRNLNLATPKDEYTMPISDLLIDAAANHAILSFMDGHAGYNQIFIA FT EADVHKTAFRCPGALGTYEWVVMPFGLKNAGATYQRAMNTIFHDLIGTIVE FT VYIDDVVVKSKRRQTHLDDLRQAFLRMRQHNLKMNPAKCAFGVSAGNFLGF FT LVHHRGIEVDENKARAIITAPPPTTKKQLQSLLGQINFLRRFIANSAGKMK FT AFSTLLKLKDSDKFVWNDEHQAAFTQIKVSLTNPPVLVPPRRGKPLKLYIS FT AAEESIGCLLAQDNDAGREQAIFYLSRNLSQPEINYPAVEKLCLAVFFAAS FT KLRHYMLPSVTQVIAQTDVIRYMLTRPIVKGRIGKWTMALSEFSLQYVPQK FT AVKGQALADFLAQHPSPYGFGGTDVEIGMVETRDNYWTMYFDGSSTSSSAG FT VGIVIQSPNHDRWYFSLKLDFDCTNNQAEYEALVIGLGLLLDLRATRALVL FT GDSELVINQXNGSFRCMSCTLAPYHMVASYLAESFDGITFEHVSRVHNTDA FT DELAQIASGAQLLGGKLGREIPMLRQLYPALVNQQILRRDNVIRTRVMSLP FT SLLDRQDSIEICAAEAVPDDWRKPIMQYLDNPNGKHSRRTRVHATNYVTYQ FT NELYRKGEDGLLLLCLGPQESARAIAEVHEGVCGAHQSGRKMRWLLRRHGY FT FWPRILKDCIEFARGCVQCQIHGPIQRVPAESLHSVIKPWPFRGWAMDVIG FT KITPTSGAAKHAWIIVATDYFTKWVEAKSYAELTSKEVCDFVEEHIVTRFG FT VPETIITDNGTIFTAERFKEYTANLKIRLEQSTPYYPQANGQAEASNKVLI FT GILEKIIKERPGMWHLKLNEALWAYRTSPRSATATTPYALTYGHDAMLPVE FT LSINSLRLIEQSSLFSAEYNQSMRQELEDLEEARLDAYNLLVAQKQIAERA FT YNQKVRQKTFGEGELVWQTVLPVGLKDPRFGKWSPNWEGPFIVHKVYGKGA FT YHLKDRTGVVHRLPINGKFLKKYYPVTWEMRE" FT CDS join(11423..9387,8510..9352) FT /product="Gypsy-43_Mad-I_3p" FT /translation="MTSKACGCLNRLAIMTTISIREPLPQSVSPLVIVQAS FT NRLSSLISPSHAIVRPQNPDLRSSQPHFPNVHHDQRFLRSILPFVLNFERL FT LFPPQLYKYRNSLICTFTLSNFLKSSAIAFQCISPIPSLRLQIPNPENPFT FT PCFFLTMASFISKLSRECDQHQKILDRSSIKTIRFENDMSTQHQILGPLFK FT ATIPPTITGLLQEHCLTPLLQGFEWSRWDAAKPQGSWPSTTTTWAAWVVRM FT ERLFGEQWKALGIYDAILLSSMEIVPDKELLLAALCFWCSATNTMVLPLGP FT IGPTILDITAILGTSATGIPVDATLSGHPSNIDLKTLFDRRAFETLNRDGH FT IPSKEDIQKLHKNFCNYNTLYLHFAGRGEEDLREGEHEAFLFYWYNKYICC FT TKSNKCLVENMPVAEALASGHVLALSSNILAQLFRCLAEATLHKVDPHQNG FT PLWVFQLWLQVYFASLRPAIADFSPTEALGPQLASRPTPPHQAEEVFRYLF FT ALDDLSNDEFLICRRRDYPSSIRLPTSTWSAEEDADLRQTWGSFVLARDLP FT LGCDGKRSGWEVYHPNFLARQLGYLQGCPVPLLSSRTVLSRGREPRSSEKE FT CRTAVREFQERCQKFRLRPATPETHCTDTFGEWWENYTQEFFGAPVEDVLS FT RLFGDRPKKASAPHPQGTCSIFLFSFNLAYHLVFSSFRILKQKSNQGETVE FT GTYKGRGNLLWRNVEALVLRMDRRFRRCLGFLERPFATVGCRWADWRSCFR FT GGRDVLVLRRSERFGHRGRFLDRALATISRGGAGLNRHLGHWRRLSASMRT FT MRQRDLVAPLTLFQXEDRGLWILGGGSLGRRNRLLWDRCLLDRGRYNWCAG FT HRGRPRWGRLCGRSRLFLDPGMAGGGRRGSTGSRRVTGDDVDLPCTFLRQL FT FDPLGRRGRLDSRLGLLARPFDQHGPTSGFVLLGHDRFFPGRGSGNCLRLS FT QRPTT" XX SQ Sequence 11612 BP; 2891 A; 2867 C; 3223 G; 2619 T; 12 other; ttttggcacg cccagtggga cccagtgcta aactacgaag ttcatgccaa ttgaaacacg 60 atcggtaaaa aagaaaacaa ctatgggaaa gtcgacagcc gatttgccga atcaaagcat 120 gggacaaagt gtgccacagg cgcagaatcc ccttagcgct gtgacacctg agtccacgag 180 cgcgactcgc cgagagagag aagttaatct cggcggtcaa ctccgtggtt tagaaatccc 240 taacagaaac acatgcgttc tcaatgaagg gatagtagag gagtgtgacg aggatggtgg 300 tgaaggatct gacccaccaa cgaggtcgtt tctccgaaag cgactggacg agcagtctcg 360 gtcagtcgag cagacgttca gtcgaggcat tgacaagctg catgacgcga tactcagttc 420 caatgatcga caaaccaggc tgctcgaaat gctggttagt caagttggtg gcagcaggcc 480 tttcgatctt cgccaacatt gtttaccagg aaacaacccg gtaccgattg taccggccga 540 gcctattcct gccccgctca aaccaattaa cttggagaaa ggaggagggt cgaatagtag 600 gtcagacggg accgaccaga gggtcgaagc aacacctgtt gatatgaccg aagttcagcg 660 gatgatcgac tcggccatga agaaagggcc gaagtttccc aagtttattc atccgtaccc 720 agcttacgtg gaaacgtttg gatacccgaa gggtttcaag atcccagatt ttagtctttt 780 tgccggtgaa tcgtccctgt cttcgttgga gcacgtggct cgtttcaccg cgcaatgcgg 840 agatgttaat agtgatttcc acaagttacg gctgttcaat ttttcattga ccggctcggc 900 atttgcctgg tacatcaatc tcccgcctaa ttccgtccaa aactgggagg agttggtcga 960 gaagttccac gagcagtttt atcggccggg gatggagatg tcagtctctt cattagcacg 1020 gatggctcaa gcatctgatg agtcaccaat ggattatctt accaggttca aatcggctag 1080 gaattggtgc cgagtgcctt tacccgaagt cgaatttgtc aggcttgctt tgaacggcct 1140 tgacgtcgaa tacaaaaaga aattcttggg ggcaaatttt cgggatatgt acgaattggc 1200 ccaacatgtc gagcagtatg attatttgct ccgcgaggaa aagacttcga agactccaac 1260 tcggggaacg atttacaaga accctactgt caattatgca tcaaccgagg atgaatgcgt 1320 tagtgtggat gcggctgaga tagtgataga taagccatac gtttgcaagg cattgactca 1380 ggttgattct agagaagcca aaagtcgctc ggccactgaa ggaacatcga aaccgtcaaa 1440 ggtttatact tttgatatta ccaaggctga cgcaattttt gaccaactgt tatcagcaag 1500 aatcattaag cttcggcctg gtcataacat tcctaaggcc gaagagctta aaggaaaggt 1560 gtattgcaaa taccacaatt cgagcaaaca cacgacaaac aattgcgtcg tatttcgcga 1620 taacgtccaa agctggattg ataatggcaa actgaagttt cccgagaaga ggatgagtgt 1680 tgatactgat ccgttcccca cggcaacagt aaatatggtc gacgcgtacc tacccaagga 1740 caaagggaaa ggcaaggccg aagtggttga gacgcaacgc ccgcggaatc agaatgttcg 1800 gccacggttc atggccgatt ttcgttcaaa caaaccacct acggctttaa cggggcccgc 1860 tattgtcaaa cctatgacgg attatagcgc cgatgaagat agtgggacgg cggttctgtg 1920 caggaaatgt agagcgaagg tcgacagtga accagaggag aagccctctt cgcaacccgt 1980 ggccgcaact cggcaaaagg tagccaatga aggccaacat catggggttt ttgggaggct 2040 cggtcctaaa gtacggatgg aagagacacc cccggtcagg cggcgcctcg attttgatgc 2100 ttcattttat gacgatgatt actataagcg taattctagc agttcagaat catcgcggag 2160 tcaaaagacc ttcaagcctc ccgagcctag agatcaacgt tggtatacat accattcttc 2220 gaagggcgtc tacaccgcgt tgtccaaatc tcagaaacgc cggcatcaac ggatagattg 2280 catggctcgc cgacaagcag cccaagaaac ttcggcccct aagtggcggc cgaaggacac 2340 agttgccact gatgaggagc gaccacctcc ascaattatg acagagttgg ctcaggggaa 2400 acggctggtc gatcaagacg tcgagaccat gtttgaagaa gctgataaac ggatcaaact 2460 tctcattcga ccaggggaaa tgaaggcacg ccttgaacat ttcaggcaag aggccgaaag 2520 caaattatcc ccgctagcta tacaagagcc tttggtcaaa attcgacgga atttgcatcc 2580 cccgttcctt ggggagtctt tggagtatat gcgagaattt cataagaaac attcggccaa 2640 cgatctgtat ggtttgccga aggcatgcca ggacaccatt gatctggtcc tgacttgtcc 2700 ggatgctgag cggatcatcc agaagacctc agatccagga ttgaaagcaa ggttccagca 2760 catacgagaa gctcgtgtcc ttggatttga agtcgacccg tacaccgata tcgatgcagc 2820 cgaccttcct ttctcgctgg aggaccttca gtatttacgg tatcactttg aagtattttc 2880 ggcggtttct ctcttcggcc ttacgaccga tgaaatcgca cgtattgccc gtctggatgc 2940 ttatctcgac actagggatg ctcggctaca ctaccaggag caggttcagg tcttgacccc 3000 aagtacattg tcaatctcga ccttacctga ggcggtcacg cagaaccaac aagtggccga 3060 agcagctccg ccgggtgacg tcgttgaaga agggacggaa gagtctcgtt gtccgactct 3120 gacgacaact gagtccgtag tcgccgacca accgaacgag gagggtctcg accagatggg 3180 cccgtcagtc ctggataata tggaaatcag tatggtccat gtgttacctg ccgattttca 3240 atcaagcacg gctcaaccaa atttcctcga tggagatgtg gttgccgagg aacccggcca 3300 tgttgatttt gtatcgattg ctgaaggcga gtcaacaaca aaagatgata gtctaaaggc 3360 cgctttggcc gaattgttcc ctcgttcatc gtcggccaag cttcaccatt taaagccatt 3420 gtatgtgacg gcccacatcg agggatatcc agtttctaaa gtttttgtcg actgtggggc 3480 taccgtcaat atcatgcccc tgaacatcat gaaggcctta cgccgttcga atgacgagct 3540 tattccgtca gggatcacaa tgagtagttt cgtcggcgac aagtcccaaa ccaaaggtgt 3600 acttccgtta actgtgaata ttgccggtcg cacccacatg accgcctttt tcgtggttga 3660 ttccaaaacc gagtataatg cactgctcgg ccgagattgg atccatcaaa ccagctgtat 3720 tccttcctcg ttgtaccaag tgcttgtctt ttgggacggc aaatcggtca ctgttcatcc 3780 ggccgatagc cagcccttcg aagccaacat gatccaagca cggtattatg acgaccacgt 3840 cggctatatt acgttgcaag gcttcaatga agacggacgg ccgactcgga tttccgttca 3900 gaaagctatc gaggttggcg ccgagactgt ccaccaggat tcggcgagac tcggattggc 3960 caactttctc cccgaatccg atgtctgaca cmgatcggga mgmacgtagg gccgcggttt 4020 catctacgat ggaacgactg ctggcccatt ggtatactat atctmggcaa ccgaattcag 4080 gcgtcaacct cgtcgagttc cttgccgagg gggatmatgg tcctgcctta tcttttgata 4140 aagttcgagc cgccccggcc gagctcgagg atcatcggcc ccaagttaag gaccccctgg 4200 aagaaattaa tgttgggacg gccgatgacc cacgaccttt gtttgttagc gctttacttc 4260 ctcaacaaat gaaggacgag ttgcgggcct tgcttacgga attcaaagat tgttttgctt 4320 ggagttatca tgaaatgccc ggcttagatc gtgctctggt cgagcatgaa ttacgtatta 4380 agcccggatt caagcctttc cgtcagccac ctcgtcgatt ctcgaccgaa gtacaactca 4440 gtgtcaagga cgaactagtt cggcttttga aagccgggtt cattcggaca gctcgatatg 4500 tcgaatggtt ggcgaatatt gttcctgtat taaagaaaag tggtgcactg cgcatctgca 4560 ccgattttcg aaatctgaat ctggcaacgc ccaaagatga gtatacaatg ccgatttcag 4620 atctgttaat cgatgccgcg gcgaatcatg cgatcttatc ctttatggat ggacatgccg 4680 ggtacaacca aatatttatt gccgaagccg atgtgcacaa aactgctttc cgttgcccgg 4740 gggcactcgg cacttacgaa tgggttgtca tgccattcgg cctcaagaat gccggcgcca 4800 cgtaccaacg ggcgatgaac accatcttcc atgatttaat tggcaccatc gtcgaagttt 4860 acatcgacga tgttgtcgtc aaatctaaac gccgacagac acatctggac gatctccgac 4920 aggctttcct ccgcatgcgt cagcacaacc tcaagatgaa tcctgccaag tgtgccttcg 4980 gtgtatcggc cgggaatttt cttggtttcc tcgtacatca tcgtgggatt gaagtcgatg 5040 agaataaggc acgcgcaatc atcactgccc cacccccaac gacgaagaaa caactmcagt 5100 ccttactcgg ccagatcaat ttcctccgcc gatttattgc taactcggca ggtaaaatga 5160 aagcgttttc cacacttttg aaactcaagg actcagataa gttcgtgtgg aacgacgagc 5220 atcaggcggc gtttacgcag atcaaggtct ccctcacgaa cccacctgtc ctggtccctc 5280 ctcggcgcgg taagcctctt aagctctata tctcggcggc cgaagagtcc atcggctgcc 5340 tcctcgcgca agacaacgat gccggacggg aacaggctat cttttacctc agccgtaatc 5400 tcagtcaacc ggagatcaat tatcccgccg tcgagaagct gtgtctcgcc gtgttcttcg 5460 ccgcatccaa gcttcggcat tacatgctcc cgtcggtcac ccaagtcatt gcccagaccg 5520 acgtcatccg gtacatgctt acccgaccaa tcgtaaaagg ccgaattggg aaatggacga 5580 tggcgttgtc cgagtttagc ttgcaatacg tgccgcagaa agctgtcaag ggccaggcat 5640 tggccgattt ccttgctcag cacccctccc catacggttt tgggggcacc gacgtcgaaa 5700 tcggcatggt tgagacscgc gacaactact ggacgatgta ttttgacggc tccagtactt 5760 cgtcctcggc cggcgtggga atcgtcattc aatcccctaa ccacgatcgt tggtattttt 5820 cgctcaagtt ggatttcgac tgcaccaata atcaggccga atacgaggcc ctggtcattg 5880 gccttggcct ccttcttgac ctgcgggcca ctcgtgccct cgtcctcggs gactctgaac 5940 ttgtgattaa ccaamttaat gggtcttttc gctgcatgag ttgtaccctg gcgccttacc 6000 acatggtcgc cagctatttg gccgagtcct tcgacggtat tacattcgag catgtttccc 6060 gggttcataa taccgacgca gacgagttgg ctcaaatcgc ctccggtgca caactcctgg 6120 ggggcaagct aggccgggag ataccaatgt tacgacaatt atacccggcc ttggttaatc 6180 agcaaatcct ccgtcgagac aatgtgatac gcaccagggt catgtccttg ccttcgttgt 6240 tagatcggca ggactctata gaaatttgcg cggccgaggc agtaccagat gattggagaa 6300 aacccattat gcagtacctt gacaatccta acggaaaaca tagtcgcagg acacgggttc 6360 acgccacgaa ctatgtcacg taccagaacg agttgtaccg aaagggcgaa gatggtttgt 6420 tattgctatg cctcggcccc caagagagtg ctcgggcgat cgcagaggtt catgaagggg 6480 tatgcggagc tcaccagtct ggacggaaaa tgcgatggct actccgacga cacggctatt 6540 tttggccgag aatactgaaa gattgtatcg agtttgcacg aggatgcgtg cagtgccaaa 6600 tccatgggcc tatacaaagg gtcccggccg aatcactaca ttcggtcatt aagccgtggc 6660 cgtttagagg atgggccatg gacgtaatcg gcaaaatcac gccgacttct ggagctgcta 6720 agcatgcatg gataatagtc gcaactgatt actttactaa gtgggtcgaa gcaaaatcat 6780 atgccgagtt aacatctaaa gaagtttgcg acttcgtgga ggaacacatt gtgacccggt 6840 tcggtgtacc agaaacgatc ataaccgaca atggaacaat cttcacagcc gaaaggttta 6900 aagaatacac ggcaaatttg aaaattcggc tggaacagtc cacaccgtat tatccacagg 6960 cgaatgggca ggccgaggca agtaataaag tgttgatcgg catcctcgaa aaaataataa 7020 aagaaaggcc tggcatgtgg catttgaagt tgaacgaggc attatgggca taccgaacgt 7080 cgccccggtc ggcgactgcg acaaccccat acgcattaac ctacggacac gatgcaatgc 7140 taccagtcga gttgagcata aattcgttgc gattaattga acaaagtagt ttgtttagcg 7200 ccgaatataa tcagtccatg agacaggaac tagaagattt ggaagaagcg cgacttgacg 7260 cttataactt actggtggca caaaaacaga ttgccgagcg agcctataat caaaaggtgc 7320 gacagaaaac attcggcgag ggtgaattgg tgtggcaaac ggtgttgccc gtaggactaa 7380 aagatcctag gttcggcaag tggtcgccga attgggaagg gccgttcatt gtgcataaag 7440 tatacggaaa aggggcgtat catcttaaag accggaccgg tgtggttcac agattaccga 7500 ttaatgggaa gtttttgaag aaatactatc cggtcacatg ggaaatgcgg gaatagaaaa 7560 tccagattcc attaagattg ataagtatta caaaaatgag taggtcgaat acattcaagg 7620 agaagaggga agaagagtgc tgagcagagc cttcaactcc aaccaccgca cgtcggccat 7680 gatgacttcg gcttgccgat tctttttgtc cagcttcagc cgctcgaccc gttttttggc 7740 cgccgcatac tcagttaggc gatccttccc gcctgactcg aagtccctcg caagctcgga 7800 agcaatggcc gaccgacgtt ttgctagttc ggccatctga cggtcgagct cggctaacgc 7860 ttctcctttt gcccgtagat cgtcaatctt cggacggagg gtgtcttgaa cggccgtggc 7920 ggcttgcagg tcctgttcgg ccttcagagc agtctggaag atactaaatg tctcccgaac 7980 gcgctccaag gcagacgatg cccgaacaat ggcatctccg ctcaggcgac cgtcggctcc 8040 aaggtcgttc agacacacgc cgagcagatc aagaccgttg cgctcaagta cttgcgatga 8100 tgagagcgac aggacttctc gcaactgggt tagggcgctt ggatcggcag cctcagtcgg 8160 agcggccgaa gggccggact ctgcagtcgt gctggagagg agggctttga attcgacctc 8220 ccatgaagcc tgcacgaaca aataaggtta agcttaaagg aagtcatgac aagaatagca 8280 agaaggtktc gtttttttaa cctgccgaga ggagacctcg gccatgtccc caggatcgtt 8340 gctcgaacct aaagaactca atggccgagc ccagtgtctc agattgcttc tcacttcacg 8400 cggccgatgg aggttatcta cgtttgatgg ccactgaggc ggccaggaaa tatagataac 8460 gcccttcggc gcatagaatt gacggtgaaa agaatgtaca ggcacctgac atttagtatt 8520 ttcctcgttt agaattctaa agcagaaaag caatcagggg gagacggtcg aaggtactta 8580 caaaggccga ggtaacctcc tgtggaggaa tgtggaagcc ctggtcttga ggatggaccg 8640 gcgattccgc cgttgcctcg ggttcctcga gcggccgttt gccacggtcg gctgccgatg 8700 ggccgactgg cgcagctgct tcagaggagg cagggacgtc ctggtcctga gaaggagcga 8760 gaggttcggc caccggggtc ggttcctcga ccgggcgctt gccacgatca gccgtggagg 8820 ggccggcttg aaccgccatc tcggacactg gaggaggttg tcggcgagta tgaggacgat 8880 gcgccagcgg gacctcgtcg ctcccctcac tctcttccag macgaagacc gagggctttg 8940 gattcttggg ggaggttccc tcggtcgtag aaaccgcctg ttgtgggaca ggtgccttct 9000 cgacagaggg aggtacaact ggtgcgccgg ccacagaggc aggccgcgct ggggccgtct 9060 ctgcggccga agccggctgt ttctcgaccc cggaatggcc ggcggcggga gaaggggaag 9120 cactgggagt cgtcgtgtga ctggagatga cgtggatctc ccgtgcacct ttcttcgcca 9180 gttgtttgac ccgcttggca ggcggggaag gctcgacagc cggctcggcc tcttggcgag 9240 gccgtttgat cagcacggcc ctaccagcgg gtttgtcctt ttgggccacg accgattttt 9300 tcccggccgt ggcagcggca actgcctccg tctttctcaa aggccgacta cctaaaaaga 9360 taaagacaat tcagtaaggc aaatcaatat gcaaggttga aggaaaagag gaaaatggaa 9420 caggtacctt gaggatgggg ggccgaggcc ttcttaggtc ggtcaccgaa gagtctgctc 9480 agcacatctt cgaccggcgc accaaagaac tcctgggtgt aattttccca ccactcaccg 9540 aaggtgtcgg tgcaatgggt ttctggggtg gccggtcgaa ggcggaattt ttggcagcgc 9600 tcttggaact ccctcacggc ggttctacac tccttctccg aggaacgagg ttcgcgtcca 9660 cggcttagga ccgttcggga ggagagaagg gggacagggc agccctgaag gtagccgagc 9720 tgtcgggcaa ggaagttcgg atgatacact tcccaacccg accgtttccc atcgcagccg 9780 agagggaggt cgcgagcaag cacaaacgac ccccaggtct gacgaagatc ggcgtcctcc 9840 tccgcgctcc acgtggaggt aggcagcctg atggaggaag gatagtctcg acgacgacat 9900 atcaggaact cgtcgttgga gaggtcgtcg agagcgaaga ggtaccgaaa tacctcttcg 9960 gcttgatggg gaggtgtcgg tcgagaggcc agctgaggtc caagcgcctc tgttggtgag 10020 aagtcagcta tggccggccg aagggaggcg aagtatacct gcaaccagag ttggaagacc 10080 cagagaggac cattctggtg tgggtcgacc ttgtggaggg tcgcctcggc caggcagcgg 10140 aagagttggg cgagaatgtt ggaactcagt gccaggacgt gaccactagc cagggcttcg 10200 gctaccggca tgttctcgac caaacacttg tttgacttgg tacaacaaat gtatttgttg 10260 taccagtaga agaggaaggc ttcatgctct ccctctcgca ggtcctcttc tcctcggccg 10320 gcgaagtgaa gatagagggt gttgtaatta cagaagttct tgtggagctt ctgaatgtct 10380 tccttcgacg ggatgtgacc gtcacggttc aaggtctcga aggcccgacg gtcgaagagc 10440 gtcttcaggt cgatattcga cgggtgccca gagagggtcg cgtcgacagg gatcccggtc 10500 gccgaagtcc ccagaatggc ggtgatatcc aggatggtgg gaccaatggg accaagagga 10560 aggaccattg tgttggtggc cgagcaccag aagcacagag cggctaggag aagctccttg 10620 tcggggacga tttccatgga cgaaaggagg atggcgtcgt agatgccgag ggccttccat 10680 tgctcgccga agagccgttc cattcgaacg acccaggctg cccaggttgt ggtcgtcgag 10740 ggccaggagc cttggggttt cgccgcatcc catcgcgacc attcaaaccc ttggagcaag 10800 ggtgttaggc agtgctcctg gagaaggccg gtgatggtcg gcggtattgt agccttgaag 10860 agaggaccca ggatttggtg ctgggtgctc atgtcgtttt caaaccgtat ggtcttgatc 10920 gagctccgat caagaatctt ctgatgctgg tcacattccc tggaaagctt ggagatgaag 10980 gacgccattg taagaaagaa gcacggcgta aaagggtttt ctgggttggg gatttgaaga 11040 cgaagacttg gaataggaga aatgcactgg aaagcaatgg cagaggattt caggaagttt 11100 gagagcgtaa aggtacaaat gagggaattt cggtatttat agagttgtgg ggggaagagc 11160 aatcgttcga aattcaaaac aaagggcaaa atcgaccgaa ggaatcgttg atcatgatga 11220 acatttggga aatgcggttg agaagaccga aggtcagggt tttgggggcg cacgatcgcg 11280 tgtgacggcg aaattaatga cgaaagacgg ttcgacgcct gcacgatgac aagtgggctc 11340 acggactgag gtagtggctc gcggattgag atagtggtca tgatggcaag acggttcagg 11400 cagccgcacg ccttagacgt cattattggg gattggccat gttagaggac gccacgtggc 11460 gagtgtggtt agcaggatca agatcgtgcg atcgtgttca ataaatgcgc cttggaactc 11520 gggcattagg gttctgagtg gtagattcgc ttcttcaagg ccgaaactcg gccgaagatt 11580 tcaggccgag gacctcagaa gcgagggggc aa 11612 // ID BoSB8B repbase; DNA; EDCOT; 99 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB8B. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-99 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 99 BP; 28 A; 27 C; 29 G; 15 T; 0 other; gccgggacag aatagcctag tggtaaaaca ctagagtgaa ctggatccca aggcacacgg 60 gttcgactcc tccgggattc cagagagcgc ccagtgaac 99 // ID Sat-1_Mad repbase; DNA; EDCOT; 454 BP. XX AC . XX DT 25-OCT-2010 (Rel. 15.11, Created) DT 25-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE Satellite sequence from the apple genome. XX KW Satellite; Simple Repeat; Sat-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-454 RA Bao W. and Jurka J.; RT "Satellite sequences in the apple genome."; RL Repbase Reports 10(11), 2022-2022 (2010). XX DR [2] (Consensus) XX SQ Sequence 454 BP; 117 A; 77 C; 105 G; 155 T; 0 other; ttttgagttt cgagggatcg tcttgattaa tattcctcgg gagatgaaag aaatggatga 60 gaaagactat taatcgtatt ttttaaattt cgagggatcg ttttgattaa tattttcgaa 120 tttcgtgatg accaaagaaa tggttataaa caattacaag tcatagacca acggatgcga 180 tcataccaac tcacatgcac cggatcccat cagaactccg cagttaagcg agtttgggcg 240 agagtagtac taggatgggt gacctcctgg gaagtcctcg tgttgcatcc cccacctctt 300 tttttgtttt cgtaattctt gttttgcgta ttttgttttc gtgattcttg ttttgcgtat 360 ttttagcggc taatttgtgg cgcgcgtcgt ttattaccga gcctcgtgct tgggagatga 420 aagaaaggaa tgggaaagac taataattct attt 454 // ID TDK2B repbase; DNA; EDCOT; 243 BP. XX AC AB060981; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Diospyros kaki TY1/copia-type retrotransposon TDK2B, DNA for DE reverse transcriptase, partial cds. XX KW Copia; LTR Retrotransposon; Transposable Element; retrotransposon; KW TDK2B; Ty1/COPIA superfamily; reverse transcriptase. XX OS Diospyros kaki OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; Ericales; Ebenaceae; Diospyros. XX RN [1] RP 1-243 RA Nakatsuka A., Iwami N., Matsumoto S., Itamura H. RA and Yamagishi M.; RT "Ty1-copia group retrotransposons in persimmon (Diospyros kaki RT Thunb.)."; RL Genes Genet. Syst 77(2), 131-136 (2002). XX DR Genbank; AB060981; Positions 1 243. XX SQ Sequence 243 BP; 76 A; 37 C; 54 G; 76 T; 0 other; gcattcctta atggagaact agaggaggag gtttatatga aacaaccaga aggattctcc 60 tctagtgatg gtgagcactt ggtatgcaag cttaagaaat ccatatatgg attgaaacaa 120 gcctcccgac aatggtactt aaaatttcat gatattatct cttcatttgg ttttgtagag 180 aatgtcatgg atcagtgtat ataccagaag gttagtggga gcaaaatatg tttccttgtc 240 tta 243 // ID Gypsy-24_Mad-LTR repbase; DNA; EDCOT; 245 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-24_Mad_; KW Gypsy-24_Mad-LTR; Gypsy-24_Mad-I. XX NM Gypsy-24_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-245 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1743-1743 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 245 BP; 49 A; 58 C; 45 G; 93 T; 0 other; tgttaagacc cttttcccat tcaggcccat ttccttagtt atttccttta tctagtagtg 60 gatcagtagt aggatagtga ctcagcatgt ttacctaaca ctcttgtctg tagtgcgggt 120 gtgggcatat tatccctgtt gcgactccca tttgggatat gaatgaaaag ctgttctttt 180 acaatttctc tgtcatttcc tttttctctg caaattcgcc tcttggtccc ctctggaacc 240 tatca 245 // ID Gypsy-27_Mad-LTR repbase; DNA; EDCOT; 473 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-27_Mad_; KW Gypsy-27_Mad-LTR; Gypsy-27_Mad-I. XX NM Gypsy-27_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-473 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1749-1749 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 473 BP; 118 A; 127 C; 89 G; 138 T; 1 other; tgacgacccg tcccgaatta atatatattt tatcctcgag tgtgtggaaa tgacgattat 60 gccctcgagg cttagtgacg tggatgtacg tatatagttt taaattattt ttctcgccga 120 cgtaattaaa ttgtackcga cgtcacgagc gcgttgacgc gagttagggt cgaatcgggt 180 tcgtaacgaa aatgttacga acgaatgagt gtaatggtag gttttggttt tgtctaacca 240 ccgttatttt cttcctagat cttggaccaa ttgcttgggc cctaatccca tagcccaatc 300 agggccttgt ttcttttatt ttggcccaat cccgtgacac acacacacac acacacgtgc 360 aaaccctcac ctctctctcc tctcttctcg aactttcttc ctcgtccgta caacccgagc 420 ccccaactct caaacaccat caaaacctca cagatcgaac ttgaggatca cca 473 // ID EnSpm3_PT repbase; DNA; EDCOT; 8677 BP. XX AC . XX DT 12-DEC-2009 (Rel. 15.06, Created) DT 12-DEC-2009 (Rel. 15.06, Last updated, Version 2) XX DE EnSpm-type DNA transposon - consensus. XX KW EnSpm; DNA transposon; Transposable Element; ENSPM3_PT. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-8677 RA Jurka J.; RT "DNA transposons from black cottonwood."; RL Repbase Reports 10(6), 789-789 (2010). XX DR [1] (Consensus) XX CC >91% identical to consensus. XX FH Key Location/Qualifiers FT CDS 922..3282 FT /product="EnSpm3_PT_1p" FT /translation="MSGKTNIFVMFYRGSIEVMDDRSWMYRDSPQGLRRMD FT YCNGVQGFINFATSIPRNFTDGGIRCPCRKCKNLKFLHQDVVTMHLLTKGF FT MEDYLCWYAHGELFVPDESMEEQVVGSTSSASNMHEVGNENSNPYRNMVMD FT AMRMSEGNVRECPIVEEEPNADAARFFDLLRDSDEPLWDGCTNHSKLSAVA FT QVFTIKSDHGLSEAGYDKIIEWARSILPEGNRLKENFYAAKSMMKPLGLGY FT QKIDICPNFCMLYYLENAEMTECMTCGHSRYKPRTGRGKTLVAYKKLRYFP FT ITPRLQRLFMSPRTAEHMTWHQSHHAVDGVMVHPSDGEAWKHFNSVHPHFS FT AESRNVRLGLCTDGFNPFGSFAAPYSCWPVILTVYNLPPGMCMRPEFMFLS FT MVIPGPSSPGRNIDVCLRPLIDELTQLWSSGALTYDISRKQNFVMRAALMW FT TINDFPAYGMVSGWSTHGKLACPYCMENNKAFTLTNGGKASFFYCHRRFLP FT HNHRYRKNRKDFFVGRVEXDVAPPRLSGEELFDVVSEYGDIVFGLQSGKQK FT FPGFGLTHNWVKRSIFWELPYWKTNLLRHNLDVMHIEKNVFENIFNTVMDV FT KGKTKDNIKARLDVALFCNRKNMELVCDGSRVAKPRASFVLEKNAQLLVYK FT WLKSLRFPDGHASNISRLVNTEECRLYGMKSHDCHVFMQTLIPLAFRDLLP FT KGIWDALTEISHFFRDICSSKLNVDHIERLEKNIVETICKLEMIFPPSFFD FT SMEHLPVHLPFEVKVGGPVQYRWMYPFERLDITVAM" FT CDS 3983..4747 FT /product="EnSpm3_PT_2p" FT /translation="MGGSAAISLSLLCLGPERKVKCYNGYFVNGYVFHTEE FT YGHGRKTYNSGVCIKGSTSSEFEVDYYGRLEEVIELQYHSEQNRVFLFKCY FT WYDTTDRGIRVDPHYGLVEINSKARHRNVNDVFVFAKQCQQVYYTYTPSFR FT KDRSRVDWLSVLKTKPKGRVEVVQDENEDTSVIDEVFQASELVEPYRVAPS FT IDLEENSNFRVFNDSLVDVDAEELNVVLSSTSGKKNVVEEDDNEIEECDEA FT DDNNSIEDEDENSD" XX SQ Sequence 8677 BP; 2435 A; 1507 C; 1858 G; 2873 T; 4 other; cactaccaga aaaccggaga aaaccaacgg aattaccgac ggaatttttc cgtcggtaat 60 ttttaccgac ggaaataatt ccgtctcaaa atctgtcggt atataccgac ggaataaatc 120 cgtcggcgaa ccgtcggtat ataccgacgg tttcgccgac ggggtataca gtttgtctgg 180 aaatatgcaa cggcgtggtg acgtcagacg attttaccga cggaatgacc gagggattca 240 aactgagata gccgtacagt gacgtggcac tgtcaccgac ggaatcaccg aggaattccg 300 gtgattccat cggaaaaagc cattatatgc acccatctgc cgacactctc ttcctctgtt 360 tctccttctt cttctttccc atcccacctc tcccctccca aactgcagcc aaccacccat 420 cccaactctc cactattctc aacacgagca ctcaagtttc ttatatcttg tacgtggtca 480 caatatccgt ttcttgtgga ttttatcatt tttttgtaag taaatctatc ctttttagtt 540 ttaacattta attgtgaatt ttattgtttt agtatatgta ttttgttaac gtttgtactt 600 gtttaattgt tatttgtcaa agaaacttgt agtatgaatg tataattttg tagttgttat 660 agtttgtttt agattttgtc aaattatatt tgtttgtaaa ttgttgaaat tttgtttgaa 720 ttacaccgaa ttaaatgtgt cgttgtgatg aaataaataa ttaatagctt gtttaacggg 780 tcttgtttaa ttgttatcaa ttctatttcg aagttgtgat ttctgtaaat ttatatatgt 840 ataaatttgt atgtatgaac gttgatagtt gataattgat aatgaatatt taacataagt 900 gttgttttag tttgttggat aatgtcgggg aaaaccaata tttttgttat gttttataga 960 ggttcaatag aagtcatgga tgatcgttca tggatgtatc gggactcacc ccaaggattg 1020 cggaggatgg attattgtaa cggtgtccag ggttttatta atttcgcaac atctattccg 1080 aggaatttta ctgatggcgg tattaggtgt ccatgcagga agtgtaaaaa tttaaagttt 1140 ctgcatcaag atgttgtaac gatgcatctt ctaaccaaag ggttcatgga ggattacctg 1200 tgttggtatg cwcacggaga actatttgtt cctgatgaga gcatggaaga acaggtggtt 1260 gggtcaactt ctagtgctag caacatgcat gaagttggaa atgagaacag taatccttac 1320 aggaatatgg ttatggatgc aatgagaatg agtgaaggta atgtcaggga atgtccaatc 1380 gtagaagaag aacctaatgc agatgcagca aggttttttg atctgttgag agattctgac 1440 gaaccattat gggatggctg cacgaaccac agtaaattat cggccgtagc acaggtgttc 1500 accatcaagt cagatcacgg gttgagtgag gccggttatg acaagattat tgaatgggcg 1560 agaagcattt tacctgaagg gaacaggctg aaagagaact tctatgctgc caagtccatg 1620 atgaaacccc tcggtttagg ataccagaaa attgacatat gccctaactt ctgcatgtta 1680 tactaccttg aaaatgctga gatgaccgag tgcatgacat gcgggcattc ccgttacaaa 1740 cccagaactg gtagagggaa gactctcgtg gcatataaaa aacttagata cttcccaatc 1800 acacctagac tgcagaggtt attcatgtca ccaaggactg ctgagcacat gacatggcac 1860 caatcacacc atgcggttga tggagtgatg gttcatcctt ctgacggtga agcctggaaa 1920 cactttaaca gtgtgcatcc tcacttttca gctgaatcaa ggaacgtgcg tcttgggttg 1980 tgtacagacg gattcaaccc attcgggtca tttgctgctc cttattcttg ttggccggtc 2040 atactgacgg tttataactt gccaccgggg atgtgtatga ggccggagtt catgttttta 2100 tctatggtca taccaggtcc gagcagtccg gggcggaata tagatgtttg tcttcgtccg 2160 ttgattgatg agttgacgca gttgtggtcc tctggagctt tgacttatga catctcgagg 2220 aaacaaaatt ttgttatgag agcggctttg atgtggacta tcaatgattt cccagcttat 2280 ggaatggttt ctggttggag cacgcatgga aagctagcat gtccatactg tatggagaac 2340 aacaaggcat tcacgctaac aaacgggggt aaagcttctt ttttttactg tcaccgtcgt 2400 ttcttgccac ataaccacag gtacagaaag aacagaaagg atttctttgt tggcagagtt 2460 gaaaakgatg ttgcaccccc gcgtctttcc ggtgaagaat tgtttgatgt tgtgtcagag 2520 tacggtgaca ttgtgtttgg tctccaatca ggtaagcaga agtttcctgg ttttggtttg 2580 acccataatt gggtgaagcg aagtatcttt tgggagcttc cttattggaa gaccaatctt 2640 ctccgccata accttgacgt catgcacatt gaaaagaacg tgtttgagaa cattttcaac 2700 accgtcatgg atgtgaaggg gaagacaaag gacaacatca aggctagatt ggatgtagcg 2760 ttgttctgta accgtaaaaa tatggagttg gtttgtgatg ggtcacgggt cgcaaaacca 2820 agagcaagct tcgtgctaga gaaaaacgca caactactag tctacaaatg gcttaagagt 2880 ctgcgtttcc ccgatggaca tgcctcgaac atatcaaggc tggttaatac ggaggaatgc 2940 agattatatg gaatgaagag tcatgactgc catgtgttta tgcaaacact catcccatta 3000 gcttttcgtg atttgttgcc aaaggggata tgggatgcac taacggagat cagtcatttc 3060 ttcagagata tatgctccag caagttgaat gttgatcaca ttgaaaggct tgaaaagaat 3120 atcgtcgaga caatatgcaa acttgagatg atattccctc catcattttt tgactcaatg 3180 gagcatctac ccgtacattt accgtttgag gtaaaagttg gaggaccggt ccagtacaga 3240 tggatgtatc cattcgagag gttagatatt acagttgcta tgtaattcat aattaaatgt 3300 ttttattttt attttaatgt ttttaattga taattatata tatatatata tatatgcagg 3360 tacttgttca atcttaaaaa aaaggttaag aacaaggcgc atgttgaggc gtcaatatgt 3420 gaggcctata ttgttgagga gatctcaaca tttatctcat actatttcga acctcatttg 3480 agaacgagga tmaaccgtgt tccacggcat gatgatggtg gtgaagtgcc ttcaagtggg 3540 aacttgtcaa tattctccaa tcctggacga cccacaccta aaaatgccgt gaggggaaga 3600 tatttgtctg aaatagagtt cagacaagca cacaattatg tcctatttaa ctgtgatgag 3660 ctgagacctt ttattaagta agtagatgtt cgacttaaac tttgtcaaga gtgtactatt 3720 tatgttttgt gataccatac actcatataa tttggaacaa ccttgcaggc aacatcgacg 3780 atacttactg tccaataact cacagctgac cgaatcccag atctttcaat tacaagatga 3840 acaatttgcc acatggttta gaacacatgt aagtcctatc acaaactcat tatctcttgc 3900 aatgtaatta attgtagtca atgttacata atatccgttt attgattatt gttgtattta 3960 atttacaagc taggtttatc aaatgggagg tagtgctgct atttcactgt ctttactatg 4020 cctgggccct gaaagaaaag tcaagtgcta taacgggtat tttgtcaatg gatatgtctt 4080 tcatactgaa gaatacgggc atggaagaaa gacatacaac agcggtgttt gtattaaggg 4140 atcgacttct agtgagtttg aagttgacta ctacggtaga ttggaagagg tcatcgaact 4200 gcaatatcat agcgagcaaa atagagtgtt tttattcaaa tgctattggt atgacacaac 4260 tgacagagga atcagagtag atcctcacta tggtctcgtt gaaatcaact caaaagctag 4320 acaccgcaac gtaaacgacg tctttgtttt cgcaaagcaa tgccaacaag tttattacac 4380 atacacccct tcctttagaa aggaccgatc aagagttgat tggttatccg ttttaaaaac 4440 aaaacccaag ggtcgtgtcg aggttgttca ggatgagaac gaagacacaa gtgtgataga 4500 tgaagtcttt caagctagtg agttggttga accataccga gttgctccgt cgattgactt 4560 agaagaaaat tcgaattttc gtgttttcaa cgatagtctt gttgatgttg acgcagagga 4620 gttgaatgtt gttctgagct ctactagtgg aaaaaagaat gttgttgaag aagatgataa 4680 cgaaattgaa gagtgcgatg aagctgatga taacaattca atagaggacg aagatgaaaa 4740 ttccgactaa ctaaacatgt tataaagcct tatttttata atgtaataat ttgaaacatg 4800 aaatatttat tcttctttaa tggtcagccc ttgttattgt gttgtgcgtg ctgtaagatt 4860 gcaattcaag attttttcac agggttacat aaaaaaataa gaaaaattta cggtttcacc 4920 gacggatata ccgacggact ataacccgtc ggtatttcac agagagttgc aaaaaattta 4980 cgggattttg ccacatcacc gacggatttc cgacggacga cccgtcggta tttcaccgag 5040 agttgcaaaa aatttacacg tgttcgctgc cgaataccga cggattaccg acgtattacc 5100 gacggcatca ccgacggatc gcgcacgtct gacacgtgtc cgtctgcaca taccgacggc 5160 ttccgacgta aataccgacg gaatcaccga cggacacgca tgtctgacac gtgtccgtct 5220 gcacaatacc gacggatttg ccgacggatc gaaaagtctg gcgggatttt cgaacttttt 5280 tggtgcgcat ttcaattaat ttccgacgga attaccgacg gaatttaatg ccaccgacaa 5340 caattaattt ccgtcggtaa ttccgtcgga aaaattgcgt ataaaccccc acccccccct 5400 tggttcattt tctcctcttc tctccctctt tctcttctct tctcctttct cttctcctct 5460 cgtttatatt tagcttttgg aaggatttta ttgttttggt ggtagtttta aaaggtatgt 5520 attctttttt ctttatcttt gtattttttt tattttaatt atgattattt tttttggtgt 5580 tctttgtttt gtgtattgtt tgtagataaa atcttaaatt caacacacta ttaaggtaag 5640 cattttttat tcccaaattt attttgaatt gatatagtgt tttttagttt tgtgtattgt 5700 ttgttttgtt tgtttgtgta gtgtttttta ttttttattt tattttaatt tatttattgt 5760 ttgtattgct ataattgtta ttggaattta tgttaaattt aattgttatt gttgatttat 5820 ttaaaatgtt aatttatata tatagaatta catttaatta gtttatctta atttaggata 5880 ttattgtttg tattgctata attgttattg ttgaatttat gttaaaatgt taatttatat 5940 gttgatgtta tatatagaat tgcatttaat tagtttatct taatttggat attattgtat 6000 tgctataatt gttattgttg aatttattta aaaatgttaa tttaattata tatagaattg 6060 cgtttaatta gtttatctta atttaggatt tattgtttgt attgtaatgt tattaatttt 6120 gttattttaa ttgttattgt tgatttactt gaaatgtaat tggaaatgag aattgattta 6180 attattttat ctcaatttat gtctattatt gaattgttat ttttttatta ttatcaattt 6240 aatgtatgac tttaataatg tttgtaactc taagtgtcag tttaacaata atgttcatag 6300 ttgaattcta tatgatgtta ttgaataaaa tgttgtgttg atgatgatga gttgggttga 6360 gatccaggat gattggatcg ggatgtgaaa taaaattgga agtgtaatat gattttgtcg 6420 aaacttggga ccccccagta taggggaggc tctgtcgaat ttttttttaa ataatcgaag 6480 ttaattatgt aattattcgt ataaatttgt gtagatgcgt agaatgaaat ctacagcacg 6540 tcgtcagaag acggttgcag ctagttcttc tagcagcgag gaggacgtat ccttaggtgc 6600 tgatcacggc gaggmatcta cgccaacttg tgatgctgcc tcttctagcg cggtttcaca 6660 gcgcagaggc ggtgtgcctt cacagcgggg tcaattcacc cgcaagtacc aggcacaatg 6720 gaaggatgac ctctcaatgt aagtttgttt aggttttagt ttttttttat atacttataa 6780 cataatttat gaacaactaa ttaatattac tattttattt aatttcaggt tcacaaacat 6840 tgaggctgcc aggacataac atcggcgttt aaatcgtcga tggagattcc attgtttcaa 6900 tggagccagg tttccagaca tcctgagtgg agacctaata tcgatgcatg gtttagcgat 6960 ttcaggtcgg tgttaatttt taatttccag cttattttta ataaatattt ttataatttt 7020 atatcttgta ctatttttat tttaatgaat tatttatata cacagcacaa atttgagtgg 7080 gataggcgga caacaatgtt gtgaggaggg tatgggagaa tcacgcggca actaggtaac 7140 atcgaaaata atatttattt ttgttttata attttatgtt ctaaattcta atttgttact 7200 atggaagtag gttgcgtgat ttttggtatg acacccaaaa aaaacaaaaa gacatgcgag 7260 ggataacggt cttgaaggat ggaatgaggt ggcggtttgg cgggaattca aaccgccatt 7320 catctcgggg gaatatggac gcatatattg agcacgtgac tcgagcggtt ccacggcgct 7380 cacagtccgg cgccgacaac cggaaccggc aaattcatgg ttcggtgacc acgcacaccg 7440 gcggctccgt cccgttcagc gcacatgcga agcggatggt aagattaatt taatgaaata 7500 tatcgttaat taatttgttg ttgcttataa tatatttaac ttcaactttt tttccttaca 7560 ggctgcgtct cttggacgtg agccgagccc aatggagctg tttgtagaga cgcacgtgcg 7620 gagtcaagac cgccaaaagg gggtgcaaca gttcgtggac aaccgtgctc agcacttcgt 7680 ggtatgttcg ttcatcattt tattttgtaa gttattattt tcttgaattg aatatgatga 7740 tttttttaat tcaggagacc tataatagcc ggttgaggga gagatatggg gacgatcctt 7800 cgacccatcc ggatttcgat ccggatttgt ggatggaggt gggatcgtct ggtggacccg 7860 ataaaaatcg ggtctacggg ctctccaaca ctacggccga aaacttgcgg cggcccgtag 7920 tgtctcaacc gttgggagct ctccatcagt atcgagcacc cagtctgagg agttcatggc 7980 cttgaaacaa caatatgaac aactctcgac gaattatgat cagctccgtc aaatggtcat 8040 ggaatagatc aaggatgggt gagatactgt gcagcccctt tttggccgta cggtcccggg 8100 aacaaccagc ctcctcctcc tcctcctcct ccagctccgc cgctattcta gtttaatttt 8160 gtttttaaac acattaaatt tgtatgaata tttggatgaa tattatttaa cattattttt 8220 atatttttaa tgtttaatac attttatttg tttattaagt tttttacatt aataattttt 8280 ttttatatat tttaaatata ccgtggtttt acagagagtt gaaacaatac cactgccatt 8340 accgacggac aatccgtcgg tattagttac ctcttaccga cggatatccg tcggtattac 8400 agagagttaa attacgccat gccacatcac cgacggaccg tcggtgatta ccgttgaaat 8460 cagacggata tccgtcggta agttccgcgg gaaatttttt ggcgcgcgct ccgtctgtaa 8520 gaccgtcggt gtgttttttt tatttcgaca gatagcgacg gaagggaatt accgacgata 8580 tccgacggac gttcctcggt gaccgtcggt aaaatttacc gacggattct cttcaccgac 8640 ggaattaatc cgtcggtaaa actgttaatg tgtagtg 8677 // ID Copia23-PTR_I repbase; DNA; EDCOT; 4634 BP. XX AC LG_VII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia23-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4634 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4634 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 220-220 (2007). XX DR Genome; LG_VII; Positions 12649963 12645330. XX CC Positions [1769-2269] - Integrase core CC 'ATGTA' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 71..4624 FT /product="Copia23-PTR_I_1p" FT /translation="METPTEMTEQEQQNTVATLDDLTTRMAQIVTQNQTQT FT QTPSVIYDTTAASIGIKLDGTNYALWSQIVEMYISGKDKLGYINGDLPQPE FT LNDPHFRRWRTENSIVKGWLINSMDPSLIGNFIRFSTAKQVWDSIATTYFD FT GSDTSQVYDLKRRVTRMKQSGESIETYYNCLQGLWREIDFRRPNPMECAAD FT IQRFNDLLQENRVYTFLDGLDDRLDNIRSDVLQLKPFPTVEQAYAYVRREA FT IRQTVMLTNNGNSTAAAMVSRGGKTYLPRQQTLQINRAGMAPTAGRNLHHL FT ARPKGQVESEGSGCSHCGNMKHTRETCFKLHGYPDWWSELKTRKQRTSSGD FT TGQASLANTKPQLSLAPLVESGEAATSLPNDQGNTESKNDWIVDSGATDHM FT TYCSDDFSNTTELRRTGISNANGVVYPVTGAGTVHISTSLLLTNTLLVPSL FT SNKLLSVSQVTEDLNCVVLMYPKFCLFQDILTKEIIGRGTKREGLYYVDDF FT NIGNVNTVRRSLLTKENQIWLWHYRLGHPSFSYMKYLFPELFLNLNYAEFK FT CETCILAKSHRVSFPISLNKSDTPFALVHSDVWGPSPITTVSGIRWFVTFV FT DDCTRMTWLYLLKRKDEVFDVFCMFEAMVHTQFSANIQILRSDNGGEYVNH FT NFVEFFRTKGILHEMSCSQTPQQNGVAERKNRHILETARALLFGAQVPGRY FT WSDSITTAVYLLNRMPSKALDFKTPLQALSQYVTLPSILLLPPRVFGCVAF FT VHIHKHLRTKLEPCAVRCIFLGYGSNKKGFRCYDPKTKRLYITMDVTFLES FT EYFYPFTAFTSPLQGEIRNEDEKWWTIGDVENIEVNEVTGAIGDVENNEGT FT GAIGDAKNNEVTGAIETVVMTSTVTDAAENTEGTLVGTTENAENVVIIDED FT DEGTESMASDSISKSPSLLVPDNDNPLHEDDPEVISHTTPTGNILNSSNSY FT HLPFRQNRGRPPSRYSPDTKGKKAKYPVSNYVSTQRLPMPLKAFTYKLSSG FT HIPLGIHEALADPKWSQAIQEEMTALEKNQTWEIVTLPQGKRTVGCKWVFS FT TKYKADGSIERHKARLVAKGYTQTYGIDYQETFSPVAKLNTVRVLLSIAAN FT LDWPLHQFDVKNAFLHGDLEEEVYMDIPPGYNSNTPGTVCRLQRALYGLKQ FT SPRAWFGRFSVAMRKYGFQQSNSDHTLFLKRQRGKVTVLIIYVDDMIITGD FT DEEEIKRLQKQLSGEFEMKDLGGLKYFLGIEVARSKRGIFLSQRKYVLDLL FT TEVGMLDCKPADTPTVQNQKLGVYPDQEPADKERYQRLVGKLIYLSHTRPD FT ISYAVSLVSQFMHCPSKDHMDAVSRILQYLKSAPGRGLMLSKNDHLKVEGY FT TDADWAGNVFDRKSTSGYFTFVGGNLVTWRSKKQKVVALSSAEAEFRGMAK FT GLCELLWIRRLLSEIGFTPKSRMNLYCDNKAAIAISQNPIQHDRTKHIEID FT RHFIKQNLEEGVICFPFVRSEGQLADVLTKAVSNKVFQDSLSKLGIEDIFA FT PT" XX SQ Sequence 4634 BP; 1454 A; 916 C; 1057 G; 1207 T; 0 other; tggtatcaga gcaaaggttc attctttgct actcaaaaat ctgacagaag gcgtaagggt 60 gaaatacaga atggaaacac caactgaaat gacagaacaa gaacagcaaa atacggtggc 120 aactcttgat gatctcacga cgagaatggc tcagattgta acccaaaacc agacccagac 180 ccagacccca tcggttatct atgacactac ggctgcatca attggtatca aacttgatgg 240 taccaactat gccttgtggt cccaaattgt ggagatgtat atctccggaa aagacaaatt 300 gggatacata aatggagatc ttccccaacc agaactgaat gatccccact tcaggagatg 360 gagaacagaa aactcgattg tgaaaggatg gctaattaac tcaatggatc cttctctcat 420 aggcaatttt attcgattct ccactgccaa acaggtatgg gactcgatcg ccaccactta 480 ttttgatgga tctgatactt ctcaagtata tgatttaaag cggcgagtaa caaggatgaa 540 acaatcagga gaatccatag aaacttatta caattgcctt caaggtttat ggagggaaat 600 tgatttccgt agacctaatc ctatggaatg tgctgctgat atacaacgat tcaatgatct 660 actgcaagag aatcgagtgt atactttctt agatgggctg gacgataggc ttgacaatat 720 acggagtgat gtactccaat tgaaaccctt cccaactgtt gaacaagcct atgcctatgt 780 caggagggaa gcaattaggc agactgtcat gcttactaat aacggaaatt ctactgctgc 840 agcaatggtt tctagagggg ggaaaactta tttaccacga cagcaaacac ttcaaataaa 900 cagagcaggg atggcgccga cagcagggcg taacttgcat cacctagcaa ggcctaaagg 960 acaggtggag agtgaaggca gtgggtgttc ccattgtgga aatatgaaac atacacggga 1020 gacatgcttt aaattgcatg gttatcccga ttggtggagt gaattgaaga caaggaaaca 1080 gagaacctca tctggggaca caggccaagc atcattggca aatactaaac cccaactatc 1140 attagcaccg ttggttgaat ccggagaagc tgccaccagt ctgcccaacg accaaggtaa 1200 cacagaatct aaaaatgact ggattgtgga ctctggtgca acggaccaca tgacatattg 1260 ttcagatgat ttttcaaaca ccacagaact gaggagaacg ggtatctcta atgccaatgg 1320 ggtggtctac cctgtcacag gggctggaac cgtgcacata tcaacctctc tattattgac 1380 caacacgtta cttgtgcctt ctctttcaaa taaattgtta tcggtgagcc aagtcaccga 1440 agacctaaat tgtgttgtgc taatgtatcc aaaattctgc ctttttcagg atatcctcac 1500 gaaggagatc attgggcgtg gtactaaaag agaggggtta tactacgtgg atgacttcaa 1560 catcggcaat gtcaacaccg tgagacgatc actactgaca aaagaaaatc agatttggct 1620 ttggcattat cggttgggac atccatcttt tagctatatg aagtacttgt ttccagaatt 1680 gtttttgaat ttgaattatg cagaatttaa atgtgaaact tgcattcttg ccaagagtca 1740 tcgtgtatcc tttccgatta gcttgaataa aagtgatact ccttttgccc tggttcactc 1800 tgatgtatgg ggtccgtcac caattaccac tgtttccggc atacgctggt ttgtaacatt 1860 tgtggatgat tgtactagaa tgacatggtt atatttattg aagcgtaaag atgaagtgtt 1920 tgatgtgttt tgtatgtttg aagctatggt tcatactcaa ttttcagcaa atattcagat 1980 ccttcgatcg gataatgggg gggagtatgt gaatcataac ttcgtagaat tttttcgaac 2040 gaaagggatt ttgcatgaaa tgtcctgtag tcagactcca caacaaaacg gagtggcaga 2100 acgaaaaaac cgacatatct tagaaacagc acgggcatta ttatttggag cacaggtgcc 2160 gggtagatat tggagtgaca gtattactac cgctgtatat ttactaaaca ggatgccgtc 2220 caaagccttg gactttaaga ccccactaca ggcattatca caatatgtta ctctaccatc 2280 catcttgtta cttccaccaa gagtgtttgg ttgtgtagca tttgttcata tacacaaaca 2340 tctacgaaca aagcttgaac catgtgccgt tcggtgtata tttttggggt atggctcgaa 2400 taaaaaggga ttccgctgct atgatcctaa gacaaaacga ctctacatta caatggatgt 2460 tacctttcta gaatcagaat acttctatcc gttcacggct ttcacttctc ctctccaggg 2520 ggaaatacgg aatgaagatg agaagtggtg gactattgga gatgttgaga atattgaggt 2580 taatgaggtt actggagcta ttggagatgt tgaaaataat gagggtactg gagctattgg 2640 agatgctaag aataatgagg ttactggagc tattgaaacg gtggtcatga cttccaccgt 2700 gactgacgct gctgagaata ctgagggaac tctcgttgga actactgaaa atgcagagaa 2760 tgtggtcata atagatgaag atgatgaagg gacagaaagc atggcatccg acagtatcag 2820 taaatccccc tctcttctag tacctgacaa tgacaatcct ttgcatgagg atgatcctga 2880 ggtaatttct catacaaccc ctactggaaa tattttgaat tcttcaaata gctatcactt 2940 acctttcagg cagaacagag gcaggcctcc atcacggtac tcaccagata cgaagggaaa 3000 aaaagcaaag tatcccgtct caaattatgt ctccacacaa aggctgccaa tgcctctcaa 3060 agcctttaca tataagttgt cctctggcca tattcctttg ggaattcatg aagcactagc 3120 agaccccaaa tggtcccaag caattcaaga agaaatgaca gccctagaga agaaccaaac 3180 atgggaaatt gtcacattac cgcaagggaa gagaacggtt gggtgtaaat gggtattttc 3240 aaccaaatat aaggcagacg ggtcaattga gcgacacaag gcaaggctgg tagcaaaggg 3300 gtacacacag acttacggga tagattatca ggagacattt tcaccggttg caaaacttaa 3360 cacagtcaga gtattgttat ccatagctgc aaatttagat tggccattgc accaatttga 3420 cgtgaaaaat gccttccttc acggagacct ggaagaggag gtatatatgg atatcccacc 3480 aggatataat tcaaacacac ctggaaccgt atgcagatta caacgagcgt tatatgggct 3540 aaagcagtct ccacgtgcat ggtttggccg atttagcgtg gctatgagaa agtatgggtt 3600 tcagcagagc aactcggacc ataccctctt ccttaagagg caacgaggaa aggtaactgt 3660 cctgataatt tatgtagatg acatgatcat tacaggagat gatgaggaag aaattaaaag 3720 attacaaaag cagctttccg gtgaattcga aatgaaggac ttaggcggac tgaaatactt 3780 cttagggatc gaagtggcta gatcaaaacg gggaattttt ctctcacaga gaaaatatgt 3840 attagatcta ctgactgagg taggaatgct tgactgcaag ccggcagaca ctccaacagt 3900 tcagaatcaa aagcttggag tgtaccccga tcaagaacca gctgacaaag aaaggtatca 3960 acgattggta ggtaaattaa tctacttatc tcatactcgt ccagatattt cgtacgctgt 4020 cagcttggtt agccaattca tgcattgccc tagcaaggat cacatggacg cagttagtcg 4080 aatactacag tacctaaagt ccgctccggg gagagggctt atgctctcca agaacgatca 4140 tttgaaggtt gaagggtaca cagatgctga ttgggcagga aatgtgtttg atagaaaatc 4200 tacatccgga tattttacat ttgttggggg aaatttggtg acctggagaa gtaaaaaaca 4260 gaaggtagtt gctttgtcaa gcgcggaggc agagttcaga ggaatggcta aaggtctttg 4320 cgaactcctt tggattagaa gattactctc cgagattgga tttactccca agtcaaggat 4380 gaatctatat tgcgacaata aagccgcaat tgcaatttct caaaatccaa ttcagcatga 4440 ccgaacgaaa cacatcgaga tagatcgaca tttcatcaaa caaaatctgg aagaaggagt 4500 gatatgcttt ccttttgtta gatcagaagg tcaacttgcg gatgtgctca caaaggccgt 4560 ctcaaacaaa gtgtttcagg actcacttag caagttgggc atcgaagata tctttgcacc 4620 aacttgaggg ggaa 4634 // ID PIGY-LTR_PS repbase; DNA; EDCOT; 2653 BP. XX AC AY299398; XX DT 09-JUN-2005 (Rel. 10.05, Created) DT 29-MAR-2007 (Rel. 12.04, Last updated, Version 2) XX DE Pisum sativum LTR retrotransposon PIGY-1 (Long Terminal Repeat). XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Long terminal repeat; Metaviridae; PIGY-1; PIGY-LTR_PS. XX NM PIGY-LTR_PS. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-2653 RA Neumann P., Pozarkova D. and Macas J.; RT "Highly abundant pea LTR retrotransposon Ogre is constitutively RT transcribed and partially spliced."; RL Plant Mol Biol 53(3), 399-410 (2003). XX RN [2] RP 1-2653 RA Toth G.; RT "Pisum sativum LTR retrotransposon PIGY-1."; RL Direct Submission to Genbank (09-JUN-2005). XX DR Genbank; AY299398; Positions 13544 10892. XX CC Long terminal repeat of envelope-class Ty3/Gypsy-like CC retrotransposon CC PIGY-1. XX SQ Sequence 2653 BP; 811 A; 493 C; 471 G; 878 T; 0 other; tgataacatg aaataatatc acatttttgg aattgattta attaaattat attgttattt 60 gattcgattt attttatatt attcgatatt actcggtatt ttctttttat ttatttcagg 120 tgtcattatt taaagcatgg gtgaaaaaga aagaagaggg gtgcaaaaag aagactttgt 180 agaatagtat ctcactaaag ctcagcccac gccaactaca aggaaaatgg ctgtgacgac 240 cgccacgggc atgtgacgag cgtcacgccc ctctacttag tgttacgacc ataacacatg 300 gtgtgacgga cgtcacacac tccactccta ttttttggca ttgacgtgcg taacagaagg 360 cggttctccc ctatttttcc tcttgactcg ttgacgcttt agaaacccta ctgaagatac 420 ttttgagaaa acagttactt tatggatgaa tataaataga cctcaaagga tccaattgac 480 atctctctac gccgtgcaat atttttcctg ctttctaatt ttccagcatt ctattttctt 540 agcattttta ttttcttttc tttgctagct taatttacta agcattcaat ttatttattt 600 tcacaatagt ttctacaccg gaaactattg tgtaattttt actggatcca accatacgtt 660 atatcatagt attttatttc cttgtttttt atttacctgt ctgatcaaga attgtgaaga 720 acaaatccaa ccgacttgtg gtggagtgtt cgagcgtcga agctaggaac aaaaccaaga 780 tttctagtaa ttttccaggt tcattaattg atttattgtt ttaatttaca tatgctttgt 840 gctgctgttt atatatattg tctgtttgat atggccgtat ttatgcatga ttattgttta 900 ggcatgttta gcatgtccgg ctaagcaatt tagatatcgg tatgtaaagt aagcggaata 960 aaggaatcaa aactgagttg gtttaaattt attttaaaat atagtcactc tttttctggt 1020 ctcaatttac agagttaata ccaaagtttt tgtacgagag taaaagacat aaagaagtta 1080 aaatcaatag aacgacggtt tgagctttta actggacagt gtaaattgaa cattaacttt 1140 aaatcagagc gaaatcaatt tttaaagtta attaaattct aatcattttc aaaaattatt 1200 tttaaaggtt aaatgtgagg acgagagtta agcatttaag tttaatcata tagtctaagt 1260 caacagagcg agagtttgag acgagggcat ttaaacggtt agtattttct taaaaagagt 1320 ttctatagat tctattgttt tcaaaaagtg attttagatt taatgaaata gtgagagcgt 1380 acgttaatat aaagtcatag tctgattcaa cagagcgaga gtttgaggaa aagactttta 1440 attaatagtg tctactgaaa agacttattt taaaactaag aaaaagacaa acgaagattt 1500 gattccctaa ttacgaagaa ctacataccg atatccgtgt tatttgatat ttaatctaga 1560 tccaatttta gttttatttt tccccctaat catcaaagta tcatccgcct tagctttacg 1620 cagtaaccct agaaaaacgg tatatcgatt cattaagtcc ctgtgggatc gatatctttt 1680 aaaactacgc gattagactg tgcacttgca gttaatactc gatagactca taaagtcgcg 1740 atcaagtttt tggcgccgtt gccgaggact tttatttagt cgatatcgta actcttctgt 1800 tacgctgtag agactaaggc aatttttatt tcccctgtct ttcgttgatt tgtatgccac 1860 acactcgctc acaaggcgag tcgtattact tacgaatcaa tgacgttgaa cgatatctct 1920 gagtcttacg ccgaattcgg gagtatcgtg ctgcaaacaa tcttcctcca atcgaaattc 1980 ctgatctcaa aaatctcctt ccttcgacga taccagagat ggcagaacca gctcgtgctc 2040 ttcgagatta cgctgctcca tcgcaagatg agccgcattc gagtattgct tcacccgcaa 2100 tcgaagcaaa caacttcgaa cataaacctt cgctgttgca ggcagtgcaa cagaaccaat 2160 tttctggaaa tcctaccgag gatccaaacc ttcatttatc cgtatttgtc caatacactg 2220 atactgttaa agctaatggt gtcacttcaa aggcaattcg acttcgtctc tttcctttct 2280 cgttaagaga taaagctaga agatggcttt agtctcttcc ttccaactca gtcaccacat 2340 ggaatgagtt gaagaaagtc tttcttgccc gatattttcc tccaagcaaa acagctatgt 2400 taagagccca gataaatgga tttaagcaga aagataacga gtctcttttc gaagcatggg 2460 aaagatacaa agacatgatg agactttgtc cacaccatgg tttagaggac tggttagtaa 2520 ttcatacctt ctacaatggt ctcttgtaca acacaaggtt aacaatagac gccgccgccg 2580 atggtgcgct tatggataaa ccttacgctg acgcttatta acttatcgag agcatggccc 2640 aaaaccatta tca 2653 // ID Copia7-VV_LTR repbase; DNA; EDCOT; 221 BP. XX AC AM466606; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia7-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-221 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-221 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 748-748 (2007). XX DR Genbank; AM466606; Positions 12384 12164. XX SQ Sequence 221 BP; 59 A; 33 C; 45 G; 84 T; 0 other; tgcagggggg tgataaggga gaatcaaatt ctccataata catgctgcat tccttttctg 60 ttagcataat atccgtttgt atagctgtag ggatatgctc aatatttgta tttgattctt 120 tcctattatg taggagttta caactgtaat tatcgtgtat ataatgaaga gttatctcct 180 tatccggtaa ggaggatttc agtcatttac cgtgtttatc a 221 // ID Copia-39_Mad-I repbase; DNA; EDCOT; 5145 BP. XX AC ACYM01026927; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-39_Mad-I; KW Copia-39_Mad-LTR; Copia-39_Mad_. XX NM Copia-39_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5145 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1309-1309 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01026927; Positions 19336 14192. XX CC Positions [2382-2723] - Integrase core CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 2754..5129 FT /product="Copia-39_Mad-I_1p" FT /translation="MTDAKLPQDMWYHACAHSVFLINRMPCSVLAQQSPYQ FT KLYNINPQLQGLKVFGTAVYPYIRPYTANKLQPRASLCVFVGYAPGYKGVI FT CFHPPTRKFIISRHVVHDESQFPYKNVSITQTGSSDQASISQSLQSSVLVP FT VPPPPRSISTVSIGSQGIESHHSTDLSSFNDIATSAPPSANTDHTGSSSAS FT ETTLSSSSTALVLPVLDPAQLEVILPLDSFPNDLSHSAPISRMQTRLQTDA FT ISRKNYAGFLATFPQLHTMKLDPSDHCHSGFSFVAALHDISEPTSFRTAAT FT HAHWQHAMQEEFDALQSQGTWILVPPPAHRSVICSKWVFKLKKNPDGSISR FT YKARLVAQGYSQALGLDYFETFSPVVRHTTVRLIISLVAQYKWELRQLDIK FT NAFLHGDLEEEVYMKQPQGFMDSNHPEYVCKLVKSLYGLKQAPRAWNAKFT FT GYLPAMGFHMSQLDTSLFIKRDDNDVIVLLLYVDDIILTGSNASKVQAVIQ FT ELGDVFELKDLGKLSYFLGLQLTYKDNGDIFINQSKYAQELIHKAGMDTCK FT PAPTPCKPNTQLLLSEGTHLIDPTTYRSLVGALQYLTFTRPDLSYSVNAAC FT QFMNNPTDVHYALVKRILRYVQGTINCGLTYSASSDQSITAFSDSDWATDP FT NTRRSITGFVVYMGNNPISWQSKKQSSVSRSSTEAEYKALAHCAADMAWIR FT LMLKDLHQFLSYPPLLHCDNLSALALCVNPVFHTRIKYLDTDFHFVREKVQ FT KKDLLVQYVPTEDQTTDVFTKGLHGPAFYKHCCNLRIGYPT" XX SQ Sequence 5145 BP; 1354 A; 1005 C; 1021 G; 1756 T; 9 other; agagcaagcg atcctcctgt ggtgtctagg catctgaaat ttcagtcggt gacggcactt 60 tgggcatttg gaagttgagt tggtgtatct gggttcatca attcatcaat tccctgtaag 120 tgtataaatt ttttttgggg gcacaaagcc attactgtgt gtttgcggca cgaagccatc 180 tacgatcaag attgtgtgtt tgggcacaaa gccatctgag aaatttgttt ttactgtgtg 240 tttgcggcac gaagccatct gcgatcaaga ttgtgtgttt gggcatgaag ccatctgata 300 aatttgtttg ttattcgtgt atctttgaac gttgaagttg ttctttttct acttgtgttc 360 ttgaaatctg catagtttgt gtaacaatgg cgtctaatac tattcgaatt gaaggtcttt 420 tgggtatgct tacaatcaag ttgaatgata agaatttttc gaaatgggtt tatcagttca 480 agtctgttat gaaagggtac aagatgtttg atcattttga tggcactgca gtttgtcctc 540 ctaaatttgt gattgataaa gagcatgggg ttactagtrt gctttctgaa gtttttcttg 600 aatgggaatc agttgattta gcactcttgg gtttgttgat agccactttg tctgatgaat 660 ctattgaaca tgtattgggt tgtaagacaa cacatgaggc ttggtctaat ctccaagatc 720 gttatgcttc aatttcgaag gctagggtga atactttaaa gactgagttt caaactttgc 780 aaaaaggtgg tgattcgata gatcaatatt tgtctaaact acggaatatt aaggatcaat 840 taattgctgc caatgaatct gtctctgata atgattttgt ggtggctgca ttatctggtt 900 tacctagaga atactctact ataagaactg ttattcttac tcgagataac tccattactc 960 ttagggagtt tagggagcaa ttgttgtgtg ctgaaaggga agttgactct atggttaata 1020 ctatgactca taatttttct gggttgtata tgcaaggctc ttcttctcag tctgtttagt 1080 ctcaaggttc atctagccat tctgatgaca ttccatgtgc tactgttggg acaattactc 1140 gagtacctaa tgggggttct aatctgagta taccatatca tcctcaaggt tctgttgctt 1200 tgccctttaa ttctcacggg tctgctgctt tgcctgttaa tcctcaaggg tcttcctttt 1260 ctgcaccacc attttcatct aatggtctca tgtattctcc tgatcaattt ccattaagtt 1320 cttatgtcat gccacaatct ccatctgtgt atccagagtt ttctaattca tatggttttg 1380 ttggcaatgg taatgcttct cggtcattca atacctctaa taatggttcc agaccatttt 1440 ttggcccgaa gtctaatggg gggtatcgag gttctaatgg cagaggacag tcatccggta 1500 ctaagtccag tggcagtact tggcaatctt ggtctggaaa cacagaaaat agaagctata 1560 ttgttccaga atgccaaatt tgttccaaga gagggcatac cgctcctaat tgctggaaaa 1620 gatctactaa tcctaatcaa gtaggtcagg ttgttgagtg ccaaatctgt ggaaaacgag 1680 gtcatagtgc cttggattgt catcatcgta ataactttgc ttatcaaggc acggcacctg 1740 caccttcttt aactgctatg caagcacaag gttcgtctac attcttgcct caagattcct 1800 ggatagttga cattggtgct tcccatcata tgaccgctga tgtcaattca cttcaacaag 1860 tcactcctta tcaaggcact gataaaatca ctattgrcaa tggtgaaggt ttgccaattc 1920 aacatattgg ttctgctcaa ttaaatactc tccctacttc tttaytttta agaactgttt 1980 tacatgtrcc aaatattgyt gtgagtttaa tgtcagtgca acaactttgy aaagataatt 2040 tywgttggtt catttgtgat gatcatgagt tctttgtgca ggacaaggta accaaagttg 2100 tactttacca crgaaggagt aatgggggag agttgtttcg gataccagtt tagttgctat 2160 ctggttcttc tactcattca tccaatacat cagtggcttt acttggacag aaagtgaaaa 2220 cagcaatctg gcatcaacga tttggacatc ccagcaatgc aatcctgtct gctatgttga 2280 aacagtcaga tatagttagt attcccgatg accaacaaca cttatgtcct cattgtattt 2340 ctgggaagat gtctaggtta cctttctctg ctaaaacaga aacttgtacc tttccatttc 2400 aaaaagttca tactgatctt tggggaccat cacctactaa gtccatagac ggttacaagt 2460 attatgttag ttttgtagat gagtttacca gatttgtatg gatatttccc ttaatcaata 2520 catcagaatg ttttgatgtc tttcgacagt tttatagttt tgtcttggct cagtttaatg 2580 ttggtatcaa atgtttacaa acggatggtg gtggtgaata tgttagtacc agatttgcga 2640 atttcttaaa acaaaaaggc atcatttata tgctctcttg tccatatacc cctcagcaaa 2700 atggcattgc tgagaggaaa cattgacata ttgtggagac tgccattact cttatgactg 2760 atgcgaaatt acctcaagat atgtggtatc atgcatgtgc ccactctgtc ttcttaataa 2820 atagaatgcc ctgttcagta ttagcacaac aatctccata tcagaagttg tataatatca 2880 atcctcagtt acaaggtctc aaagtgtttg gtactgcagt atatccatat attagacctt 2940 atactgccaa caagttacaa ccaagggctt cattgtgtgt ttttgtggga tatgctccag 3000 ggtataaagg agtcatttgc tttcatcctc caactaggaa atttattatt tctaggcatg 3060 ttgtgcatga tgaaagtcag tttccatata agaatgtttc tattacacag actggttctt 3120 ctgatcaagc ttctatttct cagtccttgc aatcttccgt gctagttcct gttcctcctc 3180 cgccaagatc aatctccacg gtctctatag gttcacaggg tattgaaagt catcatagta 3240 ctgatttgtc ttccttcaat gatattgcta catctgctcc tccttcagca aatactgatc 3300 atactggctc ttcttcagca tctgaaacaa ctctctcctc ttcctccaca gctttagtct 3360 tacctgtcct tgatcctgca caactggagg taattcttcc tcttgactct ttccctaatg 3420 atttatctca ttctgctcca atttcgagaa tgcaaactag actacaaacc gatgctattt 3480 ctcggaagaa ttatgctggt tttcttgcta cattccctca gttacacact atgaaacttg 3540 atccttctga tcattgtcat agtggctttt cttttgttgc tgcattacat gatatttcag 3600 aacctacctc ttttcgaact gctgcaactc atgctcattg gcaacatgca atgcaagagg 3660 agttcgacgc tctacaaagt caaggcactt ggatccttgt tcctcctcct gcacatcggt 3720 ctgttatttg tagtaaatgg gtttttaaac tgaaaaagaa tcctgatgga tccatttcaa 3780 ggtataaggc acggttagta gctcaaggtt atagtcaagc actcggttta gattactttg 3840 agacttttag tccggttgtg cgtcatacta ctgtgagatt gattatctct cttgttgctc 3900 aatacaaatg ggagttaaga caacttgata tcaaaaatgc cttcttacat ggtgatttgg 3960 aggaagaagt gtatatgaag cagccacagg gttttatgga ctctaatcat cctgagtatg 4020 tttgtaaatt ggtgaaatct ctctatggtt taaaacaagc acctcgtgcc tggaatgcta 4080 aattcacagg ttatttacca gctatgggat ttcacatgtc tcagttggat acgagtctct 4140 ttatcaaacg tgatgacaat gatgtaatag ttcttctact ctatgttgat gatataatct 4200 tgacaggttc caatgccagc aaagttcaag cagttattca ggagttaggt gatgtgtttg 4260 agctgaaaga tttgggaaaa ctttcatatt ttttgggact gcaacttacc tataaagata 4320 atggtgatat ctttattaat caatccaagt atgctcagga gttgattcat aaggctggaa 4380 tggacacttg caaacctgcc cccacaccat gcaagccaaa tactcaattg ttgttatctg 4440 agggtactca tttaattgat ccaactactt ataggagttt ggtgggtgca cttcaatatt 4500 taacgtttac acgaccagat ctttcttatt ctgtcaatgc tgcgtgtcag tttatgaaca 4560 atcctacaga tgttcattat gctcttgtca aacgcattct tcgatatgta caaggcacta 4620 tcaattgtgg tcttacatat tctgcatctt cagatcagtc tattactgca ttttccgatt 4680 cggactgggc aaccgatcct aatactcgac gatcaataac tggttttgtg gtttatatgg 4740 gcaacaatcc tatttcctgg cagtctaaga agcaatcttc ggtttctcga agttccaccg 4800 aggcagaata taaagccttg gctcattgtg ctgcggatat ggcatggata cgtcttatgt 4860 tgaaagattt gcatcagttt ctgtcatatc ccccacttct ccattgtgat aatctctcag 4920 cccttgcttt atgtgtgaat ccagtatttc ataccaggat taagtacctt gatactgact 4980 tccacttcgt tcgtgagaaa gtccagaaga aagatttact ggtgcaatat gttcccactg 5040 aggatcagac aactgatgtc tttacaaagg ggcttcatgg acctgcgttt tacaaacatt 5100 gctgcaatct ccgaattggt taccctacct gagattgagg gggga 5145 // ID Copia-92_Mad-I repbase; DNA; EDCOT; 4720 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-92_Mad_; KW Copia-92_Mad-LTR; Copia-92_Mad-I. XX NM Copia-92_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4720 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1722-1722 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1516-2016] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 409..3960 FT /product="Copia-92_Mad-I_1p" FT /translation="MSDTKSVVKQVEELQVIVHELDEENLGLKEGFVVGSI FT IEKLPSNWKDFKIYLKHLTEDMSMDQLILKLRVEEDHRKNEKYDVSSLEAK FT ANVVEGGDSHKARHHQKNKGKDAAAKKALTAVKGKTFKKIKGGCWVCGKTG FT HRAKDCRHKKDQNSENSNQANVAEDKFVAVVSEVNLLTNSNDWWVDTGATR FT HVCADRNLFVTYQSVDGGENLYMGNATASAVAGKGKVTLKLTSGKELSLTN FT VLHVPDIRKNLISGSLLSNKGFKIVFESDKFVITKGGVYVGKGYLAEGLFK FT LNVLSADAINNNNKPSASSAYLIESSTLWHARLGHVNFRSLQRMVNLGLLP FT KCSMNKVSKCEICTESKYARHSYKSVEKSNEILGLIHSDLCDFKSTPTRGG FT KNYYISFIDDCSKYCYVYLIHSKDEALNMFKTFKAEVENQLDKRIKVLRSD FT RGGEYESNDFAEFCSTHGIIHQTTAPYTPQQNGVAERKNRTLKDMINSMLN FT SSGAPHNLWGEALLAANTILNRIPHKKTNQSPYEIWKGRLPTYKTLKVWGC FT LAKVQVPLPKRQKLGPKTVDCIFIGHANNSSAYRFLVHKSEIADIHVNTIL FT ESAEAEFFEEIFPYKDRSYVLNKRVHDDTTRNDDENHASTSRVQSQDLEPR FT KSKRAKIAKDFGPDFLTFITEEEPQTYKAALESSEAPYWKEAIQSEMESIM FT QNNTWELVNLPPGNKPIGHKWIFKRKLRPDGTIDKYKARLVAKGYRQKEGL FT DYFDTYSPVARITSIRLLIAIASVYNLEIHQMDVKTAFLNGELDEEIYMEQ FT PEGFIVKGQEKKVCKLIKSLYGLKQAPKQWHEKFDHNMITNGFVINESDKC FT IYVKQTKNACVIVCLYVDDMLILGTNKDVINSTKKMLNSSFDMKDMGIADV FT ILGVRILRNSDGYVLTQSHYVEKVLKRFGHYDCKPAVTPFDPIHKLTKNEE FT ESVSQLEYTQVIGCLMYIMNCTRPDLAYSISRLSRYSSNPGRDHWNALIRV FT LRYLKHTMNYGLHYTQYPPVLEGYSDANWISGSTDSKSTSGYVFTLGGAAV FT SWKSSKQTCIARSTMESEFIALDAAADEAEWLKNFLEDIPLWPKPVTAVCI FT HCDSMAAQGRAKNAEYNGKSRHIRRRHKTIRQLLKNGTISIDYIKSKENIA FT DPLTKGLSKDQVAFTSRGMGLKPTQ" XX SQ Sequence 4720 BP; 1598 A; 781 C; 1004 G; 1336 T; 1 other; atctaagaca gaaattattg tgaaaccatg gatcaatcaa atgttggtgt cgtcaagcaa 60 cacgttgaga aacctgagaa attcaaggga gttgatttca aacgttggca acagaagatg 120 ttgttctact tgacaactct gaacttgagt catgtgatta cttctgaggc ccctaaagca 180 ccagaagagg gagatattcc tgccgaaatt ctgcaggcta tagaagcctg gactcacagt 240 gaatttctat gcaggaacta cattctgaat gctttagatg actctctgta tgatgtttat 300 tcatcatata agacagcgaa agawctgtgg gagtctctgg acaagaagta taagtctgaa 360 gtggcaagtt ccaagaagtt tgtaattgga aaatttctga attacaagat gagtgacaca 420 aagtctgttg tcaagcaagt tgaagaactc caagtgattg ttcatgagtt agatgaagaa 480 aatcttggtc tgaaagaagg ttttgtggtt ggctctatta tagagaaact gccttcgaat 540 tggaaggact ttaagattta tctgaagcat ctaactgaag acatgagcat ggatcaattg 600 attctcaaac tgcgtgtgga agaggatcat cgcaaaaatg agaagtatga tgtctcatcg 660 ctggaggcaa aagccaatgt tgtggaagga ggtgactcac acaaggcaag gcaccatcag 720 aaaaacaaag gcaaggatgc tgctgcaaag aaagcactga ctgctgtgaa agggaaaacc 780 ttcaagaaaa tcaaaggagg ttgctgggtt tgtggaaaga caggtcatag ggcaaaggat 840 tgccgccaca agaaggatca gaattctgag aattccaatc aagcaaacgt tgcagaagac 900 aagtttgttg ctgttgtgtc tgaagtcaat ttattgacta attccaatga ctggtgggtt 960 gatacaggag caacaaggca tgtgtgtgct gatcggaatt tatttgttac ttaccaatct 1020 gttgatggtg gagaaaatct gtacatggga aatgcaactg catctgccgt tgcagggaag 1080 ggaaaagtga cgctcaaact cacttctgga aaagagcttt cactcaccaa tgttctgcat 1140 gttcctgata ttcgcaagaa tctgatttct ggatcgcttc tgagtaacaa aggtttcaaa 1200 atagtctttg aatctgataa gtttgtaatc accaagggtg gggtgtatgt gggaaagggc 1260 tacctggctg aggggctctt caaattgaat gtactttctg ctgatgctat taataacaat 1320 aacaagccta gtgcttcttc tgcttacttg attgagtcat ctacattatg gcatgcaaga 1380 ttaggtcatg ttaattttcg ttctcttcaa agaatggtta acttaggcct attgcccaaa 1440 tgttccatga acaaagtatc taaatgtgag atatgcacag aatccaaata tgcaagacac 1500 tcatataaat cagtggaaaa atccaacgaa atacttggtt taatccatag tgatctttgt 1560 gatttcaaat ccacaccaac tcgtggagga aagaactact atatttcttt cattgatgat 1620 tgcagcaagt actgttatgt ctatttgatt catagtaaag atgaagcttt aaacatgttt 1680 aagacattta aagccgaagt cgaaaatcaa ctagacaaaa gaataaaagt cttaagatcg 1740 gatagaggtg gtgaatacga atctaatgac tttgcagaat tttgttcaac acatggaata 1800 atacatcaaa cgacagcacc atatactcct caacaaaacg gagtggctga acgaaaaaat 1860 cgtacattga aggatatgat taattccatg ttgaacagtt ctggtgcacc acataattta 1920 tggggtgagg cactccttgc tgcaaacacg attttgaacc gaattccaca taagaagact 1980 aatcaatctc cttatgaaat ctggaaaggt aggttaccta catacaaaac cttgaaagtg 2040 tggggttgtc ttgcgaaagt tcaagtgcct cttccgaaga gacaaaaact tggaccaaaa 2100 acagtggatt gtatatttat tggtcacgcc aataatagtt cggcatatag atttttggtt 2160 cataaatctg aaattgcaga cattcatgta aatacaatac ttgaatctgc cgaagctgag 2220 ttctttgagg aaatttttcc ttataaagat aggtcatatg ttttgaacaa aagagtacat 2280 gatgatacta caagaaatga tgacgaaaat catgcttcaa cttctagagt tcaaagccaa 2340 gatttggaac cacggaagag taaaagagca aagattgcaa aggattttgg tcctgatttc 2400 ctcactttta taaccgaaga agagcctcaa acttataagg ctgcattaga atcctctgaa 2460 gcgccttatt ggaaagaagc tattcaaagt gaaatggaat ccatcatgca aaataataca 2520 tgggaattgg ttaatttgcc tcctggaaat aaaccaatag gacacaaatg gattttcaag 2580 aggaaattga gaccggatgg taccatagac aagtataaag ctcgtctagt tgccaaaggg 2640 tatcgtcaaa aagaaggact tgactacttt gacacttatt caccagtagc tagaataaca 2700 tctataaggt tattaatagc tatagcgtcc gtgtacaatc tcgagataca tcaaatggat 2760 gtcaagactg catttctaaa tggtgaatta gacgaagaaa tatatatgga acaacctgaa 2820 ggtttcattg tcaaaggtca agaaaagaaa gtttgcaaat tgattaagtc attatatgga 2880 cttaaacaag ctcctaagca atggcatgaa aaattcgatc ataatatgat cacaaatgga 2940 tttgtgatca atgaaagtga taaatgcatt tatgttaagc aaacgaaaaa tgcttgtgtt 3000 attgtatgtc tatatgttga tgacatgctt atactgggaa caaacaaaga tgtgattaac 3060 tccacaaaga aaatgctaaa ttctagcttt gatatgaaag atatgggaat agctgatgtg 3120 attcttggag ttcgaattct aaggaattca gatggatatg tcctaactca atcacattat 3180 gttgaaaagg ttctaaaaag gtttggacat tatgattgta aacctgcagt aactccattt 3240 gatcccattc ataaacttac taaaaacgaa gaagagagcg tatctcaatt ggagtatacc 3300 caagttatag gttgcttgat gtacattatg aattgtacaa gacctgatct cgcttattca 3360 ataagccgat taagtaggta ttcaagtaat cctggaagag atcattggaa tgctttaata 3420 agggtattaa gatacttaaa gcatacaatg aactatggtt tgcattacac tcaatatccc 3480 ccagtattag aaggatatag tgatgcaaat tggatttcag ggagcacaga cagtaaatcc 3540 acaagtggat atgtatttac acttggtgga gcagctgtgt catggaaatc atctaagcaa 3600 acgtgtatag cacgttcgac aatggaatca gagtttatag ccttagatgc agctgctgat 3660 gaagctgaat ggcttaaaaa ttttctggaa gatattccat tatggcccaa gcctgtgact 3720 gcagtatgta tacattgtga cagcatggct gcacaaggtc gagccaaaaa cgctgaatat 3780 aatgggaagt cgagacatat aaggcgacga cataaaacca ttagacagct actcaagaat 3840 ggaactatct ccattgacta tattaaatct aaggagaata ttgccgatcc tttgacaaaa 3900 ggcctatcca aggatcaagt ggcatttaca tcgaggggaa tgggtttaaa gccaactcaa 3960 tgagttataa cttgacggaa acctaaccta gctaattgga gatcccatgg tctaggttca 4020 ataggcaaac tagttgagga aaactcaagg taagaaacac acaatcctta ctcattccta 4080 tgatggaaaa cagtgtgttg cctgtaagac gtagagggtg aatcattatt cttaataatg 4140 ctaatatctt atggttaaga tgaatagaac aggctattct taattagcat tacctatatg 4200 agattgatgt ggggtcgcat ctttgagaat tgatatggct acaattctct aaaggtctca 4260 tgaaatcagg atatgttcag gaccaaaatg aacacaaccg tatgaattga agtgtgtcaa 4320 gatgtgatat gtgtgatact tattgtttcg atttactact aacaatgatc agttcaagat 4380 attaaattca ctgcttcatt aggtaaatcc gataagtact cactagagaa ggttcaagtc 4440 caaaagacac ctatcccgat gcatatcata tctaagttct ctggaaagac gttactaatt 4500 tagttagtat cttattttct attcaaatgt ggggtattgc tagagtttga atagaaaatg 4560 tggggtattg ttggaacttg tgagtgggac tcagtcccac atcgcccaaa cactttttga 4620 aagtcccctt tataagtgtg ttccctcact tatggtttga aaagaattgg gccaaagcca 4680 tggaccttgg gccttacaaa tggaggctct tgggctcgga 4720 // ID GmGYPSY11_LTR repbase; DNA; EDCOT; 1126 BP. XX AC . XX DT 07-JUL-2009 (Rel. 14.07, Created) DT 07-JUL-2009 (Rel. 14.07, Last updated, Version 1) XX DE Gypsy-like retrotransposon from Glycine max,LTR. XX KW LTR Retrotransposon; Transposable Element; Gypshan4; Medicago; KW soybean; consensus; GmGYPSY11_LTR. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-1126 RA Sobol A. and Laten H.M.; RT "GmGYPSY11_LTR: LTR consensus sequence in Glycine max."; RL Repbase Reports 9(7), 1381-1381 (2009). XX DR [1] (Consensus) XX CC GmGYPSY11_LTR is a LTR consensus sequence related to Gypshan4 CC from Medicago truncatula. The GmGYPSY11_LTR consensus sequence CC was generated based on an alignment of 13 full-length unannotated CC copies in Genbank (26 LTRs). XX SQ Sequence 1126 BP; 316 A; 237 C; 207 G; 366 T; 0 other; tgatgaggac atgaccaaga gcaagggcaa ggatccactt gaaggacttg gaggacctat 60 gacaagggct agagcaagga aagccaagga agctcttcaa caagtgttgt ccatactatt 120 tgaatacaag cccaagtttc aaggagaaaa gtccaaggtt gtgagttgta tcatggccca 180 aatggaggag gactaaatga caccactttg tctcaatttt agagtgttta gtttgtctaa 240 ataatggccc aatccttgta aagttggctg accaaaaata tgttttgggt taatcaacta 300 aaagggcttt agttaggttt agttcaagtt gtaataaggg cccaattggc aacctaggca 360 tcagcctttt gggagaccaa atggtggctg acttgttggc tgttgggggt gacttttggt 420 tgccacaatt tcagttacac tcagccatta agtttttttt aattccctag gttaatggca 480 ttaagttatt ttaattctag gttagtgggt cattactaaa atctgctgta aagcttctat 540 ataagctgaa ccattttatc aataaacaca agttgagttt tattcagaaa attagagttt 600 atctctttta tcttagtgag agtgattctc ctaaattctt gagtgattca agaacaccct 660 ggctgtatca aaggactttc acaacctttg tgtgttgccc tcgccggaaa gagtgattct 720 ttccttcctt tcatcttcaa ccttgttctt tcaaaccaca attccagaaa atccacttct 780 gcccagaatt atctcgtggc cataactccc attttacgca ctcaaattaa gtgattcttg 840 agcctaaatt gaatttcaaa acgagacctt tcacctcgtt ttggaatcac ctcatttgga 900 gccctgtagc ttgagttatt gccatttcta tatttctgtc cagccaccac ttaacctacg 960 ttttatcatc tcattcttcc attttatgcc aagaaccacc ttattaagac ccacgaaatt 1020 aaccacctta ttttccatcc tttccttaat caatttccgc attttccatc aaggtttaat 1080 cctagacgat cctaagtcag cccttgtgcc atgagggttc atatca 1126 // ID Copia36-PTR_LTR repbase; DNA; EDCOT; 391 BP. XX AC scaffold_3831; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia36-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-391 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-391 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 249-249 (2007). XX DR Genome; scaffold_3831; Positions 539 149. XX SQ Sequence 391 BP; 121 A; 65 C; 60 G; 145 T; 0 other; tgttggaaga ttgcttcatg agctggcaaa gaaccagtca aagaagaagt agtcaaagat 60 ttatttatgc tctgtatttc ctgttttcat gcaaataatt aactgcgtcc tagtctctag 120 gaattaggtg atctgttagt atgttaacag attgtagcag gttttttatg ctttattgta 180 gcatttctgt tttgtttttc agtataaata tctgtaaaga ttgcaacata aagtgcaatc 240 atattcttca atcctcagct aataaaacag taaaaacttc tactgttcag atcaagattt 300 ctggcaattc tcaacagtaa caaactgtta ctgtaaacat caaaactgtc cattctttct 360 aagtttcatt tttcttttct aaacactgtc a 391 // ID SINE1_SO repbase; DNA; EDCOT; 200 BP. XX AC . XX DT 23-OCT-2006 (Rel. 11.1, Created) DT 24-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE Short Interspersed Element from Solanum demissum. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; SINE1_SO. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-200 RA Shankar R. and Jurka J.; RT "A SINE consensus sequence from Solanum demissum."; RL Repbase Reports 6(10), 506-506 (2006). XX DR [1] (Consensus) XX CC The consensus sequence of SINE element from Solanum demissum. XX SQ Sequence 200 BP; 75 A; 39 C; 35 G; 50 T; 1 other; cagtgacaga gtyagaattt ttactaaggg ggttcaaaat ataaagaagt aaacacacga 60 agaagtcgaa gaggttcaat atacatctac tatatataca taaaaataaa atcaatttta 120 accatgtata aacagtgtaa ttttccaacg aagggggttc gaatgaaccc cctgagccct 180 tactagctcc gcccctgctc 200 // ID Gypsy-41_Mad-LTR repbase; DNA; EDCOT; 1497 BP. XX AC . XX DT 18-OCT-2010 (Rel. 15.1, Created) DT 18-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-41_Mad-LTR. XX NM Gypsy-41_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1497 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1777-1777 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 1497 BP; 445 A; 382 C; 300 G; 369 T; 1 other; tgtttgggtt aaaacttgaa ctttgggctc aagagggagt tggcccaaaa gaagaggcct 60 agaaggagag aagcccgaag cccagccgaa gcccagaagg cagaagaggc cttttccgac 120 taggtgcaga tcatttggac cacttgctca cctacccaga ggccaagtgg tgtagaccag 180 ccagctaatc agcccaaaag tactttacag tggcagtaca agtaaaatag ctgatgagtc 240 actacccttc aagctgcatt cgggcaagat tgctgctaca ggaggccaag ccaagttgtc 300 tataaaagga gaaagagaaa tcagaaataa ggacactcaa tcaaacaaac aaatacaagc 360 acaaactctg ctcaaagcca gatttgcctt caaaacgaag ctgtagtcag cccaagcctt 420 catccctttc gggatcaacc ttcacccaaa gcctttgtaa tagctctgct accctgtcta 480 aatcttgctg tagtatcgat tcccttctgt aaactcatct ccctacccct ctttctaagc 540 tctcaaaccc cttgataaac cacaaagata ggaagttgca agacgatcag ccttgcccga 600 ccctctttgt ttttgtcttt tcattcatta gcctagcaat atgttgtata cttccagttg 660 tatccaagtt atttctagca agatgackat taaaaggctc tctcagtgct tggatccgat 720 ttgaatatgt cttcacagtt caaaccagat ctaagttcta agccctcggg catgtaagat 780 tgatcattaa aagtccttgg cctcaaggca taaaaaagaa ccttatgtgg acttaaccca 840 tccacgacaa tccttgataa acaagaagtc cgaagttact tggggcgcaa gtaatcgacc 900 tatctcttag ttttatttct gttatattat gattaccata gaacgtttga gtatagaatg 960 aattctgatg ggaagcctca aggcctacac ctaaggcccc acaaaggcac ctatttgggt 1020 tcattctgct cttcgggctc gggtaatcag aagtataata gttataagac tcctgcaacc 1080 aatgaaacaa acattatatg ttcgagtact gggttagtta ttgattggaa gcctcaaggc 1140 ctacacctaa ggccccacaa aggcacctgt cataactaac acggtctctc gggtatatat 1200 acaactaaaa ctcaacatcc gttttacatc tgccatgctg aagatggcag tggcacgcct 1260 gagcacttaa aagttaatct tgattgtgag cctcaaggcc tacacctaag gccccacaaa 1320 ggcacctttc aaagttaact ctgtccttct ctttcagcct tgcccgacaa gccttgcccg 1380 acaagcccgc cagtgaagca gaagcccgac agaaagcatc aaccggcgcc aacctctcgg 1440 ggagctgtgt gctcgtcggc caggaaacat ccccgacgga aattcctgcc acgaaca 1497 // ID Gypsy16-VV_I repbase; DNA; EDCOT; 8582 BP. XX AC AM462489; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy16-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-8582 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-8582 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 712-712 (2007). XX DR Genbank; AM462489; Positions 17293 8712. XX CC Positions [2743-3198] - Reverse transcriptase CC Positions [4738-5217] - Integrase core CC 'CTGCC' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 367..2340 FT /product="Gypsy16-VV_I_1p" FT /translation="MPRAPREESSDSTHFSAKRQRDKKSQLSSSMRARLGP FT QEPGRSRPLVATTRAPRPDPMIAPMVQNVPPHRDPMVTPVMRNVHSHPAER FT PAGKNLPNEPPIGSISKRLDDMLSTPFCSHITHYEPPRGFLVPKFSTYDGT FT NDPFDHIMHYRQLMTLDIGNDALLCKVFPASLQGQALSWFHRLPPNSIDNF FT RDLSEAFVGQYLCSARHKQNISTLQNIKMKDNESLREFVKRFGQAVLQIEV FT CSMDAVLQIFKRSICPGTPFFESLAKKPPTTMDDLFRRANKYLMLEDDVRA FT ATQQVLVARQASRDNADRHAKPPDRPKPVDRRQDGPSRPDRPPVTPLSVSY FT EKLLPMIQGLSDFRWPRPLETDPSIRDRSKKCAFHKDHGHTTETCRSLQYL FT VERLIKAGHLKQYLRSDTGGRDVSQHHNSGAPRAPVAPKAVINYINGGPSD FT EEYDSRRKRQKLLRAASIRERINSIRPGLTGEGPRPIDGTIIFPPVDPTWT FT LQPHRDALILSLEIGDFDVRRILVDPGSSADLVQASVIGHMGHSLAGLENP FT GRILSGFNGSSTTSLGDIILPIQAGPVTLNVQFSVVQELSPFNVILGRTWL FT HYMKAIPSTYHQMVSFLTDEGQTDLYGSQLAARQCYQIAREAVANQEDASP FT PEPSIARDQ" FT CDS 2842..4134 FT /product="Gypsy16-VV_I_2p" FT /translation="MLSFLDAFSGYHQIPMFPDDEEKTAFITPHSLYCYKV FT MPFGLKNAGATYQRLMTKIFKPLIGLSFEVYIDDIVVKSKTREQHILHLQE FT VFYLLRKYGMKLNPSKCAFGVSAGKFLGFMVSQRGIEVSPDQVKAVMETPP FT PRNKKELQRLTGKLVALGRFIARFTDELRPFFLAIRKAGTQGWTDNCQNAL FT ERIKHCLMHPPILSSPIPKEKLYMYLAVSEWAISAVLFRCPSPKEQKPVYY FT VSRALADVETRYSKMELTALALRSAAQKLRPYFQAHPVIVLTDQPLRSILH FT KPDLTGRMLQWAIELSEFGIEFQPRLSKKGQVMADFVLEYSRRPNQHHESS FT EQEWWTLRVDGASRSSGSGVGLLLQSPTGEHLEQAIRLGFPASNNEAEYEA FT ILSGLDLALALSVSKLRIYSDSQLVVRHVQKEYEAKD" FT CDS 4297..5604 FT /product="Gypsy16-VV_I_3p" FT /translation="MQANPSVTEDSTCNTIEANQTDDQEWTHNIAEYLRAG FT TLPEDPKQAHKIRVQAARFTLIGGHLYKRSFTRPYLRCLGHSEAQYVLAEL FT HEGICGNHTGGRSLAHRAHSQGYYWPTMKKDAAAYVQKCDKCQRYAPIPHV FT PSAALKSVSGPWPFVQWGMDIVGPLPAAPAQKKFLLVATDYFSKWVEAEAY FT ASIKDKDVTKFVWKNIVCRFGIPQIIIADNGPQFDSIAFRNFCSELNIRNS FT YSTPRYPQSNGQAEATNKTLINALKKRLEQAKGKWVEELPGVLWAYRTTPG FT RPTGNTPFALTYGMDAVIPTEIGLPTIRTDAAKQKDANTELGRNLDWADEV FT RESASIRMADYQQRASAHYNRKVRPRNFKNGTLVLRKVFENTAEVGAGKFQ FT ANWEGPYIVSKANENGSYHLQKLDGTPLLRPWNVSNLKQYYQ" XX SQ Sequence 8582 BP; 2499 A; 2266 C; 1911 G; 1898 T; 8 other; ttggcgccgt ttgtgggaat acttttactt ttcattttga ttcagtcact agcaaagatg 60 gccacacctt cccaaagtcg atcatctggt agaaaggagg aagataatca cgaatggcgt 120 caggccatcg aaaaaagaca gttggcaagc gaaaaacagc taagagctct cctcctggag 180 acggagaggt taagggaaga aaacgcagtg ttacgcattc aagcctcaac atcaggtcct 240 cctcgtcgtc agcgttcgag aggctaggtg gcaaactcaa ggccagaatc agaatcaata 300 tatcctgggt caacaggagc tgtcccagga gcatacaacg caaggcccca tgagccacgc 360 acacccatgc ctcgagctcc ccgtgaggaa agctcagact ctactcattt ttcagcaaaa 420 agacaacgtg ataaaaaatc ccaattgtca agttctatgc gcgcaagact aggcccacaa 480 gagcctggga gatcaaggcc actagtagcc acaacccggg cgccacgccc tgatcctatg 540 atcgctccca tggtgcagaa cgtacctccg catcgtgacc ccatggtcac cccagtgatg 600 cggaacgttc actcacaccc agcggaacga ccagctggaa aaaacctccc aaacgagcca 660 cccattggct ccatcagcaa aaggctggat gacatgctct ccacgccctt ttgctctcat 720 atcacccatt acgagccccc aaggggattc ctcgtaccaa agttttccac atacgatggg 780 accaacgatc ccttcgatca catcatgcac tatcgacagc ttatgacgct cgatataggc 840 aacgatgcat tgctatgcaa agtatttccc gccagccttc aagggcaggc cctctcatgg 900 tttcatcgcc tacctcctaa ctctattgac aatttcaggg acctctcaga agcattcgtg 960 ggacagtatt tgtgctctgc tcgacacaag cagaatatca gcaccctcca gaatataaaa 1020 atgaaagaca acgaatcttt aagggaattt gtgaaacgat ttggccaagc tgtactccaa 1080 atagaggttt gcagcatgga tgctgtccta caaatcttca agagaagcat ttgtccaggc 1140 actccatttt ttgaatcact ggcaaaaaag cctcctacaa cgatggacga tttgttcaga 1200 cgtgctaaca aatacttaat gctcgaagat gacgtgcgtg cagccactca gcaagttttg 1260 gttgccagac aggcttctag agataacgcg gacagacatg ccaaacctcc ggaccgtcca 1320 aaaccagttg accggagaca ggacgggccg agtcgtccgg acaggccgcc cgtcacaccc 1380 ctatccgtat catacgaaaa acttctccca atgatccaag ggttgtccga cttcaggtgg 1440 cctagacccc tcgaaacgga cccatccata agagaccgca gcaagaaatg cgctttccac 1500 aaagaccatg gtcatacaac agagacatgt cggtccctcc agtatctagt tgaaaggctc 1560 atcaaagcag gacatttaaa acagtacctc cgctcagata ctggaggaag ggacgtatct 1620 cagcatcata actctggggc cccgagggcc ccagtcgccc ccaaggctgt cataaactat 1680 atcaatgggg gcccgtctga cgaggaatac gattccaggc gtaaaaggca gaaattgctg 1740 cgggccgcgt caatacgcga acgcattaat tccatccggc cgggtcttac tggagagggc 1800 cctcgcccca tagatgggac aatcattttc ccaccagtag atcccacctg gacgctacag 1860 ccacatcgcg acgccctcat tctctcccta gaaataggag atttcgatgt aagacgtatc 1920 ttggttgacc caggcagttc agccgatctg gtacaagcat cagtcattgg ccatatggga 1980 catagtctcg cgggtctcga aaaccccgga cgaatcttat ccggattcaa cggatcatca 2040 accacgtcct taggagacat tatactgccg atccaagctg gcccagtcac tctcaacgtg 2100 caattctcag tggtacaaga gttatcaccc ttcaatgtca tcttgggacg cacatggctt 2160 cactacatga aagccatccc gtccacatat catcaaatgg tgagtttcct caccgacgaa 2220 gggcaaactg acttatatgg cagccagtta gccgctcgtc agtgctatca aatagcacgt 2280 gaggcagtcg ctaaccagga ggatgcatct ccccctgagc ctagcattgc acgcgaccaa 2340 tagcaattat tgggttcggc ggacaaagat cccccggtag cagatccctt acaaacaatc 2400 caaatttcgg aggaaagcga tcacctcaca aacatcagtt ccctcatgac acaagaagaa 2460 actcggggca tgcaaaaaat cctcagacag aaccatgaca tcttcgcgtg ggcacattct 2520 gacatgaagg gaattcatcc ctccattgca tctcacaggc ttaacgtctt ttcaactacc 2580 agacccgtcc ggcagaggat taggcgcttc cacccggata gacaaagaat catccggaac 2640 gagattgata aattgctcga agccggattc atcagagaag tttcgtatcc ggattggctg 2700 gcaaacgtag tcgtggtacc caaaaaagaa ggaaaatgac gagtttgtgt agattacacc 2760 aatctcaaca gtgcatgtcc aaaagacagt ttccccttac cacgaataga tcagattgtg 2820 gattccactt ccggacaggg gatgctctct ttcttggatg ccttctccgg atatcatcaa 2880 atccccatgt tcccggatga cgaagaaaaa acagcattca taacgccaca cagcctctat 2940 tgctacaaag tcatgccatt cggactcaag aacgctggcg ccacgtatca aagattgatg 3000 actaaaatct tcaaacctct gataggcctc tcgttcgaag tatacattga cgatatcgta 3060 gttaaaagca aaacgcgaga gcagcatatc ctccatttac aagaagtttt ttatctcttg 3120 cgaaagtatg gcatgaagtt aaatccttcc aaatgtgcct ttggcgtgag tgctggcaaa 3180 tttctgggat ttatggtcag ccaaagaggc atagaagtca gcccggatca ggtcaaagca 3240 gtcatggaga cacctcctcc caggaataaa aaggagttac aacgcctcac aggcaagctc 3300 gttgcgttag ggcgtttcat agcccgcttc actgatgagt tgcgaccctt cttcttggcg 3360 atacgaaaag ctggaacgca gggatggacg gacaattgcc aaaacgcgtt ggaaagaatt 3420 aaacattgtc ttatgcatcc acccatcttg agcagtccca tcccaaagga gaagctatac 3480 atgtatctag ctgtctcaga atgggcaatc agcgccgttc tattccgctg cccttcaccc 3540 aaggagcaga aacctgtcta ctatgtcagc agggcattgg cagatgtaga aaccaggtat 3600 tcaaaaatgg agctaacagc cttagctctt cgaagtgctg cccaaaagct ccgcccctat 3660 tttcaagccc acccagtgat tgtactgacc gaccaacccc ttcgtagcat tctacacaaa 3720 ccagatttaa ctggacgaat gctacaatgg gccatcgaat tgagcgaatt tggaatcgaa 3780 ttccaaccca gattatccaa aaaaggccaa gtaatggccg actttgtgct cgaatattca 3840 cgaagaccca accagcacca cgaatcaagt gaacaggagt ggtggacact acgagttgac 3900 ggagcctcac gctcatcagg ctctggagtt gggctcttat tacagtcccc aactggggaa 3960 catctggagc aagccatccg gctgggattc cccgcgtcta acaatgaagc agaatacgag 4020 gccatcctgt ccggattgga cctcgccctt gctctatccg tytccaaact ccggatctac 4080 agcgactcgc aactagtggt aaggcacgtc cagaaagaat atgaggctaa ggackcacgy 4140 atggcgcgat acttggccaa agtaagaagc accttacagc arttcaccga gtggacaatc 4200 caaaaaatta rgcgagctga caataggcac gctgacgctc tggccggcat agctgcctcc 4260 ctccccatca aagaagccat tctactgccc atacatatgc aagccaatcc ctctgtcaca 4320 gaagattcca cttgcaacac cattgaggca aaccaaacgg atgatcaaga gtggacgcat 4380 aatattgcag aatatctccg ggcaggcact ttacccgaag atcctaaaca agcacacaaa 4440 atccgggtgc aggctgcccg tttcaccctg atcggggggc acctgtacaa gcgatccttc 4500 acaaggcctt atcttcgctg tcttgggcat tcggaagccc agtatgtgct agctgaatta 4560 catgaaggaa tatgcggaaa tcatacggga ggacgatccc tggcacatag agctcattca 4620 cagggatact attggccaac aatgaagaaa gacgcagcag catatgtcca aaagtgtgat 4680 aaatgtcaga gatacgctcc cattccgcat gtgccttcag cagcgttgaa atcggtatca 4740 ggcccatggc ctttcgtgca gtggggcatg gacattgtgg gacccctccc agcagcacct 4800 gcccagaaga aattcctcct tgtcgccact gattacttca gtaaatgggt agaagctgaa 4860 gcatatgcaa gcatcaaaga taaagatgtc accaaattcg tatggaagaa cattgtttgc 4920 cgctttggaa ttccccaaat catcatagct gacaatggtc cacaatttga cagcattgca 4980 ttcaggaatt tctgttcgga attgaatatc cggaattcat actccacgcc acgttatcct 5040 caaagcaatg gccaggcgga agccacaaac aaaactctaa tcaatgcctt aaagaaaagg 5100 ctggagcaag ccaaagggaa gtgggtggag gagctacccg gcgtcctgtg ggcttatcga 5160 accacacccg gacgaccaac aggaaatact ccttttgccc tcacatatgg aatggatgca 5220 gtcattccca ctgaaatagg tcttcctact atccggactg atgcagcaaa acaaaaagac 5280 gccaacacgg aactaggaag aaatttggac tgggcagacg aagtcagaga aagcgcgtcc 5340 atccggatgg cagattatca acaaagggca tcagcgcatt acaatcgaaa agtcaggccc 5400 agaaacttca aaaatggtac gctagtactt agaaaagttt ttgaaaatac tgctgaagta 5460 ggcgcgggaa agttccaagc caattgggaa ggaccttaca tagtgtctaa ggcaaacgaa 5520 aatggatcct atcatttaca aaagctagat ggcactccgt tactcagacc atggaatgtg 5580 tccaatttaa agcagtacta tcagtaaaaa gtatacacaa gtgcaaatga gaaaaaagta 5640 tgttttattg atatgaataa atgtaattac aaagagatct ccggaccaca aaaaatacag 5700 aaggaaaaat tacagyagaa aaattgcaaa aagagataaa ctatcaggga gcaggtttct 5760 catggagctt cttttcttca cttggaagaa ttgaaggggt atctcgcttt ataccgttct 5820 tcttcatgca gcagcgatac ccaaagataa atgtatcatc cacttgtttc tggtaatccg 5880 ctgcaagttc ctctctttcc acagcaaact cccgttcaag ttcctctttt tgcacatcca 5940 gacgcagctg caaatcttcc ttctgtttct tttcattcaa aacttctgtc cggagttgac 6000 tcaattcatc ccttarccgg gctgcctcac cctccgcctc atgaaggcgg cccgcagttg 6060 attcttttca ttcaaaaagt caaaaagcaa aaacacaaga caacgatata ccrtttctat 6120 catatcaaac atctgagcag agggcttgat ggctttccag tctggtgtaa tatgctttaa 6180 cttaacttcc aactccgcat agctgaaagg gctagcagga gcggcatcgt cagcagggtc 6240 ttcctcagat gaggaagcag aaggtaactc ttgtcctgga atcggaaccc ccatatcttc 6300 gtccggacac ataggtccgg atgcatcctc agccggaatt attgccgggg cggctgaggt 6360 ctcagtagcc atctccacct cgcctccatc cggatgagcg tcatgggcag aaacgcagct 6420 aatttcaatc tcttgctgcc gctcttgaag ccactcaaag agtccggact gtagatcgcg 6480 cgtcaaacgc ggcttcttga ggggaggccc tttcaccagg actatggcca ggcgatccgg 6540 gtcgtcggaa ggctgacttt ggctttctgc ccccgcttcc tccaacgggg ccgtttcagc 6600 tgcatcagca tccggattaa ggttgcccgg atggttgata gatgcaactt cctcagccac 6660 gttagccaga tgcgcagccg cgactaagga aggacctgaa tgattcaacc ccgacatgcg 6720 tccggggccg cttgagatag agtgcggagc agcatttact ggctcctcta tcattacttc 6780 cccctcatag gtagtttgtg gaggaggaaa ctccttggga ggagtgggtt ccttcgcatc 6840 cttcccatgc ttcttcacca gcttccccat ttttcctgaa gttttctttg gaggagagtc 6900 cggaccccgc ttctgtccgg gagccttccg gatagtgcct tcagtctttt tctgatctct 6960 atcctccagg agctttcgcc gcctttcagc gtcagcctct ttagcttcct gatagagggg 7020 gagctccttc acagtataat gctccccagg cactatctca tcctttgcca gtttcctggg 7080 aaggatattg ataacatatt cctggggctc ccggatgacc gctatcaaat tccgcgcgga 7140 aagcaatgtc ttgtaggccc tctccttggg atctatctcg aataacttgc agacacaggc 7200 gaaggacgcc ttttccaccc aatccacaag gtggcccctc aattccagac ctgcattgac 7260 agcaacaaaa ggtgagaatt ccgttcgaaa aaaatcagaa aaaatcagca aagcaaaatc 7320 cggacaaaaa atcgcaaaac aagattaccc ggaattttta aggtataatt tggagaaaaa 7380 ggcctcgacg gatgctgcga tagccccgcc catccacccc ggaccgccac cagccccttc 7440 gcccctccct ttgtcgaatc tggcagttct ggcaccattt gaagggaggg caggtgagcg 7500 gacacactga agatatcatt ctttgctttc ttcagggaat agacaaagaa caactccagt 7560 agcgtaaggt cgaggctgta cagcatgttg atgatgctgc atcccatcag cacccggaca 7620 aggttgggat gaatgaagat gggtggaatc tgagagaagt ggaggaattc cttgaacaac 7680 gccggcagag ggaaccggag ccccgcgttg aattgttcct ttgtgaagag gataacgttt 7740 tctccacctt tctcagtagg catagctgcc tcctcgttca ccaagtctat caatacgtca 7800 tgggggaggc agaatcgctc ccggaactcc ttcgcattta atttatctat cgccttttcg 7860 ccagcctcgc tgacccggac agacgaaaca gtcttttttg gagccatttc ttaccacaaa 7920 gcaaaaccaa aatctacata caaaaacaat gcaacggttc aaaacaagca gtcagaaaaa 7980 cccctcaaaa acccctccga acaacaacaa agtaccaaca ttcaacaaca attgcaaacg 8040 actcgatcaa aacaaacgcc caaacaagcc agaaaacaag tttaaaagaa ccagcaaatg 8100 caaccaaaag aatggcagta gcaaagaggt acgtaccaaa taaagctctg aagaagaaga 8160 acgggtactg ccttgataca aaatcaccag caacaaacaa acaaagtcgc gatacaaaag 8220 caccggtaca aaagagctct cgaagttttt ctcagaggag caaaggacgc aggaaaaagc 8280 agtaagaaga aaggctctca agagaatgca gtaggaaaaa ttgcaaaaag aggtacagtg 8340 ccctatttat agcaggacag cccctcagaa aagcaaacca acagccatgt tatcattgaa 8400 acgacatatt gcctggggat acacagggtc ggcggctcgc cataaatgcc ttttttggct 8460 tccgcacccc cactcgccac gtggccaagt tagacgaatg gactttttca attttcaaaa 8520 acccagttat ttttaacccg cccatttttt gggcaaaata ggcaagttaa aaaggggggc 8580 aa 8582 // ID Helitron-1_Mad repbase; DNA; EDCOT; 7323 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Helitron family DNA transposons from the apple genome. XX KW Helitron; DNA transposon; Transposable Element; Helitron-1_Mad. XX NM Helitron-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-7323 RA Kojima K.K. and Jurka J.; RT "Helitrons from the apple genome."; RL Repbase Reports 10(10), 1642-1642 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~90% identical to consensus. This consensus can be incomplete. CC ORF can be broken. XX SQ Sequence 7323 BP; 2248 A; 1319 C; 1574 G; 2167 T; 15 other; ctkactttat tagttttttc catttttatc cagaccaaag cttccatctt tacttcaaat 60 gtagtcctac aaataaaggg tatcctttgt tttggttaat tagtcagtgt atgttgttct 120 tgttttagaa ttttagggag agaaaattat gggatctggt aatggggttt attcagttgg 180 ggatttcgat ttggatgcca agtggctgat cgatccaaaa catcttttgt tggtccgagg 240 attggggaag gcgcacatgc caaagtgtat gaaggaaagt aggtacaacc tctgtgtttg 300 ttttgtctta aattctgaat ttctggtctc tcaagtttag caatttaata tgatgcctta 360 gatcttgtta aatataaatg caaatttgag ttgggtttta gcagaactaa tcaaagatca 420 aaacttgatt tggtgttctg caattatggt gtttatgatg ccgaatatgt gtttttcgtg 480 tcgagttaca acgatgatgt tctgttctgt tgtgttctta atctgtttgt tggttgcgtt 540 ttgtttgttc tagatataag aatcaaaatg ttgctgtaaa aaatgttcat agaggagaaa 600 ccccagagca gattgccaag agagaagcgc ggtttgcgag ggaagtggca atgatgtcga 660 aagtgcagca caaaaactta gtgaaggttg ttgtctagtt ttcgataagt atttgtgatc 720 actaaatggg cgtgttagcg ataagtattt ggggattttt aactttgtga ttctgaggtt 780 gtttttgttt ctcaatcaaa ggggcttgaa agagtcggat gtggacagtt ttgttgatga 840 tgtccttgtg aatcacaaac catgggcttc cggagtgcaa gaggcgttga ctggctccca 900 tgtaatgtat gtgcacatgg tgtcgagata atagatgtgg tgtttggacc tgttttgcac 960 cgaagattct tataacgctg tcgtgacgtc caccagcagc cgcagttgaa cctacctgcg 1020 caccacctta aaactacaaa agaaaggaaa ttgcatcgta aagcagttat acaatttatt 1080 ttttaaaatt tgatggtaac atttatacaa attaaattgt gggaggaata ccactcacgc 1140 gttatcgaca cggcagtgac atcattgccc catgcaaaaa atttaaaagg gccgcctaca 1200 ctggggaagc ttgggaaaga ttgactttgg ttatttgaaa gccaagctgc acttctacag 1260 gctgcaatgg atgccagcag ctccgmccat ggagccgsck ctgccgcctc ttcgtcttcc 1320 tcgcggagct caaaccgctg gaagtacgag gtgttcctga gctttagagg tgaagacacc 1380 cgcaacacct tcacagacca cctcttcatt gcgttacgca atgccggaat taacacgttt 1440 atagacamac agctcagaag gggggaaaac atacagagtg aacttgacca agaaatcgaa 1500 gggtcgagaa tcgccgtcat cgtcttctcg aagaggtacg csgagtcccg atggtgcctg 1560 agggagctgt cgaagatcat gaggtgccta aaagatcaag aggggaaaat agtctgtcca 1620 atattctacg acgttgaccc ttctcaagtc aggaaacaga aagatagttt tggggaagca 1680 tttcagaagc atgaaaagga tgaagatcca aatgwggtca agcagtggag agaggatctt 1740 aaggcttctg cakatttggc cggctggaac ctcaaaacca cggccgacgg gtataatttt 1800 ttgtttactt caaatttcat atcaccatat ttcactaatc aaccaaaatt aagatattat 1860 aattaaggca ttgaatcctg attttatatg ttataagaaa aattggatcg ttggtccgtg 1920 aactatgata gaactgtaat tttggtcact acataaaaat ttattagaat tggtatatga 1980 attttataaa aggtagagca tttgcataag aatttccgtc aaaattaagg aagtgaaacg 2040 cagggtacat gctttgtttt ttatgggtgt gtgaaggaca aatgctccac actttatcaa 2100 attaaaatac caattgtaat ggattcttaa ttatataact gaaagctaca attgcgtagt 2160 agtccaatca ccaatggtct aatgtattca cattataatc gaagattaga tacgtggttg 2220 aattgagctc agtaaatcac agtttattca aatctgtttc aatatgtaaa tatatagtca 2280 tgatgaataa ggcatttagt atggctctcg taatttggaa tttctactcg taggcgtgaa 2340 ggagtgttta tcgagaaaat tgctggggac gtcaagggac tattgaaacc cacagactta 2400 aaagccaagc actcagttgg aatggctctt cgcgtgcaag aattcagcac tgaatactta 2460 gacgttggag gttcacctga tgttcaaata attggaattt ggggtacggg cggtataggt 2520 aaaacaacgc ttgccaaagc cgtttgtagc aaatatggtc atagtttcag cagtcaatgt 2580 taccttgaag aggtgaggag taacaagaaa aatatggtta gtctgcaaga acaacttctt 2640 cgagatattt tgaaacggcc tgacattaag gtaagcagtg ttgccgaagg gaccaaggag 2700 atagagaaaa gacttggaag catgaaggta cttgtcgtgg ttgatgacat agatgatgcg 2760 gaccaattag atgaattggc aatagcacat gactcgtttg gtccagggag taggattatt 2820 ataacgacaa gagatgaaca agtgctgaat atacaaaagg tggataaaag gtataaggca 2880 caaggaatga ctgatgacga agctcttgag ctccttagtt ggcatgcctt tggaaatgat 2940 tgtcccgacg aagaatatat tgaactcgca agagatgttg ttgattattg tggaggattg 3000 cccctagctc ttgaagttgt tggccgtttg ttggctacga aaaagagtaa aagcatatgg 3060 aaaagtacat tggataaatt gagaaatatt ccagatggaa aaattcatga aacgcttaaa 3120 ttaagctacg atgggctacg tgacgatcat gtgaagggtg tgttccttga catatctagt 3180 ttctttattg gagtgtgtat aagtgtggtc acgacaatat tggatggttg tagtcgtttt 3240 tctgtagaag cagaaattac cacactttgc gatcgatgtc tcttatatat tgatgaaggg 3300 ggagmattga ggatgcatga tttgattcga gatatgggaa gagaaattgt gcgggcagaa 3360 tctcctgtgg aactgggaaa acgtagtcga ttgtggcata gtgaagatgc aaaaagcgtg 3420 ctaaggaacg aatctgtaag tacttttgca ataaaaaatg ttatgttaag tacatgtgaa 3480 gaaagagaag tatatacgca tatcctgcat atatataatg tatgacgtac atagtatatt 3540 cgaagaaaaa gaagaaaaga aaaggctttc atccactggg taawttgaaa gagaaaatac 3600 ataattatgt tgtatgccct acctttctag tagttcattc atccgattca cggctctgct 3660 tcgtgtgaat attatccttt tcttgttttt tttttttatc tctaacaggg aacagaagca 3720 gttgaaggac tagaattatt tttgccagaa cattctgatg acgagcaaag cttcagtacg 3780 gaagcgttta agaagatgtg gcgtctgaga tttctctggc tgggaaatgt aaagctgact 3840 ggaagctaca aacatctttc caaggagtta agattattgt attggattgg atttcctctt 3900 gaagccatac cagcagattt tgatcaacga aacctagttt atatggaact gtggtmcagc 3960 aagattgtac gagtttggga ggattcggac ctggtacgat ataattatca atgtccttgt 4020 aaatatcaac atcagtcatc gtcatgcatt ctctctttta tttatttgga tttttattat 4080 tgttttctct ttttgagtaa cagttgccta agaagttgaa gttatctcgt tcttgtasac 4140 tgccgtaacc tgactgaatt accagacttt tcaaaactcc cacatctccg gtacttgacc 4200 atcagaggct gtaagggttt gtgtgggggt taccattttt tagcacaact gaagatgatt 4260 gaggaattac atctcagcga ctgcaatata acagatggtg ccgttctcga aataattggg 4320 agtctatctt ctttaacagt tttagatcta ggtgggaatg gttttaatag gctacccatt 4380 ctcagtggcc tttctcagct tcggggttta tgtctaaatc attgcacaaa ccttcaggca 4440 atcccagatt tgccgaacag tttgcgtgta ctggaagcga attactgcac tgcactggaa 4500 ataatgtccg acttttcaga gatgtcgaaa atgaggaaat tgcaactgaa agactgccgc 4560 aaactcaaag atattccaaa cttggagaac tcattggact acatggattc aatttatatg 4620 gaagggtgta ccagtctcac tgatactttt aaggagaacc tccgaacggt atggtactct 4680 ctctctctct ctctctctgc tttttgtatt gttgcttata ctaactttgc accccatgct 4740 gtagaaaaat gcatttggtg gaatttttct ctctggaaat gatattccta accggttagc 4800 ctatgtcgcg agagaggatg aaactgtcaa atttgaagtg ccgccaagta ttgattatat 4860 aggagggttg gctttgggca tcgtttattc ttcggacaac tccgactcta ctgggtttct 4920 awccattgat gttgttaatc gtacccagcg aactaatttt cgcatctggg caattgaggc 4980 caccgtaact gcttcccatg aatattatct ttggttggga aatctttcaa acaagaagct 5040 caatctgaaa ggcggcgaca tggttcttgt aaaagcagaa ttttatggac kagataatac 5100 aattattaag gtgaacaaaa caggagtgga tattgtaaaa tgggatttgt ctgatggtcg 5160 tactaattgg gacaactatg agactatgtc atatgagtct gatgaagaca ctactgtgtc 5220 atatgagtct gatgaagaca ctgatgacga tacactgtcg agctatcgcc acgttttcct 5280 ctgctacaag acccccgagg cctggccatg gcgcatcgaa ggctctgagt ccgatccact 5340 ccctaagttc ttcgcatccg ctctcaaagc tcgcaagaac gacatcaccg ttaaggtctg 5400 ttttccagct caattcgtcg gcgtttctga ttgctttttc ttaccgtttc ttatttcctg 5460 gagctactga gttctggtgt tgagctgagt tgactccatt actcactttt ttcttggttt 5520 ttgatagacg ttgctgacag taattgaagg acgcgaagga actgagtttt ccgacggcga 5580 tgtgttgatt ttcccacaaa tgatcaaata caggtaaatt ttaatccgaa tttataggat 5640 ttacatacca tcaaatgata gcaactaact cctgatatca actgctggat gaaaaacctt 5700 gcctgatgca aaacaacaat taaattgaaa aagtatgtaa gttttagtta tattataact 5760 gactatttat gtaaaaatgc ttcagaccta actttcccta tctgaaacta gacgaaaatc 5820 gagatggatt ccatttcagg ggacattcag acatcccata tttgagactc tacactaaaa 5880 tcatttccaa tgaaattttc tctgcatttg aaactacttt atctcatcct cactaaatct 5940 gccagcactg catattctct cgaagagttc tcacccagcc gtgtactcca tcacaatggc 6000 aagatgaggt ggtgtgagca gaaccaacaa gaaagacacc gcactactct caagtcttaa 6060 acacaaacct atttatcaat tatcacaaat aagcactcta aagactattt ccacttcaca 6120 gtaaaacaaa gtgcaggaag tatagatcat atttttagca gagttatttt gacaactatt 6180 ctgcaagtgg tggattgccc cggtgggtag ggcattttct cttagtccta ctgcattccg 6240 ggctcaaagt tctaaccatc ccctatacca gtttaagcac accaaaggcc aaatttagca 6300 tgttctgtct tcatccaccc accctcagca gatacttata aaaaattcaa acacaacttg 6360 ccaaattcat tcttaaaata caaaatgaaa aagtttatga tcactgacct cttggaatca 6420 aacgatattc agatgcagtg atctgtggtt catgatttcc ccttgaacat gttcatctat 6480 ctgcatcacc aaaaaataaa ggtcgtaccc agtgcacaag gctcccgctt tacgcagggt 6540 ctgggagagg tgaatgtcgg ctagccttac ccccatttat gaagaggctg ctcccaagac 6600 tcgcccacca aaaaatatat acatttaaaa aaatacaaag tttaaaggat gagaaataaa 6660 gaaaattcag aaaaagggaa gatataagag tcgaagaaga cagaaccaaa acatccaaga 6720 ctcgcccacc aaaataatca agacatccaa gataacatcc aagactcacc caccacccat 6780 ctagctagca aacacacamc taaaggctaa aaaggatacg gtcttcgtca aattaggtgt 6840 taggcaagtc ttggatgttt tagctatggt caacctaaac caaaatcaag tgacaaataa 6900 acaaaggcat gcataaatca ttttctttcc gttaacttta attaataaga ttgggtttgg 6960 atctatctta gtctgctttc tgatgttaac atgtaagagt agaatgtagt actacaaaga 7020 gaaagccatc attgcaagcc tatatcatgg caagcaaggc agattcactc tcacctccat 7080 atattaccaa atcttagtct atatgatttt gccagagcta cctaatgttg aatatatatc 7140 tgttgaatgt tctataacat caacattata aaggtttcta attgaatcat acatttaaaa 7200 tccaagcatg aaagctttac agagacaaat aaacaaatgt aaataactaa ttaggcaata 7260 cacagcagag aagggggggg ggggagagag agagagagag agaggcaaag cagcattcca 7320 agt 7323 // ID BoSB6D repbase; DNA; EDCOT; 341 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB6D. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-341 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 341 BP; 98 A; 62 C; 85 G; 96 T; 0 other; gtggaagcac cgtagcctag tggttaaggt ttaaaggctt ctacacccag gctggggttc 60 gaatcccaga ctatgcaatt tattgcagat tacaggaaat ccaggtttca agtcccggag 120 agagcgattt attaaacaat tatgcagact acggaagaaa ggcttacaag ggatcttcaa 180 catggtgcaa gtaaatctgg tcaggcgtgg atcttcatag gacggctcag gtgatgcagt 240 taggcgtagg tccttcataa ggcaggtagt attgtcggtt gtcgaatcgt ctatgtaatc 300 tttctcatat cataattgta atatcataat aaatcagcgt t 341 // ID SHACOP6_I_MT repbase; DNA; EDCOT; 4469 BP. XX AC AC131248; XX DT 15-JAN-2007 (Rel. 12.01, Created) DT 15-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region sequence from LTR retroposon, SHACOP6_MT, from DE Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed repeat; SHACOP6_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4469 RA Shankar R. and Jurka J.; RT "SHACOP6_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 76-76 (2007). XX DR [1] (Consensus) XX CC The internal region sequence has intact domains for Copia-like CC gag-pol polyprotein. XX FH Key Location/Qualifiers FT CDS 58..4467 FT /product="SHACOP6_I_MT_1p" FT /translation="MVEHDETLETPKASTNKSLTNKYDDPSDPLYLHHSDQ FT PGLVLVTQQLSQSNYPLWSHAMLMALTTKNKDGFVDGSIKKPSTTSSKEYK FT QWIRCNLLVKGWILNTISPSIAQSVMYNDDASKIWSELKERFSHANNVHLF FT HIEQEIHECVQGDMSIGDYYTKLKGLWDERDALSPLPLSDGNVAKKLKEYQ FT QTQHTIQFLMKLNPVYATARGQILLMDPLPPVNKVFSLIIQDEKQRDISSQ FT VTSEAVAFAVRNEPPNSNKNYQPKYPHLKCDRCNLAGHTAENCRQHLKCDH FT CGYKGHTIDICRKLKRENVQGDRKGFSNSLSRANHVNSKSDKAETTSSYNL FT TADQYHDLLELINRTKSVSVANQVSTMNNLSGIAPKYLTYGKNIRWIFDTG FT ATDHMTCSSQFFTTSSPVTNRYVYLPNHALAQVTHIGTIHFSKSLILYNVL FT CVPSFELNLISVAKLNQTSSCHATFTNNLCFVQDQHSGKTIGTGIEEAGLY FT YLDTSKFAGCRSFAAMVTSTNPHLWHQRLGHPSNKSMHAISLCSELVKFHS FT ISDCSICPLAKQTRKPFSTSSINTKSCFELIHVDIWGSYHVSTLQGAKYFL FT TIVDDFSRCTWVYLLHTKSEARKYLLTFINLVETQFESRIKIIRSDNGLEF FT SIPNTYHDKGIIHQTSCVSTPQQNGVVERKHRHLLNVACALLFQANLPKTF FT WGDAILTATYLINRTATPILQGKTPFEVLFHKPPTYHHLRVFGCLCFASNH FT HHKPSKFDTRSVRCIFLGYPYGTKGYRVYDLATGKIFISRDVMFHEHIFPY FT TSAATLSNPLTHQVPITTTVPHVAMPFFPSPTPLLLDDQQQTPPIVAPTTA FT PLETIIPTTTSTSDAATSDSTTLTLPEAPHNTPLPAPIPKRKIQAPSYLQQ FT YHVEVSLPTRSLPSSHSVLAAPKGIPHPLSQVLNYDRLSAAHRVFTTCISV FT VKEPTSFHQAVKDPKWRLAMDEELSALHDNNTWSLQDLPPNKNPVGCKWIY FT KIKFNPDGTVERYKARLVAKGYSQVEGFDYRETFAPVAKLVTVRLLLAVAS FT SMNWHLRQLDVYNAFLHGDLEEEVYMSLPPGYGRKGETRVCKLHKSLYGLK FT QASRQWFIKLSKVLVLADFTQSKSDHSLFVRRHETSFTALLVYVDDIILAG FT NNLQEIERIKAHLMEQFKLKDLGNLKYFLGIEVSRSKQGITLSQRKYALEI FT LEDMGYLAVKPANSPMEQNLSLSKTDGDFIAEPSSYRRLVGRLIYLTITRP FT DLVYPVHILSQFMDKPRIPHLEAAQRILRYIKKTPGQGIFFSSTSSLQLNA FT YCDADWARCRDTRRSTSGYCVFIGNSLISWKTKKQVTVSRSSAEAEYRSMA FT SVCCEITWLRSVLYDLGIEHQQPVKLFCDNQAALHIASNPVFHERTKHIEI FT DCHLVREKVQAGVVKTYHISTSEQPADVFTKALSVPQFSNLINKLGMINIY FT SNLRG" XX SQ Sequence 4469 BP; 1319 A; 1051 C; 789 G; 1310 T; 0 other; tcaagagcac tcaaacctct atagctcaaa tacccatttt tttccatagt ttctatcatg 60 gtagaacatg atgaaacctt agaaacaccc aaagcctcta caaataagag ccttaccaac 120 aaatatgatg atccaagcga tccactatat ctccatcact cagaccaacc aggtttggtt 180 cttgtgactc aacaattgtc acagagcaat tatcctcttt ggagccatgc catgctcatg 240 gctctcacca ccaagaacaa ggatggattt gtggatggat ccatcaagaa gccatcaaca 300 acatcttcca aggagtacaa gcaatggatc cgctgcaatc tccttgtcaa ggggtggatt 360 ctcaacacca tttcacctag cattgctcaa agtgtaatgt ataatgatga tgcctccaag 420 atctggagtg aattgaaaga acgtttctct catgcaaata atgtgcatct cttccacatt 480 gaacaagaga ttcacgagtg cgttcaagga gatatgagca ttggtgacta ctacaccaaa 540 ttaaagggat tgtgggatga acgtgatgct ctcagtcctc ttccactaag tgacggtaac 600 gtggcaaaga aattgaagga gtatcaacaa actcaacaca ccattcaatt tctgatgaaa 660 ctcaacccgg tctatgctac agctcgggga caaattttac ttatggatcc attgcccccc 720 gtgaataagg tattttctct tattattcaa gatgaaaaac aacgtgacat ttcttcacaa 780 gtaacatcag aagcagtagc ttttgctgtc agaaatgagc caccgaattc caacaagaat 840 tatcaaccaa agtatccaca cctcaaatgt gatcgctgca accttgctgg acacactgct 900 gaaaattgcc gccaacatct taaatgtgat cattgtggct acaaaggtca taccattgac 960 atttgtcgca agctcaagcg agaaaatgtt caaggggata ggaaaggttt ctcaaactcc 1020 ctttctagag ctaatcatgt gaattccaaa tctgacaaag ctgagacaac ttcctcatac 1080 aacctgactg cagatcaata ccatgatcta cttgaactca ttaatcggac aaaatcggtt 1140 agtgttgcca atcaagtgtc gacaatgaac aacctttcag gtatcgctcc taaatatctc 1200 acatatggta agaatattag atggatattt gatacaggag ccactgacca catgacttgt 1260 tcgtctcaat tcttcaccac cagcagtcct gttactaatc gttatgtcta tttacccaat 1320 catgcccttg ctcaagtcac acatataggg acaatacatt tttctaaaag cctcatactt 1380 tataatgtgc tttgtgtccc ttcctttgaa ttaaatttaa tatctgtggc taaattaaat 1440 caaacatctt cctgtcatgc aacttttacc aacaaccttt gttttgtgca ggaccaacat 1500 tcggggaaga cgattgggac gggaattgag gaagctggac tctactactt agatacgtcg 1560 aagtttgctg ggtgtcgttc gtttgctgcc atggtcactt caaccaatcc tcatctttgg 1620 caccaacgac ttggtcaccc ctccaataaa agcatgcatg caatctctct gtgttctgaa 1680 cttgtaaagt ttcattctat cagtgattgt tccatttgtc cacttgctaa acaaactaga 1740 aaaccttttt ccactagttc tatcaataca aaatcttgtt ttgagttaat tcatgttgat 1800 atttggggca gttatcatgt ttcaactttg caaggggcaa aatatttcct cactatagta 1860 gatgattttt ctcgatgcac atgggtttat ctattacata caaaatctga agctagaaag 1920 tatttactta cctttataaa tctagttgaa acccaatttg aatcccgcat taaaatcatt 1980 cgtagtgaca atggattaga attctccatc ccaaacacat atcatgataa aggaattata 2040 catcaaacta gttgtgtctc aaccccgcaa cagaatggcg ttgttgaacg aaaacatcgt 2100 catcttctta atgtagcttg tgccttactt ttccaagcca atcttcccaa aactttctgg 2160 ggtgacgcta tccttactgc cacttaccta atcaatcgca ctgcaacgcc cattcttcaa 2220 ggcaagacac cttttgaggt actattccac aaaccaccga cttatcacca cttacgggtc 2280 tttggttgtc tatgttttgc ctccaaccac catcacaaac catcaaagtt tgacacacgt 2340 tctgttcgtt gtattttcct cggttatcct tatggtacca aaggttatcg ggtatatgat 2400 ttagccactg ggaaaatttt tatttctcga gatgtcatgt ttcatgagca catatttcca 2460 tatacttccg ctgccactct gtctaatcct ttaacacatc aagttcctat taccactact 2520 gtacctcatg ttgctatgcc attctttcct tccccaacac cattattatt ggatgaccaa 2580 caacaaacac cacctattgt ggcgcccact acagcacctc tagaaacaat tattcctacc 2640 accacgtcca cttcagatgc cgcaacttcc gattctacaa ccttgacact accagaagca 2700 cctcataata cccctcttcc tgctcctata cctaaacgaa agatacaagc acccagctac 2760 cttcaacagt atcacgtaga agtgtccttg ccgactcgtt ccttaccgtc gtctcactcg 2820 gtgttggctg ctcctaaagg tattcctcat cccttgtctc aagttctcaa ttatgataga 2880 ctttctgctg cccatcgtgt tttcaccact tgcatatcag ttgttaaaga acctacctcc 2940 tttcaccagg cagtcaagga tccaaagtgg cgtcttgcta tggatgaaga actttctgct 3000 ctccatgata acaacacttg gtctctccaa gatttgcctc caaacaagaa tccagtgggt 3060 tgcaaatgga tttacaaaat caaattcaac ccagatggaa ccgttgagcg ctacaaggct 3120 cgcttagttg caaaagggta cagtcaggtt gaaggttttg attatcgtga aacatttgcc 3180 ccggttgcta agctcgttac tgttcggtta ctacttgctg tggcatcttc catgaattgg 3240 catcttcgac aattagatgt ctataatgct ttccttcatg gtgatctcga ggaagaagta 3300 tacatgtcat tgcctcccgg ttacggaaga aagggggaga cacgtgtctg caagcttcac 3360 aagtctttgt atgggctaaa gcaagcctca cgtcaatggt ttatcaaatt gtccaaagta 3420 ctcgttcttg cggattttac tcaatcaaaa tcagatcact ccttatttgt tagacgccat 3480 gaaactagct ttaccgctct ccttgtttac gtcgatgaca taattttggc aggaaataat 3540 ctccaagaaa tcgagagaat taaagctcat ctcatggaac aattcaagct aaaggatctc 3600 ggtaacttga aatacttttt gggcatagag gtatctcgat ccaaacaagg aatcacactt 3660 tcacaaagaa aatatgcact tgaaatattg gaggacatgg gatacttggc agtaaagcct 3720 gccaattctc caatggagca gaatttgtct cttagcaaaa cagatggtga tttcattgct 3780 gaaccatctt cttaccgaag gcttgttggg agattaatct atttgaccat tacaaggcca 3840 gatttggtgt atcctgttca catcctcagt caattcatgg acaagcctcg cattccacac 3900 ttagaagctg cgcaacggat actacgctac atcaagaaaa cacctggaca aggcattttt 3960 ttttcatcca caagttcact gcagctgaat gcttattgtg atgcagattg ggctcgatgt 4020 cgagacacac gcaggtcaac ttcaggttat tgtgttttta ttggaaattc cttaatttct 4080 tggaaaacaa agaagcaagt cactgtatcc cgctcaagtg cagaggcgga atatcgttcc 4140 atggcatctg tttgttgtga gatcacttgg ctacggagtg ttctatatga tcttggaata 4200 gagcatcaac aaccggttaa attattttgt gataatcaag ccgctctaca tatagcctca 4260 aatccggtat ttcatgaacg gacaaaacac atagaaatag attgtcacct tgttcgcgaa 4320 aaggttcaag ccggagtagt caaaacttac catatttcaa catcagaaca accagcagat 4380 gttttcacta aagcattgag cgttccacaa ttttccaacc ttatcaacaa gttaggaatg 4440 atcaacatct attccaactt gagggggag 4469 // ID GmCOPIA11_I repbase; DNA; EDCOT; 4086 BP. XX AC . XX DT 21-JUL-2008 (Rel. 13.09, Created) DT 21-JUL-2008 (Rel. 13.09, Last updated, Version 1) XX DE Copia-like retrotransposon from Glycine max internal region. XX KW Copia; LTR Retrotransposon; Transposable Element; retrotransposon; KW gag; reverse transcriptase; polyprotein; soybean; consensus; KW integrase; LTR; GmCOPIA11_I. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-4086 RA Wright L.N. and Laten H.M.; RT "Intact, full-length transposable element consensus sequences in RT Glycine max assembled from robust collections of BAC-ends."; RL Repbase Reports 8(9), 903-903 (2008). XX DR [1] (Consensus) XX CC Related to AtCOPIA78. XX FH Key Location/Qualifiers FT CDS 33..4079 FT /product="GmCOPIA11_I_1p" FT /note="gag-pol polyprotein." FT /translation="MANGGFPFQMPMLTKNNYDNWSIKMKALLGAQDVWDI FT VENGFEEQDEASLSQGVKETLKESRKRDKKALFLIYQSVDEDTFEKISNAT FT TAKEAWDKLQTCNKGVEQVKKIRLQTLRGDFERLFMEESESISDYFSRVLA FT VVNQLKRNGEDVDEVKVMEKILRTLNPSFDFIVTNIEENKDLKTMTIEQLM FT GSLQAYEEKQKRKIKQKEATEQLLQLNVKEANYANYKSQRGRGRGQDRGRG FT RGHGGEGRGGYNNHSNKFNNGERSWNPQVTRGRGRGNSWSRYDKSQIKCFN FT CNKIGHYASECRFSKKVEEKANFVEEKGGEEETLLLACQNKFEEKRNKWYL FT DTGASNHMCGDKSMFVEINEAATGDVSFGDDSKIPVKGKGKILIRLKNGSH FT QFISNVYYVPNMKNNILSLGQLLEKGYDIHLKEHSLFLRDCRHNLIAKVPM FT SKNRMFLLNIQNDVAKCLKACYTDSSWLWHLRFGHLNFDGLERLAKKEMVR FT GLPSINHPDQLCEGCLIGKQFRKSFPKESTTRATKPLELIHTDVCGPIKPN FT SFGKNKYFLLFIDDYSRKTWVYFLKEKSEVFENFKKFKALVEKESGLSIKA FT MRSDRGGEFTSNKFNKYCEDHGIRRPLTVPRSPQQNGVAERKNXTILNMVR FT SMLKSKKMPKEFWAEAVACAVYLTNRSPTRSVHEKTPQEAWSGRKPGISHL FT KVFGSIAYTHVPDEKRTKLDDKSEKYVFVGYDSRSKGYKLYNPNSRKIVIS FT RDVEFDEEDCWDWSVQEDKYDFLPYFEEDDEIEQPIIEEHITPPASPTPRL FT DETSSSERTPRLRSIEEIYEVTKNLNDINLFCLFGDCEPLSYQEAAENIKW FT KDAMDEEIKSITKNDTWELTTLPRGHKAIGVRWVYKAKKNAKGXVERYKAR FT LVAKGYSQRQGIDYDEVFAPVARLETIRLIISLAAQNKWKIYQMDVKSAFL FT NGFLEEEVYIEQPLGYEVKGQEEKVLKLKKALYGLKQAPRAWNVRIDKYFQ FT DKNFIKCPYEHALYIKAQSGDILIVCLYVDDLIFTGNNPSMFEEFKKDMSN FT EFEMTDMGLMAYYLGIEVKQEDKGIFITQEGYAKEVLKKFKMDDANPVGTP FT MECGSKLSKHEKGENVDPTLYKSLVGSLRYLTCTRPDILYAVGVVSRYMEA FT PTTTHFKAAKRILRYIKGTTNFGLHYYSSDNYNIVGYSDSDWSGDLDDRKS FT TTGFVFFMGDTAFTWMSKKQPIVTLSTCEAEYVAATSCVCHAIWLRNLLKE FT LKMPQEEPMEICVDNKSALALAKNPVFHERSKHIDTRYHFIRECIEKKEVK FT LKYVMSQDQAADIFTKPLKLETFVKLRSMLGVTNQV*" XX SQ Sequence 4086 BP; 1417 A; 727 C; 972 G; 966 T; 4 other; aagtggtatc agagcttcaa gatcctcaaa agatggcgaa tggaggtttt cctttccaaa 60 tgccgatgct cacaaagaac aactatgata attggagtat caagatgaag gcgctactag 120 gagctcaaga tgtgtgggat atcgtagaga atggcttcga ggagcaagat gaagcctcgc 180 taagccaagg tgtaaaggag acgttgaagg agtcaagaaa gagagacaag aaagctctct 240 ttctcattta tcaatcggtg gatgaagata catttgagaa gatatccaac gcaacgacgg 300 ccaaagaagc atgggataag cttcaaactt gcaacaaagg agttgagcag gtaaaaaaga 360 ttcgtcttca aactcttaga ggtgactttg agcgtttgtt tatggaggag tccgagtcaa 420 tttctgatta tttttctcga gtattggccg tagtcaatca acttaaaaga aatggtgaag 480 atgttgatga ggtgaaggtc atggaaaaaa tacttcgaac tttaaatcca agttttgact 540 tcattgttac caacattgaa gaaaacaagg atttaaagac catgactatt gagcaactca 600 tgggttcctt acaagcatac gaagaaaaac aaaagagaaa aattaaacaa aaggaggcta 660 cggagcaact actacaactc aacgtaaagg aagcaaacta tgcaaattac aagagccaaa 720 gaggacgagg tcgcggccaa gatcgtggac gtggacgagg acatggagga gaaggaagag 780 gtggttacaa caaccactcc aacaaattca acaatggaga aagaagttgg aatccacaag 840 taacaagagg tcgtggaaga ggaaattcat ggtcgaggta tgacaaatca caaatcaagt 900 gcttcaattg caacaagatt ggtcactatg catccgagtg tagattctcg aagaaggttg 960 aagagaaagc taactttgta gaagaaaaag gcggagaaga agaaactttg ctactcgcgt 1020 gccaaaacaa atttgaagag aaaagaaaca agtggtacct cgacaccggc gcaagcaacc 1080 acatgtgcgg cgataaaagc atgttcgtgg agatcaatga agcggcaact ggcgatgtct 1140 catttggaga cgactcaaag ataccagtca aaggcaaagg taaaattctc atacgtttga 1200 agaatgggag tcatcaattc atatccaatg tctactatgt gcctaacatg aagaataata 1260 ttttgagctt gggacaatta ttagagaaag gctatgacat ccatttgaaa gaacatagtc 1320 ttttcttaag agattgtaga cataacttga ttgctaaggt gcctatgtca aagaatagaa 1380 tgttcctctt gaacattcaa aatgatgtgg caaagtgtct caaggcttgc tataccgact 1440 cttcgtggct atggcatcta cgattcgggc acctcaactt cgacggtcta gaacgtttag 1500 cgaagaagga gatggtgaga ggcttgccta gcatcaacca cccagaccaa ctttgcgaag 1560 gatgtctaat tgggaagcaa tttcgtaaaa gttttccaaa ggaatcaaca acaagagcaa 1620 caaagccgct agagctcata cacaccgatg tctgtggacc aatcaaaccc aattcatttg 1680 gtaagaataa gtactttctc ctctttattg atgattattc cagaaaaacc tgggtttatt 1740 tcttgaagga gaaatcagaa gtgtttgaaa actttaagaa gttcaaagcc ctcgtggaga 1800 aagaaagtgg tctttccatc aaggccatga gatctgatcg aggaggagag ttcacttcaa 1860 ataagttcaa caaatattgt gaagaccatg gaatccgtcg cccactgaca gtgccaagat 1920 cgccacaaca aaatggagta gcagagagaa agaaccrgac catacttaac atggtgcgaa 1980 gcatgctcaa gagcaagaag atgccgaagg agttttgggc tgaagcagtg gcatgtgcag 2040 tttacctaac aaaccgttcc ccaacaagaa gcgtgcatga gaagacacca caagaagcat 2100 ggagtggaag gaagcccggg atctctcacc tcaaagtgtt tggaagcatt gcctataccc 2160 atgttccaga cgaaaagagg acaaagctcg atgataaaag tgagaagtac gtgtttgtgg 2220 gttacgactc aagatccaag ggrtacaagc tctataatcc aaatagtaga aagatcgtca 2280 taagtcgcga cgtggagttc gacgaagaag attgttggga ttggagtgtt caagaagata 2340 agtatgattt tcttccttat tttgaagaag atgatgaaat tgaacaacca atcatagagg 2400 aacatattac accacctgcc tcaccgacac caaggctgga tgaaacaagt tcaagtgaga 2460 ggacaccgcg actaaggagc attgaagaga tttatgaggt aaccaaaaac ctaaacgaca 2520 ttaacctctt ttgtcttttt ggtgattgtg agcctctaag ctatcaagaa gcggcggaaa 2580 acataaagtg gaaagacgcc atggacgaag aaatcaagtc aatcacgaag aatgatacgt 2640 gggaacttac tacacttcca cgaggacaca aagcaatygg agtaagatgg gtgtacaagg 2700 caaagaagaa tgctaaagga gawgtggaga gatacaaagc aagattggtg gctaaaggct 2760 atagtcaaag acaaggaatt gactatgatg aggtatttgc tcctgttgct cgtcttgaaa 2820 ctattagact gatcatttct ttggcagccc aaaataaatg gaagatctat caaatggatg 2880 tgaagtcagc cttcttgaat ggttttctcg aagaagaagt ctatattgag caaccactgg 2940 gctatgaagt aaaagggcaa gaagaaaaag tcttgaagtt gaagaaggcg ttgtacggtc 3000 tcaagcaagc accgagagct tggaatgttc gaatcgacaa gtactttcaa gacaagaact 3060 tcatcaagtg tccatatgag catgcactct atatcaaagc gcaaagtgga gatattttga 3120 ttgtgtgttt gtatgtagat gacttgatct ttacagggaa caatccaagc atgttcgaag 3180 agttcaagaa agatatgtca aatgaatttg agatgacgga tatggggctc atggcatatt 3240 atctcggcat cgaagtaaaa caagaagaca aaggaatttt catcacccaa gaaggctatg 3300 ccaaagaagt ccttaagaag ttcaagatgg atgacgccaa tccagttggc accccgatgg 3360 aatgtggcag caagttgagc aagcatgaaa aaggagagaa tgtggatcca actctttaca 3420 aaagtttggt tggaagttta cgttacttga catgtacaag gccggatatt ctctatgctg 3480 taggagtagt aagtcgctac atggaagctc caaccacaac tcacttcaag gcggcaaaga 3540 gaatccttcg atacatcaaa ggtacaacaa actttggctt gcactattac tcttctgaca 3600 attataacat tgttggctat agtgatagcg attggagtgg agacttggat gatagaaaga 3660 gcactactgg ttttgtgttc tttatgggag atactgcttt cacttggatg tcaaagaagc 3720 aaccaatagt cacactatca acttgtgaag ccgagtatgt cgctgccaca tcatgcgttt 3780 gtcatgcaat ttggctaagg aacttgttga aagagttaaa aatgccacaa gaagaaccta 3840 tggaaatatg tgttgacaat aaatcagcac tcgctttggc aaagaatcca gtctttcatg 3900 aaagaagtaa gcacatcgac acccgttacc acttcataag agaatgcatt gagaagaagg 3960 aggtaaagtt gaagtatgtg atgtctcaag atcaagctgc cgacattttc acaaagccac 4020 tcaagttgga aactttcgtg aagctaagga gtatgcttgg agtcacaaat caagtttaag 4080 ggggga 4086 // ID Gypsy17-PTR_I repbase; DNA; EDCOT; 4627 BP. XX AC LG_XIV; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy17-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4627 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4627 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 312-312 (2007). XX DR Genome; LG_XIV; Positions 4332847 4337473. XX CC Positions [1975-2400] - Reverse transcriptase CC Positions [3544-4023] - Integrase core CC 'TAATG' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(37..1461,1465..4626) FT /product="Gypsy17-PTR_I_1p" FT /translation="MPPETRATDIKRIEDSIAAVAQDHGQKYELLVDMFKG FT QTLKIDQTIENQGGQINDIRNMMGTMAQQLEYTLQKISQASSSSSLSRDKQ FT SLHPDRADLRGKELREDRFATYKVHKPKHFFPTFHGEDVHKWLFKCTQYFE FT IEEVADSDKLQIASYYLDGVALYWHQNFLRSLEGQNTSWEEYVEAICYRFG FT GRKDPLEELMELRQHGDLEEYIQDFDILWNKAEINEKQALVIFLGGMELEI FT KNTVKMFDPKTLKHAFNLARLQANTLSYRKSPGYIRKTSTLCTNPTANTPL FT TFPQQNPRNPANSQANPSKPNSVQWTTNPNNNIYPNSSKPTKFIRNQEFEE FT RRLKGLCFWCDEKFVPGHRCRNKKVYSLSVVEEEEVYQEEEVEAEEAFSRE FT VTPHISLDALEGTVGLNTMKVNGKMEKTTVCILIDSGSTHNFLNSAVVRKL FT RYHLTPIKPMTVQAANGDKMVCKSMCKGLKKMQGISFQADVYIIDLSNCEM FT VLGIQWLSLLGDILCNYKHLWMSFDWQGQRVLLKGENPPKFQGIELKQLSA FT LVQSRQPGEDYLIYSLQLMEVEEVSQGHNPQFQGVTDTSLLTLLESYQDVF FT QEPQGLPPLRDHDHKIPLKTRSEAVNLRPYRYSGLQKDSLERMVTEMLDTG FT IIRTSNSPFASPVILVKKKDSTWRLCVDCRALNQLTIKDKYPIPMIEELLE FT ELVGDTIFSKIDLKSGYHQICMAVGEEFKTAFRTHSGHYEFLVMPFGLTNA FT PATFQSLMNEVFRKHLRKFILVFFDDILVYSQTMIDHYEHLAMVMQLLRTH FT QLVARATKCFFGHSQVEYLGHIITEHGVATDPLKIQAIVDWPIPQTLKQLR FT GFLGLTGYYRRFVKGYGNISKPLTLLLRKDTKGWNEEATHAFNNLKVLMTS FT APVLALPDFTKVFVVETDASLTGIGAILLQEGHPIAFISKSLGPKQQTLSV FT YEREMMAILHAVTKWKHYLWGRHFHIRTDHISLKYLLHQKLTTPAQHLWVV FT KLLGYDYDIEYKQGRENVPADALSRIPSQEIYALTTSTISTSLMEDIKSSY FT QNDPMIQTIIKDLLSSADSHPHYTWVHDHLNRKGKVVVGNNRAVRSQIIAL FT FHNSAVGGHSGMTVTSKTVSSLFYWKGQQKHIREHVRECTICQRNKHENVA FT SPGLLQPLPIPSAPFIDISMDFVEGLPKSEGKDVIMVIVDRFSKYAHCVAI FT SHPYAAPTIARAFMDNVYKLHGTPASITSDRDPVFLSRFWKELFNNQGVNL FT NHSTAYHPQTDGQTEVVNKCIEHYLRCMTGDCPHQWAKWLPLAEWWYNTNY FT HSATKMTPYEVLYGFPPPIHIPYFPRDSAVASVDEYLNTKEEVIKRVKAHL FT QLAQNRMITIANRKRSDRSFEIHDYVYLKLQPYRQQSTTYRSSQKLAAKYY FT GPYQVIAKMGTVAYKLELPSSSTIHPVFHVSQLKKHVGNQVVQQSLPITSP FT GPTLQPRAILDRRMTRQNNQAATQVLIHWAGLPPADATWEFTTELKLRFPT FT FNLEDKVGFMGEQ" XX SQ Sequence 4627 BP; 1414 A; 1000 C; 1041 G; 1172 T; 0 other; actggtatca gagccaacaa tcctcggatt tccaccatgc caccagagac gagagcaaca 60 gatatcaaac gcattgagga ctccatagca gctgtagctc aggaccacgg ccagaagtat 120 gagctgttag tcgacatgtt caaaggacag actctgaaga tagatcagac catcgagaat 180 caaggtggcc agattaatga cataaggaat atgatgggca ccatggcaca acaactggag 240 tatactctgc aaaagatttc ccaagcttcc agcagctcaa gtcttagcag agacaagcag 300 tctctgcatc ctgacagagc agatctcagg ggcaaagaat taagggagga tagatttgca 360 acctacaagg tacacaaacc aaaacacttc tttcccacct tccatgggga ggatgtacac 420 aagtggctgt ttaaatgtac acagtatttt gaaattgaag aggtagcaga ttctgacaaa 480 ttacaaatag cttcatacta tttggatgga gtggctttat actggcatca gaatttcttg 540 aggagtttgg aaggtcagaa tacatcctgg gaagagtatg ttgaagccat ttgttacagg 600 tttggtggta gaaaggatcc cctggaggag ttgatggagt tgaggcaaca tggagatctc 660 gaagagtata tccaagactt tgatatattg tggaacaagg ctgagatcaa tgagaaacaa 720 gctttggtga tctttttggg gggcatggaa cttgaaataa agaacacggt taaaatgttt 780 gatcctaaaa ccctcaaaca cgctttcaat ttagctagac tacaagctaa caccctctct 840 tatcgaaaat cccctggcta tattcgaaaa acttctaccc tgtgcactaa tcctactgcc 900 aatactcctc tcacctttcc acaacaaaac cccaggaacc ctgcaaactc tcaggccaat 960 ccctctaaac ccaactcagt tcaatggaca accaacccca acaacaatat atacccaaat 1020 tccagtaaac ctaccaaatt cattaggaat caggagtttg aggagagaag attgaaagga 1080 ctgtgtttct ggtgcgatga aaagtttgtg ccaggtcata ggtgtcgcaa caaaaaagtg 1140 tattccctca gtgtagtaga agaggaggag gtctaccaag aagaggaggt tgaagcagag 1200 gaagctttca gccgagaggt cacaccccac atttccttgg atgcgttgga aggaactgtg 1260 ggtctcaata caatgaaagt caatggaaaa atggaaaaaa ccacagtgtg catcttgatt 1320 gactcaggta gcacccataa tttcttaaac tcagcagtgg taaggaagct ccggtaccac 1380 ttgactccta tcaaaccgat gactgtgcag gcagctaatg gagataaaat ggtctgtaaa 1440 tccatgtgta agggtctcaa atgaaagatg cagggcataa gttttcaggc tgatgtttat 1500 atcattgacc tcagcaactg tgaaatggtc ctaggaatcc aatggctttc cttgctggga 1560 gacatacttt gcaattacaa acatctgtgg atgtcctttg actggcaagg gcaaagggta 1620 ttattgaagg gcgagaaccc acccaagttt caaggtatcg aattgaaaca attaagtgca 1680 ttggtccaga gtcgccaacc aggggaagat tacttaattt atagtttaca gctcatggaa 1740 gtagaagaag tttcccaggg tcacaaccca cagtttcagg gtgttacaga tacctccttg 1800 ttgactctgt tagaatccta ccaggatgtg ttccaggaac ctcaaggatt gccacccttg 1860 agagatcatg atcacaagat tcctctgaag acaaggagtg aagcagtgaa cctcagaccc 1920 tacagatatt cggggttaca aaaagacagt ttggagagga tggtgacaga aatgttggat 1980 actgggatca tcaggactag taatagtccg tttgcgtctc cagttatatt ggtgaagaaa 2040 aaggattcaa cctggcggtt atgtgtggac tgtcgtgctc taaatcaact cacgatcaaa 2100 gacaaatatc caattcccat gattgaggaa ttgctagaag agttggtcgg ggataccata 2160 ttttccaaga tagaccttaa atcgggatat catcagattt gtatggcagt aggagaagaa 2220 ttcaagactg catttcgcac ccacagtggc cattacgaat tcttggttat gccttttggg 2280 ttaaccaatg ccccagccac ttttcagagt ctcatgaatg aagttttcag gaaacacttg 2340 cgcaaattca ttttagtatt ctttgatgac atcctagtgt acagtcagac tatgattgat 2400 cactatgaac acctcgcgat ggttatgcaa ttattaagaa cacatcagct ggtggccaga 2460 gctaccaaat gcttttttgg tcattcgcag gtggaatatc taggccatat catcactgaa 2520 catggtgtgg caactgatcc tctcaagata caagccatag ttgattggcc tattccacaa 2580 actctaaaac agttgagggg atttttggga ttaactggtt attatcgcag gtttgttaag 2640 ggctacggca acatcagtaa acctttgaca ctgctactca ggaaggacac taaggggtgg 2700 aatgaggaag ctacgcacgc attcaataac ttgaaggtat tgatgacgag tgctcctgtc 2760 ctggctctgc ctgatttcac caaggtattt gtggtggaaa cagacgcctc attgacaggt 2820 ataggggcca ttttgttaca agaaggtcat cccattgctt tcattagcaa atccttaggg 2880 ccaaaacaac aaaccctctc agtttatgag agggaaatga tggcgatcct acatgccgtt 2940 accaaatgga agcattattt gtggggaagg cactttcata tccgtactga ccacatcagc 3000 cttaagtatt tgttacatca aaaactgact acaccagctc agcatctatg ggtggttaag 3060 ctcctgggtt atgactatga tattgaatac aaacaaggaa gggaaaatgt gccggctgat 3120 gcattgtcca gaattcccag ccaggaaatc tatgctttga ctacttccac aatatctacc 3180 agcttgatgg aggatattaa aagttcttat caaaatgatc ccatgattca gactattatc 3240 aaggacttac taagctctgc agactcccac cctcactata cttgggtgca tgaccatttg 3300 aacaggaaag gcaaggtggt ggtgggtaat aatagggcag tgcgtagtca gatcattgcc 3360 ttatttcaca actcagctgt gggtggccat tcgggcatga cggtgacatc taagaccgtg 3420 agcagcttat tctattggaa ggggcaacag aaacacatca gggagcatgt gcgtgagtgt 3480 accatttgcc agaggaacaa gcatgagaat gtggcaagtc ctggcctcct acaacccctg 3540 ccaatcccta gtgccccatt tattgatatt agcatggact ttgtggaagg cttacctaaa 3600 tcagagggaa aggatgtcat aatggtcata gtggatcgtt tcagtaaata tgctcactgt 3660 gtggccatca gtcatcccta tgcagctcct accattgcaa gagcatttat ggacaacgtc 3720 tacaaacttc atggcacacc agcttcaatt accagtgaca gagacccagt atttcttagc 3780 cggttctgga aagaactatt caacaatcaa ggagtcaact taaatcattc caccgcgtac 3840 catccacaaa cagatggcca gaccgaagtg gtgaacaagt gcattgaaca ttacctaagg 3900 tgcatgactg gggattgtcc acatcagtgg gcaaaatggt tgcctttagc cgaatggtgg 3960 tataacacca actaccattc agccaccaag atgactccct acgaagtgct atatggtttt 4020 cctcctccca ttcatattcc ctattttccc agggactcag cagtggcttc ggtggacgag 4080 tatttaaaca ctaaagagga ggtaattaaa agagtcaagg cacatctaca acttgcacag 4140 aacagaatga ttacgatcgc aaacaggaaa agaagtgatc gcagttttga aattcatgat 4200 tatgtatacc tcaaactaca accatacagg caacaatcca caacatacag atcatctcag 4260 aaactagcag ctaaatacta tgggccatac caggtgattg cgaaaatggg cacagtggcg 4320 tataagcttg agcttccatc ctcctccacg attcatcctg tgttccacgt ctctcaactc 4380 aagaagcatg tgggtaatca ggtggtgcaa caatcacttc cgattacatc tccaggtccc 4440 accttgcagc ctcgtgcgat tttggacaga cgaatgacta ggcaaaacaa tcaggcagcg 4500 acacaagttc ttattcattg ggcaggtctg ccacctgcag atgctacttg ggagttcacc 4560 actgaattga agctccgatt tccaacattc aaccttgagg acaaggttgg tttcatgggg 4620 gagcaat 4627 // ID GmGYPSY11_I repbase; DNA; EDCOT; 5176 BP. XX AC . XX DT 06-JUL-2009 (Rel. 14.07, Created) DT 05-JAN-2011 (Rel. 16.02, Last updated, Version 2) XX DE Gypsy-like retrotransposon from Glycine max, internal region. XX KW Gypsy; LTR Retrotransposon; Transposable Element; consensus; KW Medicago; soybean; Gypshan4; GmGYPSY11_I. XX NM GmGYPSY11_I. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-5176 RA Sobol A. and Laten H.M.; RT "GmGypsy11: Consensus sequence in Glycine max."; RL Repbase Reports 9(7), 1380-1380 (2009). XX DR [1] (Consensus) XX CC GmGYPSY11 is a consensus sequence related to Gypshan4 from CC Medicago truncatula.The GmGYPSY11 consensus sequence was CC generated based on an alignment of 13 full-length unannotated CC copies in Genbank. The gag-pol open reading frame extends into CC 196 bp into the 3' LTR (which is included). XX FH Key Location/Qualifiers FT CDS 593..5176 FT /product="GmGYPSY11_I_1p" FT /note="Gag-pol polyprotein: gag, protease, reverse FT transcriptase, ribonuclease H, integrase." FT /translation="MSGTNPNDGVGLSQFQMQALMQHLERLMKQRDDALHE FT RLDQMENRDHNEEERRRRGNDGVPRQNRIDGIKLNIPPFKGKNDPEAYLEW FT EMKIEHVFSCNNYEEDQKVKLAATEFSDYALVWWNKLQKERARNEEPMVDT FT WTEMKKIMRKRYVPASYSRDLKFKLQKLTQGNKGVEEYFKEMDVLMIQANI FT EEDEEVTMARFLNGLTNDIRDIVELQEFVEMDDLLHKAIQVEQQLKRKGVA FT KRSFTNFGSSSWKDKGKKDGAATSSSSTPIPSKTRSKSQEEPSKRSRDVKC FT FKCQGLGHYAYECPNKRSMVLRDGEYISESDVEEEEESEYVEEEETPEGDL FT LMIRRLLGGQLKHEEESQRENIFHTRCLINGKVCMVIIDGGSCTNVASARL FT VSKLNLATKPHPRPYKLQWLSKDGEVQVRQQVEVDVSIGKYNDKVLCDVVP FT MEASHLLLGRPWQFDKRANHDGYTNKISFMHQDKKIVLKPLSPQEVCEDQK FT KMREKLLQEKREKEKVSKTLESEKKRETLERKKSEQKKSETLEVRESYLAT FT KSEVKRLFRAKQSLYILFCKNQILTTNTFDDFEVPSSVKTLLQDFQDMFPP FT NVPSGLPPLRGIEHQIDLIPGASLPNRPAYRSNPQETKEIQRQVDELISKG FT WVRDSMSPCAVPVILVPKKDGTWRMCSDCRALNNITIKYRHPIPRLDDLLD FT ELHGACYFSKIDLKSGYNQIRIREGDEWKTAFKTKYGLYEWLVMPFGLTNA FT PSTFMRLMNHILREFIGKFVVVYFDDILIYSTSLDLHIDHLKSVLTVLREE FT QLYANLEKCIFCTNHVVFLGFVVSSKGVQVDEEKVRAIQEWPTPKSVTEVR FT SFHGLASFYRRFVKDFSTLAAPLNEVLKKNVGFKWGEKQEEAFNVLKQKLT FT NAPILALPNFQKSFEIECDASNVGIGAVLMQEGHPIAYFSEKLSGPTLNYS FT TYDKELYALVRALKTWQHYLYPKEFVIHSDHESLKYIKGQGKLNKRHAKWV FT EFLEQFPYVIKHKKGKGNIVADALSRRHALLSMLETKLIGLECLKSMYEND FT ETFGEIFKNCEKFSENGFFRHEGFLFKENKLCVPKCSTRNLLVCEAHEGGL FT MGHFGVQKTLETLQEHFYWPHMKKDVQKFCEHCIVCKKAKSKVKPHGLYTP FT LPIPEYPWIDLSMDFVLGLPKTSNGRDSIFVVVDRFSKMAHFIPCKKVDDA FT SHVADLFFKEIVRLHGLPRSIVSDRDSKFLSHFWRTLWSKLGTKLLFSTTC FT HPQTDGQTEVVNRTLGTLLRTVLRKNLKTWEACLPHVEFAYNRVVHSTTNC FT SPFEVVYGFNPLTPLDLLPMPNVSVFKHKEGQAKADYVKKLHERVKDQIER FT KNKSYAKQANKGRKKVVFEPGDWVWVHMRKERFPEQRKSKLQPRGDGPFQV FT LERINDNAYKVELPGEYNVSSTFNVSDLSLFDADGESDLRTNPSQEGENDE FT DMTKSKGKDPLEGLGGPMTRARARKAKEALQQVLSILFEYKPKFQGEKSKV FT VSCIMAQMEED*" XX SQ Sequence 5176 BP; 1665 A; 807 C; 1205 G; 1499 T; 0 other; tttggtatca gagctccggt tctaggatca acacttcctt tgctggaaat attgggtaac 60 atccttcttt attctctttg ccatttatat taccttctta ttcatatatt tttttttagg 120 ctgaaccatt gcaaaagtta agccttttga tctctttgtt ataaaaaaaa aaaaaagcag 180 aatttcgtat aagcaaaatt aaaaaaaaaa taaaattggg ctgaatggtt catgcttgaa 240 gaactttaaa aaaaaatctc tttaaggtaa tatattggtt gcatgaagga ttgttacttg 300 aattcctaaa ttctgaattt tatttccttc atttgtgcct aaaaacattg ttagcctttt 360 tcttggttaa ccttttcctt gtctctctag ccttacctta cacatattgg tgaattgttc 420 tttgttgtgg ccataatctc ttgaattgcc taagaactca aggggaatta gagtggtaaa 480 aggcaagagt gtttcattag agaaaagcca taattgtgtg atacacttga gtgggtgagg 540 tattcaaaca acaactataa ttgtcttgtt acgtttgatt tgtttgtttg agatgtcagg 600 tactaatcct aatgatggag tggggctttc gcaattccaa atgcaagctt tgatgcaaca 660 tttggagagg ttaatgaaac aacgagatga tgcgctccat gagaggttgg atcaaatgga 720 gaatagagat cataatgaag aagaaaggag gagaagaggg aatgatggtg ttcctagaca 780 aaaccgaatt gatggtatta aactcaacat tcctccattt aaaggaaaga atgatccgga 840 ggcctacttg gagtgggaga tgaaaataga gcatgttttc tcatgcaaca actatgagga 900 ggaccaaaag gtgaagcttg ccgccacgga gttttccgac tatgctcttg tgtggtggaa 960 caagctacaa aaggagagag caagaaatga agagccaatg gttgatacat ggacggagat 1020 gaaaaagatc atgaggaagc ggtatgtgcc ggctagttac tcaagggact tgaaattcaa 1080 gctccaaaaa ctaacccaag gcaacaaggg ggttgaggag tatttcaagg aaatggatgt 1140 gctcatgatt caagcaaata ttgaagaaga tgaggaggta actatggctc gatttcttaa 1200 tggtttgact aatgatatcc gtgatattgt tgagctgcag gagtttgttg aaatggatga 1260 tttgcttcac aaagcaatcc aagtagagca acaattaaaa aggaagggag tggctaagag 1320 gagttttacc aactttggtt cttctagttg gaaagacaaa ggtaagaaag atggggctgc 1380 tacttctagt agttccacac ctatcccatc aaaaactcgc tcaaagtccc aagaggaacc 1440 ctctaaaagg agtagagatg tgaagtgttt caagtgccaa ggcctaggac actatgctta 1500 tgagtgccct aacaaaaggt ccatggttct tagagatgga gaatatataa gtgaatctga 1560 tgttgaagag gaagaggaga gtgagtacgt agaggaagag gagactccgg agggagattt 1620 gttgatgatt aggcggttac ttggtggtca attgaagcat gaggaggaga gccaaagaga 1680 aaacatcttt cacactagat gtttaatcaa tggcaaggtg tgcatggtga tcattgatgg 1740 aggtagttgc accaatgtgg ctagtgctag attagtgtca aagctaaatt tagctactaa 1800 accacatcct aggccataca aacttcaatg gcttagtaag gatggggagg tgcaagtgag 1860 gcagcaagtt gaagtggacg tttccattgg gaaatacaat gataaggtac tttgtgatgt 1920 tgttcctatg gaggccagtc acttactttt ggggagacca tggcaatttg ataaaagagc 1980 caatcatgac ggttacacca acaagatctc tttcatgcac caagacaaaa agattgtgct 2040 caagccattg agtccacaag aagtgtgtga ggatcaaaag aaaatgagag aaaaacttct 2100 tcaagagaaa agagaaaaag aaaaagtgag caaaacactt gagagtgaga aaaagaggga 2160 aacacttgag aggaaaaaga gtgaacaaaa gaagagtgaa acacttgaag tgagggagag 2220 ctatttagcc acaaaaagtg aggtcaagag gttgtttcgt gctaaacagt cactatatat 2280 cttgttttgc aaaaatcaga ttttgaccac taacactttt gatgattttg aagtgccttc 2340 tagtgttaaa actcttttgc aggattttca agacatgttt ccaccaaatg tgccaagtgg 2400 actaccacct ttgaggggaa ttgagcatca aattgatctc attccgggag cttctttgcc 2460 caataggcca gcctatagaa gtaatccaca agaaaccaaa gagattcaaa gacaagtgga 2520 tgaactcatt agcaaaggtt gggtaagaga tagtatgagt ccttgtgctg tcccagtgat 2580 tttggtccct aaaaaggatg ggacatggcg catgtgttcc gattgtagag cccttaataa 2640 catcaccatt aaatataggc atcctatacc taggcttgat gatttgcttg atgaattgca 2700 tggtgcatgt tacttctcta aaatcgattt aaaaagtgga tacaatcaaa ttaggattag 2760 agaaggggat gaatggaaaa ctgcttttaa aacaaaatat ggtttgtatg aatggttggt 2820 tatgcctttt ggcctaacta acgctcctag cactttcatg agattaatga accatatctt 2880 gagagagttc ataggaaagt tcgttgtggt gtactttgat gatattctta tctatagcac 2940 ttcacttgat ttgcatattg atcatttaaa atctgtcttg actgtgctta gagaagaaca 3000 attgtatgcc aatcttgaaa aatgcatctt ttgtactaac catgttgtgt ttcttggttt 3060 tgttgtgagt tcaaaaggag tgcaagttga tgaggagaag gttagggcta ttcaagaatg 3120 gcctacacct aagtccgtga ccgaggtgag gagttttcat ggcttagcaa gtttttatag 3180 acgatttgtg aaggatttta gcacattggc agcacctctc aatgaagtgc tcaagaaaaa 3240 tgttggtttc aaatggggag agaaacaaga agaagctttc aatgttctta agcaaaagct 3300 aactaatgcc cccatacttg cgttgccaaa ctttcaaaaa tcttttgaaa ttgagtgtga 3360 tgcttcaaat gttgggattg gggctgtgtt gatgcaagaa ggccatccaa ttgcttattt 3420 tagtgaaaag ttaagtggtc ctacccttaa ctattcaact tatgataagg agttgtatgc 3480 cttagtacgg gctttgaaaa catggcaaca ctacctttat cccaaggaat ttgtcattca 3540 tagtgaccat gagtccctca aatatatcaa ggggcaaggc aagcttaaca aaaggcatgc 3600 gaagtgggtg gaattcctag agcaattccc ttatgttatc aaacataaaa agggaaaagg 3660 taatattgta gccgatgctc tttctcggcg tcatgcatta ctttctatgc ttgaaacaaa 3720 attgattggt cttgaatgtt tgaaaagcat gtatgaaaat gatgaaactt ttggagaaat 3780 ttttaaaaat tgtgaaaaat tttcagaaaa tggtttcttt agacatgaag gctttctttt 3840 caaagaaaac aaattgtgtg tgcctaaatg ttctactaga aatttgcttg tttgtgaagc 3900 acatgaagga ggtttaatgg ggcattttgg ggtccaaaag actctagaaa cattacaaga 3960 acatttttat tggcctcata tgaaaaagga tgtgcagaaa ttttgtgaac attgcattgt 4020 atgtaaaaag gcaaagtcta aggtaaagcc tcatggattg tatactccat tgccaattcc 4080 ggagtatcct tggattgatt tatccatgga ttttgttttg gggctgccaa aaacaagcaa 4140 tggtagagat tccatttttg tggttgttga taggttttct aaaatggctc attttattcc 4200 atgtaaaaaa gttgatgatg cttcccatgt ggctgatttg tttttcaagg agattgtgag 4260 actccatggt ttgccaagga gcattgttag tgatagggac tctaagttcc taagtcattt 4320 ttggaggact ttgtggagca agttgggcac taaattgtta ttttcaacca cttgtcaccc 4380 acaaaccgat gggcaaacgg aagttgttaa taggactttg ggaactttgc ttaggacagt 4440 tttgaggaag aacttaaaaa cttgggaagc ttgtttaccc catgttgaat ttgcttacaa 4500 tagagttgtt catagcacca ctaattgttc tccttttgaa gttgtttatg gttttaaccc 4560 actaactcct cttgatcttt tgcctatgcc taatgtttct gtttttaagc ataaagaagg 4620 tcaagcaaag gcggactatg tgaagaagct tcatgagaga gtcaaagatc aaattgagag 4680 gaaaaataaa agctatgcta aacaagccaa caaagggaga aagaaggttg tcttcgaacc 4740 cggagattgg gtttgggtgc acatgagaaa agaaaggttt ccggaacaaa ggaaatcaaa 4800 gcttcaacca aggggagatg gaccatttca agtgcttgaa agaatcaatg acaatgctta 4860 caaagttgag ctgcccggtg agtataatgt tagttccacc ttcaatgtct ctgatttatc 4920 tctttttgat gcagatggag aatccgattt gaggacaaat ccttctcaag agggagagaa 4980 tgatgaggac atgaccaaga gcaagggcaa ggatccactt gaaggacttg gaggacctat 5040 gacaagggct agagcaagga aagccaagga agctcttcaa caagtgttgt ccatactatt 5100 tgaatacaag cccaagtttc aaggagaaaa gtccaaggtt gtgagttgta tcatggccca 5160 aatggaggag gactaa 5176 // ID RTIP1_I repbase; DNA; EDCOT; 10281 BP. XX AC AB000394; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-JUL-2004 (Rel. 9.06, Last updated, Version 2) XX DE Ipomoea purpurea retrotransposon RTIP1_I, internal region. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-like internal region; RTIP1_I; internal portion. XX OS Ipomoea purpurea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea. XX RN [1] RP 1-10281 RA Hisatomi Y., Hanada K. and Iida S.; RT "The retrotransposon RTip1 is integrated into a novel type of RT minisatellite MiniSip1, in the genome of the common morning glory RT and carries another new type of minisatellite, MiniSip2."; RL Theor. Appl. Genet 95, 1049-1056 (1997). XX DR GenBank; AB000394; Positions 589 6352. XX SQ Sequence 10281 BP; 2680 A; 2740 C; 3027 G; 1834 T; 0 other; ctggcgccgt ctgtggggat cgaaacaaag agtcgcgtgc cttctgagca aagcgagtcc 60 gagagatcat cgagaagagt cctggtcgcg aggaattgaa agactttacc atgacaggaa 120 gccaagagca attgagccaa cgcaatgggc taggagccga cctaagagat caattgaatc 180 ggagaagcac ccaaagccgg gaaaacgatg caacaccgcc accaacacca caaataaata 240 cacagccgac tgcggtacca ctcaccccgg atcaactaca cgcaatagga cgcgctttcg 300 ccgaggcaag tcggggaata cgggagcaat ccgctactcg gataccgcaa caagaccccc 360 caccgccgcg aaggccggac aatcgacaat caacccgccg ggcggtgagt caacccgtcc 420 agtccgttca ttctcggcta ggccctggtg tcgagcgacg gtcggcgaga aaacggctgg 480 gacgaagaga accctccgcg ctcctgtaga acccacggtc ggcagaccgc acgtgagctt 540 aaccgtgcgg ggaaaggctg gacggttgtt cgccgcgtgg agcagcccgc ccgagaccat 600 aaccaacccg ccgagtcaga ggttggcgaa agcgcggaat cgacaggaaa ccacacccaa 660 gagagggtcg aaatggccaa cctagcccaa gaggtgagaa atctgaaaga acaggtagaa 720 ggaagaacca aggcccccgg acgagcactg ctaaccgcgt tacccttctc cgctgagatc 780 atggccttta agttaccggg cgactttaag ttcccggagc aagccacgtt cgacggatca 840 ggcgacccgc gagaacatct actgagttta ccaagctaag atgcaagtcc taggggtacg 900 ggatccggtc atgtgccgtg ccttcttacc cacgctgaag gggtccgccc aaaggtggct 960 tgtgggacag cccccagggt cgattcacag cttcgaggag ttggcagacc gcttcatgag 1020 ccactatgcc gctaacatca agccacagaa ggatctgaca cacttaggcg acatccatca 1080 ggatgagggc gagtccttaa aagcctatct agctcgctgg taaaaggaga tccagtcgat 1140 agaagaagtg gaggaccaaa cagcgctcac cttcttcatt gaatctttgc ggtccggaca 1200 gctgtatcga gacctaaggg acaaccgccc ggcaacatac gcggaagcta tccagatggc 1260 caacaagagg gccaacacag agcaggctat gaagcataaa cggtagcgcg aggtcggcgg 1320 gtccgcagcg gaaaaaggac gcgggccgag acgagagaaa ggcgctcgga tgtagcccgg 1380 gaccagaggt caggcgaccg tatgaccgcc tcgtcgttca cacctatcga ccggttccag 1440 agcgaccggt ccacgaagta caagcagtcg ccccgcctcc gcctccgccg attgacgacc 1500 gttcagcgat gaggatactg gtaagacttc taaataatgt cgctatcaca aatcttatac 1560 tcacagcacg gaagaatgct tttatctaaa caagatcatg gaggggatca tccagcaagg 1620 gacgccgccc cctaaccaat ggaagcgaag gtcgaccagt cgaggagacg aggggctttc 1680 cgccgacgga gaaaacagcc gaggcaagca gccggcttcc gaggaggacg aagcccaatg 1740 gcgccagaag ccagtcatta acatgatagt cggcgggcca gagggcggcg atttcgcgaa 1800 cacccgaaaa gcctgggctc gacaactata tgtcggaaca gtctatggcc gagaggagag 1860 ctccaaaaag atatgccggg agcccatcgt gttcaccgat aaggacctgc cagccgggga 1920 aacccgcatc gagacgcgtt ggtcatcgcc atggacatca acggtgtggt cgttcgccga 1980 atcctggtcg acaccgggag cagcgtcaac gtactgtacc tagagacctt taccaagatg 2040 gggctgaccc gagaacagct cagaccagtg aacacccctc tcgccggctt caccagggac 2100 tcggtggagg cggaagggtc catcactctc cctgtggaga tcggcagcta tccggacgta 2160 caaaagctga gcatgaagtt tatcgtggtc gatctagctt gctcacacaa cgccatactc 2220 ggccgcccgg gtttggaaga cctcggggcc ctgatctcaa tcgaacatct atgcctgaag 2280 tttcgcacgc cgaacggaat aggaacggtg cgttgtgacc gcaaggtcgc ccgcgactgc 2340 tatctacaag cgtgtagagg aatgggcaag cgtggaatgc aggtccacga gatcaccaag 2400 aggcccccta agaaaacagt gatacctcgc ccagagccgg ccgtcgagct agaggaaatt 2460 gagattgacc cagcacagcc gagcaggcga gtgagaattg gagtcggcct ttcggagaag 2520 ttaaaggggg aaatcatgaa agtgctccaa gagcacaggc tggtttttca cctggggccc 2580 agaagatatg cccggcgtgg atcgatcgat cgtatcgcat cgactcgccg tagacccaga 2640 gcaccggccg gtcgtgcaaa agaaacggta cttggccaac gaccggaggg agtttgtgaa 2700 gaaagaagtt agcacgctgc taacagccgg gcacgtccgt gaggttaagt acccggaatg 2760 gttggctaac gtggtcctcg tgcccaagcc cccgacgtgg cgaatgtgtg tagactacac 2820 tgatcttaac aaagcatgcc caaaagatcc atttcctctg ccccgaatcg accagttagt 2880 cgacgagacg gccgggtcgg cgctgctcag ttttatggac gccttcagag ggtaccatca 2940 aatattcatg cacccggcgg atgaggagaa gaccgccttc ctgactccgg acggagttta 3000 ttgctatcga gtcatgccat tcggactcaa aaatgccggg gctacgtaca cccgaatggt 3060 tgcccggttg tccaccacct gctaggaaaa tcgatggccg catacgtcga cgacatgctc 3120 gtcaagagtc gagaggagga caagcacgcg gaagatttag ccgactgctt taaagtaatg 3180 ataaagtaca acctccgact gaaccccaag aagtgtgcat tcgccgtcca gggtggtaag 3240 ttcttgggct acatggtcac caagcgaggc attgagccta acacagagaa agtacaagtc 3300 atcctcgaca tgcagcctcc tactactatc aaggacctac aacgcttgac cggacgactg 3360 gctgctctca gccgttacct gagcaaatcg gcggataaaa ctgtgccttt cttcgaagcc 3420 atgaagaaga aagagggatt cgctggacta ccgagtgcca acagtcgttc gaggaattaa 3480 aacaatatct gtcgactccc ccagtactgt ctacccccca ggagggcgag cccttactgt 3540 tgtacctcgc cgcctcggcc aaagcggtaa gctcggtgtt ggtttgagag gaggaccgag 3600 ttcagcaccc ggtttactat gtaagccgtt cactgaaagc tgctgagaca cggtacaccg 3660 tcctggaaaa gatcgtgtat gccttggtag tcaccgtgcg caagttggcg ccttacttcc 3720 aagcccatac cgtccgggtc tgacggatca gccactcggg agtgtgctac ggaacccctt 3780 gtcctccggc cggctggtaa agtgggccgt cgagttgact cagtacggga tcgagtacca 3840 acccaggcct tccatcaaag gccaagcttt ggccgacttc ctggtcgagt gtaccgcgag 3900 tgaggaagag aaggaacacg cctcggagag caatccgggc gagtggtggg agatgcatgc 3960 ggatggagca tcgagtcgac agcactgcgg aggcggcgtc atgctcatca ctccggaggg 4020 atttcggctg tattacgccc taagatacct gttctctgca tcaaataacg aggccgaata 4080 cgaagcagta ttgaacggcc tccgactcgc caagaaccta ggagtcgaat ggctacgaat 4140 caaaaccgac tcccgactgg tagtcggaca gatctcgggt acgtgcgaag taaggaacgc 4200 gagaatggcg ttgtacaaag aatgtgccac caagatgttg aaggggtttg aagcttatga 4260 aatagaatac atatcccggg cggacaatgt agaggctgac atcttgtcta aaatcgccct 4320 gaagggggtg ccggaccact taataagaat ttgccagaag gaagaactaa gttggccgag 4380 tatcgaagag gcgccgctag atgtccagca agtaaacatc ggagggtggg atcgagagaa 4440 aaaccctgag atgttctgga tagacgacat ctgacgattc aaggaaacgg gcgagttgcc 4500 aactgaccca gcagtcgccg caagggttcg gcggaaagcc ccttccttcc ggattgtcga 4560 cggacagcta tataaacagt cgttcggagg acccttgctg aaatgcctgc ttaggcctga 4620 ggccgagaag gtaatggatg aagctcatag gggcattttt gctgcgcacc agggtgctca 4680 cacgctcgcc cgaaaattgg tcgttcaagg gtattactgg ccgaccatga tgcgagactg 4740 tattgaaagg atgtccaaat gtggcgtttg tcaggcattc gccaggaaag acactcggcc 4800 ggccaccttc tatacaccgg tcaccactgc cattcccttc gccaaatggg gaatagacct 4860 gttgggacca ttacccgtcg ccccgggagg attgaagttt tgcgtcgtgg ccatcgatta 4920 cttcaccaag tgggtcgagg cggagcccct ggctaccatc accgagtacc agtgtcgacg 4980 ttttctgtgg aaaaaggtga tctgtcgctt cggtttgccc gaacacatcg tcagcgataa 5040 cgggcgacag tttgactgcc agcattcgcc gaattctgcc gccgacacgg tatcaagcat 5100 accaaggtgt cggtggccta cccccaagca aatgggcagg ttgagaatgt gaatcgaacc 5160 ttggtcgatg ggatccagaa gaaactcgag gacattcgag gaaactgggc ggacgagctt 5220 gatcgagtcc tatgggctta tcgcactacc cagcggtgag cgacgggaga gagtccgttc 5280 tcgctcgcat acggctttga ggccaaggtt ccagtcgaag tggtcgaacc cacccaccgg 5340 gttcgcacct actcggacgc agcgaatgaa gagaacctgc aaattgagaa aaaatttcta 5400 gaggaaagaa gggaagtcgc gagtccacga atggttgagt accagcaggc ggtgaaaaga 5460 taccgcgacc gtagaactcg cccgcgaacc ttccaggttg gcgacctagt gctacgagat 5520 cgacaagcca gccagcctac tgaaggaggc aagctcgcgg tcaagtggga agggccgtac 5580 cgcatcacgg ctgtagtcca ggccggaact tacaaattag agattatgga aggcaagctt 5640 atagatcgta tatggaatgc tactcatttg aaaaggttct atcagtagcc aatgataggt 5700 catgtatgag ctcgaggatt ccaagaaatc tgaataaagt gcatgggtta cagccaatcg 5760 tcccaggaac tcggcgagga aaaagtgagg ttcaaagcct tagaagaatg ccaatattaa 5820 aagaactcaa agacaaattc cgtgaaaaga gaaggaaaaa ctgtttttta ttaaaataag 5880 gccgataagg aggccagccc ttacaaaagg agggtctatt ctaaaagacc ctaggctact 5940 ggggaggggg tgtcgatggc gaccccttca acttgcgccc ccgccgatgg tccagcaagg 6000 ggaacagagg aagggtcctc cgcctgagga gaagactcgg cgagctctgg agcgtcgccg 6060 caggaagagt cgccgggtca gtaggcgcag ccggcccatc agcgtccagc accggcttga 6120 gaccccagct ctcgggaatg aacgaggagt cgcgagccaa caaggtggcg tgaatctcca 6180 tctgcgcctc gcggaaaccg aggcggtaat cccgctcgcc caggtctaag aggaaatcat 6240 cgccttggga tcggcagcca ctccttggcc acctctctcc tccgagctgc caccgctgcc 6300 tgcacatccg cctcgaaggc cgccgacttc gtgtaatctt cgacagaagt cgcggcgatc 6360 gtggccgctc tatccctctc ctcctcccac tgacgggtga ccctcagcaa ctcggcattg 6420 tgcacctcca ccatcttgag ttcttcgcct gctcttccag gaaagcttcc tctgtctggc 6480 gcacttcgcg accatggccc gcatatcatt cctaaagccc tggaaccgat tgcccagttc 6540 catctggagg gtgaggtcct gcacaccaaa ccgtcagtcg aacggaaaag agaaaagtaa 6600 acagagggaa aggtcgaatg aataacactt acgcgatacg actgccggag caaggcctcg 6660 atgatgaacc cgtcgccgag agcatgggtc gactccacat cttttggcag gaggacatcc 6720 ttgcacactt gcgaatggag gtgttgccca tccagatttg ggcgtcctca tccacctcgt 6780 ggcacagcct gatcctcttc ggagtcggcc cctccgtatg ctcagcagac cgcttagaac 6840 tcggactctc agtagaagga ggaggcggct gccgactggg cgataccacg ggcgagggtg 6900 tgaggtcgac cacgttgtga gaaggtggag gagtcggccg aaccaccgac gacggctgag 6960 aagaggacgc ggcggcagca ccggtggagc gttgcgtcaa gcgacgcctc atctttttcg 7020 ctctatctgc catctcagga gtcggtgcga ttgcctcgtc ggagctggag gagtcggaat 7080 cgtacgggcc tgtaaaagaa acccactcac ttgtgagtgt tcccgcatga agtaagaagc 7140 aagtcgagaa agagatgaaa aagacgctac ctatggtggc ggcgcctccg gcagaaggcc 7200 atgcttggcc atgggccgga cccggaccag tacttgaccg agtatggccc caggcccttc 7260 aagaagtcgc cgcccttgac agcatcctcc gtaaagacgg cgctccgaga gcaaggcttg 7320 aagagagtcg ccggccatag ggtcggaaag gtgaaggaag aagagcgagg tcggacgaag 7380 aaataaaggg gcttccactc ttttatcgtg tcggacaacc cctcgaaaag ttgccgcccc 7440 ggacgggcag cgacttggat gaagccgggc gagtgagagc cgaccttgtt cacggtgaag 7500 aggtaccgga acaggtccaa atctggctcg cactgccacc aatggcagag aattgatgaa 7560 gctggtgagg agtcggtgag agttaggcac taactggccc gggaccaagt tatagtgccg 7620 aaagagaagc gaaagaaatg ggtgtggggg cactcggaag ccgaatgcaa ccgactgcag 7680 gtggataccc acaaaaccct ccggcgggtc gtggatatgc cggctctccg ccgcgacgac 7740 cagggctgaa gggccaagca gaaagcgggc catgtccagg tccgccgctg ttgcagacga 7800 cggaagaccg gacggcggac aaccgagtca aacttgcctc gcggccgttc aacaccgtcc 7860 ggcaaagcgc caccgtggtc aacggggctg ggctcatcgg ggtggccgcc cagaagaaga 7920 aggggttaag aatgaagaag agagacaccg cctggaagcc cgccggcatt tccaggcggc 7980 ggacgacgga agaagaagga gaggacgtcg gttgtcaaaa gacggccgac gggtggaaga 8040 agaatgagaa gaggaaggca ttacttacag attggagttg aggctgagaa gacgatgaag 8100 gagcagaagc ttggtgggag aattgaagaa gaagaatgga aggaaggggc tttttaaaga 8160 gagaaagaag tccaagaggc tgccacgcgg cgcctcctca gtggaggaat cggaggcgac 8220 aagacgtcga agggacgccg catttaatac ctcgataggc ggggcgacgg ttcaggccta 8280 gggctagcct gcaagcggcg cgtctaccct aggccgagcc tgagttacgg tgacccggcc 8340 tgctaggcaa aggccatcaa ggcgaaagct atgggggccc atcaagatca tgctggaagt 8400 ttctagaagt gacccagctg ggtccggcca aattgggatg ccggacgagc ttcaggtcgc 8460 aaggtcggcc gacggatttg tcgagtcctt catccacaag gattagtcgg gcagagtcta 8520 caagccggtc atgacgacca agagtcggcc aaaggaacac gcaaaaccaa gaaccaaaaa 8580 gtaaaaacgt gattttattc cataaagaca ggggtacaag gccgaggact cggccacaag 8640 cattacaaag aaaagacggg cctagggctt agcttcctcc tcctccgcgt gacgcatcgg 8700 ctgcggaccc tccaggtagt agtgggggcg gaaaggcagg ggactcggct caggctcggg 8760 ctcgggcagt tcgtccagat acacggcagg cttcccatca acaaccatcc gcaggggtct 8820 ctccagagca ctcggcgaca tggccacgcc aaaaagcgga ggagcctccc agtctaggtc 8880 ctcctccggc tccgggtcct ctaccatggg ctccatctcg tcctcctccg gctccacgat 8940 catcaggtca agcatgtcag gaggcaccac gatgggatca gaagtggagt cgcccaccaa 9000 gtgccctccg ttagccgctc tcttccgcca gagctcctcc agccgggcat gctccttatt 9060 gcggatggac caacgacgat caccgtccct gaaactcata gcttgaggtt ttgaaatgtg 9120 aaatggtgag aaaacacaga gctaccaaga gcccttatat agagcctcga gagggcaacg 9180 accgagcgca aatcacggag ggaatcgtaa ctgacataac tgagccagat tggatgggca 9240 gcgcgaatct ctgtcagaga ttaatcccat ccaattagct cggaagggtg agattcgcac 9300 gctaaactga aaaagcctag ctcgccctgg gaagcgagat tttacaggtg tcaagcggag 9360 ggaggactcg acattgcggc caactcctca accattcaga cgggcgaatg cgctgaatat 9420 accaaaaaaa aagatgaaaa cagaaggccg agaatatttt attataagat aagaaggtgc 9480 aggttacaag gagcttatta cagagtaagc aagtgctcct aaaagaacta cccctctaga 9540 gtatccagcc gaccccagtc cacaagatca ctcacccggc gaagaggagt cgcttccaaa 9600 gaaccctccc gatggtccag gaggggaggg gcaaagcgag tcccagaacg ccggcatgag 9660 tggtggcaca accagttctt cgtcgtccgg gtacatttcc tgatagcgag caaagtcttc 9720 ctcgttcatt agccccgtaa ccggaccgtc caagtcatcc agaggaatag aaaaggtcat 9780 acggaaggtc agttgctctg ggacaggcac gtcaacaacg gtaccgccta gggaagttac 9840 tcgagcagtc ccggaggggg agaagggcga gaagtcggag cgacttcacg acgagcagga 9900 gtcggcggat gaagagccat ggaggcagcg ccaacaggtg atctctgtgg agtcggacgg 9960 ggagccttct ttttgggctc cctctcaggc cgagtccgtt tcgaatgcaa ggggcgccag 10020 ggcgacccaa agtcaatccg cttccctttc aatggtgagc gacccatgag gaattagtaa 10080 gttaagagaa gaacggccaa ggtcatttat aggtgccagg ccagggcgag gagatcagaa 10140 cggtcccgcg agatccggga gatagcgaat aatctggacc aatcctgagt cattcatggt 10200 agggattcgg tgagcaggag acggttacta cttttccaaa cccaggttgg tggaccgggt 10260 atggaaaagt gagggactag t 10281 // ID Copia-5_Mad-LTR repbase; DNA; EDCOT; 276 BP. XX AC ACYM01007529; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-5_Mad-I; KW Copia-5_Mad-LTR; Copia-5_Mad_. XX NM Copia-5_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-276 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1345-1345 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01007529; Positions 3774 3499. XX SQ Sequence 276 BP; 91 A; 51 C; 39 G; 95 T; 0 other; tgatagacaa gatggagaca atcatgctca tcaggccacg aaatcatctg tccaatagat 60 gatttcgtga tcatactcat ttgccttatt aagatccctg attttatgta aatattgatt 120 tgtagaatct ttccttatgc aaattgtcaa agcttgtaaa ccctctgtaa aactgtataa 180 atacaatata atgagatcaa ttgaagacat ccaaaatttc aaacaaaaac ctgtgcgtgt 240 tctttatgtt attcccttgc actgtttaat ctttca 276 // ID ENSPM1_VV repbase; DNA; EDCOT; 6087 BP. XX AC AM429952; XX DT 22-AUG-2007 (Rel. 12.08, Created) DT 22-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE DNA transposon from Vitis vinifera. XX KW EnSpm; DNA transposon; Transposable Element; ENSPM1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6087 RA Obukhanych T. and Jurka J.; RT "ENSPM1_VV."; RL Repbase Reports 7(8), 669-669 (2007). XX DR EMBL/GenBank/DDBJ; AM429952; Positions 1481 7567. XX SQ Sequence 6087 BP; 2037 A; 911 C; 1138 G; 1982 T; 19 other; atcactacaa gaaataggat ttttggtgac ggttccaacc gtcaccaaat cttatatatc 60 cgtaaccaaa acctattgtc acggtcttat gaaaccgtga ccaagcgtca cagtatgagg 120 cgtagctaaa agtattggtc acggtttcct aagtgatcgt gaccatatga tttccttttt 180 tgtgacggcc atacaaaaac tgtgacaaaa aaagttaaga atactttgct acttattaag 240 ttgatttagt cacgatcagg taataaaccg tgaccaaatg taatcttatg gtcacggtca 300 atgtccttga ccgtgactaa atgtaacctt atggtcacgg ttaatgcccc tgaccgtgac 360 taaatgtaac cttgtggtca cggtcagtgt ccctgaccgt gactaaatgt aaccttatgg 420 tcacggtcag tgtccctgac cgtgactaaa tgtaacctta tggtcacggt cactgtccct 480 gaccgtgact aaatgtaacc ttatagtcac ggtcagtcat cgtcgatttt tgccaattga 540 tcatagattt cgacgtgata aaaagtcctt tratggaaat gaagagcata gagcagcacc 600 taaacaattg tctggggaag atgtcctaca tcaattagat ggaatggaac atattacttt 660 agggaagaca tcaaaaaata agatgtcagc aaaaagaaaa agagaacatg ttgaacttga 720 gcataattgg aaaaaaaaaa aaagcatatt tttccaattg ccatattgga aaaccctcat 780 tttacgtcac aatttggatg taatgcatat tgaaaagaat atatgtaaca gtatagttgg 840 caccttgttg agtattgatg gtaaatcgaa agataacttc aatagtcgtc ttgacttgca 900 agctatgggt atcagagatc aacttcaccc catacaaaga gggaataggg ttatattgcc 960 tgctgcatgc tattcactaa cttcaaatga aaaaaaggaa ttctgtaaat ttttgaaaga 1020 agtaaaggtt ctagatggtt atgcttctaa catctctcgg tgtgtacaag tgaatgaaag 1080 aaagatattt ggattgaagt ctcatgattg tcatgttctc atgcaacaac tccttccact 1140 tgcaattcga ggagttctac ataagaatgt ttgtgctgtt atagttgaac tatgtagttt 1200 cttcaaacag ttgtgttcta aagtgttaaa gactgatcaa ttggagcact ttgagaatga 1260 cataatagtc acactttgca aattagaaag aatatttcct ccatcattct ttgatgttat 1320 ggtgcattta tctattcatc ttgcaagtga ggcaaaggtt gctggaccag tgcaatatcg 1380 atggatgtat cctatcgagc ggtatgttct cattcaatta atcttatgga tattaggttt 1440 catatagttc atgaaacaaa tctatcatat tgtgaaatga caggtattta cgtacattaa 1500 agtcttatgt ccgtaataag agtcgtccag aaggttctat tgcagagagg tacatagcag 1560 aagaatgtac aaccttttgc tcaagatatt tgcatgatgt tgaaacgaag catgaccatg 1620 aagaaagaaa ttatgtcatt gaaaataaca taacaaatgg tggagggtta accattttca 1680 aatgcatggg acgtacaata gggaagtcaa catctcgtgt tcttagcaca gaagaatggt 1740 cccaagcaca tttatatgtg ttgactaatt gtgaggaagt gacgtcattt attgagtaag 1800 acacttattt gaataaaact ttatactaat tctcatacaa aaatttaatt ttggtctttg 1860 tgagcattat aattaatttt ttctttttta tcagagagca taagcaatct ataagggtta 1920 agcctcgtat tcgtgcacga gatgtagatt tgattctcac aagagaattc attagttggt 1980 ttgaagaacg tgtaagttca ttcactacat aaattgttct attatctaat acacatgtat 2040 gtattaacat cttatatttg aatctataga ttatacaaat gcgacatgaa ggtccaattt 2100 ctgaacacat actatcattg tctcgtggac caagtacatc agttacatgt tataaaggat 2160 acatcattaa tgggttcaga tttcacacaa gagaacgaga aaaggggaaa aaaactcaaa 2220 atagtggagt tgttgtgacc gcagaggtat caagctttgc aagtgcaaga tataagaacc 2280 caattcctgg tcatgtttct tactatggtg tgctaactga tgtaattgag ttacattacc 2340 ttggtggaaa tagagttatt ttattcaagt gtgactggtg ggatgtaatc aatagtggaa 2400 ggggaataaa aaaggatgaa tatgggttca cgtgtttgaa ttttgaacgt accatatgca 2460 tagatgagcc atttgtgctt gcatctcaag caaaacaagt cttctatgtt caaaattcaa 2520 atgaggaaaa ttggcacacc rttgtagaga tacaaactcg aggggtttat gatatgaata 2580 agaaagtatc tactaatgat ccagagccat atcaacagtt tataacacct catagtcaac 2640 gtgatgtgca tgagttggcc gagaatgatt taatcaattg ggatagaart gatattgcag 2700 gagaaactat ccaaacagat gttctactat cacgacaaga aaacattgtt gaaagacata 2760 atgaatttat tcaggatgat gtgtagctaa taatattggt aagtacataa atatatactt 2820 acaaaatata caaattgtaa tttatttcat attatttttg taacttattt tgtattactt 2880 tttctaattt actttattat gtaggaaatg tcacatcgaa gaggaagagt acaaatagtg 2940 tctccagaag atgagttgga caatctacaa ctcttagaca tacaacctgc tgcaactact 3000 actcctagta gttctgatcc ttccgattct tcagatcctt cagttgttgg tatgattaag 3060 aaaattatgt ttaactttac atatgataaa tttacatatg tttaatttct tgaatgatag 3120 gtttttaatg tttaatttta tataagataa gtaaattatg tttcttttaa tttcattatt 3180 actcttaata ggttcatcct ctagcaaaaa gaggacacgt ggcccaacac gtaacttaga 3240 tttacttagt atgaaacctg gggaaaaaaa aactacaaga ttcaatacca gagggcaagt 3300 tgtttatgat ggaaaagggg aaagattgtc aagctatatg ggaacattgg tgcgatctca 3360 acacaatgtg cccatccaag ttcaagattg gaatcatgtt agtgaagatg tgaaggaaaa 3420 gatttgggcc ttagtattgg tatatgctag ttactattca atctaaattg taatgttatt 3480 gtttaaaaat gatacctctt atttatacat gacattttaa tgcaatacag gaaaaatatg 3540 aactagaaga aacatgtaag agctacattc ttcaatgttg tggaaatttg tttagaagct 3600 atagaaataa aatgaaggcc aagtattata acccttataa tacagatgag gagagattgt 3660 gtcatcgacc tccacactta tcagatgatg attggaggtg gctcatccac ttttggggta 3720 cacctgargc caaggtaaag ataatgatmt tttcttrata atgtatstta tgatactcat 3780 attcacataa aatkatattt attagttata tctaacmtaa yacttcatrt atataacttt 3840 tattatgttt ctattaccta tataggtgac ttgctatttt ttaattgatg taggatatct 3900 cataaaaaaa aacaaggcaa atagggcaaa gcaagtgata aagcatacat cgggatcaaa 3960 aggttatgct caaattcgat atgaacaggt tggaaattta ttattaatat gatttgtttg 4020 tacataaata attcatcata aataactcaa ttgttttact tgtaagaata ggcacaaaag 4080 aaggaggatc gaagtgagcc caatagaatt gagatgtttg ccttgacaca cataagaaaa 4140 gatgggaygc ctgttgatga tcattctaag gagattatgg taatgaagta aataaatttt 4200 atatacttgt atttcaatca tagccacata ctaaattatt ttaaaagtct aacaattttt 4260 tttttttttt tataattcca ggatcaattt cagcaaattt actatcccaa cctgaakgga 4320 catctttctt ctacttctgc atcatttgga gcatctacat ctgtatcatc tacatctgta 4380 gcatctacat ctatagcata tacatatgta gatgagatat atactcaagt catgggtcya 4440 gagaggcatg gtcgtgttcg agggtatgga tttggtcctm ctcctacctc agtctttggt 4500 tctactagta gaaggygatc aggagctatt ctttcaacac aacttsaaaa cgcccaagag 4560 atgctaatag ctgcagaaca aaagtttaca actrcaactg aagaactctc aaatgtgaaa 4620 gasgaactct cacatgtgaa agaaacattt gaagagaggt tgatagaagt tcaaaggaac 4680 acacgagaag aagtgaaaga aaagtttgaa gaaaaaatta tggaaatgca aagaaaaatg 4740 caagtacaaa tgcaagcaca aattcaagaa cagataatgc aaatgatgca acaattttag 4800 caaaagcagt agaaatttga agattttgct acatctttat atgatagatt ctcttaactt 4860 tttttaagat tatgctactt atttatatga tagattctcc taactttttt tgctttctat 4920 gactattatg tgatgtttgg ttggttgatt tgttatatta tgttagaatg tcaaactaaa 4980 tttgaatttc tttgttcttt gtttgttttt tttttttttt ggttatatta tgtttgtttt 5040 atttaatgac ttatattgat atataagttt ttaactagct tgggataatt gattgtaata 5100 tattaaaatt gttttaattg cttaattgca tatacaggtc taaaatgggt ttgtttgggt 5160 ttataacagg tttgggaaat ttgaatttat aaaaaattaa tgtccaaata taacaaattt 5220 tagtcacgac cactaaaaaa ttgtgaccat aaatgtactt ttagtcatgg tcagtaatga 5280 atcgtcacca aaatttgggg aaggcagcca tcatatgatt aatttcagtc acggtcatta 5340 aaagtcgtga ccgtgtacat tttgtcataa tagacctaat gattagtcac agtcacttaa 5400 ttactatgac catataccta catttagtca tgattaatga attgattgtg accatacaat 5460 ccatttagtc acgattaggg gcattgaccg tgactaaatg tatgtctata gtcacggtta 5520 agggcattga ccgtgactaa aatgtatgtc tatagtcatg gttaggggca ttgaccgtga 5580 ttaaatgtat gtctatagtc acggttaggg gcattgaccg tgactaaatg tatgtttata 5640 ctcacggtta ggggcattga tcgtgactaa aatgtatgtc tatagtcacg gttaggggca 5700 ttgatcgtga ctaaatgtat gtttatactc acggttaggg gcattgactg tgactaaaat 5760 gtatgtctat agtcacgatt agggcattga ccgtgactaa atgtatgtct ttagtcacgg 5820 ttagggcatt gaccgtgact aaaccaactt aataaatagc aaagtattct taactttttg 5880 gtcacagttt ttgtatgact gtcacaaaaa aagaaatcat atggtcacga tcacttagga 5940 aaccatgacc aaaactttta gctacgcctc atactgtgac actcgatcac ggtttcataa 6000 gactgtgaca ataggttttg gtcacggata tataagattt ggtgacagtt ggggaccgtc 6060 accaaaaatc ctatttcttg tagtgat 6087 // ID Gypsy12-PTR_LTR repbase; DNA; EDCOT; 643 BP. XX AC scaffold_214; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy12-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-643 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-643 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 303-303 (2007). XX DR Genome; scaffold_214; Positions 215990 216632. XX SQ Sequence 643 BP; 229 A; 112 C; 149 G; 153 T; 0 other; tgtaacagtc ccggcagcgc ctaaaggagc aagatcaagt tgaggccggg ggaagaaatg 60 aaggaggcgt atgggagaag acttacctgc agcaaagaaa gaaagtgagc aagtgtaggg 120 tcaagattag aaaagaagaa cttacgtgga tggctgagat gatgaactcc tgcagctgac 180 agctggcaaa ggcgtaaatc ccaaatgcaa aacggcacag tttgagagaa gaaaaggagt 240 ccaaatacgg cacagtttgg gagaaggaaa aaagagtcca aatacaacac tgataaataa 300 aacagctgtc aattctatct attatcttgt tatttcaatt aaccgagagt tacaataaaa 360 gggagaggga ggagcagcag agaggcagga aattgctttg aagcaaatct cattcaccca 420 ggaggcccgg gctaccttga agctgcccag aaatctagat tagggtttat caaaattgca 480 ttgttctttc aattcaagtc tttaagatat ttcgtttcag ttgttatttc agtttcctca 540 atttcttttt gttaaaacct gtaaggctca ggtccaagaa aagctataat aaaagtaaaa 600 gaaaaattcc agacattctc ccttacttat caagatcatt aca 643 // ID Gypsy12-PTR_I repbase; DNA; EDCOT; 2754 BP. XX AC scaffold_214; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy12-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2754 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-2754 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 302-302 (2007). XX DR Genome; scaffold_214; Positions 216633 219386. XX CC Positions [1669-2148] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 70..2739 FT /product="Gypsy12-PTR_I_1p" FT /translation="MKQQQEAQQQNQQNQQQILEDIVQQLRNMSTRMDQMA FT KAQGKRPMGSPPHSPTRTNNGITRHEVVPQEGFQQVQLKSIRLEFPRFNGD FT DPIGWVYKANQFFNFHNTPAQHRLFIASFHMEGKAITWYQELEETGILTSW FT EAFIKALQIRFGTSSYDDPMEALISIKQVSTVELYKTQFEMLSNRVRGLSD FT SHRLSCFLGGLKEEIRMGVRMLNPQNLVAAYELARMQEENLTIMRKSWRPS FT AMGFQGRNPTLTQPRAENKPIPVQRLTPAQMKEKRDKGLCFKCDASGIGLG FT AVLMQEGRPISYFSKSLKGRELSLSTYEKEFLALVTAVQKWRPYLLGQAFK FT VKTDQQSLKYLLEQRVGTPTQQKWLSKLIGYDFVVEFRAGRENLVADALSR FT QEDTTEKGTLWAISTPIVNWADRLKDSYKTDPEIQTIMQQLDQETIGSLKY FT RLRGGILYYKHRVYISQSSPIKNDILNYIHDSPTSGHTGFERTLKRARRDF FT FWVGMKSDIQNYIKHCDVCQRAKGENTKPSGLLQPLPIPTRPWSSISMDFI FT EGLLKSNQYSVIMVVVDRLTKYAHFIPVSHPYSATKIANLFSQNVVKLHGL FT PNNIVSDRDPTFTSKFLGELFQIQGVKLLMSTAYHPQTNGQTEATNKTLEG FT YLRCYVGDNPKEWSNWLTMAEYCYNTSYHSSLKSTPFEATYGYPPPSLTDY FT IPGSTKNQATEEHLQHRTEQIAEIKHNLSQAQARQKKQADKGRKEIQFSEG FT EWVYLRLQPYRQSSMQRKKNVKLAYKYFGPFQILKKVGEVAYQLDLPKEAR FT IHITFHVSLLKKWVGKGIVPEPKLPSLETKLKSQPEPAEIIDRRSQVSRGK FT KKEEVLLRWEGQPKEDAVWVDEEWLEGSYPHLEGKVF" XX SQ Sequence 2754 BP; 917 A; 627 C; 622 G; 588 T; 0 other; agtggtatca aatccagatc tcgagctgaa ggaacaagag tttcacaatt gatagaaaca 60 gtatcaggaa tgaaacaaca acaggaggcg caacaacaaa accagcagaa tcagcagcaa 120 atattggaag acatagtcca gcaattaaga aacatgtcta ccaggatgga tcagatggct 180 aaggcccaag ggaaaaggcc catgggctcc cctcctcatt ctcccaccag gacaaacaat 240 ggaattacca ggcatgaagt agtaccacag gaaggatttc agcaggttca gctcaagtca 300 atcaggttgg agttcccccg gttcaatgga gatgatccta ttggttgggt gtacaaagcc 360 aatcaattct ttaactttca caatactcca gcccaacaca gattgtttat agccagtttt 420 cacatggaag gaaaggccat aacatggtat caggaactag aagaaactgg aattctcacc 480 agttgggagg ccttcattaa agccctccaa attcgttttg gaacctcatc ttacgatgac 540 cccatggagg ccctcataag tatcaaacag gtctcaacag tagagctcta caaaacccaa 600 ttcgagatgc tttcgaaccg ggtcaggggg ctgtctgact ctcacaggct cagctgcttc 660 ctaggtggat taaaagagga gataagaatg ggagtacgaa tgctaaaccc tcagaaccta 720 gtggctgcct acgaattagc aaggatgcag gaggaaaatc tgacaatcat gaggaaatca 780 tggagaccta gtgccatggg gtttcaaggc cgaaacccca cgctaactca gcccagggct 840 gaaaacaaac caattccagt acaaagactc acccctgcac agatgaagga aaaaagagac 900 aaggggcttt gctttaaatg tgatgcctca ggaataggac tcggagctgt gctaatgcaa 960 gagggccgac ccatctccta tttcagcaag agtctaaagg ggagggaatt atcactatcc 1020 acttatgaga aggaattctt ggcactagtt actgctgttc agaagtggag gccttactta 1080 ttgggccaag cctttaaagt taagacagac caacagagcc tcaagtattt attggagcag 1140 cgggttggga cacccacaca gcagaaatgg ttgtccaaat taattggata tgactttgtg 1200 gtcgaatttc gagcaggaag ggaaaaccta gtagctgatg cactctctag acaggaggat 1260 actacagaaa aaggtacact atgggctatc tctaccccga ttgttaactg ggctgaccga 1320 ttgaaggata gttataaaac tgatccagaa attcaaacta tcatgcaaca actagaccaa 1380 gagactatag gttccttgaa atatcgtctt aggggaggga tactatacta caaacacaga 1440 gtctacataa gccaatccag ccctataaaa aatgatatac tgaattatat tcatgacagt 1500 ccaacctcag ggcacacagg gtttgagaga acactaaaaa gggcaaggag agatttcttt 1560 tgggtaggga tgaaatcaga catacaaaat tatataaaac actgtgatgt ctgtcaaaga 1620 gcaaaaggag aaaacacaaa accctccggg ctcctacagc ccttgcctat acccaccaga 1680 ccatggtcat ccatatctat ggattttata gaagggctcc ttaaatctaa tcagtactca 1740 gtaattatgg tagttgtgga taggcttacc aaatatgccc attttattcc cgtatcccac 1800 ccctacagcg cgacaaaaat cgccaacctg ttttcacaaa atgtggtgaa gctgcatggg 1860 ctcccaaaca acatagtatc cgatcgggat cctaccttca ctagcaagtt tttgggggaa 1920 ttattccaaa ttcaaggggt caagctactg atgtccacag cctaccaccc ccaaaccaac 1980 gggcagaccg aggccaccaa caaaacactg gaagggtatt tgagatgcta tgtaggtgat 2040 aacccgaaag agtggtccaa ttggctaacc atggctgaat actgttacaa taccagctac 2100 cactcatccc tcaaatctac cccgtttgaa gcaacctacg gctacccgcc cccaagtctc 2160 acagattaca tccccggttc aaccaaaaat caagcaacag aagaacattt acaacacaga 2220 acagagcaaa ttgcagaaat caaacacaac ttatctcaag ctcaggcgag acagaagaaa 2280 caagcagaca aaggcagaaa agaaatccag ttctcagaag gggaatgggt ttacctccgg 2340 ctccagccat accgacagtc cagcatgcaa aggaaaaaaa atgtgaagtt agcttataaa 2400 tatttcgggc cgttccaaat cttaaaaaaa gtgggagaag tggcttacca gctagatctt 2460 cccaaggaag cccggatcca tatcaccttc cacgtctcac tgttgaagaa atgggttgga 2520 aagggaatcg ttcctgaacc gaagctaccc agtctcgaaa ccaagctgaa atctcagcca 2580 gaaccagcag agataattga ccgaaggagc caagtctcga gggggaagaa gaaggaagag 2640 gtgctgttaa gatgggaagg acagcccaaa gaagacgccg tttgggtcga tgaagagtgg 2700 ttagaaggtt cctaccctca ccttgagggc aaggtttttt aagggggaga gagt 2754 // ID Copia12-VV_LTR repbase; DNA; EDCOT; 295 BP. XX AC AM468287; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia12-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-295 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-295 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 721-721 (2007). XX DR Genbank; AM468287; Positions 20372 20078. XX SQ Sequence 295 BP; 87 A; 42 C; 42 G; 124 T; 0 other; tgttgaattt tgacttagta tttgctggaa tttgaatttt gaatattgca gctggagtct 60 tgcacaaaat ctgcaacatc tagatatttt cttattttta tttggtcaag atttgatttc 120 tattttatag gaagtagttg ttcatcatct agtagcttga ttttctgcta ttctaatgtc 180 atttttagtt acaagctcat gtataaattc agcactcttc atcaataaaa ttagttccag 240 cagcccaaaa atatattttt tgtataagta tttagatcca aatatttgtc caaca 295 // ID Copia-71_Mad-LTR repbase; DNA; EDCOT; 146 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-71_Mad_; KW Copia-71_Mad-LTR; Copia-71_Mad-I. XX NM Copia-71_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-146 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1681-1681 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 146 BP; 52 A; 19 C; 19 G; 56 T; 0 other; tgtaaaacat tagtgttagt caagttagtt agttgttaga atagttacaa atagttacca 60 ctgtaactat tctctttacc tgtgtaaatc tagtttatat aaatacctca gtgtaactaa 120 ttataaagta atgaaatcat ttctca 146 // ID RAS1_MT repbase; DNA; EDCOT; 408 BP. XX AC . XX DT 29-NOV-2006 (Rel. 11.11, Created) DT 04-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW non-autonomous; Inverted repeat; Interspersed repeat; RAS1_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-408 RA Shankar R. and Jurka J.; RT "RAS1_MT: A putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 596-596 (2006). XX DR [1] (Consensus) XX CC It's flanked on both termini by 9 bp TSDs (TAATTTAAA). XX SQ Sequence 408 BP; 160 A; 45 C; 52 G; 151 T; 0 other; ggcaaattct atggtacact caaaaatttg agtgtaccgg tacaccaaat catcaaatta 60 atattgaaac gagttgtttt tttgaagaaa aagaattgtt ttctatcatt aacaattaca 120 ataattagat cttagttacc aaaagtgtcg acgaaataaa attttacatt ttttgaattt 180 ttgttacata taacaaagaa tatttattat tttttatgag aaaatgttaa aaatttaata 240 tgattcttat aaacaatgaa atgatgttta ttcttataaa atgatgtctt ataaaatata 300 aatattgata aataactctt tatttcataa aataatcgtt aaattataaa tatttgaagc 360 aggagtaccg gtacacctca atttgtgagg tgtaccgtag aagttccc 408 // ID RT_CA repbase; DNA; EDCOT; 686 BP. XX AC AJ411783; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Cicer arietinum Ty1/copia-type retrotransposon RT_CA, RT gene for DE reverse transcriptase, partial sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; RT_CA; KW retrotransposon; pseudogene; reverse transcriptase. XX OS Cicer arietinum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; OC Cicer. XX RN [1] RP 1-686 RA Staginnus C.; RT "Thesis (2001) Department of Plant Molecular Biology, University RT of Frankfurt / M., Frankfurt a.M., Germany."; RL Direct Submission to Genbank (22-JUN-2001). XX DR Genbank; AJ411783; Positions 1 686. XX SQ Sequence 686 BP; 186 A; 131 C; 129 G; 240 T; 0 other; aacatatcgt caacgtaagt atactcagtt acctgatttt gtctattcca cttactgaac 60 ttcgtttgtt tctttcttaa cctctattcg cagtttgtct gagccctctt cctataaaga 120 ggttgttctt gatcctcttt ggcagcaggc tatggcagaa gaactatctg cattgcacaa 180 aaccaatact tgggaattag tacctcttcc tcctggaaaa tgtgttattg ggtctcgttg 240 ggtatacaag atcaaaacta agtctgatgg gtcaattgag cgctacaaag cacgtcttgt 300 tgctaagggt ttctctcaac aatatggtat ggattatgaa gaaacattta ctcatgtagc 360 caagatgacc actattcgta ctcttattgc agttgcatct attcgttaat ggcatatttc 420 ccaaatggat gtcaaaaatg tttttttaaa tggtgagctt catgaagaag tctatatggt 480 ccctccacaa ggagtttctc ataatcaagg ggaagtatgt aagttaaaaa aaggctctat 540 aaataggctc atcgagcttg gtttgagaaa ttctctattg tgatcacttc tcttagtttc 600 tgctctagtg aacatgattc tgcattgttt ataaggtcta ccacttatgg tcgcattata 660 ctttctctat atgtcgatga tatgct 686 // ID DNA9-13_Mad repbase; DNA; EDCOT; 952 BP. XX AC . XX DT 25-OCT-2010 (Rel. 15.11, Created) DT 25-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-13_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-952 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1853-1853 (2010). XX DR [2] (Consensus) XX CC TSD is 9-bp long. Imperfect TIR (72% identical) is ~60-bp long. CC Elements are >92% identical to the consensus. XX SQ Sequence 952 BP; 334 A; 111 C; 103 G; 404 T; 0 other; tagaaaactt cattttaatc cttaaaaaag atgagtttta gattataacc atgtgtaaga 60 ttaaaatcca attttagtcc ctagcacatt taatcatatc atttattagt tgtattttga 120 tgttttattt tatcttttta tttttatttt aatgtattaa ttacatttaa atttaatttt 180 tatttcattc atcataatat attttaatgt ctacatttag gcaactaatt tttttataat 240 atatattccg ataacaattt tgtatgttct tcatttaggt acattaatac atttgaatat 300 tttggtatat ccatcggtac aaacatgtag ttacattgat tcaatataat gcatttcggt 360 caatataatg tatttcgtta cgtacacttt ggtacacaca tttgagtatt gacttttagg 420 tacattaatt caatatatta tatttcggta aatacattta ggtacataca ttttggtatt 480 gatatttagg tacatacatt ttcggtattg acatttaggt acatacattt cggtattgac 540 atttaggtac attaattcaa tataatacat ttcggtacat acatttaggt tcattataat 600 atatttcggt acaatcatgt aggtacaaat atttcggtac aaaaaagtca attttatata 660 ttttggcaca gtcatttctg tacacttatg tatttatata tttttgtatc acaaatttct 720 tttaatattt tctcatttac gttcatttct aattaaaaaa aactaaatat gtgcatatta 780 ataaaattaa aatttaatat ggagagatta aataaaaata cacattaaat aacaaaaatt 840 gaatgtaaat tttgataaaa gtacacttca agggattaaa ttgaatattt aatctagcac 900 caggtttttt ttaaatttta atcttttgca aggactaatg ttcaaaaacc cc 952 // ID Gypsy-11_Mad-I repbase; DNA; EDCOT; 4649 BP. XX AC ACYM01129965; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-11_Mad-I; KW Gypsy-11_Mad-LTR; Gypsy-11_Mad_. XX NM Gypsy-11_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4649 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1334-1334 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01129965; Positions 2311 6959. XX CC Positions [3527-3799] - Integrase core CC 'GTGGG' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 39..2837 FT /product="Gypsy-11_Mad-I_1p" FT /translation="MPRHTTNSRMSTVESRLSAVEATLEAMGAIPQLIQTS FT NANSDTRFTALETKFALLLEHLHRDPGPQGGAGSSTAPPPLVPDPHIPPPI FT VTDDGDFRCLDTPRFQRRDSFEGGGFTPRPQRSHRLDFPRFSDGDDPSAWI FT YKAEQYFAYYHTPENQKVLTASFHFKNEPLYWFRWRDCVHSTPTWGEFTTA FT LCQEFGPPEFEDCTESLFKLRQTGPLRDYIVEFRRLATRTYDVGPILLKSC FT FLGGLKKELRYDVKLLRPSSVHEAISFAAQLNAKLTDLKPSPPKPHPPLKP FT PLALPLPSLTRPHPQTLPYKKLTPRKFKRKKDKGECWFCNEKWVRGHKCVH FT NKQLLMLDVCNELEPTECELLEPTECELLEPIDLSLSSMELSACAFYGTTE FT PSTVQTMKVAGVLHTLPVTILLDSGSTHNFVDSRLLKQLGWPCHTTKPFDV FT MIADGGKVRSQGCCQQIPLELGAYRCHTNLYALPLGGCDVVLGVKWLSSVS FT PVLWDFHNLTMEFSVGKDHYKLVHSTAPAYLVQDTVCQQLEKEFKYSNWGV FT LLYSMETNPLEASNLNPQQLIELQGMLRQFETVFKPPTTLPPPRAHDHQIP FT LLPGSKPPSIRPYHYGPMQKTEIERAVQELLDAGFIQPSHSPFSFPVLLVK FT KKEGTWRLCMDYRELNSITIKDKYPIPLVDDLLDELHGAQYFSKLDLRSGY FT HQIRMSPSDVEKTAFRTHQGHYEFLVMPFGLTNAPATFQALMNDIFKPYLR FT KFILVFFDDILVYSKTWEDHLSHLHQTLELLQKHQLAVKKSKCSFGQSQVE FT YLGHIVSRDGVAADPTKIQAIIDWPIPKNVKELRGFLGLSGYYRKFIPGYG FT KVCQPLYQLTKNDGFNWSPEATAAFQALKRTMTSPQLLALPNFAIPFTLEC FT DASGNGIGAVLQQNGRPIAFTSQALGPRN" XX SQ Sequence 4649 BP; 1220 A; 1096 C; 1032 G; 1300 T; 1 other; attggtatca gcctctcgat cctgagtctc cctcttgtat gccccgccac accacaaatt 60 ctcgaatgtc cactgttgaa tcgcgcctct ccgccgtgga agctactctg gaagccatgg 120 gagccattcc tcagctgatc cagacttcca acgccaattc cgacacccgc ttcaccgctc 180 tcgaaaccaa attcgccctt ctcctggagc atctccatcg cgaccctggt cctcaaggcg 240 gtgctggctc ttcgactgca ccaccacctc tagtgccaga tccacatatt cctcctccca 300 ttgtgaccga tgatggcgat tttcgttgtc tcgacactcc acggtttcag cgccgtgatt 360 cttttgaagg cggcggtttt actcctcgcc cgcagcggtc acatcgtctg gattttcccc 420 gtttctccga cggtgatgat ccctcagcgt ggatctataa ggccgaacaa tattttgctt 480 attatcacac tccggagaat cagaaggttt tgaccgcctc cttccacttc aagaatgagc 540 cgctgtactg gtttcgttgg cgcgattgtg tacattccac tcccacctgg ggtgaattca 600 cgactgcttt gtgccaggaa tttggtccac cggagtttga ggactgcact gagtcgctat 660 tcaaactccg ccaaaccggc cctcttcgtg attatattgt ggaatttcgg cgccttgcca 720 ctcgaaccta tgatgttggt cctattctct taaagagttg ctttctgggg ggtctcaaga 780 aggaattgcg ttacgatgtt aaattgcttc gcccttcctc agttcatgag gccatttcct 840 ttgctgccca attaaatgct aaactcacgg acttgaaacc atctccccca aaacctcatc 900 ccccactcaa acctcctctc gccttacctc taccttccct taccaggcct catcctcaaa 960 ccctccctta taagaaactt accccgagga agttcaaacg gaagaaggac aagggcgagt 1020 gttggttctg taatgaaaag tgggttcgag ggcacaaatg tgtccataat aaacagctcc 1080 ttatgcttga tgtttgtaat gagttggagc ctaccgagtg tgaattgctg gaacctacag 1140 agtgtgaatt actggagcct attgatcttt ccctatcaag catggagttg agtgcttgtg 1200 cgttctatgg cactactgag ccctccacgg tacaaaccat gaaagtggct ggtgtgcttc 1260 acactctacc tgttaccata ctacttgact ctggtagcac ccacaatttt gtggattcta 1320 ggttgcttaa gcagctcggg tggccttgtc acaccaccaa acccttcgat gtcatgattg 1380 ccgatggggg taaagtccga agtcaaggct gttgccaaca aattcccttg gaattgggtg 1440 catatcgctg ccacactaac ctctacgcac ttcctctagg gggttgcgat gttgtattgg 1500 gtgtgaaatg gctctcatct gtgagtccag ttttgtggga ttttcacaac ttaaccatgg 1560 aattttctgt gggaaaagac cactataaac ttgttcattc cactgctcca gcgtacttgg 1620 tacaggatac tgtttgtcaa cagcttgaaa aagagtttaa atactctaat tggggcgtct 1680 tattgtattc aatggaaact aatccgttgg aggcatccaa cttgaatccc cagcaactca 1740 ttgagctgca gggtatgctc aggcaatttg aaacggtttt taagcctcct actaccttac 1800 cacctccacg ggctcatgat caccagattc cattgcttcc tggttccaag cctccgagta 1860 ttagaccata ccattatggt cctatgcaaa aaactgagat tgaacgagct gtgcaagaac 1920 ttttagatgc tggattcatc cagccaagtc atagtccctt ttcatttcca gttctcttgg 1980 tcaagaagaa ggagggcact tggaggcttt gcatggacta tcgtgaattg aacagcatta 2040 ccattaagga taaatatcct attccattag tggatgattt gttagatgaa ttgcatggcg 2100 ctcagtattt ttctaagctt gatcttaggt ctggatatca tcagatccgt atgtctccct 2160 ccgatgtgga aaagactgcc ttccgaactc accaagggca ttatgaattc ttagtcatgc 2220 cctttggtct tacaaatgct cctgccactt tccaagccct tatgaatgac atttttaagc 2280 cttacctccg gaaattcatc ttggtgttct ttgacgacat tttggtgtac agcaagacct 2340 gggaggacca tctttcacac ttgcaccaaa ctttggagtt attacagaaa caccaattag 2400 cagtgaagaa atcgaaatgc tcttttggcc aatcacaggt ggaatacttg gggcacatcg 2460 tctctcgtga tggggtggct gcagatccta ctaaaattca agcaattata gattggccga 2520 taccgaaaaa tgtcaaagag ttgaggggat ttctcgggct ctcagggtat tatagaaaat 2580 tcatccccgg ttatggcaag gtgtgtcaac ccttgtatca actaacaaaa aatgatggtt 2640 tcaattggtc ccctgaagcc acggcagctt tccaagcatt aaaaagaaca atgacttctc 2700 cgcagctatt agccttaccc aattttgcta ttcccttcac tttggaatgt gatgcatctg 2760 gcaatggaat aggggctgtg ttgcaacaga atggcagacc tatagctttc acaagtcaag 2820 cattgggacc acggaattaa gcattgtcta catacgaaag agagttgatt gccattgtta 2880 gtgctatcaa aaaawggcaa aaactacctt caagggcgcc atttcatcat aaagacagat 2940 catagcagct tgaaatactt tctgagtcaa agaactacta ccccgttcca acagaaatgg 3000 gtggccaagt tgttgggatt tgattatgag atacaatata ggcaaggcaa tgacaacata 3060 atggctgatg ccttatctcg agtagttggt tcgtctcaat tacaagagaa acctctcagt 3120 gacttattgg agtgcaaagc tatcacatac ccctacttcg ggtggctaga tgaacttcgg 3180 agagggttag aacaagatag ttggattcaa agcaaggtgc agaaggtgtt agcatattct 3240 taagctgctg caattgaccc caatctgtcc aagtaccatt tagacaacgg tttcctcaaa 3300 tacaaaggac ggatcgtgct tagcccagat tcaagttgga aaaggaaggt ctttgaggaa 3360 catcactctt ctccaagtgc aggccatgaa aggggttcta aagacttatc agatattgaa 3420 gaggggcttc tattgggtag gaatgaagaa agatctcagg tcatgggtgg ctgaatgtcg 3480 ggaatgccag caaaataagt atgaaaccat ttcccctccc ggattacttc aacctctgcc 3540 gatccctaca catgtatgga aggatataag catggatttc atcactggtt tacctctgtg 3600 caaaggcaaa tcagtgatcc tggtaatcgt agacaggctg tccaagtatg ctcatttcat 3660 ccccttagca catccgtata cggcaagcat ggtagctcag gaatatgttg ataatgtgtt 3720 taaactccat gggatgccct ctaccattgt gagtgacagg gacaccattt tcatgagtgt 3780 tttttggaaa gaattttttt aagttgcaag gctccaagtt gtgtatgagc tcgggttacc 3840 atccacagag tgatggccag acagaggtgg tgaatcggtg ccttgaaact tacttgcgat 3900 gcttcactag ctgtcaacct aagaagtggc tccactggct tccatgggca gaatggagct 3960 ataacacttc ctaccacact tcctcaaagt tcaccccctt cgaagtggtc tatggttatc 4020 caccaccaca catcgcgtct tatgagcttg gcactgctaa gttggatata gtggagcaag 4080 ggctgctaac tagggacaaa atattagcaa tgctcaggac caatttacta gtagctcaga 4140 accggatgaa aacacaagca gataagcatc ggagtgagag ggttttcgag gaaggagatt 4200 tggtgtattt gaaattaatt ccctatcaat tgcaatcttt gtcatctcat gcttaccata 4260 agcttcatcc ccggtactat ggtccttatg aggttttgga aaatattggg aaggttgcct 4320 accgattgaa actgcctgag aattcaaaaa ttcatccagt ctttcatgtt agttgcttga 4380 agaagcactt gggagacaag gtcacataac tccattcttg cctactgtca ctgatgatgg 4440 gttgctacca ctcgaaccac tcaaggtgct acaaatgagg gtctacaaga agggccaagc 4500 tgctggagtt cagttgttaa tccagtggaa gaacaacaaa gaggacgaaa ctacatggga 4560 ggattatgac gagtttgctg ccagatttcc tgatttcagt ctttaattct aaccttgagg 4620 acaaggttta ttttgtaagg gaggggtag 4649 // ID RT_VS repbase; DNA; EDCOT; 229 BP. XX AC . XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Vicia sativa Ty1/copia-type retrotransposon RT_VS, reverse DE transcriptase gene - a consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; RT_VS; KW retrotransposon; Ty1/COPIA superfamily; reverse transcriptase. XX OS Vicia sativa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Vicia. XX RN [1] RA Pearce R.S., Harrison G., Li D., Heslop-Harrison J., Kumar A. RA and Flavell J.A.; RT "The Ty1-copia group retrotransposons in Vicia species: copy RT number, sequence heterogeneity and chromosomal localization."; RL Mol. Gen. Genet 250(3), 305-315 (1996). XX RN [2] RP 1-229 RA Jurka J. and Drazkiewicz A.; RT "RT_VS: a Ty1/copia-type retrotransposon, RT gene from Vicia RT sativa."; RL Direct Submission to Repbase Update (18-SEP-2002). XX DR [2] (Consensus) XX SQ Sequence 229 BP; 69 A; 37 C; 43 G; 80 T; 0 other; ggtgatttgc atgaagaagt atatatggag ctacctcctg gttttcctag tacaaaggca 60 aatcaggttt gcaagttgaa gaaatcttta tatggcttga agcaagctcc cagacattgg 120 tataagaaat ttgactcttt cattattaac cttggataca ctcaatctaa tgctgatcat 180 tctctgtcta ctataaaagg ctgataatga tttcataatt ttgttggtt 229 // ID LTR-12_Mad repbase; DNA; EDCOT; 2371 BP. XX AC . XX DT 01-NOV-2010 (Rel. 15.11, Created) DT 01-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE Putative LTR-retrotransposon from the apple genome: long terminal DE repeat. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR-12_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-2371 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 2003-2003 (2010). XX DR [2] (Consensus) XX SQ Sequence 2371 BP; 577 A; 481 C; 587 G; 725 T; 1 other; tgtaacgacc cgtccccaaa aattacggtt tttataattt taaaatgtga atttacgaaa 60 atgcccttcg aggcaaatac gttgactttt gttgaccgcc ttgtcgtgtc acgtaagatc 120 cgttttcttg gcgtatcctc gtagtactcg tcgctacgaa cgcgtgggcg caaacggaac 180 gtaatttgga gttataacga aggagttatt aacgaacgaa gtcgagggca aaatggtcaa 240 ttgatcattt tctggaaggc tccagatttt tggagcaaaa tctggaaagc cacgtgtgtg 300 gccgagattg aaggaaatga gagatggacg gtggagatgg aagataaagg agagaaatga 360 gggagaggtg aggccaatca ggaaagggag agaagagagt gaccaatcag agaggagaga 420 aaggagggga aatgagagag tggaggagca ccggatcacc cttgacccgg ttcctccccg 480 ccgacccgac ccggtttcca tgcattccga cgcgtttccg gcgtttttcc ggcgaattga 540 ccgtcgccac cacctgcaaa caactccacg acctcccttc ttcaatttcc acccaaaacc 600 cgatggattt ggccccggtt tcgtggggat ggcgccggcg gtccgagggt gcctcggcgg 660 agatccgcca tttctgaagg taattccttc gaccaccacc accattagac tccccttgag 720 cccaggaaca aagcccaaac aaccgttggg gcgtcggagt cgatttgagg acgaatcgaa 780 gaacacccat ttctagggtt tccggcgggt tcgagggaaa ttggggcttt tcccggccaa 840 attggcctta gtcacaggta tgaaagttgt tcctctcatc gagatcttca ttcctgtaaa 900 atttgggaat ttttggagtt gttggatttt ccggcgagtc ggggcggccg accgccacgt 960 ggcggccgtg cggcggcgcg tggaggaaaa acccgaggtc cctccttagg tttttcgaca 1020 tgccgaatcc gccatccgtt ttcccaaatt ctaacgtttt agtakagttt tactaaaagg 1080 tccctaattg tgtttaggcg cgttggcggg aagcgacgtc atcctcgcta gttcgagcgg 1140 ctctcgggca atggaaaacc tgtgagtgga ccccttctta acttatatat ttttataaaa 1200 tattagccta gcatgcattt catatttcat gatttgaata tgttttatat tatgctttac 1260 ggatttctat aattatggtt taagagaatc atgatttata aattgctttg aatatttgat 1320 ttatcgaaat tacgttttac taaaggtata acggatatga attattggat ttgcatatat 1380 ggatttctat tgatatgatt tatatatgga tttacgaata tggttatttg attttatgat 1440 agatttatat gatttatgag atgaggcttt gagcttttga gctccggatt tgatacgaga 1500 ttttgagata tgtttttggt acttacctag tgggttatca tacggcacat ccgcacacca 1560 cgggtataga tgtctatggc cataggacac agatgatgga ggagtgagat atgatatatt 1620 atataccccc agcttcactg ccgaaagcgg tgtcggacag cttcactagc cacggctagt 1680 gtcggtgtgg atgttatgct attttattca gcttcacctt cgggtgatgg acaggttatt 1740 cagcttcacc ttcgggtgat ggacaggtta ttcagcttca ccttcgggtg atggacaggt 1800 actgccttcg ggcgactatg atacccctag ttgagtactt cactgatgag atttacggat 1860 ttgccttcgg gcgacgtttt cagcattttg agcatggttt tacacgtaca tgttttacga 1920 atgttttgca tggcatgcta gggttttcat aaaacctata tgtagtatta tatatgtttt 1980 caaaacaggg ggttactatg ttcaaaaata aaatggtttt cctattatta gtattattat 2040 tataaacttt ggtccactca ccttttctgt ttttgcgccc cctcaggagt taggatcgag 2100 gcacatgatc ccggcgtcag ggcacttacg gcataggtat cctcgagtct tctcagtata 2160 ggtatcattt ccttgttcgt atcttttcct agtaattctt tcatattatt cttagttagt 2220 tgtatgctct gaacacgttc ctgctttggt ttaatcgttc taattgcata tttttatttg 2280 tatgcatgtt taaaatggct tcgtcaccct cgggtgtcgg ccagcacgtg cctaccctgg 2340 tatgtgggga tatcggggtt ggggcgtgtc a 2371 // ID Copia27-PTR_LTR repbase; DNA; EDCOT; 209 BP. XX AC LG_XIX; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia27-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-209 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-209 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 229-229 (2007). XX DR Genome; LG_XIX; Positions 1013919 1014127. XX SQ Sequence 209 BP; 61 A; 32 C; 38 G; 78 T; 0 other; tgaagagaaa gtttaggctt ctgttaagga agtagttagg atttgcattc agtttaataa 60 gtcctagtcc ataggattgt tagtttatat tttgcaagat tttctacgtg aatagctcct 120 ctgctgagat tatgtaaggc tgtataaagc caaccttctt ctttcaataa aagcattctg 180 atcctgcatt attatcagtt tctataaca 209 // ID Copia10-VV_I repbase; DNA; EDCOT; 7110 BP. XX AC AM486050; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia10-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-7110 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-7110 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 731-731 (2007). XX DR Genbank; AM486050; Positions 2277 9386. XX CC Positions [2311-2811] - Integrase core CC 'GTCTC' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 56..1579 FT /product="Copia10-VV_I_3p" FT /translation="MAIPSSSSQTENFSKHRAPFFTGTDYPYWKARMTWFL FT QSTDLDVWDVIEDGPTFPTKLVDGVLVPKPKKEWNELDRRNFQLNAKAVFT FT LQCAMDRNEYNRICQCKSAKEIWRLLEITHEGTNQVKESKINILVHNYELF FT SMKETETIVEMITRFTEIVNGLEALGRVINESEKVMKILRSLPSKWHTKVT FT AIQEAKDLTKLPMEELLGSLMTYEISLTKQPQESEDKKKKNIALKATTKEE FT EDVEEEKPSEEDDDLALITRKLNKYMRGERFRGKKFTSRRNPSRRESSSHG FT DKEKWEEKSDLICFKCKNPGHIKYDCPLYKIEAKRRMKKAMMATWSESEES FT SEEEKEKEVANMCFMAIDDLDEVNSNSSDEDMHVIFEELYEDFEKLSLKNT FT SLKKRIQELEKELEEVKEKFSIDEISKTHLEKEHEILRNENEILKKKNEWL FT TSSLSIFSCGQKSFEMILASQKCVFDKQGLGFKSSKNQKYFKNYFVKESSS FT ECPSTICNFCGR" FT CDS 1786..3075 FT /product="Copia10-VV_I_1p" FT /translation="MTGDESKFAFLTKRKGGYVTFGDNAKGRIIGQGNIGN FT GTSSLIESVLLVDGLKHNLLSISQLCNKGFKVIFEASHCIIKDIQNDKTIF FT MGHRCENVYAINISKYDGHDRCFSSMHDQSWLWHRRLGHANMDLISQLNKD FT ELVRGLPKINFQKDKICEACQMGKQIKNSFKNKNFISTSRPLELLHMDLFG FT PSRTPSLGGKSYAYVIVDDFSRYTWVLFLSQKSEAFYEFSKFCNKVQNEKG FT FSITCIRSDHGREFENFDFEEYCNKYGINHNFLAPRTSQQNGVVERKNRTL FT QEMARTMLNENNLPKYFWAEAINTSCYVLNRILLRPILKKTPYELWKNKKP FT NISYFKVFGCKCFILNTKDNLGKFDAKSDVGIFLGYSTSSKAFRVFNKRTM FT VVEESIHVIFYESNNFLQERESFDDDLGLETSMGKL" XX SQ Sequence 7110 BP; 2279 A; 1282 C; 1519 G; 2028 T; 2 other; attggtatca gagctagacc tcttgcttaa rgacttaaat cgtctaagra ggaaaatggc 60 tattccatca agttcatctc aaactgaaaa tttttcaaaa catagagctc cattctttac 120 gggaaccgac tatccctatt ggaaagctag gatgacttgg ttcttacaat caactgattt 180 agatgtatgg gatgtcattg aagatggccc aacttttccc actaaattag ttgatggagt 240 tttggttcca aaacccaaga aagaatggaa tgagcttgat agaagaaatt ttcaattaaa 300 tgctaaagcc gtttttactt tgcaatgtgc tatggatagg aatgaatata atagaatatg 360 ccaatgtaaa tctgctaagg aaatttggag attgcttgaa ataactcatg aaggaacaaa 420 tcaagtgaaa gagtcaaaaa ttaatatact tgtccataac tatgaattgt tttcaatgaa 480 agaaactgaa actattgttg agatgatcac taggttcact gaaattgtca atggccttga 540 agcattggga agggtcataa atgaatccga aaaggtgatg aagatattga ggtctctccc 600 ctcaaagtgg catacaaagg tcaccgctat tcaagaagct aaagacttga ccaagctacc 660 tatggaagaa ctcttagggt cattgatgac ttatgaaatc agtttgacaa agcaaccaca 720 agagagtgaa gacaaaaaga agaaaaacat agctctcaaa gctacaacca aggaagaaga 780 agatgttgaa gaagaaaaac caagtgaaga agatgatgat ttagctctca tcacaagaaa 840 gctaaacaag tacatgagag gtgaaaggtt tagagggaaa aagtttacct ctagaagaaa 900 tccctcaaga agggaatcct catcacatgg tgacaaggaa aaatgggaag agaaaagtga 960 tttgatatgc ttcaaatgca aaaatccggg acacattaaa tatgattgtc ctctctacaa 1020 aattgaagcc aaaagaagaa tgaagaaggc aatgatggcc acttggagtg agagtgaaga 1080 atcttccgag gaagaaaagg aaaaagaagt ggcaaacatg tgcttcatgg caatagatga 1140 tcttgatgag gtaaactcta actctagtga tgaagatatg catgttattt ttgaagaact 1200 atatgaggat tttgaaaaac ttagtttgaa aaatacttct cttaaaaaga gaattcaaga 1260 acttgaaaaa gaacttgagg aagtgaaaga aaagttttca attgatgaaa tctctaaaac 1320 tcatcttgaa aaagagcatg agattttaag aaatgaaaat gaaattttga aaaagaaaaa 1380 tgaatggttg acctcctctc tttcaatttt ctcttgtgga caaaagtcct ttgaaatgat 1440 cctagcaagc caaaaatgtg tttttgacaa acaaggacta ggattcaaat cttcaaagaa 1500 ccaaaaatat tttaaaaact attttgtaaa agaatcctca agtgaatgtc cttccactat 1560 ttgtaacttt tgtggaagat gaggacacat tagtagtaca tgtcccttaa gaaatggtgc 1620 tcaaaagaat tcaaatacta aggttaaaaa ggtttggatt gaaaaatcca aagtcactaa 1680 ccctcaagga cccaaaaaga catgggtacc taaaccaact tgaattctat tttgtaaggc 1740 tcaaaggaag ataagtggtt tttggatagt gggtgctcaa gacatatgac cggggatgaa 1800 tccaagtttg ccttccttac aaagagaaaa ggaggatatg tcacctttgg agacaatgca 1860 aaaggaagaa tcattggtca aggtaacata ggtaatggta catcctccct tattgaaagt 1920 gttttattag tagatggttt aaaacacaat cttttgagca ttagccaact ttgtaacaaa 1980 ggttttaaag taatttttga agcatctcat tgtatcatca aggatattca aaatgacaaa 2040 accatcttca tgggccatag atgtgaaaat gtatatgcta taaatatttc aaaatatgat 2100 ggccatgata gatgtttttc aagcatgcat gatcaaagtt ggttgtggca taggaggttg 2160 ggacatgcta acatggacct catttcccaa ctcaacaaag atgaactcgt tagaggcctt 2220 cccaaaatta attttcaaaa agacaaaatt tgtgaagctt gtcaaatggg aaagcaaatc 2280 aaaaactctt ttaaaaacaa aaatttcatc tcaacatcta gacctcttga attgctacac 2340 atggatttat ttggtccttc taggacacct agtctaggag gaaaatctta tgcttatgtc 2400 attgtggatg atttctctag atacacatgg gtcttgtttt taagtcaaaa gagtgaagct 2460 ttttatgagt tttcaaaatt ttgtaacaag gttcaaaatg aaaaaggttt ttcaatcact 2520 tgcattagaa gtgatcatgg gagagaattt gagaattttg actttgagga atattgcaat 2580 aagtatggta tcaatcacaa ttttttggct cctagaactt ctcaacaaaa tggggtagtt 2640 gaaaggaaaa atagaactct tcaagaaatg gctagaacca tgctaaatga aaacaatttg 2700 ccaaagtatt tttgggccga agcgataaac acctcttgct atgttttaaa tagaatattg 2760 ttgaggccca ttcttaagaa aactccctat gagctttgga aaaacaagaa acccaacatt 2820 agctatttca aagtctttgg gtgcaaatgt tttatattaa acaccaaaga taatcttgga 2880 aaatttgacg caaaatccga tgttggaatt tttcttggct actcaacttc aagtaaagct 2940 tttagagttt tcaacaaaag aaccatggtt gtagaagagt ccatccatgt cattttttat 3000 gaatctaaca attttcttca agaaagagaa agttttgatg atgatttagg attggagact 3060 tccatgggaa aattgtaaat tgaggacaaa agacaacaag aagaaagtgg agaggatccc 3120 aagaaagaag aatcaccttt ggcactacct cctcctcaac aagtgcaagg tgaatcaagt 3180 caagaccttc caaaagattg aaagtttgtc atcaaccatc cacaagatca aatcattggt 3240 aatccattaa gtggggtaag aactagatca tcccttagaa atatttgtaa taatcttgca 3300 ttcatctctc aaattgaacc taaaaacata aaagatgcta tagttgatga aaattggatg 3360 attgctatgc aaaaagaatt aaatcaattt gaaagaagcg aagtatggga actagtacca 3420 agaccttcaa atcaaagtgt tattggaact aaatgggtct ttagaaacaa aatggatgaa 3480 aatggcatca tagtaagaaa taaggcaaga ttggtagccc aaggatataa tcaagaagaa 3540 ggaatagact atgaagagac ttttgcccct gtagctagat tggaagcaat tagaatgttg 3600 cttgcttttg catgtttcaa agactttatt ctatatcaaa tggatgtgaa aagtgctttt 3660 ctaaatggct tcataaatga ggaaatatat gttgaacaac cacccggttt tcaaagcttc 3720 aactttccaa accatgtttt taaacttaaa aaggcacttt atggtttgaa acaagcacct 3780 agagcttggt atgaaagact aagtaaattt cttttgaaaa agagttttaa aatgggaaaa 3840 attgacacaa ctcttttcat taaaaccaaa gaaaatgata tgctcctagt tcaaatatat 3900 gttgatgata ttacttttgg ggctactaat gactctcttt gtgaagattt ctctaagtgt 3960 atgcatagtg agtttgaaat gagcatgatg ggggaactca attacttcct tggacttcaa 4020 atcaagcaaa gtatataaag gaccttctca agaggtttaa catgggtgaa gccaaggtga 4080 tgaaaactcc aatgagctca tccatcaagc ttgacatgga tgaaaaaggt aaatctattg 4140 actcaactat gtatagaggc atgataggat ccttgcttta tttgaccgct agtagacccg 4200 atatcatgta tagtgtgtgc ttgtgtgcta gatttcaatc ttgtcctaaa gaatctcact 4260 taagtgccgt taaaagaatt cttagatatt tgaaagggac aatgagtatt ggtttgtggt 4320 atcctaaggg tgataatttt gaattgattg gtttctcgga tgccgatttt gccggttgta 4380 gagttgaaag aaagagcact agtggcactt gtcattcctt aggacactca cttgtctcat 4440 ggcatagtaa gaagcaaaat tcgatagctt tgtcaacggc ggaagccgaa tacacagcag 4500 ccagtttgtg ttatgcacaa atcctttgga tgaaacaaac acttagtgat tttaacttgt 4560 cttttgagca tgttcctatc aaatgtgata acactagtgc cataaatatt tcaaaaaatc 4620 ccgtgcaaca ctctaggacc aagcatatag aaattagaca tcattttctt agagatcatg 4680 cacaaaaagg tgacattaca cttgaatttg taagcacaaa agatcaactt gccgatattt 4740 ttacaaaacc tctaagtgaa gaacaatttt ccgatattag aagacaacta ggggttattt 4800 ctctttgatc tgatgtttgt ataatgaatt cttgttggaa atgcattatg attgcataaa 4860 tttcatctca tacgcatcat atagcaatcc cttagaaaat aggtcaattt ttgaccaaaa 4920 atcaaaattc ccatggcatt ggacatcaaa aattggggat ttcaactgaa aagagcaggg 4980 ggaggatcac gagacaagaa tacgcaaaaa aaattggaaa atgtaaccgt tgaccattga 5040 ccaggcggtc aaccggttga ggaaccggtc gaccggttcg tcggggttgg gaatttaaaa 5100 ggcccccgcg cgtcagtttt ttccactatt ctttggcatt ccttgaagac tcttcatctt 5160 cccgccttca gagaccagtt taggctactc cttggaccga tttcaggttg tggagtgatt 5220 tttaacgaga ttttgaggct agggtttcat ctctggacag atttggactt cggatcttga 5280 cgggttcctc tctgtttgcg cgccatcttc tggtttctgc tcctttcccg cgcgcctagg 5340 gcttcttggg gttagtcttc tctctttgcc tactcgcttc agttctccaa gcatatctcc 5400 atttttggat tttggatggc tcctcgaaaa gagacgggta cttccagggc tcagggcaag 5460 tgccttgcta agccctctca gtagcccgag cagaccgagg ctcgccgaaa ggcgaggtac 5520 gacaccgccc tcttcggctc agttgaggat tatcagaggt acaagacgca tttcgccaag 5580 agaaaggtgg ttccagggag aaacataaat ttcttccaac ttcagagtct cgggtttgag 5640 ggactcttca tcaagatggg atggctgcca gttgtgacgg tctatgagcc tatcttttcg 5700 accttagtgc gtgcattcta ctccaggata acctatggac ttggagggcc gattaggact 5760 actgtctaag gagttgagat tgagctgagt ccggagagca tcggtgtcgc atcgcttgac 5820 attcctcccg ttggtctcag agtatatgag gccaaggcat ggcctactat ccccgggttc 5880 gagcctagag aggccattca gaggctgtgc ggacttgcag atgcccatgg gatgggcaaa 5940 ccttcagcac atagcctgac cgtgcctagc cgagtccttc atcatatgat ctgctccatc 6000 ctattaccac ggggtggaca tcgggacgag gtctcctact atgaggcttt tcttgtcgac 6060 tcacttctca ccgggaggcg gatacatgta ggatatgtga tgatgaggca tatgatgtcc 6120 tgttgtgaga gcaccacacg agtgcttccc tacggccgct tcctcactcg tgtcttcaag 6180 gatgctgggg tagacttgag tagagagaca gagtttgagg cacccagcat ctatgacact 6240 tatgacgagc attctctggg gtgcatgaag cttgagaagg cccccgatgg ctcctgggtt 6300 aggaaagccg agcgacaggc ccagggacat gatcagctac accccggagt agaggaagag 6360 gacgagatca gagagatgga ggatgggttg gaccctcaga gggaccttga gcagcgaggg 6420 ccagagcttg acattccgcc tccacatcag tcagagggca ttcatgttga ggctaccttc 6480 tcagagccta tgatgactga gccatccttc ccagcaggcc cttcatctca gccatcattt 6540 accgagctac catctcaggt tcctcatgct cctgagcatc caccttggat ggatttgtcg 6600 gcacagatta gctctctcgg gactcgtatg gaggagttag ctatagttca tgatactcgt 6660 ttttattcca tggaggatcg catcgatcag tatcaggccg gcttcacctc tcagtttaag 6720 cagcttgtac agaggattga gcgtcttgag agccaccagg agagtcagca cgaggagatg 6780 atgacttacc tccgttctgt gtttccacca ccacctcctc agccttgact ttgtttggga 6840 tcccccttca tttctttttg atgttgccaa agggggagat atgttaggat agggacctta 6900 ggagactttt tcattttcat gcatatcata cttatgcttt catgtactct tgttcttgct 6960 tatatatgat atgacactct tattgattta cattgtctta ttgctttaac tttcctaaat 7020 tttgtgttga ttatcccatg gttggtttga gggggagatt tctctgtctc ctagataacc 7080 aaggtttgtc atcatcaaaa agggggagat 7110 // ID Copia41-PTR_I repbase; DNA; EDCOT; 4641 BP. XX AC LG_XI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia41-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4641 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4641 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 260-260 (2007). XX DR Genome; LG_XI; Positions 13417106 13421746. XX CC Positions [2025-2555] - Integrase core CC 'ATATA' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 459..4595 FT /product="Copia41-PTR_I_1p" FT /translation="MAESTFVQAAIPRFDGHYDHWSMLMENFLRSKEYWPI FT VEAGIEEPAVTVVLTETQKTELEGRRLKDLKAKNYLFQAIDRPILETILSK FT ETSKDIWDSMKLKYQGSTRVKRAQLQALRRDFETLQMQIGEPVTNYCARTM FT EICNKMRFHGEKMDDNVIVEKILRSLSPKFDYVACSIEESRDVEKLSIDEM FT QSSLLVHEQKMIRGSHTNEQALKATNYSHSSNFRGRGRGRGRDGNRDRGDG FT YRNQFRAVDNFGRGRGNFRGVEGNKGNYRGVEGQNRGKGDKSKVECFRCHK FT FGHYRSECYARIHNDKAEMSHFAERREEETLLMAVETTQKLKQGSREQQQG FT SEIWFVDTGCSNHMCGCKSSFIYLNEDFNSTISFGDNSTVNALGKGDIEIR FT TKNGFVETISDVLYVPDLKSNLLSAGQLQEKGYEINIKNGICEIYDPLRGS FT IAVVKMSSNRLFPLEIVISQPCFIAEIENPTWLWHFRYGHLNFSGLKTLQQ FT KNMVKGLPEIDIPSQICEDCVVSKQHRSPFPQGKSWRAKHALELVHSDICG FT PISPSSNGGKKYLITFIDDFTRKTWVYFLQHKAEAFYVFQSFKAKAENEAG FT KLIKTLRTDRGGEFCSTEFDVFCGEHGIRKELTASYTPQQNGVSERKNRTI FT LNMVRSLLARGKIPKEFWPEAVNWSIHVLNRSPTFSVQNMTPEEAWSGRKP FT NVEYFRIFGCIAYAHVSDEKRKKLDDKGEKCVFLGMSECSKAYKLYNPLTK FT RIVTSRDVVFDEVQTWDWDRQQPMHADFEIDADLGPAAAAILQQPCSETAA FT EIHSTTGAAAGNFPPTAVAPVAAAPPCPRIRKRPTWMEDYEVNGIEDPITY FT FALFADCDPMTFESAVKEEKWRQAMDDEIDAIERNDTWELIDLPPGQKSIG FT VKWVFKTKLKANGEVDKYKARLVVKGYKQEYGIDYTEVFAPVARHDTIRLI FT IALAAQNSWPIFQLDVKSAFLHGNLEEQVFVDQPLGHIKIGYEHKVYRLKK FT ALYGLKQAPRAWYSRIESYFLREGFHKCPYEHSLFVKIGDGGTLLIVCLYV FT DDLLFTGNDTDMFKDFKSSMMVEFEMSDLGLMHYFLGIEVMQTVNGIFIGQ FT KKYVHDILERFQMKDCNPVSTPTEFGLKLNKDHGGKKVDSTLYKQIVGSLM FT YLTATRPDIMYSVSLISRYMENPTEMHLLTAKRILRYLQGTKDFGLFYKKG FT EKMELVGFTDSDYAGDQDDRRSTSGFIFMFGTGAVSWSSKKQQIVTLSTTE FT AEFIAATACACQAIWIRRILEELQVQQIGATTVFCDNNSAIKLSKNPVLHG FT RSKHIDVRYYFLRDLSNDGMINLVYCRSEDQVADIQTKPLKLAAFMKLRGL FT LGMCSRSAVIKNTEEG" XX SQ Sequence 4641 BP; 1470 A; 785 C; 1089 G; 1297 T; 0 other; gtggtatcag agccttaccc aacatcccta atatccctac ccgtgagcaa cctgcgaaaa 60 aagccaaaaa aaaaaaaaaa aaaaaaaaaa acacccaaaa tccctttcac ttcattttgt 120 aagcagacga gagagagaga gccaaaataa ttcaactttg gtagacgaga gatcgaacca 180 aaatccaaaa ttcacaaacc caattcgaat ttctgcaatc tccatcgtgt gcagctgaga 240 gtaacgagag tatcaaaatt tcagtcattt tcttctccaa tttccatcgt gagcagccga 300 gagaaaccca cccaaattac agaaatcagt tcctgccgtt ttcatcgtga gcaaagagag 360 aaacccagct atttgttttt ctcaaatcgt gaccagacga gagaatccaa tttttcaacc 420 attttcttca tccatttttc agaagcacaa gtacatcgat ggcagaatca acctttgttc 480 aagcagccat tccacgtttt gatggtcact atgaccattg gagcatgcta atggagaatt 540 tccttcggtc caaggagtat tggccgattg ttgaagctgg aattgaagaa cctgcagtga 600 ctgtcgtctt gaccgagact caaaaaacag agttggaagg gagaaggctg aaggatttga 660 aggcgaaaaa ttatctgttt caagccatcg atcgtcccat tttggaaaca attcttagca 720 aagaaacttc caaagacata tgggactcca tgaagctgaa atatcaagga tcgacaaggg 780 tgaaacgtgc acaacttcag gccttgcgac gggattttga gactttacag atgcaaattg 840 gggaaccagt cacaaattat tgtgccagga cgatggagat atgcaataaa atgaggtttc 900 acggtgagaa gatggatgat aatgtgattg ttgaaaaaat attgcgttca ttgtcaccca 960 aatttgatta cgtagcttgt tcaattgaag agtcacggga tgttgaaaaa ctctccattg 1020 atgagatgca aagctccttg cttgtgcatg agcagaaaat gattcggggc tcacatacta 1080 atgagcaggc cctgaaagct acaaattatt ctcattcctc aaatttccga ggaagaggca 1140 gagggagagg tagagatggg aaccgagaca ggggagatgg ttatagaaac cagtttaggg 1200 ctgttgataa ttttggcaga ggcaggggga attttagggg tgttgagggg aacaaaggca 1260 attatagggg tgttgaggga caaaatagag gcaaaggtga caagtccaaa gttgaatgct 1320 tcagatgtca caaatttggg cattaccgat ctgagtgtta tgccaggata cacaatgaca 1380 aagctgagat gtcacatttt gccgagagaa gggaagaaga aactctgcta atggctgtgg 1440 agacaaccca gaagctgaag caggggtctc gggagcagca gcaggggtct gaaatttggt 1500 ttgtggatac gggctgcagc aatcatatgt gtgggtgtaa gtcttccttt atttatttaa 1560 atgaagattt taattcgaca ataagctttg gtgataactc tactgtgaat gctttaggaa 1620 agggtgatat tgagattagg accaagaatg gttttgtaga aacaatttct gatgtgcttt 1680 atgtgcccga tttaaaaagc aatttattga gtgctggtca attgcaagag aaggggtatg 1740 agataaatat aaagaatggt atttgtgaaa tttatgatcc tttgagaggg tcaattgcag 1800 tagtgaaaat gagctcaaat aggctgtttc ctttagaaat tgtgatatca cagccctgtt 1860 ttattgctga aattgagaat ccaacatggc tttggcattt ccgttatggc catttgaatt 1920 ttagtggcct aaaaactctt cagcagaaga atatggtaaa aggtcttcct gaaattgata 1980 ttccttcaca aatatgtgaa gattgtgttg ttagcaaaca acatcgttct ccattcccgc 2040 aaggcaaatc gtggagagca aaacatgctc ttgaattggt gcactcggac atttgtggac 2100 cgattagtcc atcttcaaat ggaggtaaaa agtatctaat caccttcatt gacgatttta 2160 ctcggaagac atgggtttat tttttacagc acaaggcgga agctttttat gtgtttcaaa 2220 gctttaaagc taaagctgaa aatgaggcag ggaagctcat taagactctc cgaacagacc 2280 gtggtggtga attttgttca actgaatttg atgttttttg tggagagcat ggcattcgca 2340 aggaattaac agctagttat acaccacagc agaatggtgt atccgaaaga aaaaacagaa 2400 caattctcaa catggtgagg agcttgctag ctagaggaaa aatcccaaag gaattttggc 2460 cggaagcagt aaattggagt attcatgtgc tgaatagaag ccctactttt tcagtccaga 2520 acatgacacc tgaagaagca tggagtggga ggaaacccaa tgttgagtat ttcagaattt 2580 ttgggtgcat agcctatgca catgtctcgg atgagaagag aaagaagcta gatgataagg 2640 gtgaaaagtg tgtgtttctc ggcatgagtg agtgctccaa ggcctataaa ttgtacaatc 2700 ctcttacaaa aaggattgtg accagccgtg atgttgtgtt tgatgaagtg caaacttggg 2760 attgggatag gcagcagcct atgcatgctg attttgaaat agatgcagat ttggggccag 2820 cagcagcagc cattttgcag cagccttgct cagaaacagc tgctgaaatt cactcaacaa 2880 caggagcagc tgctggaaat ttcccaccca cggcagtagc tcctgttgca gcagctccac 2940 cttgtcctcg tatccgtaaa aggcctactt ggatggaaga ttatgaggta aatggaattg 3000 aagatccaat tacctatttt gctttgtttg cagattgtga tcccatgacc tttgaaagtg 3060 ctgtcaaaga agaaaaatgg aggcaagcaa tggatgatga gatcgatgct attgaaagaa 3120 atgatacttg ggagttgatt gatcttccac caggacaaaa atccattggc gtaaaatggg 3180 ttttcaaaac caaattaaag gcaaatggtg aagttgataa gtataaggca agattggtag 3240 tcaaggggta taagcaagag tatggaattg attatacgga ggtctttgct cctgttgcaa 3300 gacatgatac aattcggttg ataattgcat tggctgcaca gaattcatgg cctattttcc 3360 agcttgatgt caaatcggca ttcttgcatg gaaacttgga ggagcaggta tttgttgatc 3420 aacctcttgg tcatattaag atcggatatg agcataaagt atatcgtttg aaaaaggctc 3480 tttatggttt aaaacaagct ccacgagctt ggtatagtcg tattgagtct tatttcttaa 3540 gagaaggatt tcataagtgt ccatatgagc attcattatt tgttaaaatt ggagatgggg 3600 ggacattact tattgtttgc ttatatgttg atgatcttct atttactgga aatgatactg 3660 atatgtttaa agatttcaag agttctatga tggttgaatt tgaaatgtcc gatcttgggt 3720 tgatgcatta ctttcttggc atagaggtga tgcaaactgt aaatggcatt tttattggtc 3780 agaagaaata tgtgcatgat attctggaaa gatttcagat gaaggattgc aatcctgtta 3840 gcactccaac tgaatttggt ttaaagctca acaaagatca tggagggaag aaagtggaca 3900 gcacacttta caagcaaatt gttggcagtt taatgtattt aactgcaaca agacctgaca 3960 ttatgtattc tgtaagccta atcagcaggt atatggaaaa tcccacggaa atgcacttgc 4020 ttacagccaa gagaatcctc cgttacttgc aaggaactaa ggattttggg ttgttctaca 4080 agaaaggaga aaagatggag ctggttgggt ttactgacag cgattatgca ggtgatcaag 4140 atgacaggag aagcacctcg ggatttattt ttatgtttgg cacaggtgca gtttcgtggt 4200 cttcaaaaaa gcaacaaatt gttactttat ccaccaccga agctgaattt attgctgcca 4260 cagcttgtgc ttgtcaagct atttggataa gaagaatcct tgaagaatta caggttcagc 4320 aaattggagc tacaacggta ttttgtgata acaactcagc tatcaaactc tccaaaaatc 4380 cggtgttaca tgggagaagc aaacacattg atgtgagata ctacttcttg cgagatctca 4440 gtaatgatgg catgatcaac ctagtttatt gcagaagtga agatcaagtt gcagatatac 4500 aaaccaaacc tcttaaactt gctgcattta tgaaattacg cggtctactt ggaatgtgtt 4560 cgcgatcagc agtaattaaa aatactgaag aaggataatt tctcttaaac tgttatctgc 4620 agatttcagt ttaagggagg g 4641 // ID Copia-66_Mad-LTR repbase; DNA; EDCOT; 795 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-66_Mad_; KW Copia-66_Mad-LTR; Copia-66_Mad-I. XX NM Copia-66_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-795 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1671-1671 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 795 BP; 223 A; 220 C; 159 G; 192 T; 1 other; tgttaaagag caaacctgtc agaggaatat tgcacatggt ttcaacacat gccttgacag 60 ctaaactgcc cacgtgggct gtgcatctgt gtttgtgctt tatgggcagt ttctgcacta 120 tgggcagcga ggactccacc ttcatttata cttagtttaa tgcatgcgtg tacgtatcca 180 atgtataaag caatgctgcc attgcagcag tatgaatata cagaaatatc aaacttaaca 240 tggtatcaga gcgcaggtaa tcctttgctc tgctctgcct tcactctttc gctgctatac 300 tgtgaacagc gacatctgct actgcagcaa ccagtgcact gcaagctgca cactcgctgc 360 cttgccgtcg caaaaccgct acacagccat cgtcgctgct ctacctgtca cagccattaa 420 gcacagccgc agagcacagc caagcacagc cactgcacac tgtctgtgaa catggcaact 480 gactcttcca gcaaacacac caaatacgaa gatcccagcg atcctcttta tcttcatcac 540 tccgatcagc ctggagcgat tctcgtcaca caaccattga atgacgaaaa ttactccact 600 tggagccgag ccatgaccat ggccctcaat gccaagaaca aggaaggatt catcaatgga 660 accattmaaa ggcctgagtc gacgtccaca attgaatacc aacagtggac tcgttgcaac 720 aacctcgtga aatcctggct gctcaactct gtctcaaaag atattggtgc aagtgtcatc 780 tacaacaatg ttgca 795 // ID COP3_I_MT repbase; DNA; EDCOT; 4345 BP. XX AC AC159872; XX DT 14-DEC-2006 (Rel. 11.12, Created) DT 14-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Internal region of LTR retroposon, COP3_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; internal region; KW Interspersed; repeat; LTR; retroposon; COP3_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4345 RA Shankar R. and Jurka J.; RT "COP3_MT: LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 607-607 (2006). XX DR EMBL/GenBank/DDBJ; AC159872; Positions 23475 27819. XX CC The sequence has two ORFs. XX FH Key Location/Qualifiers FT CDS 80..1936 FT /product="COP3_I_MT_1p" FT /translation="MATPTTESTKFHPALAVSNIKNHISITLEIENVQYAT FT WAELFKIHARSHKVLHHIIPPATGKSKGPKTDDEKELWSTLDAAVLQWIYS FT TISHDLLHTIIEPDATAMEAWNRLRDIFEDNKNSRAVTLEQEFSSTNMEDF FT PNVSAYCQRLKELSDQLKNVGAPVSNNRLVLQIVAGLSEAYNGVATLIRQS FT DPLPQFYQARSMLTLEEAGLMKKVATSGGAAMMARETSDSPSLSKNYQQNR FT NNHGGKHGQNRQNSGKNNGGRGSGKNSRGGGRGGIRNGGGQQQYDQQRPGQ FT QQWSAGQWQWPWMPWGMPPCPYPSSPWARPNFQHGQHAQQHQPGILGSKPP FT QAYTAAAPLTPTDIEAAMHTLGLNPTDPNWYMDTGATSHMTSEQGNLSSYF FT NLSNNRGIIVGNGHSIPIRGYGHTNLSFPNPPLTLKNVLHSPQLIKNLVSV FT RKFTTDNSVSVEFDPFGFSVKDFQTGMRLMRCESRGDLYPITTSQAISPST FT FAALAPSLWHARLGHPGAPVVDSVRKNKFIECNKASGSHICHSCSLGKHIK FT LPFVSSNSCTVMPFDIIHSDIWTSPVLSSSGHRYYVLFVDDYSNFLWTFPL FT SKKSQVFSIFFIFSNIYPNPI" FT CDS 1824..4340 FT /product="COP3_I_MT_2p" FT /translation="MFCLWMTTLIFCGHFHCLKNLKFFPFFLSFRTFIRTQ FT FEREVKNIQCDNGKEFDNRHFWEFCKENGVAFRLSCPHTSSQNGKAERKIR FT TINNIIRTLLVHASLPPSFWHHALQMATYLINILPNKQLAYQSPLKILYQK FT EPSYSHLRVFGCLCYPLFPSTTINKLQARSTPCVFLGYPSNHRGYKCYDLS FT SRKIIISRHVIFDETQFPFAKLHNPQPYTYGFMDDGPSPYVIHHLTSQPSL FT GQPAQHDLPNTQPTTQPTTPEEQHAHSPPSSSPNTSPSTTATPSPPYQPTP FT ISVPKPVTRSQHGIFKPKRQLNLNTSVPRSPLPRNPVSALRDPNWKMAMDD FT EFNALIKNKTWELVPRPPDVNVIRSMWIFTHKEKSDGVFERYKARLVGDGK FT TQQVGVDYGETFSPVVKPATIRTVLSLALSKAWSIHQLDVKNAFLHGELKE FT TVYMHQPMGFRDPNLPNHVCLLKKSLYGLKQAPRAWYKRFADYVSTIGFSH FT STSDHSLFIYQKGTTMAYILLYVDDIILTASSDALRMTIISLLSTEFAMKD FT LGSLHYFLGIAVTHHTGGLFLSQRKYAAEIIERAGMAACKSSSTPVDTKPK FT LSANSSAPYADPSHYRSLAGALQYLTFTRPDIAYAVQQVCLFMHDPREEHM FT HALKRIVRYIQGTLDHGLHLYPSSTSTLISYTDADWGGCLDTRRSTSGYCV FT FLGDNLISWSAKRQATLSRSSAEAEYRGVANVVSESCWLRNLLLELHCPIR FT KASLVYCDNVSAIYLSGNPVQHQRTKHIEMDIHFVREKVARGEVRVLHVPS FT RYQIADIFTKGLPLVLFEDFRNSLSVRQPPVSTAGVC" XX SQ Sequence 4345 BP; 1140 A; 1062 C; 858 G; 1285 T; 0 other; ggtatcacaa gtctagggta cgatccatat tgcttccgcc gcaccctagc tctcttctcc 60 ttccttctct aattctctca tggcaacccc cacgactgaa tctaccaaat tccacccggc 120 tcttgctgtt tctaatatca agaaccatat ctccatcact cttgagatcg aaaacgtcca 180 atatgcgaca tgggcagaac tgttcaagat tcatgcccga tctcacaagg tcctccacca 240 catcatcccg ccggcgacag gcaaatcgaa gggccctaaa acagatgatg aaaaggaatt 300 gtggtcaacc cttgatgctg cggtcctcca atggatctat tcaacaattt cgcacgatct 360 gctgcatact atcattgaac cagacgccac cgcgatggag gcgtggaata ggttgcgtga 420 tatattcgaa gacaacaaaa attctagggc tgtaacactt gagcaggaat tctcctctac 480 caacatggaa gatttcccaa acgtttctgc ctactgtcaa cgactcaagg agttgtcaga 540 tcaactcaaa aatgttggtg caccggtctc aaacaaccgt cttgtccttc aaattgtggc 600 tggcctctct gaagcgtaca atggagtagc cacactcatc cgccaaagtg atcctcttcc 660 acaattctat caagctcgct caatgctcac tctagaagaa gccggtctca tgaagaaggt 720 tgcaaccagc gggggtgcag ccatgatggc tcgtgaaact agtgacagtc cctccctctc 780 taaaaattac caacaaaacc gtaataatca tggcggtaaa catggtcaga atcgtcaaaa 840 tagtggcaag aacaatggtg gccgcggaag tggcaagaac agccgcggtg gtggtcgtgg 900 tggcatccgc aacggtggcg ggcagcagca atacgatcaa cagcgaccgg ggcagcaaca 960 gtggtctgcc gggcagtggc agtggccttg gatgccgtgg ggtatgccac cttgcccata 1020 cccctcctca ccatgggcca gacccaattt ccaacatggg cagcacgcgc aacaacacca 1080 gccaggcatc cttgggtcaa aaccacctca agcatacacg gcagcagctc cgctcactcc 1140 aactgacatt gaggcagcga tgcacactct tgggcttaat cctacggatc caaattggta 1200 catggacact ggtgccacat cccacatgac ttccgagcaa ggtaatctct cgtcttattt 1260 taatttgagc aataatcgtg gtatcattgt cggtaatggt cattcaattc caattcgggg 1320 ttacggtcac acaaatttgt ctttcccaaa tcctccctta accttgaaaa atgtcctgca 1380 ttcccctcaa cttattaaaa acttagtgtc agttagaaaa tttacaactg ataattcggt 1440 ttctgttgaa tttgaccctt ttggcttttc tgtgaaggat ttccagacgg ggatgcgtct 1500 aatgagatgt gagagccggg gagaccttta tcccatcacc accagccaag ccatttcacc 1560 atctactttt gcagctttag caccatcttt gtggcatgct cgtttaggtc atccgggggc 1620 acctgttgtt gattccgttc gaaaaaataa atttattgaa tgtaataagg ctagtggttc 1680 tcatatttgt cactcttgtt ctcttggaaa acatattaag ttgccatttg tttcttctaa 1740 ttcttgtact gttatgccat ttgacattat ccatagtgat atttggacat ctcctgtttt 1800 gagttcttcg ggccatagat attatgtttt gtttgtggat gactactcta attttttgtg 1860 gacatttcca ttgtctaaaa aatctcaagt tttttccatt ttttttatct tttcgaacat 1920 ttatccgaac ccaatttgaa cgggaagtaa aaaatattca atgtgataat ggtaaagaat 1980 ttgataatag acatttttgg gaattttgta aagaaaacgg ggtagctttt cgcctctctt 2040 gtccacatac atcatctcaa aatgggaaag ccgagagaaa aatccgtacc atcaacaata 2100 ttattcgtac actccttgtc catgcatctt taccaccttc attttggcat catgctttac 2160 aaatggccac ctatcttatc aacattctgc caaacaaaca attagcatat caatcacctc 2220 tcaaaattct ttatcaaaag gaaccttctt attctcatct tcgggtgttt gggtgtttat 2280 gttatccttt atttccctct accaccataa acaaacttca agcccgttct accccgtgtg 2340 tttttttggg atacccatct aatcatcgtg gttacaaatg ttatgatttg tcctctcgta 2400 aaatcataat cagtcgtcat gtcatttttg atgaaaccca atttcccttt gctaagttgc 2460 acaatccaca accttataca tatggtttta tggatgatgg accctctcct tacgtgattc 2520 atcacttaac ctcacaacct agcctaggtc aaccagccca acatgacctt cccaacactc 2580 aacctactac tcaacctaca acaccagaag aacaacatgc ccatagccca ccatcgtcat 2640 caccaaatac ctcacctagc acaacagcta caccttcacc tccatatcag ccaactccta 2700 tttcggttcc caaacccgta acacgtagtc agcatggaat tttcaaacct aagcgacaat 2760 taaatcttaa tactagtgtc cctagatccc ccttaccacg taatcctgtg tctgcccttc 2820 gtgacccgaa ttggaaaatg gctatggatg atgaatttaa cgctcttatt aaaaataaga 2880 cgtgggagtt ggtgccccgt ccacctgatg taaatgtgat tcggtctatg tggattttca 2940 ctcataaaga aaaatctgat ggtgtttttg agaggtataa ggcccgtctt gtaggtgatg 3000 gcaaaacgca acaggttggc gtggactatg gggaaacttt tagtccagtg gtcaaaccgg 3060 ccactatccg cactgttttg agtttagctc tctctaaagc atggtctatt caccaacttg 3120 acgtgaagaa cgctttcttg catggagaac tcaaagagac tgtgtacatg catcaaccca 3180 tggggtttag ggatccaaat cttcctaatc atgtatgctt gttaaagaaa tctctatatg 3240 ggctcaaaca ggcccctcgg gcttggtaca agagatttgc tgattatgtt tctactattg 3300 gtttttctca cagtacttcg gatcattctc tctttattta ccagaaaggc acaactatgg 3360 cttacattct tttatatgtg gatgatatta tactgacagc ctcctctgat gctcttcgca 3420 tgactatcat atccctcctt agtacagaat ttgctatgaa ggatttgggg tcattacatt 3480 acttcttggg tatcgctgta actcatcata caggtggatt gttcttatct caacgaaagt 3540 atgcagctga gatcattgaa cgggctggca tggcagcatg taaatcatct tctactccgg 3600 ttgacactaa accgaagctt agtgctaatt ccagcgcacc atatgcagat ccatctcatt 3660 atcgaagcct tgcaggtgct cttcaatacc tcacttttac gagacctgat attgcttatg 3720 ctgtgcaaca ggtgtgttta ttcatgcatg acccaaggga agaacatatg catgctctca 3780 agcgcattgt gcgctacatt cagggtactc tggatcatgg tttgcatctc tatccatcct 3840 ccacatccac tctcatttct tatacagatg ctgattgggg tgggtgtctg gatacccgac 3900 gctctacgtc tggttattgt gtgtttcttg gtgataattt aatttcttgg tccgccaaac 3960 ggcaagctac tttgtcacgt tctagtgcgg aggcagaata ccgaggcgtt gccaatgtgg 4020 tttctgagtc atgttggtta cgtaatcttc ttcttgagct tcattgtcct attcgaaagg 4080 ctagtttggt gtattgtgat aatgttagtg cgatttatct ctctggaaat ccggttcaac 4140 atcagcgcac taaacatatc gagatggata ttcattttgt tcgcgaaaaa gttgctcgtg 4200 gggaagttcg agtcctacac gtcccctcac gctaccagat tgcagatatt tttacaaagg 4260 gccttccctt ggttctgttt gaggattttc ggaacagtct cagcgtacga caacctcccg 4320 tttcgactgc gggggtgtgt tagag 4345 // ID Gyp_LTR_MT repbase; DNA; EDCOT; 2338 BP. XX AC AC144656; XX DT 13-DEC-2006 (Rel. 11.12, Created) DT 14-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Long terminal region sequence of LTR retroposon, Gyp_MT, from DE Medicago truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; Gyp_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2338 RA Shankar R. and Jurka J.; RT "Gyp_MT: LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 623-623 (2006). XX DR EMBL/GenBank/DDBJ; AC144656; Positions 48631 50968. XX CC The LTR sequence flanks both termini of an internal region coding CC for gag and pol. XX SQ Sequence 2338 BP; 791 A; 519 C; 295 G; 733 T; 0 other; tgtcataccc caatttttga cccaagatac cacttacacg cgtcatttaa ctccgaccgg 60 tcttagcctt tcgagcaaaa attcggcagg gaggtatttt aaaatacctc atgtttgatt 120 ccgagtcggg ctctcttctc tcaattttca tttaatttta atttccatct tttattaact 180 ttaaattcgt tttttaatct ttattttatc tcatctttgt tttttatttt taatccttta 240 gatgtcccaa aaaattaatc aaaaaccatt gtcggataat atccaaacag ctcacccaca 300 gttcattcac acagctcaaa acaggctgtc atgttcctct ccaagcaaca aaattctgct 360 ctataaatac aacacacaaa ccagccaaga aaggcggggg ggcccaacag acaaaaacat 420 agaatttcaa ttgcaaaaac ctgcaatcac aatatccaaa aaccaatcac agaaaaaaaa 480 cccaactcat ttcaaaccat caccgatcca taaacaaaca aagaaccaca catcacaaac 540 tgtttcacgc tcacagaacc ttttttttca acgaacaaaa cacaaatcca gtagccataa 600 accccaaatc acaaatccaa tcaaccacaa accaaatcta aacagcacaa acacaaaatc 660 atcatcaacc gcaaatccat acaaccaagt ctgacccata caagaatctc acaaaccgaa 720 acacaaatcg gcttaagctt taaaggttac tttttctttc tttcgtctct tttagatcta 780 gggttgaagg gtttgatttt gggaatttta aggctaaaaa cgtatagagg agagagagta 840 gaagataaag aacaaaaaat aataaaaaag aggagtacat aatcactccg gcgcggcggc 900 gcggccatct tggctggccg gccaccgcgc cagccaccgg agaagaaggt ggcgacggag 960 aagaattcta gagagaaggc agagcctctc tctctagaaa taagagaaga gagagagaag 1020 tttgaaataa aaatgattaa aaaaaccgga gctgtgtatt tataaaaggg attggaccgg 1080 ttcaacccct gaaccggtct gaaccggtct attccaggcc cacacgcgcc cggcctcacc 1140 caaggcccaa atcctcttca ttttattttc tgcaccctcc tttactgctc acacacaccc 1200 cagcatctca tttttctaat ttctttttca tgcattttaa ttctctctct atctgttaat 1260 ctagagtact ctggtcctat attaactatt aatattatat ttttgtttaa tttaattatt 1320 ctccagaaca atctggtcct tgttaattaa attaatccag agtgctctgg tcctatatta 1380 actgttaata ttatattttg tttaattcaa ttattctcca gaacaatctg gtccctgtta 1440 attaaattaa tccagagtgc tctggtcctc aattaactgt caatattata atttgttatt 1500 ctccagaata atctggtcct tgttaattaa tttaatccag agtgctctgg tcctaaatta 1560 tttgttaata ttatattttt gtttaattta atcattctcc agagtgcttt ggtcccctgc 1620 ttttattttc ataacttcgt tagtttaatt ttatttacta tttcaaaaca acaaaaacat 1680 tcaaatatca aaaaatcaca aaaaaaactt ttcacaaaaa aaaccttgat cttaaatcaa 1740 gtgaccgtct ttttatttta tttttcttaa tcaaatttca aatcaattct aattcaactt 1800 caagtcaatt tctttcaatc taaaaaacac aaatcaattc tcatttgcca cttggctttt 1860 ttttttcttt caaaaactaa taaaaaacac aaaacaaatc aaacgtcaat ttctaccccg 1920 aactacgagg ttttgatccc tcacgggtac gtaggcagag gaccttgtcc ttccaaatca 1980 attaaaaaac aatttccttt tttttctttt caactttcaa ctcaaaaaca attttctttt 2040 tttttctttt caactaaaat caattttcat tttcttttca attctatttt catctcttca 2100 aaagcaagca aatttaagca caaaaagttg aataaaaatc aagaggttct cgtagagtac 2160 tacaaatatt tagggtgcta acaccttccc taaatataac caaccctcga accctaaatc 2220 ttttcaaaat ggatggtttg gaacattttc cccttcaaaa aaatttgttc agtcgtgaga 2280 taaaaactga gtcaaacgct aatcaaatgg cctttgacct ccgaaaaatg gcgcgaca 2338 // ID Copia-17_Mad-LTR repbase; DNA; EDCOT; 171 BP. XX AC ACYM01116382; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-17_Mad-I; KW Copia-17_Mad-LTR; Copia-17_Mad_. XX NM Copia-17_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-171 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1362-1362 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01116382; Positions 478 648. XX SQ Sequence 171 BP; 57 A; 28 C; 27 G; 59 T; 0 other; tgttagcgtg agtcaacctt aaatttcagg aatgtaatca tatattttag gaataggatc 60 acatgattga ttcattgtgg gattcttgtt tcctaattta taggacctct tgtacaacta 120 tatatgcacc tcccagagag aagaataatt tattattaaa ccctaaacac a 171 // ID Copia-20_Mad-LTR repbase; DNA; EDCOT; 354 BP. XX AC ACYM01133918; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-20_Mad-I; KW Copia-20_Mad-LTR; Copia-20_Mad_. XX NM Copia-20_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-354 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1366-1366 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01133918; Positions 11145 11498. XX SQ Sequence 354 BP; 102 A; 59 C; 68 G; 125 T; 0 other; tgttagttga ttaaggtcta aactgtattt tccttacttt agcaagtgta aataaatcag 60 ttagtgatca agggctgaga ttagatgata ttgtgctagg cttggatgta aacatgtgtc 120 aagatctcat agggtcttgt aatgaatggt atgatgagct cataggctat gtagcttctc 180 tctccctagt agtcatgtaa atgttgagga aagaaggaat atatgcagca gagcattctt 240 tggctctctc tgagattttt gagaactctc tctgtctttt cattttctct ctaaaaactt 300 cttcttctta tgcacatttc taaatacatc actacataac aggaaagtcc aaca 354 // ID Copia-43_Mad-LTR repbase; DNA; EDCOT; 324 BP. XX AC ACYM01028651; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-43_Mad-I; KW Copia-43_Mad-LTR; Copia-43_Mad_. XX NM Copia-43_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-324 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1393-1393 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01028651; Positions 5 328. XX SQ Sequence 324 BP; 78 A; 54 C; 73 G; 117 T; 2 other; tgttcagttt aagggaggat gttaaaattg ttgggatcct agccgttagc agataagtct 60 tgttgctagg gttcctagtt gttagggttt ctaaccacgt aggagtctaa taaagtccta 120 gtcttaaggg acacccaagt agtcgttacc acgattgtag gtcctgtaaa atcktgggma 180 gtttcattta ctttctgatc agttgtaagg ctatttaatg gccggtgttg atgctttcaa 240 ttaataagaa tactccctgt ttttcatgca agctttcgaa cttggcttta ctgtgattcc 300 ttgtttaagt tctaggttct aaca 324 // ID hAT-2_PTr repbase; DNA; EDCOT; 3354 BP. XX AC . XX DT 17-DEC-2009 (Rel. 15.02, Created) DT 17-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE hAT-type DNA transposon - consensus. XX KW hAT; DNA transposon; Transposable Element; hAT-2_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3354 RA Kojima K. and Jurka J.; RT "DNA transposons from black cottonwood."; RL Repbase Reports 10(2), 112-112 (2010). XX DR [1] (Consensus) XX CC >94% identical to consensus. 8-bp TSDs. XX FH Key Location/Qualifiers FT CDS 724..3147 FT /product="hAT-2_PTr_1p" FT /translation="MENQGSKRGKTMFSFFKPNEQTSTSKGHSPSNVDVSN FT RSEQPPFKSQRVEIDVNTLERDPGLRIPVWKHPINQQDEIRRAYIKMGPYQ FT PKLAEYPRTESGRQYRRFQYTWFDQFPWLEYSPSKDAVFCFPCFIFENKVP FT RHLTFTTEGFRSWKRVNDGVRCALLMHVGSPTSPHNNAVKSAEDLMKVSRH FT IDKVLNAQTVEEVQKNRLRLMTTIESVRWLSLQACAFRGHDESSASNNRGN FT FLEMIRLMGRLNVDIDDVVLEKAPKNAKYTSPTIQKEILHILANKVRKKIC FT EEVRDAKFCILVDEAKDASNKEQMAIVLRFVDIQGFVRERFFGIVHVSDTT FT SSTLKKEICDVLARYNLHIFNMRGQGYDGASNMRGAWNGLQALFLRDCPYA FT YYVHCFAHRLQLALVAAAGNEISIWLFFSKLTTIINLICASPKRHTELHYA FT QAIEIAHMVATGERETGRGANQIGNLHRSGTTRWSSHFDSICSLIDMYGAT FT ITVLESMVQEGSSNSIRGEAGGCLIVMKSFEFIFILYLMHKIMGITDLLCR FT ALQQKSLDILNAMDLVSTTKALLQTLRDAGFDLLLANVQSVCTKYEIDIPH FT MNASYKKATGRSCQQQGSVTVYQHYHYDIFNSTIDFQLEELNSRFSDGTVE FT LLVLSSALEPKDNFKSFKVDAIYKLAEKFYPEDFNEQEMYYLRSQLEHYQI FT DVIHHESFQNMSTISELCRGLAETNKSQHYHLIDRLIRLVLTLPVSTATTE FT RAFSAMKHVKTVLRNKMKEEFLADSMMIYIERELVEDIDSDSIIDEFYSTK FT HRRVQL" XX SQ Sequence 3354 BP; 1048 A; 566 C; 618 G; 1121 T; 1 other; caggggcgga gccttttaca aggctaagga gggctgtagc ccaggttaaa aaaaaattaa 60 tgacccactt tcccctttwt cttttacaca gcaaacctat gtcccacccc tttcccatct 120 tttacagcaa acctagtgtc ccacttttcc ttgcaataca aattaattac tagccattag 180 ccgccacttt actttcccta gcaacactaa ttaattagcc acccaccttc ccttgcaata 240 ctaattaatt agttatattt tacagcaaat ctatctaaat ataaataatt aattggttca 300 catgtcttct aagtaacttg gggttttagc tatttttctt ctcaacaata tacaatttta 360 gcttggattt tgaagaagaa tctatacaga gagccgcaag agtgtaaaat catcaggtaa 420 gaatttacaa gccctgactt ttcattttga attcaatgtt tcacattcat tacagtagat 480 tgttagtgga gtaaacagta gactgtaccc tagaaatgga tgcatgctaa cacactagta 540 gtctagtact aataatttac tggttatttc aaagttaagt tctccaaatc tcccagtagt 600 ttgcatcact agtttatcct tgtatattct gcatttcatg aatattctat tgtggcatta 660 gtatcttttc atcttgcacc tgacttccct aatccctttt acttgaatag gttataaatt 720 ataatggaaa atcaaggaag caagagagga aaaactatgt tttcattctt taaaccaaac 780 gaacaaacat caaccagtaa aggacattct ccatccaatg ttgatgtctc aaatcgtagt 840 gaacaacccc ctttcaaatc tcaaagagtt gaaattgatg ttaatactct tgaacgagat 900 cctgggttac gaattccagt gtggaaacat cctattaatc aacaagatga aattagaaga 960 gcttatatca aaatgggtcc atatcaacct aagttagcag agtatccaag gactgaatca 1020 gggagacagt atcgtcgatt tcaatacact tggtttgatc aatttccttg gctagagtac 1080 tctccatcaa aggatgcagt attttgtttt ccatgcttta tctttgaaaa caaagtgcct 1140 cgtcatctca cattcaccac cgaaggcttt agaagttgga agagggttaa tgatggggtt 1200 agatgtgcac ttttgatgca tgtgggaagt cccacttcac cacataataa tgctgtgaaa 1260 tctgctgaag atttaatgaa agtaagtaga catattgata aagtgttgaa tgcacaaact 1320 gttgaagaag ttcagaaaaa tcggttgaga cttatgacaa caattgaaag tgttcgatgg 1380 cttagcttac aagcatgtgc atttagaggt catgatgaat cttcggcttc taataatcga 1440 ggcaattttt tggagatgat aagacttatg gggagactga atgttgacat tgatgatgtt 1500 gtcttagaaa aagctccgaa aaatgcaaag tatacctcgc cgactattca aaaagagatt 1560 ttgcatattc tcgcgaacaa agtgaggaaa aagatttgtg aagaagttag agatgcaaag 1620 ttttgtattt tggttgacga agccaaagat gcatcaaata aagaacaaat ggctattgtt 1680 ttgagatttg ttgacattca gggttttgta cgagagcgtt tttttggtat tgtgcatgtt 1740 tcagatacta cttcttcaac acttaaaaaa gaaatttgtg atgtgctcgc tcgatataac 1800 ttgcatattt tcaatatgcg aggtcaaggg tatgatggtg ctagcaatat gcgtggcgca 1860 tggaatggac tacaagctct atttctcaga gattgtcctt atgcatatta tgtacattgc 1920 tttgctcacc gactacaact ggcattagtt gcagcagctg gaaatgagat ttctatttgg 1980 ttatttttct caaaattgac aaccattatc aaccttattt gtgcttctcc caaacgtcat 2040 accgagttac attatgctca ggctatagaa attgcacata tggtagctac tggagaacgt 2100 gagactggta gaggggctaa tcaaattggt aatttacatc gaagtggaac tactcgctgg 2160 agctctcatt ttgattctat ttgcagctta atagatatgt atggtgcaac tattactgtg 2220 cttgaaagta tggttcaaga aggatcttct aattctatac gtggagaagc tggtggttgt 2280 ttgattgtga tgaaatcttt tgaatttata ttcatcttat atttgatgca taaaataatg 2340 gggattactg atttactttg tcgagctttg cagcaaaaat ctcttgacat cttaaatgca 2400 atggatcttg tatcaactac taaagcattg cttcaaactt tgagagatgc cggatttgat 2460 cttctccttg caaatgtgca atctgtttgc acaaaatatg agattgacat accacatatg 2520 aatgcttcgt ataaaaaggc tacaggtcgt tcatgtcaac aacaaggttc agtgacagtt 2580 taccagcatt atcattatga tatatttaac tcaacaatag attttcagtt ggaagaatta 2640 aattctagat tcagtgatgg gacagtggaa ctccttgtac ttagctctgc tttagaacct 2700 aaggacaact ttaaatcatt taaagttgat gctatttaca agcttgctga gaaattttat 2760 cctgaagatt tcaatgaaca agagatgtat tatttgagat ctcagctaga gcattatcag 2820 attgatgtga ttcatcatga gagctttcag aatatgtcta ccatttctga attatgtcga 2880 ggattagctg aaacaaataa gtcgcagcac tatcatttga ttgacaggtt gattcgtctt 2940 gttttgactt tgcctgtttc cactgccact acagagcggg cattttcagc tatgaaacat 3000 gttaaaactg tgcttcgcaa taaaatgaaa gaggagttct tagcagattc tatgatgatt 3060 tacattgaac gagagcttgt tgaagatatt gattcggatt cgatcataga tgaattctat 3120 tctacaaaac atcgaagggt gcaactttga tagtataatt tatttttatt tttattttga 3180 attttatgta ctttaaattt tattttttat atattttatg ttatgtattt gaattaaaac 3240 tttattgtta acttgacaaa tttatatatc cgagtgaatg attgatctta aaaaataatt 3300 tatgtgtatt tatatcatag cccaggatag gaaaaattcc tggctccgcc cctg 3354 // ID Copia20-VV_I repbase; DNA; EDCOT; 4436 BP. XX AC AM444110; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia20-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4436 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4436 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 699-699 (2007). XX DR Genbank; AM444110; Positions 13946 18381. XX CC Positions [1807-2301] - Integrase core CC 'CCATC' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 2440..4434 FT /product="Copia20-VV_I_1p" FT /translation="MSSNGRVYISRDVIFNETSFPYSKTIQVSSCLPSTVS FT PSTSHLSPSASPPVLSPTMLPAPTSPISSARPISEMDNIVSTHPHAPNSAD FT TTLTPAQVVSNPVATPVQHVVSSIADASVTRTIAKDADNTHPMITRAKSGI FT VKPKIFIAAVREPSSVSAALQQDEWKKAMVAEYDALQRNNTWSLVPLPAGR FT QAIGCKWVYKTKENPDGTVQKYKARLVAKGFHQQAGFDFTETFSPVVKPST FT IRVVFTIALSRNWAIKQLDVNNAFLNGDLQEEVFMQQPQGFIDEKNPNLVC FT RLHKALYGLKQAPRAWFEKLHQALLSFGFVSAKSDQSLFLRFTPSHITYVL FT VYVDDILVIGSDTTTITSLIAQLNSEFSLKDLGEVHYFLGIQVSHTNNGLH FT LSQTKYIRDLLQKTKMVHCKPARTPLPTGLKLRAGDGDPVDDLHGYRSTVG FT ALQYVTITRPELSFSVNKVCQFMQNPTEEHWKAVKRILRYLQGTLQHGLHL FT KKSSNLDLIGFCDADWASDLDDRRSTSGHCVFLGPNLISWQSKKQHTVSRS FT STEAEYRSLAGLVAEITWLRSLLSELQLPLAKPPLVWCDNLSTVLLSANPV FT LHARTKHIELDLYFVHEKVIRKEVEVRHVPSADQLADVLTKTVSSTQFIEF FT RHKLRIENLSTLSLRG" XX SQ Sequence 4436 BP; 1239 A; 901 C; 856 G; 1417 T; 23 other; tggtatcaga gcmrtgagtc ttcttcaatg gaggycaata tcagtcctgc aatagcaaac 60 cctaatgctt tgtcttccac tcgttttgtt ccaattaact tcaatcactc actgtccgtg 120 aagcttgata acaagaattt cttgatctgg aaacaacaaa tygtctctgc gattcgaggc 180 tatgggctac agaaatttgt gtttagtgat gatgaagtac cagttcaatt tctcaccaga 240 gaagatgcga gatctggaaa agcaactaag gaattcctcg agtgggaaca acaggatcaa 300 ctactgctct cttggcttct ctcatctgtt tctgagtcaa tacttcctcg rttagttggc 360 tgtgatacat cctytcttct ttggggacga ttagagcaat attttrcgtc tcagactcga 420 gccaaggcga aacarttcaa gactcaactt cagcatacca agaaggragg ttcaacaatt 480 gatgaatatc ttgcgaagat caaggtttgt gttgattcac ttgcatctgt tggtgtttct 540 ttgtcaacya aagatcatgt tgaatcaatt cttgatggtt tacccaatga ttatgagtct 600 ttcrttacct cagtcatttt gaggaatgat gatttttcag ttgaagaaat tgaagctctc 660 ttgatggctc atgaatccag agttgagaag aacaacagtt ctcttgactc ctctccttct 720 gctcatgttg caagctctaa cgctgtagaa aaagggaatc gttttaagca agattattat 780 gctgctaact ctcaaggtaa tcattcaggt tacaatggta gttttggacg aggtggagac 840 tttggtcgta gaggtggctt caatggtggt cgtggattca attggaatta caatggaaga 900 agcaatagag gtggttttcg tggtagaggt ggttttcgtg gtagaggaaa cagaggtaat 960 tttcaagcaa gacctccttg gaactctgat aatcagaatg agaaaccagc atgccaacta 1020 tgtggtaaaa taggccatgt agtagcacag tgctattaca ggtttgacca tactttccaa 1080 gtaccacaga atctatcagg caggaaccct tctcctcggg cttattacar yttttcaccc 1140 caagtaaatg gtgttatccc aacttctgaa gtttttagtg atgacaattg gtatccrgac 1200 tctggagctt caaaccatgt gacacctaat cctgcaaatc tgatgaaaag tgytgagttt 1260 gctgggcaaa atcaggttca tgttgggaat ggaacaggtt tgtccattaa gcatattggt 1320 caatctgaat tcttatmtcc tttttcatct aaacctcttt tacttaatca cttacttcat 1380 gtaccttcca ttaccaaaaa tctcttgtca gtttccaaat ttgcaaagga taataaagta 1440 ttttttgaat ttcattctga ttcctgtttt gtcaaggatc aggtaaccca agctgttcta 1500 atggttggga aggttagaga tggattgtat gcttttgact cctcacatct tgctctcaga 1560 ccaactcaaa gcttatcgaa gtctccttct rttgttgcta gttcmttttc ttccaaagtt 1620 tgtayarctt ctttgtcatc tacctttgat ttgtggcata aaaggttggg gcatccttcg 1680 gctgcaacaa ttaaaaatgt tctgtccaaa tgtaatgttg cccatataaa taaaatggac 1740 tccaacttct gttcttcttg ttgcttgggt aaaatacata kgtttccttt ctctttgtct 1800 catacaactt ataccaaacc ccttgagtta attcattcag atttatgggg tccagccccg 1860 gtattatcta atagtggata taggtattat attcactttg tggatgcctt ttcacgattt 1920 tcttggatat ttttactcag aaataaatct gaagctatca aaacctttgt taacttcaaa 1980 actcaggtgg aattgcaatt tgatttaaaa atcaagtcct tgcaaactga ctggggaggt 2040 gaatttcgtg cttttcaatc ttatcttgct gaaaatggca ttgtacatcg tgtttcttgt 2100 ccacacactc aacaacaaaa tggtgttgct gaacggaagc ataggaccat agttgaacat 2160 ggtttaactc ttctccatac agyttctctt ccccttaaat tttgggatga atcatttagr 2220 actgttgttt acctatcaaa taggcttccc actgcagtac ttcatcacaa atgtcccatt 2280 gaagtcttgt tcaagtccat acctgactat tccttcctca aagtttttgg ctgctcctgt 2340 tttcccaact tacgtcccta taacacccat aaacttcaat acaggagtga agaatgcact 2400 tttcttggct atagtctaaa acacaagggt tacaaatgta tgtcttctaa tggtcgagtc 2460 tatattagtc gtgatgtcat ttttaatgaa acctccttcc cttattctaa aactattcaa 2520 gtttcatctt gtttaccttc cactgtttcc ccttctactt ctcatttgtc tccttcagcc 2580 tctcctccag tattgtctcc aacaatgctg ccagctccta cttctcccat ttcttcagct 2640 agaccaataa gtgaaatgga taatattgtt tccactcacc cacatgcacc taatagtgct 2700 gatactactc taacacctgc acaagttgtt tctaatccag ttgctactcc tgtacagcat 2760 gttgtctctt ccattgcaga tgcaagtgtg actaggacaa ttgccaagga tgctgataat 2820 actcatccaa tgattactag agcaaagagt ggaattgtta aacccaaaat ttttattgct 2880 gcagtaagag aaccttcaag tgtttcagct gcccttcaac aagatgagtg gaaaaaggct 2940 atggtggctg agtatgatgc attacaaaga aacaacacct ggtcactagt tcctttaccc 3000 gctggtagac aagctatagg ttgcaaatgg gtttacaaaa ctaaagaaaa tccagatggc 3060 actgttcaga agtataaagc acgattggtt gccaaaggct ttcaccaaca agctggcttt 3120 gattttactg agacctttag tccagtcgtt aagccttcta caataagagt tgtcttcacc 3180 attgctctct caaggaattg ggcaatcaag caactagatg taaataatgc gttcctcaat 3240 ggagatttgc aagaagaggt gttcatgcaa caaccacaag ggtttattga tgagaagaat 3300 cctaatttgg tttgtagact tcataaggcc ttgtatggtt tgaaacaagc cccacgagcc 3360 tggtttgaga aacttcatca agcattattg agttttggat ttgtatccgc caagtctgac 3420 cagtcactat tcttaaggtt cactcctagt catattacct atgtcttggt ttatgttgat 3480 gacattttgg tcattggtag tgacacaact acaattactt ccctaatagc tcaattgaac 3540 tcagaatttt ccttgaaaga cctcggggaa gtacattatt tcctaggaat acaagtttct 3600 cataccaata atggactaca tttatcccag actaaatata ttcgagactt gctccaaaag 3660 acaaaaatgg tgcattgcaa acctgccaga actcccctgc ccactggtct aaaattgaga 3720 gctggagatg gtgatcctgt ggatgattta catggttatc ggagtacagt aggagctctt 3780 cagtatgtga ccatcacaag gccggagctc tccttcagtg tgaacaaagt atgccaattt 3840 atgcagaatc ctacagagga gcattggaag gctgtgaaac gaatcttgag atatttacaa 3900 ggcactttgc agcatggttt gcatttgaag aaatcatcca accttgattt aattggattt 3960 tgtgatgctg attgggcatc tgatttggat gatagacgct caacctcagg ccattgtgta 4020 tttttgggac caaatttgat atcttggcaa tccaagaaac aacatactgt ttcaaggtct 4080 agcactgaag ctgaatatcg aagtcttgca ggtttggtag ctgaaatcac atggttaagg 4140 tcattgttga gtgagttgca acttccccta gctaagcctc ctttggtttg gtgtgataac 4200 cttagcacgg ttttgctgtc tgcaaatcct gttcttcatg caagaacaaa gcacatagag 4260 cttgatctct attttgttca tgaaaaagtc attcggaagg aggtagaagt tcgccatgtc 4320 ccctcagctg atcaacttgc agatgtattg acaaagacag tttcctcaac tcaatttatt 4380 gaattcagac acaaactcag gatagaaaac ctttctaccc taagtttgag ggggga 4436 // ID POPCOP2_LTR repbase; DNA; EDCOT; 330 BP. XX AC . XX DT 09-APR-2007 (Rel. 12.04, Created) DT 03-MAY-2007 (Rel. 12.04, Last updated, Version 1) XX DE Copia-type LTR retrotransposon - long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; POPCOP2_LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-330 RA Jurka J.; RT "POPCOP2: Copia-type LTR-retrotransposon from black cottonwood."; RL Repbase Reports 7(4), 152-152 (2007). XX DR [1] (Consensus) XX CC LTRs are ~97% identical. XX SQ Sequence 330 BP; 99 A; 62 C; 63 G; 106 T; 0 other; tgttggttat tgggttaggc ctggtccgcc catgatggat gggcctggtc caagttatta 60 gaggagttac taaaggaagt aaccgcctcc tctaatcata tataaaggga cataacccat 120 atggaaaaat aagttttcat ttattgaaag aacatagttc tctctttctc ttttcccatc 180 ttgactctct gcattaactt gacaagattt acaaagacgt tcgtactgtg gaatatcact 240 ttggttctag taattgaagt gacactgaag taattgatcc aggaataaga aaacgaattc 300 tcacaagtaa gttttccttt ccgatctaca 330 // ID RAVLIN5_MT repbase; DNA; EDCOT; 5875 BP. XX AC AC152406; XX DT 26-JAN-2007 (Rel. 12.01, Created) DT 26-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A LINE element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Interspersed; KW ORF; Poly-A tail; retroposon; repeat; RAVLIN5_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5875 RA Shankar R. and Jurka J.; RT "RAVLIN5_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 48-48 (2007). XX DR EMBL/GenBank/DDBJ; AC152406; Positions 77940 83814. XX CC The element is present in high copy number most of which are CC incomplete and 5' truncated. It has intact ORFs, showing domains CC for CCHC zinc finger binding protein, exo/endo-phosphatase and CC reverse transcriptase. XX FH Key Location/Qualifiers FT CDS join(9..1460,1464..1514,1518..1592) FT /product="RAVLIN5_MT_1p" FT /translation="MNSDFVFSAHDTTNMQQSKKPPDPSKPSTQKLSFRDK FT LLESNKEIPIREKEDMIEKKLVRIELEDGNRLLPKIYIEPQVFQELCTTWK FT DALVVKLLGKSLGYTTMKERLQKTWKLQGGFDIMDNDNGFYMVKFDQAADK FT EKVITGGPWLIFDHCLAVTHWSPEFASPNAKVDRTVVWVRFPGLNLVYYDE FT SLLLAMATTLGQPIKVDTNTLKVERGKFARVCVEIDLTVPVVGKIWVNGHW FT YKVQYKGLHLICTNCGCYGHLGRNCCSKPPAAEPVTLNHLKTTGDHHTQKT FT NPTQSQTDPHQNPTDPQAIHSRSLSAVTQSLPADHNRTTLNAGLMETTSEK FT GKSTISNEGNHLLHGDWLIVSRRKKFHNNSTLNAPKTVTQKNNRFNALSSL FT TNQNLTDPTNHKIPQWSKTNETSRGRTNFGPKGADMRTHICQSLRFSSANP FT LAILKPLLSLSLDPPLKLRTRLFPKSLQLNLKCLIKCPTTKKSRQNYPQHT FT NHSHHPYIVFTPPFNHSDQRSYCHGYYFSF" FT CDS join(1573..1680,1684..1719,1723..2232,2260..4182, FT 4186..4266) FT /product="RAVLIN5_MT_2p" FT /translation="MDTISPSEMLDDTDVSLANSDDTLENSNSKGEDMVTL FT FNLSRLGLPTLMEALLDTTILSWNIRGAQNSKAKRQLKELMRKFRPSFFAI FT YETHVPFTRLSSFWTNDGYTPEHIIEANGHSGGIWLLKHSADNTTSTITDS FT NPYSITFTISLGDATTTCTCIYASPNSTMRTTFWNYLSNLNRTITGPWMLI FT GDSMKQSSLVNKEGDYSTTLEQPSSPILQQLVAASLGTATTTVFEFFPRNL FT TEVLPILIGGFLFPEAFVEVLCRTHSDHNPLLLRFGGLPLARGPRPFRFEA FT AWIDHKEYADLVSRAWISSNHNTTVALNNVRENSISFNHDVFGNIFKRKKH FT IENRLKGIQIYLERVDSLRHSLLEKELQQEYHHILFQEEMLWYQKSRENWV FT KFGDKNNSFFHAQTIIRRKRNRIHRLQLSNGIWSSETSILQDEAQRYFKNL FT FCSTVHHQNRHFHVGLHPTIDDDEKNSLTKPITKEEVSAALNSMKPYKSPG FT PDGFQCIFFKQYWHIVGEDIFQLVSKAFQTGFFDTTISDTLIALIPKIDPP FT KTYKDFRPISLCNITYKIITKVLVNRLSRFSIILLVPTKVVFYQVRAPLTT FT LLFCRKLFTSCGDPSEKKGFVAFKLDLEKAFDNVNWEFLNSCLHDFGFPSA FT TIKLIMHCVTSSTFSVLWNGNKLPPFKPTHGLRQGDPLSPYLFILCMKKLS FT LAINNAVIQGDWDPIRISTTGPHLSHLLFADDVLLFSKAKNSQFRFIKDLF FT DRFSQTSGLKINLSKSRAFYFSGIPHQKIANLTSISGIRRTPSLDKYLGFP FT ILKGRPKRSDFNFIIEKMQTRLASWKYKLLNRPSRLALASSVLSSIPAYYM FT QINWLPSICDNIDQTTRNFIWKGANNKWVPLVG" XX SQ Sequence 5875 BP; 1720 A; 1426 C; 1025 G; 1704 T; 0 other; taaatataat gaactctgac tttgtgttct ctgcacatga tacaaccaat atgcaacaat 60 ccaaaaagcc acccgatccc tctaagccct ctacccaaaa gctatccttc cgagacaaac 120 tgctagaatc taacaaagaa atccctatcc gcgaaaaaga agacatgatc gagaagaaac 180 tcgttcgaat agaactagaa gatggaaacc ggctcttgcc taaaatctac attgaaccac 240 aagtttttca agagctgtgc acaacctgga aagacgcatt ggtagtaaag ctgctgggaa 300 aaagccttgg ttacaccacc atgaaagaac gcctccaaaa aacatggaaa ctccaggggg 360 gattcgatat catggacaat gataatggct tctatatggt gaaattcgac caagctgcgg 420 acaaggagaa agtcatcact ggagggcctt ggctaatctt cgaccactgt ttggcagtca 480 ctcattggtc tcccgaattt gcctcaccga atgcgaaggt cgaccgcacg gtggtatggg 540 tacgttttcc tggattaaac cttgtttatt atgatgagag cctcctgctt gccatggcaa 600 caacgttagg ccaacccata aaggttgata ctaacactct taaggttgaa agaggaaaat 660 tcgctagagt atgcgttgaa attgacctta ctgttccggt ggtggggaaa atatgggtga 720 acggacattg gtacaaggtt caatacaaag ggctacactt aatttgtacc aactgcggat 780 gttacggtca tctagggaga aattgttgtt cgaaaccacc tgctgctgaa ccggtaaccc 840 taaaccacct caaaaccacc ggcgaccacc acacacaaaa aaccaacccg acccagtccc 900 aaactgaccc gcatcagaat ccaactgacc cgcaagccat tcattcgcga tcattgtctg 960 ctgttacgca atcattacct gctgaccata acagaaccac attaaatgct ggattaatgg 1020 agacaacatc tgaaaaagga aaatcaacca tcagtaacga gggaaatcat ctgctgcacg 1080 gtgattggtt aattgtctct aggaggaaga aattccacaa taacagcaca ttaaatgccc 1140 ctaaaactgt tactcaaaaa aacaataggt ttaatgcttt gtcttctctg accaaccaaa 1200 acttaaccga ccctaccaat cacaaaattc cccaatggtc caaaaccaat gagacctcac 1260 gtggcagaac taattttggc ccaaaaggcg cagacatgag gacccatata tgccaatcac 1320 taagattctc cagcgccaat cccctagcaa tcttaaaacc attattgtcc ctgagcctgg 1380 acccaccctt aaaattaagg acacgtttgt ttccaaaatc cctccaactg aacctcaaat 1440 gtctgatcaa atgtccaacc tgaacaaaaa aatcccgaca aaattacccc caacacacaa 1500 atcattccca ccactgacct tacatcgttt tcacccctcc cttcaaccat tctgatcaaa 1560 gatcatactg ccatggatac tatttctcct tctgaaatgc ttgatgacac tgatgttagc 1620 ttagccaaca gtgatgatac ccttgaaaat tctaattcaa agggagaaga tatggtgact 1680 tagttattca atctctctcg tcttggtttg cccacccttt aaatggaagc actcctagat 1740 actactatcc tctcttggaa cattagaggg gcccaaaaca gtaaagctaa aagacaactg 1800 aaagagttga tgcgaaaatt tagaccctcg ttctttgcaa tttatgaaac tcatgtccct 1860 tttactagac tttcctcctt ctggacaaat gatggttata ctcctgagca catcattgaa 1920 gctaacggcc attcaggagg tatttggctt ctcaaacatt cagcagataa tacaacttct 1980 accataacag actccaatcc ctactccatc acttttacaa ttagtcttgg agacgcaaca 2040 accacttgca catgcattta tgctagcccc aactctacta tgagaaccac cttttggaat 2100 tatctctcta atctcaaccg caccataacc ggcccgtgga tgttgattgg tgattcaatg 2160 aaacaatcct ccctagtgaa caaagaaggg gattattcaa ccacactaga gcaaccctct 2220 tctccaattt tatgaatcat tgtaacctcc tggacctaac aacaactggt ggccgcttca 2280 cttggcaccg caaccacaac ggtcttcgaa ttctttccaa gaaacctgac agaggtattg 2340 ccaatattaa ttggaggctt tctttttccg gaagcttttg tggaagtcct ttgtagaaca 2400 cactctgacc ataatcctct ccttctccgc tttggtggtc ttcctcttgc aaggggccct 2460 agacctttcc gctttgaagc agcttggatt gaccacaaag agtatgcaga tttggtaagc 2520 agggcttgga tttcttctaa ccataacact actgttgctc ttaataatgt tagagaaaac 2580 tctatctctt tcaatcatga tgtcttcggc aatattttca agagaaagaa acatattgaa 2640 aaccgtctca aaggcattca aatttatctt gaaagagttg actctctcag acattctctc 2700 cttgaaaaag agcttcaaca agaatatcat catatcctct ttcaagaaga aatgttatgg 2760 tatcaaaaat ctagggagaa ttgggttaaa tttggtgaca aaaacaactc ttttttccat 2820 gctcaaacca tcattagaag aaaaagaaac agaatccata gacttcaact ttcaaatggc 2880 atatggtctt ccgaaacctc catcctccaa gatgaagctc aaagatactt taagaattta 2940 ttttgcagca ctgtccatca tcaaaaccgc cactttcatg ttggccttca ccccaccatc 3000 gatgatgacg aaaaaaattc cctcaccaaa cctattacca aagaggaagt ttcagcagcc 3060 ctcaactcca tgaaacccta caaatctcct ggtccggatg gtttccaatg catcttcttc 3120 aaacaatact ggcacattgt tggcgaagac atcttccaac tcgtttccaa agcctttcaa 3180 actggttttt tcgacacaac catatccgac actctcattg ccctcatccc taaaattgat 3240 ccacctaaaa cctacaaaga ctttagacct atcagccttt gcaacataac ctacaaaatc 3300 atcaccaaag tccttgtcaa ccgcctcagc cgattctcaa taatattatt ggtccctacc 3360 aaagtagttt tctaccaggt aagggcacct ctgacaactc tattgttttg caggaaattg 3420 ttcacttcat gtggagatcc aagcgaaaaa aaaggcttcg tcgctttcaa acttgacctt 3480 gaaaaagctt tcgataatgt aaattgggag ttccttaatt cttgtcttca tgattttggg 3540 tttcctagcg ccaccatcaa gctcatcatg cattgtgtta cgtcatcaac tttctccgtc 3600 ctttggaatg gaaataaatt gccgcctttc aaacctactc atggccttag acaaggtgat 3660 cctctatctc cctacctctt catcctttgc atgaaaaaac tttctcttgc catcaataat 3720 gccgtcattc aaggggattg ggaccctatc cggatatcga ccactggccc tcatctttct 3780 cacctcctct ttgcggacga cgtcctcctt ttctccaaag caaaaaactc tcaattcagg 3840 ttcatcaagg atctttttga tagatttagt caaacatctg gtctcaagat taatctctca 3900 aaatctagag ctttctattt ttcaggtatt cctcatcaaa aaattgctaa tcttacttcc 3960 atatccggta tcagaagaac accatccctt gataaatatt tgggttttcc gattcttaaa 4020 ggtcgtccaa agagaagtga ttttaatttt attattgaga aaatgcaaac gagacttgct 4080 tcttggaaat ataagcttct caataggcct agcagattgg cccttgcttc ctctgttctc 4140 tcttccatac cagcctatta catgcaaatt aactggcttc cgtaaagcat ttgcgataat 4200 attgaccaaa caacccgtaa ttttatttgg aaaggtgcca ataataaatg ggttcctcta 4260 gttggttgaa aaaaatagct aaacataagc atctaggagg tttgggttta agagcagcca 4320 gggaggtaaa tacttgtctt ctagggaagt tggtttggga tttaactcaa agaaataata 4380 agctttgggt caatattctt gcgaataaat attcagttgg ccataatttt ttatatgctt 4440 caacaaccag cagtagctca cccacttggt cttccatcat ccgggcaaaa aatgttctat 4500 ttagcggtta ctcctggcga gcgggatccg gttcctcctc cttttggttt agctcttgga 4560 gtaattttgg ccccctcggg tctcttgttc ccgttattga cattcatgac cttcacctta 4620 ctgtcaaaga tgttataaca actaatgagc agaggaccca atcactgtat actcctcttc 4680 ctcctgctgt gtccaagttc ataaataata gcaacttcag gttcaacgcc gcaattgaag 4740 acgtcttcat ttggcatcac aacacaaatg aaatttattc agctaaaagt ggttacaact 4800 ggctgctctc ccttcaaggt actcacgatg tcactcaatc ttggtcatgg atttggaagc 4860 acaaaatttc ggaaaaatgc aaattcttca tttggttggc ttgtcaaaat tctattccta 4920 ctttatcatt gcttcatcac aggaatattg ctccttcggc aacttgcact cgttgtggtg 4980 attttgaaga aaccatcttt cactgcgttc gtgactgtaa attttccaga gatatttggc 5040 aacatcttgg tttctcggac cactctttct ttgcggctgt atgtgtcaga gattggatca 5100 aggatgggtt gaacggtgct aattctatct tgttcgcgac aagtttatgg tggatttgga 5160 gacaccgcaa ctcaatgtgt ttgagcgatg aagccatgcc tctcaacaga ctgacctgga 5220 acatcatgac ttttgttaat gacgtgaagc tttgtttcca tcagcagcac ccagttaccg 5280 aatctgtcag acacatcaga tggaataaca acaatttcga ctgtgcaatt ctcaacgtcg 5340 acggtagttg tattggttct ccaactcgga caggttttgg cggtttattt cgcaacaacg 5400 caggtttcta cctgctagga ttttcaggtt cccttccttc atcagcagat attttagaag 5460 cggaactgtc tgcaattttg cacggtctta ctttagcttt ggataacgac attgaagagt 5520 tggtttgcta ctcggattct ctcctttcta tcaacctcat aaccggtaac tcttctaagt 5580 ttcatgttca tgctgttctc atccaggata ttaaagataa attgtcacag ttgaattgtt 5640 ctctccatca cacgcttcgc gaagggaatc attgtgcaga ttattttgcc aagcttggtg 5700 caagttcaga cgcggcctta ctacttcact cctctcctcc tgatgatcta cgaccttctt 5760 tgaggaatga tgctactgag actttgttcc ctagacctta ggctttcttc cttgcctctt 5820 ttcttctgtt tctgtttttt tcccttttta gctttgttac caaaaaaaaa aaaaa 5875 // ID Copia-11_Mad-I repbase; DNA; EDCOT; 4772 BP. XX AC ACYM01091843; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-11_Mad_; KW Copia-11_Mad-LTR; Copia-11_Mad-I. XX NM Copia-11_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4772 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1353-1353 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01091843; Positions 5509 738. XX CC Positions [2030-2530] - Integrase core CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS 1967..3562 FT /product="Copia-11_Mad-I_1p" FT /translation="MLCSTCLEGKFTKLPFPVSQFKSVKPFEIVHSDMWGP FT APCLSIEGFKYYVTFIDECTHYTWIFPISNKSDVYPTFVSFYQYFTNQFAV FT SVKTLQTDGGWEYIGKSFQAFLLNKGILHHMSCPHTPEQNGLAERKHRHII FT ETSITLLQTASLPPLFWSYAVQTSVYLINRMPSSTLDNKSPFELLFHDIPE FT IQHLRVFGCSCYPLLRPYNSTKLQPRTTKCVFLGYASKFKGYICFEVAKRR FT VYISRHVIFDEFEFPYSNLVSFDKPVLSSVLTSHGSHPVLVPNNDNVMVVP FT SASSSSLMQSSSSQSAPNNSLDTRSHPITTNSLSNGSSLSMPSATSSHHTL FT TGALNEAAPITSTADQSLSSSVLVVPEFQLDQLQVVIYVSSFNLHPMQTRS FT KSGISKKVAFMSVIHEHGGADLTKIEPATYKSSLTSSVWCEAMKEELSALH FT NQGTWSLVPLPPHKNLVGCKWVFKIKKNADGSIGRYKAKLVDKGFNQEEGI FT DYGETFSPVVKPTTVRVVIALATHYGWCLRQLDVKN" XX SQ Sequence 4772 BP; 1276 A; 960 C; 901 G; 1621 T; 14 other; tggtatcttt gctggaaaaa gtataaagcc ttacggtgta tcgatctggg atttctgtat 60 ctgcttccgc ttctgatcgc acatatatgt gcttctctct tctgtctatt acttcttgat 120 ttggggcttt tctaatcgaa ttagggctct tcaatttgtg tttggttttc tgcacaccaa 180 gtgttcgacg tttgttctct gtcaatctcg gtgaagcaat tccatcaaaa tggtgaccgt 240 gtcttagttg caaatcttgc aatcgcctat tacatctttt atttcctctg tttctacgtc 300 cgtaaccatg aagttggatg ataccaatta cttgacttga catttttaga tgcagctttt 360 gttggaaggc tatggcatta tggggtttgt tgatgggtct actccttgtc ctcttcgatt 420 ttctaatgtg atttatgggg attctgaagt tgtttttggt tgttctactg cacaagttga 480 atatgatgca tacaagattt ggaaaatgca tgatagagcg ttgatgcagc tcatttctgc 540 aactctttcg gctcccgcaa tttcttgtgc aatagggagt agcagttctt tggatttatg 600 gactcgtctg aaagaacaat tttccacagt ttctcgaacc agcattttcc aaatgaaatc 660 tgagctccaa actatcaaga aaggtaatga ttccatcact ttgtatcttc aaatgattaa 720 ggaagctcga gattatttgt ctgctgctgg tgtctatttt gaggatgatg atattgtaat 780 tcttacgttg actggtttac cttctgagtt caataccatt cggtcagtca ttaggggtca 840 agatactgtt atttcattaa aagatcttcg ttctcaacta cttgccaaag aagcaatgct 900 tgaaaatatg aatgctgccc ctatgcttac tgctttggtt gctcaacagt ctggttttcc 960 ttcaaagaat tctggtggtt tttcatctca acatcctaac tccaactatc agtataatgg 1020 ttctcgagtt ttcaataaca agaataaagg cagggattgg tttaattcta ataacaggtt 1080 tggaaccaac aagcaattct tctccaatta tggtcctgga atcttgggaa actctccaca 1140 atagcttggt tcttctccat tgatgacatg tcaaatctat ggcaagcata atcatcttgc 1200 agacacttgt cgatttagaa atactcctgc ttctccaagt tgccaaatcc gtgggaaaca 1260 taatcatttt gctgatactt gtcggtttcg aaatactagg gttaattcag gctatcaaat 1320 atgtgggaat tctaaccata gtgctgattt ttgcttccag aagaattcta atgtttcaat 1380 gactgccatg tatgctcaca ccaactctgg tcctcagttt atttcttccc agacatctgt 1440 tccatctcag caagtttggc tcactgactc gggagcgaca aaccacatga caactgagtt 1500 gcagaatctg tctcttgcaa ctcattatcc atccaatgag actatataag ctgctaatgg 1560 tgaaggttta gccatatctc atattggctc caccactctt caaactccat tacattctct 1620 gaaattaaat tctgttttat atgtttcgaa attaacacag aatctgctat cagttcatag 1680 aatctgcttg gacaataatt gttggttaat atttgatgca ttgtgtttct ggattcagga 1740 caaaaccaca gggaggatac tctacaaagg actgtgcagt aatggggtgt atccgattat 1800 ctcaccaaca tccagtgctt cttcaaaact tgcctatgct gctgcttacc ttggacaaca 1860 aatcaattca agattatggc ataacagact aggtcatcct tctaatccta tagtatctca 1920 aattttaaga aagtccagat tgtcttgtaa tcctgattcc ttgcctatgt tgtgttctac 1980 ctgtttggaa ggaaaattta caaaacttcc ttttcctgtg tctcagttca agtctgtaaa 2040 accttttgag atagttcata gtgatatgtg gggtcccgct ccttgtttgt caattgaagg 2100 gttcaagtat tatgtaacct tcattgatga gtgtacacat tatacttgga tttttccaat 2160 aagcaataaa agtgatgttt accctacttt tgtttctttt tatcagtact ttacaaatca 2220 atttgctgtc tctgttaaaa cattacaaac cgatggggga tgggagtata tagggaaatc 2280 ttttcaagct tttcttttga ataaagggat tcttcaccat atgtcatgtc cccatacccc 2340 tgagcaaaac ggcttagccg agcgaaaaca tagacatata attgagactt ccatcacact 2400 attacaaaca gcttccctac cacctctttt ttggtcctat gcagttcaaa cttctgttta 2460 tcttatcaat aggatgccat cttctacatt ggataacaaa tccccatttg agctcctctt 2520 tcatgacatt ccagaaattc aacatcttag ggtttttggt tgctcttgtt atccactact 2580 gagaccttat aacagtacca aacttcaacc tagaactaca aagtgtgttt tcttggggta 2640 tgcttctaag tttaaagggt acatatgttt tgaggtggct aagagacggg tttatatatc 2700 cagacatgta atttttgatg aatttgaatt tccttattcc aacctagtgt cttttgataa 2760 accagtcctt tcttcagtac ttacctcaca tggttctcat cctgttttgg taccaaacaa 2820 tgataatgtg atggttgtgc cttctgcttc ttcttctagt ctgatgcagt ctagttcctc 2880 acagtctgct ccaaataatt cattagacac taggagtcac cctatcacta ccaatagttt 2940 gtcaaatgga tctagtctgt ctatgccatc tgcaacatca agtcaccata ctctcactgg 3000 tgctctcaat gaagctgcac ccattactag cactgcagat cagtcattat cctcttctgt 3060 ccttgtggta cctgaattcc agcttgacca actccaagta gtcatatatg tttcatcatt 3120 caatttgcat ccaatgcaaa ctagatcaaa gagtggtatt tccaagaagg ttgcattcat 3180 gtctgtgata catgaacatg gaggggctga tcttactaaa atagaacctg ctacctataa 3240 atcttctttg acatcttctg tgtggtgtga agcaatgaaa gaagaactct cagccctaca 3300 taatcaaggt acttggtcct tggtacctct tcctcctcac aaaaatttag tgggctgtaa 3360 atgggtgttc aaaataaaga agaatgctga tggttctata gggagatata aggccaaatt 3420 agttgacaag gggtttaatc aagaagaagg tatcgattat ggggagactt tcagccctgt 3480 ggttaaacca accactgtga gagtagttat tgctttggct acacactatg gctggtgttt 3540 aagacaatta gatgtgaaaa atgycttttt acatggcatt cttcaagaag aggtatatat 3600 gtctcaacct cctggtttcc atgattctaa acatgaggat tatgtttgca agctccataa 3660 gtccttatat ggtttgaaac aggcccytag ggcatggaat gacagattta ccaagtttct 3720 accttcattg ggatttcagt ccacttattc tkattcttca ctatttgtca agcatgctrg 3780 tgattatatt gtgattcttt tattrtatgt tgatkatata atcatcacag gtagtgcaag 3840 tcaatgtgtt aytgatgtta ttcatgcctt ggcacatgag tttgatatta aggacttagg 3900 accattgcat tactttctgg gtatacagat tgtgcagcaa ccaaaaggga tttttttgtc 3960 tcaatataag tatgtcacag atcttctcac caagtcagac atgttgtctt cyaagccctg 4020 tgccactccc tgtttacctt acaatcggtt attgaaagat gatgggaaac catataacaa 4080 tccagcattg tatagaagtc tagtgggtgc tcttcagtat ctcactttca cacggcctga 4140 tattgccttt rcagttcaty aagtgagtca atttatgcgg gcacccatgg aatctcattt 4200 tctggccgtc aggagagttc ttagatacct tcgggcaaca cagggatgtg gtcttcgata 4260 tgttcacggc ggtttggatc ttacagcttt tagtgatsca gattgggcag gggatcctaa 4320 tgataggcaa tccaccactg gtttggttgt tttcctaggc tcgaatccga tatcctrgtc 4380 ttccaagaaa caacaaactg tctctcggty atccacagag gctgmgtata gggcataggg 4440 cattatcttc tacaacagct gagattgatt ggattaaaca gttgttggca tttctgtagg 4500 tttcagtatc ttatacacca actttgtatt gtgataatct ttcagtacta gccttaacat 4560 taaatcatgt tcagcatcaa cggacaaaac atatagaggt tgtcatacat tttatgagag 4620 aaagagttgc caaacaactt atgcaagtgc attttgtatc ctctggtgag cagtttgcag 4680 atattttcac aaatgggttc tttgcacctt tgtttcagcg ccattgcaac aatctccagc 4740 tcagtttctc tgctcctgag cttgaagggg ga 4772 // ID HELITRON1N_MT repbase; DNA; EDCOT; 1323 BP. XX AC . XX DT 07-JUL-2003 (Rel. 8.06, Created) DT 07-JUL-2003 (Rel. 8.06, Last updated, Version 1) XX DE HELITRON1N_MT, a nonautonomous rolling-circle DNA transposon - a DE consensus sequence. XX KW Helitron; DNA transposon; Transposable Element; Nonautonomous; KW HELITRON class; HELITRON1N_MT; nonautonomous DNA transposon. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1323 RA Kapitonov V.V. and Jurka J.; RT "HELITRON1N_MT, a nonautonomous rolling-circle DNA transposon in RT the Medicago truncatula genome."; RL Repbase Reports 3(6), 114-114 (2003). XX DR [1] (Consensus) XX CC HELITRON1N_MT is a nonautonomous rolling-circle transposon. CC Some copies are less then 1% divergent from the consensus CC sequence. CC HELITRON1N_MT elements are inserted into the AT target site, and CC they CC have a 19-bp palindrome followed by the 12-bp 3' terminus. CC The M. truncatula genome harbors many families of Helitron CC transposons, CC including autonomous elements. Similar to autonomous Helitrons CC present CC in the A. thaliana and O. sativa genomes, autonomous Helitrons CC from CC M. truncatula encode the Rep/helicase and RPA1-like proteins. XX SQ Sequence 1323 BP; 460 A; 261 C; 132 G; 469 T; 1 other; tcttcttata tattaaagtt aacaagtaag ccctaatttt aacctaaacc ctattgcata 60 attttactgt tttaacccta atgttcacac ctaatctcct attttcatga acaatcttct 120 tatatattaa agttaacatg taagccctaa ttttaaccta aaccctattg cataatttta 180 ctgttttaac cctaatgttc acacctaatc tcctattttc atgaacaatc ctaatgctct 240 cwcctaatct tcttatcttc ttatatatta aagttaacaa gtaagcccta attttaacct 300 aaaccctatt gcataatttt actgttttaa ccctaatgtt cacacctaat ctcctatttt 360 catgaacaat cctattgctc tcacctaatc ttcttatata ttaaagttaa cccgtaagcc 420 ctaattttaa cctaaaccct attgcataat tttaccgttt taaccctaat gctcacacct 480 aatcttatat tttcatgaac aaccctaatg ctcacaccta atctcatatt ttcatgagcc 540 ctaattttaa cctaaaccct gttgcataat tttaccgttt taaccctaat gctcacacct 600 aatcttctat tttcatgaac aacgctaatg ctcacaccta atctcctatt ttcatgaaca 660 aagcaaatcg gcatcgcttt atttccccta tttcttcaaa acaaatcgcc ctatttcttc 720 aacaaaacaa atcgccctat tggaataaaa gggttttgaa agattatagc aacatttttt 780 tttgttaata ttacactttt catccaaatt agaactgaac tctctttgtt aaatatttac 840 cacaaaatgc acctgaattt tgcaatctat ataaacaggt ggaagaaaca tttcaacaaa 900 cagttaaagg gtatcattta cggtaaatgc caaatattcg ataaaaggaa aattatttaa 960 ataaaacatt ttacatgttg aggttaagaa tgaactattt ttaggtacat aatataacat 1020 taacatataa tttttacaaa agaatgaagt aacatttttt caaaaaaaaa aaaaaaaata 1080 tgaagtaaca taccaataat ataatattga catataattt taacaaaaga atgaagtaac 1140 acacgattga taaaaattaa tatttttttg gtgaataagc gtggtgtctg aggttcgaat 1200 tccaacatct gcatatattt gggaccacat atttcattct ctttgatatg cattgagatt 1260 tgtttttgtc tactatatct acaatgtata tgacccgtgc ggcagcacgg gtggaaagtc 1320 tag 1323 // ID REP-1_Mad repbase; DNA; EDCOT; 1516 BP. XX AC . XX DT 26-OCT-2010 (Rel. 15.11, Created) DT 26-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE repeatitive sequence in the apple genome. XX KW Nonautonomous; REP-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1516 RA Bao W. and Jurka J.; RT "Repetitive sequences from the apple genome."; RL Repbase Reports 10(11), 2020-2020 (2010). XX DR [2] (Consensus) XX CC ~75% identical to the consensus. The 5'-terminus is not CC determined. The 3'-end may or may not represent a real terminus. XX SQ Sequence 1516 BP; 351 A; 377 C; 404 G; 384 T; 0 other; ttgtgttatt tttttcatag atgtcatcgc ggttgatcac cagtggtcgc cgctctgcct 60 ccgcttcggg tcagagtgac ccggcggcag agatacccac cagccactgc cgagtcggcg 120 gccggcccac tacatctgct tcatcgggcc gggtgccccg atctgccagg cgtgttcaca 180 gccggagacg gcacgaggct gtgccaaccc cctgttgacg ccgcggaggc cgatgccgat 240 tcggcggccg tgcgcccgac gggagacgga gaactcccag ccgggaagaa ggtcaaagtg 300 caggggatct gtagaggctt gtcctcgaac cggatcaccc gcataacgca aaacaagatc 360 gtggtcgatt acaacccact ccatcggcga gcgagcctga aagtcaacag cctgttgact 420 cacgacatgg gtgccatcat ccgcaccaag tgccccatgc tcgccccttc atggaagaag 480 ctcgcccccg aggtgcatga ggagatgatg agagagatct cggtaagtgt ttatttatta 540 tttattttta cttttactta tttaatgtat tttttaacta atacacttgt ttttttgtct 600 atttcaggcc aacttctcca tcgacatgga gcacccgggt atgtacgagt acataaaccg 660 ggtgtggact gagcggtaca aggagtggaa gtacgagctg cacatgtact acaagacttg 720 tgcatctcct gctgaagctc ctaccgatcc acccccggag tttgcggaga ggatgacgag 780 tgggagtggc tgtgcaaaat ttctggtagt ttttttaatt taatttcaat ttttttattt 840 tttatttaat taatttttta attcacagcg aaaatcgacg gcaaataagg ctaaccggga 900 agcgaagccg taccttcatc actctggttc tcggcccctc actttccggg tcgaggaaca 960 gcgtgagaag ggttcgcttt tcccggaagt cgaggcttgg gggatacgca tgccaattat 1020 ggcaaccagg tggctgacga catttatgta agtattccgt tcaaaatttt atttcaaatt 1080 tcattacact taaaaatttt aaaattatga tcgataatct taattggttt tttttttttt 1140 tttgtaggct tctatgttgc agaagaagga cgagtacctc gccaacctct cccagcagca 1200 accagacacg ccaatggagg agctgacacc tgatccagag gtgtctctac agttgctgat 1260 ggacggggtt gggcgacgga aaggcaaaga gctccgcggc ctaggagcgg gtcgggttcg 1320 ggacctcggg ggatcttctt catctagctc tcagcctcca agcgggacgt cttccagact 1380 gcagcagttg gagatggagc tagaggccat gcgccagcga gaagaagaag ctgtgcgcca 1440 gcgagaggag gactttctgc agtacattgc tgggatggcc caagcaatgg cagcctctgg 1500 cattcgcctt cccgat 1516 // ID Copia-81_Mad-LTR repbase; DNA; EDCOT; 237 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-81_Mad_; KW Copia-81_Mad-LTR; Copia-81_Mad-I. XX NM Copia-81_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-237 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1701-1701 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 237 BP; 59 A; 43 C; 36 G; 97 T; 2 other; tgtatccaac ccaccagatt agattctttc acttagctgt taagcttgkg atgtgtagtg 60 attagttata tgcattatgc tgagctggca catatattgg gataggatat ttatgtataa 120 ataccttgtg tatkgttctg ttgaattaat gagaatcaca attatatttt tctctctctc 180 tctacaattc tctctctctc tctataactg atttctctct ctgaattctg agtttca 237 // ID Ogre-PT1_LTR repbase; DNA; EDCOT; 2218 BP. XX AC AC149300; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 10-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-PT1; Ogre-PT1_LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2218 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC149300; Positions 19339 17122. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). XX SQ Sequence 2218 BP; 812 A; 392 C; 403 G; 611 T; 0 other; tgtcataacc caatttttga acaaataata aaaaaattaa atatagttgc caatggggtt 60 aagataacaa aatttgaagt ttgaggatgt aatttgagag ttaattgatc aattttgaaa 120 gaattaaaag ttaaagattt aattaagggt taaattgaac aatccaggaa ttaaggactg 180 ttttgtaaac agtgttataa tttaaggatt taattgaaat taatccaaag ggacaaaatt 240 aaaaggaatt tttaatttct tagaggtcca attgccgaat ttccaaagtt caggggtcaa 300 aatgaaaatg tccattgctg cttgaaacgt cgccgttgct ggtggaatcc attcctgccg 360 aaacgtcgtc gctgctggta gaacagccgt gttcgtcttc tccatcccga ttcaacaggc 420 tgaaaatctg caacggattc gatccaatcg aggaccacgt ctctcgccca cgatctcgtt 480 cgtggaagat aacagtcctg caaaggcagg actggttaga ggcaatcagc tgggaagtct 540 ataaaaggga gaagaaaacc tagaaccagg aaaaggagaa aacccagaaa aaaacagagc 600 aatcaaccta gaaaagcaga gcacacaaaa cacaacccaa agaaaataca gagtcaagaa 660 cggaaacatc aacccaaaac agagcaaaaa aaccaaaaaa aaaacagagc ataaaccaaa 720 aaatatatac acagaaaagg agagaaaggc agaggggagt cacggatcag ccctgttttc 780 gtccctgcaa gaaaacaatt gatcaccgaa ccatcagtta ttgacagaaa gcagtgaacc 840 cacaccggcg ttgcagcttt cttcaccatc gccagaaacg gaaagcagtc gaaccccacc 900 agcgttgcag ccttcttcgc aatctccaga aacaggtgcg cccgtttccc tttgtttttg 960 ctcttctgtg ttcaaattgc atttgaacag tgcgaaggta atttaattac cttcgcactg 1020 ttgatgcacg cgtgaaagtg cttcacgcgt gcatcagctg tttgcccagc tggtcactgg 1080 cttgggccag tgaccgggcc gggctggctg ggcctagccc agcccctgtg gggctgagct 1140 cagcccagcc accaatatat atgctgggct ggatttagcc cagcccagcc caaaaataaa 1200 aaataaaaag ataaaaaata aaaaaatata atacaaattg tgtatgtaaa taaatttcat 1260 tttttattta ttcattgacg ccagagtcag aataaaaatt tcattgtatt ttattattta 1320 gttatataaa aataaaaaat gtgcatgcaa aaaaaaaata acataagata aaaataaata 1380 aatttatttg gtatattcac tgacgccaga gtcaggaata aaaaatacta atgcaaattt 1440 attttatttt attttgtttt ttgttttttt tgctacataa taaaaaatgt gtgtatgtaa 1500 ataaaaaaat aaatatgaat ttattatttt tattcattga cgccagagtc agaatacaac 1560 tattgattca aatttatttc cttgtgtttt ctttaaaaat aaaaaatatg catgcaaaaa 1620 taaaataaaa taaaataaaa taaatttatt ggtttattca ctgacgccag agtcaggaat 1680 aaagatacta agtaaattta ttttatttta ctttgttttg tttttttagc tacataaaaa 1740 taaaaataat gcgtatgcgt aaaaaaaaaa attgatttta tttgtttatt cactgacgcc 1800 tgagtcagga ataaaaaaaa atgatgattt aaatttattt attttcatac ctacgtaata 1860 tttaccaacg ccagagttgg aaatatccgt agctgaatat tcactggcgc cagagtcagg 1920 aatattgcac gcaaacaatc atagtataaa ccaacaaaaa tgttagcaat taatgacaaa 1980 tgtaagcaat gcagcctgcc ttaggcagga cgtttaaggg gtgataatat cttccctttt 2040 acgtaaccag tctcggacca tagaatctct gttgaccagt tagggttcct agtaaccata 2100 atactaggtg gcgactcctt aaacaaagaa tatccccata aaagaacagg atgccagaaa 2160 tccgttcttt tcaaagattt aatagatttt taaggccgcc gcgatgtcgg gtgcgaca 2218 // ID Gypsy20-VV_LTR repbase; DNA; EDCOT; 1798 BP. XX AC AM483798; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy20-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1798 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-1798 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 719-719 (2007). XX DR Genbank; AM483798; Positions 5804 4007. XX SQ Sequence 1798 BP; 566 A; 323 C; 352 G; 557 T; 0 other; tgattactac tcaaaaggtg ttatttcata gcttgtaatt aactctttta aacacttttg 60 agtagtagtt atcacctttt aacccaatta acatattaag gacctttgca agcatttcta 120 atcaaagtgt gtaagttttg gtgtttttgt tagtaatttg atcaccaaag caatccgaga 180 ttaaggagag ttctctggaa tccatggcaa atcaatggaa agttcaaaac atgaagaacc 240 aaagctttaa agtcctttgc cataagcaaa tcaggaatgt aaggagggga agcaaacaag 300 aaccagccat gaaacattct tgatgacagt catttcagcc acttttggag cacttaatgg 360 agttcaattt atgcattcta tatgttgttt cgaagctcag gaagtcaaca atccaatgct 420 tcaaacagtg cacgatttgg agttgaaacg aaggagttac agccattaca agaaaatcac 480 tccaagttaa aggaagattt ttgcacggct gcgaaatcag ccttttgctg cgaaaatctt 540 gtcctatttg ctgtgaaatt ttcgcagcca ttttgcacag tgcatggggt gttctcctga 600 agcttcccaa tatttgcgac cgacattttg agattttttt gctttagata tttgatgtct 660 aaatccccaa actctccttg taacccacct atcataggat tccttagtct ttaagcaaga 720 acaaggggta aattaagcca tatttaatgg ttgtaagttt cctcagagac ggacggacgg 780 aagaaaggct tgtacacaga cgctttgtat aattttgaag gaagtaaaat acagagcttt 840 gctctacctt acctactcaa tttgattgta tttttcattt actagctaaa caagctctaa 900 gaaagtttcc tcagagaatg agtggctagg cttttagttc cttggagcta aggttgccgg 960 gaaaggttcc aaatgcaaga attagtagct ttgtggtttc agccattaat gaagagaaag 1020 tgtgatcctt taatgatttc tatgttttta gttaacttaa aacaccttca attcacttga 1080 gccaacactt ggtaaggcaa gtgatctccg tccatggaga tgcactagtt tacctcttgc 1140 gagcttttgg gaagtgactt gaaggtagga ttttctagaa ttgccaacac ttggtaagct 1200 tttggactcc aaggagacat ccattagtta tctcttgcga gcttgagaag ggaagtgcaa 1260 agttaatgat cactttgaat ggcaaatgct aagtgagagg tacaagccat tgcaagttgc 1320 atcagtgaga gggaattaga gctgaaatcc atttaaggaa tacatctgta caacaccggt 1380 tagagaattg actatatgtt aattctctaa tgcgaggaaa tgaaccaagt gaccgaagct 1440 ttgtttttgc atgaggaatc tcccctgtga acctaaacct tcaaggaatg ttttttttca 1500 taagtaattt ccattacttt ctttttagtt agcttgaaac aaaacctcga tcaaccaaag 1560 tttgtgtttt atttcttaag ctaaccttga aatgaaaaaa caccaattta acgttgaatt 1620 aatatcagtt gtgagttgaa aacccttcac agagaatgat cctagagcca ctatgctata 1680 ttagctaaag ctatcctaat gcatggtgat ataggttata aattttgttg attacaccct 1740 caatcaaaaa gcaccagctg aacacgaatc agctgagaca ccaattggga atgaatca 1798 // ID COP7_LTR_MT repbase; DNA; EDCOT; 821 BP. XX AC . XX DT 28-DEC-2006 (Rel. 11.12, Created) DT 28-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE LTR sequence of a copia type LTR retroposon, COP7_MT, from DE Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; internal region; terminal; COP7_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-821 RA Shankar R. and Jurka J.; RT "COP7_MT: A copia type LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 614-614 (2006). XX DR [1] (Consensus) XX CC The LTR flanks well conserved internal region and flanks both CC termini of the internal region. XX SQ Sequence 821 BP; 204 A; 137 C; 211 G; 269 T; 0 other; tgttggaatt gacttcaaat tagtggttta ggagaacaga ggaatcgtgt cacgattttg 60 cagtcgtgac acgatcaggg aggcagtgag ctaagtttgc tggaagcaaa atcgtggcac 120 gatcttggga aatcgtgaca cgattcagaa acttgctggt taagtatctc tgataaggac 180 tggtcaactt ggggaccgtt gcagatcgtg acacgatcta gggaaatcgt ggcacgattt 240 cctcaggaca ggactagtat ttaaagtgtt cttgtgctct tttgaaggta accttaagag 300 acaaccttaa gacaaccttg agaggttgga agagagataa cttggagatc aaagagggga 360 tcctttgggg tgtgttcctt tgatgagagt gtatcttagg ttgggaaaac aacattgtaa 420 tcaccttggg attatgggtt catagtgtga ggttgggaaa ttaccaaagg gtaggtctag 480 ggttttgtct tgtgtaaagc ttgataagct agattcttgt aactcttttg taacacattc 540 acatattgga ttggagagct gctctctccc ccagattagg ccacattggc tgaactgggt 600 caacaatctt gctcggtgtt ttgttcgttt tcgtttatcg ttttatcttg tatgcttgtt 660 aactcttagt gtggttgtgc tacacattag gcttaggctg ttttgttgtt gttagcttgg 720 aagccatttg ctctcataga ttatctctat cacttgctcc acacatcatt gatttattct 780 cattggtgtg aaggttcatt agttgagccg gattcacaac a 821 // ID Copia-40_Mad-I repbase; DNA; EDCOT; 4870 BP. XX AC ACYM01026881; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-40_Mad-I; KW Copia-40_Mad-LTR; Copia-40_Mad_. XX NM Copia-40_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4870 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1310-1310 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01026881; Positions 8802 13671. XX CC Positions [2122-2457] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 2134..4062 FT /product="Copia-40_Mad-I_1p" FT /translation="MVAVQYNRNIQVLRSDNGGEYVNMELRSFLELQGIVH FT QTTCPYTPQQNGVAERKNRHLLEMVCASLIAAHLPLHYWGEALTSAAYLIN FT RLPSRTLNFHTPFQALTSQTSSPPTPNLPPRVLGCVAFVHLHPPQRHNKLE FT PRAVRCVFLGYAATQKGYRCYHPSSKKMFITQDVSFHENEMFFGSPASSLQ FT EEYRNSEVLTRDNSKVLSFDELHEEQPYAASGELQPYTAPRELQQPMAFEH FT GQQPCFGHQPTEQLTDEGQQTLQVDDQSTGPMRFGLDDDQQPTSWNGTEQQ FT LQQVSRDFSPGVISGSSWNSPSDNSHNQSSSTPDAPPLRHLPERINRGIPK FT PTYEADPKCKHKYSVSEPNSDSRVKYPLNNYVSTSHLSKSNKSFVYQLSTV FT SIPNSVQEALADSRWKDAMNEELRSLKKNATWEITDLPAGKKPVGCKWVYT FT VKYKADGTVDRFKARLVAKGYTQKYGIDYTDTFAPVAKINTVRVLLSLAAN FT LDWPLQQFDVKNAFLHGDLTEEIYMDLPPGWSDPDIRKQKVCRLKKSLYGL FT KQSPRAWFGRFTKSMKAFGYRQSNWDHTLFLKHRNGNVTALIVYVDDMVVT FT GDDPVEQAALKKYLSTEFEMKDLGSLKYFLGIEVSRGKSGIFLSQ" XX SQ Sequence 4870 BP; 1341 A; 957 C; 1153 G; 1413 T; 6 other; ctctttcttc ttggcaccrg agccgggtta gaaaagaaaa acactgaacc ctaactgttt 60 ttttcctgcc gtgtccctga tcaaattgca gcgagcaact tagaggagtt gttgctgccc 120 gtgtttcttg atttattgca gcgaacaact gtgaagttgc tgctgccctc tgttttgtcc 180 gaagggtccc atcaatgctg cactgttgct tcttgttttg tctgaagggt ctcatcaacg 240 ctgctgcccc tgtttctgtc cagttttgtt agtcaattcc caagttccaa aatcccatca 300 actctgcagg ttttatgctc taccgacaac aagagagatg gctgaagaaa aggggaccgg 360 ctctaagatt gttccagtgg ctgctccaat tatggtgcag tcagagaatt ctagttttaa 420 tattggtatg gttttggatg aaaagaacta tgatttatgg gctcctctca ttcaaatcca 480 tattgctgga tggaagaaga tgggatatct tcgtgggtct atcaaggcac ctaacgtgga 540 cgatcctaaa tatgatgatt ggttctctga agatcaaaaa attaagagtt ggcttttgtc 600 ttccatgaag cctgagatta tgaaacggta cattcggttg tctacatcaa aggaaatttg 660 ggattccctt aaggctgcat actttgatga gaatgacgag gctagaattt attccttgaa 720 tcagaaggca tcacgtcttc gtcagaatgg ccgacctttg gctacctatt ttggggagct 780 gactgagatt tttcaagaat tggatcactt taataaagta tctatggagt gtgaaaacga 840 catcaaagtg ttccagaaat ccaytgagag acaacgagtt tatgtgtttc ttggtggtct 900 tgatgatggg tttratcagg tgtgtggaga agtgctacgg aaggatcccc tacttggcct 960 tcaggcttct tatgcatatg ttcgtcgaga agccgatcga aatgaagcaa tgaagacgga 1020 ggttgacaag agtgaactcg atgccctggc aacaaaggcc cgtgggtcat cttttgggtc 1080 taaccgtgaa gggtcacaaa gttggcctgg acaaactcgg cctagtcaga caagccggga 1140 tcgtccccaa ggtaagtgca cacactgtgg catgacagga cactcaaaga gtcgctgttt 1200 tgagctgatt ggatatcccg agaattggga taagacccgt gatcctcgat ggaacaaatc 1260 tcgagcctcc gttgcagaaa ccaagaacga cttagaccag atagaggaca aagcatctgc 1320 catgattgct gcggcaggta gtgatggtaa ggcactcagt acttctactt ctgttatgaa 1380 taatacatgg ataattgatt ccggagctac tgaacatatg acttgtgatt ctaracaggt 1440 tccatcacta aaaacatcca tccaaaccga gtcaatgttg ctaatggtaa tgtcgtccct 1500 gttattgggg aaggcactgt ttccctttct gataccatga aacttgacac tgttcttgtg 1560 gttccctctt taaattataa tttgttgtcc gttgctcaaa taacccttgt cttacattgt 1620 ttggttattt tttggcctca tttttgtgtt tttaaggaca tccggacgcg gaagacgatt 1680 ggttatggta ttagaagagg aaaactttat tacttggagt tgaccaccag tagttctagc 1740 ttgctgactc aagctctctc agttgatgat tctcaagggg atattaataa agtgtcagac 1800 atttggatgt ggcacaggcg ccttgggcat gcttccttta gttatctgca taagttattt 1860 cctagtttgt ttgtcaagac tgatgtttct cagtttaagt gtgatgtttg tgaaatggct 1920 aagagccatc gaacttmttt tcctcccagt ttcaataaaa gtaccgttcc ttttatgatt 1980 gtgcattctg atgtttgggg accgtaaaaa atagctactc ttggtggtgc tcattggttt 2040 gttactttta ttgatgattg taccagaatg acttgggttc ttttgttaaa gtcgaaaagc 2100 gaagttagtt cggcctttta acggttccat aaaatggttg cggtgcaata taacaggaat 2160 atccaggttc ttcgaagtga caatggtggt gaatatgtta atatggaact tcgttccttc 2220 ctggaactgc agggtattgt tcatcagacc acgtgcccgt atactcctca acagaatggg 2280 gttgccgaac gtaaaaatag acatttgtta gaaatggtct gtgcttcact cattgcggca 2340 catctgcctc tacattattg gggagaggca cttacgtctg ccgcctatct tattaatcgt 2400 cttccttctc gtactcttaa cttccataca ccatttcagg ctctcacatc tcagactagc 2460 agtccaccga ctcccaatct tcccccaagg gtcttggggt gtgttgcttt tgttcacctc 2520 catcctcctc aacggcataa taaacttgag cctcgagccg ttcgttgtgt ttttttgggt 2580 tatgctgcta cccagaaagg atatcgttgt tatcatcctt caagtaaaaa aatgtttatt 2640 actcaggatg tgagtttcca tgagaatgaa atgttttttg gatcccccgc gtcctcactt 2700 caggaggagt accgaaatag tgaagttctg actcgagata atagtaaagt tttaagcttt 2760 gatgagctgc atgaagagca accatacgcg gcttcaggag aattgcagcc atacacagca 2820 cctagagaat tgcagcagcc catggcattt gaacacgggc agcagccctg ctttggtcat 2880 cagcccactg agcagctcac tgacgaaggg cagcaaacat tgcaggtgga tgatcagtcc 2940 acgggtccca tgaggtttgg gcttgatgat gatcagcagc ccactagttg gaatggaacc 3000 gagcagcaac tgcagcaagt gtcacgggat ttttctcctg gtgttatatc aggttcaagt 3060 tggaactcgc cttctgataa ttctcataac caatcgtctt ctacaccgga tgcacctcca 3120 ctccgtcacc ttccagagcg tattaatcga ggtattccca aacctactta tgaggcagat 3180 cctaagtgta aacacaagta ttccgtgagt gagccaaatt ccgattcaag agtgaaatac 3240 ccattaaaca attatgtgtc taccagtcac ttgtcaaaat caaataagtc atttgtatat 3300 caattatcta ctgtatctat tcctaacagt gtgcaggagg ccttagcaga ttcccgctgg 3360 aaagatgcaa tgaacgagga attgagatcg ttgaagaaga atgctacctg ggaaataact 3420 gacttgccag ccggaaagaa acctgtggga tgcaaatggg tttatacagt gaaatacaaa 3480 gcggatggaa cggtagaccg ctttaaggca agattggtgg caaaggggta tacacagaaa 3540 tatggcatcg actacactga tacattcgca ccagtggcaa agatcaatac agttcgtgtt 3600 ctactgtcat tagcagcgaa tctagattgg cctttgcaac agttcgatgt aaaaaatgca 3660 ttcctccatg gagatctaac tgaggagatt tacatggacc ttccaccagg gtggagtgat 3720 ccggacatac ggaaacaaaa ggtatgtagg ctcaagaagt cattgtatgg gttgaagcag 3780 tctccaagag cctggtttgg tagatttacc aagtccatga aagcattcgg gtataggcaa 3840 agtaattggg atcacacgtt attcctgaaa catcggaatg gaaatgttac agctctcatc 3900 gtatatgtgg atgatatggt ggttactggt gatgatccgg ttgagcaagc agccttgaaa 3960 aaatatttgt ccacagaatt tgaaatgaag gatcttggtt ctttgaaata tttccttggg 4020 attgaagtat cgagaggaaa gtctgggata tttttatcac aaakgaagta tgttcttgac 4080 ctgttggaag aaaccggtat gacggcgtgc aaactggtgt ctactccgtt ggccgaatga 4140 atgaaattgg gtatcgatca gaaccaagta ctggttgata aagggaggta tcaaaggtta 4200 gtaggaatat tgatgtactt ggctcacact aggccagatc ttgctcatgc tttaagtgta 4260 attagtcaat atatgcacaa tccaggataa caacatatga gtgcagttat gagaatattg 4320 agttacttga aaggaagccc tggtaaagga gttttatttc gaaaaaatgg gcatttcaga 4380 attgagtgct atacggatgc tgactgggca ggatcaacgg atgataagcg ctcgacatcc 4440 gggtacttta cctttgttgg gggaaatcta gtaacgtgga gaagcaagaa gcagaatgtt 4500 gtatcaagat caagcgcaga agccgaattt agaggtatgg cactcggtat ttgtgaactc 4560 ttatggctca agtttctgtt acaagatgtg ggggccaaac atggtcagcc gatgaggtta 4620 ttttgtgaca ataaagctgc tcgtgatatt gctcataatc cagtgcaaca tgataggacc 4680 aagcatgtag aggttgacag attctttatt aaagaaaagc tagatagcaa agtaattgag 4740 gttcctccta taggaacgaa cgaccaagta gcagatattc tcactaaggc ggtttctagt 4800 gacaagttct ccaagtttct agacaagttg ggcatgtgca acatctatgc accaacttga 4860 gggggagtgt 4870 // ID Copia22-VV_I repbase; DNA; EDCOT; 4345 BP. XX AC AM472139; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia22-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4345 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4345 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 687-687 (2007). XX DR Genbank; AM472139; Positions 6864 2520. XX CC Positions [2010-2510] - Integrase core CC 'CTTACA' target site duplication CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 1287..2900 FT /product="Copia22-VV_I_1p" FT /translation="MEMLQKLLSPLLSVQSQTGSSSNQVIGSGTLAHKGNF FT LSAFTAGKKRKKPWIVDSGASDHMTGDATIFDTYSSCPNNLTVRIADGSLS FT KVAGTGSVVLSRDLTLNSVLLVPNLDCNLLSISKLTKEKRCITNFSSTHCE FT FQDLDSGKTIGNAEECSGLYILKERHDPQEQPQMTVGSNSFSVSCQNNDSA FT IRLWHYRLGHPNVMYLKHLFPSLFNKNPQSFECEICQLSKQVRSHFPIQPY FT KESSPFSMIHSDIWGPSRIKNVTGTRWFVSFIDDHTRLTWVFLMKEKSETS FT QIFKNFKNMIQTQFQSKIQILKSDNARDYFNSILGEFLAQEGIVHLSSCVD FT TPQQNGIAERKNRHLLEVARSLMFSMNVPKLFWGQAVLTAAYLINRMPSRV FT LKFQTPCQTLLKSFPTTRLISTVPPKIFGCSVFVHINQQHRSKLDPRSLKC FT IFLGYSSNQKGYKCYSPVTRKFYNSMDVTFFETQPYYPKNDIQGENSTQEY FT QFWDLESFSESPITTENHIPPESFNQPESIVDLWDKEHIQEE" XX SQ Sequence 4345 BP; 1357 A; 875 C; 857 G; 1237 T; 19 other; tgtaagagta gtttatttac tttccatgta agagtagttt atttaattcc catgtaagag 60 tttattcact ttccatgtaa gggaaattcc attccggaat tgtctcatat ccgtaggcta 120 tttatttatg ytttcattca ttgtaaaggt aggaatcaca gaatgaattg aggtgttcct 180 ccatattttg tcttcaaatt ccttcatatt tttcttcaaa ttcttcatgg tatcagagca 240 ggtttaatcc tgtytcatcg tcttcatctt tagtcagttt ttactcaatt ctattcttct 300 aatttatgcc taaatacggt ccagcctttg gaatggctac caactcatca tcctctactt 360 ctgatatcat catctcatcg tcttcatcct ctcatcagat ggaaacctct catcttccaa 420 tcacagccca taaactgaat gggcaaaatt atttgcaatg gtctcagtcc atattaatgt 480 ttatamgggg aaaggagaaa gatgactaca tcaccggagc ttcggcggca ccagaaacca 540 cagcatcaac ctacaaaaag tggatagcag aaaataatat ggtcatgtcc tggctagtca 600 actctatgac cgctgacatt ggtgaaaatt ttctgtcatt tgatactgcc aaagaaatct 660 gggacactgc aaaagaaact ttctcagaca aggaaaacac atctgaaatc atccagattg 720 aaggcatcct ccacaatttg cgtcaaggaa accttacggt aactgaatat ttcaatactc 780 ttactcgtct atggcgtcaa cttgacacgt ttgaggttca taattggaat tgtgttacag 840 atggtttttt gtataaaaag attgtcgaag ggaaacgtgt gtttaaattt ttgttaggtt 900 tgaacaaamr tcttyatgam wttarwggaa gaatcatggg agtaaaaccc ctacctagcc 960 tcagagaggc attctctgaa gtccgtcgcg aagaaagtcg raaaaatctc atgatgggat 1020 cccatcaaca actgaatatg gcagaaagct cggctcttaa kactcaattc gctccttttg 1080 amaaccgtca aaaaattaaa ggaggtagac cttggtgtga tcattgcaga aagccgggac 1140 actcaagaga aacttgctgg aagattcatg gaaagccagt agattggaag ccacgtcaac 1200 cacttgagaa agaaggacga ggcaatcatg tggctaccga tgaacaatcg ccacaacctg 1260 aagctagccc ttttaataag gagcaaatgg agatgcttca gaaactactg tctcctcttt 1320 tgtcagtaca gtcacaaact ggctcatctt ccaaccaggt cattggttcc ggaaccttgg 1380 ctcacaaagg taattttttg agtgccttca ctgctggtaa gaaacgtaaa aaaccttgga 1440 tagtggactc aggagcatct gatcatatga cgggagatgc gacaattttt gatacatata 1500 gctcatgtcc aaataattta acagtccgaa tagcagatgg ttcactatca aaggttgccg 1560 gaacaggttc agttgtgcta tcaagggatc ttactctcaa ctctgttctc cttgttccta 1620 acttggactg taatctattg tcaattagta aactcactaa ggaaaagagg tgtattacta 1680 atttttcctc cactcactgt gaatttcagg atttggattc ggggaagacg attggcaatg 1740 ctgaggaatg ctctggactc tacatcctta aggagcgcca cgatccacaa gaacaacctc 1800 aaatgacagt tggtagtaat tctttttcgg tttcatgtca aaataacgat agtgcaatta 1860 ggttgtggca ctatcgctta ggtcatccaa atgttatgta tctcaagcat ttatttcctt 1920 cattatttaa taaaaatcca caatcctttg agtgtgaaat ctgtcaatta tcaaagcaag 1980 tccggtctca ttttcccatt caaccctata aagagtctag tccattctca atgattcata 2040 gcgatatctg gggtccgtca agaataaaaa atgtaactgg tactaggtgg tttgtctcat 2100 tcatagatga tcacactaga ttaacttggg tattcctcat gaaagaaaaa tctgaaacga 2160 gtcaaatttt caaaaatttt aaaaatatga ttcagaccca attccagtca aaaatacaaa 2220 ttctaaagtc tgataatgct agggattatt tcaactccat tctaggagaa tttctagcac 2280 aagaagggat agttcactta agttcatgtg ttgatacccc acaacaaaac ggaatcgctg 2340 aaaggaaaaa taggcatttg ttagaggtgg ctagatcact aatgttctcc atgaatgttc 2400 caaaattatt ctgggggcaa gctgtcctta cggcagccta cctcatcaat aggatgccgt 2460 ctagggtact aaaattccaa acaccttgtc aaacactcct aaaatccttt ccgactactc 2520 gtctcatctc caccgtccca cccaaaattt tcgggtgctc tgtctttgtt catatcaatc 2580 aacaacatag aagtaaactt gatcctaggt cactcaagtg catctttctt gggtattctt 2640 caaatcaaaa agggtataag tgttactctc cggtcacaag aaaattctac aattcaatgg 2700 atgtcacctt ttttgaaacc cagccttact atcccaaaaa cgatattcag ggggagaatt 2760 caactcaaga atatcaattt tgggatcttg agtcattcag tgagtcaccc atcaccactg 2820 aaaatcacat tcctccagag tcatttaatc aacccgagtc cattgttgac ttgtgggata 2880 aggagcacat ccaagaggaa atrgaggaaa gagcactttc tcaacaaacc catgaggcag 2940 aaccgggtcc taatccaarc aaacttccag gtaacaaygc tcctaatggt actgttgatt 3000 ccgagttaga aaatgatatt cttaatatgc ccatagcttg gaggaaagga gttagatcat 3060 gcactcagca tcccattgga aattttattt cttatgataa gctatcacct acgttttgtg 3120 cattcacttc tagcatcaca gagatacaag ttcctcagaa tattcaagaa gctttcaagt 3180 atcctaagtg gaaggcgrca gtcgatgagg aagttcgggc actggaaaag aatggtacgt 3240 gggaaattac tgacctccca agatgtaaga aaccagttgg gtgtaagtgg attttcacag 3300 taaagtacaa ggcagatggt aatgtggaca ggtataaggc tcggttggtc gccaaaggat 3360 tcacccaatc ctatggcatt gactatcaag aaacttttgc tccagttgcc aagctcaata 3420 ctgttcgtgt acttttatcc ttggcagcta atctcgattg gtcrcttcac caacttgatg 3480 tgaagaatgc attcctcaat ggtgacttag aggaagaagt ttacatggac attcctactg 3540 gacttgagac gacatcaaat ttcaacaagg tttgcagact ccgaaaatcc ttgtatggtc 3600 tcaaacaatc tcccagggcc tggtttgaac ggttcactaa ggtagtgaaa gggtacagat 3660 tcgttcaatg tcaatccgat cacacattat ttgtgaaaca cttcccagaa gggaaactga 3720 caattatcat tgtatatgtg gacgacataa ttttgacagg tgatcatgaa gagaaaattg 3780 acttacttaa aaaattactg acaaaggaat ttgagatcaa ggatcttgga aacctcaagt 3840 actttctcgg aatggagatt gctaggtcaa agaaaggtat agcagtctca caacgcaaat 3900 acgttctgga cttattgaat gaaacaggaa tgctaggatg caagccggca gaaacaccta 3960 tggatacaac tgtcaaactg gaagaaagtg atggaagtgc gccagttgat aaaggaagat 4020 atcaacgtct tgtggggaaa ctcatctatc tttctcatac aaggccagac atcgrcttct 4080 ccgttagtgt ggtaagtcaa ttcatgaata atccaaccga aaaacacatg actgctgtga 4140 tcagaatatt gagatacctc aagatgacac cgggaaaggg tctcttcttt caaagaacaa 4200 caaagaaaga gattgaaatt ttttcagatg cagattgggc aggttcagtg actgatcgga 4260 gatcaacttc aggctattgt tcatttgtct gggggaactt ggttacatgg cgaagcaaga 4320 aacagtcagt ggtagcccgt agcag 4345 // ID SONATA1 repbase; DNA; EDCOT; 243 BP. XX AC . XX DT 21-MAY-2006 (Rel. 11.05, Created) DT 23-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE Nonautonomous DNA transposon from Solanum - consensus. XX KW DNA transposon; Transposable Element; SONATA1. XX OS Solanum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae. XX RN [1] RP 1-243 RA Jurka J.; RT "SONATA1: Non-autonomous DNA transposon from Solanum species."; RL Repbase Reports 6(5), 267-267 (2006). XX DR [1] (Consensus) XX CC This family is relatively young and may still be active. TSD is CC "TA". Putative Mariner superfamily. It is present in other CC Solanaceae (Petunia, Lycopersicon, Nicotiana). XX SQ Sequence 243 BP; 88 A; 26 C; 49 G; 80 T; 0 other; tactccctcc gtcccatttt atgtgaggta gtttgactcg gcacggagtt taagaaagaa 60 aggaagactt ttaaaacttg tggtctaaaa tgaatgatag aaatttgtgt ggctataaat 120 catttcatta agggtaaaat agatatttta aagttaaatt gttacttaat atagaaatgt 180 gtcattcttt tttagactga ctaaaaagga aagtaagtca tataaattgg gacagagaga 240 gta 243 // ID Ogre-MT4_LTR repbase; DNA; EDCOT; 1884 BP. XX AC AC145061; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 10-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE Autonomous LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-MT4; Ogre-MT4_LTR. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1884 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC145061; Positions 77054 78937. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). CC In Medicago truncatula, there are distinct subfamilies of CC Ogres differing in their LTR sequences. XX SQ Sequence 1884 BP; 611 A; 366 C; 265 G; 642 T; 0 other; tgtcataccc caattttgga ccgtttaaaa tctcttgtcc gtattttaaa atggttcacg 60 ttccctttta ttcgtttttt tgtaccattt aaaattcggg tttcttgtct ttagtcattc 120 aaaaagtttt tatttttaca tttaaatcaa cgttcgcatt tcacactttc atttttacgt 180 cgcatagtct tttttttaat cgtaacgatc acgtcaaaaa aaaagagaag gcctgatcgc 240 attttaaaag gcgttttttt tattaatcat ttcaaacaaa atttcggcag ggaggatact 300 ttgaagtacc tcatgtcaga tttcgaaggg attttttttt attttctttt ttaggctagt 360 ttgtttatta ttattattat tttttttact tttatttttt ttagaaaaaa aagaaaaaaa 420 caaaagtcac tcacgtgact ttcttctttc ccttttcttt tcttttttta ttatttattt 480 ttttacttat tttactcatt ttgttttttt atttatttat ttatcttttt tgtcaaatct 540 ttttctccaa gtctcagctg caggggcatt ttggtcattt gtttgtacca gagccaaccc 600 tagtttgtca ctataaaaac cctgtcaatc attgggaaat gggccagaag tcactgttca 660 cgtcaaaaaa tcagcagcaa ttcacaaaca ctcattttct acttttccaa ccctttttca 720 gatcaaacac taaaaattac agagaaataa catgaacaca tgaagaacat tcatatattc 780 atcaaaatcc agcaacacaa aacttaaaca aaacctcaaa tcagcccata caaccacaaa 840 tcatcatcat cccaaaccaa ggaagaactg aaccgtagca aaagaggggg aaacgaaccg 900 gaccgaaccg gaaggagagg agcagaaccg gaccggaccg gaaggagaga agcagaaccg 960 tagcaaaaga gggggaagag aaccggaccg gaaaagctag gaaaggagga gaccggaaaa 1020 agagcatgca tattcaattt tctcatcatt ttattttgtc attgacttag tatgtataaa 1080 tagggaattg atgtaatttt atttcttgca ttttattttg gcataaaggc cttagggttg 1140 tatttaggaa ttgatgtaat aatgtaggta acacaagcac cgacacatgc accgacacta 1200 ccacatttta tttaccgctt tccgttagtt ttttacgacg ttacgttagt tttcaccgtt 1260 agtttagaaa aatcattttt cacaaaaaaa atcaaatatg tcaaattcaa aaaatatttt 1320 ttcttagcaa cattttccct ttattttctt aatcaaattt ttaatcaatt ttaattcaac 1380 ttcaatcatt ttcaaaattt aaaatcaatc aacctcactt atttctttta tctcatgcct 1440 tgaggcctct ttctcttctt aaaaccattt tcaaaaaaat cttaaaatca acctaaccca 1500 ccaaagaaat ttttgagtgg aactacgtcg gttttgatcc ctttcccaaa aagggtacgt 1560 aggcagagga ctcgtccttc caaatcaaat aaaaataacc aaaaacatac ttcttctccc 1620 tccattctct catttagaca ttaggcaata attttttcaa gtaaacaagt aacttagcac 1680 aagataatct aagtaagagg ttcctatgga ataccataga cgcttaggat gctagcacct 1740 tcccttcgcg taaccaaccc ccgaatccaa agtctcgata agggttttta ctcatttttt 1800 cccttcccaa gaataaaaat cgagagttca aagattgacg attcaaatca attaatggtt 1860 tgacatccga aaatcgcgag caca 1884 // ID Copia48-PTR_LTR repbase; DNA; EDCOT; 145 BP. XX AC scaffold_954; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia48-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-145 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-145 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 275-275 (2007). XX DR Genome; scaffold_954; Positions 11642 11498. XX SQ Sequence 145 BP; 56 A; 17 C; 17 G; 55 T; 0 other; tgattgagta accgaagatt agttttgatt cttagtaatt atagttttta atgctattta 60 taattcttgt aacagtcaaa caaattctgc tatacatata actatatatt gtaaacagaa 120 gtaataagaa aaaccatttt ctaca 145 // ID HRS60_NT repbase; DNA; EDCOT; 182 BP. XX AC X15068; X78472; X78473; X78474; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 25-MAR-1997 (Rel. 2.02, Last updated, Version 2) XX DE Nicotiana tabacum repeat element, consensus sequence. XX KW BamHI repetitive sequence; GRS; HRS60; HRS60_NT; NTTDNA; KW T-DNA integration; consensus; eco repeat; tandem repeat. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RA Matyasek R., Koukalova B. and Reich J.; RT "Isolation and sequencing of HRS60diml, a dimeric member of the RT HRS60-family of a tobacco DNA repeat."; RL Nucleic Acids Res 17, 4377-4377 (1989). XX RN [2] RA Gazdova B., Siroky J., Fajkus J., Brzobohaty B., Kenton A. RA and Bezdek M.; RT "Characterization of a new family of tobacco highly repetitive RT DNA, GRS, specific for the N.tomentosiformis genomic component."; RL Chromosome Res 3, 245-254 (1995). XX RN [3] RA Suter-Crazzolara C., Brzobohaty B., Gazdova B., Schell J. RA and Reiss B.; RT "T-DNA integrations in a new family of repetitive elements of RT Nicotiana tabacum."; RL J. Mol. Evol 41, 498-504 (1995). XX DR [3] (Consensus) XX SQ Sequence 182 BP; 48 A; 32 C; 61 G; 40 T; 1 other; ggggaccccg ggcccacggc ggaaggcatg ggctatagca cacgaaaatc tgggaatcgg 60 gcggaattcc agttttatgg ctgtaaaatg ccaaaaaatg aggaacggtc atggaggggg 120 ggtgaatatg gtttcttagg tcgtatttga tgtccgggaa aaattttagg cgatccaggt 180 cn 182 // ID Copia10-PTR_LTR repbase; DNA; EDCOT; 205 BP. XX AC LG_I; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia10-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-205 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-205 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 193-193 (2007). XX DR Genome; LG_I; Positions 3192332 3192128. XX SQ Sequence 205 BP; 75 A; 28 C; 32 G; 70 T; 0 other; tgttaagaaa ggattaatga atatcccaaa gttacgtaat ggtttaggaa agaaatatgt 60 agacctgatc tatcaactat actattccta ttgtaattca tattcctaat atagcatagc 120 acaattgtag ggaaatactt gtatataagc ggcagagtat cattgaataa atataaggca 180 aatattttct cttctctgtt ttaca 205 // ID TLP1 repbase; DNA; EDCOT; 662 BP. XX AC . XX DT 02-MAY-2002 (Rel. 7.04, Created) DT 24-OCT-2006 (Rel. 11.11, Last updated, Version 2) XX DE Putative non-autonomous DNA transposon - a consensus. XX KW DNA transposon; Transposable Element; TLP1. XX NM TLP1. XX OS Solanum pimpinellifolium OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-662 RA Lavelle T.D., Oldroyd E.G., Dalhbeck D., Staskawicz J.B. RA and Michelmore W.R.; RT "Direct Submission to Genbank."; RL Direct Submission to Genbank (04-JAN-2000)Center for Engineering RL Plants for Resistance Against Pathogens (CEPRAP), University of RL California, Davis, One Shields Avenue, Davis, CA 95616, USA. XX RN [2] RP 1-662 RA Jurka J. and Drazkiewicz A.; RT "TLP1: a non-autonomous DNA transposon from currant tomato."; RL Direct Submission to Repbase Update (16-APR-2002). XX DR [2] (Consensus) XX CC Originally [1] described as tomato inverted repeat CC element 4 (80%, bases 57212-57850). XX SQ Sequence 662 BP; 232 A; 100 C; 98 G; 216 T; 16 other; tacataaata tgacctttaa cttggcttca aatkacattt atgacctcca actttgagtg 60 tgcacaagta gacacttaaa cttgtataaa attgaacaaa tagacacatg agtcctacat 120 gacataatac gtcccacgta gggtcctaca tgtattatgt catgtaggac atgtgtgtct 180 atttgttcaa ctgttataca atttaagtgt ctacttgtgc acactcaaag ttgaagggca 240 taaatgtaat ttgaagccaa gttaagggtc atatttatgt attatgcctt tntatntaan 300 attnttaaaa twttctygat tnanactnac ntttagatan aatnnagnat atatatatat 360 tattanataa taggcataat acataaatat gacctttaac ttgacttcaa attataatta 420 tgacctccaa ctttgattat gcacaagtag acacttaaac ttgtataaaa tttgaacaaa 480 tagacacatg agtcctacat gacataatac acgtaggaca ccacgtagga caaaaaatgt 540 catgtaggac atgtgtgtct atttgttcaa cttttataca agtttaagtg tctacttgtg 600 cacactcaaa gttgaagggc ataaatgtaa tttgaagcca agttaaagga catatttatg 660 ta 662 // ID HAT-4N1_Mad repbase; DNA; EDCOT; 1680 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-4_Mad; HAT-4N1_Mad. XX NM HAT-4N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1680 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1613-1613 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >90% identical to consensus. 8-bp TSDs. The 3' terminal 365 bp is CC ~98% identical to that of HAT-4_Mad. XX SQ Sequence 1680 BP; 482 A; 273 C; 422 G; 503 T; 0 other; cagtgaagaa aatatcgata atatcggcga tatttcgccg atattatcgt tttttttggg 60 gtccgatatt tttttaacta tccaaattgt tttcgtcaaa atatcgcgat attatcgata 120 atatcgataa tatcgcgata ttttcgaaac tatcgcgata ttttggcact gttcaaatcg 180 gagaagaacg ccggagcaaa ttaaccgaat ccctaaatcc ccaaattcga tttcaaagca 240 aatgaactga atccctaaat ccccaaattc gaattcaaag caaatgaact gaatccctaa 300 ttcctaaatc cctaaaatcg aattcagtac aaaaatggtg caacatgcag aaaattcgaa 360 atctgtacaa aaattaaatt acaagccgag aagaatatgg tagtaggagc ctgggaacgt 420 cgtcttcctc acgaatccaa gacggctggg acaacgtcgt gctcctcacc gacgactacg 480 atgaattccg gtccatcgtc cggtgtccgc tgcctccgct cagtttctcc acaaccgttg 540 atttgcgatg acgcgacagt tacgactcga cgactgggac taacgacacg gcttctccat 600 ggaacaaggt ggtttagaag gcggttatgg agtggtgtcg acggctgggt ttagggcggg 660 tgagatggga ggagcagagg gagacgcgga cgaggaggat cgagagatgg atcgagattc 720 gagagatgat gtctgtgtgt gtgtgtggaa gaactggaga agggggaagg gagaagactg 780 agaacaatta caggaaggga gaagactcag agagagaaga gagagaagga aggatcgaga 840 cgattcgaga gagaaggaag gattgagggt gtgtgtgtgt gtgtgtgtgt gtgtggggag 900 gggtggcaca cggttttgtg tgaaccaggt tgtgtgtgtg tgtgtgtgtg tgtgtgtgtg 960 tgagaaaatg aggtgtgtgt gtgtgtgttg tggcacacgg ttttgtatga aaccatggtt 1020 ttgtgtgtgt gtgtgtgtgt gtgtgtgtat ggttatggcg cgtgtgtgtg tacatggtta 1080 tggttgtgtg tgtgtgtgtg tgtatggtta tgtgtgtgtg tgtgttatcc gagagaaaaa 1140 gaaaaaaact ttgagggtgt gtgtgtgtgg cacacggttt tgtatgaaag aattggaagt 1200 gactttgcac agaagaacca aatattctgt cagagaagaa ccaaaaaatc tgcttacttt 1260 atcttcttct ccacgtgaag accaaattct gtcagagaag aaccaaaaat gcaatgtaca 1320 aagtgtaaaa tattgtacta attcattata tataaatgat tatggtgtgt ttagacctct 1380 ttcattaatt actacatatt ttctacactc acaatgtttg tcagctcgct atataatcaa 1440 cttgataatg ttaaatccat catgcaatgc atttccttcc aattttttgt gataaactaa 1500 tagataattg actaaataaa catcctgcaa agtttcaata aaaatttcca agtttttctt 1560 acaatttccg tggtttccat gtaattttta tcgatatcga tattatcccg atatttccat 1620 cgatatttcc gtgttttcgg actaccgata tttccgatat taccgatatt ttcttccttg 1680 // ID Copia-99_Mad-LTR repbase; DNA; EDCOT; 1824 BP. XX AC . XX DT 25-OCT-2010 (Rel. 15.11, Created) DT 25-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome, consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Copia-99_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1824 RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1824 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1984-1984 (2010). XX DR [2] (Consensus) XX SQ Sequence 1824 BP; 561 A; 338 C; 384 G; 541 T; 0 other; tgttggaaat gtgccctaaa accaatcata tgatgatact ttacggacat ttcacatgtt 60 aaactaatat agtttaattt aaagggcaaa gattattgtt tgaagccgtc tcatataaat 120 gttatacgct taaacgataa gtccaaggaa tatgtaattg ggagaatgcg atctaaagaa 180 gttagattca tgagaccatt ctctttcgta tacatatcct aaacgttcct gatcatagga 240 ttgccaattg ggcattgaca gtccgttaag atcagtacgt gctatgtctt ctcttaggga 300 gagtgactgg tctcgagtca ttggtgtgac tgacaccaag acaagcatgt aggtgctcaa 360 tagagaatga gtccactgaa cacgatcaac aaggagttct catactcatg tcacatgaga 420 actcatggtt gggataatgc aaagtagtcc tttgacctga ggcatcatag ttgtcttgtg 480 gttaggtcct tgatctttga ctatgtcaaa gtcactccgt cagagggtgt ccacggcata 540 gttggggtta agccacttag ccatggaggc aagtgaatgc gcaacaaggg atctctaacc 600 ttcaaactgt ttgagggaga atactctatg atatgattaa gaatctctgg ccagagtatg 660 aatgagattt aggaagtcgt tccaaatcac attcaaggta atcatataag taaatgaatc 720 acattggata gtagacatga ataaactatc aaaccaaaca atgtggtcaa gagtattgta 780 ttagagaaag accgtattgc attgtaatcc taaactgaat aggttctcca cctcttctga 840 ttagcttggg taaccatgac atactgctag gtgtcactca tggtttgtgg aagccctaaa 900 cgtgtataat cactaaaggg agaattgaaa gtaagtttca attcacaatc gatttgaaag 960 agttctaatc gcccactgcc tcgctaaaag gaacctaatg gatcgtacac cgtgtaaggt 1020 agagattgaa gaaacaacgg agatgagtaa ggacaattaa atggtttaat tgtttatggc 1080 aagaattaat taatatgtta attaatcaaa cgaataaagt tcgttttaaa ccttgagtta 1140 gttttgggcc ttaaagccca aattgggctt cgaatcgtca agcccattag cttaagttgt 1200 atgacaactt aacaaacaaa attcaagaag cccaaaacag cccaaaggct tgggaaaacc 1260 ggccatatag agaggggtag tgggcttggc tttattgcaa gtttgccact ccaatgtgag 1320 gtaggtataa aggcaacttt atagccattt catccttagg gtttcttttg gagaaaagat 1380 gagaacacaa gtctcccctt ttctctctaa gaggccggcc accctggagg attttagcta 1440 gcaatcttac ctcctccaag gtcactcatc tcttcttcaa gtccttcctt ggtgtggaga 1500 cttagaggtt ctcaactttg ggaacttgga gaatcctttc aaccatcctc atccaagaaa 1560 tccatggagc taagaagcaa ggaatgaagg ccctctcctt gggtgattag cctttgctta 1620 tgcaaagagg aatcaacaaa ggtataaaat ttctcaactc actttgttct tgagttgagt 1680 cttggttcac ctttctacta ggctttgaat ttcatgggta atgttttgtt tttgagtgca 1740 tacaagcatg attccgcctt taattgttaa ttgcatgcca tagatgttgc tcaaatgaac 1800 atgtttttca caaaatttcc ttca 1824 // ID MuDr2_MT repbase; DNA; EDCOT; 366 BP. XX AC . XX DT 28-DEC-2006 (Rel. 11.12, Created) DT 28-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Non-autonomous DNA transposon - consensus. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW MuDr2_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-366 RA Jurka J.; RT "MuDr2_MT: MuDr-type non-autonomous DNA transposon from barrel RT medic."; RL Repbase Reports 6(12), 635-635 (2006). XX DR [1] (Consensus) XX CC Present -in ~300 copies phg, >90% complete and 68-98% identical CC to consensus. XX SQ Sequence 366 BP; 110 A; 69 C; 65 G; 122 T; 0 other; ggctaaaata tggttttggt ccctgcaaat atgcctcgtt ttggttttag tccctgcaaa 60 aaaaatttgt tgtttttggt ccctgcaaat atgtctcatt ttggttttgg tccctggctc 120 cacttttgtg ataatttgca cacgtgtcac atgatgactg aacccattta ttagagaaat 180 agtccctgca aaatcttttg attttgaaaa aggtccctgc aaaatatttt gtttttggaa 240 atagtccctg cagggactat ttccaaaaac aaaatatttt gcagggacca aaaacaacaa 300 atttttttta cagggactaa aaccaaaacg aggcatattt gcagggacca aaaccatatt 360 ttagcc 366 // ID DNA9-7_Mad repbase; DNA; EDCOT; 392 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-7_Mad. XX NM DNA9-7_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-392 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1488-1488 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 106-bp long. ~84% identical to the consensus. TSD is 9-bp CC long. XX SQ Sequence 392 BP; 124 A; 80 C; 80 G; 108 T; 0 other; gggggcggat ccgtggcacc actttttttt acacaacttt tgacacatgt ttttgtgggg 60 cccactccgt aatgtatttc aacgatccga accatctatc ttttagaaca tcattcatag 120 atcatccttg caaaaaatta gacaaatcca aaaccattaa gacattcatt tgtagtgaag 180 aaaatggacg aatacggttc tacaaagaaa ccctaaaccc ttaatccaac ggtcatatgg 240 tttcagattt gggtgatttt tggtagacat gatctttgag ggaagaccta aaagatagac 300 ggttcggatc gttgaaatac attacgaagt gggccccaca aaaacgtgtg tcaaaagttg 360 tgtaaaaaaa gtggtgccac ggatccgtcc cc 392 // ID MUMET2 repbase; DNA; EDCOT; 5516 BP. XX AC AC135233; XX DT 19-JAN-2007 (Rel. 12.01, Created) DT 22-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE MuDR-type DNA transposon. XX KW MuDR; DNA transposon; Transposable Element; MUMET2. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5516 RA Jurka J.; RT "MUMET2: MuDR-type DNA transposon from barrel medic."; RL Repbase Reports 7(1), 42-42 (2007). XX DR EMBL/GenBank/DDBJ; AC135233; Positions 20113 25628. XX CC No TIRs have been identified. XX FH Key Location/Qualifiers FT CDS 941..2647 FT /product="MUMET2_1p" FT /translation="MGLFDVVFHHGGEFVMDKRIFYRGGVQTVVSGIESNN FT WGVCDIQNIVASWGYEKNKFRVWSQIEVVFEEFFQINQDHIAEEISGYSVA FT NKVHAHIFVEHNVLDITVKVDVPSFLDLDAGYDKEDVMVCSDDDGAAVVGF FT NDSEDERTTALEDGFEEVEVEAPVNGTNRVTVNNKTLRIKKCGSKTPKKKS FT PKKNNSGRMNVVAPVSLLKNGEGKDVVDEEIDGDYLSEELGSSDPDDSDDD FT TIKYQQFRMVQLNKDFKFKVGMEFNTLVEFKEAIIEWNVLNGYQIKMPKNE FT SYRVRVECRDQCGYKVLCSKVGDRRTFQIKTFEGPHTCAPVLENKSSNSRW FT VAKKVVPKMQVTKKMSVQEVYNEMAVNYGVGITMDRAWRARNIAKKIIEGD FT ADKQYAMIWRYAAELKRVCRDNNVKINVVGPSATIQPRFGSFYFCFDGCKK FT GFTSSCRPFVGVDGCHLKTRYGGQLLIAVGRDPNDQYFPLAFGVVETECKE FT SWKWFMQLLMEDIGQDKRCVHIRSTKGMFRSIHVSSIYVFNVLDLMKSIFI FT YCFQSIFRSKFIYCYAGVVVSF" FT CDS 2625..3584 FT /product="MUMET2_2p" FT /translation="MQGLLSVFDEMFDSIDHRLCLRHLYANFKKKFGGGSQ FT IRDLMMGAAKATYYQAWLEKMNELKKIDLGAWEWLMAVEPKKWCKHAFTFY FT SKCDVLMNNISESFNATILSARDKPIISMAEWIRHYLMRRMTTSATKLQKW FT QHNVMPMPRKRLDKEITLAAHWTATWSGIGEQFQVIHLYNRQQFIVDIAKR FT SCSCNFWEIVGIPCRHVVAALGHRKQRPELYVDDYYSRSKYVMCYSFAISP FT INGMDMWPEVEAPELLPPEYKNGPGRPRKLRIREFDENGARMKRQGVAYRC FT TKCDQFGHNQRRCKSAVQNPEAAKRKVY" FT CDS 3735..4439 FT /product="MUMET2_3p" FT /translation="MAHVSASQPTVPHASDTHSTMPHAPSSQPLMHTEPVQ FT RPPKLTSVQGPSRFTSVQGPPMEVAKLVHQNIHLERPFKIQKVSSSNATNT FT VPEKIVTDFYNALPASQIESGLGPDVFDDPDDHVLAAITDQMFDAAENKFQ FT ILNNEKDVKNLNEQKLKTLGLKKHVRPKNSRKSTRLMKLKTKAIKGAGSSI FT AEPMVIEESEEGTLTQENDGVIKSGTCMEVLRGLPKLVMRASKPN" XX SQ Sequence 5516 BP; 1783 A; 866 C; 1174 G; 1693 T; 0 other; agggttaata ggggtttacc cccctgccat ttggggtact tttggtttac ccccccacaa 60 aaaaaaaact tgtagattcc cacttgtaat atgaagattc cttggtttac ccccctacac 120 ccaatagtca gcatatgact ggataaaaac ggtgacgtgg ttgtctgact aggtattatt 180 ttttttaatt tccacctaga ttattaaaca ccaaaagtcc aaaaatgttc ttattggcat 240 acacccctgt catttccccc aaaacttaaa cctaatttca aaaactgaga agaacaaagg 300 gagggacgaa gaacaaaggg acgaacaaag aaatagggtt ttcctttctc gaaatcgaaa 360 ttgagaacaa agggagaagg gacgaacgga agaacaaagg gttttcgttt tattggcata 420 cacccctgtc actttcttga aatcgctaat ttctccaggt agatttctgc gattcgaacc 480 aagatttctg ggtttttgag atttcgaagc aagattactg caaatctggg aagctgcgaa 540 tccgcgagca agattactga gacctttcga actcgattta gggtttctgc gaatctggtg 600 acgaacggag aaagagaaat tgaagggaac gacgaaggtt ggagacgaag cttgtggtaa 660 gtttactgat tctctctttt tctttatgca tgcgtgtctc tttgttgtta ctatttgtag 720 atggtaaaga aaggaaaaaa tgtatgttgt ggtcccaaaa gtctgatgct atattccatt 780 actgtctctt tgcatgcgca aaagttcgaa ttttagggtt tatttattga agctttttgt 840 tttttctgag ttgtttatat aaacctggtt taaaccaatg ggttgcagac acgtgtcaat 900 ctgattttga taaaaaaata attttttttt accatagata atgggtttgt ttgatgttgt 960 tttccatcat ggtggggagt ttgttatgga taaacgtatt ttttatagag gtggtgtaca 1020 aactgttgtg tctggtattg aaagtaacaa ctggggtgtg tgtgatattc agaatattgt 1080 ggcttcttgg ggatatgaga agaataagtt tagggtatgg agtcaaattg aagtggtttt 1140 tgaagagttt tttcaaatca atcaggacca tattgctgag gagatttctg ggtattcagt 1200 tgctaataaa gtacatgcac atatctttgt tgagcacaat gtgttggata taactgtcaa 1260 agtagatgta cctagttttt tagatttgga tgcagggtat gataaggaag atgttatggt 1320 ttgtagtgat gatgatggtg ctgcagttgt tgggtttaat gatagtgagg atgaaagaac 1380 cactgcactt gaagatgggt ttgaagaagt tgaagttgaa gcacctgtta atggtaccaa 1440 cagagtcaca gttaacaaca aaacattaag gatcaagaag tgtggttcca aaacacctaa 1500 gaaaaaatct cctaagaaga ataatagtgg taggatgaat gtggttgcac cagtgtctct 1560 tttaaagaat ggggaaggga aggatgttgt agatgaagaa atagatggag attaccttag 1620 tgaagagttg ggtagctcag accctgatga ctcagatgat gacacaatta aatatcagca 1680 gtttaggatg gtacaattaa ataaggattt taagttcaag gtaggtatgg aatttaatac 1740 tctggtagag tttaaagaag caattattga gtggaacgta ttaaatggtt accaaattaa 1800 aatgccaaaa aatgaaagtt atagggtaag ggtggagtgt agggaccaat gtggctataa 1860 ggttttatgt tcaaaggtgg gggacaggag gacttttcag ataaagacat ttgaggggcc 1920 ccacacttgt gcaccagtgt tggaaaataa aagttccaac tcaagatggg ttgctaagaa 1980 agttgtgcca aaaatgcaag ttaccaaaaa gatgagtgta caagaggtat acaatgaaat 2040 ggctgttaat tatggtgtgg gtattaccat ggacagagca tggagagcaa ggaatattgc 2100 aaagaaaata attgagggtg atgcagataa gcagtatgca atgatatgga ggtatgcagc 2160 tgagttgaag agagtgtgta gggacaataa tgtcaagata aatgttgttg gtccttctgc 2220 aactattcaa ccaagatttg ggtcttttta tttctgtttt gatgggtgta agaaagggtt 2280 cacatcttct tgcagaccct ttgttggagt ggatggttgc cacttgaaaa caagatatgg 2340 gggccaactg ttgattgctg tagggagaga cccaaatgac cagtactttc cactagcttt 2400 tggggtagtt gaaactgagt gcaaggaaag ttggaaatgg ttcatgcagt tgctgatgga 2460 agatataggt caagataaga gatgtgttca tatcagatca acaaaaggta tgtttagatc 2520 tattcatgtt tcatctatat atgtatttaa tgttttagat ctaatgaaat ctatatttat 2580 ttattgtttc caatctatat tcagatctaa atttatttac tgttatgcag gggttgttgt 2640 cagtttttga tgagatgttt gatagtattg atcatagatt gtgcctgaga catttgtatg 2700 caaatttcaa gaagaagttt ggaggaggca gtcaaataag agatttgatg atgggagctg 2760 caaaggcaac ttactatcaa gcatggttgg aaaagatgaa tgaactaaag aagatagatc 2820 tgggagcttg ggaatggtta atggctgtag aaccaaaaaa atggtgtaag catgctttta 2880 ccttttactc taaatgtgat gtactgatga acaacatatc tgaatccttt aatgccacaa 2940 tattatctgc tagagataaa cctattatta gtatggctga atggattaga cattatctaa 3000 tgagaaggat gacaacatct gccactaaac ttcaaaagtg gcaacataat gtcatgccta 3060 tgcctagaaa aagattagat aaagagataa ccttagctgc tcattggaca gcaacttggt 3120 ctggaatagg tgaacaattt caggttatac atttatataa ccgtcagcaa tttattgttg 3180 acattgcaaa aaggagttgc agctgtaact tttgggagat agtgggaata ccttgcagac 3240 atgttgttgc tgcacttggg cataggaaac aaaggcctga actgtatgtt gatgattact 3300 actctaggag taagtatgtc atgtgttata gttttgcaat tagtcctatt aatggtatgg 3360 atatgtggcc tgaggtagag gctcctgaac ttctacctcc agaatataag aatggaccag 3420 gaaggcctag aaagcttagg attagagagt ttgatgaaaa tggagctagg atgaagaggc 3480 aaggggtggc atatagatgc acaaaatgtg atcaatttgg acacaatcaa agaagatgca 3540 agagtgctgt tcagaatcca gaggctgcaa aaaggaaggt atattaatac atcttaatgt 3600 tgaataatta tacttaatga ttatgtacaa attaatataa cttatgtttg tttatgttgt 3660 agaggaaaac accaagaagg aaggccgctt caaatgcacc tgtgcaagaa agtacacctg 3720 tgcaagaacc aacaatggct catgtatctg cttctcaacc aacagtgcct catgcatctg 3780 acacacactc aacaatgcct catgcacctt cttctcaacc actaatgcac actgaacctg 3840 ttcaaagacc accaaagttg acatctgttc aaggaccatc aaggttcaca tctgttcaag 3900 gaccaccaat ggaagttgca aaattagtgc atcagaacat tcaccttgaa cgtccattca 3960 agatacaaaa agtttccagt tctaatgcta ctaatactgt accagaaaaa attgttactg 4020 acttttataa tgcccttcct gcatcacaga ttgaaagtgg ccttgggcca gatgtgtttg 4080 atgatccgga tgaccatgtg ttagcagcca tcactgatca aatgtttgat gcagcagaaa 4140 acaaatttca gattttgaat aatgagaagg atgtgaagaa cttgaatgaa cagaaactga 4200 agaccttggg gttgaagaaa catgtaagac ctaaaaatag taggaagagc accaggctga 4260 tgaaattgaa gaccaaggca atcaaaggtg ctggttccag cattgctgaa cctatggtca 4320 ttgaagagtc tgaagaggga accttgactc aggagaatga tggtgtcata aaaagtggga 4380 catgtatgga agtgttaaga ggcttaccaa aactggttat gagagcctcc aagcctaatt 4440 aaacaagtga ttttggtttt atgcttgtgt ttgtctaagt tcagtttaag acttatgcac 4500 tataagtgct tttggttgta tgcttatgtt tgtctaaatt tactttaaga cttatgcact 4560 ataagtgctt ttggtttaaa acttatgcat tataagtgct tttggttgta tgcttatgtt 4620 tgtctaagtt tactttaaga cttatgcact ataagtgctt ttgtttaagt tacagacata 4680 tgcttatgaa atgccatacg cactttaagt gcttttcatt attgcttatg ttatggcctg 4740 tttagaatga tgcaaagatc acttcaaact tttttataga ttactaaagg agttacatta 4800 gttgctgaga taaacaaaaa cattaatgct gaaaacaatt acattaactt gaaaacaatt 4860 acaatgacat taatcataac attacaatga cattaacttg aaaacaatta cattaacttg 4920 aaaataactg agaacacaat ccaagacaca gctagcgcaa caatgaggcc taaatttttc 4980 ttcttctcag cttcaaactt cattttcaac ttctcatgtt tctttgcact tattcctttt 5040 ccatcttctt ttccacgttc tatgccatat tcttttccaa actcttttcc aaactctttc 5100 ccaaaatctt tgccaaattc tctcaaaaac tccattgtca ttacacagct gttgcaacca 5160 gattcagact tcaaaccaga agaacaacct aggtcgtagt actttccaga tttttttaca 5220 aattcatcaa gttcatcatc ccaaatgaac agctcgcaac tatactcagc ctacaataag 5280 ttccaagtta taggtttacc aactattaca aactgcagat gtaagcaaaa ttttaaactc 5340 acacaaaatt aacatctaaa ataaataaat aaaatcactt actccagaaa atcgacatct 5400 ccaaaacttt ctcttgggat tttcatctgt gtttgaaatc cacatcttca taaccttctc 5460 acaaccgcag attggtggtc tgtttccatc atggttacta attgatgaag ttctgc 5516 // ID Gypsy-30_Mad-LTR repbase; DNA; EDCOT; 410 BP. XX AC . XX DT 08-OCT-2010 (Rel. 15.1, Created) DT 08-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-30_Mad-LTR. XX NM Gypsy-30_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-410 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1755-1755 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 410 BP; 116 A; 104 C; 91 G; 99 T; 0 other; tgttggtacc atatattggg cctcgtcttt gggcctcatc cctaagccca tgacaaatgt 60 aaaaggggag ggagccctta ttctataaaa gggactctcc ctcaccctca tgaggagagc 120 ctcacatcca gaagagaaac aaagggtctc agatccatcc ctcacaacaa tagagggcaa 180 taccctctca gccaaacaga gagcaaaatg gcaagggctg catccacaga gagctccctt 240 gccgatctat tgtaatccat acattcatac agtaaatgga atcaacatca gtgtggacgt 300 agcccaaaca ttggggtgaa ccacgataca tctttgtgtt cttgtgcgtt tgtgtgattc 360 acggccggat ttacgttggt ccaagatcct ccggattttg tgcatcaaca 410 // ID Copia-98_Mad-LTR repbase; DNA; EDCOT; 735 BP. XX AC . XX DT 01-NOV-2010 (Rel. 15.11, Created) DT 01-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Copia-98_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-735 RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-735 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1982-1982 (2010). XX DR [2] (Consensus) XX SQ Sequence 735 BP; 204 A; 102 C; 185 G; 244 T; 0 other; tgttgtgttt ggctcatata cttatgagtt ggcaacaatt ttgatagtgt aactttctga 60 gtgctacagg gaaatggcag tagccacttt gtgtttggct ttcggttgtg gcatggatgt 120 cttgtttcaa gagaagacat ggtgactacc acaagcaaag ttggaagcaa gacttgactt 180 tgtggttgct tgcacacaat tgtgcatgtt ttattttata tgcattaaat gacaaatgga 240 gaaaagttgt actttataga ctaggtatag actttgatgc atgctaggta ggctaggtga 300 taattatgtc atgtgaactt aagacttttt ggtcttgttt gttggcatag ttgctagtgt 360 atgcctataa ctagatgcaa tatttgtgca tttagaaatg cattgagaga gcatccgaag 420 gagaacacaa aggagagaaa atatagagtg agagtgagaa actcttgggg tagagtgagg 480 ctcttagtaa aattctgtga gggtacaagg gattggggtt tgggttatgt tgatttaact 540 caagtgtatc ttgtactagt tattctcata gtgaagagca atatctcttg gaggacgtag 600 gcagattttt gccgaacctc gtaaatttct cagtgtattt atttcttgta atttaaactg 660 ttcaactgtg ggtctgtagt ttggtgagac aatctgaatc tcacttccgc actgacgaac 720 ggccaaggca caaca 735 // ID VIHAT3 repbase; DNA; EDCOT; 3980 BP. XX AC . XX DT 13-SEP-2007 (Rel. 12.09, Created) DT 13-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE DNA transposon from grapevine. XX KW hAT; DNA transposon; Transposable Element; VIHAT3. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-3980 RA Obukhanych T. and Jurka J.; RT "VIHAT3."; RL Repbase Reports 7(9), 1003-1003 (2007). XX DR [1] (Consensus) XX CC This is a hAT-type DNA transposon from Vitis vinifera. CC Individual copies are ~98% similar to their consensus. This CC transposon has ~16-bp imperfect TIRs and 8-bp target site CC duplications. XX FH Key Location/Qualifiers FT CDS 871..2025 FT /product="VIHAT3_1p" FT /translation="MDNESETQVDSSASGRRDPGWKYGRLVNEKDLNTIIC FT IFCDKVTKGGIYRHKQHLVGGYRNAKKCRKCPEHVREEMEEYMSSKKNQKE FT QMNMGSEYVNEDLFGLEDEDIGEEINSRTNVTNISSGGSNRGGSGGRTFSS FT KKPRQKGPMDHFFTPNAEMVVQNQRSGKMNQTTINDAYKKEARERACMLIT FT RWMYEAAIPFNAVTYPSFQPMIEAIGQYGVGMKGPTFHEVRVTNLKKELAL FT TKDLMKDHMVEWGKNGCSIMSDGWTDRKERTLVNFLVNCSKGTMFMQSIDA FT SSMIKTGEKMFELLDKWVEQVGEENVIQVITDNHSSYVMAGNKYYFLNFYL FT LLKFELFILRTYVNLLSTISYREVVRIKASTFVLDTMCCTLP" XX SQ Sequence 3980 BP; 1241 A; 609 C; 911 G; 1219 T; 0 other; catagttctg aaaggcgcgc ctaggctcgg ggcggcgcga cgccaccctc cggcgcctcg 60 cctgaaggga ggcgacgccc cttcacgaag gcgccgctta ggcgcgcaag gcgctcgcct 120 ccagcaaggc gcgaggcggt cgcccgagtc gcctccgacg gcccgaccag gtacgcgctc 180 ctccttctcc ttctccttct tcttcttctt cttcttcttc ttcttcctcc tccagtcggg 240 ttgcagagac gcggcggcag ccctaatttt tttttttttt ttatgggccc aaaacgacgc 300 cgttttggac cctgtgcact taagtgaaca gggaccaaaa cgacgtcgtt ttggagcctg 360 ttcatttaag tgaacaggga ccaaaacgac gtcgttttgg accctgttct ttaaaaaaaa 420 aaaactcctt ccatccagcc cccttttctg gtctttctca acccgagacc actgccattt 480 tttgccctag cctcttccgt gctggagaag tgaagaagaa gaagaaaaag aagaagaaaa 540 atagggggaa aataggagaa aaataaaggg gaaatagtca cgtaccttcc ggacctcggt 600 atttttcttt tttcttcact tttctgcatt tttttccatt cttacctcat aactctcatt 660 ggtaattttt ttttttaaat ataaatatta tattttgagt ttttgacatg aaaattttac 720 aaaataaaaa taaataaata aaaagcactc atatgcatat ttgttgttaa tgtgatattt 780 gataatgtga tatgcatttt ttttttcaat tttttttctt aatttaatta taattatttt 840 attgtggagt atagataatt tgtttgcaag atggataatg agagtgaaac tcaagtggac 900 tctagtgcaa gtggaagaag agatccgggg tggaaatatg gtcgtttggt taatgaaaaa 960 gatttgaaca ccatcatatg cattttttgt gataaagtaa ccaaaggagg catctataga 1020 cacaaacaac atcttgttgg tggatataga aatgctaaaa agtgtagaaa atgtccggaa 1080 catgttagag aagaaatgga agagtatatg agttccaaga aaaatcaaaa agagcaaatg 1140 aatatgggga gcgaatatgt taatgaagat ttgtttggtt tggaagatga agatattggt 1200 gaggagatta atagtagaac gaatgtcacc aacatttcta gtggaggtag taaccgagga 1260 ggaagtggtg gtaggacgtt ttcttcaaaa aaaccaagac aaaaaggtcc tatggatcat 1320 tttttcactc ctaatgcaga gatggttgtt caaaatcaaa ggagtggaaa gatgaatcaa 1380 actaccatca atgatgccta caaaaaggaa gcaagagaaa gagcttgcat gcttatcaca 1440 agatggatgt atgaggctgc tattccattt aatgcagtca catatccgag tttccaacca 1500 atgattgagg ctattggcca atatggtgtg ggtatgaagg gaccaacttt tcatgaggta 1560 agagttacta accttaagaa agaattggct ctcacaaaag atttgatgaa agatcatatg 1620 gtggaatggg ggaaaaatgg atgttcaatt atgtcggatg gatggaccga taggaaagag 1680 agaactttgg tgaacttttt ggttaattgt tcaaagggaa ccatgttcat gcaatccatt 1740 gatgcttctt caatgattaa gacgggagaa aagatgtttg agttacttga caaatgggta 1800 gagcaagttg gtgaagagaa tgttattcaa gttataacag ataatcactc aagttatgtg 1860 atggcaggta ataaatacta tttcttgaat ttttatttac ttttaaaatt tgaattattt 1920 atcttgagaa cttatgtaaa tttattatct acaatttcat atagggaggt tgttagaatt 1980 aaagcgtcca catttgtatt ggacaccatg tgctgcacat tgccttgact tgatgttgga 2040 agatattgga aagctaccaa acatcaagag gacattggag agggctatat cactaaatgg 2100 gtatatttat aatcgctcag ggctactcaa catgatgagg cggtttactg gacaaaggga 2160 attgcttagg cctgctaaga ctcggtttgc aactgctttc atcacattat cgcgattgca 2220 tgaacaaaaa aacaatttga ggaagatgtt tacaagctca gattggtcag atagtaaatg 2280 ggcaaaagag cagaagggga aaactatagc caacatagtt ctaatgcctt cattttggaa 2340 cactattgtg ttttgcttaa aggtttcggg tcccctagtt cgtgtgcttc gtttggttga 2400 tggtgaaaaa aaagctccta tgggatacat ctatgaggcc atgaatagag ctaaggatgc 2460 aattgtgaga agttttaatg gaaatgaaga gaagtacaaa gaaatcttca acatcattga 2520 taagaggtgg gagattcagc ttcatcggcc tttgcatgca gcagggtact ttttgaaccc 2580 ggaattcttc tatgataagc cagaaataga gcatgatgcc gagattatga gtgatttgta 2640 taaatgcatc ttaaggctaa caagagaccc tgctaagcaa gaaaaagttg tggccgaagt 2700 gagtttgttc acaaatgccc aaggactatt cgggaatgag ttagctgtta ggacaagaaa 2760 gactagagca ccaggttagt tatttagttt tgtttattta aatgattaga ttgtattttt 2820 gctaaaatag gtgaattgtt tcactaaatt gttaatatct atactacagc tgaatggtgg 2880 gctgcatatg gagcttcagc tccaaatttg caaaagtttg caatgaaagt cctcaactta 2940 acatgcagtg catcaggttg tgaacggaat tggagcatct ttgaaaatgt gagtgaccaa 3000 atccaaaata attacaagta atagtctaat agagtcttga atgtaactta aaagttaaaa 3060 ctttaaaata tatttatgag cttatgaatt tttgcagatt catagcaaga ggagaaatag 3120 gttagatcat caacgcttga atgatttggt gtacatcaag tataatcgag ccttgaagag 3180 aagatacaat gaacgtaaca ccattgaccc aatttccttg aaagatatag atgatagcaa 3240 tgaatggttg atagggagaa tggaagatga ggattctcat ggaggtgcac aagatgattt 3300 tgtatttgat gatgacaatt tgacatgggg tgatgttgct agagctgctg gagctgagga 3360 ggccaggttt gatactagag ctagagctag agcaagctca agcataatac caccaacaag 3420 ggggatagct tcaagttcta gaactttgcc ttctcattca ctaatagatg aagatgaaga 3480 tggagacatg gttgattcag cagatgaaga agatggggaa ggctacaaat gtggtgatgg 3540 aaatgatgat gatgatgatg attttgttga tttagaggag gagtgatgat tgcttgttgt 3600 ggacaaattt gtgatttaag tgttttttaa tgatgttttt gaattgtgga caaatttcat 3660 gttttggacc tttaggtttg gaaactttgg atttggatat gtattaggca attagcaata 3720 tggatttgga tttgttttta tgcttggagt tctttatttt tatgtttttt gtttattaaa 3780 ttgaagtttt ggatgatatt tgatgattta tgtgtttagg acaaataaat gattgttaaa 3840 tttgattata ttatataaaa atatatatgt aaattagggt gcgcctcact tcactaaagc 3900 ccgcgcctta gatgcgcctt gcgcctcagg ctccaggact actttgcgcc ttggtgcgcc 3960 ttgagccttt taaaactatg 3980 // ID Gypsy-27_VV-LTR repbase; DNA; EDCOT; 1815 BP. XX AC chr20; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-27_VV_; KW Gypsy-27_VV-I; Gypsy-27_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1815 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr20; Positions 11533950 11535764. XX SQ Sequence 1815 BP; 588 A; 285 C; 341 G; 601 T; 0 other; tgtgctctaa tggcacatat tcgatatgat ttgtgcacca aaggacattc aaatcaccca 60 acctgaccta aatcaatgct aaggccctag ccatgagttt aatctatact ttggagattt 120 atctcaggtt caagggaaga aaattgtgca aattgaatga ctttagattt tgaaagatca 180 agaaagggct aaatgaggaa ataagtgaat caagactcat tgaacgtaag gaaaggcaaa 240 aaaaggatat catgaggttg gaggatgata aatgaccatt atgaagtaag aaagaaggca 300 agaaagaatg ggaaatgagg catgaagcaa gatttagttg cgtggaaatt tagaactcaa 360 aaatctgatg gcattatata ctttgacttt gaggacaaat tttgagaact ttctggagtc 420 cattatatgt atactatata tcgtttcgaa gctcgggaag tcaggagtcc aacacttcaa 480 acggtttgca aatcggagct gaaatgaaga agttatggcc atttgaagac aactgcacca 540 agctggaggg tcatttcgaa atgatttcga aattcaactt atgaattcga aatccacttc 600 gaaatgacac caatttcgaa ttcacccact gccactttga tgttccgctt cctctacctc 660 gggaattgca tctaaagcac tccatccgcc ctaggtggac cccacacaac tagaaatcac 720 aattttatta ttttttaatc atttttagga aattattttg taataagtgg ccaatgagag 780 tgtgccacat gttaggtaag tgaggatatt atataaactc tctcaattct aggttttagg 840 gatcttgaat cttggatttt tttctggaga gtttgacatt gaaggtggaa gaagacgaga 900 actttggttt gttttctttt tcttctttat tgaatatatt gtttttagtt tcttttgatt 960 caaattatgg atttttaccc tattatggat tatgaatgtg acatcacccc aatgagaggc 1020 taagatccaa cttggggctt gaagcatgaa aacctaaggt ctaggaaacc tatagggaca 1080 atgggtgaat tattataaca atgagattaa ttattggttg agtgacaatt tatcaatttt 1140 tttatcctat ccttgtgagt tcatttaggg aatgatacgg taggttatta cttgatacta 1200 gtgattcttg gtaattcttg atcattagtt atcctcattt tacctaccgt tatttgcccc 1260 taaacaaagc tataaggagt aggaatagtt aaaaagccaa atcttaaatt gataatcaat 1320 ctcattcatt tgatggtttt aggaatctgt tttaaaaagg aaaaattagg tttcggatgc 1380 aattttgagt tatagaactc aacttgatcg cgagtagcca aggatcccaa aaccttaaga 1440 tcatattact taaaataccc ttgttttcta taatttctat accctaggtt ggattgtgga 1500 aaaccccaaa cttgaatcaa ttgaatttaa aatcaatatt cattttctct tattaattta 1560 atttctttta cttagtttca cattattcac gtattgtttt tttacttaag gatttaaaca 1620 aaaacaattc atttattcta gtattgacaa ttttcataag ccagtccttg agaacgatat 1680 ccggaatact acaaaggttg tagtgactct ttctctagtt tttctttacc agagttacta 1740 cgtaaaaagg ctaagtattt tggtacaata gagaaatttc ggtcaagaaa atggcgccgt 1800 cgccggggat tggca 1815 // ID Gypsy3-PTR_I repbase; DNA; EDCOT; 4628 BP. XX AC scaffold_210; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy3-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4628 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4628 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 330-330 (2007). XX DR Genome; scaffold_210; Positions 194162 198789. XX CC Positions [3491-3985] - Integrase core CC 'AACTG' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 368..4588 FT /product="Gypsy3-PTR_I_1p" FT /translation="MTGQEFLKSGFHIPLPRMELSTFRGEDPRGWMRKCKK FT YFRIHSIPAHQWIEVVSYYLEGKADVWFEGLVRGSDSLIEWEEFSQDLCRR FT FGSKDDIVEEFNKLIQDENMDDYIERFEELRSLMGDLNPLLPEAYYVSSFI FT SGLKDEIKPMLKILKPARVLVAFEQAKWQEEANNALTKKTRSLQRSNPPFH FT SGRIPGNAPSKYFGPSRTKGVKPFSDSLYEQRKKLGQCFKCGDKYMPGHRC FT NSKGLHMIEGVEGGEDEEIGEFEDNMQGTDQIDEYGLSLNALADNDTYNTI FT RIKGNCQGQNLIILIDSGSTHSFINESTIKALNATTSKTTLLAVTVANGNV FT MLCEKHCPAFTWFMHNYEFKSNLRVLELGRHDLVLGVDWLKKYSPVLFDFI FT KLRLSFKKDGRMIELKGISQGAELQMITTLKEHRSFKNVIGGLVGQFFAMD FT SGKENKPTETRAEIKSLLVEFAGIFEEPRTLPPARRFDHKIPLKPGSQPIN FT IRPYKSSFIQKGEIEKLVKEMLSNGVIQHNVSPFASPVLLVKKKDNTWRFC FT IDYRQLNEQTIKNKFLIPLIDDLLDELHGSSFFSKLDLRSGYHQVRMHEED FT IEKTAFRTHHGHYEFRVMPFGLTNAPATFQALMNSILEPYLRKFVLVFFDD FT ILIYSPTFERHLVHLRQVLETLSKNQLLAKRSKCAFGEQQVEYLGHVISIT FT GVSTDRKKTEAVNNWPVPQALKELRGFLGLVGYYRKFIRHFGVISKPLTEL FT LKKNNFGWNDQSQQAFDHLKKALCEAPVLALPDFSKTFFLETDACDSGLGA FT VLSQEGRPIAYFSKALSPKHMGLSIYEKEYLAILMAVEKWRHYLEQEQFVI FT QTDHESLKYMLDQKIHTSIQKKGLTKLLGLRYTILYRKGRENIAADALSRK FT HNNSSLVTVVGELKAVASILPAWYEEVHATYDKDLKLQTIIMGKMMGDTGN FT SDYTYAEGVLRYKGRIVVGQEGELRAKLVKSVHDSYVGGHAGIQNTFRRLK FT ANFYWSGMKTMVKRIVEECDVCKQAKADRVTYPGLLQPLPVPNGTWEAITM FT DFIEGLPSSDGKTAIMVVVDRFTKYGHFIALSHPYTAQDIAQLFLDHVYKF FT HGLPAVIITDRDKIFTSIFWKELFKKLGVQVLMSTTYHPQTDGQTERVNQC FT LETYLRCMTMHHPKRWFHWLSLAQWWYNSSHHSTLGMSPFQALYGYLPPQR FT EWIAQESTPVAAVEDVLQRRANMDLALKKQLEAARHKMKQVADKHRSEREF FT SIGDLVFLKLQPYRQNSVALRRNLKLNPRYYGPYPIIRRIGMVAYELRLPE FT GSLVHPVFHVSLLKKKIGDTTITSSKLPRTDKEGRMQIVPIAILDRKIMKK FT DNRAVTAGLIQWSNLFPEDATWEDLEELLKQFPESIATLLTSTT" XX SQ Sequence 4628 BP; 1471 A; 878 C; 1140 G; 1139 T; 0 other; attggtatca gagcttgcaa caagctgcga acctcattca acaatggtgg acggtaacaa 60 attcaagata gtagatgaac attgcaaaag gttagataac cagctgcaga cttatcatct 120 agaatggcag gaatccatgg caggaaacaa ggagcaaggg gccaagattg agcaattggt 180 catacaaatg gaactactat cctcacagtt tcaataattt gtagctgccc aaacaacaag 240 gacataaatg gcgggaggcc attccagagg tatcctagca acaccaggaa gagacaggag 300 cgtagaagtg aatgcatcta ctgaaaaaat aacaccagga cttagaactc agagtcgtgg 360 tgagtagatg acagggcaag agtttcttaa gtcaggattc cacataccat tgccaaggat 420 ggagctatca accttcagag gagaggatcc tcgaggatgg atgcgaaaat gcaagaaata 480 cttcaggata cactcgatac ctgcacatca atggatagag gtggtctcgt attacttgga 540 aggcaaggca gatgtgtggt ttgagggctt ggtacgaggt agtgattcac ttatagaatg 600 ggaagagttt tctcaggatc tttgcagaag gtttggaagc aaggatgaca ttgttgaaga 660 attcaacaaa ctgatccaag acgagaacat ggatgactat atagaaaggt ttgaggagct 720 gagatcactg atgggggatc tcaacccact gttgccagaa gcttactatg tctccagttt 780 tattagtgga ttgaaagatg agatcaaacc gatgctcaag attttgaaac ctgcaagggt 840 gttggtggca tttgaacaag ccaaatggca ggaggaggct aacaatgcct taactaagaa 900 gactcgatca ctgcaacgaa gcaatcctcc atttcacagt ggaagaatac caggcaatgc 960 tccctccaaa tattttggtc catccaggac taaaggagtg aaaccatttt cagatagtct 1020 ctatgaacaa cgaaagaaat tgggacagtg ttttaaatgt ggggataaat acatgcctgg 1080 gcatagatgc aattccaaag gtttacacat gatagaaggc gtggagggag gagaggatga 1140 agaaatagga gagttcgaag acaatatgca ggggactgat cagatagacg aatatggtct 1200 gtcattaaac gcattagcag acaacgacac ttacaatact atcaggatta aaggaaactg 1260 tcaagggcag aaccttatca tcctcatcga tagtgggagc acacatagtt ttattaatga 1320 aagcacaatt aaggcgttga atgctaccac cagtaaaact acattgttgg cagttacggt 1380 agccaatgga aatgtcatgc tatgtgaaaa acattgccct gcattcactt ggtttatgca 1440 caactatgaa ttcaagtcaa acttgagggt gctggaattg ggtaggcatg atctggtgct 1500 gggagtcgac tggttgaaga agtattctcc agtgttattt gatttcatca aattgcggct 1560 gtcatttaaa aaagatggca ggatgattga gctaaaaggc atttcacaag gggcggaatt 1620 acagatgata accaccctga aggaacatag aagcttcaag aatgtgatcg gggggctagt 1680 aggccagttc tttgcaatgg acagtgggaa ggaaaataaa ccaactgaaa caagggctga 1740 gattaaatct ttgttggtgg agtttgctgg aatctttgag gagccacgaa ccttacctcc 1800 agcaaggcga ttcgatcaca agatacctct gaaaccaggg tcacagccta ttaacatcag 1860 gccttataaa agctcattca ttcaaaaagg agaaatagag aagctggtga aggaaatgct 1920 atctaatggt gtgattcagc acaacgttag tccttttgca tctcctgtgc tgttggttaa 1980 aaaaaaagac aatacatgga gattctgtat tgattacagg caactcaatg aacaaaccat 2040 aaaaaacaag tttctcattc ctcttattga tgatcttctg gacgaactgc atggctcaag 2100 cttcttctca aaactggacc tgaggtcagg ttaccatcaa gttaggatgc acgaggagga 2160 cattgagaag acagcattca ggacgcatca tgggcattat gagttcaggg tcatgccatt 2220 cggccttacc aatgcgccgg ccaccttcca ggcgttaatg aacagcatac tggagcctta 2280 cctgcgcaag tttgtactgg ttttctttga tgacatactc atttacagcc caacatttga 2340 gagacacctt gtccatctcc ggcaggttct ggagacctta agtaagaacc agctgctggc 2400 caagagatcc aaatgtgctt ttggggaaca acaagtggaa tacctggggc atgtaatttc 2460 tataacagga gtatcaaccg acaggaagaa aactgaagca gtgaacaatt ggcctgttcc 2520 acaagctttg aaagaattaa gggggttctt gggattggtt gggtactata ggaagttcat 2580 ccgacatttt ggagttatca gcaaacccct cacagaattg ctgaagaaga acaattttgg 2640 gtggaatgat caatctcaac aagctttcga tcatttgaag aaagccttgt gtgaagcacc 2700 agtcttagct ctacctgatt tctctaagac cttcttcttg gagaccgatg cttgtgattc 2760 aggattgggg gcagtcttaa gccaagaagg tcgtcctata gcttatttca gcaaagcctt 2820 aagtccaaaa catatgggac tatccatcta cgaaaaagaa tacttggcca tcctcatggc 2880 tgtggagaaa tggagacatt acttagagca agagcaattt gtcatacaaa cggatcatga 2940 gagcttgaag tacatgttgg atcagaaaat tcatacgtcc attcagaaga aaggtctgac 3000 aaagctcctg gggttacgtt ataccatact ataccgaaag ggcagggaga acattgctgc 3060 cgatgcatta tccaggaagc acaacaatag ttcgttggtc acagttgtgg gagagttaaa 3120 agcagtagcc agtatactac cagcttggta tgaggaggtt catgcaacct atgacaaaga 3180 tcttaagttg cagaccatta tcatgggcaa aatgatgggg gacacaggaa atagtgatta 3240 cacttatgca gaaggggtgt tgaggtacaa aggcaggata gttgtgggac aagaggggga 3300 actcagagct aaactggtta aatccgtgca tgattcttat gtgggagggc atgctggtat 3360 acaaaacaca ttcaggaggt tgaaggccaa cttttattgg tcaggaatga agactatggt 3420 gaaaagaata gtggaagaat gcgatgtttg taaacaagct aaggcagata gagtaactta 3480 tccaggctta ttacaaccat taccagttcc taatggaacg tgggaagcca tcaccatgga 3540 ctttatagaa gggctgccaa gttcggatgg aaagactgct attatggtag tcgtagacag 3600 gtttactaaa tatggacact tcatcgcgct cagtcatcct tacacagcac aagatattgc 3660 gcagctattc cttgatcatg tctacaagtt tcatggacta ccggctgtta ttatcaccga 3720 cagggacaag atctttacca gcatcttttg gaaggaattg ttcaaaaaat tgggagttca 3780 ggtgttgatg agcacgactt accacccaca gacggatggg caaaccgaga gggtgaatca 3840 gtgtttggaa acgtatctgc gttgcatgac catgcatcat ccaaaacgtt ggtttcattg 3900 gttatcgctg gcacaatggt ggtataattc cagccatcat tcaacattag gcatgagtcc 3960 ctttcaggcc ctctatggct atcttcctcc gcagagggag tggattgctc aggaatcgac 4020 accagtggct gcagtggaag atgtgctaca acgaagggcc aacatggacc ttgcattgaa 4080 gaagcagctc gaagcagcaa ggcataagat gaagcaagtg gctgataagc acaggtcaga 4140 gagggagttt tcgattggag acttggtttt tcttaaactt caaccttatc gacaaaatag 4200 tgtggcatta agaaggaacc tcaaactcaa cccccgatat tatggaccct atccaattat 4260 tcgcagaatc gggatggtgg cttatgagtt aaggctgcca gaaggaagtt tggtgcaccc 4320 agtgttccat gtctccttac tcaagaagaa gattggtgat acaacaatca cttcttctaa 4380 attgccaagg actgacaagg agggacggat gcagattgtg ccaatagcca tattagatag 4440 aaagataatg aagaaggaca atcgggcagt aacagcaggg ttaattcaat ggtccaatct 4500 ttttcccgaa gatgctacct gggaagacct ggaggaatta ctaaaacaat ttccagaaag 4560 catcgcaaca ctcttgacaa gcactactta gcattcatgg gacaagaatg cattcaagag 4620 gggagtat 4628 // ID Copia3-VV_LTR repbase; DNA; EDCOT; 200 BP. XX AC AM448401; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 03-SEP-2008 (Rel. 13.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; LG_I; KW Copia3-VV_I; Copia3-VV_LTR. XX NM Copia3-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-200 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-200 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 680-680 (2007). XX RN [3] RP 1-200 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1/copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9, (2008). XX DR [3] (Consensus) XX CC LTR = 200 bp CC LTR are 100 % similar to each other. CC Direct flanking repeats = gaagt. XX SQ Sequence 200 BP; 67 A; 16 C; 37 G; 80 T; 0 other; tgttgaaata atgccaaagt taggacttta atttaggaat aaaaaaggag agatcattta 60 ggatatttcc ttatgattta gtttcctaat tttaggagag aattaagcta gattgatttt 120 ttcttattca gttatttgtg tatatatatg tgtatggtgt gtaccgatta atattaataa 180 aggagttcag aaattcttca 200 // ID Copia-33-I_VV repbase; DNA; EDCOT; 3657 BP. XX AC CU469250; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-33_VV, LTR retrotransposon Ty1-copia like, internal portion DE from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Gentil-B05; KW Copia-33-LTR_VV; Copia-33-I_VV; Copia-33_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-3657 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL; CU469250; Positions 207844 211500. XX CC Full size = 4251 bp CC LTR = 297 bp CC LTR are 99.7 % similar to each other. CC Direct flanking repeats = gttgt. XX FH Key Location/Qualifiers FT CDS 147..2285 FT /product="Copia-33_VV_1p" FT /note="incomplete putative gagpol polyprotein." FT /translation="ISHNFKATTLGMTRKTMRNRGFEPWTFRSCLGYQHFV FT INDNNRDQRKKDSKKTSIATVAEIKTEANVAEKASTLVAAIDHGGKFLNTF FT TPVINSAWIIDSGATDHMTFDSRQVSPLRPSSQKIVSTANGNTTPIIGEGS FT LTLTDTLNLDSVLVVPSLDYNLLSVSQITAALSCIVIFLPEFCVIKDIQTK FT QTIGCGIKRGKLYYLDLQSKDSNKLQQALMADGSEGEKKKSEIWLWHRRLG FT HASFGYLKKLFPSLFAKSDISGFCCDICELVKSHRVSFPLILNKSPFPFMV FT IYSDVWGPSKVPTLSDSRWFVTFIDDCTRMTWLCLMKTKDEVKLLFQKFHK FT MIETQYNAKVRVLRSDNGGEYQSSDLQKYLEGHGIIHQTTCSNTPQQNGVA FT ERKNRHLLEVVRASLIAAKTPISYWGEAITSAAYLINRVPSSSINFQTTLQ FT ALTNVVVAPTIPNLPPRVFGCVAFVHLHKHQRTKLTSHALQCVFVGYALHK FT KGYRCYHPPTRQMYITMDVVFHEDSMYFSSESELQGEYHKEIQTLDYDYHI FT SKENESGQSELVNQETGELDMSGQQFGSEDVFTEIPNQSSSVEGVLNLEPD FT PFMKRLPHRHNRGIPKPTYEPELSTKVKYPMSNYVSNHRLSESNKSFVNQL FT STVAIPNSVQEALANPRWKAAMNEEMKSLQKNETWELVECPPGKKSVGCRW FT IYTVKYKADGSIE" XX SQ Sequence 3657 BP; 1131 A; 646 C; 781 G; 1099 T; 0 other; tggtatcaga gccatggaac tgaaatcctg gatattttgt cgctatggta gttcgacagt 60 gatcatccat cctaagacaa gccctaatat tgataagtca accttcaaat gcactcactg 120 caataagatt gatcccacca atctgaatat cccacaattt caaagcaacg actcttggta 180 tgaccaggaa aacaatgagg aaccgagggt ttgaaccatg gacctttaga tcatgtttag 240 gctatcaaca ctttgttatt aatgataata atcgtgatca acggaagaag gattccaaga 300 aaacttcgat tgcaactgtt gccgaaataa aaacagaggc taatgttgct gagaaagcct 360 ctacattggt agccgctata gatcatggtg gtaagttttt aaatactttt acacctgtta 420 ttaatagtgc atggataatt gattctggtg ctacagatca tatgactttt gattctagac 480 aggtttcacc ccttagacct tcctcacaaa aaattgtttc cacagccaat ggtaacacaa 540 ccccaatcat tggggaagga tccttaactc ttactgatac tttgaatttg gattctgttt 600 tagttgttcc atctttagat tacaatcttt tgtcagtttc tcaaatcacc gcagccttat 660 cttgtattgt catttttttg cctgaatttt gtgtgattaa ggacatccaa acaaaacaga 720 cgattggttg tggtattaag cggggaaaac tctattactt ggacttgcag tcaaaggatt 780 caaataagtt gcaacaagcc ttgatggcag atggatctga gggggagaag aaaaagtctg 840 aaatttggtt gtggcatcga cgtctgggac atgcttcctt tggttattta aaaaaattgt 900 ttcctagttt gtttgcaaaa agtgatattt ctggtttctg ttgtgatatt tgtgaattgg 960 ttaaaagcca tcgtgtttcg tttccgttaa ttttgaacaa aagtccattt ccttttatgg 1020 ttatatattc tgatgtttgg ggcccatcca aagtcccaac tttgagtgac tcacgttggt 1080 ttgttacttt tattgatgat tgtaccagaa tgacatggtt atgcttgatg aagaccaaag 1140 atgaagtgaa attgttgttt caaaaatttc ataaaatgat tgaaactcag tacaatgcaa 1200 aggttcgggt tctgcgtagt gataatggtg gagaatatca aagttctgat cttcaaaagt 1260 atttggaagg acatggcatc attcatcaga ctacttgttc caatacaccc caacaaaatg 1320 gagtcgctga acggaaaaat cggcacttgt tagaggttgt tcgtgcttcc ttgatagcag 1380 cgaaaacgcc gatatcttat tggggagaag caatcacatc tgccgcatac ttgatcaatc 1440 gggtaccttc cagctcaatt aacttccaaa caaccctcca agctcttact aatgtcgtag 1500 ttgccccaac tatcccaaat ctacctcctc gtgtttttgg ttgtgtggca tttgtgcatc 1560 tacacaaaca ccaacgcacc aagttaactt cccatgcatt gcaatgtgtg tttgttggat 1620 atgcattgca caaaaaggga tatcgatgtt accatcctcc aactcgacaa atgtatatta 1680 caatggatgt ggtgtttcat gaagattcga tgtatttttc atctgagtct gaacttcagg 1740 gggagtacca taaggaaatt cagactctcg attatgatta tcatatctct aaggagaatg 1800 aatctggaca atctgaacta gtgaaccaag aaacgggtga gttggatatg agtggtcaac 1860 aatttgggtc cgaagatgtc ttcactgaaa taccaaacca atcgtcgtct gttgaaggtg 1920 ttcttaattt ggaacctgat ccattcatga aacggttacc acaccgtcat aatagaggta 1980 ttcctaaacc cacatatgaa cctgaattgt ctaccaaagt caaatatcct atgagcaact 2040 atgtctctaa ccatcgtttg tctgaatcaa ataagtcatt tgtaaatcaa ttatctactg 2100 tagctattcc taacagtgtg caggaagcct tagctaatcc aaggtggaaa gcagccatga 2160 atgaagagat gaaatcattg cagaagaatg aaacatggga actcgtagaa tgtccaccag 2220 gaaagaagtc agttgggtgt cgttggatct atactgtgaa gtacaaggca gatggtagta 2280 ttgaatgatt taaagcaaga ctggtagtaa aagggtacac tcaaacttat ggaattgact 2340 acacagaaac atttgtacct gtagctaaga tcaacacagt tcgagtatta ttgtctttag 2400 ctgcaaacct agattggcca ttacaacagt tcgatgtgaa aaatgccttt ctgcatggcg 2460 agttatctga agaaatatat atggatcttc caccaggatg catggtgtca gaaaagcaat 2520 gtcagaaggt gtgcaaattg aagaagtcat tgtatgggtt gaagcaatcc ccgagagcat 2580 ggtttggaag gttcacaaag tcaatgagag tttttggcta tcgtcaaagt aattcagatc 2640 atactttgtt cctgaaaaag caacatggta agattaccgc actcatcgta tatgtggatg 2700 atatggtagt tacaggaaat gatcctgaag aaagaaaagc tttgcaaaat tatctatcta 2760 gagaattcga aatgaaagat ctaggtcctc tgaaatactt tcttgggatt gaagtttctc 2820 gatcaagtga aggaattttt atgtctcaca gaaagtatgc cttagatctt ttacaggaga 2880 ctggaatgtc gggatgtcaa cctgttaata caccaataga agaaggtctg aaattgtgtg 2940 ttgagcataa tcaagtatca accgataaga gaagatacca aagacttgtg gggagattaa 3000 tgtacttagc tcatacaaga ccagatcttg cttatgcatt gagtgtagtg agtcaataca 3060 tgcataatcc tggagagcaa catatgaatg cagttatgcg tattttgagg tatttgaaga 3120 atgctcctgg gaagggaatt ttgttcgcta aaaatgttaa tcatcagagt atagaagtat 3180 atactgatgc tgattgggcc ggtgcattgg atgataggcg atctacatct ggttacttta 3240 cctttgtagg tggtaatctt gtgacatgga aaagtaagaa gcagaatgtc gtcgctcgtt 3300 caagtgcaga agcagaattt agaggtatgg ctctaggact ttgtgaggca ttatggctaa 3360 gacttctctt acaggattta ggttacctat ctaggcaacc aatccgattg ttttgtgaca 3420 ataaagccgc atgtgacatt gctcataatc cagtacaaca tgatcgtaca aagcatgtcg 3480 aggtggatag attcttcatt aaggaaaagt tggatgataa gattgtggaa ttgcctaaga 3540 ttcgatcaga acatcaattg gccgatatcc tcaccaaagc tgtctcaagt caagtgttct 3600 caaaattttt agacaagttg ggcatgtgtg acatctatgc accaacttga gggggag 3657 // ID Copia4-PTR_I repbase; DNA; EDCOT; 5426 BP. XX AC LG_XI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia4-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-5426 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-5426 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 256-256 (2007). XX DR Genome; LG_XI; Positions 7936702 7942127. XX CC Positions [2477-2995] - Integrase core CC 'ATCTA' target site duplication CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS 1160..4276 FT /product="Copia4-PTR_I_1p" FT /translation="MDIDYAIRKDEPPALTNTSTAADITLHERWERSNRLS FT MMFIKTRISAGIHGSVDQHEKVQDLLKAIDEQFITSDKALASTLIMKFSSL FT RLTSVRGVREHIMQMRDLVAQLKKLEVEMSESFLVHYILNTLPHQYGPFKI FT SYNTHKENWSINELMTMCVQEEGRLVMEQGESAMLAIRGKGKSQAYQKGKG FT KIPPQASIKKDSKCFFCKKKGHMKKECAKFQKWLEDKGNPTSFVCYESNMV FT NVNINTWWIDSGSTIHISNSMQGLQNLRKPVGSEQSILSGNKMGSHVEAIG FT TCYLILSTGFILKLEKTFYVPSFSRNLISVLRLLPFEYSFNFSESSFSLFY FT KSDCVGNGILSDGLFCINLQNHITYDSMHVHTGIKKCVIDENSSKLWHQRL FT GHISINRIKRLVNEGVLNTLDFTDFETCVDCIKGKQTNKSKKGATRSSDIL FT EIIHTDICSPDLDSHSHKYFISFIDDYSRYMYLCMLYNKNEALDAFKNFKA FT EVEKQCGKQIKIVRSDRGGEYYGRYTEDGQALGPFAKFLQEHGIVAQYTMP FT GSPDQNGVAERRNRTLLDMVRSMLSSSKLPKSLWVEALKTTVYILNRVPTK FT DVPKTPFELLKGWKPSLRHMRVWGCPSEVRIYNPQEKKLDPRTISGYFIGY FT AERSKGYRFYCPYHITRIVESRNAKFLENDLISEIDQTRNIVSENDHSESQ FT PSSSSDKLNIVYNTPQVQTDVEQPIIEVPQIADDILIDQVVQELPRTFEQR FT VEPHTSQEYDGTTLRRSIRPKRSEIPNDYVVYLQEYDYNVGAENDPESFSQ FT VMSCKETELWYNAMKEEMNSMKSNQVWDLVELPNGVKAIGCKWVFKTKKDS FT LGNIERYKARLIAKGFTQKEGVDYTETFSPVSKKDSLRIILALVAHFDLEL FT QQMDVKTTFLNGDLEEEVYMKQPEGFLSSDGEQLVCKLKKSIYGLKQASRQ FT WYLKFHNVISSFGFVENVMDQCIYQKVSGSKICFLVLYVDDILLATNDKGL FT LHEVKQFLSKTFDMKDMGEAFYVIGIKIHKDRF" XX SQ Sequence 5426 BP; 1848 A; 792 C; 1036 G; 1750 T; 0 other; tttggtatca gagcatggtt ttatctctgc cttggtttat aaagttgctc tatttatctt 60 tatttatggt cgaaagtttg ataaaattta aataagaaaa tcgaaatttg caacccagta 120 tggaggttga ggacgaccca ataaataaat aaataataat gacacgcagc tttgtttttt 180 taacaaacaa tgacatttaa tttccacttt ataaatagtt gggaattgtg ttaataattg 240 ttataatata ctgttgtgat tataattttt atttgattta attatatgcg atttagatta 300 ttattgtgca aatttaatta ttatgctcgt atttagtttg catgaattga ttatttttgc 360 tctatattaa tacatgcaat ttttatgagt atatatatag ttaaaagcgt gaaattaaat 420 gttatgcata atattatagt tttgattatg caatatttat gcttatatta tgataatatt 480 ttgtgcataa taataacatg ttagtattag ttaaaattat gtgcttcata atattaagtt 540 agtcttatgc gatttaatgt ctaatgatcc atataatttt aattaattag agaatagcca 600 caacatcttt aattgattaa aattatatat tatgaattat taggatcaca taaagaatat 660 tagacattaa ttgtaattat ttatacttaa tataataaat tttatcccac aggaattttt 720 atttatttat attattaatt aggataaaat atcaagttat tcataactta cccacaggaa 780 ttatgaatta aataaattac ttgatagttt tatcataaaa gtttaatttg agataaaata 840 tatatcaaat tataatcata atatatcctt tagaattatg aattaagtaa ataatttgat 900 cataaagaat aattgaatct acttgaatta agaatttagc ccacaggcat ttttatgtca 960 ttagatttga tatttaagca tgatttacat tggtaaagca tgaatattta ttgcctcaat 1020 tttaacttaa gcatgtaatc tataattgta tgcagtttta caacctgcaa atatctctga 1080 tgttcgttat gatatccctg aacttaaagg agataactat aagatctgga aggaaagagt 1140 tcttcttcat ttagggtgga tggacataga ctatgctatt aggaaagatg aaccaccagc 1200 actcaccaat accagcactg cagcggacat cacgcttcat gagcgatggg agcgatctaa 1260 tcgcctcagc atgatgttca ttaagactag aatttctgct ggtattcatg gttctgtcga 1320 tcagcatgaa aaggtccaag acttgctaaa agctattgat gaacaattta tcacttcaga 1380 taaggcgcta gcaagcacct taatcatgaa gttctcatcc ctaaggctca ccagtgtgag 1440 aggtgtgcgc gagcacatca tgcaaatgag ggaccttgtg gctcaattga agaaactcga 1500 ggttgaaatg tcggagtcct tcttggtgca ctatatcttg aacacccttc cgcatcaata 1560 tggacccttc aaaatctcat acaacacaca taaggaaaat tggtcaatta atgaactcat 1620 gaccatgtgt gttcaagaag aagggagact ggtgatggaa cagggtgaaa gtgcaatgtt 1680 ggcaatacgt gggaagggaa aatctcaagc ctatcaaaag gggaaaggta aaatacctcc 1740 ccaagctagt atcaagaaag attccaagtg tttcttctgt aaaaagaagg gacacatgaa 1800 gaaggaatgc gccaaatttc aaaaatggct tgaggacaaa ggtaatccaa cttcatttgt 1860 ttgttatgaa tctaatatgg ttaatgtcaa tattaacaca tggtggattg attctggatc 1920 aacaatccac atttcaaatt ccatgcaggg tttgcaaaac ctaaggaagc cagtgggaag 1980 tgagcaaagc atcttatcag gaaacaagat gggctcacat gtggaagcta taggaacttg 2040 ctatttaatt ttaagtactg gttttatttt aaagttagaa aagacctttt atgttccaag 2100 tttctctaga aacttgattt cagttttaag acttttacct tttgaatatt cctttaattt 2160 ttcagaatca tcattcagtt tattttataa atctgattgt gttgggaatg gtattttgtc 2220 tgatggtctt ttctgcatta atttacaaaa tcatatcact tatgattcaa tgcatgttca 2280 cactggtatt aaaaaatgtg ttattgatga aaattcctct aaattatggc accaaagatt 2340 aggtcatatc tcaataaata gaattaaaag attagtaaat gaaggagtac ttaatacttt 2400 agattttact gattttgaga cttgtgtgga ctgcataaaa ggaaaacaga ccaacaagtc 2460 aaagaaaggt gccactagga gttcagacat attagaaatc atacatactg atatatgtag 2520 tccagacttg gactcacata gtcataaata cttcatttct tttatagatg attactctcg 2580 atatatgtat ctctgtatgc tttataataa gaacgaagca ttagatgcct ttaaaaattt 2640 taaggctgaa gtagagaaac aatgcggtaa gcaaattaag atcgtgaggt cagatagagg 2700 tggagaatat tatggtagat acacagagga tggacaagca cttgggccat ttgcaaagtt 2760 tcttcaagaa catgggattg ttgcccaata caccatgcct ggttcaccag atcaaaatgg 2820 tgtggcagaa agaagaaacc gaacattatt ggacatggtg cggagtatgc tcagcagctc 2880 caaacttcct aaatcattat gggttgaagc acttaagacg acagtgtata tattaaaccg 2940 agttccaacc aaggatgttc ccaaaacacc ttttgaatta ctgaaaggtt ggaaaccgag 3000 tttgcgacat atgcgcgttt ggggatgtcc gtctgaagtg agaatttata atccacaaga 3060 aaagaaactg gacccaagga ccattagtgg gtatttcatt ggatatgctg aaaggtctaa 3120 gggttacaga ttttattgtc catatcacat tactaggatt gtggaatcaa gaaatgcaaa 3180 gtttcttgaa aatgacttga ttagtgagat cgatcaaacc agaaacattg tttctgagaa 3240 tgatcattca gaatctcaac cttccagttc aagtgataaa ttgaatattg tttacaacac 3300 ccctcaagta caaactgatg ttgaacaacc aatcattgaa gttccacaaa ttgctgacga 3360 tattctaata gatcaagtag ttcaagagtt gccaagaact tttgaacaac gagttgaacc 3420 acatacttct caggaatatg atggtacaac attaagaaga tctattagac caaagagatc 3480 agaaattcct aatgattatg ttgtgtattt gcaagaatat gactataacg ttggagccga 3540 aaatgatcct gaatcctttt cacaagtcat gagttgcaaa gaaacagaac tatggtacaa 3600 tgccatgaag gaagagatga attctatgaa gagtaaccaa gtctgggatc ttgttgagtt 3660 gcctaatggt gtaaaagcca ttggatgtaa atgggtcttt aaaacaaaga aagactcatt 3720 gggcaatatt gagagataca aggcaagact cattgctaaa ggattcactc agaaagaagg 3780 agttgattac acggagactt tctctcctgt atctaagaaa gattccttgc gtattatttt 3840 agcattagta gcccattttg acttagagtt gcaacaaatg gatgtgaaaa caacatttct 3900 caatggagat ctagaggagg aggtttacat gaagcaacct gaaggattcc tctctagtga 3960 tggtgagcaa ttggtttgca agctcaagaa atctatatac ggtttaaaac aagcatcccg 4020 ccaatggtat ttgaaattcc ataatgtaat ttcgtcattc ggttttgtag aaaacgttat 4080 ggatcaatgt atataccaga aggtcagtgg gagtaaaatt tgttttcttg ttttatatgt 4140 ggatgacatt ttgctagcaa ccaatgataa gggtttgcta catgaggtga aacaattcct 4200 ctctaaaact tttgatatga aggatatggg tgaggcattt tatgttattg gcattaaaat 4260 ccataaagac agattttgag gtatcttagg tttgtctcag gaaacctata ttaataaagt 4320 tttagagaga tttcggatga aggattgttc tccaagtgta gctcctatta tgaagggtga 4380 tagatttagt ttgaatcaat gtccgaagaa cgatcttgaa aaggaacaaa tgaagaacat 4440 tcaatatgct tctgctgtcg gaagccttat gtatgctcaa gtatgtacaa gacctgacat 4500 tgcatttgtt gtgggaatgt taggacgata tcagagtaat ccaggtttag accactggag 4560 agctgcaaag aaagtgatga ggtaccttca aggaaccaaa gactatatgc ttatgtatag 4620 acgaacaaat aatctggaag taattggcta ctcggattct gactttgcag gctgtattga 4680 ttcacgcaaa tcaacatcag gatatatatt tttaatggct ggtggagctg tatcatggag 4740 gagtgctaag cagaccttga ctgcaacttc cactatggaa gccgagtttg tctcttgttt 4800 tgaggctact tcacatggta tatggcttaa gagtttcatt tctgggctta gaattatgga 4860 ttctatccat aggccattga gaatgttttg cgataattta gctgctgttt ttatggctaa 4920 gaacaacaaa agtggaagtc gaagtaaaca catcgacatt aagtatttag ccataagaga 4980 acgtattaaa gaaaagaaag tggtcattga gcacatcagc actgaactaa tgatcgctga 5040 tcctttgact aagggcatgc caccgttgaa attcaaggat catatagtgg atatgggact 5100 ttgttccatt atgtaatttt tcattgtttg aacaatgtta ttttcttaac tattttgata 5160 ttcttctcat attgatgtgc accttaattt gattttgaga aaaattcatt tgtgttggac 5220 caagaataaa catagggttt attcattaag aacttgttgc tacataaatt ataatgttta 5280 aagaaataaa tacatagtaa tatatggaag ataatactca tcaattagag gacccatcgc 5340 catgattcat gtatttatta ctaaaacata ttgtctatgg gtttaagatg aaatattaga 5400 ttacaaatgt ggaccaagtg ggagaa 5426 // ID Copia-3_TC-I repbase; DNA; EDCOT; 4754 BP. XX AC CACC01000721; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-3_TC_; KW Copia-3_TC-LTR; Copia-3_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-4754 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01000721; Positions 1618 6371. XX CC Positions [2037-2528] - Integrase core CC LTRs are 91% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS 1452..3215 FT /product="Copia-3_TC-I_1p" FT /translation="MDSGASDHIAYSLNKFISARPVTNSFVQLPNNKRAIV FT THVGVVKLTSLLTLKNVFCVPSFRFNLVSVGQLTRTKNTSVLFIDKYCVVQ FT DTHSWTVIGVARTFSGLYAMEPKKDEQELSNYSFDKLVKLPFNLSVNACST FT GHKAFDLCHFRLGHAPCEKLNIIHQQRANVKCSNQLLCEIRPLAKQRKLPF FT PVHVKNTKIPFELMHVDICGPYENPTISGQRYFLIVVDDHTRFTWIFIMKA FT KSEVSIIIPSFNAFVQKQFNSAIKSIGTDNAKELGLLYFFENTGIVHQLSC FT VEAHQQNGIVERKHQHILVVARGLLHQSNVPIYFWGDAVLTAVHIINRLPS FT KVLHNKTPYELLHHKLPSYDHLRVFGCLCFMFTLTQNRKKLDKRATKCIFL FT GYPNNMKGYKVYDLSANNVLKSRNVIFHEQTFPFRIKQHDQQPLTFHQTPA FT VHDIYLDHFDHNPAVIPSQNHEQVEFDLSEPMSPQLNHTNSNTNNVSPDSS FT PSSSLPIADSTNQPELATNENTFCACKKKYNNQTCSKIFGSILYRITTSNQ FT SCYLLSNCQIPVTSKTFSFTQVLYHFIVTYTRTCFLSSGCE" XX SQ Sequence 4754 BP; 1580 A; 905 C; 869 G; 1400 T; 0 other; tggtatcaga gctgggcaca aaattcctgc aaatagtact cttcagctag tgatcggaca 60 gcatctatag cagagatctc ttgtcatatt atcatcagca ttcctctctt agtaaggttt 120 ctgataatca actttactca agctcatttg ttcttttgat tttcattgct tctcaacttg 180 atctgtcaat ctacaaaaca ctatgtctga atctggatcg aatgagtcaa ggtctcaaac 240 catggtcaaa cacaaatctc accaacaaga gatccccaat cgccatattt tattcatcat 300 acagaccatc caggttctat agtgattaac cccaagctga ccacaagcaa ctatgttact 360 tggagtaggt ctttccagtt agctctttct gttagaaaca aaatgggctt catcaatgga 420 accatagtca aaccagacat ttcagatcct ttgctctccc cttggatccg tgtaacaacc 480 taatagtggc ttagctattg gattcaattt caccacctat agcatcaaca gttttctaca 540 tggacactac cttagaaatc taggctacac tgaaacaaat ctttgcacag cctaatgaca 600 ctaggatatg caatctgtaa tacactcttg gcaacataac acaaggttca cgaccagtgg 660 atacatattt cattgaacta aagggggtat gggaggagtt aagaagcttc agacccttac 720 cacattgtga gtgtgaaaat tgcaatccaa actgcttcaa gaagtattct gaacagcata 780 aaaaagacat ggttttcagg tttttgaatg gcttgaacaa atccttttct gttgtgagat 840 cccaaataat tctcatggat cctattccaa ctcttgacaa agtatacaat ctagttctga 900 gggaggaagc acagagaagc atgctttttc gaacacaacc aactcttgaa acagctgcaa 960 tgtacactgc agcagaagga aagaagaaag ttaagaagta catagtttgt aatcattgtg 1020 gaaagaaggg acatgtaaag gagaagtgct acaggctgat tggattttca gaggacttca 1080 aattcaccaa agggaagaac aatgtcagaa aaggaaaagc agctgtaaac aatgtcttta 1140 cattgactga ctcatcaact ggagagagtc aatttgacaa gtaagaagag tctggaggga 1200 attcatccat gtctcaaatg tccatcatca agtagcaagt aaggagacta atggagctct 1260 taagtgagaa tggtttaaca gattctgatg gtaagaactt ttcatcaaac actttgcaga 1320 gaaacccttc cttgatcaac tcagcctttg caggtattat ttcaggccat ttatgtttta 1380 acacaatcaa taacatgcca tttaatttta gaaatgttaa tgttgacatg ataaaatcaa 1440 atttctagat tatggactca ggagcatcag atcatattgc ttattctcta aacaagttta 1500 tttcagctag gcctgttact aatagttttg ttcagctgcc taataacaaa agagcaattg 1560 taacacatgt aggagttgtc aaattaacat cactgttgac tctaaaaaat gtcttttgtg 1620 ttccaagttt tagattcaat ctagtctcag taggacaact cactagaaca aaaaatacct 1680 ctgttctctt tattgacaaa tattgtgtcg ttcaggacac tcattcatgg acagtgattg 1740 gggtagctag gaccttttca ggattgtatg ccatggaacc taagaaagat gagcaagaat 1800 tgtcaaatta ttcctttgat aaacttgtca agttgccttt caatttgtca gttaatgcct 1860 gtagtacagg acataaagct tttgatttat gtcatttcag acttggtcat gctccttgtg 1920 aaaaattgaa tattatacat caacaacgtg caaatgttaa gtgttcaaat caattacttt 1980 gtgaaattcg ccctttggca aaacaaagaa agttgccttt tccagtacac gttaaaaaca 2040 caaaaattcc ttttgaactg atgcatgttg acatttgcgg accttatgaa aacccaacca 2100 tatctggtca acgctatttt ttaattgtag ttgatgatca tacaaggttt acctggattt 2160 tcataatgaa agctaaatca gaagtttcta taatcattcc ttctttcaat gcttttgttc 2220 aaaaacagtt caattctgcc attaaaagta taggaacaga taatgcaaaa gaactaggat 2280 tactttattt ttttgaaaat actggtatag ttcaccagtt gtcatgtgtt gaagctcatc 2340 aacaaaatgg aattgttgag aggaagcatc aacacatttt agtagttgca agaggcctac 2400 tgcatcaatc aaatgtacct atatattttt ggggagatgc tgttttgaca gcagttcaca 2460 tcatcaatag gctgccaagt aaagttcttc acaataaaac accatatgag ctcctccatc 2520 acaaattgcc ttcgtatgat catttgagag tatttggatg tttgtgcttt atgttcacat 2580 taacacaaaa taggaagaaa ctagataaaa gggccactaa atgcatattc ctagggtatc 2640 caaataacat gaagggttat aaggtttatg atcttagtgc taacaacgtc ctaaaatcaa 2700 gaaatgtgat ttttcacgaa caaacatttc catttcgaat taaacagcat gatcagcagc 2760 cattaacttt tcatcaaaca cctgctgtgc atgacatata tcttgatcat tttgaccata 2820 accctgcagt aattccatct caaaaccatg aacaagttga atttgaccta tctgaaccta 2880 tgtcacccca attgaaccat accaattcaa ataccaataa tgtctcacct gattcatcac 2940 cttcaagcag tctgcccatt gcagacagca caaatcagcc tgaactagct actaatgaaa 3000 acactttctg tgcctgcaag aaaaagtaca acaatcagac atgctccaaa atatttggaa 3060 gcatactata cagaattacc accagcaacc aatcatgtta cctcctatcc aattgccaaa 3120 ttcctgtcac ctcaaaaact ttctccttca cacaagtcct ttaccacttc attgtcacat 3180 atacaagaac ctgtttctta tcatcaggct gtgaatgatt cccactagag agaggccacg 3240 gctcttgaat tgcatgcttt ggaggataat gatacatgga ctgttgtacc tctaccttca 3300 aattgtcata gcattggttg caggtgggta tataaggtga aactgaaagc aaatggtgaa 3360 gtggaaagat tcaaagcacg cctggttgct gaaggataca atcaggtagc aggatttgat 3420 taccaggaaa cattcagttc tgtagcaaaa cagacaacag tgagagtttt tctttgcact 3480 tgcagcaaca tgtaattggc attagtctta gctggatata aataatgcct ttctaaatgg 3540 agatttagaa gaagaagtat atatggattt acctgagggg tattctgtca agggggagta 3600 cactgcaaag tcaagactgg tttgcaaatt acataaatct ctgtatggtt tgaagcaggc 3660 agcaaggcaa tggaatgcaa aattctctgc agccattttg aagtatggtt ttcaatagtc 3720 agactcagat cattcactat tcactatgaa aacaagggat ggaaaattta cagtattact 3780 tgtttatgta gatgatattc ttattggcag cacatcagtt caggaatcaa acaaagtcaa 3840 ggattttctg aactctcttt ttaagcttaa agacttagga acaataaagt attttttggg 3900 gttagaagtt gctaagtccc ctgaaggtat atctatatgc caaaggaagt atacccttga 3960 tcttctggaa gagaatggac ttcttggagc taaaccagta agtacaccaa ttgattataa 4020 tcacaaactc tccagagtca aggatgagga agtattatca gaccctacaa gctacaggca 4080 aatgattgga aagctgatat acttgacttt cagcagacca gatatctgtt atgctgtata 4140 ggttctatca caatttatgg acaaaccatg aaaagaacac ctagttgcaa ctcatagggt 4200 tttgaagttt ttgaaagcat caccaaagca gggaatactg atgaagtcaa aatctgctct 4260 aaaaatatca ggttatgcgg atagtcattg ggaaggatgt cctgacacca ggaggtcagt 4320 tactggattt tgcgtcttta ttggggactc acttgtaaga tggaaatcaa agaaacagtc 4380 agtagttgca aggagttcag ctaaagcaga gtacagatca atggcttcaa cttgctgtgt 4440 aatgatatgg atcaaaagtc ttttggaaga ttttggaatc aaacaagatg aagcaatgga 4500 tctctattca gatagtcagt ctgctataca catcagcaaa aatccagtgt ttcatgaaag 4560 gaccaaacac atagaaatag attgccattt tattagagag aaggtcctca ctggcttgat 4620 caaaccaaag cacatttcaa ccaacataca gattgcagat attcttacta aagcattaca 4680 gccgaatcaa ttctataaac tcttgagcaa gatgaacgtt cacgatgttc accattcctc 4740 ttgaggggga gtat 4754 // ID HARB-N2_Mad repbase; DNA; EDCOT; 420 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW HARB-N2_Mad. XX NM HARB-N2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-420 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1501-1501 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >94% identical to the consensus. 3-bp TSDs are usually TWA. XX SQ Sequence 420 BP; 98 A; 84 C; 124 G; 114 T; 0 other; gagcaactcc agccttctac tttgctcggg ggacgggctg caggaagggg cccgagggcc 60 ggttgattct tctccagcca tggagggccc gagtgagggt gggagcccga gcacaagggg 120 ggtggatagt tgacaggcct gcagcccgag ggccaaggca tttttttatt gttttttgtg 180 tcagcccgag gccctacagc cccatttccc tgtttttttt tattttatat tatttaaaca 240 aacaaaaaaa actactattt tattacctat tgccaggggg gagggctcca agggtggaga 300 tgcaaaaggt aattactgtt cattaatggt agttactatt cattaaaggc agttactgtt 360 caatagggtg gattcaatag tggattgcca gggggaaggg ctccaagggt ggagttgctc 420 // ID Copia-28_Mad-I repbase; DNA; EDCOT; 4409 BP. XX AC ACYM01055761; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-28_Mad-I; KW Copia-28_Mad-LTR; Copia-28_Mad_. XX NM Copia-28_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4409 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1301-1301 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01055761; Positions 18828 23236. XX CC Positions [1990-2325] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 120..1664 FT /product="Copia-28_Mad-I_2p" FT /translation="MATNSSASDSEIHPSPVTNQFPNPSQSLISSITIQNI FT GSLVPIKLTTTNYLTWSALFAPIFRRYNLTGIVGGSMVAPPKFLGDSTGNR FT TSTVNPKFVTWYENDQNILIWINSTLSDSLIPYTVCVSSSRELWSKLESRL FT ASASQSHIHELRSRLRTITKGDSTAAVYLQQIEEIADALASADAPVEDSEL FT ISVTLHGIPPDYDSFIDAIQFRLGSTTIDELHGLLLSKELQLNSRKKISSA FT SIQAFNASPGLLPTPHDPPFSQAYVAQHFTNFHQGRGMDRNFSHSRNSQTR FT GMDMNFSTYRNNNPRNNFTRQNNQRYNRGSRSHFTNYGKRISCQICKQFDH FT EAVDCPHRMNTNYGTKSQMALCASTSSTAPTWLLDSGASSHMTNSYANLQN FT PESYNGPEQVYIGDGKGLPIIHSSSSTISTSSHNFDPYNVLHVPALKQDLL FT SANKFILDNSCSIHLYHFHFTVKDISTEKTFFKGPVKDGFYPFHASSPFAG FT HPHAFATTSKLLKMYGISV" FT CDS 2248..3261 FT /product="Copia-28_Mad-I_1p" FT /translation="MPTALKCSPWESLFHRCPDYSTIRIFGCQCFPWLKLY FT NNSKLAPKSQSCVFLGYSLHHKGYKCLDIATKKMYISRHVIFHEHVFPFHH FT ISTSPSPTATVPSPLFSTSIPSTLTFTSRSSSPNSSAPSPSISHPILASTF FT ISSSPTLPPNPLLPPPLPQPLSATNAHPMQTRSKSGISKPKAYTTTKHSIP FT PHLTQDFIPSTYLQAFKCPQWRQAMQEEFNALLNTGTWSLVHSHPSQNLVG FT CKWVFRIKRKPDVSIDRFKARLVAKGFHQQQGLNYTETFSPVAKPVTIRLL FT LTLASKFNWFLNQLDVSNAFLHGNLSELVFMIQPPGFDDSLQANHV" XX SQ Sequence 4409 BP; 1150 A; 1111 C; 710 G; 1437 T; 1 other; tggtatcact cacatttgtc taaagacttt ctcctctccg atcctctttg ctcttcaccg 60 cttctgcacc gacgaacagt tcttcgtctt tttcctctct caaaccctag atttcaccca 120 tggcaactaa ttcctctgcc tctgactctg aaattcatcc ctctccggtc acaaatcagt 180 tccctaaccc ttctcaatca ctgatttctt caatcacgat tcaaaatatt ggatctttgg 240 ttcccatcaa gctcaccacc acgaattatc ttacctggag tgctctcttc gctccaattt 300 ttcgccggta caatctcact ggcattgttg gtggctcgat ggttgctccg cccaaatttc 360 ttggcgattc gactggaaat cgcacatcta cggtgaatcc taagttcgta acctggtacg 420 aaaatgatca gaatatcttg atctggatca actctactct ctctgattct ctgattcctt 480 acacagtttg tgtttcatct tctcgggaat tgtggtctaa acttgaatca cggcttgcgt 540 cggcttcgca atctcacatc catgaacttc gatctcgtct tcgtactatc acaaaagggg 600 attctacagc tgctgtttat cttcagcaaa ttgaagaaat cgctgatgct cttgccagcg 660 ccgatgctcc agttgaggat tctgaattga tatctgtaac gcttcatgga atacctcctg 720 actacgattc attcattgat gctatccaat ttcgtcttgg atccaccacg attgatgaat 780 tacatggact tcttcttagt aaggaacttc aactcaacag ccgcaagaaa atctcgtcag 840 cttctatcca agctttcaat gcatcccctg gccttcttcc tacaccacat gatccgccat 900 tttctcaagc gtatgttgct caacatttca ccaattttca tcaaggccgt ggcatggatc 960 gaaatttctc tcactctaga aattcccaaa ctcggggtat ggatatgaac ttytccacct 1020 accggaataa caatccgagg aataacttca ctcgtcagaa taatcaacgg tataatcgtg 1080 gttcaagatc tcatttcacc aattatggca aaagaatctc ttgtcaaatt tgcaagcagt 1140 ttgatcatga agctgtagac tgtcctcatc gaatgaatac caactatggc acaaaatctc 1200 agatggcatt atgtgcaagt acatcctcca ctgctcccac ttggcttctt gattctggtg 1260 cgagctcgca catgaccaac tcatatgcta atctgcagaa tcctgagtcc tacaatggtc 1320 ctgaacaagt atacatcggt gatggaaaag gtttacctat tatccactct agctcttcaa 1380 ctatatctac ttcttcacat aattttgatc cctataatgt tttacatgtg cctgcactca 1440 aacaagattt gctttctgca aataaattca ttcttgataa ttcgtgttct attcatctat 1500 atcattttca ctttactgtg aaggatattt ctacggagaa gacgtttttt aaaggccctg 1560 tgaaagatgg attttatccc tttcatgctt cttctccatt tgctggtcat cctcatgctt 1620 ttgcaacgac atctaagctt ctcaagatgt atggcatcag cgtctaggac atcctacttt 1680 caaaataatg aatcaaattg tttccaagtc ttgtatttcc atttctgata gaataagcaa 1740 gtcactgtgt tcaagttgtg ccttgggaaa gtgttccaaa ctttcttttc atactatttc 1800 ttgtaataca cgaaaacctc tggaaatagt acatactgat gtatgagggc cctcaccaac 1860 tctctctgta catggttttc gatattacat catctttgtt gatgacttta ccaagtactc 1920 ttggttattt cctcttaaat acaaatctga agcatttgcc atctttactc agttcaagtc 1980 tatgattgaa aatcttttgt ctaccaagat tgttacttta aggtccgact ctggtggcga 2040 attatcaata ctcagttctc tacttttcta agagaccatg gcatatctca tcaactcagt 2100 tgccttcaca ctccagaaca aaatggctgt gctgagagga agcacagaca tcttgtagaa 2160 actgcaagaa cttttcttac cgcttctaaa gttccacata tctactgggt tgaagctttc 2220 tctactgcca tctacttgat caacataatg cctactgcac tcaaatgctc accttgggaa 2280 tctctttttc atcgatgtcc agattactct actattcgga tttttggctg tcaatgtttt 2340 ccttggttaa agctatacaa taattctaag cttgctccaa agagtcaatc ctgtgtcttt 2400 ctgggttata gcctccacca taaaggctac aagtgtttgg atattgctac taagaagatg 2460 tatatttctc gccatgttat tttccatgaa catgtctttc catttcacca catatccaca 2520 tctccaagtc ctactgccac agtaccctca cctttattca gtacctcaat cccatcaacc 2580 ctcaccttta cctctcgaag ttcttcacca aattcatccg ccccatctcc atctatatcc 2640 caccctattc ttgcttccac atttatttcc tcatccccca ctttaccacc aaatccacta 2700 ctcccacccc cacttcctca acctctttct gcaactaatg cacaccctat gcaaaccaga 2760 tccaaatctg gcatttccaa gcctaaagct tatacaacca ctaaacattc aatccctcct 2820 catctcactc aagactttat cccttctacc tatcttcaag ccttcaaatg cccacaatgg 2880 agacaagcca tgcaggagga atttaatgcc cttcttaata ctggcacttg gtctctagtt 2940 cattctcacc cttctcagaa cttggtaggc tgcaaatggg ttttcagaat caaaaggaaa 3000 cctgatgtat ctatagaccg gttcaaagct cgtttagttg caaagggatt ccatcagcaa 3060 caaggcctca actatacaga aacattcagt cctgtagcca aaccggttac aattcgattg 3120 cttcttacct tagcatccaa gtttaactgg tttctcaatc aacttgatgt gagtaatgct 3180 tttctccatg gcaatctttc tgagttagtg tttatgattc aacctccagg atttgatgat 3240 tctttacaag ctaatcatgt gtgaaaattg cacaaatctc tgtatggtct caaacaggct 3300 cctcgcgcct ggtatgaaaa attgcacaca gctttatcct ctcttggttt tttgggatct 3360 caaaatgatc attctctgtt tgttaaacag actcctgatc ttgtattcat cttggtctat 3420 gtggatgaca tccttgtcac tggtcccaat tcccaagctt gccaggatac ccaagcttgc 3480 caggatacaa tctctcagct cagtgctctc tttcccatta aagacttggg tccactacat 3540 tttttccttg gcattgaagt aaaaaggtcc tcatctgaca tctttatctc tcagcccaag 3600 tatatattgg atttacttaa gagagcacat atggatggtg ctaaaccatg tgttactcct 3660 ctaagtactt cctccctgga tcatacttct ccactgttgt ctaatcctgc agagtataga 3720 tccttggtgg gtggactgca atatttaacc tggtccagac ctgacttatc ttttgcagtc 3780 aatttggtat gtcaattcat gcagcaacct agagaatcac atctccaagc agtcaagcga 3840 atacttaggt atctcaaagg caccattgat cttggtctct ggtttcccaa gtgttccaag 3900 ccccttagcc tcaatgtttt ttcagatgct gattgggcag gttgccattt ggatagacga 3960 tccactggtg ggttttgtgt ttttctggga gattccctta tcagttggag cgccaagaaa 4020 caacctatag tggcacgctc ttccactgag gctgagtaca gatcccttgc aaatacaact 4080 gcagaaatca catggatatg caaattattg gttgatgttg gcttggttct tccctgtcct 4140 cctacactat aatgtgacaa tatttttgct atctctttag ccaaaaatcc catctttcat 4200 gcaaggacta aacatgtgga aatcgattat cactatatta gggaaaaagt gatgtctaat 4260 gctatatcag ttcaatttgt ttgttcacat gaccaacttg ctgatatctg caccaaatcc 4320 ttgcctaagg ccagatttct atttctccga gatgaactat cacttcatct acctcagttc 4380 agtttgaggg ggcatattag agataatat 4409 // ID SHACOP9_LTR_MT repbase; DNA; EDCOT; 190 BP. XX AC AC144731; XX DT 16-JAN-2007 (Rel. 12.01, Created) DT 16-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of LTR retroposon, SHACOP9_MT, from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW terminal; Interspersed; repeat; SHACOP9_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-190 RA Shankar R. and Jurka J.; RT "SHACOP9_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 83-83 (2007). XX DR EMBL/GenBank/DDBJ; AC144731; Positions 77103 77292. XX SQ Sequence 190 BP; 70 A; 20 C; 26 G; 74 T; 0 other; tgtgaataag gagttgactt gttctcctta ttatatttat tagataaatc agaaattgat 60 ttgtttccaa taattgtaat tatttagtat aattatatat tatttagtgt aattatatat 120 atagccttgt aacctctata tatacacaag aaataacaag gagaaaggca tcaagccatt 180 atttgtgaca 190 // ID CAULIV-2_Mad repbase; DNA; EDCOT; 8427 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Caulimovirus-like sequence. XX KW Caulimoviridae; Integrated Virus; CAULIV-2_Mad. XX NM CAULIV-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-8427 RA Kojima K.K. and Jurka J.; RT "Integrated Caulimovirus-like sequences from the apple genome."; RL Repbase Reports 10(10), 1647-1647 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >93% identical to the consensus. XX FH Key Location/Qualifiers FT CDS 2141..6727 FT /product="CAULIV-2_Mad_1p" FT /note="retropepsin, reverse transcriptase and FT ribonuclease H." FT /translation="MELFRKKGKEVVRAEDIYPNEEEAQEFIRRGFERTQK FT NKYNLYQLGLFENRSRIVSSISQHEVSCIDKEVTLNLISKEAVTHLRKSHF FT SQIHIGTILIGIAGLTRAQVGTKALVYIYDDRWDNHQQAAIATAEVDLSSN FT LAVIGCIPNYVMTINEFSKYIKVSIRTKNYNMKGEYKNLCISLMYIGKVSD FT RYNHKFNLEFQNLVQTFGSKHVNMIEAKPVDNSFLEGTQWTLPNLQVAXNR FT QPDKVQIYETSTGQATIRFSNYKQLEKIEEDESEIENESIHMAFDNLDINL FT VEQNFDHIVDKLIEDIDHLDEEQYLEKYKTYDLGLHKISDEEMKILILEIG FT VEHILGSKEYNNLLELKAECNPAEESSTSGVENPGHASRTDQQFLRPTNEQ FT YNEKAKVDYIEESMIKPRKNRIPYLRGLEQINIAGNILNLDNVDPQDWERT FT IERWEKGCVHAALMLDFSNSQNMLDYFEHTLDGLVFYYFQSWKVQNPEQHQ FT AAKTHFNIDGFVTLIKQEFLDHNRLDGRSEQEQIRAIRNLEQLQICDLQYI FT AEYTTDFFKYLGRTGRISDINLLDTYMTKIKGPIGEKIWNEWQKHPKKNDI FT AIGPRIQHVYDILRQECSQIKAKRQIRKQFYMSCKNIDLPQQYGCHKKNKH FT KKIYKKKYKSYKPYKQHKNFSIRPSRTYRKRKYIPKQFRKRSGRPWIRKYK FT APKDKSSCKCYSCGEAGHIRPKCPKLGKQSKEKVHLMELFKLEEDEDIQSI FT YSLDDLSDNESIYSIESINMIDSDSEDSSSTNSDLEEYMCAFIEEQHEEEY FT KYINLGWPEKCHKCSKLVANKYYNTYSILCEKCYSNRLLEVNSAESQESTE FT ILGNIVHSIEKPKNSSLITINCEIELAKEHKIQTTAMIDTGSTKSVIREEL FT VPEKYRQKLAKPVRITQFDERPVYLTHCINNEFIKVEKQQFNLPLTFVSPV FT GSYPFILGLNFLKSLQGFLFMNPNITFFKRGITITDQSNTVEAYKSISIEE FT SSGQDSYHLENSKENDEHNNVEEFDEDIFEHEYPILEEGTRIEILQLDRPK FT SLEELLQLAEQTRIIGEDPQLHWSKNKILAKLDIINPDLTIKTADMPCSLI FT DKQEFEQQIKELLNLKVIRPSKSRHRSAAFIVRKHSELKRGKARIVYNYKR FT LNDNTYEDSYKLPNKDELINKIQESKYFSKFDCKSGFWQIRLAEESIEWTA FT FTCPEGHFEWLVMPFGLKNAPSIFQRKMDQIFKKYDNFCSVYVDDILVHSK FT NRNEHRKHLEIVLQEFINNGIVISKNKIALEKQDIEFLGMYIKSGTIQLQD FT HIAKKVLEFPDKLEDKKQLQAFLGLLNYARNFIPDLGRKIAVLHSKTSKTG FT QKYFNSEDIKLVQKIKEEITKLKPLTLPLDDSYKIVETDASSLGWAGILYQ FT KKHRESPKSDEQVCRYSSGKFSDVQSRLPSTDLEILGIINSLEAFSLFLHN FT EVFTIRTDCQNIVSHYNKIHANKQAARRWVNFVDSITGNGFKPIFEHIKGN FT DNTLADILSRLIC" XX SQ Sequence 8427 BP; 3410 A; 1130 C; 1499 G; 2386 T; 2 other; aagattgggt cagttttctg caaagttcat gtggatacat ccaaaagaag aaaaaggaga 60 ttgacatttt cagaaaacat tcgcatgcaa aagaatacgc ggcaaacatt gcaacaacca 120 agacaacata gattcgcatg caaaagaaaa tgtggcaaac tctgcagcaa ccaagacaac 180 ataaattcac atgacattca agcaaagaca agacagccag ctttcagaaa cagtgctgac 240 agctttcaga aacagtgtgc tgtcactatt caaaaagttg taaatagttg aaacgttatt 300 ttgtttagga attagatttt gtatataagg gagcctttcc tcccatacag acgacctctc 360 tcaacacctg aacaccacac acatatctca acatctgaaa atcatacact caagcattcg 420 tagccttcat agcatccttg taaacacttc tttgtaatca ctttcttgta aacaactatc 480 tctgtaaaca ttccatatat caataaaagt tcaagtgtac atattcaagc aatctccaag 540 tcttaagtaa gttttctttt ccttctttag tgtgtttgtt taattagact tctagtccaa 600 aacagggaaa cactattgtg gttatattat taacctgcta aactgacgat catactttgt 660 tcgagcactc tgttatagtt gaatgcttgc catacaaata actggacatt aaccagggta 720 cctctgagtt cttcgtacct ctgagttcag ccgttaaggc cttatacttg tactgtgagt 780 ggccgtcatg ctgaaacatg tcgagttcca tgtgcaaggt tctatgtcta gttgttataa 840 tggtcatccg actatttaac cgggcatgct tttcgaattt ggtatcagag ccaagtttag 900 cattttaata gtataattat aatagtaaag taccttgagg acggaagtca ttgatacaac 960 tgatatcaca cttgtttatt ttgtatgaac aacagatatt attgtccctg tagaccttgt 1020 caaccacaac caccaggtat ttattgtccc agacatccaa ctataactag cataaagaga 1080 agattagcat atatatccaa aagaattatc agtactttga agaagcaaaa gttttatctt 1140 ggttatcttg aacatccttc atttattcgt aaatataata acacagaagt gcagcataaa 1200 gttttagaag caaaaagagc aacagatcaa gttttagaga ccttgagaga agaaagagag 1260 tttctaagaa accagttagc cgtaactcta gagaaaggta gactgtagtt tatgatagat 1320 tatcttaatt tagaaattag tgaacctcaa aaaagaaaaa taactttaga ccaaaatagt 1380 ttagtttgtt attttccatc gagaaagcat aatcatattt tgcacagtga agaaaatcca 1440 caagccaata gtattgtaga tcttattatt agtcaagcag aaaatataaa attagaaaat 1500 aataagcata atcatttgtt aaaccagttg ttagagcatt ttcagaaaaa ttccataaaa 1560 ataattagac aaaatttaga ttatattaca tctcagttag aagataataa taaaaatatt 1620 caaaggtttc ctagcaaaag agagataaaa gagcttgttg acctcataga tagtaagccg 1680 aagcaagtag aacttaggtc attagaaata gttgaacagc taaaattaga agttcaaaaa 1740 attcaattag tacaaaagga gttgagtgaa caagtagata agttgcataa taaaatagat 1800 aaattattag tttaatgaca gattctagaa ctagcagaaa atatatccaa gctttgaaag 1860 aaattagtaa gttagataaa gaaccagtag gtttaacaga tttttcaaca caagtatcca 1920 gtagtaatat tcccattagg caaaataatt tgattatcca attagtttta agtttggctg 1980 aaaaattaga tcaagttgaa gaacaaatag cagaaataaa ccaagtttta cataacgcat 2040 cttcatcact tccaccatcc ttgctagata aattagaaaa tttaactttg agtgcaaata 2100 ataatagaag acctaagcta aatccttttg ataatagaaa atggaactct ttaggaaaaa 2160 aggaaaagaa gtagttagag cggaagatat ttatccaaat gaagaagaag cacaagaatt 2220 tattcgaaga ggttttgaga gaacacagaa aaataaatat aacttgtatc aattaggttt 2280 atttgaaaac agaagtagaa ttgtaagcag catcagtcaa catgaagtta gctgtattga 2340 taaagaagtc acacttaatc taattagtaa agaagcagtt actcatttga gaaaatcaca 2400 ttttagtcag attcatatag gaacaatatt aattggaata gcaggattaa ccagagcaca 2460 agtaggtaca aaagctttag tatacatata tgatgataga tgggataatc accaacaagc 2520 agcaatagca acagctgaag tagacttaag ttcaaactta gcagtcatag gttgtattcc 2580 aaattatgtt atgacgatta atgaatttag taaatatatt aaagtgagca taagaacaaa 2640 aaattataat atgaaaggag agtataaaaa tttgtgtatt agcttaatgt atataggtaa 2700 agtgtctgat agatataatc ataagtttaa tttagagttt caaaatttag ttcaaacatt 2760 tggcagtaaa catgtaaata tgatagaagc aaaacccgta gataatagct ttttagaagg 2820 aactcagtgg acattgccta atttacaagt agcacmaaat agacaaccag ataaagtaca 2880 aatatatgaa actagtacag gtcaagcaac aattaggttt agtaattata agcaactaga 2940 aaaaatagaa gaggatgaga gtgaaatcga aaatgagagt atacatatgg cttttgataa 3000 tttagatatt aatttagttg agcaaaattt tgatcatatt gtagataagc ttatagaaga 3060 tattgatcat ttagatgaag aacaatattt ggaaaaatat aagacatatg atttaggact 3120 acataaaatt tcagacgaag agatgaaaat tttaatctta gaaataggag tagaacacat 3180 tttaggatca aaagaatata ataatttatt agaattgaaa gcagaatgta atccagcaga 3240 agaaagtagt acatcaggag tagaaaatcc aggacacgca agtagaactg atcaacaatt 3300 tttgagacca acaaatgaac aatataatga aaaagcaaaa gtagactata tagaagaaag 3360 tatgataaaa cctagaaaaa ataggattcc atatttgaga gggttagaac aaattaatat 3420 agctggtaat atattaaatt tagataatgt agatccacaa gattgggaaa gaacgattga 3480 gagatgggaa aaaggttgcg tacatgcagc attaatgtta gattttagta attcacaaaa 3540 tatgttagat tactttgagc atactttgga tggtttagtt ttttattatt tccagtcatg 3600 gaaagtccaa aatccagaac agcatcaggc agctaaaaca cattttaata ttgatggttt 3660 tgttactttg attaaacaag agtttttaga tcataatagg ttagatggca gaagcgaaca 3720 agaacaaata agagcaatta gaaatttaga acaattacaa atttgcgatt tacagtatat 3780 agctgagtat accacagatt tctttaaata tttaggaaga acaggtagaa ttagtgatat 3840 taatttatta gatacttata tgacaaaaat aaaaggacca ataggtgaaa agatttggaa 3900 tgaatggcaa aagcatccga agaaaaatga tattgcaata ggacctagaa ttcaacatgt 3960 atatgatata cttagacaag agtgtagtca aataaaagct aagagacaaa ttaggaaaca 4020 attttacatg agttgtaaaa atatagattt accacaacag tatggttgcc ataagaaaaa 4080 taagcataag aaaatataca aaaagaaata taagtcatat aaaccctaca aacagcataa 4140 gaatttcagt ataagacctt caagaacata taggaagaga aaatatattc caaaacaatt 4200 tagaaaaaga agtggcagac cttggattag aaaatataaa gcaccaaaag ataagagtag 4260 ttgtaaatgt tattcatgtg gagaagctgg acatattaga cctaaatgtc caaaattagg 4320 taaacagtcg aaagaaaaag tacatttgat ggagttgttt aagttagaag aagatgagga 4380 tattcagtca atatacagtt tagatgattt aagtgataat gagagtattt atagtataga 4440 gagtattaac atgatagatt cagactcgga agattcaagt agcacaaata gtgatctaga 4500 agagtatatg tgtgcattca tagaagaaca acatgaagaa gaatataaat acattaattt 4560 aggttggcca gaaaaatgtc ataagtgtag taaattagtt gcaaataaat actataatac 4620 atattcaata ttatgtgaaa aatgttatag taataggtta ttagaagtta attcagcaga 4680 atcacaagaa agtactgaaa tattaggaaa tattgttcat agtatagaaa aaccaaaaaa 4740 tagttcttta attaccataa attgcgaaat agaattagca aaagaacata agatacaaac 4800 aacagctatg atagatacag ggagtacaaa gagtgtcata agagaagagt tagtaccaga 4860 aaaatataga caaaaattag caaaaccagt gagaataaca caatttgatg agagaccagt 4920 ttacttaaca cattgtataa ataatgagtt tattaaagta gaaaaacaac aatttaattt 4980 accattaaca tttgtttcac cagtaggatc atatccattc attttaggtt taaacttttt 5040 gaaaagtttg caaggttttt tatttatgaa ccctaacata acatttttca aaagaggcat 5100 tacaataact gaccaaagta ataccgtaga agcatacaaa agcataagta tagaagagtc 5160 tagtggccaa gatagttatc atttagaaaa ctcaaaagaa aatgatgagc ataataacgt 5220 agaagagttt gatgaagaca tatttgaaca tgaatacccg attttagaag aaggaacccg 5280 tatagaaata ttacagttag atagaccaaa gagtttagaa gaattgttac aattagcaga 5340 acaaactagg attataggag aagacccaca gttacattgg agtaaaaata aaatactagc 5400 aaaattagat ataattaacc cagatttaac cattaagacg gctgatatgc cttgtagtct 5460 aatagataaa caagagtttg agcagcaaat aaaagagttg ttaaatttaa aagtaattag 5520 accctctaag tctagacata gatcagcagc atttattgta agaaaacatt cagaactaaa 5580 gagaggtaag gctagaatag tttataatta caagagatta aatgataata catatgaaga 5640 tagttataag ttaccaaata aggatgagct tataaataaa attcaagaga gtaaatattt 5700 tagcaaattt gattgtaaat caggtttttg gcaaatacga ttagcagaag aatcaattga 5760 gtggacagct tttacttgtc cagaaggaca ttttgagtgg cttgttatgc catttggact 5820 taaaaatgct ccatcgatct ttcaaagaaa gatggaccaa attttcaaga aatatgataa 5880 tttttgtagt gtttatgtag atgatatttt agtacatagt aaaaatagaa atgaacatag 5940 gaagcattta gagatagttt tacaagaatt tatcaataat ggaattgtga ttagcaaaaa 6000 taaaatagca ttagaaaagc aagatataga atttttagga atgtatatca agtcaggtac 6060 aatacaatta caagatcata tagctaaaaa ggtgttagaa tttccagaca aattagaaga 6120 taagaaacag ttacaagcat ttttaggatt gctaaattat gcaagaaatt ttatccctga 6180 tttaggaaga aaaatagcag tattacatag taaaactagc aaaacaggac aaaaatattt 6240 taatagtgaa gatattaaat tagttcaaaa aataaaagaa gaaattacta aacttaagcc 6300 attaacatta ccattagatg atagttacaa gatagttgaa acagatgctt catcattagg 6360 atgggcaggt atactatacc agaaaaagca tagggagtct ccaaagtctg acgaacaagt 6420 ttgtagatat tcctcaggaa agtttagtga tgtacagtca agattaccat caacagattt 6480 agaaatttta gggataatta attcacttga agcattttct ttatttttac ataatgaagt 6540 atttacgatt agaacagatt gtcaaaatat agtttctcat tataacaaga tacatgctaa 6600 taaacaggca gcccgaagat gggttaattt tgttgattca attacaggaa atggttttaa 6660 accaattttt gaacatataa aaggtaatga caatacatta gctgatatct tatcaagatt 6720 aatttgttga acaggtatgg aatatcgtgg accatcatca gcaaatagca caaggccgca 6780 aggcagaaga gtttctttca atggcatgat gatgcaccat caacctccac cattcagtgg 6840 atttcaaaat agcatgagca gaccagcatc accaccagta cctacgttca actttaatgg 6900 caatattgtt gaaggaatca gaaatccaac tctgagatat aggtcaaggg taccagggct 6960 ttctgatagg cagcaggttc tcttagataa tttttggaat atccaaatca agcagccaag 7020 catgaggtta ggtcatgaaa aattaattag agccttggaa caagagtttg atagctttaa 7080 ttttaatttc caccaaagcc agcaacatat tcattctctt gagcacaacc ttcaagtcat 7140 ctctagggac catgagtcat tacttggtaa gtttaccaaa atgaaccaag aactccaatc 7200 tcttagaatg cagcaaaagg caagtgacac cttgaaaaga gaattgaaaa taggtttaga 7260 aattgatcag cataagaata aaggaaaaga ggttattgaa cccatagaac aagaggctaa 7320 tgagcccata gaagaaatta agattgagct cttagaagaa gacgttgaaa tggagcagca 7380 tcaaagtaat gagcagcatc aggttctgag tgacaaagaa aaacaagaaa aatatgaaag 7440 ttttcttagg aatatatctt cagacttaat attagatgat gttttattag aagaaatttc 7500 aaaagcaaaa ctaagaataa tgccaacaga tatgcaaaat gagatcctga gcagagcatc 7560 acagtccatg aaagagttac aattacaatt acaatgcgcc ttgtatcagt ccatctttga 7620 tccaaaacca gggatggata ttattacaaa gatgtatcct ccatgtcttt gtgatagtac 7680 agagaattgt atttgtaaac cagaggttag cgtagctgtg gccaggatta acatgagaga 7740 ttttaaacca tggcatttta gttatgagca tcagaaaaag cataatgtgg tagaagttac 7800 ccctgcctta ctattagagt ttggttatct cgataaaata tttattaacc gtatttctca 7860 actagaatca tttcctgaaa aacttataaa agtagcagaa gattatctag aaaggtggaa 7920 agaaatttgc ataagtttta ttagtagtcc tccagattgg tatgtacata tgcataagga 7980 gaaagctagg catatagcca tgatcaatga agagtccttt agactaamcc ctatctcctc 8040 acataggtgg actccttcat acaaagatat tttaaaattt agagggatcc aaatgtttgc 8100 tttagatgag tttgaagatt ttaggtatga catggtacta gtagcagaag aagaagagat 8160 gtatatttac agcaagacaa gaatcagtca tcagccttat tggaagcccc aaaatttcaa 8220 agaagaaaca gcagaaatat attacaaggt gaaagaagat agagaaagag atgcggagct 8280 agtagaaggc gatgaacagt attggaataa tttgacagaa gaagagctgc ataacatcga 8340 caacatgatg gaagcctgaa gagctagctg taaattagca taagtttaat agcataatgt 8400 aaaataatgt attcctagac agaaatg 8427 // ID Copia-51_Mad-LTR repbase; DNA; EDCOT; 207 BP. XX AC ACYM01038468; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-51_Mad-I; KW Copia-51_Mad-LTR; Copia-51_Mad_. XX NM Copia-51_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-207 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1401-1401 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01038468; Positions 4430 4224. XX SQ Sequence 207 BP; 58 A; 35 C; 36 G; 78 T; 0 other; tgtgccacat aaggcaattg ccacgttagc actagcttta gagataagct acttttgata 60 tgtggtataa ataggcttta tattcttttc tttttctgtt aagtcggtgt gtatgtaaaa 120 acagaagatc agagaaatac aattgagctt tctttcttcc tctacaagat tactagggtt 180 tatttttctc acagattctt cagctca 207 // ID Harbinger-3N2_VV repbase; DNA; EDCOT; 221 BP. XX AC . XX DT 05-FEB-2009 (Rel. 14.03, Created) DT 05-FEB-2009 (Rel. 14.03, Last updated, Version 1) XX DE Harbinger-3N2_VV, non-autonomous DNA transposon - a consensus DE sequence. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW PIF; TIR; MITE; mPifvine-3.2; Harbinger-3N2_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-221 RA Benjak A., Boue S., Forneck A. and Casacuberta J.M.; RT "Recent amplification and impact of MITEs on the genome of RT grapevine (Vitis vinifera L.). submitted."; RL Repbase Reports 9(3), 708-708 (2009). XX DR [1] (Consensus) XX CC Harbinger-3N2_VV (mPifvine-3.2 in [1]) is a non-autonomous DNA CC transposon of the MITE type. Unlike the Harbinger-3N1_VV, this CC element is not a deletion derivate of the autonomous CC Harbinger-3_VV but it has the same TIRs as Harbinger-3_VV. It is CC almost a prefect palindrome. Individual copies are >80% identical CC to the consensus sequence. TIRs are 18 bp-long and flanked by 3 CC bp-long TSDs. There are approximately 1300 highly conserved CC copies present in the genome. XX SQ Sequence 221 BP; 87 A; 27 C; 21 G; 82 T; 4 other; ggtggtgttt gttttttgay traatagaaa aaatcaaaat atttgatttt ttctattcaa 60 ctaaaagtaa ttcattgaca tcaaccaaca taattaaact aaacttatta ataataagtt 120 cactttaatt atgttggtta atatcaataa ggtactttta gttdaataga aaaagtcaaa 180 tattttgrtt ttttctattc aaccaaaaaa caaacaccac c 221 // ID Gypsy-50_Mad-LTR repbase; DNA; EDCOT; 391 BP. XX AC . XX DT 03-NOV-2010 (Rel. 15.11, Created) DT 03-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-50_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-391 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1998-1998 (2010). XX DR [2] (Consensus) XX SQ Sequence 391 BP; 132 A; 58 C; 94 G; 107 T; 0 other; tgttgtaaat atgtgtggat ggtccacatg aatagtttgc tactatatgc acagtatttt 60 cactattcat ttgtgaaaaa tttgcaaagt gaatagtgct ttcttttctt tatataaagg 120 caaacagaga tcaaatgagg tgagttcacg ggagagaagg aaggaaagga gagagaggaa 180 gagagaggaa ggaagaggaa gagagaaaag agaggaagat gagaggagat aatagagaga 240 gttatctttg tactcctatt atttcaaatt ataatgaaag caccactgct gccccgagga 300 cgtactccag tcacactgac tgtagaggaa cctcgtaaat tttgtgtctt gtttcattta 360 ttccactgca cccaccgtcg attttacaac a 391 // ID Gypsy-14_Mad-I repbase; DNA; EDCOT; 4583 BP. XX AC ACYM01085282; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-14_Mad_; KW Gypsy-14_Mad-LTR; Gypsy-14_Mad-I. XX NM Gypsy-14_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4583 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1417-1417 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01085282; Positions 5447 865. XX CC Positions [3468-3962] - Integrase core CC 'TCCAG' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 41..1003 FT /product="Gypsy-14_Mad-I_1p" FT /translation="MPRSTNTARFAAMDDRVASIEATLANLPTLITSAVNS FT AFDSNFNSHLDARLPLYFEQFRRELGCQRLGVGATTSSPDAPLPSSDLDPL FT PPPRSPFVLGGGGGAPPRLPWSPRIDFPRFVEGDDPLAWIYKAEQYFSFYN FT TPDDQRVLTASFHFEWEVLHWFRWLDCLHTTPTWWEFTKALCMEFGPSAFE FT DSAEALFKLRHTGSLRDYISEFRRLATRSPEIGPILLKSCFIGGLRKELKF FT DVKLLKPVNVHEAISIALQLDTKLTELKTPTLKSTVTSKPSTTTTPHPFPV FT NRQGAYPVKKLSPEEIQKKRERGGVLVLH" FT CDS 1050..2012 FT /product="Gypsy-14_Mad-I_2p" FT /translation="MLDVLDTEGVELPHSDILCSEPSMELSSCAFYGTGEN FT HTTRTMKVDGQLNGHHVRILLDSGSTHNFIDSKLLKQWGQPVSPTTNFEVM FT IADGGKVRSSGCCKDATLSLGGYTCKVDFFSLPLGGCDVVLGVQWLSTVSP FT VLWDFQLLTMEFTKDHHRYTLSPTVTPSQCIHEISLQNLEKALGSSNLGLF FT LYSIEGKKLESFDLSEDHLQELQAVLKQFTDIFQVPTKLPPSREHDHHIPL FT VQGATPPNIRPYHYGPLQKTEIEKAVQELLIAGFIRPSHSPFSFPVLLVKK FT KEGSWRMCIDYRELNALTIKDKYPIPLID" FT CDS 2088..3755 FT /product="Gypsy-14_Mad-I_3p" FT /translation="MAASNVEKTAFRTHEGHYEFLVMPFGLTNAPATFQSL FT MNDIFKPYLRKFVLVFFDDILIYSKSWNEHLQHLQTVFEVLRDNQLYLKKS FT KCSFGQSNIEYLGHIISQNGVAADPSKLSAIQDWPTPKSVKELRGFLGLTG FT YYRKFVPNYGKICHPLYQLTRKDGFHWGPEAAQAFDHLKSIMISPQVLTFP FT NFSQPFELECDASGIGIGAVLQQRGRPIAFASQTLGPRNQALSTYERELIA FT IVYAVKKWQNYLQGRHFVIKTDHNSLKYFLSQRASTHFQQKWVSKLMGYDY FT EIQYKQGAQNMVADALSRLHNTPWEKTPVTDNGENSECVAISYPYAGWLDE FT LRRSSEHDAWVREKKQMLLQATHNGVESSKLSHYSIDNGFLCYKKRIVLGP FT TSDWKVKIIAEYHSTPSSGHQGVLKTYQRIKRGFYWKGMKHDIRQFITECP FT TCQQNKIENISPPGLLQPLPIPQRIWSDISMDFIVGLPNCKGKSVIWVIVD FT RLSKYAHFIAMSHPYTASSVAQLFVEHIFKLHGMPNSIVSDRDPVFTSAFW FT KELFKLQDS" XX SQ Sequence 4583 BP; 1260 A; 1011 C; 1016 G; 1285 T; 11 other; ttggtatcac ccatttgatc tctggttctc cttgttgtgc atgccccgtt ccaccaacac 60 tgctcgcttc gctgccatgg acgaccgtgt cgcttccatc gaagcgaccc tcgccaatct 120 tccgaccctc atcacctctg ctgttaactc ggcgtttgac tccaatttca attctcacct 180 cgatgctcgt ttgcctctct acttcgagca gtttcgtcgt gagttgggtt gtcaacgtct 240 tggcgtcggt gcaaccactt cctcgcctga tgcgcctcta ccgtcctctg atctggatcc 300 cttgccacct ccgcgcagtc cttttgtact tgggggggga gggggtgctc caccacggct 360 accatggtct ccacgtatcg attttccgag atttgtcgaa ggtgacgatc cccttgcttg 420 gatctacaag gcagagcagt atttctcctt ttacaacact ccagatgatc aacgagtcct 480 cactgcttct ttccatttcg aatgggaggt tctccactgg tttcgttggt tggattgcct 540 gcatacaaca cctacttggt gggagttcac taaggccttg tgtatggagt ttggaccctc 600 tgcgtttgaa gatagtgctg aagcactctt caaactccgt cacactggta gtcttcgtga 660 ctatatatcg gaatttcggc gtttagccac tcgctcacct gaaattggtc ccatcttgct 720 caagagttgc ttcatagggg gtttacggaa ggaattgaaa tttgatgtga agctattgaa 780 acctgtgaat gttcatgaag ccatttccat tgctcttcag ttggatacca aactcactga 840 gctcaaaact cccactctga aatccactgt cacctccaaa ccatccacca ctaccactcc 900 tcatcccttt ccagtcaatc gacagggtgc atatcctgtt aagaaattat ccccggagga 960 gattcagaag aaacgggagc gggggggagt gttggttttg cactgataag tggactgcgg 1020 ggcataagtg tgggttaaaa caactgttaa tgctggacgt ccttgatact gagggggtcg 1080 aactgcctca ttcagacatt ctttgctcgg aaccgtccat ggaacttagt tcctgtgctt 1140 tttatggtac tggggagaac cacaccaccc gcactatgaa ggttgatggc caacttaatg 1200 ggcaccatgt ccgaattcta ctagactcgg gaagcactca caattttatt gactccaaat 1260 tattgaaaca atggggtcaa ccagtttctc ctaccaccaa ctttgaagtc atgatagcgg 1320 atggaggcaa ggttcgtagt tcaggttgct gcaaggatgc tacactctca ttgggggggt 1380 atacctgcaa ggttgacttc ttctccttac ccttgggtgg ttgtgatgtg gtactaggag 1440 tccaatggtt gtcaacggtg agtccagtcc tgtgggattt ccagctgctt acaatggaat 1500 tcaccaagga tcaccaccgt tatacattgt cccctactgt gaccccatcg cagtgcatac 1560 acgagatttc tctgcaaaac cttgaaaagg cactcggcag ctctaatttg ggactatttc 1620 tctattctat agaagggaag aaactagagt cctttgattt gagtgaggat catttacaag 1680 aacttcaagc agtgttgaag caatttactg acattttcca agtccctact aaattacccc 1740 catccaggga acatgatcat cacatccctc tagtccaggg agcaacacca ccaaacattc 1800 gaccatatca ctatggtccg ttacagaaga cagaaattga gaaagcagtt caggaattat 1860 tgattgccgg gttcattaga ccgagccata gtccattctc attccctgtg ctgttggtta 1920 agaagaagga gggcagctgg agaatgtgta tagattacag ggaacttaat gccttgacca 1980 tcaaggataa ataccccata ccccttattg atratctatt ggatgagtta tatggtscya 2040 agtactttac taagcttgat ttgcgatctg gttaccacca gattagaatg gcagctagta 2100 atgttgaaaa aacggcgttt cgaactcatg agggtcayta cgaattttta gtgatgcctt 2160 ttggacttac caacgctcca gccactttcc aaagcttgat gaatgatata ttcaagccat 2220 atctcagaaa gtttgtgttg gtatttttcg atgatatttt gatctacagc aagagctgga 2280 atgagcattt acaacattta caaactgtgt ttgaagttct aagggacaat cagttgtatc 2340 ttaagaaatc taaatgctcc tttggacagt caaatattga atatcttggg cacatcattt 2400 ctcaaaacgg ggtagcagcc gatccttcta agttatctgc catacaagat tggccaactc 2460 caaaatctgt caaagagtta agagggttcc tcgggttaac tggatattat cgcaaatttg 2520 tgccgaatta tggcaagata tgtcatcctc tctatcagtt gactcgaaag gatggatttc 2580 attggggtcc tgaagcagca caagcatttg accatcttaa atccatcatg atttcacccc 2640 aagttttgac tttcccaaac ttttctcaac cctttgaact ggagtgtgac gcctctggaa 2700 ttggcattgg ggctgttctt caacaaaggg gacgacctat cgcattcgct agtcaaactc 2760 tcggtcctcg gaaccaagct ctctctactt atgagagaga gttgattgct atagtgtatg 2820 cagtgaaaaa atggcaaaat tacttgcagg gcagacattt tgttatcaaa actgaccaca 2880 atagccttaa gtacttctta agtcaaaggg ccagtactca ttttcaacaa aaatgggttt 2940 ctaagctcat ggggtatgac tacgaaattc aatataaaca aggggcacaa aatatggtag 3000 ctgatgcact gtccaggctg cataatacac cttgggaaaa aacacctgtc actgacaatg 3060 gtgagaacag tgagtgtgtt gccatctctt atccctatgc aggttggttg gatgagttga 3120 gaaggagcag tgagcatgat gcctgggtta gggagaaaaa gcaaatgtta ctacaagcta 3180 cacataatgg cgtggaaagt tcaaaactga gccattattc tattgacaat ggtttccttt 3240 gttataagaa gagaattgtg ctaggcccca cttctgattg gaaggtcaag attattgcag 3300 aatatcattc aactccatcc tcaggtcatc agggagtgct taaaacatac caaagaatca 3360 aaagagggtt ttattggaag ggaatgaaac atgatattcg gcagttcata actgagtgtc 3420 ctacttgcca acaaaataaa attgagaata tttcaccccc tggattgtta caacccctcc 3480 caataccaca gagaatttgg agtgatatca gtatggactt cattgttggt ctacctaatt 3540 gcaagggcaa atcggttata tgggtgatag tggacaggct ctctaaatac gcccatttca 3600 ttgctatgtc acacccctac actgcctcct ccgtagcaca actctttgtg gagcacatct 3660 tcaagcttca tgggatgccc aactctattg tgagtgatag agacccagtt tttacaagtg 3720 ctttctggaa ggaactcttt aagttacagg attctaaktt gtgcatgagt tcggggtacc 3780 accctcaaag tgatgggcaa tctgaagtaa tgaacagatg tttggagact tatttgaggt 3840 gttttgtagg aggrcagcct argaaatggg ttcaatggct accatgggca gaatggtgyt 3900 tcaacacctc mtttcacact tcatcgaaac acactccctt tgagatagta tatggatacc 3960 ctccaccaca agtaattcct tatgagatgg gcactacaaa gatggaaact gtggaacaag 4020 agttaatgaa cagagataag gtgttgtcaa tattgaagaa caatttggtg gtggcrcaaa 4080 awcggatgaa gcaatatact gataggaaga ggactgaaag gtatttcgaa gtgggtgact 4140 tggtttactt gaaattgata ccctatcact tgcaggcctt atctccacat agctaccaca 4200 agttacaaca aaggtactat ggaccctatg aaattttgga gaagattgga ccggttgctt 4260 ataaactcaa actaccccca gagacaagaa tccatcctgt tttccatatg agctgtctca 4320 aaaagcaact tggaccaact aacattccac agactgagct accccaagtc actgatgatg 4380 ggttgattca caatatacca caggccatac ttgctaggag gatatataaa aaaggagatt 4440 ctgcaggggt gcaagtgttg gtgcaatgga aggatcaaga agaagcaagc tcaacttggg 4500 aggattctga tgagtttcag agcaaatatc cagattttcc actctagaac cttgaggaca 4560 aggttgtttg aaggggagag cat 4583 // ID SHACOP16_LTR_MT repbase; DNA; EDCOT; 709 BP. XX AC AC174347; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of LTR retroposon, SHACOP16_MT, from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; terminal; SHACOP16_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-709 RA Shankar R. and Jurka J.; RT "SHACOP16_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 60-60 (2007). XX DR EMBL/GenBank/DDBJ; AC174347; Positions 7793 8501. XX CC The LTR is present in the genome in few intact copies and just a CC single intact set flanking the internal region. XX SQ Sequence 709 BP; 214 A; 110 C; 160 G; 225 T; 0 other; tgttggcccc accacgtgtg ggttatgtcc agccaaagac aattgctaca agcaattgcc 60 aaagtttcaa ctatgcagta aatgtatgat gtaaaatctt cttctacagt gaggctatgt 120 tgtagcttgc ggtgctgata tctttgaaaa gtaaatgtga tgcagatttc acatttggct 180 tgtagtatca tttgacaaag gagaattgaa ttcacatagc cacatttcat gtataaatag 240 aggccttggc atgtgaagaa aatcatccga agctcaaaga aaatacaagc ttcagtattg 300 aagcagaagt gaaaatacaa agcttctgtg tgtgtagaag tgtgtgagag gaaaaataga 360 gtgttgagta aatccagaga gtgtgggaaa aatacaccgg gtgggtatca tctctataac 420 ttctaggtgc tataaaataa tagcattaga ataaaagtag gtctcacggg aaacactata 480 ttgtatctct tgtgtgtgtg agagagtgga gagaatattg taatattctt taatatagtg 540 gaatattttt cggagtttgt cccgtggttt ttccctcggt attagagggt tttccacgtt 600 aaatattggt gttcattttt ttatcgctac cgctgcgctg caagatccag tctcttttgg 660 attttggaat tttaatttac acttgcgtta agctcgtcga gcccaacaa 709 // ID Copia-77_Mad-LTR repbase; DNA; EDCOT; 285 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-77_Mad_; KW Copia-77_Mad-LTR; Copia-77_Mad-I. XX NM Copia-77_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-285 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1693-1693 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 285 BP; 100 A; 54 C; 31 G; 100 T; 0 other; tgattgtagt gaaataagtt aattaattaa taaagaaaat aatataatta attaattaat 60 taatttaaaa ggatatgaac agttgtattt caacttgaaa agttataact tctcctgaag 120 aacacaactc ctccagaaag gttatttcca tctctatata tttgtcaaat ccctttctgt 180 cagaatatac attcaattcc attctcactc tctgttcata tccttcacac catattgtga 240 tcgatagtct aaacgacatc cgtttccgat cctgtgaact accca 285 // ID DNA3-8_Mad repbase; DNA; EDCOT; 875 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative non-autonomous Harbinger family DNA transposon from DE apple. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA3-8_Mad. XX NM DNA3-8_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-875 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1472-1472 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TSD is 3-bp long. TIR is 21-bp long. XX SQ Sequence 875 BP; 247 A; 204 C; 239 G; 185 T; 0 other; ggcctcgttt ggcagctcgg actgtactga ctatttctgt cggataggat aaatagccac 60 cggatagtac tgactaaatt agtcgggcgt ttggtgcagt atcggactaa tgaccgtatt 120 atttatactg tgtttggttt tataccggat aggaggaatc aaacttaaaa taaaattaaa 180 cttataaaaa taaaaaaaaa ctgaaaccat cccttcttgt tcccagatct ctccgccgca 240 cccctcaaac tccctccctc tctctccctt cttcttcccc gcctgcctgc acatttggtg 300 agcaaccatg agtcatcaga tccacatcaa cccaaatcaa gatgcaacaa acgaaacaaa 360 ctaccgcttt cttgacaagg ttacctcccc gactgcagaa gaatcccaaa tggaatcgac 420 tggcggcggt ttgacagaga gaaggagagt agttcgctgg cgttttgaga agagaggtct 480 cccagacacc atgccgggca agagagtgca tgcttctttg caagacccag ttgcagggga 540 ggacgacgac gcgatgggga gggcgacaga cggcgacggg gagggcgacg atggtgagag 600 aaggtgacgg ggggggggga ggacgacgac gcctagagag agagagagag agagaggaga 660 gaagggagag agagagggcc gagagaaggc gagagagaga gggccgacta ataatccggg 720 ccttttggtt ggttttatta gtccggcgta taccgtgcta aataagcaga ccggttaaat 780 taatccggcg cttatttagt acgagtgaac gccaaacacc cgcgtccgta taactagtcc 840 tatccgatcc tctatccgat ctgccaaaca gggcc 875 // ID Gypsy-48_Mad-LTR repbase; DNA; EDCOT; 1897 BP. XX AC . XX DT 29-OCT-2010 (Rel. 15.11, Created) DT 29-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-48_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1897 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1994-1994 (2010). XX DR [2] (Consensus) XX SQ Sequence 1897 BP; 517 A; 326 C; 345 G; 709 T; 0 other; tgataggagc atatttatgc gacttagtta gcttgttttc ttgcattttc atagtttgtt 60 tgtgtttatt atagtgtttt aagctatttt cgtgtgtttg taggtccata tgacaaagtt 120 ggcaagaaag tgcaatttgg agcattttga ggcagttttg ggcaccaaat ggatagctta 180 tgaatggagc aagatggatg gacgaatttg aagttcaaga ggctaggaat gtgctgaaaa 240 gagtgaagaa ataaatccaa gtcaaggaag ataagaaatc agctcaaaag aaggaacatt 300 atccaaaacc ttatccaacc ttatcttatc ttatcctatc ctaatcctat cctaacttaa 360 ttccagttgc aaaggggatt tattttcaga ttaaaacaca ttaaaatagg tttctagaag 420 cccttatcca ctcctacaaa ggtgccgcac cttatccctt gtttttctag aaatcagcca 480 caaaacaacc tttctagaag gccttatccc ttgtcctaca aatctggcgc cccaaacctt 540 tctagaagtt ctagaaacct gattattcct ttcccccttg gtttctaaaa gccttagcct 600 tttccttcaa ggattgtgtg ttattttcct atacaaatta ggcctttaaa tccttttcct 660 ttgctacata ggggctgcga atttcagcct ataaatacca acctttgctg caccatttag 720 tcaccaccct ctaccatata ttcactacac cattcaccca aacatccctc ttgtgccgtg 780 agtattgcaa aggagaagga aggagaccct tggagccgtg cctatgccat tcaaggagct 840 tggattgttg gagcgtttct aggtgttttc tatcttttaa tttcaatgtt taatttaagt 900 tatctttgtt tatttgcgaa catgaggaac taatttcttt atagttagag gtgaattcga 960 agccatgatc atatgtttta tatgaattga tttcctccag ttattgtttc atgaatcgtg 1020 aatgtggttt acttatctgt tttattgaga acttgttctt gtatgttgat tgagggtggc 1080 caacttagtt tgcatgcatg aatttgatgc tagagtataa gggaatttca cctaatcgtt 1140 atgaacttat attcatgagt agtaaaagtc gctagtcacg attgtgttaa gtaaatccta 1200 ggcaagagta acatgctttt catagttatg aatgcctcgt caatgcttat ggtttccatt 1260 gaacttaatg atctttgtta agtgtttcta tcatgcgtat tccatagtta gggaacttga 1320 taaagaataa tttggttgtg atgcgttttc cattcaattc aatgaatcta gggaaatctg 1380 agaattaatt agttcaatac aattaatttg gggcattgtc attcatggtt tgtcgaaaga 1440 ataattggaa atcgattcgt atgcatatgt catgtgtgga gaaggaaccc tctaactagc 1500 ctttcaccat tctatttcat caatttcgtg tcttcttaag tttgttttac aagtttctgt 1560 ttttaagttt taatttcgtc aaaacaaaat ccctttttct taagtcttgt ttttagagtc 1620 aaaacctgtt ttcttttagt cttttgagtc aagttaagtc ttattttcgt ccaaatcact 1680 tgttaggtct agaattgagt cttttttatt gtttcttgct gttttgagtg ttttaagtta 1740 gttttgagtc tatagagtct agtttagtgt ttttgagtct tatttgtgtt gattagcatc 1800 cctagttaat ccccggtcta gaacgatccc tacttgctta atactacaat tgtcatcaat 1860 agggtttaat ttgtgtgtca agttaatttt cacatca 1897 // ID BoSB2 repbase; DNA; EDCOT; 150 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB2. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-150 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 150 BP; 29 A; 38 C; 47 G; 36 T; 0 other; accagaggtc gttagctcaa ctggaaagga ccctggccat tgtgtcagag gtccccggtt 60 cgagtgaccg ctgggacgaa actaatatta catgttgtgg tttcgggcct ggggggatta 120 cgggcttcgg ccccgaacct cctggtattc 150 // ID Copia-50_Mad-I repbase; DNA; EDCOT; 5228 BP. XX AC ACYM01045729; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-50_Mad-I; KW Copia-50_Mad-LTR; Copia-50_Mad_. XX NM Copia-50_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5228 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1320-1320 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01045729; Positions 14160 19387. XX CC Positions [2582-2917] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1793..2578,2582..3883) FT /product="Copia-50_Mad-I_1p" FT /translation="MTAQSQSTFNLNQAWIMDTGATHHMTGDINDLEMIAP FT FEGDQKITVGNGKCLPVKNTGSNSLYTQSKILYLASMLHVPTLAASLLSVY FT TLCKDNNCCVILDEYGFLVQDKATKAILMRGRSSGGLYYIPKSLFFKHHKQ FT QSVSLPKAFLGQVVKASLWHHRLGHPSNDVLHSMLSNSKVLYKPDVNKHIC FT SFCLSGKMSRQVFSSSSHLSVRPFQRISSDVWGPSPVVSLEGYKYHVSFID FT DYTKFTWLFPLVYKSQVLSVFTFFAFVQNHFHTSIQYFQSDGGGEYTSFSF FT KKFLNSKGVVHLISCPHTPQQNGTAERKHRHIIETAITLLTTASLPHNFWM FT HACSHAIFLINRMPCKSLAWQSPYFKLFGTHPLVNSIKVFGSAVYPYLRHY FT TKHKLDPRTDECIFLGYVLGYKGVVCYHRGKQRLFISRHVVHDEQVFPFQQ FT SSIVQRTVNGPHYQFKHPVVTPFVLPIYSGARFGQQHQTTSSVHNGSDLVV FT QDTSLVNDSPMFSGMGQDERSSSPTQTSHHTTTPQSFHPTTSLLPVHCPAS FT LEVPFSLPYANDLSSGSIHNDTSDSSNVHSMTTRLKSGVIARKDYSTYSAM FT AAPISSGSYSSFDDHVLLGCTAVLDISEPIEPASYKHVVAHSHLRDAMTEE FT FSALQKQRTWDLVPLPSNKNIIGSKWIYKVKRDQNGAVSRYKARLVA" XX SQ Sequence 5228 BP; 1413 A; 942 C; 1083 G; 1780 T; 10 other; tagctgttat gatggtatca agagcttagg ttcttcaaga tcctgwrttt ttttcttccg 60 gtggtgattg cggtcaacgc cgatttgtgg ttttactcag gttctgttct tggttgattc 120 ttgacatttc gtctttcaat tcgagataat ttgttgatca ttgaggcacg aagccagaat 180 tggatatatt tgtgaaatct tgtgtgatat atcatgatga aatttgagca cgaagctggg 240 ttgttcttgg attacaattt ttcttgagtc tgttgaagtg cgattagggc actgaattga 300 aatttatgat taaattggtt ctgttgttga cgtttggtga tgaattgttg agcacgaagc 360 ttttgttagc ataaacaaaa tttcacaaat ttggaaaatt aagggcacta agctcatctt 420 attcgtatac gaagatattg tttgtctgag aaatttgggg gtttgttgtt ctgcgctcat 480 ctctcatttg gttcaccata ctaagcacga agcgtgtggt tgattctgtc tgagttcaca 540 aatggcgtct tcttcattca aaattgaaag tttattggga gtgctcacta tccacttaca 600 ggatgataac tttgctaagt ggtcatttca gtttcgctct gttttggaag gatatgattt 660 gtttgatttc tttgatggga atagtgtttg tccaccaaag tatgtgatct ctctggaagg 720 tggggtgaca aaggagatta cagcggccta tcgtgattgg gttaaaacag ataaagcatt 780 gttaagcttg ttgattgcta gtcttggtga tgaagccatt gaatatgtgg ttgggtgtaa 840 gactgcttat gaagcgtgga ccaatcttaa tgatcgatat gccacagtgt ctagagcacg 900 gatcaatcat cttaagactg aacttcacac gataaaaaag ggatctgata ctgttgagaa 960 atacttgcta cgtcttaagg gcttgaaaga tcaattactt gctgcagggg aaattgtttc 1020 agataatgat ttaattgtag cagctttggc tggattgccc tctgagtata acatgatcaa 1080 aactgtgatt gtggcacgca agtctcctct tactcttaaa gaatttcgtg cacagttgtt 1140 gagtgctgag aaaactgctg aagagtttca aggtggtttt caatttccta tgattggcat 1200 gtattctcat ggagagtctt ctaatgctgg ttctcaacat ggacagacgt ttaatggtaa 1260 ctatggaggt ctacgattct atccaggaga atcatccaat gctagtrmks aacaaggama 1320 aawttttaat ggkggaagkt ttggttttgt tggtcaaaat cagcggtcta atggtaatgg 1380 tcaagctaat atatcacaac aatttcattc caatcgtaac aatggtaata gtcagcgcta 1440 taattccaga tcaagattca atggtggtaa tgggtttcat tttggctcta ccaacagagg 1500 caatggctat ggtaattcag gtgggaattt tcagaataaa gggggttcga attggtcaac 1560 ttggactggg aattctggtc agaagtctgc cattatccct gaatgtcaga tttgcaacaa 1620 acgtggtcat actgctccaa attgttacta tcacaatgaa caacaatctc aagcgcctgc 1680 tgctattcct gagtgtcaaa tctgtggaaa aaagaggcac attgctctca attgtttcca 1740 tcgaagtaac tatgcatatc aaggagcaaa tccacctccc actttgattg ccatgactgc 1800 tcagtctcag tctactttca atctgaatca ggcatggatc atggacacag gggctactca 1860 tcatatgacg ggcgatatta atgatctgga aatgattgca ccatttgaag gggatcaaaa 1920 gatcacggtt ggcaatggaa aatgtcttcc agtgaagaat actggttcca actctcttta 1980 tactcagtct aaaatcttat atcttgcttc tatgttacat gtccctacct tagcagctag 2040 tttattatct gtgtatacat tgtgcaaaga taataactgc tgtgtgattc ttgatgaata 2100 tggttttttg gtgcaggaca aggcaacaaa ggcaatccta atgagaggaa ggagtagtgg 2160 aggtctgtat tacataccca agagtttgtt tttcaagcat cacaagcaac aatcagtttc 2220 tcttccaaag gcatttcttg gtcaagtggt gaaggcttct ctttggcatc atagactagg 2280 acatcctagc aatgatgtgt tacatagtat gctttctaat tccaaggtct tgtataaacc 2340 agatgtgaat aaacatatat gcagtttctg cctaagtggc aaaatgtcta gacaggtgtt 2400 ctcttctagt tcacatttgt ctgtaagacc ttttcaaagg ataagtagtg atgtatgggg 2460 accctctcct gttgtatcac ttgaaggata taaataccat gtgagcttta ttgatgacta 2520 tacaaagttt acatggttgt ttcctctggt ttataaatct caagtgctct ctgtttttta 2580 gacctttttt gcatttgtcc agaatcattt tcatacttct attcagtatt ttcagtcaga 2640 tggtggtgga gagtatacaa gcttttcctt caagaaattt ttgaattcaa aaggggttgt 2700 tcatcttatt tcttgtcctc atacacctca gcaaaatgga actgctgagc gaaaacatcg 2760 acatattata gagactgcta tcacattatt gactactgct tctttgcctc ataatttttg 2820 gatgcatgct tgttctcatg ctatttttct tatcaatcga atgccttgca aatccttagc 2880 ttggcagtct ccttacttca agttgtttgg gactcatccg ttagtcaatt ctattaaggt 2940 ctttgggtct gctgtttatc cgtatcttag acattatact aagcataaat tggaccccag 3000 aaccgatgaa tgtatatttc tgggatatgt tttaggttac aagggagttg tttgctatca 3060 tagagggaag caaagattat ttatttcgag gcatgtagtt catgatgaac aggtgtttcc 3120 atttcaacaa agttctatag tgcaacgtac tgtgaatgga cctcactatc agttcaagca 3180 tccagtggtt actccttttg tgctaccaat ttattctgga gcaagattcg gtcaacaaca 3240 ccaaactaca tcatctgttc ataatggttc cgatttagtg gttcaggata catctttagt 3300 gaatgatagt ccaatgttct ctggtatggg tcaagatgaa agatcttctt ctccaacaca 3360 gacctctcat cacaccacta ctccacaatc ctttcatcca actacatctt tgttgcctgt 3420 ccactgtcct gcatcattgg aggtaccttt ctcacttcca tatgctaatg atttgtcttc 3480 tggttccata cataatgata cttctgattc ttccaatgtt cattctatga ctactcgact 3540 taaatctggg gttattgcta gaaaagatta tagtacctat tctgcaatgg ctgctcctat 3600 ttcctctggt tcatattctt cttttgatga tcatgtttta cttggttgta ctgctgtctt 3660 agacatatct gagcctattg aacctgcatc ttacaaacat gttgttgctc attctcattt 3720 gagagatgct atgacagaag agttctctgc acttcagaaa caaaggactt gggatcttgt 3780 tcctttgcct tctaataaga atattattgg aagcaagtgg atttataaag tcaagaggga 3840 tcaaaatggt gcagtttcca gatataaagc tagactagtt gcttaagggt tcagtcaaac 3900 acatggttta gattatgatg aaactttcag tcctgttgtt cgacacagta ctgtcagaat 3960 tgttttggca cttgctgctt ctcacaaatg gtctttgaag caattagatg tcaagaacgc 4020 atttcttcat ggagatttgc aggaggaagt gtttatgcaa cagccccaag gtttcaagga 4080 tcctcaacat cctgattatg tttgtaagct cagaaaatca ctgtatggat tgaaacaggc 4140 acctcgggcc tggaattcta agtttacaac ttatttgcct accttgggat tccttgtttc 4200 agattcggat cctagtttgt ttgttaaaac tcaaggcagt gcagtggtta ttcttcttct 4260 atatgttgat gatataatca tcacaagttc tgattcagtt ttggttcaac aagttattga 4320 tgaattggga atggtatttg atatgaaaga catgagacaa ctcactttct tcttgggttt 4380 acaaattact tatcaagcta atggtgatct atttgtgtct caatcaaatt atgataaaga 4440 gctaattaaa aaggctggta tggtatcgtg taaagcttgt ctaactactt gcaagccaca 4500 tagtcagttg cttaaagatg aaggcatacc actgattgat cctactgagt ttcgcagttt 4560 agtaggagca ttacagtatc tcacttttac tagacccgac atcgcttttg cagtgaacta 4620 tgcttgccaa ttcatgtcaa ctcctactga tgttcatttt catttggtaa agcggattct 4680 tcgatatctt caaggtactt tggagtgtgg ccttacatat tcatctacac atactttgga 4740 tttattagca tttagtgatg tagattaggc atctgatatc aacacaagac gatcgactac 4800 tggatatgtg gtgtttttgg gacagaatcc agtctcctgg cagtccaaga agcaagcaag 4860 tgtatcgcgt agttccacag aggctgagta taaagctcta gctaatgctg ctgccgatgt 4920 tgcctggata cgattgatct tgaaagattt acacattttc ttgccctcac ctcctactct 4980 gcactgtgac aatatttcaa ctttggcttt gtgttctaat ccggtttttc actctcggat 5040 taaacatctt gatatagact ttcattttgt tcgtgaaagg gtgcaaaaag gagatttaca 5100 tgttgagtat atttctactg ctgatcaggt ggctgatatt ttgacaaagg gtcttcatgg 5160 acctttattt gttcaacact gtcacaatct caagctgggg ttccccagtt gagattgagg 5220 gggaatat 5228 // ID LTR-15_Mad repbase; DNA; EDCOT; 3046 BP. XX AC . XX DT 03-NOV-2010 (Rel. 15.11, Created) DT 03-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE Putative LTR-retrotransposon from the apple genome: long terminal DE repeat. XX KW LTR Retrotransposon; Transposable Element; LTR-15_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-3046 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 2005-2005 (2010). XX DR [2] (Consensus) XX SQ Sequence 3046 BP; 746 A; 476 C; 736 G; 1080 T; 8 other; tgtgaaatcc cgttcccgga tttcactgtt ataatctacg tatttgtact attgagattt 60 tatattattt ctcgagaatt tattttaaat tgtttggatt ttggatttta attaaactag 120 ttacgaagag tgaagtttgg aaawtaatta tttaaaattc gttgaccttt cgaggtcaca 180 agtaacgttt tcgaataggt ctcgaagcca cgagcgcata ggcgaaagcc gtttgcgagt 240 ccgagttata acggtatagt tacggacgtt tgaagttgtg agctatagat tgtgggaatt 300 atttaattcc cacatgtggg ttaaaggtta agtgagttta ataaaagggg gagggaccaa 360 tggaaagaga aaaggaaaaa agaaggaggg gtctggtttt gacccctttt tggggcgatt 420 tcgacccttt aacccgcaaa cttgacccgc tcatatctcc ttcatccgag ctccgttttg 480 ggtgatcttg gtgtccatgg aaagctcttg acgagcccta catctctgta gtgttagatt 540 ttccattttc ttatccattt ttccagttcg aggcagcaaa gttccgtggg ttttccggcg 600 gttttatcat ttttccggtg attccggcaa ccatttcctt cgagtgaggt atgaaacttc 660 atctactctt cataatcttc aagttggtat gcttggtttg tgctttcgta ttcgttttag 720 agttgggtgt gtagaaccct agaaacccgg ttttccccga tgaaattgga tggtttccgg 780 ttagaatttg tcgttggcct agttgtgaat aatgtttccc ttgttgagct ctagttacca 840 cgtaaatttg agcccwtgtg gttaakgttg aaaatttggg ttttcaaacc cttcaccatg 900 gctagcatcg cgtgtggcgg tgcgtgggac cgtccacgag tgttgtctaa gtaccaaata 960 ccttctagtg accctatgaa cctatgtcta gctcggtttc ccgaaattca attgtttggt 1020 gtggtgatca aattggacca ccacttgttt gcgtgattga cgacaatccg atcgttggat 1080 cgtcgtacaa ttttgtgagc accctagtta tcagttgttg gaccttagga acttactagt 1140 gaaaatctag tggttggatc ttacggagca agtgatgtaa gatcatggac catacctttg 1200 atcgacggtt tgattctcat taaatgtcgt tgtgggagac ttatgagagt tttgggcatg 1260 tgaatttatc gagagaaatc taaatgtgga cttgtgcttt gtttttggcg gtgatagagc 1320 ttgatgcctt gaattccatg ctagagtgcg ttagtgtgga cctcaggtga gtgactttaa 1380 tatatgtgat attggtgatt accctatttt cgtaattgtt atcctatgtg gatatgactt 1440 ggttttataa atatgttttc tattgaattg ttatttttaa tgcttagcca ttgatttaag 1500 tttatgaaat gagatttgac atgtatatat tgaaatatgg tttgattggt ttgattggca 1560 tgttgtgatg aaatgtgagg actagtggta gaccgttaac ccgtggtgat ggggatttgt 1620 tgcttcgata tggtttcatc tcccgcttcg ttgattcgtt ctaaatttag tatttgtgcc 1680 ttatttccct tggttgagct tttgtaaatt aagtaacttg tgcttgtctc atttctttga 1740 gccgttgtat atatggttgt tggccttccg cgattccgtt gagtgatggt ccggaatcgt 1800 atccactcgg attccgttga gagatggtcc ggaatccttc ctactccgat tccgttgagt 1860 gatggtgtga tttgagatgg tcgaatcgcg attccgttga gtgatggtcc gggatcgtat 1920 ccacctcggg tttcattgag tttggattga gatagcttca aagatgtagg cttcggccga 1980 actgcgtccc tctagcccta gtttttaatg tacatatgaa cgatggattt tgagaatctt 2040 gtgctttgaa ttagaaaagt cgttggatgt ctaggtgact ccttcgaagt tgtcagtgac 2100 ttgattatga tttcataaag catgattcta tacttgatgt ttatagattg tgatcgatgc 2160 actaatttta catgcaagaa accgattgat aattttggtt ccgttaagtg atccggaacc 2220 cgatgtggtt ggattccgtt gagtggtcgg aatcgtatcc tgatttggat tccgttgagt 2280 ggtccggaat ccctactctt gctcatttcc ataagattag acttgtaccc tggattcgag 2340 tgaatgggaa ttacccacaa tagatcttgt gaatataaat tagaattatc aagttattac 2400 ttgaaatcca ggcagggaat tatatagaag tcctttaatt aattttgtgc attgagatgt 2460 gatctgattg actgattaac ataattaaat gttaatatcg tgcctctttg atatcatgga 2520 atgggttact tgagatgatt gtggaaggat gttgaatatg attgttatta awacgattag 2580 attagttgat caatgcgact agaggataat attgtgcttt attgattctt tgatatgtta 2640 catgatatga atwgcgatwt tatgttgaaa cataatgatk tatatgatgg atgaaataga 2700 aaccttgatt gtcatgtcgg gttgttatgt agctttgaat cgaataattc atgctcgtca 2760 agttcaaatg tttgattgag gaatgttatg cattttggct tgaacakact gtgttatatg 2820 tcgagttata gtgaatgttg aactacgaat ggcttgatcc ctattgaggg tacgtaggca 2880 gtctaacgag gaggttagat gcagccataa agtatacgga aaattattac gcaattggat 2940 cttgagttgt gctttgtcat atccggaggc ggggtatgtt agatatacgg gtatttggtg 3000 acgtcacgtg tcgatcctgg acgtatgttg ggatcggggc gtgaca 3046 // ID Gypsy-34_Mad-I repbase; DNA; EDCOT; 8476 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-34_Mad-I. XX NM Gypsy-34_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-8476 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1762-1762 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 145..1554 FT /product="Gypsy-34_Mad-I_1p" FT /translation="MVQTRSGTAQIAQFDPEPERTLHRQRRENNLVWDCXL FT QGTFLQELFAGFVDSKITMALQLPAAGRPLRESLAARANDVPNCIVYPAQE FT DGDSFEIKHHMLEILPTFRGLPNEDANLHVAKFIVGCKNILIRGFSAEAIK FT LRLFPFTLKDKAETWLFTLPANSITTWQQLHTRFLNKYYPASKTLNYKREI FT MTFTQKPNEEFHEAWERYTEMYIKCPHANIDPDTQMNIFFDGLNPTSKSHV FT NASAGGSLSNKSAREAFELFDTMATESQQWAAEHSQKRGIFELSAGSPNMS FT AQMEKMEKKIDAKFDIILQQIANSTQQQPPAATVCTICSMATHDILGCPHK FT ESYPELVEQHVNMMNSYQRPRNDAYATHYNPGWRDHPNFKWGDNQNNAKPF FT QHAQKPFVPSKPSLEDQLAKLAATTQTFMEGSNQRIQNVEASIKSLEQQFG FT QLAAQISDREKGKFPSQTVPNPRGT" FT CDS join(2255..4573,4230..5567) FT /product="Gypsy-34_Mad-I_2p" FT /translation="MDEDLKTPIILGRPFMATARTLIDVEAGTLTLRVQDQ FT SVVFNLFEATKRPAEQQECMRIDVLDSMVQGSFYASSNTDQLLHVLQGEIG FT TDSEDEGVLEYIHALDSLPTQLPRFRNVYESLGEPKQPLKPSRQQPPKLEL FT KPLPEHLKYAHLGAAETLPVIVAADLTPTEEDKLLRVLRKYQDALGWTIAD FT IKGISPAICMHRILMEDDVKPTVDAQRRLNPIMKEVVRTEVMKLLDAGMIY FT PISDSKWVSPTQVVPKRTGXTVVKNDNNELIPTRLTTGWRMCVDYRKPNAG FT TRKDHFPLPFTDQMLERLAGRAFYCFLDGYSGYNQIPIAPEDQEKTTFTCP FT FGTFAYRRMPFGLCNAPATFQRCMMSIFSGLVERIVEVFMDDFSVFGDSFD FT QCLHNLSLVLERCQETNLVLNWEKCHFMVKQGIVLGHSISSKGIEVDKAKI FT DVIAKLPPPTSVKGVRSFLGHAGFYRRFIKDFSKISRPLCNLLAKDAPFNF FT DEACLEAFNKLKSLLTSAPIIAAPDWGLPFELMCDASDYAVGAVLGQRKDK FT LPHVIYYASRTLNDAQLNYATTEKELLAVVFALEKFRSYLVGAKIIVYTDH FT AALKYLLSKKDAKPRLIRWVLLLQEFDLEIKDKKGSENVVADHLSRLIIPA FT AKEADSLPLSESFPDEQLFAAQINTPWFADLVNYLATGVVHPDFSFQQKKK FT FLSDVKHYFWDEPYLYKYCPDQIIRRCIPEVEQDSVLRFAHQYACGGHFGQ FT KRTAEKILQSGLFWPTLFKDAKVRVFQMSSSLLPKLIHPGLLILLIIWLRV FT LCIPIFHFSRKRSFCLMSSIISGMNHTYISIVPTRLFAGAFLRLNKTVFCV FT LLISMHVGDILDRKGQQRKFCKVGCFGLHYLKMQNNWCRACDRCQRVGNQS FT KRNEMPQQSILIVELFDVWGIDFMGPFPSSHGNQYILVAVEYVSKWVEAIA FT TPTNQGSVVLKFLQGVIFPRFGIPRVILSDGGKHFINKQFDALLAKYGITH FT RVATPYHPQTSGQVEVSNRELKRILEKTVGSTRKDWSLKLNDALWAYRTAF FT KTPIGMSPFRLVYGKACHLPMELEHKAFWAIKELNFAYDSAGEKRKLELNE FT LYEIRNDAYESSKIYKDKTKAFHDSKILRREFYTGQKVLFFNSRLKLFPGK FT LKSRWTGPYVVTKVYSHGAVEIKNEVTGHEFKVNGHRLKPYLESPYDTARE FT SLTLRDPVT" XX SQ Sequence 8476 BP; 2469 A; 1528 C; 1839 G; 2623 T; 17 other; agaaattggc gccgctgccg gggactattt tagataattt ttgtttaaac tttttctgat 60 tatttttttt tatattattt ttcgtcaaaa aaaaaaatca atttatttta acgcttttgt 120 kttattgcag attctgtaaa ctgcatggtc cagaccagat caggaactgc ccagattgca 180 cagtttgatc cagaacccga acgcacactg catagacaga ggagagaaaa taatttggtt 240 tgggactgtk cactgcaagg cacatttctg caggaattgt ttgctggttt tgtggacagt 300 aaaatcacaa tggcgttgca attgcctgca gcaggcaggc cactcagaga gtcattggct 360 gcccgagcca atgatgttcc taattgtatt gtgtatcctg cccaggaaga tggcgattca 420 tttgagatca agcaccatat gcttgaaatt ttacctactt ttcgtgggct gcctaacgag 480 gatgcgaact tacatgttgc aaaattcatc gtgggttgca aaaatatttt gatcaggggt 540 ttttctgccg aggctattaa gttacgtctt tttcctttta ctttgaagga taaggcagaa 600 acttggttat tcactctacc agctaatagc attactactt ggcaacaatt gcatacaaga 660 ttcctgaaca aatattatcc ggcatccaag acattgaatt acaagcggga gattatgaca 720 ttcactcaaa agccaaacga agaatttcat gaagcgtggg agagatatac agagatgtat 780 ataaagtgtc cacatgctaa tattgatcca gatacacaaa tgaatatttt ctttgatggg 840 cttaatccta catccaaaag ccatgttaat gcatcagctg ggggttcatt gtcaaataaa 900 tctgcaagag aagcatttga attatttgat acgatggcta cagaatctca acaatgggca 960 gcagaacatt cacagaaaag gggcattttt gagttatcag caggttctcc taatatgtct 1020 gcacaaatgg aaaaaatgga gaagaaaatt gatgcaaagt ttgacattat tctacaacag 1080 atagcaaatt ctacacagca gcagccacct gcagcaacag tttgcactat ctgcagcatg 1140 gctacacacg acatattggg ctgtccacat aaagaatctt acccagagct tgtggagcaa 1200 catgttaata tgatgaacag ctatcaaagg cctaggaatg atgcatatgc aactcattac 1260 aatccaggat ggagggatca tcctaatttc aaatggggtg acaatcagaa taatgcaaaa 1320 ccattccagc atgcacaaaa accttttgtg ccatccaaac catccttgga agatcaactt 1380 gctaaactgg cagcaacaac acaaacattc atggaaggca gcaatcaaag aattcaaaat 1440 gttgaagcat caattaaaag tttggagcaa caatttgggc agctagctgc acagatttca 1500 gacagagaaa aaggcaaatt tcctagtcaa acagtgccta atccaagagg tacatgaaga 1560 ctgcaatgct gtwcggactt tacggtgtgg aaaaagttat gacaaccgtg maaattgtac 1620 tgaacagaat ctgcctgcag tgccaattct gcagaatctg aaaaaacagc agcagaacct 1680 gccaawtctg cagcaaaaca gaatctgaca gtgcagaaac tgtcccaaaa cagatttctg 1740 agcgtgttta tgaccctcca ctgcctaccc tgaacgttta attcctaagg caagagatca 1800 gcagctcaaa gatttcatgc agacattgtc caaggttcaa atcaacattc cattgctgga 1860 tgcaatcaag aaaattccat cttatgccaa atttttgaaa gaggtttgca gtagsaaaaa 1920 gaagcttgcg gattcggasa aagttgtkct gacagaacag tgcagtgcag ttttgctaca 1980 caaactgcca cccaaagaag aaagatccag ggagttttam tatttcttgt actattggaa 2040 attctgattt taaaagtgct ttaattgatt taggtgctag tgtwaactta atgccttwtt 2100 ctgttttcaa acgtttgggw caaggagagt taaagcctac atcaagtatt cttcaactgg 2160 ctgaccgttc aatcacttat cctagagggt cattgaagat gttattgtta aggttgacaa 2220 tctttattta ccggcggatt ttgtggtttt agacatggat gaagacctga aaacacccat 2280 cattttgggg aggccgttca tggcaacagc taggactcta attgatgtgg aagctggaac 2340 actaacttta cgagttcaag atcaatctgt tgtatttaat ttgtttgagg caaccaaacg 2400 tcctgctgaa cagcaagaat gtatgcgcat tgatgtgtta gacagtatgg ttcaaggtag 2460 tttttatgcc agttcaaata cagatcagtt gctgcacgtt ttacaagggg aaattgggac 2520 agattctgaa gatgaaggtg ttcttgagta cattcacgca ttggacagtc tgcccacaca 2580 gttgccaagg tttagaaatg tttacgagag cttaggggag ccaaaacagc cccttaagcc 2640 gtccagacag cagccaccaa aattggagct gaagccctta ccagaacatt taaaatatgc 2700 acatttaggg gctgcagaaa cgctgccagt tatagttgca gctgatttaa ctcccacaga 2760 ggaagataaa ttgcttcgtg ttttgaggaa atatcaagat gcactaggat ggacaattgc 2820 cgacatcaag ggtattagcc cagcaatctg tatgcacaga attttaatgg aagacgacgt 2880 gaagccaaca gttgatgctc aacgccgcct taacccaatt atgaaagagg tggtcagaac 2940 agaggttatg aaattacttg atgcaggtat gatttatcct atttcagaca gtaaatgggt 3000 gagtcctacg caggttgttc ctaaacgtac tggcatkaca gtagttaaaa atgacaacaa 3060 tgagcttatt cctacgcgct taactacagg ctggcgtatg tgtgtggatt ataggaagcc 3120 aaatgcaggt acamgaaaag accattttcc tctaccgttt actgaccaaa tgttagaaag 3180 attggctggc agggcttttt attgtttctt ggatggctat tctgggtaca atcagatccc 3240 aattgcacca gaggatcaag agaagacaac atttacatgc ccatttggga catttgccta 3300 tcggaggatg ccatttgggt tatgcaatgc acccgccact tttcagcgtt gtatgatgag 3360 tatcttttct ggcttggttg aaagaattgt ggaagttttt atggatgatt tttctgtgtt 3420 tggagattca tttgatcagt gcctacataa tttgtcatta gttcttgaga gatgtcaaga 3480 aacaaattta gtgctgaatt gggaaaagtg tcattttatg gtgaaacagg gaattgtttt 3540 gggtcattca atttctagca aaggcattga agttgacaaa gctaaaattg atgtgattgc 3600 aaagttgcca ccccctacat cagtaaaagg tgttagatcg tttttgggac atgcaggatt 3660 ttatcgtcgg ttcatcaagg atttctccaa gatcagccga cctttgtgca atttattggc 3720 taaagatgca ccatttaatt tcgatgaggc ttgcttagaa gcgttcaaca agttgaaatc 3780 actcctaact tcggcaccca tcattgctgc accagattgg ggtttaccat ttgaattaat 3840 gtgtgatgct tcagattatg ctgttggggc agttttagga cagcggaaag acaagcttcc 3900 ccatgtcatt tattatgcaa gtcgtacact caatgatgca cagctcaact atgctaccac 3960 agagaaagaa ttgttggcag ttgtgtttgc cttagagaag tttcggtctt atttggttgg 4020 ggctaagata attgtttata ctgatcatgc tgcattaaaa tacttgttgt ctaagaagga 4080 tgcaaagcct aggttgattc gttgggttct tttacttcaa gaatttgacc tagagattaa 4140 agacaagaag ggcagtgaaa atgtggtggc tgaccattta tccagattaa ttattccagc 4200 agctaaggag gcagattctc taccattgag tgagagtttt ccagatgagc agctctttgc 4260 tgcccaaatt aatacaccct ggtttgctga tcttgttaat tatttggcta cgggtgttgt 4320 gcatcccgat ttttcatttc agcagaaaaa gaagtttttg tctgatgtca agcattattt 4380 ctgggatgaa ccatacttat ataagtattg tcccgaccag attattcgca ggtgcattcc 4440 tgaggttgaa caagacagtg ttttgcgttt tgctcatcag tatgcatgtg ggggacattt 4500 tggacagaaa aggacagcag agaaaattct gcaaagtggg ttgttttggc ctacattatt 4560 taaagatgca aaataattgg tgcagagctt gtgacaggtg tcaaagagtc ggcaaccaat 4620 ccaagaggaa tgagatgccc cagcaaagta ttctaattgt tgagttattt gatgtttggg 4680 gtattgattt catgggacca ttcccatcat ctcatgggaa tcagtacatt ttagttgctg 4740 tggaatatgt ttctaaatgg gtcgaggcca ttgcaacacc aactaatcaa ggatcagtgg 4800 tactgaaatt cctccagggg gttatatttc cacgttttgg aattccacgt gtgattctta 4860 gtgatggggg gaagcatttt attaataaac agtttgatgc tttattagca aagtatggga 4920 ttactcatcg cgtggctaca ccctatcatc cacagacatc tggtcaagtg gaagtttcaa 4980 acagagaatt aaagcggatt ttggagaaaa cagttggctc tacacgtaag gattggagtt 5040 taaaattaaa tgacgcgctg tgggcttaca ggacagcttt taaaacccca attgggatgt 5100 cgccatttag acttgtgtat gggaaagcat gtcatttacc tatggaacta gagcacaagg 5160 cgttttgggc cattaaggag ctaaattttg catatgattc agctggggag aagcgtaagt 5220 tggagctcaa tgagctctat gagattcgta atgatgcata tgaaagttca aaaatctaca 5280 aagacaagac taaggcattt catgacagta aaatccttcg cagggaattt tacacagggc 5340 aaaaggtgtt gtttttcaat tccagattaa agttgtttcc aggcaaactt aagtcacgtt 5400 ggacagggcc atatgtggtc actaaagttt attcgcatgg ggctgtggag ataaaaaatg 5460 aggtcacagg tcatgaattc aaggtcaatg gtcacaggct caaaccatac ttggaatcac 5520 cctatgacac agcacgcgag tcattaactc tgagggatcc agtgacttag ccaccagatt 5580 tctgcaacgt ctagctacag actttaaata aagcgcttat tgggaggcaa cccaactttc 5640 taactttttc tttactttgt ttcatttttc tttcattact ttcaatttct agctgcattt 5700 aaattcctag gctgcatttc atgttcttaa aaaaaaaata ataaaattaa aaaaaaaata 5760 aaacaaacaa aacaaaaaaa aaaaacaaaa caaaacaaaa cattctttgc ttttacttgt 5820 tttattttac cgatagtatc ttctacattt ttatctctga tttcaacacc tgatttttat 5880 gcagccagca aacaagacaa acaaaactta atgcacagag agatcatttt agacggaatc 5940 atgcatccag tagcagatct gtcatacaca agcagggatg tgatgttata cctctctatt 6000 ttgctaagcg gccattcttc agtgtaagct aatggttttg tcatcacgtt tcctttgccg 6060 atctggggta ttttccctgc aacagaacaa tcaagtgtat gagttccagt ggaaacaggt 6120 gtatcaattt gggggtcatc attggtggag aacaaaattt ttacctctgc atgcctcagg 6180 tccgaaatgt cgtctctgtt gccgtgtcct tgctcctgtc cagcatccag ctcaagcacc 6240 tttgcacacc aacgagacac atagcttata catttgcatg gtggagttat aggcgacatg 6300 gaagtcacca cactacgata gttggtgtga agatgtgtac ctctgtggga tgattggagc 6360 tgcactgtgc atcatttcta tggcagacac taactggttt cggattttgc tgacaatccg 6420 aatgcgtggt gtacatcggc tcagatctgc aagtttggag gacttcctac ggataaacac 6480 acatgcatgt gttagatctt gtttcctttc acccaaatac atcaagctga cacggaagta 6540 acacaaattg aggaggattt ttaccttcag catcttcact tttcagctca ctctaccacg 6600 gctcgggact cacagaggtt tgtttgttgc ggttctggaa ggctacggag acagctcttc 6660 gagaggatgc aagagctgct gtgacatgga ggtttgactt actggttggg ttgcgagttt 6720 tgaacatggc aagagctccg tgagtctctt cggattttct agagagagaa gacggaaatt 6780 tttttctttt cattttggag agaaatgggt tctgaacttc tgagagataa gagagaggga 6840 tctgttatgg aggtgcagct tgcgagaaat aatgcggtct aggggttcta aatgccatct 6900 gacataacaa tgggtgactg taacacattt cagcgtctct attggaatcc taaggagttt 6960 attacacgga tgtatgacac gtgttttcat cgtgtggccc tgtgtctctg tccgagaggg 7020 ttattttgaa ctgggaaaat acagtgccgt ttggctctcg atttggtaaa aagaaaagag 7080 ccgtttgggc tcatttactg acaakgactg tgaggactgc tcgtgacttt tcttcttcag 7140 acatgggaac tagcataatc ccactttcca atgcacatgc cagctgcatg ccattccaat 7200 ttcaaatcgg catccaatgt tcctttcggc ttctttggtt tgtgggctgg gttataatcc 7260 aaagggtcat cacgaggcta tgtgcatcat tttgtcacgg cccaatgttt sttatgtcag 7320 gtgatttttt attttttatt ttttactttt cctttttgtt attttttttg ttctcttatt 7380 tatttcattt tttttaattt ctttgtttca tttctatttc cctttttctt ttagttcttt 7440 ggtctagact tttgttttta tcttttctag ttttgctttt tgttttttta gtttatattt 7500 attttccaca ccttgaggac aaagtgtgaa ataagtttgg gggtgggaaa gtagtaaaaa 7560 tttagggttt ttatttttgt gtcagttaaa ttttttcgtt tttaagctaa tatccataga 7620 ttattttaaa cgttagaaca aatggacatg gtaaagatta atcccacagt agagtctttt 7680 ctatttatcg ttacttagac accaattcac gaattatact ttgacaattg cacatcacac 7740 caacatggtt tgtggggagt gagattgaaa cacttgcttt ttgtccaagt gtatttttat 7800 ttttgttcta aataaagtaa agttagtatg tgttataaag taataattgt ctcacccgag 7860 gttctgccta gtaaccgggc cagtcctgcc taatcagcag tgattctcgc gtcaaacggt 7920 agagttttgg catgaggcag ggtggttagt tggtttcgta gccttttcag ctcgggttaa 7980 taagtcctta ggggtgttct acacctagtg ccctaaagcc ctagtggttt gggagtcatt 8040 gacctaaagc tcgctacatg ggttggatmg aaagcttaag tgaaccgaca ttgcacgacc 8100 actactgtta cttcaaaaaa aaaaaaaaaa aaaaaaaaaa aaaatctatg tgaagttagt 8160 gtgtgaagta tgaataaagg gatgagaggt aagagttttg gtcgagtctc tttaactatg 8220 ttggttcact ttacaccaaa ggaagtttgt gaattctttt ctaattgatt ctaaatggct 8280 tagactctgt ggtgggattg gttggaactt ttgaaaagat gttctgattt ttaacatttt 8340 ctatggattg caacttgaaa gtgagaattt tgttttagct aagttttagt taagtgtcca 8400 gtttgttagt ttttattttt gttttctagt tttattttgc ttgaggacaa gcaaaaagct 8460 aagtttgggg gtattt 8476 // ID Helitron-3_Mad repbase; DNA; EDCOT; 6510 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Helitron family DNA transposons from the apple genome. XX KW Helitron; DNA transposon; Transposable Element; Helitron-3_Mad. XX NM Helitron-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6510 RA Kojima K.K. and Jurka J.; RT "Helitrons from the apple genome."; RL Repbase Reports 10(10), 1644-1644 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC 5 sequences are >95% identical to consensus. This consensus can CC be incomplete. XX FH Key Location/Qualifiers FT CDS join(1294..2736,3066..4847,4798..5511) FT /product="Helitron-3_Mad_1p" FT /translation="KLTLVRYFGDDCVIFLFIGVDPDYVDFGPRNSQCQYC FT GALFWSTERLKTNVSSIRRPQFTACCMSQKVKFPPVKPTPAYLEHLLNSTN FT SQESSHFKTNVRLYNSMMAFTSMGAKVDASINKGQGPYVFKINGQVHHLMG FT SLLPPEGESPKFAQLYIYDTQNEINNRMSCFPHSEESSKVDEQIVSGLIKM FT LDECNELVQLFRVARDRINEQSTSSLRLRLHGTPSNHDAQYNLPTCDGIGG FT LIVGDIGQFHTERDIIVEHRATGLQRITKLHPKYMALQYPLLFPYGEDGYS FT KGLPWNPDFRGKKPKTGGVSMRAFVGYQIQDRPGQDSTLLKGGRLFQQYLV FT DAYATLEEDRLDFIRTNQNSLRTERLKGIHEALRKGNASGSDIGKRIILPT FT SFTGSARYMINNYQDAMAICRHLGNLDLFITFTCNAKWPEIIEDLRERPGC FT RVEDRPDIVSRIFKAKLDHMVKYIKSGKPFGKVESGKKKKCLKRFPKHFSN FT ETTFESDGFVKYKRREMENRFVVKNGVKLNNAFVVPYNRELLLKYQAHINV FT ESCCQSMLIKYLFKYITKGVDRARAVFEDQEFDEIVAYLNCRYLCPYEAVW FT RLLQFHIHFREPAVQRLCVHLPSDQNVVFQEDDNLNYVVNQPNLESTMLTK FT WFEMNAQDPDACQLSYVEFPSKYVWNSENKEWTRRKSGRCLGRVAYVHPAA FT GELYYLRLLLNYQKGGFCFDDLRTIKGVLQPTFQAACNSLGLLGDDKEWNN FT AMLEAVVTASSYQLRQLFVTLVLFCDVADPTTLFEAHWKMMCDDILTKMVN FT AFGLQDMSKYEDELRNSLLYELEKLFVVSNSSLSKHHLPVPNKDLMDRLKN FT RSLREELNYDTESLKEQHSLLMAQLNQEQKIVYDSVIEVVDGNKPGLFFVH FT GHGGTGKTFLWTTIIAKIRSENRIVLAVASSGIASLLLPGGRTAHSRFKIP FT ISITDCSLCEIKKGTHLAQLISNAALIVWDEAPMNHKQCFETLDRSLRDVL FT KGSKPGFDDLPFGGKPILFGGDFRQILPVVPNGTRADIVEASLTXSYLWXY FT LTVFFSQRKHEAFKNWFELFFFLKENMRLSKTGLNEQEKQELADFANWILQ FT IGNGNVANSILSTDEESSWVEISKDFLINFDDDPIENMVSAVYTDFETNFH FT DVSYLKERAIVTPRNNTVTEINDFMLTMVPGEGRTYLSFDSVSSSTENVEN FT LDILYPLEFLNQLDLPGLPHHKLALKVXMPVMLLRNLNQSCGLCNGTRLVV FT MQLTDRIVEAKIITXSNIGDKFTFQESLLSHQKINIRLLCGEDNFLXEFVM FT Q" XX SQ Sequence 6510 BP; 1910 A; 1014 C; 1264 G; 2312 T; 10 other; aacaccctta tcggtttaat aattaagtgt tattactact cattttcaca cctttttagc 60 tttgattaat tcatttctgc ctttgacaaa aaaaaaaata tatcatttct accttaatgc 120 aatttttccc tgattttgtg atttgacaga attgatgttc atattccatt tactatatca 180 caaaaataat cacattattc agtggtgatt catgttttgc ttctgcttcg atttaccttg 240 atttttttgt tatttatgtt tattgactgg twaatccatt gtttagctag gattgttctt 300 ctcttttttt attccgttgt gttgtgtatg tgcttacatw tttagccttt tttggttggt 360 tattttttta ttatccaggt tttcgcaatt aattgcttac gcttgccagt gattcctttt 420 gcaactgaaa ctggttagct ttctcgattt ttacatatga attggtttta aaattaaact 480 ttaatctcat ttactttctt tattttattt tagaggatta aaaaagtagt tagttttggt 540 aaatgtggat gaatgtttta ggtcttaaca tagtttacat gtggtttctt tgattttgtt 600 attttatgcc taaaaacttg agaatgtttg acaagaccgg taatattaag tggtttttat 660 tgctggtgtt gacctaattt aattaggtga tttaattagg attttgtttt tgtggttata 720 ttttggatgt atttgtgttt ttaatagtgc cttctttacg tgtggcgatt tgattagtga 780 gtaaggctta gtcattcgca tgttcttttt gtttttattt gcgtagtatt atgcctagga 840 aagtcagaat atctggaggg cagctaaaat tcaacacgcc agcttaggcg tttttaatgg 900 cgatgtttat ccggatgatg tgattttgca agatgtccca acttcttatg atcaagaata 960 taacaacgtt tcacactctt tactgtttca taacaataca accaatcatg tccaacccaa 1020 tacatctgtt ttgaaacaaa atgcatttat tgccaatgga ttcaactcat cttcgtccgc 1080 tgctagcact tcacatgaaa ttaccgtccc tgttttcctt gccaatgatg ccactttgcg 1140 tggtatattg atctctgata ctcaagacga tcatcctgtt agaagctcac atgtgattgg 1200 ccaggccgct tatcaaaaaa aaagaaaacg tatgcgctct gacaatatag tcctctttgc 1260 atcctctttg catttttttt aaacttattt taaaagttaa ctttggttcg ctactttggg 1320 gatgattgtg tcatctttct tttcataggt gttgatccag actatgttga ttttggccct 1380 agaaattctc aatgtcaata ttgtggcgct ttgttttggt ctacagagcg gttaaaaaca 1440 aacgtttctt ctattagaag gccacagttc actgcatgct gtatgagtca aaaagttaaa 1500 ttcccacctg ttaagcccac tcctgcttat ttggaacatc tgctaaattc aacaaattct 1560 caagaaagtt cgcatttcaa aacaaatgtt aggttgtata attcaatgat ggcattcact 1620 tcaatggggg ctaaagttga tgcatcgata aacaagggtc aaggtcctta cgtttttaag 1680 attaatggtc aagtgcatca tttaatgggt tctttgttgc ctcctgaagg cgagagccct 1740 aaatttgcgc agctctacat ttatgacact caaaatgaaa tcaacaatcg tatgagttgt 1800 tttcctcatt cagaagaatc ttcgaaggtt gacgaacaaa ttgttagtgg gctcattaaa 1860 atgttagatg agtgtaatga gttggttcag ttatttagag tcgcaaggga taggattaat 1920 gaacagtcaa caagttcttt gcgcttgcgt ttacacggca caccgagcaa ccatgatgcg 1980 caatataatc tgccaacatg tgatgggata ggagggttaa tagttgggga tatcggtcaa 2040 tttcataccg aaagagatat tattgtwgaa cacagggcaa ctggtctgca aaggataaca 2100 aagttgcatc caaaatatat ggcccttcaa tatcctcttc ttttcccata tggtgaagat 2160 ggatacagta aaggtctccc ttggaatcca gatttcagag ggaaaaaacc caagactggc 2220 ggagtgtcta tgagagcatt tgtgggttac caaattcagg atagaccagg acaggatagc 2280 accctgttaa agggtggcag attatttcaa caatatttag tagatgcata tgccacactt 2340 gaagaagata gacttgattt cattaggaca aatcaaaatt ccttgagaac tgagcgtctt 2400 aagggaattc atgaggcgtt gagaaaagga aatgcaagtg gttccgacat tggtaagagg 2460 attatcttgc caacttcatt tactggcagt gctagataca tgataaataa ttatcaggat 2520 gctatggcta tatgccgtca cttaggaaat cttgatttat ttatcacctt tacatgcaat 2580 gctaagtggc ctgaaattat cgaagatcta cgtgaaagac ctggttgtag ggttgaagac 2640 agaccagaca tcgtatccag aattttcaaa gcaaaacttg accatatggt taagtatata 2700 aaatcaggaa aaccttttgg caaagttgaa tctggttagt tattgtcttt tctcaattct 2760 caagattatt tgtttgtttt ctcttctaag cataaacatc aggcgttctg ttttgatttt 2820 tttttatctt atatttctca aaacagtgat ttacacagtt gaatttcaaa aaagaggtct 2880 cccgcattgc cacatcttgg tttgggtcag taaagagtat aagtgtcatt ctccttctga 2940 tgtggattca atcatttcgg ctgaaattcc taaccaagaa tttgacaaag atgggtatga 3000 tgttgttgca ctgtacatga ttcatggtcc atgcggtctt gcaaatgaaa aatccccttg 3060 catgaaagaa aaaaaaatgt ttaaagagat tcccaaaaca tttttcaaat gaaactactt 3120 ttgaatctga tggttttgtg aaatacaagc gtagagaaat ggaaaatcgt tttgttgtaa 3180 aaaatggagt gaagcttaat aatgcgtttg ttgttcctta caatcgtgaa ttgttattaa 3240 agtatcaagc acatataaat gttgaatcgt gttgtcaatc aatgcttatt aaataccttt 3300 tcaagtatat aaccaagggt gttgataggg ccagagctgt ttttgaggat caagagtttg 3360 atgaaattgt ggcttatcta aattgcagat atttatgccc ttatgaagca gtttggagat 3420 tgttacaatt tcatattcac tttagagaac cagctgttca aagattgtgt gtccatcttc 3480 cttctgacca aaatgttgtc tttcaagagg atgataattt aaactatgtt gttaatcaac 3540 ctaatcttga aagcacaatg ttaacaaaat ggtttgaaat gaatgctcaa gatcctgatg 3600 catgccagtt atcttatgtt gaatttcctt cgaaatatgt ttggaatagt gaaaataaag 3660 agtggactcg aaggaaaagt ggtagatgtc taggtagagt tgcgtatgtt caccctgctg 3720 ctggtgaatt atactatttg agattattgc ttaattatca aaaaggtggc ttttgttttg 3780 atgatttaag aacaattaaa ggtgttcttc aacccacatt tcaagctgca tgcaactcgc 3840 taggtctgtt aggagatgat aaggagtgga acaacgcaat gttagaagcg gtggtcactg 3900 catcatcgta tcaattgcga cagttgtttg ttacattagt tttgttttgt gatgttgctg 3960 atccgacaac tttgtttgag gcacattgga aaatgatgtg tgatgacatc ttgacaaaga 4020 tggttaatgc ttttggcttg caggatatgt ctaagtatga ggatgaactt agaaattctc 4080 ttttgtatga gttagaaaag ttgtttgtag tttcaaatag ttctctgtct aaacatcacc 4140 tcccagttcc aaacaaagat ttgatggata gacttaagaa tagaagttta agagaggagt 4200 taaactatga cactgaatca ctgaaagaac aacattcact attgatggca cagttgaatc 4260 aagagcaaaa aatagtttat gatagtgtta tagaggttgt tgatggcaac aagcctggtc 4320 tattttttgt tcatggacat ggtggaactg gtaagacttt tttgtggacc actatcatag 4380 ctaagattag atcagagaac cgtattgttt tggctgttgc ttcgtctgga attgcctccc 4440 ttttgcttcc tggtggaaga actgcacact ctcgatttaa aatccctatc agcattacgg 4500 attgttcact ttgtgaaata aaaaaaggaa ctcatctagc acaattaatt agtaatgcag 4560 ctcttattgt ttgggatgaa gcaccaatga atcataaaca atgttttgaa actttagata 4620 gatctcttcg tgatgttctt aaagggtcta aaccaggttt tgatgatttg ccatttggag 4680 gaaagccaat tctctttgga ggtgatttta gacaaatctt gcctgttgtt ccaaatggaa 4740 ctagggctga cattgttgaa gcttcattga caasttctta tctttggsct tatctaactg 4800 tttttttttc tcaaagaaaa catgaggctt tcaaaaactg gtttgaatga gcaggaaaaa 4860 caagagttag ctgattttgc aaattggata ttacaaattg gaaacggtaa tgttgctaat 4920 tctatattgt caactgatga agaaagttct tgggttgaaa tttcaaaaga ctttcttatt 4980 aattttgatg atgatcccat cgaaaatatg gtttcagcgg tgtacacaga ttttgaaaca 5040 aattttcatg atgtatcata tttgaaagaa agagccattg tcacaccgcg aaacaacacg 5100 gtaactgaga taaatgattt tatgttgact atggtgcctg gcgaaggtcg cacgtacctc 5160 agttttgatt ctgtgtcttc ttcgacagaa aatgttgaaa atcttgatat actttatccg 5220 ctagaatttt tgaaccaact tgacttacct ggtttgccgc accacaagct ggcattgaaa 5280 gttkgtatgc cagtaatgtt gcttaggaat ttaaatcaaa gttgtggatt gtgtaatggg 5340 acaaggttgg tggtgatgca gttaactgat agaattgtgg aagcaaagat cataacggkt 5400 agcaacattg gtgacaagtt tacattccaa gaatcattac tgagtcatca gaaaataaat 5460 atccgtttac tttgcggcga agacaatttc ctcwtagaat ttgttatgca atgacagtta 5520 ataagagtca aggacaatmt ttgaagattg ttgggttatt tctatctcaa acagtttttt 5580 ctcatggaca gctctacgtt gcattgtcta gggtcacctc aaaacagggt cttaaaattg 5640 tgattgctca tgatagtgat atgccttatg gatacacwaa aaacattgtt tataaagatg 5700 ttttgaattg tttacatgaa ggtgtgttga tttgtgtttg tccattcatt tttttttctc 5760 tttttgtcta tttttcaaaa ttctaatgta ttctttgttt catgtgtgtt gcacgatttt 5820 gaggatttta tttgcttcta aatttacttt atatagattg atggagcata tgccagttcg 5880 tcttttgtta ccatacaagc caacaaggaa actacaaatt aggatatgca gaatttgggt 5940 gacaaaaaat attggagctg atcgtcaacc tgcaagtttg gactgtgtct ttgttgacaa 6000 agaggttaca tctttacacc tttttctcat tattaaatag acacagtttt atatttgtcg 6060 aaatgcatct atcatacttt cagtattaat tcgatttttc cttctcattg attaacattc 6120 catctttttt gtgttcaatt gtggtttgta gaaatttctg aagtaaaata ttcattaaat 6180 gttctgtgaa ataggcattt ttcaataggg tagttgtgct gttggttttt tgatgatgtg 6240 cctaatgttt attttggatt gaatttcaac ttctacatag atttatgatt agtaaactct 6300 catggcagtt tggaaatgat aatttgttca cgagcttatt tactacttta atgattaatt 6360 taattttgtt tttcctctct aaaagggaca tgcaattcag gcgaccatga aaccctggga 6420 catccaattc tttttggacc gtctaaaagt tgggttcgtg tacgagatag ataaatttcg 6480 tcttatcaat aacagaacgt caaacaaaat 6510 // ID SHELI_MT repbase; DNA; EDCOT; 756 BP. XX AC . XX DT 29-NOV-2006 (Rel. 11.11, Created) DT 29-NOV-2006 (Rel. 11.11, Last updated, Version 1) XX DE Putative non-autonomous DNA transposon from Medicago truncatula. XX KW DNA transposon; Transposable Element; Nonautonomous; KW non-autonomous; Inverted repeats; Interspersed element; TSD; KW repeat; SHELI_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-756 RA Shankar R. and Jurka J.; RT "SHELI_MT: A putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 604-604 (2006). XX DR [1] (Consensus) XX CC The sequence is very well conserved and flanked by poorly CC conserved 8 bp TSDs (ATATACATA). XX SQ Sequence 756 BP; 275 A; 121 C; 138 G; 222 T; 0 other; gaagattgct ttttaggccc ccccaatatc tctttaggcc ccctaaaaat acaaaaataa 60 cctttataat acatccggta gttacatacc ggtagtgcat tttaaatttt cacattttac 120 accttcggta tgtacatacc agaggcacat ttacaaattt tcgcgtttat cgcattatgt 180 tatttaaatg tacatgttct gctatgttgg aaaattcaca aacttttggt agggtgcata 240 aaatttacag aaataaaagg atcaaacttt tcattgaata tgacagaact ctaaaaaaat 300 tatgcagaaa caatacgaga gaggaagaag caaggtttac cttctaaatg attgcaattg 360 agtaaagatt gacgccattt gttctattaa ttgtgatgaa aacacaacaa aaattggcca 420 aaaaacgcaa ggtatggaac aatattgaag cttagaaaat aactcttaaa aaactgcacc 480 attttataca gataacaacg tgggtggagt acggtatata tataccggag gtgtaattga 540 gaaatcgcaa aatgaatgtt cctccagaac ataactaccg aatgcgataa acgtgaaaat 600 ttgtaaatgt gcctccggta tgtacatacc gaaggtgtaa aatgtgaaaa tttaaaatgc 660 actaccggta tgtaactacc ggatgtatta taaaggttat ttttgtattt ttagggggcc 720 taaagagata ttgggggggc ctaaaaagca atcttc 756 // ID ENSPM_MT repbase; DNA; EDCOT; 8153 BP. XX AC . XX DT 31-JUL-2005 (Rel. 10.07, Created) DT 25-AUG-2005 (Rel. 10.07, Last updated, Version 2) XX DE M.truncatula ENSPM type DNA transposon - consensus. XX KW EnSpm; DNA transposon; Transposable Element; autonomous; KW ENSPM_MT. XX NM ENSPM_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-8153 RA Gentles A. and Jurka J.; RT "ENSPM-like DNA transposon from Medicago."; RL Repbase Reports 5(7), 172-172 (2005). XX DR [1] (Consensus) XX CC Flanked by 3 bp TSDs; only 3 complete copies in available CC sequence, plus fragments. Complete copies are 95% similar to CC consensus. Encodes tnp2-type transposase. XX FH Key Location/Qualifiers FT CDS join(1877..4516,4524..5435) FT /product="ENSPM_MT_1p" FT /translation="MEYYEYYRRWMYDRTFPGRTGLKPQFVEGVDGFISWA FT WEQEICRDEGGIRCPCLKCRCRHIITDPGDVKKHLKKVGFMPNYWVWTYNG FT EMFQNFGXGVNAQASTSHGGTNVETNVEYNEDVNTXQFNMMDDMVADALGV FT ELSYGEDVEDDEEEQPPNEKAQRFYRLLSESNTPLYEGSSHSKLSMCVWLL FT SHKSNYLNPDDGMDDITKMLKAVTPFKDNLPMNYHAAKRLVMKLGLSVKKI FT DCCRNGCMLFYDNEFGINDGXLEECKFCQSPRYGISKQKRVAVKSMFYLPI FT IPRLQRLFASMKTASQMTWHHSNGIXGVMRHPSDGEAWKHFDRVHPDFAAD FT PRNVRLGLCSDGFQPYVQSSAKPYSCWPIIVTPYNLPPEMCMTKPYLFLSC FT IVPGPDNPKAGIDVFLQPLIDDLKRLWVGELTYDISRKQNFKLRAALMWTI FT NDFPAYGMLSGWSTHGRFACPHCMENTKAFTLESGGKSSWFDCHRPFLPHN FT HPFRRLKNGFKKDERVFVGPPPKITSEEVWTRVCDYPKVTDYGRAVPIPRY FT GVDHHWTKRSIFWDLPYWKDNLLRHNLDVMHIEKNVFDNIFNTVMDVKGKT FT KDNEKARKDLQIYCKRKDLELKPQPNGKLLKPKANYNLSAQEAKLVCQWLK FT DLRMPDGYSSNIGRCADVNTGRLHGMKSHDSHIFMENFIPIAFSSLPKHVL FT DPLIEISQFFKNLCASTLRVDELEKMEKNMPIIICQLEQIFPPGFFDSMEH FT LPVHLAYEAILGGPVQYRWMYPFERFMGDSKRAVKNLAKVEGSIVAIYTAK FT ETTYFIGHYFVDRLLTPSNTRNEVQVNDXRDPSTLSVFNLXGRHAGKVLQY FT WMVDQKEMRSAHVHVLINCAEVKPYLEIYSYPFLLVHTTISFNAVNNFVLN FT LLFFREFIAFYAEFGEGSTVGSIHEYFPAWFKQRVYNAEPTDEVIRLRQLS FT QGPLQCANEFHTYFVNGYKFHTHSWTEGKKTINSGVYVKGVTDGGEDDFYG FT VIKHIYELSYNDNKVVLFYCDWFDPSPRWTKINKLCNTVDIRVDKKYKEYD FT PFIMAHNVRQVYYVPYPPTLPRKRGWSVAIKTKPRGRIETEEXNEEVAYQA FT DDMTHVNEIIEVDQVTSWQDSQVEGDQVDPSILEMRNEVEDENEDVVDDNN FT EGDXQDNQVDDGDVDEYNYASDNNT" XX SQ Sequence 8153 BP; 2458 A; 1315 C; 1681 G; 2590 T; 109 other; cactacaaga awaatkrccy tttgccaggg attttgacaa gggtttgaaa cccctggcaa 60 atttgccagg gamaaccgst ggcamaaaag mcagggattt gcccctcgct ttttgwcaaa 120 aatccctcgg ttwtgwtwag gcgccagwtt gaaatttgaa aakctgtggr aatctgtsct 180 tgtcagmaaw aaccgasgga waaagccagg gaamascccy tsgrtttgcg aaaaccaaar 240 gawtccctgc gttttcccag ctgagttgac aagggcctgs caaaagytra gygctgcmgg 300 cctgccaggg gcggaacccc tcggatwttg ctartwtccg tsgcwaatat caasmcgttc 360 tgcgcctact tytgcgccta cctaagtagg atttgaccga tttttccgag ggacgtgccg 420 tggcaaaggc cctggttttt tccctttcct atataagggt agcaccggtt tgatcatgtg 480 caaatgaaac yttytccttc tcttaaaacw caataccttc atacaaaaca ttcttcaawc 540 ttcwattmtt tggtaaaaaa atwmttyatt tsttatatgt tttatcatga trttaaattt 600 tamyacttat taatsttatt tattttsttt gttatttgca gctgtgttat ttatcygcct 660 cctggtgtta ggttttgcty caactcttgy tgtttttgga ttgcattgca gatttctrtw 720 gkaaagcttc aacatgttag tgatwttttt ttctcataac amtatarctg atatacatgt 780 tgatgatgtg ttgtatrtaa watatgctra ttgtttggta tttttttttt ccgaaaatct 840 gaagaaaaaa aaattatatc atgataattt tttttgtttg ttaatattat tatgcatcaa 900 tgttggcaat ttttaaaata tatccatttt ttattgtgat aaaatgaaat gcatgttttt 960 gttgtgataa aatgaattat atatatatat gcatatttta ttttttgtga tcaaatgaaa 1020 tatatgcatg ttgttttaat tttaattaaa tgaaakatwt gcatgctgtt tttttttttt 1080 tttttktgat aaaatgwaat atatgyatgt tgtagtagaa tgttaaaaaa aatatatgca 1140 tgctgtagtt aaattgtttg ttttaaacta aatctgttat taaaaatttw tttattttta 1200 aattttaata actagttttt ataaatatat tttagtttag ttaatgccat attaaaacta 1260 gtttctaaat tataaaaaca gatttttaaa cataatgctg ttttttaata aattaaaatc 1320 tgtttwtata tttaaaaatc tgttkytata ttkaaattat aattattatt ttaataaatt 1380 aaaactaatc aaagcgtwgg aaaataaaaa tgcttcataa aaaatactat actaaaaatt 1440 tcttggaaaa caatttatta aaatagtgta ttaaaaatca gttttttttw twwaaattaa 1500 aactttgtta aaaaatctaa ttttttttaa taaattaaaa tatgtttgat ttccgtgtct 1560 aaaatgttat aattattatt tttataaaat aaaacaatat aatataataa tggatattgt 1620 ttaaaaagga gggactcaaa aatagtatag tacaagaaag ttgtttatcg atgaaaatta 1680 aaactatgtt acaattattt amtaattaat tattatatgt ttaatttgcg agataaaaat 1740 ttaatttgtt tgcgcgtaaa cttatatttt attgtttgag cgggattttt tttycgcata 1800 atgttagtta tctccgttga gtaataattt atttttgacg tggaatacgt caatgaagtt 1860 gcggaacgtg tagaagatgg agtattatga atattatcgt cgttggatgt acgataggac 1920 gtttccggga agaactggac taaaaccgca atttgtcgaa ggagttgacg gatttatttc 1980 atgggcatgg gagcaagaaa tctgtagaga tgagggagga attagatgtc cgtgtctaaa 2040 atgtaggtgc agacatataa ttaccgatcc tggagatgtg aagaaacacc taaaaaaagt 2100 tggttttatg cctaattatt gggtttggac atataatggt gaaatgtttc agaattttgg 2160 ggyaggggtc aatgcacaag cttctactag ccatggtgga acaaatgtgg aaacaaatgt 2220 ggaatacaat gaagatgtca acacagawca attcaacatg atggatgata tggttgcgga 2280 ygctttaggg gtggaattgt cttacggtga agatgttgaa gatgatgaag aggaacaacc 2340 cccgaatgag aaggcgcaaa gattttaccg attgttgagt gaaagtaata cacctttgta 2400 tgaagggtct tcgcactcta agctatctat gtgtgtgtgg cttttatctc ataagtcgaa 2460 ctatcttaat cctgatgatg gtatggatga tattacgaag atgttgaagg ccgtkactcc 2520 gttcaaagat aatctgccaa tgaattatca tgctgcgaag aggttggtga tgaagttggg 2580 attatcagtt aaaaagattg attgttgtag aaatggatgc atgttgttyt atgacaatga 2640 gtttgggata aatgatggas cattggagga atgtaaattt tgtcaaagcc cgaggtacgg 2700 tattagcaag cagaaacgag ttgcggttaa gtcaatgttt tacttgccga taataccaag 2760 attacaaaga ctrtttgcat cgatgaaaac tgctagtcaa atgacgtggc atcattcaaa 2820 tggaattycc ggagtgatgc gacatccttc tgacggtgaa gcgtggaaac actttgatcg 2880 agtacatcct gattttgcag cagatccacg gaatgtgaga cttggattat gctctgacgg 2940 ttttcagcca tatgtccaat cctcggcaaa accatattct tgttggccaa tcattgtaac 3000 cccgtataat ctccctcctg aaatgtgcat gacaaaacca tacttgtttt tgagttgtat 3060 tgtaccagga ccagataacc ctaaagcagg catagacgtg tttctacaac ckttaattga 3120 tgatttgaag aggttgtggg ttggagaatt gacatatgat atttctagaa aacaaaattt 3180 caagttgaga gcagctttga tgtggacaat taatgatttt cccgcttatg gcatgttgtc 3240 cggttggagt actcatggta gatttgcatg tccacattgt atggaaaata caaaggcatt 3300 tactttggaa agtggaggga agagttcgtg gtttgactgt catcgtccgt tcttgcctca 3360 taatcacccg tttagaagac ttaagaatgg tttcaagaag gatgagagag tttttgttgg 3420 tcctccacct aagattacat cagaagaagt gtggacaaga gtttgtgatt atccaaaagt 3480 cactgattat ggtcgagctg tcccaatacc aagatacgga gtagaccacc actggactaa 3540 aaggagtata ttttgggacc tcccatattg gaaagataac ttgctcagac ataatcttga 3600 tgtaatgcac attgagaaga atgtctttga caacatattt aacacagtga tggatgtcaa 3660 aggcaaaaca aaagacaatg agaaggctag aaaagactta caaatatatt gcaaragaaa 3720 ggatttggag ttgaaacctc aaccgaatgg gaarttgttg aaaccgaaag ccaactacaa 3780 cctatctgcc caagaagcga aattagtgtg tcaatggttg aaggatttga gaatgcccga 3840 tggatattct tctaacatag gcaggtgtgc cgatgtcaac acgggaaggt tgcatgggat 3900 gaaaagtcat gactctcaca ttttcatgga gaactttatc ccaattgcat ttagttcatt 3960 gcccaaacat gtgctagatc cacttattga gattagtcaa ttttttaaaa atttgtgcgc 4020 ttcaaccttg agagttgatg aacttgagaa aatggagaag aatatgccaa tcattatctg 4080 tcagttggag caaatttttc caccaggttt ctttgactct atggaacatc ttcctgtgca 4140 tctggcatat gaagctatac ttggcggacc tgttcaatat aggtggatgt acccttttga 4200 aagattcatg ggtgactcaa aacgagcagt taaaaatctg gccaaagtgg aaggatcaat 4260 tgttgctatt tacaccgcca aggaaaccac atactttatc ggccattatt tcgttgatcg 4320 tctacttact ccatcaaata caagaaatga agttcaggtt aacgatktac gggatccrtc 4380 aaccttatcc gtattcaatc ttsatggtcg acacgcgggc aaggtgcttc aatattggat 4440 ggtagatcag aaagagatgc ggtctgctca tgttcatgtt ttgattaatt gtgcggaagt 4500 taaaccatac cttgagtaag taaatctatt cctacccatt tttactagty catacaacaa 4560 taagttttaa cgcggttaac aacttcgtat tgaatttatt gttttttagg gaatttattg 4620 ctttttatgc ggagtttggt gaaggatcga cagttggttc gatacatgaa tattttccag 4680 cttggtttaa acaaagagtg tataatgccg agccaactga tgaagtcatc cgtttacggc 4740 aattatctca gggtccttta caatgtgcca atgaatttca cacctacttc gtgaatggat 4800 ataaatttca tacccactct tggacggaag gcaaaaagac tattaatagt ggtgtttatg 4860 taaaaggagt tacagatgga ggtgaagatg atttctatgg cgtgatcaaa cacatttatg 4920 agctttcata taatgacaat aaagtggtgt tgttttattg tgactggttt gatccctcgc 4980 ctagatggac taaaattaat aaattatgca acactgttga cattcgagtc gacaaaaaat 5040 ataaagaata tgacccgttt atcatggcac ataatgttag gcaagtgtac tatgttcctt 5100 atcccccaac tctaccacgc aaacgrggtt ggtctgttgc aatcaaaaca aaaccgaggg 5160 gccgcatyga gactgaagaa csaaacgaag aagttgctta ccaagccgat gatatgacac 5220 atgtaaatga gataattgaa gtagatcaag ttacaagttg gcaagactct caggttgaag 5280 gggatcaggt tgatccttct attttggaga tgcgtaatga agttgaagat gagaatgaag 5340 acgttgttga tgataataat gaaggggacc ascaagacaa tcaagttgat gatggtgatg 5400 tagatgaata taactatgca tctgataaca acacttgaag tatattgtta tccacccttg 5460 taatgattga atttgaattt attgtaatct tgaatacatt tgtgtttgaa tgaagatatc 5520 gcttgtttaa tgatgtatat atatttgagt cctttacaat ataacttttt ttgttattta 5580 acagattcac aatgcctccg aaacaaaaag agaaaggcaa gagcaaggac mccaggaggc 5640 ggttcacaac acacattgcg gatccagcca cacttgccac aytgactccc tttcccagac 5700 caccctcttc ttctagccar ggatcgactg ggtcatccca agctagtgcc tgtgcacccg 5760 ctggagggtc tggtgttgtt gcacctgttg gttttatcct ccctacaggt taccagttgc 5820 ctcctccacc atcattacct catgggcaga ccggctttat gatccctcaa catcaacaac 5880 ccccaccacc ccaacatcaa caacccccgc cccaacccca accccaatcc caaccccaac 5940 agggtgctga tgatgatgat gaggagatgg cagattatcc gcaagatgaa caagagcgtt 6000 acatcattgt gcctagcggg aactcgtaag tctttatgta tttttgttca atatgtatat 6060 tgttataaat ttatgtaatg tttaactata tgagttttca ttgtttgtag tttcatgccc 6120 tgcaagccag ccgccagtgc cattagagac atcatccagg gaaggtatca tggattttgg 6180 aagacttatg gtgatatccc agatgatgaa aaggatgcat ggtttggtct ttttgaggta 6240 acattaatac atatcataat atattttaac ttatctgcac atatgttata atttactaat 6300 ttcctaaaat atgttaacaa atatgcagat gaagtgtgcc tggaacccca agtactatgc 6360 tcagataagg aggaactttc acattagagc ttctgcccgc ctctccgaca tgttgcgaca 6420 tgtccgactt cgtcacgaga ctgctggaaa gaggccctac tggatcgggg agccacttat 6480 gaggcagttg gtggactatt gggggagtcc agagtttaag acgaaatcag agaaggcaaa 6540 gaagaacaga gcatcagaga aagggggatg catccacacg ggaggctgca taagcacagc 6600 agagcatgcc cgtcgactgg taattaaaaa taataactct gttaattaat tttatagaat 6660 gtatgttttt aaatattttg tggttaaata tagtttaatg ttttactaac tactyaataa 6720 ttgtgtttct tgtcaattag gcaaagaagc taggtaggga gccatacata aatgagctcc 6780 acaagaagac ccacacatat cgatcaggcc agtatgttga tgatcgctcc aagatatgcc 6840 aggtaattgt tacataagtg tattttaatt aattttatta attagtggtt ataattttwt 6900 gttaatgttt atttatcttt aactatttta ttcttattta ttttaggagg agtatgatcg 6960 tcagctatca gaggcgctct cccgtggatg ctctgttgat gaagctctca cacttcgtgc 7020 atggacgaaa gttgctggtg agaagaagaa ggggcgattg tacggtgcag gaaacttagc 7080 tggaaactwc cgcaagggtg ttgctaccac tctaaagttg acccttaatg ctggggaggg 7140 ttcttctcgg caacctgagc tcactccaga aatccgggat ctgatcacta ggttgactca 7200 agaacagctt gctgcccata tgcaaaccca acaggagctg atccatgagg tggttaggaa 7260 gcaacgagaa ttcctagact ctcagttgga cacatttagg caagagcaag gctggaatat 7320 gaatgagcaa ggtggtgggc agcatagtgg aagccgagag agtgtgaggg ctcctctagt 7380 gtgtgatgat gatgcggaag acccctatga agtgtatggt gagggcgaag aggatgatga 7440 tgacgacctc gagatggatg attgatgctt atgatgcttg ttgtgtgttt tctttactat 7500 tatgttatgg tttgtatgat tttgggaggt tttccatact tcctggcaca atatttattt 7560 tcctgcacgg tttgtaatat tattaagtac actttctatt tcatgcattt taattagact 7620 tattagtgtt tgtgtgatta aactttattt atatgcattt aattgtgttt taaaaaaaat 7680 taattttttt aaatatatat tttttaatta aaaaaaatcg atttttaaat taatttaaat 7740 atattttatt aattaattaa aaaaattcgt tttcataaaa taatattttt ttaaaaaaaa 7800 taaggacatt tgccaggggt taaacccctc gcatgtccct cgttttttgc tgttgtcact 7860 tcggtcagag ccgtcgtcaa gccgtcagtc agtcagggtc agaggtgcag tctgcagaca 7920 aaagtgacgg accatgccag gggttcagcc agggagaaag tggcgcgatt tgccaggggt 7980 tcaaccccty gtttttctgc caggggtgta gcccctggca aagtgtttgc gatgagcgct 8040 tttgccaggc catctgcccc tcgttttttc cctcacaaat gtcccgtttg ccagggattt 8100 tgtccttttg acagggattt tgcccctggc aaaaggcaat gttccttgta gtg 8153 // ID MtPH-E-Ia repbase; DNA; EDCOT; 3957 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 13-MAY-2008 (Rel. 13.05, Last updated, Version 1) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-E-Ia. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3957 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC An autonomous element representing low copy number family E of CC PIF/Harbinger transposons from Medicago truncatula, carrying 22 CC bp-long TIRs. XX SQ Sequence 3957 BP; 1249 A; 574 C; 664 G; 1470 T; 0 other; gggcctgttt gaaacacttt ttaaaaacag ttttttaatt tttaaaaatt aaaaaattaa 60 aaacttgttt gattacctat ttttaaaata tatttttgaa aagtgttttg ggttttttag 120 ttttggaaac taaaaaagtg aaagagctaa aatgggtttt gcttttctat ttttagtttt 180 aagtttttaa aatagagtaa aaaataagaa aagtgaaaac acggagaaaa gtgttagttt 240 tctccaatgg catagttgta attatgtttg aagttcaggg gcattttcat attttttatc 300 aaaaaaattt ggatcaaaaa tcattcctca ttttacagaa aaactaacgt gagaacagtg 360 agaagcgaaa tggcgatttc cacggcgatt cttctccgat ctccgccgtg atttttcttc 420 ggtctacatc tcgcttcttc ttctccaccg cgcttcttct tctccaccgt gcttcttctt 480 ctctgtggtt ttttcaggtt acatctcaca tctaattgtt tttcattttt aaattaattt 540 ctgttctttg attcagaatt ttgcacctaa tatagcgatt tcttacttga ttttgtgttt 600 ttagatctat gattttcaat attaggttaa tttgtaaatt tgagattgtg gtagaattcg 660 aaatttgtaa tgctttttat atgttgttgt gtttgataaa ctctgattca ttttgataac 720 ttatttgtag cttatgtgat tgatatttgc agcttataga tctggattaa gttcctgtct 780 agataaaaaa acttatttgc agcttatagt ataagtgctt atcataataa gcacttattt 840 ataagcataa gctattttta tagcaaaata gaaaataacg ttaaattatt tttctaattg 900 ctatttataa gctatattaa agaactaaga aattatgaat ataagttgaa atcaactcat 960 gaaaattgtt aacattattt aattatggct tctatcaact tgtatctttc aatgtcatta 1020 ataagttaca atattcacac ggataccaga tacaaaactc accgatggaa aataatttga 1080 aaatctgaag taattgaacg taacatgagt caatgttgtg ttagtgctag acagtggaca 1140 ttacttcaat ttgaactgtt gatgttctta agtgtaatta gatttcagct agtgtggcat 1200 ttaattaatt tgttaatact gatagttagt tagtcaagtg taacttattg tacttattag 1260 tgagttgata tgagttataa atagtgctgc atttgatttt cagtcattca gatagacaat 1320 caataaaatg agatcattct caagttttca taatattcct ttttctagtt cttgtgtgca 1380 ttgatatgct tgttccctaa cagatggcta catatttgtt tggcttactt aacatatgaa 1440 ttttgatcca tgtattgttg aatcatttgt taacatagac atgtaataat ttgttaactg 1500 aaccttattg atatgactct ctctttgcat atctgtttta gacatgaatc tcatcatgaa 1560 tcacgattaa ttatttgaag tggtgcaggt agaaggattt gaagtagtat gaaaaacact 1620 agccaccgtc cacgtttcac tgctcctgcc tcctcatttg ttgcgcctgc agcctcttca 1680 tcagtcgtgc atgcctcctc ctcggtcgtc gctcctgctt cttctggtgc gcctgccact 1740 gctgctgatg ctacacaggt aacctacctt catctcagcc ccatgtatgc aaaatattct 1800 cattcatcta ctgcagttgc actacaccga ctctattttg ttttagtgag gcgtcacagt 1860 ttagtcatta attaaaatgt gccttagttg gttgagtaga gcagataaat gtttatgaac 1920 tagtcccttg agtctcgatt tccaagcaat ttgattatga gacttttgtt tgtttatgaa 1980 ctagttataa aatgtacgtt aaactttggt tccatgattc taataaaact gtgcacacaa 2040 ggaatagaac agaaatgaac tctctattgc taccttgatt ttatttgttc tctctgctgc 2100 tacttttata ggacataagt tgttatgaga actaatatta ctcaatgctt attctaatga 2160 agaaagagtg ttttcttaat ttctgtaatg aactgagaga caagaactac ttaagtgact 2220 cgagggatgt gcttgttgaa gagaaagttg ctacattctt attcataatt ggtcataatg 2280 ttcgtcatag agttgcttca aaccgttttc aacattccac agaaacaatc tcacgcaatt 2340 tcaaggaagt attaagggca gtgtgtcgat taggaaaaga actgataaag caagagtcta 2400 tggagttgcc tagtagaatt aagaataatc caaaatatta tccttggttc aaggtatgtg 2460 tgtaattcat attattgtta ttgtagttgt atcttcattt cacataattt aatcatttat 2520 gcgttcatat tatcaaagat atttggttgt tgtttaatta tccgtataat ttggattatg 2580 ccttgtagaa ttgcataggt gcaattgatg gtacacaaat aagtgcatgg gctcctgctg 2640 agaaacaaat ttcatgtaga ggtagaaagg caacaatcac tcagaatgtc atgtgtgctt 2700 gtgatttcaa catgatattt acatatgtat attcggggtg ggaaggaagt gcacatgatt 2760 ctaaagtttt acttgatgca attacaaatc caaatgcagg atttccttgg ccacctaaag 2820 gtaagtatta atatctaaca taaagttata caatcatatt gacgaaatta acaagtagag 2880 ctaacatgta ttttatttga tgaaggttca ttttatcttg ttgattctgg gtatccatgt 2940 accggaggtt ttcttccccc ttatagaggt gaaagatatc atgcacaaga atatcgaggt 3000 caaggtagac aaccaaaaag tccagaagag ttatttaact acaggcactc gtctttaagg 3060 atgacaatag agcgttgttt tggggtgttg aaaaacagat ttcctatttt aaagttaatg 3120 ccttcctaca aaccttcaag gcaaagactc atagtaactg cttgttgtgc tattcacaat 3180 tacatacgca agtggaattt gcctgatgag ttgtttagga tatgggagga aaatggatga 3240 tatagaactt gaggcggtga acgaggttcc taaccttgaa gggagctcga atgttgaaaa 3300 cttaacaagg ttatctaatg aaggtgcaac tgagatggca atggatagga atcatcttag 3360 agataggatg tgggtacatc gtcataatta atcgaactaa ttacactttt ttttaaattt 3420 tcttatatgc aacaatggag tatggagttt tgttagttat tttgcggatg attgtttttg 3480 tttgcttatt tgatgtttat gttatcgaca ttaatatgct ataatatttt tatatgtttc 3540 acattttaca attttgtatc gcttgaacaa attatgactt catatctaaa aaaattattt 3600 attttatgac taaattctac atttaactat agtacttaaa atttaatttg attggtaact 3660 aaggataaaa ttgtaagaaa aatacaatta tataaaaggt aatataattt atataggtta 3720 aaaaaaaaat taaaaatttg attaccaaac aagttttcta attttctatt ttttaaaact 3780 gtttttgaaa attatatcac caaatggatt ttctaatttt ttcatttcta aaacagtttt 3840 gaaaagtcac attaccaaac aagttttttc ttttactctt cttgaaatcc ctttcctaaa 3900 attagttttt aaaacatatt ttaaaaacta aaaacaaaaa gtgttccaaa caagccc 3957 // ID SHACOP7_I_MT repbase; DNA; EDCOT; 4559 BP. XX AC CT573421; XX DT 15-JAN-2007 (Rel. 12.01, Created) DT 15-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of copia-type LTR retroposon, SHACOP7_MT, from DE Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; terminal repeat; ORF; KW SHACOP7_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4559 RA Shankar R. and Jurka J.; RT "SHACOP7_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 78-78 (2007). XX DR EMBL/GenBank/DDBJ; CT573421; Positions 29656 34214. XX CC The internal region sequence is present in few copies and exists CC in highly variable forms, showing poor conservation across the CC sequences. CC It has intact domains for integrase and RT polymerase. XX FH Key Location/Qualifiers FT CDS 143..4549 FT /product="SHACOP7_I_MT_1p" FT /translation="MAIQSFDSYADFATNASNPFFLHPSENPAVELVTPPL FT EGNKNFQSWIRSMRLALTSKNKIAFVDGTFLTPAKSDALYNQWIRCNSLVL FT AWIQRSVSVNVRKSIAFFDKAYDAWKDLHARFDQGDMFRIADIHEEICRMS FT QGSLDVSSYYTELKSLWDELENFRPLPSCKCAIQCSCGAVQSLQTFRDQDY FT TIRFLKGLNDEYSHVRSQIMLMDPFPPVTKAFALVTQQERQFHIPTISDVD FT GDLKSITDNVASVNNVYSNRGRGGYNNRGRGRSNGGGRGQNQNRYCTNCKR FT SNHTIDTCYLLHGYPPGYQNRSNKGAQSGSSVNLASTVGIEERSQITHTPA FT TSNSGFSFTQDQYKSLLDLLQQNKQQASSAIHSANTTLTNSNTSSTNPFVL FT NVNSNSDFGKHSNFWIIDTGATDHITNNCSILTNSHSIKPITVHLPNKTFT FT TAIMVGTVILSDDLHLKNVLFVPTFHANLISVPQLTKTSKCSAIFTADCCY FT FLQETTKKTIGTARLVGGLYIIESISNSVCPIISHSVSNCSTNNISNSALW FT HMRLGHISFDRHQCIANKYPFVHFNKTRIPCDVCHFAKQKKLPHISSITKT FT TQIFDILHADIWGPYSHTSILGHKYFLTLVDDFSRFTWVILMKSKGETRKH FT LTNFISFVETQFDTKLKCLRSDNGVEFLMHDFLLSKGILHQRSCVETPQQN FT GTVERKHQHILNVARALSFQSNLPKTFWNFAIQHAVHLINRIPTPLLSNKA FT PYEILHNKPPVFLHLKVFGCLCYASTLHTHRTKFDSRARKAAFIGYKEGIK FT GYILYDLSSHQLFISRNVIFYEHCFPFHHSSNATTPTSPNPSSNDNSAFPF FT DSFGVENNLTAPTSPSIVSSPSSPLSPPPTSPSLPLTQPIRHSTRITNRPS FT YLQDYHCNYTSCTNPSSGINTAITYPLSSVLSYNNCSSSYKNFCLSVTTNL FT EPKTFIQASKHECWQNAMKAELDALSLNKTWTIVDLPAGKTPIGCRWVYRI FT KYHADGTIERYKARLVAKGFTQMEGVDYFETFSPVAKLTTVRVLLALAAAK FT GWFLEQLDINNAFLHGDLNEEVYMSLPPGFEISNSDCSTKVCRLHKSLYGL FT KQASRQWNHKLTTTLISLGYSQSQADHSLFVKASDSTFTALLVYVDDIVLT FT GSSMTEINFVKKILDNRFKIKDLGPLRFFLGLEVARTKDGISLNQRKYALE FT LLHDSGNLATKPATTPCDPSTKLTNEGSTPYSDHSAYRRLVGRLLYLTHTR FT PDIAFSVQQLSQYVSQPLESHFRAANRVLRYLKSAPSQGLFFPASTSLQLS FT GFADSDWACCLDTRKSITGYCVFLGSALISWKSKKQSTVSRSSCEAEYRAL FT ASLSCEIQWLHYLLADLYIPIKSPSSVYCDNASAIYLAHNPTFHERTKHIE FT IDCHVIREKIQKGTIHLLPVPSSSQLADVFTKPLHVTSFQSFISKLGLCNL FT HSPT" XX SQ Sequence 4559 BP; 1287 A; 1004 C; 730 G; 1538 T; 0 other; gttggtatca gagcttagct ctggatccgt caaaatcata tagtcctttt tcttccacct 60 ttcaaattgt tcaattcata ttttttctgt ggatttaatt catctatcaa tttcaatttc 120 ctgtttgctt gtctctgcaa ctatggcaat acagagtttc gattcgtatg ccgatttcgc 180 caccaatgct tcgaatccgt tcttccttca tcccagtgag aatccagctg tggaactggt 240 tactcctcca ttggaaggta acaaaaactt tcaatcatgg atcagatcga tgcgtcttgc 300 tctcacatcg aagaacaaga tcgcgttcgt tgacggtacg tttctcactc ctgctaaatc 360 cgatgctctt tacaatcaat ggattcgatg taatagctta gtactcgctt ggattcaacg 420 atctgtttct gtcaatgttc gtaaatccat agctttcttt gataaggctt atgatgcttg 480 gaaagatctg catgctcgtt tcgatcaagg tgatatgttt cgtatcgccg atattcatga 540 agaaatttgt cgtatgtctc agggaagctt agatgtttct agctattata ctgagttgaa 600 atctttatgg gatgaattgg aaaattttcg tcccctacct tcttgcaaat gtgcaattca 660 gtgttcatgt ggtgctgttc aatcgttaca aaccttcagg gatcaagact atactatcag 720 atttctgaaa gggctcaatg atgaatactc tcatgtgcgt tcccaaatta tgttgatgga 780 tccctttcct cctgttacca aagctttcgc cttagtcact caacaagaac gacaatttca 840 tattccaaca atttccgatg ttgatggtga cctaaaatca attactgata atgttgcatc 900 cgtaaacaat gtgtattcta atcgagggcg aggaggatac aataatcgtg gtcgtggaag 960 atctaatgga ggaggtcgtg gccaaaatca gaatcgctat tgcactaatt gcaaaagaag 1020 caaccatacg attgatacat gttacttgtt acatggctat cctccgggtt atcagaacag 1080 atcaaataaa ggtgcacaat cagggagctc tgtgaatcta gcatctactg ttggtattga 1140 agaacgcagc caaatcactc atacacctgc aacatctaat tctggttttt ccttcacaca 1200 agatcaatac aaaagtctat tggatttact tcaacaaaat aagcaacaag cttcatctgc 1260 gattcattct gccaacacaa ctctaaccaa ttcaaatact agctcaacca atccttttgt 1320 tctaaatgtc aattccaatt cagactttgg taagcattcc aacttctgga tcattgatac 1380 aggagctacc gatcatatca caaataattg ttccatactt accaatagtc actctattaa 1440 gcccattacc gtacacttgc caaacaaaac ctttactact gcaattatgg ttggaactgt 1500 tatcctttct gatgatttac atcttaaaaa tgtccttttt gttccaactt ttcatgccaa 1560 tttgatttct gttcctcaat taaccaaaac tagcaaatgt tcagctattt ttactgctga 1620 ctgttgttat tttttgcagg aaactaccaa gaagacgatt ggtacagcta gattggttgg 1680 tggtctctac ataattgagt ctatttctaa ttctgtctgc ccaattattt cccattctgt 1740 ttccaattgt agcacaaata atatctctaa ttctgctcta tggcatatga gattaggcca 1800 catttccttt gatagacatc aatgtattgc aaataaatat ccctttgttc attttaataa 1860 aacaagaatt ccttgtgatg tttgtcattt tgcaaaacaa aaaaaattac cgcatatcag 1920 tagcatcact aagaccactc aaatttttga tattcttcat gctgatattt ggggtcccta 1980 ctcccatact tctattttag ggcacaaata tttcttaacc cttgttgatg actttagtcg 2040 attcacttgg gttatcctta tgaaatcaaa aggagaaaca agaaaacatt taaccaattt 2100 tatctccttt gttgaaactc aatttgatac caaactaaag tgcttaagaa gcgacaatgg 2160 tgttgaattc cttatgcatg attttctttt atccaaagga attcttcacc aaaggtcttg 2220 tgtggaaacc ccgcagcaaa atggtactgt tgaacgaaaa catcaacata ttttaaatgt 2280 tgctagagca ctttcttttc aatctaatct tcctaaaact ttttggaatt ttgcaattca 2340 gcatgctgtg catctcatca atagaattcc cacacccctt ctttccaaca aagctcctta 2400 tgagattctt cacaacaaac ctcccgtctt cttacaccta aaagtttttg gttgtttgtg 2460 ttatgcatcc actttacaca cacataggac caaatttgac agtcgagctc gcaaggcagc 2520 cttcattggc tataaagagg gtatcaaagg atacatactc tatgatttgt catctcatca 2580 acttttcatc tctagaaatg tcatttttta tgaacattgt tttccttttc accactcttc 2640 aaatgctact actcctactt caccaaaccc ttcatccaat gataattctg catttccttt 2700 tgattcattt ggtgttgaaa acaacttgac tgctcccact tctccttcta ttgtatcttc 2760 ccccagtagt cctttatctc ctcctcccac ttctccttct ttaccgctca ctcaacccat 2820 taggcattct accagaatta caaatagacc tagttacttg caagactatc actgcaacta 2880 tactagctgc accaatccat cttcaggtat taatactgct attacctatc ctttatcttc 2940 tgttttgtct tataacaatt gttcttcttc ttataaaaat ttctgtcttt cagttactac 3000 taaccttgaa cccaaaactt ttattcaagc ctcaaaacat gaatgttggc agaatgctat 3060 gaaagcggag cttgatgctc tttcattaaa caaaacctgg actattgttg atcttcctgc 3120 aggtaaaacc cctattggat gtcgttgggt atataggatt aaataccatg ctgatggcac 3180 cattgagcgc tacaaagctc gccttgttgc taaaggcttc acacaaatgg agggggtgga 3240 ttactttgaa acttttagcc ctgtggcgaa attaaccact gttagagttt tacttgcctt 3300 agctgctgcc aaaggatggt ttttagaaca attggacatc aacaatgcct ttttgcatgg 3360 agacttaaat gaggaggtat atatgtcttt accccctggt tttgaaattt caaattctga 3420 ttgttccact aaagtgtgca gattacacaa atctctctat ggtttaaagc aagccagtcg 3480 tcaatggaac cataagctta ctacaacttt aatttctctc ggatattctc aatctcaggc 3540 cgatcactca ctctttgtga aagcttctga ctctactttc acagccttgt tagtatatgt 3600 ggatgacatt gtcttgactg gcagttcaat gactgaaatt aactttgtca aaaagatttt 3660 ggataatcgt ttcaaaataa aagatcttgg tcctttaaga ttttttcttg gccttgaagt 3720 tgctcgcacc aaggatggta tttctttaaa tcaaagaaaa tatgctttgg aattgcttca 3780 tgacagtggt aatcttgcta ctaaacctgc cacaactcca tgtgaccctt ccactaagct 3840 caccaatgaa ggaagtactc cttattctga tcattcagct tatagaagac ttgttggtag 3900 gcttctttac ctcactcata cccgaccaga catagcattt tcagtacaac aactgagtca 3960 atatgtttcc cagcctctcg agtctcattt tcgcgctgca aatcgtgtgc tcaggtatct 4020 taaatctgcc ccttctcaag gacttttctt cccagcatct acatctctac aattgtctgg 4080 atttgctgac tctgactggg cctgctgttt ggatactaga aaatctatta ctggatattg 4140 tgtatttctc ggttctgctc ttatctcatg gaaatcaaag aagcaatcta ctgtatctag 4200 atcttcctgt gaagcagaat atagggcatt ggctagttta tcatgtgaga ttcaatggct 4260 tcattaccta cttgctgacc tatacattcc tatcaaatct ccatcttcag tttattgtga 4320 caatgcatca gcaatttatc ttgctcataa ccctactttt catgagcgta caaaacatat 4380 tgagatagat tgccatgtaa ttagagaaaa gattcaaaag ggcaccattc acctattacc 4440 agttccatca tcatctcaac ttgctgatgt atttactaaa ccgcttcatg tcacctcgtt 4500 tcaaagcttc atttccaagt tgggactttg caatctccat agtccaactt gagggggag 4559 // ID MuDR-6_VV repbase; DNA; EDCOT; 10060 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-6_VV, an autonomous DNA transposon - a consensus sequence. XX KW MuDR; DNA transposon; Transposable Element; mutator; Mutavine-6; KW MuDR-6_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-10060 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 766-766 (2008). XX DR [1] (Consensus) XX CC MuDR-6_VV (Mutavine-6 in [1]) consensus is an autonomous element. CC Its individual copies are >90% identical to the consensus CC sequence MuDR-6_VV does not contain TIRs, but is flanked 9 CC bp-long TSDs. Note that there are computational protein CC predictions for the transposases of few individual copies CC (proteins stored at NCBI), but the length of the proteins as well CC as splicing sites are not always consistent. Although some copies CC are theoretically able to produce a transposase protein with CC conserved domains characteristic for Mutators, it is still CC questionable whether true autonomous copies exist in the genome. XX FH Key Location/Qualifiers FT CDS join(3184..5749,5856..6690,6802..6889,6976..7377, FT 7458..8408) FT /product="MuDR-6_VV_Transposase" FT /note="MUDRA transposase." FT /translation="MDSLLTIVCYKDGEIIDGPNGVCYSCPPKKGVLVNNL FT IKYDELEDKLCHVMSIDRTHTMLSMIFRYPILMSIGNGNINYIQLPIKDDD FT DVRLMFHVVAQIPPSNTIEMYLQTRPRDHSSELSPSFDQEIMGHDVEIPAK FT GNLAVQIDEMDENLAHNDEMGGNLAVVTQSVMGATNNYVDIPFTNENDDVE FT FYDEDEINEMHYDDEPPTNKASSDDGEHIMPSPMFKQLNWDAINSMTAEPL FT TSRTGLWNESNELFKGLRFESKEDLQYAVKRYAICRNQHLVVCESEPQLWA FT VRCKKWQEGCNWRLRACRRKSHGMFEITKYAGPHTCVYPKLSQDHSQLDST FT LIAREIQNVVQRDHTTSIATLHQIVKDKFGYDVHYRRIWEAKRKAMLRVFG FT DWDESYQALPKWMNILQLTNPGTKIVWKTIPLGGISGNVRFMRVFWAFGAS FT VEGFKHCRPIIQIDGTFLYGKYMGKLLIATSIDGNGHVFPLAFAIVEEESQ FT DSWSWFLIALRHHVTQREGICLISDRHAGINAAVRNPSVGWSPPHAQHRYC FT LRHVVSNFNDKFKNKVLKELAYRAGCQHQPRKYERYMEELKRLDEKSVAWF FT SKLDTQKWTQAYDLGYRYGWMTTNIAECINGVLKGARMLPITALVQLTFYR FT CVSYFETRRAEIRARMAVGDVYTAYAIEKFRRAEAKASGHTVTIFHRIHET FT FEVITALHGFHMDKGRNKQVVKLNEGTCSCNKWQSFGIPCSHVLAVSAHMR FT IDSWQLVEKYYRLDAYASCYAPEFNPIPHESYWPYPDFPILHPDPTSMRDK FT GRPRSSRIRNEMDLKEPSVRIRCGLCKIAGHNRRNCPTKDGGQSSNPLPHD FT N*SITARWSRDPWIPTVLHGQATHRSSVAWTGVDSKELHCRRREAIFHRTS FT VLDGRIIPLLQQAGFYGVARLGFISLDWHLITAFVERWRPETHTFHLPQGE FT CTITLQDIAMLIGLPVDGDVVTGSTCLDWRRVCYSLLGLTPGDTDIDGQRL FT HLTWLSQSFPTLAPDADEESIQRYTRAYILQLIGGFLFSGKSSDKVHLMFL FT PLLEDFEVAGRYSWGSACLAWLYRQLCRASHIDTHDISGPLILLQLWVWER FT FPFIAPHRLRIAPHDDQLPPPPLAIRWRDEFQTTSISMHVLAQYRHHLDRL FT TADQIIWQPYVDDMNVGLPDYCTAGKDIWCTISPLICFHIIEWHRPDRVLR FT QFGFRQGIPQPCDNESILHKCDLRGRHDVDWTTRHGDYIRRWSSRREHIAR FT GEMAIGSLGYHDPYMVWYRSITIRFLTRTGSFHELLTTSIHQIYDIAPPDD FT FRIRRLCTTVLEAIHEMDRLDAPFSVDATTQLQPPSGDVRPTRRGPRTREI FT RHTPVVARVRPSTDISPPPHQQPTSSITRSGGVRTRGGGPHTRSSPPPHQQ FT PISSITRSGGVRTRGGGPHTRSSPPPHQQPISPITRSGGVRTRGGGPHTRS FT SPPPHQQPISSITRSGGVRTRGRGAHTRGTRHTSVLRDAPSTDISLPPVQE FT TPITPMEVPSTPPVVPLVASSPPSIEATLVHEELVHIANDDQQGQKTNRGR FT GHGRGRGRRRGRGAHGGLHVSPIEPIVEHAHHRRPLRKRKAPSCGTH" XX SQ Sequence 10060 BP; 3106 A; 1542 C; 1950 G; 3436 T; 26 other; gggattcttg ataaatatac agcaattaga aaaagtaata tttaaaatac catagattgg 60 aaaataattc caattctacg gcacttttga acacgtagga taacccattt cctcagcccg 120 ttttccttct tttcttctct acatcaaaaa tcattttgcc cctctgcccc aaactcattt 180 tcccgcacgc cgattaggga ggggagatcc ttacctcaac accaatagga aggacctgaa 240 gtggagatct gagagaccat tgccccctgg ttttttctgt aagttttgtg gttatatttg 300 gtggtgtggt tgtgtttggt caccgagaaa gtgtgggaaa gttgaaaaaa aataaagttt 360 tcgttttttt ttttttacaa tgaaacagag tagactaaaa attatggaga aagttttcat 420 tttttttttt ttttgtggtt cggcttgttg tgattttgtt tggttgccaa gaaagtatgg 480 gaaagttgaa aaaaaataaa gttttcattt tttttttgac aatgaaaccg agtagactaa 540 aaattatgga gaaagttttc atttttttgt ggttcaactt gttgtgattc tgtttggttg 600 ccaagaaagt gtgggaaaat tgagaatttt gtttccattt ttttttccgc cagctcggac 660 acaatatttg atcctttttt tttatatata taaaaaaact atttggtgat ctgataatga 720 tttgcgggaa aaggttgtgt ttttcagcct ggctcaaaaa tcatggattt agggtttgtg 780 aaatttaaat ccaatggcac aaaagcaaag ggacccctag aacagctcca gaaagcacag 840 agagcaaaaa aacaaaagca tttttttttt cgttgggggt tttgcaagaa gagaaacaaa 900 gcaattcttc tatctaccca cttcaccttg tctaagaatc cttttttggc atcatcttct 960 ggtgtatgtt ttggttgtgc aattccattc ttgttacatt ggttgttatg gttgtttggt 1020 ttatactctt tcattcaggg agcacattag aggtttgttt ggatcttgaa aagtatgagg 1080 ggaaataaag gcgttgaaaa catcttgagg aatgaatcac tctcaattag tgtttggtat 1140 tttttttttc ttcctgtcat cctttaacat ccaagcagat ccttgtaaac caaaacttgc 1200 tcattttctc tcctgcttgg agaggtgaat aattcagtaa ttgtaacttg agttaggtgc 1260 atcaaacaat cgtcaaaaga aacatcacaa ttttgttgtg gaattggagt aaaagtagct 1320 cgttgttata gccttgtatt cccttatttt tgctttgttt ctcttcttgt gaaagagagg 1380 tgaggagaaa tttcttcatg gatatactct ctttttattt gttaaaatta aaaataatta 1440 tttgtttcat tgctttcagg tgattgtttc attcttctat gagtgaatta ttttctatac 1500 gaatccttgg tttttttgtt taataattta ttaattcctt gataatccac atacttcagt 1560 tgaaggaata aagtcaaggt gatatctata gtatggttta gatttggata agattgaatt 1620 tgttttcatc cggctagatt aattttaaaa tctatttaat attaaaatta tgatatatta 1680 taaaataaat gatgataaat gtataaaatt ttaatatatc aataatatta aaaacactat 1740 gaataaaatt atgatatatt tttactaatc aattaagcga aaaatttaat ttcaattata 1800 aaatagttat aattaattcc ttgttattta aagtattttt tttaatattg tatttatatc 1860 ataactttta atatatattt ctttagtgca tattatatat caaatggtaa gtttgcctta 1920 gtggagctat ggatacatgt tgagcctttt gttgggggtt caaatcctct caacaatagc 1980 aaaaaaaacg atgatcaatt ttgaaaattt taaaatctat ttaatattaa aacactatga 2040 ataaaattat gatatatttt tactaatcaa ttaaatgaaa attttaattt caattataaa 2100 atagttataa ttaatttgtt atttaaagtg ctttttttaa tattgtgttt atattctaac 2160 tttaaatata tatttcttta gtgcatatca tatatcataa ggcgagtttg ccctagtgga 2220 gcttgggatg catgcctaac cttttgttag gggttcaaat cctctcaaca acaccaaaaa 2280 aarctcaatt ttgagtgtta accaccaata taaaatataa aattgatatt atttataata 2340 aaaaatataa atttgataag tgtacattga ttaattttaa aatctattta atattaaaat 2400 tatgatatat ttttactaat maattaaatg aaaattttaa ttttaattaw aaaatagtta 2460 taattaawtt gttatttaag gtgttttttt ttaatattgt acttatatcc taacttttga 2520 tatatatttc tttagtacat atcatatatc ataaggcaac tttgtcctag tggagatggg 2580 gatgtatgmt gaaccttttg ttgggggttc aaatcccctc aacaacacam raaaaaagct 2640 caattttgag cstymactta taatataaat atatatatta ttataaaaaa aatataaatt 2700 tgataagtgt acattgatta attttaaaat ctatttaata ttaaaattat gatatattat 2760 aaaataaatg atgataaatg gataaatttt taatatatta ataatattaa aaacaatatg 2820 gataaaatta tgatataatt ttactaatca attaaatgaa aattttaatt tcaattataa 2880 aatagttata attaatttgt tatttcaagt atttttttaa tattgtattt atatcctaac 2940 ttttgatata tatttcttta gtgcatatca tatatcatag ggcaagtttg ccctagtgga 3000 ggtagggatg catgttgaaa tactatcttt ttttkagcat ggatatacta tctttttatt 3060 tgttaaaatt aaataattta ttttgtataa aatgaataca ttaaattgaa tatgataaat 3120 taaaataaat ttaatttgat ttagacttac atatatttta tttgattctt tttaggtaca 3180 tgaatggata gtttgcttac aattgtgtgt tacaaggatg gtgaaataat tgatgggcca 3240 aatggggtgt gttacagttg tcctcctaaa aaaggtgtct tagtgaacaa tttgatcaaa 3300 tatgatgagt tggaggataa gttgtgtcat gttatgtcga tcgatcgcac tcataccatg 3360 ttatccatga tatttcggta tccaattctt atgtcgattg gaaatggaaa cattaactat 3420 atacaattac caattaaaga tgatgatgat gtaaggttaa tgtttcatgt tgtagcacaa 3480 atcccaccat cgaatactat tgaaatgtat ttgcagacac gtccaaggga tcattcatct 3540 gagttaagtc catcatttga tcaagaaatt atgggtcatg atgtggaaat accagcaaag 3600 gggaatttgg cagtgcagat tgatgaaatg gatgagaatt tagcacacaa tgacgaaatg 3660 ggggggaatt tggcagtagt aactcagtca gttatgggag cgacaaacaa ctatgttgac 3720 atcccattta caaatgaaaa tgatgatgtg gaattttatg atgaggacga gattaatgag 3780 atgcattatg atgatgaacc tccaacaaat aaggcttctt cagatgatgg tgaacatatt 3840 atgccttccc caatgttcaa acaattgaat tgggatgcaa taaatagcat gactgctgag 3900 cctctcacat cacgtaccgg attgtggaat gaatccaatg agttgtttaa aggattgaga 3960 tttgagagta aagaagactt gcaatatgct gtaaaacgtt atgcaatatg tcggaatcaa 4020 catttggtgg tttgtgaatc agaaccacaa ttgtgggcag tgagatgtaa gaagtggcag 4080 gaaggatgta attggaggct tcgtgcatgt cgtcgtaaaa gccatggaat gtttgagata 4140 accaagtacg caggtcctca tacttgtgtt tatcctaaat tatcacaaga ccactctcaa 4200 ttggactcta cattgattgc aagagagatc caaaatgtag ttcagaggga tcacactacc 4260 tctattgcta cattacatca gatagtgaag gataaatttg gatatgatgt ccattatagg 4320 agaatttggg aagctaagag aaaagcaatg cttagagttt ttggtgattg ggatgaatct 4380 tatcaagcat tgccgaagtg gatgaacatc cttcagctaa ctaatcctgg aacaaagatt 4440 gtttggaaga caataccttt aggagggatt tctgggaacg tgcggtttat gcgtgttttt 4500 tgggcatttg gggcaagtgt tgaagggttc aagcattgca gaccaattat acaaattgat 4560 ggtacattcc tatatggaaa atacatgggg aagcttttaa ttgctacttc aattgatgga 4620 aatggtcatg tattccccct tgcgtttgca attgttgagg aagaatcaca ggatagttgg 4680 tcttggtttc ttattgcatt aaggcatcac gtcactcaaa gagaagggat atgcttaatt 4740 tcagatcgcc atgcaggaat aaatgctgct gttagaaatc catcagttgg atggagcccc 4800 cctcatgcgc aacatcgata ttgtcttagg catgtagtga gcaattttaa tgacaaattt 4860 aagaataagg tcttaaaaga gttggcgtat agagctggat gtcaacatca accgcggaag 4920 tatgagagat acatggagga gttaaaacga ttggatgaaa aaagtgtggc ttggttttca 4980 aagttagaca ctcaaaaatg gactcaagca tatgatctag gatatcggta tgggtggatg 5040 accacaaata ttgctgagtg cattaatggg gtgcttaagg gagcgcgaat gttacctatc 5100 actgcacttg ttcaattaac tttttatcga tgtgtgtcat actttgagac tcgtagagca 5160 gagatacgtg ctagaatggc agttggagat gtgtacactg cgtatgcaat tgaaaaattt 5220 agaagagctg aggccaaagc tagtggacac actgtcacca ttttccatcg aattcatgaa 5280 acatttgaag taattactgc tctccatggg tttcatatgg ataaaggacg taacaaacaa 5340 gttgttaagc tgaatgaagg tacatgtagt tgtaataagt ggcaatcatt tggcattcca 5400 tgctcacatg tgctagctgt ttctgctcat atgaggattg atagttggca attagttgaa 5460 aaatactata ggctggatgc ctatgccagt tgttacgctc ctgaatttaa tcccattcct 5520 catgaatctt attggccgta tcctgatttt cctattctcc accctgaccc aacttcgatg 5580 agggataagg ggcgtcctag atcatcaagg ataaggaatg aaatggattt gaaggaacca 5640 agcgttagga ttcgatgtgg cttatgtaaa atagcgggtc ataatcgtcg caactgtccc 5700 acaaaagatg gagggcaatc ctccaacccc cttcctcatg acaattaaag tatgaaagat 5760 tatccatttt gataatatga tatttttatg taatgtctgt aaatttgtaa tcatactaat 5820 gataacaaga attaatggtt atttggtata tgtaggtatc accgcacgat ggagccggga 5880 cccttggatt ccgacagttc tacatggaca ggccacacac aggtcatctg tagcatggac 5940 aggtgttgac tctaaggagc ttcattgtag acgacgtgag gcgatcttcc atcgcaccag 6000 tgtactcgat gggcgtatta ttccattgtt gcagcaggca ggcttctatg gtgttgcacg 6060 cttaggattc atttccttag attggcatct tattactgca tttgtcgaga gatggcgacc 6120 tgagactcat accttccact tacctcaggg ggagtgcacg attacactac aggatattgc 6180 catgttgatt ggactaccag tagatggaga tgtagttact ggtagcacat gtttagattg 6240 gaggcgtgta tgttattctc tattaggact cactcctgga gatacagaca tagatggcca 6300 gcgccttcat cttacatggt tgagtcagag cttccctact ttggcaccag atgctgatga 6360 ggagtctatt cagcgttata ctagggctta tatcttacag ctcattggag gttttctatt 6420 ttcaggaaag tctagcgata aggtgcatct tatgttttta ccccttctag aggattttga 6480 ggttgctggt aggtatagtt ggggtagtgc ctgtttagct tggctttatc gacagttgtg 6540 tcgagcctct catattgata cacatgatat atctggccca ctgattttgc tccagttatg 6600 ggtatgggag aggttcccat ttattgcacc tcatcgttta cgtatagctc cacatgatga 6660 ccagctgcct ccacctccat tggccattcg gtatatatta taaaattacg acaaatttta 6720 ctattatgag gatacatgca taaacttaaa ttctaacatt ttttatttat ttaactatgc 6780 tttgttattt taattttata ggtggagaga tgagtttcag actacttcga ttagcatgca 6840 cgtcttagct cagtataggc accatcttga tcgacttaca gcagatcagg tgataaaagt 6900 gtgattcatt tcttatactt gtttctctaa acaaattcta aaccactgat tatatctaac 6960 gtttcttggg tacagattat atggcagcct tatgttgatg acatgaatgt tggtcttcct 7020 gattattgta ctgctgggaa agatatatgg tgcactatct cacctttgat atgtttccac 7080 ataattgaat ggcatagacc tgatcgagta ttgcggcagt ttggatttcg tcaagggatt 7140 cctcaaccat gtgataatga gtcaatctta cacaaatgtg atttgagagg tagacatgat 7200 gttgattgga ctactcgaca tggagactac attcgacgtt ggagctctag gcgtgagcat 7260 attgctagag gcgagatggc tataggttca ttggggtatc atgatccata catggtgtgg 7320 tatcgctcca ttactattcg gtttcttact cggactgggt ccttccacga gctattggta 7380 attttcatgt tttatctttt tattaaagtt tattttattt ttataagaat ttaatttaac 7440 tcttatttga cttacagact accagcatac accagatata tgatattgca cctccagatg 7500 attttcgcat tcgcaggcta tgtactactg tattagaggc catacatgag atggatcgct 7560 tagatgctcc atttagtgtt gatgctacta cacagctcca gcctccatca ggagatgtac 7620 gacctacacg acgagggcct cgtacgaggg agattaggca tacaccagtt gttgcccgag 7680 tgcgaccatc gactgacatt agtccaccac ctcatcagca gcctacatca tccattactc 7740 gatcaggagg tgtacggact agagggggag ggcctcatac gaggagtagt ccaccacctc 7800 atcagcagcc gatatcatcc attactcgat caggaggtgt acggactagg ggaggagggc 7860 ctcatacgag gagtagtcca ccacctcatc agcagccgat atcacccatt actcgatcag 7920 gaggtgtacg gactagggga ggagggcctc atacgaggag tagtccacca cctcatcagc 7980 agccgatatc atccattact cgatcaggag gtgtacggac tagagggcga ggggctcata 8040 cgagagggac taggcataca tctgttctta gagatgcacc atcgactgac attagcctgc 8100 cacctgttca ggagactcct attacaccta tggaggtgcc atccacccca cctgtagtac 8160 cacttgttgc atcatcacca ccatcgatag aggctacatt ggttcatgag gagttagttc 8220 atatagcaaa tgatgatcaa caaggacaaa agactaatcg tggtcgagga catggtcgag 8280 gacgtggtag gagacgtggt cgtggagctc atggagggtt acatgttagc cccatagagc 8340 caatagtgga gcatgcacat catagacgtc cactacggaa gaggaaggct ccttcgtgcg 8400 gtacacattg aggatgttac tacatatgac ttatattttg gatactatta gtattttgca 8460 tatcattatt ttggacaaat actctagatg tatgttttta cttgttatat tttggattaa 8520 ctaacttttt attaacgtaa gttctatagt attctatcta ttttggactt attttacaca 8580 aaatagtatt gttactattt tggaaaggtg ctgattttga tatttggttt acttgttttc 8640 attggttttg gattgaatgt caaaatactg attataatgt atacaggtga taaactttaa 8700 acatttggtt gtacagtagg taatactaat taagagatag aatttttttt ttcttttgtg 8760 gaaggtgtct cttcaagaga caccttcagc ataaattcga aattttctac trtgtatgga 8820 aattgtggaa agtgtctctt gaagagacac ctttagtata attttatttt ttgggaattg 8880 tagaatgtcc cttttcaaaa ttcgamattt tcactgaaaa attgttgaaa gtgtctctts 8940 aagagacact ttcartataa agcaaaattt tttacaaata atgaaaattg tggaaagtgt 9000 ctcttgaaga gacaccttta gtataatttt attttttggg aattgtagaa tgtccctttt 9060 caaaattcaa aattttcact gaaaawttgt tgaaagtgtc tcttgaagag acactttcar 9120 tataaaccca attttttaaa aattatgaaa ggtgtycgaa tataattcca tttttttgta 9180 attatggaag gtgtytctts aagagacacc ttyagcataa attcaaaatt ttccactgtt 9240 tgaatggaaa ttgtggaaag tgtcttttga acaagcactt tcagtataaa cccaatattt 9300 ttaaaattgt ggaaggtatc aagagacaca tttcacaatt cccaaaaaat ggaattatat 9360 tgaaggtgtc tcttgaarag acaccttcta ttattttaaa aaaattgggt ttatactgaa 9420 agtgtctctt gaagagacac tttccacaat tttcatacat taaagagaga catctttaac 9480 tttaaaatca tttctacaaa taaaatacat attggatttt gtggaattgt gtaaagtgtc 9540 tttccaagag acacatttag tataaatcta attttttgga attttagaag gtgtctctta 9600 aagagacacc tttggtataa attaaaattt ttaggaattg tagaaggtgt ctcttcaaga 9660 gacatcttta gctttaaaat caaatttata agacattcaa atttttgagg aaagtgtctc 9720 ttcaagagac acctttaatg aatattggat tttttgccac gtggaaagtg tctctgcaag 9780 agacaccttt aatacatatt ggattttttg ccacgtggaa agtgtttttt caagagacaa 9840 ctttaatgta aatcaaattt tctgaaattg tagaaggtgt ctcttcaaga gacacmttta 9900 gcttaaattc aattttttca tgattttgaa aattgtggaa ggtgtctctt caaaakwcac 9960 cttccacgtg gccaaaactg cygtaaatct atcaatattt tcaaaactac cattttttaa 10020 ttataatttt ttaaaattgc cgcaaaagtt aaaaaagccc 10060 // ID L1-9_Mad repbase; DNA; EDCOT; 6579 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-9_Mad. XX NM L1-9_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6579 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1813-1813 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 395..2251 FT /product="L1-9_Mad_1p" FT /translation="MEESGQGFYPFHSLIWGLGLYWXFNLGVGVLFLCTTG FT FDVGLTVRHKCGLCEDGVKVGSNKSQSIECWDGIYGSYEMLVGSVKGAQPL FT LPPNGRYVQAYAFIAIVIALPLALNEDLRQIQDLRLLPASAHRVFSAHSKY FT SAASLGLSKVWSLLLMENPGVEELVVHLDRSLDLSTMEIGVKLVGMALTQR FT PLNRWGIRNILNSAWKDLGEVGIKWVRENLFIISVXDQSMAKKILAQVPWA FT VMKKNFVVKAWPPDLALEEVDMKTVPFWVQIRGVPLSLVSKENVTRLIRTA FT GVFLEMEDPAKARGFLRVRVLVNSENPLVLGCWLKREVNRETWVEFRYERL FT QDFCYRCGRIDHVNTECSYAANMGGAEGYGDWIKAPPVRDFVEPVRPSRLG FT VGERRTVGMVRGSDRPELRLQRPIHSEAPSRKDTSGVTAGEHGSHARDKKK FT WRRVQRQACPXSQIQVVVPQLRRQLRWECGGGSFPPVLNQVVFQGGEGGHS FT VRIRDVSEAYSGTPPDXDLEGFTGTXVCNSRQXSSLLRHEVGGIKRGVEPS FT SMDLVPSPQKKTRGPNPDADRQVIHDGTMEARDLWDHVEAVSGENESSVLA FT VCAGNLARGGGGWPSTAARSP" FT CDS join(2251..3504,3240..4217,4221..6389) FT /product="L1-9_Mad_2p" FT /translation="MILVFWNCRGLGSDTAVRALHGLIRNKRPSMIFLSET FT KMKDHRLDGVRRRMGFXXGFNVSPVGRAGGLSLWWDDSVEVQTLFSSKHII FT DVILRKGGDSNWVRITGVYGTPYREDKAXFWEWMSSYFXPSDIPWLCAGDF FT NEFLWDHEKSGGVEVLYNRPRYLETFMQATNLWDLDFNGPAFTWRGMRHGH FT LVEERIDRALINGLWQDLWPNSLVTHGTVMGSDHCPLIIQSDSESVRGRRA FT FKFEAFWAKEDECDQVVSSCWNRPDPGEILVRWTKKINDCKSSLIRWSRNK FT FKKRGQLIQELLHQLQELQRDWRSNIDVIKQKTQLVDELRAQEESYWMQRL FT ELNGFVMGMQIQNSFIILLCNEDDATRLSKLRMSLGIGWSNLVVFGSWWRI FT ILCKRLLLGEPGIGDLCWIVLARGIEGSGGKLLDAASRVKWLRDGDANTKF FT FHNSTLQRRRRNQIIKIKDELGNWVEQPGRVRKLVEDHFMQTFTSGGARNW FT GSLLDCISPRVTEDMNQALLKPVSEDEIKAAIFKMGGLKAPGPDGFQGIFY FT QSFWEHVYADVCALVRELMQGSSSPSTLNATHIVLIPKVPHPESVSQFRPI FT SLCNYSYKVLSKVLANRLKVILPMLISPSQNAFVAGRQIQDNIGIAHEMFH FT FLKGRTAKRKFEMGIKLDMQKAYDRVEWDFLDAVMERMGFCVCGEGLSWDV FT FLLLILLSFSMGSQVTSLLLLGVSGRVILYLHICLSFWGRFFRAFKLRLTI FT KGWRELGLVSRGPLFLTCSLRTILFFFLRAEVNYCWNLLSILERYCEASGQ FT KVNLQKSSIYFGANVPKGVAANLGGILGVSVVDXPGTYLGVPAIWGRSKKR FT GLAYVKGRILGKLQGWKQSALSRAGREVLIKAVVQAIPAYPMXIFKFPAVV FT CQELDALVARFWWGSHGEDRKIHWVSKEVLGLPKDMGGLGFRNFQEFNDAL FT LAKQCWRLLTEPNSLWARVIKARYFPHCSFWEAKKGARASWAWSSLLSGRE FT LLASGSHWQIMGGEDVRVWVDRWLPSLPSGHPMPLGEVSVTSNLRVSSLID FT SSSRQWDFDFLRPFLSMADQRAIQETIIGDSRWKDRLVWAANRNGKYSVKS FT GYRWLQVRSIDVRDHRLPVVRSISKXLWNCIWXLDVPPKIRHFLWVSLHLG FT LPTGXALFKRRLSPSPSCPLCRSADETVEHVFLRCPWVAAVWFGGALNYKV FT DAAGIDSWALWLQAVFSSNWGSSADRXWFQAYVAFTCWFIWKARCDFVFNQ FT VSINPSKVIFSLSTAFGNFLLAVSSXGVARPVSGSREXAAVRWCPPSSPFV FT KINVDASWSKSSRMGFAGVVARQDGGXFRAAVRSSVLAPSSFVAESFAILR FT GCELGASLGFSSVIIESDSLQAISCLNGSLENGSWEAFPILARAQRLGSAF FT QNCRWSWVPRSANMAADVLASAGLTEMCDFVWVDRPPSSLVHVLCNDGLPC FT PH" XX SQ Sequence 6579 BP; 1262 A; 1186 C; 2012 G; 2087 T; 32 other; ctctccgtcg tgagagcctt ttctcctctg tgagaatccg ccgttgtgcg agtttagtgt 60 gggtgtgggt gctctttcct gctggttctg ggttctcatc tggtgttggt ggatctccgt 120 tagggcgtcg tttgcgaggg gtgggtggat ctcttttggg gcgaagtttc gaggggtagg 180 tggagctctt tattcttctg cgattgtctt cgtttggggt tgtgtctctt ctgattgtgg 240 tggggctttg gtggggcgtc tgtccgtgtc ctgtttgtct gctgtggttc tggatttctg 300 ttggggggtt gtcagattgg ggttggtgga gctttaattt cgtcttggtg ttctgcgatt 360 ggggttcgtg cttcttctgg tggggcgggt tagaatggag gagagtgggc agggctttta 420 tcccttccat tctctgattt gggggttagg gttatactgg kcgttcaatt tgggggttgg 480 ggtcttattc ctctgtacga ctggtttcga tgtggggttg acagtacggc acaaatgtgg 540 cctctgtgag gatggagtta aggtgggttc taacaaatct caaagcattg aatgctggga 600 tggtatttat gggtcttatg agatgttggt tggcagcgtt aaaggagctc agcccctttt 660 gcccccaaat ggtaggtatg tgcaggctta tgcttttatt gccatagtta ttgcacttcc 720 tttggctctt aacgaagatt tgaggcagat tcaagattta cgactgttac cggcgagtgc 780 tcatagggtt ttttctgcgc attccaagta ctctgcggca tctctggggc tgtcgaaggt 840 gtggagtctg ctacttatgg aaaatcctgg tgtggaagag cttgttgttc atctggatcg 900 ctcgctggat ctgtctacga tggagattgg tgttaagttg gttggtatgg ctttgacgca 960 gaggccattg aataggtggg gtatcagaaa catccttaac tcggcgtgga aggatctagg 1020 tgaagtggga attaaatggg tccgagagaa tttgttcatt atctcggttc mggatcagag 1080 tatggctaag aaaatcctgg cgcaggtgcc gtgggcwgtc atgaagaaga attttgtggt 1140 gaaagcttgg cccccggacc tcgctttgga ggaagtagac atgaagactg ttcctttctg 1200 ggttcaaatc cgtggtgtcc ctttaagttt ggtttccaag gagaatgtta ctcggctcat 1260 taggactgct ggtgtttttt tggagatgga ggatccagca aaagctcgwg gtttcttaag 1320 ggttagagtg ttagttaatt cggagaaccc gcttgttctt ggatgttggt tgaaaaggga 1380 ggtaaaccgt gagacttggg ttgagtttag gtacgagagg ctccaagact tttgctatcg 1440 ttgtgggcgt attgatcatg ttaatacgga gtgctcctat gcggcgaaca tgggtggggc 1500 ggagggctat ggagattgga taaaagctcc cccagtgcgc gattttgtgg agcccgtgcg 1560 tccgtcgcgt ttgggagtag gcgaamggag gacggttgga atggttaggg gcagtgatcg 1620 tcctgagttg aggttgcagc gtccgatcca cagtgaggct ccgagtagga aagacacatc 1680 tggggttact gctggggagc atggttctca cgcccgtgac aagaagaaat ggcgtagagt 1740 tcagcgacaa gcttgtcctk ctagtcagat tcaggtggtt gtgcctcagc ttcgtcgtca 1800 gctcagatgg gagtgcggcg gtgggagttt cccgccagtt cttaaccaag tggtttttca 1860 gggkggagaa ggagggcatt cggttcggat tcgggatgtc agtgaggcat attctggkac 1920 tccaccagat gktgatttag aggggttcac ggggactgwg gtttgtaact ctmgacagwg 1980 ttcaagcctk ttgcgtcatg aggttggtgg catcaagcga ggagtggagc cttcgagtat 2040 ggacttagtt ccatccccgc aaaagaaaac tcgagggccc aacccggacg ctgatagaca 2100 agtgatacat gacggcacta tggaagcacg tgatttgtgg gatcatgtgg aggcagtctc 2160 gggagagaat gagagcagtg tcttggctgt ttgtgcgggc aatctggctc ggggtggtgg 2220 cggctggccc tcaacagccg caagatcgcc atgattctgg tgttttggaa ctgccgtggt 2280 ctagggtcgg acacggcagt tagggccctc catggtctta ttagaaacaa acgaccctct 2340 atgatctttt tatctgaaac taaaatgaaa gatcatagat tagatggtgt taggmgacgt 2400 atgggttttc wkwatggttt taatgtttct ccggttggca gggcaggtgg gctaagtttg 2460 tggtgggatg attctgtgga ggtgcaaact ctgttttctt ctaagcatat tattgatgtt 2520 atcttgcgca agggtggaga cagtaattgg gtccggatta ctggagttta tggaactcct 2580 tacagggagg ataaggctgm tttttgggag tggatgtcga gttattttwc tccttctgat 2640 attccgtggc tttgtgccgg ggactttaat gaatttcttt gggatcatga gaagtctggg 2700 ggtgtggagg tcctctacaa cagacctagg tatctggaga ctttcatgca ggctactaat 2760 ttgtgggatt tggactttaa tggtcctgct ttcacttggc gtggtatgcg ccatggtcat 2820 ctggtggagg aacggattga tcgggctttg atcaacgggc tatggcagga tttgtggcct 2880 aattctttgg ttacgcatgg gacggttatg gggtctgatc attgtcctct cattattcaa 2940 tctgattcgg agagtgtgcg ggggcgtagg gcgtttaagt ttgaggcgtt ctgggctaag 3000 gaggatgaat gtgatcaggt ggtgagctct tgctggaata ggccggatcc gggtgagatt 3060 ttggtgaggt ggacgaagaa aataaacgat tgcaaatcca gtctcatacg gtggagccgt 3120 aataaattca agaagagggg tcagctgatt caggaactcc ttcatcagtt gcaggagctt 3180 caaagggatt ggcgctctaa tattgacgtc attaagcaga aaactcagct tgttgatgaa 3240 ttgagggctc aggaggaaag ttattggatg cagcgtctag agttaaatgg cttcgtgatg 3300 gggatgcaaa tacaaaattc tttcataatt ctactttgca acgaagacga cgcaaccaga 3360 ttatcaaaat taaggatgag cttgggaatt gggtggagca acctggtcgt gttcggaagt 3420 tggtggagga tcattttatg caaacgttta cttctggggg agcccggaat tggggatctt 3480 tgttggattg tattagcccg agggtgacgg aggatatgaa tcaggcgctc cttaagccgg 3540 tttccgagga tgaaattaag gcagcgatct ttaaaatggg tggtcttaaa gctccgggac 3600 cggatggttt tcaaggtata ttctatcaat ccttttggga gcatgtctat gcggatgttt 3660 gtgctttggt gagggagttg atgcaggggt cgagtagtcc gtctactctt aatgctacgc 3720 atattgttct gatcccaaag gttccgcacc cggagtcggt ctcgcagttc cggcctatta 3780 gcctgtgtaa ttattcttac aaggtgttgt ccaaggtttt ggcgaaccgg ttaaaggtga 3840 ttcttcctat gcttatatct ccctcccaaa atgcttttgt ggcgggtcgt caaattcaag 3900 ataatatcgg gattgctcat gaaatgttcc attttttgaa agggaggaca gcgaaacgga 3960 agtttgaaat gggtatcaaa ttggatatgc agaaagccta tgatagagta gaatgggatt 4020 tccttgatgc ggttatggag agaatggggt tctgtgtatg tggagaaggc ttgtcatggg 4080 atgtgtttct tctgttaatt ttgctgtcct tctcaatggg cagccaggtg acaagtttgc 4140 tccttctagg ggtctcaggc agggtgatcc tttatctcca tatctgttta tcattctggg 4200 ggaggttctt tcgtgcatga ttcaagctgc ggttgacgat aaaaggctgg agggagttag 4260 gattggtgtc tcggggccca ttatttctca cttgttcttt gcggacgata ctcttctttt 4320 ttttacgagc ggaggttaat tattgttgga atttactctc tattcttgaa aggtattgtg 4380 aagcttcggg gcagaaagtt aatctgcaga agtctagtat ttattttggg gcgaatgttc 4440 cgaagggggt ggctgccaat ttgggtggca ttcttggtgt gtctgtggtg gatmatcctg 4500 gcacttattt gggtgtccct gccatctggg gtcgttccaa aaagcgtggc cttgcttatg 4560 tgaagggcag aattttgggg aagctccaag ggtggaagca gagtgcgttg tcgcgggcgg 4620 gaagagaagt tctgattaag gctgtggtcc aggccattcc tgcttatcct atgwgcattt 4680 ttaaatttcc tgctgtkgtt tgtcaggagt tggatgcctt ggttgcgagg ttttggtggg 4740 gaagccatgg ggaggaccga aagattcact gggtgtctaa ggaggttctg ggccttccta 4800 aggatatggg tggcctgggt tttagaaatt ttcaggagtt taatgatgcg ttacttgcta 4860 agcagtgctg gcggttactt acggagccga attcgttgtg ggctcgggtt attaaggccc 4920 ggtacttccc gcattgctct ttttgggagg ctaaaaaagg ggctmgggcg tcgtgggctt 4980 ggtccagtct tctctcgggc agggagcttc ttgccagcgg atctcattgg caaattatgg 5040 gtggggaaga tgtgagggtt tgggtggata ggtggctgcc ctctctccct tcggggcacc 5100 ctatgccgct tggtgaggtt tcwgttacgt cgaacttacg ggttagctcc ctcattgact 5160 cctcttcccg gcaatgggat tttgattttc taagaccgtt tctatctatg gcggatcaaa 5220 gggctattca ggaaacgatt attggcgact cgaggtggaa ggaccggctt gtttgggctg 5280 ctaaccggaa tggcaaatac tctgtgaaat cggggtacag gtggcttcaa gttcgctcta 5340 ttgatgtsag ggatcatcgg ctgccggttg ttcgttcgat ttctaaaamt ctgtggaatt 5400 gcatttggma gctggatgtg cctcccaaaa ttcggcattt cttatgggtt tcgttgcatc 5460 ttggcctgcc tactggtawg gctcttttta aaaggaggtt atccccctct ccctcctgtc 5520 ctctttgtcg gagtgctgat gaaactgtgg agcatgtctt ccttcgctgt ccttgggtgg 5580 cggctgtttg gtttggtgga gctttgaatt ataaagttga cgctgccggt attgattcgt 5640 gggctctgtg gttgcaggct gtgttctctt ctaactgggg ctcttcggct gacaggmagt 5700 ggttccaggc ttacgttgcg tttacttgct ggttcatttg gaaagctcgc tgtgattttg 5760 tgtttaatca ggtttctatc aacccttcta aggttatttt ttcgttgtcg accgctttcg 5820 ggaatttttt gcttgctgtg tcttctktgg gtgttgctcg gcctgtctcg ggttctcggg 5880 aggakgctgc tgtcaggtgg tgtcctcctt cttctccttt tgttaagatc aatgtggatg 5940 ctagctggtc taaatcttct cggatgggtt ttgcgggggt ggttgctagg caggacggtg 6000 ggckttttcg ggctgcggtt aggtcttctg ttttggctcc ttcttctttt gtggctgagt 6060 cttttgcgat tctgcgtggt tgtgaattgg gtgcctcgtt gggtttcagc tctgttatca 6120 ttgaatctga ctctcttcag gctatttcct gtttaaatgg ttctcttgaa aatggcagtt 6180 gggaggcttt ccccattttg gctagggctc aaaggttggg ttcggctttc cagaactgtc 6240 gctggtcttg ggttccaaga tcagccaata tggcagcgga tgttcttgcg tcagctggtc 6300 ttacggagat gtgtgatttt gtttgggttg acagaccccc atcttcgtta gttcatgttt 6360 tatgtaatga tggtcttcct tgtcctcatt agcgggttgt ggtgggtttg gggtgacact 6420 ttctcttagt gattgtgtcg gttgttgtat ccccgctcac tgctttgctt ggtctttact 6480 tcgttgtgtt tgcctcgtcg taggctctct tgcttctgtt tggcttctta gccttgggtt 6540 ttttaattaa actcaattct tcaaaaaaaa aaaaaaaaa 6579 // ID MuDR-12_VV repbase; DNA; EDCOT; 10585 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-12_VV, an autonomous DNA transposon - a consensus sequence. XX KW MuDR; DNA transposon; Transposable Element; mutator; TIR; KW Mutavine-12; MuDR-12_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-10585 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 771-771 (2008). XX DR [1] (Consensus) XX CC MuDR-12_VV (Mutavine-12 in [1]) consensus is an autonomous CC element. Its individual copies are >90% identical to the CC consensus sequence. MuDR-12_VV contains 423-447 bp-long TIRs CC which are 86% identical and flanked by 9 bp-long TSDs. Note that CC elements from this family contain an additional putative gene CC downstream of the TPase, encoding for an ULP1-like protein CC similar to CAN67356.1 (region 5103-6702). XX FH Key Location/Qualifiers FT CDS join(2100..2431,2530..4435) FT /product="MuDR-12_VV_Transposase" FT /note="MUDRA transposase." FT /translation="MEEEMFCYIHEGGELVKTAVGSVEYKGGRTNCIVVSK FT NISHSEFVSKVCGELNLEPNSIKLDFTVKFDPSCLLPXHNDXDIVKMFKFN FT DMFCRAYVSQCTEGGDGFICPTSAPTPIVASNSAHVSSIGEPPLHMSNESP FT TIESFGFSQRCAETNIVQLQPSRFEHSIVGSGHTFPNASEFRDAIYLMSLA FT GKFRYSYKRNSPKHMTVVCTIEDCPWKITARAIGDSNIVQVHTFRNVHNHC FT LEDVALSQPLVRSTRASLVIDDVIRSTPEYQPRQICKDFVRQHGIQLTYLQ FT AWQMKEKAKERIYGQPKNYYKLLPWMCERMLATNPGSSVELSYSDDDHFEQ FT LFVAHSISIEGFVRGCRPIIAIDSAHMSGPYGGALFSATAYDANDSMFPLA FT FGVMSSENYEDWLWFLEKLKIVVGNKEVIIISDRHPALLRSVPEVFGLENH FT AYCYRHLKENFSSFLSKHNTRGNKGKENALQFLDSIAYGRLEHDYNVSMFE FT LKKYNEALATWVEENAPHHWAMSKFPKQRWDKMTTNLAESFNAWLRIERHH FT SICNFLLEHMSKLASMLVKHKEESKNWKGCIGPKIEDKVLQNIAKGEVYPV FT TPFMNGVFGVCIGRALLNVDIMNRTCTCRGWQMLGIPCEHAAAVIISIGQN FT VTDFVDDCYKYPMQELIYGGSFSGIETHDMPSVDDDGLVRSITGEVFFSLK FT PPHTKRPPGRPRKKRIESQFQDKRTVYCSRCHMSGHNRKTCXNPLP" XX SQ Sequence 10585 BP; 3126 A; 1948 C; 2097 G; 3398 T; 16 other; gggaaagttg tgttttcatg ggccaatatg gtaataatat tgtttttgga acccaggttt 60 gtgaaatatg aaaaacatct gttaatgtgg aaacttatat cagtttcatg cactttgagt 120 cggttgtatt ttttctactg aaattgcccc tccaggtatc caggtcagca gcccatctca 180 gcacgggctg aaactgaatc ggttgtcttg tgcaaaatca aatattgagc ttcccacaaa 240 aacaccctgg gcgaccgacc gttcatcctc cttttctctc atttggtacc cattcctctc 300 atctttctgc agtccgtcac caaggtgaag cagagattcc cacaagaaaa ccctagctga 360 tcgaccgttc tttcttccct ctctctcatt ttggcaccca ttcctctcat ctgtcttcac 420 tcggtcacca aggcgaagca gaaaatccca taaaaatagt gtagccgagg gttctttctt 480 ccctctctct catttgatac ccattcctct catatttctt cactccgtca ccgaggcgaa 540 gcagatttca gttgagaagg ccttaatccg atttgtcaca tcttagattt tctctgtcga 600 ggtaagccat tcgttccatg ttttgcattc gcattctcat tcatgaaaat ctgctgtttg 660 tgtgggtttt ttctgaacca ggcgtggctc aaatgttggc atttaggagt tggtactgaa 720 attttaaatc tgttggtaat gaatcatcat cgtctttttc aaatatgatt ttgtactgtt 780 ttatttggat tggcaaatta tcgcaactct gttgttttga tataaagtga aggcaagaat 840 atgggttggg aattgtttcg ttgaaaaagg catttgtttt tgttttggtt tagaactgag 900 aaaaacatat tttgaattga ttagcgaaaa aggaattttt tttttcccag tggtgttttt 960 aggtattggg aaacaatgca tttttagtga aacccattta ttggattgtg tttttggatt 1020 gagctatgca gtggatgacc aaaagggaac atttttttgg gatgaagttt tcattttgag 1080 agcaaaaaaa gttcttaaga aatggtgatt tttagatggg aaagttgttc caaattactc 1140 agttttttgg gtttttgtga tattgatggt tgatgggtgc taaagttttc gttgtgtttt 1200 tttgtttttg ttttatatgt atagtttcaa atcacgtccc atttcttcaa acatatagta 1260 acatatgtat ggttactata tgttaatgtt cttgttgatt agtaattgat attgattcag 1320 agatycgttt taaaagatgg taataggaaa ggctatatag gaactattgg tatccatgca 1380 ttggtttaat tcccttcata acataaatag aaaataggga atgctggtca gaatggatga 1440 aatgcatttt tatctatatg ttgtttgttt tggtgatcag ttggttaacc ttattgtact 1500 ggtaagttaa gcttatgtac tacctcatta ttcctaaatg tacgacctta atcgactgta 1560 tgtactgyat tagtcaacat caggtactac ctgagccaac cttgggtaca agctgtgtga 1620 cgactagaaa cttcattttt taatattcaa ataattcata tgtgaataaa cgttgtcttt 1680 attgttaacc caatggggtt cagtttgtca aacataggac ctacaggctg ttttcaagtc 1740 atgcataaat taaattgtat tcacttccac atacaagcta tcatgacatt atgtgtttga 1800 ctactctgct catttggttc cccttacctt tacttgagac tgtaccatag gtactatctt 1860 aattaacctt aggtctaacc ttagtaatct ttaagtacta ggttagatat ccttaggtac 1920 taccatagtt ggacttgcac actacttgtg tgcatcggcc aattagcatg tttgaacctt 1980 aattgtgtgc ataagccaat tagcatgttt gaaccttaaa gtatatggaa tcaacatgca 2040 taattcctca atctttcgtt gttgtattgt ttttaacaaa tctttatgtc aataaggaaa 2100 tggaagagga gatgttttgt tacattcatg aaggtggtga gcttgttaag actgctgttg 2160 ggtccgtcga atataagggt ggtcggacca attgcattgt tgttagcaag aatatctcac 2220 attctgaatt cgtttcaaaa gtatgtggtg aactgaactt ggagcccaat tcaattaaat 2280 tggatttcac agtgaagttt gacccatcat gtctactccc ahtgcataat gatgncgaca 2340 tagtcaagat gttcaaattc aacgacatgt tttgtcgtgc ctatgtctcc caatgtactg 2400 aaggtggtga tggcttcatt tgccctacta ggtacctaat gtctttccac aataatgttc 2460 ccttttgtat aatcgctttt cacacttagg ttgatggatg atcaatttct ttccttgtgt 2520 tttttgcagt gccccaacac ctattgttgc ttcaaactcg gctcatgttt cctctattgg 2580 cgagccccca ttgcacatgt ctaatgagtc gcccacaatt gagtcatttg ggttttccca 2640 aagatgtgct gaaacaaata tcgttcaact tcaaccaagc cggttcgaac attcaattgt 2700 aggtagtgga cataccttcc caaatgcctc ggagtttcga gatgcaatct atttgatgtc 2760 tttggctgga aaatttcgat attcttacaa aaggaatagt ccaaaacaca tgaccgtagt 2820 atgcacaatt gaagattgtc cttggaaaat cactgcbcgt gcaatagggg attcaaacat 2880 tgttcaagta cacacattcc gaaatgtgca taaccattgc ttggaagatg ttgccttgtc 2940 tcaaccttta gtgagatcca ctcgtgcntc vttggtcatt gatgatgtca ttcgatctac 3000 tcctgaatac caaccacgac aaatttgtaa ggactttgta aggcaacatg gcatccagtt 3060 gacttaccta caagcatggc aaatgaagga gaaggctaag gagcgcattt atggacaacc 3120 caagaattat tacaaattgt tgccatggat gtgtgaaaga atgcttgcaa caaatccggg 3180 atcgagtgtt gagttgagtt attccgatga tgaccatttt gagcagcttt ttgttgctca 3240 ttcaatatct atcgaagggt ttgtaagggg gtgtcgacca atcattgcaa ttgattcggc 3300 ccatatgagt gggccttatg gcggtgctct attttcagcc accgcctacg atgctaatga 3360 ctccatgttc cccttagcct ttggagtgat gagctcggaa aattatgaag attggttatg 3420 gttcttggaa aaactgaaga tagttgtggg aaacaaggaa gttattatta tctcagatag 3480 acatcctgct ctgcttcgta gtgttcctga ggtgtttggc cttgaaaacc atgcctattg 3540 ctaccgtcac ctgaaggaga attttagtag tttcttgtcc aagcataaca cacgagggaa 3600 caagggtaaa gaaaatgcat tgcaattcct agatagcatt gcgtatggaa ggttagaaca 3660 tgattataac gtttccatgt ttgaactaaa aaaatacaac gaggctttag ccacatgggt 3720 tgaagaaaat gcgccgcacc attgggccat gtcaaaattc ccaaaacaaa gatgggataa 3780 aatgactacc aaccttgccg agtcatttaa tgcttggtta cggattgaaa gacatcactc 3840 catttgtaac tttttattgg agcacatgtc caagttagct tctatgcttg tgaagcataa 3900 agaagagtcc aagaattgga aagggtgtat aggcccaaaa attgaagata aggtgctgca 3960 aaatattgca aagggtgagg tgtatccagt cactccgttc atgaatggag tatttggggt 4020 atgtatcggg agagccttgt tgaatgtaga cattatgaac cgtacatgca cttgtagggg 4080 ttggcaaatg ttgggaatcc cttgtgaaca tgccgcagcc gtcattattt ccattggtca 4140 aaacgttact gatttcgttg atgattgcta caaataccca atgcaagagt tgatatatgg 4200 gggctctttc tccggcatag agacccatga catgcctagt gtggatgatg atggtttggt 4260 tcgatctatc actggggagg ttttcttctc tctaaagcct ccacatacaa agcgccctcc 4320 cggaaggcca aggaagaagc gcattgagtc ccaatttcaa gataaacgga ctgtbtattg 4380 ctctcgttgt catatgtccg gccacaacag aaaaacctgc arvaatcctt tgccctaaat 4440 gcatatctgt ctacttattg cattatgctg atcttgtatt actctatttc aactaactgg 4500 ttgtcaccca atcatcgtta ctatttgaat gttttgtgcc tttccattca cctgcaatgt 4560 tcattgagtt acattatatt tctctactga ttcagttctt tcacaaagtc cgaactatgt 4620 ttgcaccaca tcttgtttta atggtattta ctcaaatccc atgtatttgc taagattaca 4680 ttgcttaagc cattttaacc atactgcagt ttgtgttccc atgtatcatt tggtggcatc 4740 atttaattat ccgaaaataa atactttgaa tgagtggcat catttggtgg cattttcaga 4800 ggctggttgc taatatcagt gtcggctggc ctgttcattt aattatctgc atatttgtcc 4860 tttgatttga gtgctatttt cttttatact ccccatggtt tgaggagtgc gatcaaacca 4920 atttttgccc taacctttgc ttcatttttc atgcactcta acaaaattta tttttcacca 4980 cacttcttca tggcttgtgc aataccagcc ataactgtac gctaacagtt cttactttcc 5040 aggtttaatt aattgcgctt acattatatc catctgaacg agaaggtcat cttattctag 5100 gcatggcaat agaaaggagg aaaaggaagg aacatgtccc tgcaacatgt gaacatgtcg 5160 gcaacacgga tttcattcaa caatgcattc aatcttcaat ttcaccttta atgcatattt 5220 ccatatattc tattttccta tcactgacca atatttaatt ttaactgtag gaaaagctcc 5280 caaagtcccg atgttctgga aggaaattca tcactgtgat tgcgcgctya ccaccagaaa 5340 aacaccaagc catcacagat atgggatttg ggggcctgct aacatttgcc tgtcgggagc 5400 tgagatatga gctgtgcggg tggcttatat ctcaatatga ctttacctac cacaggctta 5460 aaatggcaac tggcagtgct gtcactatta atgaacaaca tgtcagctaa gtcatgggca 5520 tccctaactc cggggaagac ttggttattg ttaagagaac aggcccctcc aaccgcacat 5580 acactctcag ggttttggag caaaaccttg acaatctgcc cgttggtgat gattttttaa 5640 aatcattttt aattttttct tgtgccactc tgctggcacc taattccaaa cttgaaggaa 5700 gccatgacct atgggacacc atatgggatt ctgatcttgg tgtccaaagg aattgggcta 5760 agtttttggt gcaacactta gaagacgaca ttagggaata tcagtaaaag caacctactt 5820 acatccgagg ctgcctcatg ttcctccagg tacagtcaag ggtccacagt attctgcaat 5880 taggttcaac tttgtttaca ttttatttta aaactcatcg ttactgcaat tccataattt 5940 aatgcttatt gtttcgtata ctacccttgt acaactctta tatatggcat tattctatat 6000 gccatcagtt attgttgagg tgacctggcc gcttgctact gcatggagtg acgatgtcat 6060 aaagcgccgc ttagcggctg aaatatcaac tttcggtgga tatgggcatg tggatgtatg 6120 ctataaatga acatagctaa agttcaattc catagtaata aatgcaaggg tattgggaat 6180 gactataaag taatgacata aaagctaata actcttgaat tgttatgcag atgttcatcc 6240 cggtttgcga gaataatcac tagcacgtgc atgttgttaa ttttgcagct ggaagagttg 6300 agatactttc gtcattgccc ctaaggcggg gcaacaacat cagtgctgca acgcgacgat 6360 tatcaatggc actccacaaa gcactgcatg catatagaat ccatatggat gcggatgtct 6420 caagttttgt gcatgtccaa ccacaccttc tccaacagct gaatgggtaa agtattcaga 6480 tattccaacg aaaacaaaca tttctaaata atttgattta tcagatttct atcatctaac 6540 acatttctga tgtgttatag gtccgattgt ggtgtcctcg ttctaaagtt catggaattt 6600 tggaatgggg cgaccttaac tactttagtg gcagaggtta gagttggttt acactgtcaa 6660 acttggactg tttttctttg tttttttccc aaccgcatgg aataattttt tcccatttcc 6720 gtaggacaag acgaacatgt acagactcta gctagtgctg caactagtgc tcaatgaacg 6780 caacagtgtc agagatacaa ttatggccgc atgtcatttg tgacttcata attcatgata 6840 agtttcttcc tatctgttgc tacgtaccaa aatgaccaag ggttgattgt agtttgtcca 6900 aaatttatta attcatatca tgttgtgtgc tgatgtgatt tgttccaatt gtaaaaccat 6960 tatttatgtt ctatatgtga tgtatttgat gaagtattcc acatcccatt gtaacagtgg 7020 ctgttgggtt atgctgaata tgaggacttt atgtacaaga atggccaacg tgtaagggaa 7080 aggaagagta cctggtaatg ctgctgctgg agcatatggg acgcagtaac agcagtgtaa 7140 tagggttgtt catttttcct tcaatattgt aaaggaaggg agtaggaaca tggacaacac 7200 tcagtatttg ttcttttatt atagttaagg gtgctggtta gtgttgtatt ggcgactgat 7260 tggacaacaa ttgtgattgt aagatgtgat ccaaagtgat aggtttatta tggggtatgg 7320 tactaatttc ataagagaac aacaaacata gactggaacc tatttgtttg tacactgatg 7380 cagtttcagt ttatccttct atactcacat tagtaaattg tttgacggct ttcctttcat 7440 atttagttat tgtgtaagct tttacataac atcttctgtt aatgttattg gtaagttggg 7500 aggtttgttt ggtttgattt actacattag aaacagtttg ctggtatacc aatagtttgc 7560 aatggtgccc ttcaaatcct gatctaccag ggttcaggac tattgcgcat cctcattggc 7620 aagggctact cagggttcct aaatgattgt gcattttgct aattttgtgc ttcaaaccat 7680 gtacaggttg ttatagaaaa aataaatgtg gtagaaaacc aataaatatt tgcttcgcat 7740 gatcaccttc cgtatccaac caaaaccatc gtaacttgac ataaccagaa aaatgagaaa 7800 acaacagtat gattaaataa atactgagag tgaaaaattg tcgggagagc aaaatttatc 7860 gaatatggtt taaggtagtg tcatgctgca ataggtaatg aaattaacta atgaaaatct 7920 gaagtcacag aatggctaca tttctcgcag gtgcgttaag gtagtacctg aggtacatta 7980 aggtagtact tgaagaccat taaggtagta ccttatgtgc attaaggtag tacttgaaat 8040 ttcttatgat tacataaggt accgttggag taacctatga gaacataaca atgtcatgct 8100 rcaataggta atgaaattaa ctaatraaaa tttgaagyca cagaatggct acatttctcg 8160 caggtgcrtt aaggtagtac ctgaggtaca ttaaggtagt acctgaagac cattaaggta 8220 gtaccttatg tgcattaagg tagtacctga aatttcttat gattacataa ggtactgttg 8280 gagtaaccta tgagaacata acaatgtcat gctgtaatag gtaatgaaat taactaataa 8340 aaatctgaag ccatagaatg gctacatttc tcgcaggtgc gataaggtag taccggaggt 8400 acattaaggt agtacctaaa gaccattaag gtagtacctt atgtgcatta aggtagtacc 8460 tgaaatttct tatgattaca tcaggtcgat ggagtcacct atgacaacat aacaacgtca 8520 tgctacaata ggtaatgaaa tgaactaata aaaatctgaa gtcacagaat agctacattt 8580 ctcgcaggtg cgttaaggta gtacctgagg tacattaatg tagtacttga agaccattac 8640 ggtagtacct taagtgcatt aaggtacgta gtacctgaaa tttcttatga ttacataagc 8700 tatcaatgga gtcgcctatg acaacataac aacgtcatgc tacaataggt aatgaaatga 8760 actaattgtg tctgaagtca tagaagagct acatttctcg caggtgcatt aaggtagtac 8820 cggatgtaca ttaatgtagt acctcaggac cattaaggta gtacctgagg tgcattaagg 8880 tagtacatga aatttgttat gattacatac gccaccgatg gagtaaccta tgagaacata 8940 acaatgtcat gctgcaatgt gtaatgaaat gaactaattg tgtcttaagt cacacaacaa 9000 caacatttct caaatatgca ctaagatagt acctgatgta cattaatgta gtacctgatg 9060 tgcaatgtgt aatgaaatga actaattgtg tcttaagtca cacaacaaca acatttctca 9120 aatatgcact aagatagtac ctgatgtaca ttaatgtagt acctcaagac cattaaggta 9180 gtacatgttt tgcattaagg tagtacctga tgcgatgaaa caattctgtc ttcattgaca 9240 aaagatgtac actacaaatt ccaacaaaca ttacaaattc acaaacacta ccaacaattt 9300 ctactaacca acacataatt tatgcatttt aatttttatt attattatta tttttatttt 9360 tatttttatt ctcaacatat atgattgaat tatcaagttt ttcgccaata tatgatattg 9420 cctaattata ttcatcaatt attaccatca gtctaaaaat ctgaataaat acacaagttt 9480 tccacccaat ttctaaatat gtccacaaca tttttccatt tcatgagtct ccaatacaca 9540 aaaatattga gatcgaacag cctctcatgc gatccaaaat cgacattcgc ctcaacctat 9600 gccctcacca atggaggaaa aattgcaaat acaacaacca ctcgaaaatc actcttctgc 9660 tccattttaa acaaaaaaaa tattaaaaaa acaaccctaa atacaaatta attaccttca 9720 catttgatgt gaaggttaca gaaaaatgtg atccaatgag aagaacacga gatttcttct 9780 tcatgaacct aatatatcag agttgtcgtt tccattccgg ttcgctatcc taaaccagat 9840 tttcagtcaa cacgtaccct cctcaagccg tcttcttaac tcgaccttgt ttcaatgaag 9900 tgctccattt ggttcttcac arttaccaca agcaacaaaa atttcgattc aggttttcaa 9960 gtaaaggttt atactttcaa atgtgtgaaa atttgcaaat tttcacaccc tcttcgatcc 10020 agaggggtga cgaaattggg atgatcgggt ctaaatggtt aggactttga gaggagaagg 10080 ggctgaagat agaaaactag attggagttt gggattaaag gcttcagaaa ttaaatgaga 10140 gaaattgttg aaaaatatac aagattcttt gcttcgcctc ggtgacggag tgaagacaga 10200 tgagaggaat ggctgccaaa atgagagaga gggaagaaag aacgactgaa cgctagggtt 10260 ttcttgtgga aacctctgct tcgcctccgt gacggagtgt agaaagatga gaggaatggg 10320 taccaaatga gacagaggga ggaacaacgc tagggttttt gtgtttgatt ttgcaaaaga 10380 aaaccgattc agtttcagcc cgtgctgaga tgggctgttg acgtggatac ctggaggggc 10440 aagctcggta gaaaaaacac agccggctca aagtgcatga atctgatata agtttccaca 10500 ttaacatatg tttttcatat ttcacaaacc tgggttccaa aaacaatatt attaccatat 10560 tggcctatga aaacacaact ttccc 10585 // ID MuDr3_MT repbase; DNA; EDCOT; 378 BP. XX AC . XX DT 04-FEB-2007 (Rel. 12.02, Created) DT 04-FEB-2007 (Rel. 12.02, Last updated, Version 1) XX DE Non-autonomous DNA transposon. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW MuDr3_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-378 RA Jurka J.; RT "MuDr3_MT: Non-autonomous DNA transposon from barrel medic."; RL Repbase Reports 7(2), 124-124 (2007). XX DR [1] (Consensus) XX CC Present in >600 copies phg. XX SQ Sequence 378 BP; 150 A; 43 C; 46 G; 138 T; 1 other; agggttaaat aagtttttcg tccctataaa tatatcaaat tttgatttta gtccctaaaa 60 aataaaatga gatgttttca tcctcacaaa attttttgtt ttatttttgg tccytaatgg 120 atataatttt gacatgtttt tgacattttt tgaacataat atgaatatat aaatgttgaa 180 cataataaac ggacataaca tgatacaatt tgaacataaa agagttataa tcttgacatt 240 catatgaaca taaattggtc attaaggacc aaaaacaaaa taaataattt tgtgaggatg 300 aaaacattca atttaatttt ttagggacta aaatcaaaat tcgctatatt tataaggacg 360 aaaaacttat ttaaccct 378 // ID DNA-9-3N_Mad repbase; DNA; EDCOT; 1150 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; KW DNA-9-3N_Mad. XX NM DNA-9-3N_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1150 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1464-1464 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC 9-bp TSD is AT-rich. The full length forms hairpin structure. XX SQ Sequence 1150 BP; 321 A; 245 C; 282 G; 302 T; 0 other; gggtaaatta catagtagcc cctcaggttt gaggtctatt acaaccccat acaacatctt 60 taaaacattt cactttcata cctcacgtac tattttattt caaaataata cctccgttac 120 attttccatc cattgatccg ttaagcgctg acgtggctgc cacatttgtg ccacgtggct 180 gccaaatgtg tgccatgtgg caaaaaaaaa attttttatt tttttaaaac ctgaatcttc 240 taaataaaat taaaaaaaaa aaaaaaaaac caaaaacaaa agctgaaaca cacctccccg 300 caacccccac ttcgtcttcc ctccctccct cccccaccca acctgcaacc ccagaagaag 360 aagaagaaga aaaaaaacaa aaacaaaaaa cccatcttca tcttccccga ccccccttcc 420 ttgcaaccca cccctttctt ccccctcccg tcttcccaaa cccaccgcac ccatcctcca 480 cgtcctcctc cgcacccacc ctccgcaccc accctcttcc ctcctctaca caccccactc 540 cttaaatcca cacccattgg ggaagacggg atctgggttg cagggaaagg gagatgggtt 600 tttttttttc ttttctaggt tgcaggtagt gggtgcagag gaggaggtgg aggatgggtg 660 cacggtgggt ttggggaaga cgggagggag aagaaagggg tgggttgcag ggaagggggg 720 tcggggaaga tgaagatggg tttttttttt tttttttttg ggagatggga agatgggtgc 780 gcagaggagg tggaggatgg gtgggagtgg ttttggattt gggttgcagg gagggacgac 840 ggatggggaa gatgatgaag gggatggggt ttcggcggtg ggggggaggg gtggggtgat 900 gggatttggg ttttctaagt tttttttttt tgaagattta ggtttttaaa aaataaaaaa 960 aataaaattt tgccacgtgg cacaaatgtg gcagccacgt cagcgcttaa cggatcaatg 1020 gatggaaaat gtaacggatg tattattttg aaataaaata gtacgtgagg tatgaaagtg 1080 aaatgtttta aagatgttgt atggggttgt aatagacctc aaacctgagg ggttactatg 1140 taatttaccc 1150 // ID Copia5-PTR_LTR repbase; DNA; EDCOT; 360 BP. XX AC LG_XIII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia5-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-360 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-360 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 279-279 (2007). XX DR Genome; LG_XIII; Positions 3997388 3997747. XX SQ Sequence 360 BP; 105 A; 79 C; 74 G; 102 T; 0 other; tgtgtttgtt gcattaaact caatctagaa ggtcaaggaa gacaaccacc acttgtagcc 60 accagctgtc atcgcctagc caccacttgc aatcgccagc cgccagccac cagctgtatg 120 ccgccagccg ccttcacact tgaaggttga attatcttgt tttgaattca tgtataaata 180 ggtacctaag tggatgctat tctgtgtgga aagagaggaa agaaacacta gaaagaaaga 240 gagagggagt gtattcaaag cttttgttta atctttgtaa gctttttatt gttgaaataa 300 aacagtgtgt tttataccct ctgaatgttt caaagccacc accagtggtt tctcccacca 360 // ID MuDR-1_Mad repbase; DNA; EDCOT; 2638 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; MuDR-1_Mad. XX NM MuDR-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2638 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1505-1505 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~89% identical to the consensus. Partial sequence. XX FH Key Location/Qualifiers FT CDS 673..2433 FT /product="MuDR-1_Mad_1p" FT /note="transposase." FT /translation="MMEEQSSQGPHLKQVAGERNPIVGQEFGSITEAYDFY FT NQYAREVGFSVRMGSSKKKKGTNEITWKQFVCSKEGEPDETYQKTKKNTST FT KEERNVGSTRVGCKAKLSISRDKSKKKWSICNFEECHNHVLSTPTKAHLLH FT SHRKVSKAKKLYMETLSSANVPTSQQFRIMENEAGGIANVGCIDKDLRNVE FT RDLQKEIKGHDADMLLEYFHSEKEKNPSFYFEVDKDEENRLSRCFWVDSTA FT RKAYFFFGDVVAFDATYNTNKYSMIFAPFVGVNHHNQTIVFGCGFLSDEKT FT ESFIWLFEQWLKAMPSGPPQLIITDQDQAISKAIAQVFPLAFHRYCIWHIM FT DKFPQKLGPMLSVYMPQFSASVYGSETIEEYEESWKHALMQHSALENHERL FT LPMYKLRKQWVPAFCMHIFSAGMSSSQRVESGHSFFKKYVSKRNSLWDFVT FT RFERALGHQRHKELVSDHVDVNEVPKLKTLFPIEKQMRGLYTKTIFLKFQD FT EVIQSTAYLKCDAIREDEKECVYVVIRADAESSTLRHIVHDKVSSFAKCSC FT RKFEFEGIPCRHIVFFSQKYSYCRFAKPIHHEKMDQKCEG" XX SQ Sequence 2638 BP; 855 A; 430 C; 546 G; 807 T; 0 other; tgctctccta aggtcctctt tttaaggatc tgtgaggacc tcttttatta gagccatagg 60 attaatctaa cggtacaaaa actaatgagt ttatataatc cttttacacc taaacaaaat 120 caaaacacac caaaattaaa aataggattc acgctcaaga accaacgact gctgcagttt 180 gaagagttcg agatcttcac cctggatcgc ctctgaggta attttccttt ccgtttcact 240 gctcaatttt tgtctccaaa ccaaccgatt cttatgatta attaataact atatgttgtg 300 ttcgactctt ttgggaagaa tgtaaatgac ctacccagct tttcgaattg gtcgcactcg 360 aaaattgcga gatcaaagtt taattgactt ataaaaaatc gaatcctgtt gtaatttgaa 420 gaaatcaact tctgtggtat cttttaattt tggttttcgt ttggttcgtg agaaaatttt 480 gttggttttc gtttggttcg tgagaaaatt ttgaaacgag aaatacggtt cacgctcatc 540 ctccctgctc cagccctctc accgtttagt gggtgagaaa attgattata ttgcatttgc 600 ctttgtggtg gtggttcaac ctttagcccc attttttttt cttcactttt aattttaatt 660 gcatattgct ttatgatgga agaacaatct tcccagggac ctcacctcaa acaagttgca 720 ggtgaacgta atcccatagt tggccaagaa tttggatcaa taacggaagc atatgatttt 780 tacaatcaat atgctcgaga agttggattt agtgtcagaa tgggttcaag taagaagaaa 840 aaaggaacga atgaaatcac ctggaaacaa tttgtttgct caaaggaagg tgaaccggat 900 gagacttatc agaaaacaaa gaagaataca tcaaccaagg aagaaaggaa tgttggatca 960 acacgtgtgg gttgtaaggc aaagttaagc atttctcgtg acaagtcaaa gaagaagtgg 1020 tctatttgta actttgaaga gtgtcataat catgtacttt caacacctac aaaggcacac 1080 ctactacatt cacaccgaaa agtttcgaaa gcaaagaagc tttacatgga aacactaagt 1140 agtgcaaatg tacctacaag tcaacaattc agaataatgg aaaatgaggc aggtggaatt 1200 gcaaatgttg gatgtattga caaagatttg agaaacgttg aaagagattt gcagaaagaa 1260 atcaagggac atgatgctga catgcttctt gaatattttc attcagaaaa ggaaaagaac 1320 ccatcttttt attttgaagt tgataaagat gaggaaaata ggttgagccg ttgtttttgg 1380 gtcgattcca cagcaagaaa agcgtacttc ttttttggtg atgtagttgc ttttgacgcg 1440 acttacaaca caaataagta tagtatgatc tttgctccat tcgtaggggt taaccatcac 1500 aatcaaacaa ttgtatttgg atgtgggttt ttaagtgatg agaaaactga gtcatttatt 1560 tggttatttg agcaatggct gaaagctatg cctagcggtc cacctcaatt gataattacg 1620 gatcaagatc aagcaatatc aaaggccatt gctcaagttt ttcctcttgc attccaccgg 1680 tattgtattt ggcatataat ggataagttt ccacaaaagc ttggcccaat gctttcagtt 1740 tatatgccac aatttagcgc tagtgtatac ggttccgaaa ctatagaaga atatgaagaa 1800 agttggaagc atgcattaat gcaacatagc gcattggaga atcatgaacg gctgctacca 1860 atgtacaaac tccgtaagca atgggtccct gcattttgca tgcatatatt ttctgcagga 1920 atgtcaagta gtcaaagagt tgaaagtgga cactctttct tcaagaaata tgtttcaaaa 1980 cgcaactctt tgtgggattt tgttacacga tttgagaggg cactcggaca ccaaagacat 2040 aaagagttgg tttctgatca tgtggatgtt aatgaagtac caaagttgaa gacattattt 2100 ccaattgaaa agcagatgcg cggtttatat acaaaaacaa tatttttaaa gtttcaggat 2160 gaagtgattc aaagtactgc ttatttgaag tgtgatgcta taagggagga cgaaaaggaa 2220 tgtgtttatg ttgttatacg tgctgatgca gaaagctcaa cattgcgaca tattgttcac 2280 gataaagttt ctagttttgc aaagtgcagc tgtcgaaaat ttgagttcga aggaattcca 2340 tgcagacata ttgtattttt ttctcagaag tattcatatt gtagatttgc caagccaata 2400 catcatgaaa agatggacca aaagtgtgaa ggctgaaaga gtttgggatg gagatggatt 2460 ggaaataaaa gatgtgcaat acaagtcatt aatgatgagg catattcagt tatctcaact 2520 ttcatagtgc ttaattgatg aatcatccct tatggaagaa acaactgaac ttgtaagaaa 2580 aggaatcgaa tcgcttcgta ttgaagttaa gggattacgc tccagtttag gtgttgga 2638 // ID Copia6-PTR_I repbase; DNA; EDCOT; 4222 BP. XX AC LG_I; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia6-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4222 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4222 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 288-288 (2007). XX DR Genome; LG_I; Positions 14951032 14955253. XX CC Positions [1744-2124] - Integrase core CC LTRs are 87% similar to each other. XX FH Key Location/Qualifiers FT CDS 2698..4179 FT /product="Copia6-PTR_I_3p" FT /translation="MQEELHALEANQTWDIVDCPSGVTPLRCRWVYSVKIK FT VDGSLDRYKARLVALGNHQKYRVHYEETFAPVAKMGTIRTILAIAASKHWC FT LHQLDVKNAFLHGDLTEDIYMRPPAGLFSTPTSAVCKLRRSLYGLKQAPRA FT WYERFTSILLQFDFLKSKYDASLFLRKTAHGVVFLLVYVDDIVITGTDLAL FT IDQLKQHLQKSFHMKDLGPLTYFLGLEIHAGSHGIFLSQHKYAMDLVTTAG FT LQNSPPLDTPMEINLKLRKDEGDLLSDPAAYRTLVGSLIYLTNTRPDISYA FT VQQVSQFMASPRHLHMVAVTRIIRYVHGTIRRGLCYPAGTSLDLIAYSDAD FT YAGCSDTRCSTTGWCMFLGPALISWKSKKQDRVSKSSTESEYRAMSQSCSE FT IIWLHGLLAELGFQQCTPTPLFADNTSAIHITANPIFHERTKHIEVDCHFI FT RDAFAAQTISLPHVSSNLQVADVFTKTLTRQRHHYLTTKLMLMDKPASI" FT CDS join(97..1740,1744..2664) FT /product="Copia6-PTR_I_1p" FT /translation="MFVRFTGKNYTAWAFQLEIFLKGKELWGYIDDSNKGD FT LAVEGSVVAKAAWAAKDAQIMSWILSSMESHLILSLLPHRSAKAMWDHLTQ FT VYNQDNNARRFQLELAIANYTQGNLSIQDYYSGFLTLWNDYSDLVTAKISA FT EGVLAVQQVHKISQRDQFMMKLRSEYELVRASLVNRDPVPSLDACFGELLR FT EEQRLHTQTIMEQTRVAPVAYVAYRKGKDHDMSKTQSYSCKYGHIAPHCPN FT KFCNYCKQPGHIIKECSIRPPRINKAYHTAVTNAGPSAPQPLVGSPISQPP FT AHLLTKEMVQEMIVSAFSTLGLQGTGSSTLPWILDSGASNHMTNSFGGLRN FT IRKYYGSSHIQTANGNALPIVAVGDIPPLKDIFVSPKLAVNLASVGQFVDN FT NCDVSFSKHGCIVQDQMSGQLVAKGPKHGRLFFIQFHVPRTLVPSSVLSLF FT CTAPKVSNEVWHKRLGHPNPRILSHLLKSRLINTTMHSSSSMFLDCVTCKL FT GKSKVLPFPSEGSRATNLFEIVHSDVWGISPILSHARYKYFVTFIDDYSRY FT TVYFLRNKSEVFSMFKLFLVLVNTQFSATVKTLRSDSGGEYMSNDFQSFLQ FT SKGIISQCSCSYTPQQNGVAERKNRHLLDVVRTLLIENSVPPKFWVEALIT FT ATYLINRLPSQVLGLESPYFRLHHCPPIYTNLHTFGCVCFMHLPPPHRNKL FT SAQSIRCAFLGYSITQKGYLCFDPHTNRVHVSRNVIFFENQCFFPLPSSSA FT TSLASLPSFDDSSHLQSAQVDRFKPHMVYKRRLPVLPPSASVLSSAPPLHP FT SVASEVTVLAPLRRSSRVSVPPAKYGFNSFVAHNSTAALSATLSSIAIPTG FT YS" XX SQ Sequence 4222 BP; 1081 A; 963 C; 812 G; 1366 T; 0 other; aatctgttat ggtatcagag cctctctcat agaattccta aaatcttagt cttttttttt 60 tttctctcag tcatagcctc atgaaaaagt cagataatgt ttgtcagatt tactggcaaa 120 aattatactg cttgggcatt tcagctggag atctttctca agggaaagga gttatggggc 180 tatatagatg acagcaacaa aggagacttg gctgttgagg gatctgttgt tgctaaggca 240 gcatgggcag ccaaagatgc acaaatcatg tcatggattc tcagttctat ggagtcacat 300 ctgatcctgt ctttgctccc tcatagatca gcaaaggcta tgtgggatca cctcacacaa 360 gtctataacc aagataacaa tgctaggcgg tttcagcttg agttggctat tgccaactat 420 acccaaggaa atctctctat tcaagattac tattctggat ttttgactct atggaatgac 480 tattctgatc ttgttacagc taagatctct gccgaaggag tgttggcagt gcagcaagtc 540 cataagatca gccaacgcga ccaatttatg atgaaattgc gatctgaata tgaactagta 600 cgtgcctctc ttgtcaatcg tgatcctgtt ccatccttgg atgcttgttt tggagaactc 660 ttgcgtgaag aacaacgtct ccatactcag accattatgg agcagaccag agttgcccca 720 gttgcttatg ttgcttacag aaaagggaaa gaccatgata tgagcaagac acaatcctat 780 agttgtaagt atggtcatat tgcacctcat tgtccaaata agttttgcaa ctactgcaaa 840 cagccaggac acattattaa ggaatgttct attcgtcctc ctcgcatcaa caaagcctat 900 cacactgctg ttaccaatgc tggtccttct gctccacagc ctcttgttgg ctcacctatc 960 tcacagcctc cagcacattt attaaccaaa gagatggtgc aggaaatgat tgtgagtgct 1020 ttctccacac ttggtcttca aggtactggt tcttcaactc ttccttggat cttagattca 1080 ggtgcttcca atcacatgac aaactccttt ggtggcttac gtaatatccg caaatattat 1140 ggatcctcac atattcaaac agctaatggc aatgctcttc ccattgtagc tgttggtgat 1200 atacctcctt taaaggatat ttttgtctca cctaagcttg ctgtaaatct agcttctgta 1260 ggtcagtttg tggacaataa ctgtgatgta tccttttcta aacatggttg tattgtacag 1320 gaccagatgt cgggacagct ggtagcgaag gggcctaagc acggacgtct attcttcatc 1380 caatttcatg ttccacgcac cttggttcct tcctctgttt tatctctctt ttgtactgca 1440 cctaaagtgt ctaatgaagt ttggcataaa cgtcttggtc atccaaatcc tagaattctc 1500 tcccatctgt tgaaatctag attaataaac actacaatgc attcctcttc cagtatgttc 1560 cttgattgtg tcacatgtaa gcttggcaaa agtaaagtat taccttttcc ctctgaaggc 1620 agcagagcaa caaatttgtt tgagatagtt catagtgatg tctggggaat tagtcctatc 1680 ctttctcatg caagatacaa gtattttgta acctttatag atgactacag ccgttataca 1740 tgagtttatt tcttgcggaa caaatcagaa gttttctcta tgttcaaatt gttccttgta 1800 ctggttaaca cccaattttc tgccactgtt aaaactctta gatcagattc aggaggggag 1860 tatatgtcta acgatttcca atctttcttg caatctaaag gtatcatttc tcaatgctca 1920 tgttcctata ctcctcagca aaatggagta gcggaacgca agaatcgcca tcttttggat 1980 gtggtccgta ctttgctcat tgaaaattct gttcctccta agttttgggt ggaagcactc 2040 attacagcaa cttatctaat caatagactt ccttcacaag tcttgggtct agagtctcca 2100 tattttcggc ttcatcattg ccctcctata tacaccaatc ttcacacctt tgggtgtgta 2160 tgcttcatgc atcttcctcc acctcataga aataaacttt ctgctcagtc aattaggtgt 2220 gcctttcttg gatatagcat tactcaaaaa ggttatctat gttttgatcc acacactaat 2280 cgagttcatg tttccagaaa tgttattttc tttgaaaatc aatgtttctt tcctttgcct 2340 tcatcctcag ccacttctct tgcctcttta ccctcttttg atgactcttc tcatctgcaa 2400 agtgctcaag ttgacaggtt caagccacat atggtataca agagaagact tccagtgctg 2460 cccccttcag cttctgtcct gtcatctgct cctcctttgc acccttctgt ggcttctgag 2520 gtaactgttt tggctccttt acgccgctcc tctagagtat ctgtaccacc tgctaagtat 2580 ggatttaact cctttgtggc acacaattct actgctgctc tctctgccac tttatcctct 2640 attgctattc ctactggtta ttcataggca gctaaagaac catgctggca gcaggctatg 2700 caggaagaat tacatgctct cgaagctaat cagacttggg acattgttga ttgtccttct 2760 ggtgtgactc ctcttaggtg tcgatgggtc tattctgtta aaatcaaggt tgatggcagc 2820 ttggacagat ataaagcacg attggtggct cttggaaacc atcaaaaata tagagtacat 2880 tatgaggaga cttttgctcc cgtagccaaa atgggtacta ttcgaacaat tctggccatc 2940 gcagcatcta aacattggtg tttacaccaa ttggatgtga agaatgcctt tcttcatggt 3000 gatctcactg aagatatata tatgcgacca ccagccggct tattttccac tcctacctct 3060 gctgtgtgta agttacgccg ctccttgtat ggtctcaaac aagctcctcg tgcttggtat 3120 gagagattta cttcaatcct tcttcaattt gatttcctca aaagtaaata tgatgcatct 3180 ttgtttctac gtaagactgc acatggagtt gtgtttctat tagtgtatgt tgatgatata 3240 gttatcaccg gtactgattt agctctgatt gatcaactaa agcagcattt gcagaaatcc 3300 ttccacatga aggatctagg tcctctaaca tattttcttg gtctagagat tcatgctggt 3360 tcacatggca tatttttatc ccaacacaag tatgccatgg acttggtgac aactgctggt 3420 ctccagaatt cgccacccct tgatactccg atggaaatta atctcaagct acgcaaagat 3480 gagggtgatt tattatcaga cccggcagca tatcgtacac tcgtgggcag cttgatctat 3540 cttacaaaca ctagacctga tatttcttat gcagtacaac aggttagtca gttcatggct 3600 tctccgaggc acctccatat ggttgctgtt acaagaataa ttcgttatgt tcatggcaca 3660 atccgaagag gactttgcta tcctgctggt acttctcttg atcttattgc ttatagtgat 3720 gctgattatg ccgggtgttc tgacactcgg tgttcaacta ctggttggtg tatgttcctt 3780 ggccctgcac ttatttcctg gaagagcaag aaacaagacc gtgtttccaa gtcttctact 3840 gagtctgaat acagggctat gtcccaatct tgttccgaaa tcatctggct ccacgggctc 3900 cttgctgagc taggttttca gcagtgcact cctactcctc tttttgccga taatacaagt 3960 gctatacaca ttaccgccaa tcctatcttc catgagcgca cgaagcatat tgaggtggac 4020 tgccacttca ttcgtgacgc ctttgcagct caaactatat cacttccaca tgtgtccagc 4080 aatcttcagg tggctgatgt ttttaccaag actctcacac gacaacgtca tcattatctt 4140 acgaccaaat tgatgcttat ggataagccc gcatcaattt gaggggggat gtcaatagaa 4200 aggctgaagt caagcataca gt 4222 // ID DNA9-3C_Mad repbase; DNA; EDCOT; 792 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative transposons from the apple genome. XX KW Transposable Element; Nonautonomous; DNA9-3C_Mad. XX NM DNA9-3C_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-792 RA Kojima K.K. and Jurka J.; RT "Putative transposons from the apple genome."; RL Repbase Reports 10(10), 1825-1825 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~98% identical to the consensus. TSDs are likely 9-bp. It shows CC similarity to DNA9-3_Mad and DNA9-3B_Mad. XX SQ Sequence 792 BP; 291 A; 108 C; 69 G; 324 T; 0 other; ggaaaaatta gtatccggtc cctagttctt actgttcatt gactaagacc ttattagttc 60 tcaaattttg attcaagtcc ctagcattaa tgtgataatg aatttacatg tttattatat 120 aattttttaa tataaaaatt agtaattaat ttagggttta atactcacac ctctattaaa 180 cttctaatta attttcaatt caaacatttc caaaataata aaaaattaaa ttaaattaag 240 tttgtaccta ttagtttttt ttatatatat aaaaagattc tcaatttttt aatcttaaat 300 gtacccattc atataatttt tcaatttttt taatcttaaa tgtacccatt ctcaaatata 360 tcaatttgtt atatgtaaaa tgtacccttt ttttaatata aaatccattc aaatttttta 420 atccatgttt aaacttatat gggtacattc tttttcgttg atttgagaat gtatccatgt 480 tttggtacaa taactttttt tgttaatttt ggttaatgta cccatacata tatgtatata 540 cacacacaca cacacacaat ataatagaga gtataattta tattttatta tttttaatcc 600 cataaattat gggttttatt taaaatctca ttaatataaa caattacaaa tttcaatttt 660 taatttttaa ttaaaaaaat atagtaactt acattattac attaatgtca gggacctcaa 720 tcaaaaacta aaaactaaca aggtttcaat caaagaatat tgatagctag ggaccgcatc 780 caaagtgtcc ct 792 // ID EGLN3_SM repbase; DNA; EDCOT; 410 BP. XX AC AB016144; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 23-SEP-2007 (Rel. 12.1, Last updated, Version 2) XX DE Solanum melongena LINE retrotransposon EGLN3_SM, endonuclease DE region. XX KW L1; Non-LTR Retrotransposon; Transposable Element; endonuclease; KW LINE; EGLN3_SM. XX NM EGLN3_SM. XX OS Solanum melongena OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-410 RA Noma K., Ohtsubo E. and Ohtsubo H.; RT "Non-LTR retrotransposons (LINEs) as ubiquitous components of RT plant genomes."; RL Mol. Gen. Genet 261(1), 71-79 (1999). XX DR Genbank; AB016144; Positions 1 410. XX SQ Sequence 410 BP; 145 A; 43 C; 99 G; 123 T; 0 other; ttggaatgtg cgaggtctaa attgccttag taagcagagg gaagttgcat tcttctgtaa 60 caaatgagaa ctaaatttag taggactggt gaagacaaaa ataaaataca aaagtgtaga 120 tcgggttgtt taatccatgt ttgctggttg gaattattac tataaccata actctcatta 180 taatgggagg atattggtgg tatggaggga acatataaat gagataaggt ggaaagtgaa 240 ttacatcaag caataacatg tttattgaaa aacaagttgt tgatgaaaga attttactat 300 acttatgttt atgctcagaa tgggagggaa gaaaggaaag aactattgaa gtatttgaat 360 cagtggagtg ttggtatgta gaaaccatgg ctcttccccg gagattttaa 410 // ID Gypsy19-VV_LTR repbase; DNA; EDCOT; 1709 BP. XX AC . XX DT 11-SEP-2007 (Rel. 12.09, Created) DT 01-OCT-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy19-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1709 RA Obukhanych T. and Jurka J.; RT "Gypsy19-VV."; RL Repbase Reports 7(9), 795-795 (2007). XX DR [1] (Consensus) XX CC This is 5' LTR from Gypsy19-VV LTR retrotransposon. 5' and 3' CC LTRs are 97% identical and contain small indel mutations. XX SQ Sequence 1709 BP; 518 A; 306 C; 316 G; 566 T; 3 other; tgattactac tcaaaaagtg ctcttttata gcttgttata aactctttta aacacttttg 60 agtagtattt attacctttt aactcaattg gcacattaag gacccttgca aatgtttcta 120 atcagttttt ggcaagtttt ggtgtttttg atagcttttt tatcattaaa acragccaag 180 aatgagggag aattttgtat agtccatggc aaagcaagtt gaagctcaaa cacatgaaga 240 atccaagttt tggagagctt cgtagccttt gccaaatcaa tcaagtatgc aaggaagaga 300 atcagagaag aaatctaaca tccagcaatt tcgcatggct atgcgaaata ccaaaaggag 360 tacaagctgc aagactgtga aaaatgaatt tcgcaccctg tgcgaaattt cgcaagcctt 420 gcgaaattcc tcctatgtaa ttttcagata tttttgcacc gactccgtta gatttttatc 480 tcaagatatt ttgtgtaatt acctattttc tccttgtaat cagctaaaga tatttttaga 540 tatttaggat atctaaatga ggggttaaaa atatctctct atatatgtct taaaatatct 600 ctttttgtaa gcgaaagaaa tcctatgtaa aaatctcgga atctcggaag aaattccaga 660 gaacacttgt aaattctttt agtaagaaat atacagagct ttgctctgcc ttacctattc 720 attttgtttt tattttcttt ctagccaaac aacctctgag gatgttttct cagaggatga 780 gtggctaggt ttttcgtttc ttggactgaa ggaagctagg taagggatcc ggatacaaaa 840 gtgggagttt tccttgtttt aaatgaggag agttgtgacc cgttaatggt ttttattttt 900 ttaggtttaa cttaaaatcc cttaaaatca cctgggccaa cacttggtaa gcttttcgga 960 ctccatggag atccattagt tatctcttgc gagcctctgg gaggtggttt aaaggtagga 1020 ttttctagaa tagccaacac ttggtaagct tttggactcc awggagacat ccattagtta 1080 tctcttacga gcttttgaag ggtaatccaa ggttaaggat caccttgaat ggccaatact 1140 tggtaagctt ttcgggccat ggaatggatg tctattagtt atctcttacg agccattgaa 1200 agatgattca cagtgagagg tctttagtgt ttgaaaccat taatgggaag caactgcagt 1260 ctttcatgga ccagtgggat caaatcttga ttgctaaata cacaccggtt cgggagataa 1320 ccattcttta tgttattatc cccaacgcga ggaaaagatc cggaatctcc cctttttgtc 1380 taaggaacct gaacctagtg acctaaaact ccaagaaacc ttttctttgt aattaatctc 1440 agttactatt tttggttaac ttaaaaccaa cctttttcaa cccaaaatta tgttttcttt 1500 taaagctaac tcataaaaga aaaaacacca tttcagtact ttaactaata tcacktgtga 1560 tatgaaaacc catccctgtg gacgatccta gaaccactat actatgctag ctatgctacc 1620 ctagtatatg gtgaattagg tttataaatt ttgttgataa ctcccgtctg aggactgaat 1680 taaagagtac accaattggg gacgaatca 1709 // ID MuDR-5_VV repbase; DNA; EDCOT; 9997 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-5_VV, an autonomous DNA transposon - a consensus sequence. XX KW MuDR; DNA transposon; Transposable Element; mutator; Mutavine-5; KW MuDR-5_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9997 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 765-765 (2008). XX DR [1] (Consensus) XX CC MuDR-5_VV (Mutavine-5 in [1]) consensus is a virtual autonomous CC element. Its individual copies are >90% identical to the CC consensus sequence but do not contain an intact ORF due to stop CC codons and/or frameshifts. MuDR-5_VV does not contain TIRs, but CC is flanked with 9 bp-long TSDs. MuDR-5_VV has an intronless CC transposase gene. Downstream of the transposase is a putative CC gene in a reverse orientation virtually encoding for a ULP1-like CC protein similar to CAN81969.1 (region 7278-4716). XX FH Key Location/Qualifiers FT CDS 894..3320 FT /product="MuDR-5_VV_Transposase" FT /note="Intronless MUDRA transposase." FT /translation="MLLYEGDWVQNGNMYYFEGCQGKGIELKKTTTYEELL FT KIVCHILKVDPTEHNLSMKYVFNGNIPSTPIQLRDDGDVKFFIRLNCTDGK FT LPVPLCITIEKRSGNHGYESIINTDFGSHTLSGVEKEINMDPIFINSSESL FT SGFDDENRTRLSYDPLNCFDSHNLNMNKDDEDGGMNVNPNKDSQVMQIDVM FT EKAVMEYESHAEESIEEPFIVGYSEIGDDYMEEHQIYSNKKELQKKLCMIA FT LKRKFQFKTLKSSTKLLSVGCVDKECKWRLRAIKLGNSDLFQIRKYHSTHT FT CSLDMISRDHRHASSWLIGESIREIYQGVGRQYRPKDIVADIRNKFGVGIS FT YDKAWRAREFALSSIRGSPEESYSALPSYCYVLEQKNPGTITDIVIDHDNQ FT FKYFFMALGACISGFRTSIRPVITIDGTFLKAKYLGTLFVAACKDGNNQIY FT PLCFGIGDSENDASWEWFLKKLHGAIGHVDDLVVVSDRHNNIEKVVRKVFP FT HASHGVCTYHMKQNLKTKFKNVEVHKLFHDAAYTYRLSEFNVIFGQLQMIS FT PRAATYIIDAGVERWARSHSTKKRYNIMTTGIAESLNVVLKDARDLPILQL FT IEELRNLLQKWFANRKQQALSMTTELTTWADGELRVRYNTSSTYEVEAINS FT MEYNVKYNGVSDHVNLHNHSCTCRRFDLDHIPCSHAIVACRYAHMSCYPLC FT SKYYTVNSLLSSYAESIYPPGHQRDWMIPDDISSRVVLPPKTRRPAGRPRK FT ERIPSGGEGKRRRRCGRCGDYGHNRKSCKRPIPLHYQNDNSGHTEIGMQDC FT SLQSENE" XX SQ Sequence 9997 BP; 3486 A; 1545 C; 1557 G; 3409 T; 0 other; gaatctttgg ttagattata aggttatttg gataggtgac tctaaataaa ggtaaaatta 60 taaaagtaac ctcaccaatt aattgttttg agagatgacc taatttggac atttttaccc 120 ttatttattt ccctccaaaa acaaataaga tcccccacca aagacatgat atccctccaa 180 aagtagaaaa ctttagtttt acctctctca tcggtactac atctctttca ccaacactgt 240 gagtacatcc atatacacaa tctctataac ccactaataa aactgagtta agagaagcag 300 aaaagagtag tgaaacatag aagaataaga tcccccacca aagacatgat atctctccaa 360 aagcaaaaca ttttagtttt atctctctca ttggtactac atctgtctgc atatttctca 420 ccaacattgt gagtacgtcc ctatacacct ttactgcaat ccaccatcaa aattgaggta 480 atagaagtag agcatattaa agaataacat atgacgaggt tgaatgaagg tatgtaaacc 540 catttgggga aaaaaaattt atcttagttt tgctattctc aacattattt ggttgtaggg 600 aaaaaagtga aaattttaga gtaaacatga gtgaaatttt ttgttaaaaa gatttgtatg 660 aaaagagtaa agttcatatt taacatgtaa aaactggatg caactagtgt taagttcttt 720 atataaaact tgaagatagt tgagtatagt tcaacatgtt aatcgaccac tttgcgggtt 780 tgagttactt atccgaataa ctactatttt aatattgttt tttttttgta tcaataattc 840 aatttattta tttattattt atttttgtta tagtgattga tgaagtggga ataatgcttt 900 tgtatgaagg agattgggtg caaaatggaa acatgtacta ctttgaaggt tgccaaggta 960 aaggtattga acttaagaag actacaacat atgaagaatt attgaagatt gtttgtcaca 1020 ttttgaaagt agatccaaca gagcacaatc tttcgatgaa gtatgtattc aatggcaata 1080 taccatccac tcctatacag ctaagagatg atggagatgt gaaatttttc attcgtttaa 1140 attgtactga tggtaagttg ccagttccat tatgtatcac aatagagaaa agaagtggca 1200 atcatgggta tgaatcaatc atcaacactg attttggctc tcatacttta tctggggttg 1260 agaaagaaat caatatggac ccaatattca taaatagtag tgaatctttg agtggttttg 1320 atgatgaaaa tagaacaagg ttgagctatg atccacttaa ttgttttgat tctcataact 1380 tgaatatgaa caaggatgat gaagatggtg gaatgaatgt caacccgaac aaggatagcc 1440 aagtaatgca aattgatgta atggaaaaag cagtaatgga atatgaaagt catgcagaag 1500 aaagcataga ggaaccattt atagttggtt atagtgaaat tggtgatgac tacatggaag 1560 agcaccaaat atactccaat aagaaagaat tgcagaagaa gttgtgcatg attgctttga 1620 aaagaaagtt tcagttcaaa acattaaaat cttcgaccaa gttattatct gttggatgtg 1680 tcgataaaga atgcaagtgg cgacttcgtg caatcaagtt gggaaattct gatctatttc 1740 aaataaggaa atatcattca acacacactt gtagcttgga tatgatatcc cgtgatcatc 1800 gtcatgcaag tagttggttg attggtgaaa gcataagaga aatatatcaa ggggttggtc 1860 gtcaatatcg accaaaagac attgtagctg atattcgaaa caagttcggt gtggggataa 1920 gctatgataa ggcatggaga gctagagaat ttgctctaag ttctattaga ggatcaccag 1980 aggagtccta tagtgcttta ccatcttatt gttatgtgtt ggagcaaaaa aatcctggca 2040 ccattactga tatagttatt gaccacgaca atcaatttaa gtattttttt atggctcttg 2100 gtgcatgtat ttctgggttt cgtacatcaa taaggcctgt cattacaatc gatggaacat 2160 ttttgaaggc aaagtactta ggaactttgt ttgttgctgc atgtaaggat ggaaacaatc 2220 agatataccc tttatgtttc ggaattggtg attctgaaaa tgatgcttct tgggaatggt 2280 tcctaaaaaa attgcatgga gcaattggcc atgttgatga tctcgtggtg gtttcagatc 2340 gtcacaacaa cattgaaaaa gttgtgcgaa aagtttttcc tcatgcaagc catggtgtgt 2400 gcacttatca catgaagcaa aacctcaaaa caaagtttaa aaatgtcgaa gtccataagt 2460 tgtttcatga tgctgcttat acataccgtt tgtcagaatt caatgttata tttgggcaac 2520 tacaaatgat ttctccgaga gcagcaacat atataataga tgcaggtgtt gagcgatggg 2580 cacgttcaca ttctaccaaa aaaagatata acattatgac cacagggatt gctgaaagtt 2640 tgaatgttgt gttaaaagat gcaagagatc ttcctatttt gcagttaatt gaagagttaa 2700 gaaatttact tcaaaaatgg tttgcaaacc gtaaacaaca agcattgtca atgacaactg 2760 agctaacaac atgggctgat ggagagcttc gtgtaaggta caatacatca tcaacatatg 2820 aagttgaagc aatcaactcg atggagtata atgttaaata taatggtgtc agtgatcatg 2880 tgaatttaca taatcattca tgcacatgtc gacgttttga tcttgatcac ataccgtgtt 2940 cacatgctat tgttgcttgt agatatgcac atatgtcatg ctatccttta tgctccaaat 3000 attacacagt gaactcatta ttatcttcat atgctgagtc catctatcct cctggacatc 3060 aaagggattg gatgatacct gatgatataa gcagtagagt tgtattacca ccgaaaacaa 3120 ggcggccagc aggaagacca aggaaggaaa gaatcccttc aggtggagag ggtaagcgca 3180 gacggcggtg tggtcgatgt ggtgattatg gtcataatcg aaagtcatgc aaacgaccaa 3240 tccccctgca ttatcagaat gataatagtg gacacactga aataggcatg caagattgct 3300 ccttacaatc agagaatgaa tgaaactatc actaagccaa ttttatggtg aattttttgt 3360 tttttgtaga tgatgtttgg gcatataaaa tatttgatat tgtagttttt tttgtatatt 3420 gtgaataggg gcacaaaaca tgtaatcgta ctttgattca gtctctttta attgaatgtt 3480 gaacttaaag cttaaaaatg aagtttaagt tcatccctca ataccaactc atttgaaatg 3540 acaagtgaac tctttatttt ttttggaata ctagtctcgt tagtatttga tcatacatat 3600 ttggagatgt tttaatcttt tattgatgtt aagatcagac acattatgta tgttgagatc 3660 attcatatat acaactttaa ttgaggatat tcacctaaac tacactaggg ttaagtttct 3720 tttacaaata acttaacaat ggttaagttt aagttacaaa aaattacttg aacgaaagtg 3780 aagttaagtt ttttttacaa aagaacttag taagagttaa gttttaatta aggatattca 3840 atcgaactat actagggtta agtttatttt ccaaagaact taacagttgt tatgtttcag 3900 ttaaaaaaaa aatttacttg aacgaaactg aagttaagtt tttttaataa agaacttaat 3960 aggagttaag ttttaattga ggatatatac ttgaattgca ctagggttaa gtttaattta 4020 caagtaactt aacactaaat tttgaattaa aacaaatgtc ctgaacttaa ttgaagttaa 4080 gttaagtttt tttaataaag aacataataa gagttaagtt ttaattgagg atactcacct 4140 gaactgcact agggttaagt gtaagttaca agtaatttaa catcgttaag tttgaataaa 4200 aacaaatgtc ctgaacttaa ctaaagttaa gtttttttaa taaagaacat agtaggagtt 4260 aagttttaat tgaggatact cacctaaact gcattatggt taagtgtaag ttacaagtaa 4320 cttaacactc gttaagtttg aattaaaaca aatgtcctga actaaactga agttaagttt 4380 ttttaataaa gaacttacta ggagttaagt tttaattgag gatattcact tcaattgcac 4440 taggattaag tttgttttat aaggaactta acactcgtta agtttgagga aaaaaaaatt 4500 atgagctcta tattgaaata taattttcta ttattatgct tactccaata aattcaaaca 4560 tgttaacaat cataacacag tcacatttat aaaaataaaa taattttttt ttgcaaccat 4620 tcatttcttt agatgtatga aaaacatgta actgtttaaa tacctgttat aacataggaa 4680 tttgctaaac aaaaaacttc aatgtcatta cgtagaaaca tcttccacta tccaattaca 4740 atccatttac aatagtagga tcacatagga agttctttat ggaaaaataa ctccaatgcc 4800 atcttctcac gaaaccaatc catacactcg cttgttagtg tatccattgg atggttgtgc 4860 atcaggtatt ctacaaattt gattaaaaac ataccataat caccactgca taaacaaaaa 4920 aatgtgatgt taacaatatt aaatattatt gtatatataa tgaaatatgt gtgttggcaa 4980 cagtcacaaa ctgagtcacc gagccgttct ccagaaaaca ttattttctg aaaccatttt 5040 tggtccacct ccgtatactc aatgttcact tcaaaccttt atgtcatata aagaaataaa 5100 ccattcgtca acttcataaa ttacataaaa aaaattaatt gagttaataa tgtagataac 5160 ttactcttcc tcaatttcat cattaatata ttctgtatga gccacctttg cctccattga 5220 tggtggccgc aatgaatcaa agattgatga tgttatgtcg gtcttactca ttaataactt 5280 ccttctctta gtgggatctg taaatgggtg ctttagtata tgagatttct ttaccttttt 5340 tctttgctta aagatattca gtgatagttg atgtgggaaa acatgaacta ctgtcgcatc 5400 aagtgggtca tccttcaaag cctccttatc attgtctttc ctcaatgtct caattttttc 5460 taactttgat ttgaagtcta gtgttgtttc atttcccatt gttgcagtat atggctcatt 5520 actcgatttt ccaacctgaa attgcataga aatatataaa tatatttgaa aaggcattgt 5580 tagtaattca aaaaatataa agaatataag atcgtcgaaa aacattaacc ggtgtttcat 5640 tctgtgcatc atccattgaa gcctccttct tattgtcttt tctcgatgtt tcaaattttc 5700 ctaactttga tttgaagtcc atcatcatat cattccccat tgtagcatga tatggctcac 5760 ttcttgggtt tctaatctaa aattgcatag aaatatatta atatatttta aaatgtgttg 5820 gtggttttat aaaaaataaa gaatctaaca catgttacta acatccaata acaactcact 5880 caaaccatca atcttgcttt ctatttcttt caattatgtt ttgacttcat taaaatttgc 5940 ttctgtcttt tcttgaaagt tgatgaacat cataaacaat tcctttacat aagaaaaaac 6000 attataacat tagtaaaaca ttcttaaaca tgtatagtga aataatatta ataactttca 6060 ctttagttac cttgaatgaa ggtaatttag aactataacc ttcttttcca cctttcatta 6120 ctgctgctgc tgctactgta tatgcctcag ctttctcatg atcttcattt ttctcccaat 6180 tattcacatt atcttgtaag gcatcatccg attgagcttc aaattcaaag catttcacat 6240 actcttgttc atgctcttct aatgtgggaa tgagtataga atgcaaagat aactaataat 6300 tcaagataga aagaaagtgg ttaataataa gaatatggtt atgcaaataa gaaagcaagt 6360 ataagcaaaa attaagatat cactcacatt tgtctctaca aataatgatt gaatctcagt 6420 gtactttgga gttgcagtcc ttgtccaatt taaaattatg ggaaaacttc taccaatgtg 6480 acttgcatat ttcattccaa gcaatggaat gacttcatat gcccaaattt gaaaggtata 6540 tggaaatccc acaagtgcat atgcttcata tgatgcattt tctttttctt cttttttctc 6600 tacatatttt gattgtcttt tatccaaagc ccttttcaac ccaaataatg ttctttcata 6660 gcaaatttcc ccctcaggat acttgttgaa ctcctctaaa ttatcaacaa gttgaaccta 6720 ttgtaaatct atcaaattct ttccttcttt tcctagtaga acatgctcaa caaagtacaa 6780 caatgctaac ttcataatgt cttcatcaag atttgatttc ccatttaact ttgccttatt 6840 ttttgtcttc tttgtgctca ttctctttcc tttcttacat aatgcgatga aaaccttctc 6900 caatcgatca ttgagaatct tattctctct attgaaatat tgatctctta tccttaaaga 6960 tgttatgtca aattgtgaaa ttttcccaaa tttcaaccta gttatcaatg caagctccaa 7020 cgcactaaat ctcaatcctt ttgagtgaac aagtatccac atgtcatttt tttttttaat 7080 gttacattgg cataacaaca tattatgaac aatttgagca gaaaaattca aataagccat 7140 acttaagaag tggccaaaac aagatgtttt aaacatctgt agttgggttt cattcaagtt 7200 tttctttatg ttgtcaatgg taatattgtg ggataagcaa gccaccttag aagagaagtg 7260 atcttcatta cgtattttct gtatgaagat tgtttaaaaa gtagtagcct acaaagtcac 7320 atacattgtg cttcacatta agaaactata ttaagagtta caaacattct gcatgaacta 7380 aaataaatta caaaaaaaat ttaactactt ctactaaaat caaattaacg attcaattaa 7440 ttatattgta agcaagtttg aaatatttta actgagaact taactatagt tatgtttttt 7500 gtcaatgaga cttaaccttg gttaagttca agtgaatttt tattttttaa taacttaacc 7560 tttgttaagt tctttgtata taaaacttaa ctatagtgta gtttaaatga atattttgat 7620 taacatataa aaaacttaac ttgattagtt cattatttat ggcaaacttg agatataata 7680 tcatttgtag acttattatc taggattaac ttatttggta tatttttagc atatgaaatg 7740 caatagatat atattttgct attgaaggag taatctcata tacaagaatc atcaacacat 7800 taacatccca aatagtacaa aaaatacaaa ccttctcatc agattcgtca atatttgcca 7860 ttaaagatga gttgttcact ttctaggatg atcacttttg gagttatact agattgcaaa 7920 tctaagtttt ttttccttgt ccctggaaaa taaatataaa aaaaattcaa ataaaaatca 7980 tgaatttatt tattaaaatc cataagttta tactaagtat atatatatat atatataaag 8040 agagagagag agagagagag agagaaatag agaccattgt ataacattct tttacatcac 8100 cttgaaacaa tttttataaa tttgaatttt gataaaactt acactacatt tttcattgaa 8160 ttcttttaaa tcttttattg atgaaagaga ttgcataatg cacattattt tctaatgagt 8220 tcaaacactt tggttattca tgcctaaatt ttaagaacga atcatgagtc catgtcatat 8280 tacttttcct tgcatctata tctagatata aatgaagttc taaaggacca tccttactta 8340 tagaaagcac atgacagaag tattttggct atgcatatgc atcatctcac tcaatatttt 8400 aattgtgagt aatatttcaa tccttagttg ggatcattct ttgtcatgaa ttttgttaga 8460 gattactatt tcaatgttgt ggtttgcatt ctaggaccaa ctaggtccca aatttagaaa 8520 atgtcactta tgatctagta aaaacaaact gggttgaaac cttgatgggg tgcttcttaa 8580 tgttggttca catccaaggg agaacgggga ttttcttttc aatctataca agcgaaatgg 8640 aaactataga taggcaaggg atgcaaatta tttgatgaaa attgagattt tcagttaaac 8700 caacttctta tcccttagga aaagaactac aaataggaaa agattttttt cccaaactgc 8760 taaaaaacta ggcacccaat tggcaaagac tataatgatc tccaattttt tcattaatag 8820 aaaataatga ctattcatgt atatcatatt ggttccatta cttaaaagtt aagcaacaca 8880 aaaggagaat aattgacatg aatgctctta gaagaagtat tgttttcact ttatgataga 8940 agccaaaact actctaaaag aagggttttg aattttggaa aataaatcaa aaccattctt 9000 ccaacactgc tcatggaaaa agacttcagt aacaccttca atatcttcac ttggggggtt 9060 taaggaaaca aattcatttt cttatgggat gaatgaaatg tttcttccaa tcatcaggga 9120 ggagatatca aaatgggggc aaattctatt tctgttatta tgattcaact ctttagaaga 9180 ccaaattggt caacacattt gtcacttttt tactagattt ctacactata gaaacaaagc 9240 atttgccaca acatcatgat tcaaaatctt aacaactaga gaaaaacatc aaaataaaat 9300 agccaagaaa tctaattaaa gtttttttta ttattattat tcaatccaac tagatatctt 9360 ctttggtaga ccaatgtgtt ttcagagttc aaaatcaaag aggaatatgc taacaaattt 9420 aagaaaaacc cttatattta tgcttaacaa aaagtgaacc tacaaaccca ttattttctc 9480 ccgcatttct tctgaaacca tgtagaaaga aaacacacac ctaaagtgaa tatataaaat 9540 caacaaagag aaaaatctaa aaaaaaaaca aactatttca aattaataaa cttacttttc 9600 aagatcattt tcggttctct tctactttgt ttcgttctct tcaattcctg cgttttttca 9660 aaaactagag aaaaaaaaat tcacatttca atcaaatgaa taacctttta gaatcctttt 9720 agaaagataa tcaacaacaa tacaaaaatt tgaaatatat atatatatac atagagtgcg 9780 ttgcagtcta ccattcaaga gagaaccctt ggttcattct ctttaacttc ctttaggcac 9840 ttttgaattt caaacgtttc tctttaattt ttttaggggt aatttagtcc aaaatgggtc 9900 attcttcagg ttttaaaaag gcagaggtca tttttccaaa taccagctta ttttggcact 9960 tttaaccaaa taaccctaga ttatatgtgg aggaaat 9997 // ID HAT-N11_Mad repbase; DNA; EDCOT; 1473 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; HAT-N11_Mad. XX NM HAT-N11_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1473 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1633-1633 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >96% identical to the consensus. 8-bp TSDs. Both termini are ~80% CC identical to HAT-N10_Mad. XX SQ Sequence 1473 BP; 536 A; 205 C; 212 G; 519 T; 1 other; tagacccggc agtttctgac acgacacgaa aacgacacga aaataacggg tttcgggtca 60 acacgataac ttatcgggtg acccgttaag aaaaaattta ttttgataat tttaaagttt 120 aattactaaa agatttatta taaaatacaa tagccatatt aatatataca atatattcta 180 tattaaatat atagttttgt attattattc tatataagtt ttaaaaaaaa gttttagtca 240 ttatttattt ttattatgag agttccttat tatcattact aggataaatt ttacttaaca 300 tgttgttgtc caaaattaaa ataaactaat atagtatttg tataggcaag aactaagaag 360 acatacatac aagtatgaaa aatgtgaaag aatatataaa cactcgtgat tcatcattat 420 tcctccacga gtagataatg gttacactta cattatcgtt tagattttta aaatcctcca 480 aaccttcatg aataatgttt tttatttgag ggmaaaatta ataaaattaa taataattat 540 tgtagaagtg taaaaaatgt aaaaaaaata tacaatcact catagtgaca aactttacaa 600 ctttcatgaa ggggtcagct tcgaaatcca acactataat tcataaacct taaatttata 660 tttaaccgtc gattgccatt tacgctttat tcttcttact gaatttcatt tttaaaattt 720 tcttttttga aaacatgatc atctggcgga tgtaagaaga tgaacggttc agatctttga 780 tatcacgttt cgatatttac ggttaactga aatatgagtc gatgtcatat agtttgtaga 840 aactttataa acatcaagca atattttcac taaccgtaaa actctgaata taatatcaac 900 gatccaaacc gttcatcttc ctgcatcctc taatagatca agttttcaaa aaagaaaatc 960 tgaaaaaaac aaaatttgat gagaacaatg aagcgtaaat gtaaacaaca atcaacggtt 1020 aaattttgat ctatgattta tatgattata gtggcgaatt tcgaagttaa gctcttcatg 1080 aaagttgtaa agcttgtcat tacgagcgtt tatatatttt ttctatattt tttttacact 1140 tctacattaa ttaaaaaact attaaagact ttaggtaagt gaaaatatac ttaaaagaaa 1200 aatgcgtttt tatgttttgg atgtgacaat atggtatgta tatacttatt tagtattatg 1260 tttttcattt gattatttat tggtttaaaa tatattttcc ttaacgggta acgggtcggg 1320 tcatattacc tgttaatatt atcgggtcga tttcgggtcg ggtcatttta cccgtttatt 1380 ttaacgggtg ttacacgaca cgacccgtta agatatcggg tatgacacga aaacgacacg 1440 aacacggaaa acacgacacg aatgccaggt cta 1473 // ID IBGYPSY1_LTR repbase; DNA; EDCOT; 962 BP. XX AC AC073166; XX DT 09-AUG-2005 (Rel. 10.08, Created) DT 30-AUG-2005 (Rel. 10.08, Last updated, Version 1) XX DE Gypsy-like LTR-retrotransposon from sweet potato (LTR). XX KW Gypsy; LTR Retrotransposon; Transposable Element; IBGYPSY1_LTR. XX OS Ipomoea batatas OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea. XX RN [1] RP 1-962 RA Jurka J.; RT "IBGYPSY1: A Gypsy-type LTR-retrotransposon from sweet potato."; RL Repbase Reports 5(8), 200-200 (2005). XX DR Genbank; AC073166; Positions 72288 73249. XX CC LTRs differ by 1 bp deletion (possibly a sequencing mistake). ORF CC appears to be intact, indicating a recent insertion. XX SQ Sequence 962 BP; 287 A; 135 C; 181 G; 359 T; 0 other; tgatgagacc ggaatgcaac aaataaatga tccattaaaa gtctcgagcg gcccggtaac 60 aagatctaag tcaaggaaga ttcaagaggc ttttaacact tttgtgcaaa cagattggag 120 tccaacatct ttttgtgaag aagaagatca atctggaaaa ataattctgt tcaattgtct 180 tcacataaaa acttttgaaa acaattcaga cttcagtatc agatcaaatt tcccggtgtg 240 aaattatttg caaggtgtat tttttttagg tgggaaacta ctttgcaaga attgtatttt 300 ttatttttgg gtggaaatta cttttgcaaa atgttgtatt tttaattttg ggtgggaaat 360 tattttgtat tttaattttg ggtggggaat tattttgtat ttttaatttt gggtgggaat 420 tacttttaca aagttgtaat tttttttatt ttgggtggga ttagtgacct agaatattta 480 ataccttatt ttcccctata aataccccat aaacccaatg gtttgaaaaa caccttgtaa 540 gaattcaatt tgagtgaaat ttctctcttt tctttgcatg agaagtgcat tgaagtttta 600 ggttgtttgt gagaagcatt caatcttggt aggctagtga gaagctagtt tatcccctta 660 tcttgttctt tatattcaca cacatatcca aaaacccaaa aagaatacta ttactcatat 720 tatatagcta attttatttt tgtatcttaa ttctagtgct agattcctaa tactctaatt 780 cttagccttg cttaataatc taagggttga gagtattatt tgttagtttg gtgaggcatt 840 tgtagagttg ggatctcaaa atccaagagt ctacaaggta agatcctctt ttggacacga 900 aaggttcttg agtgattcct tgagtgtgca cttattgcgg gaagcaatcc gtgtacgcat 960 ca 962 // ID Copia-74_Mad-LTR repbase; DNA; EDCOT; 216 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-74_Mad_; KW Copia-74_Mad-LTR; Copia-74_Mad-I. XX NM Copia-74_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-216 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1687-1687 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 216 BP; 55 A; 41 C; 30 G; 90 T; 0 other; tgatacattc ctgatctctt gggattgttt cctgtttcat catgatttcc agatttccct 60 gttttattaa aacattccct ttatgtattc tttgtagatt aattatactt gtaaatcaag 120 tcattgtaca ctatttaaat caatgataat gcaccctcta aggtatcgag ggattgagcc 180 aaaatacctt cttttacttt tgctgtcttg tctgca 216 // ID RAM9B_I repbase; DNA; EDCOT; 3894 BP. XX AC . XX DT 22-NOV-2006 (Rel. 11.11, Created) DT 29-MAR-2007 (Rel. 12.04, Last updated, Version 2) XX DE Internal region sequence of RAM9B LTR retroposon, from Medicago DE truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR; Interspersed repeat; retroposon; internal region; KW internal portion; RAM9B_I. XX NM RAM9B_I. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3894 RA Shankar R. and Jurka J.; RT "RAM9B: LTR retroposon from Barrel Medic."; RL Repbase Reports 6(11), 594-594 (2006). XX DR [1] (Consensus) XX CC The translate of internal region exhibits intact reverse CC transcriptase, integrase and Arginine methyltransferase CC containing zinc finger domains. XX FH Key Location/Qualifiers FT CDS 211..3849 FT /product="RAM9B_I_1p" FT /translation="MVDVRRPKKKDAAEIVCFNCGEKGHKSNVCPEEIKKC FT VRCGKKGHVVADCNRTDIVCFNCNGEGHISSQCTQPKRAPTTGRVFALTGT FT QTENEDRLIRGTCYINNTPLVAIIDTGATHCFIAFDCVSALGLDLSDMNGE FT MVVETPAKGSVTTSLVCLKCPLSMFGRDFEMDLVCLPLSGMDVILGMNWLE FT YNHVLINCFSKSVHFSSVEEESGAEFLSTKQLKQLERDGILMFSLMATLSI FT ENQAVIDRLPVVCEFPEVFPDEIPDVPPEREVEFSIDLVPGTKPVSMAPYR FT MSASELSELKKQLEDLLEKKFVRPSVSPWGAPVLLVKKKDGSMRLCIDYRQ FT LNKVTIKNRYPLPRIDDLMDQLVGARVFSKIDLRSGYHQIKVKDEDMQKTA FT FRTRYGHYEYKVMPFGVTNAPGVFMEYMNRIFHAFLDRFVVVFIDDILIYS FT KTEEEHAEHLKIVLQVLKEKKLYAKLSKCEFWLKEVSFLGHVISGDGIAVD FT PSKVEAVSQWETPKSVTEIRSFLGLAGYYRRFIEGFSKLALPLTQLTCKGK FT TFVWDVHCENSFSELKKRLTTAPVLILPKSDEPFVVYCDASKLGLGGVLMQ FT EGKVVAYASRQLRIHEKNYPTHDLELAAVVFVLKIWRHYLYGSRFEVFSDH FT KSLKYLFDQKELNMRQRRWLELLKDYDFGLNYHPGKANVVADALSRKTLHM FT SAMMVREFELLEQFRDMSLVCEWSPQSVKLGMLKIDSEFLKSIKEAQKVDV FT KFVDLLVARDQTEDSDFKIDDQGVLRFRGRICIPDNEEIKKMILEESHRSS FT LSIHPGATKMYHDLKKIFWWSGLKRDVAQFVYSCLVCQKSKVEHQKPAGMM FT VPLDVPEWKWDSISMDFVTSLPNTPRGNDAIWVIVDRLTKSAHFLPINISF FT PVAQLAEIYIKEIVKLHGVPSSIVSDRDPRFTSRFWKSLQEALGSKLRLSS FT AYHPQTDGQSERTIQSLEDLLRICVLEQGGTWDSHLPLIEFTYNNSYHSSI FT GMAPFEALYGRRCRTPLCWFESGERVVLGPEIVQQTTEKVQMIQEKMKASQ FT SRQKSYHDKRRKDLEFQEGDHVFLRVTPMTGVGRALKSKKLTPKFIGPYQI FT LERVGTVAYRVGLPPHLSNLHNVFHVSQLRKYVPDPSHVIQSDDVQVRDNL FT TVETLPVRIDDRKVKTLRGKEIPLVRVVWTGATGESLTWELESKMLESYPE FT LFA" XX SQ Sequence 3894 BP; 1060 A; 571 C; 1065 G; 1198 T; 0 other; tgcatcaagt tcgagaacgg tttgaggccc gacatcaaga gggcgattgg ataccaacag 60 ctgagagttt ttccggattt ggttaatagc tgcaggatct atgaagagga tacgaaggct 120 cactacaagg tagtgaatga gaggaagggc aagggacagc agagtcgtcc taagccgtac 180 agtgcccccg ctgataaagg gaaacagaag atggtcgatg ttaggcggcc taagaagaag 240 gatgctgcag agattgtgtg tttcaattgt ggtgagaaag gccacaaaag caacgtctgt 300 cctgaggaaa tcaagaagtg tgtccggtgt ggcaagaaag gtcatgttgt agctgattgc 360 aatcgtacgg acattgtgtg ctttaattgc aatggagagg gtcacattag ttcacagtgt 420 actcagccta agagggcgcc gactactggt agggtctttg ctttgactgg tactcagaca 480 gagaatgagg atcgtttgat cagaggtact tgctatatta ataatactcc tttagttgct 540 attattgata ctggtgctac gcattgtttt attgctttcg attgtgtttc tgctttgggt 600 cttgatttgt ctgatatgaa tggagagatg gttgtcgaaa ctccagctaa gggttcggtg 660 actacttctc tcgtatgttt gaaatgtcct ttgtctatgt ttggtcgtga ttttgaaatg 720 gatttagttt gtctaccttt gagcggtatg gatgtgattc tgggtatgaa ctggttagag 780 tacaaccacg ttcttattaa ttgttttagc aagtcagtgc atttctcttc cgtcgaagag 840 gaaagtggtg cagagttttt atctactaag cagctgaagc aactggaacg cgacggtatc 900 ttgatgtttt cgttaatggc tactttatct attgagaatc aagcagtgat tgataggtta 960 ccggtggtgt gtgaatttcc tgaagttttt ccagatgaga ttcctgatgt gcctccagag 1020 agagaagttg agttttctat tgatcttgtt cctggaacga agccggtctc gatggcacct 1080 tatcgtatgt ctgcttctga gttatctgag ttgaagaaac agttggaaga cttgcttgag 1140 aagaagtttg ttagaccaag tgtttcacct tggggagcgc cggttttgct agtaaagaag 1200 aaagatggta gtatgcggtt gtgtattgat tatcggcagt tgaacaaggt aactatcaag 1260 aataggtatc cacttccgag aattgatgat ttgatggatc agttagtggg tgcacgagtt 1320 ttcagcaaga ttgatttgag atcaggttat caccagatta aagtaaaaga tgaagatatg 1380 cagaagacag ctttcagaac gcgttatggt cactatgaat ataaagttat gcctttcggt 1440 gtgaccaatg cacctggagt gtttatggag tatatgaatc gcatcttcca tgcatttttg 1500 gatcggttcg tggttgtgtt tatcgacgat attttgattt actccaagac tgaagaagaa 1560 catgctgagc atctgaagat tgtcttgcaa gtgttgaaag agaagaaact ttatgctaaa 1620 ttgtctaagt gtgaattctg gttgaaagaa gtgagttttc ttggccatgt tatttctggt 1680 gatggtattg cagtggatcc gtctaaagtt gaagcggtat cgcaatggga gactcctaag 1740 tcagttactg agattagaag cttcttgggt ttagctggtt actatagaag gtttattgaa 1800 ggattttcta agttagctct tccgctaacg cagttgactt gtaaaggtaa aacttttgtg 1860 tgggacgttc attgtgagaa cagtttcagt gaattgaaga agcgtttgac gactgctcca 1920 gtgttaattt tgccgaagtc agatgaacct tttgtggtgt attgtgatgc gtccaagttg 1980 ggtttaggag gtgtacttat gcaagaaggt aaagtggtag cttatgcttc aagacagttg 2040 agaattcatg agaagaatta tcctacgcat gatctcgagt tggcggctgt agtctttgta 2100 ttgaagatat ggagacatta cttgtatggt tcgaggtttg aggtgtttag tgatcacaag 2160 agtttgaagt atttgttcga tcagaaggaa ttgaatatga ggcagcgaag atggctagaa 2220 ttgttgaagg attatgactt tggtttgaat tatcatccag gtaaagctaa tgttgttgca 2280 gatgccttga gtaggaagac attgcatatg tccgctatga tggtcagaga gttcgagtta 2340 cttgaacagt ttagagatat gagtttggtt tgcgaatggt cacctcagag tgtgaaactg 2400 ggtatgctga agattgatag tgaatttctg aaaagtatca aggaagcaca gaaagttgat 2460 gtaaagtttg tggacttgtt ggttgctaga gatcagactg aagacagtga ttttaaaatc 2520 gatgatcaag gtgtgttgag attccgagga agaatttgta tcccagacaa tgaagagatt 2580 aagaagatga ttcttgaaga gagtcataga agtagcttga gtattcatcc gggagctacg 2640 aagatgtatc atgatttaaa gaagattttc tggtggtctg gtttgaaacg agatgtggca 2700 cagtttgtgt attcctgttt agtttgtcag aagtcgaaag ttgagcatca gaaacctgct 2760 ggaatgatgg tacctttaga tgtgccagaa tggaaatggg atagtatatc catggatttt 2820 gtgacgagtt tgccgaatac tcctagaggg aacgacgcaa tttgggttat tgttgataga 2880 ttgacgaagt cggctcattt tctaccgatt aatattagtt tccctgttgc ccagttggca 2940 gagatttata tcaaggagat tgtgaagttg catggtgttc cttcgagcat tgtatcagat 3000 agagatccaa gatttacttc tagattttgg aaaagtttgc aagaggcttt gggttcgaag 3060 ttgagattga gttcggcgta tcatccacag acagatggtc agtcggagag gacaattcag 3120 tcgctagagg atttgttgag aatttgtgtt cttgagcaag gaggaacttg ggatagtcat 3180 cttccgttga tcgagttcac atacaataat agttatcatt ctagtattgg aatggcacct 3240 ttcgaggctt tgtatggtcg gagatgcaga actccgttgt gttggtttga gtcaggtgaa 3300 agagtggtct taggaccaga gattgttcag caaactactg agaaagttca gatgatccaa 3360 gagaaaatga aagcgtcgca gagtcgacaa aagagttatc atgataagcg tagaaaagat 3420 cttgagtttc aggaaggaga ccacgtgttt ttgagagtca ctcctatgac tggtgtagga 3480 cgtgctttga agtcaaagaa gttgaccccg aagttcattg gtccgtatca gatattggaa 3540 agagttggaa cggtggctta ccgagtgggt ttaccgccgc atctttcgaa tttgcacaac 3600 gttttccatg tgtcgcaact tcgaaagtat gttccggatc catctcatgt aatccaaagt 3660 gacgatgtgc aagttagaga caaccttacg gtagagactt taccggtgag gattgatgat 3720 cgtaaagtga agacgttgag aggcaaggag atacctctcg tgagagtcgt ttggacggga 3780 gcgactggtg aaagcttgac gtgggagctt gagagtaaga tgctggagtc ttatccagag 3840 ttgtttgctt gaggtaaatt ttcgaggacg aaaatctttt aagtggggga gagt 3894 // ID Gypsy-21_Mad-I repbase; DNA; EDCOT; 4468 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-21_Mad_; KW Gypsy-21_Mad-LTR; Gypsy-21_Mad-I. XX NM Gypsy-21_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4468 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1736-1736 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [2088-2543] - Reverse transcriptase CC Positions [3537-4034] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(57..974,978..4466) FT /product="Gypsy-21_Mad-I_1p" FT /translation="MGDRDREPAPITRADLDAQAEQITNLTTQIGELREML FT VQAIGPNNHRAAGVNNLRVPRLRVQDSESESEEEDVEPHPANNPNHQNRNN FT FDDFRIKADIPTFAGNLKIEDFLDWLVEVERFFDVMEVPETKMVKMVAFRL FT KATAAVWWDQLQNTRQRQGKNRIRTWRKMKQLLMDRFLPADYEQLLYRMYI FT SCVQGNRNVTDYTDDFMRLAERNNLMETENQRVARFVNGLKPSIQEKIGLQ FT NLWSLQEAINMALKAEIIEKERRQTSFRRNVTEHFENPVVSSTDKGKSVPQ FT SSGELKPSSFPSRANEGSSRTFNKGQNRNQPPRENPYAKPMGDICYRCNKI FT GHRSNVCPERRQANLLEAEGDQEEVGDDDYEGVEFATEEGMDRLALVLQRV FT LLTPKEDGQRHRIFRSLCSVDSKVCEVIVDNGSCENFVAKKVVERLQLPTE FT PHVTPYSLGWVKKGPSVYVTETCRVPLSIGKHYRDEVLCDVIDMDACHILL FT GRPWQFDVDSTLKGRDNVVLFTWNNRKIAMAPVSPSEVPKAKNTSFLTLIS FT DKQEIEGAIKEADSFFPIVMKGLLTENEEEEQISSEVQQLLEEFHELISDE FT LPNELPPMRNIQHQIDLVPGASLPNLPHYRMSPAENEILREQIEDLLRKGF FT IRESMSPCAVPALLVPKKDKEKKKAWRMCVDSRAINRITIKYRFPIPRLDD FT MLDVLEGSKLFSKIDLRSGYHQIRIRPGDEWKTAFKSKDGLFEWLVMPFGL FT SNAPSTFMRLMNQVLRPFIGLFVVVYFDDILIYSKTREEHMMHLRHVLGVL FT KENKLYMNLKKCIFCTSKLLFLGFVVGENGIQVDDEKTKAIREWPTPKSVS FT DVRSFHGLATFYRRFVRHFSTITAPITECLKKGKFRWGDEQEQSFVLIKEK FT LCTAPVLALPNFEKVFEVECDASGVGVGAVLSQEKRPIAFFSEKLSEARKK FT WSTYDQEFYAVIRALKQWEHYLIQKEFVLFTDHQALKFINNQKHVNKMHIR FT WVTFLQKFPFVIKHKSGAQNRVADALSRRASLLITLSQEVVGFECLKELYA FT TDDDFQEIWRKCINHEPMADYSINEGFLFKGNQLCVPVSSLREKLIRDLHG FT GGLSGHLGRDKTIASLEERYFWPQLKRDVGAIVRKCYACQVSKGQVQNTGL FT YMPLPVPNDIWEDIAMDFVLGLPRTQRGVDSVFVVVDRFSKMAHFIACRKT FT ADASNIAKLFFREVVRLHGVPKSITSDRDTKFLSHFWITLWRMFGTTLNRS FT TTAHPQTDGQTEVTNRTLGNMVRSVCGDKTKQWDYALPQMEFAYNSVVHRA FT TGKSPFSIVYTATPHHVVDLVKLPRGHGLSIAAENMAEDVVAIRDEVKQRL FT EQTNVKYKEAVDKHRRVKVFKEGDSVMVFLRRERFPVGTYSKLKPRKYGPF FT KVIKRINDNAYVIDLPESMGISNTFNVADLYTFNDDEVLYPDHNSGSSSSE FT VEGT" XX SQ Sequence 4468 BP; 1309 A; 846 C; 1100 G; 1212 T; 1 other; attggtacca gagcgggttt ctcccgtctt ggcatcgttg attatcctat ctatccatgg 60 gtgatcgtga tcgtgaacct gcccctatca ctcgagcaga cttggatgct caagctgaac 120 agattacaaa cttgactact caaattggag aacttcgtga gatgttggtc caagccatcg 180 gtccaaataa tcatagagct gctggagtca ataatctacg agttcctagg ctccgtgttc 240 aagacagcga atcggagtcc gaagaagaag atgtggaacc acacccagct aacaatccaa 300 atcatcaaaa ccgcaacaac tttgatgact ttcggattaa ggccgacatt ccaacttttg 360 cgggaaacct taaaatcgaa gatttcctgg attggctagt tgaagtagaa agattctttg 420 atgtcatgga ggttcccgag acaaagatgg tgaagatggt ggccttccgt ctcaaagcaa 480 ctgccgctgt ttggtgggat caattacaaa atacccggca gaggcaagga aagaatcgaa 540 tccgcacttg gagaaaaatg aagcaactct tgatggatcg tttcttacct gcggattatg 600 aacagctttt gtatcgtatg tacatcagct gcgtccaagg caacagaaac gtgactgatt 660 atacggatga tttcatgaga cttgcggagc gaaacaatct gatggagaca gaaaatcaaa 720 gggttgcgag gttcgtgaat ggattgaaac cctcaattca agaaaagatt gggctgcaaa 780 atctgtggag tttgcaagag gccattaaca tggccttgaa ggcggagata atagagaaag 840 aaaggcgaca aacctctttc cggaggaacg tgacggagca ttttgaaaac cctgttgtct 900 cgtccaccga caaagggaaa tctgtgccac aaagttcggg agaattgaaa ccttcaagtt 960 ttccttctcg agcakcaaat gaagggagta gcagaacttt taacaagggg cagaatagaa 1020 accaacctcc aagggagaat ccgtacgcca agcctatggg agacatttgt tatcgttgca 1080 acaaaattgg gcatcgatct aacgtttgtc ctgaacggag acaagccaac ttgttggagg 1140 ctgaagggga ccaagaagaa gttggtgatg atgactatga aggcgttgaa ttcgcaactg 1200 aagaaggaat ggatcgcctc gctttggtgt tgcagcgagt tcttttaaca ccaaaagagg 1260 atgggcaacg acaccgcatt tttcgttctc tttgctccgt cgacagcaaa gtttgcgaag 1320 tgattgtaga caatggaagt tgtgaaaatt tcgtggccaa gaaagtggtg gagcgtttac 1380 agctaccaac ggagcctcat gtcaccccat actcgcttgg atgggtgaag aaaggacctt 1440 ccgtctatgt cacagaaact tgccgtgtcc cactttccat tggtaagcat taccgtgatg 1500 aagtactttg cgatgttatt gatatggatg cttgtcatat actattaggg agaccgtggc 1560 agtttgatgt ggattcgaca ttgaagggtc gagataatgt ggtgttattt acttggaata 1620 atcggaagat tgcgatggct cctgtttcgc cctctgaagt accaaaagca aagaatacta 1680 gtttcctcac tctaattagt gataagcagg agattgaagg ggccataaaa gaagcagatt 1740 ctttctttcc gatcgtgatg aagggactat tgacagaaaa cgaagaagag gaacaaatct 1800 cttcagaagt gcagcaatta ttggaggaat ttcatgaact catttctgac gagttgccta 1860 acgagcttcc tcccatgagg aacatccaac atcaaattga tttggtacct ggagctagcc 1920 taccaaatct tccccattat cgaatgagcc ctgcagaaaa tgagattttg agggaacaaa 1980 ttgaagactt gctgcgaaag gggtttatcc gagaaagtat gagcccttgt gcagtacctg 2040 ccctattggt tccaaagaaa gacaaggaaa agaaaaaggc atggcgtatg tgtgtagaca 2100 gccgagctat taaccgaatc accatcaaat acagatttcc aatacctcgg ttagatgaca 2160 tgctagatgt gcttgaaggt tcgaaattat tttcaaaaat tgaccttcgc agtggctacc 2220 atcaaattcg aatcaggcct ggagatgagt ggaaaacggc gttcaagagc aaggatggac 2280 tgttcgagtg gctagtgatg ccatttggat tgtctaatgc gccgagtacc ttcatgaggc 2340 ttatgaatca ggttcttcgt ccctttattg gtctctttgt tgtggtttac tttgatgaca 2400 tcttaatcta tagcaagacc agagaagaac acatgatgca tttgagacac gttttgggtg 2460 ttttgaaaga aaataaattg tatatgaatc tcaagaaatg catattttgt acaagtaaat 2520 tgctatttct aggatttgtg gttggtgaaa atggtattca ggtggatgat gagaagacca 2580 aggccatccg agaatggcca actccgaagt ccgtctccga cgtgaggagt ttccatggct 2640 tggctacttt ttatcggaga tttgtgcggc atttcagcac catcaccgca cccattacag 2700 aatgtttgaa gaaaggcaag ttccgttggg gagatgaaca agaacaaagc tttgttttga 2760 tcaaagagaa gctttgtact gctccggtgt tagctcttcc aaattttgag aaagtattcg 2820 aagtcgaatg tgatgcaagt ggagtgggag tgggtgctgt cctttcccaa gagaagagac 2880 ctatagcttt tttctctgaa aagctaagtg aagcccgtaa aaaatggagc acttatgatc 2940 aggagtttta tgcggtgatt cgagctttaa aacaatggga acactatctc attcagaaag 3000 aatttgtgct attcacggat catcaagcct tgaagtttat taacaatcag aagcatgtta 3060 ataaaatgca tatcagatgg gtaacgttct tgcaaaaatt tccatttgtt atcaagcaca 3120 aatctggagc tcaaaaccgt gttgccgatg ccttgagtag acgagcatca ttgctaatca 3180 ctctttccca agaagttgtg ggtttcgagt gcttaaagga gttgtatgca accgatgatg 3240 attttcagga aatatggagg aaatgcatca atcatgaacc tatggcagat tactctatca 3300 acgaaggttt tctgttcaaa ggtaaccaat tatgcgttcc tgtctcttcc ttgcgggaaa 3360 agcttattcg agatttgcat ggaggaggat taagcggtca tcttggtcgt gacaagacga 3420 tagcaagttt ggaagaaagg tacttttggc cacaattgaa acgggatgtt ggagccattg 3480 tgaggaagtg ttacgcttgt caggtttcaa aggggcaagt ccaaaatacg ggcctttaca 3540 tgcctttacc cgttcctaac gatatttggg aggacattgc tatggatttt gtgctcggac 3600 taccccgaac gcaaagggga gtggattcag tttttgtggt ggttgacagg ttctccaaga 3660 tggctcattt cattgcttgc agaaagaccg ctgatgcatc aaacatagcc aaactgtttt 3720 tcagggaggt tgttcgattg catggggtac ctaagtccat cacttctgat cgagacacca 3780 agttcttgag tcatttctgg attacattat ggagaatgtt tgggactact ttgaatcgaa 3840 gtactactgc acatccccaa actgatggac aaacagaggt cacaaatagg actcttggta 3900 acatggttcg aagcgtttgc ggagacaaaa caaaacaatg ggactatgcc ctacctcaga 3960 tggagtttgc ttataatagt gttgtgcatc gtgctactgg taagtcacca ttttccattg 4020 tttacactgc cactcctcat catgtggtgg atttggtgaa gctacctagg ggacatggac 4080 ttagcattgc tgcagaaaat atggctgaag atgtggtggc aattcgtgat gaggtcaagc 4140 aacggcttga acaaaccaat gttaagtata aggaagcagt ggacaaacat cggcgggtta 4200 aagtgtttaa ggaaggagat tctgtcatgg tgttcctgag aagagaacga ttccctgttg 4260 gaacttacag caagttaaag ccacgaaagt atggtccatt caaagttatc aagcgaatta 4320 atgacaatgc ctatgttatt gatttgccgg agtctatggg aatttccaat actttcaacg 4380 ttgctgattt gtataccttc aatgatgatg aagttcttta tcctgatcat aactcggggt 4440 cgagttcttc tgaagtggag gggactga 4468 // ID Copia-56_Mad-LTR repbase; DNA; EDCOT; 223 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-56_Mad_; KW Copia-56_Mad-LTR; Copia-56_Mad-I. XX NM Copia-56_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-223 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1651-1651 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 223 BP; 52 A; 31 C; 54 G; 86 T; 0 other; tggaagaaag aatggcaact agggttaggt taggttgcat gttcaccgta caaaggattt 60 tagggtgata gatagtgttg tcaattccct taattcaagg gatgtgtctt atttgtcttg 120 ttgtcaattc ccttaattca agggatgtgt cctatttgtt ctttttttgt tagctttagg 180 cgtaaatcaa ggagggatag gtagtcttgt tttcttctct cca 223 // ID Copia-2_CP-LTR repbase; DNA; EDCOT; 211 BP. XX AC ABIM01016427; XX DT 10-MAR-2010 (Rel. 15.04, Created) DT 10-MAR-2010 (Rel. 15.04, Last updated, Version -1) XX DE LTR retrotransposon from papaya: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-2_CP_; KW Copia-2_CP-I; Copia-2_CP-LTR. XX OS Carica papaya OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Caricaceae; Carica. XX RN [1] RP 1-211 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from papaya."; RL Repbase Reports 10(4), 576-576 (2010). XX DR Genome; ABIM01016427; Positions 7608 7818. XX SQ Sequence 211 BP; 61 A; 24 C; 34 G; 92 T; 0 other; tgttgagttt gttatttgat ttagtcaagt ttgttaataa gtcctattct ataggaagta 60 gtttcgtatt ttgttctaat ctattagcta tcttaatggg ttgttagtaa gttaacttta 120 aaagttcatt tctgtgtaac aaggctatat aaaggcctgt agtttccttt aataaaacaa 180 cttttacaaa tcatatgagt gtttctttac a 211 // ID Copia-29_Mad-I repbase; DNA; EDCOT; 5090 BP. XX AC ACYM01054283; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-29_Mad-I; KW Copia-29_Mad-LTR; Copia-29_Mad_. XX NM Copia-29_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5090 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1302-1302 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01054283; Positions 30669 25580. XX CC Positions [2278-2622] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 940..2622 FT /product="Copia-29_Mad-I_1p" FT /translation="MCAEREADSMVNILTHNFSGLYMQGSSSQSSDSQGSS FT SNSNNVPFTTGGTITRVPNNAPPVSMPFISQGSTAMHTQPPGHIFPHAPYS FT IDGSLFPQVPYSPTSYMMPPSLPPIYPDFPNVYGFIGTGNLPRPFPNSNNG FT SRSFSGSKPNEGYRGSNFGNGRGQFSGPKQSGGTWQFWSGNTDTKLHIVPE FT CQICSKHGHTAPNCWKRSTSPSSMGQVVACQICGKRGHSALDCHRRNNFAY FT QGTAPAPSLTAIQAQAPSNLLPQDSWIKDTGASHHITADLNSLQQVTSYAS FT TDKITIGNGEGLQIKNIGSARLHTLPQSLILRTVLHVPTIAVSLLSVKQLC FT KDNFCWFICDDNDFFVQDKVTKVVLYHGRTNEGELFRIPVKLLSKSPSQKS FT VALLGQKIKSEVWHQRCGHPSNEVLSVMLKQSNIVSSPDTHQHLCSCCISG FT KMSRLPFHDRTESCNFSFQKVHTDLWGPSPTTSIEGYKYYVSFVDEYTRFV FT WIFPLINKSKVFDVFQKFYSFVFTQFNIGIKCLQTDGSGEYISRRFDDFLK FT HKGIVHMISCPYTP" FT CDS join(2915..3748,3752..5074) FT /product="Copia-29_Mad-I_2p" FT /translation="MGYALGYKGVICFHPKSRKFIISQHVIHDEDLFPYKS FT QHTLQNTSQGISSQDSTYVSSPIHSAIFLPQSVSMPNDVSSLEFVEGQGSI FT DLSGSTTMNTSLQSSGTLSHSSIVPESETTPSSSSTTLMLHVLDPAQLEVI FT LPFPSSSNSGTTHHIVSSPPRMQTRLQTGAISRKTYANYIASLPELQSLQL FT DFQDSCSSGFSFVASVRDISEPKSFRSAATNVNWQIAMQEEFDALKSQGTW FT VLVPPPTHRSIIGSKWVYKLKKNHDGSISRYKARLVAGYTQELGLDYFETF FT SPVVRHTTVRLIISIAAQNKWELRQLDIKNAFLHGDLEEEVYMKQPQGFVD FT STHPDFVCKLVKSLYGLKQAPRAWNAKFIGYLPAIGFTVSQSDNSLFFKHD FT GTDVVALLLYVDDIILTGSNATKIQAVIQELGDVFDLKDMGKLSYFLGLQI FT QYSDNGDIFLNQSKYAKDLIHKAGMDNCKPASTPCKPHTQLLASEGNLLSD FT LTMYRSLIGALQYLTFTRPDMSYAVNMACQYMNQPTDVHYGLVKRIICYVQ FT GTVTCGITYSASLDNSITAFSDLDWAVDPNTIRSITGFVEYMGHNPISWQL FT KKQSSISRSSTEAEYKALAHCAADVVWIRLLLKDLHQFLSMPPLLHCDNLS FT MLALCSNPVFHTRIKHLDTDFHFVREKVQKKDLQVQYVPTKEQTADVLTKG FT LHGPTFFKHCCNLRIGNPT" XX SQ Sequence 5090 BP; 1377 A; 918 C; 1011 G; 1784 T; 0 other; gagctggcgg tcctcctgtg gttcatagtt tcttggggcg gttttctctg agagtttgat 60 cgaggttctt gatcgggggt ttcttggtgc ttcttggttt cttgcgcatc tgggtttttt 120 ggatttctag agttcttttt gtgaagcttt gattctttgt tttgtggctt atgatatcag 180 ttggggcacg aagccaattc aagattatgt agcaggcacg aagccatctg ggtaattttc 240 ttgcaaggtt tgttgtttag taggcaattt aactgataat tgttgaattg gcattttgtt 300 tctttcaaga agtagttgtt tgttttcctg atttgtgata atcatggcat cttctggagt 360 taaaattgag ggtttgcttg gaatgttgac aatcaagtta actgataaga atttctcaaa 420 atgggttttt cagtttaagt cggtgttgaa aggatataag ttgtttgatc attttgatgg 480 aactgcagtg tgtcctccta aatttgtgat tgatacgact tctggggtta ctagtgttct 540 cacagaagct tttcttgaat gggaatccat tgatttagca cttttgagtt tactgattgc 600 tactttatct gatgagtcta ttgaacatgt tttgggatgc aagactgcac atgaggcatg 660 gtctaatctt caggatagat atgcttcaat ctcaaaggct agggtgaata ccttaaagac 720 agaatttcaa acaattcaaa agggcggtga ttcaattgat cagtatttgt ctaaatgaga 780 cacattaaag aacaattggt tgcagctggt gaatttgttt cagacaatga ttttgtggtg 840 cctgctttgt ctggtttacc gagggagtat tctactatac gaactgtaat tcttactcga 900 gatacttcta tttctctatg agaattcaaa gagcaattaa tgtgtgcaga gagagaggct 960 gattctatgg ttaacatttt gactcataat ttttctgggt tgtatatgca aggatcttct 1020 tctcagtcaa gtgattctca gggttcttct agtaactcta ataatgttcc tttcaccact 1080 ggtggtacta ttactcgagt accaaataat gctccacctg tgagtatgcc atttatatct 1140 cagggttcta ctgccatgca tactcagcca ccaggtcata tttttccaca tgctccttat 1200 tctattgatg gttctctgtt tcctcaagtt ccatattctc ctacttcata catgatgcct 1260 ccatctttgc ctcctatata tcctgatttt cccaatgtct atggttttat tggcactggt 1320 aatcttccta ggccatttcc taattccaat aatggttcaa gatctttctc tggttccaag 1380 cctaatgagg gttatagagg ttcaaatttt ggaaatggaa gaggacaatt ttctggtcct 1440 aaacaaagtg gaggtacttg gcagttttgg tcagggaata ctgacaccaa acttcatatt 1500 gtcccagagt gtcaaatttg ttctaaacat ggtcacacag ctcctaattg ttggaaacga 1560 tctactagtc ctagttctat gggacaggtt gtggcatgtc aaatatgtgg caagcgtggt 1620 catagtgctt tggattgtca tcgtcgcaat aactttgcct atcaaggcac agctcctgct 1680 ccttccttga cagctattca agctcaagct ccttctaatc ttctacctca agattcctgg 1740 ataaaggaca ctggtgcttc gcaccatata actgctgatt tgaactccct gcaacaagtc 1800 acatcttatg caagcactga taagattacc attggaaatg gtgaaggttt gcaaatcaaa 1860 aatattggtt ctgcacgttt acatacttta cctcagtctt taattctcag aacagtttta 1920 catgttccca ctattgcagt tagtctactg tcagttaaac aattatgtaa ggataatttt 1980 tgttggttta tatgtgatga taatgatttc tttgtgcagg acaaggtaac caaggttgtt 2040 ctatatcatg gaaggaccaa tgagggtgag ttgtttcgga ttccagtgaa gttgttatca 2100 aagtctccat ctcaaaagtc agtggctctt cttggacaga aaataaagtc tgaagtatgg 2160 catcaacgat gtggtcatcc tagcaatgaa gtgttgtctg taatgttgaa acaatccaat 2220 atagttagtt ctcctgatac tcatcaacat ttatgttctt gttgtatttc tggcaagatg 2280 tctaggttgc catttcatga tagaacagag tcttgtaact tttcatttca aaaggtgcat 2340 actgatcttt ggggtccttc acctactacg tctatagaag gttacaaata ctatgttagt 2400 tttgttgatg agtataccag atttgtatgg atatttccgt taatcaataa atctaaagtg 2460 tttgatgtct ttcagaaatt ctacagtttt gttttcactc agtttaatat tggaattaag 2520 tgtttgcaaa ctgatggtag tggtgagtat ataagtagaa gatttgatga ttttctaaaa 2580 cacaagggca ttgtacatat gatttcgtgt ccatacactc cttaacaaaa tggtcttgct 2640 gagagaaagc atcgacatat tgtggaaact gctattacct tgatgactac tgcttaatta 2700 cctcaggatc tttggtatca tgcctgtgca cattctgttt ttttttatta atagaatgcc 2760 ttgcaaggtt ttaggcatgc aatccccata tcaaagacta tatggtgttt ctccttaatt 2820 gcaaggtctt aaagtctttg gtactgctgt ctatccatat attagacctt acactgtaaa 2880 taaattgcaa ccaagggctt ctttatgtgt ctttatggga tatgcattag gctataaagg 2940 agtaatttgt ttccatccaa agtctcggaa atttatcatt tctcagcatg tgattcatga 3000 tgaagatttg tttccatata agtctcaaca tacattacag aatacatctc aggggattag 3060 ttctcaagat tccacatatg tatcttctcc aatacattct gctatatttt tgccacaatc 3120 agtttcaatg cccaatgatg tttcatctct ggaatttgtt gagggtcaag gtagtatcga 3180 tttgtctggt tctactacga tgaatacttc tctgcaatct tctggcacac ttagtcattc 3240 ttctattgta cctgaatctg aaacaactcc ctcatcttcc tcaacaactt tgatgttaca 3300 tgtccttgat cctgcacaac tggaggtaat tcttccattt ccttcatctt ctaattctgg 3360 tactacacat cacattgttt cctctcctcc aagaatgcaa acaaggttac aaactggtgc 3420 aatttcaagg aagacatatg ctaattacat agcatcatta ccagaattgc aatcattgca 3480 gcttgatttc caggattctt gttctagtgg tttttcattt gtggctagtg ttcgtgatat 3540 ctctgagcct aaatctttta ggagtgctgc aactaatgtt aattggcaaa ttgccatgca 3600 agaagaattt gatgcattaa agagtcaagg gacttgggtt ttggttcctc caccaacaca 3660 tagatcaatc attggtagta agtgggtcta taaacttaaa aagaatcatg atggttcaat 3720 atccagatat aaggcaaggt tagtggctta aggttatact caagagttgg gtttggatta 3780 ttttgaaacc tttagtcctg ttgttaggca cactacagtt cgattgataa tttccattgc 3840 tgctcaaaac aaatgggaat taaggcaact tgacattaaa aatgcattct tacatggcga 3900 tttagaagaa gaggtttaca tgaagcaacc tcaaggtttt gtggattcta cacatcctga 3960 ttttgtgtgc aaactggtta agtctctgta tggtttgaaa caggcaccta gggcctggaa 4020 tgctaagttt ataggatatc ttccagctat aggatttaca gtgtctcaat ctgataacag 4080 tctgtttttc aaacatgatg gcactgatgt tgtcgcctta ttattatatg ttgatgacat 4140 tatcttgaca ggatctaatg ccaccaaaat tcaggctgtt attcaagaat tgggagatgt 4200 ctttgatctc aaagacatgg gcaaattgtc ttattttctc gggttgcaga ttcagtatag 4260 cgataatggt gatattttct tgaatcaatc taagtatgcc aaagatttga ttcataaagc 4320 tggtatggac aattgcaagc ctgcatctac accatgtaag ccacacactc agctcttagc 4380 atctgaaggt aatcttttaa gtgatctcac tatgtatcga agtcttattg gtgctttaca 4440 gtatcttacc tttactcgac cagatatgtc ttatgctgta aacatggctt gccagtatat 4500 gaatcaacct actgatgtcc attatggtct tgtgaaaaga attatttgct atgttcaagg 4560 tactgtaact tgtggtatta cttattctgc atctctggac aactctatta cggcattttc 4620 tgatttggat tgggcagttg atcctaatac tataaggtct attactggtt ttgtggagta 4680 tatgggacac aatccaatct cgtggcaatt aaagaaacag tcctcaattt ctaggagctc 4740 cacagaggca gaatataagg cattggccca ttgtgcagct gatgtagtat ggattaggtt 4800 gctgctcaaa gatcttcatc agtttctatc aatgccacca ttgttacatt gtgataatct 4860 ctctatgtta gccttatgtt ctaatcctgt gttccataca cggattaaac atttggatac 4920 cgattttcac tttgtaagag agaaagttca gaagaaagac ttgcaagttc aatatgttcc 4980 cactaaagaa caaacggctg atgttcttac caaaggtctc catgggccta cattcttcaa 5040 acattgctgc aatctcagga ttggtaaccc tacctgagat tgagggggga 5090 // ID Copia-31_Mad-LTR repbase; DNA; EDCOT; 187 BP. XX AC ACYM01069187; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-31_Mad_; KW Copia-31_Mad-LTR; Copia-31_Mad-I. XX NM Copia-31_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-187 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1380-1380 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01069187; Positions 12692 12878. XX SQ Sequence 187 BP; 62 A; 24 C; 33 G; 68 T; 0 other; tgttaagaaa gagatctctg attgattctg attgattggt caaatattgt aaattaatat 60 tagttattca ctttcttatt tagctccctg ttagccttga ttgtaggcaa tagagtagga 120 tcgtactatg caatgtgtat aaaagtgtaa ccctagttct atgaataaat tagaaaagac 180 aattcca 187 // ID Copia-68_Mad-I repbase; DNA; EDCOT; 4226 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-68_Mad_; KW Copia-68_Mad-LTR; Copia-68_Mad-I. XX NM Copia-68_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4226 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1674-1674 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1720-2220] - Integrase core CC 'TTTG' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(115..1254,1258..4226) FT /product="Copia-68_Mad-I_1p" FT /translation="MAGSGGGELRAPVFNGENFDFWQIRMKTIFRSHELWN FT IVEKGFTTSAKGEGDLTEAETKLRSENLVKDARALGIIQGAVSDQIFPRIA FT TLETAKEAWDILKQEYVGDKQVRSVKLQGLRRDFEYTRMSESESLAAYLAR FT LFDLINQMRSYGEDLSNQRIVQKLLISLPKTYDSIASVIENTKDIDVIDAQ FT DVVAILKGFELRLIRHEESSTERAFASLDISSKNSKFGNQHTNTGGSKYQK FT NFKFKGKQWTNRFTPSVRNEANNTGGACKYCDKLHYGECWLKGKIKCHKCG FT KPGHIARICNQNKNAQQGNFANKVGEQRNFTNKVGEPGNLFMVKQSTEVKA FT VSDAWYIDSACSNHMTSREELLVEIDRSIKAKVQVGTVLVDVKGKGTLVID FT TDKGKRYIREVMLVPGIAENLLSVGQMTEHGYFLLFGDYKVDIFDDRTLTN FT LVVSVKQKGNRCFPLVFKSNDHLVLKTNVHQSSTMWHKRFGHLNFRSLQQL FT QEHDMVLGLPEMHDSEGVCQGCAFGKNHRVSFPRESIWRARMPLELIHSDV FT CGPMQTPTMSGNRYFVTFIDDYSRMCWIYLLRHKSDVFHVFKKFKAMVELQ FT SGFSVKKLRTDRGGEFTSNEFEQFCEALGLERQLTVAYSPQQNGVAERKNR FT TIVEMAKCMLHEKGLPYSLWGEAVVTSVYLLNRCPTKALENVTPFEKFSGR FT KPGIQHLRVFGSLGYSLIPGNLRQKLDETSVIGIFIGYGTCEKGYRLLNPE FT NQKVIISRDVIFDENGTWDWDRQKIKEVYIPIAASESSEMKEADEDSDSME FT QAVAEGSQTQLTDSPLIESGSASDSISASQTDHTPLRYRSLSEIYERCHVC FT IVEPESYYEAAQDEAWKKAMKDEIGMIEKNKTWELVKRPSDKPVIGVKWVY FT KTKLNLDGSVQKNKARLVAKGYAQKPGIDYNETFAPVARLDTIRTLIALAA FT KNKWKLFQLDVKSAFLNGVLEEEVYVDQPDGFIVQGEEDKVYRLHKALYGL FT KQAPRAWYGEIDSYLTLCGFKKSTSEATLYTKWRKSSEMIIVSIYVDDIIY FT TGSCQELMDDFKSDMMLKYEMTDLGLLHHFLGMGVMQTEEYIFIHQRKYAS FT SLLKKFGLQDCKSVSIPLVPSDKLRKEDESGTADEAQYRQIVGSLLYLTAT FT RPDIMYAACLLSRFMHCPTNKHLGTAKRVLRYVQGTLDFGLEYKKGKGAIL FT MGFCDSDWSGSEDDMKSTSGYAFTFGSGVFSWSSVKQQCVALSTAEAEYIS FT ASEATAQATWLRFVLEDFGEMQTVATPMNCDNTSAIAITKNPIFHQKTKHI FT NRRYHFIKEALQQGVIELLHCPTKEQIADIFTKALAREQFSYLRELLGVKS FT VHNLKGA" XX SQ Sequence 4226 BP; 1382 A; 647 C; 1035 G; 1159 T; 3 other; gagccttgtt gggtctgaat ctctgggcgt cgattctgtg agagatagtg agcaagtgtt 60 tgcaacacat cgttgcaaag aaaatagtag agagaggtgt gatctgagtc taacatggct 120 ggatctggtg gaggggagct tcgagctccg gtgttcaacg gagaaaactt cgatttctgg 180 cagattcgaa tgaaaacaat cttccgatct cacgagttat ggaatattgt tgaaaaaggt 240 tttaccactt cagcgaaagg ggaaggagac ctcactgagg cggaaacgaa gttgcggagt 300 gaaaatctgg tcaaggatgc aagggctctt ggaatcattc agggagccgt atcggatcaa 360 atttttccac gcattgcaac cttggaaact gcgaaagaag cttgggatat tctgaagcaa 420 gagtatgtag gggacaaaca ggtacgatct gtgaaattac aaggtctgcg tcgtgatttt 480 gaatataccc gtatgagtga aagtgaatct ctagctgcat atttagctag gttgtttgat 540 ctgataaatc agatgcgaag ctatggagaa gatcttagta atcagagaat tgtgcaaaag 600 ttattgatca gtttacccaa aacatatgat agcattgctt ctgttataga aaatactaaa 660 gatattgatg taattgatgc acaagatgtg gttgccatat tgaaagggtt tgaactgaga 720 ttaatcagac atgaagagag tagcacagaa cgtgcatttg ctagcttaga tatctcatct 780 aagaatagta aatttggtaa tcaacatacc aatactggtg gatcaaaata tcagaagaac 840 ttcaagttca aagggaagca gtggactaac aggtttactc caagtgtaag aaatgaagct 900 aacaacactg gaggggcatg caaatactgt gataaacttc actatggtga atgttggcta 960 aaagggaaga ttaaatgtca caagtgtgga aaacctggtc atattgctag gatctgcaat 1020 caaaacaaaa atgctcagca agggaatttt gcaaacaaag tgggagagca aaggaacttt 1080 acaaacaagg tgggagaacc tggaaatctc ttcatggtca agcaatcaac tgaagtgaaa 1140 gctgtgagtg acgcctggta tattgacagt gcgtgcagta atcacatgac ttccagagag 1200 gagttacttg tggaaattga tagaagtatt aaggcaaaag tgcaagttgg cacakgggtt 1260 cttgttgatg tgaaaggcaa aggaaccttg gtcattgaca cggataaagg aaaaaggtac 1320 ataagagaag ttatgttggt acctggaatt gcagaaaacc ttctcagtgt tgggcagatg 1380 actgaacatg ggtattttct gttatttggt gattataagg tggatatttt tgatgataga 1440 actctgacaa atttagtggt tagtgtgaaa caaaagggga acagatgctt tccacttgtg 1500 ttcaagtcaa acgatcactt ggtactgaaa accaatgtgc atcagagtag tacaatgtgg 1560 cataaacggt ttggccacct gaattttaga agtttgcaac aattgcagga gcatgatatg 1620 gttcttgggt tacctgaaat gcatgacagt gaaggtgtat gtcagggatg tgcatttggt 1680 aagaatcata gagtgtcctt tccaagggag tcaatctgga gagcaagaat gccattggaa 1740 cttatacact cagatgtgtg tggccctatg caaacaccaa ccatgagtgg aaatcgatac 1800 ttcgttacat tcattgatga ctattcgagg atgtgctgga tatatctctt gagacacaag 1860 tcagatgtct ttcatgtatt caagaaattc aaagctatgg tggaacttca aagtggtttt 1920 tcagtgaaga aattgagaac agatagagga ggagaattta cctcaaatga atttgaacag 1980 ttttgtgaag ctttgggttt ggagaggcag cttactgttg catactctcc acaacagaat 2040 ggagttgcag agaggaaaaa tagaactata gtggagatgg caaagtgtat gcttcatgag 2100 aaaggtcttc cttatagtct ttggggtgaa gctgtagtta catctgtcta cttgctaaat 2160 agatgtccta caaaagcatt ggaaaatgtg acaccttttg agaaattcag tggaagaaaa 2220 cctggaattc aacacttgag agtgtttggc tcattaggtt attcccttat tcctggaaac 2280 ctgagacaga agctggatga aacaagtgtc attggtattt ttattggata tggcacttgt 2340 gaaaaggggt acagattgct taatcctgaa aatcagaaag taatcatttc aagagatgtt 2400 atttttgatg agaatggtac atgggattgg gatagacaga agatcaaaga agtgtacatt 2460 ccaattgctg caagtgaatc ttcggagatg aaagaagctg atgaggattc ggattccatg 2520 gaacaagctg ttgctgaagg ttctcagact caacttacag attctccact cattgaatct 2580 ggaagtgcta gcgactcaat ttctgcatct cagactgatc atactccttt gagatataga 2640 agtttgagtg aaatctatga aagatgtcat gtgtgtatcg ttgaaccaga atcctattat 2700 gaagctgcac aggatgaagc wtggaagaaa gctatgaaag atgaaatcgg catgattgag 2760 aaaaataaga cttgggaatt agtgaaaaga ccatctgata aacctgtgat tggtgtgaaa 2820 tgggtgtaca aaactaaatt gaatttggat ggatcagttc aaaagaacaa ggctaggctt 2880 gttgcaaaag gctatgcaca aaagcccgga attgattata atgaaacctt tgcacctgtg 2940 gcaaggttgg atacaatcag aacattaatt gccctggcag caaagaacaa atggaagttg 3000 tttcaattgg atgtaaaatc ggcattcttg aatggkgtac tagaagaaga agtgtatgtt 3060 gatcagccgg atggatttat tgtacaaggg gaagaagata aggtctacag gttacataaa 3120 gcactgtatg gtctgaagca ggcaccaagg gcctggtatg gtgaaataga ctcatacctt 3180 acactctgtg ggtttaagaa aagcactagt gaagcaactc tgtataccaa gtggaggaaa 3240 agttcagaaa tgattattgt gtctatctat gttgatgaca taatatacac tggaagttgt 3300 caggaattga tggatgattt caaatctgat atgatgctca aatatgaaat gacagatctt 3360 ggactcttac atcactttct tggtatggga gtaatgcaaa ctgaggagta tattttcatt 3420 catcagagaa aatatgcttc ttctctactg aagaaatttg gacttcaaga ctgtaagtca 3480 gtgagtattc cattggttcc aagtgataaa ttgagaaaag aggatgaaag tgggactgcg 3540 gatgaagctc aatatagaca aattgtaggc agtttgctgt atctcacagc aactagacct 3600 gatataatgt atgctgcatg tctgctatca cggtttatgc actgtccaac caacaagcac 3660 cttggtacag caaagagagt actaagatat gttcaaggga ctcttgattt tggcttggaa 3720 tacaagaaag gcaaaggagc aatcttaatg ggattttgtg acagtgactg gagcggttca 3780 gaagatgata tgaaaagtac atcggggtat gcattcacct ttggcagtgg agttttctct 3840 tggtcttcag tcaagcaaca atgtgttgca ttatcaacag ctgaagcaga gtacattagt 3900 gcatctgaag caactgcaca ggctacatgg ctgagatttg ttttggagga ctttggtgaa 3960 atgcaaacag ttgcaacacc aatgaattgt gataatactt cagccatagc tatcactaaa 4020 aaccctattt ttcatcagaa gaccaagcac atcaacagga gataccattt cataaaggaa 4080 gcattgcagc aaggagtaat tgagctgttg cattgtccta caaaagagca aattgctgat 4140 atctttacaa aggcattggc aagagaacaa ttcagttatc tgagggaact tcttggagtt 4200 aaatcagttc acaatttaaa gggggc 4226 // ID Copia-2_SL-LTR repbase; DNA; EDCOT; 398 BP. XX AC AC243710; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the tomato genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-2_SL_; KW Copia-2_SL-I; Copia-2_SL-LTR. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-398 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the tomato genome."; RL Direct Submission to RU (22-JAN-2011). XX DR Genome; AC243710; Positions 103887 104284. XX SQ Sequence 398 BP; 77 A; 99 C; 107 G; 115 T; 0 other; tgttgaatgc cttgaatcgg acccgctaca aacagaaagg acgggggtct cgctgcccgg 60 tcagcgagtc ggggggtcca ggggggcgac gcgccccctg gcctgggggt ccgggggggc 120 ggagacgccc ccgggccgac ggtatacaat gttgttgtat tgggccctta attttctgtt 180 gattctgtat gttgggccca agcctgttag ggcgtagctt agcactatat atagacgcta 240 tgggaaaccc tattctgtaa ttctgttttt gcctctccat aataaaactg ctccctctct 300 tcccgtggac gtagccaatt tgttggtgaa ccacgtaaat ctgttgtctt atttttcgcg 360 tttatatttt ctcgtattat ctcaaattcc gcacaaca 398 // ID Copia35-PTR_LTR repbase; DNA; EDCOT; 367 BP. XX AC scaffold_1646; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia35-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-367 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-367 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 247-247 (2007). XX DR Genome; scaffold_1646; Positions 1349 983. XX SQ Sequence 367 BP; 116 A; 67 C; 56 G; 128 T; 0 other; tgaattacat gcagctcagc tttcacatcc acaatgaagc cagcatctct gtcttctctg 60 tcttctccac accagcagct acagcagtac aatctccagc ttcaacagta acaaatatag 120 caatcttgca atcttcaatt aatatcttca gcaagcaatt gtgtagaagt tcgagtttgt 180 taaggttgtt agagttagtc aaagctgtta caagaattgg ttagctgtta gcaagaatca 240 gttattctgt taattattga ttgattattt tgtttacaag aatcagtcta tataaacagt 300 gtaatagatc attgattaga aatagtaaag ataattcagt tcatcatttt ccattttctc 360 tatttca 367 // ID Harbinger-3N3B_VV repbase; DNA; EDCOT; 312 BP. XX AC . XX DT 05-FEB-2009 (Rel. 14.03, Created) DT 05-FEB-2009 (Rel. 14.03, Last updated, Version 1) XX DE Harbinger-3N3B_VV, non-autonomous DNA transposon - a consensus DE sequence. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW PIF; TIR; MITE; mPifvine-3.4; Harbinger-3N3B_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-312 RA Benjak A., Boue S., Forneck A. and Casacuberta J.M.; RT "Recent amplification and impact of MITEs on the genome of RT grapevine (Vitis vinifera L.). submitted."; RL Repbase Reports 9(3), 709-709 (2009). XX DR [1] (Consensus) XX CC Harbinger-3N3B_VV (mPifvine-3.4 in [1]) is a non-autonomous DNA CC transposon of the MITE type. Unlike the Harbinger-3N1_VV, this CC element is not a deletion derivate of the autonomous CC Harbinger-3_VV but it has the same TIRs as Harbinger-3_VV. The CC first 100 bases are shared with Harbinger-3N3_VV. Individual CC copies are >80% identical to the consensus sequence. There is a CC number of copies that are less conserved. TIRs are 18 bp-long CC (with 1 conserved mismatch) and flanked by 3 bp-long TSDs. There CC are approximately 20 conserved copies in the genome. XX SQ Sequence 312 BP; 114 A; 28 C; 46 G; 123 T; 1 other; ggtggtgttt gtttttttac taaaatttaa atagaactta atttaactta aytctaatta 60 taacttaata gtattaagta ttaagttgtt tgtttttttc agagtgtggg gtgtgagggt 120 tgggggttag aagtatgaat tagctaactc tttagattaa gaaaaaaact acatatttaa 180 ctttttctag tcaattaaaa atattggtaa aaatgttaaa agtttaattt tttttttctt 240 tttttaaaac aaacagttgg aatctaaaag taaattgcat tcaacattaa cttaaaaaag 300 acaaacacca cc 312 // ID Copia-65_VV-LTR repbase; DNA; EDCOT; 267 BP. XX AC chr15; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-65_VV_; KW Copia-65_VV-I; Copia-65_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-267 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr15; Positions 15864262 15863996. XX SQ Sequence 267 BP; 80 A; 37 C; 46 G; 104 T; 0 other; tgttaggatt ataaaataat aagttgttaa ctattagttt gctaagctgt tagtttgtta 60 gctgttaaga ggatgttaga ttgctataac agattgttag tgttgtacac gtgtaagcaa 120 gttagttagt gagaagaaac tactgtaata taaatattga ggtttgctct gtaaaccaaa 180 aaacaaagga tttcttccag attgaatctg agccctttct ttccctcttt ctcacttctt 240 tatctcttta ttatcttagt tctaaca 267 // ID COP_I_MT repbase; DNA; EDCOT; 4489 BP. XX AC AC133572; XX DT 13-DEC-2006 (Rel. 11.12, Created) DT 13-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Internal region sequence of LTR retroposon COP_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; COP_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4489 RA Shankar R. and Jurka J.; RT "COP_MT: LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 617-617 (2006). XX DR EMBL/GenBank/DDBJ; AC133572; Positions 58288 62776. XX CC The sequence contains integrase domain. XX FH Key Location/Qualifiers FT CDS 305..4486 FT /product="COP_I_MT_1p" FT /translation="MSSTPATSSSVKSDFHPTLAVTNIKNSIPFVLEMEKD FT HYTMWAELFEVHARAHKVIDHIIPLPGKEKPVSTDANFEMWTILDSTVLQW FT IYSTISFDLLTTIMEKGSTAMAAWNRLADIFEDNQNSRAVALEQDFSSTRM FT EDFSNVSAYCQRLKQLSDQLKNVGAPVSSHRLVLQLVSGLSEPYRGVATLI FT RQSNPLPSFFQARSMLTLEESGLAKMHNTSSPTALHTAVPRDSDDSSQQRS FT NRRQNNRSGSGRNRNNQTRTGGRGQRGGSRSDGPSWTPQPWQQPQYPPWSP FT WGWTPPPWSVPPCPYPTSQWTRPAGPSRQPGILGQRPQAHTTTASPAPTDI FT AAAMHTMSLTPPDSTWYMDTGASSHTAASHGNLSSYSNLSNLNQKLIVGSG FT QGIPILGSGHTTLPTSHKHKTLNLNHVLHTPQIIKNLISVRQLTTDNNVSV FT SFDPFGFSIFDFQTGIPLMRCNSLGDLYPVTSPSHFAGLASSLWHNRLGHP FT SSSTLQSLHSNKFISSEHLSSKTICHSCVFGKHIKLPFDSSKNVTLLPFDI FT LHSDLWTSPILSTSGHRYYVLFLDDYSDFLWTFPISNKSQVFEMFTLLSNQ FT IHTQFSQTVKCFQCDNGREYNNTSFHKYCDDNGLVFRFSCPHTSSQNGKAE FT RKIRTINNMIRTLLAHSSVPPSFWHHALQMATYLLNILPRKNLSNHSPTQL FT LYHRDPSYTHLRVFGCLCYPLFPSTIINKLEPRSTPCVFLGYPTNHRGYKC FT FDLSHRKIIISRHVIFDETQFPFAHMPSLPPTAYDCFTDDLHPSIIHQWTN FT PTLQPLPHDLPSPSPPIPDPPSTSRVGPHTPGTSSSPAPLAQPAPPTRTMA FT TRSMQGIYKPKKLFNLSVTIDDPTISPLPKNPKLALSDPNWKAAMQSEFNA FT LIRNNTWDLVPRPCDVNVIRCMWIFRHKKKSNGCFERYKARLVGDGRSQIA FT GVDCDETFSPVVKPTTIRTVLTIALSKSWPIHQLDVQNAFLHGDLHETVYM FT HQPLGFRDPDRPDYVCRLRKSLYGLKQAPRAWYQRFADFVSTIGFQHSTSD FT HSLFIYRRGSDLAYILLYVDDIILITSSHELRKSIMALLASEFAMKDLGPL FT SYFLGIAVTRHVGGIFLSQSIYVGEIIARAGMASCKPSATPVDTKQKLSTS FT AGTPYDDPTLYRSLAGALQYLTFTRPDISYVVQQVCLHMHAPCTDHMLALK FT RILRYVQGTLHYGLHLYPSRIEKLISYTDADWGGCPDTRRSTSGYCVFLGD FT NLISWSSKRQPTLSRSSAEAEYRGVANVVSESCWLRNLLLELHFPLSQATL FT VYCDNVSAIYLSGNPVQHQRTKHIEMDIHFVREKVARGQARVLHVPSRHQI FT ADIFTKGLPRVLFDDFRTSLSVREPPASTAG" XX SQ Sequence 4489 BP; 1033 A; 1248 C; 824 G; 1384 T; 0 other; tggtatcacg atctgccctt ccagcgtgac cacacacaca agacagccgc cgactgtttt 60 cttcctcacc accagtccgc cgtcatcgtg ctctctctct ctctcagcaa tagaccgccg 120 ccgtcgtgct ctctctctca gcaacagact gccgccgtca tctgctctct ctcaacaaca 180 ggcctccgcc gtcgcttcct atttccggcc aatcccgtcg tctgcactgt tcacgcgaat 240 ctcacccatt cctttgggat tctttttgat tcgattcagt cgatacaccg tcactgctat 300 caacatgtct tctactcctg caacgtcatc ctccgtcaaa tccgactttc atccgaccct 360 tgccgtcacc aacatcaaaa acagcattcc ctttgtgctg gagatggaga aggatcacta 420 caccatgtgg gctgaattgt ttgaggttca tgctcgtgcc cacaaggtta ttgaccacat 480 cattcctcta cccggaaaag agaagcctgt ttccacggat gctaattttg aaatgtggac 540 aattcttgat tcaacggttc ttcagtggat ttattcaacc atatcctttg atcttcttac 600 caccattatg gaaaaaggat ccactgccat ggctgcctgg aaccgtttgg ctgatatatt 660 tgaggacaat caaaactccc gtgctgttgc ccttgaacaa gatttttcat ccactcgaat 720 ggaggatttt tctaatgttt ctgcatattg tcagcgtctc aaacaactct ctgatcaatt 780 gaagaatgtt ggggcaccag tcagtagtca ccgcttggtc cttcaactgg tttccggact 840 atctgagccg taccgtgggg ttgccacctt gattcgccaa agcaacccct tgccatcatt 900 tttccaggct cgctccatgc tcaccttgga agaatccggc ttggcaaaaa tgcacaacac 960 tagttctccc accgctttgc acactgctgt tccacgagac tcagatgatt cctcccagca 1020 gcgctccaat cgtcgtcaga acaatcgctc tggttccggc cgcaaccgca acaatcaaac 1080 tcgcacagga gggcgtggac aacgtggtgg ttctcgttcc gatggtccct cctggacccc 1140 tcagccatgg cagcagcccc agtatccacc atggtctcct tggggttgga ccccacctcc 1200 ttggagtgtg cctccttgcc cctatcctac ttctcagtgg actcgccccg ccggtccttc 1260 aaggcaacca ggcattctag gtcagcgtcc tcaggctcac actaccacgg cttcaccagc 1320 tcccacagac attgcagctg ctatgcacac catgtctctc actcctccgg acagcacatg 1380 gtacatggac actggagctt catcccatac agcggcatct cacggtaatc tctcgtctta 1440 ttctaatttg agtaatttaa atcagaaact gattgttggc agtggacaag gtattccaat 1500 tctagggtct ggtcacacaa ccttacctac atctcacaaa cacaagacct taaaccttaa 1560 ccatgtttta catactccac aaattattaa aaatttgatt tctgtgcgac aactcactac 1620 tgacaataat gtttctgttt cttttgatcc atttggtttc tcgatatttg attttcagac 1680 ggggattcct ctcatgagat gtaatagtct tggcgaccta tacccagtca cctctccttc 1740 tcactttgct ggtcttgctt ccagtctctg gcacaaccgt ctcggtcatc ctagttcttc 1800 cactttgcag tctcttcata gtaataagtt cattagtagt gaacatttga gttctaaaac 1860 tatttgtcat tcctgtgtgt ttggtaaaca tattaagttg ccctttgatt cttccaaaaa 1920 tgttacttta ttgccctttg atattttaca cagtgattta tggacttcac cgattttaag 1980 tacctctggt catcggtatt atgttttatt tttggatgat tattctgatt ttttgtggac 2040 attccctata agtaacaaat cacaagtttt tgaaatgttc acattacttt ccaatcaaat 2100 tcacacacaa ttttctcaaa ctgtcaaatg ttttcaatgt gataatgggc gtgaatataa 2160 taatacatca tttcataagt attgtgatga taatggtctt gttttccgtt tctcttgtcc 2220 tcatacttca tctcaaaatg gcaaagcgga acgtaaaata cgcaccatta acaacatgat 2280 tcgtactctt ctcgctcatt cgtctgtacc tccctcattt tggcatcatg ctcttcaaat 2340 ggctacttac cttcttaata ttcttcctcg aaagaatttg tcaaatcact ctcctactca 2400 acttttgtat catcgtgatc cctcctacac acatcttcgc gtttttggtt gtctttgtta 2460 tcccctgttt ccatccacta tcattaacaa actagaacca cgctcgaccc cgtgtgtctt 2520 cttagggtat cccactaatc acagaggata caaatgtttt gatttgtcgc acagaaagat 2580 cattatctcc cggcatgtca tatttgatga gacacaattt ccctttgccc acatgccttc 2640 cctacctccc accgcctatg actgtttcac tgatgaccta cacccatcta ttatccatca 2700 gtggacgaac cccaccttgc aacctctacc tcatgacctt cccagtccat cacctcctat 2760 acctgaccct ccgtctacct cacgagtcgg accacataca cctggaacct cctcatcacc 2820 tgccccacta gcccagcctg cacctcccac tcggactatg gccactcgta gcatgcaggg 2880 tatctacaaa cctaaaaagc tctttaacct ctctgttacc attgatgatc cgactatttc 2940 acctcttccc aaaaatccaa aacttgccct atctgaccct aattggaaag ccgcaatgca 3000 gtctgaattt aatgctctta ttagaaataa tacgtgggat ttggttccac gaccttgtga 3060 tgttaatgtt attcgctgta tgtggatttt tcgtcataaa aagaaatcta atggttgttt 3120 tgagcgttac aaagctcgtc ttgtcggtga tggcaggtca cagattgcag gtgtggattg 3180 tgatgagaca ttcagtcctg ttgtaaaacc gacgacgatt cgtaccgttc tcaccattgc 3240 gttgtccaaa tcctggccta ttcatcagct agatgtccag aatgcatttt tacatggtga 3300 ccttcatgag acggtttaca tgcatcaacc acttggtttc cgtgatcctg atcgcccaga 3360 ttatgtgtgt cgcttgcgaa aatcactgta tggtctaaag caagcgcctc gtgcctggta 3420 ccagcgtttt gcagactttg tctccaccat tggattccag catagcactt cagatcactc 3480 ccttttcatc tatcgacgtg gctctgattt ggcttacatc ttgttatatg ttgatgacat 3540 catcctcatc acctcctccc atgagcttcg aaaatccatc atggcactcc ttgcctctga 3600 gtttgctatg aaggatctgg gtccactgag ttattttttg ggcattgccg tgactagaca 3660 tgttggtggg attttcctta gtcagagtat ctatgttggt gaaatcattg cccgcgcagg 3720 catggcctcg tgcaaacctt ctgctactcc agttgacacc aaacagaagc tcagtacctc 3780 cgctggcact ccatacgatg accccacctt atatcggagt cttgcaggag ccttgcagta 3840 tcttactttc acccgtcctg acatttctta tgttgttcag caggtgtgtc ttcacatgca 3900 tgccccttgc accgaccaca tgcttgccct caaacgcatc ctacgttatg tgcagggcac 3960 cttacactat ggtttgcatc tttatccatc ccgtattgag aaacttatct cctatactga 4020 tgctgattgg ggtggatgtc cagacacccg tcgttctacc tctggctatt gtgtgtttct 4080 tggtgacaac ctcatctcct ggtcttccaa gcgacaaccc acactttcgc gctctagtgc 4140 agaagctgag tacaggggtg ttgctaatgt ggtatctgaa tcttgttggc ttcgtaacct 4200 tctcttggaa cttcatttcc cactctctca agctactttg gtgtattgtg ataatgttag 4260 tgccatttac ctttctggta atccagtaca acatcagcgc actaaacata ttgagatgga 4320 cattcacttt gttcgagaaa aggtagctcg tggccaggca cgcgtccttc atgttccttc 4380 tcgtcaccag attgctgaca tcttcaccaa aggcctaccg cgtgttcttt ttgatgattt 4440 tcgaaccagt ctaagtgttc gtgaacctcc cgcttcgact gcgggggtg 4489 // ID TAS49_NT repbase; DNA; EDCOT; 222 BP. XX AC . XX DT 23-MAY-2005 (Rel. 10.05, Created) DT 03-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE N. tabacum unclassified dispersed repeat, consensus. XX KW Transposable Element; Interspersed repeat; subtelomeric repeat; KW TAS49_NT. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RA Horakova M. and Fajkus J.; RT "TAS49--a dispersed repetitive sequence isolated from RT subtelomeric regions of Nicotiana tomentosiformis chromosomes."; RL Genome 43(2), 273-284 (2000). XX RN [2] RP 1-222 RA Gentles A. and Jurka J.; RT "TAS49, an unclassified dispersed repeat."; RL Direct Submission to Repbase Update (20-MAY-2005). XX DR [2] (Consensus) XX CC TAS49 is a member of a family of dispersed repeats, but lacks CC characteristics of known transposable elements. XX SQ Sequence 222 BP; 40 A; 28 C; 84 G; 69 T; 1 other; atttggacgt ggcttcgggt agttttggcg ggcaagtgga ggaaaatggt aatatgcagg 60 ttgagtgttg taggtatggt aggtggtggc agggtattgg tattttggtg gtgagggctg 120 atatgtgggt ggaggtgttt ggtatgtgar gggagactta gggccctggg ctaccatcac 180 ggcaccactt ctttcttgaa tccctgatgc aagttttcgt gg 222 // ID Copia-6_TC-LTR repbase; DNA; EDCOT; 518 BP. XX AC CACC01004662; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-6_TC_; KW Copia-6_TC-I; Copia-6_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-518 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01004662; Positions 8030 8547. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 518 BP; 134 A; 75 C; 83 G; 226 T; 0 other; tggtcgttac attcatattc tgacagtgat agcatgtgaa gaacaagaga agagcttcaa 60 ctttttagtg caaaacaatg acgtttattc atcagcaatt ataagttttc aaagtgtgtc 120 attttactct ttatgtttta agttggttgt actcaaaacg atgttgctca tatcgttttt 180 tagctaagtt tagttaagtc ctatacgctt cattttagtg tcatttttta gtctgtttta 240 aggcttaaca gccatggttt tctatttcaa ttttttaccg ttgagggatc attgatttgt 300 gtgtagtttg ttgttgtgat ccgatttatc aagaaatgtt tttgaattgt ttgaatatat 360 atacttgaaa taaaatgaaa tttacacttc ttcccagtaa gaaattttca gttcacattc 420 tctggaattc ttagttcttt agacttctca gacttctcta ttttttaagc tttgtttttc 480 attgcttagc tttgcagctt agcttttaat tttcttca 518 // ID SHALINE6_MT repbase; DNA; EDCOT; 5894 BP. XX AC . XX DT 22-DEC-2006 (Rel. 11.12, Created) DT 05-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE A LINE element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; retroposon; KW LINE; Interspersed; repeat; Poly-A tail; SHALINE6_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5894 RA Shankar R. and Jurka J.; RT "SHALINE6_MT: A LINE element from barrel medic."; RL Repbase Reports 6(12), 642-642 (2006). XX DR [1] (Consensus) XX CC The LINE element is present in low copy number in Medicago CC genome. The sequence has two ORFs. The first one codes for a zinc CC finger protein while another one has well conserved domains for CC endo-exo-phosphatase and reverse transcriptase. XX FH Key Location/Qualifiers FT CDS 92..1138 FT /product="SHALINE6_MT_1p" FT /translation="MVILKKVVVGENPLSMPMNTTEIWAQVHQLPFGFMDA FT KVGALVGSHIGRMVRYDDENNYGLWRRFMRVRVEIALEEPLQQSLVIEREQ FT GEDIKLVLKYEKLGKFCFVCGVIGHTENFCSDKFETSSASSEKKWGAYLRA FT ENFSSGGGSKVASRWIVDGRNKNSGGRNDEGTSINGIKSNHLMVIDGISNH FT EIYGRIKVDIDLQSRALKFFKFMECQRSDGTGLVRWWTEIDPTEEIESGSK FT KKEVITKKKLFAPNLTKSDQINKAIAEGMTEKDEFLYENGGGAEALWKLID FT LEAQQKKHKPTKFYGGGQPAGPTWGQRQGREGRSDNSGPTRGQPPDKARNT FT RTACLV" FT CDS join(1742..2599,2603..3157,3161..4255,4259..5863) FT /product="SHALINE6_MT_2p" FT /translation="MSFVAWNCRGLGNLRVIPKIKFLVRYYKPDIIFLSET FT IIQVNKIEEFRYLLGYDSCFAPDRVGRGGGVALFWRNTINCSIVNYSSNHI FT SAKIEESNGHWIFTGFYGYPEASRRRDSWNFLRRLASNINLPWCLMGDFND FT ILHADEKKGRATRPNWLIRGFRQAVQDANLVDVHMEGYPFTWFKSLGTPRA FT VEEKLDRALATNSWMHLFPNAKLENLVAPSSDHFPILLDRTPVVRPHRSKR FT SFKFENAWRIEDGLNEVVHNSWLRSAGDGVINKLATCAEDLMQWNTHCNRI FT QKDIEDCRHQLSRSRGVNGIQDEIHFDNLRKKMNHLLVQEDMYWKQRAKTH FT WFRDGDLNTKYFHVAATSRKKVNKILSLDTDEGIRVTEDAGMRSIAKNYFE FT ELFEGQESVRSPVVNLLDPVLDNEDNDQLIAPFCIEEFKEAMFSMQPDKCP FT GPDGFNPGFYQHFWSVCSDDIYNECCWLNEGQFPPSLNSTNLALIPKGSNQ FT KTMKDWRPIALCNVLYKLLSKVLANRLKKILHKCIADSQSAFVPGRSILDN FT ALVAIEVVHHMKTKTRGKDKSVALKLDISKAYDRIDWLYLKDVMHKMGFSD FT KWIQWIMMCVETVDYSVIVNKEMVGPIIPGRGLRQGDPLSPYLFILCAEGL FT SALIRDAENREVLQGVRICRNAPRVSHLLFADDCFLFFQAEERQANEMKQI FT LTRYEAASGQAISLPKSEIFYSRNVQDPLRQTITNILGVRAVLGTGKYLGL FT PSMVGRSKKATFGFIKDRVWQKISSWSSKCLSKAGRKVMIKSVLQAIPSYV FT MSVFRLPNSLLDEIEKMINAFWWGHGGANNKGMRLSWKKLSVHKNHGGMGF FT KDLAAFNVAMLGKQGWKLQVESDSLVSRIFKARYYPNSSYLDSKLGHNPSF FT VWRSIFGAKVVVRQGARWKIGSGFNIPIINEPWIGEGSSIPPIGPDMLALQ FT SYSVGHLMDHNAKVWNEHLIRQLFATETANNILNTPLHQQVLVDRLIWKAE FT KDGCYSVKSAYRMCIEEIINNDHLRKPGYWSGIWRLKVPPKVKNLVWRICR FT DCFPTRVKLRSRGVNCPSNCVMCEDPHEDSYHILFHCKAAVDVWNAANVWH FT LISPSLDLFDNASDIIFHLLKILSTTQIENIVTTIWSIWKARNLKLWQQVT FT DSPTTILVRATHLLEGWRSANRKQNPPNQSHIDTTLPRNHNIQVVDGVSNI FT RWRKPRSGRLKCNVDASFSEVNNKIGLGICIRDSTGSHVRSKIMFFSPLCY FT VDVGEALGLYHAIRWIHEFQLENVDFEVDSKRVADYFNKGRGDVTEFGSIM FT DSSIHFCRSLLTNSHVEFTRRQANEVAHNLAKAATSSSSFRIFDEIPTCIT FT ELIFNEMI" XX SQ Sequence 5894 BP; 1799 A; 1039 C; 1406 G; 1650 T; 0 other; tatggagaac aacaagttta tggtccagct ctactagaaa ggagaccttg ctaagattct 60 ggacggcagc ccctggttgt tagacaacaa catggtaatt ttgaagaagg ttgtggttgg 120 agagaacccc ttgtcgatgc cgatgaatac cacggagatc tgggctcaag ttcatcagct 180 acctttcggc tttatggatg ctaaagtcgg tgcattagta ggaagccata tcggacggat 240 ggtccggtat gacgatgaaa ataactacgg tctgtggagg agattcatgc gagttcgtgt 300 tgaaatagcc ttggaggaac cgctgcagca aagtctcgtg attgaacgag aacaaggtga 360 ggatatcaaa cttgttctta aatatgagaa attaggcaaa ttctgttttg tctgtggtgt 420 tataggccat acggagaatt tttgcagtga taaatttgaa accagctctg ccagtagcga 480 gaaaaaatgg ggggcttacc tccgggctga gaatttttct tccggtggtg gtagcaaggt 540 ggcgagtaga tggatagttg acggtcggaa caagaattcc ggtggccgga atgacgaagg 600 tacatccatt aatggcatta aaagtaatca tttaatggtt attgatggta tttcgaatca 660 tgaaatttat ggtcgtatta aagttgatat tgatttgcaa tcaagagctt taaaattttt 720 taaatttatg gaatgtcaac gctcggatgg gacggggctg gtcaggtggt ggacggaaat 780 cgatccaaca gaggagattg agagtgggtc caagaaaaaa gaggtcataa caaagaagaa 840 gttgtttgct ccgaacctca caaaatcgga tcaaataaac aaagctatag cagaaggaat 900 gacagagaaa gatgaatttt tgtatgaaaa tgggggaggt gcagaagcac tttggaagct 960 gatagacttg gaggcccaac aaaaaaaaca taagcccaca aaattctatg gtgggggaca 1020 gccagcgggg cccacgtggg gacaaaggca aggaagagaa ggaaggagtg ataactcggg 1080 tcccacaagg ggacagccgc cagacaaggc acgcaacaca aggacagctt gtcttgtgta 1140 atactttcca gcagcaggtg gtcccgcaag gacaaaaaac agcacatcaa tcattgaaca 1200 ttcaatacaa aatgactggc acggattaca gaagactttt taccaaggaa tctgcacaat 1260 taccaataaa tgctgctttt agtgctaata attgtgtcat acaggtacaa aaagtgaacc 1320 agcttcaaac tttgatgaac aaaggcaata aagaccaatc atcagccttg tctcctatct 1380 ttactgccaa tgattaccgc ccagcttttt ccacaaaaga caagaactgc caaccgagcc 1440 gagccaagcc ggacagaaaa aacaaagctg caacagctgt ccaagtgcat gggaagccgc 1500 gtaagccccc tctggtgcgc aacccagtgc agcctggctc ctttatggct gctgctcgtg 1560 gggccagcag agctagtgga cctgtagaag aaaatgggcc caaaaaaagg tccagaacag 1620 attttgctga agaagaagaa cagcgcaagg aggggcagaa agcagtagat gtttttaaca 1680 atccactttt tgagaataat aaagaatcgg cgggacctgg tcaccaggcc tgccgggacc 1740 aatgagtttt gtagcatgga attgccgagg cctgggaaac ctgcgtgtaa ttcctaaaat 1800 caaattcctt gttcggtatt ataaaccgga tatcattttc ctttctgaaa caattattca 1860 agttaataaa attgaggaat ttcgatactt gttgggctat gattcttgct ttgctcctga 1920 tagagttggt agaggagggg gtgttgcttt attttggcgt aatacaataa attgtagtat 1980 tgtcaactac tcttcgaacc atattagtgc taaaattgaa gaaagtaatg ggcattggat 2040 ttttactggt ttttatggct atccggaagc tagtagaaga agagactctt ggaattttct 2100 tcgtcgtctt gcaagcaata ttaatttacc ttggtgtcta atgggggatt ttaatgacat 2160 tcttcatgcc gacgaaaaaa agggaagagc cactagacct aattggctca ttagaggctt 2220 taggcaagct gttcaagatg ctaacctagt agatgtacac atggaagggt atccgttcac 2280 ctggttcaaa agcttgggta ctcctcgtgc tgtagaagaa aagctggata gggctctagc 2340 gactaattct tggatgcatc tgtttcccaa tgctaagctg gaaaatttgg ttgctccttc 2400 ttctgatcat ttcccaattt tattggatag aacacctgta gtaagacctc atagaagcaa 2460 aaggtctttc aagtttgaaa atgcttggag aatagaagat ggtcttaacg aggtggtcca 2520 caacagttgg ctccggagtg ctggagatgg tgttataaat aaattagcca catgtgccga 2580 agatttgatg cagtggaact aaactcattg caacaggatc caaaaagata ttgaagattg 2640 tcggcatcag cttagtagaa gtcgtggtgt taatggaatc caggatgaga ttcatttcga 2700 taacttaagg aaaaaaatga accatcttct cgttcaggag gatatgtact ggaaacagag 2760 agccaagaca cactggttcc gggatggaga tttgaatacg aagtactttc atgttgctgc 2820 tacttcgaga aagaaagtaa acaaaatact ttctcttgat accgacgaag gaatccgtgt 2880 tacagaggat gcaggtatgc gatctattgc aaagaattat tttgaagaac tgtttgaggg 2940 tcaagaaagt gtgcgttctc cagtggttaa tctgttggat ccagtcttag ataatgaaga 3000 caatgaccaa ctaatagccc cgttttgtat agaagagttc aaagaagcaa tgttttctat 3060 gcagcctgac aaatgccccg gacctgatgg tttcaatcct ggtttctacc aacacttttg 3120 gtcggtatgc agtgatgata tctataatga gtgctgttaa tggttgaatg aagggcaatt 3180 ccctccttcc ttgaattcca caaatttagc tctaatccct aaaggttcta atcagaaaac 3240 catgaaagac tggagaccta tagctctatg caacgtccta tataagctgt tatctaaagt 3300 tcttgcaaat cgtctaaaga aaattctaca caagtgtatt gccgactcac agtcagcctt 3360 cgtacctgga agatccattc tggataacgc tttagtagct attgaagtgg tccatcatat 3420 gaagactaag acaagaggca aagacaagag tgttgcactg aagctggata ttagtaaagc 3480 ttatgatagg attgactggt tatatctcaa ggacgttatg cacaagatgg gtttttctga 3540 taagtggatt caatggatta tgatgtgtgt agaaacggtt gactattcag ttattgtgaa 3600 taaagaaatg gtggggccta ttattccagg acgtggtctt aggcaaggtg atccgttatc 3660 gccttattta tttattctgt gtgctgaagg tctttctgcg ttaatcagag atgctgaaaa 3720 cagagaagtt ctccaaggtg tgcgtatttg tcgcaatgca cccagggtgt ctcatctact 3780 ctttgctgat gattgcttct tgttcttcca agcggaggag agacaagcaa atgagatgaa 3840 gcagatctta acaagatatg aggctgcgtc aggacaagcc attagccttc caaagtcaga 3900 aattttttat agcagaaatg tccaagaccc gctgagacaa actatcacca atattttagg 3960 ggttcgtgcg gtgttaggta ctggtaagta tcttggttta ccttcaatgg tagggcgtag 4020 caaaaaagca acgtttggtt ttatcaaaga tcgagtgtgg cagaaaataa gcagctggag 4080 tagtaaatgc ttatccaaag caggaaggaa agttatgatt aaatctgtcc tccaagctat 4140 cccttcgtat gttatgagtg ttttcagatt accaaactca cttctggatg aaattgaaaa 4200 gatgataaat gctttctggt ggggacatgg aggggcgaat aataaaggga tgcgctgact 4260 ttcgtggaaa aagttatcag tacacaagaa ccacggaggt atgggtttca aagatttggc 4320 agcttttaat gttgctatgc ttggaaaaca aggttggaag ctacaagttg agtcggatag 4380 tcttgtctca agaattttta aagctcggta ttatccgaat agcagctacc tagattctaa 4440 attaggacat aatccaagtt ttgtttggcg tagcatcttt ggtgcaaaag tggttgttag 4500 gcaaggtgcc cgctggaaaa ttggctcggg attcaatatt cctattatta atgagccttg 4560 gattggggaa gggtctagta ttcctcctat tggacctgac atgttggctc ttcaatctta 4620 ttcggttgga catttaatgg atcataatgc taaagtttgg aatgaacacc taatcagaca 4680 gttatttgca acggagacag ccaataatat cttgaatacc cctttgcacc aacaagttct 4740 cgtggatagg ttgatttgga aagcggagaa ggatgggtgt tattctgtta aaagtgctta 4800 ccgtatgtgc attgaagaaa taattaataa tgatcatctg cgaaagcctg gttattggag 4860 tggcatctgg agactgaaag ttccacctaa agttaagaat ttggtgtgga gaatttgtag 4920 agattgtttc ccaacaaggg taaagttacg aagcagaggt gttaattgcc cttcaaattg 4980 tgttatgtgt gaagatcccc atgaagacag ttatcatatc ttgtttcact gtaaggcggc 5040 tgtcgatgtt tggaatgcgg ctaatgtttg gcatctgata tctccatctt tggacctgtt 5100 tgataatgca tcagatatta tattccattt gttgaaaata ttgtctacaa cccagataga 5160 gaatattgtc actactatat ggagtatctg gaaagctagg aaccttaagt tgtggcaaca 5220 agtgacagat tcacccacaa caatcttggt aagagctacc catcttttag aaggttggag 5280 aagtgctaat cgtaaacaaa atcctcctaa tcaaagtcac attgatacca cccttcctcg 5340 taaccacaat atccaggtag tagatggagt ttctaacatc agatggagga aacctagaag 5400 tggtagactc aagtgtaacg ttgatgcatc attttcagaa gtcaacaaca agattggttt 5460 gggcatatgt attagagatt caacaggatc ccatgtccga tccaaaatca tgtttttctc 5520 tccgttgtgc tatgtggatg ttggagaggc gctggggttg tatcatgcaa ttcggtggat 5580 ccatgaattt caactcgaaa atgttgattt tgaagttgac tcgaaacgag tagcagatta 5640 tttcaacaaa ggtcgtggag atgtcaccga atttggttct ataatggaca gtagcattca 5700 tttctgtcgg tcacttttaa caaactctca tgtcgagttt actaggaggc aagcgaatga 5760 ggttgcacat aatctagcta aggcagccac atctagttct agcttccgta tctttgatga 5820 aatcccaaca tgtattactg aattaatctt taatgaaatg atttaagttt ctttctctcc 5880 aaaaaaaaaa aaaa 5894 // ID L1-15_Mad repbase; DNA; EDCOT; 3799 BP. XX AC . XX DT 07-OCT-2010 (Rel. 15.1, Created) DT 07-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-15_Mad. XX NM L1-15_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3799 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1819-1819 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Truncated at the 5'-end. XX SQ Sequence 3799 BP; 811 A; 734 C; 1039 G; 1200 T; 15 other; aggtttcaat cgaagaacgt taataaatag gaaccgcatc caaaatcacc cggttcaaaa 60 tttgaatcaa attagaagga tgctccacag aaatttgatg aggacaatct tagttcaaac 120 atatgacctc aagtgcagct gttaacggac atgttccttg caatctacac acgaataaaa 180 aggaaaaaaa awtwagctaa agaactacaa gcaagttgct tcggtttctt tatttcgaag 240 ctcttttatg ttaaagattg tggaggagtg ctgggccaat ctgggggtcg gtccgctgcc 300 ggggcaatgg gttcagaaac ttaacgcctg tcgggtctct ctgtccaggt ggagccggac 360 taaattccat cagcggagcc agcaaattga ggcgctctct aggcagcttg tggagcttca 420 aaagcaatgg ggaaataatt ttcaggacat tctcgagaag caaaaacaaa tggccgatct 480 tcaaacgcag gaggctagct attggcatca acggtcccgc gttaaatggt tgcgagaagg 540 agactcaaat accaagttct ttcaccattc cactttacaa cgtcgacgcc gaaatatgat 600 tctaaagctt aaagacgatg acgggcattg gattgagcac cctagtcgga ttcgccagat 660 ggtagaggaa cactttcaga ctctctttaa gtctggggga tctaggaact ggggggattt 720 attagagtgt gtatcgcctg gaatcacgga ggaaatgaat agggatttaa ttgctccagt 780 ttctgatgag gagattcgga ctgcagtgat gaagatgggg aggctgcaag ctcctggtcc 840 tgatggtttc caagggattt tttaccagac gttctgggac actttgaaga ctgatgttca 900 gttgttgatt cgtgctttga tgcatgrgga ggttgtgcct acaactatta attccactca 960 tattgttctt atacccaagg tgcccaatcc tgagtcggtt tcgcagttty gcccgatcag 1020 tctttgtaat tattcttata aggtcctttc taaggtgttg gccaatagat tgaaggtggt 1080 gatgccgaat attatctccc cttctcaaaa tgcttttgtg gaggggcgac agattcatga 1140 taacattggc atcgcccatg agatgtttca tttcttaaag ggtaggaaag ctaaatcaaa 1200 atatgagttg ggcattaagc ttgatatgca gaaggcctac gatcgtgtgg agtgggattt 1260 cctggatgcg gttatggaaa agatgggatt ctgtaccaga tggaggcaac taatcatggg 1320 ttgtgtttcc tcagtccaat ctgccattyt cttaaatggc yagcctggaa aatgcttcgc 1380 tcmttctcgt ggaattcggc agggggatcc tctctcccct tttcttttct tgttggtggg 1440 agaggttttc tcttgtttaa ttcaaaacgc ggtgcagaaa aatyttctgg atggtgtgca 1500 gttgggagct tccggtcctg tcatttccca twwttttttc gctgatgaca ctttgctgtt 1560 tcttaaggct gatggtaaaa attgtcggaa cttagttgac ttgatcaata agtattgtga 1620 ggcttcgggg caattagtca actttcaaaa atcaagtgtg tattttggag cgaatattcc 1680 taagcgggtc tccgctgatt tggctcatat ccttaatgtc aaggctgtgg aagatcctgg 1740 agcttacctg ggtgtccctg ctatttgggg cagatcgaag gtgaagggtt tggcgtttat 1800 tcgggagaaa attttgggaa aagttcaagg ttggaagcat aaacttttat cctctgcggg 1860 tcgtgaagtc ttaattaagg ctgtggtcca ggcccttcct gcttacccca tgtacatgtt 1920 taaatttcct gcctcggtgt gtcaagactt tgattcttta gttgccgatt tttggtgggg 1980 acgacagggg gcttcgagga aaactcactg ggtttcgaag gaggttcttg gcctccctaa 2040 agattggggt ggtttggggt ttcgaaattt tgctgatttt aatgatgcct tattagctaa 2100 acaatgttgg cggttgcttt cggatccgat gtctttgtgg gcacgtgttg tgaaagctcg 2160 ctatttcccg aattgctcct tttgggacgc tactaaaggc ggttgggcct cttgggcttg 2220 gtcaagtctc ttggtgggga gggaagtgtt acgtaagggg gcgcattggc aaattatggg 2280 agggcatgat gttagagttt gggtggatcg ctggctcccc tccttacctc ttggtcgtcc 2340 ggagcmgctc ggggaggtgg ctgtttctcc aaatctgcgt gttcactctc tgattagcca 2400 ggagtcgagg atttgggaca ttgatttcct actgccgttt ctctcggagg aggccaaact 2460 cgctatcaat tgtctgccta ttggtgattc caggtacaag gatagattaa tttgggatgc 2520 tagtaagaat ggcagatact cggtgaagtc gggtatcgtt ggttacagtt ggggctattg 2580 cttctcgtga tcagtggctg ccmaggtcgt ctcattccta aaaatctgtg gaaccaggtt 2640 tggaatctgc ctgctccggc aaaaattcgc ckkttctttt ggctttctct gcaccggggt 2700 ttggctacta aagagacgtt gtttcggaga aagatatgtt caattgtctc atcttgacta 2760 ttacatattg ggcaasatgg gacaattgag catatccttc tcctttgtcc gtgggtgagg 2820 gccatatggt ttggtggcgc ccttaattat cggattgatg gcgaaagcat ttcttcttgg 2880 gcggactggt tgatggaggt ccttgttcgt tttccgggtg gaacggaggt caggaaatgg 2940 gtctgctctt atgtggcgtt tactgtttgg tttatttggc gtaccaggtg cgagtttgtt 3000 tttaatcagg ttcccattct tccttttaag gtcctgttgg gggtgtcttc ggctgtcggg 3060 gctttctggg aagccatggg atggtctgga ggtggtgcag ctcggccctc tgcccgctgt 3120 ggtccgattc ctctatggat ccctcatcct gattcttttg ttaaaattaa tgttgatgct 3180 agttggtccc atgcatctcg ttcgggtttt actggtgtgg tcattcgtga tgcttctggt 3240 cagtttgtgg ctgctgagcg ttttgccttg tctactccat ctgttgcggt ggctgaagcg 3300 acgactttgc tgtgtggctg taagttgggg tcctcgttgg gctttaaatc ggtaatagtg 3360 gaatcggact ctaaggagtc cattgattgg ctttctggag atgttgaggt tggcagttgg 3420 aaagcctttc ctgtcctgac gagagttaag gtggagagtg atgcttttca gttctgtcgc 3480 tggtcttggg tgccaagatc agccaatggt gccgctgact ttctggcgtc gcggagtttt 3540 ccggagatgg gttctcgggt ttgggttcac aggcccccat cttctctggt ctttgttttg 3600 aataaggatg gtcttccttg ccctccttaa ttttgttttg gtggtggtgg gggtgacgct 3660 cgttgctggt gcgtctgctt ggtgtatccc ctatctcttc tttctgtgtt gtttgccctt 3720 gtggtgttag cctcctggta ggcttcctgt gctgtttgtt tgtttgttcc tcctttcaaa 3780 aaaaaaaaaa aaaaaaaaa 3799 // ID Copia-97_Mad-I repbase; DNA; EDCOT; 4223 BP. XX AC . XX DT 28-OCT-2010 (Rel. 15.11, Created) DT 28-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-97_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4223 RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-4223 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1979-1979 (2010). XX DR [2] (Consensus) XX FH Key Location/Qualifiers FT CDS 50..4078 FT /product="Copia-97_Mad-I_1p" FT /translation="MSDGQDENPFGSSSGFARTTVQNAKFEVEKFDGTNNF FT GMWQCEVKDVLAQQDLLAALGEKPEAMSKPEWEKLNLWACSSIRLCLAKTQ FT KYFVMRETLASVLWQKLEDKYMTKSAENRLHLKKKLYRFQYKEGTKMIRHL FT DAFNKLIADLLNLDEDIKDEDKALILLNSLPDSYEHFVTTIMHGKETVKFE FT DVSNALMNYEMRHRDKNHDSTSEALFVRGRSSERRSSSSRKKSQSRPRGNS FT KGRKPLERDECAFCHNKGHWKKDCPRLKTKGKESSEANVAEVETDFSDFAL FT TTSSSFDCATKWVLDTGCTHHMTPHKDWFSSLKEFDGGVVFMGDDNPCTTK FT GIGTVRLKLHDGMVKELTGVRYVPNLKKNLISLGTLESKGFRFHSDGQTLK FT VTYGALVVMKAPRCGHLYLLQGSTVTGEASVVSENMGTSDSDTTRLWHMRL FT GHAGEKALQGLVKXGLLKGATTCKLDFCEHCVLGKQTRVKFGTAVHQTKGI FT LDYVHSDVWGPTKTPSLSGRHWFVTFVDDYSRRSWVYTMKHKSEVLSIFLG FT WKKMVENQTGRKIKILRSDNGGEYTSDPFFKVCKEEGIVRHFSVRGTPQQN FT GVAERLNRTLLEKVRCMLSQSGLSKSFWAEAVXYACHIINRLPSAAVQGKT FT PMEVWTGKPSSDYDYIRIFGSPAYFHVTENKLDPRAKKAIFLGFSSGVKGY FT RLWCPEMKKLVISRDVTFDEESMYKDSEKNVKDVQQVELEKVASGTSNPIS FT ADVEATTSEEVGDHEDVEEVELEDSIQVEEQVSPQESIAKNRGKRQITKPA FT RYSDYVAFALPIITDDIPSNFEEAIESEEKERWCNAMGDEMNSLLKNKTWE FT LAKLPKGKKAIGCKWVYAKKEDADEKSNVRFKARLVAKGYAQKEGIDYNEI FT FSPVVKHSSIRIMLALVAQYDLELVQLDVKTAFLHGDLNEEIYMCQPDGYT FT VKGKENLFCKLKKSLYGLKQSPRQWYLRFDKFMRGQNYSRSQYDHCVYFKK FT LQDGSFIYLLIYVDDMLIASKNVEEIEKLKKQMKNEFEMKDLGEAKKILGM FT EITRDREKGLVSLNQRQYLEKLIRKFGVHDSTKPVSTPLAPHFKLSSLQCP FT KTDKEKLQMKNIPYANLVGSLMYAMVCSRPDIAHAVGMVSRYMHNPGKEHW FT QAAKWILRYLHGTRDVGLCFERDDSGIGHFAVGYVDSDYAGDLDGRKSTTG FT YVFTMAKGPVCWRSILQSSVALSTTEAEYMAVAEAIKEAIWIHGLIRDLGV FT DQKQVEVHCDSQSAIYLAKYQVHHARTKHIDVRYHFVREIVGEGEIILQKI FT PTKDNPADMLTKVVGVAKFVHCLNLAHILPI" XX SQ Sequence 4223 BP; 1233 A; 634 C; 1105 G; 1249 T; 2 other; attggtatca gagcactggt tgctcttggg tactgtctag ttgccaaaga tgtcagacgg 60 gcaagatgag aatccttttg gaagcagctc cgggtttgca agaactacgg tgcaaaatgc 120 aaagttcgaa gtggaaaagt ttgatggcac aaacaacttc gggatgtggc aatgtgaggt 180 caaagatgtg ttggctcaac aagatctact tgccgctttg ggagagaagc cggaagctat 240 gtcgaagccg gaatgggaga aattaaattt gtgggcttgc tcttcaattc ggttgtgcct 300 tgcaaaaact cagaagtatt ttgtgatgcg ggagacatta gcaagtgtgt tgtggcaaaa 360 attggaagac aagtatatga cgaagagtgc agagaaccgg ctacacttga agaaaaagct 420 ctaccgcttc caatacaaag aaggtacaaa aatgattaga caccttgatg cttttaataa 480 gttgattgcc gacttgttaa atttagatga ggatattaag gatgaagata aggccttaat 540 attgttgaat tccttgccgg actcttatga gcattttgtt accactatta tgcatggtaa 600 agaaactgtg aaatttgaag atgtgtcaaa tgccttgatg aattatgaaa tgaggcatag 660 agataaaaat catgatagta cctctgaagc tttatttgtt agaggtagat catcggagag 720 gagatcatct tctagtagga aaaaatcaca gtctcgacct agaggaaact ctaaaggtag 780 aaaacccttg gaaagggatg aatgtgcctt ttgtcataat aagggccatt ggaagaaaga 840 ttgtcctagg ttgaagacca aaggaaaaga aagttctgaa gctaatgttg ctgaggttga 900 aacagatttt tctgattttg ctttaaccac ttcctcatca tttgattgtg ctactaagtg 960 ggtgttggat acgggttgta ctcatcatat gactcctcac aaggattggt tttcaagctt 1020 gaaagagttt gatggtggcg ttgtgttcat gggagatgac aatccttgca caacaaaagg 1080 gattggtaca gttcgtttga agttgcatga tggcatggtt aaagagttga caggtgttcg 1140 gtatgtaccg aatttgaaga aaaatcttat ttctttgggt actttggaat ccaagggctt 1200 caggtttcat tcagatgggc agacattgaa agttacttat ggtgcacttg ttgtgatgaa 1260 agctcctcga tgtggccatt tgtatctatt gcaaggaagc accgtgacag gtgaagcatc 1320 tgtagtctca gaaaatatgg gcacatctga ttcagatact actagactgt ggcatatgag 1380 attaggccat gccggtgaga aagctctaca agggcttgtg aaamaaggtc ttctaaaagg 1440 tgccacgact tgtaagcttg atttctgcga gcattgtgtc ttggggaagc aaactagagt 1500 gaagtttggt actgcagtac atcagacgaa gggcattctt gattatgtgc attcggatgt 1560 ttggggtcct acaaagactc cctctttgag tggtagacat tggttcgtga cctttgttga 1620 tgattattca agaaggtctt gggtctacac tatgaagcac aagagtgagg tgttgagcat 1680 tttcttgggt tggaagaaaa tggttgagaa ccagactggg agaaagatta agattttgag 1740 atcggataat ggtggtgaat acacatccga ccctttcttt aaagtttgca aagaggaagg 1800 gattgtgaga catttcagtg ttcggggaac tccacaacaa aatggagttg cagaaagatt 1860 gaatcgaacc ttgcttgaga aggttagatg tatgttgtct cagtcgggtt tgagcaagtc 1920 attttgggca gaggcagtta mttatgcatg tcacatcatc aaccggttac cctcagctgc 1980 tgttcagggt aagacaccaa tggaggtatg gactggaaaa ccttcttctg attatgacta 2040 tatccgtatt tttggttcac ctgcttattt tcatgtgact gaaaataaac ttgatcctag 2100 agccaaaaag gctatctttc ttggttttag tagtggtgtc aaaggttaca ggttgtggtg 2160 cccagagatg aagaaacttg taatcagcag agatgtgaca tttgatgaag aaagtatgta 2220 caaagactct gagaagaatg tgaaagatgt ccaacaggtg gagcttgaga aagttgcctc 2280 tggtacttca aatcctattt ccgctgatgt cgaagccact acaagtgaag aagttggaga 2340 ccatgaggat gttgaagaag ttgaacttga agattctatt caagttgaag agcaagtttc 2400 acctcaagag tctattgcca agaacagagg aaagagacaa attaccaagc cagctcggta 2460 tagtgactat gttgcttttg ctcttcctat tatcactgat gatattccat ccaatttcga 2520 ggaagccatt gagagtgagg agaaggagag gtggtgcaat gccatgggtg atgagatgaa 2580 ttctctcttg aagaacaaga cttgggagtt agctaaattg cctaagggca agaaagctat 2640 cggttgcaaa tgggtgtatg ccaagaagga agatgctgat gagaaaagca atgtgagatt 2700 caaagcaaga ttagttgcta aagggtatgc acaaaaggag ggcattgact acaatgaaat 2760 cttttctccg gttgtgaagc actcctcaat tcgcattatg ttagctcttg ttgcacagta 2820 tgatcttgag cttgtgcaac ttgatgtgaa gacggctttc ctacatggtg atttgaatga 2880 agagatctat atgtgtcaac cggatgggta tacagtgaaa gggaaggaga atttgttttg 2940 caaattgaag aaatcacttt atggcttgaa gcaatctcca aggcaatggt atttgaggtt 3000 tgataaattt atgagaggcc aaaattattc tagaagtcaa tatgatcatt gtgtgtactt 3060 caagaagttg caagatgggt ctttcattta tttgttgata tatgttgatg atatgttgat 3120 tgcctcaaag aatgtcgaag agattgagaa attgaagaag caaatgaaga atgagtttga 3180 gatgaaggat cttggtgaag cgaagaagat ccttggcatg gagatcacta gagatagaga 3240 gaagggtttg gtcagtttga atcaaagaca ataccttgag aagttgattc ggaagtttgg 3300 agttcatgat tcaaccaaac cggttagtac ccctttggct cctcatttta aattgagttc 3360 tctacaatgt cctaaaactg ataaagagaa gctgcaaatg aaaaatatac catatgcaaa 3420 tttggttggt agtttgatgt atgcaatggt atgctctaga ccggatattg ctcatgcagt 3480 tggcatggtg agtcgatata tgcataatcc aggtaaagag cattggcaag cagctaagtg 3540 gatattgagg tatctccatg gtactcgaga tgttggttta tgctttgaga gagatgactc 3600 tggtattggt cattttgcag ttggttatgt tgattcagat tatgcaggtg atctggatgg 3660 aaggaagtct actacaggct atgtgtttac tatggctaaa gggccagttt gttggaggtc 3720 cattttgcag tcgtctgttg ccttgtctac tacagaggct gaatatatgg cagttgctga 3780 agctataaag gaggccattt ggatacatgg gctgattaga gatttggggg ttgatcagaa 3840 gcaggtggag gtacattgtg atagtcagag tgccatttat ttggctaagt atcaggttca 3900 tcatgcgagg accaagcaca tagatgtgcg ttatcacttt gttcgtgaaa ttgttggtga 3960 aggggaaatc attctccaga agattccaac taaagacaac cccgctgata tgttgactaa 4020 ggttgttggt gtagccaagt ttgttcattg cttgaacttg gctcacattt tgcctatata 4080 aagaaggcgt tgagcagtag gagttttgga gcatttggct cggcatgagt tgttctcttg 4140 ctagtgtttg ggagtgatgt tgtgtgttga ttgtgttggt tggcttatca tggcgttttt 4200 cggaacttgg ccaaggtgga gat 4223 // ID POLN2_ST repbase; DNA; EDCOT; 359 BP. XX AC AB016141; AB016141.1; GI:4126549; VERSION; XX DT 08-JUL-2003 (Rel. 8.06, Created) DT 08-JUL-2003 (Rel. 8.06, Last updated, Version 1) XX DE Solanum tuberosum LINE retrotransposon DNA, endonuclease region DE of POLN2. XX KW Non-LTR Retrotransposon; Transposable Element; POLN2_ST. XX OS Solanum tuberosum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RA Noma K., Ohtsubo E. and Ohtsubo H.; RT "Non-LTR retrotransposons (LINEs) as ubiquitous components of RT plant genomes."; RL Mol. Gen. Genet 261(1), 71-79 (1999). XX RN [2] RP 1-359 RA Noma K., Ohtsubo E. and Ohtsubo H.; RT "Direct Submission to GenBank."; RL Direct Submission to Genbank (09-JUL-1998)Kenichi Noma, The RL University of Tokyo, Institute of Molecular and Cellular RL Biosciences; Yayoi, 1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan RL (E-mail:aa77116@hongo.ecc.u-tokyo.ac.jp, Tel:81-3-5684-3269, RL Fax:81-3-5684-3269). XX DR Genbank; AB016141; Positions 1 359. XX SQ Sequence 359 BP; 113 A; 50 C; 99 G; 97 T; 0 other; ctggaatgcg agaggtctca atgaaagccc atatcatctc gtggaatgcg aggggattga 60 atgacatcaa caagtggagg gtgatcaaat ctctaattca agattggagg gctgattttt 120 actgtgttca agaaacaaca atggaaggcg aataagggga agttgtgaaa catctattta 180 gcaacaggtg ggctgattat gtgggattgg aggccaatgg aagaagtgga gggattcttt 240 atcatgtggg ataaaaagtg ctggacatgg gaattaatac agtacggtgt acattctgtt 300 tcttgtaaat taagctttac aaattaaaat tacagttggc tgatccccgg ggacttcaa 359 // ID Copia-54_VV-LTR repbase; DNA; EDCOT; 308 BP. XX AC chr4; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-54_VV_; KW Copia-54_VV-I; Copia-54_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-308 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr4; Positions 16320620 16320927. XX SQ Sequence 308 BP; 83 A; 55 C; 56 G; 114 T; 0 other; tgtaacataa tgtgcctatg ctgtgttagg ttatatatgt aaaaacaact tttttgtttt 60 tgttttgagt ggttgtcatg cttccacgtg gagagattta cacaggttaa atctctttgc 120 atctagttta aattctagac tgtacaacaa aaagtgaaga accgagaata caaagtgaaa 180 agaaacaggg tcctctgttt ttttgggact gtcttaactc ctctgttcca ggtctgttac 240 aaggtgtcac tcttccattt tttctttcta tagcctttct ttgtttcagg cttaaactgc 300 aaccaaca 308 // ID COP20_LTR_MT repbase; DNA; EDCOT; 357 BP. XX AC . XX DT 11-JAN-2007 (Rel. 12.01, Created) DT 11-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of COP20_MT retroposon from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; COP20_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-357 RA Shankar R. and Jurka J.; RT "COP20_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 16-16 (2007). XX DR [1] (Consensus) XX SQ Sequence 357 BP; 128 A; 58 C; 54 G; 117 T; 0 other; tgttagaaat taaatcaaga aatatctaga agagtataga agcttggagt tattcttttt 60 cattaagagt taaaaatatc tatattatgt agcaccacct agaataatct tgtaaccaaa 120 agaataatct agtgctgatt gtacaccacc tctataggaa taatctagca ccatccatag 180 ctagaaaaat ctagtaaccg acattaagtt taagagccta taaaaggcac atgcttgtac 240 catattgaat catcaagtct tcgacaataa aattagtgtg tgttcaaaga aattctccat 300 tgttctctta gttattactt tgtgagtttg tgtcccactg atatcaaatt ggtatca 357 // ID Gypsy5-VV_I repbase; DNA; EDCOT; 4562 BP. XX AC AM487303; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy5-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4562 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4562 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 737-737 (2007). XX DR Genbank; AM487303; Positions 10789 6228. XX CC Positions [3454-3948] - Integrase core CC 'TCTTG' target site duplication CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 704..3130 FT /product="Gypsy5-VV_I_1p" FT /translation="MEAFTLARAYETRCEEIKQSARPWHKWSSSNAANTST FT VSSTRQHAVTAVPTGPFQTATPAPASTSTTVGHKQTLLIAPTPALPIRRLT FT PTELREKREKGLCYNCDQKYFANHRCRNKFLLLLGTDDIDEDIDDDGVATE FT PTEDLVTGDISSLNALASQGNPRSLHLVGEFGSHRFHVLIDSGSTHNFIKQ FT ALVERLGLPIQPTPKFRVYIGNEDYLICQHTCLQVALKLQGKVFLLDLFIL FT PIEGPDVVLGIQWLQQLGCAAHDYAALSMEFCWEGRPIILHGDLHQSSSLI FT TFNQFQALIHSSNVHSMFALQPLAIEELETASLVTKEPVAISTTLQKFCDL FT FLPPTALLPHRTIDHKVHLIPNSKPVNVRPYRYPHFQKNEMEKLIREMLDQ FT GIIRPSQSPFSSLVLLVKKKDGIYRFCVDYRVLNAVTIKDKFPIPTIDELL FT DELGSATIFSKLDLRAGYHQIRVHNRDVYKTAFRTHEGHYEFLVMPFGLSN FT APSTFQAIMNQLFAAFLRKFVSVFFYDILVYSTTISEHVTHLEQVLTCLHK FT GSFYVKLSKCHFCQETIEYLGHIVSTGGVRPDQQKLDAMMKWPIPRTLKHL FT RGFLDLTGYCRRFIHGYASIAALLMDLLRKDAFNWTPEVTMAFDALKSSMV FT AAPVLRLPDFNETFVIETDASNVGIGTVLMQAGHLISYFSKKLGPRLQASS FT TYLKELHAIAEAVHKWRQYLLGRFFIIRTDHKSIKELLQQVVQTPDQQIYI FT RKLLGYHFRIEYKPGSANQAADALSRVHEEELEQPTLSAPSCLSFSSHPSL FT EFLTTLR" XX SQ Sequence 4562 BP; 1122 A; 1123 C; 1002 G; 1315 T; 0 other; attggtgctt tcatcgactc ctttgatggc ggagtcggat gtgctttcag cggttaaggc 60 tttgcatgat caatttgaag ctcaatttga gagccaaacg gtgtcgtttc atcgaatact 120 ccaacaatat atgtctactg tggattcgcg attggaggag ttccgttctc agtttcgtgg 180 atcgtcgaga tcgtctatgg gtcttctagg tcctccaccg gccccaccgc ctgttactga 240 gatgggtgtt ggaggtaatg agttagccat tgccttacgt tttatgaaaa tggagattcc 300 aaagtttaac agaactgatc cacacgggtg ggtatttcgc gttgaggaat ttttttattt 360 tcatggaaca cctgagccgc tctggttgcg gattgtctcc ttccatatgg aaggtccgac 420 aacaggttgg tatcaatgga tgaaggccaa taatctgttg tcttcgtgga aggcattttt 480 actcagtctg aagcaccgtt tcgaagcttc cctctatgaa gaccatcaag gtaatctctc 540 taagctcact cagacttcga ctgtggagga atttcagtcg gccttcgagg acctaatgaa 600 taaagtcacg agaatttctg agccgttgtt gattagtttt ttcattatca gcttgaaata 660 ggatattcgt tgtgagctac ttttctcacg gtcgtccacg ttgatggagg cttttacctt 720 agctcgagcc tatgaaactc gctgtgagga gatcaagcag agcgctcgcc cttggcataa 780 gtggtcctct tccaatgctg ccaacacgtc cacggtgagt tccactagac agcatgctgt 840 aacggccgtt ccgacgggcc cgtttcagac agccacccct gctccggcct caacatcgac 900 aacggtcggg cataagcaaa cactactcat agctccgacc cctgctttac ctattcgtcg 960 cctcacccct actgagttac gagaaaaacg tgaaaaggga ttatgctata attgtgacca 1020 aaaatatttt gctaatcatc gttgtcgcaa caaatttttg cttcttttag gaacggatga 1080 tattgatgag gatatagatg atgatggcgt ggcgaccgaa ccgaccgagg acttggtcac 1140 aggcgacatt tccagcctca atgccttggc aagccaaggt aatcctcgct ccctgcattt 1200 agttggtgag tttgggtctc atcgcttcca tgtgctcatc gatagtggta gtactcacaa 1260 ttttattaaa caggctctgg tggagcgttt gggcctccct attcagccaa cacctaaatt 1320 tcgagtttac attggcaatg aagattattt aatttgccag cacacttgcc tccaagttgc 1380 tttgaagttg caagggaagg tgtttctctt agatcttttt atcctgccaa ttgaaggacc 1440 tgacgtcgtt cttggtattc aatggttgca acaattgggt tgtgctgccc atgattatgc 1500 agccctgtca atggagtttt gttgggaagg gcgtccgatc attctccatg gggatttgca 1560 ccagtcctct agcttgatta cttttaatca atttcaggca ctgatccata gttcaaatgt 1620 ccacagcatg tttgccttgc agccactagc gatagaagag ttggaaactg cctctttggt 1680 taccaaagag cccgtggcta tctctactac tttgcaaaaa ttttgtgacc tgttccttcc 1740 gccaacagcc cttctcccgc accgcaccat tgaccacaag gtccatctca ttcctaattc 1800 aaagccagtg aatgttcgtc cttatcgata tccacacttc caaaaaaatg aaatggaaaa 1860 attaattcga gagatgcttg atcaaggtat aattcggcca agtcaaagtc ctttctcctc 1920 tctggtgtta ttggttaaaa aaaaggacgg tatctatcgc ttttgtgtcg attaccgcgt 1980 tctcaatgca gtaacgatca aagataaatt cccgattcca accattgacg agcttttgga 2040 cgaactagga agcgctacta tttttagcaa actggacctc cgggctggtt accaccaaat 2100 cagggtacat aatagggacg tctataaaac agcgtttcgg actcatgagg gccactacga 2160 atttcttgtc atgccttttg ggctgtcgaa tgccccatcc acttttcaag ccataatgaa 2220 ccaattgttt gctgcattct tgcgcaagtt tgtaagcgtt tttttttacg atattctagt 2280 ttacagcact actatttctg agcatgttac tcatctggag caggttttga cttgccttca 2340 caagggtagt ttttacgtca agctctccaa atgccacttt tgccaggaga caattgagta 2400 tctgggacac atagtttcta ctggcggagt acgtcccgat cagcaaaaac tcgatgccat 2460 gatgaagtgg cccatacccc gcaccttgaa gcacctccga ggtttcctcg accttactgg 2520 ctattgtcga cggttcattc acggttatgc ttcaatcgcg gctctgctca tggatttgtt 2580 acgcaaagac gcttttaatt ggactccgga ggttaccatg gcttttgatg ccctgaaaag 2640 ttcaatggtt gcagcgccag ttttacggtt gccagatttc aatgagacct ttgtgatcga 2700 aactgacgcg tctaatgtgg gaataggcac tgttctcatg caagcaggtc acttaatctc 2760 ttatttcagc aagaaattgg gtccgcgcct acaagcttca tcaacatacc tcaaggaact 2820 tcatgccatt gctgaggcag tacacaaatg gcgccaatac ctattgggca ggtttttcat 2880 tatccgaacg gatcacaaaa gcatcaaaga attattgcag caggtggtac aaactccaga 2940 tcaacaaatt tatatccgga agttgttggg ctatcatttt cggatcgaat ataagccggg 3000 gagtgctaat caagctgcgg acgctttgtc tcgggtccat gaagaggaat tggaacagcc 3060 tacgctatcc gcgccttcat gtctgtcgtt ctcgagccac ccctccttag agtttttgac 3120 cacccttcgt taggaaaact ctacactcct ggacttagtc tcccttcatc aacagttcac 3180 gatgggttcc ctctcttcgg actactccct tcatgatggc ttgttgttct tcaagcatag 3240 atactacatc agccccaact cttccttaaa ggccctactg ttgcacgagt ttcatgctac 3300 cccattcgcg agtcatggtg gagtaaaacg tacttggttc gcttggctac tcttttttat 3360 tggccacgca tgcgggcaga tgtggaacaa tatgtttcag catgcttagt ttgtcaacag 3420 acgaagtatt caacccaagc accagctgga ctcctccagc cactcccagt tccttcgttg 3480 gtatgggacg aagtcaccat ggacttcatt accaacctac ccccttcccg caattttaca 3540 attatcatgg tggtggttga ccgtctcacc aagtcagcgc atttcgaggc tttgccaact 3600 cagttcacag ccgccaaatc agcagaagtt tttgtgacaa ttgtggtcaa gattcatggg 3660 tttccgagtt cgatcatatc cgatcgcgac ctcgtcttca tgagtaaatt ttggcagaca 3720 ctctttcaac ttagcgggac atccttgcgc catagtacgg cttaccaccc acaaacggac 3780 gggcagtctg aagtcgtcaa tcgaggacta gagcagtact tacgtgcatt catgaatgag 3840 aagccacact cgtggatctc ttttctcgga tgggctgaat tttgttataa ttccagttat 3900 catagtggac taaaaatgac tccttttcag gccttattcg gacgtccccc tccgatcatt 3960 ccggcttata cctagggctc tacttcaatc caagccctcg atgaggcact tgtggagcac 4020 gatgccttgc ttcgtacctt gaaggagaat ctacgtcaag ctcaacaccg gatgacgcaa 4080 aaggccaatg cacatcggca cgacctgcag cttgaagtag gagatatggt tcttgttcgc 4140 ttacaaccgt atcagcaaac taccgtagct catcgtccct accaaaaatt ggccaaacgg 4200 tattatggac cgtaccaagt gcttgagcgg attggggccg tcgcttatca tttagcatta 4260 cccagtggct gcaagatcca tcccatgttt cacatatcta cccttaagcc ttttcgagga 4320 cccgttcctg aagaagtcta tccactccta accgaaacta tgggcatcca tcctttatta 4380 ataccaacgg ctatttgtgc tgttcgaacg attctccgac agggaaaaga agtccaacaa 4440 attctggtgc agtggaccgc cagtgaccct gagaacgcaa tctgggaaga ttttttcgca 4500 ttctgcaaac tttaccctga ttaccacctt gaggacaagg tcgattttca tggagtgggg 4560 aa 4562 // ID Copia31-PTR_LTR repbase; DNA; EDCOT; 255 BP. XX AC LG_II; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia31-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-255 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-255 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 239-239 (2007). XX DR Genome; LG_II; Positions 8202285 8202031. XX SQ Sequence 255 BP; 73 A; 41 C; 45 G; 96 T; 0 other; tgggactgag tcagttaata atatcctagc ttataggatt acaagattaa gtttgattta 60 ttctttgctt attaaccacg tctgtaggag tgtcagacgg gggttgctta tttccctgat 120 ttctgttgta atggtttgtt atataaacca actttctatt caataaagct gtggtctttg 180 actcttcatt tgaactatca aactgattgc ttagatttaa caagactaac cactagatta 240 attatcaagg ctaca 255 // ID LINE1D_MT repbase; DNA; EDCOT; 4205 BP. XX AC AC153004; XX DT 23-MAY-2006 (Rel. 11.05, Created) DT 26-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE L1-class element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; LINE1D_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4205 RA Jurka J.; RT "LINE1D_MT: L1-type element from barrel medic."; RL Repbase Reports 6(5), 249-249 (2006). XX DR EMBL/GenBank/DDBJ; AC153004; Positions 1 4205. XX CC This is a recently retroposed element. 5'-end not determined. XX FH Key Location/Qualifiers FT CDS 61..4143 FT /product="LINE1D_MT_1p" FT /translation="MEALFDTTFLSWNIRGALSNNSRRHLKDLIRKHQPTF FT ITILETHVSFAKLSVFWSNMGYTPVHIIEANGHSGGIWLFQHSASNTTTTV FT LDSNQFSITIKISRGNVTTSCTCIYASSNHAQRPNLWNYLMSIGQAMDVPW FT MLIGDFNETLLPSEQRGGIFHHNRAAFFSNLMNNCNLLDLTTTGGHFTWHR FT NNNGIRTLSKKLDRCIASVGWRVSFPEAFVEVLCRLHSDHNPLLLRFGGLP FT LARGPRPFRFEAAWIDHKDYAALVKNSWIPQNNNITDCLATIQEKSINFNH FT EVFGNIFKRKKHVESRLKGVQNYLERVDSYRHTLLEKELQQEYNHILFQEE FT MLWYQKSREQWVKFGDKNSSLFHAQTIIRRKRNRIHRLQLPNGIWSSDSTI FT LQEEAQKYFKNFFGGHQSPTATIFHEAAPTTIADIEKNSLTKPITKNEVFV FT ALNSMKPYKAPGSDGFHCIFFKQYWHIVGDDIFHMVHTAFHTGHFDPEISN FT TLIALIPKIDPPTTFKDFRPISLCNIIYKIIPKVLVHRLRPILSNLIGPCQ FT SSFLPGRGTSDNSIVLQEIIHFMRKSKRKKGYVAFKLDLEKAFDNVRWDFL FT NSCLQEFGFPDITIKLIMHCVTSSTFSILWNGNKMPPFKPTHGLRQGDPLS FT PYLFILCMEKLSLAINNAVSQGSWEPIHITNGGPQISHLLFADDVLLFTKA FT KNSQFHFINDLFNRFSRASGLNINISKSRAFYSSGTPQAKINNLTSISGIR FT STTSLGKYLGFPMLKGRPKRSDFQFIIEKMQTRLASWKNRLLNRTCRLTLA FT TSVLSSIPYYYMQINWLPQNICDSIDQTTRNFIWRGSSNKGIHLVSWKKIT FT TPKRYGGLSIRTARNANTCLLGKLVWDMVQSTNKLWVKLLSAKYTTGPNVF FT QAKASGNNSPSWTAIIRAKDILKQGYSWRPGSGSSSFWFSNWCPHGLLGSS FT VPIIDIHDIHLTVKDVISSNGQHTESLYTALPHSIAEAVNNYRATFNPTVE FT DVFIWNHNKNGVYSTKSGYSWLLSMESPNIISNGNSWSWIWTLQVPEKYKF FT LIWLAMHDVVPTLYVLHHRNMAATATCSRCGEDDESFMHCIRDCKFSKPIW FT QKLNFSDSHFFSISCAKDWIKSNVDSSRSIFFLASLWWIWLHRNNMCFNNE FT VWSLTRLSISIHNSTETIIKSFQSAAITAGTDRWISWNSRNYNCHILNVDG FT SCLGTPIRAGYGGLICNSAGFFLKGFSGHIQASTCILQAELTAILEGFRMA FT VNMGIEELVCFSDSQLSVNLVSGEVSRFHAYAVIIQDIKDIIASNHFEIFH FT TLREGNHCADFLAKLGASSNAAITEHQTPPLDLMDKLRMDAMGTYFLRA" XX SQ Sequence 4205 BP; 1211 A; 1010 C; 768 G; 1216 T; 0 other; ggaggaggac atggtaactt agtcccttcc actcttgatc tatcaatctt tctatttatc 60 atggaagctc tttttgatac tacattcctc tcttggaaca taagaggggc actcagtaat 120 aattcaagaa gacacttgaa agatttgata agaaagcatc aaccaacatt cataaccatc 180 cttgaaacac atgtctcttt tgctaaactt tcagtttttt ggtctaatat gggctacaca 240 cctgtacaca tcatagaagc taacggtcat tctggaggaa tttggctctt tcaacattct 300 gcaagcaaca ccaccaccac cgtccttgac tctaaccaat tctccataac aataaaaatt 360 agccgtggta atgtgaccac ttcctgcact tgtatctatg ctagctctaa ccatgcccaa 420 cgtcccaacc tttggaacta cctcatgtcc atcggccaag ctatggatgt cccctggatg 480 ctcataggag actttaatga aactcttctc cctagcgaac aaagaggtgg aatttttcat 540 cataatagag ctgcattttt ctctaatctt atgaataatt gcaacctact cgacctcaca 600 acaacgggtg gtcatttcac ttggcatcgt aacaacaacg gcattcgcac cctctccaaa 660 aaacttgaca gatgcatagc aagtgtgggc tggcgggttt ccttccctga agcctttgtc 720 gaggttctct gcagactcca ctccgaccat aaccctctcc tcctccgctt tggtggactc 780 ccgttagctc gagggcctag gcctttccgc tttgaggcag cttggataga tcacaaagat 840 tatgcggcac tggttaaaaa ttcttggatc cctcagaaca acaacattac tgattgctta 900 gcaacaattc aggagaaatc catcaatttt aatcatgaag tctttggcaa cattttcaaa 960 aggaagaaac atgtagaaag taggctcaag ggggttcaaa actatctaga aagagttgac 1020 tcatatcgac acactctcct tgaaaaagaa ttgcagcaag aatacaatca catcctattc 1080 caagaagaaa tgctatggta ccaaaaatcc agagaacaat gggttaaatt tggcgacaaa 1140 aatagctcac tttttcatgc tcaaactatc ataagaagaa agagaaatag aatccatcga 1200 cttcagctcc ctaatggcat ttggtcttct gatagcacca tcctccaaga agaagctcaa 1260 aaatacttca aaaatttctt tggtggccac caatcaccaa ccgccaccat cttccatgaa 1320 gccgctccta caaccattgc cgacattgaa aagaattctc tcaccaagcc tatcaccaaa 1380 aatgaagttt ttgtcgccct caactccatg aaaccataca aagcccctgg ctcggatgga 1440 ttccattgta tctttttcaa acaatattgg catatagttg gagatgacat cttccatatg 1500 gtccatacag ccttccacac aggtcacttt gatccggaga tttcaaacac tctcattgca 1560 ctcattccga aaatcgaccc ccccaccact ttcaaagatt ttagacccat cagtctatgc 1620 aacataatct acaagattat ccctaaagtt cttgtgcatc gtctcagacc tatcctcagt 1680 aatcttattg gcccttgcca aagcagcttt ctgcctggta ggggaacttc tgataactca 1740 attgttttgc aggaaattat tcacttcatg aggaaatcaa agaggaagaa aggttatgtt 1800 gctttcaagc tagacttgga gaaagctttc gataatgtca gatgggattt ccttaattct 1860 tgccttcagg aatttggttt tccagacatc accatcaagc tcatcatgca ttgtgtcacc 1920 tcctccacat tctccatatt atggaatggt aacaaaatgc cccctttcaa gcccacacat 1980 ggtctcagac aaggtgaccc gctctctcct tatcttttca tactatgcat ggaaaagctt 2040 tcccttgcta ttaataacgc tgtgagtcaa ggaagttggg aacctataca cataactaat 2100 ggaggacccc agatttctca cctactcttt gcagatgatg tgcttctctt cactaaggca 2160 aaaaattctc aatttcattt catcaatgat ttgtttaata gatttagcag ggcatcaggt 2220 ttgaacatta atatttccaa gtctagagca ttctattctt cagggacacc gcaagcgaag 2280 atcaacaatc tcacttccat ttctggcatt cgaagcacaa cttcccttgg caagtaccta 2340 ggtttcccca tgcttaaggg ccgccccaaa agaagtgatt ttcaattcat aattgaaaaa 2400 atgcaaactc ggttggcttc ttggaaaaat cgtcttctta acagaacatg tagactcact 2460 ctagcgactt ctgtgctatc ttccataccc tactactaca tgcaaattaa ttggctccca 2520 caaaacattt gtgactccat tgaccaaaca actcgcaatt ttatatggcg tggttcaagt 2580 aataagggaa ttcatttggt aagttggaag aaaattacca ctccaaaacg gtatggtggt 2640 ttgagtatta gaacagctcg aaacgctaat acttgccttc ttggaaagtt agtttgggat 2700 atggtccaat ctacaaacaa gttatgggtg aagcttcttt ctgctaaata tacaacaggg 2760 cctaacgtct ttcaagcgaa agcttccggc aacaattcac cttcatggac agctatcatt 2820 cgtgcaaaag acattctcaa acaaggttat tcttggaggc cgggctccgg ttcctcctcg 2880 ttttggttta gcaattggtg tccccatggt ctccttggtt cctcggtccc cattattgat 2940 attcatgaca ttcaccttac ggttaaggat gtgataagct ccaatggtca acacaccgaa 3000 tcactctaca ccgcccttcc tcactcaata gctgaagccg ttaataacta tcgagctacc 3060 ttcaatccaa ccgttgaaga tgtcttcatt tggaatcaca acaagaacgg tgtttactct 3120 acaaaaagtg gttactcttg gcttctctcc atggaatcac caaacattat cagcaacggt 3180 aattcttggt cttggatttg gacattgcag gtaccggaga agtataaatt tttgatttgg 3240 ctggctatgc atgacgtggt gcctacactt tatgtgctgc atcatagaaa catggctgcg 3300 accgcaacct gtagtagatg cggagaagat gacgaatcct ttatgcactg tattagggac 3360 tgtaaatttt cgaaacccat ctggcagaag cttaatttct cggactcaca cttcttctcc 3420 atcagctgcg caaaagactg gataaaaagc aatgttgaca gcagccgctc aatctttttt 3480 ctggcctctc tgtggtggat ttggctgcac cgcaacaaca tgtgtttcaa caacgaggtc 3540 tggtctctca cgcggttgag cattagcatc cataactcaa cagaaacaat cataaagagc 3600 tttcagtccg cggccattac tgctggcact gatcgctgga tttcttggaa cagcagaaat 3660 tacaattgcc acatcctcaa tgtagatggc agctgtcttg gcactccaat acgtgccggc 3720 tatggaggtt taatctgcaa cagcgcgggg ttttttctaa aggggttttc cggtcatatt 3780 caggcatcaa catgtattct ccaagctgaa ctgaccgcaa ttcttgaagg ttttcgcatg 3840 gcggtgaaca tgggaattga ggagttagtc tgcttctcag attctcaact ctcagttaat 3900 cttgtttcag gagaagtctc tagattccat gcctacgcgg tgataatcca agatatcaag 3960 gatatcattg cttcaaacca ctttgaaatc tttcacactc ttagagaagg aaaccactgc 4020 gcagattttt tagccaagct tggagcctcg tcaaatgcag ccattacgga gcaccaaacc 4080 cctcctcttg atctcatgga caagcttaga atggatgcta tgggaaccta tttcctaaga 4140 gcttaatttt tcctttttct tttcttttct gttttttttg ttagctttgt aacaaaaaaa 4200 aaaaa 4205 // ID Copia-44_VV-LTR repbase; DNA; EDCOT; 662 BP. XX AC chr11; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-44_VV_; KW Copia-44_VV-I; Copia-44_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-662 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr11; Positions 12489659 12490320. XX SQ Sequence 662 BP; 218 A; 74 C; 114 G; 256 T; 0 other; tgttatattt atatatatat atatatatat atatatatat atatatatat attgttggtt 60 aaaaaataaa gtgtaagaag agttacactt ttgagaaaat aacttttgaa aataaagtgt 120 aagaagggtt acacttttaa tgtgtgaatt aaacacatga ttaagttttg aaatgttaca 180 aaacttgaaa ggttgaggaa gacaatgagt cttctcatct ttgtaacttt ataaacttga 240 gaggttaagt gtaagagagt tacacatttg agattaaatc atgtttaatg tgtgaattaa 300 acatatgatt taatttttga atgttacaaa gatgaagaga ttgaggaaga caatggtttt 360 tctcatcctt gtaacctttt ttcaacccta agagtgctat acatgacttt tcttcttttt 420 gaaatcttat gcagaaaagt gaaaaggctt gatcaatccc aagactattt ccatttagtt 480 tccaaaagat ttctagaggt gggaggaaat agagtctttg gacaaagttc caagaacttg 540 tttgagcctt tcttgtgttc ttcttcttct tgttcttatt ttgtatcttt gagagtttta 600 ttgtatcaaa gtgagtgtgt gagagtgttt cttttctcca ttgtatccaa attttctcaa 660 ca 662 // ID Copia16-PTR_I repbase; DNA; EDCOT; 4325 BP. XX AC LG_XVI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia16-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4325 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4325 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 204-204 (2007). XX DR Genome; LG_XVI; Positions 11662024 11657700. XX CC Positions [1767-2093] - Integrase core CC LTRs are 92% similar to each other. XX FH Key Location/Qualifiers FT CDS 148..1806 FT /product="Copia16-PTR_I_1p" FT /translation="MSEGNFVQPSIPKFNGHYDHWSMLMENFFRSKEYWSL FT IEQGVPTTVEGAPLTETQMKVIQDQKLKDLKAKNYLFQAIDRSLLETILKK FT DSAKDIWDSLKQKYQGTARVKRAQLQALRKEWEILQMKVGESVNDYFARTL FT TIANKKRIHGEQMNDVVVIEKILRSMTPKFDYVVCAIEESNNVEVMSIDEL FT QSSLLVHEQRMNYHTVAEEHALKITYEANFEGRGRGRGVYRGRGRGRHRPS FT FDKSTVECYNCHDLGHFQYECPKKGLRANFADTSEEMLLMAYIEEQQISTA FT EVWFLDSGCSNHMCGKKELFSDLDETFRETVKLGNNSCMTVMGKGNIRIRV FT NENTQVFTGVFYVPELKSNLLSIGQLQEKGLAILIKNGKCKVYHPNRGLII FT EIKMSSNRMFVLLDQRPSEEQICYSSLTDDSAGIWHRRYGHLSYDGLKTLQ FT QKNMVQGLPHIKPPVILCEECMLGKQARDPFPKSSTWRATRILQLVHSDIC FT GPIKPISNSNKRYFISFIDDFSRKVWVYFLTEKSEAFYTFKRFKNLVEKET FT GVYLSG" FT CDS 1944..3578 FT /product="Copia16-PTR_I_2p" FT /translation="MNMVRSMLNEKKFPKNFWPEAVNWSVHLLNRSPTLAV FT KNVTPEEAWSHIKPSVSYFRIFGCTAYVHIPDAKRTKLDNKNLKCVFLGVS FT GEAKAYRLFDPLSKTIIISRDVKFEEDGHWDWDHGYAEAVMADLDWDDVHV FT HALDSHGDNAILESDSDVAATSTHPINTHEGVEVAVADEATAEESVPESRV FT NTGRSDAGKSVHGGVHAESSVNVGRRVHDGVHAETILPTAIESNTEEGRVR FT RPPRWMQDYIGSEQLSDTDDFAFFALYADNDPLSYTEAVKSDIWQRAMEAE FT LNAIERNDTWELTMLPAGGKVVGVKWIFKTKLNENGEVDKHKARLVAKGYT FT QQHGIDYAEVFAPVARLDTIRLVISIAAQKGWVIYQLDVKSAFLHGELNEE FT VYVAQPPGYEKKGKEQMVYKLEKALYGLKQAPRAWYSRIESYFADQGFKKC FT PYEHTLFIKTGDGGNILIVCLYVDDLIFTGNDVNMFDEFKQSMMNEFDMTD FT LGRMKYFLGIEVLQSSNGIFVGQKKYAQSILRNLRWMAAILLTFRLFLV" XX SQ Sequence 4325 BP; 1401 A; 728 C; 1044 G; 1152 T; 0 other; tttggtatca gagcctttca atttgtgtca cagggtgtgc agttgaaatt gtgagaagca 60 gcagctatct acacgagagt tagagagaaa ccaaagaatt agagaaaaaa cgagagacag 120 agagaaacac gagaaacaga gagaaaaatg tcagaaggga attttgtgca gccatcaatt 180 ccaaaattta atgggcatta tgatcattgg tccatgctta tggaaaattt ctttcgctcg 240 aaagaatatt ggtctttaat cgaacaagga gtgcctacaa cagtagaagg agcacctctc 300 acagagaccc aaatgaaggt gattcaagat cagaaattga aggatctaaa agctaagaac 360 tatttgttcc aagcaataga tcgatccctc ctggaaacga ttctcaagaa agactcagca 420 aaggatatat gggactcatt gaaacaaaaa taccaaggca cggctagggt caaacgtgcc 480 cagttacaag cacttcgaaa ggaatgggag attctgcaga tgaaggtggg tgaatccgtg 540 aatgattatt ttgctcggac tttgacgata gcaaataaga aacgaattca tggtgaacag 600 atgaatgatg ttgttgtcat tgaaaagatt ttacgatcaa tgacaccaaa atttgattat 660 gtagtctgtg ctattgagga atcaaataat gtggaagtca tgtccataga tgaattacaa 720 agtagcctcc tggtgcatga gcaacgtatg aattatcata cggttgcaga agaacacgcc 780 ttgaagataa cttatgaagc aaactttgaa ggaagaggac ggggacgtgg agtttacaga 840 ggaagaggaa gaggacgtca caggccaagc tttgataagt ccactgtgga atgctacaat 900 tgccatgatc ttgggcattt tcagtatgaa tgtccaaaga aaggactaag agcaaacttt 960 gctgacacaa gtgaagaaat gctgttgatg gcctatatcg aagagcaaca aatcagtact 1020 gccgaagttt ggtttttgga ctcaggatgc agcaaccata tgtgcgggaa gaaggaactt 1080 ttttctgatc ttgatgagac tttcagagag acggtaaaac tggggaacaa ctcttgcatg 1140 acagtaatgg ggaaaggcaa catacggatc agagtcaacg aaaatactca ggtattcact 1200 ggtgtttttt atgtaccgga gctaaagagt aatttgctga gtatagggca gcttcaagag 1260 aaggggcttg caattctaat caaaaatgga aaatgcaagg tttatcatcc taatcgaggg 1320 ctgattattg aaattaaaat gtcctcaaat agaatgtttg ttctacttga tcaacgtcca 1380 tccgaagagc agatttgcta tagctctttg acagatgact cagctggaat ttggcaccgt 1440 cgatatggtc acttaagcta tgatggattg aagactcttc aacagaaaaa catggtgcag 1500 ggactgccac atatcaagcc tcctgtgata ctgtgtgaag aatgcatgct tggaaagcaa 1560 gcgagagatc ctttcccgaa gagcagtact tggagagcca cccgaattct tcaactggtg 1620 cattcggaca tatgtggacc tatcaaacct atttcaaaca gcaacaagag gtatttcatc 1680 agtttcatag atgattttag ccgtaaagtc tgggtctatt ttttgacaga aaaatcggaa 1740 gctttttata cctttaaaag gtttaaaaat cttgtggaaa aggagacagg ggtgtatttg 1800 agtggctaag gactgatcgt ggaggtgaat tcacgtcaaa tgaattcaac aatttttgca 1860 atgaacatgg catacgacga caacttacgg cagcatacac acctcaacaa aacggtgtgg 1920 cggaaaggaa aaatagaacc attatgaata tggttcgtag tatgttgaat gagaagaaat 1980 ttcccaagaa tttctggcca gaagctgtaa attggtctgt tcatttacta aatcgaagtc 2040 ccacactagc tgtcaaaaat gtaacccccg aagaggcttg gagtcacatt aagccttcgg 2100 tatcctactt taggattttc gggtgcacag cctatgtcca tattcctgat gcgaaaagaa 2160 ccaagttaga taacaaaaac ttgaaatgtg tctttcttgg tgttagtggg gaagcaaagg 2220 catatagact atttgatcca ctgtccaaaa ctattatcat cagtagggat gtaaagtttg 2280 aagaagatgg ccactgggat tgggatcacg gctatgcaga ggctgttatg gctgatttag 2340 actgggatga tgttcatgtt catgcacttg acagtcacgg agacaatgca attcttgaaa 2400 gtgacagtga tgtagctgcc actagtactc atccaatcaa cacgcatgaa ggtgttgaag 2460 tcgctgttgc tgatgaagct actgctgaag aatcagtacc tgaatcacgt gtaaatacag 2520 ggagaagtga tgctgggaaa agtgtgcatg gtggtgtgca tgccgaatca agtgtgaatg 2580 ttgggagacg tgtgcatgat ggtgtgcatg cagaaaccat cttgcccact gccatagaat 2640 ccaacacaga agagggaaga gtgcgaagac caccacgctg gatgcaagat tacattggta 2700 gtgaacaact atctgataca gatgactttg cattttttgc tttgtatgca gataatgatc 2760 cattaagcta cacagaagca gtgaagagtg acatatggca aagagctatg gaagcagaat 2820 tgaatgctat tgaaaggaat gacacatggg agctcaccat gctgcctgca ggaggaaaag 2880 tagtgggagt taaatggatt ttcaagacaa aattgaatga gaacggtgag gtggataaac 2940 acaaagctcg tctagtagca aagggatata cgcaacaaca tggaatagac tatgctgaag 3000 tctttgcacc ggtagctcgg ttggatacca ttcgattagt catctcaatt gcagctcaaa 3060 agggatgggt tatctatcaa ttggacgtga aatcggcttt cttgcatggg gagttaaatg 3120 aagaagttta tgttgctcag cctcctggat atgagaagaa aggaaaagag caaatggtat 3180 acaagctaga gaaagcactg tatggactca aacaggcccc tcgcgcctgg tatagccgaa 3240 tcgaatcata ctttgctgat caaggcttca agaaatgtcc ttatgaacat acattgttta 3300 taaaaacagg agatggaggt aatatcttga tcgtatgcct ttatgttgac gatttaatat 3360 tcaccggtaa tgatgtgaat atgtttgatg agtttaagca atccatgatg aatgaatttg 3420 atatgactga tttggggagg atgaaatact ttctgggtat tgaagttttg caaagttcaa 3480 atggaatatt tgttgggcaa aagaaatatg cacaatcaat tttgagaaat ttaagatgga 3540 tggctgcaat tctgttaaca ttccgattgt tcctggtatg aagctttgca aggatcatgg 3600 tggatcaaga atagacagca cactatacaa acaaattgtg ggtagtctaa tgtatttgac 3660 ctccactaga cccgatatga tgtttgttgt aagtcttctc agcaggtaca tggaaagccc 3720 cactgaactt catttaatgg ctgcaaaaag ggttttcagg tatctaaagg ggacagtcag 3780 ttatgggata ttctataaga gaggaggact tgaagggctt aatgtgtatt ctgatagtga 3840 ctacgctggc gatattgaag atcggaaaag cacgtcaggt tatgtcttca tgttaaactc 3900 aggagttgtc tcatggtctt caaagaaaca acccatagtg acattgtcca ccacggaagc 3960 tgagtttata gcagtaacat cttgtgcttg tcaggcaata tggctccgga gaattttgca 4020 gcagctggga cataatcaag aaggtcctac gacaattctt tgtgacaata gctctgccat 4080 caagctttgc aaaaattcag tcttacatgg acgtagtaag catattgatg ttcggtttca 4140 ttttattcga gagcttacta gcatgggtat catagaagta acacactgtc caactcaaag 4200 tcaagttgcg gatataatga ccaaaccatt gaagactgat gcctttgtaa aattacgggg 4260 tctgatggga gtttgttctg tgtcaagtgt aaactgatgc acttggcatt cagtttaaaa 4320 gagga 4325 // ID Gypsy-24_VV-LTR repbase; DNA; EDCOT; 340 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-24_VV_; KW Gypsy-24_VV-I; Gypsy-24_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-340 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 13164545 13164206. XX SQ Sequence 340 BP; 90 A; 53 C; 78 G; 119 T; 0 other; tgatgagagt caagttggca caagaagttc cagaccaagg cgggaaaggc atccaaatcc 60 aaaatatact gcataggctt cggttgaaga agtcaataac tttattgatt aattgttgtt 120 tttattttcg ttccagtcgt ggctaaaata atgggagagt gggtcttcct tgattgtagg 180 ggttgtttcc tcttatttct gctatttgtt attcatgttg gttaggacct tcttgtattt 240 aaagaggctg aagcctgagt aataagggga gaatattttt cctgtcactt tcatacttgt 300 ttctacgata aaactttgag gctttgactg ggaccaatca 340 // ID HAT-N1_Mad repbase; DNA; EDCOT; 813 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-N1_Mad. XX NM HAT-N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-813 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1627-1627 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~95% identical to the consensus. TSD is 8-bp long. TIR is not CC obvious. XX SQ Sequence 813 BP; 201 A; 148 C; 207 G; 257 T; 0 other; caaggacgga tccacatagg gacctgggag gtcccaggac ccgtcggcga tcctaaatcg 60 ctgctagaaa ttttccgggg acccctcgta ctcgagcatg aggtctgtgc aggttgtagg 120 ttgttgcagg ttgcagtggc tgtcttcttc tcggagaaga tgaccgcgca cggagaagaa 180 agaaaatagg gacccttcca gcctctctcc tccttgcttc tgccatggtc tcatccatcg 240 gtgccaccca cttctcctcc aacctttctc tgtcgtctgg cggggcagta cataagccca 300 aatttcccca aattatttca accaccttag taatttttct tatgggtgaa atttcctaca 360 taaggttagt aagatggata tgatctgtca tgggttggtg aaatttgggg gtggagctgc 420 catggcttcg ggagaatggg gagggaggcg gttggtggag gtatggcagc tgtgttctta 480 gtgagagaga aagtggatgt ttggaaacta gtaaaagaga aaaatggtgt gtttggttag 540 aaagatagtg ggagtttggg gagagtttta tttgaccggt gttttaaatt tagtggtcca 600 tattagataa tcaataactt aggtactccc tagtaactta tgaaacctcg taatggacgc 660 ttgaattatg attttataat ttgtaatatt gttttgcata tgatttttga atgaaatgta 720 ttatatttaa attttcaatg ttgtttttgt ctataaattt tttgaccttt attattggga 780 ccccccgagt ttaaaatcct ggatccgcca ctg 813 // ID Copia-85_Mad-I repbase; DNA; EDCOT; 4318 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-85_Mad_; KW Copia-85_Mad-LTR; Copia-85_Mad-I. XX NM Copia-85_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4318 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1708-1708 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1774-2274] - Integrase core CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS 343..2820 FT /product="Copia-85_Mad-I_1p" FT /translation="MAAIFMKDAKALGIIQSAVSDQIFPRIANADSAKMAW FT DLLYGEYHGGDQVRSVKLQNLRREFEYARMRDDESLTGYLTRLNDLINQMK FT TFGETLSNERLVQKVLISLTKIYDPICLVIENTKCLESVELQEVLAILKSQ FT EQRFDLHSSDATERAFSSLTVSSKGQNRSYAQSSTFKPQRNWNQKGKKWDS FT KPKFQQKSFANVAQNSTSSQVMGQESVKPQCKVCSKFHYGECRYKGKSKCY FT NCDRFGHWARECTVGKSVQKANCASQMEVTGNLFYANCAVAETKVNGDWYI FT DSGCSNHMTGNVDLLVDVNTNVAGKVQMPTGVLVNVAGMGSLEIETNRGRK FT YIREVMYLPGLKENLLSVGQMDEHGYYLVFGGSMCTVFDGPSLECQIISVK FT MKGNRCYPLSLRPEKQLVLKTSFAHCSRTWHRRLGHLNFGGIKQLKDKDMV FT HGLPYLEEYDRVCEGCQYGKQHRESFPSGQAQRAGAPLELVHVDLCGPMRN FT ESTGGNKYFMLLVDDATRMIWVYFLRYKSEAFSCFKKFKAMTELQTGLRVK FT CLRSDRGGEFLSTEFNQFCDTEGIQRQLSLAYTPQQNGVVERKNRTVVEMA FT KSMLHDKGMPYYMWAEAVHTAVYILNRCPTKSLDNITPFEAYSGRKPGIAH FT LKVFGSVCYVHTPSELRHKLEAKSIKGVFVGYAKCEKGYRVFDPISKRLIL FT SRDVVFDEDSSWDWQGSTEKHVSMPNYEWQSVETPRSEFTEDETQVSNTLS FT PGSLRETASGTDDAQITPQAQSSESSSRSCEGARDSQAFDHTPLKWRKLDD FT VLAQCNLCIMEPEKYEDALRMSLG" FT CDS 2820..4316 FT /product="Copia-85_Mad-I_2p" FT /translation="MKAMKDELSMIEKNATWELVDRPSNKPIIGVKWVFKT FT KLNLDGTVQKNKARLVAKGYAQKPGIDYNETFAPVARLDTIRTLIALAAQK FT SWKLYQLDVKSAFLNGVLEEEVYVEQPDGFVAKGEEDRVYKLHKALYGLKQ FT APRAWYGEIDTYFSQCGFTRSLSEPTLYIKAGEEDILIVSIYVDDIIYTGS FT NNQMLEEFKEDMKRKYEMTDLGLLHHFLGMGIIQTNSSIFIHQKKYAGSLL FT DKFGLKECKSVLTPLVATEKLTTDDGSGAASEELYRSIVGSLLYLTATRPD FT IMYASSLLARFMHCPTSKHVGTAKRVLRYIKGTLDYGLEYVKGKNSMLIGF FT CDSDWGGSIEDSKSTSGYAFSFGSGVFSWASVKQNCVALSTAEAEYISASE FT ATAQAIWLRFVLEDFGEFQTEATPVHCDNTSAIAITKNPVFHQKTKHIDRR FT YHFIKDALKDGIIDLVYCPTNEQLADIFTKPLPKDRFNYLRSMLGVKSAQD FT LKG" XX SQ Sequence 4318 BP; 1356 A; 740 C; 1054 G; 1167 T; 1 other; tggcctcaga gccttgtttc gattagatct gggcgtgttt ctgtgagctc aaacatcacc 60 gtctctggac tcggtgaagt ttgccggagt ttatctgtga tctaagaact acgtgtttct 120 ggattcacac aagctcacga tggctggatc tgggagtgct gaagtgagga ccccgatctt 180 ctccggtgag aactacgagt tctggagaat caaaatggtt accattttca agtcacatgg 240 actgtggaat ctggtggaaa aagggattcc ggttcctgat tcgaagaaga agaaagctaa 300 gactgatgaa gatacagagt tgatgctgac gatgatgaga aaatggctgc aatcttcatg 360 aaagatgcaa aagctctcgg aatcattcaa agcgcagtct ccgatcagat cttccctcga 420 atcgcaaacg cagactcagc aaaaatggca tgggatctgt tatatggcga atatcacggt 480 ggggatcagg taagatctgt gaaactccag aatcttagac gagaatttga atacgctaga 540 atgcgtgatg atgaatcctt gactgggtat cttactcgtt taaatgatct gattaatcaa 600 atgaagacgt ttggtgaaac tctgtcaaat gagagattag ttcagaaggt gttaatcagt 660 ctcactaaga tatatgatcc tatatgctta gtgatagaaa acaccaaatg tttagaatct 720 gttgaactgc aagaggtact agctatattg aagagtcaag agcagaggtt tgatttgcat 780 tcctctgatg caactgagag agcattttct tctcttactg ttagttcaaa agggcagaat 840 cgaagttatg ctcagtctag tacttttaaa ccacagagaa attggaatca aaagggtaag 900 aagtgggatt caaaaccaaa gtttcagcaa aaatcattcg caaatgttgc acagaatagt 960 acttcctcac aggttatggg tcaagagagt gtaaaacctc aatgtaaagt gtgttcaaag 1020 tttcattatg gtgaatgtag gtataagggg aaatccaagt gctataactg tgatagattt 1080 gggcattggg ccagagaatg tactgttgga aagtctgttc aaaaggcaaa ctgtgcaagt 1140 caaatggaag tgacaggaaa cttattttat gcaaattgtg cagttgctga gactaaggtt 1200 aatggagatt ggtacataga tagtggctgc agtaatcata tgacagggaa tgttgatctt 1260 cttgttgatg tgaatacaaa tgttgcaggg aaagttcaaa tgccaacagg agtgttagtt 1320 aatgtggcag gaatgggatc actggaaatt gaaactaaca gagggaggaa atacatcaga 1380 gaagtcatgt acttacctgg tttgaaagag aatctactaa gtgtaggaca aatggatgag 1440 cacggatatt atcttgtgtt tggtggaagt atgtgtactg tttttgatgg tccttctctg 1500 gaatgtcaaa ttatcagtgt gaaaatgaaa ggaaacaggt gctatcctct atctctaagg 1560 cctgagaaac aacttgtgtt gaagaccagt tttgctcatt gttctcggac ttggcacaga 1620 agattaggtc acctaaactt tggtggaatc aaacaattga aggataaaga catggttcat 1680 ggtctaccat atctagaaga gtatgataga gtctgtgaag gctgtcaata tggtaaacaa 1740 cacagagaaa gctttcctag tggtcaagca caaagagcag gtgctccact cgaattggtt 1800 catgttgatc tgtgtggacc aatgagaaat gaatccactg gaggaaacaa gtactttatg 1860 ctgcttgtgg atgatgcaac aagaatgata tgggtatact ttcttagata taaatctgaa 1920 gctttctctt gtttcaagaa attcaaagca atgactgagt tgcaaactgg tttaagggtg 1980 aaatgtctga ggagtgacag aggaggggag ttcttgtcta ctgaattcaa tcagttctgt 2040 gacacagaag gcattcaaag gcaactttct cttgcataca ctccacagca aaatggagtg 2100 gtggaaagga aaaacagaac agtggttgaa atggccaagt ctatgctaca tgataaagga 2160 atgccttact atatgtgggc agaagctgtg catactgcag tctacattct gaatcgatgt 2220 cctaccaagt ctcttgacaa cataaccccc tttgaagctt acagcggaag gaaaccgggt 2280 attgctcatt tgaaggtttt tggctcagtt tgttatgttc atactccatc tgagctaagg 2340 cacaaactag aagctaagag tataaaggga gtttttgttg gatatgcaaa gtgtgagaaa 2400 gggtacagag tctttgatcc aatctctaaa aggctgatac tgtcaagaga tgttgtgttt 2460 gatgaagatt caagttggga ttggcaggga agcacagaga aacatgtgtc tatgcctaat 2520 tatgaatggc agtctgttga gacaccaaga agtgagttca cagaagatga gactcaagtc 2580 tcaaatactt tgtcacctgg cagtttgaga gaaactgcaa gtggtactga tgatgcacag 2640 attactccac aagcacagtc aagtgagtcc tctagcagat catgtgaagg tgcgagagac 2700 tcacaagctt ttgatcatac tccattaaaa tggagaaagc tggatgatgt acttgctcaa 2760 tgcaatctgt gcattatgga accagagaaa tatgaagatg cgctaaggat gagtcttgga 2820 tgaaagccat gaaggatgag ctctccatga ttgaaaagaa tgcaacctgg gagttagtag 2880 acaggccaag taacaagcct ataattggag taaaatgggt gtttaaaacc aaactcaacc 2940 tggatggaac tgtgcaaaag aacaaggcaa ggcttgttgc aaagggatat gcccagaaac 3000 caggaataga ctacaatgag acctttgctc ctgttgctcg gttggataca atcagaactc 3060 ttatagcatt ggctgcacaa aagagttgga aactctatca acttgatgtc aaatctgctt 3120 ttctgaatgg tgttctggaa gaggaggttt atgtagagca gcctgatggt tttgtagcta 3180 aaggggagga agacagagtg tataaacttc acaaagccct gtatggtcta aaacaggcac 3240 camgggcctg gtatggagag attgatacct atttctcaca gtgtggtttt acgagaagtc 3300 taagtgaacc aacactgtac atcaaggcag gggaggaaga cattttgatt gtgtcgatct 3360 atgtggatga cataatctat actgggagca acaatcaaat gcttgaagaa ttcaaggaag 3420 acatgaaacg aaagtatgag atgactgatt tgggtcttct ccatcatttt cttggaatgg 3480 gaataattca aaccaattca agcattttca tccaccaaaa gaaatatgca ggctctttgt 3540 tggacaaatt tggtctaaaa gagtgcaaat ctgtgcttac tccacttgtt gcaactgaga 3600 agttaaccac ggatgatgga agtggtgcag caagtgaaga gctatacaga agtattgtgg 3660 gaagtctcct atatctcact gcaaccaggc ctgatattat gtatgcatcc agtctgctag 3720 ccagatttat gcactgccct accagtaagc atgttggaac tgctaaaaga gtgctaagat 3780 acattaaggg caccctggat tatggtttgg agtatgtgaa gggtaagaac tcaatgttaa 3840 ttgggttctg tgacagtgac tggggtggat caattgagga cagtaaaagt acttctggtt 3900 atgccttctc ctttggcagt ggagtattct catgggcatc cgtgaagcaa aattgtgtag 3960 ctctttccac tgcagaagca gagtacatca gtgcttcaga agcaactgct caagccattt 4020 ggctgagatt tgttcttgaa gactttggtg aatttcaaac cgaagccact ccagtgcact 4080 gtgacaacac ctcagcaatt gcaatcacca agaaccctgt gttccatcaa aagaccaaac 4140 acattgacag aagataccat ttcatcaagg atgcactgaa ggatggcatc attgatctgg 4200 tgtactgtcc aactaatgag caactggctg atatcttcac aaaacctctg cccaaagatc 4260 ggttcaatta tctcaggagc atgcttggag tgaaatcagc tcaagactta aaggggag 4318 // ID SPRT1_IB_I repbase; DNA; EDCOT; 1022 BP. XX AC AB055092; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Ipomoea batatas copia-type retrotransposon SPRT1_IB_I, pseudogene DE for polyprotein. XX KW Copia; LTR Retrotransposon; Transposable Element; KW COPIA superfamily; SPRT1_IB_I; internal region; KW reverse transcriptase; Ribonuclease H; internal portion. XX OS Ipomoea batatas OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea. XX RN [1] RP 1-1022 RA Tahara M.; RT "Direct submission."; RL Direct Submission to Genbank (27-JAN-2001). XX DR Genbank; AB055092; Positions 1 1022. XX SQ Sequence 1022 BP; 335 A; 178 C; 244 G; 265 T; 0 other; gctaaccggt cagatgcctg cttatacact aaagagatag agtctaaagt agtgattata 60 tgcctaaatg tagatgatat gctaattttc agttcaaata ttgaatttat aaatgaggat 120 aagaaaacac tttgtggaag atttgatatg aaggatctag ttgaagccga tgtgatactt 180 gggataaagg ttacaaaatc caaagagtga taccttttat cccaaagtca ctatgcagaa 240 aaacttctga agaagttcga cagttatgat gtaaccccgg ctaaaacccc atatgatcct 300 agtgtcaagc tttcaaagaa ttccggggct agtgtatctc aagaaagata tgcaaagata 360 attgggagtc taatgttcct aatgaactac actagacctg ataattcgta gtaaacaagc 420 tcagtcgcta tacacacaac tcaagtgctc gacattggga tgcactaaga cgagtacttc 480 ggtatctcag aggcactata ggctggagtt ttaactataa aggattcccg gctgtgatgg 540 aagggtactg tgatgcgaac tgggtaaatg acaatgaaga tgtgagctca accagcggtt 600 ttgtgttcac catgtgtgga gccgctgtgt cgtggaaatc aaccaaacaa tcttgtatcg 660 ctagatcgac tatagaagaa gagttcatag gacttgatct accaagccaa gaggccgagt 720 ggttaagaaa tttattggct gacataccat tgcgggggag accaacacct ttagttccca 780 tacattgtga ctcacagact gtgatctgtg ttgcataaaa cagtgtctac aacgggaaga 840 ggagaaacat aagagtcatg catgagtcca tacggcagct aatgctgaac ggggtgatca 900 caatggaatt tgtgaggttt gagaggaata tagtagatcc tatcacgaaa ggcctaaatc 960 gaaaggctat ccttgagaca tcaagggagg tgggtttgaa acctgatgag gtaaggaatt 1020 ca 1022 // ID Copia-80_Mad-I repbase; DNA; EDCOT; 4386 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-80_Mad_; KW Copia-80_Mad-LTR; Copia-80_Mad-I. XX NM Copia-80_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4386 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1698-1698 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1779-2273] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 216..2930 FT /product="Copia-80_Mad-I_2p" FT /translation="MVPIKLTSTNYLTWSALFAPILRRYNLTGIIDGTMSA FT PPKYLLDSSGNQTSTLNPQYVTWFENDQNILIWINSTLSDALIPYTVGVNS FT ARELWSKLESRLATASQSHIHELRSRLRSITKGDSTAALYLQQIEEIADAL FT ANAGAPIEDSELISVILHGLPSEYESFVDAIQFRLGSTTIDELHGLLLSKE FT LQLTARKKTSPSAPVQAFNASAGLLPTPLGDFGAQAFFTQNGSSSQSYGPP FT NRGNFSQSRNYTNRGSQRNHQGFQGNQRFNRGSQGNHRYNRGPRSQYNNSH FT RKISCQICRQLDHEAVECPQRMNPNFGNKNSPAAYHASTPPTWLLDSGASS FT HMTHSSTNLQNPEPYTGPEQVYIGDGKGLPILNSGSSTLNTGSHCFDLKNV FT LHVPHLKQDLISANRFILDNWCSIHLYPFHFIVKDLSSEKTLFKGPVRAGF FT YPFHASSIAGNQKAFAASAKASQQTWHHRLGHPALKILNKLASQSCISVSS FT ALNKSVCSSCALGKSSKLSFASVSCTSSRPLELLHTDVWGPAPLISVNGYR FT YYLIFVDDYTKYTWFFPLKSKSDVFDTFVQFKVLVETLLSTKIVILRSDSG FT GEFLSLKFIKFLQEHGISHQLSCPHTPEQNGCAERKHRHLVETARTLLAAS FT KVPHSYWVEAFATAIYLINRMPTTTNFSPWELLFHRSPDYTSLKIFGCRCF FT PWLKPYTTSKLDPKSKECVFLGYSLNHKGYKCLDPSTGRVYLSRHVIFDED FT TFPFAQKDHPQPSHSSSSSSHLQPSNPIPTTLTFPPLSQPSPSPSPILSPT FT PSSPSPSQSLPVPSSTALPNPPLPSLPHPLSAPSIPLNTHTMQTRSKSGIF FT KPKALWQPSIPSLLISLPIIHHLPIFKPPNILIGVKQCRKSSMLSFKLALG FT L" FT CDS 2885..4387 FT /product="Copia-80_Mad-I_1p" FT /translation="MQEEFNALIQTGTWSLVPANPTQNLVGAKWVFRIKRK FT PDGTIDRYKARLVAKGFHQQQGIDYTETFSPVAKPVTIRLLLTLAAKFDWF FT LNQLDVSNAFLHGTLTESVFMIQPPGFEDPTKLNHVCHLHKSLYGLKQAPR FT AWYDKLTTALKSLGFSGSSNDHSLFVKKAPALIFILVYVDDIIVTGPNAQL FT CQDVISQLSSLFPVKDLGPLHYFLGIEVKRSSSGILLSQHKYILDLLSKAH FT MEGSKPCVTPLSTTKLDHDSSLLDKPEEYRSLVGGLQYLTWTRPDLSYAVN FT LVCQFMHSPRQAHFQAVKRILRYLKGTLSLGLWFPKCAKPLTLTAFSDADW FT AGCSLDRRSTGGFCVYLGDSLISWSAKKQPTVARSSTEAEYRSLANTAAEL FT TWICKLLVDVGLDLPSSPQIWCDNISAISLARNPIFHARTKHVEIDYHYIR FT EKVLANQVQVLFVCTQDQVADICTKALSKHRFHLLRDKLSLRLPQLGLRGD FT NKGKT" XX SQ Sequence 4386 BP; 1046 A; 1129 C; 788 G; 1422 T; 1 other; ctcgcctaag tcctacgaca gccgatcctc tccctctgct tcccgcttct tcctcttcga 60 atcttcaaac cctagaaatc tcccgcttcc tctcttcgat tcttccaaac ctagcaatca 120 ccacggctgg atctccttct tctggctctg cttcttgccc taattcttct ctctcctcga 180 cgacatcgtc gattacgatc caaaatattg gatctatggt gccgatcaag ctcacatcga 240 cgaactatct cacctggagt gctctgttcg ctcccatcct tcgccggtac aatctcaccg 300 gaatcattga cggcacgatg tctgctccgc cgaaatacct tcttgactcc tcgggtaatc 360 aaacctctac tctcaatcct cagtatgtta cttggtttga gaatgatcag aatatcttga 420 tttggatcaa ttctaccctc tcggatgccc taattccgta cactgttgga gttaattcgg 480 cccgtgagct ctggtccaaa ttggaatcgc gacttgcaac tgcatcgcaa tcgcacattc 540 atgagcttcg ttctcgtctt cgtagcatca cgaagggtga ttctacggct gcgctctatc 600 ttcaacaaat tgaagaaatc gcagatgctc ttgcaaatgc aggcgctcca atcgaagatt 660 ctgagttgat ttctgtaatt ttacatggtt tgccctctga gtatgagtct ttcgttgatg 720 caatccaatt tcgcctgggt tcaaccacta ttgatgaact tcatgggctg cttttgagta 780 aggagcttca actgactgct cgcaagaaaa cctcaccatc tgctcccgtt caagctttta 840 atgcttctgc tggtcttctt cccacacctc ttggtgattt tggtgctcaa gcattcttta 900 ctcagaacgg atcttcttca caatcctatg gtcctccgaa tcgtggcaat ttctctcaat 960 ctcgtaatta cacaaatcgt ggttcacagc ggaatcatca aggttttcag ggcaatcaaa 1020 gattcaatcg cggttctcag ggcaatcatc gttacaatcg tggtcctcgt tctcagtaca 1080 acaattctca cagaaagatc tcttgtcaaa tttgtcgcca attggatcat gaagctgttg 1140 agtgtcctca gcgcatgaat cccaattttg gtaacaagaa ttctccagct gcttatcatg 1200 cctctacccc tcctacttgg cttcttgatt ctggtgckag ctcgcacatg actcattcct 1260 ccacaaattt gcagaatcct gagccctaca ctggacctga gcaagtgtat attggtgatg 1320 gcaaaggttt gcctatactc aattctggtt cttctacact taatactggt tctcattgtt 1380 ttgatcttaa aaatgtcttg catgttcctc atcttaagca agatttgatt tccgcaaatc 1440 ggtttattct tgataattgg tgttctattc atttgtatcc ttttcacttc attgtgaagg 1500 atctttcttc ggagaaaacg ctttttaaag gtcctgtgag agctggtttc tatccatttc 1560 atgcatcctc tattgctggt aatcaaaagg catttgcagc ttctgctaaa gcttcacagc 1620 agacttggca tcacagattg ggtcaccctg ccctcaaaat acttaataaa ctagcatctc 1680 agtcttgtat ttcagtttcc agtgctttaa ataaatctgt gtgctccagt tgtgctctag 1740 gcaagagttc caaattgtct tttgcttctg tttcttgtac atccagtagg cctctggagc 1800 tcctgcacac tgatgtatgg ggtcctgcac cactcatttc tgttaatgga tatcgatatt 1860 atctcatttt tgttgatgac tacaccaagt atacttggtt ttttcctctc aagtctaaat 1920 ctgatgtctt tgatacattt gtgcaattca aagtgttggt ggaaacttta ctcagtacta 1980 agattgttat cttgcgatct gattctggtg gggaatttct tagtctcaag tttatcaagt 2040 ttcttcaaga acatggcatt tcccatcagt taagctgccc tcacacacct gagcaaaatg 2100 gttgtgctga gcgcaagcac aggcatttgg ttgaaactgc tcgaactctc ctagcagcat 2160 ccaaggttcc tcattcctat tgggttgaag cttttgccac agctatctat ctcatcaatc 2220 ggatgccaac aaccaccaac ttctcacctt gggaactact atttcacaga tctccagatt 2280 acacctcact gaaaattttt ggatgtcgat gtttcccatg gttgaaacct tatacaactt 2340 ccaagcttga tcccaaaagc aaggaatgtg tctttttggg gtacagtttg aaccacaaag 2400 gctataaatg tcttgatcct tccactggca gagtgtatct ttcaaggcat gttatttttg 2460 atgaagatac atttcctttt gctcaaaagg atcatcctca gccatcacat tccagctcta 2520 gttcttctca tttacaacca tccaatccta ttccaaccac attgactttt cctcctctat 2580 ctcagccttc tccctctcca tctcctatct tatctccaac tccatcttca ccctctccat 2640 cccaatctct tcctgtcccc tcttctactg ccttacctaa ccctcctctt ccctctctcc 2700 ctcatccact ttccgcaccc tcaatacctc tcaatactca taccatgcaa accagatcca 2760 aatcgggtat ttttaaaccc aaagcactct ggcaaccaag tatcccatct cttctgatct 2820 ctctcccgat tatacaccat ctacctatct tcaagcctcc aaacatcctc attggcgtca 2880 agcaatgcag gaagagttca atgctctcat tcaaactggc acttggtctc tagttcctgc 2940 taatcccact cagaacttgg ttggtgcaaa atgggtgttc agaatcaaaa gaaaacccga 3000 tggtaccatt gataggtaca aagctcggct tgttgccaaa ggcttccatc agcagcaagg 3060 cattgattat actgagacat ttagtccagt tgccaagcct gttactattc ggttacttct 3120 cactttggct gccaagtttg attggtttct caatcaactt gatgtcagca atgctttttt 3180 gcatggtacc ttgacagaat ctgtgttcat gatccaacca ccaggatttg aagaccctac 3240 caagctaaat catgtttgtc atctccataa atctttgtat gggctcaagc aagcccccag 3300 ggcctggtat gacaagctca ccactgcatt gaagtctctg ggtttctcag gttcctcaaa 3360 tgatcattct ttatttgtca agaaggctcc tgcgttgatt ttcattttgg tctatgttga 3420 tgatattatt gttactggac cgaatgctca actctgccaa gacgttattt ctcagctcag 3480 ttctttattt cctgtcaaag atcttggtcc tcttcattac ttccttggta ttgaagtcaa 3540 gcggtcatca tctggtatcc ttctctctca acacaagtat attctcgatc ttctctccaa 3600 agcacacatg gaaggttcca aaccttgtgt cactcctctt agtacaacta aattggatca 3660 tgactcttct ctgcttgata aacctgagga atatagatct ttggttggtg gtttgcaata 3720 cttaacatgg acacggccag atctgtctta tgcagttaat ttggtttgtc aatttatgca 3780 cagtccgaga caagctcact ttcaggcagt caaacgcatt ctccgatatc taaagggtac 3840 tctgtctctt ggcttatggt ttccaaaatg tgctaaacct cttactctca ctgctttctc 3900 tgatgccgat tgggccggtt gcagtcttga tcgccgatct actggggggt tttgtgtcta 3960 tttgggtgac tcacttataa gctggagtgc caagaaacag cctactgtgg ctcggtcatc 4020 gaccgaagct gaatatcgat cattggctaa cactgcagct gaactgacat ggatatgcaa 4080 gctattagtt gatgttggtc ttgatcttcc ttcttcccct cagatttggt gtgacaacat 4140 ttctgccatt tcattggcta gaaatccaat cttccatgct cgaaccaagc atgtggagat 4200 tgattatcac tacattcggg aaaaagtgct tgctaatcaa gttcaagttc tgtttgtgtg 4260 tactcaagat caggttgctg atatctgcac caaggctctg tccaagcaca gattccatct 4320 tctcagggac aaactctccc ttcggctacc tcagttaggt ttgagggggg ataataaggg 4380 taaaac 4386 // ID Gypsy-33_Mad-I repbase; DNA; EDCOT; 3369 BP. XX AC . XX DT 08-OCT-2010 (Rel. 15.1, Created) DT 08-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-33_Mad-I. XX NM Gypsy-33_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3369 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1760-1760 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 3369 BP; 971 A; 928 C; 693 G; 777 T; 0 other; tttggcgccg tctgtgggaa tcgacacgaa aagctatgtc ggttctcttt cattttttca 60 cctccaccgt gaatctgcaa aatcacaaaa acccagaaca caaaatctct aaaacccaac 120 atcggtcgca ctctcttagc tctctgcagc ttcacacccc aactccaaag tcccaaccgc 180 cctctctctc tcttcaaact caactccaaa ggcaccatct ctctccaaac acctaaagaa 240 gcccatctct ctacaaaccc aggaagccaa gaaatcgaga aaacgagatg caatttcttc 300 taggacgtcg tactgaggtc ccgagtattc aagaacccag atctcctgca gtatgatgtc 360 ctgtacgatc tcttgcactc cccgcagtgc gatctcttgc actccttagc ggacgccgcc 420 tccatcccgc gcagaaacaa atcgttcggt atgaagctcc ggcgtcggag atcctccgct 480 ggagagccga tgtcctcgat ggccacgtcc ttgtctatgt cgatgacgag atggagcggt 540 tcgtggtcag cgccgaactc ctgaaccacc cagtcttcgt tggactcctc gacgagtcga 600 gcaggggtcg actattacat tccctgatgg atactgtcct ctcgatgatg ttggaccgct 660 gctctcgccg ctgctcgtgg cggttgtcct agtacctttc gtggttgcgg cgaaagctat 720 ggaggcacaa gtgctagttc tagaacggct tacattccaa ccacaagcgg cactcaaaga 780 tcggagacca ttgctggcat cagagccgcg agtctgcaat gccgggcctc ttcgtccaga 840 tctcaagcct ctgcagtcga aggacgagcc tgtttgtaag ttcatgggag cacgggttcc 900 tggacagatg aggtgtaaga ccacgggagc aggggttccc gccattatca tcccttctca 960 gctgacctca tacattttga tcttgcgacg gccgtaaaag cgagtcaatg gaatgcaact 1020 gtccctccag accaccttca ttgtcagcaa gaatctcttg tgctgagatt gtcaagcaac 1080 gctgcagctt tgaattccgg agaaggccag gaggattggc aacagtccct ggtggtgctt 1140 gtcggcaggg agttattcgg atttggagag gttatggctg ctcatatcac agcagagagc 1200 ttcctgaaag ttatggcgcc acaaacgtgc cctgggacga tcctcattgc cagcccagtt 1260 ggctcaactc gctcaaaggg tgatactgaa tatgttgaaa agaccatgct taaagtgtgc 1320 atgcccttgc tgtttttggg tccaccacct ccactgtata acactttcag atccacagcg 1380 gctgatgaca gcaaaaaagc aaaagagaaa ggcagtggga aacaaagcga aaagaaaaag 1440 gaaaaggaaa agatgctttt acaaacggat ctccttgatt ttacaaacag gagctggcta 1500 ccaaagcgga aaggaacatc gtcaccaagc ggaagccaga tcggcaaagc agagacagaa 1560 aagagaaagc aggagaaagc aaaagcagaa agcaaaagca aggaataaac accccaccag 1620 aatgatgtga tttacttttc ttgtttttgt atgatgtaat ttatttttct tatctttcgg 1680 agacatctgt ataaacccca tcagagggta ataaaaaaaa aaaaaagggc aaagcccaaa 1740 ataaatgggc tggaatgttg tgtggagggc gaaggcccat aagcccaaaa tagctccaac 1800 caggtgatca aaagtacgcc cagtactcca caattattcg gcaacctgcc gctattacca 1860 ccaaccaggt gatcaaaagt acgcccagta ctccaaaatt attcggcaac ctgccgctat 1920 taccaccaac caggtgatca aaagtacgcc cagtactcca aaattattcg gcaacctgcc 1980 gctattacca ccaaccaggt gatgaaatgt acaacccgta ctctaatatc atttggcaac 2040 tagccattca tgccaccaac caggtgatga aatgtacaac ccgtactctc cttcatgcca 2100 ccaaccaggt gatcaaaagt acgcccagta ctccaaatta tacatgagca ttactcatgt 2160 cattcataca taaacattca tgagcatcac tcatgacaat catacataaa cattcatgac 2220 catcattcat gtcaacattc atgagcatca ctcatgttaa cattcatgag catcactcat 2280 gacaacatcc atgagcatca ctcatgtcaa tcaacataaa cattcatgag catcactcat 2340 gtcaatcagc ttcaaaagct tcatttacag agctctagct tcaaaagctt catttacaga 2400 gctctagctt caaaagcttc atttacaaaa gctccagctt cgaaagcttc atttacagag 2460 ctctagcttc aaagcttcac ttgcaaagct tcacctacaa agcttcagtg cagggtatac 2520 aaataccgcc tccgaacaac cgccacttcg gcccatacat ggattcaatt tgaagtctcc 2580 agccaacaga ctctattgac cgaagacttg ggggactaca ttatgtacca tatattgggc 2640 ctcaactggg cctcatgaaa aatacttggg ggacttagcc cattatttat gtattgagga 2700 gcgagccctt attctataaa agggactccc tcactttcat tagagagcac ccattattca 2760 tgtactgagg agcgagccct tattttataa aagggactcc ctcaccttca ttagagagca 2820 cgccgccagc tgagcaaccg cctcgccgcg agcatcactc ctagcccatc acttatgtat 2880 tgaggagcga gcccttattc tataaaaggg actccctcac cttcattaga gagcaacgcc 2940 gccagctgag caaccgcctc gccgcgagca tcactcctaa cccatcactt atgtattgag 3000 gagcgagccc ttattctata aaagggactc cctcaccatc attagagagc atcgccgcct 3060 actgagcaac cgcctcgccg cgagcatcaa ctctagccca tcattcatgt attgaggagc 3120 gagcccttat tctataaaag ggactccctc accttcaacg ccacaagccg agccaaccaa 3180 ggcaacataa gccacgagcc gagcagcctc gcagcatgtg ctacttctag ttgagcatca 3240 tttcagattg agcaccgcct catatcgagc atcagttcaa gacaacatct agttacttcg 3300 gcccacacat ggactgaatt tcaagtctcc agccaaaaga ctctcttgac tgaagacttg 3360 ggggactac 3369 // ID Gypsy-75_PTr-LTR repbase; DNA; EDCOT; 413 BP. XX AC . XX DT 23-DEC-2009 (Rel. 15.02, Created) DT 23-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-75_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-413 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 185-185 (2010). XX DR [1] (Consensus) XX CC >90% identity to consensus. 5-bp TSD. XX SQ Sequence 413 BP; 97 A; 68 C; 72 G; 176 T; 0 other; tgatggggac accgaacccg aaatattatt tatgcacgcg tatgatcata gacgatggag 60 gatagcccaa acaattgaga gattgggctt taacttatgt ttttgggttt aatttatatg 120 aacttttagt taaggtttat taatttggct ttatttgttg ggtttgattt aattattgtt 180 gggtatttta tttagtgggc cataagccca aacgcttgtt ctagttaggg ttttagtatt 240 tatatcctac ttttctaaat gttaagggac ttttgatgat taatgaaaat ttgcagactt 300 tgcatatctc caatcccctt tcttctcttt ctttgctttc tcttctcagc ttcttctcta 360 aaagcttctt tcttttcccg gctttaattc ttattattta ttgtcccgca tca 413 // ID ENSPM2_VV repbase; DNA; EDCOT; 14435 BP. XX AC . XX DT 24-AUG-2007 (Rel. 12.08, Created) DT 24-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE DNA transposon from Vitis vinifera. XX KW EnSpm; DNA transposon; Transposable Element; ENSPM2_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-14435 RA Obukhanych T. and Jurka J.; RT "ENSPM2_VV."; RL Repbase Reports 7(8), 670-670 (2007). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS join(5965..6495,6499..7665) FT /product="ENSPM2_VV_1p" FT /translation="MFQSSKIAKDLIWHAEGGEFDGKMRHPSDSPSWKVID FT HRWPDFAAEPRNLRLAISADGINPHSSLSSRYSCWPVVMITYNLPPWLCMK FT RKFMMLSLLISGPQQPGNDIDIYLAPLIEDLKTLWEIGVEAYDAYQREVFT FT LRVVLLWTINDFPAYGNLSGCTVKGYFACPIVDGNLFTVEAWEKELIYRHR FT RFLPCNHPFRKHRKAFNGEQEFRSPPQPLSGEEILLKMNAICNSWGKKRGR FT HEKSNVTYTNCWKKKSIFFELEYWRYLHVRHNLDVMHIEKNVCESIIGTLL FT NIPGKTKDGLNSRLDLMDMGLRCELAPRFESNRTYLPPACYTLSRKEKKVF FT CQTLAELKVPEGYCSNFRNLVSMEDLKLYGLKSHDYHTLMQQLLPVALRSL FT LPKHVRHAIARLSLFFNALCKKVVDVSTLDQLQNELVVTLCLLEKYFPPSF FT FDIMIHLTVHLVREVRLCGPVYFRWMYPFERFMKVLKGYVRNRNHPEGCIV FT ECYIAEEAIEFCTEYLSNVDAIGVPSSTNVDHKVGAPIPGGHITEVDCNLL FT LQAHHYVLENTTIIQPYIE" XX SQ Sequence 14435 BP; 4655 A; 2143 C; 2614 G; 5023 T; 0 other; cactactaca aaaatagaaa attatgacgc tttaatcctt ggcgctttca taaagtatca 60 ttatatttgg atatacaatg gcgttttttc aaaagggtca ttttttatat tagttttttt 120 atttcatggc gcttatttaa agtatcattg cttgctgtgg cacttataag aataactggt 180 tattccatga cactttatag cagtgtcata gttgtgatat ttcatggcgc ttatattagg 240 tgacattaaa taatagtata tatatatata tatatatata tatatgttct aaatatatat 300 taattaaatg cttttccctt tctacactca cccgccagac attccctcca caatttcaga 360 actgaagaaa ctaaaatgcc ctaatccatt ccccttgcaa agtcatttga ctccacatca 420 attgccaaaa tccattcctc ttgcaaagtc caccactaaa atgccctaat ccgttggaat 480 ggccatgtct aacttccatg catgggaggt taccattgtc aaaatctact acagagcatc 540 atagttacag gtaaatctct ttctcaagta atgttgtttt cctcaaactt gaatagatta 600 gtacaaatga agacaaatgg aagggttttc attgttccaa aaatctaata ttattgtttc 660 atagatggga aaattatttt gggaggagaa aatcagggta atggtatccc aaataaatac 720 agtgcatttt ttgttcttct tgttgtatgg tacgctgcaa gttgtaatag gtatagttcc 780 agcttctcct tttagttgtg gtgggaagtg ccgccttgtt tttgcctaat gtaatgccat 840 ggagatgtag cagccagcat ggtgatcggg atggaggttg agggtaatgt ggtgggtggc 900 tcacgcacca gcacaagggc gtgggaaagg aggtgtagtc tctgccgcct gtaggtatgg 960 acgtgtcgtg ttcgtacacc aaggagaaga caggttcggc tgcagcagtt gagaaagcta 1020 cagaatggag gatttttaaa tggtattgag aggggaacag ctggcaaagg catgacgtgt 1080 tttaaaattt tctttggtgg gcttgggttt gagttttagt tgttgggcag ccaaggattg 1140 ggggaggcac caggtccaaa atatatgggc ttggtttaaa gaagaaactt ctacagaatg 1200 taaataataa taataattta aattttactt taggggatag gaatttggac cttggatgtg 1260 gctggatttg ggcccatccg aaggccttgt ttggtccacc tcatccctcc tacaaagtca 1320 tgactgatga ctggagaggc aaaactcgtt cctgggaggg agaggttgat gtcggcgtca 1380 tgctgggcgg tgttgaagga gttggaggag atgaggactg aggcatcgta gccttcgacc 1440 atgcagtcgt ggaagaagag gcggagagtg gcagtagctg tggtggggtc gttgatttcc 1500 ttggtgctta tgatctcaca tattttaatc aggaatattc tatgcctccg cgtctttgaa 1560 aggctgtcaa gtctgactct aaatttggtg cgttgaaagg attctaaacc tgccgctgtc 1620 attgttctag ctgctgcatc ctctctcaat ctcctctgcc atggctgcga caccatcttc 1680 cactgctgaa atctctacag ctatggtgaa ctctcttctg ttttcttgcc atctgaaagg 1740 agcactgcac atatgatatg cactaaaaga cctggttatt gatgatggtg ttccaaacac 1800 tagctcctcc tcccctctca tggaaacatg cgattgtatt gagagagtca aatttctaag 1860 gggaaagaac tatttctcac tggatcctta gtggcatcgt cgttgaccca ggtttttaag 1920 tccttgcctc ctagcactct tgccggacct ccatctgtca tctccaccac tgctcttcct 1980 cccttcttga ctcaggtatc aactttgtca tctcctattc tcctcaaata aattccttca 2040 ccctattctt ttcttcttct tatttctcta caccatcata tccttctgtt cttcttcttc 2100 tttgtcacat tcttatcagt tttctatttc gaattcactg ccttcttcca ctctacttgc 2160 tgcaccgaat attaccaatc aaacttgatt ccaccaacta tcttctctga aagataaatt 2220 cctcctgttt taattagcaa cacctcttag gatagttgat ggcacttttc cttgtcctcc 2280 tcaatatacc tgtgatgccg aaggtgtaaa attgcaagtt gggattgaaa gttcaaggaa 2340 gctgccttct ttctttactt aataaaatat acattgttga aatcaaaacc cttatgatta 2400 tatatatata tatatatata tatatatata tatttaaaag tttttatata cacaaaatat 2460 taaaataatc ctttaaacaa taaattaatt ataattattt tatatgtaaa taattttttt 2520 atttaattaa attgtaaaaa gtttttaata tcattaatat attaattaaa tatatcataa 2580 ttttaatatt aaatatattt taaaattaaa catattataa ttaaatgtca caatattatt 2640 attgaataag attttatata atttaataat tataatatat atatatatat atatattaat 2700 ttttttaata aaataatttt ataatattta ttacactttt aattttattt ataagagttt 2760 tattggaccc tataatgttg aggctaagta caagggaaat tttagaaggt ttcaaggaat 2820 gatccaaaca aagaaaaatt aaaaacttga atgggcttct tctatatgct tctttcataa 2880 aagtagaggg gcaagtaaga gaaacacaca tggtcaaagt aaagaggact aagtaggtgg 2940 tcaaggggca aaataggtaa tgaaggtagc aaaaaggttc gagattaatg ttgactcaag 3000 aaatttcatt agtatgggtg acaacttact aggaacttct aattatagac ttgaagagtc 3060 ttatggactt cttcaaattt catattatcg ggtgccatta tatttagtca aatcttgagg 3120 ggaaatgaat taaattaacc ctttaaaaat attactcaaa atatggtaat ggaatatttc 3180 aaaacttgta tcatttgtgt ggattgaaat agaatattgc ttttaaaatg caatttctaa 3240 ctttctattt taaaaacaaa aaatagtaaa atattttgta taagagttgt tactattttc 3300 tattttcaaa acaaaaaata agaagtgaaa aaaaaatgaa tattagccta cttttaaaat 3360 ttacactaat tactttttag agaaaaaaaa taactttaat gtagtgtaac catatatact 3420 ttgtatacat aaggaatcaa aactaaggta taggatcata ggtattatta ttagatggtg 3480 caacttgttg gaaaaatcaa agggtggaat tgctggatgc tgaagaccta gcctgtaact 3540 tctctttcac aatatgatac aacctaacca agatgattac ggattgttaa gccaccttaa 3600 tttagaccag acttttctat ctcattcgtt taagttctac ccatcttgca gtcatctttc 3660 ttgccctaag gacttgaccc ggtcagatag tgtggttcac ggttcaccca ccattaggtc 3720 atcaccaaaa gtcataatct caaatgaaaa ggggcacaag gaataatctt cttacctttc 3780 tcatcatgca tatattttat tttatatgag tattaattac catttaaaaa aaataataac 3840 taaaatagtt gattttaata attttataaa tttttaaaaa tatctaacca ttgttgcaca 3900 tgtgaaaatc ttttttttct tacttatatg ttttttcttc ttagtttatt tcttatttta 3960 atttattttg tatttatttg ttaatatcta ctaatggatt tattttatat ctttatttat 4020 tatttgtttt gcatatacat attttaagag acagtgacct acattggact acgagaggtg 4080 tgtgatgcaa gactcgagac aaagacagag tgaggaaggt acactatttt tccttataca 4140 aaccaacata ttttaattat aataccattt ttactttggg tggttagaag aatataatgg 4200 aagcgttatt ttaaattttg tttaaatctt attgagtacc tgaattgtac gagttattcc 4260 cagcttagtt tgataccaag gcccaaattt tgacccaagg ctatgacata gactggtgtg 4320 acttgattcg caaatcatgg gccatacgta tgctttctta taataatctt gtttaatgat 4380 gaaaatagca ataattatgg aacaacttta ggtgttttat aattattaga ttattcaata 4440 agtaattgtg ttttaatttt aatcaaacat gcatgcatga aaccttagag ttcccattca 4500 actatcattg taagataaaa gtttctctta ttacatacta aagacattta agttgtcaaa 4560 ggtgaaaaag gttttatcta agccactttc aagttgacaa cttttaaatt gtctagaatg 4620 tgataaagat attttttttg caatgatgtt tgaattgtcc gattggacag tgtaggaaaa 4680 cataatatct atgaagttaa ttgcttgtgc ttaattcact ttttagaaat tttggtagta 4740 tttcctcttg ttctctgggt gcatatttga acaaggtcac atattatacc ttgttcattt 4800 tgtgtacttg gagaactatg gggaaatgct gccaaaattt ctttaaaatg aaattgagta 4860 tattggcaat taacacatag ggattatgta ttcctacatg ggataggaac aactacctga 4920 ttttggatga tggacatgtt aaaaggcata aaaacatgca tcaaaaggtt ctattgtcat 4980 attgttaatc cttttttttt tattgaggat gaggttcaaa ttttttatta cacttgaatc 5040 ctaattgttt gtccatagaa agtttaaaag aaattttgga tgtcacaaat gagaaactga 5100 aagttttgag tgttttctaa aggtaacttt tctaagtctt ttccatttca ttgtttgctt 5160 atgtttgcta tataggaatt gagttcaact attataggca aatgaatcgt tcctggatgt 5220 caaaagatag aagatcaaaa gactatgagg atggggttga aaattttatt tcatttgcag 5280 ttcaaaattc tgcaaatcaa aactccatca aatgcccatg tctacagtgt ggaaatttga 5340 tcttcaatac tcctcaaaag attagagaac acctattctt ttatggaatt gaccaaagtt 5400 accatacttg gttttggcat ggggaggcag ctctaagtag tggaccccca actacaaggg 5460 ttgaatgttt tgatagaatt catattggta atgtggatca tacagtagaa atggttgaag 5520 ctgcacaaga tgattgtaag gctaatccaa aattatttga aaggttgctt gaagatgctg 5580 aaaaaccttt gtatcccggt tgcaaaaact tcaccaaatt atctgcttta gttaaattat 5640 acaatctgaa agaagatatg ggtggtctga taaaagcttc tccgagctat taagcttact 5700 tggtgatatg ttgcctgtaa acaatgagtt gccattgtct atgtatgaag caaaaaaaac 5760 attgaatgca ttgggaatgg aatatgaaaa aatacatgca tgtcccaatg attgcatact 5820 ttttaggaat gagttaaaag atgcatcttc atgtcctaca tgtggagctt caaggtggaa 5880 ggtgaataga agaggaagca aaaagagtaa aggagttcct gctaaagtga tgtggtattt 5940 tccacctatc ccacgattta aagaatgttt cagtcctcaa aaattgcaaa agacctcata 6000 tggcatgcag aaggtggaga atttgatgga aaaatgcgtc atccatccga ctcgccatca 6060 tggaaggtaa ttgaccatag atggcctgat tttgctgcag aacctagaaa ccttagactt 6120 gccatttcag cagatggcat aaatccccat agttctttga gcagcaggta tagttgttgg 6180 ccagttgtca tgatcactta taaccttcca ccgtggttgt gcatgaagag aaaatttatg 6240 atgttatctt tgttaatatc gggtccacaa caacctggaa atgacataga tatctattta 6300 gcaccattga ttgaggacct taaaaccttg tgggagatag gggtagaagc ttatgatgca 6360 tatcaaagag aggtctttac attaagggtt gttctattat ggacaataaa tgactttcct 6420 gcatatggaa acttatctgg ttgcacagtc aaaggatatt ttgcttgtcc aattgtggac 6480 ggaaacctat tcacataggt tgaagcatgg gagaaagaac tcatttacag gcacagacgt 6540 tttcttccat gcaatcatcc ttttagaaaa catagaaagg cattcaatgg tgagcaggag 6600 tttcgatcac ctccacaacc attaagtgga gaggaaatac tattgaaaat gaatgccatt 6660 tgtaattcat gggggaaaaa aaggggaaga catgaaaaat ccaatgtgac ttataccaat 6720 tgttggaaga aaaagtctat attctttgaa cttgagtatt ggagatattt gcatgttcgt 6780 cataatttgg atgtaatgca cattgagaaa aatgtttgtg aaagcatcat tggtacatta 6840 cttaacatcc cagggaagac aaaagatgga ctcaattctc gtctagacct tatggacatg 6900 ggcttaaggt gtgaactggc accaaggttt gaatcgaatc gaacttacct tccgcctgca 6960 tgttatacat tgtctagaaa ggagaagaaa gtattttgtc aaactttagc tgagttaaag 7020 gttcctgaag ggtattgctc aaactttaga aatcttgtgt caatggaaga tttgaagctt 7080 tatggcctga agtcccatga ttatcataca ctgatgcaac aattgttacc agtggcattg 7140 cgatcacttt tgccaaagca tgtacgacat gctattgcta gattgagcct ttttttcaat 7200 gctttatgta agaaggtggt tgatgtgtct acattggatc agttacaaaa tgaacttgtt 7260 gtgacattgt gcttgcttga aaagtacttt ccgccatcct tctttgatat catgattcat 7320 ttaacggttc atcttgttag agaggtgaga ctttgtggac cggtttattt tagatggatg 7380 tacccatttg aaaggttcat gaaagtatta aagggttatg tgcgaaaccg taaccaccct 7440 gaaggttgca ttgttgaatg ctacattgca gaggaagcta ttgaattttg tacagagtac 7500 ttatcaaatg tggatgcaat tggagttcct agtagcacta atgttgacca taaagttggg 7560 gcgcctattc ctggaggtca tatcaccgaa gttgattgta atttgttgtt gcaagcacat 7620 cattatgtgt tggaaaatac aactatcatc caaccttata tcgagtaagg gtcaactatt 7680 ttgattttat gtgtagatta cttaaactaa ttttggaaac ttattgttac tttcttatac 7740 atatcttata gagaacacat gaaatggttg aaattgaaca atcctcgtca atctaagaga 7800 caaaagtggc tacaagaaga acacatgcga acattcactc attggttgcg aaaaaaggta 7860 ttgaatttat tctaaaaatt gcaccattct tagcactaat cataaaaaaa tattaataac 7920 tatggtccat tcaaacaggt agaagttgcc attgctgaca aagaacctat atctgaaacc 7980 ttaagatgga tggcacatgg tcctacccac tacgtggcca agtatcatgg ctatgttata 8040 aatgggtgtc agtacaatac aaaagaccgt gatgagttac gagttaccca gaatagtgga 8100 gttagcattg tagcaacaac aatgcaaatt tctagtgcca aggataagaa tccagtattt 8160 ggtgagctat gtttctatgg tattattact gagatatggg atcttgatta taccatgttt 8220 aggattccag ttttcaaatg caattgggtt gataataaga gcggcatcaa agttgatgag 8280 tttggctgac attagttgac ttcactaaga tggctcataa atcagatcca tttattttag 8340 cctcccaagc caagcaagta ttctatgtac aagaccaact tgatccaaga tggtcagttg 8400 tgtttgtcaa ctcctgaaag ggacttctca ttttcagcaa aggattctga tgacttcatg 8460 gataattcta ttgaacacca tcctctcatt accaccttgg cacaagttga atcatttgat 8520 acaatggatg actctgatgt catttgcatt cgaggagact gtgagggatt ctggattgat 8580 aacaaatctt ctatgtaact aaatttatga ccttgttgtt ttgttgtgaa ggttgtaact 8640 atcccattaa cttgttaata ttgaaattct gcatttcagt aaatagttta tttattttct 8700 aagtggatta aattcatcat gtctctaaat ttattgattc cctatttcat gattattatt 8760 atacacatat ctcagagtga tctaaagggt aatacaagga tatcaatttg tctcagctca 8820 aagcttatga tttctagttc cataagaaaa aagtttggtg aggatcttct agtaagtttt 8880 tattattatt atttttaaat atttcatgac aacatgtgaa tattgttatc tagcatgtaa 8940 aatgttccta gtatgttcat gttactaata tgagttcatg ttataaaaaa attcaatttt 9000 acttgcaatt aatgggtata cttatcattt ctcattgatg tgttataggc atggattcaa 9060 aggaagagaa aaccccttca caaaaaaaat atagagggac aacaaggaaa tccatgatta 9120 taaggaatag gaaaatagag ggataaagtt ggtcataaag tacaatgctg atggtatcta 9180 tgtaggagaa tcttctgtgc acctaacaag ctacttaggt gtattggcac gtacgatggt 9240 accaatcaga tataacacat ggcgagatgt ccctgaacaa ttgaaggata agttgtggga 9300 ctctattgag gttacttttt tttttttttt aacataaata agttttctac aatctctata 9360 tttctttcaa attttgagaa actaatgact ttataatttg tagattgctt ttacattaga 9420 caagaaaagc agaaggaatt gtatgcttac attgggaaaa tgttttcgat cttttaagaa 9480 cacgttgact gtgaaacata ttcttccttt caaagatgag ccagagcttc ttaagaaacc 9540 accagctgaa tatcatttta tcgatgatga agattggaat atttttgtga aaaataggtt 9600 gtctgaaaaa ttccaggtac aaatacaatt aacattaaac atactacatg catccacata 9660 tatatactaa gcatccattt taatttgtag gaatataggg aagtacaaaa acagagaaga 9720 aagaagcata tatataatca tcatctaagt agaaaagggt atgctggact tgaagaagag 9780 atggtaagtt tttgttattc ttattgtggt ttaattttat atgattgtat aagtaatgaa 9840 ggaatatttt atatgggttt cttaattgtt tcttttctga caaaaaaata gaaataaaac 9900 cacatgtgtc atctaataac tatctttaat tttccatttc tattagatga ttgaagctgg 9960 ctccacagaa agcattgata gaagtttact ttggaagagg gcaatgcaaa aaaaagatgg 10020 cagctatgat gatgtggtcc taccggtagt ggaaaaaata gtaagtagac attttgtacc 10080 caaaaatcac atctttaaca ccttatttgg ttttacttat ttgaaagtta acttcataac 10140 ttccttttgt tttaggatga attgatgaaa gagtctcaag aagtggcata agctatagtg 10200 ggagcaatga catactttct caagcactag gtactcctga gtatactggt cgggttcgag 10260 ctaaagggaa gcactacaca cgcctggacg atatttcaat agtatgtcag aacgtgttgt 10320 gagggatatt ttaaaagcaa ctcaagaacg tcaagtaagt ttgaggctga tgtgttagcg 10380 agactatctc agataggagt tgctacacca caatccgatg tgagtagttc caacatgaaa 10440 tcaaaactgt tgcttctacc agaagtagtg gagaaaccaa ttcgtaaagt tgaggaggag 10500 accttacctg tgaaaataga accacacatg aaggtgtgtt atttttagtt tacatttcct 10560 agttaatgac gtaattgtca caaattccta gataattttc ataaataatt tcttccaatt 10620 gcttttattt ttgttagatt gatacttaca ttttaggtag attctattac agtataatta 10680 ctactagtaa tattctattc cactacaact attacttata aaatatgtaa ctttatgtct 10740 taaatatagc cctaacatag tcaatgcact ttaaacttca tttattgatt atttttttat 10800 attgaaatta acaatttaat ttacttttga aggcaagaaa atgtgagttg gcagtaggga 10860 ccagagaaaa tacagtggct ggtggaacaa ttgtaatgga ttgtggtccc aactacctag 10920 ttgttttgga tgctccctat gagtcaaatc accacttcct attccattcc cattcctgga 10980 caagctacaa cagttggagc ggcagtgggc taccaagttt tatggccaac ccatttagtc 11040 aatttgagta ctaaattcat taaggtgtgt tattttcatt tgcaatagtt tataaagata 11100 tgtatatcat ttgaaaacat ggtgctttct tttataggga tctcacaaag ggaaaagaca 11160 aaaaacaaca gaaaatgact tgaaaattgg tgaaaaccct caagatatca acaattttga 11220 tgcattagta ggtctcatgc taaatgaggg gaaagcacaa ggtgtggagg tcccaaatga 11280 tgtatttggc gagagtttta agaccttcct tatgaaagaa gacatggata tgataatttc 11340 atttaaggaa gtgtcggcta attgtgtcat atattatata tggtaaataa ttttataact 11400 tgctaatgtg tgttaattta tatatatatt atatatatta tatatatata tatataaaag 11460 taaaatggtc atttcttatc aaggtatgtg gaatttaaac aggcacctac agaaaaagct 11520 aagtgatgca aggctcaccg aacgatttgc ttttatcaat ccagctttag tctctaaagc 11580 tggaatgggt gagacaacaa aggaaaatag gtcaaggttg attgcaaatc gtttaatgca 11640 tgcaaagcgt gctgactaca ttttattcca tataaccctg agtaagttat gaaaaatatt 11700 aagttttttt tttaatgtta aatagcttaa tcaatgctaa ttactaaata atatctaatg 11760 tactattgta gtttccactg ggtcttggtg gcattggata tgaggacaat gactgcgtac 11820 taccttgatc cgatgcaaaa gcaaccatgt gatgatctta aggaaattgt taacatgtaa 11880 gtgtcttcat ttccatactt gaatatagtg catagtatct aaaatgttaa ttttctttcc 11940 atgtagggca ctacgaattc atccaccaga gaaacaaaga tcatcaaaga gggagccaca 12000 tgggtaaaag tagtggtaag ttacttggtt agagtaagat atatcatatg accacttata 12060 tcaaccctaa aatttgaata tggttttatg ttttgtcact tagataataa tgacataaaa 12120 catcatgata ttaatgtttt tatggtacca taattcatat gtgtgcctat agtgcccaag 12180 acaactagga agtgtggagt gtggttatta tgtgatgaga tacatgaaag atataattgt 12240 tgatccaagc ctcctatcca caaaggtata tactcattaa taaattttat tagtttctat 12300 actttagtaa ttttttgtta acttaactaa tcatcatgta tgtacaatta attattagtt 12360 taaagggaaa aaatcgtata gtgaagttga gcttaatgaa gtacgatctg agtgggttat 12420 gttggcaact caattgattc ttacccatgc ctgaaggtat aaattaacat ctataatgct 12480 tgattttcat tattaatgaa gtcttgaatg gactaatttt tttaatttac catcttatgt 12540 atgcagatgc cctcatttca gtccagtaag agttgtagat cacattttga cgattctcat 12600 aagttctcat ctcatgagat aagtaatttt ttcctccata gtgatagaat ataatagttt 12660 tatacataaa ctatttcaat ataacaaatc aaattattac atcatcacca atgttgttac 12720 atggagaagt tatttttgtt attgttgtat ggagaagaag catataattt gtgaactcaa 12780 taaatcaaat tattatatca tgatcatcaa tgttgtcatt attattgttg ttgttgcata 12840 gagaagttgt tattgttata tgtttggact aaacaaatca aattattact aatataatta 12900 tcaccatcga tcatcaatgt tattgttatt gttattgttg ttgttgttgt tattgttgtt 12960 gttgttgtta ttgttacatg gagaaattgt tattgttgtg atggagaaat tgttattgtt 13020 gtatggagaa gttattgttg ttggaaaggt tgttgttgca tcaaaggttg ttgttgttgg 13080 atggagggat ggtagagagc tttttttttt tgtgtagggt taattattat atttgggtta 13140 taattttgga attgaaaata aaggcaagtt ttagaatggt tgttattatg acatttaacc 13200 aatgatttgt aggtttctat tgccttggtt atgctctttt aatttttagt ttaatactct 13260 ttttttcctt atggaatgtt attagttaac taaatttggt aatataggaa agttgtaaga 13320 agaaattaag tcatttgcaa atggttaata ttaaatgtct tatattacta gatatgatga 13380 tttatgattg aaactaatta taaaccatac ctattggtat attcatatat ttatttaatt 13440 atgagaaatg agtttgatat gttagacata gataagaaaa tattatatta cattccatat 13500 tgtagaattt ataccattga aagcctaact tgtttcctct aacttaataa tgaactaaaa 13560 aagtatttta atattttata aacaagtatc aaattaaaca atttttcatc ttcattgaag 13620 cataacatct cattaaatac caagttattc tcatttgcac ttctttcatg gaccatttat 13680 agatttagat ttaactttca tattgcatgt atattaacta aacatatttg tttcttctat 13740 taattttttt ttaatgtata caggtaaaag atttcaagtt caggagtgga tatgcaacca 13800 acaaaaatac ttttggctat aaatactttt ggcttcttct tcttcttctt gtaatattat 13860 ttttgataag gaatttggag accttgtttt ttggtacatg tgtacttgtt ttatatatgt 13920 tgaagttgga aaatatgctt gtaaatattt tgatacattt acaaatttgc gtattaatta 13980 actatgtaga cattagttct ttatcattat attattccca aatttattca atttcttttg 14040 gaagatgtag ttattaatat tgaagttatt gtttggtact ttataaataa tcatgcagcc 14100 aaaattatat ataacaggac atacaaaata tatcattcaa cagggggatt ttcaatatta 14160 ttatccacat aagatgacac tttttttagt gtcgaaatag acaaatgata ttttggccat 14220 tccttggcgc tagtgtaagt gttaacatag gtagatcaat aatgacgttt tttaacgtgt 14280 taatataaac caatcaacaa tgacgctgtc tagaagcgac atggttgcct gcacccattc 14340 cttgacagag gcggaaagga cgctttcgag aagcgtcatc gtatacattt attgacgcct 14400 aaaaagcgtc attattaccc ttttttctta tagtg 14435 // ID SHALINE4_MT repbase; DNA; EDCOT; 2282 BP. XX AC . XX DT 21-DEC-2006 (Rel. 11.12, Created) DT 21-JAN-2007 (Rel. 11.12, Last updated, Version 2) XX DE A putative non-autonomous LINE from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW LINE; repeat; Interspersed; Poly-A tail; SHALINE4_MT. XX NM SHALINE4_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2282 RA Shankar R. and Jurka J.; RT "SHALINE4_MT: A LINE element from barrel medic."; RL Direct Submission to Repbase Update (21-DEC-2006). XX DR [1] (Consensus) XX CC The LINE contains intact 3' end while truncated 5' end. A ORF is CC present coding for non-LTR reverse transcriptase. XX FH Key Location/Qualifiers FT CDS 310..1179 FT /product="SHALINE4_MT_1p" FT /translation="MAYTCLWPCVSDTISSAVAQSVPSATTQTVSGTTKSF FT LAALAGQNVIDDRPLPTPCIKGDALSIKICQDEYHKGXEDCKNALRGRLTL FT NKGDKPYSARDLSTKIGKLWKTTAAWKMVPLGKGYYDFHFDSADDLRKIWA FT AGTVNLKPGLLRFSQWTKDFKYHSQKQTHASLWIRLVELPQEYWRERTLKE FT IASAVGTPIDIDGPTRNRTFGHYARILVDIDLSKRAYDEILVEREGFAFKV FT EVQYERRPLFCHHCYSIGHNVTTCRWLHPQPPKDKNDRGKQIGCRGSSP" XX SQ Sequence 2282 BP; 595 A; 439 C; 510 G; 727 T; 11 other; shanmtgaag tttttcagtt gagaatttct acgctctgtt gctagggttt cccctaacat 60 gagtgccgtt tccacaaatc cttgctagtt tttcaattct acacgacata catagaaatc 120 cttcttatag acacgatgag cttgtacaat tgtcaaattt gaagctttac gtgattggtc 180 cctaaaggta caatgtcctt gcttgctaat tcatttttgt taatcaccca ccgtttgact 240 ttttgaatta gcccacctat tttgtaattg aatttgtcca attgctgaat caatcggtgg 300 atacatgtga tggcatacac gtgcctttgg ccgtgtgtgt ccgacaccat atcttcagca 360 gttgcgcaat cagtgccttc agcaactacg caaacagttt caggaacaac taagtcattt 420 ttagcagctt tagcgggtca gaatgtgatt gatgatagac ctctccctac tccatgcatt 480 aaaggggatg ctttgagcat caaaatttgt caggacgaat atcataaagg aktggaagat 540 tgcaagaatg cgttaagggg tcgattgact cttaacaaag gggacaaacc ttattctgca 600 cgtgatttaa gtactaaaat aggaaagctt tggaagacaa cggcagcatg gaaaatggtg 660 cctcttggca agggttatta tgactttcac tttgactcgg cggatgattt acgtaaaatt 720 tgggcagcag gcacagtaaa cctcaagccg ggtttgttac gattttctca atggaccaaa 780 gacttyaaat atcattctca gaaacagact catgcatcac tttggattcg tttggttgag 840 ttaccgcaag agtattggcg ggagagaact ttgaaggaaa ttgcaagtgc ggttggcact 900 cctattgata ttgatggacc gacaagaaat cgtacttttg gacattatgc aagaatttta 960 gtggacattg atttatcaaa gagagcatat gatgaaattc ttgttgaaag ggaaggtttt 1020 gctttcaagg tggaagtcca atatgagcgg agaccgttat tttgccatca ttgttactcc 1080 attggacata atgtcactac ttgtcgttgg ttacatccgc aaccaccaaa ggacaagaat 1140 gatcgtggga aacaaatcgg ttgccgaggc agctccccct aaaccatcta cagaacaatg 1200 atgtgggtgc ttccccttcg ttgttgctac cacaactcta cataggctat ttcgtcaaac 1260 tctttcagtt ttccactwca taatgttttt gacaaaattt ctcctgaaga gttgccacgt 1320 ctaygccagt gttagaggtt gtttcccctg ttgcgcacga tgacgtgcat tctgagggag 1380 tggagcagtt gcatcagaca tcgcgggagg tgttggagaa ccccacggtg gatgatgtta 1440 ctgttacgct ttctgatgat gtggaacaca atcattcgag cccrcgggag ctggtggaga 1500 gtcccaaggg ttcccatgag mgtgtaacac attcatcccc tgttgagcat tttgaggtgc 1560 atgaggtgtc tgtagaattt cagttcagac gaatacagtt gttgagcatg ttgacgtgca 1620 ttctggttca tgcggttctt tggtttcacc tgtggttatt gagcaacctc ttgttgataa 1680 tgttagcatg cccacgacaa aggaacaaga ggttgttakt ttacaacaac aagaggttca 1740 tcctagcaag aatattcagc atggtttaga tttgtgggaa agagttcgtg aatatgatga 1800 aagatcagct gaagaagact tcacgccggt tcttacaagg aagcagaaac agaaacttaa 1860 agtacaacaa gtcttggcaa agcagccttc taaaacccgt gctcggggtg atactcatcc 1920 gactgctcaa tgaattttct ctattggaat gttagaggcc tgttgattac tgtttggctt 1980 gcatctcttc ctgatgagtt gaatattgat ttctttagga tagatgtggt ttacctaatt 2040 acagatttcc ttaatctgtt ttttggttgt tttttttctg tttatttttc ttttctgttt 2100 tcttttgagg gttttggcct agtcccccct cctttgtaat tatttttccc cctttttttt 2160 aataaatttt tagagtttgg cggcatagga tggaggtttc tcggggtgcc aacctagttg 2220 ggatgtcgat gttgcctctt gatgtctgtc ctctctcctt gcttataaaa aaaaaaaata 2280 tt 2282 // ID Copia-45_Mad-I repbase; DNA; EDCOT; 4477 BP. XX AC ACYM01043826; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-45_Mad-I; KW Copia-45_Mad-LTR; Copia-45_Mad_. XX NM Copia-45_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4477 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1315-1315 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01043826; Positions 5240 764. XX CC Positions [1521-2018] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 2793..4475 FT /product="Copia-45_Mad-I_1p" FT /translation="MNVLPNKWVYRIKRKSDGSIERFKARLVANGFHQQEG FT LDYSETFSPVVTHATIRIILSVALHFNWPIRQLDVKNAFLHGSLNEEVYMR FT QPSGFVDPQFPSHVCRLRRSLYGLKQAPRAWFQCFSHHLEELGFQASMADS FT SLFIFCNGTNVIYLLIYVDDILVTGNNPAHISTLIHQLGRKFSMKDLGPLH FT YFLGMEITRTPTAMYLTQSKYILDLLKRTQMADAKPLSTPALPGRKLSLYE FT GEPLADGTTFRSIVGALQYLLFTRPDIAFAVNQVCQYMHSPTTTHWVAVKR FT ILRYLKATHDRGLVYKPSFLSLTAFADADYAGDPDDRRSTGGHCIFLGDNL FT VSWSSKKQRGVSRSSTEAEYRQMAYTAATLSWFRHIFCDLRLPLTPPKLWC FT DNISALGSGFQSSNFPPNPHLPAPSSIPSPTTAMGVAPVSPSSQRQIQPVH FT SMVTRSKDGIQKPNPKYALVSDVTNELVEPSCFTQANKSPEWRMAMAEEFN FT ALQSTGTWSLVPSHPSMNVLPNKWVYRIKRKSDGSIERFKARLVANGFHQQ FT EGLDYSETFSPVVT" XX SQ Sequence 4477 BP; 1067 A; 1219 C; 783 G; 1350 T; 58 other; gtcgaaatct ggtttccttt gttgatggaa ctagtaagtg tcccccagca ttgctgacag 60 atgaggatgg aaacatcact gacamagtca accctgattt cgacacttgg atacaacagg 120 atgcaactgt tatgtcatgg atcaactcct ycgtccatcc taccgtgctt gctgctttaa 180 ttgggaaaac cagctcccac tctgcctgga caacactacg tgatcgttay gcttctcagy 240 ccaccggtcg ccttctccar cttcgtagtg agttgatgaa tactcaccga ggtgwttctt 300 ccatttctgw awttttggat aaaattaatt gtctcgcaga taccctctct ctytctggtg 360 ctccygtttc cgactccgac atcgttgcca tcatcctcaa caacgttggt ccggcctatg 420 aaagtaccgt tgcttccgct caagcccgtg atgaggctat tacctacagt gctttggaag 480 ccctcctcct tggcgctgaa agacgacarc aaatacattc cgcrtttgrt actgacagtg 540 ggctcactgt ccttgccrcc gytygcaatg gcaaccgcgc acctgcatct tctcgaggac 600 gaggatcctc tactggcttc cgtggtcgta gtaacttcaa tactggtcgc ggctctacca 660 atcgccacta cagctcctca ccctctcacc aaggttccta ctatcaccaa gggtccaact 720 stmaccaagt atcccactcc cgcccacatg atgggattct tggcacctct ccttcccaag 780 gtacttttac tacaagccgg attcaatgcc aaatatgtaa tcgttatggt cattctgcga 840 ttgactgctt caaccgccta aatatgtctt atgaggracg tgtccctgca ccacgtcttc 900 aagcctttgc tgctcgtgct cctcctgctt ctgcaacagc ayctgccata caggaatggc 960 tgtttgactc cggggccaat gctcacatca ccaataatct wgctactgtt gcgcatcctc 1020 atccttatac tggcatggac caagtcaatg gagttgttgg tggcacaggt ttgcaaattt 1080 cacacatagg caacacttcc attcgtacac ctacctctac tttcacatta cctaatacac 1140 tactmtgccc taatgcatca accaatatta tttctatcca tcgttttact accgataata 1200 actgttctct maccttatat cccaactcat actgtgttca ggaactycac acggggagga 1260 tgcttttaca aggcccgagt agraatggat tctacccttt ttctggtgtt tcatcttcca 1320 ttaaaggcgt gtctgcattt ttaggaacta gagtgtccaa ttcaatytgg cactctaggt 1380 taggtcatcc atcttctcat attttgcaaa rtttggtttc taggaacaaa ttgcctatta 1440 aggrcgttgt mactagtrag ttatgtcact catgtcccat gggcaagagt cacaagttac 1500 cttttccatt gtctgtctct aggtcttcat ctcctttaca attggttcat tccgatgtat 1560 ggacttcacc ttctttttct atcaatggtt ttaaatatta tgtcgtrttt attgatgatt 1620 tttctcgcta ctcttggmya tatcccttwa aattaaaatc tgatgtyttt ctcacttttg 1680 tgtcctttaa gaaaytggtt gaaaacatgt tccacactac aattaaatcc tttcaaactg 1740 atggaggagg ggagtacgta aacaacaaat tcaaaatttt tttgactcaa catggcattc 1800 tacatcgttt tacatgtcca catcatcctg aacaaaatgg amtttccgaa cgtaaacacc 1860 gtcatatcgt tgaaactggt ctcacycttc ttgctcattc ctccttacca acttcttttt 1920 gggatgatgc tttccataca gcaaactatt tgatcaatcg tttaccsact aaagttctcc 1980 atgatgagtc tccctttcaa aaactgtttc aaaaatctcc tcaatatgat tttcttaaag 2040 tttttgggtg tgcatgtttt ccatttcttc gtccttataa tactaacaag ctgcaatttc 2100 gctccaaacg ttgcattttc ttaggwtatt cattaaatca acaaggttat argtgtttag 2160 atacgtccac aggtcgyatt tttttgtcac gccatgtcct atttgatgaa accaattttc 2220 catacaaaga atccatttct acamsgtcct catcctccca atcgtctatg gtactgaaca 2280 ttgacccctc ttctttccat tatccctcta ggaaccccat tttcccaact gtaccaccaa 2340 acccrcatcc gtccaactta ttccccatat tatctcaccc acctaaccct agtcctattc 2400 cctgcccttt accaccacat ccgcamcatc acatgcatcc cactatacca tccccccaac 2460 cwaaccctat ttcctctaat ttcccaccaa atccgcacct ccctgcccct tcttccattc 2520 catcccctac gactgcartg ggtgttgctc ctgtctcacc ttcctctcag agacaaattc 2580 aacctgttca ctccatggtt acacgctcaa aggatggcat tcagaagcca aaccccaagt 2640 atgctcttgt ttctgatgtg actaatgaac ttgttgagcc ctcttgtttt acacaggcaa 2700 ataagtctcc cgaatggcrt atggcaatgg cagamgagtt caatgctcta caaagcayag 2760 gaacgtggtc cctagttcct tctcatccct ccatgaatgt cctaccmaat aaatgggtct 2820 accgtattaa acggaaatct gacggttcca ttgaamgatt taaagcacgt cttgttgcca 2880 atggtttcca tcaacaagaa gggcttgatt acagtgagac gtttagtccc gtcgtcactc 2940 atgcyaccat caggatcatt ctctccgtgg cycttcattt taactggcca attcgccaac 3000 ttgacgtmaa aaatgcgttc cttcatggct ctttaaatga agaagtctac atgcgccaac 3060 cttctggttt tgtcgatccg cagtttccgt cacatgtatg ccgtcttcgy cggtccttat 3120 acggcttaaa acaggctcca cgtgcctggt ttcagtgctt ctctcaccat ctggaggagc 3180 tcggctttca agcctccatg gcagattctt cgctgttcat tttctgcaat ggaactaatg 3240 tcatttactt gctcatttac gttgatgaca tcctcgtcac cggtaataat ccagctcaca 3300 tctccacctt gattcatcaa ttgggtcgaa aattctccat gaaggacctt ggtcccttgc 3360 attatttttt gggaatggaa attacgagaa cgccaacggc catgtactta acacartcaa 3420 aatatatcct ggacctcctc aaacgaactc agatggctga cgccaaaccc ttgtctactc 3480 cagccctccc tggccgcaag cttagtttgt atgagggcga gcccttggcg gatggaacaa 3540 cctttcgaag tattgttggg gctctccaat atctcttatt cacacgtccg gacattgctt 3600 tcgctgtgaa tcaagtctgc cagtatatgc attcgcccac cactacacat tgggttgccg 3660 tcaaacgcat tcttcgctat ttgaaagcca ctcatgatcg cggtctcgtt tataaaccca 3720 gttttttgtc cctcacagca tttgccgatg ctgactacgc tggtgaccct gatgatcgtc 3780 gctccactgg tggtcattgc atatttctag gggataactt ggtctcctgg agttctaaaa 3840 agcagcgcgg cgtgtctcgc tcaagtacgg aggccgagta tcgccaaatg gcctacacag 3900 ctgccacctt atcttggttc agacacattt tttgtgatct tcgtcttcct ctcactccac 3960 caaaattgtg gtgtgacaat atcagtgcac ttggcagtgg cttccaatcc tctaatttcc 4020 caccaaatcc gcacctccct gccccttctt ccattccatc ccctacgact gcaatgggtg 4080 ttgctcctgt ctcaccttcc tctcagagac aaattcaacc tgttcactcc atggttacac 4140 gctcaaagga tggcattcag aagccaaacc ccaagtatgc tcttgtttct gatgtgacta 4200 atgaacttgt tgagccctct tgttttacac aggcaaataa gtctcccgaa tggcgtatgg 4260 caatggcaga agagttcaat gctctacaaa gcacaggaac gtggtcccta gttccttctc 4320 atccctccat gaatgtccta ccaaataaat gggtctaccg tattaaacgg aaatctgacg 4380 gttccattga aagatttaaa gcacgtcttg ttgccaatgg tttccatcaa caagaagggc 4440 ttgattacag tgagacgttt agtcccgtcg tcactca 4477 // ID SHACOP2_LTR_MT repbase; DNA; EDCOT; 263 BP. XX AC . XX DT 11-JAN-2007 (Rel. 12.01, Created) DT 02-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of SHACOP2_MT, a LTR retroposon from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; terminal; SHACOP2_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-263 RA Shankar R. and Jurka J.; RT "SHACOP2_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 72-72 (2007). XX DR [1] (Consensus) XX CC The complete intact element exists in very few copies. XX SQ Sequence 263 BP; 72 A; 58 C; 29 G; 104 T; 0 other; tgttagaata tagtatagat agaggctaaa cattgtaact atctaactag tcttaagctc 60 tagtctatca gattgtgaca tgtgtcacat atctctagct tatctcttgc atctatataa 120 actcttgtat ctctcagatt catttaatac aaagaatata tttttcctat tttctcttct 180 gtctctctct cttctctttc tctctcctct aacaaacttc tgtaacaaac ttcaaccttc 240 aaggttcatc aatggcggtt tca 263 // ID Harbinger-3N3_VV repbase; DNA; EDCOT; 347 BP. XX AC . XX DT 05-FEB-2009 (Rel. 14.03, Created) DT 05-FEB-2009 (Rel. 14.03, Last updated, Version 1) XX DE Harbinger-3N3_VV, non-autonomous DNA transposon - a consensus DE sequence. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW PIF; TIR; MITE; mPifvine-3.3; Harbinger-3N3_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-347 RA Benjak A., Boue S., Forneck A. and Casacuberta J.M.; RT "Recent amplification and impact of MITEs on the genome of RT grapevine (Vitis vinifera L.). submitted."; RL Repbase Reports 9(3), 710-710 (2009). XX DR [1] (Consensus) XX CC Harbinger-3N3_VV (mPifvine-3.3 in [1]) is a non-autonomous DNA CC transposon of the MITE type. Unlike the Harbinger-3N1_VV, this CC element is not a deletion derivate of the autonomous CC Harbinger-3_VV but it has the same TIRs as Harbinger-3_VV. CC Individual copies are >80% identical to the consensus sequence. CC There is a number of copies that are less conserved. TIRs are 18 CC bp-long and flanked by 3 bp-long TSDs. There are approximately CC 600 conserved copies present in the genome. XX SQ Sequence 347 BP; 136 A; 27 C; 35 G; 142 T; 7 other; ggtggtgttt gttttttttt tacttaadtc taaatavaah ttaatttcac ttaactctaa 60 ataaaattta tagtattaag tattaabttg tttgtttttt attattttat ttctattaag 120 tattaattat taataggatg aagaatgtgt taagattdtg ttttggttat tkcaaaaagt 180 tatttttagc attcaacaaa agctaaatat ttgccttttc ctattcatat aaattattta 240 acagaaatag taataaaaaa aaaagttaaa aacaaataat ctaaagttgt atttakagag 300 tgaaattaaa ttgtatttaa cattaagtta aaaaaacaaa caccacc 347 // ID SHALINE20_MT repbase; DNA; EDCOT; 4336 BP. XX AC . XX DT 24-JAN-2007 (Rel. 12.01, Created) DT 24-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A LINE element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; retroposon; KW Interspersed; repeat; Poly-A tail; ORF; SHALINE20_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4336 RA Shankar R. and Jurka J.; RT "SHALINE20_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 96-96 (2007). XX DR [1] (Consensus) XX CC The element has 5' truncated end while the 3' end is well CC conserved as well as the central domain is very well conserved. CC The element has a single ORF present. It has domains for reverse CC transcriptase and RNAse. Like other L1s, it too ends with a well CC conserved poly-A tail. XX FH Key Location/Qualifiers FT CDS 3085..4233 FT /product="SHALINE20_MT_2p" FT /translation="MXKMINWFGNTSSTGDLSLKEAYQFKYTTGQNINWAK FT NLWSPDIPPSKSLXVWRXMHNKLPTDDNLXHRGCNLPSMCSFCQAYEETTF FT HLFFECSFALKMWXWLASILNXSLIFNSPMDIWNILERNWSPQCKVVIKAC FT IINIFNTIWFXRNQIRFQDKMIHWRTAINIIISKVSLSGNITTKAAAANML FT EFTILKAFNVNINPPRAPIIKEVIWTPPILTWIKXNTDGASTKNPSRASXG FT GIFRNSEGVCLGGFAQFLGNANALYAELFAAMRAIEIAASMEFSNVWLETD FT SQLVILAFKSKSIVPWSLRNRWNNCIQFTHRMRFYGSHIYREGNICADRLA FT NFGLSLSSSELFWFDSIPDFIRREYNRNRLGLPNFRFVTF" FT CDS join(693..1610,1614..2375) FT /product="SHALINE20_MT_1p" FT /translation="MVRYLFFITCSTLIKXXSDHFPLLFXFKTVXTPFVSQ FT FKFLKMWTLHDDCRNLIQDSWNTNVVGCPMFXLNQKXKSLKQKLKIWNKTV FT FGNVHMLVXEAEQKLISIQDXIDINGVTDXLLDQXKXAQIALENALXKEET FT FWKEKSKVXWHSHGDRNTKYFHRLTKIKNTSKLITSIIDGDXMITDPDQIS FT THIINYFKNIFSTNYSVQDLQVDDLVDEXIPNLITDDMNNLLTMLPTHEEI FT NHAVFDLNKDGAPGPDGFGASFYQTYWDIVKKDVINAVLEFFNKDWILPNF FT NANTIVLIPKIPDASVAQYRPIALANFKFKIISKILADRLAQIMTNIISTE FT QRGFIQGRNIKDCICLTSEAINXLHKKSFGGNLAFKVDISKAFDTLEWKFL FT LKVLSSFGFNDKFCNWINTILNSATLSIYVNGKLNGYFNCKRGVRQGDPLS FT PLLFCIAEDVLSRSISKLVDQGKIELIKGTRSVQVPSHSLYADDIMIFCKG FT KLSSIHALMDLFNTYAQASGQIINPSKSTVYSGSISDXRINQIXNLIGFNK FT GSLTFYLSWSSYF" XX SQ Sequence 4336 BP; 1310 A; 685 C; 743 G; 1518 T; 80 other; gtcatttcaa aaggcactaa gaaggcgcaa aaagctctca agagcagtta cattaccaga 60 tcaaaggttg gaacctccaa accttcccaa tgaagtgcct cttctggaat ttgaggggat 120 tagctaactc cccaactaag ttagcactta aaaaactttt aattttgcat aggcctgatt 180 tatgctttat tgctgagccc tggatgcata ttgacaattt ttctaagctt tggttggata 240 gattgggaat gaaagttttc tgtgttaatg atagaggaaa tttgacacca aatctgtggt 300 gcttttgctc taaaacctta acccctacac ttattaatat ggatgatcaa catattacta 360 ttcaaatcac cctaaatgcc atgtgtttta cgttatctgc aatttatgct tcaaacagtt 420 acatgaatag gagggattta tggcaaactg aaactaatca aaaaatataa tgctccatgg 480 tgcttcatcg gagacttcaa tacaattttg ggggcccatg aacatagggg twccawtcgt 540 cctgctagwg ccatgaaaga ttttctagat tggtcagatw ctaatwatct cattcatctt 600 cctactagag gagckcagtt tacatgggcc aatggaagag gaggtagaag gtwcatagaa 660 agaaggcttg atagagcaat ttgtaatcaa gaatggttag atatttgttc ttcattactt 720 gytccacttt aattaaamtt argtcagacc attttcctct cttgtttgas tttaaaactg 780 tgmcaacacc atttgtttct caatttaaat ttctyaaaat gtggaccctt catgatgatt 840 gtagaaatct gattcaagat agttggaata cnaatgtwgt wggatgtcct atgtttrttc 900 ttaatcaaaa gytcaartcy ctgaaacaaa aactgaagat ttggaayaag actgtgtttg 960 gcaatgttca tatgctkgtt aragaggctg arcaaaagtt ratatcyatt caagacsaaa 1020 ttgacatcaa tggtgttact gatgmtcttc ttgatcaasa aaaaratgct caaatagctt 1080 tagaraatgc tttamacaaa gaagaaactt tttggaaaga aaaatccaaa gttncgtggc 1140 actctcatgg ggatagaaat accaaatatt tccatagact aaccaaaatc aaaaacacct 1200 ctaaacttat cacttccatt atagatggtg atgamatgat tactgatccg gatcaaatct 1260 caactcatat tataaattat tttaaaaata ttttttcaac taactattct gtgcaggatt 1320 tgcaggttga tgatctggtt gatgaagyta ttcctaattt aataactgay gatatgaaya 1380 atttgctcac tatgcttcct actcatgaag aaattaatca tgctgttttt gatttgaaya 1440 aggatggtgc ccctggtcca gatggwtttg gtgctagttt ttaccaaact tattgggata 1500 ttgttaagaa ggatgtcatc aatgcagttt tagaattttt taataaagat tggattcttc 1560 ctaatttcaa tgcaaacact attgttctta ttcctaaaat tcctgatgca tagtcagttg 1620 ctcaatatag accaatagct ttagctaatt tcaaattcaa gattatttcc aaaattctag 1680 cagataggct ggcacarata atgacgaata ttatttctac tgagcaaaga ggttttattc 1740 aaggaaggaa catcaaagat tgtatttgcc ttacttcaga agctatcaat sttcttcata 1800 aaaaatcttt tggaggaaac ttagctttca aagtagatat ttctaaagct tttgacactt 1860 tagaatggaa gttccttcty aaagttttaa gcagttttgg ttttaatgat aaattttgca 1920 attggattaa tactattcta aactcagcaa ctctatctat ttatgtcaat ggtaaactaa 1980 atggttactt taattgtaag agaggagtga gacagggtga ccctctatct cctcttcttt 2040 tttgcattgc tgaggatgtt ttaagcagaa gcatttctaa acttgtggat caaggcaaga 2100 ttgagctcat caaaggtact agaagtgtyc aggttccctc tcactctctt tatgcagatg 2160 acataatgat tttttgtaaa ggaaagttat cttcaattca tgctctcatg gatcttttca 2220 atacttatgc tcaggcttct ggccaaatta tcaatccttc aaaatcaact gtttattctg 2280 gttctatttc tgatkctaga attaatcaaa twrctaatct tattggtttt aataaaggtt 2340 ctcttacctt ttacttatct tggagttcct atttttaaag ggaaaccaaa aagatctcat 2400 ttgcaaccta ttgctgataa gattaagtct aagctatcag cttggaaagc ttctctgcta 2460 tctattgcag gtagagttca atctagttaa atctgtcatt caaagtatgc ttattcatac 2520 tatttctatt tattcttggc ccaattcctt gttcaaagat atggaaaaat ggataagaaa 2580 cttcatttgg agtggtgata tttcaaaaag gaaactggtr actgttgctt ggaaaaaart 2640 ttgtaaacct tttgatgaag gtggwttagg gatcagatct ttgtatactc taaatgaagc 2700 aactaatctg aaactttgct gggatcttat gcattctaat gaasattggg caattcttct 2760 yagaagtaga gttttaagag ataggaaagt cattwatcat catattttct cttctatttg 2820 gagtagtatt aaaacwgaat ttaatattat tatkgataat tctacttggc tcmttggtaa 2880 tggtraaaat attaattttt ggactgatac ttggtgtgga gaaayctatt gcttctttgc 2940 ttaattttcc agatattgtt catagcactc taacaactag ggtttctgat tacattaata 3000 attctcattg gaatattcct caatctatcc tgrattcttt ccctaatttg agtcaacttg 3060 tcanacaagt tactmttcct atggatgaka aaratgataa aytggtttgg aaacactagt 3120 tcaacaggtg atctatctct yaaagaagct tatcagttca aatatactac tggtcaaaat 3180 attaattggg cmaagaattt atggagtccg gatatccctc cytcaaaatc tctgytkgtt 3240 tggagaytca tgcataacaa actccctact gatgataacc taaygcatag aggttgtaac 3300 ctgccttcaa tgtgctcttt ttgtcaggct tatgaggaaa ctacttttca tttatttttt 3360 gaatgctctt ttgctttgaa aatgtggart tggttagcat ctattctcaa tatrtcatta 3420 atmttcaatt ctccgatgga tatttggaat attttagaaa gaaattggtc tcctcaatgt 3480 aaggttgtta ttaaagcttg cattattaat atyttcaata ctatttggtt tagmaggaac 3540 caaattagat tccaagacaa gatgattcat tggagaacag ctattaacat tatcatttct 3600 aaagtctctt tatctggaaa cattacyact aaagctgctg ctgctaatat gttggaattc 3660 acaattttra aagctttcaa tgttaacatc aatcctccta gggctcccat aatcaaagaa 3720 gttatttgga ctcctcctat tcttacttgg attaaggkta acactgatgg tgcatctacc 3780 aagaatcctt caagagcatc tkctggtgga attttcagaa actctgargg tgtttgttta 3840 ggtggctttg ctcaatttct tggtaatgct aatgctcttt atgctgaact gtttgctgct 3900 atgagagcaa ttgaaattgc tgcatcaatg gaattctcca atgtttggtt ggaaacagat 3960 tctcagttgg tgattcttgc tttcaaatcc aaatctattg ttccttggag tttaagaaat 4020 aggtggaaca attgtattca gtttacccat aggatgagat tttatggttc tcacatatat 4080 agggaaggga atatttgtgc tgacagactg gctaattttg gtttatcttt atcttcttct 4140 gagttgtttt ggtttgatag cattcctgac tttattagga gagagtacaa taggaatagg 4200 ttgggtttgc ctaattttag gtttgtcacc ttttgaaaag gttttggttt ggtccccctt 4260 ttcttttttg tacttctttt ctctttaata tattgattag atgctctttg catctctttc 4320 aaaaaaaaaa aaaaaa 4336 // ID EGLN1_SM repbase; DNA; EDCOT; 405 BP. XX AC AB016142; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 23-SEP-2007 (Rel. 12.1, Last updated, Version 2) XX DE Solanum melongena LINE retrotransposon EGLN1_SM, endonuclease DE region. XX KW L1; Non-LTR Retrotransposon; Transposable Element; endonuclease; KW LINE; EGLN1_SM. XX NM EGLN1_SM. XX OS Solanum melongena OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-405 RA Noma K., Ohtsubo E. and Ohtsubo H.; RT "Non-LTR retrotransposons (LINEs) as ubiquitous components of RT plant genomes."; RL Mol. Gen. Genet 261(1), 71-79 (1999). XX DR Genbank; AB016142; Positions 1 405. XX SQ Sequence 405 BP; 162 A; 53 C; 76 G; 114 T; 0 other; ctggaatgca agaggtctaa ataagatata taaataaaag aaacttaaag ttgtagtttg 60 ataaagtaag ccttgttggg attatagaaa ctagagttaa ggagtacaac agaaagaata 120 taataagagc aataacactt agatgggaga tacttcataa ctatgattca gcactcaatg 180 gtagattatg ccttatatag gatgggaatg aatataaggt ggcaaaaata aaaaataccc 240 acagttacta tactgtttga tcactgatag agttaaagat caataacaat tacttactat 300 tatatatgaa ttcaacatta ttgagctgtg tataaatttg tagcgggaac tgaatgaact 360 aacacacaaa attgatcaac cttggctcgt cctcggggac ttcaa 405 // ID HAT-N6_Mad repbase; DNA; EDCOT; 1215 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-N6_Mad. XX NM HAT-N6_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1215 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1628-1628 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~88% identical to the consensus. 8-bp TSDs. The consensus shows CC similarity to HAT-N5_Mad. XX SQ Sequence 1215 BP; 331 A; 219 C; 244 G; 421 T; 0 other; tagggatggg caaaataccc atgggtttgg gtaaccgcgg ttacccgccc atttaaagtt 60 cacggttacg gttatgggta accgtttaga cgaacaaacg gttatgggta taaccgttta 120 tccgtgaaat ttaaatgggc ggttatgggt attacccgcg gttataacgg gtatccatcg 180 gttatgggta ttatccgcgg ttataacgga tatccattta cccatttaat ttaatatatg 240 taaaattaaa aaaaaaatta aaaaccttaa attttcaatc tctccgccag agtctgaaac 300 gccccgtccc cgctcatctc tccctcctcg ctgccctctc tcatctccgc cgccctctct 360 ctcatctacg ccgctcatct ctctctctct ctctctctct ctctctctct ctctcggttt 420 ctctttggtt tcagtttcca tattttcttg cattttctca gaaaccaaac agggcatcaa 480 atttaatttt tctttttaac tcttattcgg tgctgggttt tgattgctca ttatttcaag 540 tttcatgaat tgggtttctc caagaattgc gatattttta tgaatttttg tgctttagca 600 attgatgaag cttgaatttc tatataattg attacgtgtt aaagaataat catctttttt 660 ttttgtcaat ggagaaaaaa gggtcttgat atgattttta gatgttcaat ttatgctggg 720 cagccttcta actttgtatt ttataggatt aagtattatg ttttctatgg ttgatgagct 780 aaaatgtcga aaaaatgggt cttcgttaat gttgtatatg ttgtgaaaca aaatgcagtg 840 tatgactgtg atgtttagtc gtctatcgag ccttcgaaat ctccgaattt tgtaattttc 900 aagttgttaa aaaaaaaaca tgtagacggg tgaaaaaatg ggtaaatggg taaaaaaaga 960 taaacgggtt caaaaacggg taaatggtta tggttaaatg ggtaaacggt tatggttatg 1020 gttaaatggg taaacggtta tggttaaatg ggtacacggt tatgggtatg gttaaccatt 1080 tataaacggt tatgggtatg ggtataaccg tttatgcaat tacccaacgg gtaaacggtt 1140 atgcgggtat gaacataaac ggttatgggt aaataaccgc ggttacccgc ccgccataac 1200 cattgcccat cccta 1215 // ID Copia16-VV_LTR repbase; DNA; EDCOT; 774 BP. XX AC AM460200; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia16-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-774 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-774 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 710-710 (2007). XX DR Genbank; AM460200; Positions 16806 17579. XX SQ Sequence 774 BP; 242 A; 107 C; 145 G; 272 T; 8 other; tgttagatat ttttcttcta atgtccyaca tgatacgtgt atggctttag tcttttattt 60 aaatagagtt atctaatcta atctctaaaa ttttggttat acaattagag aagtagtttc 120 ctattttttt gtttactctt gactttgatg ggaagtggag tagcggttac taaattgttg 180 gcagttatca aaaaggaaat gggtcatctc tctacccatt taagtaacat tacacagttt 240 ccatcttttc gtgtgtggta tgtaattttc attttgaaag aaaaagggtt aagagagaga 300 aaccgatatc ctggagaatt ctacaatttt tcagatcaag aattaaatga aagagattgc 360 tatggattta ggtatgttat ttatgtttgt gaaaatcatg atagtcaaga tcttggaatt 420 tataaagcat taagtttaaa gtttcatttt atttataaca tgtggtatca aagcaaggtt 480 aagactttca tgattttcca ttatgatcta tttgttggaa tcaattattt ggggnnnnnn 540 ntttttctta atattttcag taaccaaaca cagcaaaata gaaaccacct gaattttcct 600 caaatgggcc attttggcat ccttgaatgg atgcacttgt atttcacaat gataagcagc 660 attagcagta gtgaaaagct ggtccccatt aggatattgg acaacatgga gaagctggtc 720 cccattagga tattggacaa catggagaaa acggattcac acgggatgca ctca 774 // ID BoSB5C repbase; DNA; EDCOT; 162 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB5C. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-162 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 162 BP; 32 A; 45 C; 49 G; 36 T; 0 other; aaccaagcgc tcgtagcttg gtggtaaagg aggtacagct gtactgcccc ccacccgggt 60 tcgagccttg gccacaacgg atttaacatc ccttccgttg gggcgctgga cccctttcgg 120 ggggatagtt gggaatgtgg ctgcccagat accagagtta tc 162 // ID Helitron-2_Mad repbase; DNA; EDCOT; 4037 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Helitron family DNA transposons from the apple genome. XX KW Helitron; DNA transposon; Transposable Element; Helitron-2_Mad. XX NM Helitron-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4037 RA Kojima K.K. and Jurka J.; RT "Helitrons from the apple genome."; RL Repbase Reports 10(10), 1643-1643 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >85% identical to consensus. This consensus can be incomplete. CC ORF can be broken. XX FH Key Location/Qualifiers FT CDS 900..2135 FT /product="Helitron-2_Mad_1p" FT /translation="MLTNSIFRREAKLIRKIVDENIREWLPSTNELHVAKH FT PVGIDSRVQDIISYLSSGGSNDVLMVGIWGMGGLGKTTAAKAIYNQIHHKF FT QFKSFLADVXDATSKHGLVYLQKKLVSDILKQKPXISSVDXGIGLIKQXLR FT RRRVLVIXDNVDKVEQLNAIAGNRDWFGPGSRIIITTRDERLLXQLRVDKX FT YPAREMNEEEALELFSWHAFGNSXPDEGYLELSKKVVSYCGGLPLALEVLG FT SSLIERPIAEWESQLEKLERIPEGEIIKRLRISFXGLDDTQKAIFLDISCF FT FIGXDKDYVAKILDGCGFSATIGISVLRERCLVTVERNKLNMHDLLREMAR FT VIISEKSPGHPGKWSRLWNRQEVTXVLTNKSVSTFPIKFRINASYMKSIYV FT THVCLLYIKQHSRVNIXA" XX SQ Sequence 4037 BP; 1212 A; 764 C; 861 G; 1149 T; 51 other; caaacacaac cgttgccatt ttttcagtct gtgatccgaa ccactgctgt gccataacgg 60 tggataccgc catgacagcc cacgaagcct cctcttcgtc ctcctccaag tccaaactct 120 ggaagtacga cgtgttcttg agcttcaggg gtgaagacac gcgcnatggc ttcacgggcc 180 acctccacgc ggcattaaaa gacagagggt accaggtctt tatcgatgag gacgatctac 240 aaagagggga agaaataaaa gagaaactgt ttcgtgcaat cgaagagtcg aggatctctg 300 tcattatctt ctcaaagatg tatgcggatt cgagttggtg tcttgacgag ctggtgaaga 360 tcatggagtg cagatacaaa ctggggcgac atgttttgcc aatattctat cacgttgatc 420 cttcgcatgt caggaagcag gacggagatt tagccgaagc atttcagaag cacgaagagg 480 acatccgtga agaaaaagat gacaagaaac gtgaagctaa acaagaaagg gtaaagcagt 540 ggagagaggc tctcacagaa gctgcaaatt tgtctggcca ccatcttaaa atcgctaaca 600 atgggtaatc attcagctgc ttttcaagat ttgacagttt tagtgaatga cttaatctct 660 caattaacat gcttaattaa tacaccttaa tctctcataa acctaaaccg taattggagt 720 ttaattaata caccttaact tttatttatc aatgaattct tttattcaag ttattaaaat 780 cacatactag ctagtagcta gttagtgtat atatatatat atatatatat tataggaaga 840 aggaaagaaa attgtttatg tactgatagc tcctaccgag ccttcattga gtcccactaa 900 tgcttacgaa ttcaattttc aggcgcgaag caaagcttat taggaaaatt gttgacgaga 960 atattcggga atggcttccc agcacaaacg aattacacgt ggccaagcac ccggttggaa 1020 tcgattctcg cgttcaagat attatcagtt atctttcaag tggtggatca aatgatgttc 1080 tcatggttgg aatttggggg atgggtggat tgggtaaaac aacagctgcc aaagccattt 1140 ataaccaaat tcatcataag ttccaattca aaagtttcct tgccgacgtt ngcgacgcta 1200 caagtaaaca tggtctggtt tatttgcaaa aaaaacttgt ttctgacatc ttgaaacaga 1260 agcctnaaat aagcagcgtt gacgnaggta tcggtctgat aaaacaacan cttcgacgta 1320 gaagggtact tgtcatcatn gacaacgtag ataaagtgga acaactgaat gcaatagctg 1380 gaaatcgtga ttggtttggt ccaggaagta gaattatcat aacgacacga gatgaacgtt 1440 tactaaanca actgagagtg gacaaganat atccggctcg ggaaatgaat gaagaagaag 1500 ctcttgagct ctttagttgg catgcctttg gaaatagttg ncctgatgaa ggatatcttg 1560 aactntcaaa gaaggtcgtt tcttactgtg gaggtttgcc gctagcgctc gaagttttag 1620 gctcttctct gattgaaaga cccatagcag agtgggaaag ccaattggag aaattggaaa 1680 gaattcctga aggagaaatt ataaaacgac tcagaataag ctttganggg ctagatgata 1740 cacagaaggc tatattcctt gacatatctt gtttctttat tggannggac aaggactatg 1800 tcgcaaaaat attagatgga tgtggntttt ctgcaacaat aggaatcagt gtcctccgtg 1860 aacgatgcct tgtaactgtt gaacggaaca agttgaatat gcatgatttg cttcgagaaa 1920 tggccagagt aatcatttct gaaaaatccc ctggtcaccc tggaaaatgg agtaggttgt 1980 ggaaccgtca agaggtcacc gangtgttga caaataaatc tgtaagtaca ttcccaataa 2040 agtttcgnat taatgcatcc tacatgaaaa gcatatatgt aacccacgta tgtctattat 2100 acattaaaca acattcacgt gtaaatataa ncgcgtaggt gatttcgcct aatgataata 2160 atacatgtaa atatacgcaa ataatccntt tcttacncat gaatataacc ttttgttaac 2220 agggaactga agaagttgaa ggacttgctc tagatttgcc tatttgccaa gctctaaaaa 2280 atggctagtt tcagtacaga agcatttgcc aatatgaaga aactgagatt gcttcggctc 2340 aacnacgtan agctcantgg agaatacaaa catcttccca aagagttaat atggttgcgc 2400 tggcgtggat tccctttaaa gtccatacca gatgactttt ttaatcaacc aagactagtt 2460 gttctagaca tgcggtncag caaactggta caagtttggg agggttccaa ggtacaatcg 2520 attacacatg atgatgttct gtttctattt gtttttggat ttcctttttt tttttatgac 2580 atattccttt tggatattaa tttcaatttt cctttggttt tgtgcaacag tcgctcgaga 2640 anttgaaaat ccttgatctc ggtcgttccc gttnnttaaa aaaatcaccg gacttttcac 2700 gactcccaaa tctcgaagag ttgatattgg aaggctgtnn gagtttgtcc gagattcacc 2760 cctccatcgg tcaacttaaa agactttctt tggtgaacct taaannntgc ganaagctta 2820 gttctcttcc aggggatttc tataagtcga aatctgttga gactcttctt cttaatggct 2880 gttcagaatt cagagaactg cctgagggtt taggggagat ggtatcattg agaatacttg 2940 aagcagntnn tacagccata agacaagtac caccttccac agtaagattg aagaatctca 3000 ctcgtttatc cctagaaggt gcgaaattag ccatgacgca atcccnacga tcttgggagt 3060 ctaatttctt tacaagattt ggatcttcga gggaatgatt ttcgtaccct acccagcctc 3120 agtggtcttt caaagctcga aacnttgngg ttaaatgant gcnnnaacct tcgtacaatc 3180 cccgatttac caacaaattt gaaatttctg natgcgnntg gttgccctgc attggaaaca 3240 atgcccgact tttcggaaat gtcaaatatg agagaactga atgtaagtga ttcgcccaaa 3300 ctcactgagg ttccaggtta ggcttggata agtcattaaa ctccatgacg tngattgata 3360 tgaangggtg caccaatctc acagctgatt ttaggaagaa catcctacag gtatctctct 3420 ctctctctct cattgccttc ctatcgcgca cacgcacaca caaacgcaca tgtacacgta 3480 tttgacacta tatacattgt atatatatat gacacttgca ttgtatatat agggatggac 3540 ttcttgcgga tttggtggca ttttnctcaa tgggaattat gttcccgatt ggttcgagtt 3600 tgtcgacgac ggcaataaag tcagttttga tgttcccccg ngtgatggtc gtaattttga 3660 agggctgact ctgtgcttct tgataaaacc cgaaattana agtgaacttg ccattactgt 3720 tataaatagt accaagcgta ctaagttgcg ggcctctagg cagggatgct tggatacgct 3780 agagaggatt atctttggca gggacaatta tcgaacgata agctcaattt gcaaggcggg 3840 gacaaggttg ttattcattt tagggncatc gaagagaaca ggggttaaat ctagtatggg 3900 acaaaccttt gaaggaaaat acgcatgatt tggacattta tagatatgaa tctggaccac 3960 atccggatcg gtttatgatg agtcgagtcc aggaccaagc catgacgcat ctgataatca 4020 tcccactaat caaatga 4037 // ID L1-4_Mad repbase; DNA; EDCOT; 6391 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-4_Mad. XX NM L1-4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6391 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1808-1808 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 1890..6041 FT /product="L1-4_Mad_2p" FT /translation="MKVLFWNIRGIGNDDSRTELSNICRLHHPDLVCIAEP FT MVTFNSISAAYWDSLNLSALTFNSRGTLAPNLWLLTSSACADPLVISISDQ FT QVTVRCTFDHIPSQFTFVYASTSPIKRRDLWADFISLRPQTQVPWMAIGDF FT NAILGAHEQMGGGRPSQASCAEFSNMSDTCNFTHLNTSGAAFTWSNGWRSR FT GRTERRLDRSLCDISWFDSWPHSNCIALPKVVSDHNPLIFSGSRVLSSGHR FT PFRFQSMWVQHPSFRETVTHCWRNTVVYGCPMFIILQKLKALKTCLRQWNF FT SVFGDVHNRVANARHNLSMIQQRISTEGINNDLFEEEIVAKTTVMESLQMQ FT EAFWKDRARVKWLTKGDRNSSFFHAYARIKSSSSRISCILDGNNLLTDPLA FT IENHIVNFYQTLFGSSFTPSGIDEVCEVIQPMVTDSENDLLSALPTDEEIK FT EAVFSLSASSAPGPDGFPGFFYHHCWDIVGFDVIQFVKQFFQSNWLYPNAN FT SNFLVLIPKVEDAISMTHFRPIALANFLFKIIPKILAVRLSHVVQRIISPH FT QAAFIPGRRITDCIGLVSECFNVLDKKTRGGNMGVKVDIAKAFDTLDWSFL FT LRVLTNFGFSTCFIDWVSTILRSAKLSILINGSPHGFFSCSRGVRQGDPLS FT PLLFCLAEEALSRGLSRLQLDGLTKPTFAPRGCISPSHVLYADDLFIFCRS FT DGVTLRNLQGFFDRYSRASGQFINKAKSTFYLGSTSRHRKAVVESYLGFKE FT GKAPFVYLGVPIFCGKPKRSHLQALADKAKAKLTGWKGKLLSMAGRVQLTQ FT SVFQSMLLHSFSVYKWPSSLLRPLSRCARNFIWSGDVTSKKSVTVSWRQIC FT APKNEGGLGLRDLGSLNTTALLKLGWLIITTDSPWSIYLRERFKLHGRLYS FT CSYKRSSIWPGIKSILHILFQNCRWVIGNGSTTSLWVDKWLDKPIVDVVGA FT TEIAXSLSRTKVSNIIRMGKWVIPSIFSSTFPDLTKEILEMPLPIDEDKDV FT LIWEVSTSGVFSFSDGYEIVRHRFPVKSWASIIWRPFIPPRYSILVWKILF FT NKLPTEDQLQRRGIPLAPICQLCHKNSESIDHLFSSCEFAQRAWRWLATQF FT GTIIPPTGSLSDLWLVFLSKRFSPHLRNVWLASGFFLLMAIWKMRNKVKFE FT GKPPSFSRLCRSTSAWIRQVGALTPGHVRGILDRQLLVSLGISPNSCKAPS FT IVPVLWHPPPFSWVKVNTDGLAKGNPGPAACGGVFRDSAGYFLGGFSLSLG FT HRTSFYAELHAVILAVELAHARGWQNLWLESDSSSVISCFASGSFSPPWSL FT QTRWNNCTLRLQNMVFRCSHIFREGNVVADKLANLGLLSSSLVWHSTPPIE FT ILPPLHSDFLGMPTYRFVSSS" FT CDS join(268..288,292..1890) FT /product="L1-4_Mad_1p" FT /translation="MVLTTLNIIMGTNIVCPWGFLAETVMPTTNMPPAQPI FT LKARTFASVVSIPIEDVHLSQLPTPVVRGDKTYVKISEDLYQEQLKLFQNN FT LLGRLLLKKGSTPMKTGALKSCLEDAWRPTAPWNLVPIGKGYFDIHFNKED FT DMRRAWGGGTCTLATGLFRLSKWTPDFKPGDVLPQTHAQVWIKIFGLSQEY FT WHPRHLMEIARGVGTPLQLDSATRERQYGYYARILVDVNLADDLPTSLMVE FT RESHGFPVEVVYENLPPKCSHCGLIGHLANSCRQLKQMSRGRSRSRTRKGG FT NMGDNKTGDHSRSQLHMEYRPKKDTTIPVNVFCGSHASEPLQQVDQLLPAG FT IEAADDGNXEPILQSPLGTTPTVSGNVIPETDTADTHIGIQSPGISHISNS FT MTGSLSPDGSHPQNGLSYGQHLGNTNVPNNLGPHDLCDDSSTPPGFEQVET FT VAQNSQQLGNTDVPNNFGMQDPHDNHSIPPGFEHVATLAKDVIDIVNHIEG FT CDMDGFTPVLSNSQRKKQKQLANLNQPSDKPYPSRVRGIPARYK" XX SQ Sequence 6391 BP; 1482 A; 1418 C; 1362 G; 2126 T; 3 other; catgaggggt acctccgcct cactctcact actcagtctt ggaactcagt aaggtgcctt 60 gtacctgttc gacgaattgc cccagtcaat ctgaaagctc tcttcggtac tagcacctcc 120 tcctgccgga agcttgatct gcctctggtt gcttggctgt ggtgccttgt acctgctcga 180 cgaattgctc cagagaatct gcgttttttt tttttttttt tttttttttc agggtgccca 240 aggttattct gcgttcaacc ttgctttatg gtgttgacaa ctctaaactg aattatcatg 300 ggcacaaata tcgtttgtcc atggggtttt cttgcagaga cggttatgcc gacaactaat 360 atgccccccg ctcaaccaat tctgaaggca aggacttttg cttctgtggt ttccatccca 420 attgaagacg tccatctcag ccaacttcca actccggttg tgcgtgggga caaaacatat 480 gtcaaaatta gcgaggatct ataccaagaa cagttgaagt tgtttcaaaa taatctcctt 540 gggcgtttgc tcctaaaaaa gggttctacg ccaatgaaga ccggtgctct aaaatcttgc 600 ttagaagatg catggcgccc tactgcacca tggaacctgg ttcctatagg taaaggttat 660 tttgatatcc atttcaataa ggaagatgat atgcgacggg catggggtgg cggtacgtgt 720 actcttgcta ctggtttatt caggttatca aaatggacgc cagattttaa accaggtgat 780 gttctccctc aaactcatgc tcaggtatgg attaaaattt ttggtttgag tcaggaatat 840 tggcatccta gacacttgat ggaaattgcg agaggggttg gcactccctt gcaactagat 900 tcagctacaa gggaaaggca atatggttat tatgcacgta tattagttga tgtcaatctt 960 gcagatgatt tacctacatc tcttatggtt gaaagagaaa gtcatggctt cccggttgag 1020 gtggtttatg aaaatttacc gcccaaatgt agtcactgtg gtttgatagg gcacttggct 1080 aatagttgca gacaacttaa acagatgtcg agaggtcgtt ctcgtagccg gacgcgaaag 1140 ggtggtaaca tgggggacaa caaaaccgga gatcactctc gcagtcaact gcacatggaa 1200 tatcgtccca aaaaagatac aacaataccg gttaatgtct tttgtgggtc acatgcttct 1260 gaacctcttc aacaggttga tcaattgttg cctgcaggta ttgaggcagc ggatgatggt 1320 aatgmtgagc ccattcttca gtctcctctt ggaacgacgc caactgtttc tggtaatgtc 1380 ataccggaga ctgacaccgc tgatacgcat attggtattc aatcccctgg gatttcgcat 1440 attagcaatt ctatgaccgg atcgctgtct ccagatggat cacatcctca gaatggtctt 1500 tcttatggtc agcatttggg caacaccaat gtcccaaata atcttggccc acatgatctc 1560 tgtgacgact ctagcactcc tcctggcttt gaacaggtcg agacggtagc tcagaatagt 1620 cagcagttgg gcaacaccga tgtcccaaat aattttggca tgcaggatcc tcatgacaac 1680 catagcattc cccctggttt tgaacatgtt gcgacattag ctaaggatgt catcgatatt 1740 gtcaatcaca tagaaggctg tgatatggat ggttttactc ctgtgttatc taacagtcaa 1800 cggaaaaaac aaaagcagct tgccaatctt aatcaaccct ctgataaacc atatccgagt 1860 agggtccgag gaataccagc tcgttataaa tgaaggttct cttctggaat atccgtggca 1920 ttggtaacga tgactctcgg acggagctct ctaacatctg tcggttgcat cacccggatt 1980 tggtttgcat tgcggagccc atggtgactt ttaattctat ttcagctgct tattgggatt 2040 ctttaaatct atctgctctt acttttaatt ctagaggaac tcttgctccc aacctttggt 2100 tactaacatc ttcggcttgt gcagaccctt tagttatttc tatctctgat caacaggtta 2160 cggttcgctg tacttttgac catatcccaa gccagttcac atttgtttat gcaagcactt 2220 cacctatcaa aagaagagac ttgtgggctg attttatctc tctgcgccca caaacacaag 2280 ttccatggat ggctattggc gatttcaacg ctatcctggg cgcccacgag cagatgggag 2340 gaggcagacc gtcccaagct tcatgcgctg agtttagtaa catgtctgac acttgtaact 2400 ttacccactt gaacacatct ggggcagcct ttacatggtc taatggctgg aggtctcgtg 2460 gtcgcactga aagaaggtta gatcgctcct tgtgtgatat aagctggttt gattcttggc 2520 cccactctaa ctgcatagca ttgccaaagg tagtctcaga tcacaacccc cttatcttct 2580 ctggttctag agttttgagc agtggtcatc gtcctttccg ttttcaatca atgtgggttc 2640 aacatccatc ttttcgagaa actgtaactc attgctggag aaatacagtt gtctatggtt 2700 gtcctatgtt tatcattctg caaaaattga aagctctaaa aacctgcttg cgccaatgga 2760 atttttcggt ctttggtgac gtccataata gagtggctaa tgctcggcat aatctttcta 2820 tgattcaaca aagaatttca actgagggta taaataatga tcttttcgag gaggagattg 2880 tcgccaagac tacagtaatg gagtctctcc aaatgcagga ggcattttgg aaagatagag 2940 ctcgtgttaa gtggttaact aaaggggata gaaattcttc tttctttcat gcctatgctc 3000 gtattaaatc atccagctct cgtatcagtt gtattcttga tggaaacaat cttcttactg 3060 acccgctggc aattgagaac catattgtta atttctatca gactttgttc ggctcttctt 3120 tcaccccttc aggtattgat gaggtttgtg aggtcatcca gccgatggtc acagactctg 3180 aaaatgatct cttatctgca ttacctactg atgaggaaat taaggaggca gttttctcat 3240 taagtgcttc cagtgcgcca gggccagatg gttttccagg ttttttctat caccactgtt 3300 gggatattgt cggctttgat gttattcaat ttgtgaagca attctttcaa tcgaattggt 3360 tataccccaa tgccaatagt aatttcttag ttttgattcc gaaggtggaa gacgctattt 3420 ccatgactca ttttagacct attgctttgg caaactttct ctttaagatt attcccaaaa 3480 ttttggcagt tcgtctttct catgttgttc aacgcattat ttctccgcat caagctgctt 3540 ttatacctgg ccgacgtatc acagattgta ttggccttgt ttcagaatgt ttcaatgtgc 3600 ttgacaaaaa aactcgtggt ggcaatatgg gagtcaaagt tgatatagct aaggcttttg 3660 atactttaga ttggtcattt ctattgcggg tgcttactaa ctttgggttc tccacttgtt 3720 ttatagactg ggtttctacc atcttaagat ctgctaaatt gtccatccta atcaatggtt 3780 ccccgcatgg ttttttctct tgttcccgag gagtgcgcca aggggatcct ctctctccgt 3840 tacttttctg tctagctgag gaggctttat caaggggcct gagtcgtctt caacttgatg 3900 ggcttactaa gccaactttt gctccaagag gttgtatctc tccttctcac gttctctatg 3960 cagatgactt attcattttc tgtagaagtg atggtgtcac tctgcgtaat ttgcaaggtt 4020 tcttcgatag atatagtaga gcctctggtc aatttatcaa taaggcaaaa agtactttct 4080 acttgggctc tacctcaagg catcgcaaag ctgtggttga gagttacttg ggtttcaaag 4140 aaggcaaagc accttttgtc tacttaggag ttccaatctt ctgtggcaag cctaaaagga 4200 gtcatcttca agccttggca gataaagcta aagctaagtt aactggttgg aaggggaaac 4260 ttttatctat ggcaggaaga gttcaactca ctcaatcagt ttttcaaagt atgctcttgc 4320 atagcttttc tgtttataag tggccttctt ccttgctaag gcctctttca agatgtgctc 4380 gcaattttat atggtctggt gacgtaacct ccaagaagtc tgttaccgtt tcttggcgtc 4440 agatatgtgc tccgaagaat gaaggtggtt tgggtttgcg tgatcttggc tctcttaaca 4500 ctactgctct cttaaagctt ggatggctta ttattactac tgattcccct tggagtattt 4560 atcttcggga acgtttcaag ctacatggtc gcctatattc ttgtagttat aagcgatctt 4620 ctatatggcc tggtattaaa tccattcttc atatcttgtt tcagaattgt cgttgggtga 4680 ttggaaatgg ttctactact tccctttggg ttgataaatg gctggataag cctattgtgg 4740 acgtcgttgg tgcaacagag attgctcmtt ctttatctcg tactaaggtc tcaaatatta 4800 ttcgtatggg aaaatgggtt attccttcta ttttttcttc tactttccca gacctaacta 4860 aagagatttt agaaatgcct cttccaattg atgaggataa ggacgtttta atttgggaag 4920 tttctacatc tggtgttttt tcgttctccg atggctatga aattgttcgt catcggtttc 4980 ctgttaagag ttgggcttcc attatctggc gtcctttcat cccacctcgt tactctattt 5040 tagtttggaa gattctattc aacaagctcc caacggagga tcaacttcag cgccgaggca 5100 tcccgctggc tccaatatgc caactatgtc acaagaattc tgaatctatt gaccacttat 5160 tttctagctg tgaatttgca caacgtgctt ggcgttggct agctacccaa tttggcacta 5220 ttattccacc tacgggctcc ctctctgatc tatggcttgt ttttctgtca aagcggtttt 5280 ctccacatct tcgcaatgtc tggctagctt cagggttttt cttactaatg gctatttgga 5340 agatgcgtaa taaagtgaag tttgaaggca aacctccctc cttctcacgt ctctgccgct 5400 ccacctcggc ctggattagg caggttggag ctctcacccc tggccatgta cgaggcattt 5460 tggataggca acttttagtc tctcttggaa tatcgcctaa ctcctgtaaa gctccttcta 5520 ttgtccctgt tctttggcac ccccctcctt tttcttgggt caaagtgaat actgatggcc 5580 ttgctaaagg taatccgggt cctgcggcat gtggcggggt ttttcgwgac tctgcgggtt 5640 attttcttgg tggtttctcc ctaagcttgg gccatcgtac ttctttctat gcggagctcc 5700 atgctgtcat ccttgctgtc gaattggccc acgcgcgggg ctggcaaaat ttatggcttg 5760 aaagcgactc ttctagtgta atatcatgtt ttgcttctgg atctttctct cccccttggt 5820 cgctccagac acgctggaac aattgtactc tccgtttgca gaacatggtt tttcgttgct 5880 ctcatatttt tcgagaaggg aatgttgttg ctgacaaatt agccaattta gggcttctat 5940 catcttcact tgtttggcat tccactcccc ctatagagat ccttcctcct ctgcactcag 6000 atttcttggg catgccaacc tacaggtttg tctcctcttc ttgatgtgtg ttctcctttc 6060 ttttcctaac ctttttggat tcccttttgt tttgcagctt gtcttgcagg ttattacctt 6120 ttaggtttat agaggggttt gggcttatgt ccgcccagtc ttttccttgt attttctttt 6180 ccaagagggg tacggtctat gtccccccct cttttgtatt tcctttctca aaaggggtaa 6240 ggtgcatgtc cccccctttt ttgtatttct tttctcttgt tctatgaggg gttaggttta 6300 tgtccccccc tgtctaggtg tatcttcttt tttcttatca ataaatttcc ctcgtaccgc 6360 cgaggttctc caaaaaaaaa aaaaaaaaaa a 6391 // ID Copia10-VV_LTR repbase; DNA; EDCOT; 1241 BP. XX AC AM486050; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia10-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1241 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-1241 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 732-732 (2007). XX DR Genbank; AM486050; Positions 1036 2276. XX SQ Sequence 1241 BP; 348 A; 261 C; 247 G; 384 T; 1 other; tgttagccca agggttctcc taatcaggtt ttgatgataa caaaccatgg ttaagtgact 60 aattgtttta aattgttaag aatctcaggc ataatctcaa aaattcatca aggaccaaac 120 gaatacggga tcgagatcat ttggaagact tgtgatcata ggaaatgaat gtaagataat 180 agcatgagtg cacttaggat gttcatacat tttcatgcat cttagaaaac ttggtttatt 240 ctttaaaact ttattttctt taaaaaccga gttatatcaa atatacctta ggcaaattga 300 ttcaaaattg gcatattaac tcacctaaag accttgccta agtattggaa aagaaagaaa 360 taaaaaaagg ataggttttc agggccaaaa ggctcatccg gtcgaggcta tggccaaccg 420 gctcaaccgg ttgggtaacc ggtcgaccgr tttcccttgt ccggtcgagg tccgatcgag 480 ggaggcacaa aaaccttctc tctctcccag tagctttctc ttcccggtcg agcctcaccc 540 cttgtccggt caaggtccga tcgaggtccg gtcgaagtcc ggtcgaggca acggtaacct 600 gctatgcatt aaatgctcca acggctagtg atccggtcga ccctttgctc gtccggtcga 660 ggctactttc tgctgttttt gtctcccgag cttagaaacc tataaattga gagctcctct 720 tcatttatga ctaagagaac aattgcattc aaagcctacc tacctgttct tgatctaaaa 780 agcgctcatc ttctttctta gtgcattaaa ccatcacttg catattctta atgcactctt 840 gcaattcatc ctagctttct cttgtacttg agccttcctt aaagctaggt tgagagtttc 900 atccttgtgt aaactgagtg tgaaagcctt caagtggttc aaatcttgaa gagattgtgt 960 aagagcccat tggagccgga atccaagtgt aagacgattg aaagcttgat tgaagcttca 1020 agttagtgga accctcactc ggttaggaga ttgaggagag tggacgtagg caagggagtg 1080 ccgaaccact ataaatctga gtttgaattc tctaacttta atctcttatc ctttaattta 1140 ttttgtgcat atattattgt gtggaaaaaa attttgaaaa acccaattca cccccccctt 1200 ttgggtattt tccttattta ttcataacct ttgttttatc a 1241 // ID COPMET_LTR repbase; DNA; EDCOT; 2753 BP. XX AC AC161863; XX DT 09-NOV-2006 (Rel. 11.11, Created) DT 09-APR-2007 (Rel. 12.05, Last updated, Version 2) XX DE Copia-type LTR retrotransposon long terminal repeat sequence. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed repeat; LTR retroposon; Medicago; GYPMET; KW COPMET_LTR. XX NM GYPMET_LTR. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2753 RA Shankar R. and Jurka J.; RT "COPMET: LTR retroposon from Medicago truncatula."; RL Repbase Reports 6(11), 560-560 (2006). XX DR EMBL/GenBank/DDBJ; AC161863; Positions 72832 75584. XX CC A new LTR sequence flanking internal region of a retroposon, from CC Medicago truncatula. It shares some characteristic of Gypsy-like CC LTR but the internal region is closest to Copia type. Name CC changed from GYPMET to COPMET (Apr. 9, 2007). XX SQ Sequence 2753 BP; 914 A; 512 C; 472 G; 855 T; 0 other; tgactatata ttggtttata gtggggaccc tcaagctcat ctccggatag tacatagatc 60 atcttctgat agtacttggt gtgttgagaa ccaatgtcct gagggtgaat gcaaagaagt 120 gttgtttcgg catgactcag ttggaatatc gagatttaaa gtaatatatg ttgatcatgt 180 caaaattaaa gtaatgcaag agtggccttg tcccaaagat cctaaagggt tatgtgggtt 240 tctcggttta accgggtatt atagaaagac tgcttcaaat ggagtgagga aagctctcga 300 ggattacgag actctgtttt tggcgtaaac cgggtatcca ctgcacgtgc aactgcagag 360 actaatccct cgagccttgt gggacccaaa tgggcagcaa actctcctta agagttttaa 420 cgctgctgca tgtccaaggc tggattcgaa cccaggacct tggttaaact agaagagaca 480 tgtgccatct tatctaagcg ctcttgggta ggattatgag actttgaaac agaagatgga 540 tgaattacaa ttaatagcta cgcttaattt taactagccc tttgcgatag aaactgacgc 600 atcagggatc ggattgggtg cagtgctgat gcaacaggga aaaatgttga ccttctttag 660 caaagcattg tcagacaaag gcagattaaa gcctgtgtat gagagggaat tgatggcgat 720 tgtcctggaa gtacaaaagg gaaggcgtta cttgttgggg agctattttt atcatacgca 780 ctgaccataa aagtctaaag tatttgcagg aaaagagatt gttggatggt ggacagcaaa 840 agatggatga caaagttgtt gggatatgtc tttgaaaccc aatcctaaaa taattagtcc 900 cttcccaact tatatctaat taactaagac attccataaa aaaaatatct aattaactaa 960 gacatgctaa acatacaata acatatgttc ataagattta ttgtttttcg catatgggcg 1020 actaatgacg agattgttac tcatcccact atatattagt aaaattcaaa tgctaaacca 1080 tatacatgta ttaaattaac aatatcatgt aagtttttga ctcttttgtc aacttcataa 1140 taataaataa aatatcattt tcaacttact cgtagaaaaa aagtaaaaaa taccttgacc 1200 atgcatattt atcttgaatc aggctattca aattttcttt tgtgctctca ataaatctag 1260 aacaaaggtt gtccacaata tgcgtatacg tcaaaaaaag ctcagctcaa tacttcctta 1320 caaggagagg tgggaagaca ttttctctgt gcattaaaaa caatcataca atgagttgca 1380 tggaattcag tgacacccaa tgcctgttat tggtcaatat acttagtaac aaggtaaaaa 1440 atttatgagt atattgacca acaacagtag aatgagattg agatttctaa tgcatacata 1500 acgacttacc ccaacacctg aatctacaat tctacttcaa cattaccctc agcgtcaaga 1560 aaaccatttt cacaggcacg ctcaagatca aatacatccc ccgggtgagc cttacaaact 1620 aagtgaaatc gatctgaata aactcaaatg aaatggttag taatagtaaa gctttttttt 1680 tttttttaaa taataaaaaa cctaccaaaa caatcagttc gcccggggtc aagggggtga 1740 attatcgcta atgtgttaag tgcataaaag ttcaacattg gattgttgtc tatgtcagca 1800 aataactcaa atcgcaacga ggttcccatc cgacgaacca tgaaagtcct gcattggcat 1860 atcaatcttt acttatatct ttacaattat tcactcttca atatataaaa tagaaaatta 1920 agaaagttgc ataccattta tactctccaa gttcgatgag taaagagtca tatccagaaa 1980 tcggctttag tgtcaacaat gttttcgtat atagttttga cacattattt ccatcttcaa 2040 caatgttatg ggattccaaa agatcccgaa ttacattacg aaatgttatt ctcaacctgc 2100 gtactgagat ttgagagaga ggaaaataag catgagtata ttaaggagat cttcttgcta 2160 tgtttaaaga gatgcttacc actttcttcc tccacctcca catacaaagc aacaacattt 2220 tcttgtgctt ccacgtacaa ttcagtgact gcttttttca atgcacatgc aacatactcc 2280 tcttgttgtt ccgcagttaa ttcatcaatc ttctctttca aagtagtagc aataacctca 2340 tgctttttta gggcacacat aaacaagtaa ttaagcaaag ctctcactct attcagaaaa 2400 gacgtatcct ctttcaaatc tgctgcaatc gattcatcat ttagctgcag ccacaaacag 2460 tttctagtaa gtagttaaga aaataagaaa aacccatcta tttacagcca aaatcaagtt 2520 taccgtttgc ttattctctt ctacacattt atcatttttc tttggtttag cctacaaaac 2580 aagatttttt ttttcttcat aaacataaaa atgatgataa acatatatgc atgacacacc 2640 tttttttctc cttttttctt ggacttcttt tcagtttgaa tgagctcact ttgagtaaag 2700 tttacctcaa ttttattcct gcatccatta aataaataat tagaatatga tca 2753 // ID DIASPORA_I repbase; DNA; EDCOT; 6689 BP. XX AC . XX DT 19-OCT-2005 (Rel. 10.1, Created) DT 27-OCT-2005 (Rel. 10.1, Last updated, Version 1) XX DE Gypsy-type family of LTR retrotransposons from Glycine max DE (internal portion, consensus). XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; DIASPORA_LTR; internal portion; DIASPORA_I. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-6689 RA Yano S.T., Panbehi B., Das A. and Laten H.M.; RT "Diaspora, a large family of Ty3-gypsy retrotransposons in RT Glycine max, is an envelope-less member of an endogenous plant RT retrovirus lineage."; RL BMC Evol Biol 5(1), (2005). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 874..6546 FT /product="DIASPORA_I_1p" FT /translation="MTRGNPSDLQPFDPEIDRTFHRLVRHHFIPFDHSEHS FT ITGESVHSVIGDFEHPDLEHYNFEHSDSEHSDFEHSENMAQPPPRERTLRE FT MAAPDFTYESLCIQYPDEDVPYVLKTGLIHLLPKFHGLAGEDPHKHLKEFH FT IVCSTMKPPDVQEDHIFLKAFPHSLEGVAKDWLYYLAPRSITSWDDLKRVF FT LEKNFPASRTTAIKKDISGIRQLSGESLYEYWERFKKLCASCPHHQISEQL FT LLQYFYEGLSNMERSMIDAASGGALGDMTPAEARNLIEKMASNSQQFSARN FT DAIVIRGVHEVATNSSSSSETKKLEGKLDALVNLVTQLALNQKSVPVARLC FT GLCSSADHHTDLCPSVQQPGAIEQPEAYAANIYNRPPQPQQQNQPQQNNYD FT LSSNRYNPGWRNHPNLRWSSPQQQQQQPAPSFQNAAGPSRPYIPPPIQQQQ FT QPQKQPTVEAPPQPSLEELVRQMTMQNMQFQQETRASIQSLTNQMGQLATQ FT LNQQQSQNSDKLPSQAVQNPKNVSAISLRSGKQCQGPQPVAPSSSANEPAK FT LHSTPEKGDDKNLPNNFCAGESSSTGNSDLQKQHIPPLPFPPRAVSNKKME FT EAEKEILETFRKVEVNIPLLDAIKQIPRYAKFLKELCTNKRKLKGSERISM FT GRNVSALIGKSVPQIPEKCKDPGTFSIPCIIGNSKFDNAMLDLGASVSVMP FT LSIFNSLSLGPLQSTDVVIHLANRSVAYPVGFIEDVLVRVGELIFPVDFYI FT LNMEDGFSQGSVPIILGRPFMKTARTKIDVYAGTLSMEFGDITVHFNILDA FT MKYPSEDLSVFRAEIIDHVVDEYMTDLYSNLHASHSSCIESEIVLDHMSEF FT DAESESEIDIDCMSGGGVLPLEIDFIESDRTNHVSGSTHTSDFLYEVKAEK FT PSPSTTIQPTTPELKPLPSNLKYAYLDDSKSFPVIISASLADEQEEKLLSV FT LKKHKKAIGWTLADIPGISPSTCMHRINLEDGAKPVRQPQRRLNPVILDVV FT KKEITKLLQAGIIYPISDSQWVSPVQVVPKKTGLTVIKNEKEELIPTRVQN FT SWRVCIDYRRLNQVTKKDHFPLPFIDQMLERLAGKSHYCFLDGFSGYMQIT FT IAPEDQEKTTFTCPFGTFAYRRMPFGLCNAPGTFQRCMISIFSDFLENCIE FT VFMDDFTVYGSSFDGCLDSLEKVLNRCIETNLVLNFEKCHFMVEQGIVLGH FT IISNKGIEVDPAKISVISQLPYPSCVREVRSFLGHAGFYRRFIRDFSKVAL FT PLSNLLQKEVEFDFNDRCKEAFDCLKRALTTTPIIQAPDWTAPFELMCDAS FT NYALGAVLAQKIDKLPRVIYYASRTLDAAQANYTTTEKELLAIVFALEKFR FT SYLLGTRIIVYTDHAALKYLLKKADSKPRLIRWMLWLQEFDLEIRDRSGAQ FT NLVADHLSRIERVSDADSPIRDDFPDDHLYILYSISDSLSTPWFANIVNYL FT VASVFPPLASKAQKDKIKSDAKHFIWDDPYLWKLCSDQVIRRCIPDHETDS FT VLQFCHSSAPGGHLGVQRTARKVLDCGFYWPTIFKDAWKICSTCEQCQRAG FT SSLTWRQQMPQQPMLFCEVFDVWGIDFMGPFPVSFGFVYILLAVDYVSKWV FT EAKPTRTNDAKVVVDFVRSNLFCRFGVPRAIVSDQGTHFCNRSMHALLKKY FT GVVHRISTPYHPQTNGQAEISNREIKRILEKIVQPSRKDWSTRLDDALWAH FT RTAYKAPIGMSPYRVVFGKACHLPVEIEHKAYWAVKTCNFSMDQAGEERKL FT QLSELDEIRLEAYENAKFYKEKTKKFHDSMIVKKDFMVGQKVLLYNSRLGL FT MSGKLRSKWIGPFVVTNVFPYGTVEIKSDSTNKSFKVNGHRLKPFLTNPSL FT VDVVVEETSLLHPTLPPP" XX SQ Sequence 6689 BP; 1849 A; 1352 C; 1429 G; 2057 T; 2 other; aatttggcgc cgttgccggg gagcagtggt ccaaaggttc ataatagcta gtgattcggg 60 ttttatgttt agttgtttta agttttatgg ttgtgtgaga gtgttgtttt vgtgtgtgtg 120 tgaaagttag tgttgtttag tgtcttggta ttttgtttag tgtgtgttct gttttagttt 180 ttctgttvag cgcttcccct gtttcagttt tgggtgtttt gctgtgaata gtgttttgcg 240 acggacttag cgaccacttt ctgcttgcgg caaaaacaga gtagtagtag aaatcaatta 300 gagacggatt ttagcgacca cccatgctga attatttggg attttttgtt ttagtagcta 360 gggttgttat ttttggctga atttttttgt ggtaacttct tttaatccat attttgtggg 420 aaaaatagct agagccttta gtttggtcag atttgaaagt tccaaaaaac tagcaaattt 480 tgtgtttgtc aaaacttcaa acggccataa cttttgctcc ggttatcaga atcgcaatta 540 ttatatatgc atttggggta gaaaaaaatt tcctacaccg tggcagcctg ccataggccg 600 gctgaggtct ccatcgtcca aaaaaagcga ttctgtcaaa agttttttat ttttcaagtt 660 ttattcactt atttttctta acttaccaat tttagctttc atagttagac tttgaatttt 720 tgtctgaaat tttttgtgct atcttctcat cattttataa ggttgctcac aaaatttcaa 780 gtcatttgga tatcatttga gggtagctgt agttcaaacc tacactgtta cttgcataag 840 aaggcaacta gttgtgcatg ctgaatgtag tgtatgacta gaggcaatcc atctgactta 900 caaccctttg atcctgagat agataggaca tttcatagat tagttaggca tcattttata 960 ccttttgatc attctgagca ttccataact ggtgaatctg tgcattctgt tattggtgat 1020 tttgaacatc ctgatcttga gcattataat tttgagcatt ctgattctga gcattctgat 1080 tttgaacatt ctgagaacat ggcacaacct ccaccccgtg agaggactct aagggaaatg 1140 gctgcacctg atttcaccta cgaaagcttg tgcatccaat accctgatga ggatgtccca 1200 tatgttctta aaactggact gatccatttg cttccaaagt ttcatggcct tgcaggtgaa 1260 gacccgcaca aacatctgaa agaatttcat attgtctgct ccaccatgaa acccccagat 1320 gtccaagagg atcacatatt tctgaaggct tttcctcatt ctttagaggg agtggcaaag 1380 gactggctat attaccttgc tccaaggtcc atcacgagct gggatgacct caagagagta 1440 ttcttagaaa aaaatttccc tgcttccagg accacagcca tcaagaagga tatttcaggc 1500 attagacaac tcagtggaga gagcctatat gaatactggg agagatttaa gaaactatgt 1560 gccagttgcc ctcaccacca gatttcagag cagcttcttc tccaatattt ttatgaagga 1620 ctcagtaaca tggagagaag tatgatagat gctgccagtg gtggagccct tggagacatg 1680 acccctgctg aagccagaaa tttaattgag aagatggctt ccaactccca acaatttagc 1740 gccagaaatg atgctatagt cattagagga gtgcatgaag tagccacaaa ctcatcttca 1800 tcatctgaaa ctaagaagct tgaaggtaaa ctagatgcct tggttaacct ggtaacccag 1860 ctggccttga atcaaaaatc tgtacctgtc gcaagactct gtggtttatg ctcctctgct 1920 gaccaccata cagacctttg cccttctgtg cagcaacctg gagcaattga gcagcctgaa 1980 gcttatgctg caaatattta caatagacct cctcaacctc agcagcaaaa tcaaccacag 2040 cagaacaatt atgacctctc cagcaacaga tacaaccctg gatggaggaa tcaccctaat 2100 ctcagatggt ccagccctca gcaacaacaa cagcagcctg ctccttcctt ccaaaatgct 2160 gctggcccaa gcagaccata cattcctcca ccaatccaac aacagcaaca accccagaaa 2220 cagccaacag ttgaggcccc tccacaacct tccctcgaag aacttgtgag gcaaatgact 2280 atgcagaaca tgcagtttca gcaagagacc agagcctcca ttcagagctt aaccaatcag 2340 atgggacaat tggctaccca attgaatcaa caacagtccc agaattctga caagctgcct 2400 tctcaagctg tccaaaatcc caaaaatgtc agtgccattt cattgaggtc gggaaagcag 2460 tgtcaaggac ctcaacccgt agcaccttcc tcatctgcaa atgaacctgc caaacttcac 2520 tctactccag aaaaaggtga tgacaaaaat ttacctaaca atttctgtgc aggtgaatct 2580 tcttccacag gtaattctga tttgcagaag cagcacattc cccctcttcc attccctcca 2640 agagcagttt ccaacaaaaa aatggaagag gcagagaaag agatcttgga aacgtttaga 2700 aaagtagagg taaacatacc tctgttggat gcaataaagc aaattccaag atatgccaaa 2760 ttcttgaagg agctgtgcac taataagcgg aagcttaaag gaagtgaacg aattagcatg 2820 ggcagaaatg tctccgcatt gattggtaaa tctgttcctc aaattcctga aaaatgcaaa 2880 gatccaggta cattcagcat accttgtatt atagggaata gtaagtttga caatgccatg 2940 ctagatttag gagcttctgt tagtgttatg cctctgtcta tttttaattc tctatctcta 3000 ggtcccttgc agtcaactga tgtggtaatt catttagcta atagaagtgt tgcctatcct 3060 gttggtttca tagaagatgt cttagttaga gttggtgaac tgattttccc tgttgatttt 3120 tatattttga atatggaaga tggattttct caaggatcag ttcccatcat tctaggcaga 3180 ccctttatga aaactgctag aactaagata gatgtttatg caggcacact atctatggaa 3240 tttggtgata taactgttca ttttaatatt ctggatgcta tgaaataccc atctgaagat 3300 ctttctgtat ttcgtgctga aataattgac catgttgttg atgaatacat gactgatctt 3360 tattctaatc tgcatgcctc tcactcttca tgcattgagt ctgaaattgt acttgatcat 3420 atgtctgaat ttgatgctga gagtgaatct gaaattgata ttgattgcat gtctggtggt 3480 ggtgttttac ctcttgagat tgattttata gagtcagata ggactaacca tgtttcagga 3540 agtacacata cctctgactt tctttatgag gtaaaggctg agaaaccatc tccttctacc 3600 actatccagc cgaccacacc agaattgaag cctctgccat caaatttaaa atacgcttac 3660 ttggatgata gcaagagttt tccagtgatt atatctgcct cccttgctga tgagcaagag 3720 gagaagttgt tgtcagttct caagaagcat aagaaggcta taggctggac cctggcggac 3780 attcctggta ttagcccatc cacatgtatg catcgaataa atttagagga tggagctaaa 3840 ccagtaagac agccacagag aagactcaac ccggtgattc ttgatgtagt gaagaaggag 3900 ataaccaagc ttttgcaagc tggaatcatt tatcctatct ccgacagcca atgggtgagt 3960 cccgtccagg tagtcccgaa gaagaccggc ctcacagtga taaaaaatga gaaggaggag 4020 ctgattccta ctcgggtgca gaacagttgg agagtctgca ttgactatag gaggctgaac 4080 caggttacca aaaaggacca ttttcccctg ccattcattg accagatgct tgaacgcctg 4140 gcaggtaaat ctcactactg tttccttgat ggtttttctg gttatatgca aatcactatt 4200 gctcctgagg atcaggaaaa gaccacattc acctgcccct tcggcacttt tgcctatagg 4260 aggatgcctt tcggcctgtg caatgcccct ggtaccttcc agcggtgcat gattagtatt 4320 ttcagtgatt ttttagaaaa ttgcatagag gtgtttatgg atgatttcac tgtatatgga 4380 tcctcttttg atggttgttt ggatagtttg gaaaaagttt tgaatagatg cattgaaact 4440 aaccttgttc taaattttga aaaatgtcat tttatggttg agcaaggtat agttttaggc 4500 cacattattt ccaataaggg tattgaagta gatcctgcaa aaatttctgt tatttcacaa 4560 ttgccttacc cctcttgtgt gcgagaggtg cgatcttttc ttggtcatgc aggattctac 4620 aggcgcttta taagggattt tagcaaagta gcccttccac tgtccaactt gttgcaaaag 4680 gaggtggagt ttgactttaa tgacagatgc aaagaggctt ttgattgcct caaaagagcg 4740 ctgactacca cccccatcat ccaggcaccc gattggacag ccccttttga gcttatgtgt 4800 gatgcatcaa attatgcatt gggggctgtc cttgctcaga aaattgataa attgcccagg 4860 gtgatatatt atgcttctag gactttagat gctgcccaag caaattatac tactactgag 4920 aaagagcttc tagccatagt ttttgctctt gaaaaatttc gatcttattt gcttggtact 4980 cgcattattg tttatactga ccatgcagct ctaaagtact tgttgaagaa ggctgattct 5040 aagcctaggt tgatccgatg gatgctctgg ctccaagagt ttgacttgga gatccgtgat 5100 aggagcggag cacaaaatct agttgctgat catttgagtc ggatcgaacg tgtctctgat 5160 gcagattcac ctattcggga tgatttcccg gatgatcatt tgtatatatt gtatagtatt 5220 tctgactctc tttctactcc ctggtttgct aacattgtca attatttagt tgcctctgtt 5280 tttcctccct tagcatctaa ggcccaaaaa gataaaatta aaagtgatgc taagcatttt 5340 atttgggatg acccctactt gtggaaattg tgcagtgatc aggtcattag acgatgcatt 5400 ccagatcatg agactgactc agtcctgcag ttctgtcatt cttccgcacc gggaggccat 5460 ctgggtgttc aaaggacagc tcgcaaagtg cttgactgtg gtttttattg gcccaccatc 5520 tttaaagatg cgtggaagat ctgtagcact tgtgagcagt gtcagagagc aggaagttca 5580 cttacatgga gacaacaaat gcctcaacaa cctatgctat tctgtgaggt gtttgatgtc 5640 tggggtatag attttatggg gcctttccct gtctcttttg gttttgttta tattctcctt 5700 gcagttgatt atgtttcaaa atgggtggaa gccaaaccca ccagaactaa cgatgctaag 5760 gttgttgtag attttgttag atctaatctg ttttgcaggt ttggagtccc tagagccatc 5820 gttagtgatc aaggaaccca tttttgtaac agatccatgc atgccttgct taaaaagtat 5880 ggggtcgtgc acagaatatc cacaccttac cacccccaaa ctaatggaca ggcagaaatt 5940 tctaacaggg agatcaagag aattttagag aagattgtgc agccaagcag gaaagattgg 6000 agtaccaggc ttgatgatgc tctttgggca cataggactg cctacaaagc acccatagga 6060 atgtctcctt atcgggttgt ctttggaaag gcatgtcatc ttccagtgga gattgagcac 6120 aaagcatact gggcagtgaa gacctgcaac ttctctatgg atcaagctgg tgaggaaagg 6180 aagttgcaac tgagtgagtt agatgagatc cgcctagaag cctacgagaa tgccaagttc 6240 tacaaagaaa agaccaagaa gttccatgat agcatgatag ttaagaagga cttcatggtt 6300 gggcaaaaag tgttattgta taattctagg cttggactca tgagtggtaa gttgaggtct 6360 aagtggattg gtccttttgt tgttactaat gtttttcctt atggtacagt tgagatcaaa 6420 agcgactcca caaacaagag cttcaaggtc aacggacatc gacttaagcc attcctcacg 6480 aacccttctt tagtggacgt agtggtggaa gagacttcct tactccaccc tactcttcct 6540 ccaccatgac ttagggagtt tttcttttcc tatctccttc tttgctttta ttacacttgt 6600 ccgattctct ttgatgattt aattgttttt aatcttttaa ttgtgctaca ttgaggacaa 6660 tgtgttgttt aagtatgggg gggggggag 6689 // ID Copia2-PTR_LTR repbase; DNA; EDCOT; 414 BP. XX AC LG_V; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia2-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-414 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-414 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 213-213 (2007). XX DR Genome; LG_V; Positions 13738788 13739201. XX SQ Sequence 414 BP; 135 A; 75 C; 59 G; 145 T; 0 other; tggaatctac aacactctac atctataaac aaagaaccag aggaatccca gcaacttgca 60 gacgctgcaa tgatcacagc aggctaaagc tttgccattc ttattctgca atcttcacat 120 atatatgtaa atacagttgc aaatacagtt ggatgttatt agttagttag tcataaccgt 180 tacagttagt taaaatattg ttagttagtt ccttcttatc agttagaata tgtgtatata 240 tatattcatt catgtaatct gtaaatgtat gtgaaataca agaagaaagg taactctgca 300 tgcagtgtat acagttgtaa acaattcttg ttttcctttc aagaaattca ttctctcctt 360 ctgttacaaa cttcatctgc atattttaca ttcctcacgt tagaattctt taca 414 // ID GYPSODE1_I repbase; DNA; EDCOT; 5142 BP. XX AC AC150162; XX DT 31-AUG-2005 (Rel. 10.09, Created) DT 31-AUG-2005 (Rel. 10.09, Last updated, Version 1) XX DE GYPSODE1: Gypsy-type element from Solanum demissum (internal DE portion). XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; GYPSODE1_LTR; internal portion; GYPSODE1_I. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-5142 RA Jurka J.; RT "GYPSODE1: Gypsy-type element from wild potato."; RL Repbase Reports 5(9), 246-246 (2005). XX DR Genbank; AC150162; Positions 80567 85708. XX CC There are only 2 bases substituted between the LTRs. This appears CC to be a recent insertion. XX FH Key Location/Qualifiers FT CDS join(469..2802,2806..5097) FT /product="GYPSODE1_I_1p" FT /translation="MRQAPVPAAPAPAPAPQGQPAAAAPEVQPPPVHVTVV FT SDLKDGEMPLREQKMLGVFQRLALPIFSGAIGEDAYEFQLTCQEQLQSLGL FT LESRGADFTAHQFRGPARQWWRSYRESRPVGSPHVSWSEFSEAFLARFMPR FT SVRDRLRDQFSRLEQGPMTVSEYETRFHELSRHATMILPTEEERVRCFVRG FT LRYRLRVDTEHLVSAGRSFLDVVDHARSMEHIHREAQGGSDKRARYQGSYS FT GSQTRGRDSYDRPRQRFQQGQSSRPVQAALPASEGGQYHQGGPSTGQGSRG FT SDSLPSYRGRVTSERSASGCFDCGALDHWSRECPRRGRGAIVPAPLTPRPV FT SAVPPLVRGGGQDQGRRDSRQGTRGGARGGRLSGRSDASGRGAQGHFYAAP FT ARATAEASDDVITGMLLLCHQPATVLFDPGSTFSYVFVYFAPRLGMRSASL FT TEPIHVSTPVGESLVVDQILRSCLVTIQGCDTRVDLILLDMVDFDVILGMD FT WLSPYHAVLDCYAKTVTLAMPGISPVLWQGAYSHTPTWIISFMRARRLVAS FT GCLAYLAYVRDVSRDDSSVDSVPVVREFADVFPIDLPGLPPDRDIDFAIDL FT EPDTRPISIPPYRMAPAELRELSAQLEDLLGKGFIRPSVSPWGAPVLFVKK FT KDGTMRMCIDYRQLNKVTVKNRYPMPRIDDLFDQLQGAAVFSKIDLRSGYH FT QLRIRAADIPKTAFRTRYGHYEFLVMSFGLTNAPAAFMDLMTRVFRPYLDL FT FVIVFIDDILVYSRSRSEHEQHLRIVITLRDQRLYAKFSKCEFWLESVAFL FT GHVVSKEGIRVDPAKIEAIRDWVRPTSVTEIRSFVGLAGYYRRFVEGFSTI FT AALLTRLTRVDVPFVWSEECEASFLRLKELLTTAPILTLPVEGEGFTVYCD FT ASGVGLGCVLMQQGRVIAYASRQLKIHEHNYPTHDLELAAVVFALKIWRHY FT LYGVRCEIYTDHRSLQYIMSQRDLNSRQRRWIELLKDYDLSILYHPGKANV FT VADALSRKAVSMGSLAFLSVEERPLALDIQSLANSMVRLDISDSRCVLAFM FT RVQSSLLDRIRGCQFEDDTLVALRDRVLADDGGQATLDPDGVLKFAGRICV FT PRVGDLIQLILSEAHESRYSIHPGTAKMYRDLRQHYWWSGMRRDIADFVSR FT CLCCQQVKAEHLRPGGEFQRLPIPEWKWERITMDFVVGLPRTSRGVDSIWV FT IVDRLTKSAHFLPVHTTFSAERLARIYIREVVRLHGVPVSIISDRGSQFTS FT SFWRAFQEELGTRVHLSTSFHPQTDGQSERTIQVLEDMLRACVMDFGGQWE FT QFLPLAEFAYNNSYHSSIQMAPFEALYGRRCRSPVGWFESTEPRPRGTDLL FT QEALDQVRVIQDRLRTAQSRHQSYADQRRRPLRFSVGDRVFLRVSPMKGVM FT RFGRRGKLSPRYIGPFEILRTVGEVAYELALPPVFSAIHPVFHVSMLRRYV FT PDESHVLQYDAVELDDRLTFVEEPVAILARDVRRLRSRAIPVVKVRWRHRP FT VEEATWETEQEMREQFPSLFEPSGTS" XX SQ Sequence 5142 BP; 1018 A; 1159 C; 1534 G; 1431 T; 0 other; agttggtatc agagccccag gtttatcggt ctcacttgta cagagctaac gtctagtaga 60 gtcctgcgga tcggtgcgga gacgtccgta acttatcctc gggaggctac aggatgtcct 120 taggaaaatt tcctcttttg tttcgctttc gtgcagcgtg tgtcttattg gttccttgaa 180 atatcacttg tttcattctt tcggggtatg gctcgctcgc gaggtggtgc ggccaggggt 240 ggcgcacccg ggtctgcagg cagagcctca gcttggggta gacgttgacc ccgaggtcga 300 ggcagggccg tagcaccagc ccgagatagg gaggaggagc ctcaggcagc atatgtacct 360 ccacaaccgg tggggccgag gccagcccag ccaccacctg caccagctgc agctgcagct 420 cctgatcttc atgctctgct gactcagata ctagcagcta ttggggagat gcgacaggca 480 ccagtcccag cagcaccagc accagctcca gcgccgcagg gtcagcctgc tgcagcggca 540 ccagaggttc agccgccacc agttcatgtg actgtcgtgt cagacttgaa ggacggggag 600 atgccactgc gcgagcagaa gatgctcggg gtattccaga ggttggcact gccgatattc 660 tcaggggcga ttggggagga tgcctacgag ttccagctca cttgtcagga gcagctacag 720 tcattaggcc tcttggagtc gagaggagcc gacttcactg ctcatcagtt tcgtgggcca 780 gccaggcagt ggtggcgctc gtatcgagag tccaggccag ttggatcgcc tcatgtatct 840 tggagtgagt tctcagaggc tttcttagcc cggttcatgc cacggagcgt cagggataga 900 cttcgtgatc agttctccag attggagcag ggccctatga ccgtctcaga gtacgagacg 960 agattccatg agttgtctcg acatgctacc atgatcctac ccacggagga ggagagagtt 1020 cgttgttttg tacgtgggtt gcggtaccgt ctgagggtcg acacagagca tttagtttct 1080 gccggccgtt catttcttga tgtagttgac catgctcgat ccatggagca tattcatcgc 1140 gaggcccaag ggggcagcga taagagggca cgctaccagg gcagctacag cgggtcacag 1200 actagaggga gagactctta tgataggccc cgtcagaggt ttcagcaggg tcagtccagt 1260 cggcctgttc aggcggcatt acctgcttct gagggaggcc agtatcacca gggtggtcct 1320 agtacgggcc agggttcgag gggatcagat tccctacctt cctatcgcgg tcgggttact 1380 tcagagcgtt cagcttcggg gtgttttgat tgcggtgcgc ttgaccattg gtccagagag 1440 tgcccccggc gagggcgagg agcgattgta ccagctccac ttacacctag accagtttca 1500 gcagtgcccc ctctagttag aggtggtggt caggaccagg gtcgtcggga cagccgacag 1560 ggtaccagag gcggagctcg aggaggcagg ctaagtggta gatcagatgc atcgggcaga 1620 ggtgctcagg gccatttcta cgcagccccg gcgagggcga cggctgaggc atctgacgat 1680 gttatcacag gtatgctttt attatgccat cagcctgcta cagtattatt tgatcccggg 1740 tccacattct cgtatgtatt tgtttatttt gctcctcgat tgggtatgag gtctgcgtct 1800 ttgacagagc cgattcatgt ttcgaccccg gtgggtgagt ccttagtagt ggatcagata 1860 ttgcgatctt gcttagtgac tatccagggt tgtgatacta gagttgatct tattttgcta 1920 gatatggttg attttgatgt gattctgggc atggactggt tatctcccta ccatgcggtc 1980 ttggattgct atgccaagac tgttacctta gcgatgcctg gcatttcccc agtgttgtgg 2040 cagggtgctt atagtcacac accgacatgg atcatctctt ttatgcgggc tagacggttg 2100 gttgcttctg ggtgtttagc ttatttggct tatgtgcgag atgtgagtag agatgactct 2160 tcagttgact cagttcctgt ggttagagag tttgcagatg tgttccctat agacctacct 2220 ggcctacctc cagatcgtga cattgatttt gccatagatt tggagcccga cacccgtcct 2280 atttctattc cgccttaccg aatggctcct gcagagctca gggagctcag tgctcagtta 2340 gaggatctct taggtaaggg ttttatccgt ccgagtgtgt cgccttgggg tgctcctgtt 2400 ctgtttgtga agaagaagga cgggactatg aggatgtgta ttgactacag gcagctgaac 2460 aaggtgacgg tgaagaaccg ttaccccatg cctcgtattg atgatttgtt tgatcagctt 2520 cagggtgccg ccgtgttttc taagattgat ttgaggtccg ggtaccatca gctgaggatt 2580 agggcagcgg acatccctaa gactgcattt aggacccgtt atggccatta tgagttcttg 2640 gtgatgtcgt ttgggctgac taatgcccct gccgccttca tggatttgat gacacgtgtg 2700 ttcaggccat accttgattt atttgtcatc gtcttcattg atgacatact ggtatactcg 2760 cggagccgga gtgagcatga gcagcatttg aggatagtga tctagacttt gagagatcag 2820 cggctttatg ccaagttctc aaagtgcgag ttttggcttg agtctgtagc cttcttgggg 2880 cacgtggtgt ccaaggaggg tattagggtt gatccggcga agattgaggc tattcgtgat 2940 tgggttaggc ctacctcagt tactgagatt cggagcttcg tcggactagc aggctactac 3000 agacgctttg ttgagggctt ttctactatt gcagccctgt tgactcgatt gactcgtgtt 3060 gatgtccctt ttgtttggtc agaggagtgt gaggcgagct ttttgaggct caaggagtta 3120 ttgaccactg ctcctatatt gactcttcca gttgagggcg agggcttcac agtttattgt 3180 gacgcatccg gcgttggttt gggttgtgta ttgatgcagc agggccgggt tattgcttat 3240 gcgtcgaggc agcttaagat ccatgagcac aactacccca ctcatgactt ggagttggcg 3300 gcggtagttt tcgcgcttaa gatttggagg cactacctgt atggagttcg atgtgagatc 3360 tataccgatc ataggagtct tcagtacatc atgagccaga gggaccttaa ttcgaggcag 3420 cgtcgttgga ttgagctcct gaaggactac gacctctcta ttctctatca tccgggcaag 3480 gcgaatgtgg tagctgatgc cttgagccgg aaggcagtga gtatgggtag tctagccttc 3540 ttatctgttg aagagcgacc cttagctttg gacattcagt ccttagctaa tagcatggtt 3600 cggttggata tctcagattc tagatgcgtc ttggccttta tgagagttca gtcttctttg 3660 cttgatagga tccgtggttg ccagtttgag gatgatacct tggtggccct tagagatcga 3720 gtgttagcgg atgatggtgg tcaggctacc ttagatcctg atggagtgtt gaaatttgcc 3780 ggccgcatct gtgttccgag agttggagat ttgatacagt tgatactttc tgaggcccat 3840 gagtctagat actctatcca tccgggcaca gcgaagatgt atcgtgattt gaggcagcat 3900 tactggtgga gtggcatgag gagagatatt gctgactttg tttcccgttg cttgtgctgc 3960 cagcaggtaa aggccgagca tttgaggcct ggtggcgagt tccagagatt acccattccg 4020 gagtggaagt gggagcgtat cactatggac ttcgttgtgg ggttgcctcg gacttctaga 4080 ggtgttgaca gcatttgggt catcgtggat cgattgacca agtcagcaca cttccttcct 4140 gttcatacta ctttcagtgc cgagaggttg gctcgtatct acattaggga ggtagtccgt 4200 cttcatggtg tgcctgtttc tatcatttca gatcggggtt cacagttcac ttccagcttt 4260 tggagggctt ttcaggagga gttgggaacc cgtgtccacc ttagcacatc atttcaccca 4320 cagacggatg gtcagtcaga gcgtactatt caggtccttg aggatatgtt gcgggcctgt 4380 gttatggatt ttggaggtca gtgggagcag ttcttgcctt tggcggagtt tgcgtacaac 4440 aacagctacc actctagtat tcagatggcc ccgtttgagg ccttatatgg taggcgttgt 4500 cgctctccag ttggttggtt tgagtctaca gagcctaggc cgcgtggtac agatttgctt 4560 caggaggccc tggatcaggt gagggtgatc caggataggc tcaggacggc tcagagtagg 4620 caccagagtt atgcggatca gaggcgtcga cctttgagat tctctgttgg tgaccgggta 4680 ttcctccgtg tgtcgcccat gaagggcgtg atgaggtttg ggaggcgggg caagcttagc 4740 cccaggtaca ttgggccttt tgagatactc cggacagttg gagaggttgc ttatgagttg 4800 gctctacctc cagtattttc agccatccac ccagtgtttc atgtttcgat gctgcggcgg 4860 tatgttcctg atgagtccca tgtgctccag tatgatgcag tcgagttgga tgatcgtttg 4920 acatttgtag aggagccagt tgccattcta gccagagatg tgaggagatt gcgctcgaga 4980 gccattcctg ttgttaaggt ccgttggagg catcgtccag tcgaggaggc tacctgggag 5040 accgagcagg agatgcgaga gcagtttccc agcttgtttg agccttcagg tacttcttga 5100 tcctttcttt cgcggacgaa agtccttttt agtagtggat at 5142 // ID Gypsy-37_Mad-LTR repbase; DNA; EDCOT; 1494 BP. XX AC . XX DT 13-OCT-2010 (Rel. 15.1, Created) DT 13-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-37_Mad-LTR. XX NM Gypsy-37_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1494 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1769-1769 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 1494 BP; 438 A; 254 C; 282 G; 519 T; 1 other; tgttgagtgc ataaagttat acttttacgc cctcttttac ttaggttttt gacttaaaat 60 ctctatgcat cacaaggtat tttgttgttt gtattgtatt tcaggatgaa agtaagggct 120 tgaagaaatc atcttatttt gaatatttta agagcctaga atggatagtt tgaagcccaa 180 ctcgcccaag accagaccat agcccacaag tggcccaaga tccgccagaa aaggcccttg 240 cagaacagcc aacttgcgag ctttgccccg aagtgctcag aacgaattag aaaatgggcc 300 atatatggtt ggaaagccct ggaagtcttc tttctgatgg tctttacagc ttgtgatttg 360 gaggtttcga caagaagtta tgacagaata aagaggagct gttcagttac aaattctgat 420 aacagctagt tttcagttac tcctatacta aaagctgatt gtaatgagct ataaatgaga 480 gtcaattcaa ggatgtaaat gtgtcagatg ttagaaaact cctaagcctt ttaataggag 540 aaaaatacac agaatcagaa ggaggaaaag gaggagaaca cagaatctgg agagagcagg 600 agtcttcagc cttgagcagt ttctaggttc tagctttcct aactttttat gtattttgtt 660 atgtttttaa tttagtttat ggatacttag ggctgctttg aagccctaga catgattgaa 720 ttaatgttat gatgcagttt tagtttatca atttcatttg caagctagaa tcagttttct 780 gtctcaatca tttcaagcac atattttcaa gcttagctac cttgtttatg tttgctttct 840 gttgagaatg ataaggatga ctgccatatc ttctttcatt cattagcaac atgtggttag 900 gttcagaact aatcatgtaa actgattcca tgaagatcta ggataaatgc catgttctag 960 ggttcatgtg atgttcataa tcctcttcgt tcttaatgag tttctaggtg ctaaatctga 1020 gtatatgcca tgctaggttg cacctacaaa tataagtttt atgtatatgc catgcatcta 1080 acatgcaaag aaagtgagga ttcatacaat ctagttatat gccatgctag atatgtgaac 1140 atcttagttg tgcatttgaa atggataagt taaaagatca tmtcattgat tcatgaatgt 1200 ttaggggaag gccttagctc attttaagtc agatttatgt cctaaaaacg tttctaacct 1260 atttcatgtc ttaggtttat ttttagatag ttctaatttt tcccttttct ttctgtcttt 1320 atttcttttc caaaattact caaacccccc attttaagtc ataggagtct ttaactaatg 1380 ctaatttgta agagtcaaag gttttactaa gttgtttctc agtccctgtg gttcgacacc 1440 cttacttgtg ccactatact atccttatat ttgcactcga aaggaacttc aaca 1494 // ID COP10_I_MT repbase; DNA; EDCOT; 4470 BP. XX AC . XX DT 01-JAN-2007 (Rel. 12.01, Created) DT 06-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, COP10_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; internal region; KW LTR; retroposon; Interspersed; repeat; COP10_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4470 RA Shankar R. and Jurka J.; RT "COP10_MT: A copia type LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 5-5 (2007). XX DR [1] (Consensus) XX CC The internal region contains a single ORF, having domains for CC gag-pol polyproteins. Flanked on both termini by LTRs. XX FH Key Location/Qualifiers FT CDS 97..4467 FT /product="COP10_I_MT_1p" FT /translation="MAPRNNNGAGSSYEVALDQTSPYFVHSSDGPSSVTVT FT PLLNGSNYHSWARSMRRALGGKMKFEFVDGTISPVTDSFDPSFRAWNRCNM FT LIHSWILNSVDSSISQSIVFMENAMDVWNDLKERFAQGDLVRISELMQEIY FT SLQQDSKSVTNFYSELKVLWEELEIYLPMPSCSCRIQCSCEAMRTARKNHV FT LLYAMRFLTGLNENFNMVKSQILLMDPLPPMNRIFSMVLQHERQGNFAPII FT EDSLPSINAVNSGKPKYGNSGNMYKNTNQSSNSNYNKNRSCTFCGRSNHTI FT ETCYKKHGYPPHLQRNFNNSSYANHTASSETENPTSDEPGRVASTSITNEQ FT YEKLMSLLQVSSSKQDSVTAQASANQVFSTPSGHTSNGKHSTSCILSLTCH FT SFALNSWIIDSGASDHICGNLQWFHSYNEITPMHIKLPTGHYAIAKHAGTI FT KFSSNFSISHVLYVPEFHFNLLSVSKISDSLNCIVIFDGSKCLIQEKNTQR FT MIGSGEKREELYYLNPPDKMVCSSSIVKSPSTFLPDSALWHFRLGHLSFSR FT MNVLHSKFPFVNVDSKATCDVCHFAKHRKLPFTPSCNKAKQPFELIHFDIW FT GPISIKSIHGHSYFLTAVDDFSRYTWLTLMKTKAETRQHIVDFITLIENQF FT SYKVKTIRSDNGPEFLMPNFYSSKGILHQRSCVETPQQNARVERKHQHILN FT IVRALLFQSHLPKQFWSYAAIHAVFIMNRVTSPIIDNNTPYFLLHKQIPDL FT NQLKVFGSLVFSSTLQANINKLASRARKCAFLGYKSGMKGVVLLDIITKEI FT FVSRNITHHENIFPYQPVSSPPLWNYYSSIPSKSLDQNLDSNSSVCNDFTS FT SDQNSPTQTSLDMHIDNAPNPDITDTSLPSISKPARIRNAPSYLTDYVCNS FT SSAFASAPKSSGTLYPIASYHSYAHLSSSQKSFSMSVTQCTEPKTYKEASQ FT SECWLKAMDSELEALAKNGTWSIVDLPHNVKPIGSKWVYKIKHKADGSIER FT YKARLVAKGYNQVEGVDFFDTFSPVAKLTTVRILLAIASIKNWHLHQLDVN FT NAFLHGDLQENVYMNIPEGVSSAPNKVCKLHKSLYGLKQASRKWYEKLTSL FT LIAEGYTQSPSDYSLFTIQQGSNFTALLVYVDDIILAGSSITEFTRIKAIL FT DAHFKIKDLGILKYFLGLEVAHSKEGISISQRKYCLDLLDSSGLLASKPAS FT TPLDTSIKLHQDNSKPFADVSCYRRLIGRLLYLNTTRPDITLATQQLSQFL FT NAPTVSHYKAACRVIRYLKHNPGLGLFFPRHSDLQILGYVDADWAGCIDSR FT RSTTGFCFFLGSSLISWRAKKQATISRSSSEAEYRALSTGTCELQWLLYLL FT KDLQVTCIRQPVLYCDSQSAIHIASNPVFHERTNHLEIDCHLVREKVQKGI FT LRLLPISTEEQLADFLTKPLSPPKFNSFVSKLGMINIYHAPAC" XX SQ Sequence 4470 BP; 1343 A; 858 C; 737 G; 1532 T; 0 other; atggtatcta gagcctcttg atccaaagag agcttcttct tccgctacga ttctctcttt 60 tcttcttcgt tttcctttct ctgttcttca gttttcatgg cgcctcgcaa caacaatggt 120 gcaggttctt cctatgaggt tgctcttgat caaacaagcc cgtattttgt tcattctagt 180 gatggtcctt cttctgtaac agttacgcca ttgttgaatg gttctaacta tcattcttgg 240 gctcgttcga tgcgaagagc tcttggggga aaaatgaagt ttgaatttgt tgatggaact 300 atttctccgg ttacagattc gtttgatcct tcttttcgtg cttggaatcg gtgtaatatg 360 ctgattcact catggatctt gaattcagta gattcttcaa tttctcaatc tattgttttc 420 atggaaaacg ccatggatgt gtggaatgat cttaaggaac gttttgctca aggtgatttg 480 gttcgtattt ctgaacttat gcaagaaatc tattctttac aacaagattc aaaatctgtt 540 actaatttct actctgaatt gaaagtatta tgggaagagt tagaaatcta tctacctatg 600 cctagctgta gttgcagaat ccaatgttcc tgtgaagcta tgcgcactgc taggaaaaat 660 catgttctgt tatatgctat gcgttttctt actggtctca atgaaaattt caacatggtg 720 aagtctcaga tccttctcat ggatcctctt ccaccaatga ataggatttt ttctatggta 780 ttgcaacatg aaagacaggg taattttgca cctattattg aagattcttt accttctatc 840 aatgctgtga actctggaaa acctaagtat ggtaattctg gaaatatgta caaaaatacc 900 aatcaaagtt ctaattccaa ctataacaag aataggtctt gtactttctg tggtagaagc 960 aatcatacca tagaaacttg ttataaaaag catggatacc ctcctcatct ccagagaaat 1020 ttcaataatt catcttatgc taatcatact gcatcttcag agactgaaaa tcccacttct 1080 gatgagcctg ggagagttgc ttctacatct atcacaaatg aacaatatga aaagttaatg 1140 agtttacttc aggtttcatc ttctaaacaa gattcagtaa ctgcacaagc ttctgcaaat 1200 caggtttttt ccactccatc tggtcataca tcaaatggta agcacagtac tagttgcatt 1260 ctttctttaa cttgtcatag ttttgctcta aactcctgga tcattgattc aggagctagt 1320 gatcacattt gtggaaatct tcaatggttt cattcttaca atgaaatcac tcctatgcat 1380 ataaaattgc ctactggcca ctatgcaata gccaaacatg ctggaaccat taagtttagt 1440 tcaaattttt caatatctca tgtattatat gtgcctgaat ttcatttcaa tctattatct 1500 gtgtcaaaaa tatctgattc actaaattgc attgtcattt ttgatggttc caaatgtctt 1560 attcaggaaa agaatactca gaggatgatt ggttctggtg aaaagagaga agaattatat 1620 tacttgaatc caccagataa gatggtttgc agttctagca ttgtcaaatc accctccact 1680 tttttacctg atagtgcctt atggcatttt agactaggtc atctctcttt ttccagaatg 1740 aatgttttac attcaaaatt tccctttgta aatgttgata gcaaagctac ttgtgatgta 1800 tgtcattttg ctaaacatag gaaacttcct tttactccca gttgtaataa agcaaaacag 1860 ccttttgagc taatacattt tgatatttgg ggtcctattt ctattaaatc catacatggt 1920 cattcttatt ttctcactgc tgtagatgat ttcagtaggt atacttggtt aactttgatg 1980 aaaaccaaag ctgaaaccag acaacacatt gttgatttta ttactcttat tgaaaatcag 2040 ttttcttata aagttaaaac cataagaagt gataatggtc ctgagtttct catgccaaat 2100 ttttactctt caaaaggaat tttacatcaa agaagttgtg tggaaactcc tcagcaaaat 2160 gctagagttg aaagaaaaca tcaacacatt ttaaacattg tgagagcttt actttttcaa 2220 tcacatcttc ctaaacaatt ttggtcttat gctgctattc atgctgtctt catcatgaat 2280 agagtgacca gccctattat tgacaataac actccttatt ttctattgca taaacagata 2340 cctgatttaa atcaactgaa agtttttggt tctttagttt tttcatccac tttacaagca 2400 aacataaaca aacttgcttc tagagcaaga aaatgtgcct ttttaggtta taaatctggc 2460 atgaagggag ttgtcttgct tgatataatt acaaaggaaa tttttgtttc tagaaatatt 2520 acacatcatg aaaatatctt tccttatcaa cctgtatcat ccccacctct ttggaactac 2580 tactccagca taccttcaaa atcattagat caaaatcttg attccaattc ttctgtttgc 2640 aatgatttta cttcttctga ccaaaattct ccaacacaaa catcccttga tatgcacatt 2700 gataatgcac ctaaccctga tattacagac acttctttac catcaatttc caaacctgcc 2760 agaattagaa atgcaccttc ttatctgaca gattatgtat gtaattcttc atctgctttt 2820 gcatccgcac caaaatcctc aggtactctt taccctattg catcatatca ttcttatgca 2880 catctatcat catcccaaaa gtctttttct atgtctgtca cacaatgtac tgagccaaaa 2940 acctacaaag aagctagtca gtctgaatgt tggttaaaag ctatggattc tgaattagaa 3000 gcattagcta agaatggaac ttggtctatt gttgatcttc ctcacaatgt gaagcctatt 3060 ggtagtaagt gggtttataa aattaagcac aaggcagatg gcagtataga aagatacaaa 3120 gctagactgg tggctaaagg atataatcaa gttgaaggag ttgatttttt tgatactttt 3180 tcaccagtag ccaagcttac cacagtgaga attttacttg ccatagcttc aatcaaaaac 3240 tggcatttac atcagttgga tgtaaataat gcttttctac atggtgattt gcaagagaat 3300 gtttacatga atataccaga aggtgtctct agtgcaccaa acaaggtttg caaattacat 3360 aagagcctat atggtttgaa gcaagcaagt aggaaatggt atgagaagtt gacatcttta 3420 ttgatagcag aagggtatac acagtcacca tcagactatt cacttttcac cattcaacaa 3480 ggttctaatt ttactgcctt attagtatat gtagatgaca ttattcttgc tggttcatct 3540 atcactgaat tcactagaat caaagctata cttgatgctc atttcaagat caaagatttg 3600 ggaattctaa agtatttttt aggattagag gttgctcatt ccaaagaggg gatctctatt 3660 tctcaaagaa agtactgtct tgacctattg gattcttctg gacttttagc ttctaaacct 3720 gcttctactc ctctggatac ttccatcaaa ttgcaccaag acaatagcaa accttttgct 3780 gatgtgtctt gttacaggag actcattgga agacttctct atctcaatac tacaagacca 3840 gatatcacac tagcaactca acaactcagt cagtttttaa atgctcctac tgtatcgcat 3900 tacaaagctg cttgtagggt catcagatac ttgaaacata accctggact tggtttattc 3960 tttcctagac attctgattt acaaatcctt ggttatgtag atgctgattg ggctggttgt 4020 attgattcta gaagatcaac aacaggtttt tgtttcttct taggttcatc attgatctca 4080 tggcgtgcaa agaaacaagc aactatttct aggtcatcct cagaagcaga gtatagagca 4140 ctttctactg gcacatgtga acttcagtgg ctgctatatc tcttgaaaga tttacaagtt 4200 acttgcatca gacaacctgt gttatactgt gatagtcaga gtgcaattca catagcttcc 4260 aatccagtat ttcatgagag aactaaccat ttggaaatag attgccatct tgtcagagaa 4320 aaggtacaaa aaggaatact aaggttgctt cctatatcta ctgaagaaca gcttgcagat 4380 ttccttacaa aacctctgtc acctccaaag ttcaattctt ttgtatccaa gcttggaatg 4440 ataaatattt atcatgctcc agcttgtggg 4470 // ID Copia3-VV_I repbase; DNA; EDCOT; 5086 BP. XX AC AM448401; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 03-SEP-2008 (Rel. 13.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; internal portion; LG_I; Copia3-VV_I. XX NM Copia3-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5086 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-5086 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 679-679 (2007). XX RN [3] RP 1-5086 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1/copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9, (2008). XX DR [3] (Consensus) XX CC ize = 5485 bp CC LTR = 200 bp CC LTR are 100 % similar to each other. CC Direct flanking repeats = gaagt CC UTL size = 617 bp CC gagpol putative polyprotein size = 1486 aa. XX FH Key Location/Qualifiers FT CDS 618..5075 FT /product="Copia3-VV_I_1p" FT /note="Putative gagpol polyprotein." FT /translation="MTKYGMASSQVSSVTSPESGGRSEIPNLGGNDSSPIL FT ITGHKLNGHNYLQWSQSVLLFICGKGKDEYLTGEAVMPETTEPGFRKWKIE FT NSMIMSWLINSMNNDIGENFLLFGTAKDIWDAAKETYSSSENTSELFQVES FT ALHDFRQGEQSVTQYYNTLTRYWQQLDLFETHSWKCSDDAATYRQIVEQKR FT LFKFFLGLNRELDDVRGRIMGIKPLPSLREAFSEVRREESRKKVMMGSKEQ FT PAPTLDASALAARSFNSSGGDRQKRDRPWCDYCKKPGHYKETCWKLHGKPA FT DWKPKPRFDRDGRAHVAANSESTSVPEPSPFNKEQMEMLQKLLSQVGSDST FT TGVAFTANRGGMRPWIVDTGASDHMTGDAAILQNYKPSNGHSSVHIADGSK FT SKIVGTGSIKLTKDLYLDSVLHVPNLDCNLLSISKLAHDLQCVTKFYPNLC FT VFQDLKSGKMIGSAELCSGLYLLSCGQFSNQVSQASCVQSQSMLESFNSVS FT NSKVNKDSEIIMLHYRLGHPSFVYLAKLFPKLFINKNPASYHCEICQFAKH FT TRTVYPQIPYKPSTVFSLVHSDVWGPSRIKNISGTRWFVTFVDDHTRVTWV FT FLMKEKSEVGHIFQTFNLMVQNQFNSKIQVLKSDNAKEYFTSSLSTYLQNH FT GIIHISSCVDTPQQNGVAERKNRHLLEVARCLMFSSNVPNYFWGEAILTAT FT YLINRMPSRVLTFQSPRQLFLKQFPHTHAASSDLPLKVFGCTAFVHVYPQN FT RSKFAPRANKCIFLGYSPTQKGYKCYSPTNKRFYTTMDVSFFEHVFFYPKS FT HVQGESMNEHQVWESFLEGVPSFHSESPNPSQFAPTELSTPMPPSVQPAQH FT TNVPSPVTIQSPMPIQPIAPQLANENLQVYIRRRKRQELEHGSQSTCGQYI FT DSNSSLPEENIGEDRAGEVLIPSIDDSTLPIALRKGVRRCTDHPIGNYVTY FT EGLSPSYRAFATSLDDTQVPNTIQEALKISEWKKAVQDEIDALEKNGTWTI FT TDLPVGKRPVGCKWIFTIKYKADGSVERFKARLVARGFTQSYGIDYQETFA FT PVAKLNTIRILLSLAVNQDWCLQQLDIKNAFLNGDLEEEVYMEIPPGFEES FT MAKNQVCKLQKSLYGLKQSPRAWFDRFTKAVLKLGYKQGQADHTLFVKKSH FT AGKLAILIVYVDDIILSGNDMGELQNLKKYLSEEFEVKDLGNLKYFLGMEV FT ARSRKGIVVSQRKYILDLLKETGMLGCKPIDTPMDSQKKLGIEKESTPVDR FT GRYQRLVGRLIYLSHTRPDIGFAVSAVSQFMHSPTEEHMEAVYRILRYLKM FT TPGKGLFFRKTENRDTKVYSDADWAGNIIDRRSTSGYCSFVWGNLVTWRSK FT KQSVVARSSAEAEYRALAQGICEGIWIKRVLSELGQTSSSPILMMCDNQAA FT ISIAKNPVHHDRTKHVEIDRHFITEKVTSETVKLNYVPTKHQTADILTKAL FT PRPNFEDLTCKLGLYDIYSPA" XX SQ Sequence 5086 BP; 1454 A; 1143 C; 1107 G; 1382 T; 0 other; tggtatcaga gccagttttc tgaaacccta atcccttctg gccacctctt tattcaggcc 60 atcactcatt ccggccaaat ctctctggcc atatctcaat ccaatcatct ctctctctct 120 ctctctctct cattccggtc atcagtccct attctcagag ccaagggaga aaacgctttc 180 cggtcagtcg actcgtcgtc agaaaacact caccgccgac aactttttcc ggcgaacttt 240 ccggcgaggg tttttttttt ctacatcgca aggagcgcct ggaggagatc tccaatttgt 300 cccaaagcac cggagccaga aacccatcca cgcgccgccc acgcgcgttt ttccggccgg 360 tgactgcatc tcacgcgccg gcgcgtgagg gcgcgtgagc cactttccgg cgacgcgctt 420 cctcctccag gctcgcctga cgccgaccag ccacccttcc tacctgtttg tgcaatccga 480 gccctacacg tgcctctttt ggggttcttt tgcttccgcg ggccctctga tcagattttc 540 cggcgtcctc cggctatttt ttctcaactc cagtccctgc acgtgccttg agaagtgttc 600 ttctatcttt ccggtccatg acaaaatacg gaatggcatc atcacaagta tccagcgtca 660 cgtcaccaga atcagggggc agatctgaaa ttccaaacct tggtggcaat gattcctctc 720 ctattctcat cacaggacac aaattaaatg gccataacta tttacagtgg tcacaatctg 780 tgttgctgtt catttgcggt aaaggaaagg atgagtacct cactggagaa gcagtcatgc 840 cagaaactac agaaccgggt ttcaggaagt ggaagattga aaacagcatg atcatgtcat 900 ggcttatcaa ttccatgaac aatgacatag gcgaaaattt cttgctgttt gggactgcaa 960 aggacatatg ggatgcagcc aaagaaactt actcaagttc tgaaaatact tcagaactgt 1020 ttcaggttga atcagctcta catgacttcc gccaaggaga gcagtcagtt actcagtatt 1080 acaacacact cacaaggtat tggcagcaac ttgacttatt tgagactcac tcatggaaat 1140 gttcggatga tgcagctaca tacaggcaaa ttgtggaaca aaagagactg ttcaagttct 1200 tcctaggact aaatagggaa ttggatgatg ttagaggccg aatcatgggc attaaacccc 1260 tgccaagtct cagggaggct ttttcagagg ttaggcgtga agaaagtaga aagaaagtga 1320 tgatgggatc aaaagagcaa cctgccccaa cattggatgc ctctgccctt gctgctcggt 1380 catttaatag tagtggtgga gatcgtcaga aacgggatag gccttggtgt gattattgta 1440 agaaaccagg ccattataag gagacttgct ggaagcttca tggcaaacct gctgattgga 1500 aaccaaagcc acggtttgac agagatggca gagcacacgt ggctgccaac tctgagagca 1560 catctgttcc cgagccgagt ccattcaaca aagagcagat ggagatgcta cagaaattat 1620 taagccaagt tggcagtgac agtactaccg gtgtagcctt cactgctaat cgaggaggaa 1680 tgaggccgtg gatagtagac acaggtgctt ctgatcacat gacaggagat gctgccattc 1740 ttcaaaatta caagccaagt aatggtcatt catccgtcca tattgctgat ggttcaaagt 1800 caaaaattgt cgggacaggt tctataaaac ttactaaaga cttatatctt gactctgtcc 1860 tccatgttcc aaacttggat tgtaatcttt tgtccattag caaattggct catgatctcc 1920 aatgtgttac taaattctat ccaaacttgt gtgtttttca ggacttgaaa tcggggaaga 1980 tgattggcag tgctgaactg tgttccggtc tctacctcct ttcatgtggc caattctcaa 2040 atcaagtctc tcaagcaagt tgcgtccagt ctcagagtat gttagagtct ttcaattctg 2100 tgtcaaattc taaggtcaat aaagatagtg agattataat gttacactat cgccttggtc 2160 atcctagctt tgtttacctt gcaaaattgt ttcccaaatt atttatcaat aaaaatccag 2220 catcttatca ctgtgaaatt tgtcagtttg caaagcatac tcgaacagta tatcctcaaa 2280 tcccatacaa accttcgact gttttctctc tagtacatag tgatgtgtgg ggtccctccc 2340 ggataaaaaa tatttctggc actcgatggt ttgtgacatt cgttgatgat catactcggg 2400 taacatgggt tttccttatg aaagaaaagt cagaggtcgg gcacattttt caaaccttca 2460 atcttatggt tcaaaatcaa ttcaattcca aaatacaagt cctcaagtca gataatgcaa 2520 aggaatactt tactagtagt ctcagtactt atcttcaaaa tcatggcatt atccacataa 2580 gttcttgcgt tgacacccca caacaaaatg gggtggccga acgcaagaat agacatctct 2640 tggaggttgc ccggtgcctt atgttttcct ctaatgttcc aaactatttc tggggggaag 2700 ctattctcac agctacctat ttgattaacc gtatgccatc cagagtgctt acctttcaat 2760 ccccacgtca acttttctta aaacagtttc ctcacaccca tgccgcctct tctgatttac 2820 cactcaaagt atttggttgt acggcattcg ttcatgtgta tcctcaaaat cgtagcaaat 2880 ttgctcctcg agcaaataag tgcatttttc tagggtattc tccaacccaa aaagggtaca 2940 aatgctattc tccaaccaac aaaagatttt acaccaccat ggacgtctct ttctttgaac 3000 atgtcttctt ctatcccaaa tctcatgttc agggggagag catgaatgaa catcaagttt 3060 gggagtcttt tcttgagggt gtaccttctt ttcactcaga gtcaccaaat ccttcccaat 3120 tcgcgcccac tgagttgtcc acacccatgc cgccatcagt tcagccagcc cagcacacaa 3180 atgttccttc tcccgtgacc atccagtctc ccatgcctat tcaacctata gccccacaac 3240 ttgctaatga gaacttacaa gtttacatca ggaggaggaa aagacaggaa ttagagcacg 3300 gatcacagtc aacatgtggc caatatattg actccaattc aagtcttcct gaagagaaca 3360 taggtgagga tagggctgga gaggtgttaa ttcccagcat tgatgattct actttgccaa 3420 ttgcattgag gaagggtgtt aggagatgta cagatcatcc aattgggaat tatgttacgt 3480 atgaagggtt atcaccatct tacagagcat ttgctacttc tcttgatgat actcaggttc 3540 ccaacacaat acaagaggca ttaaaaattt cagaatggaa gaaggcagta caagatgaga 3600 ttgatgcact tgagaagaat gggacgtgga ctatcacaga tttgccagtt gggaagaggc 3660 ctgtggggtg caagtggatt ttcaccataa aatacaaagc agatggatca gtcgaaagat 3720 tcaaggctcg tttggtagct agagggttta cacaatccta tgggatagac tatcaggaga 3780 cttttgctcc tgttgcaaaa ctgaacacta tcaggatcct tctctcattg gctgtcaatc 3840 aagattggtg cttgcaacaa ctggacataa aaaatgcgtt tctaaatggg gacctagaag 3900 aggaagtcta catggaaata ccacctggtt tcgaagaaag tatggcaaag aatcaggttt 3960 gcaaactcca aaaatccttg tacggcctta aacaatctcc tcgagcctgg tttgatagat 4020 tcacaaaagc agtcctgaag ctgggctaca aacaaggtca ggctgatcat actctatttg 4080 tcaagaagtc tcatgccggg aaattggcca tattgatagt ctatgtcgat gatattattc 4140 tatctggaaa tgatatgggg gagttacaga atttgaagaa gtatttgtca gaagagtttg 4200 aagttaaaga ccttggaaat ttgaaatatt tccttggtat ggaagtggct agatcaagga 4260 agggaatcgt agtctctcaa agaaaataca tcctcgatct tcttaaggag accggtatgc 4320 ttggatgcaa accaattgat actcctatgg atagtcagaa gaaacttggt atcgagaaag 4380 aaagtacacc ggtagacagg gggagatatc agcggcttgt cgggcgcttg atttatctct 4440 cacacactcg gccagatatt ggctttgcag tgagtgctgt aagtcaattc atgcacagcc 4500 ccactgagga acacatggaa gcagtctaca ggattcttag atatttaaaa atgacaccag 4560 ggaaaggcct attcttcaga aagacagaga accgtgacac taaagtatac tcagatgcgg 4620 attgggcagg aaacatcatt gacaggcggt ccacttccgg atattgttct tttgtctggg 4680 gaaatcttgt tacctggagg agtaagaagc aatcagttgt agccagaagt agtgcagaag 4740 ctgagtacag agctcttgca cagggaatct gtgaagggat ttggataaaa agggttctta 4800 gtgaactggg acaaacgagt tcatctccaa ttctgatgat gtgtgataat caggccgcta 4860 taagcatagc aaagaacccc gtgcatcatg acaggaccaa gcatgttgag attgacagac 4920 actttatcac agagaaggtg actagtgaga cggtcaaatt aaactatgtt cctaccaagc 4980 accaaaccgc agacatcctc accaaagctt tacctaggcc taacttcgaa gacttaactt 5040 gcaagctggg attatatgat atatattctc cagcttgagg gggagt 5086 // ID Gypsy10-PTR_LTR repbase; DNA; EDCOT; 941 BP. XX AC scaffold_156; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy10-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-941 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-941 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 299-299 (2007). XX DR Genome; scaffold_156; Positions 225078 224138. XX SQ Sequence 941 BP; 297 A; 157 C; 182 G; 305 T; 0 other; tgatgtgcat catgggaatt ataatccatc ttgtaaagct aaaactaatg tgcaagagga 60 ttcagatggt ccaatgacaa gagcgagagc gaaacaacta caaagggcct tgacgagtca 120 aattggaatg attgaagctg cgtcagagtt aaaaattagc aatcagtttg aaattggttc 180 aaagatgttt atttgcctac aattggaact tggagatgag aaaagccctt aatttttctt 240 tgatgctggg ctactcgaaa tttggttgat atgcaaataa gtgaaggaat tgatgctgtt 300 tatggtcaga acagcaaatg aatttgaacc cgaatttgaa gtcatccatt gcatgtgaaa 360 acaagactaa tctaggtgga tttcaagttc agaacgtgtt ctttctagat tgttcaacca 420 tgattgcatt ggacttttgt ataagaagat atggttgttt taaatttggt ctgtttatgt 480 tagaaaggtc aaaaaacgtg tgctagttaa tttgtctagg ttagtttgtc aaagtctgtt 540 ttttgggctt gacttctgcc atgttgaatt attcctaatt tggggggatg ttccaattat 600 aaatatagta tcagaatatg taataaagaa cttttggcca agatttgaaa cttaattcac 660 agaattaaga gttgttcttc caaattgatt ttgtgaagaa ccctacctga cttatcactc 720 ttcaatcaca aagagtgtgg cgtcgaaatc ctagattgat ctttgtggcg tccagatcga 780 cttatcaaag tatcattcta gtctatcctc catcttattt accttgaaat cactataatc 840 cagcctaaac accaaaagaa agacaacaca accagaccca tccttcatcc attttcgtca 900 gattcattgt tgccgatttt caaatcattc acggcacatc a 941 // ID Copia29-PTR_LTR repbase; DNA; EDCOT; 274 BP. XX AC scaffold_97; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia29-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-274 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-274 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 233-233 (2007). XX DR Genome; scaffold_97; Positions 1081034 1080761. XX SQ Sequence 274 BP; 115 A; 43 C; 39 G; 77 T; 0 other; tgtagaagaa caagtcaaag agaaagagta tgctgcaaca accaccaaat ctgcaggatc 60 gtagctatcc aatattcaaa gtttgaaatc aaacaagatt gtatctattg tttaaaattc 120 aaactatcag atatacatgc acatatgtag gaaatcagtg agtattatca cgtatttaaa 180 ccctctgtac atgcacacaa aaacaatgaa aaaagatata gaagacagtc ttcaaatatt 240 tcttctttaa gatataaaag tttatatata tgca 274 // ID Copia28-PTR_I repbase; DNA; EDCOT; 4277 BP. XX AC scaffold_857; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia28-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4277 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4277 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 230-230 (2007). XX DR Genome; scaffold_857; Positions 10688 6412. XX CC Positions [1664-2194] - Integrase core CC 'GGTTT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 236..2734 FT /product="Copia28-PTR_I_1p" FT /translation="MSTADKFVQPSIPRFDGHYDFWAMTMENFLRSKEMWN FT LVDEGIPTLAVGNAAASEAQRKSVEEIKLKDLKVKNFLFQAIDREILETIL FT DKRTSKAIWDSMKQKYQGSTKVRRAQLQALRKEFELLAMKEGDKIDSLLGR FT TLALVNKMKTNGEAMEQSTVVGKILRSLTPKFNYVVCSIEESNDLSVLSID FT ELHGSLLVHEQRMQGQQIEEQVLKVVYDERSTRRRGRNMYRGGRGRGRGRQ FT TSNKALVECFKCHKLGHFQYECPDWEKRVNYAELDEEEELLLMSYVELHNS FT KREVVWFLDSGCSNHMTGNKQWFVELDEEFSHSVKLGNNLRMPVEGKGNIR FT LEIEGITQVISEVYYVPELKNNLLSIGQLQEKNLAILMQNGECRVYHPRRG FT LIMHTQMTSNRMFVVLANIVLHASSTCLNVSSNHLGDLWHKRYGHLSFTSL FT NLLQQKELVQGLPKFQVPTSVCTSCMKGKQHREIIPKKSNWRATQQLQLIH FT SDLCGPITPESHGNERYVLTFIDDMSRKLWVYFLHEKSETFMTFKSFKNAV FT EKESGLSIAGLRTDRGGEFTSKEFTEFCRIEGIKRQLTTAYTPQQNGVAER FT KNRTILNMVRCLLEEKQMPARFWPDAVKWTCHILNRSPTSAVKNKTPEECW FT SGVKPNVDYFRVFGCIGNVHVSNPQKLKLDARSQKCVMLGYSEESKGYKMV FT DPITKKVIVSKDVVFEEEQSWDWRKTEEDKNDMLDWGEVDADIYASSDEEN FT ETEESLEEGESSQSNDAAISHGSIPSNAAAPALPERRVTRAPAYLQDYIRG FT ENFEAEEEVQSFSLFMVSADPIYYEEAAKMK" XX SQ Sequence 4277 BP; 1473 A; 664 C; 1070 G; 1070 T; 0 other; tttggtatca gagcctaaaa aaaggggacc tgattgtgtg ggggtgtgag caagtataga 60 gtgtgtgaca gtgagatcaa acacgagtgt gagtgaaagt gtgtgagagt gtgtgtgaca 120 gtaagagcaa acacgagtgt gagtgaaagt gtgtgagagt gaaaatcaac acagagtgtg 180 tgagggtgag agtgaaaatc acaccgtgag agtgcaatca acacagaaaa tcgggatgtc 240 aaccgcagac aaattcgtgc agccttccat tccgagattt gatggccatt acgatttctg 300 ggcaatgaca atggagaatt tccttaggag caaggagatg tggaatcttg tggacgaagg 360 gattccaaca ctggctgttg gaaatgcagc agcaagtgag gcacagagga agagtgtaga 420 ggagatcaaa ctcaaagact tgaaagttaa aaatttcttg tttcaagcaa ttgacaggga 480 gattttggag acaattctcg acaagagaac atcaaaagct atttgggact caatgaagca 540 gaaatatcaa gggtccacaa aggttagaag agcacaactt caagctttga ggaaggaatt 600 cgagttacta gccatgaaag aaggagataa aattgacagc ctcttgggtc gaactctagc 660 cttggttaac aaaatgaaaa caaatggtga ggcgatggaa caaagcacag tggtgggtaa 720 gatacttaga tcattgactc caaaatttaa ctatgttgtt tgttcaatag aggagtcaaa 780 tgatctaagt gtcctgagta ttgatgaatt acatggaagc ctgcttgtcc atgaacaaag 840 gatgcaagga caacaaatag aggaacaggt gttgaaagtc gtatatgatg agagatcaac 900 cagaagaaga ggcagaaaca tgtatagagg aggacgaggt agaggacgag gcagacaaac 960 atccaacaag gctctggttg aatgtttcaa atgccataaa ttgggacact ttcaatatga 1020 gtgtcctgat tgggaaaaaa gggttaatta cgctgagttg gatgaagaag aagaactcct 1080 tttgatgtct tacgttgaac ttcacaattc gaagagagag gtcgtatggt ttcttgattc 1140 tggttgctct aaccatatga caggaaacaa acaatggttt gtggaactag atgaagaatt 1200 cagtcactcg gtgaaacttg gaaacaacct cagaatgcca gtggaaggga agggcaacat 1260 cagacttgaa atagaaggta taactcaagt aatatcagaa gtttactatg ttcctgaatt 1320 aaaaaataat ctgttgagca ttggccagtt gcaagagaaa aatttggcta ttttgatgca 1380 aaatggagag tgtagagttt atcatcctag aaggggttta attatgcata cacagatgac 1440 atcaaatagg atgttcgtag tattggcaaa tattgtgctg catgcatcat ctacctgttt 1500 aaatgtgagc agcaatcatc tcggtgattt atggcataaa agatatggcc acctaagctt 1560 cacaagtctg aatttactgc aacaaaagga acttgtccaa ggacttccaa agtttcaagt 1620 gccaacctct gtgtgtacaa gctgcatgaa aggaaaacag caccgagaaa ttattccaaa 1680 gaaaagcaat tggagagcaa cacagcagct gcagctcata cactcagacc tttgcggacc 1740 tatcactccg gaatcacatg gcaacgaaag gtatgtgttg accttcattg atgacatgag 1800 tagaaaactt tgggtgtatt tcctgcatga gaaaagtgaa actttcatga cattcaaaag 1860 ttttaaaaat gctgtggaaa aagaatctgg tctatctatt gctgggttaa gaacagatag 1920 aggaggggag ttcacctcca aagaattcac agaattttgc agaattgaag gcattaaaag 1980 acagttgaca acagcttaca ctcctcaaca aaacggagtt gcggagcgca aaaatcgtac 2040 cattctaaac atggtacgat gtctgctaga agagaaacag atgcctgctc gtttttggcc 2100 agatgctgtg aaatggacat gtcatatcct caaccgaagc ccaacctctg ctgtaaagaa 2160 taaaacacca gaagaatgct ggagtggagt caagcctaat gttgattatt tccgagtgtt 2220 cggatgcata ggaaatgtgc atgtatcaaa tccacagaag ctgaaattgg atgccaggag 2280 tcaaaagtgt gtgatgctgg ggtatagtga agagtccaaa ggatacaaga tggttgatcc 2340 cataacaaaa aaggtgatag ttagtaaaga tgttgtgttc gaagaagagc aaagctggga 2400 ttggagaaaa acagaagaag acaagaatga tatgcttgat tggggagaag ttgatgcaga 2460 catatatgcc tccagtgatg aagaaaatga aactgaagaa tcactagaag aaggagaatc 2520 cagtcaatcc aatgatgctg caatatctca cggtagcatc cccagtaatg ctgcagcacc 2580 tgctctgccc gagagaagag tcactcgagc tccagcctat cttcaagact acataagagg 2640 ggaaaacttt gaagcagaag aagaggtaca aagtttttca ttgtttatgg tttctgctga 2700 tcctatttat tatgaagaag ctgcaaaaat gaaataatgg agggatgcaa tggatatgga 2760 gattggtgca atcttaaaga atgagacctg ggagcttgtt gatgcaccaa agcaagcaaa 2820 aataattgga gtaaagtggg tttataaaac caagttaaat gaaaatggag aggtggacaa 2880 atgcaaggct cggcttgtgg caaaaggata tgcacaagag aagggggtag actacaatga 2940 agtttttgcc ccagttgcta ggtgggacac aattcgcaca gtgatagctt tggcagcaag 3000 gaatggatgg acactttttc aacttgatgt caaaagtgct tttttttatg gcgagttgaa 3060 tgaagatgta tacattgcac aacctccagg ctatgagatt aacggggaag agaagaaagt 3120 ttataaattg aagaaagcac tttatggctt aaaacaggtg ccaagagcat ggtttagcag 3180 aattgaaggt tattttgcta aggagggatt tgagagaagt agctatgaac acacattgtt 3240 cataaagaag gaagagaaga acagaattct aattgtaagt ttatacgtcg atgatctcat 3300 ttttactagc aatgattcaa ttatggtgag caagttcaaa gagtcaatga aaaaggaatt 3360 cgaaatgact gatctcggtg aaatgaagta ttttctggga gttgaaattc ggcaaagttc 3420 caaaggcatt catattggtc agaaaaaata agcagaagaa atcttgaaaa gatttgggct 3480 ggaaaattgt aatggtgtta agaatcccat ggtttcagga agcaatagac tgacaaaaca 3540 agaagatggc aagaaggcag atgcaacctt gttcaaacaa atagtgggga gtttaatgta 3600 tataacagtc acaaggcctg acttggctta tagtgtgtgt ctgataagcc gtttcatggc 3660 caatcctatg gaatctcaca tgatggcagc caaaagaatt ctcagatata ttagagccac 3720 tactgatctt ggtgtattct acagaaaggg atgtgaagat gagatgctag cttatacaga 3780 tagtgactat gcaggggact tggatgatcg aaaaagcact tctggatatg ttttcatgct 3840 aagtggagga gcagtggctt ggtcatcaaa gaaatagccg gtggtgacac tctcaactac 3900 agaagcagag tttgtggcag ctgcatcttg tgcatgtcaa tgtatttggc tgcaacagat 3960 acttaaacag attggaggta ctgaaaggaa gtgtgtcaaa gttctgtgtg ataattcttc 4020 tacaataaaa cttgccaaaa atccagttct tcatggtagg agtaagcata ttgacgtaag 4080 attccatttt ctgaggaatc ttacaaagga tgaagtaatt gacatagagc attgtggtac 4140 aaatgagcag ctggctgata ttatgaccaa gcctctaagg ctggaactgt tcgagaaatt 4200 cagagctgca cttggggtga attcagctga agaaataaac taaactgctt caagcatgtt 4260 caatttaggg gagcaat 4277 // ID DNA8-8_Mad repbase; DNA; EDCOT; 1215 BP. XX AC . XX DT 18-OCT-2010 (Rel. 15.1, Created) DT 18-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA8-8_Mad. XX NM DNA8-8_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1215 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1480-1480 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TSD is 8-bp long. TIR is 23-bp long. XX SQ Sequence 1215 BP; 335 A; 296 C; 318 G; 265 T; 1 other; taggggtggg cacgggccgg gccgggccca aaattgaagg gaccggaccg gacccgcttg 60 aaaatacaac gggccgggcc ggggcggatt ctactatttt caaactgaga accggaccta 120 acccggcccg tataaaacgg gccggttcct acgggtccaa cgggtaccct gttttttttt 180 ttccttctaa ttttcagttt cttctccagc ttctcttgct cttcttacat caaaaaataa 240 caaacaaaca ataacatctg agaagatgta tcattcagaa taacattgca aatatgataa 300 agaaacagac aaaatcaaag catgggtcat attgtaatcc actacagaaa cgaggtgttc 360 tcagttctct cccatttgag catctggcaa caaaagaaaa acggagaaag cgccgccgga 420 gcataggctg cacagatcca acttcctcgc cagagagaga aagcttgagt tgatcacgtt 480 gtgcgccttc tcagttctct ccaccactcc ccactgcagc tggacgactc aaacgtggag 540 atccggtcga accccaagct atccttcgag cactcgtacc caccaaccaa gaccatcttc 600 atcctggaca aggagtgcca gaagccagac atgcgattga aaatttcaca acttttcaca 660 aattttgtaa atcaaaatta agaaattgac gaaattggaa gaaattaggg aaatgmgtta 720 cctcggtgtt gagatcggag gaggagacgg aggagttggt gggggaggag ggcggcggca 780 gcatatcatt tctcggtggg gtgtgggggt ggtgtgtttg tgctccggga agaagagttg 840 cagagatggg gggagaaaaa acaaagcaga agaatgagga aggttcgagc gattttgtta 900 cgaagactga gaaatggggt gtgtgtgtgt gtgttggaga ttgagaaatg tcacggccca 960 cggggaggaa caaaagaagt gggcttggga ggctgggaga caataacagt acccaacaaa 1020 ggggtttttt tgcaaacggg ccggtccggg tacccatttt tctacacttt tggaaccggc 1080 ccgaacctaa aatttcaaag gcccgccccg ccccgccccg tttctctttt ttaaaattag 1140 gcccgccccg tacccgcccc gaaccgctaa tacccgcccc tacccgcggg cccagggccc 1200 gtttgcccac cccta 1215 // ID BoSB12 repbase; DNA; EDCOT; 170 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB12. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-170 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 170 BP; 34 A; 52 C; 54 G; 30 T; 0 other; ccagcggcct tgggctagtg gtacttgagg ggaaaacccc caatacgcta cccgcagttc 60 gagtcccgct ggccacccgg gctagggtta aatcccaaga atacgtggag tgccgtgggc 120 ctcgcgggaa tagtcggttg accacggtcg ccggaaaccc gcggttacct 170 // ID RAM14_I_MT repbase; DNA; EDCOT; 4119 BP. XX AC AC151523; XX DT 08-JAN-2007 (Rel. 12.01, Created) DT 08-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of a LTR retroposon from Medicago truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW internal region; LTR; Interspersed; repeat; retroposon; KW RAM14_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4119 RA Shankar R. and Jurka J.; RT "RAM14_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 45-45 (2007). XX DR EMBL/GenBank/DDBJ; AC151523; Positions 14749 18867. XX CC The central domain of this internal region sequence is well CC conserved. The sequence is flanked on both termini by LTRs. XX FH Key Location/Qualifiers FT CDS 213..1040 FT /product="RAM14_I_MT_1p" FT /translation="MLARFATGASFSADSRGGGRDSNSRFLPFMFQMARHL FT LDLGSPLQRRTMARAVSAYISSSTSDVRPSSPSGTQLTLGTEETVQFMMVN FT SLLSESYESWLQHRRAFLQRGIYHAYMQHTHGRTTARSSSVSASVQGVESG FT STGQSATTEAGQNDELLSIIRPMLVYTGLIEQLQHFFKVKKLPSATPASID FT GVSSAAEGEDESGNLEGWELVMKERLLNVKELLGFPKEMISWLDEINSASD FT LQEAFDIVGVLPEVLSGGITRCEDFVQAAISAGKS" XX SQ Sequence 4119 BP; 1323 A; 680 C; 741 G; 1375 T; 0 other; gaattggact gattaagaca agataattaa aggagaaact gaaggaatct tgtttatgac 60 aacatatata aatgattaga tcttcgagat aactcacttc accgggttta aatattatct 120 ataataggat gtccctacaa ttatgtatac actgcttgaa ttacatgaat ttgcctcacc 180 ccggtgctta agcattattt acttgtttgt agatgttggc tcgctttgca acaggagcat 240 cgttcagtgc agatagccga ggtgggggac gggacagtaa ttctcggttc ctcccattta 300 tgttccaaat ggcacgtcat ctccttgatc taggaagccc cttgcagcgt cgaacaatgg 360 ccagggctgt atcagcatat atatcctctt ctacatcaga tgtcagaccc tcttctccgt 420 ccggcaccca acttacattg ggaacagaag aaaccgtcca atttatgatg gtgaactcac 480 ttctctcaga gtcttatgag tcctggctgc agcaccgccg tgcttttctg cagcgtggaa 540 tttaccatgc atacatgcag cacacacatg gtcgtactac tgctcgctca tcgtccgttt 600 cagcttctgt acaaggtgtg gaatctggaa gtacaggcca aagtgctaca acagaagcag 660 ggcagaatga tgagcttttg tctatcattc gtccgatgct tgtctacaca ggtttgattg 720 agcagttaca gcatttcttc aaggtcaaga aattgcctag tgcaacacca gcaagtattg 780 atggggtttc gtctgcagca gaaggggaag acgaaagtgg gaacctggaa ggatgggagt 840 tggtaatgaa agagcgactc ttgaatgtaa aagagcttct tggattccca aaagagatga 900 tttcctggct tgatgagatt aactctgcta gtgatttgca ggaggccttt gatattgttg 960 gggttctgcc agaggttttg tccggtggga tcacccggtg tgaagacttt gtgcaagctg 1020 caatcagtgc agggaaaagc tgaaacaata cagctttctc ttttcattta tacaaatatt 1080 aacagcatat tatattctga gaatgtaaaa cgctcatgta ctatgttctt ttcaaagcat 1140 aaagatgata caaaatgaaa aggggttatt gtgatgaata tgaaaacaaa catgtttgaa 1200 tcaaagctat aataactact accattctga ataaacgagc atgatcgtct agtagttatt 1260 ttcccacttt tagaatgaat tttaagagaa tgaaacaacg ttagatgatt taaaaattat 1320 acatagggtt ctgtgaaaat gattcaacat aatgttcaaa ccataaatag ttttctattc 1380 tatttagaca tggcaacaaa gctcataccc gcgggcaccc gtccgaacca aactcaaatt 1440 gactattttt tttttcttct gctttgactg agtttggata ttcctcaatt tcaaaacacg 1500 ggtacgggac ggacataggg atatcagtat ccaccccgaa tcatacccaa gcccgtcctg 1560 aatgcaaaaa atcaatttat tttaccttta atataagaaa cttaaattct ttgcctttca 1620 tacgtccctc acttctctaa gttttatccc ttcttcttcc acatcgcacg ccctcgatct 1680 ctcttctcca tcacccattg accacattca tctctttgca ggataatgca ttacaacatt 1740 gagttcgggg ctgaaaaata ctttttaaaa aaaaaaaaaa attattcact gcggggatgg 1800 gtatgaaacg gagatgtcgt agggtaatga gttagtattt gggagcaagg tatatgaacg 1860 gggaaggtaa aacccgtcca caccccgccc cattgccatg cctaattggt atgacaccgt 1920 ttgaggcttt gtatggaagg aggtgtagaa caccgttgtg ttggtatgag ttaggagaaa 1980 gtgctttgtt aggaccagaa gttgtgcaat agactacata gaaggtgaat atgattgaga 2040 agatgagagc gtctcaaagt aggcagaaga gttatcatga taagaggagg aaggatattg 2100 agtttcaagt tacaaaatat tctcacatgc gtcattctta agctatgatt atgcacatgc 2160 gtcacctcta aaaatattct cacaatagta taacttttcg cccattctta aactatctaa 2220 taatgcaatt aattttaagt tacaaaactt atcatccttt cttaatatat ttgcagttat 2280 tatttatcct cttttaaaaa agatgtcgag agtagaaaat gtgagaaaga gttagtaaaa 2340 aaaaagaaaa agagaatgag aaataaattt aaagaagtgt taggaatgat ttttttgcaa 2400 tgcagtgttg gattagagga ggatttgtaa acaaatgatt tcggagttct gttttaatat 2460 attataggtt atggggaaaa acatgtgaag attaggaacc acatgaaata aatgattttt 2520 ttacttgagc catttgaaat acaatgtaaa tcaagaaaaa caaaattaaa agttgtcata 2580 tttttctcca atataattgc taaatttaaa ttaaacactt tgaaacttta cctatctaaa 2640 aaaatattgt gaagcattca ttttattgat gtgtttacag taattggtta tttaaagtta 2700 gcaattataa agggtgagtg gttatttaaa gttagcaata ttgtgaaata ttgtgaaatt 2760 ctactactat atatgaagca ggctttctaa caaaaattgt gaagcatgac aagtttgagg 2820 aggtgatgaa caagatggat gtcgcatctt tggagcatct atctatctat ctatctatct 2880 atatcttctt ctcttagtaa actaaacttg actcatttta atgcttagga ttgtgcctat 2940 gaggcacctc taaaaaaagc ttaatttcta ctctctaatt attctttcta ataaactaat 3000 ctaatatgta acttctaaca tttatttatt tttttcacaa aaatgctaac tcaatcatac 3060 aatgcataag agtacaatgg gttatgaact cactctagac aaaaaaataa caaagacgtt 3120 acgttaatga acaaaaacat cattgttttt ctataaccat gttttaagaa tctaatagta 3180 acggtttatg cacctaacaa actattcaaa cattccataa tttcttacac tatcatcata 3240 tcatcatttg atgtatctct taacattcct tcaatttttt tttgaaggaa acatttcttc 3300 aattacaacc tacaaaatgg aaaattttaa agtgtacctt tttttatatt tttaaataac 3360 cactcaccct ttataaccac aacttatgcc acattcattt tcactcaatt cctggatgtt 3420 tccaccatgc cttctattga tatcaattta acaacaaata tttttctaca cttttgttga 3480 aaatgggttg gttataatat taattaaagg ttattgtata aatttcggtg ttattatttt 3540 gcttttggat catcattatc acttacttca atcaactctt ggataatact cttcaatttt 3600 gtatcgttgt atattgaaat agcacattat tttcttaaca agattgatgt tttttatttt 3660 tagagagagc accttacttt ttaacaagat tgatgttgtt tttcttttaa ttttgttttt 3720 agtttctatg cgtaacaatt aaagagaaca ttttagagct ttgttacagc aaagtcatgt 3780 aaagaagttt gagcaattgg tttgattggc aacagtatgg tgcatttaaa atatcataaa 3840 caatattata tttcaaaatg gagtggataa tgtggcaaaa ttggtggatc aaattaaaaa 3900 tattggttag gtgtagttcc tgagaaaatt gcaagcaata ttttgatcaa accagtgcaa 3960 cgcacgggtt atatacctag ttatatgtat atgaggctcc acgacacttg agaggcattg 4020 ggatttattt tttatttttt attttttatt ttttattttt gtttatgtat ttttaggtgt 4080 gaatgtggaa caacagttaa ttgtagtagg agatatatt 4119 // ID Copia25-PTR_LTR repbase; DNA; EDCOT; 912 BP. XX AC scaffold_452; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia25-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-912 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-912 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 225-225 (2007). XX DR Genome; scaffold_452; Positions 38041 37130. XX SQ Sequence 912 BP; 315 A; 126 C; 164 G; 307 T; 0 other; tgggagattg aaggaattgt gtcctttaaa ttaatgtgca atgactaaac ttggatagga 60 caattaacgg agataattta atctgattat tttaggagtc gtagtgcttt gctagaagcc 120 aactacgatt aatagggtta aacctatagc tattataatt gggtcctatg aggtcacaca 180 cttagagatt acggactaga tcaacgaaag aaaaaaaaaa ggttaattat taatacatat 240 tagatattat taataataaa gaatattatt tatttctgaa ataaaataaa tattatttat 300 tcatattaga tatgattaat tatggagtta ttcatacagc cttttatttg ataaaaggac 360 aaagtcttca tttctattta ttgctttaaa aaccgtacgt tgaaaaagga aatgacattt 420 tctatatatt gatgtgccat aaaaggaaaa aaacgtctcc atcattgaag atggaatata 480 taaatgattt ttagaaaatc atgttttgga aataaaaatc tttccatgta acgtacgggg 540 aaaggctaat ataagaaatg aaagaggttt tgaatatata ggttttttat ttcttggctg 600 ctctcaaaaa ttgggagagg ggcaaggaga gaccaccatt tttccttttt caaccaaggc 660 aattttgatt gctccctttg tccattcgtc ctagcagtcg aaggcaagag atctattcgg 720 gctcgtgtgg actaaataga ggagcaacac gtggggcttt tatcctttta gataccacca 780 tatctgactc ggttcacgca tcaacaggta ttttccatga acaatacttt gatctatcaa 840 ttatgcttga agattctacg attagatgtt tagatatgat ctgaaattcc gcttaatgca 900 tctaattttt ca 912 // ID DNA9-1_Mad repbase; DNA; EDCOT; 181 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-1_Mad. XX NM DNA9-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-181 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1481-1481 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >93% identical to the consensus. 9-bp TSDs. XX SQ Sequence 181 BP; 52 A; 37 C; 45 G; 47 T; 0 other; ggagtaggat tctctcccct ctttttttcc ctccccttcc ctcccctcct atttgaacgg 60 tcacggttaa gccacgtcaa catcttatat taatttttta tagaaagaga aagacaaaat 120 agagaatgtg agaggagggg atggaagggg atggaaagag gaggggagag aatcctagtc 180 c 181 // ID Copia-49_VV-LTR repbase; DNA; EDCOT; 474 BP. XX AC chr19; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-49_VV_; KW Copia-49_VV-I; Copia-49_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-474 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr19; Positions 11012848 11013321. XX SQ Sequence 474 BP; 137 A; 79 C; 96 G; 162 T; 0 other; tgttggaatt ttttatgtgt ggacttacat agtcaatgtg ataatgccat aaatcaatgt 60 tattttattt ttgcattgtg gtccataatg gggttggaca catattgttg cttgattttt 120 tatgggctca ccctaattca cttgactggc ctattaagtc aagtggtcca aataatgtgt 180 gtaatgtgtg atatatataa gtgcaaagaa aggcttcttc ttcttgggct aaaaaaaggg 240 cacgcattgc acactcgtct tgagagcaca cacggactga atcttgggtg tagaaaggga 300 agaactcatt gaacccagat tttcatacca tcacggactg agcatattct tggacaccag 360 tggagcacaa aaatggcttt ctatgacatt aatcaaggta agcatttcat ttattgtcat 420 ttaatgcatg ctttaatgtc tacatgtgat cctatgtcgt ttaaaatttc atca 474 // ID MuDRA_MT repbase; DNA; EDCOT; 429 BP. XX AC . XX DT 22-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon, from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW transposon; Interspersed repeat; Inverted repeat; MuDRA_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-429 RA Shankar R. and Jurka J.; RT "MuDRA_MT: A putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 581-581 (2006). XX DR [1] (Consensus) XX CC This is a new transposon family, sharing some features of MuDr CC transposon family. It lacks the transposase domain. Flanked on CC both sides by 9 bp TSD. XX SQ Sequence 429 BP; 142 A; 77 C; 87 G; 123 T; 0 other; ggcttaaata tgtatttcat ccttgcaatt aggggtcgtt taaaaattgg tccctgtatt 60 cgctaatcct tgcaaactag ccttgcaatc attaatcatt taaaatttcg tcctttgacc 120 aacttaatca ctgccacgtc actaatttga tgacgtggca atcactgcca cacatgaaat 180 tccaattttg cccttaagaa gaggacaaaa tattgaagaa agaattggaa acccaggggt 240 aaaattggaa tttcatgtat ggcagtgatt gccacgtcat caaattagtg gcgtggcagt 300 gattaagtgg ggagagggac gaaattttaa atgattaaac aatgcaaggg taaattgcca 360 ggattagcga ttacagggac caatttttaa acgaccccta attgcaagga tgaaatacat 420 atttaagcc 429 // ID hAT-6_VV repbase; DNA; EDCOT; 5131 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE hAT-6_VV, an autonomous DNA transposon - a consensus sequence. XX KW hAT; DNA transposon; Transposable Element; TIR; Hatvine-6; KW hAT-6_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5131 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 775-775 (2008). XX DR [1] (Consensus) XX CC hAT-6_VV (Hatvine-6 in [1]) consensus is an autonomous element. CC Its individual copies are >80% identical to the consensus CC sequence. hAT-6_VV contains 13 bp-long TIRs which are flanked by CC 9 bp-long TSDs. XX FH Key Location/Qualifiers FT CDS join(975..1636,1734..3027) FT /product="hAT-6_VV_Transposase" FT /note="pfam05699: hAT dimerisation domain." FT /translation="MTSEEGENFSMPSAGSTPITGSTSTTDGTLISKRRKL FT TSVVWNDFDKIIEDGQDYAICKHCKGKLKADSKNGTKHLHVHIDRCMKRRN FT VDIRQQLLAVERKGHGKVQIGGFTFDQEISREKLARAIILHEYPLSIVDHV FT GFRDFATSLQPLFKMVSRNTIKGDIMKIYEVEKDKMISYLEKLQSRVAITT FT DMWTSNQKKGYMAITVHYIDESWLLHHHIVRFVYVPPPHTKEVLSDVLMDF FT LLDWNMDRKVSTVTVDNCSSNDGMINILVEKLSLSDSLLLNGKIFHMRCAA FT HVLNLIVKEGLDVIEVEIEKIRESVAYWSATPSRMEKFEDAARQLRIPCNK FT KLSLDCKTRWNSTYLMLSIAITYKDVFPRLKQREKYYMVVPSEEEWNMAKE FT ICGRLKLFYNITELFSGRNYPTANTFFIKVCEIKEALYDWLICSNDVVKTM FT ASSMLQKFDKYWSGCHIVMAIAAIFDPRYKIKILEFYFPLMYGSEASNEIE FT KIRGMCYELLSEYQSKSKLGQKTSSYGTSSGSTLLELNYDEQDPLSKFDLF FT VHSTIGESHTKSELDYYLEESILPRISNFDVLSWWKTNGIKYPTLQMIVRD FT IYAIPVSTVASESAFSTGGRVVSKHRSRLHPDTLEALMCAQSWLWKEKEGN FT RFT" XX SQ Sequence 5131 BP; 1558 A; 744 C; 1018 G; 1790 T; 21 other; taggaatggc aatttcgcgg gtcaatcggg tcacccgccc cgccccaccc ctcctctatt 60 gggacgagta tgggataaat taatcaggta tgggacgggt atgggaaagc tttgtgaaac 120 ccgaatcggg tttgaggcgg gtatgggttt gtagttaccc gcctcgccct agaattagaa 180 ttaccaattt acccttaaat attataaaat accaaaaatc tcctctgtat atataattta 240 ttcttccaag atttttatgg tttttctctc tcgggagaaa ggtttcgtct tctcagttca 300 aatggcccta aaagcaaaat ctttgctcta aaaaccatat ttgcaatctc gtaaacaagt 360 gattattgga gttattgtgg attccttcct tctaggtaag aaaaccctaa cttttgaaac 420 tttgttaaaa atttggcttg tttttcaaaa ttttttggtt ttagtttatg ggtttgaggt 480 tttttcaatt gtctatcagt agatttgtaa tttatatgca ctcttagtct tcgtcttata 540 tgtatttttc agttgaatca attttcgtct ttgactctta ttgttcatgt ttttgacatt 600 aattttcacc ctgtccaaat caatttcatc cacatataaa ctgatttttg gggtttatac 660 gaataagaat gatgatttat gggtttttca ttattttagg gttcaatttt ggtattcacg 720 tttttgcaga aacaagttgt tataatttca ttattttagg gttcaatttt gatattcatg 780 tttttgcata aacaagttgt tataagaaaa cgatctaatt tcatgttgtt ttttcataga 840 tgaaaaccct aatttttttt ttctaaacaa attctggaaa catattattc atgctttcag 900 aaacatacaa atagaatttt attgtggtta aattggtttc aaactatttc agaatatcct 960 aacgattaag aaaaatgaca tcagaagaag gggaaaactt ttccatgcca agtgcgggtt 1020 caactccaat tacaggcagt acttcaacta ctgatggaac attgatatct aaaagaagaa 1080 agttgacttc ggttgtttgg aatgattttg ataaaatcat agaagatgga caagattatg 1140 ctatttgtaa gcattgtaaa ggaaagctta aggccgatag caagaatggg acaaaacatt 1200 tacatgtaca catagatagg tgcatgaaac gaagaaatgt tgatattagg caacaattat 1260 tggcagtaga gagaaaaggt catggaaaag ttcaaattgg tggttttacc tttgatcaag 1320 aaatctcaag agagaagctt gcacgtgcaa ttatattgca tgagtaccca ctttcaatcg 1380 ttgaccatgt ggggtttaga gattttgcta ctagtctcca acccttgttt aagatggttt 1440 cccgcaatac aattaagggt gatataatga agatttatga ggttgagaaa gataagatga 1500 ttagctactt agagaaactt caaagtagag ttgctatcac aactgatatg tggacatcaa 1560 atcaaaagaa aggctacatg gctatcactg tacattacat tgatgagtct tggttactac 1620 accatcatat tgtaaggtta gttatgttat ttttttttaa cttccaaagt gtttttttat 1680 ttgatccttt aatgatattg tttgtgttaa tgatattttt tttcttaatg taggtttgtt 1740 tatgtgcctc ctccacacac aaaagaagtt ctttcagatg tattaatgga tttcttgttg 1800 gattggaata tggatagaaa agtatctaca gtcactgtgg ataattgctc aagtaatgac 1860 ggaatgatca atatcttggt ggagaaatta tctttgagtg attcactctt attgaatgga 1920 aaaatttttc acatgcgatg tgcggcacat gtgttgaact taattgttaa ggaaggtttg 1980 gatgtcattg aagtagaaat tgaaaaaatt cgtgagagtg ttgcatattg gtcagcaacc 2040 ccatcaagaa tggaaaagtt tgaagatgca gctcgccaat tgcgtattcc atgcaataag 2100 aagttaagtc ttgattgtaa gacacgatgg aattccacat acttgatgtt atcaattgct 2160 ataacatata aagatgtgtt cccacgtttg aagcaacgtg aaaaatacta catggttgtg 2220 ccatcagagg aagaatggaa tatggcaaag gaaatatgtg gaagattgaa attgttttac 2280 aacataacag agttgttctc aggacgaaat tatcccactg caaatacttt cttcatcaaa 2340 gtgtgtgaga tcaaagaggc attgtatgat tggttgatat gctcaaatga tgttgtgaaa 2400 acgatggcat caagtatgtt gcaaaagttt gacaagtatt ggagtgggtg tcatattgtg 2460 atggcaatag cagctatatt tgacccaaga tacaagataa agattttaga gttttacttt 2520 ccactaatgt atgggtctga agcttcaaat gagatagaaa aaattcgtgg aatgtgttat 2580 gagttgcttt ctgagtatca atcaaagtct aagttggggc aaaaaacttc atcctatggt 2640 acttcatcag gttcaactct tttggagtta aactatgatg aacaagatcc tctttcaaag 2700 tttgacttat ttgttcatag taccattgga gaaagtcata cgaagtcgga gttagattat 2760 tacttagagg agtctatttt gccaaggatt tcaaattttg atgttttaag ttggtggaag 2820 acaaatggta taaagtatcc gactttgcag atgattgttc gtgatatcta tgctattccg 2880 gtatctacag ttgcatctga gtcagccttt agcacgggtg gtagggtggt atcaaaacat 2940 cgtagtaggc ttcatccaga tactttggag gccttaatgt gtgctcaaag ttggttatgg 3000 aaggaaaaag aaggtaaccg atttacataa ttatcaattt tatgaaggga aatgaaatgg 3060 aaaatagtta atctaaaata ttttcaatct tatggaacaa ctatgttgaa ttttttaata 3120 aagttatttc ttgttattct tacttttatt gggtgatttt ttgcttgtta acccatgggg 3180 caaactcaca atcatggatg aagatgatga atcactcttg ttgtaggttc ttttcttgaa 3240 atgaaagttg gtattggaga tacattttgg gacccaagat acaccttttt tttaatgctc 3300 ttttttaacc ttaatgtggt tatatgtatg aatatgttgg gaagacttta tgtttaatgt 3360 tttttttttt ttaatgttgc catatccatg gagattttct atttttatat gttgtagttg 3420 tgatatttat ttattattca tttttatctt aatgttataa tttatattgt tatatccatg 3480 gtattaagca tcaaagttgt atcttttgcc aaagaaggca ttagtgctga cctaattgca 3540 gtaaatgaag acgttagggc tgcttgttgg ggctacagat taatataact tggaagtgat 3600 gccaaagaac ccttgtcatg ccaaggaaga aaggagctga tcaacctggc acatgaagca 3660 atgcagaatc caaatcatga atcatcaaga ggtccaactt ctaagagaaa aaaagttgtt 3720 gttcctcttg gaaaagagga aaaagtggac aagaaatttg tttatatttc tccaatgttt 3780 cttagaattg ttgttgctgg tgctagatta ttaaagaaca aaggtatatt gcctaaataa 3840 cttggatgat ttgggttgat aaatctatct tttcttctag ggtcaatcac atttaatttg 3900 ttcccaagag atggaaagca aaagagagag ggcccttgtg ttggaaccaa gggctttcgg 3960 gcacctgagg taagaacttg taatcatttt tgcttcggtg actgcattat tgttattatt 4020 ttctatgtca tgttcattcg aatcctaacc cacactattg atcaaaaggg ggtaatgatt 4080 ggtgctatca cgagtgggca gattgctgat tttattggtc gaaaaggggt aagatggagg 4140 atactctgtc gagattgttc atatttgagc atttttccta cacaaacctt ctctcacaac 4200 ttgctttctt tgtgggtgga atcaggccat ggggatgtca tccatgatct atctagcagg 4260 atggctcaca gtctacttat cttttgtagg atatctccaa ttttcaatta taattttgat 4320 atatttgtat atgtttttct tcatgtttta ccctctggat gtttcaatgt agggatcttt 4380 ttccctttat tttrggagat ttcttcgtct tatatggaat tggtgttctt tcttatgtgg 4440 tatgctttta tgagaagctt ctcttcttgg atatgaagtt ccgataatta tgcaacttaa 4500 gaagcattaa acatcttttt tttcctctgg atgaacaggt accagtcttc attgctgaaa 4560 taacacctaa gaatctttra kgagcactag caayarcaaa tcaagtagaa gtttttattt 4620 tattttattt tattgtttgc attgttttca aaagcaattt tgttgaagaa taatttatga 4680 tggaatgatt tcaatatgat tgtgtttttt tccatagaaa aayakattca aaagattgta 4740 tatttattga aaataaattt atgttttgcc acattgaytr aatgytgaat agtatgtgaa 4800 gaaaatgcta attgttgatg cttttaagag ttgcaatcta tatcattgtg atgttgaata 4860 agacaggaaa ataaccatgg aacctatgtc ayagaatttt ycaactagaa aaaacccaat 4920 acccgarcct gaactagaaa cccgmsctca ccccgccccg aaaacacatt tggtaygggg 4980 atgggattat caagtctatt gtaaacggga acgagacaca wtaactcrtc ccgccccagg 5040 tttgggacag ggatgggaaa gagattcaga taattrggac rggaatgggg taggggtggc 5100 ycggcccaaa cccgtcccat tgccattcct a 5131 // ID Gypsy-30_PTr-LTR repbase; DNA; EDCOT; 3192 BP. XX AC . XX DT 11-DEC-2009 (Rel. 15.02, Created) DT 11-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type non-autonomous LTR retrotransposon from Populus DE trichocarpa: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed repeat; Gypsy-30_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3192 RA Bao W. and Jurka J.; RT "Non-autonomous LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 235-235 (2010). XX DR [1] (Consensus) XX SQ Sequence 3192 BP; 904 A; 594 C; 636 G; 1054 T; 4 other; tgttgttact cawttttgga ccccacgtgc tggagacggt gtatacctct tttgaaccga 60 gtgtaggagt ttagctcatg tttgctggaa gattgacaaa agcagagaaa gaaatatttt 120 tttttcgaaa ccctgtttga gctgttttct gctctcttta tccttcccct ttgctgccaa 180 aatcatcagg ttttcttaga ttgatcagga gtcttcataa tgctaaattc gttccttttt 240 tatctggtct ttaaggttga ataaatccct cagaatttgc actaaaaaaa tggttctgct 300 gctgtcgcaa ttttttgttc caacttaggc tctgattctg actcggtttc gtacgatatc 360 tgaccatcct aggtatattc tgtcactcat gacatgttga aaaattgacg tacaccttta 420 ttaggtccta gggatcattg ttcttagggc agattctcag tcagatttgg atgctcagca 480 ttgtcagatc aagaaccttt ttgaccaact agattactgc cagattctgt tctctaaaat 540 gattttatct cacttcgact ccttcatcaa agttgtagtc ctagacgcgt agatgaattt 600 gggcttttga atcgcttgat ttcgatatca gaagctcaag atattcccgt ttgaatatct 660 agcgtgaagg cagagaatcc tgccgcgaga aggattgacc cgagtttcca gtcagttttg 720 agttaaattc tgttcttaag attttatctc acttcgactc cttcatcaaa gttgtagtcc 780 ggacgcgtag atgaatttgg gcttttgaat cgcttgattt cgatatcaga agctcaagat 840 attcccgttt gaatatctag cgtgaaggca gggatcctgc cgcgggaagg atttagccca 900 agttcgcggg actgattcga aggatttttt ttggaccaag gactgaatcg aaaagtgcta 960 aaatgaggga ttgaattgaa gaaggatatt gaaagctgga gaggggggct ggatcatcat 1020 aaatgacagg atttttacca caccgaataa ggaaaataag actttgcagc tgcaccctcc 1080 atctgatttc tttccttttt tctctgcaaa ttcctgctgt tttcctttmt catcacgcct 1140 gatttttgga gctgmagacc acgtttttgt tgcctcattt caaagggagc agctggccct 1200 atggaaggaa agaaaagagc cacaccatcc tctaaaactg gaaagaaatc agacgtaaac 1260 accacacaaa atcagaatat tgcagtttcc tttttgcgtt ttttttactg caaatcagta 1320 gggatttgca tcctagaatt aatgcattga atctttccta aatagagaca tgttagacta 1380 tatataagcc cctctaatga cctaggggaa gagggaaaaa cggagagaaa aagagcataa 1440 aaagaggaga aaaacgcaag agaggcagag taaaaaaaac gcagtaaata gagggagttc 1500 ctttcttgca ttctggtgtt actgtgagga aagaggagag aaaaaaagac aagacggaga 1560 gggagatttg ctgctaaacc ttgacagcaa cgttcgcttg gttttccatt tcatcttctg 1620 cagaaaaaac gttgagacct gcaggtataa gtcttaactt tctcctcctt tgctgccttt 1680 aaatctgttg tgttgacgtt ttaaaaacct gttttgtctt tgctttgcac attcgttttc 1740 aattttagac tacaatgaac gcttgccttt tgttgttcct gacgttttaa aagcctattt 1800 cttttttctt cttttctttc tttcgctggt tcataaggaa ccgtgggagg gggggctgtt 1860 gtttcttcat catcagctcc cttttctgtt cgttttcttt cctgcttctt gagagattag 1920 ccggccatgg ttttgttttt cctatataca tgaataaagc atgctttccc agtttttgtt 1980 ttgtttctct ctgttggcgt tgtgaaatga ataggcagtt ctttttaagg tgaggaaata 2040 atggggttgt gaggcacgga catagggttt gatttcaaaa tttcagtttt aagactgtgg 2100 ctccctcatg catacgggtt tattcctttc cagttacaaa attttaagtt gatttggctt 2160 tgaaggtttt tgttacgaat tgtttcaagc ttcttgtaat tcttgkaata tgtgtgatgg 2220 cttgctactt tccattttga tgtttacgtc taattgtgat gtttgcgttt tgacaaaaat 2280 ataaaaaatg ttttcttgtg tgttgcatac ggccaatacc ctaacatgtt ttgaacgctc 2340 ttttttttat acaaaaaata ttggaagttt tgaaaatgtg ttttcgcatg gatttcttaa 2400 acacaacaaa aattattttc ttgcatttct ggattttaca acatgtttgt aaaactccaa 2460 agggtattgg ccaatattcc aaaaaatata aaaatcttat tttgggggga attcatctat 2520 tattcaccgc taatgtttgg ataaagaaat ccttaaagga cgaatatcca aaatattatt 2580 gggaataatt tgttattatt cactgttaat atttggataa agaaacccgg agtggtaaat 2640 atccaaaata attttctagg aataataaat ccgcacacat ccttgaaaga agccttgatt 2700 ataatcgagg acatttcaat tttttactcc acggtttacg agccgtgaga gtataaaaca 2760 ctaagacaaa aaaaataggt ttttaaagca ccctagattt ctaaattttt gtccctcctc 2820 cttgcgattt acgagtcgca aactcttgaa atactaaggg gaaaatgagc ttttaaagca 2880 catggaacct ccttggattt ctatcttaat aaatttagtt tgaatcaaac ctagaaaaac 2940 tgatgggatt agaaaacacc aacaccatag caattataaa gcaaaccaaa caccaagcag 3000 cttaccttag gtagggcgta ctaggggtgc taataccttc cctttacgca accagtccct 3060 tgccttagaa tctctgaaag accagttagg gttcctagtg accataatac taggtggcga 3120 ctcccttatt cacaaaaaaa aagaccccga aatcaatcga gggtcgccgc gctccgccgc 3180 gagggtgcga ca 3192 // ID Copia9-VV_LTR repbase; DNA; EDCOT; 682 BP. XX AC AM473118; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia9-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-682 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-682 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 682-682 (2007). XX DR Genbank; AM473118; Positions 72016 71335. XX SQ Sequence 682 BP; 224 A; 97 C; 112 G; 247 T; 2 other; tgttagcttt ttttcctata atgtgtggcc atatataatt atatttatat gaatattatt 60 taagggtatc aattgatagg taggtgaatc aattgattgg gcatccaaga gtcttatgta 120 tggaagactc aaattacaaa tggggagtta gaaaatttaa ctcatatgaa tgtggtgttt 180 acaatttttg taaccccatc tttatgaaat ttatttgtac attatgttta tgagtaatgg 240 aggaaaatgg aaaggtataa cctatgcaat tatatggatg cattcaagtt cataacccac 300 cattacccat taatttgtac ataatgggtg taaataatga gtataactcc catatagtct 360 ttgatgggaa gactaagaga tgtacaactt attataaatt gaggtcccaa gccacactct 420 cattcttatg tctttttttc tttcttgttg tttayytttt taacaacata caccacacaa 480 gtgacccatc cactatatga gagtagtgag ttgaagacct tgacaataca attcacaagg 540 tgactcaatc tcacttcatg gatcaaggta agaatatgat cagattattt tagtactact 600 ccatttattt gtttgtatgt atccaaaatg tgttttcaaa aataattatt tccgcataaa 660 gtttatgaaa gtttggttaa ca 682 // ID Gypsy20-PTR_LTR repbase; DNA; EDCOT; 346 BP. XX AC scaffold_942; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy20-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-346 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-346 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 321-321 (2007). XX DR Genome; scaffold_942; Positions 8184 8529. XX SQ Sequence 346 BP; 86 A; 62 C; 75 G; 123 T; 0 other; tgataagaag tagcagagta cgtggaggaa gtgttgcatg gctcaaggag ctgaatacgt 60 ggaagcagct gagttcgtgg actgctattg ttttggtttt atcattgttt ttatcgccaa 120 gttgaattag tcaaataatc aaagtggtgg aagtaggaat gctaatcgca atcctggtct 180 tcagctccac tttgggaatc cctgttattt cgaattattg ttattttggg tggcctattt 240 aggttcacaa actctgtatg gaagagggca ttgaattaat aaaacaatct ttcctttctc 300 tcctctgttc cttccttatc tcttgtccca aattctcttc ttatca 346 // ID PSL repbase; DNA; EDCOT; 9932 BP. XX AC AF009516; XX DT 28-AUG-1998 (Rel. 3.07, Created) DT 26-AUG-2005 (Rel. 10.09, Last updated, Version 2) XX DE DNA transposon PSL. XX KW EnSpm; DNA transposon; Transposable Element; PSL. XX NM PSL. XX OS Petunia x hybrida OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Petunioideae; Petunia. XX RN [1] RP 1-9932 RA Snowden C.K. and Napoli A.C.; RT "A variegated Hf1 phenotype facilitates the isolation of a novel RT Spm/En-like transposable element from Petunia hybrida."; RL Unpublished. XX RN [2] RP 1-9932 RA Snowden C.K. and Napoli A.C.; RT "PSL."; RL Direct Submission to Genbank (19-JUN-1997)Environmental RL Horticulture, University of California, Davis, CA 95616, USA. XX DR GenBank; AF009516; Positions 203 10134. XX FH Key Location/Qualifiers FT CDS 1927..3582 FT /product="PSL_1p" FT /translation="MENLDRGWMYERLDGRGGYNSNFITGVDNFLKFACSQ FT QNRMSGCNVRCPCKICKNIKYWDVETVRLHLYQSGFVENYFVWVYQGEKAM FT ISALSSRSNFDGGSQSELGYENPYRQMVLDIAGPNFGPNIEQGSSWQSDSN FT VEPESSHHFESPMEEEPNPESQRFYDLLHAADAELYPGSSLSQLAVVSRML FT SIKMENTLSQRGYNQMMQLLKEALPEDNKVLDSYYQTKKLVQSLGLPVEKI FT DCCNSGCMLYWGDDEDLTSCKFCGHDRYKRRVGTRKRKSVPYKKMYYFPLI FT PRLQRLYASHATASDMRWHHEHIQEEGVMRHPSDSEAWKHFNETHSFFANE FT PRNIRLGLCTDGFQPFGQSGRKYSSWPVILTPYNLPPWMCMKEAYMFLTII FT VPGPNNPKQKIDVYLQPLIKELTLLWETGVEAFDISKKQNFQLRAALMWTI FT SDFPAYSMLSGWSTAGNKACPYCMEEAQSFRLRHGRKTSWFDSHRMFLDQN FT HPFRRDRKNFLKGQTVRMPPPPLRTGEEILNQIIELGLRKVTELDAEEVNG FT RICRS" XX SQ Sequence 9932 BP; 2961 A; 1635 C; 1998 G; 3338 T; 0 other; cactacaaaa aaatcagctt ttgccgacgg attttagcga cagagtttaa tctgtcgcta 60 attacctacc gagtaactac agaattaaga ttctgttgca acataatcaa aaaaataaaa 120 tagcgacaga ttagcgacag attaaaaaat ttgttgctaa aaagtggcgc taaatgttgg 180 cgctaaatgt tggcaccttg attttagcta aaaattttgc agagaaatta agcgccaaaa 240 ttatataata tagcgacaga tatagctacg gaaaggctgt tgccaaaact atttagtcta 300 attttataat tttataatta ttgctacgga caattctgtc gttaaaattt taaaaaatta 360 taatttaaag ttaagtgtag ctacggaata ggttctgtca ttataactct agctaaacat 420 aaattaaata tttcctgtta tgatatgaat gaaacaaggg ctttcttttg ccactttaac 480 acctaaacca tgtctgccta ttttcctccg ccatagctcc actttcctcc gccactttct 540 tccgccgctt tcctccgcca ctttctccgc ctgctgctcc tacttctcta ttaaaagacc 600 ttctattctt acaggtatat cttagatctg agctatattt ttcgccacct gctgctccta 660 ctttcaattt tgcttaaatc tgttctcgtg tgtgtgtgta tgctttagtt aaattcattt 720 ttgtgtgtgt ttgtgtgggt gtgggtgagt catttagtta aatctgttag tgggggtgtg 780 atttagttaa atctattagt taaattagag atggggtgtg atagattggt aaatattttg 840 aaaaaatttg gaactcaact actgcattct cgcttaacct tccgcaacca gttcccattt 900 tcattttctc tcttaaatta tatttgaact ctcttcatta ttatttgtaa gcaataggtt 960 catccatcat tctaactctt acatggaact ttaaattgtt gcagaggaag ttcatagaaa 1020 atatttaatc caccggggca ctcatgttat gggcgtgctg aaggtaatat tctgcactat 1080 aattttttat cataagcctt caatatgcaa tgtaattaca tttacagtaa atgggacttc 1140 aaattgatta gcatgtacaa ttggtgtcaa cattattaat cgaactatgt taaactgtct 1200 cgaactagct gccatgattc tttctgaatt tatccctgaa ttgtatacac ttatttaaca 1260 actcttgtag gatcttggca agtagatata ttggcttgca tcagtggtag cagaagtttt 1320 attcaggtac tttttttttt tcctattgtt ctttcagttt aaatgatgta tgttactgaa 1380 gaaatattga gatatgggat ttcaacttga ggctaaatta gcgctaggtt aatatgtttg 1440 attgagagtt tttttttctt attctatgca aataactgca ttcttgatgg aaaaatagtg 1500 attgttagta caacttcaac agcttacaat gaggtggtag agcttttcat tgctgattgt 1560 attagttgca ttcttgatga caatgcaact taatttacct atattttgac tatattttag 1620 tgcatatttc ttgttggtac ttgatgtgta aacacttact atatatgcac agttagtgga 1680 tgttaattat ttgagactat taaaccttct agtataacta ttgactgata ttaaggcaag 1740 ttttagtttt ttttatactc aatgaactga atcttacata aatatttctt atctgtattg 1800 gaacaagtaa taggaaggtc tttaactaat caattatgca aattccacaa tttgtttgcg 1860 tagaggtgtt taacatttgt gacttataaa ctgattattt ttactatttc tacaatattt 1920 aggaaaatgg agaatttaga tcgtggttgg atgtatgaga ggttggatgg ccgagggggt 1980 tataattcta atttcataac cggtgtggat aactttctca agtttgcatg ttcccaacaa 2040 aatcgcatga gtggttgcaa tgttagatgt ccatgtaaaa tttgtaagaa cattaaatat 2100 tgggatgttg aaacagttag attgcacctt tatcaatcgg gattcgttga aaattatttt 2160 gtttgggtgt atcaagggga aaaagctatg attagtgcac tttcttcccg tagtaatttt 2220 gatggtggtt ctcaatctga attgggatat gaaaatccat atcggcaaat ggttttggat 2280 atagctggac ccaactttgg acctaacata gagcagggtt cgagttggca gtctgatagt 2340 aatgtcgaac ctgagtcatc tcaccatttt gaatctccaa tggaggagga gcctaatcct 2400 gagtctcaaa ggttttatga tttgctacat gccgctgatg cggaattgta tcccggttct 2460 tcactctctc aactcgcagt ggtttcgagg atgttaagca ttaaaatgga gaacacttta 2520 tcacaaaggg gttataacca aatgatgcaa ttgttgaaag aggctttgcc tgaagataac 2580 aaagtgcttg atagctatta tcagaccaaa aaactggtac aaagcttggg tttgccagtt 2640 gaaaagattg attgttgtaa ttcaggatgt atgttgtatt ggggtgacga cgaggacctc 2700 acatcttgta aattttgtgg ccacgatagg tataagcggc gtgttggtac tcgtaagagg 2760 aaatcagtcc cctacaagaa aatgtattat tttcctttga ttcctagatt gcagagatta 2820 tatgcatccc atgctacagc ctcagacatg agatggcatc atgaacatat acaagaggaa 2880 ggggtaatgc gtcatccatc agactccgag gcttggaagc acttcaatga aactcattcc 2940 ttttttgcta atgaaccaag gaatataagg ttgggtttat gcacagatgg tttccagcca 3000 tttggccagt caggtaggaa atactcttca tggccagtga ttctcactcc atacaatttg 3060 cctccatgga tgtgtatgaa ggaggcatac atgttcttga ctatcattgt ccccgggcct 3120 aataacccta aacagaaaat tgatgtttat ctacaacctt taataaagga gttgactttg 3180 ttatgggaga caggtgtaga agcatttgac atctcaaaaa agcaaaactt tcaattaagg 3240 gcggcattga tgtggacaat tagtgacttt ccagcatatt ctatgttatc aggatggagt 3300 acagctggca acaaagcatg tccttattgt atggaggaag cacagtcctt tagattacgc 3360 catggtagga aaacatcttg gtttgacagt catagaatgt tccttgatca gaatcatccg 3420 tttaggagag atcgtaagaa ttttctcaaa ggtcagactg tcagaatgcc accaccacca 3480 ctcagaacgg gagaggaaat tctgaaccaa attattgagt tagggttaag gaaagtgaca 3540 gagctagacg cggaagaagt taatgggaga atatgcaggt cttaacattt gttttttttt 3600 tcttatgtta cttagcctct tcttgatgtt atttctgaaa ataccttact tcacaaaaaa 3660 atatgcagga attgtggatg gaaaaaacga agcatctttt gggatttgcc ttattggaat 3720 tctaacatga ttcggcataa tcttgatgtc atgcatattg agaaaaatgt gtttgataat 3780 gtctttaaca cagttcttaa tgatgagaaa accaaagata atgcaaagtc acggttagat 3840 atggcaatct attgtgatcg acctcagttg acaaaggatg ctcatggaaa ctatcccaaa 3900 gctgcatata cagtaaaaaa gcaagaaaga aagattctgt ttgattgggt aaaaggatta 3960 aagtttccag atgggtatgt ttcaaattta ggtcgaactt tagacacgaa cagtcatagg 4020 ttatatggca tgaaaagtca tgattgccat gtgttcatgc aacgactaat gcctattgcc 4080 tttcgtgagc ttcttccatg taatgtgtgg caagcactta cagaattgag cttatttttt 4140 aagaatctta cttcaacgac tctacgagtg gttgacatgg agagattaga ggcagacatc 4200 ccacaaatct tgtgtaagtt ggaacgcatc tttccccctg gattttttga ctcaatggag 4260 catttgcccg ttcacctgcc atacgaagct aggattgctg gacctgtaca atatcgatgg 4320 atgtatcctt ttgagaggta aaacgataac attttatttt ttgaagtgta tactacacat 4380 gccctatcta accgtccaaa tacttattag gtacctcggt actcttaaaa gaatgattgg 4440 gaataaagct agtgtcgagg gttctatttg tgaagcatac ttgatggccg agtcaaccca 4500 attattttct cattattttg aacctcatgt catgacacgt agccaaaatg tggaccgtaa 4560 taatgatggc ggtgttggag aagatcttga aggaaattta tcaatattta ctcatccagg 4620 tcgactatgg ggagaagaaa gaaagaggga tttgtcgctt caagagatta aggctgcaca 4680 aacatatatt ctactcaatt gtgaagaggt tgagccattt gtgaggtgat atttaaaagt 4740 tatacttgcc taatatagta aacatatcca tatacatgat aagttcttaa tttaatttat 4800 tttattgcaa tgaagtatgt ttgtgcaacg tttgcaacaa gaaattccga atttatctca 4860 agatcaaata gatgagagcc ttgaattgaa tttctctaac tggttcaagg attatgtaag 4920 tctccaacaa taattaactt tatagaatta tgtacttaaa ttggcttttg aaaatttact 4980 aagtcttgca ctttttcttc aataggtccg atacaaccat attgagaatg aatttttgcg 5040 tagtcttgct catggaccgt tgttaggcgt aaaatgtcat tcaatgtatt ttgttaatgg 5100 atacaaattt cacacggaat ctcacggtag tgcaagatca acaatgaata gtggagtttg 5160 tatctcggat ccaaatgttg gtgactactt tggacggata caagagatca tacaagtgga 5220 atatcgtgaa gagcctttaa agcaagttgt gttattcaag tgtgaatggt ttgatccaac 5280 catagatatt ggtgtcaaaa cgcatagtca atacaaattg gttgatgtta accatcgtcg 5340 tcggtttaag aaatatgaac cctttattct tgcgatgcaa gcaacacaag tatgttatgt 5400 gccttatcct agcatgaaaa aggacaatga tgattgggta gccgtactaa aagtcaaacc 5460 tcggaatgtt attgatttac caaaagagga agcggctgca attccagaat cgaatcttcc 5520 attccaagtt gaagaagttg aagcccatga gatagatatg aatgttgtca ttgatgaaga 5580 catactctta catgatccaa atgggggtac aattgaaata gttgaaccga ttggtgatgg 5640 attattggaa gaagagcatg aaactgaaga agagtttgaa actgaagaag agtttgaaac 5700 tgaagaagag tttgaagatg acgaatcgtc tgaagaagat atagatagtg actagtgtgt 5760 taataaaatt ctgctatata tctttaatgc attacttttg tagtaatatg tgtcgtttgc 5820 tataagtttt gtgtagtaat cagtgattgt aattttgcaa tgacaaaaag aaagatttgg 5880 tacttttaca ctacttatct aactataagt atacttctgt tccagttctg cactactgta 5940 agtacttgtg gcactacaaa caaaaagtac ttagctaact ataagtactt ttgcactatt 6000 tgtgtagtaa tcagtgactg taattttgtt acttgcttac tgctgatgta ttgtcttatt 6060 actaattatc taaccataag tgtcatcttg ttccagttct ggcaggctgc tgtaattatc 6120 acgggaagac agtgaagcta acttgggttt tcactggtgt ttgctgttct gctcttgcta 6180 cttcttctac ttcagagact acaaatcagg taagtgttgt aaatttcagg cgaaatgtta 6240 acaaaatttt gccttatgta atagtataat ttatcttgcc ttgctttttg tagtcgcatg 6300 atgattacac tagaatatga tggttgttat attacactag aggaccacca ttcaattttg 6360 aattttccag cataaactag gttgtcaaat attttttcct ggtatcgaca atggcatcaa 6420 ctggacgcgt atggtggttt aaaatgaatt cagcagttgg cttctatatc tctcttgatt 6480 ttctatatgg ctggaggctc tgggaacaaa taaagttgca tgagattgcc tgctgacaag 6540 ttacatattg gtcaatatgt atcatcagcc ttgttgttgc tttgatattt ctgaatagtt 6600 ttctttttcc tagtagaaat gactcgagga agaggaagag gccgaggtaa aataggtcgt 6660 ggaggcaggt cgatagttag gggtaatgtt actgctcgtc tgaacatgcc tactgttcct 6720 actccagaaa ttgttcctga acaaggtggc acgaattgtt ctggtggccc tactgataca 6780 ccaccggttc gaacatcagt tggtagtggt agcccaaata ttcattttga agcgtctcct 6840 gcggcaccaa atcagagtgc cacaataggc gagggtgtat ctgttcataa caacacagca 6900 ggtgaagttg agtctagtag tagccacggg cgacggacgc ttcttactct atctcctact 6960 acagggttag tccgagctct actattatct ttttactgtt caaaatgtcc tatgggcaat 7020 ttgtgatttc attgatagat tcttctggaa taacaagctt aattttttta tatctatact 7080 atgttagtca ttgcgacttc gttgatagat tatttggtct agtatgttat cttagtgatg 7140 tatcagcagt tgatgagctg agcttcttag ttgtgcagat atgtttattc atggacttta 7200 tttcgattaa tctctttatc ggcttgctct gatatcgtca accttatcaa ttaatctcgt 7260 tgtcggcttg ctatgtaaac taatatgtgc tttattcact aatatgtaca tttggtgcag 7320 gttggaaccc tctagattgt gctctgaaag catatccgcg gctttcaggc atgagcttga 7380 tcccaatgga atcaattgga aaaatgtctc tcaagagcta aaagattttt attatggaga 7440 attcaaggta aatctttcca tcatgaaatt agaaggtctg ttgtgttata tagatatgat 7500 attaacgtta gtttaaaatt ttcagaaggc attttattgg gactcctcca ttgaaaatgc 7560 agtaaagatc gcatggaaaa gaaaagcagc aagaaggtac agtgatttca tctccaaaat 7620 aaaagctgat ggaatccagc tgaactgtat tcatgataat gtgtgggcta gttggttgag 7680 actttgggaa gatcctaagt gtcgcgaaaa gtcggaaacg gctcaaagga atcgttgtgg 7740 tgggaatgaa gtcgcacttg ggactcacac gggcggctct atcaccattg gggaacatcg 7800 caagaggctt gtaagtatat cattaaaaaa attttgtgcc atcactgttg ctttagattt 7860 ggatgatata tgggatgtaa ttagtgttct gatgcagtat actcttggcc tatgatggtc 7920 ccctatttag tgaggtctct ggtggtgaaa atattttgct gttgcaccta ttatcattga 7980 tacaattttt tcgtgcttgt tgagtctact gtttggccat gtacagtttg gcccggggtt 8040 ttatcaattt tgtgacctgc tctctttgaa ttaaatgtgt ttggataatt gccggcctga 8100 tcatcaagta ataattttaa atagaagaaa agagtaaaga aaacatcaga gaacttgctg 8160 ccctgatcct tactctgtgc ttccttctcc tcagtggctt gagtattgga agttgaactt 8220 tctgcaccat cagctttgtc actgtctttg tgctagctgc atcaggatga acagaaactt 8280 agtagctttt tcatcaagaa tccactttct cccaaagcac ctttgtgtca gcaattgaac 8340 ataaagtgtt agttctagca ctgtagtgta tgcataactt ttgtagttta gtcttgcagt 8400 ttgtttagtc tgcactttat tacaggaagc aaagagctta cagttgtgta tagttaatct 8460 catgttacag aaaacaaaga gattacagta ggaacacttt actaatctta tgttcctata 8520 tgttttttcg gtataggtta ttgacaaggg tagagatgtc acaccagctg agatacattt 8580 gcacgttcat acacatggtc atgatggaaa atcttttgtt ggtgagcgat ctcgcatcgt 8640 gcatgtaagt ctaatattct ataatcttat tgactttaca tatgacatcc atttttattt 8700 aagtcgttaa ttatatgcat attgtgatta ttcttatagg agagatatga agaaatatta 8760 caacaaacac aaactcaatc tgatattgat aagtgtcaag catattacca agccgcggga 8820 ggggaaaaga agagaagagt atatggtctt gggtgtgaag cacaaaacta ctacgggcag 8880 catcttcgtc ccgcttttgg atctgatgct acctcgtcag taccgccttc gagtgctcaa 8940 caaccaccga tagggaatat ggatgagttt atgacacgat tgatccctgc tcttacagat 9000 cacatgcttc ctttatttat tgaacgcgta cgagcaatga ttccttcatc ctcaaatcaa 9060 tcaaacactg ttgccgactc tccttcatcc gtagcaccta tggttaatgc tcctactgat 9120 ggtaacattg atggtgtcca ttcatcgggt tcagatgatc aatcttaact catcaagctc 9180 gctttagttt ttcatttttg gattttattt tggtgttgtg gattttctaa actaacagta 9240 tgatatttat atggatttct attttggacc ttttaaaatt ttaagttatg tgaatgtttt 9300 tttaatttta agtgtttaaa ttatttgcat ggactatact tgaaaaggtc taattcaaat 9360 tatcaaaata aatagataaa aaatgacaaa tgttacaaca gatcgcgagg gatacttttt 9420 gtagctagaa gcagcattat aaaataaaat catgcgacag attgctacaa taatttctgt 9480 cgctaaagta attttatatg gctacaggtg tagcaacagt tgtattttgt agctggaagt 9540 agaatataaa taatacgttg tgacagattg caacaaataa tttccgtcag caaaatattt 9600 tgagaagtga ctttcaactt aactagcgac agcaatagct atagattttc tgtagctaat 9660 tatttccaaa cgacagaatt actaatgaat ttagtgacaa taataacgac agataaaatt 9720 tgtagctaaa atggcgacag attttgttgt cgctactgtg tcgctatttg ttgctacaga 9780 tctcatttct ctgtcattaa acggctagct acgagcgatt ctgcaacggt cgactatttg 9840 tcgctaaaac cgtcgttaag ccttttagcg acagatataa gccttttagc gacggaaaac 9900 gtctgtcggt aaaagcagtg ttttttgtag tg 9932 // ID Copia38-PTR_LTR repbase; DNA; EDCOT; 313 BP. XX AC LG_XII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia38-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-313 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-313 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 253-253 (2007). XX DR Genome; LG_XII; Positions 3264279 3264591. XX SQ Sequence 313 BP; 102 A; 53 C; 47 G; 111 T; 0 other; tgttgacata attagttgcg attctgtaat ctgattaatt ataggaacta gattaaatat 60 tattttgtaa tctgattact gcctattcag atcaaatctc gtataggcag taattatgtg 120 aatctgatca attataggag tcatatcaaa tcttgtacaa aattactaca ctttcttaga 180 ataggattgt tacctattca gagctctgcc tattcaggac actgcctatt tagagctctg 240 cctatatatt tcctcctaca aggagaagaa tactaatgaa aaattcagct agtagacacc 300 attgttttct aca 313 // ID TLP3 repbase; DNA; EDCOT; 328 BP. XX AC . XX DT 30-OCT-2006 (Rel. 11.1, Created) DT 30-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon. XX KW DNA transposon; Transposable Element; Nonautonomous; TLP3. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-328 RA Shankar R. and Jurka J.; RT "TLP3: A putative non-autonomous DNA transposon from Solanum RT demissum."; RL Repbase Reports 6(10), 510-510 (2006). XX DR [1] (Consensus) XX CC A putative non-autonomous DNA transposon, sharing characteristic CC with TLP1, from Solanum demissum. The terminal inverted repeat is CC not well conserved. XX SQ Sequence 328 BP; 112 A; 48 C; 46 G; 122 T; 0 other; attcataaat tctaaagtta tctttgcttt cttaacatgt cttttaactt ggtcttattt 60 tacatttatg tccttcaatt tatgtgtaca caagtaggca cgtaaacttg tataacgtta 120 aacaagtaaa cacttgaatc cacgtgacat aatacacgca ggccaatata ttgatgcaaa 180 ttatcatgta agatgtcatg taggacatgt atgcttattt gttcaatttt atacaagttt 240 aagtgtctat ttatgtgcac ccaaattaga gaacataaat gtaaatcaag ttcaagttaa 300 aggatatatt gtataatacc ttttgaat 328 // ID SINE-4_Mad repbase; DNA; EDCOT; 212 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative SINEs from the apple genome. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Nonautonomous; SINE-4_Mad. XX NM SINE-4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-212 RA Kojima K.K. and Jurka J.; RT "Putative SINEs from the apple genome."; RL Repbase Reports 10(10), 1824-1824 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~85% identical to the consensus. 11-14 bp TSDs. Relatively long CC TSDs and polyA tail indicate that it is a SINE. ~70% identical to CC SINE-2_Mad. XX SQ Sequence 212 BP; 55 A; 56 C; 61 G; 39 T; 1 other; aaccacagca agtggcccag tggtaagggc gcggactgcg gctccccaat aaacaaaaaa 60 atgtgggagg tcccgggttc gatgctccga gctggtgagt ctgcttgact gtggccacgg 120 gcagggtgaa attccccata gcctctccgg gcccgaaagk ggtggataac cgtggcttgc 180 caccagttgt ccccctttta aaaaaaaaaa aa 212 // ID Copia13-VV_I repbase; DNA; EDCOT; 4358 BP. XX AC AM455744; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia13-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4358 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4358 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 722-722 (2007). XX DR Genbank; AM455744; Positions 8008 12365. XX CC Positions [1742-2242] - Integrase core CC 'TATT' target site duplication CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 794..3082 FT /product="Copia13-VV_I_1p" FT /translation="MKVNPSKENDWILSVNTVMHLGIHQIVVGFSIQNSNQ FT NSQRTRGVVITNVVSTTRLMLQLKQLILFFPNPMALLKDFTTYLQEKRGQE FT SLNEAAGQDQDKPTALLSKFAGFLADSNPENSQGIFTAFTTALEISNFHDL FT WVVDSGASNHMSNKLTNLYNFRPCSSSTFVSVADGKDVPVQGKGKTKLVSK FT TIESEVLYVPSFPVQLLSVQQLTSTLNCDVLFTSDKVLFQDRITKKTIGEG FT FQLHGLFYFSSDDRLCKGFQASFSSTNKHSLWHQRLGHPSESVFNKIHPSL FT PKGTDGCDICHYSKSTRLPFNLSLSKSSEMFELVHSDVWGPFSLSIDGFKY FT FVTFIDDFSKVTWVYLLKSKSEVFECFKDFHRLVITHFSAHIKTLRTDNGT FT EYTSHNMKNYLISHGIVHQTSCVNTPQQNGVAERKNRDLLEKTRAIMMQMN FT VPKHFWSYGVLTATYLINRLPSRVLDFLCPLEVLQQKKPDLSHLKVFGCTC FT FVHLSATQRRDKLDPRAVKCVFLGYSQTQKGYRCYDTTAKRLFVSRDVQFV FT ETSPIFENSNQGEILSDFVPLPEVAANIEQQSIAPTIQHPTEASVESTINQ FT VVQESAPNIDISEQTTLPRRNPPRERHPPAKFRDYIAAAVRYPPEKFLSYQ FT NLSTSHLAYLTAISSVHEPKNFHEANSQPMWRKSMDDELKALEETNTWNIV FT HLPPGKHVVGCRWVYRFKFNPDGSIERPKSRVVAQGFTQHFGVDYKETFAP FT VAKMSTVKGFVI" XX SQ Sequence 4358 BP; 1250 A; 854 C; 886 G; 1364 T; 4 other; tattttcttc ttggtatcag agckaaaatt tgatcctttg ttctgctttt tattaacatg 60 gcaggcaaca acagtggtga aggctttgtc aaagatctga ttacggctcc ttctggtttt 120 gttgctgatg gtgaatcaaa cacatctcaa aggttgtgtt cggtgttgct gaatgaattt 180 aactatttac cttggtcaag agctgttaca attgctcttg gtggaagatc caagttagga 240 ttcatcaatg gaaaggagaa ggctcctgtt tttkattcac ccgaatatga gatttggtta 300 tcaaaggacc agcttgtcat gtcttggatt cttaattcca tggagcgcaa tatagctgag 360 attttcagtt attctgaatc ttctctagat ctctgggaag cccttcgaga catgtatgga 420 aatcagaaca attcggcacg aatttttcaa attcaacaag aagttaatgc tcttcgacaa 480 gatggaaggc cattcgtgag tttgcttggc aattttaaga gtctgtggag cgaattggag 540 gtctacaggc ctcatactgt tgatccagtt gttctaaaga aaagaacaga agaagacaga 600 gtttttcagg tgctggccag tctcggttcg gagtttgagg atctcagatg tcatattcta 660 atgagtccag aattgccctc cttgaagagt gtctgttcaa ctattcaacg tgaagaagtc 720 cgtagaaagg tgatgattcg tgaaactgtg actaattcct cagacacacg agcctacatt 780 gctcataaaa attatgaagg taaatccatc aaaggaaaac gattggatct taagtgtgaa 840 cactgtaatg cacctgggca tacatcagat cgttgttggg ttctccatcc agaactcaaa 900 ccaaaattca caaaggacaa gaggggtggt gatcacaaac gtggtttcaa ccacaaggct 960 aatgttgcag ctcaaacaac tgattctttt ttttcctaat cccatggcac tcttgaagga 1020 ttttacaacc tatctacaag agaaacgcgg tcaggaatct ctcaatgagg ctgctggtca 1080 ggatcaagac aagccgacag cactgttgtc taaatttgct ggatttcttg ctgattccaa 1140 tccagaaaac agccaaggta tcttcacagc tttcaccact gcactagaaa ttagtaattt 1200 tcatgattta tgggtagttg attcaggtgc ctcaaatcat atgtcaaata agttaaccaa 1260 tctatataac ttccgtcctt gctctagttc tacctttgtt tcagtagcag atggtaaaga 1320 tgttcctgtt cagggtaagg gaaaaactaa gttggtttct aaaaccatag aatcagaagt 1380 cctctatgtt ccttcatttc ctgtgcaatt actttcggtt cagcaattaa cctccactct 1440 taactgtgat gttttattta catctgacaa ggttttgttc caggaccgta ttacaaagaa 1500 gacgattggt gagggttttc agttacatgg gcttttctat ttttcctctg atgatcgact 1560 ttgcaagggt ttccaagctt ctttttcttc tacaaataaa cattcattat ggcatcaacg 1620 tctaggccat ccttccgagt cagtctttaa caaaattcat cctagtcttc caaagggaac 1680 tgatggctgt gatatttgtc attattcaaa gtctacaaga cttcctttca atttatcttt 1740 gtctaaatca tctgagatgt ttgagcttgt tcactcagat gtgtggggac ctttttcttt 1800 gtctattgat ggttttaaat actttgtgac tttcattgat gatttttcaa aggtcacttg 1860 ggtttattta ttgaaatcaa agagtgaagt ttttgaatgt ttcaaggact ttcatagatt 1920 ggtgataact catttttcgg ctcatattaa aaccttgcga actgataatg gcactgaata 1980 tacctcacat aacatgaaaa attacttaat ttcacatggt atagtgcatc aaacaagctg 2040 tgttaacaca ccccaacaaa atggagtagc agagcgaaaa aatcgtgatc tgttagaaaa 2100 gactcgggct ataatgatgc aaatgaatgt tccaaaacat ttttggtcat atggagttct 2160 tactgctaca tatctaatta atcgcttacc cagtcgagta ctggactttc tttgtcctct 2220 tgaagtttta cagcagaaga aaccagattt atctcatctc aaggtttttg gctgcacctg 2280 ctttgtgcat ttatcggcaa ctcaacgaag agataagctc gatcccaggg ctgtaaaatg 2340 tgtattcctg gggtattctc aaacacaaaa gggctatcga tgctatgaca ctacagccaa 2400 gagacttttt gtctcaagag atgttcaatt tgtggaaact agtcccatct ttgaaaattc 2460 caatcaaggg gagatattat ctgactttgt tccactgcca gaggttgctg caaatattga 2520 acaacaatct attgcaccta caatacagca tccaactgaa gcatctgttg aaagtactat 2580 aaatcaagtt gttcaagaat cagctcccaa cattgatata tctgaacaga ccactcttcc 2640 tcgacgcaac cctccacggg aacgtcatcc gccggccaaa tttcgcgatt atattgcagc 2700 tgctgtcagg tatcctcctg aaaaattctt gagttatcaa aacttatcta cttcacattt 2760 ggcttatctt acagcaatct caagtgtcca tgaacccaag aattttcatg aggctaactc 2820 tcaacccatg tggagaaaat ctatggatga tgaattgaaa gctctagaag aaactaacac 2880 ctggaatatt gtgcatcttc cacctggaaa acatgtggtt ggatgtcgct gggtgtaccg 2940 attcaagttc aatcctgatg gatcaattga aagacctaag tctcgtgttg ttgctcaagg 3000 attcacacaa cattttggtg tagattataa ggagacattt gctcctgttg ccaaaatgtc 3060 cactgtcaaa ggttttgtta tcygttgctg caaatcatgg ctggtcttta tcacaaatgg 3120 atgtaaagaa tgcttttttg cacggcgaac ttgaagaaga ggtgtacatg aaaattcctc 3180 caggacaccc tctgtgtgga gatccttctc gtgtgtgtaa gctaaacaag tcaatttacg 3240 gactgaaaca gagtcctcga gcatggcatg ccaagttaag ttctactctg gaagatcttg 3300 gctttacaag aagttctgca gattcctcgt tatatgttca aactggacaa actgaaaagt 3360 taatggtgct tatttatgtg gatgatctca ttataactgg gagtaatgct gattctattg 3420 ctgcactgaa gaagaaactc caaggtaaat ttcctgttaa ggatctcggc ccactcaagt 3480 attttcttgg cattgaggtt gcgacttctc gcaaaggctt atttcttaat cagcgaaaat 3540 acactataga tttgcttcgt gattctaata tgctcaattc caaacccgcc aacactcctt 3600 ttgatagtaa actccagctt gataaattgg gggatcctct tgattctcca aattactatc 3660 aaaagcttgt tgggaagctt atttatttaa caatcactag acctgacatt tccttcgctg 3720 tgagtttggt tagtcagtat atgcatgcac caacagttgt tcacttgtgt atggtgaaaa 3780 ggattttgag atatttgaag aaaacaattg ggcgtggcat tgtaatgaga agaaatgggc 3840 acaytgacat cattgggttc tcggattcag attgggcagg caatacaatt gatagacgat 3900 ccactacggg ctattgtatg tttgttggag ggaatctggt gtcttggaaa agtaaaaagc 3960 aacctgttgt agcacgttca agtgctgaag ctgaataccg tgcaatggcg gcagcatcat 4020 gtgagatggt gtggcttaaa aacctgctga cagatcttgg attttctcct actagtccga 4080 tgaaattgtt ctgcgacaat caagcagcta tgcacatcgc cgccaatcct gtttttcatg 4140 aaagaacaaa acatattgaa gtagattgtc acttcattcg gcaacaagtt cagtccaagg 4200 tgatccaaac acactatatc agatccagtg atcagcttgc agatgccttc actaaagttc 4260 tttcttctac tgtttttcat cgccttatgt tcaagcttgg ctccattgat ccattggcgc 4320 cagcttgagg gggagtattg gagaactatg tgagtcgt 4358 // ID Gypsy10-VV_I repbase; DNA; EDCOT; 4417 BP. XX AC AM469898; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy10-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4417 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4417 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 735-735 (2007). XX DR Genbank; AM469898; Positions 6657 2241. XX CC Positions [3309-3803] - Integrase core CC 'TTTAT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 402..1985 FT /product="Gypsy10-VV_I_1p" FT /translation="MAQMVERNSVEPLTWDEFTKAVQLRFGPIDYEDPSEA FT LTRLKQTTSIAAYQEAFEKLSHRVDGLPKNFLIGCFIAGLRDEIRINVKIK FT QPRTLADTIGVARLIEERNQLQRKPNQQTHFQPASLTPKASPNPTAGVLGP FT PPTQRMNQSSNAQPATFRRITNQEACERREKGLCYYCDEKFVAGHRCERPQ FT LFMIEDFPHMNTEDVEGAHPEQEHHEVIPEISFHAIAGTEHPQTIRVLGKL FT KNKNVMVVIDGGSTHNFIDHVIVSKFGLPVIRDKKFEVMVANREKIECTRQ FT CRGLTLTIQGYSVTADYYILPVAACQLVLGVQWLETLGPIEMDYKQLTMNF FT KVEGTPQTFQGLRRTNIEALSDKESNGLQGTGLFFKIIPSTTASSQPKSYP FT PEIGQLLAKFSHVFESPTSLPPRRSHDHQIPLHPSAGPVSVRPYRYPYYQK FT TEIEKMVKEFLQSGLIQPSNSPFSSPILLVKKADGAWRFCVDYRALNDITV FT KDKYPIPIIDELLDELHGAKFYSKLDLRSGYH" XX SQ Sequence 4417 BP; 1264 A; 1058 C; 913 G; 1170 T; 12 other; ttggtatcag agcttggtcc gaccatggac actcgcggca aaacgaatgc aaaattccgc 60 aacgatgtta acgaaatctt agcacgacac gataccagtt tcgatcaggt gaatgcaatc 120 ttacaagaag tgttaactga agcttcaagc tcttaagagc ctcccataaa ccaaaacact 180 agcccacgtg atgcctcctc acacccacat acttctcgtt ctaacattat cagttgacca 240 ccctttcatt caacacctca aactgtcctt cccaaaattt aaacggtgac gacccaaccg 300 gttggattta caaggcagaa cagtactttg atttcaagaa cattgcacca gaacaacaag 360 ttcatctggc ctccttccat ttaagaaggc attgccctgc aatggcacag atggttgaac 420 gaaattccgt ggaaccactc acatgggatg agttcaccaa ggctgttcaa cttcgatttg 480 gtccaatcga ctacgaagac ccgtcagaag ctctgactcg tcttaaacaa accacatcca 540 tagcagctta tcaagaagct tttgaaaagc tttcccaccg agttgatggc ctgcctaaaa 600 attttctcat cggttgtttt attgcaggac ttcgagatga aattcgcata aatgtaaaaa 660 ttaaacaacc gcgaaccttg gcagatacaa taggagttgc taggctgatc gaagaacgca 720 accaactgca gaggaagcca aaccagcaaa ctcatttcca accagcctca ttgacaccaa 780 aggcctcacc caaccccaca gctggtgtgc taggacctcc accaacccag cgtatgaacc 840 agagttcgaa tgctcaacca gcaacattcc gccgaatcac caatcaagag gcatgcgaac 900 gacgagagaa gggattatgt tattactgtg acgagaagtt cgttgctggc catcgttgcg 960 aacgacctca attattcatg atcgaggatt tccctcatat gaacactgag gatgttgaag 1020 gcgctcaccc ggaacaagaa catcatgaag ttataccaga aatttctttt catgcaattg 1080 caggaactga acacccacaa accatacgcg ttctgggcaa gctgaaaaac aagaatgtga 1140 tggtggtaat agatggtggt agtacgcaca acttcattga tcatgttata gtctctaagt 1200 ttgggttacc agtgatccgg gataagaaat tcgaagtcat ggttgctaac cgtgagaaga 1260 tagaatgtac tagacaatgt cgcggtctca ccctcaccat tcaaggatat tccgtcaccg 1320 ccgactacta cattcttccg gtcgcggcat gccaattggt cttaggagta caatggcttg 1380 aaactctcgg acccatcgag atggactaca agcagctcac catgaacttc aaggtagaag 1440 ggacccccca aaccttccaa ggattgagac gaaccaacat cgaagctttg tctgacaagg 1500 aatccaatgg gttacaaggc actggattat ttttcaaaat aattccttcc accaccgcca 1560 gcagccaacc aaagtcctac ccacctgaga taggccaact actagcaaaa ttctcccatg 1620 tatttgaatc acccaccagc ttgcctccaa ggcggtcaca tgaccaccag atcccattgc 1680 atccgagcgc aggaccagtg agtgtgaggc catatcgata cccttattac cagaaaactg 1740 agatagagaa gatggtaaaa gagtttttgc aatctggttt gatacagcca agtaacagtc 1800 cgttctcttc cccaattctg ttagtaaaga aagcagatgg tgcttggcgt ttttgtgtgg 1860 actatcgagc tctgaacgac atcacagtta aagataaata tccaattcct attatcgatg 1920 agctattaga tgaactccat ggagccaaat tctactctaa attggattta cggtctgggt 1980 atcattagat acgggtgcac gaagatgaca ttcctaaaac agtattctgg acacacgaag 2040 gccattacga atttatagtg atgccatttg gcctcactaa tgcaccagca accttccaaa 2100 gtctcatgaa tgatctcttc cgttcctatc tccggaaatt tattttggtt ttctttgatg 2160 acattctaat atattcaaga tcatgggaag accatctcgc acatctacaa attgttctcc 2220 aaatcctatt caactaacag tttgtttgca aaagagtcga aatttcgatt cggtgtttta 2280 caggtagagt acttgggcca cattatttcg gagcaaggtg tatcggttga tccagccaaa 2340 atacaagctg tcattgagtg gccaaccctg acaacagcaa aaggagtccg tgggttcctc 2400 ggtttagcag gctactatcg gaaatttatc cgtcatttcg gcagtatagc agctccccta 2460 acccgtctct tgagcaagga tggattcaat ggaatgaggc agcagagatg accttcacac 2520 aattaaaaga ggccttgaca tcaccaccaa ttttacgcct tcccgatttt actcaacgat 2580 tcgtgattga atgcgatgcc agcggaatcg gacttggtgc aattcttacc caagaaaatc 2640 gaccagtggc gtattttagc caagcactga agggttcggc cttatcattg tccatttatg 2700 agaaagaaat gttagctatt gtcaaagcaa tcaagttatg gcatccatac ttgcttggga 2760 aaccatttac agtccgcact gaccaaaaaa gtctcaagta cctactggag caacggatta 2820 ctacaccagc acaaacacga tggctgccaa aactacttgg ttatgattat gaaattgagt 2880 ataaacgtgg gcttggaaat caaggtgcag attctttgtc acgtgtagtt gaattccaat 2940 ttttatccat ttcccaacca cgtgaaaatt ggtggccagt gcttcaaaag gaagtccaac 3000 aggactcatt ttatgaagac ttattacaaa aaaacccctc tccaactacc cacaagttgc 3060 tccaacgtga tgaagtatgg ttcaagggaa acaaagtgta tttgagcccc aactcatcct 3120 tgatttcaaa gataatggct gactaccatt cgtcgccaat aggtgggcac tttgggttcc 3180 ataaaaccct ctctcgtatc aaacagagtt ttttttggtc taatatgcgc cggatggtga 3240 aggatttttt atagcaatgt gatatctgtc agcggttcaa aattgattgt atgaagctgg 3300 cggggttgct tcagccgcta cctgtcccta ctcaaatgtg gattgatgtc tcgatggact 3360 ttattgaggg gttaccatct tctaatgggt atacttccat catggtagtt gttgaccgcc 3420 tgaccaaata tgctcacttc gtcgccttga aacacccgtt tactgctgta attattgcca 3480 aggcatttgt tgccaacgtg gttcgcctgc acggtattcc gacatcaatt gtcagcgatc 3540 gggacaaggt gtttatcagc tccttttggc tagccttgtt ccaactgcag ggaaccaagt 3600 tgtgtatgag ctcaagttac catccccaat caaacggcca aaccgaagtt gtcaatcgaa 3660 ctttggagca atatttacga tgttttgtcg gtgaccagcc acagaagtgg ctcaaatgga 3720 ttccctgggc tgagttcagc tacaacactt caactcactc ctccaccaag atgacaccct 3780 tcgaagctgt ttatggaatt ccacctccac gtctattagc ttatgtacca ggtacttccc 3840 acgtccaagc agtagatgag tacctgcgtg atcgagatgc tatcctacgt gagctgcgay 3900 ataaccttct rctggctcaa gatcggatga aatgtcaagc tgaccaacac cggcgyragg 3960 cctctttcct tgtgggagat tatgtgtatt tgaaamtyca accatataga cagacttctr 4020 tggcttttcg ttcctccatg aarcttgccc caygtttctt tgrtccttat aaagtcattg 4080 ygaaagttgg tccgrtggct tataaactgg ctttgcctct tggttctcaa attcatgatg 4140 tgtttcatgt cagtttgtta aagaagcatt tgggaccagt cactgcaacg tccacccaac 4200 ttccccttgt ctcggatact tcgactgtcc ttccacaacc tgaagccgtt ttagatcgac 4260 gagtgatcca taagggtaaa taccgcccaa aatttgaaat attggtgaag tgggtcggtg 4320 taccagcaga agatgccacc tgggagaatg aatggtgttt caccaagtca tatcctgatt 4380 tcatccttgt ggacaaggat ccttaagcgg tggggaa 4417 // ID BAMHI_VF repbase; DNA; EDCOT; 250 BP. XX AC M16852; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 08-JUL-2004 (Rel. 9.06, Last updated, Version 3) XX DE Broad bean (V.faba) BamHI repetitive element, clone 6. XX KW Gypsy; LTR Retrotransposon; Transposable Element; BAMHI_VF; KW BamHI repetitive sequence; Gypsy-like retrovirus. XX OS Vicia faba OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Vicia. XX RN [1] RP 1-250 RA Kato A., Iida Y., Yakura K. and Tanifuji S.; RT "Sequence analysis of Vicia faba highly repeated DNA: the BamHI RT repeated sequence families."; RL Plant Mol. Biol 5, 41-53 (1985). XX DR GenBank; M16852; Positions 1 250. XX SQ Sequence 250 BP; 79 A; 50 C; 60 G; 61 T; 0 other; gatcccatca agtacatatt tgaaaagccc gctctgtctg ggagaatagc aagatgacgt 60 tggtcttaac agaatatgat atccaatata caactcagaa agcaattaag ggaagtgtac 120 tggctgatca tttggcacac caagcctgtg gacgattatc aatcattgaa ctttgatttt 180 ccggacgaag acatcatggt ggtaactgcc tgctgaagtc ctagaccgga tgaaggaccg 240 aggaaggatc 250 // ID Copia-6_Mad-LTR repbase; DNA; EDCOT; 169 BP. XX AC ACYM01089668; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-6_Mad_; KW Copia-6_Mad-LTR; Copia-6_Mad-I. XX NM Copia-6_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-169 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1347-1347 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01089668; Positions 29 197. XX SQ Sequence 169 BP; 53 A; 30 C; 22 G; 64 T; 0 other; tgtcaacgag ctgtacattc ctaattagtc taagtcaact atttgattct gcaagattat 60 aggctcataa ttactttcct agaatagttt cccaggctct gtatatataa ccttcctctt 120 gttatacata aaatgagaga tatattaatg aagtattatt ttttaccca 169 // ID Gypsy-45_Mad-I repbase; DNA; EDCOT; 5058 BP. XX AC . XX DT 22-OCT-2010 (Rel. 15.11, Created) DT 22-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-45_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-5058 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1987-1987 (2010). XX DR [2] (Consensus) XX FH Key Location/Qualifiers FT CDS 184..1446 FT /product="Gypsy-45_Mad-I_1p" FT /translation="MSSVRTMPPRREPRHSAEPSFPDIAQLGEAIANAIQS FT SLRPPQXTPLETVYNLKLNHFMGNEGHEGAEKWLNHVEKTFLVMQSQGNLP FT PDRWVETTTWFLGPEPASWWRQESYQMPPEVVADWEVFKQLFRKRFIPPEY FT IDRKKQEFTHLKQGKMSANEYYRRFTDLSRYDPEVAANPVEMLRRFRLGTK FT KKWRSIATSTPCATYQEFYEVLLRIEDSENMPSESEDEEEKNGNQRRDDKG FT KGQSSQGPRKTQSFKRSGVSSSSSSGGLSSNVQRRGGRFSGGPRFQRQRDF FT GGSGAPLCRRCNNRHFGECRRGSSACYTCGQMGHRAAHCPQNQQRPQQPSL FT PPPAPTQQASGPSGYAQTGRGGAYHYQGDAAPYASGQYQYSQDPHYQGGYP FT QYQGGSMPYQPHSAGGSQWYQGDSPSR" FT CDS 1569..5000 FT /product="Gypsy-45_Mad-I_2p" FT /translation="MTLQDAQNNPDLIMGTLNILGHFARVLIDCGATHSVV FT SHTFAQVTQPHPTPLGYDLEFSMPRGERCYVDRVYPGCPVMVEDVVMPANL FT IPLDIVDFDVILGTDWLHYNRAKIDCYGKTVTFHRPGLPEVTFVGEPSGVR FT HGVISAMKAKRLLSKGCQGYLAHVVLNDNAPSSVEDVRVVRHFPDVFPDDL FT PGLPPDRDVEFVIDLLPGTDPISLTPYRMAPAELRELKVQLQELVDKGFIQ FT PSTSPWGAPVLFVRKKDGTLRLCIDYRQLNRVTIKNRYPLPRIDDLFDQLR FT GACVFSKIDLRSGYYQLKIRSEDVPKTAFRTRYGHYEFLVMPFGLTNAPAA FT FMDLMNRVFQPYLDRFVIVFIDDILVYSKTRAEHARHLKLVLKSLREHQLY FT AKFSKCQFWLDQVAFLGHVISAQGIRVDSQKVAAVENWEQPRTVTEVRSFL FT GLAGYYRRFVKDFSVIALPLTRLTRKDVKFEWDDNCEQSFQQLKYYLTHAP FT VLALPDDSGNFEVYSDASLNGLGCVLMQHGRVIAYASRQLKPHEKNYPTHD FT LELAAIIFALKIWRHYLYGEKCKIFTDHKSLQYLFTQRDLNLRQRRWIELL FT SDYDCTIEYHPGRANAVADALSRKTPARLNAIYDCHVPLLADLRSTGVELG FT VEDREEALLANFQVRPILIDRVLEAQMNDEETQEIIQARNQGKKKDFRIRE FT TDGMLMQESRMYVPNNAELKKEILDEAHISAYAMHPGGTKMYHTIRPFYYW FT PGMKREIAEYVSRCAICQQVKAERKKPFGLMQPLPVPQWKWENITMDFVYK FT LPRTQNGYDGIWVIVDRLTKSAHFIPVREKYPLSRLAKLFISKIVKYHGVP FT VDIISDRDPRFTSKFWIAFQEALGTRLLYSTAYHPQTDGQSERTIQTLEDM FT LRSSVLQFGDGWHDCLDLMEFAYNNSYHSSIGMAPFEALYGKSCRTPLCWS FT EVGERVLVGPEIVDETTQNIQVIKSNLKAAQDRQKSLADKHATDRMYNVGD FT WVFLKLSPWKGVVRFGKKGKLSPRYIGPYMITERVGEVAYRLELPPELSKV FT HDVFHVSMLRHYVSDPSHVIPPQPLEINPDLTYDEEPVTILDWKDKELRNK FT TVRLVKVLWRNHSVEEATWETEDRMREMYPRLFYDY" XX SQ Sequence 5058 BP; 1329 A; 918 C; 1337 G; 1472 T; 2 other; gtagctttcg gtttttattt attcgtatat ttcttatcct tatcgcttcc gcactgtgca 60 catggctacg tcaccctcac gtgacggcca gcacgcctcg atcttcggtc ggggtgtgtc 120 agtttggtat cagagcctag gtttagcagt cctgtatatc ttgtgaatga tctaatcatt 180 gtgatgtctt ctgtcagaac tatgccgcct cgtagagagc cacgtcactc agctgagcct 240 agtttccctg atattgctca gttaggggaa gctatagcta atgccattca gtcttcgctc 300 cgtcctcctc aaakgacacc tcttgagact gtgtataatc tgaagctgaa tcatttcatg 360 ggaaatgaag gacatgaggg agcggagaag tggcttaatc atgtcgagaa gactttcctt 420 gtgatgcaga gtcaggggaa tcttcctcct gataggtggg tcgagacgac tacctggttt 480 ttgggtccgg agcctgcatc ctggtggaga caggagtcat atcagatgcc accagaggtt 540 gtagccgatt gggaagtgtt taaacagttg tttcggaaaa ggtttattcc ccctgagtac 600 attgatcgca agaaacaaga gtttacgcat ctgaaacaag gaaagatgtc agcgaatgag 660 tattacagga ggttcactga tttgtctcga tatgatccgg aggttgctgc taatccggtc 720 gagatgctcc gtcgtttcag gttgggtact aagaagaaat ggcgttctat agcgacatcg 780 actccctgtg ccacttacca ggagttttat gaggttttac tgcggattga ggactcagag 840 aacatgccca gtgaaagtga agatgaagaa gaaaagaacg ggaaccagag gcgagatgat 900 aaaggtaaag gtcaatcatc tcagggacct cgtaagaccc agagttttaa gagaagtggt 960 gtcagttcca gctcttctag tggaggtttg agctctaatg tgcagaggag aggtggtaga 1020 ttttctggag gcccgagatt tcagaggcag agggactttg gtggttcagg tgctccttta 1080 tgccgcaggt gtaataatag gcattttggg gagtgtagga gaggcagcag tgcatgctat 1140 acttgtggac agatggggca tagggctgca cattgccctc agaatcagca gaggccccaa 1200 cagccttcct taccaccacc tgcgccgacc cagcaagctt caggacctag tggttatgcc 1260 cagactggtc gtggaggtgc ttatcattat cagggcgacg ccgctcctta tgcttcaggg 1320 cagtatcagt actcacagga ccctcattat cagggtggtt accctcagta tcagggaggt 1380 tctatgccat atcagccaca ttcagcaggt ggatcccagt ggtaccaggg ggacagcccc 1440 agcaggtaga gattgctgct agcagtgcag gatcttcgag gcagtctggt cagccaagac 1500 aaggacgagg tattcatgct agcagaggtc gtggtggacg acagcagaat cagggacgta 1560 tccataacat gacactgcaa gatgctcaga acaatcctga tttaatcatg ggtacgttaa 1620 atattcttgg tcattttgct agagtattga ttgattgtgg tgctacgcat tctgttgttt 1680 ctcatacatt tgctcaagtg acgcaacctc atcctacacc tctaggatat gatttagagt 1740 tttctatgcc tagaggggag agatgttatg ttgatcgggt atatccagga tgtccagtga 1800 tggtggagga tgttgttatg ccagctaacc ttattccgtt agacattgtt gattttgatg 1860 tgattttggg cactgattgg ttacactaca atcgtgccaa gatagattgt tatggaaaga 1920 cagtcacttt tcatcgtcct ggattacctg aagttacatt tgtaggagag cctagcgggg 1980 tgaggcatgg tgttatttct gccatgaaag ccaaaagatt gttgtcgaaa ggttgtcagg 2040 gatatttggc tcatgtggtg ttgaatgata atgctcctag tagtgtggag gatgtgcgtg 2100 tggtcaggca ttttccggat gtgttccctg atgatttgcc tggattgccg ccagacagag 2160 atgtggagtt cgttattgat ctgcttccag gtacggatcc tatatctttg actccttata 2220 gaatggctcc tgctgaatta agggaattga aagttcagtt gcaagaatta gtggataaag 2280 gttttattca gcctagtact tcaccttggg gagctccagt cttatttgtg aggaagaaag 2340 acggaacctt gaggctgtgc attgattaca ggcaattgaa tcgggtaaca attaagaacc 2400 gttatccgtt acctcgtata gatgatttgt ttgatcaact ccgaggtgcc tgtgtgttct 2460 ctaagattga cttgaggtct ggttactacc agttgaagat tagaagtgaa gatgtcccta 2520 aaacagcwtt caggactcga tatggtcatt atgagtttct tgtgatgcca ttcgggttaa 2580 ctaatgcacc agcagctttc atggatttaa tgaatcgagt attccagcca tatttggaca 2640 ggtttgtcat tgtcttcatt gacgatattc tggtatactc taagactaga gcagagcatg 2700 ctagacatct taaattggtg ttgaaaagtt tgagggaaca ccagttatat gctaagttta 2760 gcaaatgcca attctggtta gatcaagtgg catttttggg acatgttata tcagctcaag 2820 gcattcgagt ggattctcaa aaagtggcag ctgtggagaa ttgggaacaa cctcgaaccg 2880 tcactgaggt acggagtttt cttggccttg caggctatta tagacggttt gttaaggatt 2940 tttcagtgat tgctttacca ttgacgaggt tgaccaggaa ggatgttaag tttgagtggg 3000 atgataattg tgagcaaagt tttcagcagt tgaagtatta tctcactcat gcacctgttt 3060 tagcactccc agatgatagt ggtaatttcg aggtctacag tgatgcttct ttgaatggtc 3120 tgggttgtgt attgatgcaa catggtaggg tgattgctta tgcttcgaga cagttgaaac 3180 ctcatgagaa gaattaccct actcatgatc tggagttagc ggctatcatc tttgctttga 3240 agatttggag acattatctt tatggtgaga aatgtaagat cttcacagat cataagagtc 3300 ttcagtatct ttttactcag agagatctaa atcttcggca gcggaggtgg attgagttac 3360 ttagtgatta tgattgcacg attgagtatc accctggtcg tgcaaatgca gtggcggatg 3420 cacttagtag gaagactcca gctagactta atgccatcta tgattgtcat gttcctcttc 3480 ttgcggattt gaggtccact ggagtggagt taggagtgga agatagagag gaagccttac 3540 ttgctaattt tcaagttagg ccaatcttaa ttgatcgtgt gctcgaggcc cagatgaatg 3600 atgaagagac ccaggaaata attcaagcaa ggaatcaggg gaagaagaaa gatttcagaa 3660 ttcgagaaac tgatggcatg cttatgcaag agagcagaat gtatgtgccg aataatgcag 3720 agttaaagaa agaaatcctt gatgaagcgc atatttcggc atatgcaatg catccaggag 3780 gtaccaagat gtatcatacc attcgaccat tttattattg gccgggtatg aaaagagaaa 3840 ttgccgagta tgtgagtagg tgtgccattt gccaacaggt taaagctgaa aggaagaagc 3900 cgtttgggtt gatgcagcca cttcccgttc cacagtggaa atgggaaaat attaccatgg 3960 attttgtgta caagcttcct cgtacacaga atggttatga cggcatttgg gtgatagttg 4020 atcggcttac taagtcagca cactttattc cagtgaggga aaaatatcca ttaagccgat 4080 tagctaagtt attcatatcg aagattgtga agtaccatgg tgttccagtt gatattatct 4140 cggatcggga tcctagattt acttctaagt tctggatagc attccaggaa gctcttggta 4200 cgagattact ttatagtacg gcatatcacc ctcagacaga cggacaatct gagaggacta 4260 ttcagacatt agaggatatg ctgagatctt cagtgctgca gtttggcgat ggttggcatg 4320 attgtttgga tttgatggag ttcgcctaca acaacagtta ccattcgagt attggtatgg 4380 caccttttga ggcactctat ggcaagtctt gtcgaacgcc attatgctgg tcagaagttg 4440 gtgaaagagt tttggtgggc ccggagattg tggatgaaac tactcagaat attcaggtaa 4500 ttaagtctaa cctgaaagcg gcccaggatc gacaaaagag cttagcagac aagcatgcca 4560 ctgaccggat gtataatgta ggtgattggg tatttctgaa gctatcacca tggaaaggtg 4620 ttgtgcggtt tggaaagaaa ggcaagctga gtcctaggta cattggacca tatatgatca 4680 ccgagcgagt cggtgaggtt gcttacaggc ttgagttgcc tccagagttg tccaaagtgc 4740 atgatgtgtt tcatgtttcg atgcttcgac attatgtctc agatccttca catgtgattc 4800 ctcctcaacc tttggaaatt aatccggatt tgacttacga tgaggagcca gtgactattt 4860 tggattggaa agataaggag ctgaggaata agacagtgcg tttggtgaaa gttttgtgga 4920 gaaatcactc agtggaagag gctacttggg agacagagga tcggatgaga gagatgtatc 4980 cacgcttgtt ttatgattat tagtggattg tattgttgtg tataatttcg aggacgaaat 5040 tttataaggt gggtagat 5058 // ID Copia42-PTR_LTR repbase; DNA; EDCOT; 381 BP. XX AC LG_IV; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia42-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-381 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-381 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 263-263 (2007). XX DR Genome; LG_IV; Positions 14409801 14410181. XX SQ Sequence 381 BP; 107 A; 70 C; 90 G; 114 T; 0 other; tgtagcaaat tgtcaacatt ttctcaatca ccctatccac taccaaccac cctctccttt 60 acaaccacta tatttatgct tccccttctc atgtagacag aagagaaaaa cgagagagaa 120 gagagagtgc agtgtgtgtg cagaggaaga agagagagtg caactgtgag agtgaaatag 180 tgcagatttg agagaaaaac tgagtgtaag agtgaaacac tgggttttgt gggattgtac 240 tgggttgagt tgagtgtttg tatcattcct tcaataatat acaatctgtt gcctccgtgg 300 acgtacccgg ttttggggaa ccacgtaaat ctgcttgttt gtgttttatt tgtgtttgct 360 ttcggtccag tatgcacaac a 381 // ID Copia-90_Mad-LTR repbase; DNA; EDCOT; 321 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Copia-90_Mad-LTR. XX NM Copia-90_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-321 RA Kojima K.K. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1719-1719 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 321 BP; 103 A; 50 C; 59 G; 107 T; 2 other; tgttgtaaat aatgggtatg tttgcccaca tgtgtatagt aatgtgnata gtgggtatgt 60 ttgcccacat gtgtatagta tanactcaca agctaaatag taatgttttg taattttcca 120 ttgaagtggc tctataaata gagcacttcg attgttcaaa gattagtgaa tgagaagaag 180 aaagaaaaga gaaatatatc taatagcaat aatatacatt acttcctctg caacagcttg 240 tgtcggtata atactctgca accgcttcgt tcctgccccg agtaaaggtt atctctctat 300 aaattttgcc tatttataac a 321 // ID GYPSHAN3_LTR_MT repbase; DNA; EDCOT; 380 BP. XX AC AC150244; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of a LTR retroposon from Medicago truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; terminal; repeat; GYPSHAN3_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-380 RA Shankar R. and Jurka J.; RT "GYPSHAN3_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 25-25 (2007). XX DR EMBL/GenBank/DDBJ; AC150244; Positions 19144 19523. XX SQ Sequence 380 BP; 99 A; 60 C; 91 G; 130 T; 0 other; tgttaggact gctgagtcat tagttcataa tacaactgtg ggtcccaaag tttggcaagt 60 ttattctaga aggtgtaaga aacctgctaa gggttagtta tagaatttgg tgacgtggag 120 agtggataga ggactagcaa tgacttccat tatataagga gtgggtgggg ttgagagtag 180 gcatcttgga ttttccgtga gtaatagaat ggataggcag ctgtgagctg acctatagga 240 gcttagctct agtcagatct agggattcat acattccccc atttctgtaa ttctccaatt 300 ttccatcaat aaagtccttt tacatttcaa ttgtctgaat attgtgctgt tttctctgtt 360 cttattttgg gttcctaaca 380 // ID TOPIE1_LE_I repbase; DNA; EDCOT; 3201 BP. XX AC AF220603; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 25-JUL-2007 (Rel. 12.08, Last updated, Version 2) XX DE Lycopersicon esculentum retrotransposon TOPIE1_LE_I, internal DE region. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW internal region; TOPIE1_LE_I; internal portion. XX NM TOPIE1_LE_I. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-3201 RA Lavelle T.D., Oldroyd E.G., Dalhbeck D., Staskawicz J.B. RA and Michelmore W.R.; RT "Direct submission."; RL Direct Submission to Genbank (04-JAN-2000). XX DR Genbank; AF220603; Positions 54681 57881. XX CC Flopped on July 25, 2007. Putative non-autonomous Copia. XX SQ Sequence 3201 BP; 1163 A; 439 C; 619 G; 979 T; 1 other; attggtatca aaccaggttg tcttttacag gttaacacct aagataaaag atcgagatga 60 attctgtacc acctattggt cacagcgaaa gacagtaaac tgttagactc ccaatgttca 120 atgggtctca ctttggctag tggaaagcac acatggagga tttattcaag cagaatatta 180 tgaattatgg ataggataaa tataggaccc actattgcaa tgaagattgt cgaaggactt 240 aaattacaaa aggttaagat tgacttcacc acggaagatt tatcagctct caggaaaaat 300 gctaagaaca aaaacattct tgtttgtggt cttggaccag atgagtacaa cagaatttca 360 aactatacta ctgctaaaca aatctgggat gcattggttg atgcttatga aggaacaagt 420 caagtgtgga aattcatagt agacatgcta ttcactgaat atgaaacatt caaaatgatt 480 aaggtgagcc tatgtcaaaa atgattacta gactcactaa gttggtaaac gagttgtcat 540 cactgggaaa aatcctcact actgaagaac atgttgacaa ggttctaagg atccttccta 600 aaaacaaatg agatgtaaaa gtaactgcca taagagaagc taaagacatc tcatcatgac 660 atttgatcaa cttgtggaaa atctcagaac ttatgagatg aatatggatg acttaaagaa 720 gggggaaatg cttagcgaaa aagcattagc cctaaaagtg tctgatggtg aagatattga 780 gtatgatgag gataaaatgt cacttctagc aaaaggatat aagaagtatc tcaggaagga 840 gaaggaaaat gaaaagaaga aaaccaatca aaagaagtgg ataaatgata aatctcaaaa 900 tggatgctac aagtgtgaaa aaatgggtca tcatgttaag aactgcccgc aatgggaagc 960 taattggagg aaagaaagga tggaaaagga aaggaattca aagaaaaagg aggaatatgc 1020 aatggtagct tcttggggtt caagagatgg agaatctgat gatgaaattg atgaaacaac 1080 attcttagct ctgggcgatt cagacgctaa agatgatgaa aattctgagg ttagtatcac 1140 tgatgttaaa gaaaaactgc actcattttc taaaagtaga ttaattggat taataaatag 1200 gttaattgat gaccttgaag aattaacatg tgaaagagat aagttgttta aagcctttgc 1260 agataaaaaa tttgagtaca tggatctcaa agatgacaaa attgtaactg ataaacaaaa 1320 taattgtctg aagaaacatg ttgaaaaact tgagtcatct aacctagatc taaagtctga 1380 aattttaagg atgaaaatta ctgaataagg aaaagtaaaa atgagtgtaa ctgaagaaat 1440 ttgattcacc cttttgatca taagaaagga cccaagcttg tgtgggttcc taagactaac 1500 ctctaagtta ttttgcaggt gaagtagaaa ggaagcaagt gatgaaattc ataaatattg 1560 cttgcgtaag agatataaat gaagataaat aaaagttact ttcgctcact tcgcaaaagg 1620 gggaatgtgt catttaaaaa aaaagaaaaa aaaggaggta atgcatgtgt aagggggaag 1680 caaaaacaag gtgaggatta aagtgaaact gataagagtg aattgaaaca cgttgtacca 1740 catatttcat ttgttgaaca aactaaggac atatttatag ggggaacaat gaatcttaaa 1800 actgatttga ctacaaaagt ttgtgcttgt tggctcacct tgttcttttt caaacgacaa 1860 ttgatgaatt gtgacactaa gtaaggagca ttatgaaaag aataagttag acttggggat 1920 gattgagatt gcatgaactc ccctgaatga ttggctagaa taattattct cctaacttta 1980 tgagctaaaa tgttattcaa ttaagtctta cacattcagt tgtgtgtccc aacttcagat 2040 cttttactta ttttaatcta attttgtatt agattgtgca gagaaatggt aaaaacaagt 2100 aatgatggtc acaaaattgc tcttatcagg tatgttatat attgatggag gttaatattg 2160 tataaagtga aaaagttgag gactcatgtx tcatgtatta attgctctaa tatagaaaaa 2220 aattaaccgt ccaagtgcaa gagtctcatt ctttcaaatt gttctctctc actttgtctt 2280 cttgtattat ttttgcaagc ttaaagaaga cagtttctca atttcagtta tcaggaagaa 2340 tcaactccta aaacacattt ttttctctat tccaccttga actctcatct agaaatcaaa 2400 agtgtcaaca agatgccatt atcttagagc tagcatgaaa aaaacaaaga taacatgatt 2460 tccattgtaa gttttgagga acactcaatt ccaattcatg catggttttt caaaaaacaa 2520 atatagaaaa aaaattattg agtagatgaa ccatgttgac ctatatgcgt caatgaggaa 2580 aactgctact ccaatgaaaa ggttgaagta ataatttcac taataagatt gttttactgg 2640 aggttggtca tattgcttat ggaaaaaaaa tcagatatga ctttaagctc taaagattgt 2700 tcttgataaa gattgttgac actactatct ccacttgttc cattatttgc ttcacttcca 2760 atgttagtcc ctatgttttt ttctactcat gtcaactatt tgtttttttt attagtgctc 2820 agtcgttttt gcttcattca gtatgacttt gatcttatat aaaacattat ctggtagttt 2880 gatggattaa ttattgattg ctttaatgac tcatgttctt gctctctata atacattatt 2940 atgttgcatg aagtcgttat ctgattgtct tggtgatagt cagtgagcat gaattgttta 3000 actgatcaat ctagcttgta tattatagga ttgacataac ttttcaatga tgccaaaagg 3060 gggaagataa gagttgtgca gtgtttataa tccatcgact aacttgtttc atgttagtat 3120 tttatgcttc agtgtctaca aataaaactg tttgaatgca caaagaaaag aggtttgtca 3180 tcatcaaaaa ggggaaattt t 3201 // ID Copia-4_CP-LTR repbase; DNA; EDCOT; 360 BP. XX AC ABIM01012539; XX DT 10-MAR-2010 (Rel. 15.04, Created) DT 10-MAR-2010 (Rel. 15.04, Last updated, Version -1) XX DE LTR retrotransposon from papaya: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-4_CP_; KW Copia-4_CP-I; Copia-4_CP-LTR. XX OS Carica papaya OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Caricaceae; Carica. XX RN [1] RP 1-360 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from papaya."; RL Repbase Reports 10(4), 580-580 (2010). XX DR Genome; ABIM01012539; Positions 2790 2431. XX SQ Sequence 360 BP; 111 A; 70 C; 56 G; 123 T; 0 other; tgttaaaatt aatgattttt tctgttaatg tcaaattcaa aaaatgaaaa tccaccgtga 60 ggatgtttca cggaaggata cgtaaaatcc catgcgatgt gtatgcatga ttttcggacg 120 atctaatttg atcgattggt tgatgtaatc aatttaaatt tgtattgcta tatatatatg 180 acgaaataaa gaagaagata actcattctc tccagaaaaa gcacgcctct tcataacagc 240 aaaacagagt cagttgcata agcttgctct gttttgctgc cctctctctc ctcaactttc 300 tctctctaag tttgttcatt cacagagcct cctttgaagc ttattctctt tcaatcaaca 360 // ID Copia-88_Mad-LTR repbase; DNA; EDCOT; 270 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-88_Mad_; KW Copia-88_Mad-LTR; Copia-88_Mad-I. XX NM Copia-88_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-270 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1715-1715 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 270 BP; 77 A; 47 C; 46 G; 99 T; 1 other; tgacagtagt aacagctggc aatgccacat cagcttagct aatagactat tggtggttat 60 gttggttaga ggtgttataa ctaactgata tagttactga tgtaagtmgt gcaaactata 120 taagatgata tggcattact gtaatcttca agtcagatca atacaaaagt ttctttctct 180 aaacattcat tctctctcta gaactcttct ttcttctcct tttcttgttc gagtattcat 240 tgcagatcag gatttctgta tacgttaaca 270 // ID COPIA1-LTR_LC repbase; DNA; EDCOT; 1205 BP. XX AC . XX DT 24-MAR-2005 (Rel. 10.02, Created) DT 29-MAR-2005 (Rel. 10.02, Last updated, Version 1) XX DE L. corniculatus copia-like LTR retrotransposon - LTR consensus DE sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; COPIA1-LTR_LC; KW copia-like retrotransposon LTR. XX OS Lotus corniculatus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RP 1-1205 RA Gentles A. and Jurka J.; RT "COPIA1_LC: L. corniculatus copia-type LTR retrotransposon."; RL Repbase Reports 5(2), 31-31 (2005). XX DR [1] (Consensus) XX SQ Sequence 1205 BP; 387 A; 223 C; 263 G; 331 T; 1 other; tgtaagatca agatttggtc atgtggtaca actctatgtt ttgatgataa caagtattta 60 tttgtggatg aacaactatg atactctaat gtttgtcttg agtgttttga caaacaggtt 120 ctgattctga caccagaaga tatattcgtc agaagttctg aagatcagaa gatctgaaga 180 tcagaggatc tgaggatcag aggatctgaa gatcagagga tctgaggatc tgaggatcag 240 aggatcagag gatcagagga cagaagatct gaggatcaga agatctgaag accagaagct 300 ctgagggacc agaggctctg aaggttcaga agctctgaag gtccagaagc agaagttacg 360 aaggtcagag gatccaagca tccctctgac tctgatcacc aagcttcaca agttccaaca 420 cgaagcataa ctctgatcag aagtcaatgg ttaaaggcaa atgtctctat cgagaagtac 480 aagagcagtg tactattctg aaaagcctac ctaccaaggt tcagccacag caggttctgg 540 aagttccaga aatgccctcc aacggtcata ttctctcaac agaaatatcc tttgcacctt 600 ggactataaa aggctgaaga aaagaagaaa gacaagagag agagaaacca agagctgcaa 660 tacaagaaaa gattcaagcc tctactttct tcatctgttc ttatttagtt tacactcagc 720 ttatttagaa gcaaaccttt gtaaacacca acctcaaaca gttgtttgat tttccttaag 780 ggaccgggta ggtcagtatc cttaagaaga ctaagagagt gaatcttagt ggtgattcct 840 ttaggagatc aaggttgatc ggatcctaga gaagactaag agagtgaatc ttagtgagag 900 ctaagtcagt gtattgttag tcacttgtag gtttcaagtg cagttgtaac aattatctga 960 ttagtggatt gccttcattc taagaaggaa gaaatcacct taacgggtgg actggattag 1020 cttgagggat ttatcaagtg aaccaggata aaatacttgt gtgcttttct cttctctcta 1080 tctttatccg ctgcaccatc tatcttagag aaaccgaaaa gatttacttt aaatcttaar 1140 gggaaagttt ttatattgaa aacgctattc aacccccccc cttctagtcg tttttcacac 1200 cttca 1205 // ID Copia22-PTR_I repbase; DNA; EDCOT; 4536 BP. XX AC scaffold_3565; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia22-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4536 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4536 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 218-218 (2007). XX DR Genome; scaffold_3565; Positions 807 5342. XX CC Positions [1491-2012] - Integrase core CC 'TGGTG' target site duplication CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 21..968 FT /product="Copia22-PTR_I_1p" FT /translation="METNMNSSVKVAKDVKIQLDRFDGTNYTRWMDKMIFL FT LSSLKIYYILDLNLSALPEPQEDESATIKTTRVKREEDEVLCRGHILNTLT FT SRLYDIFSKLKSPKEIRAALETHYKQEKSGSDRFLALKFFEYEITDNKPIM FT DQVHEIQMLISKLSDLDIKVPDSLQVGAVLSKLPPSWNEYRKKMLHSTDNY FT TFEQFQTHLQIEVQSRMRELQATNSKVNLVTETGLTMTQNNLKVQKKGNKF FT KKKQYANKKHRVCFHCGNKGHYIKECRFKNFNKKGGSFKVNMVEKDEVREL FT VAMVSNIQIRMITELNMATNVVKT" FT CDS 1485..3578 FT /product="Copia22-PTR_I_2p" FT /translation="MTKKPFPKVERNSQLLELVHSDICEINGMLTRGGKRY FT FITFIDDYSRFTYVYLLRTKDEAFGKFKEFNKMVENQKERQIKVLRSDRGG FT EYFSKEFSTFYEENGIIHQMTAPYTPQHNGLAERKNRTLVDMVNAMLLNAK FT LPNHLWGEALLTACHIHNRVLSKKSIISPYEAWNGRKPNLNYFKVWGCVAF FT YKSSDPQRTKLGPRGLKSVFVGYAQNSKAYRLLDLETNVIVESIHVEFIEY FT KFISDSNVQEPNLKVMTPSSTLSEKRKNLEVIGSSEPRRSQRVRKEKHIDT FT DFISTDSIVFLVEGDINTILKKTPMILNIEDEPKIFGQAMSSRDVAFLKEA FT VNDEMDSILSNNTWILVDLPPGSKPIGCKWVFKRKYNTDGSIQTFKARLVA FT KGFTQKEGVDYFDTYSPVARITSIRVLFALASIYKLYVHQMDVKTAFLNGD FT LKEEVYMEQPEGFILPGNEEKVCKLVKSLYGLKQAPKQWHEKFDKSILLNG FT FHHNGADKCMYSKFTKDSGVIICLYVDDMLIFSTNIIGIVETKRYLTIIFK FT MKDLGEVDTILGIKVKKHSNGYALNQSHYIEKMLDKFKHLNIKEANNPFDF FT SMKLNDYCDKAIAQLEYACAIGSLMYVMHCTRPDIAFAIYKLSRYTSKLNT FT DHWKAIARVFGYLKRTIDLGLFYSDFPAMMEGYSDASWMTSSSDNKSTS" XX SQ Sequence 4536 BP; 1594 A; 624 C; 883 G; 1435 T; 0 other; attttaaggt gtttattttg atggagacaa atatgaattc tagcgtcaaa gttgctaagg 60 atgtcaaaat tcaactagat cggtttgatg gtacgaatta cacaagatgg atggacaaga 120 tgatattctt acttagttca ttaaagattt actatattct tgatctgaat ctatctgcac 180 tacctgaacc acaagaagat gaatctgcca ctattaagac tacaagagta aaacgtgaag 240 aagatgaagt gctttgtcga gggcatatac tgaatacttt gaccagtcga ctttatgaca 300 tcttctccaa attaaagtca ccaaaagaaa ttcgggctgc cttggagaca cactacaagc 360 aggaaaaatc aggttctgat cgttttcttg ctttaaaatt ttttgagtat gagattactg 420 ataataagcc aatcatggat caagtccatg aaattcaaat gctgatatca aaacttagtg 480 atttggatat caaagttcct gattcacttc aagtgggggc tgttttatca aaacttcctc 540 catcctggaa tgaatatagg aagaagatgt tgcattctac agacaattat acatttgaac 600 agtttcaaac acacttgcaa attgaggttc aatctcgtat gcgtgaattg caagcaacaa 660 attctaaagt gaatttggtt actgaaactg gtttgacaat gactcaaaac aatctgaaag 720 tgcaaaagaa aggaaacaaa ttcaagaaga aacaatatgc taataagaag catagagttt 780 gtttccattg tggaaataaa gggcactata taaaagagtg cagattcaag aatttcaaca 840 agaaaggtgg ttctttcaaa gtgaatatgg ttgaaaaaga cgaagtcagg gagttagttg 900 ccatggtttc aaacattcaa attagaatga ttaccgaatt aaatatggca actaatgttg 960 taaagactta agattggtgg ctggattctg gtgcaacagt tcatgtttgc aacaataaag 1020 catggttcaa gacttatgaa gaattgaaaa aacctgaaga ggtcttgatg ggcaaccata 1080 attctgccaa agttttggga aaaggaacta ttgagttgta ctttacttct ggacaaaaat 1140 tgtctttact caatgtgttt catgttcttg aaattagaaa aaaccttgta tctgctagtc 1200 tcttgagcaa gaaagggttc aagattgttt tggagtctga taaggttatt gtaactaaga 1260 gtgggatgtt tgtgggaaag ggttattcct gtgatggcat gtttaagttc agtattaatg 1320 aaatcaatgt tatttctgct tatatggttg aatctacttc tcttctttgg catgcaagat 1380 taggacatct aaattataga tatttgaaat atatgtgtaa gcatggttat atttcatatc 1440 aacacaataa taaagaaaaa tgtgaagtat gtatttaagc aaagatgaca aagaagcctt 1500 ttcctaaagt agaaaggaat tctcaattac ttgagttggt ccattctgat atatgtgaaa 1560 taaatggtat gttaacaagg ggtgggaaaa gatattttat aactttcatt gatgattatt 1620 ctcgttttac ctatgtttac ttgttaagaa ctaaagatga agcctttgga aaattcaagg 1680 aattcaataa aatggtagaa aatcaaaagg aaaggcaaat taaagttctt agaagtgata 1740 gaggtggaga atacttttct aaggagtttt ctacatttta tgaggaaaac ggaataatcc 1800 atcaaatgac agcaccctat acaccacaac ataatggact tgctgaaagg aaaaatagga 1860 ccttagtgga tatggtcaat gccatgcttt tgaatgctaa attaccaaat catttatggg 1920 gtgaagcctt acttactgca tgtcacattc ataatagagt actatctaaa aaatcaatta 1980 tttctcccta tgaagcatgg aacggtagaa aaccaaatct gaattatttt aaagtgtggg 2040 ggtgtgtagc tttttataaa agttctgatc ctcaaagaac aaaattaggg cccagaggtc 2100 ttaagagtgt ttttgttggt tatgcacaaa attcaaaggc ttatagactt ttggatttag 2160 aaactaatgt gattgttgaa tctatacatg ttgaatttat cgaatataaa ttcataagtg 2220 attcaaatgt gcaagaacca aatctaaaag taatgactcc tagctcaacg ttaagtgaaa 2280 aacgtaaaaa cctagaagta ataggttcaa gtgaacctag aagaagtcaa agagttagaa 2340 aggaaaaaca catagataca gattttattt ctactgattc aattgtattt ttagtggaag 2400 gtgatataaa tacaatatta aaaaagacac ctatgatcct aaatatagaa gatgaaccaa 2460 agatatttgg tcaagctatg tcttctaggg atgttgcttt tttgaaagaa gcggtaaatg 2520 atgaaatgga ttcaatattg tctaacaata cttggatcct agtagattta cctccaggtt 2580 ctaagccaat aggatgtaag tgggtgttta aaagaaaata caataccgat ggttctatac 2640 aaaccttcaa ggcaagattg gttgccaaag gttttactca aaaggagggt gttgattatt 2700 ttgacactta ttctccagtg gcaagaatta catcaattag agttttattt gcattagcat 2760 caatttataa attgtatgtt catcaaatgg atgtaaagac ggcttttcta aatggagatt 2820 taaaggaaga agtgtatatg gagcaacctg agggttttat acttcctggt aatgaagaaa 2880 aagtctgtaa attggtaaag tccttatatg gtttaaaaca agctccgaaa caatggcatg 2940 aaaagtttga caaatcaatt ttgttgaatg gttttcatca caatggtgct gataagtgta 3000 tgtattccaa atttacaaaa gattctggtg tgattatttg tctctatgta gatgacatgt 3060 taatatttag caccaatatt attggaatag ttgaaaccaa aaggtatctc actattatct 3120 ttaaaatgaa agatcttggt gaagtggata caattttagg tatcaaagtt aagaaacata 3180 gtaatggcta tgcacttaat cagtcacatt atattgagaa aatgctcgat aagtttaagc 3240 atctcaatat aaaggaggct aataacccat ttgactttag catgaaatta aatgattatt 3300 gtgataaagc gatagcacaa ctagaatatg cttgtgccat tggaagtctt atgtatgtta 3360 tgcattgtac aagaccagat atagcttttg ctatatacaa gttatcaaga tatacaagta 3420 agctgaatac agatcattgg aaggctattg caagagtctt tggttaccta aaaagaacaa 3480 tcgatttagg cttgttttat tctgattttc cagctatgat ggaaggatat agtgatgcaa 3540 gttggatgac tagttcaagt gataataagt ccacatcatg atggattttc tcacttgaag 3600 gaggtgcaat atcttgggca tctaagaaac aaacatgcat ctctcattct accatggaat 3660 cagaatttat tgctatagct gctgcaggta aagaagcaga atggctaaga aatatgttgt 3720 ttgatattaa gttgtggcca caacctatgt cagccatttc tttatactgc gatagtgcag 3780 cgactatgtc tcgagcttat agtaacattt acaatggtaa gtcaagacat ataagcattc 3840 gacatggata tattcgagag ttgattacaa atggtgtaat caccattgtc tatgtgaagt 3900 ctgtgaataa tttagcggat ccgctcacaa aaggactatc tagagacatg gtacgaaaaa 3960 caactaatgg aatggggttg aaactcgtta ttaaagatac cagtaatagg aacccaactt 4020 cggattagca aaaagcttat ctcttagttt aatgggtaat aacaagttac tgttttgtat 4080 ctgttggaca ctgataatta atttgagtcc ctattctgat agtattcagt gtgttctatt 4140 acgaaaagta ggatgagcgt gggctcttaa tagaatttaa agttcgtgtc taatgtaata 4200 aagacatgta taattccacc tatatgaata taaaagtggt gccgcttttg acaagagtta 4260 gggttttctc ttgtaaatat tcaagaaaaa aaattatgat tttagcacat ggccataata 4320 gtgctaaaca gttgtaaacc tctttaagag tttggatagt attatgtgtg tagtatcttt 4380 tattctacaa caaaagtttt gatttaatct gcggacacca ataactttag taggattcaa 4440 gttctaacac taattgaagg tttaaattgc aaaatacctt cttgtaagca taattctatc 4500 aagtgaaaag accttcatta caaactagtg ggggat 4536 // ID S1_BN repbase; DNA; EDCOT; 172 BP. XX AC L24035; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 25-MAR-1997 (Rel. 2.02, Last updated, Version 2) XX DE Brassica napus S1 SINE retroposon. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; BNSINE; S; KW S1_BN; retroposon. XX OS Brassica napus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-172 RA Deragon M.J., Landry S.B., Pelissier T., Tutois S., Tourmente S. RA and Picard G.; RT "An analysis of retroposition in plants based on a family of RT SINEs from Brassica napus."; RL J. Mol. Evol 39(4), 378-386 (1994). XX DR GenBank; L24035; Positions 1 172. XX SQ Sequence 172 BP; 28 A; 46 C; 66 G; 32 T; 0 other; ttacccagga cctcgtagtc cagtggtact acctcctctt tggggagggg aggtcggctg 60 ttcgactcgc ggggaggggg aggcgtgccc agggccctaa ccggtacagg cacaggctgg 120 cgccgggcct aggtggtggg ctggtcgaag gctggtcaac acctggttaa ac 172 // ID SINE2-2_PTr repbase; DNA; EDCOT; 178 BP. XX AC . XX DT 09-DEC-2009 (Rel. 15.02, Created) DT 09-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE SINE element from Populus trichocarpa - consensus. XX KW SINE2/tRNA; SINE; Non-LTR Retrotransposon; Transposable Element; KW SINE2-2_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-178 RA Bao W. and Jurka J.; RT "SINE elements from black cottonwood."; RL Repbase Reports 10(2), 239-239 (2010). XX DR [1] (Consensus) XX CC >91% identical to consensus. XX SQ Sequence 178 BP; 49 A; 40 C; 48 G; 41 T; 0 other; tgaggggtgt agctcaactg gtcaggttct aggtttgctt tctagagatc accagttcga 60 gtctcacaaa tctcagggcc actggaggct tacatggtcg ttaacttcag ggcccgtggg 120 attagtcgag gtacgcgcaa gctggcccgg acacccacgt taataaaaaa aaaaaaaa 178 // ID Copia24-VV_I repbase; DNA; EDCOT; 4184 BP. XX AC AM477428; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia24-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4184 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4184 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 690-690 (2007). XX DR Genbank; AM477428; Positions 15428 19611. XX CC Positions [1657-2139] - Integrase core CC 'GACAT' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1822..2982,2986..4137) FT /product="Copia24-VV_I_1p" FT /translation="MIENQLNSTIKCIQSDNGGEFIAFKPYLEAHGIVHQF FT LCPHTAQQNGRAERKICHLVETGMALLAQSFLPSKYWSFAFQTSVYLINLL FT PAKLLNFQSPLQVLFHKIPNYHHLRVFACLCFPSLRPYNHHKLSYRSTACV FT FLGYASAHKGYICLDVSTSRLYISRDVLFHESSFPFQSIPAPSPLPQHTPL FT TSALINPPLLSTSSPSTMSFPVPTSSTDCTSTSDSLPPLLQVPFAPTPSPT FT PSSSSSPLNTHPMVTRVKSGIHKKKSFLMQTTSEPHTYNQASKSEPWDQAM FT QHEYQALLRNHTWSLVPPPPSAHIVGCRWIYKLKYLPNGSVERHKARLVAQ FT GFTKTPGVDYFDTFSPIVKPCTIRLILTLAVSFQWPIRQLDVENFLNGDLQ FT EEVFMAQPQGFVHPQYPHYVCKLYKALYGLKQAPRVWFQKLRVALVDYGFQ FT SSRADTSLFIHHTASNILILLVYVDDILVTGSNPKLVSHFISYLHDKFALR FT DLGPLSYFLGIQAQQQGSVLHLNQQKYIVDLLHRTQMEASKPTPTPGSLGR FT TLSQSDGVPLPDPSEYRRIVGALQYVTLTRLDIAFAVNKACQFMAKPSDVH FT WLAIKRILRYLKGTISLGLHFQPSTSMELQGYSDVDWASCPDDRRSTSGYY FT VFLGSNLISWSSSKQRLVSKSNAESEYRGLVSLTAELVWIQSLLQELCLPT FT SPPVLWCDNQSAAHLVANPVFHSRSKHIELDLHFIREKVLRQELQICYVSS FT TDQLADILTKHLSISQFCTL" XX SQ Sequence 4184 BP; 1020 A; 1145 C; 671 G; 1333 T; 15 other; tggtatcaga gccaactttg ttttcttgat tgtttttttc aagatgccgt catctactca 60 ctcttctgat cttcatttac cttcttcttc aacctccagc ctcgtttctt tatccctcaa 120 ccatgccctc ccaatcaaac ttgaccgtaa caactacatt mtctggaaaa ccyagatgga 180 aaatgtagtt tacgctaatg gctttgaaga atatatcgac ggcaccaagc catgcccgcc 240 tcaagagctc catactggcg aactcaatcc tgactttgtg caatggagac gtttcgatcg 300 catggttctt agttggttgt attccacgtt aacaccagat attatgggcc aaatcgttgg 360 gtttcagacc tcccatgatg cttggatggc tctacacaaa atcttttctt cctcatccaa 420 ggctcgtatt ctacagcttc gtcttgagtt tcagacagca aagaaagggg ctgatcctat 480 gytagaatac attctcaaga tcaagactat ttatgataat cttgctgcta ttggggagcc 540 tgttaaggaa actgatcata tcctgcaact tcttggagga ctgggttytg aatacaacty 600 tattgtggcc tccttaacag cccgtgaaga tgatctttct ctccactccg tccayarcat 660 tctgcttacc catgagcaac gcttaaacca tcagcatacc tcatctgcag acctgccatt 720 tgcggctgcc cacatagctg ytgccccttc cacccaacat ccyagacctc atcaccccag 780 attccaatct cctcaacccc gattccaatc tcattactya kgaaatcacc agcatgtccc 840 attttctcat accagacccc ataacagacc tcataacaga cctgctaaca gatcttcctc 900 atctgctcct cacagacctc ctcacctccc tactcgccct caatgycaat tgtgtggtaa 960 atttggacat accgttgtaa agtgttatca ccgttttgac atcacctatc aaggaaccaa 1020 tggtgtatct tcttcacaag actcttctcc attacaagcc atgcttgctg caacaccaaa 1080 tcatcaagat tcttggttct ttgacactgg agctacccac catctcagtc attctgctca 1140 aactctctct catgttcaac cgtactcagg tgctgatcag gtcaccattg gtgatggtca 1200 ttccttaccc atcctaaaca caggtaacaa atcctttttc tttcattcca aggtcttttg 1260 cttaaatcaa gttcttcatg ttcctcaact ctctactaac ctcatcagtg tttccaaatt 1320 ttgcactaat aatgctatct ttttttagtt tcattcaacc catttctttg tcaaagatca 1380 ggtcaccaag cagacacttc tcaagggatg gcttagggat ggtctgtatg agtttccttc 1440 ttcttcatct actcatgctt ttgtgtctac aagctccgtt cctgctctca ctcctggtgc 1500 aatttggcat tccagacttg gacacccakc arctcctatt ctttccaagg ctttagcctc 1560 ttgtaatcct tctgtttcat ttcagattaa taaaattgct ccatgtaaaa tttgtccact 1620 ggctaagtct cattctttac cttattcttt gtcatcttct catgcatccc tcacactgac 1680 ttatggggtc ctgctctttc tccttccaca tcaggtgcac aatattttct tattttcatt 1740 gatgattatt ccaggtatac ctggatttat tttctttcca ctaaggacca ggccctctcc 1800 actttcatta ccattcgaaa aatgattgaa aaccagttaa attccaccat aaaatgcatt 1860 caatctgaca atggtgggga attcatagca tttaaacctt accttgaagc tcatggaatt 1920 gttcatcagt ttttgtgtcc acatacagcc caacaaaatg gtcgagcaga aaggaaaatc 1980 tgccatcttg ttgaaacagg catggccctt ctggctcaaa gcttcctacc ttcaaagtat 2040 tggtcatttg cctttcaaac atcagtctat ctcatcaatc ttctaccagc taaactcctc 2100 aattttcaat ctcctctaca agttcttttt cataaaattc caaactatca tcatctcaga 2160 gttttcgcct gcttgtgttt tccctcctta agaccttata atcaccacaa actctcctat 2220 agatctactg cttgtgtgtt tcttggctat gcctcagctc acaaaggtta catttgtctt 2280 gatgtctcca ctagtcgtct atacatatcc agagatgttc tctttcatga atcctctttt 2340 ccatttcagt caatacctgc tccttcaccc ttaccacagc acactcctct cacgtctgcc 2400 ttaataaatc cacctctctt atctacatct tcaccctcaa ctatgtcatt tcctgttcct 2460 acttcaagta ccgattgcac ctccacttca gattctcttc caccactact ccaggtccca 2520 tttgcaccca ctccttctcc tacaccttcc tcttcttctt cacctctcaa cacccaccct 2580 atggtgacca gggtaaaatc tggaattcat aagaaaaaga gctttcttat gcagacaaca 2640 agtgagcctc acacttacaa tcaggcctct aagagtgaac cttgggatca agctatgcaa 2700 catgaatatc aagcccttct tcgcaaccac acttggagtc tagttcctcc tccgccctca 2760 gcacacattg ttggttgccg ttggatatac aaattaaaat atctccctaa tggctcggta 2820 gaaaggcata aagctagact ggttgctcaa ggcttcacca agactccggg agtggattac 2880 tttgatacct ttagtccaat tgtgaagccc tgcaccatac gcctcatcct taccttggca 2940 gtttcctttc aatggccaat tcgtcaatta gatgtggaga atgycttcct taatggggac 3000 cttcaagagg aggtttttat ggctcagcct caagggtttg tccaccccca atatcctcac 3060 tatgtttgca aattatacaa ggctctttat ggcctgaaac aggcccctag agtttggttt 3120 cagaagcttc gagttgcatt ggttgattat ggctttcagt catctcgggc agacacttct 3180 ctcttcattc accataccgc ttctaacatt cttattcttc ttgtatacgt ggatgatatc 3240 ttggttactg gtagtaatcc caagctggtt tcccatttca tttcctatct ccatgacaaa 3300 tttgccctca gagatcttgg ccctttatca tattttttag gcattcaggc tcaacaacag 3360 ggctcggttt tgcatctcaa tcaacaaaaa tatattgttg acttgctcca ccgcactcag 3420 atggaggctt ctaaaccaac ccctacaccc ggcagccttg gacgcacatt atctcagtct 3480 gatggtgttc ctctcccaga tccctcagaa tatcgtcgta tagtgggagc tttacagtat 3540 gtcactctca ctcggcttga tattgctttt gccgtgaaca aagcttgtca gttcatggcc 3600 aagccctctg atgttcactg gttggctatc aaacgcattc ttcgttattt aaagggcacc 3660 atctctcttg gtcttcattt tcaaccttcc acttctatgg agcttcaggg atatagtgat 3720 gttgactggg cctcctgtcc ggatgatcgc cgaagcacca gtggatatta tgtcttcctc 3780 ggctcaaatc tcatctcatg gtcctcctcc aaacaacgct tagtctccaa gagcaatgct 3840 gaatctgaat accgaggatt agtctctctc acggctgagc tagtatggat tcagtctctt 3900 cttcaggagc tttgcttgcc cacttctcca ccagtcttat ggtgtgataa tcaaagtgca 3960 gctcatcttg ttgccaatcc ggtctttcat tctcgttcca aacacatcga attagacttg 4020 cactttatca gggaaaaggt gttgcgacaa gagcttcaaa tctgctatgt gtcgtccact 4080 gatcaacttg ctgatattct aaccaaacat ttgtctattt ctcaattttg taccttatga 4140 agcaagctca cagtcacctc cccgcctatg agcttgagcg ggga 4184 // ID Gypsy-46_Mad-LTR repbase; DNA; EDCOT; 698 BP. XX AC . XX DT 26-OCT-2010 (Rel. 15.11, Created) DT 26-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-46_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-698 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1990-1990 (2010). XX DR [2] (Consensus) XX SQ Sequence 698 BP; 243 A; 172 C; 104 G; 179 T; 0 other; tgtagacatc gaaatttcgg tgaaataaat gttgaccaat aattaaaatt tcaacgttca 60 cgtgtcacat aaattttaca catagcatgt gactaaacga aaaatcaaaa taaatcagaa 120 aagtcatcaa acaggacacg tgtcaacacc tggcagaaat gatttatttc atctgattat 180 ttaaatccaa aaaatcaagt tttggaattc tataaatagg aggccaaggc attcattttg 240 ggacaccaat tcataaccaa ttcacctcac accaaaacct tgaagctttg aaactccaaa 300 gctcccaagc aaatcccgaa ggatcaagaa agccctcttc gttcttcgtc aaatcctcat 360 tcaagatcaa gccccaacgg cccttgaaga acttccacta attcaagatc aagccccgac 420 ggcccttgaa gaaagtgttc atcattcatc atccgttcat ccctagatca agccccgacg 480 gccctttgga tcaacgacgt caacaaatcc gcacaactgt ttatcccaag atcaagcccc 540 gacggccctt tggatcaaca acatcaaatc cacccattac aaagatagaa tcagaggcta 600 aatttgtaga agagattgta acccctaaat catcaataca aatattattt tgtacacgtg 660 ttcttgtctc gttcatcgca ggaatttccg tgtttaca 698 // ID Copia8-PTR_I repbase; DNA; EDCOT; 4216 BP. XX AC scaffold_156; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia8-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4216 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4216 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 292-292 (2007). XX DR Genome; scaffold_156; Positions 322169 326384. XX CC Positions [1544-2038] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 986..3367 FT /product="Copia8-PTR_I_1p" FT /translation="MDSAASHNISGDLNNLSIHSEYDGTDEVMLGDGSGLT FT VSHIGSLTLKSKHKNFILKNTLCVPDISKNLIYVHHFTAQNNVFIEFHPSH FT FPVKDTNSGVILAKGACENDVYIFPNTLAAALLPMVANVHEKTSLDGWHKR FT LGHPSSKIVHNVVRQFSLPFTTTQKSTLCPSCSINKAHQQPFRSTSLSSTA FT PLNLIYTDVWGPAHCVGLDGSRYYLIFIDHYTKYMWFYSMETKSGVAKIFP FT QFKNLVENRFQSKIQTIYSDNGGEYMSLKPFLSLHGISHFTTAPHTPQQNG FT VSERRHRHLVETGLTLLHDANLPLIYWPYAFHTATYLINRQPTPLLQNISP FT YQVLFGQQPNYLKLRKFGCVCYPLTKPYNKHKMEPKSRSCIFLGYSLTQNA FT YRCLDPRTQRVYISRHVLFDEDQIPLTESVSSFLSPTTSPISTVPNSVPVT FT VLPSSPPVSSVDAPAMVTAPPGNPPVSTSSNLSSQLVLSSTGNTLTPTNPT FT LPPSIHRINHTPGPRPTTQPATEPQITSHHPQPSISRPHPMTTRSMNKIFR FT LKQLNSTTKHPMPDTIEPTCVSQAVSEPHWREAMSHELTALMRHGTWELVP FT PPKHCNPVGCKWVFRVKRKSDGTVDRFKARLVAKGYHQRPGVDYTETFSPV FT VKPATIRIILSIAVMNGWGLRQLDINNAFLHGALSETVYMLQPPGFKDSSK FT PGHVCRLRKAIYGLKQAPRAWYSALKNAILQFGFKSSKADSSLFIFRHKSI FT ICYFLVYVDDLVITGNNSDFVNSIVKQLGCKFSLKDMGPCIIS" XX SQ Sequence 4216 BP; 1178 A; 1130 C; 725 G; 1183 T; 0 other; ccataactca aacgagacta cgatccctgc ttccaacatg tctctatctc aaaatctgac 60 cacccaaccc acctcccaca tagagaatcc actgattgct ctcaacatta cagctcaaat 120 caacgagaaa ttaattccct ccacctttcc acaatggcgt gcccaatttg aagctcttct 180 aatagggtat gatctgctgg actacgtcac tggtctctca gtgtgtcctt catctgatgg 240 cacctcccaa tctgcgttga aaagaaccca ttgggttcgg caggacaaat taattctcag 300 tgcaatcctt gcttccacct ccacctcaat cactcccctc atcgccacca ctaaaacatc 360 tcatgaggca tggaaaaaac taaatcacat gtatgctagt cgatctcgac tgagagctat 420 gcaactcaag gaggatctta ccttgattca aaaaggaaat cgatcgattc aggagtatct 480 ccacgcagta aaagcgttgg ctgatgaaat tgctctaatc gaccatccca tctctgatga 540 tgatctaact ctttatattc ttcatggttt gggttctgat ttcagggaaa ttgctgcacc 600 aattcgtgcg agggagaaat ccttaaattt tgaagaactt catgatctgc tggttggtca 660 tgacagctac cttcggcgga tggaatcggc tacccagcaa cttgtggcat cagcgaatta 720 cacaaatcgc aagaactcgt ttggtaattc tttccaaaag aatcaaaaac ccaatggttt 780 ctcacgaaac cagggtcccc acaaagaaaa ccggtacaat aataagccat tcggccggcc 840 ccatacaaca caaaaaaggt attaacccaa atgtcaattt tgtgaccaaa ttggtcacac 900 ggccaaaaca tgcccccgct tgaattctca tgcagtcaca gcaaactgca cttctaccgc 960 taatgccaca gacaataaat ggctcatgga ctctgctgca tcccataata ttagtggtga 1020 tctcaacaac ctatcaattc attcagaata tgatggcact gatgaagtca tgctcggtga 1080 tggttcaggt ttgactgtct cacatatagg atctttaacc ttaaaatcaa aacacaaaaa 1140 tttcattctc aaaaacacac tttgtgttcc agatatctcc aaaaacctta tatatgtgca 1200 ccattttact gctcaaaata atgtctttat tgaatttcac ccgtctcatt ttcctgtgaa 1260 ggacacgaac tcgggggtga tcctggcaaa aggtgcatgt gaaaatgatg tttacatctt 1320 cccgaataca ttggcggcag ctctcctccc catggtcgcc aatgtgcatg aaaaaacctc 1380 tcttgacggg tggcacaaac ggcttggtca tccttcctcc aaaattgttc acaatgttgt 1440 tcgtcagttt tcacttccat tcacaaccac tcaaaagtca actctatgtc cttcatgttc 1500 tattaataaa gcacatcaac aaccttttcg atccactagt ctatcaagca ctgcacctct 1560 taatctcatt tatactgatg tttggggtcc tgctcactgt gttggtttag atggctctcg 1620 gtattacctc attttcattg atcactacac caaatacatg tggttttact ctatggaaac 1680 aaaatctggg gttgcaaaaa tttttccaca attcaaaaat ctcgtggaaa accggttcca 1740 aagcaaaatc caaaccatat actcagataa tgggggtgaa tatatgagtt taaaaccttt 1800 tctctccctt catggcataa gtcatttcac taccgctcca cacacaccac aacaaaatgg 1860 tgtttccgag cgtcgtcatc gtcacctagt ggaaactggt ctcacattac ttcatgatgc 1920 aaatcttcct ttaatatatt ggccatatgc attccacaca gccacgtacc ttatcaaccg 1980 tcaaccaaca cccctgcttc aaaatatttc cccatatcaa gttcttttcg gtcaacagcc 2040 caattatctc aaactgcgaa aatttgggtg tgtgtgttac cctctcacca aaccatacaa 2100 caaacacaag atggaaccaa aatccagatc ctgcattttt ttaggctatt cccttactca 2160 aaatgcctat cggtgtcttg atccacgcac tcaacgtgtt tacatttcac gccatgtttt 2220 atttgatgaa gatcaaatac cattgaccga atctgtttcc tctttccttt cacccactac 2280 ctcacctatc tccactgttc ctaattcggt cccagttact gtcctgcctt cttcgccacc 2340 ggtgtcttcg gttgatgctc ccgctatggt cactgcacct ccaggtaatc ctccagtctc 2400 tacttcctct aatttatctt ctcaattggt tttgtcctct actggtaaca ccctcacacc 2460 tacaaatcct acccttccac cctccattca ccgtatcaat cataccccag gacctagacc 2520 cactactcaa cctgcaactg aaccacaaat cacttcccac catccacaac catcaatctc 2580 tcgaccccat ccgatgacca ctcggtctat gaacaaaatt tttagactca aacaactgaa 2640 cagtactacc aaacacccca tgcccgatac cattgaaccc acatgtgtca gtcaagccgt 2700 ttctgaacct cactggcgtg aggccatgtc tcatgaactc accgctctca tgcggcatgg 2760 gacatgggaa ctggtacctc ctccaaaaca ctgcaaccca gtcggttgta aatgggtgtt 2820 tagagtcaaa cgtaaatctg atgggacagt ggatagattt aaagcccgtt tagtggctaa 2880 agggtatcat caacgtccgg gagtggacta tacagagaca ttcagtcccg tagttaagcc 2940 tgcaacaatt agaatcatac tttccattgc tgtgatgaat ggttggggct tacgccaact 3000 ggacattaat aatgctttct tacatggggc gctcagtgaa actgtgtata tgttgcaacc 3060 cccaggtttt aaagattcaa gcaagcctgg tcatgtctgc cgacttcgaa aggccatcta 3120 cggtctcaaa caggcccctc gggcatggta ttctgccttg aaaaatgcca tacttcagtt 3180 tggttttaag agctccaagg cagattcttc attattcatt tttcggcata agtcaattat 3240 ctgctatttt ctggtatatg tggatgactt agtgattact ggaaataatt cagactttgt 3300 gaattctatt gttaaacaac ttggctgcaa attttcattg aaggatatgg gtccttgcat 3360 tatttcttag gaatggaagt catacccact ccaggtggtc ttttcctttc ccagcacaag 3420 tatattcatg atctgctctc caacaccaac atgcttgggg caaaggaagt gtgtagccct 3480 ctctccacaa gcacacctct gaaactcaat gatggcactg cttcttttga cagcaccgaa 3540 tatagaagaa taattggcag cctccagtac ttatctctca ccagaccgga tatctcattt 3600 gctgtaaaca agttgtctca attcatgcac aagcctactc agactcactg ggcagcaacc 3660 aagcgcctcc tgcgctactt gaagcaaacc atctttcatg gtattcgact gattagtcat 3720 acccatccat ccctaaccac tttttccgat gcagattggg cgggcaacct tgacgatcgc 3780 acatccacat ccgcatacat catctttctt ggctccaatc ctgtctcatg gagctcgaag 3840 aaacaacgtg ctgtagctcg atcttccaca gaggccgaat acagggctct tgcaaatgca 3900 gcttcggaaa ctgtttggat acactctctc ctgcatgaac ttggattcaa cctcaacacc 3960 actccatcac tactatgcga taatcttgga gccacacatc ttagtcacaa tccggtacat 4020 cactccagga tgaaacatat ccaaattgat cttcactttg ttcgtgattt ggttcaccgc 4080 ggggctattc gcgtccgaca tgtccacact caagatcaac ttgcagattt gttaacaaaa 4140 gcctctctcc aagcaacgca cagagcattt gagaagcaaa attgctcttg ctgatggcag 4200 ctcaattttg aggggg 4216 // ID Gypsy8-PTR_I repbase; DNA; EDCOT; 4505 BP. XX AC scaffold_1123; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy8-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4505 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4505 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 340-340 (2007). XX DR Genome; scaffold_1123; Positions 10128 5624. XX CC Positions [3402-3890] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 33..4505 FT /product="Gypsy8-PTR_I_1p" FT /translation="METRNKSNTEFRNEVTEALAQHASQFDLLKTQHESRF FT DLLNTNMTQVTSSLQNLQNAISELQTLSLRHSSNQQTIIQDVNSFTKGETS FT QKGRQPTSACSFTSTGFDRSHQQLKLSFSKFSGDDPTGWVYKAEQFFEFQN FT IANDQRVQLASFHLEGLALQWHRWLTKYKGTLTWLEFTAALLQRFGPTEYE FT DPSEALTRCRQVTTVTAYQEAFEGLSHRVDGLPEPFLVGCFIAGLRDDIRL FT DVKIKQPKTLGDTIGVARLVEERNLLQRKGNTFVRSPANSRPLPTTNSGVL FT GPPPASKPVSTAAPSSFRRITNQEARERREKGLCFYCDEKFIPGHRCQRPQ FT LFMIEDSTPEEIDTSDDCTVDVATVESFPEISFHAIAGTEHPQTIRVLGKL FT KNKDVTVLIDGGSTHNFIDQSIVSQFRLQEIRDKTFQVMVANREKIVCGGR FT CLALSILIQGHVVIADFYVLPVAACHVVLGVQWLATLGPIETDYRNLTMTF FT TDGGTKRMFQGIGRAGLEALSNKDLFNLQQTGLFLQITMTEHVDSTTTYSS FT DLAAVLDNFAHVFDTPTALPPNRSHDHRILLQPNSEPVSVRPYRYPYYQKT FT EIEKMVKELLESGLVRPSNSPFSSPVLLVKKADGTWRFCVDFRALNHITVK FT DKYPIPIVDELLDELHGARFFTKLDLRSGYHQIRVQESDIQKTAFRTHEGH FT YEFVVMPFGLTNAPATFQSLMNDLFRPYLRKYIIVFFDDILIYSKNWDEHI FT SHIISVLTILSSNSLYVKKSKCQFGVSLVNYLGHVISEKGVEVDPYKIQAV FT VDWPEPTTVKGVRAFLGLAGYYRKFISGFSNIAAPLTHCLGKEGFRWGITE FT STAFNKLKQALTSPPVLRLPDFSQRFFIECDACGTGIGAILIQQGQPIAFF FT SEALKGSSLALSTYEKEMLAIVKAIRKWRPYLLGRPFTVRTDHKSLKFLLE FT QRITTPAQTRWLPKLLGYDYVVEYKKGPDNKGADALSRKVEFNFMAVSLPQ FT PDWWIRLQQEVQQDSFYTDLFKLNSGQQRQLYTCKDGVWFKGGKVYLNPSS FT PLIPSVLADHHSSPIGGHFGYHKTLAKIRGTFFWPKLRQHVKDFLRRCDTC FT QRFKADCLSPAGLLQPLSIPTKIWTEVSMDFVEGLPPSLGNTVIMVVVDRL FT SKYAHFIALKHPFTAITVAKSFIANVVKLHGIPVSIVSDRDKVFLSSFWKT FT LFQLQGTQLNMSSSYHPQSDGQTEVVNRTLEQYLRCFTGDQPHKWVDWLPW FT AEFSYNTAIHSSTKISPFEAVYGIPPPNVLSYVPGTTRVQAVDEYLRDRDS FT VLQDLRHQLVLARDRMKTQADKHRREVHFTVGDFVYLKLKPYRQTSVAFRR FT SIKLAPRYFGPYQVLAKVGEVAYKLALPAGSQIHDVFHVSRLRKCLGSVVP FT VSRELPPVSVTSIILPQPELVLDHRVICKGQYRPKKEVLIKWKGAAVEDAT FT WENLWRFMKTYPDFILGDKDTLREGE" XX SQ Sequence 4505 BP; 1214 A; 995 C; 991 G; 1305 T; 0 other; cttatcaatt ggtatcagag cttctcattt ccatggagac tagaaacaaa agcaatactg 60 agtttcgcaa cgaggtcact gaagccttgg ctcagcatgc gtctcagttt gatcttctta 120 aaacccaaca tgagtctcgt ttcgatctcc tgaacaccaa tatgactcaa gttacctcat 180 ccctccaaaa cctccaaaac gccattagtg aattacaaac tttgtcatta cgtcacagtt 240 ccaatcaaca aaccattatc caagatgtca attctttcac caagggagaa acttcccaaa 300 agggtcgaca accaacatct gcttgttcct ttacaagtac tggttttgac aggagtcatc 360 aacagctcaa actgtcattt tcaaaattca gtggtgatga tccaacaggt tgggtttata 420 aggcagagca attcttcgag tttcagaaca ttgcgaatga tcaaagagtg caactcgctt 480 ccttccacct ggagggatta gctttgcagt ggcaccgttg gctgactaag tacaagggca 540 cactcacctg gcttgaattt acagcagcac tcctccaacg ttttggtccg actgagtatg 600 aggatccctc tgaagctcta actcgttgca gacaagtcac aacagtaacc gcgtaccaag 660 aagctttcga agggctatca catcgtgtgg atgggttacc agaaccattc ttggttggat 720 gtttcattgc aggacttcgg gatgatatcc gtctggatgt caaaattaaa cagccgaaga 780 ctctaggaga caccattgga gttgctcgcc tggtggagga acgtaatctc ctgcaacgaa 840 aaggtaacac ttttgtgcga tcacctgcca attctcgtcc tctgccaacc accaacagtg 900 gtgtattggg accaccacca gcatccaaac cagtcagcac cgccgctcca tcctcattta 960 gaaggataac aaaccaggaa gctcgtgaaa gacgtgagaa gggcctttgt ttctattgtg 1020 atgaaaaatt cataccaggg catcgttgtc aaaggccaca gctgtttatg attgaagatt 1080 ccacaccaga agaaatcgat accagtgatg attgcaccgt tgacgttgca actgtggaat 1140 cttttccaga aatatcattc catgccatcg ctggaactga gcatccacag accattcgcg 1200 tactgggaaa actgaagaac aaggatgtca cagtgttgat cgatggagga agtacacata 1260 atttcatcga ccaatccatt gtctctcaat tcaggctaca agaaattcga gataagacgt 1320 ttcaagtgat ggtggctaat cgtgagaaga ttgtttgtgg cggacggtgt cttgctcttt 1380 ccatacttat ccaaggtcat gtggtcattg ctgattttta tgtcttacct gttgctgctt 1440 gccatgtggt tttaggggtt caatggcttg cgactcttgg tccaattgaa acagattacc 1500 gaaatctcac gatgactttc acagacgggg gcaccaaacg catgtttcag ggcattggtc 1560 gtgctggttt ggaggcctta tctaataagg acctttttaa cttgcaacaa actgggttgt 1620 ttctccagat tactatgact gagcatgtgg actccactac cacttattcc agtgatctcg 1680 cagcagtcct tgacaacttt gcgcatgttt ttgacacacc gacagctttg ccaccaaatc 1740 gttcacatga ccaccggatt ctacttcaac ccaacagcga acctgttagt gttcgtccat 1800 acaggtaccc gtactatcaa aaaactgaga ttgaaaagat ggttaaagaa cttcttgaat 1860 ccggtttagt tcgtccaagc aacagtccat tttcatctcc tgttttgttg gtaaaaaagg 1920 cagatggaac gtggcgattc tgtgtcgact ttagggcact caatcacata acagtgaagg 1980 acaaataccc tattccgatt gttgacgagc tcttggatga actgcatggt gccaggtttt 2040 ttacaaaact ggatttacgt tcggggtacc accaaattcg ggttcaagag tcagacatcc 2100 agaaaacagc tttccgcaca catgaaggac actatgaatt tgtagtaatg cctttcggtc 2160 ttacgaacgc cccagctact ttccagagtc tcatgaacga tctgttcaga ccatatcttc 2220 gcaagtatat tattgtgttc ttcgacgata ttttgatcta ctctaaaaat tgggatgaac 2280 atatttcaca tataattagt gttctaacca ttttgtccag taacagtttg tatgtcaaga 2340 agtcaaaatg tcaatttgga gtatcactgg tgaattattt gggccatgtc atatcagaga 2400 aaggagttga ggttgatcct tacaagatac aggcagtggt tgattggcca gaaccgacaa 2460 cagtcaaggg tgtgcgtgcc ttcttggggt tggcaggtta ttatagaaaa ttcatcagtg 2520 gctttagcaa tattgcagca ccattgactc attgtttagg caaggaagga tttcgttggg 2580 gaataactga gtccacagcc ttcaacaaac ttaaacaggc cttgacttca cctcctgttc 2640 tgcggttgcc tgatttttct caacgtttct tcattgaatg tgatgcttgt ggcactggaa 2700 taggcgctat tctcatacaa caaggtcagc cgattgcatt cttcagtgag gcattaaagg 2760 gttcatcttt ggcactctcc acttatgaaa aagagatgtt ggccattgtc aaagccatcc 2820 gtaagtggcg accatatctt ctgggtagac ccttcactgt caggactgac cacaagagtc 2880 tcaagtttct gttagaacaa cgcatcacaa ctccagcaca gactcgttgg cttccgaaac 2940 tccttggtta tgattatgtg gtagaataca aaaagggccc tgacaacaaa ggtgctgatg 3000 cactgtccag aaaagtcgag ttcaacttta tggcagtttc cttgcctcag cccgattggt 3060 ggatacgtct gcaacaagaa gttcaacaag actcttttta cactgattta ttcaagctga 3120 attcaggtca acaacgacag ctgtatactt gtaaagatgg tgtgtggttc aaaggtggaa 3180 aggtatattt aaatccctct tctccattaa ttccttcagt tttggcagat catcactctt 3240 ctcctattgg gggccacttt ggttaccaca aaactctagc gaaaatccgc ggtaccttct 3300 tttggccaaa attgcgacaa catgtcaaag attttctccg gcgctgtgat acctgtcaac 3360 gttttaaggc agattgtttg agtcctgcag ggctgctgca gcccttgtct attccaacta 3420 aaatatggac tgaggtgtct atggattttg tggaagggtt gcctccttca ttgggcaaca 3480 cagtgatcat ggttgtggtg gatcgcttga gtaaatatgc tcattttata gctctgaagc 3540 atccattcac ggccattact gtggccaaat ctttcatcgc taatgttgtc aagcttcatg 3600 gaattcctgt gtctattgtc agcgaccgag acaaggtatt tttgagctcc ttttggaaaa 3660 ctctgtttca actgcagggt actcagctca atatgagctc cagttatcat cctcaatcgg 3720 acggccaaac tgaggtggtc aatcggacac tggagcagta tttaagatgt tttacaggtg 3780 atcaaccaca taagtgggtg gattggttgc cttgggcaga atttagttat aatactgcca 3840 ttcactcttc cacgaagatt tcaccatttg aagcagttta tggcattcca ccaccaaacg 3900 tgctttcata tgtgccagga actactcgtg tccaagccgt ggatgaatat ttacgtgata 3960 gggattcagt tcttcaggat ttacgtcatc aactagtcct tgcgagagat cggatgaaaa 4020 ctcaagctga caaacatcgc cgtgaagttc attttactgt gggagatttt gtttatttga 4080 agttgaaacc atatcggcaa acatcagttg cttttcgcag gtcaatcaaa ctggcgccac 4140 gttactttgg cccttatcaa gtattagcta aggtggggga agttgcctat aagcttgcct 4200 tacctgctgg gtctcaaatt catgatgttt ttcatgtgag ccgcctacgc aagtgtttgg 4260 gttctgtggt tccagtctct cgggagctac ctccagtatc agtgacttct atcattctgc 4320 cacagcctga gttggttttg gatcatcgtg tcatatgtaa gggacaatat cggcctaaga 4380 aggaggtttt aatcaaatgg aaaggtgctg ctgttgaaga tgctacatgg gaaaatttat 4440 ggcgttttat gaagacatat cctgatttta tccttgggga caaggatact ctgagggaag 4500 gggaa 4505 // ID SIRE1_INT repbase; DNA; EDCOT; 7258 BP. XX AC AY205610; XX DT 09-JUL-2004 (Rel. 9.06, Created) DT 01-FEB-2007 (Rel. 12.03, Last updated, Version 2) XX DE Glycine max cultivar Williams 82 SIRE1-8 retroelement: internal DE sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; SIRE1; KW SIRE1_INT. XX NM SIRE1_INT. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RA Laten M.H., Havecker R.E., Farmer M.L. and Voytas F.D.; RT "SIRE1, an Endogenous Retrovirus Family from Glycine max, Is RT Highly Homogeneous and Evolutionarily Young."; RL Mol. Biol. Evol 20(8), 1222-1230 (2003). XX RN [2] RA Laten M.H., Havecker R.E. and Voytas F.D.; RT "SIRE1_INT."; RL Direct Submission to Genbank (20-DEC-2002)Zoology and Genetics, RL Iowa State University, 2278 Molecular Biology Bldg, Ames, IA RL 50011, USA. XX DR Genbank; AY205610; Positions 1053 8310. XX CC Key Location/Qualifiers CC CDS 58..4788 CC /gene="gag-pol" CC /codon_start=1 CC /product="gag-pol polyprotein" CC /protein_id="AAO73525.1" CC /db_xref="GI:29423276" CC /translation="MNMEKEGGPVNRPPILDGTNYEYWKARMVAFLKSLDSRTWKAVI CC KGWEHPKMLDTEGKPTNELKPEEDWTKEEDELALGNSKALNALFNGVDKNIFRLINTC CC TVAKDACGEILKTTHEGTSKVKMSRLQLLATKFENLKMKEEECIHDFHMNILEIANAC CC TALGERMTDEKLVRKILRSLPKRFDMKVTAIEEAQDICNMRVDELIGSLQTFELGLSD CC RNEKKSKNLAFVSNDEGEEDEYDLDTDEGLTNAVGLLGKQFNKVLNRMDRRQKPHVRN CC IPFDIRKGSEYHKKSDEKPSHSKGIQCHGCEGYGHIKAECPTHLKKQRKGLSVCRSDD CC TESEQESDSDRDVNALTGRFESDEDSSDIEITFDELAISYRKLCIKSEKILQQEAQLK CC KVIANLEAEKEAHEEEISELKGEVGFLNSKLENMTKSIKMLNKGSDMLDEVLQLGKNV CC GNQRGLGFNHKSACRITMTEFVPAKNSTGATMSQHRSRHHGTQQKKSKRKKWRCHYCG CC KYGHIKPFCYHLHGHPHHGTQSSSSGRKMMWVPKHKIVSLVVHTSLRASAKEDWYLDS CC GCSRHMTGVKEFLVNIEPCSTSYVTFGDGSKGKITGMGKLVHDGLPSLNKVLLVKGLT CC ANLISISQLCDEGFNVNFTKSECLVTNEKSEVLMKGSRSKDNCYLWTPQETSYSSTCL CC SSKEDEVKIWHQRFGHLHLRGMKKIIDKGAVRGIPNLKIEEGRICGECQIGKQVKMSH CC QKLQHQTTSMVLELLHMDLMGPMQVESLGGKRYAYVVVDDFSRFTWVNFIREKSDTFE CC VFKELSLRLQREKDCVIKRIRSDHGREFENSKFTEFCTSEGITHEFSAAITPQQNGIV CC ERKNRTLQEATRVMLHAKELPYNLWAEAMNTACYIHNRVTLRRGTPTTLYEIWKGRKP CC TVKHFHIFGSPCYILADREQRRKMDPKSDAGIFLGYSTNSRAYRVFNSRTRTVMESIN CC VVVDDLTPARKKDVEEDVRTSEDNVADTAKSAENAEKSDSTTDEPNINQPDKSPFIRI CC QKMQPKELIIGDPNRGVTTRSREIEIVSNSCFVSKIEPKNVKEALTDEFWINAMQEEL CC EQFKRNEVWELVPRPEGTNVIGTKWIFKNKTNEEGVITRNKARLVAQGYTQIEGVDFD CC ETFAPVARLESIRLLLGVACILKFKLYQMDVKSAFLNGYLNEEAYVEQPKGFVDPTHL CC DHVYRLKKALYGLKQAPRAWYERLTEFLTQQGYRKGGIDKTLFVKQDAENLMIAQIYV CC DDIVFGGMSNEMLRHFVPQMQSEFEMSLVGELHYFLGLQVKQMEDSIFLSQSKYAKNI CC VKKFGMENASHKRTPAPTHLKLSKDEAGTSVDQNLYRSMIGSLLYLTASRPDITFAVG CC VCARYQANPKISHLNQVKRILKYVNGTSDYGIMYCHCSDSMLVGYCDADWAGSADDRK CC CTSGGCFYLGTNLISWFSKKQNCVSLSTAEAEYIAAGSSCSQLVWMKQMLKEYNVEQD CC VMTLYCDNMSAINISKNPVQHNRTKHIDIRHHYIRDLVDDKIITLEHVDTEEQVADIF CC TKALDANQFEKLRGKLGTCLLEDL" CC CDS <4789..6759 CC /codon_start=1 CC /product="envelope-like protein" CC /protein_id="AAO73526.1" CC /db_xref="GI:29423277" CC /translation="QLLLSERVQTLIARSLLGQNKFDRCFTRPSTFLIQTYIFVVISF CC SFTNTSQIFTKPFQKLCFSMATSPKETSSPVSPSVPSPPSSTKAPSNQEQPEFNIQPI CC QMIPGPAPVPEKLVPKRQQGVKISENPSLATSPREVDTEMDKKIRSIVSSILKNASVP CC DADKDVPTSSTPNAEVLSSSSKEKSTEEEDQATEETPAPRAPEPAPGDLIDLEEVESD CC EEPIVKKLALGIAERLQSRKGKTPITRSGRIKTIAQKKSTPITPTTSRWSKVAIPSKK CC RKEISSSDSDDDVELDVPDIKRAKKSGKKVPGNVPDAPLDNISFHSIGNVERWKFVYQ CC RRLALERELGRDALDCKEIMDLIKAAGLLKTVTKLGDCYESLVREFIVNIPSDITNRK CC SDEYQTVFVRGKGIRFSPAVINKYLGRPTEGVVDIAVSEHQIAKEITAKQVQHWPKKG CC KLSAGKLSVKYAILHRIGTANWVPTNHTSTVATGLGKFLYAVGTKSKFNFGNYIFDQT CC VKHSESFAVKLPIAFPTVLCGIMLSQHPNILNNIDSVKKRESALSLHYKLFEGTHVPD CC IVSTSGKAAASGAVTKDALIAELKDTCKVLEATIKATTEKKMELERLIKRLSDSGIDD CC GEAAEEEEEAAEEEEDAAEDTESDDDDSDATP". XX SQ Sequence 7258 BP; 2401 A; 1408 C; 1683 G; 1766 T; 0 other; attggtatca gagcgggcac tctaaatcac tgagtgagat ctagggagat aaattctgat 60 gaacatggag aaagaaggag gaccagtgaa cagaccacca attctggatg gaaccaacta 120 tgaatactgg aaagcaagga tggtggcctt cctcaaatca ctggatagca gaacctggaa 180 agctgtcatc aaaggctggg aacatcccaa gatgttggac acagaaggaa agcccactaa 240 tgaattgaag ccagaagaag actggacaaa agaagaagac gaattggcac ttggaaactc 300 caaagccttg aatgccctat tcaatggagt tgacaagaat atcttcagac tgatcaacac 360 atgcacagtg gccaaggatg catgtggaga gatcctgaaa accactcatg aaggaacctc 420 caaagtgaag atgtccagat tgcaactatt ggctacaaaa ttcgaaaatc tgaagatgaa 480 ggaggaagag tgtattcatg acttccacat gaacattctt gaaattgcca atgcttgcac 540 tgccttggga gaaaggatga cagatgaaaa gctggtgaga aagatcctca gatctttgcc 600 taagagattt gacatgaaag tcactgcaat agaggaggcc caagacattt gcaacatgag 660 agtagatgaa ctcattggtt cccttcaaac ctttgagcta ggactctcgg ataggaatga 720 aaagaagagc aagaacctgg cgttcgtgtc caatgatgaa ggagaagaag atgagtatga 780 cctggatact gatgaagggc tgactaacgc agttgggctc cttggaaaac agttcaacaa 840 agtgctgaac agaatggaca ggaggcagaa accacatgtc cggaacatcc ctttcgacat 900 caggaaaggt agtgaatacc acaaaaagtc agatgaaaag cccagtcaca gcaaaggaat 960 tcaatgccat gggtgtgaag gctatgggca catcaaagct gaatgtccca cccatctcaa 1020 gaagcagagg aaaggacttt ctgtatgtcg gtctgatgat acagagagtg aacaagaaag 1080 tgattctgac agagatgtga atgcactcac tgggagattt gaatctgatg aagattcaag 1140 tgatattgaa atcacttttg atgagcttgc tatatcctat agaaaactat gcatcaaaag 1200 tgagaagatt cttcagcaag aagcacaact gaagaaggtc attgcaaatc tggaggctga 1260 gaaggaggca catgaagagg agatctctga gcttaaagga gaagttggtt ttctgaactc 1320 taaactggaa aacatgacaa aatcaataaa gatgctgaat aaaggctcag atatgcttga 1380 tgaggtgcta cagcttggga agaatgttgg aaaccagaga ggacttgggt ttaatcataa 1440 atctgcttgc agaataacca tgacagaatt tgttcctgcc aaaaacagca ctggagccac 1500 gatgtcacaa catcggtctc gacatcatgg aacgcagcag aaaaagagca aaagaaagaa 1560 gtggaggtgt cactactgtg gcaagtatgg tcacataaag cccttttgct atcatctaca 1620 tggccatcca catcatggaa ctcaaagtag cagcagcgga aggaagatga tgtgggttcc 1680 aaaacacaag attgttagtc ttgttgttca tacttcactt agagcatcag ctaaggaaga 1740 ttggtaccta gatagcggct gttccagaca catgacagga gttaaagaat tcctggtgaa 1800 cattgaacct tgctccacta gctatgtgac atttggagat ggctctaaag gaaagatcac 1860 tggaatggga aagctagtcc atgatggact tcctagtctg aacaaagtac tgctggtgaa 1920 gggactgact gcgaacttga tcagcatcag tcagttgtgt gatgaaggat tcaatgtaaa 1980 cttcacaaag tcagaatgct tggtgacaaa tgagaagagt gaagttctaa tgaagggcag 2040 cagatcaaag gacaactgtt acctatggac acctcaagaa accagttact cctccacatg 2100 tctatcctcc aaagaagatg aagtcaaaat atggcatcaa agatttggac atctgcactt 2160 aagaggcatg aagaaaatca ttgacaaagg tgctgttaga ggcattccca atctgaaaat 2220 agaagaaggc agaatctgtg gtgaatgtca gattggaaag caagtcaaga tgtcccacca 2280 gaagcttcaa catcagacca cttccatggt gctggaacta cttcacatgg acttgatggg 2340 gcctatgcaa gttgaaagcc ttggaggaaa gaggtatgcc tatgttgttg tggatgattt 2400 ctccagattt acctgggtca actttatcag agagaaatca gacacctttg aagtattcaa 2460 agagttgagt ctaagacttc aaagagaaaa agactgtgtc atcaagagaa ttaggagtga 2520 ccatggcaga gagtttgaaa acagcaagtt tactgaattc tgcacatctg aaggcatcac 2580 tcatgagttc tctgcagcca ttacaccaca acaaaatggc atagttgaaa ggaaaaacag 2640 gactttgcaa gaagctacta gggtcatgct tcatgccaaa gaacttccct ataatctctg 2700 ggctgaagcc atgaacacag catgctatat ccacaacaga gtcacactta gaagagggac 2760 tccaaccaca ctgtatgaaa tctggaaagg gaggaagcca actgtcaagc acttccacat 2820 ctttggaagt ccatgttaca ttttggcaga tagagagcaa aggagaaaga tggatcccaa 2880 gagtgatgca ggaatattct tgggatactc tacaaacagc agagcatata gagtattcaa 2940 ttccagaacc agaactgtga tggaatccat caatgtggtt gttgatgatc taactccagc 3000 aagaaagaag gatgtcgaag aagatgtcag aacatcggaa gacaatgtag cagatacagc 3060 taaaagtgca gaaaatgcag aaaaatctga ttctactaca gatgaaccaa acatcaatca 3120 acctgacaag agtcccttca ttagaatcca gaagatgcaa cccaaggagc tgattatagg 3180 agatccaaac agaggagtca ctacaagatc aagggagatt gagattgtct ccaattcatg 3240 ttttgtctcc aaaattgagc ccaagaatgt gaaagaggca ctgactgatg agttctggat 3300 caatgctatg caagaagaat tggagcaatt caaaaggaat gaagtttggg agctagttcc 3360 tagacccgag ggaactaatg tgattggcac caagtggatc ttcaagaaca aaaccaatga 3420 agaaggtgtt ataaccagaa acaaggccag acttgttgct caaggctaca ctcagattga 3480 aggtgtagac tttgatgaaa ctttcgcccc tgttgctaga cttgagtcca tcagattgtt 3540 acttggtgta gcttgcatcc tcaaattcaa gttgtaccag atggatgtga agagcgcgtt 3600 tctgaatgga tacctgaatg aagaagccta tgtggagcag ccaaagggat ttgtagatcc 3660 aactcatcta gatcatgtat acaggctcaa gaaggctctc tatggattga agcaagctcc 3720 aagagcttgg tatgaaaggc taacagagtt ccttactcag caagggtata ggaagggagg 3780 aattgacaag actctctttg tcaaacaaga tgctgaaaac ttgatgatag cacagatata 3840 tgttgatgac attgtgtttg gagggatgtc gaatgagatg cttcgacatt ttgtcccaca 3900 gatgcaatct gaatttgaga tgagtcttgt tggagagctg cattattttc tgggactcca 3960 agtgaagcag atggaagact ccatattcct ctcacaaagc aagtatgcaa agaacattgt 4020 caagaagttt gggatggaaa atgccagcca taaaagaaca cctgcaccta ctcacttgaa 4080 gctgtcaaaa gatgaagctg gcaccagtgt tgatcaaaat ctgtacagaa gcatgattgg 4140 gagcttacta tatttaacag caagcagacc tgacatcacc tttgcagtag gtgtttgtgc 4200 aagatatcaa gccaatccta agataagtca cttgaatcaa gtaaagagaa ttctgaaata 4260 tgtaaatggc accagtgact atgggattat gtactgtcat tgttcagatt caatgctggt 4320 tgggtattgt gatgctgatt gggctggaag tgcagatgac agaaaatgca cttctggtgg 4380 atgtttctat ttgggaacca atcttatttc atggttcagc aagaagcaga actgtgtgtc 4440 cctatctact gctgaagcag agtatattgc agcaggaagc agttgttcac aactagtttg 4500 gatgaagcag atgctgaagg agtacaatgt cgaacaagat gtcatgacat tgtactgtga 4560 caacatgagt gctattaata tttctaaaaa tcctgttcaa cacaacagaa ccaagcacat 4620 tgacattaga catcactata ttagagatct tgttgatgat aaaattatca cactggagca 4680 tgttgacact gaggaacaag tagcagatat tttcacaaag gcattggatg caaatcagtt 4740 tgaaaaactg aggggcaagc tgggcacttg tctgctagag gatttatagc aattacttct 4800 atctgaacgt gttcaaacgt taatagcacg ttctctactg ggccaaaaca aattcgaccg 4860 ttgcttcaca cgtccctcta cattcctcat tcaaacttac attttcgtgg taatctcgtt 4920 ttcattcacc aacacctctc agatattcac gaaacctttt caaaagctct gcttctccat 4980 ggctacctca ccaaaagaaa cttcatctcc tgtttcaccc tctgtaccat cacctccatc 5040 atccaccaaa gcaccatcaa accaggaaca acctgaattc aatatccaac ccatacaaat 5100 gattcctggt ccagcccctg ttcctgagaa actggtcccc aaaagacaac agggagtgaa 5160 gatttctgaa aaccctagcc ttgcaacaag tcctagggaa gtagacacgg agatggataa 5220 gaagatccgc agtattgtga gtagcatttt gaaaaatgct tctgtccctg atgctgataa 5280 agatgttcca acatcttcca ccccaaatgc tgaagtcctc tcttcatcca gtaaagagaa 5340 atcaacagag gaagaggatc aagccacaga ggagacccct gcaccaaggg caccagaacc 5400 tgctccaggt gacctcattg atctagaaga ggtagaatct gatgaggaac ccattgtcaa 5460 aaagttggca cttggcattg cagaaagatt acaaagcaga aagggaaaaa cccccattac 5520 taggtctgga cgaatcaaaa ctattgcaca gaagaagagc acaccaatca ctcctaccac 5580 atccagatgg agcaaagttg caatcccttc caagaagagg aaagaaattt cctcatctga 5640 ttctgatgat gatgtcgaac tagatgttcc cgacatcaag agagccaaga aatcagggaa 5700 aaaggtgcct ggaaatgtcc ctgatgcccc attggacaac atttcattcc actccattgg 5760 caatgttgaa aggtggaaat ttgtatatca acgcagactt gctttagaaa gagaactggg 5820 aagagatgcc ttggattgca aggagatcat ggacctcatc aaggctgctg gactgctgaa 5880 aacagtcacc aagttgggag attgttatga aagtctagtc agggaattca ttgtcaacat 5940 tccctctgac ataacaaaca gaaagagtga tgagtatcag acagtgtttg tcagaggaaa 6000 aggtattaga ttctcccctg ctgtaatcaa caaatacctg ggcagaccaa ctgaaggagt 6060 ggtggatatt gctgtttctg agcatcaaat tgccaaggaa atcactgcca aacaagtcca 6120 gcattggcca aagaaaggga agctttctgc agggaagcta agtgtgaagt atgcaatcct 6180 gcataggatt ggcactgcaa actgggtacc caccaatcat acttccactg ttgccacagg 6240 tttgggtaaa tttctgtatg ctgttggaac caagtccaaa tttaattttg gaaactatat 6300 ttttgatcaa actgttaagc attcagaatc ttttgctgtc aaattaccca ttgccttccc 6360 aactgtattg tgtggcatta tgttgagtca acatcccaat attttaaaca acattgactc 6420 tgtgaagaag agagaatctg ctctatccct gcattacaaa ctgtttgagg ggacacatgt 6480 cccagacatt gtctcgacat cagggaaagc tgctgcttca ggtgctgtga ccaaggatgc 6540 tttgattgct gaactcaagg acacatgcaa ggtgctggag gcaaccatca aagccaccac 6600 agagaagaaa atggagctgg aacgcctgat caaaagactc tcagacagtg gcattgatga 6660 tggagaagca gctgaggaag aagaagaagc agctgaggag gaagaagatg cagcagagga 6720 tacagaatca gatgatgatg attctgatgc caccccatga ccatcagacc tttatttttg 6780 cttttacttt tactagttat tggtctgtaa tatttgcaca ttaatttcat gcattctact 6840 tttgccaaat tctgtctaaa aagggggagt agtaggatat tatattatgc atgatttatg 6900 attttgaggg ggagtagtag ttatatgatt ttgaggggga gtagtattta tactactgct 6960 gctgatgatg attgatgtaa gctactaaaa ctagtagctg atagaagatc gccgcagtga 7020 actgcttcac agcagtagga gcatggagac agggggagca gaaagctgat gtcacgtgag 7080 atgtcttgac atcctggaaa cgacttgcaa cttgcagaat tttgctgtcg ccactacaga 7140 taccgctgtg cttgattact ctgatagtga aagttgctga tcccacttgc ataactgctc 7200 gtacctgctc aggaagtgtc taagtatgtt ttagacaaaa tttgccaaag ggggagat 7258 // ID Gypsy-1_LJ-I repbase; DNA; EDCOT; 4657 BP. XX AC BABK01000660; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the Lotus japonicus genome: internal DE portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-1_LJ_; KW Gypsy-1_LJ-LTR; Gypsy-1_LJ-I. XX OS Lotus japonicus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RA Sato S., Nakamura Y., Kaneko T., Asamizu E., Kato T., Nakao M., RA Sasamoto S., Watanabe A., Ono A., Kawashima K. et al.; RT "Genome structure of the legume, Lotus japonicus."; RL DNA Res 15(4), 227-239 (2008). XX RN [2] RP 1-4657 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the Lotus japonicus genome."; RL Direct Submission to Repbase Update (02-FEB-2011). XX DR Genome; BABK01000660; Positions 593 5249. XX CC Positions [1995-2420] - Reverse transcriptase CC Positions [3549-4043] - Integrase core CC 'CAGAA' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 42..4655 FT /product="Gypsy-1_LJ-I_1p" FT /translation="MPPKKTKLAVTRMESKIDALEEEIAAMRTSLAAVTTA FT MKDLPTLLVTMVDKAMGKTVAADDENGVERREEGVGNKTPASNGEKGENSR FT QHSSHSDALTEFRQAVKKVELPMFEGRDPAGWISRAEIYFRVQETSPEVKV FT SLAQLSMEGGTIHFFNSLLESEEELTWDRLREALLERYGGNGDGDVYEQLS FT ELRQRGSVEEYIADFEYLTAQIPKLPEKQYQGYFLHGLKEGIRGKVRSLIA FT IGGVTRARLLVVTRAVEKEVKGEMGSGQTRVNRFGGSGPRPGSQSNGKGDG FT TDWVWVRGNKESGQTPNRPNINNSSSPRGDQTKNEGRRNGPRDRGFNHLTY FT PQLMERRQKGLCFKCGGSYHPNHVCPDKHLRLLILEEESDEFEDSKILAME FT VNEEDEEQEGELSLMSLGELGGKSGEIPRTMKLRGTIDGVPVVVLVDSGAT FT HNFVDCHLVRRMGWRIVDTPRMTVKMGDGFKSQSQGRCADLQLCIGSYQVE FT CSPQLFDLGGPDIVLGIEWLRTLGDTIVNWQSQVMSFWSNKEWITLQGMRS FT EGDILVALQSILSTGEKGAGQRVCGVSKTTTPLETGNITPIQLEELNLLLQ FT RFDVVFQEKRGLPPSRGREHCITIQEGQGPVNVRPYRYPHSQKNEIERQVR FT DMLEAGIIRQSTSAYSSPVILVKKKDQSWRMCVDYRALNKVTVPDKFPIPV FT IEELLDELHGSVFFSKLDLKSGYHQVLVKKEDIHKTAFRTHEGHYEYMVMP FT FGLMNAPSTFQSLMNEVFRPMLRKGVLVFFDDILVYSQTWEAHVLHLERVL FT GLLEAHCLTANKKKCQFAARSVEYLGHLISEQGVAVDPNKVASVKSWPVPR FT NVKGVRGFLGLTGYYRKFIKDYGKIAKPLTELTKKEAFVWGETAQKAFEEL FT KEKLVTAPVLVLPDFTQEFRVECDASGVGIGAILLQGNHPIAYFSKALGPR FT NLAKSAYEKELMAVALAIQHWRPYLLGRKFVVSTDQKSLKEFLHQKIVTGD FT QQNWAAKLLGYNFEIEYKPGRTNLGADALSRLAETGEFGQLLSYPRWEEQG FT VIQEEISRDPKLTKIKDELTHNPQAHPGYSLVQNTLLYQGRVVISSTSSLI FT PRLMQEFHTTPQGGHSGFLRTYRRIAANLYWQGMTRSIQDFVRACEACQHQ FT KYLASSPAGLLQPLPIPERVWEDVSLDFITGLPKSKGFEAIFVVVDRLTKY FT AHFIPLKHPYTARSVAEHFAREIVRLHGIPASIISDRDPLFCSHFWRELFR FT LQGTKLKMSSAYHPESDGQTEVVNRCLETYLRCFAADQPRTWTMWLHWAEY FT WFNTSFHSATQQTPFEAVYGRKPPVLTQWVIGETRVESVERDLQDRDEALR FT QLKQHLLVAQARMRAQANSRRRHQEFEVGEWVFVKLRAHRQSSVANRVHAK FT LSARYFGPYPIIARIGAVAYRLKLPEGARIHPVFHISVLKRAVGTFAEDSE FT LPEQLDGEEIPSTQPMAVLAQRDIHRLGETIPQVLVHWQGKTPEEATWEDL FT VTIRSEFPTFNLEDKVVSSGGS" XX SQ Sequence 4657 BP; 1269 A; 996 C; 1317 G; 1075 T; 0 other; atttggtccg acctgccgga taccttcttc cacggcggtg aatgccacca aagaagacca 60 agcttgcagt aaccagaatg gaatcgaaga tcgatgcact ggaggaggag atcgcggcga 120 tgcgcacgtc gctggcagca gtaaccaccg cgatgaagga ccttcctacg ctgttggtga 180 caatggtgga caaagcgatg ggaaagaccg tcgcagctga cgacgagaat ggcgtggaac 240 gacgcgagga gggagtcgga aacaaaacgc cggcgtcaaa cggtgaaaag ggggaaaact 300 cacgtcaaca ctcttcccac agcgatgccc tgacggagtt caggcaagcg gtgaagaaag 360 ttgaactacc catgttcgaa ggcagagatc cagctggatg gatctcacgc gcggagatct 420 attttcgcgt ccaggaaacc tcacccgagg tcaaggtgag cttggcacag ctcagcatgg 480 agggaggcac gatccatttc ttcaattcgc tgctcgagtc cgaagaagaa ctgacctggg 540 atcgccttcg cgaggcgcta ctcgagcgct acggtggtaa cggggatggc gacgtttacg 600 agcagttgtc ggagctccgt cagcggggat ctgtcgagga gtacatcgct gattttgagt 660 atctcaccgc ccaaattccc aagcttccgg agaagcagta ccagggatac tttttgcacg 720 gactgaaaga aggaatccgg ggaaaggtac gcagcttgat cgccatagga ggagtcactc 780 gtgctcgttt gctggtggtg acacgcgcgg tggagaaaga ggtaaagggt gaaatgggtt 840 cgggtcagac aagggtcaac cgattcggag gcagcggtcc aagacccggg tcccaatcaa 900 acgggaaagg tgatggaacg gactgggtat gggtccgggg aaataaagaa tcgggccaaa 960 caccaaacag gcccaatatc aataacagca gcagcccacg tggagaccaa acaaaaaatg 1020 agggacgtcg aaatgggcca agggatcgag ggttcaatca cctcacctac ccacaactta 1080 tggagagacg ccaaaaaggc ttatgtttta aatgtggcgg atcctaccat ccgaaccatg 1140 tctgccccga taagcatcta aggctactca ttctcgaaga ggaaagcgac gaattcgagg 1200 atagtaaaat cttggctatg gaagtcaatg aagaggatga ggaacaagag ggagagctca 1260 gcctgatgag tttgggtgag cttggaggga aatcagggga gattccgcgg accatgaagc 1320 ttcgaggtac catcgatgga gtaccggtgg tggtgctcgt agatagtgga gcgacccaca 1380 actttgtgga ttgtcacttg gtcagacgca tgggttggag gatcgtggac accccaagaa 1440 tgacagtgaa gatgggagat ggatttaaat cacaatccca gggacgttgt gcagatttac 1500 agctctgtat tggtagctac caggtagagt gttccccgca gctcttcgat ttgggaggtc 1560 ctgacatagt gttgggaatc gaatggttga ggaccttggg tgacaccatt gtcaattggc 1620 aatcccaagt aatgagtttt tggagcaata aggaatggat tactcttcag ggaatgcgtt 1680 cagaagggga catattggta gcattacaga gtattctctc aactggagaa aaaggggcag 1740 ggcaacgtgt ttgtggggta tctaagacca cgaccccatt ggaaacaggg aatataaccc 1800 cgattcagtt ggaggagctg aacttgctat tacagaggtt tgatgtggtt tttcaggaaa 1860 aacgagggct tcccccgagc agagggagag agcattgtat cacaattcag gaagggcaag 1920 ggcctgtgaa cgtgaggccg tatcgctacc cgcacagtca aaaaaatgaa attgagaggc 1980 aagtgaggga catgcttgag gcaggaatca tccgacagag caccagtgcg tattcaagcc 2040 cggtgatcct ggttaagaag aaggatcagt cttggcggat gtgtgtggat tacagggcac 2100 tcaataaggt cacggtgcct gacaagtttc caattccggt gattgaggag ttgttggatg 2160 aacttcatgg atcagttttt ttctcaaaac tggatctgaa atcgggatac catcaggttt 2220 tggtcaagaa ggaagacatc cacaagactg cgtttcgcac ccacgaaggt cactacgaat 2280 atatggtaat gccgtttgga ctaatgaatg ccccgtctac ttttcaaagt ctcatgaatg 2340 aggtatttag gcctatgttg aggaaggggg tacttgtgtt ttttgatgat attttggttt 2400 atagtcagac ctgggaagct catgttttgc atttggaaag agtcttagga ttattggaag 2460 cgcactgttt gacggctaat aaaaagaagt gtcagttcgc agccagatca gtggagtatt 2520 tgggacactt aatctcagag caaggggtgg cggtggatcc caataaggtg gctagtgtga 2580 aatcttggcc ggttcctaga aacgtaaagg gggtgcgggg atttttgggc cttacaggtt 2640 actaccggaa gttcattaag gactatggaa aaattgctaa accactaaca gagcttacaa 2700 agaaggaggc atttgtatgg ggagaaacag ctcagaaagc ttttgaggaa ctcaaagaaa 2760 agcttgttac tgctcctgtg ttggtgcttc cggattttac ccaggaattt cgagtagagt 2820 gtgatgcttc aggggtgggt attggcgcaa tactgcttca agggaaccac ccaatagctt 2880 acttcagtaa agcattggga ccaaggaatc ttgctaaatc tgcttacgag aaggagctta 2940 tggcagtggc actggcaatt cagcactgga gaccctatct ccttgggcgc aagtttgtag 3000 tttccaccga tcagaagagc ctcaaggaat tcttgcacca aaagattgtg accggagacc 3060 aacagaattg ggctgcaaaa ctcttaggat acaattttga aattgaatat aagccgggac 3120 gaacaaatct aggagcagat gctctttcac gcctcgctga gacaggggaa tttgggcagc 3180 tgttatccta tcctaggtgg gaagagcaag gagtcatcca agaagaaatc agcagggacc 3240 ccaaattaac aaagatcaaa gatgaattga cccacaatcc acaagctcac cccgggtaca 3300 gtttggtgca aaataccttg ctctatcaag gtagggtggt gatttcaagt acctcttcct 3360 tgattccacg gctgatgcaa gaatttcaca ccacacctca aggaggacat tcgggttttt 3420 tgaggacata tagacgcatt gctgcaaatt tatattggca aggtatgact cgatcaatcc 3480 aggattttgt gagggcttgt gaggcctgtc agcaccagaa gtacttggct tcgtctccgg 3540 cgggtctcct tcaaccatta ccaataccgg agcgagtgtg ggaagatgtg tcacttgact 3600 tcattactgg gttgcctaag tctaaaggat ttgaagcgat cttcgtagtg gtggatcgtt 3660 tgactaagta cgcacacttc attcctctga agcacccata tacggcgcga agtgtagctg 3720 aacattttgc ccgggaaatt gtgcgacttc atggcattcc cgcttccatc atcagtgata 3780 gagaccctct gttttgcagc catttttgga gggagttatt tcggttgcaa ggtactaaat 3840 tgaaaatgag ctccgcatac catcccgaat ccgatgggca aacggaggtt gtaaaccggt 3900 gcctcgaaac atatttgcgt tgtttcgccg ctgaccaacc cagaacttgg actatgtggc 3960 tccactgggc agagtactgg ttcaacacat catttcactc cgccacgcag caaactcctt 4020 tcgaagcagt gtatgggagg aaacctccag ttttgacaca atgggtaatc ggggaaactc 4080 gcgtggaatc tgtggaaagg gacttacaag acagggatga ggccctgcga cagttgaagc 4140 aacatttgtt ggtagcgcag gctcgcatgc gtgcacaggc aaactcaagg cggaggcatc 4200 aggagttcga agtcggagag tgggtctttg tgaagcttcg agctcaccgc caatcatcag 4260 tagcgaaccg ggtgcacgca aagttgtcag ctcgctattt tggtccctat ccaatcatcg 4320 cgcggattgg ggcagtggcc taccgcttga agcttccaga aggagcacgc attcatcctg 4380 tgttccacat ctctgtgttg aagagggcag tgggtacctt tgctgaagac tctgaattac 4440 ctgaacaatt ggatggggaa gagattcctt ccactcaacc gatggctgtc cttgctcaaa 4500 gagatatcca caggttaggc gagacaatcc ctcaagtgtt ggttcactgg cagggcaaaa 4560 caccagaaga ggcaacttgg gaagacttgg taaccattcg cagtgagttt cctactttca 4620 accttgagga caaggttgtg tcttcaggag ggagtat 4657 // ID Copia-55_PTr-LTR repbase; DNA; EDCOT; 1658 BP. XX AC . XX DT 08-DEC-2009 (Rel. 15.02, Created) DT 08-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Copia-type LTR retrotransposon: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed repeat; Copia-55_PTr-I; Copia-55_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1658 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 164-164 (2010). XX DR [1] (Consensus) XX SQ Sequence 1658 BP; 563 A; 241 C; 308 G; 546 T; 0 other; tgttagttta atatgccttg tagccaatcg gttggttaca cgtgacatta ttatattcat 60 gtaaatacat atttattatt aataaaggct taatttatct ttaatattca tataatatta 120 gattaatgaa tctagagtaa agataaagtc catgggacaa aaatgctttg caaaggaaat 180 tataaagttg ttataattat gagatttcta ttgcatcaaa gcattgttcc taaaatgttc 240 ctggtcgatg ctctcttaaa tactggacat ttattagagc cgtagagact ggtacatatt 300 atgttctttc ctttatgaaa ggaagcagtt gttctcataa gctgaggtat aagggatacc 360 tagaactaat atgtaggtgc ttgtcataag acatgtacac tgaactgacc cgcatgagaa 420 ttccatatgg agagatcacc tatgtctatg gaaaggctca cgtgacggtt gtgtaagtga 480 tccttagact tgagatcact aagttatctt atatagagaa tgttatgctt tgatcctgtt 540 acatgttatc ttaatcgagg taacgaaagg gcagacattg ggtataacat gaactatatg 600 aaggtacttg agtgatcaag agaggattca tcaccctagg tgaattagag aaaatgtttc 660 atctgttctc aaatagtatt gactgagaaa tccttggcca aggtggaatg agatttgaaa 720 agagtttcaa atcttattca aacgatcaat gactattatg tagagaacaa acatgattta 780 acatggcaga catacttcat gctttaatgt taaatcagaa cattattgat gaaaggatat 840 taattacact gagaaaccgg tcactgaaag gttaagtcaa accactaatg acttttctaa 900 tatttggggg atcatgacac gttgctagac gatgcacctg atcttcaaat ataaattaat 960 caattgttga attgataata aattaaattg tttaatttat ttaattataa ttataattta 1020 tatttgggcc aacatattag gaacctaatg ggtcacacac attaagaacc attagtcaga 1080 aattaaactg ggatgattta attaagtatg acttgattaa aatatatttt agaaattaag 1140 gactagaata taattaatac agggattata tttctagacc tagaaaaatc aagtaaggac 1200 ttgattgagt taatttctaa aattgtcctg aattaatata tggatattat tcaaggggca 1260 aattgatatt ttgccaattt atagggtttt tcagattttc ctataaatag taagctatgc 1320 ctcttatttt ttagtggttg tctgttagac agaaaaacta cgtaagtcac aaaatagaga 1380 gctagcactc taggcataac aatccctctc tcctaaatag ggatttagga gatttctcac 1440 tggtggttcg tgtggattac cgttggaggc cggacaattg gacgacttgt ggtttgcgac 1500 aacccagcct ttaaagaatt attcaaagcc gaagaagatc agatcttcag gtaataaatc 1560 cctaaacaac tctagatctg tctaacggga tcctagggac tcccaaataa ttttgtttta 1620 ttgtttccgc tgcgtgtatg atattcagga acccaaca 1658 // ID Copia49-PTR_LTR repbase; DNA; EDCOT; 291 BP. XX AC scaffold_3530; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia49-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-291 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-291 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 277-277 (2007). XX DR Genome; scaffold_3530; Positions 613 323. XX SQ Sequence 291 BP; 93 A; 49 C; 52 G; 97 T; 0 other; tgttaacaat tgcggtaatt atctccaagt tggatttgca gcattcaagt cctacattgt 60 ctctgatatt agctggaaag atatattcca gcatcccggt aaatacgtga ttgtatccta 120 gtagaaattt ttttccatgt aattagcaaa tcagtcctaa actataggat ctgaaacgta 180 gggattctta tgtagagtag ctatatatat tctgcttgta acagaggaag ttactaagtg 240 aaaataaaca attgaatccc tttgaaaact ctgcgtacgt tttgactcac a 291 // ID DNA-3_Mad repbase; DNA; EDCOT; 137 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA-3_Mad. XX NM DNA-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-137 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1460-1460 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >93% identical to the consensus. 41-bp TIRs. XX SQ Sequence 137 BP; 46 A; 23 C; 19 G; 49 T; 0 other; taaatttagg gaactgttat tagcactcca aaaatctcat tctacactcc tcacaagtgt 60 atttttcttt ctaattatag aaagtttgga gtgcaaaatg agatttttgg agtgccaata 120 acaattccct aaattta 137 // ID Copia29-VV_LTR repbase; DNA; EDCOT; 300 BP. XX AC . XX DT 13-SEP-2007 (Rel. 12.09, Created) DT 01-OCT-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia29-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-300 RA Obukhanych T. and Jurka J.; RT "Copia29-VV."; RL Repbase Reports 7(9), 791-791 (2007). XX DR [1] (Consensus) XX CC This is 3' LTR of Copia29-VV LTR retrotransposon. LTRs of this CC retrotransposon are 94% similar to each other. 5' LTR is shorter CC due to a ~25-bp internal deletion. XX SQ Sequence 300 BP; 95 A; 43 C; 44 G; 118 T; 0 other; tgttagaaga ataagccaag aaattaacaa ttattttttt ctccatatat atatatgatt 60 tctcctacca tatttttcct ttcttgtaaa agttgaccca tgattcttgt accaagaatc 120 tgggtaaatt ccatatagga accttaggta aatttccata taggactctt gcaatcagat 180 tgcttgattt tagggatttt ttttataggt agcctaattt aggggatctc atcagtcatt 240 ctttgtatat atgtattgta aatcaaaatg taaagatata cgagagatta tttttcatca 300 // ID TTO1_NT_LTR repbase; DNA; EDCOT; 574 BP. XX AC D83003; XX DT 04-MAR-1998 (Rel. 3.02, Created) DT 09-APR-2007 (Rel. 12.07, Last updated, Version 2) XX DE Tobacco DNA, retrotransposon Tto1 sequence encoding an ORF DE (1338AA), complete cds. XX KW Copia; LTR Retrotransposon; Transposable Element; TOBAA; TTO1_NT; KW TTO1_NT_I; TTO1_NT_LTR; Tto1; retrotransposon. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RP 1-574 RA Hirochika H., Otsuki H., Yoshikawa M., Otsuki Y., Sugimoto K. RA and Takeda S.; RT "Autonomous transposition of the tobacco retrotransposon Tto1 in RT rice."; RL Plant Cell 8(4), 725-734 (1996). XX RN [2] RP 1-574 RA Hirochika H., Otsuki H., Yoshikawa M., Otsuki Y. and Takeda S.; RT "Autonomous Transposition of the Tobacco Retrotransposon Tto1 in RT Rice."; RL Unpublished (1996). XX RN [3] RP 1-574 RA Hirochika H.; RT "Direct submission."; RL Direct Submission to EMBL/GenBank/DDBJ (10-JAN-1996). Hirohiko RL Hirochika, National Institute of Agrobiological Resources, RL Molecular Biology; 2-1-2 Kannondai, Tsukuba, Ibaraki 305, Japan RL (E-mail:hirohiko@abr.affrc.go.jp, Tel:0298-38-7006, RL Fax:0298-38-7408). XX DR GenBank; D83003; Positions 1 574. XX SQ Sequence 574 BP; 163 A; 87 C; 132 G; 192 T; 0 other; tgttagtttt tccaacaatt atggtgatgt atgggagagg taagcaatga tgcaactctc 60 cttagtgaga taagcaatga tgcaatgagt ggtaggtgag atgagaatat tgcaaattga 120 tccttcttgg taggtgagat ttgcactttt ggtccctatc tcaaaactat aaataccccc 180 ttccatttca ttgtataaca caccaaaaaa tatatcaaaa ctcaagaaga aagagtttga 240 gagggagaga gatatagttc ctttaggaat gtttcctaac aggggagtga caaaatagtg 300 agtagaaata ctagtcgggt atttttcggg aaacactttt gtgtgcgcca ctattttggg 360 tagagctcag gaattgttgt acctccaaat tattgaggaa gtctctcttt gtatgcctgc 420 taaatgtttt agtggaagtt ggtgtcggat ttgtggacgt agcctaaacg ttttaggtga 480 accacgttaa atattgtgtc atttattttt ggtttcgttg atcatttatt ttattccgct 540 gtgcagtagt gtttagtgcc accggatcct aaca 574 // ID Copia13-PTR_I repbase; DNA; EDCOT; 3896 BP. XX AC scaffold_3625; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia13-PTR_I; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3896 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-3896 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 198-198 (2007). XX DR Genome; scaffold_3625; Positions 1207 5102. XX CC Positions [1606-2085] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 1642..3645 FT /product="Copia13-PTR_I_1p" FT /translation="MSVDGFRYYVSFVDECTRYSWIFPMINKGEVYSIFVH FT FHTFLVTQFFATLRIFQSDGGGEYISTNFKNYLHTKGIVHQMSCPYTPEQN FT GLAERKHRHIVETVVTLLQTAHLPNKFWFHACVTSIYLINRLPCQLLRLKS FT PFFLLYGSSPVIHHLRIFGCACFPLLRPYNSNKLQPKTSTCIFLGYASQYK FT GYICFSLHTNRIFVSRHVLFDESLFPYISVPMPAVSLSLHVSAVSPSSPSV FT SLHNSVLPLVSSSPSFSSTPSASLPSLSPGLSLQPSSDLHSPAHSPLPVDP FT DFHPERLCVVLPLSPMNLHPMTTKSKSGISKKKAYSATVQSLALSQVEPRS FT FKIASATVEWQSAMQEEIEALHAQGTWDLVALPPDRNLVGCKWVYRLKKHA FT DGSIARHKARLVAKGFSQEEGIDYGETFSPVVKPTTVRLVLALAAHFNWSL FT RQLDVKNAFLHGILHEEVYMTQPPGFVSKAHPSDFVCRLRKSLYGLKQAPR FT AWNERFTSFLPSLGFQASLADSSLFVQHSSHGTLILLLYVDDIILTGSHSS FT LFSSVIAALSQEFDLTDLGPLHHFLGLQISYILAFTFILVLFICRPIVMPT FT RLEILMTAGLSLVLLSILVPVLFLGLLRNNILFLVRLRRLNIALSLSLLQS FT LPGFVNCFVTFIFLYFFHL" XX SQ Sequence 3896 BP; 843 A; 949 C; 709 G; 1395 T; 0 other; tggtatcaga gcgctggaac tcttgatctt gtggccatta acttctgaat tttggcttta 60 ttctcatcct cttcataaaa ttcttgtgca cttattgatg tgcctatcag ctatttgata 120 tattgcctca ctgattctct tcttcaaaac tccagttttc tattacttca ccgaacatta 180 taatcttcaa ttttctgctt tctcctacat tctaaaatgg tgactagctc tcaacttcag 240 attattcaat ctcctatcac ttctcttctt cctgcaatct ctattgctat aacagtgaag 300 cttgacgata caaactacct cgtctggcaa tttcaaatga aaattcttct tgaaagtcat 360 ggaattctag gatttgttga tggttccaga aaatgtccaa gtcgatttga tacagattcc 420 gatattgagg gtgttgaatc tgatgatcat cagatttgga aaatgcatga cagagcactg 480 atgcagctac ttattgccac tctttcttct actgccattt cctatgtcat tggctgcatc 540 agttctcatg atatgtgggt tcaattgcag gatcgttttt ctacagtaac caaggcaaga 600 atctttcaaa tgaagagtga acttcaaact atcaagaaag gttcagaacc tgtgtctcag 660 tatctgcaga gaatcaaaga tgcccgtgat catctctctg ccgctggagt ttattttgaa 720 gatgaggata ttgtgatctt ggctctcaat ggcctttctt ctgactataa cacgttccga 780 tgtatggttc gaggcagaga taatgtgtta tctcttaaag attttcactc tcaattgctt 840 gctgaagaag ctactattga gcagacccat tcctcttctc catttgtctc tgctatgcac 900 gttcagagat aatgttatca tagaggcaac ttctcctatc aaggccgtcc tccttccatc 960 aatcttagtg ctatggctgc tacctttcct ccatctccta aaccattttg ggtggctgat 1020 actggcgcca caactcatat gacatctgat ttgtctcact ctggtcctga tgctattacc 1080 actgcaggcg gttcaggttt gagcatttct agtattggct cttctgtttt gcctattcca 1140 caatgctcct tacaattaca ccaagtgttg catgttccta agctatctca acatctgctg 1200 tcagtttata ggttgtgtaa agataatcat tgtcgattta tttgtgatga ctttggtttt 1260 tggattcagg acaaaatcac ggggaatgtc cttctcaagg gcctgtgtag taatgtttta 1320 tatcatattc ctttttctgt ttcttctagt tcccacacac cttttcaact tgcattagct 1380 tcccatcgta atcagtcttg ctatcttggt caacaggttc aaaccagtct ttggcacaag 1440 cgatttggtc atccctctaa tagcataacg tccactcttc tcactcagtc tcagattccc 1500 ttcacttcag atcctaccaa gtctgtttgt accacttgtt tcgagggcaa aattactaag 1560 cttccttttc catatccagc agttaagtct attcaccctt tataaatcat acatagtgat 1620 gtttggggcc ctgcactcgt aatgtctgtt gatggcttta gatattatgt tagttttgtt 1680 gatgaatgta cacggtactc ttggattttt ccaatgatca ataaaggaga ggtttattct 1740 atttttgtcc atttccatac atttttagtt actcaatttt ttgctacact taggatcttt 1800 caaagtgatg ggggtggtga atatattagc accaacttca aaaactatct tcataccaag 1860 ggcattgttc atcaaatgtc atgtccctat acccctgaac aaaatggtct tgctgagaga 1920 aagcatagac atattgtgga aaccgtcgtc actttgttac aaactgccca tctccctaat 1980 aaattctggt ttcatgcttg tgttacttcc atctatttga ttaatagatt gccttgtcaa 2040 cttctacggc tgaaatctcc ttttttcttg ctgtatggtt cttcccctgt catccatcac 2100 ttgcgcatct ttggttgtgc ttgtttccct ttacttcggc cttacaactc taataaacta 2160 cagccaaaaa cttccacatg catctttttg ggctatgcca gccaatataa agggtacatt 2220 tgtttttccc ttcataccaa tcgcatcttt gtgtctcgcc atgtcctctt tgatgaatca 2280 ttgtttcctt atatctctgt gcctatgcct gcagtctctc tttctctgca tgtgtctgct 2340 gtctctcctt cttccccatc tgtctctctt cataactctg ttttgcctct tgtttcttcc 2400 tctccttcct tttcttctac tccttctgca tcattacctt ctttgtcacc tggtctgtct 2460 ttacagccct catctgactt gcactcccct gcacattctc ctctccccgt ggatccagac 2520 ttccaccctg agcgcctgtg tgtagttctg cctctctccc ccatgaatct tcatcccatg 2580 actaccaagt ctaaaagtgg catttccaag aaaaaggcat attctgccac tgttcagtct 2640 cttgctcttt ctcaggttga acctcgttcc ttcaagattg cttctgccac tgttgaatgg 2700 caatcagcca tgcaggagga aattgaggcc cttcatgccc agggtacttg ggaccttgtt 2760 gctttgccac ctgacagaaa tcttgttggc tgtaagtggg tctaccggct gaagaagcat 2820 gctgatggtt ctatagctcg ccataaggct cgattagtgg ctaaggggtt tagtcaagag 2880 gagggtattg actatggaga aaccttcagt cctgtggtga aacccaccac tgttcgtcta 2940 gttcttgccc ttgcagctca ctttaattgg tccttgcggc agcttgatgt gaagaatgca 3000 ttcttgcatg gcattcttca tgaggaggtt tatatgactc aacctccggg ctttgttagt 3060 aaggctcatc cctctgattt tgtttgccgg ctgaggaagt ctttgtatgg tcttaagcag 3120 gctcctcgtg cctggaatga gcggttcacc agttttttgc ccagcttggg gtttcaagca 3180 tctcttgctg attcctcttt atttgttcag cactcttctc atggcactct gatcttgctc 3240 ctctatgttg acgatatcat tcttactggc agccattcct ctcttttttc gtctgttatt 3300 gctgctctgt ctcaggaatt tgacctcaca gatttgggtc cattgcatca ttttttgggg 3360 ctgcagattt cctacatctt ggccttcact ttcatcctgg tcctcttcat ttgcaggcct 3420 atcgtgatgc cgactaggct ggagatccta atgaccgccg gtctgtctct ggttctcttg 3480 tctattttgg ttccagtcct atttcttggg cttctaagaa acaacatact gtttctcgtt 3540 cgtctacgga ggctgaatat cgcgctctcg ctatcactgc tgcagagctt gcctggattc 3600 gtcaactgct ttgtgacatt catattcctt tacttcttcc acctttaatt cattgtgata 3660 atatttctgc tatctccctt gcttccaatc cagtgttcca ttccaggatg aaacatctcc 3720 agatcgatta tcattttgtt agggagcggg ttatcatggg tgatttactg gtccagcatg 3780 tctcctctaa tgatcagttt gctgatatcc tcaccaaagg cctttccatt tctttatttc 3840 agcatcattg ctccaatctc atgcttggct cctcccagcc tgcgattgag ggggca 3896 // ID RAM12_I repbase; DNA; EDCOT; 4550 BP. XX AC . XX DT 06-DEC-2006 (Rel. 11.12, Created) DT 05-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE Internal region of RAM12 LTR retroposon from Medicago truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; internal portion; RAM12_I. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4550 RA Shankar R. and Jurka J.; RT "RAM12: LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 639-639 (2006). XX DR [1] (Consensus) XX CC The internal region is flanked by LTRs. The internal region CC sequence codes for GAG protein and RT polymerase polyprotein, CC with two different ORFs. The GAG region is poorly conserved. The CC RT polymerase polyprotein has conserved domains for Arginine CC methyl transferase, RT polymerase as well as integrase. XX FH Key Location/Qualifiers FT CDS 133..891 FT /product="RAM12_I_1p" FT /translation="MAGRNDAAIAAALEAVAQAVGQQPNAAAGNGEVRMLE FT TFLRNHPPAFKGRYDPDGAQTWLKEVERIFRVMQCSEVQKVRFGTHMLAEE FT ADDWWVSLLPVLEQDGAVVTWAVFRREFLNRYFPEDVRGKKEIEFLELKQG FT DMSVTEYAAKFVELAKFYPHYTAETAEFSKCIKFENGLRADIKRAIGYQKI FT RIFSDLVSSCRIYEEDTKAHYKVMSERRGKGQQSRPKPYSAPADKGKQRLN FT DERRPQEERCSC" FT CDS 854..4492 FT /product="RAM12_I_2p" FT /translation="MMRGGPKRRDAPVEIVCYKCGEKGHKSNVCTKDEKKC FT FRCGQKGHVLADCKRGDIVCYNCNEEGHISSQCTQPKKVRTGGKVFALTGT FT QTTNEDRLIRGTCFFNSTPLIAIIDTGATHCFIALECAYKLGLIVSDMKGE FT MVVETPAKGSVTTSLVCLRCPLSMFGRDFEVDLVCLPLTGMDVIFGMNWLE FT YNRVHINCFSKTVHFSSAEEESGAEFLTTKQLKQLERDGILMFSLMAYLSL FT ENQAVIDRLPVVNEFPEVFPDEIPDVPPEREVEFSIDLVPGTKPVSMAPYR FT MSASELAELKKQLEDLLDKKFVRPSVSPWGAPVLLVKKKDGSMRLCIDYRQ FT LNKVTIKNRYPLPRIDDLMDQLVGAKVFSKIDLRSGYHQIKVKDEDMQKTA FT FRTRYGHYEYKVMPFGVTNAPGVFMEYMNRIFHAYLDKFVVVFIDDILIYS FT KTEEEHAEHLRIVLQVLKEKKLYAKLSKCEFWLSEVSFLGHIISGSGIAVD FT PSKVDAVSQWETPKSVTEIRSFLGLAGYYRRFIEGFSKLALPLTQLTCKGK FT SFVWDAQCESSFNELKRRLTTAPILILPKPEEPFVVYCDASKLGLGGVLMQ FT DGKVVAYASRQLRIHEKNYPTHDLELAAVVFVLKIWRHYLYGSRFEVFSDH FT KSLKYLFDQKELNMRQRRWLELLKDYDFGLNYHPGKANVVADALSRKTLHM FT SALMVKEFDLLEQFRDLSLVCELSPQSVQLGMLKINSDFLNSIREAQQVDV FT KFVDLMIDSNQTEDGDFKVDDQGVLRFRGRICIPDNEELKKLILEESHKSS FT LSIHPGATKMYHDLKKLFWWSGLKRDVAQFVYACLTCQKSKVEHQKPAGLL FT TPLDVPEWKWDSISMDFVTSLPNTPRGHDSIWVVVDRLTKSAHFIPINISY FT PVAQLAEIYIHNIVKLHGVPSSIVSDRDPRFTSRFWKSLQDALGSKLRLSS FT AYHPQTDGQSERTIQSLEDLLRVCVLEQGGAWDSHLPLIEFTYNNSYHSSI FT GMAPFEALYGRRCRTPLCWFESGESVVLGPDLVHQTTEKVKMIREKMKASQ FT SRQKSYHDKRRKDLEFQEGDHVFLRVTPMTGVGRALKSRKLTPKFIGPYQI FT SERVGTVAYRIGLPPHLSNLHDVFHVSQLRKYVPDPSHVIPRDDVQVRDNL FT TVETLPLRIDDRKVKSLRGKEIPLVRVVWGGATGESLTWELESKMQESYPE FT LFV" XX SQ Sequence 4550 BP; 1216 A; 655 C; 1290 G; 1383 T; 6 other; attggtatca gagcaggttg gtccgtccgg ccaagtagta gagtcgtgtt gagccaccta 60 ggatagagtg tcaaactcta atgttgtctt tgttgttgtt ctgaattgtt atttcttatg 120 tagaaytttg aaatggctgg tcgtaatgat gctgctattg ctgctgcact tgaggctgtt 180 gctcaagctg taggacagca accgaacgcw gctgctggta acggtgaagt gaggatgctg 240 gagacctttt tgaggaatca tccaccagca ttcaagggaa ggtatgatcc tgatggtgcc 300 cagacgtggt tgaaggaagt ggagaggatc ttcagggtca tgcaatgctc tgaggtgcaa 360 aaggtgcggt tcgggacgca catgctagct gaggaggctg atgattggtg ggtaagtctg 420 ttacctgtgc tggaacagga cggagcggtg gtgacttggg ctgtgttcag gagagaattc 480 ctgaatagat actttccgga agatgtccga ggcaagaagg aaattgaatt tctggagctg 540 aagcagggtg acatgtctgt cacagaatat gctgctaagt tcgtggaact tgcaaagttc 600 taccctcact atactgcgga gacagctgaa ttctccaaat gtatcaagtt tgagaatggc 660 ttgagagctg acatcaagag agccattgga tatcagaaga tcagaatttt ctctgatttg 720 gtgagtagct gcagaatcta tgaagaggat acgaaagctc attacaaggt gatgagtgag 780 cggaggggta agggacagca gagtcgtcct aagccgtata gtgctcctgc tgacaaagga 840 aagcagagat tgaatgatga gaggaggccc caagaggaga gatgctcctg ttgagattgt 900 ttgttacaag tgtggcgaga aaggccacaa gagtaatgtt tgtaccaaag atgagaagaa 960 gtgcttcagg tgtggtcaga agggtcacgt gttagctgat tgcaagcgtg gtgatattgt 1020 ttgttataac tgcaatgagg agggtcatat cagttcacag tgcactcaac cgaagaaggt 1080 tagaaccggt ggwaaagtgt ttgctttgac tggtacgcaa accactaatg aggatcgact 1140 tatcagaggt acttgtttct ttaatagtac tcctttaatt gctattatag acactggtgc 1200 tactcattgt ttcattgctt tagaatgtgc ttataagttg ggtctgattg tatctgatat 1260 gaaaggagaa atggttgttg aaactccagc taagggttca gtaactactt ctcttgtttg 1320 tctaaggtgt ccgttgtcta tgtttggtag agattttgaa gtcgacttag tgtgtttacc 1380 gttgacgggg atggatgtta tttttgggat gaattggtta gagtataacc gagttcatat 1440 caattgcttt agcaagacgg tgcatttttc ttctgcggaa gaagagagtg gagcagagtt 1500 tctaactact aaacagttga agcagttgga acgagatgga attcttatgt tttctttgat 1560 ggcatatttg tcgttagaaa atcaagctgt gattgacagg ttaccagtgg tgaatgagtt 1620 tcctgaagtt tttccggatg agattccaga tgtgccacca gagagggagg ttgaattttc 1680 aattgacctt gttccaggaa cgaagccggt gtcgatggca ccttatcgta tgtcagcttc 1740 tgagttagct gaattaaaga aacagttgga ggacttgctt gataagaagt ttgtaagacc 1800 aagtgtttca ccgtggggag cgcctgtgtt gttggtaaag aagaaggatg gtagtatgag 1860 gttgtgcatt gactatcgtc agttgaacaa agttacaata aagaacaggt atccacttcc 1920 gaggattgat gacttgatgg atcagttggt gggtgcaaag gtttttagta agattgactt 1980 gaggtcaggt taccatcaaa ttaaggtgaa ggatgaagat atgcagaaga cggcctttag 2040 gacacgatat ggtcattacg aatacaaggt gatgcctttc ggtgttacta atgcgcctgg 2100 tgtgttcatg gagtatatga accgaatttt tcatgcttat ctggataaat ttgtggttgt 2160 atttattgat gacatcctga tttattcaaa gactgaagaa gagcatgcag aacatctgag 2220 gattgtgttg caagtattga aagagaagaa gttgtatgct aagttgtcga agtgtgagtt 2280 ctggttaagt gaagtgagtt ttcttggcca cattatttct ggtagtggta ttgcagttga 2340 tccttcaaaa gttgatgcag tatcacaatg ggagactccg aagtcagtga ctgaaatcag 2400 aagtttcttg ggtttggctg gttattaccg caggtttatt gagggatttt cgaagttagc 2460 acttccgttg actcagttga cctgtaaggg taagtctttt gtatgggatg ctcagtgtga 2520 gagtagtttc aatgagttga agcgaagatt gacgactgct cctattttga ttttgccgaa 2580 gccggaagaa ccgtttgttg tttattgtga tgcgtctaag ttgggtttgg gaggtgtttt 2640 gatgcaagat ggtaaggtgg tagcgtatgc ttctagacag ttgaggattc atgaaaagaa 2700 ttatcctact catgatttgg agttggctgc ggtggttttt gttttgaaga tttggaggca 2760 ttatttgtat ggttccagat ttgaagtatt cagtgatcac aagagtctga aatatttatt 2820 tgaccagaag gaattgaaca tgaggcagag gagatggcta gagttgttga aggattatga 2880 ttttggtttg aattatcatc cgggtaaagc taatgtagtt gcagatgcct tgagtaggaa 2940 gacgttgcat atgtctgctt tgatggtaaa agaatttgat ttgcttgaac agtttagaga 3000 cttgagcctt gtstgtgaat tgtcacctca aagtgtgcag ttgggtatgc tgaagatcaa 3060 tagtgatttc ttgaatagta tcagagaagc acaacaagtg gatgtcaagt ttgtggattt 3120 aatgattgat agtaatcaaa ctgaggatgg tgatttcaag gttgatgatc agggtgtgtt 3180 gagattcaga ggcagaattt gtattcctga taatgaagaa ttgaaaaagt tgattttaga 3240 agaaagtcac aagagtagct tgagtattca tccgggagct acgaagatgt atcatgactt 3300 gaagaagctg ttttggtggt ctggtttgaa gcgtgatgtc gctcagtttg tgtatgcatg 3360 tttgacttgt cagaagtcta aggttgaaca tcagaagcct gcagggttgt tgacaccgtt 3420 ggatgtaccg gagtggaaat gggatagtat ttctatggat tttgtgacaa gtttaccaaa 3480 cactccgaga ggacatgatt ctatatgggt tgtkgttgac aggttgacga agtcggcgca 3540 ctttattccg attaatatca gttatccggt agctcagttg gcggagattt acattcataa 3600 tattgtgaag ttgcatggtg ttccgtcgag tattgtgtca gatagggatc caaggtttac 3660 ttcaagattt tggaagagtt tacaggacgc gttgggttcg aaattgaggt tgagttcggc 3720 ttatcatccg cagactgatg gtcagtcgga gaggacaatc caatctttag aggatttgct 3780 aagggtatgt gtacttgagc aaggtggagc ttgggatagt cacctaccat tgatagaatt 3840 cacatacaac aacagttacc attcgagtat tggtatggca ccgttcgaag ctttgtatgg 3900 tcggaggtgc aggactcctt tatgttggtt tgagtcggga gaaagtgttg tgttgggacc 3960 ggatttggtt catcagacta cagagaaagt caagatgata agagagaaga tgaaagcgtc 4020 gcagagtcga cagaagagct atcatgacaa gcgtaggaag gaccttgagt ttcaggaggg 4080 tgatcatgtw tttttgaggg ttactcctat gacaggtgta ggacgtgcat tgaagtcgag 4140 gaagttgact ccaaagttca ttggtcctta tcagatttca gagagagttg gaactgtggc 4200 gtatagaatt ggtttgccac ctcatctttc gaatttgcat gacgtgtttc atgtgtcaca 4260 gttgcggaag tatgtacctg atccttcgca tgttattcca agagatgatg tgcaagttag 4320 agataacctg acggtggaga ccttaccttt gaggattgac gatcgtaagg tgaagtcttt 4380 gagaggtaaa gagatacctc ttgtaagagt tgtttggggt ggagcaactg gtgaaagctt 4440 aacttgggag ctggagagta agatgcaaga atcgtatccg gagttgtttg tttgaggtaa 4500 gatttcgagg acgaaattct ctaagttggg gagagttgta acgccctagt 4550 // ID Gypsy-29_VV-LTR repbase; DNA; EDCOT; 3037 BP. XX AC chr3; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-29_VV_; KW Gypsy-29_VV-I; Gypsy-29_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-3037 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr3; Positions 16901186 16904222. XX SQ Sequence 3037 BP; 676 A; 624 C; 712 G; 1025 T; 0 other; tgtagaccct caattttgtc cctcgacact ggcatttatc cttcgggtgt cacatccacc 60 catcgttcgc atatggcacc actagggccc cttttgggct tagtcggtgt ccgagcctca 120 tatgggtttg tctgtggtcc attgcggtgc atatgtggtt cattttggag ggtcaccatg 180 gccattttcc tagttgttca catcacgcta taggaaggaa gtaaggtcat cccgatgttt 240 tagcttagtt ggggtttata ggggcatgtt gaggttcgga gcactcgggc ttgttttgat 300 cgtatctccc tcatccaaac tcggaatcaa gaaccgtttc tttttatgga ttccttattc 360 ttccagacac attctgtaaa attttcaaaa ttttttgcaa ccggtcggct ggttggcagc 420 cggttcagcc ggttcatcga gtcagccggt gtagaacact gatttttggt aattgttttg 480 atcatatctc cctattccaa acttggaatc atgtaccgtt ttttttaatg aattccttac 540 tctactagga atattctgta aaattttcag aatttttttc catcgattcg accagttggc 600 atccagttcg gccggatcag ccgattcatt gagtcagctg aggtaaaaca ctaattctag 660 taattttgag gcccaaatcc tacatggctc aggaccgtaa gctccagatc ggttttggga 720 aatgttgtgg gtccattttg ggccttggtt tgggttcctt gcagcccacc acgaatccat 780 atggattctt ggtggtgaag taagctgaaa actgaaggag tgagctagcc ttgtaagttt 840 aagaggagta atgaggggtg tggttcccat gctgatgaag gggatttcgg tgctgaaggg 900 gaaggaaccc aggaggctca aatgctgaga ggggtatgag tataaaaggt gagaggatag 960 gagagcaaaa gaccttttgg catttttgag agaggggata ttttgttggt gagaagaaca 1020 gagggtgggg agcatcttct gagttgagag tgtggaggaa agctacagcg tctcggtttc 1080 tggaagtcat catcagcgta catggatcat atttggtgga gattctgagg taagtatgct 1140 aaaaattttt tacctacagg tcatcttcat cgtcttcgta tgctttttct tctttctcat 1200 cctcttttat ttcctttgat gtgaagattg tattgcttgg gtgtggataa taaaggccac 1260 acatgtttgt tgttgattgg ttatgaatgg ttgaggatta ctgttgagga tgattgtttt 1320 cttgatgtgt tagaatcacg tttaggctca agtttaattc attcatcgtt ttcaattttg 1380 caccatggtt ggttgactct gtcagtcacg aggaacatct gaccttgctt tgtctggttc 1440 tcactcatcc gggctcggaa ttgagaaccg tttcttttgt ttgcttcctt aatcacttag 1500 gaactttctg accgaattta ggatttttta ccaaccggtt gaatcggttt ggaaccggtt 1560 caaccggttc agcaccatag ctggcagcct ctgtcagcca tgaggaacac ttgcctttct 1620 ttgtctggtt ctcactcatc cgggctcgga attgagaacc atttcttttt tttgcttcct 1680 taatcactta ggaactttct gaccaaattt gggatttttt accaaccggc tgaaccgatt 1740 tgaaaccggt tcaaccggtt cagcaccata gctggcagcc tctgtcagcc atgaggaaca 1800 cttgcctttc tttgtctggt tctcactcat ccgggctcgg aattgagaac cgtttctttt 1860 gtttgcttcc ttaatcactt agaaactttc tgaccaaatt tgggattttt tatcaaccag 1920 ctgaattggt tgggaaccgg ttcaaccggt tcagcaccat agctggctgc ctctatcagc 1980 catgaggaac acctgccttt ctttgtctgg ttctcactca tccgggcttg ggattgagtg 2040 tcgtttcttt tgtttgaatc ctcactcatt taggagtttt ctagaaaaat ttgggaattc 2100 ttctcaatag gttgtaccag ttgagaacta gttcaacctg ttctgctgga ggactttagg 2160 tagcccttga ttttggcatt tttcgagccc ttatccatgg gggctcaaac ccatttgcta 2220 tagggcactt gtgagccatc ttgaaggttt aagtcagtgt ttgatttcag ttagtatggg 2280 caattttgaa gttatgggtg gtgtggtcta gatgagtcta gtttgatttg tatgacattt 2340 ggggaatccc tacctcattt caaccagcta tcttcctttt ggcacaagct ttgatgcttg 2400 attttgaata catgttgcgt gactgactca ccctctgcta cagcgcttgg ctagggacca 2460 taggtacgca ccgttggctt tggttgttga attcatatgc atgcatggtg cttaatcttg 2520 actgtttgtt atgtgtttat ctgtgtttgg ctgacctttt atgcagcgct tggctaggga 2580 ccataggtac acacccattg ttttgtttgg ttgaattcat atgcatgcca aataccaatt 2640 aggattgtgt gattcatgac atctatttag cctagggttt catttgacct ttgacccata 2700 tgctcccaca tacccaattc attagtagag accgagtttc gggcctagag gggtgctacc 2760 tcgcatgagg taccttccca acgggtaacc tgatccccga acccagaatc tagttttcgt 2820 agaccgcttt ttccatactg gggtcattag gggtttttgt tcttacttaa ttttccccat 2880 tttaaaaaca aaaataaaaa gtaagtggcg actccaaaca acaccgttcc tcaccggggg 2940 cgggtttttc aaaactggaa aataccaact ttttcatttc tttcttttct tttaaaagcg 3000 agtcgcatcg gtccagtaga tcgggtgagg gtccaca 3037 // ID Gypsy-29_Mad-LTR repbase; DNA; EDCOT; 529 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-29_Mad-LTR. XX NM Gypsy-29_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-529 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1753-1753 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 529 BP; 156 A; 144 C; 90 G; 139 T; 0 other; tgtttgtacc atacttgacc aatcccgaaa ctaccaagca ccggtcaacg tcataccttc 60 aaggacccac tgaggggttc atgctgaggc acccctgccg aagcacaaga gtttccctcc 120 aaccaggagg ccaatcacag cacgacacat gtcaacgtca gaataaagct catagagtcc 180 cacatcgacc gcggacaaaa gctggagact ctcctcaact ataaaagaag accattctcc 240 tacaattaat ccctaatgtc attattgtac ttaaactagt cattagaact cactaatgat 300 gattatgctt gaacctatgt atttgtgtaa acccttcact attaatgaga actcctctac 360 tccgtggacg tagccaaact tagggtgaac cacgtacatc ttgtgtttgc ttccctatct 420 ctatctcttt acatattatc ctcactaggt gaccggagca accgagcgaa ggtcacaaac 480 ttgacacttt acgttgttcc aaagtcttca ctgattttgt gcatcaaca 529 // ID Copia-36_Mad-I repbase; DNA; EDCOT; 10968 BP. XX AC ACYM01002754; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-36_Mad-I; KW Copia-36_Mad-LTR; Copia-36_Mad_. XX NM Copia-36_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-10968 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1306-1306 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01002754; Positions 11908 22875. XX CC Positions [7237-7632] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 6115..7632 FT /product="Copia-36_Mad-I_1p" FT /translation="MVKNYLGRGLFKLLISLPRSYDSICAVIEHSKDIETL FT EIQEVVASMKGYEQRLDMHVENSTKKAFASLNVGSKFQKPSGFSGTQKSRK FT DWKNKGKKWDNKPNLVSKHNNSHDSNKTACKHCDKLHYGKCWFEGKPKCTN FT CNKFGHETRNCNGNKMVQKANYANQVDDMGTLFFACNSVTQVKVNNTWYID FT SGCSNHMTGNENLLMNVSRNLNARVKMGTGEVVSVAGIGTLVIKTKMGKKT FT HTRSDSGAGLEENLLNVGQMLEHGYYLLFGGNAVCIYDSWNLNGLFAKVQM FT TGNRCFPLTMMPATLLVLKASVSHCTQTWHKRLGHLNTRSLLQLREQEMVH FT GLPHLEDSKNVCEGCMLGKQHRDEFPRESVWRAKFPLELVYTDVCGPMQIA FT SNAGNKYFILFIDDCTRMTWVYFLRCKSEAFEYFKRFKTMTELQCGHKIKY FT LRSDRGGEFMSSEFSNYCNVSGIQRQLTMSYTPQQNGVSERKNRTMVEMAK FT TMLHEKGMPY" XX SQ Sequence 10968 BP; 3587 A; 2002 C; 1916 G; 3448 T; 15 other; ttctcccact tgagtatgac atatgaacca cagctctata aaacatggag gtgatcacca 60 agtctagagt aacagaaaac atatctccac attcaatttt acctaagcat cttaaagcat 120 ggaactcaaa agtctccttt gaccatcaca aaattaactt aagaatcaca acgtgcccaa 180 attgctctct gtattcatgt gaacatatgt ttacagtaat gtcaaaatca ttactcacac 240 ttttctaata taatctcagc acaacaattg tcaagacagc agttaataat caaaacctat 300 taactacgaa acattctata ttagaacagt acattcaata gttcaataaa ggtatcttgc 360 aacaaaatca caaaatgact tgcaaaccaa actatcatat aaatatgttc tctagtacaa 420 ttgatcacca aaatttggaa aaaattgaac ccttattgaa aaccaaaata atgactaaaa 480 actacctgag ataataaaac tcaaaacaaa acagaaacta acttagcttt tgggatagct 540 gcttcaatac aagcatgtca tagtgaagca acaacacagt cttgatacta gaacagatca 600 ctcccacttg tcaaaagatt ttaacacacc cattcgagct acatttccct tgaacacatt 660 attgggaaat gccttagtta aaggatctgc aattatcaaa ctagtcgata agaactgaat 720 ttcaatctcc cctttcttaa ccatttctct cactttaaga aacttcacat ccatcaatct 780 tgaagccgaa gttctcttgt tattcttgga aaaaaacact gctgtagaat tatcacacaa 840 cattctcaga ggtttcttca ctgaatctac aatcttcatt ttagcaataa aatttctaag 900 ccaaatagcc tatttcattc cctcaaatca tgccacaaat ttagcttcca ttgtagaagt 960 tgacataatt gtttgtttga cacttttcca agaaacagca ccttttttca tcataaaaaa 1020 tatagcctcc agttgacttc ctttcatcca catccccagt aagatctgaa tctctatagc 1080 caataatttc caaacaattt tctctgccat acaccaacat gaattcttta gttctttgta 1140 gataccttaa aactttcttt gcggttatcc aatgatattc acctggattt gattgaaatc 1200 tgcccaacaa gccaataatg aatgctaagt caagcctagt acagatatta gcacacatga 1260 gactaccaac taatgaagta taaggtttca tcttcatcaa ttcagcccca tgttcactct 1320 taggacattg atctcgagaa aacttattac ccttgtttac tggaacatca gtcttataac 1380 aatatatccc ttttaagaca aaccaagaag tttcctttgt ctatctctca caatttcaat 1440 tccaagtact taatgagcct cccctaaatc tttcatctca aagtttgtac tcaaaatggt 1500 cttggtttcc ataagcaatt gtaaatccga gctagcaagc aagatttcat caacatacaa 1560 aactaggaag atgaaattcg aacccttaaa cttaagatag atgcagtcat ccatcttgtt 1620 ctttacaaaa ccatgagttg taattacttg atcaaattta aggaaccatt gtcttgaggt 1680 ttgcttaagt ccataaattg acttcttgag cttgcagacc atcttatctt tccctctttc 1740 aacaaatcca ataagctgaa tcatttgaat ttcttcttgt aagtcaccat tcaagaaggc 1800 cgttttgaca tccatctggt gtaatttcag atcaaaatga gatgtcaaag tcataataac 1860 cctcaatgaa tccttagaag aaaccgatga gaatatgtca ttatagtcaa taccctcctt 1920 ttggttgaat ccctttgcta ccaatcgtgc tttatatctt ttaattttcc cagctgcatc 1980 tcttttagtc ttaaaggccc attttgcaac caataggctt gatttgtgat gaagagttga 2040 ccagtgtcca cactttctta tacattgatt ccaactctta ttccatagcc ttatgccata 2100 ctgttacttg agaactttga atagcttgat ggtaggtaat tggatcatta atatctctta 2160 tgtcgaactt agcttcttga agataaacat aatctgtaga aaaggccaat ttcctgtttc 2220 tattggattt cctcaaaggc tgctgaatat ttacatgatc tggacttgga atatgttgtg 2280 acttttctaa agtcggcgag gcattaacag tttcagtcat aagatgatct tttgctataa 2340 tttgtgtagt ctcggatcca attaattcct catctggatc agtagtttga gcaggtagtc 2400 ttggtaacac agagatatga ttatagtcca taagtaatga accatcatct ggttgatcta 2460 attcttcaaa ttcaaagcta tctcaaacca agtctgacac atcttcatct tctagaaaaa 2520 ttgcattatg tgtcttttga attctggtgt gtgcttagga caataaaatt tgaacccttt 2580 tgatttctca agatatccaa caaaatagca tgaactagtt cttggatcaa gtttcctttc 2640 attagggttg taaaaccttg cctctacctt acatccccaa acatggaagt gatgaaatgt 2700 tggtgttctt ccaatccata actcaaaagt tgtctttgga acagattttg aaggtactct 2760 attgagaata taatttgaag ttctcaatgc ttcaccccag agaaatccag ttaatttgga 2820 cctcgaaatt aggcttctaa caattcccat cagtgttatg ttcctcctct ctgcaactcc 2880 attctactga ggtgtaccat gagttgtgca ttgagccacc ataccttgtt gttgaagaaa 2940 gtgagcaaaa tgaccctttt gttgcccacc ttttgtatac ccaccaaaat attcccctct 3000 tctatctgat ctaacaattt taatcactaa gtttaacttt tttccacttc acttttaaag 3060 actttgaaac actcaaggac tgcaggcttg tctttgataa gaaagatata actatatcta 3120 aaaaagtcat ctataaaagc tcacaaaata tgaattccca caaatggttt taatagagaa 3180 aggtccacag acatccgtat gtataatttc aagcaaggca tgactccttt tagcatctaa 3240 ctttcttaca ttggttgtct ttcccttcat gcagtcaatg caatcagatg tgtttttaaa 3300 atcaatgtca ggtataaatt ttaatttcga cagttgcaaa atcctttctt tagaaatatg 3360 tgctaatcgt ttatgccaca atatgtaagt atcgtaaata tgcattctct tggttgttat 3420 atttaaaatc tgcaagctat ttgactccac tgaacattgc aatttccata aatcatcatg 3480 cataaaatct tttcctatta aagacccttt tctaaaaaaa ttcacgcatt catcatctcc 3540 catgaaaaca ccatcttgtt ttactaactt tgatgtagaa agcaagtttc tcctcattga 3600 gggcacataa agcacattaa ccacttgtaa cacaaaatta gttgcaaatt ttagtttaac 3660 aaggcctaca acttcaacta aaaccttagt tccctcacca acaaaaacat tatagcaact 3720 tgtttgtttt tgtttttgaa aaccttgtaa tgagttagtt atatgaatag atgcacccat 3780 gtcaaaccac caagagtttg taggaatttc aatgaggttt gattcttcac agacataaat 3840 atcagttcta cccttagccc tcaaccagtc cttgaatatc tcatagtctt ttctatagtg 3900 tcccttggtt ttagagtgat gccatctaat tttttcaaca ttcttagctt tcttcttaaa 3960 attgatcaat ttagaggaat tggaactttt agcaggtata gcagatttat cagaaaagct 4020 aggattggat ttagaaggtt taccagtatt agcattgtac tccttttttc ctttggatga 4080 atgcacgaaa ttgatagtct caacttcttt gcctttgcct ttgtcttgct tctatctgtt 4140 ttcttcttgc acacactgag ctatgagttc atccactaac caagttttat cttaggtaga 4200 ccttcaattg attgaacttt agaggtaagg cttgtagaat catgaacaca agctattttc 4260 acatatcttc atatctaacg aattcagttt cttaattgca tcagtcatct tcataatatg 4320 atccctaatt gatcctcctc cttcaaattt gtaagatgtg agaagagtca tgtactgagc 4380 aatttcagcc ttctgggatt ccttgaattt gttctcaata gctgcgaggt aatttttttg 4440 caaattcaca tctctttatg cctcctcgta caatatcagt cattccactt tccaatattg 4500 aaagtgcaac cttgtttgct ctagtccatc tttcaaactc caagttctca gctttagtgc 4560 tcttatcagt gagagccgca ggctgtggca tgtctagtac tatatcatac tcatttagtg 4620 tcaaaagcaa ttcagtttct cttctccact tcttataatt gcttccacca gtgagtattg 4680 gcacaacaac taaattcatg gttttaagtg aaactacaga atgacaacaa tgaaatcaac 4740 attttgaatc ccaaagagat tcttgatttc catcaattcc ctcacttgat tcctaatatg 4800 aatcaattta atcatatact tagccctgat ctaacaaaac aaggcaacca tagaatacac 4860 aattcacaag gaatcacaaa tagaggttca tgttcaaaat agcgacttta aagtcaccta 4920 taacatgcct acaatttctg cagaaccaaa ttagtaaaac caacaacatg tatattatgt 4980 tatagcaacg aaagcaatta ttcaatgcat agactcaaat atcagtttga aaagagcaat 5040 ttgattcaac aacgttttaa atacagccat gataaatggt aagtattaaa gcatctcaat 5100 cttgttgttg atgtttaagc tttgcaactg ctttctgatt taggtttcct gttttccttt 5160 gtaatttaag gtgtttgttc ttagtttgta atgtagggct caaattaaat caaagctaat 5220 aggctagatg tgtgtcatat ggcatagcaa ctcacttata ggtgagcatg tgttgtacac 5280 gtgagtgtgt gaggtggata agtgagttcg ccctcaacgg ctatatctca ccttccgctc 5340 tgtgcttcta aatgtatcaa ttcagtcata actgaataga atccaaagga gaaatctttt 5400 catcttcttc gcaccttcat tccttcattt tctgagcaga gatcataatc tcattgattt 5460 cttttttatt ttgttctttg aaacttcata aaatcagaaa cccctataaa atcacaaact 5520 ctaacatggc ttcagagcta ggttcatcgc tttaatctgg gcgtgaatct atgatttatg 5580 tgttcttaag tgaattgcgc tttgaaaatt tgtgaaaatc gaagatctga gtctaaatgg 5640 ctggatcaac gagttttgag cttcgcactc ccattttcaa tggtgagaac tatgaattct 5700 ggaatatcaa aatgcatacc attctcaagt ctcatggact gtgggagctc gtagagattg 5760 ggttcactat cccagaaaca tctactgtgg ttgtggtagc tgatgaaaag aaggagaatg 5820 atgcagctac tgaaactcca acaaatgttg caaagatcat aatgaaggat gcaaaggctc 5880 ttgggttgat ccaaggagct gtgactgatc agattttccc caggatctct aacgaagaaa 5940 cctccaaggg agcttgggat attctatagc aagaattcag aggtgacaaa caggttagaa 6000 atgtgaaatt acaaggttta agccgagaat ttgagtacac taggatgaga gatgatgaat 6060 ccttatctac ataccttact aaattgtttg accttatgaa tcaaatgagg ggttatggtg 6120 aagaactatc tagggagagg gttgttcaaa ttacttataa gcttgcctag aagttatgac 6180 tctatctgtg ctgtgattga acattcaaag gatattgaaa ctcttgaaat ccaagaagtg 6240 gttgcctcta tgaagggtta tgaacaaagg ctagatatgc atgttgaaaa ctctactaaa 6300 aaggcatttg ctagtctaaa tgttgggtct aagtttcaaa aacccagtgg gttctccggt 6360 actcaaaagt caaggaaaga ttggaagaac aaagggaaaa agtgggataa caagcccaac 6420 cttgtctcta agcataataa ttctcatgat tcgaacaaaa cagcttgcaa acattgtgat 6480 aaactgcact atggaaagtg ctggtttgaa ggaaaaccta aatgcacaaa ttgcaataaa 6540 tttggtcatg aaaccagaaa ctgcaatggg aacaaaatgg tgcagaaggc caactatgca 6600 aatcaggttg atgatatggg aaccttattc tttgcttgca attctgtgac tcaagtgaaa 6660 gtcaataata cttggtacat agatagtggt tgtagcaacc acatgacagg aaatgaaaac 6720 ttgttgatga atgtgagtag aaacttgaat gcaagagtga aaatgggaac tggtgaagtt 6780 gtgagtgtag caggaatagg tacacttgtc attaaaacta agatgggaaa aaaaacacat 6840 acaagaagtg attctggtgc tggcttagag gaaaatctcc taaatgtggg acaaatgttg 6900 gaacatggtt attatctact atttggtggt aatgcagttt gtatctatga tagctggaac 6960 ttgaatggat tgtttgctaa ggttcaaatg actggcaaca ggtgttttcc cttaaccatg 7020 atgcctgcta cactactagt actgaaagct agtgtatctc attgtactca gacttggcac 7080 aagaggctag gtcatctaaa cacaagaagt ttgttgcaac ttagggagca agaaatggtt 7140 catggactgc ctcacttgga agattccaag aatgtctgtg aaggatgtat gcttggcaag 7200 caacatagag atgaatttcc aagagaatct gtttggagag ctaaatttcc acttgaattg 7260 gtatatacag atgtctgtgg tccaatgcaa attgcttcaa atgctggaaa caagtatttc 7320 attttgttca ttgatgattg tactagaatg acatgggttt attttctaag atgcaaatct 7380 gaggcatttg agtatttcaa aaggttcaaa acaatgacag aattgcagtg tggacacaag 7440 atcaagtacc taagaagtga tagaggtggt gagttcatgt cttctgaatt cagtaactat 7500 tgcaatgtct ctggtattca aaggcaacta accatgtcat acacaccaca gcagaatggt 7560 gtgtctgaaa gaaagaatag aactatggtg gaaatggcaa aaactatgct acatgaaaaa 7620 ggcatgccat actagttttg ggcagaagtt gtgcacattg tagtatatct cctcaacagg 7680 tgtcccacta ggtctttgga taaaatgact cattttgaag cctatagtgg aagaaaacct 7740 ggaattgcat atttaaagat ctttggttta gtatgctatg tcccatgaat ttaagacaca 7800 agcttgaatg caacagtcac aaatgtgtct ttgtggggta tggaaccagt gagaaaggat 7860 acaaggtatt tgatcctatc actaataaaa ttatattgtc tagagaggta gtatttgatg 7920 agagtgacag gtgggattgg aatgtaagct ctgaaaaata ttttgataca tcaattacta 7980 ctgatatagc agaatatgaa ccaactcaag gattagaagt tcaggatgac attatactcc 8040 ctgagatcac ttctgatatt tcacaagaaa gcttgagttc caatgttgat ggttcaaatt 8100 cacagattga tctatcacag agctatgatt tcactccaaa gaaatggaga tccttatatg 8160 aagtttttgc acagtgtaat gtttgcatta tggaacctca aagctatgaa gaggctgctc 8220 tagatttatc atggatgaaa gctatgcaag ttgagttaga catgattgaa aagaataata 8280 catggatgct ggtagacaga ccatctagca aacctgtgat aggagtgaag tgggtataca 8340 aaacaaaact gaatcttgat ggaagcattc agaaaaaaca aagctagact ggttgcaaaa 8400 ggttattcac agaagccagg aattgacttc aatgagacct ttgcaccaat tgctaggctt 8460 gacaccataa ggactttgat agctcttgca gcttataaag aatggcaact ctttcagttg 8520 gatgtaaatt ctgcattcct caatggtgta ctcaaggagg aagtctatgt tgatcaacct 8580 caaggtttta ccatagaagg caaggaggat aaagtgtaca agttaaacaa ggcattgtat 8640 ggtcttaagt aagctccaag agcttggtat gatgaaatcg attcctactt caccaatcct 8700 agcgaagcca ttctagacac taaggttgaa aactcaggga ttctcattgt ttctgtgtac 8760 gttgatgata ttatgtacac tggtagtagt gacacattgc tggaaaattt taaaaatgac 8820 acgatgcagc actatgagat gactgatctg ggcttgctgc accattttct tggtatggga 8880 gttgtacaaa ccaagaagag catctttata catcagaaga aatatgcaat gaagttgcta 8940 gagaaatttg gactaaagag ttgtaaatct gtgggaacac cacttgtagc aaatgaaagg 9000 ttatgcaaga atgaaggaag tgaagttgca gatgagtctg agtataggaa attggtggga 9060 agccttttgt acttcactgc cactagacaa gacataatgt ttggtgctag tctcttggca 9120 agattcatgc atggtccaac taagaagcat atgggaacag caaaaagagt actaagatac 9180 attcaaggta ctatggactt tggtattgaa tatgtaaaag gaaagtcagc actgcttatt 9240 ggatactgtg atagtgactg gtctgggagt gttgatgaca tgagaagcac attaggatat 9300 gctttcaatc ttggctcagg tgtattctct taggcatcaa tcaaacaaaa cacagtggca 9360 ttgtccactg cagaagctga atacataagt gttgctgaag caacatctca taccaagtgg 9420 ttgaggtttg ttctagaaga ttttggagaa gaacaggttg aacctactat gctaatatgt 9480 gataacactt cagcaatagc tattgccaag aatcttgtgt ttcattagaa aacaagacac 9540 atcagcagaa aatttcattt catcagggat gtaatacaag agatggagat tgagcttgtt 9600 tactgcaaat ttgaagaaca aatggcagat atcttgacta aggctctacc aaaggaaaag 9660 ttcaactatt tcagagagat gttaggagtc aaatcagctg ccagcttaga ggagagtgtt 9720 gatgtttaag ctttgcaact gctttctgat ttaagtttct tattttcctt tgtaattcaa 9780 ggtgtttgtt cttagtttgt aatgtaaggc tcaaattaaa taaaatctaa taggctagat 9840 gtgtgtcaca tggcatagca actcacttat aggtgagcat gtgctgtaca cgtgagtgtg 9900 tgaggtggat aagtgagtgc gccttcaacg gctatatctc accctccatt ctatgcttct 9960 agatgtatca attcagtcat agctgaatag aatccaaggg agaaatattt tcatcttctt 10020 cgcaccttca ttccttcatt ttctgagcag agatcataat ctcattgatt ccttttttat 10080 tttgttcttt gaaacttcat aaaatcagaa acccatataa aaatcacaaa ctctaacact 10140 tgctgtcaaa cactagtctt ttcgatcaat cataggttga ttttaaattt taacaataga 10200 tctaaacaga cataccttca gtgaagattc gagattagaa gaaaacattg atcgtgatga 10260 tcaaaagtga agagaatcaa ggatttctta atcgccataa catcaagtaa agccaagaag 10320 aagttaaacc gagagcccag aaaacataac ggtcgaaatt tttaaaagga agttataacg 10380 gctctttttr kttttttttt tttttttttt ttttttttww aaaaaaacka ttgtttacgt 10440 ttwactattt ctttttgggt taractagat cccagagatg attcagtcat gttttgttct 10500 tgaaccaaat tttgaattca atggtctaaa tattaatggc tctgatacca tatgaaagat 10560 atacaaatat ataccaacgt tattcaccac aagtatgcca attaaatcac cacaaaacaa 10620 gaacaaccta aacattcatc aatcaaacat gtttatraaa attcgataca tatgcaraga 10680 cactaacctg caaaacctgg tgtaataaat raagccattg tagcttgttr atctgataac 10740 cttctccttt tttrcaaaca caaatgctct ccaaacaata ggtatttaaa atataatgag 10800 taaaccatgc caagagcagt gattaaaatc atatatatat atatagggtt aawcyaatta 10860 ttcccctatt agaattctta tagaacttga acaagtaatc cmtaaaagtg ataaaagtga 10920 ccctcaatgg acaaagtaca gaaataagtc ccacagttaa caaggact 10968 // ID SHACOP9_I_MT repbase; DNA; EDCOT; 4402 BP. XX AC AC144731; XX DT 16-JAN-2007 (Rel. 12.01, Created) DT 16-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP9_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; SHACOP9_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4402 RA Shankar R. and Jurka J.; RT "SHACOP9_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 82-82 (2007). XX DR EMBL/GenBank/DDBJ; AC144731; Positions 77292 81693. XX CC Internal region sequence is flanked on both sides by intact LTRs CC The sequence has conserved domains for gag-pol polyprotein, CC Arginine methyltransferase protein and integrase. XX FH Key Location/Qualifiers FT CDS 2487..4364 FT /product="SHACOP9_I_MT_2p" FT /translation="MGYSNSHKGFVCYDVSNHRLRVSRNVTFFDNQFMFHS FT ISPDINDIAILPNFSIMPQSIERYKPGFTYVRQRIKQVPTAPSDTEPPPDP FT EPVEPRRSGRTSRAPDRFSPDRYDSKHTSLTASLSSISIPTCYSQAVKDVR FT WIKAMNEELQALQESFTWDIVSCPPDIKPIGCKWVYSVKLNSDGSLNRYKA FT RLVALGNKQEYGIDYDETFAPVAKMTTVRTILSIAASNGWSLHQMDVKNAF FT LHGDLTEDIYMTPPQGLFSSSKGVCKLKRSLYGLKQAPRAWYEKFRSTLLG FT FSFCQSQYDSSLFIHSTSTGIVLLLLYVDDMVITGSDNASIQRLKEQLHAS FT FHMKDLGNLHYFLGLEVHATSKGIFLHQHKYATDLISMAGLQSANQVDTPL FT EVNVKYHRDDGDLLPDPLLYRQLVGSLNYLTITRPDISFAVQQVSQFMHSP FT RHLHLAAVHRIIRYLKGSSHRGLFFSIGNSPKLSAYSDADWAGCPNTRRSV FT TGWCMFLGSSLISWKSKKQARVSKSSTESEYRAMSAACSEIIWLRGLLAEL FT GFPQTEPTSLYADNTSAIQIVANPVFHERTKHIEVDCHSIRDAYDDRLISL FT PHVSTQLQIAIFLPRLFLAHVISFLLAN" FT CDS join(358..2316,2320..2610) FT /product="SHACOP9_I_MT_1p" FT /translation="MTSEKAKDFCVRFTGKNYPAWEFQFRMYVKGNKLWSH FT LDDVSKAPTEKAALEEWEYKDAQIISWILSSIDPQMINNLRSFSTAQEMWN FT YLKRIYNQDNAAKRFQLELEIANYKQGNLYVQEFYSGFLNLWTEHSAIIHA FT DVPKASLAAVQEVYNTSRRDQFLMKLRPEFEVVRGALLNRNPVPSLDTCVG FT ELLREEQRLLTQGTMSHDAFISEPVPVAYAAQSRGKGRDMRQVQCFTCKQF FT GHVARSCTAKFCKYCKQNGHVIFDCPIRPPRRTQYPTQALHATTSSAAPPT FT ITSASDGGSLQPEMIQQMVLAALSNMGIHGKSSNVSRPWFLDSGASNHMTG FT SSEYLHNLHSYHGNQQIQIADGNKLSITDVGDINSDFQDVLVSPGLASNLL FT SVGQLVDNNCNVNFSRAGCLVQEQVSGKVIAKGPKVGRLFPLQFISSHLSL FT ACNNVLNSYEDWHRKLGHPNSTVLSHLFKTGLLGNKQVVCTASISCPVCKL FT AKSKTLPFPSGAHRASNCFEMIHSDVWGMSPIASHAHYKYFVTFIDDYSRF FT TWIYFLRSKSEVFSMFKKFLTYVETQFQASVKIFRSNSGGEYMSHEFQEYL FT QHKGILSQRSCPNTPQQNGLAERKNRHLLDVTRSLLLQASVPPRFWVEALS FT TVCFLIVFLLQLLNLILLSFVYLNFSLIIVIYILLGVCVLSTYPCLKGISL FT EHSLFSVHLWGTVTLIRALFVMMSLIIAYEFRGMLHFLIINSCFILFLLT" XX SQ Sequence 4402 BP; 1092 A; 914 C; 871 G; 1525 T; 0 other; ggtatcattc taggtacgat cccaaatttt ccagcttttg agtctttctt ggttttaggt 60 ctagccgcca cttcctgtga agcacttggt ttctgttcgt gttttttgtg tgttttcgcc 120 gtcacagatc gtaatttcga tttcttggtt ctaacttgtg attcgattct gattcttggc 180 tcttgttatt tgtggctttc ccttgttttg ttatcagcgg cttctccatt cacgaattgt 240 tttgttacta tttttgttct cataaaggtc acgtgaagct cttccttgtc cacttgcctc 300 tacgtgtcag tattcctttt cacttaagtg ctgtttgttg tttggaatat tgttaacatg 360 acttccgaga aagcaaaaga tttttgtgtt cgatttaccg gcaaaaatta tcctgcttgg 420 gaatttcagt ttaggatgta tgtcaaagga aacaaattat ggagtcacct cgatgatgtc 480 tctaaggcac caacagaaaa agctgctcta gaagagtggg aatacaaaga tgctcaaatt 540 atctcttgga ttctcagttc cattgatcct caaatgatta ataatttacg ttccttttca 600 actgctcaag agatgtggaa ctatttgaag cgtatttata atcaagataa tgcggccaag 660 cgttttcagt tggagttaga gatagccaat tacaaacaag gtaacttgta tgttcaagag 720 ttttattctg gttttttgaa cttgtggaca gaacactctg ctattataca tgctgatgtt 780 cccaaggctt ctctcgcggc tgtccaagag gtctacaaca ctagtaggcg tgatcaattt 840 ctcatgaagc ttcgtccgga atttgaggta gttagaggtg ctttgctgaa taggaatcct 900 gttccttctt tggatacttg tgttggtgaa cttctcaggg aggaacaacg tctccttact 960 caaggaacca tgtctcatga tgctttcata tctgaaccag tgccagttgc atatgctgct 1020 caaagtagag gtaagggacg tgatatgcga caagtacaat gtttcacctg caaacaattt 1080 gggcatgttg ctcgcagctg taccgctaag ttttgcaaat actgcaaaca aaatggtcat 1140 gttatctttg attgtcccat ccgtccccca cggcgaacac aatatccaac acaagcttta 1200 catgccacta ctagctctgc agcgcctcct acaattacta gtgcatctga tggtggttct 1260 ctacagcctg aaatgattca acaaatggta cttgctgctc tatcaaatat gggaattcat 1320 ggtaagtctt ctaatgtttc tcgtccatgg tttcttgatt ctggtgcatc caatcacatg 1380 acgggttcct ctgaatactt gcacaattta cattcttatc atggtaatca acaaattcaa 1440 attgctgatg gtaataaact ctccatcact gatgttggtg acatcaactc tgattttcaa 1500 gacgtgcttg tatcacccgg acttgcttct aatttattgt cggttggtca attggtggat 1560 aacaattgta atgttaattt ttctcgtgct ggttgtcttg tgcaggaaca ggtgtcgggg 1620 aaagtgatcg cgaaggggcc taaagtggga agattgtttc cgcttcagtt tatttctagt 1680 catttatctc ttgcttgtaa taatgttttg aactcttatg aggattggca tagaaaattg 1740 ggccatccaa actctactgt tttgtctcat ttatttaaaa ctggtttgtt gggaaataaa 1800 caagtcgttt gtactgcttc tatttcatgt cctgtttgca aattggctaa aagtaaaaca 1860 cttccttttc cgtcaggtgc tcatcgtgca tccaattgtt ttgagatgat tcatagtgat 1920 gtgtggggaa tgtctccaat agcttctcat gctcattata aatattttgt cacatttatt 1980 gatgattaca gtcgttttac ttggatatat tttcttcgat ctaagtctga ggtgttttct 2040 atgtttaaga aatttttgac atatgttgaa actcaatttc aagcaagtgt taaaattttt 2100 cgctctaact ctggtggtga atacatgtct catgagtttc aggagtacct tcaacataag 2160 gggatcttgt ctcaacgatc ttgtcctaat accccgcaac aaaatggtct agcagagcga 2220 aagaatcgcc atttgcttga tgtgacacgc tctttacttc ttcaagcttc cgtgccaccc 2280 cgtttttggg tggaagctct ttccacagtg tgtttttaat taatcgtctt ccttctacag 2340 ttattgaatt tgattctcct ttctttcgtc tatttaaatt tcagcctgat tatagtgatt 2400 tacatacttt tgggtgtgtg tgttttgtcc acctacccct gtttgaaagg cataagcttg 2460 gagcacagtc tgttcagtgt gcatttatgg ggtacagtaa ctctcataag ggctttgttt 2520 gttatgatgt ctctaatcat cgcttacgag tttcgaggaa tgttacattt tttgataatc 2580 aattcatgtt tcattctatt tctcctgaca taaatgatat tgctattctt cccaattttt 2640 ctattatgcc tcaatctata gaacgttaca agccaggatt tacatatgtc agacaacgca 2700 ttaaacaggt tcctactgcc ccttccgaca ctgagccgcc acctgatcct gaaccagtcg 2760 aaccaagacg ttctggtcga acatctcgag caccagatag attttcccca gacaggtatg 2820 attccaaaca tacgtctttg actgcctcac tctctagcat atccattcct acttgttact 2880 cacaggctgt taaagatgtt cgctggatta aagcaatgaa tgaggaactt caggcacttc 2940 aagagagttt tacatgggat attgtttctt gtccacctga tatcaaaccc ataggttgca 3000 aatgggtgta ttctgtgaaa ctgaattctg atgggtctct caaccgttac aaggctcgat 3060 tggttgcctt aggaaacaag caggaatatg gaattgatta tgatgagaca tttgcaccgg 3120 ttgccaaaat gacaactgtt cgcacgatac tctccatagc tgcttctaat gggtggtctc 3180 ttcatcaaat ggatgttaag aacgcttttc ttcatggtga cctgactgaa gatatttata 3240 tgactcctcc tcaaggtcta ttctcgtcat ctaagggtgt atgcaagctc aaacgctctt 3300 tatatggttt gaaacaagcg cctagagcat ggtatgaaaa attccgctcc actctacttg 3360 ggttctcttt ttgtcagagt caatatgatt cgtctctatt tattcatagc acgtctacag 3420 gaattgtcct gcttctctta tatgttgatg atatggttat tactggttct gataatgctt 3480 ccattcagag acttaaagaa cagttacatg cctcctttca tatgaaagat cttggtaacc 3540 tgcattattt tcttggtctt gaggttcatg ctacatcaaa gggtatcttc ctccatcaac 3600 acaagtatgc caccgatttg atttccatgg cgggtctcca atcggctaat caagtggata 3660 ctcctcttga ggttaatgtt aaatatcatc gtgatgatgg tgatctcttg cctgatcctt 3720 tattgtatcg acaacttgtg ggtagtctta attatttgac cattactcgt cctgacatat 3780 ctttcgctgt tcaacaagtg agtcaattca tgcattctcc gcgtcatctt cacttggcag 3840 cagttcaccg tataattcgt tacttgaagg gaagctctca tcgtggccta ttcttttcca 3900 ttggaaattc tcctaagttg agtgcttata gtgatgccga ttgggcagga tgccctaata 3960 ctcgacgctc tgttactggt tggtgcatgt ttcttggctc ttcattgatc tcatggaaaa 4020 gtaagaaaca agcacgagtc tctaaatctt ctactgaatc tgagtatcgt gccatgtctg 4080 ctgcttgttc agaaataatt tggcttcgtg gtcttttggc tgaacttgga tttcctcaga 4140 cagagccaac ctcactttat gctgacaata cgagtgccat ccagatcgtt gcaaatcctg 4200 ttttccatga gcgcaccaag catatcgaag ttgattgtca ttcaattcgt gacgcctatg 4260 atgaccgact aatatccctt cctcatgtca gtactcagtt gcaaattgca atattcttac 4320 caaggctgtt cctcgcccac gtcatcagtt tcttgttggc aaattgatgc tcatcgacca 4380 gccgcatcaa tttgaggggg ga 4402 // ID Copia-95_Mad-LTR repbase; DNA; EDCOT; 286 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Copia-95_Mad-LTR. XX NM Copia-95_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-286 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1729-1729 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Begining and ending with TA-TA. XX SQ Sequence 286 BP; 81 A; 35 C; 47 G; 123 T; 0 other; tattaaccat agtcattagt gatgacatgg ttacttagta atgaagaata tagttagttg 60 aaatgtgttg gtaggttgtc ataaggataa gattggttag tatagttaga agggtattat 120 tgtaattagg ttatatggct atataaggga ttgtatagct atcatttcct taagttcttt 180 tgtatacatt ttctccattt taatcaatac aatctttctg gtttttctct ctatcatctt 240 catcttcctt tgtaccaatt cttcatcttt tacaatgtag ttaata 286 // ID RAGYPSY2_LTR_MT repbase; DNA; EDCOT; 1622 BP. XX AC AC148525; XX DT 07-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A LTR sequence from Medicago truncatula. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR retroposon; Gypsy; Interspersed element; RAGYPSY2_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1622 RA Shankar R. and Jurka J.; RT "RAGYPSY2: LTR retroposon from Medicago truncatula."; RL Repbase Reports 6(11), 586-586 (2006). XX DR EMBL/GenBank/DDBJ; AC148525; Positions 81030 82651. XX CC This sequence shares features with long terminal repeat sequence CC of GYPSY_LTR_MT, from Medicago truncatula. XX SQ Sequence 1622 BP; 664 A; 186 C; 302 G; 470 T; 0 other; tgtgctcgtg attttcggat atcaaaccat taattgatat gaatcgttaa tctttgaact 60 ctcgattttt attcgtggga agggaaaaaa tgagtaaaaa ccctcatcga gactttggat 120 tcgggggttg gttatgcaaa gggaaggtgc tagcacccta agcatctacg gtattccgta 180 ggaacctctt acctaattta ccttgtgcta aattgatttg cttacttgaa aattattacc 240 taaaaatcta agtgaaagaa tggagggaga agaagtatgt ttttggttat ttttatttga 300 tttggaagga taaaaaatcc tatgcctaca tacccttaaa gaaaagggat caaaaccaat 360 gtagttcacc tcaaaaattt ctttggtggg ttaggttgat tttaagattt ttgaaaatgg 420 gttttaagaa aagaaagagg cctcaaggca tgagagaaaa aataaggtga ggttgttcac 480 gttttaatta caagaaaatc aagtctaata tgaatattaa ttcaattaag catttgatta 540 agaaaataaa aaggaaagac acttgggtta caaaccaagg tttattaaga aaatattttt 600 ggagttttgc agattatttg catgtttttg ttgttttttg gaatattaaa tgaaaattaa 660 actaacggag caataaaaaa tataagcacg tggatttttg tagtgacgtt ggatcaccac 720 aaaatcccta atctaatttt ttgcattttt aggactctct ctaatggcgg taaagaaata 780 aaaggacaca cacacccaca cacttttctc atttatattt acattggacc taaatacatt 840 ctaattgctg gaaaataaat aacaataatt aaaatgctaa ataaaataaa ataaaaatgc 900 aaaaatgcta aaaagaaata aaatgcaaga aaataaaaga aatggacaac cgaagggaca 960 aaaattaccg aagggacaaa attccgaagg gacttattcc gaagggacag aaaaaggagg 1020 gagaagaaaa gaatagctcg tcaacacaag ctaaagaggg agaagagaga aaagttcttt 1080 gacaactcaa gagaactttt ggtgtgtgaa attgtgtgga atgagggctc tatttatagg 1140 tgaggaggtt gatgaaaaaa ggaaaaatgg tttaatggaa atgatggaca attatggtga 1200 attttgaaaa aggaatgtta aagttgacac ttgacttgaa aattttttta gatcttgtac 1260 attttatttt ggacctattg acactttgtt ttttttttac actaattaat taaaaagaaa 1320 taaaataaat ctaatacgaa ataaaataaa acaaattaaa ctaaatcatg taaagaaaaa 1380 taaaattaaa agatggaaaa taaaaaatta ttaaatataa aaaaaagtaa ctaatcttaa 1440 aattaaaatt aataaaagaa aataaaaaga gaaaagaggg tccgactcgg aataaaaaat 1500 gaggtacttc aaagtaacct ctttgccaaa atttcgtctg aaacggcgaa aattctcaac 1560 tttaaaaata cgaataaaat gggtaagaat agaggaaagt ggtcaaaatt tggggtatga 1620 ca 1622 // ID Copia-67_VV-I repbase; DNA; EDCOT; 4271 BP. XX AC chr17; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-67_VV_; KW Copia-67_VV-LTR; Copia-67_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4271 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr17; Positions 10726154 10721884. XX CC Positions [1933-2184] - Integrase core CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS 2077..4269 FT /product="Copia-67_VV-I_3p" FT /translation="MKYWHYAFQTATFLINRMPSKVLEYDSPYFTLFRRHP FT DYKSFRVFGCLCYPFIRPYNTHKLQYRSVQCLFLGYSLNHKGFLCLDYATG FT RVYITPHVVFDESTFPLAQSKSSSSSNDTSAEGSTPALITPPSFPCLLPDS FT KISHASIDSHSLSTSESPIPTTSSSPLDTSSSSPAIDLSPKSVPEPHITAL FT APRMTTRSMRGITKKKTILDLSAIKVSEPSTLKQAFKDPNWTNAMEMEIAA FT LHRNHTWDLVEQPPNVNVIGCKWVYKLKHKPNGSIERYKARLVAKGYNQTH FT GLDYFETFSPVVKAATIRIILIVALSFKWEIRQLDVHNAFLNGELEEQVYM FT SQPPGYFDTQFPNRVCRLKKALYGLKQAPRAWFQRLSSALLQWGFSMSRTD FT SSMFLHFGKATTLIVLVYVDDILVTGSSSTQISSLIAKLDSVFALRDLGQL FT SFFLGIEVSYNEGSMTLSQTKYISDLLHRTEMFDTKPAKTPGAVGKNLSKF FT DGDPMADVTHYRSVVGALQYVSLTRPDIAFAVNKACQFMQQPTTAHWLSIK FT RILRYLRGTMQDGLLFSPSSNLTIEGFTDADWGAHLDDRRSSSGYLVYLGG FT NLVSWSSTKQKVVSRSSAKFEYRGLVFATAEIVWMQALLQELCVPIPAIPL FT LWYDNISAYHMAKNPVFHARTKHIEIDLHFIRDQVMRGKIQLHFVPTEEQP FT VDLLTKHLTSSRFLSLKSQLCIAPRPFHLRG" FT CDS join(70..930,934..1929) FT /product="Copia-67_VV-I_1p" FT /translation="MASTPTQSSSSSGSIGSGQSSTMASIPSYQMLNHTLP FT VKLDWTNYILWRSQIDNVIFANGFEDFIDGTSICLEKDLSQGVMNPAFVAW FT RRQDRTILSWIYSSLTPGIMAQIISHNTSHSAWNALESIFSSSSRARIMQL FT RLELQSTKKGSMSMIDYIMKIKGAADNLAAIGEPVSEQDQVMNLLGGLGSD FT YNAVVIAINIRDDKISLEAIHSMLLAFEHRLEQQSSIEQMSANYASSSNNR FT GGGRKFNGGRGQGYSPNNNNYTYRGRGRGGRNGQGGRQNSSPSEKPCQLCG FT KFGHTAQICYHRFDISFQGGQTTISHSLNNGNQNNIPAMVASASNNPADES FT WYLDSGASHHLTQNLGNLTSTSPYTGTDRVTIGNGKHLSISNIGSKQLHSH FT THSFRLKKVFHVPFISANLISVAKLCSKNNALIEFHSNAFFVKDLHTKMVL FT AQGKLENGLYKFPVFSNLKPYSSINNASAFHSQFSSIVENKAELWHNRLGH FT ASFDIVSKVMNTCNVASRKYKSFVCSDCQLAKSHRLPTQLSNFHASKPLEF FT VYTDIWGPASIKSTSGARYFILFVDDYSRYTWFYSLQTKDQALPVFKRFKL FT QMENQFDTKIKCLQSDNGGEF" XX SQ Sequence 4271 BP; 1188 A; 896 C; 818 G; 1369 T; 0 other; gagctctcat tcaaggtttg aattttttct tctctttctc actttctctc tgtttctctc 60 gatccaaaca tggcctctac tccaacacag tcttcttctt cctctggttc gattggatct 120 ggacaaagct caacaatggc gtccattcct tcctatcaga tgcttaatca cactctgcct 180 gtgaaacttg attggacgaa ttacatccta tggagatctc agattgataa tgtcattttt 240 gctaatggct ttgaggattt cattgatgga acctctatct gtctggagaa agatctgagt 300 caaggagtga tgaatccagc ttttgttgct tggaggagac aagatcgaac aatcctcagt 360 tggatctact cgtcgctcac accaggtatc atggcacaga tcataagcca taatacttct 420 cactctgctt ggaatgcctt ggaaagtatt ttttcatctt cttcaagagc taggataatg 480 caactcagac tcgaattaca atccacaaag aaaggatcaa tgtcgatgat agactacata 540 atgaagatca aaggagctgc tgataatcta gctgctattg gagaacctgt ctcagaacaa 600 gatcaggtta tgaatcttct tggaggtctt ggatccgatt ataatgctgt tgttattgct 660 atcaacatta gagatgataa gatctctctt gaagctatac atagtatgct attagccttt 720 gagcatcgtc ttgagcaaca aagctcgatt gaacaaatgt ctgccaatta tgcctcttcc 780 tctaataaca gaggtggtgg aaggaagttt aatggaggtc gtggacaagg ctactctcca 840 aataacaata attacaccta tagaggtcgt ggacgtggag gtagaaatgg acaaggtgga 900 aggcaaaatt ccagtccaag tgagaaacct tagtgtcagt tatgtggtaa gtttggccac 960 actgctcaga tctgttatca caggtttgat atctcttttc aaggaggtca gactactatt 1020 tctcattctt tgaataatgg gaatcaaaac aatatacctg ctatggttgc ttctgcttct 1080 aataatcctg cagatgagag ttggtatttg gattctggag caagtcacca tctgactcaa 1140 aatttgggga atctcaccag tacttcacca tacacgggaa cagatagagt cactattggt 1200 aatggtaagc atctctccat ctccaatatt ggctctaaac aacttcattc tcatacacat 1260 tcttttcgac tcaagaaggt gtttcatgtt ccctttatct cagctaattt gattagtgtg 1320 gctaagttat gctcaaaaaa taatgccttg attgagtttc attctaatgc tttctttgtg 1380 aaggatctac acacgaagat ggttcttgct caaggcaagc ttgaaaatgg actttacaag 1440 tttcctgtgt tcagcaatct gaaaccttat agtagtatta ataatgcttc tgctttccat 1500 tcccaatttt ctagtattgt tgaaaataaa gcagagttat ggcataatag actaggccat 1560 gctagttttg acattgtttc aaaagtcatg aatacttgta atgttgcttc taggaaatat 1620 aaatcctttg tttgttctga ttgtcagtta gctaaaagtc atagactacc cactcagctc 1680 tcaaattttc atgcatctaa acctttagaa tttgtttata ctgatatttg gggacctgcc 1740 tcaattaaat ctacatctgg agcgagatat ttcattcttt ttgtagatga ttattctagg 1800 tatacttggt tttattcatt acaaacaaag gatcaggccc ttcctgtctt taagcgattc 1860 aagcttcaaa tggagaatca gtttgacacc aaaattaagt gcttacagtc tgataatggt 1920 ggagaatttt gatcttttac gtcttttctt caagcagttg gtattgccca tcgattttcc 1980 tgtccataca actcagctca aaatggtaga gttgagcgga agcaccgaca cgtagttgaa 2040 actgggttgg ctttgttatc tcatgcttcc ttgccaatga agtactggca ctacgctttt 2100 cagacagcaa cttttcttat caatcgaatg ccaagcaaag ttctcgagta tgactctcct 2160 tactttactc tttttagaag gcatcctgat tataaatctt ttcgtgtatt tggctgcctt 2220 tgttatcctt tcattcggcc atacaacact cataaattgc agtacagatc tgtccaatgt 2280 ctttttcttg gctatagttt gaatcacaag gggtttttat gtcttgatta tgcaactgga 2340 agagtctata ttactcccca cgtggtcttt gatgaatcaa ctttcccact tgctcagtcc 2400 aagtcttcca gttcgtctaa tgacacttca gcagaaggct ctacccctgc ccttataact 2460 cctccttctt ttccatgtct tctcccagat tcaaaaatca gtcatgcttc catagattct 2520 cattctctat ccacaagtga aagtcctatt cctacaacct cttcttcacc tctggacaca 2580 tctagttctt ctcctgctat agatttatca cctaaatctg ttccagaacc tcatatcact 2640 gctcttgctc cacgaatgac aacaaggtcc atgcgtggta taaccaagaa aaagaccatt 2700 cttgatctct ctgccataaa ggtttcagaa ccatctactc tcaaacaagc cttcaaagat 2760 ccaaattgga ctaatgctat ggaaatggag attgctgctc ttcatagaaa ccatacttgg 2820 gatcttgttg aacaaccacc caatgtcaat gtgattggct gtaagtgggt gtataaactg 2880 aaacataagc caaatgggag tatagagagg tataaagcta ggcttgtggc aaaaggatat 2940 aatcagactc atggtctgga ctattttgag acgtttagtc cagtagttaa ggctgccact 3000 attcgcatca tacttattgt tgctctcagt tttaagtggg aaattcgaca gcttgatgtt 3060 cacaatgcct tcctcaatgg tgagctagaa gaacaagttt atatgtctca acctcctgga 3120 tactttgaca ctcaattccc gaatagagtg tgtagattga agaaggcttt atatggctta 3180 aaacaagccc cacgtgcttg gtttcaaaga ctcagctctg ctcttcttca gtggggattc 3240 agcatgtctc ggactgatag ttctatgttt ctgcactttg gaaaggccac tactttgata 3300 gttcttgtct atgttgatga tatactcgta acgggcagct catccacaca gatttcgtct 3360 ctcatagcta aacttgattc agtttttgcc ttacgagatt tgggtcaact ctcattcttt 3420 ctcggtatag aggtttctta caatgaaggc tctatgactt tgagccaaac caaatacatt 3480 tcagatcttc ttcatagaac tgaaatgttt gataccaaac cggcaaaaac acctggtgct 3540 gttgggaaga acttgtctaa atttgatgga gatcctatgg cagatgttac ccattatcga 3600 agtgtagtag gggcacttca gtatgtttcc ttgacaagac ctgatatagc ctttgctgtc 3660 aataaggcat gccaatttat gcaacaacca accacagctc attggctctc aatcaaacga 3720 atacttcggt atctaagagg aacaatgcaa gatgggcttc tgttcagtcc ttcaagtaac 3780 ttgacaatag agggattcac agatgcagat tggggtgctc accttgatga taggcgcagc 3840 tcaagtggat atctagttta tctaggaggt aacttagtct cttggtcctc taccaaacaa 3900 aaagtggtgt ctcgcagtag tgccaagttt gagtatcgtg gtcttgtttt cgctactgct 3960 gagattgttt ggatgcaagc cttactgcaa gagctatgtg tgccaatacc tgctatacct 4020 ctactttggt atgataatat cagtgcttac catatggcaa agaaccctgt gtttcatgct 4080 agaactaaac acatagaaat agaccttcat ttcatacgag atcaagtcat gagaggaaag 4140 atacaactgc actttgttcc cactgaagag cagccagtag atttattgac taagcatctc 4200 acaagttcaa ggttcttgtc cctcaaatct cagctttgta tagctccaag accctttcac 4260 ttgagggggg a 4271 // ID Copia-65_Mad-LTR repbase; DNA; EDCOT; 593 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-65_Mad_; KW Copia-65_Mad-LTR; Copia-65_Mad-I. XX NM Copia-65_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-593 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1669-1669 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 593 BP; 168 A; 113 C; 137 G; 175 T; 0 other; tggtagtgct cctggttatg tatgttcttt ctcacgaggt cgcgcatccc atttcctgta 60 tgaggagata gactagaatg gaactaagtg tgttgattga gactatgcca caccctttgt 120 gggtgagtgg gagatgtagg atttatctta tgggataaat aaatatcaaa ggatattcca 180 cccacatgag gatattaacc tcctaattat ctatgtgata attagatgaa aatcaagaga 240 tattcatatt agaatatact tgggattttc atgggctttt cagtctttgt acactcttcc 300 caaccactat ataaggaggc tttggggaag agagaagaca caagaaacac aagcttttcc 360 acagttcaaa tattctagtt aggtctttag agctatcact ttcggctcta ggtcttggga 420 ggcgaaaacc aaggggcaac tcgacatacc gtagccaacc cgacgacctg cgaggttcta 480 gacgtgcacg gagggtcaga gcagttgttc gtgtttgtag gagcgtgttg agattcaagc 540 ttccgcataa aaggtacaca cgtcctttcg aatttattta tagtcttcca aca 593 // ID V1_LTR repbase; DNA; EDCOT; 625 BP. XX AC EF439837; XX DT 27-MAR-2007 (Rel. 12.03, Created) DT 03-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE Vitis vinifera retrotransposon V1 - long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; V1_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-625 RA Kalendar R.; RT "Vitis vinifera LTR-retrotransposons."; RL Direct Submission to Genbank (14-FEB-2007). XX DR EMBL/GenBank/DDBJ; EF439837; Positions 1 625. XX CC There are only 3 substitutions between the LTRs. XX SQ Sequence 625 BP; 186 A; 123 C; 150 G; 166 T; 0 other; tgtcacaaga tgcttcaaat gaccctcccc atggcttata taggaggtga gaagcttcta 60 gagacccttg gagacatcca cacttagcca ctagtgggaa gagtgtggaa ggttctagaa 120 atgcctagag aagtccacac aactctacac tatggtagaa ggcatgagaa gggtccaaag 180 ctttctagag aaatctagaa gtctcttgaa tattctagaa tagtgtagga cattctagaa 240 gtctcttgaa tattctagaa tagtgtagga cattctagaa gtctcttgaa tattctagaa 300 tagtgtagga cattctagaa tattcatgaa ttgtaaggaa ccctccaagg ttctagagag 360 ttccattggt gcctataaat aggtgagggc ctcatttggc caaggcacca agcaagtgag 420 catccaagca cttgtaaagg cttccttgag taattaagag cttccattct ttaaggagtt 480 gcctaccaag cttcttaagc ttttgagtcg cgagtgtctt agccgagcaa gctaagcatt 540 ggggagcaag gctgacttag caagatcaag cgtcttggct tgtctaagtg ccgcacgagc 600 ttagtgaacg actaagtccg tgaca 625 // ID L1-12_Mad repbase; DNA; EDCOT; 6081 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-12_Mad. XX NM L1-12_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6081 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1816-1816 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 6081 BP; 1521 A; 1131 C; 1359 G; 2067 T; 3 other; acgcgcgcga taggaaagaa cgcaaaactt tcattctcgc gacstacggt cctctgacgg 60 cgccggagct tcatctgtag gaagattttc tggagtatgt tgtgataaat catgtcaaat 120 ctgtttgagg gttctagggc aaattcttgt ccatggtttc agattccgct cctcttcccc 180 gaaattcgaa gccaccatct atgaaggcca ggacctttgc gtcaattgtc tcggattcta 240 ctgagcgtgt tagcttgagt caactcccaa ttcccgtcat acgcggcgac caaattttcg 300 ttaaaattag cgaggatttg taccaacaac aattgcaatc cttccgtacc aatttaattg 360 ggcgtttatt gttgcgcaag ggcacagccc ctttaaagwc tgcagagctc aaatcatccc 420 tcgaggcttt atggaggcca gtcgcgccat ggcttctcgt cccgctcggg aagggttatw 480 ttgatatcca tttcaatact gaagatgaca agaggaggat atggggaggt gggacttgca 540 cgttaccgaa tggaattttt cgtttatcgg aatggcaaca agatttaatc caaatgatat 600 tgcacctcct acacatgctc aagtttggat tcgaatatat gggcttagcc aggattattg 660 gcatccacgc caccttcttg aaattgcaag gggagtgggt actcctttgc aacttgataa 720 ggccacgaag gagcgccagt ttggatatta tgctcgtgct ttggttgatg tggatctagc 780 tgttgacctc ccctcctcca tcatggtgga gcatgagggt catagttttc ccattgatat 840 agtttatgaa aaattgccgg acaaatgtaa ccattgtgga atcttgggac ataccgttga 900 tcgttgccgt caccttaaga agaaaaatgt ggcaatggat tcccaacctt ctctagcggc 960 aggacgaaag gtaaataaca gaacagagta tcgggttatt caagacccaa aaagaaatga 1020 atgtgttgat ctgatagttg ttgataagat gcaacctatt gaagaggtag tccattcatc 1080 ctctccaatg gagttgaact ctcctcttgt tcagcaaccg gacaatcaac tcgcaggtta 1140 gcaaatgaaa taattgaatc agcggccaat gagatcatca atttagtggc tgatttagtg 1200 gtgaatgagc caatggaagt gactaagcca actgtaggtg ctttgattag taagccaact 1260 gggaaagcat tgcagaatga gcaaggaaaa aatgtaattg gggatgactc ggagtctgac 1320 gaggctatca cccctcattc tcaacgtttt gaagttaatt atggcgattt gggtactaat 1380 gttggtcagc ttgtgtgcca gcattcctct cctaattctt ctgatcttca agaaggtgct 1440 aaaatttgtg atattgttaa tgaagacgga atgactttag ttctttcaaa atcccaaaaa 1500 gcaaagatga ggaaaaagat tagagatggg aatatttcta aagaagtcag ggaaccctat 1560 ccaacccgct ctagggtccc cacagaacga cttgatttat gaagattctt ttttggaatg 1620 cccgaggaat ggggaatgct cccacgaaac gggttctaag aagaatggtt caacgtcatc 1680 gtccatattt aatcggtatt tctgaacctt ttattcaatt aaattctatt aaattgtctt 1740 tttggcgatc tttacgcttg tttccagttg cggttaatga caggggtgac ctacagccaa 1800 atatttggtt gctttgtgat caagccatcc aaccttctat tttattggca accgctcaac 1860 aaatcactat ttcttgtacc ttggattctg tcagttgtgt tatcacttgg gtttatgcaa 1920 aaacgacaat tattgaaagg cgtcagttgt ggcaagactt gcgatctatc aaatcctctt 1980 ttgttaatgg tccatggcta gttctagggg attttaattg tgttttaggc gctcatgaaa 2040 aaaagggtgg gcttctaccc aagactactt cttgttctga ttttcaagag atgtcttcag 2100 cttgtgattt gcttcattta cctacaaaag gattgccata cacttggacg aatagaagag 2160 gaataaaaaa tcaagtggaa atgagattgg accgttgcct tggtaacttt cagtggattg 2220 atgcatggtc tttgttggaa tgttccactt taccccgtat atcttctgat cactgtcctc 2280 ttcttgtttc tttctcaaag ttaacaatca ctccgaaggc tccgtttcgg tttcatagta 2340 tgtggttgga tcatcaggat tttttttccc tagttgagga tgtttggaag tcttctaatt 2400 tttatggttg tccaatgtat gtgcttggtg ctaagcttcg tgtgcttaag tctcgcataa 2460 aagtttggaa caagttggtt ttcggggatg ttaatatgaa tgttgataga gcttttgatg 2520 ctttggatga aattcaaaag gaaatttcca gcttgggtcc ttcagaagaa aggtttacaa 2580 aggaggataa tgcttctttg tgcgtgcaaa aggctcttat tgcacaggaa aaattttacc 2640 gtgacaagtc tcacattaaa tggctttctg aaggggataa taatacctct ttttttccat 2700 tccatggtta aaatcaggaa acttcaccag tcactggcag ttatgagaga tggtaatagg 2760 gtacttgata atcagatgga tattagtcag catgttgtta cctattttca agatcttttt 2820 tctgcagata gttctgtgac agacactggt ttggttgctc gcattattcc caaggtagtc 2880 actgccacag aaaatgagtc tttgttagca attccaactc ctgatgaaat ttttgaaact 2940 ttaaagtcca tggaccactc tagttccccg ggtccagatg gttttggcgg gtctttctat 3000 tttaggtgtt ggcccattgt gggtaatgac gtggttcaag cagtgcaaag ttttttctcc 3060 caagggaata ttctgcctca cttcaattct aacttaatga ttttaattcc aaaggtggat 3120 ggagcgaatt cggtgaacca tcttcgtcct attgctttgg ctaatttttc atttaaaatt 3180 atcactaaga ttttagcaga tcgtttaagc cctattgctg ctcgcattgt ctccccccag 3240 cagaatgctt ttacaaaagg acgatctatt gtggatccca tcattctcac ttctgaatgc 3300 atgaacctcc ttgatagacg ttgtaggggt gggaatattg caatcaagtt tgatattcga 3360 aaggcgtttg acactttgga ttggggtttt cttctccggg ttttggatgc ttttggtttt 3420 tcagcaggtt ttgtggattg gattcgttct attctaactt cagctcatct ttctgtcctt 3480 attaatggtt cagttgaagg ttttttccca tgttctcatg gtgttcgtca aggggatcct 3540 ttgtctccta ttctcttttg tctagctgag gaggttttta gcaggggttt aacaaagatg 3600 gtggaagatg atctaattga cactttttca gttcccatgg gtattgctcc accatctcat 3660 gttctttttg cagatgatat tatggttttc atgcgtggaa ctaagcgatc tatgcgtaac 3720 ctaatgcgtt ttgtagagga gtacagctta aattctgggc aatgcataaa taaattaaaa 3780 tctttagttt ttcttgggaa atatgcaagc agtcggcatg ctattattca gaaggttctt 3840 ggtgtaagtc agggaaatct gccttttact tatctaggtg tccctatctt tcagggtcgt 3900 ccgaaaatga tctattttca agccattgct gacaagattc gttgcaagtt gacggcttgg 3960 aagggttctt tgctttcgca agcagggaga ctccaactta ttaattcagt aattcaggga 4020 atcttggttt atagttttca aatttatgct tggcctacta atttgctacg tgaagttcaa 4080 gggtggatta gaaatttctt ttggtctggt gatccgttaa aacgaggtat gcctctaata 4140 gcttggagtt cttgttgtaa gttgaaagaa gagggtggtt tgggtatccg agatcttttt 4200 gaatccaacc gttctctcct tcttaaaaga tgttgggatg taatttcttc ttcctcaccg 4260 gcttcggatt ggttacgtaa cagatttctt aaagacaact ttcatttgct aaagtcttat 4320 aaaaagtctt ccgtttggtt ggggcttaaa caattatggc cctccttcta tagttccctt 4380 caatggagtg ttggtgatgg ccgtaagatt tcttttttgt atgataactg gcttggaacc 4440 actttgctct ctaatattgg tgaggttgac ataattccct tgaattcgaa ggtaaaagat 4500 tttattcagg atgcaaaatg gtctcttccc attgtcttta cttcttcttt tcctcatctt 4560 tcggagaaga ttatgaagac tccattgcca attgcacaca tggatgatgc gttattttgg 4620 acaggttcat cttcgggtac tgtttcagct aaggaggctt ttcttttttc tctcatctca 4680 tgctccacat aaaaaatggg ctaaaatggt ttggcatcaa tctattcagc cacgcaaaag 4740 cttagtagtt tggaaagctt gtcatggaat attattgact gatgatttat tgcaacttcg 4800 aggtgtggct ttagcttcgt attgcgcttt ttatcataat gttagggaat cttgtgacca 4860 ttttcttctg cattgtcctc aaacagttgc tctatggaaa tggattttca ttctttttgg 4920 caagccttat gatccttggc aatgcattga agatattttt tatggttctt tggtcttatc 4980 tttccccaca tctgtttgga aactttggtt attggttatt tgcagtttct tttggtggct 5040 ttggcacgaa aggaacaaga tcaggtttga gaacaaaagt ttcagtattg tcaagtccca 5100 acattgtctt ttacggcatt ggagggaatc agcttctact tgtttttctt ctttcactgg 5160 ttgtgtatcg attcccatat tctctatgtt aagaatttca tccctttctt tggatgctct 5220 tagtatcgtg cctatgtttt ggcgtccacc tcctgttggg tggattaaga ttaacacaga 5280 cgggccttgt aaagggaatg gtcaagtggg tagtggtggt gtttttcgtg actccagtgg 5340 tcttttttta ggagcgtttg cctcctcgtc ttcttatcca agtgcagttg ttgcggagat 5400 tgtggctgtc atcgaggcaa ttcagattgc atgggataaa aaatggcata acatttggtt 5460 agagacagat tctatgcatg tcatcagcct actatcagct cactccatgg atgttccatg 5520 gtttcttaaa gtttcttggg caaattgttt atggcatatt gctcgcttgc atttgcgttt 5580 ttcgcatatt ttcagggaag ggaattgttt ggcggatgct tttgctaatt ttggtgcaat 5640 gaatagtagc tttacgtggt gggacttggt acccgatttt gctgatgcgt cttatagaag 5700 agattgtgtc gggcttccat tcttccgttc gagctcatga ggagcaaaat gttgctatgg 5760 aagaggattt cgggaaagaa atataatcaa ctgaattatg ggaattcaat tttaggtgac 5820 tgaagctaag cacccttaaa ctagtccata tcattttcat taattgtttt tagcgggttt 5880 tggcctagtc cccccgtttg ttctactttt ccttttttct tcttattatt aataaaatct 5940 tgtagagggg ggatgggcgg ggggtttctg ggtgcaacgg tcctttctcc tttgggagag 6000 ggttggtgcc tcgcacgcga ctgttgacga agagctaatc tcgcctaatc cgtctctaca 6060 aaaatttaca aaaaaaaaaa a 6081 // ID Copia-63_Mad-LTR repbase; DNA; EDCOT; 300 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-63_Mad_; KW Copia-63_Mad-LTR; Copia-63_Mad-I. XX NM Copia-63_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-300 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1665-1665 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 300 BP; 82 A; 54 C; 49 G; 115 T; 0 other; tgttgactga tattgactca agtgaatgcc acataatctg ccatgtcatc aatatttctg 60 ttaaaagtta gttaggatgg ttatgtgtag cttacacagt aagcaaggta gttagactac 120 tagagggata taaaaggccg attgcagcct aatgtttgta agaaataacc attctatcaa 180 tacaaaacct ttcatattct ttctagtttt atttccaagt cttcttctac attctctata 240 tttcttcttt cttctttctt ctgcggttct gatcttcttt gttaagatgg tatcgagcca 300 // ID Copia-22_Mad-LTR repbase; DNA; EDCOT; 288 BP. XX AC ACYM01125589; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-22_Mad-I; KW Copia-22_Mad-LTR; Copia-22_Mad_. XX NM Copia-22_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-288 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1368-1368 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01125589; Positions 2125 1838. XX SQ Sequence 288 BP; 84 A; 48 C; 47 G; 109 T; 0 other; tgactgagat aaatcaatgg ttagatggag tgccaactca ttacttcaat caacggttag 60 aataccaaat cagtttatag ttagttagtt agttaaaaga taaagcttgc tagctaagac 120 tgtatgttgg cttataaata gcagagaaca catattgtaa ttcagttagt caattccaaa 180 gatcaataca atttctctct tcgctatttc tctctttctt taatctttct tctcagtttt 240 ctggttcttc tctgagttac tcatagtgtt ggtcttagag tgttatca 288 // ID SHACOP21_I_MT repbase; DNA; EDCOT; 4059 BP. XX AC AC161106; XX DT 29-JAN-2007 (Rel. 12.01, Created) DT 29-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP21_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Internal; Interspersed; terminal; ORF; repeat; SHACOP21_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4059 RA Shankar R. and Jurka J.; RT "SHACOP21_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 67-67 (2007). XX DR EMBL/GenBank/DDBJ; AC161106; Positions 30861 34919. XX CC The internal region contains intact gag-pol domain. XX FH Key Location/Qualifiers FT CDS join(51..3296,3300..4049) FT /product="SHACOP21_I_MT_1p" FT /translation="MATSNSNSIFSYTTNQIPVFNCEHYDYWNSQMETIFI FT SQDLWDVVEDGYEERPIQRNASSIAEKENEYKENVKKNATALRIILQGVSK FT AIYPRIFGVKKAKDAWDILKTEFQGSSKVISIKLQSLWGQFENLAMKEGEK FT VKDFFSRVTEIGNQIKSCGEQVPEKKVVEKILRSLPQKFEHVVAVIEETKD FT LTKLSQYKLMGSLEAHEERVNRYNNQPLENVFQAKMNIRSSNSRQEGSGDS FT FRGHPSNIGHGRHYGYKGRGGERIRGNSNSYCFICKKSGHESKDCRFRCTR FT CKIPNHSSRDCWHKKKENDERIKGINFSAKDDANKLFSTMINDKKSGEMWF FT LDSGCSNHVTGNQTIFEELNKNYSSHVELGDGKHVKIEGKGVIAVHTSQGN FT KQFIHDVHYSPNISQNLLSVGQIMKRGYKLIFDDDKCEIFDKKSGEHIVTV FT LQTPNNLFPLNMKSFQPAAFSSKSTDDFYLWHLRYGHLNNKGLQLLKQKNM FT VVGLPEIKTDNAVCEGCIYGKMHRVPFPKTAWRSQAPLELVHSDICGPTRT FT PSLGNKRYFLLFVDDYTRMIWIYFLDKKSEAFTKFLHFKALVENQSGCKLK FT TLRTDRGGEFIYKPFLNYCKEQGISRQLTIRHTPQQNGVAERKNRTIVEMA FT RSMLKGKELPNSFWAEAVNSAVYILNRSPTKAVRDRTPFEAWHGRKPVVSQ FT LKVFGCIAYSLVPAQNREKFDGKGEKLIFVGYSDESKGYRLINPTTSQLVI FT SRDVIFDESAAWKWEVEDVVQTPMVPVEFKQSPLNVVEPSRNNSHEDDSDS FT ETPPRKFHSLEEILESCNVTFFAQEPQCFEEAIKEKVWREAMDVEMKSIEK FT NRTWQLVDLPKGKDAIGLKWVYKTKYNEDGSVQKYKARLVAKGYSQQPGVD FT FNETFAPVVRMETIRTVLALAAQLELQVFQLDVKSAFLNGELEEEVYVKQP FT QGFEVEGKERKVYKLHKALYGLKQAPRAWNSKIDAYFLQNGFVKSPSEPSL FT YVKRSGVNFLMVCLYVDDLIYAGTNHDMVQSFKEAMMKEYEMTDLGLMKYF FT LGIQVKQTKGEIFITQEKYIHDLLKFRLESCKPVSTPMALNEKLQLNDGAE FT KADPKAYRSLVGSLIYLTNTRPDIVHSVSLVSRFMNEPSKLHFAAAKRILR FT YLQGTKKLGIKYVKEENNELVGYTDSDWAGSFDDRKSTSAYVFCLGSKAIS FT WSSKKQNSVALSSAEAEYISANEATREAVWLRRILIDLQQKVEDPTPIFCD FT NQSAISMSKNPVFHGRSKHIELRHNYIRDMVQRTEINLEYIKTTEQPADVL FT TKAVPIEMLEQFKDNMKITN" XX SQ Sequence 4059 BP; 1410 A; 646 C; 881 G; 1122 T; 0 other; gttttggtac cagagcagcc tggtttattc aaaaaataaa aaaaaaagga atggcaacgt 60 caaattcaaa ttcaatcttc tcttacacaa caaatcaaat tccagttttc aattgtgaac 120 actatgatta ctggaattct caaatggaaa ctatatttat ctctcaagat ctgtgggatg 180 tggttgaaga cggatatgaa gaacgcccaa ttcaaagaaa cgcttcctcg attgcagaga 240 aagagaatga atacaaggag aatgtgaaga aaaatgctac agcattgaga atcatcctgc 300 aaggtgtaag taaagccatt tatcctagaa tatttggtgt taagaaggcc aaagatgcgt 360 gggatattct gaagacggag tttcaaggct cgtcaaaagt gatttccata aagttgcagt 420 ctttatgggg ccaatttgaa aacttagcaa tgaaagaagg tgagaaagtc aaagatttct 480 tctctagagt aactgagatt ggaaatcaaa ttaaaagttg tggagaacaa gttccagaaa 540 agaaagtggt tgagaaaata ttgagaagcc ttccacaaaa atttgaacat gttgttgctg 600 ttattgaaga aacaaaggac ctcacaaaac tctcacaata taaattgatg ggttccttag 660 aagctcatga ggaaagagtg aatagataca acaatcagcc attggagaat gtttttcaag 720 caaagatgaa tatccggagt tccaactcgc gacaagaagg aagtggggac tcatttcgtg 780 gacatccttc caacataggt catggaaggc attatggata caaaggaaga ggaggagaaa 840 ggatacgagg taattctaat tcttattgct ttatttgcaa aaaatctgga catgaatcaa 900 aagattgtcg ctttagatgt actagatgca aaattcccaa ccattcaagt agagattgtt 960 ggcataagaa gaaagaaaat gatgaaagaa taaagggaat taatttttct gcaaaagatg 1020 atgcaaataa gttattctct actatgatta atgataaaaa atctggtgag atgtggtttt 1080 tagatagtgg ttgtagcaat catgtaacag ggaatcaaac catatttgaa gagctaaata 1140 aaaattattc ttctcatgtt gaacttggtg atggaaaaca tgttaaaatt gaaggaaagg 1200 gggttatagc agttcatact agtcaaggca acaaacaatt cattcatgat gtccattact 1260 ctcctaatat ttcacaaaat ctgttaagtg ttggacagat tatgaaaagg ggttataagc 1320 tgatttttga tgatgataaa tgcgagattt ttgacaaaaa atcaggagag catattgtca 1380 ctgtgttgca gactcctaat aacctatttc ctctcaacat gaagtcattt cagcctgctg 1440 catttagcag taaaagtacc gatgattttt atctttggca tttgagatat ggtcacttga 1500 acaacaaagg tttgcagctc ttaaaacaga agaacatggt tgttgggctt ccagaaatca 1560 agacagataa tgcagtttgt gaaggctgta tatatggaaa aatgcatcgt gttccgtttc 1620 caaaaacagc atggagatct caagcccctc ttgaactagt acattcagac atttgtggac 1680 ctactagaac tccatctctt ggaaataaaa ggtactttct gctcttcgtt gatgactaca 1740 ccaggatgat ttggatttat tttcttgata agaaatcaga agctttcacc aagttcttgc 1800 attttaaagc acttgttgaa aatcaaagtg gttgcaagtt gaagactctt agaaccgata 1860 gaggaggaga atttatctac aagccgtttc tcaattattg caaagaacaa ggcattagca 1920 gacagctcac aatcagacac acaccacaac agaatggtgt ggccgaaaga aaaaatagaa 1980 caattgttga gatggctaga agcatgttaa aaggtaaaga gcttccaaat agtttttggg 2040 ctgaagctgt taacagtgct gtttacatcc tcaatcggtc tcctacaaag gcagttcgag 2100 atagaactcc ctttgaggca tggcatggaa gaaaaccagt tgtaagtcaa cttaaggtat 2160 tcggctgtat tgcatattct cttgttcctg cacaaaatag agaaaagttt gatggaaaag 2220 gtgaaaaact tatttttgtt ggatatagtg atgaatcaaa aggataccgg cttattaatc 2280 caacaactag tcagctcgta atttcaaggg atgtgatttt tgatgaaagt gcagcatgga 2340 aatgggaagt tgaagatgtt gtgcaaacac ctatggtgcc tgttgaattc aagcaatcac 2400 ctcttaatgt tgttgaacca tcgaggaaca attctcatga agacgattct gattcagaaa 2460 cgccaccaag aaaattccat tctttggaag aaattcttga atcatgtaat gttacatttt 2520 ttgcacagga accacaatgt tttgaagagg ctataaaaga aaaagtatgg agggaagcca 2580 tggatgtgga aatgaaaagc attgaaaaga atcgtacttg gcagctcgta gatcttccaa 2640 aaggaaaaga tgcaattggt ttgaagtggg tctataagac caagtataac gaggacggaa 2700 gtgtacaaaa gtataaggca cgtttagtgg caaaaggcta ttcccagcag cccggcgtag 2760 attttaatga gacttttgct cccgtagtgc gcatggagac aatcagaact gttcttgctt 2820 tggcagctca attggaatta caagtttttc aacttgatgt caaatcagcc tttttgaatg 2880 gagaactaga agaagaagtt tatgtgaagc agccacaagg ttttgaagtt gaaggaaagg 2940 aaagaaaagt ctataagcta cacaaggctc tttacggttt aaaacaagcg ccgagagcgt 3000 ggaacagcaa aattgatgct tactttctgc aaaatggatt tgttaaaagt ccatctgaac 3060 catctctgta tgtgaaaaga agtggtgtta atttcttgat ggtttgtctc tatgttgatg 3120 atttaattta tgcaggaaca aatcatgata tggtgcagtc gttcaaggaa gcaatgatga 3180 aagaatatga gatgacagat cttggattaa tgaaatactt tcttggaatt caagtgaagc 3240 aaacaaaagg cgagattttt atcacacagg aaaaatacat tcatgatttg cttaaatagt 3300 tcagattgga gagctgcaaa ccagtctcaa ccccaatggc cttaaatgaa aagttgcagc 3360 tgaatgatgg tgcagaaaag gcagatccaa aagcctacag aagcctcgtt ggttccttga 3420 tttatctcac gaatacaagg ccagatatag tgcattcagt tagtttggtt tctagattca 3480 tgaatgagcc aagtaagctt cattttgcag cagcaaaaag gattttgcgc tatctccaag 3540 gaacaaagaa gcttgggatc aagtatgtga aggaagaaaa caatgagttg gttggctata 3600 ccgatagcga ttgggctggt agtttcgatg acagaaaaag cacttcagcc tatgtttttt 3660 gtctaggatc caaagctatt tcatggagtt ctaaaaagca aaactcggtt gcattatctt 3720 cggcagaggc tgaatatatc tcagcgaatg aagctacacg tgaagctgtt tggttgagga 3780 gaattttgat tgacttgcag caaaaggtag aagatccaac tcctattttc tgtgacaacc 3840 aatcagcaat ttcaatgtcc aagaatccag tttttcatgg aaggtcaaag catattgagc 3900 tgcgccacaa ctacattcgt gatatggttc aaaggacgga aatcaactta gaatacatca 3960 agaccacgga acagccagca gatgttctca ccaaagcagt gcccattgag atgcttgaac 4020 agttcaaaga taatatgaaa attacaaatt aagagaggg 4059 // ID TOTO1_LP_LTR repbase; DNA; EDCOT; 456 BP. XX AC AF220602; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 09-APR-2007 (Rel. 9.07, Last updated, Version 3) XX DE Lycopersicon pimpinellifolium retrotransposon TOTO1_LP_LTR, long DE terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Long terminal repeat; retrotransposon; TOTO1_LP_LTR. XX NM TOTO1_LP_LTR. XX OS Solanum pimpinellifolium OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-456 RA Lavelle T.D., Oldroyd E.G., Dalhbeck D., Staskawicz J.B. RA and Michelmore W.R.; RT "Direct submission."; RL Direct Submission to Genbank (04-JAN-2000). XX DR Genbank; AF220602; Positions 37402 37857. XX SQ Sequence 456 BP; 100 A; 75 C; 93 G; 188 T; 0 other; tgttgggttt tatttgccct gatttcttac cataaatagg tttttctttt aggaaaaggt 60 tttggattga ctaatccttt tctcgtagga aaaggtttag gactctataa atagaggtat 120 gttccttcga acttaatcag cattcacaat gtagtcttaa gggctttgag agttttgttt 180 aggggagaat ttatgggtca caagcttgat acgttatcac ttgtgtgaac ctcccatgta 240 ttctgagaga attagttgag attgtttctc tttgtatttt gtactctcat atttataatg 300 gattgctcat ctcctttgta gacgtaggtc gatagatcga accacgttaa atctttgtgt 360 cttttggtat atttctcgtt gtcttcttac tcgtggtctt ttgaggtttg ctttgctagc 420 ttccgcgttt acacctgctt attttcggtc ctaaca 456 // ID Copia20-VV_LTR repbase; DNA; EDCOT; 212 BP. XX AC AM444110; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia20-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-212 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-212 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 700-700 (2007). XX DR Genbank; AM444110; Positions 13734 13945. XX SQ Sequence 212 BP; 72 A; 33 C; 35 G; 72 T; 0 other; tgttagagaa gattagttag gattagttaa gaattagttt tggattagtc ttgacagcac 60 atgcttaaca gattgtaaca gattgtaaca atacttaaga tgcagaaata caatagagaa 120 aatagagtgc agagcagagc ttttctgtca atcttccaat aaccttttcc actatcttct 180 cttcagaatc ttctttctta agaattctat ca 212 // ID COP4_LTR_MT repbase; DNA; EDCOT; 162 BP. XX AC . XX DT 22-DEC-2006 (Rel. 11.12, Created) DT 05-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE LTR sequence of LTR retroposon, COP4_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; COP4_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-162 RA Shankar R. and Jurka J.; RT "COP4_MT: A copia type LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 610-610 (2006). XX DR [1] (Consensus) XX CC The LTR sequence flanks a well conserved internal region, coding CC for Copia type protein coding for integrase. XX SQ Sequence 162 BP; 52 A; 25 C; 24 G; 61 T; 0 other; tgttagaata attaatcaag tacttagtgg agatattgaa aagttctgac tatttagttt 60 caactccact agtcattgta ttgattgtat tgattaatct tccttattaa ttaggggtta 120 actaggagac tcttacctat ataaatgtac actctcacca ca 162 // ID Copia-15_Mad-LTR repbase; DNA; EDCOT; 201 BP. XX AC ACYM01118580; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-15_Mad-I; KW Copia-15_Mad-LTR; Copia-15_Mad_. XX NM Copia-15_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-201 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1359-1359 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01118580; Positions 6299 6099. XX SQ Sequence 201 BP; 59 A; 35 C; 25 G; 82 T; 0 other; tgcggatact tacttgtttc ccctttatat taggagtaga attgatccgt ataaatcaat 60 gtaaatcttc tttatttcct tcttagaata gacttccttg tattatataa gtcttgtatt 120 ctattgtaaa agatcaatgt gaaatattca aagtttattc ccagacttca tatttctaaa 180 ccctagccga gttacttttc a 201 // ID MuDR-5_Mad repbase; DNA; EDCOT; 3881 BP. XX AC . XX DT 15-OCT-2010 (Rel. 15.1, Created) DT 15-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; 8-bp TSD; MuDR-5_Mad. XX NM MuDR-5_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3881 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1510-1510 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 126-bp long. XX FH Key Location/Qualifiers FT CDS 1271..3190 FT /product="MuDR-5_Mad_1p" FT /translation="MLSLLAKCFESREDLIGEVRKIALMQGFATVIRRSKT FT NTYVAIGCDRGGDYRASKTSLDERKKNSGSRLINCPFEVRGRKKKCEEFWK FT LEIKSLLHNHELSNDMCGHPSCRQFSQEEILRIKEMSKAGIPPRQILSSLR FT QGNPHLQVVSRNIYNLRAKIVKESLAGRPVIQALLEELGEGGFTYNIEYDH FT EGHLTHLIFAHPLSIELTKSYPYVFVMDCTYKTNKYKMPLLDIIGVSSFNT FT SFYSCFVFMQNEKEEDYVWALKMFSKILGVDNHPMVIITDRELALMNAIRI FT VFPSTSNLLCVWHIEKNILANCKAHFEEEVDWIDFISTWTILIQSPNETSF FT NEAWSRFEVKYEEKKFVLKYILGTWLPYKEKFVSAWSEKVTHFGNRVTSRA FT EGAHATLKKYLQVSTGGLREVKEKICLAIENQFQEIKTQLSSEKVRVSHKF FT RLPFFKEVVTHVSRFALNELYNQYEASSSSDLPSQCKGHFLKTMGLPCAHM FT IREMNIEVLQLNDIHPQWRIDRRLFVNDRHVSLDNEQDQISGLLLEFKDKY FT EKLPLTQKEDTKRQLCEFIDTSLPLTLEPNVKPHKGRPMGSKNRKESSSTK FT RGPSKFEIVEKAQKRARRVCHFFYLSFNIVYYGHDYLYIRIT" XX SQ Sequence 3881 BP; 1219 A; 618 C; 726 G; 1318 T; 0 other; gggttgtgat tttcacacac ccttaattac ctttcccaca ccccttctta ttttttaata 60 cttaattgat atcttactat ttactcttcc atatataccc tttttacttt ttgactttta 120 aaagttgttt tttatttttt gattgtgttg tagattggag tagcagcccg attcttccca 180 ctcccctgct ttttcccttg ctttctcccg cttcttcccc aaaacccaga cacctcctgc 240 tttttcccca aacccagaca cctctcgcag cccgattccc tcgccgccgc aaatatttcc 300 actgcttctt cgaagcctcc cactccctcc gccgagccca acgagaccta ttctgaaatt 360 tccactgctt cttctctttc cgttcccctg tcctctttat tacttcttgt gaaaaaccac 420 aatggatgac ctgataataa cagatgaaga actccagatg gacattgagt tgcagaagat 480 attggatatg gcatgcaagg aggatggcat ggaagaaatt tcagaatgca ttcctcctct 540 taacactttt gatggtaatt ttctaaagta ttttctcaaa ttattaagat tgattttgga 600 atttagggtt tttgttctct tcttgcctca atttgttttt taggtttagt tttttctttc 660 cctaatttgt ggttcaaatg ataattgaat gaatgaatac tggtggttta agataaatgt 720 atcatgtaac aatgaagtaa ctgaatccag gggaagaaat ttagaaaaat gcgtcaagta 780 aacagaaaat cacgaaacta agtttgtaaa tgtttttgac atcagaattt tttttacaag 840 aataacgaaa aattaggcaa tgctcagaga ctaaggagca aaagattaaa aactaccatg 900 cttacgtgaa tgcaccgggc aatgctctat aacatatttt tctctcatgt acacggcaca 960 catgctattt acacatctag ataatagaga atattgattt gtgttggttt tggggaaatt 1020 aattttctat tggaatctat tggtccccaa tacactttaa cttaatggta aattggtatt 1080 aggtttaatt gttgtggttt tacctaggct ccatgttttg gtgtaaactt gatataatgc 1140 atacaatgct ttggtataaa tttgatactt aaatgtctag tccattgata aaaagtatat 1200 attctacata tataaatgtg ttggtttgtg atatatagga agtcaaccaa cgattgatga 1260 gcccgataaa atgctctctt tgttggcgaa atgttttgaa agtcgagaag acctcatcgg 1320 ggaagttcgt aagatagcat taatgcaagg gtttgcaacc gttattagaa gatctaagac 1380 aaatacatat gttgctattg gttgtgatag aggtggggat tatcgagcct ctaaaacttc 1440 actagatgaa agaaaaaaaa actcaggatc tcgcctcata aattgtccat ttgaagtcag 1500 ggggcgtaaa aagaaatgtg aagaattttg gaagctagag ataaaaagtt tattgcataa 1560 ccatgaactt tcaaatgaca tgtgtggaca tccttcttgt cgtcaatttt cacaagagga 1620 aatcttacga attaaagaaa tgagtaaggc tggtatacca ccacgccaaa ttctatcttc 1680 gcttcggcaa ggcaatcctc atcttcaagt agtttctcga aacatctata atctaagagc 1740 taagattgtg aaggagagtc tagctgggcg tccagttatt caagcattat tagaagaact 1800 tggtgaaggt ggtttcactt ataacattga gtatgatcat gaaggccact tgactcattt 1860 gatctttgct catcccttgt ctatagagtt gaccaagagc tacccatatg tttttgtgat 1920 ggattgcaca tataagacca acaagtataa gatgccatta ttggatatca taggagtttc 1980 aagtttcaac acatcctttt attcttgttt tgttttcatg caaaatgaga aagaagagga 2040 ttatgtgtgg gctctaaaaa tgtttagtaa gattttggga gttgataatc atcctatggt 2100 gattataacg gatagggagt tggcattaat gaatgctata cgcattgtct ttccgagtac 2160 ttccaatctt ttgtgcgtgt ggcatattga gaaaaatata cttgcaaatt gtaaagctca 2220 ttttgaggaa gaagttgatt ggattgattt catttctact tggacaattt taatccaatc 2280 tcctaatgaa acatcattca atgaagcttg gagtcgtttt gaagttaagt acgaggagaa 2340 gaaatttgtt ttgaaatata ttcttggtac ttggcttcca tacaaagaaa agtttgtaag 2400 tgcatggtca gagaaagtta cccactttgg taaccgtgtt acttcaagag ccgaaggtgc 2460 acatgcaacg ctaaaaaaat atcttcaagt ttcaactgga ggtcttcgcg aggtaaaaga 2520 aaaaatatgc cttgctattg aaaatcaatt tcaagaaatc aaaactcaac tttcaagtga 2580 aaaagttaga gtttcacaca agtttcgact tcccttcttc aaagaggttg ttactcatgt 2640 atctagattt gcattgaatg agttatataa tcaatatgaa gcatcaagtt cttctgatct 2700 tccatctcaa tgtaagggtc attttctcaa gacaatgggt cttccttgtg ctcacatgat 2760 tagagagatg aatattgaag tcttgcaact aaatgacata catccacaat ggaggattga 2820 tagaagattg tttgtcaatg atcgtcatgt aagcttggac aatgaacaag atcaaataag 2880 cggccttcta ttggagttta aagataagta tgaaaagttg cctcttactc aaaaagagga 2940 taccaaaagg caactttgtg aatttattga tacttctctt ccattaactc ttgagcctaa 3000 tgttaaacct cacaaaggtc gtccaatggg ttctaaaaat agaaaagaat caagctctac 3060 aaagcgtggt ccttcaaagt ttgaaatagt ggagaaggct cagaaacgtg ctcgacgggt 3120 atgtcatttt ttttatttat cttttaatat tgtctactat ggtcatgatt atttatatat 3180 acgtataact taatgttcat tgtttatagg tgtgatgagc ataatgattt gccaaagaaa 3240 ctttttgtta ataatagctt agatgtgtaa agaacacatt aaggtacata tatttttgtt 3300 gatttttccc cataaaaata ctaattaagt ttgtaatttt ctttcctttt gttgacatgt 3360 ttttattttc ttgtaggttg gagtgcatgg gtttcatatc tttttggtaa tattgacatc 3420 tccttttgaa cacaagatta aaggccaaac atagtgtagg cagaatgtga aagcttgtaa 3480 tgatatctga tgtatttttt ggggcatgag gctactatta tggggattaa agtgtatgtg 3540 gattgcttac tagtattttg tacaattcat gtaacttatg catatatgct atatcattag 3600 gtaatcgttt tatttttatt tatataatag gtgttttata cttgttttgg gatctctcag 3660 attaggcagt agagcttgag ttacaaatgg catatatggt tgagtgttag aaaaagaaaa 3720 aaacaagttt aaaataaaat aacaaaagta ttctaaaatt tcaatggtca aaaagtaaaa 3780 agggtatata tggaagagta aatagtaaga tatcaattaa gtattaaaaa ataagaaggg 3840 gtgtgggaaa ggtaattaag ggtgtgtgaa aatcacaacc c 3881 // ID Gypsy7-VV_LTR repbase; DNA; EDCOT; 1832 BP. XX AC . XX DT 29-AUG-2007 (Rel. 12.08, Created) DT 31-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy7-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1832 RA Obukhanych T. and Jurka J.; RT "Gypsy7-VV - LTR retrotransposon from grapevine."; RL Repbase Reports 7(8), 674-674 (2007). XX DR [1] (Consensus) XX SQ Sequence 1832 BP; 563 A; 324 C; 353 G; 578 T; 14 other; tgattactac tcaaaaagtg ttattttata gcttgtaatt aactctttta aacacttttg 60 agtagtagtt attacctttt aactcaattg gcatgttaag gacccttgca atcgtttcta 120 atcaaattgt gttaagtttt ggtgtttttg atagcttttt ttatcaccaa agcaatccaa 180 gaatgaggga gagctttgta taatccatgg caaagcaaat ggaagctcaw wtwcatgaag 240 aatccaagct ttggagctty atagyccttt gccaaaagcc aaatcaagaa tgcaaggagg 300 aaaaacacag agagaaatca aacatgaaga aattcaagag gacagcaatt ttaggacaca 360 tttcgagcac tttgtggagt ccaatttatg catactatat tctttttyga agcttgggaa 420 gtcaggaatc caatgcttca aacggtgyac aaatcggagc tgaaatgaag aagttatggc 480 cattggaaga caatcgcacm actagctgaa agacaatttc gcaacttgcg aaatcaaaaa 540 tttcaacttg cgaaatcaag gtccaacttg cgaagttggc aattcaactt gcgaaatcca 600 cctgtgtamt ccgagatatt tgcgcaccga ctccgtttta gattttttct tcagatattt 660 gttgtgtaaa tccctatttt ctccttgtaa tccaccaatc ataagattcc ttagttagga 720 agtaagaagg aagggtgaat aacctctmta tatatmatct attgtaattt tctttttaaa 780 agatctcggg agttttttct cagagacaaa cttttgtata gttttgaaga aagtaataca 840 cagagctttg ctctgcctta cctactcatt ttgattgctc tttatttttc ttwctagcca 900 aacaaactct gaggatgttt tcccagagga tgagtggcta ggcttttttg tttcttggag 960 tgaaggaagc tgggtaaggt tccgaatgca aaaattggaa gttttgttgt ttcagttttt 1020 aatgaagaga aagtgtgacc cgttaatggt ttttatcttt ttagttaact taaaatccct 1080 taaaatcacc tgggccaaca cttggtaagg caagtggtct ccgtccattg agatacacta 1140 gtttatctct tgcgagcctt tgggaggtgg tttaaaggta ggattttcta gaatagccaa 1200 cacttggtaa gcttttggac tccaaggaga catccattag ttatctcttg cgagcttttg 1260 acgggtaatc caaggttaag gatcaccttg aatggccaat actaggtgag aggtatgaac 1320 cattgcaaga tgattcagtg acagggattt agtgtttgaa accattaagg ggaagcatct 1380 gtaccacacc ggttcgggaa ataactatat gttaaatccc caatgcgagg aaaagattca 1440 agtgaccgga atctcccttt ttgtataagg aacctgagcc tagtgatcta aaaactccaa 1500 gaagcacttt tctttgtaag taatttcagt tactttattt ttggtttcac ttaaaaacca 1560 accttttcaa acatatttat gttttctttt aaagctaacc ttgaaaagaa aaagcaccaa 1620 ttcagttttt gaactaatat cagttgtaat ttgaaaaccc atcccwgtgr acgatcctag 1680 agccactatg ctatgctagc taatgctacc ctagtatatg gtgaaatagg tttataaatt 1740 ttgttgatta ctcccgtctg aggactgaaa tcaaagtaca ccagttgatt gaacaccaat 1800 caacaggaca tacaccagct gggcacgaat ca 1832 // ID SAT1_AGE repbase; DNA; EDCOT; 179 BP. XX AC . XX DT 23-MAY-2005 (Rel. 10.05, Created) DT 03-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE A. gemmifera satellite centromeric repeat - consensus. XX KW Satellite; Simple Repeat; satellite repeat; Centromeric repeat; KW tandem repeat; SAT1_AGE. XX OS Arabidopsis halleri subsp. gemmifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; OC Arabidopsis; Arabidopsis halleri. XX RN [1] RA Kawabe A. and Nasuda S.; RT "Structure and genomic organization of centromeric repeats in RT Arabidopsis species."; RL Mol Genet Genomics 272(6), 593-602 (2005). XX RN [2] RP 1-179 RA Gentles A. and Jurka J.; RT "Arabis gemmifera centromeric satellite."; RL Direct Submission to Repbase Update (19-MAY-2005). XX DR [2] (Consensus) XX SQ Sequence 179 BP; 42 A; 43 C; 31 G; 63 T; 0 other; ggatccgggt tgcatttctc tttcttatac tcagtcatac acaccaatct tgtcatattg 60 gactccaaga accctacaca agcttattat ggcttcccta tatggttccc aagttttgta 120 agtgaggacg aagtccctat gagttttttt gttttgcatc tacgctactt tagcagcca 179 // ID Gypsy18-PTR_LTR repbase; DNA; EDCOT; 1627 BP. XX AC LG_I; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy18-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1627 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-1627 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 315-315 (2007). XX DR Genome; LG_I; Positions 15057647 15059273. XX SQ Sequence 1627 BP; 492 A; 273 C; 304 G; 558 T; 0 other; tgatgcaacc atattattcg atagtttcaa ccacatttaa ctagtgtttt gcctatgttt 60 tatatataaa atgccttgat attctttgtt ttatgttttg aaggcacttt tggatgaaag 120 atgcaaaaag gagtaaattg gagataattg gcagatttga ccttcagtcg atgttttgtg 180 cagagcgtga gctctagagg ttgaaatgaa gtgattccag tggcattaaa aagctaacat 240 ccataccttt ctggacatct aaggcaagaa aataaaataa ggaagagcat ggaaatcgca 300 gccttcaaag ttaaatctcg caatctgcca gtgttgacct tcgaccattc aaacttgaat 360 atctggagct acagaattcc aattgatgca aactcatttt ttttggattc atgactcaaa 420 tttctataaa cgctcaacct gtaagccaaa aacgatgtca tatgagggag atatgatttt 480 tcaaagatga catctgaatt ctgccagcaa acaggtttcg tgaagaaacg agtccaaatt 540 acgttccgaa gcatctaaac cgatatccaa gtttttattt cagtaattta gctcctctaa 600 gtcaaagctt aaagatttca tgcaaggcta tttctccttt tctaggaata tagtaattga 660 agtacttaaa tgtaaacagt ctacttaatg gaggagtatt ttgtaaaata gagacctagg 720 gtttcctagg atataaaaag aatgagagaa gagaaggggg gcagccagcc atgaagagaa 780 aaacgcaccc ttcctctaag aaaccctaaa ttatgcattc ttccttcttt ttgattagtt 840 gttcaacaaa catgaaaggc taaacacttt ttcttggttg caaggacacg gagacttttg 900 atttcaagaa ctgtcagatt tattttacct tttcttttca gtttatatga taaatatgtt 960 tgttctccta tgcttatttt tcctatgatt gtttatttta attgctagag cggactctaa 1020 gttattattg taaacaatct attgctaagt ttgatatcaa aaccggagtt gtggtatatg 1080 aacttgtgaa gcaactgagt ttaataattg tggcggatct acgttattaa tcttagggag 1140 aacattcaat caaatcaaac atagactgca gacagttatg ttttcttgat taatcaactt 1200 ctctagttct taaggctgcc gttgaattaa attactagtg cggacactgt ggttgtttga 1260 tggttagggc tagttatacg gcggatccat taactaacca atgttaagaa gagataaata 1320 ttcagaatat aaattgatgt ttcatttcca tgatcagttc tgatttctgt aggtggatgt 1380 gtgcttgtga ccaaggtttg ttctcttgat aattttctga ttttattaaa tttcgtttga 1440 tagttttctg ttttcttttg ctttagccta gataacgtcc aacccccccc ccaaattgca 1500 tatcatctag cataaaaatc taacttgaat cttcctcgtg ggatcgaccc cttgcttgct 1560 ctatactatt ttgtgtgttg tgtttgaagc tagggtaatt aatttgtgcg accgcgacat 1620 cgcaaca 1627 // ID TORTL1 repbase; DNA; EDCOT; 9695 BP. XX AC U68072; XX DT 06-MAY-1999 (Rel. 4.04, Created) DT 06-MAY-1999 (Rel. 4.04, Last updated, Version 1) XX DE Lycopersicon esculentum copia-like retrotransposon ToRTL1. XX KW Copia; LTR Retrotransposon; Transposable Element; TORTL1. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-9695 RA Daraselia D.N., Tarchevskaya S. and Narita O.J.; RT "The promoter for tomato 3-hydroxy-3-methylglutaryl coenzyme A RT reductase gene 2 has unusual regulatory elements that direct RT high-level expression."; RL Plant Physiol 112(2), 727-733 (1996). XX RN [2] RP 1-9695 RA Narita O.J.; RT "TORTL1."; RL Direct Submission to Genbank (27-AUG-1996)Department of RL Biological Sciences, University of Illinois at Chicago, 900 S. RL Ashland Ave, Chicago, IL 60607, USA. XX RN [3] RP 1-9695 RA Narita O.J.; RT "TORTL1."; RL Direct Submission to Genbank (19-JUN-1997)Department of RL Biological Sciences, University of Illinois at Chicago, 900 S. RL Ashland Ave, Chicago, IL 60607, USA. XX DR GenBank; U68072; Positions 11220 1526. XX SQ Sequence 9695 BP; 3078 A; 1692 C; 2147 G; 2778 T; 0 other; tgttatttgt agttttgatg atttgacaaa cttagggacc tcataaaggt accgggtttt 60 ctacttgagt attgcaggtg tcttctttga agtattgcag atgaaacaaa cccagggacc 120 tagtagaggt accaggccct catgatgatg agtcagtcaa ctgccagctg gagacgtaca 180 gaaagtaggt gcacacttcc cgatggcgtc agaaaagtgt gacctttcca accaatggca 240 aagaagttta ggaaagtgac ttgtcatata aaaggcactt tcctaaacat ttgtttttta 300 gtttttgcaa cttgataaaa acttttcaag aactcttgca aaggctacac aaagcaaagg 360 cagaatcatt cctaggacaa cagcaacatc tggagctttt cgtctagttg tttaggaatt 420 tattctcttg ttcttaaatt gtaaaccact cctaaatcta taaaggaatt ggtgtgttgt 480 gttaaaagtc ttggttgtcc aggtgggata gcttagtggg tagattgttt ttctactttg 540 gcttgttgag caatagaggt ctattgctta acggtaagat tgataactct ttcttacgtt 600 tggtgtaatc gtgtttcact tttgcttttg aagattagtg aaaacgatgg aaaatcctgt 660 gagacaggtc gaggttttac tctcttaagc aatgaggttt ccacgtaaaa tcattgtgtt 720 gattttactg catttaactt tctggtaatt ttctgaagta aagtaaggga cctggtccat 780 tactattaag tgaagtcata cattctatca agtggtatca gagcgggcac tacctatttg 840 attaacacca aggaagtgat tttgttctaa aatggcagct ccacttaacc tcgaagaagg 900 tcagtcatca catagacctc ctcgtttcaa tggacatttc tacagttggt ggaaagttag 960 aatgcacgat tatctcatgg ctgaagatag cgagttatgg gatattatac tagatggact 1020 ctttgttcca atgatggaag taaaggatgg agaaaagacc atcactgttc caaagcccaa 1080 gcagaaatat gatgatgctg acaggaaaaa gatagaaaag ggcttcaaag gtaaaactct 1140 tatggtctgt gggataggac ctgatgagta caatagagtg tcagcctgtg agtctgctaa 1200 agaaatctgg gattgcttgt tgactacaca tgaagaaact gaacaagtca aagaatccaa 1260 gattgacatg ctcacctcac gatatgagaa cttcaaaatg aaggaaggag aaactataca 1320 tgacatgttc acaaagttgt cttccattac aaatgagctg cgaagtctgg gtgaacctat 1380 aagcatgacc aaacaagtca ggaaagtgct tcgaattctt ccaaagtctt gggagagcaa 1440 agttgatgcc attacagaag ctaaggactt gaaggtgctg accatggatg ccttgattgg 1500 aaatcttaaa acacatgaga tgaatcgaaa ccatgatttg tcaaaaaggg aagccaagaa 1560 ggacaagtca ttgatgttga agtataaatc agatgaagat tcaagtgatg atgatgatat 1620 gacatatctc atcagtagat ttcaaaagat tgtgagaaaa aacaaaatgc ataaaagagg 1680 aacaaatggg actcgaaatg ctgctcaagg tgatacttgc tacaagtgtg aaaaatctag 1740 gcacttcatc agagagtgtc ctttactcaa gaatgaaaac aaggaacatc aaaaacacag 1800 gggtgacaaa gaaaacagaa gggacctggt acctggtaac agagatcgta aagctgctgc 1860 tggtatggtt gtcaaaaggg ctcttgctgc atggggggat tcttctagtg actcagaaga 1920 tcctgatgag ccaaaagatg tgtcgatggt tgctgtgcat gaggaggaaa ctgtctttaa 1980 tgaaatgttt gctcttatgg cacacacaga aaatgaagaa gaaaacaatc aggtaactct 2040 ttttgacatg aaaaatgact tggataaata ttctcttaaa aaattgagaa ccttggcaaa 2100 agtcatgtta gattctgtga tagagttaac atctgaaaga gataccatga ttgctgaact 2160 tgaaatttta actgaaaaca aaggtcaatt tgaagacaca atgtcaagaa tggtgtctct 2220 agagttaaaa aactctgaac ttaagaacca gttgtgtcag attactgaag aagctgaaaa 2280 tctgaatgga aagccaaata gtctgcaagc tgaaattcaa gaaaaattga aaaactctga 2340 gaaaaatctt agtttgtcac ttgaaaagaa taacaaattt gaacaggatg ttgtgaaact 2400 taagaaagag cttgaaaatt ctcttaagtg gaccaaatcc tcaaagttgc tgtcaaatgt 2460 gacaaatcag agtaatttca ataagaaagg actaggaagt ctgagcataa gtcctcctta 2520 taatcctcac agtaagtatg tgtttgtgtc cgacaatctg ttgtgtctgc attgtggtaa 2580 gaatggacat ttgaagaatg agtgtgttag ctggagaaac tcatgtgaaa gacattctaa 2640 gtatgctcaa aaacaaaatg taccaaatga gagacctggt cttacagagc ctgtctcaac 2700 tcacaaattt tcaaagaaaa aatctgttcc tgctcctagg tcttttgtta gaaagattca 2760 aagtctacca tattggacta agtacaatct gatcactcct ttgtctgcct actgggaact 2820 caagctgaaa tgggttccca agcttaacaa gtgatttttg gtgcaggtga gtgagagggg 2880 aagcagtcaa tgttggtata tggatagtgg ctgctctaaa catatgattg gtgatgtaaa 2940 gaacttcctc tcactcaaga ccctccaagg tggaggtgtc tcatttggtg atggcaagaa 3000 tgggtacatt ttgggagttg gcaaagtagg aagatctctt gaagattcaa ttgacaatgt 3060 ttaccatgtg gatgggttga agtacagctg gctaagtgtg tcacaaatct gtgacaaagg 3120 aaatgaggtc aaatttactt ctgaaaaatg cactgtggtg agtttaacta caaacaaggt 3180 aattctcact gcacacagaa ggaaaaatat gtatgtggca aacttggaaa tctctcatgg 3240 agatgactta acatgtctca gtgctcaaaa taaaaatgct gatctctggc atcgtaggct 3300 gggacatgtg agtttatctt tattgaataa gttgatttca aaggacctgg tccgagggtt 3360 gcccaaaatg aagtttgctg aaaataaaat atgtgaagct tgtgttaaag gaaagcaaat 3420 cagatcatca ttcaagccca agaatcaggt tacatcatca agaaccttag agctgcttca 3480 catggacctt tgtggaccct tgaaggttca aagcagaaat ggcaagaagt acatcttggt 3540 gattgttgat gactattcaa gatacacctg gacgagattt ttgagatcaa aggcagagac 3600 agctgatgaa ctggtggtgt tcttcaaaat gattcaaagg cagaaacagc tgatgaactg 3660 gtggtgttct tcaaaatgat tcaaaccaaa ttaaatcaag ttgtttgcag cattagatct 3720 gatcatggga cagagtttga aaactcaaca ttggatagat tttgtatgga aaatggtaca 3780 agccacaact tctctgctcc aagaactcct caacaaaatg gagtggtgga gagaaagaat 3840 agaaacttgg tgaacattgc cagaactatg attattgaat caaatcttcc tcaaagtttc 3900 tgggctgaag ctgttaacac agcatgtcat gttaccaaca ggtgtctaat aagagctgtg 3960 ttgaacaaga ctccatacga actgctcaac aacaggaagc caatgctgaa ctatcttaga 4020 gcttttggat gcagatgttt tgtgctgaat aatgggaagg atgatctggg aaaatttgat 4080 cccagaagtg atgaaggagt atttgttgga tattcttcat ccagcaaagc ctacagaata 4140 ttcaacaaac gaacacaatg cattgaagaa agcattcatg ttgtgtttga tgaaaatgga 4200 agcttgaaga atgatggatc aaatgatgat gatgatgtac tcaaaatgct aagatccaag 4260 aagattgaag gtgctgaaac tgatgcagat caacaactga ataatgattg tgatgatcag 4320 aatcacagtc cacctgaaga ggatgctgag gttgaacagg atgatggggt acctggtact 4380 actcaaaact ccagccagag tacatcagac tccccagaag atgacgtcac tcctgatgaa 4440 gaagatcatg atgatctgcc aaatcagtct gctgcaaggt caggatggaa gcatagttca 4500 tcacaccctc ttgataatct catttctccc ttgaattctg gaattcaaac tagatcaaaa 4560 acaagaaatc tagttgcatt ctcaacattc atatcatcca ttgagcctaa gaatgtcaaa 4620 gaagcattaa gtgatgcaga ctgaatcaat tctatgcaag aagaacttca tcaatttgaa 4680 agaagtaagg tatggtacct ggttcctcga cctaaaggca gaacaataat aggaaccagg 4740 tgggtattca gaaacaaact tgatgaaaat ggagttatta ctagaaataa atccaggctg 4800 gtggtgcaag gatacaatca agaagaagga attgactatg atgagacttt tgcacctgtt 4860 gccagaatgg aagctattag aatcttaata gcttttgctg cttttatggg gatcaagctt 4920 tatcaaatgg atgtgaagag tgcatttctg aatgaagatc tcaaagagga ggtgtatgtt 4980 aagcaacctc ctgggttcga agatgcagag ctaccaaatc atgtgttcag attgaataag 5040 gcattatatg gtctgaaaca agctccaaga gcttggtatg aaagattgtc aaagtttctg 5100 ctgaagaatg gtttcaaaag aggcaagata gacaatactt tgttcttact aaaaagagaa 5160 caagaattgc ttatcattca agtttatgtg gatgacataa tttctggaac tacttcagaa 5220 catctctgtg aagaattctc atcattaatg ggaagggagt ttgaaatgag tatgatgggt 5280 gagttgacat tctttctggg gctgcaaatc aagcaatcat caaatggaac ttcaatatgc 5340 caagagaagt acatcaaaga gctgttgaag aaatttaata tgtttgattc caaacctatt 5400 gacacttcta tgggaacaaa tcccaagatg atagtagaaa aatctgatcc ccttgtgaat 5460 caggcaatgt acagagaaat cattggctcc ttgctgtatc tgactgctag caggcctgat 5520 attgtgtata gcgttggaat atgtgccagg tttcaagcat gtcctcgtga ttcacatctg 5580 aaggctgcaa aacgtattct tagatacttg aagaaaatag ggaacctggt tctcttttat 5640 cctgcaggtg atacttttga tctggttggt tttgcagatg ctgattttgc aggttatcaa 5700 gttgacagaa agagcacctc tggaatggct cattttcttg gatcatcact tatctcttgg 5760 ggcaccaaga agcagaactc tgtggctctt tcaactgctg aagctgaata tgtagctgct 5820 gcagcctgtt gttctcaatt gttgtggatc aggcaacact tagaagattt cggaatccac 5880 atcaaagcat ttcttctcat gtgtgacaac actagtgctg tgagtatggg aaagaactca 5940 tttcatcata agagaacaaa gcacattgat gtcagacacc attttttgag agatcatgtt 6000 gagaagggaa atattgtact cacatactgt ccaacggagg aacagattgc agacatcttt 6060 accaaggctc tcagtaagga tcaatttgag agaaatcgat taaaattggg gatgttgatc 6120 tccaagtgat gcttttagct tctaacagta gaactccctt gatggttaga tttgcagtgc 6180 aggtatcctt tgtgtgaacc ttaaatattt gaacaagatc actttttgta tcttttgtag 6240 gtatactctc aatagggacc tgctcagcaa aaaaagaggc tagaacaatt aaggaatgaa 6300 gttaaactct atcatggtac ttggtacctg tccaggttag catttttaca ttaattttaa 6360 actaaaaaat ttgaccgttg aaaaagtcac gtgtcaatca tcggttactc tgaccgatca 6420 gtccaatcgt ttctccctca aacgacgcat ctaatcaagg acctggcacc tattcacttc 6480 tttttaaaag gggtcttttc ttcttgaaac tctcatccgt ctcttaaact ttatctctct 6540 cttctatcac aaaacttctc acattcaaag gcaaatctgt cttcctcttc tttttgttcc 6600 ttcaacgacc ccttctagta tcacaaacat gtcttcttct tcgtcttctt ctaagcaaat 6660 gctggatgca cttagtgaaa tcgcgcccct tgcattttat tctccaacac ctgctcaagc 6720 cagccttcct cccctaccta gtcctccaca aaatactccg gacaaccctt tcttctccat 6780 tgatttatac acttcttcag tacctggtcc atgtgaagac atgtttcctg acaacatgtt 6840 taagggagac ctaccaaatc acagggcttc cgagtcaaat attctggcag caagtgagga 6900 acttgtgatt gagagcctgg caatgatgag tgaagaggcc agagcagaac ataatgacgc 6960 cctggaaaga gaagaggtaa gtccttctca acccatcttc gataaaaccc ctgatttagg 7020 gcggtattct tcttcctctt catctgaatc tgcaagtgag gaagcaccat taaaatggaa 7080 gttggagagt cgaaaaggga aggaaaaggt cgtggaggag actcctaaga gacgacctaa 7140 tacaaggtct gctgcacaaa aattgatggt ggatgccttg agggcaagtg cacgatctgc 7200 tgctgcagtc agaagtgcac gaaccttcaa ggtatcaaat tttaagatac ctaaaggaaa 7260 aattggttga gttgtctgga gaagaggttg aaaagaaaaa taacaagaag aagtcagaaa 7320 agaaaaggga aagggtacaa agaaggttga aaagtcacag tcaaaaggga agaaatctga 7380 aaggaagagg aagcggacac aggaacctgg tcctcaagct aggaaagttg agaatgtcaa 7440 cttgcaggaa gtagttgaca gtctgaggaa acaagcagtt ctcgctggaa gagtgtttga 7500 tatggggatt attactcctc cgggcatgga ctctctgcat gacatggtgg agatccagtc 7560 ttggctgcac ctgttcaaca agaaatcccc catcctccat gaagaagagg ttcgtgaatt 7620 ctattacaat gttcagtttc tggaagatgg gagtctcctc acacgtgtga acaatgttgc 7680 tatttctttg aatgaggagg tgttcggcaa aatcctcaga gtgcctatag aggggacccg 7740 gtccgttcag ggaaaaactt gctcttcaga atttgcatct ttgatttcta agactcccac 7800 aaccaaggtt gctgggatct ataagaaaat tatgaagagt gactatcagc tggtcttcga 7860 gtttgtcaac aaagtgattc tccctcgtac tgaaaagaga acacttgcta ctgctgctga 7920 cttgaggctg tgcagctttg aggctctgtg ccttcctagt ctcatgattg aacacattta 7980 caaaacagtt attgagagga aaggagtaca tggaatgggg tatggatact ttctcactaa 8040 agtattcaag cactttcaga ttcctcttgg tgttggaaag gtggggacag ttaaacaaac 8100 tatctctgag catactttgt ttgaatgtga atgtattgaa ggcagaggct taccaaaaag 8160 caagatggct caacttcttg aggacctgga tcaacttaaa catgagactg aagaactcac 8220 tgtgcggttg agtagtaaag aggctgaaat tgttgtactc aaagcagagc tgcttactgc 8280 acagagtgag gtacctggtt cttcagttgt acaagcactg gagaaagaga acaatgagtt 8340 gaaggcgatg ataactgccc tgcaagaaaa ggccatcaag gataatgatg ctgccaatgc 8400 acgactcact cttgctatcc agtccctatc taaaactccc ccctcttcct aaactgtcaa 8460 tcaatccttc cctgtgtctc ttttgttgtg tggctaatca tcgtgttaat ggatttttag 8520 tttgttttta atgtatttat gttataatgg catgttggtt actttattcc tttgttgttc 8580 ttcctatgtt cttttgtgaa tgtttttcct ctactgtttg attgctgttt gctctgatct 8640 tgttcattat ttatgttgac tcaatggttt actgcatatc ttttttatga tgccaaaatg 8700 gggaagtaaa ctgtaagtat ctaaataagg gggaacatac attaagggga acatacatta 8760 agggggaata ttcagaaaaa ggggaatata cagaaagggg gaatacaaag tcagggggaa 8820 cgattctggt gaagatttca gatcatatca ttgtttgtca tcatcaaaaa ggggggaaat 8880 gttatttgta gttttgatga tttgacaaac ttagggacct cataaaggta ccgggttttc 8940 tacttgagta ttgcaggtgt cttctttgaa gtattgcaga tgaaacaaac ccagggacct 9000 agtagaggta ccaggccctc atgatgatga gccagtcaac tactagctgg agacgtacag 9060 aaagtaggtg cacacttccc gattgcgtca gaaaagtgtg acctttccaa ccaatggcaa 9120 agaagtttag gaaagtgact tgccatataa aaggcacttt cctaaacatt tgttttttag 9180 tttttgcaac ttgataaaaa cttttcaaga actcttgcaa aggctacaca aagcaaaggc 9240 agaatcattc ctaggacaac agcaacatct ggagcttttc gtctagttgt ttaggaattt 9300 attctcttgt tcttaaattg taaaccactc ctaaatctat aaaggaattg gtgtgttgtg 9360 ttaaaggtct aggttgtcca ggtgggatag cttagtgggt agattgtttt tctactttgg 9420 cttgttgagc aatagaggtc tattgcttaa cggtaagatt gataactctt tcttacgttt 9480 ggtgtaatcg tgtttcactt ttgcttttga agattagtga aaaacaatgg aaaatcctgt 9540 gagacaggtc gtggttttac tcccttaagc aaggaggttt ccacgtaaaa tcattgtgtt 9600 gattttactg catttaactt tctggtaatt ttctgaaata aagtaaggga cctggtccat 9660 tactattaag tgaagccata cattctatca gggaa 9695 // ID Copia-1_TC-I repbase; DNA; EDCOT; 4074 BP. XX AC CACC01007196; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-1_TC_; KW Copia-1_TC-LTR; Copia-1_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-4074 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01007196; Positions 13838 17911. XX CC Positions [1634-2164] - Integrase core CC 'GCTTC' target site duplication CC LTRs are 98% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS 1451..3208 FT /product="Copia-1_TC-I_1p" FT /translation="MKIEHTTCVGQEIDADLWHKRLGHVNFISLSHMINSN FT TVEGLSSMSIPKQICSTCIHGKQSRMPFPLSSSWRASDKLQLVHSDVGGPV FT NTASLSGTIYYVIFIDDFSRYCWIYFLKNKSEVFEKFKSLKALVENESEKR FT VKVLRTDNGSEFCSNTFKSYLVEKGIKHQLTISYTPQQNGVCERKNRTILE FT MTHCLLHEKGLPKLFWAEAASNAVNLLNILPSSSLKNRNAHEIWLGEKPSM FT THLRIFGCICYVQIPEQKRTKLDYKTEIGIHLGCSSVSKGYRVYEVQSKKI FT SVSRDVWFDEKSRWNWETNAVGISEKVNFFDDAVLNEQNHEEDIEDESLAV FT RGTRTLQDIYSRCNTAIVEPPNFEEASADNNWRQAIETEMEMIRKNGTWVL FT VDRPVDQNIIGVKWIFKTKLNADRTVNKYKARLVVKGYSQVYGVDYWETFT FT PVARHDTIRLLTAAAAREGWKIWHMDVKSAFLNGTLSEDIFIEQLEGFAEP FT GNEGKVCKLVKALYGLKQAPRAWYDRIDTYLKSPGFIRSANEPTLYVSDST FT FSDKLIISLYVDDLLITGPSGLVLDDFKRSMKQEFEMSD" XX SQ Sequence 4074 BP; 1333 A; 678 C; 913 G; 1150 T; 0 other; tggtatcaga gctgtaagag ggatcttgag ggacctagat ttctttcatt tttcttgtca 60 tcaagtgtga aaaccagcat catcgtagta ttcttttttt gcttgcattt cattgttttt 120 tcaatggctt ctgcaagtta caatgcctcc actccaccta tttttttcag gagaaaatta 180 ccctatatga gctgttaaaa tgaaggctta tctccgagcc tttgatttgt gggaggtttt 240 agaagttggg ggagaacccc cggttatgag gcatgcaaat ccaaccatca ctcagataaa 300 gcaacacagt gaggaggtag ctgagcacta caaagctctc tcatgtattc actctgccgt 360 gactaactca atcttcacaa gaattatggc ttgtgaatct ccaaaagaag cttgggacaa 420 gcttaaagaa gaatttcatg gcagtgacaa aacgagacag attcaagtgc tcaatttgct 480 gagggagttt gaggtgctaa agatgagaga agatgaaact ataaaagact attctgaaaa 540 agtcttgaag attgtcaatc aactgaggtt attgggtgaa gagcttcctg acagaaggat 600 tgtccataaa tttctggtta gcttaccaga aaaatttgaa gcaaaaatct cctcattgga 660 agactcgaag gatatgtcta aactctcagt gactgaattg ataaatgcgc tactagcgca 720 agaacaaagg agagccattc gtcaggagga gagtgttgag actgctctta tagcaaggac 780 gaaggatctc agacttggca actacaatgc taaaaaacat gacaacatca ggcgagataa 840 agaaaagaag aatggtgatg gcaagcaaaa caaatagaga aataaatttc ctccctatca 900 gcactataaa aaaaggaatc atactcctaa atattgttgg tacaggccta atgttaagtg 960 taggtcttgt aaccaattcg gtcatgttga aaaggtttgt aaggccaaga atagtcacac 1020 agatgaaaag gcagcagttg cagaacaagt agatgcaaca gaagaacaac tctttatggc 1080 tcagattgca gatgatgagg aaagaaacac ttggctcata gatagtgggt gctccaatca 1140 catgacaggg aatgatcaac tctttactaa gcttgacaga aacttcaagg caagagttag 1200 aattggaaat gagatttatt tgaagattat gggaatagga acagtagctg tggaaacaat 1260 gaactgcacc aaatacatct cagaggtcca ttatgtgcct gaagtgacac aaaatcttct 1320 aagtgtgggt caactagctg aaaatcacta cactcttttg ttcaaagaaa aattctgcac 1380 aatttttgat ccatctggtg atgagttaat gattgtcaaa atgaaaaatc gatgctactc 1440 tattgactga atgaaaatcg agcacactac ctgtgttggt caagaaattg atgctgactt 1500 gtggcataaa aggttaggac atgtaaactt tatatctttg agtcacatga ttaattctaa 1560 cactgttgaa ggactttcga gtatgtccat tcctaagcaa atttgcagca cttgtataca 1620 tggcaaacag agccgtatgc catttcccct ttcaagttct tggagagcaa gtgacaaatt 1680 gcaacttgtt cattctgatg ttggtggtcc agttaatact gcttcactaa gtggtaccat 1740 ctattatgtc atttttattg atgacttttc tcgatactgt tggatttatt ttttaaagaa 1800 taaatcagaa gtatttgaga agtttaagag cttgaaagca ttggtggaga atgagtctga 1860 aaaaagggtg aaagtcctta gaactgataa tggttcagag ttctgttcga atactttcaa 1920 aagttatctt gttgaaaagg gaattaagca ccagttaaca atctcataca cccctcagca 1980 aaatggggtc tgtgagagga aaaataggac catattggag atgacacatt gtttactaca 2040 tgagaaagga ttgcctaagt tgttttgggc agaggctgca agcaatgcag tgaatttgct 2100 taatatcttg ccttcaagca gtctcaaaaa tcgtaatgct catgaaatct ggcttggaga 2160 aaaaccttct atgactcact tgagaatttt cgggtgcatt tgttatgtgc aaattcctga 2220 acagaaaaga accaaactag attacaagac agagatcggt attcaccttg gttgcagtag 2280 tgtctccaaa ggatatcggg tttacgaagt tcaaagcaag aaaatatctg tcagtagaga 2340 tgtttggttc gatgagaaaa gtagatggaa ttgggaaacg aatgctgttg gaatttcaga 2400 gaaagtgaac ttctttgatg atgcagtttt gaatgaacag aatcatgaag aagacattga 2460 agatgagagt ttagcagtta gaggaacaag aacattgcaa gacatatata gcagatgcaa 2520 tactgctata gttgagcctc ccaatttcga agaagcatca gcagataaca attggagaca 2580 agccatagag actgaaatgg aaatgatcag gaaaaatggc acttgggtcc ttgttgatcg 2640 gccagtagat caaaatatca ttggagtaaa atggatattt aaaacaaagt tgaatgctga 2700 tagaacagtc aacaaataca aagccaggtt agttgttaag gggtattccc aagtttatgg 2760 ggtggattat tgggaaacat tcactccagt ggccagacac gatacaataa gattactcac 2820 tgctgcagca gcaagagaag ggtggaaaat ctggcatatg gatgtcaagt cagctttttt 2880 gaatggcaca ttatctgaag acatcttcat cgagcaactg gaaggctttg ctgaacctgg 2940 caatgaagga aaagtttgca agcttgtgaa ggcattgtat ggtctcaaac aagctccccg 3000 ggcatggtat gatagaatcg acacatattt aaagtctcca ggctttatca gaagtgctaa 3060 cgagcctaca ttatatgtaa gtgattcaac tttttctgat aagctcatta tttctcttta 3120 tgtggatgac ctgttaatca ctggtcctag tgggttggtt cttgatgatt tcaaaagaag 3180 catgaaacaa gaatttgaga tgtcagacta gggggaaaca acatattttc tgcgcttgca 3240 atttcatcaa gcttctgatt ttatatttgt gcatcaacgc aaatatgctt gtgaaatgct 3300 gataagattt cgcatggaag cttgtaaatg gtggaaactc cattggttac cggtgcaaag 3360 tttaataaag atgatggagc tccagcagct gttgattcaa cttatagaag tttaattggc 3420 tctctactat acttaacagc ctcacggcct gatttaatgt tcacagcaag cttattatcc 3480 agatatatgc aagctccttc agagattcat tttttagctt tgaaaagggt tctgcgatac 3540 attaagggaa ctgtggacta tggactcaag tttgaaaaac gagaaagcaa ggagctggtg 3600 ggatattgtg acagcgattt ggctggatgc ttggatgatt ccaagagtac gaatggattt 3660 tgtttttcat ttggtagtgc tgttttttct tggaattctc gaaagcagga ggtggttgcc 3720 caatcatcag cagaggctga atatatctca gccgcttcag caacaaacca tgcagtttgg 3780 ctaaggaaaa tgcttggaga cttgggtttc gtacaaatag agggcactac tctgttcatt 3840 gatagcaggt cagccatttc aattgccaaa aatcctgtac aatatggtcg cactaaacac 3900 atcagagtga aatttcattc cattagagaa gctgtgaaga atggagaaat caaggtagag 3960 cattgcagca ctgaagatca acttgcagat atccttacta aaggattaag caaagaaaaa 4020 ttcatttatc tgagagccaa attgggagtc tgtaagtcag gaaccaagga ggtg 4074 // ID CALYPSHAN2_I_MT repbase; DNA; EDCOT; 8836 BP. XX AC AC147496; XX DT 28-JAN-2007 (Rel. 12.01, Created) DT 06-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, CALYPSHAN2_MT, from Medicago DE truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Internal; Interspersed; terminal; ORF; CALYPSHAN2_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-8836 RA Shankar R. and Jurka J.; RT "CALYPSHAN2_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 1-1 (2007). XX DR EMBL/GenBank/DDBJ; AC147496; Positions 56449 65284. XX CC The internal regions has intact domains for gag and pol in two CC ORFs with Gypsy-like arrangement. It has domains for aspartyl CC protease before polymerase and RNAse and integrase after CC polymerase, respectively. XX FH Key Location/Qualifiers FT CDS join(167..1441,1553..1777) FT /product="CALYPSHAN_I_MT_1p" FT /translation="MTTPEEAQTMKSQIAQLLEQNEALLASVETIQQQQMQ FT ERTDSHHGELDEPEPQPFSAEIWNAPVPENFKPPHLPTFNGRGDPSEHVTV FT FNTRMSVYGVADSLKCKLLAGAFADAALRWYMSLPRFSIVGYQDMIKKFTQ FT QFSGSRHRKVLSTSLFNVRQGPNESLKEYLARFNESTIKVSNPNQEVFVGA FT FQNGLRAGQFNESLAQKPADSIEEVIARAECYVKGEESNVERKARDAKERG FT SSGAERRNPYVPPNRDRGAFKKTNDRSSHRYAPDHFTPLNTRPEKILKEVL FT ESRVIPPAAEPRFKYMGLNKDAWCKYHQVLGHGTNDCIHLKREIEKLIQSG FT KLRGYTKNADDRRRPESTQDKPALEPKHTLHTISGGFAGGGESGKLRKKYA FT RQVILLGDAHEPERIPTISFSQEDFGQGNPSDGSERRTASTFQRDPVGFYW FT GEGTCTWLCHSQNDLRNRRSTKIHQDQVFGDQRTQFIQRYHWTSFHQSFRC FT LCLY" FT CDS join(1344..1355,1368..4709) FT /product="CALYPSHAN_I_MT_2p" FT /translation="MLAREMPMNQRESQLFLSPKKTSDRVIPHDDDPLVIS FT FQLLNWEIKRVLIDIGSSADVLYYDTFSKMGLSEEQLQPFKGTLSGFTGEK FT VHARGYVTLKTTFGTGDQQKSIKIRYLVINAPSSYNAIIGRPSINLLDAFV FT STKHLMMKYPLDNGRVGVIRGDQKIARECYHASLKLGGKGRETLGVNLIDL FT DPREDYQQERIVPIEDLKDIVIGSDPNRTTKIGASLKEAEERNLIQLLQEN FT FDLFAWSPSDMPGIDIKVACHHLAVSPSVKPVVQKKRKMGEEKRKAVDEEV FT KKLMEARFISEIKYPTWLENTVLVKKTSGKWRMCVDYTDLNMACPKDPYPL FT PNIDHLIDNAAGYKTLSFMDAYSGYNQIKMDPLDAPKTAFMTNQKNYHYEV FT MSFGLRNAGATFQRSMDTIFSAQIGRNLEVYVDDLVVKTPAEGQHSVDLKE FT IFQQVRKANMRLNPAKCTFGVHAGKFLGFLLTKDGIEANPDKCQAIINMRS FT PCSVKEVQQLTGRLAALSRFLSCAGDKAFSFFPSIKKKEKFEWTPECDKAF FT QRIKVFLTTPPILHRPTQGAVLSLYLSVSENALSSVLVEDSEEKEKPVYFV FT SRVFKGAELRYQKIEKLALAVVATARKLRPYFQSHRVIVRTNYPIKQILSK FT PDLAGRMVSWAVELSEYDILFAPRNSIKSQVLADFMVEFSSPIETTTPLVW FT TLSVDGSSNLKGSGAGIVLEGPGDLLIEQSLKFEFKASNNQAEYEALIAGM FT ILAREMGVENLRARSDSQLMTNQISGEYQTKDSQLSKYLTSVRSFAKSFNF FT FEVIYVPREQNARADLLAKLASTKRPGNNRTVIQEIVSAPSYETTEVLFTT FT QEAKGWMTPILQYLTGSFEPANEEERLSVKKRAAKFTIVAGKLYKRGAVTP FT LLRCLGEEETELVLLEVHEGVCGSHIGGRSLVAKLLRAGYYWPRMTQDCCE FT FVKKCDKCQRFSDKKIAPANELTSVFSPWPFHKWGVDIVGPFPPAPGQLKF FT LIVGVDYFTKWVEAEAVSKITAEQVIKFYWKKIICRFGLPRNIVTDNGTQF FT ASTRVVDFCKQLGIETKFVSVIHPQANGQAEAANKVILNGIKKKLEAAKGL FT WAEQLYEVKT" XX SQ Sequence 8836 BP; 2674 A; 2038 C; 1959 G; 2165 T; 0 other; gttggcgccg tctgtgggaa acggtaaaac tagccttaac cacgattctt tgtatcgcgt 60 tttcgatcca aggaacaact gagtcgtagt tttctctgcg atttgatacc ctaaccctta 120 ctcaaaccta aatcgcacct cacgtacgat ttagagaaaa tccatcatga caacaccgga 180 agaggcgcaa acgatgaaaa gtcagatcgc ccagctgttg gaacagaatg aagctttact 240 cgcctcggtt gaaaccatcc aacagcagca gatgcaggag aggacggact ctcatcatgg 300 cgagcttgat gaaccggaac cccagccgtt ctcagctgaa atatggaacg ctccagttcc 360 ggagaacttc aaaccgccgc acctgcctac cttcaatgga aggggcgatc cgtctgaaca 420 tgtgacagta ttcaacaccc ggatgtccgt atacggagtc gccgattctc ttaagtgcaa 480 attgttggcg ggtgcttttg cggacgcagc tttgcgctgg tacatgagcc tccctcgctt 540 ctccattgtg ggttatcagg atatgattaa gaagtttacc cagcagttct ctggtagccg 600 ccaccgaaaa gtattatcca caagcttatt caatgttcgt caaggaccaa acgaatcgct 660 aaaagagtat ctcgcccgct tcaacgagtc aacaatcaaa gtctccaatc ccaatcagga 720 ggtcttcgtt ggagcttttc agaatggctt gcgtgctggc caattcaacg aatcgctggc 780 acaaaaaccc gctgattcaa tagaagaagt aattgctcgg gccgagtgct atgtgaaggg 840 agaagagtct aatgtggaaa ggaaagctag agatgcgaaa gagagaggga gttcaggagc 900 agagcggcga aacccttatg tcccgcccaa cagggataga ggggccttca agaagactaa 960 cgataggagt tcacatcgtt atgcacctga tcacttcacc cccttgaaca cacgccccga 1020 gaaaattctc aaggaagttc tcgaatcaag agtaatcccg ccagctgcgg aaccccggtt 1080 caagtatatg ggtctgaata aagatgcgtg gtgcaaatac catcaagtgc ttggacatgg 1140 cacaaacgac tgcattcact tgaaaagaga gattgagaag ctgatccaga gcggaaaact 1200 aagaggatat accaagaacg ccgacgatag gcgccgtccg gagtcaaccc aagataaacc 1260 tgccctagag ccaaaacata cactccatac catctcggga ggttttgccg gaggcggaga 1320 gtcaggaaag ttgcgaaaga agtatgctcg ccaggtaata cttctaggag atgcccatga 1380 accagagaga atcccaacta tttctttctc ccaagaagac ttcggacagg gtaatccctc 1440 atgacgatga tccgttggtt atatcttttc agctcctgaa ctgggaaatc aaacgggtac 1500 tcatagatat cggaagttcg gcagatgtcc tatattacga caccttcagt aagatgggtc 1560 tgagcgaaga acagcttcaa cctttcaaag ggaccctgtc gggttttact ggggagaagg 1620 tacatgcacg tggctatgtc actctcaaaa cgaccttcgg aaccggagat caacaaaaat 1680 ccatcaagat caggtatttg gtgatcaacg cacccagttc atacaacgct atcattggac 1740 gtccttccat caatctttta gatgcctttg tctctactaa acatttgatg atgaagtatc 1800 ccctggacaa cgggcgagtt ggggtaataa gaggtgatca aaagatcgcg cgagaatgct 1860 atcacgccag cctcaagctc ggcgggaaag gcagagagac actcggcgta aatctcattg 1920 accttgatcc acgagaagat taccagcagg aacggatagt gcctatcgaa gatttgaaag 1980 atatagtgat aggatccgat cctaatcgga ccaccaagat cggagcttcc ctcaaagaag 2040 cggaggaacg aaacctgatt cagcttttgc aagagaattt tgacctcttc gcatggtccc 2100 cctctgatat gcctggaatt gatattaagg tggcttgtca ccatctggca gttagcccat 2160 ccgtaaaacc ggtggtacag aagaagcgga agatgggcga ggaaaaacga aaggccgtag 2220 acgaagaagt aaaaaagtta atggaagctc gttttatcag cgagatcaaa tatcctacat 2280 ggctggaaaa cactgttcta gtaaaaaaaa cctcagggaa atggaggatg tgcgtggatt 2340 atacggattt gaatatggcg tgtcctaagg atccatatcc cttgccgaat attgaccatc 2400 tgatagataa tgccgccggg tacaaaactc tgagttttat ggatgcctac tccggctaca 2460 accaaatcaa aatggaccct ttggacgccc ctaaaactgc cttcatgacg aatcagaaaa 2520 attatcacta tgaggtaatg tcatttggtt tacgaaatgc tggagcaact tttcaacgct 2580 ctatggatac aatcttcagt gcccagattg gaaggaacct ggaggtatat gtggacgatc 2640 ttgtagtgaa gacgcccgct gaaggccaac actcggtgga cttgaaagaa atttttcaac 2700 aagtaagaaa ggcgaacatg cgccttaatc ccgccaagtg cacgttcgga gtacatgcgg 2760 gcaaattcct gggttttttg ttgaccaaag atggcattga agctaatccg gataaatgtc 2820 aagccatcat caacatgaga agcccatgta gtgtaaagga agttcaacag ttaacgggaa 2880 ggttggccgc gttgtccaga tttctctctt gtgcaggaga caaagctttc tctttctttc 2940 cctcgatcaa gaaaaaagaa aaatttgagt ggaccccaga atgtgacaaa gcttttcaga 3000 ggatcaaagt gtttctcacc acacctccta ttcttcatcg cccaacacag ggggcggtct 3060 tgtccctata cctttcagtg tcagagaacg ccctgagctc cgtcctcgtc gaggactctg 3120 aagaaaagga gaaaccggta tatttcgtca gcagagtctt caagggagcg gaattacggt 3180 accaaaagat tgagaaatta gcattggctg tggtagcaac cgccagaaaa ttacgcccgt 3240 atttccagag tcacagagtg atcgtccgaa ccaactaccc aataaagcag attctcagca 3300 aaccggatct agcaggaagg atggtgtctt gggcagtaga actctcagag tatgacatcc 3360 tgttcgcccc cagaaacagc atcaaatccc aggtactggc ggactttatg gttgaatttt 3420 cttctcccat tgaaactacc acgcctttgg tttggacatt atcagtggat gggtcgtcga 3480 atttgaaagg aagtggagcg ggtatcgtcc tggagggacc tggcgatctt ctcattgaac 3540 aatcgttaaa gttcgaattc aaggccagta acaatcaggc ggagtatgag gctttaatag 3600 ctggaatgat tttagctcga gagatgggcg tggagaacct cagagctcgg agtgactcgc 3660 agttgatgac caatcagatc tccggggaat accaaactaa agattcgcag ctttctaaat 3720 atctcaccag cgtacggagt ttcgcgaagt ctttcaactt cttcgaagtg atctatgtac 3780 ctagagagca gaatgcgcgg gcagatttgt tagcaaaact agctagcact aagcgaccag 3840 gcaataaccg aacagtgatt caagaaatag tgtccgctcc aagttatgaa acaacggaag 3900 tcctcttcac gactcaagaa gcaaaggggt ggatgactcc aatcttgcaa tatctgacag 3960 gttcctttga gcctgcaaac gaggaagaaa gactgtcggt caaaaagaga gccgccaagt 4020 ttactattgt ggcggggaaa ctttacaaac gaggggcggt tactcctttg ttgaggtgcc 4080 taggagagga agaaacagag ctggtccttt tagaagtaca cgaaggagtt tgtggaagtc 4140 atatcggcgg acgatctctc gtcgccaagc ttttgcgtgc gggatactat tggcctagga 4200 tgacccaaga ttgctgcgaa tttgtcaaaa aatgtgacaa gtgccaacgg ttttctgata 4260 aaaaaatagc tccggcaaac gaattgacct cagtgttttc tccttggccg tttcacaagt 4320 ggggagttga cattgtggga ccttttcccc cagctccagg acagttgaag ttcctcatcg 4380 tcggcgtaga ttacttcacc aaatgggtcg aagcagaagc agtttctaaa ataacagcgg 4440 aacaagtaat aaaattctac tggaagaaaa tcatatgtcg tttcggactt cctcggaaca 4500 tcgtaacaga taatgggact cagttcgcca gcaccagagt agttgacttt tgcaaacaat 4560 taggaatcga aacaaaattc gtatcagtaa ttcatcctca agcaaatggg caagcagaag 4620 ccgccaacaa agtaattctg aatggtataa aaaagaagct tgaggcagcc aaaggactct 4680 gggcagagca gctttacgag gtaaaaactt gaatgtcttt cgatttaaag aaacttttta 4740 attaactttg tcactaacaa acgaaccaga aataaaggtc ttttgtctac ataaaatgcg 4800 taagtacagg ttttatggtc ataccacaca acaccacatt ctactaccgg agagacacta 4860 ttcactatgg tttacagagc agacgcaatg cttccagtgg agattgatac cccaacatgg 4920 cgacgagaaa atttcagtga agaagccaat aaggtcggag ttcagtgtac gatggatatg 4980 atcgatgaag tacgtgagtc cgcacatatc cgagaattcg ccgccaaaca aagagctgcc 5040 cagcgatata attcaaaagt catccctcgc agtatgaaag aaggcaacct tgttttgaaa 5100 caagtcgtcg cccctaccag gataggaaag ttgttgccga gttgggaggg accatataga 5160 gttaaagaaa aactccaaca tggcgcttat aagttggaag aattgaatgg gaagacagta 5220 ccaagaactt ggaatgcaat caacttacga cattattata gctgaacgcc aagtttttat 5280 ttcttttgac atttgcaaaa ctctttatgt ttcttttgca gacgacctta tgtttttctt 5340 tccttgaata gatggaataa aagaattggg ggagcactct ttttcccctg caagggcagg 5400 gtttttaacg aggcacccca atttcttcaa aaatgtgtga tcttttatgg tattacgaaa 5460 agaaaccgtg agttcgacac caaccttgtt aaaggctctg tacttgtcgc ccagtcagaa 5520 gaagccgtga gttcgacacc aaccttgtta aaggctctgt acttgtcgcc cggttaaaaa 5580 tccgtgagtt cgacaccaac cttgttaaag gctctgtact tgtcgcccgg tcagaagaag 5640 ctgtgagttc gacaccaacc tttttaaagg ctctgtactt gtcgcccggt taaaaatccg 5700 tgagttcgac accaaccttg ttaaaggctc tgtacttgtc gcccggtcgg aagaagccgt 5760 gagttcgaca ccaaccttat taaaggctct gtacttgtcg ctcggttaaa aatccgtgag 5820 ttcgacacca accttgttaa aggctctgta cttgtcgccc ggtcagaaat cgagatcaat 5880 tataataaag gttccgtaaa tttcaaaatc aagtgatatg caaatctacg tgaaaataaa 5940 atatattccg aataagatac tcgtgaacag agatccaata agaggattct acaaagcaaa 6000 ataaaaacta ttagagtaaa agtcaagtta aacgaaaggt tctcaaaaaa agtaaaagtc 6060 aagttgtcca caaaaataaa tatttgcctc aaaagaagcc aggcgttaca actcaaaagc 6120 gcccataaca gcaataagcc taaataaaat aaacaactac aaggaaaagt caagcatcag 6180 aaatcttcaa ggctcttcaa ccagctcgcc atcttgaacg aactttagag aatcaagacc 6240 cgacaaatcc agttctggat agaaatgggc cacctgtgac ttcgcccttt gaaaaccatc 6300 ctcaaagaac ccagctagcg ccatcttgcc attctcgacc tcatccttcg attttttcaa 6360 gtcatctttt aatttggtat tctgggcgtc aagctcgccc ttctctacct gccagtccga 6420 tttctctttc tctgcatcgg tgactgcttt ctccaacaca gctttttcct tcaaaagccc 6480 ctccaccctc tcttcaaaag ctatagcctt gtgcttgaat ttctccacat ccttcacaga 6540 atcctgatac tctttctcta agacttcgtg tttcttctcc atcgaccgaa tgtataacaa 6600 agttcggaga gcactggtcc cggcatcttg caccagctcg tcaaatttcc catgaaaagc 6660 agcgtcttta tccactgctg aaaatgggac gttatcctcc atatagcggc gatagttgaa 6720 atcacggtgc caaaatgaag cttcaaacgc cgcgtcagcc tccactgata aagctcttcc 6780 gcctcctttc cttgatgttt tcattttctt cttctgggga aagatggtcg cgtcgttcac 6840 ctcattcacc ataacctcgc cctcagctat cttctcagac atagcatcaa ccccgccggc 6900 gacaggttca aagctggcag ggttatctct tttcttcgca cctttacgaa gaatcacccc 6960 agcagggtcg caggagatat gttcgccaga agcattcttt tccttgagtg cttcaaggta 7020 cttccttctt tcttttccgg ataaaggcag cattggcact gtacaaacag gaaaaataaa 7080 aaccacatca gtcagacaaa tcaaccaaaa caaaaaaaaa aacacgtaat gaaatttcgt 7140 aaagaaaaga acatgaatct tcaacactca cgaaggtaca attcaaggtc ctccgaatcc 7200 ccttctttgt ttaaaagttt tcgaatgtcc gtatgacgca tccgatctaa aaagccaact 7260 acaccttgtt cgtagggggt catcttcaga tagtgatagc ctgagacagc caaaggattg 7320 gcagtccacc ctaaaggaaa cttaacctcg cccgcgacac tagcaacgct aactgtggaa 7380 tctgttgacg cttgaaccct caaaaaactc tttttccaat ccttcttaaa gttcgaagca 7440 aaaggaggga aaagctgctt cccaggatga gcgctaatag gaacccagga acctttatcc 7500 acccctttca ttccgtaaaa atggaaaaag actccggctg aaggaaccat gtctaaagcg 7560 tcgcataaaa tctcaaaatc tcgaatgaaa gcccagctgt taggatgaat ctgagttggg 7620 gcaacattga gcatgcgtag aacgtccatc tcgaacaggg taaagggaat tcttacccca 7680 aattcttcca atacggcgcc atacatgtgg aagatctctt tcaccccctt agggcgcata 7740 gaacacacct tctcgtcggg gggacagggc gccaagacaa tatcctcctc tcttgtcgtc 7800 gacgaaaccg agagcttact actaaagaag tttatcttcg cctcatcatt gtatgtagac 7860 tcgtatcgtt gcacgtcgtc tgaaaagctc tcaaatatca ttttccggac atgcaagctg 7920 agtacccttt ccatgaacca tttctgaaga agagacctcg acgatttctt ttccacaact 7980 ttctcctggg gtcgtatata ataaaacaca atcactattg tcagaatcgc tacagtcact 8040 ctcgctagaa atgttggaga aagtcatatg actaaaataa gtggaatcat acactttcca 8100 attgattaaa ccattttttc gagtcgcatg cttcaaacat tgtaatcata gtttttgtcg 8160 gtctaaagga tccgagggag gtatttctct cccactctca tcgcactccc taactactac 8220 catggtttac taaaacaaaa taaaaagagg aaaggagcaa gcggattacc tgagtctgtg 8280 cgaacggaca ggcaaaagca gaagaagcaa gaaaagagag ttctttgcca cgggagaaac 8340 ggaaacgatg aagtgaaatg aaaagtgaag gttttttcgc ctcttttaaa ggaaaaaaaa 8400 taaacttttc attttctcga aaaacgtgcg cattcagcgg atcgccaaca cgtgtaaacg 8460 attagttgaa gagttaacac gccattggaa acgcaaaggt caggagatgt ggaccgttgg 8520 atgaaaagaa aatctaagtg tcaaccatct cgatcgaagc ttgagaacgc caatgcgatc 8580 actttagaac tgaagcacca cgccttgtgc caagacttgt gcttgggggc tatggaccgt 8640 cataatattc ctcaaaagta gaaggccctc caaaaggggc ttaagaggac ctgaaaaggg 8700 cctccaaagg gtctgttggg tttaggcgcc ctctcctaaa aagacgtcgg ccttatagat 8760 cctcagaact tgcctaaatg atctcttcag cttaaaaagc accacgtctt gtgccaagac 8820 ttgtgcttgg gggcta 8836 // ID Copia18-PTR_LTR repbase; DNA; EDCOT; 255 BP. XX AC LG_III; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia18-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-255 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-255 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 209-209 (2007). XX DR Genome; LG_III; Positions 15255507 15255761. XX SQ Sequence 255 BP; 77 A; 44 C; 43 G; 91 T; 0 other; tgaaggagtc ttctcgtaaa ctatattctg gttgttagag tttgttagaa taaataacaa 60 actagaaggg agagtcctag ttttacaggg cattgcaaat tacagttagc aacctctctg 120 ttagagtttg ttacttttct gttattctgg tatcatgtat tagaggctat ataaagccaa 180 gagttcttgc tgaataatac aatttccatt tatcccagtt cacgtatact tcttcaatca 240 tccataatcc taaca 255 // ID DNA9-5_Mad repbase; DNA; EDCOT; 667 BP. XX AC . XX DT 13-OCT-2010 (Rel. 15.1, Created) DT 13-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-5_Mad. XX NM DNA9-5_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-667 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1486-1486 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TSD is 9-bp long. TIR is not obvious. XX SQ Sequence 667 BP; 289 A; 78 C; 79 G; 221 T; 0 other; ggggctttta gatccaggtc caaaaacata gagtgttttt aggagtgact ccagttatct 60 aattatatgt ttttatttct tttatactcc ttttatattt tctaaaaata ttaaaaatca 120 attaaaatct tttaatatta tgcatttttc aactccaaaa tatctaatta atatcttata 180 aacaaaaaaa aattaatata ctaacataaa tctatctgca aaacattcta ccctaactca 240 agtagcaaat atatgaatgt atattatacc tataagtgag atatgaaacc taactaaaag 300 gtagaaaaaa aacataatat acctacaagc aagacacatt aatctgtgac aggttgacta 360 tgaaaaagaa tctgtcatat aggtagataa atacaattaa cctgtgatat aggttgatta 420 taaaaattta aaaaaaaatc tataaatggg ttaaagcagg aggaagaaca agaaataaca 480 aaaaatatat aaaaagaaat aatcaaagag ataattagga agaaatttga tttttacaat 540 aagttttttc ttttaagaga taattattga taattaaata attaaattta aagaattgga 600 cttattttaa taaattggac cattcctact attggctcaa aaaattggag ttatatcaag 660 tttcccc 667 // ID LES0 repbase; DNA; EDCOT; 613 BP. XX AC U91991; XX DT 19-NOV-1998 (Rel. 3.1, Created) DT 19-NOV-1998 (Rel. 3.1, Last updated, Version 1) XX DE Nonautonomous DNA transposon LES0. XX KW DNA transposon; Transposable Element; Nonautonomous; LES0; Les0.6; KW nonautonomous DNA transposon; SOL3; TIR. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RA Oosumi T. and Belknap R.W.; RT "Characterization of the Sol3 family of nonautonomous RT transposable elements in tomato and potato."; RL J. Mol. Evol 45(2), 137-144 (1997). XX RN [2] RA Oosumi T., Garlick B. and Belknap R.W.; RT "LES0."; RL Direct Submission to Genbank (05-MAR-1997)CIU, USDA/ARS, 800 RL Buchanan Street, Albany, CA 94710, USA. XX DR GenBank; U91991; Positions 1 613. XX CC LES0 is a nonautonomous DNA transposon with 45 bp long SOL3-like CC TIR. XX SQ Sequence 613 BP; 223 A; 80 C; 80 G; 230 T; 0 other; cactacccac ccattactaa ttaaatccca ctcagttaat aaaccaattc taatatcaaa 60 atcgccctaa acaatactga aacatgacga aattacagac tcctgtaaat gattcaaaat 120 tattcgagtc cgaattgaaa ctccaattaa atttaggttg agccgcttat ttaggaagac 180 aattttaatg agattctctt tcaaacttga atttaaattt tatgattaaa agtaaagaag 240 tagtaaatcc tgaattaatt cattcacttt tttcaatata attttataaa tatttatcat 300 ttgtttgaaa tacttaaact ttaatatatt ccttttaaaa aatatatata ttaagtaaca 360 tcacataatt gagacgaatg attaattaag atgaacatag tcaaattttt aagtttatcg 420 gtaattttta attagaaatt taattgtaat atgttttgat tgtgtacgtg aatgtatgat 480 aatctacttc tacaaacatt ttctcctcaa atttttagaa acattcattg acagtaagct 540 tttcaattgt tgcattagta atggggcgga tttattaatt gggtgtggtt taattagtaa 600 tgggtgggta gtg 613 // ID Copia51-PTR_I repbase; DNA; EDCOT; 4147 BP. XX AC scaffold_354; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia51-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4147 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4147 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 282-282 (2007). XX DR Genome; scaffold_354; Positions 40971 36825. XX CC Positions [1449-1976] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 42..4145 FT /product="Copia51-PTR_I_1p" FT /translation="MASENSSILSFNTMVHMVTVKLSSTNFLLWRSQVVPL FT LQCQKYYGYIDGSTLMPSATTDSTAYNLWKQNDQLVMSLLLSSLTEEALSI FT TIGFTTSRDIWNAIETAFSHKSKARELQIKDELHLMKRGSRSISEYSRVFK FT AHCDQLSAMGCPVEDTDKVHWYLRGLGHEFSSFSTTQLSLTPIPSFKDIVP FT KAESFDLFSKSIDYTAGGPSAYMVHSSAYSNRHARPYNNQNRYKGGHSNGG FT NRGKQQSRRSPRCQICREEGHYATNCKIRYTKSDANLVEALATCTISNDTA FT DWYTDTGASAHMTPDVSQLDSIEPYTGKDRVIVGNGSSLPVTHMGSCSPTP FT TLQLKDVLVVPNLTKNLLSVSKLTNDFPLAVLFTDNKFIIQNLQTQKVVAS FT GDRVDGLYVLKRGHHVFSAIINKHNLCNSFDIWHARLGHVSPQIISMLNKK FT GFLSLTSILPNPSLCVSCQKAKSHKLSFPLSDSRSQTVLGLIHCDLWGPAP FT INSISGYRYYAIFIDDNSRFTWFYPLKNKTDFYHTFIKFQTLVENQFSAKI FT KTFQSDGGGEFTSNIFQSHLDKCGIHHQRSCPYTPSQNGRAERKHRHITET FT GLTMLFHANVPLNLWVEAFSTAVFTINRLPTPVLNGVSPFEILYGKSPTYE FT LFRIFGCLCFPYLRDYTKHKFEPRSLPCIFLGYNSSYKGFRCLDPKSHRVF FT ITRHARFDETVFPSSSSHMQPSPALSDYISFHDPSSSNSPLSSTHSSAGSQ FT SLPSITPSIPCKSCALELPQSPPILLPPVSPTIAERVSELPVESTSRIEPF FT SDIPIAPAQHSSSNQNSHSMITRGKAGISKSKHYNYVCQIPASPLLSSLLA FT MKEPKGFKSAAKSPEWLAAMDDEIRALTHNHTWELVPRPPATNVVGSKWIF FT RIKYHSDGSIDRFKARLVAQGYTQLYGLDFHDTFSPVVRASTVRIVLSIAV FT TRGWNIRQLDVKNAFLHGLLQEEVFMEQPPGYIDTSHPHHVCRLKKAIYGL FT KQAPRAWFHRFSNFLLTIGFTCSKADYSLFVHSSDNGIIYLLLYVDDIVLT FT GSNASLIDTFIHKLQQEFSMKDLGNLHYFLGLEVTQSSQGLFLSQVKYARD FT ILIRAELHDSKPIATPMIVSHHLTSDGPLFHSPTIYRSLVGSLQYLTITRP FT DITHAVNSVSQFMHAPRESHFQAVKRILRYVKGTLHFGLSISSSSHLNISA FT FSDADWVGCPETSRSTSGYAIFMGDNLISWTSKKQTTVSRSSAESEYRALA FT LTAAEVKWLLNILHDLRIQLPAQPTLLCDNTSAIFMTRNPVAQRRSRHIDI FT DVHFVRELVCNGILQVKHVPSTLQIADIFTKSPSKSLFLLFRSKLRVLPTT FT LDLRG" XX SQ Sequence 4147 BP; 1169 A; 948 C; 711 G; 1319 T; 0 other; tggtatcaga gcctctatag gattaatctc cacttgatct tatggcctca gaaaattctt 60 ccatactctc cttcaatact atggttcaca tggtaacagt gaagctatca tcaacaaatt 120 ttcttctttg gcgcagtcag gtagttcccc tgctgcaatg tcaaaaatac tatggatata 180 ttgatggctc aacccttatg ccttccgcta ccactgattc cacagcctac aatctttgga 240 aacaaaatga tcagctagtc atgagtcttc ttctttcttc tctcacagaa gaagcacttt 300 ctattaccat tggatttaca acatcaagag acatctggaa tgctattgag actgccttta 360 gtcataaatc taaggctcgt gaacttcaaa taaaagatga gcttcatctc atgaagcgtg 420 gctctcgcag tatctctgag tactctagag tattcaaggc tcattgtgat caattatcag 480 caatgggatg tccagttgaa gacactgaca aagtgcactg gtatttgcgt ggtctaggcc 540 acgagttctc aagtttctcc accactcaac tctctttaac tcccattccc agtttcaaag 600 atattgttcc taaagcagaa agctttgatc ttttctccaa gtctattgat tatactgcag 660 gtggcccctc tgcttatatg gttcattcct ctgcatattc caaccgacat gcaaggccat 720 ataataatca aaacaggtat aaaggaggcc actcaaatgg aggaaatcgt gggaagcagc 780 agtctaggag gtctcctcga tgtcaaatat gtcgagaaga aggtcattat gccacaaact 840 gcaagatcag atacacaaaa tctgatgcaa atcttgttga agcacttgca acctgcacta 900 tcagtaatga cacagcagat tggtatactg atacaggagc atctgcacat atgactcctg 960 atgtgtctca gcttgatagc atagaacctt acactggtaa ggatagagtt attgttggta 1020 atggatcttc ccttcccgtt acacacatgg gttcctgctc tcccactcca actcttcaat 1080 taaaagatgt ccttgttgtg ccaaacttaa ccaaaaattt gctttctgtc agtaaattaa 1140 ccaatgattt tcctcttgct gttcttttta ctgacaataa atttatcata cagaatcttc 1200 aaactcaaaa ggtggtggca agcggtgatc gtgtagatgg actttatgta ctgaagcgtg 1260 gacaccatgt tttctctgct atcatcaaca agcacaattt atgcaattcc tttgacattt 1320 ggcatgctcg tttaggccat gtatcccctc aaataatttc aatgcttaat aagaaaggtt 1380 ttttatctct tacctctata ctgccaaatc catccttgtg tgtgagttgc caaaaagcta 1440 aaagccataa actatctttt cccttaagtg atagtcgttc tcaaacagtt ttaggattaa 1500 tccattgcga cttatgggga ccagcaccaa taaactcaat ctctggctat cgatattatg 1560 ctatttttat tgatgataac tctcgcttca cttggttcta cccattaaag aacaaaactg 1620 atttttatca caccttcatc aagtttcaaa cactggttga aaatcaattc tcagcaaaga 1680 taaaaacatt ccaaagtgat gggggaggag aattcaccag taacattttt cagtctcact 1740 tagacaaatg tggtattcac catcaacgtt cttgtcccta tacaccctct caaaatggta 1800 gagccgagag aaaacatcga catatcactg agacaggcct tacaatgctc tttcatgcaa 1860 atgttcctct taatctttgg gttgaagcct tcagtacagc agtttttaca attaatcgct 1920 tgcccacacc tgtcttgaat ggagtttctc catttgaaat tctgtatggt aagtctccta 1980 cctatgaatt atttcgtatt tttggctgct tatgttttcc atacttaaga gattatacta 2040 aacataaatt tgaacccaga agtcttccat gtatttttct tggttacaat tcatcttata 2100 aaggatttcg atgcttagat cctaaatcac atcgagtatt tatcactcga catgctcggt 2160 ttgatgaaac agtctttcca tcatcttcat ctcatatgca gccttctcct gcactgtcag 2220 actatatttc ttttcatgat cccagttcct caaattctcc tttgtctagc actcattctt 2280 ctgcaggttc tcagtcctta ccatcaatta ctccatctat accatgtaaa tcatgtgcct 2340 tggagttgcc tcagagtcca ccaattttgc tgcctcctgt gtctcctaca atagctgaga 2400 gagtttcaga attgcctgtt gagtctactt ccagaattga gccgttttca gatataccaa 2460 ttgcaccggc tcaacattct tcttcaaatc agaactctca ttccatgata actcgtggaa 2520 aagctggtat ctccaaatcc aaacattata attatgtttg tcaaattcct gcctctcctt 2580 tattatcatc gctattagct atgaaggaac caaaaggatt caaaagtgct gctaaatcac 2640 ccgaatggct agctgccatg gatgatgaaa ttcgtgctct cactcataac cacacatggg 2700 aactggttcc cagaccacct gctaccaatg tggttggatc caaatggatt tttcggatta 2760 aatatcattc tgatggctcc attgataggt tcaaagcacg cctagttgct caaggctaca 2820 ctcaactcta tggacttgat tttcacgaca catttagtcc ggttgttaga gcttctacag 2880 ttcgcattgt cctctctatt gcagtaactc gtggctggaa catacgtcaa cttgacgtta 2940 agaatgcttt ccttcatggt cttcttcagg aagaagtttt tatggaacaa ccacccggtt 3000 atattgacac ttctcatcca caccatgttt gtcgcttaaa aaaagccatc tatggtttga 3060 aacaggcacc gagagcttgg tttcatcgct ttagcaattt cttactcaca attggtttca 3120 cttgcagcaa agcagattac agtttatttg ttcattcatc agataatggt atcatttatt 3180 tgctgctata cgtagatgat attgtcctca ccggaagcaa tgcatctctc attgacacct 3240 tcattcacaa gctccagcaa gagttttcta tgaaggacct tggcaatcta cattattttt 3300 tgggtttaga agttactcaa tcttcacagg gactgttcct aagccaagtg aagtatgcaa 3360 gagatattct catcagggct gaacttcatg attcgaagcc aatagcaaca ccgatgattg 3420 tttctcatca tttaacttct gatggtcctc tatttcattc accaacaatc tatcgatctc 3480 ttgttggttc gctgcaatat ctcaccatca ccagaccgga tattacacat gcagtaaatt 3540 cagtaagcca attcatgcat gcaccacgag aatcacattt tcaggccgtc aaacgaattc 3600 ttagatatgt taaaggcact ctccatttcg gcctcagcat cagttcatca agtcatctca 3660 atatctcagc tttttcagat gctgattggg ttggttgtcc agaaaccagt cgctcaacat 3720 cagggtatgc aatttttatg ggtgacaatt tgatttcatg gacctctaaa aagcagacca 3780 cagtttctag atcttcagca gaatcagaat atagagcatt ggcactcact gcagctgagg 3840 ttaaatggtt gctcaacatt cttcatgatt tacgtattca actaccagca caaccaactt 3900 tactctgtga caacaccagt gctattttca tgactaggaa tccagtagct caacgaaggt 3960 ctagacacat tgatattgat gttcattttg ttagagaatt agtctgcaat ggtatattgc 4020 aagttaaaca tgtgccatcc actttgcaaa tagcagatat tttcaccaaa agtccatcca 4080 aatctctgtt tctgctgttt cgatccaagc ttcgcgtgtt gccaactacg cttgacttga 4140 gggggga 4147 // ID LINE1G_MT repbase; DNA; EDCOT; 5793 BP. XX AC . XX DT 13-NOV-2006 (Rel. 11.11, Created) DT 01-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A LINE sequence from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW LINE; Interspersed element; repeat; autonomous; LINE1G_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5793 RA Shankar R. and Jurka J.; RT "LINE1G_MT: A LINE sequence from Barrel Medic."; RL Repbase Reports 6(11), 573-573 (2006). XX DR [1] (Consensus) XX CC The LINE sequence contains two ORF regions. The first ORF CC resembles nucleotide binding protein while the ORF resembles the CC RT polymerase and Endo/Exo-nuclease protein. The TSD is not clear CC in the 5' end. XX FH Key Location/Qualifiers FT CDS 439..1908 FT /product="LINE1G_MT_1p" FT /translation="RRGEKKLYFKKEKNVEAEGEVVLKDVLKVEEEMKKVE FT GKKDRLQKISKVEEKVDIFCPLLYNSKPEDRVWASEGMVATVVSGDSSLSL FT QQRVEDAGFSNVIVTPMGSDRVFLYCTGGADIWTVFNDAVHFFGMLFSDLH FT RWSSEDIIYERGAWLRIYGIPVHAWNEDFYNICVSGCGRFIRSDVCTVERA FT RLDFARVLISTTFLEVVNSSLEVVIDGCKYLLKLVEEWGCNLGEDAFLSEE FT EQDPRLESLTLKDSASLEDVKGEMNDLVDDLKEEWLNGDDFFAGITNIEVD FT PSRVPVESDRPDTTFVNLDVGVYKVESSQNHVSHKPDSCSKELKETSSSLK FT SNSKLSKRKYKQAGVAVNHSVGFIKRIARLPSKDRKEILKVLKKQDRKRKL FT LIKASKAASNSLSNSSNNSNSSVNKDWENWVVLHGKKEVAAEDVKDIGKLL FT GVNFKGDINNSFNLLSKEGRKEWRAERGTLLLKEDGEGGGKVGME" FT CDS 4438..5634 FT /product="LINE1G_MT_2p" FT /translation="KKNLGGCEVSKKIAWIKWDSICLPVNRGGLGVRRLGE FT FNLSLLGKWCWRLLIDKEGLWYRVLKARYGEVGGRIQEGGREVSGWWSMLC FT KVRDGVGSGVGNWFDVNVRREVGNGSSTFFWTDKWLGGVPLKIQFSRLYDL FT AVHKECSVADMERWGWVEGGNGWVWRRRLLAWEEESMRECITLLDNVVLQV FT HIQDRWRWLLDPVHGYSVGGTYRFLTNSEEQVANDDFIDVWHKLVPTKVSF FT FAWRLLQDRIPTRANLVCRLILQPNDNLCVGGCGLSETTGHLFIGCESFGS FT VWVLLCHWLGFSFVPPGSIKDHYIQFTHLAGLPRSTHVFFKVIWLACVWAI FT WKERNNRVFNDTVIDPLHIVEKVKLNSFLWLSSNIEPIAFGFYDWWRHPLF FT CMGVI" XX SQ Sequence 5793 BP; 1498 A; 752 C; 1567 G; 1974 T; 2 other; nmtgcagcaa ggcaactttc tattttacta atattccaga gtctttgcct gtgttccgcg 60 tgcgacaata ttttgaggta tgcggtattc tttccgatat ttacattgct cgacatctga 120 atttgcgtgg tcaagtctat ggttttgtta gatttgagtc ggtaaagaat agagacaagc 180 tagaacatgc tttgaataat atctggattg atgattatcg tgtatgggca agggaagcta 240 ggtttgatag atttgctaaa tatgatgagg aggttaaggc ttctaatatt gttgttcgaa 300 aggctggaca gtttcagccg gtggtggtaa cccatggtgt tggtatagag aatgtgcggt 360 tgggtaagaa ggaggaggag gtcagtgatg aggctggaaa aaacatagtg aaggttggtt 420 tggtggatgt tccggtagag aagaggagaa aaaaaattat attttaaaaa agaaaagaat 480 gttgaagctg agggagaggt ggttttaaaa gatgtgttga aggtggagga agagatgaaa 540 aaggttgaag ggaagaaaga cagattgcaa aagatttcaa aggtggagga gaaagttgat 600 attttctgtc cgcttttgta taattcaaaa ccggaggacc gtgtttgggc tagtgaaggt 660 atggtggcta ccgtagtgtc gggagactca tctttatctc ttcaacaaag ggtggaggat 720 gcaggttttt cgaatgttat tgtgactcct atgggaagtg atagggtctt tttgtattgc 780 acggggggag cagatatttg gactgtgttt aatgatgctg tacacttttt tggaatgctc 840 ttttcggact tacatagatg gtcatctgag gatattattt atgaaagggg agcttggctt 900 agaatatatg gtattcctgt tcatgcatgg aatgaagatt tttataatat ttgtgtgtcg 960 gggtgtggtc gctttattcg atcagatgtt tgcacggtgg agagggcgag attggatttt 1020 gctcgtgttc ttatttcgac aacttttttg gaggttgtta attcttctct agaagttgtt 1080 atcgatggtt gtaagtattt gttaaagttg gtggaggaat gggggtgtaa tttgggggag 1140 gatgcttttt tatcggaaga agaacaggat cctaggttgg aatcgttaac tttaaaagat 1200 tccgctagtt tggaggatgt aaaaggcgag atgaatgatt tggtggatga tcttaaagaa 1260 gaatggttga atggggatga tttttttgct ggaattacaa acatagaagt tgatccttca 1320 cgggttcctg ttgagtcgga taggccagac actacttttg ttaatcttga tgtaggtgtt 1380 tataaggtgg aatcctctca gaatcatgtc tctcataaac cagattcgtg ttcgaaggag 1440 ctaaaggaaa cttcttcttc gttaaaatct aattctaaac taagcaagcg taagtataaa 1500 caggcgggtg ttgctgtcaa ccattctgtt gggtttatta aaagaattgc aagacttcct 1560 tccaaagata gaaaagaaat tttaaaggtt ttaaagaaac aggatcgcaa aagaaaattg 1620 ttgattaagg cctcgaaagc agcgtccaac tcgttatcca attcttcaaa taattctaat 1680 tcttctgtta ataaagattg ggaaaattgg gttgttttgc atggtaagaa ggaggtggca 1740 gccgaggatg ttaaggatat aggtaagttg ttgggtgtta attttaaagg ggacataaac 1800 aatagtttta atttattatc caaggaggga aggaaagaat ggagggcgga aagagggact 1860 ttgttgttga aggaggatgg tgagggtggc ggcaaggttg ggatggagtg ataggagccg 1920 gtggtgaggg ttttgtgggg gtggagacgg gtggttatga agattctttc gtataatgta 1980 aggggattgg gcagttttga gaagcgcgca gaagttcgta attttattca tgaaaaaaat 2040 ccgtttgtgg tctgcttgca agaatccaag ttgagcatgg ttgatgatta cattcttaat 2100 tctgtttggg gtaatattgg ttgtgactat tcttatcagg cttctgtagg ggcttctgga 2160 ggtttggtaa cggtttggaa tcctttattg gtggaggtgt ggtgtacaat ctcgatcaga 2220 catgttttga ttattaaagg gaaggtactt tcttcagatc aagattttat cattgctaat 2280 gtgtatgctc cttgtgatac gttggccaaa caagatttat gggtccgttt atctcatttt 2340 ttaattgcca acggtgatgt gaatgtttgt gtttgtggag atttcaattc tgttagatcg 2400 gaggaagagc gaagaggtag aaatgtggtt tttcgtcagg tggatgcaga caatttcaat 2460 aacttcattg atagtagttt tttgattgat ttaccaattt gtggtagatt atttacctgg 2520 tatcgggggg atggtgagca ggttagatag atttttggtg tcttcaaaat ggtgtgactc 2580 ttggcccaat tgtatacagg ttgcgtatca aagaggttta tttgaccatg ttcctctagt 2640 gttgagtgtc gatgatgaaa attggggacc tcgtcctcta aggttgctta aatgttgggc 2700 agattatcaa gggtatgcag attttgttcg tgataaactg aactcctttg ttttggatgg 2760 atggggtggt catgtattga agatgaagct taaaatgata aaaaattctc ttaaggtttg 2820 gcatcaacaa cagtcaaaaa atgtggaatc taaaataatg gatgttaaaa atcgtatgtc 2880 ctggttagac tctaaagggg aggagtccaa cttattggaa gaagaaactc aggaaattcg 2940 tgagttgtct gtcaaattgc attccttgtc acgtgtgcat actagtatga attggcagaa 3000 ggcgatgatg aattgggtta gagaaggtga tgcaaattct aaattcttcc ataatatgat 3060 gtctaacaga cagcgtcgaa attctcttca cttgattcat gttgatggag ttcttgtcga 3120 aggggttcag aacattcgtg cggctgccct taatcatttt gccactcaat tccgtgcttc 3180 agagggtagc cgacctggaa ttcaaggttt aaattttcgg aagttgtctt atgctcaatc 3240 aggtagttta attcgtcctt tttctcttga tgaagttaaa caggctgtgt gggattgtga 3300 gagcttcaaa agtcccgggc cggatggtat taatcttggt tttattaaag atttttggaa 3360 tgagttgaaa gatgatttta tgaaatttct tctcgatttc catcgtaatg ggaagctgac 3420 gaagggtgtc aactccactt ttattgccct aattccgaag gtggctagtc cccagaagct 3480 tggtgatttt cgacctattt ctcttgttgg ttgtatgtat aaagtgttgg caaaggttct 3540 tgcaaatcga ctacgttcta ttttgagtta tgtggtgtct gataatcaat ccgcttttgt 3600 gagaggcaaa caaattcttg atggcattct tattgcaaat gaggtagttg atgaagcaaa 3660 gcgttagaag aaagatttat tattgttcaa agttgatttc gaaaaggctt atgactcggt 3720 tgatcttaat tatttgaatt ctgtgatgct taatatgaat tttccgactc tttggcggaa 3780 gtggataatg gagtgtgttg gaacagctac tgcttcggtc cttgtcaatg ggtgcccgac 3840 agatgagttt cctattcaga gggggcttag acagggggac cctttatcgc cttttttatt 3900 tttactagcg gcagaaggtt ttgatgtttt gatgaaggct tcagtgtcgt caaatttatt 3960 taatgcttat ggtattggac ctcaaagtga aattaaaatt tctcacctac agtttgctga 4020 tgacactatc attattggag aaaaatgttg gttgaatgtt cgtaccattc gggcggtatt 4080 attattactt gaagaggtgt ccgggttgaa ggtaaatttt aataaaagca tgttgacagg 4140 tgtaaacatt tctcataatt ggttgacgga agcggcttcg gtgttgaact gtaaaactgg 4200 tacaattccc tttttgtact taggattacc tataggcgga gatagtagaa gacttagttt 4260 ctggaaaccg gttgtggacc gaattgttgc tagattgtcg tcgtggaata ataaatttct 4320 atcgcttggt ggtcgcttgg ttcttctgaa atctgtccta tcctctcttc cggtttattt 4380 tctttccttt ttcaaggcac ctgcaggtat aatttcttct attgaatcta tttttaaaaa 4440 aaaaatttgg ggggttgtga ggtctctaaa aaaattgctt ggattaaatg ggattctatt 4500 tgtttacctg tgaatcgagg tggtttgggg gtgcggaggt taggtgaatt taatttatct 4560 ttgttaggga aatggtgttg gaggttgttg attgacaaag aaggcttgtg gtatcgtgtc 4620 ttaaaggcac ggtacgggga ggttggtggt agaattcagg aaggagggag agaagtgtct 4680 ggttggtgga gtatgttgtg caaggtgagg gatggggtag gatcgggagt aggtaactgg 4740 tttgatgtta atgttaggag ggaggtagga aatggtagta gtactttctt ttggactgat 4800 aaatggctag gaggagtacc tttaaagatt caatttagtc gtctttatga tttagcggtg 4860 cataaggagt gttcggtggc agatatggag cgttgggggt gggttgaggg cggcaatggg 4920 tgggtttgga gacggcggtt gttagcctgg gaggaggaga gtatgaggga gtgtatcact 4980 ttactggata acgttgtttt gcaggttcat attcaggacc gttggcggtg gttactagat 5040 cctgttcatg gttatagtgt tggtgggact tatcgttttc tcacaaattc tgaagaacag 5100 gtggctaatg atgattttat tgacgtgtgg cacaaattgg ttccgacaaa agtgtcgttt 5160 tttgcttggc ggttgcttca agacagaatt cctacaagag caaatttggt gtgtcgtctc 5220 attcttcaac caaacgacaa tttgtgtgtt ggagggtgtg gtctatccga aacgacgggt 5280 catctcttca ttggatgcga atcttttgga agtgtctggg ttttactttg tcactggctt 5340 gggttttctt ttgttcctcc aggttctatt aaggatcatt acattcagtt tactcatttg 5400 gcgggtttgc ctagatctac tcatgtgttt tttaaggtta tttggcttgc ttgtgtttgg 5460 gcaatatgga aggagcgaaa caaccgtgtt ttcaatgata cggttattga tccgttacat 5520 attgtcgaaa aagttaagtt aaattctttt ctctggcttt cttcgaatat tgagcctatt 5580 gcttttggct tttacgattg gtggagacat cccctttttt gtatgggtgt gatttaagtg 5640 tttcgacctt tatgtttagg tggtggcatc tttttaggtg ctgtggtgtt gtaacagata 5700 ttagaggatt catcatttta gcacaccttg tgcggggtga atcactctgt ttttttgagt 5760 aatatattcc attttgattt gttcaaaaaa aaa 5793 // ID Copia-40_VV-I repbase; DNA; EDCOT; 4139 BP. XX AC chr10; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-40_VV_; KW Copia-40_VV-LTR; Copia-40_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4139 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr10; Positions 7194007 7189869. XX CC Positions [1492-1995] - Integrase core CC 'ACAA' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 385..4116 FT /product="Copia-40_VV-I_1p" FT /translation="MMSLKYQDGTPMTDHLNTFQGIINQLVGMNIKFEEEV FT QGLWLLGTLPNLWETFRTSLSNSALDGIMNMDLVKSCVLNEEMRRKSQGSS FT SQSNVLVTEKKGKSKSRGPKNRDRSKSKTNKFANVECHYCHLKGHIKKYCR FT QLKRDMKQGKVKEKKNDNGGEDDQVATTTSDFLIVYDSDVVNFACQETSWV FT IDSGASIHATPRKDFFTSYTSGDFGSVRMGNDGSAKAIGMGDVRLETSNGT FT MLTLKNVKHIPDIRMNLISTGKLDDEGFCNTFRDSQWKLARGSMVIAKGNK FT SSSLYLMQARVIDSSINAVDDDSTFELWHNRLGHMSEKGLMILAKNNLLSG FT MKKGSLKRCAHCLAGKQTRVAFKTLRHTRKPGMFDLVYSDVCGPMKTKTLG FT GSLYFVTFIDDHSRKIWVYTLKTKDQVLDVFKQFHALVERQSGEKLKCIRT FT DNGGEYSGPFDEYCRQHDIRHQKTPPKTPQLNGLAERMNRTLVERVRCLLS FT QSQLPRSFWDEALNTVVHVLNLTPCVPLEFDVSDRIWSNNEISYDHLRVFG FT CKAFVHIPKDERSKLDVKTRPCVFIGYGQDELGYRFYDPVQKKLVRSRDVV FT FMEDHTIQDIEKTNPMESQHSGDLIDLDLAPLKNLPTQVEDEAHDDQHDMG FT DVETPTQVEDETHDDQHDMGDVETPTQVEVDDDVHEQSPAAEAPSDIPLRR FT FTRDRHPSTRYSVDDYVLLTDGEEPESYVEAMKDENKMKWVDAMRDEMESL FT HENHSFELVKLPKGKRVLKNRWVYRVKQEEHTSQPRYKARLVVKGFNQKKG FT IDFDEIFSPVVKMSSIRVVLGLAASLDLEIQQMDVKTAFLHGDLDKEIYME FT QPEGFVLKGKEDYVCKLKKSLYGLKQAPRQWYKKFESVMGEQGYRKTTSDH FT CVFVQKFSDDDFVILLLYVDDILIVGRNVSRIDNLKKQLSKSFAMKDLGPV FT KRILGIRIERDRASKKLCMLQKQYIEKVLAKFNMSKAKVVSSPLASHFKLS FT SRHNPSTDKEKEDMRRVLYASVVGSLIYVMVCIRPDIAYAVGVVSRFLSNP FT GRHHWEAVKWIMRYLRGISKLKLTFGSGKPILVGYTDSDMAGDVDNRRSTS FT SYLMTFSGGAVSWQSRLQKCVALSTTEAEYIAAAEACKELLWMKCFMQELR FT FKQQRYVVYCDNQNAIHLSKNSSYHARSKHIDVRYHWMRDALNNNLFEIEK FT IHTDNNGSDMLTKTLPREKLGVCCSIAGMVSPST" XX SQ Sequence 4139 BP; 1300 A; 622 C; 1014 G; 1203 T; 0 other; ttgtttgcgt ttatcccatc aaagtggtat cagagctttg gttcaagata atttgtgcct 60 tgtgtagaac aatggaaagc aatacaagta gaatgatcac tctgaatggt tccaattatc 120 atgtttggaa aggaaaaatg gaagactcat tgtatgtgaa ggattattat ttgcctgtgt 180 ttgcttctga aaaggccaga aaataaaact gatgcagaat ggaatttact tcatcgacag 240 gtttgcggtt atatcagaca gtgggtagat gataatgttc tcaatcatgt tagtgaagag 300 aaacatgcaa ggagtctatg gaataagctc gaacagttat atgctcgaaa gactggcaat 360 aataaattgc ttctaatcaa gaagatgatg agtttgaagt atcaagatgg aactcctatg 420 acagatcatt tgaatacatt ccaaggtatt attaatcagt tggttggaat gaatatcaag 480 tttgaggaag aggtgcaagg gttgtggctt cttggtacat tgccgaactt gtgggagacg 540 tttagaactt ctttgtctaa ctcagcccta gatggtatta tgaatatgga cttagttaag 600 agttgtgttc taaatgaaga aatgagaaga aagtcacagg gctcttcttc acagtcaaat 660 gttctagtta ctgagaagaa ggggaagagt aagagtagag gtccgaagaa cagagataga 720 agcaaaagca agactaacaa gtttgccaat gttgagtgcc actactgcca tttgaaaggg 780 catataaaaa aatattgtcg ccaattgaag agagatatga aacaagggaa agtgaaggaa 840 aagaagaatg acaatggtgg tgaagatgat caagttgcca ctaccacttc agatttcctt 900 attgtttatg atagtgatgt tgttaatttt gcttgccagg aaaccagttg ggtgattgat 960 agtggtgcct ccatccatgc tacacctcgg aaggatttct ttacatccta cacatccggt 1020 gattttggaa gtgttaggat gggtaatgat ggctcagcta aagccattgg gatgggagat 1080 gtacgtttgg agactagtaa tggtactatg ttgactttga agaatgttaa acacattccg 1140 gatattcgca tgaatttaat ctccacagga aagcttgatg atgaagggtt ctgcaacacc 1200 ttccgtgata gtcagtggaa gctcgctaga ggttctatgg tgatagcaaa aggaaataag 1260 agttcctcat tgtatttgat gcaggcaagg gtaattgatt ccagtatcaa tgcagtggat 1320 gatgatagta catttgagct ttggcacaac aggcttggtc atatgagtga gaagggcttg 1380 atgattttgg ctaagaataa tcttctttct ggtatgaaga agggatcttt gaagaggtgt 1440 gctcattgct tagcaggaaa gcagaccaga gttgcattca aaacacttcg ccatacaagg 1500 aagccaggta tgtttgattt agtgtattct gatgtgtgtg gccctatgaa aacaaaaaca 1560 cttggtggat ctctatattt tgtgactttt atagatgatc attcaagaaa gatttgggtt 1620 tataccttga aaacaaaaga ccaagtgtta gacgtgttta agcagtttca tgcgcttgtt 1680 gaaagacaat ctggtgaaaa gttgaaatgt atccggactg ataatggggg tgagtattct 1740 ggtccttttg atgagtattg tagacaacat gatattcgac atcaaaagac acctcctaag 1800 actcctcagt tgaatgggtt ggctgagaga atgaatagga cactggttga aagagtaaga 1860 tgcttacttt cgcagtcaca gttgccaaga tctttttggg acgaggcttt gaatactgtt 1920 gtacatgttc tcaatcttac accatgtgtt cctttagaat ttgatgtttc ggatagaatt 1980 tggtcaaata atgaaatctc ttatgatcac ttgcgtgtct ttggatgcaa ggcttttgtg 2040 catattccca aagatgagag atctaagctt gatgttaaga caagaccttg tgtatttatt 2100 ggctatggtc aggatgagct tggttacagg ttttatgatc cggtgcagaa aaaacttgta 2160 agaagccgag atgttgtgtt tatggaagac catactatac aggatattga gaagactaat 2220 ccaatggagt ctcaacatag tggtgatttg attgatttag atctagcccc tctgaaaaat 2280 cttcctacac aggttgaaga tgaagcacat gatgaccaac atgacatggg tgatgttgaa 2340 acacccacac aggttgaaga tgaaacacat gatgaccaac atgacatggg tgatgttgaa 2400 acacccacac aagttgaggt ggatgatgat gttcatgagc agtcaccagc agcagaggct 2460 ccatcagata ttccacttag aaggtttacc agagaccgac atccttccac acggtattct 2520 gttgatgact atgtattact aactgacggg gaagaacctg aaagttatgt ggaagccatg 2580 aaagatgaaa ataagatgaa gtgggttgat gctatgcgag atgagatgga gtcattgcat 2640 gagaaccatt cttttgagct tgtcaagttg ccaaagggaa aaagagtttt gaagaacagg 2700 tgggtttaca gagtgaagca agaagaacac acttcacaac ctcgttacaa agctagattg 2760 gtcgtcaaag ggttcaatca aaagaaaggt attgatttcg atgagatttt ttctcctgtt 2820 gttaagatgt catctattcg tgtggttttg ggcttggcag ctagtcttga tttggagatt 2880 cagcagatgg atgttaagac tgcatttctc catggtgatt tggacaaaga aatttatatg 2940 gaacaaccag agggtttcgt actaaaaggg aaagaggatt atgtgtgtaa gctgaagaaa 3000 agtctttatg gcttgaagca agcaccgaga cagtggtata agaagtttga gtcagttatg 3060 ggggagcaag gctaccgaaa aactacttct gaccattgtg tatttgtgca aaaattctct 3120 gatgatgatt ttgttatatt gttgctctat gttgatgata tcttgattgt tggcaggaat 3180 gtttcaagaa ttgataactt gaagaagcag ttaagcaaat cctttgccat gaaggattta 3240 gggccagtaa agagaattct tggcatcaga attgagcggg atagagcatc caagaaacta 3300 tgtatgttac aaaagcaata tattgaaaag gtgcttgcaa agtttaacat gagcaaagcc 3360 aaagtggtta gttctcctct agctagtcac tttaagctaa gcagcagaca taacccttct 3420 acagataagg agaaggaaga catgagaaga gttctgtatg cctcagtagt aggaagtttg 3480 atatatgtca tggtatgtat tagaccagac atagcttatg cagttggtgt tgttagccgg 3540 tttttatcga atccaggaag acatcattgg gaagcagtca agtggattat gagatattta 3600 cgaggcattt ccaagttgaa actcactttt ggaagtggga aaccaatact tgttggatac 3660 actgattcag acatggcagg ggatgtggat aatagaaggt ctacttcaag ctatttgatg 3720 acattctcag gaggtgctgt gtcttggcaa tcgagactac agaaatgtgt tgcactttct 3780 acaacagagg cagagtacat tgcagcagca gaagcatgta aagagttgtt gtggatgaag 3840 tgtttcatgc aagagctcag gtttaaacaa cagcgttatg tggtatactg tgataaccaa 3900 aatgctattc acctcagtaa gaattcttcc tatcatgcaa gatcaaaaca cattgatgtg 3960 aggtatcatt ggatgagaga tgctctcaat aataacttgt ttgaaattga gaagatacat 4020 acagataaca atggctcgga tatgttaaca aagacactac caagagagaa gcttggagtt 4080 tgttgttcca tcgctggaat ggtgagtccc tccacatagt cggaaagggg gagatttgt 4139 // ID Gypsy-36_Mad-I repbase; DNA; EDCOT; 8334 BP. XX AC . XX DT 13-OCT-2010 (Rel. 15.1, Created) DT 13-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-36_Mad-I. XX NM Gypsy-36_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-8334 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1766-1766 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 80..2026 FT /product="Gypsy-36_Mad-I_1p" FT /translation="MASRKAQTVPATGAKNKSVLVATGVTLGITTRSMARA FT TSAASFTSASTLPREQEHPRHEPLITLASLRAPRGESPRKYSESMLSDADS FT SDSSAMQVMTIGATSIDEQLAQMNEAIARLTRTVEEKDLQIAALVNRLEAQ FT DGDKPDPEDDPLKGGAGGDEEPPVEKIDGKPEPDQAAALMGSLSIQQLQEM FT ITNTIKAQYEGSSHTSXFYSKPYSKKIDALRMPRGYQPPKFMQFDGKGNPK FT QHVAHFVETCNNAGTEGDYLAKQFVRSLKGNAFEWYTDLEPESINSWEQLE FT REFLNRFYSTRRTVSMLELTSTKQWKDEPVIDYINRWRTLSLDCKDRLSET FT SSIEMCIQGMQWGLQYILQGIKPRTFEELATRAHDMELSIAHHGKKEPIAD FT YKNDKVLGTKVEKAAWKPTKEAMTVNTAPVKISTRGKAIQTEAFRDQEMRR FT RTLKELEEKTYPFPDSDVVAMLDDLLDKKVISLPECRRPEEMNRTDSPRYC FT KFHRFISHPTEKCFVLKDLIMKLAQKGIIELDLDDVVKSNYTTFTSGSSDS FT KFSPQPLGASSKTSKVEGWTQVTPKKLHKKHTSPPQVRQSERGQSSSCQPS FT KQRERVEDDEISTQRSSVPITMRDFLPEDFFNHSVKAPCYEDCEERLSQIA FT " XX SQ Sequence 8334 BP; 2406 A; 2287 C; 1917 G; 1721 T; 3 other; aattggcacg cccagtggga caatctctgc ctctcatctc tttctccgtt caagaaattc 60 aagcgcactt ccaaaattaa tggcatcaag gaaggctcaa actgttcccg caaccggcgc 120 aaagaacaaa agcgtcctcg tcgcaactgg tgtcactttg ggcatcacga ctcgaagcat 180 ggcaagagct acttctgccg cctctttcac ctctgcatca actctgccaa gggaacaaga 240 gcacccaagg cacgagcctt tgatcacctt agcctcacta agggcaccaa ggggggaaag 300 cccaaggaaa tactccgaat ccatgctctc cgatgccgat tcaagcgaca gttcagccat 360 gcaagtcatg accattggag caacttcaat cgatgagcag ctggctcaaa tgaatgaagc 420 aatcgcaagg ctaacccgaa ctgtggaaga aaaagacttg caaattgcag cactagtcaa 480 ccgactggag gcgcaggacg gcgataaacc cgacccagag gatgatccac taaagggagg 540 agctggcgga gacgaagagc ccccggtgga gaaaatcgat gggaagccgg agccagacca 600 agcagcggca ctcatgggat ctctttctat ccagcagctg caggagatga tcaccaacac 660 catcaaggca cagtacgaag ggagctcaca tacctcctkg ttctactcga agccctattc 720 caagaagatt gatgccctaa ggatgccgag gggttatcaa ccaccaaagt tcatgcagtt 780 tgatggaaag ggaaacccga agcagcacgt tgcccacttc gttgaaactt gcaacaacgc 840 agggaccgaa ggggactacc tcgccaagca gtttgtgcgc tcgctgaaag gaaacgcctt 900 tgagtggtac acggacctag agcctgagtc catcaacagc tgggagcaat tagagcggga 960 attcctcaac cgcttctaca gcacccgccg cactgtgagc atgctagagc taacgagcac 1020 aaagcagtgg aaggacgagc cagtcattga ctacatcaac agatggcgca ctctaagcct 1080 cgactgtaaa gacaggctct cggaaacctc ttcaatcgag atgtgcatcc aaggcatgca 1140 atggggtttg caatacatcc ttcaaggcat taaaccacgg accttcgagg aattggccac 1200 tcgcgcccat gacatggagt tgagcatcgc ccatcatggg aagaaagaac cgatcgccga 1260 ctacaagaac gacaaagttc ttgggacaaa ggtggaaaag gctgcatgga aacccaccaa 1320 ggaagcgatg acggtcaaca cagctcccgt caaaatctcc acacgaggca aggcgattca 1380 aaccgaagct tttcgtgatc aagagatgcg tagacgcact ttgaaggagc ttgaggagaa 1440 gacttatcca ttccccgact ctgatgtggt tgccatgcta gatgacctgt tggacaagaa 1500 ggtgatcagt ttgcctgagt gcagacggcc ggaagagatg aatcgtaccg acagtccaag 1560 gtactgtaaa ttccaccgct tcatcagtca tccgacagaa aagtgcttcg tgctgaaaga 1620 tctcatcatg aagctggctc agaaaggaat catcgagcta gatcttgacg atgtggtgaa 1680 gtcaaactat accaccttca cttctggctc ttccgactca aagttttcac ctcaaccgct 1740 gggggcatcc tccaagacaa gcaaagttga aggatggact caagtcactc ctaagaaatt 1800 gcacaagaag catacgtctc ctccacaagt ccgccaatcg gaaagggggc aaagcagctc 1860 ttgtcaacct tcaaagcaac gtgaacgtgt tgaagatgat gaaatttcga cacaaagatc 1920 gtccgtcccc atcacgatgc gcgacttctt gcccgaagac ttcttcaatc actcggtcaa 1980 ggctccttgc tatgaagatt gtgaggaacg cctctcccag attgcttgac aaaattcaca 2040 aattctcctc gcccgcacga gcctaaactg catggcacaa agctcctggt ctgcacgagc 2100 ataaaaggca acaccaatgc tccttgtccg cacgagccta aactgcacga accaacgctc 2160 cttgtccgca cgagcctaaa ctgcacgaac caaagctcct tgtctgcacg agcctaaact 2220 gcagacacaa gctcctcgcc tgcacgagcc taaactgcat ggcacaacgc tcctggtctg 2280 cacgagcata aaaggcaaca ccaacgctcc ttgcctgcac gagctgaaac tgcaacacgg 2340 caccaaatgc tccttgtctg cacgagctga aactgcaaac gacaccaacg ctccttgcct 2400 gcacgagttg aaactgcaaa cggcacaaaa agaaaatacc aaaaaatatg tatgtatttg 2460 aactacgtta cgacttgatc tcttctttgg aggggtacgt aggcagctcg aatattcaaa 2520 tttcgagttc agtcacatca aaataaagaa taaatgtttt attaaagaaa aaaaaaaaaa 2580 aaaaaaaaaa taatacagtt tctcaaaaaa aaaaaaaaaa taataaaaaa taaaaaaaaa 2640 ataaaaaaaa gaatggcacc agctatctcc accaaagaaa agagccaaag cccaggcctc 2700 tttatttcac aggcccagat gccaagacca agcccagcaa gaagcccaaa aggcccgtca 2760 tcttcctctc caaaacaatg actgcctatt tctccagatg gcctccgatc tctctcgacc 2820 cgtccacatg gagttctcac cgatctcgat tccccgatcc cggcgtcaac accagcagcc 2880 ggacgccacc tcgcccatcc tctcatcttg gcccactcca gtctcctcca gccggagcac 2940 cgcaaagcct tcagggaaac gacttgggat cagggctcaa ggcgctggat caggtagatt 3000 tcaaagcccc agaggaaagg cctcgtcttc tctcgtctgc tcatctcctt gcgacgcaac 3060 tgcagctcag cgacaactct gcctcacctc cagcgtaatc aattgtcggg tgagttctcg 3120 accgggctga cccagctgca gcgcttgagc aggctcgatc tcagctccag caactcaccg 3180 gtccgttcca ttcgccatcg gcaacctgac ccgcctgacc ggactccttc ttgaaaacaa 3240 cggtttctcg ggcaagccac ccagcatccc atctcccagt ctgaccacca agcagtggct 3300 ctctcctccc ctcctcctca atctccccta ccgggcgggc atggatctcc gcactctccc 3360 ggcggaggga ttactgcagt cggtacccca cttctgcttc agaaatcggt cttttcccgg 3420 atcaaaaaga gctagctgag cttcgtcaat cgcacttgag attcaacagc acttggcgat 3480 gttgcccacc aaccacggga tcggaacatg gcatcagaat ctgggtcaag aatctgaaag 3540 acgtagctct ggtgccgacg acgtcttgga gacatcaaca cgaagttctc cggctcagta 3600 gagttcaaac caccgaaaga tgctggtgaa gagcagaaca gagtgcctca gctcggactc 3660 tacggcatgt gctgcggatc gcagcttctc acgttcgcat tctccggaat ccatgctgct 3720 caggatcgtt tgggagctgc tgcaaattcg atgcgaaggc gggttcagca ccggagcccc 3780 gtcggacctg gccgcgacct gctttcagat ggtccgagag ccttcaagaa ggagcaccag 3840 acatgaatcc tctgcgggat ttggaccctc gcagcttcac aacaggcggt ctcgcttctc 3900 agccgggctt caatgggatg cagcgtcttc aatgagccgg tcatgcttct cggcttcggc 3960 tccaggacgt tctctcggga agggcagatc aaggcatcta gtgcatcgac gaactcttgc 4020 cgctgatgac acacagcaaa acttgcaatt ggttccccgg agatgattct ccagcaacag 4080 tgtacttctc tccgatgcaa atgtgctgaa gtcccaactg acgaggctcg ggttggagac 4140 cctgtgccgg ctcagccaga gggccatgcc tgtggatgga agagttgcgg ctggaagaag 4200 cgttgtcgac gaatccatgc tccggagaat cacttcttgc atcaaggaaa aagacctcgc 4260 tgtctcagct ggaacagcag accgggatgg tcatctgcgg gttgaagcat cttcgactgg 4320 ctccagttcg atgatgttca agatcgttcg catggtggga tgctcaagga catgaagcac 4380 ccatacaaag gctgctgatc caagctggac ctttgaacag cagatgactt gcagatctcc 4440 tcctcagacg agttctcctc tagagtctgc agcaatgaaa acagcatgcc gaggctctcc 4500 tctccgaccc caagcttctc ttcagctgca ccgccaactc ctccaggtga ccgcttcacc 4560 aacctcggct cacaccttcg gcctcggcgt cgacgccgac ttcaattgat cctcctcaga 4620 tccgagagcc gtgagcacac cactatcgac acccaacacg gttgacctcc atctccacca 4680 gctcgtggcc ctgcgctcca tcaccggctc cgccagctct tcctctcccc caatctgcga 4740 gcgaccaagc aggttctggc tgatgagccg gacagatcca aagatggcaa tggtgcttgg 4800 cacggatgga tcttggctct ccctgtcctg tgatagacca gaggaatgca acaatctgga 4860 tggctaattg tgtggcacgt cgcatggcac ggcaaatagg cagcatcggt aaaataatct 4920 gcagtgattg gcagtgcaat ggtgcgcagt ggcggtgctc ggtggcagta caacgggtgt 4980 gcagtggctg tgctcagtgg ttggctcagt ggctgtgctc tggtccgccg gatccgacat 5040 caaggtcacc ccctcctccg tctcttgcct cgcagctgcc aacaacttca aagaccgccg 5100 tcaaacgact agccggccga gaagcttcct aagctccagc tctcgtccgc cttcgtccct 5160 ccctgcaaat tccccagccc atcaccaaat ttataaaaaa aaaaataaaa aaaaaaaatg 5220 ggatggtgga tcaaagatgg ggaacagccc atggcagata aaaagtttat ggtggtgcat 5280 gggcaccatg tgcagaaaga aaaaaaaatt gtaaaaaaaa aataaaaaat tatggaactt 5340 ggtgcatccg gcaccaaaag aaaaaaaaaa aaaaaacaaa tgcattgaga gaaatagaag 5400 gtccatttta tttatttttc tggaaatttt acataaattt gcattataca tacctaaaaa 5460 aaaaaaaatc aaatcaaatc aaatttacaa gaggggatct tcaaggacga tcaggtgccg 5520 cctcaccact cggcagagct ccaggaagga gaggcgccgg aggttgactg tttgaagcct 5580 caccactcgg cggaactcca ggaagaagag ggccgaaggt tgatcatttg gagcttcatt 5640 acgcggtaca gccccagaag acgaaggcaa atgctgctgg aacaaaccca caaacctctg 5700 atgatcaagt aaaatctgac catcagattc ctgcatctgg tcaatcttcc tcttcatgtt 5760 tgtggcatag ctatgtgcga gcttgtgcaa ctgtttattc tcmtgcttga gccctctaat 5820 ctcctgtttg agactcatca cttcagccgc caacgattca acttgacggg ttcgagcaaa 5880 taggcgttgg gccatgttgg acacagaacc cgcacactgc acactgagag ccagagaatc 5940 cttaacagcc aactcatcag accgtttgga aagtagtctg ttatctctgg gagtgacaag 6000 gttccgggcc accaccgcag cggtcatatc attcttcacc accgaatccc caacggtaag 6060 aggaccagta ggggatatga aggatgggcg ccatatgttg tctggagaag gcgggactgc 6120 ctcttcacca aggttcaagt caaaacgacg gtcggaaggg tccagacatt ttcaaagtgt 6180 tgaagaaaga agaggtcgga caaatcaaga tcttagaagt gcaagaaggg agttttcaca 6240 agcgaaaatt caagtgtgct ttgaaacgaa ctgcgtgcct ctataaaaaa tcagcactcg 6300 acgggatttc agagatcgaa gaggcgagct cagaattcga agaggccaat tcaaaaatcg 6360 aagaggcaag ctcagaaatc ggagaagcat cttgcttttc cagacgcgtc ggcacccgtc 6420 acacgcaaac tcagctttgc ggaaatcacg ggcaatttgt cgaagcgccg atcccagata 6480 tcgaagaggc gccagtcttt ttcagcccgt cagcacccat cacacgcaaa ctcagctttg 6540 cggaaatcac gggtaatttg tcgaagcgcc gatcccagat atcgaagagg cgccagtctt 6600 tttcagccgc gtcaacacct gtcacatgca cactcagctt ggcgcaaatc acgggcaatt 6660 tgtcgaagat ttccggtgaa ggagaaagca cgtgaagcca tactgttcaa tcacgcattg 6720 gttgccgaca cgagtgaaag aatagtacct ctacaggtat taaggaactt cctataactg 6780 tccaccttca ccttccatag caaggcagac atacagagcc tttcttcatc tccgagaatg 6840 ccttcccaac gaagcctctc gagtcactca gtgttcctta ttccttgggg tacctctgca 6900 agccaatgac tccaaagcaa aagtatctca tatcaccagg gtagaaagca agagtatctc 6960 atatcatgcg ttctccctgt cctttccttt gtccttgttc ttacctacaa agacaaggat 7020 aaagaaaaca atatgccgga acttccactc aaactcgggt aaggaaccga ctgcttggaa 7080 cccttccctg attgcctacc tagcactgct ctcgagtact cgtctcccac tgctgctgta 7140 cttccaaaga agctgccaca tctgcctgga gaacagataa ggcaagtgaa aatgatacct 7200 tgcagcatgt ggagacaasg tgcagaagga acaagcagag aagaatgcgg tctgcacagt 7260 caactcagca gaaggagtcc gaactgagga actcgagaag ctgccacatc tgcctgaaga 7320 aacaagcaga gaagaatgca gcatgcacag tcaactcagc agaaagagtc tgagatgaag 7380 aactcgagaa gatgccgcat ctgcctgagg aacagataag gaaagaaaat gatacttgaa 7440 gcatgtggag acaaggcaac aaagcacgtg cgatcatccg ctacttcttc aaaatcaaaa 7500 gtatctcata tcatcagggt tgcaatcact ctggacggtg aactcgtttt gaccctcaaa 7560 ttcttgggtc gacttactag gcgttgtggg ctgcacgtgc cgattcacca cccttgaatc 7620 aaatccttaa agatcaagtc accaactgga agaagagccc atcaatcttg aagatcatac 7680 cgttgaccaa actgctcagg tgtgaattag aaagattgaa caaagcaaca agtcgtcacc 7740 ttcacctcgt gcctgcttgc catgtgttcg agtcaacctt caagaatcaa gcctcaacgg 7800 cccttgaaga agcttccagc caaattcaag atcaagcctc gacggccctt gaggaaatca 7860 caagtccgat tcaagatcaa gtgtctacca cccttgaatc aaaacctagt tcaagaataa 7920 gctgtggaaa atcaacaatt ggaggaatcc agaaaatcct ccaacccagt tcaagatcaa 7980 agctgtggaa agtcaacaag cgcaacaaaa tacgtgccga ttcacccact accaaagcca 8040 aagatcatct accacatgaa gctccttgtg gtccaatttc aaccttcaag atcaagcctc 8100 gacggccctt gaagaaattt caaacaaaag ttcaagaaca agcctcaacg gcccttgaag 8160 aaatctcaag cccaattcaa gatcaagcct caacggccct tgaagaaatc tccagcccaa 8220 ttcaagatca agcctcgacg gcccttggat cgacatctac agtaagggac ttcaaaacgc 8280 atctcctaca cgtgacaagc acatgtatac gacgcgcctt gaagtggggg catt 8334 // ID Gypsy-8_Mad-I repbase; DNA; EDCOT; 3992 BP. XX AC ACYM01138672; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-8_Mad-I; KW Gypsy-8_Mad-LTR; Gypsy-8_Mad_. XX NM Gypsy-8_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3992 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1331-1331 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01138672; Positions 4540 549. XX CC Positions [1267-1770] - Reverse transcriptase CC Positions [2869-3363] - Integrase core CC 'TTGAC' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(307..1347,1351..3945) FT /product="Gypsy-8_Mad-I_1p" FT /translation="MAARTRPPNLPVRRLTPDEIQQKKEKGECWFCSEKWV FT PGHKCLKKQLLMLDVYDEDDFGEMVPTDDQGALQAMELSSCAYYGTSTKPS FT FQTMKVDGKIHNQPVRILLDSGSTHNFVDCRLVRKLGWPLHVTKPFDVMIA FT NGGTVSSQGCCKNLSIELGGYHCDIDLFAFPLGGCDVVLGVQWLSTVSPVL FT WDFQLLTMEFHVGTASYKLYHSAPHFPLVDDMVIQNLEKELYGSNLGVLLY FT SLDGVSPIANTTLTPSQHNELQDVLDEFEAVFLLPTSLPPAREHDHKIPLI FT AGARPPSIRPYHYGPLQKDEIEKAVQELLSSGFIRPSHSPFSSPVLLVKKK FT EGTWLCMDYRELNKITVKDKYPIPLIDDLLDELCGAKYFSKLDLRSGYHQI FT RMHEADIEKTAFRTHDGHYEFLVMPFGLTNAPASFQSLMNDIFKPYLRQFI FT LVFFDDILVYSNSWETHLSHLKQAFAVLQQHQLFVKKHKCSFGQCQVEYLG FT HMVSSEGVSADPTKIQAIKDWPTPRTVKELRGFLGLTGYYRKFVPGYGKIC FT QPLYKLTSNEGFNWSPCTEQAFQALKQAMVSPQLLALPDFSVPFVIECDAS FT GNGIGAVLQQHGRPIAFSSQALGPRNQSLSTYERELIAIVYAVKKWQNYLQ FT GRHFIIKTDHSSLKYFLSQRTNTPFQQKWVSKLLGFDYEVQYRQGKDNIVA FT DALSRVPSSTLLPETHVDNKGDICSITYPYFGWLDELRRDMEQDSWVLQKK FT KEVEDNATAVLCNTKLSKYHLDNGFLKYNHRIVIGAESTWRRKVFEEHHST FT PIAGHEGVLKTYQRLKRGFYWVGMKRNIKEWVAECRTCQQNKYETISPPGL FT LQPLPLPQQIWTDISMDFICGLPNCKGKSVILVVVDRLSKYAHFIALGHPY FT TAAIVAQEFVDNVFKLHGMPLTIVSDRDTLFLSAFWKEFFKLQGSKLCMSS FT GYHPQSDGQTEVVNRCLETYLRCFTSFQPKKWLQWLAWAEWSYNTSYHSST FT KFTPFEIVYGMTHPHIATYELGSAKLDSVEQGLLARDKILAMLKTNLIIAQ FT NRMKVQADKHRSERTFEVGDLVYLKLVPYQLQSLATHAYHKLHPKFYGPFE FT VLEKIGNVAYKIKLPETSKIHPVFHVSCLKKHIGPNVSPVPLLPLVTDEGL FT QAQEPGVVLQRRIYKKNNVAGVQLLIQWKDKGADEATWEDFDDFAARFPSF FT KL" XX SQ Sequence 3992 BP; 1097 A; 845 C; 917 G; 1133 T; 0 other; attggtatca gagcctaggt tcccgacgct gcggaggggg cgacctggaa agggctacct 60 taacaggatg accaaagtgt gcaccgccgt taagagtgaa agccaccaga gtaagggccg 120 ccgtgggcgt cggcttccga agggtggtgt aatgttatga tcccacatcg actacactta 180 tgggggtgta ggggttctta agtccttggg gtcctcccac ctattggact agtcttttgg 240 gttgggctct tcccttgcgc tttaacccct cgagtaaacc acacagtcta ccctccccct 300 ttaccaatgg ccgccaggac tcgaccaccc aacctacccg ttcgtcgtct tactccggat 360 gaaatccagc agaaaaaaga aaagggagaa tgctggtttt gttctgagaa gtgggttccg 420 ggccataagt gccttaaaaa acaacttctt atgttagatg tttatgatga ggacgatttc 480 ggtgagatgg ttcccactga tgaccaaggt gcgctgcagg ccatggaact tagttcctgt 540 gcttactatg ggacctctac taaaccaagt ttccagacta tgaaggtgga cgggaaaatt 600 cacaaccaac cagttcgcat cttgctcgac tcggggagta cccacaattt tgtggattgc 660 cggttagtaa ggaagcttgg atggcctctc cacgttacaa agccctttga tgtcatgatt 720 gccaatggag gcacagtaag cagccagggt tgttgcaaaa acctgtctat cgaattgggt 780 ggctatcatt gtgatatcga cctttttgcc tttcctctgg ggggttgtga tgtggttctg 840 ggggttcaat ggctctctac tgtgagccct gtcttatggg atttccagct tcttaccatg 900 gaattccacg tgggaactgc ctcgtacaaa ctgtaccaca gtgcaccaca tttccctctt 960 gttgatgaca tggtaattca aaacttggag aaagaattat acggttcaaa cctgggggtt 1020 ctcttgtatt ctctggacgg ggtttctcct atagccaaca ccaccctaac tcctagccaa 1080 cacaacgagt tacaagatgt tttagatgaa tttgaggctg tatttctcct tcctacttcc 1140 ctgcctcctg cgagagaaca tgatcacaag attccactta ttgctggagc ccgaccacct 1200 agcattcgcc catatcatta tggtcctttg caaaaagatg aaattgagaa ggccgtgcag 1260 gaacttctca gttccgggtt cattcgccct agccacagcc ctttctcttc tcctgtctta 1320 ttggttaaga agaaggaagg gacttggtga ctatgcatgg attacaggga attgaataag 1380 atcacagtca aggataagta tcctatcccc ttgattgatg acttattaga tgaactctgt 1440 ggggctaaat atttctctaa attagacctt aggtccggct accaccaaat tcgaatgcat 1500 gaggctgata ttgaaaaaac tgcattccgg actcatgacg gacattatga atttctggta 1560 atgccttttg gcttgactaa tgcgccagcc tctttccaaa gcctcatgaa tgatatcttc 1620 aagccatact tgcgacagtt catacttgtt ttctttgatg atatcttggt ttatagtaac 1680 tcttgggaaa ctcatttatc tcatctgaaa caagcattcg cagttcttca acaacatcaa 1740 ctctttgtca aaaaacataa atgttccttt gggcagtgcc aagtcgagta tttggggcac 1800 atggtgtcta gtgagggggt atcagctgac cctactaaga tccaggccat taaggattgg 1860 cctactcctc gaactgtgaa ggaactacgt ggtttcctcg gattgaccgg ctattacaga 1920 aaatttgtac ctggatatgg taagatttgc caaccgttgt acaaacttac tagcaatgaa 1980 ggttttaatt ggtctccttg cactgaacag gctttccagg ctttgaaaca agccatggtt 2040 tctcctcaac tgttagcttt gcccgatttt tcagtaccat ttgtcattga atgtgatgcc 2100 tcaggtaatg gcattggggc agttcttcaa caacacggga gacctatagc tttctccagc 2160 caagccttgg gtcctagaaa tcagtctctg tccacctatg aaagggagtt aatcgcaatt 2220 gtgtatgcag tgaagaagtg gcaaaactac ttgcaagggc gccactttat tatcaagacg 2280 gatcacagta gtttgaagta ttttctcagt caaagaacaa acaccccatt tcaacaaaaa 2340 tgggtgtcca aactgcttgg ttttgattat gaagtgcaat atagacaggg caaggacaac 2400 attgtagctg atgcactctc acgagttccg agttctactt tgctacctga gactcatgtg 2460 gacaacaaag gagacatttg ctctattact tatccttatt ttggttggtt agatgaatta 2520 agaagggata tggagcaaga cagttgggtg ttacagaaaa agaaggaagt cgaggataat 2580 gccactgctg tgttatgcaa taccaagcta tcaaagtacc atcttgacaa tggtttcctc 2640 aagtacaacc atcgaattgt cattggtgct gaatctactt ggcgaaggaa agtgtttgag 2700 gaacaccatt ctactcctat tgctggccat gagggagttt taaaaactta ccaaaggttg 2760 aagaggggat tttattgggt ggggatgaaa agaaacatca aagagtgggt ggctgaatgt 2820 agaacttgtc agcaaaacaa atatgaaact atctcacctc ctggtttatt acaacctctc 2880 ccattaccac aacaaatatg gacagatatc agtatggatt ttatttgtgg gttaccaaat 2940 tgcaaaggaa aatctgtgat attggtggtg gtagacagac tctccaagta tgcacacttc 3000 atagccttgg ggcaccctta cactgctgca atagttgctc aggagtttgt ggataatgtc 3060 ttcaaattac atggtatgcc tttaactata gtgagtgacc gagacacatt atttctcagt 3120 gctttctgga aagagttttt caaactccaa ggttccaaac tttgcatgag ttcaggttat 3180 caccctcaaa gtgatggcca aacagaagtg gtcaatcgat gtttggagac ttacctcagg 3240 tgtttcacta gtttccaacc caagaaatgg ttacagtggt tagcatgggc agaatggagt 3300 tacaacactt catatcactc ttctaccaag ttcactccat ttgagattgt gtatggtatg 3360 actcatcccc atattgctac ctatgaactt ggatcggcta aactggatag tgtggaacaa 3420 gggttgttgg ccagagataa gatattagcc atgctcaaga ccaatctaat tattgctcag 3480 aaccggatga aggtacaagc tgataaacat cggagtgaga ggacttttga agtgggggat 3540 ctagtttatc taaaattggt tccttatcag ctgcaatcac tggctacaca tgcttaccat 3600 aaactacacc ctaagttcta tggccctttt gaagtattgg agaaaattgg caatgtggct 3660 tacaagatta aactaccaga aacttcaaag attcatccag tctttcatgt cagttgcttg 3720 aagaaacata ttggtcccaa tgtgagtccc gtaccactac taccattggt gactgatgaa 3780 gggttacaag ctcaggaacc aggagtagtg ttgcagagga gaatttacaa gaagaacaat 3840 gttgctgggg tccaactgct aattcaatgg aaggacaagg gggctgatga agctacatgg 3900 gaggattttg atgattttgc agctaggttc ccaagtttta agctttgaag tacaaccttg 3960 aggacaaggt cttattcgaa tgagagggta aa 3992 // ID MITE_MS repbase; DNA; EDCOT; 184 BP. XX AC . XX DT 28-MAR-2005 (Rel. 10.03, Created) DT 14-APR-2005 (Rel. 10.03, Last updated, Version 1) XX DE Medicago sativa MITE, a consensus. XX KW miniature inverted repeat; MITE_MS. XX OS Medicago sativa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-184 RA Charrier B., Foucher F., Kondorosi E., d'Aubenton-Carafa Y., RA Thermes C., Kondorosi A. and Ratet P.; RT "Bigfoot. a new family of MITE elements characterized from the RT Medicago genus."; RL Plant J 18(4), 431-441 (1999). XX RN [2] RP 1-184 RA Gentles A. and Jurka J.; RT "M. sativa MITE."; RL Direct Submission to Repbase Update (28-MAR-2005). XX DR [2] (Consensus) XX SQ Sequence 184 BP; 62 A; 30 C; 25 G; 67 T; 0 other; gggtcttgtt aacttgtgcc ctaagggcac aagataagaa actaaatgta gaaacttaat 60 cttgaaaatt gtgcattcat aaccttaaaa gcttaaaaac ttatattttc aatgcaatat 120 ttatttttta attctatttt aagatcctta tcttgtgccc taagggcaca agttaacatt 180 tctc 184 // ID Gypsy-32_VV-LTR repbase; DNA; EDCOT; 260 BP. XX AC chr15; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-32_VV_; KW Gypsy-32_VV-I; Gypsy-32_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-260 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr15; Positions 8379420 8379679. XX SQ Sequence 260 BP; 81 A; 32 C; 77 G; 70 T; 0 other; tgataggcct cctatacgtt atgtgtataa tagaaaaggg aagaggaatg gactgccacc 60 tggcagttag ttgtaacagc ttgagtggag gttaggtcac agttggatac gggctgagag 120 gaaggtttaa atagaaaaag agggggaatt acaggggagg gagaagattg tggatctggt 180 agggatttga ggaccagttg ggactcttgt ttcttgaaat tcttgaaatt caataataaa 240 tctccattag atacctatca 260 // ID Copia48-PTR_I repbase; DNA; EDCOT; 4465 BP. XX AC scaffold_954; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia48-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4465 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4465 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 274-274 (2007). XX DR Genome; scaffold_954; Positions 16107 11643. XX CC Positions [1639-2127] - Integrase core CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 79..2127 FT /product="Copia48-PTR_I_1p" FT /translation="MATISSALSQNIAQFTKLTETNYLTWLQQIKPYLHGA FT KLWGYVDGTIPEPSLTILTTDTQSTRSIPNPDHASWFIIDQQIVSILTTTL FT TENIAQLTIGFDTSKAIWDCLERHFSQKSVASATNLKMQLLDLNKGTQSVD FT TYLRHAKSIADALISINKPVPDEDLVIATLHGLGPDYLMLRTVLTQNPPLP FT DFTELRARILSFDAQQSRPADSPTAIALFNHHQTPSTRRDHRPNTSHQFPT FT SGRPNNGRFRRGRYSQQRTTQQSQVGSSFPMQQQHVPPLGPFTSPAWAARP FT PPNGILGPAPQWCPNCHSSHHGLSQCPHRFSGPNTATPFAGVHYAADPNWY FT PDTGATHHMTAMPINNSQPYGGPHNVYMGNGDSMSVSHTGNLPFSLGSSTF FT TLQNVFRIPSIRKNLLSVARFTKDNHVFFLFAPDFYQIYCLRTGCLLFQGP FT CKDGLYPLNLSSVSTSPQALASVHSFIWHNRLGHPSSNVFARLSPTINSKL FT SFPSFCRDCALSKSHQLPFNSNKETATTPFHIIHSDVWSSSTISISGFKYY FT VLFTDEFSRYTWIYPMRRKNEVLTHFQTLVAKIQNIFHHTIQFLQSDNGTE FT YVNNAFSHYCKALGIQQRFSCPHTPQQNGLAERKHRHIATMTRSLLLTSGT FT PHNLWVEVVLTSVYLINLLPTPTLLGYSTYSSLW" XX SQ Sequence 4465 BP; 1070 A; 1219 C; 733 G; 1443 T; 0 other; tggtatcagc ctaaacctac gatcctcacc tatttctctc ttcttttagc gtttctcttc 60 cttttctctt tttctttcat ggccaccatc tcttcggctc tctctcaaaa tattgctcaa 120 ttcaccaaac ttactgaaac caattatctc acctggcttc agcaaatcaa gccctatctt 180 cacggtgcca aactttgggg atatgttgat ggcaccattc ctgaaccatc tctcaccatc 240 ctgactactg acactcaatc tacaagatcc attcctaatc ctgatcatgc tagctggttc 300 atcatcgacc aacaaattgt tagcatcctc accaccactc tgacagaaaa cattgcacag 360 cttaccattg gtttcgacac atcaaaggca atttgggact gtcttgaacg tcacttttcc 420 caaaagtctg tagcaagtgc aaccaatctc aaaatgcaac ttcttgatct caataaaggc 480 actcaatctg ttgacactta tcttcgtcat gctaaatcca ttgctgatgc tttgatttct 540 attaacaagc ctgttcctga tgaggattta gtcatcgcca ctcttcatgg tcttggccct 600 gattatctca tgcttcgtac tgtcctcact caaaatcctc ctctcccaga tttcactgaa 660 cttcgggctc gaattctctc ttttgatgct caacaatctc gtcctgctga ttctcctaca 720 gccatcgctc ttttcaatca ccatcaaact ccttctaccc gtcgtgatca ccgccctaat 780 accagccacc aatttcccac cagtggtcgt cccaacaatg gtcgcttcag acgtggtcgc 840 tattctcagc aacgcaccac tcaacagtca caggttgggt cttcttttcc tatgcaacag 900 caacatgtgc ctccattggg gccatttact tcaccagctt gggctgctcg tcctccacca 960 aatggtattc ttggcccagc acctcaatgg tgtcccaatt gtcactcaag tcaccatgga 1020 ctttctcaat gtccacatag attttctggt ccaaacactg ccactccatt tgctggtgta 1080 cattatgctg ctgatccaaa ctggtacccg gacaccggtg caactcatca catgacagcc 1140 atgcccatca ataattctca accttatggt gggccgcata atgtctatat gggtaatggg 1200 gactcaatgt ctgtttccca tactggtaac cttccttttt cattaggctc ttccaccttc 1260 actctacaaa atgtcttccg tattccatcc attcgtaaaa atcttctatc tgttgctcgt 1320 ttcactaaag ataatcatgt tttctttctc tttgcacctg acttctatca aatctattgc 1380 ttacgcactg gatgtctatt gtttcagggc ccttgtaaag atggtttgta tccgcttaat 1440 ctatcaagcg tctctacttc tccgcaagcc cttgcttccg ttcactcctt tatttggcac 1500 aatcgtttgg gtcatccgtc atcaaatgtc ttcgctcgtc taagtcctac aattaattcc 1560 aaattgtcct ttccttcttt ttgtcgagac tgtgcactta gcaagtctca ccaattacct 1620 tttaattcca acaaagagac tgctaccact ccttttcata ttatacatag tgatgtctgg 1680 tcctcctcta ccatttctat aagtggtttc aaatattatg ttctatttac tgatgaattc 1740 tcacgctaca cttggattta ccccatgcgt cgcaaaaatg aagtcctcac tcattttcaa 1800 actttagttg ccaagattca aaacatcttt caccacacca ttcaatttct tcaaagtgat 1860 aatgggacag aatatgtcaa taatgccttt tctcattatt gtaaagcctt gggaattcaa 1920 caaagatttt cttgccccca cacgccacaa caaaatggcc ttgccgaacg taagcaccgc 1980 catattgcta caatgactcg cagtctcctt ctcacttctg gtactccaca taatctttgg 2040 gttgaagttg ttttaacctc tgtttacctt attaatcttc ttcctacacc cactctattg 2100 ggatactcca catactcgtc tttatggtag cccaccttcc tattcctctc ttcgggtttt 2160 tggatgttcc tgttttcctc atcttgggtc ttatgtctct gataaacttt cgagtcgtag 2220 cattgagtgt gtctttcttg gttacagttc tcaacacaaa ggttatcgtt gtctagatcc 2280 taccaccggt cgtgtctata tttctaggca tgttattttt aacgaaacaa tttttcctta 2340 taaacagttg caggcacatt cagtttctga cgctggctca ttggaattca cacttttgtc 2400 tagctcagaa ctcccacaac ttgctccttc tgatccaaat ccacctgctg agaacaacac 2460 tctccttatc ttgtgtctca accagagcag catgaagtgg gtattgaatt cccgattaca 2520 gcatcatcgg ctccatccca gtctctggcg cccgccgccg cccccatcct cacttatcag 2580 cgccgacgtt cattacatcc ggttacttca cagatagagt ccacctctct tcagccatct 2640 gcccctgatg caactattcc acagctggtc tcaagtgatc cttctcctgt ctctaatcct 2700 ccagcaacat ccacatcttc atcacctgct cctccgtctc ttcctgcgcc gccctcttca 2760 cccaagagga cacgtttaca gcatggtatt gtgcaaccta aaattcacac ggatggaact 2820 atcaaatatc caattcctcg tgctctcctc actgccattg aaactacaga gcccacatgc 2880 tacactcaag cttctaaaca tgcgatatgg cgtgctgcaa tggctgatga aatcaatgct 2940 ttgctgaaaa atgaaacttg gacattggtt cctccttctt cctctcaaaa tcttgttggc 3000 tgcaaatggg tatttcgagt aaagcataac ccagatggca caattcaacg tcacaaagca 3060 cgacttgtgg ctaaaggatt tcatcaacaa caaggtatag actatacaga tacctttagc 3120 cctgttatta aacctgcaac tattcgtgtt gtgctttctc ttgctgtatc tagaggctgg 3180 tcactacgtc aattggacgt gaagaacgcg ttccttcatg gccttcttaa agaagacgtc 3240 tatatgactc aaccaccggg attcatcaat cagtcacgac catctcatgt ttgcaagctc 3300 aataaggcca tctacggcct caagcaagct ccccgtgcat ggtttcaccg aatgacatgc 3360 ttcttattat caattggctt tgttcagagc ttggctgatt catctttgtt tgttttccaa 3420 cacgagtgtc atacaattta ttttctcctc tatgttgatg acattgtggt caccggtagt 3480 gatgatcgac ttttacaaag ttttattgat gctttaagtc gaggctttga catcaaagat 3540 cttggaaatc tacactactt tctcagtttg caggttatat cccacaataa aggtgttcat 3600 atcagtcaac tcaaatatgc atatgatctt ctcgtgaagc atgatatgct gcttagtaaa 3660 cctgtgagta ctccgatgtc agcaaaggat actctcactt ctaatgatgg tgctctcctt 3720 cccaatccat cggtctttca ggaaattgtt agatccttac agtcttgaca atcactcgcc 3780 ctgacattgc ctttgctgtt aattctattg ctcagttcat gagtcaacca cacatccctc 3840 acttaattgc tgctaagcgc atacttcgct acatcaaagg ctcacttgac catggcttgt 3900 tctttggtcc tcagcaccat cctacttatc ttgctgccta tgcggatgct aattgggctg 3960 gctgttcaga atctcgccat tcaacgtctg gttatcttgg cactaacttg gtctcttggt 4020 gctctaaaaa gcaacctacc attgctcgtt ccaagctgag tccgagtatc gttctctttc 4080 ccatgctagt gcagagacta cttggttagc ctacttgctc tatgaacttg gtgcttgcat 4140 ttagtttccc attctcttgc attgtgataa cctcagtgct acgtacatgg cttctaatct 4200 ggtattccat gcccgcacta aacatattga acttgattat cactttgttc gtgagaaggt 4260 tgcacttgga agccatcgtg tttgctttat cccttccata gatcagcctg tcgatctgct 4320 caccaagcct cttcacaaga atcgtcatgt tctttttact cgcaaacttg ttcgtgcagg 4380 cccgccaagt ttgagggagg gtgttagaga gatatcctct gctgattatg taactgaaga 4440 gagatttcct cttctcaatc aaaac 4465 // ID Copia-2_Mad-LTR repbase; DNA; EDCOT; 344 BP. XX AC ACYM01105711; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-2_Mad-I; KW Copia-2_Mad-LTR; Copia-2_Mad_. XX NM Copia-2_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-344 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1342-1342 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01105711; Positions 1543 1200. XX SQ Sequence 344 BP; 128 A; 52 C; 64 G; 100 T; 0 other; tgtaagagta taagtaagga caacaagcat caagagcaga gtccaagtga aagcaattca 60 agggtctaga tgaggacaag tgtcacaaga tcaacaagga agttacaagg ttgttaggat 120 atggtgctaa ggttgttaag tttgttaaaa ctgatatatt tcatatctta gcttatagag 180 caagatatgt aaggatataa atacagatat ccaaagatgt aagacgatga tgaaaaatac 240 acaagaaata taaagaaatc ttctctgaaa tctctttgtc tctatctctc taaatttcag 300 tttcttcgac taccttcatt gaagctactg cttcaatctt caca 344 // ID TGM5_GM repbase; DNA; EDCOT; 1002 BP. XX AC X13528; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 06-AUG-2007 (Rel. 2.02, Last updated, Version 3) XX DE Soybean Tgm5 transposable element. XX KW EnSpm; DNA transposon; Transposable Element; transposon; KW unidentified reading frame; Tgm transposon; zinc finger protein; KW GMTGM5; TGM5_GM. XX NM TGM5_GM. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-1002 RA Vodkin O.L.; RT "TGM5_GM."; RL Direct Submission to Genbank (03-DEC-1988)Vodkin L.O., University RL of Illinois, Department of Agronomy, Turner Hall , Urbana, IL RL 61801 U.S.. XX RN [2] RP 1-1002 RA Rhodes R.P. and Vodkin O.L.; RT "Organization of the Tgm family of transposable elements in RT soybean."; RL Genetics 120(2), 597-604 (1988). XX DR GenBank; X13528; Positions 1 1002. XX SQ Sequence 1002 BP; 310 A; 182 C; 237 G; 273 T; 0 other; tatggatgga gtgacaaaag ctttacttca ttgcttcaaa tagtgcacga tctgcttcca 60 caggataaca cattgcctaa aagctactat caggcaaaga agatattgtg tccgatgggt 120 atggagtatc agaagattca tgcttgccct aatgattgca tactatacag acatgaattt 180 gaagaaatgt caaaatgccc taggtgtggg gcgtcacggt acaaggtgaa ggatgatgag 240 gactgcagtt ctgatgaaaa ctcaaagaag ggccctccag cgaaagtgtt gtggtatctt 300 cccatcattc caaggtttaa gcgtttattt gctaatgaag acgacgcaaa agatcttacc 360 tggcatgcta atgggagaaa atctgatgga atggtccgtc atccagctga ttgctcccag 420 tggaagaaga ttgatagttt gtatccgaat ttcggcaaag aggcaagaaa tcttagactt 480 ggactagcca gtgatggaat gaatccatat ggcaatttaa gcactcaaca cagttcatgg 540 ccagttctac tagtaattta caattttccg ccttggttgt gcatgaagcg aaaatacatg 600 atgttgtcta tgatgatatc aggcccaaga caaccaggaa atgacattga tgtttatcta 660 agtccgttga ttgaagacct gagaaagttg tgggatgagg gggttttagt gtttgatggg 720 tttcgcaagg agacttttca aatgcgtgca atgctatttt gtaccattaa tgactttcca 780 gcatatggga atctcagcgg ttatagtgtt aagggtcatc ttgcatgccc catctgtgaa 840 gaagacacaa gctacataca actgaaacat ggtagaaaaa cagtgtacac tagacatcgc 900 gtttttctaa aagctcatca cccttacaga agattgaaaa aagcttttaa tggaagtcaa 960 gagcacgaaa ttcgtcggac accgttaact ggtgagcagg tc 1002 // ID Copia-63_VV-LTR repbase; DNA; EDCOT; 235 BP. XX AC chr15; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-63_VV_; KW Copia-63_VV-I; Copia-63_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-235 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr15; Positions 19152990 19152756. XX SQ Sequence 235 BP; 74 A; 52 C; 28 G; 81 T; 0 other; tgataaccac aacattcaaa ccaccgagat ttccttggct tctcacttat cttatccacc 60 agataaacac ttatccactt taagagataa cccaagagat aacccttgac tatttttaaa 120 tttctgttat tgtgtatttc aaaacttctt ctgtaattgt atataaatga gaatagccac 180 ccggtttttg gcattgaagc caataccatt ttacagattt ctacagagtc tttca 235 // ID SHAMUDRA3_MT repbase; DNA; EDCOT; 5499 BP. XX AC . XX DT 23-JAN-2007 (Rel. 12.01, Created) DT 23-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A MuDR type DNA transposon from Medicago truncatula. XX KW MuDR; DNA transposon; Transposable Element; transposon; KW Interspersed; repeat; ORF; transposase; TIR; TSD; SHAMUDRA3_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5499 RA Shankar R. and Jurka J.; RT "SHAMUDRA3_MT: A DNA transposon from barrel medic."; RL Repbase Reports 7(1), 102-102 (2007). XX DR [1] (Consensus) XX CC The sequence has terminal inverted repeats of MuDR type DNA CC transposons, flanked on both sides by 9 bp TSDs. Also the CC sequence has intact domain for MuDr type DNA transposase. XX FH Key Location/Qualifiers FT CDS 969..2897 FT /product="SHAMUDRA3_MT_1p" FT /translation="MIAYKKGEIYEYGGEWDIDEVNLKDLDNLVREIGVEG FT EYKLWYVCPGLDIIDGLRLLNTDRDVVRFINEHRNVSVAEFYVEAKDVEVE FT DCRYDSEVEEVVVFDKGKQPAESDEGDESDPEYNGDEEGEVPDYEVEDEDG FT SVDGVSVDDSDFDEXWDWTTVLPKQTVNPTPAGQSYNSNQAVVGVEVSRNP FT XATSLEDFEDENGDSDFLESSDASEEDEGSRKRKLNRFKXGDNNDPVIFEE FT GQIFATAXLIKTAVKEYALQNKKNVYLXKSEKKRIVVKCMQGCPYHMRFSR FT VPPQTYYVFSSYKSVHKCYQTGRIRVLSGQLLAKKLVPLLKHTPNMTIKGL FT KDECKNRWNVMLSSFQMYRAKLRALEMIHGASDEQYAHLRNYAEELLRSNP FT GSSVKIKCKPSAGGVVFQRIYVCFNACKRAFVSNCRPLIGLDGCFLKGXYG FT GQLLSAIGKDXNXQMIPIAFAVVEAETKDSWDWFXELLLSDLNGVEFKXWS FT FISDQQKVIFISFMKLILIVLNLILIYINKLFFQLYFVKGLVNTIAAIGDH FT VEHRFCVRHLYGNFRKRHPGEKLKEAMWKAARANTMPEFNRAMEDLKRLSE FT AAWEEMRQYAPGMWSRAGYSTHTNCDLQVNNMXEAFNSAIXXLRE" XX SQ Sequence 5499 BP; 1794 A; 786 C; 1167 G; 1713 T; 39 other; ggctaaagtg cacttttccc cccctaactt tcaaaatgtt gcgattttgg ccccctatgt 60 ataaaaacca caattttggc cctctatgtt ttagcccctt tgcatttcag tccttttgag 120 caattttgac ttggtcaatg ctgatatgtc atgccatgtg tgtatatact gattttcttt 180 tattttaaat gccaccataa tattacatga attaaaaaaa aagtaaaaca gaaaatataa 240 aatataaaaa ggactggcac gtgagagcgg tctttgttga tttaaattct agggttaaac 300 tgcgattttg gtccccaaat cgatttatct tcatccataa tttcctccaa aaatcgttac 360 caaatttgat tgttcttacc aaaaacgaaa tccagattgt tggtttctgt gtgttgtgaa 420 aatgaagtgg gtcgaaaatg gaaactcgaa ggtgagtatg tgttcagaga agacgagttc 480 gacgaagaca gaagtagcga tgaagaagaa gggtacagag aagacgagtt cgacaactga 540 aggaaacgtg ttttatcaac aaaacgtgct aaatggaggt gacaataatg tatcaaagta 600 agtgcttttt tttgtttacg tctgttttat acctgaaaag cacagcttgt tgtttgtttg 660 tgaataaaat agggttggtg gatgtattga agactgtatt tatttatgca catwaaaaaa 720 tggaaaatgc taattttata ctgctttttt ggtttacatt gctatgaaag gagtcagtat 780 gtatatagta tgtatataca gtatgtatat tgtgtatata tataaaaata cattatgtat 840 acagttgaat acagtatata cactttgaat taaatatcat acaacattta ttgattcctt 900 gtagggctta tgaggaccac tatttgaaga taaggtttca ctacaagggt tacttcattt 960 ctgaccctat gatagcttat aagaagggtg aaatatatga atatggtggt gagtgggaca 1020 tagatgaggt gaacctaaaa gatttggaca atctggtgag agagattggt gtggaagggg 1080 agtataagtt gtggtatgta tgtccaggtt tggacataat tgatggtcta aggctgttga 1140 atactgatag ggatgtggtt aggttcataa atgagcatag aaatgtatca gtagctgagt 1200 tttatgttga agctaaagat gttgaagttg aagattgcag gtatgatagt gaggttgaag 1260 aggttgttgt atttgacaaa ggcaagcaac cagctgagag tgatgaaggg gatgaatctg 1320 atcctgagta caatggtgat gaggaaggtg aggttcctga ctatgaagta gaagatgagg 1380 atggaagtgt tgatggggtg tcagttgatg atagtgattt tgatgaagam tgggactgga 1440 ctactgtgtt gcctaaacaa actgtgaacc ccacccctgc tggtcaatca tataactcta 1500 atcaagctgt agttggtgtt gaagtatcaa ggaaccctra agcgacaagt ttggaagatt 1560 ttgaagatga gaatggagac tcagattttt tagagagttc tgatgcatct gaggaagatg 1620 agggatcaag aaagaggaaa ttgaataggt ttaagttkgg tgataacaat gaccctgtaa 1680 tatttgagga gggtcagatw tttgcaactg ctkttttaat taaaactgct gtgaaagaat 1740 atgctttgca gaacaagaaa aatgtttacc tamagaaaag tgagaagaaa agaattgtgg 1800 tgaagtgtat gcaaggwtgt ccatatcaca tgagatttag tagggttcca cctcaaactt 1860 attatgtttt ctctagttat aagtctgtgc ataaatgcta tcaaactggt agaattagag 1920 tgttatctgg acaattgttg gctaagaagc tggtaccact acttaagcac acacctaata 1980 tgaccattaa gggactaaaa gatgagtgta agaataggtg gaatgtgatg ttgagtagtt 2040 ttcagatgta tagggcaaaa ttaagggctt tagaaatgat tcatggtgct agtgatgaac 2100 aatatgctca tcttagaaac tatgctgaag agttgttaag aagcaatcct gggagtagtg 2160 ttaagattaa atgcaaacct agtgctgggg gggtagtttt tcaaagaata tatgtttgtt 2220 ttaatgcttg caagagggct tttgtgagta actgcagacc attgatwggt cttgatggat 2280 gttttctgaa aggtargtat ggtggacagy tgttatcagc aattggwaaa gatgstaatr 2340 atcaaatgat acccattgca tttgctgttg tggaagctga aacaaaagat tcatgggatt 2400 ggtttmtgga actgcttcta tcagatttga atggagtaga attcaaaasa tggtctttca 2460 tatcwgacca gcaaaaggta atatttattt catttatgaa gttaatttta attgttttaa 2520 atttaatttt gatttacatt aataaattgt tttttcaact ttattttgtg aagggtttgg 2580 tgaatacaat agctgctatt ggtgatcatg ttgagcacag attttgtgtc agacatttgt 2640 atggkaactt taggaaaagg catcctggag agaaattgaa agaagctatg tggaaagcag 2700 ccagggccaa cacaatgcct gaatttaaca gggctatgga ggatctgaaa agattaagtg 2760 aggcagcttg ggaggaratg aggcagtatg caccaggtat gtggtctagg gcaggatata 2820 gcactcacac aaattgtgac ttacaagtca ataatatgtg wgaggcattt aactctgcaa 2880 tcnttgaktt aagagartaa ccaattatat cacttgttga gggattgaag ttctatatca 2940 caaataggat agttaaatta agggattaca tgttraggta tgatggtgaa atttgtccaa 3000 tgataaraaa gattttggaa aaggctaaga aggatgcaaa tggttggtca ccaatttggt 3060 gtggtgatag ggagtmtkct atgtttactg tkwctgatgg aactgacaca tatgttgtca 3120 atctcaaaga caaaacatgt gcatgtagaa aatgggattt aagtggtatc ccttgtccac 3180 atgccattgc tggaatttat tacaatcaag ctaatgctga tgattatgtg gcacattggt 3240 acaggttagt ttttttataa gtttttattg tttttttagt gttattcatt agatttttct 3300 gaatgtttaa tttgtttgta taaaattgat aggaaacaaa cttttttgga tacttatgat 3360 aattttatcc tgccttcaaa tggaccaaaa ctatggccag aagttaacct tccaccaata 3420 ctcccacctg gtgtcagaag ggcacctggg aggcctaaga agccaagaag gaaggataat 3480 gatgagccta aatcagcaag caaaaagggc aagagaaatc aggaaactgt gaggtgcaga 3540 agrtgtaaag agcttggaca taataccagg acatgtgatg gtaaaacagg tgctgatagg 3600 aggattccac ctggagggaa caaggtaact ttatgtaatg tccttwttaa actttcattt 3660 attayatcaa atactaataa ctatatatgt acaattgata ggatattact acacaatctg 3720 cacaaactgg tattgatgca caagctgcac agcctaacaa caatgcacct gcacaagctg 3780 gcacatctaa tgtgcaatca actcaaaaag gcatgctgct gcaaatggaa agaaaccact 3840 gaagaaaaag tcaaaaactg ctgctggtac acctgctgct gctgcaaatg gtacaacttc 3900 tgttaacaac attgctactg gtacacatgc tggaactgta aatggtacaa ctgttgcccc 3960 tgctgcaacc aacacatctg gaacaatgag aggtggcaac catgttgttg gtgaggtagc 4020 tttgtttgtg cctagaaagt ctaggacaac tggggttaag aggtcaagta atgaggtggg 4080 aaatgttggt actcaacagt ctgtgaacaa gacataagct agaagctagg aatgagaatg 4140 atgtactgat attttggtat gagacttgat gtaattttgg tcatgttatk taatgtcaag 4200 tactcttatt tttattttgc ttattttagt ttaattactc tacaatgtay tatgaattta 4260 agtactctaa agagtatctt ttggttatgc actytgaatg ttaagtgctt tgatgctata 4320 gtaatgcact tttcttatgt actcttaatt tactttgtca atgacaagta cttttattaa 4380 gtttatgaat gttaagcact ctatgttaag tgctttgatg mtatagtaat gcasttttat 4440 taagttctga atgttaagta ctcgtaatat gtttcaattg ttatatcatt tcttaatgca 4500 taagtttaca tatrtttaca acataccaac agtacataag tttgtttaca tcataccaac 4560 aatacataar ttttcattaa aacatcaaac tcaatacatt tcttttcttt catcataaca 4620 acgataagtt ttcattacat aacaacataa ggtaacatca ctacataact tatccaaact 4680 ttatgagaat taccaacaca cttacaaaca acaacattcc taacacaaca atagttaaca 4740 caagcaattt ctccttattc ttcaatgcat cattcttctt taacagtcct ctaattagtt 4800 tcttctgcct atcaggaact tctggatcaa accatctgaa aaaactgcat tttcttctct 4860 gcaaatactt cccacatcca tggaatctcc ttcctggatt ttcatcagtc caagctgtta 4920 ctagagggga ttcaacacca cagtaacata ccaacttcgt tttgcccata aatgatgacc 4980 cactcacggt tgaagatgaa gattgtccaa ccattttctg tttccacaaa tcgaacagga 5040 tgaacacaaa atcgaaggag aataaacgaa atttatcaaa acaagaaatg aatgatggag 5100 caggatgaat agaacaggat gaatcgaaat aaatgaatga tggggcaggt atgaatcgaa 5160 agaagaagga agaagaacaa tggagattgg ggtcagattt ggggcttttt aatccctaat 5220 ttatgaccgt tgtaaactct ctcacgtgcc agaccttttt tattttcttt tttcgttttt 5280 tttttaattc atgtaatatt atgatggcat ttaaaataaa aaaaaatcag tatatacaca 5340 catggcatga catatcagca ttgaccaagt caaaattgtc caaaaggact gaaaatgcaa 5400 aggggctaaa acatagaggg ccaaaattgt ggttttcata catggggggc caaaatcgca 5460 acgttttgaa agttaggggg gaaaaagtgc actttagcc 5499 // ID Copia51-PTR_LTR repbase; DNA; EDCOT; 292 BP. XX AC scaffold_354; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia51-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-292 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-292 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 283-283 (2007). XX DR Genome; scaffold_354; Positions 36824 36533. XX SQ Sequence 292 BP; 97 A; 48 C; 47 G; 100 T; 0 other; tgttggtgat aatagcacat tacactctgg agataatcaa ggcagcaatc aacgagaaaa 60 tcactcctaa catcaaggat caattcatgg aaatcaagac gttatgagga gctgattagt 120 tgtgtatata gaatcttaaa tagctttcct tataagagct gatactgtta ttattatcag 180 attatattcg atactattat tattattagg ctgtaatagt tttccatata atgcaccatt 240 ctacaccata agctggtagc tgtggtttca ttattatctc taaaactctt ca 292 // ID SHALINE12_MT repbase; DNA; EDCOT; 5914 BP. XX AC . XX DT 19-JAN-2007 (Rel. 12.01, Created) DT 19-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A LINE element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; LINE; KW Interspersed; repeat; ORF; Poly-A tail; SHALINE12_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5914 RA Shankar R. and Jurka J.; RT "SHALINE12_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 90-90 (2007). XX DR [1] (Consensus) XX CC The element seems to be autonomous, though present in genome in CC moderate copy number. The central 5' half is highly variable CC while the terminals are well conserved. Two different ORFs in a CC single frame are present of which one codes for RT polymerase CC while the first one codes for CCHC type zinc finger protein. XX FH Key Location/Qualifiers FT CDS 77..1021 FT /product="SHALINE12_MT_1p" FT /translation="MSAMSSEFVFSAHGEQNLQHSKNPPDPIXPLTPKLSF FT RDKLLGSSQXIPIREKEDMIEKKLVRIELEDGNRLLPKVYLEPKVFQELCT FT PWKDALVVKLLGKNLGYNTMKDRLQKTWKLQGGFEIMDNDNGFYMVKFDQA FT ADKEKVITGGPWLIFDHCLAVTHWSPEFASPNAKVDRTVVWVRFPGLNLVY FT YDESFLLAMASAIGRPIKVDTNTLKVERGKFARVCVEIDLTVPVVGKIWVN FT GHWYKVQYEGLHLICTNCGCYGHLGRNCTTTTTTTDQHKPPHQPTAASHGE FT NHQPDHHIQATIQXQSIQDFTKR" FT CDS 1865..4939 FT /product="SHALINE12_MT_2p" FT /translation="MKXMSLLLDFPLFGLIMVTPLFTSLKLMATPEVFGFL FT NIQLLTSPXLSLTPNPHSITFTISRGNATTXCTCIYASPNPTMRPNLWNYL FT MNINHTIDGPWMLIGDFNETLLPSDQRGGIFHHNRAAIFSNFMNNCNLLDL FT TTTGGRFTWHRNNNGIRILSKKLDRGIANVDWRISFPEAFVEVLCRLHSDH FT NPLLLRFGGLPLARGPRPFRFEAAWIDHNDYANLVKNSWNSXNHNTTAAXN FT KVKENSITFNHEVFGNIFKRKKHIENRLKGIQNYLERVDSLRHSLLEKELQ FT QEYNHILFQEEMLWYQKSREKWVKFGDKNTSFFHAQTIIRRKRNRIHRLQL FT PNGIWSSDSDTLQEEAQKYFKNFFSGNQHHHDRTFNEGTHPTIDDQGKTSL FT TKPITKNEVFAALNSMKPYKAPGPDGFHCIFFKQYWHIVGDDIFQMVHTAF FT QTGYFDPEISNTLIALIPKIDPPTTYKDFRPISLCNIIYKIITKVLVHRLR FT PILNNIIGPYQSSFLPGRGTSDNSIVLQEIIHFMRRSKRKKGYVAFKLDLE FT KAFDNVNWEFLNSCLHDFGFPDITIKLIMHCVTSSTFSILWNGNKLPPFKP FT THGLRQGDPLSPYLFILCMEKLSIAINNAVNQGSWEPIXITNTGPQISHLL FT FADDVLLFTKAKSSQFHFINDXFDRFSRASGLKINISKSRAFYSSGTPHGK FT INNLTSISGIRSTTSLGKYLGFPMLKGRPKRSDFNFIIEKMQTRLASWKNR FT LLNRTGRLTLASSVLSSIPTYYMQINWLPQNICDSIDQTTSNFIWKGTNNK FT GIHLVNWKKVTSPKHIGGLGIRTARDANTCLLGKLVWDMVQSTNKLWVNLL FT SNKYTSGPNILHANATSNSSPTWSSIIRAKNVLKXGYFWRAGSGSSSFWFS FT NWSSHGXLGSLVPIIDIHDIHLTVKDVFTYNGQHTQALYTNLPQAIADFIN FT NNHINFNETVEDTFIWNHNINGIYTAKSGYSWLLSLTEPXNAXTPHHFLVL FT DLEIKNSGKIQILHLASLS" XX SQ Sequence 5914 BP; 1820 A; 1382 C; 958 G; 1697 T; 57 other; taaaaatata acaaaacaac gacaaaggaa aataaactaa tagaaattag atgaaacaac 60 aagaatattt tttagaatga gtgcaatgag ctctgagttt gtcttctccg ctcatggtga 120 acaaaacttg caacactcca aaaacccacc cgatcccatt maacctctaa ccccaaagct 180 ttccttccga gacaaactgt taggatcatc ycaagawatt cctatccgtg aaaaagagga 240 catgatcgaa aaaaaacttg tccgcattga actrgaagat ggtaaccgtc tccttcctaa 300 agtctacttg gaaccaaaag tttttcaaga actctgcaca ccatggaagg acgctttggt 360 tgtcaagctg ctagggaaga acctcggtta caacaccatg aaagaccgcc tacaaaaaac 420 atggaaactc caaggagggt tcgaaatcat ggacaatgat aatggcttct acatggtgaa 480 atttgatcaa gcagcagata aggagaaagt catcactgga ggaccttggc taatctttga 540 ccactgtttg gcagtcacac actggtctcc tgaatttgcc tcwccaaatg ccaaagttga 600 ccgcacagtt gtttgggtac gttttcctgg tttaaatctt gtttattatg atgaaagctt 660 cttgctagcc atggcatctg ctattggccg cccaatcaag gtagacacaa acactctgaa 720 agttgaaaga ggaaaatttg caagagtatg tgttgaaatt gatcttactg tgccggtggt 780 ggggaaaatt tgggttaacg gacattggta caaggttcag tacgaaggac tacacctaat 840 ttgcaccaat tgtggatgtt acggtcatct gggragaaat tgcaccacta caacaaccac 900 cactgaccaa cacaagcctc cccaccagcc aaccgcagcc agccacggag aaaaccacca 960 acctgaccac cacatycaag ccaccattca awcgcaatca attcaggatt tcacaaaacg 1020 gtaacactgt atttamtgct attaakaatt tatcacctaa taatggagaa gtaattagca 1080 wtaatgaagg aaatcaagag ctacatggtg attggctact agtyactaga agaaagaaaa 1140 ccacaaataa caccacctta aatccctcta aaaccgttac tcacaaaacc aacagntwct 1200 atgctttgtc ctataaccca ccaaaagtca aacttggccc atctactcct aaatttccac 1260 cacgccccaa atcaaatgac atascacgtg ccaaccaaaa caaatctgag ccaaaaagac 1320 ggcgcagtga ggaaactact acagacccaa ttaacttccc tttccatggc cccacacaaa 1380 atttcaagcc aaacatgcta agtcacgtta ccaaaactca caaagaaata tcattcacca 1440 attattccac tagcccaacc ccacaaagtg acacacaaat agatgagcca attcccacac 1500 atgaaaaaaa tcccaacaaa actaccatgc aaatcaatam caaccaacat cctgacacaa 1560 gtaataataa cttgctttct acccttgaaa acaatattgt taccaataac aataccatgc 1620 atatcawgca agataatggt gatgataaag tggaatccag tactggacat catgactccc 1680 atgaggagga catggtcact taryctctct actttcacgg tctcrtctgt ctacctkttt 1740 gttatggaag ctctcctcga tattacaatc ctctcttgga atattagagg ggctcaaaat 1800 aataatgcaa gaagacatct gaaagaattg atgagaaaat ataacccaac kttcatagca 1860 atttatgaaa cmcatgtccc ttttgctaga ctttcctctt tttggactaa taatggttac 1920 acccctgttc acatcattga agctaatggc cactccggag gtatttggct tcttaaacat 1980 tcagctacta acatcacctc wactgtcctt gacacccaat ccccactcya taaccttcac 2040 catcagccga ggtaatgcwa ccactwcttg cacttgyaty tatgctagcc ctaaccctac 2100 catgcgcccc aacctttgga attaccttat gaatatcaac cacaccattg atggtccttg 2160 gatgctcatt ggtgatttta atgaaactct tctccctagt gatcaaagag gtggcatctt 2220 ccaccataat agagctgcta tcttctctaa cttcatgaat aattgcaacc tccttgacct 2280 cacaaccact ggtggtcgtt ttacttggca ccgaaacaat aatggcattc gcattctctc 2340 caaaaaactt gatagaggta ttgcaaatgt tgattggcgc atttccttcc ctgaagcttt 2400 tgttgaagtt ctttgtagac tccactctga ccataatcct ctcctcctcc gttttggtgg 2460 tctccctcta gctagagggc ctagaccttt ccgctttgaa gcagcttgga tcgatcacaa 2520 tgattatgcg aacctggtaa aaaattcttg gaactctcam aaccacaaca ccactgcggc 2580 tyttaataaa gtcaaagaaa actccatcac tttcaatcat gaagtctttg gaaacatttt 2640 caaaagaaag aaacatattg aaaaccgkct caaaggtatt caaaattatc ttgaaagagt 2700 tgactctctt cgacactctc tccttgaaaa agaactccaa caagaataca atcacatcct 2760 tttccaagaa gaaatgcttt ggtatcaaaa atctagagaa aagtgggtta aatttggtga 2820 caaaaacacc tctttcttcc atgctcaaac tatcattaga agaaagagaa acagaatcca 2880 tagacttcaa ctccctaatg gcatttggtc ctctgatagc gacaccctcc aagaagaagc 2940 tcaaaaatat ttcaaaaatt tcttcagtgg caaccaacat caccatgacc gcactttcaa 3000 tgaaggcacc caccctacca ttgatgacca aggtaaaact tctctaacca aaccaatcac 3060 caaaaatgaa gtttttgctg ccctcaactc catgaaaccc tacaaagccc ctggtccaga 3120 tggcttccat tgcatcttct tcaaacaata ttggcacatt gttggagatg acattttcca 3180 aatggtccat acagctttcc aaactggtta ctttgatcca gagatttcaa acactctcat 3240 tgcactcatt ccaaaaattg acccacccac cacttacaaa gacttcagac ccattagcct 3300 ttgcaacatt atttacaaaa ttatcactaa agtcttggtt caccgtctca ggcctattct 3360 caataatatt attggcccct accaaagcag ttttctgcct ggtaggggca cttctgacaa 3420 ctcaattgtt ttgcaggaaa ttattcattt catgaggaga tccaaaagga agaagggtta 3480 tgtagctttc aaacttgacc tggaaaaagc ttttgataat gtcaattggg agttccttaa 3540 ttcttgcctc catgattttg gtttcccaga cattaccatc aagctcatca tgcattgtgt 3600 tacytcatcc accttctcta ttctatggaa tggaaacaag ctgcctcctt tcaagcctac 3660 tcatggtctt cgacaaggtg atccgctgtc tccttacctc ttcatcctat gcatggaaaa 3720 gctctctatt gctatcaata atgctgtcaa tcaagggagt tgggaaccta tccawatcac 3780 aaatacgggg ccccagatat ctcacctcct ctttgcagat gatgttcttc ttttcactaa 3840 ggctaaaagc tctcaatttc acttcatcaa tgatttkttt gatagattca gtcgagcatc 3900 kggattgaaa attaatattt ccaagtctag agctttctac tcttcaggta ctcctcatgg 3960 taaaatcaat aatctcactt ctatctccgg tattcgaagc acaacttccc ttggtaagta 4020 tttgggtttc cctatgctta aaggtcgacc aaagagaagt gatttcaatt tcatcattga 4080 aaaaatgcaa actagattgg cttcttggaa aaatagactt ctcaacagaa caggtagatt 4140 gactcttgct tcctctgttc tatcytccat ccctacttac tatatgcaga ttaattggct 4200 tcctcaaaat atttgtgata gtattgatca aacaacyagc aattttattt ggaaaggcac 4260 taataacaaa ggaattcatt tggtaaattg gaagaaagtt actagtccga aacatattgg 4320 tgggttgggt atcagaacag caagagatgc taatacttgt cttcttggga aacttgtttg 4380 ggatatggtt caatcaacaa acaaattatg ggttaacctt ctttctaaca aatatacatc 4440 agggccgaac atccttcatg ccaacgccac cagcaacagc tcccccactt ggtcytccat 4500 tatccgtgcc aaaaatgtcc tcaaaartgg ttatttttgg cgwgcgggat caggttcctc 4560 ctccttttgg ttcagcaatt ggagttctca tggtcycctt ggttctcttg tccccatcat 4620 tgacattcat gatattcacc tcacggttaa agatgttttc acttataatg gacaacacac 4680 tcaagccctc tacaccaatc ttcctcaagc wattgctgac ttcattaata acaatcacat 4740 caacttcaat gaaacagttg aagatacttt catttggaat cacaacataa atggtattta 4800 taccgctaaa agtggttact cttggcttct ctcccttacg gaaccarcca acgctrttac 4860 tccrcatcat ttcttggtct tggatttgga aattaaaaat tccggaaaaa ttcaaattct 4920 tcatttggct agcttgtcat aacgcggttc ctactctatc tttgcttcat cacagaaaca 4980 tggctccttc tgcaacttgt tcgagatgtg gtgaagatga tgaaactttt ttgcattgcg 5040 ttcgtgactg taaattctct aaaatcattt ggcagaaact tggtttctcg gaccaagact 5100 tcttctcttc aaattgcact caagactgga taaaaaatgg tgcaactggt actcattcta 5160 tcattttcct agcaggtcta tggtggattt ggagacaccg caatcagatg tgtctcagca 5220 atgaaacttg gtccttaaca cggctatgca tcaacattca taattctgtc gacacaatwa 5280 agaaaagttt tcagcatgac ggtgcaataa gtcattcaga tcgtatggtt mgatggaata 5340 acaacaatta tcactgtcat attctcaatg ttgatggcag ctgtttggga tctccaatcc 5400 gagctggttt tggtggtatw attcgaaaca acgctggttt cttcctttca ggtttctccg 5460 gttatattcc aaacatcaac tgacattytg ttwgctgaac ttactgctat tcatcaaggt 5520 tttctcntag camtgratat gggaattgag gagttggttt gctactcgga ttctctgctt 5580 tccgttaatc tcatcacagg taacatttcc aagttccatg cttatgctgt tctaattcaa 5640 gatatcaaag atctcatktc ttcaagaaat ttctccattc atcattctct wagagaagga 5700 aatcaatgtg cagatttctt ggccaagcta ggagcaactt caaatgaaga ttttataatt 5760 catccaaccg cacctcatga tctcctccct ttgmttagaa aggatgccat gggaactttt 5820 ttccctagag cttaggtttt ttttttttct tctgtttttt tcctgttttt ttttttttat 5880 tagctttgta accaaaaaaa aaaaaatgaa acaa 5914 // ID HAT-6_Mad repbase; DNA; EDCOT; 3483 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-6_Mad. XX NM HAT-6_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3483 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1617-1617 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >94% identical to consensus. 8-bp TSDs. XX FH Key Location/Qualifiers FT CDS 764..3214 FT /product="HAT-6_Mad_1p" FT /note="transposase." FT /translation="MKRLRTIDSFFKKRDDGDKLESDIPSASNDNAPISTE FT QPHDSHQTSNIIEPQEKVFDDASLELERDPGKRIQIHEHPINQQDEVRRAY FT IKAGPYRPKLLEYPRSRFGSQYRRFQYSWFSQFPWLEYSPTTDRVYCFPCF FT LFGTGPASRPTLTVDGFNNWKRVNDGKNCIFLSHIGGPSSLHNTCVSRVEE FT LMNPSQHVDKVINRQSKEEILKNRLRLKATIECVRWLTFQACPFRGHDESV FT GSKNRGNFIELVKHTAKFNDKVAAVVLENAPKNAKYSSPMIQKEVLNILAN FT IVRRKIREEVGDGVFCILVDEAHDIAHREQMAIILRFVDNDGFLRERFLDI FT VWVEDTTAPTLHREIKKVLAFHELPINKLRGQGYDGASNMRGQWNGLQSLF FT IKECSSAYYVHCFAHQLQLALVAASKEVVVIWLFFSALGSIVNVITTSPKR FT HTQLQVAHTVNIEELVGAGELETGRGANQIGTIHRPGATRWGSHYDSVCDL FT IHMYDASCTVLENIKNDRSATNSLRGEATGAYNAIRSFEFTFILHLLQEIM FT GITDILCRELQNKSQDILNAMNLVTTTKDVLQKLRLDGWATFIDKVSLFCK FT KHDVDMPDMNAQYKVGTGRSCQQTDHITFEHHYHIDIFNNAIDFQLAELNS FT RFSEEAMELLILSSALEPREAFKAFNIDHICKLAEKFYPMDFTEKELHTLR FT CELKIYESDVPHHPVFQKMSTTSELCRGLVETKRSERYYLIDRLIRLVLTL FT PVSTATTERAFSAMNLIKTRRRNKMESEFLADSMVVYIEKELAEKIDSEEI FT TKDFNSIKDRRAQLE" XX SQ Sequence 3483 BP; 1078 A; 560 C; 671 G; 1174 T; 0 other; caacggcgga gccagtaaca aggctagggt gggctctagc atagggagag ttttagttgt 60 ttaaggttaa aaatactgat aatttagatt attttattat ttttaattgt tatagcccac 120 ccaataagta aaagttctga acaataggac tacttttaga aaaagtaaga gttaataaat 180 attaaataaa ttatttactt taatcaatat caaaatttat tattattata tttcaaattg 240 cacacacaca ctgacacaca cgtcccatta agtcttttta tttgattagt ttctagggcc 300 tagggagtag ttatagtgat tagtttaggt ttcctaggat agtcatccgg ttttaaaaag 360 tagatttatt attttattat tttaggtttc ctaggagttg tactagttta ttattttatt 420 tcgacttttg gggtacaaca tgaccttctt tcacctttca gcaaaagcct ttgtcccatc 480 tgtgtcgtct ctgcactgca gttcacaaca gtcacagaaa ccaagcatac atacaagtga 540 gaaagcttat tgatttttct tatcaatagg taagtttttg accactttat tcttatgtct 600 tgatgatttt atttgtttat tgctttaatt ttaagaattc gtactttaaa aattcaattt 660 caagtttaat atattttttc tgatagtcta atagatttct tagaaatata atttattata 720 taaacttgca ttattgttgt tcaatttgtt aggttaacgt tcaatgaaga ggttaagaac 780 tattgattca ttctttaaaa aaagagatga tggtgataaa ttagagagtg atataccttc 840 tgcatctaat gataacgcac caatatcaac tgagcagcct catgattctc accagacatc 900 taatataatt gaacctcaag aaaaagtttt tgatgatgct tctttggaat tggaacgaga 960 cccggggaaa cggattcaaa tacatgagca tcctattaat caacaagatg aagttcgacg 1020 tgcttatatc aaagctgggc cttaccgacc gaaacttctt gagtatccta ggtctcggtt 1080 tggatcacaa tatcgtcgat ttcagtattc ttggttttca caatttccat ggttagaata 1140 ttctccgaca acagatagag tatattgttt cccatgcttt ctttttggga ctggtccagc 1200 aagtcgtccg acactaactg ttgatgggtt taacaattgg aaaagagtta acgacggaaa 1260 gaattgtata tttctttctc atattggagg tccatcttca ttacataata cttgtgtttc 1320 gcgtgtagag gaattgatga atccatctca gcatgttgac aaggttatta atcgacaatc 1380 aaaagaagaa attttgaaga atcggttgcg actcaaggct acaattgagt gtgttcgatg 1440 gcttacattt caagcatgtc cttttagagg acatgatgaa tcagtgggtt cgaaaaatcg 1500 tgggaatttt attgaattgg taaagcatac agccaagttt aatgataagg tggctgcagt 1560 tgttttagaa aatgcaccaa aaaatgccaa atattcctca cccatgatcc aaaaggaggt 1620 tttgaacatt ctcgccaaca tagtacgaag aaaaattcgt gaagaagtcg gggatggtgt 1680 tttttgtatt cttgttgatg aagcacatga tattgctcac agagagcaaa tggccattat 1740 tttaagattt gttgataatg atggttttct acgagaacgg tttttagata ttgtgtgggt 1800 tgaagacact actgcaccaa cacttcacag ggagataaaa aaagtccttg ctttccatga 1860 gttgcctata aacaagttac gaggtcaagg ctacgatggt gcgagtaata tgcgaggtca 1920 gtggaatggg ctacaatctt tatttattaa agagtgttca tctgcttatt atgtgcattg 1980 ttttgctcat caactgcaat tggcattagt tgcagcatca aaagaagtag ttgttatctg 2040 gttattcttt tcagcattag gttcaattgt aaatgttatt actacttctc caaagcgtca 2100 tactcagctg caggttgcac acacagtgaa cattgaagag ttggtgggtg ctggtgaact 2160 tgagacggga agaggagcta atcaaatcgg tactatacat cgacctggag ctactcgttg 2220 gggttctcat tatgattcag tgtgtgactt gatacatatg tacgacgcgt cttgtacagt 2280 acttgagaac ataaagaatg atagatctgc tacaaactct ttgcgtgggg aagctactgg 2340 tgcttataat gcaatcagat cttttgaatt tactttcatc ttgcatctat tgcaggagat 2400 catgggaatc actgatatcc tttgtcgcga actgcaaaat aagtcacaag acattctgaa 2460 tgctatgaac ctagtcacta ctacaaaaga tgtcctccag aagttgcgat tggatggttg 2520 ggctaccttt attgataaag tgagtttatt ctgcaaaaaa catgacgttg atatgcccga 2580 tatgaatgct caatacaaag taggaactgg tcgttcttgt cagcaaacag atcatattac 2640 atttgagcat cattatcaca ttgatatctt caataatgca atagattttc agttggcaga 2700 gctaaatagc aggtttagtg aggaggcaat ggaacttctt attctcagtt cagctttaga 2760 accaagagaa gcttttaagg cgttcaacat tgatcacatt tgcaagcttg cagagaaatt 2820 ttatcctatg gatttcacag aaaaagagct acatacgttg agatgtgagt tgaaaatcta 2880 tgaatcagac gtaccgcatc atcctgtctt tcaaaaaatg tctactactt cggaattatg 2940 tcggggatta gttgaaacaa agaggtccga aaggtactat ttgattgata ggttaattcg 3000 acttgtattg actcttcccg tttctacagc aactactgaa cgagcttttt cagcaatgaa 3060 tcttattaaa acaagacgtc gcaacaagat ggagagtgaa tttctagcag attcaatggt 3120 tgtgtacatt gaaaaagagc ttgccgaaaa gattgattca gaagaaataa caaaggattt 3180 caattccatt aaggatcgaa gggcacaact tgaataggta ctttttcttt tatttgttaa 3240 gttgttatga caagattgat gatgtatgtt tctttctact ataagttgca acttcaaatg 3300 ttttctttgt taaatctagt tgaaacttgc tttattcata gttaaatttc ttactttaaa 3360 ttattgcttt caggcttgtc attgtgtaac tttatgtaag taacaaaaaa atttaaccat 3420 ttgatctcct agtaataatt ttagtttagc ccacccacca aataattcct ggctccgcta 3480 ttg 3483 // ID DIASPORA_LTR repbase; DNA; EDCOT; 2524 BP. XX AC . XX DT 19-OCT-2005 (Rel. 10.1, Created) DT 19-OCT-2005 (Rel. 10.1, Last updated, Version 1) XX DE Gypsy-type family of LTR retrotransposons from Glycine max (LTR DE portion, consensus). XX KW Gypsy; LTR Retrotransposon; Transposable Element; DIASPORA_LTR. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-2524 RA Yano S.T., Panbehi B., Das A. and Laten H.M.; RT "Diaspora, a large family of Ty3-gypsy retrotransposons in RT Glycine max, is an envelope-less member of an endogenous plant RT retrovirus lineage."; RL BMC Evol Biol 5(1), (2005). XX DR [1] (Consensus) XX SQ Sequence 2524 BP; 622 A; 407 C; 439 G; 1055 T; 1 other; tgttctttgg ttttgctagt tttgttggtt ttgttaattt gttagttgtg ttaatttgtt 60 aatgttgtta gtttcgtcgg atttttagtt taatattttg ggtcaatttt gtgtgcatgt 120 acgactttgc atgtttttct ttgaattata ggatatgttc aagaaatggg taattgtttt 180 gaaaataaaa gtctcttgac attttgtgac ttgaaatcct tgattctcct ctacatgtca 240 tgatagtttt gaaagctcaa tttgaaagtg atgagtttac ctttgtgaga atttgagcca 300 tccatcatca taatcatttg gtgtgttttg ccccattgat tgcttgcaca atagccttgg 360 cttgattctt gttgatgctt cctaattcac atgcatattt ggaaatgatt taggcaattt 420 tgttcttata agcttctagc caaatggact taccttgaat taattccttt gatagccctt 480 ttgagccttg tttccctttc cttgttttga agctcactac aagccttaag tgaaaaacca 540 tgatatcacc atatccttaa ggaattttgg agctttggaa ttgttttggg aataagtgtg 600 ggggggtttt tgtttcattg gataacatgt tttgttggct atgcttcatg atgtattttg 660 ggccatactt gatgtacatt gtatattggt taaatgttgg acatgctgaa tgaaatgttg 720 tttctcaaag gctacagagt aaaaaaaaaa aaattcgaaa aaaaaattca aaaaaagaaa 780 aagaaaagca ataaagttga gtgaataaga tcttaaatgg cacaagaatg atgaaactct 840 tggttctact ctttatgttt aaattttatc tttacttctt tttattttct tatttttttt 900 cttaatatgc acttattccc cattgctcct ctattccttt gggatttagc cacttattcc 960 atatttttcc ataccttgtc cttggcccca ttacaacctt aaaagacctt ttgatcctca 1020 tgtgcttgtg tttatgggtt gattgtcaat tttagaatct tgccaagttt atgtggtgtt 1080 tgttttcatg ggtgctttga gggtaaatag tagcctagac acttgagaga tagagtgtat 1140 atcttgtgag gctttatcac ttttcattct tgagctgatt aactattttg ccatgattgg 1200 gttgcttgga tgattttcat gaatgtcttg actctttgga tctcctcatg ttagatgtta 1260 cccattcctt tcattccttg atgttcattg agaaatatgt aaatgttttt gtttgtctct 1320 ctttgatatc cttggatttt gttctttatt tcattttgcc caggagtgca aaaggctaag 1380 tatggggggt tttgatgtgc cattattttc tcctatttct taaccctttt tgcaccattt 1440 taagtactga ttagtcttaa ttgtcaaatt aattaggcag ttttattatt tgggcccatt 1500 cagctaattt gatgttttta atctaatttc aggaattaat gaagcattgg gcttgaatcc 1560 agaattgggc ttggacttga agagggcaga ctattttatt ctacaaaatt agatcttatc 1620 ttatcttatc ttatctagat attatttaga tttgatctca tctagatatt atttcatcta 1680 gatcttatct tatcttatct tatctagatt tgatttgatt ttatttatgg gcttggattt 1740 aaaacagatt tgtaagcttt ggggctgaaa aactatataa cagcaccaag gttctagttt 1800 aggggcctcc tctcctcgct cttctctctc tctctcctct ctctctcttc tatttccagt 1860 ttttactttt ctctcttatc tttctctttt atttcgtttt tttctgcaat ttcgttttct 1920 gcttcaatct acaatttcgt tttctattga ttaatggaag gctaagtctc ccagcgttgt 1980 tttctcttga ggatcaagca cagttctctt tgaggttyta ttattactat taaattctga 2040 tcagtttttc ctcttcacca attactctgt atttgttgct attaatccat gcatgcttag 2100 tgcttgatta attgtctctg cgcttaattt acgttcatgc ttaatgatca tcgttcatga 2160 ttaattggtg tatgtgttgc ttaatcacat aatgaatgcc ttatgttaaa tttcgcttag 2220 taatttaatt tagggttgga ttaagtggtt gaactgataa aggataaatt ctcgtaacct 2280 aggataagag acttgcttgt gaatcaaggg gaaacaacat gttttaattc tgatattttc 2340 taattcaaat ttgctcgctg tttaatttac aaaaacaaac aacccccccc ccccaattcg 2400 ttactgtttt attactatct gttatgaacg tttggttgac cattgctcgt tgggagacga 2460 cctaggatca cttcctagat actgcatttt taatgtttat ttgattcggg tacggcctcg 2520 atca 2524 // ID Gypsy-39_Mad-LTR repbase; DNA; EDCOT; 2275 BP. XX AC . XX DT 14-OCT-2010 (Rel. 15.1, Created) DT 14-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-39_Mad-LTR. XX NM Gypsy-39_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2275 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1773-1773 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 2275 BP; 520 A; 630 C; 477 G; 648 T; 0 other; tgtgaaaccc cgccccaaat tattgtaatt tcatattcac gaaatatgaa attaccattt 60 ttgcccccta tcccctaccc aatccggatc ccctttttgg attttctcca attctcctcc 120 tctctctgcc tgccacgtgg cagcccccca tctccctttc tcttcttctc tcttctcccc 180 cccgagccac tctctctcag ctcactcact ctctctctct ctcggacctc tctccctctc 240 cctcccctct ctcccttccc ggcgacacac acacccacac acccaaccga caccacgacg 300 gacaacgaca ccaccaccac cgtgatggcc ctctctctct ctctctcgtc tctgtgaagc 360 acagagaacc caagaaccca tccggcgagc cccgtggctt tcgagccaaa atccggccac 420 ctccggccac ctcacgacga tcgaaggtac gaatctctcc ctctcgtctc tatcttcatt 480 ttggtagtta gatcgtaggt tagggtggag aaacgacgtc gaccggagct cgggaggctc 540 cggccttctt cctcgcacga gaaccgggtc gttgacccaa acccgaagcc caagtccttt 600 agcccaaacc cttgggccgg gctttcaagc ccaaaccctt taaacccaac caaacccatg 660 aaccaggcct ttgggccatc taactcgggc cttaggcccg ttaaaccctg gccaaaccct 720 ttgaaaccca acccaaccct taacccgaaa cccaaggaac ccaggccttt gggccataga 780 accggcccat ttgagagccc aaaagcccaa taggcctagc ccagccacta agccaaccca 840 aaaccccaag cccaaaccca gaatcggccc aaacctgagc ccagccgcgc gtgaggccga 900 gccggtgccg gcgcgtggag cacacgcgcc gccgtccacg gcggcgccgg cgacttttcc 960 ggccaacttt ccggcgaccc acgcggcgcg tggcccggag ccgccacctt gcggcggcgc 1020 gtgggggtac ccgaggtccc cctttatgtt tttcgacgtc ctgaatccgt ttatgacgtc 1080 cgttttccga aattcaatcg ttttggtaga gttttattaa ttggaccctt tatgtgctta 1140 ggtgcgatta ttagcggcga ttccgtcctt cctatttcgc acggctcttc gacgacggag 1200 tatctgtgag tggacccctt ctaaaatgca tgttttaata gtagaaatgc atacatgaaa 1260 agcatgattt aatggttacg ttttatgaaa cgttttatga gtaaattaga tttacacttt 1320 atgattatca tgctttactg agaatatttt ggaataccat actttatcga atttatgttc 1380 tttgtagtat atatgatgga tgactatata ctatttatga acatgttttt acactctttg 1440 tagtatatat gatggatgac tatatactat gaagatgttt tgagatatat gtacttatgt 1500 tggaaagatt atattcaatg ttttgtgctt atctagtggt cactgttctg cctacgggcg 1560 atgatactta tattggcttc ggcgggtgat gtagtggcct acgggtcgga agatacttat 1620 tggcctacgg gtcgggtgat gtagggccta cgggtcggaa gatacttata tttggcctac 1680 ggcgggtgat gtaggggcct cgggtcgatt atgataccac tagttagcac actatatacg 1740 atatatgttt tatgaaaggt tttatggcat gctagggttt tcggaaaacc tatcacatat 1800 tatgctattg agttttcata aaactttggg ggttagtacg ttgttgaata actgtttcag 1860 tattatatat atcaacttat atggtccact catgtttgtt ttgcgccccc tcaggacata 1920 ggaacgaggc atacgatccg agctacgagg cattccccta ccagtgatat cgtgccatcc 1980 tctctgcttt gacatcactt gtaatagcac cttccgcttg tattctgaat tagatgtatg 2040 ctctgaacat gtcatgcatt atcactatca ttatcattgt tggcagttga atattattat 2100 attattttat aaggtttgta tttgaatatt acattgcgta gttcgcgcga aatttatatg 2160 catgtttcac atgttctcag catatgcatt cattaaatgg cttgcgtcac cctcgggtgt 2220 cggccagcac gtggccatcc cgatgtccct cggacatcgg gatcggggcg tgtca 2275 // ID Copia-42_VV-I repbase; DNA; EDCOT; 4541 BP. XX AC chr11; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-42_VV_; KW Copia-42_VV-LTR; Copia-42_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4541 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr11; Positions 7898198 7902738. XX CC Positions [1745-2086] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 2117..4531 FT /product="Copia-42_VV-I_3p" FT /translation="MFSTHVPKFFWGEAILTAAYLINRMPSRILDFQTPCQ FT ILFQSFPNTRLISTIPFKVFGCSAFVHVHQQHRDKLDPRALKCIFLGYSPT FT QKGYKCYSPVTKQFYHSMDVTFFEQQSYFSKSDIQGETNFIQEYQLWDIEE FT SSHFFPNSDQPYPSLNHESIPPQNLFLESPYFLESPSQDQTNNSPTNPPPQ FT NLDTIQSTKNDELITYSRRRQNQKEMEQQASLEPTQESDPSSRSSEDPLGN FT YNPETNDGSDFPIAVRKGVRSCTKHPIYTFVSYEGLSPKFKTFVANLDNIQ FT VPNNIQEALGSPEWKSAVYEEIHALEKNGTWEISELPAGKRPVGCKWIFTV FT KYNEDGSVNRFKARLVAKGFTQSYGIDYEETFAPVAKLNTVWVLLSLAANL FT DWPLHQLDVKNAFLNGDLAEEVYMEIPPGFETQTTRNKVCKLRRSLYGLKQ FT SPRAWFERFTKVVKKHGYSQYQTDHTLFVKHSPAGKLAVLIVYVDDIILTG FT DYEEEIRTIKSFLAAEFEIKDLGNLKYFLGMEIARSRKGISVSQRKYVLDL FT LKETGMLGCKPADTPMDPTTKLGAKENCAPVDKGRYQRLVGKLIYLSHTRP FT DIGFSVSMVSQFMNNPNEEHMEAVYRILRYLKLTPGKGLFFEKNQRRDIEV FT FSDADWAGSVQDRRSTSGYCTYVWGNLVTWRSKKQSVVSRSSAEAEFRAMA FT HGICEGIWLRRVLQELKISDEEPMKMFCDNQSAISIAKNPVHHDRTKHVEI FT DRHFIKEKIEEGIIKMLYVPTSLQTADILTKALPRKVFDDLSSKLGLINIY FT RPA" FT CDS join(44..1018,1022..2086) FT /product="Copia-42_VV-I_1p" FT /translation="MTKYDKHNSTATVSQITSNQEAMASSNSSADSNLMPI FT TGHKLNGNNYLQWSHSVMMFICGKGKDDYLNGVAAKPNKTDEKFKVWNAEN FT NMVMSWLINSMTNDIGENFLLYGTAKEIWDAAKETYSNNENTLELFEVESV FT LHNFRQGELTVTQYFNTLNRYWQQLDLFEEHNWSCPGDGIRYKQIIERKRI FT YKFLIGLNKNLDEVRGRILGSKPLLNIREAFSEVWREESRKKIMMGSQDSV FT TNPESSALAVRGNPFNNNDHKPKKGRPWCDHCRRPGHTKDTCWKIHGKPAD FT WKPSRFANDKEGRGNLVSMDEKPSPEPTPFSKEIEVLQKLFSQSLPAAVPT FT VVGTGSLAQKGNFLSALNVKKEKLSPWIIDSGAFDHMTGDEKLFYTYNPCY FT KNLTVRIADGSLSKVAGTGSVRVSKNITLDSVLLVPKLNCNLLSISKLTWD FT LNCVTKFGSNLCEFQVLDSGKTIGSAKMCSGLYLLEVNDPPQGSTHHSDCS FT VSSSPISLSVSQSNNDSAVMLWHYRLGHPNFLYLEKLFPSLFYNKNPNEFQ FT CEICQFSKHIRNSYPNRSYKASQPFSMIHSDVWGPSRIKNVTGSRWFISFI FT DDHTRLTWVFLMKEKSEANQIFKTFNTMIQTQFQAKIQILKTDNAKEYFNS FT ILNDYLLSHGIVHQSSCVNTPQQNGIAERKN" XX SQ Sequence 4541 BP; 1457 A; 945 C; 908 G; 1231 T; 0 other; tcgatatggt atcagagcat tctctgaacc ctaattccct catatgacca aatacgacaa 60 acataattca actgctactg tttcccaaat cacctccaat caggaagcca tggcttccag 120 caatagtagt gcagatagta acctcatgcc cattacagga cacaaactga atgggaacaa 180 ctatctccaa tggtcccatt ccgtaatgat gttcatatgc ggaaagggca aagacgatta 240 tctcaatgga gttgctgcca aaccaaacaa gacagatgaa aagttcaaag tctggaatgc 300 tgaaaataat atggtcatgt catggctcat taattccatg acaaatgaca ttggagaaaa 360 ttttcttctc tatggaacag caaaggagat ttgggacgct gccaaggaaa cgtattccaa 420 caatgagaat acattggaat tgttcgaggt ggagagtgtt ctccataact tccgccaagg 480 agagttaacg gtgactcagt atttcaacac actcaatcgc tattggcagc agctggacct 540 gttcgaggag cacaattgga gctgtccggg tgatggaatc aggtataaac agattattga 600 acggaaaaga atatacaaat ttctgattgg attaaataag aatcttgatg aagtacgagg 660 aagaatctta ggatccaaac cactactaaa tatccgggaa gcattttcag aagtttggag 720 agaggaaagt cgaaagaaga tcatgatggg ctctcaagat tctgtgacaa atcctgagag 780 ctcagccctt gcagttagag gaaatccatt taacaacaat gatcacaaac cgaagaaagg 840 gcgaccatgg tgtgatcatt gccgacgtcc tggtcacacc aaggacacct gctggaagat 900 tcacggcaaa cctgcagatt ggaagccttc ccggtttgcc aatgacaaag aaggacgggg 960 caacctcgtc tccatggatg aaaaaccatc acccgaaccc actcccttca gcaaggaata 1020 gatagaagtc ctacagaaat tgttcagcca atccttgcct gcagctgtcc ccactgtggt 1080 tggtactggt tccttggcac aaaaaggtaa ttttttgagt gctctaaatg ttaaaaagga 1140 gaagttaagt ccatggatta tagactcggg agcatttgat catatgactg gagatgagaa 1200 gcttttttat acttacaatc catgctataa aaatttaact gtgagaatag ccgatggttc 1260 actctcaaag gtggctggta caggttctgt tagagtttca aagaacatca cccttgattc 1320 agttctcctt gtgccaaaat taaattgcaa tttactgtcc attagtaaac tcacttggga 1380 tctcaattgt gttactaagt ttggctcaaa tctgtgtgaa tttcaggtct tggactcggg 1440 gaagacgatt ggcagtgcta agatgtgttc ggggctctat cttctagagg ttaatgatcc 1500 tcctcaagga tcaactcatc attctgattg ttcagtgtcc agtagtccta tttctttgtc 1560 tgtgagtcag tctaataatg atagtgcagt tatgttgtgg cactataggt taggtcatcc 1620 aaatttcttg tatcttgaga agttgtttcc ttcattattc tataataaaa atccaaatga 1680 gtttcaatgt gagatctgtc aattttctaa acatattcgt aattcttatc ctaaccgatc 1740 ctataaagca tctcaacctt tttccatgat tcatagtgat gtatggggtc cttctaggat 1800 aaaaaatgtt actggttctc gctggttcat ttcatttatt gatgatcaca ctagactcac 1860 atgggtattc ctcatgaaag aaaaatcaga ggcaaaccag attttcaaaa ccttcaacac 1920 catgatccaa acacaattcc aagcaaaaat ccaaattctg aaaactgaca atgccaaaga 1980 gtatttcaac tccattctta atgattatct cttgagtcat ggtatagttc accaaagttc 2040 ctgtgtcaac actcctcaac aaaatggtat tgccgaaaga aaaaactgac atcttcttga 2100 tgttgctcgt tccctaatgt tctctaccca tgtaccaaaa tttttctggg gtgaagccat 2160 cctcactgct gcctatctca taaataggat gccatctcgt attctcgact tccagactcc 2220 ttgtcaaatt ctttttcagt cctttcccaa tactcgtcta atctcaacaa tcccattcaa 2280 agttttcggg tgctcagctt ttgtccatgt ccatcaacaa cacagggaca aacttgatcc 2340 tagagctctt aaatgtattt tccttgggta ctctccaact caaaaaggat ataagtgcta 2400 ctcaccggtc actaaacagt tctatcactc catggatgtc accttctttg agcaacaatc 2460 ttatttctcc aaatctgata ttcaggggga gactaacttt atccaggaat accagctttg 2520 ggatattgaa gaatcatctc atttctttcc taattctgac caaccctacc catcactaaa 2580 tcatgaatcc attcctcctc aaaatctctt ccttgagtct ccttacttcc tagaatctcc 2640 ttctcaagat caaaccaaca attcgcctac taatccacct cctcaaaatc tggacactat 2700 tcaatcaaca aagaatgatg agttgattac ctactcaaga aggagacaga accaaaagga 2760 gatggaacaa caagcatctc ttgagccaac ccaagagtct gacccaagtt ctagatcaag 2820 tgaagatcca ttaggtaact ataatcccga aactaatgat ggtagtgact ttcctattgc 2880 tgtgagaaaa ggtgtaagat catgcacaaa acaccctata tacacatttg tgtcatatga 2940 aggactatca ccgaagttca aaacatttgt tgccaacctc gacaacatcc aggttcctaa 3000 taatatacaa gaagctctcg gctcacctga gtggaaatca gctgtttatg aagaaattca 3060 tgcacttgaa aaaaatggaa cctgggaaat ctcagaatta ccagctggaa aacgcccagt 3120 gggctgcaaa tggatcttca cagtcaaata taatgaagat gggagtgtta atcgattcaa 3180 ggcacggctg gttgcaaagg gattcaccca atcatacgga atcgactatg aggagacatt 3240 tgcccctgta gccaagttaa acactgtttg ggttctacta tctttggctg caaaccttga 3300 ctggcctctc caccaactag atgtcaagaa tgcattccta aatggggacc tagctgaaga 3360 agtttacatg gaaattcctc caggatttga gacacaaact acacgcaaca aagtttgtaa 3420 acttcggaga tctctatatg ggctcaagca atctccaaga gcctggtttg aaagattcac 3480 aaaggtagtt aagaaacatg gctactccca atatcagacg gaccatactc tatttgttaa 3540 acactctcct gcaggaaagc ttgctgtcct cattgtatat gtggatgaca taattctaac 3600 gggagattat gaagaggaaa tccgcaccat caaaagtttt ctagctgcag aatttgagat 3660 caaggacctt gggaatctca aatacttcct aggtatggag attgcaaggt caagaaaggg 3720 aatctctgtc tcacaaagaa aatatgtcct ggatctctta aaagagactg gaatgcttgg 3780 gtgtaagcca gcagatactc ctatggatcc aacaaccaaa ctaggagcta aggaaaattg 3840 tgcacccgtg gataaaggga gataccaaag attagtaggt aaactaatat acctatctca 3900 cacacgacca gatattggtt tttctgtcag catggtaagt caattcatga ataatccaaa 3960 tgaagaacac atggaggctg tgtatagaat cttgagatac ctgaaactaa caccaggtaa 4020 aggattattt tttgagaaga accaaagaag agatattgaa gtgttcagcg atgcagattg 4080 ggcaggatca gtacaagacc gaagatcaac ttcagggtac tgcacatatg tgtggggtaa 4140 tttggtcaca tggagaagta agaagcaatc agtggtgtca aggagcagtg cagaagctga 4200 attccgggca atggcacacg gcatttgtga gggaatatgg ttaagaaggg tgctacagga 4260 attaaagatt tcagatgaag aacctatgaa aatgttctgt gataatcagt cagcaatcag 4320 cattgcaaaa aatccagtac atcatgatag aacaaaacat gtggaaattg atcgacattt 4380 cataaaggag aagatagagg aaggaataat caagatgttg tacgtgccta caagccttca 4440 aacagctgac attcttacca aggctctacc gagaaaggtg tttgatgatc tgagttccaa 4500 gctggggtta ataaatattt accgcccagc ttgaggggga g 4541 // ID DNA3-12_Mad repbase; DNA; EDCOT; 857 BP. XX AC . XX DT 26-OCT-2010 (Rel. 15.11, Created) DT 26-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE Non-autonomous DNA transposon from apple. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA3-12_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-857 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1850-1850 (2010). XX DR [2] (Consensus) XX CC TSD is 3-bp long. XX SQ Sequence 857 BP; 172 A; 225 C; 205 G; 255 T; 0 other; ggccctgttt ggcacaccgt ataaggcacc ggatagtact aataatacgg tgtacggtgt 60 ttggtggccg tttggattaa ataggcaccg gattaaataa tccgggccca ccttttttac 120 ccggtgttta cctgcttgtt ataccgtcca aattcacggt ataacttagt cggcctcgct 180 ctccgctcgc gaactcgacc ccctctctct cgccttctct tggcgtcgtc gtcctccccg 240 tcaccttctc tcgccatcgc cgtcctcccc gtcgccttct ctcgccatcg ccgtccccgt 300 cgccttctct cgccatcttt gctctcctag tcctcgtcgc ctcctcgtcg tcctctcctt 360 gtggccttcc tcatcgccta ctcgccgtcc tcccctgcaa ctgggtctcc tgcaatgggt 420 tttctgccgt cgtcttctgc ggcggaagat gatttcaatt tgctgtttga atttatttgg 480 gattcttctg cagtcgggga agaagaagaa gagagagagg gagggagttt gggggtgcgg 540 cggagagatc tggggaacaa ttatttggga ttcttctgta gtcggggaag aagaagaagg 600 gagagagagg gagggagttt ggggggtgcg gagagatctg ggaacaagat ttcagttttt 660 tttttttttt tttttaagtt taattttatt ttaagttgat tcctcctatc cgatataata 720 ccaaacacag tataaataat acggtcatta atccgatact gcaccaaacg cccgactaat 780 ttagtcagta ctatccggtg actatttatc ctatccgaca gaaatagtca gtacagtccg 840 agctgccaaa cgaggcc 857 // ID Gypsy-22_Mad-LTR repbase; DNA; EDCOT; 228 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-22_Mad_; KW Gypsy-22_Mad-LTR; Gypsy-22_Mad-I. XX NM Gypsy-22_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-228 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1739-1739 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 228 BP; 65 A; 23 C; 61 G; 79 T; 0 other; tgtggtatgt gtatgttctg ctagttcaag ggacccttgt tagatgtttg acacttgtca 60 ttagattgga tggttagttg ggtggttatt gttgtagaaa cttagcttgc aagtctgaga 120 tggatatata tagcagacta attgtgcaag gcaggttatg ttaagaaaag tatattgtga 180 gtaataatac aaacagagtt tacgtgtcat gcgttgaagg ttagaaca 228 // ID Gypsy-12_Mad-LTR repbase; DNA; EDCOT; 421 BP. XX AC ACYM01056235; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-12_Mad-I; KW Gypsy-12_Mad-LTR; Gypsy-12_Mad_. XX NM Gypsy-12_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-421 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1415-1415 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01056235; Positions 29598 29178. XX SQ Sequence 421 BP; 101 A; 105 C; 92 G; 123 T; 0 other; tggttattcg caagtaggat ttagagttcg gcattctgac ggccgaacca ctttcacaat 60 caagatgtat attcgttttg aatacttgtt tccttatact atggtgtcga ttcggcttgc 120 ttattctctt accaatataa tcacagtgac tgaatccggc gccgacgatt tgtgaacttc 180 gcagaactag tagctttgtc ttcaagctct agaacctgaa ggctgatgcg tgttccttcc 240 tctgccgcaa tctcaagatc aggaagtcag ccgctcaccc aatgcaacat caacaaattt 300 tactcctcgg ctgagctcgg tcgacgagtt ggcacgcccc gcatacaacc gaaggatgta 360 gttagcttac taactattcg gcctgcgcgc cacgtaggct tggtagtttt tagggtcaac 420 a 421 // ID Copia-43_Mad-I repbase; DNA; EDCOT; 3845 BP. XX AC ACYM01028651; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-43_Mad-I; KW Copia-43_Mad-LTR; Copia-43_Mad_. XX NM Copia-43_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3845 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1313-1313 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01028651; Positions 329 4173. XX CC Positions [1651-2013] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(451..1647,1651..2748) FT /product="Copia-43_Mad-I_1p" FT /translation="MKNGETVNDYFGRTLAIANKMRTHREKMDDVVIIEKI FT LRSMTSKYDYVVCSVEESNDLDTMSIDELQSSLLVHEQRISRHVDEEQALQ FT VTHGVQQGGRGRGTYRGRGRGRGRLGFDKSTLECYHCHELGHFQWECPKKP FT KEEKANYVETKEEMLLMALVEFKGMEHTWFLDSGCRNHMCGRMDLFSEFDS FT SFKESVKLGNDSSLTVRGKGSVRMEVDGRIHVITGVFYVPDLKNNLLSIGQ FT LQEKGLTVLIQQGRCKIFHFEKGLIMETKMSTNRMFAVVARSPEEQKCLSS FT QTTDQAQLWHHRYGHLSWNGLKVLQQKQMVKGLPQFTASQKVCEDCLVGRQ FT QRDPFPKESLWRASEALQLVHADICGPINPTSNSNKRYLITFIDDFSRKTW FT VYFLVKSEAFGMFKAYKARVEKETGAFIRSLRTDRGGEFTSHEFASFCREN FT GIHRQLTTAYTPQQNGVAERKNRTIMNMVRSMLSAKQIPKTFWPEATNWAI FT HVLNRCPTFAVKNKTPEEAWNGHKPSVDHFRIFGCIAHAHVLDHKRVKLDA FT KSCKCILLGVSEESKAYRLYEPVSQKIVISRDVVFEEDQQWSWGDGYKDVI FT VADLEWNADEEISSPRVTNDPGFESNDVGDEPESESEYEGTLVGEGSQSHE FT TSPHEGRTRRPPIWMRDYETGQGLSDEEIDGMAHLALFIDRDPTTYEDAVK FT SEKWRHAMDQEIQSIEKNDTWELVKLPPGGKTIGVKWVFKTKLKENGEVDK FT YKARLLHKKGVVWT" XX SQ Sequence 3845 BP; 1210 A; 698 C; 1012 G; 921 T; 4 other; tctggtatca gagccccact acggggcctg atcgaaagct tgtaacccag gtgttcgagt 60 gaaaagaaac aaaacatggc gtctgaaaac agtttcgtac aaccagccat tccgaggttt 120 gacggacact atgatcattg gagtatgctt atggagaact ttctccgttc caaagagtac 180 tggaacttgg tggagcttgg gatcactgct gcagcagggg gatcggattc cagtgaagta 240 tagaagaaga tcttagatga actgaagttg aaggatttga aggccaagaa ctacttgttc 300 caagccatag ataggtcaat attggagacc attctgaaga aggacaccgc aaaagacata 360 tgggactcct tgaaacaaaa gtatcaaggg actgcacgtg tgaaacgagc tcaactgcag 420 gctcttcgca aggaattcga ggtgctgcac atgaagaatg gagaaacagt caatgactat 480 ttcgggagaa cacttgccat agccaacaag atgagaaccc acagagagaa gatggatgat 540 gtagtgatca tcgagaaaat tttgaggtcc atgacctcga aatatgacta tgtcgtttgc 600 tcggttgagg aatcaaatga cctagacact atgtctatag atgaactcca gagtagcctt 660 ctggtgcatg aacaaaggat aagccgccat gtggatgaag aacaggcact tcaagttact 720 catggagtcc agcaaggagg acgtggtcgt ggaacttatc gtggcagagg aagaggacga 780 ggaaggctag ggttcgacaa gtcaacccta gagtgctatc actgccatga actagggcat 840 tttcagtggg agtgccctaa gaaacctaag gaggaaaagg caaactatgt agaaacaaag 900 gaagaaatgc tgttaatggc acttgtggaa ttcaagggga tggagcacac atggtttctt 960 gactcaggat gcaggaatca tatgtgtgga aggatggact tgttcagcga gtttgacagt 1020 agcttcaaag aatcagtgaa acttgggaat gattcaagcc tgactgtgcg aggcaaagga 1080 agtgtacgaa tggaggtaga tggacgtata catgtgatca caggtgtgtt ctatgtacca 1140 gacttgaaga ataatttact aagtatcggt cagctgcagg agaaggggct cacagtyctc 1200 attcaacaag gaaggtgcaa gatctttcat tttgaaaaag gtctaatcat ggagacyaag 1260 atgagcacca acagaatgtt tgcagtggtg gctcgmagtc ctgaagagca gaagtgtctc 1320 tcctctcaaa caactgatca agcacagctg tggcatcatc gctatgggca cctcagttgg 1380 aatgggctaa aggtgcttca gcagaaacaa atggtgaagg gactacctca gttcacagca 1440 tctcagaagg tgtgtgaaga ttgcttggta ggcaggcaac agcgagatcc atttcccaaa 1500 gaaagcctgt ggagagcctc tgaggcgctt caactagtgc atgctgacat atgcggacca 1560 atcaatccaa cctcaaacag caacaaaaga tatcttatca ccttcataga tgatttcagc 1620 aggaaaacat gggtctactt cttggtatag aaatcagaag catttggcat gttcaaagct 1680 tacaaagcac gggtagaaaa agaaactggg gctttcatca gaagtttgag gacagaccga 1740 ggaggtgagt tcacctcgca tgagtttgca agcttctgtc gtgagaatgg gatacatagg 1800 cagttaacta cggcctacac ccctcaacag aacggagtgg cggaaagaaa gaatcgcacc 1860 attatgaaca tggtgcggag catgttatct gcaaaacaaa ttccaaaaac cttctggcct 1920 gaagcaacaa attgggctat acatgtgtta aatcgatgcc ctacctttgc cgtgaagaac 1980 aaaacacctg aggaagcatg gaatggacac aaaccttctg tggatcactt cagaattttt 2040 gggtgcattg ctcatgctca tgtacttgat cacaagaggg tgaagctcga tgccaagagc 2100 tgtaaatgca ttttgcttgg ggtaagtgag gaatctaagg cttatcgact gtatgaacct 2160 gtttctcaga aaattgttat aagccgagat gtagtgtttg aagaggatca gcaatggagt 2220 tggggtgacg gctataagga cgtgatagtg gcagacctag agtggaatgc tgatgaggaa 2280 attagcagcc cacgagtgac gaatgatcca gggtttgaaa gcaatgacgt tggagacgaa 2340 ccagaatctg agtccgagta cgagggcacg ttggttggag aagggagtca aagtcacgaa 2400 acctcacctc atgagggacg aactcgaaga ccaccaatat ggatgaggga ttatgagaca 2460 ggtcaaggat tatctgatga agagattgat ggaatggctc atttggcctt attcattgat 2520 cgagatccca caacctatga agatgcggta aagtcagaaa aatggcgaca tgctatggat 2580 caggagatac aatccattga gaagaacgat acatgggaac tggtaaagtt gccaccagga 2640 ggaaaaacta ttggggtgaa gtgggtgttt aagacaaagc tcaaggagaa tggagaagtg 2700 gataagtaca aggctcgatt gctgcacaaa aaaggcgttg tatggactta agcaggcccc 2760 tcgagcctgg tatagtcgca tagagtcata tttcatcgaa gaaggcttca acaaatgccc 2820 tcacgagtat accttattca tcaagacagc agaaggaggt aaaatcttaa tagcatgcct 2880 ttatgttgat gatcttattt tgtgcagcaa tgatgaaaca atgtttgaga aatttaagaa 2940 gtctatgact gctgagtttg acatgactga tctcggaaaa atgagatact tccttggtat 3000 cgaagttata caaagctctg atggaatttt tatcggacaa aggaagtatg ctcaagaggt 3060 cctggagaaa tttaatatgg aacagtgtaa tccagtacag aatccagtgg tgcctggttt 3120 aaaactcaca aggaatgaag gagtagaggt tgacagcact gtctatagac agatggtggg 3180 aagtctcatg tatctaacag ctacgagacc tgatttaatg tttgttgtga gcttgatcag 3240 ccgatacatg gagcgtccaa ctgaggaaca cttacaggta gcaaaaaagg ttcttagata 3300 cgttaaatgg acggttgacc tggggatatt ctacaagaaa tgaggaactg aggaactcac 3360 tggatacact gatagcgact acgcaggtga tcaagatgac aggaagagca cctcaggtta 3420 tgtgtttatg atgagttcgg gagctgtctc ttggtcttca aagaaacaac cagttkttac 3480 cctatccact actgaggcag agttcatagc tgcagcatcg agtgcatgcc aagttgtttg 3540 gttaagaaga atcatggaga gtcttaatca ggagcaatat ggtccaacct tagtgtattg 3600 tgataatgtt tcggctatca aactgtcaaa gaatcctgtg ttgcatggtc gaagcaagca 3660 tattgacata aggtttcatt tccttcgtga cctggtcaag gatggagtgt tagagctggc 3720 gcagtgttca tcacaagaac aagttgcaga tgtgttaact aaacctctga aggttgacac 3780 ttttctgaag atgtgagaac tgatgggtgt ctgcaagttt ccagggataa actgaacatc 3840 tgtag 3845 // ID Copia-30-LTR_VV repbase; DNA; EDCOT; 245 BP. XX AC CU469335; XX DT 01-SEP-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-30_VV, LTR retrotransposon Ty1-copia like, long terminal DE repeat from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Cremant-B05; KW Copia-30-LTR_VV; Copia-30-I_VV; Copia-30_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-245 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL; CU469335; Positions 883964 884208. XX CC LTR = 245-244bp CC LTR are 99.2 % similar to each other. CC Direct flanking repeats = atata CC UTL size = 35 bp CC gagpol putative polyprotein size = 1346 aa. XX SQ Sequence 245 BP; 76 A; 38 C; 36 G; 95 T; 0 other; taacagaaaa gataatgctt agccactaag tgataatgtc catctgttaa gtgataatgt 60 ctatctgttg taagttataa tgttttatcc ttttagttaa actaggaata ggaatgttta 120 tctttttagt taaacttgga gtaggactct ttatgtaaat atccacctct cttcctatat 180 aagttgtacg tgtttcacat tcagataata agaaattttc agcctttatt ccacaacttc 240 tgtca 245 // ID MuDR-3_VV repbase; DNA; EDCOT; 9278 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-3_VV, an autonomous DNA transposon - a consensus sequence. XX KW MuDR; DNA transposon; Transposable Element; mutator; TIR; KW Mutavine-3; MuDR-3_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9278 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 763-763 (2008). XX DR [1] (Consensus) XX CC MuDR-3_VV (Mutavine-3 in [1]) consensus is a virtual autonomous CC element. Its individual copies are >90% identical to the CC consensus sequence but do not contain an intact ORF due to stop CC codons and/or frameshifts. MuDR-3_VV contains 155-160 bp-long CC TIRs which are 96% identical to each other and an intronless CC transposase gene. Downstream of the transposase there is a CC non-functional gene in a reverse orientation virtually encoding CC for a ULP1-like protein similar to CAN69232.1 (region 7314-4751). XX FH Key Location/Qualifiers FT CDS 937..3405 FT /product="MuDR-3_VV_Transposase" FT /note="Intronless MUDRA transposase." FT /translation="MLLYKGNWVQDGNTYHFKGSEGKGITVKKNISYHELM FT RVVYRILQLDPIECSISMKYAFNGNIPTSPIQLRDDGDVKFFIRLNCTNKL FT PAPLCITVDRRSKNNAESMFMHGNGHVNDGSIESLNVVGDESITKFNYEPL FT ERSNVVEWNMNGYAIDDDYHVLDTNLTSNVQVIENRDSSNKATQIMEIHSI FT MNIKDGLMNDAPTMIEEVSNNDQDMSRIGTSDCGTNDDHIEEKQIYSSKKE FT LXKKLYIIALKEKFEFRTIKSTTKLLVLQCVDNECKWRFRATKLGSSNFFQ FT VMKYHPTHTCRLDMMSRDNRHASSWLVGESMRQTYQVGRQYRPKDIIGDIQ FT NKYGVQISYDKAWRAREFALNSIRGSPEESYGALPSYCYMLEQKNPGTITD FT IVTDVDNQFKYLFMAFGACISGFRTSIRPVIAVDGTFLKSKYLGTLFVAAS FT KDGNNQIYPLAFEIGDSENDASWEWFLTKLYDVIGHVDDLVVVSDXHGSIE FT KTVQKLFPHASHGVCTYHLGQNLKTKFKNVVVHKLFHDVAHAYRMSDFDTI FT FGQLEMISPRAAKYLVDVGVDRWARSHSNGKRYNIMTTEIVECMNVVLKDA FT RDLPVVRMVEELRNLLQRWFSNRQQQALSMKTELTTWADMELRLRFNKSSG FT YEVEPINSWEFNVKYAGVSNQVNLQTRSCTCRVFDLDHIPCAHAIAACRYG FT NMSCYTLCSQYYMKNSLISSYSKSIYPTGNNKDWVIPEDIRCRVVLPPKSR FT RPTGRPRNERICSGGETKRTRCCGRCGDYGHNRKTCKRPIPLHPRDEHSCV FT NIVESNINIQEFSLQPVHQSL" XX SQ Sequence 9278 BP; 3251 A; 1506 C; 1424 G; 3094 T; 3 other; ggggttaatt ggttaaaggg gtcaaaataa cccccatatt tgcaaatata acccaccagt 60 caaaaagcaa aaaaaatgac ccgattgaga caaaaatgcc cttcttctct tttctctctc 120 aacacataca acttctcatt tccctttccc ccctcatttt ttccttccaa gacaactttc 180 cttttccctt tgttttatag tagattcggt tttaattttt ttattcggtc gttggttgca 240 tgctcattct ctctcttttc ttgcagagaa caagtttaac ttcttaccat tgtttcatct 300 attcttcatt cttggtcacg aaaatatgaa aaaatgtaag caaccaacaa tttctttttt 360 atattatcat tttatttctt tctgtttctt gaaaattcaa aatctcactt caacattgta 420 ggtaaaaaat aaagactcca ttgttagttc tgaaaaagtg aaaagttcgt tcaaaagaag 480 ttgaaaagat ttatccatat ggcaaggtca aattatggta agcactaaat cacttgcata 540 gaaaattatt acggttttag tattgctcgt atgatttata cccattatag ttatatatta 600 tttgtttgga tatttgattt atgagaagtg ttgcattgct gcattgaaca acaaatttta 660 ctatttgtca ggtttgactt aacacaagtt gagtttatgt gtttctattc aaagcaaacc 720 tctgttttta tataaatata ctgaaaaact gagattgaat tgttgacata ttattatgta 780 gtgagttatt taataaaaat aaaaatatgt gttttaagat tcattacata gtctatagtt 840 gaaacttaat aaaagtatat cctatgttgt actattttat tattaacatg gtagtttgaa 900 atatttattt ttgcaatcat tgatgaagta ggaataatgc ttttgtataa agggaattgg 960 gtacaagatg gaaacacata ccactttaaa ggaagtgaag gtaaaggcat tacagtgaag 1020 aagaatatat catatcatga attaatgaga gttgtgtatc gcattcttca actagatcca 1080 attgagtgtt caatttcaat gaagtatgca ttcaatggta acataccgac atcaccaatt 1140 caactaagag atgatggaga tgttaaattt ttcattcgtt taaattgcac taacaagtta 1200 ccagctccat tatgcatcac tgtggataga agatctaaaa ataatgcaga gtcaatgttt 1260 atgcatggaa atggacatgt aaatgatgga tcaatagaat ctcttaatgt tgttggtgat 1320 gaaagcataa caaaattcaa ctatgagcca cttgagagat ctaatgttgt tgaatggaac 1380 atgaatgggt atgctattga tgatgactat catgtgttgg ataccaacct gaccagcaat 1440 gtccaagtga ttgaaaatag ggattcaagc aacaaagcaa ctcaaataat ggaaattcat 1500 agcatcatga atataaaaga tggtctcatg aatgatgctc caaccatgat tgaggaggta 1560 agcaataatg accaagacat gagtcggata ggtactagtg attgtggcac taatgatgat 1620 catattgaag agaagcaaat ttattctagt aagaaagaac tgyagaaraa attgtacatt 1680 attgccttga aagagaagtt tgagtttaga acgataaaat ctactaccaa gttattggtg 1740 cttcaatgtg ttgataacga atgcaaatgg agatttcgtg caactaagtt gggaagttct 1800 aatttctttc aagtaatgaa ataccatcct acgcacactt gtaggttgga catgatgtct 1860 cgggataatc gtcatgcaag tagttggttg gttggtgaaa gcatgagaca aacttatcaa 1920 gttggtcgtc aataccgtcc caaagacatt ataggagata ttcaaaacaa gtacggtgtt 1980 cagattagtt atgataaggc atggagagca agagaatttg cccttaactc cattagggga 2040 tcacctgaag agtcttatgg tgctttacct tcttattgtt atatgctaga gcaaaagaat 2100 cctgggacaa taactgatat tgttactgat gttgacaatc aattcaagta tctatttatg 2160 gcatttggtg catgtatttc tgggtttcgt acatcaataa ggccagtaat tgcagttgat 2220 ggaacattct tgaagtcaaa atatttaggg actttgtttg ttgcagcgag caaagatggt 2280 aacaatcaaa tttacccatt ggctttcgaa attggtgatt cagaaaatga tgcttcttgg 2340 gagtggtttc ttacaaaatt atatgatgtg attggacatg tagatgattt agtggtggtt 2400 tcagatcrtc atggtagcat tgaaaaaaca gtacaaaagt tgtttcctca tgcaagccat 2460 ggcgtatgca cttatcattt aggacaaaac ttgaaaacaa agttcaagaa tgttgttgta 2520 cataagttgt ttcatgatgt tgcccatgca tatcgaatgt cagattttga tactatattt 2580 ggtcagttag agatgatttc tccaagagca gccaaatatt tagtggatgt aggagtagat 2640 cgatgggctc ggtcacacag taatggaaaa agatataata tcatgactac agagatcgtt 2700 gagtgcatga atgttgtact aaaagatgca agagatcttc cagttgtgcg aatggttgaa 2760 gagttgagaa acttacttca gagatggttt tcaaatcgcc aacaacaagc attgtcaatg 2820 aaaactgagc ttactacatg ggctgacatg gagttgcgct taaggtttaa taagtcatca 2880 ggttatgagg ttgagcctat caactcttgg gagttcaatg tcaaatatgc tggggtaagt 2940 aatcaagtta atttgcaaac ccgttcatgc acatgtaggg tgtttgatct tgaccatatt 3000 ccatgtgcac atgctattgc tgcatgtaga tatggaaaca tgtcatgcta tactctatgc 3060 tctcaatact atatgaagaa ctcgcttata tcttcatact caaagtctat atatcctact 3120 ggaaataaca aagattgggt cattccggaa gacatccgtt gtagagttgt gctaccacca 3180 aaaagtcggc gaccaacagg aagaccaaga aatgagagaa tttgttcagg tggagagact 3240 aagcgcacac gatgctgtgg tagatgtggt gattatgggc ataatagaaa aacatgcaaa 3300 cgaccaatcc cattacatcc tagagatgaa catagttgtg tcaatattgt tgaaagcaat 3360 atcaacatcc aagaattctc cttacaacca gttcatcagt cactttaata atgttaccac 3420 ataatttgtt ttttggggat gatttaacta tgtatctaca tttttttttg tatagggtca 3480 tgaaggaatt tgtgagctta ttttttttat atgcttaaag caattttttt gaatgatgga 3540 ttgaattttt aagttaatgt tttaatttta tcatataaat tacttggtta agtttaacta 3600 tggttaagtt gatgatcatt tcattaacaa agaacttaac agtagttgag ttgtattaat 3660 aaaaaactta accacagtta agtttacatt cagaattttc acttgaacct aacagtagtt 3720 tagttgcatt aacaaagaac ttaaccatag ttaagttcat agtaagatat ttcacttgaa 3780 cttaacagta gttgagtttc actaacaaag aacttaacca cgttaagttc atagtcagaa 3840 ttttcacctg aacttaacag tagttgagtt gcattaacaa aaaacttaac catagttcac 3900 agtaagatat ttcacttgaa cttaacagta gttgtgtttc attaacaaag aacttaacca 3960 tagttaagtt cacagtcaga attttcacct gaacttaaca gtagttgagt tgcattaaca 4020 aagaacttaa ccatagttaa gttcaaagta agatatttca cctgaactta acagtagttg 4080 agtttcatta acaaagaact taaccacggt ttagttcaca gtcagaattt tcacctgaac 4140 ttaacagtag ttgagtttca ttaacaaaga acttaaccat agttaagttc acagttagaa 4200 ttttcaccta aacttaacaa tggttgagtt gcattaataa ataacttaat tgtggttaaa 4260 ttcacactca gaatattcac ctgaacttaa caattgttga gttgcattca caaataactt 4320 aattatagtt aagttgacta tcattgttac attacaaaaa ttgtaacttt gagcatcaag 4380 tcaaattcat ccaaaataac tgtcaacact caacaacata taaacctttt acataatcaa 4440 aatcgaaccc actacatggg tcaaattttg aagtagaaca attcagttgc cattttctct 4500 ctaaaccaat caatgcgggc accggtcagt gaactgaatg gattatcatg cattaagtat 4560 tctacatatt taatcaggaa catcccacaa tcaccactgc atgaaacaca agtaatcaaa 4620 attaagatgg ctaaattttt ttttactata taagccataa aggtgaaatg ataagatgaa 4680 gtttggaagc attgtttact tactcatact cttgttgagg aacatcatgc aaccgttcaa 4740 tgtcccactg ttcttcactc ttaggttcac cgctcttccc ataatatgat gtagcatgca 4800 aaatacgcag taacacttta gctaaaggta ttatggcaca ttttagtcaa ttatcactat 4860 taatgcctat caatgagtca tacacaaata ttctcctctg agcaaggtga actactccca 4920 atacccaatg catacttcgg acattaatag ggacatagac gatgtccacc tcaaaccatt 4980 tcatggaagg aattgggtga aacccattaa catagtcaac aagaatatca tttgcttgca 5040 tttggaattg attccacttt ttagcatgct tctcccacct tgctttcaca tatttctata 5100 taagaaaaga taaaaaagaa tagttaaact accataattt aactagtatt atgagggtca 5160 atagtaaaaa gaaactatac atacccaaaa cattgtatct gtggtagtaa aattttaagt 5220 aaatgcatgg cgcttttcta ttctccgctt acgaaaaaag tagaaagcaa tatcaatatg 5280 ctagacaaca tatataaaaa aaacattagt tatactattt cattataata ataatatact 5340 aataagtaaa agcaaacaca ataagaacat ttacaaaccg tgtctttaag ccatgaacca 5400 tgctaaacta gtgacccaaa ccattctttg tctgcatgca agtaatcaat atcaacctta 5460 aaccttattg taataatata tcaaaaaacc atggtcaagc aaagaacttg ccaaaaaaac 5520 tattacaagt ttaaagtcaa gataattact cttgttgaag actcaaccac ttatgaaagg 5580 cttctcttgc ttcctcagaa atagattgca aaggattaaa gtcagatgtt gtttctcctt 5640 cctttctaat ttttcttctc tttgtagggt ctgtgaaagg aggctgcaaa aaataggacc 5700 ttttcaactc acgtcttcac ttaaatatag tgggggacag ttgctttgga aatacataaa 5760 ccgaaaagtt gcttgataca gtagcggtat caaataattt ggaaatatca acaattggat 5820 cgaaaatcac atcatcatct ttctccatcc ctattatgtg tttttctgca gctacaataa 5880 ttgttatttc ttctgtattg gtcttcacat ctatatggtc atggttctca tcctccttat 5940 cttccatcat agtctcaaac ttgtcatcca atgaattaaa atccatacca atatcttttc 6000 cttttggacc agattttgaa aattttgtat tatctatagc acatgactca ttttgccctt 6060 tcacctaaaa taagatatgc accatacaat aagatatgaa aaatatagaa ataaaataca 6120 taatttgatt gaataaaata taaaattcaa taaatatatc actaacatcc aataaaagtt 6180 gtcttaattt gtcaatcttt ctgttcattt ccttcagttc tttcttcaaa taattggaat 6240 ttgatttaga cttttctata tgcttcatga actctatcca tagattctgc acatgttata 6300 aacaaatgaa acattaattc ttcatacatc attgtatacc aaaattatag tcataatttt 6360 aaaaaattga tgtgtactta tgatagttat gttatgttta tcaaagtaac cttcacttga 6420 ctatggttaa gtttcattga tgattaactt aactgaggtt aagtttacaa tttgaatttt 6480 tatttgaact ttatattaca atagaaatat taaaaatgac atttataaat gaatgtatga 6540 tagtggactt acctcaattg aaggtgggat agaataatcc tttttgttct tgttttccat 6600 tatagcaaca gcagcaacat atgcagtagc ttcaaccagt aatcttcatc ttttaggtca 6660 cccattgtat tatgttctgg ggttgttggt tggcttaaaa tttctggagg aacaccattc 6720 actaactcta acttattcaa atgcttgtaa taatcttgtt gacattcctc catagtaggt 6780 ttaagcagcg aacacaaaga taactattga attcaagtta agtaatttaa ttaacaaaca 6840 tagacatata taaatatgta agtgacaaca ctatcaaaat atatggtaaa aaaaattact 6900 cacattggag tccaaaaaga tttgttggag ctcggtaaac ctcggtgtgg aagtagcact 6960 ccaatttaaa atccgtgggc aactcttatc aacatgatta gcatatttca tttcgataat 7020 cggaatagtc tcatacaccc aaacttggaa gacatatgga aatccaacta gactatatgc 7080 ctcaagtgct atattacatt tttgttgctt tttaccttgg tattttgaca cccgattctc 7140 caaggcttgt tgcagcccag aaattgttct ttcataacaa atcctaccct atggatactt 7200 attaaaaact tccaaacaat caacaagacc aacccattgc atgtctatta aatttttccc 7260 ttctttccca agtagaacat gctcaagaaa gtacgataag actaatttca ccatgtcttc 7320 atctttaaga ttatcaacat ttttcttttg cttttttttt tttttttttt cacttcacca 7380 aaagaaagaa aaactttctc caaatgatca ttacgcactt tgttttcact attatagtaa 7440 acatccctta ttctcattga tgtttcatta tgctgaggaa tgggaccaaa acttaaacca 7500 atgattaatc caaactcatc ttcaccaaat cttaatccct ttgaatttac taaaaaccac 7560 atttcatcat ccttctttat aagacattga tgtaataaca tgtggtgcac aatttgagct 7620 aaaaatttaa gttctggcat aagcaaaaaa tgtccaaagc aagaatcctt gaacctctcc 7680 aactgttcct tattgagctt ctttttaata ttttctatta cactcaggtg tgatagacat 7740 gcaacctttg atgggaagtg ctcttctata ggtattttaa ctttaaaaca tgtcgagaga 7800 gtagtagtct ataaattaaa taaaattaag ttagtaaaga tttaataaaa aattacaaat 7860 attaaataat aactgattaa cacacttcag tagttcccaa aattttaaaa acattattaa 7920 ctaacaaatt taacactact caaatgtcat tacataacat ccctaaaaag ttcaaaaatc 7980 caaaaatttc ataaattctt taaaaactta tccttaatca catgtcattg catgaaatca 8040 ttatatatat tttattcact ctatatacat aattgacaat aatatataac tacaaaaatg 8100 acaaatatac catatgttat tttgaaatca attcaatagt tcccaaaatt ttaaaagtat 8160 caagtaaaga acatagacct actcaaacac cattgtataa tacccctaaa atttccaaaa 8220 atccctaaaa tttaataaat tctctacaaa cttatcccta attagatgct attacattga 8280 atatatctaa ttcactctaa acacataatt gataataata cagaaaacta aaacaatatt 8340 aatatggaat ttattatttt tcaacacact ataatagttc ccaaatattt tcaaacatca 8400 actaaaaaac ctaaatttat tcaatcaaaa tacataacta ataacaatgg agaactaaaa 8460 aaaatatatt ataaatataa caattttata ctttgaatac aattcaataa atcctaaatt 8520 tttaaaaaca tttaactaat aaacttaacc atactcaaat attattgtat aacatctcta 8580 aaaattttaa taatttatca aatgtgaagg ctacactcac cggtttagca gaatcacttg 8640 ccccttctgt tggtaattgg gatttttact tagtaacttc acattcattt gcttcatttt 8700 cttgtacttc acttttttct tctgttcgca attgccattt ttgctttttc gccacttttt 8760 aaaatctttt tctcttatca ctcttcaatg aactcattgt ttcctttgtg cttgaagata 8820 gaatatgaga taacttgaaa aaaatagaat aacaaatttt ccaaggattc ggaatgaaac 8880 agaggatgag aggatagacg agaaattttc taaggttttt gaaggaaata tgagattttc 8940 attttgtaca tcaaagaaag ataatgaaat agaagaagat gatgaaagat gaagactcct 9000 tctgtaaatg aaccggaaga gtagatgacc tttccgtttt gtgcaccaaa tgaagataat 9060 gaagtagaag aagagaaaat atgaagagtc gttttgtaaa tgaagcagaa gaagagaaat 9120 tgtaaatgag ggggaaaggg aaatgagaag ttgtatgtgt tggagagaaa aaagaataag 9180 ggcatttttg tctcaatcgg gtcatttttt ttgctttttg actggtggtt atatttgcaa 9240 atatgggggt tattttgacc cttttaacca attaactt 9278 // ID Copia27-VV_I repbase; DNA; EDCOT; 4554 BP. XX AC . XX DT 07-SEP-2007 (Rel. 12.09, Created) DT 07-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW internal portion; Copia27-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4554 RA Obukhanych T. and Jurka J.; RT "Copia27-VV."; RL Repbase Reports 7(9), 786-786 (2007). XX DR [1] (Consensus) XX CC This is an internal portion of Copia27-VV LTR retrotransposon CC from Vitis vinifera. Individual elements share 84% similarity to CC their consensus. LTRs, deposited as Copia27-VV_LTR, contain CC indel mutations and are 93% similar to each other. This LTR CC retrotransposon has 5-bp target site duplications. XX FH Key Location/Qualifiers FT CDS 1166..2326 FT /product="Copia27-VV_I_1p" FT /translation="MPFHVVSISTPWIIDSGASDHMTSFSNLFNSYSPCSG FT SEKIRIADGSFSPIAGKGLIKLSENIDLKSVLHVPKLACNLLSVSKLSKDS FT NCRVFFYDSHCEFQDQNSGKKIGSAKLIDGLYYFDDVFSNKQAQGLSSVSS FT ISVYEQIMLWHLRLGHPSFLYLKHLFPTLFKGLDCSSFYCESCYLSKSHRT FT TYYPKPYVASKPFYLIHSDVWGPSKITTISGKKWFVTFIDDHTRLCWVYLM FT KEKSEVGKLFQDFYNMVENQFQTKISIFHIDNGTEYFNEFLGSFLKEKGIQ FT HQSTCVNTPQQNGIAERKNKHLLEVARAIMFSMNVPRYFWGDAILTASYLI FT NRMPTRILKYSTPLECFKNIFPLSRMYFRFTPKSFWLHCFRSPT" FT CDS 2987..3655 FT /product="Copia27-VV_I_2p" FT /translation="MLVPRNIQEALDDPNWKLAVMEEMNALKRSGTWEIVD FT LPKEKRTVGCKWVFTMKCKADGSIERYKARLVAKGFTQTYGIDYQETFAPV FT AKINSIRILLSLAVNFNWPLHQLDVKNAFLNGDLEEEVFMNLPPGFEEKLG FT KNKVCKLKKSLYGLKQSPRAWFERFGKAIKNYGYCQSQADHTMFYKHSKEG FT KIAILIVYVDDIVLTGDDNEELERLKRRLATRI" XX SQ Sequence 4554 BP; 1464 A; 768 C; 886 G; 1432 T; 4 other; tggtatcaga gctaccctaa ttcacccaaa aaacccttgc aatttttttt ttcttctgcg 60 tatttctttt cctaaccagt agccatgtct gatgtttctt ctaagtcaaa tccacttgtt 120 tcctcttcca gcccaacaac taaacctgca acccaaaccc ataataccga atcccatcct 180 gttcagatta ccaccattcg cctcaatggt gacaattttt taagatggtc tcaatcagtt 240 cgcatgtatc ttagagggag agggaagatc gggtacttga ctggagacaa ggaggcaccg 300 gcatcggagg atcctctgta tgcaacctgg gatgcagaaa attcaatggt gatgacatgg 360 ctcgtgaatt ccatggatga ggagattrgc tccaattata tgtgctattc cacaaccaaa 420 gaattgtggg acaatgtgaa tcagatgtac tctgatttgg gtaatcaatc ccaagtgtat 480 gagttgacac ttaaacttgg tgagattcgg caaggagagg aatctgtcac caagtacttt 540 aattcgttga agcttctttg gcaggatctg gatttattca atgactatga atggaaatcc 600 actgatgatt ctaatcatta caagaagact gtggagagct cataggattt acaagtttct 660 tgttggactt aatgttgagt ttgatgaagt tagaggaaga attattggta gacatcctct 720 tccttcaatc agtgaagtct tttctgaagt tcgaagggag gaaagtcgga gacatgtaat 780 gttgggaaag aaatttatta gcggacctgt tgaaagttct gctcttagtg ggcactgcta 840 gaaggttctg ccaataataa caaccagttt atcagcgagg gyctggatga aaagccacga 900 gtttggtgtg attattgtaa taaaccacgc cacactcgag aaacctgctg gaaaatccat 960 ggaaaaccag caaattggaa gcccgttaac agcaagcctg aagagagaag caatcattca 1020 aatcccaagg ccaatgctac tgtcaatgaa tcagagtcaa gtcccttcag caaggagcag 1080 atggatcacc ttctaaaact gctaaaatct aattctccat ctggtattcc tagtgtttct 1140 ctagcacaaa caggtagtgc acctaatgcc ttttcatgtt gtttcaatat ctactccatg 1200 gatcattgat tctggagctt ctgaccatat gactagtttt tctaatttgt ttaactctta 1260 ttcaccttgt tctggcagtg aaaaaattag gattgcagat ggtagtttct cacctattgc 1320 tggaaaaggc ttgataaaat tatctgagaa catagatctt aaatctgttc tccatgtccc 1380 aaaactagct tgtaatcttt tgtctgtgag taaactatcc aaagattcta attgtcgtgt 1440 ttttttctat gattctcatt gtgaatttca ggaccagaac tcggggaaga agattggcag 1500 tgctaagttg atagatggtc tttactattt tgatgatgtt ttctccaata aacaagctca 1560 aggccttagt agtgttagtt ctatttctgt ttatgaacaa ataatgcttt ggcatttaag 1620 actaggacat cctagttttc tatatcttaa acatttgttt cctactttat ttaaaggatt 1680 ggattgttca tctttttatt gtgaaagttg ttatttatct aagagtcatc gtactactta 1740 ttatccaaaa ccttatgttg cctcaaaacc attttattta atacatagtg atgtttgggg 1800 accttcaaag attactacta tttctggaaa aaaatggttt gtgaccttta tagatgatca 1860 tacacgttta tgttgggttt atttgatgaa ggaaaaatct gaagttggaa aactttttca 1920 agatttttat aacatggttg aaaatcaatt ccaaacaaaa ataagtattt ttcacattga 1980 taatggaaca gagtatttta atgaattttt gggtagtttt ttgaaagaaa aaggtattca 2040 acatcaatct acttgtgtga atacccctca acaaaatgga attgctgaaa gaaaaaataa 2100 acatttactt gaagtagctc gtgctattat gttttctatg aatgttccaa gatacttttg 2160 gggggatgct attttaacag cttcctattt gattaacaga atgcctacaa gaattctaaa 2220 gtatagcaca ccactagaat gttttaaaaa tatttttcct ttatctagaa tgtactttag 2280 atttacccct aaaagttttt ggttgcattg ttttcgttca cctacctaat catawtcgat 2340 ctaaacttga tccaagggca gaaaaatgtg tttttatagg gtatgctcct aataaaaaag 2400 ggtataagtg ttataatccc caaaccagaa aaatttatgt tagtatggat gtctctttta 2460 ttgaaaataa atcttttttt aacaaaaatt ctcttcaggg ggagaatgat gtaatggaag 2520 aaaatttttg ggatttatct cccactccat taccaaatac aattttaact acttcacctc 2580 ttatttataa tcttaagaaa caatgtgata agtactgaca aagggggaaa ttctgagtca 2640 tatagtgcca aacattactg tatctgaaac agggggagaa tcastacaac caaagtctac 2700 tgagcgtctg gtttatactc ggagaaagac tcatcaaaag agtcaaagtc aacctgttcc 2760 tcttggtaat gaccaatctt gaccttcggg aactgaagct ctcaatatca caggtaatcc 2820 tactcctaac ctaccttcaa ttcctttcat ttcttcttta gaccttgata ttcctatagc 2880 ccttagaaaa ggtacacgaa cctgcactaa atatcccatt gccaaatatc tatcttataa 2940 aaaactctct aaaactcata aagcctttac ctcaaaaatc tcacacatgt tggttccaag 3000 aaacattcag gaagcccttg atgatccaaa ttggaaatta gcagtgatgg aggagatgaa 3060 tgctcttaaa agaagtggta cttgggagat agtggattta cctaaggaga aaagaactgt 3120 aggttgcaag tgggtcttta ctatgaaatg taaagctgat gggagcatag aaagatacaa 3180 ggcaagacta gtagcaaaag gatttactca aacctatggt attgattacc aagaaacttt 3240 tgctcctgta gccaagataa actcaattag aattttgtta tctttggctg taaatttcaa 3300 ttggccttta caccaattag atgtaaaaaa tgccttccta aatggagatt tggaggagga 3360 agtgtttatg aatttaccac ctggatttga ggaaaagctt ggaaaaaaca aagtttgcaa 3420 attaaaaaag tccttatatg gtcttaagca gtctcctaga gcttggtttg agagatttgg 3480 aaaagctata aagaattatg gctattgtca aagtcaagct gaccatacta tgttctataa 3540 acactcaaaa gaaggtaaga ttgctatttt gattgtttat gtggatgata tagttttgac 3600 tggtgatgac aatgaagaac tggagagatt gaaaagaaga cttgcaacac gaatttgaga 3660 tcaaggattt gggtgcctta aaatacttcc ttggaatgga gtttgctaga tccaaagaag 3720 gtatatttgt aaatcaaagt aaatatgtac ttgatttact tggtgaaaca ggtttactag 3780 gatgtaaagc tagccgaaac acctattgaa cccaatttga aactgcaacc atccaaagct 3840 gatgaagtga atgataaaga acaatatcaa aggctagttg ggaggctgat ttacttgtct 3900 catacacgtc cggatattgc ttttgcagta agcatggtga gccaattcat gcattcacca 3960 agacaagaac actttgatgt tgtttataga attttaagat acttaaaagg gacaccagga 4020 aaaggtctac tatttaaaaa ccgtggacac ctacaagttg aagcatttac tgatgcagat 4080 tgggctggaa gtgtaattga taggagatca acctctggtt attgtacctt tgttggaggc 4140 aaccttgtca cttggcgaag taaaaaacag aatgtggtgg ctagaagtag tgctgaggct 4200 gagtttagat cagttgctca tggaatttgt gaagttttgt ggattaaacg actatttgaa 4260 gaattgaagg tttctagtcc cttacctatg aaagtgtatt gtgataataa agcagctatt 4320 tcaatagctc ataattgcac ataatccagt acttcatgat agaactaagc atgtggaggt 4380 agataaacac tttatcaagg aaaaactcga aaatggactg atttgtatgc cctatattcc 4440 tactattgaa caagttgctg atatacttac aaaaggaatt cctacaaagc agtttgacaa 4500 tttaattggc aagctggcta tggaagatat cttcaagcca gcttgagggg gaag 4554 // ID GYPSHAN2_LTR_MT repbase; DNA; EDCOT; 409 BP. XX AC AC158209; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of LTR retroposon, GYPSHAN2_MT, from Medicago DE truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; terminal; repeat; GYPSHAN2_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-409 RA Shankar R. and Jurka J.; RT "GYPSHAN2_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 23-23 (2007). XX DR EMBL/GenBank/DDBJ; AC158209; Positions 42449 42857. XX SQ Sequence 409 BP; 142 A; 76 C; 82 G; 109 T; 0 other; tgtcatgaac cacagtgagg aagagataga ctatggacca gaaggtgatg agcccagccc 60 aagaggcaaa tccaaaagga acaagaccca acccaaatgg ttcaaggact atgtcaccaa 120 agctgataag acaaagaagg cagccaagac agatcatcag tcttaggaag ggtctagaat 180 agtatgagtc attatcacat ctgttaggat aaggtatcaa tagtactaca tgtgccagac 240 tgtaggaata tgctctttct ttgaaaaggg gataagagct atataatgta atactgatcc 300 aagaaataaa gacagataat tattgaaaga agttgttata gcatttattt tgcctttatt 360 cttttgcttg ttatcttcac tctctttccc agatttccca ccctttaca 409 // ID HARB-4N1_Mad repbase; DNA; EDCOT; 2521 BP. XX AC . XX DT 03-NOV-2010 (Rel. 15.11, Created) DT 03-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW HARB-4N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-2521 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1863-1863 (2010). XX DR [2] (Consensus) XX SQ Sequence 2521 BP; 662 A; 457 C; 555 G; 845 T; 2 other; gggcccgttt gtttgacagg attaagaagg actggactgg actagactat agtcctttgt 60 ttggtgtgca ccaggattag ctttaatgag cttagcacgg actcgctcgg attaaagacc 120 tccttagccg ttcttaacga ggatccccaa ttttgggcgg actcgtaagc cagagaaaac 180 acgagagatt ttctgcgtct tccctcatcg tcctcatctc tgcgtcttcc ctcatcgtcg 240 tccttgccgt gctccctcat cgtcgtcctc ctcaccctca tctctgcgtc ttcgctcatc 300 tgcatctgct cgccctcatc tgcctcgagt tgtctggtaa gcttcgaatc ttcgatttat 360 ttcgtcgatt tgtgtkgatt agtttgtgat attaactgag ctttatttga ttttgttgtt 420 ttgggtttga gaaattttca atcatagacc tctgcacttg aacaaattag ggttttgata 480 tttaggtgaa attgagatta gaatttgggg ttttcataag atgagatgga acttgggaat 540 ttaggatgtc aaagttgtca aacttggaag tcctacccac atgctgtttt cgatttttaa 600 aatttggggt ttcaacaatg ggagtactct gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt 660 gtgtttgtgt actctgtgtg tgtgtgtaat ttctgtgtgt gtgtgtgtgc aggttccatt 720 agtgcaagag aaacaactat accagctgga acaatgggat atcttgctct gggatacgtt 780 tattcaggtg ttccaactgt taaaactgat gtttacagct ttggtgtggt ggtgttagag 840 atggcaaggg gtagaaagct ggtggaggat gattgaacag tggtggttga ttgggtttgg 900 agcatgtggg aaaaggggaa actgatcgaa gctgctgatt caaggttgat ggggaagttt 960 gatacggtag agatggagag gatgctgatg actgtacttg cttgtgtgca cccaaacctt 1020 gtgaagaggc caatggtgaa ggaagctgca aggattctta aaggcgaaac gacgcctcct 1080 ctgctgcctt caagaaaacc gaaggtgagc cttctgcctg tttttcgtga tgagtttggt 1140 gaaatctcgt ttttctgtgg tgttcggcca agtcttgaac tcgatgatgt acaatatttg 1200 actctgaaga gccactttga caaggattag ttgctcgtaa tagatcaagt aacctcacaa 1260 ttagtaggat ttcagtgcag tttgtagaag agaaactagg agcttgttgt tgacggggga 1320 acttgaggaa cccctcactt gttcagttaa tttgcagatt ttgtagtctg aaattgtgtt 1380 tgatgtctta tagtaatgaa atgctcagtg tccttgtctg ttttatcatg attgacatgg 1440 tctcaagcat tttgttataa gctgatggac ttaataattc aaatgatgtt cgaaagattg 1500 aattaagttt cgtgtttcat ccaaatattc ctttcgaatt ttgttatttg tacaacaata 1560 gatgacttca gatcaagaca agagtgtctt tccattagtt acaaaaacag actgaaacac 1620 gtcgattctt tctttctata aaaatttgaa ttcaactccc cggtgtcttc agaaaatgaa 1680 ccttgcggcc aactccacgg cgctcggata gtatttgtcc tgcttcaact ccagcmagct 1740 ttgccaattc ttcccaagtt tatgatgcaa ctgactttac aggggactga aatgaaatta 1800 agaaatgaaa aaccatttct tcccaagttt atgatgcaac tgactttaat cgtacaatct 1860 tatgttatgg cttataactt agctttgcac tatgaagtat tttggctaat gttaactagg 1920 attttgtaaa ttatggagat ctactttgga atgctatact atagttcact ggcattttgt 1980 aaaatatcct ggatgaaagt ttagtgaatg atgttttaag agtcaatcaa tggcaaagat 2040 tgacttgtca caagtatctt cttatgtact tgtatttgtt gaagttgcat gtattgggca 2100 ctattctttt tcttcttttg ggtgatagag tttaaaccaa gctacatttg caaattaaac 2160 tcaactattt ataaatagta tgtcccaact atatatgtcc caattctatt agcaggtaat 2220 agaaacaaaa caattgtcct ctttttttaa gattcataat atacatggca aaaatatgct 2280 ccaattaacc catatcatga gatttgtagc attactctat tacacaatgg caaaaatttg 2340 tagtcctagt ctaagcaaac acaaatctgg tgaacagtac tgtttttatt atcctgcttc 2400 ttagtccgac actgcaccaa acgcttcact aagttagtcc agcttagtct agtctaagcc 2460 agtccagctt agtccctgca gctagtccag tccgagacag tccggcgcaa caaacgcacc 2520 c 2521 // ID Copia-58_Mad-LTR repbase; DNA; EDCOT; 612 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-58_Mad_; KW Copia-58_Mad-LTR; Copia-58_Mad-I. XX NM Copia-58_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-612 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1655-1655 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 612 BP; 188 A; 103 C; 99 G; 222 T; 0 other; tgttgaatat tttaaaaata tatataatat attatatata taataataat atatatatat 60 atatatgtgg atgtttgacg gagatggggt tgggtcattg acccaacaat cgcatctttt 120 caaattaaca ctgcaacctt ttgctaatac ccaacggttg ctgcatgttt tacaacatat 180 atgatccttg ggtaattggt ttttgtatca gatatgtcca tcggaaacat tgctgcaatg 240 ttagttgtat ctcatggtga gaggacacac tcaaatcaaa ggatgtgtct aaagggtgca 300 attctctcta tatatagtgg cgacattagt agaaaagaat cattcagaaa tttgttgtct 360 acataatttc tttgctctct tttctctctt catcacattc atacaatttc tttctagtta 420 tttctaaggg aatacaattc ggttttgcta atcgaatatt ccatactttg ttgtatcctg 480 gaagtgattt gccaagaacc ctttagcaaa ctcattcgag tgggggcaaa taacacttta 540 aggaaacgat tcaagtcgta cctcaaagtc atcattcgga ttattctcta tatttctaca 600 tttactctaa ca 612 // ID Copia-13_Mad-I repbase; DNA; EDCOT; 4638 BP. XX AC ACYM01095680; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-13_Mad-I; KW Copia-13_Mad-LTR; Copia-13_Mad_. XX NM Copia-13_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4638 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1289-1289 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01095680; Positions 7459 2822. XX CC Positions [1975-2475] - Integrase core CC 'TGTGT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 208..2628 FT /product="Copia-13_Mad-I_1p" FT /translation="MVTATQLQILQSPITSLISSVSSSVSVKLDDSNYLTW FT HFQMELLLDGHGIMGFVDGTNLCPSNLSDSTESSSDLHTSDAFKIWKMHDR FT ALMQLITATLSPSAISCAIDSTSARDLWVRLKEQFSIVTRATIFQMKSELQ FT NIKKGTDSISLYLQRIKEARDYLAAAGVMFADDDIVILTLNGLSSEYNTLR FT SIIRGRENVISMKDLRSQLLAEEAMLANVSVTPFLSAMVASNMSVSSKSSQ FT FEANSPHDNYSNTGPSSNGGSYGSQGSFYQYNGSGSKPPYHRNKGKGKYQY FT NSRFGNAKSGSFHNNAPGILGSSPPTAQGFFQSSCQICGKFGHLAVTCRFR FT NTENSITEACQICGKKNHSAHFCHFRNANLQSQQVSAMHVAGPSSVPSANS FT QQVWLTDSGATSHMTADLNQLSLASPFPSNETIQTAGGGAGLSISHIGSST FT LHTPFKPLHLNSVLYVPQLYQNLLSVHKLCLDNNCWLIYDAFCFWIQDKAT FT GRIIFMGHCSNGLYPIPLPVSYRSSLPNVHAAFLGQHVSSSLWHSRLGHPS FT NSIVSAILRKCNVSDISDSKSVMCHSCLEGKFCKLPFVDSVSQSLHPFDTV FT HSDVWGPSPCNSVEGFRYYVTFIDECTRHCWIFPLINKSDVCSTFIAFYNF FT VFNHFAISVKTLQSDGGGEYISKSFQQFLASKGIKHQLSCPYTPEQNGLAE FT RKHRHIVDTAITLLQTASLPPKFWSFACQVAVYLINRMPTPVLHNKSPFEL FT LFKDVPAINHLRVFGCSCFPLLKPYNSNKLQPKTTKCVFLGYASRYKGYLC FT YEVRH" XX SQ Sequence 4638 BP; 1128 A; 999 C; 869 G; 1594 T; 48 other; tggtatcatt cgccggaaaa gcttcgtgct tcacggtttc ttgatcttgg ttcttctgct 60 tccgctctgt ttcttctatt tcttgatttt ttagggttct catttccctt ttcttctctg 120 gttctcggtg tttacgatac tgcacaccag gtgtttgttc ttttgtctca gtgacatttt 180 cttcgagttc ttgattccta ttcgatcatg gtgactgcta cacaattgca gattcttcaa 240 tctcccatta cctctctcat ctcatcagtt tcatcttctg tttctgtgaa acttgatgat 300 tcaaattacc tcacatggca ttttcagatg gagcttcttc tcgatggtca tggcattatg 360 gggtttgtcg atggtacaaa tctttgtcct tcgaatctga gtgattcaac tgagtcttcc 420 agtgatttgc ataccagtga tgctttcaag atttggaaaa tgcatgatcg ggctctcatg 480 caactcatca ctgccacatt atctccttct gcgatttcgt gtgctatcga tagcacgagt 540 gctcgggact tatgggtgcg tcttaaagaa caattttcaa ttgttactcg ggctacaatt 600 tttcagatga aatctgagtt gcaaaatatt aagaaaggta cagattccat ttccttatac 660 cttcaacgca ttaaagaagc tcgtgattac ttggctgctg ctggggttat gtttgctgat 720 gatgatattg tgattttaac tcttaatggt ctgtcttccg aatataatac attgcgatcc 780 attattagag gtcgggagaa tgttatttct atgaaggatc ttcgctccca attgcttgct 840 gaagaagcaa tgcttgctaa tgtttctgtt actccgttcc tgtctgcaat ggtagctagc 900 aatatgtctg tttcgtctaa gtcttctcaa ttcgaggcca attcacctca tgataattac 960 tccaacactg gtccttcatc caatggtggt tcgtatgggt ctcaaggaag tttttatcag 1020 tacaatgggt ctggttccaa gcctccttac cacaggaaca agggtaaagg caagtatcaa 1080 tacaactccc ggtttggtaa tgccaagtct ggttcttttc ataacaatgc ccctggtatt 1140 cttggttcct ctccaccaac ggcacaaggg tttttycagt cttcttgtca aatttgtggc 1200 aaatttggac atctagctgt tacttgtcgg tttcgaaata ctgagaattc tattacagag 1260 gcttgtcaaa tatgtggcaa aaagaatcac agtgctcatt tctgtcattt tcgaaatgcc 1320 aatctccaat ctcagcaagt gtcagctatg catgttgctg gtccgtcctc tgttccgagt 1380 gctaattctc aacaagtgtg gcttacagat tctggggcta catctcacat gactgctgat 1440 cttaatcagt tgtcgttggc ctctccattt ccttccaatg agacaattca aactgctgga 1500 ggtggtgcag gtttatcaat ttcccacatt ggttcctcaa ctttacatac acctttcaaa 1560 cccctgcatc ttaattcagt cttatatgtt cctcaactct atcagaattt gttatctgtg 1620 cataaattgt gtctggataa taactgctgg ttaatctatg atgctttctg tttttggatc 1680 caggacaaag ccacagggag gatcatcttc atgggacatt gcagtaatgg actatatcct 1740 attcctctac cagtttcata ccgttcttcc ttacccaacg tacacgctgc tttccttgga 1800 caacatgtgt cttcgagtct ttggcatagt agattaggac acccatccaa ttctatagta 1860 tctgccatat tacgcaaatg caatgtatct gatatatctg atagtaagtc tgtgatgtgt 1920 cactcttgtc tagaagggaa attttgtaaa ttgccatttg ttgattctgt ctctcagtcc 1980 ctgcatcctt ttgatactgt tcatagtgat gtatggggtc cttctccttg taactctgta 2040 gagggtttta gatactatgt gacattcatt gatgaatgca ctagacattg ttggatattt 2100 cctctcatca ataaaagtga tgtttgttca actttcattg ccttttacaa ttttgtgttc 2160 aatcactttg ctatttctgt taaaacttta caaagtgatg ggggaggtga atatattagc 2220 aagtcatttc aacaatttct tgcatccaaa ggtattaaac accaattgtc ctgtccatac 2280 acccctgaac aaaatggtct agctgaaagr aagcatagac atattgttga cacagctatc 2340 acccttttac aaactgcttc cttgcctcca aaattctggt cttttgcatg ccaagttgct 2400 gtctacctta ttaacagaat gccaacacct gttttacaca acaaatctcc atttgagttg 2460 ttgtttaaag atgtcccagc tatcaatcat cttcgggttt ttggatgttc ytgtttccca 2520 ctcttaaaac cttacaattc caacaagtta cagcctaaaa caacaaaatg tgtcttttta 2580 ggttatgctt ccagatacaa aggctactta tgttatgaag tgagacatma aaaaatgtac 2640 atatctaggc atgttatttt tgatgagggt gaatttcctt atgccatgtt gtcttccaaa 2700 accttamctt catcatyytt tactcctctt ttgtcacctt ctatttctct gccttctgtc 2760 acacatgata accrggttgt ctccatagca tctacatcta yttcacctac acttgagtcc 2820 atttmtaccc caacacatgc tgaatccatt actgcaccgt ccatacagty tgtgcttcmt 2880 tcttcccctg tggctgcagt cctgtccyct ggatccaatc ctcatgatca yactgagmtt 2940 tcttcagagt ttcaacctga gagtttgcaa gtgrtttctt ctattccacc tatgaatacm 3000 catgccatgc agacaagatc caaaaatggt atcttcaagc ctaaagcttt tctctmtaaa 3060 attgragctg atattccaat tgatttaact caggtggaac cytcaacata taagtctgcy 3120 ctttcatcct cagtatggtg tgcagctatg aaagaagagc tctcygcttt gcattctcaa 3180 ggaacttggt cattagttcc tcttccttca aacaagaatt tggttgggtg taagtgggtc 3240 ttcaagatta aaagagatgc wgatgggaac atttctmgat ataaggcacg cyttgttgcc 3300 aaaggcttca atcaagaaga gggtcttgac tatggggaga cctttagtcc agttgttaaa 3360 cctacaactg tgaggttagt tttggcttta gctgcacaat ttggttggtc tttamggcaa 3420 ctcgatgtga agaatgcttt tcttcatggc attttacaag aagaggtcta tatgtctcaa 3480 cctccgggtt ttgttgactc tcarcagtcc tctcwtgttt gtcggttaca taagtctcta 3540 tatggcttaa aacaagcccc aagggcttgg aatgagaggt ttaccaattt tttgccttct 3600 ttgggttttc ttacaacatt ttcagactcc tcattatttg tgaaacatgt tggcaamtct 3660 gtggtcattc tcttgctcta tgtggatgat ataatcatca caggaagtgc tactgcagct 3720 attactgatg ttatccaggc tttagctcag gaatttgaya ttaaggattt gggactcctt 3780 cattacttct taggcatcca aattacttat cattccactg gattatttct ctcccaggct 3840 aagtatatta ctgatttgct tcataagact gatatgagtc tttccaaacc gtgtcatacc 3900 ccttgtctgc cgtwtaccag gttmcttaaa gatgatggga caccctttca caatccagca 3960 ttgtatcgca gtgtggtggg ggctttgcaa tatcttacat ttacaagacc cgacatygct 4020 ttctccgtgc atcaggtatg tcagttcatg cattgtccca tggagtctca ttttcttgct 4080 gtgaagagaa tcctyagata tytgaaaggc acgatggatt atggtgttcm cttcagcara 4140 ggagatttat gtttacatgc cttcagtgat gctgactggg ctggggatcc yaatgacyga 4200 cggtcmacta caggtttggt ggtctatttg gggtctagtc ccatttcttg gtcttscaag 4260 aaacaaaata cartttctaa atcctccact gaagctgaat accgagcmct ttcatcyact 4320 actgcagaga ttgactggat caagcaactt ttgcagtttc ttcggattga tgtttcmtgt 4380 cctgtcactt tattttgtga caatytrtct gctatagcct tggcttataa tccagttatg 4440 caccaamgga caaagcacat tgaggtagac atccattttg ttcgagaacg ggttgccaag 4500 aagctgcttc aacttcagtt tgtttcttca aatgaacaat ttgccgatat tctcaccaag 4560 ggattgtcta ctccattgtt tcagacccac tgttccaatc tcaggttgag caaacctcct 4620 cctgtgattg agggggga 4638 // ID Copia-58_VV-LTR repbase; DNA; EDCOT; 340 BP. XX AC chr8; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-58_VV_; KW Copia-58_VV-I; Copia-58_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-340 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr8; Positions 16313706 16313367. XX SQ Sequence 340 BP; 86 A; 49 C; 76 G; 129 T; 0 other; tgttgagttg aattgatttt ttctttgtaa tatgttgaag ctatccttgt aaaacatggg 60 ctaaggctaa atgggccgag ttttattgtt ttaaatgggt tttagggtta gggttggtat 120 ataataacta gaactcttgt aaactctata aataggtggc ttgggaaaac atatgtaagc 180 aagaaggtgc atgagccgtc tttcaatagt gaaatagaat tgctcgctct ctgcccgtgg 240 acgtagatca ctttgatcga accacgtaaa tcttgtgttt gttcttgtga gattgttttt 300 cttccattat tccgcgattc tattgtttgc ttgcttatca 340 // ID Copia-60_VV-LTR repbase; DNA; EDCOT; 238 BP. XX AC chr14; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-60_VV_; KW Copia-60_VV-I; Copia-60_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-238 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr14; Positions 10834973 10835210. XX SQ Sequence 238 BP; 55 A; 34 C; 39 G; 110 T; 0 other; tgtcaagatt taagttttct gattgtttag tttttttttg ttttaataat ccctattaag 60 cagggtagtt tccaactttg acttattctc tactctttac cacattattt gttagtgtaa 120 aacgtgggtt gtttttctta tcaattagtt attgtaaggc tattttatta gcaccggttg 180 ttgatcaata gaggtggatt tttcccagtt ttgttccatt cagttttgat tcacaaca 238 // ID MARINER1_BV repbase; DNA; EDCOT; 3909 BP. XX AC AJ556159; XX DT 16-MAY-2005 (Rel. 10.05, Created) DT 16-MAY-2005 (Rel. 10.05, Last updated, Version 1) XX DE Beta vulgaris mariner-like transposon (Vulmar1). XX KW Mariner/Tc1; DNA transposon; Transposable Element; KW Interspersed repeat; mariner; Vulmar1; transposase; MARINER1_BV. XX OS Beta vulgaris OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC Caryophyllales; Amaranthaceae; Beta. XX RN [1] RP 1-3909 RA Jacobs G., Dechyeva D., Menzel G., Dombrowski C. and Schmidt T.; RT "Molecular characterization of Vulmar1, a complete mariner RT transposon of sugar beet and diversity of mariner- and RT En/Spm-like sequences in the genus Beta."; RL Genome 47(6), 1192-1201 (2004). XX DR Genbank; AJ556159; Positions 1 3909. XX SQ Sequence 3909 BP; 1391 A; 701 C; 764 G; 1053 T; 0 other; cttcctccgt ttcaaaatag atgggacatt gtgattaaaa cggactccta ggcaaaattt 60 cataagtatg tttaagggag gtagattaaa tctagtggtc ccatgtgaaa aggagggaga 120 aaataaaagg ttggggacca catgtttttt gcccgccagc tttggggaac aaaggggacc 180 actttttttt ccctccatat ttttggaagt acattaacct tttacacatt aaacctttac 240 aaccaaaaca gaaaattttg ggttccctct caaatttgaa accacttaaa atttaagtta 300 agtttaccac cagatttttg ttttccctat ttaaggggta caaacattcc ccaaaaaaat 360 tagtgttcct accaaccaaa ctgcttacat aattaaggag aacattctct cctacacatt 420 cactgcacac acgcagcact atattaagca accaaaatct aaggcaaaaa aattcagttt 480 gttaatctct tcgtcatttg ctgcatctgg acaaaatgga tgcagcacaa gaaatgtaca 540 atgctgttgt tgatgaagag gacttggatg agtactatct acaactactt gaagagattg 600 tgcccaactt caacagtcaa atctcctctg aaccagaatc tgctgcacaa gaccaaaaca 660 gaaaaattaa acctgagatg aagcatgaaa agagaaggaa agctgtagat gaattgttaa 720 ttatggaaga gaacggaata ttaccatatg tgcattgaag aagacagcag agaagtatgg 780 tgtttcaaga cacacaatag agagattatg gaaaagagca tgcaatcaaa gagttacagg 840 tgatgtcatt gatgtcaggt caaggaaaaa gggaattgtg gggaggaaat caatggaata 900 tagtgaggag ttctccaatc agtgccactg aatttacgca cttcagttag atgctttgct 960 ggggcactta aagtgtctcc ttcagcaatt tatagactgc tgaagaaggg gaagctcaga 1020 agccatacaa gtagtaacca tcgaagtttg acagagactc acaaattgga gaggatgaag 1080 tgggtgctat cccacattct acctgcacac ccactgtaca agcagagttt atacacatgg 1140 agaacatcat acacattgat gagaaatggt tctacttgaa cccagataca aggagatttt 1200 atttattgcc aagagaagat gatccatata gatgttgcca atcaaagaga ttcaaaatta 1260 aagctatgtt tataggggta gtatcaaaac caatgtatga tgctcaaggt aatctcattc 1320 atgatggcaa gtttggcatc tttccttttg tagagagggt ggcagcaaaa tacactacca 1380 aaaacagaga taagggcact attgaaacaa aggttgttga gaggatcact cagaaggtca 1440 tcagagacat gattatacag aatgtactgc catctataat gagtaagtgg cctgctggta 1500 tgtccaagga tatattcatc caacaggaca atgctaggcc tcacatacaa ggaaatgatg 1560 aggcattcaa ggcagcagca actcaaaatg agttcaacat catgctcatt caacagccac 1620 ctcagtcccc agatttaaat gttcttgatt taggtttttt tagagccata caagctttaa 1680 tgtatcaaac atttcctaag aacatagatg agctcataac aaatgtgcaa gatgcatatg 1740 acagatttga tcctagtgtt atgaaataca catggttaca attacagtgg attatgattg 1800 agattctaca ggttagagga ggtaataatt acaataaccc acatcatggg aaggcaagat 1860 tagaaaggtt gggtcttctc ccaaaaactg tcaaatgtga tcaagttatt gtggatgaag 1920 ctgtgcacta tttgaatgag aagttaccaa atgaaagtga acaacttgag tactttgaca 1980 atgaggggtc attgatgaag attaaaatga atgtatgtgt gcattttttt gtgaagataa 2040 caattttttg gaagtacatt aaaagtgggt gaattttggg aagaagatag tttttgcaaa 2100 gaacatgttt tatttggtaa atacataaca atgccattga agtaggaact tttgttaaac 2160 tgcacaccaa acctaaatta tgtacatgta gtggaggaat gtaggtttgt aaatgcagtt 2220 tatatcaatg attatgctta ttctatttac agttatgttt cttatttaca ccattgttat 2280 tgtttttttt agttttaggg atcgaggcat acttatgaat tagcaaagaa ccacaatcac 2340 aattactcat gtaaagacat catttgacct tctacaatcc atcagggaga cttttaactt 2400 atgaaggagt tcaaatcatt aacacctcaa ggcacaatgc cgagcaaatc attgactcac 2460 ttcaagtttt tggtgagtcc ttcatcatat ggattaggga gtgattttaa aaacaggggg 2520 actcaatata caacaacaaa ccaatcccgc aacaaaagtg ctttctatat tcataagcca 2580 tcattcatca atttgacatc acccttaatc tctaggtcaa gctcaacata accaataatc 2640 agccaacaca accacagctc ccaagaacac aagcatcaaa cacaatccaa gcttatccaa 2700 cagcaagcca aacattgaac atcaccaacg gaaacattca acatcaccaa tcagattcaa 2760 gatcaccaac acaagccaaa tatacataac cattaaaaca gaagaacaca aaccaacaac 2820 aacaaatatt aacatgcaaa aaaacgcaag taaataagga taacaaaggg acagtagtca 2880 aacctccctt actgtaattt ttgttcaaat ctgtaccacc aatcactatc cccctcctct 2940 ttgaaccaga tttcatgacc gatttactcc cactaccacc actttcttta aaagaaccca 3000 ccttagcctt tccttttcgg ttgtatgaag agtaattcat ctcagaagcc atacaaggaa 3060 gagcacaaac agtaatgcat tcagaattag gtttttttga gacagagagt gggggtaaag 3120 tgggagtttt gaaaaccact ttttctttca catcttcctc ggaactcacc agatatataa 3180 tttcttcttc ttcagaggac tcacttggta aatcatcagg aaaccaaggt tccatcatgt 3240 ccttgatttc ctcaagaaca acacccaaag ctttgcaagc agttggaccc atacactttg 3300 aagcagcccc tgaatcgtaa agtctatggg gccaaggaga accattttca attgatcgaa 3360 tgacgtcaat tatgaacatc gcctctccct catccgtagt ttcaaaatgc gcatcaatca 3420 aaggttccaa attgatatca caaaccattt ttaaggagag agaaaatgat tttcaagcaa 3480 aattgcgaag aacagaaaga aaaacgaaga tgaggagaga gagagcgaag atctgaagag 3540 ttggtgtttc aggagagaga gtagatctga aaaacttata gagagatgag cagttatgag 3600 ggagagggag atgagcagtt atgagggaga tgaatgatga tgaagaaccc taggttagat 3660 gaagaggtgg ggtgggaatt caattggggg tagttggtgg gtcataaaaa atggtgggaa 3720 tcgttagttt taggttagga ttaatcggat tattagatgt agattaatgt acataacaca 3780 agttagtaag ggtaaaatgg taaaattgta aggcaaaagt tactaaataa ggaaaaaaaa 3840 aacaatgtat catctatttt gaaacaccca taaatagaca atgtcccatc tattttgaaa 3900 cggaggaag 3909 // ID HARB-1N2_Mad repbase; DNA; EDCOT; 1030 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW HARB-1N2_Mad. XX NM HARB-1N2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1030 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1495-1495 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 29-bp long. XX SQ Sequence 1030 BP; 271 A; 202 C; 240 G; 316 T; 1 other; ggccatctcc aaccgaatga gggccaaagg gctcccttta gccctatagt cctgcaagaa 60 attatatttt aatgaacagt gctaggccat attttatacc atctccaacc gagggggcca 120 aagggccata ggccaaacat agccatttga caaaaaatca tctccaaccg agggggccaa 180 agggtcatag gccaaacata atttattatt ttaattaaat taatatggtt aattaaatta 240 aactaccata ttaaaataag gttttcggac atattttgag tgtcacttgt cgccaaatga 300 ataagcctcc ggatttctta tctttatata atctcaataa ttttttggat aggatttcga 360 gtgacacgtg tcgctaacgt gagtaactct ccagatttct tatctttatg taatctcaat 420 aatttttcgg ataggatttc gagtgacacg tgtcgctaaa gtgagtaact ctccagattt 480 cttatcttta tgtaatctta ataatttttc ggataggatt tcgagtgcca cgtgtcgaga 540 tgtaattggt tgtgcaaatt ttagatagga ttcttatcta cgtgacactt cttatcttca 600 gctttcaatg ttgtaggaat ggtgtaggta tttataggaa aaaaaattag attttttttt 660 ttaaattcgt ccaaaaaaaa ttcaaattcc aacggtaacc tgacggcagc atgacgttag 720 ctagccgttg ctagctggcg tcatgctgac gccaggtagc cgttggcatt caaatgggct 780 gagctggagg gctggcaaaa tgtcaagctt gacattctgg mgctggaggg ctggcaaaat 840 gtcaagcttg acattctggc gctggagggt ggctggctgg aaatggccag cccgctggcc 900 tgatttgggg gtttgggccc ggtggggccc acaagccctt tggcctagcc ctcggttgga 960 gacggttttc gtgtcattcc gagctatttt tagccctatg accctttggc cgggtcggtt 1020 ggagatggcc 1030 // ID LTR-7_Mad-LTR repbase; DNA; EDCOT; 112 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR-7_Mad-LTR. XX NM LTR-7_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-112 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1791-1791 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 112 BP; 23 A; 22 C; 28 G; 39 T; 0 other; tgttgagagt tgtcccacat cggtgaggga caaggtttgc tatgtgctta tatggtcttg 60 ggctactccc catattgcca attggtttta tggtggaacc tcaatttcat ca 112 // ID HELMET3 repbase; DNA; EDCOT; 6573 BP. XX AC AC137702; XX DT 29-DEC-2006 (Rel. 11.12, Created) DT 03-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE Helitron-type element. XX KW Helitron; DNA transposon; Transposable Element; HELMET3. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-6573 RA Jurka J.; RT "HELMET3: Helitron-type sequence from barrel medic."; RL Repbase Reports 6(12), 625-625 (2006). XX DR EMBL/GenBank/DDBJ; AC137702; Positions 32657 26085. XX CC The sequence may be incomplete. XX FH Key Location/Qualifiers FT CDS 2615..3685 FT /product="HELMET3_1p" FT /translation="MIHGPCGPQNKSSPCILIKKCTKYFPKKFVDNTVIDS FT DGYPVYRRRDNGVFIKKKGESFVDNRWVVPYNRKLMLKYNAHINVEWCNQS FT RSIKYLFKYVNKGHDRVTATFYQGGDACYDEIKMYYDCRYLSACEAVWRIF FT SFDINYREPSVERLNFHLEGEEPVVFEDHEDIADVIKKPHIRDTKFIAWFE FT ANQKYPEARDLTYGEFPLKFTWKASQRKWTPRQRGLSIGRIHFVAPGCGEK FT FYLRTLLNYVKGPLCYDDIYTVGGVKYNSFKEACFALGLLDDDKEFVDAIN FT QASFWGTASYMRRLFVQLLVTNQFAQPEVVWSKTWQNLSDDMLHRQRRASQ FT VKYLKQFVLLNFHT" FT CDS join(4144..4779,4635..5723) FT /product="HELMET3_2p" FT /translation="MKEDYPTMPRTDISLIHESRNRLIYDELNYNQQLLEI FT EHKKLMSTMTAEQKNVYEKIISRVDDNLPGIFFLYGYGGTGKTFILRALSS FT AVRSRKEIVLTVASSGIAALLIPGGRTAHSRFGIPIIVDEISTCGIHPKSP FT LAKLVCKAKLIIWDEAPMMHKHCFEALDRSLRDILRVQNNGRTASLLVERL FT WYLVVTSDKSFPSYLKLIDKRLSTRSQLEGYPSCSKQWPNSIPFGGKVVVL FT GGDFRQILPVIPKANRQEIVNASINSSYLWPFCEVLTLSTNMRLLHGSSSS FT DIEERNQFSEWVLGIGDGSIGDANDEAIDIEIPDDLLIQSSGDHIASIVDT FT IYPSLLDERHDPSYFQDRAILTPKNATVEEIKDYVMSLIPGEEKTYLSCDS FT TLSTNSAASRPDDIHTREFLNTINASGIPNHKIKLKVGVPVMLLRNLDPTA FT GLCNGTRLIITKMGRYVLEGKVITGSNIGDTVYIPRLSLTPSDTRIPFKFQ FT RRQFPISVSFAITINKSQGQSLQKVGIYLPQPVFSYGQLYVAVSRVTSRNG FT LKLLLIDEDNNCINTTSNVVYHEVFRNL" XX SQ Sequence 6573 BP; 2072 A; 1104 C; 1330 G; 2067 T; 0 other; gaagcttacg cctattaaac ctgggaaata cattctgaag caaaaattca gtgatggata 60 tggtaaggaa aactattcac aaacaaagga taatcatgca atggcaatag atagttgtgg 120 aatggttgaa gaggatgaag ttccaaccaa agtgcatggt aaattgtcat atgaacttat 180 tataatcaaa cttctgtatc atatatgctt acattttgct taataaatta attagtattt 240 tgggattcat ctgagttgta tttctctaat actagatgcc gagcaacgcg ataaacacaa 300 attgggattc acacaagttg tgtacttacc gatggagtgc aatgagaacg gtgaggtttc 360 cgacattcct gaaaacaatt atggtaattt gacatcagaa ttgccactgc gttcatgaat 420 tgtctaattt tcccaggcca ggtgaatttt aatatttgat ataacaacaa cttcttacac 480 aattcctatg atgcagatgt agaaggcaac atagcagaaa cagttgatga tggattgagt 540 ttccttcatc atgaagattt cgaggctgag tgttatcaga acaatgaagg ggaggatata 600 tctgataatg aatatggtat gagtggaaat cattatttaa ttccaattct atacacaaaa 660 aatcaaaata atgtgaagtt ctgcggaaac taacttttgc ttttcttaac caatttataa 720 gatgatgttg aagatgaaga cgaagtagat ggagccaatg acacaggtta tttttaaact 780 ttctaccttt tgcagcataa agaaaatttg tttggacaat tatgttaaca agtctcatat 840 caaattagca tatgagatat gtatcacagc aaacttatgt gtatgcaaat ttaacgcaga 900 ttactttcaa gtgggagagc cacgttttgt ttgtgaatca tgtggtgcat taatgtggta 960 tgaggaaagg gttggaaaac atcgtgacac atcaaatccc gaatttagtc tgtgttgtat 1020 gcaagggcgt atagaaatag caccatttaa acgtcttcct cgccaactgt atgatctata 1080 ccatgagaac gacaagaaaa gtaaattctt tatggaaaat ataagatcgt tcaatagtat 1140 gtttgctttt acctctatgg gagcaactat tgacaaaacc aaaaacgatg gaaatgctcc 1200 accagtattc gtcttgaacg gagaaaacta ccaccaaatt ggtagtttgc tgcccaaaga 1260 aggtgaccaa cctaagttcg ctcaattgta tatttatgat acggataatg agctcagcaa 1320 tcgcatggca gcagtagggt acgtcggtaa atattttcaa atgtcattat attaacaagc 1380 atttatttgg tagaaatatt atatgtttcc gttcataata tactgattgt ataatttggg 1440 ggaattactt tgacaagatg aaggatgata aaaactcaat gaaaagagat attgtcaagg 1500 agctgcgcca tatccttgac cactcaaatt catttgtcaa gtcgtataga caagtaaggg 1560 acacgttaac acaagaagat gctccacata tcaagctgcg gattttagga aagaggggtt 1620 atgatggtag gcgttacaat atgcctactg cttcggaggt tgcagctttg gttgtagggg 1680 attacgatgc cgccgacttc gaaagcgtat ttccgtgttc gaaacatctt atttgccatt 1740 gcaataccct ttaatctttt caaggggcga agatgggttc cgaagagaca tcaaattttt 1800 agatagacct acaaaaaagc ctattcagcg tacttatgtt tcaatgaaag agtggtttgc 1860 gtataaaatt caacaaaggg atatattaca atctcatctg ctatggtccc gacgtttgtt 1920 ccaacaattt ttagtcgatg catacagcat gattgagtcg tggcgtttga agtggtatag 1980 agaccatcaa aaagaggtga gagcagatct atacaaaggg cttgccgaag cggtgcttag 2040 aggtgagaca agtccagcca ctgctgggaa gcgagttgtt ttgccatcaa aatttgttgg 2100 aggggcacgc tacatgattc agaactatca agatgccatg gcaatttgtg gctgggtcgg 2160 ttaccccgat ttgtttatca catttacgtg taaccacaaa tggccggagt tacttgaatt 2220 tcttaagaaa cataatctta aacctgaaga tcgtcctgat ttggtgagcc gtcttttcaa 2280 aataaagtta gatcatctca tcaaggagat aaagaagggg aaaattttcg gcaaagttaa 2340 agcaggtatt ttgacattta gtactactca ttatttattc aaaattatga tttaacagta 2400 tggtggtttg ttgtgatgat tttactattt tgtcttttat gcagttatat atattattga 2460 gttccaaaag cgcggactgc cacatgctca tattttagtg ttcttgcgtg ctgagtttcg 2520 atgtcttcat cctaatcaaa tcgacaaaat tatatcagct gaaattcctg ataagaatcg 2580 tgaccccaag ctatacgaaa tagttgcgtc gcttatgata catggtcctt gcggtccgca 2640 aaacaagagt tcaccatgta tattgattaa aaaatgcacc aaatactttc ctaaaaagtt 2700 cgtcgacaac actgtcattg attctgatgg ttacccagta tatagaagaa gagataatgg 2760 tgtgtttata aaaaaaaaag gtgaatcatt tgtcgacaat agatgggttg taccttacaa 2820 ccgtaaacta atgttgaagt ataacgccca catcaatgtc gaatggtgca accagtctcg 2880 gtcaatcaaa tatttgttta agtatgtaaa caagggtcat gaccgggtca ccgcaacatt 2940 ctaccaaggc ggagatgcat gttacgacga aatcaaaatg tattatgatt gtagatatct 3000 ctctgcatgt gaagcggttt ggaggatttt ttcatttgat atcaattata gagagccatc 3060 tgtggagcga cttaatttcc atcttgaagg tgaagaacct gttgtgtttg aggatcatga 3120 agacatagca gatgtcataa agaaacccca tatccgtgac actaagttca tagcatggtt 3180 tgaggcaaac cagaaatatc ctgaagcaag ggacctaact tacggtgagt ttccattgaa 3240 atttacttgg aaggcatcgc agcgtaaatg gacaccgcga cagaggggtc tttcaattgg 3300 taggattcat ttcgtggctc ctggttgtgg tgaaaaattc tatctcagga ccttgcttaa 3360 ctatgtaaaa ggtcctcttt gctatgacga catttacaca gttggtggag taaagtataa 3420 ttcgtttaag gaggcctgct ttgcgttggg tttattagac gatgataaag agtttgtaga 3480 cgccattaac caagcttctt tctggggaac tgccagttat atgcgccgtt tgtttgtgca 3540 attattggta acaaaccaat ttgctcaacc tgaagtcgta tggagcaaga cttggcagaa 3600 cttgagtgat gatatgctac atcgacaaag aagggcgtcc caggtaaaat atttgaaaca 3660 atttgtattg ctaaattttc atacttagtt aatatatcag gaagtaaata tgatgcaaat 3720 atatatatat atatatatat atatatatat atatatatat atatatatat gttgttctgt 3780 tttatagtgc atagagtgtt gttctgtttt caatgtacat agttgtgtgt tatataggtt 3840 atttttgaaa atcatgcagg taataatcca gtatagtata tatattgtga gctaattcat 3900 tatagtttaa ttcatgcaac taataattgg ttatgcgtgt agtttatgtg gtttaattca 3960 ttatagttta aatcatgcac ctaataattc agtatagtat atataatgtg agattagcag 4020 cacgcatatt ttttttttac aaaacttgaa tgtttgagtg cagatctggt gctggatgat 4080 gaccagctga agaattacac actagcggaa attgatagac tgttacgcag tcacggaaag 4140 agtatgaagg aagactaccc aaccatgcct cgaacagata tctcccttat acatgagtca 4200 cgaaatagat tgatatatga cgaactgaac tacaaccagc agttgcttga gattgaacat 4260 aaaaaactaa tgtctacaat gacagctgag caaaaaaatg tttacgagaa aatcattagt 4320 agggtggatg ataaccttcc tggtattttc tttctttacg gatacggtgg gacaggcaag 4380 acgttcatct tgagggcgtt gtcatctgcg gtacgctcga ggaaggaaat tgtattaaca 4440 gttgcgtcaa gcggaattgc agctttactt atacctggtg ggagaaccgc acattcaagg 4500 ttcggtatac ctattatcgt agatgaaata tcaacatgtg gaatacatcc taagagccct 4560 ttagctaaat tggtttgtaa ggcaaaactg attatatggg atgaagcacc tatgatgcat 4620 aaacactgtt ttgaagcact agatcgcagc ttgagggata tccttcgtgt tcaaaacaat 4680 ggccgaacag catccctttt ggtggaaagg ttgtggtact tggtggtgac ttcagacaaa 4740 tccttcccgt catacctaaa gctaatagac aagagattgt aaatgcaagc attaactctt 4800 catacctttg gccattttgt gaggtactaa cattgtcaac aaacatgcgt cttctacatg 4860 gttcttcgag ctctgatatt gaagaaagaa atcaattcag cgagtgggtg ctaggtatcg 4920 gtgatggtag cattggtgat gccaatgatg aagctattga tatagaaatt ccagatgatc 4980 ttctcattca aagctcaggt gatcacatcg cttctattgt tgataccatc tatccatcac 5040 tactagatga aaggcatgat ccatcgtatt tccaagatag ggctatacta actccaaaga 5100 atgccactgt ggaagaaatt aaagattatg tcatgtcttt gatccctgga gaagagaaaa 5160 cttatttgag ctgtgattcc accctttcaa ccaactcagc agcaagtagg ccggatgaca 5220 tacacacacg tgagtttttg aacacaatca atgcttctgg aattccaaac cacaaaatca 5280 agttgaaagt cggagtacct gtcatgttgt tgagaaattt agacccaaca gcaggtcttt 5340 gcaatggaac acgcctgata ataacaaaga tgggcagata cgtgcttgag ggcaaagtca 5400 taaccggcag caatattggg gatacagtct acatacctag attgtcgttg actccttctg 5460 atacaagaat tccattcaag tttcaacgtc ggcagttccc aatttccgta tcgtttgcaa 5520 taacaataaa taaaagccag ggacagtcgc tacaaaaggt tgggatatac cttcctcaac 5580 cagtcttctc atacggtcaa ctatatgttg cggtttcaag agtaacttcc aggaacggat 5640 tgaaactttt attgatagat gaagacaaca actgtatcaa cactacatca aatgtcgtat 5700 atcatgaagt gttccgcaat ttgtgaccaa tgaattctga agcacataac atgttgcggc 5760 tttgcttgca tatctatcca aaaatcatgc aggttagttc ttatctgata tagcccattg 5820 ctttcatatt atagttttta aatattgttg agtacttaag ttattctcag acttatgatt 5880 ttttttacat tgtttcagat ttgtatgtgt tgttgttagc gatactgaca acaattcagg 5940 ggcctcctat cacttatttt gtctactcaa ttatattgtc gatgatccat attaactttt 6000 cccaatttga aggttcattt tattatcctt gctgccgagc ttaccatgtt taacccagtt 6060 tttgtcggtt aaaatcatca ctcagaaaat ttaaaaaatc atgcttttta ttttgtatac 6120 aggttgtttg tgagcagaga tctatttgtt gtgaccatgc gctgctgcat acaccgtcat 6180 ttgctgattt cataaattgt gatattacat ttcaattgtt gcttgattat tgtatcctct 6240 catgaatggt gtgtatgcct attaatggat atttgtggga aaactgagac tcctatctgc 6300 tgttaagttt tgcaacatag attgttgatg catttttcat attatccatt tgtggttggt 6360 tgaaagttgc ttttgagcaa taacaatatc ataattcgac cttgcgtatt atattacctt 6420 aaaccgataa aacgtgatac atgattacgt gattatattt aactcgatca aattacccta 6480 tgaaaaaaat tatgtacaac atttagatca ataagttatt ttttaatatt atataacccg 6540 ggcggtagca caggtggaaa atctagtatt att 6573 // ID SHAGY_LTR_MT repbase; DNA; EDCOT; 297 BP. XX AC AC136141; XX DT 12-JAN-2007 (Rel. 12.01, Created) DT 12-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE The LTR sequence of LTR retroposon, SHAGY_MT, from Medicago DE truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW terminal; Interspersed; repeat; SHAGY_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-297 RA Shankar R. and Jurka J.; RT "SHAGY_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 87-87 (2007). XX DR EMBL/GenBank/DDBJ; AC136141; Positions 78431 78727. XX SQ Sequence 297 BP; 83 A; 52 C; 50 G; 112 T; 0 other; tgataggatc ctagactcac ataggagtaa aataattact actaaaccag tttggactaa 60 aagttatgtt cttaagtagt ttgggcctcc ttatgattat tgtattccct tgtaataacc 120 caggcccatc ttgtactagg ttttgagact agacctatgt ttaaaagggg agctgcgtct 180 ctatgaatga tatgaacatt ctgcaattat cttatttttt cttaatttct tgctgctttc 240 tttcttttaa tttggcatag cttagaaatt gcttgttaac ataacgtgaa cccatca 297 // ID Gypsy5-PTR_I repbase; DNA; EDCOT; 4423 BP. XX AC scaffold_3580; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy5-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4423 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4423 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 334-334 (2007). XX DR Genome; scaffold_3580; Positions 5277 855. XX CC Positions [3321-3809] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 1560..4421 FT /product="Gypsy5-PTR_I_1p" FT /translation="MQDTKGVQSPSMSQVLAKYPEIFDEPTQLPPKREIDH FT TISLKEGIEPVNVRPYRYAYFQKAEIEKQVQEMLNSGLIRPSTSPFSSPVL FT LVKKKDGSWRFCTDYRSLNAVTIKDRFPIPTVEDMLDELHGAAYFTKLDLR FT AGYHQVRVQPSDIHKTAFRTHNGHYEYLVMPFGLSNAPSTFQAIMNAIFRP FT HLRKFILVFFDDILIYSPTWEMHLHHVTQTLDILKQQQFYLKASKCAFGKQ FT ELEYLGHIVSHQGVKVDSNKIEAMVAWPQPANISELRGFLGLTGYYRKFVR FT NYGLIARALTNLLKKGQFSWNAEAEEAFQTLKKAMTTTPILAMPNFNDTFI FT VETDASGNGIGAVLQQQGKPIAFMSRALGVSKCSWSTYAKEMLAVVEAIRV FT WRPYLLGQHFIIQTDQRSLKYLLEQRITTPEQQKWVAKLLGYDYEIQYRPG FT RENSAADALSRRPASPTLHNLFVPQLAIWEEIKHAATTDDYMAVVSNLVQT FT QPEGPFTARNGLFFFKGRIVVPSDVTLRNKLIYEAHDTKIGGHSGVLRTFK FT KVATQFYWPSMHKSVQEYVKSCDTCQRTKSETLPPAGLLQPLSIPCQVWDD FT ITIDFITGLPLSQGKDTIFVVVDRLSKYAHFMSLSHPFTAKVVADKFVEGV FT VKLHGMPRSIISDRDPIFISKFLQEFFTMSGTKLKMSSAYHPQTDGQSEVV FT NRCLEQYLRSFVHQWPRRWHSFLHWAELWYNTTFHASTGMTPYQALYGRPP FT PTLPEYFDGTTPVHEVDQALLHRDELLLQLKQHLTTASNRMKQTADKNRRD FT VSFAEGDMVFLRLQPYRQSSAFKRAHQKLASRFFGPYPILQQVGRVAYRLQ FT LPEGVRIHPVFHVSLLKKYVGDATNTQTDLPPVSDDGGIILEPETILDHRW FT VKQGGKFITESLVQWKHLPPEDATWELTEFLCQQFPNLNLEDKVPLSGRG" XX SQ Sequence 4423 BP; 1288 A; 931 C; 1016 G; 1188 T; 0 other; attggtatca gagctggttt aaatggcgac taacaaagaa cgaattgaaa tgctggaggc 60 ggggctcggt ggagtgcaag aaggagtaca aagaatagag atgagcatga ctggaaaaat 120 gcaccagcta gaagaaacta tcaataaact gtcagaggcg ttgttatcca gcaaggcgtt 180 gttatcaaac aagggggaat caagccatag taacacaaac cgagagggca attctcgttc 240 aattcatgag gagaatgaag gaaacagaca agttttttct tcaaaaatgg ccaagcttga 300 atttccacga ttctctggac aagacccgac agaatggttt aatgtgtgga ccaattcttt 360 gaatttcaaa atactccagc caaccaaaaa atatcactgg cttctttcca tctggaagga 420 gaagcaaatc agtggtggca gtgggctcgt cggacatata gagaggaagg acgaatgatg 480 acatgggagg cctttgaaga ggaattatgg gcgagatttg gacctactga tggcgaggat 540 tttgatgaag ctttatcacg tataaagcag gtgggatcct tacgtgatta tcagagtgaa 600 tttgaaaagt tggggaacag agttcgtgga tggacccaaa aagctttagt tgggacgttt 660 atgggaggac ttaaaacaga aattgctgaa ggaattcgaa tgttcaagcc acagttgcta 720 aaggaagcaa ttagcctagc ctgcatgaag gatgaacaga tgaaagacaa cgccaattcc 780 tacgaccaac tcaagtcaat cgaacgccac tgtcgctacc accagcgaca cgtgcaacac 840 caaatgcacc ctttcgtaga ttaccatggg aagagatgca gaaacgtaga gcccaaggac 900 tctgttttaa ttgtaatgag agattcactg ccggtcataa atgccaagga atgcaactct 960 tgcttctgga gggcccaacc gggttcaata aaatcacata tgaagaagtt actgaagaag 1020 ctgacgtaga agaggcaaca agggaaattg atgaacctga gatcactcta catgctttaa 1080 caggatggtc tgcacctaga actatgcgtg tagatgccaa agtgggggtc ttcaaggcag 1140 tggtgctaat tgacagtggt tctacccata attttataag cactcgcatg gctgatcggc 1200 tgcggcttcc agtagttcca acagagacat ttacggttcg ggttgctaat ggggcacggt 1260 tacagtgtca aggaaaattc gaaaaggtac cggttcttct tcaagaaatt cctttttccc 1320 tgacccttta ttctcttccc ctagcagatt tagacattgt cctgggtgtc caatggttgg 1380 aaatgttagg gtctgtgata tgtaattggc gaactctcac aatgaaattc tattgggaga 1440 acttggacag acagctgtaa ggttttactg atcagcctat tcaagctgcc tccctaaagg 1500 agatttccaa agaatttcgt caaggacatt cggtatttgc aatttgccca cactccacca 1560 tgcaggacac aaaaggggtt cagtcaccga gtatgagtca ggtcttggct aaatatccgg 1620 agatcttcga tgaacctaca cagttaccac cgaaacgtga gattgatcac actatttccc 1680 tcaaggaagg aattgagcca gtcaacgttc gaccctatcg ttatgcttat ttccagaagg 1740 cagagattga aaaacaagtc caggaaatgc tgaattctgg actcatcaga cctagcacta 1800 gtcccttctc ttctccggtg ttgctcgtta aaaaaaaaga tggtagttgg cgtttttgca 1860 ccgactatcg atctcttaat gcagtcacta tcaaagatcg gtttccaatc cctacagtgg 1920 aagatatgtt ggatgagctg catggggcag catacttcac caaactagat ctacgagccg 1980 gttaccatca ggtacgagtg caaccttcag atattcataa gactgcgttt cgtacacaca 2040 acggtcatta tgaatatctt gttatgccat ttggcttgag taacgcacca tctacattcc 2100 aagctattat gaatgctatt tttcggcccc acttacgaaa attcatattg gtattttttg 2160 atgacatctt gatttatagc cctacttggg aaatgcattt acatcatgtc actcaaacct 2220 tggacatttt aaagcaacaa cagttttatc tcaaggctag taaatgtgct tttggtaagc 2280 aagagctgga atatttgggt catattgtct ctcatcaagg ggtgaaagtc gatagcaaca 2340 aaattgaggc catggtggca tggccacaac ctgctaatat ttctgagctg cgtggatttt 2400 tggggttaac aggatattac cgcaagtttg ttcggaatta tggtctaatt gctcgggctc 2460 ttacaaatct tctaaaaaag gggcaattta gctggaatgc agaggcagaa gaagcttttc 2520 agacactgaa gaaggccatg acaacaacgc ctatcttagc catgcccaat tttaatgaca 2580 ctttcatagt ggaaacagat gcttcaggta atggaattgg ggcagttctg caacaacaag 2640 gcaagcctat tgcttttatg agtcgagctc tcggtgtctc aaaatgttca tggtctactt 2700 atgcaaagga aatgctagca gtggtggaag ccattcgcgt gtggcgtcca tacttgctgg 2760 gacaacattt catcattcaa actgatcagc gtagtctcaa atacctactg gaacaacgaa 2820 tcactacgcc agaacagcag aaatgggttg ctaaattatt ggggtatgac tatgagattc 2880 agtatcggcc tggacgggaa aattctgctg cggatgcact ttctcgtaga ccggccagtc 2940 ctacactaca caatttgttc gtgccacagc ttgctatatg ggaggaaatt aaacacgcag 3000 ccactacaga cgactatatg gctgttgtta gcaacctggt tcaaactcaa cccgagggac 3060 cctttactgc acgcaatgga ttattttttt ttaaaggccg gattgtggtt ccttctgatg 3120 tcactctacg caacaaatta atttatgaag cccatgatac caaaataggg ggtcattcgg 3180 gcgtcttacg cacctttaaa aaggtggcca ctcagttcta ctggccttcc atgcacaaat 3240 cagttcagga gtacgtgaag agctgcgaca catgccaaag aacgaaatca gaaaccttgc 3300 cacctgcagg tctactccaa cctttatcta ttccatgtca ggtatgggat gatattacta 3360 tcgattttat taccggtttg ccgctttcac aaggtaaaga tacaatcttt gtggtggtgg 3420 atagactgag taaatatgct cattttatgt cattatctca tcctttcact gctaaagtgg 3480 tggcagacaa atttgttgag ggcgtagtca agttgcatgg catgccaaga tctatcatca 3540 gtgaccgtga ccctattttt atcagcaaat ttttgcaaga gttttttaca atgtcgggca 3600 caaagctgaa aatgagttcc gcataccacc ctcaaaccga tggccaatca gaggtagtca 3660 atcgatgtct ggaacagtat ttgcgcagct ttgtccatca gtggccacgt agatggcatt 3720 ccttcttgca ttgggcggag ctctggtaca atactacttt tcatgcatcc acgggtatga 3780 ctccatacca ggcactttat gggcgaccac caccaactct tccagaatat tttgatggta 3840 ccacgccggt tcacgaagta gaccaagcac ttctccaccg tgatgagctt ctgttgcagc 3900 tcaaacaaca cttgaccact gccagcaatc gcatgaaaca gactgcagat aaaaatagga 3960 gggatgtatc ttttgcagaa ggtgatatgg ttttcctcag attacagcct tatcgtcaaa 4020 gctcagcatt caaacgggct caccagaaat tagccagcag gttttttggc ccttatccta 4080 ttctccaaca ggtgggtcgg gtggcttata gacttcaatt accggagggt gtccgtattc 4140 atcctgtttt tcatgtgtcg ttattaaaga aatatgtggg agatgctacc aatactcaaa 4200 ccgatcttcc accagtatca gatgacggtg gaattatttt ggaacctgaa actatattgg 4260 atcaccgctg ggtgaagcag ggtggtaaat tcatcactga aagtcttgta caatggaagc 4320 acttaccacc agaggacgct acgtgggaac tgactgagtt tctgtgtcaa caatttccta 4380 atttaaacct tgaggacaag gttcctcttt ctgggagggg tat 4423 // ID GYCUME1_LTR repbase; DNA; EDCOT; 2646 BP. XX AC AF49972; XX DT 04-SEP-2005 (Rel. 10.08, Created) DT 04-SEP-2005 (Rel. 10.08, Last updated, Version 1) XX DE GYCUME1: Gypsy-type LTR retrotransposon from muskmelon (LTR DE portion). XX KW Gypsy; LTR Retrotransposon; Transposable Element; GYCUME1_LTR. XX OS Cucumis melo OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; OC Cucumis. XX RN [1] RP 1-2646 RA van Leeuwen H., Monfort A., Zhang H.B. and Puigdomènech P.; RT "Identification and characterization of a melon genomic region RT containing a resistance gene cluster from a constructed BAC RT library. Microcollinearity between Cucumis melo and Arabidopsis RT thaliana."; RL Plant Mol Biol 51(5), 703-718 (2003). XX DR EMBL/GenBank/DDBJ; AF49972; Positions 54497 57142. XX CC LTRs differ by deletions in minisatellite regions. No CC substitutions. XX SQ Sequence 2646 BP; 629 A; 581 C; 570 G; 866 T; 0 other; tgtaacgccc cgaattttcg aggtaaactc ttaccgtttt atgtaatttt tcgaaaattt 60 taatttttgg atttatttct gaatttctga aattttgata tttgtaaact catataataa 120 taatataata gtaattatat tattattatt attagtagtt atcattatcc ttatatatat 180 tataatatta atgttttcta ttatcattat tattattagt attattgtta ttaaataaaa 240 ttttttaagt taatatatat atgtatataa taatacttta tagattttta ttattaatta 300 atataattaa aaattaatag atatatatat ataaaataat atcctattta ttattattat 360 taaagttata tatatatata tatatatata tatatatata tatatatata tatatatata 420 tatatatata tatatatatt aataaatttt tttttaaaaa ctgtaaccct aacgcgcgcc 480 ccctctccct tttatttttt cgttttttcg gtctcttctc caccgcagcg ccgccgccca 540 tccattttct tcttcttttt ctcccttctt cgcccgtcgc cgccagccat ctctcccttc 600 gttttctcct tctccctcgt tctctccttc tcttctcctt cttcttcctt acagccccca 660 ccgacgacag caaacaccca gcccgccgca tcttcttctt ctttttcctt caccgccttc 720 aacacctcac agccgccgtc gcgcctctct gccaccatcc atctacagcc gacgcttctc 780 cagctttctc tcttcgttct accaccgccg gcatcatctc cgccatcagc ttgtgtgtcg 840 tccgcaaatc gccgccgcgt tccgccgccg ggagtgtgaa gattaaatcg gctccaagcc 900 ggctgtccaa gccgagccga gatcgcggtc caagccgagc cgaaatcgct gccaagccga 960 gccgcgatac ttgttcgagc cgagccgcca tccttgtcca agccgagccg agtgagccgc 1020 gagccgagcc gcgagccgag tgagccgagc cgcgagccga gtgagccgag ccgcgagccg 1080 agccgcgagc cgaaccaagc cgagccgcga gccgagtgag ccgagccgcg agccgaacca 1140 agccgagccg agccgagccg agccgagccg agccacctaa gccttccttc cttcatttcg 1200 gttcacggtg agttttcggt aaggtttgtt ctgatgaatt ccctaatgtt acctcgtccg 1260 attcgagttt gaatgttgaa ttaagttatg gccctacttt tctcccttga aggaagtgca 1320 gagttgacgc ctaagttctc gggttccgcg gcaggcctgg ttggagatag cttcttttcc 1380 tggggtaagt caacggatat cgcttctgac cttttaaaac ggcttctact aaagtcagct 1440 actaaaactt tcgtgtttcg tttaggtggt tctgttgagc gtggtttcga tctaggggca 1500 taaccgagta tcaggtaagg gttttcctac tactggaccc cgagtccagg ctaaaaccgt 1560 agtaatccac aggggattac acgttagtga ctgtactgaa tatctgtatg cgtgttgact 1620 gttaagtact gatattatat tctgtctgat gaaaatatac tgtgactgct gtttgtggat 1680 tgaaattata tgttgatgaa ccttaaagtt acggtttagt atgtattaaa cactgatctg 1740 gatgtggttc atgaagtttg gacggggaag gacagtgagt ccggttttgg ttgcttagtc 1800 gattggacct agggttcccc tattggtgtg cgaatcggta atgcgtaaag caactgaggg 1860 tgtagatgtt aatcctatac tatctgactg acaaagccta tggcgggact gtgatatgaa 1920 tgccgttgag atgtgactga tgtagacagt ttggtaaggg ctgaggggta acggttagct 1980 tcatctatgg ggtagtgtac cttacggata tgtgcatcct tcgggagcac tagactgata 2040 tgtgcatcct tcgggagcac tagactgata tgtgcatcct tcgggagcac tagactgata 2100 tgtgcatcct tcgggagcac tagactgata tgtgcatcct tcgggagcac tagactgata 2160 tgtgcatcct tcgggagcac tagactgata tgtgcgttct acggaaccac tagactgtta 2220 tgtagggtac ccccgaatag gaagttaact gttgttccct aacgggccca gtagtgggtc 2280 ccttactggg tatgtttata ctcacccttt cctttcttta acttttcagg taggggtaca 2340 gcgaggggca gaccgacgag aggcaggaag gatgcgtgaa ggccatatgg acgcgtctgg 2400 ttttcttttc gcttccgcta tgtattttgt cagaacattt tgactgtgat tttggactgg 2460 tgacttgaca ttttattttg tgattttctt tttgaattat ttaaaatagg gcccgaaact 2520 gtcttttgta aggtttatac tgttttaatg aatcgtatct ggtccgtttt aaattttacg 2580 ttgaatggtc gagttttggt atttggtagt gacctcagct tagtccggaa aagttgggtc 2640 gttaca 2646 // ID Harbinger-3_VV repbase; DNA; EDCOT; 3650 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE Harbinger-3_VV - DNA transposon from grapevine. XX KW Harbinger; DNA transposon; Transposable Element; PIF; TIR; KW Pifvine-3; Harbinger-3_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-3650 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 762-762 (2008). XX DR [1] (Consensus) XX CC Harbinger-3_VV (Pifvine-3 in [1]) is an autonomous DNA transposon CC from Vitis vinifera. CC Individual copies are more than 90% similar to their consensus. CC Elements are flanked by 3 bp-long target site duplications. CC Harbinger-3_VV has 23 bp-long terminal inverted repeat. XX FH Key Location/Qualifiers FT CDS join(543..866,956..1444) FT /product="Harbinger-3_VV_ORF1" FT /note="Harbinger-like ORF1. Protein with unknown FT function, usually present in elements of the FT Harbinger superfamily." FT /translation="MSQNVEISRANWTDPIQRKHFIDLCLQEANKGFRSGG FT GLKSSAWPRIAEELEKLLGKRYTSKQLKNGWDYMKRQYLIWSKMMTMTGHG FT YNSVTKTFDWPAEKWEEYLQKYPEAKQFRFKPLANVEELEALFGGVLATGS FT KNWSSGGVIASGAEESSTHSTSMPSETSISLEEDENLPRNTNDEAEGSKKK FT QKKGKKEQTQEEMNRIMNVLENFEGPSVKECMKILKRLLTYEDPLYYVAIN FT AFCKKKEYREVWVEMESDXERMGWIQSLRK" FT CDS join(1724..2302,2398..2632,2712..3169) FT /product="Harbinger-3_VV_Transposase" FT /note="Harbinger-like DNA transposase." FT /translation="MLLFHNYCFFIIDILMENLSHHSNSSSSSSSSEDEDT FT KLEVTRVLKKRLVVLLLKLLSDSSINKERVSTSSFTGSLFIQEFLNGSSST FT CYELMRMEKHGFISLCHMFREKGWLVDSKHLNVEEKMAMFLMTITHNLRNR FT LIKNKFQHSSQTIHKYFHEVLAAMVNFSKEMITPPSFNDSSNGISNRRLRQ FT IFKDVVGATDGTLIHACIPTNQQVPYRGRGRGECFQNVMAVCDFDMIFRFV FT VVGWEGTAHDSRVLTETIRNPQHNFPMPPSEKYYLVDAAYTHTRGFMAPYR FT NVRYWLSDFHSGGKAVGKEEIFNQCHARLRNVIPRAFGVVKARFPILKRMA FT PYSFTTQTKIVMTCFSIHNFLRQISVADRLFSEYDNEVELESDNANQNQNS FT TTSSFFAASDQEFMQQFRNQIANELFQVFS" XX SQ Sequence 3650 BP; 1217 A; 516 C; 607 G; 1309 T; 1 other; ggtggcgttt gtttttttgg ctttttactg aaatcaattt agttttagaa tttaggttgt 60 ttgttttttt aatttttaat gacttattac taaattttta aaatttttgg caaaatggaa 120 aaagccaaaa tatttggctt tttctattta gaaaaagcca gtttttgaaa cctcccctca 180 aaacccgacg cccaacactc gaccttagcc cacccatccc ctcaaagctt tctgcaactg 240 gcatcctcaa ccctcagctc atccccaaag cggtaatttc ttcattctcc tcctccatcg 300 ctctccatcc gagactacac agttggaaag acgcttcact ttcaatcaac attgttgatc 360 tgattgaagg taaccctcac ccaaatttat tttggatttt tggattttaa tagagcaatc 420 gagtctcatt tcccagtgct tctctctcta aaactctcat tctctttatt ttattttatt 480 ttattgtctc taattgaaaa ttgaaaatta atcattaatg ttagttggtt ttttgtacag 540 taatgagtca aaatgttgag attagtaggg caaattggac tgaccccatc caaagaaagc 600 actttattga tctttgtctt caagaggcaa acaaaggctt tagatcaggt ggaggtttaa 660 agtctagtgc ttggcctcga attgctgaag agttggagaa gttacttgga aaacgttata 720 cttcaaaaca acttaagaat gggtgggatt acatgaaaag acaatatctc atttggagta 780 aaatgatgac tatgacagga catggttaca actctgtaac caaaactttt gattggccag 840 ctgaaaaatg ggaagaatat ctacaggtag tttttttatg gatttgagtg aattttaaaa 900 ataattgtct tatatatgta tgcatgacta atttgttgtt tatcttgtaa aatagaaata 960 tccagaagct aaacaattcc gttttaaacc attagcaaat gtggaagaat tagaggcatt 1020 gtttggagga gtgttagcta ctgggtctaa aaattggagc tctggaggag tgatagcttc 1080 tggggctgag gaatcatcaa cacattctac atctatgcct agcgaaactt caattagttt 1140 agaagaagat gagaatttgc caagaaatac taatgatgaa gcagaaggtt ctaagaaaaa 1200 acagaagaaa ggaaagaaag agcaaactca agaagaaatg aatagaataa tgaatgtgtt 1260 ggagaatttt gaaggaccct cagtcaaaga atgcatgaag attttgaaga ggctcttgac 1320 ttatgaggat ccattatact atgtagcaat taatgcattt tgcaagaaga aagagtatag 1380 agaggtgtgg gtggagatgg aaagtgacva agagcgaatg ggatggattc aaagcttgcg 1440 aaaataactt tttaaatatt tgttttagat ttgtggaatg catatggtat atggcttata 1500 tgatgatttt aatttggtac atttggtttg tttgttttgg atatttgata catttaaact 1560 tttccaatta taagactttc tctctacatt ttatggatat ttgttttgga tatttgatac 1620 atttaaactt ttccaattat aagactttct ctccacattt tatggatatt tgttttggat 1680 atttattact catacattgt tataactatt tgattatatt gttatgcttt tatttcataa 1740 ctattgtttt tttataatag atattcttat ggagaatctt tcacatcact caaatagttc 1800 aagttcatca tcatcaagtg aagatgaaga tacaaagtta gaagtgacaa gagttttaaa 1860 aaaaagattg gttgtgttgt tgctcaaatt attaagtgac tcatccatta ataaggaacg 1920 agtctctact tcatcattta caggttcact tttcattcaa gagtttttaa atggttcatc 1980 tagcacatgt tatgaactaa tgcggatgga aaaacatgga tttatttctc tatgtcacat 2040 gtttcgagaa aaaggatggc ttgttgacag taaacatttg aatgttgaag agaaaatggc 2100 catgtttctt atgactatta ctcataatct tcggaatcga ttgattaaga ataaattcca 2160 acactcaagt caaacaattc acaaatactt ccatgaggtt ttagcggcca tggtgaattt 2220 ctcaaaagag atgattactc ctccatcatt caatgatagt tcaaatggta tctccaatcg 2280 tcggctaaga caaattttta aggtatatta ttttttattt ctaattattc atatcatatt 2340 tgtattattc tcatataaaa ataattattt atattttaaa gaattattac tatgtaggat 2400 gttgttggtg caactgatgg aactcttatt catgcatgta ttcccactaa tcaacaagta 2460 ccttatcgag gtcgtgggag aggagaatgt tttcaaaatg ttatggcagt ttgtgatttt 2520 gacatgatat ttaggtttgt tgttgttgga tgggaaggaa cagctcatga ttcaagagtt 2580 ttgacagaaa ctatccgtaa cccgcaacat aattttccaa tgcccccatc aggtaaatat 2640 tttattttca ttttatttaa tataatttgt atttattcat tataataatc aactcaatcc 2700 ttttttttaa gaaaaatatt atttagtaga tgcagcatac acacacactc gaggttttat 2760 ggcaccatat cgtaatgtgc gctattggtt gagtgatttt catagtggtg gtaaagctgt 2820 aggaaaagag gagatattca accaatgtca tgcaagatta agaaatgtca ttccacgtgc 2880 ttttggtgtt gttaaggcgc gttttccaat attgaagaga atggcacctt attcgtttac 2940 aactcaaaca aaaattgtca tgacatgctt ctccattcac aattttcttc gacaaatctc 3000 agttgcagat agattatttt ctgaatatga caatgaagtg gaattggaaa gtgacaatgc 3060 aaatcaaaat caaaactcaa ctacaagcag tttttttgca gcatctgatc aagaattcat 3120 gcaacaattc cgaaaccaaa ttgcaaatga actcttccaa gtgtttagtt aacttgtcat 3180 ttttagcttt ttaccattgt aagaaatgca atgtttagat attagcataa aatgtgatgt 3240 cttcagatat ttgaaaatat gtacttgaat tgttatgttt tttctttaat ttgatttagg 3300 ttttatcaat ccattatttt tcatattatt aagtttaaat attttatttt aattatataa 3360 aaaataagta tattaattat tttttgtaag aatgataatg ataaattatt tattataaca 3420 attttattat tttgaacttt tttagaaata agttaaatta tttttttttt aatacattaa 3480 aatattaaga tattggtttt cagcatataa aaaaacaaac agcttaatac ttaatagaaa 3540 aaaaatttta aaaaaacaaa caacttaata cttaatgcta ttaagcatta tttagtatta 3600 agttaaaaat aagttctatt tagaattaag ccaaaaaaac aaacgccacc 3650 // ID Gypsy-26_PTr-LTR repbase; DNA; EDCOT; 1802 BP. XX AC . XX DT 08-DEC-2009 (Rel. 15.02, Created) DT 08-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type non-autonomous LTR retrotransposon from Populus DE trichocarpa: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed repeat; Gypsy-26_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1802 RA Bao W. and Jurka J.; RT "Non-autonomous LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 233-233 (2010). XX DR [1] (Consensus) XX SQ Sequence 1802 BP; 564 A; 466 C; 340 G; 432 T; 0 other; tgttgctacc caatttttga cccatgtttt tgataaattt tcagaaaaaa ccaaaaatag 60 caaaaaaaca atgaaaaccc caaaaaaatg catttttgat atatttgcat cgtttttagc 120 attttcaacg tcatctcaga agaatttaaa ttttcaaagg tattttgaac gcgttcaact 180 tttaacgcgt taattttaca atcactgatt ttccttgttg agtcgacgtt gatattgctc 240 gctttaaaaa atacaaaaaa ataagaaaaa atcaaaatta caaaaaaaaa aagaagttga 300 gggaccaatg ttttggggac caagcacact tttcctataa atacaggtca caacacacac 360 aaaagggggg gagaaaattt acagggggaa cagagaaaaa ttagggaaac aaaaaaaacc 420 ctaaacctaa acccatctct ttcaaagcag ccgcgccccc tccctctctt tgaagaaaac 480 caaggcagcc gccccctgat ctgtcactac gatttccttc cccacagcag ccgaccacag 540 atcaacatcc cctctccccc agctccacta tcttcttctc ctccctcagc cccacatcac 600 gaccttcccc cttcagccgg cacaaactca cggtcttctc tcccaaccaa gaggcagccg 660 ccgctctccc tctccacaac agccgtcccc atcttccccc ctctagcccg atccctctcc 720 atcaccagca gtcctctgct tgcctcacgc cagccaaaga gaaagagagc agaaggaggc 780 cagcttacgc ggcctctccc ccctcctcag acctccgcct gcctcaccgc caaccaaaga 840 agaaagaagg gccgacgatc catccatcca gcaggcctca accgtgcgag ccgccgggca 900 gccgctcccc actccccaca gcaacaccgc ctccctcttc tcaacgccga ttcctccaca 960 gcagatcgcc accgaaggag agggaaagaa caacaaacca acagaacgaa agaagcagat 1020 ccgaagaagg agaagaagaa gcagatctga aaaaaaggaa agaaaactaa aacaactgct 1080 tgtgtttgct tgttgcaggt gacggtggtc tcaccgccgg cagggaaggg aagaggggag 1140 gaagccgttc cagatccccc atgttcccgg gcttttccag cggcggcgcg tggagaagac 1200 gcgccgccac tgttcctgca gtccagaagg cctctgcagt tctggatttt taggggctat 1260 tttgtaattt ttgatttgtg taatgtgttg tttggtttat tttgattttt gttatttgta 1320 attgtaaatg ggtgtatgag aaaaacataa taaaaaagga tgtgtgtgtg tttgtatttt 1380 ttttatgtat gttattgaat tataaaataa aaaagacaaa aaagaattaa atgttttaat 1440 ttgaatatgg tcaaatatct caaggacaaa taaaatcatg ttgtatttcc catgaaaatg 1500 taagaacatg tttctacata tattctggga tttaataact gatttattaa agccttagaa 1560 tttggctaat attttaaatt ttcaaatcac atcaaatcac gaagcagctt acctcaggta 1620 gggtgcgcta ggggtgctaa taccttccct agccacaacc agtcccttac cctcgaatct 1680 ctgacaagac cagtacatcc gggtttccta gtagccctca atcaaatact aggtggcgac 1740 tcccaaaaca agcaaaacaa acgaaaaaat cgccatcgac gccgcgcggg ggacgtgcga 1800 ca 1802 // ID Copia-100_Mad-LTR repbase; DNA; EDCOT; 1863 BP. XX AC . XX DT 04-NOV-2010 (Rel. 15.11, Created) DT 04-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Copia-100_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1863 RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1863 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1986-1986 (2010). XX DR [2] (Consensus) XX SQ Sequence 1863 BP; 583 A; 313 C; 386 G; 580 T; 1 other; tgttggaagt atgcccacaa agccactcat ttgatgtaat agctttttgg aatacttaat 60 gtattaaact tttatatgtt taatgaaggg caaagcttat tgttaatcac tatttattgt 120 atcatgtgtt taagcaataa gggaatccaa gggatgtatt tgatctaaga gacaagtgat 180 ctaagtgagt tagattatcg agaccattct cttatgttca ttcctaaaac gttcctagcc 240 ataggattgc caattgggca ttgacaatcc gctaaggtta gtatgtgtta tgttgactca 300 agcgtgagta tgactagtct caagtcattt ggtgttggac actaagacaa acacataggt 360 gctcgaaaga gtaatcgagt acactgaaca acgatcaaaa gagagttcga acatacatgt 420 catgtaagaa ctcgaaagtt gcaatatgca aagtagtcct ttgacctgag gcatcataga 480 tgtctaatgg ttaggtcctt gatctttgat catgtcaacg gcattccatc ggagtgtcca 540 cggcattgtt ggggtcaagc tatctagtca tgtaggcata tgaatgcaca acaagggatc 600 tctaaccttc catggtggaa ggagaatact ctaagatatg attctaaagt ctttggccaa 660 agcatatgaa tatgacttag gaagtttgtt ccaaatcata ttcaagggaa tcatatagag 720 aagtatcaca ttggatagta gacatgaaac aaactatcac tcaaacaatg tgattaagag 780 tattgtatta gagaaggacc gtattgcatt gtagttgtaa ctggataggt tctccaacca 840 attctactta gcttgggtaa ccatgacata ctgctaggtg tcactcatgg tttgtggaag 900 ccctaatgat tagcaaacac taatcataaa gggagaattg aaatgtggtt tcaattcaca 960 atcgatcgtt aagagtaaca atcgcccact acctcgctaa ttggaaccta atggatcgta 1020 caccgagtaa gggtgatagt gaagaaatta aatgaaatgg atatgcaatt aaatggttta 1080 attgaagaat ggtcaagatt aattaattag ttaattaatt ttacgaaagg ttcgtattgg 1140 gcttttaagt tggttttggg tttcggggcc caaaagcgtt ttggtccaca aggcccatta 1200 tgtttaagtt gtatgacaac taaaacaaaa tgggcaaata gcccaataac atcaatatgg 1260 ccggccatta gggtgaatgg gcaaacttgg attaattaca agtttgccac tcacttgwaa 1320 tgaagtataa aagcaacttt atagctttat ttctcattag ggtttttctt gaggaaatga 1380 ggtgaaacat tttctctctt tttctctaca aagaggccgg ccacttaggg agattatcta 1440 gcaatctctt cttccctaag tcatccattt catcttcaca cttcaccctt ggtgtggaga 1500 cttagagaca ccaaactttt ggtgttttgg agatcctttc ctcacatcct caaagaccaa 1560 aggagcacaa aaggaggagg aaatcacaag caatatccaa ggagcttgga ggtgacttga 1620 aggccctcca cttgggtgaa tcccttgtgt aaacaaggat gagcttcaag ggtaaagaaa 1680 ctctaaatct ttacttctct ttaatgttgt taaagagttt attggttcac catatactag 1740 gctttgaaag tcatgggttt tatgaattgt ttttgaatgc atgcctactt taaagtgtta 1800 atagtttgca tatgtattca aatgttctta cttgttctta gctaggacaa aatttttcct 1860 tca 1863 // ID Copia-10_TC-LTR repbase; DNA; EDCOT; 299 BP. XX AC CACC01002892; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-10_TC_; KW Copia-10_TC-I; Copia-10_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-299 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01002892; Positions 1848 2146. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 299 BP; 85 A; 24 C; 42 G; 148 T; 0 other; tgataattct attttataga attattttat ttgaattttg ttattaaata ttggctaagt 60 ccttaatttt taattataat ttatttattt ttagttattt tttataatta gtttattttt 120 aagtgagtta ttttaattct atgttattcc ttttaatttg attgttattt attagttttc 180 tatgttttgt aggatttaaa gtgattgggc ttaattttga aaagtaaggt gttgaaagac 240 ctagaatctg cttgcatatg cttcagtatt ttggccataa ctcgagatac agaactcca 299 // ID LINE1J_MT repbase; DNA; EDCOT; 3909 BP. XX AC AC144515; XX DT 21-JAN-2007 (Rel. 12.01, Created) DT 21-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE L1-type element. XX KW L1; Non-LTR Retrotransposon; Transposable Element; LINE1J_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3909 RA Jurka J.; RT "LINE1J_MT: L1-type element from barrel medic."; RL Repbase Reports 7(1), 35-35 (2007). XX DR EMBL/GenBank/DDBJ; AC144515; Positions 4795 8703. XX CC The sequence is likely to be 5'-truncated. XX FH Key Location/Qualifiers FT CDS 79..3159 FT /product="LINE1J_MT_1p" FT /translation="MKILSWNVRGLGGSAKRPEVRKLLSEKNPSIVCIQET FT KLAVIDDVFCSSLWGILTHSYSFRPAVGASGGLLIMWDSSVVEVWSSFSLE FT HVLLIHGRFIDSNDEFYLFNIYAPCDNGAKQLLWNSLSEHLHRLVGKNICL FT CGDFNAVRSMDERKSRGVAIRSFDCDPFNCFIDSNVLVDLPLQGRSFTWYK FT GDGTSMSRIDRFLLSEDWCNRWPTCMQVSCMRGLSDHCPLVLSVDDFNWGP FT KPVRMLKCWSEFPGYKEFVRSKLQSFNLEGWGGFVLREKLKHIKIALKDWH FT LTHSQNLPSKILSLKTNIDALEDRGEVNDLSEEDLTDLHDMSMDLHSLSRV FT NASISWQQSRLLWLREGDANSKYFHAIMSDRRRRNTISSILVEGHIVEGVS FT EVRAAVLNHFQHHYQVLPLNRPRVDGMNFRHLSVLEGNALIRPFTEAEVKV FT AVWDCDGYKSPGPDGVPLGFIKDFWQDLKGDIMRFVLEFHRNGRFSKGINS FT TFIALIPKIDNPHRPNDFRPIALVGCLYKILAKLLANRLRNVMGSIISDTQ FT STFVKDRQILDGILVANEVVDEARKLKKDLLLFKVDFEKAYDSVDWGYLDD FT VMGKMAFPTLWRKWMKECVTTATVSILVNGSPTEEFQMKRGLRQGDPLSPF FT LFLIAAEGLNVLMHSAVNLNLFTGYSIGSHNPTVLSHLQFADDTLLLGVKS FT WENVRALRAILVLFENMSGLKVNYHKSLLVGVNISESWLQEAASILSCKIG FT KIPFMYLGLPIGGDARRLIFWNPVIERLKSRLSDWKSRNLSYGGRLILLKS FT VLSSLPVYALSFFRAPAGIISSIESILIKKIWGGGEEHRKIAWVDWNSICM FT NKGVGGLGVKRLQEFNIALLGKWCWRCLVVREGLWYKVLFSRYGEHRGRLR FT EGGVTGSAWWREIVKIQNGIGVEGENWFEESIIKRLGDGLNTFFWSDCWVG FT TVSFMERFRRLFDLSIHNDLSVGEMYALGWEEHGEAWRWRRILFAWEEELV FT GEIRNLLTNVTLQDTQSDVWL" XX SQ Sequence 3909 BP; 963 A; 560 C; 1027 G; 1359 T; 0 other; tgtgggaagg tggttgatga agggatgcag taggagccag ttgtggggac gggttgagaa 60 ggggaggatg agggtattat gaagattctt tcctggaatg ttagggggtt gggaggtagt 120 gctaagaggc cggaagtgcg taaattatta tctgaaaaga atccgtctat agtttgtatt 180 caggagacga aattggctgt tatagatgac gttttttgtt catctttgtg gggtattttg 240 actcattcgt attctttccg gccggctgtg ggggcgtctg gtggtttatt aattatgtgg 300 gattcttctg tcgtggaggt gtggtcttct ttcagtttgg agcatgtttt attaattcat 360 gggcgtttca ttgattcgaa tgatgaattt tatctgttta atatttatgc accttgtgat 420 aatggagcaa agcaattgtt gtggaattct ttgtcagagc atctccatag gttggtgggg 480 aaaaacattt gtttatgcgg tgattttaat gctgttagga gtatggatga aagaaaatcg 540 agaggggttg caattcgctc ttttgattgt gatcccttca attgttttat tgatagtaat 600 gtgttagtgg atcttccact tcaaggccgc agttttactt ggtataaggg agatggtact 660 tctatgagtc gcattgatcg ttttttgtta tcagaagact ggtgtaatag atggccgact 720 tgtatgcaag tctcttgtat gcgtggtttg tcggatcatt gtccgttagt gttatcggtt 780 gatgatttta attggggacc gaaaccggtc cgtatgttga agtgttggtc cgaatttcct 840 gggtataaag aatttgttcg ttcgaagtta cagtctttta atttggaggg ttggggaggt 900 tttgttttaa gggaaaaatt gaaacatatc aagattgctc ttaaggattg gcatttaact 960 cattcacaaa atttgccgag caagattctt tccctgaaaa ccaatattga cgctttggag 1020 gataggggtg aggtgaacga cttgtccgag gaggatttga cggatttaca tgatatgtca 1080 atggatttac attctttgtc cagggtaaat gctagtatct cgtggcaaca atcgcgatta 1140 ctatggcttc gagaaggaga cgcgaattct aaatattttc atgcaattat gtctgataga 1200 cgtcgacgaa ataccatctc ctctatttta gttgaaggac atattgtgga gggtgtatcc 1260 gaagtcaggg cagcagttct taatcatttc cagcatcatt atcaggtgtt gcctctgaat 1320 aggcctaggg tggatggtat gaattttcgt catttatccg tgttggaagg taatgctctg 1380 atacgtccgt ttacagaggc ggaagttaag gtagcagtgt gggattgtga tggttacaag 1440 agcccgggtc cagacggtgt tcctttgggt tttattaaag acttctggca ggatttgaaa 1500 ggtgatatta tgcggtttgt gttggaattt catcgcaacg gtcgtttctc taaaggaata 1560 aatagtactt tcattgctct cattccaaag attgacaacc cccaccgtcc aaatgatttt 1620 cgccccattg ctttggtggg atgtctatat aaaattttgg ccaagttgtt ggcaaaccgt 1680 ttacggaatg taatgggatc gataatctca gacacacaat caacgtttgt aaaagatcga 1740 caaatccttg atggtattct agtagctaat gaggtggtgg atgaggctcg aaagttaaaa 1800 aaagatttgt tactgtttaa agttgatttt gaaaaagcat atgactcagt agattgggga 1860 tatctcgatg atgttatggg caaaatggct tttccgacat tgtggcggaa atggatgaag 1920 gaatgtgtta ctaccgcaac tgtttcgatt ttagttaatg gcagccctac agaggagttt 1980 caaatgaaaa ggggtctgcg tcaaggcgac cctctttctc cttttctttt ccttatagcc 2040 gcagaagggt tgaatgtctt gatgcattca gcagtaaatt taaatctgtt tactggttac 2100 tctataggat cgcacaatcc tactgtgctt tctcatttgc aatttgcgga cgacacactt 2160 ttgttaggtg ttaaaagttg ggagaatgtt cgtgctttgc gggcaatctt ggttcttttt 2220 gaaaatatgt ctggtttgaa ggtgaattat cacaagagtt tgttggtggg tgttaatatt 2280 tctgaatctt ggttacaaga agctgcttct attttgtctt gtaaaattgg taaaattcct 2340 tttatgtatt tggggctgcc cattggtggt gatgctagac gtttgatttt ttggaatccg 2400 gtgatagagc gcttaaaatc tagattgtcg gactggaaaa gtagaaactt gtcgtatggt 2460 ggtcgcttga ttcttcttaa gtctgtcctg tcttcactgc ctgtctacgc cctttctttt 2520 ttcagagctc ccgcaggtat aatctcttcc attgaatcta ttttaataaa aaaaatttgg 2580 ggtgggggtg aggaacatag aaaaattgct tgggtagact ggaattctat ttgtatgaat 2640 aagggggttg gtggtttggg ggtaaagaga ttacaagaat ttaatattgc tctgctgggc 2700 aaatggtgtt ggagatgttt agtggtcagg gagggcttat ggtataaggt gttgttttcc 2760 cgttatgggg aacatagagg gcggttaagg gagggtggag tgacggggtc tgcttggtgg 2820 agggagatag taaaaattca aaatggaata ggtgtggagg gtgagaattg gtttgaagaa 2880 agtataataa aacgtttggg tgatggcttg aatactttct tttggtcgga ttgttgggtg 2940 gggacggtgt cttttatgga gaggtttagg agactttttg acttatcaat tcataacgac 3000 ttgtctgtgg gtgagatgta tgccttaggt tgggaagaac atggggaggc ttggaggtgg 3060 agacgtattt tgtttgcttg ggaggaggaa ttggtagggg agattaggaa cttgcttact 3120 aacgttactt tgcaggatac tcaatcagat gtttggcttt gacgacctaa tattggtgat 3180 ggttacactg ttagtggtgt gtatcaaatg ctcatgcggc aagagatgca caaccacgat 3240 atcgtttcgg atgctccttg gcacaagagt gttcctttga aagtctctat ttgtgcatgg 3300 cgtctctttc gcaatagatg accaacaaag gataacttgg tgcggcgagg tgttatatct 3360 catgattcac aattgtgtgt tacaggatgt ggccaaaatg aaactttaga tcatttaatt 3420 attcattgtc ctatttttgg tggtctttgg caacaaatta aaacttggat tggtgtattt 3480 tccgtggatc cctatcaggt tctggatcat tattatcaat ttgttttctc ttttggtagc 3540 aatgcttcaa gaaggtcttt ccttcatttg gtttggcttt gtggtatttg ggttctttgg 3600 cacgaaagaa atcagagatt atttgtcaat acagcaaaaa caactgcaca attacttgag 3660 aaggttaaga tcatatctct tcaatggttg aaagcaaaaa atgtgtgctt tccttttggt 3720 taccatgtgt ggtggcagcg tccccttact tgtttgggga ttggctaatg tattttcctt 3780 ggtcttttct cttttttgtg gtttgttcgg aactctttgt aattttgttt tgtctctttt 3840 ggcactcctt gtgctaggga tcaaaacgtt ttgttaatat atctcatttt gttttgttca 3900 aaaaaaaaa 3909 // ID Copia-53_Mad-LTR repbase; DNA; EDCOT; 496 BP. XX AC ACYM01039013; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-53_Mad-I; KW Copia-53_Mad-LTR; Copia-53_Mad_. XX NM Copia-53_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-496 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1403-1403 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01039013; Positions 14160 13665. XX SQ Sequence 496 BP; 155 A; 68 C; 111 G; 162 T; 0 other; tgaatggtaa tcttgcttct agaaaagtgg ccggtgcatg cattaaaaat gctagacaat 60 tctagcatga gaatggcatg tgttcattgt gtccataagc aaagtccatg gtggtgggct 120 actttagtag agtcatgaat aatggctagg atgatttcac acttggtatt cacacttggt 180 atggttggtt atacttgcct ataaatagag tatgttgtta tgtttaagaa tgacaagtta 240 agaaaagaga aagaaggaga agtaagagag acaagaaggc tctctaccta aaagaaaaga 300 gaataagtag aagaagcatc catagcttct aagagtgttt tgagtgattc ctcttgtatt 360 agtttgtgtg agaataaaag gttttgtgtg ttataccttg agtgttcttt ttctcttgcc 420 tatcaatttc tgctgcgtta cattcttctt tggagataaa catctcaaag tagtgaagtc 480 tctttaaatc ctaaca 496 // ID Copia26-PTR_LTR repbase; DNA; EDCOT; 289 BP. XX AC scaffold_252; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia26-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-289 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-289 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 227-227 (2007). XX DR Genome; scaffold_252; Positions 143978 143690. XX SQ Sequence 289 BP; 80 A; 47 C; 47 G; 115 T; 0 other; tgttgacagt tgcctcattt gctgctgaag aagaggtctt cgatgctgtg aagagtcagt 60 caagattggt tccagattgt taggatgtta gttgaaaata aagctgtcat agatcagctc 120 tttctctgtt tttatcttct caatattttt cggaattctg ttatcaaact cttctataaa 180 agagtgattt atcaataaag aaaatacttc tattcacaac atttatatct ttatcttatt 240 gctgagttct tgcctgttct tatacaattt gtttctgtca taaactaca 289 // ID Copia-3_CP-LTR repbase; DNA; EDCOT; 134 BP. XX AC ABIM01022997; XX DT 10-MAR-2010 (Rel. 15.04, Created) DT 10-MAR-2010 (Rel. 15.04, Last updated, Version -1) XX DE LTR retrotransposon from papaya: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-3_CP_; KW Copia-3_CP-I; Copia-3_CP-LTR. XX OS Carica papaya OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Caricaceae; Carica. XX RN [1] RP 1-134 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from papaya."; RL Repbase Reports 10(4), 578-578 (2010). XX DR Genome; ABIM01022997; Positions 15639 15506. XX SQ Sequence 134 BP; 39 A; 20 C; 28 G; 47 T; 0 other; tgcaccagtt ggtccttaga aataggatcg tggtgataat ggaaccatgt ttttctatgt 60 aatcagttga atcaatctca atataaatag aactgctctc tatcgagagt tgtgtggttg 120 gtataatcat ttca 134 // ID Gypsy-6_Mad-LTR repbase; DNA; EDCOT; 1617 BP. XX AC ACYM01006063; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-6_Mad-I; KW Gypsy-6_Mad-LTR; Gypsy-6_Mad_. XX NM Gypsy-6_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1617 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1409-1409 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01006063; Positions 2575 959. XX SQ Sequence 1617 BP; 475 A; 396 C; 315 G; 413 T; 18 other; tgtttgggtt aaaaccggac tttgggccca aagatggagt cggcccaacc gaaggcccgg 60 acgaaactta tggagcagga aaagggccac ttgcttacct acccaaggac caagtggtgt 120 aggctgatca gactgcacag cctaataaag tactttttgg tggcattcat gtaaaaaagc 180 tgatgagtca tcacctccaa accgtattcg ggcaaggctg ttgctacggg aacccaagrt 240 aagtcgtcta taaaaggagg aagagaagac argaataarg acactcaatc aaacaaacaa 300 atgcaagcca aaactctgct caaagccaga tttgccttca aacgaagctg tagtcagccc 360 aagccttcat cccagtcggg ataaaacctt tatcccccgc rggataatct tttcttccaa 420 cctctgtaat agctctgcta ccttgtttaa acttgttgta gtatcgattc acttttgtat 480 cctctccctc tctctccctc taagctttca gacctttgac aaagctacaa agatagggac 540 ctgcaagaag atcagcctta actgataagg tttaatcttg cccgaccctc tttgctctgt 600 ctttgtcttt tctttcttta aaagcctagt aacatgctgt atatttccag ttatatacaa 660 gttgtttcta gcaaaatcat gatgaaaagg yttgctcagt acttgaaccc gatttgaata 720 tatcwttagt gttcaaatca gatccaagtc ccaagcccgc gggcatgtaa atctgatcag 780 tttaaaagtc mttgacctca aggcataaaa aagaacttta tgtgractta acccatccac 840 gacaatymtt gataaacgag aagtycgaag ttacttgggg cgcaagtaat cgacccacct 900 tttagttttg tttctattat gtcatgatta tcatakaacg cttaagtttr gaatgwattc 960 tgatgggaag cctcaaggcc tacacctaag gccccacaaa ggcacctatt tagattcatt 1020 ctactttgcg gtctaactgg ttcgagtaca agaacaaact ctaatgggaa gcctcaaggc 1080 ctacacctaa ggccccacaa aggcacccay ttgggttckt tctacttcks gggctcgggt 1140 aatcagaaat ataatagtga caagactctt gcaaccataa aagaccaaat atgatatgtt 1200 caagtactgg tttagtttga caggaagcct caaggcctac acctaaggcc ccacaaaggc 1260 acctgttata tctaacacgg tttctcgggc atatgcatat tcacaactaa aacttgacat 1320 ctattcgaca tctgccatac tgaagatggt agtggcacgc ttgagcacct caaaagctaa 1380 tcttaattgt gagcctcaag gcctatacct aaggccccac aaaggcacat ttcaaattaa 1440 ctatgtcatt ctctttcagc attgcccgac gagtcttgcc cgaacaagac ctgcccgact 1500 aagcccgata agaaagcaga agcccgacag cagccttcaa ccggcgccga cctcccaggg 1560 gagctgtgtg ctcgtttgcc aggaagtcat ccccgacgga aattcctgtg acgaaca 1617 // ID Gypsy-79_PTr-LTR repbase; DNA; EDCOT; 2366 BP. XX AC . XX DT 28-DEC-2009 (Rel. 15.02, Created) DT 28-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-79_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2366 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 189-189 (2010). XX DR [1] (Consensus) XX CC ~86% identity to consensus. 5-bp TSD. Similar to POPGY1 and CC POPGY2. XX SQ Sequence 2366 BP; 813 A; 449 C; 518 G; 582 T; 4 other; tgttgtaacc catttttggg tccccgcaca aaaaagaaga aaatacaaaa aaatcaaaaa 60 tatatattaa aaaatcaaaa aatatataac agtgaaaaga ggatgccaga gcgcccagaa 120 aatggtcaaa aattggttga ggaggttcaa aaatacaaag attgaaattt gacagtattt 180 tgttgactga tgagagccct gttgacaaag aaaattcaat ttgaggaaga aaagtccaaa 240 atcagatgtt tatggactca attaaatttt attgaaggtt taattgaatt tatggagggt 300 ttgattgcaa gaaaaattga ttttggagtc aatttgggct ttaattggaa gaaattaaag 360 ttctggggtc aaattataat ttttgagagt taatttggtc aaatcagggg cttaattgca 420 taaatattga agtttgatgg ccaattaggg acttaattga agaaatccga aaccaaggac 480 caaactggaa aaggcgcgta aatagagggg ctgtaattaa aaccgaatca ggggccaaat 540 tgaagaaatt agaagtttat tgactcaatt gagggtcaaa ttgcataaat tcgagaccaa 600 ggaccaaakt gaaaaaggcg gccaacttca gggccggcga ttgatatttg gcagggatgc 660 aattgaattg atttttaaaa tcaaaattgc aattkaggac ttgattgaac aaatcacaaa 720 ttgaggactg atttggactt tgacacgttt tggcgccatt ttcttttaaa tgaaacgacg 780 cgttttgtcc aaaacggcgt cgtttcatmc actgttcaaa aaaaaaaaag agcccaaaac 840 ggtgccgttt tgaacggcac tgtgggtctt cttcttcccc tggacgcgcg aagcagggga 900 agaagaagat tttttcttcc cctgttttca ccgccttctc tccctcgaaa gcctcaaaaa 960 gacgccgacc aaggaccccc acttgctaag ctctgacccg tggcctccac gtgttgggaa 1020 aaagggagga gacgtgcccc tcgggcggtc gtggggcggc tgcacagtgg ccgccccggc 1080 cacgtctctc ccctgttttt gcctataaat acaggggaga gagcagaaaa agaaggggca 1140 aagagaggga gaagagaaaa agagaaagag gagaagagaa aaaagaaaaa aaaaaagaga 1200 gagacagaag aaagagaaaa agaagaaaaa gaggaagaga gagagaagaa aaaacagaga 1260 aaaagaaaag gaaaaaaaaa agaagagaga aagagaagaa gagaaaaaca gagcgaacgc 1320 ggagaaggaa gaagacggcc gccgccggaa ccaccgccac cgccagccac cacgacaacc 1380 gacgccctcc aggtaaccct cctccccctt ttcttttcct tctgtttctt cccttgccat 1440 gcagaacgtg cacagttcac gttctgcagg cgaggcgaag ctggttactg tgctcatgca 1500 cagtaaccag ctatgtgggc tgggctggcc cagcccatgg atcttgggcc cggtccggta 1560 gcccaacaat gtgggccggg tccggcccaa caaaaaaaaa ttttttaaaa ttttgtgatt 1620 ttcccgcgtg tttgttttgt ttaatctcgg tctgtttttt tgtacaaaaa atacaaatcc 1680 ggtattaaaa tacccggttt tcgtcaaaac ttccaaaaat acaaaaaaat tgaaaaaaga 1740 aaaaaatgtt tttgtgcata cggccaagtg tctcaaagct aaaaaatcat attgtgtttt 1800 tcatacacca aaaaacaatg ttttagcatg cattttggct ttaataacca gtttattaaa 1860 gtcaagagaa cattggccaa aatttcaaaa acaacaaaaa ttttattttg ttttgtttta 1920 gtatcaggga ttacgaattt atacgtaaaa cgtattcccg atattaaaaa ggtttttttt 1980 ttgacgacat agaacagtta ggtttttacc cgataagata aggacctcct tacagaggag 2040 gacttttctt aaaccttaga cagaccaaca attagaaacc acaacaagac cttagatttt 2100 atcagacaat aaaacaatgc agcttacctt aggtagggcg takttggggt gctaatacct 2160 tccctttacg caaccagtct ccgtacccga tctctgagac cagttagggt tcctagtgac 2220 cagaatacta ggtggcgact cccattcaaa ttttccactg ataagagaca agaattcctt 2280 gtctctccat atttgccaga tagaccatta cattacattt tccctgagat ggtggacgat 2340 cgccgcgacg ccgcacacgt gcgaca 2366 // ID Copia-26_Mad-I repbase; DNA; EDCOT; 5216 BP. XX AC ACYM01137708; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-26_Mad-I; KW Copia-26_Mad-LTR; Copia-26_Mad_. XX NM Copia-26_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5216 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1299-1299 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01137708; Positions 14772 9557. XX CC Positions [2545-3045] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 3511..5214 FT /product="Copia-26_Mad-I_1p" FT /translation="MSSNEHPNITVSQVEDLQQVCLPAQNCHPMQTKSKSR FT IVKKKVFSAHIGQASDIKEPQSFSSAVKCVQGQTAMKEEMDALTQQQTWKL FT VPLPPGKNLVGCKWIYKVKKNSDGSVARYKARLVAKGYSQEAGIDYYETFS FT PVVKPTTVRLILSLAASYNWKLKQLDVKNAFLHGFLEEEVYMSQPQGFVDS FT TCLDYVCKLERSLYGLKQAPRAWNDRFSGYLLKLGFKASYVDPSLFVKCDE FT SSIIVLLVYVDDIILNESDVVKVQHVITQLIREFEMTDMGLLHFFLGQQIE FT YQSQGIFVHQSKYVKELLQKMNMLDCKPCSTPCHPNQKLLNHGSEPVSDPS FT TYRSIVGALQYLTFTRPDISFSVNQVCQFMHSPLATHFTAVKRILRYLKGT FT MIVGLSFKSGSSLLNAYTDADWAGDPNDRRLTTRFVIFLGDTPISWSFKKQ FT HTVSRSSTKVEYRAMATTTAEVIWIQQLLRDLRVACSSAPVLHYDNISAMA FT LATNPVLHSKPNILRLIVTSFVNVFNKGQLFCNLLLLQINMQICLLKGCVH FT LSSLGIAPISCLAVCHMSLRG" XX SQ Sequence 5216 BP; 1320 A; 1087 C; 1014 G; 1792 T; 3 other; tggtatcttc gccgggtgcg actcacccct ccggttgacg atcctagtgc ttccgccgtc 60 tttttccgtc aatgatcggt gtttggtgac ttctctgact agctatttcg ttttcgttgg 120 ctgcgatttt ggtgttttgg cttgctgatt gtgatcgatt gtcgatgatt tcttgatcgg 180 agtttgtgtg tcggttgatt tgctgcaatc gtaattgtct tcgtgtatca gatgctgtcg 240 attcttttgc atttgattac tgcgtatatt tgttctgcgc agtgcgaatt ccatttttct 300 gccctaagat ttgggggttt cgtgttttgt ctactcgaac gtgttggtgt cttgctcata 360 ctagttgttg tggttgctag tggcttttat tgcagttgta ttgcaattac tggttgttgt 420 aatctttcat ttgtatcgaa tatggtgact catatgcaat tagctcttac acaatcacct 480 atttcgtctt taattccaag tgttgggaat actgtcacag tgaaacttga tgattccaat 540 tatgttacct ggaattttca aatgcaactc ctcctggaag gaaatggaat tgttgggttt 600 gtaaatggtt ctattccttg tcctgctcag tttgatgatt ctgattttaa tgatgaaact 660 gttgagaata atcaccatgt ctctgatgct tatcaagtat ggaaaattca tgacaaagct 720 ttaatgacat tgatttctgc tacattgtct ttttctgcct tgtcctgcat aattggttgt 780 cagagttcca acgagatgtg gatgaatctt cgggaacatt tctccagtgt cactagaact 840 agtattgttc aactaaagat tgacttgcag aatatcaaga aatgaccaga atctgttgat 900 gtctatcttc agcggatcaa agagtctaga gattaactag ctgctgctgg tgtagctatt 960 tctgatgagg atattgttat tgtggcattg tgaagtctac ccagtgaata taacaccatt 1020 aaggcagtca ttcgtggacg ggaaaatctt gtctctctaa aggaattgcg atctcagttg 1080 aaggcagaag aatccacctt ggatgaagct actaaacaga ttcctttaat gtctgctatg 1140 tatactcaag cttctggttc tccttttgat catggagagc cattagggac aaaatctgta 1200 cctccaatgg ttcaaggttt ttctggttat cctaacttca tgtcgccctt tatgccagta 1260 tcaaataygt ctcttcaggg gtttcccggg tttcaacaat tgcctttayc tcctatgact 1320 aatgttccca tggcatttgt cactcaacaa agttytggtt catacaataa ttttagggga 1380 aataacttta ggggcaataa ttacaaagga aaaggacaag ggaagaaatt tcatggtcac 1440 aactctggag gatagtacaa tggtggtcac aactctggtg gacagtataa tggtcttgga 1500 ggatagtata atggttctgg agggtatgct caacctcaat attataatgt atctcaatct 1560 tttcagcaca atgccacacc acaatctata tcctcgactt ataatccaaa tcaaatctgt 1620 caaatctgtg atcgtaaagg tcattctgcc ttgaactgtt ttcaacatgg ctgtcagata 1680 tgtcatcgag ttggtcatgt ggcggctata tgttttaatc gaaacaatac ctcttctgga 1740 ttctcaagtc atttttctcc gggtgtacct tcatctctgc ctactccgta gcataatggt 1800 cattatggtc aggttcctat gtggaatcca ttttgtcctc cacagcctat ggtttcaccg 1860 aatcatggtt ctcagtttcc tccatctgct atgcctcagt cccatgctcc acttgctgtg 1920 cacactggtc ttggttcatc ctcctcggct cctcaacaag acttttggct acttgactct 1980 ggagccacca accatatgac ctccgatgta tcaaatctgc acatggcaac atcatatcct 2040 tccaatgata ctgtgaccag tgctagtggt aaaggtttat tgatcaaaca cattggtccc 2100 tcttttcttc ccacaaagtc ccataatttc aagttacctt ttgtgttgca tgttctgaaa 2160 ttgtctcagc atttgttatc tatgaatcaa ttgtgcaaag ataataaatg tcgctgtata 2220 gttgatgatg tttctttttg tatacaggac aaggtcacca ggagaatgat attccaaggg 2280 ctgagtaata atgttgtcta tccaatacct atgttcaaac cacagaggtc tctttctcat 2340 ggctctactc cagttgctta tatgggtcaa aaacaaattt cttctctatt gtagcattat 2400 cgattaggtc atcctacaca gtctatagtc actgcggcac ttagtaaatc tcatattcct 2460 tttgcttgta atgctcagtc tcagatgtgt aaagcttgct tgcaaggcaa gtttaccaaa 2520 ctaccttttc ctgtaattgc ttccaaatcc atcactccat ttgaagtaat tcacactgat 2580 gtgtggggtc cctcacctag tatgtctctt gaaggttaca agtattatgt ttccttaatt 2640 gatgagtgta caagatatac atggattttt ccattgacta ataaagctgc agtgttctct 2700 gtgtttgtcc atttttttgc ttttatttca aatcagtttg ctgcccatgt aaaaatttta 2760 caaagtgatg ggggtaggga gtatattagt actcaatttc aaagttttct tctttccaaa 2820 ggaattgttc atcacaaatc ctgtccttat accccaaaac aaaatgggtt ggttgagaga 2880 aaaaatcggc atattgttga gacagctatt acacttttac aacaagcttt tttaccttcc 2940 aaattctggt ttcatgcatg tgctactgca atctttctca taaacaggat gcctacaccc 3000 gttcttcata tgaagtctcc ctttgaatta ctatataccc ttccacctaa actagagtat 3060 ttgcggattt ttgggtgctt atgctatcct tctttgaaat cttacagagt tcataaactt 3120 gcaccaaaaa ctaatgcatg tatttttctg gggtatgctt cctaacataa agggtatatt 3180 tgtttctctc tcacagatca aaagttgttg gtatctcgac atgttgtctt tgatgaatcc 3240 agttttcctt cattctctga tgatgtgtct gtgcctccca aggttgtctc tgagcatcct 3300 tcattaccta tacctgttat acatcccaat acattcacac attcccctag tcttctaacc 3360 acttgttcct ttcttggttc accacactcc agttctgttt catctaggcc acagcatgtt 3420 actcagtcca ctgcttctca acacaatatt tctggtgatc ttgttccttc attcactcct 3480 gctgaggatg cttcaccggt tctttcctct atgtcttcca acgaacatcc aaatattact 3540 gtgtctcagg ttgaggatct gcaacaagtg tgtctacctg ctcagaactg ccatcctatg 3600 caaaccaagt ctaaatctag aattgtcaaa aagaaagtct tttctgctca tattggtcag 3660 gcctctgata tcaaggaacc tcagtctttc tctagtgcag tcaagtgtgt tcaagggcaa 3720 actgccatga aagaagagat ggatgcttta actcaacaac aaacttggaa actggttcct 3780 ttaccacctg gcaagaatct tgtaggctgc aagtggattt acaaggttaa gaaaaattca 3840 gatggttcag tggctcgata caaagctcgt cttgttgcta aagggtattc tcaagaggct 3900 ggtattgact actatgagac ctttagccct gtggttaaac caaccacagt taggttaatc 3960 ttgtcattag ctgcttctta caattggaaa cttaaacaat tagacgtcaa gaatgctttt 4020 ctacatggtt tccttgagga agaagtctac atgtctcaac cacaagggtt tgtggattct 4080 acgtgtcttg attatgtctg caagttggag agatctttat atggtcttaa gcaggctcct 4140 cgagcatgga atgacaggtt ctcaggctat ctacttaaac ttgggtttaa agcttcatat 4200 gtagatccct ctttgtttgt caagtgtgat gagtcttcca ttatcgttct ccttgtttat 4260 gttgatgata ttatcctcaa tgaaagtgat gttgtgaaag ttcagcatgt cattactcag 4320 ttaatccgtg agtttgaaat gacagacatg ggtctcttgc attttttcct tggtcaacag 4380 attgagtatc agtctcaggg catctttgta catcaatcca aatatgtcaa agaattgctc 4440 caaaagatga atatgctgga ctgtaagcct tgttccacac cttgtcatcc taatcagaag 4500 cttctgaatc atggtagtga acctgtgtca gatcctagta cctacagaag cattgttggg 4560 gctctacagt accttacatt tacacgaccc gatatctcat tttctgtcaa tcaggtgtgt 4620 cagtttatgc attccccatt agctactcat tttactgctg tgaagcgtat tctgagatat 4680 cttaaaggta ctatgatagt aggcttgagt tttaagtccg gatcctctct gttaaacgct 4740 tacacagatg ccgattgggc aggcgatccc aatgatcgac gattaaccac aaggtttgtt 4800 atttttttgg gtgatactcc catttcgtgg agttttaaaa agcagcatac tgtgagtcga 4860 tcgtctacta aagtggaata cagagcaatg gccacaacca ctgctgaggt catctggata 4920 caacagcttc ttcgagattt gcgtgttgct tgttcctctg ctcccgtcct tcactatgac 4980 aatatttccg caatggctct tgccactaat cctgttttgc actccaagcc aaacatattg 5040 agattgattg taacttcgtt cgtgaacgtg ttcaacaagg gacaattgtt ctgcaatttg 5100 ttgcttctac agatcaatat gcagatatgt ttactaaagg gttgtgttca cctcagttca 5160 ctcggaattg ctccaatctc atgcttggca gtatgccaca tgagcttaag ggggga 5216 // ID ALIEN2_CA repbase; DNA; EDCOT; 353 BP. XX AC X87903; XX DT 04-MAR-1998 (Rel. 3.02, Created) DT 04-MAR-1998 (Rel. 3.02, Last updated, Version 1) XX DE C.annuum Alien transposable element DNA. XX KW Transposable Element; ALIEN2_CA; Alien-2; CADNAATE; KW Inverted repeat. XX OS Capsicum annuum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Capsiceae; OC Capsicum. XX RN [1] RP 1-353 RA Pozueta-Romero J.; RT "ALIEN2_CA."; RL Direct Submission to Genbank (12-JUN-1995)J. Pozueta-Romero, RL Institut de Biologie Moleculaire du CNRS, 12, rue du Gl Zimmer, RL F-67000 STRASBOURG, FRANCE. XX RN [2] RP 1-353 RA Pozueta-Romero J., Houlne G. and Schantz R.; RT "Nonautonomous inverted repeat Alien transposable elements are RT associated with genes of both monocotyledonous and dicotyledonous RT plants."; RL Gene 171(2), 147-153 (1996). XX DR GenBank; X87903; Positions 1 353. XX SQ Sequence 353 BP; 92 A; 51 C; 83 G; 127 T; 0 other; taggggttgt ttggtagagt gtattgaaaa tgtattcatt tagacgtgaa tgccccgaga 60 cacattgtat ttattcaccg gggaatgtct cgaagtattt tgtaccagga ggacgttcga 120 gacaaaggcc cgtggcatcg gtgaggcatt ggagcttagt ctaggattag tttagaatag 180 atttacatat cttagcattt ttctatttca gaatggtatt aattggactg gacacacatt 240 ttggatttgg ttttggtttt ggtggcattt gattgattgt tttatgtgtt tttgtgtggt 300 taatacactt ataatgtcaa agttagccaa tacactctac caaacaaccc cta 353 // ID Copia-4_TC-LTR repbase; DNA; EDCOT; 277 BP. XX AC CACC01004329; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-4_TC_; KW Copia-4_TC-I; Copia-4_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-277 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01004329; Positions 12958 12682. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 277 BP; 85 A; 61 C; 24 G; 107 T; 0 other; tgaagataac aattgcaatt tcctttatcc ttaatcctct ccttctttat cttttcccat 60 atctccttaa ttctctcctt ttatcttctc aaattgatat gtacatatct tctcaaattc 120 tttagccgat aggttagcca atccttttag aaatgcttag ccgatctcaa ccaactcttg 180 tatctcaatt caactcttgt ataaatacat gtattaacaa ataaatgtta tatagtgaag 240 agttaattta ctctttaaac gtaacgccaa caataca 277 // ID DNA9-14_Mad repbase; DNA; EDCOT; 1139 BP. XX AC . XX DT 25-OCT-2010 (Rel. 15.11, Created) DT 25-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; DNA9-14_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1139 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1854-1854 (2010). XX DR [2] (Consensus) XX CC TSD is 9-bp long. Imperfect TIR is ~160-bp long. XX SQ Sequence 1139 BP; 445 A; 156 C; 160 G; 378 T; 0 other; tagaaaactt cattttaatc cctaaataag attgcttttt caataatacc gtatgtaaga 60 ttaaaaacta aaaatagtcc tccatgtcag attatagtat tccatgtcac atttaatcat 120 tttttaataa atttattgca tttttagttt ccctatatta cccttattac tctcttaaaa 180 ccaattagag aaacaaatat ataattaatt tttcaagaat gcttaattaa ctagatccat 240 aattaacatg tttgttataa cataaatctc catgtgttat tccaatcaaa gaacccagaa 300 aactcagaaa ccatgatcaa acaaaaaaag ccataaaact tacaaaccaa aaatctcgtt 360 gtattcggaa gaaagaagaa aaaaggggct tttagatgcc aaattgacgg tgaatccaga 420 gataaatgaa aaaaaaatac aaattgagaa aatagaatgt gaaatcacaa cttaattgac 480 cgtaccaaat taatcggaca tacactatat agtacctaac cgaccatacc gaatggataa 540 gacctaattg atagtaccta aatgattaag gtgcattcat ataggtacta tgatttaggt 600 gcattcatat aggtaccatg atttaggtgc attcatatag gtaccatggt ttaggtgcat 660 tcatataagt accatggttt aggtgcattt gacttggtac tatgatttat gtgcattcga 720 ctaggttata tgatttaagc acattaggac atggtttaag tgcattcgat tatgtaaaat 780 atatgatttg gctatttata tttcctctat gctttgaatg gtgataatga ataatttgaa 840 ttaggtattt gttaattctt gtaacgtatc actaatattt ttttgaatta tgtttatcat 900 tttagaaagt cagacaataa tcaatgccaa aaaatatgga gcaaattaaa atcaaatatt 960 taataggggc attataggaa ccaaaaaaac gcattaaata ttttaaaaac aagaaaatat 1020 aaattttaat atttatgctg acatggaaat ttagtcaaag gactataatg aatatataat 1080 ctaacataag gttttaattg aatttcaatc tttatcaagg attaaaatgg agaaacccc 1139 // ID Gypsy-28_VV-LTR repbase; DNA; EDCOT; 587 BP. XX AC chr20; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-28_VV_; KW Gypsy-28_VV-I; Gypsy-28_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-587 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr20; Positions 12627398 12626812. XX SQ Sequence 587 BP; 180 A; 73 C; 130 G; 204 T; 0 other; tgtaacacct agtactaatg aattaaatag gcaataatga ttattttagt acttaacttt 60 aagcttgctt aattagatgt taaaactagt ttagtgctaa tcatatttaa ttatgaatta 120 aactttgatt atggttaagt gggattagtt aatgacctaa gcatgcttat taggttctta 180 gggactaatt agggttatga gaacctaaag gactaatggg caattatggg ttttattttt 240 gataacttga aggactaaag tgcaaaattt ggacattgga gttagtggaa tgccacctcc 300 tacttaggtg attggtggca gccatgtggg ctgccacctc atgcttgggt gcttggagac 360 ccctttataa gggggctgca gctcgttttg caccatttca cctgcagcaa cttgggttag 420 agagagaatc tagagagaga aagtgtagat ttgaggtaag caagttgttt aattttgtaa 480 ttttcgttta ttttggttcc taatggtatg ttgaatagaa ttaacggtaa aaattgtgta 540 aaagttgagt ataattagct ataaacctgt tttagttaaa aatcaca 587 // ID GYPSY-I_MT repbase; DNA; EDCOT; 11810 BP. XX AC AC144893; XX DT 09-JUL-2004 (Rel. 9.06, Created) DT 09-JUN-2005 (Rel. 10.07, Last updated, Version 2) XX DE Medicago truncatula Gypsy-like LTR retroelement (internal). XX KW Gypsy; LTR Retrotransposon; Transposable Element; GYPSY-I_MT. XX NM GYPSY-I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RA Jurka J.; RT "Medicago truncatula Gypsy-like LTR retroelement."; RL Repbase Reports 4(6), 147-147 (2004). XX RN [2] RP 1-11810 RA Toth G.; RT "Internal region of Ty3/gypsy-like retrotransposon GYPSY-I_MT."; RL Direct Submission to Genbank (09-JUN-2005). XX DR GenBank; AC144893; Positions 100253 88444. XX SQ Sequence 11810 BP; 3351 A; 2605 C; 2629 G; 3225 T; 0 other; gaaatggcga cttcactggg gattcttttt agcgggtcgc gcctagtttt ctttagttta 60 tatttacgct ttgttttatt gcttacatat gtgaatactt gtttattttc atttgacgtg 120 tggggtgaga atatcaaaag tcctataccc gggctgagtg aacttatgtt taggtagaga 180 tataatcgac aattcgatcc gggggttgcc tcgtgtattg gattatgcga tcaatctcac 240 atagctgagg cattttgaaa gtgatattgt cggcgtgtgt tgtcatgctt aggcacttca 300 ctttcaattg ttcgacgaag ctatgaaccg tagttaccaa acccatccta gcctttttag 360 gacgtagtgc ggtggctaaa ttgagtgttg tctcaaactt tagtcgtcac gcgatactac 420 actcaaacta gaccttctca caaataatca tggaacgggt gtcgtcctgt actaccatga 480 tatatgtgag agaggttgca gtttgggaac tgtgttagaa ccttggttac tactatccaa 540 agcattagtt caccggacgc cgtgtccatc cgtagccccg ttactttgaa actcaaccca 600 cttttaaaca acacaatcat gcatacatgc attcatgcat aaacattttt catgcattca 660 tcgaagggtt taaacaaatg agaatttttg taaataatca caggtatgaa gaagactaag 720 tgctacaagt tcaaggaagt ggatttggtt agtttgagag agttggcact caaggtcaag 780 agtcaaacag ggttccgact ccgatatggg ggattgctta ctttgctccg aaccgatgtg 840 gaagagaagc tagtgcacac tctagtgcag ttttatgatc cgagcttccg ttgcttcact 900 ttcccggact tccagttggt tcctactctc gaggcttact ccaatctagt gggtctgcct 960 atagccgaga agacgccttt caccggtccc gggacttctc ttactcctct ggttattgct 1020 aaggatctct acctcaagac ttccgacgtc tccaaccatc ttattaccaa atctcacatc 1080 cgggggttca cttcgaagta tcttcttgat caggctaatc tcggtactac tcgtcaggat 1140 acactcgagg ctattcttgc tttgcttatc tacgggctca ttctcttccc gaacctcgac 1200 gacttcgtgg acatgaatgc tatcgagatc tttcattcca agaacccggt tcctactttg 1260 ctagcggata cctaccacgc catccatgac aggactctca agggccgtgg gtatattctt 1320 tgctgcatat ctctcttgta taggtggttt atttcgcacc ttccgagttc cttccatgac 1380 aactcggaaa actggtccta ctcgcagcgg attatggccc tcactcctaa tgaggtcgtc 1440 tggctcactc cggccgctca ggtgaaggaa atcattatgg gttgcggaga ctttctcaat 1500 gtacctcttc ttggtacccg tggaggaatc aactacaacc ccgagcttgc tatgagacag 1560 tttggtttcc ctatgaagtc gaagcccatc aatcttgcta catctccaga gttcttcttc 1620 tacacgaatg ctcctaccgg acaaaggaaa gctttcgtgg atgcttggtc caaggttcga 1680 aggaaaagtg tgaagcatct aggtgtgaga tccggtgtcg ctcatgaggc ctatactcag 1740 tgggtgatag atcgagctga ggagattggt atgccttatc cagctatgag atacgtgtct 1800 tcatccactc cgtctatgcc tctacctcta cttcccgcga ctcaggatat gtatcaggag 1860 catctagcta tggagagtcg tgagaagcaa atgtggaaag ctcggtacaa tcaagctgag 1920 aatctaatca tgactctgga tggtagagat gagcagaaga ctcatgagaa tctgatgttg 1980 aagaaagaac tagctaaggc ccggagggaa ttggaagaga aagacgagct gcttatgagg 2040 gattccaaga gagccagagg acgacgagac ttctttgcca gatactgtgg ttcagattcc 2100 gagtccgatg atgctccgac tacttcctat gcttgagggc ttcatttgtt tatcttgttg 2160 aaatttcaaa gtcttccttt tgaaaatgct atgtagtttt gattatttgc aagatttcta 2220 ttttgtttaa aaatccttcg gtggaaaaaa gaagtctttt gcattcgcat ttgcgtatca 2280 tgcatcatat gcatcatgca ttggtcacaa aggcttccaa gtgctcactc tctcctggtt 2340 tctctgcttc agtgtgaaaa gtggctcgtg ctcagaaggt ctacgaacct gatagaatcg 2400 atcgaaccag agagtacaga agaaggaaaa gggctatgga agaagagaac gctcagcttc 2460 gcaccgaatt agccactcta agggaggaat tggctaaagc taatgacgtc atgactgctc 2520 tgctagctgc tcaagagcaa tcagctacag ctatccctac aaccacagct gcaccggtga 2580 ctacaagcgt gctcccaacc acttctgcgg acactcgctt tgctatgcca gtggggtttc 2640 cgtatgggct tccaccgttc ttcactccca gtactgcagc gggcacttcg agcactgcta 2700 acaatgttct gatctctgca acaaatgctg cctccatcaa tgctactttg ccacaaacaa 2760 cagcggctgt cactgagcct cttgtgcata ccctgcccca aggtgttaac atcaacacac 2820 agcacggaag tatccccgta accaagacca tggaagagat gatggaggaa cttgctaaag 2880 aactccgtca tgagatcaag gccaatcgag ggaatgcgga ctttttcaaa actcaagatc 2940 tttgcttagt gtcaaaagtg gatgttccta aaaagttcaa aattccggat ttcgaccggt 3000 acaacgggct aacttgccct caaaaccaca tcatcaaata cgtccgaaag atgggcaatt 3060 acaaagacaa tgattccctt atgatccact gttttcagga tagtttgatg gaggatgccg 3120 ctgagtggta tactagtttg agcaagaatg acatccatac ctttgatgaa ttagccgctg 3180 ctttcaagag ccactacggg tttaacactc gattgaagcc gaatagggag tttctcaggt 3240 ccctatctca aaaaaaggag gaaagtttcc gtgaatatgc gcaaaggtgg agaggggcag 3300 ctgcccgtat cactcctgct ttagatgaag aagaaatgac ccagacattc ttaaaaacct 3360 tgaagaaaga ttatgttgag aggatgatca tcgctgcccc gaacaacttt tcggagatgg 3420 tcactatggg aacccgtctt gaggaagcag tcagggatgg aatcattgtg tttgagaaag 3480 ctgaatcttc tacgagtgca tcgaagaggt atggtaatgg acaccacaag aagaaagaaa 3540 cggaagtggg gatgatgtca gctggagccg gtcaatccat ggctactgtt gcacctatca 3600 atgcagctca aatgcctccg tcatacccat atatgccgta ttctcagcat cctttcttcc 3660 cgccatttta tcatcagtac cctctgccgc cgggtcaacc tcaagtgccc gtcaatgcaa 3720 ttgcccaaca gatgaaacaa cagttgccgg ttcaacaaca acaacaacaa caacagcagc 3780 agcaatatac cagaccaact tttcctccta taccaatgtt gtatgcagaa cttcttccaa 3840 ctctactcca gagagggcat tgtacaacta gacagggcaa gccaccacct gatccgttgc 3900 ctccaaggtt caggtctgat ctcaaatgtg actttcatca aggtgcctta ggtcatgatg 3960 tcgaggggtg ttatgctttg aagtatatcg tgaagaaact cattgatcaa gggaagctga 4020 cttttgagaa taatgttcca catgtcctcg acaatccgct accaaatcat gccgctgtga 4080 atatgatcga agtgtgtgag gaagctccta gacttgatgt ccgcaatgtc gcaactcctc 4140 tggtgcctct gcacatcaag ctgtgcaaag cttctctgtt cagccatgat catgccaagt 4200 gtctaggatg cctccgtgat cctttgggtt gccatgctgt tcaagacgac atccaaagct 4260 tgatggatga taatcttctg actgtcagtg atgtttgcgt ggtcgtgcca gtttttcacg 4320 atccgcctgt caagagtgta cctttgaaga agtgtgctga gcctttggtg ataaggttgc 4380 caggaccaat tccttatgtt tcggacaagg cagtgccata caagtacaat gctactatga 4440 tagaaaatgg agtagaggtg cctctagcct cctttgccac agtaagcaat attgccgaag 4500 ggacttctgc agcactaaga agcgggaagg ttcgtccgcc attatttcag aagaaggtag 4560 ctacgccaat cactccacaa gttgaagaag caactccaac cgtcgtttca cccattgcta 4620 cagatatgaa tcagccaggc aagtctatag aggattcgaa tttagatgag attctgagaa 4680 taataaagag gagcgactac aagatcgttg atcaattgct gcagactcct tcgaagatat 4740 ctgtattgtc attgctcttg agctccgagg ctcacaggaa taccttgttg aaagtgctgg 4800 agcaggctta tgttgaccac gaagttacgg tagatcgttt cggtggcata gtgggaaata 4860 ttactgcttg taacaacctc tggtttagtg aagaagagtt gccggaagtg ggaaagagtc 4920 acaatctggc tttgcacatc tcggtgaatt gtaaatcaga catgatatca aatgtgttgg 4980 tggataccgg ttcctctctc aatgtaatgc ccaagacgac tctagaccag ttgagctacc 5040 atgggacccc gttgaggaga agtactttct tggtcaaagc ttttgatgga tctcgaaaga 5100 atgtgctggg agagatagac ttgccgataa ccattggccc tgagaatttc ttggttactt 5160 tccaagtgat ggacattaat gcatcctaca gttgcctgct gggaagaccg tggatacacg 5220 atgcaggtgc ggttacttcc accttacatc agaagttgaa atttgtgaag aatggaaagc 5280 tcgttaccat tcatggtgaa gaggcatact tagtcagcca gctgtcttcc ttttcttgta 5340 ttgaagcagg gtctgctgaa gggactgctt tccaaggatt gaccattgaa ggtgcggagc 5400 ctaagaaagc tggggctgct atggcttcat tgaaagatgc tcagaaggtt atccaggaag 5460 gtcagactgc cggatggggc aaggtgatac agctctgtga gaacaagcgt aaagaaggtc 5520 tcgggttctc cccgtcgtca agggtttcct caggagtctt ccacagtgct gggtttgtta 5580 atgctgtctc tgaagaagca actggatctg gtctcaggcc tgcatttgtt acaccaggag 5640 gcattgcgag agattgggat gccattgaca ttccttcaat catgcatgtg tccgagtaat 5700 gtgtcttgtt gctttagcgc tttgttttca aaaataacaa tcatctcgct ctgcccaaag 5760 cgagagtgat attttctgta agggcatgtt tgtttcggca ttgccgttga ttaataaaat 5820 tttgtcgttt cttccacgac tacttttttt tagtgctttt tttcccttgg aaacaatggt 5880 aatgccagaa aaaaccaaaa catctgtatt ttcttattaa tttcaaaaaa atctgcatga 5940 aaaaaaaaac tcttcctaaa atcatccaat cattatatgc aggttgaacc ataataaacc 6000 cgttgaacac agtaatctta cggttcctcc aagttttgat ttccctgtgt atgaagccga 6060 agatgaggaa ggtgatgaca taccgtatga gatcactcgg ttacttgagc aagaaaagaa 6120 agccattcag tctcaccaag aagagattga gcttatcaac ataggtaccg aggaaaacaa 6180 gcgagaaatc aagattggtg ctactctaga ggaaggggtt aaacagaaga tcatccaact 6240 cctccgggaa tatccggata tttttgcatg gtcctatgaa gatatgccag gtctagatcc 6300 tatgattgtg gagcatcgga tccccaccaa gcctgaatgt cctcccgtca ggcagaaatt 6360 gagaaggact catcctgata tggctctcaa gattaagagc gaggttcaaa agcaaattga 6420 tgcgggtttc ctcatgacag ttgagtaccc tgaatgggtt gctaatattg tgcccgtgcc 6480 aaagaaggat ggtaaagtcc ggatgtgtgt tgacttcaga gacctgaaca aagccagtcc 6540 aaaagacaac tttccattac ctcatattga tgtgcttgtt gataatactg ctcaatctaa 6600 ggtgttctcc ttcatggacg gtttttccgg ctataatcag atcaaaatgt ctcctgaaga 6660 tagagaaaag acatctttta tcactccatg gggtactttc tgctacaaag tgatgccgtt 6720 cggcctaatc aatgctggtg ctacctacca aaggggaatg accactctgt ttcatgacat 6780 gattcacaaa gaagttgagg tatatgtgga tgacatgatt gtgaagtcag cagatgagga 6840 gcagcatgtt gaatatttaa caaagatgtt tgaaaggttg agaaaataca agctgcgatt 6900 gaatcccaac aaatgtacat tcggcgtcag atccggcaag ttattaggct tcattgtcag 6960 ccaaaagggc attgaagtcg atcctgataa agtccgggcc atccgagaaa tgccagctcc 7020 acagacagag aagcaagtca gaggtttcct gggacgcttg aattacatct cccgattcat 7080 atctcatatg actgcaacct gcgggccgat cttcaagcta cttagaaaga accagcctgt 7140 tgtatggaat gatgaatgcc aagaagcttt tgatagcatc aagaattacc tgctggaacc 7200 acctatcctt gtcccacccg tggaaggaag gcctttgatt atgtatttgg cagtatttga 7260 tgaatccatg ggatgcgtac ttggtcaaca agatgaaacc ggaaagaaag aacatgctat 7320 ctactatcta agcaagaagt tcaccgattg tgaaactcgg tatacaatgc ttgagaagac 7380 ttgttgtgct ttagcttggg ctgccaaacg cctgcgtcat tacttggtga atcatacaac 7440 ttggttgata tccagaatgg atccgataaa gtatatcttc gagaaagctg ctgtcactgg 7500 gaagattgca cgctggcaga tgcttttgtc tgaatatgat attgtgttca aagctcaaaa 7560 ggcaatcaaa ggtagcattc ttgccgatca tcttgcttac caacctcttg atgactatca 7620 accaattgaa ttcgacttcc ccgatgaaga gatcatgtat ttgaaatcca aagactgcga 7680 agaaccgttg attgatgaag gtccagatcc caatagcaag tggggtttag tctttgatgg 7740 tgctgtcaat gcttatggta aaggaatcgg ggcagtcatt gtatccccgc agaggcatca 7800 cattcctttt accgccagaa ttctgttcga atgtaccaac aatatggctg agtatgaagc 7860 atgtatcttt gggatcgagg aagcaattga catgagaatc aaacacctcg acatctatgg 7920 agattccgcg ctcgtcatca atcagataaa gggtgaatgg gagacccacc atgctaagtt 7980 gattccttat cgtgattatg cgagacgttt gctgacatat tttacaaagg ttgagctgca 8040 ccatattcct cgtgatgaga accaaatggc tgatgctctt gctactctat cctccatgtt 8100 tcgagtaaac cattggaatg atgtgccaat aatcaaagtg caacgccttg aaagaccttc 8160 acatgtgttt gctattgggg atgtgatcga tcaggctggt gaaaatgtgg ttgactataa 8220 accctggtac tacgacatca aacagttctt actaagccgt gagtatccgc cgggtgcttc 8280 caaacaagat aagaagaccc tgagaagatt ggccagtaga ttccggttag atggagatat 8340 tctgtacaag agaaactatg acatggtatt gttaaggtgt gttgatgaac atgaagcaga 8400 gcagttaatg catgatgtac atgatggtac cttcgggacc catgctacag ggcatactat 8460 gtcaaggaag ttgttacgag caggttacta ctggatgact atggagcatg attgctacca 8520 gcacgccaga aagtgccaca aatgtcaaat ctatgctgat aagattcatg tgcctccgca 8580 cgctctcaat gttatgtcat ccccatggcc gttctcaatg tggggcatcg acatgattgg 8640 aagaattgaa ccgaaggctt caaatggtca tcgtttcatc ttagtggcaa ttgactactt 8700 taccaaatgg gttgaagcag catcttatac caatgtgacc aagcaagtgg tagctaagtt 8760 catcaagaac aacatcatct gtcgatatgg tgttcccagc aagattatta ccgacaatgg 8820 taccaacctg aacaacaatg tggtgcaagc tctttgtgaa gaattcaaaa ttgagcatca 8880 taactcttct ccttatagac ctcagatgaa tggcgcagtt gaggccgcca acaagaatat 8940 caagagaatt gtccagaaga tggtaaccac ttacaaggac tggcatgaga tgttacccta 9000 tgctctgcat ggctaccgta ctactgtgcg cagttcaacc ggggcaaccc ctttctctct 9060 tgtatatggt atggaagcgg ttcttccttt ggaagtggag atcccatctc tccgtgtgat 9120 catggaagca aagttatctg aggctgaatg gtgccagagc cggtatgacc agttgaattt 9180 gattgaggaa aaacgtatgg atgccatggc tcgtggacat tcatatcaag caagaatgaa 9240 gactgccttt gataagaaag ttcatcctcg agaattcaag gtaggggaac ttgtattgaa 9300 aaggaggata agccagcaac ccgacccaag gggcaagtgg acgcctaact atgaaggtcc 9360 ttatgttgtc aagaaggcct tctccggtgg tgctttaatt cttacacaca tggatggtgt 9420 agaacttcca aatccagtga atgctgatat agtcaagaaa tactttgcct agaaatatga 9480 aaagaacagc gtggtaggtc gaaaacccga aagggcggcc taggcaaaaa tgcgcttccc 9540 ggtggatcga aaacccgaaa gggcggtcca ggcaaaaata agggacaaaa aaaaaacaaa 9600 tatgaaaagc tcgctgagat tgtaaacaac tcaggcaaga atgagcgtct cgatgagccg 9660 aaaacccgga agggcggttc atacaaaaat gagattgaaa caaaaggcaa gtaactatat 9720 ctggctaacc accgtccccc ttggggcatc tgcagctgtt aatgactatc ttcatcaaaa 9780 gctcctacac ttgcgaattc aaagtttcca ggaaatgtaa tgattactgt gttcaatgta 9840 ccaccaacca ataaaattac cattttccaa gctttgtgaa tccgtggagt cacgccttcg 9900 gctgaccacc actcttatac atcaaattga gcctgtgctt ttgtttaaaa ctctattttc 9960 ttctattttc aaagctatat acaaatcatt ttccttctat tttgataatg acaatgcttg 10020 aaacaaacat tttgaaaatt gaaaaccttt tgtctatttt gaaaagcaaa cctgagcaac 10080 agggtacttt caaatgaaac atgcatgagc gagagtatgt tgatgtctat ttcaatatat 10140 gttacaagca ggttctcctc caggatagtc tgtggtcaat ggcaagaatg aaaaaacaga 10200 atgaaaatgc atgaaaataa atgagctcgc taagttgaaa acccgaaagg gcggcttagg 10260 caaaaatgag caccccgctg gattgacaac ccgaaagggc agttcaggca aaaatggggc 10320 attgaaaaga atttatttcc ccggtggatc gaaaacccga aagggcgatc caggcaaaaa 10380 tgggatgcaa aaaatgaatg aatgaaatta agaatataac atgcaaaaag cattgaccac 10440 agatgcaatg tctacaacgt acccagcact gaaatgccca gcacaacggc gttttcccca 10500 gtaaagtctt ccaagattct atctccagca agttgcatac ctgcctgccc tcagccttgg 10560 ctccgatacg tctcccaacg acgtcatctc caaaaaggat ttccaagaat gtgtaatata 10620 gcacgagcca ctacgtgccc aatgatctga tgtcttgtct tccccgtgaa gtcgtgccta 10680 caaaatgcca acagtcatgc attacaagca ttcatacatg tataatcatg catattacgt 10740 acccatgcat attaatgaat ctgttatatc atccatgcat attgcatttc caatgtcaac 10800 atcagtctca attcaatact catgtcaggt tctctgtcaa aaccttgtga gccaataata 10860 tcggtcaatt tctacctttc aaatcaaatc gacgtcaagt caatctcaat ctacattttg 10920 ccaacaaacc aatccccagt gaatatgttt ctgtttggtc aagtggctag ttcaagtcca 10980 agaacagctt gtacctatca atttgcttat gttatcggtc gagtgcccag ctcaatccaa 11040 gagcagctcg tacctgtcaa tatgtttccg tttggtcaag tggctagctc gatccaagag 11100 cagcttgtac ctgtctatct gtttctgtcc ggtggagtaa ccagttcgca tccaagaaca 11160 agctcgcacc tgtctatttg ccttgctttc agtcgagtaa ctagttcgaa tccctaagaa 11220 caactcgtac ctgccaattt tacatgtttt cagtcgagtc accagttcga atccgtaaga 11280 acaactcgta cttgccaatt ttctcttttt cccagtcggg tcaccagttc gaatccataa 11340 gaacaactcg cactttccaa tatccccaag tgagttacca gttcgaatcc ataagaacaa 11400 ctcatgtttg tccagtaacc tctatcccct gtgaagtgac cagttcgaat ccataagaac 11460 aactcgcagt tgtctgtttg tttcatcccc ggtcaagtgg ctagtttgaa tccaagaaca 11520 gcttgtacct gtccaacttg tttctagttt cccgttactc tgctattcac tatctttgtc 11580 aatgtccacc aatcccgcaa tggatacgac atattttgtt aattccaatc cccatgaggt 11640 cttgcattca taatccaaat gatgcatggc atgcatatta tttgaaaatg ggtaggcgta 11700 tttttacgtc caaacacagt gcaaatgcta atatttaagt atcttcgtcc tgtcaagcca 11760 aagactccgt ctcttgactc tccagacaaa gaaacttaaa taggggcagc 11810 // ID Copia-52_VV-I repbase; DNA; EDCOT; 4307 BP. XX AC chr2; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-52_VV_; KW Copia-52_VV-LTR; Copia-52_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4307 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr2; Positions 17869433 17873739. XX CC Positions [1673-2203] - Integrase core CC 'TCCCG' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 524..2965 FT /product="Copia-52_VV-I_1p" FT /translation="MKPGESVSDYFSRTMAIINKMRIHGEKMEDVTVIEKI FT LLSMTPKFNYVVCSIEESKDLDELSIDELQGSLLVHEQKIIQEDKEEQALK FT ALTNNNALTMNRSTDRGRGKGRGVRGVRDGGRGRGGRGNFRVDEDQPDFQN FT RGRGQNQQFDKSKVECFRCHKFGHYRSECYTKLPNDKEKGEKSNYAEKKEV FT ETLLMAAQVNEQPQAKVWYVDTGCNNHMCGSKSSFCFLNESFRSTVSFGDC FT STVNVMGKGDINIRTKNGFVETISNVFYVPDLKSNLVSAGQLREKGYIITI FT QKGACEIYDPSRGAIAVVQMASNRLFPLKIDSVQSFLMAEVKDLSWLWHLR FT YGHLNFGGLKTLQQKHMVTGLPQISIPSQVCEECVVGKQHRSQFPQGKSRR FT AKNILELVHSDICGPINPTSNGGKKYLIIFIDDYSRKTWVSFLQEKSEAFS FT AFKSFKARVEKETGRSIKILRTDRGGEYCSNEVEHFCDDQGIRRELTAAYT FT PQQNGVSERKNRTILNMVRSLLARGKIPKSFWPEAVNWSIHVLNRSPTFSI FT QNMTPEEAWSGRKLAVDHFKIFGCIAYAHVPDEKRKKLDDKGEKCVFLGVS FT EASKAYKLFNPLTKKIVTSRDVIFDEESTWNWNGQQPTQVIFDNDAEEERQ FT QLLQQQIPTVSILESPPNDASTAAETSSTALESNVVAESRLRRVRKRPTWM FT QDFEVTGVQSDNYDTIAHYALLSDCDPITFQEAIKDLKWHKAMNEEIGSIE FT KNNSWELVELPKRQKSIGVKWVYKTKLNKDGGVDKYKARLVAKRYKQEFRS FT GLQRGVCSSSKA" FT CDS 3324..4271 FT /product="Copia-52_VV-I_2p" FT /translation="MLADFKKSMMKEFDMTDMGLMHYFLGIEVVQSSAGVF FT ISPKKYALEILDKFMLKDCNSVITPSEVGLKLSKSGAGKRVDSTLYKQIVG FT SLMYLTSTRPDIMHAVNLISRYMENPTEVHLLAAKRIFRYLKGTVDFGILY FT KRGEKSNLIGFSDSDYAGDLDDRKSTSGAVFMLNSRAITWSSKKQQIATLS FT TTEAEFVVAASSSCQAIWLRRLLEVLYNQQQGPTVIYCDNLFAIKLSKNLV FT LHGRSKHIDVRYHFLRDLCKDGVIDLVFCKSEDQIADILTKPLKPAVFMKL FT RSMLGVCSSKEVVAASGKALQIDS" XX SQ Sequence 4307 BP; 1405 A; 680 C; 993 G; 1229 T; 0 other; gtggtatcag agcccggtta acgttaaaaa agtgggttaa aaccagaaag tgagaattga 60 gagtgccaaa acagagagag agagtttatg agacagagag tcatatagca gcagctttgt 120 ttattttctt tcagcagcag aaaaaaaaac aatggcctct gaaaattttg tgcaacctgc 180 aattccacgt tttgatggtc actatgacta ttggagcatg ttgatggaga atttcttacg 240 atctaaagag tactggcaag tagtctctgg agggatagca gaaccagcaa cgaactcacc 300 aatgacggat gcgcagaaaa cagagattga aggacagaga ttaaaagatc taaaggcaaa 360 gaatcatttg ttccaagata ttgatcgctc aatcttggaa actattctgt gcaaggacac 420 ctcccagcag atttgggact ccatgaagaa gaagtaccag ggatcaacga gaaccaagag 480 gcagtagctt caagcacttc gatctgagtt cgaaacgctt cgaatgaagc cgggggagtc 540 agtttctgat tatttctcaa gaacaatggc aatcatcaac aaaatgcgaa ttcatggcga 600 gaagatggag gacgtgactg ttattgagaa aattcttctg tcaatgacgc caaaatttaa 660 ctatgttgtt tgttctattg aggaatcaaa agaccttgat gaactatcaa ttgacgagtt 720 gcaaggatct ttgttagttc atgagcagaa aatcatccag gaggacaagg aggagcaagc 780 tttaaaggct ttaactaaca acaatgcttt gacaatgaat agatcaacag atcgaggtag 840 aggcaaagga agaggagttc gaggagttag agatggaggt agaggaagag gtggacgagg 900 caattttaga gttgatgaag atcaaccaga tttccaaaat agaggtagag gccaaaatca 960 acaatttgac aaatccaagg tagagtgttt tagatgtcat aaatttggcc attaccgttc 1020 tgaatgttat actaaattac ctaacgacaa agaaaaagga gagaaatcta attatgcaga 1080 aaagaaagaa gttgaaacct tgttgatggc agctcaagtc aatgaacaac ctcaggcaaa 1140 agtgtggtat gtggacacag gctgcaacaa ccacatgtgt ggtagtaagt cttctttttg 1200 ttttctaaat gaaagttttc gttctacagt gagctttggt gattgttcta ctgtgaatgt 1260 aatgggaaag ggtgatatta atattagaac caagaatggt tttgtagaaa caatttccaa 1320 tgttttttat gttccagact tgaaaagtaa tttggtaagt gctggtcaat tgcgagaaaa 1380 gggttacata ataacaattc agaagggtgc ttgtgagata tatgatcctt cgagaggtgc 1440 tattgctgtt gttcaaatgg cttcaaacag gttgtttcca ttgaagattg atagtgtcca 1500 gtctttctta atggctgaag tgaaagatct ttcatggctt tggcatttac gctatggcca 1560 tttgaatttt ggtggattaa aaactctcca acagaaacat atggtgacag gtcttcctca 1620 aatttccatt ccttctcaag tttgtgaaga atgtgttgtt ggcaaacaac atcgttctca 1680 attccctcaa ggaaagtcgc gaagagcaaa gaatatcttg gaactggttc actctgacat 1740 ttgcggtcca attaatccaa cttctaatgg gggtaaaaaa tatctaatta tctttattga 1800 tgattatagt cgaaaaacgt gggtttcttt tttgcaggaa aaatcagaag cttttagtgc 1860 atttaaaagc ttcaaggcac gcgttgaaaa agaaacaggg agatccatca aaattctccg 1920 tactgatcgt ggtggagaat attgttcaaa tgaagttgaa catttttgtg atgatcaagg 1980 catacgaaga gaactcacag ctgcttatac accgcaacag aatggtgtat cggagagaaa 2040 aaatagaacc atcctcaaca tggtgaggag cttgcttgca aggggcaaaa ttccaaagag 2100 tttttggccg gaggcagtga attggagtat ccatgtgttg aacagaagtc ctacattttc 2160 tattcaaaac atgacaccgg aggaagcttg gagtggacgg aaactagctg tagatcactt 2220 caaaattttc ggttgcatcg cctatgcaca tgtcccagac gagaaaagga agaaacttga 2280 tgataagggt gaaaaatgtg tttttcttgg cgtaagtgaa gcatccaaag catataaatt 2340 gttcaatcca ctcacgaaga agattgtgac cagtagagat gttatttttg atgaggagag 2400 cacctggaat tggaatgggc agcaacctac tcaagtcatt tttgacaatg atgctgaaga 2460 agaaaggcag cagcttctac aacaacaaat tcctacggtt tctatacttg aaagtccacc 2520 aaatgatgct tcaacagccg ctgaaacttc atcaacagca ttagagagta atgtagttgc 2580 tgaatcacga cttcgccgtg ttcgaaaaag gcccacatgg atgcaagatt ttgaggtaac 2640 tggagttcaa tctgataact atgatacaat tgcccattat gctttgttat cagattgtga 2700 tcccattaca ttccaagaag ctatcaagga tttaaagtgg cataaggcta tgaatgagga 2760 gatcgggtcc atagagaaaa ataatagttg ggagctagtt gaacttccaa aaaggcagaa 2820 atccattggt gttaaatggg tttataaaac gaagttgaac aaagatggtg gagttgataa 2880 gtacaaagct cggcttgttg caaagaggta caagcaagaa tttcggagtg gattacaaag 2940 aggtgtttgc tctagtagca aagcttgaca ctattcgctt ggtgttatcc atggctgccc 3000 aaaactcata gtctatccat cagttagatg tgaagtcagc atttttgcat ggagagttag 3060 aagaagaagt ctatattgat caaccccctg ggtatgtgaa gcaaggttat gagaataagg 3120 tatataagtt aaagaaagca ctatacggac tgaaacaagc accaagagct tggtacagtc 3180 gtatagatgc ttattttact gaggaaggtt ttattaaatg tccatatgag cacactcttt 3240 acactaaata tggtgttgat aagaagattt taattgtgtg tttatatgtt gatgatctca 3300 tttatactag taataataaa accatgcttg ctgattttaa gaagtctatg atgaaagaat 3360 ttgatatgac tgatatggga ttaatgcact attttcttgg cattgaggta gtgcaatcat 3420 ctgctggtgt tttcatttct ccaaagaaat atgctctaga gattttggac aagtttatgt 3480 tgaaggattg taattcagtc atcaccccaa gtgaagttgg tctgaaactc tcaaagagtg 3540 gagcaggaaa gagggtggat agtactcttt acaagcagat cgttggaagt cttatgtatc 3600 tgacatctac aagaccagac attatgcacg cagtcaattt aatcagtaga tacatggaga 3660 atccaactga agttcatctt ttggctgcaa aaagaatttt tcgctatttg aaaggtactg 3720 tagactttgg gattctatac aaaaggggtg aaaaatcaaa tttgattggt ttttcagata 3780 gtgattatgc tggagatctt gatgatagaa agagcacttc tggagcagtg tttatgttga 3840 attctagagc tattacttgg tcatcaaaga agcaacagat tgcgactttg tcaactacgg 3900 aagctgagtt cgttgttgca gcatcaagct catgtcaagc tatttggctg agaaggttac 3960 ttgaagtttt gtacaaccag cagcaaggtc caacagtgat ttactgtgat aacctctttg 4020 caataaaact ctcaaagaat ctagtcttac atgggagaag caaacacatt gatgtgaggt 4080 accacttctt gcgtgattta tgtaaagatg gagttattga tttggtgttt tgcaaaagtg 4140 aagatcaaat tgcagatatc ttgactaagc ccctcaagcc tgctgttttt atgaaacttc 4200 gaagtatgct tggagtttgt tcttcaaagg aggttgtggc tgcttcagga aaggctttgc 4260 aaattgattc ctaaactgat ttctgcagat attagtttaa gggaggg 4307 // ID Gypsy-9_Mad-I repbase; DNA; EDCOT; 10065 BP. XX AC ACYM01139694; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-9_Mad-I; KW Gypsy-9_Mad-LTR; Gypsy-9_Mad_. XX NM Gypsy-9_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-10065 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1332-1332 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01139694; Positions 256 10320. XX CC Positions [4631-5134] - Integrase core CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS 840..3434 FT /product="Gypsy-9_Mad-I_2p" FT /translation="MHIFFRGLNMTTKTLVNASCGGTYKDKNAQEACLLFE FT KMAEDTQQWAVEQPQSRSAFEMPNGSPYVTAQIEKMEKRLEAKFDMLLQRM FT PGSQVAVQQPLQAACSICNLTNHDFLSCPHKDAYPEFTAEQVNSFNNFQRP FT RYDPYSNFYNPGWRDHPNLRWDKEQHTRPQFQQQVQQPAAPKAAWEVAIEK FT LANTTTQEIQNLQASVKNMEKQIGQIALQVSGRAPGTFPSQTEPNPRGGAD FT CKAVRILRSGKSFDNRDENCIQNSQVISQPKTDSGIVEKSANSKDSEQTVN FT SSENSAVIVEDRVYEPPMPYPERLKPKVKDQQLTDFMKTLSKVQINLPLID FT AIKNIPSYAKFLKDVCTKKKKLVDFEKVILTEQCSAVLLHKLPPKKQDPGS FT FTISCTIGNSHFKRALIDLGASINLMPFSVFQRLGQGEIKPTSVILQLANR FT SVAYPRGIIEDLIIKVDNLYLPADFVILDMDEDMQTPIILGRPFMATARTL FT IDVEAGTLTLRMQDQSVVFSLFEATKRPGDVHDCMRVDVLDSILHAEIMSR FT LTSDPLLNVLHGFENKYTEDEEVFEYVSALESVPFQPPRWRHVFESLGEPK FT KLLQPSKVQPPKLELRVLPEHLKYAYLGADSSLPVIIAADLSSTEEDKLLR FT ILRSHQDAIGWTIADIKGINPTICMHKILMEDGVKPAIDAQRRLNPIMKEV FT LRNEVMKLLDAGMIYPISDSKWISPTQVVPKRSGITVVKNDNNELVPTRLT FT TGWRMCVDYRKINAGTRKDHFPLPFIDQMLERLAGRAFYCFLDGYSGYNQI FT PVAPEDQEKTTFTCPFGTFAYRRMPFGLCNAPATFQRCMMSIFTGLVEHVV FT EVFMDDFSVFGD" FT CDS 4589..5572 FT /product="Gypsy-9_Mad-I_1p" FT /translation="MACDRCQRVGNQSKRNEMPQQSILIVELFDVWGIDFM FT GPFPSSHGNQYILVAVEYVSKWVEAIAAPTNQGSVVLRFLQGVIFPRFGIP FT RVILSDGGKHFINKPFANLLAKYGINHRVATPYHPQTSGQVEVSNRELKRI FT LEKTVGSTRKDWSLKLNDALWAYRTAYKTPIGMSPFRLVYGKACHLPMELE FT HKAYWAIKELNFSYDAAGEQRKLQLNELEEIRQGAYESSRIYKERTKAFHD FT SQILRKEFQPGQKVLLFSSRLKLFPGKLKSRWTGPYVVTKIFPHGAVEISN FT EAQVNTFKVNGHRLKPYMESPFDTAYESLTLKAPVI" XX SQ Sequence 10065 BP; 2995 A; 1690 C; 2114 G; 3156 T; 110 other; agaaaatggc gccgttgccg gggattattt aaaataatcc ctacgaatca gattttcaat 60 tagtattggt gtttatacat atataaaaaa aacaaaaaaa tatttaattt tcgttttcat 120 ctatttttac agattacaac agtacagatt tcagaaatct gtgcatggtc agcacccgtt 180 caacagtgca aaaattgatt ccatttgatc cagaatttga acagcattta aggaggaaac 240 gcagggaaca acatttgcag cgggttcgtc ctctgcagga gaggtttctg gaatcagtct 300 tttctgggga cctgcacaac aaagaaaaaa tggcgtttat aattccagag gcaggtctgc 360 ccctgggtga ttcactgact gcccatacca caaatatacc cagttgcatc acatatccgg 420 cagtggagga agggactgca tttgaaataa aacagcacat gttgaatatt ctacctacgt 480 ttcatgggtt ktcatctgat gatcctaaca tgcacattgc agaattttta atgggktgca 540 aaaacatttt ggtgagrgga ttttcrgcyg aatctattaa gytgcggttr tttccataca 600 ctctaaarga tcaggcaagr agatggctcc tcacactccc atcwggaagc attacaactt 660 gggcccaact cagtgaaaaa tttytaaaca agtattatcc rgcttctaag acccttgaca 720 tgagaactca gattttatct tttrcccaaa aacyraatga agagtttcat gaggcgtggg 780 agcgatttaa ggagttgatt agaaaatgtc cmcattcgsg tattaacact actgatcaaa 840 tgcacatatt tttcagaggg ttgaatatga ctacaaaaac tcttgtcaac gcwtcatgcg 900 gaggtacgta caaagacaaa aatgcacaag aggcttgttt gttatttgaa aaaatggcag 960 aagatactca gcartgggca gtggagcarc cacaatctag gtcagctttt gagatgccaa 1020 atggttctcc atatgttaca gcacaaattg aaaaaatgga gaaaaggcta gaagcaaaat 1080 ttgacatgtt attacagaga atgccaggtt cacaggttgc tgtacagcag cctttacaag 1140 ctgcctgcag catttgcaac ttgacaaatc atgatttttt gagctgtcca cataaagatg 1200 cttatccgga atttacagca gagcaggtta attcatttaa caatttccag cgtccccgat 1260 atgacccgta ttctaatttc tacaacccag gttggagaga tcatcctaat ctaaggtggg 1320 ataaggaaca gcacactaga cctcaatttc aacagcaggt acagcaacct gctgcaccta 1380 aggctgcctg ggaggtagcg attgaaaaat tggcaaatac taccactcaa gaaattcaaa 1440 atctgcaggc atcagtgaaa aacatggaaa aacaaattgg gcagattgct ttgcaggttt 1500 ctggaagggc tccaggtaca tttcccagtc aaaccgaacc aaatcctagg ggaggtgcag 1560 attgcaaggc agttagaatt ctacgttccg gaaaaagttt tgataacagg gatgaaaatt 1620 gcattcaaaa ttcgcaggtg atttcacagc ctaaaacaga ttcggggatt gttgaaaaat 1680 ctgctaattc aaaagattct gaacagacag tgaacagttc cgaaaatagt gcagttattg 1740 ttgaggatcg tgtttatgag ccacctatgc cttatcccga acggttgaag cctaaagtta 1800 aagatcaaca attgacagat ttcatgaaga ctttgtctaa agttcagata aatctgccgt 1860 taattgatgc catcaaaaac attccgtctt atgccaagtt tttgaaggat gtttgcacaa 1920 agaaaaagaa gcttgtggat tttgagaaag tgattcttac agaacagtgc agcgctgttc 1980 tgcttcacaa attgccccca aagaaacaag atccagggag ttttacaatt tcatgcacaa 2040 ttggaaattc tcattttaaa cgtgctttaa ttgatttagg tgctagtatt aatttaatgc 2100 ctttttctgt ttttcagaga ctaggacaag gagaaatcaa gcctacatca gttattctac 2160 aactagcgaa ccgttcagtt gcttatccaa ggggtattat agaagaccta attattaaag 2220 tggataatct ctaccttcct gcagattttg tgattttgga tatggatgaa gatatgcaaa 2280 caccgattat tttggggcgt cccttcatgg ctacagccag aacgttaatt gatgtagagg 2340 ctgggacact tacacttaga atgcaagatc aatctgttgt gttcagttta tttgaagcta 2400 ccaaaaggcc aggtgatgtg catgactgta tgcgtgttga tgtgcttgac agcatattac 2460 atgctgaaat tatgtcacgt ttgacatctg atccattgtt aaatgtgttg cacgggtttg 2520 agaataaata tacagaagat gaagaggttt ttgagtatgt ttcagctttg gaaagtgttc 2580 cttttcaacc tccacgttgg agrcacgttt ttgaaagttt gggggaaccc aaaaagctat 2640 tgcaaccttc taaggtacag ccacctaaac tggagttaag ggtgcttcca gaacacttga 2700 aatatgctta cttgggtgca gattcttcgc tgccagttat tatagctgct gatttatcat 2760 caacagagga agataaattg ttgcgcattt taaggagtca tcaagatgca attggctgga 2820 ctatagctga cattaaaggg atcaacccta caatttgtat gcacaaaatt ctgatggagg 2880 atggagtaaa acctgccatt gacgcacaac gtcggttaaa tccgattatg aaagaagtgc 2940 ttcgtaatga agttatgaaa cttctagatg ctgggatgat ctatcccatt tcagatagta 3000 agtggattag tccaactcaa gtggtgccta agcgttctgg tattacagtt gtgaaaaatg 3060 ataataatga acttgtgcct actcgcttga ctactgggtg gcgtatgtgc gttgattata 3120 gaaagatcaa tgcgggaact agaaaagatc attttccatt gcctttcatt gatcaaatgt 3180 tggaaaggtt ggctggtcgt gctttctact gtttcttgga tggctattca gggtacaacc 3240 agattccagt tgcccctgag gatcaagaaa agacaacctt tacttgtcct tttggaactt 3300 tcgcatatag aagaatgcct tttggtttgt gcaatgcgcc tgctacgttt cagcgttgca 3360 tgatgagcat atttaccggg ttagttgaac atgtagttga ggtatttatg gatgattttt 3420 ctgtttttgg ggattytttt gaccaatgtt tgcagaattt atctttagtt ctggacagat 3480 gcattaagac caacctggtt ttaaactggg aaaagtgtca tttcatggtt aggcagggaa 3540 ttgtcttggg ccacttgatt tctaataggg gtattgaagt tgataaggct aaaattgatg 3600 caattgaaaa gttgccaccc ccgacaactg ttaagagtgt tcgatctttt cttgggcatg 3660 ccgggtttta tagacggttc atcaaggatt tctccaagat tagccgaccc ttgtgtaatt 3720 tattggctaa agacgcccct ttcatttttg atgaggcttg tttggaggcc ttcaagaagt 3780 taaagacact cctcactaca gcacccatta ttgcagctcc taattggagc ttaccttttg 3840 aactgatgtg tgacgcatca gattatgcag tgggggcagt tcttggacag cggaaagata 3900 gacttcccca agttatttat tatgctagtc gaaccctcaa tgatgcacaa ctaaattatg 3960 caacaacaga gaaggaattg ttggcagtcg tttttgcttt ggaaaaattt cgttcgtatt 4020 tagttggagc taaagtgatt gtttatacag atcatgcagc tttgaaatat ttgttgtcta 4080 aaaaagatgc taagcctcga ttaattcgtt ggattctttt attgcaagag tttgacttag 4140 aaatcaaaga taaaaagggc agtgaaaatg tggtggctga tcatttgtct agattgatta 4200 ttcccacagt ttcagaagag attccctacc actgagggaa agttttccag atgaacagtt 4260 atttgcagtc catttccgtt caccatggtt cgctgatatt gttaattact tagttaaagg 4320 tgtagtgcat ccagatttaa catttcagca gaaaaagaag tttttatctg atgtgaagca 4380 ttatttctgg gatgagccat acctatttaa gtattgccca gaccagatta ttcgcaggtg 4440 tattccagaa gctgaacagg aaagcgtttt aaggtttgct catcattttg cttgtggagg 4500 acattttggg cagaaaagga cagcagagaa aattttgcaa agcgggttat tttggcmtac 4560 actttttaaa gatgcttata attggtgcat ggcttgtgat aggtgtcaaa gagtcggcaa 4620 ccagtccaaa aggaatgaga tgccccagca aagtattttg attgttgaat tatttgatgt 4680 ttggggtatt gatttcatgg gaccatttcc atcttcccat gggaatcaat atattttagt 4740 ggctgtggag tatgtgtcta agtgggtcga ggccatagca gcaccaacta atcaaggatc 4800 agtagtcctg aggttcctcc aaggtgttat atttccgcga tttggaattc cacgcgttat 4860 tcttagtgat gggggaaagc actttattaa taaaccattt gctaatttgt tggcaaaata 4920 tgggattaat catcgtgtgg ctacacctta tcatccacag acatctggtc aagtggaagt 4980 ttcaaacaga gaattaaaac gcattttgga gaaaacagtt ggttcaacac gaaaagattg 5040 gagtttaaaa ctaaatgatg cattgtgggc ctacaggaca gcttataaaa ctcctattgg 5100 gatgtcgcca tttcgactcg tttatgggaa agcatgtcat ctacctatgg agctggagca 5160 taaggcttac tgggcaatta aagagttaaa tttttcttat gacgcagctg gggaacaacg 5220 taaattgcag ctcaatgagc tggaggaaat tcgtcagggt gcttatgaaa gttctcgcat 5280 ctacaaggaa agaactaaag cgtttcatga cagtcaaatt ttacggaaag aattccagcc 5340 agggcaaaag gtgttgctat tcagttcaag gctaaagttg tttccaggaa aattgaaatc 5400 tcgttggact ggaccgtatg tggttacaaa aatctttcct catggggcag ttgaaatatc 5460 taatgaggct caagtcaaca cattcaaggt gaatggtcac aggctgaaac catacatgga 5520 gtcacccttc gatacagcat acgagtcttt gactctgaag gcaccagtga tctagccacc 5580 gaacttccgc aacgtctagc tacagactta aaataaagcg ctaattggga ggcaacccaa 5640 tttttctaaa ctctttgcta attttaattt ttgtttgatt ttctmyttaa aaaaaaaaag 5700 aaaaaaacat acacataaaa ataattcgga araaaaaaaa aaaaactaaa aattcaaaaa 5760 aaaaaataaa taaataaatt tggaagatgg caagttgatt ttatttaccc attttatttt 5820 tatttttatg ttccattttt taacgcgtat tggttaattg caggttgcga acatggaaaa 5880 taaagcgcgt cctaggctgg aatcctgcac ccagcagcaa gtctaacgtt cacatcaacc 5940 acatctacac taggcaggaa atttaaagca gtcaatataa aaaaaaaaaa aaaaaaaaaa 6000 aaatcattca cagatgcaag tttgggggtg attgttgtag atccagcgca taaacagagt 6060 ttagagcagt taattttctg cagctcagtt gtgcgatgca tggaggaagc acaattaaat 6120 cacagatcca tacaccacag aaccgagtac agctattatt accagatcta caacaattcc 6180 acttgcaagg atatgaaatt ttacctccca gattcaccga tctgggttct tggaagcttg 6240 tcccgttttt gtctattgca gctgaggttt cgccgtccat tttatttccc acggatcyat 6300 cagtgaccac atttcctgma yagttcacaa caagaagact aatgacactt tgattttcat 6360 gatccaggtt atgtatcact taaaacacac aagcttgtga aagtcatatt ttctgaaggt 6420 cttattagtg ttgttatttg ttcatcagtc tcccgcactt caacttcact ttcatcatat 6480 catgttagtc agtatgttgt tcgttcgatt catgttcata cccgcatata catatggttt 6540 ttgttattat ttttcaaagt tccatggacg aaataaagcg tttcatgaca tttaaccaag 6600 aacagggctg agtttatacc ttcataatcg aaagatcaaa accttcatga tgggccatgc 6660 tttatgtcca gtggatkttc agtttgagag ttctttctcg ggtctgtcac agatctgagt 6720 gttgtgcaca cataccacac cattataatt atatgcatag gtgatgaagc tattttygtc 6780 attaacctac ggagtacaag atttttacct tttgcaggaa ccagatctgc rtkgtagctg 6840 gtttgcattg cgttttcctt gtcatggcta aacttccaga tcgagaacct gtgcacataa 6900 acaaratacc acatcagtct acacatgcag tgtggagtat atgagacgca maaatggaca 6960 aggtttacct ctgtggtagg gytgttttcg gatttttgca gaggaaggtg tgtgtggttg 7020 cgcggctaag ggtgaagagg agtaaggaaa tgagagacaa atgtgataga aggagagctc 7080 tttttcattt tagagagcaa tttctgattt tagtgagagc gagggctgaa aaataaaatg 7140 gaagattggt aggaaaagga atgcagaact gagatggttt aaaagttttt tttagctttt 7200 ctagaaagag agatggacaa atgggtttat ctaaaccttt tatttggaat cctaaggtgt 7260 ggtgaaacgg atgcgcgaca cgtgtgccta ttttcagctt cacgggctac tcgaggagga 7320 tggttttgca gtggtwgaga gccgttggct ctgtggtact gactgacaca taaaaaaawa 7380 aaaaawwaaa aaaataaatm aaaaaaatat cactgaggac tgatagggat tttttttctg 7440 ayaagagaca ttgctcacgc catatgcaaa ttcgcatgcc agctgcatgc caatcaaata 7500 tctcagagca tccaatgcca ttcaaaatct cagagtttct ttaatccaat ggacgccagc 7560 tgcatgccct tctcagagca aggccctgat ggaagccacg tgatgccctg ctgatttcaa 7620 atactgtgta cagcaggcgt gcaagtgaag gtggcgtgca agttggtttt cattgcatgg 7680 gctttgtgtg gtttttattt ggccacacct atatcaacca caacgtcact tccaaagcca 7740 ggtagtcttt tttctttttc tttggttatt gttactcatt ttccttgtta taattattat 7800 ttgttagttt aagtttattt tatttttgtc attttttatt ttagtttctt ttattttatt 7860 ttctacamct tgaggacaaa gtgtrrywtw wktttrkkgk tgkgwmmgtw twwwartttc 7920 attmttsyta agttaatatc catagaktat tttaarcrkt rgaacaaatg gacatggtga 7980 aagttaatcc cacattagag tcttttctat ttatcgttgc ttagacacta attcatgaat 8040 tatactttga actttgcaca tcacaccaac atggtttgtg ggragtgaga ttgaaatact 8100 tgcttttagt ctaagtttat ttttawttyt tawtttttat tttaagtaaa gtcagttatt 8160 agtgtgaaaa aawwaaawww awaaataaag taataattgt ctcacccgag gttctgccta 8220 gtaaccgggc cagtcctgcc taatcagcag tgattctcgc gtcaaacggt agagttttgg 8280 catgaggcag ggtggttagt tggtttcgta gccttttcag ctcgggttaa taagtcctta 8340 ggggtgttct acacctagtg ycctaaagcc ctagtggttt gggagtcatt gacctaaagc 8400 tcgctacatg ggttkgatcg aaagcttaag taaaccgaca ttgcacgacc actactrtta 8460 ctggarraaa aaaaaatgtt atatatraaa aaaaaaaark kraaaarraa aaaaaaagaa 8520 aaagaaagag agttatattt aaagttacta tgtgtgaaat aaataaggac gagaggtaag 8580 ggttttagtc gagtctcctt aattatgttg gttcacttta caccaaagga agtttgtgaa 8640 ttcttttcta attgattcta aatggcttag actctgtggt gggattrgtt ggaacttttg 8700 aaaaratgtt ctagttttta aaatttrcta tggattgcaa ctttgaaggt gaaaattttt 8760 gtcagttaat tttagctagt tgtctagttt rttaagtttt tatttttgtt tgagtcttgt 8820 tttgcttgag gacaagcaaa aagctaagtt tgggggtatt tgatgagtag attttatatt 8880 atatatttta ccctaatctt agtatatttt ggttaatatw ttkgaagaat tttgatactt 8940 tgaattgtat tttcaatata ggactttcga cttcctctgg agcaaaacag gaccaaatgg 9000 acgaattttg gagtaattcy arttggagga cgttcgtgag tcamttagct tgatcgtatc 9060 aaaatttggg atttttccac caagcrgtta ttttctggcg atgaaataaa gaagcagtgc 9120 gcagtgctgg aaaatracgt ttttgggctt aaatgacgtt tttggagccc aagatgacct 9180 cggatgggtt cgtggccttc tggaaaartg ttcagaatat tccaaacatc aaatccagct 9240 atattgggcc agttttggag cagcttwtgg gccaaaacgt ggctgttcag attttagacg 9300 aattttacta tttttattta gggtttttat taattttagt tggctagggt ttgtgtggtg 9360 gcttagcaaa tatattgctt ggccgtctac agttttwgat tacgctttat tttatgcaat 9420 attggagaca gagagargkg ctagggtttt gaagattttc tacttgaagg tgttttcaat 9480 ccttttctta akaatatttt ctatgatttc aattatgaat atgcggaact aatttctttt 9540 gctagggcga agccttgagc cttagcatga atatgtgatt tttatttaat tgcttatgat 9600 cgattgcatg cgtactttga attgttaatc accgggataa aaactatcta attgtcgtaa 9660 tgcctgatca ccattaggat ctttagaaaa gtaatttgat gcaattttgg tcggaaggtt 9720 ccctgaaatt gacgctggct tcttgtgatt aataattgta atttctctta ggatgaatat 9780 cacgtcttaa ggattgcatg gtttttcaaa ggattttcat aaagcataat gagtctttca 9840 tgttcatatt tgatccgaac gtccggacgg gttgcatgtt agatatacgt tctacgttgg 9900 aggttccaag tagaatatga attaggaaaa tctaaccttc aaagtggtat gtgtagatca 9960 taagtaatgg gtaaaaattc ataggattac taggtgatgg tggaacccta gtgccttctc 10020 aatttgattt tctcaaaact gttttttttt ctctagtcct aatat 10065 // ID Copia-47_VV-I repbase; DNA; EDCOT; 6039 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-47_VV_; KW Copia-47_VV-LTR; Copia-47_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6039 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 3718804 3724842. XX CC Positions [2944-3273] - Integrase core CC 'TCTTC' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1435..3273,3277..5580) FT /product="Copia-47_VV-I_1p" FT /translation="MMYIYSCMYDAYVTNCELYYYESTSSISANVNNIPVL FT NGTNFKKWKEHVIIVLGCMDLDFALRDDRPSDLTSASTAEQRSTMEKWERS FT NHMSLMIMKHSIPEAIRGAIPEETQAKAFLDQIANRFAANEKVETSTILSK FT LVSMRYKGKENIREYIMEMSNLVTRLKALKLELSEDILMHLVLISLPTQFN FT PFKISYNTQKEKWTLNELIAQCVQEEERLKQEKIESAHLASTSQGFGTNKK FT RKKDNKGKQTAVSGTSKQKEQKKQDKEITCFFCKKAGHMKKTCTKYAAWRE FT KKGTLLNFVCSEINLAVVPTDTWWIDTGATTHISVTMQGCLRSRMPTDGER FT YIYVGNGNKVAVKAIGLFRLQLDSGCTLDLEETFVVPSFRRNLIYVSCLDK FT FGYCCSFGNGMVSLYLNSNIIGTGSLTDKLYKLNIKATNGNETLHSSNYGI FT KRKLMNENSSMLWHKRLGHISNQRIQRLVSDGILDPLDFSDFQVCIECIKG FT KQTYMKKKNANRCSDVLELIHTDICGPFPTPSWNGQQYFITFIDDYSRYDY FT LYLIHEKSQSLDVFKNFKAEVENQLSKKIKAVRSDRGGEYYGRYDGSEEQR FT LGSFAKYLMECGIVPYTMPRTPSQNGVAERRNRTLKDMVRNMISHSTLPES FT LWGEAIKIEVYILNRVPSKAVAKTPYELWTSKKPSIRHLHVRGCPVEARPY FT KPNEKKLDSRTVSCYFVGYSERSRGFKFYDPSTRSFFETGNAKFIEDVELS FT GREPLRKVVFEEEFVNIPIITTGHGHIMFNDTIQNVQSITGIQDTPEIPPA FT QVMEPIQVHQEVTQQPQVQVPLRRSTRERRSTISDDYVVYLQEHEFDMGLE FT DDPISVSQVKQSSNSEKWIEAMKDEIKSMKDNGVWDLVELPKGVKPIGCKW FT IFKTKRDSKGNIVRYKARLVAKGFTQKEGIDYKETFSPVSSKDSFRIIMAL FT VAHYDLELHQMDVKTAFLNGNIDEIIYMVQPENFESKDSKQLVCRLKRSIY FT GLKQASRQWYRKFDQVITSFGFKENTVDQCIYLKFSGSKFIILVLYVDDIL FT LASSDVGLLHETKRFLSSKFDMKDLGNASFVLGIQIHRDRSRGILGLSQKA FT YIDKVLSRFGMSNCAPEDTPVAKGDKFSLHQCPKNELEKKDMERFPYASAV FT GSLMYAQVCTRPDIAYIVGMLGRYLSNPGMDHWKKAKRVMRYLQRTKDYML FT TYRRSSHLEIVGYSDSNFAGCLDSRRSTSGYIFMLAGGAVSWKSVKKTLVA FT SSTMETEFIACYEASNHGIWLWNFVTQLRIVDGIEKPLRINCDNKAAELYS FT KNNRSSSKSKHIDIKFLVVKERVQSLQVSIEHISTNSMIVDPLTKGLPPKV FT YHEHVTHMGVVHIDDVSE" XX SQ Sequence 6039 BP; 1882 A; 1038 C; 1339 G; 1780 T; 0 other; attggtatca gagcccaatg ttgaatcact tagaattggc atataagggc aataaaattg 60 tactggcttg ttttttcctt ttaattggat tcagacgcca tttcaagcgt caatttgcag 120 tggcttgttt ttccttctaa ttggattcag acaccatttc aagcgtcaat ttgcagcgcc 180 cttgaaggcg cacttcaggc acttttagag gcgccactca gacgcctgtt tagacgccgt 240 tagggcgcgc ttcagccagc gccattgagg cgtggttcaa gtgcgtttca ggcgcagttc 300 aagagccact ccagtaccat taaggcgccg tctccggtgc ggttcagggc gctactttag 360 gcgtcgtttc tgacgccgtt aaggcaccaa cggaggcgcc gttatggcgt cattgcagtg 420 ccgtttaggc gcttcaggcg gcgcacttca ggccgcgtgc ttcaggcgtg gcctgtgcgc 480 gctgcaagcg tggcctccga tgccgttccg agggggcgct tcaggcgcgc tggtggctat 540 tggtgcgcgc tgcaggggtg gcctttgacg ccattccggg gtcgtgctct gaggcgccac 600 ttccggcatc gtctccagcg ccgttgaggt gcggttcagg cgacccactc tggcgccatt 660 agggcgcttt tccaggcgcc gttgaggcgc catctgcagc gccgacggag tgttctctgg 720 gcaccattct cggtgccgtt aaggcgcagt cgccggtgcc gttaaggcgt agtctccggt 780 gccattaaga agccttctta agcgccgttt agggcgcact ttaggtggcg tgcagttgca 840 ggctcccaac gccatgaatg gcgtttaaaa tatatatata tataaaataa aaaaaaaaaa 900 gtggaaaaat gagtaaggcc accaatgggc tcgaacccac gaccacatgg ttggaagcct 960 tgtgctcaac caactaagct atgagaactt tgtgtttata tatgatttta taccataaat 1020 gatcatgatt ttgataaatt tttgtattct cttctctata ccatgttaaa tatagagaat 1080 ttaccatttc ttattacatt tgtgttttat attttaaaat aaatgaattg tgtatgtcaa 1140 ttgccaaagt gacttgtatt atataattta tttattttat aatatgtaaa catattattg 1200 ttatttaaaa taatcggccc aaaggaagat tattttgaaa taataataga taaagtagtc 1260 ataaatatgt gatatatact gtttatcttg cattgatatg ttagtccaaa gacaaacatt 1320 ttgtgtttga ttttattgtc aatatttatg tattaatttt gtataaggat accaattaca 1380 agttaatatt tttgtccaaa gactgaatat taatgtttgt gctaggtatc ttgcatgatg 1440 tatatttatt catgtatgta tgatgcttat gtgactaatt gtgagcttta ttattatgaa 1500 tcaacatctt ctatatctgc aaatgttaat aacattcctg tgcttaacgg cacaaatttc 1560 aagaaatgga aagagcacgt tataattgtg ctcgggtgca tggatttaga ctttgcatta 1620 agggacgatc gcccatcaga tcttactagt gccagcactg ctgagcaaag gtctactatg 1680 gaaaaatggg aacgatccaa tcacatgagt ctaatgatta tgaagcactc aattccagaa 1740 gcaataaggg gtgcaatacc tgaggaaacc caagccaagg cattcttgga ccagatagca 1800 aaccgattcg ctgcaaacga aaaggttgag acaagcacta ttcttagtaa gcttgtctct 1860 atgcggtata aagggaaaga gaatatcagg gagtacatta tggaaatgtc taatcttgtg 1920 acgagactca aggcactaaa gttagagttg tcggaagaca tactcatgca cttggtcttg 1980 atctctctgc ctacacaatt caatccattc aaaatcagtt acaatacaca aaaggaaaaa 2040 tggactttga atgagcttat tgctcaatgt gtgcaagagg aagagagatt gaagcaagaa 2100 aagatagaaa gtgctcactt ggcttccaca tctcagggat ttggtaccaa caagaaaaga 2160 aagaaggaca ataaaggaaa acaaactgca gtttctggga catcaaagca aaaggagcaa 2220 aagaaacaag ataaggagat cacttgtttc ttttgcaaaa aggctggtca tatgaagaag 2280 acatgtacca aatacgctgc ttggcgtgaa aagaaaggta cacttctcaa ctttgtttgt 2340 tcagaaatta atttagctgt agtgcctact gacacttggt ggatagatac gggtgcaact 2400 actcacataa gtgtcactat gcaaggttgc ctaaggagcc gaatgccaac tgatggtgaa 2460 agatacatct atgtgggaaa tggcaacaag gttgcagtca aggctattgg tcttttcaga 2520 ttacagttag actctggatg tacattggat ttggaagaga cttttgtagt accgtcgttt 2580 agacggaatt taatttatgt ttcatgtttg gacaaatttg gatattgttg ttcatttgga 2640 aatggaatgg ttagtcttta tctaaattca aatattattg gtacaggtag tctaacagac 2700 aaactatata aattgaacat aaaggccact aatggaaatg aaaccttgca ttcaagtaat 2760 tatggcatta agcgaaaatt aatgaatgag aattcatcaa tgttatggca caaacgtttg 2820 ggtcatattt caaatcaacg aatacaaaga cttgtgtcag atggaattct cgatccactt 2880 gatttctcag actttcaagt ctgtatagaa tgcattaaag gaaaacaaac atatatgaag 2940 aaaaagaatg ccaataggtg cagtgacgtc ttggaattga tacatacaga catttgtggt 3000 ccatttccta ccccttcatg gaatggacaa caatatttta tcactttcat tgacgattac 3060 tcgcgttatg actatcttta tttgattcat gaaaagtctc agtcattaga tgttttcaag 3120 aatttcaaag ctgaagttga gaaccaacta agcaagaaaa taaaagccgt cagatctgac 3180 cgtggaggtg aatattatgg tagatatgac ggatccgaag aacaacgtct agggtcattc 3240 gccaaatatt tgatggagtg tggtatcgtt ccttaataca ccatgccaag gactccgagc 3300 caaaatggtg tagcagagag gcgaaatcgt actcttaagg atatggtaag aaatatgatt 3360 agtcattcca ccttaccaga atcactttgg ggcgaagcca taaaaattga agtttatatt 3420 ttgaatagag taccaagcaa agcagtagcc aaaaccccat atgagttatg gactagcaag 3480 aaacctagta ttaggcactt gcatgtccgg ggttgtccag ttgaagctag gccttacaag 3540 ccaaatgaaa agaaattgga ctccagaaca gtgagctgct actttgtagg gtattctgaa 3600 aggtcaagag gtttcaaatt ttatgatccc tcaactagat ccttctttga aacgggcaat 3660 gctaagttca ttgaggatgt tgagttaagt gggagagagc cattaagaaa ggtggtcttt 3720 gaagaggaat ttgttaatat tcctattatt acgactggac atggtcatat tatgtttaat 3780 gacactattc agaatgtaca gtcgataaca gggattcaag acacacctga gattcctcct 3840 gctcaagtta tggaaccgat tcaagttcat caagaggtaa ctcaacaacc tcaagtacaa 3900 gtgccactaa ggagatccac tagagaaagg agaagtacaa tttcagatga ttatgttgta 3960 tatctccaag aacatgagtt tgacatgggt ctggaagacg atccaatttc agtaagtcaa 4020 gtcaaacaaa gttctaattc tgaaaagtgg atagaagcca tgaaggatga gataaaatca 4080 atgaaagaca atggtgtttg ggacctagta gagttgccta aaggtgtaaa accgattggt 4140 tgtaagtgga tttttaaaac caagcgggat tcaaaaggca atattgttag gtataaggca 4200 cgcctagttg caaaaggttt cactcaaaag gaaggcattg attataagga gacattttca 4260 ccagtttcat caaaggactc ctttagaatc atcatggcac ttgtagctca ttatgattta 4320 gagctacatc aaatggacgt taaaactgcg tttcttaatg gcaacattga tgagataata 4380 tacatggtgc aaccggagaa ctttgagtct aaagattcaa agcaactagt atgcagatta 4440 aaaaggtcca tatatggttt aaagcaagca tcccgacaat ggtacagaaa gtttgatcaa 4500 gtgattactt catttggttt taaagaaaac actgttgatc aatgcatata ccttaagttc 4560 agtgggagca aattcattat cttggtgtta tatgttgatg atattctact tgcaagcagt 4620 gatgtgggac ttttgcatga aaccaagcga tttctgtcta gtaaatttga catgaaggat 4680 cttggtaatg catcttttgt gctgggtata cagatccata gggatcgttc aagaggtata 4740 cttgggttat cacaaaaggc ctacatcgat aaggtgttga gtagatttgg catgagcaat 4800 tgtgcaccag aagacacgcc tgtagcaaaa ggcgataagt ttagtttgca ccaatgtccg 4860 aaaaatgaac ttgagaagaa agatatggag agatttccct atgcctcggc agtaggaagt 4920 ctcatgtatg cacaagtttg tacgcgtccg gatattgcgt acattgttgg aatgttaggc 4980 agatatttaa gtaacccagg tatggatcat tggaaaaagg caaaacgggt tatgcggtat 5040 ttacaaagaa ctaaagatta catgctcaca taccgtagat caagtcactt agagatcgtg 5100 ggatattcgg attccaattt cgcgggatgt cttgatagta ggagatccac ttcaggctac 5160 atcttcatgt tagctggagg agcagtttca tggaaaagtg ttaaaaaaac acttgttgct 5220 tcttccacca tggagacaga attcatagcc tgttacgaag catcaaacca tgggatatgg 5280 ctgtggaatt ttgtcactca gttacgaata gttgatggga ttgagaaacc attgagaatc 5340 aactgtgata ataaggctgc agaattatat tctaagaaca accgaagttc gtcaaagtcc 5400 aaacacattg acatcaagtt cttggttgtg aaagagagag ttcagagtct tcaagtatcg 5460 attgaacaca taagcacaaa ctccatgatt gtggatccgc tcactaaggg tttgccaccc 5520 aaagtatatc atgagcacgt cacacatatg ggtgttgtac acattgatga tgtgtcagaa 5580 tagtgggagt ttgtatttag attttgtgtt tattttcttg atgtgatatt atgttgtgtt 5640 atctgtacag accttgattt taaagactat tgtatttgaa cactctgaat tgaaatgatg 5700 acttttagaa gcagtttagc atcaagtgtt gaaagtgtta tttgactatc ttttagtcat 5760 aaaataggac caattggaaa tagacatatt aaagatcata ttctatgtaa tttccatgct 5820 acacatccat acttgatcca tgttgctaat tttgttaatg ttgtgattaa tgataggtca 5880 agttataatt atgattaacg aaggcctctt taatcctatg ttagcataat tagtagaccg 5940 gattgtttaa ggatattttg aataagttag caaagatgag ctcaataaag tattatcatg 6000 aacattgttt gtaatatata tgtggtccaa gtgggagat 6039 // ID Copia26-PTR_I repbase; DNA; EDCOT; 4012 BP. XX AC scaffold_252; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia26-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4012 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4012 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 226-226 (2007). XX DR Genome; scaffold_252; Positions 147990 143979. XX CC Positions [1637-2137] - Integrase core CC 'AGGGT' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 494..4012 FT /product="Copia26-PTR_I_1p" FT /translation="MQKMKDSETIRDFSDRLLSIVNKIRLLGEELSDQRVV FT EKILVTLPERFESKISSLEEAKDLSKISLGELLNALQAQEQRRTIRQEESM FT EGAFPAKVQVKESDKGKRKNIKYKGAGSSNRRVGTFPPCQHCKKTNHSQNY FT CWWRPDVKCRKCNQLGHMEKICKNRTNQQHEEAQVADQQQEEQLFVATCFV FT SKHASDCWLIDSGCTNHMTNDVNLFKHLDKSSVSKVRIGNGEYILVKGKGT FT VAIEGNSGIKLISDVLFVPEIDQNLLSVGQLLEKGYSVVFKNKHCLISDPT FT GLEIFTIKMQGKSFSLDWMEEEIAAVSNTTNEADLWHKRMGHFNQATLVHM FT QRRKMVRGVPSLEEKITVCVSCQYGKQHRLGFPQNKAWRASEKLQLIHTDV FT AGPQMTDSLNGSRYYVAFIDDYTRMCWVYFLKSKAEVAGVFLRFKNWVENQ FT SGHKIQIVRSDNGTEYTSNKFAQFCHDAGIEHQYTTPYTPQQNGVSERKNR FT TIMEMARCLLFEKDLPKKFWAEAVNTAVFLLNRLPTRALQHKTPYEVWHGY FT KPSLQNLKVFGCLCFTHIPQVKRDKLDRKAEAGIFVGYSNVTKGYRVYQPA FT TEKIIISRDIKFVEAEKWNFEDTTSNASKEIMQDFDEDVDDTPVRGTRLLA FT DIYQSFNVAVLEPAEYEEAKNDPRWVTAMKEELSMIEKNQTWELVDMPTHK FT QPIGVKWVYRTKLNADGTINKHKARIVVKGYAQVFGVDFSETYAPVARLDT FT IRMLLAIAAHKGWKIFQLDVKSAFLNGYLQEEIYVEQPKGFMVEGEEDKVY FT LLKKALYGLKQAPRAWYNRIDEHLLKHGFNKSLSESTLYIKSSNTGLMAVS FT LYVDDLFVTGNNSTMIDIFKAEMMEVFEMTDLGEMSYFLGMEVQQNQLGIF FT VGQQKYAKEILKKFKMEDCKSMTTPMNLKEKFSKEDGADKVDEAIYRSLIG FT CLMYLTATRPDIMHAVSLLSRFMHCASEIHFKAAKRVVRYIKGTLNYGIKF FT SCAENFELQGYADSDWAGSCDDMKSTSGYCFSFGSGIFSWCSKKQEVIAQS FT TAEAEYVAATAAANQVLWLRKILADLDMEQREATKVNVDNQAAIAISNNPI FT FHGKTKHFKLKYYFLREVQKNEELQLIYCKTEDQLADILTKPLPKARFETL FT RNKIGVCSKRCKEE" XX SQ Sequence 4012 BP; 1406 A; 677 C; 895 G; 1034 T; 0 other; aattggtatc agagcacatt gattttaaag ggaccagctt gtgagaaaga gagcaacctg 60 tgagaaaccc ttcttccacc aaaaaaccac aaaacaccaa aaccaaaacc tttcatcatt 120 ctttcaaatg gcatccaaca cttattctct tgcaacacca ccagtattta ctggtgtgaa 180 ctaccaaatg tgggctgtga gaatgaaaac ttacttacaa gcctgcgatt tatgggatgc 240 tgttgaacaa gaacatgaac ctcagcctct ttctgcagat ccaaccatag cccaaatcag 300 aaataatcgt gaggagagat caaggaagtt caaagccaaa acttgtctct atgctgctgt 360 ttctgaagca atatttccaa gaataattgc ttttgataca gggaaacaaa tatggaatta 420 tctcaaggag gagttccatg gtaatgagag gacaattcaa atgcaggttt tgaatttgag 480 aaggtagttc gaaatgcaga agatgaagga ctcagaaact atcagagatt tttctgatag 540 attactctcc atagtcaaca aaataagact attgggagag gagctttctg atcaaagggt 600 tgttgaaaag atccttgtga ctttacccga gaggtttgag tcaaagatat cctcattaga 660 agaagccaaa gatctgtcaa aaatatcttt gggagaattg ttaaatgcct tacaagctca 720 agaacaaagg agaactataa ggcaagaaga atccatggaa ggagcttttc cagcaaaggt 780 gcaagtcaaa gaaagtgaca aagggaaaag gaagaacatc aaatacaagg gagcaggcag 840 tagcaatcga agagttggaa cctttccccc ttgtcaacac tgtaagaaaa caaatcactc 900 acaaaactac tgttggtgga gacctgatgt taaatgcagg aaatgcaatc agctgggaca 960 catggaaaaa atctgcaaga acagaacaaa tcaacaacat gaagaggctc aagttgctga 1020 tcaacaacag gaggaacaat tgtttgtggc cacctgtttt gtaagcaaac atgcaagtga 1080 ttgctggttg atagacagtg gttgcacaaa tcacatgaca aatgatgtga atttgttcaa 1140 acatcttgat aaatcaagtg tctcaaaagt cagaattggt aatggcgaat atattcttgt 1200 caaaggaaaa gggacagtgg ccatcgaagg gaattcaggt attaaactca tttcagatgt 1260 cctttttgta cctgaaatcg atcaaaacct gttgagtgtt ggccaacttc ttgaaaaagg 1320 atactcggtt gttttcaaga acaagcactg tttaatttct gatcctactg gattagagat 1380 tttcaccata aaaatgcaag ggaaaagctt ttctctagat tggatggaag aggagatagc 1440 agcagtatca aacacaacaa atgaagctga cttatggcat aagaggatgg gccacttcaa 1500 tcaagcaact ttggttcata tgcagagaag gaagatggtg agaggggtgc ccagcctaga 1560 agaaaaaatc acggtttgtg tttcttgtca atatggcaag caacacagac ttggatttcc 1620 tcaaaacaaa gcttggagag caagtgaaaa acttcagctt attcacactg atgttgcagg 1680 ccctcagatg acagattcgt taaatggaag caggtattat gttgctttca ttgacgatta 1740 tacaagaatg tgctgggtgt attttttaaa atccaaagct gaagtagcag gtgttttttt 1800 gaggtttaaa aactgggttg aaaatcaaag tggtcataaa attcagattg tgaggtctga 1860 taatggcaca gaatatactt caaacaagtt tgcccagttt tgtcatgatg cagggattga 1920 acatcaatac actacacctt acacacctca gcagaatggt gtgagtgaga ggaagaacag 1980 gacaatcatg gagatggcaa gatgcttatt atttgagaaa gatttgccaa aaaaattctg 2040 ggcagaagct gtgaacactg ctgtgttctt gttaaacagg ctgccaacaa gagcattaca 2100 acacaaaaca ccttatgaag tttggcatgg ttataaaccc tcacttcaaa acttaaaagt 2160 gtttggatgc ttatgtttca ctcatatacc tcaggtgaaa agagataagc ttgacaggaa 2220 ggctgaagct ggaattttcg ttggctatag caatgtcaca aaaggctata gagtttatca 2280 acctgcaaca gaaaaaatca ttatcagcag agacatcaaa ttcgttgaag ctgaaaaatg 2340 gaattttgaa gacacaacaa gcaatgcaag taaggagatc atgcaagatt ttgatgaaga 2400 tgttgatgac acaccagtca gaggtaccag acttcttgca gacatttatc aaagcttcaa 2460 tgtagctgtg cttgaacctg cagaatatga ggaggccaaa aatgatccaa gatgggtcac 2520 agcaatgaaa gaagagctaa gcatgattga gaagaatcaa acatgggaat tggtggatat 2580 gccgacacac aaacaaccca ttggtgtaaa atgggtttac agaacaaaat tgaatgcaga 2640 tggcactatc aacaaacaca aagctagaat tgtggtcaaa ggctatgcac aagtctttgg 2700 tgtggatttt tcagaaacat atgccccagt agctcgtctt gacaccatca gaatgttgct 2760 agcaattgca gctcacaaag gttggaaaat atttcaactt gatgtgaagt ctgcattttt 2820 gaatggttac ctgcaggagg agatttacgt ggaacaacct aaaggtttca tggtagaagg 2880 agaagaagac aaggtttact tattgaagaa ggctttatat ggactgaaac aggctccaag 2940 agcctggtat aacaggattg atgagcattt actcaaacat ggcttcaaca aaagtttgag 3000 tgaatcgacc ttatatatca agagttcaaa cactggtctt atggctgttt cactttatgt 3060 ggatgattta tttgttacag gtaacaattc aaccatgata gacatcttca aagctgaaat 3120 gatggaagtt tttgagatga cagaccttgg tgaaatgtcc tattttcttg gcatggaagt 3180 gcagcaaaat cagcttggga tctttgttgg ccaacaaaag tatgccaaag agattctgaa 3240 gaaattcaaa atggaagact gcaaatcaat gaccacgcct atgaatttga aagagaagtt 3300 cagtaaagaa gatggggcag acaaggtgga tgaagcaatt tacaggagct taattgggtg 3360 tcttatgtac cttacggcaa caaggccaga catcatgcat gcagtgagct tattatcgag 3420 gttcatgcat tgtgctagtg aaatacactt caaggctgca aaaagagtgg tgagatacat 3480 aaaaggtaca ctaaactatg gcattaagtt tagttgtgct gaaaatttcg agctacaagg 3540 atatgcagat agtgattggg ctggcagctg tgatgatatg aagagcacgt ctggatattg 3600 ttttagtttt ggatcaggaa ttttctcctg gtgttccaaa aaacaagaag ttattgctca 3660 atcaacggca gaagcagagt atgttgcagc tactgcagct gcaaatcaag tcttatggct 3720 tagaaaaatc ctagcagatc tggacatgga gcaaagggaa gctactaaag ttaatgttga 3780 caatcaagct gcaattgcaa tatctaacaa tccaattttc catgggaaaa caaagcattt 3840 caagctcaag tattattttc tgagagaagt tcagaaaaat gaagaactgc aactgattta 3900 ttgcaagaca gaagaccaac ttgctgatat attaaccaag ccattgccaa aagcaaggtt 3960 tgaaactttg aggaacaaga taggagtctg cagcaaaaga tgcaaggagg ag 4012 // ID SHACOP18_I_MT repbase; DNA; EDCOT; 3936 BP. XX AC AC147006; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of a LTR retroposon from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Internal; Interspersed; terminal; repeat; ORF; SHACOP18_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3936 RA Shankar R. and Jurka J.; RT "SHACOP18_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 63-63 (2007). XX DR EMBL/GenBank/DDBJ; AC147006; Positions 57230 61165. XX CC The internal region has a single ORF having intact gag-pol CC polyprotein with integrase domain positioned likewise in CC Copia-type LTR retroposons. Present in the genome in few complete CC copies. XX FH Key Location/Qualifiers FT CDS join(40..1641,1645..3921) FT /product="SHACOP18_I_MT_1p" FT /translation="METETSFSQVAPPVFDGENYNLWAVRMESYLEALDVW FT EAVEEDYEVPPLQNNPTMAQLKYHKERKTRKAKAKSFLFSCVSQNVFTRVM FT TLKTAKEIWDYLKEEYAGDERIRGMQVLNLMREFEMQKMKESETIKDYSDR FT LLSIANKVRLLGTQFADSRIVEKILVTVPERYEASITTLENTKDLSKITLA FT AVLHAMQAQEQRRLMRQDHVVESALPAKHHVVGSTAGNQSKDRGKKKNYPP FT CEHCGKMGHPPFRCWRRPDAKCSKCNQLGHEAVICKGKFQQLEVKAQVVEQ FT DEEDQMFVATCFSSKSSSECWLIDSGCTNHMTYDKTIFKDLKPTHISKVRI FT GNGVYIPAKGKGTIVISTSSGIKTISDVLYVPDIDQNLLSVGQLLEKGFKV FT SFENQLCLIFDITGREILRVKMRGKSFSFDPIEEEQTAYFTQVSPIELWHK FT RLGHCHIQRMLNLKKKDMSRGLPVLSDDLPNCNACQFGKQNRIPFPKTVWR FT ATKKLQLIHTDVAGPQRTPSLQGSLYFILFIDDFTRMCIYFLKFKHEVAGV FT FLKFKKMVETQSGSKIQFLRSDNGKEYTSAQFNLFCEEAGIEHQPTAPYTP FT EQNGVSERRNRSVMEMARCILHEKELPKQFWAEAANTAVFLQNRLPTKALQ FT DKTPFEAWYEYKPSLTFLKVFGCVCFAHVPKVKRDKLDKKALPGIFVGYSS FT VSKAYKVYHPQTETLTITRDVHFNEDQQWDWKNPPKTSGSLSIIEYTHPEK FT QTTELCLNELEDDPSIRGTRLLSDIFQRCNVAICEPSCCEEARKDPKWKNA FT MEEEMSMIQKNKTWELVEKPQDRKVIGVKWVFRTKLNVDGSINKYKARLVV FT KGYAQIFGVDYSDTFAPVSRLDTIRLVLAVAAQRGWKVFQLDVKSAFLNGV FT LQEEIYVEQPEGFVMQGEEDKVYLLKKALYGLKQAPRAWYSRINDHLMSIG FT FVKSLSESTLYVKHTGNNILIVSLYVYDLLVTGDDTRLVEKFKQEMMQAFE FT MTDLGLMTYFLGIEIKQSDNEVFICQKKYAKEILRKFQMEECKAISTPMNQ FT KEKLSKEDGADKVDEGYYRSMIGCLMYLTATRPDILFVVSLLSRFMHCASE FT THLVAARRILRYVKGTVDYGVKYENCQNFKLCGFSDSDWAGSIDDMKSTSG FT YCFSIGSGVFSWCTKKQETVAQSTAEAEFIAATAAVNQVLWLKKILCDLHL FT QQNHKIEVFIDNQAAIAISKDPVCHGKTKHFNIKLYFLREMQQNGEVTLVY FT CKSKDQLADMFTKPLPVNKFEFLRQKVGVCRS" XX SQ Sequence 3936 BP; 1340 A; 654 C; 869 G; 1073 T; 0 other; aattggcacc agagctatca tcttacgggg cctgtgaaaa tggaaactga aacaagtttc 60 tcacaagttg ctcctcctgt ctttgatggg gagaactata acctttgggc agtaagaatg 120 gagtcttacc tggaggcttt ggatgtttgg gaggctgttg aagaggatta tgaagttcct 180 ccgctgcaga ataatcctac catggctcag ttaaaatatc acaaggagag aaaaactcga 240 aaagcaaagg caaaatcatt tcttttctcc tgtgtttcac aaaatgtttt caccagagtt 300 atgaccctca aaacagcaaa agaaatatgg gactatttga aggaagaata cgcaggggat 360 gagaggattc gaggcatgca agtactgaac ttgatgaggg aatttgagat gcagaaaatg 420 aaagagtctg agacaatcaa agattactct gacagattgc tttctattgc aaacaaggtt 480 aggttactcg gtactcaatt cgctgattct agaattgttg aaaaaattct ggttacggtg 540 cctgagagat atgaagcatc aataaccacc ttggagaaca caaaagactt gtctaagatc 600 accttagcag cagtgttaca tgcgatgcag gctcaagagc aacgaaggct tatgaggcaa 660 gatcatgtgg ttgaaagtgc tttaccagcc aaacatcatg tagttggaag tactgcaggc 720 aaccaaagca aagatagagg taaaaagaag aattacccac cttgcgagca ctgtggtaaa 780 atgggtcatc caccgttcag atgttggaga agaccggacg caaagtgcag caagtgcaat 840 cagcttggac atgaagctgt catttgcaaa ggaaaatttc aacaacttga agtcaaagcc 900 caggttgtag agcaagatga agaagatcaa atgtttgtgg caacatgttt ttcatccaag 960 agtagttcag aatgctggct gattgacagt ggttgtacaa accacatgac atatgataaa 1020 accatcttca aagatttaaa accaactcat atctcaaaag tcagaattgg caacggtgtc 1080 tatattcctg caaaaggaaa aggaaccatc gtaatttcaa cgagttcagg tataaaaaca 1140 atctcagatg ttctgtatgt acctgatatt gatcaaaatc tgctaagtgt tggtcaatta 1200 ttagaaaaag ggtttaaagt atctttcgaa aatcaacttt gtctcatctt tgacatcact 1260 ggtcgggaga ttcttagggt caaaatgaga ggtaaaagct tctcatttga tccaattgag 1320 gaggagcaga ccgcttattt cactcaagtc agtcccattg aactttggca caagcgactt 1380 ggtcactgtc atattcaaag aatgttgaac ttgaagaaga aagacatgtc aagaggtcta 1440 ccggtacttt ctgatgattt gccaaactgc aatgcttgcc agtttggtaa acaaaacaga 1500 attccatttc ccaaaactgt ttggagagcc actaaaaagc tgcaactcat tcacacagat 1560 gtcgcaggac ctcaaagaac tccatcatta caaggtagcc tatattttat tcttttcata 1620 gacgacttta caagaatgtg ttagatttat ttcttgaaat tcaagcatga agtggctgga 1680 gtatttttaa agtttaagaa gatggtggaa actcaaagtg gctccaagat tcaatttcta 1740 aggtctgata atggcaagga gtatacatca gcacaattta atttattttg cgaagaagct 1800 ggaattgaac atcaaccgac agctccttac actcccgaac aaaatggagt tagtgaaagg 1860 agaaatagat cagtaatgga gatggctaga tgtattttgc atgagaagga attgcctaaa 1920 caattttggg cagaagcggc aaacacggcg gtgtttcttc aaaatcgact tccaaccaag 1980 gctttacaag ataaaactcc ttttgaagca tggtatgagt ataagccttc actaaccttt 2040 cttaaagtgt ttggttgtgt ttgttttgca catgttccaa aggttaagcg tgacaaactt 2100 gacaaaaaag cacttccggg catttttgtg ggatatagtt cagtttcaaa ggcttacaaa 2160 gtgtatcatc ctcaaaccga aacactgact ataactagag atgtacattt caacgaagac 2220 caacaatggg actggaagaa tccaccgaaa acatctggat ctctaagcat tattgaatat 2280 actcatcctg aaaaacaaac aaccgaattg tgtctgaatg aattagaaga tgatccatcc 2340 attagaggca caaggctgct gtcagacata tttcaaagat gtaatgtagc aatatgtgag 2400 ccttcttgct gtgaggaagc acgaaaagat ccaaaatgga aaaatgcaat ggaggaggag 2460 atgtcaatga tacaaaagaa caaaacatgg gagctggttg aaaagcctca agatagaaaa 2520 gtcattggag ttaaatgggt tttcagaaca aagctcaatg ttgatggctc aatcaataaa 2580 tataaggcca gactcgtagt taaagggtat gcacaaattt ttggtgttga ttattctgac 2640 acttttgcac ctgtatccag attagacaca attagattgg tgttagcagt tgctgctcaa 2700 aggggctgga aagtatttca gttagatgtc aaatcagctt ttttgaatgg agttttacaa 2760 gaagagatat atgtggagca gcccgaggga tttgtgatgc aaggtgaaga agataaagtc 2820 tatctattga aaaaagccct ttatgggtta aaacaagcac caagggcttg gtacagcagg 2880 ataaatgatc acttgatgag tataggcttt gtaaaaagtt tatctgagtc cactctttac 2940 gtgaaacata caggaaataa tattctcata gtttctctct atgtttatga tcttttagtg 3000 accggagatg atacaaggtt ggttgagaaa ttcaaacaag aaatgatgca agcatttgaa 3060 atgacagatc ttggtcttat gacatatttt cttggaattg agatcaaaca aagtgacaat 3120 gaagtgttta tctgccaaaa aaaatatgca aaggaaatat tgagaaaatt ccagatggag 3180 gagtgtaagg caattagcac accaatgaac caaaaggaga agttgagcaa ggaagatggt 3240 gctgataaag ttgacgaagg atactacagg agtatgattg gatgtttaat gtatctcact 3300 gcaacaagac cggacatttt atttgttgta agtctcctct cccgctttat gcattgtgct 3360 agtgaaacac atttagtagc agcaagaaga atattgagat atgtaaaagg cacggttgat 3420 tatggtgtca aatatgagaa ttgtcaaaat ttcaagctgt gtggattctc tgatagtgat 3480 tgggctggat ctattgatga catgaagagc acttcaggat attgtttcag tataggctct 3540 ggagtttttt catggtgcac aaagaagcag gaaacagtag cacagtccac tgcagaagct 3600 gagttcatag cagcaacagc agccgtaaat caagttttgt ggttaaagaa gattttatgt 3660 gatttgcatc ttcaacagaa tcataaaata gaagttttta ttgacaacca ggcagcaatt 3720 gcaatttcaa aggatccagt gtgtcatggc aagactaaac attttaacat caagctctac 3780 ttcttaagag agatgcagca aaatggagaa gtaactttgg tttattgcaa gtcaaaggat 3840 caattagcag acatgtttac aaagccactt cctgtcaaca agtttgagtt tttaaggcaa 3900 aaagttggag tttgcagatc ctaaagcaag gaggag 3936 // ID Copia-11_Mad-LTR repbase; DNA; EDCOT; 262 BP. XX AC ACYM01091843; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-11_Mad_; KW Copia-11_Mad-LTR; Copia-11_Mad-I. XX NM Copia-11_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-262 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1354-1354 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01091843; Positions 737 476. XX SQ Sequence 262 BP; 87 A; 32 C; 45 G; 98 T; 0 other; tgttaggagt attatatgaa tagctaagat gttgccaaat gtcaagggat tagtattgta 60 gttataaggc tgttataaga tagcttagtt aggtagctgt caaagatagt ataaatatcc 120 tttgtaatga aatagttggg taaagaataa gaaatataca atacaattca gaaatatctt 180 gctctctaag tattttttca atctcatctc tctcttccta tcaatcttct tcttatcgga 240 tatatatgta gattggttta ca 262 // ID Copia-26_Mad-LTR repbase; DNA; EDCOT; 212 BP. XX AC ACYM01137708; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-26_Mad-I; KW Copia-26_Mad-LTR; Copia-26_Mad_. XX NM Copia-26_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-212 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1373-1373 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01137708; Positions 9556 9345. XX SQ Sequence 212 BP; 60 A; 25 C; 39 G; 88 T; 0 other; tgttagagtt aatgatatga tgagtgctta ggattatgac aagtgtctat gtattattgg 60 tggtggtatt agtagagaga tgtataaata ccaagagttg taattattct aagtgtgttg 120 aataaaaata attcattcag ttgtaaacaa atttccctct ctactttctc tctcttgttt 180 tcttagcttc taaggttttt ccattgttat ca 212 // ID Gypsy-43_Mad-LTR repbase; DNA; EDCOT; 937 BP. XX AC . XX DT 21-OCT-2010 (Rel. 15.1, Created) DT 21-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-43_Mad-LTR. XX NM Gypsy-43_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-937 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1781-1781 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 937 BP; 231 A; 232 C; 256 G; 218 T; 0 other; tgtttgggcc caaaataaca gtttgggccg agggtaggat cactctcggc ccgggaggcc 60 gtgcggcgag agggccatgg atcgttcagc tcgtgggctt ccaagcctag gtcggttagg 120 tcagaacgca agtcgagtcc tagtacaata gggagtctcg gcgggatcag aaaccaggaa 180 gcgaatccgg ctcagttaag gactaggttc acagtcctag tggagatagg actggtcgag 240 gtgatgttga tccggagagg gaaacctagt ccgagtagga ttttaactcg ggctcggggt 300 ccagtgctat aaatagagga cgctgtgcat caggaaaagc cccgcaaaaa tcaatacaaa 360 attgccctgc gcaaactctc acaacttgag atctttttct tttccttttt cgctgacaca 420 tcttccgttg gcatcaacag cactgtggaa gcaaccggtg atatcttaag tcggcataga 480 tagctctgtc accgtagaat cagtcggtct cgcagtatct tccgttggca tcaacagcac 540 tgcggcgaga acggttgatt acctatccaa gtctcggtcg agaagggttt ccgaatcctt 600 gttggtcgag gtcatctcat cagccttctc ggcgaagtga ggtgttacag ttattacatt 660 cggcacattg aaagccgaat ttgatatgtg aacttcgtaa gaatagcagc cttgtcttca 720 ggctcgagag cccaagaggc cgagacgtgt tcctttctcg gccgcaatcg caagacgcag 780 aagtcagtag cgcgacccaa cgcaacatca acaaatttac tcctcggccg agctcggccg 840 acgagttggc acgccccgca atcaccgaag gacgtagtta gcttagaaat tactcggcct 900 gcgcgccacg taggctttgt agtttctagg gtcaaca 937 // ID SHATAG_MT repbase; DNA; EDCOT; 3882 BP. XX AC . XX DT 17-JAN-2007 (Rel. 12.01, Created) DT 19-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A DNA transposon from Medicago truncatula. XX KW hAT; DNA transposon; Transposable Element; Interspersed repeat; KW SHATAG_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3882 RA Shankar R. and Jurka J.; RT "SHATAG_MT: A TAG1 type DNA transposon from barrel medic."; RL Repbase Reports 7(1), 108-108 (2007). XX DR [1] (Consensus) XX CC The DNA transposon has intact domain for a transposase like CC protein CC resembling the hAT type transposase as well as has hAT CC dimerization CC domain. It has 22 bp TIR, a characteristic feature of TAG1 family CC of CC hAT transposons. The element exists in Medicago genome in few CC copies. XX FH Key Location/Qualifiers FT CDS 813..1763 FT /product="SHATAG_1p" FT /translation="MASSEAPTQPSAEASTQESQTQRNVRAKTDIAWGHAK FT IVLDGDKEKPQCIYCNKVMKGGGINRLKLHLAGETGQVEACSQAPEEVRFK FT MKQNREEQTQREQPRSVVVASQKGTNNGSFDNYFLPRTTPGSQPTIKSVLQ FT TKEVVEKCDLALAKWFIAASIPFNAANSPYFQSAVDALCCMGAGYKAPSIH FT DLRGPLLNKWVDETKKKIEKYREIWKNTGCTLMADGWTDGVRRTLINFLVY FT CPKGTVFIKSVDASGASKTGEMLFKLFKEVVLYIGSENVVQIVTDNAANYV FT AAGRLLMKKSSLACIGLLVQLIALT" XX SQ Sequence 3882 BP; 1151 A; 662 C; 770 G; 1299 T; 0 other; ccatagtttt cagactcggc tcggaccggc cggtcggacc ggtcggaccg tgaaccggtg 60 ggtaggccgg ttcgagccat catttggatc ggccatgcag ataacccggt caaaaccggt 120 gactcggccg agtcgtgggt cagaccggtt caattttttt tttttttttt ttgcttacca 180 aaacgacgtc gttttggatt tgttaattga aaaaaaaaaa aaaaaccgga attagaaggg 240 tcagagaaac taaaacgaaa cctcatactc tgttcttagt tttcacgtac agagagaaga 300 gaagctaaaa cgaaaccggt ccactccacg ccattctccg tcgccgccgc gaaaactcca 360 ggtcgccgtc gccctcgcca tcgccgcttc cgcttccgct tatctcacgt acgtacaccg 420 tcgttgcaga gaaccctttt tttttttaga ttgttattct ttgcttcttt ttgatttgtt 480 gttttgattt cttgtttaat gtttaatttc atgtagattc tgattgttta atgtttaatt 540 tcatgtttaa ttatgaatct ctgattgttt atatgttgat tcctcattcc atgtttaatg 600 ttgactcctc tgttttatac ttattccatg ttttatactg actcctctcc tctcctctgt 660 tttatactcc tcattccacg tacgttgttg attctgataa actgattgtt aaatggttca 720 tttcatgtta atgtttaatt ctgattgttt cataattcca tgtaaatgta atgtaaatgt 780 ctctgatata tcatatgtat ttgtgattag ttatggcctc ttctgaagca ccaacacaac 840 catcagcaga agcttcgact caagaatctc aaactcaaag gaatgttagg gcaaaaaccg 900 atatagcttg gggtcacgct aaaattgtcc tagacggtga caaagaaaaa ccacaatgta 960 tctattgtaa caaagttatg aagggaggtg gaattaatag attaaagtta cacttggctg 1020 gagaaactgg acaagtcgaa gcatgcagcc aagctcctga agaagtccgc tttaagatga 1080 aacaaaatcg tgaagagcaa acacaaagag aacaacctag gtcagtggtt gttgcatctc 1140 aaaagggaac gaacaatgga agctttgata attacttttt gcctagaaca actcctggat 1200 cacagcctac tataaaaagt gttttgcaaa ccaaggaagt tgtagaaaag tgtgatcttg 1260 cacttgcaaa atggttcatt gctgcatcta ttcccttcaa tgcagcaaat tcaccatatt 1320 ttcagtctgc ggtcgatgct ctttgttgca tgggagccgg atataaagct ccttctatac 1380 atgatttgcg tggtcctttg ctaaataagt gggttgatga aacaaagaaa aagatagaga 1440 aataccgtga gatttggaag aatactggtt gtactcttat ggcagatggg tggactgacg 1500 gggttaggag aactctgata aactttttag tttattgccc taaaggaact gtttttatca 1560 aatctgttga tgcttcaggt gcttcaaaaa ctggtgagat gttgtttaag cttttcaagg 1620 aagtagtgtt atatattggc tctgaaaatg ttgttcagat agtgacagat aatgctgcaa 1680 actatgttgc tgctggtagg ttattgatga aaaagagttc cctggcctgt attggactcc 1740 ttgtgcagct cattgcatta acttgatgtt tcaagacatt ggaaaattac ctgaagttaa 1800 agaggcagtt tcacatgcca caaatgttac caagtatata tataatcatt gctatccatt 1860 gtatttgatg aggaaattta ctcatggaag agagatactt cgtcctgctc caactcgctt 1920 tgccactaat ttcattgctt tgcagagtat tttgtctcag aaaaatgcac ttagagccat 1980 ggtaacatct caagaatgga caacttctgc ttatgcaaaa gaagccaagg ccaaacaatt 2040 tgtggaacaa gtcttgaaca ctaacttttg gactgcttgt gctgacatag tgaaactcac 2100 agaaccactt gtatgtgtgt tgcgtctcgt ggacagtgaa gataaacctg ctatgggttt 2160 tctttacaga aatatgtata aggctagaga ggagatggtg aagaggtttc aaagaaataa 2220 gacaaaagtg gagccttact tgaagatcat agatgatcga tgggattcac aacttcgaaa 2280 aaatcttcat gctgctggtt attggttaaa tccatcttgt agattcagtc ctgagtttga 2340 gaaacacaag tccaccacat ctggtcttat agatgtcatt gaaaagtatg ctcgtaataa 2400 tcatgagttg cgagcaaagt taaatactga gacaagtata tttagaaatt ccgagggcga 2460 ctttggaagg aaatctgctg tagaagctcg aaattcacca tttccaggta tcttacattt 2520 cattgtatca tatacactta cgatgatcca tttacaaata tcttaccttt cattgtatca 2580 tataaactta cggtaatact gtattaattg atgaaatttt gcaattttat agatgaatgg 2640 tgggaacttt acgggtgtca agcaccacat ttgcaaaaat tggcaattcg ggttctaagt 2700 caaacttgta gctcttctgg ttgcgagaga aactggagtg tgtttgagca tattcactca 2760 aaaaaaagaa ataggttgga gcatcaaagg cttaacgatc tagtctttgt tcgttacaac 2820 ttaatgctag aaaataggta tgtatttcta ctatatttta gttatattaa tccattgata 2880 aaatagtgtt tgtttctttg cataatggga ttgttcacaa taaaccttat atgttcatca 2940 ttttttattt ttacatttag atagaaatct ttatattttt ataatgaatt ataggaacaa 3000 caaaattcga aactatgacc ccatcaatga tgaattactt gatgatcatc atgataattg 3060 ggtgttggag gattcaccgc catttttaac agttgaggag ttggaatcat tacgcaatga 3120 tcttgccaat atgaccatcc aacctatttc aaatgatatt ggtatgtatg tgttttctta 3180 taaggttaaa atttcataat ttcactatat ggttatatac caattgttaa tatttattta 3240 aattgatgtt ttcatagatg gattgaattt ggatgaggat gatgattatg gcaatgatgc 3300 acctgacact aatgcagaaa acatggatca aagtaatgtt tttgatgaag ctgctggaga 3360 agatgttgaa ttccttgatg agcttcaaat tcaatcaata ttgactcctt ggaattaaga 3420 tgttattgat gataatactt gtgttggaat tatattttct tgggatcttt ttgaattttt 3480 ataacagggg caatctcttt ttttaattta tgttggaatc atactttttt gggatctatt 3540 tggattttta ctaccaagat gtattttgag ttatgactat gttttgaatt tgagcaatta 3600 gctatgaaat tattattgtt ggatagtttt tttcttattt tataggggtc attattttag 3660 tttctaaagt gaccgagtca ccgattaaat ccgagttaat ccgagttaat ccggttatat 3720 aactatataa atttaatcta aggaccgagt tatctaaccg agtcatccga gtggttccgg 3780 ttcagtcatg cggttcgacc aatgactcac tggttcgacc attgacccat tgacccagta 3840 cccccgccga gtcgatgacc gagccgattc tgaaaactat gg 3882 // ID MuDr-5N1_Mad repbase; DNA; EDCOT; 148 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW MuDr-5N1_Mad. XX NM MuDr-5N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-148 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1514-1514 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TSD is 8-bp. TIR is 40-bp long. ~96% identical to the consensus. XX SQ Sequence 148 BP; 37 A; 38 C; 30 G; 43 T; 0 other; ggggtgtgct atccacacac cccattttac ttctcacaca ccccttgtta atttctgtcc 60 gttgatcttc ttcaattcat ccgatccgac ggccgaaaat taaaaaggtg tgtgagaagt 120 aaaatggggt gtgtggatat cacacccc 148 // ID RTIP1_LTR repbase; DNA; EDCOT; 588 BP. XX AC AB000394; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Ipomoea purpurea retrotransposon RTIP1_LTR, long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Long terminal repeat; KW RTIP1_LTR; retrotransposon. XX OS Ipomoea purpurea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea. XX RN [1] RP 1-588 RA Hisatomi Y., Hanada K. and Iida S.; RT "The retrotransposon RTip1 is integrated into a novel type of RT minisatellite MiniSip1, in the genome of the common morning glory RT and carries another new type of minisatellite, MiniSip2."; RL Theor. Appl. Genet 95, 1049-1056 (1997). XX DR Genbank; AB000394; Positions 1 588. XX SQ Sequence 588 BP; 168 A; 142 C; 176 G; 102 T; 0 other; tgatggggtg agaaccccgg cccaagaaaa gaggcccaga gaggaaggac caaagaggga 60 agaatgggct gatgtaaggc gggctcaaag aatgcatgcc gagtccagga ctcggcccag 120 gtccaaagag gaaggcccag ttcagagccc gaaaggacgg cccaatgcca accggggacg 180 aggagtcggt ccaggcccgg cccaggggaa gactcggtcc agagagccgt tgagggagct 240 ttcagagcag tcaaggcaag gagccgttga ggcattaaaa gtcggactcg gtccgccggt 300 tactagccag agagagccgt tggcagagtc cgtaacgtcg cccaacagct cggcacattg 360 attgtaatct ttaagtcggc catcatgagc ctttaagtca gtggaggagg agccactata 420 aaagggctcc tccgcccttg taagagtcag attcgagaac ccggagaggg aaatagaaag 480 tactattaca tcatacttca ctaaaaatct agactttttg tgaaaggtgt atcctccagc 540 ttaaggttgt gttggacctc cttgggcccg aaaacccaaa aaccatca 588 // ID HAT-N7_Mad repbase; DNA; EDCOT; 347 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-N7_Mad. XX NM HAT-N7_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-347 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1629-1629 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >86% identical to the consensus. 8-bp TSDs. The consensus shows CC similarity to HAT-4_Mad. XX SQ Sequence 347 BP; 117 A; 68 C; 51 G; 110 T; 1 other; cagtgtttaa aatttcttcg atacggtcga tatttccatg gaaatatcca aaaaatcaga 60 gaaagatatg gaaatggggg gtgaagtcta aacttcacct catatcggag aaactcttaa 120 gtttaggcta aaatcgacax atatcgtcga tatttctgac acatctgtta aatatcggag 180 aaactcttat atttcgtcca aaccaatgtt tgacaatccc taaagtttca ttttaaattt 240 ccatcatttc catcgaaagc aaccgatatc gatattcgat atatccgtcg atatttccac 300 aaatttgcat atcgatattt ccaccgatac cgatatttta aacactg 347 // ID Gypsy-23_Mad-I repbase; DNA; EDCOT; 4605 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-23_Mad_; KW Gypsy-23_Mad-LTR; Gypsy-23_Mad-I. XX NM Gypsy-23_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4605 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1740-1740 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [3489-3983] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 47..1660 FT /product="Gypsy-23_Mad-I_1p" FT /translation="MPRKPAATRSATMDARLSSLEASFADLQSIIADVVKT FT SVHSALESDLPAHLDRRLPVYFEQFRREFSFQGVGDTSMPQPVPPPPLPPD FT LDLHPPHRHLNWAGGGHPHRTQWTQRVDFPRFSDGDDPLAWIYRAEQFFTF FT YNIPEHQRVLTASFHLEGEALQWFQWMNCLTSTPDWLAFTKVFCREFGPNE FT FEDSAEALFKLRQTGTLRDYVVEFRRLANRTTGIGPILLKSCFFGGLKREL FT KFDVKLLKPATVHEAIAIAGQLDSKLTELRATAPRTSIPVKPQPLLLPPSA FT PAGPRAGHVPVKKLTHAEIQLKRDKGECWFCPDKWVPGHKCGLKQLLMLDV FT VDSDAHCEFTDVDDAPPELLAMSLSECAFYGTTAKQSVQTMKVDGVVLGQS FT VKILLDSGSTHNFIDSRLLKKWGRQAQSTQAFEVMIADGGTVRSSGCCRDT FT ALCLGGYNCVVDLYSLPLGGCDVVLGVQWLSSVSPVLWDFQLLTMEFSANA FT QHYKLTHSPPTAPLIQEVSLQHLDKEFSNSHLGLFLYSMEGQ" FT CDS 2646..4565 FT /product="Gypsy-23_Mad-I_2p" FT /translation="MMSPQVLALPDFTQPFEIECDASGNGIGAVLQQGKRP FT IAYTSKALGPKNQALSAYERELIAIVHAVKKWQNYLQGRHFIIRTDHNSLK FT YFLSQQANTSFQQKWVSKLLGFDYEIQYKKGNDNVVADALLRIPETLQFDI FT GDPPVSAIEMSCAAISYPYFGWLDELRRDIEKDEWVIAKTREVLPPTHGTP FT GASVASKYTLDNGFLCYKHRIVLSPISPWRQKIIEEYHSTPAAGHQGILKT FT YHRIKKRYYWQGMKKDIQAFVSQCGICQQNKFETVSPPGLLQPLPIPSKVW FT TAISMDFIVGLPLCKTKSVIMVVVDRLSKYSHFMALAHPYSAATVAQVFID FT NVFKLHGMPSSIVSDRDPIFLSNFWKEFFKLQGSKLSMSSGYHPQSDGQSE FT VLNRCLETYLRCFVGGQPKKWVQWLSWAEWCFNTSYHTSSGFTPFEVVYGY FT PPPHICPYEEGSTRVESVEQLLQQRDRILDVLKHNLDLAQNRMKVQADKRR FT SERVFEVGDLVYLRLVPYQLQSLAPHQYHKLQPRYFGPYEVLERIGAVAYK FT LKLPEGTKIHPVFHVSNLKKKLGTDVVAGATLPQVTDDGLFQAIPKAVLAR FT RMYKKGTVAGVQLLIQWVDHDDSEATWEDYDTFTMKFPDFQV" XX SQ Sequence 4605 BP; 1145 A; 1028 C; 1051 G; 1379 T; 2 other; ttatcactaa cattggtatc acccttcgat cctggtccct ccgtgtatgc cccgtaaacc 60 cgctgctacc cgctctgcta ccatggacgc tcgcctctct tctctggaag cttcttttgc 120 agatcttcaa tctatcatcg ccgatgtggt gaagacctct gtgcactccg ctttggagtc 180 cgatctcccc gctcatctcg atcgtcgcct tccggtgtac tttgagcagt ttcgccgtga 240 gttttctttt cagggcgtcg gcgacacttc tatgcctcaa cccgttccgc ctccaccact 300 tcctcctgat ttggatctac atccacctca tcggcacctc aattgggcgg gtggggggca 360 tcctcatcga actcagtgga cacagcgggt ggattttccc cgtttttccg acggtgatga 420 cccactcgcc tggatctaca gagcggagca gtttttcaca ttctacaaca ttccggagca 480 ccaacgcgtg ctcactgcat cctttcatct ggaaggggaa gcattgcagt ggtttcaatg 540 gatgaattgt ctcacatcta ctccggactg gttggcgttc actaaggttt tttgtaggga 600 atttggccca aatgagttcg aggatagtgc tgaggcatta ttcaaattga ggcaaacagg 660 tacccttcgc gattacgttg tggaatttcg tagattagcc aatcgtacca ctggaattgg 720 gcctattctc cttaagagct gtttttttgg gggattaaaa cgtgaattga agtttgatgt 780 taagcttttg aaaccggcaa ctgtacatga ggctatcgct attgctgggc aattagactc 840 taaacttact gagctcagag caactgcacc tcgaacttct atccctgtta aacctcaacc 900 gctacttctt cctccttctg cccctgcggg tcctcgagct ggtcatgtgc ctgttaagaa 960 attaactcat gccgagattc aattgaagag agacaaagga gaatgctggt tttgtcctga 1020 taaatgggtt ccggggcata aatgtggcct aaaacaatta ctcatgttgg atgttgttga 1080 ttctgatgct cattgtgaat tcactgatgt tgatgatgct cctcctgagt tattggcaat 1140 gtccttaagt gagtgtgctt tttatggaac cactgctaaa cagtctgttc aaactatgaa 1200 ggttgatggt gtggttcttg gacaatctgt caagatttta ttggactcag ggagtactca 1260 taatttcatt gattctcggt tgcttaagaa atggggtcgc caagcacaaa gtactcaagc 1320 ctttgaggtt atgatcgctg atggaggaac agtccggagc tcgggttgtt gtagggacac 1380 tgccctttgt ttgggagggt acaattgtgt agttgactta tactctcttc ctttaggtgg 1440 ttgtgacgtg gtgcttgggg tccagtggtt gtcttctgta agtcctgttc tttgggactt 1500 ccaactattg accatggaat tttctgccaa tgctcagcac tacaaactga ctcacagccc 1560 acctactgcc ccacttattc aggaagtttc attgcaacac ttggataaag agttttctaa 1620 ctctcatttg ggtctcttcc tctattctat ggagggtcag ttmttgcacc attctgcatt 1680 atctcctcaa caatcacacg aactaaatga gttacttggg gccttcgaag mcatctttgt 1740 gttaccttct aagctcccac cttctcgggg tcatgaccac cacattcctt tggttccagg 1800 cgccaaacct ccaaatttgc ggccatatca ttatggtcct atgcagaaga ctgaaattga 1860 aagaactgtg caagaattac ttgactcggg gtttattcgt cccagccaca gtcctttttc 1920 cttccctgtc ctcttggtta agaagaaaga gggcacttgg cgtatgtgta ttgattatcg 1980 ggagctaaat gcactgactg tgaaggacaa gtatccaata ccgcttattg atgatttact 2040 tgatgagctc tttggtgcag tctacttctc taaacttgat cttcgatccg ggtatcatca 2100 aatactaatg agtcttgaag atgttgagaa aactgcattc cgtacccatg agggccacta 2160 tgagttttta gtaatgcctt ttgggcttac taatgctccg gccacatttc aaaacctcat 2220 gaatgattta ttcaaacctt ttctgcgaaa atttgttctc gtctttttat gacattttgg 2280 tctacagtaa gacatggaca gatcatttgc accatttgca attggtgttt caggttttac 2340 aacagaatca attatttctc aaacactcta agtgttcttt tgggcagaat tgtgtggagt 2400 atttaggcca tgtagtctct ccagatgggg tgcaagctga tccatctaag ttacaggcta 2460 tcaaagattg gcctcctcca aagacagtga aagggttaag gggtttcctt gggcttactg 2520 gctattacag gaagttcatc cctggctatg gaaaaatatg tcagccgctg tacaatttaa 2580 ctaagaggga cgggtttact tgggatgcca ctgcctagga tgcatttgac catcttaagt 2640 cccttatgat gtctccgcag gtattagctc ttccagattt tacacagccc tttgagatag 2700 aatgtgatgc ctcagggaat ggcattgggg cagtcctaca gcaaggcaaa cgacccatag 2760 cttatacaag caaagcctta ggcccaaaga accaagccct ctctgcctat gagcgagaac 2820 ttattgccat agttcatgca gtgaagaaat ggcaaaatta cttacaaggg cgacacttca 2880 tcataaggac tgaccacaac agtcttaagt attttcttag tcaacaggcc aatacttcct 2940 tccaacagaa gtgggtttct aagctccttg ggtttgatta tgagatacag tacaagaagg 3000 gcaatgataa tgtggtggcc gatgctctct tgagaattcc tgaaacacta caatttgata 3060 ttggtgaccc tccagtttct gccattgaga tgagttgtgc tgccatttcc tacccctact 3120 ttgggtggtt agacgagctc cggcgagata tcgagaagga tgaatgggta attgccaaga 3180 ccagggaagt gctccctccc acccacggta caccaggggc ttcagttgca tccaaatata 3240 ctctggacaa tgggtttctg tgctacaagc atcgaattgt acttagtccg atttctccat 3300 ggcgacagaa gattattgag gagtatcatt ctactcctgc agctggacat cagggcattt 3360 taaagactta tcaccggatc aaaaaacggt attattggca gggtatgaag aaggatatcc 3420 aagcttttgt gtctcaatgt ggtatttgtc aacaaaacaa atttgaaaca gtgtctcctc 3480 ctggactctt acaaccccta cctattccga gtaaggtgtg gactgctata agcatggact 3540 ttatcgtggg cttgcctctc tgtaaaacca agtctgtcat aatggtggta gtcgaccggc 3600 tgtccaaata tagccatttc atggctttag ctcaccccta cagtgctgcc acagtggccc 3660 aagtcttcat tgataatgtg tttaagctcc atggcatgcc aagctctata gtgagtgatc 3720 gcgatcccat ctttttgagc aatttttgga aggaattttt taaattgcaa ggatctaagt 3780 tgtcaatgag ttcggggtac catccacaaa gtgatggtca atcagaggtg ttgaatagat 3840 gtttggagac ttacttacgg tgttttgttg gaggccaacc gaagaaatgg gtgcaatggt 3900 tatcttgggc tgaatggtgt ttcaacacct cttatcacac ttcttctggc tttacccctt 3960 ttgaagtggt ctatggttac cctcctccac atatctgtcc ttacgaagaa gggtctacac 4020 gggtggaatc agtggagcaa ctcttacaac agagggatag gatcctggat gtactcaagc 4080 ataaccttga cttggctcaa aaccggatga aagttcaagc tgacaagaga aggagtgaaa 4140 gggtgtttga agttggtgac ttggtttacc tgcgactagt accatatcag cttcagtcct 4200 tagcaccaca ccagtatcat aaacttcaac ctcgctactt tggaccttat gaagtattag 4260 aaaggattgg agctgtagcc tacaaattga aactccctga gggtaccaaa atacatccag 4320 tgtttcatgt gagcaatctt aaaaagaaat tgggtactga tgtggttgct ggtgccactc 4380 ttccacaggt tactgatgat ggcttgttcc aagctattcc taaggctgtt ctagctcgca 4440 ggatgtataa gaaaggcact gttgcaggag tccaattgct gattcaatgg gttgatcatg 4500 atgacagtga agccacctgg gaggattatg acacctttac aatgaagttt ccagatttcc 4560 aagtctgaac cttgtggaca aggttttgtc gaaagggggg agtat 4605 // ID TONT1_LE_I repbase; DNA; EDCOT; 4633 BP. XX AC AF220603; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Lycopersicon esculentum retrotransposon TONT1_LE_I, internal DE region. XX KW LTR Retrotransposon; Transposable Element; TONT1_LE_I; KW internal region; internal portion. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-4633 RA Lavelle T.D., Oldroyd E.G., Dalhbeck D., Staskawicz J.B. RA and Michelmore W.R.; RT "Direct submission."; RL Direct Submission to Genbank (04-JAN-2000). XX DR Genbank; AF220603; Positions 31049 35681. XX SQ Sequence 4633 BP; 1615 A; 715 C; 975 G; 1328 T; 0 other; atcttaagga aattattaaa tctgtgtttc tggtggagac aaaaatcttt gtgattttat 60 actcctttaa gtctgcaatt atatttttat tgcttactta tattgtatca attttgttta 120 tcagaaatgg aaaacactgg tgttacagtg gctgttgctg caccaaccca acctcttgta 180 tcacaagcag agaaaccggg taaattcaca ggtgtgaatt ttaaaggatg gcagcaacga 240 gtatttttct ggcttaccac tcttggtctg cagaaattta caagtgaaga tactccagtt 300 cctactgatg atatgccaga cagggaaaaa tttatgattg ttgaagcatg gaaacagtca 360 gacttcctat gtaaaggtta cattttgagt gctttagaag atgacttata taatgtctat 420 agtgcaataa caacttctaa agagttgtgg aatgcacttg agaagaaata taagacagaa 480 gatgcatgct tgaaaaagtt tgtgatcgca aagtttttag actataaaat gacagatagt 540 aaaactgttg gatcacaagt gcaggaactt caacttattc tccatgatct gattgctgaa 600 gatatggtag taaatgaagc ttttcaagtg gctgcaatga tcgagaagtg cctccttcgt 660 ggaatgattt caagaattat ctaaagcaca agcgtaaaga aatgaagctt gaagatcttg 720 tgattcagct caagattgag gaagataaca gaaatgccga aaagaagtcg cataagagtt 780 caacaatcat tggagttaat attgttgaag aagctcctac caaagacaaa aatagaaaga 840 agtccaacgg gcagaagtca gaataggcca agaagaaatt caaaggcaac tattataatt 900 gtggcaaggc tggtcataga tcttctgatt gtcatgctcc aagaaaggac aaaaacaaag 960 gcaaaggcaa aaatcaagca aacatcgtgg aaaaaatgga agatgcagat gacttgtgtg 1020 caatgatatc ggagtgtaac ttagttggaa atctcaagga gtggtttctc gactcaggtg 1080 ccactagaca tatttgctct gcaaaagaag cctttgcaac atacactcct actgagtacg 1140 atgaagattt attcatggga aacacagtaa cagcaaggat tgcaggaact ggcaaagtaa 1200 tgttgaaaat gacatccggc aaagtgttga ctttaaacaa tgttctgcat gtccctacta 1260 ttaggaagaa tttagtttct gctgcactac tcgttaagaa cgggtttaag tgtgtcctag 1320 ttagtgataa agctgtaata agtaagaatg aaatgttcat aggaaagggc tatctcaatg 1380 agggtctttt caaactaaat gtaatagtta ttgacagtat caataaaaat tctgcttctg 1440 tttacttatt ggagttaagt gatttatggc atgcccgttt gggacatgta aattacaaag 1500 ccttgcgaaa attggttaat ttagaagtat tgtctgattt taaatgcgat aagtcaaaat 1560 gtgaaatttg tgtggaaagt aagtttgtta aacatcctta caagtctgtt gaaagaaatt 1620 ctaaaacttt agacttaatt cacacagata tatgcgatat gaagtcaaca tcatctcgtg 1680 gtggaaaaaa gtactttata acttttattg atgactgcac tcgattttgt tatgtatact 1740 tgcttaatag taaggatgaa gcaattgatg catttaagca atacaaaaat gaagtggaaa 1800 accaattgaa tctaaagata aaaatgattc ggagtgatag gggtggagaa tatgaatctc 1860 cttttgcaga gatatgtttg gaatatggta ttattcatca aactactgca ccttatacac 1920 cacagtcaaa tggtttgaca gaacagaaga acagaacatt aaaggaaatg atgaatgcct 1980 taatgatcaa ttctggttca ccgcgaaatc tttgggggga agccattctt acagctaata 2040 aaatactcaa tagagtaccc catcgaaaaa cacgatcaat tccatatgag ttgtggaaag 2100 gaagaaaacc caacttgaaa tattttaaag tgtgggggtg tttagccaag gtagaggttc 2160 ctttaccgaa gagggttaaa attggaccca aaacaataga ttgtgtcttt attggatatg 2220 ctatgaatag taaagcctgt cgatttttgg ttcacaaatc tgataatcct gagattcatg 2280 ttaatacgat aattgaatca gataatgcaa agttttttga aaacatttat ccgtataaaa 2340 ctgaaagtga gtcaacaagt gaaagatcta aacgaccacg agaagaatca atgaaaaata 2400 ttctaactag tgaggaacct agacgaagta ctcgacgacg aaaatatgtt tctttcggac 2460 cagattttgt agcactattg cttgaaaatg agcctcaaac atttaaacca gttatgtctt 2520 cgtcagagtc aacttattgg aaagaagcag tcaatagtga gattgaatca attttaagca 2580 atcacactta ggaattgact gatcttcctc caggaaataa acctttagga tcaaaatgga 2640 tctttaaaag gaaaatgaaa cctgatggga ctattgacaa atataaggct agactggtag 2700 tcaaagggta cagacaaaaa gaaggcctgg actactttga cacatattct ccagtaacaa 2760 ggataatatc aattaggatg ttaatagcac ttgcaacagt gcatgatctt aaaatccacc 2820 aaatggatgt aaagacaacc ttcttaaatg gagagttaga ggaagaaatt tacatggaac 2880 aacctgaagg gtttatagtt cctggtaaag aaaagaaagt atgcagactt gtgaagtcaa 2940 tttatggact caagcaagca cccaaacaat ggcatgctaa atttgatcaa gtaatgttgg 3000 caaatggatt caagattaac gaatgtgata aatgtgttta catcaaaaat gttatgaatc 3060 atgaagtcat tgtttgtttg tatgttgatg acatgttaat aatgagtaaa gaaattgatg 3120 atataaatgc tactaagcgc atgttgtcca acaagttcga tatgaaagac ttaggagttg 3180 ctgatttgat cttaggggtc aggattatca aaactcccta gggactagca ttatctcaat 3240 ctcattatat tgaaaaagta ttggataagt tcaattactt gaatttcaat gtagtcaaaa 3300 ctccaattga tttaagttgt acatttaaaa agaatgaagg tcaaagtgac tctcaattgg 3360 aatatgccag agtgttggga agtttgatgt atattatgaa ttgcacacga ccagatatag 3420 catgtgctat tagtaaactg agtcggtaca ctagtaatcc gaatcaaact cactggatgg 3480 ttatgaaacg tgtgttgggt tatctagaat ggacacaaca ttatgctttg cattataata 3540 aatattctgc tgtgattgaa ggatatagtg atgcaaattg gatcaccggg tcaaatgatg 3600 taaaatccac gagtggttat gtattcatac ttggtggagg agctgtctct tggaaatctt 3660 ccaaacagac atgtattgct cgctccacaa tggaatctga attcattgct ttggataagg 3720 ctggtgaaga agcagaatgg ctccggaatt tcatagagga tattccattc tggcccaaac 3780 ctgtcggacc aatttgcata cattgcgata gtcaagcagc aataggtagg gcagggagcg 3840 ttatgtacaa tgggaagtct cgtcatatac gacgtagaca taacaccata agacaactgc 3900 tctctagtgg aattatcaca attgactatg taaagtcaag cgataatgtg tcagatccac 3960 taacgaaagg cctagtgaga gaggcagttg aaagatcatc taagggaatg ggtttacggc 4020 ttaggacaag tcagcatgac ggtaactcta tctagcagac tggagatccc aagagctaga 4080 ttcaaggaga aaaacaaagt tgtggctgac ggttcgacat tgtcaaataa ctcaatccat 4140 tctcatgatg aagacaatgt tcaggaaaag gttaagactt taaggcttgt taatgaggta 4200 ataaagctta aagtttttaa tgatttgcta agtttggtag atttgaccaa atagtgtatc 4260 tacgagatga cacggtcaga aatcacctat gtgagtgtga ggtggaagcc gcttcaaaga 4320 gaatttatgt caaaagccta ttctctatac actcatgaaa ccaggaggtg ttcatggctg 4380 aaacgaacac aaccgtaaga atcataaaca gtaaagggtt aattgtgtga catatggttg 4440 tctaggtata caccaaagtt cgacggttca aagatatcac atctaccgat tgactgagta 4500 tatccgacat atgttcacta cggaaagtcc aaggggaaac ctacttatcc agatgcgatt 4560 aatccttgct tgtaaagtac ataattgtcc gtgcattcct atgttataac tattccccat 4620 caatgtgggg gat 4633 // ID SINE1_MT repbase; DNA; EDCOT; 132 BP. XX AC . XX DT 05-JAN-2007 (Rel. 12.01, Created) DT 05-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE SINE-type element. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; SINE1_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-132 RA Jurka J.; RT "SINE1_MT: SINE element from medic barrel."; RL Repbase Reports 7(1), 109-109 (2007). XX DR [1] (Consensus) XX CC Present in >1000 copies in the genome. The poly(A) tail indicates CC that it is propagated by L1-type LINE element. XX SQ Sequence 132 BP; 32 A; 26 C; 35 G; 39 T; 0 other; aacccacttg ggttggccta gtggtattgg cttgggacct gggagtgtgc tcctcctcaa 60 ggtctcaggt tcgattctct ctggtgccaa tttgaggggg ttagtttagc ttcttcaaaa 120 aaaaaaaaaa aa 132 // ID LINE1_CA repbase; DNA; EDCOT; 590 BP. XX AC AJ411789; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Cicer arietinum LINE-like retrotransposon and partial RT gene for DE reverse transcriptase LINE1_CA. XX KW L1; Non-LTR Retrotransposon; Transposable Element; LINE; LINE1_CA; KW RT gene; long interspersed nuclear element; KW reverse transcriptase. XX OS Cicer arietinum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; OC Cicer. XX RN [1] RP 1-590 RA Staginnus C.; RT "Thesis (2001) Department of Plant Molecular Biology, University RT of Frankfurt / M., Frankfurt a.M., Germany."; RL Direct Submission to Genbank (22-JUN-2001). XX DR Genbank; AJ411789; Positions 1 590. XX SQ Sequence 590 BP; 189 A; 65 C; 150 G; 186 T; 0 other; gggatcctgg gcctgatggt ttacattttg ggtttgtgaa agagttttgg gagaacataa 60 aaggtgactt tatgagattt ctaggtgatt ttcatgcaaa tgggaggttg gtaaaatgat 120 caaattactc atttatagtt ttaattccca aaaaagacaa tctgcaagtt ttatctgatt 180 ttagactcat gtcattagtg ggatgtatgt ataaagcttt gtcaaaagtg ttggcgaata 240 gattgagtca ggtgattggt ttagtaatag ttgaatctca atcagcattt gttaaaggca 300 gacaaatttg agttggaatc ttaattgcaa atgaagtggt cgatgaggca aaaaagaaga 360 aaaaaaaaag ctaattttgt tcaaagtgaa cttcgagaag gcatatgact cagttgagtg 420 ggattaccta gagcttgtga tggcaaagat ggatattcta gagaaatgac gtaaatggat 480 tttggaatgt gttggttcaa cgtcagtttc tgtgctagtg aatgagagtc ctacataaga 540 gtttgttatg cagaggggat tgagacaggg tgatccattt agacccgaaa 590 // ID Copia-92_Mad-LTR repbase; DNA; EDCOT; 506 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-92_Mad_; KW Copia-92_Mad-LTR; Copia-92_Mad-I. XX NM Copia-92_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-506 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1723-1723 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 506 BP; 158 A; 84 C; 92 G; 172 T; 0 other; tggacggaaa aacacaagtt aatttttacg tttttgattt ttggattcag ttttttccga 60 aaggataaaa ctgatgaaca gttacgtccg ttctgaaaga taagatgaac ggctataact 120 gttcaagtta cgccattata tatatggccg tcagatcaga aacgaataca atcaattcca 180 tcgctccttt tattcttcac agagaaacac acaaccaatt cgccaagaat ccaagttcga 240 gtgcaagaac ttggattaga tagttgtatc ctgcaagata gacgtccgtt gaactactgc 300 actggtgtag gggcgaattt ctgtcttagg agattgctct gcaagcctct atcttcaaag 360 aacaagtcag tgatttgtga ttttatatgc aatttcatta agtgttcgta ttttgatata 420 ttgtatctgt tgttgaattt tccattcgaa ataaactgtg caaattatat atatattata 480 taattgacat ttgattggtt ctaaca 506 // ID Gypsy-75_PTr-I repbase; DNA; EDCOT; 3536 BP. XX AC . XX DT 23-DEC-2009 (Rel. 15.02, Created) DT 23-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: internal DE portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-75_PTr-I. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3536 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 184-184 (2010). XX DR [1] (Consensus) XX CC >90% identity to consensus. XX FH Key Location/Qualifiers FT CDS 136..969 FT /product="Gypsy-75_PTr-I_1p" FT /translation="LQKKTVHHHDVIGSPQRHPPSCSASHAANHSGKPTTE FT KTCTSVHSDRPFSSTPITANDHNQTQAHADLLPSTPTAPSLHQQQPQPSPT FT TSVTIIVAPPPSPTNTDSNRSRNRSPTPAAVDLRRRRPSTSSSSPRHRQVG FT PPAATTSRHKNPQSHTSCCLHSRSSSSASAQPPLIAPSSSSSTSRSHHNWS FT FRPSTSAVTPRRQQTTKGNSAIAAQKKAFEAKLINPATSSATPPCHVNMIT FT TSPATSAASHVICHVSSHVIQFATSAATNSSFLPLSR" FT CDS 1493..3535 FT /product="Gypsy-75_PTr-I_2p" FT /translation="MFRRIEPQESFRIRHSKTNKYHKNNHYGQVHSERHQY FT DYHLGYSKHDDFDERVLSPNKIEAPTFDGRHDPWIFDMWIRDMDRFFEWHN FT LSDNRKVRFAKMKLIDEAKIYWRDVEDCLEMRGKPPITDWIKMKQKLQEKY FT LPQSYRNKLLDQWNNLRQGNKSINEYITQFNDYMIRCAIRENEAMTLRRFC FT KGLNDDLRREVVFQGVSTLNQAYTLVQDYKLVTKNQWXNRQGSYSIPTRSQ FT FRSSDSLLGAPPHRPNPSSAQLCKKDKGKRVVNEVSKVSSKVKCTNCLGFG FT HISLDCTSKPLVIQKHKDIGKEEYCSVEVYEPNLEDFSDLDDEDVQEEGPN FT TMSPHELENEVKKESDMSALMVEEVLGNSSVESPIEMSMVLEESHDISPPK FT LPDSSSHMLGVQHIISLEQHVELFDPLPHARDEEDEDNPSLLDCVHTISTQ FT VSNNVCLIPHPQSFSVHSYKPEKPIEHLPISPHDRMSKSAESLPCRVHNLH FT IEIMKQIQASNEQYKFRADLLKYHDALNVGDYFMIQIRPERCPLETDHKLQ FT VSSARPFKVLQMIKSNNYVIKLPLNFDISSTFNMKDLSIYKIQPIPDAPFD FT TPTSLSISLAQKEHINATLNAQVVFTRDGELQQIPVYGLDDQIQTILGLSE FT RHHNSLILIFESVIGVALAYTRRGRVLPTPGE" XX SQ Sequence 3536 BP; 1103 A; 813 C; 643 G; 976 T; 1 other; aatttggtat cagagccagg gttttaattg ttcttacaat taaacgatcc acaatgttta 60 tgctaaaccc tagatccggt ttgatctaaa aaaaaaattg tcactgttaa aaaaaaaaaa 120 cacctactgt tctgattaca aaaaaaaact gttcatcatc acgacgtaat cggttctcca 180 cagcggcacc cgccatcttg ctcagccagt cacgccgcca atcacagcgg caaacccacc 240 accgagaaga cctgcacatc agtccacagc gatcggccat tctcctcaac gccgatcaca 300 gccaacgacc acaaccagac acaagcacac gccgatttac tgccttcaac tcccacagca 360 cctagcctcc accagcagca gccgcaaccg tcaccaacca cctctgttac aataatcgta 420 gccccgccac cgtcaccaac caacacagac agcaaccgca gccgcaacag gtcgcccaca 480 ccagcagcag tagatcttcg tcggcggcgg ccatcaacca gctcatcctc tccccgccat 540 cgacaagtcg gacctccagc agccaccact tcgcgccaca agaacccaca gagccacacc 600 agttgctgtc tccacagtag atcttcgtct tcagcctcag cccagccacc actaatcgca 660 ccctccagca gcagcagcac cagccgcagc caccacaact ggtccttcag accatcgaca 720 tcagcagtca cgcctcgccg ccagcaaacg acaaaaggaa actcagcgat tgcagcacag 780 aagaaggcat tcgaggcaaa attaattaac cctgccacgt catcagccac gccaccctgc 840 cacgtcaaca tgatcaccac gtcacccgcc acgtcagcag ccagccacgt catctgccac 900 gtcagcagcc acgtcatcca gtttgccacg tcagctgcaa caaattccag cttcctccca 960 cttagtcggt gaatcactct ccttttattt gttgaatttt acctcttttg gtattgcact 1020 tgtcatttaa agttatcatt aatattactt ttgtgccaaa aaaaaaaaaa ataaaaaaaa 1080 atctcaccta gcatttttaa ttgttaattt ttgttcatca acctctttca tcagtgatag 1140 ctaatatctt attctatttg ataattatga gttcttgctt gtgacatcgt gtttgattaa 1200 tcatttacac ttaagaatct agtattacat gcttacaatt ttattagtgt aatttgttct 1260 tgattaatct ccacatttaa aaaaaagata aaaaaaaatt agctttattt ttgtattgtg 1320 attttacttg caagaaccat ttgtgatctc aattccattt ataagttagt gttgcatgca 1380 tttgtgtcat gatcatctag tgtccaagct taagtttaca cttaccgtag actcaaccct 1440 tagtgatact cttatgacca tttaaaggga actgcaaact taggtgatca acatgtttag 1500 aagaattgag ccccaagaga gttttcgaat aaggcactca aagaccaata aatatcacaa 1560 gaataatcat tatggacaag ttcactctga gcgccaccag tatgactatc atttaggtta 1620 ctctaaacac gatgactttg atgagcgagt cttgagtcct aacaaaatag aagcccccac 1680 ttttgacggt cgtcatgacc cttggatatt tgatatgtgg attcgtgata tggatagatt 1740 ctttgagtgg cataacttgt ctgataatag gaaagttaga tttgctaaga tgaaactcat 1800 tgatgaagcc aaaatttatt ggagagatgt tgaggattgt ttagagatga gaggtaaacc 1860 tcctataact gattggatca aaatgaaaca aaaacttcag gagaagtacc taccccagtc 1920 ttataggaat aaactcttag accaatggaa caatctaaga caagggaata agtctatcaa 1980 tgagtatata acgcagttta acgattacat gattagatgt gccataagag agaatgaagc 2040 catgactttg cgtagatttt gtaaaggctt aaatgatgat cttagaagag aagttgtatt 2100 tcaaggtgta tctaccctta accaagctta taccttagtt caagactaca agttggtcac 2160 gaagaatcag tggawgaatc gtcagggctc ttatagtatc cctactaggt cccaattcag 2220 aagtagtgat tctttgttag gtgctccacc ccacagacct aatcctagta gcgcccaact 2280 ttgtaagaaa gataagggca aacgagttgt caatgaagtg tctaaggtga gttcaaaggt 2340 taagtgtact aattgtttag gttttggtca tatctcttta gattgcacct ctaaaccctt 2400 agtcatccaa aaacataagg atataggtaa agaggaatat tgtagtgttg aagtgtatga 2460 gcctaatctt gaggatttta gtgacctaga tgacgaggat gtgcaagaag agggacccaa 2520 cacaatgagt ccacatgagc ttgagaatga ggttaagaaa gagtctgata tgtctgcttt 2580 aatggtagag gaagttttag ggaactcttc agtggaatcg cctatagaga tgagtatggt 2640 cttagaagag tctcatgata ttagtcctcc taaactacct gattcctcat cccacatgct 2700 tggtgtccag cacatcataa gtttagagca acatgttgag ctttttgacc ccttaccaca 2760 tgcacgtgat gaggaagatg aagataatcc tagtttactt gattgtgtcc ataccatatc 2820 tacacaggtt tcaaacaatg tttgtctcat tccacaccct caatcattta gtgttcatag 2880 ttacaaacct gagaagccta tagaacacct tcccatatct cctcacgata ggatgtctaa 2940 gtcagctgag tcgttaccat gtagggttca taatttgcat attgagatca tgaaacaaat 3000 tcaagcaagt aatgaacaat acaaatttcg agctgattta cttaagtatc atgatgcact 3060 taatgttgga gattatttca tgatacagat tagacctgaa cggtgtcctt tggaaaccga 3120 tcataaattg caagtaagta gtgctagacc attcaaagtg ttgcaaatga ttaaatcaaa 3180 taattatgtc attaaattgc cattaaactt tgatattagc tctactttta acatgaaaga 3240 cctcagtatt tataaaatac agcctatccc tgatgctcct tttgataccc ctacctcatt 3300 atccatatct ttggcacaaa aggaacatat taatgctact ttgaatgcac aagttgtttt 3360 taccagggat ggtgaacttc agcaaatccc agtatatggg ctcgacgacc agattcagac 3420 tatacttgga ttatcagaga gacatcacaa cagcttgatc cttatctttg agagcgttat 3480 cggagtcgcc ttggcctata ctcgacgggg tcgagttctt ccaaccccgg gagaat 3536 // ID RTE-1_Mad repbase; DNA; EDCOT; 8343 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE RTE retrotransposons from the apple genome. XX KW RTE; Non-LTR Retrotransposon; Transposable Element; RTE-1_Mad. XX NM RTE-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-8343 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1821-1821 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~95% identical to the consensus. XX FH Key Location/Qualifiers FT CDS 104..3259 FT /product="RTE-1_Mad_1p" FT /translation="MKMNPEQNRAKARASPVSGALCGPSTVISEQGSLYLH FT RHPDAVLNEQGGHRNFFSNDSTQSCLGAYAPINFTRDTQKKYFDPIRRGRV FT KKLGQKGRVQESKMRLGTWNIGTLTGKSMEVVEVMVRRRINIMCLQETKWV FT GSKAKDLENSGFKLWYSGTNRTRNGVGIIVDKTLVQDVVDVKRVGDRIMAI FT KIVIGQELINVISAYAPQVGLDTSSKEKFWEDLGDLVQGIAQTEKLFIGGD FT LNGHVGRETGNYGGFHGGHGFGERNEDGEAILDFAMAYDLFLANTFFKKRE FT EHVITYKSGSSKTQIDFLLMRKGDRITCKDCKVIPGESVANQHRLLVMDVH FT IKRVRQKNKTWKCPRTRWWNLKEEKQAIFKEKVITQCVWDREGEASQMWDS FT MASCIRKVAKEVLGESKGFAPHQKESWWWNEEVQTKVKAKKECCKALYKER FT TDENGERYRKAKQEAKKAVREAKLAAYDDMYKRLDTKEGELDIYKLARARE FT KKTRDLNQVRCIKDEDGKVLATENAVKDRWRGYFHNLFNEGHEMSASLGEL FT SNSEECRNYSFYRRIRKEEVVVALKKMKHRKAIGPDDIPIEVWKLLGETGI FT TWLTDLFNRILKTKKMPNEWRTSTLVPIYKNKGDVQNCMNYRGIKLMSHTM FT KLWERVIEHRLRQETRVSDNQFGFMPGRSTMEAIYLLRRLMERYRDGKKDL FT HMVFIDLEKAYDRVPRDILWRILEKKGVRVAYIQAIKDMYEGAKTAVRTHE FT GQTESFPITVGLHQGSSLSPYLFALVMDELTGHIQDDIPWCMLFADDIVLI FT DETQEGVNAKLNLWREVLESKGLRLSRSKTEYMECKFSANGGQNELGVRIG FT DQEIPKSDRFRYLGSILQKNGELDGDLNHRIQAGWMKWKSASGVLCDRRMP FT LKLKGKFYRTAIRPAMLYGTECWAVKHQHVHKMGVAEMRMLRWMCGHTRKD FT KIRNEDIRGKVGVAEIEGKMRENRLRWFGHVQRRPTDAPIRRCDYGTEVQG FT RRGRGRPRKTLEETLRKDLEYLDLTKDMTQDRAQWRSKIHIADPTQ" XX SQ Sequence 8343 BP; 2635 A; 1736 C; 2047 G; 1925 T; 0 other; ctccgcctat gtcttacatg gccggtccca agcccggata aaggaggagg gggagggcgt 60 caggtagtcg acagccggca ctccatgatc acgtcgaatc cttatgaaaa tgaatccaga 120 acaaaatcgc gctaaagcta gggcgtcacc cgtaagtggc gcgctgtgtg gcccgagcac 180 agtgataagt gagcaagggt cgctgtatct ccatcggcac ccggatgcag tgttaaatga 240 gcaagggggc catagaaact tcttttcgaa cgactccact caaagttgtt tgggagcata 300 tgctcctatc aactttaccc gggacacaca aaagaagtac tttgatccta ttagacgggg 360 gagggtgaag aagctaggac agaagggtag agttcaagag agcaaaatgc gtttaggaac 420 gtggaatata ggaaccttaa cgggaaaatc tatggaagta gtggaagtta tggtgaggag 480 aaggataaat attatgtgcc tacaagaaac taagtgggtt ggtagtaagg caaaggatct 540 agaaaactca gggtttaaac tttggtattc gggcacaaat agaacgagaa acggtgttgg 600 catcatcgtg gacaagacct tggtacaaga tgttgtagat gtcaagaggg taggagatag 660 aatcatggca atcaagattg taataggaca agaacttatc aatgtgatta gtgcgtacgc 720 acctcaagta gggttggata cgagttcgaa ggagaaattt tgggaagatc ttggagactt 780 ggtgcaagga attgctcaga cggagaagtt atttatagga ggagatttaa atggacacgt 840 gggcagggag acaggcaact atggaggttt tcatggtggc catggttttg gggagagaaa 900 cgaggatggg gaagctatct tggattttgc aatggcatat gatctcttct tagccaacac 960 cttctttaag aagagagaag aacatgtgat cacctacaag agtgggtcgt caaaaacaca 1020 aatagatttt cttctaatga ggaaagggga tcgtataact tgtaaggatt gcaaagttat 1080 accaggagag agcgtggcta atcaacatcg cttgttggtg atggatgtac atatcaaaag 1140 agtaagacaa aagaacaaga cttggaagtg cccaaggact agatggtgga atctaaaaga 1200 agaaaaacaa gccattttca aagagaaggt aatcacccaa tgtgtgtggg atagagaggg 1260 ggaagctagc caaatgtggg attccatggc tagttgtatc cgaaaagtag caaaagaggt 1320 attaggagag tccaagggct ttgccccaca ccaaaaggaa tcttggtggt ggaatgagga 1380 ggtacaaaca aaggtgaagg ctaagaagga atgttgtaaa gccttataca aggagaggac 1440 cgatgaaaat ggtgaaaggt atagaaaagc gaagcaagag gcgaagaaag ctgtcagaga 1500 agctaagtta gcggcttacg acgatatgta taaacgacta gataccaaag aaggagagtt 1560 ggatatctat aaactagcta gagcaaggga aaagaagaca agggacctaa accaagtgag 1620 gtgcatcaag gatgaggatg gaaaggttct tgctacagag aacgcggtta aagacagatg 1680 gagaggttat tttcataatc ttttcaatga aggacatgaa atgagtgctt ctttagggga 1740 gttgagtaac tcagaagagt gtagaaacta ctctttttat cgtcgaatcc ggaaggaaga 1800 agtggttgta gctttgaaga agatgaagca tagaaaagca ataggcccag acgatatacc 1860 aatcgaagtg tggaaacttt tgggagagac aggtataaca tggctcactg accttttcaa 1920 taggattttg aaaacgaaga agatgccaaa tgagtggcga acgagcactt tggtgcctat 1980 ctacaagaat aagggcgacg tacaaaattg catgaactat aggggtatta agctaatgag 2040 tcatacaatg aagctctggg agagagtcat tgagcataga ttgaggcaag agacacgggt 2100 ttcggacaac caattcgggt tcatgccagg gcgctcaacc atggaggcaa tctatctctt 2160 acgaagattg atggaaagat atagagatgg gaaaaaggat ttacacatgg tctttataga 2220 tttggaaaaa gcgtatgata gggtcccaag agacattctt tggaggattt tagagaagaa 2280 aggagtacga gtagcatata tccaagctat aaaggatatg tatgaaggag caaagactgc 2340 cgtaagaact catgaaggac aaaccgaaag ctttcccata actgtaggat tacatcaagg 2400 ctcatcctta agtccttacc tttttgcgtt ggtaatggat gagttaacag gacatattca 2460 agatgatatt ccttggtgta tgcttttcgc agacgatata gtgttgatag atgaaactca 2520 ggaaggggta aatgcaaagc ttaacctttg gagagaagtg ttggaatcta aaggtcttcg 2580 cctaagccga tcaaagacag aatatatgga gtgcaagttc agtgcaaatg gaggccaaaa 2640 cgagttaggg gtgaggatcg gagatcaaga aataccaaag agcgaccgtt ttcgttacct 2700 aggatctatc ttgcaaaaga acggagaatt agatggagat ctcaaccata gaatacaagc 2760 tggatggatg aagtggaaga gtgcatccgg cgtgttgtgt gaccgccgta tgccactgaa 2820 gctcaaggga aaattttata ggacggcaat aaggccggcg atgctgtatg gcacagaatg 2880 ttgggcggtg aagcatcaac acgtacacaa aatgggtgta gcggagatga ggatgcttcg 2940 ttggatgtgt gggcacacga gaaaggataa gattaggaat gaggatatcc ggggtaaagt 3000 aggagtagcc gaaattgaag gaaagatgag agaaaatcgg ttacggtggt ttggacatgt 3060 gcaaagaagg cctactgacg ctccgattag aagatgcgac tatgggacag aggttcaggg 3120 ccgaaggggt agaggaagac ctaggaaaac tttggaagag actctaagaa aagacttaga 3180 gtacttggat ctaacgaagg acatgacaca ggatcgagca caatggcgtt ctaagattca 3240 tatagccgat cccactcagt gacttggatt ttccaagtct ccaaccgaga agttttcctc 3300 actcgggaaa ttaagggaac actaccccaa cctacatgct ccactcagaa agcttcaaca 3360 tacaagcttc aacaaaagaa aattcaaaga acttagcgaa gaaggctttg gtgtatttaa 3420 cacaatacgt tgaaatgaag gaaagcttat ttattgatat ccccgataag ctacaaatat 3480 gtacatatac atgagtcaaa ataaacacac aagagggagc cttcacaaag gttgcttagg 3540 agaagtctca gcagtcggta gagccccaga aagagaaggc accggagggg gatcatttgg 3600 agcctcagta ctggacagaa ccctagaagg aggaggcatc agaggttgat catttggagc 3660 ttcattacgc ggtacagccc cagaagacga aggcaataaa tgcctttgga acaaacccac 3720 aaatctctga tgatcaagta aaacctgacc atcagtttcc ttcatctggt caagcttcct 3780 cttcatgttt gtagcatagt catgtgcgag ccggtgcaac tgtttattct catgcttgag 3840 ccctctaatc tcctgtttga gactcatcac ttcagccgcc aatgattcaa cttggcgggt 3900 tcgagcaaat aggcgttggg ccatattaga cacagaacct gcacactgaa cactgagagc 3960 cagcgaatcc ttaacagcta actcatcaga ccgtttggaa agtagtctgt tatctttggg 4020 agtgagaagg ttcctggcca ccaccgcagc ggtcatatca ttcttcatca cggaatcccc 4080 aacggtaaga ggaccagtag gggagacgaa ggatgggcgc catatgttgt ctggagaagg 4140 cggggctgcc tcttcaacaa ggttcaagtc aaaacgacgg tcggaggggc cagacatttt 4200 caaaggtgtt gaagagagaa gaggtcggac aaatcaagat cttagaagtg caagaatgaa 4260 gcttctactg gtggagattc aagtgtgctt tggaacttaa tgccagcccc tataaaaatc 4320 tgcactcgac ggagcttcag aaatcgaaga ggcgcctgct cagaaatcga agaggcgttt 4380 gctttctcaa aagctgggct gcttagagat cacgagggtt gatctcagaa atcgaagagg 4440 cgtttgcttt ctcaaaagtt gggctgctca aagaccacga aggccgatct cagaaatcga 4500 agaggcgctc gctttctcaa aagctgggct ccccagagac cacgagggcc gatctcagaa 4560 atcgaagagg cacctacttt tccagccttg tcagcacctg tcacacgcac actcagcttt 4620 gcggaaatta tgggcattct gtcgaagact tctggggaag tagaaaacac atgaatctta 4680 ctgttcaatc acccacttcc cacacgcaac aatagctcat gggtaccaca gataactttg 4740 ccaaagttct ctgccaaagt tgagcacgtg aagcttgcag ctcccactac atcgctctga 4800 ccaagaaggg taaaagaata gcaaagaaac agcactaaca aagtttagac ccataaattt 4860 tgaaggtcta gctaccatat tattacccac aagggtaaag gaacagtacc actgctggat 4920 aattggaaag tccctgtgtg tcaacctctg tgcttcgtgg caaggtagac tagcaaacat 4980 gcccaacctt tactcacatt cgagaaaaca ctcccaataa gattgcttgc tccaaaatcg 5040 aagaggcacc gtcctccgaa tctcgagagc cagactccca acatgactac tttcttaaaa 5100 atcgaagaga gggtaaagga acagtaccat tgctggataa ttggaaagtc cctgtgtgtc 5160 aacctctgtg cttcgtggca aggtagacta gcaaacatgc ccaaccttta ctcacattcg 5220 agaaaacact cccaacaaga ttgcttgctc caaaatcgaa gaggcaccgc cctccgaatc 5280 tcgagagcca gactcccaac atgattactt tctcaaaaat cgaagagaca ctgctccccg 5340 aatcttcgag agccagaccc ccagcatgat tgctttctca aaaatcgatg aggcatcgtt 5400 ctccgaatca atcgaagagg cgctcgcttt ctcaaaagct gggctgctca gagaccacga 5460 gggccgatct cagaaatcga agaggcacct acttttctag ccttgtcagc acctgtcaca 5520 cgcacactca gctttgcaga aattatgggc attctgtcga agacttctgg tgaagtagaa 5580 agcacatgaa tcttactgtt caatcaccca cttcccacac gcaacaatag ctcatgggta 5640 ccacagataa ctttgccaaa gttctctgcc aaagttgagc acgtgaagct tgcagctccc 5700 actacatcgc tctgaccaag aaaggtaaaa gaatagcaaa gaaacagcac taacaaagtt 5760 tagacacata aattttgaag gtctagctac catattatta cccacaaggg taaaggaaca 5820 gtaccactgc tggataattg gaaagtccct gtgtgtcaac ctctgtgctt cgtggcaagg 5880 tagactagca aacatgccca acctttactc acattcgaga aaacactccc aacaagattg 5940 cttgctccaa aatcgaagag gcaccgtcct ccgaatctcg agagccagac tcccaacatg 6000 actactttct caaaatcgaa gagagggtaa aggaacagta ccattgctgg ataattggaa 6060 agtccctgtg tgtcaacctt tgtgcttcgt ggcaaggtag actagcaaac atgcccaacc 6120 tttactcaca ttcgagacaa cactcccaac aagattgctt gctccaaaat cgaagaggca 6180 ccgccctccg aatctcgaga gccagactcc caacatgatt acttcctcaa aaatcgaaga 6240 gacactgctc tccgaatctc gagagccaga cccccagcat gattgctttc tcaaaaatcg 6300 aagaggcatc gttctccgaa tctcgagagc cagataccac agaccacttt ttcaaagtgc 6360 tctgacagag ttaaaacatg tgaaactggc agctcccact accgtgctat gaccaagcag 6420 ggtaaaggaa tagcattact acttgttgtt agggagactc ctatatatgt cgacctccat 6480 ccccaacgga caggcagacc tgcaaaaatg ctcaaccctt catcatatct gagagggcac 6540 tcccaacgaa gcctttcgaa atattcagct ttctttcccc ccgataatac ctctgcaaac 6600 aagctatact agagcaagaa tatctcatat catcagggtt aaaagcaaga gtatcccata 6660 tcatgctttt tccctgtctt ttcctttggc cttgttttta cctgcaagac aaggagaaag 6720 agagcaatca gtcagcactt ggaatcaagc ttccagccag gaactgactg cctggaaccc 6780 cttacctgat tacttacctg gcattgctct cgagtactca tcttcaacat cttatgtttc 6840 cagggaagat tccgcatctg cttgaggaac agatagggca agtgcgaagg atacaaggaa 6900 gcatgtggag acaagcgtaa cagcacacgt gccgatacat ccattactct gtcaaaagca 6960 aaagtatccc atatcagcag ggtggaacgt actctagatt tgatggactt gttttgaccc 7020 tcaaattctt cagtcggcct tatactctgg aggaaaccag aaaaccctcc agctcagttc 7080 aagaataagc ctgtggaaag ttacttcttc aaaagcaaaa gtatctcata tcatctcttc 7140 tcatttttct tctctttatc cttcatgctg ctgcaagatg gggagaaggt gaacaatcag 7200 tcggagctct gattgcttac cttgtctgtc acctctttca gcagaccccc tagctcggcg 7260 acttggggga ctcctactac atggtttgta tcgcgcttga ccaagcctga aactacaagt 7320 aagcttcaag tgaaattgat acattacctt gtgcatctcc accagttaaa gataccaccc 7380 ctggatggag gaagagtact tccagagaag atgccacatc tacctatgag acagataagg 7440 caagtcaaga cgacaccaca ctccgatact tagaagtttc gtgattacga gatcattctc 7500 ccacaatatt tcctaatgtc atttgtacta aatcattcac ttgtactcac taaaggagag 7560 cttgaaccta tgtacttgtg taaacccttc acaattaatg agaactcttc tattccgtgg 7620 acgtagccaa tctgggtgaa ccacgtacat cttgtgtttg ctttcctatc tctatccatt 7680 tatatactta tccacactaa tgaccggagc aatctagcga agatcacaaa aagcgaccgt 7740 tttcgctacc taggatctat cttgcaagag aacggagaat tagatggaga tctcaaccat 7800 agaatacgag ctggatggat gaagtgtaag agtgcatccg gcgtgttgtg tgaccgtcgt 7860 aggccactga agctcaaggg aaaattttat aggacggcaa taaggccagc gatgttgtat 7920 ggcacagaat gttgggcggt gaagcatcaa cacgtacaca aaatgggtgt agcggagatg 7980 aggatgcttc gtgggatgtg tgggcacacg agaaaggata agattgggaa tgaggatatc 8040 cgaggtaaag taggagtagc cgaaattgta ggaaagatga gagaaaatcg gctccggtga 8100 tttggacatg tgcaaagaag gccgactgac gctccggttc gaagatgtga ctacgggaca 8160 gaggttcagg gccgaagggg tagaggaaga cctaggaaaa ctttggaaga gactctaaga 8220 aaagacttag agtacttgga tctaacggag gacatgacac aaaaccgagc gcaatggcgt 8280 tctaggattc atatagccga ccccacttag tgggaaaagg ctttgttgtt gttgttgttg 8340 ttg 8343 // ID DEM1_I repbase; DNA; EDCOT; 3790 BP. XX AC AJ291492; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 15.11, Last updated, Version 2) XX DE Malus domestica retrotransposon DEM1_I, internal region. XX KW LTR Retrotransposon; Transposable Element; internal region; KW internal portion; DEM1_I. XX NM DEM1_I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3790 RA Yao J., Dong Y. and Morris A.B.; RT "Parthenocarpic apple fruit production conferred by transposon RT insertion mutations in a MADS-box transcription factor."; RL Proc. Natl. Acad. Sci. U.S.A 98(3), 1306-1311 (2001). XX DR Genbank; AJ291492; Positions 2774 6563. XX SQ Sequence 3790 BP; 1204 A; 466 C; 916 G; 1204 T; 0 other; gttggtatca gagcatggtt gcaatcttgg acatcttgag aagtttatag tgaattctgt 60 cagaactaca ccgcctcgta gcaaaccacg tagttagagg aatttagtct ccctgattta 120 gcggtttggg ggaaactatt attatggtga ttcagtatat tatcaaaatg gacattttaa 180 gacgggttat gagttgaatt tgaatcacct tatgaaatga tgaacctgag ggagcggagt 240 gacggtttaa ccaattggaa aagatgtttc agattatgca agtcaaagga aatttccttc 300 tgacaggtgg gtcgagacga ctacctggtt ttgggtatga atttgcatcc tggtggaaac 360 aggaatgtta attgttgtca ccagaggaat cagccgattt aaaatttttt aaggaaaagt 420 ttatccctcc ggcatttatt gatggtagta aacaagagtt tacaaatatg agacaaggaa 480 ggtgatgatc gagggatatt atagaaagtt ttcagacttg ccttgttcca tccagatatt 540 gttgttattg gtggaggtgt tatgttgttt taagctgggt ggcaaaaagg gaagtggtat 600 tttgggtgac cactatccat tatacttctt accaggaata tacgagatgc tgttgagtct 660 tgaggactct gagaatatga tcagctagag taaagaagaa taagaaaaga ttgggaatta 720 aaagaagacg ataaagttaa tgattcgtca tatcaaggat atagaaagat tcagagcttc 780 aaaagaagtg aagctagagt taattcttcc agcagaggtt ttaatgtcgc tggtcagaat 840 aaaagtgatg gatatactgg taatcccaga tatttgagac aaggtgtctc gagtaaagga 900 aatatacttt gtgcagcagg tacaaaatta acactttggg aagtgtgaaa ttaatgaatg 960 tgtttatgtg aacagagggg acacagaatt gtgaatcgtc cctagaatca gttgtactca 1020 acaattttcc atgaaatcat agtgtcgatt cagcagagtt atggatttag tagtttggtc 1080 ggattgaccg tgagtacaga gatatttgat gagttatatg ttcagccgta cggaccatga 1140 gaaatggatt tgactgacac atgagaaatt ggtgagttat aggctcggcc gtgccgacca 1200 cgcggagtgg atccggccga cgtattattg agataagagt tgaatcaacc gtattggtca 1260 ttctagttga cttcggctga tatatttctt attatgtatg atattaccta gagagtagta 1320 aataaatgta gttgagacga gtgtatgtat tttgcattga gtgacaaaat agtaatgtta 1380 tatctttgag agtggttgcc tacttatcga gacaacgatg atttatcagt atgcgggctg 1440 cagaccgtaa tattaataac tcattcgtgg attcgttaag caagcaaacc ggtagattat 1500 tttatgttag tataataaaa tatatattgt atcagttaat tctgttccat tagattggtt 1560 ggttataatt gtgataagac ggaatgttac gggaaaccag tactttccat cgatctggat 1620 gaccagagat tacttttgta agtatgcaaa atggattgag tcaggccgtt attaatgctg 1680 tgagagcaaa tagattgttt tcgaaaggct gtcaaaaata cttagctcat gtggtactaa 1740 aggatgttgc tcggagaagt gtgaaaaatg aaaaaggggt tagacttttt ttgatgtctt 1800 ccttgaaagt atacctggat tgccttcagg cagagatatg aggttcacta ttgaattgtt 1860 gccaggtata aatcttatga tagagattgg ttcatgatga gttaagtgaa ttggaaattc 1920 agttgaaaga attggttgat aaaaaatttc attcaaccta gtacaacact tttgaggagc 1980 accagtttgt tggtgagaaa gaaaatggac ttagagattg ttcattgatt atagacaatg 2040 gaattggtaa cgatcgagaa ccgttatcca tgatagtgta ctgatgttta gttgataagc 2100 tcagagatgt ttgtgtaatt tcaaagattg attgaggtct ggttattacc aattgaagat 2160 tttgagcgac attgatcata agatggtttt ctggatttgt tatgatcttt tatgagcttt 2220 ggtgatgcta taagaaaact cacgttgttt taggagttta tggatgaagt attccacgaa 2280 tgtcgtgata aattgttatc atttgtcatt gacgatattc tggtacattc tgagccagag 2340 cagagcatgt aaacatatta agttggtgaa gcaaagattg gaagaatgtc gattgtatgc 2400 aaagtttagc aaatgcgaat gttggatgaa tcaggtagta ttctgagatt tgttatatac 2460 tcttaaggta ttcaagtgaa tccttaaaag atagcagaaa ttagaatttg gaacaaccac 2520 gagtcgaatt gagatttgga atttcttagc ttaccaggct atcttggatg gttgtgaaag 2580 atttttttag tcattgattt gtcattgatg agactgttga gaaaagagat tatgtatgag 2640 tgggaaggaa attgtgagca aaggattcaa taactgaagt atttcctcac tcatgcacgt 2700 attttggtat tcccagagaa tagtggtaat cataaatttt tagtgatgtt tcttgaatgg 2760 tattggaggc atgttgatgc aaatgttagg gtgattgcat acgtttcacg ataaatggaa 2820 tctcataaga tgaattaccc tactggtgat ttggaagtca cgattaccat tcttgctgtg 2880 aagttatgga gacattatat tttagtggga atgcaagatt tttttttacg aatccaaaaa 2940 gtcttcaata tccattactt ggaaggattt tgatatgagg cagcgaaagt gaattgtatt 3000 gcttaatgaa catgattgta cgatcagggt gatcgtaaaa tttgttctag ctgaagcact 3060 tggtgagaag actacagtaa gattaatatc tggccgtttg ccaagagtat cattttgtgg 3120 attgaaaacc aacggaagaa aaattaagaa tggaagatcg agaagaagtt atacttgtta 3180 agtaacaagt tagtacattt actccagtgt tgagtaacaa cctttcccag acagtgcaac 3240 actacttatt tgttttatgg aaaagagaat tggtttacgg aactgctgag tttcttaagt 3300 atgttggttg tgcagtttcc gaagtaacgc cataaggatc atgaaatgtg tcatgtgagt 3360 cggtttttga tgacttgtga atggaatgtt tctgggtaga gaaggattcg atcaagaaag 3420 agttttagta gaccctgaga ctatggatga gtttcctcaa agtattcagg tgattaagtt 3480 aacctgaagt aaccaggaat ggcaaaagac atcaacagat ggatatgcca ctaatcgagt 3540 atataaggta aatggtttta tattttagaa gtgttcacct tagaaaagta gaatttggat 3600 tggaaaaaga aggtcctgag agttaagata gagtaaatgg taaaagtttt gtgaaggaat 3660 cattcagtgg aagaaaatta cgtgggagaa aaagaatcgg atgaaagaaa cttaccgagg 3720 ttggtataag tgttgatgaa ttggttggtt gctggaattt cggggacaaa attctataag 3780 gagggaagat 3790 // ID Copia-78_Mad-LTR repbase; DNA; EDCOT; 386 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-78_Mad_; KW Copia-78_Mad-LTR; Copia-78_Mad-I. XX NM Copia-78_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-386 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1695-1695 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 386 BP; 111 A; 51 C; 81 G; 143 T; 0 other; tgttgaatta taagtatttg agctgaaaag ttttttagaa taagtttctg ttttgaattg 60 gtgtattcac ttgtgcaaat gaggcaaagt gtaaatgtct agttttgtaa aaaggccatg 120 agtgccatgt gttgagtgat ccatgaaatt agaaagatgt gtgtctagga tgaaatgtag 180 tgtatgtgtg gtcccaagtt caggccatca gttatgtaaa agcatgtgct tcgtgctttt 240 tcattgacac agaaagatat tcctctgcaa ttttgcagag agaagaagaa aactattcat 300 cttccattgt gttcttcggt ttgtttttgc tcttagttaa gctttctttc ttaagtttaa 360 atctcttgaa ttcagaaaca ctaaca 386 // ID TE-7-1_VV repbase; DNA; EDCOT; 1460 BP. XX AC . XX DT 05-FEB-2009 (Rel. 14.03, Created) DT 11-DEC-2010 (Rel. 16.01, Last updated, Version 2) XX DE TE-7-1_VV, unclassified transposable element - a consensus DE sequence. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; Mila; KW TE-7-1_VV. XX NM TE-7-1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1460 RA Benjak A., Boue S., Forneck A. and Casacuberta J.M.; RT "Recent amplification and impact of MITEs on the genome of RT grapevine (Vitis vinifera L.). submitted."; RL Repbase Reports 9(3), 711-711 (2009). XX RN [2] RP 1-1460 RA Jurka J.; RT "Classification: hAT."; RL Direct Submission to Repbase Update (11-DEC-2010). XX DR [1] (Consensus) XX CC TE-7-1_VV (named Mila in [1]) is an unclassified transposable CC element that does not seem to be related to any known type of CC TEs. Individual copies are >90% identical to the consensus CC sequence. There are approximately 180 conserved copies in the CC genome. It contains neither TIRs nor LTRs and is flanked by 7 CC bp-long TSDs. It does not have any ORFs nor have any putative CC similarities to known proteins, but it is highly transcribed as CC there are around 100 ESTs (NCBI database for Vitis) that match to CC this element. XX SQ Sequence 1460 BP; 533 A; 209 C; 219 G; 477 T; 22 other; tcagggattg aaaaatcggr aaatatcgcc gatatttcga agaaatatcg gatatcgggc 60 ggcaycgaaa cgataatcgt caccgattat cgatcgacdg aaaaatcggc aaaaaatcga 120 caaaatcgyc gatatatcgg cgaaatatcg gtgaagcacc gatttatcgg agaaaaatcg 180 cgagtggatc tgacgcgcgg agcaaycgga ggagaatttw aaaaaatcgc cgaaaatatc 240 gccgatattt yggtattttt accgattttt cggaaaattt cccgatattt cctaccartc 300 cagcccgcrc acaggataca aaatctggct caaaaatcgt ggatttaggg ttcgtgaaat 360 ttaaatccaa tggcacaaca rcaaagagac ccttaaaaca gatccagaaa wcacagggag 420 caaaagaaaa gcaaattttt tggttttctt tgggggtttt kaatggattt tctcggaaat 480 caaacgagga tgaattttcc cggaaatcga atgggggatg gattttcttg graatcaaac 540 gggggttgca aaaaaaaata atatcaacgt gattagatta gtacctgcga ggattgagag 600 tggcagagga agataggtcc tttttaggaa ctctctcggc trgagggcaa cttcagaaaa 660 ggggagagaa aaggggaatt ctctcggctg gagggcaact tcaaaagtgg tggccctttt 720 aatttttaga tttagtagag gtaaaaaaaa aaaaccaaat catgagaaca attttcctct 780 atccatataa ataattataa attatcaaat tttattttga ttattaaata aattaatatt 840 aataaaaaaa agttgttact atatattttt aataaaattt taaaaattaa atctcaaata 900 aaatatttat ataaattaat ttaattttca tttaaaatat aataaaacat gttttaakaa 960 aartatttta aaatwtttta aataaatatt atcttcaaca aattgggtca tcttcatcta 1020 acaatataat gaaatcacat cgatctyttc cttartataa ggactattgt aatatcatat 1080 gtattatatt tatgtataaa ttrtttttat tyaataaaat caaatatttt ttaactcaat 1140 tctaactcta tatactttca aaattcatat atattatttt taaaattcaa atatcgaaty 1200 taccaatata tctttgttta cgatattttt cttcttaatt atatatatgt caattacact 1260 tacaagataa ctttaaaatg tgtattttta cttattttat cattttttga agttttttca 1320 agcattccta ttaattttaa ataattttca ctctatcgat atttgtgaaa aaatatccac 1380 cgatatttct ccgatatttc cgatatatcc gtaaaatcga agtaccgata tatccgtaaa 1440 aaccgatatt tcaatccttg 1460 // ID Gypsy-14_Mad-LTR repbase; DNA; EDCOT; 381 BP. XX AC ACYM01085282; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-14_Mad_; KW Gypsy-14_Mad-LTR; Gypsy-14_Mad-I. XX NM Gypsy-14_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-381 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1418-1418 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01085282; Positions 864 484. XX SQ Sequence 381 BP; 95 A; 60 C; 98 G; 128 T; 0 other; tgttatgaac tgtaagaaag ggttactcag tcgaggaaat aaacaagtag tggttatata 60 ggactgtttt gtgagggatt ttgggttaaa aagtgtaagg gttttgtaac caggttcaat 120 tgtatttacc taagtccttt tgagagtcta gttaattagt gagtgatgtc cagctggcaa 180 ttgtagtggg gagaactttc attgttgcgt ggttaaatgg tggccagagg aatttgtaag 240 ggcagatttg atttactgaa tagaatatcc tttccttttc ctctctactc tatcccttca 300 ccactgtcgt tacagctgcc atcgcaggtt gagaccattg caggtctggg ttgtgtgcca 360 ttgcaggtcc gtgacatatc a 381 // ID Copia45-PTR_I repbase; DNA; EDCOT; 4294 BP. XX AC LG_XVIII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia45-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4294 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4294 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 268-268 (2007). XX DR Genome; LG_XVIII; Positions 3737634 3733341. XX CC Positions [1593-2123] - Integrase core CC 'GTAAT' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1014..2324,2328..4190) FT /product="Copia45-PTR_I_1p" FT /translation="MLLMAFLEEEESKSDKWYLDSGCSNHMCGNKELFSCL FT NENYKDTVKLGNGMFITVMGKGNVRFYAKDNTVQTISSVFYIPELKSNLIS FT MGQLQEKGYTIIITAGCCKIHHPEKGVIAKARMTSNRMFPLYMQDQIQTCF FT STKMHDSTWLWHFRYGHLNFDGLKALQEKNMVTGLPKITCPTELCEECVVG FT KQPRDSFPKGKAWRAEQTLHLVHSNICGPINPTSNGNKRYFISFINDCSRK FT TWVYFLQDKSEAFTVFKKFKAHSEKECGNPIKILRTDRGGEFTSHEFANFC FT EMHGIQRQLTAAYSPQQNGVAERRNRTIMNMVRSMLLKGKMPKSFWPEAVK FT WSVHILNRCPTFAVKNITPTEAWCGSKPMVDHFRIFGCIAYAHVPDAKRTK FT LDDKAVKCVFLGVSEESKAYKLYNPITRNIVISRDVQFDEENTDWNKTDAN FT LFQDSDLYEDASYGTEEGFIGDRKIESHIQPPECEIHTEEQLQVPIPHEGT FT IVPHGEGTSNIPQRQRTAPAWMNDYVNGNEFSDEDTFAQFALFAGSDPIKF FT EDAVKEDKWRRAMDTEIHAINKNNTWELVDLPRGQKTIGVKWVYKTKLNEN FT GEIDKHKARLVVKGYKQQHGIDYDKVFAPVVRHDTIRLVISLAAQHTWPIF FT QMDVKSAFLNGDLEEQVYVDQPSGYVKQGYEEQVYKLNKALYGLKQAPRAW FT YSRIDAFFTKAGFRKCPHEHTLFVKTAGGGKFLFVCLYVDNLIYTGNDGIL FT LQEFKDSMKAEFEMTDLGMMRYFLGIEVMQSTTGIFITQKKYAKEILERFH FT YQNCNPVKNPIEPGLKLHKDLDGQRIDSTYYKQMVGSLMYLTATRPDVMCA FT VSLLSRYMESPTSLHSQAAKRVFRYLQGTIDFGIHYKKREASRLIGYADSN FT YAGDLDDRRSTSGSVFMMNSGAVSWSSRKQQVVTLSTTEAEFIAAATSACQ FT AIWLRRILDDLHVQQHDPTIIHCDSSLTIKLSKNPVLHGRSKHIDVRYHFL FT RDLSNEGTIELVYCRSEDQIADIMTKALKLDAFEKLRNLLGMCSFQVLEQG FT N" XX SQ Sequence 4294 BP; 1436 A; 717 C; 991 G; 1150 T; 0 other; agtggtatca gagccagaga gtgttagagt gtgacaaatc agaaagttaa gggaaacaca 60 gggaagagag atcgtgagat tgagagaaac actgggaaac acagggaaaa agagagatag 120 tgagttttgt gtcttttgct gcagcaaaga aaatggcatc agaaaataat tacgtgcaac 180 ctgcaatccc acgctttgat ggtcattatg accattggag tatgttgatg gaaaatttct 240 tgaggtcaaa ggagtattgg agtcttgtgg aacaagggat caatgaacca acggttggaa 300 gtgtgctgac agaagcacaa accaaaatcc ttgaagatca taaactgaag gatcttaaag 360 caaaaaatta cttgttccaa gcaattgatc gggggatttt agagatcatt cttcacaaga 420 acacatccaa gcagatttgg gactcaatga agaagaagta ttaagggtca acaagagtga 480 agagggcgca gcttcaaact cttcgcaaag agtttgaaat tcttcacatg aatactggag 540 agtcagtcga tggctatttt tcacgcactc ttgcaattgc aaatagaatg tgaatacatg 600 gtgataaaat ggaggatgta acgataattg agaagattct tcgatcaatg tctgcaaagt 660 ttaactatgt agtctgctcc attgaagaat cacacaacat taaagaactt tcgattgatg 720 agctacaaag ctcattgcta ttgcatgagc agcggatggt gagcattatt cctgaggaac 780 aagttctgaa agtatcaatg aatggtggag taccttcaag gggatatgga agaggtcgca 840 gctggggcag aggaggtaca ggccgtggtg gaagaggtcg tggttatgat caaaaaccat 900 ttgacaaatc atgagttcaa tgctataatt gccacaggta tggccattat caatatgaat 960 gcacagataa agaggagaag gtgaatcttg tagaagctga agccgaagaa gaaatgcttt 1020 taatggcatt tcttgaagaa gaagaatcca aatcagacaa atggtatttg gattcagggt 1080 gcagtaacca catgtgtgga aacaaggaat tattttcttg tttgaatgaa aattacaaag 1140 atacagtaaa gcttgggaat ggcatgttca ttactgttat gggaaaggga aatgtgagat 1200 tttatgcaaa agataacaca gtgcagacaa tatccagtgt cttctacatt ccagaattga 1260 agagtaatct gattagtatg ggacaattgc aagagaaggg atatacaata atcattacag 1320 caggttgttg caaaatacat catccagaga agggagtaat tgctaaagca agaatgacaa 1380 gcaatcgcat gtttccatta tacatgcagg atcaaattca aacatgtttt tccacgaaaa 1440 tgcatgactc aacttggtta tggcattttc gttatgggca tctaaatttc gatggcttga 1500 aggcactgca agagaaaaac atggtgactg ggcttcctaa gatcacttgt cctactgaat 1560 tatgtgagga atgtgttgta gggaaacaac ctcgagattc ctttccaaaa ggaaaagctt 1620 ggcgagctga acaaactctt catttggttc actcgaacat ctgtggacca attaatccaa 1680 cctcaaatgg caacaagagg tattttatct cctttataaa tgattgcagt cgaaagacat 1740 gggtttactt cttgcaagat aagtctgaag cttttactgt gttcaagaag tttaaagctc 1800 atagtgaaaa ggaatgtggt aatcccatta aaatccttcg aacagaccgt ggtggtgaat 1860 ttacttcaca tgaatttgca aatttctgtg aaatgcatgg aatacaaagg caacttacag 1920 cagcatattc accacaacag aatggggtgg cggaacgaag aaatcgtaca attatgaaca 1980 tggttcgtag tatgttactg aagggaaaaa tgccgaagag tttctggcct gaagcagtta 2040 aatggagtgt tcatatattg aatcgttgcc ctacgtttgc tgtaaagaat attacaccaa 2100 cagaagcctg gtgtggatct aagcctatgg ttgatcactt cagaatcttt gggtgcatag 2160 catatgcaca tgttccagat gccaaaagaa caaagctgga tgacaaggca gtaaagtgtg 2220 tatttcttgg agttagtgag gaatcaaaag cttacaagct ttataatcca atcaccagaa 2280 acatagtcat cagtcgtgat gttcagttcg atgaagaaaa cacataggat tggaataaaa 2340 cagatgcaaa tctgtttcaa gattctgacc tgtatgaaga tgcaagctac ggaacagaag 2400 agggttttat tggtgatcgc aaaattgagt ctcacattca gccacctgaa tgtgaaattc 2460 acacagaaga gcagctgcaa gttcctattc cacatgaagg aaccattgtt ccacatggtg 2520 aagggacatc caacatacct caacggcaaa gaacagctcc tgcatggatg aatgactatg 2580 tcaatggaaa tgaattttct gatgaagata cctttgctca gtttgcttta tttgcaggtt 2640 ctgatcctat aaaattcgaa gatgcagtaa aagaagacaa atggagaaga gctatggata 2700 cagagattca tgccatcaac aaaaataaca cttgggaact tgtagatctt ccaagaggac 2760 agaaaactat tggcgtaaag tgggtctata agaccaagtt aaatgagaat ggggagattg 2820 acaagcacaa ggctcgtcta gtggtaaagg gttacaaaca gcagcatggc atcgattatg 2880 ataaggtatt tgccccagta gtcaggcatg ataccattcg tcttgtaatt tcattggcag 2940 cacagcacac ttggcctatt tttcagatgg acgtaaagtc tgctttcctg aatggggact 3000 tggaagagca agtttatgtt gatcagcctt ctggatatgt gaagcaagga tatgaggagc 3060 aggtttacaa attgaacaaa gctttatacg gactgaaaca agctcctaga gcttggtaca 3120 gtcgtataga tgcgttcttc actaaggcag gtttcagaaa atgcccacat gaacacactt 3180 tatttgttaa aactgcaggt ggaggtaaat tcctgtttgt gtgtttatac gtggataatc 3240 ttatttacac tgggaatgat gggattttgc ttcaagaatt caaagactcc atgaaagctg 3300 aatttgagat gactgatttg ggtatgatgc gttattttct tggaattgaa gtcatgcaat 3360 caacaactgg aatcttcatt acgcagaaga aatatgcaaa agagatcttg gaaagatttc 3420 attatcaaaa ttgcaatcca gtcaagaatc caattgaacc aggactgaag ctacataagg 3480 atcttgatgg acaaagaatc gacagcacct attacaaaca aatggttggg agcttaatgt 3540 acttaacggc tactaggccg gatgttatgt gtgcagtgag tcttcttagc aggtacatgg 3600 agtcaccaac aagtctgcat tcccaagctg cgaagagagt gtttcgttat ttacagggaa 3660 caattgattt tggtatacac tataagaaaa gagaagcttc aagactcatt ggctatgctg 3720 acagtaatta cgcaggtgat ttagacgaca ggagaagcac ttcaggaagc gtgttcatga 3780 tgaattcagg tgctgtgtct tggtcttcaa gaaaacaaca ggtggttact ctatccacaa 3840 ccgaagcaga gttcatagcc gcagcaacat cagcatgtca agccatatgg ctgagaagaa 3900 ttcttgatga tctgcatgtt cagcaacatg atcctacaat aattcactgt gacagcagct 3960 taacaatcaa gctttctaaa aatccagtcc ttcacgggag aagcaagcac atagatgtgc 4020 gatatcattt ccttcgtgat ctttcaaatg aagggaccat cgaattggtt tactgccgaa 4080 gtgaagatca aatcgcagac atcatgacaa aggcactgaa attggatgca tttgaaaaac 4140 tgcgtaattt acttggaatg tgttcgtttc aggttcttga gcaaggaaat tgatgacagc 4200 agctatgttg tttgtttaat aaaactgcta tgatgaaacc tccatagtag taccatctta 4260 aactgttttt tgcagaaatc agtttaaggg aggg 4294 // ID SAT-1_PTr repbase; DNA; EDCOT; 182 BP. XX AC . XX DT 10-DEC-2009 (Rel. 15.02, Created) DT 10-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Satellite sequence - consensus. XX KW SAT; Satellite; Simple Repeat; Nonautonomous; SAT-1_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-182 RA Bao W. and Jurka J.; RT "Satellite sequences from black cottonwood."; RL Repbase Reports 10(2), 237-237 (2010). XX DR [1] (Consensus) XX SQ Sequence 182 BP; 38 A; 39 C; 40 G; 65 T; 0 other; agctgtcact cagttttcag tgatgatttc aaggtctaca gtgactctgt tttcgctgac 60 gatttatgga tcagcagtga catagcgttt ttgacaattc catgcgtcag ccatgactct 120 atttttgcta tcgatttgat gcgtcggtcg tgaattcatt gacgctgtcg attccatacg 180 tc 182 // ID GmCOPIA10_LTR repbase; DNA; EDCOT; 1091 BP. XX AC . XX DT 27-JUN-2008 (Rel. 13.06, Created) DT 30-JUN-2008 (Rel. 13.06, Last updated, Version 1) XX DE Copia-like retrotransposon from Glycine max. XX KW Copia; LTR Retrotransposon; Transposable Element; soybean; KW consensus; LTR; GmCOPIA10; GmCOPIA10_I; GmCOPIA10_LTR. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-1091 RA Wright L.N. and Laten H.M.; RT "Intact, full-length transposable element consensus sequences in RT Glycine max assembled from robust collections of BAC-ends."; RL Repbase Reports 8(6), 647-647 (2008). XX DR [1] (Consensus) XX CC Related to retrotransposon V14 from Vitis vinifera. XX SQ Sequence 1091 BP; 358 A; 170 C; 185 G; 367 T; 11 other; tgtagatgca attggctttg atgttttgat gatgatcatg atgatgtgtt gcaattgatg 60 caaatgggct tttcaagatt aaaattcaag acaatacttc aagattacaa gkcacaacat 120 caagatgatc actagaatat taggaaggga attcctaatt gaattagcaa aggtttggcc 180 aagtgattta aaataaaaag tgtttttcaa aggttttact ctctggtaat cgattaccag 240 aggatgtaat cgattaccag tggccaaata crttttataa cagctataaa aatttgaatt 300 cgaaatttta ramkstgtaa tcgattacac aattttggta atcgattacc agcagttagt 360 aaacgtttta attcaaattt taaaagctgt aatcgattac acaattactg taatcgatta 420 ccagacagga atttcagaaa aataatttca agagtcacaa cttttcaaag gctttactca 480 tgaccaccaa tggtctatat atatgtgact taaacacgaa attgctyaga gattttcaga 540 acaacaaagt gtttatcctc tcaaaragca awttcatttt atcctcttaa gaattccttg 600 gccaattcaa ttgcaattca ttaaggaatt aattgagtgc tcaatctgta aaatccatct 660 ctttctagag agatttgttc ctcttcttct tctcattctc taagggatta agagactgtg 720 agtctcttgt tgtaaagrat ctctaaacac aaaggaaggg ttgtccttgt gtgtttagaa 780 cttgtaaaag gaatttacaa gttagtggaa ctctcaagcg ggttgcttgg ggactggacg 840 taggcacaag ggtgtggccg aaccagtata aaactgagtt tgcattttct cttcccttaa 900 tctcctttat ttattattgc tttatattca tattcaagtt gcttcatttg aattaatatt 960 taagaagatt gtcattaagg gaattcataa cttaagtaaa aagtaagata gatttttaat 1020 taggrgaaaa gtttggaata tcttaattca acccccccct tcttaagata tctgaggcca 1080 cttgtctaac a 1091 // ID PDR1_LTR repbase; DNA; EDCOT; 156 BP. XX AC X66399; XX DT 28-APR-2000 (Rel. 5.03, Created) DT 28-APR-2000 (Rel. 5.03, Last updated, Version 1) XX DE PDR1_LTR is a long terminal repeat from the PDR1 LTR DE retrotransposon. XX KW Copia; LTR Retrotransposon; Transposable Element; PDR1_I; KW PDR1_LTR; Ty1/copia-like LTR retrotransposon. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-156 RA Lee D.; RT "PDR1_LTR."; RL Direct Submission to Genbank (21-MAY-1992)D. Lee, John Innes RL Institute, Colney Lane, Norwich N4 7UH, UK. XX DR GenBank; X66399; Positions 1 156. XX SQ Sequence 156 BP; 55 A; 18 C; 21 G; 62 T; 0 other; tgttgtaaat attagattgt aaatagtaat tatgtctatt agtaatgagg tccattagtc 60 aaagcccatt aggttttcta ttctctctta tttaaagcat gtagatgtaa catgtaagaa 120 tcacttttta atatatcagt aaaatatttt acaaca 156 // ID RAVLIN_MT repbase; DNA; EDCOT; 3807 BP. XX AC . XX DT 12-JAN-2007 (Rel. 12.01, Created) DT 06-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE A long interspersed element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW LINE; Interspersed; repeat; Poly-A; ORF; polymerase; RAVLIN_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3807 RA Shankar R. and Jurka J.; RT "RAVLIN_MT: A LINE from barrel medic."; RL Repbase Reports 7(1), 49-49 (2007). XX DR [1] (Consensus) XX CC The sequence contains a single ORF having domains for AP CC endonuclease and RT polymerase, with well conserved poly-A tail, CC all characteristic features of an L1 element. The 5' end is CC truncated and in general the element exists in very scattered CC poorly conserved form with low copy number. XX FH Key Location/Qualifiers FT CDS join(317..595,599..2041) FT /product="RAVLIN_MT_1p" FT /translation="MWTPHDDCXKMITSSWNXNIVGCHMYILNXKLKNLKT FT KLKVWNKXVFGDVHXAVKIAEXNLXQIQNDIDLQGFTDTLLDQEKXAQINL FT ELCLKQEDFWREKAKVNWXLXGDRNTXYFHRXXKIKKTSKLITTLQDGDNM FT ITDPDQIANHIINYXKTLFXTNFVLQDQLLVDEVIPTLISDDKNAVFTTLP FT SSLEIKXAVFDXNKDGAPGPDGFGALFYQTYWDIVKKDVVNAVLEFFTRDW FT ILPNFNSNIIVLIPKIPDATSMGQYRPIALANFKFKIITKILADRLAQLMP FT KIISTDQRGFIQGRNIKDCICIASEAINFFHKKSYGGNIAFKVDIXKAFDT FT LDWNFXLHVLKXFGFNEIFCNWIHTILQSANLSIYVNGKPDGYFNCTRGVR FT QGDPLSPLLFCIAEDVLSRAISKLVDQGKLELIKGTRXVNVPSHSLYADDI FT MIFCKGKNASISNLIDLFNIYALESGQIINSAKSIMYPGSISVSRIQQLST FT MLGFNIGSFPFNYLGVPIFKGKPKASHLQPIADKIKSKLATWKASLLSIAG FT RVQLVKSVIQGMLMYTISISILGPRLC" XX SQ Sequence 3807 BP; 1157 A; 625 C; 664 G; 1309 T; 52 other; tggtttttta ttggggactt caatgctgtt tttggagccc atgaaaatag aggtatcctc 60 ctccagttyc aatggargag ttcttgaatg gacaagctaa taatctctat cacattccca 120 ctagagcaga gtacacatgg tctaatagga gaggagatgg aagcattgca caaagacttg 180 acagggctat ctgcaatgaa caatggattg ttgttctctt acttgttcaa ctttaataaa 240 acataatctg accatcatcc tcttttactg ttccaagtga cccctcagtt ttgcttccca 300 attcaaattc ttkcaaatgt ggacmcctca tgacgattgt maaaagatga tcaccagtag 360 ttggaatwca aatattgttg gatgccatat gtacattctt aattmcaagc taaagaatct 420 yaaaacwaaa ttgaaagtyt ggaataarrc agtctttggt gatgtgcata mngcagttaa 480 aattgctgaa saaaatctta mtcaaattca raatgatatt gatttgcaag gtttcactga 540 cactcttytr gatcaagaga aakawgcmca aattaacctt gaactttgct tgaaataaca 600 agaagatttt tggagagaga aagctaaagt caattggyat ttaratggtg acagaaayac 660 trmatatttc catagamtar ccaaaatcaa aaaaacctct aaactgatca ctactctgca 720 agatggtgat aatatgatta ctgatcctga tcaaatagca aatcatatta ttaattattk 780 caagacttta ttttstacta actttgtttt gcaggatcag ttacttgtag atgaagtaat 840 ccccactcta atctctgatg acaaaaatgc agttttcact actctwcctt catcattgga 900 gattaagnaa gcagtttttg atmtgaacaa ggatggcgca cctggtcctg atgggtttgg 960 tgcacttttt tatcaaactt attgggacat tgtcaagaag gatgttgtca atgcagtttt 1020 agaatttttc acaagagatt ggattcttcc aaatttcaat tctaacatta ttgttctgat 1080 tcctaaaatt ccagatgcta cttctatggg tcaatataga ccaattgctc tggccaattt 1140 caaattcaaa atcattacca aaattttagc tgatagatta gctcagctta tgccaaagat 1200 catttctaca gatcaaagag gmttcattca aggtaggaac attaaagatt gcatctgcat 1260 tgcttcagaa gctatcaatt tctttcataa gaaatcttat ggtggaaata ttgctttcaa 1320 agtagatatt tsaaaagctt ttgatacttt agattggaac ttcyttcttc atgttttgaa 1380 awgttttggt tttaatgaaa ttttttgtaa ttggattcat actattctac aatctgctaa 1440 tctttcaatt tatgtcaatg gtaaaccaga tggttatttt aattgcacta gaggagtgag 1500 acagggagac cctctctcwc ctcttctatt ttgcattgct gaagatgttt taagcagagc 1560 gatttctaaa ctagtggatc aaggaaagct tgaactcatt aaaggaacta ganrtgttaa 1620 tgttccttcc cactctttat atgctgatga catmatgata ttttgtaaag gtaaaaatgc 1680 aagtatctca aatcttatag atctatttaa catatatgct ctggaatctg gacaaattat 1740 aaattctgca aaatcaataa tgtatcctgg ttctatctct gtttctagga ttcaacaact 1800 ctccacaatg ttaggcttca atataggatc ttttcctttt aattatctag gggttcctat 1860 ttttaaaggg aaaccaaaag cttctcatct tcaaccaatt gctgacaaaa tcaaatctaa 1920 actagctact tggaaagcct cccttctatc tattgctggt agagttcaac ttgttaaatc 1980 tgtaattcaa ggtatgctga tgtatactat ttccatatcy attcttggcc caagactctg 2040 ttgaatgatg ttgaaacatg gtcaagaaat ttcatttgga gtggtgatgt tgataaaaga 2100 aagtttgtga ctgttgcttg gaaraaagtt tgtaagcctt tctctgaagg tggtttaggt 2160 atgaggtcta tttatactct caatgaatca acaaatctaa aactttgctg ggakatgttg 2220 aattcaacrg aagattgggc aatcttgttg agatctagag ttttgagagg cagaaaagca 2280 atttctcacc acattttctc ttctatatgg agcagtatca aaaatgaatt caatgatatc 2340 aataataatt gtatttggct ccttggtaat ggtcaaaata tcaatttttg gcttgataac 2400 tggtgtggag cacccctttc tcaagcytta artattcctc atgcaatatc agttcattta 2460 acatcaactg ttagtgatta cattgttaat ggtgaatgga atattcctga aactctttct 2520 caaatgtttc ctcttctcag tcaacttgtg caacaagtta ctattcctct ggaagccaaa 2580 gatgataaaa taatttggaa acattcagct aatggttwct tgtctttcaa gcaagcttat 2640 gttttcaaga gaaataataa tgaagatctt aagtgggcaa agttgatttg gagtacggat 2700 attcctcctt caaaatctct tttggtttgg aggctcatgc ataacaaggt tcctactgat 2760 gataatctta tggatagagg ctgtcagctg gtttccatgt gttacytctg ttgtaagaat 2820 tctgactctt ttatccattt gttctttgac tgcccttttg ctttaaaatt gtggtcctgg 2880 ttatctgcat ctttaaatat gaatatgcag tttacagact tggatgacat ttggaaaatt 2940 tttgaaagaa cttggtctcc tcaatgtaaa attgttatca aagctgctct gattaatata 3000 attaacacaa tttggtttag gaggaatcaa gctagattca aaaataagtt aattcactgg 3060 aagtcagcca tttaaatgat tattgctaaa atatctctat ctggtaacat cactaccaaa 3120 gcatctaaag gtgatatcag agaattcata attttaaaag ctttcaaagt caacattaat 3180 cctccaaagg ctcccatcat caaagaagta atttggacgc ctcctttgac tcattgggtt 3240 aagggcaata cagatggagc atctataaag aatcctggta gagcatcttc tggtggaatt 3300 ttcagagact ctgaaggtat ctgtattggt tgctttactc aatgtctagg taatctcaat 3360 gcttatcatg ctgaattagt tgttgccatg acagctattg aaatggcgta tcagaagcat 3420 tggaaatttc tttggttaga gacagactct cagttggtga ttttagcttt taagaattcc 3480 actctagtgc cttggaattt aagaaacagg tggaacaatt ttcagcttaa attaactaat 3540 atgaattttg trgtttctca tatttacagg gaaggaaacr catgtagctg atactcttgc 3600 taactttggt ctgtctctgg atctctttga ttttttggat catatacctt tgtttcctag 3660 gggagagtac attaggaaca ggttgggtat gcccaacttt aggttttctt cttgagaaag 3720 ttttttggtt tggtcccctt tctcttcttt gtttcctttt ctcttttaat ctatcctttg 3780 tggcttgcta aaaaaaaaaa aaaaaaa 3807 // ID Helitron-4_Mad repbase; DNA; EDCOT; 7342 BP. XX AC . XX DT 02-NOV-2010 (Rel. 15.11, Created) DT 02-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE Helitron family DNA transposons from the apple genome. XX KW Helitron; DNA transposon; Transposable Element; Helitron-4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-7342 RA Bao W. and Jurka J.; RT "Helitrons from the apple genome."; RL Repbase Reports 10(11), 1904-1904 (2010). XX DR [2] (Consensus) XX CC The 5'-end is not determined. XX FH Key Location/Qualifiers FT CDS join(2265..3221,3561..6692) FT /product="Helitron-4_Mad_1p" FT /translation="MFPFEADDFNLINENEIQPNEDVPPRQHXMGTRPIHN FT CARNFNENMGIPRFHMPNPTTCPDCHARLFSHETFEMCCLRGKLALPLTPS FT PPEMTELFCNQSAQGRHFRQNIRAYNHIFAFTSMGVHVDENLATGRRGIYT FT FRAQGSIYHKIGSLLPIGDSRPRFLQMYIYDTAHEIDNRMRESEALNRDVV FT EKIQQILNQYNPFVQTFHHLAQRQDLQSCRLIIKEQPANQRQYCLPSASQV FT AAIIVGGEGSENIRGRDIVVQTTDGQLKSIKDCVGYYDPLQYPLLLPYGTY FT GWDVNTRNNTNRKVTCCDYYSYVLQVTWVETKQTYLDLLTTFNKTNTGNIG FT RRRTILPSSFVGSPRDMYQRYQDAMTLVQKYGRPDIFLTMTCNPNWEEISD FT ELLPGQAPQDRPDLLTRVFRAKFEQLKNDVIKKSVLGRVLAYVYVIEFQKR FT GLPHVHMLLMLEENDKLNSPDDYDRMVRAEIPIPNEEPELYGAVLRHMIHG FT PCGIHNSRSPCMKRGSCKRNYPKPFAPTTVQGNDSYPVYRRRDNHNPVPLD FT QNARIMVDNRWVIPYNSWLLLRYDCHINVEICCSIKSVKYLYKYVYKGPDR FT VAFEVHPEPIQDEIKQFVDARWVCAPEALWRIFKFVTNRLYPSVERLQIHL FT PEGQTVHFYPHQRVSDILADDTNSMTMLTEFFTKNTTCPEARRYLYREFPE FT RFRWSQRDKVWSERMNNHKVIGRIYAVSPNEGEKFYLRILLNHVRGPTSFX FT DLRTVNDIVQPTFKKAVEQRGLLEDDDSIRQCLREASNIRMPSALRRLFVT FT ILVYCEPHGVRRLWDEFHSFMVEDYSVSSTINNTSILNKLLQDLNGLLVQH FT SKSVSDYDLPQITQDCVRDNTLPRIIQDEVSLDISEADLNAVHNLNEDQMA FT AYNSIVSAIERRDNAIFFVDGPGGTGKTYLYCALLATLRSDGHIILATATS FT GIAATILPGGRTTHSRFKIPLSPDASSTCSISIQSDLAELIRKTSAVVWDE FT APMAHRFAFETLDRTFKDIIGVDLPFGGKVMIFGGDFRQVLPVVPKGTRSE FT LMQASMINASFWGHVKIIRLRHNMRSINDQDFSEFLLHVGNGEQETMIDDM FT MQLPSSMVIPWNGEESIVQFVNEVFPDLECHVCDSRYLVERAIITPKNEDA FT DKLNKMIIDKFPGTEHILYSFDSVEDDVRNLYQQEFLNSISPGGMPPHQLT FT LKKGAPIMLLRNIDPKMGLCNGTRLACHGAYNNLIDAEILSGQFAGTRVFL FT PRISLKTTESAGLPFEMMRKQFPVKLSFALTINKSQGQTIPNVGIYLPDHV FT FSHGQLYVALSRGVSASTTKVLVKKGELHGHEGVFTRNVVYKDILLPSNST FT " XX SQ Sequence 7342 BP; 2462 A; 1310 C; 1335 G; 2225 T; 10 other; ctgtcttaat tttggttatg gtggtatatg tttggctccc tcctattagt ttgtgttagt 60 ctgtgttttt tccttttcga aattctcaat gttatgtgct ttgtcaattc gatagtgtac 120 aatttcatga atcttttaac tgtgatctaa tttgtgcaag catcattttc cattgttgaa 180 tttcaatgct atgttttcat atttttcttc aattttacct ttattaagaa tcatcaaatt 240 gaaatttcag ttttaagatt tccagaggac ttcaacatat caagtatgga gggaattgat 300 agaagcaata tgtcagaggt tgcttacctt atctgcatta ttcctcttct gtagagatga 360 tttatttttt cttcttttca aaaataaaaa taaaattcat tctctttggc aatttctcaa 420 tgtaggtcgg caatgaagaa gttcacttcg gacaaacaaa tgttcacaat tctcaacagt 480 cagaccaaag gtatcgtagg agcaatcaac aaaggcaaag acgacaatct atgaattcat 540 cacagcgggc tcgaatttca mtgcgacgac gtgccaatta tcaagcccga ttgaactcgg 600 taaatatagt acaaaatcaa acggaagtaa accaagatga cataggacca acatcggcgg 660 gtaactatga attttttttt gtctctatta attatatata tatttgtaaa tccatatgtt 720 gtatgaatat tttttgtacg aattattaag acacatccat taagattgaa cggawtagtk 780 attttacatt gtcattgcct tttcgtacta tcaatgsaaa catccattta ataattctgt 840 tatgtctata acaattccaa catttggatt gtatatatct accacactga ccaacgtttt 900 aacaagtact ccaaacaaaa aaaaaaaaaa taaataaacc aattaaggaa aaaaattaaa 960 aaatgaaaaa taaaggaaag gaatatgtct ggaacgatag gtgatacaaa wttttatgwa 1020 aacttggaat aacagttcaa ctataatagt caagagaaaa cttaaaaata acatcgcata 1080 aagatatagt atatctatac caaaaggaga ccccaaattg tggactcaaa aaaacgtcat 1140 gatgcgatca accaaaattt atagtccact attaaagggc aaaaatttta ggaaatgata 1200 atgggtacag atacagaata tcgatctagc aacacaattt aaaaaaatga aaagttctac 1260 ttcaaaatta gtggagtgaa cctccgtttt tattgttttt ccgttttttt taaccccaaa 1320 acactaagkt agtagaaacc atttctttgt cctcctctcc aaacgtgtca ctatgtggta 1380 aatcaagtct gctgtataca actaatttta ttttaccact gttataatat ttactcttta 1440 ataaactaag tctaccgtaa actatttttt atttttagtt tccaatcaaa cgaaaaaaaa 1500 aaaaaaacgt aatgtatacc actgattcaa ttacaaaaac aaaaggaaaa aaaaaataag 1560 tatgtaggta cttaaataat attctatgct tactaatatt tttcgtacac cattacgttt 1620 cttggtttag agcaacaaaa tgcatatgtk actgatgaga gacaaagcca acgagagcaa 1680 tggcgggatc aacaacgtat gaggcggaat tcaatgagtt caaggcaaag acatgattac 1740 ttagcacggc gacgatccaa ttatcatgtt caacaaattc aacgctcaaa cataatgtta 1800 tttggtggcg ataccgatca agttcaacac cctaacatag tgcaattcga tgaaggcagt 1860 agcaatcatg ttgaacgact caacatagtg ccgtttggag aaggcagtag caatcaagtt 1920 ccaagaacaa tgcgcttaac tcatataagg caaattgccc gatcgaatag gacacgcttg 1980 cctcaggatg gacttattca aagttttact aataatggta attgcacaaa ctaccatagt 2040 acaactttga aaaagataaa catcaatatc atcattattg taaacaccac ttattacctt 2100 acttccattt cattttatta taacagaaaa tacaacagcg caatcattcc attcgaatat 2160 tccaatgaat cattcttatc cacccatcat caatgaaggt atcagttttg gaatgttaat 2220 acctacattt tttactatgc tctctaaacc ataaaacact tttaatgttt ccttttgaag 2280 cagatgattt taatctcatt aatgaaaatg agatccagcc taacgaggac gtaccacctc 2340 gacagcatmc gatgggaaca aggccaattc ataattgtgc tagaaacttc aatgaaaaca 2400 tgggaatccc aagatttcac atgccaaatc caaccacatg tccagattgt catgcccgtt 2460 tgttctctca tgaaacattt gaaatgtgtt gcttacgtgg aaagcttgct ctaccattga 2520 caccgtcccc tcctgaaatg actgagcttt tttgcaacca atctgcccag ggaagacatt 2580 ttaggcagaa tatacgagct tacaaccaca tttttgcctt cacttcaatg ggagttcatg 2640 ttgacgaaaa cctagcaaca ggaagacgtg gtatttacac atttcgtgct caaggttcca 2700 tataccataa gattggaagt ctcttgccta ttggagatag tagaccaaga ttcctacaaa 2760 tgtatatata tgacactgct catgaaatag acaatcggat gagagaaagt gaagcactaa 2820 acagagatgt ggttgaaaaa atccaacaaa tcttgaatca atataatcca tttgtgcaaa 2880 catttcacca ccttgcgcaa cgtcaagatt tgcaaagttg tagattgatt atcaaggagc 2940 agcccgcgaa tcaacgacaa tattgtttac cgtctgcatc tcaggttgct gcaatcatag 3000 taggtggtga aggatcagaa aacattagag gtcgagatat tgttgtgcaa actacggatg 3060 gtcaacttaa gagtatcaaa gattgtgtcg gctactatga ccctttacaa tatccattgt 3120 tgttacctta tggaacgtac ggatgggatg tgaatactcg aaataatacc aacagaaaag 3180 tgacatgttg tgactattat tcgtatgttc ttcaggtaac ctaagacctt catctctgtc 3240 aataaatatt aatttttaaa acttatattg tgttgaacaa tgaattttat cattttagat 3300 ccgtcaacat gatgaatcgc ttctacttcg tggtggccgc ctattgcagc aatatgtagt 3360 tgacaactac gtaaagatcg aatcacaaaa gcttagatgg atgcgtgata atcaacacac 3420 aattcgatct gaattttatc gaggactaca agactcatta attgcaggac aaaataatgc 3480 aggtatgagg ctaatcagtt tataataaaa aaatatattc ttcatgttca tgttttgtca 3540 cattaaatga gacttattaa tgggttgaaa caaaacaaac atatttagac ttattaacga 3600 cttttaacaa aacaaataca ggaaacatcg gtcgtcgtag gactatatta ccatcatctt 3660 ttgttggtag tccccgtgac atgtatcaaa ggtatcaaga tgcaatgact ttggtgcaaa 3720 aatatggaag accagatatt ttcctaacaa tgacatgtaa tccaaattgg gaagaaataa 3780 gtgatgagct actacctggc caagcaccac aagatcgacc agatttgctt acaagggttt 3840 ttcgtgcaaa attcgaacag ttgaagaatg atgttataaa aaaaagtgtt ttaggcagag 3900 ttcttgcata tgtatatgtc attgagtttc aaaagcgcgg tctcccccat gttcacatgc 3960 ttctcatgtt agaagaaaat gataagctta atagtccaga tgattacgat cggatggtac 4020 gtgctgaaat accaattcca aatgaagagc ctgaattgta tggtgccgtg ttaaggcata 4080 tgatacatgg tccatgtgga atacacaatt cacgatcacc ctgtatgaaa cgtggtagtt 4140 gtaaacgaaa ttatcctaag ccatttgcac caactacagt tcaaggaaat gattcttatc 4200 cagtctatcg tagaagagac aatcataatc cagtcccatt agatcaaaat gcacgtataa 4260 tggtggataa tcggtgggtc attccgtata actcatggtt actcctcaga tatgattgtc 4320 atattaatgt tgagatttgt tgcagcatta agagtgttaa gtatctgtac aaatatgttt 4380 ataaaggtcc cgaccgagta gcttttgaag tccatcctga acctattcaa gatgaaataa 4440 agcagtttgt tgatgcaaga tgggtttgtg cacctgaagc tttatggaga atattcaaat 4500 ttgtaactaa tcgactttat ccatcggtgg aacgattaca aattcatctc cctgaaggac 4560 aaactgttca tttttaccct caccaaagag tgtcagatat tttggcagat gacacaaact 4620 cgatgactat gttgacagag ttttttacca agaataccac ttgcccggaa gcacgacgat 4680 acttataccg ggagttccct gaacggttca gatggagtca aagagataaa gtctggagtg 4740 agaggatgaa taaccataaa gttattggcc gaatatatgc agtttcgcca aatgagggtg 4800 aaaaattcta cttacgcatc cttcttaatc atgttagagg accaacatca tttgamgatt 4860 taagaacagt caatgacatc gtacaaccaa catttaaaaa ggcagtggaa caacgaggtt 4920 tgctagaaga tgatgatagc atcagacagt gtcttcgtga ggcctctaac attcgaatgc 4980 cgtcagcttt acgaaggttg tttgttacca tcttggttta ctgtgaaccg catggagtaa 5040 gaagattgtg ggatgaattt cattcattta tggtagaaga ttattctgtc tcaagtacca 5100 taaataatac ttctatctta aacaagcttt tgcaagactt gaatgggcta ttagtgcaac 5160 atagtaagtc tgtatctgat tacgatctac cacaaataac acaagattgt gttagagaca 5220 acacacttcc aaggataata caagatgaag tttcacttga catctctgaa gcagacctca 5280 atgcggtaca taatctaaac gaagaccaaa tggcagcgta taattcgatc gtgtctgcta 5340 ttgaacgtcg agacaatgcc atattttttg tggatggtcc cggagggacg ggaaagacat 5400 acttatattg tgctttgtta gcaacgttaa ggagcgatgg tcatattata ttggcaacgg 5460 caacatctgg aattgcagca accatattgc caggcggaag gacaacacac tctagattta 5520 aaattcccct cagtccagat gcatcttcca cgtgttctat tagtatccag tcagatttgg 5580 cagaattgat aagaaaaaca tcagctgttg tttgggatga agcaccaatg gcacacaggt 5640 ttgcatttga gacactcgat cgaacgttca aagatataat aggtgttgac ctgccatttg 5700 gaggaaaggt catgattttt ggaggagatt ttcgacaagt tcttccagtt gttccaaaag 5760 gtacaaggtc tgaattgatg caagcaagta tgattaatgc ttcattttgg ggacatgtga 5820 aaatcattcg tcttaggcac aacatgagat ccatcaatga tcaagatttt tcagagttct 5880 tacttcatgt cggtaatggg gaacaagaaa ctatgataga cgacatgatg caattaccat 5940 catctatggt cattccatgg aatggtgaag aatccattgt ccaatttgtt aatgaagttt 6000 tccctgattt ggaatgtcat gtatgtgatt caagatactt ggtggaaagg gcaattataa 6060 ctccaaaaaa tgaggatgct gacaagctta ataaaatgat catcgataaa tttccaggga 6120 ctgaacatat cttatactct ttcgattcag ttgaggacga tgtgagaaat ttgtatcaac 6180 aagagttctt gaattcaatc tcacctggtg gaatgccccc tcatcagtta actttgaaaa 6240 aaggtgcccc aataatgctt ttgagaaata tcgatccgaa gatggggttg tgcaatggta 6300 caagactggc ttgccatgga gcttacaata atctaattga tgccgaaatc ttatctggac 6360 aatttgctgg aactagagta tttttaccaa gaatctcttt aaagaccaca gaaagcgcag 6420 gactcccatt tgaaatgatg agaaaacagt ttccagtgaa attgagtttt gcactaacca 6480 taaataaatc acaagggcag acaataccaa atgtgggtat ttatctacca gatcacgtat 6540 tcagtcatgg acaattgtac gtggctttat caagaggagt atcagcgtct acaacaaaag 6600 tcttggtaaa gaaaggagaa ttacacggtc atgaaggagt cttcacaagg aatgttgtgt 6660 acaaagatat tttgcttccc tcgaattcaa cataaggtta tattctttct tttaatgttt 6720 aattcccgtt ttcaaatttt aatgcaattc aattacaaat aatgctaata tttgattcta 6780 accgaacgca ttaaattttc aacaggacgg cgatatgagt tcatgatatg aagaaccgtc 6840 aagtgtatca aggccaattg aagttcttgg attgttttta tactttttac ttagctttta 6900 gttgcaacta aattataagg atcttctatg ttatttatta cttttttttt ttttacaaat 6960 tctagataaa tactttaaat tactacctgt attattagag atgataatcg tctttatttt 7020 atgtttctat acattgaacc aatcctcgca tataaataca tctaaaatgt gtaagtcgcg 7080 cgtagcgcgc cgtgatgaaa aaagtgtctt tcgcacgcgc gtgaggacac tgtaataggc 7140 actgctgtgt gtgagagagt atccacgtca acaacttcaa atttattgct tcctgttatg 7200 tgcagccata tcatactttc taaaccatat acattgacaa ttacaatgga aaaaaactaa 7260 cacaatacac atttaggggc gcgtagcgcc cgtgatgcaa aaatgcctct cgcacgcacg 7320 ttagtgcgtg cagagaggct ag 7342 // ID Gypsy2-PTR_I repbase; DNA; EDCOT; 4607 BP. XX AC scaffold_41; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy2-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4607 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4607 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 318-318 (2007). XX DR Genome; scaffold_41; Positions 2372329 2376935. XX CC Positions [1955-2458] - Reverse transcriptase CC Positions [3524-4003] - Integrase core CC 'CCTAC' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 38..4606 FT /product="Gypsy2-PTR_I_1p" FT /translation="MPPETRSQDVRRCDGSLEAANQRIDGIEIKLNTQSDD FT LGQLKAMMKEIATQQIAIKHTLQTLTGETSSSQRPHAPQPPTTNCSQGWVG FT EGSQGSYRFHKPKRNFPTFEGEDVHKWLYKCNQYFDLEEIAEPDKLKLASY FT YLDGLALYWHQNFIRNLEGQDTTWADYVEALCCRFGGQKDPLEELTEHKQA FT GNLEDYIKEFDMLWNRAQVSEKQALVFFLGGLETEIKNLVKMFEPKSLKQA FT YNLARLHDNTLTYRKNTPHYTKLPAQTNTYQHNQRPAYPTPSSSSTSNSTF FT TTFKSPQPALLPTPNRPPFNNATVNSNPRPSRPIRTREMDERRAKGLCFWC FT DEKFVPGHRCKNRKLYSLCIIEDEEENSEEEETIETMNVEALTPHLSLHAL FT QGTTGCHTIKVWGKLDKCPIFILIDSGSTHNFLNANLASKQNCLLTPIKPM FT LVEAANGGTMSCTKLCKNLQWKMQGVQFQADVFVMPLQSYDMVLGIQWLKL FT LGNVLANYEDKWMNFWWEGNEVTLKGDNPILTQSIRLEELNGLLARKTLLA FT EVNICSLRVLEVEGTTLSYQEGYLPAQHAEEFPIQALLDTYSHIFREPVEL FT PPARGHDHRIPLKDENLTVNLRPYRYSGLQKDTLEKLVAEMLDAGIVQPSH FT SPFASPVVLVKKKDHTWRFCVDFRALNKLTVKDKYPIPIIDELLEELEGAT FT IFSKIDLRAGYHQIRMDPKDVYKTAFRTHNGHFEFLVMPFGLSNAPTTFQS FT LMNDIFRQHLRKFILVFFDDILIYSKSQTDHLYHLTVVFELLCANQLVAKK FT EKCVFDSNQMEYLGHIITKEGVATDPNKVVAMMNWPIPTNIKQLRGFLGLT FT GYYRKFVKGYGELCRPLTQLLKKGSFNWTSSATMAFNQLKAAMANPPVLAL FT PNFDKTFVVETDASGVGMGAVLMQAGHPLAFISKALGPRQLNLSAYERELL FT AIVYAVTKWKHYLRGRRFLIRTDHSSLKFLLDHKATHEAQQVWLTKLLGFD FT YDIEYRKGKDNLAADALSRISSTELSALTLSSISTNIMEEIRQTWAADPNL FT QRVIKEVRKDANSHPAYAWVNNTLLRKGKVVVGRDSQLQTKLTSFYHDSAA FT GGHSGATVTAKRLGQVFYWRKLQKLVRQYVRECSICQQNKTENVKLLGLLQ FT PLPIPIAPFIDISMDFIEGLPKSEGKEVILVVVDRFSKYAHLMALSHPYSA FT PTVAKVFMEHVYKLHGMPATIVSDRDSIFLSQFWKELFKHQGVNLHYSTAY FT HPQSDGQTEVVNKCIEGYLRCMTGNAPTLWGKWLSACEWWYNTNYHTSTKK FT TPYEILYGMVPPIHIPYTHKDSPVEAVDHYLTQREEMFKEIRSNLLQSQHR FT MTQQANKKRSERSFLVGDSVYVKLQPYRQHSVHKRVSHKLSAKYYGPYTVI FT KKIGTVAYELQLPATAAVHPVFHVSQLKKHVGHHVVHSDLPNPQHRSLLQP FT LQIIKRRMIKQSNTAVTQFLVVWKDIPLTEATWENADEFCFRFPEFHLEDK FT VVVMEGA" XX SQ Sequence 4607 BP; 1423 A; 1086 C; 996 G; 1102 T; 0 other; aagtggtatc agagcttcat ctttggatct cctcaaaatg cctccagaga ccaggtccca 60 agatgtgaga aggtgtgacg gttccttgga agctgctaac caaagaatcg atggaataga 120 aatcaaactg aacacacagt cggatgatct tggccaactc aaggctatga tgaaagaaat 180 agctactcag cagattgcga taaaacacac cctacaaact ctcactggag agactagctc 240 ctcccaaagg ccccatgctc ctcaaccgcc tacaacaaac tgcagtcaag ggtgggttgg 300 agaaggttca caagggtctt acaggtttca caagcccaag aggaattttc caacatttga 360 aggcgaagat gtgcataagt ggttgtataa atgcaatcaa tatttcgacc ttgaagagat 420 agcagagcca gacaaattga aactagcctc ctactacttg gatgggttgg cactgtattg 480 gcaccagaac ttcatcagaa acttggaagg acaggacacg acttgggcag attatgttga 540 agccctgtgc tgtcggtttg gaggacaaaa ggaccccttg gaggagttaa ccgaacacaa 600 acaagctggg aatcttgaag actatatcaa ggagtttgac atgctctgga atagagctca 660 ggtatctgaa aagcaagcct tagtattttt cttgggaggg ttagagactg agattaagaa 720 cttagtaaaa atgtttgaac ccaaatctct caaacaagca tataacctag ctaggctcca 780 tgataacaca ctcacgtata gaaaaaacac tccccattac actaaacttc cagctcaaac 840 aaatacttac caacacaacc aaaggccagc ttaccccact ccctccagca gttcaacttc 900 caactccacc ttcactacgt ttaaatctcc ccagcctgcc ttactaccta cccctaacag 960 gccaccattc aacaacgcaa ctgtcaactc caaccccaga ccctccagac ctattagaac 1020 cagggagatg gatgagcgta gagccaaggg attatgcttt tggtgtgatg aaaaatttgt 1080 accaggacat agatgcaaaa accgaaagct atactcacta tgcatcatcg aagacgaaga 1140 agaaaactct gaagaggagg aaaccattga aaccatgaat gtagaagccc ttacccctca 1200 tctatcatta catgcattgc agggcaccac ggggtgccac accatcaagg tatggggcaa 1260 actagacaaa tgccctatat tcattttgat tgactcaggc agcacccaca acttccttaa 1320 tgccaacctc gccagtaaac agaattgtct cctgacaccc atcaaaccta tgctagtaga 1380 agcagcaaat gggggtacca tgtcttgtac taagctctgc aagaacctgc agtggaaaat 1440 gcaaggcgtc cagttccagg cggatgtttt tgtaatgcct ttacaaagct atgatatggt 1500 cttaggcata cagtggttga agttactggg aaatgtatta gccaattacg aagacaaatg 1560 gatgaatttt tggtgggaag gaaatgaagt gacactaaag ggggacaatc ctatactcac 1620 ccagtccatt cgactggaag agttaaatgg actacttgca cgtaaaacac tgctggcaga 1680 ggtgaatatt tgcagtctaa gagtgctgga ggtggagggc acaacactca gctatcagga 1740 agggtacctt cctgcccagc atgcagagga gtttccaatt caggcactat tggatactta 1800 ttcccatatt ttcagagaac cagtggaact acctcctgcc agaggacatg atcataggat 1860 acctctgaag gatgaaaacc tgacagtcaa cctaaggcca tacagatact cagggttgca 1920 aaaggatacc ttggagaaac tagtggctga aatgctagac gctggaattg ttcaaccaag 1980 ccacagtccg tttgcttctc cagtagtgct agtcaagaaa aaagaccata catggcgatt 2040 ttgtgtggac tttcgcgctc tcaacaagct gactgtaaaa gataagtatc ccatccctat 2100 tattgatgaa ttattagaag aattggaagg agcaaccatt ttctctaaaa ttgacttaag 2160 ggcaggctat catcagattc gaatggaccc taaagatgtg tataaaacgg catttcgcac 2220 tcacaatggc catttcgaat tccttgtcat gccctttggg ctctctaatg ccccaacaac 2280 cttccagagt ttaatgaatg acatctttag gcaacatttg aggaagttca ttttagtttt 2340 ttttgacgat atattgatct atagcaagag ccagacagac cacttgtatc accttactgt 2400 tgtgtttgaa ctattatgtg ccaaccagct ggttgcgaag aaagagaagt gtgtatttga 2460 cagcaatcag atggagtatt tgggccacat tatcaccaaa gaaggagtgg ccaccgaccc 2520 taacaaagtg gtagcaatga tgaattggcc tattcctact aatatcaaac aattgcgggg 2580 atttttgggg ttgactggat actataggaa gtttgtgaaa gggtatgggg aactctgcag 2640 accccttact cagctgttga agaagggctc cttcaactgg actagttcgg ccactatggc 2700 cttcaatcaa ttaaaggccg ccatggctaa tccccctgtt ctggcattgc caaacttcga 2760 caagactttt gtcgtagaga cagatgcatc aggagtgggt atgggagcag ttttgatgca 2820 agcagggcat ccactcgctt ttatcagcaa agctctggga cctcgacaac taaatctatc 2880 agcatatgaa cgggagctct tggccattgt ctatgctgtc actaaatgga agcattacct 2940 aagaggaaga cgcttcctaa tcagaaccga ccactcaagt ctcaaattcc tactcgatca 3000 caaggcaact catgaggcac aacaggtttg gttaactaaa ctcttaggct ttgattatga 3060 tatagaatac aggaagggca aagacaactt ggcagcagat gctctttcca ggatctcaag 3120 cacagaattg agtgccttaa ccctatcctc aatctccacc aatatcatgg aggaaatcag 3180 acagacctgg gcagctgatc caaacttaca gagagtcatt aaggaagtga gaaaagatgc 3240 caactcgcat cctgcctatg catgggtcaa taacactctc cttcggaaag ggaaggtagt 3300 ggtgggtcga gactcacaac tacaaactaa gctcaccagc ttttaccatg actctgcagc 3360 tggaggacat tcaggagcca cggtcactgc aaagagattg gggcaggtat tctactggag 3420 aaagttacag aaattggtaa ggcaatatgt ccgcgaatgc tccatttgcc aacaaaacaa 3480 gaccgagaat gtgaagcttc taggactttt acaacctcta cccattccta ttgccccctt 3540 cattgacatc agcatggact tcattgaagg cctacccaaa tctgaaggga aggaagtcat 3600 cctggtagta gtcgatcggt ttagcaaata tgcccatctc atggctctct cccaccccta 3660 ctctgccccc actgtagcta aggtcttcat ggagcatgtc tacaaactcc atggaatgcc 3720 agccaccata gtaagcgaca gggacagcat ttttctcagt caattttgga aggaattgtt 3780 caaacaccag ggcgtcaatc tgcactactc caccgcctat catccccaat cggatggcca 3840 gacagaggtg gttaacaagt gtatcgaagg gtacctccga tgcatgacag ggaatgcccc 3900 aaccttatgg ggaaaatggt tgagtgcttg cgagtggtgg tacaacacca actaccacac 3960 ttcaacaaag aagacacctt atgagatact ctatggcatg gtaccaccaa ttcacattcc 4020 ctacactcat aaggactccc cagttgaggc tgtggatcac tacctcacac aacgcgaaga 4080 aatgttcaaa gaaatcagaa gtaatctcct acaatctcaa cacagaatga cccagcaagc 4140 caacaagaaa agaagcgaac gaagtttttt ggtgggggat tcagtgtatg tcaaactaca 4200 accttacaga caacactccg ttcacaagag agtttcccac aagctatcag ccaaatatta 4260 tggtccctat acagttatta agaaaattgg caccgtagca tatgaattac agttacctgc 4320 tacagcggcg gttcaccccg tcttccacgt ctcccagctc aagaaacacg tgggccatca 4380 tgtcgtccac tccgatcttc ccaatcctca gcatcgatcc ctgttgcagc ctctacaaat 4440 catcaagaga agaatgatta aacaaagcaa tacagcggtt actcaatttt tagtagtatg 4500 gaaggacata cctttgacag aagccacctg ggaaaatgct gatgagttct gtttccgatt 4560 tcctgagttt caccttgagg acaaggtggt ggtcatggag ggggcat 4607 // ID Gypsy22-VV_I repbase; DNA; EDCOT; 5609 BP. XX AC . XX DT 24-SEP-2007 (Rel. 12.09, Created) DT 15-SEP-2008 (Rel. 13.1, Last updated, Version 2) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW internal portion; Gypsy22-ZM; Gypsy22-VV; Gypsy22-VV_LTR; KW Gypsy22-VV_I. XX NM Gypsy22-ZM_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5609 RA Kohany O. and Jurka J.; RT "LTR retrotransposon from maize."; RL Repbase Reports 7(9), 955-955 (2007). XX DR [1] (Consensus) XX CC Positions [2008-2463] - Reverse transcriptase CC Positions [3578-4069] - Integrase core CC LTRs are 93% similar to each other. CC Originally annotated as maize sequence by mistake. XX FH Key Location/Qualifiers FT CDS 274..3417 FT /product="Gypsy30-VV_I_1p" FT /translation="MSTEGLYRYLGTLAGLVERQARATGSNGQGQSSSTRG FT SSFDDFKKLGPPYFSGTSDPTEAEAWIMKIEKFFDVIDCSEEQKASYAAFM FT LDKEADHWWRMTKRLLEDQGPIVWSQFREAFYKKYFPDSVRRQKVGEFVRL FT EQGDLTVAQYEAKFTELSRFAPQLIATEEEKALKFQDGLKPYLKNKISILK FT LSVYSEVVDRALIAEKDNEELHQYREQQRKRNRNDGAHGNQAQKRSAPSRN FT QNKGKAAQNLDGICPTCGKKHGGRPCYRETGACFGCGKQGHMVRDCPESRK FT FVFGKPKEENKEDRQKPRAQGRVFAMTHRDAQATSDVVTGTLRIHTLFARA FT LIDPGSTHSFVSVSFAGLLGMPIDNMDFDLFVATPLGDFVVVNKILRDCCV FT MIGYREMTVDLVLLDLQDFDVILGMDWLASYHASVDCFGKRVTFSIPGQPD FT FSFEGKHVDKPLRMISALRASSLLKKGCQGFLAYVVNEENDLKLEDIPIVR FT DYPDVFPEDLPGLPPEREVEFTIDLAPGTAPISKAPYRMAPMELKELKIQL FT QELLDKGFIRPSVSPWGAPVLFVKKKDGSMRLCIDYRELNKVTVRNKYPLP FT RIDDLFDQLQGACVFSKIDLRSGYHQLRVRGEDVPKTAFRTRYGHYEFLVM FT PFGLTNAPAAFMDLMNRVFKPYLDQFVVVFIDDILVYSKSREEHERHLSIV FT LQTLRDKQLYAKLKKCEFWLDKVSFLGHVVTKDGISVDPGKVDVVSNWRRP FT NTVTEIRSFLGLAGYYRRFIEGFSKIALPLTRLTQKGVKFEWSDDCECSFQ FT ELKNRLVTAPILTIPSGSGGFVVYSDASHQGLGCVLMQHGKVVAYASRQLK FT PYERNYPTHDLELAAVVFALKIWRHFLFGETCEIFTDHKSLKYLFSQKELN FT MRQRRWIELLKDYDCIIQYHPGKANVVADALSRKSVGSLAAIRGCQRQLLE FT DLRSLQVHMRVLDSGALVANFRVQPDLVGRIKALQKNDLNLVQLMEEVKKG FT SKPDFVLSDDGILRFRTRLCVPNDGDLRRELLEGAFRGSSLF" FT CDS 3449..4681 FT /product="Gypsy30-VV_I_2p" FT /translation="MYKDLRQNYWWSGMKRDIAQFVAQCLVCQQVKAEHQR FT PAGFLQPLSIPEWKWEHITMDFVTGLPRTLGGNNAIWVIVDRLTKSAHFLP FT MKVNFSMDRLASLYIKEIVRMHGVPVSIVSDRDPRFTSRFWHSLQKALGTK FT LSFSTAFHPQTDGQSERVIQVLEDLLRACALDLKGNWDDYLPLVEFAYNNS FT FQASIGMAPFEALYGRRCRSPICWDDVGEKKLLGPELVQLTVEKVSLIKER FT LKAAQSRQKSYADNRRRDLEFEVGDHVFLKVSPMKSIMRFGRKGKLSPRFV FT GPFEVLERVGTLAYKVALPPSLSKIHNVFHVSTLRKYIYDPSHVVELEPIQ FT ISEDLTYEEVPVQIVDVMDKVLRHAVVKLVKVQWSNHSIREATWELEEEMR FT EKHPQLFQDSGMSSLED" XX SQ Sequence 5609 BP; 1599 A; 794 C; 1390 G; 1821 T; 5 other; gagtggtatc agagcactag gttgtgatct tgatgggaac ttgtttagtt tacctttggg 60 aatagatgag tgacgcatta gtttaagttt caacttcatc tagtctgatt ccttttattc 120 cttacaattc tgatttgctt atttggcttc ttagtgacta atttagttat acctgttgct 180 ttataggaca ccatgccacc aaggagacct gcatcttccc aaaacagtca ggctaatgat 240 gatatacctc ctccasctga ggctttgccc cctatgagta ctgaagggct ttatagatat 300 ttagggactt tggctggctt ggttgagcgt caagctagag ctactggaag taatggtcaa 360 ggacaatcct catctactag gggtagctcc tttgacgact ttaagaagtt gggtccccct 420 tacttttctg gtacttcaga tccaacagag gcagaggctt ggattatgaa gatagagaaa 480 ttctttgatg tcattgattg ttctgaggag caaaaagcct cttatgcagc atttatgtta 540 gacaaagagg cagaccattg gtggcgcatg actaagaggc ttttggagga tcaggggcct 600 attgtttgga gtcagtttag ggaggctttt tataagaagt actttcctga cagtgttcga 660 cgacaaaagg tgggagagtt tgtccgtttg gaacaggggg atttgactgt ggcccagtat 720 gaggctaagt ttaccgaact atcacgtttt gccccacagt tgattgctac agaggaggaa 780 aaagcattaa agtttcagga tggactgaag ccttatttga agaataagat atcaattctg 840 aagcttagtg tttattcaga ggtggtagac agagccctta ttgcagagaa ggataatgaa 900 gagcttcacc agtataggga acaacaaagg aagaggaata gaaatgatgg tgctcatggt 960 aaccaagcac agaaaaggtc tgctccaagt agaaatcaga ataaaggaaa agcagcacaa 1020 aatttagatg ggatttgtcc tacttgtggc aagaagcatg ggggtaggcc atgctataga 1080 gagacaggag cttgctttgg ttgtggaaaa caaggacata tggttcggga ttgtccagag 1140 agtaggaagt ttgtatttgg gaagcctaag gaggagaata aagaggatag acagaagccc 1200 agggctcaag ggcgggtatt tgctatgact catagagatg ctcaggctac ttctgatgta 1260 gtgacaggta ctcttcgaat tcacacctta tttgctagag ccttaattga tcctggatca 1320 acacactctt ttgtttccgt atcttttgct ggtttgttgg gtatgccgat tgataacatg 1380 gactttgatt tatttgttgc tactcctttg ggagattttg ttgtggttaa taaaatactt 1440 agagattgtt gtgtgatgat tgggtataga gagatgacag ttgacttagt acttcttgac 1500 cttcaagatt ttgatgtgat tttggggatg gattggttag cttcatacca tgcatctgtt 1560 gattgttttg ggaaaagagt gacgtttagc attcctggtc agcctgattt tagttttgag 1620 gggaagcatg tggacaaacc actgcgtatg atctcagcct tgcgagctag ttctttgctc 1680 aagaaaggtt gtcaaggctt tttggcttat gttgtgaatg aggaaaatga tttaaagttg 1740 gaagacatac ccattgtaag ggactatcct gatgtctttc cagaggatct acctggcttg 1800 ccaccagaga gggaggtgga gttcaccatt gatttggcac cagggacagc tcctatctct 1860 aaggcccctt ataggatggc acctatggag cttaaggagt tgaagattca acttcaggag 1920 ttgttagata agggcttcat taggcctagt gtttcacctt ggggagctcc tgttttattt 1980 gtaaagaaga aggatggatc tatgagactc tgcattgatt atagagagtt gaataaggtg 2040 acggtgagga acaagtatcc ccttcctcgg attgatgatt tgtttgatca gcttcagggt 2100 gcttgtgtgt tctctaagat tgatcttcgg tctggttatc atcagttaag ggttagaggt 2160 gaagatgtac ccaagactgc ttttcgaact agatatgggc attatgagtt tttggttatg 2220 ccttttggtt tgactaatgc acctgctgct tttatggact taatgaatag ggtattcaag 2280 ccctatctag atcagtttgt ggtggttttt atagatgata ttttggtgta ctcaaagagt 2340 agggaggagc atgagcgcca tttgagtatt gtattacaga ctctcagaga taagcaattg 2400 tatgctaaac taaagaagtg tgagttctgg ttagacaaag tttctttcct tgggcatgtg 2460 gtgaccaagg atggcatctc agttgaccct ggaaaggtag atgttgtgtc aaattggagg 2520 agacctaata ctgtgactga gattcgaagt ttcttgggac tggctggtta ttataggcgg 2580 tttattgagg ggttctctaa gattgcccta cctctaacca ggttgactca gaaaggggtt 2640 aagtttgagt ggtctgatga ttgtgaatgt agtttccaag agttaaagaa cagattagtg 2700 acagctccta ttttgactat cccttcaggt tcaggagggt ttgtggtgta tagtgatgcc 2760 tctcatcagg gtttgggttg tgttcttatg caacatggga aagttgtagc ttatgcttct 2820 agacagttga agccttatga acgaaattat cctactcatg atttggagtt agctgcagtg 2880 gtttttgcac ttaagatctg gagacatttt ctttttggtg aaacttgtga gatattcaca 2940 gatcataaga gtttgaagta tttattttcc caaaaggagt tgaacatgag acagaggagg 3000 tggattgaac tacttaaaga ctatgactgc attattcagt atcacccagg gaaggcgaat 3060 gttgtggctg acgccttgag taggaaatct gttggttcct tagcagctat tagaggttgt 3120 cagaggcaat tattggaaga tttgaggagt ttacaagtcc atatgagagt tttggactcg 3180 ggagctcttg tggcgaactt tagagtacaa ccagacttag ttgggagaat taaggcccta 3240 caaaagaatg atttgaattt agtgcaactt atggaagagg ttaaaaaggg cagtaagcct 3300 gactttgttt tatcagatga tgggattttg aggtttagga ctagactttg tgtcccaaat 3360 gatggagact taaggagaga gcttttggag ggagctttta gaggaagctc attgttctag 3420 gcttgcgatc cacccaggag ggacaaagat gtacaaagat ttgagacaaa attattggtg 3480 gtcaggtatg aagcgagata ttgcacaatt tgtggctcag tgtttggtgt gtcaacaagt 3540 gaaagctgag catcaacgac cagcagggtt tttgcaacca ctttctattc ccgagtggaa 3600 atgggaacat attactatgg attttgtgac agggttacca aggaccttag ggggcaataa 3660 tgctatttgg gtgattgttg atcgattgac aaagtctgct cattttctgc ctatgaaagt 3720 caatttttct atggatcgtt tggcttctct ttatattaag gagattgtga gaatgcatgg 3780 tgtacctgtt tctatagtat ctgacagaga tcctcgtttc acttctagat tttggcatag 3840 tttacagaaa gcattaggta ctaagttgag ttttagtact gcttttcatc cgcaaactga 3900 tggtcaatca gagagggtaa ttcaggtctt ggaagatttg ttgagagctt gtgctttgga 3960 cctaaaaggt aattgggatg attatttgcc cttagtggag tttgcctata ataatagctt 4020 tcaagctagc attgggatgg caccttttga ggcattgtat ggtaggagat gtcgatctcc 4080 tatttgttgg gatgatgttg gagagaagaa acttttgggg cctgaacttg tgcagttgac 4140 tgttgaaaag gtctctttaa ttaaggaaag attaaaagca gcacaaagta gacagaagag 4200 ttatgctgat aatcgtagac gagatttgga gtttgaggtg ggtgatcatg ttttcttgaa 4260 agtttcacct atgaagtcta taatgagatt tggaagaaaa gggaaactca gtcctcgttt 4320 tgtgggacca tttgaggtat tagaaagagt aggcactttg gcttataaag tggccttgcc 4380 cccaagtcta tctaagattc ataatgtatt ccatgtttcg actttgagga aatatattta 4440 tgatccctct catgttgtgg agttggagcc tattcaaatt tctgaggact tgacctatga 4500 agaggtaccc gttcaaattg tggatgtgat ggataaggta ctacgacatg ctgttgtcaa 4560 gttggtaaag gtccagtgga gcaatcatag tatccgagag gccacttggg agttagaaga 4620 agagatgaga gaaaagcatc ctcaattatt tcaagactca ggtatgtcaa gtttagagga 4680 ctaaactttt gttaaggagg ggaggatgta acgcccaagc attttttttt aagggtaatt 4740 taggaaatta ttaataataa ttaaattaat taattaatta atttaataaa atggaagagg 4800 ggtaaaaatg taattttacg aataaatacc ctaggtataa attagaaatt ttattcttcc 4860 tgttcttttc tgaatagmgt tcctgttcgc agaaagttcc agagaacgta aggttggagt 4920 cagatttcag ggtttgaaga acagatctct ataggtaaga ttctaacccc tagattaata 4980 ttttagattc attagttaat ttcaaacaca ttagatatat tttttttgga aaaccccaaa 5040 tctagattag ggttagttta ttttttttta attcgtttta atatcaaaat agtgaaaatt 5100 taagattttg attttattgt tggaatttgg gagatcttaa gtttttagat gaaaaaaaaa 5160 aaaaaaaagg attccttgga agatttcgat tttagrttag ggttaattta tttttttttt 5220 aaaattaaat aaatatattg ttaattgtgg cttaagggat tagaaaaaaa aaaaaaaaaa 5280 acacgtgtgc actggttgca tgcgtgtggg aactgtgcat ccactttttg tagaattatr 5340 taaggatttc atggttgaaa tctagttggt ggattttcac atactctatt attagacttt 5400 gatggataca tgggtatgta atattaatag tagcaagact ccgtattatt agactttgat 5460 gggtaatgta ttatttaata aaaawagata tgtatggatg gtattggggt ggttaatata 5520 tatatatata tatatatcta ttattatatt agcaataatg gagaattgtt atgtatagat 5580 tatgtttggt aaaaaataaa acttgaaag 5609 // ID Copia-59_Mad-I repbase; DNA; EDCOT; 6752 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-59_Mad_; KW Copia-59_Mad-LTR; Copia-59_Mad-I. XX NM Copia-59_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6752 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1656-1656 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [3357-3887] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 1517..2494 FT /product="Copia-59_Mad-I_1p" FT /translation="MSNLNKLDFTALEVSGRNYLKWVQDVKLHLTAKNLRP FT AIEEATDKPVGEAEKATAMIFIRRHIHDALQTEYLAEEDPRALWVALADRF FT DHQKDIFLPEARHDWQHLRFQDFKSVNEYNSEVCRIRSLLKFCNETLTEED FT LLEKTYSTFSASNIVLQQQYRAQKFTKFSDLISVLLLAEKQNQLLMKNHQA FT RPTGATAVPEAHYSTNQHPKRQKRRGKGGQKPSHQGQQSQGPSKGGNKAQK FT RPNLAPKAPNFKNKGKAPATMNDDMCYRCGSKDHWSRICRAPKKVVDAYHS FT RRTKFESNFLQVDEPETTKMEVSDFQEDTTPMED" FT CDS 2748..6329 FT /product="Copia-59_Mad-I_2p" FT /translation="MTSGKVSCLADSATTHTVLRERIYFTNFVPKNAPLTT FT LSGPSNLIEGYGKARIMLSNGTILTIAEALYSPRSGRTLLSFKDIRDNNYH FT AETHVENGVEFLCVTSYEYGQKRILEKMERNPSGLYTTTIRPIECHYVAGP FT TTGTAHEITLWHDRLGHPGRIAMRRILKTSHGHPLTRSLGSIHEIACQTCS FT MGKLITKPSYDKIRSNPPIFLQRIQGDICGPIQPPCGPFRYFMVLVDASTR FT WSHVCLLSTRNAAFSKLLAQVIKLRAHHPDYPIKSIRLDNAGEFTSKTFDD FT YCMSVGVEVEHPVPHVHTQNGLAEAFIKRLQMIARSLVIRTKLPIAAWGHA FT ILHAAKLVRLRPVATQPFSALQLVTGCEPDISHLRVFGCAVYVPISPPLRT FT KMGPQRRMGIYVGYDSPSIIRYLEPLTGDLFTARFADCHFYETVFPSLGGD FT KNVNVPNERRELSWTTPTLSHLDPRTAQSEAEVQRILDLQSIAQSMPDAFT FT DLARVTRSHIPAANTPAKMDVPNVRRTTLLEARDANSGDPRTLAASQSSAP FT TQKRGRPLGSKDSHPRKRKTTAQGPEEPTVNPTIAYSFYPTHEEILDYGSV FT LEETNPPPENREISVYYASLDDVWRRNEMIVDDALAFAVATEIMLSDDIEP FT RSVDECRRRADWSNWKQAIQVELDSLAKRKVFGPVVPTPPHVKPVGYKWVF FT VRKRNEKNEIVRYKARLVAQGFSQRPGIDYDETYSPVMDVITFRYLISLVV FT SEKLDMQLMDVVTAYLYGDLDTEIYMKVPEGLTLTGSNISKPRNTLSIRLR FT RSLYGLKQSGRMWYNRLSEYLTSQGYVNNELCPCVFIKKSHSGFAIVAVYV FT DDMNLIGTPEELARTASHLKSEFEMKDLGKTRYCLGLEIEHCSDGILVHQS FT NYTQKVLRRFNEDKAKPSSTPMVVRTLDAKRDPFRPKEDDEEILEPEVPYL FT SAIGALLYLAQCTRPDISFAVNLLARYSNAPTRRHWTGVKDIFRYLKGTTD FT LGLFYPYESSSDAAPYAHRVDSRLVGYADAGYLSDPHKARSQTGYVFTVGG FT TAISWRSTKQTLVATSSNHAEILALHEATRECFWLRAVVGHIRSSCDLHPA FT VNAPTTIFEDNAACIEQLKKGYIKGDNTKHIAPKFFFTHQQQEHQKIEVTQ FT IRSQDNLADLFTKSLPKATFQKLVHGIGMRKLSEL" XX SQ Sequence 6752 BP; 1797 A; 1613 C; 1443 G; 1899 T; 0 other; cgttatcagc acgctcctac cgctgcgctt aggaatctga cgttggagat tttttttctg 60 catcaaacca gttcatccat atcatcacgc aatcaggttc tttccaaaca acggctttta 120 actcgatatt ttgcaagccc tgatagcatg aacattcacc atgatgcatg acccaacttt 180 acgtttaacg tattttagat tctacataaa ttgtgtatgc ttcataacca aaattgctac 240 aattatgtga atttgatatt tgtcatgaat tgaatcttac atatgtacat gcattgaaac 300 tattatttgc atatgcatca acgtaaatat gtgattcatt agaattatac atgcatataa 360 tataattgaa ttgaaaaaaa aaaaattttt gcgattgggg aattagggtt ctttcgaacc 420 cgtgcacttg caccatgcaa gccacaagcc accaggcccg cagcctgcga tggcccaact 480 catcccccat gctttcccga gccgagaacc aatcctggag ccacggctcc aggcccaaca 540 cccagacccg acgcccagaa ggcgtcgccg ccctgaaatc gccgaccaac atggcctgca 600 gccatgcccg gttacccccg acgacccgca gtcgtccccg acgaattttc gctgaaattt 660 cttttttttt aaattcaatc gaatttctag ggttttacaa tgaacgtcga gatttttttc 720 aaatctccgt tcacccccat ggtcaccatg actcgatcga gccttaaaca acaccccgac 780 cgacgccaga gcgccaggtc cggtgttctt ctccggcgac acacacccag caccgctggg 840 gtgtttggtc ccaaacccga gccctatggg ctcctgtccc tcggcccgcg tcggcgccct 900 ttgggcttgc tgctgctctg agatgtcgcg gcccagcccg tgcgggaaaa gaaaaaaaaa 960 aaaagaaatt tttggctcgc ctgaagcggc ccgtgagaaa aaaaaagaaa ttttttttag 1020 ggctgcacgc agcagcccat tccccttgcc cctcaccccg tgggcctgca gctcccaccc 1080 gagggttctt ggcctatatt tttaggcccc gagattttat tatttaatat ttttaaataa 1140 tatgggtttt tatattttca cccacacttt aatttggccc cgaagaccaa aaataaatta 1200 attcaattat cattatacaa tatttctgca tatattcttt gcatatttgt ttgcatatat 1260 atttgtgttt gcctgcagga atatatgaac ctgaagttca taattacttt gaaacccgaa 1320 gtttcttata aacatgcctt gtttgaaaac ccgaagtttt cacttaaaca tatcacccat 1380 gaaaacccga agtttttcat gcaaaattaa accaatacat gtctattaga acctgtatgt 1440 tctactccta tgtgaatgga ttgatttttc tccattacac taaccacatc ttgtccatct 1500 attttgtgat aggaacatgt cgaatttgaa caaactcgac ttcaccgctt tggaggtttc 1560 tggaaggaac tacctcaagt gggttcaaga tgtgaagctc cacctcactg caaagaactt 1620 gcgtcctgct attgaagaag caacagataa acctgttggc gaggctgaaa aagccactgc 1680 tatgatcttc atccgaagac atatccatga cgctctgcaa actgagtacc ttgctgagga 1740 ggatccacgt gcattatggg tcgctttggc tgatcgtttc gatcaccaaa aggacatatt 1800 cttgcctgaa gcaagacacg actggcagca cttgcgcttc caagacttta agtctgtgaa 1860 tgaatataat tctgaagttt gtcgaatccg atcacttctc aagttttgca atgaaacttt 1920 gactgaagag gatctcctgg agaagaccta ctcgaccttc tctgcttcta atattgtcct 1980 gcagcaacaa tatagagctc agaagttcac taagttctcg gatttgatct ctgttttact 2040 tcttgctgaa aagcagaacc agctgttgat gaagaatcat caagctcgac ctactggggc 2100 tactgctgtg cctgaagcac attatagcac taatcagcac ccaaaacgcc aaaagaggcg 2160 tggtaagggc ggccagaagc catcccacca aggtcaacag agccaaggcc catccaaggg 2220 aggaaacaaa gcccagaagc gcccaaacct cgctcccaag gccccgaact tcaagaataa 2280 gggcaaagca cctgccacaa tgaatgacga tatgtgctat cgttgtggtt ccaaggacca 2340 ttggtcccgt atttgccgtg ctcccaagaa ggttgtggat gcatatcatt ctcgtcgtac 2400 gaagtttgaa tcaaacttcc tgcaagtgga cgaaccggag actacaaaga tggaggtttc 2460 tgactttcag gaggatacca ctcctatgga agattagaat cttagacata gacttatttt 2520 tcagttaaaa taagacaatt ggggccgaat tccaccttgt ggccgaaccc caccttgttt 2580 tttggttgat tttgaacaat tttcctttat gttttggatt attagttggc gatttatttt 2640 ggatattaag ttttaatcct tgaataaatg aaattatttt gaattgatac ttgtttttat 2700 aaacttttat gcatgtgacc gattcaaatt aatttttcat tctaggtatg actagtggga 2760 aagttagttg tctggcagat agtgcaacca cgcatactgt tttgcgtgaa cgcatctatt 2820 tcactaactt cgtacctaag aatgcacctc tgacaaccct ctcaggccca tccaacctga 2880 tcgaaggata cggtaaggca cgtataatgt tgtccaatgg tacaatcttg accattgctg 2940 aggcactcta ttctccacgt tccggaagaa cgttactaag tttcaaggac attagagata 3000 acaattacca cgctgaaacc cacgtagaaa acggagttga atttctgtgc gtaacttcct 3060 acgaatatgg ccagaagcgt attctagaga agatggagcg taacccgagt ggtctgtata 3120 ctacgaccat acgccccata gaatgccact atgtggccgg ccctaccaca gggaccgcgc 3180 acgaaattac actttggcat gatcgtttgg gacatcctgg acgaatagcg atgcgccgta 3240 tcctcaaaac ttcacacggg catccactaa cccgaagctt aggttcgatc catgaaattg 3300 catgtcaaac atgttctatg ggaaagctta ttactaagcc ttcttatgac aagattcgtt 3360 cgaatcctcc catttttcta caacggattc agggggacat ttgtggaccg attcaacctc 3420 cctgcggacc atttagatat tttatggttt tggttgacgc ttctacacgt tggtcacacg 3480 tgtgcttgtt gtccacaagg aacgctgcat tctccaaact gttggctcag gttatcaagc 3540 tcagggctca ccaccctgat tatccgatca aatctattcg attggataat gctggagaat 3600 tcacatctaa aacttttgat gactattgca tgtcggttgg ggttgaagtt gaacatcctg 3660 taccccatgt tcacacccag aacggcctgg cagaggcttt cattaagcgt ttacaaatga 3720 ttgctcgatc gttggtcata cgtaccaagc tcccgatcgc tgcttggggc catgcaatat 3780 tgcacgcagc aaagttggtc cgcctgaggc ctgttgcgac acaaccattt agtgcccttc 3840 agttggtcac cggatgcgaa cccgacatat cgcatctgcg cgtttttggt tgtgcggtct 3900 atgtgccgat ctcgccgccc ttacgtacaa aaatggggcc tcagcgaagg atgggaatct 3960 atgtcggata tgattctcct tcgattattc gttacttaga acctttgaca ggcgatctgt 4020 ttaccgctcg tttcgcggat tgtcacttct atgagacagt cttcccgtcg ttagggggag 4080 ataagaacgt caacgttcct aatgaacgac gcgaattatc gtggacgact cccactttgt 4140 ctcatttaga tccccgcacc gctcagtctg aagctgaagt gcagcgcata ttagatctcc 4200 agagcatagc tcagagcatg ccagatgctt tcaccgatct agcgcgcgtg acaagatcac 4260 atattccagc tgcgaatacg cctgcaaaga tggatgtacc aaatgtacga cggactaccc 4320 tcctggaagc ccgggacgcc aattctggtg atccacgtac attagcggct agccaatcat 4380 ctgcccctac acaaaagcgt ggcagacccc ttggttcaaa ggattcacac ccccggaaga 4440 ggaaaaccac ggcacaaggt cctgaagagc ctaccgtgaa tccgactatc gcttactcat 4500 tttacccaac tcatgaggaa attctagatt atggaagcgt ccttgaagag acgaatcctc 4560 ctcccgagaa tcgtgagatt tcggtctatt atgctagctt agatgatgtg tggcgtagaa 4620 atgagatgat tgtcgacgat gcattagcat ttgcagtagc tactgagatc atgttgagcg 4680 atgacattga accgcgttcc gttgatgaat gtcgacgtag agctgattgg tcaaactgga 4740 aacaagcaat ccaagtcgaa cttgattcac ttgcgaaacg taaggtgttt ggacctgtag 4800 ttcctactcc tccacatgtg aagcccgttg gctacaagtg ggttttcgtt cggaagcgta 4860 atgagaagaa cgaaattgtg cgttacaaag ctcgtcttgt agcacaaggt ttctcacaac 4920 gccccgggat tgactatgac gaaacttact cacccgttat ggatgtgatt acttttcgat 4980 accttatcag tttggtagtt tccgaaaaac tggatatgca gctgatggac gtagtaaccg 5040 cgtatctcta tggggatctt gatacggaaa tttatatgaa agttcccgaa ggacttacat 5100 tgactggttc aaatatttcc aaaccccgga acacgctctc aattcggctg aggcgttcac 5160 tatacggttt gaaacaatcc ggaagaatgt ggtataaccg tttaagtgag tatttgacta 5220 gtcagggata tgtgaataac gaactatgcc cttgtgtgtt cattaagaag tcacattccg 5280 gatttgcgat tgttgcagta tatgtcgatg acatgaatct catcggaact cctgaagagc 5340 tcgcgagaac tgcttcgcac ctgaagtcgg aatttgagat gaaagatcta ggtaagactc 5400 gatactgtct cggtctcgag atagagcatt gttcggatgg aatcctagta catcaatcga 5460 actacaccca gaaggtgttg cgccgtttta atgaggataa agcgaagcct tcgagtactc 5520 ctatggtcgt tcgtacgcta gatgcaaagc gagatccctt ccgtccgaag gaggatgatg 5580 aagagatttt ggagcctgaa gttccttatc taagtgcgat aggcgcttta ttgtacttag 5640 ctcaatgcac tagacccgac atctccttcg ctgttaatct tttggcaaga tacagcaatg 5700 caccaacacg cagacattgg actggcgtga aagacatctt ccgttacctt aagggtacta 5760 cggatttggg cttattctat ccctacgaat cctcgagtga tgccgcaccc tatgctcatc 5820 gggttgattc tcgccttgtt ggttatgccg acgctggata cttatctgat ccgcacaagg 5880 cgcgttctca aacgggttat gtctttaccg ttggaggcac cgcaatatct tggaggtcaa 5940 ctaaacagac cttagttgcc acttcgtcta accatgctga aattctcgcc ttacatgaag 6000 caactcggga atgcttttgg ttgagagcag tagtgggcca tattcgaagc tcctgtgatc 6060 ttcatcccgc cgttaatgcc ccgacgacga tttttgaaga caacgcagct tgcatcgaac 6120 agctcaagaa gggttacatc aaaggagaca acaccaagca tattgcgccg aagttcttct 6180 ttacacatca acaacaagag catcagaaga ttgaagtcac gcaaatccga tcacaagaca 6240 atctggccga cctcttcacc aaatcactac cgaaggcgac gtttcagaag cttgttcatg 6300 gaattggtat gcgtaaactt tctgagttgt aactttgcta tttctctttg gaattatgtc 6360 aaactcaggg ggagtatctt ctggatactt gcttgatctt aatgtactct ttttccctac 6420 gattaggagc atttttccca ctgggttttt gctacctaac taggttttaa cgaggcaccc 6480 accttgggct ggtcatatcc ctgatgacgt cctgtagacg tttcttttga ctttgcattt 6540 ctcacgcatt tttccttaga ctatggattt tgtccctact tgggtttttg ccatagcctt 6600 agggtttttt agtgagactt actacttatg caagttccta ccttattgag aataagcgtt 6660 gttccttgga atcaatgccg acgagtcgac ttcctcaact tctgcatgat gctgaatcta 6720 ccttgagtat ttacccactc aagggggagt gt 6752 // ID Copia21-PTR_I repbase; DNA; EDCOT; 4955 BP. XX AC LG_X; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia21-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4955 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4955 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 216-216 (2007). XX DR Genome; LG_X; Positions 16196645 16201599. XX CC Positions [2234-2731] - Integrase core CC 'AATA' target site duplication CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS 491..4948 FT /product="Copia21-PTR_I_1p" FT /translation="MTELTSDPANSPPSPPPPRQPPRPHPSHPALAVSNIN FT TFIKVTLDIEKGQYITWSELFKIHARAYQVLDHIIPPSAAEMKQDTSLQDT FT DPDLWSRVDAIVLQWIYGTISEDLLNTILERDSTAALAWNRLRDIFSDNKN FT SRALYLEQEFSKVQMEHFADASSYCQHLKSLSDQLSNVGSPVTNERLVLQL FT VSGLTDAYASVGSQMRHGDSLPPFYKARSMLVLEETARMKKAAQTSSNSAF FT FVSPVAHSSGHTAGNPFHHRSNHTSNRSSSTRNSRGGGSGARSSKGRGRGG FT GRGGQLHQQQYTTPWQPMSSQQQQWSFPPWAGPWQPWATPSCPYPTANHLS FT HQPSSQRQTGLLGPRPQQAHMTASTQQAPSSYAPTDIQAAMHTLSITPPAN FT QWYMDTGATSHMTANGGNLTSYFNMSNNHNITVGSGHTIPIIGCGNALLPN FT PNPSFSLNNVLHAPKLIKNLVSVRKFTIDNDASVEFDPFGFSVKDFQTGMP FT LLRCNSTGDLYPVTTTPPIGISPPSTFTVLSPELWHSRLGHPGAPVLSSLR FT KNNLIVCNEFQDNFVCHSCPLGKQVKLPFYDSLSYTSLPFDIVHSDIWSSP FT TLSSGGHRYYVLFLDDFTNFLWTSPIATKSQVHSIFLSFRTHVKAQFEREI FT KCFQCDNGGEYDNGPFHKFCQLNGMTFRFSCPHTSPQNGKAERKIRTINNI FT IRTLLAHASLPSSFWHHALQMATYLLNILPNKKLAFQPPTKILYQKDPSYS FT HLRVFGCLCYPLLPSTSRNKLQARSTPCVFLGYPSNHRGYKCYELSSRKIL FT ISRHVTFDEYTFPFSKLHAPPSPTYDFLDAGITPLFHSPNQPNPFEAQVYP FT TPLVDPPAQPTPPLQAQQTPLITPILTSPVRDLSPHQSASPNRTLPSPSNS FT SPRPISPSPTDQLNSHSSPPPMDTTQAIPLDRPPHSPQMTTRSQHGIFKPR FT KLLNLHTSSDNSISPLPTNPLNAFHDHNWKMAMKDEYDALIENKTWDLVPR FT PVNTNIIRSLWIFRHKKKSDGSFERYKARLVGDGAGQQTGIDCGETFSPVV FT KPATIRTVLSIALSKSWCLHQLDVKNAFLHGNLEETVYMHQPPGFRSSEHP FT DYVCLLKKSLYGLKQAPRAWYQRFTDYVTTLGFSHSFSDHSLFIYRQGNDM FT AYILLYVDDIILTASSAALRQSIMSKLDSEFAMKDLGPLSYFLGISVTRHS FT GGLFLSQKKYAKEIIERAGMSSSNPSPTPVDTKAKLSISSGNPYHDPTEYR FT SLAGALQYLTFTRPDISYAVQQICLFMHDPRTQHMSALKRIIRYIKGTIEF FT GLHLYLSSVHKLISYTDADWGGCPDTRRSTSGYCVYLGDNLISWSAKRQPT FT LSRSSAEAEYRGVANVVSESCWIRNLLLELHCPIPKATLVYCDNVSAVYLS FT GNPVQHQRTKHIEMDIHFVREKVARGQVRVLHVPSRYQIADIFTKGLPLQL FT FDDFRNSLNIRSPPVSTTGVY" XX SQ Sequence 4955 BP; 1245 A; 1378 C; 852 G; 1480 T; 0 other; accctaaatc catctccttc acaccaagcc gccgccaagg aactttgttc tctgtaaata 60 aatcttctct acacacacct ccccggtggc cttcattttt cagacccatc tagttccacc 120 tttccctttc ccttccttct cccttggctc aaaagagctg ctaaccgatt cccccatcct 180 ctctgctgtt cccccactct ttgacatcga accagtgcag ccttccttcc ctccctctca 240 gctgctcctt tttccagccg ccagctcaca atgaaccgtt tccatgcaag accagccacc 300 cgcacacttc atttctgaag ctgacagacc cagccttcgt catttctatc tccttccccc 360 ttcgtcattt ttttttttcc ttcttctggc cagttaagag ctgagctccc ttctcccccg 420 cagctttccc tcttcttctc cttcggtccc agcatctagg ctgcctcaaa actgcctccc 480 cacaaacacc atgacagagc tcacatccga cccagcaaac tccccccctt ctcctcctcc 540 tcctagacaa cctcccagac ctcatccctc tcatcctgct cttgcagtat ccaacatcaa 600 caccttcatc aaagtcacct tagacattga aaagggtcaa tacattacgt ggtcggagct 660 atttaaaatc catgctaggg cttatcaagt tcttgatcat atcattcctc cctcagcagc 720 agagatgaag caggacacat ctcttcaaga cacggaccct gacctctggt cccgtgttga 780 tgccattgtt ctacaatgga tttacggcac tatctctgaa gatcttctca acaccatcct 840 tgaacgtgac tccaccgctg cacttgcatg gaacagattg agggacattt tctcggacaa 900 taaaaactct agggctcttt atctagaaca agaattttca aaagttcaaa tggagcattt 960 tgcagatgcc tcatcctact gtcaacatct taagtccctc tcggatcagc tgtcaaatgt 1020 tggatctccc gtaacaaatg aaaggttggt tcttcaactt gtttcgggtt taactgatgc 1080 ctatgctagt gttggttccc agatgcgtca tggtgattct cttcctccct tttacaaagc 1140 acgatctatg ctggttttgg aggagaccgc aaggatgaaa aaggctgccc agacctcttc 1200 caactctgcc ttctttgtct ctccagtcgc ccattccagt ggccatacgg ctggaaatcc 1260 attccaccac cgctccaatc acacttccaa ccgaagctcc tccacccgta atagcagagg 1320 aggtggcagt ggtgcccgta gtagcaaagg cagaggaagg ggtggtggcc gtggaggcca 1380 gttgcaccag caacagtaca ctacaccctg gcagccaatg tcctcacagc agcagcaatg 1440 gtcttttcct ccttgggctg ggccgtggca accttgggct acaccctcat gcccataccc 1500 aacagcaaac cacttgtctc accagcctag ctctcaacgt cagacaggcc ttctcgggcc 1560 aaggccacag caggcccaca tgacagcctc tacacagcag gccccatcat cttatgctcc 1620 aaccgacatt caagcagcta tgcatacact ctcaattact cctcctgcca atcaatggta 1680 catggacacc ggagccacat ctcatatgac cgcaaacgga ggtaatctta cgtcttattt 1740 caatatgagc aacaatcata atattactgt tggtagtggt catactattc caattattgg 1800 ttgtggaaac gcattactac ctaaccccaa cccctctttc tctttgaata atgtcttgca 1860 tgccccaaaa ttgattaaaa atcttgtctc tgtgagaaaa tttaccattg ataatgatgc 1920 ttctgttgaa tttgatcctt tcggtttttc tgtgaaggat tttcaaacgg ggatgccttt 1980 actgagatgt aacagcacag gtgacctata tccagttacc acaacaccac ccattggaat 2040 ctcaccacca tcaactttta ccgttttgtc tcctgaatta tggcatagtc gtttaggaca 2100 cccaggagct cctgttttaa gctctcttcg taaaaacaat ttaattgttt gcaatgaatt 2160 ccaagataat tttgtttgtc attcatgtcc tcttgggaag caagttaaat taccttttta 2220 tgactctctc tcatatacct ctttgccttt tgatattgtg catagtgata tttggtcatc 2280 ccccactctt agctcgggtg gtcatcgcta ttatgttttg tttcttgatg atttcacgaa 2340 ttttctatgg acctctccaa ttgccactaa atctcaagtg cactccattt ttctatcatt 2400 tcgtactcat gttaaggcac aatttgaaag ggaaatcaaa tgtttccaat gtgacaatgg 2460 cggggagtat gataatggac catttcacaa attttgtcaa ttaaatggaa tgacctttcg 2520 attctcttgc cctcatacat ctcctcaaaa tggaaaagcc gagagaaaaa ttcgtaccat 2580 caataatatc atccgcactc tcctcgctca tgcctctctc ccatcctcct tttggcatca 2640 tgcacttcaa atggccacct atcttcttaa catactcccc aacaaaaagc ttgctttcca 2700 accacccaca aaaattctct atcaaaaaga cccgtcctac tctcaccttc gagtttttgg 2760 gtgtttatgc tatcctcttc ttccatctac ctctagaaat aaattgcaag ctcggtcaac 2820 accatgtgtt tttttagggt atccatctaa tcatagaggt tataagtgtt atgagttatc 2880 gagtcgtaaa atacttattt cacggcatgt gacttttgat gaatatacat tccccttttc 2940 taaattacat gctcctccat ctcctactta tgattttttg gatgcaggaa ttacacctct 3000 ctttcactca cctaatcaac caaatccatt tgaagcccaa gtctatccca ccccactcgt 3060 tgatccacca gcccaaccta cacctcctct acaggcccaa caaacaccac tcatcacccc 3120 aattcttact tctccagtta gggacctctc cccgcaccaa tccgcttccc ctaaccggac 3180 gctgcccagc ccatccaact cctcaccacg gcccatatct ccttctccca ccgatcaact 3240 aaattcacac agttcacctc ctccaatgga cacaacccaa gccattccac ttgaccgtcc 3300 acctcactct ccacaaatga caacacgatc ccaacatggt atttttaagc cccgcaaatt 3360 acttaacctt catacctcat ctgataactc catttctcca ttgcccacaa atccccttaa 3420 tgcattccat gatcataatt ggaaaatggc catgaaagac gaatatgatg ctcttattga 3480 aaataagacg tgggacttgg taccccgtcc agttaatact aatatcattc gaagtttgtg 3540 gattttcagg cataagaaga aatctgatgg ttcctttgag cggtataaag cccgtcttgt 3600 tggtgatggt gcaggtcagc aaacgggtat tgattgtggt gagaccttta gtccggtggt 3660 caaaccggcc actattcgaa cggtactcag tattgcttta tctaaatcct ggtgtcttca 3720 tcaattggat gtaaagaatg cttttttgca tgggaatctc gaggaaacag tttatatgca 3780 tcaacctcct ggcttccgaa gttcagaaca cccagattat gtttgcttgc ttaagaagtc 3840 cctttatggg cttaagcaag cccctcgtgc ttggtaccaa cgttttacgg attatgtgac 3900 tacattgggt ttctctcaca gtttttcaga tcattcttta ttcatttatc gtcagggcaa 3960 cgatatggca tatattcttc tttacgtgga tgacattatt cttactgcat cttcagctgc 4020 tcttcgccaa tccatcatgt ctaagcttga ttctgagttt gctatgaaag atttgggtcc 4080 cctaagttat tttttgggca tctctgttac cagacattca ggaggtctct ttctttccca 4140 aaagaaatat gccaaggaaa tcattgagcg ggccggtatg tcttcttcta acccatctcc 4200 tacaccggtg gacacgaaag ccaaactcag tatctcttca ggaaatcctt atcatgatcc 4260 aactgaatat cgtagtcttg ctggcgcctt acagtacctg acatttacaa gaccggatat 4320 ttcttatgct gttcagcaaa tttgtttgtt tatgcatgac cccagaactc aacacatgtc 4380 tgctttgaag cgtatcattc gctacattaa gggcactatc gaattcggtc tccaccttta 4440 tctctcttca gttcataaac tcatttccta caccgacgcc gactggggtg gctgtccaga 4500 cactagacgg tcgacttcag gttattgtgt ctatcttggg gacaacttaa tctcttggtc 4560 tgcaaaaaga cagccgacct tgtccaggtc tagcgctgag gctgagtatc gtggggtagc 4620 taatgtagtg tctgaatctt gttggattcg aaacttactc ttggagctac attgtcctat 4680 tccgaaagcc actttagtat attgtgataa tgtcagtgcg gtgtatttgt ccggtaaccc 4740 tgttcaacat caacgcacta agcatattga gatggatata cattttgtaa gagagaaagt 4800 cgctcgtggt caagttcgag ttctccacgt cccttcacgt tatcagattg ctgacatctt 4860 cactaaggga cttccgctgc aactatttga tgattttaga aatagtctca acattcgatc 4920 acctccagtt tcgactacgg gggtgtatta gaata 4955 // ID Gypsy-30_Mad-I repbase; DNA; EDCOT; 2405 BP. XX AC . XX DT 08-OCT-2010 (Rel. 15.1, Created) DT 08-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-30_Mad-I. XX NM Gypsy-30_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2405 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1754-1754 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 2405 BP; 671 A; 540 C; 512 G; 675 T; 7 other; tttgrygccg tctgtgggaa acgacacgaa aagctatgtc ggttatcttt cattttttca 60 tctcactatt gtgaaacctc accacaatag ccactgtgaa tctgcaaaaa cccaaaccca 120 aagcacaaac aactccgcca aaaagtccat gttgttgtcc tcggctgcag ctgcagcctg 180 ggaagaccca gctgcggcat tagccaatgc tcgccatgag tttggtgagc acggtggtgt 240 caacatgtcg attgaggcct ccgccacgtt caccgtgatg gagcccgaga ctcttcgcaa 300 aatgttcttc gacgagctgg gtgccgaccg cgacttcttc atttacagcc gccactttaa 360 ccctaccgtg ctcaatctca gtccccagat ggcagtcctc gagggcatag aggccgccta 420 ctgcacgtcc tcagggatgt caaccatatc cttcgtcctg ctccagcttg acagcagcgg 480 ggaacacatc gtagcctcaa aaaccgttta cggagggacc cacgccgtca tgtcccactt 540 cttccccagg gcatgcaaca taacgacgac gtttgtggac atcaacgaca tgaacataat 600 gaggaatact attgaggtcg agaagaccaa ggtactctat ttcgaaggca tgtcgaaccc 660 aactctcacc gtcgccaaca taccggagct cagccgtatc ggccacgaaa agggggtcac 720 ggttgtggtg gacaacacgt tttctctcat ggttctctct ccggtgaaac ttggtgctga 780 tgttattgtt gacagcattt ccaagtttat tagcggcggt gctgatatta ttgcaggtgt 840 tgtgtgcaga cctacaagcc tggtgaactc aatgatggat ctacaccaag gctccctgat 900 gctcctgggt cccacaatga atgccaaggt ggcatttgag ctctttgaga ggattcccac 960 ctagggttga gaatgaagga gcactaccac agggcaatgg tttatgccca aaggatgaag 1020 aagatgggcg aaaacaaata tgaaactttg tattttgata tgaatacggg agctaagatc 1080 ccatatgttg gtcttagaac atggaaggmt gaaccaagtg tggtcggtca agctgtcatc 1140 gctgaagtca agaatggcta casgcatatt gactgtgcat cagtacaaca tggcgtcacg 1200 gcaatgatgc ttggatctgc agtggtcctc ttcccaacct gattgggttg caacgaagaa 1260 gataagtttt ttattattaa ttattttatt attgtttgcc atctgccaaa agaaagaaaa 1320 ataaagagaa aggaaaaagt aaaactctca agtaggcgta gtgcgcacca acaatctgca 1380 actgttgacc accaacgtgg aaaaacataa acactttaac tttgggttga tttgtttaaa 1440 attatcattt gtttatttaa tagtttatta ttattttgtg ttggttgatg ctttacaata 1500 tgcataatga ggccacatca tttctatcac acctatatag tacgttccca gtttgatttg 1560 ctttacaatg ggcatatgct ttacaaacgc tagtctgcaa tcttccttac aattatttta 1620 ttaattaata ttttattatt gcatctttaa tcattcatga cttcattatt taaagtggta 1680 ggataaaact ttattataca atatttattg acctagagta ttgtgattgt cattaaacta 1740 tgtcacttat acaacatgtg atttaccaca cgatcgaata aattatttat ttacagaagg 1800 cacatggtac aatattttgc cttgacaaac tttgtcaatt tgatttattc attatacggt 1860 catgcttata ctgtcattta ttgtcaggaa ttattgagca atcagatcca ttgatcaaca 1920 ctgttgctga ttaaagaagt ctaccaactt atagactgat gggccacatg cttatggtga 1980 caaatattta gttcgaatag tgatctcttg tctaacccaa caagtggatc cgagtcatgt 2040 cgagaattaa ctcatactga gtgcatgtcg acataaagta aatacttgca atgaggaata 2100 ccacgagccg agccgcctca tagcgagcat agcctctagc cgagcagcct cgcaacgagc 2160 atcgcctcta atcgagcaac cgccttgccg cgagcatagc ctctagccga gcagcctcgc 2220 aatgagcatc gcctccaacc gagcaatctc gtaacgtgtg atacatctag ctgaatattg 2280 ttttatgttg agcattgcct tgggttgagt actggttcaa gacatctagc cacttcggcc 2340 tgkacatgga ttggattgaa gtctccagcc aaaakactct tttgactgaa gasttggggg 2400 actcc 2405 // ID COP12_LTR_MT repbase; DNA; EDCOT; 351 BP. XX AC . XX DT 02-JAN-2007 (Rel. 12.01, Created) DT 06-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of COP12_MT LTR retroposon from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; COP12_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-351 RA Shankar R. and Jurka J.; RT "COP12_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 8-8 (2007). XX DR [1] (Consensus) XX CC The LTR sequence flanks a well conserved internal region on both CC sides. XX SQ Sequence 351 BP; 96 A; 49 C; 57 G; 149 T; 0 other; tgttgactaa ttgacctata aaacttttct gaatacttta ttgtttatgt tactttattg 60 cttatgtgtg taattatttt aacttgtttt gttagtaaaa ctatgctgca caagtaagat 120 tatctgcaca agttaagtag gtttatgtca tatatatgac atcagctaag cataggctga 180 gtcattactt agtatttggc tataagtatg taagaaggat gtatggatgg tatgtatcaa 240 atttgcagca tagtaaacat tgttattgtc cctttctctt ccattttttt ctctaatttc 300 tgttttctgt ttttgagctt attgcttctg ctgccattac aaaagctaac a 351 // ID Copia30-PTR_LTR repbase; DNA; EDCOT; 249 BP. XX AC scaffold_225; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia30-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-249 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-249 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 237-237 (2007). XX DR Genome; scaffold_225; Positions 13463 13711. XX SQ Sequence 249 BP; 96 A; 38 C; 39 G; 76 T; 0 other; tgaatagcat aacaaactca acaaaatcag gaacagaatc aagcatggga gaaagatcag 60 aggaagatca gaagaagatg aataaagata atctgttata gtttaaaatt caaatacctg 120 cacttatctt attttcaaga ctgtacgcat atatatatat atgtacactg taaaacattg 180 tgtatgcaga gaatataatt ttcttcatct tctgtcagct ctcatttgct gtaatcttac 240 atggtatca 249 // ID BoSB3 repbase; DNA; EDCOT; 296 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 13-JUN-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB3. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-296 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 296 BP; 58 A; 76 C; 85 G; 77 T; 0 other; aaccaagtgg tggtagccta gtggcaatct cttggggctt ggtgtgtacc cacatcagtc 60 atgggttcga ttccccctgg gaactaaatt atcactactt ggccagtctg ggcttgggct 120 tcggcccaag tggtttacat ggtggaccat aacagatgat tggtccaccc cctggcatta 180 gtcggaaggt attccaaact cgggtcaggc agtgtggtac gctttcgggc tagtccactc 240 tgtagcacta agtgcgttcc tcccggggcc gaccggatca gccgataggg tttatc 296 // ID TE-3_Mad repbase; DNA; EDCOT; 1535 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative transposons from the apple genome. XX KW Transposable Element; Nonautonomous; TE-3_Mad. XX NM TE-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1535 RA Kojima K.K. and Jurka J.; RT "Putative transposons from the apple genome."; RL Repbase Reports 10(10), 1828-1828 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >94% identical to the consensus. TSDs are likely 3-bp. XX SQ Sequence 1535 BP; 443 A; 241 C; 282 G; 569 T; 0 other; atattggtga aaacaatgtc ctttgacttt aattccagat ttccactgta atttttcgat 60 attgtggtct aggtttgaca tatttgtttt tcctttctat aacacttgca ggttgtctat 120 ggctcagtgg aattctgggc tagatagctt acaactggta tcagcacggc atggagacca 180 atgtgaggat cattcacacc aggtaatttt gatatttgag gattaacttg attagtagat 240 gtctatatct tcttgtttac actgataaag attataaaca atgatgaatt aggatgcttt 300 agtatagttt atttatgttt ccaggtgcat atgcttatgt tctagagtta taacctactt 360 agctaggtga ttggtattgt tatgtttata taaattatag acctttcaag gatttatatg 420 atctacttat catgctgcct tgtttacaga gtgtgagaat catgttgcct tgctgtttat 480 aatgtttatc ttgttgttta cagtgatgaa tgacatataa gtagttgatg ctaacttgat 540 tattacctgg tatctattaa acatgtaatt ttgctaggtt gtgatgctgc atggcgttgg 600 taagttaact tgattagtag atatctttat cttgttgttt acacatttat ggtttcataa 660 gttatttgtt tagaaatacc actctagtgt ggccttgcgt ttccttaatg tcaatgatat 720 ttagcaccct taacgtttgc taatcaagtt ttttaatttg tttttcttct acagttgttt 780 gatactggaa tgtttcatga tgatcctcac cgtttcccga tttcatgatg ctgcatatca 840 acgtgatgag gactatagtg agaatggtga tacttaagga tattttatct atattatagt 900 aatgtcgaaa tgaaaacata gatatttttg tattttgtaa ctaaaccgaa ttgtgaacct 960 tacattagtt tatattacat gaattttgtg ttgttcctac attaattctt cattcacgcc 1020 ccttctcgat ctcttaagct tgcttgtttg tgatggttaa aaatattatt aaataaaaat 1080 tagaaaatat tggacttgac atgttttgtc ggcacaaaat taattagccg acaaatgttt 1140 ttgttcacaa aagattcaac cgactaatta ttttgtctac acaagtaatt tgagccgaca 1200 aaccaatttg ttgtcatagg actacgtagc cgaaaaacca ttttgtcacg acaagattac 1260 ttagccgcca aaatgttttg tcgcgacaag attactcagc cgacaaaatg ttttgtcgcg 1320 acaagatcac taagccgaca aataacttca tcgcgaaaaa acaacctatg ccgacaaaat 1380 attttgtcgc aatgttgttt tggtgacggg cacagtttga cggctgagat ttgtcgcctt 1440 aaaaatgagc cgacgaaata tcaagattcg tcgagaaaga tcttgcgcga catgctttta 1500 gcgacaaaat tgccgacaaa atttttcgtt gggaa 1535 // ID RAS2_MT repbase; DNA; EDCOT; 409 BP. XX AC . XX DT 29-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE Putative non-autonomous DNA transposon from Medicago truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW non-autonomous; Inverted repeats; Interspersed element; RAS2_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-409 RA Shankar R. and Jurka J.; RT "RAS2_MT: A putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 597-597 (2006). XX DR [1] (Consensus) XX CC The sequence is present in Medicago genome in high copy number CC with high level of sequence conservation. Flanked on the both CC sides by 3bp TSDs (TAA). XX SQ Sequence 409 BP; 160 A; 50 C; 46 G; 153 T; 0 other; ggcaaattct atggtacacc caacaatttg agtgtattgg tacaccaaat ccttaaatta 60 atagttaaat gagttatttt ttgtaggaaa aaattatttt ctatcaccta taattataat 120 aactaaatct tatttaccaa aaacgtcaac gcaataaaat ttgatttttc tgaattctta 180 ttactcataa tagagaattt tgattatttt ttacaataaa atgtaaaaaa aatttagtat 240 gatttttata aaaaatgaaa tgatgttttt ttcttataaa atgatatttt ctaaaatata 300 tatgtcaaca aacacctatt ttcttcataa aaaatgatag ttaatttata aaaattgtaa 360 gcgagagtac cggtacaccg taatttacgg gtgtaccata gaagttccc 409 // ID GYPSOL2_LTR repbase; DNA; EDCOT; 1580 BP. XX AC . XX DT 17-OCT-2006 (Rel. 11.1, Created) DT 17-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE Gypsy-type LTR from potato. XX KW Gypsy; LTR Retrotransposon; Transposable Element; GYPSOL2_LTR. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-1580 RA Jurka J. and Shankar R.; RT "GYPSOL2_LTR: Long terminal repeat from potato gypsy-like RT sequence - consensus."; RL Repbase Reports 6(10), 490-490 (2006). XX DR [1] (Consensus) XX CC This LTR matches a diverse group of LTRs. No intact internal CC portion was identified to date. XX SQ Sequence 1580 BP; 463 A; 257 C; 345 G; 513 T; 2 other; tgttgatata ccgtggtttc acggtattat taatactttt tccttaagtt tagtgtgtgy 60 caaaagccct ttttgtacta atttttatat aagtttctct ttgttttgca ggaaatctgt 120 ccaaagctga atgcggagat tttgagcgaa aaatgcagaa gagaccacct acggagctta 180 tgacggtccg tcgtgcttgt gacggtccgt aggtggcagc gtagtgaagc tgctgaagga 240 agatggggaa gtctgaccaa gtgtgggatt acgaagcttg tgacggtccg tcatggctat 300 gacggtccgt cctgcaggtt catcgtgaag atcagagaag tagtcctagt acccagatty 360 caagatttta agtattttgg aacgaagacc ctcgacggac cgttgtgctt atgacggtcc 420 gtcatacttg ccgtcgaggg taactgaaga aagcagcaga agaaattgca ccaagtatgg 480 gacgacggag tccacgacgg tccgtcgtga ccacgacggt ccgtcgcgtg gtccgtcgac 540 ccagccgcgt tttggcagat ttccagtaat tagagtcctt gtttaattag gtttttattt 600 ttttataaat agttcgaaaa acctcgtttt tgaggttaga ctctatgata ttaaacatta 660 tattgttaga cttgtgtttg gagtgtttga ttgttagatt tttgattcat tgcaagtgat 720 ttttggtgat ttgaatcaag caaatttttg gattttattc tttctcattg aagtaagtac 780 atgaattctt atttaatata tttgaatatt gtgattatga ctatgggtaa ctaaactcca 840 taactagggt tgtgggaacc atgggcaaat aatgagataa aacctaacta aaataacaat 900 tctagaatag tgtcttgcat gtattaataa ttctttcgct tagaagtctt tttaacggat 960 ggccaacgtt agaactcgcc ttattgctac ttgccggacc aaggaggtag ataataggaa 1020 aagaattatc aacatagatt tagtgtgata ctatctaata ggctagtgtt gattggtacg 1080 aggtaataac ttagtcaaat atcgaatatg atgcttaata tgaggtaaag ataagggtta 1140 gtaaagcata cacacgtagc cggaccaagg tgcggagtga aattttctag atgccggacc 1200 aaggatttag agatacataa cttatcactt tgcatgcaag atactaggaa agaattgtta 1260 tagctagaat tatcaagtta tgaacctgtg gggaacacgt aaaccctagt tactttcatt 1320 acttgattaa aatccaacat ttaaagctgt taagtgtttc tttcaagtta gttagttatt 1380 tttactcatt aagaaataca aacccccctt ttatgatttt actttccaag gaagtcattg 1440 actaaacaaa agtaataata ggttgaagtt aagtctaaac tattttcctc gtgggaacga 1500 tcccaacctc actagttggg ttctttactt gatacgaccg cttatacttc ttatttgaga 1560 agtatagttt gagcgtatca 1580 // ID hAT-N2_Mad repbase; DNA; EDCOT; 973 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW hAT-N2_Mad. XX NM hAT-N2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-973 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1637-1637 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >87% identical to the consensus. TSD is 8-bp long. XX SQ Sequence 973 BP; 279 A; 166 C; 255 G; 273 T; 0 other; cagtgttcta aaaatcggcc taggcggccg tctaggcggc gcctaggcgc tgggcggtgg 60 agctccgacc cgatttagac caaaacgttc agttaggcgg ggaggatata ggcggccgcc 120 tatgcgctcg ctaggcgcct gaggcgggct aggcggcgct aggcggtagt ctaggcggtt 180 tgaatctagc tgcaaattcc aaacttgctg caattttcgc aaaggatcta caacttccga 240 tctcgtacgt agcagcagag acccggaaaa ttttatgtag ctcgtctctg tgaagatgag 300 ggaagagaga gtgcgaagag agagagagag agagtgagac tgcccgtgaa gataatttca 360 taatttctgc agctcatctg tgaagatgag agcagagaag agagtgcgaa gagagagtgc 420 gaaaagagag agagagagag agactaacat ttctgtgttg gtggtgcaag ttgaggacta 480 aaagcctggg tgatgtgaaa gagcatggac ggtttgtgat tttaaaattg aaaaccatgg 540 actttgatgg ttttgtggat gggtgacgtg aaaaccacct tgggtggacg ggtgatggat 600 gggtgatgga cggtttgatg gtttaacaat gaaaaccacc cactatgtgg gttttttata 660 tttttaaaag tttgggatat atattatgtg tgtatatata tatcttatat aaattataaa 720 ttatttagat aatattttgt ttttttttcc taggcaagca tttcatatat gtacataaaa 780 cattcacata tgtatgttct tctataagaa atagcatatt agtcaataat tatttacatt 840 ttatatagta aatttaatta attcatataa tatatcagaa atttacctaa atccgcctag 900 accccgccta gccgcctagg cgctaggcgc tagcccaccg cccgactagc gcctagcgtt 960 ttttagaacc ttg 973 // ID Gypsy11-VV_LTR repbase; DNA; EDCOT; 1441 BP. XX AC AM477421; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy11-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1441 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-1441 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 727-727 (2007). XX DR Genbank; AM477421; Positions 1610 3050. XX SQ Sequence 1441 BP; 430 A; 270 C; 239 G; 502 T; 0 other; tgattactac ccaaaaagtg ctattttaca cctttaatgc attatgtttt aagcactttt 60 gtgtagtagt tctccatctt tagtccaatt ggcatgttaa ggacctatca atgtcttcta 120 atcatatttg tagctagttt taatgttttg acagcttttt ggatcattaa gacaagtcaa 180 gcaaaggaga gaagcaaagt gaaaaaatca gaggacagca gctgcagtcc tctttcgcac 240 ttttggagca cttcccgaag tccatttttt acatactata taccatttca aatatctgga 300 agtcaagaat ccaacgcttc aaaccgtgta tgatttggag ttgaaatgag gaagatatgg 360 ccttcggaat ccaactgctc caggttatgc gaaattcgca taacaccttc aaaattcgca 420 taacccatgc gtgttgcgaa ttttcctctg cttttgccga ctccacttta gatattttcc 480 tttgtatttt gtgatttaat ttcctttctt atccttgtaa ctaaccaatc acaagctttt 540 tcttttgtaa agactatata aggggtggaa atcacctctt ggaatatata gaatacatat 600 tacgtttgac acttagaaaa atatacagag ctctctcgtt tctcttttct ctttactatt 660 ttctttttct tgaaagccaa acaacctctg aggatgtttt cccggaggat gaaaggctaa 720 actttcggtt tcttggagtg aaggaagcta ggtgaaaagt ccagatgaaa aggtggaaag 780 cttccgtgca ttaaattcag gtagttggaa ttcataaatg gcttctaaat ccaaagtttt 840 gctttaaatc ccttagaatc actttgaatg accaatacat ggtaagcttc aggtctttat 900 ggatgcttat tgctagatcc atattagttc attagttatc atgtacgagc cattggaaag 960 tgattcaagg tgaagaccca tagtgtctta agccattaat ggaccttgac taccattcct 1020 attaaccttt tatggattaa atcttctttg tcaaacctat acctgttcgg gaaataacta 1080 taggttaaat ccccaatgcg aggagaaaaa tccgaaattt tccactttct attctgaact 1140 tgatcctagc aacccttaga tccaggaaac tttctttctt ccatttttac tcagtttatg 1200 ttagtttatt ttcaaacact ttcaaaacaa attttatttt cttttaaact ttaagttttt 1260 gataaaggaa atcattaaat ccaatttcta attttgagta tatcattggt agaatgaaaa 1320 cccatcccag agttcgaccc tagagccact atactatagt agctttgcta cgttagtatg 1380 aggtcatagg ttttataaat gtttttgatt aaatgaccca atcggagtta cacgcgaatc 1440 a 1441 // ID EnSpm-6_VV repbase; DNA; EDCOT; 13814 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE EnSpm-6_VV, an autonomous DNA transposon - a consensus sequence. XX KW EnSpm; DNA transposon; Transposable Element; CACTA; TIR; KW Cactavine-6; EnSpm-6_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-13814 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 758-758 (2008). XX DR [1] (Consensus) XX CC EnSpm-6_VV (Cactavine-6 in [1]) is virtually an autonomous CC element because its individual copies do not have an intact ORF CC due to premature stop codons and/or frameshifts. Individual CC copies are >95% identical to the consensus sequence. EnSpm-6_VV CC contains 13 bp-long TIRs which are flanked by 3 bp-long TSDs. XX FH Key Location/Qualifiers FT CDS join(5418..7648,7746..8054,8126..8213,8325..8894) FT /product="EnSpm-6_VV_Transposase" FT /translation="MDRDWMWLPNRLSRDYVEGVKSFIQVAKEHLRWDNKT FT RCPCRDCQNARFNDLLTIERHLIRFGFSRSYQKWIFHGEEHESQPNEQNDI FT GVDTEIVDATDADILNEVVDALNDACGHIDNDINLEESTTHGKFDYLLGEA FT NKELYPGCKKFSALTFLVKLMHIKVLNRWSDKSFDMLLQVLVDAFPERSNI FT PKTYYDAKKMLRDLGLGYDSIHACKYDCALFWKENETLDKCPVCDEPRYKF FT CNGKGKKIPQKVLRHFPLKSRLQRLFMSRHTTSDMRWHKEKRISEEGVLRH FT PADSEAWKDMDTQFPWFSQEPRNVRLGLATDGFNPFGSMSNSYSMWPIVLV FT PYNMAPWRCMKEMFFMLSLLIPGPQAPGRDIDVYLRPLIEELKELWHEGVQ FT TFDVSTGENFRMHACVLWTINDFPAYGNLAGWSTKGYKACPVCNEDTSSLG FT IRSKICYMGHRRFLPLDHGWRRSRQHDGKPEFRPPPRMFSSDEILQQLCCL FT KHRKPGKHPNNVDRKRKRVPEELNWTKKSIFFELEYWSKLKLRHNIDVMHV FT EKNVCDSVVGTLLNIVGKTKDTNKARLDLADMNIRKELHLQIQGNKLVKPH FT ACYTLTVEERKEFCKFLKSVKFPDGYAANLSRNVSINDGKISGLKSHDCHV FT LLQKLLPIAIRPYFNKDLCTTLVELCSFFQKLCAKTLYVNDLEKLEEGIVL FT ILCKLERIFPPAFFDVMVHLMVHLPREAKLAGPVSYRWMYPFERNLGTLKR FT YVRNKARPEGSIAEAYIVNEALMFCSMYLTGIETRFNRSERNEDRFEHRVQ FT GCLSIFSQQARPLGSRQHLQFSKEELTKAHWYIMNNCPELRPYLDEHTKEL FT ERTSSHNLEKRQEQEFPKWLADRMKALRVKQSPEATDELYSLACGPDNRVH FT TYMGCIVNGVRFHTKDRDDRRITQNSGICVSGEHDGEEIDFYGVLSNVVVL FT NYVLGYKVILFKCTWFDTNQKKKRIKHDYNFTTIQVTSTWYDNDPFILATQ FT AQQVFYLDDYKNGHNWKVVQKVNHRHMWDVPERDTNIEIDEEVCGGSDEEA FT YQDNESHEA" XX SQ Sequence 13814 BP; 4872 A; 1632 C; 2160 G; 5043 T; 107 other; cactacaaga aaacttattt ttcctgacaa aaatttaggg gcgaattgta attttgtcgc 60 taaaaggaac ttttaccgat gaaattttag atatcgttgc taatgtcaaa tttctgaaaa 120 cttttggtaa cgaatttgaa tttttcgtcg ccaaaagaca tggcgggaaa atttagcggc 180 ttttttttgg cgcaaacgtt attgtgatga aaaaaaaact atttgccaac gaaaatattt 240 gttactaaat acaatttttt tgtgacgaaa ataatttcct tactaaaagt tacaaatttt 300 tattcatatt tgcttacaaa atggtttcat cagtaaatat attattttct gacaaaatga 360 gtaattttgt cactgaatag tgttgctaaa ttgtaatagt aataagtcat attgacaaat 420 agataaaagg tttatgctat aaaataatat aatacgtatt ttttgagact tgatatttaa 480 attataatat tttatttata tatataataa taatactaat taaagattca taaaattaaa 540 tactagaata tagatttata gaaatttaaa tgtttttttt atgtaataat agtattgtta 600 tgaaataata aaaaggtaaa ttatttaagc aattaatttt tatagtgtaa tatatatgtt 660 atawtttttt tatatagata ataacaaata atccaagata taatataaat ttatttaaat 720 ttcaatatta ttatatratg ttaaccaaac ataaataatt ttaaatcttt tttattatac 780 aatgtaaaag ttatttttgc aagtttaata tagtattgaa cttaaattag ttatgaataa 840 gtaatgatcc tctaatttgt tcttattcaa aatcatgtca tctactcaag aagtaaattt 900 atactaatat ttaactacct agtttaaatt aatagatttt tataattatt acttggtttt 960 taaatagttk ttcataattg aaattatcaa ataaattacc taatgtytat aaagacakta 1020 tatttgcata kaatttcaaa taatacytgt gtgtataaaa aatatcatat attatcaata 1080 catatatgat tgcaattaaa tattatatga tatgatatat ggcattatat gcctaactac 1140 tataatatta ataacaaaat aaaaaatgtg ycatatatat atacacacac atawtataat 1200 gggtatatga agaaattaat atatgaatga tataaattgt aacattttat aataatcaac 1260 artatttgaa rrcatattta atgttaaaat gataatttat ttactttata atatgtgaat 1320 aattattata tttttatttc attcatgatt tttgtgcttt caataataaa ttaaatgraa 1380 aataaaatta aatatttaaa attaatagat ttattaaaac tttatcttaa tattttarta 1440 tttaaaatrt atataaaatt taggtgtaaa cataattata tataatgtat aggcacttta 1500 ataactcaaa tgaatkatta tcctagtggt gtatagttaa cttygtaagc ttgggaagtc 1560 tgaacacttt attgatctca ttataaattt ttatttttaa ttgttaaata ttaatttatc 1620 ataaatgagt tacttattaa aaataaaatc ataaattata tcacaaaata gtaaatgttg 1680 tacctactaa cttgtaaaga agtttttata tttgtataca attttttaat aaaacatgta 1740 aaacaaatat agttatcwaa ataattgtaa catatcataa aatagtatat catttatatt 1800 tatagtgttt tattgcattt gatatttttg tttgaaatat aagagaaaga aaatgaaaaa 1860 agagataaag atgacttgtt gacacgaatt gttgcactta ggcttattca ctttgaaagt 1920 aaatttatac taatatttaa ttacctagat taacctaata aaaatatttt ttttaattat 1980 tgtttagttt ttaaataatt gttaatatta gaaattatca aataataacc taatttttgt 2040 caagatattc tattgacgta aattccaaat atggtttatg tttataaaga tatcatatat 2100 cattaatgaa tatatgattg taagttaaat atcatatgat acaatacatt gtaccatatg 2160 cataactact atattattat tttagaaaat aaaaaatgca ttatatatta gtaatatatt 2220 atatacataa aaaaaaaata attgtaaggt atctaaccac ttcttaatta acaattgatt 2280 agtttaattt ttaaataatt ttatgatkta ttaatgatct ttagcttaac tactaaaata 2340 agataataaa ttatgccaca aaagtagcaa ttattatagc tactaatttg ttaaggattg 2400 ttttacactt ttatatgttt twttaataaa atatttaatc tatgattttt attccttact 2460 ttaaatttca atttttattt tactctaatt tckaatatat aaattctgat ttaaaaattt 2520 taaattttaa atttcaaatt tctaaatttt aaataataca aaactcataa atcttacatt 2580 ttatttttag tcaaatttgt aatttataaa ttctaatttt tatttttatt ttttttattt 2640 tctaaatttt aaataataaa tagtcccaat aataggcaaa taataaagtt tcaattttat 2700 ttttaatcta atttttaatt tatattttta attttaattt twwattttaa aawttttaaa 2760 ttctaaattt taaataatat aaaacataaa acatcatgaa atgcattaaa tgcgccgagt 2820 tgtagcagca wgctwctgag atttggttgy agagacggca caatggatgg tgtggagtat 2880 tggttgggaa atgaaatgaa aagaaagtga aataaaaaag aaaaaaacac aatctcccaa 2940 gcacccacgt agcactrgga ctttgaaaag tgagaagact ttctcaccaa ctctccatca 3000 tttgcctgca actttgaaaa tgaaaaagag catcactttc tggttcccac cacatctcta 3060 acatctacca taacctcctg aaccttccac cattttcacc atctcatcta ccttcttaaa 3120 aaatcgtttc ccacttgcaa gccatatcca ccattctcca ccaaagttta ccgagccggc 3180 aaagcttctt atctgccatt ttcataggtc tgttatacta cagaaatcta ccaccggtat 3240 gttcccctta taatttttat tggttttttt ttatttgttt acatgtttgt taatacttga 3300 ttattctctt tatttcactt aaaatgttga aataatttgt gtttaaattt aataagtatt 3360 tatttttctt tctctccaat ggacttaatt tcttaacaaa attttctaat aatttggttt 3420 gagttgagct aaaaataatt tgaaattgaa aatgtaaact aatttcttaa caaaattttc 3480 taataatttg gtttgagttg agctaaaaat aatttgaaat tgaaaatgta aactaatgta 3540 aaaataattt tagttaaaat tcaggttttt agagtagaat aaaatttttg actagtggaa 3600 acaagcaaat tatatagaaa aawctagatg tgagagaata taaattaggt tattaaaaat 3660 tagtttatag aaaattagtt aaaataatgc tagtttatgg tagtttaaaa aamtgaaata 3720 attttgtgag ttaatccaaa cattatatta ataaataaat agtcatcatt tgaattaatt 3780 tatttagttt caactttatt agtaaaataa taaaaaaata ataaagtagt tattagggaa 3840 gggtaatttt tgcatggatt aagtaatttc aatgaaaara agaatattaa aaaaatgaaa 3900 taatttttgt gagttaatcc aaacattata ttaataaata aaagtcatca ttttaattaa 3960 tttatttaat ttcactttat tagtaaaata atacgaaata ataaagtagt tattagggag 4020 gagtaatttt tgcatggatt aartaatttc aatcaaaaga ataatattta aaataaaatt 4080 gttatttttt taaagttaat ttaattaagg aamatacatt ttgataagaa aatagaattt 4140 taagctaata aataaaatct gatttgttac ctttgaccta tccatttcaa tatattagat 4200 attatataat ggattaatat tataatttta tcatctatcc atgttctatc aattaaattt 4260 ataaatgaca atgtttatat aattttattt atttgtgctt taccacattg ttgcctagat 4320 ttgcttcaag gattaggtaa aaatgtagtg cttttcattt acatttttat tatcacaaaa 4380 tgaattattt agagtttcaa caacttatgt taaaatggta cattacataa ttccctttat 4440 aatttgtaat taaaaaaaaa tcatttttaa ttattttatt tattatgtat tatatcttgg 4500 aatgttaatt ataccattat ytttatcttg taattataat tttttttctt catattaaga 4560 caatataagt tagaagaact aaacttgata aaataagttt aggaaaaaca acaaacatct 4620 ttttattaat aatgaaacta catgcatgaa accttagata tctcgttcaa gtattagtgt 4680 aggacaagtg tatcttatca tatacttaaa gacaaataag ttgtaaaatt atgaaaatga 4740 ctctctttga gccaaattca agttgacaac ttatatgtct agcatatgat tagtgatttg 4800 tcttcaaata atgcttgaat tgtccgtttg gacagtttag gaatgcataa tatttattca 4860 atcactgatt ggtgctttgt ccatattgaa agattatgac agttattcct attgttctct 4920 gggtgcatat ttggacaagg tgacatattg ttagttgctt aattaagcta actaatagtt 4980 tgtttgtgcc ttggccaagt cgtgtacttg gagaactatg gggaaatgct gccgattttt 5040 tctcaaaatg gatcgaagca acttggtgat tgactcttag atattatgca atcctaaatg 5100 ggataggaac caccacctaa tttatgtagg aagtacaact catgcattag attttaacat 5160 ttacatgtat ataacaaaat atgtaaggtg agttagagtt ttatgttggt taagcccaag 5220 tttccatctt attcaaaaca agccaatgag ttgggtaatt gaattttagt gcaatattgg 5280 ggaaaatgac atttcatgga attcaatatt gggcatatga aataatatga gaaaaacaat 5340 gtaagattga gaaatagaaa tcaatatttt atctttattg aatatgagat tcatttttaa 5400 tttacaggat aataagaatg gatagggatt ggatgtggtt gccaaatagg ttatctagag 5460 attatgttga aggggtcaag tcattcattc aagttgcaaa agaacacttg cgatgggata 5520 acaagacacg ttgtccatgt cgagattgtc aaaatgcacg attcaatgat ttgttgacaa 5580 ttgaacgtca tttgattagg tttgggtttt ctagaagtta tcaaaaatgg atttttcatg 5640 gggaagaaca tgaatctcaa cctaatgagc aaaatgatat tggtgttgat acagaaattg 5700 ttgacgctac tgatgctgat atccttaatg aagttgtgga tgcattaaat gatgcatgtg 5760 gacacataga caatgatatt aacttagagg aatccactac tcatggaaaa tttgattact 5820 tacttggtga agctaataaa gaattgtatc cgggttgtaa aaagttttct gctttgacat 5880 tccttgtgaa gttaatgcat attaaagtcc tcaatcgttg gagtgacaag tcttttgaca 5940 tgttactcca agttttagtt gatgcttttc cagaaagatc aaacattcca aagacatact 6000 atgatgctaa gaagatgtta agagatttgg gcttaggata tgattcaatc catgcatgca 6060 agtatgattg tgcattgttt tggaaggaga atgagactct tgataaatgt ccagtgtgtg 6120 atgagccacg atataagttc tgtaatggaa aaggtaaaaa aattcctcaa aaagtattgc 6180 gtcattttcc actaaaatca aggctacaaa ggttattcat gtcaaggcat acaacatcag 6240 atatgaggtg gcataaagaa aaacgaatca gtgaggaggg agtcctaagg catccagcag 6300 attctgaagc ttggaaggat atggacaccc aattcccttg gttttcgcaa gaacctcgaa 6360 atgttcgatt agggcttgca acagatggtt tcaatccatt tgggagcatg agtaatagtt 6420 atagcatgtg gccaattgtt cttgtgccat acaatatggc accatggaga tgtatgaaag 6480 agatgttttt catgttatca ttactaattc caggcccaca agccccaggg agagatattg 6540 atgtatacct acgtcctttg atagaagaat taaaagagtt atggcatgaa ggtgttcaaa 6600 catttgacgt gtcaacagga gaaaactttc gcatgcatgc atgtgtttta tggacaataa 6660 atgactttcc tgcttatggg aacttggctg ggtggagcac aaaaggatat aaagcatgtc 6720 cagtttgtaa tgaagacaca tcgtcactag gtattagaag taaaatatgt tacatgggcc 6780 atcgacgttt tttacctctt gatcatggat ggcgaaggag tagacaacac gatggtaagc 6840 cggagtttcg accaccccca agaatgttct ctagtgatga aatattgcaa caattgtgtt 6900 gtcttaaaca tcggaagcct ggtaagcatc caaacaacgt tgatagaaag cgaaagcggg 6960 tgcctgaaga attaaattgg acaaaaaaga gtattttctt tgagttggag tactggtcaa 7020 agttgaagtt gagacataat attgatgtta tgcatgttga aaagaatgta tgtgatagtg 7080 ttgtgggaac tttgttaaat attgtaggaa aaacaaaaga tacaaacaaa gctcgcttag 7140 atttggctga tatgaatata aggaaagaat tgcatttgca aatacaaggg aacaaattgg 7200 taaaacccca tgcatgctac acattgactg tagaggaaag gaaagagttc tgtaagtttc 7260 taaagtctgt taaatttcca gatggttatg ctgcaaattt atctagaaat gttagcatca 7320 atgatgggaa gatctcaggg ttaaagagtc atgattgtca tgttttgctg caaaaattac 7380 tccctatcgc tattcgtcca tattttaata aagatttgtg tacaacactg gttgagttgt 7440 gtagtttttt ccaaaagtta tgtgcaaaga ccttgtacgt gaatgatttg gaaaaattag 7500 aagaagggat tgtcttaata ttgtgtaagc ttgagaggat attcccaccg gctttctttg 7560 atgtcatggt tcacttgatg gtacatttac cacgtgaggc caaacttgct ggaccagtta 7620 gctatcgatg gatgtatcca tttgagaggt acatttttac ctttttttgt ttattaatat 7680 tctcatctaa ctatgttaca caatacatgt gttaaggctt atttatttac actatttcta 7740 tttaggaact taggaacatt gaaaagatat gtgagaaata aagctcgacc agaaggttca 7800 attgcagagg catacatcgt gaatgaagct ttaatgtttt gttcaatgta tcttactgga 7860 attgaaacac gttttaatcg aagtgaaagg aatgaagatc gatttgaaca tcgagtacaa 7920 ggatgtcttt ccatattttc acagcaggct cgaccattag gcagtcgaca acatctccaa 7980 ttttcgaagg aagagttaac taaggcacat tggtatatca tgaataattg cccagagttg 8040 agaccatact tagagtaagt tttagaatca acattaaaga tatttcttta gtacctcgtt 8100 acttaatatc tatttaatga tgtagtgaac atacaaaaga attggagagg acaagttcac 8160 ataacttaga gaaacgacaa gaacaagagt ttcctaagtg gcttgcagat cgtgtaagtt 8220 ttatttgtgt aatttgcttg ctacaatata gttgtaatga actaatataa ttttaataag 8280 atttgatatt aaactataaa taattatgta tatctatatt gtagatgaaa gctttgcgtg 8340 ttaaacaatc accagaagca actgatgaac tatactcatt agcatgtgga ccagataatc 8400 gagtccacac atacatgggt tgtattgtta atggagttcg cttccataca aaagatcgtg 8460 atgatcggcg tatcacccaa aatagtggga tatgtgtttc tggggagcat gatggtgagg 8520 agattgattt ctatggtgtt ttatcaaatg tggttgtttt gaactatgtc ttggggtata 8580 aggttattct tttcaagtgc acatggttcg acacaaacca aaagaagaag agaataaaac 8640 atgactataa ttttaccaca atccaagtta cctccacctg gtatgacaat gatcctttta 8700 tacttgctac acaagcacaa caagttttct acctagatga ctacaaaaat ggtcataatt 8760 ggaaagtagt acaaaaagtg aatcatagac acatgtggga tgtaccagaa agggatacta 8820 atatagaaat cgatgaagaa gtgtgcgggg gaagtgatga agaagcttac caagataatg 8880 aatctcatga agcttaactg gtttgtagag caagatgatg gatttgaatt tcaacgatct 8940 gaccgcttaa acattgatcc agaagttgtt aatgataatg ttttgatttt agagaacatg 9000 aatgacaatg atgataactt catatgtgat gacattgagg aagaagatga aacactagat 9060 gattatgcta atgagaatga aatgtggctt tccaagtgat agtgaaagtg aaagtgatta 9120 aagagactgg taagctacat tttatttact ttattatatg ttaaataaca taatgtaatc 9180 tagatctagt tctttaaatt tatgttatgt gttgtgatat tccttttgta ttattattta 9240 tttgtcttta ttgttatttt attatagatg gctcctggac gaaagcggtc accttctgag 9300 ttaactcaac cacccacaac aacacccatg actccttttt atgttgatgt tccaatgcac 9360 acatccaatg agggcactag tagttgtaag aaacttctta catttatata ttttacttat 9420 tataattttg taagatattt tattttattt tttttwaatt ttaaattgta atgagatgta 9480 atttattttt agtcttttta ttaactctta ttaattgtta aagtttaatc aataatttca 9540 tggtagcacc taataaaaga aatgtaagag gcaaaactag aggtgtcatt cttgacaaac 9600 ttattgaagc taatgggggc aaacctcttc cgatcacaat caagccatca gatgggaagc 9660 aaacaggaaa atattgtgag aaattgtcaa atgagattgg gttaacagtg agacaacatg 9720 cacctgttag agtggaaaaa tggaagcaaa tgcctcgagc tgagatcaat acaatgcttg 9780 atcgaatcaa ggtaaagttg cttgaaatat atatatatat attttttttt agcttgtaat 9840 tataactaat tgttggttat ctctaaactt actttatctc atattagttc ttcccttgtt 9900 tgactatgaa ggaaaagttt gccctagatt tgacacaaga gcatgtgaag aaaagtttag 9960 aaaaacaatt atctgaccgg tttagaaatt ggagatgcga tttgcacaag cacttcaaaa 10020 agttcccaac tgtggtggag gctaagcgaa atcctcatga atctgtgtca aatcargaag 10080 attgggacta tctttgtgat agattttcaa gtgaagaatt taaggtaaag ttttcaatga 10140 ataatcattc aaacctattt cttattgaat attctactaa ctatatttat attattttca 10200 ataataacta ttattacagc gtcgttcagc aatcaattca gtaaatagat caaagatgcc 10260 ttttcatcat cgaggaggct ctcgttcatt tatccaacat ggtctacaag tggtaaaata 10320 taaaactaag gttctttagt tattcatata actkataatt cttaatatgg tggaggctaa 10380 tgcataatac tcatgacacg tcaactcaag agaatggaga gatggttggc caaattgaac 10440 tattcaagtg actagttcat tggaaaagtc aagatggatg gataaatcaa gaggctagag 10500 attattatgt aagattattt tgactagctt tctattagtt taaatcatgt ttgggattat 10560 gacatctttg tggaagtgtc aattcartga gtagttcata tttaccatgt gatgataaat 10620 aaggcacttc cttggtagtt ttcataaatc tttaaatttt gatttggtaa tattgattgc 10680 ttgggtgttc aatgttgtta aattgattaa tagcagggaa aatttggcaa agtctaaaaa 10740 ttaggggaka ctacttgcca gtcaaatttc tattgaaatt ttatcttacc aamttgaact 10800 attcaaacta gttcattgga aaagtcaaga tggatggata aatcaagagg ctagagatta 10860 ttatgtaaga ttattttgat arcttttcta tgttwaaaty atgtttrrga ttatkartct 10920 ttgtggaagt gtyatcrtrw taryttrtwt acyatgtgat gatwmwtawk kcahttcctt 10980 krtaktattt matrwrtswt taaawkytra ttwggttmtt cttaggtaga wtscttgrrt 11040 gtwmamtktt gttwrggcat tgattaatca kmarkvaaaa tttggcaaag tctaaaaatw 11100 aggggagact atgccaaaat ttctattgaa attttatctt accaacttga attattataa 11160 cttttcttac tcaaaattac atttaagatt attagtactt gtaaagtatt attatatgat 11220 caacttgtat actagattct tatttcaatt tttatattat ttaatgtgtg attacaagct 11280 aattaggttc ttcttaggta gaatccttga agtaaacttt tgtttgggca ttaactaatc 11340 ataaatcttt attgttaaat attttattat gtggttggta aaaatttgtg gaaatagtaa 11400 agaattaaag agggattagt atattattaa cttgaatata taataggtca aattttggaa 11460 aaaaactaag aaatataaga gaatatgcca aaatttaaat aggattttta acttgttaac 11520 ttcttgttat aattttcctt gcttaaaatt aagttgagat tctaagtact tttcaatttt 11580 ttaccatttt attatgtata taagaatctt gtttacgtga taacaagttt agatactttt 11640 ytttagccat ttctttgctt aaaatgaagt ttaggattat atgtgcttgt ggggtgttac 11700 aatatttgta taaaaaatat catatcctta tttgaaatct aatattaagg gattattcca 11760 aaatttaatt aggattttta acttattaac ttcttgttgt aattttcttt acttataatt 11820 aagttgagat tctaactact tttcaatttt tatcatttta atatgtatat atgaatcttg 11880 tttatgtgat aacaagttta gatacttttt taggaatttc tttgcttaaa atgaagttta 11940 ggattatatg tgcttgtggg gtgttataat atttgtataa aaatatcata tccttatttg 12000 aaatctaata ttaagggact attccaaaat ttaattagga tttttaactt gtcaacttct 12060 tgttataatt ttmtttactt ataattaagt tgagattcta actacttttc aatttttayc 12120 attttagtat gtatataaga wtcttgttta tgtgataacr wgtttataaa cactttgtta 12180 ggcatttctt agcttaaaat taagtttagg ataatgtgtg ctaatgggat gttacaatgt 12240 ttgtataaaa atactatatt cttgtttgaa atctactatt atttgccata taataacaaa 12300 ttaaggcact tggatgtttt gttgtgctaa aaatcaattt gattattaac taatttgaaa 12360 ttccaatgct tatatttatt atatatagta ggtataattt aaaaaatatc tactaaatat 12420 gggagatcat gcccaaattk aatggraatt ttaatttact aacttattaa ttatgttttg 12480 gttcttttta tttttkwttt wttttttatt ttgcatatat aggagaagat gttggagctc 12540 caaygccagc ctattgcaga aggagctgtg gctatgactg aggcagaaat ttgtgagaga 12600 gttttgggac aaaaatcagg atatgtcaag ggccttggtt ttggccctaa accaatctca 12660 ttttctaaat ctagaccatc atcttctgag cgtgaaattg agttggagca tagacttgtt 12720 gagactcaac tacttgtgga gactcaacaa caacaacttg agactcaaca agatcgaatt 12780 gaccaattgg aggccttggt acaaaaacaa aaccaacaac atcatcaaca atttgaagaa 12840 atattgcgtc atctacgatc aagccaaggg tcctcatgat cccttttttt atgatgtgca 12900 tatgatggac gttcatttct tttttttttt gcctatgcta atatagtttt tttgtgagag 12960 acactttgtt aaactaatac tttattttgt tatgtagtta tattagcata gatattatac 13020 tactatgatc acatgttatg gttacatata ttaattacca atgaagttat gtgatatata 13080 ttttgatttt tgtaagcagg tttcagaatt aacttttcta ttataattaa tgttttaaat 13140 accaaatacc atacatttgt aatatgaaaa ataaaaaatg taaatacatt tcctgacaaa 13200 aaaaaaaatt attactaaag atatttcctg atgaaatatc tttgttgctg aagattgttg 13260 tatcatccac aactaattta taattcactg gcatacgttt tagggacgaa atcattttgt 13320 aaataaaagg atttagcaac gaaatgaatt tgtcagtatt aatgataaat attttagttg 13380 aaaaaatcct ttagcaatga aatatctatt tcatcaagaa aaacttttag tgacaaaatg 13440 gaactttcgt tgggattgca aagcctaggg agacgaaatt aaattgttac aaaaaatatt 13500 tggyagcaaa ataaattcgt cagcactaag tattgacgac tttgaggaca aaaatttata 13560 ttttttagtg gcaaaaattc ttacttttgt taatgaaaaa tttcgttggg gaaaatattt 13620 agtaacaaaa tttttatttc atcagggaaa atattgggcg acgaaatagg atttttgtcg 13680 ggatactttt agcgacgggt ctagggcgac gaatgtgaca cgaaacattt ttcgttggga 13740 aatatttttg cagacgaaat ttagactttt agtgacaaaa tattttatca ctgaaagtca 13800 attttcttgt agtg 13814 // ID SHACOP12_LTR_MT repbase; DNA; EDCOT; 213 BP. XX AC CR931729; XX DT 24-JAN-2007 (Rel. 12.01, Created) DT 24-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of LTR retroposon, SHACOP12_MT, from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; terminal; repeat; SHACOP12_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-213 RA Shankar R. and Jurka J.; RT "SHACOP12_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 54-54 (2007). XX DR EMBL/GenBank/DDBJ; CR931729; Positions 80487 80699. XX CC Present in the genome in just 9 copies. XX SQ Sequence 213 BP; 65 A; 29 C; 20 G; 99 T; 0 other; tgttacatgt taatatttaa tttaattatc attaactata acctattagt tagcctgctt 60 attagtattc tattcaattg tatttataca tgttgattag tcttctcttt attttagtgt 120 ataaataaac ctgtcatgta cttttacaca tagatcaatg agaattatat atcacttgtc 180 tttctatttt ctactgtgtt ctaaatatta aca 213 // ID Copia40-PTR_LTR repbase; DNA; EDCOT; 209 BP. XX AC scaffold_2111; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia40-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-209 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-209 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 259-259 (2007). XX DR Genome; scaffold_2111; Positions 474 266. XX SQ Sequence 209 BP; 72 A; 35 C; 31 G; 71 T; 0 other; tgtaagcaag tatccaagta tggaactaac tccaactgaa cctcctgaag aataggattt 60 aagctagtga taagatttgt atagaatgga actctaatta ttgtgtttga ttagaactct 120 gcaacattat ctttattgta tatatataac ctctgattca atgaataaac atgagtttct 180 acgtttcaca atcagatttc atctccaca 209 // ID HARB-N5_Mad repbase; DNA; EDCOT; 697 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW HARB-N5_Mad. XX NM HARB-N5_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-697 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1504-1504 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >88% identical to the consensus. 3-bp TSDs are usually TWA. XX SQ Sequence 697 BP; 205 A; 131 C; 169 G; 192 T; 0 other; ggccatctcc aaccgaagga gggccaaagg gccatgttta gccctatagc cctgcaagaa 60 attatatttt aatgaacagt gtcagaccat attttatacc atctccaacc gagggggcca 120 aagggccata ggccaaaaca tagccctttg acaaaaaacc atctccaacc gaggggggcc 180 atagcccctc aataatttat tattttaatt gaattaatat ggttaattga attaaactac 240 catattaaaa taaggttttc ggacatattt tgagtgccac ttgtcgctaa atgaataagc 300 cttcggattt cttatcttta tatatgaaaa ggatgtgaaa aattggtgaa gaatttgaaa 360 taaaatgagg taagatagta tggaatggtg aaaagtatgt gagaaatggt gtaggaatgg 420 cttaggtatt tataggaaaa aaattagatt ttttttaatt tcgtccaaaa aaaaaaaatc 480 aaatccaaca gtaacctgac gtcagctagc atgggtttgg gctggtgcaa acgggctggc 540 tggctggctc ttggccagcc cgctggcctg gtgggtggtt ttgcccggtg ggggcccaca 600 agccctttgg cctagccctc ggttggagac ggttttcgtg tcaaaacggg ctatttttag 660 ccctatgacc ctttggccgg gtcggttgga gatggcc 697 // ID Copia-82_Mad-LTR repbase; DNA; EDCOT; 519 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-82_Mad_; KW Copia-82_Mad-LTR; Copia-82_Mad-I. XX NM Copia-82_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-519 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1703-1703 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 519 BP; 148 A; 79 C; 115 G; 177 T; 0 other; tgttaggatt ttggctcgtc aaatatgtcc tagtttgttt aggattgttt taggaaacct 60 agaggtgtac cgattcttgt cctagaggga ttaggaaaga atttcagttt ccttattcaa 120 tttaggtttg gattcctaga agtctatttg gatttggata agtgtaattt cctattccac 180 ttagaaatag gaattcaatc agctttggga catgtaagcc gcaccctatg cctataaata 240 gggtgcggca aggctgattt tttaaagaga gaaagaaaac agccagacag ccaagagttt 300 tgagattagt tctagggttt gcaaaagttc tgtaatctct attattaatc aaaggagcgg 360 tgatttctct acctagagaa atcacaactg gacgtaggca aaagttctgc cgaaccagta 420 taattcttgt gtgtttctaa gttttctaat atttgctagt ttagtctatt gccgttggtt 480 acattaaaga acaaggtcta gtgtgcgggt ttttcaaca 519 // ID DNA8-6_Mad repbase; DNA; EDCOT; 1941 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA8-6_Mad. XX NM DNA8-6_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1941 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1477-1477 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >83% identical to the consensus. Likely 8-bp TSDs. XX SQ Sequence 1941 BP; 594 A; 416 C; 447 G; 478 T; 6 other; tagggctggg cacgggccgg gccgggccca tttttgaagg gaccggaccg gacccggaat 60 taaaggagac ggggcgggcc gggccgggca ttacaattct gaaaatagga accggacctt 120 acccggcccg gttgaaacgg gccggttcgg tccgggtaca cgggtccttt ttttttcctg 180 tttaaaaatg tttgctgcac acagaaactg cacagattgc agtttttaca cataacanat 240 ttcacatatt gcagtttgaa aaaactgcac aaatttcaca gattccacaa attgcagttt 300 gaaaaaactg cacagattgc agtttgtcaa actgcacaga ttgctgcaca gattgcagtt 360 tgaaactgca cagattgcag ttnaaaactg cacagattgc agttaaaaac tgcacagatt 420 gcagttttta actgcacaga ttgcagtttg aaaaaactgc acagattgca gtttgatttc 480 gcantgcaca gattgcacag tttcaaaaaa actgcacaga ttccgcaaat ttcacagatt 540 ncacattcca cagattgcag tttgaanaaa ctgcacagat tccacagatt gcaatttgaa 600 aaaactgcac agattgcagt ttgcattttg cagtgcacag attgcacaga ttgaaaaaaa 660 atacgagcaa agaagctaca gaaaccatta tagttaagta tagtaattct ttagtagccc 720 agacgggtaa acaatcatat catagaaact tgctaataaa caacacaatg aatcaaaacc 780 attgatacaa ctcacaaacg taatctttaa tgttcactct aaatacacta aaaaattctg 840 ctctttatac agaaatcaaa tttgtcaatg ttgtggaatt gtaacaaaca attagttatg 900 caatctaaac ttgccaatta attaaaaatc gcagattagg caagggaaaa tgtaataatc 960 agccaattcg ataacggtat ttaaccggct tgaaactgtt taccaatcaa caccagaaac 1020 cccacaatta tgcttctgga tagatgctgc aaatcactaa cattttacgg ttctcatatc 1080 ccaaaaaccg aaaaggctga ttacgattct ttttcttctc tcattttcct gcattttctc 1140 agcaaccaaa cactgcctaa cggcattcca aaaattacac aaaaacaatt tgacatttct 1200 caagttgcac aatcccaatt ttgcccaaat gagaaatcag atgaattttc gatagaaaat 1260 gacgaaacag agagagatac ttacatgcta gaacggcaaa gatgatggcc cccaaggttt 1320 gtgcagggga aacgacgccg tattgtggtt ctctgactcg ctagggtttc gaagtgtgag 1380 gagtggggaa ggtgtgcaca gagagacttc cagttcctac ttcctagagg tttatggcgc 1440 gcttgatttc ctcaatttta cggcggaggt ggtgatgggg ggtgatgatg ttggtcgcga 1500 ctcgcgacag cgctgtgaga gtggcgaggt gagcactgtg agtcggagtc gagggagagg 1560 gatagggaga gggataggga gagggactca gggagatgga gtcgagggag agtctgagtc 1620 tctgagaatc cgagagactg aggtctgagg ctgctgaggc tgaggatgct tctggaactc 1680 gggactcggg gaaggttggc tagggttgaa agttgaaaac ttgaactgac ggttgagatt 1740 ggatggagag atgatattaa atctcgtccg tccaatctaa cacaaacggg ccggtccggg 1800 tacccgcgga tcctataatt ttggaaccgg cccgccccgc cccgatctat tttacaaaac 1860 taaaaccggc ccgcacccgc cccgtacccg tntttacaga accggcccgt acccgccccg 1920 tacccgtatt acccgcccct a 1941 // ID DNA9-16_Mad repbase; DNA; EDCOT; 1492 BP. XX AC . XX DT 26-OCT-2010 (Rel. 15.11, Created) DT 26-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-16_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1492 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1856-1856 (2010). XX DR [2] (Consensus) XX CC TSD is 9-bp. TIR is 430-bp long. XX SQ Sequence 1492 BP; 425 A; 386 C; 326 G; 355 T; 0 other; gggttaatct ctgtttacta ccctgaagtt tcgtggtttt caacatttgg tacatgaagt 60 ttttttcatc ccagagtcat acctcaagtc ttaattttag gacagtttca tacctccgtt 120 aagttttccg ttagaatttc tgttaattga tgatgtggcg ctcacgtgga caataattga 180 gcgccacgtg tcaatatgga cccactttaa tattaaaaaa ttaaaaaaat acaaaaacac 240 aaaaataatg aaaaaaaagc ccaacttgtc cctcaccccc gcacccttct ctcttctgca 300 aatcccagca cctcacccaa atcccagcac ctctcgattt cttctctctc tctctctctc 360 tctctctctc tctctctcac tacactcact ttcttcctcc gccttattcg ccgtgaaaag 420 aagacgacga gaaacatcca gcaaacccca ccaccgccgc caatctctct gccaatctct 480 ctgaacccac accctacaaa acccagcaga aacccagcaa atcaatctct cactgcgatt 540 ccctaacctt tctggttctc catgtcctcc gaatcgagag cttcgacctc cggcggcaaa 600 gcctccgagc cacaccctaa ccctgaccat ctagatcttg agtgaagaac actcactgtc 660 aacacatcta gtacggtcgc aagaaaagag agtagaagag agagaaagag agctctaagc 720 gccggactcg acaaaatgca agatccggcc aacccgaaac cggatccgag ctccagctct 780 caggactctc accacccacg catggcgccc gccgtttcca gacacgactc cgagcacccc 840 gttccagggc tcctaccacc gtcgaaccca atccgaggcc atttccagat ccctgacgac 900 ctggatctgc tccaggaccc gttcgacggc ccgtcctgcg gcttcaaaga gttgggcagc 960 tccgatgacg acatcttcga cacctacatg gacatagaga agctcagatg tgcttggaga 1020 gagagaggtg aagagggagg tgtgggagag atcgggaaag agaaaaggaa gggatcgggg 1080 aagagggggg gcgggtgggt tttctttctc gtcgtcttct tttcacggcg aataaggcgg 1140 aggaagagag tgagggtagt gagagagaga gagagagaaa gaaatcgaga ggtgctggga 1200 tttgcagaag agagaaggtg ggtgcggggg tgaggggaca ggttggcttt tttttttgta 1260 tttgtttttt aattttttaa tattaaagtg ggtccatatt gacacgtggt gctcaattat 1320 tgtccacatg aaccccacat catcagttaa cagaaattct aacggaaaac ttaacggaag 1380 tatgaaactg tcccaaaatt aagacttgag gtatgactct gagatgaaaa aaacttcatg 1440 tatcaaatgt tgaaaaccac gaaattttag ggtagtaaac agagattaac cc 1492 // ID Copia-16_Mad-I repbase; DNA; EDCOT; 4097 BP. XX AC ACYM01086656; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-16_Mad_; KW Copia-16_Mad-LTR; Copia-16_Mad-I. XX NM Copia-16_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4097 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1360-1360 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01086656; Positions 7648 11744. XX CC Positions [1440-1949] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 1497..4046 FT /product="Copia-16_Mad-I_1p" FT /translation="MEVESLGRNKYFVTYIDDASRRVWVYLLKSKDQVFQT FT FQEFHAMVERETGKPLKCLRSDNGGEYTSHQFREYCVKHGIRHEKTVPGTP FT QHNGVAERMNRTIMEKVRCMLRTAKLSKQFWGEAVRTACYLINRSPSVPLG FT LDVPERVWTGNDVSYSHLKVFGCKAFVHVPKEQRSKLDYKATPCIFLGYGG FT EDFGYRLWDPYQKKFIRSRDVVFYEDQTIGDSDKEAQPDGAVRGVDPLASD FT EESHDDIPEATANEVPAESDNADQEEPDQDVPDHEIADQGEPSQEEQIQGE FT SNQGEPQAPQENEDQVRRSSKSRRPSTKYSSSEYIMLTNYGEPETYEEARA FT HNDSDKWMKAMESEMDSLLKNNTYELVELPKGRKALKNKWVFKLKNDDNMT FT RYKARLVVKGFGQKKGVDFDEIFSPVVKMTSIRVILGMAASMDLELEQLDV FT KTAFLHGNLEEEIYMEQPKGFEVKGKETLVCKLKKSLYGLKQAPRQWNKKF FT NSFMVSNGYKRTHADSCVYIKQFSGGKFIILLLYVDDMLIVGQDAFMIKKL FT KEELSKSFDMKDLGPAKQILGMEIIRDRKSKKLWLSQEKYVERVLERFNMK FT AAKSVSSPLANHIKLSKESCPKTYEEKEKMAVVPYSSAVGSIMYAMVCTRP FT DIAHAVGVVSRFLSNPGKDHWEAVKWILRYLKGTSKMCLCFGGSKPILEGF FT TDADMGGDLDGRKSTSGYLFTFAGGAVSWQSKLQKCIALSTTEAEYIAATE FT ACKELLWLKRFLQELGLKQSDYGVYCDSQSALDLSKNTTYHSRTKHIDIRY FT HWIRDAIENKMLQLKKIHTDNNSSDMLTKVVTKSKLEFCIKAAGMDSR" XX SQ Sequence 4097 BP; 1261 A; 721 C; 1048 G; 1056 T; 11 other; agtggtatca gagcccggtt ggctcgtact rcgagatgga aggaagtggc actatgatca 60 aactcaccaa ctccaattgg gtaacatgga agccaaggat grakgacatt ctctattgca 120 aggatttgca tgagccaatt gaaggagatg ccgctaagcc cgagagcatg tccgatgccg 180 agtggaagaa gatgaatcgc aaggctattg gcacaattag acaatgggtg gatgatagtg 240 tttttcacca tgtgtctaat gaaaccaatg ctcgcgagtt ttggacgaag cttgagtcct 300 tgttcgagaa gaagacccca gccaagaaag ccttcttgat caaagagctc atcaatgtga 360 agtacaagga tggtttaagt gtagcagaac acttgaacaa tttccagaat atcatcaacc 420 agttggctac tatgaaaatg acgatcgagg acgagctaca agcgctcttg ttacttggat 480 ccttgccaga cagttgggag acctttgtgg tgagtataag taactctgct tctaatggtg 540 ttcttactct tgataatgtt aaaaatagca tgctcaatga agawacaagg agaaagactt 600 ctggcacaga tagcagccaa gtatttgtca cagagaaccg cggaaraagc amgagtagag 660 ggcctagagg tcatggcagg agtccwagcc gatccaagtc aaggttcagg ggtgcatgcc 720 accattgtgg caaagaaggc catatgaaga aaaattgtcg agtttggaag agagagcaaa 780 gggaaggaaa caatcagaag aaagatgata ctggcaatac caccgctgtc atmtrtggtg 840 atgtaccaga aatattgtct gttggtgaat gtctgcatat gggcaactct gacagagaca 900 ttgaatggat ctttgataat ggagcttcct tccatgctac gtccaaacgg gagttcttca 960 gtacatacaa agaaggtgac tttggcatag tgaagatggg gaatgaaagc tattccaaaa 1020 ttcttggaat tggtgatatc tgcttaagaa ctaatctcgg ctgccaattg atgttgaaag 1080 atgtgagaca tattcctgat atacgtctca atctgatatc catcggtacc cttgatcgac 1140 aaggatatta tcaccatatt ggcgaaggaa aattgaagct tactaaaggc ttaatggtgg 1200 tagcaagagc acgactttgt tgtacgttgt accggtcaaa tgccaaggtt ttgaaaggtg 1260 agttgaatgc tgtggaagac tcatctctag acttgtggca taagaggcta ggccacatga 1320 gcgagaaagg cctacaagtt ttggcaaaga agtctcatat tccctttgcc aaaggtacgt 1380 cgttaaactc ttgtgagcat tgtttattcg gaaaacaaag aagagttagt ttttctgtty 1440 catctacaaa gaaaggaaac ttgttagatc ttgtttattc agatgtgtgt ggtcccatgg 1500 aagtcgagtc acttggaaga aataaatatt ttgttactta tattgatgat gcttcacgaa 1560 gggtgtgggt gtatttgttg aaatccaaag accaggtgtt tcagacattc caggagttcc 1620 atgccatggt ggagagggaa actgggaaac ctctcaagtg ccttcgtagc gacaacggcg 1680 gcgaatacac atctcaccag tttagagagt attgtgtaaa acatggcata cgtcatgaga 1740 agacagttcc tggaactcca caacataacg gtgttgctga aagaatgaac cgaaccatca 1800 tggagaaagt caggtgtatg ttgaggactg caaagttatc taagcagttc tggggtgaag 1860 ctgtaaggac agcctgctat ttgatcaacc gatctccatc agtaccatta ggtcttgatg 1920 ttccagagag agtatggact ggtaatgatg tgtcttactc tcatctgaag gtgtttggtt 1980 gcaaagcttt tgtgcatgtg cccaaagagc agagatcgaa gttagactac aaagctacac 2040 cgtgcatctt tcttggttat ggcggtgaag attttggtta cagattatgg gacccatacc 2100 agaagaagtt tatccgaagt agagacgtgg tcttttatga agatcaaaca attggggatt 2160 cggataaaga ggcacaacca gatggcgcag tcagaggagt tgatccatta gcttcagatg 2220 aagaaagtca cgatgacatc cctgaagcaa ctgccaatga agtgcctgca gaatcagata 2280 atgctgatca agaggagcct gatcaagatg tgccagacca tgagattgct gatcaggggg 2340 agcctagtca agaagagcag attcaaggag aatccaatca gggggagcct caagccccgc 2400 aagagaatga agatcaggtc agaagatcca gcaaaagtcg aagaccgtct accaagtatt 2460 cttcatcaga gtatatcatg ttgactaatt atggagagcc cgaaacttat gaggaggcca 2520 gagctcataa cgacagtgat aaatggatga aggcaatgga gtcagagatg gattccttat 2580 taaagaataa tacctatgag ctggtggagc ttccaaaggg cagaaaagca ttgaaaaaca 2640 agtgggtgtt caaattgaaa aatgacgaca acatgacaag gtacaaggct cgtttggttg 2700 tcaaaggttt tggtcaaaag aaaggagttg actttgatga gattttctca ccggtggtga 2760 agatgacttc cattcgagtt atccttggta tggcagcaag catggatctt gagctcgagc 2820 agttagacgt taaaactgca tttctccacg gtaacttaga agaggagata tatatggagc 2880 aacccaaagg ctttgaagtc aagggtaaag aaactttggt gtgcaagctc aagaaaagct 2940 tatatggtct taagcaggct ccgagacagt ggaataagaa gttcaactca ttcatggtga 3000 gtaatgggta caagagaact catgctgact cttgtgtcta tatcaaacaa ttttctggag 3060 gtaaattcat cattttgttg ctttatgttg atgacatgtt gattgtcggt caagatgctt 3120 ttatgattaa aaagctcaaa gaagagttat ctaagtcctt tgacatgaag gacttagggc 3180 cagccaagca gattttgggc atggagataa ttcgtgacag aaaatccaag aagttgtggc 3240 tgtcacaaga aaaatatgtt gaacgggtgc ttgaaaggtt caacatgaaa gcagccaaat 3300 cggtaagctc acctttagcc aatcatatca agttragcaa agagtcgtgt ccaaaaacat 3360 atgaagaaaa ggagaaaatg gcagttgttc cctactcttc agcagtagga agtatcatgt 3420 atgcaatggt gtgcacacgg ccagatattg ctcatgcagt aggtgtggtg agcaggtttc 3480 tctctaatcc agggaaggac cactgggaag ctgttaagtg gattctcaga tatttgaagg 3540 ggacttctaa gatgtgcttg tgctttggcg gttccaaacc aatcttggaa ggatttacag 3600 atgctgacat gggaggtgac ctggatggta gaaaatctac gtctgggtac ttgtttactt 3660 ttgcaggggg agccgtgtct tggcaatcca agttacaaaa gtgcattgct ttgtccacaa 3720 ccgaggctga atacatagcc gctacagaag catgcaagga gttgttgtgg ctgaaacggt 3780 ttctccaaga gttgggtttg aagcaaagtg attatggcgt ttattgtgat agtcagagtg 3840 ctctggattt gagcaagaac actacatatc attcacgcac taagcacatt gatattcgtt 3900 atcactggat tagagatgct atcgagaaca agatgctaca gctgaagaag attcataccg 3960 ataataattc ttcagacatg ttgacaaagg tggtcacaaa atcaaagttg gaattctgca 4020 ttaaggctgc tgggatggac tccaggtaac ttggagtcat gatcggaatt cctccctcat 4080 ggactggagg gggagat 4097 // ID Ogre-MT3_I repbase; DNA; EDCOT; 11878 BP. XX AC AC151524; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 16-APR-2007 (Rel. 12.03, Last updated, Version 3) XX DE Autonomous LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-MT3; Ogre-MT3_I; internal portion. XX NM Ogre-MT3_I. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-11878 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC151524; Positions 78558 90435. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). CC In Medicago truncatula, there are distinct subfamilies of CC Ogres differing in their LTR sequences. CC Additional annotations: 6027..6312: putative intron. XX FH Key Location/Qualifiers FT CDS 733..2157 FT /product="Ogre-MT3_ORF1" FT /translation="MDSKTRSIKKYTFKKPDLTRLRELASHVTNPRDFRER FT HGRLLDLLKVKVEDGILETLVQFYDPICHCFTFPDYQLVPTLEEYSFWVGL FT PVSEGEPFNGLEPSPKNATIAEALHLKPSDLVHPHFTIKNNLQGLTAKFLY FT QKASDFVKAKKTNAFESIFTLLIYGLFLFPNMDNFVDLNAIKIFLAKNPVP FT TLLANTYHSIHHRNIREGGLIVCCAPLLYRWYASHLTKSVFSKENSGKASW FT SERIMPLTPADIVWVHAGTNTAGIIGSCGEFENVPLIGTCGGITYNPTLAM FT RQYGYPMKGRPDSLSLSNEFYLNKNDHTNLRMRFVQAWHSIRKFDGIQLGR FT KQSFAHESYTQWVIDRATAFGMPYTLPRFLSSTVPEIPLPLLPQTKEEYQE FT RLAEAEREIHMWKRECQKKDKDYETVMGLLEQEAYDSRQKDVIIAKLNERI FT KEKDAALDRIPGRKKKRMDLFDGPHSDFED" FT CDS join(2595..6026,6313..9774) FT /product="Ogre-MT3_ORF2" FT /note="gag-pol." FT /translation="MAAAEQTNNDLREEVSSLKEGMEKITAMMMDMMAAQA FT QASQAKIVQTVQGDVEVSQPAGSTATISTTQPLVNQFSSGDMTNMYSSGFR FT PTGSLGSSIPPQYHMPPGYPWGMPLANNEGVRHNAPEMQFPFGHQQTPFYQ FT SGQPFPQATMTYAGPLVHAGHQEVEQVYHSNSVAGDDRVGNLEERFEAVHK FT ELKTIRGKEMFSQNVNDLCLVPDVVIPHKFKMPIFEKYTGDTCPEMHLVTY FT VRKMVAHKNNEPLLIHCFQDSLTGPAHTWYMNLKGITTFEELANAFIQQYK FT YNSYLAPNRKELQSMTQGDKESFKEYAQRFIQKSAQIRPPLDEREVSDLFY FT ETLSPFYSEKMLGCASQKFTDMVDMGVRIEDWVRKGRVSKDGASSGGSSNG FT NRKFGNGSSKKNAQEVGMVAHGGSQPIYPSYPYVANIPPPTLTPQNPNYQL FT QRPQAPHPYYPPLYQPQPYQPQPFYQQPYYPPPPQQQQPRPRAQQQHTRPQ FT RNQFPPIPMTYEALLPSLLARGLVQTLPPPRVQNPLPPWFRADRNCAFHQG FT APGHDIEHCYPLKEAVQKLIHNKDLSFTDPNPAAPDHPLPPHGPTVNMVED FT YQEGGLVTRSQDIKTPLVPLHVKMCEAAMFSHNHNSCEVCSVDPRGCAQVQ FT DDVQGLMDREELVVTREEKSVCVVIPVFKDSAKPIDGVTPVFKDSSKPAVA FT PLVICVPRPKPFFSQNAMPYNYEPTSIENGKEISWSPSTSVSNIAENSQIL FT RSGRILPAVVQAKKKAPVIESVPIPDPSKGKSMVQPGETDNDEILKLIKKS FT DYKIVDQLLQTPSKISIMSLLTSSDAHRDALMKVLNQAYVDHDVTLGQFGS FT IVGNVTACNNLSFSDEDLPVEGKNHNMALHISVMCKTDSLSNVLIDTGSSL FT NVMAKTTFDKLTYSDGFIRPSCVSVRAFDGSRKTVWGEVDLPITVGPQEFK FT VTFQIMDIQASYSCLLGRPWIHEAGAVTSTLHQKLKFVSRGKLVTVSGESA FT FLVSHLSSFSFIGGESPDGTSFQGLSVESGTTRGETCMASLKDAQRVIQEG FT KAEGWGKLVQLPENKRKEGLGFSSNNQVMFDPTRGTFHSAGFINAPPETNA FT ILEDQSEEVAPDFVTPGGNCCNWIAVDIPSAIPLSKLNIHEPVEHSDPMLP FT SNFEFPVYEAWVEEDEEIPDELRWMLEQERKAFQPHKEEIELINLGTEDDK FT KEIKIGASLEASVKKKIIELLREYDDIFAWSYKDMPGLDHDVVEHRLPLKP FT ECPPVKQKLRRSHPDMALKIKEEVRKQIDAGFLITSEYPQWLANIVPVPKK FT DGKVRMCVDYRDLNKASPKDDFPLPHIDVLVDSTARCKVFSFMDGFSGYNQ FT IKMAPEDREKTSFITPWGAFCYLVMPFGLINAGATYQRGMTKIFHDMIHKE FT IEVYVDDMIVKSGTEEEHVEYLSKMFQRLRKYKLRLNPNKCTFGVRSGKLL FT GFIVSQKGIEVDPDKVKAIREMPAPKTEKQVRGFLGRLNYISRFISHMTAT FT CGPIFKLLRKDQGIVWTEDCQKAFDSIKGYLLEPPILVPPVEGRPLIMYLT FT VLEDSMGCVLGQQDETGKKEHTIYYLSKKFTDCESRYSMLEKTCCALAWAA FT KRLRHYMVNHTTWLISKMDPIKYIFEKPALTGRIARWQMLLSEYDIVYRTQ FT KAIKGSILADHLAHQPIEDYQPIKFDFPDEEIMYLKMKDCDEPLFGEGPDP FT DSKWGLIFDGAVNVYGNGIGAVILTPKGTHIPFTARLRFDCTNNIAEYEAC FT IMGIEEAIDLRIKNIDIYGDSALVINQIKGKWETHHDGLVPYRDYARRLLT FT FFNKVELHHIPRDENQMADALATLSSMIKVNHGNDVPLISVKFLDRPAYVF FT AAEAVFDDKPWFHDIKVFLQTQEYPPGASRKDKRTLRRLSGNFFLSGDVLY FT KRNFDSVLLRCVDRREADLLMHEIHEGSFGTHSSGYSMAKKALRAGYYWIT FT MHADCHHYAKKCHKCQIYADKIHVPPSMLNVISSPWPFSMWGIDMIGRIEP FT KASNGHRFILVAIDYFTKWVEAASYANVTKQVVVRFIKNNIICRYGVPNKI FT ITDNGTNLNNKMMKELCDDFKIEHHNSSPYRPQMNGAVEAANKNIKKIVQK FT MVVTYKDWHEMLPYALYGYRTSVRTSTGATPFSLVYGTEAILPVEVEIPSL FT RVLMEAELSEAEWYQNRYDQLNLIEEKRMAALCHGQLYQTRMKQAFDKKVR FT PREFKEGDLVVKSIKSFQPDPRGKWTPNYEGPYVVKRAFSGGALILTTMDG FT EDLPRPVNSDAVKKYFV" XX SQ Sequence 11878 BP; 3393 A; 2357 C; 2629 G; 3499 T; 0 other; gaaatggcga cttcactggg gacttaaatt ctacgcgggt taaacccacc ttatttttat 60 tttattttgt gctgtactat ttgtttatgc tttgtgcata tttgcttgca taccttgtta 120 cgtgagtggt gagataagtc ctacacccgg gcttgagtga agcataagat aggacggagt 180 acgatcatag tgccatacca ggagcggtcc tgcgatatgt gtacacgtga tgtaactcca 240 ctcaacatag gtctttcaaa agtaataata tgtcgtcatg agcagtcgtg attggcgtta 300 ttatttttga agtccgctaa acgttgagga cctttagatc acccttaacc catcttggct 360 ttttttttag gacgtagtgc ggtggctaaa ccaagagcag tcttgacttt ggtcgacacg 420 cgatactaca ctcaaactag acttacttat ggatgttatt ggactaggag cggtcctata 480 caccgatatg ttcataaggg aagttgtaat ttgggaactt ggtagaaccc gtgatacagg 540 tacaatttga aaccatagtc cttaccaaat ggcgttgtca ccttttgact ccaacattgt 600 ggacttaacc tcattatgta ttctatgtac ttcagcataa gcatgcatcc atgcattcat 660 tcataaatgt attttttttc atccattaaa ttgtcgaagg acttagacaa gcattttttg 720 taaatattgt agatggattc taagacgagg agtattaaga agtacacttt caagaaaccg 780 gatttgacaa ggctaaggga gttagcatct catgtgacta atccaagaga ttttcgagaa 840 cgtcatggga gattacttga cctcctcaaa gtgaaggtcg aagatggaat tttagagact 900 ttggtgcagt tttacgaccc aatttgtcac tgcttcacgt ttcccgacta ccagttggtc 960 cccactcttg aagaatattc cttttgggtt ggcttaccag tatccgaggg agaacctttc 1020 aacggccttg aacccagccc caaaaatgca actattgcag aagcccttca cctcaaacct 1080 tctgacttgg ttcatcctca cttcaccatt aaaaacaacc tccaaggctt aaccgccaag 1140 ttcctctacc aaaaagcctc cgactttgtg aaagccaaaa agaccaatgc ctttgaatct 1200 attttcacct tactcatata cggccttttc ttgtttccca acatggacaa ctttgtcgac 1260 ctcaacgcaa ttaagatttt tctagccaag aacccagttc ccactttact tgcaaacact 1320 taccattcta ttcaccacag aaatatccga gagggtggac tgattgtttg ttgtgcaccc 1380 ctgctataca gatggtatgc ttcacattta actaagtctg tcttctccaa agagaactcc 1440 gggaaagctt cttggtctga gaggatcatg cctctcactc cagctgacat tgtgtgggtc 1500 catgcgggta ctaacaccgc aggaattatt ggcagttgtg gagagtttga aaatgtgccc 1560 cttatcggta cgtgtggagg aattacttac aaccctactc ttgctatgcg tcagtacgga 1620 taccctatga aggggagacc tgacagtctt tctctgtcca atgagtttta tcttaacaaa 1680 aatgatcata caaatttgag gatgcggttt gtgcaagctt ggcactctat tcgtaagttt 1740 gatggaatcc aattgggaag aaaacagagc tttgcacatg aatcgtatac acagtgggtg 1800 attgatagag ctacagcttt tggtatgcct tataccttgc caagattctt atcttcgacc 1860 gttccagaaa tacctttacc tctactccca caaaccaagg aagagtacca agagcgttta 1920 gccgaagcgg aacgtgagat acatatgtgg aaaagggagt gtcagaagaa ggataaggat 1980 tatgagactg taatgggctt gctggagcaa gaagcctatg atagccgaca gaaagatgtg 2040 ataatcgcca agctgaatga aagaatcaag gagaaggatg ccgcccttga tcgaattccc 2100 gggcgaaaga agaagcgtat ggatctcttt gatggtccac attctgattt tgaggattag 2160 tccgcttcag gagcttgaga gtctcagttt gtttttcatg tctttttctt agtttttctt 2220 tatgtatttt ggagtctatc ccttgactca gtttgttaaa agggaattat ttgtgtttta 2280 ctttaaagtc tatctcttgg ctttgttgtt agaaagggaa ttatcttgtg atcaactttg 2340 ttttttagtg aattgtttag gttgatatgt ttacaaaatt gcttctatag gtccttcgat 2400 aaaaaaaata tatatataaa aattgcatat tctggcatat agcatatcat gcatcatatt 2460 gcattcataa aaagtgtcaa agccaagtct catactttcc tcatttctgc ctcaggagaa 2520 aagcaaaggt ggcccggcgt attcagtaca aacctacccg tgttcatcat acccgagcat 2580 acatcaagaa gaaaatggca gctgctgaac aaacgaacaa tgatcttagg gaggaggtta 2640 gtagcctcaa agaaggtatg gaaaagataa ctgcaatgat gatggacatg atggccgcac 2700 aggcacaagc ctctcaagca aaaattgttc agactgttca gggagatgtt gaagtctctc 2760 agcctgcggg ttctactgca actattagta ctacacagcc cttggtgaat cagttttcct 2820 ctggtgatat gacaaatatg tatagttcag ggtttcgtcc tactggctct cttggttctt 2880 ctattcctcc tcagtatcat atgccgccag gctatccgtg gggcatgcca ctcgcaaata 2940 atgaaggtgt tcgtcataat gcaccagaaa tgcagttccc ttttggacat caacaaacac 3000 cgttttatca gtccggccag ccttttcctc aggccactat gacctatgct ggacccctcg 3060 ttcatgctgg tcatcaagaa gtagaacagg tttatcactc taatagtgtg gctggtgatg 3120 atagggtagg aaacttggaa gaaaggtttg aggcggtgca caaagagtta aagactatcc 3180 gtggtaaaga aatgttcagt cagaatgtga atgacctctg cttggttcca gatgtggtga 3240 tacctcataa gtttaaaatg ccgatctttg aaaagtacac aggggatact tgccctgaga 3300 tgcacttagt cacatatgtc aggaagatgg tagctcacaa gaataatgag cctctgctta 3360 ttcactgttt ccaggacagt ttgactggtc ccgcacacac atggtatatg aatttgaagg 3420 gcatcacaac ctttgaggaa ttggccaatg ctttcatcca acagtacaag tataactctt 3480 atctggcacc taaccggaaa gaactgcaat ctatgactca gggtgataag gaatctttca 3540 aggaatacgc tcaacgcttc attcaaaagt ctgctcaaat ccgtccgcct ctggatgaaa 3600 gagaagtgtc cgatctattc tatgagactc tgagcccttt ctactcagag aagatgcttg 3660 gttgtgcctc acaaaagttt actgatatgg tagatatggg tgtgcgcatt gaagattggg 3720 tccgtaaggg acgtgtgagt aaagatggtg cttcttcagg tggttcatct aatggtaata 3780 ggaagttcgg aaatgggtcc tcaaagaaga acgctcaaga ggttggtatg gtggcccatg 3840 gcggatccca gcctatatac cctagctacc cgtatgttgc taacattcca ccacctaccc 3900 taactccaca aaatccaaac tatcaactac aaaggcctca agcaccccat ccatattatc 3960 caccactata tcaaccacaa ccttatcaac cccaaccgtt ttatcaacaa ccatactatc 4020 ccccaccacc tcaacaacaa cagcctcgcc ctcgagctca acaacaacat actcgccctc 4080 aaagaaacca atttccccct atccccatga catatgaagc cttgttacct tccttgcttg 4140 cccgaggtct tgttcagacc ctaccacctc ctcgtgtgca gaacccttta cccccttggt 4200 tccgtgctga tcgaaattgt gccttccatc aaggggcacc aggacacgac attgaacact 4260 gttaccccct taaagaggca gttcaaaagt tgattcacaa caaagattta tccttcactg 4320 acccgaaccc tgctgctcca gaccatcctc tgccacccca tgggcctact gttaacatgg 4380 ttgaagatta tcaagaaggg ggtcttgtca ctcgctctca ggatatcaaa actccgttgg 4440 ttccattaca tgtgaagatg tgtgaggcag ctatgtttag ccataatcat aatagttgtg 4500 aggtatgttc tgtggatccc cgcggttgcg cgcaagttca agatgatgtg caagggctaa 4560 tggatcggga agagctggtt gtcacaaggg aagagaagag tgtctgtgtt gtaatccctg 4620 tgttcaagga tagtgcgaaa ccaattgatg gtgttactcc ggtgttcaag gacagttcca 4680 agccagctgt cgctcctctg gtaatttgtg tgccgagacc caagccgttt ttctctcaaa 4740 acgccatgcc gtataattat gaacctacaa gcatagagaa tggtaaagaa atatcctgga 4800 gtccctcaac ttccgtgagt aacattgcag agaatagtca aattctgaga agtggacgca 4860 tccttccggc agttgtgcaa gcaaagaaga aagctccggt gatagagtca gtgccaatac 4920 cagatcctag caagggtaag agtatggttc aacctggtga aactgataat gatgagattt 4980 tgaagctgat caagaaaagt gattataaga tagtggatca gttattgcag actccatcaa 5040 agatttctat catgtcacta ttgacaagct ctgatgctca tagggatgca ttgatgaaag 5100 tgttgaatca agcctacgta gaccatgatg tgactttggg tcaatttggg agcattgttg 5160 gaaatgtgac ggcatgcaac aatctgagtt tcagtgatga agacctccca gtggagggga 5220 agaaccataa tatggccttg catatctctg ttatgtgcaa aacagattct ttgtccaatg 5280 tcttgataga taccggttct tccctcaatg tgatggcaaa gacgaccttt gataaattga 5340 catattcaga tggattcatt aggcctagtt gtgtatcagt aagggcattt gatggatcca 5400 ggaagacggt atggggagaa gtagatttac ctatcactgt tgggccccaa gagtttaaag 5460 ttacattcca gataatggat attcaagctt cctacagctg tttacttggt agaccgtgga 5520 ttcatgaagc cggggcagta acatccaccc ttcatcaaaa gttaaagttt gtgagtcgtg 5580 gaaaacttgt tacagtaagt ggggaatcag cttttttggt tagccatttg tcgtcttttt 5640 ccttcattgg tggtgaaagt ccggatggaa cgtcattcca agggctttcg gtcgaaagcg 5700 gtactacaag aggtgaaaca tgcatggcct ctctaaagga tgctcagaga gtaattcaag 5760 aaggaaaagc agaaggttgg gggaagttag tacagttgcc tgagaacaag cgcaaggaag 5820 gtctgggttt ctccagcaat aatcaagtga tgttcgaccc aactagaggt acttttcaca 5880 gtgctggatt cattaatgcg ccacctgaaa ctaatgcaat cttggaagat caatcagaag 5940 aggtggcacc tgactttgtg actccgggtg gaaactgctg caattggatt gctgttgaca 6000 tcccttctgc gatacctctt tctaagtaat gtgtttgtct tttttgttgc ttttttaaga 6060 aaactccttt cgtcctaccc cagacgaagg tgaaatcttg tagggtttgt ttttgctttg 6120 agtttatttt cagtattaat gaaaattgtc gtttctgtca cggccgttat tttattttag 6180 tgctttttct ggaaaaatgg taatacaaaa aaccaaaaaa cttgttctct ttttctttta 6240 aaaaaaaaat atcaatttca aaggtctgca ttcactcttt tgctaaaaaa tcaatcatga 6300 atcatatgca gactgaacat acatgagccc gttgaacata gtgaccctat gctgccttcc 6360 aactttgagt tcccagttta cgaagcttgg gtagaagagg atgaagagat tcccgatgag 6420 ctccgatgga tgttagagca agaaagaaaa gcctttcagc ctcacaagga agaaatagag 6480 ttaatcaacc tgggcactga ggatgataaa aaagaaatta agattggagc gtcgttggag 6540 gcgtctgtca agaaaaagat aattgagctt ctcagagagt atgatgatat atttgcatgg 6600 tcctacaaag acatgccggg gttagaccat gatgttgtgg aacaccgttt gcctttgaag 6660 cccgagtgtc ctccagtcaa gcagaagtta agaagatctc atccagatat ggctctcaag 6720 atcaaagagg aagtgcgaaa gcaaattgat gcaggtttct tgattacctc tgaatatcct 6780 caatggttgg ccaacatagt gcccgttcca aagaaagatg gtaaggtcag aatgtgtgtt 6840 gactatcggg atttgaacaa agctagtccg aaggatgatt tccctttacc tcacattgat 6900 gtattggttg atagtactgc tagatgcaag gtattctcct tcatggatgg attctccggg 6960 tataaccaga tcaagatggc tccagaagat agagaaaaga cgtcgttcat cacgccttgg 7020 ggcgcgttct gctacttagt aatgccgttt gggttgataa atgctggtgc cacttaccag 7080 agaggcatga ctaaaatatt ccatgatatg atacataaag agattgaagt gtatgtggat 7140 gacatgatcg tcaaatcagg cactgaagaa gaacatgttg agtatttgtc gaagatgttt 7200 caacggttga gaaagtacaa actccgtttg aatcctaaca agtgtacctt cggtgttaga 7260 tccggcaagc tcttgggttt tattgtcagc cagaagggta ttgaagtgga tcccgacaaa 7320 gtcaaagcta tcagggaaat gcctgctcca aagacagaga aacaagttag aggttttcta 7380 ggaagactga actacatctc cagattcatc tctcatatga ctgccacatg tgggccgata 7440 ttcaagttac tccgtaaaga tcaagggatt gtttggacgg aagattgcca gaaagctttt 7500 gacagcatca aagggtattt gttagaacct ccgattcttg tccctccggt cgaagggagg 7560 cctttgatca tgtatttgac tgtgttagaa gattctatgg gctgtgtgtt gggtcaacaa 7620 gacgagactg gaaagaaaga gcacaccatt tactacttga gtaagaagtt tactgattgt 7680 gagtcccgat attctatgct tgagaaaacc tgttgcgctt tggcatgggc tgctaagcgt 7740 cttcgtcact atatggttaa tcacactact tggttgatat ccaaaatgga tccgatcaag 7800 tacatttttg agaagccggc tttaacagga agaattgctc gttggcagat gttattgtcc 7860 gagtatgaca ttgtctaccg cactcagaaa gccatcaaag gtagtattct tgctgaccat 7920 ttagctcatc aaccaattga agattatcag cctatcaagt ttgatttccc agatgaagag 7980 atcatgtatt tgaagatgaa agattgtgac gaaccattgt ttggtgaagg tcctgatcca 8040 gactctaagt ggggtttgat atttgatggg gccgttaatg tctatggtaa tggaataggg 8100 gcggttatcc ttactccaaa gggtactcac attcctttca ctgcaagact ccggtttgat 8160 tgcacgaaca acattgcaga atatgaagct tgcatcatgg gtattgaaga agccattgac 8220 ttgaggatca aaaatattga catatatgga gattcagctc ttgtgattaa ccagatcaaa 8280 ggaaaatggg aaactcacca tgatggtttg gtaccttaca gagactatgc aagacgtttg 8340 ttgactttct tcaacaaggt ggaactgcac cacattcctc gggatgagaa tcaaatggca 8400 gatgccctag ctactttatc ttcaatgatc aaagtgaatc atggcaatga cgtgccgctg 8460 atcagtgtca aattccttga taggcctgct tatgtgtttg cagccgaagc agttttcgat 8520 gataagccgt ggtttcatga tattaaggtg tttcttcaaa ctcaagagta ccctcctggg 8580 gcatcccgta aagataagag aactttaaga agattgtctg gtaacttctt tctaagtgga 8640 gatgttttgt acaaaaggaa ctttgattca gttttgctcc gatgtgtgga ccgacgagaa 8700 gcagatttat taatgcatga gatacatgaa ggctcatttg ggacccattc tagtggatat 8760 tcaatggcta agaaagcatt gagggcaggc tactactgga taacaatgca tgctgattgc 8820 catcactatg ccaagaaatg tcacaagtgc cagatttatg cagataagat tcatgtacca 8880 ccgtctatgc tcaacgttat ctcgtctccg tggccgttct ctatgtgggg cattgatatg 8940 attggtcgga tcgaaccaaa agcttccaat ggacatcgtt tcatactagt ggccattgac 9000 tacttcacca agtgggttga agcggcttct tatgccaatg tgaccaagca ggtggtggtc 9060 cggtttatca agaacaatat catatgtcgc tatggtgtcc ctaacaagat tatcacggat 9120 aatggtacga atttgaacaa taagatgatg aaggaattat gtgatgattt caagattgag 9180 catcataact cttctcctta tagaccccag atgaatggtg cggtcgaagc tgcaaacaag 9240 aatatcaaga aaattgtgca gaagatggtg gtcacctata aggactggca tgagatgtta 9300 ccctatgctt tgtatggtta ccgtacttca gtgcgtactt caacaggggc aacccctttt 9360 tccttggtgt atggtacgga agcgatactt cctgtagaag ttgaaatccc gtctttgaga 9420 gtcttgatgg aagctgagtt gtcagaggct gaatggtatc agaataggta cgatcagttg 9480 aatttgattg aggagaagcg catggctgct ttgtgtcacg gacaactata tcagacaagg 9540 atgaaacaag catttgataa gaaggttcgt ccccgtgaat ttaaagaagg agacctagta 9600 gtcaagagta tcaagtcttt tcaaccagac cctaggggca agtggacacc taattacgaa 9660 ggtccctatg tagtgaagag agctttctct ggtggtgctt taattcttac aaccatggat 9720 ggagaggatt tacctcgtcc tgtgaattct gatgcagtca agaaatactt tgtctaaatg 9780 tttataaaag aacagctcgg taggttgaaa acccgaaagg gcggcctaaa ccaaaaatga 9840 gcgtctcggt ggactgaaaa cccgaaaggg cggtccaggc aaaaattaga gacaaaaaaa 9900 aaaaaaaaaa aaaaaaatat atatatatat atatatcctg atagattgaa aacccgcaag 9960 ggcgatctat gcaaaattta aggattatga caagtaactg catcagatga agcatcactc 10020 acttggggca cctaagccgt caaaagatct tcgatattga agcaatcgaa atagtggaat 10080 ccaaagttgg taggaagtat gatggttatt gtgttcaatg taccttcccc atattaatta 10140 ccatgttcca aactttgtga tctgtggtgc catacctttg gttggttacc atttatttta 10200 aatcaatttg agcccgtgcc ttttatttga agttcctatt tattctatgt gcaagttctc 10260 ttccattttt actgttaata cttgaggtaa aaactttgaa aattcctttt aaaaaaaatc 10320 tttatgtttt cttttggaaa aagcaaaatt gacaaacatt ttatctttaa ttcacgtatc 10380 gtagaaacat gtgtcaatgt tcgattcaaa agcacgggta tggtcattgc taaaaaaata 10440 taaaaaaaaa aaaaaaaaaa aaaaaaagaa aaaaaatgaa ctcgctaagt tgaaaacccg 10500 aaagggcggc ttaggcaaaa aagagcatcc cggtggattg aaaacccgaa agggcagtcc 10560 aggcaaaagt tagggatttc aaagtatacc aaaggaaaag caatgactat ttgaagcatg 10620 agcttgtgaa agtactccag ttcaatccag aaatggcgac ttcgtctagt ggtctgacta 10680 ttggttcatt gccccatcag tgttttgctt aaagggttgt gccctgatga agattaccgg 10740 gttgtttgta ctatggtacc gggccatttc cgttctggac ctgcccaatc acccctcaaa 10800 aatcttgcca ttgtattgtc atatgtgtct catacatatt cattcattca tgcatagata 10860 gcacgcatac aaatatcatt catgtatggt tgcattatta ccaggtgtct tatttcagtg 10920 tgtcccgtaa aaagtatctt ccccaatgtg tttaattcaa ggttgtcacc agttaaagct 10980 tatttcaagt ggcaggtccc tccgagcaat ctttgtgtca attcagttta gctccccagt 11040 aacttttgta agctatcctc gtactggtag cagttgactt ttattatgtt ggtcgttacc 11100 cgagttgagg taactgacgg tatttatttt tcgtatgttg gtcgttatcc gagttgaggt 11160 aactgacggt atttattttt cgtatgttgg tcgttacccg tgttgaggta actgacggta 11220 tttcctttcc ttttcgtaag ttggtcgtta tccgaattga ggtaactgac ggtttttcct 11280 tttcttatcg tatgttggtc gttacccgag ttggggtaac tgacggtatt tccttttcat 11340 aagttggtcg ttatccgagt tgaggtaact gacggtattt atttttcgta tttcggtcgt 11400 tacccgtgtt gaggtaactg acggtatttc cttttcataa gttggtcgtt atccgagttg 11460 aggtaactga cggtatttat ttttcgtatt tcggtcgtta cccgtgttga ggtaactgac 11520 ggtatttcct ttttgtaagt tggtcgttac ccgtgttgag gtaatcgaca gtattttctt 11580 ccgtatgtcg gtctttacct tagtaagggt aatagacaat ttttctctcc gcataatggt 11640 aaatggtttt cctccccaat aatatttatc tgtatgtccc ccagtcagta ggtgttcact 11700 atccttgcat tcgtaagtgc atcgtaagta ttcatattat tacagtcatg agcatggcat 11760 tcttagcatt tcaattggtc aaaattagcg tacttaatat ttaagtctct cccacccatg 11820 gattctaaag ttgatatttg taaatccctg tgacggagaa acttaaatag gggcatct 11878 // ID Copia-100_Mad-I repbase; DNA; EDCOT; 6104 BP. XX AC . XX DT 04-NOV-2010 (Rel. 15.11, Created) DT 04-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Copia-100_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6104 RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-6104 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1985-1985 (2010). XX DR [2] (Consensus) XX FH Key Location/Qualifiers FT CDS 2231..4174 FT /product="Copia-100_Mad-I_1p" FT /translation="MPKIIPTIILDKRGLKGQRFLAWYRHIENVSKVKDIL FT YVLKQSPPHVPPTKLASKEECQNYVRHYEDDLQAKCLILTSLSEELMKLHK FT HMDTSCAMVESLHKMHDIETSNVRFSNVCSLMNAKMAKGTSVHKHGQKMEK FT IFKDLKSLGTSIDGKMAQDFFLASLSDDFTKFIVNYKVNRFDHXLNEMIDM FT CCKFEKGFKRDSGSENAITRKRLHKKKAKKSKGTCFHCGKDERWKKKYRVR FT IASLMTRTFEETISVIESAFTVSSNSWIFDSGASQHICNTXQGLAGSRSLR FT NGEMVVRVGNGTKISAKAIGTYMLNLPSGEVLELKNCLYFPSCIKNLISIS FT KLLRDGHSVLFDKMSCTLYLNGRIISHGNMIEGLFHLETNSGMHCIESGNT FT SKPKRAREEVNQEKMWHLKLGHVNLDKIRKMSKDGYIRPLGNDQMGTCECC FT LKGKMTKSPFTGKGERATEILGLIHTDVCGPMSTTSRGGFSYYITFTDDHS FT RFGYVYLMKYKSESFERFKEFKNEVEKQTGKQIKTLRSDRGGEYLSNEFLD FT YLKECGIISQWTPPGTPQLNGVSERRNRTLMNMVRSMMSSADLPVTFWGYA FT LYTAAYLLNRVPSKSVPQTPYEIWHGRKPSLKHIKIWGCEAYVKKLEAEA" FT CDS 4086..6086 FT /product="Copia-100_Mad-I_2p" FT /translation="MRYGMEESQVLNILRFGVVKHMSRSLKLKLEARSVRC FT YFVGYPKETMGYEFYHPDDQKVFVARTAXFLEDEFVLKGTSKIESMEINEI FT NDEPQTSTRQVDNPVPEPLAPRRSERVSKPPKRYGLDNDFDELYLLGDNET FT KEDPRDYTEAMSDIDSKRWQEAMKSEMDSMYQNQVWTLVDPPEGIVPVGNK FT WVFKRKIGVDGNVETYKARLVAKGYRQREGIDYEETFSPVAMIKSIRILLA FT IAAYHDYEIWQMDVKTAFLNGYLEEELYMTQPEGFVSKSEKTKVCKLQRSI FT YGLKQASRSWNIRFDTEIKTFGFTQNEDDNCVYQKVVGDAVVFLVLYVDDI FT LLFGNDTAVLSSVKVWLSKTFHMKDLGDASYVLGIKLYRDRSRKLIGLSQS FT MYIDKVLSRFQMEQSKKGFLPVRHGIHLSKSMEPKTPEEIRQMSGIPYASA FT IGSLMYAMICTRPDIAYAVSITSRYQSNPGSEHWAAVKTVLKYLRRTKDMF FT LVYGGATELRVEAYTDADFQSDVDDRSSNSGYVFTLNGGAVSWKSKKQSVI FT ADSTTEAEYVAAAEAGKEAFWMKKFITELGVVPTITSPVTLYCDNSGAIAQ FT AKEPRAHQKNKHFDRRFNIIRRYAAEGKVNILKVASADNVADPLTKPMSQI FT QLDRHMEKMGIRYMGRWL" XX SQ Sequence 6104 BP; 1893 A; 1080 C; 1333 G; 1794 T; 4 other; agtggtatca gagcctaggc ctagtttatg gtgaatcctt ttgggttttg tgattttcat 60 gatttgtgat ttaaatgttg taaatgttac aagctttgtt cttgcttttg aatatataaa 120 ttttgctaga aaatttagca tctcaaatgt tgtagatgta tttcatttaa gcatgaatat 180 tggaactaaa atttggtgcc atgtattttg ggaaattcgg ccaaatccaa agggtgattt 240 tttgggttca tgtttgtctt gttaaaatgg ttttaaggtg acttttggaa cccctaagta 300 ccctaggata ttagccctct tttgagtggt gaaaaattga gttttggtga gtgaaaacat 360 tcatggagct attatgagtt ttcatggtgt tcttcaatgt tcttgaagtt cttgccaaga 420 acaaaaaggt ttgaagtttt gattcaaaag ttttatgttt ttcataaagt tttggtttat 480 ttttgatggg tgatggttat tggtgaagca ttaatattgg ctttaatgtt tgtcaaaact 540 cattaatgtt ttacaaaaca ttttcttaca aaccatcaat ttcaccttta cctcacccac 600 caaaatcaac ttgcataaaa ccctttcaca ctcttcacca ctccaaaacc ggccaccccc 660 tagtgggggt acttttgggg ccttttatgc aattacataa agttttgata cttttgtgta 720 tttgcacttt ggcccaaaag tttacgtttt tacgttaagg cccaaaaact ctaaaggaca 780 aattgttttg atcctttaat gatgttttta cattattaaa attttgggat ctagttgtaa 840 ttacatgaag ttgtggactt ttgtgttttt acaaagtgac cccaaaagtt tttgtatttg 900 cattatggcc caattgttgt ggtcatagtt tccttttggc ccaaataaaa tgagaacaaa 960 attgttttgt ctctttaatg agaattggat tttcatttca tttagttcca tttaaatcaa 1020 ttctatggat ccaaaaacca attgtttaaa gttgctttct tagttaatgt gattgattaa 1080 gaaaagggtg attatgaacc aaaggcctcg ataattgagc tatgtgattg gccgctttac 1140 attatgaatg tttgggttta gtagtgtaga tttgaatgta atttgattaa ttcaatttgt 1200 tgtaaatgga cataagtcca tcatttgtgt tgtaaaaggg cataagccct tcttattatt 1260 tcatgtattc ctttttgttt atatgtatgc aaaatggaat agttgggtcc aacgcccaat 1320 aggaaataac ggtttaattg gattaaacgc gtaactaaaa tcaacaacta tctaccttaa 1380 acccaaggtc caacacaagg ctcgtgttgg atcaaatcaa acggttcata atcatcctaa 1440 aacctaatat gactatatag tccatatgag gatgcaatgc attcgttagt agttccatat 1500 agtctcgctt gtttcatcga aatagtggga gtattataaa ctactaaatt catattaact 1560 tggaccaatg gttgtgatag gcccaagttc ttttaataag attaaaatga ttttgatgta 1620 gcccaaaact actccctcaa caaaacgaat attaagttga taagcgagag atgttttgaa 1680 catctcttcg taggccttcc accgtggtgg gctccaatcg tttgtgactc atgcaccggc 1740 ttcaccctat catgggggag ttcaaagtat gtgcttacat ccaggaggag tccataaaca 1800 tatgatgagg tgagtgtagg caacgaggat ggccgacatc gtatcatcgt gaggctattc 1860 ttgaacccct tcacaaacta agcatggtgg gaataactta aactaagtgc aatggagccg 1920 acatcgtatc atcgtgaggc aacattctct agaggccaaa cggatgggta attacaaaag 1980 gttgtaaatg aataawgcgt tattctctca tcattatttt tgctaaccaa catcgtatca 2040 tcgtgaggtg ggcttggtaa tggtgagtct cccatacccc gctaagagtt caatataact 2100 ctcgaattct attgagggat gtggaatttg ccaaaaatag tgggtggtac tatttgattc 2160 aaagacccaa tcaaatagtt ttaaaacaaa caatctaata cgatttctgt tatgttatgt 2220 agttaacgac atgcctaaaa ttatacccac cattatactt gacaaaaggg gccttaaggg 2280 ccaacgtttc cttgcttggt atcgccacat tgagaatgtc tcaaaggtga aagacatatt 2340 gtatgtgctt aagcaatccc ctcctcatgt acctcctacg aaactagctt caaaggagga 2400 gtgtcaaaat tatgttagac actatgagga tgacttacaa gccaaatgct taatcctcac 2460 ttcacttagt gaggagctta tgaagctaca taagcacatg gacacttctt gtgccatggt 2520 tgaaagtttg cataagatgc atgacattga gactagtaat gtacgattct caaatgtttg 2580 tagtctaatg aatgccaaaa tggcaaaggg gacatcggtc cataaacatg gacaaaagat 2640 ggaaaagata tttaaagatc ttaaaagttt aggaacttcc atcgatggga aaatggccca 2700 agactttttc cttgcatctc tctcggatga tttcactaag tttattgtaa actataaagt 2760 gaatagattc gatcatkctt tgaacgagat gattgacatg tgctgtaaat ttgaaaaagg 2820 tttcaaaagg gacagtggga gtgagaatgc aatcacaagg aaaaggttgc ataagaagaa 2880 ggcaaagaaa tccaaaggaa catgctttca ttgtggaaag gatgaacgtt ggaagaagaa 2940 atacagggtg cgcattgcga gccttatgac acgaactttt gaagagacta tttctgtcat 3000 agagagtgct tttacagtga gctccaattc ctggatattt gattcaggcg ctagtcaaca 3060 tatctgcaat acgwtgcagg gactagcagg gagcaggtca ctgcgcaatg gggagatggt 3120 tgtgcgagtt gggaacggca ctaaaatctc tgcaaaagca ataggcacct acatgcttaa 3180 cctaccctct ggggaagtcc tggaacttaa aaattgttta tattttcctt catgtataaa 3240 gaatttgatt tccatctcta agcttttacg agatgggcac tcagtattgt ttgacaaaat 3300 gagttgcact ttatacttga acggtcgtat tatctctcat ggtaatatga tagagggact 3360 ttttcaccta gagacgaata gtgggatgca ctgtattgaa agcgggaata cctcaaaacc 3420 caaaagggct agagaagaag ttaaccaaga aaagatgtgg catcttaaac ttggacatgt 3480 gaaccttgat aagattcgca agatgtcgaa agacggatat atccgcccat taggtaatga 3540 ccagatgggt acttgtgaat gttgcttgaa agggaagatg accaaatctc catttactgg 3600 aaaaggagag cgtgccactg aaattctagg gttaatccac actgacgtat gtggacctat 3660 gtctactacg tcgagaggag gcttctccta ctatatcaca ttcaccgacg atcactctcg 3720 gtttggctat gtgtatctta tgaagtacaa gtcagaatcc tttgaaaggt tcaaagaatt 3780 caagaatgaa gttgagaagc aaactgggaa acagataaag accctaagat cggatcgagg 3840 gggtgaatat ctgagtaacg agttcctaga ttatctcaaa gagtgtggaa taatatcaca 3900 gtggactcca ccgggaactc cacaacttaa tggagtttct gaaaggagaa atcgaacctt 3960 gatgaacatg gttcgttcta tgatgagttc cgctgatcta ccagtaacat tctggggata 4020 cgctctatat acagcagctt acttgcttaa tagagtacct tccaagtcag ttccacaaac 4080 gccctatgag atatggcatg gaagaaagcc aagtcttaaa catattaaga tttggggttg 4140 tgaagcatat gtcaagaagc ttgaagctga agcttgaagc gagatcagtt agatgctatt 4200 ttgtggggta tcctaaagaa actatgggat atgagttcta ccaccctgac gaccagaaag 4260 tctttgtcgc cagaactgct awgtttctag aggacgaatt cgttctcaaa ggaactagca 4320 agatagaatc gatggaaatt aatgagatta atgatgaacc acaaacaagc actcgacaag 4380 ttgacaaccc tgttcctgaa cccctagctc cacgtagatc tgaacgggtt agtaagccac 4440 ctaagaggta tggcttagac aatgactttg atgaattgta ccttctaggt gacaatgaaa 4500 caaaggagga ccctagagac tacactgaag caatgtccga cattgattca aagagatggc 4560 aagaggccat gaaatccgag atggattcca tgtatcaaaa tcaggtctgg actcttgtag 4620 accctccaga aggtattgta cctgttggaa acaaatgggt cttcaagagg aagataggcg 4680 ttgatgggaa cgtggagact tataaggcta gactagtagc caagggttac aggcaaagag 4740 aagggattga ctatgaagaa accttctctc ctgtagccat gattaagtcc attcggattt 4800 tgcttgctat agctgcgtac catgattatg agatatggca aatggacgtg aagacggcct 4860 ttctgaacgg ctacctagag gaagagctct atatgactca acccgaaggt ttcgtgtcca 4920 agtctgaaaa gactaaggta tgcaagcttc aaaggtccat ttatggactt aagcaagcct 4980 ccaggagctg gaacattcgt ttcgacactg aaatcaaaac gtttggtttt actcaaaacg 5040 aagacgacaa ttgtgtttat caaaaggtcg ttggggatgc agttgtattc ctagtgttat 5100 atgtagatga catattacta ttcgggaatg acactgcagt actttcttct gtaaaagtgt 5160 ggttgtccaa aaccttccac atgaaagatt tgggagatgc atcttatgta cttgggataa 5220 agctctatcg tgatagatcc agaaaattaa ttggattatc ccaatctatg tacattgata 5280 aggtgctaag taggttccag atggaacaat ctaagaaagg ttttcttcct gttagacatg 5340 gaattcacct ttctaagtcc atggaaccta agactcctga agagatacgg caaatgagtg 5400 gtattcctta tgcttccgcc ataggaagtc tcatgtatgc catgatatgc acaaggcctg 5460 atatcgcata tgctgtgagc attactagtc gatatcaatc taacccagga tcagaacact 5520 gggcagctgt caagacggtc cttaagtact taagaagaac taaggacatg ttcctcgtgt 5580 atggaggagc aacagagttg cgagtggaag cctatacaga cgcagatttc caatctgacg 5640 tcgatgatag aagttccaac tccggatatg tattcactct gaatggtggg gctgtcagtt 5700 ggaaaagcaa gaaacaaagt gtaattgctg attccacgac agaggctgaa tatgtcgctg 5760 cagctgaagc cggcaaagaa gcgttctgga tgaagaagtt catcactgaa cttggagtgg 5820 ttccaaccat tacatcacca gtaactttgt actgtgataa tagtggggcg atagctcaag 5880 ccaaggaacc cagggcacat caaaagaaca agcattttga caggcgcttt aatatcatta 5940 gaagatatgc tgccgagggg aaagtcaaca tcctcaaagt tgcctcagcc gataacgtag 6000 cagatccact gacaaagcca atgtctcaaa tccagcttga ccgtcatatg gaaaagatgg 6060 gtattagata catgggaagg tggctttgag tgcaagtggg agat 6104 // ID Copia-44_Mad-I repbase; DNA; EDCOT; 5044 BP. XX AC ACYM01035308; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-44_Mad-I; KW Copia-44_Mad-LTR; Copia-44_Mad_. XX NM Copia-44_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5044 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1314-1314 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01035308; Positions 8586 3543. XX CC Positions [2414-2728] - Integrase core CC 'AAAAA' target site duplication CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS 629..1567 FT /product="Copia-44_Mad-I_1p" FT /translation="MTFITATLSTTALSCVIGCTSSKQMWTNLCERFANMT FT RTNIVQLKIDLQNITKGPELIDDYLQRIKDARDKLAIVGVVISNEDIIIVA FT LRELPPEYNTIKSVIRGRENLVSLPELRSQLKAEEITLDDVPKQVPLLSAM FT VAHTSSSVYDAGGTSGTKSISLGSLFCGPSNSSVSYSPVFNSYQQMPSLQP FT MPQLQQMSFPQMPLSLPQMVMPQVPIPSPYAFVSQTGSSSYNNFRGNNFKS FT KGKWKKLFYGSNHSQQPHLYKSNGFPVSHPSSPFDHQMQSPQGFQPFLKCQ FT ICDKNGYSSINCFQQGCQICH" FT CDS 2858..4393 FT /product="Copia-44_Mad-I_2p" FT /translation="MPTSLLGIKSPFEVLYQSPPRLDHLKVFGCLCYPSVK FT PYRSDKLEQKTMECIFLGYNAKYKGYICYSVHNKKFIISRHVLFDETQFSS FT WSNISSQVFKSPGSQFSRVSSTPVVHNNTFQHPPVILIPLPHVFVPSPNAT FT VQPNNVSPSSIVPSSSTSDSPRFSKLHPDTTVSQVSKLQCVSLPSHNSHPM FT QTRSKSGIVKKKQAYNTAIHSNCDIEPTSFTAASKSPQWKKAMVEEMDALL FT QKHTWSLVPLPPNKNLVGCKWIYKIKKHLNGAIAQYKAKLVAKGFPQEAGL FT DYYETFSPVVKPTIVHLILSLAATKGWKLKQLDVKNAFLHGFLDEDVYMSQ FT PQGFIDKDHPEYVCKLERSLYGLKQAPRAWNDRFTTFLLLLGFQSSFADPS FT LFVKHDGKSIIVLLLYVDDIILTGDNDGCIQTVVSQLTREFDIKDLGILHY FT FLGLQIDYQSRGMFVHQTKYVHNLLIKTYMFHCNPCITPCHPNQKLLNHGN FT SSFSNPTLYRSIVGAL" XX SQ Sequence 5044 BP; 1346 A; 1055 C; 921 G; 1722 T; 0 other; tggtatcttc gcctctcatg gttaacaccg gtggtcgtcg gtcctttgct tccgttcttg 60 ggtcatcttt ctggtaattg tagtcgccgt cgccgttcga gtttctgtgc aattgacgga 120 gttgtttggt tgtttggtcg ccgtcgctgt tcgttcgtca atcctagagt ttgggtgctt 180 gttgattctt gcagtttcgt cgattcttta gaggtgatat ctttcgtctt acttgtttct 240 tggagatttt gtcgtgaatt ttctaattgc tttagtggtt ggcacattct ttgtttcgtg 300 aattgttgat ttcttgcgct tatctctggc ctattcaatt tgtttgtgaa ttggtaaaca 360 tggtgacctc tgttcaacta gctcttacac aatcacctat ttcttcgtta attcctagtg 420 tgggaaatac tgttacggtg aaacttaatg attcgaatta tgtaacttgg aaatttcaac 480 tcgaattact actggatggc aatggaattt taggatttat tgatggttct ataccctgtc 540 ttatcctgag tctgaaactg gaactgtggt gaatgatatt gttatgtctg atgcatttaa 600 gatctagaaa atccatgata aagccttgat gacctttatt actgctactt tgtctactac 660 tgctctatca tgtgttattg ggtgtacaag ctccaaacaa atgtggacaa atctgtgtga 720 gagatttgct aatatgacca gaaccaatat tgtgcaactg aagattgatc ttcaaaacat 780 cacgaaaggt cctgagttaa ttgatgatta tctgcaacgt attaaggatg ctagagataa 840 attagctatt gttggtgttg tcatttctaa tgaggatatt atcattgttg cgttacgtga 900 acttcctcct gagtataata caatcaagtc tgtcattcgt ggcagagaga atcttgtctc 960 tcttccagaa ctacggtctc aactgaaagc tgaagaaata actttggatg atgttccaaa 1020 acaagtacct ctactgtctg ctatggttgc tcatacctcc agttctgtat atgatgctgg 1080 tggtacttct ggtaccaagt ctatctctct aggctctctt ttttgtggtc cttccaattc 1140 ttcagtttca tattctccag tatttaactc atatcagcag atgccatcac ttcagccgat 1200 gccacaactt caacaaatgt catttcctca aatgccatta tctttgcccc aaatggtaat 1260 gcctcaggtg cctataccga gtccatatgc atttgtgtct caaactggct caagtagcta 1320 taacaatttt aggggaaaca attttaaatc taagggaaaa tggaagaaat tgttctatgg 1380 tagcaatcat tctcagcaac cacatttgta taagagtaat ggttttcctg tttcacatcc 1440 gtcttctcca tttgatcatc aaatgcagtc tcctcagggg tttcaaccat ttctaaaatg 1500 tcaaatttgt gataagaatg gttattcatc gattaattgc tttcaacaag gatgtcagat 1560 ttgtcattga gtgaggcaca ctgctgccac ttgttttgat agaaaccagc agaatataca 1620 aggctattca ctgcatcccc aacagtttca acaggctaca cagggttact catcctctgc 1680 acattgttat cctcataccc agaattctgg aatgtcttca gttcaatttt agaatctttc 1740 tatgatgcag catcctctgt atgcttcaca tggggtgcct cctccatctc attcacctat 1800 tgctatgaat gctcgaacta ccatcagtca cacagcacct ccacatgaat tttagcttct 1860 agattctgga gccacgaatc atatgacttc cgatctgtcg aatctcaatg tggccgcacc 1920 ctatccttct aatgaaacag tcattggagc tagtggtgag ggtttacgta ttgctcacat 1980 tggcaattct actcttccta ctcccaatta taattttcaa ttgaattatg tccttcatgt 2040 tccacgattg tctcaacacc ttttgtccat gcatcaatta tgtaaggaca ataattgtcg 2100 atgcattgtt gatgaggtgt ctatctctat acacgacaag gcaactgcga aaacattgtt 2160 ccacggaccg agtagtaatg caatgtatcc tctacctatc atcaagtcta caaaagcttc 2220 accagcgaca tttcttagac ataaagtctc ttctacaata tggcataatc gattagggca 2280 tcttacaaat tctattgttc gtacagcact acgtaaagca tcaatttcag acagtatgag 2340 tcttgtcctg acacatgtat tccttgtctt aagggcaagt tcacaaagtt acccttttcc 2400 tataactact tcaaaatcta tcattccctt tgaagtaatt cattcaaatg tgtggggcca 2460 tgcacctagt gtgtctatag aaggatataa gtattatgtg tcctttatag atgaatgtac 2520 tcgatacact tggatctttc cactcattaa taaaactgct gtgtttggta tttttgtgca 2580 atttcaagct tatgtttcaa actgttttgc tgccaatgtt aaaattctgc aaagtgatgg 2640 tggtggggag tatgtgagtg ctcactttca aaggtttctt agcaccaagg gtattcttca 2700 tcaattatct tgtccttata ctcctgaata gaatgggttg gtcgagcaaa aaaatcgaca 2760 tgtggttgaa accgccatta ctcttcttca aacagcatct ttgtcatctt cattttggta 2820 tcatgcgtgt gctactgcta cctatcttat aaataggatg cctacatcac ttcttggtat 2880 aaagtctccc tttgaggttt tatatcaatc tccacccaga cttgatcact taaaggtgtt 2940 tggctgctta tgttatccct ctgtgaaacc ttatagatct gataagcttg aacaaaaaac 3000 aatggagtgt atcttcttgg ggtataatgc taagtataaa gggtatatat gttattctgt 3060 gcacaacaag aagtttatta tctctcgaca tgtgttattt gatgaaacac agttttcttc 3120 ttggtcaaat atctcatctc aagtgttcaa gtcccctggt tctcagtttt ctagggtgtc 3180 ttctactccc gtggttcaca acaacacttt tcaacaccct ccagttattc ttataccttt 3240 acctcatgtt tttgtcccat cacctaatgc tactgtacaa cctaataatg tctctccttc 3300 atctatcgtc ccttcaagct ccacatcaga ttctccaagg ttttctaagt tgcatccaga 3360 tacaactgtt tctcaagtat caaaattaca gtgtgtgtct cttccttccc acaatagtca 3420 tcctatgcag actcgatcta aatctggaat tgttaaaaag aaacaagctt acaacactgc 3480 aatacactca aattgtgata ttgaaccaac ctcattcact gcagcttcca agtcacctca 3540 atggaaaaag gctatggtcg aagaaatgga tgctcttcta cagaaacata catggtcttt 3600 ggttcccttg cctcccaata aaaatttggt gggctgcaaa tggatataca agattaagaa 3660 acatctcaat ggtgccattg cacaatataa ggccaaatta gtggctaaag gcttccctca 3720 agaggccggt ttagattatt atgaaacctt tagtcctgtg gttaagccaa ccatagtaca 3780 cttaatattg tctcttgctg caactaaagg gtggaaactc aagcaactcg atgtcaagaa 3840 tgcgttctta catggttttc ttgatgaaga tgtctatatg tcacaaccac agggtttcat 3900 cgacaaagat catcccgagt atgtttgtaa attggaaaga tctctctatg gactcaaaca 3960 agctcctcga gcttggaatg acaggtttac tactttctta ctgttactag ggttccaatc 4020 ttcttttgct gatccctcct tgtttgttaa acatgatggc aagtcaatta ttgtgttgct 4080 tctatatgtg gatgatataa ttcttactgg agacaatgat ggttgtattc aaactgtggt 4140 ttctcaattg actagggagt ttgacataaa agatttaggc atccttcatt attttttggg 4200 attgcaaatt gattatcaat ctcggggtat gtttgttcat caaaccaaat atgttcacaa 4260 tctcctcatc aaaacataca tgttccactg caatccatgt attacaccat gtcatccgaa 4320 tcagaaactc ttgaatcatg gcaactcatc attctctaac cctactttat acagaagcat 4380 tgttggtgct ttataatatt tggcattcac tcgtccagat attgcatact cggtaaacca 4440 ggtgtgccaa tttatgcatt ctcctttgga atctcatttt attgctgtga agaggatact 4500 gagatatctc agaggtactt taggttgggg aatttgtttt cggccgggtt cattggatct 4560 taaagcatac acagacgctg actgggctgg taatcccaat gatcggcgtt ctacaatagg 4620 ttttgtggtc tttcttggct ccaatccaat ttcatggagt tctaagaaac aacacacagt 4680 cagtaggtcc tctactaaag ccaagtatcg cgcaatggct actacaactg ctgagatagt 4740 ttggcttcaa cagttgctca aagatcttca tattgacagt tctttccctc atcttcttca 4800 ttgtgataat atctctgcta tggccttggc tacaaatccc gttttacaat ttaaagctaa 4860 acacattgaa gtggattgtc actttgttag ggaacgggta caacaaggcg tcatttctct 4920 tcagtttgtt gcctctgcca atcagtatgt agacattctc acaaaagggt tatgttcacc 4980 tctgtttact caccattgtt ccaatcttat gcttggggat tcccaacata agattgaggg 5040 ggaa 5044 // ID Gret1_I repbase; DNA; EDCOT; 8774 BP. XX AC AB111100; XX DT 27-MAR-2007 (Rel. 12.03, Created) DT 27-MAR-2007 (Rel. 12.03, Last updated, Version 1) XX DE Vitis vinifera gypsy-type retrotransposon Gret1 - internal DE portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gret1_LTR; internal portion; Gret1_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-8774 RA Kobayashi S., Goto-Yamamoto N. and Hirochika H.; RT "Retrotransposon-induced mutations in grape skin color."; RL Science 304(5673), (2004). XX DR EMBL/GenBank/DDBJ; AB111100; Positions 5496 14269. XX CC LTRs differ by 4 bp substitutions. XX FH Key Location/Qualifiers FT CDS join(695..2341,2345..5605) FT /product="Gret1_I_1p" FT /translation="MLSTPFCSHIINYEPPRGFLVPKFSTYDGTSDPFDHI FT MHYRQLMTLDIGNDALLCKVFPASLQGQALSWFHRLPPNSVGNFRDLSEAF FT VGQYLCSARHKQNISTLQNIKMQDNESLREFVKRFGQAVLQVEACSMDAVL FT QIFKRSICPGTPFFESLAKKPPTTMDDLFRRANKYSMLEDDVRAATQQVLV FT AGRPSGSNTERNTKPPDRPKPSDRRQEGPSRPKMPPLTPLSISYEKLLPMI FT QGLSDFKWPRPIATDPSTRDRSRRCAFHKDHGHTTETCRSFQYLVERLIKA FT GHLKQYLRTDTGGRDVSQHNNPGAPRAPVATKAVINYINGGPSDEEYDSRR FT KRQKLLRAASIRERINSIRPGLTGEGPRPIDGTIIFPPVDPTRTLQPHRDA FT LILSLEIGDFDVRRILVDPGSSADLVQASVVGHMGHSLTGLENPGRILSGF FT NGSSTTSLGDIILPVQAGPVTLNVQFSVVQELSPFNIILGRTWLHYMKAIP FT STYHQMVIFLTHDGQIDLYGSQLAARQCYQIAREAGANQEDASPPEPSIAR FT DQQLLGPTDKDPPAADPLQTIQISEESDHLTNISSLMTQEETQGMQNILRQ FT NHDIFAWAHSDMKGIHPSITSHRLNVVSTARPVRQRIRRFHPDRQRVIRNE FT IDKLLEAGFIREVSYPDWLANVVVVPKKEGKWRVCVDYTNLNNACPKDSFP FT LPRIDQIVDSTSGQGMLSFLDAFSGYHQIPMSPDDEEKIAFITPHDLYCYK FT VMPFGLKNAGATYQRLMTKIFKPLIGHSVEVYIDDIVVKSKTREQHILHLQ FT EVFYLLRRYGMKLNPSKCAFGVSARKFLGFMVSQRGIEVSPDQVKAVMETP FT PPRNKKELQRLTGKLVALGRFIARFIDELRPFFLAIRKAGTHGWTDNCQNA FT LERIKHYLMQPPILSSPIPKEKLYMYLAVSEWAISAVLFRCPSPKEQKPIY FT YVSRALADVETRYSKMELISLALRSAAQKLRPYFQAHPVIVLTDQPLRNIL FT HKPDLTGRMLQWAIELSEFGIEFQPRLSMKGQVMADFVLEYSRKPGQHEGS FT RKKEWWTLRVDGASRSSGSGVGLLLQSPTGEHLEQAIRLGFSASNNEAEYE FT AILSGLDLALALSVSKLRIFSDSQLVVKHVQEEYEAKDARMARYLAKVRNT FT LQQFTEWTIEKIKRADNRRADALAGIAASLSIKEAILLPIHVQTNPSVSEI FT SICSTTEAPQADDQEWMNDITEYIRTGTLPGDPKQAHKVRVQAARFTLIGG FT HLYKRSFTGPYLRCLGHSEAQYVLAELHEGIYGNHSGGRSLAHRAHSQGYY FT WPTMKKEAAAYVKRCDKCQRYAPIPHMPSTTLKSISGPWPFAQWGMDIVRP FT LPTAPAQKKFLLVATDYFSKWVEAEAYASTKDKDVTKFVWKNIICRFGIPQ FT TIIADNGPQFDSIAFRNFCSELNIRNSYSTPRYPQSNGQAEATNKTLITAL FT KKRLEQAKGKWVEELPGVLWAYRTTPGRPTGNTPFALAYGMDAVIPIEIGL FT PTIWTNAAKQSDANMQLGRNLDWTDEVRESASIRMADYQQRASAHYNRKVR FT PRSLKNGTLVLRKFFENTTEVGAGKFQANWEGPYIVSKASDNGAYHLQKLD FT GTPLLRPWNVSNLKQYYQ" XX SQ Sequence 8774 BP; 2553 A; 2316 C; 1956 G; 1949 T; 0 other; ttggcgctgt ctgtgggaac ttttctttac tttgattcag tcactaaaaa caatggccac 60 accatcccaa agtcattcat ctggtagggg agaggatgat aattttgaat ggcgcctagc 120 catcgaaagg agacagttgg caagcgaaag acagctaaaa gctctcctcc aggagacaga 180 aagattgaga gaagaaaacg ttgtgttacg catccaggct tcaacatcag agcctcctcg 240 acttcaacat tcgaggggcc aagtagcaaa ctcaaggcct cagcaagaac cagagtcaat 300 ataccctggg acaacagggg caatcccagg ggcatgcaac gtgaggcctc atgagccatg 360 cacgcctatg ccttgagctc cccgtgagga aagctcagac tctactcact tttcagcaaa 420 aaggcaacgt gataaaaagt cgcggttgtc aaattcgatg cgcgcaagac taggcccgca 480 agaacctaga agatcaaggc cacctatggc cacaacctgg gcaccacacc ctgaccccat 540 ggcaaccccc atggtgcaaa acgatcaccc gcatcgtgac cccatagtca cccctgtgat 600 gcggaacgtt catctgcacc tagcggaata gccaactggg agaaacatcc caaacgggcc 660 acccgttggc tccatcagca aaaggctgga tgacatgctc tccacgcctt tctgctctca 720 tatcattaat tatgagcccc caaggggatt cctcgtacct aaattttcca catacgatgg 780 aaccagcgat cccttcgatc acatcatgca ttatcgacag ctcatgacgc tcgatattgg 840 caacgatgcg ctgctatgca aagtatttcc cgccagtcta caaggacagg ccctctcatg 900 gtttcatcgc ctacctccca actctgttgg caatttcagg gacctgtccg aagctttcgt 960 gggacaatac ctgtgttccg cccgacacaa gcaaaatatc agcaccttgc agaacataaa 1020 aatgcaagat aacgaatcct taagggaatt tgtgaagcgg tttggccaag ccgtacttca 1080 agtggaagct tgcagtatgg atgctgttct acagatcttc aaacgaagca tctgtccagg 1140 cactccattt ttcgaatcac tggctaaaaa gcctcctact acgatggacg acttattcag 1200 acgagccaac aaatattcaa tgctcgaaga tgacgtacgt gcagccaccc agcaagtttt 1260 ggttgccgga cggccatccg gaagtaatac ggagagaaat accaaacctc cggatcggcc 1320 aaagccgtct gaccgaaggc aggaagggcc aagtcgcccg aaaatgccgc ctctcacacc 1380 tctttctata tcatatgaga aacttctccc aatgatccaa ggcttgtccg acttcaagtg 1440 gcctagacct attgcaacgg acccatctac aagggatcgt agcaggagat gtgccttcca 1500 caaagatcat ggccatacaa cagagacgtg ccgatctttc cagtatttgg tcgaaagact 1560 cataaaagct gggcatttga agcaatacct ccgcacggat acggggggta gggacgtttc 1620 ccagcacaac aaccctggag cccctagggc cccagttgcc accaaggccg ttatcaacta 1680 tattaacgga ggaccatctg acgaggagta tgactccaga cggaaaaggc aaaaattgtt 1740 gcgggctgca tcaatacgcg aacgcattaa ttccatccgg ccgggtctaa ctggagaggg 1800 tcctcgcccc atagatggaa caataatttt tccaccagta gatcccaccc ggacactaca 1860 accacatcgc gacgccctca tcctgtccct agaaattggg gacttcgatg tgcggcgtat 1920 cttagttgac ccaggcagtt cagccgacct ggtgcaagca tcagtcgttg gccacatggg 1980 acatagtctc acgggccttg aaaaccccgg acgaatctta tccggattca acggatcatc 2040 aaccacatcc ttgggagata tcatactgcc ggtccaagct ggcccagtca ctctcaatgt 2100 acagttttca gtagtacagg agctatcacc cttcaatatc attttggggc gcacatggct 2160 ccactacatg aaagctatcc cctctacata ccatcaaatg gtgatttttc ttacccacga 2220 tggtcaaatc gacttatatg gcagccaatt agccgctcgc cagtgctatc agatagcacg 2280 tgaagcaggg gccaaccagg aggatgcatc tccccctgaa cccagcattg cacgcgacca 2340 atagcaatta ttgggtccga cggacaaaga tcccccggca gcagatccct tacaaacaat 2400 ccaaatttcg gaggaaagcg atcacctcac gaacatcagt tccctcatga cacaagaaga 2460 gactcagggc atgcaaaata tcctcagaca gaaccatgac atcttcgcgt gggcacattc 2520 tgacatgaag ggaattcatc cctccattac atctcacagg cttaacgtcg tttcaactgc 2580 cagacccgtc cgacagagga ttaggcgctt ccacccagat agacaaagag tcatccggaa 2640 cgagattgac aaattgctcg aagccggatt catcagagaa gtttcttatc cggattggtt 2700 ggcaaacgta gtcgtggtac ccaaaaaaga aggaaaatgg cgagtttgtg tagattacac 2760 caatctgaac aatgcgtgtc caaaagacag ttttcccttg ccgcgaatag atcagattgt 2820 ggattccact tccgggcaag ggatgctctc tttcttggat gccttctccg gatatcatca 2880 aatccccatg tccccggatg acgaagaaaa aatagcattc ataacaccac acgacctcta 2940 ttgttataaa gtcatgccat tcggactcaa aaatgctggc gccacttatc aaagattgat 3000 gactaaaatc ttcaaacctc tgataggcca ctcagtagag gtttatattg acgatatcgt 3060 ggttaaaagc aaaactcggg agcagcatat ccttcatttg caagaggttt tttacctctt 3120 acgaaggtat ggcatgaagc taaatccttc taaatgcgcc tttggcgtaa gtgccagaaa 3180 atttctagga tttatggtca gccaaagggg catagaagtc agcccggatc aagtcaaagc 3240 agtcatggaa acaccccctc ccaggaacaa gaaagagtta cagcgcctca caggcaaact 3300 cgttgcatta gggcgtttca tagcccgctt cattgatgag ttgcgaccct tcttcttggc 3360 gatacgaaaa gctggaacgc acgggtggac ggacaattgc caaaacgctt tggaaagaat 3420 taaacattat cttatgcaac cacccatctt gagcagcccc atcccaaagg agaaattata 3480 catgtatcta gcagtgtcag aatgggcaat cagtgccgtt ctattccgct gcccatcacc 3540 caaggagcag aagcccatct actatgtcag cagggcattg gcagacgtag aaaccagata 3600 ttcaaaaatg gagctaatat ccttagccct tcgaagcgct gcccaaaagc tccggcccta 3660 ttttcaagcc cacccggtga tcgtgttgac tgatcaaccc cttcgcaaca ttctgcacaa 3720 gccagattta accgggagaa tgctacaatg ggccatcgaa ttaagcgagt ttgggattga 3780 attccaacca aggttgtcca tgaaaggcca ggtaatggct gacttcgtgc tagaatattc 3840 ccgaaaaccc ggccaacatg aaggatcaag gaaaaaagaa tggtggactc tgcgagttga 3900 cggagcctca cgttcatcag gctctggagt cgggctctta ttgcagtccc caactgggga 3960 acatttggaa caagccatcc ggctgggatt ctccgcctct aacaatgaag cagaatatga 4020 ggctatcttg tccggattgg acctcgccct tgctctatcc gtctccaaac tccggatctt 4080 cagcgactca caactcgtgg taaaacatgt ccaggaggaa tatgaggcta aggacgcacg 4140 catggcgcga tacttagcta aagtaagaaa caccttgcag caattcactg aatggacaat 4200 cgaaaaaatc aagcgagctg acaataggcg cgctgacgct ttggccggca tagctgcctc 4260 cctctctatc aaggaagcca ttctactgcc catacatgtg caaaccaacc cctctgtctc 4320 agaaatttca atctgcagta ccactgaggc accccaagcg gacgaccaag aatggatgaa 4380 tgatatcaca gaatatatcc ggacaggaac tctacccgga gatcccaaac aggcacataa 4440 agtccgggtg caagctgccc gttttacctt aattgggggg cacctgtaca agcgatcctt 4500 cacaggacca tatcttcggt gcctagggca ttcagaagct caatatgtgt tggctgagtt 4560 acatgaggga atatacggaa atcattcggg aggacgatct ctggcacata gagcccattc 4620 acaaggatac tattggccaa caatgaagaa agaggcggca gcatatgtca aaagatgtga 4680 taaatgtcaa aggtatgctc ccatcccaca tatgccatca acaacgttaa aatcaatctc 4740 aggtccatgg cccttcgcac agtggggcat ggacatagtg agacctctcc caactgcacc 4800 tgcccaaaag aaatttttgc ttgttgccac agattatttc agtaagtggg tggaagctga 4860 agcatatgct agcaccaaag ataaggatgt caccaagttt gtatggaaaa atattatctg 4920 ccgttttgga attccccaaa ccatcatagc cgacaatggt ccacaattcg atagcattgc 4980 atttagaaat ttctgttcag agctaaacat ccggaactca tactccacac cacgatatcc 5040 tcaaagcaat gggcaagcag aagccacaaa caagacccta atcactgcct taaagaaaag 5100 gcttgagcaa gccaaaggaa aatgggtcga ggagctgccc ggcgtcctat gggcctaccg 5160 aactacaccc ggacggccaa caggaaatac tcctttcgct cttgcatatg gaatggacgc 5220 cgtcattcct atcgaaatag gtctccctac tatctggacc aacgcagcaa aacaaagtga 5280 tgcaaacatg caattaggaa gaaatttgga ttggacggat gaagtgaggg aaagcgcgtc 5340 catccggatg gcagattatc aacaaagggc atcagcacat tacaatcgca aagtgagacc 5400 aagaagctta aaaaatggta cgctagtcct tagaaaattt tttgaaaata ctactgaagt 5460 aggtgcaggg aagttccaag ccaattggga aggaccttat atagtgtcta aagcaagtga 5520 caatggagcc tatcatttac aaaagctaga cggaactcca ttacttagac catggaatgt 5580 gtctaattta aagcagtatt atcaataaga aagccaaggc aagttcaaat gagaaaagaa 5640 gtatttttat tgacatagct aaaaatatgt acaaaagagg tctccggacc acaaaaatac 5700 aaaaggaaga ttacagaaga aattgcaaaa agagaaactg tcagggagca ggcttgtcat 5760 aaagtttctt ttcttcaccc ggaggaattg aaggcacgtc ccgcttgata ccgttcttct 5820 tcatgcagca ccgataccca aagatgaacg tatcatccac ctgtttttta tattctgctt 5880 caatttcctc cctctctaca gcaaactccc gttctagctc ctctttttgt gcaaccaagc 5940 gcagctttaa atcttccctc tgtttctttt caatagaaac ttctgtccgg agttgcctca 6000 cctcccccct cagttgggtt atctcatctg ctgcctcatg caggcggtcg gccgctgatt 6060 cctcctgact ctttgcctca gccaaatcca cccggagggc ttcattttct tttcgaatgg 6120 tggataagcc agcttcagcc tcttccagtt tcaggcgcag ttggttttcg ctttctttat 6180 gccaagaggc aaagatcctc atataatcag tggtccgcag caaatcaaaa aagagatcgt 6240 ggtgttgggc catgccgcgg agaccactca ccagctgaca cacaaacaag caatgcaaag 6300 ttacaaatca taccacaaca acacaacaaa atgataaaac aatcaaaaag cacgaaaaac 6360 agttttacca tttccacatt ttcgaacatc tgggctgagg gcatgatatc aggcgagccg 6420 ggtggaatct ctttcagctt atcttccaac tccgcataac taaaagagtt gtcggaggag 6480 caagatgcgt cattaacagg tccacccccg gatgaagcag cagaaggcga tttttgttcc 6540 gagtgagggg ccccaacatt tccggccgga tgggcctccc caggtgcaac ctcagccggg 6600 accaccatcg ggacggatgg agcctcagtt accatctcca cttcgccccc ctccggatga 6660 gcgtcgtggg cagatgagca actgacttca atctcttgct accgctcttg aagctgcccg 6720 tggagtccgg acttcagatc gcgcaccgag cgaggcttct ttgaggatgg ccccgtcact 6780 agaacaagag ccagcaggtt cggatcgtca gagggctgac tctggctttc tgctcccact 6840 tcctccatgg gggtcgcgca aatggcctca gctgcatcgg catccggatt gcaggagtcc 6900 ggatggttga cagacgcagc ttcctcagcc aaattcacta gacgcgcaac tgctgccaag 6960 gaggtgcttg agtggttcag ccccgcaagg tgtccggacc cgcttgagat ggaatgaggg 7020 gcagcgttca ctggctcctc tatcattacc tccgcctcgt gaataatggg cgaaggagca 7080 aattccatgg gagaactggg cttcttcaag tccttcccat ttttcttcac cagcttcctc 7140 tttttcgctg gaattttctc tggaggagag tctgcgtcac gattctgtcc gggagccttc 7200 cgaagggtcc cttcgttctt cttcttctcc cgatcctcca ggagaagtcg acatttttta 7260 acgtcagcct cttttaacgc ctcgtaaatc gggaaatcct tcacagtata atgctcccca 7320 ggaacaactt cctttggcat cttcctgggg agaatgttga tgacatattc tcggggctcc 7380 cggacgaccg ccgtcaggtt ccgcgcggtc agcagcgtct tgcactgcct ctccttggcg 7440 tctatctcga acaatttgct gagacagcca aaggacgcct tctccaccca gtccacaagg 7500 tggcccctca attccggacc tacattaaca gcaacaaaag atgagaatgc catccggaag 7560 agtcaacaaa aaatcaacaa agtaaaaacc ggacaatagt cacaaagcaa acctacccgg 7620 aaccaccaag gagtagtttg gagagaaagg cctcgccgga tgctccaaaa gccccgccca 7680 tgcaccccgg accaccacgt gtcccgtcgc ccctcccttt gtcgaatctg gcagctccgt 7740 caccagttgg agggagggca ggtgtgcgga catgctgaag atgtcatttt tgaccttctt 7800 caaagaatac acaaaaaaca cctccagcag cgtgagatcg aggttgtaca gcatgtttat 7860 gatgctgcat cccatcagca cccggacgat gttgggatga ataaagacgg gtggaatctg 7920 ggtgaagtgg aggaactcct tgaacaacgc cagcagaggg aaccggagcc ccgcgttgaa 7980 ttgttccttc gagaagatga tagttttttc ttctgctttc tcagaaggaa caagcaccct 8040 cccattcagc aattcgatag ccacgtcatt tgggatacag aaccgttccc ggaattcctt 8100 cgcgtccaac ttatctatcg cttttccacg aacctcggta ccccgagaag atgaaacagt 8160 cttttttgca gccatttctt accacaaaca caagcccaaa actacacaca agaagcgcaa 8220 tgggtaaaac acaagtaacc cagaaaatac acaaacccta acccgaacaa atcagaaacc 8280 aaaaccaaca aaacgcaaca aaaggaacag caatagcaaa agtacacgta ccaaatgaag 8340 ctctgaagaa gaaaggtcgt cgtttcgaat acaagaacac cagcagcaaa caaatgtcgc 8400 gacacaaaat caccggtaca aaagtgtttt cgagtttctt tactcagaaa aagcaaagga 8460 cgcaacaaaa gcaagaagaa gaaaggatct caggaaaatg cagtagaaaa aatgaaaaag 8520 aaggtacagt acgatattta tagggggacc agccctcgga aagccaaacg tccaaacagc 8580 gctatcattg aaacaacatg ctgcctggga attcccagag tcgccggctc atcataaatg 8640 ccttttatgg cttccgcacc ccctctcgcc acgtggctca gtcagacgaa gagacctctt 8700 caaaattcaa aaagccagtt attttttaac ccgcccattt tttggcaaaa taggcaagtt 8760 aaaaaggggg gcaa 8774 // ID MuDR-3_Mad repbase; DNA; EDCOT; 4304 BP. XX AC . XX DT 06-OCT-2010 (Rel. 15.1, Created) DT 06-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; MuDR-3_Mad. XX NM MuDR-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4304 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1507-1507 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 223-bp long. XX FH Key Location/Qualifiers FT CDS join(1079..2116,2098..2991) FT /product="MuDR-3_Mad_1p" FT /translation="MLEIKLNLERKFVVTNFVAEHSHVLVPASSSHLLRSQ FT RLIEPSQAKLIDQMHXAGLQPSQIFSYFTTEAGGSQKLNFIQSDCNNLIMR FT KRIGVLKKGDSECLLEYFKKKQTEDKSFFYSLRTNEENEICGCFFCDGNSR FT RDYTIFGDVVCFDTTFKTNRYNMVCAPIVGINNHGQTILFGCGLLDGETTD FT ACEWLFKAFLQAMDGKAPGTIFTDQAQSIAAAISEVFPNCHHRLCLWHIYQ FT NAARNLNHVFSEFKSFTQDFKRCIYDPETVEEFESSWNKLLDDYELRGNDW FT LEGIYLLREKWAQVYGRDHFCAGITLDQFLLYYFVHIIHKFLFPLYCDQFP FT FFSSISIFFLGMTTTQRIESMNKFLKKYFARNLLLQEFVVQYDKAVADRKE FT KERQAENATKQKWRSLYSDWNVEIEATKQYTSKIFYCFQEEVKKVLNLRPL FT KLESDDGXTRTYTVMNSGKRGINRTLMYDLANQTVLCSCKKFEFEGILCAH FT ALKLYYDLDLSSIPSNYYLKRWSKDAKCGIGFDSYGEPAVSNLDSSSLVQY FT SELSNIAQRIIAKGAKNSQNCSFLKSELLKLEKKMEKHANFGEQDDVNYVK FT HVTEAEKNLKIQDPKVQKSKGRGKGRMKSALESNQPKKKGPYKRKG" XX SQ Sequence 4304 BP; 1405 A; 656 C; 824 G; 1407 T; 12 other; gggtgcattt ttgctcaccc acactaacta tagggtatgc tcaccacccc tttcaatgtt 60 tgccatgtgt aatccacact aactctagtt aagccttatt tttttttatt tttgctttaa 120 ttaataggtg agagaatcct acttttactt atttacttcc atatatatcc tttcttttta 180 aatattttat taaaacttta aacttccttt ttgaatacaa acagactcaa tctctctcct 240 gatgaccaat tcaaccttgc acgcaatctg gattcactgc tatgctttcc atctgctcgt 300 attggttttt ccatctgcta cctatcttct gggttttcca tctgcaattt tttctccgac 360 tagaaaaagg tatgcaattc ccatttattt gctttttagg actattatag gtaaggatgg 420 gcattgaaca cccatttcgt gttgaggatg aggcggtggt ggtgtaaccg acgggatagt 480 actacccaga gtctacatct tcatcttcat cataatactt taaattatgt tccatcatgg 540 attataggat gtcaatatat atgcttttct taggattatt atagggtgtc aaaatatatg 600 ctttttatga ttattatagg gtgtcaatat atatgctttt taggattatt atagggtgtt 660 aatttaattc aatattaagt aatttgatac ttatacagat ggaacatcaa gatgatgagt 720 ttcatactcc atcttctagt gatgccaaag aatcagttga ttgtatacac ttagattcag 780 attcagattc cgaaaccttt gaagtcttgg atcaaaatga agaaaaagga gaatttacaa 840 gcaaagttgg tgatatttct ctggggatga cttttgataa tgaggatgat gcatataatt 900 actacaatgc atatggtaga agggttggat ttagcgtgag aaagaacaga gagaataagg 960 acaggtcagg tgtgctaaag aaaaaacaat tttgttgttc ttgtgaaggt ttttataaaa 1020 aaaaaaaaaa agaactccaa agaagaaaag agaagaaaca agatgtggct gcaaggcaat 1080 gcttgaaatc aaacttaatt tagaaaggaa gtttgttgtg acaaattttg ttgctgaaca 1140 tagtcatgtt cttgttccgg catcaagttc ccatttattg aggtcacaac gattaataga 1200 gccttctcaa gcaaaattga tagatcaaat gcattmtgca ggactacagc catctcaaat 1260 cttctcatac tttaccacag aagcaggagg gtctcaaaaa ctaaacttta ttcagtctga 1320 ttgtaacaat ttgataatga gaaagcgcat cggggttctt aaaaagggcg actcagaatg 1380 tttgcttgaa tattttaaga aaaagcaaac tgaagacaag tcatttttct attctcttcg 1440 aacaaacgag gagaatgaaa tatgtggttg ttttttctgt gatggaaatt cgaggcgcga 1500 ttatactata tttggtgatg ttgtgtgttt tgatacgaca ttcaaaacga atagatataa 1560 tatggtgtgt gccccaatag ttggtatcaa taatcatggt caaaccatac ttttcggatg 1620 tggtttgcta gatggagaga caacagatgc atgtgagtgg ctgttcaagg cctttttaca 1680 agccatggat ggaaaagcac caggaaccat atttacagat caagcccaat caattgctgc 1740 tgcgattagt gaagtatttc ctaattgcca ccaccgactt tgtttgtggc acatatatca 1800 gaatgctgcg aggaacttga atcatgtttt tagtgagttt aaatcattta cacaggattt 1860 caaaagatgc atatatgatc cggagactgt tgaagaattt gaatcaagtt ggaataagtt 1920 acttgatgat tatgaattga gaggaaatga ttggctagaa gggatatatc tattacgtga 1980 gaaatgggca caagtttatg gtcgagacca cttttgtgca ggtattactc ttgaccaatt 2040 cctattatat tattttgtac atattattca caagtttctt tttccactat actgtgatca 2100 atttccattt ttttcttagg tatgacaaca acacaaagaa ttgaaagcat gaacaagttt 2160 ttgaaaaagt attttgctcg aaacctcctt ctgcaagagt tcgtcgtcca atatgataaa 2220 gcagtagcgg atcgaaaaga aaaggaaagg caagcagaaa atgcaactaa acagaaatgg 2280 cgtagtttgt attctgattg gaatgtggag attgaagcaa caaagcagta tacaagtaag 2340 attttttatt gtttccaaga ggaggttaag aaagttttaa atttgaggcc actgaaatta 2400 gaaagtgatg atgggcwaac acgtacatac acagtaatga actcaggaaa acgaggaatt 2460 aatagaacac ttatgtatga ccttgcaaat caaacagtat tgtgcagttg caaaaagttt 2520 gagtttgagg ggattctttg tgcacatgct ctaaagttat actatgattt agacttgtca 2580 agtataccat ccaattatta tttgaaaaga tggagcaagg atgctaaatg tggtattgga 2640 tttgattctt atggtgaacc ggctgtgagt aatttagact catcttcctt ggttcagtat 2700 agcgagctat ctaatatagc acaaagaatc atagcaaaag gtgcaaaaaa tagccaaaat 2760 tgtagttttt tgaaatctga gttgttaaag ttggagaaaa aaatggaaaa gcatgccaat 2820 tttggagaac aagatgatgt aaattatgtt aagcatgtga ctgaagctga gaaaaatctt 2880 aagatccaag atccaaaagt tcagaagtcc aaaggtcggg gcaaaggtag aatgaagagt 2940 gctttggaat ctaatcaacc taaaaagaaa ggtccataca agagaaaagg ttagcacata 3000 tttggcttgt ttttatttac tatttgattc acaatttgca tttgtcaatg taattattat 3060 tttaattgtt taatagcttt taaagaatcc aattcaaatg catacgagat gaacggacca 3120 tcaacaagat atgcacaaac tcaggtttaa agtttagcaa ttttttgtca tgaatgtttt 3180 atttatttat ttatattttt gtccattagc attgttttaa tatatttctg atggatcaat 3240 tggaattggt atctagggac atattggaat gccaagtcaa aaccaattca atatggcacc 3300 cgtaagtcaa gtcacacatt ttccttatgg atttccaatt gttccttgtg ttcaagggat 3360 tcaaaatccg ctagttcaag gattcaaaat caccaacttg gatttcaagc tataagtccc 3420 atgatgtcca attactcatt tatgtatcct cgggtttgta ccttcactga atgtactata 3480 tatatagtgt actatatttt tgttctctag tttcataagt aatttttttc tttttattwa 3540 tttgcaggaa aacattcaac caatacctct gggaaccact cctcaactaa aattttcaaa 3600 tccatcaaca tcaaacattc aaccaatacc tctgggaacc actcttgaac tgaatttttc 3660 aaatccatca acatcttaga tcawgttgta atagaattta gagaattttt ttttttggaa 3720 cgacatcctc tgaagtggag aatattcatc ctactagctt tgtacaattt tattttgatg 3780 agtttcatct caaacaattg tattttgttg gatattgatg agtttcatat maagacaatt 3840 gtatgttttt ggactagctc gcttttgtac aattttattt tgatkagttt catctaaaac 3900 aattgcagat cctttttacg attttggaaa atccagatac gtagcaggcc gcatggaagc 3960 agcaagcaac gcatgaaagt gtaatctaga tacgcatgca agkttatggg gaattggtag 4020 tgtwtccaaa aaggagagag gagatgccgc agccggttgg cggcgctggc cgttgagtcc 4080 tgtttgtatt caaaaaggaa gtttwaagtt ttaataaaat acttaaaaag aaaggatata 4140 tatggaagta aatgagtaaa agttggattc tctcwcctat taattaaagt aaaaataaaa 4200 waaaaataag gcttaactag agttagtgtg gattacacat ggcaagcatt gagakgggtg 4260 gtgagcatac cctagagtta gtgtgggtga gcaaaaatgc accc 4304 // ID MtPH-A6-1-Ia repbase; DNA; EDCOT; 4075 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 13-MAY-2008 (Rel. 13.05, Last updated, Version 1) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-A6-1-Ia. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4075 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC An autonomous element representing subfamily A6-1 of CC PIF/Harbinger transposons from Medicago truncatula, carrying 15 CC bp-long TIRs. XX SQ Sequence 4075 BP; 1316 A; 611 C; 734 G; 1414 T; 0 other; gagtctgttt ggttggagat ttttggtggg gaggggaggg gaggggaggg aatattttaa 60 aatttatttg tttggttcaa tttttaaaag ggaaggggag ggatggagag ggaagcaaaa 120 tcccttatat gctcatttat tgcttcccat caaattggag tttttttgtg ggaaggggag 180 ggaagctctt taagatttta ttacactgtc aaaattatcc ttaaattatt ttaaaattcc 240 aagaatatcc ttctcacaat ttttattatt aggttatcta tcattgttat ttcttacatg 300 taactactct tccaacccta ctcctacttt gctgtcgttg tcgtcgcggt tgtttcagaa 360 ctttacgatg tgagtattgc ttattaattt ttgtcagatg atggatgaat aatgtttatc 420 tatattgctt tgtcacgttt tcttggccat tagtttttca cgttattatt ggatatgtta 480 gtgatgcttt caaaaccacc actgtgattg tcacgttatg ataatgaata atcttcttta 540 tgtttgtttt ctttttttgt taacaaagcc attattttta tcatcatttt tattgtttta 600 taatccatta tcccatgatg atgatcaatg atctcttgtt tgtttttttt tcctttttat 660 tctagtttat tatttcaagt cagttgcagc tttttttctt ctaattgtat taatttattt 720 attttataag ttgttgcatt ttattgtgtg ggatatgagt tatatattat ctagaaaata 780 attttataaa tatcttatgg aattagatgg aaaatcaaga tcaggaaatt gctatcaata 840 gatggtttga tttgcgtcga agagctgtag ctcaactcat gtgtgctatt gtttattgtt 900 atttacgggt gtttcataaa agaaaaataa gtatagtatg agttttgaga gagaaagggt 960 ccgtgaagaa gtaatgtatc gaattagaaa cagtgaaagt agtcgaaata tattaagaat 1020 gggtcctcga acttttttaa agctatgtga tatgttagaa agtgaagggg gcttacgacc 1080 tacacgatgg tcaagtgtgg aagaacaagt tgcaaaatca atctacatac taacccataa 1140 tgttaaaaat cgtgaagtca acttttggtt tcgtcgtttg ggtgaaacaa ttagccgtca 1200 tctccatcaa gtattgaaag ctattcttga attggaagaa aaatttatcg tacaacctga 1260 tggctcaagg atccccttgg aaatttctag tagcactaga ttctacccat actttaaggt 1320 aaatttttta ttaataattt gtccaacaat aaaatataag caagatttgt atagatcata 1380 tacatatatt tattgataaa aaaaatatta tgtcagaatt gtgttggtgc tatagatgga 1440 acacatatac gagttaaggt atctgcaaaa gatgtccctc gatatcgtgg taggaaagac 1500 tacctaacac aaaatgtttt agcagcgtgc acttttgatt taaagttcac ttacgtgctt 1560 gcgggatggg aaggctctgc ctctgactca agaataataa agaatccatt aacacgagaa 1620 gataaactta aaattcctca aggtaatata agaatcacca tacacatata actattacat 1680 ttattgtttc aaactataac attaatgttg acaagtatta tcctttacca taggaaaata 1740 ttatcttgtt gatgccagct tcatgttgac aagtggactt attacgcctt atagaggagt 1800 tcggtatcac ctgaaagaat attcggcaag aaatccaccc caaaatttta aagaattgtt 1860 caatcttcgg cattcatctt tacgaaatgc aattgaaaga gcctttggtg tgttaaaaaa 1920 agatttgaga ttttatcgaa ttcaacaaaa cccacttatg gagtcaaagc gcaaaaatta 1980 atcatttttg catgttgcat tcttcacaac tatctaatga gcgtagaccc agatgaagac 2040 cttatagctg aagtagatgt tgaacttgca aatcaaaatg catctcatga aaatcatcaa 2100 gcatcaagtg atagggatga atttgctatg ggtactttaa taaaaaatgg tgtagcccat 2160 caaatgtggt cgaattatga aaatgatggt tagacctaaa tggtttacct tgtaatttaa 2220 attattattt tgatgtttgt tgttctttga ggaagcagta ctgattttat tgtcatgttt 2280 attagatact tgtgtttgga ctaaatgttt atttgatatt tatgtcaagt gaatgatatt 2340 gggacttcat gttgattata tttattaatt taattgtgct ataattgacc attttcatat 2400 agtatggcat caaaaaagca aattccaacc aacaatggta attctgggac tttgagttgg 2460 aatagagcca tggatgatgc tcttgttgaa gctttcatgc aagaacttga aaatggtaac 2520 aaagtcaacg gtaactttac gacaacaaca tataacaata ttacagctga acttgtgaaa 2580 ttatttggtg acaaaattga taagttaaag gtacaaaatc gctggaaaac tttgaaaaga 2640 aacttcagtg aatattacga aatttttaaa ggtggtatga gtggattttc ttggattgaa 2700 actacacagt tatgggatgc cgaggaagaa gtttggaaag ctctaattga ggtaaatttt 2760 gtaaatcttg aattttgcaa tattttatta atcaatagtt ttataaattg tctgaaacct 2820 acttttcagt cgaaaccaaa agcagcaagt tggagatttg ttccatttcc aaattatgag 2880 aaaatgttga aactccatgg acccaaccga gctgatggag atgaatctga gacttttaaa 2940 gaaacaagaa aacgaggggc atcgatcacc gaggaagatt ttaatgaaac tattcaagat 3000 attgatggcc aagttgctca aaatgaggtg aatttggaga gttttgttcc tgattatgat 3060 tttactgtac ctgaaacaca atcaccagat ccttcaccca ttgcaagtgg tggcaaaagg 3120 aagaaactga aagtggttaa aaacaaagag gcaaaaaatg agattattga acttaaagag 3180 tcaatgaatg tggttgcaga ggcactcaga gaaggaaatg cagcaatacg cgaaggaaat 3240 gaaataacga aagaacgtca taaacatgag ttgcctccga tttcaggaga agaaacctgg 3300 aatttaataa aggagtgtgg gtgtgacaaa gattcattgc ctaagatata ttgtgctgtc 3360 atgaaggata aagacaaact tagaatgatt cttcagtgtc caccggaagc gcacaaagcg 3420 gtgataatgc aaatggtctc tggctagttt gaatactaca atgtttatga atattttatt 3480 tgcatttaat atgtttttga atatttcgaa tactgaatat tttcatttta attatttgtg 3540 ttgtttatga atgaacatat ttctctcccg tgtgaaattt aagttttagt caagttccaa 3600 ttttttttat aacttctttt tttacaacga cgaaagatgt aactcatatt tgaatgaatc 3660 atggtttctt gcttcatttg caaatgagtt ggtaacctta aatttttaac catattgcag 3720 gtttgcatga atcatattta catggctcta gtcctttggt tccgttttca atttttctat 3780 tactaatttt caaccaactg catttattta aaattgttaa ataagcattg cacatgtttt 3840 tgaaaaatat atttaattaa atttaagggt aaaactgtaa aatagtttta aaatccctcc 3900 cctccccacg tgaaccaaac acatttttaa ttaaaatccc tccccttccc tcctttgaac 3960 caaacatatg tttaattaaa atatcatccc tccccttccc ttcccttccc ttccctcccc 4020 tcccatccat taaaatccct cccctcccct ctcctccgtt gaaccaaacg gaccc 4075 // ID POPCOP1_I repbase; DNA; EDCOT; 4086 BP. XX AC scaff_2371; XX DT 06-APR-2007 (Rel. 12.04, Created) DT 06-APR-2007 (Rel. 12.04, Last updated, Version 1) XX DE Copia-type LTR retrotransposon - internal sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; POPCOP1; internal portion; POPCOP1_I. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4086 RA Jurka J.; RT "POPCOP1: Copia-type LTR-retrotransposon from black cottonwood."; RL Repbase Reports 7(4), 149-149 (2007). XX DR EMBL/GenBank/DDBJ; scaff_2371; Positions 2501 6586. XX CC LTRs are ~95% identical. XX FH Key Location/Qualifiers FT CDS 29..4084 FT /product="POPCOP1_I_1p" FT /translation="MTSNNNYSQFHMPRLTKQNYDLWCIQYKALLRSQELW FT ELVEDGYTEPREDAVMSNAERQALRESRKKDNKALFTIYQGLDEATLEMVA FT PAKTSKEAWEMLSKTYSGVEKTKRVRLQSQRGDFEKLNKEGNETISNYFTK FT VITLVHQMRRNGENIDDVRVMEKILRSLDSKFDHVVVAIEESKDLEELTVE FT ELMGSLQAHEQKIDRRGEGRTLEHALQTQLTLKNSNESNRGAFQRGRFLHR FT RGRGGRSYRNQEFHGARNQNFNGRGRGRFRGRSRGGYSNWRHNNAGVQCYN FT CKEYGHFASDCSQYRFEDKVVNFAEKVSDSEEPALLLACGKFDDSRSSTWY FT LDTGASNHMCGMKEAFADIDESYKGKITFGDLSQIPVEGRGRILIQLKNGE FT QKFITEVFYVPDMKSNILSLGQFLEQDFEVQMKNKNLKIFDETGALIASVK FT MTKNRMFPLDLNVCMSNCFKAESSNLTNLWHLRYGHLNCGSLMMMEKHRMV FT LGIPQLEHTNDLCEVCVMGKQHRKSFPKKSSRASQPLELVYSDVCGPITPT FT TIGGNRYFLTFTDDFSGKTWVYVLKEKKEVLSKFKEFKNLVEKQSECKLKN FT LRTDRGGEYVSHAFDYYCKENGIAHQLTMPQTPQQNGVSERKNRTIMNMVR FT CMLKEKNCPKEFWGDAVVCAVYLLNRFTTKRLHMLTPEEAWSMKKPRVDHL FT RIFGSIAYAKIQDEKRTKLEDKSQKCILLGYGENSYGYKLFNPVTKKVIMS FT RDVRFDEEQEWNWSTEEQLQKLVVEEEQMQNDEEEIIINPAPSTSSPASPS FT SSARKTKSIQEIYDATERMNLDDVNMLCLFSGNDPITFEEAYQEDKWKKAM FT KEEINSIQKNNTWELTTLPEGHNAIGVKWIFKTKKNAEGEIEKHKARLVAK FT GYKQQYGVDYEDVFAPVARIETVRLVISLAAQKQWKIFQMDVKSAFLNGNL FT EEEVYVEQPAGFVVKGEEEKVCRLKKALYGLKQAPRAWNSRIDGYLSQKGF FT TKCPYEHALYVKKNLHGRIMFVCLYVDDILFTGDDPTMIQDFKQSMVKEFE FT MTDLGLLAYFLGLEVKQCSNGIFVSQAKYATEVLKKFAMEDCDPADNPVEY FT GTRLTKEGEGDLVNPTYYKSIVGCLRYLTCTRPDILFGVGLVSRYMERPRS FT SHLKAAKRILRFIKGTLNYGLCYSSSQNFQITGYSDSDWAGSLEDRKSTTG FT FIFFMGETAFTWTSKKQSIVALSTCEAEYIAAASCVCHAIWLRKLMEDLQQ FT KQSEATKIFVDNKSAIALAKNPVHHERSKHIDTRFHFIREHIKEGDVELVH FT VNTHEQIADIFTKPLKTEVFCYLQKKLGIVKIDETSLRGV" XX SQ Sequence 4086 BP; 1484 A; 605 C; 960 G; 1037 T; 0 other; aaattggtat cagagcccga gagacaacat gacttccaac aacaactatt cccaatttca 60 tatgccccgc cttaccaaac aaaactatga tttatggtgc atccaataca aagcactact 120 tagatcacaa gagttatggg agctggttga agatggttat actgaaccaa gagaagacgc 180 tgtgatgagc aatgcagaga gacaagcact gagagaatca agaaagaaag acaacaaggc 240 gttattcaca atttatcaag ggcttgatga agcaaccctt gagatggtgg caccagcaaa 300 gacatcaaag gaagcatggg aaatgctaag taaaacttat agtggagttg aaaaaacaaa 360 aagagttcgg ctacaatctc agagaggaga ttttgagaag ctgaacaaag aaggcaatga 420 gacaatctca aattacttta caaaagtaat cactttggtt caccagatga gaaggaatgg 480 tgaaaatatt gatgatgttc gtgtgatgga gaaaattttg agatcactgg attcaaagtt 540 tgaccatgtg gttgtagcaa ttgaagaatc aaaagattta gaagaattga cagtagaaga 600 gttaatggga tcactgcaag cccatgagca gaaaattgac agaagaggag aaggaagaac 660 acttgaacat gctttgcaaa cacagctaac tttgaagaat tcaaatgaat ccaacagagg 720 agcattccag agaggcagat ttttgcatag aagaggaaga ggaggaagat catatagaaa 780 tcaagaattt catggtgcac gaaatcagaa tttcaatggc agaggcagag gcagattcag 840 aggaagaagt cgtggaggat actcaaactg gagacataac aatgcaggcg tgcaatgtta 900 taattgcaag gaatatggtc atttcgcctc tgactgttca caatacagat ttgaagacaa 960 agttgttaat tttgctgaga aggtaagtga ttcagaagaa cctgcactgc tgctggcatg 1020 tggaaaattt gatgatagca gatctagtac ctggtatcta gacaccggag catcaaatca 1080 tatgtgtggc atgaaggaag catttgcaga tattgatgag agttacaaag gaaaaatcac 1140 ttttggagat ctttctcaga tacctgttga aggaagaggc cgaattctta tacaactcaa 1200 gaatggtgag cagaaattca taacagaagt attttatgtt ccagacatga agagtaacat 1260 cttaagtctg ggacaatttc tggagcaaga ttttgaagtg cagatgaaga ataagaactt 1320 gaagattttt gatgaaactg gagctttaat tgcctcagtc aagatgacca aaaataggat 1380 gtttcctctt gacttaaatg tgtgtatgtc aaactgtttc aaggcagaaa gttcaaatct 1440 gacgaacttg tggcatttgc gttatggaca tctgaattgt ggatcattaa tgatgatgga 1500 gaaacacagg atggttctgg gaataccaca gctcgaacac acaaacgatt tgtgtgaagt 1560 gtgtgtgatg ggaaagcagc accgaaaatc cttcccaaag aagagttcta gagcatctca 1620 gcctctggaa ttggtgtatt cagatgtgtg tgggccaatt acacctacaa caataggggg 1680 aaacaggtat ttccttacat tcactgatga ttttagtgga aaaacatggg tatatgtgtt 1740 gaaagaaaaa aaagaagtgc tgagcaagtt taaggaattt aaaaatctag tagaaaagca 1800 aagtgaatgc aagctgaaaa atctgagaac tgatagggga ggagagtatg tgtctcatgc 1860 ttttgattat tattgtaaag agaatggtat agcacatcag ctcacaatgc cacagactcc 1920 acaacagaat ggagtatcgg agaggaaaaa taggactatt atgaacatgg ttagatgtat 1980 gttaaaagaa aagaattgtc ctaaagagtt ttggggagat gcagttgtgt gtgctgtgta 2040 tttgttgaac agatttacaa caaagaggtt gcatatgctt acaccagaag aagcctggag 2100 catgaagaaa ccgagagttg atcacttaag gatttttggc agcatagctt atgccaaaat 2160 tcaagatgaa aaacgaacca aacttgaaga taaaagtcag aaatgcatac tgctaggata 2220 tggagaaaat tcgtatggtt acaaattgtt caatccagta acaaaaaagg tgatcatgtc 2280 aagagatgtg agatttgatg aagagcaaga atggaactgg agtactgagg aacagctgca 2340 gaaattggtt gtagaagaag aacaaatgca gaatgatgaa gaagaaatca taatcaatcc 2400 agccccatca actagcagcc ctgctagtcc ttcaagttca gcaagaaaaa caaagagcat 2460 acaagaaatc tatgacgcaa cagagagaat gaaccttgat gatgtcaaca tgttgtgttt 2520 gttttcagga aatgatccca taacatttga agaagcatat caggaagaca agtggaagaa 2580 agcaatgaag gaggagatca attccattca gaagaacaat acatgggaac tgacaacact 2640 tcctgaaggt cacaatgcaa tcggagtaaa atggatcttc aagacaaaga agaatgctga 2700 aggagaaatt gaaaaacata aagccagatt agttgcaaaa gggtacaagc aacaatatgg 2760 agtagattat gaagatgttt ttgctccagt agcaagaatt gaaactgtga gattggtgat 2820 ttcattggct gctcagaaac aatggaagat atttcagatg gacgtaaaat cagcattctt 2880 gaatggcaat cttgaagagg aagtatatgt tgagcaacca gctggctttg tagtaaaagg 2940 agaagaagaa aaggtgtgca gattgaagaa agccctttac ggactcaaac aagcaccaag 3000 agcatggaac tcaagaattg atggctatct ttctcagaag gggtttacaa aatgcccgta 3060 tgaacatgca ttatatgtga agaaaaactt gcatggtaga ataatgtttg tttgtttata 3120 cgtggatgat attttgttca caggggatga tcctacaatg attcaagatt tcaagcaatc 3180 catggtaaag gaatttgaga tgacagactt aggtcttcta gcatattttc tgggattaga 3240 agtgaagcaa tgcagtaatg gaattttcgt ttctcaagcc aagtatgcaa cagaagtgtt 3300 aaagaaattt gctatggaag attgtgatcc agcagacaat ccagttgagt atggaacgag 3360 gttaactaaa gaaggagaag gagatttagt taatcctaca tattacaaaa gtattgtggg 3420 gtgtttgcgt tatctaactt gtaccagacc agacattctg tttggagttg gtttagttag 3480 cagatacatg gagagaccaa ggagttcaca tttgaaggca gcaaagagga tccttcggtt 3540 tattaaagga acattaaact atggattatg ttattcatca tcacagaatt tccaaatcac 3600 aggttatagt gatagtgatt gggcaggaag cttggaagac aggaaaagca caactggatt 3660 catatttttc atgggagaaa cagcattcac atggacatcc aagaaacaat ctattgttgc 3720 attatccaca tgtgaagcag aatacattgc tgctgcatca tgtgtgtgtc atgcaatatg 3780 gctaaggaaa ttgatggaag atctgcaaca gaaacagagt gaagccacaa aaattttcgt 3840 tgataacaag tctgctatag ctcttgcaaa gaatccagtg catcatgaac gttcaaagca 3900 tattgatact cgatttcatt ttattagaga gcacataaaa gaaggcgatg tggagttagt 3960 tcatgtcaac actcatgaac agattgctga tatttttaca aagccattga agactgaagt 4020 tttttgttat ctgcagaaga agcttggaat cgtgaagatt gatgaaacaa gtttaagagg 4080 ggtgaa 4086 // ID HAT-8N1_Mad repbase; DNA; EDCOT; 807 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-8N1_Mad. XX NM HAT-8N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-807 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1623-1623 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >95% identical to the consensus. 8-bp TSDs. The 5' terminus is CC ~80% and the 3' terminus is ~96% identical to those of CC HAT-8_Mad. XX SQ Sequence 807 BP; 264 A; 158 C; 133 G; 252 T; 0 other; tagggctgga aaaaaatccc aaaaatccca aaccgaacca aaaaattccc gaaaccaaac 60 cgaaaaaatc ccaaaccgaa attcccgaaa atttcggtac ccaataccga accgatcccg 120 aaatttcggt acgggaatcg gtctcaagtt tttgggattt cggtattccc aaaccgaacc 180 aaaaaaaaat atatatatat atatattgtt taatttttaa atatatattt agatttttaa 240 tagctgtcgg attctgttga gatttaatct caaccattga atataaattt gattatttga 300 ttatttgata ccttgcccct ccttaataat tcttcatctg gatggttcac atatgcattg 360 agatgaaaga ttcatgtgct atatagaaat ttaagctggc gtattatttt ttatgctaca 420 attgtactta ctggtgtaca cagactttct ttttccttcc atccattatt aaatccattt 480 ttacttactg gtgtacacgg actcaaattt gtgcacaaat tagtacaaac atgccttgcc 540 atttgattgg cagattagta gaaacaaatt ggcaaattga gctcaaaagc ataatatgtc 600 aaattttagt ccaaaagccc aaaagcccaa aaccatttcg ggattcccga tttgtcccga 660 aatcccgaaa ctatttcggg attcccaaaa attgggattc ccgaaaattt ggtttgggat 720 cggtattgaa attgggattc ccgaaaattt cggtttggga attgggacaa gggtttcggt 780 atgggatccc ataccgaacc accccta 807 // ID Harbinger-1_VV repbase; DNA; EDCOT; 4378 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE Harbinger-1_VV - DNA transposon from grapevine. XX KW Harbinger; DNA transposon; Transposable Element; TIR; PIF; KW Pifvine-1; Harbinger-1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4378 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 761-761 (2008). XX DR [1] (Consensus) XX CC Harbinger-1_VV (Pifvine-1 in [1]) is an autonomous DNA transposon CC from Vitis vinifera. CC Individual copies are 95% similar to their consensus. CC Elements are flanked by 3 bp-long target site duplications. CC Harbinger-1_VV has 20 bp-long terminal inverted repeat. XX FH Key Location/Qualifiers FT CDS join(1021..1383,1465..2082) FT /product="Harbinger-1_VV_ORF1" FT /note="Harbinger-like ORF1. Protein with unknown FT function, usually present in elements of the FT Harbinger superfamily." FT /translation="MSSNIVQPLQQPSGEESEKQSKAYWDDITMDAFIKVC FT VTETLAGNRPNSHFSKLGWKNVIKAFNNLTGRNYQYRQLKNKWSSLKKDWQ FT LWNTLIGKETGLGWDPMRQTINASNEWWDKKLKENPEAIKFKTKGLKNVEQ FT LDILFKDIIATGEGAWAPSQGFVGQDVDDSSKVGEHEDNIIEGQDDSSCNP FT SLDTISHSFEATTQPSMEKKNEGRRKRKRNETKSELVAIQLERICSAVENR FT SSISSRGDKPGCSIAEVMKIIRGMPEVKNDFELYMKATDIMVVKENREMFV FT ALEDPIDQIAWLKHKHVGVVSWFLYGNIFLLPNIV" FT CDS join(2341..3087,3170..3631) FT /product="Harbinger-1_VV_Transposase" FT /note="Harbinger-like DNA transposase." FT /translation="MPSNNNDQNFDDESDDEHDFYQLVXAGCAAAATFTSF FT KEKKPCRTSSHTXYKFVMDVLNGHEIRCFEQFRMEKHVFMNLLETLTKRYG FT LKEGFDMPLIEVLXXFLTTIGHGLSNRMIQERFQHSGESVSRWFEIVLDVV FT CLMAVDIIKPSDPQFKEVPDKIRNDDRYWPYFKNCIGVIDGTHIPVVVPRD FT RKIXYIGRKGVTTQNVMAVCDFNMCFTFAWAGWEGAAHDARVFLEALRRPE FT LGFPHPPRGKYYLVDAXYPQMSGYLGPYKGXRYHLPDFRRGSSPKGKKEIF FT NHRHSSLRCTIERTFAVLKNRWRMLREMHSFPLEKQVKIVIASMALHNFIR FT MVMLEWIWNLNLMMMIKGCFHLMKKRVEWIHLLRKMVHIIQERWKNNVIEL FT QIFXYLIDV" XX SQ Sequence 4378 BP; 1410 A; 550 C; 769 G; 1631 T; 18 other; tagcccgttt ggcagtgatt tttaaaagtg tttctaccct taaaaacact taaagtgttt 60 ttgggatgaa aataaagtgt ttggcaattt ttaaaaaaca cttttgaaaa tctggaaaaa 120 cacttgaagt gatttttaga gaatcacttg acaggtgttt tttwaaaaaa aacacttcaa 180 tttttttgaa atattccaaa aatgccccca gtgattcccg atatctttct tctctttcgt 240 tcatacctct ctcctttatt ctcctcctcc atcgctctcc atctgagaac aacatagtaa 300 acctctattt tcattcgaga tcgtggatcg aaggtaaccc tctattcttt ttttgttttc 360 cttttccata ttttttttaa tgtctgattg ccttgaaatg ttagttaggg ttttgggttt 420 taggattgtt tggttaggag gaaagtatga gaaaatgaaa tctgtaaatc ctcaaatgtt 480 tttataaatt gtgtttgatg tcatagaaac tgtggttaca ctgatctggc ggagccacag 540 aatggcacca tgtcattaga gattctatga catcactttc agtcttttct caaaatttta 600 ttttatagta atataattaa aatatatttt ttttatgtac araccagtgt tccatatgta 660 agttaatcgt cccttcatca tctgcatagt aattgtgcag gtgatgtatt catcaattgt 720 catgattgag acaaaacagc agggttagcc aatgaagtaa ttgatgtttg gttcgatatg 780 aagagtgggt tatattcaga acattaatcc attytgcatt acctattcta gattaaagca 840 tggtccacac tagcaaatta tggaaattct aaactttgca ctgattgttt atcaattaat 900 ggaccacata tattcttgat gttttgttcc ttaattcttt ctttattctt cattttaatt 960 gtgtgattct ttgtttgaaa attattattt ctctaaaata tatatwtttt taaatagaga 1020 atgtctagca atatagttca accattacaa caaccaagtg gtgaagaaag tgaaaaacaa 1080 agcaaggctt attgggatga tattacaatg gatgctttta tcaaagtttg tgtgactgag 1140 actttggctg gaaatagacc aaatagtcac tttagcaagt tgggatggaa aaatgtgata 1200 aaagccttca acaatttgac tggaagaaac tatcaatata ggcaacttaa gaataaatgg 1260 agttctctta aaaaggattg gcaactttgg aataccttga ttgggaaaga gactggcctt 1320 gggtgggatc ctatgagaca aaccatcaat gcaagcaatg aatggtggga taagaaattg 1380 aaggtatgtt ttgtttattc attaaattta tttgattaat ttatatattg gttatgaaat 1440 atgataaatt aaatactctt gtaggagaat cctgaagcaa taaagtttaa aacaaaaggc 1500 ttgaaaaatg ttgagcaatt agacatactt ttcaaagata ttattgctac tggtgaagga 1560 gcttgggcac catcacaagg ctttgtagga caagatgttg atgattcatc taaggtgggg 1620 gaacacgaag ataatataat agaaggccaa gatgactcta gttgcaatcc gtcacttgat 1680 actatctccc atagttttga agctactact caaccttcta tggaaaaaaa gaatgaagga 1740 agaagaaaga ggaaaagaaa tgaaaccaaa tctgagcttg tggctatcca gttagagcgc 1800 atttgtagtg ctgtggagaa taggtcttct atctcatcta gaggagataa gccaggttgt 1860 agcattgctg aagtgatgaa aatcatacgt ggcatgcctg aagtgaagaa tgactttgag 1920 ttatatatga aagccacaga tatcatggtt gtcaaggaaa atagagagat gtttgttgca 1980 ttagaagacc caattgatca gattgcatgg cttaaacata aacatgttgg agttgtttct 2040 tggttcttat atggaaacat atttttgcta cctaatattg tttagttgtt aggttgaggg 2100 gaggaaagag atgttggttt gctttatgtt agttgttatt ttatatttca tcttagtcat 2160 ttaacttttt ttttkaggtt tattatttct ataagatatt tttttttaat acaaaatgtc 2220 tagtaatggt aggaattcta aacttcaatt gtgtactttc taatttttta aaataactat 2280 agtaattgaa aatatacatt attgttgttt attaacatat ttcctttttt atttgtgtag 2340 atgccttcta ataataatga tcaaaatttt gatgatgaaa gcgatgatga acatgatttt 2400 tatcagttgg tgsttgcggg ttgtgctgca gctgcaacat ttactagttt caaagaaaaa 2460 aaaccttgta gaacttcttc ccacacakga tacaagtttg taatggatgt cttaaatggc 2520 catgaaatta ggtgttttga gcaatttaga atggaaaaac atgtgtttat gaatttatta 2580 gaaacactta ctaaaaggta tggcctaaaa gaaggttttg atatgccctt aatagaggtt 2640 ttarcawtgt ttctcactac aataggtcat ggactaagca ataggatgat tcaagaaaga 2700 tttcaacact ctggtgaatc tgtatctaga tggtttgaga ttgtattaga tgttgtttgt 2760 cttatggctg tagatattat aaaaccaagt gatccacagt ttaaggaagt ccctgataaa 2820 ataagaaatg atgatcggta ttggccatat tttaagaatt gtattggggt aattgatgga 2880 actcatatac ctgttgtggt tcctagagat agaaaaatac satatattgg tagaaaaggt 2940 gtgactaccc aaaatgttat ggcagtatgt gatttcaata tgtgtttcac atttgcatgg 3000 gccggatggg aaggtgctgc tcatgatgca cgagtctttt tagaggcatt aagaaggcca 3060 gaattgggtt ttcctcatcc acctagaggt ttgtgaatga taatatcaaa cttgtttttg 3120 tgatcaaatt tttattatct aatatatatw tttttktttt tgttttatag gtaaatatta 3180 tttggtcgat gctrgttatc ctcaaatgag tggatattta ggcccttata aaggcragcg 3240 ttaccatctt ccagattttc gacgaggtag ttcacctaaa ggtaaaaagg aaatatttaa 3300 tcataggcat tcatccttga ggtgcacaat tgagagaacg tttgccgttt tgaagaatag 3360 atggagaatg ctacgagaaa tgcatagttt tcctcttgag aaacaagtaa agatcgttat 3420 tgcttcaatg gctcttcaca acttcataag gatggtaatg ctagaatgga tatggaattt 3480 aaaccttatg atgatgatca agggttgctt ycacttaatg aagaagagag tagagtggat 3540 tcacttgttg aggaagatgg ttcacatcat acaagagaga tggaagaaca aygtgatcga 3600 attgcaaatc ttctyatatc tcattgatgt ttgattatga ctctaatatg taagaatata 3660 atttccccca atttttttgc tatgaaaaca cttgtcttct tatttacttt taattataat 3720 tttttttttg aggaaactaa taggtaatca tatattrttt tactttgaaa tttatctttt 3780 attcaatgtt cttttttatt gatttagata ttttttgtaa atatttttaa aaattttaat 3840 atattgataa aaaaaattat tatttttaat tagaaaaatc tttttttttt ttaaaattaa 3900 taggtggtca tatattgttt tacttttaaa attatctttc attcaatgtt cttttttttt 3960 tatttattga tttagatgtt ttttgtaaat attttttaaa attttagtat agtgataaaa 4020 aaattattat ttttaattag aaaagtcttt tttttttttt agaaattaat aggtaatcat 4080 atattgtttt aattttaaaa ttatcattta ttcaatgtta ttttttttag tgatttagat 4140 gttttttcat taataaaaag tttttttgtt tatcatacca tttttttaaa ttaaaattgt 4200 atgtcctttt tggtaattta ttaatattaa aagtgttttt atatttatac aatatattat 4260 caaaaacact ttagaatcat tttttctgat tatcataaaa gtgtttttca cagaaacact 4320 ataacagaaa acacttcaaa taaaaacact tccactagaa tcactaccaa acgggctc 4378 // ID Gypsy17-VV_I repbase; DNA; EDCOT; 7330 BP. XX AC AM437405; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy17-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-7330 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-7330 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 714-714 (2007). XX DR Genbank; AM437405; Positions 7787 15116. XX CC Positions [4868-5362] - Integrase core CC 'CTCCC' target site duplication CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 4811..5791 FT /product="Gypsy17-VV_I_2p" FT /translation="MCRSCDRCQRLGKLTKRNQMPMNPILIVDLFDVWGTD FT FMGPFPMSFGNSYILVGVDYISKWIEAIPCKHNDHRVVLKFLKENIFSRFG FT VPKAIISDGGTHFLNRPFETLLAKYGVKHKVATPYHPQTSGQVELANREIK FT NILMKVVITSRKDWSIKLHDSLWAYRTAYKTILGMSSYRLVYGKACHLPVK FT IEYKAWWAIKRLNIDFIRAGEKRCLDLNEMEELRNDAYINSKVAKQRMKRW FT HDQLISNKEFHKGQRVLLYDSRLHVFPGKLKSRWIGPFIIHQVHPNGMVEL FT LNSKITDIFKVNGHRLKPFIEPFKPEKEEINLLEP" FT CDS join(249..1229,1233..3611) FT /product="Gypsy17-VV_I_3p" FT /translation="MRNWIRDSGGRLVKRDIPHNKELELSLNIMEATPEDQ FT HSHHGHQDNPNEFISMRDRMHPPRMSAPSCIVPPTEQLVIRPHIVPLLPTF FT HGMESENPYAHIKEFEDVCNTFRDGGASIDLMRLKLFAFTLKDKTKIWLNS FT LRPRSIHTWTDLQAEFLKKFFPTYRTNGLKRQISNFSAKENDKFYECWERY FT MEAINACPHHGFDTWLLVSYFYDGMSFSMKQLLETMCGGDFMSKNPDEAMD FT FLSYVAKVSRGWDEPHRGEVGKMKSQPSAFNAKAGMYTLNEDDDMKAKFAV FT MTRRLEELELKKMHEVQAVAETPVQVKLCPICQSYHLMEECPTILAVREMF FT GDQANVVGQFKPNNNAPYGNTYNSSWRNHPNFSWKARTPQYQQSAQPSQQS FT SSLEQAIENLNKVVGDFVGDQKAIKAQLEDFVGAQKAINAQLSQIIDSVES FT TLNKKMDGMQNDLSQKIDNLQYSISRLTNLNTVQEKGRFPSQPHQNPKGIH FT EVKTHEGESSQVRDVKALITLRSGKKVEPPTLKPYVEEKKDKETKKEEEMK FT GKKKDFNENSEGEEDHGSTVNANPEKELIKEELMKKRTSPPFPQALHGKKG FT IKNASEILEVLRQVKVNIPLLDMIKQVPTYAKFLKDLCTIKRGLNVNKKAF FT LTEQVSAIIQCKSPLKYKDPGCPTISVMIGGKVVEKALLDMGASVNLLPYS FT VYKQLGLGELKPTSITLSLADRSVKIPRGVIEDFLVQVDNCYYPVDLVVLD FT TDPTVKEANSVPIILGRSFLATSNAIINCRNGLMQLTFGNMTLELNIFYMS FT KKQITLEEEEGAKEVCIIDTLVEEHYNQNMQDKLNESLKDLEEGLSEPPDV FT LATLQGWRRREEILPLFNKEEGEAAEEETPKLNLKPLPVELKYTYLEENNQ FT CPVIISSSLTSHQEISILEVLKRCKKAIGWQISDLKGISPLVCTHHIYMEE FT EAKPIRQPQRRLNPHLQEVVRAEVLKLLQAGIIYPISDSPWVSPTQVVPKK FT SGITMVQNKKGEEIATRLTSGWRVCIDYRKLNLVTRKDHFPLPFIDQVLER FT VSDHPFYYFLDGYSGYFQIEIDVEDQEKTTFTCPFGTYAYRRMPFGLWQCT FT CNIRKMYVEYLQ" XX SQ Sequence 7330 BP; 2311 A; 1273 C; 1586 G; 2160 T; 0 other; aatggcatcg ttgtcgggga aggtgccaac ttcatagtga tactatttca gagtacttgt 60 gattttcatc acaagtttgg taacttttct ttcattttac taattttttt ttttattgta 120 tctttacttg ttcataatct aatatatctt ttaaattcag tttagtttat tttagttatt 180 ttttggtaga cctgttttct tttgttttct tttattttca ttttagttac aattgatact 240 agttgtgtat gcgaaattgg atacgagata gtggaggaag gcttgtcaaa cgtgatatac 300 ctcataataa ggaattggaa ttgagcttga atatcatgga agctacacct gaagatcagc 360 atagtcacca tggtcaccag gacaatccca atgaattcat atcaatgagg gaccgaatgc 420 atccacctcg tatgagtgca ccatcatgta tagtgccccc tacagagcag ctagtgatca 480 gaccccatat tgtgccactt ctaccaactt tccatggaat ggaaagtgag aatccctatg 540 cccatatcaa ggaatttgaa gatgtttgta atacattccg agatggagga gcttctatcg 600 acctgatgag gcttaaacta tttgctttta ctttaaagga taagaccaag atttggctta 660 attctttaag gccaaggagt atccatactt ggactgattt acaagctgaa ttcctcaaga 720 agttcttccc tacttacaga acaaatggct tgaaaaggca aatttcaaac ttctcagcta 780 aagagaatga taaattctat gagtgttggg aaagatacat ggaagccatt aatgcttgtc 840 ctcaccatgg ctttgataca tggctgttgg tgagttattt ctatgatggg atgtctttct 900 caatgaagca actcctcgaa acaatgtgtg gaggggattt catgagtaag aatccagatg 960 aagctatgga tttcttgagt tatgtggcca aagtctcaag gggatgggat gaaccgcaca 1020 gaggagaagt gggaaaaatg aagtctcaac cgagtgcttt caatgctaag gctgggatgt 1080 ataccttgaa tgaagatgat gatatgaaag caaagtttgc ggtcatgaca agaagattgg 1140 aggagctaga actgaaaaag atgcatgaag tgcaagctgt tgctgaaaca ccagtgcaag 1200 taaagttgtg tcctatttgt caatcttatt aacacttgat ggaggagtgc cctacaattc 1260 tagctgtaag ggaaatgttt ggagatcaag caaatgtcgt tggacaattc aagcccaata 1320 acaatgcacc gtatggaaat acttacaatt caagttggag gaatcatcca aatttctcat 1380 ggaaggcaag aacacctcag taccaacaat cagctcaacc atctcaacaa tcttcaagtc 1440 ttgaacaagc aatagagaac ctcaacaagg ttgtgggaga ttttgttgga gaccaaaaag 1500 ccatcaaggc tcaactggaa gactttgttg gagcccaaaa agccatcaat gctcaactca 1560 gtcaaataat tgacagtgta gagagtactt tgaataaaaa gatggatgga atgcaaaatg 1620 atctatctca aaagatagat aatctccaat actcaatctc aaggctcact aacttgaaca 1680 cagtgcaaga gaagggtaga tttccttctc aacctcacca aaaccccaag ggtatccatg 1740 aagtgaaaac tcatgaggga gaatcttcac aggtgagaga tgttaaagcc ttgatcactc 1800 taaggagtgg aaaaaaggtt gagccaccaa cactcaagcc atatgttgaa gagaagaaag 1860 acaaagaaac aaagaaggag gaggaaatga aaggaaagaa aaaagatttc aatgaaaatt 1920 ccgaagggga ggaggaccat ggttcaacag tgaatgcaaa tccggaaaaa gagcttatta 1980 aggaagaatt gatgaagaaa cgtacatctc caccttttcc tcaagctttg catgggaaaa 2040 agggaataaa aaatgcatca gaaatccttg aagtattgag acaagtgaaa gtcaatattc 2100 cattgctaga catgattaag caagttccaa catatgcaaa gttcctaaag gacctgtgta 2160 ctatcaaaag agggttgaat gtgaacaaaa aagccttctt gactgagcaa gtgagtgcca 2220 tcatacaatg caagtctcct ttgaagtaca aagatccggg atgtcctacc atttcagtca 2280 tgattggagg aaaggtagtg gagaaagctt tgttagacat gggagcaagt gtgaatttgc 2340 taccatactc tgtctacaag caattgggac ttggtgagtt gaagccaaca tcaatcaccc 2400 tatctctagc agatagatca gtaaaaattc caaggggggt aattgaggat ttcttagttc 2460 aagttgataa ttgctactat ccggtagatc ttgttgttct tgatacggat cctactgtaa 2520 aggaagctaa ttcagttcct atcatccttg gaaggtcatt ccttgctacc tcaaatgcaa 2580 tcatcaattg taggaatgga ctcatgcaac tcacttttgg caacatgaca cttgagctca 2640 acatttttta tatgtctaaa aagcaaatca ctctggaaga agaagaaggt gcaaaagaag 2700 tatgcattat cgacactcta gtggaggagc actataatca gaatatgcaa gacaagctga 2760 atgaaagtct taaggatctt gaagaagggt tgtctgaacc ccccgatgtg cttgctactc 2820 tacaaggttg gaggaggaga gaagagattc tacctttgtt caataaagag gaaggagaag 2880 ctgctgaaga agagacccca aagctcaatt tgaagcctct gcccgtggag ctcaaatata 2940 cataccttga agaaaataat caatgtcctg ttattatatc ttcatctctt actagtcatc 3000 aagagatttc tatacttgaa gttctcaaga ggtgtaagaa agcaatagga tggcaaatat 3060 ctgacttgaa aggaatcagt cctttggttt gtacacatca catatatatg gaggaagaag 3120 ctaaaccaat tcgtcaacct caaagaagat tgaatcctca tttgcaagag gtggtgcgag 3180 ctgaagtgct gaagctactc caagcaggta ttatttatcc catatctgac agcccttggg 3240 tgagtcctac tcaagtggta ccaaagaagt cagggattac tatggttcag aataaaaaag 3300 gagaagaaat tgctacacgc ctcacttcag gttggagggt gtgtattgat tatagaaagt 3360 tgaatcttgt gacaaggaaa gatcattttc cactcccgtt tattgatcag gtgctggaga 3420 gagtctctga ccatcctttt tattatttct tggacgggta ctcagggtat tttcaaattg 3480 aaattgatgt ggaagaccag gagaaaacca ctttcacatg tccgtttgga acatacgcct 3540 atagaagaat gccttttggt ttatggcaat gcacctgcaa cattcgaaag atgtatgttg 3600 agtatcttca gtgatatggt ggagcgaatt atggaggttt tcatggatga catcaccgta 3660 tatggaggta catttgagga atgcttagtc aatttggaag cagttcttaa cagatgcatt 3720 gagaaggact tggtgctcaa ctgggagaaa ttccatttta tggtacgtca aggaattgtc 3780 cttggccata tcatctccga gaaaggcatt gaagttgata aagcaaagct ggagcttatt 3840 gtcaaattgt cgtccccaac aactgtgaaa ggggtaaggc aatttcttgg ccatgcaggg 3900 ttctatagga gatttataca agacttctct aagctttcaa aacctctttg tgagcttttg 3960 gctaaggatg ctaagtttat atgggatgaa agatgtcaaa atagttttga tcaattgaag 4020 caatttttga caaccgctcc aatagtaagg gctcctaact ggcaactacc ctttgaagtg 4080 atgtgtgatg ccagtgactt tgctatagga gctgtacttg gccaaagaga agatgggaag 4140 ccctacgtga tctactatgc aagcaaaaca ttgaacgaag ctcaaagaaa ctacataact 4200 acagagaaag aattgttagc tatggtgtat tgccttagac aagtttcatg cttatctagt 4260 agggtctttc atcattgttt tcactgacca ttcaaccttg aagtatttat tgacaaagca 4320 agatgcaaaa gcaaggttga ttagatggat tcttttgtta caagagttcg acctccaaat 4380 cagagacaaa aaatgggtag aaaatgtggt agctgaccac ctgtcaaggt tggctatagc 4440 acacaattcc catgtcttac ctattaatga tgactttcct gaggaatcac ttatgttgct 4500 agagaaagct ccttggtatg ctcatatcgc taactatttg gttactggtg aagttccaag 4560 tgagtggaat gcgcaaaata ggaagcactt ctttgcaaag attcatgctt attattggga 4620 agagcccttc cttttcaagt attgtgcaga tcagatcata agaaagtgtg tccctgaaga 4680 agagcaacaa ggaatcctca gccattgcca tgagaatgcc tgtggaggcc attttgcctc 4740 ttagaaaaca gccatgaagg tcttgcaata agggtttact tggtcatcgc ttttcaaaga 4800 ttcccacatc atgtgtagga gttgtgatag atgccaaagg cttgggaagc taacaaaacg 4860 aaatcaaatg cctatgaacc ccattctaat agttgatcta tttgatgttt ggggcactga 4920 cttcatggga cctttcccaa tgtcttttgg taattcttat atcttggtgg gggtggacta 4980 tatttctaaa tggattgagg caattccctg taaacataat gatcacaggg tggttctcaa 5040 gtttctcaaa gagaacatat tctcaaggtt tggggtgccc aaagccataa tcagtgatgg 5100 aggtactcat tttttaaata gaccttttga aaccctatta gccaagtatg gagtgaagca 5160 taaggtagct acaccttatc atcctcagac ttccgggcaa gttgagttag caaacaggga 5220 aatcaagaat atattgatga aagtggtgat cacgagcaga aaagattggt ctattaagct 5280 tcatgattca ctatgggcat acagaacagc ttacaagact attcttggta tgtcttctta 5340 tcgcctagtc tatggcaaag catgtcatct ccctgtgaaa attgaatata aagcttggtg 5400 ggcaatcaag aggttgaaca tagacttcat cagagctggg gaaaagaggt gcttagacct 5460 taatgagatg gaggaattaa gaaatgatgc ttacatcaat tccaaagttg caaaacagag 5520 gatgaagagg tggcatgatc aattaatctc caacaaagaa ttccataaag gacaaagagt 5580 cttgctttat gattcaagac tccatgtctt tccagggaag ctcaagtcga ggtggatagg 5640 ccctttcatt attcaccaag tgcatcccaa tggaatggtg gaattattga attccaaaat 5700 cactgacatt ttcaaggtca atggtcatcg tctcaagcca ttcattgagc cattcaaacc 5760 agaaaaggag gaaatcaacc tccttgagcc atagaaagcc tgatcagaga agggttagat 5820 ggacttggtt tcaccaaagt ccataatttt gttaaatatg ttaattttta agtcttgtaa 5880 attatttgat tgtaaatttg atcttaaatt ttgttaattg taaaatcagg agctcaggcc 5940 cagcacattg ccatcctgag gcagatccaa catcatctcg gcattacatc agctcctgag 6000 catgccattt cccaactcat caaagccatc acaggcccct ccttttgttg atcagcctat 6060 gcctcatcag gagcctccta caggagaggc agctgagcat cactccacgt cattcaggag 6120 gtaccacttc ctccctattg ttcaatcgtt tttgtcacat tgaggacaat gttcagcttg 6180 gttggggaga gagttgaaga agtaagtttt attattaatg ctaagttatt ttggtaattt 6240 agttgttttt gtttaatttt taaaattttt gaaagttttt tattctactc tccatggtta 6300 ttaaggaaat attttcaaaa tgaaatggga gaaattgaat atttttgtct ttttacttga 6360 cttagagttt gtattatgct tactaaagtt gatgaattgt tgaaactgct attgaattca 6420 accttagttc ttccacttta agctattcac acactgtgca taataggttc cgagtataag 6480 atgaaaaacc attttcctct tgacttagga aaatttagac ttggtacctt tgacctcatt 6540 taatagtgtt gggacacctt ataaaaggcc aatgagtctt tgaaaaaaaa aataaaacaa 6600 tgtttgcttg ccttgaaacc cgagcaaggt ctgaggggta tatggtgaaa atctttaaaa 6660 cctggtgccc taagccttca ttggttggga gtcgccgacc tcaatgctcg ttacaagggt 6720 ggataggtgg agtctaacat actgtaggtg cttgggtatt aaaatttatt ctcaaaagtc 6780 cgggataaaa tctgaggagt tagtggttga aagatcctta aatcttgatg ccctaaacct 6840 taataagttg ggagtcatcg atggaccccc gttgcatgga caaattagaa aagaatacct 6900 ttaagcctta cactcctgca atgaaaaaaa aagggtgcgt tcttagccta ttgaagttgg 6960 tcaatttgct aagtgttgaa aagagctagg ttggggggag agattagttt agcatactat 7020 atttggaagc tatcaagtaa tacctagatt tttgtggaag agtaaggatt ggtcctttgg 7080 aagtggaaat gattttaaag cttaaatttg cataatgtct tctctttaag aattgtgatt 7140 agacaagtta tttgataact cttgatgaag tttaagtttt atttctttaa tgttccatgt 7200 gagagttaga tgatcatgcc acttggaaat tgttttttga tcagcatgat gttgtaaatt 7260 atagtactgt ttatttttat ttttctctcc ttcattgtta agggactagc aatatgtcgg 7320 ttggggggag 7330 // ID Copia14-PTR_LTR repbase; DNA; EDCOT; 401 BP. XX AC LG_XI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia14-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-401 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-401 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 201-201 (2007). XX DR Genome; LG_XI; Positions 12517670 12518070. XX SQ Sequence 401 BP; 103 A; 61 C; 66 G; 171 T; 0 other; tgttgaagtt tggtacctaa gctagaacag gattacttag cagtaatcta ctgcatgatt 60 atctagttgt tagctgagat tactatctag attaggatat ggttttaatt cttttgttaa 120 gtttatctag gattaaacta acttgtaaac atctccttaa aataaaggag aagttggctg 180 gtacgtttct agagtttgtt tctctttgta attctgtttt cttttcctat aaataaaagg 240 gcatgggatg gtagtaacca actactcaat tctgctcttt gttctttata cttaaatact 300 aagttctgtg ttctttcttt tgttcttttc catcgtggac ttagttcttt gttcttttct 360 cttttatcag caaacataag gcagttcttt atatttctac a 401 // ID BVBNR1 repbase; DNA; EDCOT; 324 BP. XX AC Z38074; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Beta vulgaris TY1-copia type retrotransposon BVBNR1, DNA for DE reverse transcriptase (partial). XX KW Copia; LTR Retrotransposon; Transposable Element; BVBNR1; KW retrotransposon; Ty1/COPIA superfamily; partial sequence; KW pol gene; reverse transcriptase. XX OS Beta vulgaris OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC Caryophyllales; Amaranthaceae; Beta. XX RN [1] RP 1-324 RA Schmidt T., Kubis S. and Heslop-Harrison S.J.; RT "Analysis and chromosomal localization of retrotransposons in RT sugar beet (Beta vulgaris L.): LINEs and Ty1-copia-like elements RT as major components of the genome."; RL Chromosome Res 3(6), 335-345 (1995). XX DR Genbank; Z38074; Positions 1 324. XX SQ Sequence 324 BP; 89 A; 69 C; 80 G; 86 T; 0 other; aaggcttttg acagtgtctc atggagattt ttagaatgga aacttcaaca aatgaacttt 60 ccattgaagt ggcgagatgg attagaggat gtgtaatgtc ggtgtcggct agtatactca 120 ttatcggcac atcctcacac ctagtgaagc tacatcgagg gataaggcag ggggaccctt 180 tgtccccctt ccttttcgat gtgatagcag agacactcaa tctctaatta aaaaggcaac 240 ctccttgtga ctttgggagg ggatcgaaat ttgcaaaggt ggatccaaaa tcactcacct 300 tcagtacgcc gacgtgcggg tacc 324 // ID HAT-1_Mad repbase; DNA; EDCOT; 3634 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-1_Mad. XX NM HAT-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3634 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1606-1606 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 14-bp long. XX FH Key Location/Qualifiers FT CDS 1120..3495 FT /product="HAT-1_Mad_1p" FT /translation="MERFFKRKSSSGSGSSNNVDSSNTVGSSRTPSSRQSQ FT LDDVLGNLQADPGLRTRIIDYDANMRDEVRRLYLQKGPCQPRGHNFPITNM FT SGINRRFIPQWFDEFDWLEYSVSKDAAFCLYCYLFKTNFEQVGSEAFTGDG FT FKNWKKGRERFKMHVGPVGSVHNKAREAATNLMNQATHIETAVSKHSDQTR FT KAYRTCLIASIKCTKFLLRQGLPFRGHDESATSSNRGNYLELLQFLADNND FT KVREVVMENAPGNLKLLAPSIQKEIVNSCALETLDAIMDGLKDRFFSILVD FT EARDVSVKEQMAMVLRYVDDNGHVIERFVGIQHVTDTTSSSLKDAIDTLFS FT RYGLSISKLRGQGYDGASNMRGELNGLKTKILREQPCAYYVHCFAHQLQLA FT LVAVAKNNIDIASFFATANNVVNHVGASCKRRDSLRGQLQEELVIAFENDC FT LITGRGLNQETSLKRAGDTRWNSHYGTLISIISMFSSVVHVLQMVIDDNPN FT ESAGEANTLMRVILTFEFVFHLFLMKVILGLTNDLSQALQRKDQEIVNAMA FT LVKSCKEKLYWMRNNGFDALVDEVSSFCEKHHIDVPNMEEAFILPGRSRRY FT APIKTNRHHYRVELFIYVIDEQITELEDRFNEVNTELLICMACLSPKDSFV FT AFDKPKLLRLAQFYPQDFSDEDRLALEDQLEIYIHYVCSSSDFSQLEGIGD FT LAKKMVETRMHQVFNYVYLLITLSLVLPVATASVERAFSVMNIVKGPLRNK FT MGDQWLSDSLLVYIERDIFACIENEAIMLRFQNMKPRRGQL" XX SQ Sequence 3634 BP; 1045 A; 583 C; 761 G; 1245 T; 0 other; caggggcgga tccacagtgg ggtcgtcggg gtcgcacgac cccttggaaa ccatggaaac 60 aaccttgaag ctcccatatg cgacctcttg gagctggggt cgtcggggtc gtcggggtcg 120 gactcgcacg ccaactgttc gacaaaaagc ctgaacgaag ctcggcagga agaggaagaa 180 gaagcagcgc tcgcgcgcgc ttcttttttt tcaaaacaga cgggcaaaac ggcgtcgttt 240 tggcccagga aattttttta aatgacctgg ccaaaacggc gtcgttttgg gccaggccga 300 acaaaaaaaa aaaaaaaaaa ttcccaccgt gtcccccccc agtcccagcc ttcctacccg 360 acccctatac aatcaaaagc cccaattttt catcctccaa ccctaactca atccccccaa 420 accctcaact cctctcctcc cttgctgctg ctgcccccaa accctcaacg tcaactccat 480 ctcctccctt gctgctcctc tgctggcggc tccaactcca tctcctccct ttgtttatat 540 attgtgatgt gagtatttat tttgaatatt ttgtatatgt agaatatatt taattaattg 600 aaattcaatt catatttatt ttgtgagttt ttattgtgag tttttattga tggtttgttt 660 atattgatga tttgtttata ttgtgagttt ttattggttt gtttttattg atggtttgtt 720 tatattgatg gtttgtttat attgtgattt tttattttca ttattttgta tatgtagaat 780 gcaagatgag atatttaatt taattgaaat ccaattcata tttattttga ttatgtttat 840 ggtttgttta tattgtgagt atttattttg aatattttgt atatgtagaa tatatttaat 900 ttaattgaaa ttcaattcat atttattttg attatattga tggtttgttt atattgtgag 960 tttttatttt cattattttg tatatgtaga aattagaatg caagatgaga tatttaattt 1020 aattgaaaat ccaattcata tttattttga ttatgtttat ggtttgttta tattgtgagt 1080 atttattttg aatattttgt atatgtagca agcattatta tggaacggtt ttttaagaga 1140 aagtcatcat cgggttcggg tagttcgaat aatgttgata gttcaaatac tgttggtagt 1200 tcaagaactc caagttcaag acaaagtcag ttagatgatg ttttgggtaa tcttcaagcg 1260 gatcctggat taagaactcg aataatagat tatgacgcta atatgagaga tgaggtccga 1320 agattatatc tacaaaaagg accttgtcaa cctagaggtc ataatttccc aataactaat 1380 atgtcgggaa ttaatcgacg cttcattccc caatggtttg atgagtttga ttggttggag 1440 tatagtgtat ctaaagatgc ggcattttgt ctctattgct atctctttaa aaccaatttt 1500 gaacaagtgg gtagtgaagc tttcactgga gatggattta agaattggaa gaaagggaga 1560 gaaagattta agatgcatgt tggaccggtt gggagtgttc ataataaggc tagagaagct 1620 gctacaaatt tgatgaatca agctacacat attgaaacgg cagtgagcaa acactctgac 1680 caaactcgta aggcttatcg cacatgcttg attgcttcaa tcaagtgcac taagttttta 1740 ttgcgacaag gtcttccttt tcgtggccat gatgaaagtg ccacttcaag caatagggga 1800 aattacttgg agttattgca attccttgca gataataatg ataaagttag agaagttgtg 1860 atggaaaatg ctccggggaa tctcaaatta ctagctcctt ccattcaaaa agaaattgtg 1920 aattcatgtg cccttgaaac acttgatgct atcatggatg gtctaaaaga tagattcttt 1980 tcaatattgg tggatgaagc acgtgatgtg tctgtgaaag agcaaatggc tatggtgttg 2040 cgttatgtgg atgacaacgg gcatgtaatt gaaagatttg tgggtatcca acatgttacc 2100 gacactactt caagttcact aaaggatgct attgacacat tgttttctcg ctacggtttg 2160 agcatttcca agctacgagg acaaggttat gatggtgcta gcaatatgag aggtgagttg 2220 aatggcctta aaacaaagat attgagagaa caaccttgtg catattatgt tcattgcttt 2280 gctcatcaac ttcaactagc tcttgttgcc gtagcaaaga ataatataga cattgcctct 2340 ttttttgcaa cggctaataa tgtggttaat catgttggag catcttgtaa gcggcgtgat 2400 tcacttagag ggcaacttca agaagagctt gtgatagctt ttgaaaatga ttgtcttata 2460 acggggcgag gcttaaatca agaaacaagt ctcaaacgtg ccggtgacac acgatggaac 2520 tcacactatg gtaccttgat tagcatcatt tctatgtttt catccgtggt tcatgtgctt 2580 caaatggtta ttgatgataa tcccaatgaa agtgcgggtg aagcaaatac gttaatgaga 2640 gtgatactta cttttgagtt tgtgtttcac cttttcttga tgaaagtcat attgggactc 2700 acaaatgatt tgtcacaagc attgcaaagg aaagatcaag aaattgtgaa tgcaatggct 2760 ttagtgaaat catgcaagga aaagctatat tggatgagga ataatgggtt cgatgcattg 2820 gttgatgaag tatcttcttt ttgtgaaaaa catcatattg atgttcctaa catggaagag 2880 gcatttatac ttccagggag gtcaaggcgt tatgctccaa taaagacaaa tcgtcatcat 2940 tatcgtgtgg agctctttat ttatgtcatt gatgagcaaa ttacggagtt agaggatcgc 3000 tttaatgagg taaataccga gttgcttatt tgtatggcat gtttgagtcc gaaagattca 3060 tttgtagctt ttgataaacc aaagttactt cgtcttgctc aattttatcc tcaagacttt 3120 tcggatgaag atcgtttggc acttgaagat caacttgaga tttatattca ttatgtgtgt 3180 tccagtagtg atttctctca attggaaggg attggtgatc ttgcaaaaaa aatggtggag 3240 acaaggatgc atcaagtatt caattatgta tatttgctca ttacattgtc tttagtttta 3300 ccagttgcaa ctgcttcagt ggagagagca ttttctgtca tgaatattgt taagggtcca 3360 cttaggaaca aaatgggaga tcaatggttg agtgatagct tgcttgttta tattgagaga 3420 gatatttttg cttgtattga aaatgaagct ataatgcttc gttttcaaaa tatgaaacct 3480 cgtcgtggac aattatagtt tgtaatattg tttccattat gaattatgaa tgaaagtact 3540 atgatttcat tttcaatatg tttttccatc ctaaattttt atttgaactt ttacactgcg 3600 accccttggg gtaagattcc tggatccgcc actg 3634 // ID COP18_I_MT repbase; DNA; EDCOT; 4117 BP. XX AC . XX DT 10-JAN-2007 (Rel. 12.01, Created) DT 06-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, COP18_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed repeat; terminal; ORF; COP18_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4117 RA Shankar R. and Jurka J.; RT "COP18_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 13-13 (2007). XX DR [1] (Consensus) XX CC The region has domains for gag-pol polyprotein. XX FH Key Location/Qualifiers FT CDS join(35..1567,1571..1780,1862..4054) FT /product="COP18_I_MT_p" FT /translation="MSHKFDIEKFDGKISFSIWRVQMRAVLTQNGLKKALH FT GKTKKSTSMTDEQWDELDEKALSSIQLCLSKEVLREVVNEMTAAGLWLKLE FT TLYMTKNLANKLHLKERIYTIRMVEGTPIQSHLDEFNSIILDLENIDVKID FT DEDKVVLLVVSLPSTYKHFKEIMLYGNNDTLSFEDVKSNLLFKEKFDLEVH FT SVDKGEGLSVRGRTQEKGSTSHKKSRSKSRGRKSNKTCRYCKKSGHEISDC FT FILKKKQEKQEKGKSPQSPEAANIEADSGDDITLFVVSSNKRSKTEWILDT FT GCTFHMCPYKDLFTTFERVDYGVVLMGNDAQCKVAGIGTVQFKTNDGVVRT FT LTNVRYIPDLKRNLISLGTLESLGCKYSAEGGVLKVSKGSLVLLKANRIGS FT LYVLQGTVVTGSAVVSSSIPENDVTKLWHMRLGHMSEKGMHLLSKQGRLGK FT QCIDKLEFCKHCVFGKQKKVSFSTATHRTKGILDYIHSDLWGPSKVTSYGG FT RRYMMTIIDDFSRKVVYFLRHKNETFPTFKKWKILVETQTGKNVKKLRTDN FT GLEFCSGDFNEFCSNHGIARHKTIMRNPQQNGVAAEAASTACYLVNRSPHS FT ALDFKVPEEIWSGNPVDYSNLRIFGCPAYAHVNDGKLAPRAVECIFLGYAS FT ESKGYRLWCSDPKSQKLILSRDVTFNEDSLLSSGKQSFVSSSTSTGNLQST FT SEKVEFVLKPASPNVDVPSTSTNESNIDDHSIDDDDDDSTTSPIQQQGDDY FT SISRDRVRRQIRKPARYTDNDNLVAYALSIAQEVNDGVEPISYTEAVSCVE FT SSQWLVAMNEEIESLQKNGTWALTELPNGKRPLRCKWIYKKKDDIPGVEDP FT RCKARLVVKGFNRKEGIDFNEIFSPVVRHTSIRVLLAFVALFDLELEQLDV FT KTAFLHGELEEEIYMEQPEGFISPGKEHLVCRLKKSLYGLKQAPRQWYKRF FT DSFMIGQNYCRSQYDDCIYFQNFQNGSFIYLLLYVDDMLIASRDKSLIKKL FT KTQLSNEFDMKELGATKKILGMEIRRDRQAGKLFLSQQKYIERVLDRFNMN FT NCKPVSTPLAAHFKLSSEFCPNTKEEMEHMSYVPYASAVGSLMYAMVCTRP FT DLAYAVSIVSRYMHNPGKSHWSAVKWIFRYLKGTSGIGLVFDRKMATTNDV FT AGYVDSDYGGDLDGRRSLSGYIFTLCNSAISWKATLQSIAALSTTEAEYIS FT ATEGVKEAIWLRGLVNELGLTQGVLTVFCDSQSAIHLTKNNRYHDKTKHID FT VRRHFIRDIVVAGEIAVEKIHTSKNPEDMLTKPLPNTKFQHCLDLVGLYST FT " XX SQ Sequence 4117 BP; 1244 A; 699 C; 885 G; 1289 T; 0 other; agtggtatca gagctcttag ttgggaattt caaaatgtct cataaatttg acattgagaa 60 gtttgatggc aagattagct tttctatttg gcgagtccaa atgagggccg ttcttactca 120 gaacggatta aagaaagctt tacatggaaa gacgaagaaa tcgacttcca tgaccgatga 180 gcagtgggac gagttggatg aaaaggcgct ttcatcaatc caactttgct tgtccaaaga 240 ggttctccgt gaagtagtca atgaaatgac cgctgcagga ttatggctga agttagaaac 300 tctatacatg accaagaacc ttgcaaacaa gcttcatctc aaagaacgca tatataccat 360 tagaatggtt gaaggtactc ctattcaatc tcatcttgat gaatttaact ctatcatttt 420 ggatctggaa aatattgatg ttaaaattga tgatgaggat aaagttgttt tgttggttgt 480 ctctttacct tctacctaca aacatttcaa agaaatcatg ttgtatggaa ataatgatac 540 cttatccttt gaagatgtta aatctaattt attgttcaaa gaaaaatttg atcttgaagt 600 tcattctgtg gacaagggtg agggcttaag tgttagaggt agaactcaag aaaaagggag 660 taccagtcac aaaaaatcca gatccaaatc cagaggacgc aaatccaaca aaacctgtcg 720 ctattgcaag aaatctggcc atgagatttc tgattgtttt atcttgaaga aaaagcaaga 780 aaaacaagaa aaagggaaat ctccacaatc ccctgaagct gccaatattg aagctgattc 840 tggcgatgac attactttat ttgttgtatc ctctaataag aggagtaaaa cagaatggat 900 tcttgatact ggatgtactt ttcatatgtg tccttataag gatttattta ccacttttga 960 acgtgttgat tatggtgttg tcttgatggg taatgatgcc caatgcaagg ttgcaggtat 1020 aggtacagtc cagttcaaga ctaatgatgg tgtcgtcagg actttgacta acgtccgcta 1080 tatacctgat ttgaagcgga atttaatctc tcttggcact ctcgagtctc ttgggtgcaa 1140 gtactcagct gaaggtggag ttctaaaggt atcgaaagga tctcttgttt tactgaaagc 1200 taaccgaatt ggtagtttat atgtcctgca agggactgtt gtgacagggt cagcagttgt 1260 atcatcttct atacctgaaa atgatgtcac caaattatgg cacatgcgcc taggccatat 1320 gagtgaaaaa ggcatgcatc ttctgagcaa gcaaggtcgt cttggtaaac aatgcatcga 1380 taagttggag ttttgtaaac attgtgtttt tgggaaacag aaaaaggtta gtttctctac 1440 tgcaactcac cgtaccaaag gtattcttga ttatattcat tctgaccttt gggggccttc 1500 aaaagttact tcctatggag gacgccgcta tatgatgact attattgatg atttttctcg 1560 taaggtttga gtttattttt tgcggcataa aaatgagact tttcccacat tcaagaagtg 1620 gaaaattctt gttgaaactc agacagggaa aaatgtgaaa aagctcagaa cagataatgg 1680 attagagttc tgcagtggtg actttaacga gttctgctca aatcatggta ttgctagaca 1740 caaaaccatt atgaggaatc cccagcaaaa cggtgttgca taacgaatga acagaactct 1800 acttgagaga gcttgatgta tgctctcaaa tgttgggtta tggcatcgac gtgatctttg 1860 agccgaggca gcatctactg catgttactt ggtcaaccgt tctccacatt cagcacttga 1920 cttcaaagtt ccagaagaga tttggtcagg taatcctgtt gattattcta atttaagaat 1980 ttttggatgt cctgcatatg cacatgtcaa tgatggcaaa ttagctccaa gagctgttga 2040 gtgcatattt cttggttatg catctgagtc taaggggtat cgtttgtggt gctctgatcc 2100 aaaatcacaa aaattaattc ttagtagaga tgtgactttt aatgaggatt cattattatc 2160 ttctggaaaa cagtcttttg tgtcttcttc tactagtaca ggtaatctgc aaagtactag 2220 cgagaaggtg gagtttgtat taaagcccgc atctcctaat gttgatgtcc catctacttc 2280 aacaaatgaa tccaacattg atgatcattc tattgatgat gacgatgatg atagtaccac 2340 ttctcctatt cagcaacaag gagatgatta ctctatttcc cgagacagag ttagaagaca 2400 aatcagaaag ccagccagat acactgataa tgacaattta gttgcttatg cactgtctat 2460 tgcacaagag gtaaatgatg gtgttgaacc tatcagctat actgaagctg tttcttgtgt 2520 tgaatcttct cagtggctag tggctatgaa tgaagaaatt gagagtcttc aaaaaaatgg 2580 tacttgggct ttgacagagc ttcctaatgg caaacgacca ttaaggtgta aatggatcta 2640 taagaagaaa gacgacattc ctggggttga agatccaaga tgcaaagcac gactagtcgt 2700 taaaggcttt aatcgaaagg aaggtattga ctttaatgag atattctcac ctgttgttcg 2760 tcatacttcc attcgtgttt tacttgcatt tgttgctttg tttgatttgg agttagagca 2820 acttgatgtt aagacagctt tcctacatgg agagctggaa gaagaaattt acatggaaca 2880 acctgaggga tttatttctc ctggaaagga gcatcttgtc tgtcgtttga agaaatcttt 2940 atatggcctt aagcaagctc cgaggcagtg gtacaaaagg tttgactctt tcatgattgg 3000 gcaaaattat tgcagaagtc aatatgacga ctgcatttat tttcaaaatt ttcaaaatgg 3060 atctttcata tacttgttac tttatgttga tgatatgtta attgcatcac gtgacaagtc 3120 tttaatcaag aaattgaaaa ctcaactcag taatgagttt gatatgaaag aattaggtgc 3180 aacaaagaaa attcttggta tggagattcg tagagaccgt caagctggta aactattctt 3240 atctcaacaa aagtatattg agagagtgct tgataggttt aatatgaata attgtaaacc 3300 tgtttctact ccacttgctg cgcatttcaa gttgtcttca gaattttgcc caaatacaaa 3360 ggaagagatg gagcatatgt catatgttcc ttatgctagt gcagttggta gtcttatgta 3420 tgccatggta tgcactagac cagatctagc atatgctgtt agcatagtaa gccggtatat 3480 gcataatcct ggcaagagtc actggagtgc tgtaaaatgg atttttcggt atctaaaagg 3540 tacttccggt attggcttgg tttttgacag aaaaatggct acaaccaatg atgttgcagg 3600 ttatgttgac tcggattatg gtggtgatct tgatggcaga agatctcttt ctggttacat 3660 ctttactcta tgtaatagtg ctatcagctg gaaagctaca cttcaatcta ttgctgcatt 3720 gtctacaact gaagcagaat atatttcagc aacagagggt gttaaagaag ctatttggct 3780 tcgaggtttg gtcaatgaac ttggtcttac acagggtgtt cttactgtat tttgtgacag 3840 ccaaagtgct attcatttga ccaagaataa tcgttatcac gacaagacca aacatattga 3900 tgtaagacgt cactttatcc gagatattgt tgttgctggt gaaattgcag ttgaaaagat 3960 tcacacttct aagaatccag aagatatgct taccaagcca cttccaaata ccaagtttca 4020 gcattgcctg gacttggttg gtctctacag cacttgaacg cccttcgggg ctttatttgg 4080 cgatgagcac ttgtcgaatt cgaaccaagg tggagat 4117 // ID Copia4-VV_I repbase; DNA; EDCOT; 4551 BP. XX AC AM469526; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia4-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4551 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4551 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 741-741 (2007). XX DR Genbank; AM469526; Positions 6771 2221. XX CC Positions [2148-2438] - Integrase core CC 'ATATA' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1290..2144,2148..4541) FT /product="Copia4-VV_I_1p" FT /translation="MVSADEFAKFSQYQESLKISTPVTTLAETCKTCLISS FT SNKWVIDSGATNHMTDNPKTFSSFRSHLASSPVTIADGSTSNVVGSRTVKP FT TSSITLSSVLSLPKLAFNLISVSKLTKDLNCCISFFLDHCLFQDLMTKQII FT GKGHVYDGLYILDAWVPRSVACSSIASSVKAHCRLGHPSLPVLKKLCPQFH FT SLPSFNCESCHFAKHHYSSLSPRVNKRAESIFELVHFDVWGPCPITSKTGF FT RYFVTFVDDFSRMTWIYFMKNRSEVFSHFCAFCAEIKTQFNISVTLRSDNG FT KEYMSNSLQSYMTQHGILHQSSCVDTPSQNGVAERKNRHLLETARALLFQM FT KVPKQFWADAISIACFLINRMPSTVLNDPIPYSILFPKKSLFPVEPRIFGS FT TCYVRDVRPSVTKLDPKALKCVFLGYSRLQKGYRCFSPDLNKYVVSTDVVF FT SEDTPFYSSPPNSESEGEGENWLIYQETIPSTPTDSSEQPQAVVDLLPAPA FT KPPIVQEYSSHQETKDTCPAPTSSLSDPPSDLDLPIGLHKGKRQCKSVYSI FT VNFVSYDHLSPSSSAFVASLDSVSIPKTVKKALNHPGWYNAMLEEIQALEV FT NHTWNRVDLPIGKNVVGCKWVFAIKVNPNGSVARLKARLVAEGYAQTYGVD FT YSNTFSPVARLASVHLIISITASQHWPLHQLDIKNAFLHGDLQEEVYMEQP FT PGFVAQVEYGKVCHLRKSLYGLKQSPRAWFGKFSEMIQEFGMNKSKVDHSV FT FYRQSANGIILLVVYVDDIVITGSDCAGISSLKLFMHSKFHTKDLGELKYF FT LGVEVSRSKRGIFLSQRKYVLDLLAETGKMEAKPCSTPMIPNVHLTKDDGD FT PFDNLERYKRLVGKLNYLTVTCPDIAYAVSIVSQFMSAPTVKNWAALEQIL FT CYLKRAPGLGILYSNHGHAQIECFTDADWAGSKADRRSTTGFCVFVGGNLV FT SWKSKKQNVVSRSSAESENRAMAQATCEIMWLYHLLIEIGIKTPMPAKLGC FT DNQAAIHIASNPVYHERTKHIEVDCHFIREKIQENLISTSYVKTGEQLGDI FT FTKALNGTRVEYFCNKLGMINIYAPA" XX SQ Sequence 4551 BP; 1291 A; 863 C; 941 G; 1456 T; 0 other; tggtatcaga gccacgtttg gctcaaggga attttctggg ttttgggttt tgttccgaac 60 aatctggaac agtaacctgt tacgtttttt tgagtctgga ttgcgtcacc gccgacccag 120 ggaggagcgc attcttgttt ccggagcgtg ggagcgcgtg agaccaccgt ttcttcaccg 180 atttgacttt ctgacgtttc ccatctcttg atctgacttt ccgacgtttc tcatctcttt 240 ccgaccattc tcaggtggca ctccggtgtt cgatcaactg ttgagaggaa catctccttg 300 gcaggttctg tcccctttga tttgttctct gattccttgt ggaaattcat tttgggtatc 360 aacttttttt ggtttgctgc tggaattata tttattgtgg cgattgaata tcagttaaaa 420 tgactgacaa caaagcttct ataactgaaa tagttccagc actgtccaaa ataactgatc 480 ataaattaaa tggcactaat tatctggaat ggagcaagac aattagagtt tatttgcata 540 gtgttgaaaa ggatgaccac ctgaccatgg aaacccctga taatgaaact agaaagactt 600 ggataaggga tgatgcacgt ttattcctac aaataaggaa ttctattgat agtgaaattg 660 ttggactact taatcattgt gagtttgtta aagaattaat ggattatctg gagttcttat 720 attctggcaa agggaatctg tcccgaatgt atgatgtgtg caaagccttc tatcgtgttg 780 aaaaggaggc caaatctctc acaacttatt ttatggattt taagaagact tatgaggagt 840 tgaatgtact tttacctttc agtactgata ttaaggtgca acaaactcag agagaaaaaa 900 tggtagtaat gagtttttta attggccttc catctgaatt tgaaactgct aaatctcaaa 960 ttctttccag ttctgagatt ggttcacttc aagaagtgtt caatagaatt ttgcgtactg 1020 aaggtacctc atctatccag cagactaata atgttcttgt tgccaaatga ggaagcaatg 1080 atactgggag aaaatcaaac aacaggagag gaagcaagac ttctgatagc tataacaatt 1140 attcaagcaa cattgtttgc tactactgtc atgagccggg ccataccaag aaatactgta 1200 agaaattaca aaactgtaat aaaagaaatc agattgctaa tgttgccacc gccactagta 1260 cttcttcaag ttcttttgat aagacggtca tggtctcagc cgatgagttt gcaaaattct 1320 ctcagtatca agaatcattg aagatttcta ctccggttac tactcttgct gagacatgta 1380 aaacatgtct tatctcctcc tcaaacaaat gggtaattga ttcaggtgcc actaatcaca 1440 tgacagataa tcctaagaca ttctctagtt ttcgatcaca tttagcctct tctcctgtta 1500 ccattgctga tgggtcaacc tctaatgttg tgggttctag gactgtcaaa ccaacatcct 1560 ctatcacttt gtcatctgtt ctaagtttac ctaagcttgc ctttaacttg atatctgtca 1620 gtaaacttac caaagatctg aactgttgta tctcgttctt tcttgaccat tgcctttttc 1680 aggatcttat gacgaagcag attattggta aaggacatgt atatgatggt ctttacattc 1740 ttgatgcgtg ggtacctcgg tcggttgctt gttctagcat cgcttcttca gttaaagctc 1800 attgtcgttt gggacatccc tctttaccag tgttaaagaa gttatgtcct cagtttcata 1860 gtttaccttc gtttaattgt gaatcatgtc attttgcaaa gcatcactat agttcgttaa 1920 gcccaagagt taataagagg gctgaatcta tttttgagtt agtacacttt gatgtttggg 1980 gaccttgtcc tattacttct aaaactggat ttcgatattt tgttacattt gtggatgatt 2040 tttctcgaat gacttggatt tattttatga agaatcggtc tgaagttttc tctcattttt 2100 gcgcattttg tgctgagatt aaaacacagt ttaatatctc tgtatgaaca ttgagaagtg 2160 ataatggtaa agaatatatg tctaactcat tgcagagtta catgactcaa cacgggattc 2220 ttcatcagtc ctcttgtgtg gatactcctt ctcaaaatgg agttgctgag agaaagaata 2280 gacatttact agaaacagcc cgggcactct tgttccagat gaaggttcct aaacagtttt 2340 gggctgatgc gatttctatt gcttgctttt tgattaatcg catgccatct acagtactca 2400 atgatcctat cccatacagt atattgtttc caaagaagtc tctatttcca gttgaaccac 2460 gaatttttgg aagcacttgc tatgttcgag atgtaaggcc atctgtgact aaactagatc 2520 ctaaagccct gaagtgtgtg ttcttagggt attctcgtct tcagaaaggt tatcgatgct 2580 tttctcctga tctcaacaaa tatgtggtat cgactgatgt ggtattttca gaagatacac 2640 ctttttattc ttcaccccca aattcagaaa gtgaggggga aggtgaaaat tggctcatat 2700 atcaagaaac catcccaagt actcccactg attcttctga gcaaccacaa gctgttgttg 2760 acttactgcc tgctccagct aagccaccaa ttgttcagga atactccagt catcaggaga 2820 caaaagatac atgtcctgca ccaacttctt cgttatctga tcctcccagt gaccttgacc 2880 tccccattgg tcttcataaa ggtaaacgtc aatgcaaatc agtttattcc attgttaatt 2940 tcgtttctta tgatcacttg tctccttcct cgagcgcttt tgttgcctct ttagattctg 3000 tctctattcc caaaactgtc aagaaagcct tgaatcaccc tggatggtat aatgcaatgc 3060 ttgaggaaat acaagctcta gaagtcaatc acacatggaa tcgagttgat ttaccaatag 3120 gaaagaatgt tgtgggatgt aagtgggtct ttgcaataaa agttaatcct aatggctcag 3180 tggcacgact gaaagccaga cttgtagctg aaggctatgc tcagacttat ggggtggact 3240 attctaatac tttctctcca gtagccagac ttgcttcagt ccacctgatt atatcaatta 3300 ctgcttctca gcattggccc ctgcaccagc tggatataaa aaatgcattc cttcacggag 3360 atctccagga agaagtatat atggagcaac cacctgggtt tgttgctcag gtggagtatg 3420 ggaaagtgtg tcatctcaga aaatctctct acggattgaa gcagagtcct cgagcttggt 3480 ttggcaagtt tagtgagatg attcaagagt ttgggatgaa caaaagcaag gttgatcatt 3540 cagtcttcta tagacagtca gcaaatggta ttattcttct cgttgtttat gttgatgaca 3600 ttgtcattac aggaagtgat tgtgcaggaa tttcttctct caaattgttt atgcattcca 3660 agtttcacac aaaggactta ggcgagctaa aatatttctt gggagtagaa gtatcaagaa 3720 gcaaaagagg aatcttcttg tcacagagga aatatgttct tgacttactt gcagaaactg 3780 gaaagatgga agccaagcca tgtagcacac cgatgatccc taatgtacat ttgacgaaag 3840 atgatggtga tccatttgat aatctagaaa gatacaaaag attggttggg aaattgaatt 3900 accttacagt gacttgccca gacattgctt atgcagttag tattgtcagt cagtttatgt 3960 ctgcacctac agtgaagaat tgggcagcct tggagcagat tttgtgttat ttgaaaagag 4020 ctcctggtct gggcatattg tacagcaatc atggacatgc tcaaattgag tgttttacag 4080 atgctgactg ggctggatcc aaagctgata gacgatccac aacaggattt tgtgtctttg 4140 ttggtgggaa tcttgtatct tggaagagca agaagcagaa tgtggtatct cggtctagtg 4200 cagaatcaga aaacagagcc atggcgcaag ccacgtgtga aattatgtgg ttgtatcatc 4260 ttctaattga gattggaata aagactccca tgccagcaaa acttgggtgc gacaaccaag 4320 cagctattca tatcgcctca aatccagtat atcatgaaag aactaaacat attgaagtag 4380 attgtcactt tattcgtgag aagattcaag aaaatctgat ttccacaagt tatgtgaaga 4440 ctggagaaca actgggagat attttcacaa aggcgttaaa tggaactcgg gttgaatatt 4500 tttgtaacaa gctgggcatg attaacattt atgctccagc ttgaggagga g 4551 // ID MuTRI_MT repbase; DNA; EDCOT; 2251 BP. XX AC . XX DT 14-NOV-2006 (Rel. 11.11, Created) DT 03-JAN-2007 (Rel. 11.11, Last updated, Version 2) XX DE A MuDR like non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; mariner; KW Inverted repeats; MuTRI_MT. XX NM Piggy1_MT. XX OS Medicago OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae. XX RN [1] RP 1-2251 RA Shankar R. and Jurka J.; RT "MuTRI_MT: A putative non-autonomous transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 584-584 (2006). XX DR [1] (Consensus) XX CC The sequence is present in multiple copies and flanked on both CC termini by 9 bp TSDs. This sequence exhibits two additional long CC range internal inverted regions, which could be another CC transposon insertions. XX SQ Sequence 2251 BP; 825 A; 320 C; 298 G; 808 T; 0 other; ggtgaggcct acgttaccct ctcttgttta gagggtaatt taccctctca tgatatcaac 60 caatcaaaat gtaatataca taggtaacat taaatgtcaa ataaatgagt agattttttc 120 taaaaataaa agagttaatc ttaattattt ttttttgaag gagagttaat cttaatcata 180 aggtaacttt taatactttt aatttttatt taattttttt tttgaaacaa caaatgattt 240 aatttttttt ttttatatta aggtgttcaa tcttaattaa tttacactac aagacttata 300 acaaataaaa ttttacatca aatttctttc atctggatgt ccttaaattc atcatttaca 360 ttcataaaat ttcttccatt ccagaacccc gaacgtgaga acaaaaacat ctccttcttt 420 caaatttctt cttctttatt cttccatatt gatcaatttt tgtttctttt tcattcttct 480 tcccattttg attgttcaat tttgtcgttc caaattgccg caatttccaa ttatcgtgag 540 aattgtcgtt gtttctagaa ccgcgtcagg tatcgtgact tatttttttt atttaagcag 600 ccaacctaat aaaatctgtt aacacgcata gacctgtctc actatcagca aaagccttta 660 agtccaaata aaagaacaaa agcctcatca cataaccatt tcagcagcaa ccaaaaaaat 720 gctagcaaac tcccacaaca tcacagcggc aacacctgct agcagccctc aaagtacaac 780 ggatgattta ctcaattgtt ataattaact acctcacaac caagaaaaat caaatcaaaa 840 agaaaaatca agtcatcata cctgacgttg tactggaaat aacggcaatt ctcacgatat 900 ttgaaatcat gacgattctc acgaaaattg aaaaatgcgg cagttgggaa cgacaaaatt 960 gaacaatcaa aatgggagga ataaatttta tgaatataac tgataaattt aaggacattc 1020 agatgaaaga aatttgatgt gaaattttaa ttgttctaag ccagtcctgt agtgtaaatt 1080 aattaagatt gaacacctaa atataattaa ggcaatatta cattatgggt cctttatctt 1140 atttatttgt aacactttgg tcctttgtct ttattttttc ccgtttaggt cctttatctc 1200 tcttaaaagc acatatacat cttttttcgc attttttttt attaaaaaat acataatttt 1260 atttttaaaa atatattttt attaaaactg aaaaaaaaat ccaaaaatat gatgaagatg 1320 ttcatcatct tcatcttctt cctttgaatc ttcatcatct tctttaaata aataaaaaat 1380 tctactaaaa tatatctcca aatatcgtga attaatgtta tattcacctc aaatcttatt 1440 ttaaacacaa aaatcaaaac cttaatttca caaatgttgc aaggcggatg gtggaggctt 1500 agtcactggc ggaagggtta ggctttacga aagttaagat tgttctggaa acaacaaaat 1560 tgatgtgcaa agctgctatc aattttgggg ttatttttat gtcgggcttg aatattgagt 1620 tagaaaataa taataataat aataatatac agcgtgacaa tttatataac taattttttt 1680 ttttttttgt gatgaaacta aatctctttc tctatagggg tttgattttt gtgtttaaaa 1740 gaagatttga ggtgaatata acattaattc atgatatttg gagatatatt tgtgtagaaa 1800 tttttttgat tcaatgaaga tgatgaagat tcaaaggaag aagatgaaga tgatgaacat 1860 cttcatcata tttctggatt tgtttcattt ttaataaaaa gatattttaa aaaataaaat 1920 tatgtatttt ttttaataaa aaaaatgaga aaaaggatgt atatgtgctt ttataagaga 1980 taaaagacct aagcggaaaa aaaataaaga taaaggaccc aagtgtaaca aataaataag 2040 ataaaggatc tctaatgtaa tcatgtctat aattaaataa aaattaaaag tattaaaagt 2100 taccttatga ttataattga ttcttttttt agaaaaaaaa ttgactcatt tatgacattt 2160 aatgttgcca atgtatatta cattttgatt ggttgatatc atgagagggt aaaataccct 2220 ctaaataaga gagggtaatc tagaaaaaac c 2251 // ID Copia-47_VV-LTR repbase; DNA; EDCOT; 459 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-47_VV_; KW Copia-47_VV-I; Copia-47_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-459 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 3718345 3718803. XX SQ Sequence 459 BP; 140 A; 91 C; 89 G; 139 T; 0 other; tgatagaata aatgtggacc gacaatatat taaacattgt ctaggattaa gctatctttt 60 cacatgcaat ttatgattta atcttgagta tgggccacct aatgtgtaga gcccaatgcc 120 atcacgggct ttagatgatg ggcctgaggc ccatgaggcc caataaccaa tgggtatggt 180 ccctaaggca agagggtata aaagggcttt ggcttgtgtc ttttgtcaca atcacatctt 240 ttgaaaagaa cttaaccgct ctctctcccg ctcccattgc ctgagagaat ccagaggtgg 300 tgccctccat cagtcttaga agattcatac cgtcttcatc aaacacacaa atggaattag 360 gttggtacaa ttttaatagt atttatgaca taatttcttc atgtgattca acatatgatc 420 ctgtatgatc attgaataaa tagaatatga aatctcaca 459 // ID SINE_SO repbase; DNA; EDCOT; 189 BP. XX AC . XX DT 17-NOV-2004 (Rel. 9.1, Created) DT 17-NOV-2004 (Rel. 9.1, Last updated, Version 1) XX DE SINE element from nightshades - a consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; SINE_SO. XX OS Solanaceae OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales. XX RN [1] RP 1-189 RA Gentles A. and Jurka J.; RT "SINE elements from the nightshade family."; RL Direct Submission to Repbase Update (SEP-2004). XX DR [1] (Consensus) XX CC Average similarity to consensus 84%. XX SQ Sequence 189 BP; 64 A; 33 C; 37 G; 54 T; 1 other; gtggcggagt caaaattttc attaaggggg ttcaaaatat gaagaagtaa acacacgaag 60 tagttaaggg ggttcaacat ctactatata tacataaaaa ataattttaa ccatatataa 120 atagtgtaat tttccgccga agggttcgga tgaacccctt cctcataayt tggctccgcc 180 cctgattgt 189 // ID Copia-62_Mad-LTR repbase; DNA; EDCOT; 181 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-62_Mad_; KW Copia-62_Mad-LTR; Copia-62_Mad-I. XX NM Copia-62_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-181 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1663-1663 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 181 BP; 52 A; 27 C; 30 G; 72 T; 0 other; tgttggagag ttgacctttt gtaattagtt tagttaccta tttgagtcct tgtaatcaga 60 ttgtaattag gttatttgat gtttctttcc ttgtaaatca ctcttgtaca ttatatattt 120 tcctccttgg tgagaagaat gatatcagga aattaaaccc caaaataagc cctaattagc 180 a 181 // ID Copia-35_Mad-I repbase; DNA; EDCOT; 4305 BP. XX AC ACYM01061940; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-35_Mad-I; KW Copia-35_Mad-LTR; Copia-35_Mad_. XX NM Copia-35_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4305 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1305-1305 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01061940; Positions 10257 5953. XX CC Positions [1708-2034] - Integrase core CC 'AATAT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(913..1704,1708..2904) FT /product="Copia-35_Mad-I_1p" FT /translation="MLLMSYVKLPEQTDAWFLDSGCSNHMCGSQGMFTNLD FT ESFVHSVKLGNNSRLNVVGKGNVKLFLNGVTHVVHEVYYVPELKNNLLSIG FT QLQERGLAILIREGVCKIYHPTKGLIIQTELSKNMMFILRAQTLVSTDVQP FT ARCLHTSSQDLLYLWHRRYGHLSHKGLRILQHKKMVRGLPQLQTSNTTCTD FT CIQGKQHRNDMPTKGTWRASQPLELIHVDVYGPISSTSNSGKRYTLCFIDD FT FSRKSWVYLLTAKSEALHCFQFFKMVEKEKGLSIKCLRIDRGGEFTSTEFA FT AFCKENGIKRQLTTAYTPQQNGVAERKNRTVMNMVRSMLSEKKLPKTFWPE FT AVNWAIYVLNRCPTLAIKDITPQEAWSGVKPLVEHFRVFGSLAHVHVPDVK FT RGKLDDKSFPCVLLGVSEESKGYRLFDPIATKIIVSRDVIFEEEKQWDLDV FT SYEGQIMLDLEWEENEENGEGEERVRENENGSEAREERNVGESSVSESSEE FT TQGCNLNELGEDEGRVYEGKVRRPPSYLSDYVTGEGLSEDEAHMVQVVPIE FT DPIHFEEAVKEEKWRQAMDSEISSIEKNKTWSLSELPTGAKRIGVKWVYKT FT KYNEHGEIDKHKARLVAKGYSQKHVIDYTEVFVPVARMDTVRMIIALAAQK FT GWRIFQLDVKSAFL" XX SQ Sequence 4305 BP; 1391 A; 678 C; 1123 G; 1111 T; 2 other; aactggtatc agagcccctc actggggcct gagaaccgaa aagcagcagc ttttgagtga 60 cttccaaaca caagagagga aaatgagttc tgaaggaaac tatgtgcagg cgtacattcc 120 acgttttgat ggtcattatg atcattggag catgctcatg gaaaatttcc ttcgaagcaa 180 ggagtattgg agtttgattg aaactggtta tgaagaacca gtaaaggggg cacaacccct 240 atcagaagca cgacagaaag agcttgatgc agtgaaactc aaggatctca aagccaaaaa 300 ctatcttttc caagcaattg ataggagtat cctagagaca atgttggaaa aggacacctc 360 caagaagatt tgggattcca tgaagacgaa atatgaaggg aatgcacgag tgaagcgctc 420 aagtcttcaa gccctacgaa gagactttga gactcttgag atgaaggttg gtgaaacaat 480 cactaattac tttgctagag taatgaccgt agcaaacaaa atgagagtct atggggagac 540 catgactgat gtcacgatct gtgaaaaaat cctacgatct ccacatacaa atttaattat 600 atagtttgtt cgattgagga atctrgggat ttggatgcaa ttaccattga tgaacttcaa 660 agctcgctca ctgtacatga acagaagttt cacagaagta gcggtgtgga gcaagctcta 720 aaggtaacca ctgatgccaa aactgagggg ggtatcaaca gttatagagg atgaggatgt 780 ggaaggggag gccaagcgtt caacaaggat actgtggaat gctacaagtg tcacaatctt 840 ggacactacc agtatgaatg tccaaagtgg gaaaaggaga ctaattatgc agaagtaatt 900 gaagaagatg atatgttgtt gatgtcatat gttaagttac ctgaacagac tgatgcgtgg 960 tttcttgact caggatgttc caaccatatg tgtggcagtc aaggtatgtt cacaaatcta 1020 gatgaaagtt ttgttcattc agtcaaattg ggaaataaca gtaggttgaa tgtggttggc 1080 aaagggaatg tcaagctgtt tttaaatgga gttacacatg ttgtccatga agtgtactat 1140 gttccagagc tcaaaaacaa tctcttgagc ataggacaac ttcaagaaag gggcctggct 1200 atattgattc gagagggagt ttgcaaaata tatcatccga ctaagggtct gattattcag 1260 actgagttga gtaagaacat gatgtttata ctgcgagctc agacgctagt ctctacagat 1320 gttcaaccgg caaggtgtct tcacacaagc tcacaggatc tcctttatct ttggcatcga 1380 agatacggtc acctaagcca caagggattg agaattttac aacacaagaa gatggttcgt 1440 ggactccctc aactccaaac ctcaaatacc acatgcacag actgcattca aggcaaacaa 1500 catcgtaatg acatgccaac aaaaggtacg tggagagcaa gtcaaccctt ggagcttatt 1560 catgtagacg tctatgggcc catttcttct acatcaaata gtgggaaaag gtatacttta 1620 tgctttattg atgattttag tcgtaaatca tgggtgtact tgttgacagc aaagagtgag 1680 gcactgcatt gcttccagtt tttttaaaaa atggtggaaa aggagaaagg gctgagtatt 1740 aagtgcctac ggatagatag agggggcgaa ttcacctcaa ctgaattcgc tgccttctgc 1800 aaagaaaatg gaatcaagag gcagttaacc actgcctaca cgccgcaaca aaacggagtg 1860 gctgaaagga aaaaccgaac tgtcatgaat atggttcgtt ctatgctgtc tgagaagaag 1920 cttccaaaaa cattctggcc agaggcggtg aactgggcta tctatgtcct gaatagatgt 1980 cccacattgg caataaagga tattactcca caagaggcgt ggagtggcgt aaaaccctta 2040 gttgagcatt tccgtgtctt tggaagctta gcacatgtcc atgttccaga tgtcaagcga 2100 ggtaaactag atgacaaaag ctttccttgc gttttattgg gagttagtga ggagtctaag 2160 ggatatagat tgtttgatcc tatagctacg aaaattattg taagcaggga tgttattttt 2220 gaggaagaaa aacagtggga tttggatgtg agttatgagg gacagatcat gttagatttg 2280 gaatgggaag aaaatgaaga aaatggtgag ggagaagaaa gggtgagaga aaatgagaat 2340 ggcagtgagg ctagagaaga aagaaatgtg ggtgagagca gtgtgagtga gagcagtgaa 2400 gaaacacagg gttgtaatct taatgaactt ggtgaggatg aagggagggt ttatgaagga 2460 aaagtaagac gccctccttc ttacttaagt gactatgtca ctggagaagg gctaagtgag 2520 gatgaggcac acatggttca agtcgttcca attgaagatc ctatccattt tgaagaagca 2580 gtgaaagaag agaaatggag gcaagctatg gacagtgaaa tcagctccat tgagaagaac 2640 aaaacatggt ctttaagtga gttgcctact ggagctaaaa ggattggggt caagtgggtc 2700 tataagacca agtacaacga acatggagag attgacaagc acaaagcacg tctagtagcc 2760 aaaggctact cccagaagca cgtcatagac tacacagagg tctttgtacc agtggcaagg 2820 atggacacgg tgaggatgat cattgcattg gcagcacaaa agggttggag gattttccag 2880 ttagatgtca agtcagcgtt tcttmatgga gagctaagtg aagaggttta tgttgagcaa 2940 ccaaagggtt acgagaagga aggaagagag catttggtct acaaactgca caaagctttg 3000 tatggtttga aacaggctcc acgagcttgg ttcagtcgga tcgaggcgca ctttatcgag 3060 gagggatttc agaggtgtga tagtgagcaa accttgttca taaagaagaa tggagcagga 3120 aagatcatca ttggaaggaa gggagcattt ggtctacaaa ctgtacaaag ttttgtatgg 3180 tttgaaacag gctccacgag cttggtttag tcgaatcgag gcgcacttta tcgaggaggg 3240 ttttcaaagg tgtgaaaatg agcaaacctt gttcacaaag aagaatggag caggaaagat 3300 catcattgta agtatttacg ttgatgattt aatttttact ggtaatgata aagatatgat 3360 gtgggagttc aagaagtcca tgatgagaga atttgatatg attgatatgg gaagcatgag 3420 gttttttctc ggcattgaag tacttcaaag aactgatggt attttcatac ataaaaaaaa 3480 atatgccctg gaggttctaa agagatttag aatgttggaa agtaatgaag tgagcagtcc 3540 gattgtccca ggtgttaaga tcggtaagga tgaaaatggg attactgtgg atgagacata 3600 cttcaagcaa gtggtgggaa gcttgatgta tctcactgcc acaagaccag acatgatgtt 3660 tgtcaccagt ctctaaagca gatttatggc aaaaccaacc gagcttcacc tgcaagctgc 3720 aaagagagcg tttcgatact taaaagggac gatgaattat ggtattcatt ataagaaagg 3780 tggagatggt ggactgtttg ctttcacaga tagtgactat gcaggagatg tggaggatag 3840 gaagagcaca agtggttatg tgttcttact gagctcgggt gctgtgacat ggagttcaaa 3900 aaaataacct attgttacac tgtctactac agaagctgaa tttgtagcag ctgtagtgtg 3960 tgtgtgtcaa gcaatatgga tgaagagagt gctgaaggag cttgagtaca ataatgagat 4020 gtgtacttta attagatgtg ataacagttc aaccattaag ctgtcaaaga atcctgtgat 4080 gcatggtcgc agtaagcata ttgatgtaag gtatcatttc ttaaggaatc tcacaagaga 4140 gggttcgatt gctttgattc attgtgggag cgaagatcag gtggcagaca taatgaccaa 4200 gccattgaag tttgatgttt tctagagact tcgaagcatg atgggagttt gtgaaattgt 4260 tggtataaac taactgtttg ataacagtaa gtttaaggga gggat 4305 // ID Copia45-PTR_LTR repbase; DNA; EDCOT; 315 BP. XX AC LG_XVIII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia45-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-315 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-315 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 269-269 (2007). XX DR Genome; LG_XVIII; Positions 3733340 3733026. XX SQ Sequence 315 BP; 88 A; 50 C; 47 G; 130 T; 0 other; tgttaaatgt ttattgttta tttgttattt gatttactct gtatttgaat aagttcctat 60 ttaccaggaa ccagtcaatt gtttacctat tccttaggaa aatcccagct gactaggtga 120 cagttagtca tgggatagat gctgcatatt tttctactta tctattattt gtatttctat 180 ttaagttgaa ctcttcttaa tgaaatatat agagttgcac ttccacgttt gttgttacaa 240 agctttagct tcactgtcac gttttcaata caaaacttta gctttgaatt agtgcaaaac 300 acttagtgtt caaca 315 // ID Copia-8_TC-LTR repbase; DNA; EDCOT; 352 BP. XX AC CACC01018230; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-8_TC_; KW Copia-8_TC-I; Copia-8_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-352 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01018230; Positions 6397 6748. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 352 BP; 119 A; 48 C; 66 G; 119 T; 0 other; tgaataagct cgaagcaatt gtaaagaatt ctgtgaagaa gactcaagca gaaggaggaa 60 ataggaagtt tggaaataaa ggaacagagc tgtgcgcacc gttttgaaga aagcaagagg 120 aagaacttga aataaaatga aacgctgcgt tttatttcat tagttttaaa tttctgttat 180 gttagttaaa tattataatt attagttgtt ttatctgttt ttaactctta aaacactgta 240 tataaacaac ctttctttag gtattctgta aaatgaaaat acttgggatg actttttttc 300 ctaaaaagga tgagccgcct actgctttct ttcttcctgc agctttctga ca 352 // ID Gypsy-27_Mad-I repbase; DNA; EDCOT; 6874 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-27_Mad_; KW Gypsy-27_Mad-LTR; Gypsy-27_Mad-I. XX NM Gypsy-27_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6874 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1748-1748 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [5723-6220] - Integrase core CC LTRs are 92% similar to each other. XX FH Key Location/Qualifiers FT CDS 2947..5103 FT /product="Gypsy-27_Mad-I_1p" FT /translation="MGHRAIQCPQNQQKPQPPALPPPVPIQQVPGPSGYTQ FT TGYGGAYHYQGDIAPYSGGQYQYPHDPYHQGGYAQYPGGYAPYPPYPGGGS FT QWYPGGQSQNVEVASSSAGSSRQPNQPGQGRGTQGRGNQANRGRGGRQQPQ FT GRVHHITLQDAQNNPDLIMGTLNILGHFARVLIDSGATHSVISHTFAQTTQ FT PYPTPLGYELEFSMPRGETCYVSWVYQGCPVLVEDVVMPANLVPLDIVDFD FT VILGMDWLHYNRAKLDCYEKTVTFHRPGLPVVTFVGVRSGLRHGVISAVRA FT KRLLRKGCQGYLAHVVLNEDTPTRVEDVRVVRHFPDVFPDDLPGLPPDREV FT EFTIDLLPGTDPISLTPYRMAPAELRELKTQLQELVDKGFIQPSTSPWGAP FT VLFVRKKDGTLRLCIDYRQLNRVTIKNRYPLPRIDDLFDQLRGACVFSKID FT LRSGYYQLKIRSEDVPKTAFRTRYGHYEFLVMPFGLTNAPAAFMDLMNRVF FT RPYLDRFVIVFIDDILVYSKSKAEHTRHLTLVLKKLREHQLYAKFSKCQFW FT LDQVAFLGHVISAQGIQVDPQKVAAVENWEQPRTVTEVRSFLGLAGYYRRF FT VKDFSTIALPLTRLTRKDVKFEWDDDCERSFQQLKYCLTHAPVLALPDDSG FT NFEIYSDASLNGLGCVLMQHGRVIAYASRQLKPHEMNYPTHDLELAAIVFA FT LKIWRHYLLWGKVQDFHGS" FT CDS 5489..6811 FT /product="Gypsy-27_Mad-I_2p" FT /translation="MLMQGSRMYVPNIAELKKDILDEAHVSAYAMHPGSTK FT MYHTIRPFYYWPGMKREIAEYVSRCAICQQVKAERKKPFGLMQPLPVPQWK FT WENITMDFVYKLPRTRNGYDGIWVIVDRLTKSAHFIPVRENYSLSRLAELF FT ISGIVKYHGVPVSIISDRDPRFTSKFWVAFQEALGSRLLYSTAYHPQTDGQ FT SERTIQTLEDMLRSSVLQFGDAWHKRLDLMEFAYNNSYHSSIGMSPFEALY FT GKSCRTPLCWSEVGERALVGPEIVDETTQNIQVIKANLKAAQDRQKSLADK FT HATDRVYKVGDWVFLKLSPWKGVVRFGKKGKLSPRYIGPYQITERVGEVAY FT RLELPPELSKVHDVFHVSMLRHYVSDPSHVIPPQPLEINPDLTYDEEPVTI FT LDWKDKVLRNKTVRMVKVLWRNHSVEEATWETEDRMRDLYPRLFYGY" XX SQ Sequence 6874 BP; 1726 A; 1377 C; 1772 G; 1993 T; 6 other; tcgtgttcct cgcgasctcg cgagcctaac catacccttt gttcgaagaa aggacgtcgg 60 gaacccgaga acccataagc tccggcgagg tgctctgtta ctccgacgtg atcgtgggca 120 tttcacgggg ttttaaggct caagaaggtt cctaaacaac tccmtaagga ccttggaaca 180 attttggagt ggtttggacg tcggaacacg cgggttcgtg gagttgcagg ttggccggaa 240 tgttcgagga ttttccgacc attttccgtc ggttttagga cctcaaatag gtaagattgt 300 gttctmctcg tcgagagctt caaatccata taaaattcgt gaaatttggt tgagaaatga 360 agtagatatt aaggtttaaa aatttttcca gaaaccggcg acgcagcggc ggcccggcga 420 accaccggag aagaaaagag aatattccgt caactttgac ggaatatact gacggcgtca 480 ggtaacccgt tatttaacgg aatattccct aacgccgtta gggattccgt ccagtgtgcc 540 aggcacgtgc ctgcgcgtgg ccggcgcgtg ggcatcgaaa aatttttcta aaaatatggg 600 gatgctcgtg gtgttgagta ggccacgatg gtatattcaa acaccccaat tgagcaacgt 660 atgagaagtt attacacggt tttggttatg tgcttaaaat taacgttaaa ttagttgttt 720 cacatatagg tgagacgttc ccggaggacg agcgcggcca ggcgagactc gggggttacg 780 accctgctac ataccagtga gtgggctttt ggttttctat atatatatat atacgtatat 840 atgctttaca ttttcccaga aattgtttta aatggattta cgttttaaat gccatgtcaa 900 ttgcattaca ttttagtata tgcattagta tagatatgca tattattgca tgatgctgcg 960 gacgcccagg taagcttcag gtgagtacat attgatgata gtgattgcak tgtgtatggt 1020 tatgtttaga tgcatttagt gctcattatc ctgcaccccg gtgttagtgc tccgcccgag 1080 gccagggcct agccttcacg tgatcgttca cctcccgcac cacacgctca ccttggatcc 1140 aaggcaggtg ccagcctgtc gtacagacca cattaggtgg ttccgactcg taggtgactc 1200 gcgatcttcg cacaaccttc acgtgatcgt agcacttgag cgtacttatt tacacccagc 1260 ctgtcgtaca gaccacatta ggtggttccg actcgtgtgc aggaattggt tgatgagcta 1320 taggttcagc cgtacaggtc acgttaggtg actccggctg acatatcatt ttacattgat 1380 ttatttcacc tggcttactt atttattgct gagatacttg acatggcata tacttggttt 1440 tcactactct cgagcatgat ttctatatac gtatgtagta ttattttctg ggaaattata 1500 cgggttttac ggtgaggggt tattattttc ggaaagagaa atggttttga aaagctttgt 1560 ttttgcccac tcacgttttc tgttttgcgc ccctccaggt tctagtagaa gttcgtgttg 1620 gtggctcacg aggactctac ggcggttctg acagacatcc atcaatgtag ggttttcttt 1680 catgtcctgt ataattagta cttagcctgc tggactgcac cttggtacct acgctctgat 1740 tatgtgtatc tacactctaa cactttcact cgcacttata tactagtcta gtgtaagtta 1800 gttagtttgg tttttattta cccacatttt catatcacca tcacttccgc actgcgcaca 1860 tggctacgtc accctcacgt gacggccagc atgcctcgat ttaggtcggg gtgtgtcagt 1920 ttggtatcag agcctaggtt tggcagtcct gcatattttg tgagtattct aatcattttg 1980 atgtcttatg tcagaaccat gccgcctcgt agagagccac gtacttcctc tgagtctaat 2040 tttccgatat tgsccaactt ggtgaagcta ttgctaatgc cattcagtcc tcacttcgtc 2100 ctccccagag gactcccttg gagactgtat ataacttaaa gttgaataat tttgttggta 2160 ctgaggggcc cgagggagct gagcgttggc tcaatcatgt cgagaaaact tatcgagtga 2220 tgcagcgaca ggggaatctc cctgaggata gatgggttga gacgactact tggtttttgg 2280 gtgaggaggc tgcatcctgg tggaggcagg aatcttttca gttgtcacca gaagaagccg 2340 cagactggga ggtttttaag cagctattcc agaagagatt tgtacctcca gagtatatag 2400 atcgtaagaa gcaagaattc acgcgtctaa agcaagggaa aatgtcagct aatgagtact 2460 atagaaagtt cactgattta tctcggtatt gtccggagat tgctgagaat cctgctgaga 2520 tgcttcgacg atttaagtgg ggtactcgaa agaagtggcg ttctatggcg accacgactc 2580 cctgttctac atatcaggag ttttatgaga ttctactcgg gttgaggatt ctgaaaacgt 2640 gcccagtgac agtgaggaag aggaagaaaa agataataac cagaagaaaa ataataataa 2700 agataaaggc cagtcatcac agggacctcg caagacgcag agttttaaga gaagtggtac 2760 tagttccggt tcttctagtg ggggttcgag ttccactgcg ccgcggaggg gcggccgttc 2820 aggggttccc gcttccagag acagagagat tctagcggtt ctggtggtcc attttgccgt 2880 aggtgtaata gtcgacattt tggggagtgt aggcaaggta gcagaggatg tttcgcttgt 2940 ggccagatgg gacatcgggc tattcagtgc ccacagaacc agcagaagcc ccagccacct 3000 gccttgccac caccagttcc tattcagcag gttccagggc ctagtggtta tacccagacg 3060 ggttatggtg gagcatatca ttatcagggt gatatagctc catattctgg aggacagtat 3120 cagtacccac acgatccgta tcatcagggt ggttatgctc agtacccagg aggttacgcg 3180 ccatatccac catatccagg tggtggatca cagtggtatc ccggaggaca gtcccagaac 3240 gttgaggttg cttctagcag tgcaggatca tcgaggcagc ctaaccagcc tggtcaggga 3300 cgaggtacgc agggacgtgg aaatcaagct aacagaggtc gtggaggacg gcagcagcca 3360 caaggccgtg ttcaccatat cactctgcag gatgctcaga acaaccctga tctgattatg 3420 ggtacgttga atattcttgg ccattttgct agagtattaa ttgattctgg tgccacacac 3480 tctgttattt ctcatacgtt tgctcagacg acgcaaccct accccacacc tctcggttat 3540 gagttagagt tttcgatgcc tagaggtgag acatgttatg ttagctgggt atatcaagga 3600 tgtcctgttc tggtggagga cgtcgttatg ccagctaatc ttgttccatt agatattgtt 3660 gatttcgatg ttattctggg catggattgg ttacattaca atcgtgccaa gttggattgt 3720 tatgagaaga cagtcacttt ccatcggccg ggcttgcctg tggttacctt tgtgggtgtg 3780 cgtagtggac tgagacacgg cgttatttct gccgtgaggg ctaaacggtt attgaggaaa 3840 ggttgtcagg gttatttggc tcacgtggta ttgaatgagg atactcctac ccgtgtggag 3900 gatgtacggg tagttaggca tttccctgat gtttttcctg atgatttacc tggattacca 3960 ccagatagag aagtggagtt cactattgat ttacttccag gtacagatcc tatttcctta 4020 actccttatc gaatggctcc tgctgagttg agggaattga aaacccagtt gcaggaattg 4080 gttgataagg gtttcattca gcctagtact tcaccttggg gagctccagt tttatttgta 4140 cggaagaaag acgggacttt gaggctgtgt atcgattatc gacagttgaa tcgggtaacg 4200 attaaaaacc gttatccgtt gccgcgtata gatgatttat ttgaccagct tcgaggtgcc 4260 tgcgtgttct ccaagattga tttgaggtct gggtattatc aattgaagat cagaagtgaa 4320 gatgtcccta agacggcttt taggactcga tatggtcatt acgagttcct cgtgatgcca 4380 ttcgggttaa cgaatgcacc cgcagctttt atggacttga tgaatcgagt atttaggccg 4440 tacctcgaca ggttcgttat tgtcttcatt gatgatattt tggtgtattc taagtctaag 4500 gcggagcata ctcgacatct cactttggtt ttgaagaaat tgagggaaca ccaattatat 4560 gctaagttta gcaaatgcca gttttggtta gatcaagtgg cattcttggg gcatgtaata 4620 tcagctcagg gtattcaggt ggacccacag aaagtagctg cagttgaaaa ttgggagcag 4680 ccacgaaccg tcaccgaggt acggagtttt ctcggcctag caggttatta tcgacggttt 4740 gttaaagatt tttcaaccat agctttacca ctgacgaggt tgactagaaa agatgttaaa 4800 ttcgagtggg acgatgattg tgagcggagt ttccagcagc taaagtattg tctcactcac 4860 gcacctgttt tggcgcttcc agacgacagt ggtaattttg agatttacag tgatgcttcc 4920 ttgaatggct taggctgcgt gttaatgcag catggtaggg tgattgctta tgcctcgcga 4980 cagttgaagc cccacgagat gaattatcct actcatgatc ttgagttagc agccatcgtt 5040 tttgccttga agatttggag gcattatcta ttatggggaa aagtgcaaga ttttcacgga 5100 tcataaaagc ctccagtacc ttttcaccca gaaagatctt aaccttcggc agcggaggtg 5160 gatagaattg ctcagtgatt atgattgcac gattgagtat caccctggtc gtgcaaacgc 5220 ggtggcagac gcacttagca ggaaatctca aggccgaatt aatgctttat atgcttgccg 5280 tatccctctt ctcacagaat tgagatctac tggagttgat ttgggagtgg aagatcggga 5340 agaagcttta cttgctagtt tccgggtcag accaattttg atagatcgtg tgctcgaggc 5400 tcaagtggag gatgaggaat ctcaggaatt aattgaggca gtgtcacgag ggaagaagaa 5460 agatctcagg attcgggaat ctgatggcat gcttatgcag ggaagccgga tgtacgtgcc 5520 aaatattgca gaattaaaga aagatattct tgatgaggcg cacgtatcgg cctatgcgat 5580 gcatcctggg agtaccaaga tgtatcacac tattcgacct ttctactatt ggcctggcat 5640 gaaaagagag attgctgaat atgtgagtmg atgtgcaatt tgccagcaag tcaaagctga 5700 gaggaagaaa ccttttggat taatgcagcc acttcccgtt ccccagtgga aatgggaaaa 5760 tattactatg gatttcgtgt acaagcttcc tcgtacgcga aatggttacg atggcatttg 5820 ggtgatagtg gatcggctta ctaagtcagc acactttata ccagttcgag agaactattc 5880 tttaagccga ttagctgagc tgtttatatc agggattgtt aaataccacg gggttccggt 5940 tagtattatt tctgatcggg atcctaggtt cacttctaag ttttgggtgg catttcagga 6000 agctcttggt tcgagattgc tttatagtac ggcgtatcat ccacagacag acgggcaatc 6060 cgagaggact atccagacac tagaagatat gctgagatct tcggtactac agtttggtga 6120 cgcttggcat aagcgtttgg atttgatgga gtttgcctat aataacagct accattctag 6180 catcggtatg tcacctttcg aggcacttta tggtaaatct tgtcgtactc ctctatgttg 6240 gtcagaagtt ggtgagaggg cgttagtggg cccagagatt gtagatgaga ctactcagaa 6300 tattcaggta attaaagcta acctgaaagc ggcccaggat cgacaaaaga gtcttgctga 6360 taaacacgcc actgataggg tgtataaagt tggagattgg gtatttttga agctatctcc 6420 gtggaaaggc gtagtacggt tcggtaagaa aggtaagtta agtcctcgct acattggacc 6480 gtaccagatc accgagcgag tcggtgaagt tgcctacagg cttgagttac ctccagaatt 6540 atcaaaggtg cacgatgttt ttcatgtttc tatgcttcgt cattatgtct ctgatccatc 6600 acacgtgata cctcctcagc cactagaaat taatccagac ttgacatatg atgaggagcc 6660 agtgacgatc ttggattgga aggataaggt tcttaggaac aaaactgtgc gcatggtgaa 6720 agttttgtgg aggaaccatt cagtggagga ggctacttgg gagacggaag atcgtatgcg 6780 agatttatat ccacgcttgt tttatggata ttgatatgtt gtatgctagt gtacagaaat 6840 ttcggggacg aaattttctt aagggggtag gttg 6874 // ID Copia-56_VV-I repbase; DNA; EDCOT; 4610 BP. XX AC chr6; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-56_VV_; KW Copia-56_VV-LTR; Copia-56_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4610 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr6; Positions 3228440 3223831. XX CC Positions [1722-2222] - Integrase core CC 'GTTAG' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 3599..4600 FT /product="Copia-56_VV-I_1p" FT /translation="MFIKHSNDGKIAILIVYVDDIILTGDHVTEMDRLKKS FT LALEFEIKDLGSLRYFLGMEVARSKRGIVVSQRKYILDLLKETGMSGCRTV FT DTPIDPNQKLGDTNDGNLVNTTRYQKLVGKLIYLSHTRPDIAFAVSIVSQF FT MHSPYEVHLEAVYRILRYLKSTPGKGLFFKKSEQKTIEAYTDADWAGSVTD FT RRFTSGYCTYIWGNLVTWRSKKQSVVARSSAEAEYRAMAHGVCEILWLKKI FT LEELKRPLEMPMKLYCDNKAAISIAHNPVQHDRTKHVEIDRHFIKEKLEAS FT IICMPFVPTTQQIADILTKGLFRSSFEFLISKLGMIDIYAPT" FT CDS join(39..1388,1392..3320) FT /product="Copia-56_VV-I_2p" FT /translation="MAKTAMTGASKTSSSSEATTENVQSETAMRSSADFST FT SLSSFQLTIHKLNGKNYLEWAQSMKLAIDGRGKLGHLNGEVSKPVADDPNL FT KTWRSENSLVIAWLINSMEPAIGKPHLFLPTAKDVWEAVRDMYSDLENSSQ FT IFDLKSKLWQSRQGDREVTTYYNQMVTLWQELDLCYEDEWDCPNDSVRHKK FT REENDRVYVFLAGLNHNLDEVRGRILGRKPLPSIREVFSEVRREEARRKVM FT LTDPEPKSNPEIESSALVSKGSDLDGDRRKKPWCDHCKKPWHTKETCWKIH FT GKPQNFKKKNGSDGRAFQTMSADSQGPQINSEKPNFTKEQLSHLYKLFQSP FT QFSNPSCSLAQQGNYLIATLSSIKSNVHCPWIIDSGATDHMTGSSQIFSSY FT KPCAGNKKIKIADGSLSAIAGKGSVFISPSLTLHNVLHVPNLSCNLLSISK FT ITQDHCQANFYPSYCEFQELTSGRTIGNAREIGGLYFFENGSESRKPIQST FT CFESISVASSDDIILWHYRLGHPSFQYLKHLFPSLFRNKNPSSFQCEFCEL FT AKHHRTSFPLQPYRISKPFSLIHSDVWEPSRISTLSGKKWFVTFIDDHTRV FT SWVYLLREKSEVEEVFKIFYTMVLTQFQTKIQVFRSDNGKEYFNKALGKFF FT LEKGIVHQSSCNDTPQQNGIAERKNKHLLEVARALCFTTKVPKYLWGEAIL FT TATYLINRMPTRILNFKTPLQVFTNCNPIFRLSSTLPLKIFGCTTFVHIHD FT HNRGKLDPRARKCVFVGYAPTQKGYKCFDPISKKLFVTMDVTFFESKPFFA FT THLQGESTSEDSDLFKIEKTPTPNPNNLLEPSNSNQFVYPNIETSGLDTTK FT SDMSFEKTAEILGKKNGVLNIESLDGSSFLPSHNQNHSNTNNGNRTSTKNS FT ELMTYSRRKHNSKESNPDPLPGHESELREEPNSSECPGNNQTDSCQPVQFI FT SNSNSESFDDLNIPIATRKGVRSCTKHPMSNYMSYKNLSPSFFAFTSHLSL FT VEIPKNVQEALQVPEWKKAIFEEMRALEKNHTWEVMVCQKERQQWVANGCS FT QSSIIQMDLSKDIKHDWWPKVLLKPMVLIILRPLLQ" XX SQ Sequence 4610 BP; 1535 A; 838 C; 916 G; 1321 T; 0 other; tggtatcaga gctttggctc tctatcattt aagctttaat ggcaaaaact gccatgactg 60 gggcaagcaa gacttcatct tcctcagaag cgactacaga gaatgtgcag tctgaaactg 120 ccatgagaag tagtgcagat ttttcaacat cactttcctc ctttcaactt accattcaca 180 aattgaatgg aaaaaattac ctagagtggg cccagtctat gaagctagca atagatggca 240 gaggcaagct tggtcattta aatggagaag tgagcaaacc agtagcagat gaccctaatc 300 tgaaaacatg gaggtcagag aactcgttgg taattgcttg gcttatcaac tcaatggagc 360 cagctattgg aaaaccacat ctctttttac caactgccaa agatgtttgg gaggcagtac 420 gtgacatgta ttcagatctg gagaattcgt cacaaatttt tgatttaaaa tctaagttgt 480 ggcaatcaag gcaaggagat cgggaagtca cgacatacta caaccagatg gtgacgttat 540 ggcaagagct agacctatgc tatgaagatg aatgggactg cccaaatgat agcgtgaggc 600 acaagaaaag agaggaaaat gatcgagttt atgtgtttct cgcaggactc aatcataact 660 tggatgaggt aagaggtcgg atcctgggca gaaaacctct accatccatc agagaagttt 720 tttcagaagt taggcgggag gaggctaggc gaaaagtgat gttgacagat ccagaaccta 780 agtccaaccc agaaatagaa agctcggctc ttgtttctaa aggatctgat ttagatggag 840 atagaaggaa gaaaccatgg tgtgaccatt gcaaaaaacc atggcatacg aaagagacat 900 gctggaaaat ccacggcaag ccccagaatt ttaagaagaa gaacggaagt gatggcagag 960 catttcagac catgagtgca gattctcagg gaccacaaat caattcagag aagcctaatt 1020 tcacaaagga acaattaagc cacctgtaca aactctttca atctccacaa ttctcaaatc 1080 cttcttgctc tttagctcaa cagggtaatt atctcattgc aactctctct agtataaaat 1140 caaatgttca ttgtccttgg atcattgact ctggagccac tgatcacatg actggttctt 1200 cacaaatatt ctcttcctat aagccgtgtg caggaaacaa aaagatcaaa attgcagacg 1260 gttctctttc agctatagct ggaaaaggat cagtgttcat ttctccttct cttacacttc 1320 ataatgttct ccatgttcca aatttatcct gcaatttatt atccataagt aaaataaccc 1380 aagatcatta gtgtcaagct aacttttatc cttcttattg tgagtttcag gaactaacct 1440 cggggaggac gattggcaat gctagagaga tcggtggact ttatttcttt gaaaatggat 1500 ccgaatcgag aaaacctata cagagtactt gctttgaatc tatttctgtt gctagtagtg 1560 atgatataat attatggcat tatagattag gccacccaag ttttcaatat ttaaagcatt 1620 tgtttccaag tttgtttaga aataaaaatc catcttcatt tcagtgtgaa ttttgtgagt 1680 tagctaaaca tcatcgtacc tcatttccat tacaaccata cagaatttca aaaccttttt 1740 ccttaataca tagtgatgta tgggagcctt caagaatttc aacactttct ggaaaaaaat 1800 ggtttgtcac ctttatagat gaccacacaa gggtaagttg ggtttattta ctacgagaaa 1860 aatcagaagt ggaggaagtt tttaaaattt tttacaccat ggtgttgaca caatttcaaa 1920 caaaaattca agttttccgt agtgacaatg gaaaagagta tttcaacaaa gctttgggaa 1980 aattcttctt agaaaaaggc atagttcacc aaagttcttg taatgacact cctcaacaaa 2040 atggaatagc tgaacgaaaa aataaacatc ttttggaagt ggctagagct ttatgtttca 2100 caaccaaagt acccaaatac ctttggggtg aagctattct cacagctacc tatctcataa 2160 ataggatgcc tactaggatc ttaaatttca aaacaccttt acaagtgttc acaaactgca 2220 atcctatatt taggctatca tctacacttc ctctaaaaat ttttgggtgc actacctttg 2280 tccatattca tgaccataat aggggaaaac ttgatcctag ggctagaaaa tgtgtttttg 2340 taggctatgc acctactcaa aaaggatata aatgctttga tccgatttca aaaaaattgt 2400 ttgtcaccat ggatgtaacc ttttttgaat ccaaaccttt ttttgcaact catcttcaag 2460 gggagagcac aagtgaagat tcagatttgt ttaaaataga aaaaacacca acaccaaacc 2520 caaacaattt gcttgaacca tcaaattcaa atcaatttgt ttacccgaat attgaaactt 2580 cgggattgga tacaacaaaa tctgatatgt cctttgaaaa aactgcagaa attttgggca 2640 aaaaaaatgg tgttttgaat attgaaagtt tggatggctc atctttcctg ccatctcaca 2700 atcaaaatca cagtaatact aacaatggga atagaacaag tactaaaaat tcagaactca 2760 tgacctactc gaggaggaag cataactcaa aggaaagtaa tcccgatcct ctaccaggcc 2820 atgaatctga actaagggaa gaaccaaact catctgagtg tccaggtaat aatcaaactg 2880 attcgtgtca acctgttcag tttatttcta actctaattc tgagtccttt gatgatctta 2940 atattcccat tgctactcgt aagggcgtac gatcttgtac caaacacccc atgtctaact 3000 atatgtccta taaaaatctt tctccttctt tttttgcatt tacttcacat ctctctttgg 3060 tagaaattcc aaaaaatgta caggaagctt tacaggttcc cgagtggaag aaggctattt 3120 ttgaagaaat gagggcactt gagaaaaatc atacatggga agtgatggtc tgccaaaagg 3180 aaagacaaca gtgggttgca aatgggtgtt cacagtcaag tataattcaa atggatctct 3240 cgaaagatat aaagcacgat tggtggccaa aggttttact caaacctatg gtattgatta 3300 tcttgagacc tttgctccag tagcaaagtt gaatactgtg agagtgcttc tttcaattgc 3360 agtaaatctt gattggcctc ttcaacagtt agatgtgaag aatgcatttc taaatggtaa 3420 tttggaggag gaagtttata tggatccacc gcctggattt gatgaacact ttggatctaa 3480 ggtgtgtaag ctaaagaaat cattatacag actcaagcaa tctccaagag cttggtttga 3540 atgattcact caattcgtaa aaaaccaagg atatgtccaa gctcagagtg atcatactat 3600 gttcataaag cactccaatg atggtaagat tgcaattttg atagtatatg tggatgatat 3660 tattcttaca ggggatcatg tcactgaaat ggatcgattg aagaaaagtc tagctttgga 3720 atttgaaatt aaagatttgg ggtctctaag atactttctt ggaatggaag ttgctcgttc 3780 aaaaaggggt attgttgtct cacaaagaaa atacattctt gatcttctta aagaaacagg 3840 aatgagtgga tgtagaactg ttgatactcc aattgatcct aatcagaaac taggagatac 3900 caatgatgga aatcttgtga atacaactcg gtaccagaag ttggtgggaa aactgattta 3960 tttatctcac acccgaccag atattgcatt tgcagtcagc atagtaagtc aatttatgca 4020 ctcaccctat gaagtacatc ttgaggcagt ataccgtatc ctaagatatt tgaaaagtac 4080 tccaggaaag ggattgttct tcaagaagag tgagcaaaag actattgaag catacacaga 4140 tgcggattgg gcaggttcag ttacagatag aagattcaca tcaggttact gcacctacat 4200 atggggaaat ttagtcactt ggaggagcaa gaaacaaagt gtagtagcac gaagtagtgc 4260 agaagctgag tatcgggcta tggcacatgg agtatgtgag atattgtggt taaaaaagat 4320 tcttgaagaa ttaaaaagac cactagagat gcctatgaaa ttatattgtg acaacaaagc 4380 tgcgattagc attgcccata atcctgtgca gcatgacaga accaaacatg ttgagattga 4440 cagacacttc ataaaagaga aattggaggc tagtattatt tgtatgccgt ttgttccaac 4500 gacacaacaa atagctgaca ttcttacaaa aggattgttc agatcaagct ttgagtttct 4560 catcagcaag ttgggcatga tagatatcta tgctccaact tgagggggag 4610 // ID VLINE2_VV repbase; DNA; EDCOT; 6448 BP. XX AC . XX DT 21-AUG-2007 (Rel. 12.08, Created) DT 21-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE Non-LTR retrotransposon from Vitis vinifera. XX KW L1; Non-LTR Retrotransposon; Transposable Element; VLINE2_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-6448 RA Obukhanych T. and Jurka J.; RT "VLINE2_VV."; RL Repbase Reports 7(8), 767-767 (2007). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 991..2565 FT /product="VLINE2_VV_1p" FT /translation="MGVWEFTVSVAVAGEEDVRQGREMGESTRQKFEPHSW FT TGGRKRVEEARSTAGGRSSDGAVGRMKEGRGCQKAEIAPVGTRGKKRPTVG FT NSWSQPSPSFSLNSNILRTGSAGPRQDGEVWAGGDKAQSTVEEGLRASKQV FT RRAQSSLKPSPQFETDLGWKRGVSLKGPISLLGQEMGGKQPIFAKGSLRRD FT DPSAKGKGKVGYEDSEAQLRGSALKCGSKKLWNALFPPSSGCRQGGRSRSE FT PLTLERPSSVSDALPKEDAFEAGTQLERSFSASPSRSSGFRKRCSEEGTSP FT TRGDADQRSLLKAPFLSKGKEKMRNFSKGEDRAGFKGFVGFPHRGSSVTVF FT PSYPVTREKGLNSVGSCGMMVVENFEVSSHQHSQSSLSFLSPFSGLALPHL FT SPSVPVLPNSAIQSQFPTKPRVISEIFSKKNDDGAFCLGSVGNPNRDVAVS FT QLASLNHLSESFKSFKTKPSTPLGAPNLVTVSQGDAEFPPMGGFQIEGLSP FT SKMAKVCEVLSSLDIKVYSRRKNRFSTDI" FT CDS 2616..5450 FT /product="VLINE2_VV_2p" FT /translation="MKIISWNTRGLGSRKKRRVVKDFLRLENPDVVMFQET FT KREVCDRRFVGSVWSVRNKEWAALPACGASGGILIIWDSKKMSSEEVVIGS FT FSVSVKFLLDGCGPLWLSAVYGPNSPLLRKDFWVELLDIFGLSFPLWCVGG FT DFNVIRRSSEKLGGSSFTSSMRDFDGFIRDCELLDPPLRNAPFTWSNMQES FT PVCKRLDRFLYSNEWELFFPQSLQEVLPRWTSDHWPIVLDTNPFKWGPTPF FT RFENMWLQHPSFKECFSSWWREFEGNGWEGHKFMRKLQFVKAKLKDWNKNT FT FGMLKERKKSILDEIANIDAIEQEGVLSSDLSAQRVLRKGELEELILREEI FT HWRQKAKVKWVKDGDCNSKFFHKVANGRRNRNFIKFLENERGLVLDNSESI FT TEEILLYFKKLYSSPPGESWRVEGIDWSPISEESASRLDSPFSEEEIFNAI FT FQLDRDKAPGPDGFTIAVFQDCWDVIKEDLVRVFAEFHSSGIINQSTNASF FT IVLLPKKSQTKKISDFRPISLITCLYKVIAKVLSGRLRGVLHETIHSTQGA FT FVQGRQILDAVLIANEIVDEKRRSGEEGVVFKIDFEKAYDHVKWDFLDHVL FT EKKGFSPKWRNWMRGCLSSVSYAILVNGNAKGWVKASRGLRQGDPLSPFLF FT TIVADVLSRMMLRAEERSLLEGFRVGRNRTRVSHLQFADDTIFFSNSCAEE FT LQTLKSLLLVFGQISGLKVNLDKSNLFGINLDQNHLSRLALLLDCKASDWP FT ILYLGLPLGGNPIACGFWDPVIERISRRLDGWQKAYLSFGGRITLIHSCLS FT HIPSYFLSLFKIPASVAAKIERLQRDFLWSGVGEGKRDHLVSWDVVCKPRV FT KGGLGFGKISLRNLALLGKWLWRYPRESTALWHQVILSIYGTHSNGWDANT FT LVRWSHRCPWKAIAQVFQDFSKYTRFVVGDGERIRFWEDLW" XX SQ Sequence 6448 BP; 1685 A; 1090 C; 1753 G; 1919 T; 1 other; agagaatggt aaggacgttg aaggtctctg tggagaggaa gaccttcttg gttaggttcg 60 aaggtgaggt cggtggaaaa tggtgttcgc ttacagagca cagtagaggc tctgttttcg 120 ccttaggctt tgagaaggaa gaggttggtt ggttgataga acatttgacg aaggccattg 180 agatgaagaa tttcatgggt ttcaacagaa aattcagagg aaaaaccaga gtccatttaa 240 tggaggtttg cttcaacaat catggtaggt ttataaggct atcagagttc gcctccaaca 300 gaaagtcaac tttcctggta atacctgagg gagagaatgg caggggatgg gaacatttaa 360 agattgcgtt gtcttcaatg ttggtggtcc cctcctcgag tattgatgaa aagggaaggc 420 agtgcaggga agaaaggact tttcacaaac atgtgggtcc tttgtaccgg tccttcgcga 480 atgtagtcag agaagaagga ccgaggagag gaggccttgt tccagtcggg agatgggcga 540 gagctgtggt gtgcgaatgt catgctggtt ctgttaactg ggctgaggtt ggccgggcta 600 tggcgaaaag attagggcat aaaggtgtgg tgactatcgt ccccttctcc ggtggaaaag 660 gattattttt tgtagaaacc atagaggaag ctttatcact ccacgattta aggtttatca 720 ggattaaggg tgggcttaca gtcttgttga gaagatggtc gccaaaggaa aattcagaag 780 tagaggggaa attcaragaa ggttggatag aattacgggg tttgccattt catttatggt 840 ctgaggtaca tctgaagaaa attatggagc agtgggggac ggtgacagag atcgattggc 900 gaacgttgaa actgtttgat cttagcaagg caagggtgag agttgtaatg aaggaacgat 960 cagttctccc agctttgatc gaggtgttag atgggggtat gggagttcac agtttcagtt 1020 gcagtggctg gagaggaaga cgttaggcaa ggtagagaaa tgggtgagtc aactcggcag 1080 aagtttgagc ctcactcgtg gacaggtggc agaaagaggg ttgaggaggc tagatcaacg 1140 gctggaggga ggtcttctga tggggcagtt ggcagaatga aggagggaag aggttgtcaa 1200 aaggctgaaa ttgctcctgt ggggacacgt ggcaagaaaa gaccgacagt ggggaacagc 1260 tggtcccaac cttcaccgtc tttcagtttg aattcaaata ttctgagaac agggtctgct 1320 gggccaaggc aggatggaga agtttgggct ggaggggaca aagcccaatc aactgttgag 1380 gaagggcttc gggcctccaa acaagtgaga agggcccaat cttctcttaa gcccagtcca 1440 cagtttgaaa ctgacttggg ctggaagagg ggagtttctt taaaaggccc gatttcgttg 1500 ttgggccaag aaatgggagg caagcaaccc atctttgcga agggctcttt acgcagagat 1560 gacccctctg caaagggaaa ggggaaggta ggctatgagg attctgaagc tcaactgagg 1620 ggctccgcgt tgaagtgtgg ttcaaagaag ctgtggaatg ctctgttccc tccaagttct 1680 ggatgccgac aagggggtcg aagtcgaagc gagcctctaa cgcttgagag accgtcgtca 1740 gttagcgatg ctcttccaaa ggaagatgct ttcgaagcgg gaacacagtt ggaacgaagc 1800 ttcagtgcga gtccaagtcg ttcgtcaggg tttcgaaaaa ggtgttccga ggaaggaacg 1860 tcgccgacga ggggagacgc ggatcaaagg tctcttctta aggctccttt tctttcaaaa 1920 gggaaggaga aaatgcgcaa tttctctaaa ggtgaagaca gagcaggttt taagggtttt 1980 gtgggttttc ctcatcgtgg ctcatcagtc acggtttttc cttcttatcc agtaaccaga 2040 gaaaaagggc tcaactctgt ggggtcttgt ggaatgatgg tagtggaaaa cttcgaggta 2100 tcttctcatc aacattctca gtcatctctg tcttttcttt ctcctttctc tggcttggct 2160 cttccacacc tgagtccttc tgttcccgtt cttcccaatt cagccattca gtctcagttt 2220 cctacgaaac ctcgagttat atctgaaatt ttttccaaaa aaaatgacga tggggctttt 2280 tgtcttgggt ctgttggcaa tcctaaccga gatgttgcgg tgtcccagtt agctagtttg 2340 aaccatttgt ccgagagttt taaatctttt aagaccaagc ccagcacgcc tcttggggcc 2400 cccaacctgg ttacagttag ccagggtgat gcggagttcc ccccgatggg tgggttccaa 2460 atagaaggtc tttcccccag caaaatggct aaagtttgtg aggtcttaag ttctctggat 2520 attaaggtgt attcaaggcg gaagaacaga ttttccacag atatttgaga tctgttggcg 2580 ttggtttgga ggtttagggt cagtgaggtg tttttatgaa aatcatcagt tggaatacta 2640 ggggtttggg atctaggaaa aaacgaaggg tggttaagga ttttttgcgg ctcgagaatc 2700 cggatgtagt gatgtttcag gaaacaaaaa gagaggtgtg cgacagaagg tttgtaggta 2760 gtgtctggtc ggttaggaat aaggagtggg ctgctcttcc ggcgtgcggg gcttcaggag 2820 ggattttgat catttgggac tcaaagaaaa tgagcagtga ggaggtggta attggatctt 2880 tttctgtctc agtcaagttt ttgttggatg gatgcggacc cttgtggttg tccgcagttt 2940 atggcccaaa cagtccctta cttaggaagg atttttgggt ggagctgtta gacatttttg 3000 gcctttcttt tcctttatgg tgtgtgggag gtgattttaa tgttataagg agaagttcag 3060 aaaaattggg tggctctagt ttcacttcta gcatgaggga ttttgatggt tttataagag 3120 attgtgaatt acttgatccc ccattacgga atgccccttt cacttggtca aacatgcaag 3180 agtcaccggt gtgcaagaga ttggatcggt ttctttattc aaatgagtgg gagcttttct 3240 tccctcaaag ccttcaagaa gttcttccta gatggacatc ggatcattgg ccgattgttt 3300 tggataccaa tcctttcaag tggggcccaa caccttttag gtttgagaat atgtggctgc 3360 aacatccaag tttcaaagag tgctttagta gttggtggag agaatttgaa ggaaatggtt 3420 gggaaggtca caagttcatg aggaagttac aatttgttaa ggcaaaattg aaagattgga 3480 ataagaatac ttttggaatg ctaaaggaaa ggaaaaaaag catcttggat gaaatagcta 3540 acattgatgc cattgagcaa gaaggggttc tctcttctga tctttctgct caaagagttt 3600 taagaaaagg ggagctagag gaattaattt tgagggaaga aattcattgg agacaaaaag 3660 ctaaggtgaa atgggttaaa gacggggatt gcaattcaaa gttttttcac aaagtggcta 3720 atggcagacg aaacaggaat ttcatcaagt ttttggagaa tgaaagaggt ttggtgttgg 3780 ataattccga gagcatcaca gaggagatct tactatattt taaaaagctc tactcgagtc 3840 ctcctggaga gtcttggaga gtagaaggca tagattggtc ccctatctca gaagagagtg 3900 cttctaggct ggattcccct ttctccgaag aagagatctt taatgccatt tttcagttag 3960 atagggataa ggcgccgggg cctgatggtt ttaccattgc agtgtttcag gattgttggg 4020 atgtgatcaa ggaagactta gtgagggtgt ttgcagagtt tcacagtagc gggattatta 4080 atcaaagcac caatgcctcc ttcatagttc ttttgcccaa aaaaagtcag acaaagaaga 4140 tttcagattt tagacctatt agcttgatca cttgtctcta taaggtaata gccaaagttc 4200 tatcagggcg attaagagga gtactacacg aaactatcca ctctactcaa ggtgcttttg 4260 ttcaagggag acaaattttg gatgcagttc ttatagccaa tgagatagtg gatgagaaaa 4320 ggcgatcagg ggaggaagga gttgtattca aaattgactt tgaaaaggct tatgaccatg 4380 tgaaatggga ttttttggat cacgtgttgg agaagaaggg gtttagtcct aaatggagga 4440 attggatgag aggttgtctg tcttcggtct cttatgctat tctagtgaat ggaaatgcta 4500 aagggtgggt caaggcatct agaggattaa ggcaaggtga ccctttatcc ccttttctgt 4560 tcactattgt cgcagatgtg ttgagtagaa tgatgttgag agctgaggaa agaagtttgt 4620 tggagggttt cagggtaggt aggaatagaa ctagggtgtc ccatctgcaa ttcgcagatg 4680 ataccatctt cttttctaac tcttgtgcgg aagaactgca aactcttaag agtttattgt 4740 tagtgtttgg gcaaatttct gggcttaagg tcaatcttga caagagtaat ctttttggca 4800 tcaaccttga tcagaatcat ctctctaggt tagccttgtt gcttgattgc aaggcttctg 4860 attggcctat actctacctg ggtcttcctt tgggagggaa tccaattgct tgtggattct 4920 gggatccagt gattgagaga atctctagga gattagacgg gtggcaaaag gcttacttat 4980 ctttcggtgg taggataact cttatccact catgcctttc ccacattcct agctactttc 5040 tttctctgtt taagattccc gcttcagtgg ctgcaaaaat tgagagattg caaagggatt 5100 tcctttggtc aggggttggg gaaggtaaaa gagatcatct tgttagttgg gatgtagtgt 5160 gtaagccgag ggtaaaaggg ggtttggggt ttgggaagat ttctttaagg aatctcgctc 5220 ttttagggaa gtggttgtgg aggtatccta gggagagtac agctctgtgg catcaggtca 5280 ttctaagcat ttatgggaca cattcaaatg gttgggatgc caacacttta gtcagatggt 5340 cacatcgttg tccttggaag gctattgcac aagtctttca ggatttttcc aagtatactc 5400 ggtttgtggt aggagatggg gaaagaattc gcttttggga agatttgtgg tgagggggac 5460 caacctttga aatcccaata tccaagacta tttagagtag tcacggataa aaatattcct 5520 atatcttcaa ttctcggttc tgctcgccct ttctcttgga actttaattt ccgtcgtaat 5580 ctttccgatt ctgagataga agatctagaa tgcctcatgc gatctcttga ttgtatgcat 5640 ttatccactt cggcttcaga tgcgagatcc tggtctttat cttcttcagg attgtttaca 5700 gtcaagtctt tctttatagc cttgtcccaa atgcctgatt tatctccatt tttccctact 5760 aagtttgtat ggaattctca agtccctttc aaagtcaagt cctttgtctg gttagtggca 5820 cacaagaagg taaatactaa tgacttgcta caattgagaa gaccctacaa agctcttagt 5880 cctgacattt gtaagttgtg catgaagcaa ggagaatcag cagatcatct tttcctacat 5940 tgttctttgt cgatggggtt gtggcacaga ttatttcagc tagccaagat ggattgggtt 6000 cctccgagaa gcatttcaga catgatgtcc atcaattata aaggttttgg caattccaag 6060 agagggatag ttttgtggca aaatgcgtgc attgctttaa tttgggttgt gtggcgggaa 6120 agaaatgcta ggatatttga ggacaaagct aggaattcag agaatctttg ggattccatt 6180 catttccttg cttctctttg ggctttttgt tccgtggttt ttaagggcat tccccttaac 6240 gtgttacaac tagattggct agcagtgtgt agttccaacg ggatggtcta gccaagagag 6300 cttgttcgta gttttcatag tgtagtttct tgttattttt ttgtgttgtt tagttttatc 6360 tttggtggga ggattcctca tccttctttt gtacttcttt ttctatcaat atatatattt 6420 gttgtttcct atcaaaaaaa aaaaaaaa 6448 // ID Copia-30_Mad-I repbase; DNA; EDCOT; 4760 BP. XX AC ACYM01067653; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-30_Mad_; KW Copia-30_Mad-LTR; Copia-30_Mad-I. XX NM Copia-30_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4760 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1377-1377 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01067653; Positions 11234 15993. XX CC Positions [2136-2636] - Integrase core CC 'ACAAT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 2415..4163 FT /product="Copia-30_Mad-I_1p" FT /translation="MLHQISCPYTPEQNGLAERKHRHLIETTVTLLQYAKL FT PSQFWSFACQAAAYLINRMPTPVLNHKSSFELLFGTSPVITHLRVFGCSCF FT PLLKPYNTSKLQPKTTQCVFLGYASKYKGFLCFDVLKGRIFISRHVVFDES FT SFLYQQLLAQSKCVIACASSPASSDIHPSLLLAAASIPYIISPQPLSTLDS FT STLTPTDASSPQSITVSASSSSLLPVDPEFGPNHLQPVLPIAPLNMHPMQT FT RSKNGIVKKKAFLSSLSDSSYVDLSLCEPATYKSAIKVPVWYKAMQEEIEA FT LHTQDTWSLVPLPFQKNLVGCKWIFKLKKNSDGSISRHKARLVAKGFSQEP FT GLDYGETFSPVIKPTTIRLILALVAHFNWSLRQLDVKNAFLHGLLHEEVYM FT AQPPGFEDPTHPEFVCKLHKSLYGLKQAPRAWNERFTNFLPSLGFASTYAD FT SSLFVKHIGTKIVILLLYVDDIIVTGSASSIIQQVIDFFTVEFDIKDLGNL FT HYFLGIQIDRIGTGFFLSQAKYIQELLQKAEMVDCKPCDTPCLPYNRLLKD FT DGSPFNNPAAYRSIVGALQYLTFTRPNIAFSVHQVC" XX SQ Sequence 4760 BP; 1205 A; 1023 C; 885 G; 1637 T; 10 other; tggtatcaat caccggatca gctaaacgct actctgttcg atccttctga ttacttccgc 60 ttctccacat tgatataata tctacgtttg ccggtcttct tctctacgtt tctcggcgtc 120 gttgctgctc gtgcttgtgt tctttctctg tacgagtgca ctcttcttct tctctccatt 180 tctagggttt gctgcaagtt gggatctgtg acgttgtgtt gaagctttgc tgcacaccag 240 gtgtttgttt tggtgtctca gtgacaagtt gttcttcgaa cattgccaat atggtaactg 300 catcacaact tcagattctt caatctccaa ttactgctct tatttccaca attcctactt 360 ctgtgaatat taagcttgat gatacaaatt acttgaattg gcaatttcaa atgcaattgt 420 tattagaagg tcatgggatt atgcagtttg ttgatggttc taatctctgt cctcctcgat 480 ttcttgttaa ttcgagtgaa tctggtatag tatctggtaa ttcttcttct caaattgaga 540 atgatgcata tgttgtttgg aaactgcatg atagagcctt gatgcaactg attactgcaa 600 cgttatcaca tgctgccatt tcatgtgcta ttggaagttc tagtgcctgt gatctttgga 660 atcggttgaa agaacagttt tctactgttt caagaaccag catattttag atgaaatcaa 720 atctgcaaac cattaagaaa ggatcagatt ctgtgtctaa atatttgcag cgcattaaat 780 aggctcgaga ttacttgtct gctgctggag tttactttgc tgatgaggat attgtcatca 840 tggcactcaa tggcttacct cttgagtaca atacttttcg ctgtgttatt cgaggaaggg 900 aaagtgtcat ttctcttaaa gattttaggt ctcaattact cgcagaagaa ctaattgtgg 960 agagcaatgt ctcatctcag tttttgtctg ccatggttgc caataccaat accatatctg 1020 aacctcagtc ttcctcttat cacactcaat ctcatcctcg tcatgtgccc tatagttcat 1080 ctaatggatc ctctaatggt cataatggtg gtttcaaaca gtttgccaat aataggcaga 1140 agggtaaagg aaagttcaat ccagggtatc ggtatcctgc atcaagacca catttcttta 1200 atcagactca tgtccctacc tctggtgttc ttggtccatc tccaatcgtg ccttttgctc 1260 aatctgtgtt ttgtcagttg tgtaatgcat atggtcatac tgcaccattt tgtcactcca 1320 agacagtgga taaatctagt tgtcagattt gtggaaagaa caaccacaca acttggtttt 1380 gcttttacaa tgataaaggt ccttcataca ttggtccaca gcacccatct atggctccgt 1440 attcctatgc tccttcagca cctcagttcc cttctcaacc tgcgatgcaa gcyatgcata 1500 cartggttcc atcctcttct caggcatctt cctctcagyc ttccyctcaa ctttggcttg 1560 ctgattytgg ggctacgaat cacatgacca ctgatctcag taacttgtct ttagcctctc 1620 catatccaac caatgagacc gttcaaactg ctaatggaga aggtttgaca gtatctcatg 1680 ttggcagcac tgttattcat acaccagttc atcatatcaa attaaattct gttttatatg 1740 tgcctaaatt gtctcagaat ttattatcag tgcatagaat ctgtcttgat aacaactgct 1800 ggttgatttt tgatgcgtcc tgtttttgga ttcaggacaa ggccacaggg aggatcctct 1860 acaaagggct atgcagtaat ggactttatc ctatctcatc cctttccaaa catcctggtt 1920 cttattcacc aagtaatgtc aaggtttctg catatctggg acagctyatt agttcatctc 1980 tttggcatag taggttaggt caccctacca ataatattgt ttctactatg ctcaataaag 2040 ctaatatcag gtgttccaag gatgatgtac ccatagtatg tcatagttgt ctagaaggaa 2100 rgtttamaaa aytgcctttt caatctagta ctcatcaatc tcaaatacct tttgaagttg 2160 tayacagtga tctttggggc cctgcaccct gtaattcaat tgatggtttc aaattctatg 2220 taactatcat tgatgaatgt actagattct gttgggtgtt cccacttata aataaatcag 2280 acttttttga tacatttgtc tccttttatg cctttgttaa agctcagttt tctgcaacca 2340 ttaagagttt acaaacagat ggtgggggag agtatataag tcataaacta caagcttttc 2400 tcaaagtcca agggatgtta catcaaattt cttgtccata cactcctgag caaaacggct 2460 tagccgaaag aaaacatagg catcttatag aaactactgt taccctgctg caatatgcta 2520 agcttccctc tcaattttgg tcttttgctt gtcaagctgc tgcctattta atcaatagga 2580 tgcctacacc agttttaaat cataagtctt catttgagtt actatttggt acatctcctg 2640 tgattactca tcttagagtt tttgggtgtt cgtgttttcc tttactaaag ccctataaca 2700 cttccaaatt acaacctaaa acaactcagt gtgtttttct ggggtatgcc tctaaatata 2760 aaggctttct ttgttttgat gtcttgaaag ggaggatctt tatatctcgg catgttgtgt 2820 ttgatgaatc cagttttctg tatcaacaat tactagctca gtctaagtgt gtcatagcat 2880 gtgcctcatc acctgcctct tctgatattc atccttcact actcttagca gctgcatcaa 2940 taccatatat catatctcct caaccacttt ccaccctaga ctcttctact ttgactccca 3000 cagatgcttc atctcctcag tccattactg tctcagcaag ctcttcctcc ttactccctg 3060 tggatcctga gtttggtcct aatcatctac aaccagtgtt gcctattgct cctttaaata 3120 tgcatcctat gcaaactcgg agcaagaatg gtattgttaa gaagaaagct ttcctcagct 3180 ctctcagtga ttccagttat gttgatttgt cactgtgtga gcctgcaact tataaatctg 3240 ccattaaggt ccctgtttgg tataaagcta tgcaagaaga gattgaagca ctgcatactc 3300 aggacacttg gagtttggtt ccattacctt ttcagaaaaa cttagtaggt tgcaaatgga 3360 ttttcaagct taagaagaac tctgatggtt ctatttctcg gcataaagct cggctggtag 3420 ccaagggctt tagtcaagaa cctggtctgg attatgggga aacttttagc cctgtcatca 3480 aacctactac tattcgatta atactagctt tggttgccca ttttaattgg tcattaaggc 3540 agctcgatgt taaaaatgcc ttcttacatg gcttgttgca cgaagaggta tatatggctc 3600 agcctccggg gtttgaagat ccaactcatc ctgagtttgt atgtaagctg cacaaatctt 3660 tatatggttt gaaacaggcc ccaagggcat ggaatgaaag gtttaccaat tttctgcctt 3720 ctcttggttt tgcttccact tatgctgatt cttctctgtt tgttaagcac attggtacta 3780 agattgtcat tctactactc tatgttgatg acataattgt cactggcagt gcttcttcta 3840 tcattcaaca agtcattgac ttttttacag ttgaatttga tattaaagat ctgggaaatt 3900 tgcactactt ccttggcatc caaattgatc gaattggtac aggttttttc ttgtctcagg 3960 ccaagtatat acaagagtta ttacagaaag cagaaatggt tgattgcaag ccgtgtgata 4020 caccttgctt gccttacaat cgcttactca aggatgatgg ttctcctttc aacaatcctg 4080 cagcttatcg aagtatcgta ggtgcattgc agtatcttac tttcaccagg ccgaacattg 4140 ctttttctgt tcatcaagtg tgttagttta tgcaggctct tatgatttct cactatactg 4200 cagtcaaaag aatattgcga tacttaaagg gtactatgac ctttggtata tcatattctg 4260 ctagtgactt acagttaaaa gcttttagtg atgtagactg ggctggcgac cctaatgatc 4320 gaagatctac aacgggctta attgtgttct taggtggcaa tcccatttcc tggtcatcta 4380 agaagcagaa taccgtgtca cgatcctcta cagaggcgga atatcgggct atttcttcca 4440 cttccgctga acttgattgg atccagcagc ttcttcagtt tctgcacatc caacttccaa 4500 cagctccagt tctcttttgt gataatttgt ccgccatagc cttgtccttc aatccggttt 4560 aacatcagcg tacgaaacac attgagatag atgttcactt tgtgcgtgaa agggttgcca 4620 aacatcgtct catggttcag tttgtatctt ccagggagca gtttgcggat attctaacaa 4680 aaggacttag ttctcctttg tttcggtctc attgtaccaa tctcatgctt ggttcatcca 4740 aacctgagat taagggggga 4760 // ID Copia33-PTR_I repbase; DNA; EDCOT; 4510 BP. XX AC scaffold_117; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia33-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4510 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4510 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 242-242 (2007). XX DR Genome; scaffold_117; Positions 920244 915735. XX CC Positions [1955-2455] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 1325..4510 FT /product="Copia33-PTR_I_1p" FT /translation="MHANFPSSTSTEQFWVADTGATTHMTSDIAQLNLATP FT FSGSDTIATADGSGLSISNVGSSILDVPQCSFKLPQVLHVPKLSQHLLSVH FT RLCKDNNCRFICDAFGFCIQDKLTGRILLQGLSRDGLYPIPLSIPQSRLSQ FT SFSLSKHQFCYLGHQVKTSLWHKCFGHPSNKITSALLHQSKIPFTSDHSKS FT VCTACLEGKFVKLPFPYPAIKSATPLEVIHSDVWGPSPTISIDGFRYYVSF FT IDECTRFTWIFPMRNKGEVYSIFVSFHAFLVTQFSANLRIFQSDGGGEYLN FT HSFKQYLLAKGIIHHISCPYTPEQNGLAERKHRHILETAITLLQTAHLPSK FT FWYHACATSIYLINRMPCSILQLKSPYILLHGSVPVLTHLKIFGCACFPLL FT KPYNTHKLQPKTSTCIFLGYAGQYKGYICFSLLTNKCFVTRHVIFDESIFP FT YTSVSAASSSPSHLSPLVPPSVSLDTLPSPTLPSPIISSNRSGLDSTTQLS FT PPEDPDFHPENLCVVLPLSPMNLHPMTTRSKNGISKKKAYSTTVQSLDFSS FT AEPSSFKIASKIAAWQSAIQEEIDALHAQGTWDLVPLPHAKNLVGCKWVYR FT IKKNADGSIARHKARLVAKGFSQEEGIDYNETFSPVVKPTTVRLVLALVAQ FT FHWPLRQLDVKNAFLHGILQEEVYMTQPQGFTSKIYPDFVCRLRKSLYGLK FT QAPRAWNDRFTGFLSSLGFQASLADPSLLVQHSSHGTVILLLYVDDILLTG FT SHSSLLTSVIDALTQEFDMKDLGQLTYFLGLQVSYSSSGLFVSQSKYIKEL FT LDRVDLQNSKSCATPCLPYHHLLKDDGKPYSRPQQYRSIVGALQYLTFTRP FT DIAFSVNQACQFMHNPMESHVVAVKRILRYLKGTLDYGIHFQPGTLNLQAY FT SDADWAGDPNDRRSVSGFVVYLGSSPISWASKKQHTVSRSSAEAEYRALAI FT AAAELTWIRQLFCDMHVPLLIPPLIHCDNISAISLASNPVFHSRMKHLQID FT YHFVRERVIKGDLLVQHVSSADQFADILTKGLSSPLFHHHCSNLMLGSSMH FT TIAGE" XX SQ Sequence 4510 BP; 1096 A; 1054 C; 807 G; 1553 T; 0 other; gagctgtctt cctaatcctc tgcttccgca cgtcctgctc tgtctctgct tcttctctaa 60 tcaacaagca aatctttcca gttgattctc tatttctgca ttccaaaaac aaaacaaaat 120 ggtgactcct tctcaactcc agattgtcca atcccctata acctccttac tttctacagt 180 tgctactgct gtgccaatca aacttgatga tactaattac ctcacatggc actttcagat 240 gaaaatcctt cttgaaagtc atggtatttt aggttttgtt gatggttcaa ggcagtgtcc 300 tagccgattt aatgcagact ctgaccttga gggaactgaa actgatgact atcaggtgtg 360 gaaaatgcat gatcgagcat taatgcagtt gctcattgcc actctttcct ctactgcaat 420 ttcctatgtt attggatgtg tcagtgctca tgatatgtgg attcagctga aggatcgatt 480 ctctacagtc accaaagcac gcatttttca gatgaaaagt gagcttcaga atattaagaa 540 ggggtcagaa ccagtttctc attatctgca aaagattaaa gatgcaagag atcatctttc 600 tgcagcagga gtttcttttg aggatgatga tattatgatc ctggctctca atggcctgcc 660 ttctgactac aacacgttta gatgtatgat tagaggcaga gataatacat tgtctcttaa 720 agattttcga tctcagttac ttgctgaaga agctactctt gaacatactt agtctgcatc 780 tccctttgtt tctgcaatgt tggctcaaaa tcagacattt caaggcaagg ctcttgttct 840 tgatgaagga tcttctcctt ctcattctca ttctcatctt caatctcagg gatattcttc 900 aaactcaaag accttcccat cttctcaccc ttcatctgga tttaatgggg gtttctatgg 960 tcccacgggt ggttttaatg gtcctaatgc catgtttacc aacagtggcc actctaatag 1020 aggctcttat tttaaaggac gtggaagaag ccgtggccat tatcaatctg gtccacgccc 1080 ttatcaagtt tcttctccta gtcctggtat tcttggcccc ggtattgaca ttcccatctg 1140 tcaaatttgc agcaagaaag gccatatagc tgcagattgc tatcaacgac ataatcaatc 1200 accttcttct acctcttcag tccaatgtca gatttgttgg aaatttggcc attctgctat 1260 ccagtgctat cacagaggca atttttccta ttaaggcaga ccaccctcca ctaatctcag 1320 tgcaatgcat gctaattttc cttcttctac ttctactgag caattttggg ttgctgatac 1380 tggagcaact actcatatga cttctgacat agctcaactc aacctagcca cccccttctc 1440 aggatcagat actattgcta ctgcagatgg ttcaggtttg agcatttcta atgttggttc 1500 ttctattctg gatgttccac agtgctcatt caaattacca caagttctgc atgtgcctaa 1560 gctgtcacaa cacttgctat cagttcatag gttatgtaaa gataacaatt gcagattcat 1620 ttgtgatgcc tttggttttt gcattcagga caagcttaca ggaaggattc ttctccaggg 1680 actgagtaga gatggtttat atcctatccc tttatccatt ccacagtctc gactttcaca 1740 gtctttttcc ctttcaaagc atcaattctg ttatcttggt caccaagtaa aaacaagtct 1800 ttggcacaag tgttttggcc atccttctaa caaaatcact tcagctcttt tacatcaatc 1860 taagattcct tttacttcag accactccaa atccgtctgc actgcctgtt tagaaggcaa 1920 atttgtaaaa cttcctttcc cttatccagc aatcaagtct gcaacacctt tagaagtcat 1980 tcatagtgat gtgtggggtc cttctcctac catttctatt gatggttttc gatattatgt 2040 tagcttcata gatgaatgta ctcggtttac ttggattttt ccaatgagaa ataaaggaga 2100 ggtttattcc atctttgttt catttcatgc tttcctggtc actcagtttt ctgccaatct 2160 acgaattttt cagagtgatg gtggtggtga gtacctcaat cattccttca agcagtatct 2220 ccttgctaaa ggtattattc atcacatctc ttgtccatac acccctgaac agaatggtct 2280 tgctgagaga aagcatcgcc acattctaga aacagcaatc actttgttgc aaactgctca 2340 tctaccctct aaattttggt atcatgcttg tgccacttcc atctatttga tcaaccggat 2400 gccttgttca attcttcaac ttaaatctcc ttatatttta ctgcatggtt ctgtccctgt 2460 cctaactcat ttaaagatct ttggctgtgc atgttttcct ctactcaaac cttacaatac 2520 tcacaaactt cagcctaaaa cttccacctg tatttttctg ggatatgcag gtcaatacaa 2580 gggatatatc tgtttttctc ttcttactaa taagtgcttt gtgactcgtc atgtcatctt 2640 tgatgaatct atatttccat acacttctgt gtctgcagct tcctcttctc cttctcattt 2700 gtcccctctt gttccacctt ctgtctcttt agatacattg ccttcaccca cattgccttc 2760 acccatcatt tcttcaaatc ggtcaggttt ggattctacc acacagcttt ctccccctga 2820 ggatcctgat tttcatcctg aaaatctttg tgtagtcttg cctctgtccc ctatgaatct 2880 tcatcctatg acaaccaggt ccaagaatgg tatctccaaa aagaaggctt attctactac 2940 tgttcagtct cttgactttt cttcagctga acccagttca ttcaagattg cctctaaaat 3000 tgctgcatgg cagtctgcta tacaagaaga aattgatgct cttcatgctc agggtacttg 3060 ggatttggtt cccctgccgc atgccaagaa tcttgtaggc tgtaaatggg tgtatcgcat 3120 caagaaaaat gcagatggct ctattgctag gcataaagca cgccttgttg caaagggttt 3180 tagtcaggaa gagggcattg attataatga aacattcagt cctgtagtga aaccaaccac 3240 tgttcggttg gtgctggcac ttgtagctca gttccattgg cctttaaggc aacttgatgt 3300 taaaaatgca tttctgcatg gcattcttca agaggaggtg tatatgactc aaccacaagg 3360 ttttaccagc aagatttatc ctgattttgt ttgcagactt cgcaagtcct tatacgggtt 3420 aaaacaggct cctcgtgcct ggaatgacag gtttacaggt ttcctttcca gcttgggatt 3480 tcaggcttct cttgctgatc cttctttatt agtccaacac tcctctcatg gcactgtgat 3540 attgcttctt tatgtagacg atattcttct cacaggcagt cattcatctc tccttacatc 3600 agttattgat gccttaactc aggaatttga tatgaaggat ttaggccagt tgacatattt 3660 tctgggactg caggtttctt attcttcctc cggcttgttt gtatctcaat ctaaatatat 3720 caaggaattg cttgatcggg ttgatttaca aaattcaaag tcatgtgcca ctccttgtct 3780 tccctatcat cacctgctca aggatgatgg taaaccttat tctcgtccac agcagtatag 3840 gagtattgtt ggagctctgc agtatctaac cttcacacgt cctgacattg ccttctctgt 3900 caatcaagct tgccaattca tgcataatcc catggagtct catgttgttg cagtgaaacg 3960 aatcttgaga tatctcaagg gtactcttga ctatggtatt cactttcagc ctggcacact 4020 taatttgcaa gcatacagtg atgctgattg ggctggtgat cccaatgatc gtcgttctgt 4080 ttctggtttt gttgtctact tgggatccag tcctatttcg tgggcttcta agaagcaaca 4140 tactgtctca cgctcgtctg ctgaggctga atatagagct ctggctattg ctgctgctga 4200 gctcacatgg attcgtcaat tgttctgtga tatgcatgtt ccattgctta ttcctccttt 4260 aattcattgt gataatatct ctgctatttc tcttgcttcc aatccagtgt ttcattccag 4320 gatgaagcat cttcagattg attatcactt tgttagagaa cgtgttatca aaggtgactt 4380 gcttgttcaa catgtttcct ctgcagatca gtttgctgac attctcacta agggtctttc 4440 ttctccattg tttcatcacc attgttccaa tcttatgctt ggttcctcca tgcatacgat 4500 tgcgggggaa 4510 // ID Copia-76_Mad-I repbase; DNA; EDCOT; 4223 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-76_Mad_; KW Copia-76_Mad-LTR; Copia-76_Mad-I. XX NM Copia-76_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4223 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1690-1690 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1831-2217] - Integrase core CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 19..1212 FT /product="Copia-76_Mad-I_1p" FT /translation="MVGSGSSGGDLRTPQFDGANYDFWAVKMETILIAHDL FT WDVVELGVQPQQILEEEEDSGDEGSEAEQVPVEAPTISREDRIKNAKALSL FT IQGAITDELFPRIRNEKTAKGAWDILRREFRGDKKVRAVKLQAVRADFEYM FT RMTDSENLDDYLGRFFGIVNNLKSLGEDVTEQRIVQKLLMSLSRRYKSIVS FT IIEETRDLDAIRVEEVIASVKVYDKREDLHDERDKLTGTERAFSSLRVGNN FT QATGTYKGSQSRPNQKWQGQYKKGSNWSQSGNLNDNDGSNWNNNSGGNWNN FT RFNSQNKQGSSSQSCVKPQCQVCQKYHFGVCRYKGKAKCGKCDRFGHIAKD FT CDSHKQVANCAKEEEVTTGTMFYACHSSITQDRSVWFVDSACSNHMTSQES FT VLIN" FT CDS 1651..2625 FT /product="Copia-76_Mad-I_2p" FT /translation="MCVKVVFQGNITESHLTKEKCGEQAIHLSWYTQICVD FT QCKMSPLEGIGTSSHSLMISQECVGLYFLRNKSDTFNVFKKFKAFVELQSG FT FSLKKLRSDRGGEYTSHEFLDYCTSMGMERQLTIAYSPQQNGVAERRNRTI FT CEMARSMMAEKGIPVIFWAEAVSTAVYLQNRCFTTSVIDKTPFEAFTGRKP FT GIKHLKVFGCICYTHVPSPLRQKFDDKTRKGIFMGYGSCEKGYRVYDLQSK FT KIVLSRSVIFSEDKSWKWESNQVESISIPLNLEGNGAENEVSEEQTDVISL FT IMLEILIQTPLLMNQLRRIVEVTAKAQHLAPLQ" FT CDS 2666..4174 FT /product="Copia-76_Mad-I_3p" FT /translation="MCIIEPENYQEAVGDKAWQEAMNAELEMIEKNDTWEL FT VERPVDKPVIGVKWVFKTKLNLDGTVQKHKARLVAKGYAQKPGIDYNETFA FT PVARLDTIRTLIALAAQKGWKLFQLDVKSAFLNGVLEEEVYVEQPEGFELA FT NAGHKVYKLRKALYGLKQAPRAWYSEIDAYLSLCKFKRSTSEATLYTRSDD FT EGGLIIVSIYVDDIVYTGSSDEMLSEFKREMMERYEMSDLGLLHHFLGMGI FT LQTDQGVFIHQSKYAKSLLVKFGLEDCKPVSIPLPTGEKLKKVDGSELADE FT GLYRKIVGSLLYLTATRPDLMYAASLLSRFMNGPTKKHLGVARRVLRYVQG FT TLNYGIEYVKDKSAILIGFCDADWAGSEDDSRSTSGYAFSFGSGAFSWASV FT KQNTVALSTAEAEYVSASEATAQSIWLRFVLDDFGEMQTEATPLFCDNMSA FT ISMAKNPVFHQRTRHINRRYHFIREALQEGVIDLQFCRSEEQLADIFTKAL FT PKDRFNH" XX SQ Sequence 4223 BP; 1384 A; 693 C; 1074 G; 1071 T; 1 other; ctgatactca ctaagaaaat ggtgggatcg ggttcttccg gtggagattt acgaactcca 60 cagttcgatg gcgcaaacta cgatttttgg gctgtcaaga tggagactat cctcatagcg 120 catgacctat gggatgtggt agaactcgga gtacaaccgc agcagattct cgaggaggaa 180 gaagactctg gagatgaagg aagtgaggct gagcaagttc cagtggaagc acccaccatc 240 tccagagaag acagaataaa aaatgccaag gcgctgagtc tcatacaagg agccataaca 300 gatgagctct tccctcgcat cagaaatgag aagactgcaa aaggggcatg ggacattctg 360 agaagagagt tcagaggaga taaaaaggta agagctgtaa aacttcaagc agttagggct 420 gattttgagt atatgagaat gacagatagt gaaaacctag atgactattt gggtaggttt 480 tttggaattg tgaacaatct gaaatctctt ggtgaagatg tgactgaaca aagaattgtg 540 cagaaattat tgatgagtct aagtaggagg tataaatcca ttgtgtccat tattgaggaa 600 actcgagatc tggacgctat tagagttgaa gaagtcattg catctgtcaa agtctatgat 660 aaaagggaag acctgcatga tgaaagggat aaattgacag gaactgagag ggcctttagt 720 agcctcagag ttggaaataa ccaagctact ggtacctaca agggttcaca gagtagacca 780 aatcaaaagt ggcagggaca atacaagaag ggatcaaatt ggtctcaaag tggaaacttg 840 aacgacaacg atggctcaaa ctggaacaac aattctggag gaaattggaa caatagattc 900 aactctcaga acaagcaagg aagtagtagt caaagttgtg tgaaaccaca gtgtcaagtt 960 tgtcagaaat atcatttcgg cgtgtgcaga tacaaaggaa aagccaagtg tggaaagtgc 1020 gaccgatttg gacatattgc aaaggactgt gatagtcaca agcaagtagc taactgtgca 1080 aaagaagaag aggtaaccac aggaaccatg ttctatgctt gtcactcttc aattacgcaa 1140 gatagaagtg tgtggtttgt ggacagtgcc tgcagcaacc acatgacatc tcaagagtct 1200 gtgttaataa acmttgacag atctgtgact tgtaaagtca aaatgggcac tggagatctt 1260 gtacaagcaa ctggaaaagg cactctggtg gttgaaacac agcatgggaa aagatacata 1320 aatgaagtgt tgctggttcc aggtttggat gagaatttac tgagtgtagg ccagatgatg 1380 gagcatggat actatgttct atttgggggt aatatggcag taatctttga tgatagcagc 1440 ctcgacaatg ttgtagcaaa ggtgatcatg gcaggaaatc gatgttttcc tctgtcacta 1500 gaatctataa ccctgcagca agaaaagcat cagtgattga agactcttgg atctggcaca 1560 gaaggcttgg acatttgaac ttcgctagca tgaagaagat gcaacagaag gaaatggtac 1620 ttggattacc tgctttgaca gaaatggaag atgtgtgtga aggttgtgtt tcagggaaac 1680 atcacagaga gccatttgac aaaggaaaag tgtggagagc aagctatcca cttgagttgg 1740 tacacacaga tttgtgtgga ccaatgcaaa atgagtccat tggagggaat aggtacttca 1800 tcacattcat tgatgatttc tcaagaatgt gttgggttat actttctcag aaacaaatct 1860 gataccttca atgtgttcaa aaaattcaaa gcttttgttg aactgcaaag tggtttcagt 1920 ttgaagaagc taaggagtga tagaggtggt gaatacacct cacatgagtt cctggattac 1980 tgtacaagca tgggaatgga gaggcaacta accattgcct attctcctca gcaaaatgga 2040 gttgctgaga gaaggaacag aacaatttgt gagatggcaa gatccatgat ggctgagaaa 2100 ggaatccctg tgattttctg ggcagaagct gtgagtacag ctgtgtatct ccaaaataga 2160 tgctttacaa catctgtgat agacaaaaca ccttttgaag ctttcacagg taggaagcct 2220 ggaattaagc atctgaaagt atttggttgt atctgttata ctcacgtccc atcacccctg 2280 aggcagaaat ttgatgacaa aaccagaaag gggatcttca tgggatatgg aagctgtgaa 2340 aagggatata gagtgtatga tctgcaatct aagaaaattg tactctcaag gagtgtgatt 2400 ttcagtgaag acaaatcatg gaagtgggaa agtaaccaag tggagtctat ctcaatacct 2460 ctcaatcttg aagggaatgg agcagaaaat gaagttagtg aagaacaaac tgatgtaatc 2520 agtttaataa tgctggagat actcattcaa acaccactgt tgatgaatca gttgaggaga 2580 atagtggaag tcacagccaa ggctcaacac ctagctccac tccagtaaag tgagaactct 2640 ggaagatata tatgcaagat gtcacatgtg tattatagaa ccagagaact accaagaagc 2700 agtaggtgat aaagcctggc aagaagctat gaatgcagag ttggaaatga ttgaaaagaa 2760 cgatacttgg gaacttgttg agaggccagt tgataaacca gttataggtg tgaaatgggt 2820 gtttaaaact aagcttaact tggatggaac agttcaaaaa cacaaggcta ggcttgtagc 2880 aaaagggtat gcacagaaac ctgggattga ctacaatgaa acctttgcac cagtggcaag 2940 gttagacaca attcgaactc tcattgctct tgcagcacaa aagggttgga agctatttca 3000 gttggatgtt aagtcagcat tcctaaatgg tgtacttgag gaagaagtgt acgttgagca 3060 gcctgagggt tttgagttgg caaatgcagg tcacaaggtc tataagttaa ggaaggccct 3120 atatggactt aaacaggcac ctagagcctg gtacagtgag attgacgcat atctctctct 3180 gtgcaagttc aaaaggagca caagtgaagc cacactatat acaagatctg atgatgaagg 3240 agggttgata attgtgtcaa tatatgttga tgacattgta tatactggaa gtagtgacga 3300 gatgctcagt gagttcaaaa gggaaatgat ggaaagatat gaaatgtctg atctcggcct 3360 tctacatcac ttcttaggca tgggaatact gcaaactgat caaggtgtgt tcatacacca 3420 aagtaagtat gctaagtctt tacttgtgaa atttgggctc gaagattgca aaccagtgtc 3480 tattcctttg cccactggtg aaaagctaaa gaaagtggat gggagtgaat tggctgatga 3540 aggactttac aggaaaatag tgggaagtct gctgtattta acagcaacta gacctgacct 3600 gatgtatgct gcaagtttgt tatcaaggtt catgaatggt cccaccaaga agcatttggg 3660 agttgcaaga agagtactaa gatatgtgca agggaccctc aactatggca ttgagtacgt 3720 gaaggacaag tctgcaattc tcattggatt ctgtgatgca gattgggcag gaagtgaaga 3780 tgatagcaga agcacctctg gttatgcatt cagctttggc agtggagcgt tttcttgggc 3840 atctgtgaaa caaaacacag ttgcactgtc aactgctgaa gctgagtatg tctcagcatc 3900 tgaggcaaca gcacagtcca tttggttaag gtttgttctt gatgattttg gggaaatgca 3960 aactgaggca acacctttgt tctgtgacaa tatgtcagct atatctatgg ccaagaatcc 4020 tgtttttcat cagagaacta gacatataaa caggaggtat cacttcataa gggaagctct 4080 gcaagaaggt gtgattgatt tgcaattctg cagaagtgaa gaacaacttg cagacatatt 4140 tacaaaggct ttgccaaaag acagatttaa tcattgagat tgaggcttgg agttaagcca 4200 gtaagcagct taggagaggc tgt 4223 // ID CUMULE repbase; DNA; EDCOT; 12078 BP. XX AC AY582736; XX DT 20-SEP-2005 (Rel. 10.09, Created) DT 20-SEP-2005 (Rel. 10.09, Last updated, Version 1) XX DE MuDR-type DNA transposon from muskmelon (a complete sequence). XX KW MuDR; DNA transposon; Transposable Element; CUMULE. XX OS Cucumis melo OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; OC Cucumis. XX RN [1] RP 1-12078 RA van Leeuwen H., Garcia-Mas J., Coca M., Puigdomenech P. RA and Monfort A.; RT "Analysis of the melon genome in regions encompassing TIR-NBS-LRR RT resistance genes."; RL Mol Genet Genomics 273(3), 240-251 (2005). XX DR EMBL/GenBank/DDBJ; AY582736; Positions 90166 102243. XX FH Key Location/Qualifiers FT CDS join(1165..3585,4345..5283) FT /product="CUMULE_1p" FT /translation="MAHVRILVRHGGEWDEGRRKYEGGVLKGIVVPKEITH FT KDLQSELYDLAEVDPTKFDIKIRCIYEIKGEKEAPPFELSNDRDLKFYILS FT ENPLEVPLYLSFEPTSNRSMKVLNKDYNSVSGSNQVQNLNPHPPPIGMDRL FT DENEVDIGEVEGGLCHNMIGTNSAIWESYESYHSIDDTFTLESVEMYNELF FT DIPEQRDAPTKDCKGKGKVDYRSSSRKLKTKGSGWSEESSTSEELDVGQIF FT FCKRDLSMRLSVLAMKKNFQFVVKKSTKEVLFVRCIDNKCGWRLRAVRLKD FT SNIFKIKKYVKVHSCSLEFLNRDHRQAKSWVVGELIKSKFKGPGRIYKPRD FT IIEDMRQDYGINMSYEKAWRARENAYERVRGSPEESYNLLRRYGEALKFTN FT SGTIFHMELEDDRFFKYLFMAVGACVRGFLNCIRPVIVMDGTFLKNKYRGQ FT LIVAVCLDGNNQIYPLAFGVVDRETDDSIQWFLEKLKGAIGEVPNLGFVTD FT RKTCFAKGISSVFPSAFHGLCVQHLSQNLHDKYKNDTVATLFYNASRTYRE FT STFVEAWRHLLSFPNGSGKYLNDVGIARWSRVHCPGRRYNMMTTNIAESMN FT SILKEPRDLPIASFLENVRALLQPLVLGASRRSIKVTSTLTKWAELVIQKK FT QEGALTMKVNPIDCYQFHVKDLDKEEVVNLQTKECTCKEFQAEQLPCSHAI FT AAARVRNINVYSLCANYYTNECLLAAYAEAVYPVGNQSDWKTSEDYVHMTV FT LPPKVVKRVGRPKKKRIPSVGEAPKLHKCGRCKQIGHNRLTCTNPISYTDK FT SSIQDFSSTLKGIFPNFSYYNVTLFLCLYFKRFNFCLQKLSLCSYIIIVKR FT LGFRVRLLSSIYYIHFRMAVPSEKYFPATVSCQVHKIGSLIKDKLTKDQLQ FT MFEKTIFGPLLNVNMVFNGQLIHHFLLRQIPEDGNADGICFSVLGKNVRFT FT QKEFNIITGLWPTNNPLEKDCDSKRLQSLLFGSENKKVITCLEIEEIFKNF FT EFTNDDDAVKVALAVFIETVMVGKDKKTQFDMDILGRVDDEEAFKSFDWST FT FFYTRLLNSLKTSLQGKKEAYELKKTRSSKAVSYYNIKGYVLAFQVIFISS FT YTLSKCQLNIKV" XX SQ Sequence 12078 BP; 3988 A; 2252 C; 2226 G; 3612 T; 0 other; ttgggaaatt gccaaaaata ggttaaaaaa agagatttaa atgaattttg ggacaagttt 60 tcaaaagaaa gacttttagg acaatttggg tgtgaataga caaaaatgcc cttcctttcc 120 tttccctctt ccacgttgct ttcccttctc tgattcgttc tctttcgcgt atagttccgt 180 ttcccttctc ttttctttcg tgtagaacac ttgaacctac tccggccatc gtcagttgtt 240 catcgtcact tgcccatcgt cgcttgccca tcgtcgtttg cccttcgtcg cttgcccttc 300 gtcgcttgcc cttcgtcggt cgttgtccag tgcatttcgt cgctcctatt cggaccattc 360 aatcaacttc gagcgtctta tttaggtgag tttcatgtat aaccgatttt caatttatct 420 gctgtaagta aatgtttgtt agggtatttg gtgctatttt catccgtaat tgtctggttt 480 ttggaattgg acttatttgc cgtaaattag tttagtcaaa ttttggtttt aggttcttag 540 aaagttcaat gttcaatggc tagtgaaaaa tgaattgaac tagaggatga ggatttagtt 600 ggatcaaata gaggaggagt aagcaatagg aatagaagga attaaggttt ttttttttta 660 tctcgcattt tttttttatc tcgcacttat ctcgcacgta tctcgcacgt tccaaacttt 720 cactatttat ttcaaaatca acttggtaca cctcctaatc catttagagc tattctttgc 780 atgtttagta actctcttag gccctcatgc tttatctcgc acgtatctcg cacgtatctc 840 gcacacatct cgcacgttcc gaactttcac tatttatttc aaaatcaact tggtacacct 900 cctaatccat ttagagctat tctttgcatg tttaataact ctcttaggcc ctcatgcttt 960 atctcgcacg tatctcgcac acatctcgca cgtatcttcg cacacatctt cgcacacatc 1020 tcgcacgttc caaacttcca ctatttattt caaaatcaaa ttggtacacc tcctaattca 1080 attctttaca tcttgcacgc atttgtaggt tcttaaagtc aaatcaattt tttaagatac 1140 aaaagtactt aaggtagttt aaggatggca catgttcgga ttttagtgcg tcacggtggt 1200 gaatgggatg agggacgaag aaaatatgaa ggaggagtgt taaaaggcat tgttgtccct 1260 aaagaaataa cacacaaaga tttacagtct gaactatatg accttgcaga agttgaccct 1320 acaaagtttg acataaagat aagatgtata tatgagatca aaggggaaaa ggaagctcct 1380 ccatttgagt taagcaatga ccgtgatttg aagttttata ttcttagtga aaatccattg 1440 gaggtccccc tatacctatc gtttgagcct acaagcaatc gaagcatgaa agtgttaaac 1500 aaagattaca attcagtatc tgggagcaac caagttcaaa atttaaaccc tcatcctcct 1560 ccaattggaa tggatagatt agatgagaat gaagttgata ttggtgaagt cgagggtggc 1620 ttgtgtcata acatgatagg gaccaattcg gctatatggg aatcatatga gtcatatcat 1680 tcaatagatg atacttttac attggagtca gttgagatgt acaatgaatt gtttgacatc 1740 ccagaacaaa gagatgctcc tacaaaagat tgcaaaggaa aaggtaaagt tgactacagg 1800 tcctctagtc ggaagttgaa gacaaaagga agtggctggt cggaagaaag ctctacaagt 1860 gaagagttgg atgtaggaca aatatttttt tgcaagagag atttgtcaat gagattaagt 1920 gtgttggcaa tgaaaaaaaa ttttcagttt gtagtaaaaa agtctacaaa agaggttctt 1980 ttcgttagat gcatcgacaa caagtgtggt tggagattgc gagcggttag actgaaggat 2040 tcaaatatat tcaagattaa aaagtatgtg aaagttcatt catgttctct tgagtttttg 2100 aatcgtgacc ataggcaagc aaaatcttgg gttgttggag aattaatcaa gtccaaattc 2160 aaggggcccg gtcgcatata caaaccacgt gatatcatag aagacatgag gcaagactat 2220 ggcataaata tgagttatga gaaagcatgg cgtgccagag aaaatgcata tgaacgagtg 2280 cgagggtctc ctgaagagtc atataatctt ttgcgtagat atggtgaagc actcaaattt 2340 acaaattcag gtacaatatt tcacatggaa ctcgaagatg atcgtttctt taaatatctt 2400 tttatggctg ttggtgcatg tgttagagga ttcttaaatt gcattagacc ggtcatagtc 2460 atggacggaa catttcttaa gaacaaatat cggggtcagt tgatagtggc cgtttgttta 2520 gatggtaaca atcagatcta tcctctagcc tttggagtag ttgatagaga aacagatgac 2580 tcaatacagt ggttcttaga aaaattgaaa ggtgcaatag gggaggtgcc taatctaggc 2640 tttgtgacag atcggaaaac atgcttcgcc aagggtattt catcagtttt cccatctgca 2700 ttccacggcc tttgtgtcca acatttgagt caaaatttgc atgataaata taagaatgac 2760 acggttgcta ctttgtttta taatgcatcg agaacatatc gtgaatcaac gtttgttgaa 2820 gcgtggagac atcttctttc atttcctaat ggttcaggga aatatttaaa tgatgttgga 2880 atagcacgat ggtctcgtgt tcactgccca ggaagacggt ataacatgat gacaacaaat 2940 atagcggagt ccatgaattc tatactgaaa gaacctagag atttgcctat tgcttcattc 3000 cttgaaaatg ttcgagcttt gctacaaccg ttggttttgg gagcgtcgag aagaagcatt 3060 aaagtgacgt ctacattgac caaatgggca gagttagtta ttcaaaagaa acaagaagga 3120 gctttgacaa tgaaggtcaa cccaattgac tgttaccaat ttcatgtcaa agatttagat 3180 aaggaggagg tcgtaaacct tcagactaaa gaatgcactt gcaaggagtt tcaagctgag 3240 caactaccat gctcacatgc cattgctgca gcacgggttc gtaatataaa tgtttatagt 3300 ttatgtgcta attattacac taatgaatgt ttgttggctg catatgcgga ggccgtctac 3360 ccagttggga atcagtcaga ttggaagaca agcgaagact acgtacatat gactgtttta 3420 cctccaaaag tagtcaaaag agttggtcga ccgaagaaaa agaggattcc aagtgttggt 3480 gaagctccga aattgcataa gtgtggtcgg tgtaaacaaa taggtcacaa cagattaacg 3540 tgtaccaatc caatttcata taccgacaag tcgagcatac aagattagaa atttccctac 3600 caatgtacca agtattacac taattaatga atgtttgtta atgatgtgtt ttcttaatga 3660 tttgtcccaa cattcttact ttctgtgcgt ccaaatggat gaagaagacg aaaataacga 3720 ttgacttatt catttaagaa cacaaacact ggttttatga tcgtttaaaa ataactaaat 3780 gttcgtttaa aaatatgtaa acgatcgttt aaaaataact aaacgatcgg ttaagaacaa 3840 ccaaacgatc gtttgaaaac aactaaacga tagtttaaaa caaaactaaa cgatcggtga 3900 aacaaaacta aacgattggt caaacaaaac taaacgatcg tttaaaacaa ccaatcgata 3960 ccttgaaatt aactaaacga tcagttaaac aaaactaaac gattggtcga acaaaactaa 4020 acgatcgttt aaaacaacca atcgatcgtt tgaaattaac taaacgatcg actataaaaa 4080 actaaacgat cgtttacata aactaaacga tcttttgaaa caacgaaaga cacccgcgaa 4140 ttgtttacaa ccgcgattca acatttcaaa aaaagtatgc gaatttacaa tattgcccct 4200 ttggtaaaaa cgaccgatat atatatacgt tccgccttct cacttttcgt ttttcgtcac 4260 tacgcaatac acaaccgcac tgatcacacc ttcgttttct ctcagtccat tgttctctca 4320 gaccattttt gtctcagtcc atagttttcg tcaacgttaa aaggtatttt cccgaacttt 4380 tcctactata acgttacact tttcctttgt ttatatttca aacgtttcaa cttctgtctt 4440 caaaaactat cactgtgttc ttatattatt attgtgaagc gtttagggtt tcgggttcga 4500 cttctgtctt caatatatta tattcatttc aggatggctg tacctagcga aaagtatttc 4560 cctgccactg tgtcatgcca agtgcacaag attggcagtc ttattaagga taaactgacc 4620 aaggaccagc tgcaaatgtt cgaaaaaaca atttttggtc cattgctgaa tgtgaacatg 4680 gtattcaacg gccagttgat ccatcatttc ttgctgaggc agatacctga agacggtaac 4740 gcagatggaa tctgtttctc ggttttaggg aagaacgtcc gttttaccca aaaggaattc 4800 aacatcataa ctggattgtg gccaacaaac aatccattgg agaaagattg cgatagcaag 4860 cgactgcaaa gtcttctatt cggatcagaa aataagaaag taataacatg cttggaaatt 4920 gaggaaattt tcaagaattt tgagtttaca aatgatgacg atgctgtgaa ggtcgccttg 4980 gccgtcttta tagaaactgt gatggtcggg aaggataaga aaacacagtt tgacatggac 5040 attttgggaa gagttgatga tgaagaagca tttaaaagct tcgattggtc aactttcttc 5100 tacactcgtc tgctcaacag tttaaagaca agtctccaag gcaaaaaaga agcatacgag 5160 ctgaagaaga cacgaagttc caaagcagtg tcatactata acatcaaagg ctacgtcctt 5220 gcttttcagg tgatttttat ttcttcatac actttaagta aatgccaatt gaacatcaaa 5280 gtttaacata tttgtttaaa tgttgtaggt gtgggcttat gaagtactct caaccgcaaa 5340 tgagcacctg gccacaagaa acagtaaggg attaatccca aggatattga gatggaattg 5400 tacacaagct ccatcttaca aaatgctgca gaataacata ttcgacaaca aaaatgtaag 5460 taaaacctgt cagtcatcgt ttaatataat tacacaatcc aataatacaa ttacattgca 5520 gactgttgtt caacctaaac tcaagatgtc aacccaagag aaggctttca tggagagtcg 5580 aattcgaggg gatgataaca tgcaaatgga ggaggatgaa tccattggag caatgaacaa 5640 caaatcattg gagcaatcag actcatctcc acaaagagaa caactctcac cccaaaggga 5700 acaaagtcaa acagtggctg aggagtctga aatgcatcca atcaccaaga agaaacattt 5760 cagatcaaag aagtccaatg acaaagaaga acgaagtcat tcaaaatcct acaagaaact 5820 gaagaaggaa ataaagaagt tcgtaaggat ttatccacac tgacttctat agtctgtagg 5880 atggatgaca caatcacaaa gcagtcattg gagctgtatg aaatgaagca gatgctggag 5940 agattggtcc aggtaaaatt tgttttcatc atacattaga taaacgatcg tataactttg 6000 atagacgatc gtttatcaaa gttactcgat cgtttaactt cgatagacga tcgtttatca 6060 aagttacgcg atcgtttact tttatataca cgatggttta acaatacatt atttttttaa 6120 ttttatgttc gtttttattt gtttgttaga atcaaactga aaatcaaggg aatgatcata 6180 ctgatcagaa tgacaatgag tatgttgttc aagaacaaca tactcaacaa caacctactg 6240 aagaacaaca tactgaacgt caagaggaaa cccaaaggtt aacatttcat tcattgttta 6300 ctagtttata aatacctaac aattgtattt ttttttctta ttctcatgtt tcttctcatt 6360 ttgtttaggg aacatgaaga ggaacgtggt agtgatataa gcatagacgg tagggatgca 6420 gacttgctaa tgactataag agatatatcg gatagtctaa gtcatcaaat tcagaaagaa 6480 tcagacctgc cacagatgat tactaccctt ccatatgtga gccaacctct tgcactttgt 6540 gaattggctc caatggatca aactgtacaa attgtaaatg aagaatctca actggtatgt 6600 atacacaaca aatttgtagt cgtttgaatg aatagtttgt tacttgttta atacgattac 6660 attgcaggaa acaacaaaaa aacaggttga gatgaaaaaa aatgatgaag cagttacttt 6720 ggttgaaaaa gaaccagtaa ctgtgcctga taaagatgtg gaagaaaaac caataaagag 6780 aagaaagcta tgtaaaatag caaataaaga ggtgcaacat gaagatgaac aaggtaatcc 6840 acccacaaca tctgctcaga tcatatcagt atctacaaca cctgtcccag atgtggaaat 6900 cagagaagta gatccatata atccgatgtg gaaagtggat ccaaaattat ggaaggaata 6960 cttgcaatgg aaaaaatcaa gaaaaacaac ccatgaagaa aggaaagtag tctccacaac 7020 cagaaagaaa gactttttca gacagcttga agaaaacaca tgggtacatg gagacgtaag 7080 tactcttccc aaacgatcgc ttatatttga tatacgatcg cttctattaa ctaaacgatc 7140 gcttctatta aataaacgat cgttaagtta atattacacg atcgcttact acgtaaacga 7200 tcacatgtac atttcttatg cgatcgctta tcctctcctt tcattcatta aacgatcgtt 7260 tattttttct ttgtagacat tggatctgct attcgcccac ttgcagaata aaatgttgca 7320 tctcaagcac cattgcaagc gttcttttag aatattacat tcctcttttc tggtaagttg 7380 ttattcttta attttttttt ttgtatacaa gttaaactgc atcattatat tctgattaaa 7440 ttttgacttg ttcttgaaga ctggaatcaa taaaccagac tgcattgttt ggaaccacat 7500 ttttgatact catctggtga caccagataa taagaaagct gaatggacag acccaacagc 7560 acacctaagt atatggacag aaaaagatgt cgaatactat ttcaacactg ctgttggtga 7620 ttacaacgac ataccagggt ggggagatgt caactacgtg attacctgca tcaacataaa 7680 agaacactgg ttggctattg cagctgatat gagaaaatgc aggatctacg tgttcgactc 7740 aatgccaaat tatgttgagc agaaacttgt tgatgaagct cttcaaatgc ctgcacgatg 7800 cattgcctca ctcgcgattg caattggagt caacctccat tcagatcgtt tcacatatgg 7860 cccttggcca atacgcagat cgaaggccac attacagaaa gggcgttcat tggattgtgg 7920 aattttctgt accaaatttg ttgaatgcct tgtaactgct agtgaccttg gttgtctaac 7980 tgtgccaaac atgaaactgt ttagacaaca atatgtgctg gaactttggg ccaataaata 8040 cttttgttaa tatttgtatt cgtttatata atttttttat gtaattttta tagatagaat 8100 aacatattat aattttaaac tttgttataa aataaatact ttgtgatatt ttcaattaaa 8160 cgcgaccaaa attgagaaag aatatttgag ttaatatttg tattcgttta gatacatatc 8220 acaaaatatt cgtgtagaga aatactcatc gcgcacatat gtataaacga tcttcttaat 8280 aaacgatgtc taaacgatct tcttaataaa tgtcaaaata ttaagcgatc gtttagtaaa 8340 gtctaaacga tcgtttggta aagtctaaac gatcgttcgg taagtgtaaa cgatcttctt 8400 aataaacgat gtctaaacga tcttcttaat aaacgtcaaa atattaagcg atcgtttagt 8460 aaagtctaaa cgatcgtttg gtaaagtcta aacgatcgtt tggtacagtc taaacgatcg 8520 tttggtaaag tctaaacgat attcttaaaa tcataaaaaa attcagcgat cgtttagcta 8580 caagtagttt tgcaacatag agaataatcg atactactaa ttgaaatgca acatacacaa 8640 taatagaaca gccaattgat acttgtgatt tatgttaata tttcaataca taggagtgtt 8700 ggttggtcca tacttgaaat gctaattgtt ttctaaagta tgacatgttt tcttgacata 8760 atgtatctaa accaacacca gcagctatgt actcaaaata cttaattgcg aatacgccac 8820 aatcacaatt atttcgttga agtggaattg ggtcaacaat gacaactggc caaggttcct 8880 tgtatgtcga tgatctacct ctcctatcaa agaagccagt actatctaac aactttggca 8940 ccaactgtcg aatgggcagt aatatgtttg tcatctcttc ggcagttgta agtgacggaa 9000 gcgaatccca taccttcact tgacaactta ccaaatccaa gcataataga acccaatggt 9060 tgccatggac attgaatgga gagtaaacgt aatcaacact tgcccaagga tcttggaagt 9120 ccacttttga cccgacaaca tagtcaacca acctatactc ttcgtcccag tcaaacgggc 9180 gattctcttt aatacattct ttgtataggg gccacttcga aactaaaatg cgctgcaaag 9240 aaaaacatac aaacgcaaat atcagaccga aagacaaata tcaaacgcaa atacatacat 9300 aaagtaacga gacgattaca aaccataaag attgtgtccg cagttgtgaa gttctgagaa 9360 gaaggtatcc cggctgcctt aatcttcaag cgaatgaaaa gaaaaagtgc atccaaatgc 9420 taatacaaac aaaagtaagc agtaaatgta tagaaccata acaatgataa aattataatt 9480 gcataaatga taagataatc ccatacctca tccgacaacc accggcgaca cataaacaag 9540 tctctgaaaa aagccttcga ttttttccca tgaaaggttt cacgcagctc atcgtctgta 9600 cgcttgtctg taatccacgc tcgaagtcta tctaaatgga cgtcaagtat tttgtgcata 9660 ggatcataaa caattgcttc agactcagag gtgctggtgg ttgatgtcag agaccgttta 9720 ggtagagttg tgaatggggt tgataggtaa acacttgcac gcttcctacg ggcgggccga 9780 acgtgtggtc gttgagtgag aaatggttct atctctatga cgtcctcatc gtcaacgaca 9840 tctattggct cctctaaacc aatatcaacc ttcttctcca acacatcttc gtcaccctat 9900 ggaagctcat aatgcattag tgtatataat gatagaaatt aaacatcaat attagcatga 9960 acatggaacc aaaccttctt tttaacttca atgtgttcat cctccaagcc ttcggacacc 10020 ttgtggtccc cttcgtcacc ctatggaacc tcaaaatgaa ttagcgagaa catggttacc 10080 aaatatgaaa caactaacgt gaatacactt aacagtttca ttcctaacct ttctttgaag 10140 tccaatgtgc ttcaatatgg ttgacatcag gcccttcaat tcgtcaatat cggattttat 10200 agtattaagt tggccttcaa caaccgctac tcgatcttgg agatttcgaa tagccttttt 10260 catcttaatc ttggacttct gtttcttact ctttttcaac tcatcttcat cgttaacaac 10320 ttctcgtact ctttttgaac caccattctt cgactgaata atggtagatg agcggaagtt 10380 ttcaaaaagt tcacctgaag caattttcaa ttgctcctct tcaggtgtca tctcaatgac 10440 cgccttaact ataaactgca aatagaaaaa ggcaaatgta tttaggacaa agaaataagc 10500 acaaaatcac gcgatcctta agtaagttac tattgcttgc tacttaccat tggcgagtca 10560 aacacctggc ttatagtttg ggactttggt gattgttggc acacccacct cagcattcgt 10620 ggtatggcat gatcgtttac tttatctaca ccacatccaa tgatggttgg tatagactca 10680 tatgcccaaa cctattccac atttgacaaa caagtttaga aagtgccaca agatatatat 10740 agatatataa acaagtggtt atacaatcgt ttgaaaacaa ctatacgatc atttaacata 10800 actaaacgat cgttaaaaag aactaaacga tcgtttaaat aactaaacga tcgtttaaaa 10860 taactaaacg atcgtttaaa ataactaaac gatcgtttca aataactaaa cgatcttttt 10920 aaagttttga agtaagaagt aagaagtcaa atacctgtaa tgcatgcgga aatccattga 10980 tagtatattt ttttgtctgt gttgatttct tctttccctt ggcatattgc ttgtccaagg 11040 ctcttttcaa tgcacttagc gtgcgtacaa aaacaatccg accccaatca taattattaa 11100 atgaattcca atcatcagca atcttcaaaa aaccaatgtc cactttggtt cgcctatctt 11160 ttcccaacaa agatatctct ataaagtaga ctaaagctaa tttgacgata tcatcgtcat 11220 caccctcgta ttccaaaaat atatcttcta agtcgctaac gtaaacacag tccttgtctt 11280 tgaaaaactt ctccaacagt cgactgttcc cacccaactg aatatagtcc tctttaggac 11340 cccatagtcc agttacgatg ttaaactctc tcctaccgaa agtacaaaca acgcccccta 11400 gtaggaaact tatagaatcc tttccttcat cttccacctc ccttaacagt aagtagtgga 11460 tgagtggccc attgaagaca atatttaggt ccaaaaagtg cccaaacttt gttttcctaa 11520 ataaggctaa ttgatcgggt ttgagtttgg ccttaatatt atgtgttgtc ttttccaaat 11580 gagacaaaca gcttactagg gaataaaaat gatgggaagg attaatcttg tagaagggtc 11640 cgtcggtcga tgttgaagtc gatgtcatga ttcaagccaa gaaaaagcaa atatattgaa 11700 aatgggttac agataaaact cactgaaata agagaacacg ctcaaagttg attcttaggt 11760 tcgaaaagga gaagcgacga aatgcactgg aggaccgacg acagacgaac agtcggagta 11820 tcttcgaaga gcagagcggg aaatttgaaa agccaaagaa aggagatgtt tttttttttt 11880 ttacttcagg tgttctatgc gaaagagaag ggaaagcgaa cgtgggtagg cgaaacaatc 11940 aatagagagc gatagaaatt taatgaaggg catttttgtc tattcacacc caaattgtcc 12000 taaaagtctt tcttttgaaa acttgtccca aaattcattt aaatctcttt ttttaaccta 12060 tttttggcaa tttcccaa 12078 // ID HAT-N15_Mad repbase; DNA; EDCOT; 499 BP. XX AC . XX DT 04-NOV-2010 (Rel. 15.11, Created) DT 04-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-N15_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-499 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1902-1902 (2010). XX DR [2] (Consensus) XX CC TIR is 16-bp long. XX SQ Sequence 499 BP; 157 A; 100 C; 88 G; 153 T; 1 other; cagggccggc cctgaggggg tgcaagtggt gccaccgcac agggccccca aatcggaagg 60 gcccccgatt tttcaatttt gcatgcatwt acgtatatat agtagtatgt gtagaatatt 120 acaaacttga gtcttagcgc aagtggtatt attgcttctt tacatcggcc taggggatgg 180 gttcgaaact catctccatc attttttcag tttatatttt tattaaatgc ataagcttcc 240 acaaaataat ataaaaattc cacacaataa catgaaaatt cgaaccctga ccctctaaat 300 agttaaggaa aaacaatacg ccacctttcc acttgttgat ttgttaaatt tgtttgtgct 360 attagaattt atagaagctc aattgaaaac taaaattatt tttttgaaca aaaaaataaa 420 aaaaataaaa ttcttagtac tttttagggc ctccaattca ctttcgcaca gggcccctga 480 aatctcaggg ccggctctg 499 // ID HT1_MT repbase; DNA; EDCOT; 760 BP. XX AC . XX DT 15-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon, from Medicago DE truncatula. XX KW DNA transposon; Transposable Element; Nonautonomous; KW Inverted repeat; TSD; Interspersed element; HT1_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-760 RA Shankar R. and Jurka J.; RT "HT1_MT: A putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 570-570 (2006). XX DR [1] (Consensus) XX CC This sequence has target site duplication of 4 bp (TAAA). CC Sequence is self-complementary. XX SQ Sequence 760 BP; 273 A; 97 C; 112 G; 278 T; 0 other; gagtaaatta cactcccctc ccctcaaaga tgcttgaatt acactcccct cccctcttat 60 gttaaaatat acactcccct cccttgaaaa gtaaaattta tactcccctc ccctataaga 120 tgcttgaatt acaaccccct cccttaataa ttaaatatgg actacacttt aatctatttt 180 aacataaata aatattttta taatatatat taattttgaa tcaccattta aaaaatataa 240 attcgtttct ttataatcta aatgtcaatg acaattaaat ttaaatattt tgttattaat 300 tttataattt agagtataaa attcactttt aaataaccat acttaatcga ctttagtaat 360 ttttcacata ttttaatttt attttgggtt gtttcatatt ttataatagg gtttaaaact 420 atatgttaat gaaattgtga ataaaaaata gagaaagata tgtattcaaa atttgattat 480 attaaaatga acccgcaatg ctatttttct ttgaagtgtg ttagattatt tttttgctag 540 attattagaa ataaaaaaaa aaaaaaatta ttgagggact aaagtgtaga ttttaactta 600 agaggggagg ggaatgtaat tcaagcttct ctcaagggag gggagtgaaa tattttctaa 660 tatgttttga ataagagggg aggggagtgt atattttaac ataagagggg aggggagtgt 720 aattcaagca tctttgaggg gaggggagtg taatttactc 760 // ID VIHAT3-N1_VV repbase; DNA; EDCOT; 845 BP. XX AC . XX DT 05-FEB-2009 (Rel. 14.03, Created) DT 05-FEB-2009 (Rel. 14.03, Last updated, Version 1) XX DE VIHAT3-N1_VV, non-autonomous DNA transposon - a consensus DE sequence. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; TIR; KW MITE; mHatvine-3.1; VIHAT3-N1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-845 RA Benjak A., Boue S., Forneck A. and Casacuberta J.M.; RT "Recent amplification and impact of MITEs on the genome of RT grapevine (Vitis vinifera L.). submitted."; RL Repbase Reports 9(3), 713-713 (2009). XX DR [1] (Consensus) XX CC VIHAT3-N1_VV (mHatvine-3.1 in [1]) is a non-autonomous DNA CC transposon which is a deletion derivate of the autonomous VIHAT3. CC Individual copies are >90% identical to the consensus sequence. CC TIRs are 16 bp-long (with 2 conserved mismatches) and flanked by CC 8 bp-long TSDs. There are approximately 30 highly conserved CC copies present in the genome which could place this family in the CC group of MITEs. XX SQ Sequence 845 BP; 200 A; 202 C; 189 G; 241 T; 13 other; catagttgtg aaaggcgcgc ctaggctccg gggcggcgcg acgccaccct ccggcgcctc 60 gcctgaaggc aggcgacgcc ccttcacgaa ggcgccgctt aggcgcgcaa ggcgctcgcc 120 tccggcaagg cgcgasgcgg tcgcctgast cgcctccgrc ggtccgacca ggtacgccct 180 cctccttctc cttctcctct cttctcttct tcttcttctt cttcttcttc ttccgagatg 240 gcgggagcca gagaagccct aatttttttt tttattttgt gggtccaaaa cgacgtcgtt 300 ttggcccttt ttaatttaaa aggaaagaca ggccaaaacg acgtcgtttt ggascctgtt 360 cctttaaaaa aaaaaacagg ccaaaacgac gccgttttgg ccctgtyytc chttccarcc 420 cccttttctg gtctttytca acccgasacc actcccaatt cdtgccctag cctcadccgt 480 gcagtggaga agtgaagaag aagaagaaga agaagaagaa aaataggggr aaaataggag 540 aaaaatagag gaaaaatagt cacgtacctt ccaattagca atatggattt ggatttgttt 600 ttatgcttgg agttctttat ttttatgttt tttgttgatt aaattgaagt tttggatgat 660 atttgatgat ttatgtgttt aggacaaata aatgattgtt aaatttgatt atattatata 720 aaaatatata tgtaaattag ggtgcgcctc acttcactaa agcccgcgcc ttaggtgcgc 780 cttgcgcctc aggctccagg actactttgc gccttggtgc gccttgtgag ccttttaaaa 840 ctatg 845 // ID Copia-86_Mad-I repbase; DNA; EDCOT; 4454 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-86_Mad_; KW Copia-86_Mad-LTR; Copia-86_Mad-I. XX NM Copia-86_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4454 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1710-1710 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1681-2199] - Integrase core CC 'ATAA' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 79..4410 FT /product="Copia-86_Mad-I_1p" FT /translation="MASHSKWENPNHPLYLHHSDQPGAILVPQPLVEDNYN FT TWVQSMSMALTVKNKLGFVDGTINKPSEDNFEELQQWNRCNNLVKTWLLGS FT MSKEISGSVINYKDARQMWTDLQERFSHVNIVQLFHVENEIHDCVQSNMSV FT SSYFTKLKSLWDERDTLCSIPACSCGTKNEMNSYVETQKTMKFLMGLNESY FT ATVRSNTLLLEPLPTVNKAYALVLRHERQAEVSNGKSTQLETAVFAVKNPS FT REPTPEDKEMRCGKCNKTNHITKNCRAHLKCTFCGWKGHTFDFCRKRKAAA FT ETESNRLFSSKGNQVSQSNKQETVPNFPFSQEDCKQILQMLNKNKSSFANQ FT VSNPPSHEELSGKAFSFSCKGTKSIWILDSGATDHIVCSPSLLTHSRAVEN FT HTVELPNGSVAKVTHVGQVVFSHNLILENVLCVPFFRLNLISISKLAYDSL FT YVTIFFTQFCVIQDLRSGKMIGTGTERDGLYYLDPSKKGTCNNIQTVSPKL FT WHQRLGHPSHKATSLLPLFNNKACDLEKCLICPLAKQTRSPFPLSSISTKS FT CFELLHIDIWGGYQVASISGAKYFLTIVDDYTRSTWVYLMKHKSDTKDILV FT GFIQMIETQFNTRVQIIRSDNGPEFKLEQFYALKGIIHQSSCVNTPQQNGV FT AERKHRHLLNVARALLFQACLPKRFWGDAILTSAYLINRTPTPLLQGKTPY FT EKLFHKAPNYSHLKVFGSLCFASTHAQRPSKFDPRAIQCIFLGYPYGQKGY FT KLFDIKHNKTFVSRDVVFFEDHFPFQNRTTSAAPSPSNITPSPITFDLTSP FT IESHSSLAPEEINITSPTLADITPLSSPLPTTTPPPDTLSTPSHTLHSSPP FT PTTPSPDQPPPLRRSTRPTKTSTFLQDFHVEVALPSRVAPTSSTSMVQSSG FT TSHPISRYLSYDHVSPTHKTFLTTLTIIKEPTSFSQAVQDPKWRDAMQKEI FT VALHDNRTWTLVPLPPHKHPIGCKWIYKVKLKPDGSVERYKARLVAKGYSQ FT IEGLDYRETFAPVAKLTTVRVLLSIASIRGWHLHQLDVNNAFLHGDLYEEV FT YMSLPPGFGRKGETRVCKLHKSIYGLKQASRQWFIKLSSALKTAGFHQSWS FT DYSLFVRNRQGSFMALLVYVDDVILAGNNLREIEETKLFLSQHFKLKDLGK FT LKYFLGIEVARSKQGIALCQRKYALEILEDAGFLGAKPSRLPMEPNLSLTQ FT TDGTLLHDPSSYRRLVGRLIYLTITRPDLTYVVNMLSQFMDKPRQPHLEAV FT HKVLRYIKQSPGQGILLPSTGSLQLQAFCDADWARCKDTRRSITGYCIFLG FT QAPISWKTKKQSTISRSSAEAEYRSMATTCCEVIWLRNILKDLQVNHAQPV FT TMFCDNQAAMHIASNPVFHERTKHIEIDCHLVREKIQTGMVQTAYIRTSNQ FT PADLFTKPLSSAQFEVLISKLGVIDIHTPT" XX SQ Sequence 4454 BP; 1309 A; 1078 C; 858 G; 1209 T; 0 other; atatggtatc agagctgtga tctgggaaaa accacaaaac acagctctaa agcagccacg 60 aggtcaacca ttctaggcat ggcctctcat tcaaaatggg aaaatcccaa ccacccgctc 120 tatctccacc actcggatca acctggtgca atcctcgtac cacaaccatt ggtggaagac 180 aactacaaca catgggttca atccatgagt atggccttaa cggtcaagaa caaacttggt 240 tttgttgatg ggacgatcaa caaaccaagt gaggataatt ttgaggagct gcagcaatgg 300 aatcgctgca acaacttggt caagacatgg ctactaggct ccatgtcaaa ggagatttca 360 gggagtgtca tcaactacaa ggatgctcga caaatgtgga ccgatctgca ggagaggttc 420 tcacatgtga atatagttca gctgttccat gttgagaacg agatccatga ttgcgtccaa 480 agcaatatga gtgtaagttc ttacttcact aaacttaaaa gtttatggga tgaacgtgat 540 actttgtgtt ccattccagc atgcagttgt ggaacaaaga atgagatgaa ctcatatgtt 600 gaaactcaga aaaccatgaa gttccttatg ggactgaacg aatcgtatgc tacggttcga 660 agcaatactc ttcttctcga accactgcct acggtgaaca aggcatatgc gttggtcctt 720 cgacatgaac gccaggcaga ggtttccaat gggaaaagca cacaactaga aactgctgtc 780 tttgcagtga agaatccgtc gcgagaacct acacctgaag acaaggagat gcgatgtgga 840 aagtgcaata aaaccaatca catcaccaaa aattgtcgtg cacatctcaa gtgcactttt 900 tgcggatgga aaggccacac cttcgatttc tgtcgaaaac ggaaagcagc cgcagagacc 960 gaatccaatc gtctcttttc ttcaaagggg aatcaagttt cacaaagtaa caagcaagag 1020 acggtgccta atttcccgtt ctctcaggag gactgcaagc aaatccttca gatgttgaac 1080 aagaacaaat catcatttgc caatcaagtc agtaatcctc ctagtcatga agaactttca 1140 ggtaaagcct tctctttttc atgtaaagga accaaaagta tttggatcct ggacagtggt 1200 gccacggatc acatagtttg cagtcctagt ctccttacac actcacgagc tgttgaaaat 1260 catacagttg aactgccaaa tggttccgtt gccaaagtca ctcacgttgg acaagttgtt 1320 ttctctcata atcttatcct tgaaaatgtc ctatgtgtgc cgttctttag gttgaattta 1380 atatctatca gtaaactagc ctatgattcc ttatatgtca ccattttctt cacccaattt 1440 tgtgtcattc aggaccttcg ctcggggaag atgattggga cgggaactga aagggatgga 1500 ctttactacc tcgacccatc aaagaaagga acatgcaaca atattcaaac cgtctcacca 1560 aagctttggc accaacgcct aggacaccca tctcataaag ccacttcgtt attaccttta 1620 tttaacaata aggcttgcga tttggaaaaa tgtttaattt gcccattggc caaacaaaca 1680 agatcgccct ttcctttgag ctctatttct accaaatcat gttttgaatt attgcatatt 1740 gatatttggg gtggttatca agttgcttct atttcaggtg ccaagtattt ccttaccatc 1800 gtagatgact acactagaag cacttgggtt tatttgatga aacataaatc tgacacaaaa 1860 gacattttag tcggattcat tcaaatgatt gagactcaat tcaataccag agttcaaatc 1920 atacgaagtg acaatggccc tgagtttaag cttgagcaat tttatgctct caaaggcatc 1980 atacatcaat ctagttgtgt caacacacca caacaaaatg gtgttgccga acgtaaacac 2040 cggcatttgc tcaatgttgc tcgggctttg ctctttcaag cttgtttgcc aaaacgtttt 2100 tggggggatg caatcttaac ctcagcctac ctcatcaata gaacacccac tccacttctc 2160 caaggtaaaa caccttacga aaaactgttt cacaaagcac ctaactattc ccatttaaag 2220 gttttcggta gtttatgttt tgcttctaca cacgcccaaa ggccctctaa attcgacccc 2280 cgtgcaatcc aatgcatttt tcttgggtat ccttatggtc aaaagggtta taaattgttt 2340 gatataaaac acaataagac ttttgtttct agggatgttg ttttttttga agatcatttt 2400 ccattccaaa atcgtaccac ttccgctgcc ccgtctccat caaacattac accctcaccc 2460 atcacgtttg acttgacctc tcccattgag tcgcactcaa gccttgcacc cgaagaaata 2520 aacatcacct ctcccacact tgccgacatc acaccactct catctccttt acctactaca 2580 actccaccac cagatacctt atcaacacct tcacataccc tacactcttc accacctcca 2640 accactccat caccagacca accacctcca ctccgtcgta gcactcgacc gaccaaaact 2700 tccacatttt tgcaggactt tcatgttgag gtggccctcc cttcccgtgt tgctcccaca 2760 tcttccacaa gcatggtcca gtcatcaggt acatctcacc ccatatctcg ttatttatct 2820 tatgaccatg tatcccccac tcacaaaacc tttctcacca ccctcaccat tatcaaagaa 2880 cccaccagtt tttcgcaggc tgttcaggat ccaaaatggc gtgacgccat gcaaaaagag 2940 attgttgccc ttcatgacaa tcgcacttgg actcttgtgc ccttaccacc tcacaaacat 3000 cccatcggtt gcaaatggat ctataaggtg aagcttaaac ctgacggcag tgttgaacgc 3060 tacaaagctc gtctcgttgc taaaggctac agtcaaattg aggggcttga ttatcgggaa 3120 acttttgctc cagttgccaa gctcaccacc gtccgcgtcc tcctgagtat tgcctccata 3180 cgaggctggc atcttcatca acttgatgtg aacaacgcat ttttgcatgg tgacttatac 3240 gaggaggttt atatgtccct gcctcctggg ttcggacgaa agggggagac acgagtatgc 3300 aaattacaca aatccattta tggtttaaaa caggcctcga gacaatggtt tatcaagctg 3360 tctagtgctc tcaagactgc tggttttcat caatcatggt cagattactc attgttcgtc 3420 cgaaaccgtc aaggcagttt catggcatta cttgtgtatg ttgatgacgt gatacttgca 3480 ggtaacaatt tgagagaaat tgaagagact aaactcttcc tttcccaaca ttttaaacta 3540 aaggatttgg gaaaactcaa atactttttg gggatagaag ttgcaagatc taaacaaggg 3600 attgccttgt gccaacgcaa atatgcgttg gagatactag aagatgctgg gttccttggt 3660 gcgaagccct cacgattacc aatggaacca aacctgtccc ttacacaaac tgatgggacg 3720 ctcctacatg atccttcttc atacaggcga ctcgtaggga ggctgattta cttaaccatc 3780 acgcggcctg acctgactta tgtggttaat atgttgagcc aattcatgga caagccacga 3840 caaccacacc ttgaagcggt gcataaggtt ctcaggtaca tcaaacaatc tcctggacag 3900 ggaattcttt tgccttctac aggttcacta caattacaag ccttttgtga tgctgattgg 3960 gctcggtgta aagacactag aaggtcaata accggttatt gtatcttcct tggacaagca 4020 ccgatatctt ggaaaacgaa gaaacaaagc acaatatctc gttctagtgc agaggcagaa 4080 taccgttcta tggctactac ttgttgtgaa gttatatggc taagaaacat tttgaaggac 4140 ttgcaagtaa atcatgcaca accagtcaca atgttttgtg ataatcaagc tgccatgcac 4200 attgcttcga acccagtgtt tcatgaacga acgaagcata tagagataga ctgtcaccta 4260 gtacgtgaga agattcaaac gggaatggtg caaacagctt acatacggac ctcgaatcaa 4320 cctgcagact tgttcaccaa accactaagc tcggcacaat ttgaggtctt aattagcaag 4380 ttgggtgtca tcgacattca cactccaact tgagggggag tgttaaaatg catgaaataa 4440 acatgttgga ataa 4454 // ID Copia-64_VV-LTR repbase; DNA; EDCOT; 524 BP. XX AC chr15; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-64_VV_; KW Copia-64_VV-I; Copia-64_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-524 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr15; Positions 13486282 13485759. XX SQ Sequence 524 BP; 153 A; 78 C; 133 G; 160 T; 0 other; tgtagagatt gccaactatc aagtgacaag tggcaaggct gttgactaag caaataacag 60 atgggagcat ttgttagtta gttagaggct tgtgattgat ataaaagggt gcagtctcgg 120 gagaaacaga gtggaggcat tcagttgtat agaacagaga gcaagaaaca gagagcaaga 180 aacagaaaag agagctttgc aaatccataa ccataggtct gtttaggtta tcttgagata 240 gagagaaaca gaggtgagga gggttcttgg gaaaagcttg taatttcttt gttttgattc 300 ttgtgtaatc tctggttagc acacttgaat aaaggcttca ggaaatcagt gtggatgtag 360 atcaagttga tcgaaccacg ataagtctct tgtgttcttg accttggttg attgcgtacc 420 agctgtttga ttttagtcct aagagaagtt cttgcaaact ggttgttttt ccttttagtt 480 tctgctctaa cagtccctag ttcaaggctg gttcttcttc aaca 524 // ID COPIA2-I_LC repbase; DNA; EDCOT; 10324 BP. XX AC . XX DT 24-MAR-2005 (Rel. 10.02, Created) DT 15-APR-2011 (Rel. 16.04, Last updated, Version 3) XX DE L. corniculatus copia-like LTR retrotransposon - internal DE consensus sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; integrase; KW gag-pol; copia-like retrotransposon; 5 bp TSDs; COPIA2-I_LC. XX NM COPIA2-I_LC. XX OS Lotus corniculatus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RP 1-10324 RA Gentles A. and Jurka J.; RT "COPIA2_LC: L. corniculatus copia-type LTR retrotransposon."; RL Repbase Reports 5(2), 33-33 (2005). XX RN [2] RP 1-10324 RA Toth G.; RT "Copia-type LTR retrotransposon from rice."; RL Direct Submission to Repbase Update (09-JUN-2005). XX DR [1] (Consensus) XX SQ Sequence 10324 BP; 3055 A; 2199 C; 2147 G; 2880 T; 43 other; attggtatca gagcgcaagt tctgattacc acacctaaca gtgttcagtg atccgggccg 60 gtgtgaaaaa caatggctgc caccaccagt gaaactcaaa gagatggtta caatgcaaag 120 cctcctatgt tcgacggtca aaggttcgaa tattggaaag atagactgga aagtttcttt 180 ctgggtttcg atgcagatct ctgggatatt attgtggatg gctatgagcg tccagttgat 240 gcagatggca agaagatccc aaggtcagag atgactgcag atcaaaagaa gctgtactca 300 caacatcaca aagcaagagc aattcttcta agtgctattt cctatgaaga gtaccagaag 360 attacagatc gtgagtttgc taaaggcatt tttgaatctc tgaagatgtc tcatgaagga 420 aacaagaaag tcaaagaatc aaaggcattg tctttgatcc aaaagtatga atccttcatc 480 atggagccaa atgagtccat tgaagaaatg ttctccagat ttcagttgct tgtagctggc 540 atacgacctc tcaacaagag ctacacaaca aaagatcatg tcataagggt catcaggtgt 600 cttcctgaaa gttggatgcc tttggtgact tcaatagagc tcacgagaga cgttgagaat 660 atgagtttag aagaactcat cagcattttg aaatgccatg agctgaagcg ctcagagatg 720 caagatctga ggaaaaagtc catagccttg aaatccaaat ctgaaaaggc taaggttgag 780 aagtcaaagg ctcttcaagc tgaagaagaa gaatctgaag aagcatcaga agattctgat 840 gaagatgagc tgactctgat ctccaagaga ctcaaccgca tctggaagca caggcagagc 900 aagtwcaaag gctctggaaa ggcaaaagga aagtctgaat cctcaggyca gaagaagtct 960 tcaatcaagg aagtcacatg ttttgagtgc aaagaatcag ggcactacaa aagtgattgt 1020 ccaaagttga agaaggacaa gaagccaaag aagcacttca agacgaagaa gagtctgatg 1080 gtgacatttg atgaatcaga gtcagaggat gttgactctg atggtgaagt ccaaggactc 1140 atggcaattg tcaaagacaa agaagcagag tcaaaggaag ctgttgactc tgactcagaa 1200 tcagaaggag atcctaactc agacgatgaa aatgaggtat tcgcttcttt ctctacctct 1260 gaactgaaac atgctttgtc tgatatcatg gataagtata actctttatt gtctaagcat 1320 aaraagytga aaaagaactt atctgctgtt tccaagactc cttctgaaca tgagaaaatt 1380 atttctgatt tgaaaaatga taatcatgct ttggtcaatt ctaactctgt gcttaagaac 1440 cagattgcta agttagaaga aattgttgcc tgtgatgcct ctgattgtag aaatgaatct 1500 aagtatgaaa agtcttttca aagattccta gctaaaagcg tggatagaag cttaatggct 1560 tcaatgatct atggcgtaag cagaaatgga atgcatggca ttggctattc taaaccaatt 1620 agaaatgagc cttctgtgtc taaagctaaa tccttgtatg aatgctttgt tccctctggt 1680 accatattgc ctgatcctgt acctgctaaa gttgctaaaa accctcttaa aaagggatct 1740 ttctctatga ctaaatatca tgcaaatatt cctttaaaat atcatgttga gacacccaag 1800 gtgatcagaa cctctggggt aactaacaag agaggaccca gaaagtgggt acctaaggac 1860 aagattatct atgttgcaga tatccttgat agctccactg aaacaccaat catggtatct 1920 ggacagtgga tgctcgcgtc acatgacggg agaaaggcgt atgttccgag agctgaaact 1980 taagcctgga ggcgaagttg gctttggagg aaatgaaaag ggtaaaattg ttggtactgg 2040 tactatttgt gtagatagta gtccatgcat tgataatgtt ttattggtag acggcttaac 2100 acataactta ttgtctataa gtcaattagc tgacaagggt tatgatgtta tattcaatca 2160 aaagtcctgc cgggctgtaa gtcagatcga tggctctgtt ctgtttaaca gcaagaggaa 2220 gaacaacatt tataagatca gattatctga gttggaggct cagaatgtga agtgccttct 2280 gtctgttaat gaagagcagt gggtatggca tagacggtta gggcatgcca gtatgagaaa 2340 gatttctcag ctgagcaagc taaaccttgt caggggctta cccaatctga agttcgcttc 2400 agacgctctt tgtgaagcat gtcagaaagg caaattcaca aaagtccctt tcaaggcaaa 2460 gaatgttgtc tcaacctcaa ggccgttrga acttctgcat atcgaccttt ttggaccagt 2520 gaaaactgag tctataggtg gcaagagata tgggatggtt atcgttgatg actatagccg 2580 ctggacatgg gtaaagtttc taacccgcaa ggatgagtct catgctgtgt tctctacctt 2640 cattgctcaa gtgcaaaacg agaaggcttg taggattgtg cgtgtcagaa gtgaccatgg 2700 tggagagttt gagaatgaca agtttgagag tctgtttgat tcctatggaa ttgcacatga 2760 tttctcttgt cccagaactc ctcaacaaaa tggtgttgtt gagaggaaga acagaactct 2820 tcaggagatg gctagaacca tgctccaaga aactggcatg gctaagcact tttgggcaga 2880 ggcagtaaat acagcatgtt acattcagaa cagaatctct gtgagaccaa ttctgaataa 2940 gactccttat gaattgtgga agaacataaa acccaacatt tcttattttc atccttttgg 3000 ctgtgtttgt tatgttctca atactaagga tagattgcat aaatttgatg ctaagtcttc 3060 taagtgtcta ttacttggtt attctgatag atctaaaggt tttagatttt ataatactga 3120 tgctaagact attgaagaat ctattcatgt tagatttgac gataagcttg actctgacca 3180 gtcaaagcta gttgaaaagt ttgcagattt aagcattaat gtttctgaca aaggcaaagc 3240 tccagaggaa gttgagccag aggaagatga accagaggaa gaagctggtc cctctaactc 3300 acaaactctg aagaagagca gaatcactgc agctcaccct aaggaattga ttctgggcaa 3360 caaagatgaa ccagtcagaa ccagatctgc cttcagaccc tctgaagaga ccttgctcag 3420 tctgaaagga ttggtgtcct taattgaacc caagtccata gatgaagctc ttcaggacaa 3480 ggattggatt ctggccatgg aagaagaatt gaatcaattc tccaagaacg atgtttggag 3540 cttagtgaag aagcctgaga gtgtccatgt tattggaacg aaatgggtat tcagaaacaa 3600 gctgaatgag aaaggagatg tagtcagaaa caaggcaagg ctagttgctc aaggctacag 3660 ccagcaggaa ggaatagact acactgaaac atttgctcca gtagcaagac tggaggcaat 3720 cagactgttg atctccttct cagtaaatca caacatagtt ctacatcaga tggacgtaaa 3780 gagtgccttc ctaaatggtt atatctcaga ggaagtctat gttcatcaac ccccaggttt 3840 tgaagatgaa aagaaaccag accatgtgtt caaattgaag aaatcactct acggtctgaa 3900 gcaagctccc agagcatggt atgagagact tagctcattc cttctggaga atgagtttgt 3960 aaggggtaaa gtagatacaa ctcttttttg caagacttat aaagatgata tcttaattgt 4020 gcaaatttat gttgatgata ttatatttgg ttctgctaat caatctctat gcaaagaatt 4080 ttctgagatg atgcaggctg aatttgagat gagtatgatg ggagaattaa agtactttct 4140 gggaatacaa gttgatcaaa caccagaagg aacatatatc catcagagca agtacactaa 4200 agaacttctg aagaagttca atatgctgga atctacagtg gccaagactc caatgcatcc 4260 tacatgcatt ctggagaaag aagataaaag tggtaaagta tgtcagaagc tctatcgtgg 4320 matgataggt tcacttctat acttaactgc atctaggcca gacatattat ttagtgttca 4380 tttatgtgct cgtttccaat cagatccaag ggaaacccac ttaactgctg ttaagaggat 4440 cctaaggtat ctgaaaggca ccactaacct tggcttgatg tataagaaaa catcagagta 4500 taagctttca ggttattgtg atgctgatta tgctggagat agaacagaga gaaaaagtac 4560 ttctggaaat tgtcaatttc tgggaagcaa tctagtctca tgggcaagca agaggcaatc 4620 aaccattgca ctatcaactg cagaggcaga atatatctca gcagcaatat gcagcactca 4680 gatgctctgg atgaaacatc agctggagga ttatcagatc cttgagagca atatcccaat 4740 ctattgtgat aacactgctg caatctcatt gagtaagaat cctatcttgc attcaagggc 4800 aaagcacatt gaggtaaagt atcactttat tagagattat gtacagaagg gcgtacttct 4860 tctgaagttt gttgatactg accatcaatg ggcagatatc tttacaaagc ccttagcaga 4920 ggatagattt aattttattc tgaaaaatct raacatggac ttttgtccag agtgaagatg 4980 gatcagaacc tctgactatg atacttcttg atcagaagat gtctagtcca gaaggtaact 5040 caatcagagt gtgtgtaccc actggtactg actctgaagc tgagacarca acacgtgtgt 5100 cagtatttct gatgcatagt tccttgtgcc cgtgtgacag tctgttatga ttgcgtgtag 5160 atrtgcttct ctcctgtgtg tgattgtgta ttttactgtt actatctatc tttaattttc 5220 aaccgttgat cttaaagtgc tttttgaatc aacaacggtt atttgataaa acccactata 5280 cacacacgtt ctcsttcact tccggttttc actctcgctc tctctgcttt tcaaaaccgc 5340 ttaccctcga tttctctctc gatctctctt catctttcaa acttcatctt ctacctcaaa 5400 ccttcaacct cttcaaaatg gtgagacaaa ccagaagatc tactgcagat gcacctcagt 5460 tccctcacat ggtagttggt ctagcaacgg gtcaaagggg ccctgagaat ccggcacaag 5520 aacaagttca agctcaagag cagattgttc cwattgcaga acggggctgt gccgttcact 5580 gcgtatatgc tcctgaggaa ctccaagtcc tggcagaatg gagattcgac ctcgacaacc 5640 tggctgcaaa tgggtatgat cttcgtcctg aagtccaagc tcaaggttgg ggaaattact 5700 tcaacagact tcgaggaccg gtgtatgaga aaytggtcaa ggaattctgg aagcacgccg 5760 actgcgatga tactcaggtg gtatctcaca ttcttggcag gaagatcatc atcactgaga 5820 agtcattcgt gaatctgctg ggtgcagaaa ctgcttatgg gtatcgtttc caactsacgg 5880 aatcgaagct gaaacccagc accaaggaca aaaycaacaa ggccctgtac accacctwca 5940 aaccgggcaa gacgarttac aaggtgatgg aycttcatcc caagctcagg atctggcaca 6000 agatcctgct caactgcatc aaycagagac craagggcag ttccccagac tacatcaact 6060 tcaaccagaa ggcgatgctg ttcttcatcc aagaymagaa gaagatctgc cttccctact 6120 tcctgttctc ctacttgaag gaatgyatcc ggaagtctcg caccactgcc tccatcaagt 6180 ctgcaatcaa gtatatccct tttgggagac tgctstcaga tctcttcatt gagagtaacc 6240 tcgtkcaaga tctgatcaat gctggttgca cagaggatyt gagcacaatt gtcagtgatg 6300 tcttcactgc aaactctctg aagaagatgg gcttagtcca gaagaagatt gctcctgctc 6360 atgaagacac atcttctgag atcagaggaa gaaggatgcc tctgaatgac taccctctgt 6420 ggactcaagc agacaatcct gaagccatca gatgctatgt tgaagacctc agggctcaag 6480 gattcgagat tgatcttgat gatttcttca gcagactgcc gccagctcca gagtttcctt 6540 ctcctcccaa gaagaaagct cagaggaaga tggttctgga agaatcctct gaggaatctg 6600 atgtccctct ggtcaagaag aagaagctgc aaagagaaag catgatgaca gcaagcctga 6660 tgatgatgat ggtgataatg aggatggtcc tccwaagaag aagaagaagm aggtcagaat 6720 cgtggtgaag cctactcggg tggaaccagc tgctgcagtg gtcagaagga ctgaacctcc 6780 tgccagagtg actcgatcat cagcacattc aagtaagcct gcacttgctt ctgatgatga 6840 tttgaattta tttgatgcac tccccatttc tgccttgctc maacactcct caaatcccct 6900 cactcctatt cctgaatccc aaccagcygc acaaaccacc tctccaccac attccccaag 6960 gtcttccttc tttcaacctt ctcctactga agcacctctc tggaatttgc ttcagaacca 7020 accctctagg tcagaagatc caacctctcy cattaccatt ccatacracc cattatcttc 7080 tgaacccatc atccatgaac aaccagagcc caaccaaaca gaaccwcaac ccagaacgtc 7140 tgatcactct gttcccagag catcagaacg tcctgctgcc agaaccacgg atacagactc 7200 ttcaacagcc tttacacctg tatccttccc aaccaatgtt gctgactctt ctccctccaa 7260 taactctgaa tccattagaa aattcatgga ggttagaaaa gaaaaggtgt ctgccttaga 7320 agagtattac cttacctgtc caagccctag gagatatcct ggccctagac ctgaacgtct 7380 agttgaccca gatgaaccta tcttggccaa tcctttmcaa gaggcagacc ctttagctca 7440 acaagctcac cctgtccctg accaacaaga gcctattcaa ccagaccctg aaccagaaca 7500 atcagtgtct aaccaatcct cggttagatc acctcatcct ctggttgaaa cttcagamcc 7560 tcaccttgga acctctgaac ccaatgctca aatgwttaac attggttctc cacaaggtgc 7620 ctctgaagct catagcagca atcacccagc ctctcctgaa accaacctct ccataattcc 7680 ctayactcac ctccaaccca catctctctc tgagtgcatc aatattttct atcatgaagc 7740 ctccttgagg ctccgcaatg tgcacggtca gactgacctc agtgagaatg ctgaacatgt 7800 ggctgatgag tggaacaatc tgagcacttg gctagtggct caagttccaa ttatgatgca 7860 gctcctgcat gcagagggaa gtcagaggat tgaggctgca aagcaaaggt ttgctagaag 7920 ggtggctctt catgaacaag aacagagaaa taagcttctt gaagctattg aagaagccaa 7980 gagaaagaaa gaacaagcag aagaagctgc acgtcaagca gcagctcaag ctgaacaagc 8040 cagayttgag gcagagcgac ttgaagctga ggctgaagct tagagcactt gcaccagttg 8100 tgtttactcc tgctgcttct gcttccattc cagatcctca agctgctcag aatgttcctt 8160 ccagttctac tcagacaagc tcatccagac tcgacatcat ggaacaacgt cttgacactc 8220 atgaatccat gctgattgag atgaagcaaa tgatgatgga acttctgcgt cgcactgaca 8280 aaccttagtt ttaggatctc ttckttttct ttctttttct ttaactttgt tttatttttg 8340 ttaaactctg tttctttttt atttatttat tttactttgt tcgtttgtga ttatatatgc 8400 atatctatat atttatgtca catatgtttg caaaactttt tttattcata attgttttat 8460 gtttacatca tacatttctt tacatcataa aatctagaat ggaggatccc tcctcattct 8520 tctgcactcc tggcgctgct ctgacctatc cttctccaga cgctccagtg catgctggat 8580 gttgttgagt ctgaccttta gctcatccct ctccagaatc tcttctgaag tcttgagctt 8640 ctcttccaar ctctcttttt cttccagcag cttgagttca agccggctga gttcttgcac 8700 ctcctccacg aaggcaagaa attccttcag gtctctctcc aactctggac gcaggtcctc 8760 ttccagcagt gtccgtgtca gctccgcgat ggtcgttgta ccctctggat gcctgatgtt 8820 caggaacaag tcctcctcaa aggccttctt cctcagctct tctagtgcta cgatgtatga 8880 tgccattttt ttttactgaa aattgttcga ggtgtgaagc ttacctttct ctccaacgct 8940 ttatataggc ttcactttct ctctgaaagt taatgctcct acagtttctc gaggttaagt 9000 tcttggtaac tgacccttct ctttactcmc ttgaccggtg gtaaacgttc ttcycttgca 9060 ttaactcttc tatttatttc gcctaactct gattcttaca tcgttttcat tttctttaaa 9120 cttagacctt ctctaagggg gagtaccttg tacttcaagc taagtttttc acaccccaag 9180 ctttttgctt atgacaaaaa gggggagtaa acccagtttt tgatgtgtaa gatgtgttag 9240 tgtgatttat ttttcttttg gagaatttaa gagttccacc ttcatgacca tagatgtgtc 9300 actgggcaaa tacaaggaat acatttcact tcttctgaag tgattctaag ttgactctga 9360 tacccaagac tctgatacct tgtccgtgac tctgattact tatgcgctct gattattcgt 9420 ttttcatcta tgtcataagt ttttcactct gaactcttat attatttagc tcagaatcta 9480 gactttacta acgttttcat caagtattag attcaggggg agctaagctc agaatcaagc 9540 agtgacttga attcagaatg agcaagataa actattcaca tcaggataag tcttattcta 9600 tatctctaaa ctctgagtga attcagttta atgtttaaga attgttcatc aaaaatctta 9660 gttttgtcat catcaaaaag ggggagattg taagatcaag ttttgatcta gtagtacaac 9720 tctatgtttt gatgattaca agttaacctt ttgatatgaa caattgtggt actctaacgt 9780 gtttttctga gtgtgctatt tacaggctct gacctcaact caatctcaca caaatcagaa 9840 gcactgtgta taaagagtga cccaagcaac gctttcgcat tcaccatgtt cagtatgaac 9900 agtggaaaag cttcagaagt tctgaagcta tacaaactct gatgtggact cagtcrctag 9960 aagctctgaa gatccagaag ttctgataac caagaaacac tgaaggttca gatgttctga 10020 tggtgtagaa gactctgaag atccagaagc tgaatagtgg aaactctgaa gtccagaagc 10080 aagaaactct gaaggccatg ttcttccctc tgagttcaga atcagaagat acaatggtca 10140 gaggatctgt gctttccctc tgactctgat caaccggctt cacaagttcc aatatgaagc 10200 attcccctga tcagaagtct cctaggttwa aaggtcaagt cgctatccaa gtacaaaagc 10260 aagtgtacct tcctgacgac ctacctaacg ttctcagcca cagcagaagc tggattttcc 10320 agaa 10324 // ID HARB-2_Mad repbase; DNA; EDCOT; 4243 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; HARB-2_Mad. XX NM HARB-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4243 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1498-1498 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >91% identical to consensus. 3-bp TSDs are TWA. XX FH Key Location/Qualifiers FT CDS 491..2023 FT /product="HARB-2_Mad_1p" FT /note="transposase." FT /translation="STIHPHKSHTNFLKISIIIHSFCFLLHQNQNCIIIHS FT FCFLLTMSSSSRMMWEIDQQEEELFNQSEGMFNLQVAQNEREEDEERRRRD FT DEARMGRASHSRRVIQVVGQICRPSRSGNLDRSRQRRGTELLDDYFVRNSA FT FPDTYFRRRFRMERHLFNKIMIAVCNHDSYFVQKNDAFGAMGLLPEQKITA FT ALRMLAYGASADQVDEIARMGKSTILESLMRFCGAIESIYTAEYLRKPTDM FT DLQRLLKKGEMRGFPGMIGSIDCMHWTWKNCPSAWQGAYGDRK*AKSIILE FT AVASFDTWIWHAFFGVPGAQNDLNVLAQSPVFNDVLQGKAPKVTYWVNGRK FT YDGPYYLADDIYPRWSSFVKTVPRPRSAKEKHFASCQEGCRKDVERCFGIL FT QARWAIVRGAARMFDVESLRSIMMTCIILHNMIVEDEYDYDAVDEYEPDTM FT NNSRTQIYCAHDATEEPVQHEPLERDGRYNERLIQRYTALQRPYMHNARQI FT DLIEHQWELKQAQDT" XX SQ Sequence 4243 BP; 1216 A; 888 C; 855 G; 1284 T; 0 other; gagcagttcc agcgtgggaa aggccccccc aggctattca ctattcaatc cacccagtga 60 acagtaactg cccttaatga acagtaactg ccttttgcat ctccacccct gcacttgaat 120 agccctggca ataggcaata aaatattagt atttttttat ttataaaata atacaaaata 180 attttatttg taatttcgga taagattttt aatcgttctc gttgcgccac gtgtcattat 240 ccgaaaagac aattattggt gatggatttc cgataagatt tttaatcgtt ctcgttgcgc 300 cacgtgtcat tacccgaaaa tacaattatt ggtgatggat ttccgataag atttttaacc 360 aatcacgtcg cgccacgtgt cacaatctgt ttacaatctt tgaggataga tttcgatcag 420 atttttaacg aatgacggca tgccacgtgg cattatctac aacctaatcc tttctgaatc 480 ctccatataa tccaccatcc atcctcacaa atctcacacc aattttctca agatctctat 540 cattattcat agtttctgct tccttcttca ccaaaatcaa aattgtatca ttattcatag 600 tttctgcttc cttcttacaa tgtcttcttc ttcaaggatg atgtgggaaa tcgatcagca 660 agaggaagaa ttgtttaacc aatcagaagg aatgttcaat ctccaggtgg cccaaaatga 720 gagggaagag gatgaggagc gtagaaggag agatgacgaa gcaagaatgg gcagagcctc 780 acattcccgt cgagtcatcc aagttgtggg tcagatctgc aggcccagcc gttccggaaa 840 ccttgataga agcaggcaac gacgaggtac ggaactcttg gacgattatt ttgtccgtaa 900 tagtgcattc cctgatacgt actttagacg tcgttttaga atggaacgac atttgttcaa 960 caaaatcatg attgctgttt gcaaccatga ttcttacttt gtgcaaaaga atgatgcttt 1020 tggtgctatg ggtctccttc ctgagcaaaa aattactgct gccttgcgga tgcttgcata 1080 tggagcatct gcagaccaag tggatgagat agcgaggatg gggaaatcaa ccattcttga 1140 gtccctgatg aggttttgcg gagcaatcga atctatctac accgcagagt acctccggaa 1200 acctactgac atggacttgc aaaggcttct gaagaagggc gagatgcgag gttttcctgg 1260 gatgattgga agcatcgatt gtatgcactg gacctggaaa aactgtccaa gtgcatggca 1320 aggcgcttat ggggacagaa aatgagcaaa aagtatcatt ttggaggcgg tggcatcttt 1380 tgatacatgg atttggcacg cctttttcgg ggttccggga gctcaaaatg acctcaatgt 1440 ccttgcccaa tccccagtgt tcaacgatgt cctgcaagga aaggcaccaa aagtcacgta 1500 ctgggtcaac ggacgtaagt acgacgggcc atactaccta gcagacgaca tttacccaag 1560 gtggtcatcg tttgtcaaaa cagtgccacg tccgcgaagt gcaaaggaaa aacactttgc 1620 aagctgtcaa gaggggtgca ggaaggatgt ggagcgttgt tttggtatcc tccaagctcg 1680 atgggcgatt gtcaggggtg ctgccagaat gtttgatgta gagtcgcttc gatccatcat 1740 gatgacgtgc atcattcttc acaacatgat tgtggaagat gagtacgatt atgatgccgt 1800 tgatgaatat gagccagaca cgatgaacaa ttccagaaca caaatatatt gtgctcatga 1860 cgccaccgaa gaacccgtgc aacatgagcc attagaaagg gatggacgtt acaatgaaag 1920 gctcattcaa cgatatactg cacttcaaag gccatatatg cacaatgccc ggcaaattga 1980 cttgatagag caccagtggg aattgaaaca agctcaagat acttaagttc atttagtgtg 2040 tttgttttta tttggtgtgt ttatttaatt ttatttggtg tgtttttttt agttcatttt 2100 tttttatttg gtgtgttttt tttagttcat ttagtgagtt ttttattatt tggtatgttt 2160 atgtaatttt atttggtgtg tttatgtcat ttgaataaag attctcttag tataaataaa 2220 ttaccaaatt aaataaattt actctcactt taaataaagt actaaattca ataaattgga 2280 aacaacataa agtactctat tcaataaata ataaattaca acccaaagtg attggaaaat 2340 tatgggctcc gattacaaaa agtactctat tcatcatcac ttaaccaatt tgtggtgcta 2400 ggatgatctt ctcttgtcgt gctaggacca tctcctcttg ctctcgcttc tcttgcacgc 2460 ctccttcgca ccacgtccgc tttctccgac ttccaaaaat atttagaatt tggagacttc 2520 ccttctaaag gcgtgttcat aatgtcacga tctcgttgag ccattctttc ttctctaaca 2580 tgttcccttt cttgcctaag tagctctctt tctctctcat tagcttgaaa ttctctctca 2640 acagctgcag cttttgcctc atctctagcc ttatcagcct caaatttcgc catttcccgc 2700 gccaaagtca attcaccttg gcgagcaagt tcttccatat actttgcata atcattcttg 2760 gaagcactcc cttttctctt tgaagccttc ttaccttgag gcctaattgg ataacgggtc 2820 gaccccgacg cttgttcagg gggggcgttt cgggcacttc ttctgcgtca tcttcatgaa 2880 catgcgaggc atgatcgggt gtagagtgta gaggggtgct gttcatgaaa acttctggac 2940 cgacaggcac aactctgaat ttaggacaat ctttgacaat attccaacat tcccaccggt 3000 tgaatgattt gtttttgctt ttggttttgg cactatacca agcttgtgct tgaagttcct 3060 acacaatgcg ggagaagaaa taattataat gaaagtaggt aacaaataaa taatacaaac 3120 aaataattat aatgaaagta ggtaacaaat aaataataca aacaaataat tataatgaaa 3180 gtaggtaaca aataaataat acaaacaaat aattataatg taaatttggg tatagtacaa 3240 acaaataaat aatatattgt tacctgatcc gctaaatttt ccccacttcg aagattacta 3300 ctagcttgtg ccaaggcgtc tctccacgta ctaaacgatt ggctaagtaa tttccaacga 3360 ctggacatcg attctttggt tcttttccca cccattttct caagataatt ggtatgaata 3420 agactccaca tttctcgcaa ctgcatctca ttacccgtaa gcgaatcatg agtaacttca 3480 acccagctag tacacaacgc aacatcttca agaagcgtcc aattcgtacc tgcatcagta 3540 gtcattttgt tggaaaaaaa attggattga aactttgaga gaaagatagg aatgtggttg 3600 aaagtagttg agaaaatatg aaattgtggt gtaaggtaga agataatgag aaggtattta 3660 tagaaaagta aaatcatttt ttttttcgga tttttattaa ttttttacat tttttttaaa 3720 tttttattca cctaattaat ctctgccgtt ggattaaaaa aaattgaatt ccaacactcc 3780 agattgtgcc acgtggcaca acggtaacat ttctaatttt taaactgttt tttctttttt 3840 tttaatttat aaaggcgaat aacgtggacc gttgatctca gatccaacgg ttgatattaa 3900 ataaggtttt taaatttttt ttaccgttgg aaatccaacg gtccaaaata aatagccgtt 3960 gagatccaac ggacgtggga agccacgtgg cctcccaacg gtaacattga cgaaggcctg 4020 cgcacgcggg ccccagcgcc tgacgcaaaa cagaaaaaaa acgtggctga cgtcagcctt 4080 gcgtcagacc cacttcgggc tctcgggctg gcaactcctc acaggcctgt cgctcgggcc 4140 tgctcgggct ccctcgccag cacacgctgg gcttcatcgc tcgggctatc tggccctgtt 4200 ccctcgcctg tccctcgagc tgcagcccac ggtggagttg ctc 4243 // ID Gypsy-27_VV-I repbase; DNA; EDCOT; 7085 BP. XX AC chr20; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-27_VV_; KW Gypsy-27_VV-LTR; Gypsy-27_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-7085 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr20; Positions 11535765 11542849. XX CC Positions [4599-5102] - Integrase core CC 'AAATA' target site duplication CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 1863..4478 FT /product="Gypsy-27_VV-I_1p" FT /translation="MIKQVPAYAKFLKDLCTVKRRIKLSKKAFLTQQVSAI FT IENKAMVKYKDPGCPTISVQIGDSFVERALLDLGASVNLLPYSIYKQLGLG FT ELKATTITLSLADRSIKVPRGVVEDVLVQVEKFYYPVDFVVLDTEPLKKGM FT NYVPIILGRPFLAIANALINCRNGLMQLSFGNMTVEMNVFNLCKQPMDHDD FT VENEEACLIEALVQEHTENLMEENIDEFFSTIVKEECVQVATEWKEKYTIQ FT SLNSVKNDEESKNEEVEISKPELKPLPHGLKYVYLEANEEKPVVISATLTE FT EQEMKLLKVLKENKRAIGWSISDLKGINPLICMHHIYLEENAKPVRQPQRR FT LNPLMQDVVRNEVLKLLDAGIIYPISDSSWVSPTQVVPKKSGITVMKNDEG FT ELIPTRLTTGWRVCIDFRKLNAVTKKDHFPLPFLDQVLERVASHDYYCFLD FT GYSGYFQIAIALEDQEKTTFTCPFGTYAYRRMPFGLCNAPATFQRCMLSIF FT SDMVERIMEVFMDDLTVYGKTFDDCLLNLKKVLKRCIEKDLVLNWEKCHFM FT ATSGVVLGHIISKEGIQVDPAKIELISKLPSPTTVKEVKQFLGHAGFYRRF FT IQDFSKIAQPLCALLLKDAEFIWTKACQEAFKRLKSLLTTAPIVRSPNWSL FT PFELMCDASDYAVGAVLGQREDGKPYMVYYASKTLNEAQKNYTTTEKELLA FT VVFALDKFRNYLLGTSIVIFTDHSALKYLLNKKDAKARLIRWILLLQEFNI FT QIKDKQGVENVVADHLSRVKVESHFKEAQINDEFPDDALCAVEKLPWFANI FT VNYLATGELPSEWNMETKKYFLSRAKHYAWDDPYLYKFCPNQIMRRCVPED FT EQQDILRMCHEGACGGHFA" FT CDS 4608..5546 FT /product="Gypsy-27_VV-I_2p" FT /translation="MPQNHICVVEVFDCWGLDFMGPFPPSFGNLYILVGVD FT YVSKWVEAVACKSNDHKVVLKFLKENIFSRFGIPRAIISDGGSHFCNKPFS FT TLLQKYGVRHKVSTPYHPQTNGQAELANREIKRILTKVVNTTRKDWSTKLS FT DALWAYKTAYKTVLGMSPYRIVYGKACHLPVELEHRAYWAIKKMNFDSDQA FT EAKRKYDLNELVAYRNESYECLRNAREKHKFYHDKLILRREFKQGEKVLLY FT DSKLHIFPGKLRSRWNGPYVVKEVFPYGTVTIQNLRTGNEFKVNGQRLKYF FT IERFETQEENLHFLDGDVQKG" XX SQ Sequence 7085 BP; 2301 A; 1162 C; 1507 G; 2115 T; 0 other; atcgtcataa ctaggatata gtgcattgct ttgttttagt tattttattt tatttttatt 60 attattatta ttattattta tctttataca tatttttctt ctattttatg cttggttggg 120 aaagagatat ttcaggtaga cttcaaagaa caactgagga atctcaacca aatatggagg 180 acactgaaga attcaatagt aataacaaca ggccacgacc accggtgcag gggcaaagaa 240 ctatgagaga gcttctaaat cctcccaggt tgagcacacc atcatgtttt atgctacctc 300 aaaatcatga tcatgttacc attcggcctt aagtggtgtc tcaactaccc atttttaggg 360 ggacagaaaa tgaaaatcca tactctcaca tcaaggaatt tgaggacatc gtttcaattt 420 ttcgagaagc caacactcct ttggagatct ttcgcatgaa gctattcccc ttgtcattga 480 aggataaagc taagacttgg ttaaatagtc ttaggcccta tagtatcaga aattggggtg 540 atctacaatc agtgtttttg taaaaattct ttccaacaca tagaaccagt gcattgaaaa 600 aggagatctc gaatttcaag gctatggagg atgagaaatt ttttgcatgt tgggaaagat 660 tcagggagat tgttgcagct tgcccccatc acggatttga caactagatg ctagtttcgt 720 atttctatga aggcatgcca ccaccaatga aacaacttct cgagactatg tgtggaggag 780 atttcatgaa taaaaacccc gatgaagcat ttcaattcct tgattatgtt gctgaggtat 840 ctagaagttg ggatgaacca atcgtcaagg aaccatctag agatagaaca atgaacaggg 900 caagagctag tggagtgtat accttaccag agggtttaga tgtccaagca aagttagcaa 960 ccgttatgag aaggttggat gatttggaag ccaagggagt tcaagaggta taaatagtca 1020 atgatggggt aactcaattg tgcttgatat gtaagtctac ggaacatggt gtgcaatctt 1080 gtcccactct acctgcagtg caagatatgt ttacggagca agccaatgcc ttagggacat 1140 acaagcaata ttctagcaat tctccatatt ccaacactta taatctgggt tggaggaatc 1200 atccaaatct atcatggagg ggaggtaaca atggccagtt tcagcagcaa ggaaaccgat 1260 ttcagggtaa tcagactaat gggcagcaag gttttcaacc acaaggtatg ccatctcaga 1320 attttcaaca gcaacatcaa acctcatcat ctaactcaag cctggaagac atgatgagag 1380 agtttataca gaagcaagac aagcgtaaag aagatcaaaa taggataaat gctcaaacat 1440 ctcaagaact agtagatatt cgaaccactt tgagccaact tgctgtaagt ttatctcaag 1500 agaaaggaaa attcccagct caaccacaga aaaatccgag aggagtaaat gaagtttctg 1560 aagtgcaaaa ggaagattgc aatgtcgtta tcacactcag aaatgggaaa gaatacgaag 1620 ggcccaagtt acctgtaagt gaagaagata ttcctgctag agatgaacca actgtggaga 1680 aaaatgttag aaatgagaaa gcgtctgaaa aatatgagga agtcattgtg agcaaaaata 1740 aaatgagtgt ttccaatcat ttgcctttcc cttcagctat gcaaagacac aaagtagggg 1800 ataagacttt agagattttg gaagttttga agtaagtgaa gatcaacatt ccactccttg 1860 atatgatcaa gcaagttcct gcttatgcaa agttcctcaa agacttatgc actgtaaaga 1920 gaaggattaa attaagcaag aaagcattcc tcacccagca agtcagtgcc atcattgaga 1980 ataaagcaat ggtgaagtac aaagatccag gttgtcctac catctcagtc cagattggag 2040 attcattcgt ggaaagggct ttgttagatt tgggagctag tgtgaatttg cttccatatt 2100 caatctataa gcaattggga ttgggagagc ttaaggctac taccattaca ctctctttag 2160 cagatcgttc gattaaagta cctagaggag tagtcgaaga tgttttggtg caagttgaaa 2220 agttctacta cccagtggac tttgtggtgt tagatacaga accattgaaa aagggtatga 2280 attatgttcc aattattctt gggagaccct tccttgctat agccaatgct ctcattaact 2340 gtcgaaatgg attgatgcaa ttatcttttg ggaacatgac agtggaaatg aatgtcttca 2400 atttatgcaa gcaaccaatg gaccatgatg atgtggaaaa tgaggaagca tgccttatag 2460 aggctttggt gcaagaacac acagaaaatt taatggaaga aaatatagat gaatttttct 2520 ctacaatcgt taaggaagaa tgtgttcaag ttgctacaga atggaaagaa aaatatacga 2580 ttcaatcttt gaacagtgtt aagaatgatg aagaaagcaa aaatgaagag gttgagatca 2640 gcaaaccaga gttaaagccc ctgccacatg gtttaaagta tgtttattta gaggcaaatg 2700 aagaaaaacc tgtggtaatt tcagctacat taactgaaga gcaagaaatg aaacttttga 2760 aggtgcttaa agagaataaa agagcgattg gttggtccat ttcagatttg aaagggataa 2820 atcccttgat ttgcatgcat catatttatt tggaagagaa tgcaaaacca gtaaggcaac 2880 cacaaagaag gctaaatccc cttatgcaag atgtagtcag aaatgaggta ttgaagcttt 2940 tagatgcagg tattatttat cctatctctg acagtagttg ggtgagcccc actcaagtag 3000 tacctaagaa aagcgggata actgtgatga agaatgatga aggagagctc attcctacaa 3060 ggttgactac aggttggcga gtatgcattg attttaggaa gttgaatgca gtcaccaaga 3120 aagatcactt tccattacct ttcttagatc aggttttgga gagggtagct agtcatgact 3180 attattgctt cttggatggc tattcaggtt attttcaaat tgccattgca ttggaggatc 3240 aggagaaaac cacattcaca tgcccatttg gcacttatgc ttataggcgc atgccttttg 3300 gtctttgtaa tgcaccggcc acatttcaaa ggtgtatgct tagtattttc agtgacatgg 3360 tagagagaat catggaagtt ttcatggatg atctaactgt ttatgggaag acctttgatg 3420 attgtctctt aaatttgaaa aaagttttga aaaggtgcat tgagaaggat ttggttctaa 3480 attgggagaa gtgtcacttc atggcaacct caggggtagt acttggtcat atcatctcta 3540 aagagggtat tcaggtagat ccagcaaaaa ttgagctcat ctcaaagcta ccttcgccta 3600 ctactgttaa agaggtgaaa caatttttgg gacatgcagg tttttataga aggttcatac 3660 aagacttctc aaaaatcgct caacctcttt gtgctttact acttaaggat gcagaattca 3720 tatggactaa agcatgccaa gaagctttca agaggctaaa gtcactcctc actactgcac 3780 caattgtgag atctcccaat tggtctctcc catttgagtt gatgtgtgat gctagtgact 3840 atgcagtggg agctgtacta ggtcaaaggg aggatggaaa accatatatg gtgtactatg 3900 ctagtaaaac ccttaatgag gctcagaaga actacacgac tactgaaaag gagctccttg 3960 cagtggtgtt cgcacttgat aaattcagga actacctttt gggaacttca atagtaattt 4020 ttactgatca ttcggccttg aaatatctac tcaacaaaaa ggatgccaaa gcaagactta 4080 ttagatggat ccttctcctt caagaattta acattcaaat caaggataag caaggggtag 4140 agaatgtggt tgctgatcat ctttcccgag ttaaagtaga gtcacatttc aaggaagcac 4200 aaattaatga tgagtttcct gatgatgcac tttgtgcagt ggagaagttg ccttggttcg 4260 caaatatagt caattacttg gcaaccggag agcttccatc agaatggaac atggaaacaa 4320 agaagtattt tctttcgcgg gcaaaacact atgcttggga tgatccatat ttgtataagt 4380 tttgcccgaa tcaaattatg cggagatgtg ttccagagga tgaacaacaa gacatattgc 4440 gaatgtgcca tgaaggagct tgtggaggtc attttgcttg aaggaagact tcaacaaaaa 4500 ttctacagag tggattctat tggccaacta tgttcaagga ttgtaacact cattgcaaaa 4560 gttgtccata atgtcaacaa cttgggaaaa tcaacacaag gtatcaaatg cctcaaaatc 4620 atatttgtgt tgttgaggtc tttgattgtt ggggcctgga ctttatggga ccatttcctc 4680 cttcttttgg taatctctat attttggtgg gagtggatta tgtctctaaa tgggtagaag 4740 cagtggcatg caagagcaat gatcacaaag tggtgctcaa atttttaaag gagaatattt 4800 tctctaggtt tggcattccg agagcaatca ttagtgatgg aggttcacac ttttgtaata 4860 agcccttttc cactcttttg cagaaatatg gagtgaggca taaagtgtct accccatatc 4920 accctcaaac aaatgggcaa gctgagctag caaatcggga aattaagaga atcctcacca 4980 aagtagtcaa tactacaaga aaagattggt ctaccaagtt gagtgatgca ctttgggcat 5040 ataagacagc ctataagact gtccttggca tgtcaccgta ccgaattgtt tatggtaaag 5100 catgtcactt gcctgtagaa ctcgaacatc gtgcatattg ggctataaag aagatgaact 5160 ttgattcgga tcaagctgaa gctaaaagga aatatgattt gaatgaactt gtggcatatc 5220 gaaatgagag ttatgaatgc ctacgtaatg caagggaaaa acacaaattc taccatgaca 5280 agcttatttt acgaagggag ttcaagcaag gtgaaaaggt gttgttgtac gactccaagc 5340 ttcacatttt tccaggaaag cttaggtcaa ggtggaatgg cccttatgtg gtaaaggaag 5400 tcttccctta tggcaccgtg accattcaaa atctgaggac aggtaatgaa ttcaaagtta 5460 atggtcagcg cctaaagtat ttcattgaaa gatttgagac acaagaggag aatctccatt 5520 ttcttgatgg ggatgttcaa aagggttgaa gcattttctg aaaatccagt aggtaaaact 5580 tttattttgt tttattttat ttatttattt ttctttattt agttttgcat tttcaattag 5640 tcattagcaa tatggttaac atttttttat tttatttttt atttttttat tttttattta 5700 tttttagttg tttttaactt actaatgagt ttatgagttg tagcaactta gcttgcaaac 5760 atccgagtga tataggtaaa tgcgaacttc aagggagtga aaaggtaagc ctcatatgtg 5820 ttcaaggtga caaagctcct acagtttata tgaagtcctc ataacacact tctcacttga 5880 tgatcttgag gtaacatatt catttttcct ttcttttgac ccattatcct acacattggg 5940 gacaatgtgt aatttaggtt gaggggggaa ggctattagc ctattagccc taattttttt 6000 caaacatctt tggttagcta atgagattct tgatttgcct tggtaactca tggtttattt 6060 ggcatgagaa tgctttaagt agtattattt ctttagaatt tgaaaaaaaa tgcagttaga 6120 gcaagagtat tagttcactt accttatctt tatatacctt taagtgcaaa aatagttagg 6180 ttgaattctt ggaatacctt caatttttct ttgatggtta ttttctattt aagactcaaa 6240 gcacacacaa agcacgtgta cccttatggt atcttgatta agataatttc tttagcttaa 6300 aaagagttgt tcttaagcaa taaaatgagg aaataaaaaa aaattgaaaa tgactgattt 6360 aagcttgagc aattatctga gggggtaatg gccttgtgtc ttcaagccct gctgcccaaa 6420 accaactggt taggagtcat cggtatcttg ctcgttacat aagctaaact cagtttaaga 6480 aaaaaaaaag ataaatgaaa aatgaaaaaa aaaatgttta ggaaattcga ccttgttcta 6540 ccttgagcta gggtgatacc tgaggggtaa gtggcctata aaggtcctca atacctggta 6600 ccttgggtga aaactcggga gttgccggtg gatccctatt aagccatata gaaggagatt 6660 tcctaaacta agaaagaaaa atcaaaataa attttcctcc tctttaactt aaagaataat 6720 gaaatttgag tttaagaaaa agtcttaaga aaaatactat gaggggacac caaaattaag 6780 cacatgaggt ttaggtggaa agaaccaatc aagggaaaat caagagacac taagaggaat 6840 gctaaacatg gatgcacatt tatgtatacg aagataaggt gagaaaacta agaaattgca 6900 tatcttgtgt catcttgctc aattctagga aatttgtcta cttgggcatc ttgtgtgtga 6960 aacatgttat gttgagttaa tatggtttca tgaatctcat tacatatttt tcattcttct 7020 ttattctttt catttgctag ggactagcaa agtttaggtt gaaggggatg attggagcca 7080 aaata 7085 // ID LINE1F_MT repbase; DNA; EDCOT; 5850 BP. XX AC AC140545; XX DT 26-MAY-2006 (Rel. 11.05, Created) DT 26-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE L1-class element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; LINE1F_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5850 RA Jurka J.; RT "LINE1F_MT: L1-type element from barrel medic."; RL Repbase Reports 6(5), 251-251 (2006). XX DR EMBL/GenBank/DDBJ; AC140545; Positions 80431 86280. XX CC This is a recently retroposed element. The 5' sequence terminus CC is approximate. XX FH Key Location/Qualifiers FT CDS 1..1617 FT /product="LINE1F_MT_1p" FT /translation="MSSEFVFSAQGEPSFEKPPDPPKAKLSFRDKLLGTQN FT AIPSREKENLIEKNLVRIELENGNRLLPKVFLEPKTFQELCTPWKDALVVK FT LLGKSLGYNTMKERLQRTWKLQSGFEIMDNDNGFYMVKFDQEADKEKVITG FT GPWMIFDHCLVVTHWSPEFASPEAKVERTVVWVRFPGLNLVYYDESFLLAM FT ASAIGRPIKVDTNTLKVERGKFARVCVEVDLTVPVVGKIWINEHWYKIQYE FT GLHLICTNCGCYGHLGRSCSVKPTKTATSNPHHHPTAATQQENSHHSQREP FT ATISINSMSQNSNGNEINAINEVEPILNGGVITINEGTQELHGDWLLVSRR FT KKPANIQQSTHSKNASQNKANRFSVLTNTAHQSKPNSYPSRTSIQVIPQNT FT KNSTDLKRRRHNNDNDDIIIQNLSITPKAILKSLHKSLHKPVLDKVIPDVT FT NLTQVNHKKTTMDPPHLSQPDSATPPHNNNPITPTPQINTPRQHANCSGTN FT ELDVQDLEDEAMASQDNLQSMQAHETSEGKHKASSDTKEDMIT" FT CDS 1661..5437 FT /product="LINE1F_MT_2p" FT /translation="MEALLDVSILSWNIRGAQNNNARRQLKDLLRKFNPTF FT LAIYETHTLYANLASFWNNNNYRPVHIVDANGHSGGIWLMTHTATNFTSTV FT LDYNQYSITFNISRGIATTTCTCVYASPNASMRTNFWNYLSSISNTITNPW FT MLIGDFNETLLPSDQRGGIFHHNRAAMFSNLMDNCNLLDITTTGARYTWHQ FT NFNGLRILSKKLDRGMANVDWRMHFPEAFVEVLCRLHSDHNPLLLRFGGLP FT LVRGPRPFRFEAAWIDHKDYESLVRDSWNSANHDTISALNIVKDNSIIFNH FT EIFGNIFKRKRHVENRLKGVQNYLERVDSLRHTLLEKELQQEYNHILYQEE FT MLWYQKSRDMWVKFGDKNTSFYHTQTIIRRKKNKIHTLQLPNGFWSTDCDT FT LQDEAHKYFKDFFTKSQPHHNRTFNIGTHPTVDELGASSLTKPVTKIEVLA FT ALNTMKPYKAPGPDGFQCIFFKQYWHIIGDDIFHMVQSAFQTGTFDPNISD FT TLISLIPKTDPPSTFKDFRPISLCNIAYKLITKVLVHRLRPILNVIIGPYQ FT SSFLPGRGTTDNSIVLQEIVHFMRKTKKKKGYVAFKLDLEKAFDNVNWKFL FT HNCLHDFGFPDITIKLIMHCVSSSTFSVLWNGNKLPNFKPTHGLRQGDPLS FT PYLFILCMEKLSIAINDAVNQRRWEPIRINNTGPFLSHLLFADDVLLFTKA FT KSSQFKVVSELFEEFSIASGLKINLTKSRAFFSKGVPQAKIHKLTTISGIR FT STTSLDKYLGFPIPKGRPMRSDFAFIIEKMQNRLASWKGKLLNKAGRLTLA FT SSILSSIPTYYMQINWLPQNICDNIDQVTRNFIWKGNNNKGVHLVNWKKIA FT APKQFGGLGIRTAREANTSLLGKLVWNLVQKNDKLWVNLLSNIYSSGPDFL FT FNASAKHNSSPNWFSIIRAKNVLKNGYVWRAGSGSTSFWYSNWSALGTLGS FT HVPYVDIHDIQLTVQDVITNNGNHTQSIYTILPPNLAEVINNIRLNFNHSI FT EDAFIWPQNKNGTYSTSSGYSWLISRQSAEVQNSKSWSWIWRLKVPEKFKF FT LVWLACHEAVPTLQLLYHRNMVTSPLCTRCGENDETLFHCLRDCRFSKVVW FT EKIGFFNHNFFSTNAVHIWLHDGASSSCSTLFLSALWWIWRQRNLMCLGNE FT TLPLPQLCSNIDNLKVSINTAYNSTPSAPTLDRFIRWNNNNFQCIILNVDG FT SCSGDPIRTGYGGVIRNNTGGFISAFSGHINHSQDILYAELSALFTASP" XX SQ Sequence 5850 BP; 1797 A; 1409 C; 1037 G; 1607 T; 0 other; atgtcctctg agtttgtctt ctccgctcaa ggtgaaccaa gcttcgaaaa accacccgac 60 ccccccaaag ccaaactttc ttttcgagat aaactgttag gaacccaaaa tgccatacca 120 tcacgtgaaa aagagaactt gatcgaaaaa aatcttgtcc gcattgaatt ggaaaacgga 180 aaccgtctac taccaaaggt cttcttggaa ccgaagacat tccaggaact ctgcacccca 240 tggaaggatg cgttggtggt caaattgcta gggaagagcc tcggttacaa taccatgaag 300 gagcggctac aaagaacttg gaagcttcaa agtggttttg aaatcatgga taatgacaat 360 ggcttttata tggtcaaatt cgatcaagaa gcagataagg agaaagtcat caccggagga 420 ccttggatga ttttcgacca ttgtttggtt gtcacccact ggtcaccaga atttgcatca 480 ccagaagcca aagttgaacg gacagttgtt tgggtacgtt ttcctgggct aaatttagtc 540 tattatgatg aaagcttctt actagcaatg gcctctgcta ttggccgccc gataaaggta 600 gacactaata cactaaaagt tgaaagagga aaattcgccc gtgtatgtgt agaagtggat 660 cttacagtgc cagtagtggg aaaaatttgg attaacgaac attggtataa gattcagtat 720 gaaggattac acttaatctg tactaattgt ggttgctacg gtcatctggg aagaagctgc 780 agcgtcaagc caaccaaaac tgccacatcc aaccctcacc accacccaac cgccgccact 840 caacaagaaa acagccacca ttctcagcgt gagccagcca ccatttccat caattcaatg 900 tcgcaaaaca gtaacggaaa tgaaataaat gccattaacg aggttgaacc aattcttaat 960 ggaggcgtta ttactattaa tgaagggaca caagagctac atggggattg gctcctagtt 1020 tctaggagga aaaaaccagc caacatccaa cagtcaaccc attctaaaaa cgctagccaa 1080 aacaaagcca acagattctc tgtcctgact aacacggccc accaatcgaa accgaacagc 1140 tacccctcaa ggactagcat ccaagtgatt ccacaaaata caaaaaactc aactgaccta 1200 aaacggcgca ggcataacaa tgataatgat gacataatca ttcaaaacct aagtatcact 1260 cctaaagcca ttcttaaaag ccttcacaaa agccttcata aacctgtcct tgataaggtc 1320 atacctgacg tcactaacct cacacaagta aaccataaga aaacaactat ggacccaccc 1380 cacttgagcc agccagactc ggctaccccc ccacataaca acaatcccat aactcctacc 1440 cctcaaatta atactcctag gcagcatgca aattgcagtg gcactaatga acttgatgtg 1500 caagatttgg aagacgaagc catggctagc caagacaatc ttcaatctat gcaagctcac 1560 gaaacatcag aaggaaaaca taaggcctcc agtgacacca aggaggacat gattacctaa 1620 tatctcttga accaatgtcc tatcttcctt cattattttt atggaagctc tactagatgt 1680 ttcaatcctc tcttggaata tcagaggggc acaaaacaat aatgctcgaa gacagcttaa 1740 agatttattg agaaagttca atcccacttt cctagctatt tatgaaaccc atacacttta 1800 tgctaacctt gcatcctttt ggaacaataa taactacaga cctgtccaca ttgttgatgc 1860 aaatggccac tccggcggaa tatggctgat gacacacacc gctactaact ttacctctac 1920 cgtccttgat tataaccaat attctatcac tttcaacata agtcgaggca tcgcaaccac 1980 cacttgcact tgcgtttatg ctagtcctaa cgcttccatg cgcactaatt tctggaacta 2040 cctttcatcc atcagcaaca ccatcaccaa tccttggatg ctcattggtg acttcaatga 2100 aactcttctt ccgagtgatc aaagaggggg catcttccac cataatagag cagcaatgtt 2160 ctcgaatctt atggataatt gcaacctgct tgacatcacc acaactggag cccgctatac 2220 ttggcatcaa aatttcaatg ggcttagaat tctttccaaa aaacttgatc gcggtatggc 2280 aaatgtagat tggcgcatgc acttccctga agcttttgtc gaagttcttt gtaggcttca 2340 ctctgatcac aatccacttc tcctccgttt tggtggcctc ccactggtta gaggacccag 2400 accgtttcgc tttgaagccg cttggattga tcacaaagac tatgagagcc tggtaagaga 2460 ctcttggaac tctgccaacc atgataccat ttcagcttta aatattgtca aagacaattc 2520 tatcattttt aaccatgaaa tctttggcaa tatttttaaa agaaaaagac atgtggagaa 2580 caggctgaaa ggggttcaaa actatcttga aagagtggat tctcttagac acactctttt 2640 agaaaaagaa cttcaacaag aatacaatca cattctttat caagaagaga tgctttggta 2700 tcaaaaatcc agagatatgt gggttaaatt tggtgataaa aacacttcct tctaccatac 2760 ccaaaccatt atccgcagaa agaaaaacaa aatccacacc ctccaactcc caaatggatt 2820 ttggtccaca gattgtgaca ccctccaaga tgaagcacat aaatatttca aagatttttt 2880 tactaaaagc caacctcatc ataaccgcac ctttaacatt ggcacacatc caactgtcga 2940 tgaactaggc gcttcttccc tcaccaagcc cgtcaccaag attgaggttc tagccgccct 3000 caatacaatg aaaccctaca aagcccctgg accagatggc ttccaatgca tattttttaa 3060 gcaatattgg cacattattg gagatgacat ttttcatatg gtccaatctg ctttccaaac 3120 tggtaccttt gatccaaaca tctctgatac cctcatttcc ctcattccca agaccgaccc 3180 ccccagcact tttaaagact ttagacccat tagcctctgc aatattgctt acaaactcat 3240 cactaaagtc ttggttcacc gcctcagacc aattcttaat gttatcattg gcccctatca 3300 aagtagtttt ctacctggta ggggcaccac tgacaattcg attgttttgc aggaaatagt 3360 acacttcatg aggaaaacca aaaagaagaa agggtatgtg gctttcaaac tagatcttga 3420 aaaagccttt gataatgtta attggaagtt tctccataac tgtctgcatg atttcggttt 3480 ccctgacatt accatcaaac tcatcatgca ttgtgtctca tcctccacct tctctgtttt 3540 gtggaatggc aataagcttc ctaattttaa gcctactcat ggtcttcgtc aaggcgatcc 3600 gctctctccc tacctgttca tcctatgtat ggaaaaactc tccattgcca taaatgatgc 3660 agtcaaccaa aggagatggg agccaatccg tattaacaac accgggccgt ttttatctca 3720 tcttttattt gcggatgatg tgcttctatt caccaaggca aaaagctccc aatttaaagt 3780 ggtatcagaa ttgtttgaag aattcagcat cgcgtctggt ttaaaaatca atttaacaaa 3840 gtctcgtgct tttttctcta agggagtccc ccaagccaag atccacaagc tcactactat 3900 ctccggaatc cgtagcacca catctcttga taaataccta ggttttccta tacccaaggg 3960 gcgtccaatg agaagtgatt tcgctttcat cattgaaaaa atgcagaata ggttagcttc 4020 ttggaaaggt aagctcctca acaaagcagg cagattgacc ctcgcttcat ctatactttc 4080 ttccatccca acttattata tgcagattaa ttggcttcca caaaacattt gcgacaacat 4140 cgatcaagtc actcgtaatt ttatttggaa aggcaacaat aacaagggcg tacacctcgt 4200 taattggaaa aaaattgccg ctccaaaaca atttgggggt ctaggaattc gaacagcaag 4260 ggaagcaaat accagtcttc ttggtaaact tgtttggaat ttggttcaaa aaaatgataa 4320 actttgggtg aatcttcttt ccaatattta ttctagtggt ccggatttcc ttttcaatgc 4380 atcagctaaa cataacagct ctcccaactg gttttccata atccgtgcta aaaatgtact 4440 caaaaatgga tatgtctgga gagcaggatc aggcagcacc tctttttggt acagtaattg 4500 gagcgcgctt ggcactcttg gttctcatgt tccgtatgtt gatatacatg atattcaact 4560 cactgttcaa gatgttatca ccaataatgg taaccacaca caatccatct acaccattct 4620 cccacctaac ctagcagaag ttataaacaa catccgttta aacttcaacc actcaattga 4680 agacgctttc atttggcccc aaaacaaaaa tggaacctat tcaactagca gtggttatag 4740 ttggttaatc tcacgccaat ctgcggaagt tcagaacagt aaatcttgga gctggatttg 4800 gagattgaaa gtgccggaaa aattcaaatt cttggtttgg ttagcatgtc acgaagctgt 4860 acccacctta caattgttat atcacagaaa catggttact tcacctttgt gcaccagatg 4920 cggtgaaaat gatgaaactt tgtttcattg cttgcgggac tgtcgctttt ctaaggttgt 4980 ctgggaaaaa atcggattct tcaaccataa tttcttctca accaatgcgg tgcacatatg 5040 gttacacgac ggtgcgtctt cttcttgttc aaccctcttt ctatccgccc tatggtggat 5100 ttggagacaa cgcaatctca tgtgtctagg taatgaaact ctaccattac cccaactctg 5160 cagcaacatt gacaatctga aggtatccat taatactgcc tacaacagca caccttctgc 5220 acctacgctg gacaggttca ttcgatggaa taacaacaac ttccaatgca taatcctaaa 5280 tgtagatggc agctgcagtg gcgaccctat cagaacaggt tacggcggtg ttatccggaa 5340 caacactggc ggcttcattt cggctttctc gggtcatatt aatcactctc aggacattct 5400 ttacgcagag ctttcagcac tcttcacggc atcaccttag ctattggcct aaattatgat 5460 gaagtggctt gctattcgga ttcccttctc actgtcaatc tggtcaagga agagttaaat 5520 cagttccatg tttacgctgt ccttattcag aatatcaaag atctcctcta tccgagaaac 5580 tactcccttc accactcttt acgcgaagga aatcagtgcg ccgattgctt ggccaagctt 5640 ggagcttcga ataatgaggc ttttacaatt cacaacagcc ctccagagac ccttctccct 5700 tttctacaag cggatgaagt agggacgctt ttcctaaggc gctagttctg tttttttctg 5760 tcagtttttc tatttctttt tgtttttgtt tagcattgta accaaaaaaa aaaaagctaa 5820 agattctttg taccaaaaaa aaaaaaaaaa 5850 // ID Copia-62_VV-I repbase; DNA; EDCOT; 4253 BP. XX AC chr14; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-62_VV_; KW Copia-62_VV-LTR; Copia-62_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4253 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr14; Positions 23405508 23409760. XX CC Positions [1678-2172] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(73..2985,2989..4251) FT /product="Copia-62_VV-I_1p" FT /translation="MSSTASQSSSSSGSAQSSSMASIPSYQMLNYSLPVKL FT DRTNYILWRSQIDNVIFANGFEDFIDGTSVCPEKELRPGEINPAFVAWRRQ FT DRTILSWIYSSLTPGIMAQIIGHNSSHSAWNALEKIFSSCSRARIMQLRLE FT FQSTKKGSMSMIDYIMKVKGAADSLAAIGEPVSEQDQIMNLLGGLGSDYNA FT VVTAINIREDKISLEAVHSMLLAFEQRLEQQGSIEQLPAMSANYASSSNNR FT GGGRKYNGGRGPNFMMTNSNFRGRGRGGRYGQSGRQNSSSSERPQCQLCGK FT FGHTVQVCYHRFDITFQSTQNNTTGVSNSGNSNSMPAMVASSNNLADDNWY FT LDSGASHHLTQNVANLTNATPYTGADKVTIGNGKHLTISNTGFTRLFSNPH FT SFQLKKVFHVPFISANLISVAKFCSDNNALIEFHSNGFFVKDLHTKRVLAQ FT GKLENGLYKFPVISNRKTAYVGITNDSTFQCSTIGNKRELWHHRLGHAATD FT IVTRIMHNCNVSCGKYKATVCSSCQLAKSHRLPTHLSSFHASKPLELVYTD FT IWGPASVTSTSGAKYFILFVDDYSRYTWLYLLQSKDQALPIFKQFKLQVEN FT QFDAKIKCLQSDNGGEFRSFMSFLQESGILHRFSCPYNSSQNGRVERKHRH FT VVETGLALLAHAGLPLKFWSYAFQTATFLINRMPSKVLQNASPYFALFKRN FT PDYKFLRVFGCLCYPFIRPYNNHKLQYRSLKCVFLGYSLHHKGYLCLDNLT FT GRVYVSPHVVFDETQFPFAQNISSSPSKDASDESVIPAIIVSSNPSTLSFH FT GSNHSMASPNLTSALTHPTPPTDTPTTRSLREPVLEAEVTLPAQQQVVVPP FT PRVTTRSMSGITKRKHIFNLAAFKISEPTTLKQAIKDPNWAEAMQTEIAAL FT HKNQTWDLVDPPKDVNIIGCKWVYKLKSKPDGSVDRYKARLVARGFNQTFG FT LDYFETFSPVVKAATIIVLTIALSYRWELRQLDVQNVFLNGDLVEQVYMAQ FT PPGFLHPNHPNKVCKLKKALYGLKQSPRAWFTKRSSALLSWGFNSSRIDSS FT MFVHFGTHSTLIVLVYVDDIIVTGSSPVLIQQLIHKLHSLFALRDLGQLSY FT FLGIEVAYDGGSMHLSQSKYITNLLQRTSMLDSKAAATPGTVGLSLSQFDG FT DLMDDVTMYRSVVGALQYATLTRSDIAFSVNKACQFMHRPTSTHWSSVKRI FT LRYLKGTTTHGLLLQPSAHFTVQAYTDADWGAQPDDRRSSSGYLVYLGNNL FT VSWTASKQKVVSWSSAESEYRGLAIATAEIIWTQALLSELCISLTSIPTLY FT YDNISAYYMAKNPVFHARTKHIEIDLHFIRDQVLHNKLQLQYIPSTDQPAD FT ILTKHLTSSRFLSLRSHLCLVPRPFSLRG" XX SQ Sequence 4253 BP; 1137 A; 940 C; 834 G; 1342 T; 0 other; gtttttctat cttggtatca gagcataaat tttttttctc tccgtttctt ctccttttct 60 tccgatccaa tcatgtcttc cactgcttct cagagctcat cgtcttctgg atctgcgcaa 120 tcttcgtcaa tggcgtccat tccttcttat cagatgctca attactctct acctgtgaaa 180 ctcgatcgga caaattatat cttgtggcga tctcagattg ataatgtaat ctttgccaat 240 ggttttgaag atttcatcga tggaacttct gtttgtccag agaaagaact tcgtccggga 300 gagatcaatc ccgccttcgt tgcttggagg agacaagatc gaacaatcct cagctggatc 360 tattcatcgc tcacaccagg tattatggca caaattatag gtcataattc ttctcactct 420 gcttggaatg ccttagagaa aatcttttca tcttgttcga gagcaagaat aatgcaactc 480 agacttgagt ttcaatcaac aaagaagggc tcgatgtcta tgatagatta cataatgaaa 540 gtcaaaggag ctgcagatag cttagcagcc attggagaac ctgtttctga acaagaccaa 600 attatgaatc ttcttggtgg tcttggatcc gattataacg ctgttgttac tgctattaac 660 attagagaag ataagatctc tcttgaggca gtacatagta tgcttttagc ttttgaacag 720 cgtcttgagc aacaaggctc gattgaacaa cttccggcta tgtcggccaa ttatgcctct 780 tcttctaata acagaggagg tggaaggaaa tataatggag gtcgtggacc caacttcatg 840 atgactaaca gtaacttcag aggtcgtggt cgtggaggta gatatggaca gagtggcaga 900 caaaactcca gctcgtctga aagacctcaa tgccagttat gtggaaagtt tggccacaca 960 gttcaggtct gttatcacag atttgacatc acctttcaga gcactcagaa caatactact 1020 ggtgtttcaa attctggtaa ttcaaattct atgcctgcta tggttgcttc ctctaacaat 1080 cttgcagatg ataattggta ccttgactct ggagcaagtc accatctcac tcaaaacgtg 1140 gcaaatttaa ccaatgctac accttacact ggggcagata aagttacaat tggtaatggt 1200 aagcacttaa ccatttccaa tactggtttc acccgtctat tctctaatcc acactccttt 1260 cagctcaaaa aggtgtttca tgttcccttt atctcggcaa acttaattag tgtggctaag 1320 ttttgctcgg ataataatgc tttaattgaa ttccactcca atggtttctt tgtgaaggat 1380 cttcatacga agagggtgct tgctcaaggc aaacttgaga atggccttta caaattccca 1440 gtaattagca acaggaagac tgcttatgtt ggtattacta atgattctac ttttcagtgt 1500 agtactatcg gaaataagag ggagttatgg catcataggt taggtcatgc tgccactgac 1560 attgtgacta gaataatgca taattgtaat gtttcttgtg ggaaatataa agctactgtt 1620 tgctcttctt gtcagctagc taaaagtcat agattaccca ctcatctctc ttcttttcat 1680 gcatctaagc ctcttgaact tgtttacact gacatatggg gacctgcctc tgtcacgtct 1740 acttctggtg caaagtattt tattttgttt gtggatgact attctcggta cacatggctt 1800 tatcttcttc aatcaaaaga ccaagccctt cctattttta aacagtttaa gcttcaagta 1860 gagaatcaat ttgatgctaa aatcaagtgc ttacaatctg ataatggtgg tgaattcaga 1920 tctttcatgt cttttcttca agaatctggt atattacatc gtttttcatg tccttacaac 1980 tcatcccaaa atgggagagt tgaacgaaag cataggcatg ttgttgagac tgggttagcc 2040 ctattagctc atgctggttt gccattaaag ttctggagct atgccttcca gacagctaca 2100 tttctcatca atcgaatgcc tagcaaagtc ctgcagaatg cctctcctta ctttgccctg 2160 ttcaaacgaa atccagatta taagtttctt cgagtgtttg gctgtctgtg ctaccctttt 2220 attcggccat ataacaatca taagttgcaa taccgatctc ttaagtgtgt ctttcttggc 2280 tacagtttgc atcacaaagg gtatttgtgc cttgataatc tgactgggcg agtttatgtg 2340 tcaccacatg ttgtttttga tgaaacacag tttccctttg ctcaaaacat atcatcttca 2400 ccatccaaag atgcttcaga cgagtctgtt attcctgcaa ttattgtctc ttctaatcct 2460 tccactttga gcttccatgg cagcaatcat tcaatggcct ctcctaatct cacgagtgct 2520 cttactcatc ccactcctcc tacagataca ccaactactc ggtctttacg cgagccggtt 2580 cttgaagctg aggttactct tcctgctcaa cagcaagttg ttgttcctcc accacgagta 2640 actacgaggt ctatgagtgg aattacgaaa agaaagcaca ttttcaatct tgcagccttc 2700 aagatatctg agccaacaac cttgaagcaa gctatcaaag atcctaattg ggcagaggcg 2760 atgcaaacag aaatagcagc tctacataaa aatcagacct gggacttagt tgatccacca 2820 aaagatgtga acatcatcgg ctgtaagtgg gtttataaac ttaaatccaa gccggatgga 2880 agtgttgaca gatacaaagc gcgtctcgtt gcaagaggct tcaatcagac ttttggtttg 2940 gattattttg aaacttttag tcccgttgtg aaagcagcaa cgatatgaat tgtgttgact 3000 atagctctga gttacagatg ggagcttagg cagcttgatg ttcagaatgt ctttctcaat 3060 ggtgaccttg ttgagcaggt ttatatggcc caacctcctg gttttcttca tccgaaccac 3120 ccaaacaaag tttgtaaact aaagaaagct ctctacggtc tgaaacagtc accccgagct 3180 tggtttacca agcgaagctc tgctctgttg tcctggggat tcaattcttc aagaatagat 3240 agttctatgt ttgttcactt tggaacacac tctactctca ttgtcctagt ctatgtcgat 3300 gacataattg ttacaggaag ttctcctgtc ctcattcagc agctgataca caaacttcat 3360 tctctgtttg ctttacgcga tttgggccaa ttgtcctatt ttctaggaat tgaagtggcc 3420 tatgatggtg gatctatgca tctcagtcaa agcaaatata ttacaaatct tctgcagagg 3480 acttccatgc ttgatagcaa agctgctgca acgccaggca ctgtaggctt gtctctctct 3540 cagtttgatg gagatcttat ggacgatgtc actatgtaca gaagtgtagt cggggctctt 3600 caatatgcaa ccttaactcg gtcggatata gctttttcag taaacaaagc ctgccaattc 3660 atgcaccgac ctacttccac tcattggtct tctgtcaagc gtattttgag gtatttaaaa 3720 ggcacaacta ctcatggtct gctccttcaa ccatccgctc actttacagt tcaagcctat 3780 acagatgctg actggggcgc acaacctgat gaccgacgaa gctcaagtgg ctaccttgtt 3840 tatcttggca ataatctagt ctcctggaca gcttcaaagc agaaggttgt ctcttggagt 3900 agtgctgagt ctgagtaccg aggacttgcc attgccactg cagagattat ttggacacaa 3960 gctttgctga gtgagctgtg catttctcta acttcgattc ctactcttta ttatgataac 4020 atcagtgctt attatatggc caagaatcca gtcttccatg ctaggacgaa acacattgaa 4080 attgacctcc attttattcg ggatcaagtt cttcataata agttacagct gcaatatatt 4140 ccaagtacag accagcccgc tgatattctc acgaagcatc tcacaagctc tcggttcttg 4200 tcactacggt ctcatctatg tcttgtgcct agacccttca gcttgagggg gga 4253 // ID SOD_SINE repbase; DNA; EDCOT; 245 BP. XX AC . XX DT 27-OCT-2006 (Rel. 11.1, Created) DT 27-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE A short interspersed nucleotide element from Solanum demissum. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Nonautonomous; SOD_SINE. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-245 RA Jurka J. and Shankar R.; RT "SOD_SINE: A SINE from nightshade potato sequence."; RL Repbase Reports 6(10), 507-507 (2006). XX DR [1] (Consensus) XX CC This sequence is a short interspersed nucleotide element, present CC as an insertion in some well conserved regions, from Solanum CC demissum. XX SQ Sequence 245 BP; 76 A; 50 C; 48 G; 71 T; 0 other; tgtattacgc gtaaccacaa gtcctttctt gatatacatg agacactaga aattactgaa 60 ttttttgaag acagaactga tggatagtct attggaaaca acctctctgc cccacaaagg 120 taaggttaag gtttatgtac atcctaccct ctttagagcc ccaccggtgg aattattcta 180 ggtaagttgt tgtaggacta tagagaactc aatagctcca tgctgcagct gagaactgaa 240 aatct 245 // ID Gypsy3-PTR_LTR repbase; DNA; EDCOT; 247 BP. XX AC scaffold_210; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy3-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-247 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-247 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 331-331 (2007). XX DR Genome; scaffold_210; Positions 193915 194161. XX SQ Sequence 247 BP; 70 A; 38 C; 57 G; 82 T; 0 other; tgttacagct ggattgttac agctggattg ttgttacaag gaggtggcgt ggggcacttg 60 tgtgaaccgt tagagtcagt tagaagttag ttaaccatgg aaataaacgt gtaaagcatg 120 ggaagggtag tataaataga cagtggagtt tacgtataca acacggaaaa tttaatacaa 180 aacttctatt cctctgttct cattctctgt ttctctcttt cttattcttg ttaagctgag 240 cttaaca 247 // ID Copia-40_Mad-LTR repbase; DNA; EDCOT; 163 BP. XX AC ACYM01026881; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-40_Mad-I; KW Copia-40_Mad-LTR; Copia-40_Mad_. XX NM Copia-40_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-163 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1390-1390 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01026881; Positions 8639 8801. XX SQ Sequence 163 BP; 45 A; 17 C; 30 G; 71 T; 0 other; tgacttatat taggttccct ataattatgg gattcctacc atatttagtt tcctagttta 60 ggatgtaatt attctttcct ttattctgat aggattgtat gtggttgtat agggttgtat 120 atatatcttg ttttgagatg aaatagaata tcattgaaaa gca 163 // ID Ogre-PT3_LTR repbase; DNA; EDCOT; 2990 BP. XX AC AC149300; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 10-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE Autonomous LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-PT3; Ogre-PT3_LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2990 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC149300; Positions 92345 95334. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). XX SQ Sequence 2990 BP; 883 A; 715 C; 581 G; 811 T; 0 other; tgttgtaacc catttttggg tccccacaaa atatatataa aaatatatag ccaaaggagg 60 ttaggaaaat aacaggaggc agaagcgctc agaaaatggt tggaaaattg gtcaaggagg 120 gtaaaaatac aaagattgaa tttttgacag tatattcttg aaggaggaga gccctgttga 180 gaagggaaat ttgaaatttg aggagaaaag cccaaatttg gatgtttatg gacttaattg 240 gatttttaaa tgaatttata ggagatttga ttgtaagaaa aattgatttt taagtcaatt 300 tgggctttaa ttagaagaaa tttaagttct ggggccaaaa tatatttttt aggaatttat 360 tagttcaaat caggggctta attgcataat tattgaagtt taagggccaa ttagggactt 420 aattgaagaa atctgaaacc aaggaccaaa ttggaaaagg cgcgcaagta taggggctgc 480 aattaacaaa atccgggggc caaattgaag aaattgaaag tttaatggcc aattagggat 540 gaaattgcat aaatccgaga ccaaggacca tattgcaaaa ggcgcgaaac tttggggccg 600 aaggtgaagt tatgtcggga ctaaattgca tcaaatcaga agttttaggg tcaattaggg 660 aataatattg aacgaaattg aaagtcggag gactaaattg aaaattggca aagaaatccc 720 tatttttatc aaaacggcac cgttttgcac ttaaaaaaaa aaaaaaagag aagaggcagg 780 aaccaggcga cgcgtcgccc ggtactgttc actgtcttcc ccgccgagct gcccgagtgg 840 ccgacttcca ggcgtgtttg ctgcctcgtt tggcccccaa atccgacaaa gcatgcaccg 900 acatgtccac ctggaaccca tttatcctgg ggagtggtcc ggtcgggtca aaaaggtttg 960 gaacagctcc gttttgtggc ccaaatcgtg cacctcgggc agtctgcaaa tttggcagtt 1020 cgaggtgcac actttgaacc aacggtttga attactcaag gcgaatcaag ggctgggatg 1080 tttttccaat tgaagacgag attaccctct gtccggccct ataaatagga tcaattttca 1140 tgctcaaacg gttggcaaag gagagctcaa aattggcaca aaaataagct ttttcctacc 1200 cggttttcct gcaaacagcc ttccctctct tttttttctc tccaccgtag tccagccccc 1260 cacagaccca cacacccgaa cagccctcac acacctctcc cctccccttg attttcttct 1320 tcccctcagc agccagcaaa aagggacaac cccctctctt gcaaagccaa accggggcag 1380 cccccttcct ttcctctcat tctcttccag cagtcccaaa gaaacactgt cccctctccc 1440 tcccatcaac acaacgccag caacagatct tcacctcagc ttctccttca ccgcagcttc 1500 aacagcccca gcaacgcctc ccgcggcctc ctcagcagtg acagcctcca caggagcaag 1560 cctccgcctt ccagcttctt caccggccaa cagcagtcct ccttcctcca gtgacaccca 1620 gcagcaaccg gagtagcagc tccttcctca gtcacaccaa cagctccagc cgagagcttt 1680 ccttctcctc tgcaggaatc gaccccttct tcttccagcc gggaccagtg cacgccagtg 1740 aaaccaccag cctccaccgc agcaccgccg acataccagc aacgcaccgc cgcctccacg 1800 ccaggtgctc ttctcccccc tctttgcaca ttgtttgggt tcttctcctg catgcagaac 1860 gagcagcgtt ctgcatgcag gaagggggga aaataattcc ccccgtttgt ttttaattat 1920 gctgggccag attggttctg gcccagcaat gtggttttct cctgtgggcc ggactgatcc 1980 tagcccagcc ctactggctg ggctggttcc ggcccatgat aaaatagatt ttgtttgggc 2040 cgagatcgac ccaatacccc ttggcccgag atcggcccag cccagcccaa ttatgtatta 2100 tatactatgt atattgtatt gtgttttgta ttatttatat ctagatatat acatagaaaa 2160 attaattaat ttcttcgaaa attattccaa aaaatatgtg attttctgca agtttattac 2220 tgtattttga tcaatatcgg tttgtatttt tatactgtaa agatacaaat ccggtattca 2280 aatacccggt tttcgtcaag acacaaaaaa aaaaaaaaaa tattttaaaa aatgttttgt 2340 tttcatgcat acggcctagt ctctccaata tatatatata aatattataa catcatattt 2400 ttcacacaac aaagaaaatt tcaaaacaat atatgtatta gcatgcattt tggctttaat 2460 aaccagttta ttcaagccat gagaactagg ccaatatttc aaaaattcta aaaaaatctt 2520 tttgtcttct tttagtattt gggattacga atttatacgt aaaacgtatt cctgatatta 2580 aaaatatggt tttttttttt ttttttacat agacattaga acggttaggt tttacccgat 2640 aagataagga cctccttatt gaggaggact tttcttgaac catagacgga ccaacaaagg 2700 aaacacaacg agaccttgaa ttttatcaga caactaaaca atgcagctta ccttaggtag 2760 ggcgtatttg gggtgctaat accttccctt tacgcaacca gtccccgtac ccaatctctg 2820 agaccagtta gggttcctag tgaccaaaat actaggtggc gactcccatt ccattttcct 2880 accaacaaaa gacaatattt tcttgtctct ccacatttgc cagatagata ccatacacac 2940 ttcctagatt taaaaagtgg aaaactcgcc gcgacgccgc gcacccgcga 2990 // ID LTR-2_Mad-I repbase; DNA; EDCOT; 536 BP. XX AC . XX DT 26-OCT-2010 (Rel. 15.11, Created) DT 26-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome, consensus. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR-2_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-536 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1999-1999 (2010). XX DR [2] (Consensus) XX SQ Sequence 536 BP; 143 A; 85 C; 151 G; 157 T; 0 other; tggtatcaga gcaggtttga tccttcggga tttaatctgc ttcgggttgg tatctgtttg 60 cttgtttccg ttgtcgttcg tgttcagatt gttagttggt attgattgtt tgcaagaaga 120 aaaaaattgt tcgttcgttt tttgtcccgt gactctgctt ctgcaccttt gaacgccgca 180 gcctgcagga gtatccgcaa gtctgtattg ctgcaaagga aaaaagagga aaaagtagaa 240 tggaatgaaa aaagaaggaa aaaaagggga gtaaaaaaaa aaaaaggaag aaacaagaaa 300 aaattggttg cttgtttgag gcccatgcgg gcaaagggaa aaaaaaaatt tggttggatt 360 ttttgtttgt ttgttcggaa gttggcatcg gcattggtat tggcatcggc atcggcatcg 420 gcatcggcat cggcattggc atcggcatcg gcattggcat tggaatttgg aggcttgcat 480 ccacatctgc ttgttggcaa actcatgtcg tgtaccgcca tgagtttgac gggggg 536 // ID Gypsy-28_PTr-LTR repbase; DNA; EDCOT; 891 BP. XX AC . XX DT 09-DEC-2009 (Rel. 15.02, Created) DT 09-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-28_PTr-I; Gypsy-28_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-891 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 176-176 (2010). XX DR [1] (Consensus) XX SQ Sequence 891 BP; 239 A; 167 C; 194 G; 291 T; 0 other; tgatgtggac cagcccagaa acaccagcaa ggacccatta catgttccaa atggtccaat 60 gactcggtcc aagacaaagg cattgaaaga ggcattgaat gcattggttt tgaatgtttc 120 aaccaagtca gaattgaaag gtccattaga gtatcaagag gagaccctag tacatcttat 180 ccatgtgcaa gaggggtcca acacaacctt atttgggcca tgaggtgagg acaacaaagg 240 aaacaaaaga atcctactac aacttggaaa caacatgggt ggctaccttt tccttttgtt 300 tctaggatta atgggctgca tggaaggcta taaataagcc ttgaatcagt tctataatat 360 tttacttctc ttcttctcat gacagaacat ggatttaata ttatgggctt tattttattt 420 tgttagctac agcccaaggc ttgtttgggc ttaattaata ctttgttttc agctaggatc 480 caaggcttgt ttggattagg ttatgggctt ttcagtttag ggttttgggt cagtttttaa 540 gtgggcctca tttaagtcca cataaggggt ccattagggt taatttttca agaactattt 600 aaactcatgt aagcctaaat ttcggcagct ttgatgaata atacttctga atttttcagt 660 tttaacgtgt gagagtgatt cttgcattct tcagttcttg aacgaactga atctgactta 720 tcgaagatta actggcttcg tggcgtcatt ctacttcatt ccaatagtgt tggtgccttg 780 gggcaggttt ccattgtgtc acactcctat cagacctatt tcggctttcc gggatcagat 840 ctcaatcttg attgtgggtt gcgtgaccac gtgatcacga ggttcgcatc a 891 // ID BoSB10A repbase; DNA; EDCOT; 159 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; BoSB10A. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-159 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 159 BP; 23 A; 50 C; 50 G; 36 T; 0 other; caagagctct tggtctagtg gtattggaac tccggctgga gtgcccgccc tgggttcgag 60 tcgccttggc caccttcccc gcctataacc gtgcgtgccc ggatggaagg cctcgtgggg 120 attagtctgg gcttaccgcc tgggaacccc acggtcatc 159 // ID Gypsy-25_Mad-I repbase; DNA; EDCOT; 4637 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-25_Mad_; KW Gypsy-25_Mad-LTR; Gypsy-25_Mad-I. XX NM Gypsy-25_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4637 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1744-1744 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [3508-3738] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(445..1569,1573..2856) FT /product="Gypsy-25_Mad-I_1p" FT /translation="MASFHMENEALQWFQWVNCVKNYPKWEDFTKIFCREF FT GSPDLVDCTENLVKLRQTGLLRDYIMEFRRLANRTVEMTPRILKSCFIGGL FT KPEIRHDVKILRPFDVHEAIAYSQQVDAKLAELKVKSFSRNPFPTSQFKPT FT HLSDITNIPKPESSTRNDNFRRLTAAEIEFRRKNRLCFNCDEKFSKDHVCA FT GPKCQILLIDVYENGHLIEHESDDTDEPEVTACAVYGMPAPKSIRTMKVNG FT LVLNCPAIFLIDSGSSHNFIDIALVKQLRGHLDTTHPFSVKIANGGSLTSP FT GCLAQVSVRIQNYAAVLDFYALPLGGCDIVLGVQWLRTLGPVLWDFEKMVM FT QFVVGTTTFSITSPQVQDPQSISSLQMDRLLNDHCLGAALFVLQLSEETIL FT PSNPPQLPSPQEQDLQVLLNQFQSIFQPPSGLPPSRSHDHRIPLIEGCKPP FT SARPYKYGPFQKTEIEKCVQELLDSGFIRPSHSPFSSPVLLVKKKEGTWRM FT CMDYRALNLLTIKDKYPIPLIDELLDELFGAKYFSKLDLRSGYHQIRMHPK FT DIDKTAFRTHEGHYEFLVMPFGLTNAPASFQGLMNEIFKPYLRKFILVFFD FT DILIYSASWELHLHHLNLALSLLRDNHLFVKLSKCAFGRTQIEYLGHTVSD FT KGVAADPSKLKAIAEWPKPASVKALRGFLGLTGYYRKFIPHYGRICGPLTP FT LTKNDGFHWTPAATAAFQELKSAMMSPTVLALPDFSKPFIIESDASGTGIG FT AVLQQEGRPIAFTSQSLGPKNQALSTYEREMLAVIHAVKKWQSYLLGNHFI FT I" XX SQ Sequence 4637 BP; 1276 A; 947 C; 967 G; 1436 T; 11 other; ttggtatcat cagagccagt cacgatcttt catcccttct ctgtgccgta tgactcgtgc 60 ttctacaaag aaagccatgg attcacagaa tcaacttgct gcaataaaca acactctcaa 120 catcctgctt cagaggtttg acgccatgga agaacgccaa gattcatctg acgctcgatt 180 tgagaaattt catcgcgatt ttgtggcgaa atgtgatatg ggttttcatg tggactcctc 240 agatgcgacc ccttcagatc ccaatttgca tgaagatgca ggaaatcagc aattcaatcg 300 ccaagattca ggttttcacc caagacctcc attggtgaaa ttggattttc ctcgatttca 360 tgaaggtgat gaccctctcg gctgggttta taaagtggag cactacttcg attacttcac 420 cattccggca gataagaagg ttcgatggcc tcattccaca tggaaaatga agcacttcag 480 tggtttcaat gggtgaattg tgtcaagaat taccctaaat gggaagattt cacaaagatt 540 ttttgtcgcg aatttggatc acctgatctt gtggattgca ctgagaattt agtgaagctt 600 cgccaaactg ggttactcag ggattacatc atggaattcc gtcgattagc gaatcgtact 660 gtggaaatga ctccaagaat cttaaaaagc tgcttcattg ggggtttgaa accggagatt 720 cggcatgatg tcaagatcct tcggcctttc gatgttcatg aagctatcgc ctattcgcaa 780 caagtggatg ctaaattggc agaactcaag gtaaaatctt tttcaagaaa tccattccct 840 acatcacaat tcaagcctac tcatctgtct gacattacca atataccaaa acctgaatct 900 tcaacacgaa atgataattt tcgacgacta acagctgcag aaattgagtt tcgaagaaag 960 aatagattgt gtttcaattg tgatgagaaa ttttctaaag accatgtgtg tgctggtcct 1020 aaatgtcaaa ttttactgat agatgtgtat gaaaatggcc atttgattga gcatgaatct 1080 gatgatactg atgaacctga agttacggct tgtgcagttt atggtatgcc tgctccaaag 1140 tctattcgaa ctatgaaagt caatgggttg gtgttgaatt gtcctgctat ttttttgata 1200 gattcaggta gctctcacaa tttcattgac attgctttag taaaacagtt gaggggtcac 1260 ttagatacta cacatccatt ttctgttaaa attgcaaatg gaggttcact caccagtccg 1320 ggttgtttag cacaagtctc tgtgagaatt cagaattatg cagctgtgtt ggatttttac 1380 gctcttcctt tgggagggtg tgatattgtt cttggagtac agtggttaag aacgttggga 1440 cccgttttgt gggattttga aaaaatggtt atgcagtttg ttgttggcac tactaccttc 1500 tctatcacaa gtcctcaagt tcaagatcct cagtcaatat cttccttgca aatggataga 1560 ttactcaatm atgatcattg tttgggagct gcactatttg ttttacaact cagtgaggag 1620 actatacttc cttccaatcc tccgcaactg ccttctccac aagaacaaga tctgcaggtt 1680 ttgttgaatc aatttcagtc tatatttcaa ccaccatcag ggttgcctcc gtcacggtca 1740 catgatcaca ggattccttt aatagaaggg tgcaagcctc ctagtgcaag accctacaaa 1800 tatggtcctt tccaaaagac tgaaatcgaa aaatgtgtcc aagaattgct agattctggt 1860 tttataagac caagccatag tcctttttcc tctccagttt tgttggtgaa gaaaaaagag 1920 ggtacttgga gaatgtgcat ggattatagg gcactcaatt tgttgacaat taaagacaaa 1980 tatcctatac cattgattga tgagctctta gatgaactct ttggtgccaa gtatttctcg 2040 aaactggatc ttaggtcggg ctatcaccag attcgtatgc atcccaagga tattgataaa 2100 acggcatttc gaactcatga gggacattat gagttccttg ttatgccatt tggcttaact 2160 aacgccccag catcctttca aggtctaatg aatgagattt tcaaacctta tttgcggaag 2220 tttatcttgg tattttttga cgatattttg atatatagtg cttcttggga attacatctc 2280 catcacttga atcttgcttt gagtttactg cgagataatc acctctttgt caagctctct 2340 aagtgtgcat ttgggagaac gcaaattgag tatttggggc atacagtttc tgacaaagga 2400 gtggctgctg acccttcgaa attaaaagca attgcagagt ggcctaaacc ggcttctgtg 2460 aaagctttaa ggggtttttt aggcctcact gggtattaca gaaaatttat tccccattat 2520 ggcagaatct gtggtccttt gactccactc actaaaaatg atggatttca ttggacccct 2580 gcagcaacgg ccgcatttca ggaactcaag agtgccatga tgtctcctac agtcttggct 2640 ctcccagatt tttcaaaacc cttcattatt gagagtgatg cttcaggtac gggtatagga 2700 gcagtgttgc aacaagaggg taggccgatt gcttttacaa gccagtcttt aggaccaaag 2760 aatcaggctt tatcgactta tgaaagggaa atgttagccg taattcatgc agttaagaaa 2820 tggcaatcgt atctccttgg gaaccatttc attatatgaa cagatcatca cagcctcaag 2880 tattttctgc agaatcgtgc taattctcct tttcagcaaa aatgggtttc gaaattactt 2940 ggttttgatt acgaaattca gtacaagaaa gggagtgata acaaggcagc agatgctttg 3000 tctcgaatgt tctcagattc gaggattcca cctgacacta cttcaaccac tctggatgtt 3060 tctgccacga atagtgttgc tcctaattcc gtgcttccgg gagtacttgg cagtgaactt 3120 actgccatat cttatcctta tatgtcttgg ctcgatgacc ttcgccgaca tgttgagcaa 3180 gatgattgga tcttagccaa atcacaatca gttttgaata aaacttcgga ttctgttcca 3240 ttgcaattct tgagatatca ctttgctaat ggttttttga gatacaaaaa taggattgtc 3300 ctaagtccta caagttcttg gagggcgaaa ttgtttgaag agtttcactg cacacctagt 3360 gcaggtcatg caggttttct taagacttac aaacgcatct ctaagtcttt ttattgggaa 3420 ggtatgaaga acaacatcag ggatatggtt gctggttgtg atatctgtca gaaaaacaag 3480 tatgagtccc ttgctcccgc aggactactg aatcctttac ctattcccca aagagtgtgg 3540 actgacatat ccatggactt catcactgga cttcctcctt gcagaggcaa atctgtcata 3600 tttgttgtgg ttgaccgact ttcaaaagct gcacactttc tatccatgtc tcatccttat 3660 actgctcact ccgtagctca gcttttcatc gatcaagtgt tcaaactaca tgggatgcca 3720 acctccattg tctcagattg agatcccatt ttcatcagct ctttttggaa agagttcttt 3780 aaacttcaag gctccagatt gtgtcttagt tcaggatttc acccccaaac tgatggacak 3840 actgaggttt taaatcgatg tttagaaaca tacttaaggt gtttttgtag cttacagccc 3900 aagcaatggt tgaaatggct tccatgggtg gaatggagtt acaatacatc ttatcatact 3960 gcaacgaaac ttacacccta tgaagtagtg tatgggcagt ctcctccaca tattccaatc 4020 tatgaatctg gaactacaaa gattgactcg gtggatcagt gtttacaaga tcgaactcgg 4080 attttatctc ttctcaagac caatctggaa gcagctcaag taagaatgaa aagtcaggcg 4140 gataaacatc gaactgagag gtcttttgaa gttggtgatt atgtgtatct caggttggta 4200 ccttaccaac aaaagtcact wgctctacat ccttwtcata aattgcatcc tmggttttat 4260 ggtccctttg aaattcttac gaaggtsgga cctgtggcct acaagttaag gttgccacct 4320 cattctaaga ttcacccagt tttccatgtt tcttgcctca agaaacaact gggcacatca 4380 gcctctacta ctataccgct wccatctgct atgatgcggg tctgattcaa gatgaaccaa 4440 cagctatcct ggatcgacgg gtattaaaca tgggtcgact cttgtcaccg aagtcttagt 4500 gcattggcgg aatcatcatg ttgcmgatgc atcttgggag gtttggatga tttgaaagct 4560 cgatttcctg amttccagcc ttgaggacaa ggctaatttc aaaggggggg gtaattgata 4620 ggaatctaag kgatwaa 4637 // ID MSAT-105_GM repbase; DNA; EDCOT; 105 BP. XX AC . XX DT 07-DEC-2010 (Rel. 15.12, Created) DT 07-DEC-2010 (Rel. 15.12, Last updated, Version 1) XX DE 105-bp minisatellite in Glycine max. XX KW MSAT; Satellite; Simple Repeat; minisatellite; retrotransposon; KW soybean; MSAT-105_GM. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-105 RA Laten H.M., Mogil L.S. and Wright L.N.; RT "A shotgun approach to discovering and reconstructing consensus RT retrotransposons ex novo from dense contigs of short sequences RT derived from Genbank Genome Survey Sequence database records."; RL Gene 448, 168-173 (2009). XX RN [2] RP 1-105 RA Mogil L.S. and Laten H.M.; RT "Retrotransposon-associated minisatellites in Glycine max."; RL Repbase Reports 10(12), 2178-2178 (2010). XX DR [2] (Consensus) XX CC Consensus sequence (average identity 96%) from 100 copies of a CC 105-bp minisatellite sequence found in tandem arrays on all CC soybean chromosomes. Over 10,000 monomers in the genome. Many CC arrays located in noncoding regions of several different families CC of LTR retrotransposons. XX SQ Sequence 105 BP; 19 A; 25 C; 24 G; 37 T; 0 other; tgtcataccc taatttcgtc cggggacctt tgcttgatga catgcgacct ttctttggtc 60 cttgtgaggt gcttggcacc catcattagg caatttgtga aattc 105 // ID Copia-98_Mad-I repbase; DNA; EDCOT; 1291 BP. XX AC . XX DT 01-NOV-2010 (Rel. 15.11, Created) DT 01-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Copia-98_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1291 RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-1291 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1981-1981 (2010). XX DR [2] (Consensus) XX SQ Sequence 1291 BP; 367 A; 204 C; 379 G; 341 T; 0 other; attggtatca gagctttgtt ggaagctttg gttcattgac ggttcagatt tgttattcac 60 catgatgact acaaacatgt cattttcagt tgagaagttt aatgggaaag gcagttttac 120 tctttggcag atgagagtaa aggatgtctt gactcaacaa ggcttggcta gagctttgaa 180 gggaaaagat gggaagcctc aagaaatgac agatgaccag tgggaggagc tggaggcgcg 240 ttgtgttagc acgattcgac actgtatagc tgataacatt atcaataatg ttatggatga 300 agattctgcg cctgcacttt gggagaagtt ggaaaaactc tatattgcta agagtttgac 360 caacaagtta catctgaagc ggaagctgta caagctaaag atggatgaag gcgggaatct 420 catggaccac atgaatgtgt tcaacggata cttggatcaa ttgcggaaag ttgatgttaa 480 ggttgaggaa gaagacaaag ccctcttact tcttacctca cttccagatt cgtatgaaaa 540 tcttgtgaca accttactgc atggaaaaga tacagtaagt ttggagcagg tgcaggcttc 600 tttggtgtct tatgatacac aaaagaagaa gaccattgtt gatggtgggc acgagactgc 660 tttagctgtt caaggttgga atcgtggaag aaaattggga ggaggatctg agagagacaa 720 caggttcaaa tccggttccg gaggcaaggg tctacaatgc tacgactgca aagaattcgg 780 gcataaaaag aaaaattgtc ctttgagaaa aagaaaggat gatcttggtc cgggttgtag 840 caattttgtg gcggaagact tcgagtatgc cctctaggta ctcgaagcaa cacttctcct 900 ggtgatgttt agtctcaagt gttgcagggg ttttgcagca ggtggagcta tgggattcac 960 aggtgatgag atggtcctga aggaggagga agtgtgggaa tatttgtctg gctcgacggg 1020 ttgttgctgg aaacgggtgc actgacgagt ttccaggttg cagacaatga agagggggaa 1080 aacctgctgg aggagacgag gatgtgtcga gatcctgtct gaagctaaat ggtgattttt 1140 agcttgcagc agctgcacat gcattggcag tgactgaatc ggaacaggac caacgaggtt 1200 gattcagggt gtgtatgctg gtacgtaagg ccaatggact ttggtgatgg gtgcaaggat 1260 ttttgcacgg tatattcgcc aaggtggaga t 1291 // ID Copia7-VV_I repbase; DNA; EDCOT; 4149 BP. XX AC AM466606; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia7-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4149 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4149 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 747-747 (2007). XX DR Genbank; AM466606; Positions 16533 12385. XX CC Positions [1629-2012] - Integrase core CC 'TGTT' target site duplication CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 1884..4148 FT /product="Copia7-VV_I_1p" FT /translation="MFHARVPLSLWDEAFSTAVFLINRLPPPSLAGKTPYE FT LLFGKQPDYSMLRTFGCLCFPYLRDYSPNKLSPKSTPCVFLGYSTLHKGFR FT CLDRKTHRVYVSRHVQFYEHTFPYNGDSVQNLPSNIDYIHFSESQECVSSS FT SNVSTSDSLPSPSFSNSLCLPCNDIPHLSSTSSPGLQVPLDEDSLLDSVAT FT DSTTPSPISSSPRVTTSNHPMITRGKAGIFKPRLYHAMHISSSSQLFQAFL FT ALKEPRGFKSAAKHPEWLSAMDDEIHALKKNDTWVLVPRPQHHNVVGCRWI FT FKTKLHSDGSIERHKARLVAQGFSQVHGLDFGDTFSPVVRPATVRIILSLA FT VTSGWRLHQLDVKNAFLHGFLNEEVYMEQPPGYTDPQFPQHVCRLKRALYG FT LKQAPRAWFHRFSSFLLKHGFHSSQADSSLFFYHSSLGTVYLLLYVDDMII FT TGSTPSLVHTFITRLSNEFSMKDLGDLHYFLGVEVQANEKGLFLSQTKYAL FT DLLQRASMIDAKPISTPFVVGQHLSAEGTLFSDPTLFRSLAGALQYLTITR FT PDLSFSVNSIFQFMHAPTEDHFRALKRILRYVKGTAHHGLQLHKQSTRDLL FT GYSDADWAGCPDTRRSTTGYAIFFGANLISWSSKKQSTVSRSSAEAEYRSL FT AVATADIAWIIQLLRDLHVTLSVPPKILCDNQSAIFMAVNPVTRPRSKHIA FT IDYHFVRELVDKGTLKIDFVPSHLQLADSLTKGVTKPQFYLFRSKLSVLPS FT TTLT" XX SQ Sequence 4149 BP; 953 A; 1007 C; 766 G; 1422 T; 1 other; aacaccttta tggtatcaga gcaaggtttc tttcgattct gaccatggct gtttcgtctt 60 cttcacctcc tactcttccg ctcaatacaa tggtgcatat gctcaccatt aaactgacct 120 cctccaatta tctattgtgg agaaatcagt ttgttcctct gctaactagt caagagcttt 180 ttagttattt ggacggtagc atcacggctc cttctcccat gattactgcc tctgatggca 240 ccccaaaatc caatcctgca tatacctctt ggctgcatac cgatcagaca ctgctcagtt 300 tactctattc ttctctcaca gaggaatcta tgagtgaggt actgggtttc cgtcactccc 360 acgaggcttg gcatgcgctt gaagtctcat tttcacaccg atcaaagact cgcgaactgc 420 aactaaggat gaactccagc tgatgcacca tggctctcag tccattgttg agttttctag 480 caccttcaaa ggcctttgcg atcaactggc tgctattgga cgtcccattg acgacacgga 540 taaagtccac tggtacctat gtgcattggg acccgactac aagatctttt ctaccaccat 600 gatgtcacaa cttcctctac catcctttgc tgaaattgtt ccgaaagctt tgagccatga 660 aatctttgaa cggtcagtct cccattcatc ttccaactct gcttattttg tgcagcaaac 720 ttccaaagtg gctggtcaca agcaagtgaa gcatcggtct tcagcttctc ctacaccgtt 780 tgccaactca aagtcattat ccaactcctc cgtccactgt cagttgtgcg acaaagaggg 840 ccacttggct aaacgttgct ggaatttcct gaaactcaag aagaagcaat cggctaacct 900 tgctgaggct ttttctgcct actcgattca ggattttaat gactctgaat ggttccctga 960 ctctggtgca acgtcccaca tgactagtga caccgaaggt gtgaatcaac cggatgtcta 1020 ttctggtaat gaacgtgtca tggttggcaa tggtcagtcc ttagcaatct ctcacactgg 1080 ttccatttca tctcttattc cgtctagtcc tcttctttta tctaatgtct tagttgttcc 1140 tggaattaag aaaaatctta tttctattag ttwacctact aaagacaata attgttgtgt 1200 tacctttttt tcctttggtt ttaccataca ggatcgggtc acaagagtgg tactgggagt 1260 cggaagatgt gaaaatggtc tctacgtgtt ggatcgtcgt catcatgcct tagtgtccac 1320 tacttcttca ccgcgagcat ctgttcgttt atggcatact cgccttggtc atccacatta 1380 tcgtactgtt gcttctcttt ctaaattagg atttatttct tgtagtaata aattgtgaac 1440 aatgattctg aaatttgtgt tggttgtaga ctcggcaaaa gccaccgttt acctttttct 1500 ctaaataatg aacgttgtgc tatgcctttt gatcgtttac actgtgacct atggggtccg 1560 tcaccagttt cttcttttaa tggatataga tactatgcgg ttttcattga tgattgtact 1620 agatttagtt ggatatttcc ttaaaacaca aatctgattt ctttgataat ttcatcaatt 1680 tacaacattt tattgagaca cagttttcca ccaaaatcaa atcatttcag tgtgatggtg 1740 gaactgagtt tactaataat aagtttcgct ctcatttgca ttcatgtggc attgatcttc 1800 gtctggcatg tccttacact cctagtcaaa atggaattgt cgaacgtaag catcgttatg 1860 tcacagaaat aggtcttact cttatgtttc atgctcgtgt gccgctctcc ttatgggatg 1920 aggctttctc tactgccgtt tttctcatta accgactccc gccaccatct cttgctggca 1980 aaacacctta tgagctcctg tttggtaagc aacccgatta ttctatgctt cgtacttttg 2040 ggtgtctttg cttcccttat ttgagagatt actcacctaa taaattgtct ccaaaatcta 2100 ctccttgtgt ctttttaggt tacagtaccc ttcataaagg atttcggtgc ttagatcgta 2160 agacacatcg tgtctatgtt tctcgacatg tgcagtttta tgaacatacc tttccctata 2220 atggtgattc tgtgcaaaat ctgccgtcta acattgacta tattcatttt tctgagtctc 2280 aggaatgtgt ttctagttct tctaatgtta gtacttcaga ttctttgcct tcaccatctt 2340 tctcgaattc actatgtctg ccttgcaatg atattccaca cttgtcttca acttcttctc 2400 ctggtctgca agttcctctt gatgaggact ctctcttgga ttctgttgct acagattcga 2460 ccactccttc accaatttcg tcctctcctc gtgtgaccac ttccaaccat ccgatgatta 2520 ctagagggaa agctggtata ttcaaaccac ggttgtatca tgctatgcat atctcatctt 2580 cttctcagtt gtttcaggct tttcttgctc tcaaagagcc acgcggcttc aagtctgctg 2640 caaaacaccc tgaatggctt tcggctatgg atgatgaaat tcacgcactg aagaaaaatg 2700 atacgtgggt tcttgtacct cgtcctcagc atcataatgt ggttggctgt cgctggattt 2760 tcaaaacaaa gcttcactct gatgggtcta ttgagcgtca taaggcacgt cttgtggctc 2820 aaggattttc tcaagttcat ggtcttgatt ttggtgacac ctttagccct gtggtgcgtc 2880 ctgctacagt cagaatcatt ctatccttgg ctgttacttc tggatggcgt ttacatcagc 2940 tagatgttaa aaatgccttt cttcatggct ttctcaacga agaggtgtac atggaacaac 3000 cgcctggcta cactgatcca cagtttcctc agcatgtttg tcgtctaaaa cgtgctcttt 3060 atggcttgaa acaagctcct cgagcttggt ttcatcgatt tagctcattt ttgctcaaac 3120 atggttttca ctctagtcag gctgattctt cgttgttttt ctatcactcc tcgcttggta 3180 ctgtttactt acttctttat gttgatgaca tgatcatcac tggaagtact ccttctttgg 3240 ttcacacctt tattactcgg ctttccaacg aattctccat gaaggatttg ggtgatcttc 3300 attattttct cggagttgaa gtccaagcta atgagaaggg tctatttctt agtcaaacaa 3360 agtatgctct tgatctcttg caacgtgctt caatgattga tgccaagcct atttctacac 3420 cttttgttgt tggacagcat ctatccgccg aagggacttt attctccgac cctactttgt 3480 ttcgttctct tgccggtgct cttcaatacc tcacaatcac caggcctgat ttgtccttca 3540 gtgtcaactc cattttccag ttcatgcatg ctcccaccga ggatcatttt cgtgctctca 3600 agcgtatctt gcgctatgtt aaaggcactg ctcatcatgg tctccaactt cacaaacagt 3660 ccactcgtga tcttcttggc tactctgatg cggactgggc tggatgtcct gatacacgtc 3720 gttctactac cggctatgct atcttttttg gagctaattt aatctcttgg tcttctaaga 3780 aacaaagcac tgtctctcgt tcaagtgcag aagccgaata tcgctcctta gctgttgcta 3840 ctgctgatat tgcatggatt attcagttgc ttcgggacct ccatgttaca ctctcagtgc 3900 cacctaaaat tctttgtgac aatcaaagtg caatttttat ggcagtcaat ccggttactc 3960 gtcctcgatc caaacatatt gcaatcgact accattttgt tcgtgaactt gttgataaag 4020 gcactttgaa aattgatttt gttccttccc atctacagct tgctgattca ctgaccaaag 4080 gagttaccaa gccacagttc tatctctttc gaagcaagct cagcgttctc ccttctacca 4140 cgctcacct 4149 // ID Gypsy16-PTR_LTR repbase; DNA; EDCOT; 346 BP. XX AC scaffold_465; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy16-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-346 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-346 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 311-311 (2007). XX DR Genome; scaffold_465; Positions 41498 41153. XX SQ Sequence 346 BP; 100 A; 51 C; 73 G; 122 T; 0 other; tgataaacca cgaaggtcta atagggtgcc tatcaagaat ccaagatatg agggttgagc 60 tgggacacgt attatgagga ttcagctgtg ggcaattgct gattttgttt aatttgcttt 120 ttttgaattg gtcaataaag ttagaaggaa taagtcaatt agtgggggct atttctctgt 180 caactagccg ttccacgtcc ttctaattag cgaagtagtt atgtttttat ttgtatttaa 240 atcattgttt ccagcaagtt gagacaagaa aagtattaca aggtttattc tcaccttaaa 300 cagagtattt tcttattttc ttaaaggctt tgactgggac ctaaca 346 // ID Copia-8_Mad-I repbase; DNA; EDCOT; 4675 BP. XX AC ACYM01089008; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-8_Mad_; KW Copia-8_Mad-LTR; Copia-8_Mad-I. XX NM Copia-8_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4675 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1349-1349 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01089008; Positions 4029 8703. XX CC Positions [2294-2545] - Integrase core CC 'GGCGT' target site duplication CC LTRs are 90% similar to each other. XX FH Key Location/Qualifiers FT CDS 3056..4675 FT /product="Copia-8_Mad-I_1p" FT /translation="MQTSSKFGIFKKKQVFHAQIHSASDTEPSSFNIASKF FT SHWTNAVNEEMSALHQQHTWTLVPLPADKNLVGCKWIYKIKRHFDGSIARY FT KARLVAKGVSQEAGLDYYKTFGLVVKPTTVRLMLSLAATKGWKLKQLDVKN FT AFLYGFIEEEVYMSQPPGYIDKTHPDYVCKLQRSLYGLKQAPRAWNERFTK FT FLLSLGFKSSYADSSLFVRHDGYSIVILLLYVDDIILSGDNSDQIQCVISQ FT LTTEFDMKDLGILHFFLGLQIEYQSQGLFVHQSKYVKELLVKSDMFNCKPC FT LTPCHPNKKLLNHGSSVYLDPKTYRSIVGALQYLTFTRPDIAYSVNQVCQF FT IHSLLESHFVAVKRILRYLKGTLDWGICFRPGSLSLKAYTNADWAGDPNDR FT RSTTGFVIFLGNNPVSWSSKKQHTVSRSSTEAEYRTMATTTAELMWLQQLL FT KDLHIDTSLPPLLHCDNTSAMSLATNLVLHSKEKHIEIDCHFVRERVQQGT FT ISLQFVASVDQYADILTKGLCSPLFSAHCSNLMLGQSQHKIEGE" XX SQ Sequence 4675 BP; 1231 A; 909 C; 891 G; 1642 T; 2 other; tggtatcttc gccgatcaag gcttgcgcca tcggttgatg atcctattgc ttccgctcat 60 ttgatttttc gtgttgtttg atcggagtgc tgcctttgtt gctctgtaac aacgtctaat 120 cgttagagtc ggtggagtcg ctggtgtttg tcggtagtga ttgtcggtga agtcggtgtt 180 gtcgtcgtcg aagttcctca gaaaccctag tgtttggggg atttattgcg gtgttgaatc 240 gtcagagtta cgaaggtggt attcttctga ttgtttcatg attcttgatc ccttgcctct 300 tgattcttgt tcgtctaaac cctaattttt gggaattgtt gttcatgatt cctactgtat 360 tatgtgtttc tacgatctgc ctatatgtgc catacttgat ctatttgtat cttcacaatg 420 gttacctctg ctcagttaat gcttacacaa tcgcctagtg cttctctgat tccaagtgtg 480 agtaatactg ttactgtgaa gttagatgac tctaactatg tgacttggaa ttttcaattg 540 gagttgttgt tagatggttt catggttttg ttgatggatc aattccgtgt cctaccaaat 600 ttgttgattc tgaatttgag ggggaggttg ataatccaat gccaataatc tctgatgcat 660 acaaggtgtg gaaaattcat gataaagcat tgatgactct tcttattgct actttgtcca 720 ctgctacttt atcttgtgtg attggatgtc agagttctca agaaatgtgg cttagtctta 780 gagaacggtt tgcgaacatg actaagacta gcatatttta aatgaaaatt gatttgcaaa 840 atatatagaa aagatctaaa tcaattgatg agtatcttca aagaattaag gataccagag 900 atcaacttgc tactgttagg gtcttcatat ctgatgagga tattgtgatt gtggctcttc 960 gaggcctccc ttctgagtat aacaccatca agtctgtgat tcgtggtcgt gaaactattg 1020 tgtccttgaa agagttacgt tcatagctta gagctgagga gtccactttg caagaaattt 1080 caaagcaagt tcctttgatg tttgcaatgc tagctcaatc ttccaaatct ggcacacata 1140 tgggtagctt ttctgcttct tcatagtttc atgaatccca gtcacttcaa caaatgcctt 1200 ttccaaatca gttctcccaa ctgcctgtgt ctggaccatt tgcttttgtg tctcaaactg 1260 gtacagggtc ttacaacaat ttctgaggaa acaattggaa gaacaaaggc aaaggcaaaa 1320 agtttttatt cggattccaa ccttctcaat cttaattctc aggaagtccg tcatatcctc 1380 aacaatttca gtctggtgtt caaccttcag gacaacaaat gtcatcacct caggcttatc 1440 aaccttttta gaaataccaa atttgtgata ggaaagggta ttctgctctg aattgttatc 1500 aaaatggatg tcaaatctat catcgtgttg gacatactga tgctacatgt tgtttgcaag 1560 ctacagatgt ctttgtattg tctcaaacaa gctccaagag cttggaatga aaggttcacc 1620 aagtttctgt tgtctttggg attcaagttt tcatacgcag atccatctct ttttgtcaga 1680 catgatggtt attctattgt catcctcctc ttatatgtgg atgatataat acccactggt 1740 gacaattctg atcaaattca gtacttcatg ttcctcagtt gtcacaacat ctgcttcaat 1800 gaatcagttg tgtcgtgata atcattgcag atgtatcatt gatgattctt ctatttgtgt 1860 gcaggacaag gtcacccaaa agactctatt tcaagggttg agtaacaatg tgttttaccc 1920 tattccagtg tttaaacttc cacctcattc tccagtagca tacttagatc aaaaagtttc 1980 ttctactttg tggcactgta ggttgggtca tccaattaat tcagttgtta aaatagctct 2040 tagtaagtcc tctatcccct ttacttgtaa ttcatcacct cacacttgta cagcttgctt 2100 ggaaggcaag tataatcact taccttttga ggtcattcat tctgatgtat ggggtcctgc 2160 acctcaaatg tctatagagg ggtatagata ctatgtgtct tttatcgaag aatgtactcg 2220 gtatacttgg atttttccac tcatcaataa agctgttgta tttgctgtat ttggtgtttt 2280 tgtgcaattt tagcagtttc aagcttttct tcacaataaa ggtatccttc ataaaaaatc 2340 atgtccatat accccagctc aaaatggttt agctgagcgc aaaaatagac atgtcattga 2400 gagtgctatt actttacttc aagcagcctc tttgtcttct aattttttgt atcatgggtg 2460 tgccattgct acctacttaa ttaataggat gccaacacct gttttgggta tgcaatctcc 2520 ttttgagtcc ttatatcatt ctccatctcg tttagatcac ttgaaagtgt ttagttgtgc 2580 gtgttaccct tctctgaaac cgtaccgatc caataaactt gaacctaaga ccactatgtg 2640 tattgktttt ttgggtatac tgcttattat aaggggtata tttgttattc tctcaagaaa 2700 ctccttgttt ccagacatgt tcttttttat gaagcagtgt ttcctacttt aaaacccgat 2760 gttacaactg aacccaaagt tgctgtgtct aattaagttg ttcatccaaa tacctttgtt 2820 cttactccag tcattcccat acctttacca gttgtttttt cacatagccc ctgcatgttc 2880 ttctattact cagacccwtc tttgcaatat tggtgatctt gtccctactg ggtattcttc 2940 aactctgagg cctaattctg agttctcagc tgatttagaa ttacatccac ctactactac 3000 ttcacaagtg tcagagcttc aacttgtgca tatttcatct tagaattctt atcctatgca 3060 aactagctca aagtttggga tttttaaaaa gaaacaggtt tttcatgctc aaatacattc 3120 tgccagtgac acagaaccat cttctttcaa tattgcttct aagttctctc attggacaaa 3180 tgctgtgaat gaggaaatgt cagcacttca tcaacaacat acttggactc ttgttccttt 3240 acctgctgat aaaaatctag taggatgtaa gtggatatac aagatcaaga ggcacttcga 3300 tggatctatt gccaggtata aggccagatt ggtggccaaa ggggtttcac aggaggcagg 3360 tcttgattat tataagacat tcggtcttgt tgtcaaacca accactgttc gattgatgtt 3420 atctttagct gcaacgaaag gctggaaatt gaagcaacta gatgtaaaaa atgccttttt 3480 atatgggttt attgaggagg aagtttatat gtctcagccc ccaggatata ttgacaagac 3540 acatccagac tatgtttgca agctacagag gtctttgtat ggtctcaaac aagctccaag 3600 agcttggaat gaaaggttca ccaagtttct gttgtctttg ggatttaagt cttcatacgc 3660 agactcatct ctttttgtca gacatgatgg ttattctatt gtcatcctcc tcttatatgt 3720 ggatgatata atactcagtg gtgacaattc tgatcaaatt cagtgtgtca tctctcaact 3780 aaccactgaa tttgatatga aagacttggg aattctccat ttttttctgg gactacagat 3840 agagtatcaa tcccagggac tatttgttca tcagtctaaa tatgtcaaag agttattggt 3900 taagtctgat atgttcaatt gcaaaccatg ccttactcct tgtcatccca ataaaaaact 3960 attgaatcat ggtagttcag tttacttaga tcctaagacg tatagaagta ttgtgggagc 4020 tctacagtac ttaactttta ctcggcctga tattgcatat tctgttaatc aagtgtgtca 4080 gtttatacat tctcttttag aatctcactt tgttgcggtc aagagaatac tgagatatct 4140 taaaggtact ttggattggg gtatttgttt tagacctggg tctttatctc ttaaagctta 4200 cactaatgca gattgggctg gggatcccaa tgacagacga tctaccactg gttttgttat 4260 atttctgggc aataatccag tttcttggag ttctaagaaa cagcacactg ttagtcggtc 4320 atctacagag gctgaataca gaacaatggc aacaactact gccgaactta tgtggctaca 4380 acaattactc aaagacttac acattgatac ttctctacct cctttacttc attgtgataa 4440 cacctcggct atgtctttgg caactaatct tgttttgcat tccaaagaaa aacacataga 4500 gattgattgt cactttgtga gggagcgtgt tcagcaaggc actatttctt tgcagtttgt 4560 ggcttctgtg gaccaatatg cagacattct caccaagggt ttatgttcac cattgttttc 4620 tgctcattgc tctaatctta tgcttggaca atcccagcat aagattgagg gggaa 4675 // ID MuDi_MT repbase; DNA; EDCOT; 820 BP. XX AC . XX DT 07-DEC-2006 (Rel. 11.12, Created) DT 07-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; TSD; Inverted; repeat; KW MuDi_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-820 RA Shankar R. and Jurka J.; RT "MuDi_MT: A putative non-autonomous DNA transposon from barrel RT medic."; RL Repbase Reports 6(12), 634-634 (2006). XX DR [1] (Consensus) XX CC The sequence has 85 bp TIRs with 9 bp TSDs flanking both termini. XX SQ Sequence 820 BP; 253 A; 160 C; 146 G; 261 T; 0 other; gggagcccct aatatggacc tcaatttaaa gggaccattg gtgaaccttt gttacttact 60 tactatagcc ggtcactatc ttttatgttt tgttttgagg cttaattact ggatttaatt 120 tcatcttctc tctttacatc tcttctctct ggttcatgtc aaagtctagt ctatgctggt 180 gaacaaacct caaacctcaa ctatccacct tcaatctgtc cattgtcgat tcgtttccta 240 attactcgga ttaccctttg tgattatgaa caccgtccta ttttgcccat tcctttatac 300 acgtcactct tagtgaatgg gtcaatcctc ttcatttgtg tgagtgtttc taattagatt 360 tgtctctagg agagtactag taatctgttg ggctattttg tcatcaacaa caacaaacaa 420 ccacaatgtc acatttgtcc ctttaactcc cttcacccaa aagcttcaaa tttcaaccac 480 aactacaaaa actacaatca cctcagatat cccctctgat tcaatttttg tttggaggct 540 ttaaaaaggc aaacaacatc aaataataat actaaacttt gtggtttgta aagatgaaaa 600 tgaaatatga aagaagagag aggattgggg gaagggaatg gagtggtgga gccaaaaatg 660 acgttggtga agaaacaatt gaagcatata agaggggata gagaagagta agagagttaa 720 tttgattaca gtaaaaaaaa aaaaatgacc ggctataata agtcactttg tgaggttcac 780 caatggtccc tttaaattga ggtccatatt agggtctccc 820 // ID NPG1_NT repbase; DNA; EDCOT; 462 BP. XX AC X71015; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 25-MAR-1997 (Rel. 2.02, Last updated, Version 2) XX DE N.tabacum transposon in Npg1 gene for polygalacturonase. XX KW Transposable Element; NPG1_NT; NTNPG1. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RP 1-462 RA Lonsdale M.D.; RT "Direct submission."; RL Direct Submission to EMBL/GenBank/DDBJ (24-FEB-1993). D.M. RL Lonsdale, Cambridge Laboratory, Colney Lane, Norwich NR4 7UJ, UK. XX RN [2] RP 1-462 RA Tebbutt J.S. and Lonsdale M.D.; RT "Identification of a defective transposable element in tobacco."; RL Plant Mol. Biol 23(2), 397-400 (1993). XX DR GenBank; X71015; Positions 1 462. XX SQ Sequence 462 BP; 153 A; 75 C; 79 G; 155 T; 0 other; cagaaaattc atccaaccat ttttaaagtg aaaatagcac gggctagcta gttgttggac 60 tggtaattaa aaaatagtca gtaaagtcat taaaaatagc tactattttg ctgcaacacg 120 gaaagttcca gcataatata ctggagattg gtgcacctgt gtatgaactt ccagcatatt 180 atgctggaac tcaaacacac ggaaagttcc agcataatat actggagatt ggagcacctg 240 tgtatgaact tccagcatat tatgctagac cagtatatta tgttggaact ccagtatatt 300 atgctggaat atttttcgaa ttttgaacaa tgttttcgtt cagatttatc attacatgaa 360 aagtggctaa atttcgatta cttttgaaac tgtgactatt tttcaattac ttgtaaatct 420 ggctattttt aaatctcgcc catttttaaa aacaaatttt ag 462 // ID ENSPM-N3_VV repbase; DNA; EDCOT; 2584 BP. XX AC . XX DT 06-SEP-2007 (Rel. 12.09, Created) DT 06-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE Non-autonomous DNA transposon from grapevine. XX KW EnSpm; DNA transposon; Transposable Element; Nonautonomous; KW ENSPM-N3_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-2584 RA Obukhanych T. and Jurka J.; RT "ENSPM-N3_VV."; RL Repbase Reports 7(9), 793-793 (2007). XX DR [1] (Consensus) XX CC This is a non-autonomous CACTA-like DNA transposon. Individual CC elements are 97% similar to their consensus. ~21-bp imperfect CC TIRs. 3-bp target site duplications. XX SQ Sequence 2584 BP; 978 A; 359 C; 316 G; 931 T; 0 other; cactacaaga aaattgactt ttagcgacaa aatattttgt cactgaaagt ctaaatttcg 60 tctacaaaaa cattccccaa cgaaaattct ttcgtgcctt gttcgtcgcc ctagacccgt 120 cgctaaaagt ttcgtgacaa aaatcttatt tcgtcgccca aagttttcct tgatgaaata 180 aaattttgtc actgaaggtg ttttccaacg aaatatttca tcgacaaaag taagaatttt 240 tgtcacgaaa aaaataaaat ttgtcccaaa agtcgtcaat atttaatgcc gacgaatttt 300 atttttgttg ccaaatattt ttggtaacaa attaatttcg tcggtgatag tctaccgtct 360 ctgttagttg acttggccac gccccaggcc ttcgccattc acccacagtg ctagctcacc 420 cgtcaaacat gtgaccaagc tctgatacca cttgtagatc gaggtgctct gtacttccca 480 gtgggtcacc catcctaaga tttctttgac tgcagcacgc ttaaccacag agtattttat 540 gacaaggccc ccatttgttc tgaaaaccaa ttggtgatca gaatagggac cttatattat 600 ttaagttcac tctccatagt ccattagggt ggtcgttggc cccccataag gccaacacta 660 tttatttatt aaataaggta tgcaagtcga catgaatttg acttgaactc aattatactc 720 aacccaaaat catgaaaggg tgttagattc aagtcatatt gacaagtcat atcaaatttt 780 gtcacctcta aacaaaccta atgttgaatg agaacaaatt agaggactat agtttattaa 840 tagctagaat aaattcaatt ccagacttat ggattaaagt gataaatttg aaatataaaa 900 taaaagtaca attgaaagac aatgttagga gaatgccaaa gtgtaatact catattgaca 960 ttaataaaat aatgatcaaa atgaaattag gattctacat catttttttt ttctttccct 1020 ttctcatcta ttccaaacaa aaatatcaaa cataatgaaa cactataaat ataaatcata 1080 taataattta tgatatattt caattatttt tataactaca tttgttttaa atatttgatt 1140 aaaaatgcat acaagtataa aaactccttt acaagttagt agccatagaa gttactattt 1200 tgcggtataa tttaagattt tattcttaat aactaatcaa ttttgataaa ttagtaatta 1260 ataattaaaa ataataaata tataattgat caataaaaaa taaaataacc aattattaat 1320 aaagatgtgg ttgaaaactt ttaaaaaaac tttatattta tatagaattt cacatgtgct 1380 atatatatca gacatttttt attttgtaaa tatgaaaata gagctaggca tatagtactt 1440 gcaatatatt atatcatata atatttaact tatacttatt tatttattaa taatatatga 1500 tatcttcgta cacataaata atatttggaa ttttatgtag gtagaatgtt tttatagata 1560 ctagacaatt tatttgagaa agttaattct gaccaattat ttaaaaacca agtaataatt 1620 aaaaaaaaaa tctattaatt taaactaggt aactaaatgt tagtataaat ttacttcttg 1680 agtggataag gtatgatttt gaatgagaac aaatttgagg actataactt attcatagct 1740 aacataaatt taatactaca ttggacttgt atggataact tttacctaat ataataaaaa 1800 tcatttagta gtatttatgt atgtgtagca ccatataata atattgaaat ttaaataaat 1860 ttatatcata ggatgtaatc ttacatatct tggattatct attgttatta tttatatata 1920 tataaatata aataacatat tacactataa atattaattg cttaaataat ttacattttt 1980 gttatttcat aacaatacta ttattacata atagaacatt taaatttaaa taaatctaca 2040 ttctagtatt taattttgtg gatccttaat ttttattatt atttatataa ataaaatatt 2100 atagtataaa tattaagtgt caacaaatat atattgtatt atttcatagt ataaataatc 2160 tacttattta ttaatattct ttattaatat cacaatttaa taacattatt tggtgacaaa 2220 attactcaat ttgtcaggaa ataatataat taccgacgaa accattttgt aagcaaaaat 2280 agataaaagg ttgtaacttt tagtgaggaa attattttca tcaccaaaaa ttataattag 2340 tgataaatat tttcgtaggg aaatagttta tttttgtcac aaaagtgttt gcgccaaaaa 2400 aaaaagcgcc aaattttccc gccacatctt ttagcgacaa aaatttcaaa ttcgttagga 2460 aaagtttgta gaaaattggc attattgaca acatctaaaa tttcatcggt aaaagttact 2520 tttagcgaca aaattagaat tcgcccctaa atttttgtca cgaaaagtac attttcttgt 2580 agtg 2584 // ID Copia-96_Mad-LTR repbase; DNA; EDCOT; 270 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Copia-96_Mad-LTR. XX NM Copia-96_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-270 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1731-1731 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 270 BP; 83 A; 58 C; 41 G; 88 T; 0 other; tgttgcagtc ctatttagaa taggaatgtg attgtgtaaa tcctaggaaa tatgggaatg 60 tatcttatat tcctattagg attagattac ctattaaatg ttgtaatcct aaagggaaag 120 gttttaccct tcctactact ataaataaag gcacaatggg gtgagataac acacacccac 180 aattacacat ctctctattc ttctctctat tgccgcaccc cctctctctc taaggcctcc 240 ataattgttc agtaaattat gcctacaaca 270 // ID Gypsy-50_Mad-I repbase; DNA; EDCOT; 5439 BP. XX AC . XX DT 03-NOV-2010 (Rel. 15.11, Created) DT 03-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-50_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-5439 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1997-1997 (2010). XX DR [2] (Consensus) XX SQ Sequence 5439 BP; 1781 A; 1081 C; 1074 G; 1499 T; 4 other; cgttatcagc acgagaagct ctcatgtcag tggaaagcac aacgccacaa atcatgttca 60 cctccttcag ctggaatctc acagataaga aaaaattttc atttcatctt caaatctcag 120 tacaattgat tttcttgaag caactatata tattgttgta tgactgtata tcatcctttg 180 cagaagcaaa agagtacaga ctcaaaattc gtaagagaat ttgacagcca tgtaaacagc 240 ctcggaactc caacttgcgg acctcggatt gaaatacttt cttcttgaaa gttgttcgtc 300 cgctcagtat ctacaacata tcaaaatttc agaaaacttt aacggtgcga tcgtcgcaga 360 tgtctgaaat accaaaccag tttccaattt ccgcagaaaa ctggacagcc accttatgag 420 taccaaaact ccatttcggt agctcaaatc gaaattgttt cttcacgaaa gttgtttggt 480 atcctcttat ccatatcata ctaaaatttg aactaaatct aacggtttga tcttctcata 540 agttgcagac actcttgact ccaaaactta tgggaaccgt ttcgactttt tcgaaactca 600 ccggaggagg aacaccaatt ggaacttatt gttactatta tttcctgagt aaccaaaatg 660 acttcagaac tgtgaaataa aaataaaaat aaaagggatg aaacaaaaga agtggcagac 720 caagaaaatg aaaaagcaaa acatgaggac ttaatcattg cattttctgt tttggcatat 780 ttatgtgcat ggtgttggtt taaagcccat gtcacaagtt ctatttattt aaagcaattt 840 atttatagtg ggtagaatta ttaccctttg ctttaaagct ttgatattta tgtgaatggt 900 gctgaatcaa agcccttgtc acaagcttta tttactttaa agcaatttat ttaccatgga 960 cggttttacc gcctattgct ttaagttttg atggtgctga attaaagccc ttgtcacaag 1020 ctttatttac ttaaatgcaa tttattcatt atggctggaa ttaccgccta ttgctttaat 1080 ttatttattg tacttatctt ttgttacaat gagtatatac aggacctgaa gttccttgat 1140 cagatcagaa cctgcagttt cttgatcctc atcatataaa atgattggac ccgaagttcc 1200 atcatacaaa aggatcaggc atgaagtccc ttgatcctga agatcaggac atgaagttcc 1260 tagatgagta ccgtaagttt gaagtgccgc agtgcctcaa cttaattgta ataaaggmca 1320 taagagtctc agttcacaga ctattaaata aggaccagaa gttccttatg tccatactca 1380 aaatggttta gcagaagcat ttattaagcg gatgaaattg attacccgcg ctctgctcat 1440 gaaaacgaaa ttgccagttt tctacatggg gacatgtaaa ctttacatga tgcattatta 1500 attcggttga gacatgttac caaccatcaa tacttctcag tacaactcgt gtttgggaac 1560 cagccaaaca ttatacattt acgagttttt ggttgtgtta tctatgtgcc tgtwgsactg 1620 ccacaacgta ctgaaatgag gcatcatcgc agattaggca ttgatgttga acaccatcta 1680 tcattcaata tttggaaccc ttgactgggg atatgtttac cgcatggttt gcggactgtc 1740 attttgataa gacaattttc ccgccattag ggggagaaaa taacatcgtt ccagaagaac 1800 gatgagaaaa tatcattcca gaagaatgat gagaaaagac cgttccagaa gaacgaagag 1860 aatttgtctt attttgattc acgaagcaat caatgagaaa atgaaatagg aataattgaa 1920 tgatgcaacg aaagtgatga aatcatatat acttgctgca aatgtgccta caagaattga 1980 tgtccctgtt ggacaaaata atgagacagt aaatgattta tctgttgcac gcctgaagcg 2040 tggcagactt ttagactcaa aaggttcagt cattcgaaag aagaagaata tggcactact 2100 gaactattgc attcccgaag cataactgtt gcatgccaga agcatgacag tcgccgcatg 2160 gatacacgtc ccagatagga caatccacgg acatgggaat attgatgtct catgcatgga 2220 gcatgataga cgtataggtt ccaatgactc aactcccgga agtggagatt aaaatccaag 2280 ctctataacg ctcaagagga ggttatgatc cgcattctct aaattatgac tatcctggaa 2340 gagatagtgt catgcccttg aagaggcaat ggatatccaa agaaatgaaa agcttttatg 2400 catgcgcatg cacatgagaa tatgggatca cggattgatg ataaccaatg gtaattttgg 2460 tttttacaag tagctactaa attcatcaat gagctgtgtt aatattgagt cacgttcttt 2520 tgttcgtcga caaaaggaaa attattggcc aaaatggaga aaggcaattc cattacaatt 2580 ttgtaagaac gtggaaaaat ggacctatat atatttgaat acaatacaaa tagccaaaag 2640 atgttgaacc aaggaggtta catatgggca tttgtaatac agtgtaatac actcacatga 2700 tatgacacaa ggttactatt gaaacctgaa attatactct tgtaaacgag ttcatatgaa 2760 tggagaatta tatacgaagg gttgtgagtc gcccacatca tatctccata agtaaatccc 2820 tcaagtatac atgggagcaa attgctctgt ataaattcca aaggaaaatg tgtcatgaag 2880 tgtagaaaat ccctgaagga ttcaaattgc ttgaagtaag cccccgaagg gtaaagcata 2940 aaatatgtac tcaataccaa tggatggtat aaattgcctt agtgagtact atcattatga 3000 tattgttgca acatactaaa atctcttgca agagtcaatg acattaaatt agaactcctg 3060 aagagttgat gatattaaat tgggactcct gaagagtcta gaaaaattat aaagtgttga 3120 gggaattatt gtctcgagct gcagatcgaa caatctacca acacgaatct tatccatgat 3180 gtttatgata ttaaaagaac catatggatt gaagattatg agttgaatac tcaaatgatg 3240 aagacactaa gaataatcat ttatcttcgt gagggtaaag ataaattaat atttggtcca 3300 gaagtaccac atcttagtga agtatatgct ttattgtatt tggcacaata cattgaatga 3360 aataaagctt atctattaat atctccaaga aattacagat atgtacatac acatgagtta 3420 aaacaaacaa acaggatgga gccttcacaa aggttgctca tgtgaagcct cagtactcgg 3480 aagtacccca gaagggggag gcactggaga ttgatcatgt ggcaccccag tacttagcaa 3540 aacaccagaa ggggaaggca tcagttgctt tcggaatcta gcaacgaacc tctggtgatc 3600 actttgaatc cgactttcgg attcctgcag ttggtcgagc tttcttttca tgctcgtaga 3660 gtaactattt gcaagcacgt gtaacaccct attctcgtgc ttgagccctc tgatctcttg 3720 tttaagactt gccacctcag ccatcaatga ttcaacttgg cgagtttgag caagtaggcg 3780 ttggcccata ttggaaacag agccagcaca ctgaacactg agagccaagg agtcttgaac 3840 ggccgactct tcagaccgtt ctgaaaggat cctgttatcc cttggagtga gaagattcct 3900 agctaccaca gtagcggtta tgttattctt catcacagag tccccaaccg taagaggacc 3960 attagaagat aagaaggacg ggcgccatat attatcctga cgctgctcgt ctgtatcact 4020 cctaagactc aaatctaagc aaatgttaga tgggcaagtc atttttcaga aatgatgaag 4080 gaaaaacaga ggtcaaataa aatttcagaa gtgcaagaag ggggaaattt ctacaggcag 4140 caactttctg agcatactct tgaacacaat tgatgtctct ataaaagaag aggcagcaga 4200 gccacttgtt cagagatcga agaggcaccg ctctccgaat ttcaaaagcc agattttcct 4260 gaataaagtt cgttggcatt tttcagacgc aatcccagct ttttcggatg tcgcgtgcaa 4320 ctttgtcaaa gatctctgac aaagttgaaa acgcgtaaat cttactgttc tatttacacc 4380 acagttgctg acaagagtaa aagcacagca ccaccacttg ctattgggaa atctctatat 4440 atgtcgacct ctgttctcca taacaaggca gacctgcaac actgcaagaa tacctaactc 4500 ttcctcatct ccgagaatgc atcttcaaca tagcatctcg aaatactcag ttttcttcct 4560 ctccgagaat acctcttcaa acaagtcaca ccagagcaag attatcwcat atcttcaggg 4620 accagagcaa gattatctca tatcatgcaa tctccctgtc ctttcctttg tccttgttct 4680 tacctgcaaa gacaaggata aagaaagcaa tatgtcggaa cctccactca aactcccggt 4740 aaggaaccga ctgcctggaa cctttcctga ttgcttacct agtattgctc tcgagtagtc 4800 atcttcaact gttgttggag ctgggtctcc agtcaccaag aagtgatgaa ccatccaaat 4860 gcaagggttg cattccactc ctgcatcaga gggcaaatac tgcaggagaa gatgccacac 4920 atgcatgggg gaaaagcagg gaaaatacta cttaagcaag gggagcaagt aaggaaagtg 4980 aaaatgatac attgaagcat gtggagacaa gcgcaacaaa cacgtgctga ttcatccccg 5040 acaaagccga agatcacttg ccacgtgaag ctcctcatgg tccaatttca ttcaagatca 5100 agcctcgaag gtccttgaag aaatcacaag tccgattcaa gatcaagtgt ccaccaccct 5160 tgaatcaaat tccgctccag ataaaaggag taaattcaga cctttggagc aagtctagca 5220 gaaggtcctc cagcccagtt caagaaaaag cctgtggaaa gttaacaaca agtaaagcac 5280 ctctttcggc aactcttctc gctaagagac tgaagcagaa tgatcaacga tcagcctaaa 5340 tgatttgaaa tcagggggag atactcatca gggggagcat ccaagacaga tcaagatttt 5400 aacgagtcaa tcgaagactt gtggccatcc aagggggag 5439 // ID Gypsy14-VV_I repbase; DNA; EDCOT; 9584 BP. XX AC AM472713; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy14-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9584 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-9584 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 728-728 (2007). XX DR Genbank; AM472713; Positions 37850 47433. XX CC Positions [4798-5160] - Integrase core CC 'CTATT' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 4423..5382 FT /product="Gypsy14-VV_I_3p" FT /translation="MFLVKTPWYAHIANYLVTSEIPSEWNAQDRKHFFAKI FT HAYYWEEPFLFKYCADQIIRKCVPEDEQQGILNHCHENACGSHFASQKTAM FT KVLQSGFTWPSLFKDAHIMCKSCDRCQRLGKLTKRNQMPMNPILIVELFDV FT WGIDFMGTFPMSFGNSYILVGVDYVSKWVEAIPCKQNDHRVVLKFLKENIF FT SRFGVPKAIISDGGAHFCNKPFEALLSKYGVKHKVATPYHPQTSILMKVVN FT ASRKNWSIRFHDSLWAYRTAYKTILGMSPYRLVYGKPCHLLVEIEYKAWWA FT IKKLNMDLIRAGAKRYLDLNEMEELRND" FT CDS join(241..1821,1825..2808) FT /product="Gypsy14-VV_I_1p" FT /translation="MPNWIRDSGGRLVKRDTPHNKELELSLNIMEATPEDQ FT HSHQGRQDNLNEFRSMRDRMHPPRMSAPSCIVPPTEQLVIRPYLVPLLPTF FT HGMESENPYAHIKEFEDVCNTFQEGGASIDLMRLKLFPFTLKDKAKIWLNS FT LRPRSIRTWTDLQAEFLKKFFPTHRTNGLKRQISNFSAKENEKFYECWERY FT MEAINACPHHGFDTWLLVSYFYDGMSSSMKQLLETMCGGDFMSKNPEEAMD FT FLSYVADVSRGWDEPTKGEVRKMKSQLSAFNAKAGIYKLKEDDDMKAKLAA FT VTRRLEELELKKVHEVQAVAEAPVQVKLCPNCQSYEHLVEECPAISVEREM FT FRDQANVVGQFKPNNNAPYGNTYNSSWRNHPNFSWKARATQYQQPDQPSQQ FT SSSLEQAIANLSKVVGDFVGNQEATNAQINQRIDRVESTLNKKMDGMQNDI FT SQKFDNIQYSISRLTNLNTVQEKGRFPSQPHQNPKSVHEVESQEGESSQMK FT DVKALITLRSGKKIEKPTPKPHVEKEEEIKKDGMEDKEKEISEKKDSDSTM FT NAIPEKELLKEEMLKKSTSPPFPQTLHGKKGIRNVAEILEVLKQVKVNIPL FT LDMIKQVPTYAKFLKDLCTIKRELTVNKKVFLTEQVSAILQCKSPLKYKDP FT GSPTISVMIGGKVVEKALLDLGASVNLLPYSVYKQLGLGELKPTAITLSLA FT DKSVKIPRRVIEDVLVQVDNFYYPVDFVVLDTDPTIKEANLVPIILGRPFL FT ATSNAIINCRNGLMQLTFGNMTLDLNIFYMSKKQTTPEEEEGLEEVCIIDT FT LVEEHCNQKMQDKLNKNLANFEEGLSEPPNVLATLQSWRKIEEILPLFNKE FT EE" XX SQ Sequence 9584 BP; 2927 A; 1834 C; 2040 G; 2765 T; 18 other; aatggcgccg ttgccgggga cggtgtcgag tttatagtga tactatttta gagcacttgt 60 gattttcatc acaagattgg tactgtttct ttcactttac taattctcat tctttttcta 120 ctaattcata atccaaagtt atcttttaaa ttcagcttag tttaattttg tttttcgtag 180 ccctgttttc ttttgttgtc ctttattttc attttattta cagaaagata ctagttgtgt 240 atgccaaatt ggatacgaga cagtggaggg aggcttgtta aacgtgatac acctcataac 300 aaagaattgg aattgagctt gaatatcatg gaagctacac ctgaagatca gcatagtcac 360 caaggtcgtc aagacaatct caatgaattc agatcaatga gggaccgcat gcatccacct 420 cgtatgagtg caccatcatg tatagtgccc cctacagagc agctagtgat cagaccgtat 480 cttgttccac ttctaccaac tttccatggg atggaaagtg agaatcccta tgcacatatc 540 aaggaatttg aagatgtttg taatacattc caagagggag gagcttcaat tgacttgatg 600 aggcttaagt tatttccttt tactttaaag gataaggcca aaatttggct taattcttta 660 aggccaagga gtatccgcac ttggactgac ttacaagctg aattcctcaa gaaatttttt 720 cccactcata gaacaaatgg cttgaaaaga caaatttcaa acttctcagc taaagaaaat 780 gagaaattct atgagtgttg ggaaagatat atggaagcta taaatgcttg ccctcaccat 840 ggttttgata cttggctatt ggtgagctat ttttatgatg ggatgtcttc ctcaatgaag 900 caactcctcg agacaatgtg tggaggagat ttcatgagca aaaatccgga ggaagctatg 960 gatttcttga gttatgtagc tgatgtttca aggggatggg acgaaccaac caaaggagaa 1020 gtgcggaaga tgaagtctca actgagtgct tttaatgcta aggctgggat atataaattg 1080 aaagaagatg atgatatgaa agcaaaattg gcagctgtga caagaagatt ggaagagctg 1140 gaactgaaaa aagtgcatga agtgcaagct gttgctgaag caccagtgca agtgaagctt 1200 tgtcctaatt gtcaatcata tgagcatttg gtggaggaat gccctgcaat ttcagttgaa 1260 agggaaatgt ttagagatca agcaaatgtt gttggacaat tcaaacccaa taacaatgca 1320 ccgtatggaa atacttacaa ctcaagttgg aggaatcatc caaatttctc atggaaggcc 1380 agagcaactc agtaccaaca gccggatcaa ccatctcaac aatcttcaag tcttgaacaa 1440 gcaatagcga atctcagyaa ggtagtggga gattttgttg gaaaccaaga agccaccaat 1500 gctcaaatca atcaaagaat tgacagagtg gagagtactt tgaataaaaa gatggatgga 1560 atgcaaaatg atatatctca aaagtttgat aatatccaat actcaatttc aaggctcaca 1620 aatttgaaca cggtgcaaga aaagggaaga tttccttctc aaccccacca aaaccccaag 1680 agtgtccatg aagtggaaag ccaagaggga gaatcatcac agatgaaaga tgtcaaagcc 1740 ttgatcactc taaggagtgg taaaaaaatt gagaagccaa cacccaagcc acatgttgag 1800 aaagaagaag agataaagaa agrggatgga atggaagata aagagaagga gatcagtgaa 1860 aagaaggact ctgattcaac aatgaatgca attccagaga aggaacttct gaaggaagaa 1920 atgctgaaga agtcaacttc tcctcctttt cctcaaacat tgcatgggaa aaaggggatt 1980 agaaatgtag ctgaaatcct tgaggtattg aaacaagtga aagtcaatat cccactgctg 2040 gatatgatta aacaagttcc aacatatgca aaattcctaa aggacttatg tactatcaaa 2100 agagagttga ctgtaaacaa gaaagtcttc ttgactgagc aagtaagtgc aatcttacaa 2160 tgtaagtctc ctttgaagta caaagatccg ggaagtccta ccatttcagt catgattgga 2220 gggaaagtag tggagaaagc tttgttagac ttgggagcaa gtgtgaattt gcttccatat 2280 tccgtctaca agcaattggg acttggagaa ttgaagccaa cagcaatcac tctatctcta 2340 gcagataaat cagtgaaaat tccaaggagg gtaattgagg atgtcttggt tcaagtggat 2400 aatttctact atccggtaga ttttgttgtt cttgatacag atcctactat aaaggaagct 2460 aatttagttc ctatcatcct tggaaggcca tttcttgcta cctcaaatgc aatcatcaac 2520 tgcaggaatg ggctgatgca actcactttt ggcaacatga cacttgatct caatattttc 2580 tatatgtcta aaaagcaaac cactccggaa gaagaagagg gtctagaaga ggtgtgcatt 2640 attgacactt tggtagagga gcactgtaat cagaagatgc aagacaagtt gaataaaaat 2700 cttgckaatt ttgaggaagg tttgtctgaa ccccctaatg tgcttgctac tctacaaagt 2760 tggagaaaga tagaagagat tctacctttg ttcaataaag aagaagagrc agctgctgaa 2820 aaagaaattc caaaactcaa tctaaagtct ctgcctatgg agcttaaata tatatacctt 2880 gaagaaaata atcaatgtcc tgttgtaata tcttcatctc tgaccagtca tcaagagaat 2940 tgtttaatgg aagtactcaa gaggtgtaag aaggcaatag gatggcaaat atctgacttg 3000 aaaagcatta gtcctttagt ttgcacacat catatatata tggaggagaa agcaaagcca 3060 attcgtcaac ttcaaagaag attgaatcct catttacaag aggtagtgcg agctaaggtg 3120 ctgaagctac ttcaagtagg tattatttac cctatatctg atagcccttg ggtgagtcct 3180 actcaagtgg taccaaagaa gttagggatt actgtggttc agaacgaaaa aggggaagag 3240 attactacac gcctcacttc aggttggagg gtgtgtattg attatagaaa gttgaatgct 3300 gtaaccagga aagatcattt tccattgcca tttatcgatc aagtgttgga aagagtcttt 3360 ggacatccgt tctattgctt cttggacggg tattcagkgt attttcagat tgaaattgat 3420 gtggtagatc aagaaaagac cacttttaca tgtccatttg gaacatatgc ttacagaaga 3480 atgccttttg gtttatgcaa tgcacctgca acatttcaaa gatgtatgtt gagtattttc 3540 agtgatatgg tggagcgaat tatggaggtt ttcatggatg acatcaccat atatggaggt 3600 acatttgagg aatgcttaat taatttggaa gcggttcttc acagatgcat tgaaaaagac 3660 ctrgtgctca actgggagaa atgtcatttt atggtacgtc aaggaattgt ccttggccat 3720 atcatctctg aaaagggcat tgaagttgat aaagcaaagg tggagcttat tgttaaattg 3780 ccatcaccaa caactgtaaa aggagtaagg caattccttg gccatgcagg gttctatagg 3840 aggtttataa aaggtttttc aagtctttca aaacctcttt gtgagctgtt agctarggat 3900 gctaakttta tatgrgatga tagatgtcaa aatagctttg atcaactgaa gaaattttta 3960 acaacaactc caatagtgag agcccttaac tggcaactac cctttgaact gatgtgtgat 4020 gccagtgact ttgctatagg agctgtgctt ggccaaagag aagatggaaa gccctatgtg 4080 atctactatg caagcaaaac actgaatgaa gctcaaaaga actacacaac tacagagaaa 4140 gaatttttag ctgtggtatt tgctttggac aaatttcgtg cttatttagt ggggtctttc 4200 atcattgttt tcactgacca ttcagccttg aagtatttat tgacaaagca agatgcaaaa 4260 gcaaggttga ttagatggat tcttttgtta caagaattcg atctccaaat caaagataag 4320 aaatgagtgg agaatgtggt agctgaccac ctttcaaggt tagttatagc acataattcc 4380 catcccttgc ctattaatga tgactttcct gaagaatcac tcatgttcct agtaaaaact 4440 ccttggtatg ctcatattgc taattattta gttactagtg aaattccaag tgagtggaat 4500 gcacaggaca ggaagcactt ttttgcaaaa attcatgctt attattggga agagcccttt 4560 ctttttaagt attgtgcaga tcagatcata aggaagtgtg tccctgaaga tgagcaacaa 4620 gggattctaa accattgtca tgagaatgca tgtggaagcc actttgcctc tcaaaaaaca 4680 gccatgaagg tgttgcaatc agggtttact tggccatctc ttttcaaaga tgcccacatc 4740 atgtgtaaaa gttgtgatag atgccaaagg cttggaaagt taacaaaaag aaatcaaatg 4800 cctatgaacc ccattctaat agttgagcta tttgatgtat ggggcattga tttcatggga 4860 actttcccaa tgtcttttgg taattcttac attttggtgg gggtggatta tgtttctaaa 4920 tgggttgagg caatcccctg taaacaaaat gatcacaggg tggttctcaa gtttcttaaa 4980 gagaacattt tctcaagatt tggggtgccc aaagccatca tcagtgatgg aggtgctcat 5040 ttttgcaaca agccttttga agctctatta tccaagtatg gagtgaagca taaggtagct 5100 acaccttatc atcctcagac ttccatattg atgaaagtgg tgaatgcaag cagaaaaaat 5160 tggtctatta ggtttcatga ttcattgtgg gcgtatagaa cagcttataa gactattctt 5220 ggcatgtctc cctatcgtct tgtctatggc aaaccatgcc atctccttgt ggaaatcgaa 5280 tacaaagctt ggtgggcaat aaaaaagctg aacatggact tgatcagagc cggagcaaag 5340 agatatctag accttaatga gatggaggaa ttaagaaatg atgyttatat caattccaaa 5400 gttgcaaaac agaggatgaa gaaatggcat gatcaactaa tctccaacaa ggaatttcag 5460 aaagggcaaa gagttttact gtatgacaca agactccata tctttcctgg aaagctcaag 5520 tcacggtgga taggcccgtt cattattcac caagtatatg tcaatggagt ggtggaatta 5580 ttgaattcta acggcaaagg cacctttaga gtcaatggat attgtctcaa gccattcatg 5640 gagccattca aaccagaaaa ggaggaaatc aatctccttg agccacaaaa agcctaagca 5700 aataagggtt tggtggacgt ggttttacca cagtccaaaa tttttgtaaa ttttgtaaat 5760 ttcaaagttt tttccatact tttgatctta gtttttgatc taaaattatg tttttatatt 5820 tgttttaatc tttttgaatg atctcaggtg gaagaaattg caaagaaatt gaaaggaaga 5880 aatcggagca aaaacagagt gaaaatagag caaaaatagg gctctacgag attttgcaac 5940 ctaagggaat cttctgcgag aacagcactt tgctgacaaa ccattccgca actcatttga 6000 ctcctctgcg aaaattttcg cagytgcgaa gccaagtttg gcacacgagt gccactgcac 6060 agcacaggag cccccaattc gcagctgcga aacggctgcg aagcgataaa gcgtgaaaat 6120 ccctratttc gcaaccaaag ttccattccg caggatattt cgcaattgcg aaagcgattt 6180 tggcacacgt gtgycacttc gcagcacagt gacactcaat tcgcagttgc gaaacgcatt 6240 gcgaagtggg ctgcgaaaat gactttttgc tgcgaaattr gcctttttct gcgaaactca 6300 aaatgaccct taatattccr ttatttttat atataccggt catttgagct gcgaaagggt 6360 ttcaaaaaga gagtgtgcca tacttgcaga ctgttcatct ccttgctcga gcccgacgcc 6420 gcacaaacct ccgttcatct tctccggtcg tcacttccgg ccaaatttcg gcaacccgaa 6480 atggcgcgaa ccagaraagc taaatcttcc tctccttcaa gtcgcaagaa agtcccgcga 6540 ggggagaccg ttccagatcc cacttctgag cctccgcggc caaaagcagt ttctcctccg 6600 gtgaagcccg cgccgcagaa gcctccgacg aggcgttatc tcaccaggtc agggggtcgg 6660 ccactgcaaa agagagctag ggttgaaagc tcagagccca ttgatttaac ggagtagtcc 6720 ccagaaccct cgccggttcc atctccagtt ccatctccgg cgccgccaac agagcctgag 6780 aagcctcaac caccacttcc cgaaccccaa aatccatctg agatagctcc tgaagcagta 6840 atcaagcggc cgatgctgac tcagcctcca attgagggga atttggactg tagagctcgg 6900 ccattccact ccgagctgtg ctttgacaca gccacgttcc aatttgcggc cggagcttgc 6960 acagtcattc cacctgctgc gaagatacca catggagcgc ctgttgactc caagagactt 7020 cttctacccc agggtagcca tggattttta tcagtccatg actaccaact aggtcaggca 7080 tcctactcta atccatttta ccattgatgg gaggcatggc atattgggag ctcgccatat 7140 agctgaggcc ttacaaatac catatgagcc aactcatttt gaggatttta gagtgtggac 7200 caatcccact gagctggaaa tgatgcatat cctgtttaga ggagcttcca cacgaccaca 7260 tctgttgagg ggggagcttc cttcaatcat gtttcttatt gatgcatttt tgtgtcataa 7320 cctctaccca ttgcagcatt ggactcagag gagaggagtg cttctagagg ccttattcaa 7380 gatttctgag ggatatttct tcggccctca ccatctgatt atggctgccc ttctctattt 7440 cgaagagaag gtgcataaaa agaagytgca gagagctgat gccattcatc ttctctttcc 7500 aaggctgttg tgccaaattc tagagcacct rgggtatcca tcaaagcctc agttggagcg 7560 caagcgcatt tgccgagagg tatttactct cgacaaatgg aacaacataa cagcctatag 7620 agttgagcag ctagagcgcc cacagccagc tgctaggaga gcatccccac gacacatacc 7680 tgagggtata cctattgttg ctcctgtcat tcccagagct ccaccagtta ctccagcttc 7740 atctaagcca tccacttcag ctgaaccaag gatggccatc cccatttcta aatacagaga 7800 gttatgtcat gcattgcaga ccctcacagc atctcagagc agccttgctt aggagatggc 7860 agccattcga gcatgccaag agcagatgtt ggccacccag gctcaacaca ctgccatctt 7920 gaggcagctc cagcatcatt tcgacctgcc ttcagctgct gagccctcca cctccacctc 7980 caccactgca gtgctacact ctcatcccac agagcctcaa gccccttctg gagcagctac 8040 tgaagaggca gacccatctg cctagcccca gcaccaccca ctcatcagat cattatatat 8100 atctattgca tatgtatttt atgtatttcg ttttttttag tttttaagaa atcccattat 8160 tttggtacca tatatgggat tgcttatatt gccttctttt tcattgtact caaatggatt 8220 caaagtaata caagtctaat attttttttg ttaaccttta gcattaattt atttttattt 8280 ccttttctca cagcttttat tctttttgaa acatgtggtt tctccaatca gtattcgaaa 8340 ttgatatcac tcaggaggta ccacttcctc cctttaattg caatcaccca tatcacattg 8400 aggacaatgc tcaattcggt tgggggggag aaatgaggaa ggaatgaagt atgataagtt 8460 aaaggaagta tgctaaatct ttttggtaat gcaattaggt tggtaatcag ttgtagtttt 8520 tgctttttac tctttttatt ctattctcca tggattttga ggaaaaattt tcaaattaaa 8580 ataggagaaa ttgaactgtt gcttttcact tgacttagag tatggattat gtttactaaa 8640 gtggttcaat tgttgaagct tctattgaat tcaaccttag ttcttccact ttaagctatt 8700 cacatactgt gcacaataga ttccgattat aagatgaaaa actatttccc tcttgactta 8760 gaaaaatttt gggacttggt acctttgacc tcagttgata aagttgagac accttatgaa 8820 aggccaatga ccctttgaaa taaagaaaga aaaatgtttg cttgccttga aacccgagca 8880 aggtctgaga ggtatatggt gaaaatcttt aaaacctggt gccctaagcc ttaattggtt 8940 gggagtcacc gacttcaatg ctcattacaa gggtggatag gtggagttta gcatatggta 9000 ggtgcatggg tattaaaatt tcattctcaa aagtccgggg aaaaatccga ggagttagtg 9060 gttgaaagat ccttaaagct tgatacccta aaccttaatt ggttgggagt catcgatgga 9120 cccccgttat atggacaatt cagaaagaat acccctttaa gcctcttaaa aaaaaaaaaa 9180 aaaaatatgt gttcttttct tattgatttt ggtcagtttg ctaagtgttg aaaagagata 9240 ggttgggggg agagattagt ttagcatact atattcggaa gctaaggaat cttacactta 9300 gatttttgtg gaagagtaaa ttttggttct ttggaagtga aaatgatttt aaaacttcag 9360 tttgcataat gcattccctt aattgatagt gtttagcgta gtttgttata actcttgttg 9420 aaatttgggt gtatatttct ttgatgtatc atgtgagaat tagattatca tgccacttga 9480 aaattgtttt tcagcatgat gttgtaaatt atagtttagt ttgcttttat atttttctct 9540 ctcctttatt gctaagggac tagcaatttg tcggttgggg ggag 9584 // ID Gypsy-49_Mad-I repbase; DNA; EDCOT; 4981 BP. XX AC . XX DT 29-OCT-2010 (Rel. 15.11, Created) DT 29-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-49_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-4981 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1995-1995 (2010). XX DR [2] (Consensus) XX FH Key Location/Qualifiers FT CDS join(62..4030,4012..4923) FT /product="Gypsy-49_Mad-I_1p" FT /translation="MFSVRIMPPRRERRESRRTPDPNFPDIAQLGEAMAQA FT FQNVIRPPPPPQRTPLETMYNLKLDRFMGDEGHEGAEKWLDHIEKTFQVMQ FT SQGNFPADRWVETTTWFLGREPAGWWRNQTQFMSPAMASDWEVFKDNFKKR FT FVPPEYIDRKKQEFTRLKQKNMTAHEYYRKFTDLSRYDPDTAGNQGEMLRR FT FKLGSKKKWRTFASALPCADYHEFFEILVRMEDSDNLPSESEDDEDKNDGQ FT KKDDKGKGISIPGPRKTQNFKKSGASSSSSSGGYSITGPRRGGGRFSGGPR FT FQRQRDSGGAGGSGAPWCRRCNFRHHGECRRGSGACFTCGQMGHRASQCPQ FT GQQRPQQTTMPPPAPIQQSFGPGGYGQSGRGGAYHYQGDAAPYAPGPYQYP FT QEPYSQTGYSQDFGGYSSYSSMPAGGSQWHQGGQPRQGEVATGGAGSSRQP FT SQSGQGRAPQGRGNQGSRGRGGRQQAQGRVNHISLQEAQNHPDLIMGTLNV FT LGHFAKVLIDCGATHSVISHTFAQMTQPHPSPLGFDLEFAMPRGDKCYVDS FT VYLGCPVMVEGIVMPADLIPLDIVDFDVILGADWLHYNRAHIDCYGKSVTF FT YRPGLPEVTFVGERGGVRHGVISAIRARKLLSKGCQGYLAHVVLNDVVPTS FT IEEVGVVRHYPDVFPDDLPGLPPDREVEFSIDLLPGTDPISLTPYRMAPAE FT LRELKIQLQELLDKGFIQPSSSPWGAPVLFVRKKDGTLRLCIDYRQLNRVT FT IKNRYPLPRIDDLFDQLKGACVFSKIDLRSGYYQLKIKEEDVPKTAFRTRY FT GHYEFLVMPFGLTNAPAAFMRLMNEVFQQYLDKFVIVFIDDILVYSKSKAD FT HIRHLNLVLRKLREHQLYAKFSKCQFWLTEVAFLGHVVSAQGIQVDPQKIA FT AVENWEQPRTVTEVRSFLGLAGYYRRFVQDFSMIALPLTKLTRKDVKFEWD FT ENCERSFQQLKYCLTHAPVLVLPDDSGNFEIYSDASLNGLGCVLMQHNRVI FT AYASRQLKNHERNYPTHDLELAAIVFALKIWRHYLYGEKCKIFTDHKSLQY FT LFTQHDLNLRQRRWMELLSDYDCTIEYHPGRANVVADALSRKPQGRLNALY FT ASRVPLLAELRATGVRLELEDRSGAFLASFQVRPVLVDRILEAQMVDEEIQ FT EMVQLRSEGKKKDLRIRESDGMLMQENRMYVPNNEELKKEILDEAHCSAYA FT MHPGGTKMYHTIRPFYYWPGMKREIAEYVSRCIICQQVKAERKKPFGRMQP FT LPVPQWKWENITMDFVYKLPRTRNGFDGIWVIVDRLTKSAHFIPVREKYPL FT NKLAKLFIRRLVVHSKIVKYHGVPVNIISDRDPRFTSKFWVAFQEALGTQL FT LYSTAYHPQTDGQSERTIQTLEDMLRSSVLQFGDSWHDRLDLMEFAYNNSF FT HSSIGMSPFEALYGRACRTPLCWSEVGERVLEGPEIVDETTQNVQVIKSNL FT KAAQDRQKSLADRHTTDRVYDVGDWVFLKLSPWRGVVRFGKRGKLSPRYIG FT PYVITERVGEVAYRLELPPELSKVHNVFHVSMLRHYISDPSHVIPPQPLEI FT NPDLTYDEEPVTILDWKDKVLRNKTVSLVKVLWRNHSVEEATWETEDRMRE FT MYPRLFYGY" XX SQ Sequence 4981 BP; 1284 A; 860 C; 1351 G; 1485 T; 1 other; gtttggtatc agagcctagg ttgcagtcct gtataattgt taatgcttta atgatctttt 60 gatgttttct gtcagaatta tgccgcctcg tagagagcgt agggagtccc gccgtactcc 120 tgatcctaat ttcccggata tcgctcagtt gggggaagca atggctcagg cttttcagaa 180 tgtgattcgt cctcctcccc cacctcagag gacacccctg gagaccatgt acaatttgaa 240 actggatcgt tttatgggtg atgaaggtca cgagggggca gagaaatggc tagatcatat 300 tgaaaagacg tttcaggtga tgcaaagtca ggggaacttt ccggctgata ggtgggttga 360 gaccactacc tggtttttgg gtcgagagcc ggcaggttgg tggaggaatc agacgcagtt 420 tatgtcccca gctatggcat ctgattggga agtatttaaa gataatttca agaaaagatt 480 tgtcccccca gagtatattg atcgcaagaa acaggaattc actcgattga aacagaagaa 540 tatgacagct catgagtact acagaaagtt tactgatttg tctcgttatg accctgatac 600 agctggtaat cagggagaga tgcttcgacg tttcaagttg ggatctaaga aaaagtggcg 660 gacttttgcc agtgcacttc cctgcgccga ttaccatgag tttttcgaga ttttggttag 720 gatggaggac tctgataatc ttcccagtga gagtgaggat gacgaggaca agaatgacgg 780 tcagaagaag gatgataaag gtaagggtat ctctattccg ggacctcgca agacgcagaa 840 ttttaagaag agtggagcga gttcgagttc ttctagtggt ggatatagta ttactggccc 900 gaggagaggt ggtggtagat tttctggtgg gcctagattt cagaggcaga gggattctgg 960 tggtgctggt ggttctggcg ctccgtggtg ccgccgttgt aattttcgtc atcatggtga 1020 gtgtaggaga ggtagtggtg cttgttttac ttgtgggcaa atgggacatc gggcttctca 1080 gtgtccccag ggtcagcaga gaccgcagca gaccactatg ccacctccag cgccgattca 1140 gcagagcttt ggaccaggcg gttatggcca gtcgggtcgt ggtggtgcct accactacca 1200 gggggatgct gctccgtatg ctcccggacc ttatcagtat ccccaggagc cttattctca 1260 gacagggtat tctcaggact ttgggggtta ttcttcttat tcatccatgc cagctggtgg 1320 atctcagtgg catcagggag gtcagccccg tcagggggaa gttgctactg gtggtgcagg 1380 atcatctagg cagcctagtc agtcaggcca gggacgtgct ccccaggggc gaggtaatca 1440 aggcagtaga ggtcgtggtg gacgacagca agctcagggg cgtgttaatc acatctcact 1500 gcaagaggct cagaaccatc cggacttgat catgggtacg ttaaatgttc ttggtcattt 1560 tgctaaggtt ttgattgatt gtggtgctac gcactctgtg atttctcata cgtttgctca 1620 aatgactcaa cctcaccctt cacctctagg atttgattta gagtttgcca tgcctagagg 1680 agataaatgt tatgttgata gtgtgtatct tgggtgtcca gtgatggtag agggcatagt 1740 tatgccagct gatcttattc cgttagatat tgtggatttt gatgtgattc taggagctga 1800 ttggttgcat tataatcgtg cccatattga ttgttatggt aaatcagtta ctttttatcg 1860 ccctggacta cccgaggtta cttttgtggg cgaaagaggt ggggtgagac atggtgttat 1920 ttctgccata agagcgagga aattattatc gaagggttgt cagggatatt tggcacatgt 1980 ggtattaaat gatgttgttc ctactagtat agaagaagtt ggtgtggtca gacattatcc 2040 tgatgtattt cctgatgatt tgccggggct gccgccagac agagaggtgg aattctctat 2100 tgatttgctt ccaggtactg accctatatc tctaactcct tatagaatgg ctcctgctga 2160 gttgagagaa ttgaaaattc agttgcaaga attacttgat aagggtttca ttcagcctag 2220 ttcgtcacct tggggtgccc cagtattatt tgtgaggaag aaagatggaa ctctgagatt 2280 atgcattgac tataggcaat tgaaccgggt aacgattaaa aaccgttatc cattgcctcg 2340 catcgatgat ttgtttgatc agctgaaagg tgcgtgtgta ttttctaaga ttgatttgag 2400 atccggttat tatcagttga agattaaaga ggaagatgta cctaagacgg ctttccgaac 2460 ccgttacgga cattatgaat ttctggttat gccatttggg ttgactaatg cacctgcagc 2520 tttcatgagg ttgatgaatg aggtattcca gcaatatctt gataaatttg ttattgtttt 2580 tattgatgat attctggtat actctaaatc taaagcagat catatccgac atcttaactt 2640 ggtgttaagg aaattgaggg agcatcagtt gtatgctaag ttcagtaaat gtcagttttg 2700 gttgactgaa gtggcatttt tggggcatgt tgtatcggct caaggaatcc aagttgatcc 2760 tcaaaagata gcggcagtgg agaattggga gcaacctcga accgtcactg aggtacgaag 2820 ttttcttggt ttagcaggtt attatcgacg gtttgttcag gatttctcta tgattgcttt 2880 gccgttaacg aagttgacca ggaaggatgt taaattcgag tgggatgaga attgtgagcg 2940 gagtttccag caattgaaat attgcctcac tcatgctcca gtgttggtac ttcctgatga 3000 tagcggtaat tttgagattt atagtgatgc ttcsttgaat ggtttgggat gtgttttgat 3060 gcagcataat agggtgattg cctatgcttc tcggcagttg aaaaatcatg aaaggaatta 3120 tcctactcac gatcttgaat tggcagcaat tgtttttgct ttgaagattt ggaggcatta 3180 tttatatggt gagaagtgta agatcttcac tgatcacaag agtcttcagt atttgtttac 3240 tcagcatgat cttaatcttc gtcagcgaag gtggatggaa ttgctaagtg attatgattg 3300 tactattgag tatcatccgg gtcgtgctaa tgtggtagct gatgcactga gtaggaaacc 3360 tcaaggtaga ctcaatgcct tatatgctag ccgtgttcct cttcttgctg aactgagggc 3420 aactggagta aggttggagt tggaagatcg aagtggagcc tttcttgcta gttttcaagt 3480 caggccagtt ttggttgatc gtatactcga agctcagatg gtggatgagg aaattcagga 3540 gatggttcag ttaagaagtg aagggaaaaa gaaagacctc agaattcggg aatcagatgg 3600 tatgcttatg caggaaaaca gaatgtatgt tccgaataat gaggaattaa agaaggaaat 3660 tttggatgaa gcgcattgtt cagcttatgc gatgcacccg ggaggaacta aaatgtatca 3720 taccattcga ccattttatt attggccggg tatgaaaagg gaaattgcag agtatgtgag 3780 tagatgtatt atttgccagc aagttaaagc agaaagaaag aagccatttg ggcgaatgca 3840 gccacttccc gttccccagt ggaaatggga aaatataacc atggatttcg tgtataaact 3900 tcctcgtaca cgaaatggat tcgatggtat ttgggtgatt gtggatcgac ttaccaagtc 3960 agcgcatttc attccagtga gggagaagta ccctctgaat aaattggcta agttgttcat 4020 tcgaagattg tgaagtatca tggagttcca gtgaatatta tctctgatcg agacccaaga 4080 tttacttcta aattctgggt ggcttttcag gaagctctgg gtacgcaatt gctttatagc 4140 acagcttatc atcctcaaac tgatgggcaa tcagagagga ccattcagac gttggaggat 4200 atgttgagat cttcagtatt acaatttggt gattcctggc atgatcgtct ggacttgatg 4260 gagtttgctt acaataacag ttttcactcg agcattggta tgtcaccatt tgaggcactt 4320 tatggtaggg cgtgtcgaac gccattatgt tggtctgagg ttggtgaaag ggtgttagaa 4380 ggcccagaga ttgtggatga gactactcaa aatgttcagg taattaagtc aaacctgaaa 4440 gcagcccagg atcgacagaa gagtttagcg gatcggcata ctactgatcg agtgtatgat 4500 gtgggtgatt gggtgttttt gaaattgtca ccttggagag gtgtggtacg atttggaaaa 4560 agagggaagc taagtccgag atacattgga ccttatgtga tcactgaaag agttggtgaa 4620 gttgcctacc ggttggagct gcctccggag ttatctaagg tccataatgt gttccacgtc 4680 tctatgcttc gacattatat ttctgatcct tctcatgtga tccctcctca accgctagag 4740 attaatccgg atttgacata tgatgaggaa ccagtcacta tcttggattg gaaagataag 4800 gttctaagga acaagacggt gagtttggtg aaggtgttgt ggaggaacca ttctgtagag 4860 gaagctacct gggagacgga agatcggatg agagagatgt acccaaggtt attctatggg 4920 tattaagtgg tttatttggt tatgggaatt tcggggacga aattctataa ggaggggaga 4980 t 4981 // ID TPS38RT repbase; DNA; EDCOT; 231 BP. XX AC AJ405244; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Pisum sativum Ty1/copia-type retrotransposon TPS38RT, partial DE archaic reverse transcriptase gene. XX KW Copia; LTR Retrotransposon; Transposable Element; retrotransposon; KW TPS38RT; Ty1/COPIA superfamily; reverse transcriptase. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-231 RA Pearce R.S., Knox M., Ellis N., Flavell J.A. and Kumar A.; RT "Pea Ty1-copia group retrotransposons: transpositional activity RT and use as markers to study genetic diversity in Pisum."; RL Mol. Gen. Genet 263(6), 898-907 (2000). XX DR Genbank; AJ405244; Positions 1 231. XX SQ Sequence 231 BP; 45 A; 51 C; 51 G; 84 T; 0 other; gaattggagg aggaagtgta tatggatcaa cctccaggtt ttaccgttcc tggcaattca 60 agacttgttt gtcggcttca tcgttctctt tatgggctga aacagtcttc acgtgcttgg 120 tttggtagat ttagttctgc cttgatataa tttttttgca ttctgttttc ttccttcatt 180 cttccaccga tcaacgcact tacttgtggc tacggacgac ctgcaggcac g 231 // ID SAT_VP repbase; DNA; EDCOT; 185 BP. XX AC . XX DT 03-JUN-2005 (Rel. 10.05, Created) DT 03-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE Vicia genus tandem repeat, consensus. XX KW Satellite; Simple Repeat; tandem repeat; SAT_VP. XX OS Vicia OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae. XX RN [1] RP 1-185 RA Macas J., Pozarkova D., Navratilova A., Nouzova M. RA and Neumann P.; RT "Two new families of tandem repeats isolated from genus Vicia RT using genomic self-priming PCR."; RL Mol Gen Genet 263(5), 741-751 (2000). XX RN [2] RP 1-185 RA Gentles A. and Jurka J.; RT "Consensus of Vicia tandem repeats."; RL Direct Submission to Repbase Update (03-JUN-2005). XX DR [2] (Consensus) XX SQ Sequence 185 BP; 61 A; 21 C; 30 G; 73 T; 0 other; ttaaagatta ttgtgtgcta cagtacataa aattcacgat gaccgttaaa ttgctaaatt 60 tggtcatttg gaagattgtc ttgtgttata ctacataaaa gtcacgaagt tcattaaact 120 tgcaaaattt gggatttttt ttatgattat catgtgctac agtgcataaa atttagtttt 180 attaa 185 // ID Copia24-PTR_LTR repbase; DNA; EDCOT; 224 BP. XX AC LG_XVIII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia24-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-224 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-224 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 223-223 (2007). XX DR Genome; LG_XVIII; Positions 5893762 5893985. XX SQ Sequence 224 BP; 63 A; 32 C; 40 G; 89 T; 0 other; tgttaggact aagtcagtca ataatatcct ggttaatagg atcaaggatt acatttgatt 60 tattgtttgt ttgttggcca cgtttatagg agagtcaaac gtgggttgct tatttatcta 120 atttctgttg taatggtttg ctatataaac cagccttcat tcaataaaac atgtgaagtc 180 tttctcttca tcttgaactg ttaatcaatt gcttagaatt atca 224 // ID EnSpm1B_PT repbase; DNA; EDCOT; 3265 BP. XX AC . XX DT 14-DEC-2009 (Rel. 15.06, Created) DT 14-DEC-2009 (Rel. 15.06, Last updated, Version 2) XX DE EnSpm-type DNA transposon - consensus. XX KW EnSpm; DNA transposon; Transposable Element; EnSpm1B_PT. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3265 RA Jurka J.; RT "DNA transposons from black cottonwood."; RL Repbase Reports 10(6), 788-788 (2010). XX DR [1] (Consensus) XX CC >86% identical to consensus. XX FH Key Location/Qualifiers FT CDS 2516..3106 FT /product="EnSpm1B_PT_1p" FT /translation="MELFVETHVRSDDRQKGVQQFVDSRAQHFVVCWFSTI FT FFLSYYFLEFDEFIFSFQDTYNSRLKERYEDDPLTHPDLDPDLWLEAGSSG FT GPDRNWVYGLSNTTAENLRTTRSVSTVGCSQSIPSTQTPEFAAMLDQRVQA FT RTTHLNEKYERLTADYEELRRLVMEMRSQMGGTCAPPNWPHGPGDDQPPPP FT PPAPPLF" XX SQ Sequence 3265 BP; 871 A; 562 C; 645 G; 1186 T; 1 other; ataccgacgg aatgtgtccg tcggtatatt ccagtggcga tgggaactgt tccccttctc 60 ctggcactgt tcatggtgtt cattacatac gggtataccg acgaaatgtg tccgtcggta 120 tattccagtg actatgagaa ctgttcccct tcttcatggc actgttcatg gtgttcatta 180 cacatgggta taccgacgga atgtttcgtt ggtatattcc agagtatggg aattgttccc 240 ttctcctgca tgttcagatg ttattacaca cgatataccg atagaatttc gtcggtatat 300 tccagagact atgggaactg ttcacttctc aatggtgata attaatgttt ttttgactgt 360 cgagttttcc cgacaaaatc accgcagaat gaaaagccgt tggtaatatt tgaagggctt 420 tctaaaattt tttgaaaatt aaaaatttta atttgacttt acgacgaaat aaktcgttag 480 taattccgtc ggtaaaacta aattaaaaga ccagaatcag aacagacggg gcttcatctt 540 cttctttctt cttcttctct cacacgcctt tctctctctt tctcttctct tctctctcat 600 cttctcagcc aaaatcaagc attctcttct cttctcatcc tcaggtatgt tgtctttctt 660 catttttctt cttatttttt tttttgggtt tattaacaat ctcttttctt ttttcttttt 720 taattatcag ccgaaattaa gcatgccatt aaggtaagaa tttttcattc ctttttcttc 780 cttttttgtg tttttttttt cattattttt gtttttttgt cattattttt gttcaatttt 840 gtgttcttaa taattttatg aattaataaa tgtgttgaat tttagttgtt attgaaataa 900 tttttgcatt attttgttga attttagtta tttttttttc aaatttgttc aatttcaatt 960 aaatgtgtag gattaatttt aattattatt ttgtatttat tccatttaga ataatttttt 1020 aaatttagga ttaaaaatat tatcacttag aaataattgt gttgaatttt agttgttatt 1080 gtaataattt ttgcattatt ttgttgaatt ttagttgttt ttttttcaat tttgttgttc 1140 aatttcaatt aaatgtgtag gattaatttt aattattatt ttgaatttaa attttttttg 1200 taaatttagg attaaaaata ttatcacgta gaaaatgaaa attttctacg aaattgaatt 1260 atgctaaatt gttagaagaa attgaataaa atcaactggt ttgtggcata tatgttgtgt 1320 atttgcaggt ttaaaaattt tgggtagtct cccgtatagg ggaggtgctg ccgaattttt 1380 ttaaaaaaat aggaatcgtt taattttttt atccgttaat ttgtgtagat gcctagggga 1440 aagtctattg cacgtcgcga ggacagatca ctgctagttc ttctagcagc gatgctgacg 1500 accacgagtc attaggtgcc gaccaagaac aggcacttga ggcacaagca tcgactcacg 1560 acgcaggctc gtcgagtgcg atgccgcaac atcgaggggg gtcccttcac agcgggatcc 1620 atttacccgc aagtacgagg cctagtggaa ggacgacctt tcaatgtaag tttgttttgc 1680 tttcacaatg acatgtttaa taatttttga aaaaataatt tcatttaacg aatgcaattt 1740 caggtttaca aacattgagg ctgcgagaac aataacatcg gcctttaaat cgtcgatgga 1800 aatttcattg tttcaatgga gccaggtttc caaacatcct gaatggaaac cgcaggtcga 1860 tgcatggttt tcaaggttca aggttagtat taacttaaat atttttttat gttaatttgg 1920 ttagtttatt gaaattactg aaattttcct tttataaatt tttacttcaa gggaaaattt 1980 gaatgggaga gagctgataa taatgttgcg aggagggttt gggagaatca cgctgcaatt 2040 aggtaagatc gaattcagga taattttttt tattccaaat attaaaattt tatttttcat 2100 ttactaacag ataattaatt tgtaccatat aggttgcgtg atttttggta cgaggcgcaa 2160 aagaaagcca aaaaatatgc gaaagaaaga gagcttccag gctggaatga cgtggcggtt 2220 tggaaggatt tcagaccgcc gtacgtctca gaggctgtat gggcggaata cattcagcac 2280 gtgatgtccg cgcgtttcac gcgacggtca cagtccggtg tggaaaatca gaaccggcgt 2340 gttcacggtt ccgttaccac gcacaccggc gactccgttc cgttcgtttc gcatgcgaag 2400 cggatggtag gttttttatt acatccattt tttattagtt gtttttttat aaatatattt 2460 aactgacaat atttttatct tgcaggctac ggttcttgga cgcgagccaa gcccgatgga 2520 gctttttgtt gaaacgcatg tgcggagtga tgaccgccaa aaaggggtgc agcagttcgt 2580 ggatagccga gctcagcact ttgtggtatg ttggttttca accatttttt tcttaagtta 2640 ttatttcctt gaatttgatg aatttatttt ttctttccag gatacatata acagccggtt 2700 gaaggagaga tacgaggatg atcctttgac ccatccggat ctcgatccgg atttgtggtt 2760 ggaggcagga tcgtccggtg gacccgatag aaattgggtg tacggactct ctaacactac 2820 ggccgagaac ttgcggacga cccgtagtgt ttcgaccgtt ggatgctcgc aatcgattcc 2880 gagcactcaa actccggagt tcgcggcgat gttagaccaa cgagtacagg ctcggacgac 2940 ccatcttaat gaaaaatatg aacgactcac tgctgattat gaagaactcc gccgattggt 3000 aatggagatg agatcacaga tgggtggtac atgtgcaccc cctaattggc cccacggtcc 3060 cggcgacgac cagcctcctc ctcctcctcc agcgccgcct ctattttaga tttattgtat 3120 ttgaacgtac aaatgtttaa atttgtaata aatatttgat ttttatatta ttttaattat 3180 ttttctactt ctgttcaata tattttttaa aaatattttt aaaatattac tgacggggtt 3240 accgacggaa caactccgtc ggtat 3265 // ID Copia53-PTR_I repbase; DNA; EDCOT; 4607 BP. XX AC scaffold_352; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia53-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4607 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4607 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 286-286 (2007). XX DR Genome; scaffold_352; Positions 21754 26360. XX CC Positions [2034-2540] - Integrase core CC 'GTTTA' target site duplication CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS 1389..3239 FT /product="Copia53-PTR_I_1p" FT /translation="MRSCTKLKKPEADSANATTDEVQDALILAVQSPIDDW FT ILDSGASFHCTPHHEMMQNYVAGDHGVVYLADGQPMDIVGIGDVQIKTMNG FT STWNLQNVRHVPGLKKKLISVGQLDDSGHSILFSGGIWKVSKGAMVLARGK FT KTGTLYMTTRFADIIASTEAENQAQLWHCRLGHMSQKGMKILQSKGKLPEL FT KNIDLDICESCVLGKQKKLSFLKVGRTLRPRKLELVHTDLWGPSLVASLGG FT SRYYVTFIDDFSRKVLVYFLKNKSNVFETFKKWKTMVETESGLKLKCLRSD FT NGGEYIDGGFKEYCAVNGIRMEKTVPGTPQQNGIAERMNRTINERARSMRL FT HSGLPQTFWADAVHTAVYLINHGPSVPLEFRLPEEVWRGKEVQLSHLKVFR FT CVSYVHIDSDARNKLDAKSKKCFFIGYGDEEFGFRFWDDQNRKIIRSRNVI FT SNEKVLYKDRSSVETDMADSDTSPQKSEFIRLEGLPDVTEQNRNQESLQED FT SNTSVPTTTQEDAEPSEPTVYVRRSSRTVKPPQWFTLLLNYILLTDGGELL FT SYEESLQDGNSSEWELAMKDEMSSLLKNKTWELTTLPEGKKALQNKWVYRV FT KTEHDGSKRFKARLVVKGF" XX SQ Sequence 4607 BP; 1495 A; 852 C; 1053 G; 1207 T; 0 other; actggtatca gagcttgttc ttgaaaaaga gggtgtttga tccaaaccta gaaatcaaag 60 ttctcaaaac gtgtttttaa agataccatc gtgtagaggc agacaagaca aatccactgg 120 tgaaaacccg gcgaagaacc gacatgctgc atgccctcac gcgccgacgt caggactgtc 180 cacgcgcacc aacgtgccac acgcacctca cgctccttct tcgcccgaat tcctgcaact 240 gaaccgggtt gacccgccac ctcatcatcc agtcagcaga cacagcagca atttcgcata 300 gtcatcagcc acgtcatctg accagtcatc atccacgtca gctgaagcca cgtccgcaat 360 aatttcgcac ggctgtgaca cgtcatctat agtgggccca gtgttcttac gtgtctgcca 420 cgtaatctat gccacgtcat catcttgagt tttgatccag tgcgccgcag acactatttc 480 atcgaacacg cggcttcatc tgcatcgtcc attgatccta aactttgatt gataagatct 540 gagccatccg aagtccgatt tgggcgatct cagtgtcgtt tccaatagtt ttggccgttc 600 cggacacatc tataaggtca gatttgacag attcaaatcc gagacgtatt aaaatggaag 660 atgaaataaa ggctgctaga attgaaaaat ttgatggaac aaattttgga tattggaaaa 720 tgcagattga agactatcta tatgggaaga aactttatct tcttctgttg gggagcaaac 780 caaagaatat gcaagaagaa gattagttac ttcttgatag acaagttttg ggtattatcc 840 ggttatcctt atcaagaaga gttgctcaca atgttacaaa agaaagatcc actacaagat 900 taatggaagc cttgtctggg atgtatgaga agccctcggc aaacaataaa attcacttga 960 tgaagaagtt gttcaacttg aagatgacag aaggcatatc tgtcacacaa catctcaaca 1020 atttcaatac tatcacaaat caattgtcat ctgttgagat tgagtttgat gatgagattc 1080 gtgcactcat tttgctagct tcacttccaa gcagttggga aggtatgagg acagccgtga 1140 gcaactcagc tggaaaatcc aaactgaaat atgatgacat ccgagacttg attttggctg 1200 aagaagtacg aagaaaagac tcaggtgaaa attcaagttc aggttcagct ctcaacatca 1260 acactcaagg gaggagacag gatagaggct tatctagagg cagatcaaaa tccagatgca 1320 gaagtaaaag caagtttgga cccagaaagt aggttgaatg ttggaattgt ggcaaacctg 1380 gtcatttcat gaggagttgc acaaaactga aaaaacctga agctgactct gcaaacgcta 1440 ccacagatga ggtacaagat gctttgattc ttgctgtaca aagtccaatt gatgattgga 1500 ttcttgattc tggtgcttca ttccactgta caccacacca tgagatgatg caaaactatg 1560 ttgctggaga tcacggtgta gtctatttgg ccgatggaca accaatggat attgtgggta 1620 taggagatgt gcaaatcaag acaatgaatg gatctacatg gaatttgcaa aatgtaaggc 1680 atgttcctgg actaaagaag aagttgatct cagtcggaca acttgatgat agtggtcatt 1740 caatcctttt ttctggaggt atatggaagg tatcaaaggg agcaatggtt ttggctcgtg 1800 gaaagaaaac cggcaccttg tatatgacca caagatttgc agacattatt gcctctactg 1860 aagcagaaaa tcaagcacag ctatggcact gtagactcgg ccatatgagt caaaagggga 1920 tgaagatact tcagtcgaag ggaaagctgc cagagcttaa aaatattgat ctagacattt 1980 gtgaaagttg tgttcttgga aaacagaaga agctcagttt cttaaaggtt ggcaggacct 2040 taagaccaag aaagctagaa ctggtacaca cagatttatg gggaccttct ctagtggcat 2100 ctcttggagg ttctcggtat tatgtgacct tcattgacga tttcagcagg aaggtattgg 2160 tctactttct gaaaaataaa tctaatgtgt ttgaaacatt caagaaatgg aagactatgg 2220 ttgaaactga atcaggtctg aagttgaaat gcttaagatc tgataatgga ggagaatata 2280 ttgatggagg tttcaaagag tattgtgctg ttaatggtat cagaatggaa aagaccgttc 2340 caggcacacc gcaacagaat ggcattgctg aacgaatgaa ccggaccatc aatgaacgag 2400 ctagaagcat gaggttgcat tcagggctac ctcaaacatt ctgggctgac gcagttcata 2460 ctgcagttta cttgatcaac catggaccat cagttccttt ggaattcaga ttgcccgagg 2520 aagtatggag aggaaaagag gtacaacttt ctcatctaaa ggtctttagg tgtgtttcct 2580 atgttcatat agattctgat gctcgcaaca agttagatgc caaatccaag aaatgtttct 2640 tcattggcta tggagatgaa gaatttggat ttcggttctg ggatgatcag aatagaaaga 2700 ttatcagaag caggaacgtg atctccaatg agaaagttct gtacaaagac agatcaagtg 2760 tagaaacaga tatggctgat tcagatacaa gtccacaaaa atctgaattc ataagattag 2820 aagggcttcc tgatgttacc gagcagaaca gaaatcaaga gtctttacaa gaagattcaa 2880 acacatctgt acccactact acacaagaag atgcggagcc aagtgaacca actgtttatg 2940 ttcgcaggtc ttcaaggact gtaaagcccc cacaatggtt cacacttcta ctgaattata 3000 ttttactgac agatggtggt gagctgttaa gttatgaaga atccttacaa gatggaaact 3060 caagcgagtg ggagttagcc atgaaggatg agatgagttc gttgttgaag aataagactt 3120 gggaactaac cacattacct gaaggaaaga aggctttgca aaacaagtgg gtttacagag 3180 taaagactga gcatgacgga agcaaacggt tcaaggcaag acttgttgta aaagggttct 3240 aacaaaagaa agggattgac tactctgagg tattttctcc aattgtgaag ctcacaacaa 3300 tcagagttgt tctggggata gtagcagcat aaaatttaca tcttgaacaa ttagatgtaa 3360 aaacagcatt tcttcatggt gaattggagg aagacattta catgcaacaa ccagaggggt 3420 ttgcaacaca aggaaaggag aaccaagtct gcaagctaaa gaaaagccta tacggtttga 3480 agcaagctcc aagacagtgg tacaagaagt ttgacaactt catgtgtagt ttgggataca 3540 caagatgcca ggctgatcat tgttgctatg tcaaatattt tgacaactcc tacatcattc 3600 tactattata tgtggatgat atgttgattg caggatccag cattgaggag attgataagc 3660 tgaaacaaca attgtcaaaa cagtttgaaa tgaaggatct gggagctgct aaacaaatac 3720 ttggcatgat aatcatcaga gataaagaca aaggcatact aaagctttca caaatagagt 3780 atgtcaagaa ggttctcaac aggtttagta tggataatgc taaaccagta agtacacctc 3840 tagggaatca tttcaagctc agcaaagacc agtcaccaaa aactgagcta gaatgtggat 3900 acatggatat gattccatac gcctcagcta tcgactcttt gatgtatgct atggtctgta 3960 ccagaccaga cattgcccat gcagtgggag ttgtaagccg atatatgagc aatcctggaa 4020 agcaacattg ggaggcggta aaatggatca tgaggtactt aaaaggtttt ttggaaactt 4080 gtcttagttt tcacagctgg tggtttgaaa cttgaaggtt ttgtagacgc tgatctagca 4140 ggagatgttg atagcagaaa gagtactaca ggatatgtat acactctagg aggcactgct 4200 gtttcttgga gttctacctt gcaaaagatc gtcactcttt caacaacaga agctgaatat 4260 gttgcagtct cagaatctgc aaaagagatt gtatggttgc agagtttcct gaaagaattg 4320 ggcaagatgg atggaaaggg tactttgtat agcgacagtc agagtgcaat cttccttgcc 4380 aagaatccag catttcactc caagactaag catattcaga tcaaatatca cttcatccga 4440 caattgctag acgatgagca attgacgcta gaaaagatct gtggaagtaa gaatccagct 4500 gacatgttaa ccaaaggagt tacgcttgat aaactgaagt tgtgtaaaac ttcagttggt 4560 cttcaaggat aaaagataat ctcattgttt gtctccaagt gggagat 4607 // ID Copia-30_Mad-LTR repbase; DNA; EDCOT; 226 BP. XX AC ACYM01067653; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-30_Mad_; KW Copia-30_Mad-LTR; Copia-30_Mad-I. XX NM Copia-30_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-226 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1378-1378 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01067653; Positions 11008 11233. XX SQ Sequence 226 BP; 66 A; 33 C; 33 G; 94 T; 0 other; tgttagaata tatatattag tgtgtgggat tatgacactt gtcaatagat tgtgctttag 60 ttagttagtt tgttacatgt atttgagctt ctatataagt ctaaatgtaa tgacttcatg 120 agtaagaaag atataacaca agatattcat ctctttctct ctgcttactt tctctctcta 180 agttcttaat aattctctct ctgatatatc tgcatacata ttgaca 226 // ID Copia-4_Mad-LTR repbase; DNA; EDCOT; 185 BP. XX AC ACYM01011892; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-4_Mad-I; KW Copia-4_Mad-LTR; Copia-4_Mad_. XX NM Copia-4_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-185 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1344-1344 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01011892; Positions 9564 9380. XX SQ Sequence 185 BP; 63 A; 18 C; 34 G; 70 T; 0 other; tgttgccgtg agtctatatt tggaataagg aatgtagtga tattttgagt atgtaattga 60 tatcctaata tatttaggat atttacttcc tagttggtag gggattgtat aagtatatat 120 atattcctct atgtgagatg aataatatag aaaaacatat tcatgaaaac cctagaattc 180 tatca 185 // ID Copia29-PTR_I repbase; DNA; EDCOT; 4200 BP. XX AC scaffold_97; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia29-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4200 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4200 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 232-232 (2007). XX DR Genome; scaffold_97; Positions 1085234 1081035. XX CC Positions [1736-2056] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 0..0 FT /product="Copia29-PTR_I_1p" FT /translation="MASSSSSNSTTPPTIPTLSNLPFTMTIKLHSSNYPVW FT KAQVVPYFCGHDLYGYLDGTISIPPKELNISDSTSGTSQTIPNPLYHQWLR FT QDSLILATINSSLTEDVLTQVMSYTTSREVWLALENNFSSLSRAKVIQIRT FT QLANAKKGAMTANEFFLSVKRMADELALAGQPLPNDDIITYILAGLGQEYD FT SLASTISSRRDPVSLEELFSLLLICESRINHNNQPLLPSANLVTTSPQQFH FT RQTGTVQHSNRYRGHYRSRGRGGRSHFHDSTHSSSLICQVCLKPGHSARKC FT YHRFDLSYQAPPHSKNQPQALLAAHYLQPYKEWHPDTGATHHLTNDVNNIQ FT FSHANHDTQDHVQVANGAGLKIVRSGTSTLSSPSKSFTLNQILLVPDIQKN FT LLSVHRFCLDNNVFFEFHASFFIVKDYSGNTLHRGPLSNGLYNFSASLAHL FT QPQAFSSVRVSSQIWHRRLGHASFPVIHQAISLPSPNKNRPICSDCQLAKS FT HAMPFIKMHVAVSQPLELIYSDVWGPASTLSTSGARYYISFLDDATKFLWL FT FPLKLKSDAYQTFLSFTAVERQFGSKIKAFQSDWGGEYRSLNRYLHNQGIN FT HRITCPYTHQQAGAIERRHRQIVEIGLALLAHSKLPQKFWEDAFLTATFII FT NRLPTPILNHKSPYEMVHHQKPDYNFLRTFGCACWPYLRPYNQHKLDFRSR FT NCIFIGYSIGHRGYKCLDVSTGRIFVSRHVVFDENLFPYTALNSLSPPSPT FT PSVTLPSNLNLCSAGYSFSTGATPQSTASSTLHVASPSGPQTDHGDHLISP FT TLTFTEPPHTDPPPHIPLPSASAPPLQNLHPMTTRSKNNIHKPKLPPDFHV FT KYPIPKALLSAIQTPDTEPTCYTEAVKYPHWRTTMNTEFDALLQNGTWNLV FT PKPPTANLVGCKWVYRIKRKANGDIDRFKARLVAKGFHQQEGVDFSETFSP FT VVKPTTVRLVLSLAVSRGWPLRQIDIQNAFLHGHLNEDVYMAQPPGFSHSQ FT FPNHVCKLEKSLYGLRQAPRAWFSRLTDKLKSIGFLGSQADHSLFVYHHNS FT ILLYFLIYVDDIIITGSDIGSINQVITLLQGDFAVKDMGELSYFLNIEAIR FT TDDGLYLSQRRYILDLLMRSKMDRAKPCLTPTSTSLPLSKFTSITFHDPSL FT YGSIVGGLQYLSFTRPDIAFAIHKVSKFMHNTMDMHWAAIKRILRYLKHTI FT SHSLLIQPAANVTLQTFSDADWASDPDDRRSVGAYCVYLGNNLISWSCKQQ FT QTVARSSTESEYKALANAAAELQWIKSVLNDLGVPSVHSPILWCDNIGATY FT LTSNPIFHARTKHIEIDFHYVRDQVMSGQLIVRFISSKDQYADALTKPLPS FT VRFHTLRDNLRVRSLPFRLQGR" XX SQ Sequence 4200 BP; 1116 A; 1091 C; 698 G; 1295 T; 0 other; gagcccctac aaagacaaac gtcttctctt ctctaaactc taaatggcat cttcatcatc 60 ctcaaattcc actacccctc caactatccc aaccctttcc aatcttccat tcactatgac 120 tattaaacta cactcctcta actaccctgt gtggaaagct caagttgtgc catatttttg 180 tggtcatgat ctttatggct atcttgatgg cacaatctct attccaccaa aagagctcaa 240 catctctgac tctacctcag gtacaagtca aacaattcct aatcctctct atcaccagtg 300 gcttcgtcag gattccttaa tcctagccac catcaactcc tccctcactg aagatgtact 360 cactcaagta atgtcctaca ccacctcacg tgaggtatgg cttgcacttg aaaacaattt 420 ctcctccctt tctcgtgcta aagtaatcca gattcgaact caattagcaa atgctaagaa 480 aggcgccatg acagctaatg aatttttcct ctctgtcaaa cgcatggctg atgaacttgc 540 ccttgctgga caacctctcc caaatgatga tatcatcact tatattcttg ctggacttgg 600 ccaggaatat gattccctgg cctccaccat ttcctcacgg cgtgatcctg tcagtttgga 660 ggaactcttc tctctgcttc tcatatgtga atcacggatc aatcataata atcaaccact 720 tcttccttca gccaacctgg tcaccacctc accccagcaa ttccatcgcc aaactggcac 780 cgttcaacac tcaaatcgtt atcgcggtca ctatcgtagt cggggccgcg gcggccgttc 840 tcactttcat gattccaccc actcatcatc ccttatatgt caggtatgcc tcaaaccagg 900 tcacagtgct cgcaaatgct atcatcgctt tgatttatct tatcaggctc cacctcattc 960 caagaaccag ccacaggctc tccttgctgc ccactatctg caaccatata aagaatggca 1020 tcccgacaca ggggcaactc atcatctcac caatgacgta aacaatattc agttttctca 1080 tgccaaccat gatacacaag atcatgttca ggtggctaat ggtgcaggtc tgaaaattgt 1140 gcgcagtggc acttctacat tatcttctcc atctaaatca tttactctta atcaaattct 1200 gcttgttcct gatattcaaa aaaatttgtt atctgtccat cgtttttgtc tagataataa 1260 cgttttcttt gaatttcatg cctctttctt cattgtgaag gactactcgg ggaataccct 1320 acatcgcggc cccctcagta atggcctata caacttctca gcttccttag ctcatcttca 1380 gccgcaggct ttctccagtg ttcgtgtgtc ttcccaaatc tggcatcgtc gtcttggaca 1440 tgcttccttt cctgttattc atcaagctat ttctttacca agtccaaata aaaatcgccc 1500 catctgttct gattgtcagc tggccaagag ccatgctatg ccttttatca aaatgcatgt 1560 tgctgtttca caacctttag aattaatata ttcggatgtt tgggggccag cttctacatt 1620 atcgacctct ggtgcacgct attatatcag ttttttggat gatgctacta aatttttatg 1680 gctttttccc ttaaaactca aatctgacgc atatcaaacc tttctcagct tctaaactgc 1740 tgttgaacgc cagtttggca gcaaaattaa agcctttcaa agtgactggg ggggagaata 1800 ccgtagctta aatagatatc tacacaatca aggcatcaac catcgtataa cctgtcccta 1860 tacccatcaa caggctggtg ccattgaaag gcgtcatagg caaatcgttg aaattggact 1920 cgccttgctt gctcactcca aattgcctca aaagttctgg gaagatgcgt tcttaaccgc 1980 aacttttatt ataaatcgac ttccaactcc aatcttaaat cataaatctc catatgaaat 2040 ggttcatcat caaaagcctg attataattt tttacgcacc tttggttgtg catgttggcc 2100 ctatttacgt ccatataatc agcacaaact tgattttcga tcccgaaact gcatttttat 2160 tgggtatagt attggtcatc gaggttacaa atgtctagat gtttccacag gcagaatttt 2220 tgtttcccgt catgttgtct ttgatgaaaa tctcttccca tacactgcac taaactctct 2280 cagtcctcca tcaccaactc cttctgttac cctaccatcc aatctcaatt tgtgttctgc 2340 aggttactct ttttctacag gtgccactcc tcaatctact gcatcaagca ctctgcatgt 2400 ggcttctcca tctggtcctc aaacagatca tggtgatcat ttgatctctc ccacactcac 2460 tttcactgag cctccacata ctgatcctcc accccatatt cctttaccct ctgcctctgc 2520 tccaccccta caaaatttgc acccaatgac tacaagaagc aaaaacaaca tccataaacc 2580 gaagttgcca cctgatttcc acgtcaaata ccccattcct aaagctcttc tatctgcaat 2640 ccaaacacca gacacagaac caacttgtta cacagaggct gttaaatatc cacactggcg 2700 cacaactatg aacaccgagt ttgatgcttt actacagaat gggacttgga atttagttcc 2760 caaaccacct actgctaatc tagttggatg taaatgggta tacaggatca aaaggaaagc 2820 taatggtgat attgacagat ttaaagcaag acttgtagcc aaaggattcc atcaacaaga 2880 aggtgttgat ttcagcgaga catttagtcc tgtggtaaag ccaaccacag tgaggttggt 2940 tctctcatta gctgtttcac gtggctggcc tcttcgccaa attgatattc agaatgcttt 3000 tttacatggt cacctgaatg aagatgttta catggctcaa cctcccggtt tttctcactc 3060 tcagtttcca aatcatgttt gcaagctgga aaaatctctc tatggtcttc gtcaagcacc 3120 acgagcatgg ttttcgcgtt tgacagataa gctcaaatct attggatttc ttggaagtca 3180 agctgatcac tccctctttg tttatcatca caattccatt cttctttatt ttttgattta 3240 tgtcgatgac ataatcataa ctggcagtga tattggttcc ataaaccaag tgatcacatt 3300 gttgcagggt gactttgcag tcaaggatat gggtgaacta agctactttc taaacattga 3360 agctattcgc actgatgatg gtctgtatct atcacaacga cgctatattc tagacctctt 3420 aatgcgcagc aaaatggaca gagccaaacc ttgtcttact ccaacgtcaa cctcgctgcc 3480 attatcaaaa tttactagta ttactttcca tgatccttct ttatacggaa gtatcgttgg 3540 agggcttcaa tatctttcat ttactcggcc agacattgcg tttgccattc ataaagtcag 3600 caagtttatg cataatacta tggatatgca ttgggcggcc atcaaacgca tattgcgtta 3660 tttgaagcac acaatttctc attctttact cattcagcct gctgcaaatg ttactttaca 3720 aacatttagt gatgcagatt gggcgtccga tcctgatgac agacgttccg ttggcgccta 3780 ttgtgtatac ttgggcaata atcttatttc atggagctgc aagcaacaac aaaccgttgc 3840 tcgcagcagt acagaatccg aatacaaagc cctcgccaat gcagcagcag agcttcaatg 3900 gattaagtca gtgctcaatg atcttggtgt tccatctgtg cattctccta ttctatggtg 3960 cgacaacata ggggctactt acttaacaag taatcccatc tttcatgctc gcacaaagca 4020 tattgaaatt gattttcatt atgttcgtga ccaagttatg agtgggcaac ttattgttcg 4080 cttcatttcc tctaaagatc agtatgccga tgctctcaca aaaccgcttc catctgtcag 4140 atttcatact ttgcgagaca atctcagggt tcggtcccta ccctttcgat tgcaggggcg 4200 // ID Copia-57_Mad-LTR repbase; DNA; EDCOT; 810 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-57_Mad_; KW Copia-57_Mad-LTR; Copia-57_Mad-I. XX NM Copia-57_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-810 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1653-1653 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 810 BP; 254 A; 137 C; 134 G; 284 T; 1 other; tgttggaaat ttgagtagtt tgagtagaaa tttccttgtc ccacattggc cattcccaaa 60 agattttatc actttataag gctttgtcct ttatagaaag tgattggagt aataggcctg 120 gagamtaaaa ttgggctcac ccttggggtt gggctttggg gtgtactaat taattggtaa 180 ttaatatata attaattata taattaatat atatttaatt gtcaaaagat gggccttggg 240 gctctaataa ttaaattatt taattaatta ttttcggatt tattaattat ttttaattaa 300 ttcgaattta attaattatt tattttttac caacagactc atcctttcag atgaagtctg 360 agagttctgt aagaacacag agcaaagcac ccatctgaga gatgtctccc aacagtcgca 420 tcccatcctc atacctgttg cgaacaggca tcaatcacgt tatatataca tccatctgca 480 tggcatttag aacacagaaa atcataaatc ttcttctaca atcctaaaca tccttactga 540 gagaaccaca ctaaattcgc cagaagtcaa gttttccggt gctggaattt taacttagat 600 cgttgaatcc tggtgaagca gacgtccgta gaactacaag cacagagtag ggacgaaatt 660 tctgtttcaa ggacattgcg gtacgcaagc ctcgatcttc aagttgtctg ttttataatt 720 catattctag tttatattct gttaatttta ttgcatttat tatttattag catatataaa 780 ttatcacaga ttgttgacat atatccaaca 810 // ID Gypsy22-PTR_I repbase; DNA; EDCOT; 4628 BP. XX AC LG_V; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy22-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4628 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4628 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 324-324 (2007). XX DR Genome; LG_V; Positions 5839138 5843765. XX CC Positions [3323-3619] - Integrase core CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 883..3123 FT /product="Gypsy22-PTR_I_1p" FT /translation="MQRRRAQGLCFNCNDKFTAGHKCQRPQLLLLESLSEP FT VRVMCEEVTDDIPVEDIAEENTEPEISLHALTGWSTPRTMRIEGRVGNHTL FT TVLIDSGSTYNFINSKIAEELQLPIIPMGPFIVRVADGNRMKCQGRFEQVQ FT VILQNIPFSLTLYLIPITGLDLVLGVQWLEQLGPVVCNWKKLTMDFWWKNQ FT AQTLNGSNSQAIQPASLTAITKDVCHGCSTFTVYCQSIEKMERPNMQTNMK FT EIINNFEDIFYEPTQLPPSREVDHCIPLKEGIEPINMRPYRYAYFQKTEIE FT KQVQDMLKLGLIKPSTSPFSSPVLLVKTKDGTWHFCTDYRAFNSVTIKDRF FT PIPTIDDMLDELYGAAFFTKLDLREGYHQVRVNPKDTHKTAFRTHNGHYEY FT MVMPFGLCNAPSTFQAIMNSNFRPHLRQFILVFFYDILIYSPNWTMHLEHV FT TKVFEILRQHIFFVKANKCTFGQSELEYLGHIVTNKRVKVDSSKITAMVNW FT PRPSTISDLPGFLGLTGYYRKFVRNYGLLAKPLTNLLKKGQFRWSQEAEAA FT FLQLKQAMTTTPILAMPNFNESFTIETDASGEGIGAVLTQQGKPIAFLSRA FT LGVAKLSWSIYAKEMLAILQAIRTWRPYLLGKKFFIQMDQRSLKYLLEQRI FT GTPEQQRWVAKLLGYDYEIIYHPGRDNSAADALSRVSGSPILNALFVPQVS FT LWEDIKKGLHWTPIYGTNYSASSNQSWKTLYMARWVSFLQNTCCGAS" XX SQ Sequence 4628 BP; 1405 A; 938 C; 996 G; 1289 T; 0 other; attggtatca gagcttgcgc aatggcaaca aacaaataac gaattgagct tttggagaca 60 agacttggtg gagtccaaga tgacatacag cgactggaag attccatgat caacagattg 120 cacaacctgg aggaaaccat caacaagctt tcagaggcca tgatcgcttc caaggcgtct 180 tcaagttacc acaacaacga tcgggatggc ttctcacgca cacatcggga tgacactgat 240 tggggaaaga agaaaactga taatgagtgt ggatgccacg tcttctcatc aaaaatggcc 300 aagttagact ttccacaata ttctggggat gatccaaccg aatggttcaa ttgggtggac 360 caattttttg aatatcaaga gactgttgac aatcaaaaag tatcattggc ctcattccat 420 ttggaaggag aagccaacca atggtggcaa tggttgcatc gagcctacaa ggaagaagga 480 cgcactgtca cgtgggagat atttgaagaa gagctttggg cacggtttgg gcctacagaa 540 tgtgaggatt ttgatgaagc attatcaaag atcagacaag tgggttcctt aagggactat 600 cagaaggaat ttgagaggtt gggcaatcga gttcatggtt ggactcaaaa ggcgttggtg 660 ggcacattca tgagtggact taaagtagaa atttctgatg ctattcggat gttcaaacca 720 cggactttga aaaaggctat cagtttagct agaatgaagg atgaacaatt aacgcgtaag 780 ggaaatttac acggccaaca caatcaactc gcacaccatt gactcttccc cccaccaaaa 840 tctagttttc cagttccgat aaaaagacta acatgggatg aaatgcagag acggcgtgca 900 caagggctct gttttaattg caatgacaaa ttcactgctg gacataagtg ccaaagaccg 960 caactgttat tactagaaag ccttagtgaa cctgtcagag tcatgtgcga agaagttact 1020 gatgacattc cagtagagga catagctgag gagaacactg agccagaaat ttcactccat 1080 gcactcacgg gttggtccac accacggacc atgaggattg aaggacgagt tgggaatcac 1140 actctaacag tgctcatcga cagtgggtct acctataatt tcatcaattc taaaatagca 1200 gaggagcttc aattacctat tattcctatg ggacctttca ttgtaagggt ggcagatggc 1260 aatcgaatga agtgccaagg aaggtttgaa caagtccagg ttattctcca aaacattcca 1320 ttttcattaa ccctttattt aatacctatc acaggccttg atcttgttct tggtgtacaa 1380 tggcttgaac aactcggacc agtggtgtgt aattggaaaa aattgacaat ggacttttgg 1440 tggaagaatc aagctcaaac attaaatggt tctaatagcc aagctataca acctgcttca 1500 ctaacagcaa ttactaaaga tgtctgtcat ggctgttcca cttttacagt gtattgtcaa 1560 tccatagaaa agatggaacg acccaatatg caaacaaata tgaaggaaat catcaacaac 1620 tttgaggaca ttttttatga gcccacacag ttacctccat ctcgtgaagt tgatcattgc 1680 attcctctta aagaaggtat tgagcctatt aatatgaggc cctacaggta tgcctatttt 1740 caaaaaactg aaattgaaaa acaagttcaa gacatgctta aattggggct tataaaacca 1800 agtactagtc ccttttcttc acctgttttg ttagttaaaa caaaagatgg cacctggcat 1860 ttttgtactg attatagagc tttcaatagc gtaaccatta aggatcgatt tcctattcct 1920 accattgatg acatgcttga tgagctctat ggagctgcct tttttacaaa attagactta 1980 agagaggggt accatcaagt acgagtaaat ccaaaagaca ctcacaaaac tgctttccgt 2040 acccataatg gccactacga atatatggtc atgccctttg gtctttgcaa tgctccttcc 2100 actttccaag ctattatgaa ttctaatttt cgtcctcatc tccgtcaatt catattagtt 2160 tttttttatg atattttgat ttatagcccc aattggacca tgcatcttga acatgttaca 2220 aaggtttttg aaattctgcg gcaacatata ttttttgtaa aggcaaataa gtgtacattt 2280 gggcagtcag agctcgagta ccttggtcac attgtgacta ataaaagggt caaggttgat 2340 tcaagcaaaa ttacagctat ggtaaattgg ccaaggccaa gcactatttc agacttacct 2400 ggttttctag gccttacagg ttattatcga aaatttgtgc gcaactatgg tctgctggca 2460 aagccattaa ccaatctctt gaagaaaggg caattcagat ggagtcaaga ggcggaggca 2520 gctttcctac agctcaaaca agctatgaca accacaccca ttttagctat gccaaatttc 2580 aatgaatcat ttacaattga aactgatgct tctggagagg gtattggtgc agtgttgaca 2640 cagcaaggta aacccattgc tttcctcagc cgagcactcg gagtggccaa actttcatgg 2700 tcaatatatg ccaaagaaat gcttgccatc cttcaggcaa tacgcacttg gagaccatat 2760 ctactgggca aaaagttctt cattcaaatg gaccagcgca gtcttaagta tctattggag 2820 caaagaattg ggacaccaga acaacaacgt tgggtggcta aattacttgg ctatgactat 2880 gaaattatat atcacccagg acgcgacaac tcagcagctg atgcattatc aagagtgtct 2940 ggaagcccta ttcttaatgc cttgtttgtg ccacaagtca gtttatggga agacataaaa 3000 aaaggcctcc actggacacc catatatgga acaaattatt cagcaagctc gaaccagtcc 3060 tggaaaacct tatacatggc gagatgggtt agttttcttc aaaacacgtg ttgtggtgcc 3120 tcctaacaca gctgtgatag aacaattact acaagaattt catgatacaa agatgggcgg 3180 ccattctggt atattaggta cattcaaacg tctatctcag cagttttatt ggccatctat 3240 gtatcgttct atcaaagaat atgtccacac atgcgtgaca tgccagaaaa ctaaagctga 3300 taatcttaaa ccagctgggc tcttgcaacc tcttcctatt ccatgtcagg tatgggatga 3360 tgttactatg gattttattg aaggtttccc tacttcacat ggtcgcgata ccattttagt 3420 ggttgtggac cgtctaagca aatctgctca cttcttggcc ttagcacatc ctttcacagc 3480 aaagatggtg gcagaaaagt ttgtagatgg tgtggtgaag ctacatggca tgcctcgttc 3540 tattgtgagc gacaaagata aagttttatt agtaagtttt ggcatgaatt ttttaagatg 3600 tctggtactc agcttaagat gagctcagca tatcatcctc aaacggatgg ttaatcagcg 3660 gtggttaatc gttgtgtgga gcaatatttg cgctgttttg ttcaccaaag accacaacag 3720 tggagccaat ttcttccttg ggtagagctg tggtataata cagcttacca ttcatcaaca 3780 ggaatgacac cttttcaagc tctttatgga cgcttaccac ctacatttcc actttatgct 3840 acaggctcct caccagttaa tgaagttgat cacagtcttc aggtacggga cacactgctt 3900 aggaatctca aacagaattt agcgaatgct aggaatcgca tgaaacagtt ggctgatcgt 3960 gggcgaaggg atgtcgaatt catagaaggt gaccttgtgt atctcaaatt acaaccttat 4020 cgtcaacata ctgcttttcg acgagctcat caaaaacttg cttgcaagtt ttatggtcca 4080 ttcccaattg aaaaacgagt tggtgctgtg gcctacaaac tcaagcttcc agagggggca 4140 catttacatt cagtttttca tgtgtcgttg cttagaagga agttgggtga caaagcagac 4200 actagtatgg aacttccatc tattgatgaa gagggcacca ttgtggtcac accagaagct 4260 attctggaca cacgttggat tccacatggg gcaagattta ttgaggagag tttggtgaag 4320 tggaaacatt tgtctacaga tgatgccacc tgggaaccaa cggctgaact actaacgaac 4380 cacccaagct tggaccttgg ggacaagcgt ccacttgatg tggggggtaa tgatacgcag 4440 cttggagagc tgctgccacg aaggacccaa cgtatcataa agaagaattt gaaatatcgt 4500 gattaaaagg agttacatgc aagtcaattg gaatcatgct tccgattcaa tgggtgaaaa 4560 taaagcaacc actttcacat tatttgcatt tctgttttgt aatctgttat ttccatttcg 4620 gcgggatt 4628 // ID Gypsy-17_Mad-LTR repbase; DNA; EDCOT; 232 BP. XX AC ACYM01052055; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-17_Mad-I; KW Gypsy-17_Mad-LTR; Gypsy-17_Mad_. XX NM Gypsy-17_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-232 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1421-1421 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01052055; Positions 1553 1784. XX SQ Sequence 232 BP; 60 A; 42 C; 41 G; 89 T; 0 other; tgttaggtcc ttactgtgta ggccctcgat ataacgttat tatccttagt acagtagtaa 60 atgggtgtta ggtgatgact cagcttatga gatattttgt ctattgtgtt gaatggatat 120 aaatccccct tttgtaatga agttgaaagc aatgaatgaa aatagtcttt aatttcttct 180 tttcccttat cctttctcat ttccttcctg acctgtaact aggaccctaa ca 232 // ID Copia-70_Mad-I repbase; DNA; EDCOT; 4862 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-70_Mad_; KW Copia-70_Mad-LTR; Copia-70_Mad-I. XX NM Copia-70_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4862 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1678-1678 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [2131-2631] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 640..2916 FT /product="Copia-70_Mad-I_1p" FT /translation="MHDRALMQLLTATLSPSAVSCAIGSSSAHDLWQRLKE FT QFSIVTRATIFQMKSELQNIKKGTDSISIYLQRIKEARDYLFAAGVQFDDD FT DIVILTLNGLSSEYNTLRSIIRGRENVISMKDLRSQLLAEEAMVENVPITP FT FLSAMVARNNGSVSKPEGHSTDTSYGGSSPSTFYSSGPSGFRPNHSKNKYK FT GKFQYNSQSRFGNSKSTYGNYNVNSAPGILGSSPPKQQGFSSNSCQICGKF FT GHFAPTCRFRNSDSAISEGCQICGKKNHSAKYCHFRNSNPSTQAPTALHVS FT SSQHHQPSAHPQQFWLTDSGASSHMTADLSNMSLASPYPADETIQTASGAG FT LSISHIGSSTLHTPLKPLQLNSVLCVPGLSQNLLSVHKLCLDNHCWLIYDA FT FCFWIQDKATGRILFQGKCSNGLYPIPLPARVRAISSQPQAAYLGRQVSSS FT LWHSRLGHPSNSVVSVMLKKCNLSVSPDSLPVMCHTCLEGKFCKLPFVKSV FT SKSLHPFEVIHSDVWGPSPCTSIDGFRYYVTFIDECTRHCWLFPILNKSDV FT FSTFVGFSNFVSNHFSTSIKTLQSDGGGEYLSKSFQKFLLDKGIKHQLSCP FT YTPEQNGLAERKHRHIIETAITLLQTASLPPIFWSFAVQTAVYLINRMPSP FT TLHNKSPFELLFNDVPDVHHLRIFGCSVFPLLKPYNSTKLQPKTTKCIFLG FT YASSYKGFICYDIVHTRFYISRHVVFDESEFPYPTLSATRPVSITPPLHLY FT PLPHLHSY" XX SQ Sequence 4862 BP; 1195 A; 1089 C; 918 G; 1653 T; 7 other; tcttgagagt cttatgttag cttagtagct aagcaatgta gctagatata tacacaatgt 60 aatcagtgtt aatgttgttg aattgaattg aaaaataata catacgtttt ctttctctct 120 atctctttct tcctctctgt ttacatggta tcattcgcct gaaaagcttc ggcttgaagg 180 tttctcgatc ttggttcttc tgcttccgct ctatattctg catcaacggt ctgtcttctt 240 tttctccggg ccttgatttt tctctgtgtc ttcgactggg tgcatccttc tctttgcaca 300 ccaagtgttt gttataattc ctctgagaaa ttcttcattt gggtttcttc cttcttcggc 360 tgcaatggtg acttctgctc aactgcagat tcttcaatct cccatcacgt ctctcatatc 420 cacaatttct tcttctgtga ctgtcaaact cgatgattcc aattatctaa cttggaattt 480 ccagatcgag ttgctacttg aaggccatgg tcttatgggt tttgtcgatg ggtctcatcc 540 atgtcctgct cgattcgatg tccctatttc tgagggttcc tctgtccctt cgagtgatgt 600 ttcatcttcg actgaaagtg atgattcaag gtttggaaaa tgcacgatcg ggcattgatg 660 caattactca cagctacttt atctccttca gcagtttctt gtgcaattgg tagttccagc 720 gctcatgatc tgtggcagcg tctcaaagaa caattttcga ttgtcactcg agcaacgatc 780 tttcagatga aatctgaatt acaaaacatc aagaaaggta cggattcgat ttcgatatat 840 ttgcaacgca ttaaagaagc tcgtgattat ctgtttgctg ctggagttca gttcgatgat 900 gatgatattg tgattttgac cttgaatggt ctctcatctg aatataatac tctgagatct 960 attattcgag gccgtgagaa tgtcatctcc atgaaagatc tccgatctca gttacttgct 1020 gaggaagcaa tggttgaaaa cgttcccatt acacctttct tgtctgctat ggttgctcga 1080 aataatggca gtgtctctaa acctgagggt cattccactg atacttctta tggtggttct 1140 tctccgtcta cattttattc atctggtcct tctgggttca ggccaaacca cagcaagaac 1200 aaatacaaag ggaaatttca gtacaattct cagtctcggt ttggaaattc caagtccact 1260 tatggcaatt ataatgtgaa ttcagctcct ggcattcttg gttcttctcc accaaagcaa 1320 cagggttttt ctagtaactc ttgtcaaatt tgtggcaagt ttggacactt cgctcctacc 1380 tgcagattcc ggaattctga tagtgccatt tctgagggtt gtcaaatctg tgggaagaag 1440 aatcatagtg ctaaatattg ccatttcagg aactctaacc cttctactca agctccaact 1500 gctttgcatg tttcttcatc acaacatcat cagccaagtg ctcatcctca acaattttgg 1560 cttactgatt ctggagcatc ttcccatatg acagctgact tgagtaatat gtccctggcc 1620 tctccatacc ctgctgatga aaccattcag actgcgagtg gtgcaggttt atcaatatct 1680 catattggtt cctccactct tcatactcct ttaaaaccat tgcaattaaa ttcagttctt 1740 tgtgttcctg gattatctca gaacctgtta tctgtgcata aattgtgctt agataatcat 1800 tgttggttga tmtatgatgc cttttgtttt tggatccagg acaaagccac agggaggatt 1860 ctctttcaag gcaaatgcag taatggattg tatcccatac cacttccagc aagagttcga 1920 gctatctctt ctcagcctca agctgcctat cttggccgtc aagtatcttc tagtctttgg 1980 catagtaggt taggtcaccc atctaattct gtggtctctg tcatgttaaa gaagtgtaat 2040 ctgtctgtct cacctgattc cttgcctgta atgtgtcata catgtctgga aggcaagttt 2100 tgtaaattgc cctttgttaa atctgtgtct aagtctctcc atccatttga agtcattcat 2160 agtgatgtat ggggtccttc tccttgtact tcgatagatg gttttcggta ctatgtgaca 2220 ttcattgatg aatgcactag acattgttgg ttgtttccca ttcttaataa aagtgatgtt 2280 ttctctacct ttgttggttt ttctaatttt gtctccaatc atttttccac ttccattaaa 2340 acattacaaa gtgatggtgg aggagaatat cttagtaaat cttttcaaaa gtttttgttg 2400 gacaaaggca tcaaacatca actgtcctgc ccttatacac ctgagcaaaa cgggttagcc 2460 gaaaggaagc ataggcatat cattgaaact gctataaccc tgttacaaac agcttcctta 2520 cccccaattt tctggtcttt tgctgtccaa actgctgttt accttatcaa tcgaatgccc 2580 tcacctacac ttcataataa atctcctttt gaactattgt ttaatgatgt tccagatgtt 2640 catcatctca gaatatttgg ttgctcagta tttccgttac taaaaccata taacagtacc 2700 aagttacaac ccaagacaac caaatgcatt tttctaggct atgcttccag ttacaagggt 2760 ttcatttgct atgacattgt tcatacccgg ttttatattt ccagacatgt agtgtttgat 2820 gagtcagaat ttccatatcc caccttgtct gctacacgtc ctgtctccat aactccacct 2880 ctacatctgt accctcttcc ccatctccat tcatattagt cactggtacc aatcatattg 2940 tgtccctccc acattctagg acacctatta tgccagagac tatgtcacat ccatgttctg 3000 atcaacacag tggtacttct actccattac agtccattac tgcatcaaca ggccaccaat 3060 cctcttcttc attccctgtg gctcctgcga ttccaaatgk gtcatgttct gagatctttc 3120 atgagtctcc tactctgcct tcgagtgctc ctggtgttgc catacaacat gagtttcaac 3180 ctgacagatt gcaggttctt cttcctattc ctcctatgaa cactcattct atgcaaacac 3240 gagccaaaaa tggtatttcg aagaagaaag cttttctttc agtggttcaa gatgctgaat 3300 cagttgatct ttctcaaatg gaacctgcca cctataagtc ggctctaaag tctccattat 3360 ggttttctgc tatggaagaa gagttggctg ctcttaaaac acaacatact tggtctttgg 3420 tcccattacc tcataacaag aatttggtag gctgcaagtg ggttgttcaa gcttaagaga 3480 catgctgatg ggactatttc caggtacaaa gcaaggcttg ttgccaaagg tttcaatcaa 3540 gaagagggta ttgactatgg agaaactttt agtccggttg tcaaacctac aactgtgagg 3600 ttggtcatag ccttggcagc aaattttggg tggtctttgc gtcaacttga tgtgaagaat 3660 gcctttcttc atggcattct taatgaggaa gtgtatatgt ccagccacca gggtttagtg 3720 atccacataa tcctacacat gtttgcagat tgcataagtc cttgtatggc ttaaaacaag 3780 ccccaagagc atggaatgag aggttcacat cttttcttcc ttctctgggg ttcctttcaa 3840 catattctga tccgtctcta tttgtcaagc atgatggama ttctgtggtc attctcctcc 3900 tttatgtgga tgatattatc atcacaggga gtgattctgt ccctattgct gcagtgatta 3960 aggctttgac cgaggaattt gatattaaag atttaggtcc tcttcattat tttcttggga 4020 tccaaatcac acagaatgca agtggaatgt ttctctctca gtctaaatat gtgtctgatt 4080 tgttggttaa agcwgacatg gttcattcta agccgtgctc cacaccttgc ttaccgtata 4140 ataggttatt gaaagatgat ggccatcctt tcaataatcc ttctctctat agaagcattg 4200 tgggtgctct tcaatatctc actttcacca ggcccgatat ctccttctcg gttcatcagg 4260 tttgtcaatt catgcactgt cctatggact ctcattatgc tgctgtgaag aggattcttm 4320 ggtatttaaa aggtactatg gaccttggca ttcagtttcg caaaggagac ttggatcttc 4380 atgcattcag tgatgctgat tgggctggag accctaatga cagaaggtct accactggtt 4440 tagttgtgtt tctcgggcca aatcccattt cttggtcatc caagaaacaa aatacagttt 4500 ctcgttcatc tacagaggct gaataccgag ccctctcaag tacttctgca gaaattgatt 4560 ggatcaaaca gattcttcac tttatgcaga ttgatgtgcc ttgtccgacg accctgtwct 4620 gtgataatct ttctgccatt gcccttgcct ataatcctgt catgcatcag cggaccaaac 4680 atattgaggt tgatgttcat tttgtccgag aaagggtkgc aaagaagctt ctgcaggtgc 4740 actttgtttc ctcgaatgag cagtttgctg atatccttac aaaggggttg tctgctcctc 4800 tgtttcaaac acactgctac aatctcagac ttggcaagcc ccactctgag attgagggag 4860 ga 4862 // ID HAT3_MT repbase; DNA; EDCOT; 4030 BP. XX AC AC144404; XX DT 04-JAN-2007 (Rel. 12.01, Created) DT 04-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE hAT-type DNA transposon. XX KW hAT; DNA transposon; Transposable Element; HAT3_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4030 RA Jurka J.; RT "HAT3_MT: hAT-type DNA transposon from barrel medic."; RL Repbase Reports 7(1), 31-31 (2007). XX DR EMBL/GenBank/DDBJ; AC144404; Positions 85938 81909. XX CC The closest non-autonomous DNA transposon is Murbi_MT. XX FH Key Location/Qualifiers FT CDS join(1010..2284,2423..3259) FT /product="HAT3_MT_1p" FT /translation="MSSQANEEPTQAGANTTQAEANATQEEETQAEPIVGR FT KRKKTSVIWKDFDEKEITKGVFRAVCKHCKAQYTTGTVGSSTSQMKRHLVS FT CTAKKLQDATEKRQAAIPFKRVSSGNPFLTSGVGYSNERMREIIATAVMVH FT EYPFNVVEDDVWMWAFEYANPEFRKVTHKTTRSDCLKLFENEKKILKKQLE FT SVSKISLTTDMWKSSHQVVEYMVITGHFIDAGWNLQKRVLSFVKVPAPRRG FT IDVADAIHKCLKTWRIESKIFTVSVDNAAYNDLCLKYLKDNISMSRKLILN FT GDLFHVRCCAHILNLLVQDGLSKIKDIIFNIRESVKYVNHNDARLKNFCDV FT VEQKGLKERKLVIDCPTRWNSTFNMASTALKFKIVFSAYKEREPHYDHAPS FT FEEWDKVEKVCKLLEVFNSATHVISGSFSTILSFNITILNVGSEYPTANLY FT LPEVWRVKQVLDMADEDEDLFMREMAKPMKKKFDKYWGESNLLMAIASVLD FT PRCKFHSVCICFPKIYKSKEVSDENIEKVRRSLELLYDEYVALSLEESYLM FT PAVNLDNSSSSQTNVKNATGIDDLLQTIREQQAISPTKSELQDYLDQGVHV FT VPNSESFSALEWWRNNSMKYKILSKMAADILAIPISTVASESTFSAGGRVI FT DEFRSRLNEESVEALICGGDWFRHKYGVKNKSKVILCHDILLIFIHIFIWY FT CLVQ" XX SQ Sequence 4030 BP; 1186 A; 631 C; 797 G; 1416 T; 0 other; tagggttggg aataggctag gccggcctac aggggcctac gacctggcct atttaagcct 60 ggcctggcct ggcctattta ttaaaaaggc caggttaagg cttttttaaa agcctatttg 120 atcaaatagg ccaggcttag gcttttaaaa aagcctgtta agcctgatag gccggcctat 180 ttacacccat aagttaagcc taataggcct aattattatt atattaatat atatcaataa 240 aaaataattc ccatcccaat tcccattatc agctaaaaat atgaaacggc aaattgtatt 300 tcccaatttc cattcaatat cattcccaat taatggcttc tcttgaattg cttccttctt 360 ttgaatcgcc gccgctgcta gtaggtttga atcgctgctg cctgctgcct tctcttgaat 420 cgcagcctgc caccttatca ccgccgccgc cgtatcaccg tcgccgtatc aggttttctt 480 ctttcttctt tcttttcttt tttttgaatc gctgcctgct gccttctttt catttgaatc 540 gctgatacct tttcttcttt cttttctttt tttttttttt ttttatctct tcatagtgtt 600 cttcttatat tcgttatttg gattgaaact tcattttttc agctaaagat tgaatctttg 660 agatttttct gttattgggt ttttgtttaa tgttctctga cttgatttta gaaacccatt 720 tttttcagct aaagattttg ggtttcaact cataatctct gttacttgga agtttaatgt 780 tctctattat tgggtttctg tttaatgttc tcttcttcat cgtgttctac ctttcactgt 840 ttaaggttct agaatggaca actacaggtt gcaacctaga aatggagaaa aggaatatag 900 gaaaaccaaa ttttttagtt ttatggatca gaggcattta ataaaattga ttaatagttt 960 tctacttaat ataacacatt ttcattaatg tttttaccat ttacagcaaa tgtcttctca 1020 agcaaatgaa gaaccaactc aagcaggagc aaacacaact caagcagaag caaatgcaac 1080 ccaagaagaa gaaactcaag ctgaaccaat tgttgggaga aagaggaaaa aaacaagtgt 1140 aatttggaaa gatttcgatg aaaaggaaat tactaaaggt gtgtttagag ctgtttgtaa 1200 acactgcaaa gcacaatata ctactgggac ggtaggatcc agcacgagtc aaatgaaacg 1260 acatcttgta agttgcactg ccaagaaatt gcaagatgct actgaaaaga gacaagctgc 1320 tattccattt aagcgtgtga gttcaggtaa cccctttctt acttctggtg ttggatactc 1380 taatgaaagg atgagggaaa taattgcaac tgctgtaatg gttcatgaat atccttttaa 1440 tgttgttgag gatgatgttt ggatgtgggc attcgaatat gcaaatcctg agtttcgcaa 1500 ggttactcat aaaacaacaa gaagtgattg tttgaaacta ttcgagaatg agaaaaaaat 1560 cttaaagaaa cagttggaaa gtgtgagcaa gattagttta acaacagata tgtggaaatc 1620 tagccatcaa gtggttgaat atatggttat cacaggacat ttcattgatg cgggatggaa 1680 tcttcagaaa agagttttga gttttgtgaa agtgcctgca ccaagacgtg gtattgacgt 1740 ggctgatgct attcataaat gtttgaaaac ttggaggatt gaaagtaaaa tatttacagt 1800 atctgttgat aatgctgctt acaatgattt gtgcttgaaa tatcttaagg ataatatatc 1860 gatgagtaga aagttaatcc ttaatggtga tttgtttcat gttaggtgct gtgcgcatat 1920 tttgaatttg ttagtgcagg acggccttag taaaattaag gatatcattt ttaatattcg 1980 tgagagtgtc aaatatgtta accacaatga tgcaaggcta aagaacttct gtgatgtggt 2040 tgagcaaaaa ggtttgaaag aaaggaaact cgtcatcgat tgtcctacaa gatggaattc 2100 aaccttcaat atggcgtcaa ccgctttgaa atttaaaatt gtattttcag cctacaaaga 2160 aagagagcct cactatgatc atgccccttc atttgaagaa tgggacaaag ttgagaaagt 2220 gtgtaaattg ctagaagtgt tcaattctgc tactcatgtg atctcaggta gtttctcaac 2280 tatttaattg ttgtacttta ttactcttag aaatgtttaa tataactagt gtttaatata 2340 aatatttttg tactttatta ctcttaaaaa tgtttaatat aactagtgtt taatattact 2400 attttaaaaa tgtttaatat aactatcgtt taatataact attttgaatg taggtagtga 2460 gtatccaact gcaaatttgt atttgccaga ggtctggagg gtgaagcaag tacttgatat 2520 ggcggatgaa gatgaagatc tctttatgag agaaatggca aaaccaatga aaaagaagtt 2580 tgacaaatac tggggggaga gtaatttgtt gatggctata gctagtgttt tggatcctag 2640 gtgcaaattt cacagtgttt gtatatgttt tcccaagata tataaatcca aggaagtttc 2700 tgatgagaat atagagaagg ttaggcgttc cttggaatta ttatatgatg agtatgtggc 2760 cttatctttg gaagagtctt atttgatgcc tgctgttaat ttggataatt catcttcctc 2820 tcaaacaaat gttaaaaatg ccactggaat tgatgacttg ttacaaacca ttcgggagca 2880 acaagccatt tctcccacga agtcagaatt gcaagattat cttgatcaag gtgttcatgt 2940 tgttcctaac tctgaatcct ttagtgcttt ggaatggtgg aggaacaaca gcatgaagta 3000 taagatcttg tctaagatgg ctgctgatat actagctatt ccaatctcaa ctgttgcatc 3060 agagtccaca ttcagtgctg gaggtagagt tatcgatgaa tttcgctcta gattaaatga 3120 agaatctgtt gaagctctca tttgtggtgg tgattggttc cgtcataaat atggtgtgaa 3180 gaacaaatca aaggttattc tttgtcatga tattttacta atatttattc atatattcat 3240 atggtattgt ttagtccaat aactaaagta tttttttctt ttggttccca aggttgataa 3300 agatgagata caaatcaact tgaagatttg atatcatttt ggttttttgg gctggtttgt 3360 gtacatgaag ctgatgagtg atttgttgac ttgtgtgata tgttgaatta tgctgacttt 3420 tgctacacct tgaagatttg atatcatttt ggttttttgg gtggtctctg tacatggagc 3480 tgactatgag tgatatgttg acatgctgac ttttgctaca cttgagtttt gactaagacc 3540 atgtgactat gagtctatga ctaatgagtg tcactctatc actcatttct ttttttgttt 3600 tctcatatca agcactttat gaaatcatat gattttctat tttttggtga attgtactca 3660 aatggttgat aaacattgat gagtactaac gaaagattat tattattagc tctaaattca 3720 ttgtgatttg ttgttttgtt gttataggct tttaaagagc ttgttatgtt gttaaatttt 3780 gtttttagta aaataggctt aaaggcctgt ttagcctatt tagtacgtaa aatgaactat 3840 ttgatgacca taatgttaaa taggcttcaa attaggcttt caggccaggc caggcttttt 3900 aataggccag gccaggccaa gaaaaacggc ctatgatagg ccataggcca ggcttaggct 3960 tgtatatttt ttcgtaggcc aggctcaggc ctttcaaagc ctggcctggc ctggcctatt 4020 cccaacccta 4030 // ID Gypsy-31_VV-I repbase; DNA; EDCOT; 4527 BP. XX AC chr5; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-31_VV_; KW Gypsy-31_VV-LTR; Gypsy-31_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4527 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr5; Positions 21421281 21416755. XX CC Positions [3415-3909] - Integrase core CC 'TCATA' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 1027..4332 FT /product="Gypsy-31_VV-I_1p" FT /translation="MTENDGVPNEVQLAATEVTIQGEQPELMIDHPQISFH FT AFTRQLIPSTLKLAGSINGQSVVVLIDGGSTNNFIQSRLTKHLGLTVQTSP FT HLKVTIGNGDSLGCAGACSRVPLVLGEAYFAVDLLLLPIYGADLVLGVQWL FT SELGPILFDYKKLWMEFDYKGVKTKLHGLTQPSIAQMTLNPLSRSLQTDSI FT AHFYLLSVDHVPTSTEPKIGVQAPPHFRQQLQSLLNQFRQNFAPPSSLPPQ FT RQLDHRIPLLPNTTPVNVRPYRYPHFQNEEIEKLVGEMLRDGIIRPSTSPF FT SSPVLLVKKKDGTWRFCVDYRALNAVTVKDRFPIPTVDELLDELYGASVFS FT KLDLRAGYHQVRIHPPDIEKTAFRTHEGHYEFIVMPFGLSNAPSTFQALMN FT SVFRDKLRKFVLVFFYDILVYSKSWEDHQKHLEMVFSVLASHSLFAKLSKC FT EFGCVELSYLGHRISDQGVAVEPDKVSAIQKWPLPATIKELRGFLGLCGYY FT RRFVYRYASTTAPLTKLLCKNAFVWTKEATGAFEALKHALATTPVLAMPDF FT SNPFVLQTDASGSGIGAVLVQKGHPIAYFSKELPSKLRRESAYCREMFAIT FT EAIQKWRQYLLGRRFIVETDHQSLRALHNQTIQTPEQQKWLTKLLGFDFDI FT CYRPGRENQPADALSRLVEHTYMALQIVSKPVMAIWDALKEFYQQHPPSAH FT LMQSAQQDDSTGYAVREGLLWFNGKVVVPPDSALQRLILTEFHNTPVGGHA FT GMQRTLSRIASMFYWPKMRQLVRDFVARCQVCQAIKPFNKAPQGLLQPLPI FT PGKIWDSISMDFVTHLPPASGKSVIMVVVDRLSKQAHFAVLPGAFNAPMVA FT ALFIKEIVRLHGFPTTIISDRYPVFMSSFWQELFKLQGTTLATSSAYHPQT FT DGQTEVLNRCLEDYLRCFVADHPKQWLHYLSWAEWHYNTAYHSTIKMTPFE FT AVYGRPPPSLLDYLGDSASIDAVDALLKDRTQILSTLKDSLLRAQTRMRNQ FT TNTHRTDITFQVDDWVFLKLKPYRQTTVAHRQSQKLSKRFFGPFRIITKIG FT AVAYKLALPEDARIHNVFHVSNLKKMSRRLAGAATNSTTRPIQRL" XX SQ Sequence 4527 BP; 1212 A; 1244 C; 902 G; 1169 T; 0 other; tttttggtgc tttcattgaa ttccatggct gagggtgctg tcactcgtgc caaagaccat 60 gctgagcaaa ttagcaaact ccacgacaaa taccaagaac acactaccac catcgctgac 120 ctccaaaaat acaccgctga caaactttcc accctcacca cagccatctc ttctcattcc 180 accattctac agtatgttgt ggccaagcta tccaccctca ctttacctac cacaaccgcc 240 cctccaccac ctctactccc attaccacaa ccttcatcaa aactttccag cccctttgcc 300 actggttcat catccaatac ctttccccca ccaggtgacc cttctgtttt tccacctcct 360 cggctcccaa aattggagat ccctcttttt agcggtgata atgttcaagg ctgggtgttc 420 ccgatggaac gtttctttac ctatcaccgt acacccccgg attagaaaat gaccatcgca 480 gctttttaca tgactggtat tgctctgcaa tggttccaat ggatgcactc tacctcacaa 540 ctttcctctt gggaagtttt cactcaccaa ctggacctgc ggtttggacc ctccaagttc 600 atcaaccatg aggcacaatt atacaaactc aaacaaacct ccactgtgga agcatatctg 660 gcggattttg agaatgtttc aactcgcgtg acagggttaa gccacgctaa catgcttaac 720 tgtttcatat ctggactccg tgacgatatt caacgcgagt tatccatact caaaccttac 780 accttgcatg aagctatggg attagccaaa ctcttggaag ataagtgtaa tacggccaaa 840 ccgttcttta agaaaagcac cgccctcccc acaccatcag caccgaccaa accagccact 900 cctctacctc tcaaacgcct cacgccagct gaaatggcaa ctcgctgagc acagggtttg 960 tgttttaact gcgatgacaa gtttgtaccg ggccatcgtt gccgccctcc gcagtttttg 1020 tgcctgatga cagaaaatga tggagtgccc aatgaagtac aattggcggc cacggaggta 1080 acaatccaag gagaacagcc tgagctgatg atagaccacc cacaaatctc gttccatgcc 1140 tttacaaggc aactcatccc ttcgacactg aaattggctg gttccattaa tggacagtca 1200 gttgtcgttc tcatcgacgg aggctccaca aataacttca ttcaatccag gttaacaaaa 1260 catttgggcc ttacggttca aacatcacca cacctgaaag taacgatcgg caatggcgat 1320 tctttgggct gtgcaggggc ttgctcacga gtaccactgg ttttaggaga agcctatttt 1380 gctgtggatc tattactact accaatatat ggtgcagatc ttgtccttgg ggttcaatgg 1440 ctttctgaac ttgggccaat tctttttgac tataagaaac tatggatgga atttgactac 1500 aaaggggtta aaacaaagct ccatgggcta acacagccgt ccattgccca aatgacacta 1560 aacccactat ccagatccct ccaaaccgac agtatagccc acttttacct attatcagtt 1620 gaccacgtcc ccacctccac agaaccaaaa atcggggttc aagctccacc acacttccgc 1680 caacagcttc agtccctcct caatcaattt cgtcagaatt ttgcaccacc atccagcctt 1740 cccccccaac gccaactaga ccaccgcata cccctactac ccaacacaac cccagtcaat 1800 gtcagacctt acaggtaccc acattttcaa aatgaggaaa tcgaaaaact ggtcggagag 1860 atgcttcggg atgggattat ccgcccaagc accagccctt tttcttctcc agttttactg 1920 gtcaaaaaga aggacggaac atggcgcttc tgtgtagatt atcgcgccct gaatgctgtc 1980 acggttaaag accgttttcc aatccctaca gtcgacgaac tgctcgacga gctgtatgga 2040 gcttcagtct tctcaaagct ggatctcaga gcaggatatc atcaggtccg aattcatcca 2100 ccagatattg aaaagacggc gtttcgcaca catgaaggcc attacgagtt tattgtaatg 2160 ccattcggcc tatcaaatgc gccatccacc ttccaagctt taatgaattc tgtttttcgt 2220 gacaaactga gaaagtttgt tttggtcttt ttttatgaca ttttggtcta cagcaaatca 2280 tgggaagacc accagaaaca cttggaaatg gtattctcgg tccttgcttc ccattcctta 2340 tttgctaaat tgtctaaatg tgagtttggc tgtgtggagt taagctatct gggccatagg 2400 atctctgacc agggtgtagc ggttgaacca gacaaggttt cggctataca aaaatggccg 2460 ctgccagcaa cgatcaaaga actgagaggt ttcctcggct tatgcggata ttatcggcgt 2520 ttcgtttatc gctatgcctc cactaccgcc cctctcacca agctgttgtg caagaatgcc 2580 tttgtctgga ccaaggaagc cactggcgct tttgaagctc tgaagcatgc gctagccacc 2640 acaccagtcc tcgcaatgcc tgatttttct aacccttttg tcttgcagac agatgcatcc 2700 ggctcgggca taggagcggt tttggttcaa aagggtcacc ctattgctta cttcagtaag 2760 gaattacctt cgaagctcag aagggaatcc gcctattgca gagaaatgtt tgccatcaca 2820 gaagcaatcc aaaaatggcg acaatacctc cttggccgca gattcatagt ggagactgat 2880 catcaaagcc ttcgcgcatt gcataatcag acaatccaga cccctgagca acaaaaatgg 2940 ctaacaaaat tgcttggttt tgattttgat atttgttaca ggcctggaag agagaaccaa 3000 ccagctgacg ctctgtctcg ccttgttgaa cacacctaca tggcgcttca aatcgtatcc 3060 aaaccggtga tggcaatctg ggatgctctt aaagaattct accaacaaca ccctccgtcg 3120 gctcacctaa tgcaatcagc acagcaagat gattctactg gttatgctgt ccgtgaaggg 3180 ttgctttggt tcaacggcaa agttgttgtt cctccggatt cagctttaca acgcttaatc 3240 ctgacagaat ttcacaacac tcctgtggga ggacatgcag gcatgcaacg gaccctgtca 3300 aggattgcta gcatgttcta ttggccaaaa atgcggcaat tggttcgaga ttttgtggca 3360 aggtgtcaag tctgtcaagc tatcaaacca ttcaacaaag caccacaggg attacttcag 3420 ccacttccaa tcccgggtaa aatatgggat tctatctcaa tggattttgt tactcacttg 3480 ccgcccgcat cgggaaaatc cgtaatcatg gtggtggttg ataggctatc caagcaagct 3540 cactttgcag ttttaccggg tgcattcaac gcccccatgg tggctgccct cttcattaaa 3600 gagattgtcc ggttacatgg ttttcccacc accatcatct cggaccgata tcctgtcttc 3660 atgagttcgt tttggcaaga gctcttcaaa ttacagggca cgactcttgc aacaagtagc 3720 gcataccatc cccaaactga cggacagacg gaagtcttaa accgctgcct tgaggattac 3780 ttaaggtgtt ttgtggctga ccatcccaag caatggttac attacttgtc atgggcggaa 3840 tggcactaca acacagcata ccattcaaca atcaaaatga caccatttga agctgtgtat 3900 ggccgtcccc ctccatcact gttagactac ttgggagatt cggcctctat agatgctgtt 3960 gatgccctcc tgaaagacag gactcaaatc ctgtcaactc tcaaagacag tctgctgcgt 4020 gcacaaacca ggatgcgcaa ccaaaccaat acccatagaa ctgacattac attccaggtt 4080 gatgactggg tttttctcaa gctgaagccc tacagacaaa ctacagtagc ccatcgccag 4140 tctcaaaagc tctccaaacg gttctttggt ccgtttcgca tcatcaccaa gatcggcgca 4200 gtggcttaca agctagccct tcctgaggat gcccgaatcc ataacgtctt ccatgtctcc 4260 aatttaaaaa aaatgtcgag gagactcgct ggagcagcca caaattccac tacccgcccg 4320 attcaaagac tctaacccca ttctccaacc tgctcatgtt ttgggattcc ggcagatttc 4380 gcagttgggc aaactttgtc ctcaactctt aattcagtgg gaaggacaag acccctctga 4440 tgccacctgg gaaaacactc acgaattcca gcaagatttc cctgatttca accttgagga 4500 caaggtcagt ttcgaagaca agggtaa 4527 // ID GmOgre_LTR repbase; DNA; EDCOT; 1668 BP. XX AC . XX DT 16-SEP-2008 (Rel. 13.09, Created) DT 16-SEP-2008 (Rel. 13.09, Last updated, Version 1) XX DE GmOgre_LTR consensus. XX KW Gypsy; LTR Retrotransposon; Transposable Element; GmOgre_LTR. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-1668 RA Laten H.M., Gouvas E. and Badal E.B.; RT "LTR of an Ogre-related retrotransposon in Glycine max from RT consensus sequence assembled from robust collection of RT BAC-ends."; RL Repbase Reports 8(9), 905-905 (2008). XX DR [1] (Consensus) XX CC Ogre-related consensus sequence based on collection of 80 CC sequences from the Genbank Genome Survey Sequence database to an CC average density of 31 sequences. XX SQ Sequence 1668 BP; 496 A; 359 C; 337 G; 465 T; 11 other; tgtcataccc taatttcgtc cggggacctt tgcttgatga catgcgaccw ttctttggtc 60 cttgtgaggt gcttggcacc catcattagg caatttgtga aattccagga catgccgaaa 120 aaccaaaaaa atattgatgc acaatccgta agtttccgtg acacaccgga aatcaaatgg 180 aagcatcgtt gcataattaa gtgaggttcc gtaacattcc gtaagtcaaa aaggggatga 240 ttatgtaatc cgcaaggttc cgtaacatta cggaaagaaa acaagtatcg ttacgaaatt 300 cgtaagtttc cgtaacttta cgaaaaaaga atcaccaaaa aaaagcagag gggggtgtac 360 ttagtaaaaa tgggggtgca aatagcaccc aggcccactt gggccctcca gaatattcct 420 ccagaaggct gttgcttctg gaggaagcaa cctggctcgc ctgggcgagc tgrgctcgcc 480 tgggcgagct gggcggcaac cacctcccct attttgctat aaatagggga ggaagtgaag 540 aagaaaaggg ttcagcccct twggcacttc tctctctttc gaatttgctt ggaaaaattg 600 tttccgtgaa gaaaatctaa gccgaggcgc ttccgaaacg tttccgtaac gttttccgtg 660 argaatttcg caaaggtttc aaccgttctt cgacgttctt cattcgttct tcatcgttct 720 tcgatcttca acgggtaagt acctcgaacc aagcttttcg attcattcta tgtacccgta 780 gtggtccaca ttgtgtttcg tgcattttta ttctcgtttt gtttactttt tataccccct 840 gttgacgtgc ttaagccatt ttacttaagt crtttctcgc ttaacttaaa aataaaataa 900 atttccaccg aacgtttgaa ttgtattatc cattaacttc ggttaaaata aattccgacc 960 gttcggtcrt gccgtaacca cgttggaaat caaaaagagg taaaaaataa tataataatc 1020 aaaaaracat cttttagtaa aataaagcgg aaaatcaatc ggacgttttc tctttgggat 1080 ttctcattct taaycgaatt gattaataac taaagtgaaa ctaaggctaa aatcaactcg 1140 cctagtcaag ctcgtccaca aaaataggct tttgaagttt gtcatttcaw tttctcacta 1200 agtaaaatgg atcattttta aggtccaacg ccttaaaatg atcaccwctt aagtaaaaaa 1260 gaatcacttg ataagaaaga actacgtagg tctgattttc tcatcccaaa ttgaggaata 1320 cgtaggagca aagggaaaca cccttgtcga ccacaaaaaa ggaaaaaata taaaaagggt 1380 ataaaggata taagaacata aaagggaaca taaaaatcaa agtcatgttt gcacattcga 1440 ttaaaggctg ccgtcccttg ggacggrcgt gtggggtgct aataccttcc ccgtgcgtaa 1500 atacaactcc cgaacctttc acttaaaagt tcgtagatcg cgtcttttcc ggtttttccg 1560 acgttttcct caaataaacg ttggtggcga ctccgcgcgt attcctttcg tggaacacgc 1620 atcccgcgag tctcgcgtcg ccctcccgcc gaagggtagg ttgcgaca 1668 // ID SHACOP3_I_MT repbase; DNA; EDCOT; 4647 BP. XX AC . XX DT 12-JAN-2007 (Rel. 12.01, Created) DT 21-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP3_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; ORF; polyprotein; KW SHACOP3_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4647 RA Shankar R. and Jurka J.; RT "SHACOP3_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 73-73 (2007). XX DR [1] (Consensus) XX CC The internal region is complete and intact. It is present in 5-6 CC complete copies in the Medicago genome. It has a single frame in CC which intact domains of gag,integrase,pol and CCHC zinc finger CC motif are present. On both sides it is flanked by intact LTRs CC which are highly identical to COP4_MT LTRs (>90%). XX FH Key Location/Qualifiers FT CDS 31..4644 FT /product="SHACOP3_MT_1p" FT /translation="MSTSSPSDAQRVTAAASKTFKQVVSVKLDDTNYLQWK FT QQVEGVLRGTKMVKFVISPDIPPVFLTDAAREAGTENPAYTEWEEQDSLLC FT TWILSTISPSLLSRFVLLRHSWQVWDEIHSYCFTQMKTRSRQLRSELRSIT FT KGSRTVSEFIARIRAISESLASIGDPVSHRDLIEVVLEALPEEFDPIVASV FT NAKSEVVSLDELESQLLTQESRKEKFKKAAISEPVSVNLTETANSESQSHG FT PNSQNHNYTDGTGNNQFPNSNPNFGGRNGQFRGRGGRFGGRFRGRGGRFGG FT RSNVQCQICSKTGHDASYCHYRFFVPQNDYYSPYGSPGGYGAPPNVWMQNM FT SRPQHSGQFLRPPTQAANQRGQAPQAFLTGSDPYNSFNNAWYPDSGATHHV FT TPDASNLMDSTSLSGSDQVHIGNGQGLAITSVGSLQFTSPLHPQTTLKLNN FT LLLVPSITKNLVSVSQFAKDNNVYFEFHPNHCFVKSQDSSKVLLRGILGHD FT GLYQFEHTKSFKTTAPVSQNSSVNTVCNKVPAQTDNSASFHLSPSTGFNFN FT NFQCNNVEHLPSSSTSSSTQSFPSMYGIWHSRLGHPHHEVLQSIIKLCNIK FT LPNKSLSDFCTACCHGKVHRLPSFASQMTYTKPLELIFCDLWGPAPVESSC FT GYTYFLTCVDAYSRYTWIYPLKLKSHTLSTFQNFKTMIELQLNHKITSVQT FT DGGGEFLPFTKYLNSLGITHRFTCPHTHHQNGSVERKHRHIVETGLTLLSH FT AQMPLKFWDHAFLTATYLINRLPTPVLANKSPFFLLHLQFPDYKFLKSFGC FT ACFPFLRPYNSHKFDFHSKECVFLGYSNSHKGYKCLDASGRIFISKDVVFN FT EVKFPYLDLFPSQKVCSVLPDGPTLSTFLPTPVSTTFTVNSHTPQNSHSES FT GPHIVNSPTPQTSHSESVPTTPISNTPQTPSISSHHSESSHRNNVVLNPTP FT ITILSPSASQNSSPESSASVTSSQSTNSESPPPVPHRIHPQNCHTMRTRGK FT HGIVQPRINPTLLLTHVEPTTYKTALQDPKWHLAMQEEYNALLHNQTWSLV FT SLPANRLAIGCKWVFRVKENPDGTVNKYKARLVAKGFHQQAGFDYNETFSP FT VVKPVTVRTVLTLAVTYNWTLQQLDVNNAFLNGVLTEEVYMVQPPGFESSD FT KNLVCKLHKALYGLKQAPRAWFERLKSSLLSFGFKSSRCDPSLFTLHTQAH FT CIFILVYVDDIIITGNSKLAIQNLVHQLNSEFSLKDLGILDYFLGIEVHHS FT PSGSLLLSQTKYIKDLLQKANMINANSMPSPMASSTKLSKFGSSTVSDPTF FT FRSIVGALQYATITRPEISYSVNKVCQFLSNPLEDHWKAVKRILRYLQGTL FT HHGLMLTPASSTEPIAITGFCDADWASDPDDRRSTSGACIFLGPNLVSWWA FT RKQTLVARSSAEAEYRSLAQASTEIIWIQSLLNELQIKSKIPHVYCDNLSA FT VSLAHNPVLHSRTKHMELDIFFVREKVIRKELNVSHVPAQDQWADVLTKPL FT STARFLYLRDKLRVCDTLRLKG" XX SQ Sequence 4647 BP; 1293 A; 1075 C; 819 G; 1460 T; 0 other; atggtatcta gagcttcttg atccagagcc atgtctacgt cttctccctc tgatgcgcaa 60 cgcgtaactg ctgcagcatc caaaaccttc aaacaagtag tttctgttaa gcttgatgat 120 acgaactacc ttcaatggaa gcaacaagtc gaaggtgttc ttcgcggaac gaagatggtg 180 aaatttgtga tttcacctga tattccaccg gtttttctca cagatgcagc gcgcgaagct 240 ggaacggaga atcctgctta cactgaatgg gaagaacaag attcattgct ctgcacctgg 300 attctttcaa cgatttcgcc ttcgctactt tcgcgattcg ttctccttcg ccactcatgg 360 caggtttggg atgagatcca tagttactgc ttcacgcaga tgaagacgcg ttcgcgtcaa 420 cttcgatctg aacttagatc cattacgaaa ggttcacgca ctgtctctga attcattgct 480 cgaattcgcg caatttcaga gtctcttgct tcaattggag atccggtctc tcacagggac 540 ctaattgaag ttgttcttga agcacttcct gaagagtttg accctattgt tgctagtgtg 600 aatgcaaaat ctgaggttgt ttctttagat gaacttgaat ctcagcttct cacacaagaa 660 tctagaaagg agaagttcaa gaaagctgct atcagtgaac ctgtttcagt taatctcact 720 gaaactgcaa attcagaatc ccaatctcat ggtcctaatt ctcaaaacca caattatact 780 gatggcaccg gaaacaatca gtttcctaac tctaacccta attttggagg aagaaatggc 840 cagttcagag gacgtggtgg ccgttttggt ggtagattca gaggacgtgg tggccgtttc 900 ggtggaagat ccaatgttca atgccaaata tgttcaaaaa ctggtcatga tgcaagctat 960 tgtcactacc gtttctttgt cccacaaaat gattactaca gtccctatgg ctcaccagga 1020 ggctatggtg cacctccaaa tgtatggatg cagaacatgt cacgtcctca acattctgga 1080 cagtttctta ggcctcccac acaggctgcg aatcagagag gtcaagctcc ccaggccttc 1140 ttaactggct cagatccata caattcattc aacaatgcct ggtaccctga ctcaggtgct 1200 actcatcatg tcacccctga tgcatccaac ctcatggatt ccacgtctct ttcaggttct 1260 gatcaggtcc atattggaaa tggacaaggt ttggctatta cctctgttgg ttccttacaa 1320 tttacttctc ctttacatcc tcaaactact ctaaaactaa ataatctcct tcttgttccc 1380 tctataacca aaaatcttgt tagtgtgagt caatttgcta aagataacaa tgtttacttt 1440 gagtttcatc ctaatcattg ttttgtcaaa tctcaggatt cttctaaggt gcttttaaga 1500 ggtattctag gacatgatgg tctctatcaa tttgagcaca ccaaatcatt caagaccact 1560 gctcctgtct ctcaaaattc tagtgtcaac actgtttgca ataaagttcc agcacaaact 1620 gataattctg cctcttttca tttaagtccc tcaactggtt tcaatttcaa taattttcaa 1680 tgcaataatg ttgaacattt acctagtagt tcaacatcta gttctactca gtcttttcct 1740 tccatgtatg gtatctggca tagcagactt ggacatcctc atcatgaggt gctccaaagt 1800 attatcaaac tttgtaatat aaaattacca aataaaagct tgtcagattt ctgtactgct 1860 tgttgtcatg gtaaggttca tagactgcct tcttttgcat ctcaaatgac atatactaaa 1920 cctcttgaat taattttctg tgatctttgg ggacctgcac cagttgaatc ctcttgtgga 1980 tatacctatt ttcttacttg tgtggatgct tattctagat acacatggat atatcctctg 2040 aaactcaaat ctcacacact ttctacattt cagaatttta aaaccatgat tgaattgcag 2100 ttaaatcaca aaattacttc tgtccaaact gatggaggtg gtgagttttt acctttcaca 2160 aaatatctca atagccttgg catcactcac agattcactt gtccacacac tcaccatcaa 2220 aatggctcag ttgaaaggaa acatagacat attgttgaaa ctggtctcac tcttttatct 2280 catgcacaaa tgccattaaa gttttgggac catgcctttt taactgcaac ttaccttatc 2340 aacaggttac ctacaccagt tttagcaaat aaatcaccct ttttcttact tcaccttcaa 2400 tttccagact ataaattcct taaaagcttt ggttgtgcat gttttccctt tttgagaccc 2460 tataactctc ataagtttga ttttcattca aaggagtgtg ttttcttggg atattccaac 2520 agtcacaaag gatataaatg tttagatgct tcaggtagaa tttttatatc caaagatgtt 2580 gtgtttaatg aggtaaaatt tccttatctt gacttgtttc catctcagaa agtgtgttct 2640 gttttaccag atggtcccac tttatccact tttcttccca ctcctgtctc aacaaccttt 2700 actgtaaact cacatactcc ccaaaattct cattctgagt ctggtcctca cattgttaac 2760 tcacctactc cccaaacttc tcattccgag tctgttccta ctactcccat atcaaacacc 2820 cctcagactc catctattag ttctcatcac tccgagtcct cacacagaaa taatgtggtc 2880 ctaaatccca cacccatcac cattctatct ccctctgcat ctcaaaattc ctcacctgag 2940 tcatctgcta gtgttactag ctctcaatct actaattctg agtctcctcc tcctgttcct 3000 cacagaattc atcctcaaaa ctgtcacaca atgagaacca gaggtaaaca tggaattgtg 3060 cagcccagaa ttaaccctac actccttttg actcatgttg agcccactac ttacaaaact 3120 gctcttcagg atcctaagtg gcatttagca atgcaagaag aatataatgc tttacttcat 3180 aatcagacat ggtctctagt atctcttcct gcaaacagac tggccattgg atgtaaatgg 3240 gtatttaggg taaaagaaaa tccagatggc actgtaaaca agtacaaggc acgtttagtg 3300 gctaagggtt ttcatcaaca agcaggtttt gactacaatg agactttttc ccctgtagtc 3360 aaacctgtta cagtgaggac agttctgaca cttgcagtta cttataactg gactcttcag 3420 cagttggatg tgaacaatgc attcctaaat ggagtgctaa ctgaggaagt ctacatggtg 3480 cagcctcctg gctttgaatc ttctgacaag aaccttgtat gcaaactaca caaggctctc 3540 tatgggttaa aacaggctcc cagagcatgg tttgagagat tgaaatcatc tttacttagc 3600 tttgggttca agtcaagcag atgtgatcct tctttgttta ctttgcacac tcaagctcac 3660 tgcattttta tattggttta tgttgatgat attatcatca ctggaaactc aaaactggct 3720 attcagaatc tagttcatca gctcaattct gagttctccc ttaaagattt gggtatacta 3780 gattattttc tcggcataga ggtgcatcac tcaccatctg gctctttact tctttctcaa 3840 accaaatata tcaaggacct tcttcagaaa gctaacatga ttaatgctaa tagcatgcct 3900 tcaccaatgg catctagtac aaaattgtct aaatttggtt caagtacagt ctcagatcct 3960 acatttttca ggtcaattgt tggtgcattg caatatgcaa ccataacaag acctgaaata 4020 tcctactctg tgaacaaagt ttgccagttt ttatcaaatc cccttgaaga tcactggaag 4080 gcagtcaaga gaatacttag atatctgcag ggtactttac accatgggtt aatgcttaca 4140 cctgccagct ctactgaacc tattgcaatc accggatttt gtgatgctga ctgggcttca 4200 gatcctgatg acagaagaag cacatcagga gcctgcatat ttctgggccc caatctagtt 4260 tcctggtggg caaggaaaca gacccttgta gctagatcta gtgcagaggc tgaatataga 4320 agccttgcac aagcttcgac tgagattatt tggatccaat ctcttctcaa tgaattgcaa 4380 attaagagta aaattcctca tgtctattgt gataatctca gtgcagtttc tcttgctcac 4440 aacccagtcc tgcactcaag aaccaagcac atggaattgg atattttctt tgtgagagaa 4500 aaggttataa ggaaggaact gaatgtctcg catgtgcctg ctcaagacca gtgggcagat 4560 gtcttaacta agcctctgtc cactgccaga ttcctttatc ttagagacaa actgagggtt 4620 tgtgacaccc tccgtttgaa gggggac 4647 // ID BoSB5D repbase; DNA; EDCOT; 223 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB5D. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-223 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 223 BP; 44 A; 64 C; 68 G; 47 T; 0 other; aaccgggcct cgtagtctgg tggtaaagga acctcggctg aggtgcccgc cacccgagtt 60 cgagccccgg ccacgagggg tatttacatg ggctgcctct cgccctccag accacttcgc 120 gtaaccaggg gcccttaagt ggacgcttaa aaatcctgta atggcttggg cttaggcccg 180 gtgggctagt cgatcacgca aagtggtcgg atactggatt atc 223 // ID Copia-32-LTR_VV repbase; DNA; EDCOT; 247 BP. XX AC CU459295; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-32_VV, LTR retrotransposon Ty1-copia like, long terminal DE repeat from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Gans-B08; KW Copia-32-LTR_VV; Copia-32-I_VV; Copia-32_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-247 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL; CU459295; Positions 604139 604385. XX CC LTR = 247 bp CC LTR are 100 % similar to each other. CC Direct flanking repeats = gtagt. XX SQ Sequence 247 BP; 66 A; 32 C; 46 G; 103 T; 0 other; tgttgagata ttatgatata ttctaggaaa gtagttgcta ttgtttagga ttgtttccta 60 aatgttgaga tattatgatg tattctagga gctattgttt aggattgttt cctaaactct 120 cggcattgtt taggaatgtt tcctaaactc acggttttcc cttaattagg tttgcttgat 180 gtactatata tttacatgga tgaatatcaa ttagggttaa gctttgaccc tttaatcaca 240 ctttaca 247 // ID MuDR-2_Mad repbase; DNA; EDCOT; 4021 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; MuDR-2_Mad. XX NM MuDR-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4021 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1506-1506 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 292-bp long. XX FH Key Location/Qualifiers FT CDS 501..2729 FT /product="MuDR-2_Mad_1p" FT /translation="MLIFFCTIPFSILQIRLKMIDSEEANNINNDDSNEFD FT CTPRCGMEFDSQEAAYNLYNAYGRKVGFSIRKERHYKNKKTNEVTSRIFAC FT SKEGFRLQDKRDYKIKKPRAETRTGCHAKMVIKLNRSNGRFFVHEFEEQHN FT HALQKPECAHMLPSQRKISDSQAAELDLAEESGIPLRESYELMAKHVGGRE FT SLGYTRVDQKNYLLSRRQRKMVYGEAGSLLRYFQGKTVENPSFFYAVQLDN FT EEQITNIFWADAKMISDYGHFGDVVSFDTTYKTNRAGRPFAVFSGLNHHRE FT IVVFGAALMYDETAPSFIWLFETFLVAMSNKAPKTIFTDQDAAMMNAIPHV FT MPDTYHRLCLWHMMQNALKNVNCVFKGNSGVREVLKKFIDEYEDEDEFLVA FT WDEMLVKHNVQGKALEWLKGIKKLRKKWAKAYVKMAWSAGMTTTGISESFN FT GRLKEYLQSDYNVVQFFMHFERVLDDQRYKEYQAEYNLCYKNAQVKVPAMM FT VKQAGDTYTKAIFEEFQEQYGESLDLRIKSTVDDGEVVVYTVFPPYGAFME FT RHVRRERDSNIIWCSCRLFEIKGILCSHAIKILREVMDTLEIPSQYILKRW FT TKKARAESIQDMHGKEIQVDPRLQQSSRFRSLCHAFTQISSRAAESDETYE FT IALSCAHKLGKLTEDKLSLQINGKTEDEGEDSAPIMALNHSNDVPNLNNAT FT VVQAKGLKKRETCRGRRRLKSCLEKAIAKRKRSSNSHLSKVKF" XX SQ Sequence 4021 BP; 1247 A; 673 C; 911 G; 1188 T; 2 other; ggacctggat tgtctgccct cttagttacc atccccttcc ataccctcct acttttctag 60 ccattgattt catctaatgc tccatatttt gccacctcac caacagctca aaaacatctt 120 taaagcctcc cgcctcttcc acttttccta atcttcactc tcccgcctct tccacttttc 180 tgctgccttt cccgtagtgc ctttccgatt gctgcctttc ccgtcacctc cttccgattc 240 acctgatttc tccaatcttc ccaggtcagt ttatgttaat tttctttgct tgtttttgct 300 attggatttg tattttcttt tttataacat gttggggtcc tctttttccg atttaatgtg 360 tcccattatt tgttcttcta gagtaattga gaacaagaga gattcgtggg actgtttaat 420 gttgaaatgt tgatttttga aaatctggag agggatttgt tctagattgc ccacaacctc 480 cgtaaagaaa caactttgaa atgttgattt ttttctgtac catacctttt tctatactgc 540 agatccgatt gaaaatgatt gattctgaag aagcaaataa tatcaacaat gatgactcga 600 acgaattcga ttgtacaccg aggtgtggta tggagtttga ttcgcaagaa gcagcctata 660 atttatacaa tgcctacgga cgaaaagtgg gatttagtat tagaaaagag cgtcactaca 720 agaataagaa aactaatgaa gtcacttcaa gaatttttgc ttgtagtaag gagggttttc 780 ggctccaaga taagcgggat tacaagataa agaagccaag ggcagagaca cggacaggtt 840 gtcatgctaa aatggttatt aagttgaata gatctaatgg aaggtttttt gtgcatgaat 900 ttgaggaaca acacaatcat gctcttcaga aaccagagtg tgcacatatg ctaccatctc 960 agcgaaaaat atcagactct caggctgctg agttagactt ggcagaagaa tctggtatcc 1020 cacttcggga atcttatgag ttgatggcta agcatgttgg aggaagggaa tctcttggtt 1080 atacaagggt tgatcagaag aactatcttt tgtctagaag gcaaagaaaa atggtgtatg 1140 gtgaagcagg aagcttgttg agatattttc aaggtaagac agttgaaaat ccttcatttt 1200 tttatgccgt acaattggat aatgaagagc aaataaccaa tatattctgg gcggatgcta 1260 aaatgataag tgactatggt cattttggag atgttgtttc atttgacact acctataaaa 1320 ctaatcgagc aggtcgtccg tttgctgtgt tttctggctt gaatcatcat cgagaaattg 1380 tagtttttgg ggcagcattg atgtacgatg aaactgctcc ctcgtttatt tggttatttg 1440 aaactttttt ggtagcaatg tccaacaagg ctcccaaaac catttttaca gaccaagatg 1500 ctgctatgat gaatgccatt ccacatgtga tgcctgatac atatcatagg ctttgcttgt 1560 ggcatatgat gcaaaatgca ctaaagaatg ttaattgtgt attcaagggt aacagtggag 1620 ttagagaagt cctaaaaaag ttcattgatg aatatgagga tgaggatgag tttttagtgg 1680 cttgggatga aatgcttgtg aaacataatg tgcaggggaa agcattagag tggttgaaag 1740 gaataaagaa gttgagaaaa aaatgggcta aggcatatgt aaagatggca tggtctgcag 1800 gaatgacaac tacgggaatt agtgagagct tcaatggtag gttaaaggag tatttacagt 1860 ctgactataa tgtggtacaa tttttcatgc attttgagag agtacttgat gatcagaggt 1920 ataaggagta ccaagccgaa tataacttgt gttataagaa tgcacaagtg aaagttccag 1980 ctatgatggt caaacaagca ggtgatactt acacgaaagc aatatttgag gaatttcaag 2040 aacaatatgg ggaatctctt gatttaagaa taaaaagtac cgttgatgat ggtgaagttg 2100 ttgtgtacac agtttttcca ccttacggtg cttttatgga acgacatgtg aggagggaga 2160 gagattcaaa cataatctgg tgcagttgca gattgtttga gataaaaggt attttgtgta 2220 gtcatgccat aaaaatcctt agagaggtaa tggacacctt ggagatccct agtcaatata 2280 ttttgaaaag gtggactaaa aaagctaggg ctgagagcat acaagacatg catgggaagg 2340 aaatccaagt tgatcctaga ttgcaacaga gctctcgatt taggtccttg tgccacgcat 2400 ttactcagat ctcgtccagg gctgcagaaa gtgatgaaac atatgaaata gctcttagct 2460 gtgcacataa gttgggtaaa ttgactgaag acaagctcag tttacaaatt aatggtaaaa 2520 cagaagatga gggtgaggat tctgccccca ttatggctct aaaccattct aatgatgttc 2580 ccaacttgaa taatgccact gttgtccaag caaaaggatt aaagaagaga gagacttgtc 2640 ggggaagaag acgactcaag agttgtttgg aaaaagctat agccaaaagg aagcgatcat 2700 ctaactccca tttatcaaag gtaaagtttt aattttctaa aaattataat agcagtaaac 2760 taagtcatat ggtttactta tctatattgt gagttgtgac atcttaaagg aaacttgtgt 2820 tccaaaggag accgttgcag cgggatgtta tattgcttct cctccaccct ttttttgtgc 2880 tcccgtgatg gctgaaccaa ggggaccttt tccagtggtg agtactttga attcggtgag 2940 tggtaattaa cctccttata ttctttttta tattatgttt attagttatt tatgcaattt 3000 tcatagtcac agggacatga catgcttaaa tacatgccat ggatgacata tgaagaacct 3060 cagtatagta catttcaaga gctactccaa acaaatccca ctggttattc cgttgcacat 3120 caagatttga atgtaagcgg tgaccactgg agatgaagag aggaagccaa cttactgtta 3180 ttgcagaagc aaatactggc atgaaaactc attttttgag tctgcagatt tttgtgtgta 3240 attctgaatc tcgtagcggg ttkcwggaaa acaaattttt tgtgtggtaa ttttgaatgc 3300 tccagattct gtgcttataa tggatgtact ggcatgaaaa ctcatttttt tgtgtgtaat 3360 tttgaatatg cagaaaagtt ctacttgtaa tggaagcatg taagtacatg aaaactcatt 3420 ttccaaccag gccttacttt tgtcttagca tcaaaacatg atataaaaca gagcaatgta 3480 aaatacttat cagaaacaaa ggcatcttaa aagcagatag gaggaggggg cgggaaaggc 3540 agcagaaaaa gggagaaaaa ttaggcttta aagatgtttt ggaagagtcc tcataatctc 3600 tgtgtttccg ttggaagagt cctcataatc tctgtatatc gtccgcacac gcgcacccac 3660 ttttccagga attcttcaaa gccattaggt tactcaccgc acccgatcca cccaattagg 3720 cgaatcggcc aagcaaagaa aattaacata aactgacctg ggaagattag agaaattagg 3780 cgaatcggaa ggaggtgacg ggaaaggcag caatcggaaa ggcactacgg gaaaggcagc 3840 agaaaagtgg aagaggcggg agagtgaaga ttaggaaaag tggaagaggc gggaggcttt 3900 aaagatgttt ttgagctgtt ggtgaggtgg caaaatatgg agcattagat gaaatcaatg 3960 gctagaaaag taggagggta tggaagggga tggtaactaa gagggcagac aatccaggtc 4020 c 4021 // ID DNA3-3_Mad repbase; DNA; EDCOT; 374 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative non-autonomous Harbinger family DNA transposon from DE apple. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA3-3_Mad. XX NM DNA3-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-374 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1467-1467 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >90% identical to consensus. 3-bp TSDs are TWA. Putative CC Harbinger family. XX SQ Sequence 374 BP; 123 A; 57 C; 53 G; 141 T; 0 other; gaccatctcc aaaggagatg tcaaatttta aacacaaaat ttaaatttga aggcttatgt 60 ggcacattga tctttttata aattttgttc tccaaccgat atgtcaaatt taaactatta 120 tttattacat tatttacttt ttatagttgt aattagtatt ttaaaacaaa agataagtat 180 aaaaattatg aaaagcattt attaattact aaaaatagat ttgaagctgc tgtcaaattt 240 gacagcaact tcctctgctg cctttccatg tcatgccaca taggaattga catttcggtt 300 ggaaaacact agtgatgtct tttattaccg ttattgctga tgtggacttt ttgacatctc 360 ctttgaagat gctc 374 // ID Gypsy-20_Mad-LTR repbase; DNA; EDCOT; 294 BP. XX AC ACYM01079178; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-20_Mad_; KW Gypsy-20_Mad-LTR; Gypsy-20_Mad-I. XX NM Gypsy-20_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-294 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1425-1425 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01079178; Positions 6474 6767. XX SQ Sequence 294 BP; 84 A; 46 C; 60 G; 104 T; 0 other; tgttatgaac ggtaaacaat gtgattttct taatcacatt ttaataagtg agttagtatt 60 aagcagggga ttagttacaa tttagttatg ttttattgtt gtgttctgaa ggagccagct 120 agcttagttt gtatgacttt atatagctgt tgggttgtag agtcaagcag gcattatatt 180 gaatagaaaa tattattcca aaaaatagga gcgtagctcc cttcgtatcc atcactccca 240 tcctccattg ctatatcttg ctgccacagg tcaaggttga atcgggtctt aaca 294 // ID HAT-3A_Mad repbase; DNA; EDCOT; 4397 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-3A_Mad. XX NM HAT-3A_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4397 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1609-1609 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Pos 300-1738 is different from the corresponding region of CC HAT-3_Mad. XX FH Key Location/Qualifiers FT CDS 1813..4251 FT /product="HAT-3A_Mad_1p" FT /translation="MERYYKRKSSSISSDNHIPNSSSPNLDSSNPIPNSSP FT PIPSSSNPIGGNSTPQQNELKVDLDNLERDPGKRIPMKDYPPDIRDEVRRA FT YILMEPFRAKDHDFPFTLHSNKKRRFVDNWLKEFHWLEYSISKDAAFCFYC FT YLFKVNFEQSGSDVFTEVGFQNWKHARACFEKHVGMVGSFHNKAVEAAGNL FT MNQKTHIETVVVKQSEEARMAYRTCLNASIDCTKFLLRQGLSFRGHDESDT FT SNNRGNYLELLQFLADHDEKIKAVVLDKAPGNLKLIAPSIQKDLVHSCSIE FT TIKTIISDMKNARFFSLLVDEARDVSIKEQMAVVLRYVDKNGKVIERFVGV FT QHVPDTTSNTLKESIDAFXHFNELSFSNLRGQGYDGASNMKGEFNGLKTKI FT LNDQPCAFYVHCFAHQLQLALVAVAKDNVDVNTFFLLANNVVNNIGASCKR FT RDALREMQQKELMKALENDSLMTGRGLNQETSLKRAGATRWNSHYGTLISL FT ITMFSSVVNVLEMIVDDNTNDSVAEANRLLKDIQSFEFVFLLFLMKSILGI FT TNDLSQALQKDDQEIVNAMALVNTCKEQLLYMRNDEGFDLLVDKVLSFCVQ FT HHIEVINMDETYVAHGRSRRNTHKKTNRHRYKVELFFVVIDSQLTELNDRF FT NETSTELLICLASLSPNDSFAAFDKEKLLRLAQLYPQDFTKQDLLALEDQL FT DIYIHSMRSRSDFSQLQSISDLAKKMVEKRLHRVFQYVYLLIELALVLPVA FT TASVERAFSAMNIIKSPLRNRMGDQWLNDSLVVYIEKDVFSCIDNETIMTR FT FQSMRSRRGQI" XX SQ Sequence 4397 BP; 1297 A; 783 C; 866 G; 1449 T; 2 other; caggggcgga tctattaagg gaccaaggtg gtcccaggac cacccgaagc tcggaaaaat 60 ggctgtgagg atcttcaagg accacccaag tctgggcagt gatggagaag aacagcagcc 120 atggctgctc tggtcgctgg gcatttcaga atgaggaaga agaaagcaaa tttttttttt 180 aaaatgactt ggccaaaacg acgtcgtttt gagccaagtc attaaaaaaa atttaaaacc 240 tcactgctca ctcacgtgag aacactcagg ctcagctcct tcacacaaca atcggaactt 300 cactttacca aatcgttcaa cgctcttcgt tctcgttacc aaatccttca cacaacaagg 360 tctgctcgct ctcattcctt acggcgtcag catcgatcaa ctctcttctg cactgcactc 420 tagtttctga atctgaatct gattgcttgc actgcacaac aatcagaact tcactctctt 480 ctcgctctcg ttccttcagg tttgtactct actactctgc tctctttaac tctgtccatt 540 aaatgatttt gccatccact atctgaatct accgttagtc tgatagtatt agtaatgtta 600 gtaaccaaga taatttcact cagtccatga tttattgctg tccgtttata cgaaatagtt 660 tcacataact caaacttcat tcaaaacctt tctgcatccc ctcccaaaaa agaagaaata 720 agcctagcat aaatttttcc aagcaactca taagtcaatc aactgaaatt gaaccatgat 780 ttggttccag aaacaagtcg aaattttttt ggggcatgga gtttatgcat aaataagaac 840 agttgtggtg cattatgcat cttgcaatga tgagttgacg gggagaagtg ggttgtgaat 900 aggtaactcc ttcactctct ccctttcttt gtggtatcat ggatttctgt aacagtaatg 960 atgttgcctg tgttggatta tttgtgtatg gatctcctaa ttagcatgct gttgaatcta 1020 agtgactgca ataatcgggg ttgtcacgtg ctgcgttcag tacacatctt cattttctct 1080 ttgaaattat taacttatcc agacaagcga ttagggacaa gtacacatga ttatacttca 1140 ttgcatctcc tacttgttga tgtttcgtaa tgtaagtgaa atatgtacta aattgttttg 1200 ttgtgcagag atgagggcaa ggtcaggaaa gtgttgaagg tggagcctct cccagacgaa 1260 tctggccatt tctttaacct gagtaatcat cttttccttg aaatcttggt ggtgacattt 1320 atcttcacct tattatacca taatatgtga tttgatgctg caatttctta attttcagtc 1380 aacattttga gtatagtcaa tcgttcgtac atcaatgctt taggcaaact tttctcattt 1440 attcatccgc ctatagactt tgcagttgta aagttcataa ctaaacacca ttatgctgca 1500 tggttaagta atggataagc aatacatatg atgcatgtat ggttgtgctt ttatggtgtt 1560 ctctttttaa agaaaaaaaa aattgaaaaa gaagcttgca gttagatgga gaaacagatg 1620 atacatgtat ggttgtgctt ttatggtgtt ctcttttata gtgttcttta tacatatctc 1680 tagcattgcc tttgtgtctg catttttgct atatgcatct ctagcattgc catagtgttc 1740 atataatatt tktttagttt catcaattga tatagatttt tttattaatt gatatgtgta 1800 gaaattagaa gtatggaacg atattacaag cgaaaatcat catcgattag ttcggacaat 1860 catattccaa atagttcatc tccaaacttg gatagttcca atcctattcc gaacagttcc 1920 cctccaattc caagtagttc taatccaatt gggggtaatt ccactccaca acaaaatgag 1980 ttaaaagttg atttggataa tcttgagaga gaccccggaa agagaattcc aatgaaggat 2040 tatcctccag atattcgaga tgaggtccga agagcatata tattgatgga gccttttaga 2100 gctaaagatc atgattttcc attcactttg cattcgaata aaaagcgacg gttcgttgat 2160 aattggttga aggaatttca ttggttggaa tatagtatat ctaaagatgc tgcattttgc 2220 ttttattgct atctattcaa agtcaacttt gaacaatcag gcagtgacgt ctttactgag 2280 gtaggctttc aaaattggaa gcacgcaaga gcctgttttg aaaaacatgt gggaatggtt 2340 ggtagctttc acaataaagc tgttgaagct gctggtaatc taatgaatca aaagacacat 2400 attgaaacag ttgtggtcaa acagtcagaa gaagctcgta tggcttatcg cacttgcttg 2460 aatgcgtcaa ttgattgcac taagtttttg ttgcgacaag gtctttcatt tcgtggtcat 2520 gatgaaagtg acacttcaaa caatagaggt aactatttgg agctcttgca attccttgcg 2580 gatcatgatg agaaaataaa ggccgttgtg ttagataaag ctccgggaaa tctcaagcta 2640 atagctcctt caattcaaaa agatcttgtt cattcatgtt ctattgaaac cattaaaact 2700 atcataagtg atatgaagaa tgctaggttc ttttctctat tggttgatga ggcacgtgat 2760 gtttctataa aggagcaaat ggcggtggtt ttgcgttatg tggacaaaaa tgggaaagtc 2820 attgaaaggt ttgtaggagt tcaacatgtt cccgacacca cttcaaacac attaaaggag 2880 tctattgatg ccttcwttca tttcaatgag ttgagcttct ccaatttacg agggcaaggt 2940 tacgatggtg ctagtaatat gaaaggtgag ttcaatggac tcaagacaaa gattttgaat 3000 gatcaacctt gtgcattcta tgttcattgc tttgctcatc aactccaatt agctcttgtt 3060 gccgtagcaa aggataatgt tgatgttaac acattcttcc tattggctaa taatgtggta 3120 aataatattg gagcttcatg taagcgtcgt gatgcactta gagagatgca acaaaaagaa 3180 cttatgaaag ctcttgaaaa tgattctctt atgacgggac gaggcttaaa tcaagaaact 3240 agtctcaaac gtgccggagc tacaagatgg aattcacatt atggtacttt gattagtttg 3300 attactatgt tctcatccgt ggtcaatgtg cttgaaatga ttgttgatga taataccaat 3360 gatagtgtgg ccgaagcaaa taggttattg aaagacatac aatcttttga gtttgtgttt 3420 ctcctatttt tgatgaaatc tatattggga atcacgaatg atttatcaca agcattacaa 3480 aaggatgatc aagagattgt gaatgcaatg gctttagtca acacatgtaa agaacaacta 3540 ctctacatga ggaatgatga ggggtttgac cttttggttg acaaagtatt gtcattttgt 3600 gtccaacatc atattgaggt tattaacatg gatgagacat atgtagctca tgggaggtcg 3660 cgccgtaata cccacaaaaa gaccaaccgt catcgttaca aagtggagct cttttttgtt 3720 gtcattgatt cccaacttac agagttaaat gatcgcttca atgaaacaag taccgaattg 3780 ctcatttgtt tggctagttt gagtccaaat gattcttttg cagcttttga caaagaaaag 3840 ctacttcgcc ttgctcaatt gtaccctcaa gattttacga agcaagacct attggcactt 3900 gaagatcaac tcgatattta tattcattct atgcgttcga gaagtgactt ttctcagttg 3960 caaagcatta gtgatcttgc taagaaaatg gtggaaaaaa ggttgcatcg agtatttcaa 4020 tatgtgtatt tacttattga attggctttg gttttacctg ttgcaactgc ttcagtggag 4080 agagcatttt ccgccatgaa tatcattaag agtccactcc gcaacagaat gggggatcaa 4140 tggttaaatg atagcttagt tgtttacatt gagaaagatg ttttttcttg tattgacaat 4200 gaaactatca tgacacgttt tcaaagtatg agatcccgtc gtggacaaat ttagtatttc 4260 tagcttgttt agcacaaaga ttatgaatga aaattgtagt ttgccattta tttgttcaat 4320 gatattttcg tctttttttt ttttttggag cttttatatt gggaccaccc taagttaaaa 4380 tcctggatcc gccactg 4397 // ID COP8_I_MT repbase; DNA; EDCOT; 4468 BP. XX AC . XX DT 01-JAN-2007 (Rel. 12.01, Created) DT 06-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region sequence of LTR retroposon COP8_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; Internal; LTR; KW retroposon; Interspersed; repeat; ORF; COP8_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4468 RA Shankar R. and Jurka J.; RT "COP8_MT: A copia type LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 19-19 (2007). XX DR [1] (Consensus) XX CC The internal region is flanked by LTRs on both termini. The CC internal region has ORF for reverse transcriptase. XX FH Key Location/Qualifiers FT CDS join(18..611,615..1295,1299..3590) FT /product="COP8_I_MT_1p" FT /translation="MAASLKEMTSDFVKLEKFDEGNFICWQKNMKFLLTTL FT KVAYVLNMARPEEKDDETVAETRDRQKWDNDDYICLGHILNGMSDSLFDIY FT QSSPSAKDLWDKLETRYMREDATSKKFLVSHFNNYKMVDNKSVMEQLYEIE FT RILNNYKQHNMNMDETIVVSSIIDKLPPSWKDFKRTMKHKKEDISLEQLGN FT HLRLEEEYKQEGIKNHVTQEKVHVMEEGNSSKSSKKRNHENDKSHHNHNGN FT NNKKKRKGECYFCGKEGHFKNECRFFKKKNKEKNSRATNDDFVAVISEINM FT IEDVDSWWIDSGATRHVCKNKKMFKTINKDVSVLYMGNDSTVQVQGKGTIE FT IEFTSGKTLTLKDVFYVPEVRKNLISVPLLNKNGFKSVFEGDKFILSKGGV FT FVGKGYLCENMFKCNVANINNNNNMISAYIVSCDLWHMRLGHVNFRKLEDM FT MKSNLIPNFDKNFDSCTTCMLTKITRQPFKSVKRSSRVLDLIHSDVCDLHG FT WPTIGGKKYFVTFIDDCTRFCYVYLMHSKDEVLDKFKIFKAQVELQHETFI FT KCFRSDRGGEFYHPSYFESTGIVHQVTAPYTPQQNGIAERKNRTLVEMVNA FT MLSYSGLSKGYWGEAMLTACYILNRVPNKRNKITPYELWKQRKLTLNYLKV FT WGCRAIVKVPEPKRKKLGERGIECVFLGYAENSKAYRFLTIESNDSYFVNT FT VIESRDAIFQEDRFNSISYPKDIVHSNVQNLENNESDIDTLDGSELRRSKR FT IRKEKDFGSDFFMFLVEGTGKSINSYGPICFNLESDPVTYEEAIKSQDSAF FT WKEAIQEEMDSIMGNKTWKVVDLPPGSKPIGCKWIFKRKMKVDGTIDKFKA FT RLVTKGFTQKEGIDYFDTYAPVARIASIRMLIALASIHKFVIHQMDVKTAF FT LNGELDEEVYMKQPEGFVIKGQEDKVCKLTKSLYGLKQAPKQWHQKFDQVV FT LANGYIINESDKCIYSKFQNGKGVMICLYVDDMLIFGTNINEVEETKAFLS FT NNFDMKDLGEADVILGIKIIRDGNHIGLSQSHYIEKVLQKFNHLDCKPIST FT PFDQTVSLQPNKGCPVAQLEYSKVIGCLMYAMTCTRPDIAYAVGRLSRYTS FT NPSKEHWHAVKRVLKYLKGTMNYCLTYSGDPSVLEGYTDASWVTYVEDHAS FT TSGWIFNLGGGAVSWGSKKQTCIADSTMAA" XX SQ Sequence 4468 BP; 1572 A; 646 C; 921 G; 1329 T; 0 other; ctttaggttc gatttctatg gctgcttcat tgaaagaaat gacttctgac tttgttaagt 60 tggaaaagtt tgatgaggga aatttcatct gctggcaaaa gaatatgaag tttcttctta 120 caacattgaa agtggcatac gttctgaaca tggcaaggcc tgaggagaag gatgatgaaa 180 ccgttgctga gacaagagac agacagaaat gggacaacga tgattacatc tgcttaggac 240 acatcctgaa tggtatgtct gactctttgt tcgatatcta ccagagcagc ccttctgcaa 300 aagacttatg ggacaaattg gaaaccagat acatgcgtga agatgcaaca agtaagaaat 360 tccttgtctc tcattttaat aattacaaaa tggtagataa taagtctgtt atggaacaat 420 tatatgagat tgaacgtatt cttaacaact acaaacaaca taacatgaat atggatgaaa 480 caattgttgt atcatccata attgacaaac ttcctccttc ttggaaagat ttcaaacgaa 540 ccatgaaaca taagaaggaa gacatttctc ttgagcaact tggcaatcac cttcgtttag 600 aagaagaata ctgaaaacaa gaaggtatta agaatcatgt tactcaagag aaggttcatg 660 ttatggaaga aggaaattca agcaaatctt ctaaaaagag aaatcatgaa aatgataagt 720 ctcatcataa ccacaatggt aataacaaca aaaagaaaag gaaaggtgaa tgttactttt 780 gtgggaaaga aggacacttc aagaatgaat gcaggttctt taaaaagaag aacaaagaaa 840 agaattcaag ggcaacaaat gatgattttg ttgcggtcat ttctgaaatc aacatgattg 900 aagatgttga ttcatggtgg atagactctg gtgctactcg ccatgtgtgc aaaaacaaga 960 aaatgttcaa gaccatcaat aaagatgtga gtgttttgta catgggaaat gattcaactg 1020 tgcaagtcca aggaaaaggg accatagaga ttgaattcac ttctggaaaa acacttactc 1080 ttaaagatgt attttatgtt cctgaagtta ggaagaactt gatttctgta ccattactta 1140 ataagaatgg gttcaaatct gtatttgagg gagataaatt tatcctctca aaggggggtg 1200 tgtttgtagg aaagggatat ttgtgtgaga atatgttcaa atgtaatgtt gcaaatatta 1260 ataataataa taatatgatt tctgcttata ttgtttagtc ttgtgattta tggcatatgc 1320 gattgggaca tgttaatttt agaaaattgg aggatatgat gaaatcaaat ctaattccta 1380 attttgataa aaattttgat tcatgtacta cttgcatgtt gactaaaatt acaagacaac 1440 cttttaaaag tgttaaaaga agttctaggg tgctagattt aattcattca gatgtatgtg 1500 atttacatgg ttggcccacc attggtggta aaaagtattt tgttactttc attgatgatt 1560 gcactcgatt ttgttatgtt tatttaatgc attcaaaaga tgaagtttta gataaattca 1620 aaatatttaa agcacaagta gaacttcaac atgaaacttt cattaaatgc tttagaagtg 1680 ataggggagg agagttctat catccgagtt attttgaatc cactggtatt gtgcatcaag 1740 taactgcacc atacacccca caacaaaatg gaatagcaga aaggaagaat agaactttgg 1800 tagaaatggt taatgccatg ttgtcctatt ctggattatc taaaggatat tggggtgaag 1860 caatgctaac agcatgttac atcctcaata gggttccaaa caaaaggaac aaaataaccc 1920 catatgaact ttggaaacaa agaaagctta ctcttaatta tttgaaagtt tggggttgta 1980 gagcaattgt gaaagtgcct gaaccaaaaa gaaagaaatt gggtgaaaga ggaattgaat 2040 gtgtattttt aggctatgca gaaaatagca aagcatacag attcttgact attgaatcga 2100 atgactcata ttttgttaat acagtaattg agtcaagaga tgcaattttt caagaagata 2160 gatttaactc aatttcttat cccaaggata ttgttcattc taatgttcaa aatttagaaa 2220 acaatgaatc tgatatagat acattggatg gttcagaact tagaagaagt aagaggatcc 2280 ggaaagagaa agattttgga tctgatttct tcatgtttct tgtagaagga acaggtaaat 2340 ccataaatag ttatggacca atttgcttta accttgagag tgatccggta acatatgaag 2400 aggctataaa atctcaagat tcagcttttt ggaaagaagc tattcaagaa gaaatggatt 2460 caattatggg taataaaact tggaaagtgg tagatctccc acccggatcc aaaccgatag 2520 gctgtaaatg gatctttaaa aggaaaatga aagtggatgg taccattgat aaattcaagg 2580 ctagactagt tactaaagga tttacgcaaa aagaaggcat tgattatttt gatacatatg 2640 cacctgttgc aagaattgca tcaatcagaa tgctaattgc actggcatcc atccataagt 2700 ttgtaatcca tcaaatggat gttaaaactg ctttcctaaa tggagagttg gatgaagagg 2760 tatatatgaa acaaccggaa gggtttgtga tcaaaggtca agaagataaa gtgtgtaaat 2820 taactaagtc tttatatggg ttgaaacaag cacccaaaca atggcaccaa aagtttgacc 2880 aagttgtgtt agccaacgga tacatcataa atgaatctga caagtgtatt tacagtaaat 2940 tccaaaatgg aaaaggtgtc atgatttgct tatatgtaga tgacatgttg atctttggta 3000 caaatataaa tgaggttgaa gaaactaaag ctttcttatc caacaatttt gatatgaaag 3060 atttaggaga agctgatgtg attttaggaa ttaaaatcat aagagatggt aaccatattg 3120 gtttatccca atctcattac atagaaaagg tgcttcagaa attcaatcat ttagattgta 3180 aaccgatctc taccccattt gaccaaactg tcagtttgca accaaacaaa ggttgtcctg 3240 tggcacaact tgaatattct aaagtaatcg gatgcttgat gtatgctatg acttgtacta 3300 gacctgacat agcatatgct gttggaaggt taagtcggta tactagcaat ccaagtaaag 3360 aacactggca cgctgtgaaa agagtattaa aatacttaaa gggaacaatg aattattgtt 3420 taacatatag tggagaccct tctgttttgg aaggatacac agatgctagt tgggtaacgt 3480 atgttgaaga tcatgcttcc acaagtggat ggatcttcaa ccttggtgga ggtgcagttt 3540 cttggggttc aaagaaacaa acatgcattg ccgactccac catggctgca taatttattg 3600 cattggctgc agggagtaaa gaggcagaat gactaagaaa tttattgtat gacataccag 3660 tttggcaaaa gccaatggcg ccagtatcca tacattgtga tagtcaatcc acactatcaa 3720 aagcttatag ccaagtttat aatgggaaat caaggcatat tggtttaaga catagctatg 3780 taagagactt gatttctaat ggaataattt ccatcatgtt cgtaagaaca gagaagaatc 3840 ttgcagatcc tttgacgaaa ggtctgacaa aggatatggt gttgaagaca tcattgggga 3900 tgggactcaa gcccatatct aattgattac caatagtgga aactcaaccc acacttgagt 3960 agcatcaagt cttgggttca atggtgaaag tacactatta gagtaattgt agtacttgac 4020 aatagataca tcccaaaggt aaaagtactt ggaccataag aagaaaaaag gtaggatgag 4080 gttttcctct taatggacat atagcatata tttgttggaa tgcatactta tggggcattc 4140 ccgatatagt ctacctatgt gagaatgaag tttggccgct tcacggagtt caagggcttg 4200 actcttaaat tctcatgaaa agggatatat gacacaaggc cttcttaatg tgtcatctta 4260 caagtctctt tatcaatggt accgagattc tatgtgtaag ttatgcacac ttgttctaat 4320 ggatagttgg ttcaaagctt gcctaccata ctatttggga atgagcgaaa acttaactta 4380 ctaagtaatg gttcaaattg cgagatacca ttatctgaag gcatggaatt tccggattta 4440 tgtgatttag tattttgaaa atggtggg 4468 // ID Gypsy1-PTR_I repbase; DNA; EDCOT; 7611 BP. XX AC LG_XI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy1-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-7611 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-7611 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 296-296 (2007). XX DR Genome; LG_XI; Positions 11644962 11637352. XX CC Positions [4452-4865] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(120..2528,2532..4865) FT /product="Gypsy1-PTR_I_1p" FT /translation="MRSNKNQPLLPYNSEIERTARGLRKKTRKTQNSSGIM FT ADNENPEQDTRALRDFALPQVTGIRSVIRKPRIEANNFEIKPAILQMIQTS FT IQFYGLPSDDPNAHIASFLEICDTFKHNGVTDDAIRLRLFPFSLRDRTKNW FT LNSMPADSVISWENLAQKFLAKFFQPAKTAKKRIEIANFAQLESEPLYEAW FT ERYKDLLRRCPHHGLPKWMQVQNFYNGLNASTRTLIDAASGGAFMSKSQDD FT AYNLLEEMAMNNYQWPNERSIQKKTVGVHEIDAITALTAQVHSLTQQLKTT FT QLSANAIHTTCDFCHGNHTSEECQVGNPFSQAEHAHFVSNYSRQNNPYSAT FT YNPGWRNHPNFSWNNQTIMKNPAMPSSSEHMKEKSKLEEAMTQLANNTIRF FT MTETNTNLQNQAASIRNLEVQVGQLANMLTGRQQGNLPSTTEINPKEQCKA FT ITLRSGKEVEQTAGNKSAGREEEEQVAKPLQNMKKSDPLPEPTQEIMQRIP FT FPQRLKKNKLDKQFSKFLDVFKKLQINIPFADGLEQMPSYVQFLKDILSNK FT RKLEEYETVALTEECSAILQKKLPPKLKDPGSFTIPCSIGNSIFEKALCDL FT GASINLMPLSIFKKLGLGEARPTTVTLQLADRSLKHPRGIIEDVLVKVGKF FT IFPADFIILDMEEDNEIPILLGWPFLATGGALIDVKKGELRLRVNEEEVIF FT NLFKAIKQPDMGESCFSIQVVDSLINDKVKLPTDPLEACLVNNVLEEDAEI FT AEYTCWMDSFEPNRRRYFEDLGQPAPKIKSTSEQAPVLELQPLPEHLRYAY FT LEASTYPMIVSAKPTKTEEEKLLRVLRKHKAALGWVLADIKGISPSICMHK FT ILLEDEVKPTVEHQRRLNPTMKEVVRKEVLKWLDAGVIYPISDSSWVSPVQ FT VVPKKGGMTVVKDANNNLIPTRPVTGWRICMDYRKLNKATRKDHFPLPFID FT QMLDRLARHEYYCFLDGYSGYNQIAIAPEDQEKTTFTCPYGTFAFRRMPFG FT LCNAPATFQRCMMAIFSDMVEQIIEVFMDDFSVFGTSFDDCLAKLALVLER FT CEKTNLILNWEKCHFMVKEGIVLGHRISEKGIEVDRAKIEAIDKLLPPTTV FT KGVRSFLGHAGFYRRFIKDFSKISKPLCSLLLKDIKFQFDEECKTAFMLLK FT KKLVTAPIVIAPDWEKPFELMCDASDYAVGAVLGQRKNNVFHTIYYASRTL FT NDAQLNYATTEKELLVVVYAFDKFRPYLMGNKVLVYTDHAAIRHLVSKKDA FT KPRLIRWILLLQEFDVEIKDKKGTENVVADHLSRLELTQQLEPKFTVINEC FT FPDERLLAISTNKFFPWYADYVNFLAGKIIPPDFSYQQKKKFFSEVKHYFW FT EEPILYRHCADQVIRRCVPEEEMTNILKHCHTLEYGGHFGTQRTAAKVLQS FT GFYWPTMFKDANAFVTACDRCQHTGNISRRNEMPLQNILEVELFDVWGIDF FT MGPFPSSYNNKYILLVVDYVSKWIEAIATPTNDGKVVLNFLRKNIFTRFGT FT PRAIISDEGTHFCNKQFEALLSKYGVRHKRALAYHPQTNGQTEVSNREVKQ FT ILEKTVSNSRKDWA" XX SQ Sequence 7611 BP; 2492 A; 1354 C; 1648 G; 2117 T; 0 other; agtttttggc gccgttgccg gggattttag ataaaattac taataatatc aatataaatt 60 aaatttgatc taatttgatt gccttttgtc ttcagctttt taggtgtgtt gtctagtgca 120 tgagaagcaa caaaaaccag ccgttgctac cttataattc tgagattgag agaactgcaa 180 ggggattaag aaagaaaacg cgaaagactc aaaacagttc aggcatcatg gcagacaatg 240 aaaatcctga gcaagacaca cgggcattga gagattttgc tctcccacag gtgacaggaa 300 tccgttctgt tatcaggaaa ccaaggattg aggccaataa ttttgagatc aaaccagcaa 360 tactgcaaat gattcagacc tcaattcagt tttatgggtt gccaagtgat gatcctaacg 420 cccatattgc aagtttcttg gaaatttgcg acacatttaa gcataatggc gttactgatg 480 atgccattcg cctcagactg tttccatttt ctctgcgaga tagaacgaag aactggttaa 540 actccatgcc tgcagattca gttatcagtt gggaaaattt agctcagaaa ttccttgcta 600 aattttttca accagccaag acagcaaaaa agcgcattga gatagctaac ttcgcccaac 660 ttgagagtga accattgtat gaggcatggg agagatacaa ggatttgctc aggcgatgcc 720 cccaccatgg actaccgaag tggatgcagg tgcagaattt ttacaatgga ttgaatgcct 780 ccacaagaac actaattgat gcagcttcag gaggagcttt tatgagtaag tcacaggatg 840 atgcttacaa cttattagaa gaaatggcta tgaacaatta ccaatggcca aatgaaagaa 900 gcatacagaa gaagactgtt ggggtgcatg aaattgatgc aatcacggca ttaacagctc 960 aagtccattc actaactcag caactgaaaa ccactcaact gtcagcaaat gccatccata 1020 caacgtgtga tttttgccat ggaaatcaca caagtgaaga gtgtcaggtt gggaacccat 1080 tctctcaagc agagcatgct cattttgtgt caaactacag ccggcagaac aacccctaca 1140 gtgcaacata taatcccggt tggagaaatc atcctaattt ctcttggaac aatcaaacta 1200 tcatgaagaa tccagccatg ccatcttcaa gtgagcacat gaaagagaaa tcaaaacttg 1260 aagaagctat gacacaatta gcaaacaaca ccatcagatt catgactgaa acaaatacta 1320 atctgcagaa ccaagcagct tctattcgaa atttggaggt tcaagttggt cagttagcca 1380 acatgctcac gggtagacaa caaggaaatc taccaagcac aactgaaatt aatcctaagg 1440 agcaatgcaa ggccataact ttaagaagtg gaaaagaagt ggagcagacc gctggaaaca 1500 agagtgcagg aagagaagag gaggagcaag tggccaaacc acttcagaat atgaaaaaat 1560 ctgatcctct gccagaacca acgcaagaaa taatgcagag aattccattt ccacaacgtc 1620 tcaagaagaa taaacttgat aagcaatttt ctaaatttct tgatgtgttt aaaaaattgc 1680 agattaacat tccttttgca gatggtcttg aacaaatgcc aagctatgtg caatttttga 1740 aggacatcct ctcaaacaaa agaaagctag aggaatatga gactgttgct cttactgagg 1800 aatgcagtgc cattttgcag aagaaactgc ctcctaaact taaggatcca gggagtttta 1860 ctataccatg ttccattgga aattctatat ttgaaaaagc tttatgtgat ttaggtgcaa 1920 gtattaatct catgccttta tctattttta agaagcttgg tttaggtgaa gcaaggccaa 1980 ccacagtaac actgcagcta gctgacaggt cattgaagca tccaaggggc ataattgaag 2040 acgtactggt gaaagtgggc aagttcatct ttccagcaga cttcatcata ctggatatgg 2100 aggaggataa tgagattcct atcttgcttg gctggccatt cttggccact ggaggtgcgt 2160 taattgatgt gaagaaaggg gagctgcggt taagggtgaa tgaagaggag gtgattttca 2220 atttgttcaa agccatcaaa cagccagata tgggggagag ttgcttcagc attcaagtgg 2280 tggactcttt aattaatgac aaagtcaagc ttccaactga cccgttggaa gcatgtttgg 2340 taaataatgt actggaagag gatgctgaaa tagcagaata tacatgttgg atggactctt 2400 ttgaacctaa ccgcagaaga tactttgaag atttgggaca accagcacca aaaataaaat 2460 caaccagtga acaagcaccg gttctggaat tgcaacctct gccagaacac cttcggtatg 2520 catatctttg agaagcttcc acctatccta tgatagtctc tgcaaagccg accaaaacag 2580 aggaagaaaa attgttgagg gtgttgagaa aacataaggc agctctcggg tgggtattgg 2640 cagatatcaa aggcatcagt ccctctattt gcatgcataa aattctgttg gaggatgaag 2700 tcaagccaac agtagaacat cagagaaggc ttaacccgac catgaaagag gtagtccgaa 2760 aagaagttct gaaatggtta gatgctggtg ttatttatcc aatctctgac agctcatggg 2820 tgagcccagt tcaagttgtg ccaaagaaag gaggaatgac agtggtaaag gatgcaaaca 2880 acaacttgat acctactaga ccggtaactg gatggaggat ttgcatggat tatcgaaagc 2940 tcaacaaggc aactcgcaaa gatcacttcc ccctaccatt cattgatcag atgctggaca 3000 ggttagctag gcatgaatac tactgtttcc tagatggcta ttcaggatac aaccaaatag 3060 ccatcgcacc tgaggaccag gagaagacca ctttcacctg cccttatggt acttttgctt 3120 ttagaagaat gccttttggg ttgtgtaatg caccagctac ttttcagagg tgcatgatgg 3180 ctattttttc agatatggtg gagcaaatca ttgaggtctt catggatgac ttttctgtat 3240 ttggaacttc ttttgatgac tgccttgcaa agttggcgtt ggttttggag cgttgtgaaa 3300 agacaaactt gattttgaac tgggaaaaat gtcacttcat ggtaaaggaa ggtatagtat 3360 tggggcaccg gatttcagaa aaaggaatag aggtagacag agctaaaatt gaagcaatag 3420 acaaactttt gccgccaact acagtaaaag gggttaggag tttccttggt catgcgggat 3480 tttataggag gttcatcaaa gacttctcta aaatatccaa accgctatgc agtctgctgc 3540 taaaagacat aaagtttcaa tttgatgagg aatgcaagac agcctttatg ctgttgaaaa 3600 agaagttagt gacagctcct attgtaattg caccggattg ggagaaacca tttgagctta 3660 tgtgtgatgc aagtgattat gcagttggag cagtactagg gcaacggaaa aataatgtgt 3720 ttcacaccat atactatgcc agcagaacac tcaacgatgc ccagctcaat tatgccacaa 3780 ccgagaaaga gttgcttgtt gtggtctatg catttgataa gtttcggcct tacctgatgg 3840 gaaacaaagt actggtgtat actgatcatg ctgcaattag acacctagtg tctaagaaag 3900 atgccaagcc tagactcatc cgttggatcc tattactgca agaatttgat gtagaaatta 3960 aagataaaaa ggggactgag aacgtggtgg cagatcatct ttcaaggctg gaattgacac 4020 agcagctgga gcctaaattc acggttataa atgaatgttt tcctgatgaa agactcttag 4080 caatttccac taacaaattc tttccttggt atgcagatta tgtcaacttt cttgcaggta 4140 aaatcatacc gcccgatttt tcttaccagc aaaagaagaa atttttttct gaagtcaaac 4200 actacttctg ggaggagccg atactctatc ggcattgtgc agatcaagtc atcaggaggt 4260 gcgttccaga agaagaaatg acaaacatat tgaagcattg ccacacactt gaatatgggg 4320 ggcactttgg aacacaacgc actgcagcca aagttctgca gtcaggtttt tattggccca 4380 ctatgtttaa agatgctaat gcttttgtta ctgcttgtga tagatgtcag catactggga 4440 atatatctcg acgaaatgaa atgccactgc agaatatctt agaagttgaa ttatttgatg 4500 tttggggcat cgatttcatg ggaccttttc cttcatcata taacaacaaa tacattctct 4560 tagtagtgga ttatgtatca aagtggatcg aggcaattgc aacgcctaca aatgatggca 4620 aggtggtact taattttcta cgaaagaaca tctttaccag atttggtact cctcgagcca 4680 tcatcagtga tgaaggaact catttttgca acaagcagtt tgaagcactg ctatctaagt 4740 atggagtcag acacaaacga gcactggctt atcatcctca gacaaatggc caaacagagg 4800 tatcaaatag agaggtgaag caaatcttag agaaaacagt aagtaattct cggaaagatt 4860 gggcatgaaa gctagatgat gcattgtggg catatcggac agcattcaaa acaccattgg 4920 gaatgtctcc gtatcgatta ttttttggaa aagcatgcca tcttcctgtt gaattagaac 4980 ataaggcata ctgggcaatg aaacaactga acatggatct gcaggttgca ggtgagaaaa 5040 gaatcctgca acttaatgag atggatgaat ttcgcaatga gtcctatgag aatgccaaga 5100 tatacaagga aagaaccaag gcatggcatg acaaacacat tgtacgcaag gagtttgtcc 5160 ctggttagca ggtattactt ttcaattcac ggctccgctt gtttcctggt aagctcaaat 5220 cacggtggtc aggaccattt acggttgtga aggtatttcc ttatggagca gtagaggtca 5280 ctcatgatga aaagggaaca ttcacagtga atgggcagcg tctgaagcat tataggaatg 5340 gagagtctat tggaaaaagg gatgatatcc ctctcacttc atcttagcta aatggaaaag 5400 tcaagctaat gactataact aagcgctgat tgggaggcaa cccaaaaaaa aaaaaaaacc 5460 ttattggttt tattgagttg tgcagggatt gatcatacaa gcaaataacc aggagcaaca 5520 acaaactcac acccacatag tcaaaaggaa gtattcgtaa gcctttctat tctttgtttt 5580 tccattgagg acaatgtgat atttaagttt gggggagaca ttgcatgctt tgactatgaa 5640 agacactgca cactggaacc atgaaaacag agggtgaaaa gtgatatgca tttaagacca 5700 actttgacat ttttaggtgc ttcatgatgt atccatgata ttcctaggct tagagtggat 5760 aatatcttat aaagttggat taagcatgac tattttctgt tgaattattg aagtacactt 5820 ttccaacaca gtcaggtgaa ttgtgtagtt atgcataaga gataagtgtg ctgttctttt 5880 ttgttattac cctctaagaa aaatatcaaa acaaggagtg ataatgagta tgaaagtgaa 5940 tgaataagta tatgatgtgt atctactcca atgttttgag ttgcttagta actaggagta 6000 ttcatcataa atgtttactt ttatgtcaaa cggcagctta aaatatgagt atgcaaagca 6060 ttttaagttt atgacctgtt aagtaaccgg gtgcattcat cacaaatgtt tgtattcgcg 6120 ttaaaagaca agtgataaat tttaaaaaat cacccttgtc aaaagacaag taaaagtgtg 6180 ttattactcc taaagttggc taccttgttc aaaaaaaaaa aataataatg gcagaatgac 6240 tgtgcacggt tcaaggatgc taaacacatg aaacacatgg atgagttgga agtttgtaca 6300 acggtctgca cagagagtag gaatgcttag ttttccatta tctaatattg tctatgagct 6360 aagtcaagaa gtgaatgttg catgatggag ccttttaaat gtcaaagttg aacttatcat 6420 gagcttttag cactatgctt tcatggtttc ctttttgctt gaggacaagc aaacattcaa 6480 gtttgggggt atttgataag ggaattttta gcatgtatat tttctgttat tcatgcttga 6540 tttttaaata ttttggatat gttgcacaag acaattagac ttttgaatct ctttttgaac 6600 tattgacctc gtgggaaatt aatgtgtttt cagatcttag gttactgaac aggcagagcc 6660 gggcagtgaa actgaacaat gattcattat gtgctgcaaa gaagctatac aatttagtcc 6720 cggatgttcg taaccatttt caaatagctg agatgaaggt ctacaaaaca tatgaaggac 6780 atataactca gttttgttgt ttcgaagccc aaaaagcgag ttgaaaaaca aggattgaac 6840 cagcccgaaa ttcctgcact gcaaagactg tttcggttta tagcccatat ctcaacgctc 6900 agaggtccaa aaattgcaag atcagtgtcg ttggaaagaa aatttgattc tctacaattt 6960 ctccagaaat agagagtttt taattcgcac gtttcctacc tcaaatctgg cccgcaatgt 7020 ctgggtagga gaaatcaatg cagaaaagga aattttcttc attactgcag gggtagaaaa 7080 gccacaatat aaaagaagag ttacggggtc taaaaaacag aggagagaca cttggaaaac 7140 cctataacag agcaaagaaa aacagaggag gcgacaccaa acaggaacaa aaagaacaga 7200 ggcaaaaata ttgaagaccg agaggacacc tatctcttcc actgaaattc tctgcttttg 7260 agtgatgttc atcgtatcaa gtttgtttct ctttaattta actatggagt agacttttat 7320 tctgggattt ttgatgtaac cttactatga atatgtgaac aatttcttcg attgaattat 7380 tacattaaga tgttgagtat ttcattctat gtgtaatgct tgcgtgtgtt tggccaacat 7440 ctgcatgatt tagaattcaa tttgaaactg agaagtgata attgttttag ctattgtttg 7500 aaatacctta agaaatctat aggatagaga tatcctagga acttttgtag tcgatacagg 7560 ttttacagta cttaataaat ttcgacaagt tcaggacttt catagagtat a 7611 // ID Copia-73_Mad-LTR repbase; DNA; EDCOT; 201 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-73_Mad_; KW Copia-73_Mad-LTR; Copia-73_Mad-I. XX NM Copia-73_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-201 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1685-1685 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 201 BP; 49 A; 22 C; 49 G; 81 T; 0 other; tgagaagtaa gagtagtctt gtgaggagtg tgagtggtct agagtttgtc tctagaaagt 60 gagtagtgtc atagcttcta aagtgtcttt gagagttttg agtgttgtaa tattttgtga 120 gtgtaataca agtaatttgt ttacttgttt tgtctctcca acacttgtgt tagagttgtg 180 tactctaatt tttcctcaac a 201 // ID MtPH-D-Ia repbase; DNA; EDCOT; 3160 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 13-MAY-2008 (Rel. 13.05, Last updated, Version 1) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-D-Ia. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3160 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC A single autonomous element of lineage D of PIF/Harbinger CC transposons from Medicago truncatula, carrying 12 bp-long TIRs. XX SQ Sequence 3160 BP; 1080 A; 410 C; 600 G; 1070 T; 0 other; gcctttgttt gggttctttt agcctctctt tttgtctcat tgggttaagg cttgagtccc 60 cccaattgtt ctctgcacca cttttttctg caatttaatt ttctctgcct ttattaaaaa 120 aaaaaaatat gtttgcttac atatttacga ttcataaata tacacaagtt tctaatatat 180 gtattgttgc agttcatggc ttctaaagaa agccttccaa atagttctga aaacttagga 240 aaagcaaagt gggatacatt tagtaccaaa atgttacttg acatttgtat ggttgagatt 300 cgtaaatgcg gaaaaccagg aattggtttt agaaataaaa aatgggaaga aatacgtgat 360 gagtacaaca agcgtgctaa taaaatctat actcaaaagc agctgaagaa taggatggac 420 actttaagag gtgagtggac tatatggaaa caattactag gtaaagaaac tggtttagga 480 tggaatcatc agataggaaa tattgatgtt gattctgctt ggtgggatgc taagataagg 540 gttagtacta tgaactttaa tttttattca ttgaaagtaa gtaggagaat ttagatagcc 600 taaattttat ctaattttat tggttacaca ggagaatgtg aaatatgcga aatttcgatt 660 tcaaggtttg aaatttcgag atgaattgga attcatattt ggagagattg tggcaactag 720 tcaatgtgca tgggcaccag ctatgggtgt gccattagag tctgctggaa aaaatactac 780 cacagatgtg gcccatgaaa ttattgaatc tgatgatgaa ctcaacattg atgtgttaag 840 ccctgtggaa aacactcaat caaaaaatat aagaaaggtt tcaccaaata tggatgagaa 900 agcaacaaat aggaaggcaa aggttgggac tgcaccagct atgagaaaaa cattagaacg 960 attagtccaa gtagcagaaa atcataatga agttgaaaag gctgaaattg aagcaacatc 1020 tcatgtcaat ggaaaatatt ctatttcaac atgtgttgca atattaaaaa gtgcaaagga 1080 agaaggactt ttggatggga aacaatttat ttatgcttta gaaatggtta aggatgagca 1140 aaacagagtc ttactaatga ctctgaaaga ttctatgaag gatttgatag agtgggttct 1200 atacaagtat aagtgataga gtctatgatt taggttaaga ttgagtttta taattcttat 1260 ttcagttggt tttatgcttt ggttgaaatt tgaggttttt tatgtatttg cattctatca 1320 ttttagtttt tggaattata tgtttatggt tgagaaattt atgcatttga actactataa 1380 tgaatattta tttgtatttg attatgttgt tgtttataaa ttgttctaca gatgccttgt 1440 aatgaaatca atgggcattc aagaaaagtt aaaaaaagac gatgctcatt ttacaaaata 1500 tattacgctg ctgcagcaat tgcaatttat tatcatatga agtacttact aaagcaaggt 1560 aatagatttc tttattcaca tggatggaat tgggttcgag aaactcttaa cactccaggc 1620 gaaagttata acatgtttag gatggaatct aatgctgtgc tgaaacttga aaaattatta 1680 gttagtaagg gatggttaca tccatctaat gaaatgacat cgttggaagc tttgactatg 1740 tttctttgga gttgtgcaca tagtgagact aatcgaaatg tccaaaataa atttggaaaa 1800 tcaggagaga ccgtaagtag gaagtttggt gaagttctgg atagtttatg tttattagct 1860 accgaaattg tcaaacctcc tgattttaac tttgtagaaa ttccatccaa aattagagat 1920 gataataggt attggcctca ttttgaagga tgcattggag ctatagatgg aactcatatt 1980 cctgccattg ttcctactga agaacaaatt cgttatattg gtagaaaagg atttccaaca 2040 caaaatgtca tgttagtgtg caacttagac atgttattta cttttgttgt cgttggctgg 2100 cctggtactg cacatgatac acgtattctt tcaactacga ttgaagaaat gaaagatgtg 2160 tttcctcatc ctcctgaagg taaggatatt ctcactgttg taataaatta ttatattttt 2220 taaattaaaa ttttcatcta tattaacaaa aattgtttta ttatttttag gaaagtacta 2280 tctagttgat gctggatatc caaatatgaa agggtatcta gcaccataca agggtgaaag 2340 atatcacatt ccagatttta gagcaggaag tcaaggagaa ggcgtacatg aagtattcaa 2400 ccatgcacat tcttcactaa gaaatgtaat tgagcgaaca attggggttt ggaagaaaat 2460 atggcatata ttatctgata tgagaccatt tccattgatg aaacaacaaa agatcatagt 2520 tgcaacaacg gcacttcata attttattcg aaagtgtggt attgaagatg aagaatttaa 2580 caaatgtgac catattccag gatatatgat tgaccatgga gaagaaagaa tcaatcatga 2640 agacatggat tcatttaatc caagaagagt acaagatgga ggctatatgg acagagctcg 2700 aaatcgaata gcagtcgggt tggttggaaa tagaaatcgt tagagttttt gataatttat 2760 atttctaatc atgaattatt ttctaaagtc ttttaatatt gtttatggtt tttttttttt 2820 tacaagaata ttgtttatgg tactgttaag ctctttttgg atgatttacg ttttataaaa 2880 atattttgag agatactttc atatgacagt ttatgaaatt ttattcacat ttgtctttta 2940 tttttaaata ttcactcatt tatatcatat atagtttatc ctaaaacatt aagcttttaa 3000 atatgtattt tactaaacaa cttttagctt aaaaatcact ttgaagttaa aaaaaaagac 3060 acttaccaaa caacttttag ctttgcttct aaagcactta ttgttaactt tggcttccac 3120 aaagcttata agccctaaaa aagcttggcc aaacatagcc 3160 // ID SHAGY_I_MT repbase; DNA; EDCOT; 5249 BP. XX AC AC136141; XX DT 12-JAN-2007 (Rel. 12.01, Created) DT 12-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of gypsy -like LTR retroposon, SHAGY_MT, from DE Medicago truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; ORF; SHAGY_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5249 RA Shankar R. and Jurka J.; RT "SHAGY_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 86-86 (2007). XX DR EMBL/GenBank/DDBJ; AC136141; Positions 73183 78431. XX CC The internal region has two different reading frames. The first CC frame has intact domain for retroelement gag protein while the CC second reading frame has intact domains of RT polymerase followed CC by integrase, a hallmark of Gypsy-like LTR retroposons. The CC complete sequence is present in few copies. XX FH Key Location/Qualifiers FT CDS join(2142..4103,4107..5246) FT /product="SHAGY_I_MT_2p" FT /translation="MFQTPHGLPPTRPHDHRIPLQPNTSPINVKPYRYPHS FT QKEAMSTIIREMQDEGIITPSNSPYSSPVLLVRKKYGTWRFCVDYRALNVV FT TIRDRFPIPTIDELLDELGSANVLTKLDLRSGYHQIRVMPNDVHKTAFRTF FT DGHYEFLVMPFGLSNAPSTFQSAMNDLFRPFLRKFVLVFFDDILIFGNSLV FT EHFSHLKLVLDLLSQNQFFAKLSKCVFAVPQVDYLGHVISASGVGHDPEKI FT NSILDWLIPHSLTALREFLGLTGFYRIFVRNYATIAAPLTDLLKGSKFTWN FT TLAETAFTEFKIAMTTTPVLSLPDFSKPFTLETDASAVAIGAVLSQDGHLL FT AFFSRKMCPRMQQASVYVRELFAITEAVKKWRQYLVGRHFNIYADQKSLKE FT LLVQTIQTPEQQKWAAKLQGFSFSIHYKPGKTNLVADALSRKHADTTPLLL FT LTISSAIPDLLQNLRKFYNQTEGKQLVYDLFQPEDPAAQYAFREGLLFFKD FT RIYIPDLPDWRAAIISEFHNAPSAGHSGSKPTPSRLATTFLWPGAHTNVKE FT WVKKCSVCQQNKYLPSKKQGLLQPLETPNQVWEDLSIDFITHLPNSHGHTT FT VWVICDRLSKFVHFIALPTRFGAKDLALRFSIDICKLHGIPKSIVSDRAPI FT FLSTFKELFRVQGTTLKFSLAYHPETDGQTEVVNRSLETYLRCFASDHPRQ FT WFKFLHLAEYWFNTSFHSAIRMTPFEALYGRPPPSIRNYVRGHTTVLKLDT FT TLAHIEHILHTIKENLERSKQRMGTLANQKRKDCTFVVGQLVWLRLQLYRQ FT HTVHRRTSPKLAKRYYGPFLILRRIGPVAYELDLPPSSRIHPVIHVSQLRE FT YHGQDPDGHFRPIPPEVANNLFNESPENNHQDTAEGRQEPETGKEGQEKEK FT VISQMREKEPGIEKVNYSSTNVSSAVFKQGQMTLVPLDASQPQDACSTTQD FT KYPPLNPITTVGNQTLTDAPASPKITPSFIQSPPSDPTTNHINGQHTTPCQ FT LTESHRAPSHTEEHKPNLEVKVSSGPDS" FT CDS join(194..313,317..1390,1394..1921) FT /product="SHAGY_I_MT_1p" FT /translation="MRTSTSFSTPNMTRSPHCSPPPCDNALLRPTLHRHQK FT PQVLLPPLSQTLYFTLPLPHHNPKLTLFQSILHPFLPHYHNLSQPPPCFHS FT TTSILLFFTPSTSPIPVSLPITFHHTPQPQPTIYPPSYHQSHFTPQIPPFH FT NNIPFGAFHNQQSPYPTLQPNLYMTPPPHNQFQPSFPTPKIQLKPFDGTEP FT LEWLFQAEQFFSFYNITNENRLSLASFYMKGDALSWYKWMYQNHQLFDWPT FT FSKAVELRFGPSTYENHQAQLFKLRQYSTVADYQTQFEKLGNRVFGLPPKA FT LLNCFISGLIPEIRHELAVQKPYTISQAIGLAKLIEAKLKDSKTRPNKPYT FT NQPTQNTTLPPHLPSPKPITTTGPITSTPPSTQPTQSSKLPIRRISSAQMQ FT ERRAGLCYNCDEKYVMGHRCATGRYLLLILDPTMDDKADETIPDTAILTEP FT VDSYFHLSPQALTGQPSPKSLKALKFKGSIHGLSVSVLIDTGSTHNILQPR FT TATHLHIPHSPTQPLSVMVGNGSYIDCAGFCSSVPISLQNTLFHIPFHLFP FT IEGADVVLGLDWLTTLDPFHSIHILYS" XX SQ Sequence 5249 BP; 1508 A; 1534 C; 847 G; 1360 T; 0 other; tggtgctttc attgctgaac tcccatgcct ccaaaaccat caaacccatc aaccaaagat 60 ctagaagagg ctattcaagc caatcaacaa cggtttgaag aatcccttca tgctacccaa 120 caccagttca gggagcaact tgggctcatg aacacccgcc tggaaaatca gcaacaattg 180 cttgaatcca gagatgagaa cttccaccag cttctcaacg ccaaacatga ctcgctcacc 240 gcattgctca cctccgccct gcgacaacgc cctcctccgt ccgaccctcc accgccacca 300 gaaacctcag gtataactcc ttccacctct ctctcaaacc ctttacttca ctctcccact 360 cccccatcac aaccccaaac taaccctatt tcaatctatc cttcatccct tcttaccaca 420 ctaccacaac ctctcacagc caccaccatg tttccactca acaacatcca tacttctttt 480 ttttacgccg tccacttcac ctattccggt atcattacca atcacatttc accatacacc 540 acaaccccaa ccaacgattt acccaccctc ttaccaccaa tcacacttta caccacaaat 600 acctcctttc cataacaaca ttccctttgg agccttccat aaccaacaat ccccttaccc 660 aactctacaa ccgaatctct atatgacccc tccaccgcat aaccagtttc agccttcttt 720 tcccactccc aaaattcaac ttaaaccctt cgatggtacc gaaccgttgg aatggttatt 780 tcaagccgaa caatttttct ccttctataa cattaccaat gaaaaccgat tgtctttagc 840 ctctttctac atgaagggtg atgcccttag ttggtacaag tggatgtacc aaaaccacca 900 attatttgat tggccaacct tttccaaagc tgttgaactt cggtttggac cctccacata 960 cgaaaaccac caagctcaac tgtttaagct tcgacaatat agcacagttg cagattatca 1020 aacacagttt gaaaagttag gaaatcgggt gtttggtctt cctccgaagg cacttctcaa 1080 ttgtttcatt tcggggctca taccggaaat ccgccatgaa ttagcagtcc aaaaacccta 1140 caccatcagc caagcaattg ggcttgctaa actcatagaa gccaaactca aagactccaa 1200 aacgcgaccc aacaaaccct ataccaacca acctactcaa aacactacac tgccacccca 1260 cttgccaagc ccaaaaccca tcaccacaac cggccccatt acttccacac cgccctcaac 1320 tcaacccact caatcatcca agctcccaat tcgtcgcata tcctccgctc aaatgcaaga 1380 aaggcgtgct taaggccttt gctataattg cgacgaaaaa tacgtcatgg gacaccgttg 1440 tgccacggga agataccttt tgctcatctt agacccaaca atggatgaca aggccgatga 1500 aaccatacct gataccgcaa ttttgaccga accggtagat tcctattttc atctctcacc 1560 acaagctttg accggacagc cttcccctaa atcactcaaa gcactcaaat tcaagggatc 1620 cattcacggg ttatccgtat cggtcctaat tgatactggg agcactcaca atatcttaca 1680 accacgcact gctacccacc tccacatccc tcactcccca acccaaccct tatccgttat 1740 ggtgggcaat ggttcataca ttgattgcgc tggtttttgt tctagtgtac caatctccct 1800 ccaaaacact ctatttcata ttcctttcca ccttttccct atcgaaggtg ctgacgtggt 1860 tctcggttta gattggttaa caactctcga tcccttccat tccatccata tcctttattc 1920 ataacaacta gcccatcacg cttcaaggtg atgcttccaa ccaacccacc caagccactt 1980 ttcaccacat ctgtcaactt ttacataagg attctatagc ctcaattcat gttcttagtt 2040 gctcccccac aaccaatcac gaacacaccc atgcaaaact agccgtagtt ccatccacta 2100 caccactgga aatccagaac ctaatccaca catatgaatc tatgttccaa acaccccatg 2160 gactaccccc tactagacca catgatcacc gaatcccatt acaacccaac acttctccta 2220 tcaatgtcaa accctatcgt tacccccatt cccaaaaaga agcgatgtct accataatcc 2280 gggaaatgca agacgaaggt attataacac caagcaacag cccgtactca tcacccgttt 2340 tgttggtccg aaaaaaatac ggcacgtggc gcttttgtgt tgattaccga gcactcaacg 2400 tcgtgaccat tagagaccgt ttccccatcc ccaccattga tgaacttttg gatgaattgg 2460 ggtcagcaaa tgttttaact aagctggatt tacgttccgg ttatcatcaa attcgagtta 2520 tgccaaatga cgttcacaaa acagcttttc gcacttttga cggccattat gagtttttgg 2580 ttatgccatt tggtttatct aacgccccct ccactttcca atcagctatg aatgatttat 2640 ttcgtccttt tttacgcaag tttgtgttgg tattttttga tgatattctg atttttggca 2700 attctcttgt ggagcatttc tctcacttaa aattggtttt ggacttactt tcacaaaatc 2760 agttttttgc aaaattgtca aaatgtgttt ttgcagtgcc tcaagtggac tacctcggac 2820 acgttatatc agctagcggc gtgggtcatg atcccgagaa gatcaactcc atcttggact 2880 ggctgatccc tcattccctc accgctcttc gcgaattttt ggggctcacc ggtttttata 2940 ggatatttgt ccgcaactat gcaactattg cggcaccact tacagatttg ctcaaaggat 3000 ccaaatttac atggaataca cttgcggaga ccgcttttac agaatttaaa atagctatga 3060 ctactacacc agttttaagt cttccggact tctctaaacc attcacactc gagactgacg 3120 cttcagctgt tgctattggg gctgtcctct cccaagatgg ccatctgctt gccttcttca 3180 gccgcaaaat gtgtccgcgt atgcaacaag catctgtcta tgtccgtgag ctctttgcaa 3240 tcaccgaagc tgtcaaaaag tggagacaat acctagttgg gagacatttc aacatttatg 3300 ccgatcagaa gagtcttaag gagttattgg ttcaaacaat acaaacgccg gaacaacaaa 3360 aatgggctgc aaaactacaa ggtttcagtt tttccatcca ttacaaacca gggaaaacaa 3420 acctcgtagc agacgctttg agtcgtaaac atgcagacac cacaccatta ctacttctca 3480 ccatttcttc agccattccg gacctgctcc agaacctgcg taaattttat aaccaaacag 3540 agggtaagca attagtctat gatctgtttc aacctgaaga tccagcagca caatatgcct 3600 tcagagaagg actgttattt ttcaaggacc gtatatacat tccagattta cctgattggc 3660 gcgcagcgat catatctgag tttcacaatg ctccttctgc aggccattca ggctcaaaac 3720 ccactccgtc tcggctggca acaacttttc tctggcctgg cgcacacaca aatgtaaagg 3780 aatgggtcaa gaagtgctca gtgtgccaac aaaacaaata tttaccatca aaaaaacagg 3840 gactgttgca gccgttagaa acaccaaatc aagtatggga agatttgtca atcgacttta 3900 tcacacattt acccaactca catggtcaca caacagtttg ggttatttgc gaccgattgt 3960 caaaatttgt tcatttcata gctcttccaa cacggtttgg tgccaaggac ctagctcttc 4020 gcttctccat cgacatctgc aaacttcatg gcattcccaa gtcaatcgtc tctgaccgcg 4080 ccccaatatt cttgagtact ttctagaagg aacttttccg cgtccaaggt actaccctga 4140 aattcagttt agcttatcat ccggagacgg atggacaaac ggaagtcgta aacagaagtc 4200 tagaaacata cttacgctgt ttcgcaagtg accatccccg tcaatggttc aagttcttac 4260 atttggccga gtattggttc aatacatcct tccattcagc catccgaatg actccgtttg 4320 aagctctcta tggaagaccc ccaccatcta tccgcaacta tgtcagagga cataccactg 4380 tcctgaagct ggacaccacc ctagcacaca tagaacacat actgcacaca atcaaggaaa 4440 atctcgaacg tagtaaacaa cgaatgggaa cattagcaaa tcagaagagg aaagattgta 4500 cctttgtggt aggacaacta gtttggctta gattgcaact ctacagacaa catactgttc 4560 accgtcgcac ctctcccaaa ctcgctaaaa gatactacgg cccatttctc atcctccgcc 4620 gtattggtcc agtagcttac gagcttgatc ttcctccctc atcacggatc caccctgtga 4680 ttcacgtttc ccagctgagg gaataccatg gccaagatcc cgacggtcac tttcgaccca 4740 ttcctccaga agttgcaaac aacttgttca acgagtcacc ggaaaacaat caccaggaca 4800 ctgcggaagg aagacaggaa ccagaaacag gaaaggaggg tcaggaaaaa gaaaaggtta 4860 tatctcagat gagagaaaaa gaaccaggaa tagagaaagt gaattactcc tcaactaatg 4920 tgtcttctgc tgtctttaag cagggtcaaa tgacactagt tcctctggat gcatctcaac 4980 ctcaggatgc ctgctccaca acccaagaca aatacccacc cttgaaccca attactacag 5040 ttggtaacca gactttgact gacgcgcctg ctagtcccaa gatcactcct tcattcattc 5100 aatctccacc atctgatcca accaccaacc acatcaacgg tcagcacacc actccctgcc 5160 agctcactga gtcacaccgt gctccttccc acactgaaga gcacaaacca aaccttgagg 5220 tcaaggtttc ttctggacca gatagtagt 5249 // ID Gypsy-31_VV-LTR repbase; DNA; EDCOT; 362 BP. XX AC chr5; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-31_VV_; KW Gypsy-31_VV-I; Gypsy-31_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-362 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr5; Positions 21416754 21416393. XX SQ Sequence 362 BP; 114 A; 82 C; 66 G; 100 T; 0 other; tgatgcaggc ccactggaca aatcagcatc ggaagcgagt gaagcccagc aaaatccagt 60 agcaaccaac aacaaacatg tgactagaat cagaaacgca ccaaaacggt ttaaggattt 120 cgttatggcc accaaatagg gaccacacaa tgagtagcaa tgatgaattc tgttatggga 180 atcactggca atgatgtatt ctgttatgag tttgttacaa atatgcctat aagaatgaaa 240 ggaccctgac atgatggggg catgaaaatt attcctcaaa tattctatct tctctgcaaa 300 tctttttctt ctactctcct tcccttctat tctgtcttct tcctttccct acgtaagcaa 360 ca 362 // ID Gypsy20-VV_I repbase; DNA; EDCOT; 9884 BP. XX AC AM483798; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy20-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9884 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-9884 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 718-718 (2007). XX DR Genbank; AM483798; Positions 15688 5805. XX CC Positions [4820-5323] - Integrase core CC 'ACAAG' target site duplication CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 4454..5530 FT /product="Gypsy20-VV_I_3p" FT /translation="MLLEKAPWYAHIANYLVTGEVPSEWKAQDRKHFFAKI FT HAYYWEELFLFKYCADQIIRKCVPEEEQQGILNHCHENACGGHFASHKIAM FT KVLQSGFTWPSLFKDSHIMCRICDRCQRLGKLTKRNQMPMNLILIVDLFYV FT WGIDFMGPFPMSFGNSYILVGLDYVSKWVEAIPCKHNDNRVVLKFLKENIF FT SRFGVPKAIISDGGTHFCNKPFKALLSKYGVKHKVATPYHPQTSGQVELEN FT REIKNILMKVVITSRKDWSIKLHDSLWAYRTVYKTILGMSPYRLVYGKACH FT LPVEVEYKAWWAIKRLNMDLIRAGAKRCLDLNEMEELRNDAYINSKVAKQR FT MKRWHDQLISNKEFQK" FT CDS join(340..1224,1228..3960) FT /product="Gypsy20-VV_I_1p" FT /translation="METTPEDQQSHHGHQDNPNEFRSMRDRMHPPRMSAPS FT CIVPPTEQLVIKPHIVPLLPTFHGMESENPYAHIKEFEDVCNTFREGGTSI FT DLMKLKLFPFTLKDKAKIWLNSLRPRSIRTWTDLQVEFLKKFFSTHRTNGL FT KRQISNFSAKENEKFYECWERYMEAINACPHHGFDTWLLVSYFYDGMSSSM FT KQLLETMCGGDFMSKNPEEAMDFLSYVAEVSRGWDEPHRGEVGKMKSQPNA FT FHAKAGMYTLNEDVDMKAKFAAMTRRVEELEPKKMHEVQAVAETPMQVKPC FT SICSYEHLVEECLTIPVAREMFGEQANVIRQFKPNSNVSYDNTYNSSWRNH FT PNFSWKPRAPQYQQPAQPSQPSQQASSLEQAIVNLSKVVGDFVGDQKSINS FT QLSQRIDSVENTLNKRMDGMQNDLSQKIDNLQYSISRLTNLNIVQEKGRFP FT SQPHQNPKGIHEVETHEGESSQVRDVKALITLRSGKKVESPTPKLYVEEKV FT EKETKKREEMKGKKKDISEGKEDHDSTVNANPEKELIKDELMKKRTSPPFP FT QALHGKNGIKNASEILEVLRQVKVNIPLLDMIKQVPTYAKFLKDLCTIKRG FT LNVNKKAFLTEQVSVIIQCKSPLKYKDPGCPTISVMIGGKVVEKALLDLGA FT SVNLLPYSVYKKLGLGELKPTSITLSLADRSVKIPRGIIEDVLVQVDNFYY FT LVDFVVLDTDPLVKEANYVPIILGRPFLATSNAIINCRNGLMQLTFGNMTL FT EFNIFHMSKKLIPPEEEEGPEEVCIIDTLMEEHCNQNMQDRLNESLEGLEE FT GVTEPADVFATLQGWRKKEEILSLINKDEGQDDVKEEFPKLNLKPLPMELK FT YTYLEENNKCPVVISSSLTSHQEISLLEVLKRCKKAIGWQISDLKGINPLV FT CTHHIYMEEKTKPIRQPQRRLNPHLQEVVRTEVLKLLQAGIIYPISDSPWV FT SPTQVVPKKSGITVVQNEKGEEIATRLTSGWRVCIDYRKLNAVTRKYHFPL FT PFIDQVLERVSGHPFYCFLDGYSGYLQIEIDVEDQEKTTFTCPFGTYAYRR FT MPFGLCNALATFQICMLSIFSDMVERIMEVFMDDITIYGGTFEECLVNLEA FT VLKRCIEKDLVLNWEKCHFMVHQGIVLGHIISKKGIEVDKAKVELIAKLPS FT PTTVKGVRQFLGYAGFYKRFIQDFSKLSRPLGELLTKDAKFVWDERC" XX SQ Sequence 9884 BP; 2946 A; 1979 C; 2086 G; 2873 T; 0 other; aatggcgccg ttgccgggga aggtgccaac ttcatagtga tattgtttca gtgtacttgt 60 ggttttcatc acaagttggg tgaattttct gtcattttac tcactctttt agtgtttctt 120 ttactcgttt atattctagc atagctttta atttagtttt agttaaccga actctttttg 180 gtagttttgt tttttttgtt ttcctctgtt tttgtttttt tttttttttg ttacaattga 240 tactagttat gtatgccaaa gtggatatga gatattggag gaagacttgt taaacttgaa 300 acacctcata acaaggagtt ggaattgagc ttgaacatca tggaaactac acctgaggat 360 cagcaaagtc accatggtca tcaggacaat cccaatgaat tcagatcaat gagggaccgc 420 atgcatccac ctcgtatgag tgcaccatcg tgtatagtgc cccctacaga gcagctagtg 480 atcaaacccc atattgtgcc acttctacca actttccatg gaatggagag tgagaatccc 540 tatgcccata tcaaggaatt tgaagatgtt tgcaatacat tccgagaggg aggaacttca 600 atcgacctga tgaagcttaa attatttcct tttactttaa aggataaggc caagatttgg 660 cttaattctt taaggccaag gagtatccgt acttggactg atttacaagt tgaattcctc 720 aagaagttct tttctactca cagaacgaat ggcttgaaaa ggcaaatttc aaacttttca 780 gctaaagaga atgagaaatt ctatgagtgt tgggaaagat acatggaagc cattaatgct 840 tgtcctcacc atggctttga tacatggcta ttggtgagtt atttctatga tgggatgtct 900 tcctcaatga agcagctcct cgaaacaatg tgtggagggg atttcatgag taagaatcct 960 gaagaagcta tggatttctt gagttatgta gctgaagtct caaggggatg ggatgaaccg 1020 cacagaggag aagtgggaaa gatgaagtct caaccaaatg cttttcatgc taaggctggg 1080 atgtacacct tgaatgaaga tgttgatatg aaagcaaaat ttgcagctat gacaagaaga 1140 gtggaggagc tagaaccgaa aaagatgcat gaagtgcaag ctgttgctga aacaccaatg 1200 caagtaaagc catgttctat ttgttaatct tatgaacact tggtggagga gtgccttaca 1260 attccagttg ctagagaaat gtttggagaa caagcaaatg tcattagaca attcaagccc 1320 aatagcaatg tttcgtatga caatacttac aactcaagtt ggaggaatca tccaaatttt 1380 tcatggaagc caagagcacc tcagtaccaa cagccggctc aaccatctca accatctcaa 1440 caagcttcaa gtcttgaaca agcaatagtg aatctcagca aggttgtggg agatttcgtt 1500 ggagaccaaa aatccatcaa ttctcaactc agtcaaagaa ttgacagtgt agagaatact 1560 ttgaataaaa ggatggatgg gatgcaaaat gacttatctc agaagataga taatcttcaa 1620 tactcaatct caaggctcac taatttgaac atagtgcaag agaagggcag atttccttct 1680 caacctcacc aaaaccccaa gggtatccat gaagtggaaa ctcatgaggg agaatcttca 1740 caagtgagag atgttaaagc cttgatcact ctaaggagtg gtaaaaaggt tgagtcacca 1800 acacccaagc tatatgttga agagaaagta gaaaaagaga caaagaagag ggaggaaatg 1860 aaaggaaaga agaaagatat cagtgaagga aaggaggacc atgattcaac agtgaatgca 1920 aatccggaga aagagcttat taaggatgaa ttgatgaaga aacgcacatc tccacctttt 1980 cctcaagctt tgcatgggaa aaatgggata aaaaatgcat cagaaatcct tgaagtattg 2040 aggcaagtga aggtcaatat tccattgctg gacatgatta agcaagttcc aacatatgca 2100 aagttcctaa aggacctgtg tactatcaaa agagggttga atgtgaataa gaaagccttc 2160 ttgactgagc aagtaagtgt cattatacaa tgcaaatctc ctttgaagta caaagatccg 2220 ggatgtccta ccatttcagt catgattgga ggaaaggtag tggaaaaagc tttgttagat 2280 ttgggagcta gtgtgaattt gttaccatac tctgtttata agaaattggg acttggtgaa 2340 ttaaagccaa catcaatcac tctatcttta gctgataggt cagtgaaaat tccaagaggg 2400 ataattgagg atgttttagt tcaagttgat aatttctact atctagtaga ctttgttgtt 2460 cttgatactg atcctcttgt taaggaagct aattatgttc ctatcatcct tggaaggcca 2520 tttcttgcta cttcaaatgc aatcataaat tgtaggaatg gacttatgca actcactttt 2580 ggcaacatga cacttgagtt taatatcttt catatgtcta agaagctaat tcctccggaa 2640 gaagaagaag gtccagaaga ggtatgcatt attgacactc taatggagga gcattgtaat 2700 cagaatatgc aagacaggtt gaatgaaagt cttgagggtc ttgaagaagg ggtgactgaa 2760 cccgctgatg tgtttgctac tctacaaggt tggaggaaga aagaagagat cctgtcttta 2820 atcaataaag atgagggaca agatgatgta aaagaagaat tcccaaagct caatttgaaa 2880 cctctgccca tggagttaaa atatacgtac ctggaagaaa ataacaaatg tcctgttgtt 2940 atatcttcat ctcttaccag tcatcaggag atttctctac ttgaagttct taagaggtgt 3000 aagaaagcaa taggatggca aatatctgac ttgaaaggaa tcaatccttt ggtttgtaca 3060 catcacatat atatggagga gaaaactaaa ccaattcgtc aacctcaaag aagattgaat 3120 cctcatttac aagaagtagt gcgaactgag gtactgaagc tactccaagc gggtattatt 3180 tatcccatat ctgacagccc ttgggtgagt cctactcaag tggtaccaaa gaagtcaggg 3240 attactgtgg ttcagaatga aaaaggagaa gaaattgcta cacgtctcac ttcaggttgg 3300 agggtgtgta ttgactatag gaaattgaat gctgtgacaa ggaaatatca ttttccactc 3360 ccgtttattg atcaggtgct ggagagagtc tctggccatc ctttctattg tttcttggac 3420 gggtactcag ggtatttaca aattgaaatt gatgttgaag atcaggagaa gaccactttc 3480 acatgtccgt ttggaacata cgcctacaga agaatgcctt ttggtttatg caatgcactt 3540 gcaacattcc aaatatgtat gcttagtatc ttcagtgata tggtggagcg aattatggag 3600 gttttcatgg atgatatcac catatatgga ggtacatttg aagaatgctt agtaaatttg 3660 gaagcggttc ttaaaagatg cattgaaaaa gacttggtgc tcaactggga gaaatgccat 3720 tttatggtac atcaaggaat tgtccttggc catatcatct ccaagaaagg cattgaagtt 3780 gataaagcaa aggtggagct tattgccaaa ttgccatccc caaccactgt aaaaggagta 3840 aggcaatttc ttggctatgc agggttctac aagagattta tacaagactt ctctaagctt 3900 tcaaggcctc ttggtgaact tttaactaaa gatgctaagt ttgtctggga tgaaagatgt 3960 taaaagagtt ttgatcaatt gaagcaattt ttgacaaccg ctccaatagt gagggctcct 4020 aactggcaac taccctttga agtaatgtgt gataccaatg actttgctat aggagctata 4080 cttggccaaa gagaagatag gaagccctat gtgatctact atgcaagcaa aacattgaac 4140 gaagctcaaa gaaactacac aactacagag aaagaattgt tagctatggt gtttgcttta 4200 gacaagtttc gtgcttattt ggtagggtct ttcatcattg ttttcactga ccattcggcc 4260 ttgaagtatt tattgacaaa gcaagatgca aaagcaaggt tgattagatg gattcttttg 4320 ttacaagagt ttgatctcca aatcagagac aagaaagggg tggagaatgt ggtagctaac 4380 cacctttcca aggttggcta tagcacacaa ttcccatgta cctattaatg atgactttcc 4440 tgaggaatca cttatgttgc tagagaaggc tccttggtat gctcatattg ctaactattt 4500 ggttactggt gaagttccaa gtgagtggaa agcacaagac aggaagcact tctttgcaaa 4560 gattcatgct tattattggg aagagctctt ccttttcaag tattgtgcag atcagatcat 4620 aagaaagtgt gtccctgaag aagagcaaca agggatcctc aaccattgcc atgagaatgc 4680 atgtggaggc cactttgcct ctcataaaat agccatgaag gtcttgcaat cagggtttac 4740 ttggccatcg cttttcaaag attcccacat catgtgtagg atttgtgata gatgccaaag 4800 acttgggaag cttacaaaaa gaaaccaaat gcccatgaac ctcatcctta tagttgatct 4860 tttttatgtt tggggtattg acttcatggg acctttccca atgtcttttg gtaactctta 4920 tatattggtg gggttggact atgtttccaa atgggtggag gcaatcccct gtaaacataa 4980 tgataacagg gtggttctca aatttcttaa ggagaacatt ttctcaagat ttggggtgcc 5040 caaggccata atcagtgatg gaggtactca tttttgcaac aaacctttta aagccctatt 5100 atccaagtat ggagtgaagc ataaggtagc tacaccttat catcctcaaa cttccgggca 5160 agtggagcta gaaaacaggg aaatcaagaa catactgatg aaagtggtga ttacaagcag 5220 aaaagattgg tctattaagc ttcatgattc attatgggca tatagaacag tttataagac 5280 tattcttggc atgtctccct atcgtcttgt ctatggcaaa gcgtgccatc tccctgtgga 5340 agttgaatat aaggcttggt gggcaatcaa gaggttgaac atggacttga tcagagctgg 5400 ggcaaagagg tgcttagacc ttaatgagat ggaggaatta agaaatgatg cttacatcaa 5460 ttccaaagtt gcaaaacaga ggatgaagag gtggcatgat caactaatct ccaacaaaga 5520 atttcagaaa tgacaaagag tcctactcta tgactcaagg cttcatatct ttcctgggaa 5580 actcaagtcc aaggtggata ggtcctttca ccattcacca agtacatctc aatggagtgg 5640 tggaattact gaattccaat ggcatagaca cctttagagt caatggtcat cgcctcaatc 5700 cattcattga gtcgttcaag ccagaaaaga aggaaatcaa cctccttgag ccacaaaaag 5760 cctaatcaga gaagggttag atggacttgg tttcaccaaa gtccataatt ttgttaaata 5820 tgttattttt tatagttttg taaattattt gattgtaatt ttggtcttaa attatgttaa 5880 ttgtaactaa cttaatcttt tttaatgatt aaaatcagga gaaattgcaa aaaaatcgaa 5940 aaaaggaagc taggaatcaa aataagctca aaagcaagga gaaagctttg gctacgaaaa 6000 tttcataagc aaaagagggt cgctgcgaaa attgcattcc gctgcgaaaa aatttcgcag 6060 ccctcaggtg ctgctgtgaa aatcccactt cccgcttcga aaatcgatct ccgctgtgaa 6120 accatttcgc agccacctta cacccgctgc gaaaattttc gcaactacga aagcccttct 6180 tgacacacga gtgccatttc gcagccgggt accaccgttt cgtagctgcg aattggctgt 6240 gatttttccc acgcctggag acccgccttt tcgcagccga agcaccattt ggaaggatgt 6300 ttcgtagctg cgaaaccccc ctttggcaca ctagcgccag ttcgcagagc cgtacgctcg 6360 tttcgcagct gaaaatgggt tgcaaaatcg ataccgaatt ttccctcact gcgaaaacgc 6420 ctagctgctg caaaattcgc acctcctcgt tgcgaaaaaa cccatctgct gcaaaaagga 6480 acagtgacct tttgtgttct ttttaaaaga tataaattcc atttttccta tttttgtacc 6540 gttacttgaa ctttaaaaag gtgccaagag gagccaagcc agagcatcct ctcgtctgcc 6600 tccttcacct gagcaagtcg cgcccatttc cggcagtttc cactgacatc gccatggcca 6660 gaacacgagg agcaaagtct tcgtctccat cgactcgcct gagaatccca agaggcgcgc 6720 ctgtccaaga ctccacctct gagctgccgc ggcctcgcct cgctctacca ccagtcaaga 6780 gcgcacctac cagtcctctg gccaggcgct ataatacaag gagatcactt accattgtcg 6840 gtgcgagctc ttccggaccc ccaaagaaga aagcaaaggt ctcagagccg atcaatctga 6900 ccgagtcctc ttcgaagcct gaatcagagc ctacaccgtc tccttcgcct gctaaaaagt 6960 ctccattgct tgctaaaaat tctccacccc ctgtcaagaa gcctcagcca tctcaggcgc 7020 caacaagaga atctcaaatt cccttggata tgactcttga ggaagccatc agacacctca 7080 tggtgacaca gctgccaatt gcaagaaatc tggattgcag agcaaggcca tttcattctg 7140 agctcttttt cgacatagcc accttcataa ttcaacctga gctcagggtg tcctttcatc 7200 tgctacagag gtatcatgtg gagcatttgc tgactcctaa ggattttttc tatcctcgag 7260 tggcattgga cttctatcag tccatgacca caaaccaggt ccgcgatcct atagccatcc 7320 attttaccat agatggacga catgggattt tgggagctcg gcatatagca gaggcactcc 7380 atatccctta tgagccagca tgtccagagg attttcaagc ctggattagc ccttcataga 7440 gtgatattgt tcatactctg tctagagggg catcctcacg ccattacatc ctgaggaagt 7500 agcttccccc caacatgttc ttcattgatg cactcctgcg ccataacatt tttccacttc 7560 agcattgggt gcagaagaga ggagtgttgc tggaggcctt gtttaggatc tctgagggat 7620 acttctttgg cccttctcat ctcatcttgg ctgctcttct atactttgaa gagaaggtgc 7680 atcgaaagaa gctactccga gcagatgcca tcccactcct cttccccagg ctattatgct 7740 agatattgga gcacctggga tacccagtag agcctcagca tgagcgtaaa cttttttgtc 7800 gagagatttt cactctcaac aaatggacta gtatgacagc ttatggtggt gcagaccagg 7860 gagcaccagc tggagcagag cagccaaagg agccagtcga gccacctgct gacactcatc 7920 cacctgcccc tgcagtggcc cctagtgagc ttccaccaga gattccatcc tctgcctctc 7980 atgccacacc acagcctccc cctgtcattc cacctccatc agcaccatct ccttcagctg 8040 agctaagggt agctattccc atcctcgagt atagaggcct ttcccacact taccaggcat 8100 tggccacttc tcagagcatc atcactcagc agatcacaac ccttcactct cagcaggagt 8160 agattcttgc cactcaggcc cagcacattg ccatcctgag gcagatccag catcatctcg 8220 gcattatatt agctcctgag catgccattc ccagctcatc agagccatca caggcccctc 8280 attttattga tcagcctatg cctcatcagg agcctcctac aggagagaca gctgagccat 8340 catttccaca gcatcatcca cccaccatct gatcatttat acatttcctt tatatttctc 8400 ctatgtattt cgtttatgtt gatcttttat gaaatcccat cattttgata ttatatattg 8460 ggattacttg tattgcttaa tttccaactg tactgacatg aattaaagta atacaaatct 8520 atcatttttt ttatcactct tagcattcct ttattcttat ttcctttact cacatctttt 8580 attctttttg aaacatgtgg tttctccaat caatattcga aattgatatc cctcaggagg 8640 taccacttcc tccttataat ctcaatcact catgccacat tgaggacaat gctcagctcg 8700 gttgaggggg ggggggggga gttgaggaag gaagtttttt gttacttatg ctaagttatt 8760 ttggtaattt agatgatttt tgcttaatta taaaaaattt taaaagtttt tactctaatc 8820 tccatggttt ctaaggaaaa attttcaaat taaaatggga gaaactgaac ttttgctttt 8880 cacttgactt agagtttgga ttatgcttac taaagttgtt caattgttga agcttctatt 8940 gaagtcaagc ttagttcttc cactttaagc tattcacaca ctgtgcacac taggttccga 9000 atataagatg aaaaactatt tccctcttga cttataaaag tttagacttg gtacctttga 9060 cctcatttaa tagtgttggg ataccttaca aaaggctaat gagcccttga aaaagaaaga 9120 aaaaatgttt gcttgccttg aaacccgagc aaggtctgag gggtatatgg tgaaaatctt 9180 taaaacctgg tgccctaagc cttaattggt tgggagtcac cgacctcaat gctcgttaaa 9240 agggtgaata ggtggagttt aacttactgt aggtgcttgg gtattaaaat tcattctcaa 9300 aagttcggga taaaatccga ggagttagtg gttgaaagat ccttaaatct tgatgcccta 9360 aaccttaatt ggttgggagt catcgatgga cccccgttat atggacaagt tagaaaagaa 9420 tacctttaag ccttgcaccc ctacaataaa aaataaaata aaaatggtga aacaagaggg 9480 tgcgttctta gcctattgaa tttggtcagt ttgctaagtg ttgaaaagag ctaggttggg 9540 gggagagatt agtttagcat tctatattcg gaaactatca tctcacattt agactttggt 9600 ggaagagtaa ggtttggtcc tttggaagtg gaaatgattt taaagcttca atttgcataa 9660 tgccttctct ttatcaaagg tgtttagcaa agtttttgat aactcttgtt gaaatttgag 9720 tttatatttc tttaatgttc catgtgggag tatgatcatc atgccactta aaattttttg 9780 gaagtgataa gcatgatctt gtaaagttta ttacttttta gtactttttt tttttttttc 9840 tctctttcat tgctaaggga ctgcaatatg tcggttgggg gaag 9884 // ID SHAMU_MT repbase; DNA; EDCOT; 526 BP. XX AC . XX DT 02-JAN-2007 (Rel. 12.01, Created) DT 02-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW Inverted; terminal; repeat; Interspersed; SHAMU_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-526 RA Shankar R. and Jurka J.; RT "SHAMU_MT: A putative non-autonomous DNA transposon from barrel RT medic."; RL Repbase Reports 7(1), 106-106 (2007). XX DR [1] (Consensus) XX CC The DNA transposon sequence is present in multiple copies but CC poorly conserved. It has features of MuDR type transposons with 9 CC bp TSDs. Does not have any well retained transposase domain. The CC sequence has terminal inverted repeats. XX SQ Sequence 526 BP; 165 A; 70 C; 110 G; 179 T; 2 other; ggcttaaaca cttttttggt cccttatctt tatttcgggt tcatattggt cccttaatta 60 aaaaaaatag tgcatataga tcctttaatt tgtttaattg gtatcatgtt agtcctttcc 120 atgcgaattc atggttttga agtacgagat ccatgtgaat ttgtgttgga tccatcctct 180 gcatcattgt tcaacgattt cagaaaggaa gctgatgagg aacctcgtga atttgacatg 240 tttgctcaga tggagaagaa gattggttgc aatctctaat ttggggtgaa gaatttgggg 300 atatatgggt tccaatgaac cttaattttg atttataggg gaattgataa agtgggaaga 360 atgagatgtt acatatactg caattaatgt cgttagcctt tgatggatgr aaaggactaa 420 tgtgrtacca attaaataaa ttaaaagacc tatctgcatt tttttttaaa taagggacca 480 atatgaaccc taaaataaag ataagggaca aaaaggtgtt taagcc 526 // ID SHALINE21_MT repbase; DNA; EDCOT; 2100 BP. XX AC . XX DT 29-JAN-2007 (Rel. 12.01, Created) DT 29-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A LINE element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW Ta-type; Interspersed; Poly-A; ORF; repeat; SHALINE21_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2100 RA Shankar R. and Jurka J.; RT "SHALINE21_MT: A LINE element from barrel medic."; RL Repbase Reports 7(1), 97-97 (2007). XX DR [1] (Consensus) XX CC The element is 5' truncated and resembles Ta type L1. It has an CC incomplete ORF having domain for reverse transcriptase like CC domain. It is present in the genome in highly disrupted CC incomplete copies. XX FH Key Location/Qualifiers FT CDS join(32..1084,1088..1345,1349..1366,1370..1462) FT /product="SHALINE21_MT_1p" FT /translation="MFDWQAESAPSATPSATTVPAPPNPPVAASFAQALSA FT SQPTSSNDNLPQPSIRGETLSIKITQEVYEKGXDVCKRNLRGRLVLNKGDK FT PYSTKDIELKLQKLWKTSGAWTMLSLGRGYYEFFFASEDDLRTVWAXGTVN FT LKPGVLRLFEWTKDFNMHTQRNTHAQVWIRLMELPQEYWMERTLREIASAV FT GTPLVIDNATTKRLFGHYARILVDMDFSRKIFHEIVVEREGFAFPVEVVYE FT RMPDFCTHCQNIGHDVTACRWLYPRKEKEDNTAKEKVAQGKKQVPTKKTEW FT VPIKDNPSGIGSSXAFQQPISRPAATEEXIPTQHFCSTEPTCNPQQHLFGL FT LQLYQHVPXGKQLSKLPNSSXRVXQDINSTEEFVALEATLHEVERTNEVSK FT KNKCFNDVSTDLQMEAHMTFRMLXXXXIKRCCLXHLFMFXRKLKLXKKMRT FT LPXHXIDVMALEQSANNPDQQRQKRKCSS" XX SQ Sequence 2100 BP; 608 A; 410 C; 464 G; 565 T; 53 other; tctccttttt tgtctgatct cagtcgctgc catgtttgat tggcaggctg agtctgctcc 60 ctcagccact ccttctgcta cgacggtgcc tgctccaccc aatccaccgg tcgcagcctc 120 ttttgctcar gctttgtcag catcgcaacc aacttcatct aatgataatc tgcctcagcc 180 atccattcga ggggagactc ttagtatyaa aattactcag gaagtgtatg aaaaaggawt 240 ggatgtttgt aagcgaaatt tacggggtcg actggttyta aacaagggag acaaacccta 300 ttcgacaaag gatattgagc tgaaacttca aaaactttgg aagacttcag gtgcatggac 360 catgctgtct ctaggaaggg gttattatga attcttcttt gcctctgagg atgatttacg 420 aacggtttgg gcagygggaa cggtaaattt gaaaccgggt gtgttacgat tatttgaatg 480 gaccaaagat ttcaatatgc atacgcaacg aaacacacat gcacaagttt ggattcgctt 540 gatggaatta ccacaagagt attggatgga gaggactctt cgtgagattg ctagtgcggt 600 tggcaccccg cttgttattg ataatgcgac aacaaagcga ctttttggnc actatgcacg 660 aattctagtt gacatggatt tttcacgkaa gatytttcat gaaattgttg ttgaaaggga 720 aggctttgct tttcctgttg aggtggttta tgaacggatg ccggattttt gcacwcattg 780 tcagaatatt gggcatgatg tyacagcttg tcgttggttg tatcctcgga aggaaaaaga 840 agataataca gcgaaagaaa aagttgctca agggaagaag caagtgccaa caaagaarac 900 tgartgggtg cctattaagg acaacccttc tggtataggt tcatctanag cttttcaaca 960 acctatttct cggccagctg ctacagagga arctattccg actcagcact tctgttccac 1020 agaaccaact tgcaatccac aacaacatct cttcggccta cttcaactct accarcatgt 1080 tccctgagkt ggaaaacaac tttcaaaact tcccaacagc agcycacgag tgratcagga 1140 tatcaattcc actgaggaat ttgtagcttt ggaggccact ttacatgagg tggaacgtac 1200 aaatgaggtc agcaaaaaga ataaatgttt taatgatgtt tccacagact tgcagatgga 1260 rgcacacatg acattcagaa tgttgamrwc grtatmaatc aaragatgct gcctwsaaca 1320 tctgttcatg ttctkgagra aattgtagaa actccasaag aaaatgtagc ggacactgcc 1380 gyatcacwtt atagatgtta tggcattgga acaatcagca aacaatccag accarcagag 1440 gcaaaagcgc aagtgcagca gytaatgagc tyactgctga tcaggtgcgt gwagtttcaa 1500 ttcaccaagg aaatccaggt ttcgaaaaat gtycaaartg acttggatta tgggctcgma 1560 ttcgkgagta tgatcaatgk atggcggmcg aaggwttcac gcaagttytr tcyaaaaaac 1620 agcagcaarc aktgaaaaag caagtkttag graaagcttc gtacaacacc cgtgcraagg 1680 gtwcamctcc cccttctcaa tgaatttctg aatgttagag agaattgaga agttggcttc 1740 gatggatatt agagactact tcagtagtac tcaattctat caaccatgtg ctgggatata 1800 gtagtaccaa cgcatagaag aattcttaaa catgttgttt atgaagcaaa ccaactatta 1860 catgagattt cttgaatctc ttacgagcaa tttattgggc ttggtctcag ctttaatgca 1920 aagcaaaaag agttgggatt gggagaagat cctaacgcta ataatgcagg cttggtcaat 1980 aatatgggtc atgagattca gggttctttt tggttagtct cgctgcctgc tgagttgcat 2040 attgggatgt cggtgttgcc tcctgatgtc tgtctcactc cctgcttaga aaaaaaaaaa 2100 // ID Gypsy1-VV_LTR repbase; DNA; EDCOT; 471 BP. XX AC . XX DT 31-AUG-2007 (Rel. 12.08, Created) DT 31-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy1-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-471 RA Obukhanych T. and Jurka J.; RT "Gypsy1-VV - LTR retrotransposon from grapevine."; RL Repbase Reports 7(8), 672-672 (2007). XX DR [1] (Consensus) XX CC This is a long terminal repeat (LTR) sequence of the Gypsy1-VV CC LTR retrotransposon family. LTRs are 95% identical. XX SQ Sequence 471 BP; 102 A; 74 C; 122 G; 168 T; 5 other; tgataggcca mggcgttctg taaggagcya taagccgaat cccaartatt tgggatgagc 60 ttgtacgtaa gagatcattg catgcagcat gcatgcaacg taggcagtgg gtctcacgtg 120 aagaataatg aaggagggac tgggtcgtgc agttgagagt ttttcgtgtg aatgggtctc 180 cagttatgaa tgggtcctca gttggttgcg agttttacgt cacttttctt catgcagtta 240 tgtttggttt ttacgtgtat ttgcaggtgt tgtttacgtg tccagttgtt agtttctagt 300 ttccttttat ttcggtttgc ttgttgtacg tggctttgct tatttaaagc agccatcagt 360 tgttaagggg aggtcaagaa ktcatttgta atccaaakct tgtggttctt tctcacccga 420 agagaaatct atttatttat tcgttgtatt agctgtgatt gggacctatc a 471 // ID Copia53-PTR_LTR repbase; DNA; EDCOT; 393 BP. XX AC scaffold_352; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia53-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-393 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-393 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 287-287 (2007). XX DR Genome; scaffold_352; Positions 21361 21753. XX SQ Sequence 393 BP; 117 A; 70 C; 93 G; 113 T; 0 other; tgttagtaaa gtgtagacaa acaatgctca ctcccacttt atgctagtag gaacaactca 60 tctcccactt agtataaagt ggaagcacat ggtgggaaca actcatccca ctagcacaaa 120 gtaggagttc atgatggcca tgatttcttg ccccctgctc tgtctataat tagacacatt 180 gaagagctga ggatgtgtgc agagaataga gagaacgaga gcagaagaat agagagagct 240 tgagtgagta gagttgagtt gagaagagtt ttctcctcct ctttgtttgt attgtttctt 300 tgattgatta atacagacca gtagctccgt ggagtaggca aattgccgaa ccacgtaaat 360 ttgtgtgtgt ttgatttctg gaactgtata aca 393 // ID Copia22-VV_LTR repbase; DNA; EDCOT; 491 BP. XX AC AM472139; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia22-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-491 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-491 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 703-703 (2007). XX DR Genbank; AM472139; Positions 2519 2029. XX SQ Sequence 491 BP; 148 A; 97 C; 107 G; 139 T; 0 other; tgctgaggca gaatttcgtg ctatggcaca aggtatctgc gagggaatct ggttgaacag 60 gctgttagaa gaattacggg ttccattgaa gcatcccatg gtgttatact gcgacaatca 120 agctgccatc agtatcgcta agaatccggt tcatcatgat cgaactaagc acgtggagat 180 agatcgacac tttatcaagg aaaagattga agaaggagtt ttcaaagtca gctacactcc 240 gacaaactgt caaacggctg acattctcac aaaagctctt gctcgagtta acttcgaaga 300 tctgacagaa aaacttggaa tgatcaacat ctacaacgcg gcttgagggg gagtgttgga 360 aatcaagcca gcatcctctg tttacttccc taattagtgt aatgtactgc ctttattata 420 attgatttag gagtaattct agcaaggtac tttattcact ttccatgtaa gagtagttta 480 ttcactttcc a 491 // ID Gypsy-35_Mad-LTR repbase; DNA; EDCOT; 1155 BP. XX AC . XX DT 13-OCT-2010 (Rel. 15.1, Created) DT 13-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-35_Mad-LTR. XX NM Gypsy-35_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1155 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1765-1765 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 1155 BP; 308 A; 270 C; 274 G; 302 T; 1 other; tgtttggacc caaatttaca tcatcggccc gtgtaatcga gaccgtagag taaacatagt 60 tctcagccgt cggatggaaa agtgaaaata tttttgttaa aagataatat tatggttttt 120 atcatgatta tcttttaatt tgaattatct tgacatattc ttaaacggga tggatatgat 180 gcaaattata tcctcaagta agagtgtttg ggctcaaatt aacatgttgg gccgagtata 240 gaaccactct cggcccggga ggcctggcga caggggagcc ttggatcatt tagtacgtgg 300 gctcctaaac ctaggtcggc taggtcatat tacatttact agtcgagtcc taacgcgata 360 agkagtctcg gcaagggtaa taacccggaa gtgaatccgg ctcaatagag gactaggctc 420 acaatcctag taaacatagg actggtcgag tgggtgtttg atccggagaa gaagacctag 480 ttcgagtagg gttttgactc gacttcaaag gtatctagtg ctataaatag aggaggctgt 540 gcatcattca agaggacccc tccaacacac acaaaactgc cctgcgcaaa ctttctcaac 600 accttgagat ctttttattt tcttttttcg ccgacacatc ttccgttggc atcaacagca 660 ctgtgaaggc aaccggtgat atcttaagtc ggcatagata gctctgtcac cgtagaatca 720 gccgatctcg cagcatcttc cgttggcatc aacagcacta cggcgaggac gactggttac 780 ctatccaagt ctcggtcgag aaggatttcc gaatcctcat tggtcgaggt catctcatca 840 gccttctcgg cgaagtgggg tgttaccagg ttactgtatt cggcacattg acagccgaat 900 ttgagatgtg aacttcgcaa attagcagcc ttgtcttcag gctctagaac ccaagaggcc 960 gagaattgtt ccttcctcgg ccgcaatcgc aagacacaga agtcagcagc gcgctcaacg 1020 caacatcatc aaatttactc ctcggccgag ctcggccgac gagttggcac gccccgcaat 1080 caccgaagga cgtagttagc ttagaatata ctcggcctgc gcgccacgta ggctttgtag 1140 tttctagggt caaca 1155 // ID Gypsy-23_VV-I repbase; DNA; EDCOT; 15437 BP. XX AC chr11; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-23_VV_; KW Gypsy-23_VV-LTR; Gypsy-23_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-15437 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr11; Positions 9298761 9314197. XX CC Positions [8518-9054] - Reverse transcriptase CC Positions [10636-10914] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 4951..10914 FT /product="Gypsy-23_VV-I_1p" FT /translation="MDRLEQRMRQMRVSDGDISWDDFDGAPVVSLPTQFRM FT PEIERYTGIGCPKIHLRLYSSVMRAHGLDEAHLIMLFPMSLSGAAQRWFAS FT LDASRRRTWDDLAQEFLRQFAFNTVIDVSRRELEALRQGPDESVTSFISRW FT REKIAQIVDRPSEKDQISMILRSLQPRFARHLMGFPHTDFGSLVQALYGIE FT EGIARGLWPESSPYDSKGKKPLGGQRPGDVSAISSVGSRSPRRYQTFGQTS FT RAYYPQRYAQYRPPRPMIPTYLHQTPEPVFAAQVSERPPTLYPRPRAPQTT FT IPLVQRPTRQFSQLGMPLSRAFQKLMEGGLLTQLAPRPVPQPVPPRFRMDL FT HCSYHQGPGHDTDHCAALRHAIQDLIDQGLVNLGQPSVTTNPLPAHSTHTV FT PPPPGGIHHIDFVEDDSIHMMSWDDGVPEPIVLDDGYEVDTVGSQTFTPFS FT LISDWIPFELTPIAPSAIARQGPPAPFILRLDDDDLEGRDVQIVTRSGRVA FT QPPPLVARPFDGAVSREENRREDDEILRQLQSTQARISIWSLLASSSTHRD FT ALIRALSQIRVETTTTPEGLIHMMTADRATCIVFSDDDLPPEGSDHTHPLY FT IIVGCSGRRVPSVLLDNGSALNVCPLATAIALGYAPSDFGTSTQTVRAYDS FT TKREVMGTLMIELMIGPTTFPILFQVLRIPASFNLLLGRPWIHGAGAIPSS FT LHQKVKFIHDGQVITVHSTRDIFATSEPVLQISHSEDDLLLTGFTFDEIQT FT LEIEDFCRDFVAMSFDQHSSIVVLDMMRGMTFLPGMGLGRRQQGPSEFIAA FT IDHDTTFGLGFIPTEADYRHMARLRKERVRARLSHTPFDYPIRPYRMSLTD FT YFVRGSETRPRLEEIHSVAHTDGETDLQHLFHQLQLSDGGPDTSFPLTITP FT TSPDRASMLSLCFPEEITGDGVIVDPTEVIDGVVPHDEYRDEMDMMTVSQI FT AGIVQLQPVSAFDMFGVSTIEVFEGTQTLPVPELPDDDSSLFEGIVSPVEG FT ASDVVDPPLSFDVLSGFVSRSDDVSVASFMDLSIFEYSPVSCDSISTSAPH FT SPITPIFDIDDEIAHPSSDRDSFDHDSGPIDERVSPAAGDVETVDFGTEDQ FT PRELKIGSPLSTDERDRLIHLLRSYLDVFAWSYEDMPGLDPSIVQHHLPTL FT PHVRPVKQKLRRLHPHWSLQVKEEIQKQLSVGFISVVEYPEWLANVVPVPK FT KDGKVRVCVDFRDLNKASPKDDFPLPHIDLLVDGTAGHSMLSFMDGFSGYN FT QILMAPEDMEKTAFITEWGTYCYRVMPFGLKNAGATYQRAATTLFHDMMHR FT DVEVYVDDMIVKSRGRADHLDALERFFERIRKFRLRLNPKKCTFGVTSGKL FT LGHMVSDRGIEVDPDKIKAILDMPVPRTEKEIRGFLGRLQYISRFIARLTD FT VCEPIFRLLRKNQPTVWNDGCQIAFEKIKEYLLSPPILVPPMPGRPLLLYL FT SVSDMALGCMLAQLDDSGKERAIYYLSKRMLEYEMRYVMIERMCLALVWAT FT RRLRHYMTEYSVCLISRLDPLRYLFDRPALTGRLMRWLVLLTEFDIQYVSQ FT KSIKGSIVADHLASLPISEGRPVDDDFPDEEFIAMTSLSGWRMYFDGAANQ FT SGYGIGVLLVSPQGDHISRSVRLAFSDRHPATNNIVEYEACILGLETALEL FT DIRQMEVFGDSNLVLRQIQGDWKTRDVKLRPYHAYLELLVTRFDDLRYVHL FT PRAQNRFADALATLASSVDIPIDVVIRPLLIELRSAPAYCCLIGETEVQDD FT LPWYHDIYQFLRYGTYPEVATTKDRRALRNLATRFVICGDTLYRRSADDML FT LLCLDRASADRVMREVHTGVCGPHMGGHMLARKIMRTGYFWLTMETDCCQF FT VQKCPECQIHGDLIHAPPSELHALTSPWPFSVWGIDIIGKVSPKSSSGHEF FT ILVAIDYFTKWVEAASYARLTSARVASFIRSHIICRYGVPHELISDRGVHF FT RAEVDTLLQKYAI" XX SQ Sequence 15437 BP; 3836 A; 3081 C; 3367 G; 5153 T; 0 other; gagcgctcta tagagaaagg aaggtggcta gtttttttta ggagagaata agagagagga 60 tgaggaggac ggaaaaggaa gaggggacca ttgagaaaga aagtgatttt ctggaagaaa 120 gtggcagccg cgccgggaaa gggaggaatt ttggcattaa gaaagaagga acaaggggtg 180 ccatctagag gggagagagg tgattcacat ctccatgttt gactgggaaa gagaggtgac 240 gactagagat tatctctggt ctcagccttg agaaagatca gcatcgtgct ttctctcaaa 300 ccaaccagac gtctcaccac gggaacacca gcttcaccac taccagtccg ctcatcttga 360 tgattcgcct atcaccataa cgagaaacac ttgcgatgtc gtattaatca tcatcggacc 420 aatatcttct catctcgccg catgcctttt ccccctcccc tcacgatctg catccgtcat 480 cagtccacgc atcaagcctt catccacacg actgccactt tgagaggaaa gcaatccacg 540 caccaataga gcctccacgg gtggcacttt tgagcaccat ctccatgctg caacctattg 600 ctacctgtcc ctaaacacca cagcaaacca aacgccattc ggattgcttt ggagcaggca 660 tagccaacca gatttgactc atcataccat ccacttacac agctgccact tttgagaaga 720 acagtccacg cacctagccg ttggtaagtt gatttgtttt ctacattggg ttgctttgaa 780 aatatatata tatataaaaa tttggtttca tttcagttta gattattata tcaggttgaa 840 tgctttacag ggtccagtac gttttcattt gaataaataa aaaatgttac ttgtggttta 900 attgtttaag ttattacatt tggtggagct ttgatgtctc gtgatgtacc attttcggat 960 tattatattg ggttgagtgg gttgatttgt ttattagctc cgatacgtgt ttgctttaat 1020 atggcaatac aatctcacat ttgtttattt attttttctt tattcatcac gttaaaggtt 1080 agttttaatg tattatatta aattcataaa atatgatttt agatagcttc atatgaaaaa 1140 taaatatata tactttaatc ttcatttgat atggttttga ttcatttaat tattgattgt 1200 ttatttattt acttgttacc aatttaatgc tttgtaattt atttaattat aaataaaatt 1260 gattctatag gatagagatt tagttttaaa aatcattttt gttagttttt ttaattttac 1320 cttagattta agcactcttg taaaatttta gttcattaaa ataattgatc atatatatat 1380 ttatccaatt ataaattaat taattaatta ttattgattt attattccat cttgaaaatt 1440 atgatctttg tctaatgtgg ttacaattca ttttcttagt ttgacaaatt agtttttttt 1500 tagtattggt ttgggcaatt tttgttaata atggaaaagt taggatttct ttagagttta 1560 gataatttgt gatgatagtt aaaaatttag aattttgatt ggcattattt ttgttctcaa 1620 ttaggaaatt cataatttct ttttagttta gttttaattt atcttttagt ttaaatgtta 1680 ttaaaattca gtttattagt tcaattgctt ccatgtcact cttttcatat ctaaaggttg 1740 ttaaatttaa ttcatgattc atccttttag tttattagtt ttagaattta agttggttaa 1800 tttatttcat tccgcgttga tatattcatg ttttaaaata aaataaaaaa taaataaaat 1860 ataaataaat aaataaatgg ttattttagt tttgattgat cctgttttag ttgatatttt 1920 ttagagtttt aattaatttg gttggtttca tattgtttag tttatgttaa gattttttat 1980 tccatttttc cattaattct atgctttcga attgtaggct attagtttaa tgtattccca 2040 tgttgtcatt ttgtgtttaa aaatagttca ttttagtttt tgactaattt tatttattct 2100 atgtgtttgt tttcttttat tcaattgtta gttagccgat tagatttatg actcaaaatt 2160 gtcaatatta gttaatacgt atcgcttgta ctgttttaaa ggtcacataa tatttagtgc 2220 ttgattaagt ttatcttaag attaaatgtt tttaaagttt cagtgcttat aagatctaag 2280 gttttggttt atcactttgg tcatcctttg tcaaaatcaa tttttagagg ctatcagaaa 2340 atagtgaaga ttggcctcca ttcccaccac ttcaatttta tcggttgtca aaaactctac 2400 tttgtgattt tgttcttttt tttttttttt tttttctttt gcttgatatt ttgattcata 2460 cattttattg ttttcaaatt aactttttta tctttaaaac ataacaatat tctcaaaatc 2520 tcatttcctt aaaaacaaac catttcaaaa attcatttag agttctcaga atcaaaatcc 2580 ccttcccttt aaaaattcat ttcaaggatt cctttaggat tcttaaaatc aaaacctcac 2640 tttcttaaaa taatatgcaa ccattttttt tatcggtttg catctttctc ggtttttaac 2700 gaaaattttg gtttgaaatc agacacgaat caaagcttgt ggtcccacat aaatgggata 2760 attttgagct aaattcgtgt atatcaattg gggaattggt gaaaccccta cataaaaaaa 2820 aatcttttca aaaaattatt tttgttgcca cttttgtcac ttgttgaaat tatgtctatt 2880 ttttcaggaa ttgtatataa gatgagtgtg ataactagtg ttttcatata ctttgataat 2940 ttctgctatg ctaattagat aacgagcatg ctaggattcc tatattttat tatttattat 3000 ctaacccctc atgtcttatg gaagcgcatt gtaagtcatc tatgttatcc aggtacgtat 3060 cacctacttt ctaaattttg taaacaatca tgtcattgtg aaatatgcat atgtttgata 3120 atccttaggt gcttagatgt atgctagatt cactatgatt aaaaacaaat gttgtgtgat 3180 gtatctccaa actaatctct tatgttttat gatagcgctt gggaagccgt ccaggtacgc 3240 atttttaact ctccttaatt gtgattcgat tttgtttgat atgttatgtt tttttttgga 3300 atcacctagc ctacttaggt atccgagatc aaccatttaa ttgccacgct tcccttaact 3360 tagtcagtag agacctcttt agggcttaga ggggtgctac ctcctagagg taccttccca 3420 ataagtaacc tgatccccga accaagactt gggttttcaa agacacgctt ttccaaaaat 3480 tatggagtca tttttttagg gttttatttc ttgttttatt ttcccttcaa aaataaaaat 3540 aaaataagtg gcgactccaa ctttttttta aaattaattt ttcacaataa aaagcgagtc 3600 ttgccgatcg agtggggacg cacgtgtaaa atgcgggtcc acaaattggc gactccactg 3660 gggattttga ggatcaagct tgaacactag ttaaggaaaa tgtggcgttt aattggtcga 3720 ttagagggta cccccttttc ctaggcaagg tgattcgatt tgcttgtttg tttggtttga 3780 tatcttaaca tgtttgattg ccttggatga tcacttgatt gttttgctca cttagcatga 3840 ttcactctca catatgttag ataggacttt gtttgtttga tatttatttg cttcgtatga 3900 ctgtttggat gatcacttga ttgcttgctc acttcagcat gattcacttt cacgtatgct 3960 agataagact ttgattgtat gatacttatt tgcttggtat gactgcttgt tgcatgacaa 4020 ccctttctct tgcatgattg tatgattgct tgtctttgtt cactatctca ctttagatct 4080 taggtttttc ggatgcaccc acattcttca ccgtgcactt tagattatcc ttgagtgttg 4140 agagatggga gagccttcac ccttaagaaa ccccctggga acgcgaggaa gtgcatgtgt 4200 ggaggtgatg accaccttgc atggaagcac cccgtctcct tggaggcgtg cagagggttg 4260 cgtaccgccg gagggtacga tcgcttctgc tagggatcct ttaatccacc catttttttt 4320 tatcttatag aaccaccaca accttatagg ctagcctaga cccaattagg atttcactct 4380 tacacgtgga tgcatttgtg gaccttcaga gctgccttgg ttacaattgg gttcgattac 4440 cctctccata gtcccatttt ggtatgatca gatacgagta tcagtttgag tatacatggg 4500 ctatatgctt gattaccttt tagtcggttt ctatagagtt acccttgtac agcgtctcat 4560 ctagtgtttc cgtgtttata ggagtatttt ttggtgccca gtctggattc gccttcgtgg 4620 actagagtta gaggcagatt gaccagagta tcagatcagc cagaccaggg agtagatcag 4680 agagatatgg actcccaggt agtcacagtt gaccagtttg ctacggccat ggcttcgatt 4740 caggaggcta tagccggcct tggccagagg atagacgggc agcaggcccc accttaggat 4800 ggtgcacagt atgactctac ggcaccacca ccccctccac tcagtcagcc agttccacac 4860 ccgacaccgt atgttttgca tagtcagact gatgctaccc cacttcctgt tgtagcaccc 4920 attcaggcat cagaggatgc acatgctcgt atggatagac tcgagcagag gatgagacag 4980 atgagggttt cggatggaga catcagttgg gatgattttg atggagcacc ggtagtcagt 5040 ttaccgactc agttcaggat gccagagatt gagaggtata cgggcatagg ttgccctaag 5100 attcatttga ggttatacag tagtgtgatg agggcccacg ggttggatga ggcccatttg 5160 attatgcttt ttcccatgtc cttgagtggt gcagcacagc gttggtttgc ttctttagac 5220 gcttcacgcc gtaggacttg ggatgacttg gcccaagagt ttttgagaca gttcgcgttt 5280 aacactgtca ttgatgtctc gaggagagag ttggaggcct tgagacaggg gccagatgag 5340 tcagttactt catttatctc ccgatggagg gagaagatcg cccagattgt tgatcgtcct 5400 tccgagaagg accagattag tatgattttg aggagtttac agcctagatt tgctagacat 5460 ttgatgggat ttcctcatac ggattttgga tccttggtac aggccctgta tggcatagag 5520 gagggcatcg ctagagggtt gtggcccgag tcttctcctt acgattcaaa ggggaagaaa 5580 cccttaggag gacagagacc aggagatgtg agtgctatca gttcagtagg atcgagatct 5640 cccaggcgct atcagacatt cgggcagact tcacgagcct attacccgca gcgttatgct 5700 cagtatagac cacccaggcc catgattcct acatacctac accagacccc agagcctgtt 5760 tttgctgcac aggtctcgga gaggcctcct accttatatc ctcggcctcg agctccacag 5820 actactattc ctcttgtaca gaggccgaca cgacagttct cccagctagg tatgcctttg 5880 agtcgagctt tccaaaagct catggagggt ggtttgttga ctcagttggc acctaggcct 5940 gtaccccagc ctgtgccacc acgcttcagg atggatctac attgttccta ccatcagggc 6000 ccagggcatg acacagatca ttgcgccgcc ttgagacatg ctatacagga cttgatagat 6060 cagggtctgg ttaacttagg gcagccgagt gtaaccacga accctctacc ggctcactct 6120 acacatacag tgccaccacc cccgggtggt atacatcata tagattttgt agaggatgac 6180 agcatacaca tgatgagttg ggatgatgga gtgccagagc cgattgtttt ggatgatggt 6240 tatgaggttg acacagtggg ttctcagact tttactccat tcagtttgat ttcagattgg 6300 ataccatttg agttgactcc tattgcacca tcggccatag cacgtcaggg cccgcccgct 6360 ccatttatcc tacggctaga tgatgatgat ttagagggga gagatgtaca gattgtgacc 6420 cgtagtggga gagtagctca gcccccacct ctagtagcta ggccatttga tggcgcggtt 6480 tctcgtgagg agaataggag agaggatgat gagatattga ggcagttaca gagtacacag 6540 gcacgcatat ctatctggag tttgttagca tcttctagta ctcatagaga tgcattgatt 6600 cgagctttga gccagatccg cgtagagacc accactaccc cggaggggtt gattcacatg 6660 atgacggccg acagggccac atgtattgtg ttttcagatg atgacttacc accagagggt 6720 tcggaccaca cacacccttt atatattata gttggttgtt caggtcgtag agtcccatcc 6780 gtcctattgg acaatggctc agccttgaac gtttgcccat tggctactgc tattgctctt 6840 ggttatgcac cttcagactt cggtacctct acacagacgg tcagagcata tgatagtact 6900 aagagggagg tcatgggtac tctgatgata gagttgatga ttggtccgac tacatttccc 6960 atcctatttc aggttttgag gattcccgca tccttcaacc tgcttctggg ccgaccatgg 7020 attcacgggg ccggggctat tccatcttcc cttcatcaga aggtgaagtt tattcatgat 7080 gggcaggtca tcacagttca ctctaccagg gatatattcg ccacttctga gccagtactt 7140 cagattagtc atagtgagga cgacctactt ctgactgggt ttacttttga tgagatacag 7200 actctcgaga ttgaggattt ttgtagagac tttgtggcta tgtcatttga tcagcacagt 7260 agcatagtgg tccttgatat gatgaggggt atgacctttc tacctggcat ggggttagga 7320 cgacgtcagc agggaccgag cgagttcata gctgccattg accatgatac gacatttgga 7380 cttggattca tccctactga ggccgattac cgtcacatgg cgcggttgcg caaggagagg 7440 gtgagagctc gcttatccca cacaccattt gattatccta ttcgaccata taggatgagt 7500 ttgactgact actttgtcag aggatcagag actcgacctc gtctagagga gattcatagt 7560 gtggctcata cagatggaga gaccgatctt cagcatctat ttcaccagct acagttgagt 7620 gatgggggtc ctgacacttc tttccctttg acgattaccc ccacgtctcc agatcgagct 7680 agcatgttgt ctttatgctt tccagaggag atcactggcg atggggtgat tgttgatcct 7740 actgaggtga ttgatggagt tgttccccat gatgagtacc gtgatgagat ggacatgatg 7800 accgtgagcc agattgccgg cattgttcag cttcagcctg tttcagcatt tgatatgttt 7860 ggggtgtcta ccattgaggt ttttgagggg actcagactc ttcctgttcc agagcttcca 7920 gatgatgata gtagtttgtt tgagggcatt gttagcccag ttgagggagc gtccgacgtt 7980 gtggacccac ctctttcttt tgatgtttta tcgggatttg tctcccgctc tgacgatgtt 8040 tctgttgctt catttatgga tttgagcatt tttgagtatt cgcctgtctc ttgtgatagt 8100 atctctacat ctgcacctca ctcacccatt acaccgatat ttgatataga tgatgagatt 8160 gcacatccca gttcggatag ggactctttt gatcatgact ctggtcccat agatgagaga 8220 gtttcacctg ctgcagggga cgttgagact gttgattttg gcacggagga tcagcctaga 8280 gagctgaaga ttggttcacc cctatctaca gatgagagag atagactcat ccatttactc 8340 aggtcatact tggatgtctt tgcgtggtct tatgaggaca tgccaggtct tgatccctct 8400 atagtccagc accatttacc taccctacca catgttagac cagttaagca gaaactgaga 8460 cggttgcatc cacattggag tctacaggta aaagaggaga ttcagaaaca actcagtgtt 8520 gggttcatat cagtagttga gtatccagag tggttggcta atgtcgtccc tgttcccaaa 8580 aaggatggca aggttagagt ttgtgtcgat ttcagagacc ttaataaagc tagccctaag 8640 gatgattttc ccctcccaca cattgatttg ttggttgatg gcaccgcagg ccattcgatg 8700 ttgtctttca tggatggatt ctccgggtat aatcagattt tgatggctcc agaggatatg 8760 gagaagacgg ccttcattac cgagtggggt acctactgtt acagagttat gccatttggg 8820 ttgaaaaacg caggagccac ttatcagaga gccgctacca ctttgtttca tgacatgatg 8880 catagggatg tcgaggttta cgtggatgat atgattgtga aatcccgagg tagagcagat 8940 cacctagatg ctttagagag attctttgag aggatccgga agtttagatt gaggttgaat 9000 cccaagaagt gcacctttgg agtgacttct gggaaactgt tggggcatat ggtcagtgat 9060 cggggcatag aggtcgaccc agataaaatc aaagccatac ttgacatgcc tgtgccgagg 9120 actgagaaag agatcagggg ttttctaggc aggttacagt atattagtcg tttcatagcc 9180 agattgacag acgtatgtga gcccatcttt cgtcttttga ggaagaatca gccaacggtt 9240 tggaatgacg gctgccagat tgcatttgag aagatcaagg agtatttgct ttctcctcct 9300 attttagtgc ctcctatgcc aggacgtcca cttcttctat atttgtcagt ttcagacatg 9360 gccttgggat gcatgttagc tcagctcgat gactccggga aagagcgagc aatttactat 9420 ttgagtaaga ggatgctgga gtatgagatg agatatgtta tgattgagcg catgtgttta 9480 gcgttagttt gggctaccag gagattgagg cactacatga ctgagtattc ggtgtgcttg 9540 atttctcggt tagatccttt gaggtatctg tttgatagac ctgcattgac tggtagattg 9600 atgagatggc tcgtactcct gacagagttt gatattcagt acgtttctca gaagtctatt 9660 aagggaagta ttgttgccga tcatttggct tcattgccga tatctgaggg tagaccagtt 9720 gatgatgatt ttccagatga ggagttcatt gccatgacta gcttatcagg ttggcgcatg 9780 tacttcgatg gtgcagccaa tcagtcaggg tatgggatag gtgttctatt ggtatcccct 9840 cagggtgatc atatttcgag gtccgttcgt ttggcattct ctgatcgaca tcctgccacg 9900 aataacatag ttgagtatga ggcttgtatc cttggtttag agactgcact ggagcttgac 9960 attagacaga tggaggtatt tggtgactcc aatctagtac tcaggcagat tcagggggat 10020 tggaagacca gggatgtgaa gcttaggcca tatcatgctt atttagagtt gttggttacg 10080 agatttgatg acttgagata tgttcatctg cctagagcgc aaaaccgatt tgctgacgcc 10140 ttagctacct tagcttcctc cgtagacatt ccgattgatg tagtcatacg tccattgctg 10200 attgagttga ggtctgcacc cgcctattgt tgtttgattg gagagacaga ggtacaggat 10260 gacctacctt ggtatcatga catttatcag ttccttagat atggcacata ccctgaggta 10320 gccactacca aggatcggag agcactgagg aatttggcca ctagatttgt gatttgtgga 10380 gataccttat acaggcgatc agctgatgat atgcttctat tatgtttaga tcgagcctct 10440 gcagatcgag tgatgagaga ggttcataca ggagtttgtg gtccgcatat gggaggacac 10500 atgctagccc gtaagatcat gaggacgggc tatttctggt tgactatgga gacagattgt 10560 tgtcagtttg tccagaaatg cccagagtgt cagattcatg gtgatctcat acatgcacca 10620 ccatcagagt tacacgcctt gacttcgcca tggccatttt cagtatgggg tattgatatt 10680 attgggaagg tttcaccaaa atcttccagt ggtcatgagt tcatcctagt tgccatagat 10740 tatttcacca agtgggtgga agccgcatca tatgcgaggt tgacatctgc tagggttgcc 10800 agttttatca gatcacacat catttgccgc tatggggttc ctcatgagtt gatttccgac 10860 agaggggtgc acttccgagc tgaggtagat actttgttgc agaagtatgc tatctgacat 10920 catagatctt cagcatatag gccacagacc aacggggcag tagaggctgc aaacaagaat 10980 attaagagga ttttgaggaa aatggttgag acttctcgag actggtcaga gaagcttccc 11040 tttgcgttgt gggcatatcg tacatctttt cgtacttcta caggagctac gccttactct 11100 ctagtgtatg gtatggaggc tgttttgcca gtcgagacag aaatgggctc attgagagta 11160 gcccttgagc agcagatttc tgagacagag tgggctcagg ctcgatttga tcagcttaac 11220 cttttagatg agaggagatt gagagcggca gatcatgttc aggcctatca gagaaagatg 11280 gctcgtgcct tcaagaaacg ggttaagcct agaccattgc aaaaagggga cttagttttg 11340 aggattctca gaggtttgat tggagaccct agaggaaagt ttagacctaa ttggagtggg 11400 ccttatgtta tccgagagtt gactccagaa ggggctgcat ggttgacaga cttagatgga 11460 aaccaatttt cggagcctac caatgtggat cagctgaaga agtattatgt ttgagaccgt 11520 ggtcgcagga tgggtggcca tcatttcggt tagcctcata ctttatcacc tctatatatt 11580 agaccgttgc tagcccattg agcttcgcgt ggtatgttat agccttattt ctttcttata 11640 gctttgatta ccatttctat acccgggttg gggcctttga tgtatacgca tgctttgcta 11700 ggaaagtctc atgagcttta gacttatagg tcatcttctc attttgttac catcctctta 11760 tcaccctatt tgttctattt ttattatcac cacatattca ttctctttct tgtctctatc 11820 attatttgct ttatctgatc tattctcttc cttgggttga tgattcttca cgtcttagtg 11880 caaagagggc aagttatatc actctattca ttccatcatt tgacattgat tcggagatct 11940 tagtttgaga ggttgtctca agggttgggg ttcatgtatt catcagtggt tagagagagt 12000 ttgttcattc cttatatttt ttccattgga gtttgattta ttgatgatca gagcatgcgc 12060 aaaaaaaaaa aaaaaaaaaa aaaaaaaaag agaaagaaag aaaaaaaaaa aagaaaaaaa 12120 caaaaacaaa aaaaaaaaaa ggaaaagaaa agcgcaatga tatgctcatg tatggtatct 12180 cgttccattg ggtatttatg ccaccttttg aggttcattt attgggtata tttgtcattg 12240 tgggtttttg tgagttttta tgagttttta tgagtttttc agtccttgag ccactcttgt 12300 tatgcatttg gagtgtcgag ggttcatatg agagttctat gagatcctat gctttttgga 12360 tcatgtttga tatatactag gtatgagaga tgagtaatct ttttactaag gtctccggat 12420 cattgcctta cccaccattc catcattggt gatatgactt tcctttattg tactaacatg 12480 ggttgatcat cactcattcc actttctcat tgctttcttt tgtatcccat taccgcattc 12540 cagatctttg ttccaccttt tattcattcc ctacatattg atactcatta ctgatttgat 12600 accttcttca catcattcac atatttcatt gatggtttga ccattcatcc ttcctctcat 12660 ttcgttatcg gcattccctt tggttacttc taagtccatg actcatgaga tttttctatg 12720 cattacatct tgtacacgag ggtacgggtt tgatcattgg gtatttgagc ctagtttccc 12780 ttcatttctt tcaccctatc accttggcct acgttacgtc ccgtgtctta agaccaccct 12840 gaggccacga gatcagacgt tatctttgac agtcttcact tggacaggtt tttggtagat 12900 tggttgaagt atggtcgtta ctatgttatc ttttatggaa gatacttttg gaagcatttg 12960 gtctctctct tgcttgacat attgattttg atggattttt gggtttggag acagttcatt 13020 gaggatatcg gattcatcat tttctcgtgc accagacatc cacactgggg catatttccc 13080 catctcgaga ttgtcacatc cctcatcatt ttggctattc atttgaggtt ggatttagag 13140 tgtctccctt gagacattgg tcgatacttt attctgactt cttagcagat tattgttgag 13200 ctgaggatag ttgattgatg atattggatt catcctttgg ttgtgcatta tatattcaca 13260 ctggggcata ttcccccttc ctctgagatt cttatctgtt attgtatacg gttcgaggat 13320 ggatgatcat tgttaggttg tttacctgac gacttcgaca ttaggttatc cacactgggg 13380 catattcccc tctccttgac gagatttctt tgggcagtga tatgaggatg gatgattggt 13440 gtcggttgtt tagcttatga ctttgacatc aggtctcata ctggggcata tttccccatt 13500 ttctttgagt atccttaagt ttgggacagt agccagtttg gtttcagatt gagtactagc 13560 cctgagcgtt cgatgattga ctgtatcagg acccccctat atggatttgt tgagatagag 13620 atggatcaca tcaggtttca cccgaggagc atggatggat cctttagcta gatgctcatg 13680 agatagatta ttttcttcat tgattatctt gtggatcggg ttatctagct tgtgagacat 13740 agagggctct tttagttcag aattttcaga ggtttgtcac gatgcatcgg ttacagaaac 13800 cttgatttta gcgaatgatt gatttattgg ttgtttcagc actgcgagca ccttggatac 13860 cggggcatat tttctttcct aagcttacaa gtctaaccct ttagcatttc gatcacacga 13920 ctttgatcca tttggttcct accccctttt gagttagtct ccatttcttt tccatttaga 13980 gcccagagct ctcgacctag agtcattttc ttcgtttatg acccagagtc atttcttttc 14040 catttagagc ccagagctct caacctaaag tcgattttcc atttagagcc cagagctctc 14100 gacccagagt cgtttttttc gtttatgacc tagagtcatt tcttttccat ttagagccca 14160 gagctctcga cccaaagtcg tttttttttt tttttttttt tttttttttt ttttttttca 14220 tttatgaccc agagtcattt attttccatt tagagcccag agctctcgac ccagagtcga 14280 ttttccattt agagcctaga gctctcggcc cagagttgat tttccattta gagcccagag 14340 ctctcgaccc agagtcgatt tcccagttag agcctagagc gctcgaccca gagtcgattt 14400 tccatttaga gcccagagct ctcgacccag agtcgatttc ccatttagag cccagagctc 14460 tcgacccaga gtcgtttttc atttatgacc cagagtcatt tcttttccat ttagagccca 14520 gagctctcga cccggagtcg atttcccatt tagagcccag agctctcgac ctagagtcga 14580 attttccatt tagagcctag agctctcgac ctagagtcga ttttccattt agagcccaga 14640 gctctcgacc cagagtcgat ttcccattta gagcccagag ctctcgaccc agagtcgatt 14700 ttccatttag agcccagagc tctcgaccca gagtcgattt tccatttaga gcctagagct 14760 ctcgacccag agtcgttttt catttatgac ccagagtcat ttcttttcca tttagagccc 14820 agagctctcg acccagagtc gattttccat ttagagccca gagctctcga cccagagtcg 14880 tttttcattt atgacctaga gtcatttctt ttccatttag agcccagagc tctcgaccca 14940 gagtcgattt tccatttaga gcccagagct ctcgacccag agtcgatttt ccatttagag 15000 cccagagctc tcgacccaga gtcatttctt ttccatttag agcccagagc tctcgaccca 15060 gagtcgattt tccatttaga gcccagagct ctcgacccag agtcgatctt tcatttatga 15120 cccagagtca tttctgttcc atttagagcc tagagctctt gacccagagt cgatttttca 15180 cttatgaccc agagtcattt ctttcactta tgacccagag tcattctttc tgtgtaaagc 15240 tttgagctca cgacctgaag ttattccttt tttgtgattg cgtccccgtg tttagagctt 15300 attctcgtca tgtgctagga caaaatctca ggtccttttc ttttagttct tcggtatagt 15360 tcacttcgtt ccgctcatta ttcgtacttt tactcacatt ccctacactc gtgatctcta 15420 ccaaagaggg gcatatt 15437 // ID COP3_LTR_MT repbase; DNA; EDCOT; 153 BP. XX AC AC159872; XX DT 14-DEC-2006 (Rel. 11.12, Created) DT 14-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE The long terminal repeat region of LTR retroposon, COP3_MT, from DE Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR; retroposon; Interspersed; repeat; COP3_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-153 RA Shankar R. and Jurka J.; RT "COP3_MT: LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 608-608 (2006). XX DR EMBL/GenBank/DDBJ; AC159872; Positions 23321 23473. XX SQ Sequence 153 BP; 56 A; 21 C; 24 G; 52 T; 0 other; tgtaaatagc aataagtagc atatcaatca gtagtatgat actgagttaa ttagtttcgg 60 ttaccaccat aattatggct aagtcaacta ttgtaattgg tgtatataac cacaatcctg 120 ttaatgaaat aaggaagcaa ttatattctt tca 153 // ID HAT-8B_Mad repbase; DNA; EDCOT; 3449 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-8_Mad; HAT-8B_Mad. XX NM HAT-8B_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3449 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1621-1621 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >88% identical to consensus. Incomplete 5' terminus. XX FH Key Location/Qualifiers FT CDS join(101..451,417..1997,2057..2497) FT /product="HAT-8B_Mad_1p" FT /note="transposase." FT /translation="MLNCGCDILMCIVILFVRMDGSSSQSSTPMVSVLGKR FT KQTQPSGTLQLGTPSPQDYLHNDYYEDCWDDDPDMEEDIALEQIEEEGEEE FT EGEEEEGEEEEEXVEVVRQWEGASSEKGQDNGRVPPRKKGNRRKGPSPAWN FT DAKRVTITDNNGEKSFMAECKHCKLLVPAHPRTHGTTGILKHLRKCPGSSL FT FENADPNQPTLTQARMGGPVVAHTFNQKRLDXRCVRWIIIAEMPFRAVDQE FT DFRDFIRDLNPKYKLPNRHKVAAAVLELYFEEKXKIKSVIEGLRVSITTDT FT WTSIQXINYMVVTAHFLDTNWALHKRILNFVQVTSHKGDDIGRCLEVCLND FT WGIDKVFSITVDNASANDTAIAYMKRRLKSNGTLLLDGAHLHMRCACHILN FT LIVKDGMTELSREIXAIRNCVKFIHSSPARLESFREYCVLLRFDRMSSIPF FT DVVTRWNATYEMLNSAFKFKEVFSKMAXECDXFIAYFKEEVSKEVDGVTTK FT AKRVGPPEVDDWERSVSFAHFLKKFYDATLTLSATLTPTSHLILGTVIALQ FT VEIEEXIXNASNATLQSVATSMKLKFDKYWGDIEKVNPILFVAQALDPRYK FT FEMLEASLEELGYGCDEIXEXKARVKGXVTELYNAYKEGXVLSSSSMIVGG FT VMXDIDVAXRMAKKIQRKRAAAQQNEIANEVDMYFNDPHQSLTYEGFNLLD FT WWKGNCGXYPTLSKVAKDVXALPSSTVASENAFSLGGRVVDPFRASLTPKT FT VEALVCTSDWLRGNEFCFYKEPTLDEFYFYEELERLEKSK" XX SQ Sequence 3449 BP; 965 A; 596 C; 874 G; 976 T; 38 other; ctctttaatt ttctctgtta attntatgtt ctgttcgntt tatgctattt gaattgctga 60 tttttgacat attttattta ttgattggaa tattggatat atgctgaact gtggttgtga 120 tatattaatg tgcattgtta ttttatttgt taggatggac gggtctagta gccaatctag 180 tacacctatg gtctcggtat taggaaaacg aaaacaaacc caacctagtg gtacccttca 240 actaggcact ccctcacctc aagattattt gcataatgat tattatgaag attgttggga 300 tgatgatccg gatatggagg aggatattgc gttagaacaa atagaagaag agggagagga 360 agaagaaggt gaggaggaag agggggaaga ggaagaagag gnagtagaag tagtgagaca 420 atgggagggt gcctcctcgg aaaaagggca ataggagaaa gggtccaagt ccggcgtgga 480 atgatgctaa gagggtaacg atcaccgata ataatgggga gaaatcgttc atggccgaat 540 gcaagcattg caaactccta gtaccggcgc accctagaac tcatgggacg acgggaattc 600 ttaagcattt gaggaaatgc ccgggttcta gtctcttcga gaatgcggat ccgaaccaac 660 cnacgttgac acaagcgagg atgggaggtc cggttgtcgc tcacactttc aatcaaaaaa 720 gacttgatan gagatgtgtg aggtggatta taatagcgga gatgcctttt agggcggttg 780 atcaagagga ctttcgagat tttattcgtg acttgaatcc aaagtacaaa cttcctaata 840 ggcataaggt ggcggcggcg gttttggagt tgtattttga agagaaggna aaaataaaaa 900 gtgtgattga gggnttgaga gtgagtatca caaccgatac ttggacctcg atccaaanga 960 taaactacat ggtcgtgacg gcncattttt tggacactaa ttgggcgttg cataagagga 1020 tcctaaactt tgtccaagtt acttctcaca agggtgatga tattggaagg tgtctagagg 1080 tttgcttgaa tgattggggc atagacaagg tgtttagcat taccgttgac aatgctagtg 1140 caaatgacac cgctattgca tacatgaaga gaagactcaa gtcaaatggt actcttttac 1200 ttgacggggc tcacttgcac atgaggtgcg cttgtcacat cctcaatttg atagttaagg 1260 atggaatgac ggagcttagt cgtgagattg angccataag gaattgtgtg aagtttatac 1320 actcatcccc ggcgaggttg gagtctttta gggaatattg cgtcttgttg agatttgata 1380 ggatgtcgag tatccctttt gatgttgtca caaggtggaa tgccacctat gaaatgctca 1440 atagtgcttt caagtttaag gaagtgttct ctaagatggc gtntgagtgc gacnctttca 1500 tcgcttactt taaagaggag gtctcgaaag aggttgatgg ggtgacaaca aaggccaagc 1560 gggtgggtcc tccggaggtg gatgattggg agaggtcggt gagttttgct cactttctta 1620 aaaagtttta tgatgccacc ttgacactna gtgcaaccct tactccaacg tcacacttaa 1680 tacttggcac ggtgattgcc ttgcaagtgg agatagaaga anagatttna aacgcctcta 1740 atgccacttt gcaaagtgtg gctacctcaa tgaagctcaa gtttgacaag tattggggtg 1800 acattgaaaa ggtnaaccct attctctttg tagcccaagc actcgacccg aggtacaagt 1860 ttgaaatgtt ggaggcaagt ctagaagagc tcggctatgg atgtgacgaa atangggagg 1920 ngaaggcaag ggttaaaggn nacgtgaccg agttgtataa tgcgtataag gagggagngg 1980 tccttagtag tagtagttag tagtactagt agtagtgcta cctcaaatgt ggagcaaaga 2040 ccaagtgttg tgctagatga ttgtgggggg tgtgatggna gatattgatg ttgctncaag 2100 gatggcaaag aagatccaac gaaagagagc ggcggcncaa caaaacgaga tagccaatga 2160 agtggatatg tacttcaatg atccacacca aagcctaaca tatgagggtt tcaatctttt 2220 ggattggtgg aaaggaaatt gtggnanata tccaactctt agtaaggttg ctaaggacgt 2280 nttngccctt cctagtagca ccgttgctag tgagaatgcc tttagtcttg gtgggagagt 2340 tgtngatcct tttagagctt ccttaacacc taaaacggtt gaggctttgg tgtgtactag 2400 tgattggctt agggggaatg aattttgttt ctacaaggag cctacacttg acgaattcta 2460 tttctacgag gagcttgaac gcttggaaaa aagtaagtaa acaatttaat ttcctctttt 2520 attttcttag tatttattat ctattagact ataattcaat ntaaatgatt tgtggtttat 2580 cgttttaggc ncggctaatt tgggaggtga ggagaataca acacaagaaa atgaaatgcc 2640 acctccacct cctcgaccac ctcaagttca agttcaacaa cgtcaaaatc gatcactacc 2700 tccacgacca cccatttcaa gggcatcacc aacgaagaag ggctcaacca tcaacaaggg 2760 gaaggggtcc accacaagca ccaacaagaa gggggcaacc acaagcgtca acaaggtcaa 2820 ggggccgaag gggccgaaga ggccaacaat cttcataaac tttaagcttt gcttttttgc 2880 ttttggtttg taacttaatt tatttcgaaa ctttggcttg taactaattt ttttgctttt 2940 gggtttgtta ctttatttat tttaaaacct tggcttgtaa ctaatttttt tgcttttgga 3000 tttgttactt aatttatttt tgttgcatgc atgtgtagta gaaattgaat gggctgatgc 3060 tattgtgcac agatttgcat tgcctgaatt gatttgtgcg cagattgggc agtctgcgct 3120 atgcgcattg ggctgtattc agttgcagca gtgcaaaatt gntttttgct aatcaggttg 3180 gctatacggg cttntttaaa tgacgacant tgggcatatt gttaaaaggc tacaatttta 3240 ggccaagccc aanatttttg tccaaaggcc caaaagccca aaaccatttc gggantcccg 3300 atttgtcccg aaatcccgaa accatttcgg gatcccgaat cgggatcccg aanctgtttc 3360 gggatcgata aatcccggtc ccgaaangtt tcggtttggg aatcgggata ggggtttcgg 3420 ttcgggatcc cgtacccgaa ccaccccta 3449 // ID Ogre-PT1_I repbase; DNA; EDCOT; 13364 BP. XX AC AC149300; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 16-APR-2007 (Rel. 12.03, Last updated, Version 3) XX DE LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-PT1; Ogre-PT1_I; internal portion. XX NM Ogre-PT1_I. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-13364 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC149300; Positions 17121 3758. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). CC Additional annotations:.6203..6440: putative intron. CC Note: ORF2+3 (gag-pol) is disrupted by two mutations generating CC stop codons at 7596..7598 and 8922..8924. XX FH Key Location/Qualifiers FT CDS 574..2550 FT /product="Ogre-PT1_ORF1" FT /translation="MAVNREVTTVEYGLESESLHMTEGDCPRLDDSGIPLL FT KDVRCVINDAIRLLPLTKYLADETEFTKIYGRILHLLNVPVLPLAIKALIH FT FWDPDYRCFTFRDVDMVPTLEEYGVLTEFPEDIHKVYFHQRIEDTIEELAK FT LLGIQQMSLYREKSDSGGLRWKRLEELLITKKSNPCAKLEVYRILALGIFG FT LILCPSTAGIISVEAANLFVEYEKTKINPSAAILAETFLSLNHCKKSGKGF FT MRCCVPLLFIWMVSHIESETPIFRNFWWFDQRPLELFVSNEWNFFSEDDWR FT VKLQGIPRSNFNWRAPWMRNVTYLMGCGKKPWVPLIGVTGYISYAPALVAR FT QFGGIQSIPRTVDLAQFIGVYKGATMEMLESIRQDWKSLVLVKKETGLRNP FT TVSEKYPEWRNGGVSYMAEVSESVGIRRKRVNCEEELRKQVKSLQAELKAK FT EEQRVSLERQLAKEKGVRKIAEEERDSVGQDLIKAKADLETQKIINQDMTY FT YMAKAKHWEELAIKTQAILKMRRADIVKFKDQLGKAEALTKIQEERKTELN FT SHKAEAEALRSKLDKEKLKTVQLIGNQKMLKQHNQTLDDANNFLSRNNLIH FT TERIRELQDQIDRAAAEAHLLRVEARQVGGDIMKYRRSTDNTDLFLKAIAT FT RGSVFSPVID" FT CDS join(2843..6202,6441..9584) FT /product="Ogre-PT1_ORF2+3" FT /translation="NIGPQPKRIHNTRSRKKMENEERNQLEIQHQRELESL FT KEDVARLTSLLEQALRPRAGEGTSSQQTFTPQPPPPFIPPSEPQHAAHFVP FT TQSAHPMRVPHSVLIEEEPQRNKIIEENGHEKLAALEERMKAIEGNSLYDP FT VKAVEMCLVPNVVIPRKFRVPEFVKYTGTQCPITHLKAYCNKMAEVVYDEK FT LLIHFFQDSLSDAALAWYMRLDNTKIKGWKDLVKAFIRQYKFNMDIAPDRS FT SLQAMEKGNKESVREYAQRWRESAAQVNPPLSEREMTGLFSNTFKAPYFEY FT LVGSAAQNFSDLVVIAERIEQAVRTGRIVDPTEKRGFIGKRKETEVHNVER FT ESRGKNTYQDIYSFKSITPTPSISNIKFSSPTNTQNNPISNQTNNAYRPRR FT NFPIDQVQLPPLPMSLTEMHQRLLGIGQVAPVPLEPLQPPFPFWYKPDQKC FT EYHAGAVGHHIDGCVAFKRKILQLIKAGWISFDESPNVNSNPLPNHASGGG FT GVNSLEIGRGSTTTLRVTMDRLYGMLRQTDYLKTPVKIQAVRSANEYCKYH FT QQLGHDIDSCEEFHLEVENIMTLGMLRLMKLKEDELVGTMTGCNQKVEVCR FT YIPTEKGPPRMILAKPMNTVSGSYNAQPYNYGYSFHSTNPAPVFHAEIGGL FT TRSGRCFTPEELENHRKAKGKDMVELTKTDEVNKPVSDEEANEFLKLMKHS FT EYSVVDQLKKTPARISLLSLMLSSELHRNALQKVLNEAYVPQDITQDSIEH FT LVGRIQATNYLYFTDDELDHEGTGHNKPLHITVKCKDCVIAKVLIDNGSAL FT NVLPRHVLDKMPVDASHMKPSTMTARAYDGSPRPIIGSIDVELIIGPQPFQ FT VTLQVMDIHPSYSILLGRPWIHAARAVASSLHQRVKFIINGNLVTVRAEET FT LSMIKNVSIPYIETEESKDGNLHAFEVVNAEWVPENTVRRKPEISEAAKMA FT AKYFLKHELPFQYDHTTGMPERVNVIKMKCADQRFGLGFKPGKADFKRAAE FT IRRKKRIARIERREPDEDRIEIPPIHVTFPRSAYVIKTEDYEGGLRKEFNS FT VTINYLEKVGEQDLKEEDSTHEQLPQLTIGVLEDGSSEFVRKLAEGEDLAN FT WEIHEVPIVFKKKSESGSSYTSQTHCTVDNWLNFDETIIAMDEEEFGEEDI FT HEFTRLGEQSDRTWKPAKEELELIDMGTEHNKRELKIGKLISAGVRSELVA FT LLREYVDVFAWSYADMPGLDTDIVVHKLPLIEGCKPIKQKLRRTRPDILIK FT VKEEITKQWDAGFLEVVDYSQWVSNIVVVPKKDNKIRVCVDFRDLNRASPK FT DNFPLPHIDVLVDNAAKSSTYSFMDGFSGYNQIKMAEQDKKKTTFVTPWGT FT YCYRVMPFGLKNAGATYQRAMVTLFHDMMHKEIEVYVDDMIAKSKDEGNHI FT PALKKLFERLRKYQLKLNPAKCTFGVKSGKLLGFVVSNNGIEVDPDKVKAI FT QAMSAPKTEKEVRSFLGRLNYIARFISQLTVTCEPIFRLL*KKNPGVWDED FT CQEAFDKIKQYLQKPPLLVPPVPRKPLILYLTVTESAMGYVLGQHDESGRK FT EQAIYYLSKKFTECESRYSMIEKLCCGLVWSAKRLRQYMLYYTTWLISKID FT PLKYIFEKPYMSNRLARWQVLLAEYDIIYKTRKSVKGSAIADHLADNAVED FT YEPLNFDFPDEDVLVIESDWWTMYFDGAVNVSGNGAGAVIISPEGKQYPIS FT IKLQFSCTNNTAEYEACIHGLEAALELKIRKLGVYGDSMLIICQTKGEWQT FT KDEKLKPYQEYLSKLAENFKEIEFNHLGRDKNQFADALATLASMATIDCGI FT RVHPIGIDIRSSPTHCCLVEEEVDGSPWYTDIKRFIQYREYPSEVSKTDKK FT TLRRMVMEYFIDGEILYKRSFDGTLLRCLDRSEANKALCEVHEGICTTHAN FT GHMMARQIQRAGYFWLTMEKDCI*FVRKCHKCQVYSDKINAPPVPLFNMVS FT PWPFAMWGIDVIGPINPKASNGHRFILVAIDYFTKWVEACSYAHVTQKVVK FT RFIERDLICRYGLPERIVTDNAKNFNGKMIVELCTKWKIKHSNSSPYRPKM FT NGAVEAANKNIKKIVQKMVVTYKDWQEWLPYALHAYRTAIRTSTGATPYSL FT VYGMEAVMPLEVEIPSLRVLMESELEEAKWAEKGQIRYDQ" XX SQ Sequence 13364 BP; 4459 A; 2376 C; 2821 G; 3708 T; 0 other; gaatggcgac tccactgggg acctaagact aagctttgtc tttatttgtt aaaattgcta 60 caaatgcttg ttgtgttgtt tggttttttt ttttattatt attattttat tattttattt 120 tatttattgt tacagcttta gcatccatat ttattcatgt catcatacat atatcggata 180 tggatttatg ccttcacaca ccacgcattt cataataaat atctgctata tcgactttat 240 gttaagtggg agagtagcgg taccccaatg gctttagcct gggtaagact cgtgaaacca 300 tccaactttc gcttgattgt ttactcgata gtggttggta tgcctaaact gatatcattc 360 agggcctcta tcttcacgct acttgtaagc ctcacatcaa cctttcgagg aagatcactg 420 agcatgcgag agacctttca aagactagtt agcaacctac cctgagcatt taatgactag 480 aacttaccct ttaggttgtt ccctatgtaa gtttcactaa ggcaagctta acatatatca 540 ttttcattac aggattattt tttgggtgac ataatggcag ttaatcgaga agtcaccact 600 gttgagtatg ggcttgaatc tgaatcattg catatgactg agggagactg ccctagactg 660 gatgacagtg ggataccgct gctaaaagat gtgagatgtg taataaatga tgccattcgt 720 ttgcttccac tcaccaaata cttggctgat gagacagaat ttactaagat atatgggaga 780 attttgcatc ttctaaatgt tccagtactg ccattagcca taaaagccct gattcatttc 840 tgggatccgg attatcgatg ttttacattt agggatgtcg atatggttcc tacccttgaa 900 gaatacggtg ttttgacaga atttcctgag gatatacata aggtgtactt tcatcaaagg 960 attgaggata ctatagagga gcttgctaag ctattgggaa tccagcaaat gagcttatat 1020 agagagaaaa gtgattctgg gggtttgaga tggaaacgac tagaggagtt gttgattact 1080 aaaaagtcta atccatgtgc taaattagag gtatacagaa tattggcttt gggaatattt 1140 gggttgattt tgtgtccttc aactgctgga attatcagtg tagaggcggc caatttgttt 1200 gttgagtatg agaagaccaa aattaatcct tctgctgcga tcttggctga aacttttttg 1260 tccctcaatc attgcaaaaa gtccgggaaa ggttttatga gatgttgtgt tccattattg 1320 ttcatttgga tggtaagtca catagaatcc gagacaccaa tattccggaa tttttggtgg 1380 tttgatcaaa ggccactcga gttatttgta tcaaatgaat ggaatttttt ttctgaagat 1440 gactggaggg taaaactaca aggaattcca cgaagcaatt ttaattggag agctccttgg 1500 atgagaaatg taacgtattt aatgggttgt gggaagaagc cttgggtacc tttgattgga 1560 gtgactggat atattagcta tgcgcctgct ttagttgcaa gacagtttgg gggcatacaa 1620 agcatcccaa gaacggttga tttagctcaa tttattggag tatacaaagg agctaccatg 1680 gagatgttgg agagcattag gcaggattgg aaatctttgg tactggtgaa aaaggagacc 1740 ggattaagga atcctacagt tagtgaaaag tatcccgaat ggcgtaatgg aggagtctct 1800 tatatggcag aagtttctga atctgtgggc attcgaagga aaagagtaaa ctgtgaagaa 1860 gaattaagaa aacaagtaaa atcgttacaa gctgagctta aagcaaagga agaacagaga 1920 gtgtctttag agcggcagct agccaaagaa aagggtgtaa ggaaaatagc tgaagaagaa 1980 agggactctg tgggtcaaga cttgataaag gcaaaggctg acttggaaac acaaaaaata 2040 attaatcagg acatgacgta ttatatggca aaagctaagc attgggaaga gttagctatc 2100 aagacacaag ctatattgaa aatgcgtcgg gcggacattg ttaagtttaa agaccaattg 2160 ggaaaagctg aggctttaac taaaattcag gaagagcgaa aaacagagtt gaacagtcat 2220 aaggctgaag cagaagcatt gagatctaag ctggacaaag aaaaattaaa gaccgtacaa 2280 cttataggaa accaaaaaat gttaaagcaa cataatcaaa cattggatga tgccaataac 2340 tttttgtcta gaaacaactt gattcatact gagaggataa gggaactaca agatcagatt 2400 gatcgagcag ctgcagaagc ccatttatta cgagtggaag ctcgtcaagt gggaggagat 2460 ataatgaaat atcgaagaag tacggataat accgatcttt ttttaaaagc aatagctact 2520 agaggcagtg ttttttctcc tgtaatagat tagattaatt tttcattgta agcttctgaa 2580 tgagtaataa aagggtttga gacccacatt tttcaatgca aaaatatatg tatatgacgg 2640 aaagcccaaa tgtcaaaaag ctaagcagat ctcttctcgg catcacaaca atgatatcaa 2700 gttcaagctc aacccacata tctaaagaat gacggccata tgtcaccaac aaagagcaaa 2760 tctatatcca atatgttgca ttcacattca tgcatctcat acatttgctt atagattgtc 2820 atattctgca tataacaggt gaaatatagg tccccaaccg aaacgtatcc ataacactcg 2880 ttcacggaag aaaatggaaa atgaagagag aaatcagtta gaaattcaac accaaagaga 2940 gttggaaagc ctgaaagagg atgtagcaag gcttaccagc ctgcttgaac aggctttgag 3000 gcctagagct ggagaaggga catcttctca acaaacattt acacctcagc ctccgcctcc 3060 atttattccg ccatctgaac ctcagcatgc tgctcatttc gtacctactc aatcagcaca 3120 tccaatgagg gtcccccatt ctgtgttgat agaggaagaa cctcaaagga acaagataat 3180 agaggaaaat ggtcatgaaa aactagctgc tttagaagaa agaatgaagg caatagaagg 3240 gaatagtttg tatgatccgg tgaaggccgt tgaaatgtgt ctagtgccta acgtggttat 3300 tcccagaaaa ttcagagttc cagaatttgt taaatatact ggaactcaat gcccaatcac 3360 ccatcttaaa gcatattgta ataagatggc tgaagtagtc tatgatgaga agttattgat 3420 ccattttttt caagacagtt taagtgatgc ggctcttgct tggtatatgc gtttggataa 3480 taccaagatt aaaggatgga aggatttggt taaagctttt attagacagt ataagttcaa 3540 catggatatt gccccagata gatcaagtct gcaagccatg gaaaaaggca ataaggagtc 3600 tgtaagagaa tatgcacaaa ggtggcgcga atcagccgcg caagtaaatc ctccattgtc 3660 ggaaagggag atgactggtt tattttccaa cactttcaaa gccccgtact ttgaatactt 3720 ggtaggtagt gctgcacaaa atttctctga tttggttgtc atagctgaaa ggatcgaaca 3780 agctgttcgg acgggtagga tcgtggatcc tactgaaaaa agaggtttta ttggaaaaag 3840 gaaagaaacg gaagttcaca atgttgaaag ggaaagtaga gggaagaaca cttaccaaga 3900 catttacagc ttcaaaagta ttacacctac cccctctata tccaatataa aattctcttc 3960 acctacaaac acccaaaata acccgataag caaccaaacc aataatgcct accgcccaag 4020 aagaaatttt ccaatagatc aagtgcaact tccaccatta cccatgtctc ttactgaaat 4080 gcaccaaaga ttgcttggta ttggccaggt agcacctgtt cccttagaac ctttacaacc 4140 accatttcct ttttggtata aacccgatca aaaatgtgaa taccatgctg gtgctgttgg 4200 tcatcatatt gatggatgtg tcgcattcaa aagaaaaatc cttcagctca tcaaagctgg 4260 gtggatttct tttgatgaat ctccaaatgt gaattctaac cctctaccaa atcatgcttc 4320 tggaggtggg ggagttaata gcttggagat aggaagggga agtacaacaa ctttaagggt 4380 gactatggat agattgtatg ggatgttgag gcaaacagat tatctaaaga caccagtcaa 4440 aatacaagct gtaaggagtg cgaatgaata ttgtaaatat catcagcagc ttgggcatga 4500 tattgactcg tgcgaggagt ttcatttgga ggtagaaaat ataatgacgt tgggaatgtt 4560 aagattgatg aaactcaaag aagatgagtt agtaggaaca atgactggtt gtaaccagaa 4620 agtggaagtt tgtagatata taccaaccga aaagggtcca ccaagaatga tcctagccaa 4680 gcctatgaat actgttagcg gaagctataa tgcccaaccc tataattatg gttattcctt 4740 tcacagcaca aatcctgccc ctgttttcca tgctgaaata ggaggactca ctcggagtgg 4800 gagatgtttt actcctgaag agttggaaaa ccatagaaaa gccaaaggaa aggatatggt 4860 ggaattgaca aagacagatg aggttaacaa gccagtaagt gatgaagagg ctaatgaatt 4920 cctgaaattg atgaagcata gcgaatatag tgtggttgat cagctaaaga aaacacccgc 4980 taggatttct ttgttgtcat taatgttgag ttcagaattg cataggaacg cacttcagaa 5040 ggttcttaat gaagcatatg ttcctcagga tatcacacaa gactccatag aacatttggt 5100 gggtaggata caagccacca attacctcta ttttaccgat gatgagctgg atcatgaagg 5160 gaccggtcat aataaaccat tgcatatcac ggtaaaatgc aaggattgtg tgattgctaa 5220 ggtgcttata gataatggtt ctgctctcaa tgtattgccg agacatgtac ttgataaaat 5280 gccagttgat gcctctcaca tgaagccaag taccatgact gctagggcat atgatgggtc 5340 acctagacca atcattggga gtattgatgt tgaactaatc attggcccac aaccattcca 5400 agtcacatta caagtaatgg acattcatcc atcatatagc attttactgg ggagaccttg 5460 gatccatgca gcccgagctg tcgcatcttc tttacatcaa cgggtcaagt ttatcatcaa 5520 tgggaatttg gtgactgtga gagctgagga aactttgtca atgataaaaa atgtgtcgat 5580 cccttacata gaaactgaag aaagtaagga tggaaatctg catgcattcg aagttgtaaa 5640 tgctgaatgg gtaccagaaa atacggtacg aagaaagcca gaaatttccg aagcagcaaa 5700 aatggctgct aaatacttct taaagcatga actgccattt caatatgacc acactaccgg 5760 aatgcctgag agggttaatg tgataaaaat gaagtgtgcg gatcaaaggt ttggcttagg 5820 gtttaagcct gggaaagcag atttcaaaag agcagctgaa attagaagaa aaaaaagaat 5880 agcccggatt gaaaggagag aaccagatga agatcgaata gagatcccac caatccatgt 5940 aacatttcca agatccgcat atgtgataaa aactgaggat tatgaggggg gactaagaaa 6000 agaattcaat agtgttacta ttaattatct tgaaaaagtt ggtgaacaag atttaaagga 6060 agaggatagt actcatgaac aattgcccca gctgactatt ggcgttttgg aagatggctc 6120 atcagaattc gtgagaaaac tggctgaggg agaagattta gcaaattggg aaattcatga 6180 agtcccaatt gttttcaaaa agtaatgttt gtttgcttgt tcgttgtttt cattatttgt 6240 attgtttgaa taattgtgcc ttgccaaatc atcatgcttc aagagattgg caataaggtt 6300 ttgtggttga gcccttctat cctttaaatt tcaatgagat catgcaaatt ttctttcaat 6360 cgtgtttttc tttttctctg ttcatttatt tactttccca taaccataca ctcacaatcg 6420 aaacactttc cgctttcagg aaatctgaaa gcggatcgtc gtatacctca caaactcatt 6480 gcactgtgga taattggctt aactttgatg aaactataat tgccatggat gaagaagagt 6540 ttggggagga agatatccat gagttcacaa ggttagggga acaatctgat cgcacatgga 6600 agcctgcaaa agaagaacta gaactgatag atatgggcac cgaacataat aaaagagagt 6660 tgaaaatagg gaagctaatc tctgctggcg taagaagtga attggtcgct cttttacgag 6720 aatatgttga tgtgtttgcc tggtcatacg ctgatatgcc tggtctggat actgatattg 6780 tggtacataa actacctttg atagaaggat gtaagccgat taagcaaaag ttgaggagga 6840 caaggccaga tatactaatc aaagtgaagg aggagataac aaaacagtgg gatgctggat 6900 tcttggaagt agttgattat tctcaatggg tgtccaatat tgtagtagta cccaagaaag 6960 acaacaaaat cagggtatgt gtggattttc gagatttgaa tagggcaagc ccgaaggata 7020 attttccttt accccacata gatgtactgg tggataatgc tgctaagagt tctacttact 7080 cttttatgga tggtttctct gggtataatc agattaaaat ggccgagcaa gacaagaaga 7140 aaacaacatt tgttaccccg tggggaacgt attgctatag agttatgcca ttcggactca 7200 aaaatgctgg agcaacttat caaagagcaa tggtgacact atttcatgat atgatgcata 7260 aagaaattga agtctatgtg gatgatatga tcgctaagtc taaagatgag ggaaaccata 7320 tcccagctct aaagaaatta tttgaaaggc tgagaaaata tcaattaaag ttgaaccctg 7380 caaaatgcac atttggagtg aagtctggga agttattggg attcgtggta agcaataatg 7440 gtatagaggt agaccctgat aaagtgaagg ccatacaagc tatgtcagct cctaagactg 7500 agaaagaagt tcgaagcttt ttggggcgtt taaattacat tgctcgattt atttcacaac 7560 ttacagtcac ttgtgaacca atctttcgat tactttgaaa gaaaaaccct ggagtatggg 7620 atgaagactg tcaagaagcc tttgataaga tcaaacaata tctgcagaaa ccacctctat 7680 tggtgccacc tgtgcctagg aagcctctca ttttgtattt aacagtgact gaatcagcaa 7740 tgggctatgt gcttggccaa catgatgagt ctgggagaaa ggagcaagcc atctactacc 7800 ttagtaagaa attcactgag tgtgaatctc gttacagtat gattgagaag ctgtgttgtg 7860 gtttggtatg gagtgcaaaa aggctccgac agtatatgtt atactatacc acttggttaa 7920 tttcaaagat agatcctcta aaatatattt ttgaaaaacc atacatgtca aataggctgg 7980 ccagatggca agtgttgttg gctgaatacg atatcatcta caaaacaaga aaatctgtga 8040 aaggaagtgc aatcgcagat catttagctg ataacgccgt tgaagactat gagccgttaa 8100 attttgactt ccctgatgaa gatgtgctgg taatagaaag tgattggtgg accatgtact 8160 ttgatggtgc ggtgaatgtg tctggtaatg gagctggtgc tgtaataatt tctccagaag 8220 gaaaacaata tcccatttcc attaagctac agtttagttg cacaaacaac acagctgaat 8280 atgaggcttg cattcatgga ttagaagctg cattggaact gaagataagg aaattagggg 8340 tatatggaga ctctatgttg ataatttgcc agacgaaggg ggaatggcag acgaaagatg 8400 agaaattgaa accatatcaa gaatatctct ccaaattggc tgaaaacttt aaagagatag 8460 agttcaatca tttaggaagg gataagaatc agtttgcgga tgccttagca accttggcct 8520 ccatggccac aatcgattgt ggtatcagag tacatcctat aggcattgat atcagaagtt 8580 ctcctactca ttgttgttta gtagaagaag aagtagatgg cagtccttgg tatacagata 8640 taaaaagatt catccaatat cgagaatatc cttctgaagt ttcaaaaaca gataagaaga 8700 ctctgagaag aatggtaatg gagtacttta tagatggaga aatcttatac aaaaggtcat 8760 ttgatgggac tttattaaga tgtctggaca gatcagaagc caataaagcc ttgtgtgaag 8820 tgcatgaagg aatttgcacc acccatgcaa atgggcatat gatggcaaga caaatacaaa 8880 gagctgggta tttttggttg accatggaaa aggattgtat ataatttgtc cgaaaatgtc 8940 ataaatgtca ggtgtatagt gacaaaatca atgcaccccc agtgccctta ttcaatatgg 9000 tgtcaccttg gccattcgcg atgtggggaa ttgatgtgat tgggcctatt aatccaaaag 9060 ccagcaatgg tcatcggttt atcttggtcg caattgatta ttttacaaag tgggtagagg 9120 cctgctcata tgctcatgtg actcagaagg tggtcaagcg attcattgag agagatctaa 9180 tttgtaggta tggtttgcca gaaaggatag taaccgataa cgccaagaac ttcaatggga 9240 agatgatcgt ggaattatgc actaaatgga aaatcaagca ttccaattca tccccttaca 9300 gaccaaaaat gaatggtgct gttgaagctg ctaacaagaa cataaagaag attgtccaga 9360 aaatggtggt cacatataaa gattggcagg aatggcttcc ttatgctcta catgcctatc 9420 gaacagcaat aaggacgtca acgggggcta caccttattc attagtttac ggaatggagg 9480 cagtgatgcc cttggaagta gagattcctt ctctaagggt cctcatggaa tctgagctag 9540 aagaggctaa atgggctgag aaggggcaga tccgatacga ccagtgagaa gagattagct 9600 gcaatttgtc accaccaact gtatcaaaac aggatagcaa gagcatatga cagaaaagtt 9660 cgaccaagag agtttaaaga aggagatctt gtattgagaa aaatcctatt actacctagt 9720 gagaatcata gcaagtgggc acccaattat gaaggtccct atgtagtaaa gaaggcattc 9780 tctggaggag cattgatatt gacaggaatg gatggagaag atttgagtag gccagtgaat 9840 tccgatgccg tgaagaaata ttatccatga ttgtataagt tctcatcaaa tcaataaaag 9900 ttttgccaag aaattcactt tgcatatctt ttctatctct cataaatgtt tattgatatc 9960 aaagaatcag taaatacact cttgaagcct tgcatgatct catagattca attcattact 10020 tttaccaaaa tcagtttccc tatttgagtt tcaaaaaatt tgatctggca ttttgatttc 10080 aaaaataatt tgatgtttat tcaaaaatga tatttttgac attctacttg tagaatgaca 10140 agtgaatcaa gcaactcctt catagaggtg accaaaatct aaaaagaaaa agaaaaaaga 10200 aatgaataaa tacccttacc ccatgactct tgaataatgt gtttttaaat gtatgaataa 10260 cggtatgtag tgaacttgtt gctcataact catgaaatgc atctttgcaa agactaaacc 10320 atcatactag atgaggtcaa agtttattga tcatagctgc ttgcgcttga aatgaggaaa 10380 ggccatcttt gttattcctt tcacgttctg aaataagtac atcccttgcg atcccttttt 10440 gagcctgaat aatttttctt tcataaaaac atcccgacta agatcacacc ctacactggg 10500 gcaagtgaaa tttcaatgat caagaaagat gataaagccg tgagaaagcc gaaaggcaaa 10560 agagcccaag aaactcaaat gctagggggc atgaccaaat cacaagaaaa agtgataacc 10620 aagataaagt gagtatgctc tagcgaagca atgaaagaga aaaacagaaa aagggcaagt 10680 aaaataagag cggcaaaaga aaagatgaat gacgtcaaga gtcaaactgt tgactgtgat 10740 cttcagtctt tgaaaccctg aaaacactct ttgagcctta tgaatccttt tctttcatag 10800 ccaaaaacca cagcctatgt tacgtgcctg tagaagtcct ttctaatcaa gcaagcaagc 10860 aatctagaac aataaataat gctctcaaaa tgcaaagaat attttttcat aagattcatg 10920 atatcaagaa taaactactc attattattc atgctgataa aaataaatgt tcaaaaaaaa 10980 aaagacaagt tttttctcat acaaaacctc gagctttttc tcgagccctt cacttcgaaa 11040 caaaaggtca tctcataaca tattttcacc gaagacctca ttgccaaaca caagagcaaa 11100 taatctcttt ttcaagaaag aaaataacca aggagttgca agatttcaaa aacaaattgt 11160 tttagactcg catcgaaata atttttgttt tcaaaatgca agatcaagat ttcaagattc 11220 attctagacc catacttctt caccaaactg aaaaggagag aaatgagaga atggtctctt 11280 aaaaccatta tttgtctaag tcgctgacag ggcacacttg ggggcaatga ccagtacaag 11340 ggggcaatat tgtgcttaag aaaaatctat atgttctaaa aaaaaaaagg gaacatttcc 11400 tacaacaaga caagggggca ttatggttta cgaaagacag tttgatcctt tcatcaagtg 11460 acaccaaata tttttatcag tgagacgagg agtaatgaat gatcccctca aactatttga 11520 cgagacagaa aatctctagc aagcaagtgg gtcatgatgg gcaccaccaa ggctgagttg 11580 tgcaaacaaa tctggaaaaa gtcttatatg ggctaactcg agtgggctaa aaagccaagc 11640 gacaaagatg actcaaatca gatagcaaga tctcaccaac caagcaacga gaagactaag 11700 aagaaattgg gggcctatat ttcaaatcag gtaaagatgc atgcatatca tttaaacttt 11760 gagacattgg acaatgagtt ttgcaaattt tattagagaa aattctaacg gaatccatca 11820 agcggaaggc caacttgaaa tggcgaacat tgaaattgct tttgaaaaat tttcactttt 11880 gagaattctt caatctgggc aggtcgccca tgagaattag gccacctgaa aaatcttttt 11940 atttttccac cacctttcag tttccactcc tgaggtagtg cattttctat cctacctcat 12000 tttgagttct tttcgagcac accttcgagc cctcgtctta tttcttttcg agcgcgcctt 12060 tgagccctcg accatcaaag gtagtgcatt tcctatccta cctcaattca agcgcgcctt 12120 cgagccctcg tcttatttct tttcgagcgt gccttcgagc cctcgaccat caaaggtagt 12180 gcatttccta tcctaccttc ttttgagtgc gccttcaagc cctcatttcc ttcgagcttc 12240 catctattaa ataatgcgcc ttcgagccct atcatgtctt attaaaaaaa aaaaaaaaat 12300 tcatattttt ccactgggca ggtaacccat tacaatatac catctgggca ggtaacccat 12360 tacaatgtga ccatctgggt aggtaaccca ttacaatata ccatctgggc aggtaaccca 12420 ttacaatgtg accatctggg taggtaaccc attacaatat accaactggg caggtaaccc 12480 attacaatgt gaccaactgg gtaggtaacc cattacaata taccatctgg gcaggtaacc 12540 cattacaatg tgaccatctg ggtaggtaac ccattacaat ataccatctg ggcaggtaaa 12600 ccattacaat gtgaccaact gggtaggtaa cccattacaa tataccatct gggcaggtaa 12660 cccattacaa tgtgaccatc tgggtaggta acccattaca atataccttc tgggcaggta 12720 acccattaca atgtgaccaa ctgggcaggt aacccattac aatataccat ctgggcaggt 12780 aacccattac aatgtgacca actgggtagg taacccatta caatatacca tctgggcagg 12840 taacccatta caatgtgacc atctgggccg gtaacccatt acaatatacc aactgggcag 12900 gtaacccatt acaatgtgac caactgggta ggtaacccat tacaatatac catctgggca 12960 ggtaacccat tacaatgtga ccatctgggc cggtaaccca ttacaatata ccatcataaa 13020 aaaaaaaaaa tcctcgtatt tttcaatcat tgggtaggtc gcctggaaca attagaccac 13080 tcgcgaaatt cttcgcgttt cttttatcat tgggcaggtt gcccaaaaca atttgatcca 13140 tttcaaaaaa aaaaaaaaaa aaaaacaaca acaacaacaa aaaatgggtc gtcttccaaa 13200 taacttgttc tctctgtaaa agtcatatgt caatctactg ttttcaaagt tttcaagact 13260 tttttttgta tctacttttc tttataaatt tactacacaa agctaaggaa aaatgaaaat 13320 tttcaatatc tttgtattgt aaatattata aagagggggc aact 13364 // ID LINE_CA repbase; DNA; EDCOT; 580 BP. XX AC AJ411792; AJ411792.1; GI:14715217; VERSION; XX DT 08-JUL-2003 (Rel. 8.06, Created) DT 08-JUL-2003 (Rel. 8.06, Last updated, Version 1) XX DE Cicer arietinum LINE-like retrotransposon and partial RT gene for DE reverse transcriptase, clone CaLi9. XX KW Non-LTR Retrotransposon; Transposable Element; CAR411792; KW LINE-like retrotransposon; LINE_CA; RT gene; KW reverse transcriptase. XX OS Cicer arietinum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; OC Cicer. XX RN [1] RA Staginnus C.; RL Thesis (2001) Department of Plant Molecular Biology, University RL of Frankfurt / M., Frankfurt a.M., Germany. XX RN [2] RP 1-580 RA Staginnus C.; RT "Direct Submission to GenBank."; RL Direct Submission to Genbank (22-JUN-2001)Staginnus C., Plant RL Molecular Biology, University of Frankfurt M., Biocentre, RL Marie-Curie Strasse 9, D-60439 Frankfurt a.M., GERMANY. XX DR Genbank; AJ411792; Positions 1 580. XX SQ Sequence 580 BP; 169 A; 95 C; 110 G; 206 T; 0 other; tgggatcctg ggcctgatgg cattgatgga tgttccttca agcactcatg cgatatggta 60 ggtcttggtc tttttaatcc aatgcatcaa ttttgtttta atggatggat tatgccaaaa 120 tataattcaa acattgtagc ctttattctt aagactcctg gagctgacat gattgagtgt 180 tttagaccaa ttatatggct aacttcaaat ttaaggtaat ttcaaaaata ttggtagaca 240 tgttggctat tattgctcca aaaatcattt atgaacacta gagagaattt actaagggga 300 gacatatctc ataatgcatt ttcactactt cacatgccat taatctttta gactaaaaat 360 catttggttg taacttggca ttcaagatct atatcaagaa ggcttttgac actctttata 420 ggggatttct gattcaaacg ttgcaggctt ttgcattcaa taatactttt tgtaattgga 480 tactacaagc caagctttcc ttattggtga atggtaaggt cgtggttgat ttaatttcac 540 ttgaggatta ggtcaaggag accccttaag tccgaattcc 580 // ID Copia-66_Mad-I repbase; DNA; EDCOT; 4014 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-66_Mad_; KW Copia-66_Mad-LTR; Copia-66_Mad-I. XX NM Copia-66_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4014 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1670-1670 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1399-1890] - Integrase core CC LTRs are 90% similar to each other. XX FH Key Location/Qualifiers FT CDS join(202..1986,1990..2967) FT /product="Copia-66_Mad-I_1p" FT /translation="MQFQQSQKTMKFLMGLNESYAAVRGQLLLMDPLPAVN FT KAFSLIIQDEKQRAVSIHAPGRSSITDAAAFAVRDNMRNSGRNFSPRNSHL FT KCGRCDATGHTSETCRAHLKCDYCNWRGHTIDQCRKLKKAKDNSDKGDYQD FT RRGSDSQGFNSKANHVDIKPTPPATSPSSYGLTPEQYHNLLALLDKSQSKS FT TSNHVGTTSTMNDLSGRVFCASALNKGRNWIFDTGATDHMVCSPSLMTTSV FT PVYNRQVHLPNHALADVTHIGTVRLSNDLVLHNVLCVPSFKLNLISVSKLT FT NTSSCFVIFTDKMCLLQGQRSGKMIGTGTEREGLYYLDNVTKTGCNSVSVV FT APSSSQLWHQRLGHLSNKTLRAISPCVKNLNFCSIDDCLICPLAKQTRAPF FT PLSSINTKAPFELIHVDIWGGYHVPTITGAQYFLTIVDDFSRCTWVYLMNH FT KSDARSYLITFIHLVETQFSTRVKVLRSDNGPEFFMTQFFSDKGILHQTSC FT VSTPQQNGVAERKHRHLLNVARALLFQSHLPKKFWGDAILTATYLINRTPT FT PLLHGKSPYEILHHKQPAYAHLRVFGCLCFSSTHHHRPTKFDARATRCFLG FT YPYGTKGYRVYDLQTGKIFISRDVIFHENVFPFSSSAAVSPVVFPHTQDTD FT CDDTIIHPSLPLEQDSVDPSSSSPVSPASVSTPFLSPSPPRLKRPTHAPGY FT LQQYHVDINLPSRSVPSSHSALTTVAGTSYPLSDVLTYDRLSARHRAFTTS FT ISAAIEPSSFSQAIRDPQWRLAMEEELAALAANRTWSLQPLPPGKKPVGCK FT WVYKIKFRSDGSVERYKARLVAKGYSQIEGLDYRETFAPVAKLTTVRLLLA FT VASVQQWHLHQLDVNNAFLHGDLEEDVYMSLPPGFGRKGETRVCKLHKSLY FT GLKQASRQWFIKLSCAL" XX SQ Sequence 4014 BP; 1078 A; 1036 C; 783 G; 1113 T; 4 other; gctgatattt ggaatgagtt gaaggaacgc ttctctcaca caaacagtgt ccatctcttc 60 catatcgaac aagagataca tggaagtgtt caaggaaatt tgaacattgg tgcatattat 120 accaaactga aaagtttttg ggatgaacgt gatgccttgt gcgctctccc aacctgtgca 180 tgtggagctg cgaaagaatt gatgcagttt cagcaaagtc agaaaaccat gaagtttctc 240 atgggtctca atgaatccta cgctgcagtt cgtgggcaac tcttacttat ggatcctctc 300 cctgctgtca acaaagcttt ctcactcatt attcaagatg agaaacagag agcagtctca 360 atacatgctc ctggaaggtc ttcaatcact gatgccgcag ctttcgccgt gcgggacaac 420 atgcgaaact ctggtaggaa tttttctcct agaaattccc atctaaaatg tggccgttgc 480 gatgcaaccg gacacacttc agaaacctgt cgtgcacacc tcaagtgcga ctactgtaat 540 tggagaggtc acaccataga ccaatgccgc aaactgaaaa aggcaaagga caacagcgat 600 aagggagatt atcaagatcg caggggttcc gactcgcagg ggttcaactc caaggctaat 660 cacgttgaca tcaaaccgac gcctccagca acatctcctt catcctacgg cctcactccc 720 gagcaatacc acaacctgct tgcactcctt gataagagcc aatccaaatc cacatctaat 780 catgtcggta ccacctctac tatgaatgat ttatcaggta gagttttttg tgcttctgct 840 ctcaataagg gaaggaactg gattttcgat actggcgcca cagaccacat ggtctgctca 900 ccaagcttga tgaccacaag cgttccggta tacaatcgac aagtgcacct acccaatcat 960 gcacttgccg atgtcacaca cattggcaca gttcgtctct cgaacgatct cgtccttcac 1020 aacgtgcttt gtgttccatc atttaaactg aatttaattt ctgtcagcaa actcactaat 1080 acctcatctt gctttgtcat cttcactgat aaaatgtgtc tacttcaggg ccaacgatcg 1140 gggaagatga ttgggacggg aactgaacga gaaggactct actaccttga taatgtgacg 1200 aaaaccgggt gcaattcagt gtcagttgtc gccccttctt cttctcagct ttggcatcaa 1260 cgccttggcc atctttccaa caaaacctta cgggctatct ctccttgcgt taaaaatttg 1320 aatttttgta gcattgatga ttgtttgatc tgcccattag ccaaacaaac acgtgctcct 1380 tttcctttga gttctattaa cacaaaggct ccttttgagt taattcatgt tgacatttgg 1440 ggaggttacc atgttcccac tatcacaggg gcacaatatt tcttgaccat tgtggatgat 1500 ttctcacgat gcacatgggt ttatttaatg aatcacaaat cagatgcacg atcatatctc 1560 atcacattca tccaccttgt tgaaacacaa ttttccacac gagttaaggt tcttcgtagt 1620 gataacggtc cagaattttt tatgacccaa tttttttcag ataaggggat tctccatcaa 1680 acaagttgtg tctctactcc ccaacaaaac ggggtagcag agcgcaaaca ccgccactta 1740 ctcaatgttg ctagagcctt actttttcaa tctcatcttc ccaagaaatt ttggggtgat 1800 gcaatcctaa ctgccactta tctcattaat aggactccca ctcctcttct tcacggcaaa 1860 tcaccctatg aaatacttca tcacaaacag ccagcgtatg cacatttgcg agtgtttggt 1920 tgcttatgtt tctcttccac mcaccaccat cgtcccacca aatttgatgc aagagccaca 1980 cgttgtmttt ttcttggcta tccatacggc acaaagggat atcgagttta cgaccttcaa 2040 acgggtaaaa tctttatctc ccgtgatgtt attttccatg aaaatgtgtt ccctttttca 2100 tcttccgctg cagtttcacc tgttgtgttt ccacatactc aagatactga ctgtgatgac 2160 accatcattc atccgtccct tccactggag caggattcag tcgacccatc ctcttcttcg 2220 ccggtgagtc ctgcttcggt ttcgactcct tttctwtccc cttcaccacc tcgtcttaaa 2280 cgccccactc atgcacctgg ttatcttcaa caatatcacg tcgacatcaa cctcccttct 2340 cggtccgtcc cttcatctca ctcggcgttg accacagtgg caggtacttc ttaccctttg 2400 tctgatgtac tcacatatga tcgcttatct gctcgccatc gtgctttcac cacttccatt 2460 tcagctgcca tagaacccag ctcattctca caggctatac gcgaccccca atggcgttta 2520 gccatggaag aagaactggc agcccttgct gcgaatagga catggtctct tcaaccattg 2580 ccccctggca agaagccggt tggatgtaag tgggtctaca aaatcaaatt tcgatccgat 2640 ggatccgttg agcggtataa agcacgcttg gttgccaaag gttatagcca aattgaaggc 2700 ttagactatc gagagacttt cgctccggtt gcaaaactga ctacagtccg cctacttctt 2760 gccgttgcct cagtccaaca atggcacctc caccaacttg atgttaacaa tgccttcctc 2820 catggtgacc ttgaagaaga tgtctacatg tccttgcccc ctggtttcgg acgaaagggg 2880 gagacacgag tttgtaaact tcataaatct ttgtatgggc ttaagcaagc ctctcgtcaa 2940 tggtttatca aactctcttg tgctcttagm aaagccggtt atcaacaatc caaggcagat 3000 tattcattgt tcgtccgaaa ccatgatggt aaattcactg ccctccttgt ctatgttgat 3060 gatattatcc tggcaggaaa taacatacaa gcaattgagg ataccaagtc tttccttatg 3120 aagcaattca agttgaaaga ccttggccaa ctaaaatatt tcttgggcat cgaaattgct 3180 cgctctagca aggggatcac tctctcacag cgaaaatatg cccttgaaat acttgaggat 3240 gcaggttacc ttggcgcgaa accagccacc tctcctatgg agcaaaactt atcactcaga 3300 aaggacgaag gacaatgcat cactgatcct tcttcttatc gacggcttgt tgggagacta 3360 atctacctga caatcacgcg ccctgatttg gtctatgctg tccacattct tagtcaattt 3420 atggagaagc ctcgaactcc acacttggag gcagcccacc gagtcttacg atacgttaag 3480 cacacaccag ggcaaggtat ttttctctct gcaagaagtc caatccaact gaatgccttt 3540 tgtgatgcgg attgggccag atgtcgtgac acacgacgtt ctaccaccgg atactgtgta 3600 tttcttggag aatccttgat ctcctggaaa agcaagaaac aaaacactgt gtcacgttct 3660 agtgcagagg cggagtatcg ctcaatggca gcaacttgtt gtgaagtcac ttggctgaaa 3720 tacgttttac aagacttggg tatcaaacat aaacatccag tcaagttgta ttgcgataat 3780 caagcggcac ttcacatcgc ttcgaatccg gtctttcacg aaagaaccaa acacatagaa 3840 attgactgcc accttgtacg agaaagggtt caaagtggaa tgatcaggac atctcacatt 3900 tcaaccacga agcaaccagc cgacatcttc acaaagccac tgagcttaca ccagtttacg 3960 actttgctcc gcaagttagg aataatcaac atccattcca aacttgaggg ggag 4014 // ID GYPSHAN4_I_MT repbase; DNA; EDCOT; 4479 BP. XX AC AC131249; XX DT 28-JAN-2007 (Rel. 12.01, Created) DT 28-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, GYPSHAN4_MT, from Medicago DE truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Internal; Interspersed; terminal; repeat; ORF; GYPSHAN4_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4479 RA Shankar R. and Jurka J.; RT "GYPSHAN4_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 26-26 (2007). XX DR EMBL/GenBank/DDBJ; AC131249; Positions 93571 98049. XX CC The internal region has intact domains for gag-pol polyprotein CC with Gypsy-like arrangement. XX FH Key Location/Qualifiers FT CDS join(121..1479,1483..3732) FT /product="GYPSHAN4_I_MT_1p" FT /translation="MLIEENEDLEEEDYVVNDEGGEEEEDGENGEFLMIRR FT MLGNQAKEEESNQRESLFHTRCLVQGKVCSLIIDGGSCTNVASAHMVGKLE FT LETRPHPRPYKLQWLSESVEMLVDKQVEVCFKIGKYEDVVVCDVVPMEACH FT LLLGRPWQFDRGVQHDGRSNKYSFMHFGKKIILAPLSPNDVREDQKKMKEK FT YAQEKEKERKEKETEKEKKESFMAKKEEIKNAIVTKQPLYLLFCKEVVLFT FT NNSNTQKFPSCVESLLQEFEALFPKEIPNGLPPLRGIEHHIDLIPEASLPN FT RPAYRSNPQQTQEIQSQVAELVSKGWVRESLSPCAVPVILVPKKYGSWRMC FT TDCRAVNNITIKYRHPIPRLDDLLDELFGACLFSKIDLKSGYHQIRIREGD FT EWKTAFKTKYGLYEWMVMPFGLTNAPSTFMRLMNHVLREFLGKFVVVYFDD FT ILIYSKNFEHCGHLRAVLEVLRKEHLFANLEKCVFCTDHVIFLGFVVSSKG FT IHVDEEKVRAIKDWPPPKNVSEVRIFHGLASFYRRFVKDFSTIAAPLNEIV FT KKNVFKWGEKQEQAFAALKEKLTKAPILALPNFFKSFEIECDASNVGIGAV FT LMQEGHPIAYFSEKLKGASLNYSTYDKELYALFRSLQTWQHYLLPKEFVIH FT SDHESLKHLKGQGKLNKRHAKWVEFLEQFPYVIKHKRGKANVVADALSRRY FT ALLSTLETKVFGLEQIKSLYESDIDFSSKFLACEHAAINGYFRHNGYLFKE FT KRLCVPKCSIRTLLLKEAHEGGLMGHFGVVKTLELLQEHFYWPHMKIDVQK FT LCERCIVCKKAKSKVLPHGLYTPLPTPEFPWVDISMDFVLGLPRTKNGKDS FT IFVVVDRFSKMAHFIACKKVDDARHVADLFFKEIVRIHGVPRSIVSDRDTK FT FLSHFWRTLWGKIGTKLLFSTTCHPQTDGQTEVVNRTLSTLLRSVLTRNLR FT MWKECLPHVEFAYNRVVHSTTKMSPFEVVYGFNPLTPLDLLPMPNSSFLKH FT KDGKDKAEFVKKMHEQVKLQIEKKNEGYAKNANKGRKRVIFEPGDWVWVHM FT RKERFPKQRKSKLQPRGDGPFQVLERINDNAYKLELPGEYDISATFNVADL FT APFDVGNSDFNSWTNSFQEGGDDEGMVVHDTSASIQGLGGPMTRSRTKKAK FT EALTQLVAKVLESKPTLESMEDKMVMCIKPLEEGWGASLAAHFI" XX SQ Sequence 4479 BP; 1490 A; 669 C; 965 G; 1355 T; 0 other; agtgatccta aaggtaaaaa cattacttca tcccaaaatg tttctactaa caagattgtt 60 acgtgtttca agtgccaagg taaaggacac atagcttctc aatgtccaac aaagagaact 120 atgttaattg aagagaatga ggaccttgag gaggaggatt atgtcgtgaa tgatgaagga 180 ggggaagaag aggaggatgg tgaaaatggt gaatttctca tgattaggag gatgttggga 240 aaccaagcta aggaggaaga atcaaatcaa agggaaagtc ttttccatac aagatgctta 300 gtgcaaggaa aggtatgttc tctaattatt gatggaggta gttgtactaa tgttgctagt 360 gcacacatgg tgggtaaatt agaattagaa acaagacctc accctaggcc ttacaaactt 420 caatggctta gtgaaagtgt agaaatgctt gttgacaaac aagtagaggt ttgttttaaa 480 attgggaagt atgaagatgt tgttgtgtgt gatgtagtac caatggaggc ttgtcatttg 540 ttgctaggaa gaccatggca atttgataga ggagtgcaac atgatggccg aagtaataag 600 tattctttta tgcactttgg gaaaaaaatt attcttgcac cattgagtcc taatgatgta 660 agagaagatc aaaagaaaat gaaagaaaaa tatgcgcaag aaaaagaaaa agaaagaaaa 720 gaaaaagaaa cagaaaaaga aaagaaagaa agtttcatgg caaaaaaaga agaaataaaa 780 aatgccattg tcaccaagca gcccctatat ttgctatttt gcaaagaggt ggttttgttt 840 actaacaatt ctaacactca aaaatttcca agttgtgttg aatcgctttt gcaggagttt 900 gaggctttgt tccctaaaga gataccaaat gggctgccac ctttaagagg tattgaacat 960 cacattgacc tcattccaga agcatcttta ccaaatcgtc cagcctaccg aagcaatccc 1020 caacaaacac aagaaattca aagtcaagtt gctgaattgg taagtaaagg atgggtaaga 1080 gaaagtttaa gtccttgtgc tgtccctgtt attttagttc caaaaaaata tggtagttgg 1140 agaatgtgca ctgattgtag agctgttaac aatattacca ttaagtatag acatccaatc 1200 cctaggctag atgacttact tgatgaattg tttggtgcat gtttattttc taaaattgat 1260 ttgaaaagtg gctatcacca aataagaatt agggaggggg atgaatggaa aactgctttt 1320 aaaacaaaat atggtttgta tgagtggatg gttatgccgt ttggtttaac taatgcgcca 1380 agtactttta tgagactcat gaaccatgtc ttgagggaat ttttgggaaa atttgttgtt 1440 gtgtattttg atgatatctt gatatatagc aaaaatttct aggaacattg tggtcattta 1500 agggctgttt tagaagtttt aagaaaagaa catttgtttg caaatttgga aaaatgtgtc 1560 ttttgcacgg atcatgtaat ttttttaggt tttgttgtaa gctccaaggg aatccatgtg 1620 gatgaagaaa aggtaagagc aatcaaggat tggccaccac ccaaaaatgt aagtgaggta 1680 agaattttcc atggtttagc aagtttctat aggaggtttg tcaaagattt tagcaccatt 1740 gctgcacctc taaatgagat tgttaagaaa aatgttttta aatggggtga gaaacaagag 1800 caagcttttg ctgcacttaa agaaaaactc accaaagcac caattttagc attaccaaat 1860 tttttcaaat cttttgaaat tgaatgtgat gcttctaatg ttggaattgg ggctgttttg 1920 atgcaagaag gacatccaat tgcttatttt agtgaaaagt tgaagggtgc ttcccttaat 1980 tactccactt atgataagga attgtatgct ttgtttagat cattgcaaac ttggcaacat 2040 tacctactgc ccaaagaatt tgtcattcat agtgaccatg aatctttgaa acatttaaaa 2100 gggcaaggta agttgaacaa gagacatgcc aagtgggttg agtttcttga acaattccca 2160 tatgtgatca aacacaaaag aggtaaagct aatgtggttg cagatgcact ttcaagaagg 2220 tatgccttac tctccactct tgaaactaaa gtttttggac ttgaacaaat taagagttta 2280 tatgaaagtg atattgattt ttcatcaaaa tttttagctt gtgaacatgc tgccattaat 2340 ggatatttta ggcacaatgg ttatttgttt aaagaaaaaa gattatgtgt gccaaaatgt 2400 tccataagaa ctttgctttt aaaagaggcg catgaggggg gattaatggg acactttggg 2460 gttgttaaaa ctttagagtt gctgcaagag catttttatt ggccacatat gaaaattgat 2520 gtccaaaagt tgtgtgaaag atgcatagtg tgtaaaaagg ccaaatcaaa agttttgcct 2580 catggtcttt atacaccgtt accaactcct gaatttcctt gggttgacat ttccatggat 2640 tttgttttgg gtttacctag aacaaagaat gggaaagatt ctatttttgt tgttgttgat 2700 aggttttcca agatggcaca ttttattgca tgcaaaaagg tagatgatgc acgccatgtg 2760 gctgatttgt ttttcaagga gattgtgcgc attcatggag ttccaaggag catagtttca 2820 gatcgtgaca caaaattttt aagtcacttt tggaggacct tgtggggtaa gattggaaca 2880 aagttactat tctcaacaac ttgtcaccct caaacagatg gtcaaactga ggtagtaaat 2940 agaactctct ctactcttct tagaagtgtt cttacaagaa atttgagaat gtggaaagaa 3000 tgtttacccc acgtggaatt tgcttacaat cgtgtggttc atagtactac aaaaatgtca 3060 ccatttgaag ttgtttatgg ttttaaccca ctaactccac ttgatttgtt acctatgcct 3120 aacagttctt ttttgaagca taaagatgga aaagacaaag ctgagtttgt gaagaaaatg 3180 catgagcaag tgaagttgca aattgaaaag aaaaatgaag ggtatgctaa aaatgcaaac 3240 aaaggaagga agagggtgat ttttgaaccc ggtgattggg tttgggtgca tatgaggaaa 3300 gaaaggtttc ctaaacaaag gaagtcaaaa cttcaaccaa ggggtgacgg accatttcaa 3360 gtgctagaaa ggatcaatga caatgcatac aagcttgagt tacccggtga gtatgatata 3420 agtgctactt ttaatgttgc tgacttagct ccttttgatg taggtaatag tgatttcaat 3480 tcgtggacga attcctttca agagggaggg gatgatgagg gcatggttgt ccatgacaca 3540 agtgcttcaa ttcaagggct aggaggacca atgacaaggt cgagaaccaa gaaagctaag 3600 gaggccctaa ctcaattggt ggcaaaagtc ttggagtcca aacctacact agaaagcatg 3660 gaggataaaa tggtcatgtg catcaaacca ttggaggagg ggtggggcgc atctcttgct 3720 gcccatttta tttagttgtt cttgttatgt tataataaaa agtgtaagag accaattttg 3780 gtccaaaaac actaagtatg gttattttgt gtgtttaatc catttcgaag cttccaaagc 3840 tttgaatgga atgttttgtg tgtttatttc gtgcaaagga gtgctgaaga caaaagaaaa 3900 acaaggcatt aacgagcatt taatctgaag gatgaaagaa tgcaagaatt gaagaggaaa 3960 gggacaagac ttcaatgaga caatgaaggc atttcatttc agcatatgaa accaccatca 4020 tcatcaaatt cacgtccatc atcatgatca tcaagaccag ccaccctcat tcattgattt 4080 gtcttgtaac catttcttgt attcatgtta atttacttca gccataggaa ataatgatag 4140 attaatttgg ctgaaggaat cctaagagct atttgcattt ttctttgtaa ttcagcaagt 4200 gtccctccta cctatatata ggacacgaaa attgaataaa agacaagtta attttcgtta 4260 aaaaaaagtg agtaattgct ctttaggttc tggattggac cttgtattga tcatatcaag 4320 aatcctttct tgtggtgatc ttcattccat agacttatca ttttctagga ttagaaagtg 4380 tggcgtccct aaactctcca ttccatttct tgtttgaaac cacagatcag cctaaacacc 4440 aattcaaaaa accaaattct catttttcaa ctccaaatc 4479 // ID Copia2-VV_LTR repbase; DNA; EDCOT; 265 BP. XX AC . XX DT 29-AUG-2007 (Rel. 12.08, Created) DT 31-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia2-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-265 RA Obukhanych T. and Jurka J.; RT "Copia2-VV - LTR retrotransposon from grapevine."; RL Repbase Reports 7(8), 668-668 (2007). XX DR [1] (Consensus) XX CC LTRs of this element are 96% identical. 5'LTR has a ~50 bp CC internal deletion. The submitted sequence is for 3'LTR. XX SQ Sequence 265 BP; 64 A; 29 C; 43 G; 129 T; 0 other; tgttgaaaat ctcaatcata tcagaatttt tctgatctgg ttgttaccta ttttttaggg 60 ataatctggt tgttacctat tttttaggga taatttgttg ttgtttttta gggataagtt 120 gtatatttta aatttatttt gttcctagaa atttgggtgt acagttgtag atttagtttg 180 atttgttgta gcttttctat aaaaggaagc atgtttccct tccttattca attaatatac 240 gacatttttt ttttcctttt ctaca 265 // ID Gypsy-4_Mad-I repbase; DNA; EDCOT; 4880 BP. XX AC ACYM01134511; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-4_Mad-I; KW Gypsy-4_Mad-LTR; Gypsy-4_Mad_. XX NM Gypsy-4_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4880 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1327-1327 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01134511; Positions 6429 1550. XX CC Positions [3771-4292] - Integrase core CC 'AGATT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1070..2386,2390..3817) FT /product="Gypsy-4_Mad-I_1p" FT /translation="MFLGGLKEDIRHDILALEPDSLHQAQKLAKIFETKLH FT SKRSTRPNFPRSFLTNNISAPSSFSSPTPPITTKQPLLPHSAFKRLTPTEV FT QDKRRKNECFSCHEQYSPTHKCKTPLLILLDPTLPEDDSTTFHDCQDDNTT FT VEEPSCHMLELFSIPSLNIGRPMRLHGSISSKPIIVLIDSGAACNFMNPHI FT ADQLGLPVHPIAPMKFTTAANDRYSSKRVTGVSLQIQDYTFTRSFILLDVP FT GCDLILGVEWLESLGFIGWHFKQKTMVFSVGGRTYTLQGLTPSSSLFPTCL FT QMEKLLDNPYTLLASITSPNSNPTPPRDTHPAILSLLHKYKHLFTNPSGLP FT PERPIDHKIPLLPGTKPVNVRPYRYPHCQKAEIEKQVQDFLNSGVIRPTSS FT PFSSPVLLVKKKDNTWRLCIDYRALNAATIKDRFPIPVVDKLLDEHGATIF FT SKLDLRSGYHQIRMHADDIAKTAFRTHEGHYEFTVMPFGLSNAPATFQSLM FT NSIFRPYLRKFVLVFFYDILVYSPSVASHLSHLETIFEILSEHSLKVKLSK FT CSFGKDRVDYLGHVISGEGVAVDQSKIQAITSWPQPTSLKSLRGFLGLTGY FT YRKFVKHYGLIAKPLTNMLKQGGFLWSPESTTAFQALKNMLATAPVLALPD FT FSKQFVVETDASGTGIGAVLSQDGHPIAYLSKALSGRNLGLSTYDKEMLAI FT VFAVQHWHPYLLGQQFRIITDHQPLKHFLEQRITTPQQQHWLVKLLGYNYS FT VEYRPGSQNTAPDALSRQAELLLVMGLSTPVFDCIPQLQHSYAHDPDVQKV FT WSLLLSAPNTLIKGFSLINDVVHYKQRVFVPLTSQWRPKLLAEFHASLQGG FT HSGFLRTYKRLTRNFFWPGIKRETKQFVAECTECQRQNIENIHPRIVAALA FT HSCRHMAGHRP" XX SQ Sequence 4880 BP; 1286 A; 1505 C; 890 G; 1199 T; 0 other; attggtatca gagcccgtcg acagatgggc aaaaacacac aatccgctag ctctgacccc 60 gacgtcgtcg ccgctgcagt ggatgttcgt cacgagcacc tccgtaacca agtcgaggat 120 gtatgtgaca caatcgccat tctggaaaat cagcaagctt cattccagaa atctttggac 180 caactcagcg attccaacac agctttccaa accaccatga cctcccagtt cgcatccttt 240 caaaccatac tgttagagga gctgcgccac cttaaatcag ccctcccacc aaccccgacc 300 actaccgttc cacccacttc cacccccgca acctccgtcc acccaaaccc caccctcaac 360 ccgagagcct ccacctccaa tttgcaaccc tccttccgct ccctatttcc cgcaccgagt 420 tcttctccct tgggcctggg tctctctaac ccacccaacc tcaacctact cccaacctcc 480 accccttcaa cccggcccac accatcccct attactatca cacccaggcc ggcccactcg 540 caacccaacc cagcctcttc ctctcattac tcaccgcacc cctacaccca cacccaccca 600 acaccatata cttctcactc cttccatatt tccccgtccc ccacccctcc ttctactcac 660 cacacccaac caccaccata cacttcccaa caccctccca acaacttcaa acccatcaaa 720 atggaactcc cgcgtttcac tggggaagac ccttacgggt ggttagccat ggcggaacga 780 tatctcgact attacgaggt cccccctcaa caatgggtcc ttgttacagc ttgtaatttt 840 ggtgcagatg cctctatttg gatgaggggt tttgaacaaa ggcacgacag gagataattg 900 gggtttattt gttgacttgt tgcttcaacg ttttggtggt ggtgaccgcg caaacattga 960 atcccagctt actcatattc aacaaaagac tactgttgat gactatctgg cagagttcac 1020 acggctttct tgccgggtca ctgattggac tgaaaaccaa ttgaaacata tgtttctggg 1080 cgggttaaag gaggacatac gtcatgacat ccttgctctc gaacctgact ctctccatca 1140 agcccagaaa ttagccaaaa tttttgaaac taagctgcac tccaaacgtt ctacccgccc 1200 caattttccc cgctctttcc tcacaaataa catctctgct ccgtcctcct tctccagtcc 1260 gacaccaccc atcactacaa aacaacccct cttgccccat agcgcattca agcgccttac 1320 accaactgaa gtacaggaca aacggcgcaa aaacgaatgt tttagctgcc atgaacaata 1380 ctctcccacc cacaaatgca aaaccccact gctcatattg cttgacccta ctctgcctga 1440 ggacgattcc accacattcc acgattgcca agatgacaac actacagtcg aggagccctc 1500 ttgtcacatg cttgaactgt tctctattcc gagtctcaat atcggtcgac ctatgagact 1560 gcacggttcc atctcctcta aacccatcat cgtcctaatc gattcaggag ctgcatgcaa 1620 cttcatgaac ccccacattg ctgatcaact aggtttaccg gtacatccaa ttgcccccat 1680 gaaattcaca accgcagcaa atgatcgtta ttcatccaaa cgtgtcacgg gtgtatcgct 1740 ccaaatacag gactacactt tcactaggtc ttttatctta ctggatgtac ccggttgtga 1800 cctcatttta ggtgttgaat ggttagaatc tctcgggttc attggctggc acttcaaaca 1860 gaaaaccatg gttttttcgg tgggcgggcg aacctacaca ttacaaggct taacaccctc 1920 atcctcattg ttccctacct gcctccaaat ggaaaaatta ttggacaacc cgtacaccct 1980 cttagcctcc atcacttctc caaacagcaa ccctacccca cccagggaca cacatccagc 2040 cattctctcc ctcctccaca aatacaagca ccttttcacc aacccgtcag gacttccacc 2100 cgaaagaccc atcgaccaca aaatacccct actccctggt accaagcccg tcaatgttag 2160 accatatcgt tatcctcatt gtcaaaaggc tgagatcgaa aagcaggtgc aggatttttt 2220 aaattcaggg gttatccgcc caacttccag tccattctct tctccagtcc tcctggtcaa 2280 gaagaaagac aatacatggc gcctctgtat tgattaccgt gctttaaatg cagcaactat 2340 caaagatcgt tttccaatac cggttgtcga taaactgctt gatgaataac atggcgccac 2400 cattttttca aaactggacc tccgatcagg ttaccatcaa atccgaatgc acgccgatga 2460 catcgccaag acagccttcc gcacccatga aggccactac gaattcacgg taatgccctt 2520 cggcttatca aatgcccctg ccacatttca atccttaatg aattcgattt tccgtccgta 2580 cttacggaaa tttgtcttag ttttttttta tgacatactt gtctatagtc cttccgtcgc 2640 atctcacctc tcccatttgg agacaatttt cgagattctt tctgaacaca gcttgaaggt 2700 taaactaagc aagtgctcat tcggcaagga ccgagtggat tacttgggtc atgtaatttc 2760 tggagaaggt gttgctgtgg atcaatccaa gatacaggcc atcacctcct ggccacagcc 2820 aacatcccta aaaagtcttc gcggtttcct cggattaacg ggctattaca gaaaattcgt 2880 taaacactac ggactcattg ccaagccctt aaccaacatg ctcaaacaag gaggcttctt 2940 gtggtcacca gagtccacta cggcattcca agctttgaag aatatgttgg ccacagcacc 3000 agtccttgcc ttaccagatt tttccaagca gttcgtggtc gaaacggatg catcgggcac 3060 gggtattgga gctgttttaa gccaagatgg acatccaatt gcatacctta gcaaagctct 3120 ctcggggcgt aaccttggac tgtcgaccta tgacaaagaa atgctcgcca ttgtatttgc 3180 agtacaacat tggcatccct acctcttggg ccaacaattc cgcatcatca ctgatcatca 3240 accactcaag cacttcctag aacagcggat tacaacccca caacaacaac attggctggt 3300 aaaactactc gggtacaact actcggttga gtaccgcccc ggttctcaaa acacggcccc 3360 agatgccctc tcccgtcaag ccgaactact gctagtaatg ggactctcca cccctgtctt 3420 tgactgcatc cctcaattgc aacattctta tgcgcacgat ccggacgtgc aaaaagtttg 3480 gagtctctta ctttctgcac caaacactct cataaaaggc ttttccctga tcaatgatgt 3540 ggtgcactac aaacaaaggg tctttgttcc actcacttcc caatggcgcc ctaagctact 3600 ggccgaattc catgcatccc ttcaaggtgg tcactccgga tttcttcgca catacaaacg 3660 ccttaccaga aatttttttt ggccagggat aaagagggaa accaaacaat ttgtggctga 3720 atgcacggaa tgccaacgcc aaaatattga gaatatccac cctcggattg ttgcagccct 3780 tgcccattcc tgcaggcata tggcaggaca tcgcccttga ttttgtggag ggactaccca 3840 attccaacgg gtacactgtc attcttgttg ttgtcgatcg cttatcgaag tatggccact 3900 tcattcccct gaaacatcct tacacagccg cctcggttgc cgacattttc accaaggaga 3960 ttttcaaact ccatggcatg ccaaaatcga tagtctcaga cagagaccca atcttcctca 4020 gcaacttttg gcaagaattc ttcaacctcc aaggtagcaa actttgccac agctctgctt 4080 accaccctca aacggatggg caaacgaagg tcctcaacag aacattggaa cactaccttc 4140 ggtgcttctc aagtgacaaa cctaccaaat ggtcatctct cattccttgg gctgaatggt 4200 ggtataacac aagcttccat tctgccatta aaatgtcctc gtatcaagct gtctacggta 4260 tcgaaccacc aaccattcgc atgtacatgc ccgggtccac ggcagtccac tcggttgatg 4320 cggcattaca agaccgagac aagttgataa gccgtctgcg ggccaatctg cagcttgcac 4380 agaatagaat gaaacaaatc tatgaccaca agagaaccga gcgggtgttt aacgttggtg 4440 gctgggttta cttgaagctg caaccttacc gccagcactc ggtgactacg aggacgacaa 4500 acaagttagc acccaagttc tatggcccat tccagattac aaagcaagtc gggtctgtgg 4560 catatcagct tcgtttacct ccaaactcca agatccatct cgtctttcac gtgtctctcc 4620 tcaaacccaa gctcggcagt gcttctcctc cactctctga cttgccttct ttcgactcct 4680 ccggaactct acaatggcaa ccagaaaccg tgcttgacag gggcatgttc aagaaaaaca 4740 acaaagcagt gacaaaatgg ttgatcaagt ggtccggcct acccaccgaa gacgcaacct 4800 gggaggaagc cgacaccatc ctggctcgtt accctgaatt ccaggcctga ggacaggcct 4860 tttctcaagg gggagggagt 4880 // ID PEABODY_LTR repbase; DNA; EDCOT; 1720 BP. XX AC AF083074; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Pisum sativum Ty3/gypsy-type retrotransposon PEABODY_LTR, long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Long terminal repeat; PEABODY_LTR; Ty3/GYPSY superfamily; KW gag-pol pseudogene; retrotransposon. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-1720 RA Volman P.G., Shilo J., Weinhouse H., Ohana P. and Benziman M.; RT "Direct submission."; RL Direct Submission to Genbank (09-AUG-1998). XX DR Genbank; AF083074; Positions 1 1720. XX SQ Sequence 1720 BP; 493 A; 210 C; 414 G; 603 T; 0 other; tgtaacaccc cgataacata agataattat ttaatttaag ttaaacttat atttattaat 60 ttaattagat aattagaata ttattggatt attagtggaa tatatttaag ttggaaataa 120 gaataagagt tccattttgg taaaacggtt ttcacgtgaa aacagagaag cgacgcaaaa 180 gaggaaaaag ggtaaagagg cagagcaaga ggagataggt cgaagaaggt gaaagcagca 240 tgttagagat tgccggattt tctcaggtaa ggggtgttta tcgtcgttta atgggtatta 300 ttgattaaca tgtcatgggt agtgataaac cgttgaagtg accctaattg ggatgttgaa 360 tgctaaatat tgtgatgaat aagttgtatt aaagctgaaa ttgagtccgt aatggtgtga 420 gtcgtgttcc cccgaacgta tagcttttta cggaaattga atcggaggtc cggaagtcct 480 ccaacggcgg gaaatgcgga gaactctgca ttctgccttg tgttagcgca ggaactgctg 540 ttttggctgc gttaaccggt taacccaggg cgttaaccgg ttaacactgt tatattttgt 600 ggaaatgtgt tgttttgcct gcgttaaccg gttaacccag ggtgttaacc ggttaacact 660 gttgcgtttt gccagaaagt gtgttttgtc ctgcgttaac cggttaaccc agggcgttaa 720 ccggttaaca ctgttggaaa ttagaaaaat tggtatttta atgttgtgaa cataattggt 780 gattggccta ttatcgttaa tgttgatgag aaattttgtt cggttatgtt atggagtgtt 840 gatacaaata tgttgataag ttgtgttaaa gttgttgaaa atactgagtt gtaggcttgg 900 tgagccaaag ttgattataa gttgattcta ttgaaaacac tattatgttg ctattattat 960 tatgttgtcg acagtttaaa gtcgtgtatg ccatgtacat tcatatgcat taagtcggag 1020 ctttgctcac accacgttgg cctggattgg caaattttaa gttgaaagtt gaaggcttat 1080 gccttgatgc ccaataaaat ggcaatgatt ttaagttggg agttttactc cgaatggtac 1140 cacatgcatg acgagtcgag tctcattaga gttgcatttt gttggcttgt tgtatgaata 1200 tttaatttaa ttgaggagtg gaattgtgtt gatattaagt atgatgttta agttgatgtg 1260 ccgttactga atgtatgttg cgattagggt gatgaaatgt gtaaatttac ttagcattac 1320 atgatgattt ataatgctta ttatatcgat tgaggaactc acccttacaa ctatttttca 1380 ggtaacgagc aatgagttga gtagaagcta atgcttggag tctagtgtag tctcctaagt 1440 gggtcatgct ctgatagatg taacatcggg acgggatgtt tttaattgtt ttattgttgg 1500 ttgttgaatc attttacatg taatatgtta tatgttttga atggttgatt taatttctat 1560 ccgctgcgtg tgatgcaaga aatgtttatt ttgattgaat aaagagcatg acagttatta 1620 tggtgtgaaa tgttgtgtga cacccttgaa tgcatttatt tctgatcgaa aagttgtaac 1680 tttaattaaa taattggggt attttaggag ggtgttaaca 1720 // ID RAM4_LTR repbase; DNA; EDCOT; 707 BP. XX AC AC138014; XX DT 08-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A new long terminal repeat sequence from Medicago truncatula. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW RAM4_LTR. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-707 RA Shankar R. and Jurka J.; RT "RAM4: LTR retroposon from Barrel Medic."; RL Repbase Reports 6(11), 593-593 (2006). XX DR EMBL/GenBank/DDBJ; AC138014; Positions 100057 100763. XX CC A Copia-like long terminal repeat, flanking a large internal CC region. The flanking repeats share about 98% identity. XX SQ Sequence 707 BP; 240 A; 115 C; 117 G; 235 T; 0 other; tgttagccaa tatttgtgaa aatatgatca tttaatgcag tcaagggttt gaccaaaaaa 60 tgaggcgtag ctttgtggat ggaattcatc gaaaaggata taaatctact tcagcaggaa 120 tcgaagaata agtttttgtt caacgagtaa aggaagttgt cgacgcgcct tccaagtttt 180 tggatagagc caagcggtta gcaaacggct agttttcgaa cggctagttt cgatttgaat 240 cgaaagatag gattaggtag ttacaggact atctgtataa atagtagttt tttcttaaga 300 aaaagggtca caattcaatc atactaaaaa cttacactca atactgtccg tatggaagcg 360 acaaacgagt tacaagttgc aaagtatgaa tatgtgtacc aactttcctt aagtctttac 420 aaattcaata caatctttta aacacttttg caatttaagt cttgttttac taagtctttc 480 aaaacatttc ttttacatta cagttaatta caacatttcg attgaattca acacggattg 540 gattcgattc tttacatttt gttcttatct ttacaattat cgaaaatact ttacgaacaa 600 gtattactcc tattttcaat tagtaaaaac acaatatgct cctaagattt accggttgat 660 cttgcaagtt aacatcattg aaaccagcga ttgtttacca aaaatca 707 // ID Copia-81_Mad-I repbase; DNA; EDCOT; 4470 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-81_Mad_; KW Copia-81_Mad-LTR; Copia-81_Mad-I. XX NM Copia-81_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4470 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1700-1700 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1835-2332] - Integrase core CC LTRs are 92% similar to each other. XX FH Key Location/Qualifiers FT CDS join(152..1087,1091..2347) FT /product="Copia-81_Mad-I_1p" FT /translation="MATAANSSNSPSPPPANPNSPANLPHSDISNPSIMSI FT GSISIANVAGMVPTKLNRQNYITWRSLFIPVLKRFKLLGLVNGEDLCPPKF FT VRNSSGACVLNASFETWCERDQILMIWINSTLSEDLLPLTIGMEDSRSLWQ FT SLERRFSGASRTHVHSLRSKIQTIQKGDSSMTDFLNSIKDISDKLAAAGEP FT LSESDLVAYILSGLPDEYESFVDSIETRNESVTADELHGLLLSKEISLQKR FT KTRASSSSTAPFHAYAAQSATSGGNSNRGNSHGRFQNRNRYNQNRNFGGNK FT PNNWNNNNSSGILGAGPSRQFGQSSSSGRSVQCQLCLQYGHWAPTCNRLSQ FT FALNNFTQAPTAMSAMTSSAPPSYWLTDSGASHHVTPDPSALNSAIPYSGS FT DQLFVGDGKGLCISHTGSALIRTKNATFRLNDVLLVPQASHNLLSVYKFVY FT DNWCSLTFDPFGFYVKDLRTGKMLFQGPSEGGLYPFYWNASNGVSGIAISP FT TALMIAKADIHIWHRRLGHPSSGALHSVVHKNHLPVIGSVNNLSVCTACQL FT GKASRLPFSTLPCTSTRPLQLLHTDVWGPSPTSSCTGYRFYLIIVDDFTKY FT SWLYPLYFKSDVFSTLKTFILKIQTLLDFKVQSIRSDSGGEFLNKSLQGFL FT NDQGITHQLSCPHTPEQNGCAERKHRHVVEMGRTLLSQSGLPAKFWVEAFQ FT TAIYLINRLPPQSSVISPWELCFMLLPSITH" XX SQ Sequence 4470 BP; 1086 A; 1117 C; 826 G; 1440 T; 1 other; acatggtatc atcaccattg tctaaccgac tccgatccgg cgcttccctc cttcttgaaa 60 ctttcttgcg tttcttgaat tttcttacct cccaaacaga tcgctgcttc tctgatttct 120 tccttttccc ctcaattcag caaatcttga tatggcgact gctgcgaact cctccaattc 180 tccttctcca cctcctgcaa accctaattc cccagcgaat ctccctcaca gtgacatctc 240 caacccttcg atcatgtcga ttggatcgat ttccattgca aatgttgctg gaatggttcc 300 gacgaagctc aatcgtcaga actacatcac ttggcgcagt ctcttcatcc ctgtcctgaa 360 gcgtttcaag cttcttggac tcgtcaatgg cgaggatctg tgtcctccta aatttgttcg 420 caattcctct ggcgcttgtg ttctcaatgc ttcttttgag acctggtgtg agcgtgatca 480 gattctgatg atttggatca actctacact ttccgaagat cttcttccct tgaccattgg 540 catggaagac tctcgctctc tttggcaatc tcttgagcgg cgtttctctg gtgcttcccg 600 cacacatgtt cacagtcttc gatcgaagat ccaaacgatt cagaaaggtg actcttccat 660 gaccgacttt cttaattcga ttaaagatat ctctgataaa cttgctgctg ctggtgaacc 720 actgtctgaa tctgatctcg ttgcatacat tttatctggt cttcctgatg aatatgagtc 780 atttgttgac tctattgaga ctcgcaatga atctgtgact gctgatgaac ttcatggcct 840 cctattgagc aaagaaatct cactccaaaa acgcaaaacc agagcttctt cctcctccac 900 tgcaccattt catgcttatg ctgctcaatc tgccacttct ggtggtaact cgaacagagg 960 caactctcac ggtcgttttc aaaatcgaaa tcggtataat cagaatcgta attttggggg 1020 aaacaaacct aacaactgga acaacaacaa ctctagtggt attcttggtg ctggtccttc 1080 tcgccagamc tttggtcaat cctcctcctc tggtcgctct gttcaatgtc agttatgcct 1140 tcaatatggt cactgggctc ctacgtgcaa tcgtctctct caatttgccc tcaacaactt 1200 cactcaagct cctactgcaa tgtctgccat gacttcttct gcacctccta gctattggct 1260 cactgatagt ggtgcatctc atcatgtcac acctgatccc tccgcactca actctgccat 1320 tccctactct ggcagtgatc aactgtttgt tggtgatgga aaaggtctgt gcatttctca 1380 tactggttct gccctcattc gcacaaaaaa tgctactttt cgattgaatg atgttctttt 1440 agttcctcag gcatctcata acttgttatc tgtttacaag tttgtatatg acaattggtg 1500 ttctctgaca tttgatcctt ttgggttcta tgtcaaggac ctaagaactg ggaagatgct 1560 tttccagggc cccagtgaag gaggcttgta ccccttctac tggaatgctt caaatggtgt 1620 ctctgggatt gcaatctcac caactgctct gatgattgct aaggctgata tccatatttg 1680 gcatcgacgg cttggacatc cttctagtgg agctttacat tctgttgtgc ataagaatca 1740 tctccctgta attggttctg ttaataattt gtcagtgtgc actgcttgtc aattagggaa 1800 agcttctagg ctaccatttt ccactttacc ttgtacttcc actaggccac ttcaattgct 1860 ccacactgat gtatggggtc cctctcccac atcttcatgt actggttaca ggttctatct 1920 aataatagtg gatgatttta ctaaatatag ttggctctat cctctatatt tcaagtctga 1980 tgtcttctcc actctcaaga cttttatttt aaagattcaa actcttcttg acttcaaagt 2040 tcaaagtata aggtctgatt cagggggtga attcttgaat aagtcactcc aaggttttct 2100 taatgatcaa ggcatcaccc atcagttgag ttgccctcac actcctgagc aaaatgggtg 2160 tgcagagaga aagcatcgac atgttgttga aatgggcaga acattgttat ctcagagtgg 2220 tttacctgca aagttttggg ttgaagcttt tcaaactgct atctatctca ttaatcggtt 2280 gcctcctcag tcttctgtga tcagtccttg ggaactctgt ttcatgcttc tcccaagtat 2340 cacacactga agacttttgg atgtgcttgc tatccatggt tgcaacctat tcgagtgaca 2400 agttggattc caagagtaaa caatgtgtgt ttctgggtta tagcctgaat cacagtggct 2460 ataggtgctt ggatcctatc actaataggc tctacatctc aagacatgtg gtgtttgatg 2520 aatccttatt tccttacaag catctgtctt ctcaggtctc actcacagtc catgtgtcac 2580 ttcccctcca cctcctatgt ctctctcttc cattgccagt gtccatcctg agaaacaacc 2640 cacctgcagc tctccagagg cagcaatgca cctctccatc catatcttcg actgctgaac 2700 agaccctaca tcttcttcta tcagagtcca tacatactcc tccagcatct tccagccctg 2760 cagagtctcc acccttcatc ctccagctcc tgtcaatact catcctatga ttacaagagc 2820 aaaggcaggt attcataaac ccaaggtgtt cactgccact aaacaccaac ttccatccac 2880 tgttgattct cttacaaagt taccccctac tccatcaacc tttctccaag cctctaagca 2940 ttctcactgg atggaagcta tgcaatctga atttcaagca ttgcagtcca ctggaacttg 3000 ggaattggtt cctaataatt ccaattacaa ccttgtaggc tgcaaatggg tcttcaaagt 3060 taagcacaaa ccagatggta ccattgaaag gtacaaggca agacttgttg ccaaaggttt 3120 tcatcaacag gaaggtttgg atttctcaga aacctttagt cctgttgcaa agcctactac 3180 tatcaggatt ctactttcca ttgcagttaa ctatgattgg tttatacatc aattggatgt 3240 cagtaatgct ttccttcatg gtcatttaaa ggaagatgtt gtatatgatc cagcctcctg 3300 gttttgtgga tccttccaaa cctcatcatg tctgcaagct taggaaatca ctctatggtc 3360 ttaaacaggc tcctagagct tggtatgagg ctttctacaa tgctattctc tctctgggat 3420 ttagttcctc atactctgat accagtctct ttattaaaag agatacttcc attactttta 3480 tattggttta tgttgatgat ataatcatca ctggaagttc aaccactgag tgtcaatcca 3540 tcatctccaa gcttcaagct atgtttcctg tcaaggatct gggagatatt cattattttt 3600 taggcattga agttcacaga tcagccaagg gcttgtttat gcatcagtct aagtatgctt 3660 tagacttgct caaaaagaca gatatgcttg gagctaaacc ttgtgcaaca cctgtgtcta 3720 cttccaaact ggatcactca ggcactcttt tatctgatcc cacttcttat aggtccacag 3780 ttggtgcttt acaatatctt aacttggaca aggcctgatt tagcctttgc tgtcaatcaa 3840 gtttgtcaat atatgcattc tccaagaacc attcatctgc aggcagtcaa gcgcatcctg 3900 agatatctca agggcactgt tgattcagga ctttggttca ctaaaggcct caatgtctca 3960 ctgcttggtc tgatgcagat tgggcaggtt gccctgtgga tagaagatcc accagtggct 4020 attgtgtgtt cctaggccct aatctcatct cttggagtgc taagaaacaa gccacagtgg 4080 ctagatcatc aacagaggct gagtataggt ctcttgctaa tactgctgct gagataacct 4140 gggtgtgcaa gattctgcaa gatatatcct tccctttgct aaagacacct atcatctact 4200 gtgataacaa aagtgccatt gctcttgcat tcaatcctgt tttccatgct cgaactaagc 4260 atgttgaaat tgactatcac tacatccggg agaaagtttt acttggtcat attggtgtca 4320 acatgttgct tcccttcttc aaattgcaga catttttacc aagtctttgg ctgctgatcg 4380 atttgctgct cttacttcca agctctcagt tcgatcacct tccttcagct tgagggggtg 4440 tgttaagagt acaacctcac acagcagcaa 4470 // ID Copia20-PTR_I repbase; DNA; EDCOT; 4627 BP. XX AC scaffold_180; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia20-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4627 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4627 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 214-214 (2007). XX DR Genome; scaffold_180; Positions 426981 431607. XX CC Positions [2068-2595] - Integrase core CC 'CCTTT' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 518..1429 FT /product="Copia20-PTR_I_2p" FT /translation="MSSDKLDLFHIRLNGKNYSAWEFQFQLFVKGKELWGH FT INGSNPAPTDVDALSRWEIMDARVMTWILSSIEPHLVLNLRPYKTAAAMWN FT YLNKVYNQDNTARRFQLEYEMANFTQGSLSIEEYFSGFQNLWANYSDIVYA FT NVPTAALSAVQAVHDTSKRDQFLMKLRSDFETARSNLMNRHPVPSLDACLS FT ELLCEEQRIITQAAMEHRANVSAPVSVAYTAQGEIKVEICMLSNVLVVKVL FT VILLGIALRNSATTVRNMVISSLLVPFDLKGNKELLIMPPLVPLVLLHCLL FT PHLLFLFLLLQA" FT CDS 1459..4617 FT /product="Copia20-PTR_I_1p" FT /translation="MVQQMIISALSALGFSGNHKLLFKPWYLDSGASNHMT FT NTTVPLSNVRNYDGNLKISTVDGSSLPISVVGDLSPSLTDVFVSPYLSTNL FT ISVGQLVDNNCDVHFSHSGCVVQDQASGKMIAKGPKVGRLFPLHISHSTNI FT SSFPLLSFACNFIGSENKRWHKRLGHPNSDVLRTLINSGLLGHKTCSSLDL FT SFDCTSCKLGKSKVLPFPHHASRASKCFDIIHSDVWGIAPIVSHAHYKYFV FT TFIDDFSRFTWVYFLRAKAEVFSVFKRFLALLETQFSASIKVLRSDSGGEY FT MSNEFQGFLQSKGIISQRSCPSTPQQNGVAERKNRHLLDVVRTLLLESSVP FT PRFWCEALSTSVHLINRLPSPTLNNVSPFFKLFGHSPLYSDLRTFGCVCFV FT HLPAHERHKLIAQSVKCVFLGYAIPQKGYVCYDPHACRIRVSRNVIFFENQ FT YFFPSHVELPSAPLPLLPSFSDSTTMVERFRPGFVYERRRRHESDSTSLVP FT LSDLDPVPDSAPISTTLRRSTRLSRPPDWYGFFTPVSLVTTLSTISIPSCY FT KQAMKHTCWQNAMQAELQALEENHTWDIVPCPSTVKPIGSKWVFSVKLRSN FT GSLECYKARLIALGNKQEYGVDYEETFSPVAKMTTVRTILAIAASQSWQLH FT QMDVKNAFLHGDLHEEIYMKLPSGMITSSPHNVCKLRRSLYGLKQAPRAWF FT EKFRSTILSFSFIQSQYDPSLFFHISVSGIVLLLVYVDDIIITGTDCGLIT FT KLQQQLHATFHMKDLGQLTYFLGLEVHHRPNGIFVNQHKYIQDLITLAGLE FT DTSSVDTPMEVNVKYRKDEGDLLDDPTLYRSLVGSLIYLTTTRPDISYAVH FT QVSQFMSSPRHLHLAVVRRIIRYLRGSPNRGLFFPTGSSLQLVAYSDADWA FT GCPDTRRSTTGWCMFLGNALISWKCKKQDRVSKSSTEAEYRAMSTACSEIV FT WLRGLLEELGFPQVTSTPLHADNTSAIQIATNPVFHERTKHIEVDCHFIRN FT TLENQVISLPHISSDLQIADVFTKAMTRQRHQFLIGKLLLVDLPASI" XX SQ Sequence 4627 BP; 1081 A; 997 C; 877 G; 1672 T; 0 other; tggtatcaga gcttcttcca aatccttgct tgcctctgtc ttgaattttc ctttggctct 60 tgctgtagtt gccttactca tcttgggccc atctttttca tattactcct ggtggaaagt 120 gtgcaggcga gagagaagga gtggttgttg gatccttaat ttccaacttt gtgttattct 180 tgttttctct gctgctattc ttagttcttg gtttcaaaat ctgcaaatct gtcgtgcttt 240 tctggtgtta ttcttggcag cttcagatct tccttctttc gtggtgttct tggtattttc 300 agaatcattc ttcttcgttt cagatattgg gtttctagtg caactcttgg ctgtttcaga 360 tcttggtttt ctgctgctat tctcagtagt ttcagatcag tctttttgct gctattctca 420 gcaactcttg gcttcagaat ctggtgtgta tccctcttcc attgcactaa ttccctgtca 480 gtttcagttt caaaatctat ttcttttcag ctttatcatg tcttcggata agctagactt 540 gttccatatc cgtcttaatg ggaaaaatta ttctgcttgg gagtttcaat ttcaattatt 600 cgtcaaaggg aaagaactgt gggggcatat taatgggagt aatcctgcac ctacagatgt 660 cgatgctttg tctagatggg aaatcatgga tgctcgcgtt atgacctgga tccttagctc 720 aatagaacct catcttgttc tcaatttgag gccttataaa actgctgctg ctatgtggaa 780 ttatctaaat aaggtttata atcaggataa cacagctcgg cgttttcaat tagagtatga 840 gatggctaac ttcacacaag gaagtctctc tattgaggaa tacttttccg gttttcaaaa 900 tctttgggct aattattcag atattgttta tgctaatgtt cctactgcag ctctctctgc 960 tgttcaagca gtgcacgaca caagcaagag agatcaattc ttgatgaagc tccgttctga 1020 ttttgaaact gcacgctcta atttgatgaa tcggcatcct gtaccatctt tagatgcctg 1080 tttgagtgaa cttctttgtg aggagcagcg tatcataact caggcggcaa tggaacatag 1140 ggcaaatgtt agtgcacctg tttctgtggc ttatacagca cagggagaaa taaaggtaga 1200 aatatgcatg ttgtccaatg ttttagttgt aaaggttttg gtcatattgc tcgggattgc 1260 cctaagaaat tctgcaacta ctgtaagaaa catggtcata tcatctctgc ttgtcccatt 1320 tgacctgaaa ggaaacaagg aactgcttat catgcctcca ttggtgcctc tggttctgct 1380 gcattgccta ttgcctcacc tgttgttcct attcctactc ctacaggctt agcaaacccg 1440 aatacactta ctcctgaaat ggtacaacaa atgatcattt ctgctctttc tgctcttggg 1500 ttctcaggta atcataaact tctttttaag ccatggtatt tagactctgg tgcctccaac 1560 catatgacca atactaccgt tcctctttcc aatgtcagaa attatgatgg aaatctgaaa 1620 attagtaccg ttgatggcag ttctctgcct atcagtgttg ttggtgatct ttctccttct 1680 ttaactgatg tttttgtgtc tccttacctc tccacaaatc ttatttctgt tggtcaattg 1740 gttgataaca attgtgatgt tcatttctcc cattctggtt gtgttgtaca ggatcaagcg 1800 tcagggaaga tgatcgcgaa ggggcctaaa gtgggacgac tctttcctct tcatatttct 1860 cattccacca atatttctag ttttccttta ctttcctttg catgtaattt tattggttct 1920 gaaaataaga gatggcataa acgtttaggc catccaaact ctgatgtact tcgcactttg 1980 attaattctg gattattggg acataaaaca tgttcttctc ttgatctttc ttttgattgt 2040 acatcatgca aacttggcaa aagtaaagtt ttaccttttc ctcatcatgc atctcgtgcc 2100 tccaaatgtt ttgatattat tcatagtgat gtttggggga ttgcacctat tgtttctcat 2160 gctcattaca aatactttgt tactttcatt gatgacttta gtcgttttac gtgggtttac 2220 ttcctccgag ctaaagctga agttttttcg gtttttaagc gatttcttgc acttcttgaa 2280 actcaatttt ctgccagcat caaagtcttg cgctctgatt ctggtggtga atacatgtct 2340 aatgagtttc aaggctttct tcaaagcaaa ggaatcatct ctcaacgttc ttgtccttcg 2400 acaccacaac aaaatggtgt agctgagaga aaaaatcgtc accttcttga tgtagtaaga 2460 actcttttac ttgaatcatc tgttcctcct cgtttttggt gtgaagctct ttctacttca 2520 gttcatttga ttaatcgttt accttctcct acattaaata atgtttcccc tttctttaag 2580 ttatttggtc attctccttt atattctgat cttcgtacat ttggttgtgt ttgttttgtg 2640 catctccctg ctcatgaacg acataaactt attgctcaat ctgttaagtg tgtttttctt 2700 ggttatgcta tccctcaaaa gggttatgtt tgttatgatc ctcatgcttg tcgtatacgg 2760 gtttctagga atgtgatttt ctttgaaaat caatatttct ttccatctca tgttgaattg 2820 ccatctgcac ctttacctct tttgcctagt ttttctgatt ccacaacaat ggtggaaagg 2880 tttagacctg gttttgttta tgaaagacgt cgtcgacatg agtctgattc cacttctcta 2940 gtgccccttt ccgatcttga cccggtgcct gattctgctc ctatttctac cactcttcgt 3000 cggtctactc gtctttctcg accccctgat tggtatggat ttttcactcc tgtctctctt 3060 gtcactactt tatccactat ttccattccc tcttgttaca aacaggccat gaaacataca 3120 tgttggcaaa atgcaatgca agcagaactt caagcacttg aggagaatca tacttgggat 3180 attgttcctt gtccttctac agtcaaacct attggcagta aatgggtctt ctctgtaaaa 3240 ctacgttcta atgggtcttt agaatgttac aaagctcgcc tcatagctct gggtaacaag 3300 caggaatatg gggttgacta tgaggagaca ttttctcctg ttgctaaaat gaccacggtt 3360 cgaaccatct tagctattgc cgcttcacag tcatggcaac tgcatcaaat ggatgtgaag 3420 aatgcctttc ttcatggtga tctccatgaa gagatttaca tgaagctccc ctctggtatg 3480 attacttctt ctcctcacaa tgtctgtaaa ctaagacgtt ctttgtatgg gctcaaacag 3540 gctccccgag cttggtttga gaagtttcgc agtacaattc tttcattcag ttttatacaa 3600 agtcagtatg atccttctct cttcttccac atatccgtgt caggtatagt ccttctcctg 3660 gtttatgtgg atgatattat cattactggc actgactgtg gtttgattac taagcttcag 3720 cagcaattac atgcaacttt ccatatgaaa gatcttggcc agctcacata cttcttagga 3780 ttagaagttc atcaccgacc taatggtatt ttcgtgaatc agcataagta tattcaagat 3840 cttatcacct tggctggttt ggaagacact tcttctgttg atactcctat ggaagtaaat 3900 gtcaaataca gaaaagatga aggggactta ctagatgatc ctactctcta taggagcctg 3960 gttggaagtc ttatatactt gaccactact cgacctgata tatcctatgc tgtccatcag 4020 gtcagtcagt ttatgtcttc tcctcggcat ctccatcttg ctgtagttcg acgcatcatc 4080 cgctatcttc gaggctcacc taatcgtggt ttgttcttcc ctaccggctc ctctcttcaa 4140 cttgttgcct atagtgatgc tgattgggct gggtgtccgg atacacgtcg atctactacg 4200 ggttggtgta tgtttttagg taatgcctta atttcttgga aatgtaagaa acaagaccgt 4260 gtttctaaat cctccactga ggctgagtat cgtgccatgt ctactgcttg ttctgaaatt 4320 gtatggctgc gcggtcttct cgaagagctt gggtttcctc aggtcacctc taccccactt 4380 catgctgata atactagtgc tattcagatt gccaccaatc ctgttttcca tgaacgcacc 4440 aaacatattg aggttgattg tcattttatt cgcaacacct tggaaaatca ggtgatatct 4500 cttcctcaca tatcttccga tctccaaata gctgatgtct tcactaaagc tatgactcga 4560 cagcgacatc aatttcttat tggcaaattg ttgttggttg acttaccagc atcaatttga 4620 gggggga 4627 // ID COP10_LTR_MT repbase; DNA; EDCOT; 324 BP. XX AC . XX DT 01-JAN-2007 (Rel. 12.01, Created) DT 16-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of COP10_MT, LTR retroposon from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; COP10_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-324 RA Shankar R. and Jurka J.; RT "COP10_MT: A copia type LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 6-6 (2007). XX DR [1] (Consensus) XX CC The LTR sequence flanks a Copia type internal region having CC intact gag-pol polyprotein. XX SQ Sequence 324 BP; 112 A; 58 C; 37 G; 117 T; 0 other; tgaagaataa cacagatcat atggaaacac aaatgatcaa agataaagag aaggaacata 60 ctacacacta gtaacttgtg caacaaagtt aactaaactc ttagctagtt ttattgttct 120 aacaacctac aaagttagtt acaactagag ttacaatcat atatgtaaga ttcatattag 180 cttagtgtgc actatcttat gatacactat aaataaaggt tctcttgtaa tctctattca 240 ttcaatgaaa cccatagttt cttttccatt tttctctttc tgttattttc tctttctttt 300 ctgttacaat tcagtttctc aaca 324 // ID Copia-52_Mad-I repbase; DNA; EDCOT; 5431 BP. XX AC ACYM01039178; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-52_Mad-I; KW Copia-52_Mad-LTR; Copia-52_Mad_. XX NM Copia-52_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5431 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1322-1322 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01039178; Positions 451 5881. XX CC Positions [2606-3106] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(644..1507,1511..5428) FT /product="Copia-52_Mad-I_1p" FT /translation="MSSSNFKVDGILGMLTIKLKDDNFAKWAFQFQSVLRG FT YKLFGHFDGTTVCPSKYVVSIEAGVTKEISEVFVNWESTDMALLSLLLATL FT SDEAMEYVLGCRTAHEAWINLVDRYASVSKSRVNHLKTELHTIQKGTDTID FT KYLLRLKSIRDQLTAAGESISDNDIIIAGLAGLPKEYGVIRTVILARESSI FT TLKEFRAQLLGVEREIDGEITVLSQSLSAMYVQGSTSGSNGASSSNAQTHN FT HIPGNTGGIITAGSYGSTPPISESSLNNSLIQPNFQQPVYSAPPQQFQPFY FT SAPPLQPIMFPGQPYGYGFVGNSTEQNNSATQFNGGFQFGARGQSSNQYRG FT NNYRNNNTFRGRGYGSSNSRQSGHNSWSGNTNTRSNVVIECQICNKRGHTA FT VNCYQRNSNSSNSSFVIECQICGKRGHLALDCYQRNNYSFQGQSPPTSLSA FT MNAQQAPQFSPQDNWIVDSGASHHMTADINALTQVTPFEGSDKIIIGNGTG FT LSIHNIGSATIQTNNHLLLLNKILHVPRIARNLLLVKQLCADNKSWFICDE FT SQFFVQDKRTREIVYHGKSKPEELFHIPVVPQKRGVQVSSSNPAAYLGKAI FT KSEVWHQSLGHPTQEIMSSMLQKSKISGYIDDKHTICVPCIQGKMSRTPFP FT VRSNTCTFPFEKIHSDTWGPSPVKSLEGYRYYVTLIDEYTRYVWIFPMSNK FT SDVFTIFVRFYNFVLTQFGKHIKSLQTDGAGEYVSHRFTLFLAQKGIVQCI FT SCPYTPQQNGMAERKHRHIVETAITLLNTAGLTPEFWYFACAHSVFLINGM FT PCKTLLMCSPYQCLYQKVPDVQSLKIFGSAVFPWLRPYNANKLQARSAMCI FT FLGYSMGYKGVICFDLKTRKYIISRHVIFDESCFPAKLPQQHTVIDQHQQA FT SQQFMPVLIPVPVRHRGSISSTQLPDLVTSDTSGHNQPCTSEQGNVSISGS FT QDSDTVSSDHLTLSTPVDTPHLLPVLDPAQLQVVLPFTASSSSNNSDPNDV FT RPNGPQTRLQTGAISRQNYASFIASLPQLLSLQLMDSASEIQHMEQCHGGF FT SFLADISDVEEPKNFKSAVHKVQWQKAMQEEFDALKAQGTWKLVPPSSNQS FT VIGSKWVYKVKKNPDGSVSRFKARLVAQGFTQEHGIDYSETFSPVVRHTTV FT RIILALAAQFSWPLRQLDIKNAFLHGDLEDEVYMTQPQGFVDPQQPDHVCR FT LVKSLYGLKQAPRAWNSKFTSYLPSLGFTTSLSDTSLFIKVDDADINLLLL FT YVDDIILTGSNPTKVQSVINDLAGVFDLTNIGKLTYFLGIQVQYHTDGSLF FT LNQSKYAKELLKKAGMESCKPTSTPSKPHTQVLANERVLLTDPSQYRNVVG FT ALQYLTFTRPDLAYSVNMVCQYMTQPTDVHLHLVKRILRYVQGTVHCGLHY FT TKGSDFKLTAYSDSDWAADITTRRSISGFVVYLGSNPISWQSKKQSTVSRS FT STEAEYKALAHCAADVFWIRSVFKDIHQHLSTPPSLYCDNLSALALSSNPV FT FHSKIKHLDIDYHFVREKVQKGDIHVHYIPTDDQVAYVFTKGLHSPLFLKH FT CRHLGLGVLSSLQQTKLDSSMLSLRGE" XX SQ Sequence 5431 BP; 1499 A; 1042 C; 1147 G; 1743 T; 0 other; taatttctaa gagttaatat ggtatcatcg ccggctatgg gtaacttccg tcttcgatcc 60 taaggtgttc cgctgccagt gctatttcag agtcggtcgt ctgcggttca agatagggtg 120 actcaaaatc cgaggggttt cgtcagtgac gatcgtctgt ggtggaagat agggcgacta 180 aaaaatcgga ggggtttcgt ctgggttttc tgctattctt tttggtgatc aggttcttcg 240 tctttctgtg gctttctgaa ttcgacacat acttcttttc tgtcaattgg cgatctgggt 300 tgatttgtgt gctttgggat gtttgttttg ttaatctgtt gaagtttttg tggaagtgtc 360 attctttcat atatgcataa tcagtagtat cgttcttgtg gaagtgtcat tctttcacga 420 attcaagaaa gtgtcattct ttcttggtca agaatttggt agttcagaag aggttcttgt 480 ggaagtgtca ttctttcacg aattcaagaa agtgtcattc tttcttggtc aagaatttgg 540 tagttcatga gagtgtcatt ctttcctgtg tgtttcgatc ggagtgtcaa tctctatttt 600 ctaattccat ttggtacata gtgttggtgt gttgaagata gtcatgagtt cgtcaaattt 660 taaggttgat gggattttgg gtatgcttac cataaagctc aaagatgata attttgctaa 720 gtgggcgttt cagtttcaat cagttctaag agggtacaaa ttgtttggtc attttgatgg 780 cacaactgtg tgtccatcca agtatgttgt tagtatcgaa gctggggtta caaaagaaat 840 ttctgaggta ttcgtgaatt gggagtctac ggatatggca ttgttaagct tgttacttgc 900 tacactgtcc gatgaagcaa tggagtatgt gcttgggtgc aggactgctc atgaagcatg 960 gatcaatctt gttgatcgtt atgcgtccgt gtccaagtct agagtcaatc atcttaaaac 1020 ggaattgcac acgattcaga aaggcaccga tacaattgat aaatatcttt tgaggctgaa 1080 gagtataaga gaccaactga ctgctgcagg ggagtccatt tctgataatg atataatcat 1140 tgctggcctt gctggtttac ctaaggagta tggggttatt cgtacggtta tattagctag 1200 ggaatcttcg attaccttga aggaatttcg agcacagtta ttgggagttg aacgggaaat 1260 tgatggggag attactgttt tatctcaaag cctgtctgcc atgtatgttc aaggttctac 1320 ttccggttct aatggtgcat cctcctcaaa tgcacagact cataatcata ttcctggtaa 1380 tactgggggg ataattactg ctggatctta tggttccact cctccgattt cagaaagttc 1440 gctcaataat tcactcatcc aacccaattt tcagcagcca gtctattctg ctccacctca 1500 acagttttag cagccatttt attctgctcc acccttgcaa cctattatgt ttcctggcca 1560 gccgtatggc tatgggtttg ttgggaattc aactgaacaa aacaactctg caacacagtt 1620 taatggtgga tttcagtttg gggctcgagg acaaagtagc aaccagtatc gggggaacaa 1680 ttatagaaat aataacacct tcaggggtag aggatatggt tcaagcaatt ctcgacagag 1740 tggtcataat tcttggtccg gtaatactaa taccagatct aatgtggtaa tcgaatgtca 1800 aatctgtaac aaaaggggac atactgcagt taactgttac cagagaaaca gtaactcatc 1860 aaactcaagt tttgttattg agtgtcaaat ctgtggaaaa aggggacatt tagctcttga 1920 ttgctaccaa aggaacaact attcctttca aggtcagtct ccaccaacat ctctgtctgc 1980 tatgaatgct caacaggctc cacaattcag tcctcaagat aactggattg ttgattcagg 2040 ggcgtctcat catatgacgg ctgacatcaa tgctttgact caagttacac cttttgaggg 2100 gtccgataag ataatcattg gaaatggtac aggtttatca atacataata ttggttcagc 2160 aactatacaa accaataacc atttacttct tcttaacaaa atactacatg tccctcgtat 2220 tgctagaaat ctcttattgg ttaaacaatt atgtgctgac aataagagtt ggtttatatg 2280 tgatgaatct caattttttg tgcaggataa gaggacaagg gagatagtgt atcacggaaa 2340 gagtaagcct gaggagttat ttcacattcc ggtggttcca cagaaaagag gagtacaagt 2400 tagttcgagt aatccagcag catatttggg aaaagctata aagtctgagg tttggcacca 2460 gagcttggga catcctaccc aagaaatcat gtcttctatg ttacagaagt caaagatcag 2520 cggttatata gatgataaac atacgatttg tgtaccttgc attcaaggga aaatgtctag 2580 aactcccttc ccagttagat caaatacatg tacctttcca tttgagaaaa tacattcaga 2640 cacttggggt ccttctcctg tgaagtcctt agaaggatat aggtactatg taactctaat 2700 tgatgaatac acaagatatg tgtggatttt tccaatgagt aataaatcag atgtgtttac 2760 catatttgtt agattttata actttgtact tactcagttt ggcaaacata ttaagagttt 2820 gcaaacagat ggagcaggag agtatgtaag tcacagattt actttatttt tagctcagaa 2880 gggtatagtt cagtgtattt cctgccctta cactccacaa cagaatggca tggcagagag 2940 aaaacacagg catattgtgg aaacggctat cacattactt aatactgctg gtctaactcc 3000 tgagttttgg tattttgctt gtgcacattc agtttttttg atcaacggga tgccgtgtaa 3060 gactttatta atgtgttctc catatcaatg tttgtatcag aaagtacctg atgttcaatc 3120 actgaaaata tttggctccg cggtgtttcc ttggttgaga ccatataatg ccaacaagct 3180 acaggcaaga tcggctatgt gcatttttct aggttactcc atgggatata aaggagtcat 3240 ttgttttgat ttgaaaacta ggaaatacat catatctcgg catgtgatat ttgatgagtc 3300 ttgtttccct gcaaagctac cccaacaaca tactgtaata gaccaacatc aacaagcatc 3360 acagcagttt atgccagttc ttatccctgt tcctgttcga cacagaggat cgatttccag 3420 tacacagctc cctgatttag ttacttctga tacaagtggt cataatcagc cttgtacttc 3480 agaacaagga aatgtctcca tttctggttc tcaggatagt gatacagtgt catctgatca 3540 tcttactctt tccactccag ttgatacacc tcatttgctt cctgtcctcg accctgcaca 3600 attacaggta gttcttcctt tcactgcatc ttcttcatct aataattccg atcctaatga 3660 tgtgagacca aatggtcccc aaactagatt gcaaacaggt gcaatttcac gccagaacta 3720 tgccagtttt attgcctcat tgcctcagtt gctttcttta caactgatgg atagtgcttc 3780 tgagattcaa catatggagc aatgtcatgg tggtttctca tttctagccg atatatctga 3840 tgtggaggaa ccaaagaatt tcaaaagtgc agttcataaa gtacaatggc agaaggctat 3900 gcaggaagaa tttgatgccc tcaaagctca gggtacatgg aaattagtcc ccccttcatc 3960 taatcaatct gtcataggta gtaaatgggt atacaaagta aagaaaaatc ctgatggttc 4020 tgtttccaga ttcaaagctc ggttggtggc acaagggttt actcaagagc atgggatcga 4080 ctattctgaa acatttagtc cggtagttcg ccacactaca gtacggatta tccttgcatt 4140 agctgctcag tttagttggc cgttgagaca actagacatt aaaaatgcgt ttttgcatgg 4200 agatcttgaa gatgaggtat acatgacgca acctcaaggg tttgtggacc ctcaacagcc 4260 tgatcatgtt tgtcggttgg tgaagtctct atatggttta aagcaggcac ctagggcctg 4320 gaattctaaa ttcactagtt atctcccaag ccttggtttt acaacatcac tatctgatac 4380 aagcctgttt atcaaggtgg atgatgcaga cattaatcta ttactgttat acgtggatga 4440 tattattctc actggctcta atccaactaa ggtgcagtct gtgatcaatg acttagcagg 4500 tgtgtttgat ctcacgaaca taggcaaact cacatacttt ttgggaatac aggttcaata 4560 ccatactgat ggttctcttt ttctcaatca gtccaagtat gccaaggaat tgttaaagaa 4620 agcaggtatg gagtcttgta agccaacctc gactccgtct aagccacata ctcaagttct 4680 tgcaaatgaa agagtgttgc tgactgatcc gagtcaatat agaaatgttg tgggggctct 4740 tcagtattta accttcacaa gaccggatct tgcttattct gtgaatatgg tgtgtcaata 4800 tatgacccaa ccaaccgatg tccatttaca tttggttaaa cgaattcttc gatatgtcca 4860 agggactgtc cattgtggtt tgcactatac aaaaggttca gatttcaagc tcactgccta 4920 ttcggattcc gattgggcag ctgacataac tactagaaga tcaatatccg gtttcgttgt 4980 ttatcttgga tccaatccta tttcttggca gtcaaagaaa caatctactg tttctcgaag 5040 ttccactgag gcagaatata aagctttggc acattgtgca gctgatgtgt tttggattcg 5100 atctgtattc aaggacattc atcagcatct atccacacct ccttcactgt actgtgataa 5160 cctttctgct ttggcgttaa gttctaatcc agtgtttcac tctaagataa agcaccttga 5220 tattgactac cacttcgttc gggagaaggt tcaaaaagga gatatccatg tccattatat 5280 tccgaccgat gatcaagttg cctatgtgtt tactaaggga ttacacagtc cacttttctt 5340 aaaacattgc agacatcttg gtttgggcgt tttgtcatct ctacaacaaa ctaagcttga 5400 ttcctccatg cttagtttga ggggggagta a 5431 // ID Copia-35-LTR_VV repbase; DNA; EDCOT; 291 BP. XX AC CU459357; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-35_VV, LTR retrotransposon Ty1-copia like, long terminal DE repeat from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Wintz-B01; KW Copia-35-LTR_VV; Copia-35-I_VV; Copia-35_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-291 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL/GenBank/DDBJ; CU459357; Positions 76972 77262. XX CC LTR = 291 bp CC LTR are 99.3 % similar to each other. CC Direct flanking repeats = aaaac. XX SQ Sequence 291 BP; 86 A; 34 C; 55 G; 116 T; 0 other; tgtgggaaaa cgtgaattat ggttgtaaat taatgacttg tattttgctg tgtatagtaa 60 ttatgctagt ttaggagagt ttgtttgtaa cagccagaat tcctagaatt aggttaattt 120 agttagtttc ctattttgtt agagtatccc ataaatcatg ggatttgata tagcctagta 180 attagtttcc ttttctatag ctaagatttt tctgtataaa gctaatgtag ttttctgaga 240 aggaaggaga ataaaattat ttccacaatt ctgctctctc aatttacgtc a 291 // ID Copia-36_VV-I repbase; DNA; EDCOT; 4230 BP. XX AC chr1; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-36_VV_; KW Copia-36_VV-LTR; Copia-36_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4230 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr1; Positions 11070643 11074872. XX CC Positions [1707-2201] - Integrase core CC 'TATTT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(36..3134,3138..4214) FT /product="Copia-36_VV-I_1p" FT /translation="MEETSRTTSFLPVSFPHPVSSKLDNHNFLVWRKQILT FT TLRGHKLQHFLSETSVLPSEFLSSDDETQNHVNPKFQDWEQQDQLIMSWLL FT ASITDALLTRMVNCDTSAQVWKTLELYFATQVRAKVTQFKTQLHNTKKGDL FT SISDYLLKIRNVVDLLALVGHKISVKDHIDAIFEGLPQDYETFIISVNSRL FT DPYTVEEIEVLLLAQESRIEKNIKIADLSTPSLAHLITTNRNGSPHFNYRA FT STRNSNFRPPTHSGNGMQHFRGNFTQQGRGRHGRGSWKGNNKPQCQLCGRI FT GHVVMQCYYRFDQSFTGPSQLQGNRPQGNMAHLHQQLSENFFPGTSSVKPT FT TAEIIQDNNWYPDSGATHHLTPNLNNLLTKSQFPSSDEVFVGNGKGLPIHH FT IGHTSFSSSFIPSKTLALKQLLHVPEITKNLLSVSKFAADNHVFFEFHPTS FT CFVKDLSTRTVLMHGQLKGGLYVFDNTQLKLPLHNSSCFASTALPSKEPTV FT PASSTSPFTLWHNRLGHPSSHIVSLVLNKCNLPHLNKIPSLICSACCMGKI FT HKSPFLHSKSSYTKPLELIHTDLWGPISTPSSHGHQYYIHFIDAYSRFTWI FT YMLKHKSEAFQVFLHFKSQVELQLGHKIKAVQSDWGGEYRSFTQYLTSNGI FT IHRISCPYTHEQNGLAERKHRHIVEHGIALLAQASLPFKYWDEAFRTSVYL FT INRLPTPVLKNKSPLEVLFHQKPSYSQLKVFGCMCYPNLRPFNHHKLQFRS FT IPCTFLGYSLNHKGYKCLSPNGNILISRDVIFDEHAFPFAQRQSQKQTTSS FT FSSSSTSLPCQTSLPLMVLPSSTSCSTSSPTNPSIFPATSNHNVASQPPPS FT SAPPFPSHHMITRSKNGIFKPKAYLISTTPTSVPEALQLSHWKQAMTDEYL FT ALLRNNTWDLVPLPTDRKLIGYKWVFKVKENPDGTINKYKARLVAKGFHQI FT VGFDFNETFSPVVKPTTIRIVLTIALNLQWKVRQLDVNNAFLNGDLHEDIF FT MHQPQGFIDPVNPNHVCKLNKSLYGLKAPRAWFEKLHQALGILGFSSTKSD FT QSLFINITPTHSTYILVYVDDILITGNNDQFVQHVITQLNNQFALKDLGDI FT DYFLGIQVKHTSAGMHLSQAKYISNLLQKTKMLHVKPVPTPMVSNQSLSNS FT RSAPFSNTQLYRSTVGALQYATITRPDITYSVNRVCQFMQAPLTAHWKVVK FT RILRYQAGTLHHGLHLQHSSNSHLNITGFCDADWASDVDDRHSIIGYCLFL FT GPNLVSWHSRKQHTVSKSSTEAEYRSVATLVAEISWLQSLLRELNISSSTT FT PVIWCDNLSTVYLSANPILHARTKHIEIDLYFVPEKVLQKQIQIHHVPSSD FT QLADVFTKATPNSRFLTIRAKLSVNQSPP" XX SQ Sequence 4230 BP; 1205 A; 1160 C; 644 G; 1221 T; 0 other; tggtatcaga gcaggcttta gcttagttat ccaccatgga agaaacctca agaaccacca 60 gttttctccc agtttccttt ccccatccag tctcatccaa actagacaat cacaactttc 120 tggtttggcg aaaacagata ctcaccacat taagaggcca taagctgcaa cacttccttt 180 ctgaaacttc agttctaccc tcagagtttc tctcctcaga cgatgaaacc caaaatcatg 240 taaatcccaa attccaggat tgggaacaac aagatcagct tattatgtct tggcttcttg 300 catctataac tgatgctctt ctcactcgta tggtgaattg tgacacttca gcccaggtat 360 ggaaaaccct tgaactatac tttgctactc aagtgagagc caaagtaact caattcaaaa 420 cgcaattgca caacaccaag aagggagact tgtctatatc tgattacctc cttaaaatca 480 gaaatgtagt tgaccttctt gctctggttg gccacaagat ttctgtcaaa gatcacatag 540 atgcaatttt tgaaggtctc cctcaagatt atgaaacctt catcatctct gtcaattcca 600 gacttgatcc atacacagtt gaggaaattg aagttcttct tcttgctcaa gaaagccgta 660 ttgagaaaaa catcaagatt gcagaccttt ccactcctag cttggctcat ctcatcacaa 720 ctaacagaaa tggttctcca catttcaact acagagctag caccagaaac tcaaatttcc 780 gtccacctac acattctgga aatggaatgc aacactttcg tgggaatttc actcaacaag 840 gaagaggacg tcatggtcga ggctcctgga aaggcaacaa caaacctcaa tgtcaacttt 900 gtggaagaat tggtcatgtt gtcatgcagt gctactaccg atttgatcaa tctttcacag 960 gaccctcaca acttcaagga aatcgtccac agggaaacat ggctcatctt catcaacaac 1020 tatctgaaaa ttttttccca ggaacctcat cagtcaaacc aacaacagca gaaataatcc 1080 aagacaacaa ctggtaccct gattctggag ccactcatca ccttacacca aacctcaaca 1140 atctcctgac caaatcacag tttccttcat cagacgaagt cttcgtggga aatggtaagg 1200 gtctccctat tcatcacatt ggtcacacct cattttcatc atcattcatt ccctccaaaa 1260 cacttgcctt aaaacaactt ctccatgtac cagaaattac aaagaatctt cttagtgttt 1320 ctaagtttgc tgctgataat catgtgtttt ttgaatttca tcctacctct tgttttgtca 1380 aggatctttc cacccggaca gtcctcatgc acggccagct taagggggga ttatatgtgt 1440 tcgataacac acagctgaaa ctccctcttc acaactcttc atgctttgct tctacagctc 1500 tcccgtccaa ggaaccaaca gtacctgctt catctacatc tccctttaca ttgtggcata 1560 atagacttgg tcatccttcc tcacatatcg tttctcttgt actcaataaa tgtaatctcc 1620 cccaccttaa taaaattcca tctcttatct gttcagcctg ttgcatggga aaaattcata 1680 agtccccatt cttgcattca aaatcctcct acaccaaacc cttagaactt atacatactg 1740 acctatgggg gccaatatca acaccctcct cacatggaca tcaatactat attcacttca 1800 ttgatgccta ctcccgtttc acttggatct acatgcttaa acataagtct gaagcatttc 1860 aagtctttct tcacttcaag tctcaagttg aacttcaact aggccacaag atcaaagctg 1920 tgcaatctga ttggggtgga gaatatcgtt cattcactca ataccttacc tccaatggaa 1980 ttatccaccg tatttcatgt ccttatactc atgaacaaaa tggacttgct gaacgtaaac 2040 accgacacat tgtcgaacat ggcattgccc tccttgctca agcctctctt ccttttaaat 2100 actgggatga agcttttcgc accagtgttt atctcattaa tcgattgcct actccagttc 2160 tgaaaaacaa atctccctta gaagttctct tccaccaaaa accatcctat tctcagctca 2220 aagtctttgg ctgcatgtgc taccccaacc tccggccctt taaccaccac aagctgcaat 2280 tcaggtccat tccctgcaca ttccttggat atagtcttaa tcataagggc tataaatgtc 2340 tcagccctaa tggtaacata ttgatttccc gtgatgttat ctttgatgaa catgcctttc 2400 catttgccca gcggcagtcc caaaaacaga caacctcttc tttcagctct tcatccactt 2460 cccttccctg tcaaacctct ctcccactaa tggtcctccc ttcttcaacc tcttgttcaa 2520 cctcttctcc aaccaatcca tcaatatttc ctgccacctc taaccacaac gtagcatcac 2580 aacctccacc atcctctgcc cctccttttc ctagccatca tatgatcact cgatccaaaa 2640 atggcatctt taaaccaaag gcctatctca tttctacaac tcccacttca gtccctgaag 2700 ccctccaact tagccattgg aaacaggcca tgactgatga atatctcgct ctcctccgaa 2760 acaacacttg ggatcttgtt cctcttccca ctgatcgtaa attgatcggc tacaaatggg 2820 tgttcaaagt caaggagaat cctgatggaa ctataaacaa atacaaggcc cgtttagttg 2880 ctaagggttt tcatcagatt gttggatttg acttcaatga aacttttagt ccggttgtca 2940 aaccgactac cattcgcatt gttctcacta ttgctttaaa tctacaatgg aaagttcgac 3000 aattagatgt caataacgcc tttctcaatg gcgacctaca tgaagacata ttcatgcatc 3060 aacctcaagg ctttatcgac cctgttaacc caaaccatgt ctgcaagctc aataaatctc 3120 tttatggcct caaataggcc cctagagctt ggtttgaaaa gctacatcaa gcacttggca 3180 ttcttggttt ctcatccacc aaatcagatc aatctctatt tatcaacatc acacctactc 3240 actccactta cattctagta tatgtggatg atattcttat caccggcaac aatgatcaat 3300 ttgttcaaca tgtgatcact cagcttaaca accaatttgc tctcaaagat cttggagata 3360 ttgattactt tctgggtatc caagtcaagc atacatccgc tggaatgcac ttgtcacagg 3420 ccaagtatat ctccaatcta cttcaaaaaa ccaagatgct tcatgtcaag ccggttccta 3480 cacctatggt atctaatcag tccctatcca actctagaag tgctccattc agcaacactc 3540 aactctatag aagcactgtt ggtgccctcc agtatgccac catcacaagg ccagatatca 3600 cttatagtgt caatcgagtt tgccaattca tgcaagctcc tctgactgct cattggaagg 3660 ttgtcaagag aattctacgc taccaagctg gcactcttca ccatggactc catcttcagc 3720 acagctccaa ctcacacctc aacataacag gtttctgtga tgcagattgg gcatcagatg 3780 ttgatgaccg ccactccata ataggatatt gcctttttct tggtccaaac ttggtttcct 3840 ggcactcacg aaagcaacat acagtctcta agtcatccac cgaggcagaa tatcgaagtg 3900 tagctacctt agttgctgaa atttcttggt tgcagtctct cctcagagaa ttaaacatat 3960 cttcctccac aactccggtc atctggtgtg acaacctcag cacagtgtac ctttcggcta 4020 atcccattct tcatgctcgg actaagcaca tcgaaattga tctttatttt gtcccagaaa 4080 aagttcttca gaagcaaata caaatccatc atgtgccttc ctctgatcag ctggcagatg 4140 tcttcaccaa ggcaactcct aactccagat tcctcaccat acgtgccaaa ctcagtgtca 4200 accaaagtcc accctgagtt tgaggggggc 4230 // ID MUDRAV_MT repbase; DNA; EDCOT; 451 BP. XX AC . XX DT 24-NOV-2006 (Rel. 11.11, Created) DT 04-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW DNA transposon; Transposable Element; Nonautonomous; transposon; KW non-autonomous; Interspersed repeat; TSD; TIR; MUDRAV_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-451 RA Shankar R. and Jurka J.; RT "MUDRAV: A new putative non-autonomous DNA transposon from Barrel RT Medic."; RL Direct Submission to Repbase Update (24-NOV-2006). XX DR [1] (Consensus) XX CC This putative non-autonomous DNA transposon sequence lacking CC transposase domain. It has well conserved termini as well as TSD CC sites of 8 bp (TATATTTT). XX SQ Sequence 451 BP; 160 A; 81 C; 67 G; 143 T; 0 other; ggcttaatta cctttttggt cctctaacta tttaattggt atcagattgg tcctctaact 60 aaaaattgat ttatttcggt cctctaagtt tctcaccgtt actacattta gtcctttctg 120 ttagttttat tcaaataaac gttagggttt gtgttatgtg ggtacctgac ctcctgtttc 180 acacatacat atgaaccata acagttacca ataatatcag tcactattta atcataatac 240 cttaacaagg catatgacca aaatgatact aataaataaa gttagaggac ccacataaca 300 caaaccctaa cgtttatttg aataaaacta acagaaagga ctaaatgtag taacggtgag 360 aaacttagag gaccgaaata aatcaatttt tagttagagg accaatccga taccaattaa 420 atagttagag gaccaaaaag gtaatttagc c 451 // ID RAM13_LTR_MT repbase; DNA; EDCOT; 1155 BP. XX AC . XX DT 27-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE Long terminal repeat sequence of LTR retroposon, RAM13_MT, from DE Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR; retroposon; Interspersed element; internal region; KW RAM13_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1155 RA Shankar R. and Jurka J.; RT "RAM13_MT: LTR retroposon from Barrel Medic."; RL Repbase Reports 6(11), 591-591 (2006). XX DR [1] (Consensus) XX SQ Sequence 1155 BP; 386 A; 208 C; 181 G; 380 T; 0 other; tgatagaatt tttttggcaa gtgtaccaaa tactatcgaa gtagtaaaaa tatcgttccc 60 acgagtactg tgttaatctc aattcagcaa taaggttaat atttaggatg tgtaaattat 120 tttagtgcct gaggcagtag ttttggtttg cataaaatta aataaacaga atgtaaagat 180 agttttggaa agaataagag agagatgaga tcaggtcttt cgaatcatct atgttcccct 240 aattggtata ctgcacctat tcttatgaat gattttctag ttccacgata gtcaacaaaa 300 tagtcctaat caatcccttg agttaggacc ctcttctcaa actacaaccc ctaattactt 360 aggtggtcta ataatctttg aaggttttaa gaacgttaac ctaatatcac taataaagga 420 ttatccattc ctagactaac catgattatt agaacaattc aattctgtct aagtagaaat 480 ctatggtcag tagtcattca ttctcactaa atcatgttta tatttgatca ggatataaaa 540 agcattaaga acaattgaat tgaataaaaa ctagattgtc attcataata aatagagttt 600 cacaacatca tggttcaata agggttacaa agaatcatct cagacctaat ctctaagaga 660 tttagctact cataattgag tttacaaata gcataatcaa tagtggaatc aaaacataca 720 tgaactgata gaaggttgaa gaaatcgccc tcctagccgt ctttaggtct caaaatcgca 780 ctttgctctc tccaaatcgt aacccttgtc tttagaatag acttcagctt aaataggcac 840 agaatttcgc ctaaaatcat gccacgattt aagtaaatcg tgacacgatt ctccttgaat 900 tgcaaatcac tgaattaggg tttcctcaga tcgtgccacg attatgccat cgtgacacga 960 tttcttcaat gtcgaagctt gattttggtc ttttaaaatc gtgtcacgtt tttaccaaat 1020 ctcgacatga ttctcttctt tgtattttct tcagttttct actctttggc tgcataagtt 1080 gccttgtgaa ctccaatttg tgatcaaaat acatataaaa agactctaaa aatagcgaat 1140 gactgactgt catca 1155 // ID Copia9-PTR_LTR repbase; DNA; EDCOT; 281 BP. XX AC scaffold_750; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia9-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-281 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-281 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 295-295 (2007). XX DR Genome; scaffold_750; Positions 4007 4287. XX SQ Sequence 281 BP; 68 A; 51 C; 39 G; 123 T; 0 other; tgttgaatta tcattagttt taaagtttcc ctgttttaag cctatttctg ttatgttgaa 60 taattcctcc ttgtcttgag gaacaagatt gttttttctg ttacagtagc catgtaccac 120 gattatagga ttttaaatcg ttggttgtta ttcttttctt cttccagtgt aaggctattt 180 aatagccaca tcagttgctt aattatattg aacttcttcc atctcttgtg taatcaaacc 240 tgtcaaagct ctcaaagctc tttacttttc tttattctac a 281 // ID COPIA3-LTR_MT repbase; DNA; EDCOT; 1460 BP. XX AC . XX DT 23-MAY-2005 (Rel. 10.05, Created) DT 02-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE M. truncatula LTR sequence - a consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed repeat; copia-type; COPIA2-LTR_MT; COPIA3-LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1460 RA Gentles A. and Jurka J.; RT "M. truncatula LTR consensus COPIA3-LTR_MT."; RL Repbase Reports 5(5), 103-103 (2005). XX DR [1] (Consensus) XX CC There are 10 or more copies in M. truncatula with 97-98% CC similarity to the consensus. Flanked by 5 bp target CC site duplications. The corresponding internal sequence is not yet CC identified. XX SQ Sequence 1460 BP; 470 A; 271 C; 229 G; 488 T; 2 other; tgaagggatt ttaagagggg tttttcaaaa ttttataatc ctctttgcgg aagaaatccc 60 antgaaacgg atcttgatta aatcattaat cacaaatcaa acagaaactt aaacacttta 120 agattcatgt gtttacctct tgaagagcag aacctttgta gaagaaatat ttctgatcac 180 gagcaaagca aagcagcgat gcctctactc agtccacacg aacagaactt ctccgatgac 240 cggtgctagc caattccaac ggagattcag agagaacaag gtttagagag cggcggctag 300 ggtttcacaa cttttgtgaa ttaggttaag cactcacaaa aagggttagt aatgcttcaa 360 cacaagggtt ctattttttt atagaatcac ttgtgtggac aacaagacaa cacttaaata 420 caccgtacct tacggtgnac cgcgttttct ctattttttc ggtaaattaa ataataaagt 480 catatttaat tatttaatta ttaataagtc tcacttatta ttttataaat aagtctcact 540 tattatatta taaataagtc tcacttatta ttttataaat aagtcttact tatttattta 600 taactctcat ctatctgtcc tttgtgtgtg accctatagg ttcccgtaac gttggcaata 660 atattaaatc acatatttaa tattataaac agtgagcggt atctagcaac acatcactgc 720 tacccaagtg acgagaatgt catgtgatct gacgaaacct ttctgtgata atgatcatgt 780 gtataattac ccttttgccc tcatgtctat attgaacaca aggcatagac cgtgtcatcc 840 ttgtctagtt caatattggg cccgtagaca tttctcctgt tatgtaggag gggcaaattc 900 catctaggtc actcatgtcc ctcagcatga ttcatggagt acccatcaac caactttata 960 gtcatcctgt tacggacaac gtttgaatgg tgacaaagca ctcgactcca acatctaggg 1020 tacatagtgg tttcaggtcg aagggtggaa tacaccacta tcactatgag aatatcttat 1080 gacacttttc ataactttta ctatgtagta ttctcatggc ggatcaatcc aatataaata 1140 ttactcctaa tatttatatc tatgtgaaga cttgataact ctttatccat gatctgtgag 1200 atgtgatcat cagtctacct acataatagt ctctatgctt taatgatatc ccacttctca 1260 ataaagcttg actacggata ctttgagaat agtttcctta tgtttaatgg ggtctcacaa 1320 ttaagttaat tatacttaat gttccattaa acggactaac tattctaggg actttattat 1380 tttgaaacaa aacaaaatca ataaagaaat gccttgttat ttatatatat tcacaatata 1440 ttatttatta atcaatatca 1460 // ID DNA3-7_Mad repbase; DNA; EDCOT; 1144 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative non-autonomous Harbinger family DNA transposon from DE apple. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA3-7_Mad. XX NM DNA3-7_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1144 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1471-1471 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TSD is 3-bp long. TIR is 14-bp long. XX SQ Sequence 1144 BP; 297 A; 262 C; 257 G; 328 T; 0 other; ggcctcgttt ggcagctcgg actgtactga ctatttctgt cggataggat aaatagccac 60 cggatagtac tgactaaatt agtcgggcgt ttggtgcagt atcggactaa tgaccgtatt 120 atttatactg tgtttggtat tataccggat aggaggaatc aaacttaaaa taaaattaaa 180 aaaaaaaaac tgaaatcctc tcttttgttc ccagatctct ccgccgcaaa ccccccaaac 240 tccctccctc tctatccttt cttcttcttc cccgtctgct ccctgaacga aaccccacca 300 caaaggcagc aacaagaaac ccagcaaaac ccacctttca aattctcatc gtttttttcc 360 caatccttct cttttttttt ttagctacaa atcagcccag caaaagtact gaggaggact 420 gggttcgctg gaagaactga ggaggaagaa gaagaagaat acgatggaat ttgaaccata 480 accatttagt acaatgatat agtattattt tgaattcagc gaaccataac catttagcta 540 caaccgggtt cttcttcttc tttcttccct gtattcttct tcttcttctt caaatctttg 600 aatttcccaa tccttctctt tcttccccgt attcttcttc ttcttcttca aattccatcg 660 tttttttttt tagtttctgc tttgcaggtt cgccggcaaa ggaattgggt tttgggattt 720 gtgggaagga gggggaagaa caaagggagg ggaaacgaag aagaagatgt tcacctctgt 780 tgactgcgtg gtggtgggcg gtggaatcag tgggctctgc atcgctcagg tgctggctac 840 caagcacggc gacgccgttc cgattgtcat agtcacggag gctaaggacc aggtgggagg 900 caacatcatc accgtcgaga aggacggcta tgctggagca gagacacggc tgcgtctgga 960 gaggaaggac ccgactaaac tgtcccgtgg ttttggagag gataaacaag cgggtgttta 1020 ccgtataaag taggtgggac cggattgttt aatccggtgg ctatttaata caattggaca 1080 ccaaacaccg tactccgtat tattagtact atccgatgtc ttatacggtg tgccaaacgg 1140 ggcc 1144 // ID GmGYPSY10_LTR repbase; DNA; EDCOT; 982 BP. XX AC . XX DT 31-JUL-2008 (Rel. 13.07, Created) DT 31-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE Gypsy-like retrotransposon from Glycine max. XX KW Gypsy; LTR Retrotransposon; Transposable Element; consensus; KW soybean; GmGYPSY10; GmGYPSY10_I; GmGYPSY10_LTR. XX OS Glycine max OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; OC Glycine. XX RN [1] RP 1-982 RA Mogil L.S.; Laten,H.M.; RT "Intact, full-length transposable element consensus sequences in RT Glycine max assembled from robust collections of BAC-ends."; RL Repbase Reports 8(7), 686-686 (2008). XX DR [1] (Consensus) XX CC Complete consensus sequence based on alignment of 320 GSS entries CC with an average overlap density of 35 sequences (range: 17-48). XX SQ Sequence 982 BP; 254 A; 205 C; 190 G; 322 T; 11 other; tgcaatcctc cctaggaagg gaccartcac tagagccatg agcaagaggc tccaagagga 60 ttgggctaga gctgctgaag aaggccctag ggttctcatg aacctyaggg tagatttctg 120 agcccatggg ccaaggttgg gtccaattat ctttgtacat attagactag gatgtcatta 180 tatttggtcc ttgtatttag ggctccataw tgtaggtagg gtaccctaga aatataggat 240 ttttcagccc ttgtatttta gggcacctag actagttttt gtattagggg tagttttgta 300 atttcacatg cactaagtgr atatttgatg tgtgtgkttg gaaataaatt taattgaatt 360 ggtagaagcc caatccaatt aaattttaga gggggaggtg agcatttgct tactacaccc 420 cattgccaca tcatatagtc acactttgtg catgtccttc atgctttwca tgcctcatga 480 cacctaagca cacttagtgg agaatcttgg aattgatctt ggattagtgg gctgaaccat 540 aactaaaatt cactaatcat aattagtgaa attttggctc caaagtttgg ctccacaaat 600 tcaatttcaa attcaagtga aatttgaatt gawmaatttc cctccaattt tgtgtgacac 660 ttaggctata aatagaggtc atgtgtgtgc atttttttca actttgatca tttgaatatt 720 aaacttcaga tttcagagct cttttagagc acaaaatttc gtgctcttct ctycctctcc 780 cttcattcat ctccttcttc ctccaagctc ttatccatgg cctcctatgg tggtgagctt 840 cttctagact catcttctcc ttgaagtggc gtctcctctc tctcttcctt ctccattccg 900 ctgccattya tcttccaaga agcaaaggaa tccattgatg aagaagatcc taggcctaca 960 agctccaatg gagcttrcat ca 982 // ID Gypsy-18_Mad-I repbase; DNA; EDCOT; 6402 BP. XX AC ACYM01061902; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-18_Mad-I; KW Gypsy-18_Mad-LTR; Gypsy-18_Mad_. XX NM Gypsy-18_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6402 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1340-1340 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01061902; Positions 7694 1293. XX CC Positions [3461-3880] - Integrase core CC 'AAATT' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 1312..2922 FT /product="Gypsy-18_Mad-I_1p" FT /translation="MIADGGIVKSQGCCRHVQLTVGQYNCYTDLFVLPLGG FT CDVVLGVQWLATVSPVLWDFQSLTMEFQVGSQLFKLTHWAPSQSPIQDISV FT HHISKGRSTSNLGLLLYSLEVETSDTELTPSQYNELHTVLNKFEVVFTIPS FT TLPPSRTHDHRIPLLPGAKPPNIRPYHYGPLQKAEIEKAVQELLHSGFIRP FT SHSHFSFPVLLVKKKEGNWRLCMDYRELNGITIKDKYHIPLIDDLLDELFG FT ARYFSKLDLRSGYHQIRMHAEDVEKTAFRTHEGHYEFLVMPFGLTNAPASF FT QSLMNDIFKPYLRKFILVFFDDILVYSKTWEEHLSHLHQTLELLLQHQLYV FT KKSKCSFGQPQVEYLGHIVSGDGVATDPTKIQAILNWPAPRNVKELRGFLG FT LTGYYRKFVQNYGKICQPLYQLTKKDGFIWSEAAKSVFQELKRVMTSPKVL FT ALPDFSIPFVIKCDASANGVGAVLQQQGKPIAFSSKALGPKNQALSTYERE FT LIAVVHAIKKWQNYLQGQHFIIKTDHNSLKYFLNQRATTPF" XX SQ Sequence 6402 BP; 1862 A; 1265 C; 1395 G; 1871 T; 9 other; ttggtatcat cctttcgatc cttggcctcc ctcttgtatg cccggccaca ccaacaattc 60 tcgcatgtct acactggaat ctcgcctctc tgccgtggaa actgttctgg aagctcttct 120 tcagcagctt caggcagctt cggacgccag attcacttcc ctcgagccga aattcggcct 180 tctcttggag catctccatc gtgaccctgg cgtttccggc ggctctggat cttctgctgt 240 tccacctcct ccgggtccgg cgcagccgca tcatcctcct gacgacggcg aattccatta 300 tttagagact ccacgttttc cacgtcgcga ctcttttgac ggcggcgggt tcactccgcg 360 ccctcagtgg ccacaccgtt tggattttcc ccgtttcact gacggtgacg atccctctgc 420 ttggatctac aagactgagc agtactttgc ttattaccat acccccgatc atcagaaggt 480 cctgaccgcc tcttttcact ttgagaatga gccactgcaa tggttcagat ggcgtgattg 540 catccattcc acaccaactt ggaccgagtt taccactgca ttgtgctagg aatttggccc 600 ttctgaattc gaagactgca ccgaatcctt gttcaagctc aaacaaacag gtattctcaa 660 agattacata ctcgaattta ggcgactcgc taatcgaact actgatgttg gcccgattct 720 gctgaagagt tgttttatgg gtggattaaa acgtgaattg aagtatgatg ttaaattgct 780 gaaacctaat tcggtgcata aggccattgc tcttgcggtg caaattgatg ctaaattcat 840 ggatattaaa acagtgaccc acaaacagat cccttcagcc aaaccaaacc ctttccctac 900 ttccatcccg ggacggaacc gcgttcctgc tttgccttat aagaaattaa cacctgagga 960 ggttcagcgc aaaaaggaac agggtgagtg ttggttttgt aatgacaagt gggataaggg 1020 acataaatgt gctcataaac aactttttat gttggatata gtttctgatg atgaggatgg 1080 agttgatgaa ccaattgatt ttcctatgga gttacacaac atggcattga gtgagtgtgc 1140 cttttatggc agtagtgcca aaccttcggt tcaaactatg aaggtggaag ggttggttaa 1200 gaatcatact gttaaactac tgttagattc tggaagcacc cataatttca ttgactctag 1260 attagtcaag cacttggggt gtccagttca tccaacaagc ccttcgaggt gatgattgct 1320 gatgggggta tagtgaaaag tcaaggttgc tgtagacatg tgcagttgac agtaggacaa 1380 tataattgct acactgatct atttgtttta cctcttgggg gttgtgatgt tgtcctaggg 1440 gtccaatggc tagcaacagt aagtccagta ttgtgggatt ttcaatctct gactatggag 1500 tttcaagtgg gatctcagct atttaaattg actcattggg caccttcaca gtcccctata 1560 caagatattt cggtgcacca catcagtaaa gggagatcca cttcaaactt gggattatta 1620 ttatattctt tggaggttga aacaagtgac actgagctca ctccttccca atacaatgaa 1680 ctacacacgg ttttgaataa atttgaggtg gtttttacta ttccttccac attacctccc 1740 tcacggaccc acgaccatag gattccattg cttccaggag caaaaccccc caatatccgg 1800 ccttatcatt atggacctct acaaaaagct gaaattgaaa aagcagtcca ggaattgctg 1860 cactcgggtt ttatcagacc tagccatagt catttttcct ttcccgtctt actggttaag 1920 aagaaggaag gcaattggag attatgtatg gattacaggg agttgaatgg tatcaccatc 1980 aaagataaat atcatatccc actcatagat gacctgttag atgagctatt tggggctagg 2040 tacttctcca aactggattt aagatcgggt tatcatcaga ttcgaatgca tgcggaggat 2100 gtggagaaaa ctgcctttag gacccatgag ggacactatg aatttttggt gatgccattt 2160 ggccttacca atgccccagc aagttttcaa agcttgatga atgacatttt taaaccctat 2220 cttaggaaat ttatattggt attttttgat gacatattag tctatagtaa aacatgggag 2280 gagcacctat ctcatttgca ccagactttg gagttgttgt tgcagcacca attatatgtc 2340 aagaagtcta aatgctcttt tggtcaacca caggttgaat acttgggtca catagtttca 2400 ggtgatggag tggcaaccga tcccactaag atccaagcca ttttgaattg gccagcccct 2460 aggaatgtga aggagctgag gggttttttg gggttgacag gttactacag aaagtttgta 2520 caaaactatg gcaagatatg tcaacctttg taccaactca caaaaaaaga tgggttcata 2580 tggtctgagg cagcaaagtc agtttttcaa gaattaaaaa gggtcatgac atctcctaag 2640 gtgttagccc tacctgattt ctcaattcca tttgttataa aatgtgatgc ttcggcaaat 2700 ggggtaggag cagtcttaca gcaacaagga aaacccattg ctttctccag taaagctttg 2760 ggccccaaga atcaggctct gtccacttat gaaagagaac tcatagctgt ggtgcatgcc 2820 atcaagaaat ggcaaaatta cctccagggg caacatttca tcatcaaaac agatcacaat 2880 agtctgaaat attttttaaa tcaaagagct accactccat tttaacaaaa gtgggtttca 2940 aagctattgg gatatgatta taagattcaa tataaacaag gtgtggaaaa tgtggtggct 3000 gatgctttat caagggtacc taacgcccct atagtgccta caacccacag tgaagagtta 3060 gtggaatgtg tcactatcac atacccttac tttgggtggt tggatgattt gagaagacaa 3120 ttggaaaaag atgagtgggt taagcaaaag aaggaagaat tgagggctgc cacccacggc 3180 aacaatgtca ctccccactt atcaaagttc cacattgata atgggttctt aaaatacaaa 3240 gataggattg tgattggtcc tgattcaact tggagacaca agatctttga cgagcatcat 3300 tgcactccta tggcaggcca tgaaggtgtt caaaaaacct accacagatt gaaaataagt 3360 ttttattggg tggraatgaa aaaggacatt aaatcttggg tagctgaatg cagggtgtgc 3420 caaacagaat aagtatgaga ccttgtcacc accaggttta ctccagccac taccaatacc 3480 tgaacatgtg tggagggaca ttagcatgga ttttattagt ggcttactca actgcaaagg 3540 caagtctgtt attctagtgg ttgtggacat gttatcaaaa tatactcact tcattactct 3600 tggacaccct tacactgcaa ctatggtagc tcaggagttt gtagaacatg tgttcaagct 3660 gcatggcatg ccaacaacta tagtgagtga tagagacact atattcctca ataccttttg 3720 gaaggaattt ttcaaactta gtgggtctaa gttgtgtatg agttcgggat accatcctca 3780 gagtgatgga caaactgagg tggttaaccg gtgcttggaa acctatcttc ggtgcttcac 3840 aagttgccaa tgttggaaat gtgccctaaa gccaatcatg tgatgatact ttacggacat 3900 ttcacatgtt aaactaatct agtttaacat ataaagggca tagattattg tttgagccgt 3960 ctcatataaa tgttatatgc ttaaacgata aagtccaagg aatatgtgat tgggagaatg 4020 taatctaatg aagttagatt cttgagacca ttctttcgta gacacatcct aaacgttcct 4080 gatcatagga ttgccaattg ggcattgaca gtccgtcaag atcggtacgt actatgtctt 4140 ctctcaggga gagtgattag tctckartca ttggtgtgtg tgacatcaag acaagtrcgg 4200 taggtgctca atagagaatg agttcactga acgcgatcaa cgaagagttc tcatattcca 4260 tgtcacatga gaactcatgg ttgggataat gcaaagtagt cctttgacct gaggcatcat 4320 agttgtcttg tggttaagac cttgatcttt gattatgtca aagtcatccc accaggaggg 4380 tgtccacggc atcgttgggg tcaagccgct tagctatgga gacaartgaa tgcgcaacaa 4440 gggatctcta accttcaaac cgtttgaggg agaatactct ctgatatgat ttgaatctct 4500 ggccagagta tgaatgagat twgggaatgc gttcckaatc acattcaagg taatcatata 4560 agcacaagac acacattgga tagtagacat gagaaaataa actatcaaac caaacaatgt 4620 ggtcaagagt attagattag agaargaccg tattgcattt gtaatcccag actgaatagg 4680 ttctccacct cttctgatta gcttgggtaa ccatgacata cggctaggtg tcactcatgg 4740 tttgtggaag ccctaaacgt gtgtaatcac taaagggaga attgaaaata gtttcaattc 4800 acaatcgatg taaaatggtt ttaatcgccc actgcctcgc taaaaggaac ctaatggatc 4860 gtacaccgtg taaggtagag atggacgaaa taaatgaaat gagtaagatt aattgaatgg 4920 tttaattatt tatggcaagg attaattaat atgttaatta atcaaacgaa taagttcgtt 4980 aaagaccacg ggatagtttt ggaccttaag gcccaatggg cttcgaacgt caagcccatt 5040 aacttaagtt gtatgacaat ttaatgaata aagattcatt aaagcccaaa agcccaaaaa 5100 tccctaaatg gccggccata aggaatgaat tagggttttg gttatttagg tcacttaaag 5160 aagtgactat ataaatgact ttataactaa atattcatta agtaaaataa gggtttattt 5220 ttggggaaaa tgggtgagaa ttgtctctcc attttctctc taaagaggcc aacaccttgg 5280 aggtgattag ctagtcatct aatcctccaa ggtcactcat tcatcatcca atctctcctt 5340 ggtgtaraga cttagaggtt ctcaattttg ggaacttgga gaacctattc ttccatccaa 5400 atccatggat ctaagaagca aggaatgaag gcccctatct ctttgggtga ttagcctttg 5460 cttatgcaaa gaggaatcta caaaggtatt aatttcaact cactttgttt ttgagttgat 5520 tattggttca ccaatctact aggctttgaa tttcatggtc atgttttgtt tttgagtaca 5580 tacaagcatg attccgcctt ttaattgtta attgcatgct atatgatgtt gctcaaatga 5640 atatgtttta caaaataatt ccttcagcca acccaaaaag tggctctatt ggctcccatg 5700 ggctgaatgg agttataatt cttcagttca caattcatcc aagttctctc cttttgaaat 5760 tgtttacgga tttccccctc cacatattgc ttcttatgaa aatggcactg ccaagctaga 5820 tatagttgaa caaggattgt tggctaggga taatctatta gctatgctca agactaatct 5880 attggtggct caaaatagaa tgaaagctca agctgataag cacagaaggg aaaaagtgtt 5940 tgaagttgga gacttggttt atttgaaatt ggtaccctat caattgcaat ccctggctgc 6000 acatgcttat cataagttac atcccaggtt ttatggccct tatgaagttt tggagaggat 6060 tgggagtgta gcttacaaac tcaagcttcc tacagattct aagatacatc ctgtcttcca 6120 tgttagttgt ttgaagaagc atttgggccc aatggttagt cctctaacag ctctacctgt 6180 agtgacagaa gatgggttga agtctcagga accaatggag attctgcaaa gacgagttta 6240 caaaaaaggt gaaggggcgg gagtgcagct acttgttcaa tggaagggca gcaaggaaga 6300 agaggctaca tgggaagatt atgatgagtt ggctaagaaa ttcccagatt ttcctctgtg 6360 attacaacct tgtggacaag gtttatctga aggagtgggc aa 6402 // ID MuDR-N3_Mad repbase; DNA; EDCOT; 1396 BP. XX AC . XX DT 21-OCT-2010 (Rel. 15.1, Created) DT 21-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW MuDR-N3_Mad. XX NM MuDR-N3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1396 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1513-1513 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 570-bp long. XX SQ Sequence 1396 BP; 470 A; 222 C; 226 G; 478 T; 0 other; gagtaaactg tcgatttacc ccctgaactt tcacttaact ttcgatttcc cccctgaact 60 tttctattgg aaaattaagg actcaaacta atttttttag ccgatttgcc ccctaccgtt 120 agtttttcat atattccatc catatttctg ttaagtgaga ccatgtgcac aacatgtgag 180 ggtagttaag tcatttcact cttaaaaatg attaaaaaac tgaaaataaa taaaaaaaac 240 aaaactttcc ctctattttt tcccgctaat tcctatcctc aattttattt ttccctctca 300 ttcctatgca tgagaaatga catatggtgt tattgtcttc ataagtagct aagttagtct 360 ttttcttgaa gcatgtacta ccatttttat tttctctaac aaattaataa tttgacaaat 420 gctcatggtg ttattgtctc caaagcagtg cattaatata agaaacatgt tcataatact 480 cataaaaaaa tgctcaagat aattacatac ttttcataat gtcataataa tcccaataca 540 attccacaaa atgatcctta agaagttgga aaacataaca ccctcaacct tactcagcca 600 tcagaaatga aaataggttt aggtacaaga ttccaaccaa acgaggaagg ccatggaaag 660 tgtagttgat ctccacgtgt catatgtacg tttcgagcag aatgtttgtg ctcttgtttt 720 gataactaaa accttatttt gcttgtgttt ggttaagtgg aatgcccata ttttgtaatc 780 gagattctat gggttatata ccttatggat ggtaaaatct cttatgtttt ccaacttctt 840 aaggatcatt ttgtggaatt gtattgggat tattatgaca ttatgaaaag tatgtaatta 900 tcttgagcat tttttatgag tattatgaac atgtttctta tattaatgca ctgctttgga 960 gacaataaca ccatgagcat ttgtcaaatt attaatttgt tagagaaaat aaaaatggta 1020 gtacatgctt caagaaaaag actaacttag ctacttatga agacaataac accatatgtc 1080 atttctcatg cataggaatg agaggaaaaa taaaattgag gataggaatt agcgggaaaa 1140 aatagaggga aagttttgtt ttttttattt attttcagtt ttttaatcat ttttaagagt 1200 gaaatgactt aactaccctc acatgttgtg cacatggtct cacttaacag aaatatggat 1260 ggaatatatg aaaaactaac ggtagggggc aaatcggcta aaaaaattag tttgagtcct 1320 taattttcca atagaaaagt tcagggggaa atcgaaagct aagtgaaagt tcagggggta 1380 aatcgacagt ttactc 1396 // ID DNA9-6_Mad repbase; DNA; EDCOT; 399 BP. XX AC . XX DT 14-OCT-2010 (Rel. 15.1, Created) DT 14-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-6_Mad. XX NM DNA9-6_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-399 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1487-1487 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 197-bp long. TSD is 9-bp long. XX SQ Sequence 399 BP; 127 A; 76 C; 70 G; 126 T; 0 other; ggataatgct tgcattcccc cttaggggat gagctcattc ccccacttgc aaataacgta 60 tctcaccgta aaaatttcat aatcggaacc gttcaatctc ttaatcttca tttgaagatc 120 atccctacaa aaaattcatt gaatcgttta gtcatctaaa tgtatcaaat aaatcaacgg 180 ttcatcatga atatgctact tggtacctac accgttgatt tatttgatac atttggatga 240 ctaaacgata tccgattcga atgatttttt gtagggatga tcttcaaatg aagattaaga 300 gattgaacgg ttccgattat gaaatttcta cggtgaaaat acgttatttg caagtggaga 360 atgagctcat cccccaaagg gggaatgcaa gtattatcc 399 // ID MUMETRAV repbase; DNA; EDCOT; 752 BP. XX AC . XX DT 29-JAN-2007 (Rel. 12.01, Created) DT 29-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW transposon; Interspersed; terminal; Inverted; repeat; MUMETRAV. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-752 RA Shankar R. and Jurka J.; RT "MUMETRAV: A putative non autonomous DNA transposon from barrel RT medic."; RL Repbase Reports 7(1), 43-43 (2007). XX DR [1] (Consensus) XX CC The putative non-autonomous DNA transposon is present in the CC genome in high copy number with few complete copies. It lacks the CC transposase domain. It shows features of MuDr type transposons CC with 9 bp TSDs as well as long inverted repeats at termini. XX SQ Sequence 752 BP; 250 A; 132 C; 122 G; 248 T; 0 other; ggtggattct agggtgaggg ttcaattaag tccctcaccg gtgaagcaca aataaaacac 60 catttgattg aatcaatggt ccacattatt tgaaaataaa tatgagaaca tccatctttt 120 tccacacaca attatgtcca tatctctatc ctctccaact atttttccac gcatatcatc 180 tccaacttga gaagatgcag aactagtgtg tggttttgtt ttcgggttga caaaataagt 240 aaccattatg tttcagcaaa tcaatttcgc atcatttaac aaacaataac acatgattat 300 aatcgaattt tggatggtgg taccaaacca atccaagtcg aaagtccttt aacgttcatt 360 caatcaaata gattgcaact tctctgttca tagtagttat agaaatggaa atttaattaa 420 gtggttggtg aaatttaaac ctctattcta cctttgccat taaacccagt aaaaaaaaca 480 tataaacaac cataaatttc accatggtgt tgccaatttt tattgaggtt gattatcatc 540 acaacaagtt ctagtaaact tttctgcata tttgtggtga actaagaagg atccaaatga 600 gaaagagata gaggtaggat tgtgtgtgga aagaactaaa tgttcttatt tttattttca 660 aataatttgg accattgatt taatcaaatg gtattttttt tttgtggtcc actgatgagg 720 gacttagttg aaccctcacc ctagaatcca cc 752 // ID Copia-2_TC-LTR repbase; DNA; EDCOT; 172 BP. XX AC CACC01006997; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-2_TC_; KW Copia-2_TC-I; Copia-2_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-172 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01006997; Positions 13459 13288. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 172 BP; 44 A; 38 C; 27 G; 63 T; 0 other; tgtaactcct tataactacc aagtagctag taggctgtat atattgtttg gattatgaat 60 gaagtgtgtg cttttccttc attttgccaa tactctgttc gtccctgttc tactcaacct 120 aaaacagagg ctccctagca ggagccatat tttcatcctc tataatttat ca 172 // ID Copia-92_PTr-LTR repbase; DNA; EDCOT; 345 BP. XX AC . XX DT 22-DEC-2009 (Rel. 15.02, Created) DT 22-DEC-2009 (Rel. 15.02, Last updated, Version 2) XX DE Copia-type LTR retrotransposon: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Copia-92_PTr-I; Copia-92_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-345 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 169-169 (2010). XX DR [1] (Consensus) XX SQ Sequence 345 BP; 102 A; 60 C; 63 G; 120 T; 0 other; tgttgaaagt aaactgattt ctggaaatta gttgaaccgg tcgaccagtt gggaaccggt 60 caaccggttg agaagatcga ccggttcagt cggcagaata caattcctgt tcagattagg 120 attttcttgt attagtttaa ttccttgatt gtctaggact ttatgcctat aaaaaggctt 180 gtaattcagc attattaaag tacaaaaaga gagagaatag ctaagagagc ttagaaagaa 240 acacttaata aaagtattcc ttcctctcaa tcttcttctt gttcttgagt ttttggcttt 300 gcattgttat tttaatcttc taccacacct atttttcttc caaca 345 // ID L1-3_PTr repbase; DNA; EDCOT; 5227 BP. XX AC . XX DT 18-DEC-2009 (Rel. 15.02, Created) DT 18-DEC-2009 (Rel. 15.02, Last updated, Version 2) XX DE L1-type element - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-3_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-5227 RA Kojima K. and Jurka J.; RT "L1 elements from black cottonwood."; RL Repbase Reports 10(2), 159-159 (2010). XX DR [1] (Consensus) XX CC The consensus is not complete at its 5' end. XX FH Key Location/Qualifiers FT CDS 1..1332 FT /product="L1-3_PTr_1p" FT /translation="IKVPIKQRDGRSYKEVVNEKPVRNVTYQTSEEDREWL FT SRSLVGLFSNGTDYAKIKNKMLMTLHNMEGFRFLGASKAILTFKTQQDMQL FT AADEEKEFWGQYFEELRPWCITDKASDIFSWILISGLPIVAWNMECIKRLV FT GGDCKVLGYDLTSVSKGAISGLTILVGKPPTVSINGTVNLTIDKEKVEINI FT SEIKYEACTDLASLIYSXGVNQEFDSELDCTSSPSDPEIVATKEQPYMXAN FT KNSSFTDLEYVTEVIMMQCFSRCEAEKERDAHGYEAQVYFPEILDDYMIQD FT LTARGKWQTSTPTISNIPRKDKEKGTDNMSVMEEDQQSWPTSNLARSMTLR FT NGKQLGATKCHEGHRKAAISTDSNSSAGNEDSIDSCIRAVNQRLQLSQPPS FT DLPTACDEVGAMKEIGQKLGIEFGTTGESIEVTIQEAIDAEQDHWDRYVQ" FT CDS 1298..4114 FT /product="L1-3_PTr_2p" FT /note="This protein includes endonuclease and FT reverse transcriptase domains." FT /translation="MQNRTIGTGMSSRLLCICAWFYVPFMILSWNVCGLGS FT SSKRKAISKYIKDFNVIVCFIIETKLSCSDSMVSSLWHGQNIKWFSIEAQG FT RSGGLLAMWDEDLFRVDSIEYAGSWISLFGSFVDDAFDCVITGYYGAGSRA FT ERAASWLELTELKHAFSDYPWFLIGDFNETLSKTDRSSGLLDRRGASEFQT FT FIDGCELVEYPLVNHRFTWFRGGSMSRLDRAFAHTQCLSHFSSLKLIRLDH FT GLSDHCPLIVGKEQVNWGWKPFKCLDCWLMAPSFQNTLKVFWQEIVHDIPG FT DFQVIRRISALRLKLGQWNKTEFGNQDWALQNIQSSIRLLEDQAESGKISD FT SERKRLYELKGMQWKLCRYVESIWRQKARQSWLKLGDRNTRFFHISAKVRG FT CKNYIRQXIYNGKILSSPTEIKEGAKAYFSNIYSESLTSRPTMGNADFMKL FT SENQAAWLEREVTIEEVHLAIFSSEGSKAPGPDGFNFNFYKKFWELMKHDL FT FTMVLEFFRRGYLPKGINTSYIALIPKVAGSSSFNDYRPISLLNGLYKIIA FT KILATRLKXVMQSVVSPSQSAFIAGRNILDSVLIANEMLDSMKSRSCQGFL FT LKLDFRKAFDTVSWSYLNDVMGYMNFGARWRKWIMACVSTARLSVLINGSP FT TSEFTASCGLRQGDPLSPFLFCLAAEGISVLISRSLKMGALYGVXSAGTKY FT IHHLQFADDTLLFLPNDLQCLLNTKRMLRWFSLCSGLNVNFHKSSLVGVGV FT DGIYAEGISGVLRCRCDTLPIKYLGLPLGANPKRISTWKPVLSQIRGRLNS FT WKGRLLSMAGRAILIKSVISAIPLYYMSIFCIPKAVARKITAMQSRFLWGG FT SIDNRKIHRLLGKQWRKKKTGAVLVLGLYRQKTKLSSSSGFGNWEAMTKLV FT GQTSLRKNTDPVHKWGAPIQEKTLRDLARXXLYHY" XX SQ Sequence 5227 BP; 1452 A; 1000 C; 1255 G; 1508 T; 12 other; atcaaagttc caataaagca aagggatggg cgttcttaca aagaggtggt aaacgagaaa 60 ccagtaagga atgtcacata ccaaacaagt gaggaagatc gtgaatggct gagtcgtagt 120 ctggttgggc ttttttcaaa tggtackgat tatgctaaga ttaaaaacaa gatgttgatg 180 accttgcaca acatggaagg ctttcggttc ctaggggcgt caaaagcaat cctcaccttc 240 aaaacacaac aagatatgca gcttgcggca gatgaagaga aggaattttg gggacaatat 300 tttgaagagt taagaccctg gtgcatcacg gataaggcct ctgacatttt ctcttggata 360 cttatctctg gtctccccat tgtagcttgg aatatggaat gcattaaacg actagtgggg 420 ggagactgta aggtccttgg gtatgacttg acttctgtta gtaaaggagc tatatcgggg 480 ttaacaatct tggtaggcaa gccacccacg gtttctatta atggaacagt taatctcacg 540 atagataagg aaaaagtgga aattaacatc tcggagatta aatatgaggc ctgcacggat 600 ttggcctcgc tcatttactc cmttggggtt aatcaagagt ttgattctga gctggattgc 660 acttcatcac caagtgatcc tgagatagtg gctacaaagg agcaaccata tatgkctgca 720 aacaagaact cctcctttac ggacctagaa tatgtcacag aagtgattat gatgcagtgt 780 tttagcagat gtgaggcaga gaaagaaagg gatgcacacg gttatgaagc tcaggtttat 840 ttcccagaaa tcctggatga ttacatgatt caagatttga ctgcaagagg gaaatggcag 900 acatctaccc ctacgatttc taatattcct cgtaaagata aggaaaaagg aacagacaac 960 atgtctgtca tggaagaaga tcagcagagt tggcctacat cgaacctagc ccgcagcatg 1020 actctcagaa atggtaaaca gcttggtgcc accaaatgtc atgagggtca caggaaggca 1080 gccatttcaa ctgattcaaa tagtagtgct ggaaatgaag actcaatcga ctcttgcatc 1140 agagctgtca accaaagact ccaactatct cagcccccat cagacctccc tacagcttgt 1200 gatgaggttg gggctatgaa agaaattggc cagaaattgg gtattgaatt tggaacaact 1260 ggtgagagta ttgaagtcac gatacaagag gccatcgatg cagaacagga ccattgggac 1320 aggtatgtcc agtaggctat tatgcatctg tgcatggttt tatgttcctt ttatgattct 1380 tagctggaat gtgtgtgggt tgggatctag ttctaaaaga aaggccatta gcaagtacat 1440 taaggatttt aatgttattg tatgttttat tattgaaact aaactttcat gctcggactc 1500 tatggtctct agtctgtggc atggccagaa tattaaatgg ttcagcatag aggctcaggg 1560 tagatcaggt gggttgttag ccatgtggga tgaggatctc ttcagggtgg attcaattga 1620 atatgctggg agctggatta gcttatttgg ctcctttgtt gatgatgctt ttgattgtgt 1680 gatcactggg tattatggag ctggctctag agctgaaaga gcagcctcct ggttggaact 1740 tactgaactc aaacatgcat tttcggatta cccctggttt ttaataggtg actttaatga 1800 gaccttatcc aagacagata gaagcagtgg tctgctagac aggagagggg cttcagaatt 1860 ccaaactttc attgatggtt gtgaattggt agaatacccg ctggtgaatc atcggtttac 1920 ctggtttaga ggtggttcta tgagtaggct agatagagcc tttgctcaca cacaatgcct 1980 atctcacttt agttcattga agctgattag actggatcat ggtctctcgg atcattgccc 2040 cctgattgtt ggtaaggaac aagttaactg gggatggaag ccattcaaat gtctagactg 2100 ttggctcatg gcaccatctt tccaaaacac tctgaaggtc ttctggcagg aaattgtgca 2160 tgatatccct ggcgactttc aggtgatcag acgaattagt gctctgcgac tgaagctagg 2220 ccagtggaat aaaactgagt ttgggaatca ggactgggct ctgcaaaata tccagtcttc 2280 tattcggctc cttgaggatc aggctgaaag tggtaagatt tctgactcag aacgaaaaag 2340 gctatatgag ctgaagggaa tgcaatggaa actctgcaga tatgttgaat ccatatggag 2400 acaaaaggca agacagtctt ggctcaagct gggggacaga aacactcggt tctttcacat 2460 ctcagcaaaa gtcaggggat gcaaaaacta tattcgtcag mttatataca acgggaagat 2520 tctctccagt ccaactgaaa tcaaagaagg agccaaagca tatttctcaa acatctactc 2580 tgaatctctg acttcaagac ccacgatggg caatgcagac tttatgaagc tcagtgagaa 2640 ccaggctgcc tggcttgaaa gagaggttac catagaagag gttcacttgg ccatcttcag 2700 cagtgaaggc tccaaggccc caggacctga cggkttcaac ttcaattttt ataagaagtt 2760 ctgggagcta atgaaacatg acctgttcac aatggttctt gaattcttca ggagaggcta 2820 ccttcctaaa ggtattaaca ccagttatat tgctttaatt ccaaaagttg ctggcagctc 2880 ctcttttaat gactatagac ctattagttt attaaatggg ctatataaga ttattgctaa 2940 gattctcgcc actagactaa aagmagttat gcagagtgtg gttagtccct cccagtcagc 3000 tttcattgct ggcagaaaca tcctggactc agtccttatt gccaatgaaa tgctggattc 3060 catgaaatct cggagctgtc aaggtttcct tcttaaactt gatttcagaa aagcttttga 3120 cactgtgtcc tggtcctatc ttaatgatgt tatgggctac atgaattttg gtgctcgatg 3180 gaggaaatgg attatggcat gtgtctcgac tgcaagacta tcagttttaa tcaatggttc 3240 ccctacttct gagtttacag catcttgtgg tcttcggcag ggggatcccc tctccccttt 3300 tctcttttgt ttggctgctg aaggcatmtc agttctcatc agcaggagcc tgaaaatggg 3360 tgctctgtat ggcgtggant ctgcaggaac aaaatatatt catcatctgc aatttgcaga 3420 tgacactctt ctcttccttc caaatgatct tcaatgcttg ctaaatacca agagaatgtt 3480 acgatggttc agtttatgct cagggctcaa tgtcaacttc cataagagta gtttggtggg 3540 tgtgggggtg gatgggatat atgctgaagg gatttctggt gttctcaggt gcagatgtga 3600 tactcttcca atcaaatact tggggctccc tctaggtgct aatcccaaaa ggatttccac 3660 atggaaacct gttctctcac aaattagagg gcggctcaac tcttggaagg ggcggctatt 3720 atcaatggcg gggagagcaa ttttgatcaa aagtgtaatc tctgccattc ctctctatta 3780 catgtccatc ttctgcatcc caaaggcagt ggcccgtaag atcacagcca tgcagtctcg 3840 gtttttgtgg ggtgggagta ttgataacag gaaaattcac aggctgcttg ggaaacagtg 3900 gcgaaagaaa aagacagggg cggtcttggt gttgggacta tatcggcaaa aaacaaagct 3960 ctcctcttca agtggatttg gaaattggga agcaatgaca aagctagttg ggcagacttc 4020 attaaggaaa aatacagacc cagttcataa atggggtgcc ccaattcaag aaaaaactct 4080 cagggatttg gcgaggwatc wgctctacca ttactagtaa ggatcttgat agcwctctta 4140 ttcgagctgg ctgtaaactt aaaatgggta atggtaacca tgtwaacttt tggtcagata 4200 cttggttgac tggcttctgt ttagctaact cttatccggc tctcttccgc ctgtcctcct 4260 ccaaagcagg gattgttagt cagatgggat actggataga ggatacttgg tattggaatc 4320 tgaaatggat aaggcccctc agaactagtg agaacctgat gtttcaaaga ttaatgtctg 4380 atcttaatct tgcagttatt catcgattga aagaagacag gttgatttgg gaatggggga 4440 aggatggagg ctatactgta aactcttgta tgcttgccct tgaaaggatc aggtatgctg 4500 gttctaaaac ttatgtcaca gatgtttgga aatccatttg ccctccaaaa acagaaatga 4560 ctttatggct ggccttaaat gaaggccttt gcacaagagc cttcctggtg aagagacaca 4620 ttctaagccc tcaggaggac tggtgccctt tttgtgagca gcattcagaa actgtctccc 4680 acatcctcat gcattgccca gtggtctgga aactatggaa taaaattgta gcttggagag 4740 gtctgagctg ggtaatgccg tatgcccttg acgaccttca atgtcaatgg ctaggtcttc 4800 tgcagggcaa ccactgtaag tttgaaagat ctgtttgggg gggctttatg tttagcattg 4860 tctggactat atggaatgcc aggaacaact tgatatttga ggaaaaaaag ccaatctggg 4920 aagatatcct atggcatttg ttttactttg ctgcaggttg gatcaggaat ctgaactctt 4980 cattttggta taccggtgct gatctgtaca ggaatcacga atgcatttcg gcttggtctg 5040 cttaagttct gatttcgtgt ggttttgttt tgcttgctcc attagtaggg ttatatgttt 5100 ccttgtattt ctttcttgta attaggctga tgcctaggct acaacctatg tagctaaagc 5160 tctgctcaca ctgttcaggt tttctctttt tattatatat ctattctcga tttcaccaaa 5220 aaaaaaa 5227 // ID Helitron-N3_PTr repbase; DNA; EDCOT; 1693 BP. XX AC . XX DT 15-DEC-2009 (Rel. 15.02, Created) DT 17-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Helitron-type non-autonomous DNA transposon - consensus. XX KW Helitron; DNA transposon; Transposable Element; Nonautonomous; KW Helitron-N3_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1693 RA Kojima K. and Jurka J.; RT "Non-autonomous helitrons from black cottonwood."; RL Repbase Reports 10(2), 231-231 (2010). XX DR [1] (Consensus) XX CC ~83% identity to consensus. XX SQ Sequence 1693 BP; 358 A; 265 C; 310 G; 760 T; 0 other; tataaactaa aagaggtggt gcttttactg tgcaccacct cacaaaacac tattcatttc 60 aatagtgttt tttttttttc aaatctatat ttctttctct aatttcatac ttcaacattt 120 agtttattgg agattgagct tcataattta ttgtggtttg ctttatacgt ggttagctcg 180 gtctcataac ccgtgtcacg ggtttggcgg gttaactcgg ttgacttgag ttttttttaa 240 ttgatatttt ttttcaattt catccttcaa cattgggttg attgagaatt aggcttcatg 300 atttattttg gtttgctttc tatgaggtta tctcggtctc atgactcgag tcgcgggttt 360 ggcgggttaa cccagttgac tcgagttttt tttttttttt ttaattggta ttttttcaat 420 ttcatccttc agcattgagt tgattatgaa ttaggcttca tgatttattt tggtttgctt 480 tctatgaggt tatcccggtc ttatgactcg ggtcacgtgt tttgcgggtt aacccgtgta 540 gactcaggtc gttttattgt gtcctgtttt tagattgaat tttttttctt caatttcaac 600 ctttaacaat gagtttattg aaaattaggc ttcataattt gttttgattt gcttctatga 660 ctcagttatt tttttgttta ctttctatga ggttatcctg atctcatgac ccgggtcacg 720 agtttggcag gttaactcag gtcatttttt tttgttattt ttttttcaat ttcatccttc 780 aacatttggt tgatttggaa ttaggcttca taatttgttt tgatttgctt tatataaagt 840 tatcccggtc tcattacccg ggtcacagtt tggcgagtta acccgggttg acttgggtct 900 tttttgtttt tattttttta atttcatcct taaacattga gatttcttat ctcgagtcgc 960 gggtcaactc aggtttgttt gtcatttttt agtttaattt tttttcctaa tttatccttc 1020 aacatttggt tgatttggaa ttaggcttca tatttttttt tgctttctat gaggttatct 1080 cggtcttatt acatgggtca cgagtttggc tggttaacct gggttgactc aattttttta 1140 attgattttt ttttcaattt catccttcaa cattggattg attgagaatt gagcttcata 1200 atttgttttg atttgtttta tatagagtta tctcagtcac atgacccggg ttgcagcttt 1260 gacaggttaa cccgagttga cttgagttgt ttgttttttg gtctcttttt ttattgattt 1320 ttttttcaat ttcatccttt aacattggtt taattgggaa ttgagtttca tatttggttt 1380 tgatttgctt tctatggggt tatcccggtc ttatgatccg ggtcgtggat ttgacaggtt 1440 gacccgggtc gatccaatat gttttcatct caatattttt ttaaaaacat gtcgtcttga 1500 atttttttag tcaaactata tttttaacgg tttttcaggt tgtctttgga tccgtcaagt 1560 tgaccgggtc acatcaggtc aacccctaca tgttttaatt tttttctact agaaaacacg 1620 ttagtaacac ctagatattt tttgcattaa aaaaattaat ctgacctgca gcatagtgcg 1680 gacaacgatc tag 1693 // ID DNA-3-2_PTr repbase; DNA; EDCOT; 936 BP. XX AC . XX DT 09-DEC-2009 (Rel. 15.02, Created) DT 09-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Non-autonomous DNA transposon - consensus. XX KW DNA transposon; Transposable Element; Nonautonomous; TSD 3-bp; KW DNA-3-2_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-936 RA Bao W. and Jurka J.; RT "Non-autonomous DNA transposons from black cottonwood."; RL Repbase Reports 10(2), 193-193 (2010). XX DR [1] (Consensus) XX CC TSD is 3-bp long, TIR is not detectable. XX SQ Sequence 936 BP; 328 A; 173 C; 128 G; 307 T; 0 other; agagtccgtt tgtctacgcg gctgcggctg cggttgaaat aaaacgcagc aaatatatgt 60 ttggttacag aaaaaaacgt tgtttactgt tcatgggtcc caccttttac tgcgttgcaa 120 actcagtaat cgcgaagcag caggaggctg cttttgtttc aacagtaaac aatgggcaac 180 acatatttac gcactgtgca tgctaattaa ttagcatgca cagtgtaact tgcatacact 240 gtacactgta tgcatgttac actgttcatg ctaattaatt agcatgaaca gtgtaacatg 300 catacagttc cggttggacc ggttccggcc aaaccggttc cggttcaaag cttaaaatac 360 attgaaccag gtccaaccca gtaaaataaa aattattttt aattttttaa ttgtttttta 420 ttcgaaaaac tagtgtttaa cattatttaa tgacactaca taaattagac agagatcgct 480 tgataaagta gcatttgcag aatttgatcg caatcccaat ttcgttcttg attatatttt 540 acctgatgtt attgcgcgct taaaaaacca aaaaaactgt agtccttgtc ggatgtattt 600 catacgtgat ggaattgtag atattttaat ggaacaataa aaaatatttt atataaagta 660 ttatttattt catgatgtaa taacaaaagt taaatctaca atatttaaat taaaaactat 720 caatattaat atatattttt taaaattatt ttataacctc aatttcaaaa gcattattaa 780 ccaaacacat taaactactt tttcttcaac ctcaatttca accacagttt taaccaaaca 840 cctatttttt caaaccaacc tcaactaaaa gtacttttta taaaacaatt tttttcaaac 900 cacaaccaca acagctaccg caataccaaa cacact 936 // ID Gypsy-11_SL-I repbase; DNA; EDCOT; 6188 BP. XX AC AC243708; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the tomato genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-11_SL_; KW Gypsy-11_SL-LTR; Gypsy-11_SL-I. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-6188 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the tomato genome."; RL Direct Submission to RU (22-JAN-2011). XX DR Genome; AC243708; Positions 213468 219655. XX CC Positions [3982-4479] - Integrase core CC LTRs are 92% similar to each other. XX FH Key Location/Qualifiers FT CDS 1699..2625 FT /product="Gypsy-11_SL-I_2p" FT /translation="MASVMFDPGSTFSYVSSSFANGLNLHCELLDMPIRVS FT TPVGESVVVEKVYRSCLVNFVGSNTYVDLVILEMDDFDVILGMTWLSPQFA FT ILDCNAKMVTLAKPGTNPLVWEGDYTSNPVRIISFLRAKKMVSKGCLAFMA FT HLKDDTTQVPLIESVSVVREFSDVFPADLPGMPPDRDIDFCIDLELGTRPI FT SIPPYRMAPAELREIKAQLQELLSKGFIRPSASPWGAPVLFVKKKDGSFRM FT CIDYKQLNKITIKNKYPLPRIDDLFDQLQGACVFSKIDLRSGYHQLKIRAT FT DVPKTAFQRGMDITNLW" FT CDS 3412..5127 FT /product="Gypsy-11_SL-I_3p" FT /translation="MELLKDYDITILYHPGKANVVADALSRKAGSMGGLAH FT LQVSRRPLAREVQTLPNDMMRLEVNEKGGLLSSLESRSSFLDKIKGKQFND FT EKLMRIRDKVLKGEAKEAQIDEEGVLRMKGRVCVPRVDDLINTIMTEAHSS FT KYSIHPGATKMYRELKQLFWWGRMKRDIVDFIAKCQNCQQIKYEHQRPGGT FT LQRMPILEWKWERIAMDFVVGLPKTMGKYDSIWVIVDRLTKSAHFITVKVT FT YNAENLAKIYTSAIVRLHGVPLSIISDRGTQFTSMFWKTLHAELGTRLDLS FT TMFHPQTDGQSERTIQVLEDMLRACVIEFGGHWDSFLPLAEFSYNNRYHSS FT IDMAPFEALYGWRCRSPICWFDAFEIRSWGTDLLRDSIEKVKSIQEKLLAV FT QSRQKEYADRKVRQLEFMEGERVLLKVLPIKGVMRFGKRGKLSPRYIGPFE FT VLKRVGEVAYELALPPGLSGVHPVFHVSILKRYHGDGNYIIRWDSVLLDEN FT LSYEEEPVAILDREVRKLRSREIASIKVRWRNRPVEEATWEKEADMREKYP FT HLFTDSGTPFRPCFPSCDHSGTNDG" XX SQ Sequence 6188 BP; 1740 A; 1085 C; 1605 G; 1758 T; 0 other; aacttagtat cagagcatta ggttcgttgg tctcatcaca caagaacagg tctagtagag 60 tcttaagtaa cggtaggggg acgcctttac ttttccttga gagggtataa gactttagga 120 aaattttact ctttcattct ttctttcgtg ctactacttg ggtccaatta gtatctaggt 180 gatacaaatt ggtatctgac catcttcact ctatttcgca gatggttaga actagaggaa 240 cgactacgcc agcaccaaca ccaacacaag caaggcacga tataactgag ccagccactg 300 gggctgtggc tcgagaaaga gcaaggtcgt gggaggacgt cctctagagg aagaggacaa 360 acaccaagcc catctgatac tatggcagtg agtcctccac cgactgagga ggtgataaga 420 gaaggggagg atggggaaaa tgaacaagtg cagaatgagg gattgccacc tctgcctacc 480 ccagagatga tcaatcaggt tctcgcctat ctcagtgggt tgtctgatca aggtcaggca 540 cctccagtgt tttctgcgcc aacacctccg gtttcagaag tacaacatgc agccactatg 600 gctcctcgta tggaagcctc atttgacata ggcacctttc cacgtctgac taatgggcct 660 ataatgacaa ctgatcaaca tgaacttttc agtatgttct tgaaactgaa acctccggtc 720 ttcaagggtg ctgaatcgga ggatgcttat gattttctgg ttgactgtca cgagctacta 780 cataagatgg gtatagtaga acggtttggt gtggagtttg tgacttatca gtttcaaggg 840 aacgccaaaa tgtggtggcg gtcacatatt gagtgtcaac caacagaggc accacctatg 900 acttgggcct cattctctaa cttgtttatg gagaagtata tcccccggat gttgagggat 960 aggaaaaggg ataagttctt gagcctagag caaggtagga tatcggtcaa tgcatatgag 1020 gctaagttcc gtgcactatc cagatatgcc acccaacttt gcttcagtcc acaagagcgg 1080 atttgtcgtt ttgtgaaggg gttgaggtca gagttgcgga tttcagcctt acaggtagcg 1140 gctacagcaa aatccttcca agaagtggta gatttcgtgg tagaggtgga aggtgtgaag 1200 ctagatgaat tcaccatggc atagacatca aagaggtttc gaaagggagg tgagtttaat 1260 ggttcttact ctagaggata gggttcctga ggttacgcag ttcgacccat tcagtcttca 1320 ctacagactg tagttggggg tccacctccg accgatcaac acttctctaa gagacctatg 1380 catgaaccca gagagtgcta tggatgtgga gagattggtc atattaagag atattgtcca 1440 aaaaagagtt acagacctcc aaatgttaga ggtagaggtg gtcatggtag aggccgttat 1500 tcaagaggac gtggtggacg aggtaatggt ggccaccaga acggctgagg tgatgggcaa 1560 cctgtagcaa ctaaatcaca acatggtagg ggcaacggac agacgggtga gagggcccat 1620 tgctacgctt tccctaggag atctgaagcg gaggcatctg atgctgtcat cacaggtaat 1680 cttctggttt atgattgcat ggcttctgtt atgtttgatc ctggatccac tttttcttat 1740 gtatcttcct catttgctaa tggtctaaat ttacattgtg aattacttga tatgccaatt 1800 cgtgtttcta ctccggtggg tgagtctgtg gtagttgaaa aggtatatag gtcctgtttg 1860 gtgaactttg tggggagcaa cacttatgta gatttggtta tcttagaaat ggatgatttt 1920 gatgtaattc tgggtatgac ttggctttct ccgcaatttg cgatcttgga ttgtaatgct 1980 aaaatggtga cgttagccaa gcctgggaca aatccgttag tgtgggaggg tgactacact 2040 tccaatccgg tgcgtatcat ctcctttctt cgtgctaaga aaatggttag taaagggtgt 2100 ttagctttca tggcacatct caaggatgac actacccaag tacctttgat tgagtcggtt 2160 tcggtagtcc gcgagttttc ggatgtgttc cctgcagatc ttcctggtat gccaccagat 2220 agggatattg acttctgtat cgatcttgaa ctgggcacac gccctatttc tataccccct 2280 tatagaatgg ctccagcaga gttaagggag ataaaggccc aacttcaaga gttgttgagc 2340 aaaggcttca ttagaccaag tgcatctcct tggggtgctc cagttttgtt tgtgaagaag 2400 aaggatggga gttttcggat gtgcatagac tacaaacaac tgaataagat aactattaag 2460 aacaagtatc ctcttcctcg cattgatgac ttgttcgatc aattacaagg tgcttgtgtc 2520 ttctctaaga ttgacttgag atctggttat catcaattga aaatacgggc aacggatgtg 2580 ccaaagactg cttttcaacg aggtatggac attacaaatt tgtggtgatg tcttttggtc 2640 ttacgaatgc ccctgctgca ttcatgagct tgatgaacgg gatttttaag acatttggac 2700 ctcttcgtga tcgtacttat tgatgatata ttggtgtact caaagagcaa gaaggaacat 2760 gaagagcatt tgagaatggt attggaaatg ttgagggaga aaaagcttta tgccaagttc 2820 tctaagtgcg agttttggct agatgcagtg tccttcttgg ggcacgtggt ttctaacgag 2880 ggagtgatgg tggatccttc caagattgag acagtgaaga attgggtaag acctactaat 2940 gtgtcagaaa taaggagctt tgttgggtta gctagctact accgtcgatt tgtcaaggga 3000 ttctcttcta ttgcttccca attgatgaac ttgactaagc agaatgttcc atttgtatgg 3060 tcagacgaat gtgaggaaag ctttcagaag ctcaagacct tgttgactac cgcacctatc 3120 cttaccttgc cagtagaggg taagaacttc attgtttatt gtgatgcatt ctattcttgt 3180 ttgggtgcag tactgatgca agagaagagt gtgattgctt atgctttaag gcaattaaag 3240 gtgcatgaac gtaactatcc gacccacaat ttggaattgg ctgcggtagt gtttgtatta 3300 aagcaatgga gacactattt atatagggtt aagtgtgagg tctacacgga tcatcgtagc 3360 ctttagtatg tctttactca gaaagatttg aacttaagac agaggagatg gatggagtta 3420 ttaaaggact acgatatcac tatcttgtat catccgggaa aagcgaatgt tgtggcagat 3480 gctttaagta gaaaagcggg aagcatgggg ggtctagctc acttgcaagt ttctagacgt 3540 ccattggcta gagaggttca gactctgcct aacgacatga tgaggttaga ggtaaatgag 3600 aagggaggat tgttgtctag tctggagtca aggtcttctt ttcttgacaa gattaaggga 3660 aaacagttta atgatgaaaa attgatgcgg atccgagata aagtgttgaa aggagaggct 3720 aaggaagcac aaatcgatga ggaaggtgtt ttgagaatga agggaagggt atgtgtaccc 3780 cgagttgatg atttgattaa cactattatg acagaggctc atagttcaaa gtattcgata 3840 catccgggtg caaccaagat gtaccgtgaa ctaaagcaac tcttttggtg gggtagaatg 3900 aagcgtgata ttgttgattt tattgccaaa tgtcaaaact gtcaacaaat aaagtatgaa 3960 caccaaaggc ccggaggaac acttcagaga atgcccattc tggaatggaa atgggagaga 4020 atcgcaatgg acttcgtggt tggtcttcca aagacaatgg gtaagtatga ctctatttgg 4080 gtgattgttg acaggttaac taagtctgct catttcatta cggtcaaggt gacttacaat 4140 gcagagaact tagccaaaat ctatacctca gcaattgttc ggttgcatgg ggttccactc 4200 tccatcatat cagatagagg tacgcagttt acttctatgt tttggaaaac attgcatgcg 4260 gaattgggta ctagattgga ccttagtacc atgttccatc ctcagaccga tggtcagtct 4320 gagcgaacga ttcaagtgtt ggaggatatg cttcgtgcat gtgtgataga gtttggcggc 4380 cattgggata gcttcttacc cttagcggag ttttcataca ataatagata tcactcaagc 4440 attgatatgg ctccatttga agcattgtat ggttggagat gtaggtctcc catttgttgg 4500 tttgatgcat ttgagattag gtcttggggt actgaccttt tgagggattc gatagagaaa 4560 gttaagtcta ttcaagaaaa gcttctagcg gtgcaaagta gacaaaaaga atatgcagat 4620 cgaaaggtta gacagttaga gttcatggag ggagaacgag tcttgctgaa ggttttgccc 4680 attaaagggg tgatgaggtt tggtaaaagg ggcaaactaa gtccaaggta cattggacca 4740 tttgaagtac ttaagcgagt aggagaggtg gcttatgagt tagccttgcc tccagggctg 4800 tccggagtac atccggtatt ccatgtgtcg atattgaaaa gataccatgg ggatggaaac 4860 tacattatcc gttgggattc agttttgctt gatgagaact tgtcttatga ggaggaacct 4920 gttgccattc tagatagaga agttcgcaag ttgagatcaa gggagattgc atcaatcaaa 4980 gttcgatgga ggaatcgacc cgttgaagaa gccacttggg agaaggaggc ggatatgcga 5040 gaaaaatacc cacatctgtt tacagattca ggtactcctt ttcgcccttg ttttccttct 5100 tgtgatcatt cggggacgaa cgatgggtaa attggtatct attgaaatga cctgtttagt 5160 cgttttgagc agcagatttc aattctggaa aaacaggctg aggcgatgga cccaacgatg 5220 gaccctcatg ggcacgacgg accatcgcag ggcctcgttt caaaacactt agaaaaactg 5280 aaaattgggt actgaaaatc gactctctga acttcgtaac gaaatggcag gacggaccgt 5340 cacaggtgtg acggaccgtc acagaccctt ggtggaaatt taggtctttg aactttgcga 5400 cgacctgcag gacggaccgt cgcaggcacg acggcccgtc acaggttgcg caatcccagt 5460 ccgagtcgga tttctttata tgttttaagg gacgtttttg actattcctg ccttaattat 5520 aaagttagtg ggttaatgtt aataagtcta attacttggg ggttaaaaga gttaacattt 5580 agttaattag tgggttatta ttgccatctt ttattcttaa ttatatgtta attagggtaa 5640 aagaaagagg gttggaataa gaaaaataag aaagaacaaa gagagacaga aaaagaaaga 5700 gaacgagtag agagagagag aaacgaagag gatagcaagg attctgagaa gatagcttgt 5760 tgatcgcaat tcttcggtgg aggtaggtta tggttttcat gccattcgta gtaaactctt 5820 aatagcgaat gatatgtgtt agtagtattg tgaaccttct atatgcttaa ttgtatgctt 5880 gcatgaatga tgtgattatg ttattatgaa taaataagca tgatgaagct attgaatccc 5940 aaatcttgaa aagaaaccct aatctacttt gttaatgatg atgccttggt ataaaagaag 6000 gcttgatgaa tgaaagtagt gagataaggg gatcgggtgc cacgttctgg taccaggata 6060 gtatatgagg atcgaagtgt cacgttgcga caccaggata gaatatggat cgggtgccac 6120 attccggtac caggatagaa tatggatcgg gtgtcacgtt ctgacaccag gatagaatat 6180 ggatcggg 6188 // ID Copia47-PTR_LTR repbase; DNA; EDCOT; 197 BP. XX AC LG_XVIII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia47-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-197 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-197 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 273-273 (2007). XX DR Genome; LG_XVIII; Positions 10474322 10474126. XX SQ Sequence 197 BP; 67 A; 24 C; 43 G; 63 T; 0 other; tgttagcata ggcagtagtt gttattgata gaaatacagc tgaaatagga gtgtaattat 60 aggataagta tcttcctata atttaggcct aaattatagg aatgtgatgt aaatcaggat 120 tgatgtaaat caggattcct tcctatttaa gggacgggac tctcatgtaa agaggtattc 180 attcagccaa ttagaca 197 // ID Gypsy5-VV_LTR repbase; DNA; EDCOT; 539 BP. XX AC AM487303; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy5-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-539 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-539 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 738-738 (2007). XX DR Genbank; AM487303; Positions 6227 5689. XX SQ Sequence 539 BP; 129 A; 132 C; 110 G; 168 T; 0 other; tgatacattc gtggccatcc ctttacagca acatgtacag acaactgaag catccgttgt 60 ggaagagccc aatacaccta aagtacctcc cacggaagag cccaatgctg ccactcagct 120 agtcaccaag cattccaagg cccagtccaa ctcaggccca cgcaggccca gaaaaccacc 180 aacttggatg aacgactatg tcgtgtaagg aaagggatgt gaagctccgg ttttatcttt 240 tggtttgttt tttttttttt cctacaattt actatttctg gttgtaacca attctgttag 300 acagttgtgt cgctttggtt tcaattttcc caagagaagg cataaaactc tcgggagagg 360 tctgcatgaa ggaggctatg agattttgga tctgaacttt ctctcttttc cttattcttc 420 ctttttctgc tcaacctctt ctttgttttc tcccttcttc gttctggaga tattggagct 480 gacactcgct cgaagagtgc ccttgtgcta accggtcatt ttgcaggaag aacgtatca 539 // ID Gypsy14-PTR_I repbase; DNA; EDCOT; 4822 BP. XX AC LG_V; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy14-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4822 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4822 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 306-306 (2007). XX DR Genome; LG_V; Positions 10703814 10698993. XX CC Positions [1957-2382] - Reverse transcriptase CC Positions [3679-4161] - Integrase core CC 'GATC' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 54..1145 FT /product="Gypsy14-PTR_I_2p" FT /translation="MVLTKSGYQTIGEPLSVLQSHRHSTRKATTPSSMSSE FT EEEVTPDQSNLSDKVDRLTTQLEAVLKWIQSQPSSSASPGLKNVDDGISPP FT RARLTTEKEKSQDEDAHPRFVTGIRPQPFKVEARIDIPTFDGTIDAEKLDS FT WVDQLETYFTLYGFSSGEKVAFARLKLTSHALAWWNAFLKNNDDREISWKE FT FTQLLQQEFYPMGYVQDRWTRWHNLRQRQNQSVQEYTTEFHRLAVTLGIGL FT DHEDVFTKFVAGLWQHIQNELRLYQAVNISAASSIAMAIEQKNKPRGQRPT FT DNDKERNSGNHNFKKFTQGNPSSVSKSTKFCEHCRVSGHDKATCWKLRPDL FT FPTKWKKGRQGQAHNDNNNPQ" FT CDS 787..4776 FT /product="Gypsy14-PTR_I_1p" FT /translation="MSSRNLWLAYGSTFKMNYGYIRPLISLLPVALLWLSN FT RRINLVGNVLPTMTRRETVATTILRSSHKVTPHLYPNLLSFVSIVEFRGMT FT KRRAGNYVLTFFLLNGKKDDKGKRTMTTTILNDHIELGQMEEADMSLSLMA FT MPKETTSNLLTPPDEKEELFTLRIQVKQEIIDAIVDTGSQKNLISASLVQK FT LGLETNPHPKPYPLGWIQKDVELKIDRQCRFRFAITSQYIDEVTCEVVPLD FT ICQVIFGNPYLWERDAIYHRRAQQYHLVKDGKTYIVHKDRSSQKADLVTAC FT QARRMINASQKFVLMMIRPLTDEVTPSRFTLSCKAIDNKLNELLNKYTNLF FT AEVGGLPPKRAIEHEIQLISDSTLPNICMYRNSVLENEEIKKQVTELLDTG FT VIKPSSSPCGSPIVLVPKKDGGWRMCIDYRALNKITVKNRYPLPRIDDLLD FT QLRHATIFTKLDLKSGYHQVPIRKEDSWKTAFKTRQGLFEWLVMPFGLCNA FT PATFMRLMNDVLRPFIDHFVIVYLDDILIYSCSLEEHLVHVQQVFAVLEEH FT HLRLNRKKCEFGKKTLIYLGFIVGGGELQVDPAKVQVITEWPRPRTVTDVR FT SFMGACQYLRKFIQNFSLLASPLHSLTKANQAFVWTKAHEDTFQLLKRKIS FT EAPVLALPDLQKPFEIEGDASGYVMGAVLMQGGRPVAYHSEMFQGAAKNYP FT TYDKELLALHQAVKPFEIEGDASGYAMGAVLMQGGRPVAYHSEMFQGAAKN FT YPTYDKELLALHQAVKHWRVYLLGKETVVHTDHQPLQYLQSQARLQQARHM FT KWMTYLQQFHLVIKYKKGSHNKLADMLSRPPVTAICLSVFMQVHPALHEEY FT VDWYKEDPDFQSTWEEVLSSRPSEFMLRDGLLYKGKLLCIPRSDERVRYIR FT EAHTSKIAGHFGVTKTLQNLSRYVFWPRIQHDVARFIRGCVLCSTSKPANR FT KVGLYTPLPVPTRPWESISMDFLGGLPMTRRGNDYLFVVVDRFSKMVVLMP FT CKKTITSDGAARLFFENVWKLFGLPNSIISDRDSRFLSKFWCALWAMMDTK FT LKRSTAFHPQTDGQTEVVNRTVVHLLRGYNARHPKTWDESIPFLQFAINHA FT VHGSTNKSPAEVCLGFLPQSPFDLEFTIESNSALDKGEGERLRAQRFVDQI FT RKIHSEVEQQLTKAQQKYKERHDRHRVQGHFQEGDLVWLHLGKDRLRGVGK FT KLKPIRYGPFKILRKIGDNACQLELPAYMEMYSVVNVDKLKLFEPSMLDDE FT PDGTLPTVEDLVTEQEIILSEDTIVERKTTTTRRGERESFRIGSKGQRPSK FT AKWFSRETGQAQFPHLQF" XX SQ Sequence 4822 BP; 1451 A; 1050 C; 1100 G; 1221 T; 0 other; gatcaagttg gtatcagagc aatcgttcct ccctgtggaa aaacttttag ttaatggtgc 60 tgaccaagtc tggatatcag acaattggtg aacccctctc tgttttgcag tcccatcgac 120 attcaacaag gaaggccaca acaccatcaa gcatgtcaag cgaagaagaa gaagttacac 180 cggatcagtc taacctttca gacaaggttg ataggctgac cacgcaacta gaagctgttc 240 taaaatggat tcaatctcaa ccatcatcat cggcatcacc aggactgaag aatgttgatg 300 acggcatttc tcctccaaga gctcgtctga cgactgaaaa ggaaaagagc caggatgaag 360 atgcccaccc tcgattcgtc actggcatac gacctcaacc ttttaaagtt gaagccagga 420 tagacatacc aacattcgac ggcaccatag atgcagagaa gctagattct tgggtggatc 480 agttggagac ttatttcaca ctttatggtt tcagtagtgg tgagaaggtt gcattcgcaa 540 gattgaaatt aaccagccat gcattggcct ggtggaatgc attcttgaag aataacgatg 600 atagagagat aagttggaag gaatttactc aactcttgca acaggaattc tacccaatgg 660 gatatgttca agatcgctgg acacgatggc acaatttgcg acagaggcag aatcaatcgg 720 tgcaagaata caccaccgaa ttccacagac tagcagttac actgggaatt ggactggacc 780 acgaagatgt cttcacgaaa tttgtggctg gcttatggca gcacattcaa aatgaattac 840 ggctatatca ggccgttaat atctctgctg ccagtagcat tgctatggct atcgaacaga 900 agaataaacc tcgtgggcaa cgtcctaccg acaatgacaa ggagagaaac agtggcaacc 960 acaattttaa gaagttcaca caaggtaacc cctcatctgt atccaaatct actaagtttt 1020 gtgagcattg tagagtttcg gggcatgaca aagcgacgtg ctggaaacta cgtcctgacc 1080 tttttcctac taaatggaaa aaaggacgac aagggcaagc gcacaatgac aacaacaatc 1140 ctcaatgatc acattgaact cggccagatg gaggaagcgg atatgagttt gtctttgatg 1200 gcaatgccga aggagacaac ctcaaatctg ttaacccccc ctgatgagaa ggaggagctt 1260 tttaccctac gaattcaagt gaagcaagag atcattgatg caatcgttga cactggcagt 1320 caaaagaatt tgatctcggc cagtttggtt caaaaattgg gacttgagac aaatccacat 1380 cctaaaccat atccacttgg atggatacaa aaggacgtgg aactcaagat tgatcggcag 1440 tgcagatttc gttttgctat cactagtcaa tatattgatg aggtaacctg tgaagtagtc 1500 cctttggata tttgtcaagt gatttttggc aatccatatt tgtgggaacg agatgctatt 1560 taccaccgac gggctcaaca atatcatctt gtgaaagatg ggaagacgta cattgtccac 1620 aaagatcgat catctcaaaa ggcagactta gtcactgcct gccaggcgag aagaatgata 1680 aatgcatctc agaagtttgt cctcatgatg attcgaccac taacagatga agtcacacct 1740 tctcgtttca cactatcatg taaggcaata gacaacaagt tgaatgagtt acttaacaag 1800 tatacaaact tgtttgcgga agtaggcgga cttcctccca aacgggcaat tgagcatgaa 1860 attcaactca tttcagactc cacattgcct aatatttgca tgtatcgcaa ttcagtactg 1920 gagaatgagg agatcaaaaa acaagtaact gagttgctgg acacgggtgt tattaaaccc 1980 agcagttccc cttgcggctc accaattgtg cttgttccga agaaagatgg aggatggcgg 2040 atgtgtatcg attacagagc acttaacaaa attactgtta agaaccgata ccctcttccc 2100 cgtattgatg atctattgga tcaactacgt catgctacca tctttaccaa gcttgatctg 2160 aaatcggggt atcatcaagt tccaattcgc aaggaggatt cctggaagac agcattcaaa 2220 acacgacaag gattatttga atggttggtc atgccattcg gtctttgcaa tgccccagca 2280 acatttatgc gactcatgaa tgatgttctc cggcccttca ttgatcactt tgtcatcgtc 2340 tatctcgatg atatcttgat ctacagttgc tctttggagg aacatctcgt acatgtgcaa 2400 caggtatttg ccgtcctaga agaacatcac ttgcgcctaa accgcaagaa atgtgagttt 2460 ggaaaaaaaa ccttaattta tcttggattc atcgtgggtg gcggtgaatt gcaagttgat 2520 cctgctaagg ttcaagtgat cacggaatgg ccacgacctc gtacggtcac agacgtccga 2580 agctttatgg gtgcatgcca ataccttcgt aagttcattc aaaatttctc tcttctggcg 2640 tctcctctcc attccttgac taaggccaac caagcctttg tttggactaa ggcacatgag 2700 gacacgttcc aattattgaa gaggaagata agcgaagcgc cagttcttgc cttgccggat 2760 ttacaaaaac ccttcgagat tgagggggat gcatcaggat atgtaatggg agccgttttg 2820 atgcaaggag gacgaccagt agcctaccat tcagagatgt ttcaaggcgc tgcaaagaac 2880 tatccaacat atgacaaaga gctcctagca ctacaccaag cagtgaaacc cttcgagatt 2940 gagggggatg catcaggata tgcaatggga gccgttttga tgcaaggagg acgaccagta 3000 gcctaccatt cagagatgtt tcaaggcgct gcaaagaact atccaacata tgacaaagag 3060 ctcctagcac tacaccaagc agtgaaacat tggcgtgttt atcttctggg caaagaaacg 3120 gtggtccaca cagaccatca gccattacag tacttacagt cacaagctcg attacaacaa 3180 gcccgacaca tgaaatggat gacataccta caacaatttc acttggtgat aaagtacaag 3240 aaaggcagcc ataacaagtt ggcagatatg ttgtcacgac ctccagtgac agcaatttgt 3300 ttatcagttt ttatgcaagt gcatccggct ttacatgagg agtatgttga ttggtataaa 3360 gaagatcctg actttcaaag cacatgggaa gaggtgctgt ctagtagacc gtcagagttc 3420 atgctacgag atggccttct atacaaaggg aaactcttat gcataccccg atcggatgaa 3480 agggtgagat acatacggga ggcacacaca tccaaaattg ctggtcattt tggggtcaca 3540 aaaacattac aaaatttgtc tcgttatgtt ttctggcccc ggattcaaca tgatgtggct 3600 cgtttcataa gagggtgtgt actgtgtagc acatctaaac ctgctaatcg taaggtggga 3660 ttgtataccc cactacctgt tccgacacgc ccatgggaga gtatttctat ggatttcttg 3720 ggaggccttc caatgacccg gcgaggtaat gactatctat ttgtggtggt cgatcgattc 3780 tccaaaatgg tggtactcat gccctgcaaa aagacgatca ccagtgatgg agcagcacgc 3840 ctcttctttg aaaatgtatg gaaattattt ggtctcccta actcgattat atctgatcga 3900 gacagccggt ttttaagcaa attttggtgt gctttatggg ccatgatgga cactaagttg 3960 aaaagaagta ccgcattcca tcctcagact gacggacaaa ccgaagtggt gaataggact 4020 gttgttcacc ttctacgagg atacaatgct cgtcacccca aaacttggga tgaaagcatt 4080 cccttcctgc agtttgccat taatcatgcc gtacatggtt caacaaacaa gtctcccgca 4140 gaagtgtgtt tgggtttctt gccacagagc ccttttgact tggaattcac aattgaatca 4200 aactctgcat tagataaagg ggaaggcgag aggttacgag cacaacggtt tgtggatcaa 4260 attaggaaga tacattcgga agtggagcag cagctcacaa aggctcaaca aaagtataaa 4320 gagcgtcacg acagacatcg cgtccaaggt catttccaag aaggtgacct tgtttggttg 4380 cacctgggca aagaccgact gcgtggagtc ggaaagaaac tcaagccaat ccgttatgga 4440 ccattcaaaa tccttcgtaa gattggtgat aatgcgtgtc aattggagtt accagcttac 4500 atggagatgt attctgtggt caacgttgac aaattgaaac tctttgagcc ttccatgctg 4560 gacgatgagc ccgatggaac tctacctacg gtggaagatt tagtaactga acaggaaatc 4620 atcctatctg aagatactat cgtggaaagg aaaacaacta ccactcgacg tggtgaaaga 4680 gaatctttcc gcattggcag taaaggtcaa cgtccaagta aggcaaaatg gttctcccgg 4740 gaaactggcc aagctcagtt tcctcacctc caattctaga accagcagga gctggctcgt 4800 cctaacaagg ggagtcatga tc 4822 // ID VHARB4_VV repbase; DNA; EDCOT; 5067 BP. XX AC . XX DT 14-SEP-2007 (Rel. 12.09, Created) DT 14-SEP-2007 (Rel. 12.09, Last updated, Version 1) XX DE DNA transposon from grapevine. XX KW Harbinger; DNA transposon; Transposable Element; VHARB4_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-5067 RA Obukhanych T. and Jurka J.; RT "VHARB4_VV."; RL Repbase Reports 7(9), 1002-1002 (2007). XX DR [1] (Consensus) XX CC This is a Harbinger-type DNA transposon from Vitis vinifera. CC Individual copies are 94% similar to their consensus. XX FH Key Location/Qualifiers FT CDS 3910..4512 FT /product="VHARB4_VV_1p" FT /translation="MCACDFDMMFTFVYAGWEGTTNDARVFLDALTRPEVN FT FPWPSEGKYYVVDSGYPCISGFLPPYRGERYHLQEYRGRRNQPIRYKELFN FT YRHSSLRNIIERCFGVLKTRFPILRMMPCYKPSRQPSIVVACCTLHNWIRL FT STRNDQLFREYEVEDLSIQGEEESTSSTNHSIDLSDESAAAMAACRDQIAQ FT VMWANYINVNP" XX SQ Sequence 5067 BP; 1705 A; 730 C; 862 G; 1769 T; 1 other; gggcctgttt gtttagtgtt ttcaagaact gttttctgtt cttgaaaaca aaaaacacca 60 aaaacttgtt tggttgagag agtcattttt gtttttgttg ttccccgtgt tctcaaaatg 120 gcactgttta gagaacaaca aaatgttgtt ttccccgttt ttttactgtt tacaaaacaa 180 aattaaacaa caaaaaaacc atctgttctc cgtgtttttt ttttcttccc gttctcatct 240 cttctccagc acagtcgcgt cgcctcttct ccagcacagt cgcgacatct ccagtagcaa 300 gaaacgaagg taatttccac atatgttgaa gttatttttt atagatctag taaaataggc 360 tttttttggc aatatttgtt gagagaaatg ttagatctgg gtaaagagat atcagttatg 420 ttattcgaat gagatttgag cttttttttt tttatcacct gctgttagtt tctttttttc 480 ccgtttatat tttcctgttt ggatgctgag aaaagtgggg aacgagaatg aaaatagaat 540 gagatctgag cttttttttt tatcacctgt tgttagtttt tttttttttt ccgtttatat 600 tttcctgttt ggatgctgag aaaagtgggg aacgagaatg aaaatagaaa aaaaaattcc 660 tgattttttc ccgttttgat ttttcttgag ttgttctgtt aaaaaaaaaa acaaaaacct 720 tacttaaaga catggaaatc aaacgggaaa atccaggctt gacgggtaaa atacctcaag 780 gaaaatggaa aaaatgaaga gaatcagaag aagatgaggt gttgaatcac caagaaccct 840 ttctctctgt agatctgctc ttcctctctc tcatccagac tccaaagctt ataaaatacc 900 tcaaggaaaa tggaaaaaat gaagagaatc ggaagaagat gaggtgttga atcaccaaga 960 accctttctc tctctagatc tgctcttcct ctctctcatc cagactccaa agcccggtta 1020 aatcyagttg atgaccatgg acctccactc tttgcttctt cccttcttcc caccttccga 1080 tttcatgaaa gcaaaaataa ttaaaaaatt ataataaagt aaaaaataaa aataaaaaat 1140 aaaatcaaaa ttattaaatt attttctata tactacttca aacttatttt aattttttca 1200 tatgattata taatttaaaa tatataaatt ttaattaatt ttaatggtat atttttgtaa 1260 taaatcaaac attaaaaaat taatttttta acattattga aatcaaacgg tcaaagggga 1320 atatccatca gcatattctg agggctaggt cagtcttgaa ctcggactct gcactgatta 1380 gctcttggat gttactcatc tattttcttg gggtggtgga gaatcagtgg aaagagatgt 1440 gaccatctcc ttacttgcat ttattttgat gtcttattta ttttatttag attagttata 1500 aatattaaat taattctttt taaaactttt tatctcatct taatagaata tactataatt 1560 tttaataaaa ttaaatatta aatcaataaa aataataata aaaatgattt tatcatgttt 1620 gatttatttt aaaaaaatat aaaaaaatat tttaatttta aaattaatca aatataaaat 1680 taatcaaact attattattt ttatttactt ttctttcatt tttttccccc aatttttgtt 1740 tcaaatttta taaaaactaa aaaaaaaagt ctttaaaatc taattaatat caaatctatt 1800 tttattttta tttatttttc tttcatattt ttatacacta cactatacgt caacaatctt 1860 aattctcatt taaacatagc cttaagttct attggtggtt ttaaaagttg tctcctcata 1920 gagttcttat ttgtgatggg attgtacaga tgacaactga gataacagat gttgaggatg 1980 caggaacatg gagaggtaat atagagaaaa tctttattga catcatggta aatgaagtta 2040 ataaaggtaa catggatagt ggtacattta gtaccaacac atggagaagg atcttacttg 2100 aggtcaatag tcaagggaaa agaaatttca atttgaagca gcttaaacaa aagtttaata 2160 gactacgtgc aatgcaccgt gagttctctg atcttttaaa gcatactgga tttggttggg 2220 atgctgaaac taacacagtg catgctctag aggaaacctg gcaaaattac attcgggtaa 2280 aaataacttt taaactaatt actttttaat ttaaatattt ggtatacact aagagtgagt 2340 ttttttttcc ttctattagg cacacccaaa tgcaaaaaga ttccgctcaa agggatgccc 2400 aaactacaac ttgctgggat tgatctttaa tccatcaaca gcaaccggtg ccctccacta 2460 ctcttccacc caagatccac caaacactga tgatgaggat gagatggatg acaatttgga 2520 acatggtgga gtgcatgtgg atgtagatac tgagatccct gatgatcctc tacaaccaga 2580 gatggtagga ggagtgacca cccgttctgg aaagcgtgca actgattctc tattagagcg 2640 tagaggtaag aaagaatcca gattaagtca aatgggagat gctttgaaag cttgggttga 2700 ggcatcaaag gctagaacag aaacatctcg agctagaact gaggcattat tggctagagt 2760 ggacagatat aagagtggaa ctagtagtga agctactagt ggaggtacta atgattttag 2820 cataacaagg tgcatgacag ccttacaaac cattgaattg ttggataatg acaaatattt 2880 aaaagctgtt gagaaattca caatgccgga gtggagagag atatttatga atatgcctga 2940 tgagaggaaa atggcatggc ttgataggct ttaaatgtga atgtttggat gaataactat 3000 tatgatgaca ttgtaatatg tactatttct cttttggtta gaatctttta ccatgctctt 3060 tagtttgtca ttgtatggat gttatttatg gttatgaaac ttatattata actactttaa 3120 tgttcatttc gtgctatttt atattgtgag ttaatttgtt ttgtgtagta accaatggat 3180 gataatagca caagcagtgg ttcactatat gagtcaactt catcttctga agaggatgat 3240 gatttagatg aaatttttat tgctcacata atgaatgagt atgaggaaat atttttatgc 3300 aagacacctc aaaggacatc aatgttaagt ggtgcacaat ttgtaagaga tatgatagaa 3360 ggtcatcctc agacatgcta tgaactattt cggatggata aagaaacatt tatgaacctt 3420 tgtgatcatc ttaagagaca tgaaaactta caggatacac gattagtcac agttgaagag 3480 gcagttgcta tgttcttact aatcgtagga cataatgtga gaatgagggt tgtagcagac 3540 cgttttcaac actccacaga gactgtcgct cgacacttta aagaagttag acgtgcatta 3600 tgtcgactag gcaaaattct catatgtcct aacaatatga ccaatgaggt gtcttcatat 3660 gttgctagta atcctaaata ttttccatgg tttaaggtaa gagtttataa aaaaatattt 3720 ataaatgtga atttcatgta cataaatagt tttcatgacc attatttaat ttatttcctt 3780 aataataata aatgtttgtt gttgtaggac tgcattggtg caattgatgg cactcatatt 3840 agtgcatggg tcccagctga tagacaaacc agttttaggg gtagaaaaac agttataaca 3900 caaaatgtta tgtgtgcatg tgattttgac atgatgttta catttgttta tgctggttgg 3960 gaaggaacaa caaacgatgc acgtgtcttt ttggatgcat tgactagacc agaagtcaat 4020 tttccttggc caagtgaagg aaaatattat gtagttgatt ctggttatcc ttgtatatct 4080 ggatttttgc caccatatcg aggtgagcga tatcatttac aagaatatcg gggtagacgt 4140 aatcaaccta tcaggtataa agaacttttt aattatagac attcatctct tcggaatatt 4200 attgaaagat gttttggtgt tttgaagacc cgatttccaa tattaaggat gatgccttgt 4260 tataagccaa gtaggcaacc atcaattgtt gttgcatgtt gtacccttca taattggatt 4320 cgtctatcaa ctcggaatga tcaattgttt agagaatatg aggtagaaga cctttcaatc 4380 caaggtgaag aagagagcac aagtagcaca aaccattcaa ttgatttatc agatgagagt 4440 gcagcagcta tggcagcttg tagagatcaa attgctcaag tgatgtgggc aaattatatt 4500 aatgtcaatc catgacttat cttattttta attttaaata tttgtcaata ctttagtgtt 4560 ttgttagaat ttatatatat ttgttaactt aactagttct cattagtgtt atgtgatgtt 4620 tgttgtaatt tctaatgatt aaatattgct tataaattta atttataatt gtaaaagtag 4680 gatggacaaa agacccatgt gaaatacata catcatattt tattttattt ttaataattt 4740 atcaacttat ataaaaaatt taaaattaaa taatttttta aatttaaatg aaatgtgtat 4800 ttaaaaatat ttataaattt ataatataaa gttacttgaa gaaaatattt tattaattgg 4860 aaaagaaaaa aaaaatcttt caaacatgtt tttttattaa ctaagccaaa catgtttttt 4920 tttttgtttt tgagaacaaa aactgttttt caaaattcag ttcccaaaca caattttttt 4980 tctaaaaaca ccaaaaactg ttcttaaaaa ctgttctcaa aaactgtttt ccagaacagt 5040 tttcaaaaac agcaaccaaa caggccc 5067 // ID Gypsy-22_Mad-I repbase; DNA; EDCOT; 4636 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-22_Mad_; KW Gypsy-22_Mad-LTR; Gypsy-22_Mad-I. XX NM Gypsy-22_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4636 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1738-1738 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [3492-3986] - Integrase core CC LTRs are 92% similar to each other. XX FH Key Location/Qualifiers FT CDS 1381..2442 FT /product="Gypsy-22_Mad-I_1p" FT /translation="MIANGGTIASMGCCSQVKINIQDYEYISDLYVLQLGG FT CDVVLGAQWLRTLGPILWDFEKLKMEFTLGQQHYCLYSSPPPAPRSVTACQ FT VERLLNQGSFGVVLFLIAPDNDVTILGDLSGIQQAELDELLSQFESVFQSP FT TTLPPSRSHDHKIPLLEGSKPPSARPYRYNPMQKSEIEKCVQELLDSGFIR FT ASNSPFSSPVLLVRKKDNSWRMCMDYRALNLLTIKDKYPIPLIDELLDELW FT GAQFFSKLDLRAGYHQIRVHPADIEKTAFRTHNGHYEFLVMPFGLTNAPAT FT FQSLMNELFRPFLRQFVLVFFDDILVYSSTWEDHLLHLTTVFQVLQQHQLF FT VKRSKCDFGKS" FT CDS 2697..4397 FT /product="Gypsy-22_Mad-I_2p" FT /translation="MLSPTVLALPDFSKTFVIETDASNTGIGVVLQQEGRP FT IAFTSKALGPRSQAMSAYEREMLAIVHAIKKWQTYLHGNHFVIRTDHHSLK FT YFLQNRAHTPFQQKWISKLLGFDYEIQYKQGTENQVADALSRLHSEAQLCA FT ISYPYMGWLDDLRRHLEQEPWVISKLKDPSVAQGAVDTSSSNYHYDNGFLK FT HKGRIVLSPTTNWRDKIFHEHHSTLMAGHSGFLKTYKRISRSFYWQGMKAD FT IRRMVAECQVCQQNKYETLASPGLLNPLPIPQTVWTDISMDFIVGLPPCKG FT KTIIFVVVDRFSKYAHFVALSHPYTAHSVAQIFVDHIFKLHGMPATIVSDR FT DPVFLSAFWKEFFALQGSKLCLSSGYHPQSDGQTEVVNRCLETYLRCFCSL FT QPKKWLQWLSWAEWSYNTSYHSSSKLTPYEIVYGQLPPAVPTYESGTTKLD FT MVDRCLQTRSQILSQLKTNLEAAQVRMKQQADKHRTERTFAVGDMVYLRLV FT PYQHQSLASHPFHKLQPKFYGPFEVMERIGTVAYKIKLPAHSKLHPVFHVS FT CLKKAVGGGCGSYYYASRCH" XX SQ Sequence 4636 BP; 1199 A; 974 C; 1038 G; 1419 T; 6 other; aggttcttat tattggtatc agccaattta ggatcccacg tttcccttgc gtatgccgag 60 agcaaccact cgtgccacaa agatggatgc tcgcgtcacc gcccttgaag cttcgaactc 120 cagaatcgaa gaatcggtcc agaacctcgc agcccaaatg accaaattca tggcgtcaat 180 cgatacccgt ctctcgttgg tcgaatctcg ttctgctacc atggaagaac aaggccgcga 240 tcgtgctaat cgtgtgggtc cgtcggaatt ggggggcaat cccattgatt cggaagaaac 300 cttcagcgat caaaatcttg atcccaatct tcaattccag cgtcaagatc ctcgattccg 360 ccatcaagat tctcaatttc agtttcgcca accaccgatc aagcttgaat ttccaagatt 420 tgttgaaggt gacgatccct tagcttgggt gtacaaggcg gaacattttt ttgactattt 480 ctcggtcgcc gacgattgca aggttcaatt ggcatccttt cattttgatc gtgaagccct 540 tcaatggttt caatggcgga attgtctcaa gaattttccc cgttggcctg attttgttaa 600 gattttctgt catgagttcg gcccttcgga gtttgaggac tttctctgaa gccttggttc 660 aattgaggca aactgggttg gttagagatt atatmacaga gttcaggcgt ttggctaatc 720 gaacccatga gattgctccg tcgatgctta aaagttgttt cattggggga ttgaaaccgg 780 agctccgtca cgatgtcaag cttctgcggc cattggatgt ttatgaggct caggctattg 840 ccttacaact cgatgccaaa cttgctgatt ctaaggcccg atccttctcg aaagccccaa 900 atttctcttg gcataattcg gttggcagta aggctacacc aggttttacg gatccaggta 960 accccaattc ttctgttaat tttcctaagc agaacaatgt taagaagatg acatttgagg 1020 aaattagaga acgccgagaa aaagggtctt tgtgattact gtcctgtgaa atggtttaaa 1080 ggacatgttt gccaaaacca gcaactttta ttacttgatt tgtctgatag atctgaagag 1140 aktcttgatg ttgatmctgt ggtagaagag gatgatgaat tgttgaatgc tcgcattact 1200 gcttgtgctg tgtatggtgt ctctgctcct gataacattc cgactatgaa agtcgtaggg 1260 tccattaaaa attgttctgc agtgattctt ttttactctg gcagctctca caatttcatt 1320 aaccttgctt tggccaagaa gatgggctag agaatagatc cactcaagaa atttgatgtg 1380 atgattgcca atgggggtac aattgctagt atggggtgtt gttctcaggt caaaattaat 1440 atccaagact atgaatacat ctcggattta tatgtgttgc agttaggggg ttgtgacgtt 1500 gttttgggag ctcaatggct gagaactttg ggacccattc tctgggattt tgagaagtta 1560 aagatggaat ttacattggg ccaacaacat tattgcttat atagttctcc tccccctgca 1620 ccaaggtcag taacagcttg tcaagtagaa aggctgttga atcaagggtc ttttggagta 1680 gtcttgtttc ttatcgctcc ggataatgat gtgacgatat tgggagattt atctggcatt 1740 caacaagctg aattggatga gttgttgtct cagtttgaat cagtcttcca gtcacccacc 1800 actttgcctc catcacgatc tcatgaccat aagattccac ttctggaagg tagtaaacca 1860 cckagtgcaa gaccttatcg gtacaatcct atgcaaaagt ctgagattga gaaatgtgtc 1920 caggagttgt tagattctgg tttcattcga gccagtaata gccctttttc ttcccctgtt 1980 ttgttggttc ggaagaagga taatagttgg aggatgtgta tggactatcg agccttgaat 2040 ttgttgacta tcaaggataa atatcccatt cctttaatcg atgaattgtt ggatgaactg 2100 tggggtgccc agtttttttc caagctggat ttaagggccg gttatcatca gattcgwgtc 2160 caccctgcag atattgaaaa aacagcattc cgaactcata atggacatta tgagttcctt 2220 gtgatgccgt ttggactcac aaatgctcca gcaacctttc agagcttaat gaatgagcta 2280 tttcgaccct ttttgcgtca atttgttctg gtattctttg atgacatttt ggtttacagt 2340 tctacttggg aggatcatct gctacatctc actacagttt ttcaagtact gcagcagcat 2400 cagttgtttg tcaagaggtc aaaatgtgat tttggcaaat cacakatcga gtacttgggg 2460 catgtggtat ctcgaaatgg agtggcagcg gacccttcaa aactccgagt cattcaagat 2520 tggcccttac ctgcttcaat taaagctttg cggggattct tgggtttgac gggtattacc 2580 gaaagtttat accaggttat ggcagaattt gtggcccatt aacttccttg actaaaaagg 2640 atgccttcca ttggaattct gaggctacga ctgctttcaa taagcttaag gaagtgatgt 2700 tatctccgac agttctcgcc ctcccagatt tttcaaagac atttgttatt gagacagatg 2760 cctctaacac aggcattggt gttgtcctac agcaagaagg cagacctata gcctttacaa 2820 gcaaagctct tggtcctcga tctcaagcta tgtcggcata tgaaagggaa atgcttgcaa 2880 ttgttcatgc tattaaaaaa tggcagactt accttcatgg caaccatttt gttatacgaa 2940 cggaccatca tagtctgaag tattttttgc aaaatagggc ccatacccca ttccaacaga 3000 aatggatttc taaactgttg ggatttgatt acgaaatcca gtacaaacaa ggtactgaaa 3060 atcaggttgc tgatgcattg tctcggctgc attcggaggc tcaattatgt gctatttcct 3120 acccttacat gggatggttg gatgacttgc gcagacattt ggagcaggag ccttgggtta 3180 tttctaaact caaagatccc tctgttgctc aaggggctgt tgatacatct tcctctaact 3240 accactatga taatggtttt ctcaagcata agggccggat tgtgttaagt cctactacta 3300 attggaggga taagatattt catgaacatc atagtacctt gatggcgggg cactcaggtt 3360 ttctgaagac ttacaaaagg atttctcgct ctttttactg gcaaggcatg aaggcggata 3420 ttagacgaat ggttgccgaa tgtcaagtgt gtcaacaaaa caaatatgaa accttggctt 3480 ccccaggtct attgaatcca ctgccaatcc ctcaaactgt ttggacagat atttccatgg 3540 attttattgt tgggttgcca ccttgcaaag ggaagactat tatttttgtg gttgttgatc 3600 ggttctctaa atatgcacat tttgtggcac tgtctcaccc ttacacagcc cattccgttg 3660 ctcagatttt tgtggatcac attttcaagc tacatggtat gcctgccacg atcgttagtg 3720 atcgggaccc ggtgtttctc agcgcatttt ggaaggaatt ctttgcttta caagggtcta 3780 aactgtgtct aagctctgga taccatcccc aatctgatgg gcaaaccgag gtagtcaacc 3840 gatgtctgga aacatacctg cgttgttttt gcagccttca accaaagaag tggctccaat 3900 ggttatcgtg ggctgaatgg agttacaata cctcttacca ctcttcttca aagctcacac 3960 catacgaaat tgtgtatggc caactccctc ctgcagttcc gacatatgaa tctggtacca 4020 ccaagctgga tatggtcgat aggtgtttgc aaactcgatc acagatttta tcacaactca 4080 aaaccaattt ggaagctgct caagtgcgaa tgaagcaaca ggcggataaa catcgtactg 4140 aacgcacttt tgcagttggt gacatggtct atctcagact tgttccttac caacatcagt 4200 ccttggcttc tcatccattt cacaagctac aacccaagtt ttatgggcct tttgaagtga 4260 tggaaaggat tgggacagta gcttacaaaa tcaaacttcc tgctcactcc aaattacatc 4320 ctgtttttca tgtgtcgtgt ttgaaaaaag cagttggggg tgggtgtggc tcctactact 4380 atgcttcccg atgtcactga tgatggtttg ttacaggcta ccccattaac cattcttcag 4440 catcgtgtgg tcaccaaggc caactctcag gttcctgaag ttcttgtgca ctggaaaaat 4500 cattgcaagg aggatgccac ttgggaagaa tatgaagaat tcaaacgtcg gtttccctgt 4560 tttcaacctt gaggacaagg tttgtttcta tgggcggggt aatgttagga tactaagaag 4620 ggatagccaa attaag 4636 // ID Helitron-N4_PTr repbase; DNA; EDCOT; 2104 BP. XX AC . XX DT 17-DEC-2009 (Rel. 15.02, Created) DT 17-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Helitron-type non-autonomous DNA transposon - consensus. XX KW Helitron; DNA transposon; Transposable Element; Nonautonomous; KW Helitron-N4_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2104 RA Kojima K. and Jurka J.; RT "Non-autonomous helitrons from black cottonwood."; RL Repbase Reports 10(2), 232-232 (2010). XX DR [1] (Consensus) XX CC ~88% identity to consensus. XX SQ Sequence 2104 BP; 563 A; 281 C; 363 G; 897 T; 0 other; taagaaaagc taaacatgtg gggaaagcac tgtagctttc ctcacaaaac actgtggatt 60 gctacagtgt ttccccacat gttttttttt tacacatggt tttttttctt ttcttttttt 120 tttttttttt tgttatgatt tttttcaaaa ttatttttgt caattttatt ttttaatatt 180 gagatggttg agaatttagc tttgtaattt ttttcttttt attttgtctt tctatgaggt 240 tagcgtggtt tgcgggtttg tcgaggtaac ccaggttgcc tagtttatgg atttggtggg 300 tttttttaat tgaacttgac ttttttatag tctatttttt tctcatattg ttaaaaaaat 360 agttttagag aaaaaccatg ttattaaact ttatgaagta acaaaaatta aaggatgtgg 420 gggaaaccat tgttcaccca acacccattg cactgtggat tacaatagta atccacaatg 480 ttttgctttt tcttttttta tttttgttat gatttttttt tcaaatctat ttttgtcgat 540 ttcatctttt aaaattgaga ttgttgagaa tttagcttcg taatttgctt ctttttattt 600 tgcctttata tgaggttagc gtggtttacg ggtttgccaa ggtaacccag gttgccccgg 660 tttacgagtt tggtgggttg tctttttttt tttttaattg aacttgactt tttttatagt 720 ctattttttt ctcatatagt taaaaaaaaa tagttttaga gaaaagtcat gttattaaac 780 tttataaagt aacaaaaatt aaagggtgtg aggaaaccat tgttcaccca cacacattgc 840 actgtgaatg acaatagtaa tccacaatgt tttgctttct ttcttttttc tttatgtttt 900 tgaatttttg ttatgatttt ttttcaaatt tgtttttgtc gatttcatct tttaatattg 960 ggatggttga gaatttgact tcataatttg tttcttttta ttttaccttt ctataaggtt 1020 agcatggttt gccagggtaa cccgggttgc cctggtttac gagtttggtg gggtgtcttt 1080 ttttttaatt gaacttgact tttttatcgt ctattttttt ctcatatagt taaaaaaata 1140 gtttcagaaa aaagttatgt tattaaactt tataaagtcc atggacctat tcacaggttt 1200 ggctggttga cttggttcgc gggtctgaca agtttaactt ttttaaatta gttttttttt 1260 catccttaga tactgggtta attgggaatt cagtttcata attggtttcg tttcgccttt 1320 tatgaggtta tcatgatcta aaaaaaacat ctcggtattg ggttggtgtt tgatttcgca 1380 atcatctatt tttgttatca tatagttaaa taaaaaatag attaaaaaaa caaattataa 1440 tcccagtgga gtccataacc cagttcacag gtttggcgta ctagcccggc ttacccgatt 1500 cacaggtttg acgagtttac ccaccgatag gatatgtttt ttttgtcttt taattgtttt 1560 taatttattc ttttttattt catcatttaa tattggattg gttgggaaat ggactgcatt 1620 attgattttt gtttgctttc tagggataat tgtctcaaat aagtgtctat ttttaggttg 1680 gtgctcaatt ttgtgagcat ctatttttat catataatta aataaaaaaa tataaaaaaa 1740 gttattaaac ccaatagagt ccatgacccg ggtcgcgggg gggcgaggtc aatctgtcat 1800 tgtctcaata tttttttaaa aaaattatca tcttgaagtt tttttaaaag ctaagtcatg 1860 tttttatcga tcatcaaggt tgcatttgga cctatgaaat cgatcgattt aagtcgagct 1920 agctctcaca cggtttaatt aaaaacttga gttagacaaa gagttgagtc gggaggtttc 1980 aaaattaacc cacttggtca ggtttaataa cactattaaa aaaattcttc gtactcttaa 2040 tattttttta tatattttta aaaaattaat tcaacccgcg gcggagcgcg ggccaatata 2100 ctag 2104 // ID OGRE-LTR_PS repbase; DNA; EDCOT; 5040 BP. XX AC AY299398; XX DT 09-JUN-2005 (Rel. 10.05, Created) DT 09-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE Pisum sativum gypsy-like LTR retrotransposon Ogre (Long Terminal DE Repeat). XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed repeat; Metaviridae; Long terminal repeat; KW OGRE-LTR_PS. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-5040 RA Neumann P., Pozarkova D. and Macas J.; RT "Highly abundant pea LTR retrotransposon Ogre is constitutively RT transcribed and partially spliced."; RL Plant Mol Biol 53(3), 399-410 (2003). XX RN [2] RP 1-5040 RA Toth G.; RT "Pisum sativum gypsy-like LTR retrotransposon Ogre."; RL Direct Submission to Genbank (09-JUN-2005). XX DR Genbank; AY299398; Positions 14501 19540. XX CC Long terminal repeat of Ty3/Gypsy-like retrotransposon Ogre. 5bp CC target site duplications. XX SQ Sequence 5040 BP; 1197 A; 1040 C; 1012 G; 1791 T; 0 other; tgtagcacct caaatttgca cctatcattg tacatacatt ctcatattag gtcataacat 60 aacatggtcc actgcataac attgcattgt cccttttgcc tcaagtgcaa gtcatcagga 120 gaattaggtc aaactggtca ggagatcagt cagtcaagca agcaagtgca tttctcaagg 180 agccaaggcc ttagggttgg tccaacatgt tcacatgact tggggatcca tttgaagtgt 240 ttaggtcaag gattggatgt tcagaagtca tcagtcaatg cacaatcagt cagaaaccct 300 aaaagtcaac tgttggtcaa ctgtccattt aatcagtgat ttgatgatgg gatttggttt 360 gagaggtctc attcatgtcc atatagtctt catatatcat ttcaaacacc atcatgaagg 420 aatttgaagc cagatcagaa atttccaaaa agggaaactt gacctgtaac tgaaacttac 480 caaaaatgga aagtcttgat cctcaaacat acatcatgat acaagcttca aatgaatttt 540 tgcccaacat gaaagttgaa gatcttgttc tcccatttcc aaaaagtcca agaactctca 600 attcccatgt atggttggca agttatgatc aattcatttt caaaaattct tgaacttcaa 660 aaggccatat ctctcaaacc atttggccaa attgggtggg gttttctgca acaagtcaca 720 tttgatgccc tctttccaaa tatgtcatca tcattcacca aaacttcacc aatcaaaatg 780 gaatttttgg acttgcatga attgatttca agtgtggtac aaaagtgaat ttttgagata 840 gctatttcta atcaatttgg ccattcaaat atgttcagaa atcatatttt ggtcatgtta 900 caaagcccat ttcgtgcagt acacatagcc atgcctaact tgcttgaaat ttggacaaaa 960 gtacattttc tcaccaaatc tatcccacct tttcatgaac catgcttggt accatcaaac 1020 agagtacaaa aacatcattt tctgcaagaa gcaaccctag cagccacact tgacaaaaca 1080 gaaaacttca ttctctcaaa accatcattt tcttcatttt gcaattctgc aaaaaaaacc 1140 ttcaaagagc atgagcttag gatgtctatt ttatcatatg ccaccatttt ggagcccttt 1200 gaagatgtga taacccagct gtaaagtcat ttcgtggcac tgtttcacca agaactctcc 1260 catggcagtt caaagtttgg accatcccaa gccttctcga gctcaaaatc tttaaccatt 1320 catcattgca aacaactagg agcatctgtt ttgagcatac atggccaaat aaccaccaca 1380 ccacgactgt tcttcacttt tggccaggta tcgaatctct catttttcaa aaccatgcta 1440 tgcttctcat agatctttgc atgctgattc ttttggtctt taaatcgtgt tgaatggttg 1500 cccatgctga aagaaatgct gagttgaagt tttacatcca aacttgtttt tgcttattgc 1560 ttctttgata gtgtgattca ttgaaaatgg atgttgtaat gttgatgtac actgtttgct 1620 ggtttgaatg atgtattcgt tgccaaaatc tggaaagttt gttcttcatg ttcatgaaca 1680 cgatcactgt agctggaacc ctaattttca aaacccagaa atgcatttga tccatggaac 1740 tcgtgtttgc atgtgtttcc aagtttctgg gccatgtggc caatgactgc ttgccacgtc 1800 tgggagcgct gcgctgcgtt tcattaaacg cccagccaaa ttacaagttt gccaccgtgc 1860 cctaattaaa ccattaaatc atgttatttt tcaattttta tttcattttg tgacaccaac 1920 ttacaaaatt cataactcgt ccattttaac tccaaatttc atgggatttt ttgcattgtg 1980 ttcatctgga tctctagttt tttatcatga tttttccaga tttttttggt gagtggattt 2040 taattggtat tagggtttgt gacatgtgct catattttgt acactttgcc aaaacatttg 2100 tgaaatggtg atactttatc caatggctcc caaatttttt gtgcttaaac tagacacact 2160 catggtgatt ttggtgtaga gtttgtgaat ttatcatttc tggtttgtga gttatgattt 2220 tttgaagtag ggtgtgacaa tttgtgtcac accattgatg tgcaacttca tgatttttat 2280 taccatgctt cttgacctca aaatgctttg aatttttgca tgaatgtact cttgtatgtc 2340 tagtttacat gtgaattttc ttggaattgt ttgtggcatt tcctaattgt ttgagatttt 2400 ctcccctgct tagtcatatg ttgacttttt gtgatacatg ttcccatttc atttgtgaaa 2460 ttctcatact ttattagatg gacatgaaat tttacatgag ataactagac ctcctcagct 2520 ttgccatggt tttgatccca ttcatttatc atatgccatc cctgatttat gaatttttca 2580 agttgatgca tgtttggttg acttctttga gcatgttcaa aattgttttg actttctgat 2640 tttcattgac tgccttccac ttgtccaaat gagatgaaat ttgacatgct taccatgata 2700 tgtgttgtga ttgatcatga tttatttggt gatttttgga aatgtttgag ttgacttttg 2760 atgcaagtct tgctgttgac ccctatgagc ttctaagtgc catgttttga cctaattcgt 2820 tcatgaaatg atgatgatga ttgatatgaa tgtgaaacca attgggtttg tttcttgatt 2880 gtttgaacgt gattttggac acttgtcatt tgctgttttg actttctcat tctcttttga 2940 ccctaggctt gtcctagtgg tcctgttact cacctttgag ctcatgtttt caggttgacc 3000 aataaatgat caatgagacc aattcttttt gattgagctt gcctggatat cattgattaa 3060 cttgtttgtt ttgtaggtgg cttaacccat atgatttgag tcttgtgctt tgcacatttg 3120 attatctgat ttgactgttg attcctattt cctttgtttt aacttgtgaa ctgtgtactg 3180 acctgtttga ccatttcagg taccattagt tgcttaagtt ctttgaactt gctttgcttt 3240 gctatttagc aacttgcttg aggtataatt tctttttctt catgtagtct ggaagacctg 3300 gcctgttact tggccaggca actgtctgaa gtcctcctta agaggcaatg cttgtgtatg 3360 tttaatttgt ccttgtacat agtcaaagtc ctcctaagtg aagaggcaat tggcagaacc 3420 caagggataa gcaacctatc ccctgctatt cagtgtgcct tctgttttgc tcacaccact 3480 gtgttgacgc attacagata aaaacccaag atcttgtgca attgtacagt tgagtcagta 3540 tctaatgtgt agaaaggttc ccactttctg aacccacaca ttcttgtcaa atgctctccc 3600 tggccaggga taagagcaat gaggcacacc cctcatctcc tttcatctgc ttcaccttgg 3660 ctctcaatgt caaggttaag agcaacatcc acccagttcc agaggtttgt ttgttgaggt 3720 tgatatgacc cctcgactaa aacctagcct tgtttgagcc ccttgcttgt gtatagtgtg 3780 tgctacctgt gcttgtgtgt ttgtttggct tgcttcatgt gcaagttagg tttagtttag 3840 actaatccct gtttgctttc gccctcgttg cgatcctttc tctcgccctc gttgcgatcg 3900 agactttccc tttctcttgc cactagttgc aatcgagacc cttgcttcct gtgcaagtta 3960 ggtttagttt agacttgctt cctgtgcaag ttaggttttg cttggcttgc ttcctgtgca 4020 agttaagtgt gggtgtggct tgcttcctgt gcaagtcatg tttaggatag gcttgcttcc 4080 tgtgcaagtt agctagaaac cttaacttag ggacgatttt gcatgataac atctaggctc 4140 gagtcgtagt ctccctagtt gtgtctccct ctgttatctg attaggctag tcctgtatcc 4200 ctccgtaggg gaactacgtc gccctgatcc tcataccaga tggggtacgt aggcaggaga 4260 tgagctgatc tctccgggcg cctgagtctt tgttttgtct tgttgtgtgc ttggaagccg 4320 atgtaagtcc atcgagtggc atttgggttc cagtgtgcgt gtgtttggtt cggatgctga 4380 tgtaagtcca gtgattggca ttcaggctcc atgtttgcct tcttgggttt gtttggttcg 4440 gatgctgatg taagtccagt gattggcatt caggctccat gtttgcctct ttgtgtgtgt 4500 tttggttcgg atgctgatgt aagtccagtg attggcagtc aggctccacg tttgcctgtg 4560 tttgtttgtg tgcgtgtcag ccgagctacg aatgctctga ttcttctctc gtccgagaag 4620 atacgtatgc ataaggtgcg ataccttagc gagcatgtgt cgtttcccca gtccgaacta 4680 cttcgactct gatgtctatg cctgatagac taagtaggcc caggatgcga tatcctgccg 4740 agtcagtttc agtctgtttt cttgcgtctc tttcagccag tgtgtgtgag tgtgagcagt 4800 gttttagcaa ccatttttcc ttccttttgt gcgtggatcc cgtcgagtat gacggatgcg 4860 taggggtgct aataccttcc cttcgcataa ccgactcccg aacccattct ctttggtcgc 4920 gagaccatgt cttttcccag gtttactctg agcgtttcct ttccctcttt tgggataaat 4980 aacgcacggt ggcggctctg ttgttcttgt tttcccgccg gtttttcgcg tgatgcgaca 5040 // ID EnSpm-13_VV repbase; DNA; EDCOT; 12363 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE EnSpm-13_VV, an autonomous DNA transposon - a consensus sequence. XX KW EnSpm; DNA transposon; Transposable Element; CACTA; Cactavine-13; KW EnSpm-13_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-12363 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 760-760 (2008). XX DR [1] (Consensus) XX CC EnSpm-13_VV (Cactavine-13 in [1]) is an autonomous element. Its CC individual copies are >90% identical to the consensus sequence. CC Cactavine-13 contains short TIRs which are flanked by 3 bp-long CC TSDs. Downstream of the TPase gene (region 6793-9981) is another CC ORF encoding for a ULP1-like protein similar to CAN79325.1. CC Although ULP1 (Peptidase C48) -like proteins are usually found in CC Mutator elements, our study shows that such proteins are common CC in CACTA elements as well. This feature is not restricted only to CC Vitis as similar examples were found in rice [1]. XX FH Key Location/Qualifiers FT CDS join(2757..5221,5311..5416,5497..6150) FT /product="EnSpm-13_VV_Transposase" FT /translation="MDRSWMSKDRRSKDYADGVESFIAFALQHSSYKNSIK FT CPCLQCGNMIFHTSQKIREHLFFYGIDQSYHTWYWHGEAAPSGPPTSRAEC FT HHKVQFNDVDSTIEMVQAAHDDCKNDPELFETLLEDAQKPLYPGCRNFTKL FT SALVKLYNLKARYGWSDKSFSELLRILGDMLPLNNELPLSMYEAKKTLNTL FT GMESEKIHACPNDCILYRNELKDASSCPTCGTSRWKLDRTRTKKRKGVPAK FT VMWYFPPIPRFRRLFQSPKIAKDLIWHAQEREFDGKMRHPSDSPSWKLVDH FT RWPDFASEPRNLRLAISADGINPHSSMSSRHSCWPIIMVIYNLPPWLCMKR FT KFMMLSLLISGPRQPGNDIDVYLAPLLDDLKMLWEVGVESYDAHQQELFTL FT RVVLLWTINDFPAYGNLSGCVVKGYFACPICGEDTYSHRLKHGKKNSYTGH FT RRFLPCNHPFRKQKKAFNGEQEFRSPPQPLSGEEILRKIDVICNSWGKNKI FT TRGKLNVKTTNCWKKKSIFFDLEYWKYLHVRHNLDVMHIEKNVCESIIGTL FT LNIPGKTKDGLNSRLDLMEMGLRCELGPRFESNRTYLPPACYTLSKVEKKV FT FCQTLSQLKVPEGYCSNMRNLVSMEDLKLYGLKSHDYHALMQQLLPVSLRS FT VLPKHVRHAICRLSFFFNALCSKVVDVPALDKLQNDVVVTLCLLEKYFPPS FT FFDIMLHLTVHLVREVRLCGPVYLRWMYPFERFMKVLKGYVRNRNRPEGCI FT AECYIAEEAIEFCTEYLSNVDAIGIPISANIDQKVGAPIPGGQVVTVDSNL FT WLHAHHYVLENTTIVQPYIEEHMEWLKLKNPRQSKRQKWLQDEHLRTFTYW FT LRKKIEAAIGNNEPISETLKWIAHGPSHYVSKYHGYVINGCRYHTKERDDL FT RATQNSGVSIVASTMQIASAKDQNPVFGELCFYGIITEIWDLDYTMFRIPV FT FKCDWVDNKNGIKVDDLGFTLVDFNKIAHKSDPFILASQAKQVFYVQDQLD FT PRWSVVLSTPQKDFLDKEGGDDLVDNSIEHHPFIGALPQVEAFDAMDDSDA FT ICMRGDCEGIWIENKSSM" XX SQ Sequence 12363 BP; 4115 A; 1777 C; 2260 G; 4211 T; 0 other; cactactaca aaaaatataa tttatgacgc ttatataaag tgccattatt tattctaaaa 60 aatgggtatt aatgacgctt gcattatctt ggtgctttaa tgagagaaaa taatgacgtt 120 tttaaataat ggcgcttttt taagcgtcat tgtacaatga atttcaaata atgacgtttt 180 tttaagtgcc attgtaggag aacctcaacc ttggcgcttt taaaagcgtc attgtacaat 240 gcatttcaaa taatgacgct tttttaagtg ccattgtagg agaacctcaa ccttggcgct 300 tttaaaagcg tcattttcta ttcattttat aattactcac atttttcaat taaaaaaaaa 360 agagagataa atgtaataaa gccttttcca gacccgatgc ccacactcaa gtttcattac 420 caaatccgtc tctaactgaa ccagcaagtt ccagccaatt tcgattgaga aaatgaagtt 480 cttactccaa atcaagaaga tagcattcat ggatgttccg ccgatttgac tatttgggtg 540 ctggattgag agaaaggaaa tgaatggaga catgagagaa aactagggtt tttttagatt 600 cgtaggttgg gagagacaag aggcaacaaa ggcaggtgcc ttcggttgaa gaggtaagca 660 aggaggaaag gtcgaagaac cagaggaaca gaggaaagaa aagaagggag aagaaaaaac 720 ccagaagaga gttgtcgagc acgagcccat atgttctcgt tttcccatgg attcacattc 780 ttcactattg atttctggga tttgagtgtg aatgcttgta aatctgttgt ggtttttgtt 840 tattatcagt tattttcttg gtttgcatct ccaataaaaa gatattatac ctctgttttt 900 aggctcagtt gtgtctctcc tctgtttttg ttctctggtt cttatgttct ctagaagatt 960 tggaaatggt tctggtgttg ttccatttgt gtacaatggt tcatgccgaa aggagcttgc 1020 tttccatgga gttgtaggta ctgccaataa cttgtttgat gaaatgccat ttcgagatat 1080 gggctcttgg aatgcataga aagtttttca acaattttta ttaagggatg tagtgtcatg 1140 gaactcgata attgctgcct atgagcaaaa tcatgtggct ttcgaattaa ataaaaaaaa 1200 tttctaatta ataataataa cgaagtgcaa catttactac taatttaagc ttcacaatct 1260 tacataggct tcattgctta tgttacaaaa gatgctattc aaattcattt ttaaatgggt 1320 tacacaacat gttatctaat taataataac gtcatgtttg gttcatctat tcaataaact 1380 aattgagatt tgacacccca cttatgacca caaactagaa tggtcacccc caacataagt 1440 agaacacatg tcaaggtgcg gcttagctct actttagcct tacttgggaa atctacccaa 1500 gtctaagcct aaaaacaaaa tgaaaaaaat atcatgatat tatattaata caaattatat 1560 gtatctacat tgattatcta attaatcaag actctaaaaa atgagtaact ttgataaatc 1620 attttggggg ttggagatga accaatttta acatgaactt tatgtagtgg gtctttaatg 1680 gatttagcca agtttgtgaa cttaggccta aaatgtgatg cttacaaaca atattttcct 1740 attctcacca ttgcaattga tatgaataat ttataataca taactagatg taatatttta 1800 ataagtattt atgttttagt tttaatcaac tatgcatgcg tgaaacctta gaattcccat 1860 tcaagtatca ttgtgagaca gaagtttctc ttattacata ctaagacaat aagttgtcaa 1920 aatgtgaaat gtgggtatat ttaagctagt ttcaagttga caactactaa atttgtcttc 1980 catgtgataa agatcttttc tctgcaaatg atgtttgaat tgtccagttg gacagtatag 2040 gaaaacatga tatctatgaa gttaattgtt tgttcttaat tcaattttaa aaaaatttgg 2100 tagtctttct tcttgttctc tgggtgcata tttggacaag gtcacatatt gtgccttatc 2160 cattttgtgt acttggagaa ctatagggaa atgctgccga aatttcttta aaatgaattt 2220 aagtatattg gcaattgaca catagggatt atgtattcct atatgggata ggaaccacca 2280 cctagttaag gatgttggag atgttagaat gtctaaatca tgtataaatt acttgcttct 2340 attcattcga atcttagttc cattcgttaa ttgttttagt tcatggtatc attgtctcat 2400 gtggttatgt gtttttaaaa ttttcaaact tggtgtattc aataatataa gagaagacta 2460 aaatttagat cttgcttttc attcctattc atgaataaag caaacatcat gaatgaacta 2520 agatccattt tttatgctaa tattgaataa cctaatgtac taattatgtt tcttgtcata 2580 ttgcttattg ttagatgact tgcacattgt cattttttgg attggtctaa gttttgtgac 2640 aatgtgggaa attttaattt ggtagattat atattttaag cctattaata ggattttatt 2700 aataacttta gttgttggtg gtatctaggg agttgtgttt atctcttgta catcaaatgg 2760 atcgttcttg gatgtcaaag gataggagat caaaggatta tgcggatggg gtagaaagct 2820 ttatcgcatt tgcattacaa cattcctcat ataaaaactc cattaaatgt ccatgccttc 2880 agtgtggtaa tatgatattc catacttctc aaaaaattag agagcattta tttttctatg 2940 gaattgatca gagttaccat acatggtatt ggcatggaga agctgctcca agtggaccac 3000 caactagtag ggcagaatgt catcataagg ttcaatttaa tgatgtggat agtacaatag 3060 aaatggttca agctgcacat gatgattgta agaatgaccc agaattgttt gaaacattac 3120 ttgaagatgc tcaaaaacct ttatatcctg gttgtagaaa ctttacaaag ttgtctgcat 3180 tggtcaaatt atacaaccta aaagcacgat atggatggtc tgataaaagc ttttcagagc 3240 ttttaagaat tcttggagat atgttacctc taaacaatga gttgcccttg tctatgtatg 3300 aagcaaaaaa aacattgaat acattgggaa tggaatctga gaaaatacat gcttgtccta 3360 atgattgcat attgtatagg aatgagttga aggatgcatc ttcatgtcct acttgtggaa 3420 cttcaaggtg gaagttagat agaacaagaa ctaaaaagag gaagggagtc cctgcaaaag 3480 taatgtggta ttttcctcct attccaagat ttagaagatt gtttcagtcc ccaaaaattg 3540 caaaagacct catatggcat gcccaagaaa gagaatttga tggcaaaatg cgtcatccat 3600 ccgactcccc atcatggaag ctagttgatc acagatggcc tgattttgct tcagaaccta 3660 gaaaccttag acttgccatt tcagcagatg gtataaatcc tcatagttca atgagcagta 3720 gacatagttg ttggcctatt ataatggtca tttataacct tcctccttgg ttgtgcatga 3780 aaaggaagtt tatgatgcta tctttgttaa tatcaggtcc acgacaacct ggaaatgaca 3840 ttgatgttta tttagcacca ttattggatg acctaaaaat gttgtgggag gtaggggttg 3900 aatcttatga tgcgcatcag caagagctct ttacattaag agttgttcta ctatggacaa 3960 tcaatgattt tcctgcatat ggaaacttat ctggttgcgt agttaaagga tattttgcat 4020 gtcccatatg tggggaagat acatactctc atagattgaa gcatgggaaa aagaactcat 4080 atacaggtca cagacgattt cttccttgca atcatccttt taggaaacaa aaaaaggcat 4140 ttaatggtga acaagagttt cggtcacctc cgcaaccatt gagtggagag gaaattctaa 4200 ggaaaattga tgtcatttgt aattcatggg gaaaaaataa gatcactcga ggtaagttga 4260 atgtcaaaac tacaaattgt tggaagaaga agtccatatt ctttgatctt gagtattgga 4320 aatacctaca tgttcgtcat aacttggatg taatgcacat agagaaaaat gtttgtgaaa 4380 gcatcatcgg taccttactc aacattccag gtaagacaaa ggatggactt aattctcgtc 4440 tagaccttat ggagatgggc ttaaggtgtg aattagggcc aaggtttgaa tcaaatcgaa 4500 cttatctccc acctgcatgt tatacactat ctaaagtgga gaagaaggtt ttttgccaaa 4560 ctttatcaca attaaaggtt cctgaaggtt attgctctaa catgagaaac cttgtgtcaa 4620 tggaagactt gaagctttat ggtcttaaat cccatgacta tcatgcatta atgcaacagt 4680 tattgccagt gtcattacga tcagttttgc caaagcatgt aaggcatgct atttgtagat 4740 tgagtttttt tttcaatgct ctttgtagca aagtggttga tgtgcctgca ttggataagt 4800 tacaaaatga tgtagtggtg acattatgct tgcttgagaa gtacttccca ccttccttct 4860 ttgatatcat gcttcatctt actgtgcatc ttgtaagaga ggtcagactt tgtggaccag 4920 tttacctaag gtggatgtac ccatttgaaa gattcatgaa agttttgaaa gggtatgtac 4980 gaaatcgtaa tcggcccgaa ggttgcatcg ctgaatgcta tattgcagag gaagctattg 5040 aattttgtac agagtactta tcaaatgtag atgcaattgg gattcctatt agtgcaaaca 5100 ttgaccaaaa agttggggca cccatacctg gaggtcaagt tgtgacagtt gattccaatt 5160 tgtggttgca tgcacatcat tatgttttag agaatacaac tattgtccaa ccttatattg 5220 agtaagaact actaacactt aatatttatc tgttatactt aaaataactt tatgacatta 5280 actttgaatt tcttataaat aattacatag agagcacatg gaatggttga aattgaaaaa 5340 tcctcgtcaa tctaaaagac aaaagtggct ccaggatgaa cacctgcgaa cttttactta 5400 ttggttgcga aaaaaggtat tggattggtg ctaaaatttg aactattctt tttactaatg 5460 ttgaacatac atactaacta ttatttataa ttacagattg aagctgcaat tggtaacaat 5520 gaacctatat ctgaaaccct taagtggata gctcatggtc ctagccatta tgtctccaaa 5580 tatcatggat atgtcattaa tgggtgtcga taccatacca aggagcgtga tgacttacga 5640 gctacccaaa atagtggagt tagtattgta gcttcaacaa tgcaaattgc aagtgctaag 5700 gatcaaaatc cagtgtttgg tgagctttgt ttctatggga ttattaccga gatctgggac 5760 cttgattata ccatgtttag gataccggtt ttcaagtgtg attgggttga taataagaat 5820 ggcataaaag ttgatgatct tggctttaca ttagttgact ttaacaaaat tgctcataaa 5880 tcagatcctt tcattttggc atcccaagct aagcaagtat tttatgtgca agaccaactt 5940 gatccaagat ggtcagttgt tttgtcaact cctcaaaaag atttcttgga taaggaggga 6000 ggtgatgacc ttgtggacaa ttctattgaa caccatccct ttataggggc attgccacaa 6060 gttgaagcgt ttgatgcaat ggatgactca gatgcaatat gtatgcgagg tgactgtgag 6120 gggatttgga ttgagaacaa atcctctatg tagctgtatt ttaatgctaa tgtatgaata 6180 aaggccatgg aatgggttgc aacagccaca aaataggtaa tttttatcct ttctttattt 6240 ttttgcacaa aatattgacc attctttaac atctcccaat aacatattta ctaaaacctt 6300 ttccttaaat tgtgcatgga aaatactaaa ttagttatgt ttgtgagtaa aaaaattatg 6360 aaatttttta ttatcaatat gcatgttgtg ttttccaaac ttaatgtaac acaaaccgat 6420 agtccaaaag ctttcataag ttcttatgga cttgatgaac ttgttgaaac cacgtgctcc 6480 ttccatgttg attcttatag gaaattccta ctacaaattt agctttctta tacaaaggcc 6540 cttgggttgc ttaaaataaa taaaatgtta aacaaagcgg gacaaaaaaa agtttaaatg 6600 aagtgttatc cttgttatat gatgaacaat tctaaaaaga tctattgaat tcatgatcta 6660 ttgcatttca ttgtgcaatg attatggatt tgtttctttg aaaagttatg ttttataatt 6720 attctttgac taggttatat gcaatataat tttaactaat ctttatcatt ttttattttt 6780 tttgttacaa gaatggagac aaaggaagga gaaaaaccca taaaaaggaa gtacagaggg 6840 atgacacaga agcatatgat tataaaaaac agaagcaagg ggattaagtt gccggttaag 6900 tacaaatgta caatcttgat ggcattttca taggagaatc agcagttcat ctaacaagct 6960 acttaggcgt gttagcacgc actatggtgc caataagata taaaacttgg catgttgtac 7020 ctaaacagtt gaaggataag ttatgagaca acattgaggt aaccatttct tatttaaatc 7080 actttgatgc aaaatgtcta tcattcttaa cctcttgaaa ttactaaagt ttggtattaa 7140 tgtgcagact gatttttcat taaatcataa aagcaggagg aattgtatgt taacaatggg 7200 aaaatgcttt cagtccttta agaacttgct aacagtgaag tacattcttc ctttcgaaga 7260 ccaactggag cttctcaaaa gaccaccaat tcaatatact tttattgagg atgaagattg 7320 gataatattt gtcaaagata gattgtctga caactttaag gtataattaa gactctttac 7380 atacctctta ttcacattca ttaattataa aattttaatt tataggaata tcaagaaatt 7440 aaaaaagaaa gaagaaagat aaacatttat aatcaccatc taagtaggaa aggatatgcc 7500 ggtcttgagg aagagatggt aagtgtaagc ctattaattg ttttttattt attttatgca 7560 taatacataa tagggttata tgataattat attatagatt gtcctatttt gaaagatggt 7620 tgcaagtgga tcaactgaaa ctattgatcg aagcatattg tggaagaaag caagggaaaa 7680 aaaaggacgg cacctttgat gaagtggcca taccagtaat tgagaaaata gtaagtgaat 7740 atttttcaat tttaattaca tagatttata ataagttatt tacaataaca aatttgcaat 7800 ttaactttat aattaatatt ttttaaggac aagctattga aagagtctca agagaatggt 7860 agaagtgtta gtggaagtaa tgatatactt gtggaagcat tgggtactcc tgagtatagt 7920 ggtcgagtta gggccaaagg gaagcactac acacctcacc aatatttcaa tagtgttgca 7980 gatcgtgcta tcagggactt catagcagca tctaaagaag aacaaagaat atttcaggca 8040 gaagtgctag caaaactgtc tcaagtagga gctgctactc cccaatctga tgttagcagt 8100 tcaaacatga agcaaaaaca acttctccta ccagaagcag tggataagcc aatccgtaaa 8160 gttgaagatg tgaccccacc agaagcaata gaaccacaga agaaggtatt tattcagtta 8220 agctaatttg atgacaaagt ttcctctaat acgagaaata atttaattta attttgttgt 8280 ttgaattgac ttcaaatgtt ggtgacaaca tatatggtct tctttgatgt ggcaacatat 8340 aatatgatgt ctaaattatg ggttgagtta tatgcaatgg actgaaatgt tatcattcaa 8400 gtttgttgca attgaatgta aatgaaattg catttatcat tgtaatagga gttataaggt 8460 gattgatgat gataatgcat ttatgttagt tttgtataaa cccactaata ttgaagtgat 8520 tattgtgaat tgagttttgt aggttagaaa atttgagctg gccataggca ccaaggaaaa 8580 tatagtggca ggtggaacaa ttatacttga atgtggtccc aactatttag tagttgttga 8640 tgctccttat gattcaagtg caccccttcc cattcctatt cctggacaaa ctactactgt 8700 tggggctgca attggttacc aagttttgtg gccaactaat ttggtcatca tctgtactcc 8760 catcttagta agtaaatcta attaccaaac tttatagtga ctttatatat atataaacta 8820 gttaatttga tttgtaccat ggttcttaat tgtacaggca tctaagaaag caaagaaaca 8880 aaaagtaaat gaagttgaag tcaaatccaa gggtgaaaaa ccacaagata tgaaaaattt 8940 tgagacactg gttatcaaga acacacccta taaacttcct agatgatgtt tttggtgaga 9000 gtttcaagac cttcatgatg aaagaaaata ttgaaatgat aatatcatca aaagaagtgt 9060 catccaattg tattttatac tacatctggt aagggatttt ataatttttg aatgactttt 9120 cacaagatta tgagatagaa ggttattttc taatgaccta taatgattgt tgataacttg 9180 tcatgtgggt tataatcagg catttgcata gaaagttgat tgatgcaaag caggccgaac 9240 gatatgtttt tgtcaatcca gcattggtct caaaagctgg aatgggagag ggaagcaagg 9300 aaaacaggtc aaaggttatt gcagatcgac taaagaatac aaagcatgct gaatatatgc 9360 ttattccata caacccagag taacctttta tcctaaatat caatatggtg tttgtaagtt 9420 agtttgtcat gtttgaattt gtggatacta tattacaatt ttcatttctt ttctttagtt 9480 tccattgggt gttagtggca ttggagatga agaaaatgat tgcatattac cttgatccaa 9540 tggcctgtca accatgtgat gatcttaagg acatagttaa catgtaagta tatattttct 9600 cctattttaa tacaattgat agtgtctaaa taacatcttt ttaattcttt ttgtagggca 9660 atgagaatca acccaccgga aaaacagaaa acatcaaaga gagagccaac ttgggtgaaa 9720 gtggttgtaa gtacttattt gtttagatta aaatatattg cttcaccact taatttatga 9780 caaaaataga aaatggatgg ttattaatat gatcatcaat aagatgctaa agaagtaaga 9840 acatcattct agtgtttatt gcaattgttg atacttttcc catagtgccc aagacaacca 9900 ggtagtgtgg aatgtgggta ttacgtgatg agatatatga aggaaatcat tgctaatcca 9960 aaccaactaa catcaaaggt ttgcactcaa ttcaattcat atggttggtc attttactat 10020 agcatttttt tttttttttg gtcaattgaa cttagtgaat tgtatatgtc actccaattc 10080 agttttgcgg gaagaaatca tatagtgaaa tggaaattaa tgaagttcga tcagattggg 10140 ttatgttagt gactcagtta atcattactc atgtttgaag gtacctctta taacttatag 10200 tctaatacaa cttcatattc ttttaaagat gtagtcaata ttttgttaat gttaatttta 10260 taatggattt attcacaatg ataatttgtt aatgtatatc tttgtactcc tagttggtag 10320 tgttttcaat atggatcatt ttgggggttg ctctattatg attgatgtat agttggcata 10380 ttgagaggtg aagccaagta gacatggtag gtgtaacaac ttttgtatat ttcctctaca 10440 aattattatc agttagattt ggagaaatcc tacaatagca tagctacaaa aattcttgca 10500 tgtccaagct cattttcgta gagcctttag tttcattaca tgtgcatgaa ttaggaattt 10560 gtctattctc tacaaaagca tttttggtct ttaagattac tagctttata aacttcttta 10620 atctaaattt ataaaggtct cctactatac taatgggctt aaagtctata atatcttgta 10680 cttccatttt cttttacata aaaaatagga agttagttta agacttctta caaataagcc 10740 tatggaaaga aatagcacct cttactaatt ggttgttaaa ttgtttatta tatattcttc 10800 aggttgtaca aaaaggcata ggtcattcta ttaacaacgt cactattgct cttgatgaag 10860 gacacccaca aacaattcaa aatatatcat caaaagaatt ttgaggtaac atgttgtggt 10920 tattgtaagt tttatgaatc aattccatgt ttagagatca tttcatgcaa gttccatatt 10980 tagataatag atatcatcat attattaaat gttgatatac taatacaata agaagaacat 11040 agatatttta acacaatttt ataattttac ataaatatgt taatttacaa ttttataatt 11100 tttcggactt ctagtttttt ttgttttttt tttcattcct tagttccttc ttatgcaaaa 11160 catctaatgt cttgtacaat ctataagaag aatgagaaga tgttaatggt tgaagtttca 11220 taaataagat aaaaatcata ccaaaatagt caatgagata aaaacttttt tttttctgtt 11280 ttttttttaa aatagaataa gagttttaaa atatttagaa atttggtgta ataaaattat 11340 tggagtttgt tgagttcttt tgatattttg aaatttattg caatggaaga aagatatttt 11400 ggaaatttaa aaattggcat atacacattt catttacaaa gttgcttctt aactatttgt 11460 taatactaat aaatatgtaa ccctctcaat tattttgcag attgagcatc tagaaagtga 11520 gttacaacca tccttttgca cttggaagaa aaatgatgta aaactagatg tagtaaaggt 11580 tatgaacaat tcaaagttga agaagaagtt gtaaaattgt tggttttagt tgttgattat 11640 gtatgatgtt tatggataaa ttgtaatagt gaaaaaggaa gaccatattt gatacttttt 11700 gtcaatggag attcttaaat taagttttca ttattaattt aattgttgat agaaaattat 11760 aaaacagggc ataattagga cattttaatt tatgggctat taaaatttta tatgagataa 11820 gatgacgctt ttttaaagcg tcatgcttta cttgaataaa cagaagatga cacttctcaa 11880 aagcgtcaag gttgatgtta aaaaaacatg acattttttt ttagtgtcaa ggcataaaat 11940 gctatacgat gacacttatt atgagtgtca atgttgctcc tacaaataaa aaaactataa 12000 gatgacactt atattgagtg tcaatgttgc ttctacttat acaatgacgc tttattaagt 12060 gtcaacgttg ctcctacaaa taaaaagtta taagatgaca cttatattga gtgtcaatgt 12120 tgcttctacc tatacaatga cgcttcattg agtgtcaata ttgacatgaa tgaaattatt 12180 aacatatgat gacacttata aagcgtcaat gtttcaaata atgacactta ctatgagcgt 12240 cagggttgac gtgcaaagaa gatgacgctt ctaaaaagtg tcaacatatg tgatttaaaa 12300 agatgacaat ctaatatatg acgcttttaa aaagcatcat cttttgacat tttccttgta 12360 gtg 12363 // ID SHAMUDRA2_MT repbase; DNA; EDCOT; 589 BP. XX AC . XX DT 17-JAN-2007 (Rel. 12.01, Created) DT 21-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A putative non-autonomous DNA transposon from Medicago DE truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW SHAMUDRA2_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-589 RA Shankar R. and Jurka J.; RT "SHAMUDRA2_MT: Putative non-autonomous partner of SHAMUDRA_MT DNA RT transposon from barrel medic."; RL Repbase Reports 7(1), 101-101 (2007). XX DR [1] (Consensus) XX CC The DNA transposon resembles non-autonomous MuDr type transposon, CC with intact TIRs but imperfect TSDs. Present in Medicago genome CC in poorly conserved incomplete copies. Closest to SHAMUDRA_MT DNA CC transposon. XX SQ Sequence 589 BP; 197 A; 93 C; 84 G; 206 T; 9 other; ggctaaagtg cacttttccc ccctaacttt caaaaacttg caattttggc cccctaagta 60 caaaaactac aattttggcc ccctaagatt tagccccttt gcaactttgg tcctttaggt 120 caattttgac ctggtcaacg cttacgtggc atgccacatg tgtaattatt aaattaaaaa 180 aatttaaaaa gccacataat catttataaa ttaaaaaaaa aataaaaaaa attaaaaatt 240 aaaagaaaat raaaaaggaa gaaacgtgac rtttgatttg tttcttcttc ttctttaatt 300 tttttccatc tcttcttaaa ytcatcaytt caatttcata ttcaaattta tttttaattt 360 yttttttnat ttatttaatt tataaatgat tatgtggctt tttaattttt tttaattcaa 420 taattacaca cgtggcatgc cayataggcg ttgaccgagt caaaattgac caaaaggacc 480 aaagttgcaa aggggctaaw tcttrggggg ccaaaattgt agtttttgta cttaaggggt 540 caaaattgca agtttttgaa agttaggggt ggaaaagtgc actttagcc 589 // ID Gypsy15-PTR_I repbase; DNA; EDCOT; 4377 BP. XX AC scaffold_523; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy15-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4377 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4377 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 308-308 (2007). XX DR Genome; scaffold_523; Positions 26865 22489. XX CC Positions [3533-3766] - Integrase core CC 'TTCAT' target site duplication CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS join(26..2008,2012..3529) FT /product="Gypsy15-PTR_I_1p" FT /translation="MDTRGKSNAEFRSEVNEALARHETNFDQVHGTLQTIL FT TELQALRVSRSPRMNPPELNPFAPAESSGHNSGNHQSSLKLNFSKFSGEDP FT MGWIYKSEQYFEYNNVPPVQRVPLASFHLEGIALQWHRWMTKFQGPLTWEE FT FTKALLRRFGPTDFEDPSEALSRLRQTSTIAAYQEEFEKLSHQVDGLPETF FT LIGCFIAGLRDDIRLDVKIKHPTTLSDTIGVARLIEERNQLQKKVTHPFRI FT QPTAATTKPSMSNTVGVLGPPPNLRQSMNSTSNARRISTQEARERREKGLC FT YYCDEKFSPGHRCQRPQLFMICDSNDQESVEQSEILPAAEDQEAFPEISFH FT AITGTAHPQTLRVMGRLRSKEVMVLIDGGSTHNFIDQSIVHKYELPVIPDK FT KFQVIVANGEKIDCTGLCPSLTILIQGQIVTADYFILPVAACPVVLGVQWL FT VTLGPVETDYKRLTMSFKKDGNLCVFQGLKQSGLQELTEKEFNTMYVSSQF FT FAIIPVGSTTQPKSHSSEIAQLLSNFSHVFNPPTALPPKRPHDHQIMLQPN FT VQPVSVRPYRYPYYQKSEIERMVKELLHAGFIRPSHSPFSSPVLLVRKADG FT DWRFCIDYRALNDLTIKDKYPIPVIDELLDELHGAKFFSKLDLRAGYHQIK FT VQEEDIPKRRSTRIEFVVMPFGLTNVPATFQGLMNDLFRSHLRKFILVFFD FT DILVYSKSWEDHLSHLHTILTILSTNILLAKESKCRFGVTSVDYLGHVISE FT QGVSVDPSKIIAVLEWPTPTTVKGVRGFLGLAGYYRKFIRNFGTIAAPLNQ FT LLSKDGFKWNDMAEKAFNDLKQALTSPPVLALPDFTQPFVIECDACGVGLG FT AVLSQNNHPIAYYSEALKGSTLILSTYEKEMLAIVKSIKKWRPYLLGKPFI FT VRTDQQSLKYLLEQRITTPAQTRWLPKIMGYDYIIEYKKGVDNQAADSLSR FT VAECQFLSISTPHIDWWQKLQYEVAHDPFFTPLADSTTSTAAFSYQNGVWF FT KKGKIYLSPTSSLLQDIITECHSSPTGGHFGYHKTLSRLKQSFSWPQMRGT FT VKEFLRSCDVCQRYKTDSMRPAGLLQPLSIPDRIWVDISMDFIEGLPPSSG FT HTVVMVVVDRLSKYAHFVPMKHPYTAATVAQAFVSHIVRLHGIPASIVSDR FT DRVFISSF" XX SQ Sequence 4377 BP; 1242 A; 1003 C; 924 G; 1208 T; 0 other; attggtatca gagcctggtt tcaacatgga caccagagga aaatctaatg ctgagttccg 60 cagtgaggtc aatgaagctt tggctagaca cgaaaccaac ttcgatcagg tgcatggcac 120 tttacaaacg atactgactg agttacaagc cttacgcgtc tctaggagcc caagaatgaa 180 tcctccggag ttgaacccat ttgctcctgc tgaatcatca ggccacaact caggaaacca 240 tcaatcttca cttaaactga atttttcaaa attcagcggg gaagatccta tggggtggat 300 ttacaaatct gagcagtatt ttgagtacaa taatgtccca cctgttcaac gagtaccgct 360 tgcatccttc cacctagagg gaatagcctt acaatggcat cgatggatga ctaaattcca 420 gggaccatta acatgggaag aattcaccaa agcccttctc cgacgttttg gcccaactga 480 ttttgaagac ccctctgaag ctctttcaag actgcgacaa acttctacca ttgcagccta 540 tcaagaagag tttgaaaaac tctcccatca agttgatggc cttccagaaa cctttcttat 600 cggctgtttc attgcaggtc taagagatga cattcgcttg gatgtcaaga ttaaacatcc 660 aaccacacta tcagatacca tcggtgtcgc aaggttgatt gaagaacgaa accaacttca 720 aaagaaggta acacaccctt tccggatcca accaaccgca gctacaacaa agccaagcat 780 gagtaatact gtcggggtgc ttggacctcc accaaatctg cggcagagca tgaattccac 840 gtcaaatgcc agacgtattt ccacccagga agcacgagaa cggcgagaaa aaggtttatg 900 ttactattgt gatgagaaat tcagtccggg tcatcgctgc caacgacccc aattattcat 960 gatttgtgac tcaaatgatc aggagtctgt ggaacaatca gagatactac ccgcggcaga 1020 ggaccaggaa gcttttcctg aaatttcctt ccatgcaatt acaggtacgg ctcaccccca 1080 aacccttcgg gtgatgggaa gattgaggag caaagaagtc atggtattga tagacggtgg 1140 aagcacacac aatttcattg atcagtccat agtccacaaa tatgaattac ctgtgattcc 1200 tgataaaaaa ttccaggtga tagtagccaa cggggagaag atagattgca ctggattgtg 1260 tccatcactc accatcttga tacaaggaca gattgttaca gcagattact ttattcttcc 1320 agtagcagca tgcccagtag tgttgggcgt gcagtggctg gtgacactgg gaccggtgga 1380 gaccgattac aagagactca caatgtcttt caaaaaagat ggaaatttat gtgtgttcca 1440 agggctgaaa caatccggcc tacaagagtt gacagagaag gagttcaata ctatgtacgt 1500 atctagccaa ttctttgcta tcattccagt aggctctact acccagccaa agtcacactc 1560 ctctgaaata gcccaactct tatccaattt ctctcacgtt ttcaaccctc ctacagcctt 1620 accacctaaa cgaccacatg accaccaaat tatgctgcag cccaacgtcc agccagtcag 1680 tgtaagacct tacagatatc catattatca aaagtctgag attgaacgga tggtaaaaga 1740 gctactacac gcagggttca tacgtcccag ccatagccca ttctcttcac cggtcttgtt 1800 ggtcaggaaa gcagatgggg attggcgttt ctgcatagac tatcgagctc taaatgatct 1860 taccatcaag gataaatatc ctattccagt cattgatgaa cttcttgacg aattacatgg 1920 agccaaattt ttttccaagc tcgatcttcg tgcaggttat caccaaatca aggtacagga 1980 agaagacatc cctaaaaggc gttcaacatg aaggatcgag tttgttgtca tgccgtttgg 2040 acttactaac gtacctgcaa ccttccaagg tcttatgaat gatctctttc gttctcattt 2100 acggaaattc attcttgtct tctttgatga cattttggtg tattcaaaat cttgggagga 2160 tcatttaagt cacctccaca ctattttgac aatcttgtct actaacattt tattggcaaa 2220 ggaatctaaa tgcaggtttg gggttacttc agtggattat ttaggccatg ttatatcaga 2280 acaaggagtt tctgtcgatc cgtccaaaat catagcagtt ctggaatggc ctactccaac 2340 caccgttaaa ggggtccgag gatttttggg tttagccggg tactaccgaa aatttattcg 2400 gaatttcggt accattgctg ctcccctcaa ccagttgtta tccaaggatg gtttcaaatg 2460 gaacgatatg gcagaaaagg cgttcaacga tttgaaacaa gcattaacat ctcctcccgt 2520 tttggctcta ccagatttta cacagccgtt tgtcattgag tgtgatgctt gcggagttgg 2580 cctaggagct gtgctgtctc aaaacaatca tcccatagct tactatagtg aggctctgaa 2640 aggttcaacg ctaattctct ctacatatga aaaagagatg ttagcaattg tgaagtccat 2700 taagaaatgg agaccctact tgcttggcaa accattcatt gtgcgcacag accaacaaag 2760 tctcaaatat ttgttggagc agcgcattac tacaccagct cagactcgtt ggttaccgaa 2820 gattatggga tatgactata ttatcgagta caagaaagga gttgacaatc aggcagctga 2880 ttctctttca cgggtagctg aatgtcagtt tctttccatc tctactccac atattgattg 2940 gtggcagaag cttcaatatg aagtagcaca tgatccattc tttacacctt tggctgacag 3000 tacaacttcc actgctgcat tttcatacca aaatggagtt tggttcaaaa agggtaagat 3060 ttatttgagt cccacttctt ctttacttca agatatcatt acagaatgtc attcttctcc 3120 tacgggagga cattttggtt atcataaaac cctatcccga ctcaaacaaa gcttctcctg 3180 gccgcaaatg cgtggcacag tcaaagaatt tttgcgaagc tgtgatgttt gtcagcgata 3240 caagacagat tccatgcgac ctgctggatt acttcagcct ctatcaattc ctgacaggat 3300 atgggttgac atatccatgg atttcattga agggttacca ccatccagtg gtcatacagt 3360 ggttatggtg gttgttgatc gtttgtctaa atatgcacat tttgttccca tgaaacatcc 3420 atatacagct gccacggttg cacaagcctt cgtttctcac atagtccggc tgcatggaat 3480 tccagcttca atagttagtg atcgggacag agtatttatt agttcttttt agcgcacact 3540 gtttcgactt cagggcacga agttaggcat gagttcaagt taccaccctc aaacagacgg 3600 gcaaactgag gtgattaatc gtgtcttgga gcagtacttg cggtgttttg caggggacca 3660 accacgcaaa tggattgact ggattccatg ggcacaattt agctataaca ccttagtcca 3720 ttcagcaacc aaaatgacac catttgaggc agtgtatgga gttccacctc caaccttatt 3780 gatgtatgtc cctggaactt ccaacgtaca ggttgtggat ggatacttgc gtaatcgaga 3840 tgccatcctc tgtgagttga gaaagaatct ctcattagct caagcgcgga tgaaatgtca 3900 agcagatcag cggcgccgtg aggttaacta tgaagtgggc gactttgtct acttgaaact 3960 gcaaccatac cgacagactt cggtggcctt tcgcagttct ttgaagctat cacctcggta 4020 ttttggtcct taccaaatta cagaaaaagt tggaccagta gcttatcgat tgactttgcc 4080 tttggggtct ttgattcaca acgtctttca tgttagcatg ttaaaaaaac atgttggccc 4140 cgtcactacc atttctactc agcttcctcc tgtgaatgat gaagccaata ttctgcctca 4200 acctgagaca gttctggatc gcagagtcat ccaaaaaggc caatatcgtc caaaggttga 4260 agttctcatt aaatggacag gcgcctcact tgatgatgcc acttgggaag atgaacgccg 4320 attggctaag tcctatcctg cattccttgc ggacaaggaa tcctaagggt ggggaat 4377 // ID MboI_TP repbase; DNA; EDCOT; 163 BP. XX AC . XX DT 31-MAR-2005 (Rel. 10.03, Created) DT 15-APR-2005 (Rel. 10.03, Last updated, Version 1) XX DE T. pratensis MboI tandem repeat, consensus. XX KW tandem repeat; MBOI; MboI_TP. XX OS Tragopogon pratensis OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; campanulids; Asterales; Asteraceae; Cichorioideae; OC Cichorieae; Scorzonerinae; Tragopogon. XX RN [1] RP 1-163 RA Gentles A. and Jurka J.; RT "T. pratensis MboI tandem repeat."; RL Direct Submission to Repbase Update (31-MAR-2005). XX DR [1] (Consensus) XX SQ Sequence 163 BP; 50 A; 26 C; 29 G; 58 T; 0 other; gatcacacct ttgtgtaaaa agtcaatttt tcggtcaaaa agtcaaccgc tcgttttttg 60 accgttagat taacagttaa agtttgtgct tggttctttc tagttatttt tggcataaaa 120 actaactgaa gaagtttcgt gaaatttcgc aactgtcgaa aaa 163 // ID Copia5-VV_LTR repbase; DNA; EDCOT; 445 BP. XX AC AM470769; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia5-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-445 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-445 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 744-744 (2007). XX DR Genbank; AM470769; Positions 1122 678. XX SQ Sequence 445 BP; 133 A; 61 C; 85 G; 162 T; 4 other; tgttggaaaa ttttatatgg gctaacatta attgaataat ttgtatttgc aaaaacgggt 60 taatggatag tctattctat aatgagccca attaactagt gatcacattt tggattgggt 120 tttgcatctt ttgagtagaa gcttagttga gtggcaagtg taggctatgg gtctcattga 180 agcccattat gggagggccc aatgagaayc caatattgag ttatgctaag tccyctctct 240 aatctagata aaaagggttt tctgttttcc catagagcca mcatagytat tatcaagatc 300 atagagagga agacttggtt acaacaatca atcacgtttt tttttatcat ggctcaaaca 360 ggtatgttct ttatagtgat ttcctattat tagtatcctt taatcatgta tgattaatct 420 atgtgattat gtaaatattt ttaca 445 // ID Copia-1_TRe-LTR repbase; DNA; EDCOT; 267 BP. XX AC GU443966; XX DT 20-NOV-2010 (Rel. 15.12, Created) DT 20-NOV-2010 (Rel. 15.12, Last updated, Version 1) XX DE LTR from putative autonomous Copia family element. XX KW Copia; LTR Retrotransposon; Transposable Element; KW reverse transcriptase; retrotransposon; Copia-like; KW Copia-1_TRe-LTR. XX OS Trifolium repens OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Trifolium. XX RN [1] RP 1-267 RA Hand M.L., Cogan N.O.I., Sawbridge T.I., Spangenberg G.C. RA and Forster J.W.; RT "Comparision of homoeolocus organisation in paired BAC clones RT from white clover (Trifolium repens L.) and microcolinearity with RT model legume species."; RL BMC Plant Biology 10, 94-94 (2010). XX RN [2] RP 1-267 RA Laten H.M., Hand M.L., Cogan N.O.I. and Forster J.W.; RT "LTR retrotransposons in white clover, Trifolium repens L."; RL Repbase Reports 10(12), 2167-2167 (2010). XX DR EMBL/GenBank/DDBJ; GU443966; Positions 26647 26913. XX CC 5' and 3' LTRs are identical and flanked by 5 bp target site CC duplications, suggesting recent origin. Unusual 3' ends CC terminate in TA rather than CA. CC Genbank Accession GU443966 positions 21803-22069 and 26647-26913. XX SQ Sequence 267 BP; 76 A; 41 C; 41 G; 109 T; 0 other; tgacaaagta tagaatagtt tactagtgtt aattggcaag tcagacagtt acatttagtt 60 agaatggtag ttaggttgtt acagttagtt gaataagttg gttacactat catctcatgt 120 atataacact acacattgta atctcaattc attcattgaa tcaataacag ttttcatttc 180 tcactttatc ttcttccagc ttgagctatt ttcctccatc aatggagttt gttacatttg 240 ttttggtatc agattatctt cttgtta 267 // ID TOPSCOTCH_LP_LTR repbase; DNA; EDCOT; 239 BP. XX AC AF220602; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Lycopersicon pimpinellifolium retrotransposon TOPSCOTCH_LP_LTR, DE long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Long terminal repeat; KW TOPSCOTCH_LP_LTR; retrotransposon. XX OS Solanum pimpinellifolium OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-239 RA Lavelle T.D., Oldroyd E.G., Dalhbeck D., Staskawicz J.B. RA and Michelmore W.R.; RT "Direct submission."; RL Direct Submission to Genbank (04-JAN-2000). XX DR Genbank; AF220602; Positions 30265 30503. XX SQ Sequence 239 BP; 76 A; 37 C; 28 G; 98 T; 0 other; tggaaattag ttagcttagt tagttattat attcatttag ttagttagtt tgtaaagtta 60 gttacattga taaatgtgta gtaactaaat tctgttttag gattagtgta tatatataca 120 cagaatgtac tctgcaatat tacaatgaat attaagcctt gaataaattt ttcttttcct 180 ctcaactctt cttccccaaa gctcttcttc ctcacaaatc ttcttccaaa tttaaaaca 239 // ID EnSpm-5_VV repbase; DNA; EDCOT; 21507 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 18-OCT-2008 (Rel. 13.11, Last updated, Version 2) XX DE EnSpm-5_VV, an autonomous DNA transposon - a consensus sequence. XX KW EnSpm; DNA transposon; Transposable Element; TIR; CACTA; KW Cactavine-5; EnSpm-5_VV. XX NM EnSpm-5_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-21507 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 757-757 (2008). XX DR [1] (Consensus) XX CC EnSpm-5_VV (Cactavine-5 in [1]) is an autonomous element. Its CC individual copies are >90% identical to the consensus sequence. CC EnSpm-5 contains short TIRs which are flanked by 3 bp-long TSDs. CC Downstream of the TPase gene (region 15815-19903) is another ORF CC encoding for a ULP1-like protein similar to CAN79821.1. Although CC ULP1 (Peptidase C48) -like proteins are usually found in Mutator CC elements, our study shows that such proteins are common in CACTA CC elements as well. This feature is not restricted only to Vitis as CC similar examples were found in rice [1]. A MuDr-like element was CC masked by "x". XX FH Key Location/Qualifiers FT CDS join(11886..14359,14445..14550,14643..15284) FT /product="EnSpm-5_VV_Transposase" FT /translation="MDRSWMSKDRMSREYEEGVEYFINFALEHCPNQSGIR FT CPCMRCGNLIHHTPNKIREHMFFNGIDQSYHTWYWHGEAGPTSRQPTEMAQ FT CYDTMDCGDVASTVEMVHVIDDEFMTDPMSFKKLLEDAEKPLYPSCIKFTK FT LSALVKLYNVKARYGWSDKSFSDLLQILGDMLPVNNEMPLSMYEAKKTLNA FT LGMEYKKIHACPNDCILYRNELNDASSCPTCGMSRWKVNKAGARNTKRIPA FT KVLWYFPPIPRFKRMFQSPKIAKDLKWHAQGRENNGKLRHPVDSPTWQLVN FT QMWPEFASDCRNLRLAISADGINPHSSMTSRHSCWPVLTITYNLPPWLCMK FT RKFMMLSLLISGPRQPGKDIDVYLAPLVDDLKALWEVGVKAYDAHQREFFT FT LKAILLWTINDFPAYGNLSGCTVKGYHACPICGEETNSHWLKHGNKNSYTG FT HRRFLPCNHPFRKQKKAFNGEQEFRLPPKELTGDEIFTKVDMIHNSWGKKK FT KVKQCESFANPTSCWKKKSIFFELEYWKYFYIRHNLDVMHIEKNVCESIIG FT TVLNIPGKTKDGVKSRLDLLEMGLRPGLAPTFGLKRTYLPPACYTLSRKEK FT KIVLQTLADLKVPEGYCSNFRNLVSMEELKLNGLKSHDYHALMQQLLPVAI FT RSVLPKHVRYAITRLCFFFNALCAKVVDVSRLNDLQQDIVVTLCLLEKYFP FT PSIFDIMLHLTVHLVREVRLCGPVYMRWMYPFERYMKVLKGYVRNHNRPEG FT CIAECYIAEEALEFCTEYLSGMDAIGIPSSMKDEWKCGKPLLGGRAITIHD FT YKLVEQAHHYVLQNTTIVQPFIDEHMKYLKTKYPRQSKRVKWLEDEHVRTF FT SYWLRKNVSDDISKKEPIEKELKWLAQGPRQQVLTYPGYIINGCRYHIKDR FT DEARVNQNSGVSIVASTMQIASSKDKNPVLGDMCFYGIVTEIWDLDYNMFN FT ICVFKCDWVDSKNGVKVDELGFTLVDLSKIGHKSDPFILATQAQQVFYVED FT QVDPRWSIVLSRPKMELFDIEGDDNIADNCMEHHPFANGMPNIKSFDEVED FT YDEICMRTDCEGIWIEH" XX SQ Sequence 21507 BP; 7385 A; 2908 C; 3444 G; 7273 T; 497 other; cactacaaga aaaagagtca ttgttgacat atattatctt tacttaaagt agtatatgtc 60 aatatttttt atttaaatgg gcaactatga catataaaac ttagttaaaa gaaataatga 120 catatatgaa ttccagttat tattccatga cctatgacga tgcaaccttg acagagaatt 180 tataagtcaa tataaaatta atatatttgt atgtcaaggt agctaaataa aggcaataat 240 gacatatatg gaatttgcta aaattttctt taatttatag taatacaatc ttgatagaaa 300 aattataagt caatatatat agttaaaata ttcgtatgtc aaggttggta aaagctatct 360 tgacaaataa tttataagtc aatgtaattt catttataaa tctattaagg ttatattagt 420 aaatattgaa aatctcactt ctcatttttt ttcttttaat tcttttattt ttcttttaat 480 tctatctaga cccattccca tctagaagca acttgaaaga aaatcctaag aggccaccat 540 taaaaatttt gtgaaaagtt aaaatatttt tcatgaaaat ttattggatt agatatttat 600 tctccatgca aatatatatc ctttataggg tttaaatttt tgttttttgt tttttttttt 660 ttttgcattt tttatgacat ttattaaatg atgtaacatg aattcctttt atttggttta 720 ttattgcaac cataataatt atgaaaaaat tcattatagt attttaggaa aatttggaac 780 ttaaaaaaaa gtggtcctta attattttag gaaactatgg tactgtttag aagtaccatt 840 atataattca tttagacaac aagagaagac ataaaaattg tatatcaaat ttcattaatt 900 ataattttaa gataatgaaa ttgttttata tttatgcata aaaagttgga aataaaatat 960 gtaattttaa ttctctctta tctaagtcct aaggatgctt tgatctcata atatgatata 1020 aaccactggc atgaggttgt ccataatcta accttaaata tgaatgaaaa tttctttgat 1080 cttgagctcg ggttgtgcaa ggaatgctta cttaaggttc aagaacatta atcaaaggaa 1140 catgaaatta aagccaagtg aaaggcccat gaaatcttct tgaagaaata attaaaaaag 1200 agaataacaa ttaatgcaac aatgtttgtt ctcctatagt gcatctgtga catatcttca 1260 agtttagaag cgacttgaaa taattgttgt gtcagttaaa gaaaaacaca agattatata 1320 tatatattca taaaactgaa aatgtggctc atgaggtgga gtgtccaagg ttatttaatt 1380 cctcacttct atattaacca aaatttgata tcatatgatg taggagtcta ccaatgagaa 1440 aaaacccaaa atggaaattt gttgaaatta actattttgt ttttccatta tgcatccaag 1500 atgttatgtt agaatacaag atgcaagagc ttagcaaact acaaagcttt ttttgtcatt 1560 tttcgttgta ttgatgatca tttgttatga atttgtaaaa tataaacaaa attaaatata 1620 caaagaaaca aatattaata tagataacat ctatagagtg xxxxxxxxxx xxxxxxxxxx 1680 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 1740 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 1800 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 1860 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 1920 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 1980 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 2040 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 2100 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxatt 2160 aaacttaaat ataaataaaa taatgataaa ttatatttat ttaaaataaa taaattatga 2220 aagcctattt atgaacttaa ataaaaatat gataatattt tcataaatta tgatcctatg 2280 gacatgatgt aatattatga actaaaatta aaatataata aattttaaat ttaaattgaa 2340 cttatataga catgatatta tataccactt agatatggta tataaaaaat tattaattaa 2400 caaaagaaaa caagacatgt tgaccacgga ttattaaaga acacatggaa aagtggaatg 2460 tacaagttgc accacatacc gaaggctaat aaaaaattat ttctaaatcg taattatttt 2520 tttagattaa aaccaagtga atggattgta tcttgtgcct tggtgttttt ctcaggtcaa 2580 cttgatttat accatccaaa accacggaat ttgaatagtt caattaagat aaaattctga 2640 catattggaa tcatatcaac taatgatcaa cttaacgtaa gtaaatgaaa cccatttttc 2700 ggcttactgg acgtgaccct ttttagttcc acaactaaat ttttagttga gataatttgc 2760 taatcctttg aatagtaggc cccttataga acacaccaat cttctacaaa taccggtaag 2820 aagaaatctt agctcatcat tgccacttcg atatgaatgg acataatgaa gagaggcaag 2880 ttctcattaa gatacaagca ttcaatgcct tagaatttaa gctaaaagag gcgccatggc 2940 tagatttgag gtcatgtact tgagagccaa atctgataaa agaaacaaat tgagaaattg 3000 aaatgggggt gacatacctg aaatcatttt ttctactaat atcagaggcg aagtgccttc 3060 agatgcagta aaatgccttc tttcatggtc aactgagttg tcctcatcct tagctgctaa 3120 acaccatagc gtttaaaagt ttctttgttt gtattttcct tttctcaata tcacttcatg 3180 tatagcccgt gtttaagttg aaattgagaa tgcaagtttt tcccttgtaa aattttttta 3240 tgaaatgtag aagatagcat aaccctttct ttgcaaatta ttcctccaca tacaagaaat 3300 ataaatacgt agtctaatgc cctggctgcc cataaaccag atgttattat atatcaataa 3360 atctaaccat ggatattcat caaccaacat gtaaatttga aattaacatg acagtctaca 3420 gtttcatgac aatggtactc caaaaaagca aggcgggaaa actaatatat aataattaac 3480 cgagtaacta gtacacatgc tatgttattt tccaaatgat caagtccttg aatccaaggc 3540 catgatggtg ctaagattca tggggttcat gtacatggtt gagctggtca tgatctgttg 3600 tactatcagt ctgtttacct tttcggatgg atggaatgca tcccaaaacg catactggcc 3660 tcagttgggg cacaggtttg agagcaccgt gcaaagtccg agcccattgt tgggtccttg 3720 cccacaagat gctatctttg atgttgtaaa ccctatccaa tcataacata catgaataat 3780 gccattacat ttagtcctac tatgattaac aaattatctt ttaatttgtt gcatgcctaa 3840 ttaaattcca agcataccct tttcatgatg gaagtctttt tcaaaaagaa ggaaaagaga 3900 atcaatatat agttacatat atagaaacta acgtaccaaa tgcctaagga tcagttatga 3960 agtccgtatg catttcttgt gtattagcag cgatgaaaac atctgcatga aactttttat 4020 tgagtcctta tagcatctga atgagttgtg ggttgaacag ggctgaagct tgctgcaatt 4080 tagctgcgca ctctccgttt ttgctcctca tgacatgttt tgctggtaca caccccattg 4140 gtctagtgcc cgtcacaaaa acccttcgtg ttccaagctt atatagcctc tgcaaccata 4200 agtttagacc atacatataa gtcactaaaa tatataacat taatacattg tattttgtta 4260 gaaaatggga caacccaacg cacaaaatag taatagtgct tatttataaa gtttacatgc 4320 attggaaaag gctctaatgt aacaagtgtc tctacctacc aaaacaagtc tcttgtgata 4380 gactatcata tatgcaatac cataatgcat ttgccctcaa ctcatcccca attcctcatt 4440 agatttaata gtgaatattt tatgcagatt aggccaaaat gtaacacatg ctggggagaa 4500 ttaccattag aatttttcgg cacttagaga tgagatagca aacataattg ggaagagtaa 4560 attggcgaga tcttgtagag ttgggcacca agtagtagtt gttgacaaag tcgtttctgc 4620 ctagagtgat gaggacgagt gctttaaaca aaaggaaaca agacatgttg gccacagatt 4680 attaaagaac acctgggaga agtggaatgt acaagttgca ccatgtatgg aaggctaata 4740 aaaagttatt tctaaatagt aattattttt ttagatttta aacaaaagga aacaatacat 4800 gttgaccaca gattattgaa gaacacatgg gagaagtgga atataaggat gcaacacata 4860 ccaaaggcta ctgcctgaaa atgatgacgg accaagcttg aaaaagaaag tgaagcacag 4920 ggttgtctct gaagaaatta ttagttggaa aaacgcactc aaaatctcgt tagtaatagg 4980 atatcaccct tgagattgtg gaccaaaagc gagatggatg gactctccct atgtcctcat 5040 ctttcctttt ccggttcaag gtggccacct caacgccatg cttaaactca cccaaatact 5100 gcgtgttgag cctccagctc aaataccatt gccacaattt ttttaatcca tacaacttac 5160 aagaaaaaca aaagcattcc aaattctagt aaatgacatg caaaaaaaaa gtaaagaaaa 5220 caacataaaa tcacaaacgc acaaacaaaa tgattcaaat ggttcaccca ataaagttgt 5280 attgataggc aagggcagtg aacaaacttt accaattata taaaaaaatt tacctcttct 5340 agaaaaccca ccaaaaagca cccataacca taaagcttga aacgaaaact attttaattc 5400 aattgattta cctcaaagtc cacaaaaatt aatatctaag acaagagctg aacacttgtt 5460 gcatgtcaga ttccccacgg tgagttctga tggagttgac aactgtgttc tacatgatga 5520 gctaaaaaac gtttgggtct agccatcccc tccacctctt cacgaatcat ttgttgcata 5580 ttgaaactgc tatggtgttt agtttgaagg aaagaagaag acgacatcac aatgagacta 5640 ggtgctgctg atctaaatgt gcatgtgtgg agggataaag agggagaatt aatggacggg 5700 aagcatggat atcattatga caaatgggtt ttgggcagcc caaagcatgg gatgtgtcag 5760 aagaaagacg cttgatgtct gatgaaggtg gtagggatag gtttttttat tgcctaaaga 5820 atatgttgtt gcagggtatg gcatggtcta aagtacttgt cttgagcaac taaaaataag 5880 ctttaaagag agagtggtat ggcagatacg ttttaagcca tctgaaatat gagcagtagc 5940 aagtagtaac aaagcacaat tgatgggtga gagaaatggg aagctaggct aacgacctat 6000 ggagactatt gatggacggt tgatgcatgg gttagtttaa ggtgtgtttg gtatgtttta 6060 aattagatga aatctaagta taaatatttc ataaaatcat acaagttgca tatttgtttt 6120 ttatttagaa aattaattta ttttatgttt tgatatgtga attttaatat catataaact 6180 ttacttatga ttcatgatat ccaaaaataa taactatttt cgcatgttta ttataaaaaa 6240 aaaacacatt ttgttttata ttttaagaca tgaattagat aaccataata aactcaaatt 6300 ttaattttgt ttttggttca taaagtatta aaaagagaat tgctttgata tattaataaa 6360 ctaaaatctt tattttgatt taggattcct gtgatgttaa aaaattaaat tattttatca 6420 taaaataaag ctttgaatat atatttaata accttaacat attatttctc aatttaatca 6480 ttcaatatat tgattaatac ctcaatttct ataatttata agataaagtt aacaaaaaaa 6540 cttgaatctt attaaatcat tcttaaaaaa gaaaaaaaaa agaaaaaaaa gaaaaaactc 6600 attccaattc attatcaaaa ccttattgta ttttatattt ttaaagaata tgatatcaat 6660 tattatatta ttttaaaaca tgaatttatt tgtaagaatt aaggttttag aattctaaac 6720 aaacctaaat atgttgtaaa tcaataataa taaaaaataa aaataaaaac aaagtcctaa 6780 actaataatt aagggtcact acaaacaaaa tagggatcca cttagtctct ccaaaatatc 6840 taattgaaaa tccaaaacta gtgatcaata tagtcttagt ggaccatcaa ttaataagag 6900 ctaaacacaa ctcaaaaaat gaccacaatt gcacactaaa gcatcaaagg atgtaggagg 6960 acaatcctat atgaaatgtg tcaagagaac aaaatagagg gtttataata ttctaagaaa 7020 aaaaaaaaca cattaccata tacataatca ctttgtaaaa aatgttttca ttaggattat 7080 aattgaaatg ttgatataga aattaaataa gatgtagaaa ttcattatgt ttcttatata 7140 ttattgtatt tggatgccat ataaaattat aaataagaat tcattggaaa acaaatataa 7200 atcttgttta actaactatc aaatgaaaac tagatgaagc aaaatataat tttaaagtat 7260 tgtgttttcc tttatttgtg ttttataatt tttaatctat ttagtctttt catgtttttt 7320 tttttttaaa aaaaaaaggc aaaaaaaatt gctcttaaga agctccctat attgttaatg 7380 aaaaaacaat tatctgataa tgttgttaat ttctaaaaat aatatttagt ttttaaaaat 7440 gaaactatat tttgaatggt atggtagaac tattacaaaa tattgttatg attgactaag 7500 ttttcttacc tcataaaaca aaaggttctc cctccaatta caaaatgtct gttttgagat 7560 tactttattt tatttttttc ttattttctc tccttctaag ctttcttttt gttttatgat 7620 tctctaagca taatatgtgt ttgtctttat atatattata ataattataa gagatggatg 7680 aatgcacctc cctatttcaa ttttaatttt ggattattgg tcaagttgta ataccattat 7740 atatatatat atatatatat atatatatta tttcaattct tcaaagtaca gtgatctttc 7800 tcattagcca tttaaaaaat atatatatta atacaataag ctttaaaatt tcatttccat 7860 cttgaatttc tcgaataaaa gattctatta agaaaattag agaagagaat ggattaagaa 7920 aattagggga gagaaaatgg acgaatgtga aatttgaaaa aaaaaggtta tattaaaact 7980 tcataagtcc ttttctgata tgttatgtaa tctagattat aatatatgtt atattaaaaa 8040 atattattat tttttaaata tcccattatt ccaactggtg gtcttggtag tgagatacta 8100 aatgagtata cgtttactta attccagaat tgcaagaagc atgacaaaga ggccattgaa 8160 aaatatattg gacatgttat cctagcatcc tgcaagtgta aaggcaatgt tggaaaagtt 8220 tagagtagag ccttggaggt agtggagtca cgtcatcagc atcctaacta ttaagtgctt 8280 aaatgctgca tgctagatgg gaagtggagg actacttata ggctatagga tagtggagaa 8340 aatgtcatct ctccaatcat catccctaaa ttgttagcta cttatagctt gtcaaaatat 8400 tgaacattac cacccaatcg gtggagaaaa aaataaataa aaagcaggaa aaaaaatcca 8460 taaaaagttg ttgctatata tttaaacgtt tttgatatat ataattagaa tcaaggataa 8520 aaatatcaat aattacaaat atattggtac ttcgatttta gggatatatc gaaaatatca 8580 taaaaatatc aatgaatatt ttttcccaaa tatgggtgga gcgaaaatta tttaacattc 8640 ataggaatgc tcggaaaaac tgtaaaaacg ataaaataag caagaataca cattttgaaa 8700 ttattttgta agtataattg acatagatgt gataaaaaga aaaaaacata gataaacaaa 8760 catatatcgg tagattcaat atttcaattt taagaataat aaatatgcat tttggaaatg 8820 tataaagtta gaatagagtt aaaaaaatat ttgtttttat tgaataaaaa taatttatac 8880 atatgacatt gcaataggac ttagtatcaa aatgaagatc gatatggttc tatcatattg 8940 ttagatgaag ggagtctatt ttgttgaaga caatatttat tttcaaaatt ttaaaatact 9000 tttatcataa catgttttat tacattttaa atgaaaaatg aaattaattt atatcaaata 9060 ttttatttga gatttattaa aattattaat aaattatctt atgaaattaa ttttaatttc 9120 taaaatatgg cctttagaaa gcaaaattgt tgatttcatc aagcgaaatt tctcataatt 9180 tgtttcattg tttttttttt ttttttttac taaatctaaa aataaaaaag ccacccactt 9240 cctttgactc ggccatgaag aagccatttt tgaagttgcc ttccacaaga gagaatccct 9300 aaaaaggcca ttgtttcctc tgccactctc attgaagttg ccttccacaa gagagaatcc 9360 ccaaaaaggc ctttgtttcc gctgccactc tcattcaacg caggtactga tctaataagt 9420 ttattattac tattattatt attgcaatcc ccatttgatt cccatgaaaa tccatcaccc 9480 attccatttc caagaagatt cttcctctgt tgatttcgaa gacaatccat gcaaaacccc 9540 catggaaaac cataaaataa aataaaaatg cttttttctt tgctctgtgt ggtttctgga 9600 tgtgttgtaa gggtctctta gcttttgtgc cattggattt aaatattatg aaccctaact 9660 ccacgatttt tgaggcaggt tgaaaaactc aacctttacc tgcaaatcat ggtcatatta 9720 ttgaatagca tgttatgtct ttttttaaaa aaaaaaaaaa acggacagat tttgtatcct 9780 gtgcgtggct tggactagta ggaaatatcg gtaaattttc cgaaaaatcg gtaaaaatac 9840 cgattaatac caaaatatca gataaatttt ggaaaattta ccaaaatttc tgtggaccaa 9900 taattggtta cgaattttgt gttggagtcg gctgatcaat gatatttctc tctgaaatag 9960 tattttattt ataattatta tgaaagcaat gataaacaat ttattaaaaa acatgacaaa 10020 ttttatggta aaattattta ttaatcaaaa attgtttata tgaaaaagat aaacattaaa 10080 tatgaaaatt ctaaaattat tgaaagaaaa atattataaa ataaatatca taaataattt 10140 aagatggata ttttataatt ctaatttatt tattacaaaa atcattataa aatattttat 10200 tgctatgtaa taatggtaca caattaccaa cccattgtag aaataagcaa agctttctca 10260 aactgcatgg atacgtaatg atgatcctat ctttttatcc aaaaagtaga acaagaaaca 10320 tgaaacctgg atgagaaaag aggaaacaaa caaggggaaa aagaactaag agttttaatg 10380 gatattgatg ttctatttgt tgtttaaaag ttcatatcct tgtaccaaaa atgcaggtcc 10440 tcctaatcat gggttagttt tttaatttct caatcattag aggacaattt caagggacaa 10500 gtcttgttaa ggtaattctt tactctctca tgtttctctc tctctatact ttcccatgaa 10560 actctaactt gtcaatactt catttttttt taaaggaaat tgaacatata taatcaaact 10620 tgtagttgag ttatttgatg gttagtagat ttggtctagt gggtgggttt acttttgatt 10680 taatttgatt ccattgaatg tgacgttgat gactttatat tttgagtatt aacttttgtt 10740 tgtttgtggc caagtgtaat taaatttctc tactcatgat ttttcaagta aatatatttc 10800 ttttttccgc tactaggcaa ataacaaata tgttaaagga attaaatgta tttcatttta 10860 atgtgttaag gatacttaga tagaatttaa ataagttcat gcatgaaaca ttagacttcc 10920 cattctagca tccttgtatg acaaaaattt ctcttattac atgctaagga catttaagtt 10980 gtcaaagaat gcaaatggtt cattgatgaa ctagtttgaa gttgacaact tctaacttag 11040 tctagcatgt gaatgagact ttttttctac aaatgatgct tgaattgtcc aattggacaa 11100 tataaggaaa acataatatc tttgaagtta cgctcttatg cttcattcat tttttagaaa 11160 tttcgacatt cgttcctttt gttctctggg tgcatatttg gacaaggctg aataatatgc 11220 cttctccatt ttgtgtactt ggagaactat agggtaatgc tattgaaatt tttctaaaat 11280 gaaacgaaat agaatagtag ttgacatgta gggattatgt tttcctatat ggaataggaa 11340 ccaccaccta aactagaaag ttggagatgt tagaatgcat atgacatgta gtttaacttg 11400 attttagttt aacaagatag aatcatgaga gttaattatg tttcttggtt taatattttg 11460 atatataaat ttattttaat tttacagata tatgcataat aaatgatctt tgacgattcg 11520 ctattgaata aagacttgaa aaagtgtaac atatatttat ttctcatttg tatggtagtg 11580 cataaactag ataggatcat aattctataa gagaaccgca ttttttactt tggttcaata 11640 cctaatgaaa ttaaatgtat ttaataagat gaaatatcat gaactaatag gaattttaaa 11700 tggataattt atggcattac ctacaatgac atgaattgaa tatgacaatt tttataatta 11760 actatctcac tttgatatac ttgtagacaa catggctata ttacatgatg aatccttttg 11820 atatatgaca caacattaat gttaaaattc ctcatgatta attcattgtg tatttcaatc 11880 atagaatgga tcgaagttgg atgtctaaag atagaatgtc acgggagtat gaggaaggag 11940 ttgaatactt cattaatttt gcattagaac attgtccgaa tcaaagtgga attcgttgtc 12000 cttgtatgcg atgtggaaac ttaatacatc atacacctaa caagattcgg gaacatatgt 12060 ttttcaatgg tattgaccag agttatcata catggtattg gcatggagaa gcaggtccta 12120 ctagtagaca accaactgaa atggcacaat gttatgacac gatggattgt ggtgacgttg 12180 ctagtacagt agaaatggtt catgttatag atgatgagtt catgacagac ccaatgtcat 12240 ttaaaaaatt gcttgaagat gctgaaaaac ctttgtatcc tagttgtata aagttcacaa 12300 agctttctgc attagttaaa ttgtacaatg tgaaggcacg gtatgggtgg tcagataaaa 12360 gcttttcaga tttactccaa atattagggg atatgctacc ggtcaacaat gagatgccct 12420 tatccatgta tgaggcaaag aaaacattga atgcattagg gatggaatac aaaaagatac 12480 atgcatgccc aaatgattgc atactataca ggaatgagtt aaatgatgca tcttcatgtc 12540 ctacttgtgg aatgtcaagg tggaaggtaa acaaggctgg ggcaagaaac actaagagga 12600 ttcctgcaaa agtgttgtgg tatttcccac ccatccctag gtttaagagg atgtttcaat 12660 ctcccaaaat agcgaaagac ctaaaatggc atgcacaagg tagagaaaat aatggtaaac 12720 ttcgacaccc agtggattcc ccaacatggc aactagtgaa ccaaatgtgg cctgaatttg 12780 cttcagattg taggaacctt agacttgcta tttcagcaga tggtatcaat cctcatagct 12840 ccatgaccag taggcatagt tgttggcctg ttctcacaat aacttacaac cttccccctt 12900 ggttatgcat gaagaggaaa tttatgatgt tatctttgct aatatcagga ccacgacaac 12960 ctggtaagga tatcgatgtt tatttggcac cattagtcga tgatttgaaa gcattgtggg 13020 aggtaggggt gaaagcctat gatgcacatc aacgagagtt cttcacatta aaggctattt 13080 tgttatggac gattaatgat ttccctgcat atgggaactt gtctggttgc actgttaagg 13140 gatatcatgc ttgtccaata tgtggtgaag aaacaaattc acattggcta aaacatggga 13200 ataagaactc atataccggc catagaaggt ttcttccatg caaccatcca tttagaaagc 13260 aaaagaaggc atttaatggt gaacaagagt ttaggttacc tccaaaagaa cttactggag 13320 atgaaatatt tacaaaggtt gatatgattc ataactcatg gggaaagaaa aagaaggtta 13380 aacaatgtga atcctttgct aatcctacaa gttgctggaa aaagaagtct atattttttg 13440 aacttgaata ctggaaatat ttttatatcc gacacaactt ggatgtcatg catatagaga 13500 agaatgtttg cgagagcatc attggaactg tgcttaacat tccaggtaaa acaaaggatg 13560 gagtaaagtc tcgacttgat cttctcgaaa tgggcttaag gcctggctta gcaccaacgt 13620 ttgggttgaa gcgaacttat cttccccctg catgctatac tctaagtaga aaggagaaaa 13680 aaatagtatt gcagacttta gctgatttga aggttcctga aggttattgt tcaaacttta 13740 gaaaccttgt gtccatggaa gagctaaagc ttaatggtct taagtcccat gattatcatg 13800 cacttatgca acaactacta ccagtagcaa taagatctgt gttgcctaag catgtcagat 13860 atgccattac aagattgtgt tttttcttta atgcactttg tgcaaaggtg gtggacgtgt 13920 caagattgaa tgatctacaa caggacatag tggtgacttt gtgcttgcta gagaagtatt 13980 ttccaccttc catctttgac atcatgcttc atttaacagt gcatttggta agagaggtta 14040 gattatgtgg accagtgtat atgagatgga tgtacccatt tgaaaggtac atgaaagtcc 14100 tcaagggtta tgttcgaaat cataatcgtc cagaagggtg cattgctgag tgctatatcg 14160 ctgaggaagc cttagagttt tgtacagagt atttatcggg catggatgca attgggattc 14220 cttctagtat gaaagatgaa tggaaatgtg ggaaaccatt acttggtggt cgtgcaataa 14280 ctattcatga ttataaattg gtggagcaag cacatcatta tgttctacaa aatacaacca 14340 ttgtacaacc ttttattgag taagtgtcat atatgtgaat atatgagttt gaaactctag 14400 ctaatgttta tacaaaccat gacttgccta tttttccttg atagtgaaca tatgaaatat 14460 ttgaagacaa aatatcctcg tcaatcaaag agagtgaagt ggctagagga tgaacatgtg 14520 cgcacattta gttattggct tagaaaaaat gtatgaaact caatattcat actcccctta 14580 aaatttaatg cttacaaaat tttaaattac attaacttac atatcattaa tgaaccttat 14640 aggtttcaga tgacataagt aagaaagaac ctattgaaaa ggaacttaag tggcttgcgc 14700 aaggaccaag acaacaagtt cttacttacc ctggatatat cattaatggt tgtcgttacc 14760 atatcaagga ccgtgatgag gcacgagtca accaaaatag tggtgtcagt attgtggcat 14820 cgaccatgca aattgcaagt tccaaagata agaatcctgt gcttggtgac atgtgttttt 14880 atgggattgt cacagagata tgggaccttg attataacat gtttaacatt tgtgttttta 14940 agtgtgattg ggttgatagc aagaatggtg tcaaagttga tgagcttggt tttacattag 15000 ttgatttgag caagatagga cataaatcag atcctttcat tttggcaacg caagcccaac 15060 aagtatttta tgtagaagat caagttgatc caagatggtc tattgtatta tcaaggccaa 15120 aaatggagtt gtttgacata gaaggtgatg acaacatagc cgacaattgt atggagcatc 15180 acccatttgc gaatgggatg cctaatatta agtcttttga tgaagttgaa gattatgatg 15240 aaatttgtat gcgtactgat tgtgagggga tttggattga acattaagct taatattttt 15300 ttttgttttt tagggttgtg ctttgtgact actaagtgta ttatgtgttt tttgagttat 15360 tgttaatata caatgtgata ctcaacaatg ttatgttttt attttattct tctcaaatat 15420 atttttacta ttatatactt gataagctat tctaaataaa tgcagttagt atcatattta 15480 tatatattga gatttaagat taattttcat gtattgcaaa gtttgtacaa caatgattta 15540 ttcctactta tgaaatcatt ttgtaactaa tttctttaga tttagttgag atacattttc 15600 aagtgttgtt tattagtgca taattcttaa ttatttggga acttaggtga aaagtgcaac 15660 atctttacgg atgtctcaac caagaagaga taaagagcaa gtaaccatta aaatatcatg 15720 atttactttt gaatgtaaga tatatatata tatatatata tatgtattat gagattgatc 15780 atattctttt gattgtcatg tagatggatg aaaaaggaag gggaacagaa gattacttca 15840 ccaaaaaggt tcagaggccc aactgtaaaa cctgaaattg ctaaaaagag aagtgaagga 15900 gtgaaaattg acattcaata taatgataat ggtgagggag tgggtgaggg atatgtacag 15960 cttgtatcat acttggggat gctagcacga accatggtgc cagtatatca tactaattgg 16020 agagtagtgc ctatggaatt gaaggagaaa ttatgggatt gcattaaggt atataataat 16080 caattgaaat tattttccta tattttgtgt agaccttaca cgattattaa ataattaaga 16140 tcttcttata aggtatatag taatctactt aaattatttt cctatatttt gtgtacacct 16200 tacatgctta ttaaataatc aagatcttat attttagggt gcattcttgg ttgatgagaa 16260 tagcaaatac aacgtcatat catcaattgg gactagcttt aggtcattca ggcacacatt 16320 gacgaaaaag tatatcctgc cttacaagga taagcccgag taccttttgc aaccaccaat 16380 tgaagactgg agaaagttag tggctaatag gttgtcaaca gagtttcaag ttaaatcaaa 16440 aaaaggaaaa gaaaggaggg aaaaatactt ttatattcac caagtgagta gaaaaggata 16500 tgcaggactt taagaagaat tggtgagttg aatttgtgta ttttattttg ttggacattt 16560 acttttgtaa agtttaatta cttcactttt ttgttttttt atagatgcaa aagacaggtt 16620 caaggaaacc tattgataga tgggtcttgt ggaagctagc aagactgaaa aaaggtgaat 16680 atgatgatgt tacaaggcct atagaggaaa agattgtaag ttgtcaaacc tatacttagt 16740 tttagtcaat ttcatttgtt tttgtttttt ttttttaata tgactcttga agcatcttat 16800 atttttctga ggatgagtta gcaaaggctg ttgaggaaga gaagatcaca tgtgttggcc 16860 aaaatgatat cctcacttta gcattgggta catccgagca tcttggacgg gttagaggaa 16920 aaggtgggaa aaaaaaaagc caaaaaaatt cttcaccaca ccaaaaccca caaaaactct 16980 tgaagaagag gaatgtcaaa ggatgttaag ggagaaagta aagagcttgg aagaggagat 17040 catttctttg aaagctaaaa aaaaaaaaaa gaacccctca caccccactc taaagtgagc 17100 agcacaaaca taaggaaaca attgttggaa catgaagaaa tacgagggaa aactcattat 17160 agtgctcatg tggagaacct atcagtagaa ggaactcgaa aagcttctcc actaactcag 17220 gtatatatgg cttttcctaa gttaaattta taaaaacaat atataaaata actataatga 17280 aagactaagg attataaaat atgtttttac aggtttataa atgcaaatta gctcttgaaa 17340 ctgaagagaa cattgttgca tatggaactt atttgcgaga ttcaaagatt tccattgatg 17400 gaactgatat attagtggtc atcctttacc ctcttcaacc taatgcactt cttccattcc 17460 cgctgtctga aaacattagt acaataaggg agggtgttgg atatgaggtt ttgtggcctg 17520 ttgcatttgt gataaatgat gaaaatgatg aggtgaataa tcttataccc aaactttcaa 17580 agttgagtta tattttccta cactcttggt ttatttattt ttcattttaa tgtcatgcat 17640 ctatttatgt gtttaggatt ttggcaaaag gaagaataaa atgaagaaga tacaagcatc 17700 cccaaagaaa atcaaatatg agaatcctag agatatacaa ctgttttcta atacagtttc 17760 agcaatgttg gagggtaaac cggcacccaa agttgacttt ccaatcaatg tttttgggat 17820 gaaatttcaa accttcctct tgacaactga aatgaaggat gtaatttctg caaaagagtt 17880 gactatgaat tgtatatgtt tctatatttg gtgagatttg ttgtaaatct ttatgttaca 17940 ttcatgatat aaataagtag aagctgtttt tttttttttt tttaagtaat tctaaattag 18000 gtgatatttc attaggtggc tgcatgaaca tctagatgat acactacatg agaaaattat 18060 atttgttcat ctcggaatgg tgtctaaggc tggaacaata gccccacaaa ttgaaaaaag 18120 agcaaggttc attgctgatc gcctaattga ctccaaattg gcatatctga tttttcttcc 18180 gtataaccca aggtaatttg ttaattataa ttgtttttaa tttcttagcc ttataaatgc 18240 tatttttcta aattatatgt taatatattg taggtttcat tgggttttgg ctgtaattga 18300 cctcaaatca caaacagtat actatttaga ctcactatta caacagccat accaagatat 18360 aaaagatatt gtgaacatgt aagtctacca taattttagt tttcatgtct caaaataaac 18420 actaatgtaa tcttattttt tgtaggaggt ttcgaatttt tgtatctcaa aagaaaaaag 18480 gatctaaaaa agagctcaag tggatagtta ttgaggttac atttttttct tcttctaaac 18540 tttttgaaga cttacccaca tttaagttgc tttcttgaat taaaagttta cttgattttt 18600 gaaatgtaaa gattctatat ggcttcctct cacatgaata tatacctata tatatgaatt 18660 ttcttagctt ataattgttt ttgttattat ttcctattca taagttgagt ggagaaggat 18720 accatatacg tttgtttcac caccttatga aaatataatc taaattgcta tgaatacaat 18780 gtacccattt gtctattatt ccactagtaa tgaagtagta ctaaaaaaga acaaacctat 18840 agtatttaca atcctttaca acaatttaga tatatgtgtg ggtaaggaag caatgaggat 18900 tcatttagat agctttgatc atgttactta ggtgtgagtt gttctttata tctttctttt 18960 ggccttagta tgtcttatat acatcctatt atttagttta gatatttatt gtaaggcaca 19020 acctctctct ctctctttct ctctttaatt taaacttttt actcttttat ccatcttcaa 19080 tcaaatggtt caaatgtaaa acatttattc cttataatta ctaattgtat ttctcttcta 19140 taatgtcaat ctatgagatg taaaaggatg ctaatactac atatttccaa atatattatc 19200 gataattgct cttgaagctt gattgattta ccttaatgaa gtcttaaaag tcatgatctt 19260 ttctaaggga tattttcaca cggacaaaag ttaactattt tttttaaaag ttaatcacta 19320 ttcttaataa atataattaa tcattacctt tatctattcc tttttttgtc catatttcac 19380 atatacatgt tatttgacat tcttatattt tacccaattt aaccctccaa gttgtaaaca 19440 ggggagctta gggtattatg ctagacatga attgacttaa tttatgtgca aattttactt 19500 gaaactaaca ttatgtcatc cattgttttt ttaaatttta aatgtgaagg atgaaaaaat 19560 tgaccaaatt tatatgttgt catatttgat cgtgaaattt gattgatata attttgctta 19620 tagggaccca aacagttgga tggtgtcatg tgcggatatt ttgtcatgcg atacatgcga 19680 gacataattg caaatagaag tctcctaaca tctcaggttt atttacctat gtattttcat 19740 aagtacatga gaacttatac atatatttaa tgtttcatgt taacatattt tctcttctca 19800 tatattttag ttcgaaggga aaaaaaccta ttcgcgagtt gagttagatg aagtgagatc 19860 tgaatgggtc tcatttttta gcactcttat cttagaccaa gtatagtggg tatgtgaatt 19920 ttatagtttt ttaataaaat ctcaaacata aattttaatt aatgttgcat cttttctctt 19980 tgcaaggtat atggtgacac ttgcagttgt tgcaattttg agatttcaag atcatacgta 20040 agatcttatt gtcatgcata gatgctgaag ttttggatac ttttgggtac atacctatat 20100 cttttaaaag atacatttga tgaaattacc aattcatgtt tttgtttttt attattctct 20160 atgtttgttg gattctttta gcataaattt tcgtacatgt taatatcatt ttagtaaaat 20220 tttaaatata gacttaaagt aatgtagttt gtttatctac ttgcaagaag ttgaataaca 20280 tttgtagtag ttggaatttt gagaatacaa catcagcata ggttcttact atcatgtatg 20340 taaagttgca attagttttt tcttttattg gatattctta ggtacatatc ttatctatat 20400 ttttttcctt aaaagttcat tgctagattt tattttattt ttttttatgt attttggtac 20460 atgtttatat ctttttaatt agtactttta aatataaaca taaactaatg ttgttttttt 20520 cttatttgca agaggttggg tgatatttgc aacatttaca atttttaaag tacaagatca 20580 tgcataagtt tttgtcatca tgtatagcta ttagattttt tggtaaatat ttgtcatttt 20640 atatatatat atatatatat atatatatat atatttgata agagtacaag atcgtgtata 20700 gttgcttggt tgtttgtgaa tacatttgga tatatttggg tacatgctta tatttttttt 20760 ttaaaaagtt tgaaacataa acataaagta atgttgtttt tttgtccata tttgcctttt 20820 ttggatgtat atgtgatgat aatacaagat tatgcaagga tattaagctt tttttttttg 20880 tcaatatatt tgcctacatg ttcatattta aaaaaaaaaa ttatacattc atgtacttta 20940 tccatatata tacacacata acaggttcaa tttttatgta gatcatttgg gcaacaggtt 21000 aggttgttga catgttccat atgcaacctt gatatgaaat aaaacaattt cttttatatg 21060 aataaagaaa tcttgacata aaagacattg tattccttga cataagaata aaggaacctt 21120 aacatattaa aatttcaact ttcaaaaaaa aaacaaatcc ttgtcatatg tgtaaattaa 21180 atttaaaagc atatacaaca acattgacat atatcatact taagcttaac atatattgaa 21240 tataatcttg acaaaacaat gagttaacct tcacatatgt ttaacctaac cttgattgat 21300 gtggaagaaa cattaacata tgtcatatta ataagattcc tacgttgata gaaataaggt 21360 ataccttatt tcatgcatat gtcaagctaa cttttatcat ttcttgacat tagcatagat 21420 aacatttgtg aatactgatc taccttaaca gatatacctt atcttgacaa tgaaaaactg 21480 tcaatgaaga ccttttttct tgtagtg 21507 // ID Copia11-VV_I repbase; DNA; EDCOT; 4005 BP. XX AC AM443574; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia11-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4005 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4005 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 677-677 (2007). XX DR Genbank; AM443574; Positions 565 4569. XX CC Positions [1416-1916] - Integrase core CC 'GATTT' target site duplication CC LTRs are 81% similar to each other. XX FH Key Location/Qualifiers FT CDS 1320..2858 FT /product="Copia11-VV_I_1p" FT /translation="MVPRFSTLSSLPCESCQLGKHTRVSFPKRLNNRAKSP FT FELVHTDVWGPCRTASTLGFQYFVTFIDDYSRCTWLFLMKNRAELFSIFQK FT FYAEIQTQFNISIRVLRSDNAREYFSAPFTLFMSHHGILHQSSCAHTPQQN FT GVAERKNRHLVETARTILLHSNVPFRFWGDAVLTACYLINRMPSSVLHDQI FT PHSLLFPDQPLYFLPPRVFGCTCFVHILTPGQDKLSAKAMKCLFLGYSRLQ FT KGYRCYSLETHRYFISADVTFFEDSPFFSTTSESLPISEVLPIPIVSPPDA FT MPPRPLQVYHRRPRVAAPLPFAEAPADSFPTPSASPAPALPSPDDLPIAIR FT KGTRFTRNPHPIYNFLSYHRLSSPYSAFVSAISSVSLPKSTHEALSHPGWR FT QAMVDEMAALHSTGTWDLVVLPSGKSTVGCRWVYAVKVGPDGQVDRLKACL FT VAKGYTQVYGSDYGDTFSPVAKIASVRLLLSMTAMCSWLLYQLDIKNAFLH FT GDLVEEVYMEQPPGFVA" XX SQ Sequence 4005 BP; 863 A; 1027 C; 812 G; 1303 T; 0 other; tggtatcaga gccaagggag aaaacctaat tctttctagt ttcccgtgtc atcaactccc 60 ggaaaccttc cggtgaccgt gtttcattcc ggtcaccttc ctcatctccc aatactttcc 120 ggtcagtcgg atcgtcgtca gaaaacactc accgccgaca aaattttccg gcgaactttt 180 ccggcgaact ttccggtgac gtctttttcc gacaccaacc ataccagaag gagcgcctgg 240 aggagatctc caacttttgt gaaggcaccg gaaccaaaat cttatccacg cgccggccac 300 gtgcaacttt ccggtcggcg actgaatctc acgtgccggc gcgtgagggc gcgtgaggcc 360 ttttccgatg acgcgcctcc tcctccagct tcgcctgacg ccgaccagcc tccctacatc 420 cttggttctc ccattcgagc cctacacgta cctcttttgg ggatttttgt ctccgtcggc 480 cctccaaaca gtctttccgg cgaagctccg actatttttt ctccacccca atccctgcac 540 gtgccttggg aagtgttctt ccacctttct ggtggtacca cgccgcgatc tgaggtcgtc 600 tccctttttt ggtggtgcca cgccgcaatc tgaagccgta ttaaggctct cttcgatcca 660 aacatacttc attctccaga taagtggata tggctactaa aactcgcgat cgttgctatc 720 agttacatgg acggcctcct cgcactgccc atatggccca gtcctctgat tctccgctgc 780 ctcagcctcc gagctcctcc gcatctcaga catctcaggc ttctattgcc tctgttgccc 840 agcctggtaa tgcctcagcc tgccttaccc acacatcttc tcttggaccc tggattttag 900 attctggagc ttctgatcac ctatctggta ataaggatct tttctcctcc attactacta 960 cctctgcttt acctactgtt accttaacta atggttctca aactgtggct aaaggtattg 1020 gtttagccct tcctttgcct tctctacctt tcacttctgt cctttatact cctgaatgtc 1080 cttttaatct tatttccatc agcaaactca ctcgtactct taattgctct attacctttt 1140 ctgataaatt tgtgaccttg taggaccgga gtacggggaa gacgattggc ataagacgtg 1200 agtctcaagg cctctatcac ctcacctcgg attcatctgc tgcagtttgc atttccactg 1260 atgctcctct cctcattcac aatcgtctgg gtcatcctag tctctccaag ttccagaaga 1320 tggtccctcg tttttccact ttgtcgtcgc ttccgtgtga gtcatgtcag cttgggaaac 1380 atactcgtgt ctcattccca aagcgtttga ataatcgggc aaagtctcct tttgagcttg 1440 tccacactga tgtttggggt ccttgtcgga ctgcgtctac tttaggattt cagtattttg 1500 tcactttcat tgatgactat tctcgatgta cttggttatt tttaatgaaa aatcgagctg 1560 agttattctc tattttccag aaattttatg ctgaaatcca aacccagttc aatatttcta 1620 ttcgtgtgtt acgcagtgac aatgctaggg aatatttttc agccccattt actttgttta 1680 tgtctcatca tgggattctt catcagtctt cttgtgctca tactcctcaa caaaatgggg 1740 tagctgaacg caagaatcga catcttgttg agacagctcg tactatcctc ctccatagta 1800 atgttccttt tcgtttttgg ggggacgctg ttcttaccgc ttgttatttg attaatcgta 1860 tgccctcctc tgtcttacac gatcagattc ctcactctct tctcttccct gaccaaccac 1920 tttatttcct tcctcctcgt gtctttggtt gtacttgctt tgttcatatt ctcactcctg 1980 gacaggacaa gctttccgcc aaagccatga agtgcctttt cttgggatat tctagacttc 2040 aaaagggtta tcgttgttat tcccttgaga ctcatcgata ctttatctcc gctgatgtca 2100 ccttctttga ggactcacca ttcttttcca ccacttctga gtctcttcct atttctgaag 2160 tcttgcccat tcccattgtc tccccacctg atgctatgcc tcctcgacca cttcaggttt 2220 atcatcgtcg ccctcgtgtc gctgctcctc tcccttttgc tgaggcacct gctgactcat 2280 ttcctacccc ttcggcttct cctgccccgg ctctgccttc tcctgatgat ttacccattg 2340 ctattcggaa aggtactcgc tttactcgta atcctcatcc tatttacaat tttttgagtt 2400 atcatcgatt atcttcaccc tattctgctt ttgtttctgc tatatcctct gtttctcttc 2460 caaagagcac ccatgaagct ctttctcatc caggctggcg acaggcaatg gtggatgaaa 2520 tggctgctct gcactctact ggcacttggg atcttgttgt tttaccctct ggtaaatcta 2580 cagttggctg tcgttgggtc tacgcagtta aggttggtcc tgatggtcag gttgatcgcc 2640 ttaaggcctg cttagttgct aaaggctata ctcaggttta tggttctgat tatggtgaca 2700 cattctcccc tgttgccaag attgcttctg tccgtctgct tctctccatg actgctatgt 2760 gttcttggct tctttatcag ttggatatta aaaatgcctt ccttcatggt gatcttgtcg 2820 aggaagttta tatggagcaa cctcctggtt ttgttgctta gggggagtct ggtttagtgt 2880 gcaggttacg ccgttttcta tatggcttga aacaatctcc tcgagcatgg tttagccgtt 2940 ttagttctgt tgttcaagag tttggcatgc ttcgcagtac agcagaccat tcagttttct 3000 atcatcataa ctccttggga cagtgtattt atctggttgt ttatgtggac gacattgtca 3060 ttacaggcag tgatcaggat ggtattcaga aactaaagca acatcttttt acccactttc 3120 agaccaaaga cttggggaaa ctcaagtatt tcttgggaat tgagatagct caatccaatt 3180 ctggtgtggt cctttcccaa aggaagtatg ctttagacat cctggaagaa accggtatgt 3240 tagactgtaa accggtagac acacctatgg atccgaatgt caaacttgta ccaggacagg 3300 gggagccttt aggagacccc gggagatatc gacggctcgt aggtaaattg aactatctca 3360 ccattactcg tccagacatt tcttttcctg tgagtgttgt tagtcaattc ctacagtcac 3420 catgtgatag ccattgggat gccgtaatcc gcattctttg atatatcaaa agtacaccag 3480 gccaaggtgt attgtacgag aacagaggtc atactcaggt tgttggttac acagatgcag 3540 attgggctgg ctcacccata gatagacgtt ccacttcagg gtactgtgtt tttattggag 3600 gtaatctaat atcttggaag agtaagaaac aagatgtagt ggccagatct agcgttgaag 3660 ctgagtatcg agctatggct ttggcaacat gtgaactcat atgattgaga catcttcttc 3720 gggagttgag atttggaaag gatgaacaga tgaaactcat ctgtgataac caggccgcat 3780 tacatattgc atctaatcca gtctttcatg aaaggaccaa gcatattgaa gttgaccgtc 3840 atttcattag agagaagatc gcatcaggat gtgttgctac aagttttgtt aattcaaatg 3900 atcaactagc ggacatcttc actaaatctc tcagaggtcc taggattaaa tatatttgta 3960 acaagcttgg tgcatatgac gtatatgctc caacttgagg gggag 4005 // ID DNA9-10_Mad repbase; DNA; EDCOT; 154 BP. XX AC . XX DT 20-OCT-2010 (Rel. 15.1, Created) DT 20-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-10_Mad. XX NM DNA9-10_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-154 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1491-1491 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TSD is 9-bp long. TIR is not obvious. Termini are similar to CC those of DNA9-11_Mad. XX SQ Sequence 154 BP; 47 A; 36 C; 16 G; 55 T; 0 other; gggaacttta acgaaaagca cccggtactg ttcactttaa cgaaaaacca catttttaca 60 ctaaaaagtc aatcctggta ctattcactt taccctttat tttgtcctta tcattaaaac 120 tcaaagtttt caagcccttt tcattagttt tcct 154 // ID Copia10-PTR_I repbase; DNA; EDCOT; 4428 BP. XX AC LG_I; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia10-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4428 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4428 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 192-192 (2007). XX DR Genome; LG_I; Positions 3196760 3192333. XX CC Positions [1779-2102] - Integrase core CC 'AAGAT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(84..2102,2106..3986) FT /product="Copia10-PTR_I_1p" FT /translation="MNNLLRKAKTMPSILFFLYHSDHPGLVLVSKPLNGDN FT YSTWCRSMTISLNAKNKLGFIDGTVQIPPAKSQPNDYASWKRCNDMILSWI FT LNSISPELADSVIYSTTAQEVWEDLRDRFSQSNAPRIFQIERDIACTSQGQ FT MTVATYYTKLKGLWDELGSYSSTVCSCGADHKRRQLMQFLMGLNDSYKAIR FT GQILLLNPLPDVRQAYSSIIQEEKQHSLNDTQEAAETTAMTIQRDALTALA FT VRSGQGASSRSNSFNCKPLHCSYCDNDHHVRDTCWKLHGYPLGHPKHKASR FT FNRQGSRPPYNKSAYPSANYVKEGPTRQEMQSVMNGFSDLQFQQILSIMNN FT NGIEQSSQPQANAAVNSSGLLQAPYSLPQLILDSGATDHITSSPNLLVNSR FT QNSILPPVTMPSGEQAPITSTGTLPLNSVISLKNVLVVPSFKVNLMSISQV FT TRGLNCLVTFFPYWCILQDLATKTTIGLGKQRGRLYYLVALASPTPTPKFQ FT SSAAIATKSFCSHVISSTELWHRRLGHLSSSQLNFMANNLLNFPFKLHDAC FT DICALSKQCRLPFSASSISSIRPFELIHCDIWGPYKIPSLSGAKYFLTIVD FT DYSRFTWVFFMHHKHETQNLLTNFFSFVKTQFNASIANIRVDNGGEFFSMR FT NFFRQHGTTYQHSCVYTPQQNGVVRKHRHILESARALRFQAHLPLHFWAEC FT VLTAVHLINRLPIPLLSHQTPFEKLYGKVPTYSHLKIFGCLAYATEVHAAH FT KFAPRATRCVFLGYPVGQKAYKLYNLSTYKFFTSRDVVFHEHIFPYKSSPP FT ILAHHASTPDSAAPSPVLPLSIPDAPTADYPVSNPASPTSVPPNFSPSVPS FT NITQSSPPLIPVQPLRRSQRHHNPPPALRDYICNQVTSPKPSLASSSGSSK FT GTRYPLCNFLSYHRYSPQLCFYTATISQDIEPRSYTEAASFPQWQAAMQSE FT LAALEANNTWSLTSLPPGKTPIGCRWIYKIKRHSDGTIERHKARLVAKGYT FT QLEGIDFHDTFYPTAKMITVRCLLALAATQNWSLHQLDVHNAFLHGDLHEE FT IYICPPPGLRRQGENLVCRLNKSLYGLKQASHQWFAKFSAAIQAAGYVQSK FT ADYSLFTCRNGKSFTALLIYVDDILITGNDLKAVYTLKRFLHSHFRIKDLG FT DLKYFLGIEVSRSQKGIAISQWKYTLEILKDGGILGAKPVNFPMEQNTKLS FT DAGDLLNDPSQYRRLVGRLIYLTITRPDIMYSVYVLSRFMHAPRKPHMEAA FT LRVLRYLKGAPGQGLFFSSQNDLSLRAFCDSDWAGCPMT" XX SQ Sequence 4428 BP; 1166 A; 1061 C; 821 G; 1380 T; 0 other; tggtatcaga gctggtaacc tagctctctg ccgttttttt tcttgctcca attttccctg 60 ccaattgtcc agtattatgg agcatgaaca atcttctaag gaaggcaaaa acaatgcctt 120 cgatcctttt ttttctctac cattctgacc acccaggatt ggtgctggtc tccaagcctc 180 tcaatggcga caattattcc acctggtgca ggtctatgac gatttctttg aatgctaaaa 240 ataagttggg atttatagat ggaacagtac agataccacc tgccaagagc caaccaaacg 300 attatgcttc atggaagaga tgcaatgaca tgattctgtc atggattctc aattcaatct 360 cgccagaact tgcagacagt gttatatatt caactacagc acaggaggtt tgggaggacc 420 ttcgtgatcg gttttctcag agcaatgccc cacgtatctt tcagattgag agggacattg 480 cttgtacttc tcaggggcag atgaccgttg caacttacta caccaagctg aagggattgt 540 gggatgaatt gggttcctat agcagcactg tttgctcctg tggagcagac cataagagaa 600 gacagctgat gcagttcctc atgggactta atgactctta caaggccatt agaggacaga 660 tcttattgct gaatcctctc cctgatgttc gccaagcata ttcctctatt attcaagaag 720 agaagcaaca cagcttaaat gatacacaag aggcagcaga aactacagcc atgacaatcc 780 aacgagatgc cctcacagct ctagcagttc ggtcaggaca aggcgcttcc tctcgctcca 840 attcttttaa ctgtaagcca ctgcattgct catactgtga taatgatcat cacgtacgag 900 atacatgttg gaaactgcat ggttacccac taggccatcc aaaacataaa gccagtcgtt 960 tcaaccgtca aggaagtcgt cctccttaca acaagtctgc ttatccttca gccaattacg 1020 tcaaggaagg tcccacaagg caagagatgc agtcggtcat gaatggcttc tctgatttac 1080 aatttcaaca gatattgtcc attatgaaca acaatgggat agaacaatcc tctcaacctc 1140 aggccaatgc agctgttaat tcttcaggtt tgttgcaagc accatatagc ctacctcagt 1200 tgattcttga cagtggtgca acggatcaca ttacttcttc tccaaatctg cttgtcaata 1260 gtcgtcagaa ttctatttta ccaccggtta ctatgcctag tggagaacag gctccaatta 1320 cttctaccgg gactttgcct ttaaattctg ttatttctct caagaatgtg cttgttgtgc 1380 cgtcctttaa agtgaatttg atgtctataa gtcaagttac aagaggtcta aattgtttag 1440 taacattttt tccctattgg tgtattttgc aggacttggc gacgaagacg acgattggtt 1500 tgggtaaaca acgaggcaga ctttattact tggttgcctt agcatcacca acaccgacac 1560 caaaattcca atcctcagct gctattgcta ccaaatcatt ttgttctcat gtcatctcct 1620 ccaccgagtt gtggcatcgc cgattagggc atttatcttc ctctcaatta aattttatgg 1680 ccaacaattt actcaatttc cctttcaaac tccacgatgc atgtgatatt tgtgctcttt 1740 caaaacaatg tcgacttcct ttttctgcta gttcaatttc atctattcga ccgtttgaat 1800 tgattcattg tgatatttgg ggcccttata aaattccttc cctgtccggt gctaaatatt 1860 ttttaacaat cgtggatgat tattctagat ttacatgggt attctttatg catcacaaac 1920 atgaaacaca aaatttactc acaaattttt tttcctttgt caaaacacaa ttcaatgcat 1980 ccattgcaaa tattcgcgtt gataatggag gggaattttt ttccatgcgg aatttttttc 2040 gtcaacatgg cactacttat caacactctt gcgtttatac acctcaacaa aatggggttg 2100 tatagcgtaa acatcgtcat attcttgagt ctgcacgtgc ccttcgcttt caagctcatc 2160 tccctttgca tttttgggca gaatgtgttc ttaccgctgt gcatttaatt aatcgcttac 2220 ctataccact tctttctcac caaacccctt ttgagaaact ttatggcaag gtccccactt 2280 actcacatct taaaattttt ggttgccttg catatgccac tgaagtgcat gctgcacaca 2340 aatttgctcc tagagccaca cgttgtgttt ttctcggtta cccggtcggc caaaaagctt 2400 acaagctcta caacctttcc acctataaat ttttcactag ccgtgatgtt gtcttccatg 2460 aacacatttt cccttacaaa tcatctccac ccattcttgc acatcatgca tcaacccctg 2520 attctgcagc tccctcccct gtcctacctc tttccatacc tgatgctcct actgcagact 2580 accccgtctc caatcctgct tctcccactt cagttcctcc aaatttttct ccctcggttc 2640 ccagtaatat cactcagtca tctcctcctc tgattcctgt gcagccctta cgccgttccc 2700 agcgccatca caaccctcca cctgctttac gtgattacat ctgcaaccaa gtaacgtctc 2760 ccaaaccatc gttggcttcc tcgtctggtt catcaaaagg tacacgctat cctctttgta 2820 attttctttc ttaccatcgc tactcaccac aactttgctt ctatactgcc accattagcc 2880 aggacattga gccccgttct tacactgaag ctgcttcctt tccccagtgg caagctgcca 2940 tgcaatctga attagcagca ttggaagcta ataacacctg gtccctcact tctctccctc 3000 ctggaaaaac acctattgga tgtcgctgga tctacaaaat caaacgccat tcagatggta 3060 ccattgaacg tcacaaagcc cggttggtgg caaagggtta cacacagcta gaaggtatcg 3120 acttccatga cactttctat cctactgcta aaatgatcac cgtccgttgt ttgttagctc 3180 tggcagcaac acagaattgg tcccttcacc aactagatgt gcataatgct tttcttcatg 3240 gtgatcttca tgaagaaatt tatatatgtc cacctcctgg tcttcggcga cagggggaga 3300 atttggtgtg tcgcctcaac aagtcattgt atggattaaa gcaagcttct catcaatggt 3360 ttgctaaatt ctctgcagct attcaagctg ccggatatgt tcagtctaaa gcagattatt 3420 cattattcac ttgtcgcaat ggtaaatcct ttactgcatt gttgatatat gttgacgata 3480 ttttgatcac aggtaatgac cttaaggctg tatacacact taagagattt ctgcatagtc 3540 atttccgaat taaagatttg ggcgacttga aatactttct gggaattgag gtttctcgat 3600 cacaaaaagg cattgctatc tcacaatgga agtacacttt ggaaattctg aaggatggtg 3660 gcattttggg tgccaaacct gtgaactttc ctatggaaca aaacacaaaa ctctcagatg 3720 caggtgattt acttaatgat ccatctcagt ataggcgact tgtgggtcgt ctaatttact 3780 tgactattac ccgaccggat atcatgtatt ctgtatatgt gctaagtcga tttatgcatg 3840 caccacgcaa accacacatg gaagctgcct tgcgtgtgtt gcgttatctg aaaggtgcac 3900 caggacaggg tttgttcttc tcttctcaaa atgatttatc tctgcgggct ttttgtgatt 3960 cagattgggc tggttgccca atgacttgaa gatccactac aggttattgt gttttcttag 4020 gatcttcact tgtttcttgg cgaataaaaa gatagaaaac agtatcgctc tcctcagcag 4080 aagccgaata tcgagtcatg gcaggtacat gctgtgagtt gtcgtggtta cgttcattat 4140 taaaagattt acggatatta catccgaaac cagcattact acattgtgac aacaaagcag 4200 ctttgcatat agcggctaat ccagtttttc atgagagaac caggcatata gaaatggatt 4260 gtcattttat tcgggataaa atataggatg gatccattat aaccaaattt gttatttcgg 4320 cagatcaact tgcggatgtc ttcactaagc cattgggaaa ggagattttc tctaccatga 4380 ttcgcaagtt gggagttctc gacattcact ctccaacttg agggggag 4428 // ID Copia31-PTR_I repbase; DNA; EDCOT; 4254 BP. XX AC LG_II; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia31-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4254 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4254 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 238-238 (2007). XX DR Genome; LG_II; Positions 8206539 8202286. XX CC Positions [1666-2166] - Integrase core CC 'ACAA' target site duplication CC LTRs are 88% similar to each other. XX FH Key Location/Qualifiers FT CDS 373..2745 FT /product="Copia31-PTR_I_1p" FT /translation="MRLKDLKVKNYLFQSIDRTIMETILNRDSAKGIWDSM FT RQKYQGSTKVKQAQLQALRREFELLGMKDGENIDDYFGRTLTIANKMKSHG FT ERMEQIVIIEKILRSMTAKFDYVVCSIEESNNLAEMTIDELQSSLLVHEQR FT MKGHKEEEQVLKVMSEAREDVRFGGRGRNRGGFRGNFRGRGRSWGRQSFNK FT AIIECFRCHKLGHFSYECPGYEKTANYAKLDCEEEMLLMSHVELHNSTREE FT VWFLDSGCSNHMSGNKLWFTELDEKFRHSVKLGNNSRMAVMGKGCVKLKVA FT GAIQKIDKVYYIPELKNNLLSIRQLQEKGLAILIQHNACKLFHPTRGLIME FT IAMTVNRMFIMFAATPLNESVAFFQAGEESETQLWHSRFAHLSFKGLRTLY FT YKKMVEGLSPLKAPTKVYVDCLVGKQHRENISKKSHWRASSKLQLIHSDIC FT GPVNLESNSGKRYLITFIDDFSRKCWVYFISEKSEALNMFKMFKNLVEKKA FT GSLVGCLRTDRGGEFTSKEFNEYCSMNGIKRQLTAAYTPQQNGVAERKNQT FT IMNLVRSILSEKCIPREFWPEAVNWCMHVLNRSPTAAVPDITPEEAWSGVK FT PSVEYFRVFGCIGYVHVPHEKRTKLDPRSTKCILLGISEETKGYRMYNPET FT RKLIVSRDVIFEENASWNWAEDNINTLLRWRGDDNSISEEEFEGNEDEERE FT QEQIEETENEVSAGDEVENMKKNIMSLFKLLLSEIKGHHTGWRIMSQEQVC FT LKRRKHKIWSSTPLLKIHTPMKKPKKIKNGGKPWIMKLLQ" XX SQ Sequence 4254 BP; 1511 A; 628 C; 1038 G; 1077 T; 0 other; agtgagagtt cttgagaaga gaggagtgaa gagagaaaca ctgagagttt ttttttagtg 60 agaccatcaa gaaagcatag aggagtgaag agagaacagt gagagttcta gtgaacctga 120 gaggagtgaa aagaaaacag tgagagttcc agttaagaga ggtgagactt tcaggagatc 180 aatcaaagtc atggctgaag gaaattttgt tcaaccagcg attcccagat ttgatggtca 240 ctatgaccat tgggccatgc taatggaaaa tttcttacgt ccaaagaata ttggagctta 300 atagagattg gaattcccac aaatacaact ggcgcagaac acacggaggc tcaacaaagg 360 aacgtggagg agatgagatt gaaagatttg aaagtaaaaa attatctctt tcaatccatt 420 gatcgtacta ttatggaaac aatcttgaac agagactctg caaaaggaat atgggattca 480 atgcgtcaaa aatatcaagg gtctactaag gtgaaacaag ctcaactaca agcactgcgg 540 agagaatttg aactgctcgg aatgaaagat ggtgagaata ttgatgatta ttttggaaga 600 actcttacca ttgccaacaa aatgaagtca catggtgagc gtatggaaca aattgtcatt 660 attgagaaaa ttctgaggtc tatgacagca aaattcgact atgtcgtatg ctccatcgaa 720 gaatcaaaca accttgctga aatgactatt gatgagcttc aaagtagtct actcgtgcat 780 gagcagagga tgaagggaca caaagaggaa gagcaagttc ttaaggtcat gtctgaagca 840 agagaagatg ttcgatttgg aggaaggggt agaaaccgtg gaggattcag aggaaatttc 900 agaggcagag gcaggagctg gggaagacaa tctttcaata aagctattat tgaatgcttt 960 cgatgtcata aactaggaca tttctcttat gaatgtcctg gttatgaaaa aacagcaaat 1020 tatgcaaaat tggattgcga agaagaaatg ttgttgatgt cacatgtgga acttcataac 1080 tcaactagag aagaggtatg gtttttggac tccggttgca gcaatcatat gagtgggaat 1140 aaactgtggt ttacagaatt agatgaaaaa tttagacatt cagtcaagct tggcaacaat 1200 tcgagaatgg cagtaatggg aaagggatgt gtaaaattga aagtagctgg tgcaatacaa 1260 aagattgata aagtttatta cattccagag ctgaaaaaca atttactcag cataaggcaa 1320 ctgcaggaga aaggactagc aatacttatt caacacaatg catgcaaact gtttcatccc 1380 actagaggtc tcatcatgga aatagctatg acagtcaaca gaatgttcat catgtttgca 1440 gcaacacctc tcaatgaatc agtagctttc tttcaagctg gtgaagaaag tgaaacacaa 1500 ctgtggcaca gcagatttgc tcatctcagc ttcaaaggat tgaggacgtt gtattacaaa 1560 aagatggttg aagggctgtc accacttaaa gctcctacta aagtgtatgt tgattgctta 1620 gttggcaaac aacacagaga gaatatttca aagaaaagcc actggagagc atcatccaaa 1680 ttgcagctca ttcattcgga catctgtgga cctgtgaatc tagaatccaa cagtggcaag 1740 aggtatttaa tcactttcat tgatgacttt agcagaaagt gttgggttta cttcatttca 1800 gaaaaatcag aagctcttaa tatgttcaaa atgttcaaga atctagttga aaaaaaggcc 1860 ggttctttgg tgggatgttt acgaactgat agaggtggag aatttacttc aaaagagttc 1920 aatgagtatt gcagtatgaa tgggatcaag agacaattaa cggcagcata tactcctcag 1980 caaaacggcg ttgctgagag gaagaatcag acgatcatga atctagttag aagcatattg 2040 tccgaaaaat gcattcccag agaattctgg ccagaagcag taaactggtg catgcatgta 2100 ctaaacagga gtcctactgc agcagtgccg gatatcacac ctgaagaagc atggagtgga 2160 gttaaacctt cagtggaata ttttcgtgtg tttggatgta ttggctatgt acatgttcca 2220 catgagaaaa gaacaaagct ggatccaagg agcacaaagt gtatactgct gggcatcagt 2280 gaagaaacaa aaggttacag aatgtataat ccagaaacaa ggaaattgat agttagccgt 2340 gatgtgatct ttgaagaaaa tgcaagttgg aactgggcag aagacaatat caatacactg 2400 ttacgttgga gaggcgatga taacagtata agtgaagaag aatttgaagg aaatgaagat 2460 gaagagcgag aacaagagca gattgaggaa actgaaaatg aagtcagtgc tggagatgaa 2520 gttgaaaaca tgaagaagaa cataatgagt ttattcaagc tgctgctgtc agaaatcaaa 2580 ggacaccaca ctggatggag gattatgtca caggagcagg tttgtctgaa gaggaggaaa 2640 cacaaaatat ggtcttctac accactgctg aagatccaca cacctatgaa gaagccgaaa 2700 aaaatcaaaa atggagggaa gccatggata atgaaattgc tgcaatagaa aggaatgaca 2760 cataggagct gactgtactg ccgaataatt caaggaagat tgaagtaaag tggatattca 2820 agacaaagct aaatgaaaaa ggtgaagttg acaaatacaa ggctagactt gtagcaaagg 2880 gatatgcaca gcaacatggg attgactaca ccgaagtatt tgcaccaatg gcaagatggg 2940 acacaatccg gatggttcta gcaatagcag cgcagagaca atagaaggtg tatcaactgg 3000 atgtaaagag tgcattcctt catggagaat taaatgaaga tgtatacgta gagcaacctc 3060 tcggttatga gaagaaggga gaagaacaca aagttctcaa gttgaagaaa gcattatacg 3120 gtttgaaaca ggcaccacgg gcatggttta gcaggattga atcatatttt ctgaaggaag 3180 gttttgttag atgtccaagt gagcatactt tattcgtcaa aaatcaagaa gagaaaattc 3240 tgatagtatg catatatgta gacgacttgg tgttcactgg aagtgatgaa agaatgtttg 3300 ctgagttcaa agcttaaatg aaacaagagt ttgatatgac tgacttaggt aaaatgaagt 3360 tctttcttgg agtagaaatt gtgcagaatg atgaagggat ttatttaagc caaagaaagt 3420 atgcgcttga aattctagaa agatttggct tagaaaatgc aaattcagtt cgcaatccaa 3480 tggtaccggg tatgaaactg atgaaaaatg aagatggaga gcaagtggat atgactcgat 3540 acaaacaaat ggtaggaagt cttatgtatt tatcagtgac taggccagat atcatgtttg 3600 tagttggtct gattagtaga tacatggaga aacctacaaa tcttcatatg caggctatta 3660 agagaattct aagatatgtg aggggatctg tgaatttggg aatttattat aaaagggaag 3720 ctgcaagtga tgagaggtta atggcttact ccgacagtga ctatgccggg gatcaagatg 3780 atcgtaggag tacttctgga tatgttttta tgcttagtga aggagtagtt gcttggagct 3840 cgaagaaaca accggtggtc tctctgtcaa caactgaggc agaatttata tcggctactc 3900 actgtgcatg tcaagcagtg tggatgagaa gagtgcttga aatgttagat tgcaaacaag 3960 gtacatatac tatcatacac tgtgataata tgtctacaat taaattagca aagaatccgg 4020 ttatgcatgg cagaagcaaa catatagatg ttagatttca ttttctgcgt gaactttgta 4080 aagaaggagt aattgagttg aagcactgca atacacaaga tcaaattgct gatattatga 4140 caaaagcttt gaagatggat gcatttgaga aactgagaag cctgctgggt gtatgtgaga 4200 tgccaagcag ataaactgtt tgctgccagc aatgcagttt aagggaggaa ttgt 4254 // ID RAM14_LTR_MT repbase; DNA; EDCOT; 250 BP. XX AC AC151523; XX DT 08-JAN-2007 (Rel. 12.01, Created) DT 08-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR region of LTR retroposon, RAM14_MT, from Medicago truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR; retroposon; Interspersed; repeat; RAM14_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-250 RA Shankar R. and Jurka J.; RT "RAM14_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 46-46 (2007). XX DR EMBL/GenBank/DDBJ; AC151523; Positions 14486 14735. XX CC The LTR is present in intact form on both ends of internal CC region. XX SQ Sequence 250 BP; 103 A; 30 C; 37 G; 80 T; 0 other; tggctatatt ataattgata gcagattaca aattacaaac atagtatata tacaaccatg 60 taataataat gaaataatga ggaattaaag ttgacgttgt tgacttattc taagctacaa 120 ctataacata atgacacaat gaattgaaat gaatatttgc aatctgatgc aataaactac 180 tgatatgaaa attgatgtgt tgactttgaa attgatgcat ctagaaacag ctgtacatta 240 atgtctaaca 250 // ID MtPH-A5-Ia repbase; DNA; EDCOT; 5965 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 13-MAY-2008 (Rel. 13.05, Last updated, Version 1) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-A5-Ia. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5965 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC An autonomous element representing low copy number family A5 of CC PIF/Harbinger transposons from Medicago truncatula, carrying 21 CC bp-long TIRs. XX SQ Sequence 5965 BP; 1786 A; 858 C; 1128 G; 2193 T; 0 other; ggggatgttt gtttgagggt tacaaaaata attcctagga atctaaggct ggaattgaat 60 attgctttgt ttggtagatg ggaataacac aaatatgcca aggaatacat ttttcccagg 120 aaagtctttt acccacgttc tcccccacgt tctacccatt tttcctgtct ttcattccaa 180 tgagatagca tgggaaagtt ttatttccag ggaataaaaa ccatgatctc caacaaaata 240 cctcttctac ccttgccatt cccgctattc tttttctctg attcccgcta aacattttca 300 cccatgatat tctgtataaa aagaaaccca tgatctttgt gtgtgcatca actgcttgcc 360 aattgggttt ttgatttcac tcttctgttc aaggtatcat ctaatttcat cataattctt 420 ccattactca acatagattt ggtgattgat atcaattctc tgtttttttg tctgctgttt 480 gttgcttatt gctttgtctc aacccatttt tgttcatttt ttatgagaaa tttaactcag 540 ttttgtttca tatttttttt cccactgttt ggcaattctt gttttttccc aatcatgaat 600 caatgaaaaa aaaggttaga gacaacttgt ttttattaaa ccaccttctt ctaacttttt 660 ccaaaatatg ctaataacca taacgctgaa ttctttgttc gtaaaacttc agcatgtgct 720 agtaataacc aataagcctg tgttataact ctaattttga aaatgaagta tataacatgt 780 tcttttttca acttttatac tgcttaatat tatccataga tgatgttccc aaatgtgaca 840 tattatctaa gaaagtgaga tttgtcaaat ttggaatcat tatatattta ttagttgtgt 900 aatgacatca attatacttt gaattcattt actctattgg ttgtgtatct agaaccatgt 960 agccatagga tacatcaact gagctcctag ttgtattgtt aaagcttagt aacttgatag 1020 tgaaaatctg caagatgtgg tacataatct aagtcaagta gtatgatgtt caatgttaca 1080 tctttgtgca taatttgaca ttcttttgtt tccatcatga tatttccaag tgtgaaatat 1140 tatctaagaa agtgagattt gtcaaatttg gaatcactat atatttggat gtttgtgctc 1200 tgtttagaat gttatatatg gtgtaattcc tatgtctcta atatagtatt atgatgtgca 1260 gcaatttttt gtttttaatc atgacacatt tgatggaaat acgtgaaagg aagaaaaaaa 1320 ttatagcaat gtttatgata tatatggaga tgttgaatta ctttatgttg atgacaattg 1380 tgttatgcta ccttgagtta agtaagcgtt caaaaaagcg aaaaaggtca tgggattttt 1440 atgaaagaag tttaattaga gaagtccatt ttcgtagaat tatttacata agtgatttgg 1500 cttgcattga aaatacaagg atggatagag ctgctttcca taaactatgt gacatgttgc 1560 aagttattgg tggattgctt cctactcgac acatgtgtgt ggaggagttg gtggccatgt 1620 ttttacatat attggcacat catgttaaga atagattgat tagaagacaa tttgttaggt 1680 ctggtgaaac gattagtagg catttcagta atgtattatt ggcagttttg aagtgtcata 1740 aagaattgtt aaaacaacct aaaccaattt tggagggcaa cacagacgaa cgatggaaat 1800 actttaaaaa ttgtttagga gctcttgatg gcacttacat caaggtcaat gtgctggaag 1860 ctgacaaaag tagatataga acaaggaagg gtgagatagc tacaaatgtg ttaggtgtat 1920 gctcaccaga tttacaattc atatatgttt tgcctggttg ggagggatca gctgctgact 1980 ctagagtcct tagagatgct atttctcgac caaatggttt aaaggttcct caaggtacaa 2040 tagtataaat taatataaaa ataaaatatg tcttgcatag tttatggatt ttaacttcag 2100 gtttatttat gatagggtat tattatttat gtgatgctgg atacatgaat ggagaaggat 2160 ttcttactcc ttatagaggt caaaggtatc accttagtga gtagaggaat ggattacaag 2220 catctacccc taaagaattt ttcaatatga aacattcttc agctaggaat gtaatagaaa 2280 gatgttttgg acttttgaaa ggatgttggg ctatattgag agagaagtca ttttatcctg 2340 taaaaactca aggaagaata atagcagctt gttgtcttct acataatcat attcgcaaag 2400 aaatgacatt ggatcctttg gaattgaatt taggagatga tgagttctct gatgaagtca 2460 tgtccggtga catgataact acggtggagc caagtacgac gtggagtcaa tggagagata 2520 gtttttcatt agatatattt aataggtgga gaggtggaaa tcattgaaag ttttcatatt 2580 tttttatttg acatttcaat ttgattgtaa tttttatttt cagtgtactg ttgactttga 2640 tttaaaagtt ttattaatca aatctgtttc tttttatgag tttttatttg taaaatatgt 2700 acttgtaata tgattttatt tattgtttat tgttatatat tttgacatgc acgcacttgt 2760 tgagttgttg aatagatgga cgggtcgtct gaaaatcaaa atgtaagaat cacaaagcga 2820 caatggactc atgaagaaga tgaagtattg gtggaaggtt tgttgaaatt agtggatgag 2880 ggttggaagg ctgatgcaaa ctcatttaaa cctgggtata ctaaagcttt ggagaaatat 2940 attcacaaca aattctcagg ttgcacacta aaagctaccc tgcatattga atcaagagtg 3000 aaactgctta aaagacagta ttctgcaatc aaagatatgt tgggtccagg tgcaagtggt 3060 tttgggtgga atgatgctaa aaagatgatt aaagtagaga aggagattta tcgtcaatgg 3120 tgcaaggtaa tataagatat actattccac aattgataaa ttcatgataa tttttcttgc 3180 attaaattta tatttctaaa caatttttcc tttaatgcag tctcacccta ccgcagttgg 3240 tttgtatgaa aaaccatttc cacactatga tagcttggat actgtatttg gaaaagataa 3300 agcagctggt actgtaacag aagatatcat tgatatgact attgagatgg agaaggaaaa 3360 tgttcaatca acacaagagg gcggatcagg aattaatttg aatgatgatg atgatgctga 3420 gaattttgag tcgcagatgc cagaaacacc cacagctaac actactgctc cgggttcaaa 3480 tccaacaaac cagtcacaac gtgattctac taattatagg accggaaagc gtgggggaaa 3540 aagggtgaag tataacgatg atgcttctga tagcatgtca aattcattga acaaattggg 3600 tgagatttat gcttatggtg ttgagaatat gaaacaagtc ttcacttctt gttttgtgca 3660 cgagaaacac acagctgata ggaggaacca gattgtctct attttaaaag aaattgaagg 3720 actgtctgat gcagaagtgg taatggctgg tatgcttatc accaaagaca ataacctttg 3780 cgactatttt ttcataatgg atactcctgg attgaggaag cggtttgtgg acattgtttg 3840 agtaacaatg gttctaggta gaatttagaa tgttcaatgc tttttgaatt tggtaaaaaa 3900 aactcattag ccactgtttt taattccttt tattatttag ttgaatccgt tattatggtc 3960 tttattagtt gtgtaatcac ttcgattata cttaaaattt atttactcta ttggatatgt 4020 tactagtgca acttttgatt tatttttgaa aaagtgattt tgctagtctc gtattggttt 4080 cagtttatgc ataactagtt tttagtgtct ttttttagtt tgttcttgtg gactttgaaa 4140 tcttctttaa tagtgaagat ggggacaaaa ctgattataa gtttatgtgt aacatcagtg 4200 gtgtctggtg tgatttcaac aggtaggggc tgatttcaaa tcattgatga tataaagagc 4260 agtgtaggtt tagccttgtt tttgctgtcg gatctgcaat ttagtgcagt tccattccat 4320 acttgtatga ttttttaggt ttttgtggct gctattgctt ttcatttagt tttgaggctg 4380 gtatgttcaa ttttcagtgc agttttatgc gttgttttcg acctgctttg gctggttttt 4440 ttcttttctt ctttctacta tcgtttctac tatctcgctg cttcagtagt tttgtttgta 4500 ctcttcttgt gcgtttccaa gtataccttg tgcttggacg agtgtttatc aataccttgt 4560 gctggtatgt tgctgcaatc tgtgacagac tgcacattgt tttacatata aaacacttga 4620 acaatttcat gtgatttctg cataatttgt tgactgattg tagcaacatc tattgtatga 4680 ctctaaaaaa tgagcttgtt tcttgatctc caagagcatg gtagtcgaac aatgcatgaa 4740 ctccttgacc aatacatcct cattctgatc ccagcagggt atatgtttat tttttcttta 4800 cctctattac caagctattt actagtggtt atctgctggc actgaacttg tagtctaact 4860 gtatttgttt agggaaaagt ccaatttact ccctctaact taggattaag atcatgtgct 4920 tttagtgctc aaacattaaa aatgtgaata aaatcctcaa actttaaaac tgttagcatg 4980 tgttataact ctaattttga aatgaagtat ataacatgtt cttttttcaa cttttatact 5040 gcttaatatt atccatagat gatgttccca agtgtgacat attatctaag aaagtgagat 5100 ttgtcaaatt tggaatcact atatattatt agttgtgtaa tgacatcaat tatactttga 5160 attcatttac tctattggtt gtgtcactag tctgatgttg gtgttgttta catctgtcac 5220 atttaagttt ttggtattga aaatataatt catcaggttg tgagttttat actcaaaaag 5280 ttaacagatt ggtgactatg cattagaaaa gtgtggttca atatgtgaag tatcactgcc 5340 acatcttgtc tttatgttta aattgtgtaa tattgtaaaa aaaaatatgt tacaatactg 5400 tgacagaata ttggttttat gtttttcata cacaagctca aaagtagacc attgcagaac 5460 atgatgtaga agtagtgact aaggatgact ctgagatttg tatttggttg atgaggtaag 5520 agtggtgaca ttctctgttt tctggttttg cacaaggagg ttagcttctg tttgtggact 5580 ttgcttggtt cttctatcta ccattttagc agcaactttt tggttcctgt ttgtattgca 5640 attctgatct ttctcaagta attgggttgt aacttgtacg gtttacctac aactcatgtt 5700 gtaaatatgg aaaagaagac gttggtttca tggtttattc aatagggata tttatgtgat 5760 tataacattt attcccagga ttctacatct caagccaaac atattttatc tattccttgg 5820 aattatttta aaacaattcc taggaattaa acaattaacc aaacaccttt ttctatattt 5880 tcctgggaat aaaattttca ccttcacatt cctgggaaaa tgaataccta ggaataaatt 5940 ttgtaaccct caaacaaacg ccccc 5965 // ID SHACOP15_LTR_MT repbase; DNA; EDCOT; 574 BP. XX AC CR931743; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of LTR retroposon SHACOP15_MT, from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; terminal; SHACOP15_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-574 RA Shankar R. and Jurka J.; RT "SHACOP15_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 58-58 (2007). XX DR EMBL/GenBank/DDBJ; CR931743; Positions 37487 38060. XX CC The complete intact pair of LTRs flanking an intact internal CC region exists in just two copies in the genome. Otherwise, there CC are several disrupted copies or incomplete sets. XX SQ Sequence 574 BP; 155 A; 99 C; 111 G; 209 T; 0 other; tgtgaacatg tgtgaacaca taagccataa agtcaccttt tgttgatatg ttttcacatg 60 gcagtaatac atgtttgaca aaagggtttt gcaatttacc attcagattt tcggtgccaa 120 cattgtcaac ataaattggt tggcagtttg gctattatct atggtaataa atgaaaatgg 180 ttgaggcatg gcttttacgg tcctataaat agcatgtccc ttgcaccatt ctactcatcc 240 caaatcagta acaacacaag aacaagtaaa gcttgtttag atagtgagag aaaaaatata 300 gagaggaaaa atagtttctc ctgtgaggtt tctcctagtt tgtgttagtt agtattctcc 360 tatttataag agagagtggt atttgtactc tccttgtagt tagagagagg tcctgtaatt 420 tcttccactt agtgaaagtt ctctactctt gccccgtggt tttttcccct tatttgttga 480 ggggtttcca cgtaaaatat tgtgtgttca gttcctcttt tctcgtctct tattttagct 540 gcgtgataat attttgttac tctggtacct aaca 574 // ID Sharbinger_MT repbase; DNA; EDCOT; 425 BP. XX AC . XX DT 27-NOV-2006 (Rel. 11.11, Created) DT 01-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A harbinger like putative non-autonomous DNA transposon, from DE Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW Sharbinger_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-425 RA Shankar R. and Jurka J.; RT "Sharbinger_MT: A putative non-autonomous DNA transposon, from RT Barrel Medic."; RL Repbase Reports 6(11), 603-603 (2006). XX DR [1] (Consensus) XX CC The sequence is flanked by 4 bp TSD (CAAT). It lacks intact CC transposase domain and contains 49 bp inverted repeats at CC termini. SHarbinger_MT is short Harbinger like putative CC non-autonomous DNA transposon from Barrel Medic. XX SQ Sequence 425 BP; 158 A; 80 C; 59 G; 128 T; 0 other; ggaaaattct atggtgaagt catgagaatg acttttctgg tgaagttaac actataacat 60 caaaaatgta gtgagtaaca ccccactgtt tgtacagtgg catcaaaagt tcagtcctca 120 tagtatcatc aattcatcag attaacaaga ctacacttaa tctaatttta tcctaccttg 180 ttttaagtgt aacaccccac aaagtgtaac acttaagact atcacataat atcatcaact 240 ctgtttgcat gttaaagatg ccaacgataa aatagtacct gtaagtccaa gatgttgcaa 300 gcattactag atgaattact attgatcatt aatcagtaat caacaattta aaaatgaatc 360 aaacattaag atcaaaatta actttttcaa aaaagtcagt ttcctgactg caccgtagaa 420 gctcc 425 // ID Copia17-VV_LTR repbase; DNA; EDCOT; 374 BP. XX AC AM481163; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia17-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-374 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-374 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 684-684 (2007). XX DR Genbank; AM481163; Positions 541 914. XX SQ Sequence 374 BP; 110 A; 81 C; 74 G; 109 T; 0 other; tgtaagctga atacacgttc acacgttctc acttcatgat gtggtccaac actttgacca 60 cgtcctccac catctcactt ccgctgcggt taaggagcac gttccaccaa ctgctcaaca 120 tggtggcaag agcaacgtgg tttgatggaa gccattgtta caaagttttc agaaaatggt 180 cccgaactca ctctgttttt atcttcagaa acaccatcta aaaaagagag attagagttt 240 ggaaaccaaa ggttgaaccg attccagcaa cttgatccga tggctggagg taagtagact 300 acaagtcttt tacagattga attcatgttg taagtgttca ttgaattgtt tatatacatt 360 atgaactgct taca 374 // ID Gypsy-78_PTr-LTR repbase; DNA; EDCOT; 1721 BP. XX AC . XX DT 23-DEC-2009 (Rel. 15.02, Created) DT 23-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-78_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1721 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 188-188 (2010). XX DR [1] (Consensus) XX CC ~94% identity to consensus. 5-bp TSD. XX SQ Sequence 1721 BP; 477 A; 305 C; 425 G; 510 T; 4 other; tgccgaaacg tgtgttgcct gcagcgaatt agcgattcac tgccgaaatt gagtgtttgc 60 agcgaattgt gattcgctgc cgaaactgwg tcgtctgcag cgaattagca ttcgctgccg 120 aatgtgtgtg ttctgcagcg aacttgtgat tcgctgccga agttgwgttg tctgcagcga 180 atttgcgatt cgctgccgaa gttgtgttgt ctgcagcgaa attgtgattc gctgccgaaa 240 ttgagttgtc tgcagcgaag tagcattcgc tgccgcaaat tgtgctgsct gcagcgaata 300 gtattcgctg ccgaaactgt gscgccagca gcgaaacagt tttcgctgcc gaattggctg 360 cctgcagcga aacagttttc gctgccgaat tgggcagcct gcagcgaacc agttctcgct 420 gccgatttct acaataagcc tcctaggcag aaatgactta aatgctagta acaatttcat 480 ggtatgatgg tgtaaaatgt ggaacacttg aatgtgaaca tatgaactct tgaaataagt 540 gtggtgacga atgtgattca aaaatacaaa tgtactgatt tgtgaccatt gatgtcttag 600 gtggtgcggt cgggattgga ccatcgtcaa gacaagaaca acccacaggt ggagcaggta 660 ggtgacttgc accttccttt ttcatacgtt gaataatgaa atactttatc atgaatgtta 720 ccgtattgtg ttagaacaga tatcagattg tcgaacgctt aaatgttgac aaatggttga 780 ttagcttcgg ctaatggcat ccgaatggat ggccgggaca aatgaatgat tagcttcggc 840 taatggcatc cgaatggatg gccgggacaa atgattgatt agcttcggct aatggcatcc 900 gaatggatgg ccgggacgaa tgaatgatta gcttcggcta atggcatccg aatggatgac 960 cgggacaaac gattgattag cttcggctaa tggcatccga atggatgacc gggacaaacg 1020 attgattagc ttcggctgat ggcatccgaa gtggatggcc ggggtgagtg aacggttaac 1080 ctcggcaaat gatgccttaa gaggatagcc gggtttaaga ttatggctga ttgcaagaat 1140 tggtgcatct atatgtacta caagttgttt ataccaagta catgaaggaa ctataaatgt 1200 cacgcttcaa acatgggata atgttaatgc ttcattaaac tgccagaccg tttaattatc 1260 attattatta ttattaagta attgcattct cttaaatgtt ttgtactgca gcagggacgt 1320 cacaccaacg aggtgcctag gaaacccaat acacgggaac ctacttttgc aaggaatcat 1380 gtagttgcat tctaaatcac gatgtatttt gtatgaatca atgtactgaa cgtataactt 1440 ttattagatc cttttgttta aattcgtgat ggctattagt aggataggaa tgcaaactca 1500 tgtctatgta tgtatatttt taatgtgaac ttctaatcat gcaaacataa tattatgtgt 1560 ttatgtaaga ttcactttta aatgaaatgt tgattgttga tgtatggatt gtatcttgat 1620 gatgtgaggg aacaggttcg ccgattaccg acacgatgtg tgtcaagtat atataaaaaa 1680 aatttaccgt tgttttgggc ttgaaaagcc gggttgttac a 1721 // ID Copia-84_Mad-LTR repbase; DNA; EDCOT; 184 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-84_Mad_; KW Copia-84_Mad-LTR; Copia-84_Mad-I. XX NM Copia-84_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-184 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1707-1707 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 184 BP; 59 A; 20 C; 28 G; 76 T; 1 other; tgaggatgcc aaatcatgac atacattctg tttttaatta actaattgta atgtgctatg 60 tgtacaagtt agttagaaag gttattagtt gttgttgttg ttatgactat aaataccata 120 ctsatgtaat tatttttcgt taagtaatga aattgtaata tttcagaaac acattttctt 180 ctca 184 // ID LHI1 repbase; DNA; EDCOT; 916 BP. XX AC U91988; XX DT 19-NOV-1998 (Rel. 3.1, Created) DT 19-NOV-1998 (Rel. 3.1, Last updated, Version 1) XX DE Nonautonomous DNA transposon LHI1. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; DS; KW LHI1; Lhi1.4; nonautonomous DNA transposon; TIR. XX OS Solanum tuberosum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RA Oosumi T. and Belknap R.W.; RT "Characterization of the Sol3 family of nonautonomous RT transposable elements in tomato and potato."; RL J. Mol. Evol 45(2), 137-144 (1997). XX RN [2] RA Oosumi T., Garlick B. and Belknap R.W.; RT "LHI1."; RL Direct Submission to Genbank (05-MAR-1997)CIU, USDA/ARS, 800 RL Buchanan Street, Albany, CA 94710, USA. XX DR GenBank; U91988; Positions 414 1329. XX CC LHI1 is a DS-like (hAT-like) nonautonomous DNA transposon; it is CC flanked by 8 bp target site duplication and it has 38 bp long CC TIRs. XX SQ Sequence 916 BP; 341 A; 110 C; 142 G; 317 T; 6 other; cagaggcgga tctaggattt gaaggtcggg ggtgccacaa cattcaagta tgataaaaag 60 actgttgcnt taattttaga ttacaattca ggttattaat tttattttat tttataaata 120 aatcgatcaa atatgcctat agtaatatct tattttacat attatgtgat cagagataac 180 taaacaattc aatttttatt ttctttttga aattgaatgt cttatttgct gaaactttga 240 gannnnnaaa gtcaaatttg agcttgtata aaccatcata ataatattaa cataatatat 300 tagtcttcca ttgactttat gtgttgttgg agatatacag ttgggaaaaa aattaaaaat 360 tgtagtttca gtctattcgt cttacttagc aaaaacgtcg gtgaagatcg aaagaacctt 420 taaattaaaa aaatatattt ttgaaacttg tgttttttct aaaaattatt atttaaatat 480 attcttaata atatttattt gacgctcatt attcaatact cactatttga taaaacaaaa 540 taaatctgtt acacttaaat caatagatta ataattagtg caagagcaag ttaaaaaata 600 aaatttaatt atcaaaaagg ggtcatttga attaataaat aatagtaaat aaataagaat 660 gattggagaa aaagaaaaga aaaagaatga aaaagagcag gcaaaaaaaa ttaaatgttg 720 gtgcgtgagg tttgaacagg ggttgatgag atgtagaccc tctcctttgc ctattggacg 780 attccgttgt atagtcattg ggtggcgaaa ttaatatata tttaattatt atacatatat 840 acacgtgtat acaacgtttt ctccgaaaac actgggtgcc gtggcatccc tacctttaca 900 cctaaattcg tccctg 916 // ID Gypsy18-PTR_I repbase; DNA; EDCOT; 7283 BP. XX AC LG_I; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy18-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-7283 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-7283 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 314-314 (2007). XX DR Genome; LG_I; Positions 15059274 15066556. XX CC Positions [5074-5337] - Integrase core CC 'CAATC' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 990..2951 FT /product="Gypsy18-PTR_I_2p" FT /translation="MPTDRSIIDAASGGALVDKTPEAARQLISNMAANSKQ FT FGTRGDFANKRVNEVSISNLENKVNDLTSLERSLACGNVQQVKVCSICSLQ FT GHASDMCPTMQEDYIEQANAVDGVFNGQPQRKYDPFSHTYNPGWRDHPNLR FT YGNQPQQGNQGRQFHPHGFQPQQNYQARQPPPFTNSNVMGSSSSDDLREMM FT KTLASNTVTLQQNVMSFQQETRSSIHNLEKQMGQVASSVGKLEAQMNGKLP FT YQALNPKENVSAIMLRNGKELEEKRSKQIEMEEEEEIETELSAKKEHPSPS FT QIETMTNTLKVSPHSMNSSFKTIAPFPVSSSRSKKEDKGKEILEVFKKVEL FT NIPLLDAIKQIPKYAKFLKELCTTKRAFKLKGHEMVSMGEVVFAIVQKNMP FT LKQKDPGAFAIPCVIGNASFERALCDLGASISVMPKHVYDSLSLEPLNKTS FT IVIQLADRSFVYPLGVIEDVLVKIDSLVIPCDFYILDMEHDSCDSSNNTPI FT LFGRPFLKTANTKIDCGKDTLFMEVGDEKIEFNFHDAMKYPYSNVYSITCY FT DQVDKCVQQVFDFDCKDGLSVALSYGYDFTEIEEMERHICVPQNVHESALA FT LQSLQTVPHGNVFVDLLLSHKKLLPSILQAPELELKPLPDNLKYVFIGDNN FT TLPIL" FT CDS 3062..4387 FT /product="Gypsy18-PTR_I_1p" FT /translation="MCMHHILLEDNAKPIREMQRRLNPPMMEVVKAGILKL FT LDAGVIYPITDSKWVAPIHVVPKKTGITLVKNKNDELIPTRISSGWRMCVD FT YRKLNLATRKDHFPLPFMDQMLERLAGKSFYCFIDGYSGYNQIVINPEDQE FT KTTFTCPFGTYAYRRMPFGLCNAPATFQRCMMSIFSDYVERIIDVFMDDFT FT VYGDSFDKCLENLSLILKRCIETNLVLNYEKCYFMVEQGIVLGHVVSSRGL FT EVDKAKIDVISSLPYPSCVREIRSFLGHAGFYRRFIKDFSKITAPLCKLLA FT KEVDFVFDQACKDAHDELKRRVTSAPIIQPPNWDEPFEIMCDASDYAVGAV FT LGQRIGKNLHVIAYAARMLDGAQCNYHTTEKELFAVVFGLEKFRSYLLGIK FT VIVFTDHAALRYLLKKKESKPRLIRWILLLQEFDLEIKDKKRCRKSCG" XX SQ Sequence 7283 BP; 2246 A; 1215 C; 1499 G; 2323 T; 0 other; aattttggcg ttgttgccgg ggaagtaatt ttagttgatt cttgtgctat tatttttatt 60 tgctgtgatt gtcatttctt tttctgaaaa aaaaagagaa tttttgcttg atgcggtact 120 gttcattacg gcagcggtac tgttcaaaac agattttttg gtggaattag gtatcggtct 180 tttgtttctt gaagggaaac gacgttctaa acaggcctag tggcgtacaa ctagccccac 240 cctatcgagg ccaaattcca ctgttttcta gggtttttgg gcaggttttg ttttctaccg 300 taggattttc gtacaatttg cattgttttc gatctcttgt gtggttggtt tcttttgagt 360 tttcttgatg atttacgcca gtaacccgtt ctactaatca aagtcaagtg cagttggatc 420 tcgaaataga aaaaacttta cgcaggttac gaaaggaagc tcgccttaac accatggctg 480 ttgcacgaca acaaacactc aatgagcttg ctgctcctaa cgtggaaaat cagccattgt 540 gcataaacat cgacaataat gtaaactttg agctcaaatc tggttttata catttgctac 600 caacttccaa tggtcttgca ggagaagatc ctcatactca tctcaaggaa ttccatatgg 660 tttgcgttgg catgaaaccg aatggagttg atgaagaaca ggttaagttg aaagctttcc 720 ctttctcttt aaaaggggca gcaaaggcat ggcttttctc cattctccca ggttcaattg 780 gaacgtggaa tggcatgaag aagattttcc ttgagaagta tttcccagca tctcgagttg 840 ccaacataag gaaagaaatg tgtgggattc gacaatctca tggagagaca cttttcgagt 900 attgggaaag atttgagcaa ctatgcattc aatgccctca tcatcaaata ctcgattagc 960 tgctcattca atatttctat gaaggattga tgcctactga ccgtagtatc attgatgctg 1020 caagtggagg ggcattggta gataagacac ccgaggctgc acgccaattg atctcaaaca 1080 tggcagccaa ctcgaaacaa tttggcactc gtggagactt cgcaaataaa cgagtgaatg 1140 aggtaagtat ttctaacctt gagaataaag ttaatgatct tacttctctt gagcgttctt 1200 tggcttgtgg caatgtacag caggtgaaag tttgtagcat atgttcctta caaggacatg 1260 cttcagatat gtgcccaaca atgcaagaag attatattga acaagctaat gcagttgatg 1320 gagtattcaa tggacaacct cagcgtaagt atgatccttt ttcccacacg tacaatcctg 1380 gatggagaga tcatcccaac ctacggtatg ggaaccagcc tcaacaaggc aatcaaggcc 1440 gacaattcca tccccatgga tttcagcccc aacagaatta tcaagcaaga caaccccctc 1500 cattcacaaa ctccaatgtt atggggtcgt catctagtga tgatcttcgt gagatgatga 1560 aaactttggc ttctaacact gtgaccttgc aacaaaatgt catgtctttt caacaggaaa 1620 caaggtcaag tattcacaac ttggagaagc aaatggggca agtagcttca agtgtgggga 1680 aattggaagc acaaatgaat ggaaaattgc cctaccaagc attgaatcca aaagagaatg 1740 ttagtgcgat catgctgcga aatgggaaag aacttgaaga gaaaaggtcg aaacaaattg 1800 agatggagga agaagaagag atagaaactg aattgagtgc aaaaaaggaa catccttctc 1860 cttcacaaat tgaaaccatg accaacactt taaaggtaag tcctcactca atgaattcta 1920 gttttaaaac aattgcaccc tttcctgtga gttcttctag gtcaaagaaa gaggacaaag 1980 gaaaagagat tttagaggtt ttcaagaaag tagaactcaa cattcctttg cttgatgcta 2040 tcaagcaaat tcccaagtat gctaaattct tgaaggagtt gtgtactacc aagagagctt 2100 tcaaactaaa aggtcatgaa atggtaagta tgggtgaagt tgtatttgct attgttcaaa 2160 agaatatgcc tttgaagcaa aaagacccag gtgcgtttgc tatcccatgt gttattggta 2220 atgctagttt cgaaagggcc ttgtgcgatt taggtgcatc cattagtgtt atgcccaaac 2280 atgtttatga ttctcttagt cttgagcctt tgaataaaac tagcattgta atacaacttg 2340 cggatcgtag ttttgtttac ccacttggtg tgatagaaga tgtcctagtc aagattgata 2400 gtttggtcat tccatgcgac ttttatattc ttgatatgga acatgattct tgtgattcat 2460 caaacaacac tcctatattg tttgggagac cattcttgaa aactgccaat acaaagatag 2520 attgtggtaa ggatactttg tttatggaag taggagatga aaagattgaa tttaattttc 2580 atgatgcaat gaaatatcct tatagcaatg tttattctat cacatgctat gaccaagttg 2640 ataagtgtgt gcaacaagtt tttgattttg attgtaagga tggattaagc gtagctttga 2700 gctatggcta tgattttacc gagatagaag agatggagag gcacatatgt gttccccaaa 2760 acgtgcacga atcagcattg gctttgcaat cattgcaaac tgttccccat ggtaatgtct 2820 ttgttgattt attactttca cataaaaagc ttttgccatc tattttacag gcacccgagt 2880 tagaattgaa acctttgccc gataatttga agtatgtatt cattggcgat aacaatacac 2940 ttcccatatt atagcaacag gtttgacaaa tacgcaagag gaaaaacttg tgaagttgtt 3000 gtgtgatcac aagacggcca ttggatggac tttagctgac atcaagggca ttagtccctc 3060 aatgtgtatg catcacatac tattggagga caatgcgaaa ccaataaggg aaatgcaaag 3120 gaggttgaac ccgcctatga tggaggtagt gaaagctgga attttaaaac tgttagatgc 3180 aggagtcatt tatcccatca cggacagtaa atgggtggcg ccaatccatg tggtgcctaa 3240 aaagaccgga atcacgttgg tgaaaaacaa aaatgatgag ctcattccta ctcgcatctc 3300 gagtggatgg agaatgtgtg ttgattacag aaagctaaat cttgctacac gcaaagatca 3360 ttttccatta ccatttatgg atcaaatgct tgaacgccta gcaggtaagt ctttttattg 3420 ctttattgat ggatatagtg gatacaatca gattgttatt aatcctgagg atcaagaaaa 3480 gactacattt acatgtccat ttggtacata tgcatatagg agaatgccct ttggtctctg 3540 taatgcacct gcaacttttc aaagatgcat gatgagtatt ttttctgact atgttgaaag 3600 aataattgat gttttcatgg atgatttcac ggtgtatggt gattcttttg ataaatgtct 3660 agaaaattta tctttgatct tgaaaaggtg cattgaaact aaccttgtct taaactatga 3720 aaagtgttat tttatggtag aacaaggaat agttcttggg catgttgtgt cttcacgtgg 3780 attagaggtt gataaagcta aaatagacgt tatttcatca ttgccttacc cctcctgcgt 3840 gagggaaatt cgttcttttc ttggccatgc aggtttctat cgacgcttta tcaaagattt 3900 ctcgaagatt acagcaccct tgtgcaaact attagccaaa gaagtggatt ttgtgtttga 3960 tcaagcatgt aaagatgccc atgatgagct taagaggcgt gtcacatctg cccctatcat 4020 ccaaccacca aattgggatg agccttttga gataatgtgt gatgcaagtg actatgcggt 4080 aggggctgtc cttgggcaaa gaatagggaa gaatttgcat gttatcgcct atgctgcccg 4140 catgttggac ggagcacaat gcaactacca tacaactgaa aaggaacttt ttgcagtggt 4200 gtttggtctt gaaaaattta ggtcatatct acttggtata aaagtcattg tttttactga 4260 tcatgcagct ttaaggtatc ttttgaagaa aaaggagtcc aaaccaagat tgattaggtg 4320 gatcttgctt ttacaagaat ttgatcttga gatcaaagat aaaaaaaggt gccgaaaatc 4380 atgtggctga tcacttgagc cgactgagga ctgaggatat acaaaccgaa acaatacgag 4440 agacattccc cgatgagcag ttgtatgtgt tacattcctc tacaagacca tggtatgctg 4500 atttggtgaa ctatttagtc accaaagaat tccctccagg tttgtctaca tcccaaaaaa 4560 aaagatacga gctgatgcta aatattattt ttgggatact ccttatctgt ggaaattttg 4620 tgtggatcaa gtagttagga gatgtgtacc acaagatgaa tttcattcca ttcttacctt 4680 ttgtcattct cattcttgtg gtgggcattt tggagcaaaa agaacggccc acaaggtact 4740 tgaaagtggt ttttattggc cttctatttt taaggatgca tatcattttt gcaaataatg 4800 tgaaaaatgc caaaaaacag gtaatatcac tcataagaat caaatgcctt taacgaatat 4860 tcttgtaagt gaaattttta atgtttgggg tattgatttt atgggtccat ttccttcttc 4920 ttttggcaat ctttatatcc ttcttgctgt tgattatgtg tccaaatgga ttgaggcgaa 4980 agccacacga actaacgatg ctaaggttgt tttagatttt gtcaggactc atatatttga 5040 caggtttgga atccctaaag ctatcattag tgatcgtggc actcattttt gcaatcgttc 5100 aatggaagca ttgtacgcaa atatcatgtg actcatcgga cttccacagc ataccatcct 5160 caaacgaatg gccaagctga aatttcaaat cgagaaatca agtccatttt ggagaagaca 5220 atgcaaccta accggcgaga ttggagtcta cgacttggtg atgcactttg ggcttatcgg 5280 actgcttaca aatcacctat aggaatgtca ccttatagga tgatttatgg aaaagcatgt 5340 catctaccgg tggagcttga acacaaagct ttttgggcca ttaaaaaatg taacatggat 5400 tatgatgctg ctgggattgc aagaaagttg caattgcaag agttggaaga gattcgaaat 5460 gatgcttacg aaaatgcaag gatttacaaa gaaaagacta agagtctcca tgaccgaatg 5520 attacaagaa aagagtttaa tgttggagac aaagtccttc tttatcattc gcgtttgaaa 5580 ctttttcctg gaaagttacg ctctcgttgg attggaccat ttgttgtttc taatgttttt 5640 ttcttatggt gcagttgaaa ttacaagttt agaaaccaac aaaatactca aggtcaatgg 5700 gcatgcttga aacctttcta tgaaggttgg acgacagaac tcaccacttc tgtggagtta 5760 gctgaaccaa tctataaaga atgagcatgc aacatgtcga gccaatgaca taaaacaaaa 5820 gcgcttactg ggaggcaacc cagcacaaaa agaaaaaaaa aacagatttg ctttcctttc 5880 ccttatcttt tatttttcgc attttacttt atttttgtca ttcttctata ttccttttct 5940 tttatttcaa cattgaggac aatatcgtgt tttaagtgtg ggggtattgg gagaatgttg 6000 gttttctaat tttggttttc tttgttattt ttcaaaaaaa aaaattatgt ttgatctttt 6060 gaactgccat tggtttttga gaatatgagt attatatatg agaattagtt gaaatagatg 6120 aagatataaa tcaaatgaag gagtgtgcat gcaagtttta agatttaatt ggtttaggga 6180 ttgactttga gaatatgcca tgttgacttt atagtgttat accaatgcaa gcttttgagc 6240 cttcaacatt atattctttt attgtgcctt ctttcaatga tatgtatctc tagaacttgc 6300 ttcatatcct gttgagatta cattcacatt acatatatac atgaagatga taaaggcatt 6360 aggaatttta accatttgag ccaaaaagtc aacctaaagc atattatctt tagtgaaccc 6420 cttttgagct tgtttatctt ttctttgatt tatccatgta taagccttaa ctttttatat 6480 gttttccttt ttccctggcc aaggattagt agagcatata cttatgatat cgaatgaaat 6540 tatggttgga aattatgtga aaagaaagaa gaagtgatgc ttaatgaaaa gatgggcaaa 6600 gttgccaaag gtaaaaaaaa aatggaaaag aaaaggaaaa ggaaaagaaa aaaaaaaaag 6660 tgttccttta tgttcttaag attttatgtt gaaaaagctt gaaatcaaaa gaagttaagc 6720 attggtgatt aaagatggaa aatttatgtg ctttgatgga atatcttgtt tgaaatatca 6780 tttttcagaa tgctctactt tctttggttt gaaccttttc ttttactctc ttttacctca 6840 ccttaacctt agccccatta caaccagaaa ataagacctt ttgattcatt cattgtttgt 6900 aatatgttag taatggagat gagattgcag agcaagctta tggtagaaca tattcattga 6960 ttgaatttga gagatttaaa cacataagcc ctaaacatgt gagtgttgga gtgtatatca 7020 atgagaggac ctatcacttt ggcatggcat agatttcatt taaatcccga cgattaattg 7080 aattttgaag tttgcatgta aataaattca tgaaaattta tactctttat ccttcttaat 7140 tgtgttcttg tttataatgc atatattctt ggatattgat gggagattag aagattagtc 7200 atagtgattt aatttaattt aacttcaatt tgattttacc aatcctttct cgaggacgag 7260 caagagctaa gtgtgggggt att 7283 // ID HarbN_I repbase; DNA; EDCOT; 205 BP. XX AC . XX DT 20-OCT-2006 (Rel. 11.1, Created) DT 26-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE Harbinger type putative non-autonomous DNA transposon. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW HarbN_I. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-205 RA Shankar R. and Jurka J.; RT "HARBINGER type I: A non-autonomous putative DNA transposon."; RL Repbase Reports 6(10), 491-491 (2006). XX DR [1] (Consensus) XX CC This sequence is a putative non-autonomous transposon, with 3 bp CC TSDs and GGG/CCC termini characteristic for Harbinger family. It CC is flanked by 12 bp long inverted repeats differing by one point CC mutation ( A->G). XX SQ Sequence 205 BP; 61 A; 33 C; 46 G; 65 T; 0 other; ggggttgttt ggtgtgagag ataaaaataa ataatgatgg gataaaattt ttgtatcttg 60 tttggttgtc atgtttggga taacttatcc caccatttat aacacagtga tgggataagt 120 tatcccatat acatggtggg ataagttatc cccggatagc tggataacta atcctgggat 180 aacttgttcc caaccaaacg acccc 205 // ID SPRT1_IB_LTR repbase; DNA; EDCOT; 432 BP. XX AC AB055092; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Ipomoea batatas copia-type retrotransposon SPRT1_IB_LTR, long DE terminal repeat, partial sequence. XX KW Copia; LTR Retrotransposon; Transposable Element; KW COPIA superfamily; Long terminal repeat; SPRT1_IB_LTR; KW partial sequence; retrotransposon; reverse transcriptase; KW Ribonuclease H. XX OS Ipomoea batatas OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea. XX RN [1] RP 1-432 RA Tahara M.; RT "Direct submission."; RL Direct Submission to Genbank (27-JAN-2001). XX DR Genbank; AB055092; Positions 1023 1454. XX SQ Sequence 432 BP; 129 A; 69 C; 91 G; 143 T; 0 other; tgatggacac cacatccgtg atcaaacgag tcatggaaag gacttacacc tatactatga 60 gtatatactc tgtgacctaa atgggtggtc tatgttaaga tagacttgac agagttaaag 120 tctatgacgg gatagactag acagggaatt tcgaggtcaa tgtatttgac tgtgcaaggc 180 ttgagttatt tagttatttt gcacgcttaa gttcaaaatt tagttattcg gcgaattcaa 240 gaagcaattc actctcgggc agtaaattac ttaacgttgt tgcatgtcag ttcaagtccc 300 agaccctgac ataaaaatta acttttgcaa ttttagctca gatagtatct tatccagcct 360 ttacctttaa atgtgtgggg attgttggga tacatttaaa aggttaaggc tatttatgag 420 tttgtctttt aa 432 // ID PDR1_I repbase; DNA; EDCOT; 3612 BP. XX AC X66399; XX DT 28-APR-2000 (Rel. 5.03, Created) DT 28-APR-2000 (Rel. 5.03, Last updated, Version 1) XX DE PDR_I is an internal portion of the PDR1 LTR retrotransposon. XX KW Copia; LTR Retrotransposon; Transposable Element; PDR1_I; KW PDR1_LTR; Ty1/copia-like LTR retrotransposon; gag; KW internal portion. XX OS Pisum sativum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Pisum. XX RN [1] RP 1-3612 RA Lee D.; RT "PDR1_I."; RL Direct Submission to Genbank (21-MAY-1992)D. Lee, John Innes RL Institute, Colney Lane, Norwich N4 7UH, UK. XX DR GenBank; X66399; Positions 157 3768. XX SQ Sequence 3612 BP; 1017 A; 698 C; 745 G; 1152 T; 0 other; tggtatcaag aactcccgat tttgggattc cgttccgcct aaaccctagc cgccttgtag 60 cggagttttt tttactgcag tttgcagttt gttgttgttt ttgggtgttt gggtcattgt 120 tgttttgtgt tgtagcacat cgtgcttctt gttttttgtt cactcatctt tgaaacccta 180 acccatcctg tttcttggtt tgttttctct cgattgtcct ttcaatggct gagattactg 240 gtaagagttt gtgttcccga gtggtaatat tcctaagaat gcgtggattc ttgactctgg 300 tgctactaat catatgacat ttgattccac attattatgc tcttatacca caccttcgag 360 tattccttat atcactgttg ctgatggctc tcatgcttgt gttgttggca ctggaaatat 420 tgacttgcaa cctccattcc agttgcaatc tgtgcttcat gttcccacac tttcccacaa 480 tttaatttcc atccataagc ttacccgtga tctgaattgt aaagtaattt tttctatgtc 540 ccattgtgtt tttcaggacc ttaccacggg gcagacgatt ggaattgcta aggaaaagga 600 agggtatact acttctctga tgaccatcca aaggtgttgt cctcctgttt ccagtctcag 660 tcttcctctt cagcctcaca aatttggctt cagcacaagc gtctcggtca tcctccattt 720 tatataatta agtctatgtt tccgtcgttg ttcttacacc attctgttga gtcttttaag 780 tgtgatgttt gtcagttggc aaaacacaat cgtgtatctt ttccttccag ttttaataaa 840 agtgatgaac cttttgattt gattcattct gatgtttggg gacctgcccc tacctctaat 900 atttttggtg caaaatggtt tgtctcattt attgatgatt gtactcgggt aacttggatt 960 ttcttgatga atactaaatc cgaagtacca caaatattta tccaatttta taatatggca 1020 caaacgcaat ttgggaaagg cataaaaaga attcgttctg acaatggtaa agaatatgtc 1080 aatcatacct tttccaattt cactagtaaa catgacattc tccatgaatt cacatgtgtt 1140 gacaccccac aacaaaacgg tgtcgcagaa agaaaaaatc gtcatttact tgaagttgct 1200 agatctctcc tttttcaaat gtctgttcct acctcttatt ggggtgaggc aattcttact 1260 gctgcctatc tgattaaccg ggtcccatct tgagtgttag gtaataaaag tcctgtccaa 1320 tttatgcttt cacgttttcc atttgttcct atcttacaca ctcttgagtc tcgcattttt 1380 ggttgtgttg cttttgttca tgttcacaaa caatatcgca acaaattgga tccccgtgct 1440 gtcagatgta tctttctggg ttatgcaccc aacaaaagag ggtacaaatg ttatcatcct 1500 ccgagtcgaa aattctttgt ctccaaagat gtcacctttc atgaaaatgt gtcatatttc 1560 actcgttctc agtctcagag ggagaacata agtgacttag agtcagagtc aaagtctgag 1620 tccgagtttc tgatccttgg tcctagcctc cctagaacac ctatcagtgt tccctctctt 1680 gaacccgagt tgtcacctag tttgagtcct agttcaacac ctgaatctga gtcagtaagt 1740 gttcctggtc cttcaaggcc ttctgtttta caggaatcag cacctccagc accaactcta 1800 gtgtatcaga gaagaagtaa acctgacctt ctccagaaac aaattcaatc gcctgaaccg 1860 gagtaagtac tgaaaatgat tcctctagtg atgattgtgc catttctgat acttgtgaca 1920 ctaatccagt tgatttaccc attgctttga ggaaggataa aagatcttgt ccctccctat 1980 atcgacaccc tatctctcaa tatgtctcca taacatcttt ccacacaata tcaaagtttt 2040 attgcagcgg ttgattctgt gaaaatccca tcatctgttg aagaagcatt gcaaaataga 2100 aattagatcc aagctatgga tgaggaaatg agagcacttg aaaaaaatgg tacttgggag 2160 attattgaaa ggaaaagaga caaaagtcca gttggatgca gatggatcta tactgtaaag 2220 tacaaatctg atggtacact tgatcggtac aaagcaagac tagtggcaaa gggttatact 2280 cagacgtatg gtattgatta tgaggagaca tttgccccag tggcaaagat gaatactgtt 2340 cgaattttac tatctcttgc tgcttcatgt ggatgggaat tgcaacggtt tgatgttaaa 2400 aatgcatttt tgcatggaga cttagaggaa gaagtgtata tggagattcc accaggtgtt 2460 ggcataacaa atggagctaa caaggtgtat aaattgaaga aagccttata tggactaaag 2520 cagtcccctc gggcatggtt tggaagattc acaaaggcaa tgatgtgttt ggactataag 2580 caaactcaag gagaccacac tttatttttt aaacattcac aaggaggaaa actgactgta 2640 cttcttgttt atgttgatga tattattgtt acaggagatg atttgattga gagacatttc 2700 ctcaaagaga aattatcagc agagtttgag atgaaagacc ttgggcaact caagtatttc 2760 ttgagaattg aggtagccta ctcaaagcaa ggcatcttta tttctcaaag gaaatatgtg 2820 cttgatcttt tgcaggaaac tggcaaactt ggatgcaaac ctgcaagtgt tcccattgaa 2880 caaaatcaca ggataagctt tgaggaggaa agtgacaaag ttgacaaggg tcaatatcag 2940 agattagtgg gaaaattgat ttacttggca cacactagac cagatttggc atatgcagtc 3000 agtgtggtga gccaattcat gcatgatccg agggtgagac atttgcaggc tgtagaccgc 3060 gttctacaat atcttaaagc aactccaggg agaggacttt tgtttaaaag aggtggaaat 3120 ctaactatgg agacttacac tgatgcggat tatgccggat cagtgagtga cagaagatct 3180 acgtcaggct attgtacttt tctgtgtggt aaccttgtag cttggaagag taagaagcaa 3240 agtgtagttg ctcgatcaag cgccgaggca gaatttagag ctatggcact aggaatttgt 3300 gagctattgt ggatgaaaca aattctagaa gacttgaaga tacaatgtga aggtcctatg 3360 acattgtttt gtgacaataa atcggctatt agtattgctc ataatcctgt tcagcatgac 3420 aggactaaac acattgagat tgaccgacat tttatcaaag ataagttgga tagtggactg 3480 ataactacat cttacgttcc ttccaggcat cagctggcag atgtgttaac aaaagactta 3540 ccaacagaaa gattcagaca acttacttgc aagctgggaa tgatagatat cgattcacca 3600 gcttgagggg ag 3612 // ID Copia-3_CP-I repbase; DNA; EDCOT; 4373 BP. XX AC ABIM01022997; XX DT 10-MAR-2010 (Rel. 15.04, Created) DT 10-MAR-2010 (Rel. 15.04, Last updated, Version -1) XX DE LTR retrotransposon from papaya: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-3_CP_; KW Copia-3_CP-LTR; Copia-3_CP-I. XX OS Carica papaya OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Caricaceae; Carica. XX RN [1] RP 1-4373 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from papaya."; RL Repbase Reports 10(4), 577-577 (2010). XX DR Genome; ABIM01022997; Positions 20012 15640. XX CC Positions [1601-2092] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 50..4318 FT /product="Copia-3_CP-I_1p" FT /translation="MSTSSHSTLSHSSPLQFSTVPSPSINQVISVKLTQEN FT YLLWSAQILPYLRSQGLVGFVDGSTPAPSQTITIEPSEATNGRSIVINPEY FT TVWYHQDQLVLSLINSSVTEEVLGTMIGIITAREAWTTLEKQFASTSRARA FT MQIRMELTTIQKKDMKIADYFRKIKRLGDTLAAIGKRVEDEELIAYMLQGL FT GPDYDSLVTSITTRTDVYTISDVYAHMLTYEMRHLRNGTIDQLSSANNVNR FT MTTRGGINGARNGRGRGRQSYGGRRQTGRIGINPGRQQPRTQSSSDKNNLC FT QICGKPNHNALQCWYRFDQAYQAEDNIKQAALATSGYTSDANWYIDTGATD FT HITSELDRLTTRERYTGTDQIQVANGSGLSISHIGNSLIPGSSRSLVLKHI FT LYAPKINKHLISVKRLASDNDAFVEFHPNCFLVKDRVTKELLLTGKCKNGL FT YILPNSSNQALLTAKLSKEQWHRRLGHPASPVTVRILQDNNLAVDTSVSSS FT LICHACQLGKAHQLPFASSQHVSTAPLQLIHTDVWGPAISSVNNSKYYVSF FT VDDFSRYVWIYFLKYKSDVESVFLQFQKHVETMLNSKIRSVQSDWGGEYHR FT LHNYFKSTGIEHRISCPHTHQQNGIAERKHRHIVDTGLTLLAQSNMPLSYW FT DEAFNTACFLINRMPTRTIQQDTPLHKLFNKNPDYLTLRVFGCACWPNLRP FT YNNKKLSFRTTKCVFLGYSSSHKGYKCLDRSTGRIHISRDVIFDENLFPFN FT ESKSPAKIKHSHQPALLPVLINPTVYTEHALTNVEPVISDSHMSYGQSDDI FT ANDASVLSLLPADNTTHHEVIAEHEAENSSTNNQNRAQEQLPEHDISRDTI FT PEASNQHSMKTRSKNNIVRAKQFTDGTVRYSDTSRSFAGTAAVNNLKHTIM FT TDAVAEPNNLEEAMRNPGWREAMNNEFSALQKNETWVLVPPKPGINLIDSR FT WVYKVKRKADGSVERLKARLVAKGFKQRFGIDYSDTFSPVIKPSTIRVILS FT LAVTKGWNMRQVDIQNAFLHGILEEEVYMRQPPGFQDPDKPQNYICKLKKA FT LYGLKQAPKAWHSRLTGKLMELGFKASVADSSLFILKNRDITIYMLIYVDD FT IIIVSSSDQATESLIQNLKTDFAVKDLGDLKYFLGIEVKKTRDGLILSQRR FT YALNLLKKANMEKCKPMSTPMSSAERLLREQGIPLSTDEQFKYRSTVGALQ FT YLTMTRPDLAFAVNKVCQYLHAPTDTHWGAVKRILRYVKGTLDFGVKIQKS FT QTMMLSGFSDADWAGCPDDRRSTSGFAVFLGVNLISWSSRKQATVSRSSTE FT AEYKAIANLTAEMIWIKSLLKELGVYQSKAPRLWCDNLGATYLTSNPMFHA FT RTKHIEVDFHFVREQVARKAMEVRFISSSDQVADILTKPLSRYPFITHCNN FT LNISRTCCD" XX SQ Sequence 4373 BP; 1393 A; 935 C; 838 G; 1207 T; 0 other; tggtatcaga gcaggttgat tcacaaactt ccagcttcca ctgctaacca tgtctacctc 60 ctctcattca acactctctc attcatctcc tctccaattt agcactgtgc cttctccatc 120 tattaaccag gtaattagtg taaaactcac ccaagaaaat tatctgctgt ggtctgctca 180 aatccttcct tacttacgca gccaagggct agttggtttt gttgatggat ccacacctgc 240 acctagccaa acaatcacca ttgagccgag tgaagcaaca aatggccgca gcattgttat 300 caaccccgag tacacagttt ggtaccacca ggaccagctg gtgctcagtc tcatcaactc 360 gtctgtcaca gaagaagttc tcggaactat gatcggcatt atcacggcac gagaagcctg 420 gacaacgttg gagaaacaat tcgcttctac gtctcgagct cgagcaatgc aaattcgcat 480 ggaactcacc acgatccaaa agaaggacat gaaaattgca gattattttc gcaaaatcaa 540 acgcctcgga gacacacttg cagccattgg caaacgagta gaagatgaag agcttattgc 600 atacatgcta cagggacttg gtccagatta tgattctctg gtcactagca ttacaacaag 660 aacagatgtc tacaccatca gcgatgtata tgctcacatg ctgacttacg agatgcgaca 720 cctgcgtaat ggtacaattg atcagctttc atctgctaac aatgttaaca ggatgactac 780 tcgaggaggc atcaatggag ctcgcaacgg tcgtggtcgt ggccgtcaat catacggtgg 840 ccgtagacaa acagggcgta tcggaatcaa tcctggacgt caacaaccac gaacacaaag 900 cagctcagac aaaaacaatc tctgtcaaat ttgtggtaaa cccaatcata atgccttaca 960 atgctggtac aggtttgatc aagcatatca agccgaagac aacatcaaac aagcagctct 1020 agcaacaagt ggatatacta gtgatgcaaa ctggtatatt gatactggag ccacagatca 1080 tatcaccagt gaactagaca gacttaccac cagagaacgt tacactggca ccgatcagat 1140 tcaagttgca aatggctcag gtttgtctat atctcatatt gggaattcat taattcctgg 1200 ttcatctaga tctcttgttt tgaaacacat tctttatgct cccaaaatca ataaacattt 1260 aatttctgta aaaagattgg cctctgataa tgatgctttt gtggaatttc acccaaattg 1320 ttttcttgtt aaggatcgag tcacgaagga gctcctactc accggtaaat gtaagaatgg 1380 tctctacatt ctaccaaatt cttccaatca agccttgctc acagccaaac tttcgaaaga 1440 acagtggcac agaagacttg gccatcctgc ctctcccgtt actgttagga ttttacaaga 1500 taataattta gctgtagata ctagtgtttc atcttcccta atttgtcatg cttgtcaact 1560 aggaaaagct catcaattac cttttgcttc ttctcagcat gtatccacgg caccacttca 1620 gttaatccat actgatgttt ggggtccagc tatttcctca gtaaacaatt ctaaatacta 1680 tgtctctttt gttgatgatt ttagccgata tgtttggatt tattttttga aatacaagtc 1740 tgatgttgag tctgttttcc ttcaatttca aaaacatgtt gaaaccatgc taaattcaaa 1800 aatacgctct gtccagtcag attggggggg tgaatatcat cgtttgcaca attatttcaa 1860 atctactggt attgagcatc gtatctcttg tcctcacaca caccaacaaa atgggatcgc 1920 agaaagaaaa cacagacaca ttgtagatac tggccttact ttacttgctc aatcaaacat 1980 gcctctgtca tattgggatg aagccttcaa tacagcatgt ttccttataa atcgcatgcc 2040 cactcgaaca atacagcagg acacccctct tcataaattg ttcaacaaaa atccagatta 2100 cttaactctt agagtgtttg gttgtgcctg ctggcccaat ctcaggcctt acaacaacaa 2160 gaaactaagt ttcagaacca ctaaatgcgt gttcttgggc tatagctctt cacataaagg 2220 ttacaaatgc ttagacagaa gtacaggccg aatccacatt tctagagatg taatctttga 2280 tgaaaacttg tttcctttta acgaatctaa gtcaccagct aaaatcaaac actcacatca 2340 acctgctctt cttccagtat taatcaaccc cacagtctac actgaacatg ctctcacaaa 2400 tgttgaacca gttattagtg attctcatat gagttatggt caatctgatg atattgctaa 2460 tgatgcatct gttttaagtt tgcttcctgc agataataca acacatcatg aggtaattgc 2520 cgaacacgaa gctgaaaata gctcaaccaa caatcaaaac cgagctcaag aacaactgcc 2580 agaacatgac atttctcgtg atacaatccc tgaagcaagt aatcaacact caatgaaaac 2640 acgatcgaaa aacaacattg tgagagcaaa acaattcact gatggaactg taagatactc 2700 tgacacctcg agaagttttg caggaactgc tgctgtcaac aatttgaagc ataccataat 2760 gacagatgca gttgctgaac cgaacaactt ggaggaagcc atgcgcaacc caggatggag 2820 agaagcaatg aataatgaat tctcagcgtt gcagaagaat gaaacttggg ttctcgttcc 2880 tcccaaacct ggaatcaatc tcattgacag tagatgggtg tacaaagtaa aaagaaaggc 2940 agatgggtca gttgaaagat tgaaagcaag attagttgcc aaagggttca aacaaaggtt 3000 tggtattgat tacagtgata ctttcagtcc tgtaattaag ccttcaacaa tcagagttat 3060 tctctcatta gcagtaacaa aaggctggaa tatgaggcaa gtcgacattc aaaatgcatt 3120 tttacatggt attttggaag aggaagttta catgagacaa ccaccaggat ttcaagaccc 3180 agacaaacca cagaattaca tatgcaagct caagaaagcc ctgtatggtt taaaacaggc 3240 acccaaagcc tggcactcaa ggttgactgg aaaacttatg gagttaggtt tcaaggcttc 3300 ggtagctgat tcatctttgt ttatcctcaa aaacagggat ataaccatct atatgctcat 3360 ctatgttgat gacataatta ttgtgagctc atctgatcaa gccaccgaaa gtctgattca 3420 aaatttaaaa acagattttg cagttaaaga tttgggtgat cttaagtatt ttctgggtat 3480 tgaagttaag aaaacaagag atggtctcat actatcacaa agaagatacg ctttgaacct 3540 gttgaagaaa gcaaacatgg aaaaatgcaa gccaatgtct actccaatga gttctgctga 3600 acggttattg agagaacagg gaataccctt atcaactgat gaacaattca agtatagaag 3660 cactgttgga gcactacaat atttgacaat gactagaccc gatctagctt ttgcagtgaa 3720 taaggtttgc caataccttc atgcacctac tgatactcat tggggcgcgg taaaaagaat 3780 cctccgctat gtcaaaggta cgctagattt cggtgttaaa attcaaaagt ctcaaacaat 3840 gatgctgtct ggattttcgg atgctgattg ggcaggatgt cctgatgatc gacgatcaac 3900 tagtggattt gctgtgttcc ttggagtaaa tttgatttca tggagttcaa gaaagcaagc 3960 tacagtgtcc aggtcaagta cagaggcaga gtacaaagcc attgcaaatc taactgcaga 4020 aatgatctgg atcaaatcat tactaaagga gcttggagtg tatcaatcaa aggctcctcg 4080 tctctggtgt gataatttag gagctacata cttgacttca aatccgatgt ttcatgccag 4140 aacgaaacat attgaagttg acttccattt tgttcgagag caagtggcac gcaaggcaat 4200 ggaagttcga ttcatttcat caagtgatca agtagctgat attctgacca aaccactgtc 4260 tagatatcct tttattactc attgtaacaa tctcaacata tccagaactt gttgtgattg 4320 agggaagctg ttagaattag tcaaataact gttatgtaag tggagtaaga taa 4373 // ID Gypsy-27_PTr-I repbase; DNA; EDCOT; 5668 BP. XX AC . XX DT 09-DEC-2009 (Rel. 15.02, Created) DT 09-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type non-autonomous LTR retrotransposon from Populus DE trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed repeat; internal portion; Gypsy-27_PTr-I; KW Gypsy-27_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-5668 RA Bao W. and Jurka J.; RT "Non-autonomous LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 234-234 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 966..2096 FT /product="Gypsy-27_PTr-I_1p" FT /translation="MSDQNNTPPHPEGELTFQMQAMTQMMERMNFVMGNVC FT DRLDRVEKRGNEAGTSTQNVRKLGAEPKANSGSRAERPRWADYEDFEEAVD FT DIGDGGFEDEAIGHREGFRQPRNRRDYGNRTRGQFGQRENFRSVGGHADLD FT GDLDAIKLKIPSFQGKNDPEAYLEWEKKVDWIFDCHNYSEAKKVKLVVIEF FT TDYALIWWDQNVISRRSGERPVASWEEMKVLMRRRFVPNHYYRDLYLKLQG FT LNQGSRSVDEYFKEMEIAMIRANVIEDREATMARFLNGLNRDIANVVELQH FT CVELEDMVHMATKVERQIKRRGSTRFQTNSASSSSTWRPNLKREGAVQPKP FT YAKAEPPKAKKDTHTDGKGKSESQPTRDRDIKCF" FT CDS join(1996..2520,2514..5666) FT /product="Gypsy-27_PTr-I_2p" FT /translation="MQRPNHLRPKRILIRMGKVNLNLNLLVIEILNAFKCL FT GKGHIASQCPNRRVMLTRDNGEVESESDKSESEEMPPLVDCSDEEIAYPVE FT GEALVIRRALNMQIKEDDVDQQRENIFHTRCHIQNKVCSMIIDGGSCANVA FT SDTLVKKLNLSCIKHPRPYRLQWLNECGEVRVTKQVAGLIAFAIGKYSDEI FT LCDVVPMHASHLLLGRPWQFDRKAIHDGFRNRFTIVKDGKTITLVPLSPKQ FT VYDDQMKLKKECEDGKSENSREDNGERKPSDSAKPKSLIKPVESGGKNRGV FT KKVSLCDDNSVEKLKKQPNFYAKGSQIRSAFFTNKPMILLVYKEAYFNTND FT LDSAIPSVAVSLMQEFDDVFPEDIPNGLPPLRGIEHQIDLVPGASIPNRPA FT YRSNPEETKELQRQVDELMMKGYIRESMSPCAVPVLLVPKKDGTWRMCVDC FT RAVNNITVKYRHPIPRLDDMLDELHGSCIFSKIDLKSGYHQIRMKEGDEWK FT TAFKTKHGLYEWLVMPFGLTNAPSTFMRLMNHVLRAFIGKFVVVYFDDILI FT YSKNLNEHLDHLRNVLSVLRSEQLYANLKKCTFCMEKIVFLGYVVTAQGIE FT MDEEKVKAIRDWPTPKSVSEVRSFHGLASFYRRFVKDFSTIAAPLTEIVKK FT SVGFKWNDEQDKAFNLLKDKLCSAPVLALPDFTRAFEVECDASGIGIGAVL FT MQDRRPIAYFSEKLNGAALNYPTYDKELYALVRTLETWQHYLWPKEFVIHS FT DHESLKHLKGQGKLSRRHAKWVEFIETFPYVIKYKQGKENIVADALSRRYV FT LLSTLDARFLGFEHIKELYKDDSDFANVYNACETSAFGKFYRLDGYLFKES FT RLCVPLSSMRELLVREAHGGGLMGHFGVVKTLDVLHEHFYWPKMKKDVQRI FT CDKCITCRKAKSRTQPHGLYTPLPVPKEPWVDISMDFVLGLPRSKRGRDSI FT FVVVDRFSKMAHFIPCHKTDDATNIADLFFREIVRLHGVPKSIVSDRDVKF FT LSYFWKVLWGKLGTKLLFSTTCHPQTDGQTEVVNRTLTQLLRAVIQKNLKN FT WEDCLPFIEFAYNRSVHSTTEFSPFEIVYGFNPLTPMDLIPLPVDERVSLD FT GNRKAQVVKTLHESVRQQIEKRNRVYATKANKGRKHVVFQPGDWVWVHMRK FT ERFPAHRKSKLQPRGDGPFQILERINDNAYKVDLPGEYGVSATFNVSDLTL FT FDVGDDSRSNPFEERG" XX SQ Sequence 5668 BP; 1642 A; 870 C; 1420 G; 1736 T; 0 other; tttggtatca gagcttggct ccattaatca ggttatatcc ttctgaaatt tttgtttctt 60 gttgattccg caaaaattcc ttagtatcca atttcttctt ctccttgaat ttgcggcata 120 taaaaaaaaa aaaaaaattg ttatttcatt ctgttactgt ccaaaatata tcagtagcat 180 aaaaaaaaga gaaaagaaaa aaaaatcgtt caaaaagacg tttattggtt tctgccgcag 240 aaaactaaac aagggaaaat tggatcaaat caactcggaa ttagctcaaa tttgatactc 300 tgattactgg ggtcctaatc gcaccacata ttaattttgg ggtcaattgg atatcgtttg 360 ctttggtttt caatttcggg tctaattagg tctgattcat aacgtttttg cgtcagcata 420 tcaaacctta tcgtaaattg ctcaaacttt atattctgtc tatttgggtt gatatcgcac 480 tatatctgaa attttagctc aattggacat catttacttt aggttccaga ttcggactta 540 actcgtcgta aacgagtctg ttttgcgtca acttttgaaa ttcgctttct ttttgttgtt 600 ttcatttctt gcagtatatt ttcacatatc caacatattt gggtgttgtt tcatcatttt 660 gcatatttcg tttctatttt tattcgagtc ttcagtttcg ttcatatttc ggatagattc 720 gcttgctact cgcgagacta tcatcgcagt tttgttttgc ttgtttttct ggtttttatt 780 gcttcttgag tcatatatat atttggattg cgctgccaag ttggttctat ttggtgttgg 840 tttcagttcc gcaagaaggt gagacgagag gtgtgagcgt gtgaggatat taagagtgtt 900 tgagcgaaac acgagcgacg tgaggatatt ttttttacca ctaaccaatt tttgcaggta 960 ctatcatgtc agatcaaaac aacacaccac cccatcccga gggagaactt acgttccaaa 1020 tgcaagccat gacgcagatg atggagagga tgaattttgt gatgggaaat gtgtgtgaca 1080 gacttgatag ggtggagaaa cgtggtaacg aggctggtac aagcacccaa aatgtgagga 1140 agcttggggc tgaaccgaaa gcaaacagtg gcagtagggc cgaaaggcca aggtgggctg 1200 attatgagga ttttgaggag gccgttgatg atattggtga tggtggtttt gaggatgagg 1260 ccataggcca tcgggaaggt tttcggcagc ctagaaaccg aagggattat gggaatagaa 1320 ctaggggcca attcggccaa agggaaaatt tccgtagtgt tgggggacat gctgatttag 1380 atggtgattt ggatgctatc aaactgaaaa taccttcttt tcaaggtaaa aacgatcccg 1440 aggcatattt ggagtgggag aaaaaggtgg attggatttt tgattgccat aactattcgg 1500 aggcgaagaa agtgaaattg gtagtcatcg aattcacgga ttatgcactg atttggtggg 1560 atcagaatgt tattagtagg aggagtggag agaggccggt agcgtcgtgg gaggagatga 1620 aagtgttgat gagaaggcga tttgtgccta accactatta tagagatttg tatctgaaat 1680 tgcagggttt gaatcagggt tctaggtccg tggatgagta tttcaaggag atggagatcg 1740 ccatgattcg ggccaatgtg attgaggatc gggaagctac tatggctaga tttctaaatg 1800 ggctgaatag ggacattgcg aatgttgtag aattacaaca ttgtgtggaa ttggaggaca 1860 tggtccatat ggcaacgaag gtggagaggc aaataaagag aaggggcagt acacgttttc 1920 agaccaattc ggcttcatct tcctcaacat ggaggccgaa tttgaagaga gagggggctg 1980 tccaaccaaa gccttatgca aaggccgaac cacctaaggc caaaaaggat actcatacgg 2040 atgggaaagg taaatctgaa tctcaaccta ctcgtgatag agatattaaa tgcttttaag 2100 tgtttaggga aggggcacat tgcatctcag tgtccaaacc gaagagttat gcttacaaga 2160 gacaatgggg aggttgaatc tgaaagtgac aaatctgaaa gtgaagagat gccacctttg 2220 gtggattgta gtgatgagga gattgcatat cctgttgagg gggaggcctt ggttataagg 2280 cgtgcgctga acatgcaaat caaagaagat gatgtagatc agcaacggga aaatatattt 2340 cacactcgat gtcacatcca aaacaaggta tgtagcatga taattgatgg aggtagttgt 2400 gctaatgttg ctagtgatac tcttgtgaag aaattgaatc tgagttgtat taagcatcct 2460 aggccttata gattgcaatg gttgaatgaa tgtggtgaag tgagggttac taagcaggtt 2520 tgattgcgtt tgctattggg aagtattctg atgagatttt gtgtgatgta gtcccaatgc 2580 atgctagtca cttacttttg gggcgtccat ggcagtttga tcggaaagcg attcatgatg 2640 ggtttagaaa taggttcact attgtaaagg atggtaaaac catcactctt gtacctcttt 2700 ctccaaaaca agtgtatgat gatcaaatga aattaaaaaa ggaatgtgag gatgggaaga 2760 gtgaaaattc acgtgaggac aatggtgaga gaaaaccatc agattcggct aaacctaaat 2820 cattaattaa accggttgag agtggaggta aaaaccgagg agtgaagaaa gtaagcttgt 2880 gtgatgataa tagtgtggaa aaattaaaga aacaacctaa tttttatgca aaaggatctc 2940 aaatcagatc tgcatttttc actaataagc caatgatctt acttgtgtat aaggaggctt 3000 attttaacac taacgatctt gattctgcta ttcctagtgt ggctgtttct ttgatgcagg 3060 agtttgatga tgtattccct gaagacatcc ctaatggatt accaccatta agggggattg 3120 aacatcaaat tgaccttgtg cccggagctt cgattcctaa ccgtccagcc tatagaagca 3180 accccgagga gacgaaggag cttcaaaggc aagtagatga gttgatgatg aaggggtaca 3240 ttcgtgagag tatgagtcct tgtgctgtgc cagtgctact tgtgcctaaa aaggatggaa 3300 catggaggat gtgtgtcgat tgtcgtgccg tcaataacat aacggtaaag tatcgacatc 3360 ctattcctag gcttgatgac atgctagatg agttacatgg atcatgtatt ttctctaaga 3420 ttgacttaaa aagtgggtac catcaaatta ggatgaaaga gggtgatgag tggaaaactg 3480 catttaagac taagcatggt ttgtatgaat ggttagtcat gccgtttgga cttacaaatg 3540 cgcctagcac gtttatgcgt ttaatgaatc atgtattgcg tgcgtttata ggtaagtttg 3600 ttgttgtgta ttttgatgac attttgatct atagcaagaa cttaaatgag catcttgatc 3660 atttgcgtaa tgtacttagt gtgttgcgta gtgagcaatt atatgctaat cttaagaagt 3720 gtaccttttg catggaaaaa attgtgtttc ttggctatgt cgtaactgcg cagggtatcg 3780 agatggacga ggagaaagtt aaggccatcc gggattggcc tacaccaaaa tcggtaagtg 3840 aggtaaggag ttttcatgga cttgctagtt tttatagaag gtttgtgaag gattttagta 3900 ctattgctgc acctttaact gaaattgtga aaaagtctgt tggattcaaa tggaatgatg 3960 aacaggataa ggcttttaat ttgttgaaag ataaactttg ttcggcgcct gttttagctt 4020 tgccagactt tacgagagct tttgaagttg aatgtgatgc gtcaggtatt ggtataggag 4080 ctgtgttaat gcaggatagg aggcccattg cgtatttcag cgaaaaactt aatggggcag 4140 ccttgaatta ccctacatat gacaaggagc tctatgcctt ggtaagaact ttagagacgt 4200 ggcaacatta cctgtggccc aaggagtttg tgatacattc tgatcatgaa tcattgaagc 4260 acttgaaagg gcaaggtaag ttgagtagga gacatgccaa atgggttgaa tttattgaaa 4320 cctttccgta tgtgatcaag tataagcaag ggaaagaaaa cattgtggct gatgcacttt 4380 cgcgcaggta tgttctttta tctactttgg atgctagatt tctaggattt gaacacataa 4440 aagaattgta caaggatgat agtgattttg ctaatgttta caatgcttgc gaaacttcgg 4500 cttttggaaa gttttataga cttgatggat atttgtttaa agagagtcgt ttgtgtgttc 4560 cattaagttc tatgcgtgaa ttgcttgtac gtgaagcaca tggaggcggg ttgatggggc 4620 attttggtgt tgttaagact ttggatgtgt tgcatgagca tttttattgg cctaaaatga 4680 aaaaagatgt gcaacgcata tgtgataaat gcataacttg taggaaagca aagtctagga 4740 ctcaaccaca tggcttgtat acccctttgc ctgtaccgaa agaaccatgg gtagacattt 4800 cgatggactt cgtcttaggt ttacctaggt caaaacgggg tagggattcc atctttgtag 4860 ttgttgatag gttttcaaag atggcacact tcattccatg tcataaaact gatgatgcaa 4920 ctaacattgc tgatttgttc tttagggaga tagtacggct tcacggggtc cctaagagca 4980 ttgtttctga tagagatgtt aagttcctta gctatttttg gaaggtgtta tggggcaaat 5040 tgggtactaa actgttgttt tcaactactt gtcaccccca aacagatgga caaaccgaag 5100 tagttaatag gaccttaaca caacttctgc gtgctgtcat tcaaaagaac ttaaagaatt 5160 gggaagattg tttgccattt atagagtttg catataatcg tagtgtgcac tctactactg 5220 aattttcacc atttgaaatt gtgtatggat ttaacccttt aactccaatg gatttgattc 5280 ctttgcctgt tgatgaaagg gttagtttgg atggtaatcg taaagcacag gtggtgaaga 5340 cacttcatga gagtgtgcgg caacagattg aaaagaggaa tcgtgtgtat gcgaccaaag 5400 ccaataaggg gcgcaaacat gttgtctttc agcccggcga ttgggtttgg gtgcatatgc 5460 gcaaggagag atttccggcc cataggaaat caaagctaca accacgagga gatgggccat 5520 ttcagatcct tgagaggatc aatgacaatg cttataaagt tgatttgcca ggtgagtatg 5580 gtgttagtgc tacctttaat gtttctgatc ttactctgtt tgatgtaggt gatgattcga 5640 ggtcgaatcc ttttgaagag agagggga 5668 // ID SHACOP16_I_MT repbase; DNA; EDCOT; 4038 BP. XX AC AC174347; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 06-FEB-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP16_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; terminal; ORF; cysteine peptidase; KW integrase; gag-pol; SHACOP16_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4038 RA Shankar R. and Jurka J.; RT "SHACOP16_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 59-59 (2007). XX DR EMBL/GenBank/DDBJ; AC174347; Positions 8502 12539. XX CC The internal region has intact domains for gag-pol polyprotein CC and the pattern of domains arrangement is Copia-like. In Medicago CC genome, almost all copies are incomplete or disrupted. XX FH Key Location/Qualifiers FT CDS join(48..1622,1626..3992) FT /product="SHACOP16_I_MT_1p" FT /translation="MEENTGTMIKLTSTNYSIWKPKMEDILYYKDMYDPVE FT KGDTKPDKVTDEDWKKSHRKAVSLIRQWVDLSVFHHVATETNAQTLWKNIE FT KMYQRKTAQNKTFAIRKLVNLKYREGRSVAEHLSDFQDLVNQLVAMKLVLN FT DELQALLLLSSLPKSWETLVVSLSNSAPDGALTLSQVKDSMFNEETRRKYM FT GSSSSHALVTENRGRSKSGGRSNKSKDRSQSQPRRKFKCFHCNEEGHIKRN FT CKSWKNKEKKDRRNQRPDEDENTTTPVVDGEVVLFSVEEEECHVADSCVEW FT VIDSAASYHATSNKEFFTMYKVGDFGKVKMGNNSIADIVGIGDVCVQTNTG FT FTLTLKNVRHVPDLRLNLISVHALDLAGFQNNFGDGKWKLTKGSLMIARGV FT VYSTLYKTQVKLIKDGLNAAENVALADLWHKRLAHLSEKGLQILSRKSLIP FT SDKGTKLNPCDYCLFGKQHRVSFSRTSKLKDNKLDMVYSDVCGPMEVETLG FT GSRYFVTFIDDASRKVWVYFLKSKDQVFQFKRFHAMVERSTGKSLKCLRSD FT NGGEYTSHEFKSYCSEHDIRHEKTVPGTPQHNGVAERINRTIMEKVRCMLK FT MAKLPKPFWVEAVQTTCYLINRSPSVPLGFDIPERVWSGHDISYSHLKVFG FT CKAFAHVNKEHRQKLDDKAIPCIFVGYGDEEFGYRLWDPEKRRIIRSRDVV FT FHEQETMSDSTILETPKRYGKVDLTLTTPPVRVATEGGDLDEDPGVDGEPV FT VEDGDDEDVQDGEQSTTSHLRRSSRDHHPSTRYPSSEYILITDEGEPDSFD FT EVQTHKDKIQWMKAMQEEMDSLQKNDTYELVKLPEGRKALKNKWVFKLKKD FT GDKLVKYKARLVVKGFGQKRGIDFDEIFSPVVKMSSIRVILGLVASLDLEL FT EQMDVKTAFLHGDLDEEIYMVQPEGFEKTRKEHLVCKLKKSLYGLKQAPRQ FT WYKKFDSFMMSHEYTKTDADHCVYVKTFRGNKFIILLLYVDDMLIVGQDKD FT MIGDLKKELSKSFDMKNLGPAKQILGMKILRDRKARKLWLSQQQYVDRVLE FT RFNMKGAKPVSTPLANHFKLNRVSCPTSQDEKEAMVAIPYSSAVGSLMYAM FT VCTRPDIAHAVGVVSRFLSNPGKEHWEAVKWILRYLKGSSNKCLCFGGSDS FT LLKGYTDADMAGDLDGRKSTSGIVFTFAGGAVSWQSKLQKCVALSTTEAEY FT IAMAEAGKEMLWLKRFLDQLGMKQERYVIHCDSQSALDLSKNAMYHSRTKH FT IDVRYHWLRQAAGEQQFMLEKIHTDKNPADMLTKVVAREKLQLCAELIGMD FT RK" XX SQ Sequence 4038 BP; 1303 A; 659 C; 1001 G; 1075 T; 0 other; gtggtatcag agctccggtt ggagctcgag agtatagtgt aaattaaatg gaggagaaca 60 ctggtacgat gattaaactc acttctacaa actactccat ttggaagcca aaaatggagg 120 atatacttta ctacaaggat atgtatgatc ctgtagaaaa gggagacacg aagccagata 180 aggtgacgga tgaagactgg aaaaagtctc atcggaaggc tgtcagtctg attaggcagt 240 gggtggatct tagtgtattc caccatgtgg ccacagagac aaatgcccag actctgtgga 300 agaacatcga aaagatgtat caaagaaaga ccgcacaaaa caaaactttc gctattagaa 360 agttggtgaa tctaaagtac cgggagggaa gatcagttgc cgagcacttg agtgactttc 420 aagacttggt aaaccaattg gttgccatga agttggtgct gaatgatgaa ttacaagcac 480 tattactttt gagttctttg ccaaaaagtt gggagacttt ggtggtgtca ttaagcaact 540 ctgctccaga tggagcgctc actttgtccc aggtaaaaga tagtatgttc aatgaagaaa 600 caagaagaaa atacatggga tcaagtagct ctcatgccct tgtcacggag aacagaggca 660 gaagcaagag cggggggaga tccaataaat ccaaagacag atcacaatct caacctcgaa 720 gaaagttcaa gtgttttcac tgcaacgaag aaggtcacat caaaagaaat tgcaaatctt 780 ggaagaacaa agaaaagaaa gaccggagga atcaaagacc agacgaagat gaaaatacca 840 caaccccagt agttgatggg gaagtggtgt tgttttctgt tgaagaagaa gaatgtcatg 900 ttgcagattc atgtgttgaa tgggtcattg actcagcagc ttcttatcac gctacttcca 960 ataaagaatt ctttacgatg tacaaagtag gagactttgg caaagtaaag atgggcaata 1020 atagcattgc agatattgtt ggaattggtg atgtgtgtgt tcaaaccaat accggtttta 1080 cactaacact gaagaacgtg cgacatgtgc cagatttgcg tctaaatcta atctctgtcc 1140 atgctcttga tttagccgga tttcaaaaca actttggtga tggaaaatgg aaacttacca 1200 aaggatcgtt gatgattgct agaggcgtcg tgtattcgac gctttacaaa actcaagtca 1260 agctgatcaa agatggcttg aatgcggccg agaatgttgc tttggcagat ttgtggcata 1320 aaaggctggc tcatttaagt gaaaaaggat tgcaaatttt gtcaaggaag tccctcattc 1380 cgtctgacaa aggtactaag ttgaatcctt gtgattattg tttgtttggc aagcaacata 1440 gagtttcttt cagcagaact tcaaagctga aagataataa attggatatg gtgtattctg 1500 atgtgtgtgg acccatggaa gtggagactc ttggtggtag cagatatttt gtgacgttta 1560 ttgatgatgc ttcaagaaag gtgtgggtgt acttccttaa aagtaaggat caggtgtttc 1620 agtaattcaa aaggtttcat gcgatggtgg agagatcgac tggtaaatct ttgaagtgtc 1680 ttcgttcgga taatgggggt gaatatactt cccatgaatt taaaagttat tgttctgagc 1740 acgacatcag acatgagaag acggttcctg gcaccccaca acataatggt gtagctgaaa 1800 gaatcaacag aaccattatg gagaaagtga gatgtatgct gaaaatggct aagctgccaa 1860 agccattttg ggtagaagct gttcaaacca catgctacct gattaacaga tctccatctg 1920 ttcctttggg ctttgacatt cctgagagag tatggtccgg acatgatata agttactctc 1980 acctgaaggt atttggatgc aaagcctttg ctcatgtaaa taaggagcat agacaaaaac 2040 ttgatgataa agccattcct tgcatatttg tgggctatgg agatgaggaa tttggctata 2100 ggttatggga tccagagaag agaagaatta ttagaagcag agatgtagtg tttcatgagc 2160 aagaaactat gtcagattct actattctag aaacacctaa acgttatggt aaggttgatc 2220 ttacacttac cactcctcct gtaagagttg ccacagaagg gggagatctt gatgaagacc 2280 ctggggttga tggtgagcca gtagttgaag atggtgatga tgaagatgtt caagatggag 2340 agcaatccac aacatctcat ctcaggagat caagcagaga tcatcatcca tctaccaggt 2400 accctagttc ggagtacatc ctcatcactg atgaggggga gccggacagt ttcgatgaag 2460 ttcaaactca taaagataaa atccaatgga tgaaagcaat gcaagaagag atggattcat 2520 tgcagaaaaa tgatacttat gaacttgtga aacttcctga aggcagaaaa gccttgaaga 2580 ataaatgggt gttcaagctc aagaaagatg gtgacaagct agtgaagtac aaagctcgct 2640 tagtcgtaaa aggttttgga caaaagcgag gaatagattt tgatgaaatc ttctctccag 2700 ttgttaagat gagttcaatt cgagttatac tcggattggt tgctagcttg gatttggagc 2760 ttgaacaaat ggatgtaaag actgcatttc ttcatggaga tttagatgaa gagatctaca 2820 tggttcaacc agaaggattt gagaagactc gaaaggagca cttggtttgc aaattgaaga 2880 agagcttgta tggattaaaa caagcaccaa gacaatggta taagaaattt gactcgttca 2940 tgatgagtca tgaatatacc aagacagatg cagatcattg tgtatatgtc aaaacatttc 3000 gaggtaacaa attcatcatc cttctgttat atgtagatga tatgttgata gtggggcaag 3060 acaaggatat gattggtgat ttgaagaagg aattgtcaaa atcctttgac atgaaaaatc 3120 taggccctgc aaagcaaatc ttaggcatga agattttgcg agaccgaaaa gctagaaagc 3180 tatggttgtc acaacaacag tatgtggacc gggttctaga aagattcaac atgaagggtg 3240 ctaaaccagt tagcacgccg ttagccaatc actttaaact caacagagtg agttgtccta 3300 ctagtcaaga tgaaaaagaa gctatggttg caatacctta ctcctcagca gttgggagtt 3360 tgatgtatgc aatggtttgc accaggccag atattgctca tgcagttgga gttgttagca 3420 ggtttctttc caatccggga aaagaacatt gggaagctgt gaagtggatc ttgaggtatc 3480 tgaaaggaag ctctaataag tgcttatgct ttggaggatc agattcgctt ttgaaaggct 3540 acacagatgc ggatatggca ggtgacctgg atggtagaaa gtctacttca ggaattgtgt 3600 ttacttttgc agggggagct gtatcttggc aatctaaatt gcaaaaatgt gtagccttat 3660 caacaactga ggcagaatat attgccatgg ctgaagcagg gaaggaaatg ctttggctaa 3720 aaagatttct tgatcaattg ggaatgaagc aggaaaggta cgttatccat tgcgatagtc 3780 aaagcgcttt ggatttgagt aagaatgcga tgtaccactc tcgtacaaag catattgatg 3840 tcagatatca ttggttgcgt caagcagcgg gagaacaaca atttatgttg gaaaagattc 3900 acaccgataa aaatcccgcg gatatgttga cgaaagttgt agcacgtgaa aagcttcaac 3960 tttgtgccga gttgatcggc atggatcgca agtgaatgaa ttgcgagaat atctcccttt 4020 ggctggaggg gggagaat 4038 // ID MuDR-21_VV repbase; DNA; EDCOT; 11895 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-21_VV, an autonomous DNA transposon - a consensus sequence. XX KW MuDR; DNA transposon; Transposable Element; mutator; Jittery; KW Jitvine-1; MuDR-21_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-11895 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 774-774 (2008). XX DR [1] (Consensus) XX CC MuDR-21_VV (Jitvine-1 in [1]) is an autonomous Jittery-like CC element of the Mutator superfamily. It's individual copies are CC >90% identical to the consensus sequence. It does not contain CC TIRs, but is flanked by 8 bp-long TSDs. Downstream of the CC transposase gene is a putative gene in the opposite orientation CC encoding for a ULP1-like protein similar to CAN77890.1. XX FH Key Location/Qualifiers FT CDS 1778..4084 FT /product="MuDR-21_VV_Transposase" FT /note="MUDRA transposase, intronless. Contains FAR1 FT domain (pfam03101)." FT /translation="MDKGKGKEFIIDLNDEDFDYQYDSNVKTESDEEAILV FT SEKIFNDLTVEDVWKMEFSSIEEAEEFYNLFAKVTGFSVRKDDVKRDKNQN FT IVSRKWVCSKEGYRHRVCLENENRKREPKAVTRVGCEATFRIGFNKQMNKW FT IVKEFMADHNHPLVEQKNTQFLRSHRVIKNADKAQLNAMRGVGMGTSQIMD FT YMVQQSGGYNNVGFTKKDLYNHVDADRRVHLRDGDAEGALAYLCGKSEMDP FT SFYYKYNVDEDNRLANLFWADSTSKLDYTCFGDVLAFDTTYRTNAYKKPLV FT ILVGINHHHQTIVFGCALLVDESVSTYTWVLETFLDAMNNKKPLSVITDGD FT KAMRKAIKRIFPDSCHRLCAWHIQRNAFTNVHVKDFTNHFSKCMFMEGTVE FT EFECAWNDMLEMFNLHGHKWVTDIYAKRSRWAEAYLRGHFFAGMKSTQRCE FT SMNAYLNRFLKTRLKLFEFVKHFDRALSRIRHNEAKAEFETHHSSAVLTTK FT LYALEKYAGTVFTRQSFLKFRDEMKNAELFFPVSTENHGGYRVHTLTKFRS FT PDKIWKVCYGNSDRSMKCTCMMFESVGFPCPHMIVVMKIEHLEEIPESCIM FT KRWSKLAKETVQVHHDNESQGDATNIIRYGALSSMCSRMSYFASQSEKAFK FT EARCEIQRLTCQMEELCKNSAEESEREDLKATKHHVRDPIIVKTKGNPGNL FT KDKFKKPRHCGKCKKVGHTVRKCPEFVNTHNAFINIEDSIEDMVCSNTHSL FT NSLIIHFIVIFIWLNWLK" XX SQ Sequence 11895 BP; 4107 A; 1809 C; 1836 G; 4060 T; 83 other; tatgggttgt tctatggtac ccactcttca tttyggggta yctacycaca tttgayccya 60 ataaaaatat gayatgtgta aagtacatat cattaaaaaa tttataaaaa cttatcaaac 120 ygrtaragat gacttrttgg tgagaaataa tcacatgcat ttcatatata tatatatata 180 tctaaatatt acaatttttt ataatttatt attaaatatc aaatataatt tgttatttaa 240 tgcattacct aactcyatct aaaaaaagaa aatcttacct actactctta tactctcatt 300 attcatatat aaaaaaaaag gatagtaatt taatatgaaa attaaataat ttcaactacc 360 aaattacaaa atatataaga tgtattttga tgaatcaaat ttcaagatca agttcaaaac 420 tttttgagag agaaaattta aaatttgtat tatatgaaga agatgaagga tttcaagtga 480 ttacaagtgt caaaggtaat atttgatatt ttttttatcc aaatataatt gttgtaggaa 540 gaaatgtgat gttaaataac gattttagaa tttwttatga gtttattata aaattttgtt 600 atcaaattgt tattaatatt tttatataat ttttttcata tatatatata tatatatata 660 tatatatata tatatayata tatatatata tatatatttt gttcatagat taaatttgaa 720 gatgaagctt tatatgtctt gaagaaacat acaaggatgt caagtgatta caagtgttaa 780 aaggtaacat ttgatttmtt ttttttttcc atttacatat aactattgta ggtagaaatg 840 tcatgttaaa tgacatttaa atatgtaatg atttataata tctagatttt ttaatttttt 900 ttctgagtta tttttaatca aattgagagc atttagtmat ttgttatgaa attrtcatca 960 atattttgta agagagggta cgractttct aagrgwgggt acgractttc taagggaggg 1020 tacaracttt ctaagggags ktacgaactt tstaagggwg ggtacgaact ttctaaggga 1080 gggtacgaac tttctaaagg tgggtacgaa ctttctaagg gagggtacga actttctaag 1140 tgaggatacg aactttctaa gggtgggtac gagactttct aagggagagt acggactttc 1200 taagggtgga tacggacttt ctaagggtgg gtacgaactt tctaagggag ggtacgcact 1260 ttctaagggt gggtacgaac tttctaaggg tgggtacgaa ctttctaagg gagggtacga 1320 actttctaag ggtgggtacc aactttctaa gggtgggtac gaactttcta agggagggta 1380 craactttct aagggagkgt acgaamtttc taagggaggg tacgaacttt aagggagggt 1440 acgaactttc taagggaggt tacgaacttt ctaagggagg gtacgaactt tctaagggag 1500 ggtacgaact ttctaaggga gggtacgaac tttctaagrg akggtacgaa ctttctaagr 1560 atgggtacga aatttttaag ggagggtacg aaatttctaa gggagggtac gaacttttta 1620 agggagggta ygaactttct aatagagggt acgaactttc taarrgaggg tacgaacttt 1680 ctaagacygg gtacgaaatt tataagagat ggtatgacta gataatgtaa ttttctaact 1740 actctatctt ttatatttca gtttcttcat agatacgatg gacaaaggca aaggaaagga 1800 atttatcatt gatttgaacg atgaagactt tgattaccaa tatgatagca atgtdaaaac 1860 tgagtctgat gaagaggcca ttctagtttc ggagaagatt tttaatgatt taactgttga 1920 agatgtatgg aagatggagt ttagctcaat agaggaggca gaagaatttt ataatttatt 1980 tgctaaagtt accggattca gtgttagaaa ggatgatgtg aaacgagata aaaatcaaaa 2040 tatagtatct cgtaagtggg tttgctcgaa agaaggatat cgacatagag tgtgtttaga 2100 gaatgaaaat cgaaaacgag aacctaaggc agtaactaga gttggttgtg aggcaacatt 2160 tcggattggg tttaacaaac aaatgaacaa gtggattgtg aaagagttta tggctgatca 2220 taatcatcct ttggtggaac aaaaaaatac ccaattcctt cgatcccata gggtcattaa 2280 aaatgcagat aaggctcaat tgaatgcaat gcgaggtgtt ggcatgggaa ctagccaaat 2340 tatggattac atggtgcaac aatcaggtgg atataacaat gttggcttca caaaaaaaga 2400 tctatataac catgttgatg ctgatcgtag agttcatcta agagatggtg atgcagaggg 2460 tgctttggct tatttgtgtg gaaagtctga aatggatcca tcattttatt acaagtacaa 2520 tgttgatgaa gacaaccgtc tagcaaacct gttttgggca gattctacaa gtaaattgga 2580 ttacacttgt tttggagatg tgttagcatt tgatacaact tatcggacta atgcttataa 2640 aaaaccgttg gtcatactag ttggcattaa ccatcaccat caaactatag tgtttggatg 2700 tgcattattg gtagatgaga gtgttagcac ttatacttgg gtcttggaga cttttttgga 2760 tgcaatgaat aacaagaagc ctctttctgt tattactgat ggggataaag caatgcgtaa 2820 agccattaag aggatatttc cagactcttg tcatcgatta tgtgcttggc atattcaacg 2880 caatgcattc actaatgtcc atgtcaaaga ttttactaat catttttcta agtgcatgtt 2940 catggaaggc accgttgaag aatttgaatg tgcatggaat gacatgttgg aaatgtttaa 3000 tcttcatgga cataagtggg tgacagatat atatgctaag cgttctagat gggcagaggc 3060 ttatttaagg gggcatttct ttgctggtat gaaaagcaca caaaggtgtg agagcatgaa 3120 tgcatacttg aatcgtttcc ttaaaactcg tttgaagctg tttgagtttg tcaagcattt 3180 tgatagagca ctctcacgta ttcgtcataa tgaggcaaag gcagagtttg agacacacca 3240 ttcttcagct gttctaacaa ccaaactcta tgcacttgag aaatatgcag ggactgtttt 3300 cacaaggcaa tcttttctaa aatttaggga tgagatgaag aatgcagaat tgtttttccc 3360 tgtcagtaca gaaaatcatg gaggttatcg tgtccataca ttgaccaagt ttagaagccc 3420 tgacaagatt tggaaagtat gttatggtaa tagtgatcgg tctatgaaat gtacttgtat 3480 gatgtttgag tcagttggtt ttccatgtcc ccacatgatt gttgtaatga agatagaaca 3540 ccttgaagaa atacctgaga gttgtattat gaaaaggtgg tctaagttag caaargaaac 3600 ggtccaagtt catcatgaca atgaaagtca aggtgatgcg actaacatca tacgatatgg 3660 tgcactcagc tctatgtgct cacggatgtc ttattttgca tctcaatcgg aaaaagcttt 3720 taaagaggct agatgtgaaa tacaaagact cacttgtcaa atggaagaac tttgtaaaaa 3780 ttcagcggaa gaaagtgaac gagaagattt gaaagctaca aaacaccatg ttcgagatcc 3840 tatcattgtg aagacgaaag gtaatccggg taacttaaaa gacaaattta agaaaccaag 3900 gcattgtggg aaatgtaaga aagtaggaca cactgttcga aaatgcccag agttcgtcaa 3960 cactcacaat gcatttatca acattgaaga ttcaattgaa gatatggtat gttcaaacac 4020 acattcacta aattcattaa ttattcactt tatagttatt tttatttggt taaattggtt 4080 gaaataaaaa attgaattct ttatattaat acagggggac atgccttcat tactaaatca 4140 caacatggaa ggtggatcaa gacacgggac aaatgaattt tctcaaaatg taagtttaac 4200 attttttaag taatttttat tatgatgtga aaaatattac ttattagagt aattgaaaaa 4260 ttaaatcata ttacagacaa cacttggcac atttcaraat ggtccagaaa caagcttaaa 4320 tgattcatgg ctcgggttac atccaccaaa ttacttcaca aaccaagtaa gagtcataga 4380 ataaattatt tacaccacat atcatatatc tatatattga cagaagttcc twaacattta 4440 gtatttaatc atatggattt tctttcaaaa tattatgtat aactgtaaat attttcaatg 4500 taggtcacca tgaaccactt tacatccgga atttcgggag caagttctac atatcataac 4560 caatgagttg tactacaatg caaaaaatta tgtacaaaaa aaaaaaawtc aactcttgat 4620 tgtattctat actcttcttc tctttatttt tgcatgattc tgaactttat ctaatattat 4680 agctttctca ctattttcat catcaagaag taattcgatt gccaatttgt gtcttatagc 4740 tgtagagtcc caatgggaag gggttgaact tgagtccatg aaatcggatc ttcgcatatg 4800 attaatgaca tggactccac aatcccacct aacaaatraa atgagyaaac atttatctag 4860 ttmgtacata saaatattat cttgaacaca ttatayttga acacattagt acatgctacc 4920 aagagtccat gaaacaatta tgcttgctta cccattggct tgcacatcta cccatgtagg 4980 tctttcaatg ggaacacttg ataaattctt tagatgccca ttgagattaa aaaaatgtgc 5040 acactcttca acctaatatt catatcgtta tatcttttag caaaataaaa catgctattt 5100 aacaactaac attaaaaagt rataaaattc attaaaatat aagacatacc acagttctca 5160 yagatgaagt tcgcatgtca tccctttcta ttgatggtaa tgaatccaat atatgaatat 5220 tatgttgatg aagatttata acacacaaat accaatgatc ckgacatgta tcgtgcatcg 5280 ggatgtatat ctaaacaaaa cacamatttt agcattgata attatttaca actatgctat 5340 gaatccaact tcaaatatgt accttattgc aatcattcat ttcatccatg tgtttgataa 5400 tatgtgtgaa catcttggta gcagttgcca attttctacc accatgtaag attatttgct 5460 atgccaaaaa aaaaaaaaac atatatatat atcacaatat ttattaggtt tatttttttt 5520 ctttaataag aaatataatg gatgaacata ttttttaata agaaatataa tggatgaaca 5580 taccgcaaat gtggtgggta agtagcatct ggtaggycrt attcctttga atttgttctc 5640 aaaaytatta agttkgcatg caaatacatt tatgatctaa aaatgaaaca caaaaaagtt 5700 aacaatgtta attatgtaat agaattaata agaattgggt ttatccttgt attactcacc 5760 acatcgagta attcttgtct aggccctaaa gtcaagaaat ctgctcgact tgcatgctca 5820 tattgaaaat taacaagaag ttcactgcaa aatataagat atttaataag tataactttt 5880 aaaacatgac atacataaag tatagtcaaa ataattggtt tacacacctt ttgtccaatg 5940 aaacatcaaa cacataagca acaactagag actcaagtgt actcaaggaa tgtgaatcct 6000 ccacgttcgg caaaatggac atggggatta tctatattga aaacatctct aacaaacatt 6060 agttatcgtt cactatatta ttaagtattt taaaaatact acaccaatga agtaacatat 6120 tacctctaat accttttgtg atccaacaac tatgcttggg aatctcttag gctttggcat 6180 cttattggat tgatgaatgt agggtgacac cttgaattta ctaggcttgc gttccattgt 6240 tgatcgtgtt ttcttcaatt gacrtgggag caccaccaat gaacttagtt gttcttcttg 6300 tttttcaaca tatggaacat caacattaac ctatcacgta tttgaamatt agtatatata 6360 tatatatata tatatatata tgtatatata gaactttgta aaaaactagg tcttcataat 6420 atgcaaatac cttttcatcg tgacattgat tgttgacaat gggagaaaca tgtaactcca 6480 tgtcaccaca tgagtcattc tcactcaatc tctcttctac gacaacattg ctcataggaa 6540 aaaaacaaac gtttcaattc catatatttt tcttcaaatt ctctaaaagt tgattcttta 6600 caactttcat ccatattaga aacatttgtt tgtagcacaa attttttcaa cttctcaaaa 6660 gcttcctcca tacccatcaa acttttttct tcaacctagt aacaaataaa aatttccaat 6720 atcatgaaaa aaaaagtttg agatgaataa actaatgtat ataaatatag tatgaaaaag 6780 taccttatgc ccttcttctt gttgttcatg aacttttgca tcttgtttat caccatcttc 6840 tacatttctc atatcattat ctttatgatc acttgttatc tcatctttct caaccacctt 6900 cattttttca tcattttcat tttcygcacc attattttgc tctatatcca cactttgccc 6960 aatttttata atccatatcg tgacctataa tttatccata aactttatta taattgcaac 7020 atcacataaa caaataagtt tttcagttag taaatgtatc ttacctttgg atcatcataa 7080 cctccaagtg ttttgatttt acgtttcatc ctagaaacct catcatctcc ccattcattt 7140 atacgagggc tatatgcatt aaaacgtaag ttcataccct tctttgtgga aatgtggtct 7200 aggtagaaaa tctgcaagaa ataaattcca aaataaktat agagttgaat atatcacaaa 7260 ctctattatt gttaaaaata tcataatata tcaactttgt taaaagtgta ttaccattag 7320 aaaaaaataa acatcyagaa atcccactgc ttcgtttctt ggatttaaag tcgtttatgc 7380 ctcgtacaag gaagaaraat actatttgag cccaatttat cttctttatt gatgcggtgt 7440 cttgaaggag atggaggaag gaaggcttga cactaacttt catcgttgga cataacaagg 7500 cacccaaaac aaataataca aaacgaattt taaattcatc cccacatttc ttttcttgtc 7560 gtatttggtt ttctaacatc aacaatgrca attttccctt cccatcacaa tacatgttgt 7620 ataaatcatt ccgtttactt gtgcatctct ctatatctac ctccactcyc ttagccttca 7680 agcccaaaat taactcaaca tccattgggg ataatttaat ggaagtgtta tgcacactta 7740 atgtgcatga aagagtgtca aaattctcta ccaaccaatg acataaacta tgatcaagtt 7800 tagtacatcg caatcctaaa atacctccaa accctatttc ttgtatgacg rccttttgat 7860 taggttgcaa gtgttgaagt agtttataca cccgatcagg cgaacaacgc gtgtgaagat 7920 atgactggaa gtcataaata tacataagca tatatatttt aaattgaaag aaaatattat 7980 cataatttaa aaacataaat ttcgaatttc ttacctttga tgcatttttt gagtttcgac 8040 ccttttgttt tatatattca tgagggcatt ttttagactt ctctaagaac tctttttttt 8100 tttctccatt tgaaagggat tgccactttt tcccaatctc ttttcgcaac tgtaatatta 8160 aattagttag ttatcatata gagtataaaa gttgactaaa aaacatatta tgcaaatatt 8220 catttctttt cttacatcat tatttattat caattccttg ttatmttttt ttcttgcgag 8280 tacttgttct tgactgcaaa aaacatcaca taaaaatgat tatattttca acatatgaat 8340 aaatatccaa aatgaattaa ctatatatgt atatatattc ttacaaataa taaagccatr 8400 aacycatagg aagttttggg tttgaagggg gatcattctc ytcaaatgat tgtttgctcc 8460 trtttaaaac acaacattat gaatgtaatt tacaactaat taaamctatg tactatattc 8520 aaataattaa gtgacaaata taaaatctta catatttggc tttctaagtc aagatgcagt 8580 aagactgctc aaaataagat aaactcctct tatattaagc aactgtgtag cctgtaacat 8640 agtgagcata ccrataagaa ttaagttttg aatttgacaa caatgagttt gaaaatattt 8700 gtaacaaaat ggagtttttt ttctaaaaat attaatcatt atttaatcat tagatcgatg 8760 agttaaacta attaaaataa atttaaatta tcaaataaaa ataatttatt tactttaaat 8820 cttttttttt tattttatct tatcyttttt acatagcata gcaaaaaggc attttttaaa 8880 attatatcaa ttaatttata atttttttaa atataataat gttgtattgg attagaaata 8940 gaaaattaaa aaaaaaaagt taaatttaga gtatgctatt ttaaaaattt ttatctttaa 9000 aaaaaagtca ttagtgagca tatgtccaaa tgttttaagc tcttttatca ttcttttcat 9060 ctccttagga tcttgtttca ttgtatggtt tagtcgcatt ttgtaatttc caaatttcat 9120 tacaagtcct ctaagcttcr tarctgaaag tccaccatac ttttctttta aygcttccca 9180 catttcatga gaagtttgat atacctcata ctcaatcata agatcatctt gcatacaact 9240 taacaacgtt atgygagcta aagaattttt ttgtgagaga tgccacatca acaagataaa 9300 tatacatgtc atgtctgrca tatcaaatta tttacatgtt atgtacaaaa cataaaaaaa 9360 aaatgtaata aatagaagga aaactaatct tctcccttga aactaaaaga aacaatgtta 9420 ggattataca cagtgtcttc tataactcta gaagttgttt tcaataacca taaccctcta 9480 agatttttat gcctactaga atttgaaaat cttgcatttc gcaagttagg agaaatagaa 9540 agcactgttg ttcgtmtgat ggcattcttc acgaagcatg tttccyagtg ttccttgaaa 9600 atagctacta ggtcatcaaa agacctattt gtgaaaccat gaggcccttc ttgaatggat 9660 tcccatatat tttcaagaac ttttttctca ggttctgtta atgacatttg tagaatatgc 9720 attttacggt ttgactctaa gatatattcc tcttcgaaac gtttgaacat attagccaca 9780 tgatccacat gttcatttgt agaatggcta gggtccytct tgtagttcaa gattgtatcc 9840 aaacgcggcc aaggtccact accccttagt actttcctag ttctcctcaa tygtaccatt 9900 ttgcacctga ccaaaagaat ttaatttaat tttaatgagt aacatatact catactttaa 9960 ttaaatattt gaacaaatga aattttaatt agaaacacac aattataaaa acaaaatgtc 10020 ttttattgtc cctcaaattt ttattattat tttatacaca agtcaacatt cataatttca 10080 aataaacaat ataacactaa taaatggtat tttatatcat atcaaggtac tttattttga 10140 gatttaggtt cgaatccatg ttgcattatt atttctaaca ctaaaaggtt caaaagtcta 10200 aaattttatt acattttaaa tgaaaaataa aattaattta tataaaatat tttatttgag 10260 atttaggttc aaatccatgt tgcattatta tttctaayac taaaaggttc aaaagtytag 10320 aattttatta cattttaaat gaaaaataaa attaatttat ataaaatatt ttatttgaga 10380 tttargttca aatccatgtt gyattattat ttctaacact caaaaatcta gaattttatt 10440 atattttaaa tgaaaaataa aattaattta tataaaatat tttatttgat atttaatttc 10500 taaaatttta ttaaaaatat gtgataacaa ttttttctat taacattaat gtatttaaat 10560 aattaaaatt attaataatt tatcttatca aactattttt aattcataaa atatcagtaa 10620 taaaattcga aagttcaatg gtaaagattt aatcaaaata taaatggata attactattg 10680 gtaatgattt aaacaaaata taaatggata attactaatg gtagtgattt aatcaaaata 10740 taaatggata attattaatt atttatatat aaagacaaat tcctaaaatg ccctatttta 10800 actgcctctc acactcgggg ctaggggcgt caaagaaggc cttttctccc tctcgagaat 10860 ccctaaaaag cctcagcctc cagaccaaga atccctaaaa agaggctcca gctccgacca 10920 ctctcaatcc tcgcaggtac taatctaatc atgttatcat tttttttttc aatacccatt 10980 tgattctcaa caaaatccat cccccatttt tggatctgtt tgaagggtct ttttgctttt 11040 gtgccattcg atttaaattt catgaaccct aaatccacga ttttttagcc aggttgaaaa 11100 acacaacctt tgcctgtaaa tcatgaccag attactaaat agtatctttt gtttttttca 11160 aaaaaaatgg acagattttg tatccttgtg cgcagcctgg acttgtagga aatataggga 11220 aatttccaaa aaaaaaatcg ataaaaatac caacatttta ctgatatttt tgaattggtc 11280 aaaatatcat gtttgtgcgt ggcctggact ggtaggaaat atcgggaaat attccaaaaa 11340 cttggtaaaa atatagtctt tctcaaaaat attactggaa atttttgaca tttcaatcac 11400 taccatataa cataagatga gtgaagtacc tgttctggaa gagtaggtag agttgcctgc 11460 agggggagat tggtttcgga tccgccaaag cccgcctgat tcttttcttg ctgatttctc 11520 cttcaaaatc cccactcaac tcactctctc tgtaaatatt catttcaccc gaaaattcca 11580 tctccacacc ctcaaatttc tgaagcttaa ctctctaaaa tccgggaaag ttgtaatgcc 11640 catcaaacta atagctcatc tctccgaaaa taggcgtcaa gtgtaatacc catcagataa 11700 atttttgtct ttagacaaga ttaagcaaga tagaagcggg aaatcaggtg accggcaaca 11760 tgttgttatt tttttatata tttttaaatt tttttaaaat acataaacca attggacggt 11820 ccagattgaa ccattttcat ccaatggtca aaattgtttt ttgggtaggt accgaagtgg 11880 tactgtagaa ttttc 11895 // ID Gypsy3-VV_LTR repbase; DNA; EDCOT; 739 BP. XX AC . XX DT 10-SEP-2007 (Rel. 12.09, Created) DT 01-OCT-2007 (Rel. 12.09, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy3-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-739 RA Obukhanych T. and Jurka J.; RT "Gypsy3-VV."; RL Repbase Reports 7(9), 799-799 (2007). XX DR [1] (Consensus) XX CC This is a sequence of 5' LTR of Gypsy3-VV LTR retrotransposon. 5' CC and 3' LTRs of this retrotransposon are 98% identical. XX SQ Sequence 739 BP; 207 A; 222 C; 151 G; 159 T; 0 other; tgtagggacc cctccccctg agaacacgtg gcacacatct cctagtgaca cgtggcacgc 60 attctcatcc ggatcaccct catccggatt ttccccaaga gtacacgtgg cgcgcttctc 120 ctatccggac tccctcaagg agaggcacac gacactcata aacataacat ccggacgact 180 tccacaatac atccggacga ccaacatatg ctatccggat atgtttgtcc ggatcattga 240 ctgaagtaag caagtcttac acgttatcac aacagcctgc catggcccac gttccgccac 300 ctgcagagtg aaaggacaag aatgaagtga caacaagtca cttcccacga tcacttccca 360 cgatctctga cagccgcatc acctaccacg atctctgtca gccgcccgta gggtgatgat 420 ggccctgcca ccacctagtg tcatcatgac aacacaaaat atctccctac cattaaagag 480 ggaaacaaag cttctgatac tatatatatg aaccttcaca caaagaggaa ggtaagcttg 540 ctatacctag taaaaggcca actgatttat ctctctctct ctaaccatgg ctgacaaaac 600 catcggaggg tgcgtccgga caccctgtcc ggacgccttt tgcaggtaga acgactgaat 660 caagaatcta tattggttga gatcgtgcgt ccatccattt ggcaactacg tggatcacca 720 gggacgcgag gcctcaaca 739 // ID Copia-50_VV-I repbase; DNA; EDCOT; 4370 BP. XX AC chr20; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-50_VV_; KW Copia-50_VV-LTR; Copia-50_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4370 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr20; Positions 25312406 25308037. XX CC Positions [1737-2231] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1092..2540,2544..4355) FT /product="Copia-50_VV-I_1p" FT /translation="MAMIQKNNGGNSQHFANATGINKPSSKIIPNCPHSNM FT CWIIDSGATDHVTSSAELLDPKILPKTTTISLPDGGQAHIESIGSLHVTPH FT IKLDDVLKVPQFQVNLLSVSKLTRALQCIVMFSSDFCVVQDATTRKTMGLG FT KQHNGLYYLAQDQNPALAYAIHKHSDLWHQRLGHPSSGPLQVLAKVNSEIY FT FDSKHVCDIFPLAKQTRLSFPSSFISSHAPFDLIHCDIWGPHRINSHSGAR FT YFLTIVDDHTRYTWIHLMSFKSETQGILQSFISWVETQFNRCIKTLRTDNG FT TEISSMKQYLDTKGINYHHSCAYTPQQNGVVERKHRHLLNVGRALRFQANL FT PLKFWGESIQTACYLINRLPTPILSDKSPYQLLYNKLPSYHHLRTFGCLCY FT ATNLLPTHKFDQRARRCIFVGYPLGQKGYRVYDLETHKFFYSRDVVFHEHI FT FPFHTNPQEEQHDVVVLPLPQTSYEPITTETTKPQADDPPPLLSSLESTSN FT ECTLDLDTIVSPPPPATRRSDRIKQPNVQLRNFHLYHTTKVTSSQSSSLSG FT TRHPLTRYISYAQLSQKYRNFVCAITTLVEPITYEQAVLDPKWREAMAAEL FT HALEQNHTWTLTPLPSGHRPIGCKWVYKIKYNSDGTVERYKARLVAKGFTQ FT REGIDYKETFSPVAKLTTVRCLLAIAAVRHWSLHQMDVHAFLHGDLLEEVY FT MQLPPGFCRQGETPMVCRFNKSLYGLKQASRSWFQKFSATIQQDGFYQSRA FT DYSLFTKISGNSFTVVLIYVDDMIIAGNDENVIATLKESLHTKFRIKDLGQ FT LRYFLGIEVARSTDGISISQRKYTLDILDEAGLLGAKPLLTPMEENNKLLP FT TVGDLLKNPSIYRRLVGQLIYLTITRPEISYSIHILSQFMQEPRKPHLHAV FT HHLLRYLKGALGQGLYFPAKGNLLLRGFCDADWARCSITRRSVTGYCIFLG FT EALISWKTKKQTTVSRSSAESEYQAMASITCELTWLKYLLDDLKVEHSQPA FT KLFCDSKAALHIAANPVYHERTKHIEIDCHVVRERIQSGVIVTAHLPSSCQ FT LADLFTKPLNSSIFHSLLNKFGILDIHAPT" XX SQ Sequence 4370 BP; 1278 A; 979 C; 817 G; 1296 T; 0 other; tggtatcaga gcatcaaacc tggtgactct gaattcttcc aagcgtttcc gcaacttatt 60 tcctcgttac agctgctgcc atggacatca acaaaacgag attgacatca tctaaggcta 120 ccacagaagc tttagatccc ttctctctac accactcgga ccacccgggt atggtacttg 180 tctccaaagt acttgaagga gataactaca gcacatggag tcgggctatg aggattagtt 240 tgagtgctaa agacaaaact ggatttgtca caggttccat taagccaccc tcttcgactg 300 atgatagttt tccttcttgg caacgttgca atgatatggt gatctcatgg ctattgaatt 360 ccattcatcc agacatagcc agcagtgtga tttatgccga aacagcatca gaaatctggg 420 cagatctgcg agaatgtttt tcgcaaggaa acgattcaag aatttatcag atcaagcgag 480 acattgtgga gcataggtag gggcagcaat caatttcagt ttattacaca aagcttaaag 540 ctttttagga tgaactttca tcctatcatg aagtgttatc ctgttcttgt ggaggattag 600 agaaacttaa ggaaagggat gaaaaagaga gagttatgca atttctcatg ggattgaatg 660 atagttatgc tgccattcgt ggacaaatct tattgatgca acctctaccc gatacacgct 720 gagtttactc acttgtcctt caacaagaaa aacaggttga agtttctctc aataatggga 780 acaagaacca ttatgccatg cttgcagatc gggacaataa ggcgacttca gcacactagg 840 ttcaaaagca aaagactcca ctgcactgct cctattgtga ccgtgattgt cacagcattg 900 agaagtgtta ctacctacat ggctttccga ttggccacaa gctccatggg aagaacgtga 960 agcctcccaa tcaacgtcac tcaaatgcaa ataatgtgaa agtggaaaca aataaggctg 1020 tggagacaga agcaaaactt cttccaacaa atgatggacc aaggctcaca actgaggaat 1080 acaaccaatt aatggctatg attcagaaaa acaatggtgg taattcacaa cactttgcaa 1140 atgccacagg tataaataag ccatcatcca aaattattcc gaattgccca cactcaaata 1200 tgtgttggat tattgatagt ggagccacgg atcatgtgac ttcctcagct gaattattag 1260 atccgaaaat tttgcccaaa accactacca ttagtttgcc agatggtggt caagcacata 1320 ttgagtcaat tggttcattg catgttaccc cccacattaa acttgatgac gtactcaaag 1380 ttccacaatt tcaagttaat ttactatcag ttagtaaact aacgcgggca ttacaatgta 1440 tagtgatgtt ctcttccgat ttttgtgttg tgcaggacgc tactacgagg aagacgatgg 1500 gcctgggcaa gcaacataat ggcctctact acctcgcaca agaccaaaat ccagccttgg 1560 cttacgccat tcacaaacat tctgatcttt ggcatcaacg tcttgggcac ccatcatccg 1620 gtcctcttca agttcttgct aaagttaatt ctgaaattta ttttgattcc aagcatgttt 1680 gtgatatttt ccctttagcc aaacaaactc gtttgtcctt tccatctagt ttcatttctt 1740 ctcacgcacc ttttgatttg atacattgtg atatttgggg accacatcga ataaattctc 1800 actctggggc tcgttatttc ctaacaattg ttgatgatca tactcgatat acttggatac 1860 atctcatgag ttttaaatct gaaacacaag ggatattgca atcattcatt tcttgggtgg 1920 aaactcaatt taatcgttgc attaaaaccc ttcgaaccga taatgggact gaaatttcct 1980 ctatgaaaca gtatttggat actaagggga tcaattacca tcattcatgt gcttacaccc 2040 cccaacaaaa tggggtggtt gagaggaaac atcgtcatct tttaaatgtg ggaagagctc 2100 ttcgttttca agcaaacttg ccgttaaaat tttgggggga aagtattcaa acggcttgct 2160 atttaatcaa tcgcttacct acacccattc tttctgacaa atcgccatac caacttctct 2220 ataacaagct accttcatat catcatctac gaacttttgg atgtctttgt tatgccacca 2280 atctcttacc cacacataaa tttgatcaaa gagctcgtcg ttgcatattt gttggttatc 2340 ctcttggtca aaagggttat cgggtttatg atcttgaaac tcataaattc ttttattccc 2400 gagatgttgt ctttcatgaa catatatttc cgttccacac taatccacaa gaagaacaac 2460 atgatgtggt cgttcttcct ttaccacaaa cctcatatga acccataacc acagagacaa 2520 ccaaaccaca agccgatgat tagccaccac ccttgctttc atctcttgag tctacctcta 2580 atgaatgtac acttgatctt gacaccattg tgtcacctcc acctcctgct actcgtcgtt 2640 ctgaccgcat caagcaacca aatgtccaac ttcggaattt tcatctctac cataccacca 2700 aggttacttc cagccaatct tcttccttgt caggtacgcg tcaccctttg actcggtata 2760 tttcctatgc acaactctca caaaaatatc ggaattttgt ttgtgccatc accactcttg 2820 tggaacctat aacttatgaa caggcagtat tggatccaaa atggcgggaa gctatggctg 2880 cagaactcca tgctcttgaa caaaatcaca cttggacact cacgcctctc ccttctggtc 2940 atcgtccaat tgggtgcaaa tgggtgtata agatcaaata taactctgat ggcacagttg 3000 agcgatacaa agctcggttg gtggcgaaag gcttcactca acgcgaaggg attgactata 3060 aggagacctt ttctcctgtg gctaagttaa ctacagttcg atgtttactt gctatagctg 3120 ctgtccgaca ttggtcactt caccaaatgg atgttcatgc ctttctccat ggtgatttgc 3180 ttgaagaagt ctatatgcaa ttgccgcccg gtttttgtcg acagggggag acacctatgg 3240 tatgtcgatt caacaagtca ttatatggac ttaaacaagc ctcccgtagc tggtttcaga 3300 aattttctgc caccattcaa caagatggtt tctatcaatc aagggctgat tattcacttt 3360 tcacaaagat ctctggtaat tctttcacag ttgtgctcat ctatgtagat gacatgatca 3420 tcgccggcaa tgatgagaat gtaattgcaa ctcttaagga gtctctccac accaaatttc 3480 gcatcaagga cctcggtcaa ttacgatatt tccttggtat tgaagttgct cgttctactg 3540 atggtatttc aatatcccaa cgaaaataca ctcttgatat tttagatgaa gcaggcttgc 3600 ttggggccaa accattgttg acacctatgg aagaaaataa taaactcctg cccacagtag 3660 gagatttatt gaagaatcca tccatctaca gaagattggt cggacaactc atttatctta 3720 ccattacaag gccagagata agttattcaa ttcacatttt aagccagttt atgcaagaac 3780 caagaaagcc tcatttgcat gctgttcatc atcttctacg atatcttaaa ggtgcacttg 3840 gacaaggatt atattttcct gcaaaaggaa atttgctact aagaggattt tgtgatgcag 3900 attgggctcg atgttcgatc acaagacgat ctgtgactgg atattgcatt tttcttggag 3960 aagctctcat ttcatggaaa accaagaaac agacaacagt gtcaaggtca tcagctgaat 4020 cagaatatca agcaatggct tccattacat gtgaacttac atggctcaag tatttgttgg 4080 atgacttgaa ggtagaacac tcgcaacctg ccaaactatt ctgtgatagt aaagcagcac 4140 tccatattgc tgctaatcca gtttaccatg aacgtaccaa gcatatagaa atcgattgtc 4200 atgttgttcg agaacgaatt caatcaggtg tcatagtaac tgctcatctt ccatcgtctt 4260 gccagcttgc tgatttgttc actaagccac tcaattcatc aatttttcat tcccttctca 4320 acaagtttgg cattcttgac atacacgctc caacttgagg gggagtatta 4370 // ID Copia-34-LTR_VV repbase; DNA; EDCOT; 168 BP. XX AC CU459252; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-34_VV, LTR retrotransposon Ty1-copia like, long terminal DE repeat from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Rangen-B07; KW Copia-34-LTR_VV; Copia-34-I_VV; Copia-34_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-168 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL/GenBank/DDBJ; CU459252; Positions 1408756 1408923. XX CC LTR = 168-147 bp CC LTR are 91.9 % similar to each other. CC Direct flanking repeats = aatgc. XX SQ Sequence 168 BP; 48 A; 27 C; 29 G; 64 T; 0 other; tgttaatgta tattatgggt atattatatg ggtacattat gttatgggct ttaggcccag 60 ttaggttact tgtaccgcac acatatgcct cctatataaa ggcactgatg tatattcttt 120 cttccatgaa atacaataca attgttcagt atttctaaca tggtatca 168 // ID Ogre-PT2_I repbase; DNA; EDCOT; 12216 BP. XX AC AC182676; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 16-APR-2007 (Rel. 12.03, Last updated, Version 3) XX DE LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-PT2; Ogre-PT2_I; internal portion. XX NM Ogre-PT2_I. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-12216 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AC182676; Positions 39382 51597. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). CC Additional annotations: 6320..6557: putative intron. CC Note: Coding regions are disrupted by mutations generating stop CC codons at 1709..1711, 3761..3763, 7704..7706, and 9576..9578. XX FH Key Location/Qualifiers FT CDS 686..2677 FT /product="Ogre-PT2_ORF1" FT /translation="MKRILGHSQNIDEAAFFGKYGRLLEIAKIGVLNPAIK FT ALINFWDPDYRCFSFGNVDLCPTIEEYGMLMEFPKHLHQVYFPLRNDKVIP FT ELSKLLKIPHLSRFLEKNGSGLKWKFLEVELEKKKEQYALVLERDRLIALG FT IYGLVLFPSLKGVISLEAAAAFVEYENTHVNPTTAILAETLLTLNHFRKTG FT KGAVRCCTQLLYIWMVSHVETKKPIFNNFWWFNQKPLKIVEEEELGILGDQ FT GWMKKLQELPSSNFSWKAPWVKSVDVIVSCGQKCWVPLIGITGYVSYAPAL FT VIRQLGGIQHIPRTVGLAEFSGFFKDQSAREVLETIKQDWSQLTLIQKE*E FT SLRDPSSSEGYEKWRNLTLIATPKKPCSEDGPSRIEERSLKRKKVSNEEDL FT MEQIERLQIELGKSKGDKAALERMMMEGDKSRVFLNEQLESKDAKIGMLEL FT QLSKGKAVIEESEKERGRLILDLMQSSSELEALKADFDGYQENVEYNQDKF FT LHVKAELLDRIEKHDELNKKYMMIESRLAELQEFERKGNEEEVVKADLAAK FT KIEIRILKVKFDKEREKVKQLTNRLEVSEKHKEQIDTNNNTLNRNNMVLIE FT KMAKVDEQMDEAAIHARIIRANARRVGRDIFRYRQSLAETDAFLEKIENRG FT LAFLPVARDMDEEED" FT CDS join(3020..6319,6558..10004) FT /product="Ogre-PT2_ORF2+3" FT /note="gag-pol." FT /translation="MENEERAHIESHYQTELESVKNEVSRLTDLLEQLLRA FT KNGEGTSARQLEGAPAVHIPQASQNQGANSANEQQFVPITPILPPHTPVTV FT DLTTEGVPDNRSPSLIDQDKLFALEERLRAVEGNDWFDPMRAAEVCLVPNI FT VVPKDFRIPEFIKYTGLECPNTHLRSYCNKMAEVIRDDKMLIYFFQDSLAG FT SALSWYMRLDSIRIKSWRDLVEAFLKQYKFNMEIAPDRTSLMAMEKRSQES FT VRAYAQ*WRDEAMHVQPPLIETEMVSLFANTFKAPYYEHLMGSSSQHFYDA FT VRIAERIEQGIKAGRIAMPVEKKGFIGRKREGDVNNLEDGYKGKKVDSHNP FT QVPTSQFSRINFNQSFSPNRTNNQSNYQNHYQRPHTRYPSEQLPPLPMPLK FT DMYAKLLSIGHIAPIPTLPLQPPFPIWYKPELTCEYHAGNPGHGIETCYAF FT KKRLLELIKIGWVSFEDKPNVNSNPLPKHASSSSGIGMIEVGNQCKVLKVS FT MEKMYYLLVRSGFLEANMEGHSEGGSYCEFHGRDGHYIEDCIEFCEKIAKM FT FKMGQLRIEPMENGGEVSMMEGQMEMTGVCRVQQTANGPPRLILVKPSYTK FT GNHNAMPYNYGYASNVQAPLPLFQTEISGLTRSGRCFTSEELRKEKGKEVV FT DLDKALEVNKPVTEEESNEFLKLIKHSEYCIVDQLKKTPARISLMSLILSS FT EPHRNALQKVLNKAYVPQDIEHKTMEHLVGRIHATNYLYFTADELDAEGTG FT HNKPLYITVRCKDCLIGKVLIDNGSALNVLPKHMLEEMPIDESHIKPSTMM FT ARAYDGSPRPIIGTLEVELYVGPQMFLVTLQVMDIHPSYSMLLGRPWIHAA FT GAVASSLHQCLKYIMNGMLVTVKAEETVSMIKNVAVPFIEAGDCKGNNIHA FT FEIVNTDWVPENTVLRRPRISEAARMASLCFLNRGIPFQYNFIIRIPEGVN FT LARMKSAAQKFGLGYQPNQKDYRWAAGWRRARRMARIKGREPDEEKLEIPP FT LCVSFPKAAYIMQHDKEAESLDQELSNMSINTLGENKVEEDDMKTVARKGD FT EALPQLTVYTIEEVSAKTFVRKLAQDEKFQNWVTQEAPVVFKMNPESGSPT FT TSHIFSIKNKWPNLNEHVIAMEEEEWDESNISEFTRLVEQQEQTWKPIAEE FT LETINVGSDQLKKELKIGTLVTSEQRTKMIALLQEYADVFAWSYEDMPGLD FT TNIVVHKIPLEEGCKPVKQKLRRAHPDVWIKVKVELEKQWDAGFLEVVRYP FT QWVSNIVVVPKKEGKIRVCVDFRNLNKASPKDDFPLPHIDVLVDNAARSST FT YSFMDGFSGYNQIKMAPEDKTKTTFVTPWGTFCYKVMPFGLKNAGVTYQRA FT MVTLFHDMMHKEIEVYVDDMIAKSKRGEDHVEVLRKLFERLRKYELRLNPA FT KCSFGVKSGKLLGFVVSDRGIEVDPDKVRAIQAMSSPKTEKEVRGFLGRIN FT YIARFIAQLTTTCEPIF*LLRKKNPGTWNEECEEAFNKIKHYLQNPPLLVP FT PVSGKPLVLYLTVTEAAMGCVLGQHDETGRKERAIYYLSKKFTECESRYTE FT IERLCCALVWAAKRLRHYMLYYTTWLISKVDPLRYICNKPFLSSRIARWQV FT LLAEYDIVYMTRKAVKGSAIADHLADNAVEDYEPLDFDFPDEDILSIEKEE FT ENTDWWTMFFDGAVNVYGNGAGAVIISPDKKQYPVSVKLHFECTNNTAEYE FT ACILGLEATLELKIKKLDVYGDSMLIICQVKGEWQTKEEKLRSYQEYLSML FT AKEFEEIRFTHLGREGNHFADALATLAAMTTIDLKCKVQPVHIDIRNDPAH FT CCLVEGEIDGQPWYYDIKNLVQNQEYPVGASKTDKKTLRRLATDFYLDGEI FT LYKRSFDGTLLRCLNEADARKALREVHEGICSTHASGHMIARKIQRAGYFW FT MTLEKDCIDYVRKCHKCQVYSDKVNMPPAPLFNLISPWPFAMWGIDVIGPV FT NPKASNGHRFILVAIDYFTKWVEANSYAHVTQKVVKRFIEKDLICRYGPPE FT KIVTDNAQNFNGKMIVELCTKWKIKHSNSSPYRPKMNGAVEAANKNIKKII FT QKMVVTYRDWHEMLSFALHAYRTTVRTST*TTPYSLVYGMEAVMPLEVEIP FT SLRVLIDSELEEAEWAKVRYEQLNLISEKRMAAICHHQLYQKRMAKAYDKK FT VRPRLFQEGDLVLKKILSLPGDDQSKWAPNYEGPYIVKKAFSGGALKLARM FT DGEDLARPVNSDSVKRYYA" XX SQ Sequence 12216 BP; 3912 A; 2169 C; 2952 G; 3183 T; 0 other; gaatggcgac tccactgggg accttgtgga ctaagctttg tttttgtctg atttgtgttc 60 gtgtgtttat tgttaatata cctttccttt tgttacctgc ttatacgctt taaatatttt 120 tacacatatt gttcatgcat ttatagaact gtctcataca tcttatagaa ctgtcacatg 180 catcacatac tttgattatt gagagtacac acaaacttta agttaagtgg gggactagca 240 gcttacctta cgactgttag tcaaggttta agtttgtgta aaccccaact cttcgctgag 300 tgcttagact ggtaatagtt ggtacatgtg accatctcat tgcctacaag cccccatatt 360 gcctccacga gggcaatcac tgggacagca agagaccctt tttagagact gaatagccaa 420 cctaccctcg tcaaacacaa aagatttaga accaggctat agggtgtatg cccccacaaa 480 atacattttt gcataacata acctaaacca taaagtattt ggttttcagg tcattttgaa 540 acgataagat ggccatcatt accaaattta ctactgtgga atatgggcag aattctgaat 600 tgtcacaact atagagggag attgttctag atatgatgca aggaagcttc cagtagtcaa 660 agacctgaat tgtgtagtat atgagatgaa gagaatattg ggccatagtc agaatattga 720 tgaggcggca ttttttggga agtatgggcg attattggaa attgcaaaga taggagtatt 780 gaatccagca attaaagctt tgattaactt ttgggatccc gattacagat gcttttcctt 840 tggaaatgtg gatttgtgtc ccactataga ggaatatgga atgttgatgg agtttcccaa 900 acacctgcac caagtttatt ttcctttgag aaatgacaag gtgattcctg agttgtcgaa 960 attattgaag attccacatc tgagcagatt tttggagaag aatggcagcg gtttaaagtg 1020 gaaatttttg gaggttgaac tagaaaagaa aaaggagcaa tacgccttag tgttagaaag 1080 agacaggtta atcgctctgg ggatctatgg tctcgtgtta tttccaagct taaaaggggt 1140 tataagtcta gaagctgctg ctgcattcgt ggaatatgaa aatactcatg tcaaccctac 1200 aactgccata ttagctgaga ccttgctgac cctcaaccat tttagaaaaa cagggaaagg 1260 cgcagtaaga tgttgtactc agttattata catctggatg gtaagccatg ttgaaaccaa 1320 gaagccgatc tttaataatt tttggtggtt taaccaaaaa cccttgaaga tagtagagga 1380 agaagaattg ggaatcctag gtgatcaggg ttggatgaaa aaactccaag agttacctag 1440 tagcaacttt agttggaagg ccccttgggt taaatcagtt gatgtcatag taagttgtgg 1500 acaaaaatgc tgggtacctt taattgggat cacaggttat gtcagctacg ctccggctct 1560 ggtgataaga caattaggtg gcatacaaca catcccaaga actgtgggac ttgctgaatt 1620 ttccggattt ttcaaggatc aatccgcgcg agaagttctt gaaaccatca aacaagattg 1680 gagccagttg actctaattc aaaaggagtg agaaagtttg agagacccta gctcaagtga 1740 aggatatgaa aagtggagga atttgaccct gattgccact ccgaaaaagc catgttctga 1800 agatgggcct tcacgaattg aagaacggtc cttgaaaaga aaaaaagtca gtaatgaaga 1860 agaccttatg gagcaaatag aaaggctaca aatagaattg ggaaagagta agggagataa 1920 agcagcatta gaaaggatga tgatggaagg agataaaagc agagtgtttc taaacgaaca 1980 gctcgaatcc aaagatgcaa aaatagggat gttggagctg caattgagca aaggaaaggc 2040 cgtaatagaa gagtctgaga aagaaagagg aagactgatt ttggatttga tgcaaagcag 2100 ctctgagttg gaagcattga aagccgactt cgatggctat caagagaatg ttgagtacaa 2160 tcaggacaaa ttcttgcatg ttaaagcaga gttgttagac cgaattgaga agcatgatga 2220 gttaaacaag aaatatatga tgatagaaag tcggctggct gaattacaag agttcgaaag 2280 aaagggaaat gaagaagagg ttgtgaaggc agatttggca gctaagaaaa ttgaaattag 2340 aatattgaag gtgaagtttg acaaagaacg agaaaaggtg aaacagttga ccaacaggtt 2400 ggaagtttca gaaaaacata aagaacagat cgacaccaac aacaatacct tgaatcggaa 2460 caacatggtg cttatagaga agatggccaa ggtagatgag caaatggatg aagctgccat 2520 tcacgcacga attattagag ccaatgctcg aagggtggga agggacatct ttcgttatcg 2580 acaaagcttg gctgagacag atgccttttt agagaaaatt gagaatcgag gcctcgcgtt 2640 cctaccagtg gctagagata tggatgaaga ggaagattga tgtatttctc tttttattat 2700 tttgtaccct ctcttcaaga gatgtattag ccaatattaa tgaaaagagg ctttgaccca 2760 tcttttataa atataagcct accaaagcag cagcttgagc acaactactc ctgataagga 2820 acgtgacaaa aagagtccat gcccattaca caagaggaat gttggccatc gatcgttttt 2880 ttttttaaaa aaaacaagtt tctaagagta ttcatgcatt gtttctttat catacattca 2940 tttacatttt tccatgcgtc ccagaccgtg aaacataggt cccacatcca aaatccacaa 3000 cacccggtct cgagcgagaa tggagaacga agaaagagct cacatagagt cacattatca 3060 gaccgagttg gagtctgtaa agaatgaagt ttctcggcta accgacttac ttgagcagct 3120 tctaagggct aagaatgggg agggaacatc agcacgacag cttgaaggag cgccagcagt 3180 tcacattcct caagcatctc aaaaccaggg ggcaaactcg gccaatgaac aacagtttgt 3240 gcctattact cctatcctac cacctcatac tccagtcact gttgacctaa caacggaggg 3300 agtcccggat aataggtctc ccagtttgat agaccaagac aagctatttg ctctggaaga 3360 aagattaagg gcagttgagg gtaatgactg gtttgaccct atgcgagcag ccgaagtatg 3420 tttggtacca aacatcgtgg taccaaaaga ttttcgaata ccagagttca ttaagtatac 3480 cgggttggaa tgcccaaaca ctcaccttcg atcctactgc aacaaaatgg cggaagtaat 3540 ccgtgatgat aaaatgttaa tctatttctt tcaagatagc ctagcaggat ccgctttaag 3600 ctggtacatg aggttagaca gcatcaggat caagagctgg agagacttgg tggaggcttt 3660 cctcaaacag tacaagttta acatggaaat cgctcctgat cgaacaagtc taatggcaat 3720 ggagaaaaga agccaggagt cagtaagggc ttatgcgcaa tgatggaggg atgaggcaat 3780 gcatgtccaa ccccctttga tagaaacgga gatggtgagc ttgtttgcca ataccttcaa 3840 agcaccttat tatgagcacc taatgggtag ctcctctcaa catttctatg atgcggtacg 3900 catagctgag aggatagaac aagggattaa agctgggcga atagcgatgc cagtggaaaa 3960 gaagggtttt attggaagaa agagagaagg cgatgttaac aatttggaag acgggtataa 4020 gggtaagaaa gtagattccc acaatccaca agtacctacc tctcaattct cacgcataaa 4080 ctttaaccaa tctttttccc ctaatcgaac aaataaccaa tcaaactacc aaaatcacta 4140 ccaaagaccc catacgagat acccttcaga acaactacca ccgctaccca tgcctttgaa 4200 ggacatgtac gccaaactgt tgagcattgg gcatatagct cctatcccta cactaccatt 4260 acaaccacca ttcccaattt ggtacaagcc cgagttaact tgtgagtacc atgcgggtaa 4320 tcctgggcat gggattgaaa cctgttacgc tttcaagaaa agattgctgg agcttattaa 4380 gataggatgg gtatcctttg aagacaagcc caatgttaat tcaaacccgt tgcctaaaca 4440 tgcctcaagt agtagtggaa taggcatgat agaagttgga aatcaatgca aggtgttgaa 4500 ggtgtctatg gaaaagatgt actacctgtt agtacgatca ggatttctag aggcaaatat 4560 ggaaggccat tcggagggag gtagctattg tgagttccat ggaagagatg gacattatat 4620 tgaggattgc atcgagtttt gcgaaaagat tgcaaaaatg tttaaaatgg ggcaattgag 4680 aattgaaccc atggagaacg ggggtgaggt gagtatgatg gaaggtcaaa tggagatgac 4740 aggagtatgc agggtccaac aaacagctaa tggtccccca aggctaatct tggttaaacc 4800 atcctacaca aaagggaatc acaatgccat gccttataat tatggttatg cctccaacgt 4860 tcaagctcct cttcctttgt tccagactga gataagtggt ttgaccagga gtggtcgttg 4920 ctttacttcc gaggagttga ggaaggaaaa gggtaaagaa gtggtagatc ttgacaaagc 4980 gctagaagtt aataagccag taacagaaga ggagtcgaat gaattcctga agttgatcaa 5040 gcatagtgaa tattgcatag tagatcaact aaagaagact ccagctagga tctcccttat 5100 gtccctgata ctcagctctg agccgcatcg aaacgccttg cagaaggtat tgaataaggc 5160 atatgtaccc caagacattg aacataaaac catggagcat ctagtgggaa ggatccatgc 5220 aactaattac ctgtacttca cggctgatga gcttgatgct gaaggtaccg gacataacaa 5280 gcccttatac attacggtta gatgtaagga ctgcctcata ggaaaagtac tcattgataa 5340 tggctcggcc cttaacgtgt tgccaaagca catgctagaa gaaatgccga tcgatgaatc 5400 ccatataaag ccaagtacta tgatggccag agcgtatgat ggctcaccta ggccaataat 5460 tgggacttta gaagtggagc tatatgtggg accacaaatg ttcctagtaa cacttcaagt 5520 tatggatatc cacccttcct atagtatgtt gttaggaaga ccttggattc atgcagcggg 5580 ggcagtagct tcgtcattgc accaatgcct gaagtatatc atgaatggga tgttggtaac 5640 tgtcaaggcc gaggagacag tatccatgat aaagaatgta gctgtgcctt ttatcgaagc 5700 gggtgattgc aagggtaaca atatccatgc ctttgagatt gtgaacaccg actgggtgcc 5760 agagaacaca gtgctaagaa ggccaaggat ctcagaagca gcaaggatgg caagtctatg 5820 ctttttgaac cgcgggatcc catttcagta taactttatt atcaggatac cagaaggggt 5880 caatctggca aggatgaaaa gtgctgctca aaaatttggg ttagggtacc aacctaacca 5940 aaaggattat cggtgggctg ctggttggag aagggcaaga aggatggcta gaattaaagg 6000 aagagagcct gatgaagaaa agctagaaat ccctcccctt tgcgtgtcat tcccaaaagc 6060 tgcatacata atgcaacatg ataaagaagc cgaaagcctt gatcaagagc tgtcaaacat 6120 gagcataaat accttggggg aaaacaaggt ggaagaagat gacatgaaga cagtagcaag 6180 aaagggagat gaagcactcc cacaactgac ggtctacacc atagaagagg tctccgccaa 6240 gacctttgtg cgcaagttgg ctcaagacga gaagtttcag aattgggtga cccaagaagc 6300 tccagtggtt ttcaaaatgt aaaccaattt tgtttgtctt aacatgcttt tgtcattgct 6360 ttgtttggtt ttcttttgtc attgctttgt ttggttttca tttatttttg ctagtcgaca 6420 atcaaggctc aattgttggt tagactttat gtttgtcatg gagcccactt tttctttaaa 6480 taaattgtga gatcatgcac tttccacaaa ttgctttctt ttttatgcat ttacaccaaa 6540 cacttcccgc tttcaggaat cctgaaagcg gatctccaac aacatcacat atatttagca 6600 tcaagaataa atggccaaac ttgaacgagc atgtgatagc tatggaagaa gaagaatggg 6660 atgaaagcaa tattagtgaa ttcaccaggc tagtagaaca acaggaacaa acttggaagc 6720 ctatcgccga ggaactcgaa accatcaatg tgggtagtga tcagctcaag aaagagttga 6780 aaataggtac cttagttact tctgaacaaa ggacaaaaat gatcgccctg ttacaagaat 6840 atgcagatgt ctttgcttgg tcttatgaag atatgcccgg tttggacaca aatattgtag 6900 tacacaagat accgttggaa gaaggttgta aaccagtcaa acagaagctg aggagggccc 6960 acccggatgt ctggatcaag gttaaggtag aactcgagaa acaatgggat gctggctttc 7020 tagaagtagt tagatatcca caatgggtat ctaacattgt tgtggtgcct aagaaggagg 7080 ggaagattag agtgtgcgtg gattttcgga atttgaataa agctagcccc aaggatgatt 7140 ttcctctacc acacatagat gttttggtgg acaacgcggc ccggagttcc acatattcct 7200 ttatggatgg tttttcagga tacaaccaga taaaaatggc tccggaagat aagacgaaaa 7260 caacttttgt cacaccgtgg gggacattct gctataaggt catgccattt ggattgaaga 7320 atgcaggagt aacctatcaa agagcaatgg tgactttgtt ccacgacatg atgcacaagg 7380 aaattgaggt gtatgtagac gacatgattg ccaagtctaa aagaggagag gatcatgtcg 7440 aagttttgag gaagttgttt gagagattga ggaagtatga attaaggctc aatcctgcaa 7500 aatgttcatt tggagttaaa tcgggtaagc tgttaggatt tgtggtaagt gatagaggta 7560 tagaggtgga tccagataaa gtaagggcca tccaagctat gtcatcccct aagacggaga 7620 aggaagtaag aggattcttg ggaaggataa actacattgc tcggttcata gctcagttaa 7680 caacgacgtg tgaaccaata ttctgactac taaggaaaaa gaatcctgga acctggaatg 7740 aggagtgtga ggaggcattc aataaaatca agcattattt gcaaaatcca cctttactgg 7800 tccctccggt atcgggaaaa cctctagtat tgtatctaac agtgactgaa gcagctatgg 7860 gatgtgtatt gggtcagcat gatgaaaccg gaaggaagga aagagctatt tattacttaa 7920 gtaagaaatt cactgaatgt gagtctagat acacggagat agaaaggctt tgttgtgcgt 7980 tggtgtgggc agcaaagagg ttgcggcatt atatgttata ctataccact tggttgattt 8040 caaaagtgga tcctctgagg tacatttgta acaagccatt tctctcaagt cgaattgcaa 8100 ggtggcaagt gctattagca gaatatgaca tagtgtacat gacaaggaaa gccgtaaaag 8160 gaagtgcaat cgcggaccat ctggctgata atgctgttga agattacgaa cctttggatt 8220 ttgactttcc tgatgaagat atattgtcaa tagagaaaga agaagagaat acagattggt 8280 ggacgatgtt ttttgacggt gcagtgaacg tatatggtaa cggggccggt gcggtaataa 8340 tctctcctga taagaaacag tatccagttt cggttaaact acatttcgag tgcaccaaca 8400 atacagctga gtatgaagct tgtatccttg gtctagaagc gacattagag ctgaagataa 8460 agaagttaga tgtgtacgga gattcaatgt tgattatctg tcaggttaag ggggaatggc 8520 agaccaaaga ggaaaagttg aggtcgtacc aggaatacct gtccatgcta gcgaaggaat 8580 ttgaagaaat tagattcacc catctgggaa gagaggggaa ccattttgca gatgctttgg 8640 ccacgctagc tgctatgact accattgatc tcaagtgcaa ggtacaaccg gtacacattg 8700 acattagaaa tgacccagct cactgttgct tagttgaagg agagatagac ggacagcctt 8760 ggtattatga tatcaagaac cttgtgcaaa atcaggaata tccggtggga gcctccaaaa 8820 cggataagaa aaccttgaga aggttggcta cagacttcta tttagatgga gagattctgt 8880 acaaaagatc atttgatgga accttgctaa ggtgtttgaa tgaggcagat gctagaaagg 8940 cattacggga ggtccatgag gggatttgct caacccatgc tagcgggcat atgatagcaa 9000 ggaaaatcca aagggctggt tatttttgga tgacactaga gaaagactgt atcgactatg 9060 tcaggaaatg tcataaatgt caagtttaca gtgacaaggt caatatgcca ccagctcctc 9120 tgtttaatct aatatctcct tggccatttg caatgtgggg aattgatgta attggtccgg 9180 ttaacccaaa agctagcaat gggcatagat tcatcctggt ggctattgac tacttcacca 9240 aatgggtgga agctaattcg tatgcccatg taacacagaa ggtagtgaag aggttcatag 9300 aaaaggatct gatttgtcga tatggtcctc cggaaaagat agtgaccgat aatgcacaga 9360 atttcaatgg caaaatgata gtggagttgt gtaccaagtg gaagatcaag cattcaaact 9420 cttcgccata ccgaccaaag atgaatggcg cagtagaagc cgccaacaag aacatcaaga 9480 agattattca gaaaatggta gtcacatata gagattggca tgagatgttg tcattcgctc 9540 ttcacgcata ccgcactaca gttaggacct cgacatgaac cactccatat tctttggtgt 9600 acggtatgga agcagtgatg cctttggaag tagaaatccc gtcgttaaga gtattgatag 9660 actccgaatt agaagaggcc gagtgggcca aagtgagata tgagcaactg aacctgatca 9720 gtgaaaagag gatggccgca atatgtcatc accaactgta ccagaaacgg atggccaagg 9780 catatgataa gaaggttaga ccgcggttgt ttcaagaagg ggatctagta ttgaagaaaa 9840 tattgtcgct acctggagac gatcaaagca aatgggcacc gaattacgaa ggtccttaca 9900 tagtaaagaa ggcattctca ggaggagcac tgaagttggc tagaatggat ggagaagacc 9960 tagctcgacc tgtgaattct gactctgtaa aaagatatta tgcttgatgt aggctcctaa 10020 atcaataaag caaagtttgg ccattgactt ctttctcttt tgcattgatc tcacaacagt 10080 catttttgca ttaatcccaa cagtgcatgt cttgtgttat ctcatttaaa aagtttagca 10140 tcggctgaac gaatttcttc tctctataaa agcctagact agaatcacac ccctacactg 10200 ggggcaataa gagatatttt catgtacgaa agcctataga ttttaaaaac caagctaaaa 10260 catttgacaa aagcatgaca aagaggcaat gacaagtcat acattttgga aaaaggacta 10320 tttgaagaaa gtgagagatt tcttctccaa gaatatgatc ggaggcaaca cgagagatga 10380 atccagcata cgacttcaaa agcaagctca tgttaagagg gaatctcatg aactcgaaga 10440 agatgatggg gcctatgttt caaaaccagg tacgaatgca tgcatggcat ctaatcataa 10500 atcattgcat atatgttttt tttggatcgt cacaggagga gaccttaata cattccaaca 10560 aaattggaga cgaagaaaaa atcattgagt tgattctaga acaacaagaa gagaagataa 10620 taatgttcaa accctgccat caggaagagc gacatcgagc aatcggtaaa agggaatcgc 10680 tagaagggat tccaggttaa cagatttaca agatagattt ttttggtttt tgattaaagg 10740 agatcgccag aaaggatctc attatttcag cttcaaataa aaggaatcgc cagatggaat 10800 tccaagttga tggagatcgc cataagggat ctcatacttc gctatttgga ggtcgccaga 10860 tgggacctcg tattacctgt tgaaaaaagg aatcgccaga tgggattcca agttaattaa 10920 aggagatcgc cagaagggat ctcgtgtttc attatttgga ggtcgccaga tgggaccttg 10980 ttttttcatt gaataaaagg aatcgccaga tgggattcca agttgactaa aggagatcgc 11040 cagaagggat ctcgtgtttc gctatttgga ggtcgccaga tgggacctcg tattacctgt 11100 tggaaaaaaa aagaggaatc accagatggg attccaagtt gattaaagga gatcgccaga 11160 agggatctcg tgtttcatta tttggaggtc gccagatggg acctcgtttt tcatgaataa 11220 aaggaatcgc cagatgggat tccaagttga ttaaaggaga tcgccagaag ggatctcgtg 11280 tttcactatt tggaggtcgc cagatgggac ctcggttttc atgaataaaa ggaatcgccg 11340 gatgggattc caagttgatt taaggagatc gccagaaggg atctcgtgtt tcattatttg 11400 gaggtcgcca gatgggacct cgtttttcat tgaataaaag gaatcgccag atgggattcc 11460 aagttgacta aaggagatcg ccagaaggga tctcgtgttt cgctatttgg aggtcgccag 11520 atgggacctc atattacctg ttgagataaa aggaatcgcc agatgggatt ccaagttgac 11580 taaaggagat cgtcagaagg gatctcgtgt tttgatattt ggaggtcgcc agatgggacc 11640 tcgtttttca tttgaataaa aggaatcgcc agatggggtt ctaagttgac taaaggagat 11700 cgccagaagg gatctcgtat ttcgctattt ggaggtcgcc acatgggacc tcatatttcg 11760 tttgaatagg aatcgccaga tgggattcca ggtcgattaa aggagatcgc cagaagggat 11820 ctcgtatttc gctattggga ggtcgtcaga agggacctca tatttcaaca ttggttacaa 11880 ggaatcgcca gatgggattc taagattttt tgttaaagga gatcgttaga agggatctcg 11940 tatttcaata ttggttaaaa gggaattgcc agacgggatt ccaagttgag taagcaataa 12000 ttatagattt tggtttagag agatcgtcag aagggatctc aagatgataa attttgatca 12060 tagtttttga agttaaggag gattgctgta aaagacaagt ttcaggtcaa tcaagcttca 12120 accagatcag ttttgggagt tccgtttagg gtttatcttt ataaaactta ctgcgcaaaa 12180 cctctgctcc gtaagcatta taaagagggg gcatct 12216 // ID Copia-67_Mad-LTR repbase; DNA; EDCOT; 289 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-67_Mad_; KW Copia-67_Mad-LTR; Copia-67_Mad-I. XX NM Copia-67_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-289 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1673-1673 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 289 BP; 75 A; 44 C; 59 G; 111 T; 0 other; tgttagatta ttaggtttgt tggaagtagt ggttctatcc actacgtaag cttagggttg 60 tttatgtaag cagttttaac tgcatggcca aataaaccct agaatttagg gatcagtaga 120 agttgttttc ctttcagact tagtcttata ccacgtttag gttaatgttt aacgtgggtt 180 gcatgtttat ctttcgttag tttgtaaggc ttatataaag cctgtttgtt ctttgtttaa 240 tgttaagcga aattcctccc agcttgcaaa agatctcatt cgacaaaca 289 // ID Copia42-PTR_I repbase; DNA; EDCOT; 4784 BP. XX AC LG_IV; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia42-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4784 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4784 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 262-262 (2007). XX DR Genome; LG_IV; Positions 14410182 14414965. XX CC Positions [2140-2655] - Integrase core CC 'ACAAT' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 682..4689 FT /product="Copia42-PTR_I_1p" FT /translation="MADIPEEKSAGNASIPPQYIPVSNTKFEVEKFDGKGN FT FGMWKCEVMDMLVQMNLDFTLEDKPEDLDDKSWERINRLACSSIRLCLVKD FT QKYAFSEQNSAKELWQALEDKFMKNSIENRLYLKKRIFRFQHKKGTSMNEH FT LNDFNKMIADLKNLDVEIDDEDKALLLLNSLPDTYEHLVTTLLYGKEKIKF FT IDVSNALVNNEYRKKDQIVHKESTSEALTVRGRTNPRRFRGRGRSRSKSRG FT ESSNRRYLAKDECAFCHKKGHWKKDCPIKGNKEKDEPTVNVARDEDEQDSA FT FMVSSPENHSGEWVLDSACSYHMCPNKHLFSRLEEFDGGGVLMGNDDVSEI FT KGIGTIHLKMHNGVVKTLTDVRYVPDLKKNLFSLGVLESSGYKIIMYGGVL FT RAIRGALVVLRGTRISNLYFLDGSTVTGTAAVSKSIEDDKADNSRLWHMRL FT GHAGEKALQGLVKQGLLKGAKTGKHGFCEHCVLGKQTRVKFGTAVHNTKGI FT LDYVHTDVWGPSKNESLGGNRWFVTFIDDFSRRVWVYMMKHKDEVLDIFLK FT WKKMVETQTGRRVKTLRSDNGGEYTSDPFFEVCQDEGIKRHFTVRKTPQQN FT GVAERMNRTLVEKVRCMLSHSGLSKVFWGEALSYARHIVNRLPSAALDGRT FT PLEVWSGSPANDYDSMRIFGCSAYYHVTESKLDPRAKKAIFLGFSGGVKGY FT RLWCSESKKVILSRDVTFDESGMLQQEKSQEKEKQSGDAQQVELETSVIPI FT KTVQTISTEGDSDESSDEEDATTPATTQQESIATSKPKRVIKKPARYCNMV FT AYALPVIDDGIPYTYKEAVQSVESAKWNEAMDEEMKSLHKNQTWDLVQLPR FT GKKTIGCKWVYAKKEGNPGKDNIRFKARLVAKGYAQKEGIDYNEVFSPVVK FT HSSIRILLALVAQFDLELAQLDVKTAFLHGDLEEEIYMSQPDGFKVTGKEN FT WACKLKKSLYGLKQSPRQWYKRFDKFMAEHGYTRSQFDHCVYFRKLLDGSF FT IYLLLYVDDMLIASKSKVEIDRLKAQLRTEFEMKDLGEAKKILGMEIQRDR FT RKGTVCLTQTQYLKKILQRFGVDGKTKPVSTPLAPHFKLSASMSPRTEEER FT KHMAQIPYANAVGALMYAMVCTRPDISHAVSMVSRYMHDPGKGHWQAVKWI FT LRYIHGTTDIGLKFERDDRLGQNLVGYVDSDYAGDLDKRRSTTGYVFTLAK FT GPVSWRSTLQSTVALSTTEAEYMAVTEAFKEAIWLHGLIEDLGIVQEHMDV FT HCDSQSAICLAKNQVHHSRTKHIDVRFHFVREIVDEGDILLQKIGTADNPA FT DMLTKCVSGIKFQHCLDLVNISRC" XX SQ Sequence 4784 BP; 1477 A; 855 C; 1168 G; 1284 T; 0 other; aattggtatc agagcattag ggaagcttaa acgcagaaaa acacgttttt tagctctctg 60 ttcaaagttg cagaattttc aaagttctca gatcttgctt ttgaccagct gcggagattc 120 ctctcgtcca tacgaatccg gcgatataaa gatcgtcgca atcggagttg aaacgagccc 180 tgtagagctc gccgaagttt cgccggaaat ctgccggaaa aaccagacag tgccggaatt 240 ctcgcctgag tcatcatcca cgtcatccga cacgtaggcg ctgagtcatc atccacgtca 300 tcaacagagg ggccacatcg ccctgtcatc agacacgtca tcagcaatgt catctaacag 360 tgacagaata ttttcttgac agaataagaa tattccgtta ccagtaagag aatattcccg 420 tgacagaata ttctttatca gagacagaat attccttccc tgagtcaact cggtcagatt 480 ggttttttgg ccaactcagt gattttttga cccgtttttg gccgagtcaa gttggttcct 540 agcattttca accattccgg acgcaaccgt ggtgtccgtt ttgttaaaca gcataccgaa 600 gttactgttt tggcactttt gagcataaaa gtgtgtgttt taacaatttc gggattccat 660 ttgtaatcca aagacgtcct aatggctgat attccagaag aaaaatcagc ggggaatgct 720 agtatacctc cacaatacat cccggtatcg aataccaaat ttgaggtgga gaagtttgat 780 gggaaaggta attttggcat gtggaaatgt gaagtcatgg atatgcttgt ccaaatgaat 840 ttggatttca ctttagaaga taaaccggag gatttggatg ataaaagctg ggaaaggata 900 aatcggttgg cttgcagttc catccgactt tgtcttgtaa aggatcagaa gtacgccttt 960 tcagaacaaa actctgcaaa ggaattatgg caagcactgg aggacaagtt tatgaagaac 1020 agtatagaga atcgtctcta cttgaagaaa aggatcttcc gttttcagca caagaaaggt 1080 acttctatga atgagcatct aaatgatttc aataaaatga tagctgattt gaagaattta 1140 gatgtggaaa ttgatgatga agataaagct ctattgttat tgaattcact gcctgacaca 1200 tatgaacatc tcgtcaccac tttactgtat ggtaaagaaa agattaaatt cattgatgtg 1260 tccaatgctt tggtgaataa tgagtaccga aagaaggacc agattgttca caaggagtca 1320 acgtcagaag cattgacagt tagaggcaga acaaacccca gaagatttcg agggcgaggg 1380 agatctcgct caaaatccag aggagaatca tcaaacagac gatatcttgc aaaagatgag 1440 tgtgcctttt gtcacaaaaa ggggcactgg aagaaagatt gtccaatcaa gggcaacaag 1500 gaaaaagatg aaccaactgt gaacgttgca cgagatgagg atgaacaaga ctctgcattc 1560 atggtctcat caccagaaaa ccattctggt gaatgggttc ttgattctgc atgttcctat 1620 cacatgtgcc ctaacaagca cttattctcg agactcgagg agttcgatgg aggaggtgtg 1680 ttgatgggta atgatgatgt gagtgagatc aaagggattg ggactatcca tctgaagatg 1740 cataatgggg tagtcaagac actaacagat gtacggtatg tacctgactt gaagaaaaat 1800 ctcttctcac ttggagttct agaatccagt ggttataaga ttatcatgta tggtggagtc 1860 ttgagagcaa tccgtggtgc attagttgtc ttaagaggca cgaggataag caacttatat 1920 ttcctggatg gatctacagt tactggtaca gcagctgttt ccaaaagtat agaagatgat 1980 aaagcagata attccagact ttggcacatg cgcttagggc atgctggtga aaaggctttg 2040 caaggattag tcaagcaagg tctattaaaa ggcgccaaga ctgggaagca tgggttctgt 2100 gagcattgtg ttcttggaaa acagacaagg gtcaagtttg gcactgcagt acacaacaca 2160 aaagggatcc tagattatgt tcacacagac gtatggggac cttcaaagaa tgaatctctt 2220 ggaggtaatc gttggtttgt tacttttatt gatgatttct caagacgagt atgggtgtac 2280 atgatgaaac acaaggatga ggtccttgat atctttctga aatggaagaa aatggtggag 2340 actcaaactg gaaggagagt taagactctt cggtcagata atggtggtga gtacacttca 2400 gatcctttct ttgaagtttg tcaggatgaa gggatcaagc gacattttac tgttcgcaaa 2460 acaccacaac agaatggagt agcggaacgc atgaaccgca cattagtgga gaaagtccga 2520 tgtatgctat cacattcggg actaagcaaa gtgttctggg gcgaggcatt aagctatgct 2580 cgtcatattg ttaatcggtt accttcagca gcattagatg gtagaacccc cttggaggta 2640 tggtcaggct ctcctgcaaa tgattatgac tctatgcgta tatttggttg ctcagcatat 2700 tatcatgtta ctgagtccaa gctagatcct agagccaaga aagctatatt tttgggcttt 2760 agtggaggag taaaaggcta cagactctgg tgttctgaat caaagaaagt gatcttgagt 2820 agagatgtca cttttgatga gtctggcatg ttacagcaag agaaatcaca ggagaaggaa 2880 aaacagtctg gtgatgcaca acaggtggag ttggagactt cagtcatccc tataaagact 2940 gttcagacaa tctctactga aggagattca gatgaaagtt cagatgaaga ggatgcaaca 3000 actccagcaa ccacacaaca agaatccatt gcaacgagta aaccaaaaag ggttatcaag 3060 aaacctgctc ggtattgtaa catggtggct tatgcacttc cggtgattga tgatggaatc 3120 ccctacacct acaaagaagc agtacagagt gtagaaagtg caaaatggaa cgaggcaatg 3180 gatgaagaga tgaaatctct ccacaagaat cagacttggg atttggtaca actccctaga 3240 ggaaagaaga caattggttg taagtgggta tatgccaaga aggaaggtaa tcctggaaaa 3300 gacaacatcc gattcaaagc aagattggta gcaaaaggct atgctcagaa ggaggggata 3360 gattataatg aggtattctc tccagttgtt aagcattcat caatccgtat tctgttagcc 3420 ttggttgcac aatttgattt ggagttagcc caacttgatg tgaaaactgc cttcctacat 3480 ggagatttgg aagaggaaat ttacatgtct cagccagatg gtttcaaagt cactgggaaa 3540 gagaattggg cttgtaaact gaagaagtca ttatacggat tgaaacaatc tcctcgccag 3600 tggtataagc gatttgataa gttcatggca gaacatggat acacacggag tcagtttgat 3660 cactgtgtat attttcgcaa acttcttgat ggttctttca tctatttgct cttatatgtg 3720 gatgatatgt tgatcgcatc gaagagcaag gtggagattg acagactgaa agctcaattg 3780 agaactgagt ttgaaatgaa ggaccttgga gaagctaaga agattcttgg catggagatt 3840 cagagagaca gaagaaaagg cacagtctgt ttgacacaga cccaatactt gaagaaaatt 3900 ctacagagat ttggggtaga tggtaagacc aagcctgtaa gcacaccttt agctcctcat 3960 tttaagctaa gtgcttcaat gtctccacgc acagaggaag agcgcaagca tatggctcaa 4020 attccttatg caaatgcagt tggtgcatta atgtatgcaa tggtttgtac aagaccagat 4080 atttcacatg ctgtcagtat ggtgagcagg tatatgcatg atccgggaaa gggtcactgg 4140 caggcagtta agtggattct acggtacatt catggcacaa ctgatattgg tttgaagttt 4200 gagagggatg atagactcgg acaaaattta gttggttatg tggactcgga ctatgctggt 4260 gacttagaca agcgtcgttc aacaacaggc tatgtgttta cactcgctaa agggcctgta 4320 agttggaggt caacgttaca atcaacagta gctttgtcaa caactgaggc agagtacatg 4380 gcagtaacgg aagctttcaa ggaagctatt tggttacatg ggttgattga agatttggga 4440 attgttcaag agcacatgga tgtccattgt gatagtcaaa gtgctatttg tcttgcaaag 4500 aatcaggttc atcattcccg caccaagcac atcgatgttc gatttcattt tgttcgagaa 4560 attgtggatg aaggggatat tctgctacag aagattggta ctgcagataa tccagctgac 4620 atgctcacaa aatgtgtctc agggatcaag ttccaacatt gtttggactt ggtcaacatc 4680 tctcggtgtt gagcaccttc agggtgcagc gccatacggc gcgttagagg cagcattgat 4740 tgatcacgag gattgcatgg aaaaatcttg ccaaggtgga gatt 4784 // ID Copia-33_Mad-LTR repbase; DNA; EDCOT; 497 BP. XX AC ACYM01062820; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-33_Mad_; KW Copia-33_Mad-LTR; Copia-33_Mad-I. XX NM Copia-33_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-497 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1383-1383 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01062820; Positions 1511 1015. XX SQ Sequence 497 BP; 128 A; 89 C; 97 G; 183 T; 0 other; tgttagtatt ccctcctcat gaaattaaat gcccatcttt aatgtgcagc tgtctaagaa 60 gcaatatcct tggacaaaga aaggtctttc cagttttcaa gaactgagta aatgtaaagc 120 agcccaatat tgattgcttt gtctatcccc ttccatagtt ttctagaacg gagttgatta 180 tgaatattta tatgttgtta gcctgtagct caaaaataag agggttagta acagaaaaat 240 agtgagttca tccaagagtt tgtgagtgct cttgagtcag tcagcctcta aagtttagag 300 agattggtgc ttgtaatccc atttcttagt ggaagtattt tggactttgt cctgtggttt 360 ttcccttcac attggggggt tttttccaca aaattctggt gtccttttgt tcatctttaa 420 tttctgttta cttgtgtttt atttcttgtg atttacacta gcagcaagct gctgtttccg 480 ctgcagcaaa ctcaaca 497 // ID Gypsy-45_Mad-LTR repbase; DNA; EDCOT; 2319 BP. XX AC . XX DT 22-OCT-2010 (Rel. 15.11, Created) DT 22-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-45_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-2319 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1988-1988 (2010). XX DR [2] (Consensus) XX SQ Sequence 2319 BP; 564 A; 446 C; 540 G; 767 T; 2 other; tgtcacagcc cgtcccgaaa tatttatttt cgacggcgtg aaatgactaa tttacccttg 60 gacgttttgt gtggttatgt gggttaagtt ttattggacc aattcaaaga ttttcctaag 120 tttttggaac caattaggac ttaattgttt tgttggttgt agaccaacta ggaccacaca 180 cagcacccat acttttctct ctctcccgtt gactctctct ctctcccttc cctctcggat 240 tttcttccat ttccgtacaa tccgtacgga caacctcaaa ctccttcaac cagtcacgga 300 tcgacgttaa aaaggtaatg ttcttgttcc ctacaagctc ctgagtccat tcgtactatt 360 tttaggactt gaaaccttgg aaaacccgag aaaccataac ctccgatttg aggtactgtt 420 catgcacacg taaatgtgta gttttctgag agttttgaag ttatagggag ctttagatcg 480 tcttcacgaa gctcggagaa gaaaaatgaa gtgatttgga cgtcgggaag ctcgggaata 540 gggagttgca ggtttagccg gaatatcgaa ggattttccg gcgagttccg tcggttttag 600 gacttttgaa aggtaaggtt ttgttctact tgtcctaagc ttcaatttgg ttcaagtttc 660 gtggaatttg gttgagaatt ggacgagata tgaaggtttt cgtgattttc cagtttccgg 720 tgaacggcga cggcgaccgg cgaggctaac cggagaagaa gatagaatat tccgtcagag 780 ttgacggaat attctgacgc cgtcaggtag aattaacggt ttctgttact ttttaacgga 840 atattcctaa cggggttaag ggattccgtt agggtccctg cgcgtggccg cgcgtgttgc 900 cgtgcccttg cggcgcgtgg cggcgcgtgg gacgtcggaa aatttttcta aaaatatggg 960 gatgttcgtg aggttgtgta gatcacgttg gtatattcaa acatcccatt tgagcaatgt 1020 atgagaagtt attagctagt attggttatg tgctttaaat taacgttttt atagttgttt 1080 cgcatatagg ggagacttat cccgaggacg agcgcagtca agggcgactc gggggctacg 1140 acccttcgac ataccagtga gtgggctttt ggttttcagt atatacttat atacttgata 1200 ttttcccaga aaatgcgttt aaatgaaagt atgccttgaa atgccatgca tataaattta 1260 tgttcagtat atgaattagt atatgatgca taatatataa ttgtggtgct gtggacgctc 1320 aggtaagccc aggtgagttt atgaattgtg aatgtgaata acggttgtga ttaattgaga 1380 agcatagagc tcataaacct gcaccccggt gttagtgatt agccagagat atggcacagg 1440 cctgtatata atgtcacctc ccgcacccta tgctcacatt ggatccaatt taggtgcaca 1500 gtcttgtcgt acagaccatt ataggtggtt ccgactcgta ggtgactagc gatttatcgc 1560 acagctatca tgagagcgta gtattgagca taattatatt acacccagtc ttgtcgtaca 1620 gaccctttca gtggttccga cttgtgtgca gtgtagtgcc gtataggtca tttgcagtga 1680 ctccggctag attgactaat gagctatgaa ttcagccgta cagacttctg caggggttcc 1740 ggctaatgtg ttattttcca tgaatttatt ttcacctgag ttacttatcc tgttttatat 1800 cttggcatgg catacttatg attatgaata tgtgwagcat gatttgaatt gatatatata 1860 tatatatatg tatatgttta tattctattt ctgggaaaaa gtatacatgt tttacggcga 1920 ggggttagag catttgaaag tgaaatgtgt tttgaaaasc tttgtttttg cccactcaca 1980 ttttctgttt tgcgcccctc caggttttag gtagacttgc tgttggtggc attgaggatc 2040 tcggcggttc tgacagaata aaatattcgt aggatatctt ctggtactgt ataactagta 2100 cttgtcctac tggactgcac ctagactttc tatgctctga ttaggagtat ttactcttgt 2160 atctcactcc tagcactttc tgcttattag tgcacattag tagctttcgg tttttattta 2220 ttcgtatatt tcttatcctt atcgcttccg cactgtgcac atggctacgt caccctcacg 2280 tgacggccag catgcctcga tctcggtcgg ggtgtgtca 2319 // ID Copia-6_Mad-I repbase; DNA; EDCOT; 4453 BP. XX AC ACYM01089668; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-6_Mad_; KW Copia-6_Mad-LTR; Copia-6_Mad-I. XX NM Copia-6_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4453 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1346-1346 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01089668; Positions 198 4650. XX CC Positions [1840-2229] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1840..2811,2815..4443) FT /product="Copia-6_Mad-I_1p" FT /translation="MTWVFPLKQKSEVTAKFKLFYQYVATQFDKKITTLRS FT DNGGEYVNHDLHNFLSQHGIVHQTTCAYTPQQNGVAERKNRHLLEVVRASL FT FEARMPHHFWGEALCSAAYLINRTPSSTLQYQTPSQTLTTLLTMPSTPNLE FT PRLFGCVVYVQVYPHQRGKLDPCALRCVFVGYADTQKGYKCFHPPTQTVHV FT TADVSFHESEFYYSEGVSEHHLQGESSIFATDTHNIQIQQNVLEQSMSEQP FT ATVVQQDQELLETPDDGSDNFPPTTVPSPIIQSGPENSPQVTEHLNSNLST FT LPESSHTGNTGYQLPHHTTRGIPRQQYDPDPKKVKYPIANHVSLHRLSMSC FT ASFVYQLSTVSIPSNVHEALKDPKWTQVMNDEMETLQKNSTWEMTILPKGK FT RTVGCRWIYTVKFKADGTIERYKARLVAKGYTQTYGIDYEETFAPVAKINT FT IRVLLSLAANLNWPLHQFDVKNAFLHGDLEEEVYMDFPPGCKMGPNMSNMV FT CKLRKSLYGLKQSPRAWFGKFSKSMKDFGCKQSNSDHTLFLKHKKGKVTAL FT IVYVDDMVITGNDPEEKAALQHHLASEFEMKNLGALKYFLGIEVARSEQGI FT FLSQRKYILDILIDTGMLANKPADTPMELNHQLGEYLDQVPTNKERYQRLV FT GKLIYLGHTRPDIAYAVSVVSQFMHAPSEAHMDAVNRILRYLKSSPGRGLM FT FARHGHLDVEGHTDVDWAGFVTDRRSTSRYFTFVGDNLVSWQSKKQKVVSR FT SSVKAEYRGMAYGVCELLWIRNLLGELRFKPKHAMQLNCNNKAAIDIAHNP FT VQQDRTKHVEVDRHFIKEKLEAKIIEVSFVKSKDQFADVLTKAVTGRVFHS FT SLSKLGIDDTYAPT" XX SQ Sequence 4453 BP; 1342 A; 948 C; 935 G; 1201 T; 27 other; atytgagatg gtaccagagc agtcaatcat gactgyctct tgacttaacc ctagcaatcg 60 cttccgcaaa cagcagccgt caacaaaccc aacaccagca aatcactcaa agygttccct 120 atcatggcca acaatgatgg gttaacaaac accaatcaat ccttggtgtc gggaggctcc 180 aaaactacca cacaaatcgt cactttgcag agtgacacct ccagcttctc cgyaggaatc 240 aaactggatg agaataatta ttctctatgg catcaaatca tagagatgaa gatagctggg 300 cgagaaaaac atggccactt gaccggtgat attgcccagc ctgcagactc agatcccaca 360 tttaataaat ggcgtgcatc ggattgccaa gtcaagagtt ggttgttcga cgccatgcaa 420 cctaatcara ttaaacgatt tattcgttat gacacagcaa agcaaktttg ggctgcaatc 480 aagcaaacct attyagatgg tgctgatgaa gccaagattt rtgaccttca cagacggtca 540 ttcataatga agcaggctgg tgcatcagtt gccaaatatt acagtgagct mactgagatt 600 tttcaggagc ttgatcaatt aagtccaagc accatggagc atccgaaaga cgttgagact 660 agaygcaagg aggttgatcg tctccgagtg tatatatttc ttrccggttt ggacaataat 720 ttcratcaaa tcygaggaga gattttragg atggagccta agcctraact tgaggcagca 780 tatrcacata ttaaacgaga ragtaaccga cagggaacca tgtctgaagy tggtggaacc 840 tccgaagcca cagcctkggc tgctgccagg tccaaacawt ctcggccgaa caactacagt 900 atcgacccta ctcgtaaccr gcctccaatg aagtgtacca aatgtggttt agataaccac 960 acaattaagg gctgttatga gatcattggt tatccagaag gatgggtcca caaagggcga 1020 aaaaaggatt caaccaaagc ctcatttgca tccgctcagt catccgagga gactgcatca 1080 gaacctccat yaggtacatc tggctccaag gcctwggcca cctcaggtac ctcttrcgca 1140 tcttctctta cktgtaatag atcatggatt attgacactg gtgctactga tcacatgaca 1200 tctagtttta ctgggttgca ctctaccaaa ccatyaagcc aaacacatat taccagtgcc 1260 aatggcacca cctcccaagt tataggagaa tggtctatat ctcttacatc ctcattaagt 1320 cttgatcatg tcttagttgt cccttcactc gactatgact tgttatctgt tactcaaatc 1380 attgattccc ttaattgtac cgtgtgtttt ttgccattgt attgtctatt tcaggatctt 1440 ctcaccaggg ttgtgattgg atgtagtact aggaggggaa agttgtatta tctggacttg 1500 acagacgaca gtagtaagag attgagtcac gcacatcatg tgagaggaga tgagtctatc 1560 aggatgaaga aaatttggct atggcataga caattagggc atgcttcttt cggttatctg 1620 aaacttttat ttccagattt gttttcccag tttgctgaat cagactttta ttgtgaaact 1680 tgcattttgg cgaaaagcca tcgtatttct tatccattaa gattgaataa aagttctatg 1740 cctttcatga ttgtccattc tgatgtttag ggaccatcac gagttcccat tattagtggt 1800 tttaagtggt ttgtgacatt tattgatgat tgcacctgaa tgacctgggt ttttccctta 1860 aagcagaaaa gtgaagtcac cgccaaattc aagttatttt atcaatatgt tgctactcag 1920 tttgacaaga aaatcactac acttcggtct gataatggag gagagtacgt caaccatgac 1980 ctacataatt ttttaagtca acatggtatt gttcatcaaa ccacatgtgc ctatacacca 2040 caacagaatg gtgtcgcaga acgtaagaat cgacatctct tggaagttgt tcgtgcctct 2100 ttatttgagg cccgtatgcc tcatcatttt tggggggagg ctctttgttc tgctgcttac 2160 ctcattaata gaacaccatc cagcactctt cagtatcaaa ctccatctca gacattgacc 2220 actctcctca ccatgccatc cacaccaaat ctcgaaccac gtctctttgg ctgtgttgtt 2280 tatgttcaag tgtatccaca tcagcgtggc aagcttgatc catgtgcatt gcgttgtgtc 2340 tttgtggggt atgctgacac tcaaaagggc tataagtgtt tccatcctcc cactcagacc 2400 gtacatgtta ccgcagatgt aagtttccac gagagtgagt tctattactc agagggagtt 2460 tctgagcatc atctgcaggg ggagagctct atctttgcaa cagatactca taacatccaa 2520 attcaacaaa atgttttaga gcaatcaatg tctgagcaac cagccacagt ggtgcaacaa 2580 gatcaagagt tattggaaac tccagatgat ggttcagata atttccctcc tactacagta 2640 ccatcaccaa tcatccaatc aggtcctgaa aattccccgc aggtaactga acatttaaac 2700 tccaacttaa gcactttacc tgagtcgagt catacaggaa acacaggtta tcagttacct 2760 catcatacca ctagagggat tcctagacaa cagtatgacc cggacccaaa awtaaaagtt 2820 aaatacccta ttgctaatca tgtgtcccta cataggttgt ctatgtcatg tgcatcattt 2880 gtatatcaat tatccactgt atctattcca agtaatgtgc atgaagctct gaaagatccc 2940 aagtggactc aagtgatgaa tgatgaaatg gagaccctcc aaaagaattc cacttgggag 3000 atgactatcc ttcctaaagg gaagagaaca gtgggttgta gatggatata tacagtaaag 3060 ttcaaggcag atggcaccat tgaacgatac aaagcaagat tggtggcgaa aggttatact 3120 cagacttatg ggattgacta tgaggagacc tttgcccctg tagccaagat aaacacaatt 3180 cgggtacttc tttctctggc agcaaaccta aactggccat tacaccagtt tgatgtcaaa 3240 aatgccttcc tgcatggcga cctagaagaa gaagtctata tggattttcc tccaggatgc 3300 aagatggggc ccaatatgag caacatggtg tgtaaactga gaaagtctct gtatggattg 3360 aagcagtcac ccagagcatg gtttggaaag ttcagcaaat caatgaagga ttttggatgc 3420 aagcaaagta actcagatca tactcttttc ttgaaacata agaaaggtaa agtcactgcc 3480 cttattgtat atgttgatga catggtaatt accgggaatg acccagagga aaaggcagca 3540 ttgcagcacc acttggcaag tgagtttgaa atgaaaaatc ttggtgctct aaagtatttc 3600 ttaggcatcg aagtggctcg ttcagaacaa ggaatatttc tctcacaacg gaaatatatc 3660 cttgacattt tgattgacac tggaatgtta gccaacaaac cagcagatac accaatggag 3720 ttgaatcatc agcttggtga atatcttgat caggtaccta ccaacaaaga aagatatcaa 3780 cgcctcgtgg gcaagctaat ctatctagga cacactagac ctgatatagc atatgccgta 3840 agtgtggtga gtcagttcat gcatgcacca agtgaagccc acatggatgc tgtaaaccga 3900 attttgagat acttgaagtc atctcctgga agaggattga tgttcgcacg acatggtcat 3960 ctagatgttg agggtcacac tgatgtagac tgggcgggct ttgttactga caggcgatct 4020 acatctagat actttacctt tgttggagac aatctagtat cttggcaaag taaaaaacag 4080 aaagtagtgt caagatcaag tgttaaagca gaatatcgag gtatggcata cggagtatgt 4140 gagctactct ggataaggaa tttgttgggg gaattgaggt tcaaacccaa acatgccatg 4200 caactgaatt gtaacaacaa agccgcaata gacattgcac ataatccagt gcaacaggat 4260 agaaccaagc atgttgaagt tgacagacat ttcatcaaag agaagctcga ggcaaagatc 4320 attgaggtat catttgttaa atccaaagat caatttgcag atgtcctcac caaagcagtc 4380 acaggcagag tatttcacag ctcacttagc aagttgggca ttgacgacac atatgctcca 4440 acttgagggg gag 4453 // ID SINE-3_Mad repbase; DNA; EDCOT; 797 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Putative SINEs from the apple genome. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Nonautonomous; SINE-3_Mad. XX NM SINE-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-797 RA Kojima K.K. and Jurka J.; RT "Putative SINEs from the apple genome."; RL Repbase Reports 10(10), 1823-1823 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~85% identical to the consensus. It is temporary classified as CC SINEs only because it has a polyA tail. XX SQ Sequence 797 BP; 103 A; 215 C; 178 G; 296 T; 5 other; ttctctcctt cgtgagagtt cttctcaccg ctgcgtgtga gtgcatctcc cgcttctgtt 60 ctcctcctcg ctgccgccga tcctagctat ggctagggtt ggtggtagcc ccttgctcct 120 cttgttttcc ttttctttcc ttttgtccct gctcgttttt tcctctacct gctgcctctg 180 gtttcacttc ctcaactccc ctttcttcct ttccttttcc ctccacctnc ttcgtttcca 240 tcactccaca ccctaccctt tccacttggc tcactcctcc antgctctca ccctctagat 300 cggcttccac taatccacac cgtgaacgcg aatcttcgcg attcccgttt aggagggaga 360 tgtgtagagc ttcggatttt ttcgatgctc gggtgttctc accaccttct tgcctcgact 420 tggccttgtt gcctctgttg ctcgtgggtt gtttcctgcg agcttccttc gatttgtggt 480 gccgatcttc gatgtgctct ttggaggttg ttgaagtctt ctttttatcc actttggggg 540 ctcgatttgg cttgctttcn ggcgactggt tcgagtctgg aggtccttcn gatggcagca 600 gcggcggagg atgcggcggc agaggatgca agctgttcgg ttttttttct tttgttttct 660 gttgggcttg gttttgttgt actttggagg tccatacttt tgttgttgtg tttgtgttgt 720 atgtgggcct ctctcttgta antgtgtgtt gttggtaata aaacttgcag cccaatttcc 780 aaaaaaaaaa aaaaaaa 797 // ID SHACOP11_LTR_MT repbase; DNA; EDCOT; 189 BP. XX AC . XX DT 19-JAN-2007 (Rel. 12.01, Created) DT 19-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of LTR retroposon, SHACOP11_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; SHACOP11_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-189 RA Shankar R. and Jurka J.; RT "SHACOP11_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 52-52 (2007). XX DR [1] (Consensus) XX CC The LTR flanks an intact internal region present in the genome in CC low copy number. XX SQ Sequence 189 BP; 63 A; 22 C; 34 G; 70 T; 0 other; tgttggcgtg agttatgcct ctgatatatc atgaggaatc atagggattt gatttgtaat 60 cagaaataat ttaccattat ttcagtctag taaaaatagg ttttttactt gtatatatag 120 aataccttta cactcttgta atgtagattt ggaaagaaat aaaatgagac ctactgtatc 180 agtttgaca 189 // ID Gyp_I_MT repbase; DNA; EDCOT; 11807 BP. XX AC AC144656; XX DT 13-DEC-2006 (Rel. 11.12, Created) DT 14-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Internal region sequence of LTR retroposon, Gyp_MT, from Medicago DE truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; Gyp_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-11807 RA Shankar R. and Jurka J.; RT "Gyp_MT: LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 622-622 (2006). XX DR EMBL/GenBank/DDBJ; AC144656; Positions 50974 62780. XX CC The internal region sequence codes for gag and pol polyprotein in CC two different reading frames. XX FH Key Location/Qualifiers FT CDS join(2379..3815,3819..5864) FT /product="Gyp_LTR_MT_1p" FT /translation="MHHLAFHSLKSKSHTNFLLQKKVSSFQMVAPRIHYKA FT THTHYTRAAVKRKMDHLEQENRALYEEVAAMQIKMGEMAEVIKTMAEAQAQ FT VLAQAQAQALAQAQAHAQAQAPPPPPIRTQVEASSSAIPEWTICADTPTHS FT APQRSTPWFPPFTAGEIFRPIACEAPMPTSQYATHVPPPFATIPQATMTYS FT ALAIHAIPQDNKPIFHSKSMKAYGQVEDLQEKYDEMYREMKALRGKERFGK FT TAYDLCLVPNVQIPHKFKVPDFEKYKGNSCPEEHLTMYARRMSAYAKDDQV FT LIYYFQESLASPVSKWYINLDKTKIQTFHDLCEAFVEQYNYNVEMAPDRSD FT LQAMTQGVKETFKEYAQRWRDVAAQVSPRIEEKEMTKLFLKTLSQFYYEKM FT VGSTPKNFAEMVGMGVQLEEGVREGRLVKDGASASGTKKFGNHFPRKKEHD FT VNVVAHGRAQQTYPIYQHIAAITPTADVIQPPNSPRFPQYPQQNPQQQYPQ FT PTYQQRPYQQQPYQQQQPRPQKMQIDPIPVTYAELLPGLLRKNLVQTKPPP FT PVPERMPAWYRLDQTCDFHQGAPCHNIESCYAFKYAVQRLINDKKITFTDS FT APNIQTNLLPNYGAATVNMVGNCQETHPILDVQHIRTPLVPLHAKLCKVNL FT FKHDHDVCKVCLLNPWGCQKVKDDIQRLLNQGGLVVERKCDDVCVITPEEP FT LEIFYDSRKTFAAPLVICFPGPIPYTSEKAIPYKYNDTMIEGGREVPIPPL FT PSVGNIAEDSRVLRNGRVVPIVFPKKVSIPVIEEAQAKDSSAVKEVSQSNG FT AGASTEFDEILKLIKKSEYRVIDQLMQTPSKISIMSLLLNSEAHKEALMKV FT LEQAFVDYDVSVSQFGGIVGNITACNNLSFSDEELPAEGRNHNLALHISVN FT CKTDALSNVLVDTGSSLNVMAKTTYAQLSYQGTPLRRSGVMVKAFDGSRKD FT VLGEVVLPITIGPQVFQINFQVMDIQASYSCLLGRPWIHEAGAVTSTLHQK FT LKFVRNGKLVTVNGEEALLVSHLSSFSFIGADSVEGTPFQGFTMEEESTRK FT SEASISSLKDAQKVIQAGGSASWGKLIELPKNKRREGLGFFPSADLSKTKT FT VVEPIRGTFHSSGFIHAITKDDPEGVPRSFVTQGGSSRNWVVVDVPFIAHL FT SK" FT CDS join(6434..8005,8009..9247) FT /product="Gyp_LTR_MT_2p" FT /translation="MALKIKEEVQKQIDVGFLVTSKYPQWLANIVPVPKKD FT GKVRMCVDYRDLNKASPKDDFPLPHIDVLVDSTAKSKVFSLMDGFSGYNQI FT KMAPEDKEKTSFITPWGTFYYRVMPFGLINAGATYQRGMTTIFHDMIHKEI FT EVYVDDMIVKSITEEQHVEYLLKMFQQLRKYRLRLNPNKCTFGVRSGNLLG FT FIVSQKGIEVDPDKVKAIREMPAPQTEKQVRGFLGRLNYISRFISHMTTTC FT GPIFKLLRKDQGFVWTEDCQKAFDSIKAYLLEPPILIPLVEGRPLIMYLTV FT LEDSMGCVLGQQDETGRKEHAIYYLSKKFTDCESRYSMLEKTCCALAWAAK FT RLRHYMISHTTWLISKMDPIKYIFEKPALTGRIARWQMLLSEYDIEYRSRK FT AIKGSILADHLAHQPIEDYQPIKFDFPDEEIMYLKVKDCDEPPLGEGPDPK FT SRWGLIFDGAVNVYGSGIGAIIITPKGAHIPFTARLTFDCTNNMAEYEACI FT MGIEEAIDLRIKNLDIYGDSALVINQITEWETRHPGLVPYKDYARRLLTFF FT NKVELHHIPRDENQMADALATLSSMYQVNRWNEVPLVHIRHLERPAHVFAT FT EEVVDGKPWFHDIKCFLQRQEYPLGASSKDKKTLRRLSGNFFLNGDILYKR FT NFDMVLLRCVDKHEADLLMHEIHEGSFGTHSSGHTMAKKILRAGYYWMTME FT ADCYKHARKCYKCQIYANSIHVPPTALNVLSSPWPFSMWGIDMIGRIEPKA FT SNGHRFILLAIDYFTKWVEAASYANVTKQVEVKFIKNHIICRYGVPSRIIT FT DNGTNLNNKMMKELCDDFKIEHHNSSPYRPQMNGAVEAANKNIKKIIQKMV FT VTYKDWHEMLPFALHGYRTSVRTSTGATPFSLVYGMEAVLPIEVEIPSMRV FT LMEAELSEAEWVQSRYDQLNLIEEKRMSALCHG" XX SQ Sequence 11807 BP; 3570 A; 2501 C; 2478 G; 3258 T; 0 other; gcgacttcac tggggatccc ccctaagagg gttaagccta acttggcttt acttaatctt 60 tttgtgctag tacttgctaa aaaataataa atcaaataaa aagatggaaa tatgtgtata 120 tatgttcttt ttttttcctt tttctttctt gtaacgtgag tggtgagata agtcctatcc 180 cgggcttgaa ggaaaaataa gataggagtg gtagaatcat agtgacattc cgagagtatt 240 ctcgtgtttt ggaacatgtg atatgaccac gcttagcgga ggagcttgaa gtgatatatg 300 tcggcgtgtg ttttcacgtt tagactttat tgctcttaag tttccatcga agctaaggac 360 cttttagtaa cccttaaccc atcttggctt ttaagacgta gtgcggtggc taaccaagtg 420 ttgtctggga attagtcgac acgcgatgct acactcaaac gagactttcc tacgaacgtt 480 gttggactgg gtgttgtccc gtcacccaat gaaatttgga gggggttgta gactttggga 540 acttggtaga acctgtgata caagtacaat ttaaaccata gtccttacca aatagcattg 600 tacccttgac tccaacctta tggattcaac cttaccatgt tttctagcat aaacatacat 660 gcatgcatac atgcataaat actttttttt ttttcattaa acatcgaagg acttatataa 720 cctttttgta aacattaaag atatggagaa tgctataagg agaactcata ggtatgaatt 780 caagaaacca gatttagaga gcttaagaaa tctagggagg atggtgaaga atccagaaca 840 ctttcgaaac cggtatggat atctgctcaa tattctcagg acgaatgttg atgaggggct 900 catcaacact ttagtccagt tctatgatcc actctatcat tgctttacat tctcggatta 960 ccagcttgtt cccacacttg aagaatattc ccactgggtc ggtttaccag tactcgacca 1020 agtacccttc catggtcttg aacccggtcc taaaatccca gccattgcaa atgcccttca 1080 ccttgagata gctgatataa agaacaaatt catcaccaga gccggtctcc agtgtctacc 1140 ctacaacttc ctctaccaaa aagccaccat ttgttttgaa agatctgaga ccgatgcttt 1200 tgaggctatc cttgctttac tcatctatgg tattgtgctc ttcccgaatg ttgacaaatt 1260 tgtcgacatg aatgccatcc aaatcttttt aacccaaaac ccggttccaa ccctgcttgc 1320 cgacacttat gtttccatcc atgagcgtac cgataaagag cgtggaacca tcgtttgctg 1380 tgcacctcta ctccacattt ggataacctc acacttacct cgccctaagg ttaaaccaga 1440 atatctccct tggtctcaga agctcatgac ccttacccct aatgatatag tttggtttaa 1500 cccaacttgt gaccctgagc tcatcattga tagttgcggg gacttcaaca acgtacctct 1560 acttggtacg cgtggaggaa ttagctatag cccggttctt gctagacgac agtttgggtt 1620 ttatatggag atgaagcccg tttacctcat cctggacagg gacttcttcc tctacaaaaa 1680 ggatgatgca aatcaaagag cgcaattcaa gaaagcttgg tattccatta tcaggaaaga 1740 tagaaatcag ttaggaaata ggtcggttat tgcccatgaa gcttatgtaa aatgggtcat 1800 cgatcgagct aataaatgga agatgcctta ccctcgccaa aggcttgtga cctcaaccgt 1860 ttcagctata cctttacctt tacctcctga gtccttagaa gggtatcaga aacaattgga 1920 cattgaaagg cgtgagaact ccatgtggga agtgaagtac cgcaagaaga agcaagagta 1980 tgatacggtg aaaaatctac tggatcagca gattcaagcc aattgcaagg aaaagaatga 2040 aaacgctagg ctgaaagcct ctatccaaag gaaggaggat tttcttgaca agatttgtcc 2100 tgggagaaaa aagaggcgca tggatctctt taatggtcca catttagatt cagaagagta 2160 atctacttca ggggctcaag aatttcccaa ttgttcttat cttttatatc gtagcttctg 2220 ttatgaacat tggagtctat cccttggctc agtttgtaaa aagggaatta tcttgtttct 2280 atttataagt ctatcattta tcttttataa tgtttacaaa atttctttta taagtccttc 2340 gataaataaa aaatgcgtct acctttttgc ataacatcat gcatcatctt gcatttcata 2400 gtctcaaatc caagtcccac acaaattttc ttctccagaa aaaggtcagt tcgtttcaaa 2460 tggtggcacc acgcatccac tacaaggcta cccatacaca ttacactcga gcagctgtaa 2520 agaggaaaat ggatcatctc gagcaagaaa atagagctct ctatgaagaa gtggcagcca 2580 tgcagattaa gatgggcgaa atggctgaag tgataaagac aatggcggaa gcacaagctc 2640 aggttctagc acaagcccag gctcaggctc tagctcaagc tcaggctcat gcccaagccc 2700 aagcacctcc tccacctcct atcagaactc aggtcgaagc atcttcctct gctatccctg 2760 aatggacaat atgtgccgac actccgacac actctgctcc acaacgttcc acgccttggt 2820 tcccaccttt tactgctggc gaaatattcc gtcccattgc ttgtgaagct ccgatgccta 2880 cttctcaata tgcaactcat gttcctccgc cttttgcgac aattcctcaa gctactatga 2940 catactcagc acttgcgatt catgctatcc cgcaagataa caaacccatt ttccattcaa 3000 agagtatgaa ggcctatggt caagtggagg atttacaaga gaagtatgat gagatgtacc 3060 gtgagatgaa agctctccgc gggaaagaaa ggtttggaaa aactgcttat gacctctgtt 3120 tggtgccgaa cgtccagata ccccacaagt tcaaagtccc agatttcgag aagtataaag 3180 ggaactcctg ccctgaggaa catctgacaa tgtatgcaag aaggatgtcc gcgtatgcta 3240 aggacgatca ggtccttatt tattacttcc aagagagctt ggctagtccc gtctcaaagt 3300 ggtacataaa tctggacaaa acaaagatcc aaactttcca tgatctgtgt gaagcttttg 3360 tggaacaata caattataat gtggaaatgg ctccagatcg aagtgatctt caggctatga 3420 ctcagggggt caaagaaaca ttcaaggagt atgctcagcg gtggagggat gttgctgccc 3480 aagtcagccc gcgtatagaa gagaaggaaa tgaccaaact cttcttaaaa actcttagtc 3540 agttctacta cgagaagatg gtcggaagta cgcccaagaa cttcgctgag atggttggta 3600 tgggtgtgca gttggaagaa ggagtccgag aaggacgttt agtaaaagat ggagcttctg 3660 ctagtggaac caagaaattt gggaaccact tcccaagaaa gaaagaacac gatgttaatg 3720 tggtagccca tggaagagcc caacaaactt atccaatcta ccaacatatc gctgccatca 3780 cacctactgc cgatgttatt caaccaccaa atagttagcc tcgattccca caatatcctc 3840 aacaaaatcc tcaacaacaa tatccccaac caacatacca gcaacgccca tatcaacaac 3900 aaccctatca acaacaacag cctcgaccac aaaaaatgca aattgaccca atccctgtta 3960 cttacgcaga gttactccca ggattactca gaaagaattt agttcaaacc aagcctcctc 4020 ctccagtacc agaaagaatg ccagcatggt acagacttga tcagacttgt gattttcatc 4080 aaggagcccc atgtcataat attgaaagtt gttatgcctt taagtatgca gtccagaggc 4140 taatcaatga taagaagata accttcacag actcagcacc aaatattcaa accaatctgt 4200 tgccaaacta tggtgctgca actgtcaaca tggtcggaaa ttgccaagag actcacccta 4260 ttctcgacgt tcaacatatc cgaacacctt tggtcccatt acatgccaag ttatgcaaag 4320 tgaacctctt taaacatgat catgatgtct gcaaagtgtg ccttctaaat ccctggggtt 4380 gtcagaaagt gaaagatgat attcaaagac ttttgaacca aggaggactg gttgttgaaa 4440 gaaaatgtga tgatgtatgt gttataactc ctgaagagcc cttggagata ttttacgaca 4500 gtcgaaagac atttgctgct cctttagtga tctgctttcc tggtccaata ccttatactt 4560 ctgagaaggc aattccttac aagtacaatg acactatgat agaaggtggt cgtgaagttc 4620 caataccacc tttgccttct gtgggaaata ttgccgaaga tagtagagtg ctgaggaatg 4680 ggcgtgttgt tcctatagta ttcccgaaga aagttagtat tccggtaatt gaggaggctc 4740 aagctaagga ttccagtgct gtcaaagagg taagccagtc gaatggggcc ggtgcaagta 4800 cagagtttga tgagattctc aagttgataa agaagagcga gtacagggtt attgaccaac 4860 tgatgcaaac tccatcaaaa atatccataa tgtctttgtt actgaattct gaggctcata 4920 aggaagcatt gatgaaggtc ttggaacaag cttttgtaga ctacgatgta agtgtgagtc 4980 aatttggtgg aatagtggga aatatcactg catgtaacaa cctgagtttc agtgatgaag 5040 aactcccagc cgaaggaagg aaccataact tggctttgca tatatctgtg aattgcaaga 5100 ccgatgcttt gtcgaatgta ctagtggata ccgggtcgtc tctgaatgtg atggccaaaa 5160 caacctatgc tcaactctct taccaaggta cacctttgag acgaagtggg gtaatggtaa 5220 aagcttttga tggttcaagg aaggatgttc ttggagaggt ggttctgcct attacaatcg 5280 ggccacaagt tttccagatt aattttcaag tgatggacat tcaggcatca tatagttgcc 5340 tactgggccg accctggatt catgaggctg gagcagtaac gtctacactg catcaaaagt 5400 tgaagttcgt gaggaatggg aagctagtaa ctgtgaatgg tgaagaggct ttgttagtga 5460 gccatttgtc gtctttctct ttcattgggg ctgatagtgt tgaagggacg ccttttcagg 5520 gatttaccat ggaagaagag agtaccagga agagtgaggc ctctatttct tctctgaagg 5580 atgctcagaa agtgatacaa gctggagggt ctgcaagctg gggaaagttg attgaacttc 5640 caaaaaacaa acgccgagaa gggttgggtt tcttcccatc agctgatttg tccaagacaa 5700 agaccgtcgt cgagccgata aggggtactt ttcatagttc tgggttcatc catgcaatca 5760 ccaaagatga tcctgaagga gtgccacgaa gctttgtgac acaaggaggg tctagccgca 5820 attgggttgt tgtagatgtt ccttttattg ctcatttgtc caagtaatgc actttatttc 5880 gtattttatg ctttttaaag aaaatccttt cgccccgccc caagcaaaag tgaatctatc 5940 tagggttttt tgcttcaaga atttatcatc aatcaaataa aaatgtcgtt ttgttcccga 6000 ccttttgcct tgttttcttt tatgttttta gaaaaaatgg taatacaaaa aaccaaaaat 6060 ataatcatat atgcagatta aaaaccaatg aacccgttga acaacatagc cctatgatct 6120 ctcccaactt tgagttccct gtgtatgagg cggaagaaga agagaacgaa gagattcccg 6180 acgaaatctc tcggctactt gaacaagaaa gaaagaccat tcagccttat ggggaagaat 6240 tagaagcaat caacttgggt accgaagaag acaagaaaga gatcaagatt ggggcatcac 6300 ttgatgcaag tgtcaagaag cgagtgatag agcttctcaa agaaacagat atggccctca 6360 agtggtacac catttacctt tgaaacccga gtgtccgccg gtcaagcaga aattaagaag 6420 aacccgtcct gatatggccc tcaagattaa agaggaagtg cagaaacaga tcgatgtagg 6480 tttcctcgtt acatcaaaat accctcaatg gctagccaac atagtgcctg ttccgaagaa 6540 ggatggcaaa gtcagaatgt gtgttgatta ccgtgacctt aacaaagcta gtccaaaaga 6600 tgatttccca ttacctcata ttgatgtact ggttgacagc actgcaaaat ccaaagtgtt 6660 ctccctcatg gatggtttct ccggttacaa tcagatcaag atggcgcccg aagacaaaga 6720 gaagacgtct ttcatcacac cttggggcac tttctattac agagtaatgc cgttcggttt 6780 gatcaatgca ggagctactt atcaaagggg tatgactact atctttcacg acatgataca 6840 caaagagatt gaggtttatg tggatgacat gatcgtcaag tcaatcactg aagaacaaca 6900 tgttgagtat ttgctaaaga tgttccaaca gctaagaaag tacagacttc gtctgaatcc 6960 caacaagtgt acttttggtg ttagatccgg aaatcttctg ggcttcattg ttagtcagaa 7020 aggtattgaa gtagatccag acaaggtcaa agccataaga gaaatgccag ctccgcaaac 7080 agaaaaacaa gtaagggggt ttctcggacg actgaattac atctcccgtt tcatttctca 7140 tatgactaca acatgtgggc cgatattcaa actcctccgc aaggatcaag ggttcgtttg 7200 gacagaagat tgccagaaag cctttgatag catcaaagca tacttactag aacctccgat 7260 tctcatccct ctagttgaag gaagaccact aatcatgtac ctgactgtac tagaagattc 7320 catgggttgt gtgctcggac aacaagacga aactggaaga aaggagcatg ccatttatta 7380 tttgagcaag aagtttactg attgtgaatc tcgctattcc atgctcgaga agacctgttg 7440 cgcactagcc tgggccgcca aacgcctccg tcactatatg attagtcata ctacttggtt 7500 gatatctaag atggatccga tcaagtacat ctttgagaaa cccgctttga caggaagaat 7560 tgcccggtgg cagatgttat tatccgaata tgatattgag tatcgttccc ggaaagcaat 7620 caaaggcagt atccttgctg atcacttggc tcaccaaccg attgaagact atcagcctat 7680 caagttcgac tttcctgatg aagagatcat gtatttgaaa gtgaaagatt gcgatgaacc 7740 accgcttggg gaaggtccag atccaaaatc aagatggggt ttaatatttg acggggctgt 7800 taatgtttat ggtagcggaa ttggggcaat cattattact cctaagggtg cacacatccc 7860 cttcactgcc aggttgacgt tcgactgtac aaacaacatg gcagagtacg aagcatgtat 7920 catgggtatc gaagaagcca tcgatctgag aatcaagaac ctcgacattt atggtgactc 7980 agcccttgta atcaatcaaa tcacatgaga atgggagact cgtcaccccg gattggttcc 8040 ctacaaagac tatgcaagac gattactgac cttcttcaac aaagtcgagc tacaccatat 8100 tcctcgtgat gagaaccaga tggcggatgc tctggctact ttgtcttcga tgtaccaagt 8160 aaatcgttgg aatgaggtgc cattggtcca tatcagacat ctcgagagac ccgctcatgt 8220 attcgccact gaagaagttg ttgatggcaa gccatggttc cacgatatca aatgcttcct 8280 tcaaaggcaa gagtatccac ttggagcatc cagtaaagac aagaagactc taagaagatt 8340 gtctggcaat ttcttcctga acggggacat tttgtataaa agaaacttcg acatggtgtt 8400 gctcagatgt gttgacaaac atgaggcaga cttattgatg catgaaatac acgaaggatc 8460 cttcggaact cattctagcg gacatacaat ggctaagaag atattgagag caggctatta 8520 ctggatgaca atggaagctg attgttacaa gcatgccagg aagtgttata aatgtcaaat 8580 ctatgccaat agcattcatg taccgccaac tgcactcaat gtcctttcct ccccgtggcc 8640 attctctatg tggggcattg acatgattgg aagaattgaa cccaaagctt caaatgggca 8700 ccgcttcatt ctactggcta ttgactattt caccaagtgg gttgaagctg catcttatgc 8760 taatgtgacc aagcaggtgg aagtcaagtt tatcaagaat catattattt gccgctatgg 8820 tgtccctagc cggatcatta cagataatgg gacgaatctg aacaacaaga tgatgaaaga 8880 attgtgtgat gatttcaaga tcgaacacca taattcttcg ccttacagac ctcagatgaa 8940 tggtgctgtc gaagctgcaa acaaaaatat aaagaagatc atccagaaga tggtggtgac 9000 ttataaagat tggcatgaga tgcttccctt tgcattacat ggatatcgta cttctgtacg 9060 cacatcaaca ggggcaaccc ctttctcttt ggtatatggc atggaggcag tacttcccat 9120 agaagttgag attccttcaa tgcgagtttt aatggaggct gaattatcag aggctgagtg 9180 ggttcaaagt aggtatgacc aattgaatct gatcgaagaa aagcgcatgt ctgctctttg 9240 tcatggttag ctgtatcaaa agaggatgaa gcaggctttt gacaagaaag ttcatccccg 9300 tgaattcaaa gaaggtgatc ttgtgctcaa aaagatcttg actttccaac ccgactctag 9360 aggcaagtgg acgcctaact atgaaggccc gtatgttgtc aagaaagctt actcaggcgg 9420 tgccatgact cttcaaacca tggatgtgaa gaacttccac gtcctgtgaa cacagatgca 9480 gtcaagaaat actttgtcta aaagttataa gaacagctcg gtaagtcgaa aacccgaaaa 9540 gggcggctta ggcaaaatga gcgtctcggt gggctgaaaa cccgaaaggg cggctcaagc 9600 aaaaattaga gacattaaac agaaatcatt atcctggtag gctgaaaacc cgaaagggcg 9660 atctatgcaa aagttaagga taaaaagaaa aagacaaagt aactgcgtcc agtcaggcgc 9720 aatccacttg gggcatgtct gctatcaaag aatctccaaa tctgaagcat caaaagcagc 9780 agaattcaag agttgtaagg gggaatgggg ttatgaagtt caatgtacct tcccatttta 9840 aaattaccac tttttttcaa aaaaaatcca tgaagtcatg ccatctgcag gctgtcattc 9900 aatcaataat atttgagccc atggcccttc tgtttgaaat tcccctttta ttctattttt 9960 aaagttcttt ccattgtttg atgataatat ttcgaagtag aattcttaaa aacttttttc 10020 tatgtctctt aaaaaggcat aaatgcacaa gtacatatta ggacttgaga gtgaaggaag 10080 catgcgtcag cacgttcctc aaagaatggt tagaccccac cagacaacca tgattggaca 10140 ctgtgaaaat tcaaaaagag ggcacaacga cggaagtgtg tcaatggaag aacattatgt 10200 atcagcttac aaatggcgac tttttccaga cttttaatgg gttttgtccc cataaggcat 10260 atgtttgtta cttcgccccc aatgaggtca tctccaagga ggtttgccga gtttatagta 10320 ctatgatgtc agtccacttt ccaccttacc agtcttgtct tgtctcatcg agtccatcta 10380 tcatatacaa taaatacatt catgttttcg tacgttaaca cattcataca cccatacatc 10440 catgcatcag cactttcata cattcttaca cagcatatgc atcgcatcat tcgtacacgg 10500 ttgcatcagt cgcacaaagt tttgtttgat aatatcccct cagttcggtc ctcgtttcat 10560 cattatgtca agtggcaagt tctaacaaat gaacagcttg taatcatcat ttacatcaaa 10620 ggtgtcatcc ccagtgtgtc tggtcaagag atgtcacgaa tcaatcaatt tcaagcggca 10680 agtttccgac aaaaggacag cttgaatcta tttttcagtc aatttcaagc ggcaagtttt 10740 cgacaaaagg acagcttgaa tctattttca ttcactttca agcggcaagt ttccgacaaa 10800 aggacagttt gaatctattt ttcagtcaat ttcaagcggc aagtttccga caaaaggaca 10860 gcttgaatcg attttttttc aagcggcaag tttccgacaa aaggacagct tgaatcgatt 10920 ttttcagtca atttcaagcg gcaagtttcc gacaaaagga cagtttgaat ctatttttca 10980 gtcaatttca agcggcaagt ttccgacaaa aggacagctt aaatctattt tttcagtcaa 11040 tttcaagcgg caagtttccg acaaaaggac agcttgaatc tattttcatt cactttcaag 11100 cggcaagttt ccgacaaaag gacagtttga atctattttt cagtcaattt caagcgacaa 11160 gttttcgaca aaaggacagc ttgaatctat tttcattcac tttcaagcgg caagtttccg 11220 acaaaaggac agtttgaatc tatttttcag tcaaattcaa gcggcaagtt tccgacaaaa 11280 ggacagcttg aatctatttt cattcacttt caagcggcaa gtttccggca aaaggacagc 11340 ttgaatctat ttccaatcaa tttcaagcgg atggtttccg acaaaaggac aacttgaatc 11400 catttccagt caatttcaat ttcaatttcg aaagtatcat ccccggagtg aagtcgttct 11460 agtcatgaca ctagtcaatt tcaatcctgg cgtaaagctg tgccagtgat gtcactagtt 11520 agtttcaatc acctatcata catgtagtag ctagacaatt attttcccca gtgaaactac 11580 attcccctag cggagtcgga tccctttctc tagcgagttt tgggtatccc atggttgctt 11640 ctcattccag tcgagtcatc tttgtcatct gcattcgtaa ttgcatcatg tgcattcata 11700 gcatcttagg tcaaaaatgg tgtactctgt atttaagtct cttcgacccg tcaaatcaaa 11760 gattccatct tcaaatctcc ggtcgaagaa acttaaatag gggcatc 11807 // ID Copia-33_Mad-I repbase; DNA; EDCOT; 4006 BP. XX AC ACYM01062820; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-33_Mad_; KW Copia-33_Mad-LTR; Copia-33_Mad-I. XX NM Copia-33_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4006 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1382-1382 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01062820; Positions 5517 1512. XX CC Positions [1445-1942] - Integrase core CC 'AAAAG' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 1466..4006 FT /product="Copia-33_Mad-I_2p" FT /translation="MVYSDVCGPLKVKSLGGASYFVTFIDDHSRKVWAYAL FT KTKDQVLSTFKTFHAMVERETGVKLKCIRTDNGGEYLGPFDEYCKMHGIRH FT EQSVPRTPQHNGVAERMNRTIVEKIRCLLSHAKLPKTFWGEAMRTSCYLIN FT LSPSSPLNGDVPEKVWSKKGVSYGHLKTFGCKASVHIPKEERSKLDDKAKQ FT CVFLGYGDEKFGYRLWDPVSKKVVRSRDVVFFEDQTIEDFEKNAKCDQPYF FT DSLIDFDPISHVVAHDVEGGAEPDKDLDGQENVPADSNAEEIQEEQPTREQ FT DMELRRSNRQRVPSVKYSPHEYVLLTDSGEPECFQEVQYDVHKEEWLKAMQ FT EEMNSLHKNHTYDLVERPKGKKVLPNKWVFKLKETENSKPRYKARLVVKGY FT AQKKGIDFDEIFSPVVKMTSIRVVLGLAASMNLEIEQLDVKTAFLHGDLHE FT DIYMEQPEGFKIKGKEHMVCKLKKSLYGLKQAPRQWYKKFESFMVDNGFKK FT TASDHCVFIQKSSSKDFIILLLYVDDMLIVGPEADKIDKLKKKLSKSFDMK FT DLGPAKQILGMQISRDRKEGKLWLSQERYIEKVLERFNMDKAKSVSCPFAA FT HFKLSNSQCPSTKEEMEEMKKIPYASAVGSLMYAMVCTRPDLAYAVGVVSR FT FLANPGKEHWAAVKWILRYLRGTAKLCLCFGNNKPVLEGFTDADLAGDRDT FT KRSTSGYLFTFAGGAVSWQSKLQKCVALSTTEAEYIAITECCKEMLWLKRY FT FKELGLHQKTFVIYCDNQSAIHLSKNPSFHYKSKHIDIRYHWIRDVLGKKL FT LQLDKVHTNDNKSDMLTKALPKGKHEQCTTSGGLRFFDTSREGGD" XX SQ Sequence 4006 BP; 1324 A; 651 C; 961 G; 1053 T; 17 other; attggcatca gagccgggtt gctttgtaga tcatggatgt caacacaagt cgaatggtga 60 gcctaaatgg aagaaactac attatttgga agtcaaaaat ggaggactta ctgtattgca 120 aggatatgtt cggtccaatt gaaggtgaca agccggaaaa aatgtccgat gaggaatgga 180 agaaacaaaa ccgaagaacc attggagtta tcaggcaatg gcttgatgat agtgtgtatc 240 accacgtttc aaaggagact aacgcacttt cgttgtggaa gaagcttgaa agcttatacg 300 aaagaaagac agcgggcaac aaagtttttt kkatgaaaaa mytwgtcaat ttaaagtttc 360 aaagaaaggc acctccgtca acgaacactt gaacgaaatg caaaacattg tcaatcagct 420 ctcttcaatg aatatggtgt tggatgatga actacaagct ctcctgcttc tcagttctct 480 tccagacagt tgggaaacct tggccatttc tgtgaacaac tctgcttcag atggagtcct 540 gtccatgaat caagttactg ctagtttgct gaacgaagaa acgagaagaa aatccacaga 600 atcctcctac tcagaagctt tggttgtaga gaagaggggg aggaataaaa atagaagtgc 660 ttatcctcag tctcatggga ggtcaagaag caaatcaagg ccaagaaagg atgtcgtatg 720 tcattattgt ggtctaaaag gtcactacag aagagaatgc agaaagctca agaaggaaaa 780 gaaaaatgaa gaaaaacatg aagagaaaga tactgctgct atatcctctg atggtgatat 840 tattgttctc tcggagtgtg aaaaatcatg cttgaatatg tcttatgaag ataccacttg 900 gacagtagac tccggagcct cctttcatgc tacttcgaac aaggcatttt tttcatcata 960 taaggctggt gattttggca tagtgaagat gggaaataag gatacatcaa aaattgcagg 1020 gattggtgaa gtgattctag aaactgatcg tggtagcaaa ctcatgctca tggaggttag 1080 acatgtgcca gacctacgcc taaatttaat ttctgtcgga aagttggatg atgccggata 1140 caagaataag ttttcaaatg ggagatggaa gctcaaaaag ggatccctcg taattgcaag 1200 aggaagaaaa tgctgcactc tgtacagaac ccatgctcaa ctatggaagg gtgagctgaa 1260 tgcaatggaa aakgatgytt cgwtcratct atggcacaag crgctgrgtc atatgagtga 1320 gaagggtttg cagattcttg caaagaaaga aatcctccct gaaattaaag gtaygcacat 1380 aaacagctgc attcattgtt taatwggcaa gcarcataga gtttcytttc aaagaaayca 1440 tgaaagaaaa tcaaatattt tagacatggt ttaytcggat gtgtgtgggc cactgaaagt 1500 taaatccttg ggtggtgctt cttattttgt cacttttata gatgatcatt caagaaaagt 1560 ttgggcatat gctttaaaaa caaaagacca ggtgctgtca acatttaaaa cctttcatgc 1620 tatggtggaa agagagacag gagtgaaact aaaatgcatt cgcaccgaca atggcggtga 1680 gtacttgggg ccatttgatg agtattgtaa aatgcatggc attagacatg agcaatctgt 1740 tccgagaact ccacaacaca atggtgttgc ggaaaggatg aatcgcacca ttgtggaaaa 1800 aataagatgt ttgttgtctc atgcaaaatt gcccaaaact ttttgggggg aggcaatgag 1860 aacatcatgt tatttgatta atttgtctcc ttcatcaccc ttaaatggag atgttccaga 1920 gaaggtatgg agtaagaaag gtgtctcata tggacacttg aagacattcg gttgcaaagc 1980 atctgtgcat atacccaagg aggagagatc aaagcttgat gacaaggcca agcaatgtgt 2040 atttttgggt tatggagatg aaaaatttgg ctacagattg tgggatcctg taagcaagaa 2100 agtggttcga agtcgagatg tggttttctt tgaagaccag acaattgaag attttgagaa 2160 gaatgcaaaa tgtgatcagc cttattttga tagtctgatt gatttcgatc caatttctca 2220 tgttgtagct cacgatgttg aagggggagc tgaaccagat aaagatcttg atggccaaga 2280 aaatgtaccg gcagattcta atgctgaaga gattcaagaa gaacaaccca cgcgtgaaca 2340 agatatggag ttaagaaggt ccaacagaca acgtgtacca tccgtgaaat attcgccaca 2400 tgaatatgtc ctacttacag atagtggcga acccgaatgc ttccaagaag tgcagtatga 2460 tgttcacaaa gaagaatggt tgaaagctat gcaagaggag atgaattcct tgcataagaa 2520 tcatacgtat gatttggtgg aaagaccaaa gggaaagaaa gttcttccaa acaaatgggt 2580 tttcaagcta aaagaaactg aaaactcaaa accaaggtac aaagcgagat tggttgtgaa 2640 ggggtatgca cagaagaaag gcattgattt tgatgagata ttctcgcctg ttgtgaaaat 2700 gacttcaatt cgtgttgttc tgggattggc tgcaagcatg aatctggaga ttgagcaatt 2760 agatgtcaaa acagcctttc tacatggtga tttgcatgaa gatatttata tggagcagcc 2820 ggaaggtttt aaaatcaaag ggaaggagca tatggtctgc aagctgaaaa agagtctata 2880 tggacttaaa caagctccga gacaatggta caagaaattt gagtccttca tggttgataa 2940 tgggttcaag aagacagctt ctgatcattg tgtgttcatt caaaaatctt ccagtaagga 3000 tttcattata ttgcttctat atgtggacga tatgttaatt gttggtccgg aggctgataa 3060 gattgacaag ttgaagaaaa agttaagcaa atcctttgat atgaaggatt tgggacctgc 3120 gaaacaaatt cttggcatgc aaatctctcg agacaggaaa gaaggcaaat tgtggttgtc 3180 tcaagaaaga tatattgaga aagtacttga aaggttcaac atggacaaag ccaagtctgt 3240 aagctgtcca tttgctgctc acttcaagct aagcaacagc caatgccctt caacaaagga 3300 agaaatggaa gaaatgaaga aaattcccta tgcttcagcc gtaggaagtt taatgtatgc 3360 aatggtttgc actaggccag accttgccta tgcagtagga gtggtgagta gatttcttgc 3420 aaatcctggg aaggagcatt gggcagcagt taaatggatt ctaaggtacc ttagaggtac 3480 tgcaaagtta tgtttgtgtt ttggaaataa taagcctgtt ctcgaaggct tcacggatgc 3540 agatttggca ggagacagag acacaaaaag atcaacttca ggctatttat ttacttttgc 3600 agggggagcg gtgtcttggc aatctaaatt gcaaaaatgt gtggcattgt ctactacaga 3660 ggcagagtac attgccatta ctgaatgttg caaggagatg ttgtggttga agagatattt 3720 caaagaactt ggtctacacc agaaaacgtt tgtcatctac tgcgacaatc aaagtgcaat 3780 ccatctcagt aagaatccaa gctttcacta caagtctaaa cacattgata tcaggtatca 3840 ttggattcga gatgtgcttg ggaaaaaatt gttgcagctg gacaaagttc ataccaacga 3900 caacaagtct gatatgttga cgaaggctct tcctaaagga aaacatgagc agtgcacaac 3960 atcaggaggt ttgcgtttct tcgacacgag tcgggaaggg ggagat 4006 // ID HAT-N10_Mad repbase; DNA; EDCOT; 4909 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-N10_Mad. XX NM HAT-N10_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4909 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1632-1632 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~96% identical to the consensus. 12-bp TIRs. Both termini are CC 70-75% identical to HAT-9_Mad and ~80% identical to HAT-N11_Mad. XX SQ Sequence 4909 BP; 1834 A; 807 C; 673 G; 1594 T; 1 other; taggcctggc aattcctgac acgacccgat aacccgacac gacacgacac gaaattaaca 60 ggtgttcggg tcgacacgat aacgaaacgg gtcgttatcg ggtaacccga taagcacctg 120 ttaagataac gggtttgttc gggtatacac gtgggtaaca cgatacacga taagcagaat 180 attaatttaa taatttataa ccctaaaaaa atactataat aattatatat atattaattt 240 aacaatttta tacccctaaa aactataata attatatata tatatatata ttaaattaac 300 tataataatt ataataatta tatatactat aataattata cccaaaatat taactataat 360 aattatatat atatatatat attaaatttt atacccctaa aaactataat aattatacat 420 acaaaataaa tagatttaaa tctacttaat aaataaatat atatatacac acacacacac 480 cattgaactt catgggatac gaattatacg aaactaattt caacgatcca accgtcaaac 540 atgtttgtat atacttcgag atcgcatacg ccaaaaattg caaaaaacaa acattcagag 600 agcaagtaac gggacaaaac ttttcgacgg ttataaacga aaaatcacga tttaacggtc 660 attttaactc cgattttgat gattttttac aaccacactc cttgacccta tatgaataca 720 atgattgaat tcgatcttca atttaaaata tttacactag tggataccac aaaatcttat 780 gttatactta ataaaagtat gaataaactc ttaagtatta gtgaatctat tgttttgatg 840 ggatactcat tctacgaaac tagtttcaat gatccaaccg tcaaacatgt ttgtatatac 900 ttcgagatcg catacgccaa aaattgcaaa aaacaaacat tcagagatca agtaatggga 960 caaaagtttt cgacggttat aaacgaaaaa tcacgattta acggttattt taactccgat 1020 tttgatgatt ttttacaact acactccttg accctatatg aatacaagta atgaattcga 1080 tcttcaattt aaaatattta cactagtgga taccacaaaa tcttatgtta tacttaataa 1140 aagtatgaat aaactattaa gtattagtga atctattgtt ttgatgggat actcattcta 1200 cgaaactagt ttcaaagatc caaccgtcaa acatgtttgt atatacttcg agatcgcata 1260 cgccaaaaat tgcaaaaaac aaacattcag agatcaagta acgggacaaa acttttcgac 1320 ggttataaaa cgaaaaatca cgatttaacg gtcattttaa ctccgatttt gatgattttt 1380 tgcagctaca ctccttgacc ttatatgaat acaatgattg aattcgatct tcaatttaaa 1440 atatttacac tagtggatac cacaaaatct tatgttatac ttaataaaag tatgaataaa 1500 ctattaagta ttagtgaatc tattgttttg atgggatact cattctacga aactagtttc 1560 aaagatccaa ccgtcaaaca tgtttgtata tacttcgaga tcgcatacgt caaaaattac 1620 aaaaaacaaa cattcagaga tcaaktaacg ggacaaaact tttcgacggt tataaaaaga 1680 aaaatcacga tttaacggtc attttaactc tgattttgat gattttttgc agctacactc 1740 cttgacctta tatgaataca atgattgaat tcgatcttca atttaaaata tttacactag 1800 tggataccac aaaatcttat attatactta ataaaagtat gaataaacta ttaagtatta 1860 gtgaatctat tgttttgatg ggatactcat tctacgaaac tagtttcaaa gatccaaccg 1920 tcaaacatgt ttgtatatac ttcgagatcg catacgtcaa aaattacaaa aaacaaacat 1980 tcagagatca agtaacggga caaaactttt cgacggttat aaacgaaaaa tcacgattta 2040 acggtcattt taactccgat tttgatgatt ttttacaact acactccttg accctatatg 2100 aatacaatga ttgaattcga tcttcaattt aaaatattta cactagtgga taccacaaaa 2160 tcttatgtta tacttaataa aagtatgaat aaactattaa gtattagtga atctattgtt 2220 ttgatgggat actcattcta cgaaactagt ttcaatgatc caaccgtcaa acatgtttgt 2280 atatacttcg agatcgcata cgccaaaaat tgcaaaaaac aaacattcag agatcaagta 2340 acgggacaaa acttttcgac ggttataaac gaaaaatcac gatttaacgg tcattttaac 2400 tccgattttg atgatttttt acaactacac tccttgaccc tatatgaata caatgattga 2460 attcgatctt caatttaaaa tatttacact agtggatacc acaaaatctt atgttatact 2520 taataaaagt atgaataaac tattaagtat tagtgaatct attgttttga tgggatactc 2580 attctacgaa actagtttca atgatccaac cgtcaaacat gtttgtatat acttcgagat 2640 cgcatacgcc aaaaattgca aaaaacaaac attcagagat caagtaacgg gacaaaactt 2700 ttcgacggtt ataaacgaaa aatcacgatt taacggtcat tttaactccg attttgatga 2760 ttttttacaa ctacactcct tgaccctata tgaatacaat gattgaattc gatcttcaat 2820 ttaaaatatt tacactagtg gataccacaa aatcttatgt tatacttaat aaaagtatga 2880 ataaactatt aagtattagt gaatctattg ttttgatggg atactcattc tacgaaacta 2940 gtttcaatga tccaaccgtc aaacatgttt gtatatactt cgagatcgca tacgccaaaa 3000 attgcaaaaa acaaacattc agagatcaag taacgggaca aaacttttcg acggttataa 3060 acgaaaaatc acgatttaac ggtcatttta actccgattt tgatgatttt ttacaactac 3120 actccttgac cctatatgaa tacaatgatt gaattcgatc ttcaatttaa aatatttaca 3180 ctagtggata ccacaaaatc ttatgttata cttaataaaa gtatgaataa actattaagt 3240 attagtgaat ctattgtttt gatgggatac tcattctacg aaactagttt caaagatcca 3300 accgtcaaac atgtttgtat atacttcgag atcgcatacg tcaaaaatta caaaaaacaa 3360 acattcagag atcaagtaac gggacaaaac ttttcgacgg ttataaacag aaaaatcacg 3420 atttaacggt cattttaact ccgattttga tgatttttta caactacact ccttgaccct 3480 atatgaatac aatgattgaa ttcgatcttc aatttaaaat atttacacta gtggatacca 3540 caaaatctta tgttatactt aataaaagta tgaataaact attaagtatt agtgaatcta 3600 ttgttttgat gggatactca ttctacgaaa ctagtttcaa tgatccaacc gtcaaacatg 3660 tttgtatata cttcgagatc gcatacgcca aaaattgcaa aaaacaaaca ttcagagatc 3720 aagtaacggg acaaaacttt tcgacggtta taaacgaaaa atcacgattt aacggtcatt 3780 ttaactccga ttttgatgat tttttacaac tacactcctt gaccctatat gaatacaatg 3840 attgaattcg atcttcaatt taaaatattt acactagtgg ataccacaaa atcttatgtt 3900 atacttaata aaagtatgaa taaactctta agtattagtg aatctattgt tttgatggga 3960 tactcattct acgaaactag tttcaatgat ccaaccgtca aacatgtttg tatatatttc 4020 gagatcgcat acgccaaaaa ttgcaaaaaa caaacattca gagagcaagt aacgggacaa 4080 aacttttcga cggttataaa cgaaaaatca cgatttaacg gttaatttaa ctccgatttt 4140 gatgattttt tacaactaca ctccttgacc ttatatgaat acaatgattg aattcgatct 4200 tcaatttaaa atatttacac tagtggatac cacaaaatct tatgtttata cttaataaaa 4260 gtatggtata gtactattgt tttatttttt ttcataatta ttttggtaaa cttctcataa 4320 tttgaatgat ttttaatgtt tggtttttct atgcttagtt tatgcagaag atagttatga 4380 cgtggaaaac cttactgaaa acatcatcaa cataactctt gaaggcaata gatcaagcca 4440 aagttccaat gcaatttcat gatgatcgat gtaaatcgag gattttgtaa attgaggttt 4500 aaacttttga gaaagatttc acaaccttga aaacaaaaac tgtttcattt tgcatatcct 4560 tgcacattta aaatttgtaa tagattagta gtgtatgtat tattttttta ttaggctctt 4620 attttcgagt gtagatgtag tacttaaacg acaaatgtgt tttaatgttt tgaagtaata 4680 tttatgtggc aatgtgtggt atgtgcaaat ttaagaaaaa aaatatattt ttcttaacgg 4740 gtcataacgg gtcataacgg gttgggtcac tttacccgtt gggtaaagtg acacgacctg 4800 ttaaggaccc gttaagataa cgggtgtgac acgacacgac ccgttaagat aacaggtgtt 4860 acacgaaaac gacacgaaca cgactgacac gacccgtttg ccaggccta 4909 // ID EnSpm-4N1_VV repbase; DNA; EDCOT; 3266 BP. XX AC . XX DT 05-FEB-2009 (Rel. 14.03, Created) DT 05-FEB-2009 (Rel. 14.03, Last updated, Version 1) XX DE EnSpm-4N1_VV, non-autonomous DNA transposon - a consensus DE sequence. XX KW EnSpm; DNA transposon; Transposable Element; CACTA; TIR; MITE; KW mCactavine-4.1; EnSpm-4N1_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-3266 RA Benjak A., Boue S., Forneck A. and Casacuberta J.M.; RT "Recent amplification and impact of MITEs on the genome of RT grapevine (Vitis vinifera L.). submitted."; RL Repbase Reports 9(3), 705-705 (2009). XX DR [1] (Consensus) XX CC EnSpm-4N1_VV (mCactavine-4.1 in [1]) is a non-autonomous DNA CC transposon which is a deletion derivate of the autonomous CC EnSpm-4VV. Individual copies are >90% identical to the consensus CC sequence. TIRs are 6 bp-long and flanked by 3 bp-long TSDs. There CC are approximately 30 highly conserved copies present in the CC genome which could place this family in the group of MITEs. On CC the other hand, the size of this element is larger from that of CC "standard" MITEs. We suggest this family be an intermediate CC between deletion derivatives of autonomous elements and MITEs. XX SQ Sequence 3266 BP; 1087 A; 429 C; 489 G; 1251 T; 10 other; cactactaca aaaatagttt atggtgtcac tatttacggt gtcactttta aaataatgac 60 accatagggt ttataattaa taaaggtgac acatcatata aaaaatcttc aattgaggta 120 gttagatgat attaatttta tatttatagt gtcatttttt gggaagtgac atcatataaa 180 ataaattttt ttaagtatta taacttaatg agcccacttt tagaattaat aatgatggat 240 actatataaa aatcccattg tttccatatc tcacccacaa tccaaaaaat ctcaatatat 300 aaatcctata tataaaatca tgatcttctt caaccttttc tctcacccat ccatagtcaa 360 cacgctcama accgacattc ttcactttgt ggactcccag gtaacccaaa atctcttgga 420 tctatcattt ttttttcttt tattaatgyc attatattaa ttgtttcaac atctttgtat 480 tatggttttt gtgaattgtg ttttcttgag ttgtagggaa gaaaaattta ggtttaatct 540 tctagcatrg aagaaaaaac trtagattaa ttgatttttt taatctaaac caaacacatg 600 atcaagtcct taaaaaaaag tgaaaaacag gaaaaaatga atgattttta atatgtattt 660 gtgtgagaat gacaggtaca gaattttttt tragatatac tatcacataa tcttcatcct 720 ttctaaaaaa cgagagagga aaaaaaaaaa gaatgatttt tctgtttgta tctaagtggg 780 aatgagatat agaatttcgt tgagagtatc caaccccaaa aggaccaatc cgggaaggca 840 tgtgtggtat tgacgggaga tgataagatg gaaatcataa ccatagccat gttctctctg 900 tgtctttcta tcctcttcaa ttaattcatg ggcatagata ttttatttag tttttatatt 960 tagtttattt atagtttatt tagtttctaa aatccaatta gytagatatt ttatttgatt 1020 ttgtttttat atttaagtak ttgagttttg gaaagttttt atattttgtt aatagaaata 1080 gaaattttta tattttttat tattaggaat ttctattttg ttaaattgta agtatctatc 1140 tcaataagag attattaata ttcaaatgaa agtgatgaaa gagagtaaat attttaatgc 1200 tcaattatat tttaatgttw tttttttttt tacataaggg tttatttatg ttttcaattt 1260 tgaagttccc tttccaagtc cagcaacaaa agtagtgtcc aaccttaaaa tgggcatgtg 1320 tggtattgac rggaratgat aagatggaaa tcataaccat agccatgttc tctctgtgtc 1380 tttctatcct cttcaattaa ttcatgggca tagatatttt atttagtttt tatatttagt 1440 ttatttatag tttatttagt ttctaaaatc caattagcta gatattttat ttgattttgt 1500 ttttatattt aagtagttga gttttggaaa gtttttatat tttgttaata gaaatagata 1560 tgaggactta aagggtttat atttaggtag tgcttgagcc aaggaaaatg atagtccact 1620 atcttgaccc tatgcatcac aaaccatgtg aggacttaaa ggatatcgta aacatgtaag 1680 ttcttcctat tatttttcat agtattattt ttaaataaaa aaaaatacat tcacctcaaa 1740 cacatttttt ttattattta tatatattaa aacatataac atttacctat tttaaaaatg 1800 tacccattga acttatttac atagggctct tcgaatatct gcaaagaaaa catctaagag 1860 ggagccatct tagcaactag tgcaggtgac atccaaaaat ttttctttac acattagctt 1920 atgcatttgc accatttata tatgtgagta ctaatgttat tttataattg atcgattagt 1980 gtccaagaca agaaggaggg ttcgaatgtg gctactttgt tatgagattc attaaagaga 2040 taatttttta tcctacaatt attgcttcaa aggtattact tatttaatga attgtacata 2100 gttttaggct tccaaatgtt atgcatttta atgttatttt cttatttgat ttcagtttgg 2160 taataaaaaa aaacatattc tcaagtagaa ttatatttcc atttattcat cagaagaagc 2220 gcccttcgat gaaattagag gagaatgggc tacttttgtg ctacaactaa tcatgaatca 2280 tgttgatgca tcatgatcac catgcatggt gagtccctta gctactacat gaatttttcc 2340 ataggtattg tatagtaatg cttattcttt gaataatgtt tctatttgaa aaaaaaaatt 2400 aattcttaga tttgttcatt tatgataaca tagatccatg tttattttct tcaataaaaa 2460 tctctaaaac tcattaaatt ttgaaatgca ggtatacact cttgggaggg tgaaatggag 2520 aataaaaaga aagaagaagg caacaagatt ttgggttttt aaatgcaact cttatgtcat 2580 acgttgtagg acataaacgt tactttaatt gcaactgaga aatttagatt tttagatggg 2640 acttctatgt cattttatgg ttagccggtt ttatgcttat gaaatggagg tatacatgaa 2700 tcttgggatc tttaacattt ctaaatcatg ttttggtatg tattcactct tcttttttag 2760 ttttgatggg tttgatatgt tggacgtact atccttttgt gaacatttga tatacaaata 2820 ttattagatg atcaatgtat tatgagttat tccagaaaca ttacagaaaa atgagttaaa 2880 tataatatga ttgttatatt tatggacaaa atataaacag gttaatctta ttaattcata 2940 agcattacaa aaatcaacaa ctaaaaccaa tcatatattc cacaataatt tacaatgatg 3000 tgataccata actcaaaggt gatgcattta atgtgacatc ataactcaaa gatgatgtat 3060 ttaatgtgac accctatcat cactagaaat atatggtgtc acttctgaat gggtcaccat 3120 ttatctactt tggtgtcact tccaaatacg tcaccaattg gtaccctcta tggtgtcagt 3180 ggagaaggtg acgctatgtt gtagtgacac cttatgttta tggtgactcg ttataaatgt 3240 caccatatac ctttttcctt gtagtg 3266 // ID BoSB8A repbase; DNA; EDCOT; 95 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB8A. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-95 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 95 BP; 22 A; 26 C; 30 G; 17 T; 0 other; gccgggacag aatagcctag tggtaacact agagtgaact ggatcccaag gcacctgggt 60 tcgagtcctc tgggattccg gagaccgccc gtgac 95 // ID Gypsy-1_TC-LTR repbase; DNA; EDCOT; 744 BP. XX AC CACC01004890; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-1_TC_; KW Gypsy-1_TC-I; Gypsy-1_TC-LTR. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-744 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01004890; Positions 18641 17898. XX CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX SQ Sequence 744 BP; 251 A; 108 C; 135 G; 250 T; 0 other; tggctaaata ggagtaatta aacaagagat agaagagata gatggtatcc caccgtgtct 60 agcccaatcc ttttccatta tctcaatttc atttactata aaatgttaat cctaattcta 120 tcttcttcct cttaacaatt gagaatattt ttacatctgc atataattaa gttgctcgtc 180 agcttttata aaatatggga aataattagc cttataatta ggctttgtat gtgattgaag 240 acgaaaataa tggtggggga aaattaaaac caaaaaaggt ccataccttt acttagtgca 300 ggttgtcgaa aggcaatcct ttcggcatgg aaaagggacc aagatttata tattctaatc 360 tatttatagt tttttgtttt taatttatag gttctaatcc atttggtggt aggtgattag 420 gacttcctgg ttataaaatt gtcatgaact caggtcccag caaggtctcc atagataact 480 acagccaatt gattgaagaa gaaaatagtg gaatttaaac ctaaaagcaa gcctagaatg 540 cccagtcttc gtcaaaaggt tccttttgca ggaatttgta gcgtggaaaa aggataaaaa 600 ttatatacta taaattaaaa ctagcagatg gagttaataa tataagtacc agttggttcg 660 tggaaattgg tgtgatcaca aagtgtttga taagtcagtt ttcttttttc tttttaattt 720 ctagtgtact cacatagaaa gaca 744 // ID Copia-54_VV-I repbase; DNA; EDCOT; 4419 BP. XX AC chr4; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-54_VV_; KW Copia-54_VV-LTR; Copia-54_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4419 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr4; Positions 16320928 16325346. XX CC Positions [1905-2435] - Integrase core CC 'CTTAT' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1323..2939,2943..4199) FT /product="Copia-54_VV-I_1p" FT /translation="MFYACQSAAEQKNNVWFLDSGCTNHMTGNKNIFLNMD FT TTINSQVKMGNGDLVNVKGKDTIGIQTKVGTKYIRDVLFVPALEQNLLSVG FT QLVEHGYKLHFENNECTIYDKERRRNLVKKIKMEKNRSFPIVFKYAENVVL FT RMEDVEEAWLWHRRFGHLNFNSLKMLCQRKMVQGLPNTIEEKNEVCDGCAL FT GKHHRQSFPKGVAWRAKKVLELIHTDICGPMSTPSQGNNKYFVLFIDDFTR FT MTWVFFMKQKSEVFSIFKKFKSFVEKQSGCYIKTLRSDRGMEYTSSQFGNF FT CEDEGVERQLTVAYTPQQRGVVERKNQTVMEMAKAMLYEKGLSKIFWAKAI FT NTAVYLLNRCPTKALLNKTPIEAWSGRKPSVRHFKVFGCLCYSQVPKERRS FT KLDETCEKCIFMGYSSQSKGYRLYNLKTNKLIISRDVIFDEKATWNWEEGK FT ILKKTILVDELQTKAPVETGNGSTSTSSPQESPRSVPLSPSIESPTSSSSS FT PSSTPRKMRSLTDVYERCNLCIVEPQSFEEATKDEDWRKAMEKIDVIEQNE FT TWQLVEKPKDKEIIGVKWIFRVKYHSDGRVQRLKARLVAKGYSQQSGVDFH FT ETFAPVARLDTIRTIIAVAAQKGWLLYQLDIKSAFLNGKLEEEIYVEQPQG FT FVVDGEENKVYKLKKALYGLKQAPRAWYTQIDNYFIENGFIRSKSEPTLYV FT KSKDNSQILIVSIYVDDLIFTGNDEKMVEKFRNEMMKKYEMSDMGLLHYFL FT GIEVYQEEDGVFICQKRYVEHILKKFGMAGCNPVSTPLVVNEKLRKEDGGK FT MVDETHFRSLVGNLLYLTATRPNIMFAASLLSRFMHYPSHLHLGAAKRVLR FT YLQGTVELGIKYFRNIEVKLIGHCDSDWGGCIDDMKSTSGYAFSLGSGVIS FT WVSKKQGSVAQSSAEAEYISASLATSQGIWLRRILEDIKEKMKQHIYFVTT FT NLL" XX SQ Sequence 4419 BP; 1527 A; 657 C; 971 G; 1264 T; 0 other; taattggtat cagagcaacc catttcacaa atccacctct caatctaatc ttcgatccac 60 cttgctgttt ccaatctgat ctaatccact tcttcttttc aagccctttt atctcttaaa 120 acatgcctct tgtgtatgga attttaagaa atttcctctg ttttggaaag agtggatact 180 agggtttctt ttaatctgaa gaccaaaatc cgaacctaca atgcagctga attggtgatg 240 ttgctgtgca atcaaattct gtagctagaa accctcaatc ttgaagcaga cggaccaagg 300 acttgaaggg tagatcaatg gccagcacaa gtgttacaag tatgagttct caaccttctt 360 ctattccatt atttgaagga gaaaattata acttttggtg cgtaaaaatg aaaactttat 420 ttatgtctca agatgtttgg gatttggttg aaaatggttt tgatgaacct gacaatgtga 480 tcacactaac tccaattgaa aaagatcagt tgaaagaatt gaaaaaaatg gatgcaaaag 540 ctctcttatt tattcaacaa ggtgttggta ataacatctt tccaagaatt atgagagctt 600 caaaagctaa agaagcatgg gacatccttc aataggagtt ccaagaagac aaaagaaccc 660 ggtcagtaaa gcttcaagct ttaagaagag agctggaaaa catgaaaatg aaggagaatg 720 aaactctaaa tgagttttct tccaaattta tggagttagt aaatcagatg aagtcatatg 780 gtgaagaaat tagtgataaa agaattgttg agaaactgtt gatcagtcta cctaacaaat 840 ttgacccaat tgtggctgtg attgaagaaa caaaagattt ctcactactc tgtgtacaag 900 agctatttgg gtctttaaaa gcttatgaac aaagattgtt gaggcattct gaaaaatcag 960 tagaaagtgc attccaataa aaaataagcc ttaactccag aaatgttgaa aggaaaccta 1020 taagcaatga aaatagaagt gattcatcta gaggtggcag aactggacga ggaagagcaa 1080 gaggaagaga tggaagaggt agaggaagat tcaactatgg aagaaagttt actaacgagg 1140 aaggctcatc attctcaaag tgtaatattt gtaaaagaag tagtcatgtt gaaaaagatt 1200 gttggttcaa agggaagcct caatgcttca attgtaaaaa atttaggcat gtccaaaaag 1260 attgcagatt taagaacaag caacaagcaa gctgtgctga ggagaaagag gctgatgaaa 1320 acatgtttta tgcttgtcaa agtgctgctg agcaaaagaa taatgtgtgg ttccttgaca 1380 gtggctgcac aaaccacatg actggtaaca aaaatatttt ccttaacatg gatacaacca 1440 tcaactcaca agtcaaaatg ggtaatggtg atttagtgaa tgttaaaggg aaagacacaa 1500 ttggcatcca aactaaagtg ggaaccaagt acattagaga tgttcttttt gtaccagcct 1560 tggagcaaaa tttgttgagt gtgggacagc tagtagagca tgggtataaa cttcactttg 1620 aaaataatga gtgcaccatt tatgataagg agcggagaag aaatttagtg aagaagataa 1680 agatggagaa aaatagaagc tttccaattg tcttcaaata tgctgaaaat gtggttttga 1740 gaatggaaga tgttgaagaa gcttggttgt ggcatagaag atttgggcat ttgaacttca 1800 atagcttgaa aatgctttgt caaaggaaga tggtacaagg attgccaaac accattgaag 1860 aaaagaatga agtatgtgac ggttgtgctc ttgggaagca tcatagacaa tcatttccaa 1920 aaggagtcgc ttggagagca aagaaggtat tggagttaat tcacactgat atatgtgggc 1980 ctatgtctac accttctcaa ggcaacaaca agtactttgt tttgtttatt gacgatttta 2040 caagaatgac ttgggtgttc ttcatgaagc aaaaatcaga agtgttctct atcttcaaaa 2100 aattcaagag ttttgttgaa aagcaaagtg gttgctacat aaagaccttg agaagtgaca 2160 gaggaatgga atatacttca agccaatttg gtaatttttg tgaagatgaa ggggttgaga 2220 gacagcttac tgttgcatat actcctcaac aacgtggagt agttgaaagg aagaatcaaa 2280 cggttatgga aatggccaaa gctatgttat atgagaaggg tttgtctaaa attttttggg 2340 ctaaagcaat taacactgct gtgtatcttt tgaatagatg cccaacaaaa gcattattga 2400 acaaaactcc gattgaagca tggagtggaa gaaaaccatc tgttagacac ttcaaagtgt 2460 ttgggtgctt atgttattca caagttccaa aggaaagaag gagcaagctg gatgaaacat 2520 gtgaaaagtg catcttcatg ggttatagtt cacagtcaaa gggttatagg ctgtataatt 2580 tgaaaaccaa taagctgatc ataagtagag atgttatttt tgatgaaaaa gctacttgga 2640 attgggaaga aggtaaaatt ctgaagaaaa caattcttgt tgatgaactt caaacaaaag 2700 caccagttga aactggaaat ggcagcactt caacttcatc acctcaagaa tccccaagat 2760 cagttccatt atctccctca attgagtctc caacttcaag ctcatcatca ccatcctcaa 2820 ctccaagaaa aatgagaagt ttgactgatg tttatgagag atgcaatttg tgcattgttg 2880 aacctcaaag tttcgaagag gcaacaaaag atgaagattg gaggaaagca atggaaaaat 2940 aaattgatgt cattgagcaa aatgaaacat ggcagctggt tgaaaagcca aaagacaaag 3000 aaatcattgg ggtgaaatgg atttttaggg tgaaatatca ttctgatggt agagttcaaa 3060 ggcttaaagc tagattggtt gcaaaaggct attcacaaca gtcgggtgtt gatttccatg 3120 agacctttgc tccagttgct cgccttgata ctattagaac tattattgca gtggctgctc 3180 aaaaaggttg gttgttgtac caacttgaca taaaatctgc atttttgaat ggaaagctgg 3240 aagaagagat ctatgttgaa caacctcaag gctttgttgt tgatggagaa gaaaacaaag 3300 tttacaagtt aaagaaagcc ttatatggtt tgaaacaagc tccccgtgcc tggtacactc 3360 aaattgacaa ctacttcatt gaaaatggtt tcattagaag caaaagtgag cctaccctct 3420 atgtgaagag caaagataat tcccaaatcc ttattgtttc tatttatgtt gatgatttga 3480 tttttactgg aaatgatgag aagatggttg aaaaatttag aaatgaaatg atgaaaaaat 3540 atgaaatgag tgatatggga ttgttgcatt attttttggg aattgaagtc tatcaagaag 3600 aagatggtgt gtttatttgt caaaagaggt atgttgaaca tatcctcaaa aagtttggca 3660 tggctggttg taatcctgta tctactcctt tagttgtgaa tgaaaagttg aggaaagaag 3720 atggagggaa gatggttgat gaaactcact ttagaagtct tgttggaaat ctgttgtatc 3780 tcactgcaac tagacctaac atcatgtttg cagcaagctt gctgtcaaga ttcatgcatt 3840 atcctagtca tttacatctt ggagcagcaa aaagagtctt gagatatttg caaggcacgg 3900 ttgaacttgg aataaaatat ttcaggaaca ttgaagtgaa gctaattggc cattgtgata 3960 gtgattgggg tggctgtatt gatgacatga aaagcacatc aggctatgca ttctcccttg 4020 gttcaggtgt tatatcttgg gtctcaaaaa agcaaggctc agtggctcaa tcatctgctg 4080 aagcagagta tatttcagct tcactggcaa cttctcaagg catatggttg agaagaattt 4140 tagaagacat caaggagaag atgaagcaac atatctactt tgtgacaaca aatctgctat 4200 agccattgca aaaaactatg tttttcatag taggactagg catattgcag tgaagtatca 4260 ttttattaaa gaagctattt cagatggtga ggttcaattg atgtactgta aatcagagga 4320 gcaggttgct gatatcttca ctaaagcatt gcctttggag aagcttgttc acttccgaaa 4380 gcttttgggt gtagaggaac atcacattaa gggggagaa 4419 // ID SINE2-1_PTr repbase; DNA; EDCOT; 197 BP. XX AC . XX DT 11-DEC-2009 (Rel. 15.02, Created) DT 11-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE SINE element from Populus trichocarpa - consensus. XX KW SINE2/tRNA; SINE; Non-LTR Retrotransposon; Transposable Element; KW SINE2-1_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-197 RA Jurka J.; RT "SINE elements from black cottonwood."; RL Repbase Reports 10(2), 238-238 (2010). XX DR [1] (Consensus) XX CC ~98% identical to consensus. XX SQ Sequence 197 BP; 45 A; 47 C; 59 G; 46 T; 0 other; taaccatcta ggtggtggcc cagtggtaag agcttgggac caagaggttt gctccctctg 60 tggtctcagg ttcgagccct gtggttgctc atatgatggc cactggaggc ttacatggtc 120 gttaacttca gggcccgtgg gattagtcga ggtgcgcgca agctggcccg gacacccacg 180 ttaaactaaa aaaaaaa 197 // ID Copia-57_Mad-I repbase; DNA; EDCOT; 4575 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-57_Mad_; KW Copia-57_Mad-LTR; Copia-57_Mad-I. XX NM Copia-57_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4575 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1652-1652 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1525-2025] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 19..3675 FT /product="Copia-57_Mad-I_1p" FT /translation="MDQQSVNVNGAVPKYSEKPEKFKGLDFKRWQQKMLFF FT LTTMNLAHVVKEEAPKSNENPMTRETVMAIEAWNHSEFCCRNYILNSLDDN FT LYDIYSLCKTAKELWESLEKKYKIDDAGSKKFVIGKFLKYTMVDSKSVVSQ FT VEEIQKLIYELHSEGCEINEHFQVGAIIEKLPTSWNDFKIYLKHKRREMNM FT EDLILRLRVEEDHRKADRSGGFAAIEANANYVEGGNSKAKPKKNKAPAPKT FT KQFVQSALAPKGKNLKKIKGACYVCGKSGHKAQDCYHRKDGNHANGNNNNH FT ANMATTDEELAAVVSEVNMVSNVSEWLMDTGATKHICADRNLFTEYHPAAL FT GEKLYMGNSASSAVEGKGKVVLKFTSGKSLTLLNVLHVPEMRRNLVSGPIL FT IAKGFKLVMESNKFVLTKGGMFVGKGYVADGLVKLNVIAIDDANKINASTY FT IVESSNIWHARLGHVNFRSMHRMVKLELLPKFEIDFNHKCETCTESKFARQ FT TRKSILERSNELLGLIHSDLCDFKSTPTRGGKNYYVTFIDDCSKYCYVYLI FT HSKDEALNMFKTYKAEVENQLERKIKALRSDRGGEYESTAFSDFCAQHGII FT HQTTAPYTPQQNGVAERKNRTFKDMINSMLNSSGLPHSLWGEALLTANTIL FT NKVPLKKIDESPYELWKGHKPTYKTLKVWGCLAKVQVPLPKRTKLGPKTID FT CVFIGYANNSAAYRFLVVKSSISDIHVNTILESADAEFFEDIFPYKEKESG FT SNTKRVHDHSHDEASSSGVQGNDVEPRRGKRIKVSKNFGPDFIAFLSENEP FT RTFKEAMSSSEAPLWKEAIKSEMESIMENNTWELVDLPPGSKPIGHKWIFK FT KKLKADGTIDKFKARLVAKGYRQKEGLDYFDTYSPVSRITSIRTLIAIAAV FT YNFDIHQMDVKTTFLNGELDEEIYMEQPEGFVLKGQESKVCKLVKSLYGLK FT QAPKQWHEKFDHTLLTHGFKINESDKCVYIKSNDKTCVIVCLYVDDMLIMG FT SDKDVINKTKKMLNSSFDMKDLGQADVILGIQIKRNSEGYVLTQSHYAEKI FT LRRFGQFDCKPAATPFDAGCKLEKNKGDAISQLEYSQVIGSLMYLMNSTRP FT DLAYAVSRLSRYTSNPAQEHWDALVRVLRYLKNTLDYGLHYTKYPPVVEGF FT SDANWISDTTESKSTSGYVFTLGGAAISWKSSKQKCIARSTMESEFIALDL FT AGEEAEWLK" XX SQ Sequence 4575 BP; 1507 A; 776 C; 996 G; 1294 T; 2 other; atcttgaaac agaaatttat ggatcaacaa tctgtgaatg tgaatggcgc tgtgccaaaa 60 tactctgaaa agcctgagaa gttcaaaggg ttggacttca agagatggca acagaagatg 120 ttgttcttcc tgacaacaat gaatctcgct catgttgtca aggaagaagc tccgaagtct 180 aatgagaatc caatgacgag agagactgtc atggcaattg aagcttggaa tcattccgag 240 ttttgttgca ggaactatat tctgaatagt ttggatgaca atctctacga catttattct 300 ctgtgcaaga cagcgaagga gttgtgggaa tccctggaga aaaagtataa gattgatgat 360 gccggttcaa agaaatttgt tatcggtaag tttctcaaat atacaatggt ggattcaaaa 420 tctgttgtct ctcaggtcga agaaatccag aaattgatct atgaactgca ctccgaggga 480 tgcgagatca atgagcattt ccaagttggg gcgataatcg agaaattgcc aacttcctgg 540 aatgacttca aaatttatct caagcacaag cgtcgtgaga tgaatatgga ggatttgatt 600 ctgaggctac gagtggaaga agaccacaga aaggcagacc gttctggagg gtttgctgcc 660 attgaagcca atgcgaatta tgttgaggga ggaaactcca aggccaagcc gaagaagaat 720 aaggctcctg ctccgaaaac caagcagttt gtacaatctg cccttgctcc taaaggcaag 780 aatctgaaga agattaaggg cgcctgctat gtgtgtggca aatctggtca caaggcacaa 840 gattgttatc atcgcaagga tggaaatcat gccaacggaa acaacaacaa ccatgctaac 900 atggcaacca ccgatgaaga attggctgct gttgtgtccg aggttaacat ggtctcaaat 960 gtgagtgaat ggttgatgga tactggtgct acaaagcaca tctgcgctga cagaaatctg 1020 ttcactgaat accaccctgc tgcccttgga gaaaagctgt atatgggcaa ttctgcctca 1080 tctgcggtgg agggcaaagg caaagtggta ctcaaattca catctgggaa gagtctcacc 1140 ttgctgaatg tgctgcatgt tcctgaaatg aggaggaact tggtttctgg acctattctg 1200 attgctaagg gctttaaact tgtaatggaa tccaacaaat ttgtacttac caagggtggg 1260 atgtttgttg gaaagggtta tgtggctgat ggcctcgtga aactcaatgt aattgccatt 1320 gatgatgcta ataaaataaa tgcttctact tatattgttg agtcttctaa tatttggcat 1380 gctagattag gacatgttaa ttttcgttcc atgcatagaa tggttaaatt agaattatta 1440 cctaaattcg aaattgattt taatcataag tgtgaaacat gtactgaatc gaaatttgct 1500 aggcaaacga gaaagtcaat tctggaaaga tcaaatgaat tacttggatt aattcatagt 1560 gatctttgtg actttaaatc cacaccaact cgtggaggaa agaattatta tgtcactttt 1620 attgatgatt gcagtaagta ttgctatgtt tatttgattc atagcaagga cgaagctttg 1680 aatatgttta agacatataa agccgaagtt gaaaatcaac ttgagagaaa aatcaaagca 1740 cttagatccg atagaggagg agagtatgag tctactgcct tctcagattt ttgtgcacaa 1800 catggaatta tacatcaaac aacggctcca tacacaccac aacaaaatgg tgttgccgaa 1860 agaaaaaata gaacattcaa agatatgatt aattccatgt taaatagttc tgggcttcca 1920 cacagtttgt ggggtgaagc tttacttact gcaaatacca tattgaataa ggttcctcta 1980 aagaagattg acgagtcacc ttatgaacta tggaaaggac ataaacccac ttataaaacc 2040 ctcaaagtgt ggggttgctt agcaaaggtg caagttccgt taccaaaaag aacgaaacta 2100 ggacctaaaa ctattgattg cgtattcatt ggatatgcaa ataatagtgc tgcttatagg 2160 ttccttgttg taaaatcttc gatttctgac atacatgtta acactatatt agaatcagcg 2220 gatgcagaat tctttgagga tatatttcct tacaaagaaa aggaatctgg ttctaataca 2280 aagagggttc atgatcatag tcatgatgaa gcctcttctt ctggtgtcca aggaaatgat 2340 gtggaaccaa gaagaggaaa aagaatcaaa gtttctaaaa actttggacc agatttcatt 2400 gctttcttgt ccgagaatga acctagaact tttaaagaag caatgtcttc ttctgaggct 2460 cctttatgga aggaagcaat taaaagtgaa atggaatcca ttatggaaaa taacacatgg 2520 gaattggttg atttacctcc cggtagtaaa ccaattggtc ataaatggat tttcaagaag 2580 aaacttaagg cggatggaac cattgataag ttcaaggcac gtttagtagc caaaggttat 2640 cgccaaaaag aagggttgga ttatttcgac acctattctc cagtttctcg cataacgtca 2700 attaggacgt taatagcgat tgcggctgta tacaactttg atatacatca aatggatgta 2760 aaaacaacat ttttaaatgg agaactagat gaagaaatat acatggaaca acctgaaggg 2820 tttgtgctta aaggacaaga aagcaaagtg tgcaaattag ttaagtcatt atatggactt 2880 aaacaagcac caaaacaatg gcacgagaaa tttgatcata ctttgttgac acatgggttc 2940 aaaataaatg aatctgataa atgtgtctac attaagagta atgataaaac ttgcgttatt 3000 gtctgcttgt atgtggatga tatgctcata atgggaagcg ataaagatgt aataaacaaa 3060 acaaagaaaa tgttgaattc aagttttgac atgaaagact taggtcaagc cgatgtcatt 3120 ttaggaattc aaattaagag aaatagtgaa ggatatgtcc ttacacaatc ccattatgca 3180 gaaaaaatat tacgaaggtt tggtcaattt gactgcaaac ctgctgcaac tccttttgat 3240 gctggatgca agttggagaa aaataaaggc gatgccatat ctcaacttga atattctcaa 3300 gtaattggaa gtctaatgta cttgatgaat tcaactaggc ccgacttagc ttatgcagta 3360 agtaggctta gtagatatac aagtaatccg gcacaagagc attgggatgc tttagtaaga 3420 gtgttaaggt atttgaaaaa tacacttgac tacggattac actacacaaa atatccacct 3480 gttgtagaag gcttcagtga tgccaattgg atttctgaca ctacagaatc caagtcgaca 3540 agtggatatg tttttacctt gggaggtgca gcaatatctt ggaaatcctc taaacagaaa 3600 tgtatagctc ggtccaccat ggagtccgag tttatagctt tagacttggc tggcgaagaa 3660 gccgagtggc tcaaamattt tctggaggat attccaatgt ggccaaagcc ggtaackgct 3720 atatgtatac attgtgatag tatggccgcg caatcaaggg ccaaaagtca tgtatacaat 3780 gggaagtcac gtcacatcag gcgtcgacat aatactctta agaagttgct ctccaatgga 3840 ataatatcca ttgattatgt gaagtcaaag gaaaatatag ctgatccttt gacaaaaggc 3900 ctaccaagag agcaaatatt atttacatcg aggggaatgg gtctcaagcc aattcaatga 3960 atcgaactgg gcggaaacct aacctagctg attggagatc ccatggtcta ggttcaatag 4020 gcaaactggt tgagtttgat tcaaaagttg aacacacaac ttacccattc ttatgataaa 4080 atgtgtgttg tctgttgacg tttgaggggt tatgttttat acatttaatg acattaatat 4140 cttgttatca agaggaatat ggcagactat tcttaattaa tgtcacctat ataggagtaa 4200 atggggccac atttatgaga attgacatgg ctaaattctc taaagctcct acgaaatccg 4260 ggatctgttc agggccaaaa tgaacacaac cgtatgaatt gacgtgtggc agacatgata 4320 tgtgtgtagc atattgtctc ggtttactac tgcggtgaac agttcaagat cttccacatc 4380 cactgcgtca ccaagtaaac ccgatatgtt ttcactaggg taagttcaag tccaaaagac 4440 acttcacccg atgcatatca tgtctattct ctctcagttt taggcagcct agtcatccat 4500 ttgcatttac atttgcattc aaatgtgggg taattgttgg agtttgaatg aaatttcaac 4560 tcaaatgtgg ggtat 4575 // ID Gypsy-2_Mad-LTR repbase; DNA; EDCOT; 2374 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-2_Mad_; KW Gypsy-2_Mad-LTR; Gypsy-2_Mad-I. XX NM Gypsy-2_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2374 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1735-1735 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 2374 BP; 560 A; 538 C; 497 G; 779 T; 0 other; tgtgacgacc cgtccctaat tttcctatgt aatttctccc cgagtatgtg tattgacggt 60 tatgccctta ttggcaagtg acgtggacgt attcttatcg ctttcatttt atttctcgct 120 atcgcattta aattgtacac gctattacga gtgtgcgtag attttaaagt gtaaaaatat 180 ctatttcgga tagattttga tttcctttta ctgtagaaaa tccgaaaccc tatcccttgg 240 acccttttac ccaacccgtg caccccctcc attattcact ctctcacctc accaatccca 300 tctctccctc atttctgtcc cccaatcaga aaaagagaaa aaggaaactc tctctcttct 360 ctctctccct cccgtatact ccctcttctc tgcaacacct cgaacgagct tcaaagctcg 420 cagatcgaac ccaaaaacca caccattgtg ctcatctcag ccccacgatc acaaccatgt 480 ccttgaaacc tggtgtggac gagttttgac tcaccaactc ggaaggtctg ttcgacgatt 540 ctcgggcaat tactgagtta ggcaagtcct cgagagaccc ttagaacctt cgtttcaatt 600 ctatgggttg atattgatcc cttgtttgtg ttttgaacgt atggttttac ggaagaagct 660 cgagaagaga aaactcgagt ttttcatcaa ggagtgtcac tatttggccg gaactttcaa 720 ggcgtttttc cggtcaacct cgtccacttt ttggactcca aacaggtaca acgcgattct 780 ccactttact agcttcaaat cggcatatga atcactgagt tggttaagag agttagaaat 840 gaattctgga agttaggaag aaatttccag tttccggaaa tccacaaccg tggtcatttg 900 acgacggcga ggccaaattt ccgaacaact cggacgtagt cgaactttct gtcaattgag 960 ttgtacggaa tattcctggc tttaatttgg cgtcgtgtaa gtgctttggt tgagaatcga 1020 gctcgttagg agcttgaaag ttggcccaaa aatctgcaaa actgcagaaa ttcgcgagaa 1080 ggcgagtacg cctgcactcg cgggcgcatg gccgcttgtg cagccccttt ggcggcgcgt 1140 gggggcgcgt cagcctccgg ccagcgtgtg tttgaaacat gtgtgttcgt gacgtcgagt 1200 aggtcacgat ggtatattta aaccctaggt ttgagcaaac tatgggggtt ttatttaggt 1260 ttccgtatat gtgctttaat taattctatt ttagttattt cacatatagg ggaaacgtat 1320 cccgaggatg ttcgaggcca agctaggctc gggggctacg acccagcgac gtacttgtga 1380 gtgggcagtt tgtttttata cctatacata tttatagttt ccataaatgc gtatttactt 1440 cacttttacg cctatattgc caagtatcat tattgtgata taattgtgat aaatgctgct 1500 atatggttgg atattactgt catggcattc atacatattt gtacatgctc atcttgctgc 1560 acccggtgtt agtactcgcc ccagggccag ggccagtcct tcacgtgtat gttcacatcg 1620 caccgttcgc tcgccttgga tccaagttag gtgccagtcc tgtcgggtag attgcattag 1680 gcaatccgac ttgtatgtga ctgtgcttct gcaccagtct tcacgtgatc gtagtactag 1740 agcatattga ttacacccag tcctgttcgt gtcagaaact atctgttcga acttgtgtgt 1800 cagcttagat ggatgagcac ttagctatac ttgattatca catgattata ttattgtggc 1860 atttgataca tcatgacttg gcatatttct ggttataata ctgttataat attgttgatt 1920 tattgtttac atacctacgt agtatgtttt aaggaaacta tacttgtttt acggcgaggg 1980 gttagtatat tcaaagataa aggttttctt ataagcattg ttttgctgac ccactcaact 2040 ttgtttttcg cccctccagg acctagatag ctgtactctt tgtggcactc gaggaatctc 2100 ggcagttctg acattccctt ctgtttagac gtacgaactt atcactgtta tgtaataagt 2160 gtactttggt tgctttgact actcttctgt agtctcactg tctattacgc tctgaataat 2220 tgtagtgggt tcatcccacg aattgcgcac tctttcactg tttagttcta attagtttta 2280 attttattca ctttttgcat cacttaccct tatggttacg tcacctcacg gtgatggcca 2340 gcatgcttcg acctttccag gtcggggtgt gtca 2374 // ID Copia-58_VV-I repbase; DNA; EDCOT; 4122 BP. XX AC chr8; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-58_VV_; KW Copia-58_VV-LTR; Copia-58_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4122 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr8; Positions 16317828 16313707. XX CC 'AGAAG' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 50..4033 FT /product="Copia-58_VV-I_1p" FT /translation="MSSQKFEVEKFNGSNDFTLWKLKMKALLVQQKCAQAI FT EGEEKLPVGLTAAEKEEVVSRAHSAILLSLADEVLREVADETTAVGLWRKL FT ESKYQKKSLTNRLYQKRRLHTLKMSEGMQVRDHFDNFNRIILDLNGVGVKV FT EEEDQAMILLCSLPSSYENFVDTMMYGRDSISINDVKDALQSKELQKLVSG FT SGEGSVEIGLTVSRGRSMERNGGGRSKSRSKSKAEMRCFHCKEKGHFRKNC FT PQRQKRIGQGSNGNAQVVVAQKDSEKQDSSDEGEGGDVLIVSTSSSAESWI FT LDTGASYHMAYSRDLFTTFKEWNGSVKLGDDGELGVKGSGSVQIKMYDGLV FT KTLNAWYVPGLRKNLISVGTLDKNGYTFSGSGGVLRVSKGALVVMKGRLQH FT GIYTLMGSSVLGTAAVSSSMAIDSVEKKDNCTELWHRRLGHMSEKGLSILS FT KQGLLSGAETGKLKFCETCVMGKQRRVKFSMGSHTTKGVLEYIHSDLWGPS FT PVESHSGCRYYVTFIDDFSRKVWVYFLKAKDEAFRKFKEWKTMVEKRIGKV FT VKTLRTDNGLEFCNKDFDEFCRKEGIVRHRTVRHTPQQNGVAERMNQTLVQ FT RARCMRIDSGLSKKFWTEAVNTAAYLVNRSPSTAIDFKTPQEVWSGKPSNY FT SGLKIFGCPAYAHVSDGKLEPRAMKCIFLGYATGVKGYRLWCTEDRTPKFI FT ISRDVTFDESAMFGQRKEFGDLAGTSKTDLGANQKVEFEVDAPMENGVDDT FT SEEQPVIDQNDSQSIAARRPIREIRRPMRYVDCVSANITNPVAFALAVAEE FT IGREEPRSYKEAMESKDSKKWLSSMDDEMASLRKNQTWELVPLPERVKPVD FT CKWLFKIKDGISEDEPPKYKSRLVAKGFSQKEGIDYNEVFSPVVKHKSIQV FT LLAMVSVFDLELDQLDVKTAFLHGNLEEEIYMKQPEGFVDSEKSDHVCLLK FT KSLYGLKQSPRQWYKRFDAFMVSHEFMRNQYDSCVYFKTLPDSSFIYLLLY FT VDDMLIAAKNRAEINKLKQLLSSEFEMKDLGAAKKILGMEIWRDRDAGLLY FT VSQQKYIEKLMQAFHMDHSKPVSTPLAQHFKFDHSTLPSTDEEVEYMKSVP FT YSSVVGSLMYAMVCTRPGLAFAVSVVSRFMSNPGKAHWEAVKWIMRYLKGS FT SSVCLVYGNGDVSSGLVGFTDSDHGGDLMKRRSLTCYIFTLFGCAISWRAS FT LQPTVALSTTEAEYMSLTEGVKEGMWLNGFLGSLGLNLSKPVIYCDSQSAL FT CLAKNPVYHERTKHIDVRLNFIRDVIEEKLFSIEKVATEVNPADMLTKPIT FT TEKFKHSLDLVNVCKV" XX SQ Sequence 4122 BP; 1219 A; 585 C; 1135 G; 1183 T; 0 other; agtggtatca gagcccacaa acacctgggt ttagatctgc agaagaaaga tgtcttcaca 60 gaaattcgaa gttgagaagt tcaatgggtc gaatgatttc accttgtgga agctgaagat 120 gaaggcgctt ctggttcagc agaagtgtgc acaagcaata gaaggggaag aaaaattacc 180 tgtaggattg acagcagcag agaaggagga agttgtgtct agggcacata gtgcgattct 240 gttgagtcta gcagatgaag ttctgaggga agtagctgat gaaactactg cagttggctt 300 gtggaggaag cttgaaagca agtaccagaa aaagtcactg accaataggc tttatcagaa 360 aaggcgattg catactttga agatgtcaga aggtatgcag gtaagagatc actttgacaa 420 ctttaacaga attattttag acttgaatgg agttggtgtt aaagttgagg aagaggatca 480 agccatgatt ttgttatgtt ctttgcctag ctcttatgaa aattttgtag atactatgat 540 gtatggtagg gatagtatct cgataaatga tgttaaggat gctctacagt ctaaagaatt 600 gcagaaatta gtttctggtt ctggggaagg cagtgtggag attgggttaa ctgtgagtag 660 gggcaggagc atggaacgaa atggtggagg acgtagtaag tcgcgttcta aatcgaaggc 720 tgaaatgaga tgctttcact gtaaagagaa agggcacttt agaaagaact gtccacaaag 780 gcagaagaga attggtcagg ggtcgaatgg aaatgcgcag gttgtagtag ctcagaaaga 840 ttctgaaaaa caggatagtt ctgacgaggg agaaggagga gatgttttaa ttgttagtac 900 atctagctct gcagaatcat ggatcttgga tactggtgct tcgtatcaca tggcttattc 960 acgagatcta ttcactactt ttaaagagtg gaacggaagt gtaaagttgg gagatgatgg 1020 ggagctgggt gtcaaaggca gtggttctgt gcagattaag atgtatgacg gattggttaa 1080 gacattgaat gcttggtatg ttcctggact gcgaaagaat ttgatctctg tgggtacact 1140 ggataaaaat gggtacacat tctctgggag tggtggagtt cttagggtgt caaaaggagc 1200 tcttgtggtg atgaaaggca gattacaaca tgggatttac acattgatgg gaagttcagt 1260 gttgggaacg gcggctgtgt caagctccat ggctattgat tctgtagaga agaaagataa 1320 ttgtactgag ttgtggcatc gaagattagg acacatgagt gagaaagggc tctctatctt 1380 gagtaagcaa gggctattaa gtggtgctga gaccgggaag ctgaaattct gtgaaacttg 1440 tgttatgggt aaacagcgta gggtgaagtt cagtatgggt agtcacacta ctaaaggagt 1500 tcttgagtat attcactctg atttatgggg tccttctccg gtggagtctc atagtggatg 1560 caggtactat gttactttta ttgatgactt ctctagaaag gtgtgggtgt actttctgaa 1620 agcaaaggat gaagcgttta ggaagttcaa ggagtggaag actatggtgg agaaacggat 1680 tggaaaagta gtcaagacac tcagaacaga taatgggttg gaattctgta acaaggattt 1740 tgacgagttc tgcagaaaag aaggtatagt gaggcaccgc actgtacgac atacgccaca 1800 gcaaaatgga gttgcagaac ggatgaacca aacacttgta cagcgtgcta gatgcatgag 1860 gatagactct gggttgtcga aaaagttctg gactgaagca gttaacactg ctgcttatct 1920 ggtaaataga tcgccatcga ctgcaattga ttttaagact cctcaagagg tatggtccgg 1980 taaaccctct aattattctg gcttgaaaat atttggttgt cctgcatatg ctcatgttag 2040 tgatggcaag ctggagccta gggcaatgaa atgcatattt ctagggtatg cgactggggt 2100 gaaaggttat cgtctgtggt gtactgaaga tagaacccca aaatttatta ttagcagaga 2160 tgtgaccttt gatgaatctg ctatgtttgg ccagaggaag gagtttggtg atcttgcagg 2220 tactagtaaa actgatctgg gtgctaacca gaaagtggag tttgaggtcg atgctccaat 2280 ggaaaatggt gtagatgaca catctgaaga acagcccgtg atcgaccaga atgattcaca 2340 gagtatagca gcacgtagac caataaggga aatccggaga cctatgaggt atgtggattg 2400 tgttagtgct aacatcacta atcctgttgc ttttgcttta gcagtggctg aagagatagg 2460 aagggaggaa ccaaggtcgt ataaggaggc gatggaaagt aaagactcga aaaagtggct 2520 aagttccatg gatgacgaga tggcatcatt gagaaagaat caaacttggg agcttgtgcc 2580 tttgcctgaa agagtgaaac ctgttgattg taaatggctt ttcaaaataa aggatgggat 2640 ttcagaggat gaaccaccta agtacaaatc aaggcttgtg gcgaagggtt tttcacaaaa 2700 ggaggggatt gactacaatg aagtgttctc acctgttgtg aaacataaat ctattcaggt 2760 cctcttagcg atggtaagcg tttttgactt ggagcttgat caacttgatg ttaaaactgc 2820 ttttctgcat ggaaatctag aagaggaaat ttatatgaaa caacctgagg gatttgttga 2880 ttctgaaaag tctgatcatg tgtgtctttt gaagaagtcc ttgtatgggt tgaagcaatc 2940 ccctaggcaa tggtacaaga ggtttgatgc atttatggtt tctcatgagt ttatgcgaaa 3000 tcagtatgat agctgtgttt actttaaaac attgcctgat agttcattta tttatctgtt 3060 gctatatgtg gatgacatgt tgattgcagc taagaatcga gctgaaatta acaaactgaa 3120 acagttgttg agtagtgagt ttgagatgaa agatttgggt gcagctaaga aaatcttggg 3180 gatggagatt tggagagaca gagatgcagg cttgttgtat gtctcacagc aaaaatacat 3240 tgagaagtta atgcaggctt tccatatgga tcactctaaa ccggtgagta ctccattagc 3300 tcaacatttt aaatttgatc atagtacatt gcctagcact gatgaggagg tggagtacat 3360 gaagagtgtg ccttactcta gtgtggttgg tagtttaatg tatgctatgg tgtgcactag 3420 accaggtctt gcttttgctg ttagtgttgt aagcagattc atgagtaatc ctggtaaagc 3480 tcactgggaa gccgtcaagt ggattatgcg atatttgaag ggttcaagta gtgtatgctt 3540 ggtgtatggg aatggtgatg tatctagtgg attggttggg tttactgatt ctgatcatgg 3600 aggagatctc atgaagagaa gatcattgac ctgttatatt ttcactctgt ttgggtgtgc 3660 aattagctgg agagcttctt tgcagccaac agttgctttg tctacaactg aagcggaata 3720 catgtccttg acagaagggg tgaaagaagg tatgtggtta aatggttttc ttggcagctt 3780 gggtttgaat ttgtctaagc cggttatcta ttgtgatagt caaagtgctt tgtgtttggc 3840 aaagaatcct gtttatcatg agaggacaaa acatattgat gttaggttga actttattcg 3900 tgatgtgatc gaagaaaagt tattctccat tgagaaggtt gccacggaag ttaatcctgc 3960 agatatgttg actaagccaa ttactactga aaagttcaag catagcttgg acttggtgaa 4020 tgtttgcaaa gtttgagctt gaggcccttc ggggcgtagc agatgagtag ttctatattc 4080 tgaattgaaa gaagaaagaa aactcaattc aaagtggaga at 4122 // ID Copia-20_Mad-I repbase; DNA; EDCOT; 4280 BP. XX AC ACYM01133918; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-20_Mad-I; KW Copia-20_Mad-LTR; Copia-20_Mad_. XX NM Copia-20_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4280 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1294-1294 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01133918; Positions 11499 15778. XX CC Positions [1757-1981] - Integrase core CC 'GTTTC' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 2461..3750 FT /product="Copia-20_Mad-I_1p" FT /translation="METVHFSVPFSEANEGISITEIENGVCEETNISSSGL FT SCPNTRSEYVSSVHNDAPNTVNMESEIPLTETYDNTPKKWRDLNEVFAQCR FT LSVIEPENYIEASQDEAWKKAMDEEITMIEKNDTWRLVDRPSDKPIVGVKW FT IFKTKLNLDGTVQKHKARLVAKGYTQKPGIDFNETFAPVARLDTIRTLIAL FT AAQKGWKLYQLDVKSVFLNGILEEEVYTDQPDGYIVKGEEHRVYKLKKALH FT GLKQAPRAWYSNIDTHLLQSGFKKSPSEATLYVKHVDGQGTLIVSIYVDDI FT VYTGSCLEMIEDFKCDMMNKYEMSDLGLLHHFLGIGVIQQEGSIFIHQKKY FT ALSLLDKFGLKSCKSVSIPLPPTDKLRKGDGSEAADEELYRKIVGSLLYLT FT ATRPDILYSACVLARYMHCPSIKHLGTARRILRYVQ" FT CDS join(107..1033,1037..1981) FT /product="Copia-20_Mad-I_2p" FT /translation="MAGSGSGDLRAPVFDGTEFEFWKVRMVTIFKSYGIWK FT LVDKGIVIPDSKKKGEKKKTKKEKDEEDSSSSDDDEGDDDELDAHMEDQLM FT KDAKALGIIQSAVSKEIFPRIVNQETSKGAWDLLQEEFRGDEQARSVKLQS FT LRREFEYMRMKENESLSVYLTRLFELINQMKSYGENLTHQREVQKVLISLS FT SKYDPICVVIERTSYLNTVTVQEVVGSLKSYELRLSRHVDEITSTEHAFST FT MGLVPKAQNRPLTQGNHSKGKKNWKSMSRKWENNTRQPERQGEITEGVKQK FT CKICDKAHHGECWFKGKKCHNCNRFGHVVRDCHQPKKNHTANYLNHVQDNA FT MMFYACHKASVQENNGVWYLDSGCSNHMTSTESLMINIDRSIRCKVKMGTG FT ELVDSVGKGTLIVETKRGTRFIPEVMIVPGLDENLLSVGQMVEHGYWLLFG FT NFMACIFGDRELQDHIATVKMKGNRCFPLMFNHVDHIVANIATTEGNTWKW FT HRRFGHLNYDSLRMLQERSMVYGLPYLKEYNQVCEGCATGKAHREAFSKEQ FT KWRAKLPLELVHTDVCGPMSETLGGSRYFLTFIDDKSRMCWVYFLKCKSKV FT FRIFKMFKAMTELQTGYKLKKIRSDR" XX SQ Sequence 4280 BP; 1398 A; 688 C; 1029 G; 1156 T; 9 other; tggtatccag agcctaggtt cgatttcgga ctgggcgttg aattctgtga aattgtgtga 60 gagaatccaa cgtgaaatct ctccatttca ttccrattca agctaaatgg ctggatctgg 120 aagcggtgat ttacgagctc ccgtttttga tggaacggag ttcgagttct ggaaagtgag 180 aatggtcacc attttcaaat cgtatgggat atggaaattg gttgacaaag ggattgttat 240 tccagattcg aagaagaaag gagaaaagaa gaaaacaaag aaggagaaag acgaggaaga 300 ttcatcctca tcggatgatg atgaaggaga tgatgacgag ttggacgcac acatggaaga 360 tcagctcatg aaagatgcta aggcactggg cattattcaa agtgctgtct cgaaggagat 420 cttccctcgg attgtgaatc aagagacctc aaagggtgcc tgggatctac tccaggagga 480 gtttcgcggc gatgaacagg caagatctgt taaacttcaa agtttacgtc gtgaatttga 540 gtatatgaga atgaaggaga atgaatctct atctgtctat cttactagac tatttgaatt 600 aattaatcaa atgaaatctt atggtgagaa cctcactcat caaagagaag ttcaaaaggt 660 tttgattagt ttgtccagta aatatgatcc aatctgtgtt gtgattgaaa gaacttctta 720 tttgaatact gtgactgtgc aagaagtggt aggatctctt aagagttatg agcttagatt 780 gagtagacat gttgatgaaa ttacaagcac ggagcatgct ttctccacta tgggtcttgt 840 acctaaagca cagaataggc cactcacaca gggaaatcac agtaagggaa agaagaattg 900 gaagtctatg tctaggaagt gggaaaacaa cactcgacag cctgaaagac agggcgagat 960 cactgagggt gttaaacaaa agtgcaagat ctgtgataag gctcatcatg gagagtgttg 1020 gttcaaagga aaacytaagt gtcataactg caacagattt ggacatgtag tgagagattg 1080 tcaccaacca aagaaaaatc atactgcaaa ttatttgaat catgttcaag ataatgcaat 1140 gatgttctat gcctgtcata aggcctctgt gcaagaaaac aatggtgttt ggtatttgga 1200 cagtggttgc agtaaccaca tgaccagtac tgaatcattg atgatcaata ttgacagaag 1260 tataaggtgt aaggtgaaaa tgggcacagg ggaattggtt gactcagttg gcaaaggcac 1320 actgattgtg gagaccaaaa gaggcactcg gttcatacca gaagtaatga ttgtacctgg 1380 tttggatgaa aatcttctca gtgtaggaca aatggttgaa catggctatt ggttgttgtt 1440 tggtaatttc atggcctgca tatttggaga tcgtgaattg caagatcata tagccactgt 1500 gaaaatgaag ggaaatagat gctttccact aatgtttaat catgtggatc atattgtagc 1560 aaatattgct accactgaag gtaacacatg gaaatggcac agaagatttg ggcacctaaa 1620 ctatgacagc ctgagaatgt tacaagaaag gagtatggtg tatggtctgc catatctaaa 1680 ggagtacaat caggtatgtg aagggtgtgc tactggaaag gctcacagag aggcttttag 1740 caaagaacag aaatggagag caaagttgcc attagaactt gtacacacag atgtgtgtgg 1800 acccatgagt gaaacacttg gaggtagcag gtattttctc accttcatag atgacaagtc 1860 cagaatgtgt tgggtctatt ttctgaagtg caaatctaag gtattcagaa tttttaaaat 1920 gttcaaggcc atgactgaat tacaaactgg ttacaaactg aagaaaatca gaagtgacag 1980 atgaggagag tacacatctc tagaatttga aagattttgt gaagatgttg gtattgaaaa 2040 gcaactcact gttgcttatt ctccccagca aaatggtatt gctgaaagga agaatcgtac 2100 catagttgag atggcaagaa ccatgctcta tgaaaaaaaa ttaccactca agttttgggg 2160 tgaagcagtt cacactgctg tctacttgct taacaggtgt cctaccaaag cactagagaa 2220 caagactcct tttgaagaat tctgtggtag aaaaccaggg gtaaaacact tgagaatctt 2280 tggttctgtt tgctacactc atgtgccaac ccagttaaga caaaaactgg acataaatgt 2340 gtatttgttg gatatgggac aagagaaaag ggttacaggg tgtatgatct gaaacacaac 2400 aacatcattg tctcaaggag tgttattttt gatgaagatg ctgctcttaa ttgggagaat 2460 atggaaactg tgcatttctc ggtacctttc tcagaagcta atgagggtat aagcataact 2520 gagatagaaa atggtgtgtg tgaagaaact aatattagtt cctctggttt atcttgtcca 2580 aatacaagaa gtgagtatgt ttccagtgta cacaatgatg ctcctaacac tgtgaatatg 2640 gagagtgaaa ttccactcac agaaacctat gacaacacac caaagaagtg gagagatctg 2700 aatgaagtgt ttgctcagtg tagactcagt gtcattgaac ctgagaatta cattgaagct 2760 tctcaagatg aagcttggaa gaaagcaatg gatgaggaga ttactatgat tgagaagaat 2820 gacacttgga gattggttga tagaccaagt gacaaaccaa ttgttggggt aaaatggatc 2880 ttcaaaacca aattgaattt ggatggcact gtacaaaaac acaaggcaag attagttgcc 2940 aaagggtaca ctcaaaagcc cggaattgat tttaatgaga cgtttgcacc tgtggctaga 3000 ttggacacta taagaacact cattgctttg gcagcacaga aagggtggaa actgtaccag 3060 ttagatgtaa agtctgtttt cctgaatggg atccttgaag aggaagtgta tacagatcag 3120 ccagatggat atattgtcaa gggagaagaa cacagagtat ataagttaaa aaaggccctg 3180 cacggtctaa aacaagctcc cagagcttgg tacagcaata ttgatactca tttgctgcag 3240 agtggattta aaaaaagtcc aagtgaggcc accttatatg tgaaacatgt ggatggacag 3300 ggaactctga ttgtctctat atatgtggat gacatagttt atactggaag ctgtttagaa 3360 atgattgaag atttcaaatg tgatatgatg aacaagtatg agatgtctga cttaggcttg 3420 ttacatcatt ttcttggaat tggagtaatc caacaagaag ggagtatctt tattcaccag 3480 aaaaagtatg cactgagttt actggacaag tttggtttga agagctgcaa gtctgtctca 3540 atacctttac ctcccacgga taagctaagg aaaggtgatg ggagtgaagc tgcagatgaa 3600 gaattgtata ggaaaattgt tggcagcctt ctatacttaa ctgcaacaag gcctgatatc 3660 ttgtactcag catgtgtact tgccaggtac atgcactgtc cttccatcaa acatcttggc 3720 actgcaagga ggatcctcag atatgtgcaa tgaactgttg actatggaat taagtatgaa 3780 aagggaaatg cagctctact cataggattt tgtgacagtt attggagtgg agatgaagat 3840 gacatgaagt ccacatcagg gtatgctttc agctttggca gtggtgcatt ttcttgggct 3900 tctgtaaagc aacaragtgt tgcactctca actgctgaag ccgagtatat gagtgcctca 3960 aaagccacca ctcaagctac atggctgaga tttgtgctgc atgattttgg tgaagaattg 4020 atcgaaccaa ctcctttgat gtgtgataac acatcagcaa ttgcaatgtc aaagaatccg 4080 gtattccatc agaggtctaa acatatcaag aggaartttc atttcatcag agatgcaatt 4140 caagaaggaa caattgacct gcaatactgc aaaagtgagg agyaactagc tgacattttc 4200 accaaagcac ttgctaaaga cagattctgt gctttkrggg awaarcttgg ggtaatctca 4260 gttaagacct tagaagggag 4280 // ID Copia-94_Mad-I repbase; DNA; EDCOT; 4805 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-94_Mad_; KW Copia-94_Mad-LTR; Copia-94_Mad-I. XX NM Copia-94_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4805 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1726-1726 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [2131-2394] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 553..1722 FT /product="Copia-94_Mad-I_1p" FT /translation="MQLVTATLSPVAMSCAIGSASSRELWTRLKEQFSTVS FT KTSIFQMKSNLQTIKKGSDSVTRYLQKIKEARDYLSAAGVFLDDEDIIILA FT LNGLPPEYNTFRTVVRGRESVMTMKEFRTQLLAEEEIVDSHSHVPFLSAMV FT ANNNSSTVHKGSNQAFNSGGGHSFHHTGGQSYGVSGGFKPYVHKNKGKGKF FT NGGQRYYTPRPMYHTQTHVFPTPTPGVLGSSPSAPLLQTCQLCNAEGHTAP FT YCYNKSSDRQQCQICGKFNHTTWYCFYNEKGPSYMGPQYSQRAGTPMQGYS FT YNVPHVLHGSHPSSLQAMNTVFSPTSPSSHMGSVASTSQSPQVWLTDSGAT FT THMTADLNNLSLASPYPSNEVVQTANGEGLRVSHIGSSILNTSKNPI" FT CDS 2574..4805 FT /product="Copia-94_Mad-I_2p" FT /translation="MPTPVLQNQSPFQVLYGQNPVITHLRVFGCSCYPLLR FT PYNTSKLQAKTTKCVFLGYASQYKGYICYEVSKAKFFISRHVVFNETEFPY FT LSLLQLSKQNSVSHVPCSPSSFTPVPNHQNVLVVPLPPVSSSTSPPVPPSP FT DSSVAVHSPHMVASPPFSSLPSSSSITATSSTTPSLPVDHEFSPDRLQVVL FT PIAPLNMHPMQTRSKNGIVKPKVFFSSLAPSGDVDMSLIEPVSYKTAMKSS FT VWLAAMKEEIAALHSQGTWSLVSLPSQKNLVGCKWIFKIKKNSDGSIARHK FT ARLVAKGFSQEEGLDYGETFSPVVKPTTVRLVLALAAQFHWSLRQLDVKNA FT FLHGILQEEVYMAQPPGFADPVHPHFVCKLHKSLYGLKQAPRAWNERFTAF FT LPSLGFISTYSDSSLFVKHVGSEIVILLLYVDDIILTGNATAAIQQVIQSL FT TTEFDIKDLGTLHYFLGIQISCTATGMFLSQTKYVQDLLHKTEMSDCKPCD FT TPCLPYNRLLKDDGVPFSEPGTYRSIVGALQYLTFTRPDIAFSVHQVSQFM FT QNPMVSHFTAVKRILRYLKGTLSSGITYAAGEVGLKAFSDADWAGDPNDRR FT STTGFVVFLGSNPISWSSKKQQTVSRSSTEAEYRAMSSTAAELDWIQQLLT FT FLHIPLSCAPVLFCDNLSAIALSFNPVQHQRTKHIEIDVHFVRERIAQKKL FT LVQFVSSGEQFADILTKGLSAPLFRTHCTNLMLGSSPMHEFEGG" XX SQ Sequence 4805 BP; 1144 A; 1115 C; 913 G; 1627 T; 6 other; tggtatcaat cgccattgtt gctcttgctg ttttcttcga tccttcggct gcttccgctc 60 atcttctcac tctgcgattc tttctcgtcc tcgacgtcga ttcttttctg tatgcttgga 120 cgattctggt attcttcttc gccttctgtg atttctaagg ttcttggtgt ttcttgatct 180 tcttgcatcg gtgtttccag agtgtgcaca ccaggtgttt gtgatatttc ctctcttgga 240 tttctatctt ctttctgcaa aaatggtgac tgcwtctcaa ttacagctcc ttcagtcacc 300 tattactgct ctcatttcta ctatttcaac atctgtcaat gttaagcttg atgattcgaa 360 ttatcttaat tggcatttcc aaatgcaatt attgctggaa agtaatggaa tcatggggtt 420 tgttgatggt tcaacaccct gtcctgctcg atttgcccta attctggtga atctggagtt 480 aattctgcta attcctcctc tgktatagaa acagatgaat atactgtttg gaaattacat 540 gatcgtgcac ttatgcagct cgttactgcc accttgtccc cagtagctat gtcatgtgca 600 attggtagtg ctagttctmg ggagttgtgg actaggctta aggaacagtt ttctactgtt 660 tccaagacta gtatttttca gatgaagtcc aatcttcaaa ccattaaaaa ggggtcagat 720 tctgtcactc ggtatttgca gaagatcaaa gaagcaaggg attatttgtc tgctgctggt 780 gtgtttcttg atgatgaaga cattattatt ttggctctta atggtttgcc tccagagtat 840 aatacattcc gcacggttgt tcgaggccga gaaagtgtca tgactatgaa agagtttcgg 900 actcaactcc ttgctgaaga agaaattgtt gacagtcatt ctcatgttcc ttttctgtct 960 gcgatggttg ccaataataa ctcatccacc gtgcacaaag gttctaatca ggcatttaac 1020 tctggcggtg gtcattcctt tcatcatact gggggtcagt cctatggtgt ttcaggaggt 1080 ttcaagccgt atgtccacaa gaacaaaggg aagggcaagt tcaatggagg tcagcgatac 1140 tacactcctc ggccaatgta tcatacacaa acccatgtct tccctacacc tactcctggt 1200 gttcttggtt cgtcgccctc cgcacctcta ttgcagactt gtcaattgtg taatgctgaa 1260 ggtcacactg ctccttattg ttacaataag tcttctgatc gccaacagtg tcaaatctgt 1320 ggcaagttca atcatacaac ttggtattgt ttttacaatg aaaaagggcc ttcttatatg 1380 ggacctcagt attctcaacg ggcaggtact ccaatgcagg gatactctta caatgtgcct 1440 catgtgttgc atggctctca cccctcttcc ctgcaagcaa tgaatactgt attttctccc 1500 acatcaccat cttctcatat gggctctgtg gcatctactt ctcagtcacc acaagtctgg 1560 ttgacagatt ccggwgctac tactcatatg acagctgatc ttaacaattt gtccttagct 1620 tctccatatc ccagcaatga agttgttcaa actgccaatg gtgaaggttt gcgagtttct 1680 cacattggca gttctattct taacacttct aaaaatccta tcamattaaa ttccattctc 1740 tatgttccta aattgacaca gaatttattg tcagttcata agttgtgttt ggacaacaat 1800 tgctggctaa tctttgatgc attttacttc tggattcagg acaaggtcac agggagaatc 1860 atgtacaagg gcccgtgcag taatggactc tatcctatcc actcactctc tactagcttc 1920 ctaccttctc aatcttcaca tgttgctttt cttggacatc ttgttggttc cagcctatgg 1980 catactaggt tcggacatcc atccaataat gtagtttctt tacttcttaa acaagcaaat 2040 attccatgta ataaggacgt tgtctctcat atgtgtcaaa gttgtctcaa gggcaaattc 2100 acamagttac catttccttc cactcatgtc aagtctgtca taccatttca aattgttcac 2160 agtgaccttt ggggtcctgc accatgtaca tccattgatg gctataaata ctatgttact 2220 ctcattgatg agtgcactcg gttttgttgg ttgtttccct tatccaataa atctgatttc 2280 actgatgttt ttgttacctt ttgtgcattt gtctccactc aattctctac ttctgtgaaa 2340 atactacaaa ctgatggggg ggtgaataca ttagtaataa gctccacact tttctgaaat 2400 ccaaaggtat tgtacatcat aaatcttgtc cctatacacc tgaacagaat gggttagctg 2460 agaggaaaca taggcatatc attgaaacta ctgtcacttt gttacaacat gccacactgc 2520 cttctcaatt ctggaccttt gcttgtcaaa cagcaattta cttaatcaat aggatgccaa 2580 ctccagtttt acagaatcaa tctccttttc aagttttgta tggtcaaaat cctgtcatta 2640 ctcacctccg tgtctttggt tgttcttgct atcctttact tagaccctac aacacttcca 2700 aacttcaagc taagaccacc aagtgtgttt ttctggggta tgcttcccaa tataagggtt 2760 atatttgtta tgaggtgtcc aaagccaagt tttttatctc cagacatgtt gtctttaatg 2820 agactgaatt tccttatctt agtcttcttc aattgtccaa acaaaatagt gtgtcccatg 2880 tcccttgttc accttcatct tttacacctg ttcctaacca tcagaatgtt ttggtggtgc 2940 ctcttcctcc ggtttcttcc tcaacctctc cacctgtccc tccatcccct gactctagtg 3000 ttgctgttca ttctccacat atggttgctt cacctccatt ttcctcctta ccttcttctt 3060 catccattac tgctacatca agtactactc cttctctccc tgtggatcat gagttcagcc 3120 ccgatcggtt acaagtggtg ttacctattg caccattgaa tatgcatcct atgcagacca 3180 ggagtaaaaa tggtatagtc aaacccaagg tgtttttcag ttctttagcg ccatctggag 3240 atgttgatat gtctctcatt gagccagttt cttataagac tgctatgaaa tcctctgtgt 3300 ggttggctgc tatgaaggaa gagattgctg ccctgcactc tcaaggtact tggtctcttg 3360 tatctctgcc ctctcagaaa aacttagtcg gctgtaaatg gatctttaaa ataaagaaga 3420 actcggatgg ttctattgca agacataaag ctcgcttagt tgcaaagggc ttcagtcaag 3480 aggaaggatt agactatggg gagacattca gtccagtggt taagcctacc acagtaaggc 3540 ttgtcctggc cttagctgct cagtttcatt ggtctttaag gcaacttgat gtcaagaatg 3600 catttttgca tggcatactg caggaggagg tttacatggc acaacctcct ggatttgcag 3660 accctgtgca tcctcatttt gtttgcaagt tacataaatc tctgtatggc ttgaagcaag 3720 ccccccgggc ctggaatgag agattcacag ctttccttcc ttctctcggg ttcatctcca 3780 cctattctga ttcgtctcta tttgtgaagc atgttggttc tgagatagtg attttactgc 3840 tttacgtgga tgacattatc ttaacaggga atgctacagc tgctatacaa caggtcatcc 3900 agtcccttac tactgagttt gacatcaagg atttgggcac acttcattat tttttgggca 3960 ttcaaatatc ctgcacagca actgggatgt ttttatcaca aaccaagtac gttcaagact 4020 tgttacacaa gactgaaatg agtgattgca aaccttgtga cactccatgc ttaccttata 4080 atcgtttact gaaggatgat ggagttccat tttcagaacc tggtacatac aggagtatcg 4140 ttggtgccct gcagtacctc actttcactc gtcctgacat tgcattctca gtccatcaag 4200 tgtctcaatt tatgcaaaac cctatggtgt ctcacttcac tgctgtcaaa cgcattctgc 4260 gttatttgaa aggcaccttg tcttctggca ttacttatgc tgctggtgaa gttggtttaa 4320 aagcttttag tgatgccgac tgggctggtg atccgaatga caggcgctct acaactgggt 4380 tcgttgtttt cttgggctcc aatcccatct cgtggtcttc taagaaacaa caaacagttt 4440 ctcgttcgtc aactgaagcc gaatatcgag ccatgtcctc cactgctgct gaacttgatt 4500 ggattcagca acttcttaca tttctacaca ttcctctgtc ttgtgctcct gtgcttttct 4560 gtgataacct gtccgccatt gctctttcgt tcaatcccgt tcaacatcaa cggaccaagc 4620 atattgaaat tgatgttcat tttgttcgtg aacggattgc tcaaaagaag ttacttgtgc 4680 agtttgtatc ttccggagag cagtttgccg atatccttac caaaggtctt agtgctcctc 4740 tctttcggac tcattgtacc aatctcatgc ttggttcttc tcccatgcat gagtttgagg 4800 gggga 4805 // ID Copia-7_Mad-LTR repbase; DNA; EDCOT; 532 BP. XX AC ACYM01099170; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-7_Mad-I; KW Copia-7_Mad-LTR; Copia-7_Mad_. XX NM Copia-7_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-532 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1348-1348 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01099170; Positions 7292 7823. XX SQ Sequence 532 BP; 154 A; 79 C; 125 G; 174 T; 0 other; tgttagacta cgtgtgaatg acaatgagat aacaactagg tttcttgaat cacacgtaaa 60 ctcattgtgc aagttgtgtg gttgaaggaa tctgagatcc ttgatataat aggagttgtg 120 gagtttagtt attgtgcagt caattaatag gagtacttgt tgggtattca ctgagatatt 180 agagtcacga tgggacttaa acttgttata aggatagagt ttatcttcac tactgataat 240 aggccggtaa gtgtggaact ctgcgaggac aaattggtgt atatatacat attgaagaag 300 tccctgcttc cacacaataa gactctcgag aactaaaccc tatttactag tagagatcat 360 cactgtgtgc tggaagtaga agactaattc actggttcat tcaatggcag caccatcagg 420 taagtcgttt tgcagattgc acgtagagtt gtgtgttcgg gttgttcgtg ggtgtaatcc 480 tatcactacg ttgattatgt tgttagcttg tgtgtaataa tatattctaa ca 532 // ID HATSOD1 repbase; DNA; EDCOT; 4792 BP. XX AC AC149267; XX DT 21-SEP-2005 (Rel. 10.09, Created) DT 30-SEP-2005 (Rel. 10.09, Last updated, Version 1) XX DE hAT-type DNA transposon from Solanum demissum. XX KW hAT; DNA transposon; Transposable Element; HATSOD1. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RA Buell R., Liu J., Zaborsky J., Tallon L., Wirtz U., Wei F., RA Kuang H., Zhang P., Wang X., Marano M.R. and Baker B.; RT "None."; RL Unpublished (2004). XX RN [2] RP 1-4792 RA Jurka J.; RT "HATSOD1: hAT-type DNA transposon from Solanum demissum: a RT complete sequence."; RL Repbase Reports 5(9), 258-258 (2005). XX DR EMBL/GenBank/DDBJ; AC149267; Positions 7730 12521. XX CC The coding portion was identified as putative hAT family CC dimerization domain containing protein in ref. 1. Here a CC full-size sequence is reported, including TIRs. The sequence CC shows significant similarity to a human protein described by Acc. CC Nos.: AAH37313, CAD97777, CAI12902 and CAI12903. XX FH Key Location/Qualifiers FT CDS 1699..3813 FT /product="HATSOD1_1p" FT /translation="MRRFNHEWFDDIYHDWLEYSVSKDAVYCLYCYLFKDH FT NTNQGGGETFSTIGFKSWNKKSGLDKHIGLPNSIHNQSKKKCQDLLQQRRS FT IQFAFERQSNQLKHRYYMRLSASVDVVRLLISRGFAFRGHDESKSSLSRGN FT FLEILSWYAKRCDKIRDYILEHAPVNDQMTSPMIQKDIVSACKIETVKAIL FT EELNGDYFALLVDESFDVSHKEQMAIIFRYIDRMGFVMERLIDIVHVKDTS FT ASSLKETIFNLLAQHSLSPSSVRGQCYDGASNMQGEINGLKMLIRRESKSA FT HSIHCFAHQLQLTLVGVSKKCVEVGKLVVLISNIFNVLGSSFKRMDNLRDS FT QKSTIQVALDMGELTTGSGLNQQLGLSRACDTRWGSHYKSFNNFIIMFGSI FT LEVLESLALDARSMDERAKAMGHLEACQTFEIAFMLHLMRDVLAITNELNK FT CLQKKEQDIANAMLLVEVAKRRLQVLRDDEWDSLIAKVSTFCIKHNILIPN FT FEEPYVSSLRSRRKLANYTILHHYRVEVFCNIIDWQLQELNDRFDEVTTDL FT LHGIACLNPIKSFSSFDIRKKMRMAELYPDDFDESNMNILENQLASYIVDV FT RDVDERFFDLNGLCDLSKRLVQTKKHSNYPLVFRLVKLALLLPVATASVER FT AFSAMKFIKNDLRSQMSDDFFSGCLVPYLEKDVFDKISNDVIIKTFQDMKP FT RRIQL" XX SQ Sequence 4792 BP; 1459 A; 722 C; 886 G; 1725 T; 0 other; cataatacat aaattggacc ctaaacttgg cttcaaattt taagtatgac ctctaacttt 60 caaagtgcac aagtaggcac ttcaactatc caattcttaa acaaaaaaac acgcgaatcc 120 aacctggcat aatgcgtgat tgagacgcaa tttaggcacg tcaggggtat ttttcgaggc 180 ccacaacagt aaaaaaaaga accggaaatg acaattttac ccttaatgaa tcccttttaa 240 atatatcttt atttttttca aatcaaaatc ccatttttct tcttcttcct aattctagta 300 ctcaagcttt ttttctcttt ttgtgcacaa tttctggtcg ttttttatgt aatggcttct 360 aatttttttt gtcattgtgt aaaaagagct ataatgaaga tttcttggtc tgcaaataat 420 tcaggtataa aaaaaagtga atttacattc atggtgacca ggggcggatg tacagtgcta 480 cgaggggggt catccgaccc ccctcggaaa aaaaattaca ctatatatat aagattgatt 540 tttttttgta catgtatata tttaaaattg aaccacctaa atacataaca aaggtgtagt 600 ccaatggttg agggggtgca aaatttcgct attgtgagcc ttgggtcgcg ggatcgattc 660 caggcaacaa cataattttt ttttgtaatg tttagctatt ttgcagtctt taaatagacc 720 aaaacgaccc cgttttaatt ttataactaa aaaaaaaatc atattttaaa tcataatgaa 780 aatgtcaaca aataaatata tccctctttt ttagggattg caatatttat tttttctaat 840 attgatttct ctcttgttca acgctgttgg gctagctttg ctgctgctga gtgcttgtgc 900 tgcctggcgg ctgttgcttg caagttgctg acttgctgtc gagtgctgac tgccgactgc 960 cgtggtggtg tggtgccgtg ccacctgttg ctgctggcgc ctggctgctg ctgctgcttg 1020 gtggaggatt ggtggtccat tagtgatggc aacggtaagt tttcattttg gttttttttt 1080 ttttttcaaa attctatgct ttgattcttg tatttgttga tgtgctattt tatgtagctg 1140 attgaacttg gatattcact taacaatttt ttatttttca tatgaaaatt tcaattatat 1200 tcactgatta tgaaagttat aattttattt gtttgggttt atttgttgat ttaatatgtt 1260 aattatggac attcaacatt tgttcagtag atattaactt ttatttatga gattcaaact 1320 tttggtcatt gtctataatt ttgttttggt ccttattgca tattcaattc ttgtaagttt 1380 tgactaaatt tttattttac gattcagtct caatattcag tgaagaagta ttttacacaa 1440 gtaccgaaat caactttagc ctctcaaagt catagtcaat ccaatcaaaa agaaaatact 1500 aatcattcag aagtgtcatt agattcttct caagaatttg atttgagttc tttaaagttt 1560 gatcctggtg aaagaacatc aatattgaat tatcatccaa accaccgtga tgttattaga 1620 agagcatacc ttttgaatgg tccttgtcaa cctcgtttgg cggtgcaaaa gtatcctcaa 1680 acaaatattt ttggatcaat gcgtcgtttt aatcatgaat ggtttgatga tatatatcat 1740 gattggttgg agtatagtgt tagtaaagat gcagtctatt gtttgtattg ctatcttttt 1800 aaagatcata acactaatca aggaggaggg gagacatttt caactatagg atttaagagt 1860 tggaacaaaa agagtggtct tgacaaacat attggtctac cgaatagcat acataatcag 1920 tcaaaaaaga aatgtcaaga tttactacaa caacggcggt ctattcaatt tgcatttgag 1980 aggcaatcta atcaactcaa gcatagatat tatatgcgct taagtgcgtc ggttgatgta 2040 gtaagacttc tcataagtcg gggatttgca tttcgaggtc atgatgaatc taaatcatca 2100 cttagtaggg gtaactttct tgaaattctc tcatggtatg caaaaagatg tgataaaatt 2160 cgtgattata ttttggaaca tgctcctgta aatgatcaaa tgacttctcc aatgattcaa 2220 aaagatattg tgagtgcatg taagatagag accgttaaag ctattcttga ggaattaaat 2280 ggtgactact ttgctttact agttgatgaa tcctttgatg tgtcacacaa agagcaaatg 2340 gctatcatat ttcgttatat tgatagaatg ggctttgtaa tggagcgact tattgacatt 2400 gttcatgtta aagatactag tgcttcatct ttaaaggaga caatttttaa tttacttgct 2460 caacattctt tgagtccatc aagtgtgcgt ggacaatgtt acgatggggc aagtaatatg 2520 caaggtgaga tcaatggcct taaaatgttg attagacgag aaagtaaatc ggctcattca 2580 atccattgct ttgctcatca acttcaacta actcttgttg gggtctctaa aaagtgtgtt 2640 gaagtgggaa aacttgtagt attgatctca aatattttta atgtattggg atcttctttt 2700 aagcgtatgg ataatttacg agattctcaa aaatcaacaa ttcaagtggc attagatatg 2760 ggtgaactta caaccggtag tggcttgaat caacaacttg gtctttcaag agcttgtgat 2820 actcgttggg gatctcatta taaatccttt aacaatttta ttattatgtt tggctctatt 2880 cttgaggttc ttgaatcact tgctcttgat gcaaggagta tggatgaaag agccaaggca 2940 atgggacatc ttgaagcttg tcaaacattt gagattgcgt ttatgttgca tttgatgaga 3000 gatgtcttag caatcacaaa tgagcttaat aaatgcttac aaaaaaaaga gcaagatatt 3060 gcaaatgcca tgctacttgt tgaagtagca aagagaaggt tgcaagtctt aagagatgat 3120 gaatgggatt ctcttattgc caaggtatct acattttgta tcaaacataa tattttgata 3180 cctaactttg aggaaccata tgttagctct ttaagatcac ggcggaaact tgctaactat 3240 acaatcttac atcattatcg tgttgaagtg ttttgcaata tcattgattg gcaacttcaa 3300 gaacttaatg atcgttttga tgaggtgact accgatttgc tccatggaat tgcttgcttg 3360 aatccaatta aatcattttc aagttttgac ataagaaaaa aaatgagaat ggctgaatta 3420 tatccagatg actttgatga atccaatatg aatattcttg agaatcaact tgcaagttac 3480 attgttgatg ttcgtgatgt tgatgaaagg tttttcgatc taaatgggct ttgtgatctt 3540 tccaaaagat tagttcagac aaagaaacat tcaaattatc ctcttgtatt tcgcttagtg 3600 aaacttgctc tacttttacc agttgccact gcctccgttg aaagagcttt ttcggcaatg 3660 aagtttatca agaatgactt gcggagtcaa atgagtgatg atttttttag tggttgtttg 3720 gtgccttatt tagaaaaaga tgtatttgat aagatttcta atgatgttat tattaagaca 3780 tttcaagata tgaaacctcg tagaatacaa ttgtaaaaag gtatgtagtt gtattttcaa 3840 atgtaaaact atattttgat aggtttatcc gcatgtttgg tttcttaacc tcccttcaag 3900 gttgtgtagt tttgtgatgt aatgaagtca ttttatgcca agaagaattt tgtgaagaaa 3960 tagtattttc gctttgattt ttgtttttgg ttagtctttc taatgttaaa tttgtgcttg 4020 ctctaatgct ctccatttgc actttcaaga gccgaagaga attctaaagg aattgaagaa 4080 cttgtagaac tttttgaatg agttgtgcta ctttattatc attttataga tatatacttc 4140 aaatttgttt cttaagataa attgtaatgg taagaaatta tttgaactaa ggattttttt 4200 ttgtcaaccc gtttgttaat caatccgttc ataacttcat atatgacccg acccgtttat 4260 ttatgaataa tattagcgtg tttaactttt tttttgaacc cccttgatag aattcctgga 4320 tccgccactg atggtgacaa cttctaccaa aaataaactt tcaaaaagca aaaattgaca 4380 taactagact aaattgagga agaacaacac ataaacattc aaaagataag aactttgacc 4440 acaaatcttc acaattttac tttgatttgc aaagaaatta gggctagggc tccactgatg 4500 ttgagtgaaa atcgagcaaa ttgggaatag aaaatacgac cctacccttt tgtattttaa 4560 ttttttcttt tttttaatta taaaatacgt gtaatttttt aattacgtgg catccactga 4620 gtggctcaat aagccacgta ggagcgtttg tatatcacac aatttggctg ttggattcgc 4680 gtgttttttt gtttaagaat tggatagtta aagtgcctac ttgtgcacta tgaaagttag 4740 aggtcatact taaaatttga agccaagttt agggtccaat ttatgtatta tg 4792 // ID Copia-4_Mad-I repbase; DNA; EDCOT; 4889 BP. XX AC ACYM01011892; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-4_Mad-I; KW Copia-4_Mad-LTR; Copia-4_Mad_. XX NM Copia-4_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4889 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1284-1284 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01011892; Positions 14453 9565. XX CC Positions [1961-2461] - Integrase core CC 'GTATC' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 1130..2818 FT /product="Copia-4_Mad-I_1p" FT /translation="MTAHVSGHVGPKTQQDKAGSSGIAAVAAGQPRPNVSH FT LATTEAQSAGRVLEATSKIDDSGPLLSLINQISMHENSEDSGKIGTVLILS FT TKRDTGWIIDSGATDHMTYDTSLFYHMTTPSKEDVITANGDIAPVTGAGSI FT SLTPSLSIHNALLVPSLSNHLLSVGQVTEQLDCVVLMFPTFCLLQDIQTRA FT IIGRGTKRRGLYYVDDVSASRVNQVRSSQSNKDKTIWLWHRRLGHASFGYL FT KRLLSSLFCGISDSDFQCKDCILAKSHRTSYHLSLNKRTVPFELVHSDVWG FT PSPVATIHGVRWFIIFVDDCTRMTWLYNLKHKSEVGKNFQQFYHMVENQYS FT LPLKVLRSDNGGEYLSTELSQFFQDHGILHETSCPHTPQQNGVAERKNRHI FT LETTRALLIGAHAPHSYWVEAVKYAVYLMNPMPTRIHNFRTPTEVFADHVT FT LTSSLQLLPRIIGCVAYVHLHKNQRSKLDPCVVRCIFLGFTGQQKGYRCYH FT PPTKHTYITMDVTFSEHEMFFVTDHTNYNLQGELNTHEDYSWIDLPTGQPR FT ETQQDACHGTGQPRET" XX SQ Sequence 4889 BP; 1420 A; 959 C; 1151 G; 1326 T; 33 other; tggtatcaag agcaggttcg gcctgccttt gacaatcaca aacacccagt aaaactctct 60 cacggtttga atatcagact gtgttagaaa caaccaaatt gaatcgcagc ctttgtaaac 120 atcaaagcct gtgaaaatct aattaaaacc cattctagaa agttgtgcga tggctgaaga 180 acataaggca agcttgattc ccgtgcatac cgtgtccaac caaggcgaat ctaccaacat 240 caatgccatt cctttcgggt atcggttgag tgactcgaac tttaaagtat ggtcgaagat 300 gatgaaggtt catgcttcag ggttcggcaa gctagggtat ctaacaggga aaattccgat 360 ggtcgaggaa gatgatccgg gatatgcaaa gtggtcaatt gaagatgcta ttgtgagagg 420 atggttgtta aaaactatgg aaccgcatct acttggtctc tttatcgacc tacccacagc 480 aaaagatatt tgggagagtg tcacccagat gttttatgat ggttctgatg agtcgcaata 540 ttatgaactc cgatgtaagg ctacacggac cagacaagat ggtcgcccag ttaatctgta 600 cttcactgaa ttaaagggtg tatggcaaga tcttgacaaa agacgtcctc ttcgtatggt 660 ttgtggagca gatttgagaa ctcgtaaaga ggaaattgca aaggataggg tgtacgattt 720 tcttgctggg ttagacagtg gtttcgatca agtacggagt gagattctaa ggataaagcc 780 tatccctgga atcgaggaat gttttaatct agtacgacgt gaagctcagc ggcaggccac 840 tatgatggga acaaagagca tcacggcakg accttctatg gctatggcaa ctaaagtrca 900 aagttatcgt tcaccatcmt ttggaaactc tcggtcatca cgtacgcakg aggatattga 960 taaagataaa ctccattgca atcactrtaa tggaacycga cacayggagg aaacctgttt 1020 tgaaattcat ggttacccag aatggtactg ggaaaggaag aaagaattaa aagctaaggg 1080 gaataaacgt acctcgggtc aggttcgtgt ggcagctact ggacagggga tgacagcaca 1140 tgtaagtggc cacgttgggc ccaaaaccca acaagacaag gcaggtagca gcggcattgc 1200 agctgtagcc gcaggccaac cgaggcccaa tgtgtcacac ctggccacga cagaagccca 1260 atcagcaggc cgagtcttgg aagcaacatc caaaattgat gactccggtc cattattatc 1320 tctcatcaac caaatttcaa tgcatgaaaa ctcggaagac tcaggtaaaa tcggtactgt 1380 tttaatattg tctaccaaga gggatactgg ttggataatt gactctggag ctacagatca 1440 tatgacttac gacacatcat tattttatca tatgacgaca ccttctaaag aggatgtcat 1500 cacagccaat ggtgatattg ctcctgtcac gggagctggt tctatttccc ttactccatc 1560 tttgtctatt cacaatgcac tacttgttcc atcgttgtcc aatcatttac tatctgttgg 1620 tcaagttact gagcaattag attgtgttgt gttaatgttt cccacttttt gtctacttca 1680 ggatatccag actcgggcga taattgggcg tggtactaag aggagagggt tatactatgt 1740 ggatgatgtg tccgcaagca gagtgaacca agtgcgcagt agccagtcaa acaaggataa 1800 gacaatctgg ttatggcatc gtcgtttggg ccatgcctct tttggttatt taaaaagatt 1860 actttcgtct ttattttgtg gcatttcaga ctctgatttt cagtgtaagg attgcattct 1920 ggcaaaaagc caccgtactt cttatcattt gagtttaaat aaaagaacag tgccgtttga 1980 gttagtccat tctgatgtat ggggaccttc tccagttgct actattcatg gtgttcgttg 2040 gtttattatc tttgttgatg attgcaccag aatgacatgg ctttataatc tgaaacataa 2100 aagtgaggtt gggaaaaatt ttcaacaatt ttatcacatg gttgaaaatc aatactctct 2160 tcctcttaag gttctccgat cagataatgg tggcgaatat ctcagtactg aactctctca 2220 atttttccaa gatcatggca ttcttcacga gacttcttgt ccacacaccc cacaacaaaa 2280 tggggtcgct gaacgcaaaa atcgacatat tctggaaacc actcgagcac ttctcattgg 2340 tgctcacgcc cctcactctt attgggtaga agctgttaaa tatgcagttt atttgatgaa 2400 tccaatgccc accagaatac acaatttccg cactcctacg gaggtatttg ctgaccatgt 2460 gacattaacc tcttcccttc agttgttacc ccgtattatt gggtgtgtgg cctatgtaca 2520 tctccacaaa aatcaacgta gcaagttgga cccatgtgta gttcgatgta tttttttggg 2580 atttactggc caacaaaaag ggtaccggtg ttaccaccca cccaccaagc atacctatat 2640 caccatggat gttacgtttt ccgagcatga gatgttcttt gtcactgatc acaccaacta 2700 taaccttcag ggggagctaa atacacatga agattacagt tggattgatc tccctactgg 2760 gcagccacgt gaaacccagc aggatgcctg ccacggtact gggcagccac gtgaaaccta 2820 gcagaatgct tgccacgcga acagccagca aggccgactt ctgccttctg gtgaaatcca 2880 cgggcctgaa cccattagtg taggtgaggc cccatctttg aaaggttgtg cagcagccag 2940 tgagaccata tttgggagtg ggcctgacgg catggcaaca ggtgagcagt ttggtgcaca 3000 gcccagtgca cggttagaaa caccatatca aggcgacagt gaactgcaac cattagttca 3060 tagtttggac gactagtaca cttcaagaaa taaatcctct ccagttgtac ccgtccatgt 3120 gcccgaggat atccatgagg taagtttatc tcaacctaat gaagctcgtg atttgactaa 3180 tattgaaagt acatatgtgt tgccatctag acaaaatcgt gggaaaccac cagacaggta 3240 ttctcctgat ggaaaagtcc aatatgctat tgcaaattat gtctctacac atcgattgtc 3300 ttctaagtat caagccatgg tgaatacaat ggatggaatc aaaatcctaa caagagtgga 3360 agaagctttg ctagattctc ggtggacaaa agcaatggaa gtcgggatgg aggctctaca 3420 gaaaaacagg acttggagca tagagtcgct accccaaggg aaaakacyag tgggatgcaa 3480 atgggtattc accatcaaac acaacgyaga ygraacyatt gacagataca aagcaaggtt 3540 ggttgctaag gggtacacac agactttcag ggtarattat caagaaacat tcgctccggt 3600 agctaagatg aacaytatty gtgtactttt gtctttagyt gctaactttg attggccgtt 3660 gaagcaattt gatgtaaaaa atgcctttct acatrgagac mtggaakaag aggtttacat 3720 ggaacttcca cctrggtttg aggtgtcaaa caggacaggc aaggtgtgta ggttgaggaa 3780 agcgctttat ggactcaaac agtcgccgag ggcatggttt gggagattca ccgatgcaat 3840 gaagaaatat ggttacagac aaggaaatgc tgatcatact ttgtttatca aacgaaggga 3900 aggaaaggtc accttgttaa taatttatgt ggacgacatg gtagttactg gtgatgatac 3960 cgaggagatg aagaagttac aggggcatct ctctttagar tttgagatga aagacttagg 4020 aggcttgaag tacttcttgg gaattgaagt tgctcrttcc cgtgaaggta tttatttgtc 4080 acagcggaag tatgttctgg atcttttgtc tgagactgga atgttggcat gtaaacctgc 4140 agaaacgcct atagttcaga atcatcatct agcaatttat cctgaccaag ttccagcaaa 4200 cagggaaagg taccaaaggc tagtaggaag gttgatttac ttgtctctca caaggccaga 4260 tattgcatat gcagttagtg tggtgagtca attcatgcac tctcctagtg aggatcacat 4320 ggctgcagta atgcgaatct tgagttattt gaaaggtgcg cctggaaaag ggttgatctt 4380 cargaagcat rggcacttgg aagtaagagg atacayagat gcygattggg ctggaaatgt 4440 tactgatagg cgctctacat caggrtactt tacatttgtt gcaggtaatc ttgtaacttg 4500 gaggagtaag aaacagaatg tggttgctag gtccactgca gaggctgaat accgtggtat 4560 ggcacatgga atttgtgaat tgttgtggct aagaatcctc ttraccgaga ttgggttcaa 4620 accacatgga gctatgttgc tgtattgtga taatcaagck gcgagagaaa tagctaataa 4680 tccagttcaa catgatcgta caaaacatgt tgaggtggat aggcatttta ttaaagaaaa 4740 gttggatgtt aaattgrttg atattccgtt tgtgaagtct rgagatcagt tggcagatgt 4800 gttaactcat gccgtgtcat caagagtgtt tcaggactca cttaacaagt tgggcttmgg 4860 tgatatctac gcaccaactt gagggggag 4889 // ID Copia-32_Mad-I repbase; DNA; EDCOT; 4469 BP. XX AC ACYM01014620; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-32_Mad-I; KW Copia-32_Mad-LTR; Copia-32_Mad_. XX NM Copia-32_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4469 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1303-1303 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01014620; Positions 17545 22013. XX CC Positions [1796-2296] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 2615..4468 FT /product="Copia-32_Mad-I_1p" FT /translation="MAEPNMPTTPNMAAPPTTATSPQMVTSLDTATTPNMA FT ATSHVIAAISPPSSHILATSTTPPASPDHSPGHNKFCSINSLIYSTSPHPL FT PHALAAILNDPLSHEPSSYSQAAKHTHWQHAMQVEYDALMHNHTWSLVPYS FT PSMNVIGCKWVFKVKRKADGSIERHKARLVAKGFNQQEGLDYDETFSPVVK FT PATIRTILSLAVSFSWTLQQLDVHNAFLNGILHEEVYMKQPPRFVDPSCPK FT YVCKLHKALYGLKQAPRAWFQRLTSFLLTQGFFHSHSDASLFIRHGSQSSI FT FVLIYVDDIIITGYNATEISSFIDVLCSKFDSRRMGDLSFFLGLEINRTST FT TISLCQTRYALDLLKKFHMESCKPSPTPLSSSTRLSSLDGDPLIDPSTYRS FT IVGGLQYLTLSRPDIAYAVNQVCQFMHAPRTTHLQSAKRILRYVKGTLSHG FT LLFHKAPHFNLYGFLDSDWAGSVDDRRSTTGACIFLGPNLLTWTAKKQSTV FT SRSSTEAEYRALATTAAEIRWFCYLFREIGIALRVPPCIFVDNMSALHIAA FT NPIFHARTRHIEIDYHFVRELLNFGVLRTRYVPSAHQLADIFTKGLTRERF FT HSLVPKLKLHYVLSRLGGGV" XX SQ Sequence 4469 BP; 1162 A; 1067 C; 814 G; 1366 T; 60 other; tatttcttta tggtaccaga gccctaaaag ggctaacacc caaacagtcg atcctattct 60 tttcttcckc taactatcaa tggcaaaccc tgataactcg gctytctcct cygctrcatc 120 tggtgcatct mgaacctctg ayagtctgac tcaatctacc atggcgggct tcacttctgc 180 tcttcctacc tccttcaata tatctaatct cttcaacaca ycaatggatc gcacaaattt 240 ycttagttgg aagtcacaat tcgaggatgt tctcgaactt catgatcttg gtattattgt 300 taaacttgaa gataaacctg ccaagaactt atctgatggc tcactcaatc ctctctacgc 360 taaggacaag ctagtgctca gttggatcaa ggccacarca tctccctcaa taaagactct 420 tctcattcca tgttcgactg ccttcgaagc ctggattctt ctctaaaaga ggctctctcc 480 tctctctaag actcatgtaa gaactctcag ggaccaaatt cgtaccctca aaaggattct 540 ggatcaacaa atgtctgatt atcttataca tgcccggtca ctttttgact cttttgccgc 600 cgctggaaca ccgatgacag atagcgaact aattgaatat atattagatg gtctgggtca 660 tgagtataaa gagttcacca cttcccttca tcttcgtcaa actctcagtt ttgatgaatt 720 ttttgatcta ctccttcaag aggaacaact ccagaaaaga atggaagcac tttcattatc 780 aaacggagtt gcacttgcca cagatcgggt agcccaaaat catccacaca acaggcctca 840 aaccaacaac tccaagggac acggacgcgg acgcggacgt ggtcgtggtc gtaactggaa 900 caatgggcgt gacarctttg accayygtga acatggaaga aactttaatc aygatcgtga 960 tggtggttgg cggaacaacc gtaatggtgg caatmaatgg gcgyaaaata ataatgcaaa 1020 tggcaccttg tattatggaa acccacgwca taatccaatt ccaccggata atcrtccacm 1080 gctgctcccr acaccgtcaa atccctctgc atttcagttt gatgtccctt gccaacaatg 1140 tggaaatgat ggtcataatt ctcgtgtttg ccctcaacga ggcaactatg cctacacggc 1200 tgatcactct ggtgctatct cagacccaat tgattggtgt tttgactcyg gagcaaccca 1260 ycacatggtt tctgatcctc gtgcactcac caacgtgcaa ccttatrcag gtaytgattc 1320 tatcattgtt ggtaacgggt ctcacctttc tattatgtat attggggatg gaaagctatg 1380 cacaccatyg agttcattgc atcttaaagr ggwcttatgt gttccagcca ttcrgaaaaa 1440 tctattatct attcgaagat tttgtcatga taatgattgt tatttcatca traatgctta 1500 tggtttttgt gtcaaggaca acaagacggg gaaggttctt ctagttggya gtagcttcaa 1560 tggtctctat cayatccrtg cagccccaaa agtgacagag aaaatmgttt tctatggrga 1620 aaaracgayt caggaygttt ggcatactcr ccttggacac ccgtcttatc atgtatttcg 1680 gatgattttg aataaacacc atttacctat yagtggtgag attgattcta ataaaayttg 1740 ccatgtttgt cccatggsaa aatcttgcag attacctttc tytaatcgca cttctcrtac 1800 acaaaaacct ttagaattat tgcacttgga tctttgggga ccggcacctg ttttgtcaaa 1860 ctttggatat agattttatc tctccattgt ggaygatcac acccsttacg tatggctgta 1920 tccattactc aaaaaatccg atgtgcttgc cacstttatt gggtttaaaa rgataattga 1980 aaatcgacyc aatttaaata tcaaaatggt gcaaatggat ggtggtggtg aattcacaag 2040 tcggttattc atgcaatttc ttcgtgataa tgggatyggg catcaaatct cttgtcctta 2100 tacrcctcaa caaaatggcg tygtcgaaag aaaacatcgc cacatwgttg aaaaagggtt 2160 gtgtttattg actcaatctc sacttccatc aagttattgg gytgaagckt tttctacttc 2220 cgtctatctt attaatcggc tgccaaccgt gaatcttgmc aacatatctc catatgagaa 2280 actttttcag crtcctcctg attataagat gctcaaagca tttggttrtg catgtttccc 2340 acacttggtg scatataaca agcacaaact tatgcctaag tcagtaaaat gtgtgttcat 2400 tggttatgat ttacattaca agggttatcg atgtttagat cccatcacag gtcgtgttta 2460 tatttcayga aatgtaacct ttgatgaact cacattccct ttttctgagc ttacatccag 2520 gaacaaggaa gatgctccat tctccttgcc gacaccagcc ccagtcctca ttgagccaat 2580 tgctcctctt tcaagtctgg tgcacactcc tcatatggca gaacctaata tgccaacaac 2640 tcctaatatg gcagcacctc caactacggc aacatctcct caaatggtaa cttctcttga 2700 cacrgcaaca actcccaata tggcagcaac ttcccatgtt atagcagcca tttcaccacc 2760 atcatcgcat attttagcaa catcaacaac accaccagct tctcctgatc actctccggg 2820 tcataacaaa ttttgcagca ttaattcact tatttatagc acttctccac atccattgcc 2880 tcatgcctta gctgccattt tgaatgatcc actttctcat gaaccttcaa gttattctca 2940 ggctgccaag cacacacatt ggcaacatgc tatgcaagtt gaatatgacg ctcttatgca 3000 caatcatact tggtccctcg tgccctattc accatctatg aatgtcattg ggtgtaagtg 3060 ggtcttcaaa gtgaaaagga aagcggatgg ttctatcgaa aggcataaag cacggttagt 3120 tgccaagggg tttaatcaac aagaaggttt ggactacgac gaaacgttta gtcccgttgt 3180 caaacctgca actattcgca caatactctc tttagccgtc tcatttagtt ggacactcca 3240 acagttggat gttcataatg cttttctcaa tggcatacta catgaggaag tctatatgaa 3300 gcaaccaccc aggtttgttg atcctagttg tcccaaatat gtgtgcaaac tccataaagc 3360 tctttatggc cttaaacaag cccctcgtgc ttggtttcag cgactcactt catttttact 3420 cacccaggga tttttccata gtcactctga tgcctcatta tttattcgtc atggttccca 3480 atcctctatt tttgtgctta tttatgtcga cgatatcatt atcacaggct ataatgccac 3540 ggaaatctct tcctttattg atgtgttgtg ctccaagttc gatagtcgcc ggatgggtga 3600 tcttagtttc ttccttggac tagagattaa tcgtacctct actacgattt ctctttgtca 3660 aacgcgatat gcacttgatc ttctcaagaa gttccatatg gagtcatgca aaccgagtcc 3720 cacacccttg agttcctcta cgcgactatc ttccttagat ggtgaccctt taattgatcc 3780 gtctacttat cggagcattg ttggtggctt gcaatatctt acactttctc gacctgacat 3840 agcttatgca gtcaaccaag tgtgtcaatt tatgcatgct ccacgaacga cacatctaca 3900 aagtgcaaaa cgtattctcc gttatgttaa aggtactctt tctcatggtc ttctttttca 3960 caaggcacct catttcaacc tttatggttt cttggactcc gattgggctg ggagtgttga 4020 tgatcgtcgc tctaccactg gtgcgtgtat ctttcttgga cctaatcttc ttacatggac 4080 tgccaaaaag caatctactg tctcaagatc tagcacggag gctgaatatc gtgcccttgc 4140 tactacggca gctgaaattc gttggttctg ctacttattt cgtgaaattg gcatcgcctt 4200 gcgtgtacct ccttgcattt ttgttgacaa catgtctgct cttcatattg ctgcgaaccc 4260 tatctttcat gcaaggacta gacacatcga aattgactat cactttgtta gggagctgct 4320 caactttggt gtcctccgca ctcgctacgt cccatctgcc catcagcttg ccgatatctt 4380 tactaaggga ctcactcgtg aacgctttca ttctttagtt cccaagctca aactccacta 4440 tgttttgtct cgcttggggg ggggggtga 4469 // ID Copia-24_Mad-LTR repbase; DNA; EDCOT; 244 BP. XX AC ACYM01122703; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-24_Mad-I; KW Copia-24_Mad-LTR; Copia-24_Mad_. XX NM Copia-24_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-244 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1370-1370 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01122703; Positions 1421 1664. XX SQ Sequence 244 BP; 71 A; 41 C; 36 G; 96 T; 0 other; tggtagaaat gaatgacact tgtcaagaga ttacatagtc tgttataagg tagttatgca 60 gttagttctt agcttagtga gaaagctttg taacgagata taacagtttt tgtaaacagt 120 gaaataacat actgaaaaaa aatacaatca tctctctttc tttctcagcc tgattctctc 180 tctaattctt tcttctttct tctgctttct gtatcttttc ttcaagattt ttgcagttct 240 aaca 244 // ID Gypsy-11_SL-LTR repbase; DNA; EDCOT; 1017 BP. XX AC AC243708; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the tomato genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-11_SL_; KW Gypsy-11_SL-I; Gypsy-11_SL-LTR. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-1017 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the tomato genome."; RL Direct Submission to RU (22-JAN-2011). XX DR Genome; AC243708; Positions 212451 213467. XX SQ Sequence 1017 BP; 263 A; 176 C; 246 G; 332 T; 0 other; tgccacgttc cggtaccagg atagtatatg aggatcagag tgtcacgttc cgacaccagg 60 atagaatatg gatcgggtgc cacattccgg taccaggata gaatatgaat cgggtgtcac 120 gttctgacac caggatagaa tatgcatcgg gtgccacgtt ccggtaccag gatagaatat 180 ggatcgggtg tcacgttccg acaccaggat agaatatgga tcaggtgcca cgtttcggta 240 ccaggatagt atatgaggat cggagtgtca cgttccgaca ccaggatagt atattgagga 300 gccgagtgtc acgtaccgac acgaggggaa taaagataat gaatcttgaa aaatgttaat 360 atactcaatc taatgaactg aattcccaaa tgagtatgat gaggagacgt gagtcctcat 420 tgatgtgctt cgtgttgtaa ccaagggtta tggtaacttt aaatgctgca tgctaaggat 480 attagttgat tttatgatat tgcttaatat atactgtttt ctattttgag ttggccgatg 540 atatctacac agtacccgtg ttttgtactg acccctactt ttattgtttt cttcttgttt 600 atttgtggag tgcagcaaac gtgccgtcat cttcgactca acagtaattc aagcaagtct 660 taccacatcg gaaatttagg gtgagctaat gcttctagct tggactggat cttcttcttc 720 aagtcttgat gccttgaact tccggcatgg actagcttct tatgtatttt tagcttttag 780 aatactctta gtttagtcat ttgatcatag atgttcttgt ggtgatgact tccagatttt 840 ggggaatgac aagttttgag ttatagaagt tgattattga tttttattaa tgagtttaag 900 tcttccgcgt tacttcatgt tgatattata ttgaaatgta aaggtttaga ttggttggtt 960 cgctcacata ggaggttaag tgcgggtgcc agtcgcggcc cgttttgggt cgtgaca 1017 // ID EnSpm-3_Mad repbase; DNA; EDCOT; 2304 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous EnSpm elements, consensus. XX KW EnSpm; DNA transposon; Transposable Element; EnSpm-3_Mad. XX NM EnSpm-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2304 RA Kojima K.K. and Jurka J.; RT "EnSpm-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1603-1603 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >92% identical to consensus. This consensus includes only the CC protein-coding region. 8 copies in the genome. XX FH Key Location/Qualifiers FT CDS 1..2301 FT /product="EnSpm-3_Mad_1p" FT /note="transposase." FT /translation="MNKEWVHLNRTTNEYLIGRRAFISNALDVAAFQGKIK FT CPCRSCCNMFYRDPFEVDQHLYVEGMDPHYIDIPWVEHGEQVHTSDNISSQ FT TTEALNERSPENFMAAMLHDVFSNHVHMDESDHVGESSSACDETTDAHQFD FT NILREADGELYPGSRKKRLDFVVKLYQSKLLYGMSDAAFGSVLALIREHFP FT MCETLPPNLYYTKKIIRALGLDYHNIDACRNNCMLFWKEHVNAIVCAKCGA FT SRYKQRKGNSGTIQCTKVPKKVLRYFPIGPRLQRLYMSRYTAESMIWHSEI FT RTDDGVLRHPADSSAWKHLDNTYPDFARECRNVRLGLASDGFNPFGMHGKP FT HSTWPVLVVVYNLPPWMCMKQPYIMMSLLIPGKTSPGDAIDVFLQPLIDDL FT RHLWMTGLRTYDSHRQETFTMRAALLWTINDFPAYAMLSGWSTSGEKACPT FT CGDDTDSLRLKHGKKFAFMGHRRWLPMSHRYRRHKKTFNGSQEFRNPPKPR FT SAMDCLLEVTGLTFRFGKGARASGRKRGWNDDGHVVGQWTKKTIFFELPYW FT KDLLLRHNLDVMHIERNVAENVIGTLLEIEGKTKDGIRARADLVELGIRHD FT LHPRADGARTKLPAAEYNMKPGEKRMLCQVLESIRVPDNYSSNISNCVNIQ FT EKKLIGLKSHDYHMLMQVFLPIAIRKVLPKSVVTVLLELSRFFRHLCSKTG FT TEELFNGLSKSIALTLCHLEKLFPPSFFTVMVHLIIHLADEAAVAGPVPYR FT WMYPIERCQFRKTPPQ" XX SQ Sequence 2304 BP; 655 A; 437 C; 554 G; 658 T; 0 other; atgaataaag aatgggtgca tctgaatagg acaaccaatg aatacttgat tggcaggcgt 60 gcattcatca gtaacgcttt agatgttgct gcgtttcaag gcaaaattaa gtgcccctgt 120 cggagttgtt gcaatatgtt ttatcgtgat ccatttgaag tcgatcaaca cctgtatgtc 180 gagggtatgg atccccatta catagatata ccttgggttg aacatggcga acaggtgcat 240 acttctgata acatatcaag tcaaactacc gaagctctta atgaaagaag ccctgaaaat 300 ttcatggcag cgatgcttca cgatgttttc agtaaccatg tgcatatgga tgagtcagac 360 catgttggtg aatcttcttc tgcgtgtgac gaaacaactg atgcgcacca attcgacaac 420 attctacgag aagcagatgg agaattatat ccaggtagca ggaagaaaag gttggatttt 480 gtggtgaaat tatatcagtc aaaattgtta tatggaatga gtgatgctgc atttggttca 540 gtgctggcac taataagaga gcattttcct atgtgtgaga ctcttcctcc aaatttgtac 600 tatacaaaga agattattcg ggctttgggg ttggattacc ataacataga tgcgtgtcga 660 aataattgca tgctattctg gaaagagcat gtaaatgcca tcgtttgtgc aaagtgtggc 720 gctagtagat ataagcaaag gaagggaaat tcaggaacga tccaatgtac caaggtacca 780 aaaaaggttt tacgctactt tcccataggt cctagactac aaaggttgta catgtctcgt 840 tacacagctg agtcaatgat atggcattca gagattagaa ctgacgatgg tgttttgagg 900 caccctgctg attcttcggc ttggaagcat ttggataata catatccaga ttttgcaagg 960 gagtgtcgca atgtccgtct tgggcttgca agcgacggat tcaatccgtt tggtatgcat 1020 ggcaaacccc acagcacatg gcctgtttta gttgtagttt ataatcttcc gccttggatg 1080 tgcatgaaac aaccttatat catgatgtcc ctcctaattc cagggaaaac aagtcctggt 1140 gatgcaattg atgttttctt gcagccgcta attgatgact tgcggcattt gtggatgaca 1200 ggtttgcgaa catatgatag tcaccgtcaa gaaaccttca ccatgcgtgc tgccttgttg 1260 tggactatca atgactttcc tgcttatgcc atgctctcag ggtggagcac tagtggtgag 1320 aaagcttgtc cgacttgcgg tgatgacacc gattctttac ggcttaagca tgggaaaaag 1380 tttgcattca tgggacatag acgatggctc ccgatgtcac acaggtaccg gagacataaa 1440 aaaactttta atggatctca agaatttcga aaccccccta aaccaagaag tgccatggat 1500 tgtttattgg aagtgacggg attgaccttc agatttggca agggtgcaag ggcaagtggt 1560 cgtaagcggg ggtggaatga tgatggacac gttgttggtc agtggacaaa aaagactata 1620 ttctttgaat tgccttactg gaaggatctc ctactacggc ataacttgga tgtcatgcat 1680 atagagagaa atgtagctga aaatgttatt ggcactcttt tggaaattga agggaagact 1740 aaagatggta ttagggcaag ggctgatctc gtagagttgg gcattaggca tgatctccac 1800 ccacgggcag atggtgcccg tacaaagctt ccagcggcgg aatacaatat gaaacctggg 1860 gagaaaagaa tgttgtgcca ggttttggaa tcaattcggg tgccagacaa ctactcttct 1920 aatatcagca actgtgttaa tattcaagaa aagaagttaa ttggcttgaa aagccacgat 1980 tatcatatgt tgatgcaggt cttcctccct attgcaatac gaaaagtgtt accgaaatcg 2040 gttgttacag tgttgttaga gttgagcaga ttttttcgcc acctttgttc aaaaactgga 2100 actgaagaat tgttcaatgg cttgtcaaaa agcattgcct taactctatg ccatctggag 2160 aagttatttc cgccatcatt ctttaccgtt atggtacact tgataattca ccttgcggat 2220 gaagctgctg ttgctggtcc ggtcccatac cgatggatgt accccattga aaggtgtcag 2280 tttcgtaaaa cacctcctca gttc 2304 // ID METMITE repbase; DNA; EDCOT; 187 BP. XX AC . XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE A miniature element from Medicago truncatula. XX KW DNA transposon; Transposable Element; Nonautonomous; Interspersed; KW repeat; terminal; TSD; MITE; TIR; METMITE. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-187 RA Shankar R. and Jurka J.; RT "METMITE: A MITE transposon from barrel medic."; RL Repbase Reports 7(1), 36-36 (2007). XX DR [1] (Consensus) XX CC The miniature element sequence is present in a high copy number CC and well conserved too. CC It's flanked by 10 bp TSD sequence, basically rich in AT as well CC as varying across the individual copies. XX SQ Sequence 187 BP; 66 A; 26 C; 29 G; 66 T; 0 other; gggtagtgtt aacttgtgct cttagggcac atgttaataa acttaaaaga gaagaaatat 60 ttcctaaaac tttgtgcatt taattgatta aaaaattaaa gattaaatgc aatgcacatt 120 tttcaataaa ttatttctat attcgaatca ttaacttgtg ccttgagggc acaagttagc 180 atttccc 187 // ID Copia35-PTR_I repbase; DNA; EDCOT; 4378 BP. XX AC scaffold_1646; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia35-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4378 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4378 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 246-246 (2007). XX DR Genome; scaffold_1646; Positions 5727 1350. XX CC Positions [1760-2209] - Integrase core CC LTRs are 96% similar to each other. XX FH Key Location/Qualifiers FT CDS 593..1660 FT /product="Copia35-PTR_I_1p" FT /translation="MISSSSLSFNQNTTTLFTKTMSPTRFASNNSLYIRKD FT RPICSHCGISGHTVEKCYRIHGFQPGYKFNRGKNASPSVNQVSGLNTPQLP FT ITYEQCQQLINMFKPTISEHDSSVNQVSLSANKESEIPMQGESMTSAGDSS FT IIAQLSTLDSKHSIFSSSLSLTQQSSLANPAKTPWIIDTGATDHMIYSISF FT FTSITSAVSKSVRLPNGQCTSVTYIGTIKISESFVLTDVLCIPSFSFNLIS FT ISKLIKNLQCCVIFLPKFCFVQHLTSWKTIGMGKEARGVYHLLQNPVSVLP FT KNFVSVNSAKFMSNHTITDLASASFSVNFVNNSLWHYRLGHPSDFPLKLIF FT HVIPQVLHESNKT" FT CDS 1961..3835 FT /product="Copia35-PTR_I_2p" FT /translation="MSHFYASKGVIHQLSCVETPQQNSSIERKHQHILNVA FT RSIHFQSHLPLQFWGDCILTPVHLINRIPTPILQNKSPYETLFKSSPSYSH FT LRVFGCLCYANTLFQNQHKFDPRAKPCIFLGYPFGIKGYKLYDLHLYTVFA FT SRDVVFHKNIFPFALKYPISPTDSVLPLPIPMHESAIPSLDPLLTNSFPLS FT SINASPSNSSNMNSTSEPCMSSTSEITPQPSRKSSRVKHTPGYLYDYHFYL FT ATSTSNPAPSSTASGIPYSLSSVLSYDHFSSTEKFFSLSVSALVEPTSSIQ FT AVKHEEWREAMDTEIKALELNDTWTVVDLPASKHVIGCKWVCKVKLKSDGT FT LERYKVRLVAKGYNQCEGLDYYETFSHVAKLTTMRTLLAVAAVKKWHLHQL FT DVNNAFFHGQLDEEVYMSLPPRFTNQEESKVCKLHKSIYGLKQASRQWFAK FT FFSALLEFGFIQSKVDYTLFTRTLEGSFIALLVYVDDIVIASDNSTEVSKF FT IQLLNDRFKLKDLGQLKYFLGLEIARSELGISVCQRKYALEVLEDTGMLAS FT KPVQFPMEPNVKFSKDSGQILEDPTTYKRLVGRLLYLTISRPDISFVVQVL FT SQFMDKPRVPHLAAATRVLRYIKASPA" XX SQ Sequence 4378 BP; 1242 A; 912 C; 702 G; 1522 T; 0 other; ttatggtatc agagcaattt atttgaagtt ttatttctgc atcttcattc tcttcatctt 60 cttcatctag ttctttattt ccctttattt tcttggcaat ggctgaaaat accaacccta 120 catcagaaat ggattcttcc aatcccttct tcccgaatca tggtgacagt cctggagcca 180 tgattgtttc aaaatcactc aatggtgaaa attacaattc atggaaaaga gcgatgatga 240 tggctttatc agtcaagaac aaactcagtt ttgttaatgg cactttgggt cacgaatctt 300 tcaactccag aaatctatct catgtttgtc acaagaaaat aattttgtca gctcatactt 360 tattgctatg aaaggattat aggatgagtt aggaaatcac cagccaattc ctacctgcac 420 atgtggagct ttgaagacta ttttgtctta tcatcatcaa caacacgttt atcagttcct 480 aatgggattg aatgaaagtt attcacatgt ttgaggtcaa attctattga ttgatccact 540 gccttcaatc aataaggttt tctcacttgt catccaagag gagaggcaac gcatgatttc 600 ttcatcaagc ctttccttca atcaaaacac cactaccttg tttacaaaga ctatgtctcc 660 aactcgtttt gctagtaaca actctcttta tattcgaaaa gatcgaccta tatgctctca 720 ttgtggtatt tctggacaca ctgtggagaa atgttacaga attcatggct ttcaacctgg 780 ttacaagttt aacagaggaa agaatgcatc tcctagtgtt aatcaagttt ctggtttaaa 840 tactcctcag ctgcctatta cttatgaaca gtgtcagcag ctcatcaaca tgttcaaacc 900 gaccatctca gagcatgatt catctgtcaa ccaagtttcc ttatctgcaa ataaagagtc 960 agaaatcccc atgcaaggtg aaagtatgac aagtgcaggt gattcttcaa ttatagcaca 1020 actttctact ttagattcaa aacattctat tttttcatct tctttgtctt taactcaaca 1080 gtcttcactc gcaaaccctg ccaaaactcc ttggatcatt gatactggtg ctacagatca 1140 catgatttat tccatatctt tcttcacaag tattacttct gctgtttcca aatccgtaag 1200 attaccaaat ggccaatgta cttcagttac ttacattggt acaatcaaga tttcagaatc 1260 ttttgttcta actgatgtac tttgtattcc ttctttttca ttcaacttaa tatctattag 1320 caaactaatc aaaaatctac aatgttgtgt catcttctta ccaaagtttt gttttgttca 1380 gcaccttaca agctggaaaa cgattggtat gggtaaagaa gctagaggtg tatatcattt 1440 gctgcaaaat ccagtttctg ttttacctaa gaattttgtt tctgtcaatt ctgcaaaatt 1500 catgtccaat catacaatca ctgatttagc ctctgctagt ttctctgtaa actttgtcaa 1560 taatagctta tggcattaca gattaggaca tccttcggac tttcctttga aattaatttt 1620 ccatgtaatt cctcaagttc tacatgaatc aaataagact tagagcatct gtccattagc 1680 caaacagcat cgtttatctt ttcctcatag cacatctact tctacataac cttttgattt 1740 aattcattat gatatttaag gtctcttctc tacaaaatct cttactggtt catcatattt 1800 tcttaccatt gttgatgatc ataccagatt tacatggatt caccttttag acaataaatc 1860 tcaaaccaga actcacatta aagctttctt taatttggtt aagacacaat tcaatgctaa 1920 aatcaagtcc ttaaggtcag ataatggagt tgagttcaac atgagtcatt tctatgcatc 1980 aaaaggtgtt atccaccaac ttagttgtgt tgaaacacca caacaaaact ccagtattga 2040 acgcaaacac cagcacatct tgaatgtggc tagatccatt cattttcagt cacatttgcc 2100 tttacagttt tggggggatt gtattcttac tccagtacat ttgataaata ggattcctac 2160 tcctatactg caaaataaat ctccttatga gactttgttc aaatcttctc catcctattc 2220 tcatttgcga gtatttggtt gtctttgtta tgcaaatact ctttttcaaa atcaacataa 2280 atttgatcct agagctaagc cttgcatatt tcttggttat ccatttggca tcaaaggtta 2340 caaactctat gatttacacc tttatactgt gtttgcctcc agagatgttg tgttccacaa 2400 gaatatattt ccttttgcac tcaaatatcc aatatctcct actgattctg tcttaccttt 2460 gcctattcca atgcatgaat cagctattcc ttcacttgat cccttactta caaattcttt 2520 tcctttgagc tccatcaatg cttcaccttc taattcaagt aacatgaatt ccacttcaga 2580 accttgtatg tcatctactt cagaaattac acctcagccc agtagaaagt cttctagggt 2640 aaaacacaca cctggatact tgtatgacta tcatttttat cttgcaacct ccacttcaaa 2700 tcctgcacct tcgtctacag cttcaggtat tccttattca ctttcttcag ttctttctta 2760 tgatcatttt tcctctactg agaaattctt tagtctttct gtctctgcac ttgttgagcc 2820 cacatcttct atccaagctg tcaaacatga ggaatggcgt gaggctatgg atactgagat 2880 caaagcactt gaactaaatg atacgtggac tgttgttgac cttcctgctt caaagcatgt 2940 tattgggtgc aaatgggttt gcaaagtcaa gttaaaatct gatgggactt tagagaggta 3000 taaagttagg ttagttgcca aggggtataa tcagtgtgag ggattggatt actacgaaac 3060 attttctcat gtggctaaac tcaccactat gagaactctt ttagcagttg cggcagttaa 3120 gaagtggcat cttcatcaat tggatgtgaa taatgctttt tttcatggcc aattagatga 3180 agaagtctac atgtccttac ctcctagatt taccaaccag gaggagtcca aagtatgcaa 3240 gctacacaag tcaatttatg gcctaaagca agcttctagg caatggtttg ctaaattctt 3300 ttctgctcta ctcgagtttg ggttcataca gtccaaagtt gattacactt tatttacaag 3360 aactttggag ggttcattca tcgcattatt agtttatgtt gatgacatag ttattgccag 3420 tgataattca actgaggttt caaagtttat ccaactgctt aatgatagat ttaagctaaa 3480 agaccttggc caattgaaat atttccttgg tttagaaata gctcgtagtg agcttggcat 3540 ctctgtttgt cagagaaaat atgccttgga agttcttgaa gatactggta tgttggcttc 3600 aaaaccagta caattcccaa tggaacctaa tgtgaaattc tctaaggatt ctggccaaat 3660 cttagaagat cctactactt acaaacggct tgttgggaga ttgctttatc tcactatcag 3720 cagacctgac atttcatttg ttgttcaagt cttaagtcaa tttatggaca agcctagagt 3780 tcctcattta gctgcagcaa ctagagttct acgctacatt aaagcctctc cagcttaagg 3840 gttgttcttt ctagtcatat ctagtttaca aatgaaggca ttatgtaatt ccgactaggc 3900 gggttatgtg gattccagaa gatcagtgac agggtattgc attttccttg acaattcttt 3960 aatttcttgg aaatcaaata aacaaaccat tgtatccagg tcttctgctg aggctgagta 4020 cagagcaatg gcatctactt gttgtaaggt tatatggctt cgcactcttc ttcaagacct 4080 acaggttcca cctcaaactg ctctccttta ttatgacagt aaagctgctc ttcacattgc 4140 agctaaccct gtctatcatg agcgtacaaa acacattgac attgattgtc atatggttcg 4200 agagaagatt cagttaggca ttctgcgcac ttttcatgtt tcttccaaac accagctcgc 4260 ggatattttt accaaggttc ttggcttctc tcttttttat cctttgatat ccaagatgag 4320 ccttcataac atttattccc cttgatcttt ttttgcgtct catctggagg gagagtat 4378 // ID Copia-45_VV-I repbase; DNA; EDCOT; 3092 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-45_VV_; KW Copia-45_VV-LTR; Copia-45_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-3092 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 7155432 7158523. XX CC Positions [519-1013] - Integrase core CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 333..3092 FT /product="Copia-45_VV-I_1p" FT /translation="MSSTLQLSNKANLWHFRLGHPAHKIVNKVLSACSLPP FT EHWTSVCEPCQMAKSHRLPFTLSESRASQPFALVHSDLWGPAPVVGTNGAR FT YFVLFVDDHTRFSWLYLLVSKDQAISAFLQFKVMIETQFDTKVRMLQTDWG FT GEFQAFTDTLCKFGILHRVSCPSTSQQNGRVERKHRHVVEVGLSFLAHASI FT PLKYWPFAFQYALYLINRLPSSVLNFSSPYKTLYHCLPNYSFLRVYGCTCY FT PFLRPFNRHKFAYRSVKCTFIGYSSKHKGYLCLNMSNGKIHISRHVIFDEL FT DFPFAKPSTVQPPCRVSPTHCAIPLTTPITPISSLLPSSSSPSSELVPISD FT TSVSISSSEVAPIPTAQPSSSHVPSPCHPMTMRAKKGIFKPKIFLSPIETI FT FHPLCEPNSFKKAVKVPEWQQAMHLEFEALMSNKTWVLVPLPPNQNIIGCR FT WVYKLKYKPDGTVERYKARLVAKGFHQTPGFDYFETFSPVVKPTTIRVVLS FT LALSKNWFIRQLDVHNAFLNGDLSEQVFMTQPPGFVDSSKPNFVCKLTKAL FT YGLKQAPRAWFTKLSSALVKWGFSMSQVDTSMFVYCNNSAMLVVLVYVDDI FT IVTGSSSLLIEQLISSLNSCFALKDLGPLNFFLGIEVLNSGSSLHLSQAKY FT ICDLLQRAGLSESKSMASPMAAGSVLSIADGTRLEDPTLYRSLIGVLQYCT FT ITRPDIAYTVNKLCQFMHAPTSTHLQTVKRVLRYLKCSLFYGLSFQPSSSL FT DLITCTDADWASCPDDRRSTSGYCIFFGGNLVSWSASKQKVVSRSSTESEY FT RGLANTAAELTWIQSLLKELFVPLFQPPVLYCDNLSTTYLAANPVLHSRAK FT HVEIDYHFVRERVLQKTLDVRFLPSEYQVADILTKALSTQRFLHLRSKLTV FT LSCPVCLRGDVKKLTG" XX SQ Sequence 3092 BP; 779 A; 693 C; 540 G; 1080 T; 0 other; tctcgttcta atcgtttaaa tatctcaaat attggacact ccactatttc ttcagcttct 60 cggtctttaa atctaaaaat attttacatg ttccacaact tacaaccaat ctgataagtg 120 tgaataggtt gtgtactgac aataatgtca ctgtggaatt ctttactaat ggatttgtgg 180 tgaaggatca agcttcgaag aaggctcttc tccaaggtaa ccttaactat ggcttataca 240 aattgtcgtc ttcagcacct agtagaagat atcaagatcc taatgataat aaacttgctg 300 gaagaacaag cttgacaact gaggtcccat gtatgtcatc tacattacaa ctttccaata 360 aggcaaatct atggcatttc aggttaggcc atcctgcaca taaaatagtc aataaagttc 420 tgagtgcttg tagcttgccc ccagaacatt ggacaagtgt ttgtgaacct tgtcaaatgg 480 caaagagcca tcgcctacct tttactttgt ctgaatccag agcatctcag ccttttgctc 540 ttgtacattc tgatctatgg ggtcctgctc ctgttgttgg tactaatggt gcaagatact 600 ttgtgctctt tgtggatgat catacaagat tttcttggtt gtatctacta gtttctaaag 660 atcaagctat ctctgccttt ttgcaattta aagtgatgat tgagactcaa tttgatacta 720 aagttagaat gcttcaaact gattggggag gagagtttca agcctttact gatactttgt 780 gtaagtttgg gattctgcat agagtatctt gtccatccac ttctcaacaa aatggccgtg 840 ttgagagaaa acatagacat gtggttgaag taggcctttc ttttcttgct catgcttcta 900 ttcctctcaa atattggcct tttgccttcc aatatgcttt atatttgatt aatagacttc 960 cttcctctgt gctaaacttt tcttctccat ataagactct ttaccattgt ctaccaaatt 1020 attcttttct tcgtgtctat ggttgcactt gttatccttt tcttcgccct tttaatcgcc 1080 ataaatttgc atatcgatca gttaaatgca ccttcattgg ctacagctct aagcataaag 1140 gatatctctg tttaaacatg tccaatggaa aaatacatat atcacgacat gttatttttg 1200 atgaactaga tttcccgttt gctaagccct ctacagttca gcctccttgt cgtgtttccc 1260 ccactcattg tgccattcct ttaacaacac caatcactcc aatatcttcc ctcttgcctt 1320 cctcatccag tccatcttca gaattagttc caatctctga tactagtgtg tcaatttcct 1380 cttctgaggt tgcacctatt ccaacagctc aaccttcttc ctctcatgtt ccttctcctt 1440 gtcatcccat gacaatgcgt gccaaaaagg gcatcttcaa gcctaagata tttctgtctc 1500 ctattgagac tatttttcat ccactttgtg aaccgaattc tttcaagaaa gctgttaaag 1560 ttcctgaatg gcagcaagct atgcaccttg aatttgaagc tctcatgagc aataaaacat 1620 gggtcctggt cccccttcca cctaatcaga atattattgg atgtcgctgg gtttataaat 1680 tgaagtataa acctgatgga actgttgaac gctataaggc acgtttggtg gcgaaaggat 1740 ttcatcaaac tcccggtttt gattactttg aaaccttcag tcccgtggtt aaacccacta 1800 ctattcgtgt ggttctctct ttggcattaa gtaaaaattg gtttattaga caacttgatg 1860 ttcataatgc atttcttaat ggtgatttat ctgagcaagt ttttatgaca caacccccag 1920 gctttgtgga ttcctctaag cccaactttg tttgtaaact taccaaggca ttgtatggtt 1980 tgaagcaagc tccacgtgct tggttcacca aactcagctc cgccttagtt aaatggggtt 2040 tttccatgtc acaagtagat acatcaatgt ttgtttactg taacaattct gccatgcttg 2100 ttgtcttggt ttatgttgat gatattattg tcactggctc aagttccttg ctcattgaac 2160 aacttatatc ctccttaaac tcttgctttg ctctcaagga tcttggtcct ctcaactttt 2220 ttcttggaat agaggtgctc aattctggat cttctttgca tttaagtcaa gctaaatata 2280 tatgtgatct tcttcaacgt gctggtttgt ctgaatcaaa gtccatggct tccccaatgg 2340 ctgctggttc tgttctctcc atagctgatg gtaccagatt agaagatccc accttgtacc 2400 ggagtcttat aggtgtcctg cagtattgca caattactag accagacatt gcttatactg 2460 ttaataagct ttgccaattt atgcatgctc caacctctac tcatcttcaa accgtgaaac 2520 gtgtccttcg ttatctcaaa tgttcattgt tttatgggct ttccttccaa ccatcttcct 2580 cccttgatct tattacctgt acagatgcag attgggcatc ttgccctgat gatagacgta 2640 gcaccagtgg ctactgcata ttttttggag gcaatctggt ctcttggtca gcctctaaac 2700 aaaaggtggt ttctcgctcc agtactgaat ccgaatatag gggcttggct aacacagcag 2760 ctgaactcac ttggatccag tccctgctta aagaactctt tgttcccctg tttcagcctc 2820 ctgttctata ttgtgataat ctcagcacta cttatttagc tgcaaatcct gttcttcatt 2880 ctcgggctaa acatgtggaa attgattatc attttgttcg tgaacgagtc ttgcaaaaaa 2940 ctcttgatgt tcgatttctc ccatctgaat atcaagttgc tgatatcttg accaaagctc 3000 tttcaactca acgttttctt catctccgaa gcaagctcac agttctttct tgccctgtgt 3060 gcttgagggg ggatgtcaag aagttaacag gt 3092 // ID LINE1H_MT repbase; DNA; EDCOT; 3870 BP. XX AC . XX DT 13-NOV-2006 (Rel. 11.11, Created) DT 01-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE LINE sequence from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW LINE; Interspersed repeat; retroposon; autonomous; LINE1H_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3870 RA Shankar R. and Jurka J.; RT "LINE1H_MT: A Long Interspersed Element from Barrel Medic."; RL Repbase Reports 6(11), 574-574 (2006). XX DR [1] (Consensus) XX CC The LINE sequence has two ORFs with truncated 5' end. XX FH Key Location/Qualifiers FT CDS 5..547 FT /product="LINE1H_MT_2p" FT /translation="LFAAQLLSEFHKHVYSGSCNSNWRLTAFYGYPDSGRR FT RDSWDLLRHLSSLSNDPWCIIGDFNDHLSSADKRGGPDRPPWLIRGFQDAV FT NDCNLFDMPLFGYQFTWFKSIGTDSSKEARFDRALVTSSWQTLFRMQHFRL FT WLLQFLTTLLFFCSFIQYLGDNLTVVSNLTILGYLSRNSMNW" FT CDS 367..3840 FT /product="LINE1H_MT_1p" FT /translation="SPCHILLANTFPNAALQTLVAPISDHTPLLLQLHPIP FT WRQPYRSFQFNNSWLLEPELNELVKNNWEHYPPSNILTKLNHCVEDISSWS FT SSVTPNFKHLINKQRSVIEDFRTYSNDASDPQLQLLQNNLATLFLQEESYW FT RQRSKIFWLSEGDTNSKFFHASASARKRNNTIKKMRDNSGNWITSHDDMCT FT LVHDYFTSIFTARQGDHQPIISCVQPRITAEDNTILTQPFSEQEFKEAIFS FT MHPDKSPGPDGLNPAFYHRFWKDIGGEIFXTAINWLSSGVIPPDLNATHIV FT LVPKGDNPESMKDLRPISLCNVLYKIISKVLANRLRPLINKWISPEQAAFV FT PSRSIMDNALTAFEILHYMRCKRKGKKGEIALKLDISKAFDSVSWSYLQAI FT LSKLGFCSQWITWMMMCISTVEYHVIFNGDRIGPITPGRGLRQGCPLSPYL FT YIICAEGLSATIKNHELRGKIHGTRICRTAPPVSHLLFADDSFLFCKATIS FT EAQYLKDILSSYEHASGQAINYRKSAIAFSSNTPQDTISSIITCLGVYSAI FT GSGKYLGLPSMVGRSKKAIFSYLKDRIWKNCQSWSARSLSRAGKEILIKSV FT AQAIPSYCMGAFLIPTSLCEEIERMMNSFYWGSKKNGRRGINWMRWDKLTL FT HKSLGGLGFRNLEAFNLSMLGKQSWKLLSDSSSLFTRILKAKYFPRRDFLD FT ATLGHNPSYTWRSLWSTQSLLTLGHRWKIGDGSKINVWSMPWIRNLPSLKP FT STPPPLHHEDLTVNYLLNSDVNSWNITLVQSLFNSVDAAAIVSIPLFPRTA FT TDQRIWKATADGSYTVKSAYRICSDLIPAINHIQNDHRWNTIWNLQIPPRV FT RSFLWRLAHQCLPTRANLLTRGIPCDDSCVFCDPLAETHMHLFFVCTKASN FT CWELLGVNHIIRELLLTTNDFTTMLFDFIDRLHSQQQALVAMFLWSLWKSR FT NSKLWDAIDTTPISIVTRAKDTINEWSCMQRAKAPIHHANSVHSWIKPPVG FT TIKCNVDAATFNNNSIIGYGMCFRDYTGHLLIGKSDFLHSSATVLEAEALA FT LLDAIKLAISNGMHVVLFETDTKILADALTNNSSPTNEFGDLVTQCRSFLL FT NNPDFVVSYVRRQANRVAHSIARASLSHPSPHIFYHVSPTLYSLIMNEMN" XX SQ Sequence 3870 BP; 1070 A; 894 C; 721 G; 1183 T; 2 other; ttaactgttc gctgctcaac tactctcaga atttcataaa catgtctatt caggatcctg 60 caatagtaac tggagactca ccgctttcta cggatacccc gactcaggaa gacgtcgcga 120 ctcatgggac ctcctccgcc atcttagcag cctatcgaac gatccatggt gcattatcgg 180 agacttcaac gaccacctct catcagcaga caaacgagga ggccctgacc gccctccttg 240 gcttatccgt gggttccaag atgctgtaaa tgactgcaat ttatttgata tgccgctgtt 300 tggttaccaa ttcacatggt tcaagagtat tggtactgat tcctctaagg aagcgcgttt 360 tgatagagcc cttgtcacat cctcctggca aacacttttc cgaatgcagc acttcagact 420 ttggttgctc caatttctga ccacactcct cttcttctgc agcttcatcc aataccttgg 480 agacaacctt accgtagttt ccaatttaac aattcttggc tacttgagcc ggaactcaat 540 gaactggtga agaacaattg ggagcactat cctccctcca acattttaac caaactcaat 600 cattgtgtgg aagacatttc atcttggagc agttctgtta ccccaaattt caagcatctt 660 attaacaaac aacgatcagt cattgaagat ttcagaacat actcaaatga tgcaagtgat 720 cctcaacttc agctcctgca gaataatctc gctactttat ttctccaaga agagagttat 780 tggagacagc gttcaaaaat cttttggtta tcagaaggcg acacaaacag caagttcttt 840 catgcttcag cttcagccag gaaaaggaat aacaccatta aaaagatgcg tgacaattct 900 ggtaactgga taacatcgca tgatgacatg tgcactctcg ttcatgatta cttcacttct 960 atattcactg cgcggcaagg tgatcatcag cctattatat cttgtgttca gccaaggatc 1020 acagctgaag ataatactat tctcacacaa cctttctctg agcaagaatt caaagaagct 1080 atttttagta tgcatccgga taaatctccg ggcccggatg gcctcaaccc ggctttctac 1140 cacagattct ggaaagatat tggtggcgaa atattcwcta ctgctatcaa ttggctctct 1200 tcyggtgtca ttccccccga tctgaatgct acacatattg ttcttgttcc aaaaggggat 1260 aatccggaat ctatgaaaga tcttcgtcct atatccctct gtaatgtcct atacaaaatc 1320 atttctaagg tcctggccaa ccgtcttcgt cctttgatta ataaatggat ttctccagaa 1380 caagcagctt ttgttccctc tcgttcgatc atggataatg cgcttacagc tttcgaaatt 1440 ttacactaca tgcgctgcaa aagaaaagga aaaaaaggtg agatagctct gaaactcgat 1500 atttcaaagg catttgatag tgtcagctgg tcttatttac aagctatttt atccaaattg 1560 ggtttctgtt ctcaatggat cacttggatg atgatgtgca tctctaccgt tgaatatcat 1620 gtcattttta acggagaccg cattggcccc atcactccag gacgaggtct ccgacaaggt 1680 tgccctctct ccccatattt gtacattatt tgtgctgaag gattatctgc cactattaag 1740 aatcacgagc ttcgagggaa aatacatgga actcgcattt gtcgtacagc acctcctgtc 1800 agtcaccttc tcttcgcaga tgacagcttc ctattttgca aggcgacaat atcagaagct 1860 caatatctca aagacattct ttctagttat gaacacgctt cagggcaagc aataaactat 1920 aggaaatcgg ctattgcttt cagttcaaac actccacaag acacaatctc ttccatcata 1980 acatgccttg gcgtttatag tgcaatcgga agcggtaaat atctaggact cccatctatg 2040 gtaggtcgta gcaagaaggc aatcttctct tatttaaaag atcgcatatg gaagaattgt 2100 caatcttgga gtgctcggtc tctatcacgt gcaggtaagg aaattttgat caaatcagtg 2160 gcacaagcca ttccgtctta ctgtatggga gcctttctta tccctacatc tctttgtgaa 2220 gaaatcgaaa ggatgatgaa ctcattttac tggggttcga aaaagaatgg tcgtcgtggt 2280 ataaattgga tgcgttggga caaactcact ctccacaaaa gtctaggtgg ccttggcttt 2340 cggaacttgg aagcattcaa tctttctatg ctcggtaagc aaagttggaa actcttatcc 2400 gactcatcct ccttatttac tagaatcctc aaagctaaat atttccctcg acgggatttc 2460 ttggatgcaa ctcttggtca taatccaagc tacacatgga ggagtctatg gagtactcaa 2520 tctttactta ccttgggcca tagatggaag attggagatg gttctaaaat taatgtgtgg 2580 agtatgcctt ggatccgcaa tctcccctct ctcaaaccat caacaccgcc gccacttcac 2640 catgaggatc ttacggtaaa ttatttgttg aattcagatg taaattcttg gaatattact 2700 ttagtgcaat ctctttttaa tagcgtagat gctgcagcta tcgtttccat tcctctattc 2760 cctcgtaccg ctactgatca gcgcatttgg aaggctactg cagatggatc ttacactgtc 2820 aaatcagcat atcgtatttg ttctgacctt atacctgcca tcaatcacat ccaaaatgat 2880 catcgttgga atactatttg gaacttgcag atcccaccac gtgttcgatc ttttctttgg 2940 cgccttgctc atcaatgcct gccaactcgc gctaatcttc ttacccgtgg tattccatgt 3000 gatgattcgt gtgtattttg cgacccatta gcagaaacac atatgcatct attctttgtc 3060 tgcacgaaag catcaaactg ctgggaacta cttggcgtta atcacatcat ccgcgagctg 3120 ctactcacga ctaatgactt cactactatg ttgtttgatt ttattgacag gttacactcg 3180 cagcaacaag cactagttgc tatgtttctt tggagcttat ggaagagtcg taattcaaaa 3240 ctttgggatg ccatagacac tactccgatt tctattgtta ctcgagcaaa ggataccatt 3300 aacgaatgga gttgtatgca acgagcaaag gcaccaattc atcatgcaaa ttctgtccac 3360 tcttggatta aaccaccagt aggtacaata aaatgcaatg tcgatgccgc tacctttaac 3420 aataactcta tcataggtta tggaatgtgc tttcgagact atacgggtca tttgttaatt 3480 gggaaatcag attttcttca ctcatctgcc actgttttag aagcagaagc tcttgctttg 3540 cttgatgcta ttaaattggc tatttcaaat gggatgcatg ttgtattatt tgaaacagat 3600 actaagattc tagctgatgc actcaccaat aactcttccc ctactaatga gtttggagat 3660 cttgtaaccc aatgtagaag tttcttactt aacaatcccg actttgtagt gtcgtatgtt 3720 cggaggcaag caaatagggt tgctcatagt attgctagag cttcgctatc tcatcctagc 3780 ccccatattt tctatcatgt atcgcctact ttgtactctt tgattatgaa tgaaatgaat 3840 taattttgct tttgctcaaa aaaaaaaaaa 3870 // ID Copia-10_Mad-I repbase; DNA; EDCOT; 4471 BP. XX AC ACYM01115773; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-10_Mad-I; KW Copia-10_Mad-LTR; Copia-10_Mad_. XX NM Copia-10_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4471 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1288-1288 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01115773; Positions 13452 17922. XX CC Positions [1738-2232] - Integrase core CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS join(88..993,997..1959) FT /product="Copia-10_Mad-I_1p" FT /translation="MGDEKPTDVMPNASDPLTLHHSDSPGLVLVSKPLDGH FT NYGQWSRSMRIALSAKNKLGFIDGSIKAPAPSDAKFSIWQRCNDMVLSWIW FT QSVNAAISSSILYCKTASAAWKDLEDRFSQGNDSRIYQIRQEIAEYRQRQS FT SVSDYYTKLKALWDELGSYHEPIACDCEGSKTLAEREEKERVMQLLMGLND FT SYSTVRGSILMMSPLPDTRRVHGLVLQHERQLDVANSREPQSGVHAMQASR FT STMAKGSSSTGGSTSRKLLKCSYCDGDGHLVDRCFYLIGFPVGHKWHGKNV FT TPKNKRTSHVHNVEAPQPTNTVTDTTRATTTNGPMFTTEEYNQIIAMLRNG FT NGNGQQLANATGIYTSICNIAQHDPHSTLYWIVDSGATDHISRSPPTHNKT FT DTCHDFVGLPNGGQAEIKGIGSVKLSHDLTLDGVLHVPKFQVNLLSVSKMT FT RALRCFVIFFPDFCVVQDVDTKRTIGLGKHFDGLYYLTPSQNPHLANHVRH FT TTDLWHQRLGHPSSAPLHSLSTSVPEIMFESKHMCEICHLAKQTRLSFPSS FT SIKSIAPFDLIHCDIWGPHKIHTHSGARYFLTIVDDFTRFTWVHLMRFKSD FT TQSLIKSFFSWVKTQFHYDIKILRA" XX SQ Sequence 4471 BP; 1190 A; 1140 C; 880 G; 1241 T; 20 other; tggcatcaga gcaccgatcc tggtgacwct agaggctcat tcaccttccg ctacaaacac 60 agtcaatctt ccctgcaaac agcttacatg ggtgacgaga aaccaacaga cgtgatgcca 120 aatgcatctg atcctctcac ccttcaccac tcggattcac cgggtcttgt tttagtctca 180 aaaccccttg acggacacaa ctatggacaa tggagccgtt ctatgcgcat tgctctcagc 240 gcaaagaaca agctcggatt tattgatggg tctattaagg ctcctgcacc cagcgatgca 300 aagttttcca tttggcagag atgcaatgac atggtactat catggatytg gcaatcggtg 360 aatgctgcta tttcgagtag catactctac tgcaaaaccg catctgctgc ctggaaggat 420 ctggaggatc gtttctcgca agggaacgat tcaaggatct atcaaattcg acaagaaatt 480 gccgaatacc gacaaaggca gtcatctgta tccgactact acaccaaact caaggctttg 540 tgggacgaat tgggttcata tcatgagccc attgcatgtg attgtgaggg atcgaagaca 600 cttgccgaaa gggaggagaa ggagagagtc atgcaactct tgatgggatt aaatgactcg 660 tactcgaccg tacgaggatc gatcttgatg atgagtcctc tcccagacac acggcgagtc 720 catggcttag tccttcaaca cgaaagacag ttggatgtgg caaacagtcg tgagccacaa 780 tctggtgtcc acgcgatgca ggctagtcgc tccacaatgg caaagggcag ttccagtaca 840 ggcggttcta cctcgcgcaa gctgctgaaa tgcagctatt gtgatggtga tggacatcta 900 gtggatcgct gcttctatct cattggcttc ccagtrggcc ataaatggca cggaaagaat 960 gttacaccca agaataaacg cacatcccat gttgytcaca acgttgaagc acctcagcca 1020 actaataccg taactgacac aacaagagca accaccacca acggcccaat gttcacaact 1080 gaggagtata atcaaatcat tgccatgctt cgaaatggga acggtaatgg ccagcaactt 1140 gcaaatgcaa caggtattta tacatccata tgtaatatyg cacaacatga tccacattca 1200 acactttact ggattgttga tagtggggcg actgatcaca tctcccgctc accaccgacg 1260 cacaataaaa ctgatacttg ccatgatttt gtgggcttac ctaatggggg acaagcagaa 1320 attaaaggaa ttggctctgt caagytgtct catgatctga cacttgatgg agttcttcat 1380 gttccaaagt ttcaagtcaa tctattgtct gtaagtaaaa tgacacgggc tctacgatgt 1440 ttcgtaattt tctttccgga tttttgtgtt gtgcaggacg tggatacgaa gaggacgatt 1500 ggcctgggca agcattttga tgggctctat tatcttacac caagccaaaa cccgcatcta 1560 gccaaccatg ttcgccacac tactgaccta tggcaccaac gcctaggaca cccttcatct 1620 gcacctttac attccttgtc aacaagtgtt ccagaaataa tgtttgagtc caaacacatg 1680 tgtgaaattt gccatttggc aaaacaaact agattgtctt ttccttcaag ttcaattaaa 1740 tctattgcac cttttgactt aattcattgt gatatttggg ggcctcacaa aattcataca 1800 cattcagggg cacgttattt tttaaccatt gtagatgatt ttactcgatt tacwtgggtg 1860 catcttatgc gtttcaagtc tgatacacaa tccttgataa aatcattttt ttcttgggtc 1920 aaaactcaat ttcattatga cattaaaatc ttacgcgccr acaatggtgg tgagtttcta 1980 tccatgcaca attttttgga aacaaatgga accatcttcc aacattcttg tacacatacc 2040 cctcaacaaa acggagttgt tgaacgtaaa catcgrcatc ttttaaatat tggacgtgcc 2100 ctccgttttc aagccaattt accactaaaa ttttgggggg aaagtatcca aaccgcttgt 2160 tacctcatca atcgacttcc cacaccatta ttatgccacc aatctcccta tgaacgttta 2220 catggtcaac macccaatta ttcccatcta cgagtttttg gatgcctttg ttatgccaca 2280 aatcttcttc ccacacacaa atttgatgca cgtgcacgac gatgcatttt ccttggctat 2340 cccctaggac aaaaaggtta tcgtgtctat gaccttgcaa ccaagcaatt ttttacctct 2400 cgagatgttc wttttcatga gcatattttt ccctttgcac actccccacc agaacatcaa 2460 aatgatctcc ctgtacttcc tatcctacca gatgcccaat tttccaacct tcccattttc 2520 ccaccttcag ccccacctac ggacccacct actctccacc cygcaactta tcmggaccac 2580 aaccccataa accatcttcc acacgcccct gattccccca ttcctgatgc ttccccttcc 2640 tcacctaacc tcactccacc acttcaatca tcacccactg atcacttcaa tccctcccca 2700 ccttcatcct caccgccacc tccaccccct ccacttcggc agtccacccg acctaaacat 2760 ccacctgcat attttaaaga ttatacggct tatcatgcgg ctttgctcac gcccactact 2820 gcctcttcct ccacgtccgg tactcgctat cccctccaac ggtacgtttc ttatgctcat 2880 ttgtcacctg cttaccggac ttttgtttct aatgtatctc aacttgtgga accatccact 2940 tatgaacaag cttgtcataa ccctcattgg gttgtagcca tggccactga acttcaagct 3000 cttgaagcaa atcagacttg gagcatggtt tctttgcctc ctggtcagcg tccgatcagt 3060 tgtaartggg tcttcaagat caaatataaa tcggatggaa cgatagaccg ttacaaagct 3120 cgtcttgttg ctaagggttt tacccaacgt gaaggtatcg attacaaaga aacctttgct 3180 ccggtcgcga agctcaccac tgtgcgttgt ttgttgaccg tcgctgctgt tcgtaattgg 3240 cctttacatc agatggatgt gcagaatgcg tttcttcatg gtgatctcca tgaagaagtg 3300 tacatgctgc ctccgcctgg ttctcgtcga cagggggagc rtctcgtgtg tcgactccat 3360 aagtctttgt acggactcaa gcaggcctcc cgaagttggt ttcaaaaatt ccactctgcc 3420 atttgcgawa ttgggttcac acaatctcgg gctgattact ctttgttcac tcaagtcact 3480 ggtggttctc tcaccattat attactatat gttgacgact tggttattac agggaatgat 3540 gatgccgcaa tcaacaatct taaacaattc ctcaatagcc gcttccggat taaagatctt 3600 ggacccttga aatacttcct tggartcgag gtggcacgtt caaaagccgg cattaccatt 3660 tgtcagcgca aatacacact agacatactg gaagaggccg gtttacttgg tgttaagccg 3720 gcaaaggtcc caatggagcc tgacttggta ttattgccta ctggtagcga tcctctcaaa 3780 gatccaacga gatttcgacg attaattggg aagttgattt acttgacaat tacaaggcca 3840 gaaatcatat atgccgtcaa taccttaagc caatttatgc aggagccaaa gcgacatcac 3900 cttgatgcag cacatcgact cctccaatat cttaaagaag ctccaggtca agggttattt 3960 ctctctgcac aaagtaaact gaatttgatt ggttattgcg atgcggattg ggctcgttgt 4020 ccgatcacac gccgttctgt cacaggttat tgtatctttc ttgggaactc acttgtatcc 4080 tggaaaagca agargcaggt cactgtagca cgttcatctg cggaagcaga gtatcgttcc 4140 atggctgcaa taacttgtga actaacatgg ttaagatact tgttgaggga cttgcatgta 4200 actcatccta atccagcaag attattttgt gataatcagg ctgctttgta cattgcagca 4260 aatcccgtgt tccatgagcg gaccaaacat attgagcttg actgtcatac tgtccgcgag 4320 aaaattcaaa ggggagaagt tagaacggcc tatgtacaaa caggggaaca aattgctgac 4380 atgtttacca agccattgcg ggcacctgtt ttccgttcac aycttggcaa gttgggtgtt 4440 rttgatatcc acactccaac ttgaggggga g 4471 // ID CAREP1 repbase; DNA; EDCOT; 1966 BP. XX AC AJ411810; XX DT 01-SEP-2005 (Rel. 10.08, Created) DT 01-SEP-2005 (Rel. 10.08, Last updated, Version 1) XX DE Cicer arietinum Ty3-gypsy like Retrotransposon CaRep (partial DE sequence). XX KW Gypsy; LTR Retrotransposon; Transposable Element; integrase; KW pol gene; polyprotein; RNase; CAREP1. XX OS Cicer arietinum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; OC Cicer. XX RN [1] RP 1-1966 RA Staginnus C.; RT "Thesis (2001) Department of Plant Molecular Biology, University RT of Frankfurt / M., Frankfurt a.M., Germany."; RL Direct Submission to EMBL/GenBank/DDBJ (07-JUL-2002). XX DR Genbank; AJ411810; Positions 1 1966. XX FH Key Location/Qualifiers FT CDS 2..1963 FT /product="CAREP1_1p" FT /translation="QLYANLSKCEFWLEKVNFLGHVITKEGIAVDPAKIEA FT VLAWKQPQTVTDIRSLVGLAGYYRRFIEGFAKIVAPLTQLTRKDQPFAWTE FT KCEENFQLLKRKLTTSPVLVLPQSEEPHEVYCDASHQGLGCVLMQHKKVVA FT YASRQLKIHERNYPTHDLELAAVVFALKIWRHYLYGCTFTVFSDHKSLKYL FT FDQKELNMRQRRWIETLKDFDFTLQYHPGKANVVADALSRRSVSVSSLIMA FT RQQELWEAFRDLHLNVEFAPGILKFGMIKISSGLLEDIANSQDDVLIQEKR FT NLIVQGKTTEFKIGADNVLRCNGRICVPEITAMRKTILEEAHKSKLSIHPG FT ATKMYQDLRQNYWWPGMKKHVAEYVSTCLTCQKAKVEHQRPAGMLQPLDIP FT EWKWDSISMDFITGLPKTRRKNDSIWVIVDRLTKSAHFLPVRTTYKVDQLT FT EIYIAEIVRLHGVPSSIVSDRDPKFTSHFWGALHEALGTKLRLSSAYHPQT FT DGQTERTNQSLEDLLRACVLDDRGSWDHVLPLIEFTYNNSFHTSIGMAPYQ FT ALYGRKCQTPLCWYKDGENMIVGPEMVQQTTAKVKKIKEKMKTSQDRQKSY FT ADKRRRLLEFEQGDHVFLRVTPTTGVGRALKSKKLTPKFIGPYQIYARIGP FT VAYRI" XX SQ Sequence 1966 BP; 594 A; 343 C; 517 G; 512 T; 0 other; gcaattgtat gccaatctgt cgaagtgtga attttggcta gagaaagtga atttcttggg 60 acatgtgata accaaggaag gaattgctgt agatccggct aagattgagg cggttcttgc 120 ttggaaacag cctcagaccg tcactgacat acggagtctt gtaggactgg cagggtacta 180 caggaggttt atcgaaggtt ttgctaagat tgtggctcca ctgacacaac ttaccagaaa 240 agatcaaccg ttcgcatgga cggagaagtg tgaagaaaac ttccagttgc taaagagaaa 300 gttgacgacc tcacctgtat tggtattacc gcaatcagaa gaaccccatg aagtttattg 360 tgatgcatct caccaggggt taggatgtgt tctgatgcaa cacaagaaag ttgtggctta 420 tgcctcgaga caattgaaga ttcatgaaag gaactatcct actcatgatt tggagcttgc 480 cgcggttgtt tttgcattaa agatctggag gcattattta tatgggtgca cgttcaccgt 540 gttcagcgac cataaaagct tgaaatattt gtttgatcag aaggagttga acatgcgcca 600 gagacgatgg atagagactc tcaaggattt tgatttcaca ctacagtacc accctgggaa 660 ggccaatgta gtggctgatg cgttgagcag aagaagtgta tcggtgtctt cactgattat 720 ggctagacaa caagagttgt gggaagcttt tagagacttg cacttgaacg tagagtttgc 780 accgggaatt ttgaaattcg gaatgattaa gatctcgagt ggattacttg aagacattgc 840 gaattctcag gatgacgtct taattcaaga gaagaggaat ctaatagtac aagggaagac 900 gactgagttc aagattgggg cagataatgt tttgcggtgt aatggtagga tttgtgtacc 960 agaaattaca gctatgcgga aaacgatttt agaagaggcg cataagagta agctgagtat 1020 tcatcctgga gcaacaaaga tgtatcagga tttgaggcag aattattggt ggccaggaat 1080 gaagaaacat gtggcggaat atgtgtccac ttgtctaact tgtcagaaag cgaaggtgga 1140 acatcagcga cctgctggaa tgttgcaacc tttagatatt cctgaatgga agtgggacag 1200 catttccatg gattttataa ccggattacc gaagacaagg aggaaaaatg attctatatg 1260 ggtgatagtg gaccggctga ctaaatctgc tcacttttta ccggtaagga ccacctataa 1320 ggtagatcag ctaacggaga tctacattgc tgaaattgtg aggttacacg gggtaccatc 1380 gagcattgta tcagaccgtg atccgaagtt cacatcgcat ttttggggag cattacacga 1440 agcgttggga acgaagctac gattgagctc agcttaccat ccacaaacgg acggacagac 1500 tgaaaggaca aatcagtcct tggaagatct gttgagagca tgtgttttag atgatagagg 1560 aagttgggat catgtacttc cgttgattga gttcacttac aacaatagtt tccacacaag 1620 tattggaatg gcaccatatc aggctttata tgggcgcaag tgtcaaacgc ccttgtgttg 1680 gtataaagac ggtgagaata tgattgtcgg accagagatg gtgcaacaga ccacagctaa 1740 agtaaagaag atcaaggaga aaatgaagac ttcacaagat cgtcagaaga gttacgcgga 1800 caagcgtcgc agacttttgg aattcgaaca gggtgaccat gtatttctga gagtcacacc 1860 tactactggg gtaggtagag ccttgaaatc gaagaagttg actccgaaat tcattggacc 1920 atatcagatt tatgcacgaa ttgggccggt tgcttatcgg attgca 1966 // ID SINE_LC repbase; DNA; EDCOT; 141 BP. XX AC . XX DT 17-NOV-2004 (Rel. 9.1, Created) DT 15-APR-2011 (Rel. 16.04, Last updated, Version 2) XX DE Lotus corniculatus var. japonicus SINE element. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; SINE element; KW SINE_LC. XX NM SINE_LC. XX OS Lotus corniculatus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RP 1-141 RA Gentles A. and Jurka J.; RT "SINE element from L. corniculatus."; RL Direct Submission to Repbase Update (31-AUG-2004). XX DR [1] (Consensus) XX SQ Sequence 141 BP; 47 A; 31 C; 23 G; 38 T; 2 other; caggggcgga cccagcatag aggtgagggg gttcagttga accccctgga aaaaaaaaaa 60 atyacactta cccccctata taaattattt acccccttat ataaattttt ttttgaaccc 120 cctgaaaatt ttaaattgya c 141 // ID Gypsy-29_VV-I repbase; DNA; EDCOT; 11468 BP. XX AC chr3; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-29_VV_; KW Gypsy-29_VV-LTR; Gypsy-29_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-11468 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr3; Positions 16904223 16915690. XX CC 'GCCTG' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 6112..7065 FT /product="Gypsy-29_VV-I_1p" FT /translation="MVPPISRGLALISPQGDYIPRSVRLAFSDHHRLTNNI FT VEYEACITGLETALDLGIRQLEVHGDSNLVIKQTQGIWRTRDEKLKPYHAY FT LDLLIDRFDVLRYIHLPRAENQFADALATLASLIVIPAGVNVRPLLIETRS FT VPTYYCLIGEIEDQIELPWYHDIYQFLSCGTYLESASAKDRRALRQLATRF FT VVYGDALYRRSPDGLLLLCLDRASADRVMREVHARVCGPHMGGHMLARKIM FT RTGYFWLTMETDCCQFVQRCQECQMHGDLIHVPPSELHALASPWPFSVWGI FT DIIGKISPKSSSGHEYILVAIDYFTK" FT CDS 10016..11233 FT /product="Gypsy-29_VV-I_3p" FT /translation="MASLPPFSSMVPRHRARVRSPGFHHFSVLARTLLQYS FT PRAFSVLARTLLRYLPGTFSGTRSEPSPVLAQSFFGTCPNPSPVLARTLLR FT YSPGAFSVLARTLLWYLPGTFSGTRPNFTRFRYSPEPFSGTRPEHFRYLPG FT TFSGTYPEPSLILARSFFGTCPNPSLVLARSFFGTCPNPSLVLARSLLRYS FT PETFSVLARNLLRYSPGAFSGTRPELFWYLTEPFSGTCPNPSPVLARSFFG FT TCPNPSLVLAQNLLWYSPGAFPGTRPELFRTCPNPSLVLARTLLWYSPEFY FT PFSVLARIAPFSGTRPELFQYSPGTFSDTRPEPSPILAQTLLWYSPGTFSV FT LARSLLQYSPGAFLVLARNLLRYLPKPFSGTRPNFTRFRYSPGFHHFSVLA FT RTFLRYLPGSNP" FT CDS join(2277..4826,4830..6104) FT /product="Gypsy-29_VV-I_4p" FT /translation="MPLSRAFQRLVEGGLITPLPPRPPLQPTPPGFRTDLH FT YAYHQRAGHDTDSCSALRHAIQDLIDQGLVDLGRPGVATDPLPTHDTRVVP FT PPPEGVHLIEFAGDEIFMMGWDGEAPQPISLYEESDFVGYIPRQQIPRPFS FT LTPDRIYGPPPVSPVYLQHVPPMTPFILFPEEYRPPHRDVQIVTQSGRVAQ FT PPPVDRPFAGIAAREEVQREDEILRQLHTTQARISIWSLLASSSTHRDALV FT RALSQIRVDTATIPEGLIHMLTADRATCIVFSDDDLPPEGSNHVRPLFIDV FT ACLGRQVSSVLLDNGSALNVCPLVTAIALGFSPDDFGPSTQTVRAYDGTQR FT TVMGTLSTHVMIGPVSYSIVFQVLRIQSSFNLLLGRPWIHEAGAIPSSLHQ FT KVKFIHEGCIITIQSDRDIITSSKPVLHISHSEDDLHLTGFTFDEVQVISL FT EDGSRDMVPMSFDQHSSTLVLSMMRGMSYLPGMGLGRRQQGPHEFTFTVDH FT DTPYGLGYIPTEADARYMSQLRRDRVRARMSGIPFDYLLRSYTFQLADYFI FT RGSEHTPRTKGTVHIPGTVEIQDIQQALGQIHLDTGTTEAPGAMIVMPPSP FT DRASMFSMCFPEEVPDYDLPMDLGYGTDEMDMIGIGRILDATPRRPLSAFD FT ISGVSVLGDESVLDVVTSDFAFVEGASDSVDPPLSFDTMSGFVTRFDDISD FT GNNDMSIFKYLNVSQHFPLIAPPAPTTHIYDVDDVGDTDDPLGGQSECDSD FT TEDRKVTPISSSTELIDFGAPDQPREIRIGSSLSPDERSRLIDLLRSYLDV FT FAWSYEDMPGLDPTIVQHHLPILPHARPVKQKLRRLHPRWSLQVKEEIKQL FT SVGFLSVVEYPEWLANVVPVPKKNDKVRVCVDFRDLNKASPKDDFPLPHID FT MLVDSTTGHPMLSFMDGFSGYNQILMAPEDMVKTSFITEWGTYCYRVIPFG FT LKNAGATYQRAATTLFHDMMHRDVEVYVDDMIVKSRDRADHLAALQRFFER FT IRQFRLRLNPKKCTFGVTSGKLLEHIVSERGIEVDPEKIRAILDMPTPRTE FT KEIRGFLGRLQYISCFIARLIDICEPIFRLLRKNQPIVWNDDCQRAFERIK FT ECLLSPPVLVPPTPGRPLLLYLSVSDMALGCMLAQLDDLGKERAIYYLSKR FT MLEYECKYIMIECLCLAVVWATRRLRHYMTEYSMLLVSRLDPLRYLFDRPV FT LTGRLMRWLVLLTEFDIHYVTQKSIKGSIVADHLASLPISDDRSIDDDFPD FT EQIVSMTSITGWRL" XX SQ Sequence 11468 BP; 2553 A; 2611 C; 2786 G; 3518 T; 0 other; aattggcgac tccgctgggg atcgaaccca gaatctctgg tttcataaga ggatcaagct 60 tgaacttgag ttgggtatat cggagcacat ggttcattga taagtagact cttaggctac 120 atagatgact tatgatcatg tagttggttg gtatgtggct tgcacctctg atgtgttgtt 180 gcttgtgtgt tcacctgttg gattctagca tgcttgctca ttgttgattg gtatctagtt 240 atgacatttg ggattagact tagatgatta gattgtgtgt agatgtgtgg taggctatct 300 ctttgtgcat gactatttgc tgtatgactg ctccttccct tgcatgactg cttgctgctt 360 gtgtttgtgg ggcacgtgtg tatcccctta attccgaatc actagtcttg gtcaactatt 420 cctcatggat tgcttgtgtt tcttgggagt cattcccaac tgttcgcctt cgaccaagct 480 aggggtttgg aatagggtct agcataaggg ctatattgat gtttgggagc actatggaaa 540 agatgaatat ctgagcaatg aagacttgta tagccctgag ctggatttca tggagacata 600 cgtggccagc atgtcacttt gattgttgat tgattgttag ttaggacctt aggttgcgta 660 tccctgtggg tatagtcatc tagtctttta ggacttgcct tttctctctc tttttttact 720 tttgagccac attacccctg aggtatcacc atgtcagaat cccgttcctg cttgtggaac 780 cgtatatcag tttagctatt gacatcacat gtcagttcat tctctcggaa gattttagtt 840 atacgttcct agtttgattt caggattgat agtcacgggg actgacgtac ccctttcctt 900 ttgtaggatt attgattgag atcgacctgg gttcccaagc ttggatccag attggagata 960 gactggttag aggatcggat tcacccaacc agttagagca gataccagat catagagata 1020 tggaccctca gtatgctacc gttgaccagt tggctgagat taccgatacc atggcgtcac 1080 ttagggacgc tatcttagga ctgggtcaga ggattgatgg gcaccaggcc cagccattgt 1140 cgattccggg gagcaccctg catgactcta ccacaccatc accaccacca ccatctgggc 1200 catttggacc tactatacaa caggactaca tagttccacc accaccggtt cagtcagctc 1260 cccaagctgg agcatttatg ttgcatggtc agagtgagac tatgccgcat tctattgtgg 1320 caccggcaca gattgttgat gatacccatg ctcgtattga taggattgag caaagaatga 1380 gatcactaca tgtttctgat gggattatgg gttgggatgg atatgatgat atgccagtag 1440 cagctttgcc tgttgagttc cgcatgccgg acattgagag atacatgggg atagggtgcc 1500 ctcgtattca cttgcagtta tacagcactg ttatgcgtgg gcatagactg gatgaagcac 1560 aaatgattat gttattccct ctgtcattga gtggtgctgc ttagcgttgg tttgcctcat 1620 tggacccttc gagacgtagg acatgggctg atttgggaca ggagtttatt agacagtatt 1680 ctttcaatac tatagtggat gtatcccgga gggagttaga ggcccttagg caagggccgg 1740 atgagacagt cacttcattc atctcctgtt ggagagagaa gatagcacag attattgata 1800 ggcctttaga gcgtgatcag atcagtatga ttatgcgcag ccttcagccc cgctttgcta 1860 ggcatctcat gggcttccct cagacagact ttggctcatt agtgcaagcc ctctatggca 1920 ttgaggaggg tatatctaga ggtttatggg tagattcttg cccttcagac tcaaagggga 1980 agaagtcggg atcaggcccc aggccctcag atgttggtac tattggcatg acaggacacc 2040 gatcttcacg tcgtcctccg tttcagagtc agtttttagg cactccttat cagatgatac 2100 agcatggtca gtacagacca gttgctccca ttaggccagt aaggcctact tatctacatc 2160 cgccaccaca gccggtatat gctacacagg caccccaaag gccgcctatg tagttccatc 2220 atcagtatag agcaccacct ccaccgaggc cagttagaca gttcacacag cttgggatgc 2280 cattgagccg agcttttcag agattggttg aggggggact gattacccca ctaccgccta 2340 gaccaccact acaacctacc cccccaggat tcaggacaga tcttcactat gcctaccatc 2400 agagagcagg ccatgataca gacagttgtt cagcactgag acatgccatt caagatttga 2460 ttgatcaggg cttggttgat ttggggcgcc cgggtgtagc cacagacccg ctacctactc 2520 atgacactag agtagtacct ccacccccgg aaggggtaca tttgattgag tttgcagggg 2580 atgagatatt tatgatgggt tgggatggag aggctcctca gccgatcagt ctatatgagg 2640 agtcagattt tgttggatat atacctagac agcagatccc caggccattt agtttgaccc 2700 cggacaggat ttatgggccg cctccagtat caccagtata cttacagcat gtgccaccta 2760 tgacaccctt cattctgttc ccagaggaat ataggccccc tcatagagat gttcagatag 2820 ttacacagag tggaagggta gcacaacctc cacccgttga caggccattt gctggtatag 2880 ctgctagaga ggaggttcag agagaagatg agatattacg ccagctacac actactcagg 2940 ctcgcatatc catttggagc cttttggcct catctagtac acacagagat gcattagtca 3000 gagcccttag ccagattaga gttgacactg ctactatccc agaggggctt attcacatgt 3060 tgacagctga tagagctaca tgtatagtgt tttctgatga tgacttgcca ccagagggat 3120 caaatcatgt tcgaccctta ttcattgatg ttgcttgttt aggtcgtcag gtgtcgtctg 3180 ttctattgga caacggctct gccctgaacg tctgtccatt ggttactgcc attgcgcttg 3240 ggttttcacc agatgatttt gggccttcta cacagactgt tagagcttat gatgggactc 3300 agaggacagt tatgggtaca ctcagtacac atgtcatgat tgggccagtt agttactcca 3360 tagtatttca ggttttgagg attcagtcat cctttaacct gcttcttggc cgcccgtgga 3420 ttcatgaggc cggtgctata ccatcttccc ttcatcagaa ggtgaagttc atacacgagg 3480 ggtgcattat cacgatacag tctgatagag atattatcac ttcgtctaag ccagtattac 3540 atatcagtca tagtgaggat gacttacatt tgaccgggtt tacgttcgat gaggttcagg 3600 ttatcagttt agaggatggc agcagagata tggtacctat gtcatttgac cagcacagca 3660 gcactttggt gctcagcatg atgagaggca tgtcttattt gcctggtatg ggattgggtc 3720 gccgccagca agggccccac gagtttactt tcacagttga tcacgacacg ccctacggat 3780 taggttacat acccacagag gctgatgcac gttatatgtc acagctgcgc agggataggg 3840 tgagggctcg catgtctggc attccatttg attatctcct ccgctcatac accttccagt 3900 tggccgacta cttcattagg ggttcagagc atacacctcg cacaaagggg actgttcaca 3960 ttccagggac agttgagatt caggacatcc agcaggcctt gggtcagatt catttggaca 4020 ccgggactac tgaggcacct ggtgccatga tagtcatgcc cccatcaccg gatcgagcta 4080 gtatgttctc tatgtgtttc cccgaggagg tccctgacta tgacctacct atggatttgg 4140 gatatggcac tgacgagatg gacatgatcg gcataggtcg tatccttgat gcaaccccac 4200 gcaggcccct ttctgctttt gacatatctg gagtttccgt acttggtgat gagtcagtcc 4260 ttgatgtcgt tacttctgat ttcgcttttg ttgagggagc gtccgactct gtggacccac 4320 ctctttcttt tgacactatg tccgggtttg tcacccgctt tgatgatatt tctgatggta 4380 ataatgatat gagtattttc aagtacttga atgtgtcaca acattttcct ttgattgcac 4440 caccagcacc cacgacacat atatatgatg ttgatgatgt gggagataca gatgacccac 4500 taggtggtca gtcagagtgt gattctgata cagaggatag gaaagtcaca cccatttcta 4560 gtagcacaga gttgatagat tttggggcac cagatcagcc cagggagatt aggattggct 4620 cttctctatc tcctgatgag aggagtagat tgattgacct gcttaggtca tacttggatg 4680 tatttgcatg gtcatatgag gacatgccgg gccttgaccc caccatagtg cagcatcacc 4740 tgcccatttt accacatgct aggcccgtta agcagaaatt gaggagacta caccctcgat 4800 ggagtttgca ggtgaaggaa gaaatttaga agcaactcag tgttggcttc ttgtcagtgg 4860 ttgagtatcc tgagtggctg gctaatgtcg tccctgttcc caaaaagaac gacaaggtta 4920 gagtttgtgt tgactttcga gatctgaata aggccagccc taaggatgat tttccccttc 4980 cacacattga tatgttggtt gatagcacta cagggcatcc gatgttatcc ttcatggatg 5040 gtttttctgg gtataatcag attttgatgg ctccagagga tatggtgaag acttctttca 5100 ttactgagtg gggtacttac tgctaccgag ttattccatt tgggttgaag aatgcaggag 5160 ccacttatca gagagctgct actactctgt tccatgatat gatgcataga gatgtcgagg 5220 tctatgtgga tgacatgata gtaaagtccc gagacagggc agatcactta gcagccttac 5280 aaaggttttt tgagaggatc agacagttca ggctgagatt gaatcccaag aagtgcacct 5340 ttggggtgac ttctggaaaa ttgctggaac acattgttag tgagcgaggt atagaggttg 5400 atccagagaa aatcagagcc atacttgaca tgcctacccc gaggactgag aaagagataa 5460 ggggattcct aggtagattg cagtacatca gttgtttcat tgctagactg atagacattt 5520 gtgagcctat cttccgcctt ctgagaaaga atcagcctat agtttggaat gatgattgtc 5580 agcgcgcttt tgagaggatt aaggagtgtc tcctttctcc tccggtttta gtgcctccca 5640 caccggggcg tcctttgctt ctgtacttat cagtttcaga catggcctta ggatgcatgt 5700 tagctcagct tgatgatttg gggaaggagc gagccatcta ttatttgagt aaaaggatgc 5760 ttgagtatga gtgcaagtac attatgattg agtgcctttg cttagcagtg gtttgggcca 5820 ctaggagact tagacattac atgacagagt attctatgct cttggtctca cgattggacc 5880 cgttgaggta tctatttgac aggcctgttc tgaccggtag gctcatgaga tggctggtat 5940 tgttgacaga gtttgatatt cattatgtca cgcagaagtc aataaaggga agcattgttg 6000 cagatcatct agcttctttg ccgatatccg atgaccgatc aattgatgat gatttccctg 6060 atgagcagat tgtttcaatg actagtatta cggggtggcg gttgtaattt gatggtgccg 6120 ccaatcagtc ggggtttggc attgatatca ccacagggtg attatatccc cagatcagtc 6180 cggttagcat tttctgatca tcaccggttg acgaataata ttgtagagta tgaggcttgc 6240 attacaggtt tggagactgc acttgatctt ggcattagac agttggaggt ccatggggat 6300 tccaacttgg ttataaagca gactcagggt atctggagga cacgggatga gaagctgaaa 6360 ccctaccatg cttacttgga cctgttgatt gatagattcg atgtgttaag gtatatacat 6420 ttgcccaggg cggagaatca gtttgccgat gccttagcca ccttggcttc tctgattgtg 6480 atccctgcag gggtgaatgt taggccattg ctgattgaga ctaggtctgt accaacttac 6540 tattgtctga ttggagaaat agaggatcag attgagctgc catggtatca tgacatttat 6600 cagtttttgt catgcggcac ttacctagag tcagcctcgg ccaaggatag gagagcattg 6660 agacagttgg ccaccagatt tgttgtttac ggggatgcac tgtataggag atcacctgat 6720 ggcttgttat tattatgttt agaccgtgca tctgcagatc gagtgatgag agaggttcat 6780 gcaagggtct gtggcccaca catgggaggt catatgctag cacgtaagat catgaggact 6840 ggctactttt ggttgaccat ggagacagat tgttgccagt ttgtacagag atgtcaggag 6900 tgtcagatgc atggagactt gatacacgtg ccaccttctg agttgcatgc acttgcatcc 6960 ccttggccat tttcagtatg gggtattgat attattggga agatctcgcc caagtcttct 7020 agtgggcatg agtacatttt ggttgccatt gactatttca ccaagtgagt ggaagctgct 7080 ttttatgcta ggttgacagc ggccagagtg gccaagttca tcagatcgca tattatctgc 7140 tgatacgggg tccctcatga gctgatctca aacagagggg tgcatttcaa gggcgaggtg 7200 gacacgttga ttcaagagta tggcattcag catcacagat catctgcata caggtcgtag 7260 actaatggag cagttgaggc cgcaaataag aatatcaaaa ggattttgag aaagatggtc 7320 gagacttctc gggattggtc agagaagctc cctttcgcat tgtgggctta tcgtacatct 7380 tttcgtacct ctattggagc taccccgtat tctttggtgt atggtatgga ggcagtgcta 7440 cctgttgaga ttgagatgag atctttgaga gtagcactag agcagcatat atccgaggcc 7500 gagtgggccc agtctcgtta tgatcagctt agcctgttgg atgagaagag attgaaggtg 7560 gcagatcatg ttcaggccta tcagaggaag atgacctgtg catttagaaa gagggtcaag 7620 cctaggaaat tccagagagg tgacctagtc ttgaaagtcc tcaggggatt gatcaacgac 7680 cctcgaggta agtttagacc gagttggagc gggccttatg tcatccgaga tctgactcga 7740 gagggagctg cttggttgac agacctagac ggaaatcagt tcatagagcc agttaatatg 7800 gatcagctga agaagtttta tgcgtgagat catggtcaga ggatgggtgg ccgtcacttc 7860 gagtagccat attccctatt gcacacccat acattgatat atactattgc tagcccttta 7920 agcctcacgt ggtttattat ggccttttct ttcattcagc cttgcatacc ttttctgacc 7980 tgggttgggg gcctaccctt gtgcgctttg tatttattga ttggatctat gagcattgtg 8040 ggcatggtgt cattcttcgt ttgttctttc ttgcatcatt gcctgtttct tttcgtctcc 8100 attttgcatc ttcacactgt ctacctgtta gtcgagtttc tatcatcttt attcacttcg 8160 cttctgtttt cccttgtgtg atgatgatgc gctttcgtcc tagagctacc agtcaagttt 8220 gtcacactct tcgttccgcc tgtaggcttt gatccaagat tcttaggttg aaggggtcgg 8280 tcaagattgg aggtttgggg ttctttttgt tggattgtga tagtatggaa ttcggcccaa 8340 aaaaaaaaaa taataataat aataataata aaataaaata aaaatgaaaa aaaggaaaaa 8400 ttgtgcttgt ttggtattcg ttgatatact tgggatcatc agaggtggtt ttgggtttga 8460 gagatttctt tttcctttaa gagtcgggtg agagcattgt acgatccttc tcaccatgga 8520 tctgggcgac acattgggag tgaggtttgg gtttccttgg cactaggccc ttggatcatt 8580 gtctacatca ccattcccat catatagtga cttgctttga tttggcgttc ttaggatgag 8640 ttgttcgtcg ttgtcacata ttgctatatt tgtatcccag ttggtttctc cattttcttc 8700 tacacccatt catcattcat cttatccttt ttcgtctgct tctatcctcg tcgatcgtcg 8760 tttcacttca tgaacgatga gttctttggt gcgtatcacc tattgtttgt ttttttttat 8820 ttggatgcag ggttgagtca ccttgctcac atggttctgc gatgtttgac attgcacaca 8880 caggggtttg gcattatcta ttaggagatt tgggcctttg tttcccatcg tttcattcac 8940 cttttacccc tggcctacat tacggtccga gtcgtaagac caccctgagg ccatgagatc 9000 tcgtgtttgc ttcgatgcgg ttcattcgga caggcttcgt ctactgattg agtatgggat 9060 gttgacaggt ctccattatt tcgggggata tcgagggtca catattgtct ttccattcag 9120 tttacttgcc tcaggtccat gatcagagat agatgataca gagagttggg accgttgagg 9180 gcacctttgc ctgatgtttt gacacgttta tactagggca tgctcccatc tttgcatgtt 9240 ggctttagct ctttatacat gtacgcaggc attccatttc gcctagcaat gttatggaca 9300 tcaaagtttg agtaagcccc gcattcagcc caatttcttc atatagcaga gtgcttctga 9360 ggtctgaccc gagatcagat tcacggtatt catcgaccca gcaggggtgc ataccccatt 9420 cattgtcttg tttgttagtt caaatgagtg ggtcttcagt gatgtattcc agagttttca 9480 ttaagatatt tgagtttcaa atgtacacac tagggcatat cccctatcag tttttgtgga 9540 tattggatgt tgtggattag agtggagggt tttttttcct tagaaatgga tgattgtgat 9600 attttcagct ctctgacttt aaccatatgt gcggttatag gattctgaca tgatattgat 9660 atcttagact ggggcataac tcctttcttt cacctttggt cacatttgtg agtttgtcct 9720 ataggggcat acccccttct ttccatttgt tagtggtgat tatgatttct cgcttgtcat 9780 ttatcggcat tttctggtgt tacaccggga catacccctt tcttttgtca tgatgaaggt 9840 gtttgatttc tggcttcttc gagtcatctg ttggcagtcc ctggacgtca tactggggca 9900 tacccctttg ttatcaaggt tagtatgtca gcggttgcat cttgagtccc cctattttgc 9960 tctgagtttt gttttaaggc atcccctgtc tgtttaggtg ttttgagcct tagtaatggc 10020 atccctaccc ccttttagtt cgatggttcc tcggcatcgt gcccgagttc gatcgcccgg 10080 attccaccat ttttcggtac tcgcccggac ccttctccag tactcgccca gagctttttc 10140 ggtacttgcc cgaacccttc tccggtactt gcccggaacc ttctccggta ctcgctcgga 10200 gccttccccg gtactcgccc agagcttttt cggtacttgc ccaaaccctt ctccagtact 10260 tgcccgaacc cttcttcggt actcgcccgg agctttttcg gtacttgccc gaacccttct 10320 ctggtatttg cccggaacct tctccggtac tcgcccgaat tttacccgtt ttcggtactc 10380 acccgaaccc ttctctggta ctcgcccgga acattttcgg tacttgcccg gaaccttctc 10440 cggtacttac ccggagcctt ccctgatact cgcccggagc tttttcggta cttgcccgaa 10500 cccttctctg gtactcgccc ggagcttttt cggtacttgc ccgaaccctt ctctggtact 10560 tgcccgaagc cttctccggt actcgcccga aactttttcg gtacttgccc gaaatcttct 10620 ccggtactcg cccggagcct tctccggtac tcgcccggag cttttttggt acttgaccga 10680 acccttctcc ggtacttgcc cgaacccttc tccggtactc gcccggagct ttttcggtac 10740 ttgcccgaac ccttctctgg tacttgccca gaaccttctc tggtactcgc ccggagcctt 10800 ccccggtact cgcccggagc tttttcggac ttgcccgaac ccttctctgg tactcgcccg 10860 gacccttctc tggtactcgc ccgaatttta cccattttcg gtactcgccc ggattgcacc 10920 attctccggt actcgcccgg agctttttca gtactcgccc ggaaccttct ccgatactcg 10980 cccggaacct tctccgatac tcgcccagac ccttctctgg tactcgcccg gaactttttc 11040 ggtacttgcc cgaagccttc tccagtactc gcccggagct tttttggtac ttgctcggaa 11100 ccttctccgg tacttgccca aacccttctc cggtactcgc ccgaatttta cccgttttcg 11160 gtactcgccc ggattccacc atttttcggt acttgcccga acctttctcc ggtacttgcc 11220 cggatcaaat ccctaatctt tcccggcatc gtgatcgggt ctccttttat ctttctccgg 11280 catcgtgcct agatcccata gtccattccg tcagcatgac ttatttctct tagccttctt 11340 tattgttggg tggggaaaaa attgttggtc atttgggttc ttcactagag ttcatttcac 11400 tcttgcatta catgcacttc gcactcacaa ttcactcgtt cattcactct actgaagagg 11460 ggcatatt 11468 // ID Gypsy9-VV_I repbase; DNA; EDCOT; 4688 BP. XX AC AM487024; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy9-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4688 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4688 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 739-739 (2007). XX DR Genbank; AM487024; Positions 30629 25942. XX CC Positions [2092-2547] - Reverse transcriptase CC Positions [3754-4044] - Integrase core CC 'TTAG' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 844..2592 FT /product="Gypsy9-VV_I_1p" FT /translation="MLEIPNMAEEELLFNFMDNLQNWAEQELRRRGVQDLA FT TTMAVAESLVDYRRGDSSKPKPPSKGNQAKGGGDKRSQGHTPKEGSSKGPS FT GKDGKGKDKRKEFTPRTNCFLCGGPHWARDCPKRKALNAMIEEKEQEGNAK FT VGSLQLLNALKAKPMPKTPQSKGLMYVEALVNGKATKALVDIGATHNFVSE FT DETRRLELQASKEGGWLKVVNSGAKPSHGVARGVTMHIGSWEGRVDFTVAP FT MDDFKMVLGMDFLQKVKAVPLPFLRSMAILEEEKPCMVPTVNEGTLKTPML FT SAMQVNKGLKREEVTYLATLKEEKDDGSGEPMPKEIEGVLDEFKDVMPPEL FT PKRLPPRREEDHKIELEPGAKPPAMGPYRMAPPELEELRRQLKELLDAGFI FT QPSKAPYGAPVLFQKKHDGSLRMCIDYRALNKVTVKNKYPIPLIADLFDQL FT GRARYFTKLDIRSGYYQVRIAEGDEPKTTCVTRYGSYEFLVMPFGLTNALA FT TFCTLMNKIFHPYLDKFVVVYLDDIVIYSNTLKEHEEHLRKVFKILRQNKL FT YVKKEKCSFAKEEVSFLGHRIRDGKLMMDDSKVKAI" XX SQ Sequence 4688 BP; 1317 A; 1066 C; 1358 G; 942 T; 5 other; agtggtatca aagcgtggct acgaagcggg cataagggaa gcatgtcggg ctctaacgwg 60 gaggagatta gcgaacaaac ccgtgggagg gaggccgagc ctactgcacg gggcaggggc 120 agaggtaaga aggatacatc tcgtgatgtt gttgccaaca tggaggcaag gttagccaag 180 gtggagctag ccatggcaga cacccgggaa ggggtggact tgatcgagca aggcatggag 240 aagggcttag aggatctaag ggagcagatc caagaccttc gcgagggggt gctggtctcg 300 caagttcaac cggtgtcaca cgaggagttc atgtccttcc aagacaaggt tatgagcatg 360 ttcgctagtg tggagtcaag aatggaggcc ttgactgcac gagtggaggc ccgagaccaa 420 gagattcgac aagagttgac catctataag accgctgtat cagcacgagt catggccact 480 catgaggcac caagggtgga ggtgcccaag ccacacacgt tcagtggcaa gagggatgcc 540 aaggagctag ataacttctt gtggcacatg gagcgttact ttgaggcaat tgcattgacg 600 gatgaagcca ctaaggtacg cacagcgacc ctttacctca ctgataatgc tactctatgg 660 tggcgtygac gatttgccga catagagaga gagacgtgca ccatagacac atgagatgcc 720 tttaagagat aaatcaagag gcaattctat cccgaagacg tggcttacct agcaaggaag 780 agtttgaagc gtctcaagca cacgggctcg atccgtgagt atgtcaaaga attctctact 840 cttatgcttg agatacctaa catggctgag gaggagctac tgttcaactt catggacaac 900 ttgcaaaact gggccgagca agagttgagg agacgtggtg tccaagacct agccacgacc 960 atggcagtag ctgagtcctt agtagattat agaaggggag actcctccaa gcccaagcca 1020 ccatccaagg gaaaccaggc caaaggtggg ggagacaaga ggtcgcaggg ccacactcct 1080 aaggaaggat caagcaaagg ccctagtggc aaggatggca aaggcaaaga caagcgaaag 1140 gagttcacgc ccaggaccaa ttgcttcttg tgtggtggtc cgcactgggc acgagactgc 1200 cctaagagga aggctttaaa tgctatgatc gaggaaaagg agcaggaggg caatgctaaa 1260 gtgggatcgt tgcagctcct aaatgccctt aaggccaagc cgatgcctaa aacgcctcaa 1320 agcaaagggt tgatgtatgt ggaggccctt gtgaatggga aggccaccaa ggccctggtg 1380 gacataggtg ccactcacaa ctttgtctcg gaggatgaga caagaaggct ggagctccaa 1440 gcatccaagg aaggaggatg gctcaaggta gtcaattcag gagctaagcc atcacatgga 1500 gtagctcgcg gggtgactat gcacatcggc tcgtgggaag ggagggtcga cttcacagtg 1560 gcacccatgg acgacttcaa gatggtgcta ggaatggact tcctacagaa agtcaaggct 1620 gtgccactac ctttcctacg ctcaatggct atcctagagg aggagaagcc gtgcatggtc 1680 cctacggtca atgaaggtac gctcaagacc cctatgctat ccgctatgca agtaaataag 1740 gggttaaaga gggaagaggt aacctacctc gccaccctga aggaagagaa ggatgatggg 1800 tcgggagaac ccatgccaaa ggaaattgag ggggtccttg atgaattcaa ggacgtaatg 1860 ccgcccgagt tacctaagag acttcctcct aggagagagg aagatcataa gattgagttg 1920 gagccgggag ccaagccccc tgctatgggg ccatatagga tggcaccacc cgagttggag 1980 gagctaagga gacaactcaa ggagttgcta gatgcagggt tcatccaacc atccaaggct 2040 ccctatggcg cgccggttct atttcaaaag aaacatgatg ggtccctacg aatgtgcata 2100 gattaccggg cactcaacaa ggtgacggta aagaacaagt atcccatccc gctcattgct 2160 gacttgttcg atcaattggg aagggcaagg tacttcacga agctagacat aaggtccggc 2220 tactaccaag tcaggattgc ggagggagat gagccgaaga ctacatgtgt gaccaggtac 2280 ggctcatatg agttcttagt gatgcctttc ggactcacta atgccctagc aacgttctgc 2340 accctcatga acaagatctt ccacccatac ttggacaagt tcgtggtggt gtacttggat 2400 gacatagtca tctatagtaa cactctaaag gagcacgaag aacacttgag gaaggtcttt 2460 aagatcttga ggcaaaacaa gctatacgtg aagaaggaga agtgctcgtt tgctaaggag 2520 gaagtgagct tcctagggca tcgcatcaga gatggcaagc taatgatgga tgatagcaag 2580 gtgaaagcca tctaggagtg ggattcacca accaaggtac ctcaactcag atctttcctt 2640 ggtttagtta attattaccg gcggttcata aaaggttatt cgggaagggc trytccactc 2700 actgatcttc tcaagaagaa taaggcctgg gaatgggatg aaaggtgcca acaagccttt 2760 gacgacctga agaaggctgt gactgagaag ccagtgttgg cactacccaa gcacaccaag 2820 gtctttgagg tacacataga tgcctcagac ttcgctattg gggaagtcct tatgcaagaa 2880 aggcacccaa tcgcatttga gagtcgcaag ctaaatgacg cggagaggcg ttacacgatg 2940 caagaaaagg agatgaccgc tatcgtccac tgcttgcgca cttggaggca ctatctgcta 3000 gggtctcact tcatagtgaa aaccgacaat gtggccacta gctacttcca gacacagaag 3060 aagctgagtc ctaaacaagc taggtggcaa ggcttcctgg ccgagttcga ctatatgctg 3120 gagtataagc cgggaagtgc taatcatgtg gccgacgccc taagtcgcaa agtcgagcta 3180 gcgtccatga tgagtcagcc ccaatgagac ataatgggtc ttctaaggga gggactgcaa 3240 catgatccag tggctaagag cctcatcgct ctggctcatg aagggaagac taagcggttt 3300 tgggtagagg acggcctact ctacacaaaa gggagacgac tctacgtgcc taagtggggg 3360 aacataaggc agaacctgat taaggagtgc catgacacca agtgggctgg gcaccctggg 3420 taacgacgca ctagggcact tgagtcggct tactattggc ctcaaatacg ggatgaggtt 3480 gaggtctatg tgaggacttg tcttgtgtgc caacaagaca aggtggagca gcgacaacct 3540 agaggcctgt tagagccact acctgtagca gaacgcccat gggacagcgt caccatggac 3600 ttcatcatcg ggctacctaa gtcggaggac agcggctcta tcatagtggt ggtggacagg 3660 ttctctaagt atgcaacctt catagcagcc ccgaatgact gcacgtcgga agagacggcg 3720 agactattcc taaagcacgt agtcaagtac taggggttgc ctaagttcat catcagtgat 3780 cgcgacccgc gcttcactgg gaagttttgg acggagctct tcaagcttat gggttcggag 3840 cttcacttct ccacaagctt tcacccacag acggatgggc agaccgagag rgtgaacgct 3900 ttattggagc tatacttaag gcacttcgtg agtgccaacc aaaaggattg ggctgagttg 3960 ctagatatag cccagttctc atacaacttg caaaggagtg aggcgaccaa taagagccca 4020 ttcgagctag ccacagggca gcaaccgtta actcctcaca ctctaacgat tgactatacg 4080 gggagaagtc caactgcttt caaatttgcg aaagggtggc atgagcaagc tgacatagct 4140 cgctcatact tggacaaggc cgctaagaaa atgaagaagt gggctgacaa gaagcgacga 4200 cacaaggagt acaaggtcgg agacatggtg cttgtcaagc tccttcctca acaattcaag 4260 tccctaaggc cggtgcataa gggccttgtg aggaggtatg aaggaccctt ccccatactt 4320 gggaaggtcg gcaaggtgtc ctatagggtc aagctgctcc cgaggttgaa gattcatcct 4380 gtcttccacg caagctactt gaagccctat cacggagaca aggatgatcc aagccaaggg 4440 ttgtctaaga gggcacctac agcggtcgtg acctcctatg ataaggaggt agaacacgtc 4500 ctcacagatc gggtcatcag gagacgaggg gtacctcctg ctacggaata cttagtgaaa 4560 tggaagggac taccagaaag cgaggccagc tgggagccag cagaggcact atggcagttc 4620 caggagtaga tcgagcggtt ccgggcagaa gacgcgacga ggacgtctgc ggcttaggtg 4680 ggggagag 4688 // ID HARB-N1_Mad repbase; DNA; EDCOT; 785 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW HARB-N1_Mad. XX NM HARB-N1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-785 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1500-1500 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >83% identical to consensus. 3-bp TSDs are TWA. XX SQ Sequence 785 BP; 170 A; 293 C; 130 G; 192 T; 0 other; gagcagttcc agcgtggcgg aggcccccta gggctatcca ctattaatcc acccagtgaa 60 cagtaaccgc ccttaatgaa cagtaatcgc cttttgcatc tccaccccta cacttgaata 120 gccctggcaa taggcaataa aataatagta tttttttatt tataaaataa tacaaaatat 180 tttactttct tcattttccc ggaaaatatt ttactttctt tcaatccttg catccccaca 240 aaaatcccac ttctgggttt tctttcccat tcacttaatt cccccaccaa gctctcagag 300 ctctcagtct cgtttcccgt aaaaaaaacc catatctctt aacccgggct tcatctccag 360 tcaaaccctc tccttctcgc cgtcaagatc cctctccaag ctctattccc ccacctcctc 420 gccctccaag cccctctcct cccctccttc tccccaaccg ccgccgccgc aactcgccgg 480 gtcaaatcag tctctgactc gaccgaccca gtcccaaacc ctctacgaga tgatgtccga 540 cgaccagaac cgagactcca ggctcctccc ggaccggaaa atccatgaga aaatccttgc 600 atcttcaccc tgacgtcagc gtgcatcacc tccacctcgg gctctcgggc tggcaactcc 660 tgccgggcct ctccctcggg gccgctcggg ctccatcgcc agcacacgct ggacctcccc 720 actcgggctc tctggccctg ttccgcagcc tgtccctcga gcacgagctc ccgctggagc 780 tgctc 785 // ID CARO_CA repbase; DNA; EDCOT; 687 BP. XX AC AJ012823; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Cicer arietinum tandemly repetitive DNA, CARO_CA. XX KW CARO_CA; Repetitive sequence; tandem repeat. XX OS Cicer arietinum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; OC Cicer. XX RN [1] RP 1-687 RA Frediani M.; RT "Direct submission."; RL Direct Submission to Genbank (16-NOV-1998). XX DR Genbank; AJ012823; Positions 1 687. XX SQ Sequence 687 BP; 206 A; 132 C; 134 G; 215 T; 0 other; tatcgtctgg ttcaaaaata caaattttgg tccctttttg tcgaggggta cacaaattgc 60 ccaaaacgtc tagatgaaat cgaggagaag aagattcttg tagcattctt ctcctaaatt 120 tataactgag tttcgtgttc ggcgtcagat tttcaaacac tagccatcat ttggtccgaa 180 aatacgaatt tcggtcctta tttgtcgggt ggtacgaaaa tcgcctaaaa agtctagatg 240 aaatcgaaga ccaggagacc cttaaagaat tcttcaaaat ttataaatgt ctttcgggtt 300 ccgcgtccaa tttcaaacac tagccctcgt ctggtccgaa aatagagatt ttggtccatt 360 tttgttaggt ggtacaaaaa ttgcccgaaa agaccaaatg aaatttagga tcgtctaaat 420 ttataaatgt atatcgggtt ccgcgtcaca tttcaaacac tagccatcgt ctcgttggaa 480 attaaggatt tccgtccatt tttgtcgagg tgtacgaaat ctcccgaaaa gtccatatga 540 aatcgaagga tcgggcgacc cttttagcat tcttctccta aatatataac aatgtttcta 600 atttcgggtc agatttcaaa cactagacat cgtctggtct gaaaatatag attttagtcc 660 atttttgtcg aggggtatga aaatcgg 687 // ID CAULIV-1_Mad repbase; DNA; EDCOT; 7907 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Caulimovirus-like sequence. XX KW Caulimoviridae; Integrated Virus; CAULIV-1_Mad. XX NM CAULIV-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-7907 RA Kojima K.K. and Jurka J.; RT "Integrated Caulimovirus-like sequences from the apple genome."; RL Repbase Reports 10(10), 1646-1646 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~90% identical to the consensus. They appear integrated into CC (TA)n microsatellites. XX FH Key Location/Qualifiers FT CDS 295..5844 FT /product="CAULIV-1_Mad_1p" FT /note="movement protein, retropepsin and reverse FT transcriptase." FT /translation="MSRLFRSNSMASTSSRSNLGTIPDIVNEEQKFEFQTD FT SSLDFAEWNIPKISSKNIYKKKWAFASFKTEHHVKTVEQAYALSKDHETCQ FT LFTPEQINSHRKDGHNYIHIGLVQIAAKPLTRRGLNTSILLCLRDARFTDF FT SDSILGMVESSLCNGPIHFDCFPDLTISLSDPHMLKALTLNIKTSGYKVLE FT GTQPLALIYRIYYKVTGTNMNFQALTKSPKDHTLLIQTDQENANIKIPRTI FT RWSEINLPSDWCLINESRPVAIQNSLVNLDNVEQYFDGTVKINFDRPARKS FT CDSNRSLKSFTSNRNSFSGSMPNDRQGRDQELINSLANRKLKSVDTGSSVT FT QQELINDLLNFKLQSLETNAQVVQPTYHTPSIPPKEEQTSPTASDFDAEPV FT HHQLLVLTRQEPFKYDRKKLCRDIEALENVPRRNIFRSKYTTEEKLEIHKA FT WKDFMQTNRLEIFFFDFVEKHYESENQVKVITKENWLKEDKTIVSSSHPPQ FT ETILISTANTQVPASPFKLPKEDAGVKPVIEQNNFTNQSLHIIGKQLDKIE FT TKVDNLSIKPLSKEIPLTSFRESPSLKTSTSIKIEQMLHKLEKDKSVRVIN FT NPHDSETPSSIPDSEDESVDSIHQMEQAFQSLELKRLNVKRTNPTSLTKNW FT YPRPTPPDLQFEERNFQSQFTVSSDKLYEWNIDGLSEQELLNKLQHISMVA FT NSYITNHDLSQTQIVDILVSGFTGMLHSWWEKHLTEDSRNLIRNAVKQDEE FT GIPIFDEHLGRGVPDAVNTLLYTIIQHFIGIPSNITSRIHDQLSNLRCPTL FT SDFRWYKDVFMSRVMLRDDSNQPFWKEKFINGLPNLFAHKIRNTLINEDGI FT IPYNDLTYGHIISTIQKEGLKMCIDMKISRQAQSEKAIAKYELGTFCEQYG FT LPPIAPSNLKKKSTTFNRSKISKPRTNYSKYRKGKYAKPNPFYENPKQKRW FT KGKRKSSGKFHSKDNSHKGKCYKCGKEGHYANKCKVKKTISQLKISEEEKL FT QLIQALELQNTDSSHSSEDDLGSTSSSSYQSASSKHSTPNIKLGCPDACCK FT NISVLTKQEKQEELLLELISNVEDTELKRFYLKKLKNLVSQEEVGTSQSQI FT QKPQISLSSTLAKFSKTKKEITVSDLQKEINQIKEEIKLLKSDNHEIRTQL FT TRANTPPKEELSSSSSSSSHHESESDTHSEHLVLNLLHKIRIQKWYSKVTI FT VIEDFRFETIALIDSGADLNCIQEGLIPTRYFHKSKEILSAANESPMEIKY FT ELPKAHVCQNEVCFKTPFVLIKNLSDPVILGLPFIALLYPFKTHHNRITSK FT VLGQKVTFEFCLETDLKKLRHLQKDSTSRSLNIISNKTKHLQFLKDDIHHK FT RTEEQLKQEIISQKILKFEEQLVKEVCSDIPNAFWHRKQHIVKLPYIKEFN FT ESKIPTKARPIQMSQEVMDFCKAEIQDLLNKGIIRKSKSPWSCPAFYVQKS FT AELERGSPRLVINYKPLNEVLEWIRYPIPNKRDLIKRLSKATIFSKFDMKS FT GFWQIQIHESDKYKTAFVTPFGHYEWNVMPFGLKNAPSEFQNIMNEIFNQY FT SHFTIVYIDDVLVFSKSIDEHWKHLHLFARIIRSNGLVVSATKIKLFQLKV FT RFLGYNIHRSTIQPIDRVIQFADKFPDQITEKTQLQRFLGSLNYVSEFYPH FT LRQQCKPLFDRLKENPPAWSTIHTSIVKQIKNHVKTLPCLGIPTPNSFKIV FT ETDASDVGYGGILKQQTSSGSPEQIVRFHSGVWNPAQTNYSTIKKEILSIV FT LCISKFQDDLLNQKFLVRVDCKSAKHVLQKDVQNIASKQIFARWQAILSIF FT DFEIEYIKGSHNCIPDFLTREFLQGKNV" FT CDS 5840..7156 FT /product="CAULIV-1_Mad_2p" FT /translation="MSNKNTASPQGSSQQRRLPASLPPPKQEPIPGSSALA FT ITNRFTPLGSTLGSIRPNYQTALVNQYDPFSSTYRQSPSPSVSYTKTSPYV FT IKPSKEYLFSIPFNYKHLKTPEVIAKKMFPTNSHFQPSEFHKTLKYYTTIL FT NETSSITIKPIFDKTPGNQNRILYHSLTINKFLLESEWGVPLFQPKPFKSS FT SFPSHSNHYTYFDYIQAWTNIFLHQSEDFSHSWFITFDRSFRLNFPAWFPR FT WWSEHGLISDLMPDEFKQVLSGTFQKKFDRTRFDEGIPLFALFMAKYKVPW FT ILRWNYEIESNQVFRQRMIKWWDKFNHQKIIEVVLRDFPMDSNSSTCSSSS FT SSXALPEPTKEEIESLSDISPSSSLKGKAKSSKSSSSSKKKKSSKLKALAK FT ILMKELQEENEDSSDSDNSSDASSQRAVATQGNIFPPDSQDPYEF" XX SQ Sequence 7907 BP; 2714 A; 1682 C; 1239 G; 2269 T; 3 other; cttccgcacc catttggtat cagagccaag tgtggttggt tataccatta gtatctgaat 60 actctgttta tacctttaga tttattcagt ctctttatag tttaatcttt tcagtttaac 120 cttcttagtg tctcctgatc tccataaggt ctgagcagta aggcgtcacc caaacagtaa 180 gtcccggagg atagggcctg agcggcgcgc atgacccaga gagcttggtg tttagaagca 240 ctagtaagat tttctgttaa ggtttctgta ttttgattgt ttgaattttt aggtatgagt 300 agattgttta gatctaattc tatggccagc actagctcta gatcaaattt aggaacaata 360 cctgatattg tcaatgaaga acaaaaattt gaatttcaaa cagacagtag tctagatttt 420 gctgaatgga atattccaaa aatatcttca aaaaatattt ataaaaagaa atgggcattc 480 gcctctttta aaactgaaca ccatgtcaaa acggttgaac aagcttatgc tcttagtaaa 540 gatcatgaaa cttgccaatt gtttacccca gaacaaatta attcccatag gaaagatggt 600 cataattata tccatatagg tttagtgcaa attgcagcca aaccattaac acgtagaggt 660 cttaatacct ctatcctctt atgtctccga gatgctagat tcactgactt cagtgatagc 720 atacttggta tggttgaatc cagcctctgt aatggaccta tccactttga ctgctttcca 780 gatcttacca taagtctgtc cgacccacat atgttaaaag cacttacact aaatatcaaa 840 acttcaggat ataaagtcct tgaaggaaca cagcctttgg ccttaattta tagaatttat 900 tataaagtca ctggcacaaa tatgaacttt caggctttaa ccaaaagtcc gaaggatcat 960 actctcttga tccagaccga tcaagagaat gccaatatta aaatacctcg aaccattagg 1020 tggtcagaaa tcaatctccc ttcagattgg tgtctgataa acgagagtcg gccagtagcc 1080 atccaaaata gtctagttaa tttagacaac gtagaacaat actttgacgg tacggttaaa 1140 attaattttg atcgtcctgc taggaaatcc tgtgattcta atcgatcact taaatccttt 1200 acttccaata ggaattcttt ctctggatct atgccaaacg ataggcaagg tcgagaccaa 1260 gaattaatca attccctagc caataggaaa ttaaaatcag tagatacagg ctcatctgtc 1320 acccaacaag aattaataaa tgacctttta aatttcaaac tccaatcact tgagacaaac 1380 gctcaagtag tccagcctac ctatcatacc ccatccattc ctcctaagga agaacaaaca 1440 tccccaactg cttctgattt tgatgcagaa ccagtacatc accaactatt ggttttaacc 1500 agacaagaac cttttaaata tgatcgtaaa aaactctgta gagacataga agccttagaa 1560 aatgtccctc gacgaaacat cttcagaagt aaatatacta ctgaagaaaa attagaaatc 1620 cataaggcat ggaaagactt catgcaaacc aacagacttg aaatattttt cttcgacttc 1680 gtagaaaaac attatgagtc tgaaaaccaa gtaaaggtaa taaccaaaga aaattggctt 1740 aaggaagaca agacaattgt ctcctccagt caccctccac aagaaactat tcttattagt 1800 actgcgaata cgcaggtccc agcctcaccg ttcaaacttc cgaaggaaga tgcaggtgtc 1860 aaacctgtta ttgaacaaaa caattttacc aaccaaagcc tacatatcat aggaaaacag 1920 ttggataaaa ttgaaaccaa ggttgacaat ttgtcaatta aaccacttag taaagaaata 1980 cctttaacta gttttagaga gtcaccctct ttaaaaacct caacatctat taagatagaa 2040 caaatgcttc ataagctaga aaaggacaaa tcagttcgtg tgattaataa tccacatgat 2100 tctgaaacac cttcctcaat tccggattca gaagatgaaa gtgttgattc catccatcaa 2160 atggaacaag cctttcagag tcttgaatta aaacgtctta acgttaaaag gactaatcct 2220 acatccttaa ccaaaaactg gtatcccaga ccaacacctc ctgatcttca atttgaagaa 2280 aggaatttcc aatcccaatt cactgtttca tctgataaac tctatgaatg gaatatagat 2340 ggtttatcag aacaagagtt attaaacaaa ctccaacaca tctccatggt agcaaatagc 2400 tatatcacta atcatgacct tagtcaaacc caaattgttg acatccttgt ctctggattc 2460 acaggaatgc ttcattcctg gtgggagaaa catctcactg aagactccag aaatctaata 2520 agaaatgcag taaaacaaga tgaagaagga atacctatct tcgatgaaca tctaggacgt 2580 ggtgtcccag atgcagtcaa taccttactt tatacaatca tacaacattt cataggaatc 2640 ccttccaaca tcacatctag aatccatgac caactaagta acttaaggtg tccaacccta 2700 agtgatttta gatggtataa agatgtattt atgtcaagag ttatgcttag agatgatagt 2760 aatcaaccat tttggaaaga aaaatttata aatggattac caaacctttt tgcacacaaa 2820 ataaggaata ccttaatwaa cgaagatggt attataccat ataatgatct tacttatgga 2880 catatcataa gtactatcca aaaagaaggc ctaaaaatgt gcatagatat gaaaatatct 2940 agacaagcac aatctgaaaa ggctatcgcc aaatacgaat taggaacctt ctgtgagcaa 3000 tatggtttac cacctatagc tccttccaat ctcaagaaga aatcaactac cttcaataga 3060 tctaagatct ctaaaccacg gaccaactac tccaaatatc gtaaaggcaa gtatgccaaa 3120 ccaaacccat tttatgaaaa ccccaaacag aagagatgga aaggaaagag aaaatcctct 3180 ggaaaattcc actctaaaga caatagtcat aagggaaaat gctacaaatg tggcaaagaa 3240 ggccattatg ccaataaatg taaagttaag aaaaccataa gtcagttgaa gatttctgag 3300 gaagaaaagc ttcaacttat ccaagcccta gaactccaaa atactgacag tagtcattca 3360 tctgaagatg atctgggttc tacctcatca tcctcatacc aatctgcttc tagtaagcac 3420 tctaccccaa acatcaagct cggatgtcct gatgcttgtt gtaaaaatat atcagtacta 3480 actaaacaag aaaaacaaga agaattactc ttagagctaa taagcaatgt tgaggacact 3540 gaactcaaaa ggttctacct caaaaagctt aaaaacttag tttcccaaga agaagtaggc 3600 actagccaat ctcaaatcca gaaaccacaa atctctctta gttctacact agcaaagttt 3660 agtaagacta agaaagaaat cacggtcagt gacctccaaa aagaaattaa tcagataaaa 3720 gaagaaatta agcttctaaa atctgataat cacgagattc gtacacaact cactagagcc 3780 aatactcctc caaaagaaga actatccagt tcctcttctt ccagtagtca ccatgagtca 3840 gaatctgata cacattcaga acacttagtt ctgaatcttc ttcacaaaat tagaatccaa 3900 aaatggtatt ctaaagtaac aatagtaatt gaagactttc gtttcgaaac aattgcatta 3960 attgattcag gagcagactt gaattgtatt caagaaggac taattcccac taggtatttc 4020 cacaagtcaa aggaaatcct tagtgctgct aatgaatctc caatggaaat caaatatgaa 4080 cttcctaagg cgcatgtctg ccaaaatgaa gtttgtttca aaacaccttt tgttctaatt 4140 aagaacttat ctgaccctgt catactagga ctacccttta tagcactcct ctatcctttt 4200 aaaacacatc ataataggat tacctcaaaa gtcttaggac agaaagtcac ttttgagttc 4260 tgcctggaaa cagacctcaa aaaacttagg catctccaga aggatagcac ttcgcgatcc 4320 ttaaacataa tctctaataa gactaaacac cttcaattct tgaaagatga tattcatcac 4380 aaaagaactg aagaacaact caaacaagag attatatctc aaaaaatcct taaatttgaa 4440 gaacaacttg ttaaagaagt atgttctgat attcccaacg ccttttggca ccgcaaacaa 4500 catatcgtta aattacctta tatcaaggaa tttaatgagt caaaaatccc tactaaggcc 4560 agacctattc aaatgagtca agaagtaatg gatttctgta aggcagaaat acaggacctt 4620 cttaataaag gaattatccg taaaagtaaa tcaccttggt catgtcctgc attttatgtt 4680 cagaaaagtg cagaacttga aaggggatct ccccgattag ttattaacta caaaccttta 4740 aatgaagttt tggaatggat tcgatatcca attcccaaca aaagagattt aataaaaagg 4800 cttagtaaag caactatttt ctcaaagttt gatatgaaat caggtttttg gcaaatccaa 4860 attcatgaat ctgataaata taaaactgct tttgtaacgc ctttcggcca ttatgaatgg 4920 aatgttatgc cttttggttt gaaaaatgca ccatctgaat tccagaatat catgaatgag 4980 atttttaatc agtatagcca ttttacaatt gtttatattg atgatgttct tgttttctct 5040 aaatctatag atgaacattg gaaacattta cacttgtttg ctaggatcat tagatcaaat 5100 ggattggttg tgtcagccac taagattaag ttgtttcaac ttaaggttag atttttaggt 5160 tataatatcc ataggtctac catccaacca attgaccgtg tcatccaatt tgcagataaa 5220 tttccagacc agattactga aaaaacccag cttcaaagat tcttaggttc tttgaattat 5280 gtttcagaat tttatcctca tttgcgtcaa caatgtaaac ctttgtttga tcgccttaag 5340 gagaatcctc ctgcctggtc taccattcat acttctattg tcaaacagat aaaaaatcat 5400 gttaagactt tgccctgtct tggcattcca actcccaact cttttaagat wgttgaaact 5460 gacgcctctg acgttggtta tggaggtatc ctcaaacagc aaacttcctc cggatcacct 5520 gaacaaattg ttcgtttcca ttcaggtgta tggaatcctg ctcaaactaa ttatagtact 5580 attaagaaag aaatactatc tatagtatta tgcattagta aatttcaaga tgatttatta 5640 aatcaaaaat ttcttgttag agtcgattgc aaatctgcaa aacatgtttt acaaaaagat 5700 gttcaaaaca ttgcatcaaa acagattttt gcacgatggc aagccatatt atcaatcttt 5760 gattttgaaa ttgaatacat taaaggcagc cataactgca ttccagattt cctaaccaga 5820 gaatttttgc aggggaagaa tgtctaataa aaacacagct tctccacaag gcagtagcca 5880 acaaaggagg cttcctgcct cattaccacc accaaaacag gaacctattc ccggttcctc 5940 ggccttagcc attaccaata gatttactcc attaggatca actctaggaa gtatccgacc 6000 aaattaccaa acagcgttag taaaccagta tgatcctttc tcctctacct acaggcaatc 6060 gccatctccc tcagtaagct ataccaaaac atccccttac gttattaaac cctccaaaga 6120 gtatctcttc agtatcccct tcaactacaa acatctgaaa acacctgagg tcatagccaa 6180 aaagatgttt ccaaccaatt cccattttca accaagtgaa tttcacaaaa ccctcaagta 6240 ctataccact attctcaatg agacttcatc catcaccata aaacctatct ttgataaaac 6300 ccctggtaat caaaacagaa tcctgtatca ttcccttacc attaataaat tcttgttaga 6360 atcagaatgg ggagtacctc tttttcagcc caaacctttt aaaagtagta gcttccccag 6420 ccactcaaac cattatacct attttgatta cattcaagcc tggactaaca ttttcttaca 6480 ccagtcagaa gattttagtc attcatggtt tataaccttt gatcgaagtt tcagattgaa 6540 ttttcctgca tggtttccca gatggtggtc agaacatggc cttatctccg acctcatgcc 6600 ggacgaattc aagcaagtct tatcaggcac cttccagaag aagttcgata gaacacgttt 6660 tgatgaagga atccctttgt tcgccctgtt catggcaaaa tacaaggtcc cctggatcct 6720 ccgctggaac tacgagattg aatccaatca agtcttccga cagagaatga tcaaatggtg 6780 ggacaagttc aaccaccaga agatcattga agttgtgctc agggacttcc ccatggattc 6840 taactccagt acctgcagta gcagctcctc cagcwcggct ttaccagaac caaccaagga 6900 agaaatcgaa tcattatcgg acattagtcc ttcttcctct ctcaagggca aggccaagtc 6960 atccaaatct tcgagcagtt cgaagaagaa gaagtcttca aagctcaagg ctctagccaa 7020 aatcctcatg aaggaactgc aagaagaaaa tgaagacagt tcggactccg acaactcttc 7080 ggatgcttca tcccagcgcg cagtagccac acaaggaaat attttcccgc ctgattctca 7140 agacccttac gagttttgag ctttaaatgt aatagcatgt atcccaatag ggaatttcta 7200 aatccgtctc agtagatact ttgtatctag acccagtagg gtattttgta atagcgcata 7260 tgaagacaaa gccagccgca agtgaaagca gcagtagcag acaagcacta ttcatgaata 7320 gtaaaatcac ttttactatt catccatcat tcctccacag tattcaccct cgtgaaagcc 7380 acagtccccg acagcatctt ctgctttcgg cctctttaca gcagtagcac atgcagagcg 7440 ggaatcccgc ttccatcctt caatcattcc ggtcacctcc tcgcctataa gaggaccctc 7500 cagcttcatg gagggggact tcttagaaga agaaaactct gcgtattcat ttagaacaga 7560 gtccatcttc ttagcaaaaa tattttgaaa cacttgtatt ttattttatc aaggatgcct 7620 gcgagctcca agtccagtcc ttttcaaatc gtcaatagac gaaacgtttg taagtcttat 7680 ttgattttca ataaatatat tttcaatcga atatcagcat cattaatttt aattcattat 7740 tttcatcatg aatactaaat ctattttcaa tttagttttg cttatttatg ttcttgttat 7800 tgatcctatg aattttacat tgatatcaat caaattcttc gaatttccag atacatatat 7860 cgaatatttc cggctttata tgttattctg cttccgcacc catttgg 7907 // ID COP21_I_MT repbase; DNA; EDCOT; 4402 BP. XX AC AC124966; XX DT 11-JAN-2007 (Rel. 12.01, Created) DT 16-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of COP21_MT LTR retroposon from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Internal; Interspersed; ORF; COP21_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4402 RA Shankar R. and Jurka J.; RT "COP21_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 17-17 (2007). XX DR EMBL/GenBank/DDBJ; AC124966; Positions 16292 20693. XX CC The internal region sequence is represented by a single copy. It CC has intact domains for gag followed by integrase and RT CC polymerase. XX FH Key Location/Qualifiers FT CDS 70..4392 FT /product="COP21_I_MT_1p" FT /translation="MSDIPPSENSPLSSISSPITVHSTTNPDPCVIHHSDN FT PSTVLVTPLLTGDNYGSWSRAVTMALRAKNKFGFVDGSLTIPKKKEDILTW FT QRCNDLVASWILNSVSTEIRPSILYAETAEQIWSDLQDRFSQSNAPKIYQL FT KQSISALKQEGMYVSLYFTQLKSLWDELNSIALVNPCICGNAKSILDQQNQ FT DRAMEFLQGVHDRFSAVRSQILLMDPFPSIQRIYNIVRQEEKQQEINFRPV FT PAVESAALQTSKAPYRTPGKRQRPFCEHCNRHGHTITTCYQIHGFPSNPSK FT PQKKTETSPSTSANQLSSAQYHKLLTLLAKEDNVGSSVNLAGTAFTCIPFS FT WIIDSGASNHICTSLSLFSSYYPVNNQISVQQPDGSQALVKHIGTINCSPS FT LILTNVYHVPTFKFNLMSVTQLTESLNCDAIFSSSGCVFQDQATKKMIGRG FT SARNELYYLNQDLVSNKHDKDHYCLSHPLSSLFSSKHCNKFDLWHLRLGHP FT SMSRFNFIVKNSPEINANKDFSCEVCPRAKQPRLPFSLRTTNSSHCFELIH FT VDIWGPFSIPSNNGSRYFLTIVDDYSRCTWLYLMQHKSETFTMLVHFFNQI FT NRQFNIKIDQINSGNGDIFLPQLQTVRSDNGLEFLSKQMQTWFHDHGIIHQ FT RSCVATPQQNGVVERKHRHLLDVARALRFQANLPLLFWGECVLTAAYLINK FT LPTPILKFKSPHQVLLGSPPSYSSLRVFGCLCFAKNMNIQHKFDERSKPGI FT FVGYPFNQKGYRIYDMKTRQIYVSRDVQFHETVFPYQDIQSPPFNNAISIN FT TQILDNEFDDLFTGSPTHPNIPPENSHNDNSNDTIVTISTPEDDASSNPPS FT FSAESLSNNPPSTEMNPPNHRHSQRIRNPPIHLKDYICKINNVTSKINFPL FT ENYLSLSNLSNSHRAFLINIIENKEPKSYSQAMKSVEWRDAMAKEIQALES FT NNTWILCPLPEGKSAIGCKWIYKIKYHSDGSIDRYKARLVAKGYSQVQGID FT YHDTFAPVAKLVTVRLLLSIAAIKNWPLYQFDVNNAFLQGDLSEEVYMKLP FT PGFSHKKKPCVCKLNKSIYGLKQASRQWFSKFSTTLIQKGFRQSISDYSLF FT TYNCDQTTIFVLVYVDDIIITGNNENAISKIKKFLAQSFSIKDLGNLSYIL FT GIEVSRSKKGIFLCQRKYTLDILSDSGMTGCRPSDFPMEQHLRLRPNDGTP FT LSDPTVYRRHVGRLLYLTVTRPDIQYAVNTLSQFMQSPYSSHFDAATQVLR FT YLKGSVGKGLFLSASSSINLVGYADSDWAGCPTTRRSTTGYFTMLGSNPIS FT WKTKKQPTISRSSAEAEYRSLATLSSELQWLKYLLSDLGIDHPQPITIYCD FT SQAAIHIAENPVFHERTKHIEIDCHFVREKIKSGLIAPSYIRSSDQLADIF FT TKPLGGDAYKRILGKLGVIEISIPPPT" XX SQ Sequence 4402 BP; 1307 A; 989 C; 655 G; 1451 T; 0 other; tcagttgttt gtcctcttta tatcatcact ttgctccaaa tatttttccc tttgcttctg 60 tttgccatca tgtctgatat accaccatca gaaaattctc cactttcttc catctcctca 120 cccataactg tccactcaac cacaaatcca gacccttgtg tcattcatca ctcagacaac 180 ccttcaactg ttcttgtcac ccctttactt acaggtgata actatggttc atggagtcga 240 gcagtgacaa tggcacttcg tgcaaaaaac aaatttggtt tcgttgatgg atcactaacc 300 attccaaaga agaaagaaga cattcttaca tggcaacgat gcaatgattt ggttgcaagt 360 tggattctta actcagtttc aactgagatt cgtcccagca ttttgtatgc tgaaactgca 420 gaacagatct ggtccgatct acaagatcga ttttctcaat caaatgctcc taaaatatat 480 caattaaaac aatcaatttc tgccctcaaa caagaaggca tgtatgtttc tctttatttc 540 acccaactca aatctctttg ggatgaactc aactctattg ctcttgtcaa tccttgtatc 600 tgtggtaatg ctaaaagcat ccttgatcaa cagaatcaag atcgtgccat ggaattcctt 660 caaggcgttc atgatcgttt ttctgctgtt cgtagtcaaa tcctcctgat ggatccattc 720 ccttcgattc agcgtatcta taatattgta cgccaagaag aaaaacagca agagatcaat 780 tttcgacctg ttcctgctgt agaatctgct gcactccaaa cttctaaagc gccatatcgc 840 acaccgggaa aacgtcagcg tcctttctgt gaacattgca acagacatgg ccataccatc 900 actacttgtt atcaaattca tggcttccca agtaacccaa gtaagccaca aaagaaaaca 960 gaaacatcac catccacttc cgctaatcaa ctgtcaagtg cacaatatca caagcttctg 1020 actctcttag ccaaagagga caatgtggga tcatctgtga atttagcagg tacagctttt 1080 acttgtattc cgttttcatg gattattgac tctggtgctt ctaaccatat atgtacatct 1140 ctttcccttt tttcttcata ttatcccgtt aataatcaaa tctcagttca acaacctgat 1200 ggctctcaag cgcttgtgaa acacataggc actatcaatt gttcaccatc acttatactc 1260 acgaatgttt atcacgttcc aactttcaaa ttcaatctaa tgtctgttac acaattaaca 1320 gaatcactta attgtgatgc aattttctca tcttctggtt gcgtatttca ggaccaagca 1380 acgaagaaga tgattggtcg gggtagtgct cgcaacgaac tctactatct gaatcaagat 1440 ttagtctcaa ataagcatga caaggatcac tattgcctta gtcatccatt aagttccttg 1500 tttagttcta agcattgtaa taagtttgac ctatggcatt tacgcctagg tcatccatct 1560 atgtctcgtt tcaatttcat tgttaaaaat tcaccagaaa ttaatgcaaa caaagatttt 1620 tcttgtgaag tttgtccacg tgcaaaacaa ccacgtttac ccttttcctt aagaacaact 1680 aattcatctc attgtttcga actaattcat gttgatattt ggggtccatt ctccattcca 1740 tctaataatg gatcacgcta ttttctaacc attgtcgatg attactcgcg atgtacttgg 1800 ttgtatctaa tgcaacataa atcagaaaca ttcactatgt tagttcattt ttttaatcaa 1860 atcaatcgtc aatttaatat caaaattgat caaatcaact ctggtaatgg agacattttt 1920 cttcctcaac tccaaactgt tcgttctgac aatggtttag aatttttgtc caaacaaatg 1980 caaacatggt ttcatgatca tggaattatt catcaacgta gttgcgttgc aactccgcaa 2040 caaaatggag ttgtggaacg aaaacatcga catcttcttg atgtcgcaag agctttacgc 2100 tttcaagcaa acttacctct tctattttgg ggtgaatgtg ttcttactgc agcctatctt 2160 ataaataaac ttccaactcc aatcctaaaa tttaaatccc ctcatcaagt tttacttggt 2220 tctcctcctt catactcatc acttcgcgtg tttggatgtc tatgttttgc taaaaatatg 2280 aatattcaac ataaattcga tgagcgttct aaacctggta tttttgttgg ttaccctttt 2340 aatcaaaaag gataccgcat atatgacatg aaaactcgtc aaatatatgt ttctcgcgat 2400 gttcaatttc atgaaactgt ttttccctat caagatattc aatcccctcc atttaataat 2460 gcaataagca ttaacactca aattcttgat aatgaatttg atgacctatt tactggttca 2520 ccaacccatc ctaatattcc tcctgaaaat agtcacaatg ataattcaaa tgatacaatt 2580 gtgactattt ccactcctga agatgatgcc tcatctaatc ctccgtcatt ttctgcagaa 2640 tctctctcaa ataatcctcc ttctacagaa atgaaccctc caaatcatcg tcattctcaa 2700 cgtattcgta atcctccaat tcatctcaag gactatatat gtaaaattaa taatgttaca 2760 tcaaaaatta attttccttt ggaaaattat ttatcattat ccaatctaag taattcccat 2820 agagcttttc tcattaatat cattgaaaat aaagaaccaa agtcttattc tcaagccatg 2880 aaatcagttg aatggcgtga cgctatggct aaggagattc aagcccttga gtcaaataac 2940 acttggattt tatgtccact ccccgaaggt aaatctgcaa ttggttgtaa gtggatttac 3000 aaaatcaaat atcactctga tggatccatt gatagatata aggctcgttt agttgccaaa 3060 ggctattctc aagttcaagg catcgattat catgatacct ttgcacctgt cgccaaacta 3120 gtcacagttc ggcttcttct ctccattgct gccataaaaa actggccatt atatcaattt 3180 gatgttaaca atgcatttct tcaaggagat cttagtgaag aagtttatat gaaattacct 3240 cctggattct ctcataaaaa gaaaccatgt gtctgtaaac taaataaatc aatttatggt 3300 cttaaacaag cttctcgcca atggttttct aaattctcca ccactcttat tcaaaaaggc 3360 tttcgtcaat caatttctga ttatagttta ttcacttata attgtgatca aacaaccata 3420 tttgtccttg tatatgttga tgatatcatc atcaccggca acaatgaaaa tgccatttca 3480 aaaataaaga aatttcttgc tcaatctttt tctatcaaag accttggtaa tcttagctat 3540 atcctaggca ttgaagtatc tcgttctaaa aagggaatat tcttatgtca aagaaaatat 3600 acacttgaca ttttatctga ctctggtatg actggttgcc gcccatcaga ttttcctatg 3660 gagcaacatc ttcgtctacg tccaaatgac ggaacccctc tttctgatcc gacagtttat 3720 cgtcgccacg taggtcgtct cctatatcta acagtgacac gacccgatat tcaatatgct 3780 gttaatactc ttagtcaatt catgcaatcc ccatattcct ctcatttcga tgcggccaca 3840 caggttcttc gataccttaa aggtagtgtt ggaaaaggtt tatttctttc ggcatcaagc 3900 tccattaatt tagttggata tgcagactct gattgggctg gttgtcctac aactcggcga 3960 tctactactg ggtattttac catgttaggt tctaatccca tctcatggaa aaccaagaaa 4020 caaccaacaa tttctcgctc ttctgctgaa gcagaatatc gttccctcgc aactctatct 4080 tctgagttgc aatggttaaa atatcttctc tctgatctcg gtattgatca tcctcagccg 4140 atcacaattt attgtgatag tcaagctgcc attcacattg ccgaaaatcc agtttttcac 4200 gaacgcacca aacacattga aattgattgt cattttgttc gtgagaaaat taaatcaggt 4260 ctcatagctc cttcctatat ccgttcttct gaccaactag ctgacatttt tactaaacca 4320 cttggaggtg atgcttataa acgaatactc ggcaagttgg gtgtcattga aatttcaatc 4380 ccacctccaa cttgaggggg gg 4402 // ID LINE1E_MT repbase; DNA; EDCOT; 5383 BP. XX AC AC148239; XX DT 26-MAY-2006 (Rel. 11.05, Created) DT 26-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE L1-class element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; LINE1E_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5383 RA Jurka J.; RT "LINE1E_MT: L1-type element from barrel medic."; RL Repbase Reports 6(5), 250-250 (2006). XX DR EMBL/GenBank/DDBJ; AC148239; Positions 30323 24941. XX CC This is a recently retroposed element. The sequence is flanked by CC a 19 TSD AGAAGAACAAGCATCGACT. XX FH Key Location/Qualifiers FT CDS 75..1286 FT /product="LINE1E_MT_1p" FT /translation="MTSLPNLHLSDEEEELEIPIEVIPDDTTDTSASLVGR FT FLTDKPIRGHMMTSKIAEFWHPGRGVNIKEVEPNLFTFKFFHYRDMHTILK FT KGPWYFDNNLLILNTLPDDAPAQSVPLQSVPFWVRIHDIPVGFMTERVGKD FT LGNFIGEFLEYDVKNGANHLRSYMRIRVLLDVNKPLKRQKNIKRPGGNIQT FT VKFKYERLGNFCYYCGALGHIEDYCDKLYSIDSDDGARFWGPELRVDRQKN FT EGRGSRWLREEGQEWSPPSNSAPKAAGDVSVGPANGNGRALTVVTSPAKTV FT ALADLLRNPNLIRPSGSNKQQESHLSPHNETLLEEDNATIIHSNTKRSRAD FT LNGGSLSADSSNARPTSLSIPSTPAHNNSQSTPMEVVNTKSSSTSVPFLSA FT APGSQACRES" FT CDS 1286..5356 FT /product="LINE1E_MT_2p" FT /translation="MNVIAWNCRGLGNVKAVPCIKDLVRVYKPDIVILIET FT LCNNNKISGLKYAIGFDYHFSVDCIGRSGGIAVLWRNSAHCSILNYSQHFI FT NMSIQDPVKGPWRLTAFYGYPDHGRRRDSWELLRSLHSQSDDPWCIIGDFN FT DHLSPSDKRGGPDRPHWLIRGFQEAVSDCNLIDLPLNGYQFTWFKSIGTSH FT AKEARIDRALCTAPWLELFPHASLQTLVAPMSDHTPLLLQLDPPPWRAPHN FT SFRFNNSWLIEPELAHLVKDNWSYYPSSNIVTKLSYCIEDMKYWSKANHPH FT FNQRKQQLKNQIDVMRNTSDASVDPRLIELQNSLANLILQEDVYWRQRSKI FT FWLKDGDKNSKFFHLTASSRRRKNTISKLRHPNGFWLTSQDDMSAHIHDYF FT SGLFQAINGDQQPVITRIQARVTENDNATLTKPFSIDEFKEAVFSMHSDKS FT PGPDGLNPGFYQFFWDDIGAEIFSSACSWLQSGAFPTHLNDTNIVLAPKGD FT HPETIKDLRPISLCNVLYKIISKVLANRLRPLIGNLISPEQAAFVPSRSIM FT DNALSAFEILHHMRCKQKGNTGEVALKLDISKAFDSVSWSYLQGVMRKMGF FT CDQWISWMMMCITSVDYHILFNGDRIGPLTPARGLRQGCPLSPYLYIICAE FT GLSALIRHNELAGNLHGIRVCRAAPPVSHLLFADDSFLFCQATPTEVNCLK FT DILMCYENASGQALNFGKSAIAFSKNTAPDMINHITTCLGVTRSIGSGAYL FT GLPSMVGRSKKSVFNYLKDRIWKKCQSWSAKSLSRAGKEMLIKSVAQAIPS FT YCMGAFLIPTSLCEEIERTMNSFYWGSKKDGSRGINWMRWNKLSLHKSHGG FT LGFRDMEAFNLSMLGKQGWKLLTEPSSLLTRILKAKYFPRRDFLDTNIGHN FT PSYTWRSIWSSRDLIKSGYRWKIGDGSRINVWNARWIRSLPTLKPSTIPSP FT TMAELFVNNLLNPDLSSWNNDLIHSIFNYQDATAILSIPLRNRTMVDTYVW FT QHTVDGSYSVKSAYTHCMTLAANMSNAADPDQNWNIIWKQKVPPRVRSFLW FT RAAHTCLPTRSELIQKGVPCSDTCVHCDVLAETHTHLFFVCPKVVTCWELL FT QLDAVIRDLLPTSYDFSTLLFNLFDRLTTEQQSMASMVLWSLWKNRNSKLW FT ENSDSAPAFIVQNANDSLNEWRYMQHHKNPGQQVHNTVLWTKPPPPFLKCN FT VDCALFNNNSVAGYGLCIRNSTGQFIAGMSNFSHCSLMPVEAEAWGLLEAI FT KFVVANDMSHVIFESDCKAIVDIVNSSHFPQNELGDILSTCKDLLSIHASF FT IVNFVRRQANEVAHSIARASLSNPSPHVFYDVSSHLYSLISNEMA" XX SQ Sequence 5383 BP; 1440 A; 1278 C; 1090 G; 1575 T; 0 other; gttattctct cccattcttg gtgagacgta ttcctttctc tcctagtgag aagtttcttt 60 accattttgt ttccatgaca tcactgccaa acctgcatct aagtgacgaa gaggaagaac 120 tcgaaattcc aatcgaggtt attcctgatg atactacaga tactagtgcc agccttgtgg 180 ggagattcct tactgacaaa ccaattagag ggcatatgat gacatccaaa atagctgagt 240 tttggcatcc aggaagaggg gtcaacatta aggaagttga accaaacctc ttcacattca 300 aattctttca ctatcgggat atgcacacca tcctcaaaaa aggtccatgg tattttgaca 360 acaacctgct aattcttaac actctcccag atgatgcacc tgcacaaagt gtgccactgc 420 aatctgtccc tttttgggtc cgaattcacg atattccagt ggggtttatg acagaaagag 480 tgggaaaaga cctgggaaat ttcatcgggg aatttttgga gtatgatgtc aagaacggtg 540 ctaatcatct cagatcctat atgcgcattc gtgtgttgct tgatgttaac aaacctctca 600 aaaggcagaa gaatatcaag cgtccagggg gtaacataca aactgtcaaa ttcaaatatg 660 aacgcttagg aaacttttgt tactactgtg gagctcttgg tcacattgaa gactactgtg 720 ataaactcta ttctattgat tcagacgatg gagcaagatt ctggggtccc gaattacgtg 780 tcgacagaca gaagaatgaa ggcagaggtt ctcgttggct ccgggaggaa ggccaggagt 840 ggtcaccgcc atcaaactca gcaccaaagg ctgccggaga cgtttcagtt ggtccagcaa 900 acggtaacgg tcgtgcatta actgttgtta cctcacctgc taaaacggtc gctttggctg 960 acctactgag gaatcctaat ttaattcgcc catcaggaag caataaacag caggaatctc 1020 atttatctcc ccataatgag acattattgg aagaggacaa tgcaacaatt attcacagta 1080 acacaaaacg gtcccgtgca gacttgaatg gaggatcttt gtctgctgac tcatctaatg 1140 cgcgccccac atcactcagc atcccttcaa cacctgcgca taataattct cagtcaacac 1200 caatggaggt tgtgaacact aaatcatcct caactagtgt gcctttttta tcggcagcgc 1260 ctggctccca ggcctgccgg gagtcatgaa tgttatagct tggaactgtc gtggcctagg 1320 caatgtcaag gcagttccct gtatcaaaga cctcgtccgt gtctataaac cggacattgt 1380 tatccttatt gagactttat gcaataataa taaaatttct ggtttgaagt atgcgattgg 1440 ctttgattat catttctctg ttgattgtat tggtcgtagt ggcggcattg ctgtcctttg 1500 gcgtaattct gcacactgct ccattctcaa ttattcacaa cattttataa atatgtccat 1560 tcaagaccct gtcaaaggcc cttggcgtct caccgctttt tacggttatc cggatcatgg 1620 taggagacgt gattcttggg aactacttcg ctctcttcat agtcagtcag atgatccctg 1680 gtgtattata ggagacttca atgatcattt atctccttct gacaaacggg ggggacccga 1740 ccgaccccat tggctaatta gaggttttca agaagcagta tctgattgta accttatcga 1800 tcttcctctc aatggatatc aattcacttg gttcaaaagc ataggtacaa gtcatgccaa 1860 agaagcccgt attgatagag ccctctgtac cgccccctgg ctggagttgt tccctcatgc 1920 ctcgctgcaa actttagttg ctcctatgtc tgaccacaca ccgcttcttc tgcagcttga 1980 tccgcctcca tggcgtgccc cccacaacag cttccgtttc aataactctt ggttgattga 2040 acctgaactt gctcatctcg tcaaggataa ttggagctat tacccttcca gcaacattgt 2100 tactaagctt agttactgca ttgaggacat gaaatattgg agcaaggcca atcaccctca 2160 tttcaaccaa cgcaaacagc agttaaaaaa tcaaatagat gtcatgcgca acacctctga 2220 tgcttcagtt gatccacgcc ttattgaact ccaaaatagt ctcgcaaatc tcatactcca 2280 agaggatgtt tattggcggc aacgctcaaa aatattctgg ctaaaggatg gtgataaaaa 2340 tagtaaattc ttccatttga ctgcttcatc tcgtcgtcgg aaaaatacta tctctaaact 2400 ccgacaccca aatggattct ggcttacttc acaagacgac atgagtgctc acatccatga 2460 ttatttttcg ggcctcttcc aagccatcaa cggcgaccag cagccagtta ttacacgtat 2520 ccaagcacgt gtaacagaga atgataatgc aactctcact aaaccattct ctattgatga 2580 gttcaaagaa gctgttttta gtatgcattc cgacaaatct ccaggacccg acggactcaa 2640 tccgggtttt tatcaatttt tttgggatga tattggtgct gagattttca gttcagcttg 2700 ctcttggctc caatctggtg ctttcccgac tcatctcaat gacacaaaca ttgttcttgc 2760 acccaaaggt gatcacccgg aaacaattaa agacctccgc cctatctctt tgtgcaacgt 2820 cctctacaaa attatctcta aagtccttgc taaccgtctt cgccccttaa ttggaaactt 2880 gatctcaccg gagcaagcag cctttgttcc ctcgcgttcc atcatggata acgccctctc 2940 tgcctttgaa atccttcatc atatgcgttg caagcaaaaa ggtaatacgg gtgaagtagc 3000 attgaaactt gatatttcca aggcctttga cagtgttagt tggagctact tgcaaggggt 3060 tatgcgcaag atgggttttt gtgatcaatg gatttcttgg atgatgatgt gtattacttc 3120 ggtcgattac cacatccttt tcaatgggga ccgtattgga ccactcactc ccgctagagg 3180 ccttcgtcaa ggctgcccac tctcacctta tctctacata atttgtgcgg aaggcctctc 3240 tgctctaatc cgtcataatg agctcgcagg gaatttacat ggaatacgcg tgtgtcgtgc 3300 agcccctccg gttagtcatc tcctttttgc agacgacagc ttcctctttt gccaagcaac 3360 cccaaccgaa gtaaattgtc taaaagatat tctcatgtgt tatgagaatg cttcaggcca 3420 agctctaaac ttcggtaagt ccgccatagc cttcagcaaa aacacggcac ctgacatgat 3480 taatcacatt acaacctgcc ttggggtgac gagaagcata ggcagtggtg cttacttagg 3540 actcccttcc atggtcggac gtagtaagaa atctgtcttt aactatctca aagaccgtat 3600 ttggaaaaag tgtcaatctt ggagtgctaa atctctgtcg agagcaggta aagagatgct 3660 catcaaatcg gttgctcaag caattccttc atattgtatg ggagcttttc tcattccaac 3720 ctctttatgt gaagaaattg aaagaaccat gaattctttc tattggggtt ctaaaaaaga 3780 tggcagtagg ggtataaatt ggatgagatg gaacaaacta tctcttcaca aaagtcatgg 3840 tggactcgga tttagggata tggaagcctt taatctatcc atgctcggta agcaaggttg 3900 gaaactcctt acagaaccta gctccttact cactcgcatt ctcaaagcca aatatttccc 3960 tcgacgggac ttcttggata ccaatattgg tcacaatcca agttatactt ggaggagcat 4020 ttggagttcc cgagacctta taaaatcggg ctatcgatgg aagatcggtg atggttcccg 4080 catcaatgtt tggaacgctc gttggatacg ttcactccct acacttaaac cctccactat 4140 tccttctcct actatggctg agttgtttgt caacaatctg cttaatccgg atctgtcctc 4200 ttggaataat gatctcatcc attctatttt taactaccaa gatgctacag caattctttc 4260 tatccctctt aggaacagaa ctatggtgga tacttatgtt tggcagcaca cggtcgatgg 4320 ttcctactcc gttaaatcag cttacacgca ctgtatgaca cttgcagcca atatgtcgaa 4380 cgctgctgat ccggaccaga actggaacat tatttggaag caaaaagtcc ccccaagggt 4440 gcgctccttt ctttggcgtg cagctcatac ttgtcttcct acccgctccg agttaatcca 4500 aaaaggagtc ccttgttccg atacctgtgt gcattgtgat gttctcgcag aaacgcatac 4560 acatctcttc tttgtgtgtc ctaaggttgt tacttgttgg gagctgctgc aacttgacgc 4620 agtcatccgt gacttgcttc ctacttcgta tgatttttcc actcttttat ttaatctctt 4680 tgacaggttg acaaccgaac aacaatctat ggcgtcaatg gtcttatgga gcttgtggaa 4740 aaatcgtaat tctaagttgt gggagaattc agattcagcc cccgccttca ttgtgcaaaa 4800 tgcgaatgat tctcttaatg aatggcgtta tatgcaacat cataagaatc cgggacagca 4860 ggtacataac acggttctgt ggacaaagcc accgcctcca ttcttgaaat gcaatgtcga 4920 ttgtgcgcta ttcaacaaca actcagtggc aggctacggg ttgtgcatcc gtaactcaac 4980 aggccaattt atagccggta tgtcaaactt ttcacactgc tccctcatgc cagtcgaagc 5040 tgaagcatgg ggtcttctag aggctattaa atttgttgtt gctaacgaca tgtcccatgt 5100 gatctttgag tctgactgca aggccattgt tgacattgta aactcctctc atttcccaca 5160 aaacgagctg ggagacattc tatctacttg taaggactta ttatccattc atgctagctt 5220 tattgtgaac tttgttagga ggcaagcaaa tgaggttgct cattccatag caagagcatc 5280 cttatctaac cctagccccc atgttttcta tgatgtatct tctcatttgt actctttgat 5340 atctaatgaa atggcctaag cttgcctttg ctcaaaaaaa aaa 5383 // ID Copia16-PTR_LTR repbase; DNA; EDCOT; 268 BP. XX AC LG_XVI; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia16-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-268 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-268 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 205-205 (2007). XX DR Genome; LG_XVI; Positions 11657699 11657432. XX SQ Sequence 268 BP; 67 A; 48 C; 48 G; 105 T; 0 other; tgttaaatat taggatttga tttaccagtt aaactgggtc gttaataatt cctattgtat 60 aggaacactt agctgtagtt tgcttagctg tagtgtgtct ttgtctttaa ctgtccacgt 120 tgctctccac gtcacaaaag gagtgggcac gtttttagct tattcagttt ctttccattt 180 gctttgcttc tgtttgtaag gctattaaat agccaatcct ctcttaatga aagtacacag 240 ttattgttca aatcttctga gatcaaca 268 // ID POTTEN2 repbase; DNA; EDCOT; 797 BP. XX AC . XX DT 24-OCT-2006 (Rel. 11.1, Created) DT 31-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE Non-autonomous DNA transposon from Solanum demissum. XX KW DNA transposon; Transposable Element; Nonautonomous; POTTEN2. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-797 RA Shankar R. and Jurka J.; RT "POTTEN2: A non-autonomous putative DNA transposon from Solanum RT demissum."; RL Repbase Reports 6(10), 499-499 (2006). XX DR [1] (Consensus) XX CC POTTEN2 is a DNA transposon with ~10 bp target site duplication CC and inverted repeat flanks, from Solanum demissum. XX SQ Sequence 797 BP; 285 A; 112 C; 116 G; 270 T; 14 other; ggaaaagggc cwaaaatacc cttgaactat tggaaatggt ayaaaaatac ccttcatcca 60 cctattgggt caaaaatgcc cttctcgtca acttattggc tcacaaatac ccttgtcatc 120 cactttgggt tcaaaattga ccactttttt aactattttw caattaaata atattttaaa 180 tacgtggcga tcaactattg gttataattt taatttaaat caatccacta cccactcatt 240 attaactaaa cctgatccaa aaatattaat ctcgtcctaa atactattac amcacgatwa 300 aaataaattc tgatccttca ttcccaacaa ttaaattcat cttccaactt ttttcctaat 360 atattaaatg taaaaaaaat acaaataytc atgtattaaa aaaaagtttt tttcgaagta 420 agcgmatata ttgagtaaga ttgatgaaga aaaacatatt cagaattaag agtgtatttg 480 ttttaattat tttgtaattt aaggctgtaa ttaacttcra ttggtataat taatwtgaga 540 cgagtgtatt aatttgagga gtttttagta atgggtgggt ttataaatta acttataatt 600 aaattataac aaatagtcgc cacatattta aaaaaatatt taaatgaaaa ccgttaaata 660 agtggttgar ccaaaggtgg atgacaagrg tatttgggas ccaataggtg ratggaaagg 720 gtattttgga gccaataggt ggatgaaggg takttttgta ccatttaata gttcaagggt 780 attttaggcc cttttcc 797 // ID V1_I repbase; DNA; EDCOT; 1703 BP. XX AC EF439837; XX DT 27-MAR-2007 (Rel. 12.03, Created) DT 03-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE Vitis vinifera retrotransposon V1 - internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; V1_LTR; internal portion; V1_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1703 RA Kalendar R.; RT "Vitis vinifera LTR-retrotransposons."; RL Direct Submission to Genbank (14-FEB-2007). XX DR EMBL/GenBank/DDBJ; EF439837; Positions 626 2328. XX CC There are only 3 substitutions between the LTRs. XX FH Key Location/Qualifiers FT CDS 46..1689 FT /product="V1_I_1p" FT /translation="MSGSNVEETSEQTRGRETEPTARGRGRGKKDKSRDVV FT ANMEARLAKVELAMADTREGLDLIEQGMEKGLEDLREQIQDLREGVLVSQV FT QPVSHEEFVSFQGKVLSMLASMESRIEALATRMESRDQEVRQELAIYKAAV FT SARVMATQEASRVEVPKPHRFSGKRDAKELDNFLWHMERYFEAIALTDEAA FT KVRTATLYLTDTATLWWRRRFADMEKGICTIETWEDFRREIKRQFYPEDVA FT YLARKNMRRLKHTGSIRDYVKEFSSLMLEIPNMTQEELLFNFMDNLQGWAE FT QELRRRGVQDLATAMAIAESLTDYKRGDSSKVESLEDSHAMGGGDEVPRDH FT NAPKKGSGKTSNVREGRDKAERKEFTPKIKCFLCDGPHWARDCPKRKALSA FT MIEEREQEDEAHMGSMQLLGALQFNPKPSTPETSLLAGVQVKEEKGERAEV FT ARTHMEEVTKGKVNYQGKRKQHSKHRKRTGLHPSEASREKEVKNILAERVT FT RRQGVPPVIEYLVRWKGLPKRQVSWEHADALRKFWKHIERFQNEATTRTST FT A" XX SQ Sequence 1703 BP; 472 A; 356 C; 560 G; 315 T; 0 other; agtggtatca gagcgcggtt acgaggtggg catagcaaag gaagcatgtc gggttccaac 60 gtggaggaga ctagtgagca aacccgtggg agggagaccg agcctactgc acggggcagg 120 ggcagaggta agaaggataa atctcgtgat gtcgttgcca acatggaggc aaggttagcc 180 aaggtggagc tagccatggc ggacactcgg gaggggttgg acttgatcga gcaaggcatg 240 gagaagggct tagaggatct aagggagcag atccaagacc ttcgcgaggg ggtgctagtc 300 tcacaagttc agccagtgtc gcacgaggag tttgtgtcct tccaaggaaa ggtcttgagc 360 atgcttgcta gcatggagtc aaggatagag gccttggcca ctcgaatgga gtcccgagac 420 caggaagtta ggcaggagtt ggccatctac aaggctgctg tgtcggcacg ggtcatggcc 480 acacaggagg catctagggt ggaggtgccg aagccacaca ggtttagtgg caagcgggat 540 gccaaggagt tggataactt cttatggcat atggagcgat acttcgaagc tatcgcattg 600 acggatgagg cggctaaggt gagaactgcg accctctacc ttactgacac agctactcta 660 tggtggcgtc gaaggtttgc cgatatggag aaaggcattt gcaccataga gacgtgggag 720 gacttcagga gggagatcaa gaggcagttc tacccggagg acgtggctta cctggctagg 780 aaaaacatgc ggcgtcttaa gcacacaggc tcaatacgcg actatgtcaa ggaattctct 840 tcgctcatgc ttgagattcc taacatgact caggaggagt tgctattcaa cttcatggat 900 aacctgcaag ggtgggccga gcaggaatta aggcgccgag gcgttcaaga cttagccact 960 gctatggcaa tagcagaatc tttaacggat tataagaggg gagactcctc caaggttgag 1020 tctttggagg atagccacgc catgggtggg ggagacgagg ttccaaggga ccacaatgct 1080 cctaaaaagg gatcaggcaa gacgtctaac gtccgagaag gaagggataa ggcggaaagg 1140 aaggagttta cgcctaaaat caaatgcttc ctgtgtgacg gtccacattg ggcacgggat 1200 tgtccaaaga ggaaggcgct cagtgccatg atcgaggaga gggagcagga ggacgaagca 1260 catatgggct caatgcagct actaggtgcc ctccaattca acccgaagcc tagtacgcct 1320 gagacctcct tactagcagg ggtgcaagta aaggaggaaa aaggggagcg agctgaggta 1380 gcccgcacac acatggaaga ggtcaccaag ggaaaggtga actatcaggg taagaggaag 1440 cagcactcta agcatcggaa gcgcacgggt ctgcatccat ctgaagcctc acgggagaag 1500 gaggtgaaga atatcctggc tgaacgggtc accaggagac aaggggtccc tcctgtgata 1560 gagtatctag tccgatggaa aggactacct aagaggcagg taagctggga acatgcggat 1620 gccttgagaa aattctggaa acacatcgag aggtttcaga atgaggcaac gacgaggacg 1680 tcgacggctt aggtggggga gag 1703 // ID HAT-5_Mad repbase; DNA; EDCOT; 3641 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-5_Mad. XX NM HAT-5_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3641 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1616-1616 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >96% identical to consensus. 8-bp TSDs. XX FH Key Location/Qualifiers FT CDS 835..3390 FT /product="HAT-5_Mad_1p" FT /note="transposase." FT /translation="MSFRKQLSGNMKRKKKAKDNEIAESLRGSLNKFFSTK FT NESVENLRENNVGEEPQNVVGESHDHENGSDLEENVGDESQDHENGGDVDL FT NVDDDHIGVEENIESPEPIFHLNIYDPRVWDGLNAEMRDLLVENGPIRETN FT LTYPKDKLSRKFSSHYYDRKLPTGEIYDRKWLVYSKELDKVFCFCCKLFKT FT IASKSELAKDGISDWRHLGVKLDQHEKSKEHLTNSRTWVELKSRLTTNQTI FT DKEFQMRIKKETNHWKQVMLRIIAVVKCLAIRNLAFRGTNERPYEDSNGNF FT LGLLEMIAEFDPIMQKHFRLIENKEIHHHYLSHKIQNELIATLASKVKTAI FT IKKVKEAKFFSVILDCTPDASHVEQMTLILRCVDLSSRSINIREYFMEFLS FT VEDTSGQGLFNELQDVLKSLDLDIDNVRGQGYDNGSNMRGKHQGVQKRLLD FT INPRAFYMPCGSHCLNLIVCDMASSCLKAKSFFGACQCIYTVFSNSTKRWN FT ILLEHIDGLTLKSLSTTRWESHIESVKAIKSQVAQVRNALFTLVEITENPQ FT LSRDAECLASGELSSFDFVLSLVIWYDILLKINMVSKKLQSEDMRLDVAVK FT ALEALVTFFENYRETGFASAMRDAKEIALESEIDPVFQTKRHRPRKRHHDE FT VDGNEREQQSAEESFRTDYFLVIVDIALSQLKHRFEQLKAFEYIFGFLFDA FT PKLISLDDQQLKENCMNLEAHLKHGNTMDVDGADLCSELQVLQMMLPEEAF FT LSNNPWTSMEIANFVKETDMCPNVLIAYRVLLTVPVTVASAERSFSKLKLL FT KSYLRTTMTQDRLNGLAILCIEKDEIEDLEYDDIIDDFASKNARRQFLKG" XX SQ Sequence 3641 BP; 1208 A; 588 C; 715 G; 1128 T; 2 other; cagggccggc ccaggcccag tgccacaggg gcaactgtcc agggccccaa aatgaagggg 60 gcaccaaaat aaaaaaaagc ccatataact aagtattaaa aaaaaaattt cacagcccaa 120 ataggggctg gcaagagccc aaaaggcaac aaaagggccc agaaagaccc agccacagat 180 tagaagaaaa aaaaaaaaaa aaaaaaaaaa aaacataaca aaacataaca gggaccactc 240 ggtcccaatc aaaccctaat ccctaatata ctcaaccttt cccgattccc caccctttcc 300 cgattcccca cccacccacc cacctccctt ttgttcccta catcccccac tttgccttcc 360 ctgcccctcc cttttctttc tctgaatcat tgtttctgtt cctcttgatc attggagctt 420 tgctctgcca tcccaagcca tcccaacttc ttcgccgcaa gctttaatgg ttgctccaaa 480 ctctcaagcg cgaagacaaa attagttttg aggtaaacta atttttaaaa tttgaattmt 540 caatttataa tttaatataa aattttgcaa tgcaagtgac atagaattat atgataaatt 600 gataattgat gtatagaatt gttgttgttg atgaatgatg aattgaattc ttgactaatt 660 gattattgaa ttatttgatt tcatttcaaa cccaattttt aggttcaatt tttataatat 720 gtttgactat gtgttagtgt ttttataata tataatgtgt tggaatgata attttgatag 780 gaaaattttg ttatatcatg tgtaggtaat ttttgcaaac aaattatcga agccatgtct 840 tttaggaaac aactctctgg taatatgaaa aggaaaaaaa aggcaaagga taacgaaatt 900 gccgaaagtt taagaggatc tcttaataaa tttttctcta caaagaatga gtcggttgaa 960 aatttgagag aaaataatgt tggtgaagag ccacaaaatg ttgttgggga gtctcatgat 1020 catgaaaatg gtagtgattt agaagaaaat gttggtgatg agtctcaaga ccatgaaaat 1080 ggtggtgatg tggatttaaa tgttgatgat gatcatattg gtgtagagga aaatattgaa 1140 tctcctgaac ctattttcca tttaaacatt tatgatccaa gagtttggga tggtcttaat 1200 gcagaaatga gagacttgct tgtagaaaat gggccaattc gagaaactaa tctcacttat 1260 cctaaggaca aactctctag aaaattttcc tcacactact atgatcgaaa attaccaacg 1320 ggtgaaattt atgataggaa atggctcgtg tactcaaaag agttggataa agtcttttgc 1380 ttttgttgta aattgtttaa aacaattgcc tcaaaaagtg agttagcaaa agatggaatt 1440 agtgattgga gacatcttgg tgtgaagctt gaccaacatg aaaagagtaa agagcatctc 1500 actaattcga gaacttgggt tgagttgaaa agtagattga caacaaatca gacaattgat 1560 aaagaatttc aaatgcgaat caagaaagag acaaatcatt ggaaacaagt gatgcttaga 1620 attattgctg ttgtgaaatg tcttgccata cgtaatttag catttcgtgg aacaaatgaa 1680 agaccttatg aagactctaa tggmaacttc ttaggtttac ttgaaatgat tgcggagttt 1740 gatccaataa tgcaaaagca ttttcgactc attgagaata aagagattca tcaccactat 1800 ttgagccata aaattcaaaa tgagttgata gctactttag cttcaaaagt caaaaccgca 1860 atcattaaaa aggtaaaaga agccaaattt ttttctgtca ttcttgattg tactcctgat 1920 gcaagtcatg tggaacaaat gactttaatt ttgagatgtg ttgacttgtc aagtaggtca 1980 ataaatataa gggagtattt catggagttt ttaagtgtgg aagatacatc aggacaagga 2040 ctttttaatg agttgcaaga tgtcctaaag tctcttgatc ttgatattga taatgtgagg 2100 ggacaaggtt atgataatgg atctaacatg agagggaaac accaaggtgt ccagaaaaga 2160 ttgctagaca taaatcccag agccttttac atgccatgtg gttctcattg tcttaattta 2220 atagtttgtg atatggcaag ttcatgtctt aaagcaaaat ctttttttgg agcatgtcaa 2280 tgcatatata cggtgttttc caactctaca aagcgttgga atattttgct tgaacatatt 2340 gatggtttaa ctttgaagtc attgtcaact actcgatggg aaagtcacat tgaaagtgtt 2400 aaagcaatta aatcccaagt agcccaagtt agaaatgctt tgtttacgtt ggtggaaatt 2460 actgagaatc cccaattgag tagggatgca gaatgtttag catcaggaga actttccagt 2520 tttgattttg tattaagttt ggttatttgg tatgacattt tgttgaagat taacatggtg 2580 agcaaaaaat tacaatctga agacatgcgt cttgatgttg ctgtaaaggc attggaagca 2640 cttgttacct tttttgaaaa ctacagagaa actggttttg cttctgccat gcgtgatgct 2700 aaagaaattg cacttgaatc ggaaattgac cctgtttttc aaactaaacg tcatagacct 2760 agaaaaagac atcatgatga agttgatggt aatgagaggg aacaacagtc tgctgaagaa 2820 tcatttagaa cagattattt tcttgttata gtggatattg ctctttctca actgaaacac 2880 aggtttgaac agttaaaggc ttttgaatat atttttggct tcttgtttga tgcaccgaag 2940 ttgatttcat tggatgatca acagctaaaa gaaaattgta tgaatcttga agcacatttg 3000 aaacatggaa ataccatgga tgtagatgga gccgacttat gttccgaatt acaggtgttg 3060 caaatgatgt tacctgaaga agcatttctc tctaataacc cttggacatc catggaaata 3120 gcaaactttg taaaagaaac tgacatgtgt cctaatgtct tgattgctta tcgtgtactg 3180 ttgactgtac ctgtgaccgt ggcatctgca gaaagaagtt tttcaaaatt gaaattatta 3240 aaatcttact tgcggaccac tatgactcaa gataggctaa atggattagc aatcttatgc 3300 attgaaaagg atgagattga agacttggag tatgatgata taattgatga ttttgcttca 3360 aaaaatgcca gaagacaatt tcttaaaggt tgaaatttca aggagctttg ctaggaatgg 3420 ttgtatatga ttgtattttt gattgtcggg gtttaggtac tatgtccccc ccgttgtata 3480 ttttctcaag taatataatt tgggcgtgag ggcctagccc cccagcttcg actgggttcc 3540 agccctcgtt aaatattttt tttaaacata tgtttccgta ttaaaaaagg ccacattttg 3600 agctttcgca ctgggcaccc aaaaacacag gaccggccct g 3641 // ID LTR-5_Mad repbase; DNA; EDCOT; 3192 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR-5_Mad. XX NM LTR-5_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3192 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1788-1788 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 3192 BP; 814 A; 556 C; 822 G; 998 T; 2 other; tgtgaaatcc cgttcccgga tttcactatt taaaattacg tatctcatat gtagtattca 60 tattcgtagt ttcgacgcgt ttatatttac ggcgtataaa attttattcg ataagtaaaa 120 ggatgaaatt gcccctattg tgttaaacga gattctttgt ggacgtactt gatattttca 180 taatttttca gatttctttg catatctgga tagtacgtgt cgatacgaac gcgtgggcgc 240 aaacggaacg taawttggag ttataacgaa tgagttatta acgaacaaag acaagggcaa 300 aatggtcmtt taattattaa atctggaagg ctccagattt gttggagcag gaatggctgg 360 gatgaagcca cgtgtgtggc tgtgatggag agaagagaag agaaaggggt gtggaactgc 420 ccaatcaggg ggagggcgga cgaatgagag gaaagagctg ggaggggaag ggagatgagg 480 gagaaaaacc ggatcaccct ggactcgatg acccgacccg gtttagccgg acttctatga 540 gttttccgac ggttttccgt caattttctg acgaatttcg tcgagctacc acctggaaaa 600 ccttccccga tcttccctct cccatttgca cccataatcg aagaagtttg gccctaattt 660 cacgaagaac ggaactcgtc ggcgttaatg ggtgcacggc ggcgattcgc catttctgcg 720 agctccacca tcgatcacca ccatcaatcg actcctctca accccaggag caaggcccaa 780 gcattggata aggcgtcgga gttcgtttgg tgacgaatcg aagctcaccc ttttcggggt 840 ttccgacggt tcgagggatt ttccggccac ttcccggccg aactaggctt cggcccaggt 900 atgaaaaatg ttcctctcct tgagttgtac atttctgcaa aatttggtga attttagtgt 960 tggtcggaat ttggggtttc cgttcgccgg aaaccgccac ccgcggcggc gcgtggccag 1020 tgggccgacg ctgccttttt aagttaaatt cgatgttctg atttcaaatt tgataaccgt 1080 ttgatatagt tcgatagttt gaacctagta tggaatacta cgccacttga ccattttatg 1140 attcgacgat ccgaccgttg gatcgtcacc aaaccttaat acgttatagt acgtaatatt 1200 tgaggaccat aggaactgac ggattgggaa tccgacgtat ggatcttccc aaattgaatt 1260 tctaagtttg taaaaccaaa cgttgatagc aacctaattc tagcaattgg cggagatccg 1320 accgttggat cgttccgaaa ttttagaata ttgttctaga agataaatga gacccttggg 1380 aagttacgga tcggaaatcc atgggcggat gttccagatt gacttgtata gggttgtgga 1440 ccccaccttt gacagagact tgacttttgg tcaatatgct acgaattgat cttaaatatt 1500 aaaatcagta ttactagaga ctatgtaggg cttagtgggc ctatattggt tagtgagtta 1560 tcccagataa tatatacatc ggtttacgtg tatgggacgt catattgtga tatatatgtg 1620 tttatttatc ttcttaataa tgtgaatgat aagtatgata aatgttatga caatgtgatc 1680 ctagaatcct attagaagta ttctgtagaa cttatatgct tgtgtgacat attagttggt 1740 ggccatgaga agttgatggt gcaggtgact acgttgtaac tcataggggt tgaggtatgg 1800 gtaggttgtg tgttgaattt actgcaccat gtagcagtgg tacatggatg gtcctgcttg 1860 gtatatccgc gatgggggac catacgtatt tcaagggtga tcatgcttgg tatatccgcg 1920 atgggggacc atacgcattc taagagtgat catgcttggt atatccgcga tgggtgatca 1980 ctactagagt tatagatcag tcctgcttgg tatatccgcg atgggggact gttaggggtg 2040 atcatgcttg gtatatccgc gatgggtgat cactgcctac gttattagac tatgcatatg 2100 gttctgcttg gtatatccgc gatgggggac catacgcatt ctaggagtga tcatgcttgg 2160 tatatccgcg atgggtgatc actacctaga gttaggatgt ggtcctgctt ggtatatccg 2220 cgatggggga ccatacgtat tcaggggtga tcatgcttgg tatatccgcg atgggtgatc 2280 actgcctgca cgatgagatt atgcctatgg ttctgcttgg tatatccgcg atgggggacc 2340 atacgcattc taggggtgat gaggattagt tgtacttggt acatttcgat aggcgatcat 2400 attttggttg gattccgttg agtggtccgg aatccctact cttgctcatt tccataaagt 2460 tagtccgacc ctaggttcga gtgagtagga attgctcaca gtagacgtta tgtttataaa 2520 ttagaattat catgttatta cttggaatcc aggtagggaa ttatgtagaa ttcctttatt 2580 aaatttcgtg aattgatatg tgatcttatt gattgattaa cgtagttaaa tgttaatatc 2640 gtgcatcttt gattcatgga attgattaat tggagtgatt gtggaatgat gttggatatg 2700 attgttatta ttatgattag attagttgac caatgtggct agagaataat attgtgcttc 2760 gttgactgtt ctttgatatg ttgcatgcta tggattgcgg tattatgttg aaacatagtg 2820 atttatatga tggatgaaat ggaaatcttg attgtcatgt gggtttgtta tgtagccctg 2880 aatctagtaa tttcatgctt gtcaagttct aatgattgat tgaggaatgc tatgcctttc 2940 tgcttgaacg tactgtgata aatgtcggag tgtagtgaat ggtgaactac gaatggcttg 3000 atcccttttt agggtacgta ggcagtctaa cgaggaggtt agatgcagcc ataaagtata 3060 cgaaaattac tacgcaattc gaatcttgaa ttatgctttg tacatatccc ggaggcgggg 3120 tctgttggat atacggatac ttggtgacgt cacgtgtcga tcctggacgt atgtcgggat 3180 cggggcgtga ca 3192 // ID MtPH-M-2-Ia repbase; DNA; EDCOT; 5519 BP. XX AC . XX DT 13-MAY-2008 (Rel. 13.05, Created) DT 13-MAY-2008 (Rel. 13.05, Last updated, Version 1) XX DE Harbinger-type element from Medicago truncatula. XX KW Harbinger; DNA transposon; Transposable Element; MtPH-M-2-Ia. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-5519 RA Grzebelus D., Lasota S., Gambin T., Kucherov G. and Gambin A.; RT "Diversity and structure of PIF/Harbinger-like elements in the RT genome of Medicago truncatula."; RL BMC Genomics 8, 409-422 (2007). XX DR [1] (Consensus) XX CC An autonomous element representing subfamily M-2 of PIF/Harbinger CC transposons from Medicago truncatula, carrying 14 bp-long TIRs. XX SQ Sequence 5519 BP; 1739 A; 842 C; 985 G; 1953 T; 0 other; gtacgtgttt ggttacacgg tcaaaaacgg aaaacgcgct tccatctgtt caaaagcact 60 ttgaggatgt ttggctctcc ataatccttc tgccgccgcc tagcttttga caactagaat 120 cgattttgaa agaagctgct attcctagct tctacaaatc gatttcctac accttaggtt 180 tgctttctct caatttctct tttttgccct taccttcacc gccataaatc catgttgatc 240 tgaatttttc aaattttttt tgaaacattg aaggcaaagc tgttttttca cctgtataat 300 aactctatgc ttatctaaat ttactaatct cttgtcaaac attgaactct aattccttaa 360 tggaaatatg atccactttg tattaagggc ggcctccaca ttttcattaa ttcttcacaa 420 cttgtagaaa tcagtcacca acctcatagt ttcattaact atgtagttac tctctgttca 480 tacaaacttc tatatatagg ttggctcatt tatcactctt tcattcttaa acaagcaaat 540 agccaaatag ttacagtgtt tggtactcaa gggtaagctc aaacactcat cttctgtcta 600 ttaattcaat tttgataaca ttgcatttga tgtgtttgat aaaatgccta aataaaaaac 660 aatttatttc ttttgttttc cttgacctta gtatgattgt ttattttatt ttttgcctga 720 aatattaatg atattgatgg agtttgaaaa tagcttctat gtttttcatc aaatgatact 780 aatcaatatt atttgcattg tatgagtact ttagattgag ttattttcta taccatttat 840 cactatagtt tcaactttgt tgacagaagg aatgttcttc attttttttc tatcttttgt 900 caactctaga aaataaagga agagctatct atggtgttca tatgtggttt tataatttat 960 ttttaccaaa ttttctctta aacacatgta ttatatctga agttacaagt ttcaaaggat 1020 aatatctaaa gaatttatca accttgatga agaccttgaa tagtttagga ccatggatct 1080 tgaaatagtt gcaagaagag aaagctttca agcacaaatg ccacttattc atgtctgtta 1140 tttaatattt acttttgaca aggttttaga tgtgtgtgtt tttttagtag agaatatgtc 1200 tttattttat tggtgttttg gttcagtttt gctactattt tggttatgtt tttctatatg 1260 ttgatataaa caacctcaat aagctcttca aatgataatg ataataaagt ctctctttgt 1320 ttgcttcttt gttttacttg aactcatagt gatttttgtt taccaatttc acctcattag 1380 ataagtggtt attcgaatat aggtttgatt caaatagatt aatatttaac cttgtttaca 1440 taaaatggtg aataccaaga aaaatgttgt gcgtttctcc tcacctaatg atggggggca 1500 gaaaacaaaa gctaattggg attataagtc aactgaaaac tttgtgaaag catgtttgga 1560 gcaagtttcc aagagagaac gtgttggtac gagctttaca aaaaaagggt ggaacaatat 1620 taaggcccaa tttcataatt taaccggact gaagtatgag aaggctcaat taaagaatag 1680 gtatgacagt ctgagaaagg attggagagc atggtataac ttatttggga gagaaactgg 1740 attagggtgg gatccggtga acaacactgt tgtagcacct gatgagtggt gggagaccaa 1800 acagctggta tgtaatagag aaaattgtta tttcgtaagc cttagatata tatacccgtg 1860 tttcttatat gatgaattat gaaaatgtag gaaaaccctc cttatgaaaa atttaggaac 1920 aaggggcttc cattctccaa tgagttaact acacttttta aggatgtagt ggctaatgga 1980 gagtacactt gggcaccatc atgtggggta ttggcatgtg tgtttgaaaa tgatgataat 2040 gatgtagtgg ctgtagaagg atctggcgat agcgaggatg caagtgttgg agcaacaact 2100 gaatttgcaa atattagact gaattcttca caaaaaaccg atggtcaaaa gagtggtgag 2160 aagaggaaaa gagttgttag agtagacaag ccaagtaaga aaaaagcaag tgcatcatca 2220 aagatagctc cgggtaatag cagagacatg tcgttctcgc aatgatgctc cgggtaatgc 2280 atctattggt gaagtgatgg ctaagcttca caccatggat gaaatctcaa atgatcttta 2340 tttgcatgcg cagtgttgca acttgctgat gtttaagcct gcaagggaga tttttatttc 2400 cctacgaggt tcagaggaga aaaggttgga ttggcttaag catacaattg ataacccatt 2460 gccattcatg actatgtaat ttggaacctg tgtgactagg atgtaatggg aattaagcta 2520 ggaagtacta tgaattaaga agtaatctac gaagtactag taactatgaa gtactcttat 2580 gtttaatctt taatgttgta atgttctgtt gtctttaaat taagaagtaa tctaggaagt 2640 accggtaact ttgaagtatt gttatgtttt tcctttcaat taggaagtaa tctaagaagt 2700 ggtagtaact atgaagtact cttatgaagt accagtaact tatgtaatat ttctatccct 2760 taatgaagac ttatgttgtg tgataattat gcttgtattt ttggttcact tatgttgttt 2820 ttttgcttca gttttaactg ctattttggt tctgatttgc tggttttctt gttcagtttt 2880 taccaccctt ttagattgtg tgaaaatatt atcctgatca tagttatttg caatgttgtt 2940 atgatttctg cactatattc tgcacatgat ttctacacta tatttgtttt agattgcagt 3000 taacttgtgg gttgcacttg gtagtttgct gcaaaatgca cagatataca caataaagaa 3060 aactaacata tgggttgcac taggtagttt tctgcaaaat gcaatacata agatttactt 3120 tgctggtaaa cttatttaca ttgctagtac cttctgaatg tacacaataa agacacatat 3180 gtcaaataag atgcaaaaac aatgcagaca agtatatata tgtaatccga gtaaaaatac 3240 agtatatggc tgacatgtaa ttaatttctt ctacaaagct aatgcactat atttgtctat 3300 aattcaaatg ccatgatttc tgattgttct gattattgtt atgtttctta tgatttctta 3360 tgtttaatat catgttttag attgtgtgac attcaagata gctcctgata taataaatta 3420 attttttttt tgtttttctt actaattgtt tacctttgac agtagccaaa tctcattgca 3480 aaatggacta ttgtgatgaa gaatcaactg aagacgatga tttttttgaa caagcttctt 3540 tagtggctgc actaatgggt gagtatgcta gaatacatgt atgttaagag ccatgtagaa 3600 ctagtgagct aatagggcat gcatgggtga aagaagtatt gcaaggaaat cccactcgtt 3660 gttataagat gtttcgaatg gaaaaatata tttttcataa actttgcact aaattagttg 3720 atcatggttt aaatcccact aatcacatag gggtagaaga gatggttgca atgttcttac 3780 ttgttgttgg acatggagtg ggtaatagaa tgattcaaga aaggttccaa cactcaggag 3840 aaactgtgag tagacgtttt catgatgtgt tagttgcttg cttgagtttg tccatcgaat 3900 atataaagcc tcaagatcct ttgttccgtg atagtcatgc aaaaattcaa agtgatccac 3960 agtattggcc attttttaag aatgccatag gagcaatcga tggtacgcat attccctgtg 4020 tggttagtgc caatgaccaa actagattta ttggacaaaa gggatatccg acacaaaatg 4080 taatggctgt atgtgattgg aacatgtgct ttacttttgt tttagctgga tgggaaggta 4140 ctgcccatga tgctcgtgtt tttgaccatg ctctcacaaa tgcaaatcta aattttccac 4200 atcctcctcc aggtattaat attatctttt acaacttatt tattagtatt attctttaca 4260 atttataatt taatttgttt ttaggtatgt attatttggt ggatgccggt tatccaacac 4320 cgatgggata tcttggtcca tacaaatgtg aacgtttatc acctccctga ttttcggcgt 4380 tctcatgggt ttgaaaataa caacgaggta ttcaattatt atcactcaag tttaaggtgc 4440 acaatagaaa gaacttttgg tgtatggaag aatagatttg caattctacg acgcatgcct 4500 aaattcacaa ttaagacaca agttgaagtc gttgttgcaa caatggctat acataacttt 4560 attagaagga atgctgatat ggacgtcgat ttcaatcggt atgaggatga agacataacc 4620 cttgatcatg atgattatcg tacaccagtt aatttggatt tatctcaaaa tttaaatata 4680 gcttcctcat ctgagatgaa tcatgttcga aactcggttc gagatcaaat tatagagttc 4740 aacaaaaatc attagtattg tagtaatgtt taattttaaa gaccatcaga gatgagataa 4800 catgatgcac tgagaaggca tatgactatc ttgcaaagaa acaccctctc tgcaactcat 4860 caaccaaaca cttagttatg ctagggagat ggagaggatt gtctcaaaag aaatggatgc 4920 aatggatttt gtgttttcca agattgctaa tattgtctaa tgaaattgtt taattctgat 4980 tcaatgtgga actgtgaaat gattctatct ctttattatg ttcatctagg tgctgtattg 5040 ttccatagtg tacccttttc tttctttttt acagtgctca aaatcattat atacttgtgt 5100 tgactattat atcgtaagaa tttgacaaat tgatgaattt caaatccatt ggaaggttca 5160 tattcaaaaa aaaaaattat atatattccc tacatgcatt tttatttgaa tattgtgtga 5220 ttaacaatta tattaatcta gtaattttat tgtcagttaa tcaaaaataa ataaaggatg 5280 aaaaatcaaa taaatgtaaa atttatatat acacatatac aaacacacac agacacactc 5340 acattttaaa gcccatttag gtcttttata catctaaaag caattctgac tcaaaacatc 5400 caaacaaaat ttttcataca aatcactttt gttttgaagg tatccaaaca taaatcactt 5460 tacattcaac tcacttttaa ccaaaatcaa ttttttccac cgcacaacca aacacacgc 5519 // ID HAT-7_Mad repbase; DNA; EDCOT; 5020 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-7_Mad. XX NM HAT-7_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5020 RA Kojima K.K. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1620-1620 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~87% identical to consensus. XX FH Key Location/Qualifiers FT CDS 1688..4018 FT /product="HAT-7_Mad_1p" FT /note="transposase." FT /translation="MFFFRILFQSRYEESSKHSGIGYSSTGDSPEKPEDEA FT IEIDSENEIDVEGDPENDGEESEGEDEKVSNSDSRKRSWVWDHFTTYYVTK FT KQSKINEKGEKYLAEVKLRRAKCNYCPKQSSVGDYAAEPRVNGTTSMRHHI FT ERYCKFYQGNRSKKQKVLVGDKSKGNNLVAVGFSQESVLEACVKMVVIDEM FT PFSTVDKMGFRLFCAVGIPLFKVPSRRTLVRTFLNMCDESKAYLKKTLSAH FT RICLTTDTWTSTQNTNYMVLTAHFIDHEWNMHKRIINFCVIPNHYGTTIAK FT LIESCLLEWGIDKVMTITVDNASANKVALDQLMTKMNRWENSQAILGGKYL FT HVRCIAHITNIIVSHGMKRLNNGLLAIRNCVRFVRSSPQRLELFRQAVNRV FT KLTCKATVCLDCPTRWNSTFVMLDVALKFKKAFATMAEDEASPFLAYFKEV FT EDEKDEDGVIIVCQTKGRKRVGPPTEEDWSKAEVFVKFLRVFYDVTLRVSA FT STHPTVHTGLHDVIKVETAINNLESRANMQVGLPSEQLLKAMASDMRSKYE FT KYFDSYHELNPLIVIGLVLDPRFKLRHVTQLFRKKLSDIEAQLKTEEIKNI FT LRALYDEYAPNVEGGKYMKKSESLQSQPSSTSSNVATTEDDLIDEWMHFVE FT DSDEKVVGDEVDSYLFDPLVQITKEESTKYFNILLWWKVNGNKYPILAAIA FT KDILAIQVSTVASESAFSTGGRVISDFRSSLTPKSVEALICMQNWLRGDNI FT ITLEDDAPSIDHIEFYESIESGKYII" XX SQ Sequence 5020 BP; 1398 A; 882 C; 1074 G; 1664 T; 2 other; taggggtggg cacttggaac cgaaaaccga aaccgaaaca cgaatcgaat caaaccgcac 60 caaacggttt ggttttgcgg ttttgaaacg gtttcggttt caaaaccgaa ccgcggcaca 120 caaaacggtt tggtttcggt tttgggtttt caaaaccgca ccgaaaccga aaccgcactt 180 ttttattttt atttagttca ttcaactagg ttatacttat tatacatttg gttttgcggt 240 tctgggtttg caccgagtgg gtttgcactt catgactgct tctgcgccgc ctccttgcat 300 ctccgcatct gcctttgcga cctggtcacc tgactgcctg cttgcatctg cttctgcctg 360 cctgcctgcg agcgactgct tctgcctgct gctgcgagcg acggctgctt ctgcatctgc 420 ttctgcctgc ctgcaactgc ttctgcctct gcgagtcgcg gcttgctctc atctctgcct 480 tgcctccaat cttggagtcg acacacccag aggtaaaaat ttctcatcct ctgtcttcaa 540 tttcatatat gttgttagat taattcgaat gttaggcagg tttgggtttg caaaaattac 600 taatctacat gttgaagtcg acacactcat ggggtaatta ttaatctaag cagtcttcaa 660 ttttgaaaaa ctaggtttgg gatcttagta attaattcga atgtcgttag attaattcga 720 atgttaggca gtttgtttag atgtcagact gttatactat tagtaatttt ttttcgaaag 780 ttgaatatta aggtactcca ttgattcttg attgataatt tcaaatgtgc atttcttcga 840 akgttagcat gtttgggttt gcaaagtaag taattctttc tctaccttgg ggtattgcat 900 tatcattgat gattggtctt gaagttaaga gttcacatta gtttggtttg tctgatacca 960 ggaaagcttg agtattttct gttatacgtt tgcttttgct cgacatcacc catataacat 1020 tattctatgg cttgtttttc aaatgactta ggagatttag aaggtctatt tatttgtttc 1080 atttctctca ttttgagctt cttctgtcga tgttctttgt tccagtggga gttggctgtt 1140 ttccttttct gtggattctt gttgcttccg atttgttaat ctgtgactgc gttgattcac 1200 cgtcttcact gcaccatttg ttgttttcag tttgtgaatg tcttctgacc atttgcataa 1260 ttcactgatg tcttcactgc accattcact tatttgtcaa tatttaagtt ctcttttatc 1320 atcattagta aactatgtta tcattttcag caacttcagc agtttgcatt tgctaatgag 1380 atgattgttt gttgacagtt tgactgatac ctctaggaaa tatctatgca tggaccacta 1440 ctgtaacccg ttctcaaccg atgaacttca aactatggtg cgtatcgcgt cattttgcct 1500 tcctccctat ttattcagct attacatatc caattgtatt gattcctaac atgtttactt 1560 ttctggcaac tctttcaatg ttttacaatt tctttcctgc tacattataa tagaaatgtg 1620 aagtacaaag tcgatttaaa aacctaatat ctatctattt tcttagtata aaacctaata 1680 tctatctatg ttcttctttc gtattttatt tcagtcaaga tatgaagaat ccagcaagca 1740 tagtgggatt ggttactctt ctacggggga ctcccctgag aagccggagg acgaggcaat 1800 agaaattgac tcggaaaatg aaatagacgt tgaaggtgac cctgaaaatg acggcgaaga 1860 atctgagggc gaagatgaaa aagtaagtaa ctctgattca agaaaacgta gctgggtttg 1920 ggatcatttt acaacatatt atgtgacgaa aaaacagtcg aaaatcaatg aaaaggggga 1980 gaaatatttg gccgaagtaa aacttaggag agctaaatgt aattattgcc caaaacagag 2040 cagtgtaggt gactatgcag ctgaaccaag agttaatggc accacaagca tgagacacca 2100 cattgaaaga tattgtaaat tttaccaagg gaatagaagt aaaaagcaaa aagttttggt 2160 tggggataaa agtaaaggta acaatctggt tgctgttgga ttttcacaag agagtgtgtt 2220 agaagcatgt gtcaagatgg tagtcataga tgagatgcca tttagtacag ttgataagat 2280 ggggtttcgg cttttttgtg ctgttggtat tccattgttt aaagtgcctt ctagaagaac 2340 tcttgtgaga acttttctca acatgtgtga tgaatcgaag gcttatttga agaaaacctt 2400 aagtgcccat agaatttgtc tcactaccga cacttggaca agcacacaaa acaccaatta 2460 tatggttctt actgcacatt ttattgatca tgaatggaat atgcacaaga ggatcataaa 2520 cttttgtgtt attcctaacc actatggaac cacaattgca aagttaattg aaagttgctt 2580 gttggaatgg gggatagaca aagttatgac aatcacagtg gacaatgctt ccgcaaataa 2640 agttgctttg gatcaactta tgacgaaaat gaataggtgg gaaaattcac aagctattct 2700 aggtggcaag tatttacatg tgagatgcat cgctcacata accaacataa ttgtgagtca 2760 tgggatgaag aggctaaata atggtctatt agctataaga aattgtgtga ggttcgtgag 2820 gagctctcca caaagattgg agctttttag gcaagccgtg aatagggtga aattgacgtg 2880 caaagcaacg gtttgccttg attgccctac tcggtggaat tctacatttg ttatgttgga 2940 tgtagccttg aaatttaaga aggcctttgc tacaatggcg gaggatgaag caagtccctt 3000 tttggcttac tttaaggaag ttgaagatga aaaagatgaa gatggtgtga ttattgtttg 3060 ccaaaccaag gggaggaaaa gggttggacc accaacggaa gaagattggt ccaaggcgga 3120 ggtttttgtc aagtttttac gggtgtttta tgatgtgact ttgagggtga gtgcttctac 3180 acatcccacg gttcataccg gcctccatga tgtcataaaa gtggagaccg ccatcaataa 3240 cttggaatcc cgagccaaca tgcaagtggg tttaccgtcg gagcaattat tgaaggcaat 3300 ggcatccgat atgagatcaa aatatgaaaa atattttgac tcataccatg aattgaaccc 3360 tcttattgtg attggacttg ttttagatcc gaggttcaag ttgaggcatg tcacacaact 3420 ctttagaaag aaactttccg acattgaggc acaattgaaa actgaagaaa taaaaaatat 3480 attgcgtgcc ctttatgatg aatatgctcc taatgttgaa ggtggaaaat acatgaagaa 3540 atcggaaagt ttacaatcac aaccttcttc tacctcatct aatgtggcta cgacggaaga 3600 tgatctaatt gatgaatgga tgcattttgt tgaagatagt gatgagaaag tggtgggaga 3660 tgaggtggat tcttatttgt ttgatccctt ggtacaaatt acaaaagagg agtccacaaa 3720 gtattttaac attctcctat ggtggaaggt gaatggtaac aagtatccta tcttggccgc 3780 aattgcaaaa gatattcttg caattcaagt ttcgaccgtg gcatcggaga gtgcttttag 3840 caccggtggt cgagtgattt cggattttag gagttcttta actcctaaat cggtggaggc 3900 cttgatatgc atgcaaaatt ggttgagggg tgataatatt attactttgg aggatgatgc 3960 accttcaatt gaccacattg agttctatga aagtattgaa tccggtaagt atatcatttg 4020 aagtaaaaga actttcttcg ttttcttttt tcaactaaac gtcaattata ttttttatgt 4080 tttgtattgt gtagagttgg ccaaatcgac ttcaagcatt gcctctctta ctcttgatca 4140 acaaccacaa caagctccaa agcaatctca aggttctaat tcacaagagc ctccccttac 4200 gcgtttacaa ggtgcaaggt cttcacaagc tcaaaggcct cctaaacctt caaagaataa 4260 gtgtccaaaa ggaaaaggaa aggcaaaggt ttgaaacttg aacgatgcaa agtaagttga 4320 aaaccaagac tttgttgaat tccatgaacc atttattttt ttggttgtac taatgccata 4380 aggcatttga cattgaactt tgtttgaaac tttgaagttt gaactttagt tgtattatgg 4440 caaacttaac ttttcaattg ggttgtagta aagtattgtg attgattggt gatcaagttg 4500 aattttagta gatgtgaatt atgtgatgcg tttttgtgca gttttttggt gcagttttgt 4560 gcagtttttt ggtgcagttt tggtgcagtt gtggtgtaat ttttgctgca gtttwgctgc 4620 tgttttttgt gcagttttgt gttttgctgt tttgtgcagt tttttgctgc agtttcggtg 4680 cagttttttg ctgcaggttt ggtacagttt cttggtgttg ttttgctgca ggtttggtgc 4740 agtttttggt gcaattttgg tgcatattca ttaattaata tacaaggaaa ataagaccat 4800 cttatgcata aatatgtgta tattttaaat tgtacatttt tttctcaaaa accaaaccga 4860 aaccgtttga aaccgcaccg aaccgaacca aaccgaacca aacggtttgg tttcatttcg 4920 gttttggctt caaaaccgca ccgcaccgca ccgcaaaaag tttcgatttc ggttgtggtt 4980 tcactcgaaa ccgcaccaaa ccgcaccgcg cccaccccta 5020 // ID Copia4-VV_LTR repbase; DNA; EDCOT; 184 BP. XX AC AM469526; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia4-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-184 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-184 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 742-742 (2007). XX DR Genbank; AM469526; Positions 2220 2037. XX SQ Sequence 184 BP; 61 A; 22 C; 30 G; 71 T; 0 other; tgttacagaa tcaaaatcta ccttatttat gtagttgact taccttattt atgtattgat 60 tataggcttg attataggat gtaaatatag gagacttacc ttagatagac tagcatagca 120 tgtataaata gagatgtttc tgttatgaat aaattgacag tttacatatt ctctgcagtt 180 taca 184 // ID Gypsy-19_Mad-LTR repbase; DNA; EDCOT; 233 BP. XX AC ACYM01061158; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-19_Mad-I; KW Gypsy-19_Mad-LTR; Gypsy-19_Mad_. XX NM Gypsy-19_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-233 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1423-1423 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01061158; Positions 11000 10768. XX SQ Sequence 233 BP; 52 A; 53 C; 46 G; 82 T; 0 other; tgaccattgg ctcaaggccc aggctgttag gacgacaccc aggattgcgt ttcatcctgc 60 tagctagggt ttcctttcat ctgaatataa atattatggc tgtactctgt agaggggcat 120 gatgaatgaa atgagctttc ttttccctta aatctccatt ttcttctcta actctttata 180 attcctgcac tgtttatttc aatctttgct gtcggaaccg attgggcgta cca 233 // ID Copia-30-I_VV repbase; DNA; EDCOT; 4320 BP. XX AC CU469335; XX DT 01-SEP-2008 (Rel. 13.1, Created) DT 02-JUN-2008 (Rel. 13.1, Last updated, Version 1) XX DE Copia-30_VV, LTR retrotransposon Ty1-copia like, internal portion DE from Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Cremant-B05; KW Copia-30-LTR_VV; Copia-30-I_VV; Copia-30_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4320 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL; CU469335; Positions 884209 888528. XX CC Full size = 4809 bp CC LTR = 245-244bp CC LTR are 99.2 % similar to each other. CC Direct flanking repeats = atata CC UTL size = 35 bp CC gagpol putative polyprotein size = 1346 aa. XX FH Key Location/Qualifiers FT CDS 36..4073 FT /product="Copia-30_VV_1p" FT /translation="MAEKPSTHTKMIEPSSPLYLHPFDNPGATITTCVFNG FT ENYDMGEKAVKNALRAKNKLGIIDGTVNKPKGEDGNELNAWEACNSMIISW FT MFNVIDKSLHSSVAYAQTAKDMWEDLKERYAVGNAPRVHQLRSEIVNLKQE FT GMTVAAYYAKIKGMWDELNQYIEIPECTCGAAQAIVKSREDEKAHQFLMGL FT DDTTFGTVRSSILALDPLPTLGKIYAMVTQEERHRSMARGADRAEITVFAA FT RTEKPGGQTNKSGSCTHCGKTGHDVADCFQLKGYPDWWPTRQMGRGRGRGR FT GRNSYAGRGATSGRVHYANAVAEADTQEKGQCVGHDVERSIIPGLNDDNFQ FT KLMALLRSGSSNVEKLTGKNKIVEEWILDSGASMHMTGRRDLFDWLRKWET FT ACVGLPDGTKTVANEMGYVKLSKDLCLKNVLYVPSLKCNLISISQLLKEKD FT YIVTFTDSFCVIQDRTSRNPIGVGKLKNGVYYYKPLQGEKVNAVKVEEKYE FT LWHRRLGHPSDRVLASIHSLGNNVMKGIEDYVCDSCCRGKQVRNSFQLSNK FT RAFEIFNLIHVDIWGPYRTPTTSGAHYFLTIVDDHSRGVWIYLMKEKSETK FT EILQNFCFMTKTQFDKPVKCIRSDNGLEFCSGQMMSFYKREGILRESSLVN FT TPQQNGRVERKHQHILNIARTLRFQACLPIDFWGECVLTAAYLINRTPTPI FT LDGKTPYEILFGEKPNYEHLRVFGSLCYAHKKSRSNDKFDARSRRCIFVGY FT PYGKKGWKLHDLETKEQFESRDVIFHETIFPFCQSSKGDKEQKFQNNGNIE FT SYIEDDDVIVKKTCERESEKNIEREKGEENMETGEDQSQGEMLGRGHRQHK FT EPRHLQDYICYSARSLSTLCSKASSIQKVPSGKPYPIANYVTYTKFSVGHR FT AFLAAINIEKEPRTYKEAVTDNRWREAMAKEIEALETNQTWKVVDLPPEKK FT AIGCKWIYKIKYNADGSIERYKARLVAQGFTQIEGIDYQETFSPVAKMTSV FT RCFLAVVVAKRWELHQMDVNNAFLHGNLEEEVYMKLPEGFKATGKNKVCKL FT QKSLYGLKQASRQWFAKLTTALKEYGFQQSLADYSLFTYRRGNIVMNLLVY FT VDDLILAGNDNKVCEAFKNFLDRKFGIKNLGQLKYILGIEVAKGKDGLFLS FT QRKYALNIIKECGLLGARPVEFPMEENHKLALANGRLLNDPGMYKRLVGRL FT IYLTVTRPDLTYAVHVLSQFMQSPREEHLDAAYRVVRYLKKGPGQGIVLKA FT DNDLQLYCYSDSDWASCPLTRRSISGCCVKLGTSPISWRCKKQGTISRSSA FT EAEYRSMAMAASELTWLKSLLASLGVLHDKPMKL" XX SQ Sequence 4320 BP; 1528 A; 697 C; 1021 G; 1074 T; 0 other; tggtatcaga gccagatacc tgaagaaaat atatcatggc agaaaaacct tcgactcaca 60 caaagatgat agaaccatct tcacctcttt acctacatcc atttgataat ccaggggcaa 120 ccatcacgac atgtgtgttc aatggtgaaa attatgatat gggggagaag gctgttaaaa 180 atgcattgag agcgaaaaac aagcttggga tcattgatgg gacagtaaac aaaccaaaag 240 gagaagatgg aaacgaattg aatgcatggg aagcatgtaa ctcgatgatt atatcatgga 300 tgtttaatgt gatcgacaag agtttacatt caagtgtagc ctatgcgcag actgcaaaag 360 acatgtggga ggatctcaaa gaaagatatg ctgttggaaa tgctccgagg gttcatcaac 420 tcagaagtga aatcgtgaac ttgaaacaag aaggaatgac agttgctgca tattatgcca 480 aaataaaagg catgtgggat gaattaaatc aatacattga gatacctgag tgcacttgtg 540 gagcagctca agcaatagta aaaagcagag aagatgagaa ggcacatcag tttctcatgg 600 gtctagatga cactacattc gggactgtga gatcgtctat cttagccctt gatcccttac 660 ctactttggg aaaaatatat gcaatggtta cacaagaaga acgccatcgt agcatggcca 720 gaggagctga tcgtgctgaa ataacagttt ttgcagcgag gacagagaaa cctgggggac 780 aaacaaataa aagtgggagc tgtacacatt gcggaaagac gggacatgat gttgcagatt 840 gctttcaact aaaaggatat cccgactggt ggccaacacg ccagatggga cgaggaaggg 900 gacgtggacg tggccgcaac agttatgctg gaagaggagc aacttcagga cgcgttcatt 960 atgcaaatgc agttgctgaa gcagatacgc aagaaaaagg acagtgcgtt ggacatgatg 1020 tggaacgtag tataatccca ggactgaatg atgacaactt ccaaaaactc atggctctac 1080 tcagaagtgg aagcagtaat gtagaaaaac tgaccggtaa gaataaaatt gtggaagaat 1140 ggatattgga tagtggtgca tccatgcata tgacaggaag gagagatttg ttcgattggc 1200 tacgtaaatg ggagacagca tgcgtgggac tacctgatgg aacaaaaaca gtagcaaatg 1260 aaatgggata tgtgaagctc tctaaagatt tatgcttaaa aaatgtttta tatgtccctt 1320 ccttgaaatg caatttaatc tctataagcc aattattaaa agaaaaagat tatatagtca 1380 catttactga ttcgttttgt gtgatacagg accgcacttc gaggaatccg attggagtgg 1440 gtaagctaaa gaatggagtg tactactaca agccattaca aggagagaag gtgaacgcag 1500 tgaaagtaga agaaaagtac gaattgtggc acaggaggtt agggcatcct tcagatcgtg 1560 ttttagcttc cattcatagt ttaggaaata atgtgatgaa gggaattgag gactatgttt 1620 gtgattcatg ttgtcgtgga aaacaagtac gaaattcttt tcagttgagt aataaaagag 1680 catttgaaat ttttaatctc atacatgtag acatatgggg tccatatcga actcccacta 1740 cttcaggggc acattatttt cttaccattg tagatgatca tagtagaggg gtgtggatat 1800 atctcatgaa agaaaagagc gaaaccaaag aaattttaca aaatttttgt tttatgacca 1860 aaacacaatt tgataaaccg gttaaatgca tcagaagtga taatggatta gaattttgct 1920 caggacaaat gatgagtttc tataagagag aaggaatatt aagggagagc agcctagtaa 1980 acaccccaca acaaaatggg agagtggaga gaaaacacca acacatatta aatattgcta 2040 ggacattgag atttcaagct tgtctaccaa tagatttttg gggagaatgt gttttaacag 2100 cagcatactt gataaatcga acacccacac ctattttaga tggaaagacg ccttatgaaa 2160 tattatttgg cgagaaaccg aattatgagc acctgagagt ctttggtagt ttgtgttatg 2220 cccataaaaa gtcacgtagt aatgataaat ttgatgctag aagccggcga tgcatatttg 2280 taggttatcc ctatggaaag aaaggatgga aacttcacga tctagaaacc aaagaacaat 2340 ttgagagtag ggatgtaata tttcatgaaa caatttttcc tttttgtcaa agcagcaagg 2400 gagataagga acaaaaattc cagaacaatg ggaacataga atcttacatt gaagatgatg 2460 atgtcatagt aaagaaaaca tgtgaaagag agagtgagaa aaatattgaa agggagaaag 2520 gggaagaaaa tatggagaca ggagaggatc aaagccaggg ggagatgctt ggtaggggac 2580 atagacaaca caaagaaccg agacatctcc aagattatat atgttattcg gctagaagct 2640 taagtacact ttgttccaag gcaagctcaa tccaaaaggt accctcaggt aagccttatc 2700 ctattgcgaa ttatgtgact tatacaaaat tttctgttgg ccatcgagct tttcttgcag 2760 caataaatat tgaaaaggaa ccaagaactt acaaagaagc ggttacagac aacagatgga 2820 gagaagccat ggcaaaggaa attgaagcat tagagactaa tcagacgtgg aaagtagttg 2880 acctaccgcc agaaaagaaa gcaataggat gcaagtggat atacaaaata aaatacaacg 2940 cggatggatc aatcgagcgg tacaaagcga ggttagtggc gcagggattt acacagattg 3000 aaggaataga ctatcaagag acgttttctc cagtggcaaa aatgacaagt gtaaggtgct 3060 ttctagctgt agtagtggca aaaagatggg aattacacca aatggacgta aacaacgcat 3120 ttctacacgg aaaccttgaa gaagaagtat atatgaagct gccagaaggg ttcaaggcca 3180 ctggaaagaa caaagtttgc aagttacaaa aatcgttgta tggattgaaa caggcatcga 3240 gacaatggtt tgcgaaactc acgacagctt tgaaagaata tggttttcaa caatcattgg 3300 ctgattattc actctttact tatcgacgtg gaaacatagt gatgaaccta ttggtatatg 3360 tggatgattt aatattggct gggaatgaca acaaagtatg cgaagctttc aaaaactttc 3420 ttgatagaaa atttggaatc aagaatctgg gacaattgaa atacattctt ggaatcgagg 3480 tggcaaaagg taaggatgga ttatttttat cacaacgaaa atatgcttta aacattataa 3540 aggaatgtgg gctgttagga gcgagaccag tggaatttcc aatggaagaa aaccacaaac 3600 tagcacttgc taatgggaga ttgctaaatg acccaggaat gtacaagcga ctcgtgggac 3660 gattgatata cttgactgta acaaggccag acttgacgta tgctgttcat gttttgtcac 3720 aattcatgca aagcccacgg gaagaacacc tagatgcagc ttatagagtt gttcgatatc 3780 tgaagaaagg accaggtcaa ggaatagttt tgaaagcaga taatgatctt cagctttatt 3840 gttattcaga ttcagactgg gcaagttgtc cgttaacaag acgatcaatt agcggatgtt 3900 gcgttaaact tgggacatca ccaatttcgt ggaggtgcaa aaagcaagga actatatcaa 3960 gatcttcagc agaagcagag taccgttcca tggcaatggc agcaagcgag ttaacatggc 4020 taaaatcact tcttgcatca ttgggagtgc ttcatgataa gccaatgaaa ttataatgtg 4080 ataataaggc tgctttacac attgcagcaa atcccgtatt ccatgagagg accaaacaca 4140 tcgaaataga ttgtcatttt gttcgagaga aagtgcaatc cggtgagata gtgacaacat 4200 atcttccttc aaagctgcaa atagcagaca tgttcaccaa agcccttgga agacaacaat 4260 tccttttctt atcaagcaag ttgggcattc gagatcttca tgcaccaact tgagggggag 4320 // ID DNA3-4_Mad repbase; DNA; EDCOT; 442 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE non-autonomous Harbinger family DNA transposon from apple. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW DNA3-4_Mad. XX NM DNA3-4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-442 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1468-1468 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >98% identical to consensus. 3-bp TSDs are TWA. XX SQ Sequence 442 BP; 120 A; 83 C; 114 G; 125 T; 0 other; gggggcgttt gttgcgccgg actatctcgg actggactag cttcaaggac taagctggac 60 tggcttagac tagactaagc tggactaact tagtgaagcg tttggtgcag tgttggacta 120 agaagctgga taataacaaa ttctaatatt atattattta atatataaat tattaatatt 180 ttattatgat ctaggtgacc ggagatgacg aggagtctat cgggagtggt tgttgagcat 240 gacgaggacg agagaggata gtcttagcta gtcccatggt tattgggggg tctcgctaag 300 acctcttagt gaagggtttt gtccatgcta gtccccttta gtctcattaa tgttagtccc 360 agcatggaac aaacacagta ttggactaac agctagtcca gtccagtcca gtcccactta 420 gtgagggcaa acaaacgccc cc 442 // ID hAT-4_PTr repbase; DNA; EDCOT; 3687 BP. XX AC . XX DT 18-DEC-2009 (Rel. 15.02, Created) DT 18-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE hAT-type DNA transposon - consensus. XX KW hAT; DNA transposon; Transposable Element; hAT-4_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-3687 RA Kojima K. and Jurka J.; RT "DNA transposons from black cottonwood."; RL Repbase Reports 10(2), 114-114 (2010). XX DR [1] (Consensus) XX CC >94% identity to consensus. 8-bp TSDs. XX FH Key Location/Qualifiers FT CDS 1625..3316 FT /product="hAT-4_PTr_1p" FT /translation="MMELLASYNEQVGALVLGNAPQNAKYTSHQIQKEILH FT VFARNVQSSIRHEIGDARFCLIVDEARDESRREQMALVIRFVDRSGFIRER FT FLDIVHVKDTTASTLKEEISFVLSHHNLDVQNIRGQGYDGASNMRGEWNGL FT QALFINDCPYAYYVHCLAHQLQLALIAAAREISDVHTFFQNLIFIINIVSA FT SCKRNDELRAFQAATIEHLVDIGEIETGKGVNQVGGLQRPGDSRWSSHFKS FT ICSLIKMYGATCLVLENIALDGSTYSQRGDAAFSFKLLMSFDFAFILHIMK FT NVMGITDVLCQALQQKSQDILNAMHLVTTTKTLIQKLRDDGWETLLEEVTS FT FCKHQDIEVPDMDACFSSVGRSRRKKKSVTVEHHYRVDIFTAIIDQQLQEL FT NNRFNEQAIELLKLSTTLDPRNSYKLFNVEDICLLVDKFYPEDFSDQEKIH FT LRLQLQHYELDVPNHPKLKNMSSIADLCQGLVETEKSTIYPLVDRLIRLIL FT TLPVSTATTERAFSAMKIVKTRLRNRMEDDFLANYLIVYIEKEIAERFTID FT MIIDDFYSMKERRAQLK" XX SQ Sequence 3687 BP; 1166 A; 566 C; 632 G; 1323 T; 0 other; cagcggcgga accaagggga ggccccaaat ttttttttta aaatataata aataataggc 60 tttttaatac taaattatta ttttattagt tatgtttgac tttaaagcca tatctccgta 120 tctctatgta aaaggacaaa taagcttttc aatttattcc cttcctttac tgcctctctc 180 tctttcttct ctgaacccta accgaaaaaa ttaataatac aaagcataaa ggttaaagca 240 aagctgctgc caattaattc ttcatcaaac aaggtaatta gtaaattttt tttttgtttg 300 ttaagaaatt taatatatat atatatatat atatatatat atatatataa ttctgctttt 360 ttttttcaga tctactagtt ttaccatttt ttatttcttg ttatagtgaa tgttgttttt 420 tctaattaat tggatatatt ttatgggttt gtttgtttcg attatgcttg gattttttta 480 tgttttgttt ttagcagagc caccaaaatt atcaattttt tctcacgtgt accttactat 540 caccaggtcc aatatacaat tagacacgat ctttctagcc aaattgagtt ctttgaagag 600 cgtataccca actttgattc agtgtaagtt ttctttttta ggaaccagta atcctatttt 660 ttatgttaga ttgcttttat atatcaattt ctttttttaa tatgttaatt ttgctttcat 720 atgtcagtgt tgtttacatg taaaaattta tttttggttt tgattattgc ttcaacacat 780 ttttttttat gttttgtttt tagcagagcc accaaaatta tcaatttttt ctcacatata 840 tgttttgatt ttaggttgaa ccatgaacaa aataagaaga attgattcct tttttgagaa 900 aaagaggaaa aatattgata actcacagcc tagtgaacca actccaatgt gtaatgttga 960 agttatggtt gagcaacccc aatgtgcttc agtttacgaa gaacctgcat tgattagtga 1020 gcagcctcct actagaatcg acattgctca tttaattaga gatccaagca atcgtcctca 1080 aatttgggaa tacccggtta atcaacaaga tgaaattcga agggcataca ttaatttggg 1140 gccatatcaa cctttgatgt ctgaatatcc gctgactggt aaaaaacatc ctcgtcgatt 1200 tcagtctcat tggttcaaaa gttatccatg gcttgaatat tcagagaaaa atactgcatt 1260 ttgtttccct tgctatctat ttccaagtaa gccatctgga aagccaggat cagacacatt 1320 tactgttaaa ggattcaatt gttggaagaa agttaatgat ggggaacgat gtgctttttt 1380 gactcatatg ggaaaaggtc caaattcagc tcatagattt gctaccaggt gcttggaaaa 1440 tttgaaaaat cagtcatgtc atattgagaa ggtagttaag aggcaaacta ctcaagaaat 1500 tctaaataat cgattgcgta ttaaagcttc aatagatatt gttcgttggc tcacatttca 1560 agcatgtgct tttagagggc atgatgaacg tccagaataa aaaaaccgag gtaattttct 1620 tgaaatgatg gaacttttag catcatacaa tgaacaagta ggtgctcttg ttttgggtaa 1680 tgctccacaa aatgctaaat acacctcaca tcaaattcaa aaagaaattt tgcatgtctt 1740 tgctagaaat gttcagtctt caattcgtca tgagattggt gatgcaagat tttgtttaat 1800 tgttgatgaa gctcgagatg aatccagaag agagcaaatg gcccttgtta ttaggtttgt 1860 tgatagaagt ggatttatac gagaacgatt tttggatata gttcatgtca aagatacaac 1920 tgcttcaact cttaaggaag agatttcctt tgttttatct catcacaatc ttgatgttca 1980 aaatattagg ggccaagggt atgatggtgc tagtaatatg cgtggagagt ggaatggttt 2040 gcaagcttta ttcattaatg attgccctta tgcatattat gtacattgct tagctcatca 2100 attacaattg gctcttattg ctgcagctag agaaatatct gatgttcaca ctttctttca 2160 gaatttgatt tttattatta acattgttag tgcttcttgc aagcgtaatg atgaattacg 2220 ggcttttcaa gcagctacaa ttgaacattt agttgatatt ggtgagattg aaacgggtaa 2280 aggagttaat caagtaggtg gtttgcaacg acctggagat agcagatgga gttcgcactt 2340 caaatcaatt tgcagtttga taaaaatgta tggggcaact tgcttggttc ttgaaaacat 2400 tgctttagat ggatctactt attctcaacg tggtgatgcg gctttttcat ttaagttgct 2460 aatgtcattt gattttgcat tcatcttaca tataatgaag aatgttatgg gaattactga 2520 tgtgctttgc caagccctgc aacaaaaatc tcaagacatt ttaaatgcta tgcatttggt 2580 gactaccaca aagactttaa ttcagaagtt aagagatgat ggttgggaaa ctcttttaga 2640 agaagtgaca tcattttgta agcatcaaga cattgaagtt cctgatatgg atgcttgttt 2700 ttctagtgtg ggacgatctc gccgtaaaaa aaaatcagta acagttgagc atcactaccg 2760 agttgatata tttacagcta tcattgatca acaattgcaa gagctaaata atagattcaa 2820 tgagcaggcg atcgagcttc ttaagttgag cacaacttta gatcctagaa atagctataa 2880 attattcaat gttgaagata tatgcttact tgttgacaag ttctatcctg aagatttttc 2940 tgaccaagaa aaaattcatt tgagacttca gttgcagcat tatgagcttg atgtacccaa 3000 tcatccaaag ttaaagaata tgtcatcgat tgctgattta tgtcaaggat tggttgaaac 3060 agaaaaatca acaatttatc cactcgttga caggttgatt cggcttattt tgactcttcc 3120 tgtttcgaca gcaactactg aacgagcttt ttcagcgatg aagattgtta aaacaagact 3180 tcgcaatcgg atggaggatg attttcttgc aaattatttg attgtctata tagaaaaaga 3240 aattgctgaa agattcacaa ttgatatgat aatcgatgat ttctattcta tgaaagaacg 3300 acgagcacaa ttaaaataaa tatgtaagaa tcattcttta ttatttttta ctttatttca 3360 aagtttatca aacataaata atgcttcgct ttagctaatg tttcttatat actttgtatg 3420 tttatatttg ataggtacaa agaccaacaa aattaaagtg atggatacat tatgaagatg 3480 aaattaactt catagctttg actcaatttg gtattgctct aaacctctta ccttatacaa 3540 agatcatcat atgtttgtag taagttcttt gaataaaact aaatcatgca gttttttttt 3600 acaactcatg tacaataaat taaaaaaaat tatatcttgt tatattattt tggccccccc 3660 taacaaataa tcctagctcc gcccctg 3687 // ID LTR-4_Mad repbase; DNA; EDCOT; 1905 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; LTR-4_Mad. XX NM LTR-4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1905 RA Kojima K.K. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1787-1787 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >95% identical to consensus. 5-bp TSDs. XX SQ Sequence 1905 BP; 612 A; 326 C; 402 G; 560 T; 5 other; tgttggagat atgccctgaa agtcaatctt tggaagaaac ctttcaggac aatgtctata 60 tgtatggaaa actctaatac atcaaaaggc aaagtcactc attaggacta tctcaataaa 120 cgatatacgt cctaaanggt gaatccatgg acaatggatc gatggaagaa gtaatctaat 180 gatgttagac tgcagagacc ttcttcacat aaccatgatg tccaaaaagg ttcctggtca 240 taggattgtc ggagggacac tgacaataca tagaccagta catactatgt ccccttccaa 300 tgggaaggat ggaaagtctc atgccattcg tgtagtgaca ctaagacaag tatgtaggtg 360 ctcattatgg gaatgagttc actgaacaca atcaaacgag agtacttgca tggaggtcta 420 ctcacatgtc aagcaagtaa ctctactggt tggaataatg taagtaatcc tttgacctga 480 gacatcatag ttgtcttggg gatacgttgc tgatcatttg ataatgagac gtgaccacat 540 ctcatcttgg atgtgttcta tgcattgttg gggtcagtga tttattctca gaggcatgtg 600 aatgatcaac aagggatctc taatcctcgt tatgagagga tgaatactct aagatatgat 660 tcaggaatct tcggccgaag tatcgagcgt aatgatggaa agcgttccta tacgactcaa 720 tagaatcata taacttgata taatcacatt aggggtttga cattaaatat ccatacccta 780 gtaatgtgat tgtgagtatt gtattagaga aggatcgaat tacattgtaa ttccaactga 840 ataggttctc cgaacaaatt ctacattagc ttgggtagcc atgatatatg gttagatgtc 900 actcatggct tgtgggttct tctagatgat taaataagta gtcatcaaag aagaaggaga 960 attgaaagta agttttaatt cactaagtga ttggattaat acnaatcaat tggattggtg 1020 ccaatcacct cactgccttg ctaattagaa cctaaaacga ttgtacaccg aaacactctt 1080 gtggtgagac aactaaagga tgatggaatn aattaattgg attaattaag tgttatgatt 1140 aattagaaag tctaaagaaa tcatagaagc gatgaaagat cgttttggac ttaaagaaaa 1200 gttcgggttc attcgggccc attaggccca aacccattgg gcttttattc aagcatagga 1260 tgacttgaaa tgataaaagc ccaaagccca aacaacacaa aggggccggc caatacaagt 1320 gaaaggagag agagagagtc aagttgttga ctcacttctt tgacatttat aaaggaagtt 1380 tagtgaaaaa gtttcattag ggtttttgtg tgttcttttt cacaaaagag aaaaacaagt 1440 ctctctctct cnacacactt atagccggcc accaagagga gggaatagct aatcatctct 1500 tctccttttg gttattccat tatccatctc actacactag tgggtgtgga tctttagagg 1560 tcttctactt tggagactaa aggagaaagg agctctaaat ctttcaaggt ggaggaagct 1620 aggagggagg ctagactcaa ggagttccaa gaacaaagag cttggaggtg gtccatcctt 1680 ggtctcaagt ctagatcaag aggtataaaa ctataccttc actttgttct tcaatatttt 1740 cttagatgca tcatatatga acctatgctt cttgaagggg atttgcatga ctatagcttt 1800 gatattatgt gataacatgc ttccgttgcn aatgtatata aattttgaat tgtatatgca 1860 tgctagtcac tagaaatccc acataaatct cattatttcc cttca 1905 // ID Copia-72_Mad-I repbase; DNA; EDCOT; 4527 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-72_Mad_; KW Copia-72_Mad-LTR; Copia-72_Mad-I. XX NM Copia-72_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4527 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1682-1682 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1758-2258] - Integrase core CC LTRs are 90% similar to each other. XX FH Key Location/Qualifiers FT CDS 141..4517 FT /product="Copia-72_Mad-I_1p" FT /translation="MASDDEVSDPPIQSFTPGESNSTTQVVTIQNDNSNFS FT AGIKLDENNYSLWHQVIEMKIAGREKHGHLSGDTEQPAITDPPYNKWRAEN FT CQVKSWLFDAMTPNQMKRFIRYDTAMQVWDAIKKTYSDGSDEAKIYDLHKR FT SFTMKQNGAPIANYYSDLTEIFQELDQLSPTNMKDPDDILSRQQEIERLRV FT YIFLAGLDNKFDQIRGEILRMEPKPGLEGAYSHVKRESNRQGTMSESAAMP FT EATVLFTANSRSPQGPRLQNINSSTADRFRNRPPMQCTKCGLKNHTIQGCY FT EIIGYPEGWVHKGRKKESSRASFATSESSQDVSSSDHVPKALNTSGISNST FT SANTCNRSWIIDTGATDHMTSDANILHSLKTANQTFITSANGSISPVTGEG FT SLSLTSSLNLDHVLVVPSLDYDLLSVSQIIDSLNCSVSFLPLYCLFQDLLT FT RAVIGCGTRRGKLYYLDLTEECSNRLSQVHHVSRDESTRMKKIWLWHRRLG FT HPSFGYLKLLFPELFPQFKESDFHCEICILAKSHRVSYPLRLNKSSVPFMV FT VHSDVWGPARILTTSGFRWFVTFIDDCTRMTWVFPMKHKSEVPTKFNIFHQ FT YVATQFDKKIQTLRSDNGGEYVNHALHNYLQEHGIVHQTTCAYTPQQNGVA FT ERKNRHLLEVVRASLYGANMHHKFWGEALCSATYLINRTPSSTLQYQTPFQ FT TLNHLLTIPSIPNLEPRVFGCVAYVQVYPHQRGKFDPCALRCVFLGYSDTK FT KGYKCFHPPTQTLYITADVQFQEGETYFSKGDIEYPLQEENSMFEEDTQDI FT SNIKIVAEISETEINVDKSADDCNQTIHAETESSTPTSDTEVHPATLSPDG FT LGLPSSTVPHDQSAPEHNQQVTDQSNSIEIVPESSQIESTNYQLPPRKSRG FT IPKQLYDPDPRAKVKYPIANHVSLHRLSTSCEAFVNQLSTVSIPCSVEDAM FT KDPRWTRAMNEEMEALQKNSTWELTNLPKGKKSVGCRWIYTVKFNADGTIE FT RYKARLVAKGYTQTYGIDYGETFAPVAKISTIRVLLSLAANLDWPLQQFDV FT KNAFLHGDLEEEVYMELPPGCKLDPNQTNNVCKLKKSLYGLKQSPRAWFGR FT FTKSMKFFGYKQSNSDHTLFLKHKKGKITALIVYVDDMVVTGNDPEEKAAL FT QKYLASEFEMKDLGALKYFLGIEVARSQQGIFLSQRKYVLDILTETGMLAC FT KPADTPIELNHKLGEYPDQIPTNKERYQRIVGKLIYLAHTRPDIAYAVSMV FT SQFMHAPSETHMDAVNRILRYLKSAPGKGLMFSKHDHLDVKGYTDADWAGD FT VTNRRSTSGYFVIVGGNLVSWRSKKQKVVARSSAEAEYRSMAHGVCELLWV FT KNLLRDLGFRPKHAMRLHCDNKAAIDIAHNPVQHDRTKHVEVDRHFIKEKI FT EARLIEVPFVKSEDQLADMLTKAVTSSVFHNSLSKLGIHDIYAPT" XX SQ Sequence 4527 BP; 1435 A; 942 C; 900 G; 1250 T; 0 other; atttctgaga tggtatcaga gcagtcgatc atgactgact cttgaacctc aaaaacagaa 60 aaaagcttcc gccatatcat atctcaatca tcatatcagt tttattttta tttcaacttc 120 attgatctta agcctataca atggctagcg atgatgaagt atcagaccca ccaattcagt 180 ccttcacgcc aggtgaatca aactccacca cacaagtggt caccattcaa aatgataatt 240 ccaatttctc tgcaggaatt aaacttgatg agaacaacta ttctctatgg catcaagtca 300 tagagatgaa aattgctggt cgagaaaaac atgggcatct ttccggtgat accgagcagc 360 ctgcaatcac agacccaccg tataacaagt ggcgagctga aaattgccaa gtcaaaagtt 420 ggttatttga tgctatgaca cccaatcaga tgaagcggtt catccgttac gacacagcca 480 tgcaggtatg ggatgccata aaaaagactt actcagatgg ctctgatgaa gccaaaattt 540 atgatcttca taaaaggtca tttaccatga agcaaaatgg agctcctatt gctaactatt 600 acagcgatct caccgagatt tttcaagaac ttgatcaact tagtcctact aacatgaagg 660 acccagatga tatcttatca aggcagcaag aaattgagcg acttcgagtc tatatttttc 720 ttgcaggatt agacaacaag tttgatcaaa ttcgtggtga gattttgagg atggagccca 780 aacctggtct tgaaggagca tactctcatg tcaaacgtga aagcaatcga caaggaacca 840 tgtcagaaag tgccgccatg cctgaagcta ctgtgctctt taccgcaaat tctcgatctc 900 cacaaggacc tcgacttcaa aacataaact cctcaacagc tgatcgattt cgtaatcgac 960 cacctatgca gtgcaccaaa tgcggattga aaaatcatac tattcaaggc tgttatgaga 1020 ttattggcta tccagaagga tgggttcaca aaggacgaaa gaaggaatcc agcagagcat 1080 cattcgccac ctctgagtct tctcaagatg ttagctcatc tgaccatgtc ccaaaagcct 1140 tgaacacctc aggtatatct aattctacat ccgctaatac ttgtaataga tcgtggatta 1200 ttgatacagg tgccacagat cacatgacat ctgatgctaa cattcttcac tcactaaaaa 1260 cagccaacca gacattcatt accagtgcca atggttcaat ctctccggtt actggagaag 1320 gctctctttc actaacttcc tcactcaatc ttgatcatgt cctagttgta ccatccctag 1380 attacgatct tttatctgtt tctcaaatta ttgactccct taattgttct gtttcttttt 1440 tgccactata ttgtcttttc caggatctgc tcaccagggc cgtgattggt tgtggtacta 1500 gaaggggcaa actatattat ttggacttaa cggaagaatg cagcaataga ttgagtcaag 1560 tgcatcatgt aagcagagac gaatcaaccc gaatgaagaa gatttggtta tggcacaggc 1620 gattaggaca tccctcattt ggttatctta aacttttatt ccctgaactt tttccccaat 1680 tcaaagaatc cgatttccat tgtgaaattt gtattttggc caaaagtcat cgtgtttcct 1740 atccattaag attaaataaa agttctgtgc cattcatggt cgttcattct gacgtttggg 1800 gtcctgccag aattcttacc acttctggat ttagatggtt tgtgacattt atagatgact 1860 gtactagaat gacctgggtg tttccaatga agcacaagag tgaagttcct accaagttca 1920 atatttttca tcaatatgtt gcaactcagt ttgacaagaa aattcagaca ctcaggtctg 1980 ataatggagg agaatatgtc aatcatgctc tgcataacta tttgcaagag catggtattg 2040 ttcatcaaac cacatgtgcc tatacacctc aacaaaacgg tgtagcagag aggaagaatc 2100 gacatctctt agaagtggtt cgtgcatctt tatatggtgc caacatgcat cataagtttt 2160 ggggggaggc actgtgttct gcaacatatc tcataaatcg aacaccatcc agtactctcc 2220 aatatcaaac accattccaa acacttaacc accttctcac cattccatct atcccaaact 2280 tagaaccacg tgtctttggg tgtgtggctt atgtacaggt ttatccacat caacggggga 2340 agtttgatcc atgtgccctc cggtgtgtat tcttgggtta ttctgataca aaaaagggat 2400 acaaatgttt tcatcctcct acccaaactc tatacatcac tgcagatgtc cagtttcaag 2460 aaggagaaac atatttttca aagggagaca ttgagtatcc ccttcaggag gagaatagta 2520 tgtttgaaga ggatacccaa gacattagca acattaaaat tgttgcagaa atttcggaaa 2580 ctgagataaa tgttgataag tcggcagacg actgtaatca aacaatacat gcagaaacag 2640 aatcatcgac tccaacatca gacacagaag tacatccagc aacgttaagt ccagatggct 2700 tgggattgcc ttcttcgaca gtaccacatg atcaatcagc ccctgaacac aatcaacagg 2760 taactgatca atctaattct attgagatcg tacctgagtc aagtcaaatt gagtccacta 2820 attatcaact tccccctcga aaatctcgag ggattcctaa acagttatat gatcctgatc 2880 ctagagccaa ggttaaatac ccaattgcta accatgtgtc cctccatagg ctatctacat 2940 catgtgaggc atttgtaaat caattatcca ctgtatctat tccttgtagt gtagaggatg 3000 ctatgaaaga tcctaggtgg actcgtgcaa tgaatgaaga aatggaggca ctccagaaaa 3060 attccacttg ggagttaact aacctaccca aggggaagaa atcagttggt tgcaggtgga 3120 tatacacagt aaaattcaat gcagatggca ctattgagcg atacaaagca agattagtgg 3180 caaaaggcta cacgcagaca tatggcattg actacggaga gacttttgcc cctgtagcta 3240 agataagcac tattcgtgta ctcttatccc tagcagcaaa ccttgactgg cctttgcaac 3300 aattcgatgt caaaaatgct ttcctgcatg gagatttaga agaagaagtt tatatggagc 3360 ttcccccagg atgcaagctg gatcccaatc agaccaacaa cgtttgtaaa ctaaaaaagt 3420 cgttgtatgg tttaaagcaa tcaccgagag cttggtttgg gagatttacc aaatcgatga 3480 aatttttcgg atacaagcaa agcaactcgg atcatactct tttcttaaag cataagaaag 3540 gtaaaatcac tgctcttatt gtatatgtgg atgacatggt ggttacagga aatgatccag 3600 aagagaaggc agcactgcaa aagtatctag caagtgaatt tgagatgaaa gatctcggtg 3660 ctttaaagta tttcttgggc attgaggtgg cccgctcaca acaaggaata tttctatcac 3720 aacggaaata tgttcttgat attttgacgg aaactgggat gctagcatgc aaaccagcag 3780 ataccccaat tgagctgaat cacaaacttg gtgaatatcc tgatcagata cctaccaaca 3840 aagagagata tcaacgaatt gttggtaagc taatatatct tgcacatact agaccagata 3900 tagcatatgc agtcagcatg gtaagccagt ttatgcatgc accaagtgaa acacacatgg 3960 atgctgtaaa ccgtatcttg aggtatttaa agtcagctcc tgggaaagga ttaatgtttt 4020 caaaacatga tcatctagac gttaaaggct acactgatgc tgattgggct ggtgatgtaa 4080 ctaacagacg atcaacatca ggatactttg ttattgttgg aggaaatcta gtctcttggc 4140 gtagtaagaa acaaaaggtt gttgctagat caagtgctga agcagaatat cggagcatgg 4200 cacatggagt atgtgaactg ctttgggtga agaatttact gagagatttg ggatttaggc 4260 ccaagcatgc tatgcgtcta cattgtgaca acaaggctgc aattgacatt gctcacaatc 4320 cggttcaaca tgatcgaacc aaacatgtgg aggtggatag acattttatt aaagaaaaaa 4380 ttgaggcaag acttattgaa gttccattcg ttaaatctga agatcaatta gcagacatgc 4440 tcaccaaagc agtcacaagt tcagtatttc acaactcact aagcaagttg ggcattcatg 4500 acatctatgc accaacttga gggggag 4527 // ID Copia-54_PTr-I repbase; DNA; EDCOT; 4493 BP. XX AC . XX DT 08-DEC-2009 (Rel. 15.02, Created) DT 08-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Copia-type LTR retrotransposon: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; internal portion; Copia-54_PTr-I; KW Copia-54_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4493 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 161-161 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 323..4477 FT /product="Copia-54_PTr-I_1p" FT /translation="MATERDDSLQSVSVRLDGKNYSYWSYVMRNFLKGKKM FT WGYVSGTYVIPKNTEEGDAVLIDTWEANNAKIITWINNSVEHSIGTQLAKY FT ETAKEVWDHLQRLFTQSNFAKQYQLENDIRALHQKNMSIQEFYSAMTDLWD FT QLALTESAELKACGAYIERREQQRLVQFLTALRSDFEGLRGSILHRSPLPS FT VDSVVSELLAEEIRLQSYSEKGILSASNPSVLAVPSKPFSNHQNKPYTRVG FT FDECSFCKQKGHWKAQCPKLRQQNQAWKSGSQSQSNAHRPPQGYKPPHHNT FT AAVASPGSITDPNTLAEQFQKFLSLQPQAMSASSIGQLPHSSSGMSHSEWV FT LDSGASHHMSPDSSSFTSVSPSSSIPVMTADGTPMPLAGVGSVVTPHLSLP FT NVYLIPKLKLNLASVGQICDSGDYLVMFSGSFCCVQDLQSQKLIGTGRREN FT GLYILDELKVPVAAAAAATTTVDLSSFRLSLSSSSFYLWHSRLGHVSSSRL FT RFLASTGALGNLKTCDISDCSGCKLAKFSALPFNRSISVSSSPFDLIHSDV FT WGPSPVATKGGSRYYVSFIDDHTRYCWVYLMKHRSEFFEIYAAFRALIKTQ FT HSAVIKCFRCDLGGEYTSNKFCQLLALDGTIHQTSCTDTPEQNGVAERKHR FT HIVETARSLLLSAFVPSEFWGEAVLTAVSLINTIPSSHSSGLSPFEKLYGY FT VPDYSSFRVFGCTCFVLRPHVERSKLSSRSAICVFLGYGEGKKGYRCFDPI FT TQKLYVSRHVVFLEHIPFFSIPSTTHSLTKSDLIHIDPFSEDSGNDTSPHV FT RSICTHNSAGTGTLLSGTPEAPFSSTAPQASSEIVDPPPRQSIRIRKSTKL FT PDFAYSCYSSSFTSFLASIHCLFEPSSYKEAILDPLWQQAMDEELSALHKT FT DTWDLVPLPPGKSVVGCRWVYKIKTNSDGSIERYKARLVAKGYSQQYGMDY FT EETFAPVAKMTTIRTLIAVASIRQWHISQLDVKNAFLNGDLQEEVYMAPPP FT GISHDSGYVCKLKKALYGLKQAPRAWFEKFSIVISSLGFVSSSHDSALFIK FT CTDAGRIILSLYVDDMIITGDDIDGISVLKTELARRFEMKDLGYLRYFLGI FT EVAYSPRGYLLSQSKYVADILERARLTDNKTVDTPIEVNARYSSSDGLPLI FT DPTLYRTIVGSLVYLTITRPDIAYVVHVVSQFVASPTTVHWAAVLRILRYL FT RGTVFQSLLLSSTSSLELRAYSDADHGSDPTDRKSVTGFCIFLGDSLISWK FT SKKQSIVSQSSTEAEYRAMASTTKEIVWLRWLLADMGVSFSHPTPMYCDNQ FT SSIQIAHNSVFHERTKHIEIDCHLTRHHLKHGTIALPFVPSSLQIADFFTK FT AHSISRFRFLVGKLSMLVAAAS" XX SQ Sequence 4493 BP; 1044 A; 898 C; 934 G; 1617 T; 0 other; tggtatcaga gctggtttta tggaacgagg cttaatcccg aacacaactt cgcggatcca 60 acttggagtg agattttgtc ttccgcttct gcaaaatttg gtatttcgtc agtttctgca 120 attattttgg tatttcgtct tcccttcagc ttctgcaatt tggtatttgc gttcagtttc 180 tgcaaatttg ttttgtgttt tggagtaatc gtataatttc gagaagatat ttgtttagtt 240 tctgcgatct ctgttcagtt tctgcaattt ggtattttgt tttccgctgc ttttgcattc 300 tggttctctg tgattgttga ttatggctac tgaaagagat gattcgcttc agtctgtgag 360 tgtgaggttg gatgggaaga actattcgta ttggagctat gtaatgagaa attttcttaa 420 gggtaagaag atgtgggggt atgttagtgg aacttatgtg atacctaaga atactgagga 480 gggggatgct gttttgatag atacatggga agcaaacaat gcaaagatca ttacttggat 540 caacaattct gttgagcatt ctataggtac gcagttggcg aagtatgaga cagcaaagga 600 ggtttgggat catctgcaaa ggttattcac gcaatcaaat tttgcaaaac agtatcaatt 660 agagaatgac atacgagctc ttcatcagaa gaatatgagt attcaagagt tttattctgc 720 tatgacagat ctttgggatc aattggctct tacagaatcg gcagaattaa aggcatgtgg 780 tgcctatatt gagcgtagag agcagcaacg attggtacag tttttaacag cacttcgcag 840 tgatttcgaa ggacttagag gttcaattct gcatcgttct ccactgcctt ctgttgactc 900 tgttgtcagt gagttattgg ctgaagaaat acgtcttcag tcttattctg aaaagggaat 960 tctttctgct tcgaatcctt ctgtactagc agtaccttct aagccattct ctaatcatca 1020 gaacaagcct tacacaaggg ttggcttcga tgagtgcagt ttctgtaagc agaaaggtca 1080 ttggaaggct cagtgtccta agttgagaca gcagaatcaa gcttggaagt ctggcagtca 1140 gtcacaatct aatgctcata gaccacctca gggttataaa ccaccacacc acaatactgc 1200 agcagtagct tccccaggct ctattaccga tcctaatact ttggctgagc aatttcagaa 1260 gtttctctcc ttgcagccac aagcaatgtc cgcttcttcc ataggtcagt tgcctcatag 1320 ttcctcaggt atgtcacact ctgaatgggt cttggattct ggtgcttccc atcatatgtc 1380 tccagattcc tcatctttta cctctgtgtc cccttcgtcc tccattcctg ttatgactgc 1440 tgatggcact cctatgccct tagcaggtgt tggttctgtt gtcacacctc acttgtctct 1500 ccctaatgtt tatcttattc caaaactcaa attgaatctt gcgtctgttg gtcaaatatg 1560 tgattctggt gattatttag tcatgttttc tggttctttt tgttgtgtac aggatctgca 1620 gtctcagaag ctgattggga caggccgtag ggagaatgga ctatatattt tggatgagtt 1680 aaaagtgcca gttgctgctg ctgccgctgc tactactact gttgatttgt cttcctttcg 1740 tttgagtctt tcatcttcta gtttttattt atggcattcc cgtctaggtc atgtttcgtc 1800 ttctcgtttg agatttttgg catccacagg agctttagga aatttgaaaa cttgtgacat 1860 ttctgattgt agtggatgta aactggcaaa attttctgct ttacctttta atcgaagtat 1920 ttctgtttct tcttcaccat ttgatttgat tcattctgat gtatggggac cttctcctgt 1980 tgccacaaaa ggagggtctc gatattatgt ctcttttatt gatgatcata ctcgttattg 2040 ttgggtttat ttaatgaaac atcgttctga attctttgag atatatgcag cttttcgagc 2100 tcttatcaaa actcaacatt ctgctgtgat caaatgcttt aggtgtgatt tgggtgggga 2160 atacacctct aataaatttt gtcaattgct tgccttagat ggaaccatcc accaaacttc 2220 atgtacagat actcctgagc aaaatggtgt tgctgaaaga aaacataggc acattgtcga 2280 aactgctcgt tctctcttgt tgtctgcttt tgttcctagt gagttttggg gagaagctgt 2340 tcttactgct gtaagtttga ttaatacaat tccatcttct catagttcgg gtctatctcc 2400 ttttgaaaag ttatatgggt atgtccctga ttattcctca tttagagtct ttggttgtac 2460 ttgtttcgtt cttcgtcctc atgtagaacg cagtaagcta tcctctcgat ccgctatttg 2520 tgtctttctg ggttatggtg aaggtaaaaa ggggtatcgt tgttttgatc caataactca 2580 gaaactttat gtgtctcgtc atgttgtctt ccttgagcat atacctttct tttctattcc 2640 atccactact catagcctga ctaaatctga tcttattcat atagatcctt tttctgagga 2700 ttctggtaat gatacctctc cccatgttcg atcaatttgt actcataact ctgcaggtac 2760 tggtacttta ctctctggca cacctgaagc tccattctca tctacagccc ctcaagcttc 2820 atctgagatt gtggatccac ctccacgtca gtccatccgc attcgtaagt ccacaaaact 2880 accagatttt gcttattctt gttattcttc atcatttact tcctttttag cttctattca 2940 ttgtctcttt gagccctctt cctataaaga ggcaattctt gatccgcttt ggcagcaagc 3000 tatggatgag gaactttctg ctttgcataa gacagatact tgggatctgg ttcctctacc 3060 tcctggtaag agtgttgttg gttgtcgttg ggtgtataag atcaagacta attctgatgg 3120 gtctattgag cgatacaaag ctaggctggt tgcaaaagga tactctcaac agtatggtat 3180 ggactatgag gagacatttg ccccggttgc aaaaatgact actattcgta ctcttattgc 3240 cgtagcttcg attcgtcagt ggcatatttc tcagcttgat gttaaaaatg ccttcttgaa 3300 tggagatctt caagaagaag tttatatggc accccctcct ggtatttcac atgactctgg 3360 atatgtttgt aagcttaaga aagcgttata tggtctcaaa caagcacccc gtgcttggtt 3420 tgagaaattc tctattgtga tctcgtctct tggctttgtt tctagcagtc atgattctgc 3480 tctttttatt aagtgcactg atgcaggtcg tatcattctg tctttatatg ttgatgacat 3540 gattattact ggtgatgata ttgatggtat ttcagttttg aagacagagt tggctagacg 3600 atttgaaatg aaggatttgg gttatcttcg atatttcctg ggtattgagg tagcatactc 3660 acctagaggt taccttcttt ctcagtcgaa atatgttgca gatattcttg agcgggctag 3720 acttactgat aacaagactg tagatactcc tattgaggtt aacgcaaggt actcttcttc 3780 tgatggttta cctttgatag atcctacttt ataccgcact attgttggga gtttggtata 3840 tctcaccatt actcgtccag atattgcata tgttgttcat gttgttagtc agtttgttgc 3900 ttctcctact actgttcact gggcagctgt tcttcgtatt ttgcgatatc ttcggggtac 3960 agtttttcag agtcttttac tttcatccac ctcttccttg gagttgcgtg catactctga 4020 tgctgatcat ggtagtgatc ccacagatcg caagtctgtt accgggttct gtatcttttt 4080 aggtgattct cttatttctt ggaagagcaa gaaacaatct attgtttctc aatcatccac 4140 cgaagcagaa tatcgtgcca tggcatctac taccaaagag attgtttggt tacgttggtt 4200 acttgctgat atgggagttt ccttttctca tcctactcct atgtattgtg acaaccagag 4260 ttctattcag attgctcaca actcggtttt tcatgagcga actaagcaca ttgagatcga 4320 ttgtcatctt actcgtcatc atctcaagca tggcaccatt gctttgcctt ttgttccttc 4380 ttccttgcag attgcagatt tctttaccaa ggcgcattcc atctctcgtt ttcgttttct 4440 ggttggcaaa ctctcgatgc ttgtagctgc cgcatcgtga gtttgagggg aga 4493 // ID Gypsy-3_Mad-I repbase; DNA; EDCOT; 4614 BP. XX AC ACYM01138405; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-3_Mad-I; KW Gypsy-3_Mad-LTR; Gypsy-3_Mad_. XX NM Gypsy-3_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4614 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1326-1326 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01138405; Positions 4401 9014. XX CC Positions [3467-3964] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 2669..4555 FT /product="Gypsy-3_Mad-I_1p" FT /translation="MQHSRVIAYASRQLKPHEKNYPTHDLELAAIIFALKI FT WRHYLYGEKCKIFTDHKSLQYIFTQKELNLRQRRWLELISDYDCTIEYHPG FT RANVVADALSRKSQGRVNALYASLVPLLADLRSTGLQLGLEEQEDMVVGRE FT KALLASFQVRPIFIDRILEAQGIDEEVQSLIFAVSQGKKKDLNVRESDGIL FT MQDKRMYVPNNEELKKEILDEAHISAYAMHPGGTKMYHTIRPFYYWPGMKR FT EIAEYVSRCVVCQQVKAERKKPFGLMQPLPVPQWKWENITMDFVYKLPCTQ FT NGYDGVWVIVDRLTKSAHFIPVREKYSLNKLAELFITKIVKYHGIPVSIVS FT ERDPRFTSKFWTAFQEALGTRLLYSTAYHPQTDGQSERTIQTLEDMLRSSV FT MQFGDDWHAKLDLMKFAYNNSYHSSIGMAPFKALYGKSCRTPLCWSEVGER FT VLVGQEIVEETTQNVQVIKSNLKVAQDRQKSLADRHATDRVYKVNDWVFLK FT LSPWKGVVRFGKKGKLSPRYIRPYQITERVGEVAYRLELPSELSKMHNVFH FT VSMLRQYVADPSHVILVQPLEISPDLTYDEEPVTILDWKKKVLRNKTVRLV FT KVLWRNHSVKEATWETEDRMREMYPRLFYDY" XX SQ Sequence 4614 BP; 1330 A; 711 C; 1136 G; 1437 T; 0 other; ctgcgcacat ggctacgtca cgctcacgtg acggccagca tgccttgatt ttggtcgggg 60 tgtgtcagtt tggaatcaga gctctaggtt gcagtcctgc atattttgtg aacttcccta 120 attattgttg gtgtcttctg tcagaacttt accgcctcgt agcgagccac gtagttagga 180 tgagcctagt ttccctaata ttgtagtttg gggaaaacta ttgctattgt gattcagtct 240 attatctaaa ggaacccttt gagactggtt ataagttgat tttgaatcac tttatggaag 300 tgaagaacct aagggagtaa agtgacggct taatcatttg gaaaagacgt ttcggattat 360 gcaaagttaa gagaatcttc ctcccgacaa gtgggtcgag atgaatacct agtttctgag 420 tattgaatct gcattttggt ggagatagga atgttatccg atgttatcgg aagaacagct 480 gtttggaagt tgtttaaaga attgtttaag aaaaagttca ttcctccggc atattgtgat 540 ggtagtaagc aagaatttgc aaatgtgaga caaggaaaat gacggcgaat gaatattata 600 gaaagtttac agacttgcct tgtttccatt cggatgttgt tgctaatccg gtcgaagtgt 660 tatgttgttt taggttggat aataagaaga aatggcgttc tttggcgacc actatccatt 720 gtacttttac caggagttta cgagatgttg ttaaacattg aggactctga gaacatgatc 780 agcaagagta aagaggaata agaaaagatt gagaatcaga agaaagacga taaggttaag 840 atccgtcata tcaaggacct tgaaagactc agagcttcaa aagaagtgaa actagagcta 900 attctcccag ctgaggtttt agtgccactg gtcagagatg aagtgataga tttactagtt 960 atcccatatc tcaaagacaa gttgactctg gtagaggaaa tgtatcttcg taccgttggt 1020 acaatattag actctttgaa gagtgtggga agcagtgaat gtgttcatgt ggttagatga 1080 gacatagagg tatgaattgt ccctagaatc agttgttacc cagcagtctt ccctgacata 1140 ttacttggaa aaattgagga gtaagatggt aatattgcac ccttaagaat tgttgcttac 1200 ttatcgagac gacaatgagt tatcgttatt gcgggttgca gaccgtaata cccataactt 1260 atttgttgga ttcgttaagc aagtaaatag gtaggacaca ctatgttgat ttggtttatt 1320 caggatgcca atgatggtgg aagatgtagt tatgccagct aatcttgtcc cgttagatat 1380 tgtggatttt gatgtgatat tagtcacaga ttggttgcat tttaatcgtg cccaaattga 1440 ttgttacggg aaaacagtga ctttccatcg tcttggatta cctgaagtta cattcgtagg 1500 tgagcctagt ggattgaagc atgatgttat ttcagctgtg agagctgaaa ggttgttatc 1560 gaaaggttgt caagggtact tggctaatgt gatattagat gatgttgctc ctagtagtgt 1620 ggaagaagtg ggagtagtca gacattttcc tgacgtattt ccaaatgatt tacctggatt 1680 gctgctagac agagatgtgg agttcactat tgatttactt ccaggtacaa atcctatttc 1740 cttaactcct tatcgtatgg ctcctactaa gttaagagaa ttgaagattc aattacaaga 1800 attggttgat aaaggtttta ttcaacctag tacttcaccc tggggagctc cagttttgtt 1860 tgtaagaaag aaagacggaa ctttgaggtt atgcatcgat tacaggcaat tgaatagggt 1920 aacgattaaa aaccgttatc cattgccacg tatcgatgat ctatttgatc aacttcgagg 1980 tgcatgagta ttctcaaaga tcgacttaag gtcagattac tatcagttga agattaagag 2040 tgacgatgtc tacaaaacgg cttttagaac tcgttatggt cattatgagt tccttgtgat 2100 gccatttgga ttgacgaatg caccagtagt ttttatgggt ttgatgaata aagtattcta 2160 gcaatatttg gatagatttg tcattgtttt tattgatgac attctggtgt attccaagtc 2220 tgaatcagat catgttcaac atctcactct ggtgttggag aaattgagag agcaccgttt 2280 gtatgctaag tttagctagt gccaattttg gttaaatgaa gtggcattct tgggacatgt 2340 catctcagct cagggtattc tggtagaccc tcagaaaatt gcagctgtgg agaattagga 2400 acagccacga acagtcatag aagtacgaag tttccttggc ttagcaagtt actatcgacg 2460 gtttgttaag gatttttcag ttatcacttt accacttacc aggttgacta gaaaggaagt 2520 taagtttgag tgggatggta agtgtgagca gagttttcag caacttaagt atggtctcac 2580 tcatgcgcct gttttggcac ttcctgatga tggtggtaat ttcgagattt atagcgatgc 2640 ttcgttgaat ggcctgggat gtgttttgat gcagcatagt agggtgattg cttatgcttc 2700 acgtcagtta aagcctcatg aaaagaatta ccctactcat gatttggaat tagcagccat 2760 tatatttgcc ttgaagattt ggagacatta tctttatggt gaaaagtgta agatctttac 2820 ggatcataag agtcttcagt acattttcac ccagaaagag cttaatctta ggcaacgaag 2880 gtggttagag ctgattagcg attatgattg cactattgag tatcatcctg gtcgtgctaa 2940 tgtggtggct gatgctttga gtaggaaatc ccaaggtcgg gttaacgcat tgtatgcttc 3000 tcttgttcca cttcttgcag atttgaggtc cactggactg caattgggat tggaggaaca 3060 agaagacatg gtggtaggac gagaaaaagc cttacttgct agtttccaag ttaggcctat 3120 tttcattgac cgtatactcg aagcacaagg aattgacgaa gaagttcaga gtttaatctt 3180 tgcagtttct caaggaaaga aaaaagatct taatgttcgg gaatctgatg gcatacttat 3240 gcaggataag cggatgtacg tgccaaataa tgaggaattg aagaaagaga ttcttgatga 3300 agcgcatatt tcagcatatg caatgcatcc agggggcact aagatgtatc ataccattag 3360 gccattttac tattggccag gtatgaaaag agaaattgca gagtatgtta gtaggtgtgt 3420 agtttgtcag caagttaaag ctgaaaggaa gaaaccgttt ggtttaatgc aaccacttcc 3480 cgttccacag tggaaatggg aaaatatcac tatggatttt gtgtacaagc ttccttgtac 3540 acagaatggt tatgatggcg tttgggtgat tgtagatcga ctgactaagt cagcacactt 3600 tattccagtg agggaaaagt attctctgaa caaattggct gagctgttta tcactaagat 3660 tgtgaagtac catgggattc cagtgagtat tgtttcagaa cgagatccta gattcacttc 3720 taaattctgg acagcttttc aggaagctct tggtacgaga ttgctatata gtacggcata 3780 tcatccccag acagatggtc aatcagaaag gacaatacag actttggaag atatgttaag 3840 atcttctgta atgcagtttg gcgatgattg gcatgcaaag ttggatttaa tgaagtttgc 3900 ttataataac agttaccatt ctagtatcgg gatggcacca tttaaagctt tatatggaaa 3960 atcgtgtcgt actcctttat gttggtcaga ggtcggtgaa agagttttgg tgggccagga 4020 gatagtggag gaaactactc agaatgttca agtaattaag tctaatttga aagtggccca 4080 ggatcggcag aagagcttag cggataggca tgctactgat cgagtgtata aggttaatga 4140 ttgggtattt ttaaagctat cgccttggaa aggagtagta aggttcggga aaaagggtaa 4200 gctgagccct aggtacatca gaccttatca gatcaccgag cgagttggtg aggttgctta 4260 caggcttgag ttgccttcag agctgtctaa aatgcataat gtatttcatg tctcgatgct 4320 tcgtcagtat gttgcagatc catcgcatgt gattctggtt caacctttgg agattagccc 4380 ggatttgact tatgatgaag aaccagtgac tatcttagat tggaaaaaga aagttctgag 4440 aaataagaca gtgcggttgg taaaagtttt gtggaggaac cactcggtga aagaggctac 4500 atgggaaaca gaggatcgga tgagagagat gtatccgagg ttattttatg attattagtg 4560 atgtattttg gttgtgtaaa tttcggggat gaaatttcta taaggagggt aggt 4614 // ID Copia-39_VV-LTR repbase; DNA; EDCOT; 246 BP. XX AC chr10; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-39_VV_; KW Copia-39_VV-I; Copia-39_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-246 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr10; Positions 16481258 16481013. XX SQ Sequence 246 BP; 60 A; 36 C; 45 G; 105 T; 0 other; tgttgggatg ttcagttaaa gtagtcaaag ttgttagaat ttcattctgt taataattcc 60 tattttttgg gacatgttgg taggatttga ctatttcctt agccatttac cacgttctta 120 cgtgggctgt ttgtttcctt tttaatctct tttgtaaggc ttatataagc ccatagcttg 180 ttttgaattg aataagactc attctcatat tgtgagtgaa ttgcattatg tctacagttt 240 acaaca 246 // ID TS2 repbase; DNA; EDCOT; 655 BP. XX AC . XX DT 20-OCT-2006 (Rel. 11.1, Created) DT 24-OCT-2006 (Rel. 11.1, Last updated, Version 1) XX DE Solanum DNA, short interspersed repetitive element, TS family. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; TS2. XX OS Solanum demissum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum. XX RN [1] RP 1-655 RA Shankar R. and Jurka J.; RT "TS2: A SINE subfamily from Solanum demissum related to TS."; RL Repbase Reports 6(10), 511-511 (2006). XX DR [1] (Consensus) XX CC This sequence is relatively new. It has got 27 bp long target CC site sequence (TTGAGACCTCAATAACCATTTATCACA). XX SQ Sequence 655 BP; 145 A; 113 C; 210 G; 187 T; 0 other; gcggagatga gtatgttgag atggatgtgt gggcacacta ggagcgacaa gattaggaat 60 gaggtaatcc gggagaaggt gggagtggcc tctgtggtgg acaagttgag ggaagcgaga 120 ctgagatggt ttggacatgt gaagagacgg agcgcagacg ccgcagtgag gaggtgcgag 180 gtaatggtgg tagagggtac gcggaggggt agaggtaggc ccaagaagta ttgggaggag 240 gtgattagac aagacttggc tatgcttcac attaccgagg acatgactct agataggaag 300 gagtggaggt cgcgtattaa ggttgaaggt tagtagggtt agcgtgttgt cttcccttgc 360 aagggtatgg gttgttagcg tttggagtag acctagcctt atgctgttta ctgcgtttca 420 cgcatcgcat tactttcttg ttgttattgt ctcattggtt gattatacgc tatcttttgt 480 attggctgtt atgttttata tatatctctc ctgtcactta gatttgttgt tcttgagctg 540 agggtctccc ggaaacagcc tctctacctc cacgaggtag tggcaaggtc tgcgtacact 600 ttaccctccc cagaccccac ctagtggaat cccactgggc atgttgttgt tgttg 655 // ID POPGY1_LTR repbase; DNA; EDCOT; 1539 BP. XX AC AC182679; XX DT 29-MAR-2007 (Rel. 12.03, Created) DT 02-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE Gypsy-type retroelement - long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; POPGY1_LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1539 RA Jurka J.; RT "POPGY1: Gypsy like sequence from black cottonwood."; RL Repbase Reports 7(3), 138-138 (2007). XX DR EMBL/GenBank/DDBJ; AC182679; Positions 4088 5626. XX CC There are only 4 single-base substitutions between LTRs, CC indicating that this is a relatively new sequence. XX SQ Sequence 1539 BP; 463 A; 256 C; 257 G; 563 T; 0 other; tgattagtac ttaaaagtgc atttttatca aggttttata tcattatttt gcacttgaag 60 tatcaataac tccttaacta aagcatgttt tataataacg tatctaataa tataagatac 120 ctttaattta tggtaaatgt tcatcttaaa tgcaggccta tcacataaat gaaagaattg 180 attgatgagt tgaagtactg aaattgaaag gacaaagaga tggccaaact tagaaaagag 240 atgttggtgc agtccaaact ggaacattgt ttggtaatcg ggctatatct ggagctgtag 300 atctcggatt gaggtctact ttatatggat ggaaaggtaa gacatagtcc tacaactttc 360 atgcggagcc caagatttaa taaggccgtt ttcgagtcca aattgtagca acaatgaaga 420 agcccgaatc tgtcctgcaa cccagacact gttcagtgtt cagcccatat ctcgagttct 480 agaagtccaa atgatctcaa atttttatcc tggaaagatg agacaattcc ctagaacttt 540 catgatttaa gtttgttcaa attatgacgt catcaatgac gtttttggca gacaagaaga 600 taagaattgt caccaagtca agatgtggcc acccactcat caattagtca acaaatcaat 660 agttccgaat tttggcctat aaaaggaggc atttgccatg tatttaggca tcttggtgtt 720 cagatcaaga tcatgctctt gctctctctt tatattttgt aatgcttaag ttttgcttat 780 attaatttct tgcttatgct tttcatttcc tttccttgtt tatttatgtt tctttctttc 840 attatgtgtt gctaagttaa ttatgtcaag gtgaaaaggg tacactaatg gtgtaagaat 900 aagtataata taaacttaac atggacctta atgttggata ctaacatggt ttatatttgt 960 tatcttgttc acttttaata ctttgcttgt taaatggtta atctagattt atgttgtata 1020 acacttggta caacaaatac ttggcacttt catagcccat actgtatggt ataaccgaca 1080 cctgagctat gaaaggaact tgatttgttg ttaacataag ttataatcat gaatgcctga 1140 caacatttac aagtattagc attattcgaa taagataact aatgtaataa tgttaacaat 1200 ttataatctg attggaacct cctttatgtg tggtttccaa ttgaataaaa agagtttata 1260 ctatacttgt ttgaaatacc attagtggat cctctaacct tgacatttgt tgttatcatt 1320 gtttaatcct tacgttaatc ttccatctca aagtcctcat caacttcttc ctcttcttct 1380 tcactattat tattattgtt gttattgttg ttgttgtatt attgttatct ataatttata 1440 caattaacct ccctgtggtt cgaccccggt cttgccgggt tatttattac ttcgacactc 1500 ctgcacttgg gaaaagacat caatcttttg gtcgtgtca 1539 // ID SHACOP23_I_MT repbase; DNA; EDCOT; 4385 BP. XX AC CT030234; XX DT 30-JAN-2007 (Rel. 12.01, Created) DT 30-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region of LTR retroposon, SHACOP23_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Internal; Interspersed; terminal; repeat; ORF; SHACOP23_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4385 RA Shankar R. and Jurka J.; RT "SHACOP23_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 69-69 (2007). XX DR EMBL/GenBank/DDBJ; CT030234; Positions 50796 55180. XX CC The internal region has domains for gag-pol polyprotein. XX FH Key Location/Qualifiers FT CDS 26..4372 FT /product="SHACOP23_I_MT_1p" FT /translation="MAPRNNASTSNEQGAPAIDPSSPYYVHPSDGPTSVSI FT TPLLTGSNYHSWARSMRRALGGKMKYDFVDGSIPVPTDPFDPTFRAWTRCN FT MLVHSWIMNSVAESIGQSIVFMENAVDVWNDLKERFSQGDLVRVSELQQEI FT YALKQEHRTVTKFFSDLKILWEELEMYMPIPTCTCRVRCSCEAMHTARYNH FT NLLYVIRFLTGLNEEFSVVKSQILLLDPLPSLNKIFSMVIQHERQIVPHVS FT VNDDSKVLVNAAENRRSNFRNNKTGSKPGERVCTFCNKSNHTIDTCYRKHG FT VPPHLQKKGSNYAAHNVNAESSAPPALTHEQYNTLVSLLQASSISKQSTAH FT ASNQVNSFQSTDHPSVDDKGNISVISIFSSCVNNTTLGSWIIDSGASDHIC FT GSSHWFHSFHDISPIFIRLPNGNFAVAKQIGTIYFSQSFFLTNVLYVPNFS FT LNLVSVAKLCSDLPCLVSFTNSQCLVQDPQSLKTIGSAELIEGLYHVVLPD FT KIRNVSAAPCNSAVIIPENALWHFRLGHLSSSRMTLLHSDFPFIVIDQKGV FT CDVCHLAKHKKLPYQRSFNKAMKPFDLIHFDIWGPLAIKSVHGFSYFLTAV FT DNFSRYTWVTLMRSKAEVSQHVMNFVQLIETQHNTLVKTIRTDNGPEFLIS FT SFYSSKGIIHQKSCVESPQQNGRVERKHQHILNVARDLLFHSNLPKQFWCY FT AVSHAVFIINRVSSPLLDNKSPYFLMHDKLPDLKILKVFGSLAYASTLHSH FT RTKLDPRGRKCVFLGFKSGMKGSILFDLNNKEIFVSRNTTHLEHILPYNPI FT SKPSNWKYHSHGRTLGDDIPIIHPPNDTISHNTKPPDSVPLSSTLEHNLTN FT STIPEPESFTPVPRIPNQNPQPSPHQPIRQRHPPSYLADYVCNASDGSTKS FT KSSGTPYPITSYHSFSQLSPSRQVFSSSITHCTEPKSFKEASQYDCWQIAM FT KSELDALDKNGTWILVDLPPHVKPIGSKWVYKVKHRADGSIERYKARLVAK FT GYNQIEGLDFFDTFSPVAKLTTVRTLLALASIHSWHLHQLDVNNAFLHGEL FT QEEVYMTIPEGVSCTKPNQVCKLLKSLYGLKQASRKWYEKLTSLLVKEGYQ FT QSTSDYSLFTLKNGHEFTALLIYVDDVILAGTSLDEFKRIKHILDCNFKIK FT DLGILKYFLGLEVAHSKIGITISQRKYCLDLLNDSGLLGSKPAGSPLDPSI FT KLHQDDGKPYDDIAAYRRLIGRLLYLNTTRPDITFATQQLSQFLHAPTMTH FT YNAACRVVRYLKHNPGKGLLFPRNSEVQILGYSDSDWAGCIDSRKSISGYC FT FFIGSSLISWRAKKQQTVSRSSSEAEYRALSTATCELQWLLHLFKDLHVIS FT TRQPVLYCDSQSALHIASNPVFHERTKHLEIDCHLVREKVQDGTLRLLPIS FT SQEQLADFLTKALAPPKFNSFISKLGMIDIYNASA" XX SQ Sequence 4385 BP; 1318 A; 829 C; 745 G; 1493 T; 0 other; atggtatcat agagccgtaa gatccatggc acctcgcaac aatgcttcaa catctaatga 60 gcagggtgct ccagcaattg atccatcaag tccttattat gtccatccaa gcgatggtcc 120 tacctcggtt tcaattactc ctctacttac tggttccaat taccatagtt gggctcggtc 180 tatgcgtagg gctttgggtg gaaaaatgaa atatgatttc gttgatggtt ctattccggt 240 tcctacagat ccattcgatc caacatttcg tgcttggacg cgttgcaata tgctcgttca 300 ctcatggatc atgaattctg tcgctgaatc aattggccaa tccattgtat ttatggaaaa 360 tgcggtcgat gtttggaatg atttgaaaga acgcttctct caaggtgatt tagtccgcgt 420 atcagaactg caacaagaaa tttatgctct caagcaggag catcgaacgg taactaaatt 480 tttctctgat cttaagattt tgtgggaaga actagaaatg tatatgccaa tacctacatg 540 tacctgtcgt gtccgttgct cttgtgaagc tatgcatact gctagatata atcataattt 600 actctatgtg attcgttttt tgactggtct taatgaagaa ttcagcgttg ttaagtcaca 660 aattctgcta ttagatcctt tacctagctt gaataaaatt ttctcaatgg ttattcagca 720 tgaacgtcaa attgttccac atgtttcagt taatgatgac tctaaagtcc ttgttaatgc 780 tgctgaaaat aggagatcaa attttagaaa taataagact ggttcaaaac ctggagagag 840 agtttgtact ttttgtaaca aatcaaatca tactattgat acttgttatc gcaagcatgg 900 agtaccacct catttacaga agaaaggttc aaactatgca gctcataatg ttaatgcaga 960 aagttctgca cctccagctc ttacacatga gcagtataat actcttgtgt ctctacttca 1020 ggcttctagc attagtaaac aatctactgc acatgcttct aatcaggtga actctttcca 1080 atcaactgat catccatcag tcgatgacaa aggtaatatt tctgttattt ctattttttc 1140 ttcttgtgtt aataacacaa ctcttggttc ttggatcatt gattcaggag ctagtgatca 1200 tatttgtggt tcatcccatt ggtttcattc ttttcatgat attagtccta tttttattag 1260 attacctaat ggtaattttg ctgtagcaaa acaaattggc acaatttatt tttctcaaag 1320 ttttttctta acaaatgttc tttatgttcc taatttttct ttgaatctag tttcagttgc 1380 caaactctgt tctgatttac cttgtcttgt tagtttcact aattcacaat gtcttgttca 1440 ggatcctcag tcattgaaga cgattggttc tgctgaactc attgaaggat tgtatcacgt 1500 ggttctacca gataagattc ggaatgtatc tgctgcccct tgcaactctg ctgtcatcat 1560 accagaaaat gcattatggc attttagact aggccacctc tctagttcta gaatgacttt 1620 gctacattct gattttcctt ttattgttat agatcaaaaa ggagtttgtg atgtatgcca 1680 tttggcaaaa cataaaaaat taccatatca aaggagtttt aataaagcca tgaaaccttt 1740 tgatctaatt cactttgata tatggggtcc tcttgctatt aaatctgttc atggtttttc 1800 ttattttctt actgctgttg ataacttcag tagatatact tgggttactc ttatgagatc 1860 taaggctgaa gttagtcaac atgtcatgaa ttttgtccag ctaattgaaa cacaacataa 1920 cacccttgtt aaaaccataa gaactgataa tggcccagaa tttttgattt cttctttcta 1980 ttcttccaaa ggaattattc atcaaaagag ttgtgtagaa tctccacaac aaaatggaag 2040 agtagaaaga aaacatcaac atatactaaa tgtagccagg gatttgttgt ttcattcaaa 2100 tttaccaaaa caattttggt gttatgctgt gtcacatgct gtttttatca taaaccgtgt 2160 ctctagtcct cttcttgata ataaatcacc atattttttg atgcatgata agctacctga 2220 tttgaaaatt ttaaaagtgt ttggctcttt agcttatgca tctactttac attcacatag 2280 aactaaattg gatcccagag gtagaaaatg tgtgttccta ggttttaaaa gtggcatgaa 2340 aggatctata ctttttgatc taaacaataa ggaaatattt gtttctagaa ataccacaca 2400 ccttgaacat attttgccat ataatccaat ttcaaaacct tccaattgga aatatcattc 2460 tcatggtaga acactcggtg atgatattcc aattattcat ccccctaatg acactatatc 2520 acataacaca aaaccaccgg attctgttcc attatcatct acactagaac ataaccttac 2580 aaattcaacc ataccggaac ctgaatcttt cacccctgtc ccaagaatac caaatcaaaa 2640 tccacaacca tcacctcatc aacctattag gcaaaggcat ccaccatctt atcttgcaga 2700 ttatgtgtgc aatgcttcag atggttcaac aaaatcaaag tcttcaggta ctccttaccc 2760 tatcacctct tatcattctt tttcacaatt atcaccttca cgtcaagttt tttcttcttc 2820 tatcacacac tgcacagagc caaaatcctt taaagaagca agtcagtatg attgttggca 2880 aatagctatg aaatctgaat tagatgcatt ggataaaaat ggcacttgga ttctagtaga 2940 tttgccacct catgtgaagc ctattggtag taagtgggta tacaaagtta aacatagggc 3000 agatggctct attgaaaggt ataaagcacg attggttgcg aaagggtata atcagattga 3060 aggtcttgat ttttttgata ccttttcacc tgttgcaaaa ctcactacag ttagaacatt 3120 acttgctctt gcttcaattc attcttggca tttacatcaa ttagatgtaa ataatgcgtt 3180 tttgcatgga gaattacaag aagaagttta catgactatt ccagaaggtg tttcatgtac 3240 caaacctaat caagtttgta aacttcttaa aagtctctac ggtcttaaac aagcaagcag 3300 gaaatggtat gaaaaattga catctttgtt agtgaaggaa ggatatcaac aatctacatc 3360 tgattactca cttttcacat tgaaaaatgg tcatgaattt actgccttgt tgatttatgt 3420 tgatgatgtg atcttagcag gaacttctct cgatgaattt aaaaggatca aacatattct 3480 tgattgtaat ttcaagataa aggatctagg aattcttaaa tatttcctag gcctcgaagt 3540 ggctcattcc aaaattggga tcactatttc acaaaggaaa tattgtttgg atttattgaa 3600 tgattcaggt ttattgggat ccaaaccagc cggtagtcct cttgatcctt ccattaaatt 3660 acatcaagat gatggtaagc cttatgatga tattgccgca tataggagat taattggtag 3720 gttgttatat ttgaatacta ctcgaccaga tatcacattt gcaactcaac aactaagtca 3780 atttcttcat gctccaacca tgacacatta taatgctgct tgtagagttg tgagatattt 3840 gaagcataat cctggaaaag gccttttatt tcctagaaat tctgaggtac aaattttggg 3900 gtattcagat tctgactggg ctggttgtat tgattccaga aaatcaattt caggatattg 3960 tttttttatt ggttcttcct tgatatcttg gcgtgctaag aaacaacaaa ctgtatcgag 4020 gtcttcttct gaagctgagt acagagctct ttctacagca acatgtgaat tacaatggtt 4080 gcttcacttg ttcaaagatt tgcatgttat ctccacacga cagcctgtgc tatattgtga 4140 tagccaaagc gctcttcata ttgcttccaa tcctgtgttt catgagagaa caaagcacct 4200 tgaaatagat tgtcatctag taagggaaaa ggttcaagat ggtactctta gacttttacc 4260 aatttcatca caagagcagt tagcagattt tctcacaaag gctttggccc ctccaaaatt 4320 caactcattt atatccaagc ttggcatgat agacatctat aatgcttcag cttgagggag 4380 gatat 4385 // ID Gypsy-16_Mad-I repbase; DNA; EDCOT; 8070 BP. XX AC ACYM01047118; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-16_Mad-I; KW Gypsy-16_Mad-LTR; Gypsy-16_Mad_. XX NM Gypsy-16_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-8070 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1338-1338 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01047118; Positions 1379 9448. XX CC Positions [5905-6231] - Integrase core CC LTRs are 92% similar to each other. XX FH Key Location/Qualifiers FT CDS 3324..4961 FT /product="Gypsy-16_Mad-I_1p" FT /translation="MENSDHSPTLPILLRRSFMKTAHTKIDVFKGTLTMEF FT DGEVIDFNISETIRYPCDDHSCFSIDIIDSLAQGYLEELNDDALDTVITRG FT MKLNNKGAEHMLTNSLLEEFHAVPPCEEFIEMVATLESLPKHDGKPSNFES FT IPISTNKMLPSVIQAPTLELKQLPSHLKYVFLGEQETLPIIVSSSLTAQEE FT EKLVRVLKEFKSTIGWTLADIKGISPTTCMHCIFLEEGAKPTREAQRRLNP FT PMMEVVKKEIIKLLDCGVIYPISDSHWVSPIQVVPKKSGITVVKNEENELM FT LTRILTGWRVCIDYRKLNATTRNDHFPLPFIDQMLKRLAGHSFYCFLDGYF FT GYNQIVIAPDDQEKTTFTCPFGTFAYRHMPFGLCNAPAIFQRCMVSIFSDY FT VEKIIKVFMDDFSVFGDSFDDCLANLTLILKRCIETNLVLNWEKCHFMVKQ FT GIVLGHIISERGIEVDKSKVDLVCHLPSPTSVREVRSFLGHAGFYRRFIND FT FSKLGQPLCRLLQNDVPFNFNEACEEAFKHLKTLLTSAPIITPPDWSISL" XX SQ Sequence 8070 BP; 2416 A; 1487 C; 1610 G; 2545 T; 12 other; tatatcctag ccgcatcctt acaccatcag aaacctttcc aaacactttt gccgcaacct 60 ttatccatcc aaaacaccac catacctgtt cccatccatt cctccataca aacaaccctt 120 caaaccatca accacacctt gtgccgtagc aaagaagaag aaggagaatc cctggatgtg 180 cttgatgtcc aatttggatc attggagcat ttaggtgttt tcttttcttt tgtttccaat 240 gtatraattt gtttatcytt gttttgcgat taaggaacta agcccttcct ggctaggggg 300 cgattcaaaa ccatgattat acttgcatat tgaattgatt accttcaact gttatttcat 360 aagttgtgaa ttcaatttgc ttaaccgttt gattgataac ttatacttgt atgtttatta 420 agagtgcaca cttagttttc atgcagggat ttgaagctaa aatataaggg agtttcacct 480 aatagttaca aacttatatt tacaagtagt ggaggtcgct tataaacgat cgcgttaagt 540 gaattcttgg caagagaatc atgctcatca tagttatgaa tgcctcatca atacttatag 600 ttttcatgaa gcttaatgat ctttgattgt acctttattg tgcttttcac gtaggggaat 660 tttagagaat gttttgaatt gttgtatgtg ctttcctatc caattcatta acttaaggag 720 aacttgaaag ttaaaaaagt gttgtcacag ttaacgtgga gtattgagtt tcatggttta 780 ttgaaagaag caattggaaa tcaatttgaa tgcaagtgtg tcatgtgtgg agaagaaccc 840 tctagctagc ccatcatcca tctaattcaa tcaatttcgt gcaaatctat ctagttctag 900 gtcttgcttt attttacttt attttcatcc aaaaccaaat ccccctttac tttagagggt 960 ctaattagtt agaatctgtt tagtttgtgt ttttaagtgt tttgaatcaa tataaaacca 1020 aaattcgtcc aaaaagtgtg ttaaagtcag aaactgccta attattgttt ttaggcagtt 1080 ttgagcgctt ttagcttgtt ttgagtcttt tgagttagtt ttgagttctt tccgtctagt 1140 taagtgtttt ttagcctctt tttatatatt tgagtcagtt tagagtgttt tagcaatccc 1200 tcctaatccc cggtttaaga acgatcccta cttatccata ctacaattgt caacaagggg 1260 gtttaatttg ggtattaagt taattttcgc atcaaatttt ggcgccgttg ccggggatta 1320 gcaaagtttg ctaatccctt gttatttctt tattyttttt tttcgtgtgt ttttatgtta 1380 cttactgacc atgtttgttt tcttgtttta ggtactagtt tatgactcgg agttctcatc 1440 cggttcgtga gcatatcttg gactttaacg atgattttga gcggactttg agaaagaaga 1500 gaactcaacg agaatccaat ccacctagcc ctgaccccgt gcatgaagaa aaagagatag 1560 aagagcaaga ggaggccacg gcagggattt tttaagaagt cctagatatg gcggtagaca 1620 atcgaacaat catgggagag tatataargg gcatttttkg agaagttttt cccaacgtct 1680 cgagtcattc ttctacacaa aaagattagt ggcattcagc aaaaccaagg tgaatccttt 1740 ccaacttatt atgaacattt taaaactctt gttgcttcat gtccacagca ccaaatgaag 1800 gaggagcttc ttcttcaata tttctacgaa gggcttctac caattgaacg ccaaatgcta 1860 gatgcctcag cggaaggagc tttggtggac aaaacactca tggctgccaa gacactaatt 1920 gcaaatcgtg cactgaatgc acaacaatac gaaggcattg ggcaaaggga taccccatgg 1980 caacaagtaa atgaggtaag ttccatatcc gatattcaat ctcaattagc taatcttact 2040 tccattgtat ctcagatggc cgaagggatg aggatgcaag gaccaagtgt gtgtggcgtg 2100 tgttctatcc gagggcactc ctctgaaaag tgccctcaat taattgagaa tggtggatgg 2160 gaaagcgcta atgctattgg atttcaaggc caaaaccaac caagaaacga tccatactcc 2220 aacacatata atccaggttg gagagaccat ccaaatttca agtggatgga gccctaacaa 2280 acccaacaac aaggaggctt taggcagcaa cccccgggct tctacacaaa gccatatgca 2340 cccacacaag ctccacaaca atctgcccaa aacacttcag gtacttcttt ggataatgat 2400 acacttaata agttactcac caatttgtct caggggcaag aaaattaaac caaagcaatg 2460 caaaaccaag acaaaagagt ggatcaattg gagaagcaaa ttgggcagat tgccgagttt 2520 gtagggcagt ttcgagacca agaaaaactt cctggttcaa ccattgcaaa tccaaatgaa 2580 ggttttgaaa cggccaaagc aatcatctta agaagtggca aggaagtcgg ggcaggttca 2640 caaccttcaa aatcaggtca caaggaagat gaaaggttgc aaattgaaga ggaggaatcc 2700 actcaaccca cgacaaggat ggaaacatca ttaccgcaag ccccaagtgt tcctaaatca 2760 tcaaatctgc ccaataaagg taagaacgtg tccaattcaa ttcctaccaa tgttattcct 2820 tcgaatgtac cttttcctcg caggttcatg caaacaaaga aagaggaagc tgaaaaggac 2880 attctagaga catttaagaa agttcaactt aacaatccac tccttgatga aatcaagcaa 2940 gtgccaaggt atgccaagtt tttgaaagaa ctttgcataa ctaggaaaag aatttcgaac 3000 aaggaggttr taaagttaag tgaaaatgtc tcagccatct tacaacgtaa atagccccct 3060 aaatgcaaag atccgggtaa wwatacaatt ccttgtgtca ttggtaatac tcggtttara 3120 atctgccatg ttaracttag gtgcatctat aaatgtcatg ccatattcaa tttatgcatc 3180 tatgaactta agagagttga aaaatgatgg tgtgattatt caattggccg atagatctaa 3240 cacctatcca aaaaggagtt ttggaagatg ttttggtgca ggtcaatcaa ttaatctttc 3300 tggcggactt ctacatactt gacatggaaa actcagacca ttctcctaca ttgccaatcc 3360 tccttagaag gtcattcatg aaaactgccc acaccaagat cgatgtgttt aaaggaacat 3420 tgacaatgga atttgatggg gaagttattg attttaatat ttctgaaacc ataagatatc 3480 cttgtgatga tcattcttgt ttttctattg atataattga ttctttggcg cagggatatc 3540 ttgaagaatt gaatgacgat gcacttgaca cagtcattac acgtggaatg aaactcaaca 3600 acaaaggggc agaacatatg ctaaccaaca gcctacttga ggaattccat gccgtgcccc 3660 cttgtgagga attcatcgag atggttgcta cccttgaatc attgccaaag catgatggca 3720 agccttctaa cttcgagtca attcccattt caactaataa aatgcttcct tcagtaattc 3780 aggcacctac ccttgaactt aaacaattac caagccattt gaagtacgtt ttcttagggg 3840 aacaagagac cttacccatc attgtctctt cctccctcac ggcacaagaa gaagagaagt 3900 tagtgcgtgt cttgaaagag ttcaaatcta ccataggttg gacattggcc gacatcaagg 3960 ggataagccc taccacttgc atgcattgta tatttcttga ggagggggcc aaaccaacta 4020 gagaggctca acgccgtctt aaccctccga tgatggaagt tgtgaaaaag gagattatca 4080 agctacttga ttgtggagtg atctatccga tctcggatag ccattgggtc tcaccaattc 4140 aagtcgttcc aaagaagtct ggcatcacgg tagtgaagaa tgaagagaac gaacttatgc 4200 tcactcgtat cctaacaggt tggagagttt gcatagacta taggaaactc aatgccacaa 4260 caaggaatga ccatttccca ctgccattca ttgatcaaat gctcaaaagg ttagcgggtc 4320 attcatttta ttgttttctt gatggatatt ttggttacaa tcaaattgtc atagccccgg 4380 acgatcaaga aaagaccact ttcacttgtc cctttggaac gtttgcttac cgtcacatgc 4440 catttggttt atgcaatgca cctgccatat tccaaagatg catggtaagt attttctctg 4500 attatgttga aaagatcatt aaagtcttta tggatgactt tagtgtattt ggtgattcat 4560 ttgatgattg tttggccaat ttgactttaa tcttgaaaag atgtattgaa actaaccttg 4620 tgttaaattg ggagaaatgt catttcatgg ttaaacaagg tatagttttg ggccatataa 4680 tctctgaacg tggaattgag gtggataaat caaaagtaga tcttgtgtgt cacttaccct 4740 ctccaacatc ggttagagag gttcgttctt ttcttggaca tgcaggtttc tatagacgat 4800 ttatcaatga tttttcaaag cttggacaac ctctttgccg tctcctccaa aacgatgtac 4860 ccttcaactt caatgaggcg tgtgaggaag cattcaaaca tctcaagacc ttgctcactt 4920 cggcacccat tatcactcca ccagattgga gcatttccct ttgagctcat gtgtgatgca 4980 tcggattacg caattggagc tgttttagga caaaggaaaa acaagcagcc acatgttatt 5040 tattatgctt cccgtacctt aaatgatgct tattttaatt attccacaac tgaaaaagaa 5100 ctattggcta ttgtatttgc attagataag tttagatctt atttaattgg cactaaagtc 5160 attattttca ctgatcatgc agccttgaaa tacttgttca caaagaagga agctaaacca 5220 agactcattc attggatgct cttacttcaa gagttcgata ttgaaattaa ggacacgaaa 5280 gggagtgaca acgtggtggc tgatcaccta agtagattgg tgcgtgaaga tgagtccatt 5340 cccattccaa aaacgtttcc agataactac tgtccattaa ggtaagtgag ccttggtatg 5400 ctgatttggt caattatttg gtgtctaaac aagttcccac cactcttaac aagttccaac 5460 gtgataaact taaaaaggat gctagatttt atgtttggga tgacccatac ttgtggaaat 5520 attgcccaga tcagattcta tgtaagtgtg catgaattcg aatttcattc cattttaagt 5580 ttctgacaca cctatgcatg tggggggtca ttttggcacc taaatgacag cttttaaggt 5640 tcttgagtgt ggattttatt ggcctacttt gtttaaagat gctagaacct tttgcttaac 5700 atgtgatcgt tgccaaatga taggaaatat aggccaaata gacaaaatgc cgtaggtttc 5760 catacttgtt gaaatttttt atgtttgggg tatcgatttt atgggtcctt ttccttcatc 5820 ttttggtttc acttacatat tacttgcagt tgattatgtt tcaaagtggg tggaagcaaa 5880 aaccacccga attaacgatt ctaaagttgt tgcaaatttt gtgaaatctt tgccagattt 5940 gggatgccta gggtgctcat aagtgatggg gggtctcatt tttgcattcg taccattgag 6000 gtgctgctta agaaatataa tgtgacgcat aaagtttcca cgccttatca cccccaaacc 6060 aatggccaag ccgaggtttc caataaagaa atcaaacaga ttttggagaa gaccgttagg 6120 ccaaatagaa aagattggag cttgcgtatg gatgatgcac tatgggcata tcgtacagct 6180 tacaaaacac ccattggtat gtccccattt ctgctcattt atggcaaacc atgccatctt 6240 cccgtggaat tagagcacaa ggcacattgg gctattaaga ctttcaattt gaatgtggac 6300 caagctggaa ttcatctgaa gtttcaacta agtgaacttg aagaaattag gcatgaagct 6360 tatgagaatg ctcgaattta caaagagaag accacggcat tccacgacaa gataattcga 6420 ggcaaaactt tctcaatagg gcagaaagtg ttgttattca actcccgtct ttgtttattc 6480 cctagtaagt tacgttccaa gtgggttggt cagtttgtta ttactaatgt ttttgttcat 6540 ggtgcagtcc aaatcaaaag cttgaaaact cggcaagaat tcaaggtgaa tgggcatcgt 6600 ttgaagccat actatgagag ctttgttgag catgttgtgg aggagatccc ttttcaggtc 6660 gtgggctcca atggggagtg aatggaattc ttcgtccggc tacaagacat taaagcaagc 6720 gcttcttggg aggcaactca tgcattcaac aaggagaaga tggaactttc atccccaacc 6780 cagatttgcg tttctaaact cttccccttg ctgttttatt ttttcatgtt tagtttgttt 6840 gtttgtttgt ttgtttgttt ttgtgtgagt ttatgtttga aacattgagg acaatgtttg 6900 aagttatgtc tctcaaagga atcaaaagaa ttccttctag ttatcttatt tatgctccac 6960 tatccttcta ggtttaaaca cacatcatct ctacctagtt tatgtttgat tgaagtatag 7020 tggagcataa cttagaagga attcctttga gagacattat tgcagaaaac aagtgtgggg 7080 gaagaatgtt tcaaagtgtg tgttttgtgt accatagggc acggcaataa aaaaaawaaa 7140 tatatatata tatatatttc gtagaaaaag aaaaagtgcg ttgaaaagaa agaaaaagag 7200 ttctaaataa gtgagaataa actcacatgt gttggttgtt gtagataggg tccaaaagtt 7260 taaatttgac cctaaggttt tgcatgaatc ttcccttgtg tttaaaagta gatttctgca 7320 ttctaaagtg aattctaagt gccgaattca ttactttgct cactattgct ttaagaacat 7380 tcgttttccc ttacctttct ttgttaacca acacccttaa tcctgttacc accctcgact 7440 tccatcttga gtgttgtgtg tttcaatatg tggagtttgg aattggtatg agcatgtgat 7500 atcaccggtt ctcgcttcta agtagtggca ttctattcat gagatcatat atatacatgc 7560 attaataatt ccagaaattg ctttctttgt ttaaaacata tgtgagtact agttttcatg 7620 tttacatcaa tcttctcaca tatacctagt gtagggtgtg tagttagaaa atctgagtga 7680 aaatcaagtg catttctagt gaggaattga gggaattctc taaggcatgt tactaaattt 7740 aaaatgtwgt tttaattgat tacatgtgag ctagtgaatg gtgactgtga ttaagtatgc 7800 tcgagggtaa ggattgctta aatctatgtg aatggtgatc tttgacattg aaaatccctg 7860 aggcaaatgt tggaaggttt agattgtatg ctttgtttct ttttgctcaa ggactagcaa 7920 aatctaagtg tggggcaatt tgataggagc atatttatgc gacttagtta gcttattctt 7980 gtgcatttat gttgttattt cttagttaaa ttagtatttc aagccatttt catgtgtttg 8040 taggtctaaa ggagtaaaga agcaaagaag 8070 // ID SHALINE5_MT repbase; DNA; EDCOT; 7373 BP. XX AC . XX DT 21-DEC-2006 (Rel. 11.12, Created) DT 02-AUG-2010 (Rel. 15.09, Last updated, Version 2) XX DE A LINE sequence from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; retroposon; KW LINE; repeat; ORF; Interspersed; SHALINE5_MT. XX NM SHALINE5_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-7373 RA Shankar R. and Jurka J.; RT "SHALINE5_MT: A LINE element from barrel medic."; RL Repbase Reports 6(12), 641-641 (2006). XX DR [1] (Consensus) XX CC The LINE sequence has 2 ORFs. The first one codes for zinc CC binding protein and another one has domains of reverse CC transcriptase, exo-endonuclease and RNAse H. XX FH Key Location/Qualifiers FT CDS 1684..3126 FT /product="SHALINE5_MT_1p" FT /translation="MPMLHVQDSVMEELSVPYKGCLAVKLLDKKLGYNMMK FT TKLEAVWKPNKGFDLMEVGNSFFMVKFDDEEDKNKVINGGPWMIFDHYLAI FT RQWTPTFNAATATIDKTMAWVRIPNLNLVYYDESLLWAVASMVGTPVKVDI FT HTLRVARGKFARLCVEIDLTKPVVGKVGINGEWYHVQYEGLHVICTQCGCY FT GHVLKDCSHNLKSTTVTPESMVAPATAGPEVETETVHNKNGKEINVASRIS FT GVIIEEISTKAVNLSINGDPEFLHGDWIKVERKKRINKMNVRGPGGDVKAE FT KFQNLKNRIKELNAESSNILHENRNVGNNFQRNNSPNTSIKVGKNKQKRSR FT GDIGPSRIGPNNEKHNHIARSSGVYKGGYTATLIHEPQKSSCAEENGPTVK FT ACAKLDSSHSNSDIDINSKGGRNGNMSIVTNGDDSSQQHASIAATPREEIF FT LSHVVNKKKEDHDNISSMDGEDQNMGQAHDIQMHMI" FT CDS join(3129..4490,4494..6620,6624..7112) FT /product="SHALINE5_MT_2p" FT /translation="MWFSHARFLYPFIYSLMIIISWNCKGAQGLNFPKALN FT NFCRKNKVDVVALQETRCSGSVARKAIKKLGFKNHIVSEAQGFSGGIWLLW FT NRPDVEFEVIQNNFHFIHIKVKEKDVDPWLLTVVYASPRGNERDITWQQLR FT GIAANIQDLWLMMGDFNEIASLDEKKGGAQHDIRKCLNFSNWINECRLMEV FT TTTGTIFTWRGPKWNGRDRVFKKLGRVLCNVEWRLRYHEGFAKVLPRVQFD FT HHPIMVLMEGEPSNRGNRPFRFEAAWITHKDFHRFLREKWGRGSDLLHTIS FT NLTPQLKDWNHETFGNIFRRKNELLARLNGIQNSQNYGYSHFLEELEKDLQ FT EQLAVTLYQEECLWFQKSRSKWIADGDRNTKYYHAKTIIRRRKNKIMSLRD FT DSSDWVDEPDSLKNLVRSFYTNLFREDTPIRDNIVSWTTYPNVVEEQHERL FT SAIIQLNECRALFDMSPHKAPGEDGYPAVFFQQRWDTVVDSLFKFANQVWV FT NPSFISFINNTLLVMIPKLDKPEFVSQFKPISLCNGIYKIISKVIVNMIKP FT LLDRIISPYQSSFIPGRSIHHNIIMAKEMVHAMSKMKGQKGFMSIKIDLEK FT AYDRLNWNFVKNFLEECKFPPQIIQIIHHCISSPSYKIMWNGEKIDIFYPS FT RGIRQGDPLSPYLFVICMDKLSHIIADQVEANYWLPMRAGRYGPKISHLLF FT ADDLLLFAEASIEQSHCVLHCLDTFCQASGQKINRNKTHVYFSKNVDTQLR FT AEILQHTGFNQVNSLGRYLGANLATGRNSRGHFNHIVNKIQSKLSGWKHQC FT LSFAGRITLTKSVFNTIPYYHMQYAKIPKTICDEVDKIQHGFVWGDSDQGR FT KAHLISWDVCCLPKIDGGLGLRQARNMNEAFLMKILWNLINNPDKLWGKVL FT HSKYGRGKDLTANISVQPYDSPLWKALAGIWDDFKRHVVWKIGDGHSTNFW FT LDKWSPNNGSLLSISNQDYIDTTLTVRDVLTPSGDWDIDFLMNNLPDYTVS FT RVLALPAPTDKDGPDTIGWSGTNTHQFTVQSAYSLQHQNCPTVEGDWKILW FT KWHGPHCVQTFIWLAIHRRILTSLRRSRWGVGISPTCPCCGNDDETVLHVL FT RDCIHATQVWLHIVPSNVITNFFSFDCRDWFSNNLKRKMVGTSTCRWQTTF FT MTTCYLWKWRNKTIFEADFQRPNNPNILIQTFVRDIEDYNLELFHRGPKLT FT DTIYIGWKRPQEGWIKLNGDGACKDMGHISGCGGIFRDADGKWIKGYTKKI FT EACDALHAEMWGLYLGIEMAWREHFDHLIVESDSKILIDMISDEFKFNGNV FT PILVHRIRKLLRMD" XX SQ Sequence 7373 BP; 2299 A; 1211 C; 1575 G; 2288 T; 0 other; gggtgtaaat acagttgaaa acgagttact cgaatctttt taaagtttat tgagattcct 60 gaaagtcgtt gagtgttaga atcagtcaaa actcaatgga acttagcttg acaattgaac 120 aattaactca tgtttcatat taatttaggg ggtcatcgac agaggatgag aatcgcgtgg 180 gggtgccaac cttgtaggga tgtcagcgag tttccttgat gtctggacct cttgattcag 240 ctaaaaaaaa ctcgtgtttc atattatcag tgtcactaat catagtagct atgaacacta 300 gactgtctag agcgcattat gtgaaagttg cacacacatg gatagaagaa acaagaaatg 360 ccgcgaaaga gagaaaatca aatcaaatgt ggggaatcac atatttccaa caaagtgagg 420 attcacccac tatccgtgta atttttacag gccacattgt tttggttagt aggattagtg 480 tttgtctata aataccggac ttgtaaattt ttttaacata ggcaaccaat caaacaagtt 540 tttttgtcaa gtaatcttgc atctaaaatt catcttttaa gatagataaa taattttgcg 600 gctcaacaac ttctataatt tattctaaat cttattcatt ctcattttcc ttaactttta 660 aatttattgg acggcaaact agtaatataa gaattttttt ttgaaggagc aatataagaa 720 gaattatttc ttctctaata tatgagttga tgaaattaag atgaagatca taaatgtctt 780 tttcaccata cttgggtcac tgccacatat atagcgtgct gaatcactgt caattcaacc 840 gctataaagt gtcatgcgtt ggtgagagat gccatgtact aatccatctt ttaattctgg 900 aattaggtaa aaatcaattt tatacctaag aattttatca ttatttaata ttaagactta 960 agagctacaa ctgtattatt aaaaaaaaat tgtctaagag ctacttacta cttgacaaac 1020 actcaagttt ctatattaaa tgaaggaatt ttgttgcaat ataaaaagaa gcgtctgtaa 1080 aagatcctac cattaccata tctatcgaca atcaatgaaa cattattcaa tatttttgca 1140 ctttatgaga tagatggtac ctccacgatt aagtacaaaa gtttcaatat tctaaactga 1200 cttcaacggt gaatatcatg ttttttcctc cttaatccaa actataaaca aatgagaatt 1260 gtggtggtgg ggaatgttac gtttctctct ctcttttatt tttacggtct aaatcatata 1320 ttgattgtat caaatctcaa caaactcttt ggttaagaat acagttaaga ggatagtaaa 1380 gccaaagcaa taatagaaaa aaagtgctct gctagggttt cttagtatcc atgagtttca 1440 ctttcatgtc ttcacggcaa acaccagtta cgtcatcgaa acctcccgac ccacctgaca 1500 atggtggtga taagggaata ttcaatgcag aaaatagaga tgaaacaaat gggggaaaaa 1560 acccatgctc atgtccttcc gtgacaaggt tttggaatcg cagccttttg ttataaagga 1620 aaaagtggat ctggtggcaa acaagctagc acaagttgaa cacatcaaag gtataataga 1680 ttgatgccaa tgcttcatgt tcaagatagt gtgatggagg aattaagtgt gccatataaa 1740 ggatgtttgg cagtgaaact tcttgacaaa aagcttggtt acaatatgat gaagacaaag 1800 cttgaagccg tctggaagcc aaacaaagga tttgatctta tggaggtagg aaattctttc 1860 ttcatggtca aatttgacga tgaggaagac aaaaacaagg taattaatgg tggtccatgg 1920 atgatttttg atcattactt agccattcga caatggactc caacttttaa tgctgcaaca 1980 gccacgatcg ataaaactat ggcatgggtt cgaatcccga atttgaatct ggtttattat 2040 gatgagagtt tgttatgggc agtggcatca atggtgggaa caccagtgaa ggtcgacata 2100 catactttaa gagttgcgag gggaaagttt gcaagattat gcgttgaaat agatctcaca 2160 aaacctgttg taggaaaagt gggaatcaat ggagaatggt atcatgttca gtatgaaggt 2220 ttgcatgtta tttgcactca gtgtggttgt tatggtcatg ttttgaaaga ttgcagccac 2280 aatctcaaat ctacgacagt tacacctgaa tcgatggttg ctccggcgac cgccgggcct 2340 gaagttgaaa cagaaacggt tcacaacaaa aacggtaagg aaattaatgt cgcgagcaga 2400 atatcaggag taatcattga agagatttcg accaaagctg ttaatttaag cattaatggt 2460 gatccagaat ttttgcatgg tgattggata aaagtggaaa ggaaaaaaag aattaataag 2520 atgaatgtgc gtggacctgg tggggatgtg aaagcagaaa aattccaaaa tcttaagaac 2580 agaatcaaag aattgaatgc tgaaagttct aatattttgc atgaaaatag gaacgtcggc 2640 aacaatttcc agcgtaacaa ctctccaaat acaagcatta aagtggggaa aaataaacaa 2700 aagagatcta gaggtgacat tgggccaagt agaataggcc caaacaatga aaaacataat 2760 catattgcta gatcaagtgg tgtatacaaa ggagggtaca cggcaacttt aattcatgag 2820 ccacaaaaat ctagttgtgc tgaagaaaat ggacctacag tcaaagcttg tgcaaaattg 2880 gatagctccc attctaatag tgatatcgac atcaattcta agggaggtag aaatggcaac 2940 atgtccattg ttactaatgg agatgattct tcacaacaac atgcaagtat tgctgcaact 3000 cctcgtgagg aaatattttt gtcccatgtg gtgaataaaa agaaagaaga ccatgacaat 3060 attagtagca tggatgggga ggatcaaaac atgggacaag cccatgacat tcaaatgcat 3120 atgatctgat gtggttttca cacgcaaggt ttttgtatcc ttttatttat tctttaatga 3180 ttataatttc ttggaattgt aagggtgctc aaggattgaa tttccctaaa gcacttaata 3240 atttttgcag gaaaaacaaa gtggatgtgg tggctttgca agaaacccgg tgtagcggta 3300 gtgtagctcg taaggcaatc aaaaagcttg ggttcaagaa tcatattgtg tctgaagctc 3360 aaggtttctc aggaggtatt tggttacttt ggaataggcc agatgttgag tttgaggtaa 3420 ttcagaataa tttccatttt attcacatta aagttaagga aaaagacgtt gatccttggt 3480 tgcttactgt ggtttatgcg agccctcgtg gcaatgaaag agatataact tggcagcagt 3540 taaggggaat tgccgctaat attcaagatc tttggctgat gatgggggac ttcaatgaaa 3600 ttgctagtct tgatgagaaa aaaggtggag cacaacatga tattagaaaa tgcttaaatt 3660 tttccaattg gattaatgag tgcagattga tggaggtcac aactacggga actatattta 3720 cttggagagg tccaaagtgg aacgggcgtg atagagtttt caaaaaatta ggtcgtgttc 3780 tctgtaatgt tgagtggaga ttaagatatc atgagggttt tgctaaagtc cttccaaggg 3840 ttcaatttga tcaccatcct attatggtgc ttatggaggg ggagccttcc aataggggta 3900 atcgtccttt caggttcgag gcggcctgga tcactcataa ggattttcat agatttttgc 3960 gtgagaaatg ggggagaggc tccgacttgc ttcacactat ttctaacctt acccctcagt 4020 tgaaagattg gaaccatgaa acttttggga atatttttag aagaaagaat gagcttttgg 4080 ctaggttaaa tgggattcaa aacagtcaaa attatgggta tagtcatttc cttgaggaac 4140 ttgaaaagga tcttcaagag caacttgcgg ttacccttta ccaagaagaa tgtttgtggt 4200 ttcaaaagtc tcgtagcaag tggattgcag atggagatcg gaacacaaag tactatcatg 4260 ccaaaacaat cattagaagg cgtaaaaata aaattatgtc tcttcgagat gactctagtg 4320 attgggttga tgaaccagat agtttgaaaa atcttgttcg aagtttctat acaaacttgt 4380 tcagagaaga tactcctatt cgtgataata tcgtttcttg gaccacatat ccgaatgttg 4440 tggaggaaca acacgaaaga cttagtgcta ttatccaact aaatgagtgc taaagagctt 4500 tatttgacat gagccctcat aaggctcctg gagaggatgg ctaccctgct gtcttttttc 4560 agcaacgttg ggacaccgtt gttgattccc tttttaaatt tgccaaccag gtttgggtaa 4620 atccttcttt tatctctttt attaataata ctttgcttgt tatgattcca aaattagata 4680 aacctgaatt tgtttcacaa tttaagccta tttccctttg taatggtata tataaaataa 4740 tttctaaggt cattgttaac atgattaagc ctttgcttga tagaattatt tctccatacc 4800 agtctagttt tattccaggt cgaagcattc accacaatat tattatggct aaagagatgg 4860 tgcacgccat gtctaaaatg aaagggcaaa agggcttcat gtctatcaaa attgatttgg 4920 aaaaagctta tgatcgtctt aactggaact ttgtgaagaa ttttttggag gagtgtaaat 4980 ttcctccaca aatcatccaa atcattcatc attgcatttc ctctccgtcg tacaaaataa 5040 tgtggaacgg tgaaaaaatt gatatttttt atccttctag aggaattagg caaggggacc 5100 ctctttcccc ttatcttttt gttatttgta tggataaatt gtctcacatt atagctgatc 5160 aggttgaagc taattactgg cttcctatgc gcgcaggtag gtatggtcct aaaatctctc 5220 atttactttt tgctgatgat cttcttcttt ttgcagaagc ttctattgaa cagtcccatt 5280 gcgtcttaca ctgcctggat actttttgtc aagcttctgg tcaaaagatt aataggaata 5340 aaacccatgt gtatttttcc aaaaatgttg atacccaact tcgcgctgaa attttacaac 5400 acacgggttt taatcaggta aatagtttag gtaggtacct tggagctaac cttgctacag 5460 ggaggaattc cagaggacat tttaatcata ttgttaacaa aattcagagt aagttgagtg 5520 gctggaaaca tcaatgttta agttttgcag gtaggatcac tctcactaag tctgtcttta 5580 acacaattcc ttactaccat atgcaatatg ctaagatccc taagaccatt tgtgacgagg 5640 ttgataaaat tcagcatggt ttcgtgtggg gtgattctga tcagggtagg aaagctcatc 5700 tgattagctg ggatgtttgt tgtctgccta aaattgatgg aggtcttgga cttcgacaag 5760 ctcgtaatat gaatgaggct tttctcatga agattttatg gaacctgatt aacaatccgg 5820 acaaactttg gggtaaagtc cttcatagca aatacggacg tgggaaagat ctcactgcca 5880 atattagtgt gcagccttat gattcacccc tttggaaagc tttagcaggc atctgggatg 5940 attttaagcg tcatgtggtt tggaaaattg gagatggtca tagtactaac ttttggttag 6000 ataaatggtc tcctaataat ggatcacttc tatccataag caatcaggac tacatagata 6060 ctactcttac tgttagagat gttcttactc cttcaggcga ttgggatatt gattttctta 6120 tgaacaactt gccagattac actgttagta gggttcttgc tctcccggct cctacagata 6180 aggatggtcc tgatactatt gggtggagtg gaaccaatac ccaccagttc acagttcaaa 6240 gtgcttattc tctgcagcat caaaattgtc caacggtgga gggggactgg aagattcttt 6300 ggaagtggca cggcccacat tgcgttcaaa cttttatttg gttggctatt cataggcgaa 6360 tccttactag tttgcgaaga agtagatggg gtgttgggat ttctcctact tgcccatgtt 6420 gtgggaatga tgatgaaact gtccttcatg tgcttcgtga ttgcattcat gcaactcagg 6480 tatggcttca tattgttcct tccaacgtta taactaactt cttttccttt gattgtaggg 6540 attggttttc caataacctt aagagaaaaa tggttgggac aagcacatgt agatggcaga 6600 ccacctttat gactacgtgt tgatatttgt ggaaatggag gaacaagact atctttgaag 6660 cggatttcca aaggccgaat aatccaaata tactaatcca aacattcgtt agagatattg 6720 aagactacaa cttggagctc tttcatagag ggcctaagtt gacggacact atctacatag 6780 gatggaaacg acctcaggaa ggttggatca agctcaacgg cgacggtgcc tgcaaggata 6840 tgggtcatat ttccggttgt ggtggtattt ttcgtgatgc agatggtaaa tggattaaag 6900 gctacactaa gaagattgaa gcttgtgatg ccttacatgc tgagatgtgg gggttgtatt 6960 tgggtataga gatggcttgg agggagcatt ttgatcatct tattgtggaa agtgactcga 7020 agatattgat cgacatgatt tctgacgagt tcaagtttaa tgggaatgtg cctattttag 7080 ttcatcgtat caggaagctg ctgagaatgg attagcatgt gcaaatcaac catacttggc 7140 gtgaaggaaa tagaagtgcc gattggcttg ctaattttag catttctgtg aatcatttga 7200 atttgattat ttcggagact cctcctattg agcttcgaaa gctcatgttt gatgatattt 7260 cccgggcttg catgcctagg aatgtccggt taatttcgca gtttcttttc ttttgggctt 7320 tgccctctat tgtaccaaaa aaaaaataaa aaatctcaac aaataatgaa aaa 7373 // ID TTO1_NT_I repbase; DNA; EDCOT; 4153 BP. XX AC D83003; XX DT 04-MAR-1998 (Rel. 3.02, Created) DT 08-AUG-2007 (Rel. 12.07, Last updated, Version 3) XX DE Tobacco DNA, retrotransposon Tto1 sequence encoding an ORF DE (1338AA), complete cds. XX KW Copia; LTR Retrotransposon; Transposable Element; TOBAA; TTO1_NT; KW TTO1_NT_I; TTO1_NT_LTR; Tto1; retrotransposon; internal portion. XX NM TTO1_NT. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RP 1-4153 RA Hirochika H., Otsuki H., Yoshikawa M., Otsuki Y., Sugimoto K. RA and Takeda S.; RT "Autonomous transposition of the tobacco retrotransposon Tto1 in RT rice."; RL Plant Cell 8(4), 725-734 (1996). XX RN [2] RP 1-4153 RA Hirochika H., Otsuki H., Yoshikawa M., Otsuki Y. and Takeda S.; RT "Autonomous Transposition of the Tobacco Retrotransposon Tto1 in RT Rice."; RL Unpublished (1996). XX RN [3] RP 1-4153 RA Hirochika H.; RT "Direct submission."; RL Direct Submission to EMBL/GenBank/DDBJ (10-JAN-1996). Hirohiko RL Hirochika, National Institute of Agrobiological Resources, RL Molecular Biology; 2-1-2 Kannondai, Tsukuba, Ibaraki 305, Japan RL (E-mail:hirohiko@abr.affrc.go.jp, Tel:0298-38-7006, RL Fax:0298-38-7408). XX DR GenBank; D83003; Positions 575 4726. XX SQ Sequence 4153 BP; 1297 A; 770 C; 1051 G; 1035 T; 0 other; agtggtatca gagctttggt tagagtacta ttcatacgta cgagtactat tcatccatac 60 gggcactatt catatccacg gttactattc accgtcggat ttttttttta gattgcaaaa 120 gtctgtcaaa ttctgatcta aatggaggcg aggacaagca agatggtcaa cctgaatggc 180 acaaattatc acttatggag aaacaagatg aaggatctcc tgttcgtgac aaagatgcac 240 ctgccggtgt tcagttctca gaaacctgaa gataagtcag acgaggactg ggaatttgag 300 cacaaccaag tgtgcggcta catacggcaa tttgttgaag acaatgtgta caaccacatt 360 tctggtgtga cacatgcaag gtcgttatgg gacaagctcg aagagttgta tgcctctaaa 420 acaggtaaca acaaattatt ttacttgaca aaattaatgc aagtaaaata tgtagaaggg 480 acaactgtgg cagatcacct taatgaaata caagggattg tcgaccagtt gtcgggaatg 540 ggcataaagt tcgatgacga ggtacttgct cttatggtgc tggcaacact cccagagtca 600 tgggaaacct tgaaggtttc aatcaccaat tctgcaccca acggtgtggt aaacatggag 660 acagtcaaga gtggcattct gaatgaagaa atgagacgcc gatcacaagg aacatcttct 720 tcacagtcag aggtgttggc tgttacgacc agggggagaa gtcaaaataa gagccagagt 780 aacagagata agagcagagg taaatccaac aaatttgcaa atgttgagtg ccattactgc 840 aaaaagaagg ggcatatcaa aagattttgc cgacagttcc agaatgacca gaagaagaac 900 aaaggcaaaa aggtgaagcc cgaagaaagc agtgatgatg aaacgaactc ctttggtgag 960 ttcaacgttg tctacgatga cgacattatc aatctgacaa cccaagagat gacctgggtg 1020 attgatagtg gggctaccat tcatgcgacg ccacggagag aactcttctc atcttacaca 1080 cttggagact ttggtcgtgt aaagatggga aatgccaatt tctcaacagt tgtaggcaaa 1140 ggtgatgttt gcctagagac catgaatggg atgaagctac ttttaagaga tgtcaggcat 1200 gttccagata tgcgcctgaa tctgatctcc gtagacaagc tcgatgagga aggttactgc 1260 aataccttcc ataatggcca atggaagctc acgaagggct cattgatggt ggcgcggggc 1320 acgaagcagt caaagttgta cgtgacccag gcgagcatct cccaacaagt tataaatgtt 1380 gcggagaatg atagcaatat caagttgtgg catagacgtc ttggccacat gagtgagaag 1440 tcaatggcgc gtttggtaaa gaagaacgcc ttaccaggtc taaaccagat ccagttgaag 1500 aagtgtgctg actgtttagc tgggaaacaa aacagagttt cgttcaaaag attccctcct 1560 tccagaaggc aaaatgtgtt ggatctggta cactcagatg tatgtgggcc tttcaagaag 1620 tccctcggtg gtgcccgata tttcgtgacc tttattgatg atcattcacg aaagacatgg 1680 gtatacacgc tgaagaccaa ggatcaagtg tttcaagttt tcaaacagtt tctgaccttg 1740 gtggaaagag agactggtaa gaagttgaag tgcatccgga cagacaatgg cggtgaatac 1800 cagggtcaat ttgatgctta ctgtaaagag catggtattc gacatcagtt cacacctcct 1860 aaaactcccc agttgaatgg cttggctgag aggatgaaca gaactttgat cgagagaacc 1920 agatgtttac tctctcattc aaagttacca aaggctttct ggggtgaagc tctagttaca 1980 gcagcctatg tgctgaacca ttcaccctgt gtccctcttc agtacaaggc tccagaaaag 2040 atttggttag gaagagatat ctcttatgat caattacggg tatttggctg caaagcctat 2100 gtccatgttc cgaaagatga aaggagcaaa cttgatgtca agacaaggga gtgtgtattc 2160 atcggctatg gtcaagacat gcttggctat aagttctatg atccggtgga aaagaagctc 2220 gtcaggagtc gagatgtcgt gttcgttgag gaccaaacaa ttgaagacat tgacaaagta 2280 gagaagtcca ctgatgattc tgctgagttt gagttgcctc caacagtggt gccgagacaa 2340 gttggagatg atgttcagga taatcaacct gaagcccctg gtcttcctaa tgaagatgaa 2400 ctagcagata ctgaaggtaa cgaggacaat ggtgatgatg atgcagacga ggaggatcaa 2460 cctcaaccac caatcctcaa taaccctcct tatcacacaa gatctggaag agttgtgcaa 2520 cagtctacca gatattctcc acatgagtat gtgttactca ctgacggggg agaacccgac 2580 agctttgaag aagctattga tgatgaacat aaggagaagt ggatagaagc catgcaagac 2640 gagataaaat ccttgcatga gaacaagacg tttgagctgg tgaagttgcc gaaaggcaag 2700 agagctttga agaataagtg ggtgttcaag atgaagcatg atgaacacaa ttcccttccg 2760 agattcaaag caagattggt cgtcaaaggt ttcaatcaaa ggaaaggcat tgactttgat 2820 gaaatattct caccagttgt gaaaatgacc tcaatacgca cggtgctggg attagcagca 2880 agcctcaacc tggaggttga acagatggat gtaaaaactg ccttcctaca tggtgatttg 2940 gaagaggaga tatacatgga gcaaccagac ggtttccagc aaaaggggaa agaggactac 3000 gtttgtagat tgaggaaaag cctctatggc ttaaaacagg caccaaggca gtggtacaag 3060 aagttcgagt cggtgatggg gcaacacggc tacaagaaga caacttcaga ccattgtgtg 3120 ttcgctcaga agttttctga cgatgatttc atcatcctat tgctctatgt agatgatatg 3180 ttgattgttg gccggaatgt ttccagaatt aatagcttaa aagaacagct aagcaagttc 3240 ttcgccatga aagacttggg gccagcaaaa cagatccttg ggatgaggat tatgcgagac 3300 cgagaagcca agaagttatg gttgtctcag gagaagtaca tcgagaaggt acttcaacgg 3360 ttcaacatgg agaaaactaa agcagttagc tgtcctcttg ctaaccactt tagattgagc 3420 accaagcaaa gcccgtcaac agatgatgag agaagaaaga tggagcggat tccatatgct 3480 tcagcagtag gaagtttgat gtatgccatg gtttgtacac ggccagatat cgctcacgct 3540 gtaggagtgg taagtagatt tctttctaat ccaggtaagg aacattggga tgctgttaag 3600 tggattctca ggtatcttcg aggaacctcc aaactatgct tatgttttgg agaagacaac 3660 cctgtgttgg ttggctatac tgatgcagat atggccggag atgttgattc tagaaaatca 3720 acttcaggat acttgattaa cttttcaggg ggagctgtgt catggcaatc aaagttgcaa 3780 aaatgtgttg cattatcaac tactgaagct gaattcatcg cagcaacgga ggcttgcaaa 3840 gaattgatat ggatgaagaa gttcttaact gaacttggat tttcgcaaga cggttatcag 3900 ttattttgtg atagtcaaag tgctatccac cttgcgaaga atgcctcatt ccattccaga 3960 tccaaacata ttgatgtgag atataattgg atcagggatg tgttggagaa gaagatgttg 4020 cggcttgaaa agatccatac agacgaaaat ggatcggaca tgttgaccaa gactttaccg 4080 aaagggaagt ttgagttctg tagagaagct gcagggatag tggatccacc atatagttgg 4140 aagggggaga att 4153 // ID MuDR-13_VV repbase; DNA; EDCOT; 9685 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-13_VV, an autonomous DNA transposon - a consensus sequence. DE Partial sequence. XX KW MuDR; DNA transposon; Transposable Element; mutator; Mutavine-13; KW MuDR-13_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-9685 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 772-772 (2008). XX DR [1] (Consensus) XX CC MuDR-13_VV (Mutavine-13 in [1]) consensus is an autonomous CC element. Its individual copies are >90% identical to the CC consensus sequence. Elements from this family have an unusual 3' CC ending, consisting of tandem repeated blocks of sequences (>3kb CC in total). Although several copies seem to be present in the CC genome, all shotgun sequences available so far physically stop in CC this region, possibly due to assembly limitations of such CC repeated regions. Therefore the true 3' border of the element is CC not known. XX FH Key Location/Qualifiers FT CDS join(2360..2706,2802..4611) FT /product="MuDR-13_VV_Transposase" FT /note="MUDRA transposase." FT /translation="MDPSNTIYCYLHIGGELVRDEHGNVEYMGGRREGLSL FT ERSMTYNDFVSRICGKMNINIVGPTFSYTLPFDLYALQPLKNDEDLTNMFQ FT FSDRXARVYICLASTVEDDETIENGGQGLNETIVGSNSPVPYSTRDVDIRM FT QSRGFHQRCAESHVGPLESSRFESAILGSGHTFSTANEFRDAIYLMSVGGR FT FRYKFKRNCLKHMTVICVVEGCPWKVTARAVGRTKIVQVHTFRNEHNHSLE FT DVSISEPAVRCNRATTMIDDVIRSNPDYLPRQICKDFRRQYGMQLNYCQAW FT NLKEKAKERIHGVPQCSYKLLPWLCTRLIETNPGTIAEYRCSDDGHFMQLF FT VALSVSIHGFQMGCRPIISIDSSHMSGPYKGALFSASSYDADDGMFPLAYG FT LFSSENYEDWLWFLEKLKMVIGERDVIIISDRHQGIIRSVSEVFGSENHAH FT CYRHIKENFSSFLTKLNTKGRKGKENALQMLDSIAYARLDCDYEVAMDTLR FT TFNHDLAKWVEENNPQHWAISKFKKMRWDKMTSNLAESFNSWLRHERHHNI FT CVFFIEHMDKLGSLLVEHKNGLVKWNGCIGPKTEENIALNIGKGENYITYL FT HLGSSMKVSNGKAFLEVDLMERTCTCKAWQMSGIPCDHACAAIRRMGFDVS FT DYVDDWYKYNLQEKIYSGSMRTLVTHDMPMIDEDGTVRDALGHTYPFLNPP FT TTKRPPGRPRKRRIESQFM" XX SQ Sequence 9685 BP; 2998 A; 1423 C; 2095 G; 3070 T; 99 other; ggggaattta tgtaaccata caccaagggg caaaattttg ccttttggaa acttaacttt 60 ttacttttca aattcaatgg attttgtgaa aaataaayma yctttcatac actgtaatag 120 tgatattgag acccttccaa aaataccctc ctataatttg acatctctcc tagttggata 180 agttgcttgt tgtccactta agccaatgac atgactcagt tacatgtcat cagccascta 240 gacattccac atggattgat gttttaaaca atatttaccc ccaaatatct tcttctttct 300 tcaaccaaac cctaacacca aaaacccatg ttctttcttm ttcgttcaca ggcacaaccc 360 atcacaaggc gaaaggatcc ataaaaaatc tggtaggttc tcaaatcgcg ataacccatc 420 aaccccaaac gaacctccaa acttgatctc ttattttgtt tctcctccat caccataagg 480 aagacgacat cttcattttc ccaccaaaca tcaatctgaa aacaaaagtc caagtgcgaa 540 ccccttaaca aaggccaggt agacaaaaaa aaaaacccat ttccttcttc ttatttcagg 600 agtgacagtc atttttctcc tggttgtact tcctattttg cttttacatc gaaaaaggag 660 aaakaaagma attgagagaa cgagataacg aagaataaaa atattgtagt tgcatttaac 720 ttttaaagca agggtttttc caggtatata gatatatata tatgttatta aattttgtaa 780 taactttata ttttgatttg tcattttgat tctttgagat ttgaataatg tcatagttat 840 gtgatttgtg caattttgtg atttaaactt gattacattg catatttcta catgttcaat 900 gtccattaat attgtatcta aatttatatt ttaatttatt tagggtttat ttgaaatgaa 960 atatggctta aattttgata aatgatggga aaatgagatg gtggtaagct atattgattt 1020 tgttttattt ctgaattgtt gtgtttgtgt tgtatgtggt tgttgggaag aatacggaaa 1080 agagaagaaa aatatgagta ttgcatgtga agggaataca atttttagga atgttcaaac 1140 aatttgttgt ttaatgttgt ttatatggga ttcgagatgt tttgttgttt aatgttgttt 1200 atctgggatt ccaaaatgag taatttgagt gatcytttat agttgttmat tggtgaatct 1260 aatgcatggg aaaagaattc atgtttagtc atgagtagat gagtataaat tttaaaaatg 1320 attgggatta aagtttgaat aaatttctta ataaaagttt tgaatttgta atgaataagg 1380 attgaattga agaagaaaat aaaacaaatt tagtaaagcg ggcatgaatt tatgtgggaa 1440 ttagggaaaa tagtattgga gccttaggtt caaaattgat ggtcacaacc acaaatatga 1500 aatttgtttt gtttatgtgt gtagtagtca tagtaagggt ctacccttag atgaaggggt 1560 tggccgtaat ccagttaatg acatttggat gaaattattg ttttcgtaag aggttgcagt 1620 aagtgaatta aargctgacc catttgtttg gaggtagrcc cttagttgta aatattgttg 1680 tggtttaatc tggatagtag gcaaaataaa ggctgaccca tttgtttgga ggtcggccct 1740 tggttgtaaa cattgttgtg gtttaatttg ggcagtgggc aaaataaagg ttgacccatt 1800 tttttggagg tcggcccttg gttgtaaaca ttattgtggt ttaagttggg cagtaggcaa 1860 aataagggct grcccaattg tttggaggtc ggcccttggt tgtaacattg ttatggttaa 1920 atttgggcag tgggcaaaat aaaggtygac ccattgtttg agggggtggc ccgaagagag 1980 tgaaattagc acaatttggc ttgaagagtt accaaaacaa tggttagccc atgaattgag 2040 aggttcactc cctaacttat ataacataac aaattactac gaagtaaaat agaataattg 2100 cattgcttaa tgttaagtat acactatgca tgtctatatt tacaccatta attgtaaact 2160 atgaaatgta aatgaagctc gtttgtaaag tttcaaagat aaatgatgta ttaatatatg 2220 atggtcatag gcatgataat cagttttgtt ataagtaagt tggtttatgc agtgttatta 2280 agaaattagt taattgtttc agcttgacta aaggttcatg cttctaaaca ggggctgcac 2340 atgatcgagt agcatttaaa tggatccaag taatacaatt tattgttatc tgcacattgg 2400 aggagagcta gtaagggatg aacatggcaa tgtggaatat atgggtggga gacgagaggg 2460 tctaagttta gaacgatcaa tgacatataa tgattttgtt tcaaggattt gtgggaaaat 2520 gaacatcaat atagtgggac caacattttc atatactctc ccgtttgatt tatatgcact 2580 tcaaccattg aaaaatgatg aagacttgac aaacatgttt caatttagtg accgatbtgc 2640 acgtgtatat atatgtttag catcaacagt tgaagacgat gaaacgattg agaatggagg 2700 acaagggtaa gttatatcaa aaaaatatct aatcttaaat gattccatgt atttatttat 2760 tttttaatat ttatgtttat tcattagatg ttataatgca gcttgaacga aacaatcgta 2820 gggtctaact caccggtccc atattcaaca agagatgttg atattagaat gcaatcacga 2880 ggatttcatc aaagatgtgc tgaatcacat gttggtccac tagagtcaag tcgttttgag 2940 agtgcaatat tgggtagtgg gcataccttc tcaactgcaa atgaatttcg ggatgcaata 3000 tatctcatgt cagtaggagg ccgttttaga tataagttta agaggaattg tcttaagcat 3060 atgactgtaa tatgtgttgt tgaaggatgc ccttggaaag taactgctcg tgctgttggg 3120 agaacaaaaa tagttcaagt gcatacattt agaaatgaac ataaccactc tttagaagat 3180 gtgtcaattt ccgaaccagc agttcgttgt aatcgagcca caactatgat tgatgatgtt 3240 attcgttcaa atccagatta cttaccccgt caaatatgta aagactttcg tcgacaatac 3300 ggaatgcaat tgaattattg tcaagcatgg aacttgaaag agaaggctaa agaacgaatt 3360 catggtgtgc cccaatgttc atataagttg ttaccttggt tatgtacaag gcttattgaa 3420 acaaatccag ggacgattgc tgaatataga tgttcggatg atggtcattt tatgcaattg 3480 tttgttgccc tttcagtgtc aatacatggg tttcaaatgg gatgtcggcc tattatatca 3540 atagattcat cccacatgag tgggccatac aagggtgctt tattttcagc ttcttcctat 3600 gatgctgacg atggcatgtt tccacttgct tatggcttat ttagctctga gaattacgag 3660 gattggcttt ggttcttaga gaaattgaag atggtcatag gtgaaagaga tgttataata 3720 atatctgata ggcaccaagg gattatccgt agtgtttcag aggtatttgg tagtgaaaac 3780 catgcacatt gctatcgtca cattaaagaa aacttcagta gctttctaac aaagctgaac 3840 actaaaggga ggaaagggaa ggaaaatgct ttgcaaatgc ttgattctat cgcctatgct 3900 aggttagatt gtgattatga ggttgcaatg gatactttaa ggacatttaa tcatgatttg 3960 gcgaagtggg ttgaagaaaa taaccctcaa cattgggcaa tctctaaatt taagaagatg 4020 cgttgggata agatgacaag taatttggcc gagtctttca attcttggtt aagacatgaa 4080 cgacaccata acatttgtgt tttcttcatc gagcatatgg ataagttagg atctctttta 4140 gtcgagcaca aaaatggact tgtaaaatgg aatgggtgta ttggtcctaa aacagaagaa 4200 aatattgcat tgaacattgg aaaaggtgaa aattatatca cttatttaca cttgggtagt 4260 tcgatgaaag tatccaatgg aaaagcattc ctggaagtgg acttaatgga gcgaacttgc 4320 acatgtaaag catggcaaat gtctggaatc ccatgtgatc atgcttgtgc agctatacgg 4380 cgaatggggt ttgatgtatc tgattatgtt gatgactggt ataagtacaa tttgcaagag 4440 aagatatact ctggaagcat gcgtactttg gtaacgcatg acatgccaat gattgatgaa 4500 gatggaaccg ttcgtgatgc cttgggtcat acttatccct ttcttaatcc tccaaccaca 4560 aagcgacctc ctggaagacc taggaaacgt cgaatcgagt ctcaattcat gtaaaaaaaa 4620 aacagttcat tgttctcgtt gtaatcagcc tgggcataat cgtgcgacat gtaacaaccc 4680 attgytgtaa ggtttttttt ttattaaact tcataatgta agatcgactt tatattagta 4740 tgaaatagtt tgstaatctt cgttrttgtt tccttgatta taagcaatga gtaatttatt 4800 ggatttgaag tgtttggtgt acatatattg tgattgtatg ttgttcttca atattatggg 4860 atatgttaca tgataatgwa attgtaatag caaaatatgt accttggtca ttattgttca 4920 aagatggcat tgaagtgaca tagattcata tggygtcctt ggcaaaaaaa acgagattgt 4980 taactagtgg gcataatcgt ggcsaacctt tacatgtagg ggttgctgct ttttggctga 5040 tgacccttaa gcatattatt tagttttgtg tgaaatgggc artagccaaa ataaggttgt 5100 gcctgttaga tcataggcaa ccctatcgtt tttcatcttt aaaattggtt tcgtgttatg 5160 tgaggtgtct gtaaaaggga ggttgaacca ttaacaccat gggaaggcat tcraacatta 5220 gtttagtatg ttatgtgcag aaggcaatct aggggcgcac cttccatttg aaaggcatgc 5280 ctatgtgtta atgatattat ataactatac tacatgcaga aggcaaagca ggggtgcacc 5340 cttggttgca taggtatgcc catgggtatg ataactttat tgggaaattc tatatgcagt 5400 atgcaaagta ggggcacacc cttgatttta ggggcatgcc tattgctaaa accattatat 5460 tggtagrcta tgtgcagtag tcaacctaag agcaaaagct tkatggaaga cacataaatg 5520 tgggtgaaaa acttcttttt gttaagctac ttgcagtagg aaaaagaaag acatgactct 5580 ctgtcagagg catgccttta ggatgactag agttgaggtg tgggttgggc agtaaggcaa 5640 atggaggcat aytgatagct taaaaggttg gcccttgatg ttcatatgaa ataaacgttg 5700 gaaatgattc cttgttgatt caaaatcata gattttttct aatatttaaa aaaaatttaa 5760 ttgttcaatt tttaatttat tttttattat cttaattttt tttaactact ttttttattt 5820 agctcattaa taattttttt tatttatccg tttactttta tttaatttca aaattttgta 5880 tttttaaata ttacaaaaat agttgtgctt agaatatgtt acaatataac aaaaaaatat 5940 aatgaagtcc waatatttta taactaaaaa ttaatttgat tagataaatg attaataatt 6000 ttaattattt aaataaatta attttaatag aaaaattgcc acmacatatt tgtaataaat 6060 ttttagaaat catatctcaa atcaaatatt tgatataaat caatttagtt tttatttaaa 6120 atttaataaa atatrtttta ataaamgtat ttttttaatt ttaaaataaa taacttaaat 6180 atattaaatg taattatgac ccatccatgc tcagatgggg gtcccggaat cactagactt 6240 ggatgtacca aatttaatga aggatgtayc aaatttaaty aaggatgtac caaattttgt 6300 taaagatgta ccaagggctc caaagtgtga tccgaagtrg ggatcggctc caaatcactc 6360 tgttatgggt ttctaaataa aatagtggct catccatggt cagaaggggg tcccggaatc 6420 actaggctcg gatgtaccaa atttaatgaa rgatgtacca aattttgtga aggatgtacc 6480 aagggttcga aaatgcgttt ccgaagtrgg gatcgacccc caatcacttt kttatgggtt 6540 tcttaaagaa attacagacc atccatgttg aaatgggggt ctcggaatct gtcggatcgg 6600 atgtaccaaa tttaatgawg gatgtaccaa attttgtgaa gratgtacca aattttgtga 6660 atgatgtacc aagggtccaa aaatgctttc cgaartgggg atcggmccca aatmamwttg 6720 ttwtgggytt ttaaatgaaa tagtggctca tccacggtca gaagagggtc ccrgaatcac 6780 taggatcrga tgtaccaaat tttgtgaarg atgwamcaak ggtycgaaaa tgcrtwcyra 6840 agtggrgatc gacccccaat cactttgtta tgggtttcyw aawsaaatta tggaccggac 6900 catccatgtt gaaatggggg tctcggaatc trtcggwtyg gatgtacmaa atttaatraa 6960 ggatgtacmm aattttgtga aggatgtacc aaattttgtg aatgatgtac caagggtcca 7020 aaaatgcttt ccgaagtggg gatcggcccc aaatcacttt gttatgggtt tttaaatgaa 7080 atwgtggctc atccayggtc agaagagggt cccggaatca ctaggatcgg atgtaccaaa 7140 tttaatggga tgtaccaaat tttgtgaagg atgtaccaag ggtccgaaaa tgcgttccga 7200 agtggggatc gacccccaat cactttgtta tgggtttcct aaagaaatta tggaccwtcc 7260 atgttgaaat gggggtctcg gaatctgtcg gatcggatgt accaaattta atgaaggatg 7320 taccaaattt tgtgaaggat gtaccaaatt ttgtgaatga tgtaccaagg gtccraaaat 7380 gcktttcgaa gtggggatcg acccccaatc actttgttat gggtttctaa atgaaattat 7440 gcagaccatc catgttgaaa tgkgggtctc ggaatctgtc ggatcggatg taccaaattt 7500 aatgaaggat gtaccaaatt ttgtgaagga tgtaccaaat tttgtgaatg atgtaccaag 7560 ggtccaaaaa tgctttccga agtggggatc ggccccaaat cactttgttt tgggttttta 7620 aatgaaatag tggctcatcc acggtcagaa gagggtcccg gaatcactag gatcggatgt 7680 accaaatttt gtgaaggatg taccaagggt csgaaaatgc ktttcgaagt ggggatcgac 7740 cccmaatcac tttgttatgg gtttctaaat gaaattatgg accatccatg ttgaaatgkg 7800 ggtctcggaa tctgtcggat cggatgtacc aaatttaatg aagratgtac caaattttgt 7860 gaaggatgta ccaaattttg tgaaggatgt accaaatttt gtgaatgatg taccaagggt 7920 ccaaaaatgc tttycgaagt ggggatcggc cycaaatmac tttgttwtgg gtttttaaat 7980 gaaatagtgg cycatccayg gtcagaagag ggtcccggaa tcactaggat cggatgtacc 8040 aaattttgtg aaggatgtac caagggtccg aaaatgcgtt ccgaagtggg gatcgacccc 8100 caatcacttt gttatgggtt tcctaaagaa attatggacc ttccatgttg aaatgggggt 8160 ctcggaatct gtcggatcgg atgtaccaaa tttaatgaag gatgtaccaa attttgtgaa 8220 ggatgtacca aattttgtgt aaatgatgta ccaagggtcc aaaaatgctt ttcgaagtgg 8280 ggatcgaccc ccaatcactt tgttatgggt ttctaaatga aattatggac catccatgtt 8340 gaaatgtggg tctcggaatc tgtcggatcg gatgtaccaa atttaatgaa ggatgtacca 8400 aattttgtga aggatgtacc aaattttgtg aatgatgtac caagggtcca aaaatgcttt 8460 ycgaagtggg gatcggcccc aaatcacttt gttatgggtt tttaaatgaa atagtggcyc 8520 atccayggtc agaagagggt cccggaatca ctaggatcgg atgtaccaaa ttttgtgaag 8580 gatgtaccaa gggtccgraa aatgcgttcy gaagtgggga tcgaccccca atcactttgt 8640 tatgggtttc taaatgaaat tatggaccat ccatgttgaa atgggggtct cggaatctgt 8700 cggatcggat gtaccaaatt taatgaagga tgtaccaaat tttgtgaagg atgtaccaaa 8760 ttttgtgaat gatgtaccaa gggtccaaaa atgctttycg aagtggggat cgggcccaaa 8820 tcactttgtt atgggttttt aaatgaaata gtggctatcc atggtcagaa gagggtcccg 8880 gaatcactag gatcggatgc accaaatttt gtgaaggatg taccacgggt ccgaaaatgc 8940 gttccgaagt gggaatcgac ccccaatcac tctgttatgg gtttctaaat gaaattatgg 9000 acgacccatg ttgaaatggg ggtctcggaa tctgtcggat cggatgtacc aaatttaata 9060 aagaatgtac caaattttgt gaaggatgta ccaaattttg tgaatgatgt accaatggtc 9120 caaaaatgct cttcgaagtg gggatcgacc cccaatcact ttgttatggg tttctaaatg 9180 aaattatgga ccatccatgt tgaaatgkgg gtctcggaat ctgtcggatc ggatgtacca 9240 aatttaatga aggatgtacc aaattttgtg aaggatgtac caaattttgt gaatgatgta 9300 ccaagggtcy aaaaatgmtt tccgaagcag ggatcagccc caaatcactt tgttatgggt 9360 ttttaaatga aatagtggct catccatggt caraagaggg tcccggaatc actaggatcg 9420 gatgtaccaa attttgtgaa ggggatcgac ccccaatcac tttgttatgg gtttttaaat 9480 gaaattatgg accatccatg ttgaaatgtg ggtctcggaa tctgtcggat cagatgtrmy 9540 argttcatga aggatgtacc aaattttgtg aatgatgtas caagggtacc aaaaatgctt 9600 tccgaaggtg gggatcggct ccaaatcact tttggttttt tgggttttta aatgaaatag 9660 tggctcatcc acggtcagaa gaggg 9685 // ID Gypsy20-PTR_I repbase; DNA; EDCOT; 4441 BP. XX AC scaffold_942; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy20-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4441 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4441 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 320-320 (2007). XX DR Genome; scaffold_942; Positions 8530 12970. XX CC Positions [3329-3622] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 26..3622 FT /product="Gypsy20-PTR_I_1p" FT /translation="MDTRGKNNAEFRAEITEALGRHDANFDELNQNFNRVN FT NALQGVMAELQAMRIAQTHRSSEREVNPFAGGSSSHDRSSSSHTSTFDRGH FT SNLKLNFPTYAGEGEDPTGWIFKAEQYFEFQNVDAPRQVQLASFHLTSVEL FT QWYRWYTKGKGQLRWHEFVQALLHRFGPTDYDDPSEALSRLKQVTTVNAYQ FT EAFEKLSHKVDELPETFLVGCFIAGLKDEIRLDVRVKQPKTLSECISVAHL FT IEERNQFQRRTNNTFRTTTTSGQVRQQTSTMGLLGPAPSQRPPQVSHFPGG FT PARRLTGQEARERREKGLCFYCDEKYVQGHRCSRPQLFMMVDVQSQGDEDE FT VDMDIEPDEEALPEISFHALVGTSHPRTFRVTGRIGHKELIVLIDGGSTHN FT FIDQSVVIKLGLHVVKGKTFKVTVGNKEVIECTGRCFGLSLSLQGITIRAD FT FFVLPVAACQVVLGVQWLETLGPIKTDYKKLRMSFKQSGRTHVLHGITGSE FT LALLSEKELLHLSGMGFFVHMVSEVQSSQDTPLPPDLEQILSQYSHIFDEP FT TNLPPTRSHDHRIPLLPNQPPVNTRPYRYPHYQKNEIEKLVKEFLQSGIIR FT PSRSPFSSPVLLIKKSDGSWRFCVDYRALNEITVKDKFPIPVIDELLDELH FT GAKYFSKLDLRSGYHQIRVHQEDIQKTAFRTHDGHYEFLVMPFGLTNAPAS FT FQSLMNDIFRPHLRRFILVFFYDILVYSRSWEDHLLHVKQVLGILADHQLF FT VKLSKCQFGVLSVGYLGHLISSEGVAVDPEKIHAVQNWPVPTSPKGVRGFL FT GLAGYYRKFVRGFGVIAAPLTKLLTKDGFCWTEECELAFDKLKEALVSPPV FT LRLPNFSQPFVVECDACGDGLGAILSQDNQPIAYYSEALKGKSKLLSTYDK FT EMLAVVKAVRKWRPYLLGRPFVIKTDHRSLKYLLEQRLTTPSQARWLPKIM FT GFDYTIQYRQGKENQGADALSRVAAFQFQALTVPIADWWEILQQEVLNHPY FT YNSLLTNQPLNCVQRDGVWMQNGRILLSPNSTLLPAVLADGHSSPSGGHFG FT YLKTLTRISASFVWPGIRTSVKSFIRDCEVCQRCKHETLRPAGLLQPLPIP FT QRIWTDISMDFVEGLPLSQGYNVIMVVVDRLSKYAHFVPLKHPYTAVSVAK FT KFLNNVVKLHGMPLSIVSDRDKVFLSTFWKSLFKLQGTKL" XX SQ Sequence 4441 BP; 1183 A; 994 C; 1064 G; 1200 T; 0 other; gtggtatcag agcgcggttc aacccatgga cacgcgtggt aaaaataatg cagagtttcg 60 tgctgagatc actgaagctc ttggacgaca cgacgccaat tttgatgaat taaatcagaa 120 ttttaatcgg gtcaacaacg ctcttcaagg agtcatggct gaactccaag caatgagaat 180 tgctcagacc catcgttcca gtgagaggga agtaaatcct tttgctgggg gaagttcttc 240 tcatgacagg tcatcttctt cacacacttc tactttcgac agaggtcatt ccaaccttaa 300 gctgaacttt ccaacctatg ctggtgaggg tgaagaccca acaggttgga tttttaaggc 360 agagcagtac tttgaatttc agaatgttga tgctccgcga caggttcaat tggcttcttt 420 tcacttaaca agtgtagaac tccaatggta tcgctggtat accaagggca aagggcagct 480 acgctggcat gagtttgtcc aagctctgct ccatcgtttt ggaccaactg attatgacga 540 tccatctgag gcactttccc gtcttaaaca agtcactact gtcaatgcgt atcaggaggc 600 atttgagaaa ttatctcata aggtcgatga gctcccagag acgtttttgg tgggctgttt 660 tattgcaggg ctgaaggatg aaattcgttt ggatgtgcga gtgaagcaac caaaaacact 720 gtcggaatgc attagcgtcg ctcatctaat tgaggaacgc aaccagttcc aaaggaggac 780 gaacaacaca ttcagaacta cgacaacctc aggccaggtg agacagcaga cttccacaat 840 gggactacta ggacctgccc cttctcagcg accaccacag gtttcccatt tccctggtgg 900 acctgcacga agacttactg gacaggaggc acgagaacgg cgggaaaagg gcttatgttt 960 ttactgtgat gaaaagtatg ttcaagggca tcgttgctcc agaccccaat tattcatgat 1020 ggtagatgtg cagtcgcagg gggatgaaga tgaggtggac atggatattg agcctgacga 1080 agaagcatta cccgaaatat cattccatgc attagtgggt acatcacacc cacgaacttt 1140 tcgggtaaca gggaggattg gccacaagga attaattgtg ctcattgatg gggggagcac 1200 ccataatttt attgatcaat cggtggtcat taagttagga ttgcatgtgg ttaaggggaa 1260 gacattcaaa gtgacagtag ggaataaaga agtaattgaa tgtacgggga ggtgttttgg 1320 actctcatta tctctccaag gaatcacgat tcgggctgat ttctttgttc tgcccgtggc 1380 tgcctgtcaa gtagtgttgg gagtccaatg gctagaaact ttgggaccaa tcaagactga 1440 ctacaagaag cttcggatgt ccttcaaaca atcaggcaga acccacgttc tacacggaat 1500 aacaggttca gagttggcgc tgctgagtga gaaggaattg ttgcacttat ctggtatggg 1560 gttctttgtt cacatggttt cggaggtgca gtccagccaa gacactccat taccaccaga 1620 cctggagcaa attctatcac aatattctca catatttgat gaacccacca acctgccacc 1680 tacgcgcagc cacgaccatc gcattccttt actaccaaat caaccaccag ttaacacccg 1740 accttacagg tatccccact atcaaaagaa tgagatcgaa aaattggtca aagaattcct 1800 tcagtccgga attattcgcc caagccggag tccgttttca tcacccgtct tattgataaa 1860 aaaatcagat gggtcttggc gcttttgcgt cgattatcgg gcacttaatg agattacggt 1920 caaagataaa tttcccatac ctgtcattga tgagcttttg gatgaactac atggcgcgaa 1980 gtatttttca aaattagact tgcgctccgg ttaccaccag atcagggtac atcaggagga 2040 tattcagaag acggcgttcc gcactcatga tggtcactat gagtttttgg taatgccgtt 2100 tgggttgacc aacgctccag catcctttca aagtctcatg aatgatatct tcaggccaca 2160 tttgcgaaga tttatcctcg ttttttttta cgatattttg gtgtatagca ggtcttggga 2220 ggatcatctg ctgcatgtta aacaggtgct gggaattctg gctgaccacc agctatttgt 2280 caaactctcc aaatgccagt ttggggtgct atcggtgggg tatttgggcc acctcatttc 2340 ttcggagggt gtggcagtgg acccagagaa aatacacgcc gttcagaact ggccggtgcc 2400 aacatctcct aaaggtgtcc gtggcttcct gggtttggct ggttattatc gcaaatttgt 2460 acgcggattt ggtgtaatcg cggccccctt aacaaaactt ctcactaaag atgggttttg 2520 ttggactgaa gaatgtgaat tggcttttga caaattaaag gaagctctcg tctccccccc 2580 agttttacga ctgcccaatt tttcccagcc attcgtcgtt gaatgtgatg cttgcggaga 2640 cgggttaggg gcaatcttgt ctcaagacaa ccaaccgatt gcctactaca gtgaggcttt 2700 gaagggcaaa tcaaagttat tatccactta cgacaaggag atgttggcag tggtgaaagc 2760 cgtgaggaag tggcgacctt acctgttggg cagacccttt gtgattaaga cagatcacag 2820 aagcctcaaa tatttattag agcaacgcct cacaacgccg tctcaagctc ggtggctgcc 2880 aaaaataatg ggttttgatt acaccattca atatcgccaa gggaaggaga accaaggtgc 2940 tgatgctctc tcacgcgtgg cggccttcca atttcaggcc ttgactgtgc caattgccga 3000 ttggtgggaa atcttgcagc aagaggtact caatcatcct tattataatt ccttgcttac 3060 taatcaaccc ttaaattgtg ttcaacgaga tggagtttgg atgcaaaatg gacgaattct 3120 tttaagtccc aattccacgc tattacctgc tgtcttggcc gatggacatt cttcaccatc 3180 aggtggccat tttggttatt taaagaccct cacgagaatc tcagccagtt ttgtgtggcc 3240 tggtatccgc acctcagtaa aaagctttat ccgagattgt gaggtgtgcc aacgttgcaa 3300 gcatgagact ctccgaccag caggtttgct tcaacccctt cctattcctc aacgaatctg 3360 gacagatata tccatggatt ttgtcgaagg attgccactg tcacaaggat ataatgtgat 3420 catggtggtg gtagatcgtc tctcaaagta tgcccatttt gttcccttaa aacatcccta 3480 cacggcggta tcagtagcaa aaaagttcct caataacgtg gtgaagcttc atgggatgcc 3540 tctctccatt gtgagtgatc gtgacaaagt ttttcttagc actttctgga agtccttgtt 3600 caaattacag ggaacaaagc tgtgatatag ctccagttat catccacaat ccgacggaca 3660 aacggaggtg gtcaaccaaa ctcttgagca atacttgcgt tgcttctctt cggatcaacc 3720 aaaaggctgg gtggaatggc ttgcttgggc agaatatggg tataacacag cagttcattc 3780 ggcaacaaaa atgtctccct ttgaagcagt ttatggggtt cctcctccga acatgacctc 3840 ttacattcca ggcacaacaa aggtccaagc agtggataac ttactgcaaa caagggaagt 3900 catcatgcgc gacctcagga gaaatttgtt ggaagcacag actcgtatga agtctcgagc 3960 tgacctgcat cgacgggagg tcacctacga tgttggagat tatgtgtttc ttaagcttca 4020 accctaccgt caaaagtctg tagcgttcag gagttctttg aagctttctc ccaggttttt 4080 tggaccattc agaattttag ctcgcgtggg ggctgtggct tacaagctag acctaccagc 4140 aggggcacac attcatgatg tgtttcacgt cagcttgctc aaaaagaaat ggggaccggt 4200 tgttgacgat accgtgataa ctcttccccc tgtgtctaca gatgacgtca tactaccaga 4260 acctgaattg attttggata gaagggtggt ccaaaagggc aaatatcgtc ccaaaacaga 4320 ggtcttagtt cagtggaagg gagccttgcc agaagatgct tcgtgggaga atttgtggcg 4380 tttcgccaag acatatcctc aatttaacct tgaggacaag gttcttcgca gggggatgga 4440 t 4441 // ID Copia24-VV_LTR repbase; DNA; EDCOT; 196 BP. XX AC AM477428; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia24-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-196 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-196 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 691-691 (2007). XX DR Genbank; AM477428; Positions 15232 15427. XX SQ Sequence 196 BP; 59 A; 62 C; 18 G; 57 T; 0 other; tgataaccaa acagattcta acctaacctc ctctcccaca gttgtaactg aacaaccatg 60 taacaacccc caaaccaact catccaacca cctcacctag cttataaata cccacaccgg 120 tgtactctga atgcaatgag acaattcttc ttcttcttct ttttgtattt tctgacctgt 180 gtaaccactt ctatca 196 // ID Copia-13_Mad-LTR repbase; DNA; EDCOT; 265 BP. XX AC ACYM01095680; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-13_Mad-I; KW Copia-13_Mad-LTR; Copia-13_Mad_. XX NM Copia-13_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-265 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1357-1357 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01095680; Positions 2821 2557. XX SQ Sequence 265 BP; 93 A; 40 C; 34 G; 98 T; 0 other; tgataacagt atataaagca agcataacag cttgtgatca tgtggttgta atagtgacaa 60 gtgtagtcat cttgtaatca ttgtaatagc ttagaaagta agcaatctag ttagctatat 120 actatataac tatcattgta agatgatgaa atattaatat gaaaaataaa atatcttctc 180 tgtctaaaat tctatttctc tctctgaata ttcatttctt cttctgcaag aatacatctc 240 ctctatacct attgatatct ttaca 265 // ID HARB-1_Mad repbase; DNA; EDCOT; 2818 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; HARB-1_Mad. XX NM HARB-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2818 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1496-1496 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >94% identical to consensus. 3-bp TSDs are TWA. XX FH Key Location/Qualifiers FT CDS 442..1842 FT /product="HARB-1_Mad_1p" FT /note="transposase." FT /translation="MNSNFGSSSNSNWGSSSNSKLEAKWAQMRREDEESDE FT EVQVRRNKQNMAAAMAAAMVCQPTEEQPQWGGSVAGRSYKPRNRAMAHANL FT MNNYFNPNSVYTEEDFRRRFRMRRHVFERLLRDVQQVNPYFRQKRDRAGRP FT GFSPHQKVTVALRMMAYGSSADSMDETHGMSESTCLDTLEEFCNTIVQVYK FT DEYLREPNQEDLNRLLHKAEDRGFPGMIGSLDCMHWDWKNCPTGWQGGFSG FT RSRKPTVVLEAVASYDTWIWHAFFGVPGSQNDITVLGRSPLFNNLTEGKAP FT QLDYYINGREYNMGYYLADGIYPKWATLVQAIPNPRNDAEKLFTLHQEAYR FT KDVERAFGILQARWKIISEPARGWSRENLNSIMMSCIILHNMIVEDERDGY FT IDGESDDDQEDPNRSRRALAKIYDGPNLPFNPRTGSISINEYMRRYRMIRS FT RATNKYLQQDLVAHLWAKRSME" XX SQ Sequence 2818 BP; 939 A; 514 C; 600 G; 764 T; 1 other; ggccatctcc aaccgagggc tggccagagg gctcgtttta gccctctggc cctccaagat 60 tctccaagat attaatattt taatgaacag tacagggcca tatttgcctc cgtctccaac 120 cgagggccaa agggccagag ggctcgtttt agccctgtca caaaaaaccg tctccaaccg 180 agggccaaag ggccataggg ccaaacataa tttattattt aaaaactaca atttaaattc 240 aaatctaacg gctaagtgac gtcaacatga tgtcagctag ccgttggtag ctgacatcat 300 gctgacgtca gctagccgtt ggatttgaat ttttttttgc tataaatagg gtggatattg 360 ggctataatt cacacaactt taaattcaat ctatttcaat tcaatctctt gcaattcaat 420 ctctttcaat tcaagtttgc aatgaattcc aactttggat cttcatccaa ttccaattgg 480 gggtcctcat ccaattccaa attggaagca aaatgggcgc aaatgagacg agaagatgag 540 gagtctgatg aagaagttca agtaaggcgc aacaaacaaa acatggcagc agccatggct 600 gcggccatgg tgtgtcagcc aactgaggaa caacctcaat ggggtggctc tgttgctggt 660 cgctcttaca aaccacgaaa cagagcgatg gcgcatgcca atctgatgaa caactacttc 720 aaccccaact cggtgtacac agaagaggat ttcagacgtc gcttccggat gaggcgtcat 780 gtcttcgagc gtttacttcg tgatgtccag caggtcaatc catactttcg acagaagcgg 840 gacagagcag gccgccctgg tttctcacct catcagaagg ttactgttgc actccgaatg 900 atggcatatg gctcctcagc tgattcgatg gatgaaaccc atggtatgtc tgagtctaca 960 tgccttgata ctcttgaaga attttgtaac acaattgttc aggtttacaa agacgagtac 1020 ctccgagagc caaatcaaga agatctgaat cggctccttc acaaagctga agaccgtggg 1080 tttccgggca tgatagggtc attagactgc atgcattggg attggaagaa ctgtcccact 1140 ggatggcaag gaggctttag cggaaggtcg agaaagccaa ctgttgtgtt agaggcagtt 1200 gcctcatatg acacatggat ctggcatgct ttctttggag tccctggatc ccaaaatgac 1260 attacagttc ttgggcgttc acccctcttc aataacttga cggaaggtaa agcacctcaa 1320 cttgactact acatcaacgg ccgtgaatac aatatggggt attacttggc agatggcatc 1380 tacccaaagt gggcgacact tgtccaagca attccaaacc ctaggaatga tgcagaaaag 1440 ttgtttacct tacaccaaga ggcataccgg aaagatgttg agagagcttt cggtattcta 1500 caagcacggt ggaagattat cagcgaaccg gcaagagggt ggagtcgaga aaatttgaac 1560 tccatcatga tgtcttgcat catattacac aatatgatag tggaggatga gcgagatggg 1620 tatattgatg gagagtccga tgatgaccaa gaagatccaa ataggtcaag aagggctcta 1680 gcaaaaatat atgatgggcc taatttgcct ttcaatccaa gaactggtag tatctctata 1740 aatgagtata tgaggcgcta tagaatgata cgttctcgtg ccacaaataa gtacctacaa 1800 caggatcttg ttgcacatct ttgggccaaa agaagcatgg agtaggcttt taagttttat 1860 gttgttaaat gtttttaaaa atgttgttta agtttcatgt tgttaaatgt ttttttatgt 1920 tgtataattt gtatgttggt taatgttatt taatgttgtt tcatattgtt taatgttgtt 1980 tcatgttact taatttaatt taatgttgta taaatggcct aggaagttat aggaaaaaaa 2040 tagaattgaa aaaaaatatg aaacaaattt tgtgaaatag aagttatagg aaaaaaaatg 2100 gaatttaaaa aaatatgaaa caaattttgt aaaatagaag ttatatgaaa aaaaatatga 2160 atcaaatttt gtaaaataga agttatagga aaaaaataga atttaaaaaa aaattgaaac 2220 aaattttgtg aaataaaagt tataggaaaa aatggaattt gaaaaaaaat atgaaacaaa 2280 ttttgtaaaa tagaagttat aggaaaaaaa tagaatttaa aaaaaaattg aaacaaattt 2340 tgtaaaatag aattgaaaaa aaatataaaa tttgattcat atgaaaagga aaaaacaagg 2400 gaaaaaaaga agtttaaatt cataaaaaaa aaaaaaaaaa gttaatacaa cggctactag 2460 ccgttatatt aaaaaaaatt caaactatta gtgtcggtta taaccgacac taatagtaat 2520 taaaaaaaaa aatttgcctt tgaataacta ttactgtcgg ttataaccga cagtattaaa 2580 aaatccttct ttaatgctgt cggttataac cgacagcaat gggaaaactw taaaaaaaat 2640 agccagcccg gggctggctg gctggccgaa agcagccagc cctccagccc tctggccctt 2700 tgagatcccg tggggccctc ccagattcca gagccctctg gcctagccct cggttggaga 2760 cggttttagg gctattttcg gccctctggc cctctggacc cttcggttag agatggcc 2818 // ID Gypsy-74_PTr-I repbase; DNA; EDCOT; 2969 BP. XX AC . XX DT 22-DEC-2009 (Rel. 15.02, Created) DT 22-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: internal DE portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-74_PTr-I. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2969 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 182-182 (2010). XX DR [1] (Consensus) XX CC ~87% identity to consensus. XX FH Key Location/Qualifiers FT CDS 1664..2698 FT /product="Gypsy-74_PTr-I_1p" FT /note="Including Gag and retropepsin-like FT protease." FT /translation="MKSLMRRRFVPSHYYRELYQRLQSLSQGTKSVDEYFK FT EMKLAMIRANVEEDREATMARFMNGLNHDIAHIVELHHYVELEEMVHMAVK FT VEKQLKRKGTIRQSQPLGPSKPWKPNWKANTGGGPSQQNEEGKAEYPREKK FT DTSAIVKGNNVTPTSRNRDIKCFRCLGFGHVASQCPNKRVMVMKANNEVET FT DGEDEEEKMPPLEDADDVCVEYPVEGEALVVRRALNMHVKVDDSEGQRENI FT FHTRCHVHNKVCSLIIDGGSCTNVASTELVRKLNLHTTKHLIPYKLQWLND FT GGEVKVNKQVLVAFSIGKYCDEVLCDVMLCQCKLVTCCLVDHDSMIGELCM FT ME" XX SQ Sequence 2969 BP; 889 A; 416 C; 750 G; 913 T; 1 other; gttggtatca gagctaggct ccaaaaatca ggttatatcc tttattttct tcttgttagt 60 ttcggcttcc ttagctttag ttgtctttga ttcggttttt attatttcgt gtctagagct 120 tagtagtttg cgtctagggt tcctaaaaaa aggtgttatt ttagtttgtt gttgtctcag 180 aatatatcag tagcataaag agtaaaaaaa aagaagaaaa aaacgtccaa aagtcacttt 240 tgtcgaatct gccacaatac acaaacaagg gagaatttgg accaaaccaa ttcagaaaat 300 tctcaaattt tatatactgg ttctaggagt cctaatcgca ccccatataa aatttgagct 360 catttggaga tcgtttgcta tagtaaccaa ggtcgggatt aaaacttgtc gtaataggtc 420 agattcgtat cagaagggaa tttcaggtca aataaattca gaaaattctc aaattttata 480 tactgggttt taaggttcta atcgcacccc atataaaatt tgaggtcatt tggagttckt 540 ttgctatagg aactaaattc aggattggaa cttgtcgtaa cgggtctaat tcgcgtcagt 600 aattcaaact tgttttgctg ctgttatttt tcaattatga cagtataata acatcataat 660 tgatatattt aggtgtcatt taaatttttt ttatataacc tttgcatctt ttttctttcg 720 cgtcttcaaa aacatccatt tttcgtacaa attcgcttgt tactcgtgaa attgtaatcg 780 tagtttcgtc tttgcttgtt ttcatatttt tcttgcttct tgagtcatat acacatattt 840 ggatacgctg ctaaggctgt tatatttggt gttgatttca gttccgcaag agtcgaagaa 900 aggtgagacg agaggaaaaa ggcgtagcga gtatatttga gtgaaacacg agaggagtgt 960 aaacacatga gggagtgggt gaggaatata tatttcttgt caactaacca attttcagat 1020 tcaaagatgt cggaggcaag caacaacatg gcaccacaga gaggagacaa tgaaattgta 1080 actcagttac gcattatgaa tcagcggatg gatcagatgg ccaatgaatt tggagatagg 1140 ttggataggt tggagaggca acatgttaat gatcatggta gggttcaaat taggcctgag 1200 cgaagagaat ttaatgttag gagggttgtt aggcgagtta acactaatgt ggatgagttt 1260 gtggctgata atgcggacat gagtgatgtt gattttgaag atgtgtccgt gggacatggg 1320 gaacgttttg gacagcagcg gaattgtcag tttgtagggg aaagatatgg tgataatttt 1380 ggccagaggg gtaattatag gtaccgggac cataatgctg agttaggtgg agatttgggt 1440 acaattaagc tgaaaatacc ggcttttcag ggaagaatga tccagaagtt tatttagaat 1500 gggagaagaa ggtggagtgg attttttagt gtcacaatta tccagagccc aagaaagtca 1560 agcttgttgt gattgctttt actgactatg ccattgtgtg gtgggatcag ttagtgacaa 1620 accacagagg aattatgaga ggcaagttga tacttgggat gagatgaaat cccttatgag 1680 gaggagattt gtgcctagcc actattatag agaattgtat caaaggttgc agagtttgag 1740 tcaaggtaca aagagtgttg atgagtactt caaggagatg aaacttgcta tgattcgagc 1800 taatgttgag gaggataggg aggctactat ggctagattc atgaatggcc ttaatcatga 1860 tatagctcat attgtggagt tgcatcatta tgtggagttg gaggagatgg tgcatatggc 1920 cgtgaaggtg gagaaacaac ttaaacgaaa gggtaccatt cggcaaagcc aaccattagg 1980 cccttcgaaa ccttggaaac ccaattggaa ggctaacact gggggtggtc catcacaaca 2040 gaatgaggag ggcaaggccg aataccctag agagaagaaa gacacctcgg ccattgttaa 2100 aggtaacaat gttactccta cttctcgtaa ccgtgacatt aaatgctttc gttgtctggg 2160 ttttggtcat gttgcttcac agtgtccaaa caaaagagtc atggttatga aagctaataa 2220 tgaggttgag accgatgggg aggatgaaga ggagaagatg ccaccattgg aggatgctga 2280 tgatgtttgt gttgagtatc cggttgaggg agaggcactt gtggtgagga gagcactgaa 2340 tatgcatgtc aaggtggatg attcagaagg tcagagggag aacatattcc acacgagatg 2400 tcatgttcat aataaggtat gtagcttaat tatagatggt ggtagttgca ctaatgtagc 2460 tagtactgaa ttggtgagaa agttgaactt gcacactacc aaacatctca taccttataa 2520 attacagtgg ttgaatgatg gtggtgaagt gaaagtgaat aagcaggttt tggttgcttt 2580 ttctattggt aaatattgtg atgaggtgtt atgtgatgtt atgttgtgcc aatgcaagct 2640 agtcacttgt tgcttggtag accatgacag tatgatagga gagttatgca tgatggagtg 2700 acaaataggt attcctttga gatgaatgga agacctataa ctcttgtatc tttgacacct 2760 aagcaaatat atgaggagca actgaaattg aagaaggaga agatggttga aaaggagagc 2820 ttgtatatca aggggacctt ctttgctaac aaggttcttc ttggttttga tgatgatgtt 2880 attcttcggc ttggtactga tttgttgacc ttagaagatg ttttccatga tacagattcg 2940 aggtcgaatc tttttaaaga aggggagga 2969 // ID RaMu_MT repbase; DNA; EDCOT; 470 BP. XX AC . XX DT 14-NOV-2006 (Rel. 11.11, Created) DT 21-JAN-2007 (Rel. 12.02, Last updated, Version 2) XX DE A non-autonomous transposon from Medicago truncatula. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW transposon; non-autonomous; Inverted repeats; RaMu_MT. XX NM Harbinger1_MT. XX OS Medicago OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae. XX RN [1] RP 1-470 RA Shankar R. and Jurka J.; RT "RAMu_MT: A novel non autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 569-569 (2006). XX DR [1] (Consensus) XX CC The sequence is self-complementary. XX SQ Sequence 470 BP; 144 A; 91 C; 90 G; 145 T; 0 other; ggcttaattg cacttttccc ccctatagtt tgccaattgt gcgattttgc accccatagt 60 tttaaacgag cgattttgcc ccctatagtt ttcccccttt ctgattttat ggtccccatg 120 acatttagtg ctgatgtgtc tgttttttta tcaattaatg tgtgccacgt gtgtaattcc 180 atttttttgg tatttttcag attttgagag aaggaggcac gtgatatttc ttcttaaaat 240 ctgaaaaatc acgtgcctcc ttctctcaaa atctgaaaaa tacaaaaaaa tggaattaca 300 cacgtggcac acattaattg ataaaaaaca gacacatcag cactaaatgt catggggacc 360 ataaaatcag aaagggggaa aactataggg ggcaaaatcg ctcgtttaaa actatggggt 420 gcaaaatcgc acaattggca aactataggg gggaaaagtg caattaagcc 470 // ID CAREP repbase; DNA; EDCOT; 2433 BP. XX AC AJ411812; AJ411812.1; GI:14715227; VERSION; XX DT 08-JUL-2003 (Rel. 8.06, Created) DT 08-JUL-2003 (Rel. 8.06, Last updated, Version 1) XX DE Cicer arietinum Ty3-gypsy like Retrotransposon CaRep, partial DE LTR, clone 101-18. XX KW Gypsy; LTR Retrotransposon; Transposable Element; CAR411812; KW CAREP; Ty3-gypsy like retrotransposon CaRep. XX OS Cicer arietinum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; OC Cicer. XX RN [1] RA Staginnus C.; RL Thesis (2001) Department of Plant Molecular Biology, University RL of Frankfurt / M., Frankfurt a.M., Germany. XX RN [2] RP 1-2433 RA Staginnus C.; RT "Direct Submission to GenBank."; RL Direct Submission to Genbank (22-JUN-2001)Staginnus C., Plant RL Molecular Biology, University of Frankfurt M., Biocentre, RL Marie-Curie Strasse 9, D-60439 Frankfurt a.M., GERMANY. XX DR Genbank; AJ411812; Positions 1 2433. XX SQ Sequence 2433 BP; 685 A; 333 C; 576 G; 839 T; 0 other; tgtattttgg attttggctc ggaggctttt aagccaaagt taataatatt ttggagtttt 60 ataatcaaaa agatattttg atgccaatta aaatttctcg tcgataaata aattgaattt 120 aactgcgatg aatcctttac ggagaattta atgcgtttcg ggtgaaacgg taatttaaca 180 aatatctaga ttttgagata tttgttaagt tatatttatt atatttatat atgtttgttt 240 ggagggaaaa agaaaggaaa actagaagga aggaaaagga aaagaaaata gtataaaagg 300 aaggaaggaa aaaggaagaa aggaaaaaca aaggaaagaa aaagaaagga aagaaaaacc 360 atttttccat cgtctccttc ctctgtccgc ggccaatttt cctcctttct cccattttca 420 ttttcgtcgc tttcctttct tcgaaactag taacccaagg ttgggtggga gttagatcaa 480 ggttttcgca actccactct tcctctttga ttcgaaaacg aagaaaaacg gtttttgaga 540 tccaaacaca aacccctccg tttcttctag atccaaacct cattttgcga tgagtcagaa 600 gggaaggttg ctcactacca cgccacggtg ctaggggacc tatttggagg cgaagttgcg 660 agcggagatt ttaccgaaat tactcgcggt accagaaacg cacgttaaag ctaacgttga 720 ggtaaggact ccttccaaac ttctagtttg cattagggac ttatctgtgg ttgtgtggaa 780 aggaatttgt tagggtttaa tgtatcgatt tggggaaaaa acgaaactaa tgcgttttgg 840 gtaaaacctt agagttaggt tttgtttata ttgatgaatg tttcgtggta aatgaatttg 900 aagtcattgt gtgtgattat gagtaaatga aatttgatgt atctgggcgt tatgttgcgt 960 tgatttgtgt tcgttgtatt tggcgtgtcc atacttgatg tttgttaatt ggtgtggttg 1020 ttgtgaatta tggtttgaat gtgagagttt gtttccgtgg aatttgaaaa tcattagagt 1080 aaacgagtat taaaaatggg gaatctttta atacctcggt ttacttaatg tgcatttgag 1140 gaaaaggttt aagttaactg ggcgttgaaa atgaggaatc tcttaatgtc ccggttactt 1200 aactatcgtg tttgaaaatc gttccggtaa atgagtatta agaatgggga atctcttaat 1260 gactcgttta ctgaatgttt tgtgagaaaa tcgtttaagt caaaagtata ttaagaatgg 1320 ggaatctctt aatatgtctg tttgcttaac attttgtttt gaaaatcatt aagataaatc 1380 gatattaaga acggggaatc tcttaatgac ttatttattt aatgttgttt tgaaagtcgt 1440 ttaaagttaa atgggtatta aaaatgggga atcttttaat atctgcattt gcttaacgat 1500 tgttgtgaat ggagtctgtg tatgctcctg catttcattt ggtaaattgt gtcgacccgt 1560 gataggtgac accttggtaa actgtactga cccgtgatag gtggtacgtt tacgatttac 1620 atttttggta aatcgtgttg acccgtgata ggtgacacct tggtaaactg tactgacccg 1680 tgataggtgg tacgtttacg atttacgttt ttagtgaatt atgctgaccc gtgataggtg 1740 gcacctcggt aaacagtact ggtctgtgat aggcggtacg tttacgattc acgctttttc 1800 ttttagtaaa tcgtgttgac ccgtcatagg tgacacctcg gtaaactgta ctgacccgtg 1860 ataggtggta cgtttatgat ttacgcattt tagtaaatcg tgctgacccg tgataggtgg 1920 cacctcggta attggtactt tggcctgcga taggcggtac aattatgatt tacggccctt 1980 cgaggagggt tttggtttgg aattccgagt ccatgcattt tggcatatac gcattgcatt 2040 agggtgcttg gcacgtgagt cgtgtttgat tcaagtttat gattgagtgt tttgaatttg 2100 agttgtcgtg gtaattgtgt tgaaattgct aagtgttatg tattgattag catgtgcgcg 2160 tgcgatggat tgcaaaacta tttcgaaaac caattcgtcg tggtgattgt gtgggttttg 2220 ctaagtgtta agttttggag ttatgtgtga gtgtgattga attagtttaa gtatttttgg 2280 aagaataagc agggaaatcg atttcccaat cgattggatg agttgcagga agttcactat 2340 tttaacctaa tcgatttgcc aatcgattgt ataaatatat ctttcaaaat cttttaagaa 2400 atcgatttgg aaatcgattg gcagagaggc agg 2433 // ID SHACOP8_LTR_MT repbase; DNA; EDCOT; 323 BP. XX AC AC174297; XX DT 16-JAN-2007 (Rel. 12.01, Created) DT 16-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR sequence of LTR retroposon, SHACOP8_MT, from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW terminal; Internal; repeat; SHACOP8_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-323 RA Shankar R. and Jurka J.; RT "SHACOP8_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 81-81 (2007). XX DR EMBL/GenBank/DDBJ; AC174297; Positions 76310 76632. XX SQ Sequence 323 BP; 104 A; 57 C; 48 G; 114 T; 0 other; tgttaaaatt aatgtgttgt aaccgccact atctttagga agcattatga tagaattgta 60 accatcatca taatgattgt ctttatttag gtttatggta ggtttgttat caacctattt 120 gtattctcta tcagtttcct tctagcctat ataaaggctt tgtaatgcta agttgaagta 180 agcagtatgt ggtgaattca acaaaatcag tttttcttca atgttcatcc accagtggaa 240 gtatagtata aaaagtcacg tttccactca aaatcctgca acagtataat ttataacata 300 ccacctctag aataccacca aca 323 // ID Gypsy-47_Mad-I repbase; DNA; EDCOT; 10908 BP. XX AC . XX DT 27-OCT-2010 (Rel. 15.11, Created) DT 27-OCT-2010 (Rel. 15.11, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-47_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-10908 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(11), 1991-1991 (2010). XX DR [2] (Consensus) XX FH Key Location/Qualifiers FT CDS 42..2147 FT /product="Gypsy-47_Mad-I_1p" FT /translation="MTGSAQEVPNPSEDAGTRSVHARSQSQNSEPSLAMEQ FT FRRLTRELRETKKTADEALKKAEARNAVEDVTGTKRQRAEEEDKEGSSSSA FT PSSNRVEVTKNQGEGGYRGKGSKKVKDVDLREQIEKIVKGYKPQTPAELAL FT EAARGIRKSPFTEDILKAKKPAKFTQPKFRLFEGTTDPVEHIYHFQQQMAL FT EGDDEALLCKLFPSSLSGSSLTWFRQLKSRSIGSFTDLCEAFISQYVCNRR FT PRKDVTILFSTKQNVGESLKSYMTRFTEEMSTLEECDSHTAALAFREGVLP FT GTKMRRSLIETPPLDMREVMARADGIIRLEEEELIQSKRATATIAASPAGT FT TALTLKPTAQPRQERRFSRDPNDGFNERSRLDRPNTKLTVSLGKIFHENKG FT KGIFRAPAPIRTPLEKRDRNKMCAHHNDFGHATNDCRSLRNQVEAMLKKGM FT LSQYRVESRDERKNDGGLQAVTGNIGADERLLDINVIHGGPQPPEGREARY FT RSQRREAEKSRRVHNITSAPEASKALDNLGVISFSQKDLEGIQFPHNDALV FT VTLRVANSRVKRIMIDGGSSTDVLFWSTFRRMKLDEKEIRPNPTPIYAFEG FT TKAQPIGDVTLPVTAAGKTLFVTFVIIDAPSAYNAIMGRDWIHRMDGEAST FT RCQVMRCLSTDGQTTIDIKGDQLEARKCYSMATDIKTTREVQQSTDLHENK FT PL" FT CDS 2358..5501 FT /product="Gypsy-47_Mad-I_2p" FT /translation="MPGIDPEVACHQLNVDPSCPPHRQKQRRFAPERNQII FT SAEVDRLLEVGFIRDVWCPTWVSNVVVVGKKEKGKWRVCVDYTNLNRACRK FT DCFPIPKIDQTVDATAGYALLSFLDAYSGYNQIPMAVEDQEKTAFITERGL FT YCYTVMPFGLKNAGSTYQRLVNKMFKNQIGNTMEVYIDDMVVKSRERCQHI FT DHLRNTFDVLRRYHMRLNPAKCAFGVSSGQFLGHIVNKRGIEPNPAKVEAL FT CNMPDPVTPRDIQVLTGRIAALSRFISRSSDRCKPFFQAIRNRKGDVWGHE FT QREAFEQLKKYLTSPLLLTIPKQGELLYMYLAVSEGAVSAALFREEGSVQQ FT PIFYVSKSLIDAEKRYSPTEKMVLALVTAKKKLRQYFEAHTIVVLTNQPMR FT AILSKPDLSGRITKWAIELSSFDIKYRPRSAAKGQVIADFLVECYPRESLQ FT GECEEIAKVDPSEIKWELYVDGSSNQAGAGAGIILISPEGIDLECSVRLDF FT PASNNVAEYEALVLGLELAKQLKISRLTVHSDSQLIVGQATEEYTTKNARM FT EAYQQLVKGLANGFKYFELKQIPREMNERADQLACAASAAQENLRVAEVEY FT LHSPSIGAVQSDVMQIGGQRSRLDNPLPEQAQAEDNDCWMTPIVNYLTKGI FT QPEDLVEARKLRMKAVRYAILSDTLYRRSFSGPYLRCLNPRQSEWVLRELH FT EGMCGNHSGGRSLAHRALTQGYFWPYMARDAEQYVRKCDKCQKYAPVVRQP FT AEELNPIVGPWPFAKWGMDIVGPLPRAPGSNKFVLLATDYFTKWVEAEAYV FT SVTQDDVVRFVWRNIICRFGIPRAIVTDNGTQFDNRRFRSYCTEKGITLQF FT SSRSYPQGNGQAEKTNRTIFYCLKKKLEQRKGKWHEELPNVLWAYRTTKRK FT PTGESPFSLAYGTEAVIPTEVGLPTVRTLVVENGENDQQLAHNLDLVEEQR FT EIAALRLANYQNQVAAYFNKRVKSKRFRVGEWVLRKVMENTKDLNAGKLGR FT IWEGPYEVTEAFGKGAYKLRHVETGQYVPRPWNAIHLRKYHI" FT CDS join(9309..8614,8446..7931,7873..7346,6988..6296) FT /product="Gypsy-47_Mad-I_3p" FT /translation="MSRRTPWSKYGGTPPXFEIVKARDLGHVPDDIHLSPL FT PAGADMYSGLGIPAGSTVLSPDHLGVISFPLHPMIHLILFFTNTHPMQLNP FT NSYLIMSTFLALGLKLGVSLGFRDFLYLFDLTVIKGETSFFNFKPRYRKKF FT LSLGPSRARDWKNRPLLISGNWKAPELSQLSIPSAFGPKPGIYKFTFIIFF FT INMRTLLTMNFFRSFIRWSRTDHFQRPKMLAKEVCDEEDMELPTLERRAQK FT KKTKEEKTRSQGNRTRILTRIILLRWLHHLLTFHRPAALRRLHVIFLCPEL FT QAGRINVLWQIGPKSLGVVRRLSSAQPQDPCNGNRLLPPSARLVAMVPAIH FT LKLGGLSSQKEMGVTSPLATIYGAMQVPLLLWRGAWLILVTPVVLRQCSMT FT MSTPMNLIALRCFQMALLQKEKSDRLAARLESLSLTQQQVREYRAKLHGYE FT EEITSLKGARDAATSEVRRAKEELAEVKRARATEREMNMQQIRKEMASSFR FT FGWVQSQQRPEHRFVDDPDVYDRHMGIEPGGYEWYEGMDPKDRRPSDQPAS FT SDPIPGSGFVTTSGPISSLGFGGFQSGPRFGAQEPLGSTWIFMANNRKVKL FT HFRLYADVPKKRSSRRGSRGSRNVIELCSNSSSRSPGRASYSSEVPNTFRE FT SSYRSRTRSGGKQALDSIVDGMISPRLNHTTRALNPVTDRMVSPGGSYATR FT APDSIARSPDPYAGDEAGPSRAPSRHHPRCPQCFDYSLLLNERETLKGHLQ FT RAEHQVDRLRGELMAADRAVSAAHSDGIHDGFKQGVQYFRSKAKAAFPSVN FT WDSLSTPLD" XX SQ Sequence 10908 BP; 3368 A; 2295 C; 2727 G; 2515 T; 3 other; gttggcgccg tctgtgggaa acacaaaatc aaactacaaa catgactgga tccgcacaag 60 aagttccgaa tccctctgaa gacgcaggga ctcgatcggt acatgctagg tctcaatccc 120 aaaatagtga acccagtctt gccatggaac aatttagaag gttaacgagg gaattgcgtg 180 aaacaaaaaa gacagcagat gaggcgttga agaaggctga agcgagaaat gccgtagaag 240 atgtaacagg caccaagaga caacgtgcag aagaggagga taaggaaggt agctctagta 300 gcgcgccatc cagtaaccgt gttgaagtga cgaaaaatca gggcgaaggg ggctacaggg 360 gaaaaggatc gaaaaaggta aaagatgttg atttgcgaga acaaattgag aagattgtga 420 agggatacaa gccacaaacc ccagcggagc ttgccttaga agcggccaga ggaattcgca 480 aatcgccgtt cacagaggac atcctgaaag ctaaaaaacc tgccaagttc acccaaccaa 540 agtttaggct gtttgaaggc acgactgatc ctgtcgaaca catttaccac tttcaacagc 600 agatggcgct tgaaggagac gatgaggccc tcctgtgcaa gttgttcccc tcaagtcttt 660 cgggatcatc tttaacttgg ttcagacaac tgaaatcgag gtctatcgga agtttcacag 720 atctctgtga agcattcata tctcaatatg tctgcaatcg gaggccaaga aaagatgtta 780 cgatcttgtt cagcaccaaa caaaatgttg gcgagagcct caagagctac atgactaggt 840 tcacggaaga gatgtccacc ctagaagaat gtgactctca cactgccgct ttggcattcc 900 gagaaggggt gttgcctgga acgaagatgc gtaggtcgtt aatcgagaca ccaccactgg 960 acatgaggga ggtgatggcc cgagctgatg gaatcatcag attagaggaa gaggaactta 1020 tccaatcaaa gcgggccacc gcgactattg ctgcatctcc agcgggcact accgcgctta 1080 ccttgaaacc cacggctcaa ccgaggcaag aaagaagatt ctcacgtgat ccgaatgatg 1140 ggtttaatga aagatctaga cttgatcgcc caaacaccaa gctgacagtg agcctgggca 1200 aaattttcca cgagaacaag ggaaaaggaa tctttcgtgc accggcccca attcgaacgc 1260 cgctagagaa gcgagacagg aacaagatgt gcgctcatca caacgacttt ggtcatgcca 1320 ctaatgattg tcgaagccta aggaaccaag tggaagctat gctgaagaag gggatgttgt 1380 cacagtaccg cgtagaatcg agagacgaac gcaagaacga cggaggactt caagcagtaa 1440 caggaaacat tggagcggat gagaggttgt tggatatcaa tgtcatacat ggtggacccc 1500 aaccccctga gggacgtgaa gcacgctatc ggtcgcaaag acgggaggcc gagaagtcta 1560 gacgcgtaca caacataaca tcagcccctg aagcgtctaa agcattagat aatctcggag 1620 tcatctcctt tagccaaaaa gacctcgaag gaattcaatt ccctcacaat gatgcattgg 1680 tcgtgacgct acgtgttgcc aattcaagag tgaaaaggat aatgatagat gggggaagca 1740 gcacagacgt tctattttgg agcacattta gaagaatgaa attagacgag aaagagataa 1800 ggccaaatcc aactcctatc tatgcgtttg aaggaactaa ggcccagccc attggagacg 1860 tgacccttcc tgtcacggca gcaggtaaga ctcttttcgt cacttttgtc atcatcgatg 1920 caccgagtgc atataatgcc attatgggaa gggattggat ccatcgaatg gatggggaag 1980 cgtcaaccag atgtcaagta atgaggtgtt tgtcgacgga tggtcaaacg accatcgaca 2040 tcaaagggga tcagctggag gccagaaaat gctacagcat ggcaacagac atcaagacaa 2100 ccagggaagt gcaacagagc acggaccttc atgagaataa accattatag caattagcgg 2160 aggacccacc acaacaggat caggaaaacg gcgatcaaga acccccaact atagaaccac 2220 tgagggaaga ggttttggat ccaaccgatc ctgagaaacg aatatgggtg ggctccctcc 2280 tatctgatgc ggaagtcgaa gagttgctga aatttctaag gagcaacgct gatgtttttg 2340 catggtctca tagggacatg ccaggaattg acccggaagt ggcatgccat cagttgaatg 2400 ttgatccgag ttgtcctcca caccgacaaa agcagaggag atttgcgcca gaacgaaatc 2460 agattatcag tgcagaagtc gataggctcc tcgaagttgg attcattcgt gatgtctggt 2520 gcccaacttg ggtttcgaat gtcgtggtgg tgggcaagaa agaaaaagga aaatggcgcg 2580 tgtgtgtgga ttataccaac ctgaacagag catgtcggaa agattgtttt ccaattccaa 2640 agattgacca gacggtggat gctacggctg ggtacgcact attgtctttc ttagatgctt 2700 attccggtta taaccaaatt cctatggctg ttgaagatca agagaaaact gcttttatca 2760 ctgagcgtgg attgtattgt tacaccgtta tgcctttcgg actcaagaat gccggctcga 2820 cttatcaaag gttagtgaac aagatgttta aaaatcaaat cggaaataca atggaggttt 2880 acattgacga tatggtcgtc aaaagccgag aaaggtgcca acacattgat catctacgca 2940 acacttttga cgtattgaga agatatcaca tgcggctaaa cccggcaaaa tgcgcattcg 3000 gtgtatcatc tgggcagttc ttagggcaca tagtgaacaa acgaggtatt gaaccgaacc 3060 cagcgaaagt tgaagccttg tgtaacatgc cagatccggt aacacccaga gacattcaag 3120 tgttaaccgg gcgaatcgct gcccttagtc gtttcatctc acgatcatcc gatcgatgca 3180 aacctttttt tcaagccata cgaaaccgga aaggagatgt gtgggggcat gagcaaaggg 3240 aagctttcga acaactgaag aaatatctca caagcccatt gttgttaacc attcccaagc 3300 aaggggagtt gttatacatg tacctagccg taagcgaagg ggcagtaagc gctgcgttat 3360 tcagagaaga aggctcggtc caacaaccca tattttacgt gagcaaaagt ttaatcgatg 3420 cagagaagag gtattcgccc actgagaaga tggtgttggc cttagtaacc gcaaagaaga 3480 agctccgtca gtacttcgag gcacacacca ttgtggtgtt aactaatcaa ccgatgaggg 3540 ctatcttatc taaaccggac ttatcaggaa gaattacgaa gtgggccatc gaacttagtt 3600 cctttgacat aaagtatcgg cctcgaagcg cagccaaagg acaggtaatt gctgactttc 3660 ttgtagagtg ttatcctcgt gaaagtttgc agggtgaatg cgaagaaatt gcaaaagtcg 3720 accctagtga gatcaaatgg gagctttatg tggatgggtc atccaatcaa gcaggagctg 3780 gggcagggat cattttaatt tctcctgaag gtatagactt agagtgttcg gttcggttgg 3840 attttcctgc atcaaacaac gtggcggaat acgaagccct ggtactaggc cttgaacttg 3900 caaaacaatt gaagataagc cgtcttaccg tgcatagtga ttcacaactc atcgtcggcc 3960 aagcaactga agagtatacg actaaaaatg cgaggatgga ggcatatcag caactggtta 4020 aagggctggc gaatggattc aagtatttcg agctgaagca aatacctaga gagatgaacg 4080 aaagagcgga tcagctagcg tgcgcggcgt cagccgcaca agagaacctg cgggtagccg 4140 aagtagaata tctgcactcc ccgagtatcg gagcagtgca atcagacgtg atgcaaatcg 4200 gcgggcaaag gtcgagactt gacaacccgt tgccagagca agctcaagct gaggataatg 4260 actgttggat gacgccaatc gtaaactacc tgacaaaagg gatccagccg gaagatcttg 4320 tggaagcgag aaaactccga atgaaagcag taagatatgc aatccttagc gacacgctct 4380 ataggaggtc attctcagga ccttacctca ggtgcttaaa tccaaggcag tccgaatggg 4440 ttctgagaga attacatgaa ggaatgtgtg ggaatcactc aggaggaaga agcttagcac 4500 atcgagcatt aactcaaggt tacttctggc cgtacatggc tcgagacgcg gagcagtatg 4560 taagaaagtg cgacaagtgc cagaaatatg ccccagttgt tagacaaccc gccgaagaac 4620 tcaatccaat cgtaggaccc tggccattcg caaaatgggg catggatatc gtaggcccgt 4680 tgccgagggc gcccggaagt aacaagttcg tccttctcgc cacagactac ttcactaagt 4740 gggtagaagc agaagcgtat gtttctgtca cacaagatga cgttgtaaga ttcgtatggc 4800 ggaacattat atgccggttt ggcataccaa gggcgattgt gacggataat ggaacgcagt 4860 tcgacaatcg aaggtttaga agctattgca ccgagaaagg gatcacatta caattctctt 4920 ccaggagtta tccccaaggc aatggccaag cagagaagac gaatcgaacg attttttatt 4980 gcttaaagaa aaagttggaa caacgtaaag gaaagtggca tgaggaactc cctaatgtac 5040 tatgggctta tcgcaccaca aaacggaagc caacgggtga aagcccattc tctctcgctt 5100 atggtactga agcggttatc cccacagagg tcggtctacc tacggtcaga acattagttg 5160 tggaaaatgg cgagaacgat cagcagctag cccataacct cgacttagtc gaggaacaaa 5220 gagagatcgc cgcactacga cttgcgaact accagaacca agttgccgct tacttcaaca 5280 aacgggttaa gtcgaaaaga ttcagggtag gagaatgggt gttgagaaag gtcatggaaa 5340 acacaaaaga tttgaatgca gggaagcttg gacgcatatg ggaaggacca tatgaggtga 5400 ccgaagcctt cggaaaggga gcttataaac tcaggcacgt tgaaacaggt cagtatgtgc 5460 cgcgcccgtg gaacgcaatt catttgagaa agtaccacat ttaacttttc gtgtttatgt 5520 tttccgtatt taaatttctg tttccagtaa tgttgaaggg taaatccctt tctgttttcc 5580 ttgcatatcg aagggtgtat ccctagatgt ctgttgacat ctccttattg tttgataaat 5640 aaagttgcat ttcatccgaa tcttaaaata aagtctaaag ctgaagagta taaactaagg 5700 gatgaggatc gaatcaagat cgaaaacata agatcgagtg ggaaaagaaa acccaagatc 5760 ggatgggcag agacccaatc aagatcgaaa atcaaagatc gagtgggaaa agaaaaccca 5820 agatcggatg ggcagagacc caatcaagat cgaaaatcaa agatcgagtg ggaaaagaaa 5880 acccaagatc ggatgggcag agacccaatc aagatcgaaa atctaagatc gagtgggaaa 5940 agaaacccaa gatcgatggg caaagaccca atcaagatcg aaaatctaag atcgagcagg 6000 aaaggaaaac caatgggcaa agacccatcc aagattgaat agaggaaaat gaggcatgac 6060 atgtacaaag gtaaaaagct taggcagtgg gacgttgttc tcctgccgta aaagagaata 6120 tgttttattt aaaagaggaa aacctcttgg atgttggaca catagtgcga taaaagacaa 6180 gaatgagaag taaacctact agcaaaaagg gaaaaacaag gacaacatca ctactagata 6240 tcccagtagt ggttggacct aagggcccaa cttattacaa gcaaaatgac acctagtcta 6300 acggggtaga gagactatcc cagtttacgg aaggaaatgc cgctttcgcc ttggagcgga 6360 aatattggac gccttgctta aaaccatcat gtatgccatc tgagtgagca gcagacacgg 6420 cacgatcggc agccattaat tcccccctga gacgatccac ctggtgttca gcgcgttgta 6480 agtgtccctt cagagtttca cgctcgttca atagtaggga gtagtcgaag cactggggac 6540 agcgtgggtg gtgacgggaa ggtgcgcgag aaggacccgc ttcatctcct gcataagggt 6600 cgggagaacg agcgatagag tcaggagccc gagttgcgta actccctccc ggagagacca 6660 ttctgtcagt aacaggatta agagcccgag tggtatgatt tagcctcgga gagatcattc 6720 cgtcgacaat ggagtctaga gcttgttttc cacccgatct tgttcgagac cggtatgagg 6780 attcacgaaa agtgttaggg acttcagaag aataagaagc cctccctggc gaacgagaag 6840 aggagttaga acatagctcg attacattcc tagaacccct ggaacccctc cgggagcttc 6900 tttttttggg aacatcagcg tagagccgga agtggagctt cacttttcga ttgttagcca 6960 tgaagatcca ggtactacct aatggctctc aaacacccct ttatatagag gcaattcgag 7020 gttgatagaa acgaaaattc aaaatctaag gtgatcgtat cttattaaga taagttaatc 7080 tctttggttt gaaaactcaa atttaaggat aaaggatatt gttcacattc agttaaaatt 7140 gaaaatcaaa aggaacggat aggaagagtt aggcagtgga agggcgaagg cccaatttgt 7200 gaacgacaat cacgcgaaga tacaacggag ataataaagg aaaaaacata ttacaaacac 7260 agatggagtt ttagcccacg agaatggatc accaacacaa atggggttta gcccaaaaga 7320 acagaccacg cgattgcgtg agctactgag cgccgaaacg agggccggat tgaaagcctc 7380 caaagcctaa actcgagatg ggtccggaag tagtaacaaa cccgctgcct gggataggat 7440 cagaagaagc aggttggtct gagggtctcc gatctttagg atccatccct tcgtaccact 7500 cgtatccacc cggctcaatc cccatatggc gatcatacac gtcaggatca tctacaaatc 7560 gatgttccgg gcgttgctgg ctttgcaccc aaccaaatct gaagctggaa gccatctcct 7620 tacgtatttg ctgcatgttc atctcgcgct cagtggccct cgctcgcttg acctcggcca 7680 actcttcctt cgcgcggcgt acttcggacg tcgcagcatc ccgagctcct ttcaaacttg 7740 tgatctcttc ctcatatccg tgaagtttag cccggtactc tctgacctgc tgctgagtaa 7800 ggctgaggga ttccaacctg gcagctagtc tgtctgattt ttccttttga aggagagcca 7860 tctggaaaca acgttagggt taaagcttac agaaatgacg aagacatgag agaatgaagg 7920 aataccttca taaggcaatg agattcatag gagtcgacat cgtcatcgag cattgcctca 7980 aaacgaccgg cgtcactagg atgagccaag cccctcgcca cagcagtagc ggcacttgca 8040 ttgccccata gatcgtcgcc aagggtgacg tgactcccat ctctttttgt gaactcaggc 8100 ctccaagctt gagatgaatt gctggaacca tcgccactag ccgagccgaa ggtgggagga 8160 gccgattgcc attgcatggg tcttggggtt gtgccgaaga tagtcggcga accacgccta 8220 gactttttgg gcctatctgc cagaggacgt ttatccgacc tgcctgcaat tctgggcaca 8280 ggaagatcac gtggaggcga cgtaacgcag cggggcggtg gaatgtcaga aggtggtgaa 8340 gccatcgcag gagaataatt cgagtcagaa tccgtgtccg attgccctga ctcctcgtct 8400 tctcctcctt cgtcttcttc ttctgagccc tccgttcgag agtcggtcac aagtaaggaa 8460 gactctgcgc tgaactgaag gtcaagatcg agagcgaaga tagatttaag tagggggtct 8520 gggggcaacg accggtcgac caaacagtac gggaagtaaa tgatggagtt gcggagagag 8580 gtgatttgag tgagggtgtc ggcaacttct ctagagctcc atatcttcct cgtcacaaac 8640 ttctttagcc agcattttcg gtctttggaa atgatctgtt cgggaccatc tgataaagct 8700 gcgaaagaaa ttcatggtaa gtaaagtccg catatttatg aaaaaaataa taaaggtaaa 8760 tttatatata ccaggtttag gaccgaaagc agaaggaata gatagttgtg acagctcggg 8820 agccttccag ttccccgaaa tcagaagagg gcggttcttc caatctctgg ctctcgaagg 8880 gcccaatgac aagaatttct tacgatatct aggtttaaaa ttaaagaagc tagtttcacc 8940 cttaataacc gtcaagtcga agagatagag aaaatcccta aaacctaagg atacgcctag 9000 cttcagaccc aatgccagaa aggtcgacat aatcaagtaa gagtttgggt tcagttgcat 9060 agggtgagta ttagtgaaga ataagatgag atgaatcatg gggtggagcg ggaaactaat 9120 gacccctaaa tggtccggag acaaaacggt agacccggct gggataccga ggcccgaata 9180 catgtcggct ccggcaggaa gtgggctaag gtgtatgtca tctggaacat gacctaggtc 9240 acgagccttg acaatttcga agkgtggtgg agtaccacca tatttagacc agggtgtacg 9300 tctcgacatg ataaacgggt gggagactta tcgkccaaaa tttggttaga taagacagaa 9360 ggggaatttg tgctcgtaaa cgtaagtgga atgtttgaaa tattctcgca agaggggttt 9420 gaaatggaaa attacctgta aactaagagg tcactctgaa gcaagaaatc acaggcttgg 9480 agaagaaact aagcagagga agtgaagaaa agcagagatg gagaaacaca aggtaatgac 9540 acacacacac acatatacat atatatacat atatatatat atatatatat atatatatat 9600 acatgcgtgc atagagatgt acacgaatat atgaacagta cgtgcagaga tccgcatgtc 9660 agtatgcaga gatatgcaca cgtatgttgc tcgtaggtct gcctatatat gcctacgaat 9720 ccaaacatat atatgtatac acatataaag tgcatatgca tacacataca tatatatatg 9780 tgtgtataca tatagaaaag catgcaaaag tctggcaaaa tctggacgtg atgtccacaa 9840 aagatatata tatatatata tatatatatg tgtgtataca tatagaaaag catgcaaaag 9900 tctagcaagg acgtgatgtc cacaagggta cacatatata tatatatata gaaaggcatg 9960 caaaagcatg caaaaatttg gccgggacag gatgtccaca aaagtacata tagggaaacg 10020 tgcaaaagtc tgtcaagaac gtgaggtcct caaaagtatg catatatgta tgtatatatg 10080 tatgtatgta taaaggtaag acgagacggg acaatgagtt atatgataga tacgcataag 10140 tgtgacatgt cagactgcac agttaaattt cgtcagtcct ctttcgtcat gtcagtccac 10200 tttcgtaatg tcagtcctct tccgtaatgt tagtccacgt tcgtaatgtc agtcatcatc 10260 cactttcgcc atgtcagtcc actttcgtaa tgtcagtcct cttccgtcat gtcagtccac 10320 tttcgtaatg tcagtcctct tccgtaatgt cagtcctcgt tcgtmatgtc agtccacttt 10380 cgtaatgtca gtcctctttc gtaacgtcag tccactttcg taatgtcagt cctcttccgt 10440 aatgtcagtc cataatgtca gtctcttccg ttgtgtcatt ccactttcct aatgtcagtc 10500 cttcgaatgt tagtcctcag tccaccttcg taatgtcctc gtaaatcctc gttcgtaaat 10560 ctttgttcgt aaatcctcgt ttgtaaatgt cagtctgctt tcgtggaagg tgtcagccca 10620 tattttatgt gaagatgtga ggtgactttc gtaaagtaag cgaaggagcc tgtttggctt 10680 tcgcgagtca ggcacacgaa acaatgactt tggtaaactt actgaaggta agtttacccg 10740 tagaaaaagc aactcccaca aatgttggtc ttagtaagaa atgctaaaag tttagctagg 10800 ttcaaaaagc atagtttcaa ggccacatgt gatcgaaaaa cttagttttc ccctatttta 10860 catacgtaaa aaagggaaaa aggggcattg tgggaggata aaatccgg 10908 // ID Ogre-VP1_LTR repbase; DNA; EDCOT; 6438 BP. XX AC AY936172; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 10-APR-2007 (Rel. 12.03, Last updated, Version 1) XX DE LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; LTRs; Ogre superfamily; Ogre-VP1; KW Ogre-VP1_LTR; Ty3/gypsy-like; gag-pol; intron; KW plant retrotransposon. XX OS Vicia pannonica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Fabeae; Vicia. XX RN [1] RP 1-6438 RA Neumann P., Koblizkova A., Navratilova A. and Macas J.; RT "Significant expansion of Vicia pannonica genome size mediated by RT amplification of a single type of giant retroelement."; RL Genetics 173(2), 1047-1056 (2006). XX RN [2] RP 1-6438 RA Macas J. and Neumann P.; RT "Ogre elements - A distinct group of plant Ty3/gypsy-like RT retrotransposons."; RL Gene 390(1-2), 108-116 (2007). XX DR EMBL/GenBank/DDBJ; AY936172; Positions 25540 19103. XX CC The element belongs to Ogre retrotransposons which occur in a CC number of dicot plant species. This superfamily of CC Ty3/gypsy-like elements is characterized by specific CC structural features, including an extra ORF upstream of the CC gag-pol region, a putative intron dividing the pro and rt/rh CC coding sequences, and a primer binding site complementary CC to tRNA(arg). CC In Vicia pannonica, Ogre elements occur at very high copy CC numbers (100,000/1C), making up about 38% of the genome. XX SQ Sequence 6438 BP; 2101 A; 1268 C; 866 G; 2203 T; 0 other; tgtcataccc caatttttga cctaagatcc ctcttcacat tgcatacact tgcaatgcat 60 cagtcaacaa gagataggct tgcatgatga atcaattgat tagacaaggc tcaaagtcaa 120 gaaagcattc atctacaagt caaggaccaa ttagggtttc cttgatcact tcaaggcaag 180 tgatctatct tcatcaacaa tcaacatttg atccccaaca atccatgtta tcaggctcaa 240 gcttgaggat tgatcaaatt agggttttgg tccaagtaat gcattcttga cttttggctc 300 aaggcatgac caagtatcct aagaacaagg ttcaaataat cccaatacac tttgggaatc 360 aacccacaca actttcttag gtccaaggga tggatacaag aaaaatcagg aattagggtt 420 tcctcgattc ctctgataca caagggcaaa atgggaattg atgcatccaa tcaagcattg 480 gtcatcaaca tcatgattat catctcctaa aacatcaagg atttgaaaat cataacaaga 540 atcacaagtt tcccattgaa aaaatcaaga aatctcagtc aactgaaaaa gtcaactgtg 600 cagtcaaact ttgacttttc aaactttttg gtcaaccaag tcaattttgg gtcaaggatc 660 atgaaaatga agttagattt tcaatttgat caaccaaaat caagaaatca gagattgctt 720 gcatttgaag aaatttccaa cacttagaaa aatttctaag tcttttcaaa atctaacaaa 780 tgcaccactt taccttgagg ccattcaaaa ttagtgaaca attcttgggc gcatcctttt 840 ctgttttaaa gtacatctaa caagcttcac ataggccttg gaatcattca aaaagaccaa 900 gaaacaaaga agttatgatc ttgacaagat ggccaaaatc aggaaaatct gggcagccag 960 gcaggcaccc tggcaggcca aatttggcca ggtttggcac ccaagttgat ccaatcatat 1020 ctccctcatt tctaaataat tttggacaaa tgaatactct ttagaaagct ctcataacct 1080 actttcaaat gcccaaaaac atttcttcaa ttggatcatg gtttggaaga atcaagccct 1140 tactttctgc atgccaagtg tttgatcaaa tgcatggctt gacaaggcac aaacttggca 1200 actctgcatt tctgccactt tgaaacatca agattacagg tccatttgag gtatcctcca 1260 ataccactct tgttaaacat caagaacaaa gttgtatgat gccattccac ctttccaaaa 1320 catccaaaac cttaaggatt catccatggc aagtgtgact tctgattttt gaattagagg 1380 ttcaaaatct gttttttttc ttggacttta gctctatgat cacatgccaa ccatttagtt 1440 tgattctaac tagataggaa tctcagaaca cttgagtgca agcctttgaa ttcaacacag 1500 caggtctgag caaagatatt tgcttggagt ccaaataaca tgtgatactt cacttgcaag 1560 caaaagatca aacctcctta tctctttgca atctgatcct cagctcctct cctataaata 1620 gaggtgttct tagacctcta acacacacca attcacagca ttccatagct caatctctct 1680 tcttcctccc tttaacaaaa ttctgcaact ttttcttcca atgcaagaaa cattcgagtt 1740 ttgaatttga gagtgatctg aggcaaacaa accatgccaa catgattcaa atatcatttg 1800 tggtatgtcc atgccctcca tacacttgct gatccattaa atcaccaagt cactatgcaa 1860 aacctccatt gaagcttggc ctctgaattt aacaagccat attgagttcc acttgtgttt 1920 ttcttcattt caacacataa acactcccta cacatcatat atgagctgtt ccaaccattg 1980 aaacacagcc atagcacctc catcatcatc ttcaaaatct caaaatccat gtctgcaact 2040 tgaagtggag agaaagattc aaggagtttc aggaccaacc aagcattgga acatgaccag 2100 gggagctcac tgaagctatt tggatcattg ccacactctg aaagtccacc atttgagttt 2160 cacgatttca cctccatagg taaactttct gaaacttata tatcatcata catgcatcaa 2220 tttcatattg tgtttgaaga gaagtgtttt atttaagttg cttaagctat ctgaatcacc 2280 aatttgagcc atggtcgtgt ctgttaagag attgagattt tagctcagtt agggtttatt 2340 tggggatgat gaaaattcat ccaatccatg aactgttgat ggaattggat agaaccattg 2400 aattccccat gaaattgtga agaactttgt tctttacact ttgcaatttg gttgagaaat 2460 gaagaaattc gaatttcaga accagggtgg ctggaggttg aagatgaagt ctttaacacc 2520 tggtttttca aaaactaggt gtaattggct ttattttatt taatttttca tttaatttca 2580 atttatttga aaaatttgtt ttatttaatt gaccaccact aaaattccac aaaaattatt 2640 ttaagttcat aaaatattat agaatttgat tttataattt atttatgatt ttcttgcatt 2700 tttgaataaa atataaattg tgaaactttt attaacttaa ttgttttctt aattttattt 2760 tcatattttt attaatcaat aaattatgag aaaaatcatg gaagcttgaa attaatcata 2820 ttatttgatt ctaattttgg tttggcattt ttcaaagttt tattcaaaat tatatttaat 2880 tggttaaata attctttaat tgtttaatta attaaatttg ttttatttca attgatctcc 2940 atttgatttt aaagcattcc aaaattagaa tcatgatctc ttgagttttc tcatagttta 3000 cttgatttta ttttcaatca tttgaattta ttttgtcatt taattaattt ttgacttaat 3060 tttcaaatat taatatatta ggaaaatatt tgtttattct ttattcaaat ttccattttt 3120 cttctatatt tgatttccaa actctttgat cattcaatat ttgaagtatt attgctttca 3180 aattaattta taatgatcat ataattttta tcaaagcagt tagggttttg tttctgacaa 3240 atgtcaaaaa ccctaatctg acaaatcact ttgtttcaat ttcaaatttc aaactatatt 3300 attgattctt caaaatatct tgtttgatca aagcaacatt tgagacattt caaatcaatc 3360 catgaccata tacttggctc attttcaaaa caattagggt tttgactttc aaatctctga 3420 aaacccctga tgcaagttta aaaacttcaa aatttgcttt gatcaaacaa atgtttgaaa 3480 catcattctc aaatgatttt aacattgatc ataaacactt tgggcctcta atagagtgta 3540 agtccctcct ttcccttttt ctttgttttt gaacaaaaca attcatccct ttttcttttg 3600 tttttataca aagcaattaa tcaacttttc tttgtttttg acaaacaatg atcacaaact 3660 tttctttgtt tttgacaaac aaataatcat aaacttttct ttgttttaaa caaacaaata 3720 cactttgggc ctctgacaca gttgtaagtc ccaacccctt cctttttcct tgtttttaaa 3780 caaaacaaac aatcaatttt tctttgtttt tgacaaacaa taaatcaatc aacttttctc 3840 tgtttttgac aaacattgac caataaactt ttctttgttt ttgacaaaca ttgatcatca 3900 aacctttctt tgtttcaagc aaacaaatac actttgggcc tctaaaagag tgtaagtccc 3960 ttcttcccct tttctctttg tttttggaca aaacaattct tccacctttt atattgtttt 4020 tagacaaaac aatcaatcat tttctttgtt ttaaacaaac aaatgcactt tgggcctcta 4080 aaagagtgta agtcccttct cccccctttt ttctttgttt ttgacaaaca aaaatcaatc 4140 aacttttctc tgtttttgac aaacaacaac caatcaactt tctttgtttt aaacaaacaa 4200 atgcaacaac aaatgcactt tgggcctcat atacagttat actttatttg atcaaagcat 4260 aattgaaaca tttccaaaaa atcaatagca aaccatgcac ttggttgatt tcaaaacaat 4320 tagggttttg ttttcaaaat actttggaaa ccctaattca cctcaaactt caaggattgc 4380 tttgatcaaa tcaaacattc ttgcaccaat catccatgat ctttaaactt tgaaaacttc 4440 aaaattgatc atgggcatcc cttatggtgt aagtcccaac aatttttctt ttctcttgtt 4500 ttttggacaa aacaatcaaa tcttctttgt taaaatcaac ttaagaaact ttgggcctct 4560 cttacagttg taagtcccat ctcttttttc aaaacatctt tgaaaatctt ttgcaaactt 4620 ttctttgttt ttttgacaaa caatgaacaa accttttctt tgttttagac aaacaatgat 4680 caaacaaact tttatttgtt tttgacaaac aatgacacag tctttcactt tgctttatca 4740 gcaaaacaaa caaactttgt tttaaacagt gatcaaacaa acttgggcat ctcttacaat 4800 tgtaagtccc attccttttc aaaacctttt acttagtttt tgtacaaaac ttttagtcat 4860 ttactttcaa taaacattgt tgtaaatacc aattcaatac ttgtaaccaa gttactttgg 4920 gcctcactcc aagtataagt cccaatcctt tcctgtttgc ataaagattt taaagtttgt 4980 tgggcaagca caggtaagtt ttcctaacac cttcaaacct tgtatttcct tcacaacttc 5040 ccatatctgt taaatgaata tttgtatata tatacttgta tacagtcatt tcaattacaa 5100 cttagtataa cactaggttc cccaatgcct actcttgggc tttgtacaaa agaactcccc 5160 tgttgagtta gcctcctatt gggcttcata caaagaaaat caactagttt aaggtagaac 5220 acaagaatga tggtttctcg gtgaaatcca ttcttaacat agagtgatgg tttctcggtg 5280 aaatccactc ttagagccaa agccagccat acataagctt actcttgggc ttctaactac 5340 aatggattaa attcctagca aaacaagctt cctcttgagc tttcaaaatc acaaggaccc 5400 gagatgaccc gagatgaccc gagaaatgcc tcctcttggg ctaacaatac aaggacccaa 5460 agggcttctt ataagcatcc ccctaggata gaactaatca aatttagtct cccttagaga 5520 tgttgacatg attcatctct atggaaggag tatttcctct atagcattac aatcaatcat 5580 ttcaatcaca aatcacattt ttatcataaa tatctttctt atataagaac tataagtggc 5640 acacttgaac actcaagatc attgtccatt tcttattata aaaagatttc aaacatttta 5700 aacatcttat caatataaga actataagtg gtatgcttgt atactcaagc caaaaacacc 5760 catttcttgt aatgaaagat caaaaatcac ttacacatca caatgattgt aatgaaatag 5820 atgaaataca cttttcattt agatgacaaa ttgccattgt ctcttttgct tccacaagca 5880 tcatatgtgg gaactacgat tactctgact ttctcaacat ccttttgaga atacgtaggc 5940 acgaggtctt atccttggcg agtataactt tttcaattaa aaaccctttg taaccatagg 6000 tacccattag atcgagctac aattgctctg attccaacta gtggatatgt atgcagagga 6060 tttcaataat ctttgcgagc atcatcaatc aaacacttag atcatccatc aaacatatca 6120 gaaaccaagc aaatagttta gaaagccaag aagtgaacaa aagttcctat agagtactat 6180 agatatatag ggtgctaata ccttccccgt atataaccaa tccccgaacc aataagaatc 6240 tctgcgtatg cactttgcgt acaacatagg gtttatgtaa ctttttccct tttccttaat 6300 cctgttattg gaaacaataa agttcggcgg taacctttta taaaacaaaa gtaccacaga 6360 aaatgaaatc gtcgtgagag taggaagtct tgacttctta ttcccattcg tatgatttat 6420 cctattttca ccgcgaca 6438 // ID Copia18-VV_I repbase; DNA; EDCOT; 3756 BP. XX AC AM451396; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW internal portion; Interspersed repeat; LG_I; Copia18-VV_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-3756 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server i), W265-W268 (2007). XX RN [2] RP 1-3756 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 697-697 (2007). XX DR Genbank; AM451396; Positions 8310 4555. XX CC Positions [1243-1602] - Integrase core CC 'ATTTT' target site duplication CC LTRs are 95% similar to each other. XX FH Key Location/Qualifiers FT CDS 1710..3314 FT /product="Copia18-VV_I_1p" FT /translation="MCLPCPLKKDTSVTIPQPENFISLQMSPSQKINFFFP FT KSSLQGEISMMEDSPCESFEPLDLPHVSTHGDEEPVSSSVPTSVTHNFPQF FT PKVYSREKVIPEQKQVQESNSDLGNEIMVRLDPPTSTDSTDNLNLDLLIVV FT KKGTKECTNRPLYPLSHYVSLKHLSPAHKNFIVSLNTTIIPNTVYEALTKR FT EWKDAMREDMSALEKNKTWEIVERPKEKNIVDCKWIFTLKYKADGSLERHK FT ARLVAQTYGVDYQETFAPVAKMNTVRILLSLAAHYNRQLLQYDVKNAFLHG FT DLDEEIYMNIPPGFEGNTGNKVCKIKKALYGLKQSPRAWFERFAKVMKESG FT YKQSQGDRTLFVKHSAAGGVTVFLVYVDDIIVTETDEREKHEVKQIKELGK FT LKHFLGIEVAYSTQGIFISQQKYVTDLLAKIGKIGCKPVSTSMDPIHKLGE FT AKEKSVVDKRMYQRLVGRLIYLAHTRPDIAYFVSVISQFMHDPREPHLQAA FT YKVLHYLNGNPRKGILFKKNNTLALEAYTDTDYASSLVD" XX SQ Sequence 3756 BP; 1220 A; 734 C; 799 G; 1002 T; 1 other; tggtatcaga gctgtaggtt tttaagacct aggcatcatt ctagccttca tcgccatttt 60 tctagccttc atagctggat ttttttttat tcacgtgttc ttttaccaac cttcattgtt 120 gcgggttttt ttctttttcg cgatctgcct taattcccaa gagatcatat ttttttgtgg 180 aagatgtcgg aggttgcaga gatgactact acaacacaat cggaggagat tgttcgatct 240 caacatcccg aggaattgca aaacattcag gctgcgtata ggttggatgg aaaaaattac 300 cttaaatggt ctccacttgt tcgcactgtg ctgaaagaga aagggaagat cagccatctt 360 atgggtacag ggccgaaacc aggagatccc tgttttgaag catgggatga agaagattct 420 atgattatgg cgtggctgtg gaattctatg actcctgaga ttagcgacac atgtatgttc 480 ttggctacag ctaaggatat ttgggacgta atccaacaaa cgtattcaaa agctagagat 540 gcggctcaag tatatgaggt taaggtgaag acgattgcta caaaacaggg aagtaaaaca 600 gttactgaat atgccaatca attgaaagct ttgtggcaag aacttgatca ttatagggtg 660 ataaaaacca aatgtcctga ggatgccgct gttctaaagg atttcattga acaagataga 720 gtctatgatt ttcttgttgg gcttaaccca gaatttgatc aagtgagaat ccaaattctt 780 ggcaagcagg aggttccatg ctttaatgag gtggtggcat tgattcgagg cgagaaaagc 840 cgaaggagtg ttatgcttga accacaaacc ttggatggat cagccctagt tgcaaaaaca 900 aaatattcaa tacaaggaaa gaatgatcta cctaaacact taggtagaga caattagtgg 960 aaggagaaca aggacaatct ctggtgcacc ttttgcaaga aaccaaagca cacaaaagaa 1020 aagtgttgga agctaaatgg taaaccacca agttgtgaat gaggaaaccg tggaaggcag 1080 caaaggcctc aagcacacat ggcagagcag cccaaaacta gggaaaattc agcaataggt 1140 gggttcaata gtgaagaaat ggagaaactg agaagcttgt tgggttccct tgacaaacct 1200 actggaactt gttctttggc tctttcagtt actccccctt gatctgatgt tagcattgtt 1260 atacctaatt tccactcaat ggttcaaaac caatttgggg ttaaaataaa aagctttagg 1320 acagacaatg ctagagatta cttcaaccag attttgtcac cctattttca atcacagggt 1380 attctccatg actcatcatg tgttaacaca ccccaacaaa atggggtagc tgagaggaaa 1440 aatgggcatt tactcaacac aacccgagtc ttactctttc aagggaatgt tcctaagtcc 1500 tattgggggg aaattrttct tactgccaca tacatgataa atagaattcc ctcacaagta 1560 ttagacaaca aaagccccgt caagatactt aagaatttct attcacactt caaaacccca 1620 aatgggctta ctcctagggt atttggctgc actacatttg ttcatgtcca cagccaacat 1680 agagacaagc tagacccccg agccataaaa tgtgtcttcc ttgtccactc aaaaaggata 1740 caagtgttac aatccctcag ccagaaaatt ttatatctct gcaaatgtca ccttcacaaa 1800 aaataaactt ttttttcccc aagtcctctc ttcaggggga gatttcaatg atggaagata 1860 gtccttgtga gtcctttgaa cctctggatc ttcctcatgt ctcaacccat ggtgatgaag 1920 aacccgtgtc atcctctgtt ccaaccagtg tcactcacaa ttttccacaa tttcctaagg 1980 tgtattcaag ggaaaaggtc attccagaac aaaagcaagt ccaagaatcc aactcagacc 2040 ttgggaatga aatcatggta agattagacc caccaacttc cactgactca acagacaacc 2100 taaacctaga ccttctcatt gttgtcaaaa aaggcaccaa agaatgcact aaccgaccac 2160 tttatccact atcacactat gtgtctctta aacacctatc accagcccac aagaatttta 2220 ttgtgagtct aaacaccact atcatcccta acacggttta tgaggcattg acaaaaaggg 2280 aatggaagga tgctatgaga gaggacatga gtgcattaga aaagaataaa acatgggaga 2340 ttgttgaacg accgaaagag aaaaacattg ttgattgcaa gtggattttc acactgaaat 2400 ataaggccga tggatctctt gagagacata aagcaagatt ggtagctcaa acttatggag 2460 ttgattatca ggagactttt gctccagttg caaaaatgaa tactgtaaga atcctgctgt 2520 cactggctgc ccactacaat cgacaactcc tacagtatga tgttaagaat gcatttcttc 2580 atggtgattt agatgaagag atttacatga acatcccacc aggatttgag ggaaacacgg 2640 gtaacaaggt gtgcaagata aagaaagccc tttatgggct aaaacaatct cccagggctt 2700 ggtttgagag atttgcaaaa gtcatgaaag agtctgggta caaacaaagc caaggtgacc 2760 gcactctctt cgttaagcac tcggctgcag ggggagtaac tgtttttcta gtctatgttg 2820 acgacatcat agtgactgaa actgatgaga gagaaaagca tgaagtgaag cagataaagg 2880 aactagggaa actgaagcac ttcctcggaa ttgaggtggc atattccaca caagggatct 2940 tcatctctca acaaaagtat gtgactgatt tattggcaaa aatagggaaa attgggtgta 3000 aaccagtctc tacctcgatg gatccaatcc acaagttggg agaagctaaa gaaaaatcgg 3060 tggtagataa aagaatgtac cagaggctgg ttggtagact catatacctt gcccacactc 3120 ggccagacat cgcctacttt gtgagcgtga tcagtcaatt catgcatgat ccaagagaac 3180 ctcatcttca agctgcttac aaggtgctac attacttgaa cggcaacccc aggaaaggaa 3240 ttttgttcaa gaagaacaat actcttgctc tagaagcata caccgacact gactatgcaa 3300 gttccttagt ggattgaaaa tcaattacag ggtattgtac ttttcttgaa ggtaatctgg 3360 taacatggag aagtaaaaag tagaatgtgg tagcaaggtt gtctgtagaa tcagagttta 3420 gggttattac tcaaggattg tatgaactac tttggctgaa gattattcta gatgatttga 3480 gaatcaagtg ggatggtcct atgaagctct attgtgacaa caagtcaact atcaatattg 3540 ctcataaccc tatacaacac gataggacaa aacatattga gattgatagg catttcaaca 3600 aagaaaaatt ggaggaagga gtagtgtgta tgtcctatgt tccatcagaa catcaattag 3660 ctgatatcct aacaaaaggg ctgaatagtt caatatttca cgatcttgta ttcaagctgg 3720 gaatggatga catctattcc tcaacttgaa ggggag 3756 // ID Copia9-VV_I repbase; DNA; EDCOT; 4818 BP. XX AC AM473118; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia9-VV_I; KW Interspersed repeat; LG_I; internal portion. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4818 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4818 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 681-681 (2007). XX DR Genbank; AM473118; Positions 76834 72017. XX CC Positions [2063-2422] - Integrase core CC 'TTCTC' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS join(2222..3310,3314..4426) FT /product="Copia9-VV_I_2p" FT /translation="MLGTPEQNGVAERRNRTLIDMVRSMMSNSTLPEFLWG FT EALKIAIHILNRVPSKAVPKTPYELWVGRKPTLNYLHVWGCPAEAKNFNPQ FT IKKLDFETISCNFIGYPKRSKGFRFYCHGQGPKIVETRHAVFLENEYFSGR FT TELKKLTSNEVSTPMMEYGVTQEVSCNENENVPTIEVFLRRSQREKRPTIS FT NDYEVYLNECDYDVGLESDPTSYDQAINSENSTLWLYAMEEELKSMKDNEV FT WDLVKLPKGIKTIGCKWIFKTKHDSKGNVERYKAMLVAKGYTQKEGIDYKE FT TFSHVSNKDSLIIVMALVAHFDLELHQMDIKTAFLNGDLHEEVYMDQPEGF FT QDKGKAHMECKLKKSIYGLKASRQWYLKFQEILITFGFRENLVDQCIYLKI FT SGSKICIIVLYVDDMLLTSNNMGMIFETKQFLSKNFDMKDLGEASYVIGIE FT IHRDRSCGLLGLSQKNYIEKILKRFNMQNCSNSVAPIVKWDILCELQCPKN FT DLEKKQMDKIPYASAVGSIMYAQVCTRPDIAYVVGMLGRYQSNPGIDHWKA FT VKKVLCYLQMNTDYMLTYRRTDNLEIIGYSDSDYAGCKDTRKSTSGYIFML FT SNGPISWKSHKQSLIASSIMGAEYVACYEATCHAIWLRNFVSGLHVIDSIM FT RPLQIYCDNSVVARFSKNNKTTGGSKHIDIKYLVVREKVQNGVVSIEHIKN FT TLMLANPLTKGFPPKLFVDYVARMGLVASLSILD" XX SQ Sequence 4818 BP; 1625 A; 647 C; 939 G; 1606 T; 1 other; attggtatca gagccaacca attttggatc ataaacaatt agttatgtgt gtgttgttca 60 acttatgaaa caagtgttga tcaacccaat ggaggatcat caccatgttt gattatatga 120 caagagttta ataataaaag gttgatgaag tttttaccca acggtattaa acttctttac 180 gttttagtac ttttatttta ataattatgt catatctata tgatttataa attattataa 240 tccaacccaa cgaaaggatt ataataatat acttttggat tatgtgattg tagttcggtc 300 caacgaaaga actatgatat gatctcttat gtttatgatt aatgtgatat ctaacttaat 360 ttttgttgta gttagattat tgtaaagtgt ggtgttaaat attgtcatga tataaaataa 420 ttttcctttt gaattaaatt ttattttgca gcaatgaatc ctactgctat tataggctat 480 ttgtctagta ttgaacaatt aagtggggca aattttaaaa aatggaagga acaaattgga 540 attgttcttg gttgcatgga tttggactat gccttaagag agcctacacc cacaaagcct 600 acttctgaaa gtactaatga ataaaaggct ttatatgaaa agtggaagtg ctctaatcgc 660 atgagtctaa tgattatgaa aggttcaatc actcctgcaa ttcgtggagc aatctcggat 720 tcagataatg caatgaccta tcttaaatca gttgaagaat aattcttagg aacttccaag 780 tccttggcaa gcactcttat gatcaaaatg ataacaatga aatatgatgg tcatagtggt 840 gtacgtgagc acatcatgaa gatgagtgac atggattctc aattgaaagg aatggacatg 900 gcaatttctg aaggttttct tgttcacttc ataatgactt cccttccttc acaatttggt 960 cctttcaaaa ttaattataa cactcagaag gataagtgga aaatgagtga actaattgcc 1020 atgtgtgttc aagaagaaga gaggcttaaa ctggaaaagc ccgatatggc tcacctcacc 1080 attggtctaa ataaaaaatc cttcaagaaa ggtaaaggta agaaaaataa gtaaggtaat 1140 gatgtatctc acaatgggca aaaggatgaa aataagatac aatgtcattt ttgccacaag 1200 aaaggtcaca aaagaagaga ttgttctggt tttaaaggtt ggttggaaaa gaaaggtaaa 1260 actcaatgct tagcgtctta tgaatcttat ttagttgata taccaccaaa ctcttggtgg 1320 attgacacta gtgcaagcat tcacataatg aattcattgc agggatacct tacaagcaag 1380 agactaagta aaggagagcg aaccattact ttgggaaatg gaacaaaagt ggaaattgag 1440 gctattggca ctcttcattt aattttggat actggtttca ttatggattt agtagataca 1500 gtttatgttc ctgtttttac tagaaaccta atttcagtta caagacttga ttcttatggt 1560 tatgaattaa agtttggaaa taaagaagtt tccttgttct ataattcttg tttggttggc 1620 tctggcactt tacgtggtaa tctttattca ttgaatttag attgcaaata ttcacagtct 1680 cttttatctt atcatgtgta tgaattctct aaaaaacgaa atcgagtgaa tgaaaattca 1740 tccatattat ggcataagcg attgggtcac atttcaagag aaatgatgga acgtcttatt 1800 aaagatgaaa ttttgacttc acttgatttt tctgatttta ctagttgtgt tgaatgcata 1860 aagggaaaat acactaaggt taagaaaaaa ggtgcctcaa gggctactga attgttaaaa 1920 tgtattcatt ctgacatttg gggaccttat ttaattccaa ctatcaatgg acataagtac 1980 tttattagtt ttattgatga cttttcaagt attcttatgt gtatcttatt cataaaaaat 2040 cttaagcatt agattttttt agatttataa agctgatgtt gaaaatcaac tcaatcggcg 2100 aattaaaagt gtaagatctg atagaggtgg tgaatattat gctaggttca ccaaatcagg 2160 tcaacatctt agtacttttg ccttattttt aagagagtat ggtatcattg caaactacac 2220 aatgcttgga acaccagagc aaaatggtgt agcagagcga cgaaatcgta ctctaattga 2280 catggtgaga agtatgatga gtaactcaac cttgcctgaa tttttgtggg gtgaagcatt 2340 gaaaattgct attcacattc tcaatcgtgt wcctagtaag gctgtaccca aaactcctta 2400 tgagttatgg gtaggtagga aaccgacttt gaattattta catgtatggg gatgtccagc 2460 tgaagctaaa aattttaacc cacaaataaa aaaattggat tttgaaacca taagttgtaa 2520 tttcattggc tatcctaaaa gatcaaaagg ttttagattt tattgtcatg gtcagggccc 2580 taaaattgtt gaaactagac atgctgtgtt tttggaaaat gaatatttta gtgggagaac 2640 tgagcttaaa aagttaacct ctaatgaagt atcaacacca atgatggaat atggtgtgac 2700 tcaagaggtt tcttgtaatg aaaatgagaa tgtcccaact atagaagtat ttttacgtag 2760 atcacaaaga gagaaaagac ctactatatc aaatgactat gaagtttatc ttaatgagtg 2820 tgattatgat gttggcttgg aaagtgatcc tacttcttat gatcaagcca tcaatagtga 2880 aaattcaact ctatggcttt atgctatgga agaagagttg aaatcaatga aagataatga 2940 agtttgggat cttgtaaaat tgcctaaagg aattaaaact attggttgca aatggatttt 3000 taaaacgaaa catgattcta agggcaatgt cgaaagatac aaggccatgt tagttgcaaa 3060 aggatacact caaaaagagg gaatcgacta taaggaaaca ttttctcatg tttccaataa 3120 agattcctta ataattgtca tggctttagt agctcatttt gacttagagt tacatcaaat 3180 ggatattaaa actgcgtttt tgaatggtga cttgcatgaa gaggtttata tggatcaacc 3240 tgagggtttt caggataaag gcaaggcaca tatggaatgt aaacttaaaa agtccatata 3300 tggtctaaag taggcttcta gacaatggta tcttaagttc caggaaattc tcatcacttt 3360 tggtttcaga gagaatctag tggatcaatg tatatacctt aagatcagtg ggagcaaaat 3420 ttgtattatt gtattgtatg ttgatgatat gttgcttact agcaacaata tgggaatgat 3480 ttttgagacc aaacaatttt tatccaagaa ttttgatatg aaagatcttg gtgaagcatc 3540 ttatgtgata ggaattgaaa ttcatcgaga tagatcatgt ggattattag gattatccca 3600 aaagaactat attgaaaaaa ttcttaaaag attcaacatg caaaattgtt ctaacagtgt 3660 tgctcctatt gtgaaatggg acatactttg tgaacttcaa tgtcccaaaa atgatcttga 3720 aaagaaacaa atggacaaaa ttccttatgc ttctgcagta gggagtatca tgtatgctca 3780 agtctgcact cgaccagaca tagcttatgt ggtaggcatg cttggtcgat accaaagtaa 3840 tccaggtatt gatcattgga aagcagttaa gaaagtattg tgttatttgc aaatgaatac 3900 ggactacatg cttacataca gaagaacaga taatctagag attattggtt attctgattc 3960 cgattatgct ggttgtaagg ataccagaaa gtctacatct gggtatattt ttatgttatc 4020 aaatggacct atttcatgga agagtcataa gcaatcgttg atagcttctt ctataatggg 4080 ggcagaatat gtagcatgtt atgaagccac atgtcatgca atatggttga gaaactttgt 4140 ctcagggctt catgttattg attcgataat gagaccattg caaatatatt gtgataatag 4200 tgttgttgcg cgattctcta aaaataataa gactacagga ggatcaaagc acattgatat 4260 taagtacttg gttgtaaggg agaaagttca aaatggagtt gtctctattg aacatattaa 4320 aaatacactc atgttggcaa atccattgac aaaaggtttt ccacctaagc tttttgtgga 4380 ttatgttgca cgcatgggct tggtggcaag tttgtcaatt ttagattgat tgagagtgta 4440 atgtatgtga tcacattata atgagaataa agttcttgat tatgatatat tgatgattat 4500 tatgttactt ttatacatca tttttgtgca caatctagat gtttaaaagt tgatgggacc 4560 attatgtgaa tgaattagca ttattacctt aatgttgcta atgtcataaa agtcattgat 4620 tcatgttaat ggatgtgcta gtactataat ccttgaagaa tattggatcg ttgtgtgatc 4680 caatcatttc aatgatttgg tgttagtagt tccatgaaac ataatcttaa agtaaaggat 4740 gcctattttg agaaattgtt atggtcatat tatgttttaa tctattacaa atataattat 4800 gtaggccaag tgggagat 4818 // ID Copia38-PTR_I repbase; DNA; EDCOT; 4425 BP. XX AC LG_XII; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia38-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4425 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4425 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 252-252 (2007). XX DR Genome; LG_XII; Positions 3264592 3269016. XX CC Positions [1680-2180] - Integrase core CC 'CATAC' target site duplication CC LTRs are 99% similar to each other. XX FH Key Location/Qualifiers FT CDS 54..4415 FT /product="Copia38-PTR_I_1p" FT /translation="MTNLNPIVPVPQNSQTSPIIIHQDNSAFPTSIILDEN FT NYPLWSQLMEMRIGARNKTGYLTGAAKKPEPEDPMFATWITESQKVKSWLI FT DSMSPLLMQRFIRLSTAKEIWEAVSKTFYDGSDETRLFELNQKSFSIKQEG FT RPVSIYYNELVALFQEIDHRTASQGETVEGVVQLHSTMHRLRVHIFLSGLD FT FEFEQVRGEILRKDPKLDLESTYACIRREFQQRQTMGNYRTTSEHSVHSAR FT FTNQPRQGPASGIMKNRNNSSAGKYTGLVCGHCGESGHSKQRCYEIIGYPE FT WWDFSKKPRKKFAGKAMMTTTEAQTTAADKLPAVDNLPPTVNVAHSSSTGK FT ANTFSAITKDNNWIIDTGASDHMVRDTGQLQSLHSSTHSFISTANGSTSPT FT VGEGTVILTQNLTLNSVLVVPSLEHNLLSVGQITSALNCTVTFWSLFCVFQ FT DILTRKILGYGVKRGKLYYLELTENGGKRFGQAHQTRSSDTDRATIWLWHR FT RLGHLSFGYLRKLQPHLFNVVHDSEFHCNICEMAKSHRITYLPSLNKSSEP FT FAVIHSDVWGPAKISTISKARYFVTFIDECTRMTWMSLLHKKSDVFTAFQE FT FHRMVGTQYQKQIRSWQTDNAMEFLDTSVQKYLHHYGIRHQTSCTYTPQQN FT GLAERKNRQILEVVRASLFGMHMPRYYWGEAAKSAVYLINRTPSRVIDFQT FT PQQRMQSLLSTPHLPNLEPRVFGCTAYVHIPKVLRTKLDPCATRCVFVGYS FT DLQKGYRCYDPHTQKLHVTLDVSFRETESFYSKEGSIISSQGEQSSNEHLL FT QESDRNEFVELENIIEQFGSSGTNEKSQGRSSDEESQINIELPLLTPLTNE FT SSQNAESQVLLQPISDESNIFPDISYAQDVPPATAAPRCSQRSNKGVPKKQ FT YEPDHRVNIQYPINNYVSNHRLSESYALTVNQLSNISIPSNVQEALTDPAW FT ANAVNEEMQALQKNSTWELVSLPEGKKTIGCRWVFTVKLKTDGSIDRYKAR FT LVAKGYTQKYSVDYTETFAPVAKLDTIRILISIAASREWPLKQFDVKNAFL FT NGDLEEEVYMDLPPGVQCKSETRSKVCRLKKSLYGLKQSPRAWFGRFSSAM FT TAFNYKQSNADHTLFIKHQNGKVTALIVYVDDMVLTGDDPEEMQLLQEHLA FT AAFEMKSLGQLRYFLGIEVARSAHGISMSQRKYVFDLLTETGMLACKPAAT FT PMDINHKLGVFPNQVPTDMGRYQRLVGRLIYLSHTRPDIAYVVSVVSQFMH FT APSEEHLQAVNRILQYLKGTPGKGLLFSKHGVSSIEGYTDADWAGDQTTRK FT STSGYFTFVNGNLVTWRSKKQKVVARSSTEAEFRGMAHGVCELLWIQRVLT FT ELGIHYTDPMTLHCDNKAAISIAHNPVQHDRTKHVEIDRHFIKEKLDQKLI FT QFPFVQSAYQLADILTKAVSGPAFQRVITKLGMTDIYAPT" XX SQ Sequence 4425 BP; 1346 A; 931 C; 937 G; 1211 T; 0 other; tagtatcaga gcctaattaa tcaaacacga atcccacacg aatcccatac tacatgacga 60 acctcaaccc cattgttccc gttccacaaa atagccaaac atcacccatt attattcacc 120 aagacaattc tgcattccct accagcatca tattagatga aaacaattat ccattatggt 180 ctcaactaat ggagatgcgc attggtgctc gtaacaaaac cggatatctc actggagcag 240 caaaaaaacc cgaacccgaa gatcccatgt ttgcaacatg gatcactgaa agtcaaaagg 300 tgaaaagttg gcttattgat tcaatgagtc cgttactgat gcaacgattt attcgcctat 360 ccacagccaa ggaaatatgg gaggctgtgt cgaagacctt ctatgatggc tcagatgaaa 420 ctcgtttgtt tgaattaaat cagaaatctt tctctatcaa acaagagggt agacctgtgt 480 ccatttatta caatgagctg gtggctcttt ttcaagaaat tgatcacaga actgcctctc 540 aaggagagac agttgaagga gtggtccagc tgcattcaac aatgcataga cttcgtgttc 600 atatattttt gagtggcctt gattttgagt ttgagcaagt ccgaggagaa atattacgca 660 aagatccaaa actggacttg gagagtacat acgcatgcat aaggagggag tttcaacaaa 720 gacaaaccat ggggaactat cgaacaacca gtgagcactc cgtgcactct gccaggttta 780 caaaccaacc ccgtcaagga ccagcttctg gaataatgaa gaaccgaaat aattcatctg 840 ctggaaaata cacaggcctc gtctgtgggc attgtggtga atcgggacac tcaaaacaaa 900 ggtgttatga gatcattggt tatcctgaat ggtgggattt ctcaaagaaa ccaaggaaga 960 aatttgcagg aaaagccatg atgaccacaa ctgaagctca aactaccgct gctgataaac 1020 tgcctgctgt tgataacctt ccgccgactg ttaatgttgc tcactctagc agcactggta 1080 aggcaaatac attctctgca attactaagg ataataattg gataattgat acaggtgcat 1140 cagatcacat ggttagagac actggtcagt tacaatccct ccactcttcc acacattctt 1200 ttatttccac agctaacgga agtacctctc caactgttgg ggaaggcact gtcatcttaa 1260 ctcaaaatct cactttaaac tcagttctag ttgtcccatc ccttgaacat aatttgttgt 1320 cagttggcca aattacttct gctcttaatt gtacagtaac cttttggtcg ttattctgtg 1380 tgtttcagga cattctgacc cggaagattc ttggttatgg tgttaaacgt ggcaaactct 1440 attatttaga acttacagaa aatggaggaa agagattcgg acaagcacat caaactagaa 1500 gttcagatac agatcgagcc acaatatggt tatggcaccg acgtttggga catctttcct 1560 ttggatatct tagaaaatta caaccgcatc tttttaacgt agttcatgat tctgagtttc 1620 attgcaatat ttgtgaaatg gctaaaagcc atcgtattac ttatttaccg agtttgaata 1680 aaagttcaga accttttgcc gttatacatt ctgatgtatg gggtcctgca aaaatctcta 1740 ccatatcgaa agcccgttat tttgtcacat ttatcgatga atgtactaga atgacttgga 1800 tgtctttgct acacaaaaaa agtgatgttt ttacagcatt tcaggaattt catcgtatgg 1860 tgggtactca gtatcagaaa cagattcgta gttggcaaac tgataatgct atggaattcc 1920 tggatacctc tgttcagaag tatctacatc actatggaat tcggcatcaa acttcatgta 1980 cttatactcc acaacagaac gggttggccg aacgaaaaaa caggcaaatt ttagaagtgg 2040 tccgtgcctc tctctttggc atgcacatgc cgcggtacta ctggggagaa gctgcaaagt 2100 ctgctgtgta tctgatcaat cgaacacctt ctcgagtgat agattttcag acacctcaac 2160 agcggatgca atccttattg tccaccccgc accttccaaa ccttgagccg agagtgtttg 2220 ggtgtactgc ttatgttcac attccaaagg tgttacgaac taaacttgat ccatgtgcca 2280 ctcgatgtgt ttttgttgga tattcagact tacagaaagg gtacagatgc tatgatcctc 2340 acactcaaaa gttacacgtc acattggatg tctccttccg tgagactgaa tcattttatt 2400 caaaagaagg ttccatcatt tcctcccagg gggagcaatc cagcaatgaa catttgctac 2460 aagagagtga caggaacgaa tttgttgagt tggaaaacat aattgaacag tttgggagca 2520 gcggcactaa tgagaagtca cagggtagaa gcagtgatga ggagtcacaa ataaatatag 2580 aattgccttt gttaacacca ttaaccaacg aatcttctca gaatgctgaa tcccaggtac 2640 tcctccaacc tatatctgat gagtcaaata tatttcctga tatttcttat gcccaggatg 2700 ttcctcctgc tactgcagcc ccaagatgtt cccaaagatc aaacaagggt gtcccaaaga 2760 aacagtatga acccgatcat agagtcaata tccaatatcc aatcaacaat tatgtctcta 2820 accataggtt gtctgaatca tatgcactta ctgttaatca attatccaat atatccatcc 2880 ctagtaatgt gcaggaagct ttgacagatc cagcttgggc caatgcagta aatgaagaaa 2940 tgcaagctct acaaaagaac tcaacttggg aacttgtctc cctacctgaa ggaaagaaga 3000 caattgggtg tcgatgggtg ttcactgtga aacttaaaac tgatggcagc attgacaggt 3060 ataaagcccg gttggttgca aagggatata cacaaaaata cagcgtggat tatactgaga 3120 cttttgcacc ggttgccaag cttgacacaa tccgtattct catatctata gcagccagtc 3180 gggagtggcc tttgaaacag tttgatgtga aaaatgcgtt tctcaatggg gacttagaag 3240 aagaagtgta tatggacttg ccaccgggtg tgcagtgcaa gtctgaaact aggagcaaag 3300 tctgtcgttt gaagaaatct ctgtatgggt tgaaacagtc ccctagagct tggtttgggc 3360 ggttctcatc tgcaatgaca gcattcaatt ataaacagag taatgcagac catactctgt 3420 ttataaagca ccaaaatggg aaggtaacag cccttattgt ttacgtggat gacatggtgt 3480 taacaggtga tgatccagag gagatgcagc tgttacagga acatttagct gctgcattcg 3540 aaatgaagag cctggggcaa ctcagatact tcttaggcat tgaagtcgcc agatcagctc 3600 acgggatttc catgtcacaa cgcaaatatg tgtttgatct gctgacagag accggcatgc 3660 ttgcttgcaa accagcagca acccctatgg acatcaatca caagctcggt gtatttccca 3720 atcaggttcc aacagacatg ggccgttatc aacggttggt tggtcgactg atttatttat 3780 ctcatacaag accggacatc gcctatgtcg tcagtgttgt aagtcaattt atgcatgcac 3840 ccagcgaaga acatttgcag gcagtgaata gaattttaca atacttaaag ggtactccag 3900 gcaaaggttt gttattctca aaacatgggg tctctagcat tgagggatat accgatgctg 3960 attgggctgg ggatcaaaca accagaaaat ctacatcagg ctacttcact tttgtcaacg 4020 gaaatctggt tacatggcgt agtaagaagc aaaaagtggt ggcccggtcg agtacggagg 4080 cagaatttcg aggtatggct catggggtat gtgaattatt atggattcag agggtcctga 4140 cagaattagg gattcactat acagacccga tgactctaca ctgtgataat aaggcggcca 4200 tttccattgc gcataatcct gttcaacatg accgcacgaa gcatgttgaa attgatcgtc 4260 acttcatcaa agaaaaatta gatcagaaac tcatacaatt tccctttgtt cagtcagcat 4320 atcagttagc tgatattctt accaaggccg tttcagggcc ggcatttcag agagtaatta 4380 ccaagttggg catgactgat atctatgctc caacttgagg gggag 4425 // ID EnSpm2_PTr repbase; DNA; EDCOT; 12422 BP. XX AC . XX DT 10-DEC-2009 (Rel. 15.02, Created) DT 10-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE EnSpm-type DNA transposon - consensus. XX KW EnSpm; DNA transposon; Transposable Element; EnSpm2_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-12422 RA Bao W. and Jurka J.; RT "DNA transposons from black cottonwood."; RL Repbase Reports 10(2), 109-109 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 4933..7242 FT /product="EnSpm2_PTr_1p" FT /translation="MDDRSWMYRRLMDGRLRPEYITGVRRFINFAFSIDKN FT ISGGKIRCPCVRCKNQKFLKEDDVCKHLLTKGFLPCYENWTVHGEPYVAEP FT ILAGPSSVGISHVVNDVCLENPYRNLVMDAMGVGDAYSNDNVSSPVVAEEL FT PNPEATNFFKLLKAAEEPLWDGCTKQSKLSACVQLLNMKSTLNLTQTAFNK FT FIDFTKSCMPNDENLVSNFYDAKKFMRPLGLGYEKYDVCPNYCMLYYGADA FT MKINCDFCGSSRYKPRNPTSKGSNKAEKQLRYFPLTPRLQRLFMSPYHAKD FT MTWHHFHKSDNGVMVHPSDGEAWKEFNRVHLSFASDPRNIRLGLCTDGFCP FT FDMSSNTYSCWPVIVTVYNLPPWKCMTRPFMFLTMMIPGPKNPGKKLDVFL FT RPLIDELKNLWSVGVETYDVYRKENFQLRAALMWTISDFPAYGMLSGWSTH FT GNLSCPYCMEHSKAFRLKNGGKTTFFYCHRRFLPMNHPYRCQSDKFLKGVI FT ERLPPLPRPSGLEMLNEVSKYTEGHNGSSSHNDKIPGFGVKHNWVKKSIFW FT ELPYWHTNLIRHNLDVMHIEKNVFDNIFYTVMDCPNRSKDNLKARLDIQLY FT CKKPNLHLQQDTSGRVYKPKGTYCLHKKQQQEVLSWMKELSFPDGYASSIS FT RCVKEAQCKVSGMKSHDCHVFIQRLLPTAFRPYLPRPLWEALTELSVFFRD FT ICTTNLNAQHMELMQMNIIEIICKLERIFPPSFFDSMEHLTIHLPYEAKVG FT GPVQYRWMYPFERYVFILC" FT CDS join(7942..8592,9471..9941,9629..10003,10727..11083, FT 11339..11866) FT /product="EnSpm2_PTr_2p" FT /translation="MGPSTSVKCYNGYYVNGFKFHTQSYGRFKKTMNSGVC FT VKGSCYDDNERDYYGMLKEVVRLKYLGSKCKLFMFKCNWYDTKRGIRVHRS FT NGLVEIKHTSRLHGNEDFVLAQQCQQVYYTYPPGNKSSEWWTVIKTTARSR FT YNVDMGEFIEDANNVRSFDVDQSDEISQPCRVLPTQTLDDPNILVESSYYE FT EIGQHELLQLDINWGNEDEKGCGRRRRLWHLGKISVNFLFLIFNYELIYCY FT VVYIHMIMYIFFLVFSMPRRGSILDSRSDRSTQGVTGPLHPNHFKLHQGII FT TKDPHFINLCIRTQMSIIYLLWGVHILLNMIMGGLMHINIVRAFAFKICFK FT LKEVSLEITNLFMEDIIHIGVMGELMVMMMMQVHSRSDRSTSSKSFQTTSR FT HNNKGSTFHQPVYQNANEYYIPTLGSTHPPQHDYGRVDAYQYCEGFRFQDL FT LQTQGGFSRDNQLVYGGHNSYRSYGRVDGDDDDVNIRDEDEGDGSNERGVC FT DGWKKYSFPEEDESIVRNIWEDKARIALNQQLTRARKKAMSKENTTNIIDC FT LDKGPAWINNDDWNQMIKDVWSTPEFQRRSESARRNRLTKTDGKISTHSGG FT TVSFASYRANMVRIFFLCLRENYKMEMISKYGTDRENHPSFDGAAWCVASG FT GVTKGRVYGAPRMPKSIVSTSSSSHSYSVESSYPSSSYRALQKEIKDKEEE FT IKKKDDFILEMKRQMDSMKEYLVNNLGYHGGTSNIGQGMPPPLTPSMPPPM FT APQIMTPMGPTSQPIYRPTPRPLYPDQSCVDPQYHGSSSQPAP" XX SQ Sequence 12422 BP; 3932 A; 1806 C; 2203 G; 4474 T; 7 other; cactactaaa aacaggggta ttagcatctg aatttagcaa cggataattc cgttgctaaa 60 ttcagtaacg gatttgcaac ggattacaca tatattattt ttttaatatt agcaacggac 120 tttagcaacg gataatccgt tgcaaaattt acgttgaatt tagcaacgga ttttccgttg 180 ctaattgaaa aaataaaaat ttaaatstta atataaaacc aaaattatgt agaccgttga 240 ttacatgata aaatctgaac cgtttatttt cgctacagtc tctcccccca caccgaaata 300 cagagaccaa caaaaccaat tacagctgaa aattaattac ttccactctt ccagtatcct 360 ccttcgtccc taataacatc gatccataac tgttgaaaaa tcaccctctc ttcatcgatt 420 tcatcttcct ttatcccaaa ctgttcatca tcttcgcatt cgtcttcagc atccctaatt 480 ttttttcttc atcttcttct ccttcatctt aacagtttca atatttctct gcaaaccaac 540 aaaaacasag acccatggca acatcgcacc agacccatca tcatcaccat cgaacatcct 600 gatttacccc ttctccttgt aaacgggttg ggttttgcac tgttttcttc gatagctcag 660 gtaattaatt takggttttt gttttctttg ttgcaattta agttacacta aacagttcta 720 acctaacttt cccaatctca ggtgttattc tgtcgtgttg atccatctcc ctcacctgta 780 actgaagaac acaggtaaca attttttttc cgatactttg aataatggtt ttaggctatt 840 aattcgataa tataaggttt atgaaatgtt tttaccatga tttatawcct aattatgcac 900 gtttaaktga aaatttatga aaacccccaa attaattttt agggttacgg ttcataaatt 960 gaatgatttt atgcaactgg accaatgctg gcaattcttg tgtctggaag agagtgattg 1020 atggaaatta tgcatgttta attgaaaatt tatcaaaacc cccaatttaa tttttaacaa 1080 ttagtattat tgatgctggg tgttctttga tgtctgcaag tctttttgtc ctcctgtgcg 1140 cmgacaccta ggtgttttga atgtattcat atgcttatat atatataagg aaacttgctt 1200 gttgatgttg tgtttcgtta ataagattgc tgttttattt ttgtatcttc attcattctt 1260 ttttttcttg ctgttttact tgttatatat ataagtagca gaattgtgta gtgaaagagg 1320 ttagaattca tggttgcctc ctccttgcat ggtgatcagt taatttccca cattagctat 1380 atatgttgtc tgttttcact tgattgtcct gtcttgaggt cagcatgcat gatttggaaa 1440 cgttattgat caccaaatgg tttaggtggc aggcttttaa ttcagttcag ctaaaatgtt 1500 agatggtatc taatttttct ttttaatcct tccttccccc taattaatgt ccattattct 1560 caccttgcct agctagacca gcaacccacc cgtaaggatg caggatccca aaccctaata 1620 ttttttttta tctaaaatgc tcttaattat attttaatat gatagtcaca ttgagaattt 1680 aaaaaagtta gagaaacaat gtaagaaatg ggacatgatt ttttagtaca tgaaatatag 1740 taatttcact atttaatttc atttattttt tttaatattc tttctctgtt tttaaaaatt 1800 tccttaattt aactattttt ttattttatt tttttcaact caaaggcatt ctagatataa 1860 tagggagttt ggaactggct atatgactca tctatatgta tgcttcagct attgaatttt 1920 ggataaaaat ctgtaatatt tactcatttt gttacagtac ctaatgcttg ctttgttatt 1980 tggctttttt tttttttatg ggtcctgaca tgactttgtt caatatgatg gcttaggttt 2040 ttaagcgtgg catcaagtta tcttcctcaa taattaatca gcctttgggt tcttcttggc 2100 acgaaagcgg tgtgttgcgt tcttactatt atttaatatg gtctccttaa tgctttgtcc 2160 ttttgaggtc ttgtgctctt atactacatg tcatttacat ggaatatcat ttaatgcatc 2220 cagcttcctt tgttcatgca atttttctac atgtcattta ctgtttttat acaaactgtt 2280 accattttct gcatctgcta ccattgttaa ttagagttaa ttataattta gtctatgcat 2340 tttttatgat tttataagtt agtcattatg tttttgaaaa ccataagtta gttccttgtt 2400 ataaattaaa tgttagttat tttaaaattt caaaatgaat catgttcaag attgaaattt 2460 ttcaggttag atcttagaag aaaaaaattg ttatgagaag acaagtgcca aaaaaatatt 2520 aaaaattaat agtttaactt ggatatcttt ctgtttttca tagtttaact tggatttgtt 2580 ttaaagacta gcaagtgtta taactggatg ggtttaagat gttatgcaca attcctttac 2640 ctaagatgta cactagtaga tttatcaatg aatgtctact ggaattttgt ttgttgaagc 2700 ttattttaga gttatttgtt atgacattcc atttctgcaa ctgacctcat gtgtcagtta 2760 ttaactaaga ggtggacttg tgtattgtag cttcttggca ggagcagtgg atttcaagta 2820 gcatccactc atcggccatg tacaaaagga cgatgcaacg ttaagagaac tgcccttgat 2880 ggaactcagt acaatctctt actgttagac agtgaaggaa tagatgccta tgatcaaaca 2940 gtaagcgcat ttaccttatc aagatgaact gatgattgtt gtgctggttt tatgttttag 3000 cagttcaaga attgatgaaa tggctagtaa taattttatt aattgaagaa tttttttctg 3060 cgattccttc ttatttataa tttacaccat atccttttta tattcccaca cagctgctgt 3120 tttggattat gcagtaattg ttgttttggt tacctaggtc tatttacagc taagttgttt 3180 gtgctatgct ttttgtacct tgttgttttg ctctttgaac taaaagcatc tcattggaat 3240 ttccttttat gcaaaggctt ggttttgtag aaaaattatg tcctaaccat aaaaattcct 3300 attaagttat aggttttaag agataataat tagagtaaat tataatttaa ttttttaaaa 3360 ctataagtta gttccttgtt attaaattaa atgaaatttt cgcagcagat cttaaatgaa 3420 aaaatatttg ttatgagaag acaagtgcca aaaaaatatt aaaaattcat actttaactt 3480 ggatatgctt tctgtttttc atagtttaac ttggatttgt tttaaagact agcaattgtt 3540 ataacttgat gggtttaaca tactgtttat gttttttatt tttccagcaa tatgaatggc 3600 ttattggatc acaatataat ccaatagagt tggctaaatc tgattgggtt gcaataagaa 3660 aacctccacc ttgggccatt gattcttggg gcttaggtaa gtctattttg ctccattttt 3720 acatggttgc ttaattatat cgtgcataat ttttttgttg ggcatgccta ttgtaatctt 3780 ktcaagtagt tggaactctg cctttcattg ggacaatatt gatagtttgt ataagaaaac 3840 taattgaatg attttctttt attaaatctg atattgagtt tattttggat ggaaattatg 3900 agaccaaaat gaaacctaga ggtggctgaa taatatatca attaattgca aatttaaatg 3960 tcgtgctatt tgtcaagtct tgaaacatat tgtgacgttg agattgagaa gacaacattt 4020 ctcttacggt ctgctcatgt caattaatta acaataatat tatgctccat acgtattaag 4080 agaagaaaga aggcaacaaa tctactagta catgaaatta actaatttgg attgtgctta 4140 aagaatttat aaaacaaatg tatttatatt ttcatccacc agtattataa ttattatcta 4200 attattattt cactacgaca taaaagatag atacaatgta tatgataaga gacaaagata 4260 caaatgtgag taactattat aacccataat aaattatgtt tttttttata ttgcattttc 4320 atctttttaa aaaaataaaa aaaattcttt aatcttgtat tacctcgcat gtttctgatt 4380 tcatttacca tttcttagtt gagcaaaaaa agatccgaat aaaaataaaa agtttgatgg 4440 atccaataaa aataaaagga tccaaataaa ataaaaaaaa ctatttcagg tggtaacaaa 4500 agttagaagg accaataaaa aaaatgaact ccaaaactat tataaagata aatttattta 4560 atatttgttc aactaaatat ttttttttct ttatccattc attctgtata aaatactaac 4620 cgaacataat ctaaaaagta tatttttgtc actagttaga aaatataaat gacaatatga 4680 gtgtgtggga attcctcaca cactcatatt gtcacactaa acagcccata taattaaaaa 4740 ctcaataaga aaaagtagaa gaaaaacagt tatccatttt ttagcttcat atatgtgtga 4800 gctggacaaa taattaaagt ttgtttatgt ggtacatatt ttattttaaa ggattgttta 4860 agtactagta gttaaagaag tatgcttatt tctaaaaatg cttattggtg ttatcatgtt 4920 aattagatta acatggatga tcgatcgtgg atgtatcgtc gtcttatgga tggtcgcctt 4980 cgtcctgaat acattacggg tgttagaaga tttatcaatt ttgcattttc aattgataaa 5040 aatatatctg ggggaaaaat tagatgtcct tgtgtgaggt gcaaaaatca aaagttttta 5100 aaggaagatg atgtttgtaa gcacctattg acaaaaggtt ttttaccttg ttatgaaaat 5160 tggactgtac atggggagcc ttatgtcgca gaaccaatat tggctggacc ttcatcggtt 5220 ggaattagtc atgttgtgaa tgatgtttgt ctagaaaatc catataggaa tctggttatg 5280 gatgcaatgg gggttggtga tgcatactct aatgataatg tgtctagtcc tgtggtagca 5340 gaggaacttc caaatccgga ggcaactaat ttttttaagc ttttgaaagc tgcggaggag 5400 cctttgtggg atgggtgtac caagcaatcc aaattatctg cttgtgtaca attgcttaat 5460 atgaagtcaa ctttaaattt gactcagact gccttcaaca aatttattga ttttacaaaa 5520 agttgcatgc ctaatgatga aaatttggtt tcaaattttt atgatgccaa gaaatttatg 5580 cggccacttg gacttggtta tgagaaatat gatgtgtgtc ctaattactg tatgttgtac 5640 tatggggcag atgcaatgaa aataaattgt gatttttgtg gaagttcacg atacaaacct 5700 agaaatccaa ctagtaaagg ttccaataag gcggagaagc aactccgata ctttcccttg 5760 acaccaaggc ttcagagact gttcatgtct ccatatcatg ccaaagatat gacatggcat 5820 cattttcata agtcagataa tggggttatg gtgcacccat ctgatgggga ggcatggaag 5880 gagtttaatc gtgtccactt aagctttgca tcagatccga gaaatattcg gttagggtta 5940 tgcactgatg ggttttgtcc atttgacatg tcttcaaata catactcttg ttggccagta 6000 attgtgactg tttataattt gcctccgtgg aagtgcatga ctagaccatt catgtttttg 6060 acaatgatga ttcctgggcc aaagaatccg gggaaaaagc ttgatgtttt cctaagacct 6120 ttgattgatg agttaaagaa tttgtggtct gttggtgttg aaacatatga tgtatacaga 6180 aaggaaaatt ttcaattaag ggcagctttg atgtggacca ttagtgactt tccagcatat 6240 ggcatgttat cggggtggag tactcatgga aatctgtctt gtccttattg tatggagcat 6300 agcaaggctt ttagattaaa aaatggaggg aaaactacat ttttttattg tcatcgacga 6360 ttcctaccca tgaaccaccc atatagatgt caatctgata agtttttgaa aggagtaatt 6420 gaaaggctcc ctcctttacc tcgtccatct ggtttggaaa tgttaaacga agtgtccaag 6480 tatactgagg gacataatgg aagttcatca cataatgata aaattcctgg ctttggtgtt 6540 aaacacaatt gggtgaagaa gagcattttc tgggagcttc catattggca tacaaatttg 6600 attcgtcata atcttgatgt catgcatatt gagaaaaatg tctttgacaa tattttttat 6660 acagtaatgg attgtcctaa tagaagcaag gacaatttaa aggctaggtt ggatattcag 6720 ttgtattgta agaagccaaa tttacatttg caacaagata cgagtggtcg ggtttacaaa 6780 cctaaaggca cttattgtct acacaagaaa caacaacaag aagttttgtc atggatgaag 6840 gaattatcat ttcctgatgg ttatgcttca agcatttcac gatgtgtgaa agaggcacaa 6900 tgtaaggttt cggggatgaa gagtcatgat tgtcatgtct tcattcaaag acttcttcca 6960 accgctttcc gaccttactt acctaggcca ctgtgggagg cattaactga actgtccgta 7020 ttttttcgag atatttgtac aacaaattta aatgcccaac acatggagtt aatgcagatg 7080 aatataattg aaataatttg caaacttgaa aggatttttc ctccatcctt ctttgactcc 7140 atggaacact tgacgataca tctaccttac gaggcaaaag ttggtggacc tgttcaatat 7200 cgatggatgt atccatttga acggtatgtt ttcatactat gttaatttta ttcccttttt 7260 attttaaaaa ataaactaat tgacagaaat gatataggta tatgttttat ttgaagaaga 7320 aagtgaccaa taaagctaaa gttgagggtt ccatatgtga agcatacttg attgatgaaa 7380 ttaccaattt tgcatctcat tattttggtg atgacgtgca aacaatttgg aatcgagttc 7440 cacggaatga tgatggtggc cttaaaagtc tagatggatg tctctctatt ttttcctatc 7500 cagggaaaaa attatccaaa agattttata gaagacagtt gtcacatgct gaaatgcaaa 7560 ttgcgcataa ctatgtgata ttcaattgtc aagaactgaa gccttattta gagtaagtat 7620 gaaatattat tttgtactta atttataata atttattatt aactttaaca ttttaaaatt 7680 ttaggcaatg tcgtcaagag ctaaagtcac aacaaccaca tgcgagtgat gttgaaattg 7740 aaaaattatg cgaagagatc tttccaaatt ggttaaaaaa taatgtaagt attttaataa 7800 aattaattta tattttatgt caattagtta ctttaaaaaa attactaatc tcttttaaat 7860 cactatttct tatggagtta actattatgc taggtggaat accaatctaa cggaattgaa 7920 aatcaactct ttggacttgc tatgggccct tcaacttcag tgaaatgtta taatgggtat 7980 tatgtgaatg gttttaaatt tcatactcaa agttatggtc gttttaaaaa gacaatgaat 8040 agtggagttt gtgtgaaagg aagttgctat gatgataatg aacgtgatta ttatggaatg 8100 cttaaagaag ttgttcggct aaaatacttg gggagtaagt gcaagttatt tatgtttaaa 8160 tgtaattggt atgatacaaa acgagggatt agagtgcatc gttcgaatgg tttggttgaa 8220 atcaagcata catctcgact acacggaaat gaagattttg tgttagcaca acaatgtcaa 8280 caagtctact atacatatcc acctggtaat aaatcctctg aatggtggac ggttattaag 8340 acaactgcta gaagtcgtta taatgttgac atgggtgaat ttattgaaga tgccaacaat 8400 gtgagatcat ttgatgttga tcaatcagat gagatttctc aaccatgtcg tgtccttcct 8460 actcaaacac ttgatgatcc aaatatactt gttgaatcat cttattatga agaaatcggt 8520 caacatgaat tgcttcaact tgacataaat tggggaaacg aagatgaaaa aggttgcgga 8580 agaagaagaa gatgatgatg atgatggtga tggtgatggt gatggtgatg atgagagttg 8640 tggtggtggt ggtgatgacg acgacaacat ggttttgtgt gatgatgatg acatggttag 8700 gagtgatgat aataatgagt agcacaagtt aattatattt cgtagtatat gtaatgaatt 8760 atctttatta tatgtatgga tgatttcata ttatttccta tattacttga caatgtttag 8820 gctttcaatg ttttttttta ttattttatt caagtgtgtg ttatggatca cattacatat 8880 atcattttca ttgacctttg aaaccatttc taacctttca agtatcaatc tttaaattgt 8940 gattctgatg ttatagttta ttttgtgatt cgttttcttg cttatagatg ctgaggcatg 9000 aatgaaaggg ttcttcctac tcaatgtttt tatttatagg aacaaacatt aaggtaagca 9060 tactcataat tttgatttct gcttaattaa ttatttagat ttttattatt attattgttt 9120 gtgttaattg gcttttgaca atttaaactt catggctgat ttttattatt gcaaggatgc 9180 tttgatatct tttgtattgt aatacattgt gtttttcctc acttttttca acgaatcaaa 9240 taagttaggt cttgatgtta tttatatatt tgtttttgtt acagtaatac tttatttgaa 9300 gtataatatt tttggaagtg atggctatta agtggacaat ccatactgat tttgaacatc 9360 ataaactgga tattgtttgt aatgaagctg actacaaaaa tatcagaaag tttgtatgat 9420 tgaagtgaat tggaaaaaaa atgagattta acagtttgtt ttcattctag ttatggcatc 9480 ttgggaaaat atctgtgaat tttttgttcc tgatatttaa ctatgagcta atttattgtt 9540 atgttgtata tattcatatg ataatgtata tattttttct ggtttttagc atgcctcgac 9600 gaggatccat attagattct aggagtgaca ggtccactca aggagtgaca ggtccacttc 9660 atccaaatca tttcaaacta catcaaggca taataacaaa ggatccacat ttcatcaacc 9720 tgtgtatcag aacgcaaatg agtattatat acctactttg gggagtacac atcctcctca 9780 acatgattat gggagggttg atgcatatca atattgtgag ggctttcgct ttcaagattt 9840 gcttcaaact caaggaggtt tctctcgaga taaccaactt gtttatggag gacataattc 9900 atataggagt tatgggagag ttgatggtga tgatgatgat gtgaacatta gagatgaaga 9960 tgagggagac ggtagtaatg agagaggtgt atgtgatgga tggtagtaat gagagaggtg 10020 tatgtgatga ggatcaagat ggtgttccat caaaccacgg ttcaacatct tctccataca 10080 attatgatca aagtgttaaa aggaagggtt ttgacacacc aatagatcca attacaagaa 10140 aaaaagagct ttgtttgtat ggaacaacag agtaagttca aacttttaaa aactaactta 10200 ttaaggttat attttcaggt atgaaaaaaa ttacttatta ttgtgtaatt atttgtttaa 10260 tataagtttg ttattatata ttttcaggtt caataacgca tcgtgtggac gtgcaatcgg 10320 agatattttg aggtccaatt ttaagggagc atggcactct tgggaaaaag tagattcaat 10380 gtgcagggat gaactcttta aagagtttaa ggtaagaacc aacactaatt gccatattct 10440 tttcaatttt gatcacttta atgtagcatt atgaaaatta tcaactgaat agctataagt 10500 tgctgtaatt gcttttattt gtaaccataa attatcaact gaatagcagg gactgatttg 10560 tgttataatt tgttcttatt tcttgtttac tctttaatat catttaattt ctttagttat 10620 tacatcatct tgcaaattct gaacaagata acacaatatg attaattatt tatataattt 10680 gaaattttgt gcactctttt tacttggtat atatattatt tggtagaaaa aatattcctt 10740 tcctgaggaa gatgagtcga ttgttcgtaa tatttgggaa gataaggcta ggatagcttt 10800 gaatcaacaa ttgacacgag ctcgcaagaa agccatgtca aaagaaaaca ctacaaatat 10860 tatagattgc cttgataaag gtcctgcttg gataaacaat gatgactgga atcaaatgat 10920 caaagatgtt tggtccaccc ctgaatttca aaggaggtct gaatctgcta ggaggaatcg 10980 attaaccaaa acagatggca aaataagcac tcattctgga ggaacagtgt catttgcatc 11040 atatcgagct aacatggtaa ggattttttt tttatgctta agataatgaa ttaaaatttg 11100 tatatttatc ttttataata tttattaatc ttgaaagcaa gaggaagctg gtggaaaaga 11160 acctccatgg gatgatgtct tttcagcttt gcatcaaagt actaagcagt ctggtagctt 11220 cgtcgacaac aagtctaaaa aagtggttgt atgtattttt atttgattat ttcttaatat 11280 aacttaagta ttatttaaca ttcaaatgaa tttattgttg catgtatttt atttgtagga 11340 aaattataaa atggagatga tttcaaagta tggaactgat cgggaaaatc atccttcatt 11400 tgatggagca gcttggtgtg tggcttcagg aggagttaca aagggtaggg tatatggtgc 11460 acctcgtatg ccaaaatcta tagttagtac aagctcttca tcacattcct actcggtgga 11520 gtcatcatat cccagttcat cgtatcgagc attgcaaaag gagataaagg ataaagaaga 11580 ggagataaag aaaaaagatg attttattct tgaaatgaaa cggcagatgg attccatgaa 11640 agaatatctt gtgaacaatc ttggatacca tggtgggaca tcaaatattg gccaaggtat 11700 gccaccacct ttgaccccat caatgccgcc acctatggct ccccagataa tgacacctat 11760 gggtcccaca tctcaaccaa tttatcgacc tacacctcga ccactatatc ctgatcaatc 11820 ttgtgtcgat ccacaatatc atggttcgtc ttcgcaacca gcaccatgat tgtatctttt 11880 gttgtttttt tttattgtat ttcgacttaa ttgtattaat gcaagtttaa ctaaattttt 11940 ataatatgaa tattattttt attccatttt ttattagtga tacaattatt tttaatatta 12000 atttatgttg gttatatata ttctacaact tttaaaatat ccataaataa ttaattaaac 12060 aaattaaaag tcattttaat aaataaataa aaattaattt aataaaaata atataatcag 12120 caacggattc tccgttgctg attgtaaata atcatcaatc agcaacggaa atccgttgct 12180 aaaattagca acggaaatcc gttgctaatt tgcaacggaa aatccgttgc tgattgtaag 12240 caacggaatt tccgttgctg cgaaatcagc aacggataaa tccgttgcta aaaaatcagc 12300 aacgacaaat ctgcatccga tatttgccgt tgctgattcc gttgctaaat tgttttagca 12360 acggatttta gtattatttg caacggagta gttagttgct aattaccatt tttttagtag 12420 tg 12422 // ID Gypsy-7_Mad-LTR repbase; DNA; EDCOT; 540 BP. XX AC ACYM01142332; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-7_Mad-I; KW Gypsy-7_Mad-LTR; Gypsy-7_Mad_. XX NM Gypsy-7_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-540 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1410-1410 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01142332; Positions 4847 5386. XX SQ Sequence 540 BP; 160 A; 113 C; 118 G; 147 T; 2 other; tgtcacgggc cgcatgttaa aaacaaagaa aatgcccaag acatcatata tctaagccca 60 tgaagccatg tcttcatgga agcttctgga acgtcccgga gaaatcaaga acgtggcgga 120 gcattcaaga taatctaggg cattccggaa cattccacac aagtgtacat atttaagcct 180 cmcytagaat aatctagatt aggcaagttg tatctagaac tatgctagat atttttggat 240 gtaagtaggg gattctagaa ccctccattg aggaggtgac ttaggcctat aaataggagg 300 taaggccatt tggccaaacc atccaagaat tgtaagcaat tgtaaagttc tcttaagttt 360 caatacaaag cttcctttct cccatcttct aagtgatctt agcattctcc aagctatctt 420 agctttcttt gtgattcgat ccggggaagc gaggcttcga aggcttactt agcttgttca 480 tcgaggtatt caagtctaag tgccgcacgg gcggaaggct taaagagtca tcccgtgaca 540 // ID Copia22-PTR_LTR repbase; DNA; EDCOT; 560 BP. XX AC scaffold_3565; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia22-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-560 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-560 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 219-219 (2007). XX DR Genome; scaffold_3565; Positions 247 806. XX SQ Sequence 560 BP; 173 A; 90 C; 91 G; 206 T; 0 other; tgttggtgta gtttgtaaat gaataaagaa aagatgttta tcccacattg gaaagagaca 60 ctccctccta atgtttctaa gtgtgggttt ctattgtgta gtaaattaag ccatgatgga 120 caaactctcc tatttggctt cctaatgtta ttatatggac atttataata tcatttggaa 180 cttggaactc aatatgaata gtcatactat ttgatgaaca atcatattat ttcatcaaca 240 atcatattgt ttgatgaaca accatagtgt ttcatgaaca gtcatattgt ttcatcaata 300 gtcatattgt ttgatgaaca gtcatactgt ttcatcgtta tgtttcaagt ctataaaagc 360 atgttactat acagaaaaga aataacaaca aaaagacatt cttttcttgg tcttatcttc 420 tcattctttt agaggtttag agggcttagt tgtatcttgg aggtgttgtc tttgtgtggg 480 acaaataaac accttaaaga tggtgttttc acgcctctaa gccaactcca tatttgcttc 540 catcctaaat ttctctaaca 560 // ID Copia-96_Mad-I repbase; DNA; EDCOT; 6289 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Copia-96_Mad-I. XX NM Copia-96_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6289 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1730-1730 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 6289 BP; 1735 A; 1439 C; 1256 G; 1858 T; 1 other; cgttatcagc acgctcttga cgctacgcta acaagagagt ttgatcttca atttggggag 60 tattacgttt taatcattct tttcatgatt aatttaatta ttttattaaa ttgatctaca 120 tgctattgat tcaatttaat ttttctgtgt tgaacgtgat acaacgcatt ggagatgcaa 180 ttccggcttt cgaagaagga tcttctacaa attcaaaggc ttttgttgtt ttctgctact 240 caggtacgct taaaataaag gaagatattt gaaacgaccc atgaagcatg aaaacattcc 300 ccatgatgca tgaaccccct acatttatat ttaccttccg atatatatat tgtatatgtt 360 tcatatattk gtcaatatat atatttgttt catgcattac gcaataattg ctatgtggaa 420 tttgtgagtc aaagtattca attaaattag aagcatgttt cgggttttcc taaaccctaa 480 aggatttgaa aaaaaaaatg ggggaatcag gacatggtgc ggcacaccac cgcaccatca 540 ttgtgcaaat aatcaccagg cctaggcctg gattttacct cggtagggcc tgcagccctg 600 agcctatgca cactggcctt ggcccgcagc catccaacct gcccaattgt ctgggctgtc 660 ctcccataca cacgctgcaa cctttttggt tgctgggttt tgttgctctg gcccgcatac 720 atatagccag catatgctgg gcttgtcact gcgccaccca tacccaagcc cgtgacctgc 780 agtcactatg gggctgcttt cacgcaacca gccttcgctg ggatccccgt gacaacccac 840 aggccagctt gcgctagacc tgtccgtgca ctcccttgtg gcccaaaaca cgacccagct 900 gcggctaggg tctcccattc ctcacccgtg gcctgcagcc accaccaaag gaacatttgg 960 gcctcgcctt atgcttaagg cacccaaccc gtgcctctta acccccggca ttaagcccaa 1020 ttatttttgg ggctctattt tcgatccaat aatattattt taatattatt ttgcttctac 1080 gatcgacccc gaatggtccc gatctattga attaattaaa agtgacctgc agtccattaa 1140 tctgataatg aatccaaaat tattgacctg aagatcactt ttggacatta acgattcaat 1200 aatttatttc tcttctttga accgtcacat actttcgtag taacgaagct ctcacacttg 1260 agttcccgaa gacaactcaa atccactaca ctaagttagt atattgcatt ctgagtttct 1320 tgcaggaacc tctcctttat gaactaaacg ttcataaact aaattgaacc tgtagtttca 1380 aatttagtgc ctttgaaacc cgaagatttc ataaaacaat acacccatga aaacccgacg 1440 tttttcatga aaaccatgtc ttagaactcg aatgttctaa ctttgatgct tatggatgat 1500 tcattcccat agcaccaatc acaatcttgt tccctcaaat tcagtggatt gtcgaaccgt 1560 cacaagtttg attttcctga tttggacgtt ttctaataga aaccacttta ggtggggtac 1620 aagacgtgaa tctccacttg actatcaaga agctgagaaa ccattgatgc caacaatggc 1680 aaggaagagc tgaataagcc tccgccataa tcttcattcg aagacttatg ctcaaagcat 1740 tacaaatgga aatactcccc gaacgaggat tccatggctc tttggctcgc ttctatagac 1800 cgtctaatca tgaaagaaat tgcccgaagc aaaccatgat tacgtccatg aatgagtaca 1860 attctgaatt ttataaatcc gatcgaatct tgactggaga atacttttct cgtcattcca 1920 tgtttctaac tcgctcctga agcagcagtg tagaaagtgg aaatttacca aattctcgga 1980 tctgattact accacaaacg tgagagaaag gtatggaccc agttcggctg gagtctaccg 2040 aatggctcga cccagttcgg tcaaaaccta accaaatggt gatgcactgc ttcggcaggg 2100 atacactgaa tggcatattc tttcacaata caatttcgag tttgtgttca caaacatata 2160 gtataatcag ggcctgccaa ggtgtggcat catgcccgaa gcatgatcct tggtacataa 2220 gacctaaaac ttcaagaata agggataata ttctcgaacc tcaaccttgc aagaatctac 2280 tcccgtcttg atggaataga tcattggtta tgcacctgtt cgtgccccta ccaatgttgt 2340 tgaggagtac cattctagta gtcaatatgt gagattgatt ttgctccacc gaacatcgtt 2400 ggcagagcaa aatttcgaca tggatggcct tattggccga atccccttag taaatttact 2460 ttgtgaacat ttttccatgt tcttggattc aagtttggtg tatgttttac ttatggataa 2520 tcttattgat attgtcctcg aatatgagtt aattgaatca tgtttcttaa tacatgtgac 2580 cgattcaatt aaacacgtga ttaggtagga atgtgggaaa gttagttgtc tggatgaatg 2640 cgtactacgc acactaactt tacacctaaa tcacatctct aacaacgact tcaggtctat 2700 ccaacctgat taagagcatt ggcacgctcc tcgttgtatg aatgatactg aattatcatt 2760 taaaggacct taaattcttc ctgacgttga gtttttaagg atattcgaga tgacaatgat 2820 cataaatgaa accactgaag aaaatagagt gaaatatctt tgcaccacct ccaaaaatga 2880 gcctgaagct ttgatttggg gccaatgggt tgtctcccaa ctgggaatac accacatgtg 2940 gccggcctgt agcctggtga ttgagcagtt tacttgcttt ggcacgacct tttgggacac 3000 ttaggtcgaa caatgatgct acaacgcatc tccttacctg aagtaaggat cttgtgccta 3060 caagcacact ttgccaatcc tgctcattag ggaaattgat tttctatatc attccttgca 3120 aagatacgac acgactccat tttcgcagtg gattcaaggg aatatatgtg gactaatcca 3180 accaaaatgc ggaccatata aatacttatg gttttggttg atgaatcgac aaactggtca 3240 catgtttgtc cacacacatt actgctaaac ctcttggccg attaagggtt caccacccta 3300 cttatccctt aaggtctggg agactggata atgccagaga gtttatatcg acggttttcg 3360 ataaagtatt gcatgtcatt ttgggttttt aattgaacat cgaattccca tgttcacccc 3420 aaatagccta gcctagcgat cataaagcgc aatttaaatg atcgcccgaa ttttggtaaa 3480 cgtaccaagt tttcggtctt tgcctagggc tatgcaatcc ttgcacgcag ctatgttggt 3540 ccgccttgag gcccattgcc acccaaccta tatgacgtta cagttggtta ctgggtacga 3600 acctgacgac tttcgtattt acgcatttgg gtgcgcattc catgtgccaa gttgcgccgc 3660 cgcaacgtac caccatgggt cctcaaagaa ggatgtgtat cttttgtcga tcatgattct 3720 ccttcacact agctctcttc gagcccttgc acgcgatctc tttaccgctt atttgcgggt 3780 tgtcacttta atgagacagt cttcccgccg ttagggggag ataagaacgt caacgttcct 3840 gtagaacggc gcgaatttgc atggacgttg cccactatgt ctcatctcga tccccatacc 3900 gcacaagtgt gataagcaag tgcgacgaat tctagatttc agaatgttgc tccagacgca 3960 ttcctctgat ctagctaaag tgacgagatc atataccagc tgcaaacatg cctgcaagga 4020 tagacgtact taacggacgt cgagtcaaca tccctggagg gtgtgccgcc catgttggac 4080 ggtttggacg cccctgttgg acggtccggt acaccggcgg atagccaatc aatatgtctt 4140 ggcctggagc acgacatatc attcggttcg taggattcac ttccctggaa gaggaagaca 4200 cggcacaaca atgaatctaa actcgatcgc tgtctcaaat catttccatc tcatgagatt 4260 aatccggatt actcccgaga cttgaagttc ttggtccagt atactagttt ggatgagcaa 4320 aatggaattg aaatgagatt atcatcgatg atgttttcac ttatatggta gctaccgaca 4380 taaatgaaaa gcgacgatat cgaaccgtgt tccgttgatt aagtgacaac gtagaactga 4440 ttggacaact aaagttacaa tccaggtcaa attccttacc aaagtgtgta ttggacctgt 4500 cgttcctaca ctgcccaagg taaccctgtt gagttacaag tgggaaagga aacgttatga 4560 gatgaatgaa atagtgcgat atgatgcacg ccttacggcg caaggtttct ctcaaaacgt 4620 cctgtgattg atagcagcat tatgaaatgt ggttagtatt ttctccatgg ggatataaat 4680 acggagattt acgtgtaagt tcccgaagaa ttacatggac tggttcaaat agttccaaac 4740 cacggaacac cctcttaact cgttttgagg cgttcactta tggattgaaa aatccgacgg 4800 atgtggtata cccgtctaag tgattatttg atcagtcaag gatatgaatt atgcccttgc 4860 gtgttaaact atgaagtctt attccaaatt gctagagtta cagtttatgt cgttaacacg 4920 aatctcacta agactctgga agagcttgag aaaactgcct cgcacctgaa gatggaattt 4980 gagatgaagg atcttgggaa aactcgttta tgccttgacc tgaagttgaa gcattgttct 5040 gacggtattt tggtctacca gtcgaactac accccgaatg tgtcaccttt gagtataccc 5100 atgatcgtcc atacgttata tgcaaatgag actcttgaag aggctatgga atccgaaatt 5160 ccatatctaa aagttcaact ttgcgcttcg ttgtacttag ctcattgtat ttagacagga 5220 catctccttc gctgttgatc ttggtaaaga tgcagcaccg cgcctacacg caaccactga 5280 attggtatta aagacgtacc ctgaaggtac tacgtgggca aatcccaacg catcttgagc 5340 ggatctaacc cccctgatcc tcgaaatgat gcttgccttg tttgttatgc tgacgctggt 5400 tacttatcaa acccgcacaa ggcaaaatcc ccgaatggtt atgtctttac cgttagggat 5460 atcgcaatat cttggaggtc cacgatatga ccctagttgc gaaatcttcg aatcgttcca 5520 agactcacct tacttcacta tgccacaagt gagacatggt taggagttct tgttgagcat 5580 attcgaagta cttgctatat tttcatccat cgttgagtcc caacgacgat ccatgaagat 5640 tatgccacat gtatcaaccc gaccaagcca tgatacatca acgaagtcaa caccaagaca 5700 tattgcgtct acatctacat cagcaaagca tcaggagatt gaagtcatgc aaaccgatcc 5760 cagacaacct tgccgacctc tacacgatgt cactgccgaa gtcaaccttc cagaagcttg 5820 tccgaggaat tggtatgcct aactactcat atgcaatgct tgtagttctc atttggaagt 5880 tatgtcaaac tcagggggag tatccagaag tatactcact tgatcttaat gtactctttt 5940 tccctacgat taggagcatt tttcccactg ggtttttgct acctaactag gttttaacga 6000 ggcacccatc ctgggctgat catacccttg agagctcttc tacttgcgtc caaaagacgt 6060 atagttttga cttaatgcaa cttctcactt ttctccttag actatgggtt tttctcccac 6120 cttgggtttt accatagcga ggttttgtga gttttacttt ttatgcattc ttccgttgat 6180 ttgagactcg catttgccca ttgtgccgac gacttcatca actgtactta cttcatcaat 6240 gaagacttga tgcgccattt acttgagtat ttacacactc aagggggag 6289 // ID Copia-54_Mad-I repbase; DNA; EDCOT; 4458 BP. XX AC ACYM01040376; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-54_Mad-I; KW Copia-54_Mad-LTR; Copia-54_Mad_. XX NM Copia-54_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4458 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1324-1324 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01040376; Positions 8985 4528. XX CC Positions [1716-2216] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 399..1913 FT /product="Copia-54_Mad-I_1p" FT /translation="MYGNQNNAARIFELQKSLSVLNQDGKTFIEHLGRLKS FT MWNELNLYRPHTTDPAILLKQAEEDKVFQLLSSLDSTYEDLRSHILMSVEL FT PSLNTVCTIVQREEARRKVMSTKVGDPESRAFVASDRRFEGKNFKGKKGEM FT QCSHCGQKNHLRDTCWVLYPHLKPNFSKQTKPGRSANQVPRLQTASTVGNF FT TSNPSALLSEFTSFTQKKDESNLHKGNSEASTTELFEQFAKFLQTKVSSSV FT DMSGILNSFSAALASRKLANVWIIDSGATDHITNIKRYMHDFKEAVIPQFV FT SVANGTGVSVLGEGKVKLIDTNVESTALYVPSFPFQLLSVGRLTNSLNCDV FT IFSPFNVIFQDRITKKKIGEGMYKDGLYMLSLQPVEARGLQVGFLKNHLLW FT HRRLGHPSNLVQSHLFKTSENVMTQDCEVCHFSKQTRLPFDVSSTKSCKPF FT EIVHSDVWGPAPLVSFDGFRYFVTFVDDFSRCTWLYLLKSKDEVINVFQEF FT HSLVTNQFS" XX SQ Sequence 4458 BP; 1316 A; 841 C; 950 G; 1332 T; 19 other; tggtatcaga gcaggcttcc taaagaacct gttctctgaa atcttttgaa atggaagaag 60 aaaatatact tgctgcttca tccgagaaca tccttggtty ttcatcagtt tcttcaagtg 120 aagctgatgg aaatcccaat caacgtcttt gttccatact cctaactgag tttaattatc 180 ttccttggtc aagagctatt actttagctc ttggaggaag atctaagctt ggtttcatca 240 atggaactat cgtacctccc aaggttggtg attctaagta tgaagaatgg ttctgcaagg 300 atcagctcgt catgtcctgg ttgctcaact ctgctcaggt atcagaaawt ttcagctttt 360 cagaatcagc ttttgatctg tggaaggctg tcaaggagat gtatggaaat caaaataatg 420 cagccaggat atttgagctg cagaagagtc tttctgtttt gaatcaagat ggaaagactt 480 ttatcgagca cttgggaaga ctgaagtcta tgtggaatga gctgaatctc tatcgacctc 540 acactacaga cccagcaatc cttcttaagc aggctgaaga agacaaggtc tttcagcttt 600 tatccagtct tgactctacc tatgaggacc tgcgaagcca catattgatg agtgttgaac 660 taccatctct caatactgtg tgcactatcg ttcaacgaga agaagcaaga aggaaagtta 720 tgagtactaa ggttggtgat cctgagtcta gagctttcgt tgcaagtgat agaaggtttg 780 aaggaaaaaa tttcaaagga aagaaaggag aaatgcaatg cagtcattgt ggacagaaga 840 atcatctcag agacacttgt tgggtgttgt atccacacct taagcctaac ttttccaaac 900 aaaccaaacc tggtcgcagt gcaaatcaag tccctcgctt gcagactgcc tcaactgttg 960 ggaacttcac atctaatccc tcagctctct tgagtgagtt cacttccttc actcagaaga 1020 aagatgaaag caatcttcat aaaggaaaca gtgaagctag caccactgaa ttatttgagc 1080 agttcgcaaa atttcttcag acaaaggtgt catcttccgt tgatatgtca ggtattctaa 1140 actcatttag tgctgcactt gcttccagaa aacttgcaaa tgtttggata atagactctg 1200 gagcgactga tcacattaca aatataaaaa gatatatgca tgactttaaa gaggcagtta 1260 ttccgcaatt tgtctctgtt gctaatggaa ctggtgtatc agttttgggt gaagggaaag 1320 tcaagttaat tgatactaat gttgaatcaa ctgctctata tgtgccctcc tttccatttc 1380 agcttctgtc agtaggaagg ttgacaaatt ccttaaactg tgatgttata ttctcgccat 1440 tcaatgtgat tttccaggat cgtatcacga agaagaagat tggtgaaggc atgtataaag 1500 atggcctcta tatgctttca ttgcaacctg ttgaagctag aggtcttcaa gttggttttt 1560 tgaagaatca tctattatgg catagacgat tagggcatcc ctctaatctt gtgcaatcac 1620 atctcttcaa aacttcagag aatgtgatga ctcaagattg tgaagtttgc catttttcaa 1680 aacagacgag gttgcctttt gatgtctcat caaccaagtc atgtaaacct tttgagattg 1740 tgcactctga tgtttgggga cctgcaccct tggtttcttt tgatggtttt agatactttg 1800 tcacctttgt ggatgatttc tcaagatgta cctggttgta tttgttgaaa tcaaaagatg 1860 aagttattaa tgtgttccaa gaatttcaca gtcttgttac aaatcagttc tcamcccaac 1920 ttaaagtytt aaggtcagac aatggtactg agtatatgtc taatgctttt actcaatatc 1980 taacttgtca tggaataatt caccaaacga gctgtgttgg tactccgcaa caaaacggag 2040 tagcagaaag gaagaaccgt gatctactgg agaaaactcg atcacttatg cttcaaatga 2100 gtgtacctaa gaaattctgg tctcatgggg ttcttactgc tgcatatgta attaataggc 2160 ttccaagcaa ggttctcaaa ttcaaggcac ctcttgaaac acttaatggc aggaaaatta 2220 acttgtctca ccttcgagtg tttggatgtg tttgctttgt tcatattcaa accttgcatc 2280 gagataaatt ggaccctaga gctgtaaggt gtttgttctt agggtactca tctgttcaaa 2340 agggatataa gtgctatgac ccaaagcgca kgaaactttt ggtgtctaga gatgtggttt 2400 ttgacgagaa aactcctttt tttgctagta ccaggggtga agatcttctg ggggaggagg 2460 actttcttga tcaaatccwc acgccaatta tggaaatcaa tgcactgcct catcattttt 2520 cagytccaga tcaaccaagc aacaatgaaa tttcgattga tccagttgag tgtaattcat 2580 catctgacat acttgttgat aatgaatcaa ctgaagacac tgaacaaaat caaatttcgt 2640 cygaggagaa ccttgctatt actcctgaag tgatcactcc aaggagaaac cctagtagaa 2700 atcggggtaa gccaacttgg tttaaagatt atgtaagtta trcctcaaga catcctatag 2760 aaaaatatct tgaatactca agagtatctt cgtctcatgc tgctttccta agcaaaattt 2820 cagcctcatc tgaaccaagc tcattccaag aagctaactc tcaaytgatc tggmaaacag 2880 ctatggatga ggagcttaga gctctaaatg aaaacaaaac ttggagcatc accaagctac 2940 ctaaggggat gagagctgtg gggtgtcgat gggtgtayaa aaccaaattt aagagtgatg 3000 gttcagtgga gagacacaaa gctagattgg tggctagagg ttttactcaa acttatggca 3060 ttgattacaa ggaaaccttt gctcctgtgg caaagatgaa ctcggtaaga gtgcttctct 3120 cggttgctgt caaccatgat tggcccctat accaaatgga tgttaagaat gccttcctgc 3180 atggagaact taaagaagat gtgtacatgc agttgcctcc gggacatcca caagaagrag 3240 agggcatggt ttgcaagtta cacaaggcca tttatggcct caaacaatct cctcgagctt 3300 ggtatgccaa gttaagttct gtgttagaga acattggttt taaaaggagc aatgcagatt 3360 cctcactatt tgtgcgagat agttcagcag gtaaacttgt cgttctcatc tatgtcgatg 3420 atctcattgt gactggtgay agtttgacag aaattcagcg acttaagggy tttcttcaca 3480 aaaagtttgc aattaaagat ctaggaactc tgaagtattt tctaggcatt gaagttgctt 3540 catctagtaa aggcttgctc ttgaaccaac gcaagtacat acttgattta cttcaagagt 3600 ccaaaatgct tgaggcaaaa ccagtggcaa ccccaatagc ttgcaaagag aaacttggat 3660 tagatggaga tttactgata gacgttggtt tataccagag attggtaggg aaacttattt 3720 accttaccat tactcgtcct gatatcatgc atgccgtgag cctagtcagt cagttcatgc 3780 atgctcctcg atcaattcac ttacaagctg ttcgaaggat cttgcgctac ttgaaaggca 3840 ctgttggaac tgggattgtg atgaggaaga tcggaaatgc tcacattgtt ggctacacag 3900 atgcagactg gggtggctcc aaaattgatc gaagatctac tactggatat tgtacatttg 3960 ttggtggaaa tctggtgaca tggaaaagca aaaaacaaag tgtggtggct cgatcaagtg 4020 cagaagctga atatcgtgcc atggcatcta ctacctrtga gttaatttgg ctgcaaggtt 4080 tgctcaacga cttagggttc aagagaacac tgcctatgcc tcttttctgt gataaccaag 4140 ctgctattta cattgcatct aatcctgtat ttcatgaaag aaccaaacac attgaaatgg 4200 actgtcattt tgttcgagaa aaaacccaat ctgatgtcat tcaacctgtt tttgttcgra 4260 gcacakatca actagcagac atcttcacca aaggattgtc tcgggttcaa ttcaacactc 4320 ttttggtcca acttggcttg atgaatatac tagccttcgt ttgaggggga gtgttagatt 4380 atttaatatc caaagtatgg gttataggta tgggtagawt atctaatatc caaagtatgg 4440 gttataggta tgggttaa 4458 // ID Gypsy-6_Mad-I repbase; DNA; EDCOT; 6388 BP. XX AC ACYM01006063; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-6_Mad-I; KW Gypsy-6_Mad-LTR; Gypsy-6_Mad_. XX NM Gypsy-6_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6388 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1329-1329 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01006063; Positions 8963 2576. XX CC 'CTTAT' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 52..1674 FT /product="Gypsy-6_Mad-I_1p" FT /translation="MSKKKNYKFSKRESKKSLFQMAEHSENLSSPSGQVVS FT DSPTASEKSQRKGTNEELQATMIQVLKSMERISLETKGEVSRLCMLTGNLQ FT RRLDLEFSTPKGAQGSGMSQVITRNDPIIPLFPLLEEERDRGKNKTIPEGS FT QPVIEPIPEKEFPSFPLLSFNNGRQSEPEKIRYRLPAMMGETSGKGTTTTS FT DKPPPYRPPPMVNKGGGSNWRKPEPRREVNAGNDRSPKIESAIIGHNDNIA FT TQQLREELAELRRTVTQNAQPWARPVFRITYQKPYPEYIDELNPFPLNFKM FT SAFPTFTGEDNSVSSRDHIFKFSNHCVAYEDNPNYKLRLFGNSLVGLASQW FT YSLLPPNFIANWGQMEIAFHEQFYIIEPELTINDLVEVKQYDHESTEDFMM FT RFRRTRMRCQFPVNQAQLISIAQRVLKLPLRKRFYDAQFNELQELMIAATK FT YERLLQEEQQVKHTSKAPPFYKNKATIHHVEMGETRPERAESHEEENIDVC FT AAEMTTPFKPLTIKGLVQPVKDQKIVMNDGGFIPMKPPKISELFV" XX SQ Sequence 6388 BP; 1967 A; 1317 C; 1559 G; 1543 T; 2 other; tagttttggc acgcccggtg ggataatcgt gatcagactt ccagatcttg catgtccaaa 60 aagaaaaatt ataaatttag caaaagggaa tccaagaaaa gtcttttcca aatggcagaa 120 cattcagaaa atctttcttc cccatctgga caggtggtct cagatagccc gactgcatct 180 gaaaaatcac aaaggaaggg aactaatgaa gagctgcaag ctacaatgat tcaagtgtta 240 aaaagtatgg aaagaatctc cctagagacg aagggagaag taagcagact ctgtatgctt 300 acagggaatc tacaaagaag gctggatttg gagttctcta ctccaaaggg tgctcaagga 360 agtggaatga gtcaggttat cacaagaaat gatccaatca ttcccttgtt cccattacta 420 gaagaagaaa gggatagggg aaagaataag acgattcctg aaggaagtca accagtgata 480 gaaccaattc cggagaagga gtttcccagc ttcccattat tatcatttaa taatgggagg 540 cagagtgaac cagaaaaaat aaggtacaga ctgccagcta tgatgggaga aactagtggg 600 aagggtacta ctactacttc agataaacct ccaccctata ggccaccccc gatggtcaat 660 aaaggtggag gatctaactg gaggaaaccc gaacccagga gggaagtaaa tgcaggcaat 720 gaccggagcc caaagattga atcagctatc atcggtcata atgataatat agccactcag 780 caattgaggg aggaattggc cgagttaaga aggacggtga ctcaaaacgc ccagccgtgg 840 gctcgcccag tattcaggat tacttaccag aagccatatc ctgaatatat cgacgagtta 900 aatccattcc ctctcaattt caagatgtcc gcattcccga ccttcacagg tgaagacaac 960 agtgtgtctt ccagagacca tattttcaaa ttctccaatc actgtgtggc gtatgaggac 1020 aacccaaact acaaattgag gttgtttgga aattctttag tagggttggc atctcaatgg 1080 tattctctat tgccccccaa cttcattgcc aactgggggc aaatggagat tgctttccat 1140 gaacagttct atataataga gccagaattg accatcaatg atttggtgga agtaaaacaa 1200 tatgatcatg agtccactga agacttcatg atgaggttca ggaggacaag gatgagatgt 1260 caattccctg tcaaccaagc acaactcata tccattgctc aaagggtttt aaaattacct 1320 ttgagaaaaa ggttttatga tgcacagttt aatgagctgc aagaactcat gattgctgcc 1380 acgaagtatg aaaggctgtt gcaagaagaa cagcaagtca agcatacttc caaagcccct 1440 cctttctaca aaaacaaggc tactattcac catgtggaga tgggagaaac caggcccgaa 1500 cgcgcggaaa gtcatgagga agagaatata gatgtatgtg ctgctgagat gaccacaccc 1560 ttcaaaccat tgacgatcaa agggttagtc caacctgtca aagatcagaa gatcgtgatg 1620 aatgatggtg gtttcatccc catgaaaccc cccaaaatat cagagttatt cgtttgattt 1680 aactaaggca ccggagatct acgaagaact ggtgcgggca agagtaattt tgcccgacag 1740 tgccaaaaag atgcccaagc ccgaagaact cagggggaag aagtattgca aactgcatta 1800 taccttcaat cattctatag ttaattgtgt ccagtttaga gattggatac aagatcttat 1860 agtaaagggg aagctgctac ttgattcacc ccaggccagt atgatggtgg acactaaccc 1920 tttcccgaag gctcctatta atatgatcaa cctcattttt aaggagccgg ggttatcaac 1980 tgagtaaaaa tgccatgaag ggaccagagg tccgagggca ggttctaagg ttgccaacaa 2040 taaaggtgga gaagaaaagc aagtaggcaa gggggcaaag agttgcccga agccagtcca 2100 aacagagcag agctggaaga aaattacata tccattccaa aacaaaaagg agttacaaat 2160 cattctattc taaaaacttt acatctttac atagagtgat tattctagaa tgatatgttc 2220 gcatgatggc aaaaattcta ttaggttcgg ccaagacagt atggctgttt acaagttcgg 2280 acttggcttg ctctaactct gaagttgctt tctctacccc ttcgatttgg tgttcaaagg 2340 tgtctagaag agttgcttgt tctgccttga ggacaatcag ttgctcttcc agcttctgga 2400 tttcagaaga aaccacttta accctttcct tagtctgcat gctttcttcc atcagtcggt 2460 taacttgggt agaggaggtt gattctttct ccatgaagca tcttgtccgg ttagcctatc 2520 tatccactct ctagtattgt tccctgagag ccctcaagtt ctcgaaaaat gagagaaaag 2580 aatcgcgctg aggcttggac aaacgaccag ttttgaaaaa ttcagttatg accttctcac 2640 aaagggcctt gagactgaat gatgcggtga attctttctt tgcccattcc tgaaagattt 2700 gctgttcttc tgaggatatg gaggtggccg aaggctgcgt tgaagatctc aaccgcgtct 2760 caagtctccc gagcgcttcg aagagtttgg gcaacttggc agggtcagag gacgagaaag 2820 gaggagggtc cggcgtgaca gttccctccg gtgagataat gtctattgag ggggcaattt 2880 ctgtctgttt aatctgctca gctccaggga gggaagtgtc agcacctcca gaagatgaat 2940 gagggtgaga gcactttgat ttacgggcca ttagaggagg ggaaatttct tttgatggag 3000 ctcgctacaa aaatccgagg atcaggtcaa gataaactga acacaagttg aagcaaaagg 3060 ggccttggag agaagaaatt tacctgactt agccctggag tttcaccaga gaatgcacta 3120 actctttgtt ggggtgaaga ttcttcaccg ccagcaaaag aggaaagagt tgcgcctgaa 3180 cctgtgcctg catcctggat atatccaaag aaagtagtaa ttgtcagcaa aaatgtcact 3240 agaggaagaa gcaagaagaa aaatattcca gtacctgagt ctgatcttgg ggaggagaag 3300 gaggttcatc aactgtcgag caaacaaacg cctgcgaaat agttgcatct aaagctacag 3360 ggatttcagg aactatgggt tccttatccg agaccactag tgaaggaggt ggctcataca 3420 ctggagacgg ctgtgagaaa catgaatagg agttaattgg gtagcaatgt gcaaaatttc 3480 aatgaagaaa taataactca ccaagggatc atcctcatcc acgaagtgta gcataactca 3540 tgtggacgga tcaaattgag aggaatgggt cgcatccaga gcagtagaag aagccatgga 3600 tctaagagga ggtccctgac taagcaaaga ggcagatgca ccagcctagg aaaacaaaat 3660 agaatgagag aaaagacctt agccattaga tccataaatt ggagagatat ccaagaagta 3720 gagggaggga agtacctcag caggattgat ctgggagggg gaaagatttt tctctcgggc 3780 aggttgtgga gaggcctcgg gcgaggagag cctttctttc cttgcagcct gagtcagagt 3840 aatcaaattc agggttgtat gaaagtaaga aagtataaga atataggcca tacctcaagt 3900 tctcgaaggg cggtgtttcg caaatcttca gcctttttaa gcatagcagc ccttaatggt 3960 tcctccttag aagcaaggat tggcctttta gatgcttgag gtcctgttga tcaataaaag 4020 ggacaattag ataaaggaga aaggtagcag tttgatctag aaaaatagaa acttacttga 4080 tgattgttgc ttctttctgc ctgcctcagg aactggagca gatgggactg ctggtttagg 4140 gggcatagtg atccttaccc gcttactctt tcgggtgaga actggtcgtg tggttgctgg 4200 aagaggtgca gggtcaggga ttgaagtttt agtcatggcc accttctttc gtttggatgc 4260 tttggtgatt gctttgggcg tttcttcagc tcttgaatcc ccaatggatt ctgagacgtc 4320 cgtcccttcc ccggtttctc gtctctcagc ccctgcggca gcaccatgaa gaactgcagc 4380 atcagcaaaa tcattctcta attcaatggc ttcaaattca gtatccactg gagctgtaga 4440 atcaagcaaa agtaaaggaa aatggacatc agaggaaaaa caaaatcaga tggaaagaga 4500 ggcacctatt agaagtaacc ggtttttctc ttaaatcatc tccttccaat ttgcaagctc 4560 gcccgagcca ggatatgatt taagagaaag ctggttgaag atgcgatcgt gattcacctt 4620 caaatctcct ccatactttc tagtccattt atcctcccac caagaagaaa acagcgaggt 4680 acactcaaaa ttaagaacaa cagaatgtcg ggctgcttga ctcattacat ccagactgcg 4740 gcgggcggct cggaatgtca cttcagaaag agtttgtaac cagaatgaag tgccacaatg 4800 aacggagtcg aagaatggga caggtatggc ttgcctaaat cctaactgcc tgctgcagaa 4860 gttaggatgg tacacctcca atcctcgatc atacctatta ccccgaaccc cccaggccaa 4920 gtctcttggt tagatacagc tgataaactt ttccctgcaa aagggggtag catcttcacc 4980 aggggcatct tggaagactt ggtcagagaa ccaagggtat ctcctcaaga ctgacgcacc 5040 ccattccaag tctgatcgag tcctgcagac tctgaaaaag taaaaacagg caaaagtaga 5100 atggtctaca gggggagctt cagccaggat tcgggcagga gccacaccct ctgggaactc 5160 tagattggca gcccgaaatt ctggaaaata ccattgcagc cagatttgta acatccagat 5220 tggtccattc aagttggtct caaagggctc atctcaagtc atttcaaaaa gaaggtgata 5280 aagatgggaa agaaggaatg gacctgtggc tacatcatca aaattatgaa gaacctccac 5340 caaggggatc cattctaccc tcactccctt ggatttgttg gggaagacgt gcttgttgag 5400 ccagtaaaga agaaagtaca tatgctcttg atctttgtca gcccgagggg agcctgcccc 5460 aaaattctcc tttacaaaag ggatgaatcc tttaaaagag gtcccataac tcttgaaagt 5520 ggctgagtta tagttcagag gaagtaaggg gatagaagaa ctcgagctcc cggtggtaga 5580 agacggaacc caatcttgag taacatctac tgtcctgccc gatggcctca acccaaagac 5640 ctgggccata tcgagaatgg tgggagacat gggacccata cgaaaatcaa aagtatttgt 5700 gccccgtaat tccaaaagag gagggcagaa gtaagcaact cgggcttaga gacaatggaa 5760 gtctttgaaa gcatgatgag ttcataaata tcgttactca tccatttctg cttgaaggaa 5820 ggctccaatt cgtcaaccca ttgggtccag gcgggatcat tcatcaaggg aaagcctcga 5880 cgatgtaatg accattttga ggaggagatg cccaacccgg ccaaataggg atttggggaa 5940 aaacccaatt tcccctaggc atgttgcttt ccactactga ggggacccga gaaatccagg 6000 cgggacccaa tgattgtacc ccatgcgtct caaagaataa ctcagagtgt aggcctgccc 6060 gcggacgatg cagcccgttg agtaaacggc gtagagtggc gattccgtcg ccggactcat 6120 aagatggtgg ggtttggctg aatcctgaag ccatttgatg aaggtcgaga gaaagaaaaa 6180 caaggaagat gataaagatg caaccttgtc aggcaacgga araatggtgg gaagaagtag 6240 gaarttttaa tcacagaaaa ttttctttct acagaacacc ggaaattaag aagttcaatc 6300 gcgaaggatt cgtgggttta ataaggagtc tctttcaatt aatattggcg cctggaattc 6360 caggtttaat atcaattgaa gggggcac 6388 // ID Copia-2_CP-I repbase; DNA; EDCOT; 4132 BP. XX AC ABIM01016427; XX DT 10-MAR-2010 (Rel. 15.04, Created) DT 10-MAR-2010 (Rel. 15.04, Last updated, Version -1) XX DE LTR retrotransposon from papaya: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-2_CP_; KW Copia-2_CP-LTR; Copia-2_CP-I. XX OS Carica papaya OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Caricaceae; Carica. XX RN [1] RP 1-4132 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from papaya."; RL Repbase Reports 10(4), 575-575 (2010). XX DR Genome; ABIM01016427; Positions 7819 11950. XX CC Positions [1527-2027] - Integrase core CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 97..1386 FT /product="Copia-2_CP-I_1p" FT /translation="MAEGSSSGFVQPAIPKFDGHYDHWAMMMENFLRSKEY FT WDLIENGISGESNQQTEKLKDLKAKNYLFQAIDRTILETILNKDTSKSIWD FT SMKQKYKGSNKVKRAQLQALRKDFETLRMKEGETVDNLFARTLTIANKMKA FT HGETMSQTIIIEKILRSMTSKFDYVVCSIEESNDLDTMTIDELQSSLLVHE FT QRMNGHREEEQALKVSHEYSYRGRGRDRGSFRGRCRGRGRGAQQFNKATVE FT CFNCHNLGHFQYECPQRDIGANYAELNEEEELLLMSYVELNQAQREEIWFL FT DSGCSNHMSGNKEWFSDLDVHFRQTVKLGDNSRMSVMGKGNIRMQVKGITQ FT VISEVYYIPELKNNLLSMGQLQEKGVSILIQHGKCKVFHPSKGLIIESEMS FT ANRMFVLLANMKPEVTTCFQAVTEMRIICGTAGLGI" FT CDS 1425..4103 FT /product="Copia-2_CP-I_2p" FT /translation="MVNGLPSLTEPQKLCITCLAGKQHKEAIPKRSLWRAT FT QKLQLVHADICGPIKPTSNSNKRYFLSFIDDFSRKTWIYFLHEKSEALTVF FT KRFKAHVEKEADVFLKCLRTDKGGEFTSIDFEAFCKENGISRQLTAAYTPQ FT QNGVAERKNRTVMNMVRCILTEKQVPKIFWPEATKWCVHVLNRCPTLAVKD FT RTPEEAWSGVKPTIQHFRVFGCLAHVHVPDQKRIKLDDKSFKCVLLGVSDE FT LKAYRLYDPISKKIVVSKDVIFEENEKWNWNMSKEEKALDLLDWGDIEEGD FT AVENGTPGVEENRITQADSSGTSLSSLNQATGSCSSTPSSNDTDDGNSQSQ FT VQGRERRAPHWMQNYESGEGLSEEEEDLSAMTVLIEGDPITFEEAVKSKKW FT RDAMNSKIAAIERNKTWNLTDLPEGVKPIGVKWVFKTKLNENGAINKYKAR FT LVAKGYAQQYGFDYTEVYAPVARLDTIRLIIAIAAREGWNIFQLDVKSAFL FT HGELNEEVYVLQPQGYEKKGEEDKVYKLNKALYGLKQAPRAWYNKIEAHFV FT KEGFDKCHHEHTLFTKTTGGGKLLIVSLYVDDLIFTGNDSNLCEEFKKSMM FT IEFDMTDLGKMRYFLGIEVLQHSDGIYICQRKYAHEVLERFGMDRSNFVKN FT PIVPGCKLSKDEKGTEVDSSLFKQVVGSLMYLTATRPDLMYGVSLISRFMS FT CPTEQHWLAAKRMLRYLKGTTDLGILYKKGRNKQLTGYSDSDFAGDLNDRK FT STTGYVFMLSSGAVSWSSKKQPVVSLSSTEAEYIAAASCACQCIWLRRILA FT KLGFIQEQSTIILCDNSSTIKLSKNPVLHGRSKHIDIRFHFLRELVRDGVV FT DLRHCNTQDQAADILTKPLKLEVFLKLRKLLGICEVPTLN" XX SQ Sequence 4132 BP; 1377 A; 650 C; 985 G; 1120 T; 0 other; tttggtatca gagccatata acagggcctg attgtgagtg tttgtgtgaa tagaaaaact 60 gcagattttt ctattgagta aatagagtca aataatatgg cagaaggcag tagcagtgga 120 tttgtacaac cggccattcc caaatttgat ggccattatg atcattgggc gatgatgatg 180 gagaattttc ttcgttcaaa agaatattgg gatctcattg agaatgggat atcaggggaa 240 tcaaatcagc agactgaaaa gttgaaagat ttaaaggcaa agaattacct ttttcaagcc 300 attgatcgaa ctattctgga aactattctc aacaaggaca cctcaaagag catctgggac 360 tcaatgaaac aaaaatacaa aggctccaac aaggtgaaga gggcacaatt gcaagcactt 420 cggaaagact ttgaaacact ccgcatgaag gaaggcgaaa ctgttgacaa cttgtttgct 480 cgtactctca ctatagctaa taaaatgaaa gctcatggtg agacaatgag tcaaacaatt 540 atcattgaga aaatcttgag gtccatgacc tcaaaatttg attatgtggt atgctctatc 600 gaagaatcca atgatttgga tacaatgacg attgatgaat tgcaaagcag cttgttagtt 660 catgaacaaa gaatgaatgg ccatcgtgaa gaggagcagg ctcttaaggt cagtcatgag 720 tacagttaca gaggtagagg tcgagatcgt ggctcattca gaggaagatg tcgaggaaga 780 ggtcgtggtg cccaacaatt caacaaagct actgttgagt gttttaattg tcacaattta 840 ggacatttcc aatatgaatg tcctcaaagg gatattggag ccaactatgc cgaactaaat 900 gaagaagaag agctgttatt gatgtcgtat gttgagctta accaagcaca aagagaagag 960 atttggttcc ttgactccgg ttgtagcaat cacatgagtg ggaataaaga atggttctcc 1020 gatttggatg tccacttcag gcaaaccgtg aagctagggg ataattcaag gatgtcagtt 1080 atggggaagg gaaatattcg gatgcaagtc aaaggaatca ctcaggtaat atctgaagtt 1140 tattacatac ctgagctgaa aaataacttg ttgagtatgg ggcagctgca agaaaaaggt 1200 gtgtcaattt taattcagca tggaaaatgc aaagtctttc atcctagtaa gggcctgatt 1260 attgagtctg aaatgagtgc aaacagaatg tttgttttgc ttgcaaacat gaaacctgaa 1320 gttactactt gttttcaagc agtaacagaa atgagaatta tttgtggcac cgcaggtttg 1380 ggcatttaag cttcaaaggc ttgaaaactc ttcaaaacaa aaggatggtg aatggtttgc 1440 cttcactcac agaacctcaa aagctgtgca ttacctgttt agccggaaaa caacacaagg 1500 aagctattcc aaaaagaagt ctgtggaggg caacacaaaa acttcagttg gtgcacgctg 1560 atatatgtgg tcctatcaaa cctacatcaa atagtaataa gaggtatttc ctaagtttta 1620 ttgatgattt cagccgtaaa acttggattt atttcttaca tgaaaaatcg gaggctctta 1680 ctgtttttaa aagattcaag gctcatgttg aaaaggaagc agatgttttc cttaaatgtt 1740 taaggactga taaaggtggt gagttcacct cgattgattt tgaggcattt tgcaaggaaa 1800 atggcatatc caggcaattg acagcagctt atactcctca gcaaaacgga gttgcagaaa 1860 ggaagaatag gactgtgatg aacatggtgc gatgtatact aacagagaag caagttccaa 1920 agatcttttg gccagaagca actaagtggt gtgtgcacgt cctcaacagg tgtcctacct 1980 tagccgtgaa agatcgaact ccggaggaag catggagtgg tgtgaagcct actatacaac 2040 atttcagagt ttttggttgc ttggcccatg tgcatgtacc tgaccagaag agaatcaagt 2100 tagatgataa aagcttcaaa tgtgttttgt tgggagtaag tgatgagttg aaggcttatc 2160 ggttgtatga tcccatttct aaaaagatag ttgttagcaa ggatgtcatt tttgaggaga 2220 atgaaaaatg gaattggaat atgagcaaag aggaaaaggc cttggatttg ctggattggg 2280 gagatattga ggaaggagat gcagtagaaa atggaacacc tggggtagag gagaacagaa 2340 taacacaagc tgattcaagt ggcacaagct tatcatctct taatcaagca actggttcat 2400 gtagcagtac accgtcatct aacgacacag atgatgggaa ctctcagagt caagttcaag 2460 ggagggaaag acgagctcca cactggatgc aaaattacga aagtggagaa ggtttatcgg 2520 aagaagaaga agatttgagc gccatgacag tattgataga aggtgatcct attacctttg 2580 aggaagcagt aaaaagtaag aaatggagag atgccatgaa ttcaaaaatt gcagctattg 2640 aacggaacaa aacgtggaac ttgactgact tgcctgaagg agtgaaaccg attggagtta 2700 aatgggtttt taaaacaaaa ctcaatgaaa atggtgctat caacaagtac aaagctagac 2760 ttgtagcaaa aggatatgca cagcaatatg gttttgatta tacagaagtt tatgctccag 2820 tggcaagatt agataccata aggttgataa tcgccatagc agctcgagaa ggttggaaca 2880 tatttcagct tgatgtgaaa agtgcattcc tacatgggga gcttaatgag gaagtgtatg 2940 tcctgcagcc tcaaggatat gagaagaaag gcgaggaaga caaggtttat aagctgaata 3000 aagccttgta cggtcttaag caagctccgc gagcttggta caacaaaatt gaagctcatt 3060 ttgtcaagga gggttttgat aagtgtcatc acgagcacac cttattcaca aagacaacgg 3120 gaggaggtaa actcttaatc gtcagtcttt atgttgatga tttaatattt actggtaatg 3180 acagcaactt gtgcgaagaa tttaagaagt caatgatgat agaatttgat atgactgatt 3240 tgggtaaaat gagatacttt ttggggattg aagtgctgca acattctgat gggatttata 3300 tttgtcaaag aaaatatgct catgaagtgc tagaaagatt tggcatggac agaagcaact 3360 ttgtgaagaa cccaatagtt cctggctgca agttgtcaaa agatgagaag ggaactgaag 3420 ttgattcaag tttgttcaaa caagtggttg gcagtctcat gtatttaaca gccaccagac 3480 cagatttaat gtacggagta agtcttatca gtagattcat gtcatgtcct accgagcaac 3540 attggttggc tgcaaagcga atgctgaggt atttaaaagg cacaactgat cttggaattc 3600 tttataagaa aggaagaaac aagcagctca caggttactc ggacagtgat tttgctggag 3660 atttgaatga tcgaaaaagt acgacaggat atgtattcat gcttagttct ggagctgtgt 3720 catggtcatc aaagaaacaa cctgtggtta gtttatcttc caccgaagct gaatatattg 3780 cagctgcttc atgtgcctgt caatgtattt ggttaagaag aattttggca aaacttgggt 3840 tcatacagga acaatctact ataattttat gtgataacag ttcaactata aaactgtcaa 3900 agaatcctgt tcttcatgga agaagcaaac atattgacat caggttccat tttcttcgtg 3960 aattagttcg agatggggtg gtggatctaa ggcattgtaa tacccaagac caagctgctg 4020 atattctaac aaaaccactc aaattggaag tatttttaaa gcttcgtaag ttgctgggca 4080 tctgtgaagt tcctacttta aactgaatgt acatacagtt taagggaggg aa 4132 // ID Copia-45_VV-LTR repbase; DNA; EDCOT; 209 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-45_VV_; KW Copia-45_VV-I; Copia-45_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-209 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 7155223 7155431. XX SQ Sequence 209 BP; 63 A; 30 C; 39 G; 77 T; 0 other; tgtcaagaag ttaacagctt gtttaacaac ttaacaagct gtttaagtag ttaacagtct 60 ggttgttgta actaattaga aagtggttaa taactgattt ttagattcct gtatataaga 120 aacagaggac ctaacagagg gtagttttgc tgtagctcaa ttttagtttt tcatcttttt 180 ggttttctct caaacagatg ctctgcaca 209 // ID Gypsy5-PTR_LTR repbase; DNA; EDCOT; 476 BP. XX AC scaffold_3580; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy5-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-476 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-476 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 335-335 (2007). XX DR Genome; scaffold_3580; Positions 854 379. XX SQ Sequence 476 BP; 153 A; 84 C; 92 G; 147 T; 0 other; tgataagcca ccacgtcgat ctgagagagc aacaaaaccg aatcccaagt atagtgaagt 60 gcagtgaaag gcaagaccag gacaaacgtg agtcatgcag gattgatgat accaaattaa 120 agcatgagat cttcaccacg tcagctagta atgctaagca tcagtttttt ttagtttcca 180 ttcagtattt gttccgttct attttgcagt aatagtgtaa ccgttataac gggtccttat 240 atttcggatg cataaccgaa gtattgatta gtttccattt agtaattatt ctgttgtaat 300 gttgcagtaa tttaaatatt gtaaccgttc taacagatcc ttataataag gctggaaaga 360 aaggaagaag gacaatattt ttctatcata aatttatctt gtggtacgtt ctcacccgaa 420 gagaaccagt gtgaattctg ctattacaaa ttagctcttg actgggacct caaaca 476 // ID Copia-50_Mad-LTR repbase; DNA; EDCOT; 259 BP. XX AC ACYM01045729; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-50_Mad-I; KW Copia-50_Mad-LTR; Copia-50_Mad_. XX NM Copia-50_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-259 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1400-1400 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01045729; Positions 13901 14159. XX SQ Sequence 259 BP; 72 A; 39 C; 49 G; 99 T; 0 other; tgagtgatgt gtagctagga gagtttattg tatgaaatga tcttgttatg acaagtgtca 60 caatcctaga agggtagtta gttagatggt tagcttagtc attaagcaaa ctagtaagta 120 taaatagtga ggaggagcat gattgtatta tcttttgaca gttaatcaaa tatatacttt 180 ctctctatct ttctctctct taaatctctc tctaagcttt tcttcttagt ttcgaagcat 240 ccatggctgt actttctca 259 // ID Copia-91_Mad-I repbase; DNA; EDCOT; 5281 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-91_Mad_; KW Copia-91_Mad-LTR; Copia-91_Mad-I. XX NM Copia-91_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5281 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1720-1720 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1973-2497] - Integrase core CC LTRs are 94% similar to each other. XX FH Key Location/Qualifiers FT CDS 500..2809 FT /product="Copia-91_Mad-I_2p" FT /translation="MNVSFSVNPSSLNLNTVEPLTGVNYRKWKQDLEIVLG FT VMDWDLALRTEEPPALTDDSTSSQKSKYEKWHKSNRIALLIIKRSMTDVVR FT GGFPDATNAKDFLKSIEAKYRESPKTETGNLMNALTTMRYDGVQSVREYIL FT KMVDVAGKLNALEVPISDTFLVHVIMNSLPESYTQLKVYYNGLREKWDVNE FT LIAICVSEEERMKKEKFEKERIESVNFVQSATRATKPHVPDTAKKDSTKSV FT PSPKRNFKLNKPSVFKRYFCKKAGHMKKNCPKYKAWLAKQEAKKGKNVFAC FT FESNLINIPSTEWWLDSGSSIHVTNSLQDFTTRRTPNKDEVKVSVGNGRRV FT EVKALGSVRLKLEFGFYLELDNVVYVPSMKRKLISISKLVLLGFYFTINKR FT GFNVFYESSQVGHGFMSDGMFQLKLNQTEYVFNVQDDKTKTQQSSILWHKR FT LGHISKQRMELLVKNEILPPLNFNDFDFCVDCVKGKMTNTRKEGSTRSKQP FT LEIIHTDICGPFPTQTLEGNKYFITYIDDFSRFCFIYLISEKSKALETFKI FT YKSEVENQLERNIKVVRSDRGGEYYGRYTEIGRNPGPFALFLQERGIVAQY FT TTPGTPEQNGVAERRNRTLMDMVRSMICRTNLPSCLWGEAVKTANYILNRV FT PSKSVEGTPFELWTGRKPSLNHLHVWGCRAEAKIYNPGYKKLDSKTVSCHF FT IGYAERSKGFRFYCPNQNTRIVETGKAVFMESDASVDSGTRVEGFVFEEEI FT NNKEARSKTLIVTQRLWHQ" FT CDS 3151..4710 FT /product="Copia-91_Mad-I_1p" FT /translation="MKSELSSMANNQVWDLVEQAEGTKPIGCKWVFKTKRD FT SNGNIERHKARLVAKGFTQKEGVDYKETFSPVSTKDAFRVIMSMVAHFDLI FT LHQMDVKTAFLNGDLEECIYMRQPEGFKEGEGRNLVCKLNKSIYGLKQASR FT QWYLKFHRIVKEHGFTENPSDNCVYLRFSGSNFIILVLYVDDILLATNSHS FT LLDDTKTFLQKHFEMKDLGEATYVLGIEIKRDRRRGLLGLSQKAYIEKMLK FT RFNMSSCGTTEMPISKGDKLSKLQCPQTDLERKAMDDKPYASLVGSLMYAQ FT VCTRPDLAFTISVLGRFQSNAGEAHWNAAKRVLRYLQRTKDHMLVYKRTES FT LVLEGYSDSDFAGCPDDMKSTTGYVFLMACGAVSWKTVKQGTVAASTMVAE FT YLSVCETVNQAVWLKNFIVGLQVVDSISRPIQIFCDNNAAIFFTKNNKRSN FT ATRNLDIKYLIAREKVMAGLVKVDYLETGSMIADPLNKAVPTIVFKKHVTS FT MGVLAGFDAANSCRNQWEQTDAGN" XX SQ Sequence 5281 BP; 1723 A; 859 C; 1199 G; 1498 T; 2 other; gtttttatat atgtatataa cttaaagatt tacttacatt tggtatcaga gcccttcaca 60 tatcatctga ccctatgtga aaggcatcaa gaaatttcat tctgtctcgc aggttacgga 120 actggaactg tatcatcaag gaaaaatata taaacacgtt caagtgatga ctaaagttat 180 ccttgatcat aaggatatta tgtttttcaa tcgatacacg taccagtgat ggtgcttaaa 240 attcaagaca tgatcactga tcatctaaag atgatttttc tttcatgctt cgaatttgag 300 cagcatatca cttttatata tatatatttg aatcgaatta atattgtcaa accacaaagg 360 cttgtgattt tgattacaga aattcgaatg ttgactataa aagtgatatg attaaagaaa 420 gttttcacat gttcatcaat ctaaagatgt tgaagatgtg atttatggtt tggggttaaa 480 gattaatact ctttacatca tgaacgtttc cttttcagtg aatcccagct ctttgaacct 540 caatacagtt gagcctctta ctggtgtcaa ctacagaaag tggaaacaag atctcgaaat 600 cgttctggga gtcatggact gggatttggc actgagaact gaagagcctc cggcactcac 660 tgatgacagc acctcaagtc agaaatccaa gtatgaaaaa tggcacaaat ccaacagaat 720 tgccctattg atcatcaaaa ggagcatgac agatgtggtg agaggtggct ttcctgatgc 780 aacaaatgca aaagattttc tgaagtccat tgaggcaaag tatagggagt caccaaaaac 840 tgagacaggt aatctcatga atgctctcac taccatgaga tatgatgggg ttcaaagtgt 900 gcgagaatac atattgaaaa tggtggacgt cgctggaaaa ctcaatgcac tcgaggtacc 960 aatttctgat acttttctgg tacatgtcat tatgaattct ctgcctgaga gttatacaca 1020 actcaaagtt tattataatg gtctgcgtga gaaatgggat gtgaatgaat tgatagctat 1080 ttgtgtgagt gaagaagaaa ggatgaagaa agaaaagttt gagaaagaga gaattgagtc 1140 tgtgaacttt gtccaaagtg ccactagggc cactaaacct catgtccccg atactgccaa 1200 aaaggattct accaagtcgg ttccctctcc taaaagaaac ttcaaactta ataaaccttc 1260 agttttcaag cgctattttt gcaaaaaggc aggccacatg aagaaaaact gtcccaaata 1320 taaggcttgg cttgccaaac aagaagcgaa gaaaggtaaa aatgtttttg cttgttttga 1380 atcaaattta attaacatac ctagcactga atggtggctt gactcgggct cttctataca 1440 tgttacaaat tcattgcagg acttcacaac aaggagaaca ccaaataagg atgaagtcaa 1500 agtttcggtt ggcaatggaa gaagagttga agtcaaagcc ttaggaagtg ttagactaaa 1560 gctagaattt ggtttttatt tagagttaga taacgttgtt tatgtgcctt ccatgaaaag 1620 gaagttgatt tctatttcaa agctagtgtt attgggtttt tattttacta ttaataaaag 1680 gggctttaac gttttttatg agtcttctca agtaggacat ggtttcatga gtgatggtat 1740 gtttcaactt aaattgaatc aaactgaata tgttttcaac gtacaagatg ataaaaccaa 1800 aactcaacag tcttcaatat tatggcataa gagactcggc catatttcta aacaaagaat 1860 ggagctgctt gtcaaaaacg aaattctgcc tccattaaac ttcaatgatt ttgatttttg 1920 tgtggattgc gttaaaggaa aaatgacaaa cactagaaag gaaggctcaa ctaggagtaa 1980 gcaaccctta gagatcattc acacggacat ttgtggtcct tttcccacac aaaccttaga 2040 aggaaacaaa tatttcataa cttacattga tgatttctca agattttgct tcatttattt 2100 gatttcagaa aagtctaaag cacttgaaac ttttaaaatt tataaaagtg aagtcgaaaa 2160 tcaattggaa aggaacatta aggttgtaag gtctgatagg ggaggggagt actatggtag 2220 atatactgaa attggtagaa atcctggacc ctttgcgtta tttctgcaag aacgtggaat 2280 tgtagcccaa tataccacac caggtactcc ggagcaaaac ggagtggccg agaggaggaa 2340 tagaactctc atggacatgg taaggagcat gatttgtaga actaatctgc caagttgttt 2400 gtggggtgaa gcagtgaaaa ctgcaaatta tatattaaat agggtacctt caaaatctgt 2460 ggaagggaca cctttcgaac tatggacagg cagaaaaccg agtttaaacc acttgcatgt 2520 atggggctgt agagcagagg caaagatata taatccaggt tacaagaaac ttgattcaaa 2580 gactgtcagt tgtcatttta ttggatatgc tgaaagatcg aagggtttta gattctattg 2640 ccctaaccaa aatacaagaa ttgtcgaaac tggaaaagca gttttcatgg agtctgatgc 2700 aagcgttgat tctgggacaa gggttgaagg gtttgtattt gaagaagaaa taaacaataa 2760 agaagcgcgg tcgaagacgt tgatcgtaac acagcgatta tggcaccaat agttgtagta 2820 accgagaaca tgggaagcaa tgactctgac gaaccatgta acgagataga ggttgcacat 2880 gacatcgagc tgcacgataa cactgttgta caagacgtgk tcgaagaggt tgtgacagag 2940 aatcaacaac gacagcacca tgcacatgaa gacaacatca cggctgcggg tgctgcaaat 3000 ataagaaggt catctagggt tagaaaacct acaaccctaa atgatttcgt atattcgaca 3060 cgggtcgaca ctgatctttc ggagtttaat gatccgctga gttacaaaga agcaattgca 3120 ggaccagatg ctgataaatg gatagaagcc atgaagagtg aactgagttc gatggcaaac 3180 aatcaagtgt gggatctagt ggaacaggca gaaggaacaa aacccatagg atgcaaatgg 3240 gtttttaaaa caaaaaggga ttcaaacgga aacattgaaa ggcacaaagc caggcttgtt 3300 gcgaaaggct tcacacaaaa ggagggtgta gactacaaag aaacgttcag ccccgtgtcg 3360 acaaaggatg cgtttagggt tatcatgtct atggtggctc attttgattt gattttacat 3420 caaatggatg taaaaacggc gttcttgaat ggggacctgg aagagtgcat ttacatgcga 3480 caaccagaag gtttcaagga gggagaagga agaaacctag tgtgcaaact caacaaatcc 3540 atatatggat tgaagcaagc atcamggcaa tggtacttga aatttcatag aattgtgaaa 3600 gaacatggct tcaccgagaa cccttcagac aattgcgtct atctgaggtt cagtgggagc 3660 aactttatca tcctagttct ctatgtggat gatatattgc tcgccacgaa tagtcacagt 3720 ttgttggatg atacaaaaac ttttttgcag aagcattttg aaatgaagga cctgggagaa 3780 gcgacttatg ttttgggcat tgagatcaaa agggatagaa ggagaggctt gctgggattg 3840 tcacagaaag catacataga gaaaatgtta aaaaggttta acatgtcttc gtgtggaact 3900 actgagatgc ctatatcgaa gggtgataaa ttgagtaagc tgcagtgtcc acaaacagac 3960 ttagagagga aggctatgga cgacaaacca tacgcctccc tggtgggaag tttaatgtat 4020 gcacaggtgt gcacaaggcc tgacttggcc ttcaccattt ctgtgcttgg gaggtttcaa 4080 tccaatgcag gagaagctca ctggaatgct gccaaaaggg ttttgagata ccttcagaga 4140 accaaggatc atatgttggt gtataaaaga accgagagtt tggttttgga agggtacagt 4200 gattcagatt ttgcgggttg tccagatgat atgaagtcaa ctacaggtta tgttttctta 4260 atggcatgtg gtgcggtatc ttggaagact gtcaaacaag gaactgtggc agcgtcaaca 4320 atggttgcag agtatttatc agtctgtgaa acagtgaatc aagccgtttg gttgaagaat 4380 ttcatagttg ggcttcaagt ggtggactct atatcgagac ctatacagat tttctgtgat 4440 aataatgcag ccatattctt tactaagaat aataagaggt ctaatgcaac aaggaacttg 4500 gatataaagt atctcattgc tcgagagaag gtgatggccg gtttggttaa ggttgattat 4560 ttggagactg gatccatgat tgctgatccg ttaaataaag cagttcccac catcgttttc 4620 aagaagcatg tcactagcat gggagtcttg gctggttttg atgcagcaaa ctcatgcaga 4680 aaccagtggg agcaaactga tgcagggaat tagtgggagc tacgcaacag gtttaaactt 4740 ttaaatgcta gttttaattc agtagcagtt tatgttatgg aggataagta tttgagtatt 4800 aacaatgaag ttttcttagc taataaagaa taaagctgaa aggttgttca agttccctta 4860 aagggttcag cttttagcta tgataatgca tgaatatttt tgcatgctgt ttatgatttt 4920 tattcattat acagtgtcag acaacctgag ggcttcatat agaagcacat ggatcgtttt 4980 tcgattctga aggggaccaa atgtttgaca tattattaat acatgttcgg tcgtgtctta 5040 cattggctat atatcttgtt ggagtcttat gtgttggtaa gcttcactgt aagtaattat 5100 ggggacggta ctcttcagtg taagttgagt gtgttgccct ataattctca tgaatgcttg 5160 acaatgacgg agactggtaa accaagaaag tgtcgaaggc taatctcatg gccaattcag 5220 attcttccca actcaagtat agactataca actttacaaa gtatttgctc tagtgggaga 5280 a 5281 // ID Gypsy-29_PTr-I repbase; DNA; EDCOT; 5580 BP. XX AC . XX DT 09-DEC-2009 (Rel. 15.02, Created) DT 09-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: internal DE portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; internal portion; Gypsy-29_PTr-I; KW Gypsy-29_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-5580 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 177-177 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS join(834..1169,1160..5578) FT /product="Gypsy-29_PTr-I_1p" FT /translation="MSSNSVPQKKGEIPEDGLSRIQQQMEFMFGELMTRIE FT KLETRSDGGRSKRGREARKEESVAGNSADEAEDDLNRGGGFRTHRGERYEN FT RPRRGHIRPHRDFEHRGDFDDLGMFGDVDRNLGSIKLKIPAFKGKTDPEAY FT LDWEKKVEMIFDIHRYSEEKKVKLAVVEFTDYAMVWWERLVVERRRNRERP FT VSTWEELKTIMKKRYVPKHYYRELFNRLQMITQGNKSVEEYQKELEVAMIR FT ANVNEDEEVTMSRFLNGLNRDIANVVELQSYVDLEELVHLAIKVEGQLKRK FT GNTRSGAYTGSSSGWKMNYRREGSASSKPLVTSKVAEPTSMKKQVSANDKK FT LKGEVQPKRNRDIKCFKCQGLGHYASECANRRVMILRDDGEIVSTSEESDC FT DDMPPLEDASDLEYAVGDKVLVIRRSLSVQTKEDDVEQQRENIFHTRCLIN FT DKVCSMIIDSGSCTNVASVTLVRKLGLNTIKHERPYQLQWLNECGVVRVNR FT QVMISFSVGKYKDEVLCDVVPMHATHLLLGRPWQFDRKAKHDGFKNRYSLE FT KDGRIYTLAPLSPKQVYEDQIQLKKGYEEEQHVSAKVEEQKDSAKMEKQAE FT QHGEDVRKREKKVSHELKTKGNKVSALRTLGEGHGQEQKNEKKAESGEKMS FT GEKKERVRKEECVEKVGKHLNFFAKSNDLKHAYLSDLPMILLVYKEAFFNS FT DDLDSCVPSVVKVLLQEFEDVFPDDIPSGLPPIRGIEHQIDFVPGASIPNR FT PAYRSNPEETKELQRQVGELMSKGYIRESMSPCAVPVLLVPKKDKTWRMCV FT DCRAINNITVKYRHPIPRLDDMLDELHGSKLFSKIDLKSGYHQIRMKEGDE FT WKTAFKTKYGLYEWLVMPFGLTNAPSTFMRLMNHVLRAFIGKFVVVYFDDI FT LIYSKEIDEHIGHLRQVLDVLRKESLYANLKKCDFCMDRIVFLGYVVSAKG FT IEMDEAKVKAIQEWPTPKSITDVRSFHGLASFYRRFVKDFSTIASPLTEIV FT KKAVGFKWGEEQENAFSLLKSKLISAPLLSLPDFNKAFEIECDASGIGIGA FT VLMQEKRPIAYFSEKLNGATLNYPTYDKELYAVVRALETWQHYLWPREFVI FT HTDHQSLKHLKGQGKLSRRHAKWVEFIETFPYVIKYKQGQENVVADALSRR FT YVLLNTLNTKLLGFEYIKELYLDDHDFGAIYDTCKVSAKDKYFRHDGFLFK FT ENKLCVPNCSLRELLVREAHGGGLMGHFGITKTLEVLHEHFYWPNMKRDVQ FT RMCDRCITCRQAKSRVMPHGLYTPLPVPKEPWVDISMDFILGLPRSRKGRD FT SIFVVVDRFSKMAHFIACHKTDDATNIADLFFREVIRLHGLPRSIVSDRDV FT KFLSYFWKVLWGKLGTKLLYSTTCHPQTDGQTEVVNRTLIQLLRAIIQKNL FT KNWEDCLPFIEFAYNRSVHSTTDYSPFEIVYGFNPLTPLDLIPLPVDERVS FT LDGNQKAQVVKDLHAKIRQQIEKKNEQYANKANRGRKLVRFEPGDWVWVHM FT RKERFPEQRRSKLMPRGDGPYQIIERINDNAYKVDLPGEYGVSATFNVSDL FT SLFDVGDDSRSNPFEERG" XX SQ Sequence 5580 BP; 1700 A; 731 C; 1382 G; 1765 T; 2 other; gttggtatca gagctgatct aatcacaggt tatatccttc aatttgagtc tttattgttt 60 cttgtttgat tcttgataga ttcggccacc tatatatata aaaaaatagg gatcttactt 120 tttattgctt tgttgaacac ttaatcataa gttagtgttc ttttgatgct ttcttgatca 180 aaatcggcat acacacctaa gttcttgatt ttgttttgtt cttgccgaaa tatatatata 240 tatatataag gaggcttgat cttgaaatct tgattgttgc cgcacaaaaa aaaagaaaaa 300 aaaatcactt ttttttttag ttttggccga atacatgctt gagaaaacct tgatcattgg 360 gaaattggtt agtcttgatt cgtgaatctt ttagtagtct tgtttgtgtt tcttgaaaat 420 ttgggtagtt tagttgattt tcttgagttt ctggaatttt cttgaattaa atccttagtt 480 cttgataatt cgtaattgtt tagctctttt ctgatttttt ttatttcgtc ttcaaatcgt 540 catattattc gtacaaattt gcattgctat tcgtgaattt gtcatcgagt tttgttttgt 600 tagtttcgta atttcttgct tcttgagtct atatcaaatt tataaattca ctgcatagtt 660 ggttgctttt ctgaattgtt gctaagtgat ttcaagaact aaagaaaggc aatttgagtg 720 gaaaaaggcg tagggagcat attcgagtga aaagcctata aatttgtgtg aaacacgagt 780 gtgtgaggtg ttatttttat tgctaacgat tttcgtgcag gtttaaaaaa aaaatgtctt 840 ctaatagtgt gccacagaag aagggtgaaa tcccagaaga tgggctttcg agaatacaac 900 aacagatgga atttatgttt ggtgagctga tgactaggat tgaaaaatta gagactaggt 960 ctgatggagg gcgtagtaaa aggggtagag aagctaggaa ggaggagagt gttgctggaa 1020 actctgcaga tgaagccgag gatgatctta accgtggtgg tgggttccgt acacataggg 1080 gagagaggta tgagaatcgg ccaaggaggg gacatattcg gccacatagg gattttgagc 1140 atagagggga ttttgatgat ttggggatgt agaccgaaat ttgggtagta ttaagttaaa 1200 aatcccagcc tttaagggaa aaactgatcc ggaagcttac ttagattggg aaaaaaaggt 1260 ggagatgatt tttgacatcc ataggtactc tgaagaaaag aaggttaagt tagctgtagt 1320 ggagtttact gattatgcca tggtttggtg ggagagattg gtggtagaaa gaagaaggaa 1380 tagagaaaga ccagttagca catgggagga gttgaagaca ataatgaaga agaggtatgt 1440 tcctaaacac tattatcggg agttgtttaa tcgtttacaa atgattacac agggtaataa 1500 gagtgtggag gagtatcaga aagaattaga ggtggctatg attagagcta atgttaatga 1560 agatgaggaa gttactatgt ctaggttttt gaatggcttg aatagagaca tagctaatgt 1620 tgtggagttg caatcatatg ttgatttgga ggagttagta cacttagcca ttaaggttga 1680 aggacagttg aaaaggaagg gtaatacacg atctggagct tatacggggt cttcttcggg 1740 ttggaagatg aattatagga gagagggtag tgcgtcatcg aagcctttgg tgacttctaa 1800 agttgccgaa cctacctcca tgaagaagca ggtttcggcc aatgataaaa aacttaaggg 1860 agaagttcaa ccgaagcgta atcgtgatat aaagtgtttc aagtgtcagg gattgggaca 1920 ctatgcatca gaatgtgcaa atcgtcgagt tatgattcta agggatgatg gagagattgt 1980 gtccactagt gaggagtctg attgtgatga catgccccca cttgaggatg ctagtgattt 2040 agagtatgct gttggtgata aagttttggt gattagaagg tcacttagtg ttcagactaa 2100 ggaggatgat gtggagcaac aaagggagaa catcttccat actagatgcc taatcaacga 2160 taaggtatgt agtatgatca ttgatagtgg tagttgtact aatgttgcta gtgttacttt 2220 ggttagaaag ttgggattga ataccataaa gcatgagagg ccttatcaac ttcaatggtt 2280 gaatgaatgt ggtgttgtta gggtgaatag acaggtgatg atttcttttt cagtaggcaa 2340 atataaggat gaagtgttat gtgatgttgt gcctatgcat gctactcatc tgttactagg 2400 gaggccttgg caatttgata gaaaagccaa gcacgatggg tttaagaaca ggtattcatt 2460 agagaaggat ggaaggattt atacacttgc cccactctca ccaaagcaag tgtatgaaga 2520 tcaaattcaa ttgaagaagg gctatgagga agagcaacat gtttcggcca aagtggagga 2580 acaaaaagat tcggccaaaa tggaaaaaca agctgaacaa catggtgagg atgtgaggaa 2640 gagagaaaag aaagtgagcc atgagttgaa aacaaaaggg aacaaagttt cggcccttag 2700 gacattaggg gagggtcacg gccaagaaca aaaaaatgaa aagaaggccg agagtggaga 2760 gaaaatgagt ggagagaaga aagaaagggt gagaaaagaa gagtgtgtag aaaaagtggg 2820 gaaacacctt aatttttttg caaaatctaa tgatcttaaa catgcctatc tttctgactt 2880 gcctatgatt ttacttgtgt ataaggaggc attctttaac tcagatgatt tagattcttg 2940 tgttcctagt gttgttaaag ttcttttgca ggaatttgag gatgtctttc cggatgacat 3000 tcctagtggt ttgccgccaa ttagaggtat tgagcatcaa attgactttg ttccaggagc 3060 atctatacca aataggccgg cttataggag caatcctgaa gagactaagg agcttcaaag 3120 gcaagtgggg gagttgatgt cgaaaggata cattcgagag agcatgagtc cttgtgcagt 3180 tcccgtgctt cttgttccaa aaaaggacaa aacttggcga atgtgtgtgg attgtcgagc 3240 tatcaataac atcactgtaa agtatcgaca tcccattcct agattagatg atatgttgga 3300 tgaattacat ggttctaaat tgttttcgaa aattgatttg aaaagtggtt atcatcaaat 3360 taggatgaaa gaaggggatg aatggaaaac tgcttttaaa actaaatatg gtttgtatga 3420 gtggttggtt atgccttttg gacttactaa tgcacctagt acttttatga gattgatgaa 3480 tcatgtgttg cgtgctttta ttggtaagtt tgtagtcgtt tactttgatg atatcttgat 3540 ttatagtaag gagattgatg agcatatagg tcatttgaga caagttcttg atgtgcttag 3600 aaaagagtcc ttatatgcta atttgaaaaa gtgtgacttt tgcatggata ggattgtttt 3660 tcttggatat gtggttagtg caaaaggtat agagatggat gaggctaagg ttaaggctat 3720 tcaagaatgg cctacaccaa aatccataac agacgttagg agttttcatg gtttggctag 3780 tttttatagg agatttgtta aagactttag tacgatagcc tctccattga ctgaaattgt 3840 taagaaagcc gtgggtttca agtggggaga agaacaagaa aatgctttta gcttgttaaa 3900 atcaaagttg atttcggcac ctttactatc tttacctgat tttaataaag cttttgagat 3960 tgaatgtgat gcttcaggaa taggtattgg agctgtttta atgcaagaaa aacggcccat 4020 cgcttatttt agtgagaaac tcaatggtgc aactcttaac tatcccactt atgataaaga 4080 gttgtatgca gtmgtgcggg ctttggagac ttggcaacat tatctgtggc cccgagagtt 4140 tgtcatacat actgatcacc aatcgttgaa acatttgaag ggtcaaggta agttaagtag 4200 gagacatgct aagtgggttg agtttattga aacttttcca tatgtgatta aatacaagca 4260 aggtcaggaa aatgtggtcg ccgatgcctt gtcgcgaagg tatgttcttc ttaatactct 4320 taatactaaa ttgctaggat ttgagtatat taaggaattg tatcttgatg atcatgattt 4380 cggtgctata tatgacacat gcaaggtttc ggccaaggat aaatatttta ggcatgatgg 4440 atttttgttt aaggaaaata agttatgtgt gcctaattgt tctttacgtg aattgcttgt 4500 gagggaagca catgggggag gtttaatggg gcattttgga attactaaaa ctttggaggt 4560 tctgcatgag cacttttatt ggcctaatat gaaaagagat gtgcaaagaa tgtgtgatag 4620 gtgcataaca tgtagacaag ctaagtctag ggtaatgcct catggactat acacaccttt 4680 gcctgttcct aaggaacctt gggttgatat ttctatggat ttcattttgg gtctacctag 4740 gtctaggaaa gggagagatt ctatatttgt tgttgtggat agattttcta agatggcaca 4800 tttcattgct tgccataaaa ctgatgatgc aacaaatata gctgacctat tctttagaga 4860 ggtcattcgg ctacatggtc ttcctaggag cattgtatcc gatcgagacg ttaagttttt 4920 gagttacttt tggaaggttt tgtggggtaa gttaggaact aaacttttat attctactac 4980 ttgtcatcca caaacagatg gccaaactga agttgttaac cggactttga ttcaattgtt 5040 aagggctatc attcaaaaga atcttaaaaa ttgggaagat tgtttgccat tcattgaatt 5100 tgcatataat cgtagtgtgc attctactac tgattattca ccatttgaga ttgtttatgg 5160 ttttaaccct ttgacaccat tagatttgat tcctttgcct gttgatgaaa gggttagtct 5220 tgatggtaat caaaaagcac aggtggtgaa agatctccat gcaaagattc ggcaacaaat 5280 agaaaagaag aatgaacaat atgcaaacaa agccaatagg ggacgaaaat tggtgagatt 5340 tgaaccaggt gattgggttt gggtgcatat gaggaaggaa aggtttcctg aacaaagaag 5400 atcaaagttg atgcctcgag gagatggtcc ttatcagatc atagaaagga ttaatgataa 5460 tgcctacaaa gtggatctac caggtgagta tggtgttagt gctacattca atgtttctga 5520 tctttctttg tttgatgtag gtgatgattc gaggtcgaat ccttttgagg agmgagggga 5580 // ID Gypsy-71_PTr-LTR repbase; DNA; EDCOT; 2188 BP. XX AC . XX DT 15-DEC-2009 (Rel. 15.02, Created) DT 15-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon from Populus trichocarpa: long DE terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Gypsy-71_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-2188 RA Kojima K. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 179-179 (2010). XX DR [1] (Consensus) XX CC ~82% identity to consensus. 5-bp TSDs. Similar to Ogre-PT1_LTR CC and Ogre-PT2_LTR. XX SQ Sequence 2188 BP; 526 A; 486 C; 365 G; 811 T; 0 other; tgtcgcaccc gacatcgcgg cggccctaaa aaatattatg gaaaaagaac agatttctgg 60 catcttgttc ttttagggga aaatgtcttg tttaaggagt cgccacctag tattatggtc 120 actaggaacc ctaactggtc aacagagatt ctatggttcg ggactggtta cgtaaaaggg 180 aagatattat caccccttaa acgttctgcc tgaggcagac tgcattgctg attttgtctt 240 aaattgctaa acatttatta gtttatgcta tgatgatttg cttataatat tcctgactct 300 ggcgccagtg aatattcaac tacgaataat tccaactctg gcgttggtaa atattacgta 360 gctataaaat aaatttagat caatattttt tattcctgac tctggcgtca gtgaataaac 420 aaataaaata aatttatttt tacgcatgca catatttttt tatttttcta gctaaataaa 480 ataaaataca tgaataaaaa taatataaat ttaaaccggt atttttattc ctgactctgg 540 cgtcagtgaa taaaccaata aatttatatt atttttattc atgcatacac attttttatt 600 ttttctactt ttttattttt ctttttttat tttttatttt ttttggggct gggcccagct 660 cagcccacgt gggctgggct agacccagcc agcccggccc ggtcactggc ccaagccagt 720 gacccggctg ggccacagca cgcgtgaact aattcacgcg tgcatggcgc tgtgcgaagg 780 taattaatta ccttcgcaca gtgctaagtg cactgaaatt ttgaaacaaa acgaagaaag 840 agggaaagct taccttgctg caggttgctt gccggagtga ggtcttgggc gaagatcggt 900 gatggcgtcc gttgtgggac tggattcctc cttctgcctc tgccttcctg ccctctgttt 960 cttctgctct cgtctgttct cccctgctct gtttttcctc tctctgctct ctctcggtct 1020 gtttctcttg tatgctcctg tgtttttctg ctcaccttgt tcttttctct ccgtttctcc 1080 gtcctctctt ttctccccct ggctttttcg gtcccttctt ctctggttct tgcgttcctc 1140 tgttctttga gaagaaacag gggatgatag tcctattctg gttctccctc tgggttgttc 1200 tcttgttctc tctctgtgtt tgtttcctgg ctttcctctc tctctaaggt tttttttttc 1260 gtgttttctc ctctggtttc tctgcttgtt cgtcctctgt ctcctggttt ttttttccct 1320 ctctcctggg tttttttttt cttcccctcc gtctctctct tttttctccc ctatttttct 1380 gcccctgttt tcttcggtgc tcctctgttt ttatagagcc cggcgggtgg taacgggcgg 1440 cagctgaggg tcgaccacca ttaaggcgcc catactgaag ccaacggacg acgattactg 1500 ctgcaacgtt tctccttact gcagaaacgg tcccggctta aagaagaaga agatgaacag 1560 cgtcctcaaa acgacgccgt ttggagataa aatggccatt ttcaatttgg tcctgaagtt 1620 ttgaaagtct tgtaattaag cccctggttt aaactgtaat tggacccctg catttcgcgc 1680 cttttacaag ctagtccttg gactttaatc tgttgcaatt ttgccccaat taaccccaaa 1740 ctttgatatt tcttcaatta agtccctgat ttcattaatt taattaatcc aagtccaatt 1800 aagtctaaaa cttatcaatt ctccaattaa acccttgatt ggattaatta aattaattcc 1860 aagcttaatt aagtctcaaa acttatcaat tctccaatta aacccttgat tggattaatt 1920 aaattaattt caagctcaat taagtctcaa aacttatcaa ttctccaatt aaacccttaa 1980 ttgattaatt aaattaattc cagaaagttt aattaaaccc caaaacttcc aatcatgttg 2040 cccttaaccc aaattttaat tcattcttca tttatttcat tttacttgtt ttttcatcat 2100 tattattttt tttcatcatt tttttctttt cagtaaataa aataataata ataattaaaa 2160 taaaatggtc aaaaattggg ttatgaca 2188 // ID GYCUME1_I repbase; DNA; EDCOT; 4840 BP. XX AC AF49972; XX DT 04-SEP-2005 (Rel. 10.08, Created) DT 06-SEP-2005 (Rel. 10.08, Last updated, Version 1) XX DE GYCUME1: Gypsy-type LTR retrotransposon from muskmelon (internal DE portion). XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; GYCUME1_LTR; internal portion; GYCUME1_I. XX OS Cucumis melo OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; OC Cucumis. XX RN [1] RP 1-4840 RA van Leeuwen H., Monfort A., Zhang H.B. and Puigdomènech P.; RT "Identification and characterization of a melon genomic region RT containing a resistance gene cluster from a constructed BAC RT library. Microcollinearity between Cucumis melo and Arabidopsis RT thaliana."; RL Plant Mol Biol 51(5), 703-718 (2003). XX DR EMBL/GenBank/DDBJ; AF49972; Positions 57143 61982. XX CC LTRs differ by deletions in minisatellite regions. No CC substitutions. XX FH Key Location/Qualifiers FT CDS 2032..4800 FT /product="GYCUME1_I_1p" FT /translation="MAPAELKELKVQLQELLDKGFIRPSVSPWGAPVLFVK FT KKDGSMRLCIDYRELNKVTVKNRYPLPRIDDLFDQLQGATVFSKIDLRSGY FT HQLRIKDEDVPKTAFRSRYGHYQFIVMSFGLTNAPAVFMDLMNRVFREFLD FT TFVIVFIDDILIYSKTEAEHEEHLRMVLQTLRDNKLYAKFSKCEFWLKQVS FT FLGHVVSKAGVSVDPAKIEAVTGWTRPSTVSEVRSFLGLAGYYRRFVENFS FT RIATPLTQLTRKGAPFVWSKACEDSFQTLKQKLVTAPVLTVPDGSGNFVIY FT SDASKKGLGCVLMQQGKVVAYASRQLKSHEQNYPTHDLELAAVVFALKIWR FT HYLYGEKIQIFTDHKSLKYFFTQKELNMRQRRWLELVKDYDCEILYHPGKA FT NVVADALSRKVSHSAALITRQAPLHRDLERAEIAVLVGAVTMQLAQLTVQP FT TLRQRIIDAQSNDPYLVEKRGLAEAGQTAEFSLSSDGGLLFERRLCVPSDS FT AVKTELLSEAHSSPFSMHPGSTEDVSGPEAGFIGGRNMKREVAEFVSKCLV FT CQQVKAPRQKPAGLLQPLSIPEWKWENVSMDFITGLPRTLRGFTVIWVVVD FT RLTKSAHFVPGKSTYTASKWAQLYMSEIVRLHGVPVSIVSDRDARFTSKFW FT KGLQTAMGTRLDFSTAFHPQTDGQTERLNQVLEDMLRACALEFPGSWDSHL FT HLMEFAYNNSYQATIGMAPFEALYGRCCRSPVCWGEVGEQRLMGPELVQST FT NEAIQKIRSRMHTAQSRQKSYADVRRKDLEFEVGDKVFLKVAPMKGVLRFE FT RRGKLSPRFVGPFEILERIGPVAYRLALPPSLSTVHDVFHVSMLRKYVPDP FT SHVVDYEPLEIDENLSYVEQPVEVLARGVKTLRNKQIPLVKVLWRNHRVEE FT ATWEREDDMRSRYPELFGE" XX SQ Sequence 4840 BP; 1192 A; 994 C; 1385 G; 1269 T; 0 other; gttggtatca gagcctaagt tttaggttct gtagactgac ttataatgtg agtctgtgtt 60 ttgtgtcctt atggctgaaa cgatccttgc cgctcgccaa ggacgctctc atgaaagtat 120 atgtatcact ctacatgcat taccttacct aagttaaact gcaaattcaa ttaccatttg 180 tgactaaaga atcgttggtg gttgttagga aatgccacca agaagagttg cacgaagggg 240 tgcccgagag ccggaggaag gggagcagga cgcgttcagc cttgaggtgc agcctgtagc 300 ccaagcccct tgacccggct tgcgccagtt actcatgcgg acctagccgc catggagcag 360 aggtttagag atatgattat gcagatgccg gagcagcaga agcctgcctc accaactccg 420 gcgccagctc cagcgccagc tccagcacca gttcctgctc cagctccggc tccggtacca 480 gttgcacccc agtttgtgcc ggatcagttg tcagcagagg ctaagcacct gagggatttc 540 aggaaatata atcccacgac gtttgatggg tctttggagg accccaccag agctcagatg 600 tggttatcgt ccttggagac catattccgt tacatgaaat gccctgagga tcagaaggtt 660 cagtgtgctg tctttatgtt gactgacaga ggtactgcat ggtgggagac tactgagagg 720 atgctaggtg gtgatgtgag tcagatcacg tggcagcagt tcaaggagag tttctatgcg 780 aaattcttct ctgccagttt gagagatgcc aagcggcagg agtttctgaa cttagagcag 840 ggtgacatga cagtggagca gtatgatgcg gagtttgaca tgttatcccg cttcgctccc 900 gagatgatag cgaccgaggc ggccagagct gataagtttg ttagaggcct cagactggac 960 attcagggtt tggtccgagc tttcagaccc gctactcatg ccgatgcact gcgcctggca 1020 gtggatctca gtttacagga gagggccaac tcgtctaaga ccgctggtag aggttcgacg 1080 tcgggacaga agaggaaggc tgagcagcag cctgttccag tgccacagcg gaacttcaga 1140 ccaggtggtg agtttcgcag cttccagcag aaaccttttg aggcagggga ggctgccaga 1200 gggaagccgt tgtgtaccac ttgtgggaag caccatttgg gccgttgctt attcgggacc 1260 aggacctgct ttaagtgcag gcaagagggt catacagctg atagatgccc gttgagagtc 1320 acggggatcg cgcagaatca gggagcaggt gctccacatc agggtagagc ctttgctacc 1380 aacaggactg aggctgagaa ggcaggcaca gtagtgacag gtacgctccc agtgttgggg 1440 cattacgcct tagttttgtt tgattcggga tcgtcacatt cttttatctc ttccgcattt 1500 gtgtcgcatg cccgcttaga ggtagagccc ttacaccatg ttctgtcagt atctactcct 1560 tccggggaat gtatgttgtc gaaggaaaag gtgaaggcat gtcagattga gatagcaggc 1620 catgtgattg aggtacgctg attagttctg aatatgctgg acttttgatg tattcctggg 1680 tatggattgg ctgccgctaa ccacgccagc atagattgtt cacgtaagga ggtaacgttt 1740 aaccctccct cgttggccag ttttaaattt aagggaggag ggtcaaagtc gttgcctcag 1800 gtaatctcag ccatcagggc cagtaaactg ctcagtcagg gtacttgggg tatcttagcg 1860 agcgtggtgg atactagaga ggccgatgta tccctgtcat cagaaccagt ggtgagggac 1920 tatccggacg tttttcctga ggaacttcca gggttacctc cgcacaggga ggttgagttt 1980 gccatagagt tagagccggg cacggttcct atatccagag ccccttacag aatggccccc 2040 gcagaattga aagaactgaa ggtacagtta caggaattgc ttgataaggg attcattcga 2100 ccgagcgtgt caccttgggg tgcgccagtc ttattcgtta agaagaagga cggatcgatg 2160 cgtttgtgca ttgactatag ggagttgaac aaagtaacag taaagaacag atatccctta 2220 cccaggatag acgatctatt tgaccagtta cagggagcca cagtgttctc taagattgat 2280 cttcggtcgg ggtaccatca gctgagaatt aaggatgagg atgtcccgaa gacagcattt 2340 cgttccagat atggacacta ccagtttatt gtgatgtctt ttggtttaac gaatgctccg 2400 gcagtgttta tggacttgat gaacagagtg tttagggaat tcctagatac ttttgtgatt 2460 gtgtttatcg acgacatctt gatatactct aagacggagg ccgaacacga ggagcacttg 2520 cgtatggttt tgcaaacact tcgggataat aagttgtacg caaagttctc gaagtgcgag 2580 ttttggctga agcaggtgtc ctttctgggc cacgtggttt ctaaggctgg agtctctgta 2640 gatccagcta agatagaggc agttaccggt tggacccgac cttccacagt cagtgaggtt 2700 cgtagttttc tgggtttagc aggctattat cgacggtttg tggagaactt ttctcgtata 2760 gctactcctc ttactcagtt gaccagaaag ggagctcctt ttgtttggag caaggcatgt 2820 gaggacagtt ttcagaccct taaacagaag ttagttaccg caccggtact tacggtacct 2880 gatggttctg gcaatttcgt gatttatagt gatgcttcca agaagggtct gggttgtgtt 2940 ttgatgcagc agggtaaggt ggtcgcttat gcgtctcgtc agttgaagag tcatgagcag 3000 aactacccta ctcatgatct agagttggca gcagtggttt ttgctttgaa gatatggagg 3060 cattatttat atggtgaaaa gatacagata ttcacagatc ataagagctt gaaatacttc 3120 tttactcaga aagaattgaa tatgagacag cgaaggtggc ttgagttagt gaaggattac 3180 gattgtgaga tactgtatca tccaggcaag gcaaatgtgg tagccgatgc tctcagtagg 3240 aaagtgtcac attcagcagc actcattacc cggcaggccc cattgcatcg ggatctcgag 3300 cgggctgaga ttgcagtgtt agtgggggca gttactatgc agttagccca gttgacggta 3360 cagccgactt tgaggcagag gatcattgat gctcagagta acgatcctta tctggtggag 3420 aagcgtggcc tagcagaggc agggcaaacg gctgagttct cgttatcctc tgatggtgga 3480 ctgttgtttg agagacgcct ctgtgttccg tcagatagtg cggttaagac agaattatta 3540 tctgaggcgc acagttcccc attttccatg cacccaggta gcaccgaaga tgtatcagga 3600 cctgaagccg ggtttattgg tgggcgtaac atgaagaggg aagtagcaga atttgttagt 3660 aaatgcttgg tgtgccagca ggttaaggca ccaaggcaga aaccagcggg tttattacaa 3720 cccttgagca taccggaatg gaagtgggag aacgtgtcca tggatttcat tacagggcta 3780 ccgagaactc tgaggggttt tacagtgatc tgggttgtgg tggacagact tactaaatca 3840 gcgcacttcg ttccgggtaa atccacctat actgctagta agtgggcaca gttgtacatg 3900 tctgagatag tgagattaca tggagtgcca gtgtcgattg tttctgatag agatgcccgt 3960 ttcacttcca aattttggaa gggtttgcag actgctatgg gcacgaggtt ggactttagt 4020 acggctttcc atccacagac tgacggtcag actgagcgtc tgaaccaggt tttagaggat 4080 atgttacggg cgtgtgcatt ggaatttcca ggtagctggg actcccactt acatttgatg 4140 gaatttgctt ataataacag ttatcaggct actattggca tggcaccgtt tgaggccctg 4200 tacggcagat gttgtagatc cccggtttgc tggggtgagg taggtgagca gagattgatg 4260 ggtcctgagt tagttcagtc tactaacgaa gcaatacaga agattagatc acgcatgcat 4320 accgctcaga gtaggcagaa gagttatgca gatgtgaggc ggaaggacct tgagtttgag 4380 gtaggggata aggtgttctt aaaggtagca cctatgaaag gtgtcttgcg ttttgaaagg 4440 aggggaaagt tgagtccccg ttttgttggg ccatttgaga ttctggagcg gattggccct 4500 gtagcttatc gcttggcgtt gcctccatca ctctcgacag tccatgatgt gtttcacgtt 4560 tctatgttga ggaagtacgt gccagaccca tcccatgtag tggattacga gccactagag 4620 attgatgaaa acttgagcta tgttgaacaa cctgttgagg tgctggctag aggggtgaag 4680 acgttgagaa ataaacaaat tcccctagtt aaagtcttat ggcggaatca ccgggtagaa 4740 gaggctacat gggagcgtga agacgacatg agatcccgtt atcccgaact gttcggggaa 4800 taaaactttc gaggacgaaa gttccctaag gagggaagaa 4840 // ID Copia-39_VV-I repbase; DNA; EDCOT; 4170 BP. XX AC chr10; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-39_VV_; KW Copia-39_VV-LTR; Copia-39_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-4170 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr10; Positions 16485428 16481259. XX CC Positions [1541-2071] - Integrase core CC 'CAATC' target site duplication CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 114..1253 FT /product="Copia-39_VV-I_2p" FT /translation="MAAESSNFVQPAIPKFDGHYDHWSMLMENFLRSKEYW FT SLVENGIPAAVEGIEPTEAQQKAIADHKLKDLKVKNYLFQAIDRNIMETIL FT NKETGKHIRDSMKQKYQGSTRVKRAQLQALRREFEVLQMKEGESVDEYFAR FT TLTIANKMKIHGESMKQVVIIEKILRSMTSRFDYVVCSVEESNDLDTLTID FT ELQSSLLVHEQRMNGHGRDEQALKVTYNDQVAGRGGRGRGAFRGRGRGRGR FT QAFNKAIVECYKCHQLGHFQYECPKWEKGAHYAELDEKEEMLLMSYVELNQ FT SRKEDVWFLDSGCSNHMCGNKLWFSDLDEEFRQSVKLGNNSKMTVLGKGNI FT RMQVAGVTQVITDVFYIPELRNNLLSVGQLQEKGVLF" FT CDS 1304..4135 FT /product="Copia-39_VV-I_1p" FT /translation="MQTSMSANRMFILPARVMSKAPTCFQITLEDNTHLWH FT CRYGHLSFKGLRTLQYKKMVRGLPQLKASSKVCTDCMVGKQHRDAIPKRSL FT WRASQRLQLVHADICEPIKPVSNSKKRYLISFIDDYSRKVWIYFLTEKSEA FT FTTFKNYKNLVEKETGAFICCLRTDRGGEFTSLEFNAFCKTNGISRQLTAA FT YTPQQNGVAERKNRTIMNMVRSMLSEKQVPKNFWPEAVNWTAHVLNRSPTL FT AVKGVTPEEAWSGVKPNVDYFRVFGCIGHVHVPDNKRKKLDDKSFQCVLLG FT VSEESKAYILYDPVSKKIVVSRDVVFEEDKCWNWGRSNEEVRLDVLEWGDS FT NEEGSEDDAEEGVAVEGREREDNLSSSESLGSLSESLGENSGVSGESSPSS FT QQGRNRRVPFWMEDYVSGGEFSEGDVEHNLVLFTSTADPTTFEEAVQSSKW FT RAAMDLEIEAIERNETWELTDLPEGVKKIGVKWVFKTKLNENGKVDKCKAR FT LVAKGYAQQHGIDYTEVFAPVARWDTIIMVIALAARNGWSVYQLDVKSAFL FT HGELNEAVFIEQPQGYEKKGEEHKVYKLKKALYGLKQAPRAWYSRIEAYFI FT KEGFERCSCDHTLFIKTGDGGKILIVSLYVDDLIFTGNDESMFVKFKNSMK FT LEFDMTDLGKMKYFLGMEVLQNSEGIYISQRKYAKEVLERFGMEKSNSVKN FT PIVPGDRLTKNEGGVKVDATKYKQLVGSLMYLTATRPDLMYVVCLISRFMA FT SPTEMHLQAAKRVLRYLKGTVDLGVFYQKEGNGELMAYTDSDYAGDVDDRK FT STSGYVFLLSEGAVAWSSKKQPVVTLSTTEAEFVATASCACQGVWMRRVLE FT KLGHSQGKCTTVLCDNNSTIKLSKNPVMHGRSKHIDVRFHFLRDLTREGVV FT ELKHCGTQEQVADIMTKPLKLDVFLKLHELLGVSVVPRVN" XX SQ Sequence 4170 BP; 1324 A; 612 C; 1121 G; 1113 T; 0 other; atctggtatc agagccccat catagggcct gattgtgaga gaaaagaaac cgcagtttct 60 tgtagagaga aagagtgaaa agagagtaag ataagagaaa gagtgatcaa agtatggcag 120 ctgaaagtag taattttgtt caacctgcaa ttcctaagtt cgatggccat tatgatcatt 180 ggtctatgct tatggaaaat tttcttcgtt caaaggagta ttggagcctg gtcgagaatg 240 gaatccctgc tgcagtagaa ggaatagagc ctactgaagc tcaacagaag gcaattgcag 300 atcacaagct gaaagacttg aaggtcaaga attatctgtt ccaagccata gatcgaaaca 360 ttatggagac catcctcaat aaagagactg gtaagcatat ccgggactct atgaaacaga 420 agtaccaagg ttccacaaga gtcaaaaggg cacaacttca agcacttcga agggagttcg 480 aggttctgca gatgaaagag ggtgaaagtg ttgatgagta ttttgctcga acactcacca 540 tagcaaacaa gatgaagatt catggtgaaa gcatgaagca agtggtgatc attgaaaaga 600 tcctgagatc aatgacttca aggtttgact atgttgtgtg ttcagttgaa gagtctaatg 660 atttagacac tttaaccatt gatgagttgc agagtagctt gttggttcat gagcagagga 720 tgaatgggca tggaagagat gagcaggcat tgaaggtgac ctataatgat caagttgctg 780 gaagaggagg tcgtggtcgt ggagcttttc gaggaagagg cagaggaagg ggcaggcaag 840 cattcaacaa agctatagtt gagtgctaca agtgtcatca attagggcac tttcaatatg 900 agtgtcctaa atgggagaag ggagcacatt atgcagaact tgatgagaaa gaggagatgc 960 tattgatgtc gtatgtggag cttaaccaat caaggaaaga agatgtttgg tttcttgact 1020 cggggtgcag caatcatatg tgtggaaata agctgtggtt ctcggatctt gatgaggaat 1080 tccggcaatc tgtaaagctc gggaacaatt ccaagatgac tgtattggga aaggggaaca 1140 ttagaatgca agttgctgga gttactcagg taattacaga tgttttctat attcctgagt 1200 tgagaaacaa tttgctaagt gttggacaat tgcaagagaa aggagtgcta ttctgatcca 1260 acatggagaa tgcagagtct atcatcctga gaaagggctc attatgcaaa catcaatgtc 1320 tgcaaatagg atgttcatac tgcccgcaag agttatgtca aaagctccca cttgttttca 1380 aataactctt gaagacaata cacacctctg gcattgtaga tatgggcacc taagctttaa 1440 gggtctcaga acattgcagt ataagaagat ggtgagaggg ttaccacagc tgaaagcatc 1500 atccaaagta tgcactgatt gcatggtggg aaagcaacac agggacgcaa ttccaaagag 1560 gagcttgtgg agagcatcac agaggttaca gttggtacat gctgacattt gtgaacccat 1620 caaacctgtc tccaatagta aaaagaggta tcttattagc tttattgatg attatagtcg 1680 taaggtatgg atatattttc ttacggagaa gtctgaagct tttactacct tcaagaatta 1740 caaaaatctt gttgagaaag agacaggagc ttttatttgt tgtttgcgca cagatagggg 1800 tggagagttc acatctctcg aattcaatgc cttttgcaaa actaatggta ttagtaggca 1860 actcactgca gcctatactc ctcaacaaaa cggagtagct gagcgcaaga acaggacaat 1920 catgaacatg gttagaagca tgttatcgga gaagcaagtc ccaaagaatt tctggccaga 1980 agcagtgaac tggacagctc atgtgctcaa tagaagtcct acattggcag taaaaggcgt 2040 gacccctgaa gaggcttgga gtggtgttaa acccaatgtt gattattttc gggtttttgg 2100 atgcattggc catgttcatg tgccagataa caagagaaag aagctagatg ataagagctt 2160 tcaatgtgtg ttgctagggg tgagtgaaga gtctaaagca tatatacttt atgatccagt 2220 gtccaagaag atagttgtaa gcagagatgt tgttttcgaa gaagataagt gctggaattg 2280 ggggaggagt aatgaagaag taagacttga tgtgcttgaa tggggagata gcaatgaaga 2340 agggagtgaa gatgacgctg aagagggggt ggcagtagag ggaagagaaa gagaggacaa 2400 cttgtcttcg agtgagtcac ttggttcttt gagtgagtca cttggtgaaa attcaggagt 2460 atctggagaa agctcaccaa gctcacaaca agggaggaac agaagagtac cattctggat 2520 ggaagattat gtgagtggag gagaattttc agaaggcgac gttgagcaca acttggtcct 2580 atttacctca actgcagatc caactacttt tgaagaagct gttcaaagtt ccaagtggag 2640 agctgcaatg gacttggaaa tagaagcaat agaaaggaat gagacttggg agctgacgga 2700 cttgcctgaa ggagtgaaga agattggagt aaagtgggtt ttcaaaacca aactcaatga 2760 aaatggcaag gttgacaagt gcaaagctcg gttggtggca aaagggtatg cacaacaaca 2820 tggcatagac tatactgagg tgtttgctcc tgtggccagg tgggatacaa ttataatggt 2880 gattgcttta gcagctcgaa atggttggag tgtgtaccag cttgatgtca aaagtgcttt 2940 cttacatggt gagctaaatg aagcagtgtt tattgagcaa ccacagggct atgagaagaa 3000 aggtgaagag cataaggtgt acaaactaaa gaaggcattg tatgggctta aacaagctcc 3060 tcgtgcatgg tatagtcgaa ttgaagcata ctttatcaag gaagggtttg agagatgcag 3120 ttgtgatcac acattgttca tcaaaacagg agatggaggt aaaattctga ttgttagctt 3180 atatgttgat gatctaattt ttactggtaa tgatgagagt atgtttgtta aattcaagaa 3240 ttctatgaaa cttgaatttg atatgactga tttgggaaag atgaagtatt ttctgggtat 3300 ggaggtttta caaaattctg agggtattta tattagtcag aggaagtatg caaaagaagt 3360 gttggagagg tttgggatgg agaaaagtaa tagtgtgaag aatcccattg ttcctggaga 3420 tagattaacg aagaatgaag gcggagttaa ggtggatgct actaagtaca aacaattagt 3480 tggaagtctt atgtatttga ctgctacaag accagatttg atgtatgtgg tgtgtcttat 3540 tagcaggttc atggcaagtc caactgagat gcatctgcaa gctgcgaaaa gggtgttaag 3600 gtacttgaaa ggtactgtag atttgggagt tttttatcag aaggagggta atggtgaact 3660 aatggcatat acagacagtg actatgcagg ggatgtggat gataggaaaa gtacttctgg 3720 ctatgtgttt ttgctcagtg aaggagctgt ggcatggtct tctaaaaagc agcctgtggt 3780 tactttgtct actactgaag cagagtttgt ggcaactgct tcttgtgctt gtcaaggagt 3840 atggatgagg agagtattgg agaagcttgg tcattctcaa ggaaagtgca ctaccgtgtt 3900 atgtgacaat aattctacta taaagttgtc caaaaatcca gtaatgcatg gacgcagcaa 3960 gcacattgat gtaaggtttc atttcttgcg tgatttgact agagagggag ttgttgagtt 4020 aaagcactgt ggcacacaag aacaagttgc agacattatg acaaaaccac tcaagttgga 4080 tgtgttttta aagttgcatg agttactggg tgtgagtgtg gtaccaagag tcaactgaat 4140 gcattattgc aatcagttta ggggaggaat 4170 // ID Copia25-PTR_I repbase; DNA; EDCOT; 6092 BP. XX AC scaffold_452; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia25-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-6092 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-6092 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 224-224 (2007). XX DR Genome; scaffold_452; Positions 44133 38042. XX CC Positions [2819-3256] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1298..2815,2819..4072) FT /product="Copia25-PTR_I_1p" FT /translation="MSNDNLKFSLRSIVEKNKLNGTNFLDWERNLRIILRS FT EGREDVLATPVPTVTNTSSDEEKATATRVKSEALPVTCLMLAAMEPDLQKR FT FEHSDAYSIITELKTLFQDQARIERYETHKAILDSHLVKGKPVSPHVIKLT FT GLFKRMENLGTPYDQELATDIVLRSLHDGFAPFRMQYHMNGLKHDLNELHS FT MLKNAEGNIIGDKKKEVLNVNNGKGFKRVAKSKSNYQGKSKQVAKPKDGEK FT PKVAADHDCFYCKTKGHWKRNCPKYLEDKRNETVSSTSGIYVIEIMTTNVL FT TLDNGPTWVLDTACGAHITSYVQGLRNSRQVRKGEINLCVGNGASVAALTV FT GDLSLSLPSGLVLELNNCYYVPCITKNLISYAVLDHENFEFSSKNGCISIF FT KNDIFYATARVSNGLFVLDLKSELYNINNKRQKLKSLSEAYLWHCRLGHIS FT VNRMKKLHKDGLLKDMDYESIDTCESCLMGKMTRSPFKGTFERATELLGVI FT HTDVCGPMSTARGGYRYFITFTDDMSRYGYVYLMSHKSKSFEKFKEFQNEV FT ETQSGKKIKALRSDRGGEYLSHEFDHHLKNYGIVTQLSTPGTPQLNGVSER FT RNRTLLDMVRSMMSFADLPLSFWGYALTTAVLTLNRTPSRTVDKTPYEIWT FT GKVPKLSFLKIWGCEAYVKRLQTEKLAPKSDKCYFIGYPKGSFGYYFYNPT FT QQKVFVARDIVFLEREFFSNKSSGRNIHLEIVQDDEEQQTQQQEDMDDVDD FT EMITFEGLGPQIIQEPEQEDLQTVMNHVPDPVVEQVEPTRRSERPRVQPRR FT YDDFILNESLDVLMLELSEPSTYKQAVTGPDSKKWLEAMRSEMDSMFENQV FT WDLIDLPDGVKPIGSKWIFKLKTDTDGNISVYKARLVVKGFRQIHGIDYEI FT LANGVKDPFLNRFLPKRMCI" XX SQ Sequence 6092 BP; 1996 A; 942 C; 1301 G; 1853 T; 0 other; acaatggtat cagagctatc ttgcataaat tcataggatc aatgaattaa ttgttaattt 60 gatgcggatc ttgatttaaa ttggtggtga attttatatg gataaaatgt aaaattaaaa 120 tgaagatttt gattggccca tggaatttta tgaatataat atgaaatttt aggagggaga 180 tacacaaaac atatggtacg tgacttttgc ttttgatctc ctctccttaa taataaaatg 240 cctttacgat tttaattaaa aagaaagcaa aattgttttg tttcctccaa ttttaaaatg 300 tgcagacaaa ccccaaggga gtcaatatta tatggtttat tttattgttt cctaaaagtt 360 aggaaatccc atttatatat ttttcataca attttatcta ataattgcat tttatgatta 420 ataatgatta ataccatgta aggatttaat tttaaattaa gaattttttt ttttatgctt 480 gttttatatt atgatatatt gcatgcataa ggtgactagt atggcccaga aatacgatct 540 gcgtattgtt atatttttgt aatttatttt aataattaga ttattgtaaa taattttgta 600 atacaaagaa gagaaagtcc atgaagttca aggatggaga tccatgaagg gtacaaggat 660 gaagacaaaa gaagattaga tctttaatta attttttttt ttggggccat actaggatca 720 tttttttttt attgcatatt ttttttatgc tttatttatt tattttgcat tgtctttatt 780 tatgccagtt ttcacttata aataaaagat aatcaaaaac ttaagttcct acagaaaatt 840 ggggcaatgc ctttccgtgt cataacccat gaagtttatg gttttggttg gatgggtttc 900 gcaaaagcga gggtgtccta cctcaatctt aggctcgtga gggtgaatct atacgggggt 960 tcataaatct tgatacggtt gtacccaaca agagaccaaa aggcaaagtt ttggatcttg 1020 aggcatgggg atgaatccta cattggatgt ggatcatcaa ccaagaatta taataagtta 1080 taattagtaa ttgttactta ccttgaatac acaagaacta aggcagtgca aaagtacgtt 1140 ggggcttgtc tatgatggga tcttggaatc attttattca taagggacaa taacaacttg 1200 aataaaatgt gcatttactt attttaaatt gtttaattat aagtatttgc aatatcaaac 1260 ataaactgat ttgtatgtca tttatatttt gtagattatg tcgaacgata atttgaaatt 1320 ctctctacgc tcaattgttg agaaaaacaa gctcaatgga acgaacttcc ttgattggga 1380 aaggaatctg agaattattc tcaggtccga gggacgtgag gacgtcctag ctacccctgt 1440 ccctactgtg accaatacct catcagatga ggaaaaggca acagcaactc gggtaaagtc 1500 tgaggcatta cctgtaactt gcctcatgct tgctgcaatg gagcctgatt tgcaaaagag 1560 gtttgagcat tctgatgctt attctatcat aactgaacta aaaacgttgt ttcaggatca 1620 ggcaaggata gagcgatatg agactcacaa ggctatactt gatagccatc ttgtgaaggg 1680 aaaaccagta agtcctcatg tgattaaact gactgggctt ttcaagagga tggaaaatct 1740 ggggacccca tatgaccaag agttggccac tgatattgtt cttagatcct tgcatgatgg 1800 ttttgcacca ttcagaatgc aataccatat gaatggtctg aagcatgatc tgaatgagct 1860 tcatagcatg cttaaaaatg ctgagggcaa tataattggt gacaagaaga aggaagttct 1920 gaatgtcaac aatgggaagg gatttaagag ggtggctaaa agtaagagca attaccaagg 1980 gaaaagcaag caagttgcca aacccaagga tggtgagaag ccaaaggtgg ctgctgatca 2040 tgattgtttt tactgcaaaa ccaaaggaca ctggaaaaga aactgtccca agtacttgga 2100 agataagagg aacgagactg tgagttccac ttcaggtatt tatgttattg agattatgac 2160 aaccaatgtt ctcacattag ataatggtcc cacttgggta ttagatactg catgtggtgc 2220 tcacattact tcatatgtgc agggactaag aaatagcaga caagtaagga aaggggagat 2280 aaacctgtgc gttggaaatg gagcaagtgt tgctgcactc accgtaggag atttaagttt 2340 atctttacct tctggtttag tattagaact gaataattgt tattacgttc cttgcattac 2400 taaaaacctt atttcctatg ctgtattgga tcatgaaaat tttgaattta gtagtaaaaa 2460 tggatgtatt tctattttta agaatgatat tttctatgca actgctcgag tgagtaatgg 2520 actctttgta ttagatctca aatcagaatt atataacata aataacaaaa ggcaaaagtt 2580 aaaaagtttg agtgaggcct acctatggca ttgtcgatta ggtcacatta gtgtgaatcg 2640 catgaagaag ctccacaaag atggacttct aaaagacatg gattatgaat ccattgatac 2700 atgtgaatca tgtctgatgg gcaagatgac aaggtcacct ttcaaaggaa cgtttgaaag 2760 ggctactgaa ctactgggcg taatacatac tgatgtatgc gggccaatga gcacataagc 2820 tagaggtggc tatagatact tcatcacatt tactgatgac atgagtagat atgggtatgt 2880 ttaccttatg tcacataaat cgaagtcttt tgaaaagttc aaagaatttc aaaatgaagt 2940 agagactcaa agtggcaaga aaataaaagc acttcgatct gatcgtggtg gtgaatactt 3000 gagccatgaa tttgatcatc atttgaagaa ctatgggata gtaacacagt tgtctacccc 3060 aggaacacca caactgaatg gtgtgtctga aaggagaaac aggactctgt tagacatggt 3120 ccgatcaatg atgagttttg ccgatcttcc gttatccttc tggggatatg ccctcactac 3180 cgctgtactt acattaaaca ggactccgtc aagaactgta gacaaaaccc catatgagat 3240 atggactgga aaagttccaa agttgtcttt tctgaaaata tggggatgtg aagcttatgt 3300 aaaacgttta caaacagaga agcttgcccc aaaatcagat aaatgctatt ttatagggta 3360 tccaaaagga agtttcggat attacttcta caatccaact cagcaaaagg tgtttgttgc 3420 aagggatatt gtctttttgg aaagagagtt cttttccaac aagtcaagtg ggagaaatat 3480 tcatcttgaa atagttcaag atgatgaaga gcaacaaact caacaacaag aagacatgga 3540 tgatgtcgat gatgagatga ttacctttga aggcctaggg cctcagatca tccaagagcc 3600 agaacaagag gatctacaaa cagttatgaa tcatgttccg gatccagttg ttgaacaagt 3660 tgaacccact cgtagatcgg aaaggccaag ggtacaacca agacgttatg atgatttcat 3720 cttgaacgaa agccttgatg ttcttatgct agaacttagt gagccttcta cctataagca 3780 agcagtgacg ggtccagact ccaaaaaatg gcttgaggcc atgaggtccg aaatggattc 3840 gatgtttgaa aatcaagtat gggacttgat agatttgcca gatggagtaa aacccatagg 3900 aagcaaatgg attttcaaac tcaaaactga cacggatgga aatatatctg tttacaaggc 3960 aagattagtt gtcaaaggtt ttagacagat tcatggtata gactatgaaa tattggcaaa 4020 tggtgtcaaa gatccttttc taaatcgttt tttgccgaag aggatgtgta tatgacacaa 4080 cctgaaggtt ttgaagatcc aaatgaagct gggaaggtat gcaagcttaa gaagtccatt 4140 tatggactta agcaagcatc caggagttgg aactttcgat ttgatgaaaa gatcaaagaa 4200 tttgatttca ttagatgtga agaggatcct tgtgtttaca agaagtttag tgggagtaag 4260 gtagccttct tagtcttgta tgtagatgac atactactta ttgggaatga cattccgatg 4320 ctagagtccg taaaagaatg gctgaagaaa tgtttctcta tgaaagactt aggaaaggct 4380 gagtacatac ttggaattaa gatctataga gatagatcta agaggcttct tggattaagt 4440 caaggaactt atattgataa gattcttaat agattcaaga tgcaggattc caagaaggga 4500 tttttaccca tacaacatgg tatatatctc agcaagaaac agtgtcctaa aacacctgtt 4560 gagcttgaga agatgaaaca ggtcccatat gcttctgcta taggatctat catgtatgcc 4620 atggtatgta cccgtctgga tgttgcatat gctttgagca tgtgtagcag atactaatca 4680 aatcctggag aagcacactg gagtgcaact aagaatatcc tgaagtactt aagaaggact 4740 aaggatgatt tcttagtata tgggggagat gaaaaattga tcgtacaagg ctatactgat 4800 gcaagctttc agactgatcg agatggcttt gagtctcaat ctggttatgt cttcatcctt 4860 aacggaggag ctgtgagctg gaagagctcc aagcaggata caatagcaga ttctacaaca 4920 gaggctgagt acattgctgc tagtgaagca gcaaaggagg ccgtttggat aaggaagttc 4980 ctagatgaac tcggtgttgt tcctagcata tcagtgccta tcgacatcta ttgtgacaac 5040 aatggtgcca tagcccaggc aaaggaaccg agttcgagct ccaaatccag acatgttatg 5100 aggaagtatc accttattcg tcgcatcatc actatgggtg acattaggat gtgtaaggtg 5160 catactgatg acaacattgc agatccattg accaaaccta tgcctagacc caagcatgag 5220 agtcacacta gggctaaggg tcttaagcac attggagaat ggctttaagt gttgatttta 5280 tattacatta tattttatga gtgttggaca ctagttttat gtttgacttg atgattttat 5340 gatatatgat atttcatcct tatttatata ttgttttgat cgatattgaa taatatgtcc 5400 aaataattca ttattaacaa atgggatcac cttaagtgtt ctggtgaatg aaaccccatt 5460 aagtgaaatg aagttttgaa ttattaaatg tctatagttt gaaatcatca aatggacata 5520 gatgatttta taagctacta tattgtaagc tgactgatag caccaggttt catgggctat 5580 agggacatgg agatgtctag tcaattacat atatgtgtat ggatgataca tgtaggactg 5640 acccacctta agactctcca aaagagattg tagagtctta aattaaacca tgattagtag 5700 attcctcaga catgagcatg ttgtggtctc acttgatgat tggtatctct ttgacactgt 5760 taaacgcttt ccgtaaaagg gagttataaa ggcagtagtt gggattgcca aaagttgagt 5820 gggagccata gtcatacaag actggagaag tcctcctgct tcgtgcatac tgtgatgcat 5880 tgaacaggaa tggtgtctcg gccatttgaa gagcgagaac taaaaatgca tggccatgct 5940 cggatggatt atttgaaatc atccgtttaa ttgacagttc aaactcagag ttcaagaaac 6000 atatttgata atagatatga atgtcaccat atcatcaaat aagacattaa gagacaaagg 6060 tatcttatat tgcacacttg tttaaagaca ag 6092 // ID DNA8-2_Mad repbase; DNA; EDCOT; 730 BP. XX AC . XX DT 03-NOV-2010 (Rel. 15.11, Created) DT 03-NOV-2010 (Rel. 15.11, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA8-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX RN [2] RP 1-730 RA Bao W. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(11), 1852-1852 (2010). XX DR [2] (Consensus) XX CC TSD is 8-bp long. TIR is 14-bp long. XX SQ Sequence 730 BP; 206 A; 151 C; 178 G; 195 T; 0 other; cagtggcgga gccaggaatt taagacaatg gggtcaaaag ttgaacttcc attactagac 60 agggcatgcc gaaaacgcgg gtctgacgat ctggaggctg ccaggcctta aattcacggt 120 ggtgggaaga tttagcaggg ggctggagaa gaggtgctga tggagtgatg gctaacaaat 180 ggagcagcag ctcctgttgg accttaaact gcttctagtt ccaaggatcg acgacagcaa 240 gtggagctcc aatggatgag ttgctgctgc atcgaagaag aaagaagaaa aaaagggttt 300 agtcccaacg gcttgttttc agtttaaatg ctttgtatgt gtgtgtgaga gtgacaagtg 360 tgcactccag attagatcgc ttaaaacccc aatgaagggc taggatcaaa tctggaggag 420 aatgggtgta atatttgttt aagttctctt gtcccccaga ctcttaaaaa atgttttggg 480 agttggcaat gcaccaaacc ttacaaacat tccttattaa atgaagtgat ggcagatgca 540 atttgcacag ccttgtagtc gtccaacatc tctgcattct ttgttccatt tttctgtcaa 600 gttctaaacc ccaagaaact aatcaaacaa acacaaacaa actttatcag ctccttcttc 660 ttcttcttgt ttggccacaa ggttattggg gtcaaggaat cccattgccc ccaccttggc 720 tccgctactg 730 // ID Copia-10_TC-I repbase; DNA; EDCOT; 14371 BP. XX AC CACC01002892; XX DT 18-JAN-2011 (Rel. 16.02, Created) DT 18-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the cocoa genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-10_TC_; KW Copia-10_TC-LTR; Copia-10_TC-I. XX OS Theobroma cacao OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma. XX RN [1] RP 1-14371 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the cocoa genome."; RL Direct Submission to RU (18-JAN-2011). XX DR Genome; CACC01002892; Positions 2147 16517. XX CC Positions [4231-4716] - Integrase core CC LTRs are 95% similar to each other. CC We thank Le Centre de coopération internationale en recherche CC agronomique pour le développement (CIRAD) for making the sequence CC data for Theobroma cacao available. XX FH Key Location/Qualifiers FT CDS 2057..3583 FT /product="Copia-10_TC-I_2p" FT /translation="MSIYIKPIDYEMWDVITDGPFIPSTLNVITNELMPKS FT RFEWTEAETKKVQTNFKAINTLHCALTPTEFNKVSSCTTAKQVWDKLRVIH FT EGTSQVKESKITLLTHNYKMFKIELGEDITSMLDRFTNIINKLSQLGKPIP FT EHEIVKRLLRSRPKNWKPKVTAIRKAKDLNVITLDEICGSLLTHELELKDE FT KEEDRKEAKEKKKSIALKVSILEEELKELSCDDDEELSLVVRKFRKLMGRR FT NRRLARRGFRKDQGASWKFRNKNNSIKKKELICYECKKPGHFKSECPLLKD FT KTPKKNKKSKKVMVAAAWFDSDTSSSEDEDEKSEEKANLCLMAQDDEIEVS FT SSPCDISIDDLQDEYDSLYDEFEKLFSKYKILKKKTTSLENDLEKVRQEFN FT SIFEQRNFLQVELEHSKIDFEVLKLELENKSEALQKLLDEKIAPKCLKMKL FT QKEMHTTRRILLLHHLDVIVVENMDIYHMTTLREVICRKLRKFGSLKDPIL FT QLTLKDPSKYGYL" FT CDS 3799..4968 FT /product="Copia-10_TC-I_1p" FT /translation="MVGKNSQTQISHWLLVKGLKHNLLSISQLCDKGFNVC FT FDSNKCEVIDIGTNKVSFIGKRLKNMYVVFLEDLEINNEICLVANVENDSW FT LWHRRLGHVSLHTMSKLIRKNLVVRLPDLKFENEKICDTCQLGKQVRTSFK FT TKKIVSTYRPLELLHIDLFGPISTTSLGGKSYSYVIVDDYSRYTWVYFLAH FT KNDAISAFISHCRKIENEKGLAIVSIRSDHGGEFEKFCNEKGLDHNFSAPR FT TPQQNGVVERKNRTLKEMARTMLCENNLPKYFWAEAVDTTAYILNRVSIRP FT MISKTPYELYKGRKPNISHFRSFGCKCFVLNNGKQPLGKFDAKSDEAIFLG FT YALNSKAYIVFNKRTLNVEESIHVVFDESNDLQKEIHVDDDDVEILE" XX SQ Sequence 14371 BP; 4984 A; 2182 C; 2770 G; 4435 T; 0 other; agtgatggcc attcaagtga tcaatgttca tacaattatg cttcagtcca atttgcgggg 60 aacttcaaca agtagcagaa taacccatat tttaattcat acaatcatgg ttggagaaac 120 caccccaact tttcatggaa caacaacata gggcctttca atccaaaccc caacgtgcct 180 cttggttttc aacaacaatc tagaccacca attcttgaaa tgaagtccca agtggaagaa 240 cttatcttgc aatatatgtc tacgattgat gccataattc agagctatgg agccttcttg 300 agaaatcttg agacccaagt gggacagctt gcaaactcca tcaatagtag atgccaaggt 360 gccttaccaa gtgatacaca agtcaatctc aaaggtaagg aacattgtaa tgcaattacc 420 tttaggagtg gcaaagaagt tgaaagggtg agtggaaaat caattgaatc ttcaaaggag 480 catgtagatg atgacaaggc aattgttgag aaagaagttg aagtggaaaa gatagataat 540 gggcaagcta agaatcaagg ggattctcaa gcaatttatc ctccaccacc attcccacaa 600 aggttgaaaa gacaaaaaag cttgataaac agtttgagaa atttttaatg tcttcaagaa 660 gctccacata agcatccctt ttgctgaagc ttctgaaaac atgccaagtt atgttaaatt 720 cttgaaagac atcttaatta agaagagaaa actagaagat tttgaaacaa tggcacttac 780 tgttggctcc attagttttt gatgataata aattattccc attcatttgt atctaatact 840 tttacttaag tgtggaggaa aattaatgta tgaaattaat aaatcaatct ttcaaagggt 900 atatcaaaag aaaaaaggga gataaaaata ataagacatg actgcttaac aaggaagaag 960 ctcattagtt gaataaggaa gaatgttggt tggcaaggat tcaaattgga gaaatggcaa 1020 gctgaaggat attgagaaac agaaccaact tagtcgacca agaaatgggc tagtcgacta 1080 agtgcttact gccaaaacta ctagagacag ggagcaaaaa atagagacga cttagttgac 1140 taagatatca gttagtcgac taaaagcatt atgcctacaa gtttgaaatc tgcactaaaa 1200 gacagaataa tggttagaac caactcccaa ctgtctccac gactagaaaa ctattaaact 1260 cccatcagag atgtttctcc aagtataaaa aggtcttcca acagttagaa actagttttt 1320 ttaaaagtgt taaagggatt tgagtcacaa aagagttgaa aaaccagaaa atctctcttg 1380 taccttgcta cacctaaacg cccatctttg tacttgtatt ctgcactcaa ccttgtacca 1440 tttagatcaa cttgtgatca taggtacttt cttttactta tctttttgta ttcttagagt 1500 gagggattca ctctaagtgg ttgtttcaag caaggtttgc ttgaaagtgt tcaagttcta 1560 acttagcctt gaaaagttag gtgtttggtt ttactttagc ctgtgaaaaa actagtgtaa 1620 aaggttttgg ttgagcctgc taaaagccat tgtaaagctt ggtgaaagct tgtgaatttc 1680 accgattcgt agtggatttg ctgggaaaat ctttggttag ataatcaagg tagtggatgt 1740 aggtcttgga ccgaaccact ctaaattcta ctatcttttt gctctgtttt tatttcattt 1800 tcttttcttc atttgtttcg cacttgtcta gactttgaga caatatttga aagagccaaa 1860 ttgtgctatt cacccccttt ctagcacata ttattgggac caacaagtgg tattagagct 1920 agttccctat tattaaggct taacattcgt taggagaatc taaatggctc aacaaaaatc 1980 catagttgct gagagacaat aaacaaacag accacctctg tttgatggct ctaactatcc 2040 ttattagagc actaggatgt caatttacat taaacctata gattatgaaa tgtgggacgt 2100 cataactgat ggacccttta ttccctcaac attaaatgta attacaaatg agttgatgcc 2160 aaagtcaagg tttgaatgga ccgaggctga aactaagaaa gtccaaacaa attttaaggc 2220 catcaataca ttgcattgtg ccttgacccc cactgaattc aacaaagtct caagctgtac 2280 aacagctaag caagtgtggg acaaacttag agtaatccat gaagggactt cacaagtcaa 2340 ggagtccaaa attacccttt tgacacataa ctataaaatg ttcaaaatag agcttggtga 2400 agatatcacc agcatgctag ataggtttac aaacatcata aacaaattga gtcaactagg 2460 aaaaccaata cctgagcatg aaatagttaa aagacttctt agaagccgac caaaaaattg 2520 gaagcctaaa gtgactgcaa tccgaaaggc caaagatcta aatgtaatta ccttagatga 2580 gatttgtggt tctctcctta ctcatgagct ggagcttaaa gatgaaaaag aagaagatag 2640 gaaggaagca aaggaaaaga aaaagagcat tgcacttaaa gttagcatcc ttgaagaaga 2700 gctaaaagaa ttatcatgtg atgatgatga agagttatct ctggttgtaa gaaaattcag 2760 aaagcttatg ggaagaagaa accggaggct agctagaaga gggtttagaa aagatcaagg 2820 tgcttcatgg aaattcagaa acaaaaataa ctccataaaa aagaaagagc tgatctgcta 2880 cgaatgtaag aaacctggcc actttaagtc cgaatgtcca ttgttgaaag ataagacacc 2940 aaagaaaaat aaaaaatcca aaaaagtaat ggtggctgct gcatggtttg acagtgacac 3000 atcaagctct gaagatgaag atgaaaaatc tgaggaaaaa gcaaacctct gcttgatggc 3060 acaagatgat gaaatagagg tatcctcatc cccctgtgat atttccattg atgatttaca 3120 agatgagtat gacagccttt atgatgaatt tgaaaaactt ttttcaaaat ataagattct 3180 aaagaaaaag actacatctc ttgaaaatga tttggaaaaa gtgagacaag agttcaattc 3240 tatttttgag caaagaaatt tcctgcaagt tgagttagaa cactcaaaaa tagattttga 3300 agttttaaag ctagagctgg aaaataaatc tgaagctttg caaaaactgc ttgatgaaaa 3360 aatagctccc aaatgtttaa aaatgaaact ccaaaaagaa atgcatacca caagaagaat 3420 tctgcttttg catcatctag atgttatagt tgtggaaaac atggacatat atcatatgac 3480 tactttaaga gaagtaatat gtagaaagtt aagaaaattt gggtccttaa aggatcctat 3540 attgcaacta actctcaagg acccatcaaa gtatgggtac ctataaagaa aaattgaaat 3600 tttgttttgt aggttgagct gcacataaag gatacatgtt taagagctca actcaagaag 3660 aagtagcctt gctacatgaa caatggctac tcacaacaca tgacatgaga tgaactgtta 3720 tttacttagc tagacaaaag aaagggaggt atcgtatcct ttggtgatga ttctgaaggt 3780 tgaattcatg ggataggtat ggttggtaag aactcccaaa ctcaaattag tcattggtta 3840 ttggtgaagg gtttaaagca taatttattg agtattagtc aattatgtga caaaggattt 3900 aatgtatgtt ttgattcaaa taagtgtgaa gtaatagaca taggtacaaa caaagtctca 3960 tttataggaa agagattgaa gaatatgtat gttgtttttc ttgaggatct tgaaataaat 4020 aatgaaatat gtctagttgc aaatgttgaa aatgacagct ggttatggca taggagatta 4080 ggacatgtaa gcttgcatac tatgtcaaaa ttgattagaa agaacttagt tgttaggctg 4140 ccggatttaa aatttgaaaa tgagaaaata tgtgatactt gccaactagg aaaacaagtt 4200 agaacatcct tcaagactaa aaagattgtg tcaacatata gacctcttga attattacac 4260 attgatctat ttggtccaat aagcacaaca agtttaggag gaaaatcgta tagctatgta 4320 atagttgatg actattctag atatacttgg gtttattttc ttgctcataa gaatgatgct 4380 atatcagctt ttataagtca ttgtaggaaa atagagaatg aaaaaggact agccatagtt 4440 agcataagga gtgatcatgg aggagaattt gagaaatttt gcaatgaaaa gggattggat 4500 cataatttct ctgcacctag aacaccccaa caaaatggag tagtagagag gaaaaatcga 4560 accttaaaag aaatggctag gactatgtta tgtgagaata acctaccaaa atatttttgg 4620 gctgaggctg tggacacaac agcttatata cttaatagag tctcaataag acccatgatt 4680 tctaagacac catatgaact ttacaagggt aggaaaccaa acatttctca ctttaggagt 4740 tttggctgta aatgttttgt attgaacaat ggaaaacagc ctctaggaaa gtttgatgca 4800 aaaagtgatg aggcaatatt tttaggatat gcattaaact ccaaggctta tatagttttc 4860 aacaaaagga ctctaaatgt tgaagaatca atccatgtag tttttgatga gtcaaatgat 4920 ttacaaaagg aaattcatgt tgatgatgat gatgtagaaa tcctagaata acaaatggaa 4980 gaaatgagcc taaagaacaa tataaataat gaagaaagct cacatagaag agaaaatgaa 5040 actccatctt tagaagattt gcaaagaaca gaaaattagc ataatgacct tccaatgagt 5100 tgaagatttg taagagacca tccataagat caaatcatag gtgatattta tcaaagagtt 5160 agaactagga gagcaataag agaaacttgt gaattttcag ccttcatatc ataaattgaa 5220 cctaaaagtt ttgaagaagc taaaaatgag gaaagttggg taatggccat gcaagaggaa 5280 cttgatcaat tcaaaagaaa tcatgtatgg tcactagtac ctagaccttc aaatcaccct 5340 attgttggca caaaatgggt gtttagatat aaggtagata agcaaggaaa tgtagttaga 5400 aataaagcta ggttagtaac ccaaggatac aaccaagagg aatgaataaa ctatgatgaa 5460 acctttgcat ccgttgctag gatcgaagcc ataaggttgt tgttagcttt tgcttgcttc 5520 atgaatttca aattgtacca aatggatgta aaaagtgcat ttttaaatgg attcattcaa 5580 gaggaagtat atgttgaaca accaccaggg tttgaagatt ttgaaaaacc agatcatgtt 5640 ttcaaactcc acaaagcctt gtatggattg aaataagctc ctagagcttg gtatgagagg 5700 ctttcaaaat ttttggttga aaaaggttat gatagaggca gcattgatac tacattgttt 5760 attgaaagat gtttaaatga ttgaattgtt gtgcaaatat atgtggatga cattgttttt 5820 ggtgcaacta atgaggcttt atgcaagaac tttgctaaag aaatgtaggg tgaatttgag 5880 ataagcatga taggagagtt gaagtacttt cttagtcttc aaattaaaca aagtgaggaa 5940 aaaatcttca tcaaccaaga aaggtacact caagatatgc tcaaaaagtt tgatatgctc 6000 aagttgaaac taatctctac accaatgagt ccatccacaa gacttgatct tgatgaaaaa 6060 ggaaaaagta ttgatcaaaa gctctataga ggtatgatcg aatcacttct ctactttaaa 6120 acaagcagac cagatattta gtttagtgtg tgtttatgtg ctagatttca gtcacaacct 6180 aaagaatcac acctaacagc tattaagaga atttttagat acctcttaga aactcaaact 6240 ttaggattat ggtattttag agaatcatca tttgatcttg taggctattc ggatgcagac 6300 tttgcaggaa gcaaaactga tagaaaaagt actagtggga catgccaatt tctaggaaat 6360 atgctagtat ctttgtctag taagaaacaa aattctgtag cactttcaac agctgaagca 6420 gagtatattt ctctaggtag ttgttgtgct cagattttat ggatcaaaca acaactatga 6480 gattttggaa ttaaagttca taatgtacca attttctgtg acaacacaag tgcaatcaat 6540 atatctaaaa atcctgtgca gcattcaagg acaaagcaca ttgagattag acaccatttt 6600 gttagagacc atgtagtgaa aaatgacatt aaaattgaat ttgtgaatac tttgcatcaa 6660 ttagttgata tttttactaa accactaaat gaagatagat tctgtgaaat tagaagaaat 6720 ctaggtatga ttagtcagca ggaattgtga gaaaatcttt ggctcatgca catgaaacag 6780 aatgcattta gtcgactaag atgaatctta gtccattaag agtgttttgg tagcattaaa 6840 taataagact cagtgaataa aataaggaag gaataaaata atataaagaa tgtgtgtatc 6900 gagtaataag gaaagaagaa atactaccta aaatgaataa ccaaaattta gagggagttt 6960 tgaaattttg agcaaataga atagggcaat atttaaaggg gagacggacg gttcttctag 7020 gaattaactg ctaacaactt ctctttttct ctcccctgaa acctgagcct ctgaaactaa 7080 ttcaaaccct tgccacttag acaaaacctc gtcagaaaaa ttcttgattc aaaatatgaa 7140 aaacctcaca gagtaaagaa atcattgaaa agaagaaagg aaaaaggcca ctagaagaaa 7200 ggcctaaagc aaaaatactt aagaagaaat agaaaatcgc atctgcttca gtgaaagaga 7260 tatttgggaa actgaaagaa aagaagcaaa aaatagaaaa gaagaaggac aaggaatcca 7320 cactcaagaa agatactggc tcttcttctt ctaagtttag aaataagatg catgaactga 7380 ggttcagaaa aatttagaat gcacctatta cctgtggcaa atatattgac tagaagagtt 7440 ttgatgagaa tttagaaatt cagactagtt tatccgacta ttttgatgaa ctgaaactga 7500 aaggatataa cacttttaag aatagatcct accgtgcaag tctggtaaaa gagttctatt 7560 ccagcattgc tttaggagaa aaagaattag aggattctaa ggactttgtc gaaaatggcc 7620 tgaatgtgta tttgaatggg aaagaatttg ttgtcactac tgatgattta ggtagcttac 7680 tgaaaatcga gtgtgaaggg ggtgagtatg agttcctaga gaaatacgat ccctcatgat 7740 tataggaaat catcaccgga agaaaggaaa agtattcttc aaagattaat tccagtatga 7800 taatcagccc ccagataagg attctgtatt actttgtagc agcaaacatc tagggcaaaa 7860 atggaagttt aagttacatc aaccttcagg atctttggct gatggaacat gcctttaatg 7920 tggttgctct gaatgtaggt agatttatga ttgaaaagat gagaagtgca tgcaaacttg 7980 agaaaatcaa tctgccttat ggaaatgtgt ttacatcctt agtgctaaag aagggtgttt 8040 gggcaaaaag atatggtgaa gaatagagac tagattatct acttgggtag tttaactaaa 8100 atgggttact ggatggtgaa aaatttacta aaacacccta ggtctctaca attccaacac 8160 cgattgaggc accatcatct caattttcta gtgaaatgat ttttaatttt ttgatgagga 8220 tagatggaaa gctcattgat catgaaacta gattacaaaa aatggaagag aaaattgttg 8280 aactggagaa taaactgaaa ggaaaagaaa agccatcaga acttgctact gaagattcct 8340 ctaaaacact aagtgcttca ccagcacagc aaggtgctgg aagtttaggc ttgcaagtag 8400 aagaatctga tcctcatggt gtaagttatg gtgttccagt tgaaggtcat cagctagaag 8460 aggaacaatc aagaaaatca ccttcacctg agttatagga taaagatgaa tctgatcaag 8520 gtatcgaagt gattgcatct gagcaagaaa atacccctac taaaccttag cctcaactag 8580 aaccttaacc atttcctcca cactttgaaa aggttttaat catgagtttg ttccaacaaa 8640 taattcaaga ggaataagtt gagaaagggg tagttaagga aaaagcacaa aaagcagcat 8700 ctccatcagt ccctaaagta aaagtaaaat ctgggaaaga aaagcacata gtcactgtac 8760 catcacaaca gaaggaagcc attgcagcac cattgatgag gaagaaaact atggccacaa 8820 agatagcatt tctcaagaga ataaaggctt atcgattggt agagaaatct aaactagctc 8880 cagtctcttc tccccaggat ccagtcaatg tctttgacaa atcctcacta gaaccttccc 8940 cttaaaaatc atcacctcta agagaaccct ttctttgtcc tctgaatcct ttttatggca 9000 ctgaatcctt agcctctgac accttagatg actagaaacc ccttgatttg atgttgacaa 9060 aaagggaaag tagaatggta ggaactaggg aagcaggaac ctgagaatta attaaaaaaa 9120 ctgttagggt agagttatca ggaattatca gaaatgaata aggggcattt tagaaatatt 9180 gactgttgtt ttttttttcc tactagttat gccatgatgg cacttgaaca cttagtttta 9240 attttgttat ctatatggtt gtttaacaaa tggatgctga tatgattatg atatttgact 9300 gctgaaaatt aaagtttact gatattttgc tatccttggt atttttactg ctgttgacaa 9360 aatctgctgc tacattaata ttgaattata tgctgacaat taatttctgt gaataatttc 9420 tgtttgtgaa tagatataaa tgctatgtat aatgtatcag ttgaaacata aatgatgaaa 9480 acaaaatcta ataaattaac tgctgacagc tgctggaact ttgatgaaaa tctgtcaaca 9540 tttactgttg aaagtttaat gacaatctgt taatacttac ttgccgtaaa tcactctata 9600 ttgctacaca tatatatact ctaaatatac aatgtcattt tctatataac aagaataaaa 9660 tttgctggaa taaagtaagc aaaatatgca cacactaagg gagagcatat gcttagaggg 9720 agcaatcctc atgttttgca gaaactaaaa tgagtaaaaa gacactatcc tgttaatcaa 9780 ggaatgtttt gtaatcatca aaaagggaga gattgttggc tccattagtt tttgatgata 9840 ataaaatatt cccattcatt tgtgtctaat acctttacgt gagtgtgcag gaaaattaat 9900 gtatgaaatt aataaatcaa tctttcaaag ggtatatcaa aagaaaaagg gagataaaaa 9960 taataagaca tgactgctta acaaggaata agcttattag ttgaataagg aagaatgttg 10020 gttggcaaag attcaaattg gagaaatggc gggctgaagg atattaaaaa acagaaccaa 10080 cttagtcgac caagaaatgg gctagtcgac ttagtgctta ctgctagaac tgccagagat 10140 agtgagcaga aaatagagac gacttagtca actaagatat cagttagtcg actaaaagca 10200 ttctgcttgc aagtttgaaa tttgcactaa aagacaaagt aacagctaaa accaactccc 10260 aactatctcc aacggctaga aaattgtcaa actcccatca tagatgtttc tccaagtata 10320 aaagggtctt ccaacagtta gaaactagtt tttttagaag tgttaaagag atttgagtca 10380 cataagagct gaaaaactag aaaatctctc ttgtaccttg ctgcacctta acgcccattc 10440 tttgtacttg tattctacac tcaaccttgt accatttaga tcaacttgtg atcataggta 10500 ctttctttta cttctcttct tgtattctta gagtgaggga ttcactcgaa gtggttgttt 10560 caagcaaggt ttgcttgaaa gtgttaaggt tctaacttag ctttgaaaag ttaggtgttg 10620 ggttttagtt tagcccgtga aaatctagtg taaaaggttt tggctgagct tgctaaaagt 10680 cattgtaaag cttggtgaaa gcttgtgaat tttactggtt cttagtggat ttgttgggaa 10740 aatccttggt tggataatca aggtagtgga tgtaggtttt ggaccgaacc actctaaatt 10800 ctgctgtcat tttactctgt ttttgtttcg ctttcttttc ttcatttgtc tcgcacttgt 10860 ttagactttg agacaatatt tgaaagagct aaattgtgct attcaccccc ctctagtaca 10920 tattattagg accaacactt actgaggagt gtagcgtaat aattcaaaac aagcttccac 10980 caaaacttaa agatctaagg agtttttcta taccttgtac tattggtaga tttaaattta 11040 ctaaagcttt atgtgatttg ggcgcaggtg tttcaatcat gcctttgtca atggttgaga 11100 aaattggact taatgagtta caacttacca caattttttt gcaattagta gatagaataa 11160 tcaggtatcc tgttgtgatt attgaagatg tattggttaa agttgggcat ctctacattc 11220 cggtggactt cattatgctt gagatggaag aggatctgaa aattccttta atcttggggt 11280 gaccattctt ggccactata ggcgcaatca ttgatgtgag ggaagacaag ataactttca 11340 aagttggaga agaggtagtt gagtttaaca ttttcaatgc aaataaaaat cctagctcta 11400 caagttgttg ctatagagtg gagttaattg atgaatgaaa aggtgaacct atttctccac 11460 ctacaattga gcaagcacca atatttgagt ttaagccacc accttcgcct gtgagaccca 11520 agcagtcacc aacggagcat tttccaccac catctagttg tctttttgat attggacaac 11580 aagtaattat gctttctaga tcatacttca agctttttcg atggaaacac aaagaaagat 11640 ggtggggtcc tttcaaagtg gtaaaggctt atccttgtgg aataattgag atttatagtg 11700 aggatacggg aataatcatg gttaatggga tgagcctcaa accatattcc gaggatgaag 11760 aattggaaaa tggggtgctt tagtcaagct agtgactata aataagtgtt tcttaggagg 11820 caacccaagt ttctaaactt tacttatttt agcctttatt ttatttaatt ttttttagtt 11880 tagttagaat ttatttcttt tgatttatta aattttttta tatttccttt tgcaagtaat 11940 tggtaaaaaa attaaaaaaa aaggtcagtg ctgcggcact tattttgagt atcgtggcct 12000 tgaaatgaag aaaacaaggc acatgaaata gaatgtttca gcatcgcgac cctcaaaggg 12060 agcgccacgg cgctgaacaa agcaaggatt tatagaatag ttagacgccg cgacgcttag 12120 ccttcaacac cgtggtgctg gtaaggacaa tcttttttgt tttaaatata tttttttctt 12180 ctttttcccc ccatgatctc caacttcttg agagacgcag tgttgggtca gggcacaacc 12240 ttaacccttt gaaaaccctc tcatattttt ttcttcttct ttcactcttc tttttctttg 12300 acctccatcc ccactcccat tcttcctcct cctgccaatc tcttgccttc ctccgttttc 12360 tcttttccac tccaacttaa tgcatattct ttctacttgg atttttttta ttttcccttt 12420 gaaatcctac actcctaagg taagtaatct tccaaacatt ggttgtcaat tactttgtgt 12480 agagagagga tgaggttggt gttcatagta aattttataa tctttgctac ttgaatgatt 12540 ccattgtgca tgtttgttaa tgggtatttc atacttcctc atgatcaatg cttagagtgc 12600 agaaaatttt tatgattagt gccaatttct tagtacccat ataatgaatt catggacctt 12660 ttgtctgctg caaatataat tgataaatgc tttgttgatg agagtagata atgggtttgt 12720 ttaattttgg atacttggtt gagcaattag aaataaatcc tggaattgtt ggtgtaacaa 12780 catgcaataa ttgataattt tgatgagtgc attgtcatag aattattttt atattagact 12840 attgcatatt gaaaattatg attatgataa tgttgtttga atgttgtgag gaatagagaa 12900 tttatgctgc atattaagga gtgggatgga catgtctact tttcctccgt cacctacgaa 12960 ttttaactct gaggatgatt ttgatggtga cgagtgggaa gacttgtaga ctacaacttc 13020 ggagtgaggg gagtattctc gtcctttttc ttttattttc ttttatcaca ttgaggacaa 13080 tgttcagtcc atgtttgggg gagtggttta gaattttgtt agtttatttt tagttagctt 13140 tatttatgtt ttgcatgctt tattgtgttt caaaaaaaaa aaacatttga gatagttgca 13200 ccttattcat gattgtccca atcttaggat gatattttaa ttatcttttg attcttagct 13260 tttgggaagc atatatttat gatttaattt tatgtgataa tcttgtgtta gctttatttt 13320 agaatgtgac ttccaataat ttgaacacta tattctttta cttagaattt ttgtgtgatt 13380 tagagaaatt ttatgttgat gaaaaagtat agtgaagtca agaattctag aatttgtttg 13440 attctctctc gaggcgaaat cttagataac acttaggata ggaagtgatc taggctatct 13500 ttggatcgtt tgagcctttt tgagcccacc ttgttatatt tatacttagt cacccttttt 13560 tagcctaatt taccttttct ttgtaattac acaattttgt tagccttagc ctttctattt 13620 aaatctagca atttgaacct ttcaccctct aagtatttta atctttctaa ggaatggttt 13680 gagcttaaag ataaattgag ggagaaaagt gaaaaaaaac acgaaaagaa aaaaaaaagt 13740 gatggttatt agcaaaaatt accccttgtt tgtaattgtt aaaaataagt ttgggggttg 13800 aaaaagaaaa gaaaagaaat aaatgtgttg tatgaaggaa agtttatttc aagtttgggg 13860 gtgctattta aaaaaaaaaa atgagctctt tatatgtcct agattgatta agtgcttagg 13920 gtgaatttgg gcctaaatat atcctttatc ataccttgat cctagcctta cattacaagc 13980 ttgataaaga cctattgatc cttgaataag tgttaatcta cattagtaga tagaaagatg 14040 aaaagcaaac ctatgggatc ctagtactaa tctatgctta gatttggaat aaactaatcc 14100 gaattgtatg atattctttg taagagagca ttcacacaca cacacacagg aagtccattc 14160 gaaaaataag ttttcatttg aattgatgca tgaatttaag gattagctgt atgttacctt 14220 aagttggaat ttgagttaat ttctgaggta aaattaggaa atcatgattt ggtacttcaa 14280 tctcatgttc agggattttt tttttatgtt cagttttctt tttgtgattt tcttttgctc 14340 gaggactagc aaaatcttaa gtttggggtt g 14371 // ID Gypsy-26_Mad-LTR repbase; DNA; EDCOT; 2627 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Gypsy-26_Mad-LTR. XX NM Gypsy-26_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-2627 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1747-1747 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 2627 BP; 641 A; 560 C; 495 G; 930 T; 1 other; tgtgacaacc tgtccctaat tttacgattt tattaatttt aaaggagtga atggacaaaa 60 aatgccccta gagatgagat tgttgacttt cgttgaccat cattttggga catgtatgag 120 ctattatttt accgtaacct cgaagtactc gacggtacga atgcgtaggc gcaagcggaa 180 ttgaatttgg agctacgata aagattttat ggaactacga aacttgaggg tgttttataa 240 aatttgaatt ttgggtattt tattatttta atattttttg agtggacatt ttaaatattt 300 tataattttt ctggcttatg gggcccacac ccatacaaac tttccacttt tttctttcca 360 cgtttctatt tttccaccac tcttagacac tctttcttct ctctctgtta ctctcacttc 420 tccctcacct ttctcccgtg tctcaccctg caacaacaat ggcaacaccg gcgtctacca 480 acttgccatc tcctccgatg agctccaccc aaaccaccac ctaggttttc tctctcttcc 540 ctcttccctc aatttttctc tcatccccct caaagtctat cttactttcc tgtctctttg 600 ggatgcatcg agatggtgca acgaaaaaca ccgagccacc atcatcgtcg tttcgacgag 660 tttcaaccac aaaacaactc actccattct ctccttcgga tttcttactc tggactccgt 720 gcacactgca tagaaacgta acggggaacg ccgccatgtt ttctggcgag ttcgcaaact 780 cccgacaagg gtaagctatg agaacaacct aaaaattctt ggatcatgtt ttagtatatg 840 tttctagctt tcttaagggt tttgatgagg gttttggtac agaaccgctg cagggaagac 900 ttcctagatt tttcggcgac ttttgagccc ttcttttckg ccaactccgg ccacggtcga 960 ggaacccaat gatatatttt gattccttgt ttcttgggct tcaatttgat atattggatg 1020 actagtttta gtggagattt ttagttggat tggggccgtt aaaaatttct ggccaaaagc 1080 ccaaaaaaat cggcccaaac ctttgaccca tgacacatta acctaggatc cggcccggcc 1140 cacttcagac caggaatatt cttggcaaat tctttggaat attccttctg ttgacttttt 1200 tgaaattttc tcggaaactc tcctaggcta atttcgatgc ccgagttcgt ttttgacatc 1260 catttagtga aattttaaag ttttaacgta gttgaccggc tcggcgtctc ggttgacttt 1320 ttagggttga ccgttgattt ttcgttgact ttttacgaaa tttgccaggg atgcttctta 1380 acgtatttcg atgcgctgat tccgaatctg ccgtccgttt ctccaaattc aaacgtttta 1440 attgagtttt actaatgggt ctcaatatta tgcttaggta cgattaacat cggtgactcc 1500 atatttattc gtccgaacgg ccatgacttc gcaagtatct atgagtgggt cttttctttt 1560 atatagtata tatacttgtt tagtttccac atatattttt aataaagaat ttttcaacgt 1620 gattgccata attagtttaa tgcttataat aaaggccgta gtgttgagaa ttatgaaatt 1680 attctgaatc ctgcgggatg cacatgtatg cgtactatta tggaatgctt taattatatt 1740 tgtggccatg aatagtatta tggttgacta gaattatcga tttaccatta tatgatcata 1800 attatattat ctgctcatcg tgtgctacac tggtgtttgt actcgcccag gccagggcca 1860 tctttcactg tatgttcaca tcgcaccgta cgctcacttt ggatccatta taggtgccag 1920 tcctatccta gattgctata ggcaattagg actcgtatgt gatgcacata gcgccagtct 1980 tcacgtgatt gtagtactag agcgtatatc attattacac ccagtcctgt tcatgttaga 2040 atatctctgc atgaactcgt gtgtcagcat atgtcgatga gcactcgata tattatgttt 2100 gtttatgcga gattatgtga ttactagacg atagatattt gtttacgaaa tattgtgacg 2160 tattgaattc ttgagatatt gcaggctacg gtaagtattt tcatactata cgtagtatgt 2220 atattttgga aactatactt gttttacggc gaggggttat catgttttcg aaaaggtttt 2280 tataaagctt tgtttttagg cccactcacc cttgtttttc gccccttcag gttttagtag 2340 ctgagctttc gtgttgacga ggattcttgg caaatcttgg tataggtgat taccttcgac 2400 ggtataattc ttatcctacc tttactttac tttacttatg ctctgacatc acgtgtgaat 2460 tgggttcact cccgctcaca tgtgcactct tacatttagg cacttttagg tttaaattta 2520 ttcacatatt ccacctcact acactttatg gcttcgtcac cttccgggtg tcagccaaca 2580 caactcgatt cggagtccag gtggacattt caggtcgggg tgtgtca 2627 // ID Copia-48_Mad-LTR repbase; DNA; EDCOT; 169 BP. XX AC ACYM01033143; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-48_Mad-I; KW Copia-48_Mad-LTR; Copia-48_Mad_. XX NM Copia-48_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-169 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1398-1398 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01033143; Positions 6 174. XX SQ Sequence 169 BP; 56 A; 30 C; 21 G; 61 T; 1 other; tgttgagata ctagcttatg cagtaagcca tagatatata actaagatgt aagaaatgta 60 wacattcaat gacaaaagaa atatatcaga aagtctttct tcttctctct ctttacaatt 120 ctaagttttc ttaatcttct tcgttagaac tactgctgct atcttcaca 169 // ID Copia1A-VV_LTR repbase; DNA; EDCOT; 206 BP. XX AC CU459238; XX DT 22-MAY-2008 (Rel. 13.1, Created) DT 08-SEP-2008 (Rel. 13.1, Last updated, Version 1) XX DE LTR retrotransposon Ty1-copia like, long terminal repeat from DE Vitis vinifera. XX KW Copia; LTR Retrotransposon; Transposable Element; Huben-B01; KW Copia1A-VV; Copia1A-VV_I; Copia1A-VV_LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-206 RA Moisy C., Garrison K., Meredith C.P. and Pelsy F.; RT "Characterization of ten novel Ty1 copia-like retrotransposon RT families of the grapevine genome."; RL BMC Genomics 9(1), 469-469 (2008). XX DR EMBL; CU459238; Positions 1039841 1040046. XX CC LTR = 206 bp CC LTR are 100 % similar to each other. CC Direct flanking repeats = atata. XX SQ Sequence 206 BP; 56 A; 21 C; 44 G; 85 T; 0 other; tgtggaaatc cgttacaatt gtgagtagtg attggtagga taatagggaa agattgaggc 60 ccctatgtgg gtaatttgtg ttcttccata tttgtatttt tttccttttt taattgctct 120 ctgtatagtt gttaaatagg gatatgttta tgtaaaaagt aagagtttgt gaatgaattc 180 agaaaatcat tttctcagtt tcttca 206 // ID Copia-56_PTr-I repbase; DNA; EDCOT; 4639 BP. XX AC . XX DT 10-DEC-2009 (Rel. 15.02, Created) DT 10-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Copia-type LTR retrotransposon: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; internal portion; Copia-56_PTr-I; KW Copia-56_PTr-LTR. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4639 RA Bao W. and Jurka J.; RT "LTR retrotransposons from cottonwood."; RL Repbase Reports 10(2), 165-165 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS join(160..2907,2924..3733,3592..4629) FT /product="Copia-56_PTr-I_1p" FT /translation="MLSSAASPPGFSSAMAGERLLLQPTSAASAAASIISL FT SHTHQVISLKLTNTNYLYWRMQMMPYLLGQGVFGFVDGSNTCPSPHVLAAD FT GISLQVNXLFLRWKQQDQLILSALLSSLSMEVLHLVVGCQTSCSAWRTLEQ FT ALASTSNSRIMQLHGSLQDLRQGDESVTQFMQKAKALFDELAAAGRPVSLE FT DFNLYVFRGLRGEFKDLVTSLVTKAEPLSYADLHSHLLTHEFLHKSSAAIH FT APLLPTPNTPPSALVAQRQTFGNFGRNRGRFNGGWRPNQFSSRGNRSAGSR FT PDHRSFHSSSFGDSRQGNWQRNRGQNPRCQLCQTFGHTAPHCPQLQQRGYG FT QQPTANLAQRNLSSTGSADWFPDTGANQHVTPDLATLTASEPYLGNDNLHV FT GDGKGLPISHLGHTKIYTPHRSFTLSNVLHVPAITKPLLSVQKFCLDNNVY FT FEFHPRVFYVKDLNTNEVLLSGQSKDGLYALTRSSVTSVPQAYWSPCTSAS FT ADLWHRRLGHPTSRIFQLLVSKNKIICNNKRLNFQCQSCPLGKSSRLSLGP FT TGHKTSAPLELIFSDVWGPAPLFSSDGYRYFVIFVDAYTKYVWYYPLVAKS FT DVYSVFHQFQTLVERQFSLKIKSVQTDWGGEYRKLSTFFQTIGIHHRLICP FT HTHEQNGTVERRHRHIVETGLTLLGQCKAPFRFWNYAFETSVYLINRMPTP FT VLAHRSPFDCLFQRSPDYHFLRTFGCLCFPFLRPYNNHKLDFRSSPCVFFG FT YSSSHLGYRCFDIASHRIYISRHVRFHEHVFPFDNSEQIAKVSTTTPTXPA FT TATLPNLLNHPPLPTSTSHPNSPQTQLCHSKQPPDHSLHPSLAHHHMHVYL FT TIMMQVQLVNWSHLLMVLGHSLVPPLLRPPWPAFLQIRSLLTAPPLLTVLC FT LRQLLXHPLRLVFIFLSAATGLLTATIFPCVPPALSRHPMVLRPRQPKTAN FT LVASAAATTASTRVLHSPSSEPLAFSDADRYAVWHDAMCDEIAALRSNRTW FT SLVPFHPSMNVVGSRWVYRIKRRVDGSIERYKARLVARGFTQQEGIDYSET FT FSPVIKQATVRLVFSIAVSRNWKIHQLDIHNAFLNGVLTEEVYMKQPPGFV FT DSSLPSHVCRLHKSLYGLKQAPRAWYTRLSDFLLSIGFRLPRLTPPCLSYL FT MVLISFISWCMLMIFCLRVATLLCFITFFALHWFPASKVDTSLFILSDGTN FT IFYLLVYVDDILLTGSNSAMLHHLIQLLSSEFKLRDLGVVHYFLGIEVQST FT GMGLMLRQHKYILDILTRAGMTSCKPVDTPVSPSKVTILPDHSFSDPTRFR FT QIMGALQYLTFTRPDICFAVNRVCQFMHAPTDSHWAAVKRILRYLKGTTSY FT GFHITRGSSFALHGFTDADWAGSIDDRKSTGGYLVFFGQTPISWKSGKQRT FT VARSSTEAEYKALADGTAEVIWLQYLLTDLQVPSVSAPTIWCDNLGATYLS FT ANPIFHARTKHVEVDYHFVRDRVAKKEIQIRFVPSRDQLADVFTKPLPVAS FT FTAFRFKLRVDPPPSA" XX SQ Sequence 4639 BP; 975 A; 1301 C; 893 G; 1460 T; 10 other; tggtatcaga gccctcccta aaataaacta aaacactttc cctccccctc ccttctgcaa 60 tggacacagc cgccasctac atcttcctct tctgcagcac cggcagtcca gccttcttct 120 cctgccgcag tgcagccctc ttttcctgca gcgcctccta tgctctcctc tgctgcatca 180 ccgcctggat tctcctctgc catggctggt gaacgcctcc tcttgcagcc cacgtctgct 240 gcctctgctg ccgcaagcat tatctccctc tcccacactc atcaagtcat ctccctcaaa 300 ttaacaaaca ccaattatct atattggcgt atgcagatga tgccgtatct cctaggccaa 360 ggagttttcg gctttgttga tggctccaac acatgtccmt ctccacatgt tcttgccgcc 420 gatggtatct ctcttcaggt aaatcmgctc tttcttcgct ggaaacaaca ggaccaactc 480 attctaagtg ctctgctttc ctcsctatcc atggaagttc tgcatcttgt tgttggctgc 540 caaacctcwt gttctgcctg gcgcacwctt gagcaagctc tagcttccac ctccaactct 600 cgtattatgc aacttcatgg ctctcttcag gatcttcgac agggtgatga atcggtaact 660 caatttatgc aaaaagctaa ggccttattt gatgagttag ccgctgctgg ccggcctgtt 720 tcgcttgaag atttcaactt atatgtgttt cgtggccttc ggggagagtt taaagactta 780 gtaacaagtc ttgttaccaa ggccgaacct ctatcatatg cagatcttca cagtcatctc 840 ctcacgcatg aatttcttca caaatcttct gctgccatac atgctcctct gctgcccaca 900 cccaacaccc caccttctgc ccttgttgcg caacgccaga cctttggcaa ttttggccgc 960 aacaggggcc gcttcaatgg cggctggcgt cccaaccagt tcagcagcag aggcaaccgg 1020 tctgctggct ccagacctga tcaccgcagc ttccacagct cctccttcgg tgacagtagg 1080 cagggcaatt ggcagcgcaa tagggggcag aatccacgct gccaactgtg tcaaactttc 1140 ggccatacag ctccccactg ccctcaactc cagcagcggg gttatggcca acagcctact 1200 gccaatctgg cgcagcgcaa tctctcctca accggttctg ctgattggtt tccggatacc 1260 ggtgccaatc aacacgtcac acctgatctt gccaccttga ctgcttcaga accgtatctt 1320 ggtaatgata atttgcatgt tggtgatggt aagggccttc ctatatctca tctcggtcat 1380 acaaaaatat atacaccaca tcgttctttc accttatcta atgttcttca tgttcctgca 1440 atcacgaaac ctctgctctc tgttcagaaa ttttgtcttg ataataatgt ttattttgaa 1500 tttcaccctc gtgtgtttta tgtcaaggat ctcaacacca atgaagtcct tctctcaggt 1560 cagagtaaag atggtctcta tgccctgacc aggtcttccg tcacgtcagt tcctcaagcc 1620 tattggtctc cctgcacttc tgcttctgcc gatttatggc atcgtcgact aggtcatcct 1680 acttcacgta tttttcaatt gttagtctcg aaaaataaga tcatttgtaa caacaaacgt 1740 cttaattttc aatgtcaaag ttgtccttta ggaaaatcat cgcgtttgtc tttaggacct 1800 acgggtcaca aaacttctgc tccgcttgaa ttaattttta gtgatgtatg gggccctgct 1860 cccctttttt cttcagatgg ctatcgttat tttgttatct ttgttgatgc ttatacaaaa 1920 tatgtatggt attatcctct cgttgccaag tctgatgttt actctgtttt tcatcaattt 1980 cagactctcg ttgaacgtca attttcatta aaaataaaat ctgttcaaac tgattggggc 2040 ggtgaatacc gcaaactgtc cactttcttt cagaccattg gtattcatca tcgtctgatt 2100 tgtcctcaca ctcatgaaca aaatggcaca gtagagcgtc gtcataggca tattgtggaa 2160 acaggtctta ctcttctagg gcaatgtaaa gcaccatttc gattttggaa ttatgctttt 2220 gaaacctctg tttatcttat aaatcgcatg cctactcctg ttcttgccca tcgatctccg 2280 tttgattgtt tgtttcaacg gtctcctgat tatcattttt tgcgtacttt tgggtgtctc 2340 tgttttcctt ttctgcgtcc atataataat cataaattgg attttcgttc ctctccatgt 2400 gtgttctttg gttacagttc ctcgcacctt ggttatcgat gttttgacat tgcatctcac 2460 cgcatttata tctcccgtca tgtccgtttc catgaacatg tgtttccatt tgataattct 2520 gaacagattg caaaggtctc gaccacaacc cccacccmac ccgccactgc caccctccca 2580 aatctgctaa accacccacc actacccact tccaccagcc acccaaacag cccccaaact 2640 cagctctgcc actccaaaca gccacccgac cacagcctcc acccctccct tgcccatcat 2700 cacatgcatg tttatctaac cattatgatg caggttcagc tcgtcaattg gtctcatctc 2760 ctcatggtct tggggcactc tctagtccct cctctgcttc gccctccctg gccagcattc 2820 ctgcagattc ggtctctgct gacagcccct cctctgctga cagtcctstg cttgcggcag 2880 cttcttcmtc atcctctccg gctggtctga atcttgtggt tgatttatct tcttatcagc 2940 tgccacaggt ctcctcactg ccaccatctt cccctgcgtc ccaccagcgc tcagcagaca 3000 tcctatggtt ctcagaccgc ggcagccgaa gacagcaaat ctggttgctt ccgctgccgc 3060 tactactgcc tccacacggg tactgcattc tccctcttct gagcctcttg cattctctga 3120 tgctgaccgg tatgcagttt ggcatgatgc tatgtgtgat gagatcgcgg ctttgcgctc 3180 taatcgcact tggtctttgg ttccctttca tccttcgatg aacgttgttg gcagtagatg 3240 ggtatatcgg atcaaacgtc gtgttgatgg cagcattgag cgctataaag cgcgccttgt 3300 tgctagaggc tttacccagc aggaaggcat tgattattct gaaaccttca gtccagttat 3360 taagcaggcc accgtccgat tggttttctc cattgcggtt tcgcgaaatt ggaagattca 3420 tcagcttgat attcataatg ccttcctcaa tggtgttctt actgaagagg tctacatgaa 3480 acaacctcca ggttttgttg actcttctct tccatctcat gtgtgcagat tgcacaagtc 3540 attgtatggt ttgaaacagg caccgagggc atggtacact cgtctgagtg attttttgct 3600 ctccattggt ttccggcttc caaggttgac acctccctgt ttatcttatc tgatggtact 3660 aatatctttt atctcctggt gtatgttgat gatattctgc ttacgggtag caactctgct 3720 atgcttcatc acctaataca gttactaagc tctgagttca agcttcgtga cttaggcgtt 3780 gttcactact ttctgggtat tgaagttcag tctacaggta tgggtttgat gctgcgtcaa 3840 cacaaatata ttcttgacat cctcacccgg gctggtatga cttcctgcaa acccgttgat 3900 actccagtct ctccttcgaa agttactata ttgccggatc attcattctc tgatcctaca 3960 cgatttcgtc aaatcatggg tgctcttcag tatcttacct tcacccgtcc agatatctgc 4020 tttgctgtta acagagtctg tcagtttatg catgctccta cagattctca ttgggccgct 4080 gttaagcgta ttctacgcta ccttaaaggt acgacatctt atggttttca tatcactcga 4140 ggctcctctt ttgctctaca tggctttaca gatgcagatt gggctggtag tattgatgat 4200 cgcaagtcta cgggtggcta tcttgtcttc tttggtcaga cgccgatttc ttggaaatcc 4260 ggcaagcaac gcacagttgc tcgctcctct actgaggctg agtataaagc cctagctgat 4320 ggtaccgctg aggtcatttg gcttcaatac ttgttaacag atctgcaggt tccctcagtc 4380 tctgctccta ccatttggtg tgataatctt ggtgckacct atctctcagc aaatcctatc 4440 ttccatgctc gtactaagca tgttgaggtg gattatcact ttgtccgcga ccgcgttgcc 4500 aagaaagaga ttcagattcg ttttgtcccc tctcgggatc aacttgccga tgtcttcact 4560 aaaccgcttc ctgttgcatc ctttactgct tttcggttca agcttcgggt cgatccccca 4620 ccctcagctt gagggggca 4639 // ID CALYPSHAN2_LTR_MT repbase; DNA; EDCOT; 340 BP. XX AC AC147496; XX DT 28-JAN-2007 (Rel. 12.01, Created) DT 28-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of LTR retroposon, CALYPSHAN2_MT, from Medicago truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW Interspersed; repeat; CALYPSHAN2_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-340 RA Shankar R. and Jurka J.; RT "CALYPSHAN2_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 2-2 (2007). XX DR EMBL/GenBank/DDBJ; AC147496; Positions 65286 65625. XX SQ Sequence 340 BP; 124 A; 88 C; 46 G; 82 T; 0 other; tggaccgtta taatattcct aaggacctga aagacctcca agacctccaa aaggactttt 60 agacccctca ggaaggcctt agtaccttta aaagaagcca aaaagcccaa ggcgcgcatt 120 attatatcgc cgccatacta aatctctaga aacttctaga aactgcccta aatacataaa 180 taaccctatt acttggaaac taagcaacca agacccaagc ccatagaagg ctataaatac 240 cacccttgag aacactctca agtatctaat aaccagtcta aaaaccctag tatacgattc 300 ttaaccctag aatccttatt gtacttttta tgcaagtaca 340 // ID Copia-64_Mad-I repbase; DNA; EDCOT; 4238 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-64_Mad_; KW Copia-64_Mad-LTR; Copia-64_Mad-I. XX NM Copia-64_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-4238 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1666-1666 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [1723-2223] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(1111..1926,1930..4236) FT /product="Copia-64_Mad-I_1p" FT /translation="MFYVCMAAAVKKGEDVWYVDSGCSNHMTGREDLLENI FT DRSVTAKVEMGTGELVNVVGKGELMVATKQGKRYIKEIMLVPGLKENLLSV FT GQMMEHGYYLVFGGIEVRIYEDFTCSNLVVKIPMKGNRSFPLKLQPGIQIA FT MRASVRQAAEIWHRRLGHLNMNALMQLQEHDMVTGLPELRVNSTVCEGCAL FT GKHSRDAFPKETNWRAALPLELIHTDICGPMQTPTKAGNKYFITFTDDCTR FT MGWVYFLRNKSEAFGVFKRFKATVELQSGFKKKLRSDRGGEYTSLEFSQFC FT EDLGLERQLTVAYSPQQNGVAERRNRTIVEMAKCMMLEKGIPFEFWAEAVN FT TAVYILNRCPTKALNKKTPFEAYSGRKPGVKHLRVFGSLCYAQVPSQMRQK FT LDATSVKCIFLGYGTCEKGYRLFNPKTNKIVISRDVIFDENSCWDWKSGAK FT KNLSISVPSEVHGGEGSDVEAVEDDAVFECTESLQEQHEQVIASSSSQEEQ FT VDHTGSQEYDHTPLRFRSLNEVYERCNFCVIEPECFEEASGDEAWRKAMST FT EIEMIEKNDTWELVNRPFDKPVIGVKWVYKTKLNLDGSVQKNKARLVAKGY FT SQKPGVDFNETFAPVARLDTIRTLIALAAQKEWKLFQLDVKSAFLNGTLHE FT EVYVDQPQGFEVQGQEDKVYKLKKALYGLKQAPRAWYDEIDTYFNRSGFEK FT SQSEATLYTKFSDAGVLIVSLYVDDIIYTGSSDEMIQEFKKDMMKQYEMSD FT LGLLHHFLGLGIIQTDKGIFIHQKKYAKSLLEKFGLKDCKAVKTPLAIDDK FT LSKEDGSEDADEGLYRTMVGSLLYLTATRPDLMYASCLLARFMHKPTRKHM FT GTAKRVLRYVQGTLDFGIEYVKGKAAVLIGYCDSDWAGSLDDMKSTSGYAF FT SFGSGVFSWASVKQCSVALSTAEAEYVSAAEATTQAMWLRFVLSDFGEEQV FT EATPLLCDNTSAIAMSKNPVFHQKTRHINRRYHFIRDAIQDGTIELHYCST FT EEQLADIFTKALPKDRFEYLRTALGVKSAKHLEGS" XX SQ Sequence 4238 BP; 1337 A; 678 C; 1091 G; 1122 T; 10 other; ctaatatggc ctcagagcca ggttggatct caatctgggc gtgaatctgt gacaagggtt 60 gcagctaagg aactcgacag agaatcgagt ttgctgcgat tgaagaacga tctgaaaatc 120 wctgggtaac tcgataacaa gtctaatatg gctggatcga gtggtgctga tcttcgagca 180 ccgattttca atggggaaaa ctttgatttc tggcagataa agatgaagac cattttcaga 240 tctcacgatc tgtgggatat ggttgaaacg gggtataatc ctccggcgaa gaaagaagac 300 gaagaactca ctgccgctga gctaaagcag ctgaaggaga acatgatcaa ggatgctaag 360 gctctcggga ttattcaagg tgctgtgtcc gatgaaattt tcccacgaat cgccatactg 420 gagacggcaa aggaggcctg ggatatactg aagcaagagt ttattggaga taaacaggtg 480 agatctgtga aacttcaaag cttaaggcgt gattttgaat atactcgaat gggtgaacat 540 gaagcatttt ctgtgtatct tgtgcgatta tttgatctta ttacacaaat gaaaagttat 600 ggtgaagata ttggaaatca aagaattgtg cagaagttat tgattagtct tcctagatcc 660 tatgatagta ttgtagctgt gattgagaat actagggatt tggagacagt tgatgtgcag 720 gatgtagttg ctactctaaa agggtatgaa caaagaattg agagacactc tgaaaatagt 780 actgaaaaag cctttgctag tttaagtata gctcccagga agaacaatta caatggcaat 840 caaagcttca aacccacaaa gaactggmag acaaagggta agaagtggga taacaaacct 900 gtgcaccagc aagggaaatt tactggatct tctgatagtg ccaagaatgc ttgcaagtac 960 tgtgataaac ttcattttgg agagtgttgg ttcaagggga aaccaaggtg ccataactgt 1020 gataagccag ggcattttgc caaggattgc aggtcaaaga aggttactca acaggcaaat 1080 tatgtcgaac aagtggagaa caatccaact atgttctatg tgtgtatggc tgctgcagtg 1140 aagaagggag aagacgtttg gtatgttgat agtggctgca gtaatcacat gacaggaaga 1200 gaagatctac tggagaacat tgatagaagt gttactgcca aagttgagat gggcacaggg 1260 gagttggtta atgtggttgg aaaaggagag ttaatggttg caactaagca aggcaaaagg 1320 tacatcaagg agatcatgtt agtacctggt ttaaaggaga atctattgag tgtgggacag 1380 atgatggagc atggatatta ccttgtgttt gggggaattg aagtcagaat ctatgaagat 1440 tttacatgct ctaatctggt tgttaaaatt cctatgaagg gaaatcgaag ctttcctttg 1500 aagttgcaac caggaatcca aattgctatg agggcaagtg ttagacaagc tgctgagata 1560 tggcatagaa gactcgggca tctaaatatg aatgctctaa tgcaacttca agagcatgac 1620 atggtgactg gtttacctga gctcagagtg aactccacag tatgtgaggg atgtgccctt 1680 ggcaagcatt ccagagatgc ttttcctaaa gaaacaaact ggagagctgc actaccattg 1740 gagttgatac acactgatat atgtggacca atgcaaacac ctaccaaagc tggaaacaag 1800 tatttcatca ctttcacaga tgattgtacc agaatgggat gggtctattt tctgaggaac 1860 aaatctgagg cattcggcgt gttcaagagg ttcaaggcaa ctgttgaact acaaagtgga 1920 ttcaaastga agaaattaag aagtgacagg ggaggggagt atacttctct kgaattttct 1980 cagttttgtg aagatcttgg tctggaaaga cagctcacag tggcctattc tcctcaacag 2040 aatggtgttg cagagaggag aaataggacc attgtagaaa tggctaaatg catgatgttg 2100 gagaagggta ttccatttga attttgggca gaagcagtta acactgcagt ctacattctc 2160 aatagatgtc ctaccaaggc tttgaataag aagactccat ttgaagctta cagtggaagg 2220 aagcctggag tgaaacactt aagagtgttt ggatctctat gctatgcaca ggttccatca 2280 cagatgaggc agaaactgga tgcaacaagt gtcaagtgca tatttcttgg ctatggaacc 2340 tgtgagaagg gttacaggtt gttcaatcct aaaactaaca agattgttat ctctagagat 2400 gtaatctttg atgagaactc ttgttgggat tggaaatctg gtgctaagaa gaatctgtcc 2460 atctcagtcc caagtgaagt tcatggaggc gaagggagtg atgttgaagc tgttgaagat 2520 gatgcagtat ttgaatgcac agaatcatta caggagcaac atgagcaagt tattgcttct 2580 tcttcaagtc aagaggagca agtggatcat accggttcac aagagtatga tcacactcct 2640 ctaaggttca gaagcttgaa tgaagtttat gaaaggtgca atttctgtgt gatagaacct 2700 gagtgttttg aagaagcatc aggagatgag gcttggagaa aagctatgtc cacagagatt 2760 gagatgatag aaaagaatga cacatgggag ttggtcaata ggccatttga taaaccagta 2820 attggtgtma aatgggtcta caagacaaag cttaatctgg atggttcagt gcagaagaac 2880 aaggcamggc tagtggcwaa gggctattct caaaagcctg gggtkgactt caatgagacc 2940 tttgcacctg tggcaaggct tgataccatt agaactctaa ttgcattggc agctcaaaag 3000 gaatggaagt tgttccaatt ggatgttaaa tctgcattcc taaatggtac actgcatgag 3060 gaagtatatg tkgatcaacc acagggattt gaagtccaag ggcaagaaga caaggtttac 3120 aagctgaaaa aggccttata cggtctgaaa caagctccca gagcttggta tgatgagata 3180 gacacwtatt tcaatcggtc tggtttcgag aaaagtcaaa gtgaagctac tttgtataca 3240 aagttcagtg atgcaggtgt gcttattgta tctctgtatg tagatgacat tatctacaca 3300 gggagttctg atgaaatgat tcaagaattt aagaaggata tgatgaagca gtatgagatg 3360 tcagatctgg gattgttgca tcacttcctt ggtctaggca taattcaaac agataagggc 3420 atatttattc atcagaagaa atatgccaag tcactacttg agaaatttgg tttgaaagac 3480 tgtaaagcag tgaaaactcc acttgcaatc gatgacaagt tatctaagga agatggaagt 3540 gaggatgctg atgaaggttt gtacaggaca atggttggta gtttgttata cctgacagct 3600 actagaccag atctaatgta tgcatcatgt ttgctggcaa ggttcatgca taaacctact 3660 aggaagcaca tggggacagc taaaagggtc ttgagatatg tacaaggcac attggatttt 3720 ggaattgagt atgtgaaggg aaaagctgct gtgttgatag gctactgtga tagtgattgg 3780 gcaggaagct tggatgacat gaagagtacc tcgggctatg cattcagttt tggttcaggg 3840 gtattttctt gggcttctgt taaacaatgc agtgtggctc tatccactgc agaagccgag 3900 tatgtaagtg ctgcagaagc tacaacacaa gcaatgtggc tgaggtttgt gttatctgat 3960 tttggagaag aacaagtgga ggctacacct ttgctgtgtg acaacacctc tgccatagcc 4020 atgtccaaga atccagtgtt tcatcagaaa acaaggcata tcaacaggag gtatcacttc 4080 ataagggatg ccattcaaga tgggacaatt gaactgcact attgcagcac agaggagcaa 4140 ttggcagaca tctttaccaa ggctcttcct aaggatcggt tcgaatactt gagaactgca 4200 cttggagtga aatcagcaaa acatttagaa gggagtat 4238 // ID RAM9B_LTR repbase; DNA; EDCOT; 2659 BP. XX AC . XX DT 22-NOV-2006 (Rel. 11.11, Created) DT 29-MAR-2007 (Rel. 12.04, Last updated, Version 3) XX DE Long terminal region of RAM9B retroposon from Medicago DE truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW LTR; Interspersed repeat; retroposon; RAM9B_LTR. XX NM RAM9B_LTR. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2659 RA Shankar R. and Jurka J.; RT "RAM9B: LTR retroposon from Barrel Medic."; RL Repbase Reports 6(11), 595-595 (2006). XX DR [1] (Consensus) XX SQ Sequence 2659 BP; 742 A; 395 C; 626 G; 893 T; 3 other; tgatttattt tcgtgataag ttatgagttt tggaggattt gataaggata tgagaattat 60 tttattgtta aataaaataa agatttgaaa ataatataaa atatttagtt gagggctgtt 120 ttgatatttt agatagtttt gggggagaaa gtgagataag ataagtaatt aagaagagat 180 ataaatagga gatagaccta gtattttaga aactcattgt acgtacgaaa acttttggag 240 aaaagggaga aaaagcttag agaggagcaa gagcatagag agggctgcga ttttcttcat 300 aacaaggtaa gggtgagact aataattcaa taatgttaat tgttgtaatt ctgatgatta 360 attgacaaga gttaggattg atttagagaa gttttggaat taggtcaaaa ccctaaaaat 420 tgatgatcaa acggtaaaac ttgtttagat tgatgtagaa accgtccttt aaccttagaa 480 tatgtttagg atgaattctg gaatcaaaat taggcttaga accatgttat ttgatggatt 540 tttgtgaaaa acggtagtct gcccgtgcct atgttcatcg ctcgccacgg cgagckatga 600 tcctcgcctc gcgagtgatg aacattcatc gctcgccacg cgagcccttt cccttcgcct 660 cgcgagttgt ttggtgcagc tcgccatggc gagcaaccct tcctcgccat cgcgagctta 720 ggcagagtgc atgtcatatt ttgtgtttcg acctttttag ttggaccttg gatgcctttg 780 agtrcctgaa catacctagt attgattagg aatgaatgta ggatcagatt gaacccagaa 840 caaccttagt ttgggagttg agtggtactc gccatggcga gtaagaactc tcgcctcgcg 900 agcacaacca gaatgtagtt gcttgagtgt ttgtgcgatc tgtgtcgcac gtgttgatca 960 agagtgaacc cctaattggt aatgagacct aatgatgacg tttaatgcag tctgtaaagc 1020 tgtttaagat atgttgatat taattgaaca tgaattaatg tattgtatat tcatgcaaga 1080 tatgaaagtt taattatgat gcaattgatg tgctattgat ataatgatat catcttgtta 1140 tgtgacttgt ttatgctgct tccgttattt aactaagtgc attgcatata gtatgaatga 1200 gttgaagttt agctccaaat tattggatgc atgtgtgata atgttgatta cgatgttttg 1260 ttgataagag tccatgcatt agcatatcat tgagcttagt cctcaccacg aatattagga 1320 gctttgtcct ccgcacgttt tataggagct ttgtcctccg cacgattaaa gtatattaat 1380 acttatgatg acgattggta ccacatgcat ataaggagtc taagatgcat tgtcacattg 1440 tcatgattaa gatgccttgt tgataatgat tgaatatgtg attacgtgat aagtgtttat 1500 tgattatgtt atgttgttca tgatgaattg gatatatgat tacgtgataa ctgtttagca 1560 attatgcaaa gttaataatg gaatgattat gatgttaatt tatgattcgc aattacattg 1620 attaatgtta ttttgttatg aaatctcacc ccttctgctt gaaaatgttg cccttcgtat 1680 gggtaacttg caggtgatcg tgcttagtgt gcagtttgct ttcgtgagtt ggccttgcct 1740 tcactgtgtc gtctaggtcg ctctgatacg taacgggatg gggttatatg ctataacatg 1800 cttcattctc ttacgtgaac taatatgtta tttttattat gttattgatt aactctgatt 1860 tgaaatattt tggttggggc ctgcgtgcca aaacgatttt atgatttatg attataattt 1920 tccgctgcaa tgtttaagat attttgtgaa ggttaaatta ttatttaact gtttttggat 1980 tacgtttcta tgtgatatcc cgttgttatg rtgtttactc tgataaatgt ttaagaaatt 2040 tttatattgg gaaaacgggg tgttacaatt ggtatcagag caggttgatc cgtccggtca 2100 attagagagt cgtgtcgagt cttagtaata tttatattac tatcttatgt tgttgttgct 2160 acttttgtag aatatcagaa atggctggaa gaaacgatgc tgcgttagct gctgctctac 2220 aagctgttgc ccaagctgtg ggacaacaac ctaacgtgaa tgctggtgca aatgctgaag 2280 ctaggatgtt ggagacgttc atgaagaaga accctccgac tttcaaagga cgttatgacc 2340 ctgatggagc ccagacgtgg cttaaggaga ttgagaggat tttccgagtt atgcagtgca 2400 ctgaagatca gaaggtgcgg tttggtactc atcagctggc cgaggaagct gatgactggt 2460 gggttgctat tctgcctacc ctcgagcagg aaggagctgt ggtgacttgg gctgttttca 2520 ggagagagtt cctgagaaga tactttccgg aagatgttcg cgggaagaaa gagatcgaat 2580 tccttgagct gaagcaagga aatatgtccg tgacagagca tgctgccaag ttcgtggagc 2640 tgtctaagtt ctatccgca 2659 // ID Copia19-PTR_I repbase; DNA; EDCOT; 4547 BP. XX AC scaffold_130; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia19-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4547 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4547 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 210-210 (2007). XX DR Genome; scaffold_130; Positions 598492 593946. XX CC Positions [1709-2239] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS join(47..3310,3314..4534) FT /product="Copia19-PTR_I_1p" FT /translation="MEDPFKMDNAEGINRSCNMSEGEPNPNQRLGSVLLNE FT FNYLPWSRAVSIALGGRSKLGYVNGHMRPPNSSSQAYEAWQCKDQLVMSWL FT LNSMENHIAEIFSYSESSFELWEAVKEMFGNQNNAARIFQINRNLANLQQD FT GKTYVQLLGTLKGMWSELALNRPHTIDAAELRKHEEEDKIFQLLASLGSDY FT EDLRSRILMNPDLPSLTSVCATIQREEARTKVMNSDSKNSLSESRAYVVNR FT SMNNDRPFKGKRTELKCHHCHNIGHSIGRCWILHPELKPDFGKKKRSQRSY FT NTKSHVAAAHFTSTSSSNIENFSTNSSALLNEFAAYLKENGDTTMTASAFD FT SVALLGKFAGFLANSAHLSQENTEGIFTAFKTALVASIVHDFWVIDSGATD FT HITNKMTSLYNFEGFSSPTHVSIANGKHVSVKGKGKIKLMSNSIESSILCV FT PSFPFQLLSIGKITRTLNCRVIFDSQQVLFQDLATKKTIGEGFFFKGLYYF FT SSHPQNNGYHQVSALSSFHQEQLLWHQRLAHPSDIVLTKLMPNLDLKNIPC FT DTCHLSKSTRLPFMLSSSKSNKMFDIVHSNVWGPTIESFDGYKYFVSFVDD FT FSRVTWIYLLKFKSEVMHVFQNFHMLVMTQFFTKIKILRSDNGTEFMSKHM FT TQYLASHGILHQSSCVGTPQQNGVAERKNRDLLEKTRALMLHMHVPKMFWS FT HGVLSAAYLINRLPSRVLQFKSPLEVLQKQPPNLSHLRVFGCTYFVHIQNL FT HRDKLDPRAAKCVFLGYSSTQKGCKCYYPPSKKLLISRDVRFEESSLYFKN FT ENQLDDLKELFPLPNATTDLASSVDRLVVANDSSSFSDVMATDEGGASPVN FT THFEHKTIDSQADESSDHDRHLSTTATDIHSDSRVVIPIISDSGDGSANQS FT PQPHPSVIPITTDSEEVSESESANHSPFPQPRRNPTRHRAPPTRLQDFVTY FT AARHPISNYLTYQHLSTEHTAFLIAISDVHEPQNFQEANSKDEWQQAMHDE FT LQALDQNNTWSVVRLPKDKHAVGSRWVYKTKFNSDGSIERYKARLVAQGYT FT QTFGIDYKETFAPVAKMNTIRVLLSVAVNNRLMCQMDVKNAFLHGNLEEEV FT YMKLPPGHPQSSDPNLVCRLHKSIYGLKQSPRAWHAQLSAVFEDNGFKRSN FT ADSSLFIQLGPTTKVMVFVYVDDLIIVGNDGNTISHLKTTLQKHFPIKDFG FT SLKYFLGIEMVVSHKGLFLNQRRYVLDLLKDAKMTDAKPAPTPLDSKLKLE FT TTSEPLRSINYYQHLVGRLIYLTITRPDITYAVSLVSQFMHAPTVFHLCLV FT KRILRYLKGSAGRGIVMTNHGHTQITGYSDSDWAGNAIDRKSTTGFCMFVG FT GNPVSWRSKKQHVVARSSAEAEYRAMASATCELIWLKGLLSDQGFCSSTPM FT TLFCDNQAAMHIAANHVFHERTKHIEVDCHFIHQQVQSQIIKPCYTRSYDQ FT LADVFTKVLTSAHFHRLLSKLGSINPLDPA" XX SQ Sequence 4547 BP; 1319 A; 958 C; 844 G; 1426 T; 0 other; tggtatcaga gcatgttctt aatatcctgc tgtttattta agacttatgg aagatccatt 60 caagatggat aatgctgagg gaatcaacag atcctgcaat atgtctgaag gagagccaaa 120 tcccaatcaa cgtttaggct cagttttgtt aaatgaattt aattatcttc cttggtcaag 180 agctgtgtca attgctcttg gtggcagatc caaacttggc tatgtcaatg gccatatgag 240 accccctaat tcttcttcac aagcttatga agcttggcaa tgcaaggacc aacttgttat 300 gtcctggtta cttaactcta tggaaaatca tattgctgaa atattcagct actcagaatc 360 ttcttttgaa ctatgggaag cagtgaagga gatgtttgga aaccagaaca atgcagctcg 420 tatcttccaa atcaatagaa atcttgctaa tctgcagcaa gatggcaaga cctacgtcca 480 attacttggg accttgaaag gtatgtggag tgaacttgca ttaaatcgac ctcacacgat 540 tgatgcagca gaattaagaa aacatgaaga ggaggacaag atctttcagc ttttagctag 600 tctcggttca gactatgaag atctccgtag cagaattctc atgaatcctg atcttccatc 660 gcttactagt gtgtgcgcta ctatccaacg ggaagaagct cgcacaaagg ttatgaattc 720 tgactctaaa aactctttat cagaatctcg tgcttatgtt gtcaacaggt caatgaataa 780 tgacagacct ttcaagggta aacgaactga gttgaagtgc caccattgtc ataatattgg 840 tcattctatt gggaggtgtt ggatccttca tccagagttg aagccagatt ttggaaaaaa 900 aaagagatct caaaggagct ataacaccaa aagtcacgtt gccgctgctc acttcactag 960 tacttcttcc agtaacattg agaatttctc taccaactca tctgctcttc tcaatgagtt 1020 tgctgcatat cttaaggaaa atggtgatac taccatgaca gcatctgcct ttgattctgt 1080 ggccctcctt ggtaagtttg caggcttcct tgcaaattct gctcacctct cgcaagaaaa 1140 cacagaaggt attttcactg catttaaaac tgccttggta gctagtattg tgcatgattt 1200 ttgggtcatt gattcaggtg ccactgatca tataactaat aaaatgacca gcttatataa 1260 ttttgaagga ttttcttctc caactcatgt gtctattgcc aatggaaaac atgtctctgt 1320 caagggtaaa ggaaaaatta aattaatgtc caatagtata gaatcttcaa tcctatgcgt 1380 tccctccttt ccatttcaat tactttctat tggtaaaatt actcgaacac taaattgtcg 1440 tgttatattt gactctcaac aagttctttt tcaggacctt gccaccaaga agacgattgg 1500 tgaaggtttc tttttcaaag ggctttatta tttttcaagt catcctcaga acaacgggta 1560 tcatcaagtt tctgctcttt cttcgtttca tcaagagcaa cttttatggc accaacgctt 1620 agctcacccc tcagacattg tcctcaccaa attaatgccc aatttggatt taaaaaatat 1680 tccatgtgat acttgtcatt tgtctaagtc taccagactt ccctttatgc tttcatcatc 1740 taaatcaaat aagatgtttg atattgttca ctctaatgtt tggggaccaa ctattgaatc 1800 ttttgatggc tacaaatatt ttgtctcctt tgttgatgat ttctctcgtg ttacttggat 1860 ttatctctta aaattcaaaa gtgaagttat gcatgttttt caaaattttc atatgctggt 1920 catgactcaa ttttttacga aaataaaaat tctccgatct gataatggca ctgaattcat 1980 gtctaaacat atgacacaat atctagcttc tcatggcatt ttacatcagt cgagctgtgt 2040 tggcacacct caacaaaatg gggtagctga acgtaaaaat agagacttat tggaaaaaac 2100 tagagcttta atgctacaca tgcatgttcc taaaatgttt tggtctcacg gagtgttatc 2160 tgctgcatat ctaatcaatc ggcttcctag ccgagtatta cagtttaaat cacctcttga 2220 agtcttgcag aaacagcctc ctaatctatc tcatttacga gtgttcggtt gcacctattt 2280 tgttcatata caaaacttac atcgggacaa acttgatcca agggctgcta agtgtgtttt 2340 cttgggatac tcctcaacac aaaaggggtg taaatgctac tatcctcctt ctaaaaaatt 2400 gctcatatca agagacgtcc gatttgaaga aagctcatta tacttcaaaa acgagaatca 2460 actagatgac ttgaaagaat tatttcctct gccgaatgcc actacagact tggcctcatc 2520 tgtagataga ttggttgttg caaacgactc ttcctccttc tctgatgtta tggctactga 2580 tgaagggggt gccagccctg ttaatacaca ttttgaacac aaaactatag actctcaagc 2640 cgatgagagt agcgatcatg acagacactt gtccactaca gctacagata tacactctga 2700 ctcaagagtt gtcattccta ttatctcaga ctctggggat ggttctgcta atcaatcccc 2760 tcagccgcac ccttctgtca ttcctattac cacggattct gaggaagttt ctgagagtga 2820 gtctgctaat cactctccat ttccacagcc tcgtagaaat ccaacccgtc accgtgctcc 2880 tccaacaagg ctacaagact ttgtcaccta tgctgcaaga catcctatat ctaattacct 2940 tacatatcaa catctctcaa ctgaacatac tgccttcctt attgctatct ctgatgtgca 3000 tgaaccacaa aattttcagg aggcaaactc aaaagatgaa tggcagcaag ctatgcacga 3060 tgagttgcaa gctcttgatc agaataacac ctggagtgtt gtaagactcc ccaaagataa 3120 acatgctgtg ggcagtcgct gggtgtataa aaccaagttt aactcagatg gatctattga 3180 gagatacaag gcgcgccttg tggctcaggg ctatactcaa acctttggca tagattacaa 3240 agaaactttc gcacctgttg cgaaaatgaa cactattcgc gttctacttt cagtagctgt 3300 gaataataga tgattgatgt gtcaaatgga tgtcaagaat gctttcttgc atggaaacct 3360 tgaggaagaa gtctacatga aattgcctcc tggtcaccct caaagttcag accctaattt 3420 agtgtgtcgg cttcacaaat ctatttatgg gctaaagcaa tctccacgag cttggcatgc 3480 acaattgagt gctgtttttg aagacaatgg cttcaaacga agtaatgcag actcctcctt 3540 atttatccaa cttgggccaa caacaaaagt aatggttttt gtctatgttg atgaccttat 3600 tattgtagga aacgatggta acacaatatc tcatctcaag actactctgc aaaaacattt 3660 tcctattaaa gactttggca gtttgaaata ctttcttggg attgaaatgg ttgtttcgca 3720 caaaggatta ttccttaatc aacgcaggta tgttcttgat ttacttaagg atgccaagat 3780 gacagatgcc aaacctgctc ctactccatt ggatagtaaa ttgaagcttg aaacaactag 3840 tgaacctctt cggtctatca attactatca acatcttgtt ggcagactca tttatcttac 3900 tattacacga cctgatatca cctacgcagt gagccttgtt agtcagttca tgcatgctcc 3960 tacagttttt cacctgtgcc ttgttaagcg aattttgcgt tatctaaaag gttctgctgg 4020 tcgtggaatt gttatgacta atcatggtca tactcagatt actggatata gtgactctga 4080 ttgggcaggt aatgctattg atcgcaaatc aactactggt ttttgcatgt ttgttggtgg 4140 taatccggtc tcctggcgaa gtaaaaaaca acatgttgtt gcacgctcta gtgccgaagc 4200 tgaatatcgt gcgatggcgt ccgcaacttg tgaattaatt tggcttaaag gtcttctgtc 4260 agatcaagga ttttgtagca gtactccaat gactctgttt tgtgacaatc aagctgccat 4320 gcatattgca gctaatcatg tgttccatga aagaactaaa cacattgaag ttgattgtca 4380 ttttattcat caacaagttc aatcacagat tatcaaacca tgttacactc gcagttacga 4440 tcaattggct gatgtattta caaaggttct aacttcagct cacttccatc gtctgctatc 4500 caagcttggc tcaatcaacc cccttgatcc agcttgaggg ggagtat 4547 // ID DNA7-1_Mad repbase; DNA; EDCOT; 180 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA7-1_Mad. XX NM DNA7-1_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-180 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1475-1475 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~83% identical to the consensus. TSDs are likely 7-bp. CC Subterminal inverted repeats. XX SQ Sequence 180 BP; 55 A; 36 C; 34 G; 55 T; 0 other; ttagggtgat gctagagaga tcatctactc gaaccatatt ttgtagacca catgatgtga 60 cggttgatgg ttggatttct tgtttaaatc attaaagaaa gaattcaacc atcaaccgcc 120 acatcacgtg gtctacaaaa tacggtctaa aaacatggtc tccctagcat tttccgattt 180 // ID BoSB14B repbase; DNA; EDCOT; 181 BP. XX AC . XX DT 15-MAY-2006 (Rel. 11.05, Created) DT 15-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE SINE family from Brassica oleracea - consensus. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Interspersed repeat; BoSB14B. XX OS Brassica oleracea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica. XX RN [1] RP 1-181 RA Deragon J.-M. and Zhang X.; RT "Short interspersed elements (SINEs) in plants: origin, RT classification, and use as phylogenetic markers."; RL Syst. Biol 55(6), 949-956 (2006). XX DR [1] (Consensus) XX SQ Sequence 181 BP; 41 A; 47 C; 52 G; 41 T; 0 other; taaccggggc ttctagctct agtggtaaag ggcttacagc tgtgagtacc gccacctggg 60 ttcgaatccc ggccactggg gaattaacat ttcggcatcg ccagggacag aggaccgaca 120 cgtggcaaca cgtgactagt ctggatcact tctgtggggc caggatacct ctgtataatt 180 c 181 // ID Copia-66_VV-LTR repbase; DNA; EDCOT; 264 BP. XX AC chr18; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-66_VV_; KW Copia-66_VV-I; Copia-66_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-264 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr18; Positions 14100541 14100804. XX SQ Sequence 264 BP; 84 A; 47 C; 33 G; 100 T; 0 other; tgttagaata tccaaaatct gatagatgaa ttagagttaa aatcacaaat agccaaacat 60 aattcatcta actaatgtca gttaaattag ttatgtcagt tgtcaatact taacagcttt 120 attgatccat ttcaagtgta taaatagacc tcacctgtac atttttattt catctgaatg 180 taaggagaat ttcagtttca atacacgttt gagtgctcct ctgttttctc ctctgttttt 240 cttacaattc tgcatatctt caca 264 // ID L1-8_Mad repbase; DNA; EDCOT; 3879 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-8_Mad. XX NM L1-8_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3879 RA Kojima K.K. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1812-1812 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC This consensus is 5'-truncated. XX FH Key Location/Qualifiers FT CDS 10..3852 FT /product="L1-8_Mad_1p" FT /note="endonuclease, reverse transcriptase and FT ribonuclease H." FT /translation="NLHNDKVQFITFVYAYPQKHLQANLWDQILAHTPTNH FT PWCLIGDFNNIVDSTEKLGGCSNTTTYMNNFINFLNRGDLISLTASGVPYT FT WTNGHSDNTRIYERLDRGVANPQWLREFHDFSLHNFPIFGSDHSPILLTNN FT VNPVRKGSYSFKFEAMWLRHPNFRNFVKSAWTCTNTSRPQEKFVACAGTFK FT YLVRKWNKETFGNVKDRKDKLLTSLCDIQNKIMRDQDNSISMDDEVKIRSE FT LNRVLQEEEIMWAQKAKVKWLQLGDKNTKYFQTVASIRKKRNEIKSVKDSN FT GFWWNYGEGLEQVFVQEFKLRFSCDSSPSQETLATMVDIITPCIDHTHNMQ FT LLECISDEEVWEAVNSIGALKAPGPDGLCAAFYQGCWEEVKDTIIPMIKDF FT FQNNSSLRFINHTNIALIPKVDNPETVSNYRPIGLCNVSYKIITKIIIKRL FT KPLLDLCISANQGAFTPGRSIHDNILIAHELFSSFKVKKGKTGTMGVKLDL FT EKAYDLLNWDYIRYVLIRFGFNEKWINLIMECITSTSFSILINGSPHGYFY FT PKRGIRQGDPLSPYIFILCMEPLIRHFNRLASTPKSHVGILSSLGGFRISN FT LVFADDCLLFARATPKGARNVLQILEMFASAAGQQVNFHKSSIYFSNNTIN FT QDRNNIVNILSIQHKTTIGKYLGIHNIVFWKDLVNEIELIKRVKQKLAGWK FT GQTLSKAGRLTLINSNLTGMPNHVMSCFKCPNRVTTKIDKECRDFFWGRNT FT KLRPMAWKKVCSPKNQGGLGIKRIDHFNNACLAKLGWKVLTNKENWWAEIV FT KSKYLRKSDFLNSKIKQNYSLAWKGILSNRNIIHEGMRWIVGNGEDILFWT FT HQWVFPYPLFHLIPVNDRNNIDWNLKVSNFIVHNSWDSIKLATVVDGDIIR FT KICRIPLPLQESKDKLIWGLTNNGNFSIKSATWLQNRNNHSSNRLTLLKKM FT WKLTIPPKVKMFAWLMIQERLQTRKRLSRFVKNIDKLCPLCNTAEEDQCHL FT FCNCVFATKVWSSTFGXFNNGNISTNDNFFDWMESLSSNDKDGLSDLSKVI FT LNCWQIWMERNNLVFRSVPPVPARCVSIAGSVGSAFLKANGKCDPNEALPI FT SSFIKWHPPDRHDVIKLNFDGSVSNNCAAAAFVLRNSNSQVIGAGALNLDG FT TTISVAEAMGLREGLQCARRKGFTKVMVEGDSKLIIEAVQGHWGIPWRVSS FT IINDIRILARSFSHVDWKHIFREANFVADALAHLGLSLSNPHYWDFCLPDV FT ALPAFNFDCIGNGCTRGFVL" XX SQ Sequence 3879 BP; 1141 A; 665 C; 805 G; 1265 T; 3 other; tgtagttaaa atttgcataa tgataaggtg caattcatta cctttgttta tgcttatcct 60 cagaaacatt tacaagctaa tctctgggat caaattttag ctcatacacc aacaaaccat 120 ccttggtgtt taattggaga cttcaataat attgtggact ccactgaaaa gcttgggggc 180 tgctctaata ctactaccta catgaataac ttcattaact ttctaaatag gggtgacttg 240 atttccctaa ctgcctccgg tgttccctat acttggacca atggtcatag tgacaacact 300 aggatttatg agagacttga tcgtggtgtt gctaatcctc agtggttgag ggagttccat 360 gacttttctt tacataattt tcctatcttt ggatcggatc atagtcccat cttacttacg 420 aataatgtaa accctgttag aaaaggctct tattccttca agtttgaagc tatgtggtta 480 cgtcatccta attttaggaa ttttgtcaaa agtgcttgga cttgtacaaa tacttcaagg 540 ccacaagaaa agtttgttgc ttgtgcaggg acattcaagt atttggtaag gaagtggaac 600 aaagagacct ttggtaatgt caaagatcgt aaagataagc ttttaacctc tctctgtgat 660 attcaaaata aaattatgag ggatcaagat aactctataa gcatggatga cgaggttaaa 720 attagaagtg agcttaacag agttttacag gaagaggaaa ttatgtgggc tcaaaaagct 780 aaggttaagt ggcttcaatt gggagataaa aatactaaat attttcaaac ggtggcttct 840 atccgtaaga aaagaaatga aataaaatct gttaaagata gtaatggttt ctggtggaat 900 tatggggaag gtctggagca agtttttgtg caggaattta aactgcgttt ttcttgtgat 960 agttcccctt ctcaggagac attggctaca atggttgata tcataactcc ttgcattgat 1020 catacgcata atatgcaact acttgaatgt atttcagatg aggaagtttg ggaagcggtg 1080 aatagcattg gtgcgttaaa agcacccgga cctgatggtc tttgtgctgc tttttaccaa 1140 ggttgttggg aagaggttaa agatactatt attcctatga ttaaagattt ctttcaaaat 1200 aattcaagcc taaggtttat taatcacaca aatattgcct taatcccaaa agtggataat 1260 cctgaaactg tgtccaatta tagacccatt ggtctttgta atgttagtta taaaattata 1320 acaaaaatta ttattaaaag gcttaagcct ttgcttgacc tatgcatttc tgctaatcaa 1380 ggtgccttta ctccggggcg ttccattcat gataatatct taattgccca tgagttattt 1440 tccagcttca aggtaaagaa aggcaagacg gggaccatgg gtgttaaatt ggacttggaa 1500 aaagcctatg accttttaaa ttgggattac ataaggtatg ttctaattcg ctttggtttt 1560 aatgagaaat ggatcaactt aataatggaa tgcattacat caacttcttt ctccatttta 1620 attaatggct ctccgcatgg ttatttctat cctaaacgtg gcatacgaca gggtgacccc 1680 ttatcacctt acattttcat tttatgtatg gaaccgctta ttagacattt taatcgtttg 1740 gcttctactc ctaaatccca tgtgggaatc ctatcatccc ttgggggatt tagaatttcg 1800 aacctagttt ttgcagatga ttgtctactt tttgcccgag ctacccctaa aggggctaga 1860 aatgtccttc aaatccttga gatgtttgca tcggctgcag gtcaacaggt aaattttcat 1920 aaatcttcta tttatttttc gaataatact atcaaccagg ataggaacaa tattgtgaat 1980 atcttgagca ttcaacataa aaccactatt gggaagtact tagggatcca taatatagtt 2040 ttctggaagg atctggttaa cgagatagaa ttaattaaac gggtgaagca aaaacttgcc 2100 ggttggaaag ggcaaaccct ttccaaggcc gggagactaa ctcttattaa ttctaatctc 2160 accgggatgc cgaatcatgt aatgtcttgt tttaagtgcc ccaatagggt aacaactaaa 2220 attgataaag aatgcagaga tttcttttgg gggagaaata ctaaactcag accaatggcc 2280 tggaagaagg tttgttctcc gaagaatcag ggtggtttag gaatcaaacg gattgatcat 2340 tttaacaatg cttgtttagc caaattaggt tggaaagttt taaccaacaa agaaaattgg 2400 tgggctgaaa tagtcaaaag taaatactta cgtaagtccg attttttaaa ttcgaagatt 2460 aaacaaaact actcacttgc ttggaaaggc attctttcta atagaaacat catccatgag 2520 ggaatgagat ggattgtggg taatggtgaa gacatactct tctggaccca tcaatgggtt 2580 tttccttacc ccctttttca tttaattccc gtgaatgata gaaataatat tgattggaat 2640 cttaaagtaa gcaactttat agttcataat agttgggata gcattaaatt agctactgta 2700 gttgatggtg acatcattag aaaaatttgt cgcattcccc tccctctaca agagtcgaag 2760 gacaagttaa tttggggttt aaccaataat gggaactttt ccattaagtc tgctacctgg 2820 ctacaaaatc ggaacaatca ctctagtaat cgccttacat tgttaaagaa aatgtggaag 2880 ctaactattc ctcctaaggt taaaatgttt gcttggctta tgattcagga aagattgcaa 2940 accagaaaac gcttaagtcg ttttgttaaa aatattgata agttatgtcc gttatgtaat 3000 acagccgaag aagatcaatg tcatctcttt tgtaattgtg tttttgctac taaagtttgg 3060 agctcaactt ttggtakttt taataatggt aacatwagta ctaatgataa tttttttgat 3120 tggatggaat ccttaagttc taatgacaaa gacggccttt ctgatcttag taaagtaatt 3180 ctgaactgct ggcaaatctg gatggaaaga aataacttgg tgttcagaag tgtgcccccg 3240 gtcccggcgc gttgtgtttc tatcgccggt agtgttggtt cggcttttct caaggctaat 3300 gggaagtgtg accccaatga ggctttacct atctcttcct ttattaaatg gcatcctcct 3360 gaccggcatg atgtgattaa actcaatttt gatggttcag tttcgaacaa ctgtgctgct 3420 gctgcctttg tgctccgtaa cagtaattca caggtgattg gggcgggggc tcttaacctt 3480 gatggcacta ctatttcggt agcagaagcg atgggtttgc gagaagggct ccagtgtgct 3540 aggcgcaagg gtttcaccaa agtgatggtg gagggggact ctaagctcat cattgaagct 3600 gtgcagggtc attgggggat tccttggaga gtcagctcta tmatcaatga tattcgtatc 3660 ctggctcggt cttttagtca tgttgattgg aagcacattt tcagggaggc aaactttgtt 3720 gcggatgctt tagctcacct tggtctctcc ctctcgaatc ctcattattg ggatttctgt 3780 ttacctgatg ttgctcttcc tgcctttaat tttgattgta ttggaaacgg ttgtactaga 3840 ggtttcgtgc tttaatgaat ttctttgcat aaaaaaaaa 3879 // ID TND1_I repbase; DNA; EDCOT; 6529 BP. XX AC AF059674; XX DT 02-JUN-2000 (Rel. 5.05, Created) DT 02-JUN-2000 (Rel. 5.05, Last updated, Version 1) XX DE Internal portion of TND1, a copia-like LTR retrotransposon. XX KW Copia; LTR Retrotransposon; Transposable Element; TND1_I; KW TND1_LTR; COPIA superfamily; internal portion. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RP 1-6529 RA Kenward D.K., Ban R.M., Bai D. and Brandle E.J.; RT "Isolation and Characterization of Tnd-1, A Retrotransposon RT Marker Linked to Black Root Rot Resistance in Tobacco."; RL Theor. Appl. Genet0-0 (1999)In press. XX RN [2] RP 1-6529 RA Kenward D.K., Ban R.M., Bai D. and Brandle E.J.; RT "TND1_I."; RL Direct Submission to Genbank (15-APR-1998)Southern Crop RL Protection and Food Research Centre, Agriculture and Agri-Food RL Canada, 1391 Sandford St., London, Ont. N5V 4T3, Canada. XX DR GenBank; AF059674; Positions 328 6856. XX SQ Sequence 6529 BP; 2060 A; 977 C; 1160 G; 2332 T; 0 other; attggtatca aagcttaact ctctgaaagc cttaaccggt tgagaggacg atctgcattt 60 ttctgttgag aatgttgaac gcaggtataa tgagcgtagg tcactccatc tctttacctc 120 cagtatttga tggcagcaac tacgcatatt ggaaagagcg gatgagagtg ttcatccgag 180 cgaacaactt ccgtctttgg caaatcataa agtatggtga acaaatgacg gaacaagttg 240 ggcaagccat ggtaagtgaa cataatacca aggctatcaa tatgttgtac cgctctttga 300 atcaggaaat ttgtcggaaa atttcccact gcaaatctgc caaagaagtg tgggacaaac 360 ttgaggactt ttatgaaaac actcctcaag aagcggacag ctcgtgtgat gaacctaatg 420 tccgatgtta catggccgac ggagaagaag aggtaagtac ttatgactct tattcttttg 480 aagagttgca agaagccttt aacgatttat tttatgaatt gaaaaaggtt tcaaaaatcg 540 ccaaagaagc tactgcaaaa tcaaaagctt ttgaagacga aaatctgttt ttaaaaaatg 600 acaatgatga tcttagagaa aagatcaagg cgatgaatga agcttcctcg attgataaat 660 gtcttacttg tttatcgtgt gaatctttgc aattagaaaa cgcagaactt aggagtacac 720 tagaaacacg tagtgtagac gttcctaagg tagttaaaga aatcaaaaag gaattgccta 780 agaaaaataa aaggcgtagt aaaaacaaga atggagttag gaattttact gcaccaccga 840 gaaataattc tagggcttta aatgagtcta gaactaacaa ttttagacca cctagacact 900 actctaggat gtatgcaaac aagtctagaa ctaacgctct tagaccacct agacacgaat 960 ctaggatttt tgcaaacaag cctagaaata gtaattttag gcaacctaga aataattcta 1020 ggaacgagac tagacaacct agaaacgata ctaggttctt caataagtct aggattaata 1080 actttagacc acctagatac aattctagga attggaataa tgagtctaga gttaatcgct 1140 ttaattcgcc tagaaataat actaggacct tcgttgataa gtctaggatg aatcatgcta 1200 gaccacctag aaatgactct aggattttca acacgtctag gaatgacttt agatcaccta 1260 gaatgtattt ggctcaacct aggcataggc acaacccgaa tgttgtatgc cattattgca 1320 atcgcgtagg acacattgca cccgtgtatt tttctaaaca tagggattta tcttttggct 1380 ataatcatta tttgcctaac ctcaaaggac ccaaaatggt ttgggtacca aaaacctctt 1440 cgtaggtatt tttgcaggtg tgcttgaagg ctacaaaatt gtagtagatg caccaagcac 1500 gacacctaaa tgcatcaagg ggaatttcgg ttagctattc attttgataa aactgaatag 1560 tgcaaatgat tattgttgac aaatttgctg ttattgttgt tatgtgccaa ctgttgatat 1620 taacatatga ggtattaact tgattctcac cttgaaaaat gttgatgtgc tttattgtaa 1680 gaatcaatat gtgagatttc attgttgact atccttgttg tttcacatgc tgaaaatctg 1740 ttttactagt atcaattatt aaatgattga tccatgcttt gataattatt tttggtgtta 1800 attattaaat catgttttgg taatctattt caaacagcaa gtgatatcaa ttttgttttg 1860 atgtatgttt tgataaatgc ttttcaaata aagattagta tattttgaaa tatctatttg 1920 atatgttttg ttggtataat tgataaattt gtagcaatct tcatattgta tgttcctcaa 1980 tatccttcct actctattta tatggaaaaa ggaagtagcc ttattatact atcttcttgc 2040 taaaagaaga aatgtttagg cgatttgttt caagtaagaa ggaatgtcat ttcattctaa 2100 tttgccttac ttgaggagga atttgttctt ggaaagaata gattgcatga atttcattga 2160 tgatattctc ttaacaatat ctcttgtatt tcaaaaatga attttattgt tgatattact 2220 tttgaaataa atttcttgtt gatgatatca ttttgattct tatgctgatg atattatttt 2280 gatgttcgaa aatattttgg tttaaatttc gtatctgaaa ataaattttt gtgttgataa 2340 tctttacgtt gttggtgata acatttttga gatgtcaaaa atatttctat tttgactaat 2400 atttatttaa tgttgatgtt ttgattaaat gcaatatttg attatgtgta tcaattgtgt 2460 taaattttgg ttttataaca attggtattg attatgtgta ttcatgtttt atagcacctt 2520 ttctaaaaaa aaacgttttt ccaaatctga aaagttattg tcttctacca ttttttgatg 2580 gcattgtctc atccataatc aattgtcata cttccataat tgattgtcat ccaaaatcga 2640 ttgacatact tccataatcg atttttagga cttcaaattt tttggcctca gtaacaatcg 2700 attgttactt gccacaatcg attgtccgtt catttctgag tttttgaaaa ctctctgcct 2760 gttgcccatt tttttaaaac taagtgtcaa cagccccaca atcgattgtt ccttttcaca 2820 atcgattgtc caacggttca atttcaaaaa tttgttaccg ttctgaattc tgaacttatc 2880 cgaaatcgat tatcattgtt gattcatgtg ctggatattt gccatttagt taggctctca 2940 tttttaacat gcctaattgt atttgttgat atgtgttaac aattaagtta tctttgttaa 3000 caatttgtat caattcttct tgaatcacgt tttggtaatt atcattgatt tggttctcat 3060 tattgttaat gtgcttaatt gaaatagttg acatttattt taatatggtt tgctgaaaat 3120 aacattgtgt atcactgtta ataaaataac atttgatgca tttgttatgc tttccatcaa 3180 atggatttat cattgctttt ataacaatcg gtatttcctg aaaaatgtca aattgatatg 3240 tttttgctta aacagttgat gtgtcttgaa aacttttatc tatcatttat catgcatatt 3300 cctcaatgtc tttcctatct gtattgtgtc acttgaagat ttttcgataa aggaaagtag 3360 tcttaatact ctctctttgt ggcaaaagaa gaagtgttta ggcgatttat ttcaaataag 3420 gaaaaatgct ttcttttggt atgccttatt tgagggggaa ttttctttaa ggaagaaata 3480 aattgcatga atgtttattg atgttggtac tcttgaattt atgtgttgat aacactattg 3540 ttgtttcaga tttgcattgg tgatatgact gcatctcaaa atctgtattt caaaaacaaa 3600 tttatatctt gatgatattt tttttggaac aactaatatg tttgtatgca aggagtttgt 3660 aagactcatt actagcaatt taagatgtca atgatggacg agcgtaaatc tcatcttgaa 3720 gctgcaagtt aagcaaatga aagaaggaac tttcatttgt caaaccaagt attgcaagga 3780 gttgctgaat taacttgaaa taagcaacac caaagcaatg gccacatcaa tgaatatgac 3840 catcttgaca gaaatgagag aggtaaggag gttgaacacc aagatatacc gaggtatgat 3900 cgttccctac tttacttcac tgctagtaga cttgatataa tatttagcgt ttattgatat 3960 gctagatatg aatcatgtcc aaaggagtca cgtcttaatg cagctaaaaa tgaagtatat 4020 tattagaaat tttgaatgtg ggactttgct atcccaaaga ttcttcatgc caatcacttg 4080 gctattccga ttctaatttt gctagatgca aattagaccg caagagcata attggcactt 4140 gccatttgct cggtaactcc ttagtttctt ggattagcaa gaaacgtgtt aatgtcgctt 4200 tgtccgcaac cgaggccgaa tatactgcca cgggaagttg ttgttcacaa atcctttgga 4260 tgaaataaca acttttggat tatggtctta gtcttgatta cgtccctctt cgatgtgata 4320 aatactagta ccataagctt gacgaagaat taaattcttc attcaagacc aaagcctatc 4380 aaaattaggc accattttat gaaagatcac gttctcaaag gtgatgtcca aattgagttc 4440 gtaattacta aacatcaatt tgatgacatc ttcaccagac ctttagataa agagtcgttc 4500 ttccgtattc ttagtgaact cggaaatcct tgactctacg ttgatcaaat acattcactt 4560 aggttgtatt tattttataa atacttactt aattatgttt ttgcagagat atcctcaaag 4620 acaaggggaa tctattgttg gtattacaaa ataaattgtt tacttgccac aaaattgatt 4680 gtgtctaata tgtttggtgt gcaggtgttt ttggcaaatt ttattgtttg atccctattt 4740 tctgcccaga ttttattatt atttttatgt gttgtttata aaatattttt attgcagaaa 4800 catcaatttc tttccagtgc aactactcga ttatctcgta tcaataatcg attatgttga 4860 cgttgttgac tttgcaatgc tgtaattaga cttgtgatct taaccttttt gttaatgtca 4920 aaagggggaa gattaagggt atatgcatat ttatcttgtt catgcattag aagataaagg 4980 gtatatttat tttctatgct ttggagaaga taagggtaaa tgcatactta cttgcttaca 5040 tgcatacttt attaaaggga gaagatatat gcatgtttat gtttatgcaa atctctaaat 5100 atttgttgca taaatttagg gggaatcata aattaagggg gaacacatat cttgaactgt 5160 tatgcatatg aacatgtatc ttgaactgtt atgcatatat tgaactgtta ttattatgca 5220 tatcccgata caggtttgcc attatcaaaa agggggaaat tgttggaaac acgttctcaa 5280 actaaacgtg tgttgatcta tgtaggtttt gataaatgcc aaaccaacga ggatggaaca 5340 ataacagtcc aaatacaaga aggacagtac aagttcaaga atcgcaaatg cagttaactg 5400 ttgagtcgtc tttattttgt aatcttgact caacgactgt tgagtcgtct ttattttgta 5460 atcttgactc aacgacttat ttctaatatt ggctctcaca caaaatgatt tttattaaat 5520 catgcatcat tatgttttaa agaaataagt tgcatattag ccaaaatgat ttttaaacac 5580 gtcttgtgat ttttaagttc gacaatcgat tgtcaatagg caacaatcga ttgtcacgag 5640 gcagtaagtt tcttgaaaat catttttgag ctcacaatcg attgtcatgg ctaacaatcg 5700 attgttgcac agtcaaaatt caaataagaa tttcttcaat catttgtttc ttaaagtcaa 5760 gatttggtag gtgaaattga tttacaaaat ctgtgatttt caaatatctt gaccgaaata 5820 ttttgaaatt tgtaaccaca atcgattgtc tattgacaca atcgattgtt gatggttgaa 5880 aaatcccaaa cggactttta caattatttt cgttatcaaa agtcaagatt cgtttggtaa 5940 gcatttatta tacaatctga cttattcaaa atgttgtctg aaactttttg aaaaactgga 6000 caacaatcga ttgtcactat gcaacaatcg attgtcatgg ctttaaatca aagattttgt 6060 ttgatattaa ggcaacggtc agattctctt ttgacagtat taaaacctgt cttaaactcg 6120 tttttgaaaa aaacaacaac agagatgaaa gattgaatat tatctttgaa atcatttcat 6180 atcattcata tcaaatacat tatttttgag agcaaatatt gattaagttg ttgtgttctt 6240 gagctaaata ttttgtactc atatccactc tattgagaga gttattgtat aagtgagtat 6300 tgagtgtttt gtaaacactt gttgcaagag ggaatattgt atttcttctt gagaagtctt 6360 agggataggt ttccttaagc aagattgttt gaggcttgtg tgattcaagt tctcaagttg 6420 taacggttcg ttaggcaccc ggaagcttaa catggaagtc tttggggtga ggaacctccg 6480 agcagggtgt ttgaggctta tgcgatttaa gttctcaaac ggaaaggtt 6529 // ID Copia-65_Mad-I repbase; DNA; EDCOT; 6515 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-65_Mad_; KW Copia-65_Mad-LTR; Copia-65_Mad-I. XX NM Copia-65_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6515 RA Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1668-1668 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC Positions [2949-3365] - Integrase core CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 1475..2494 FT /product="Copia-65_Mad-I_1p" FT /translation="MAAKNVVADLTKGEKLVGTNYDIWHRKIQYLLNEQEL FT LEPLEASVDEPDLERDGTTAAQHTARVRSYESWFKKDRSARFTMLSSMHDD FT LIGEYEGYSTAKEMWDQLKFAFGGTSTTRLRSLVLKFEVYRMDPKHSVSEH FT LRKMSSMIRDLKAAGSILTDEQQVQAVIRSLPDSWDALKQIMTHNDQIKNF FT HDISRHVELEGERRVATQSTALLTQGGSKKGNQFKGKGKTKSEKKDAKLAP FT NSNKIKAHRGKRGKKDESKSTCFNCKKKGHFARNCTEPNRKVIPNPKSVIV FT CVCSHIHVAHTSDNWIVDTGATKHVTRDKRGFEKLSTLSSKVTLGVRG" FT CDS 3761..5545 FT /product="Copia-65_Mad-I_2p" FT /translation="MVAEYDVGGLDPSGSTQPSGSNVSINTQENTPNDGSV FT PSEIQGHTVRRSKRGHIPKRHFEVDGEAYICIPSEEDEPSSYKEALSSTAK FT EKWITAMEEEMSSMDKNTVWELVDLPPGRKTIGNKWVLKIKRKADGSIDKY FT KARLVAKGYTQQLGVDYEETFSPVVRFASIRLILAIVAQLDLELYQMDVKT FT AFLNGELDEEIYMDQPLGFEAKGQERKVCRLKRSIYGLKQASRQWNIRFHN FT SITSFGFEMIEEDHCVYLKKSGKSILILSLYVDDILIAGNDKTSIETTKAW FT LSSHFEMTDMGEAHYVLGVKITRDRSRKLLSLSQETYIKKVLERFKMENSK FT PIDTHMERGAILSLEQCPKTKKEKEQMANVPYASAVGSLMYAMLCTRPDIC FT HAVGMVSRYQSNPGQAHWQAVKRIMRYLQGTKDLALCYQGGDLKLRGYSDA FT DWASDRDERKSTSGYAFVLGGGIVSWCSKKQTCIALSTMESEYVALGSAVQ FT EAVWLRRFLRQMGVTAYAQEAVLVYCDSTSALAYTKDPKYHGKSKHIDTRY FT HFFRNKVTKGEVVLKHISTSNMLADPMTKPIIRNSFLTHVKNMGLCRV" XX SQ Sequence 6515 BP; 1983 A; 1167 C; 1513 G; 1852 T; 0 other; gtggtatcag agccactcac acactcctcg catgaaagca tgagatatat atatatatat 60 atgtatgaaa accttgaaag catgagatat atatgaatat gccatgaatg cttgtcttta 120 aaattttcgt ttttgccatg cttatttttt ctgggtttta acgcttgggt tatgttcttt 180 acattcatat gagactatag tttaaaattt ggtaaagaaa aaccaagtgg ttagagagat 240 aattgaaacc ctagtttcgt aatagcatga aaaacgaatt ttttcaaggt ttttgcgacc 300 cttttttcgt gaggttagag ttgtttttgg atttcaccaa agaagattta attgtagatg 360 gtaatttgat ctttctaacg acataaaata cgcataaaac ggatgcatat tcgctaagtt 420 atggcctctg taaacaggcc tcgtgagagt gaaaaatctg gaaattccag attttttgga 480 agaagatgat gaacagtggt tcatctcttc cactctcggc ctaagcaagt acgagtacat 540 cgctaggctt tcgtggatgt tagctacacc gttggattca tctcagggag ttcaatccaa 600 cggaggtcaa aagaacggca tcggaccgcc agaaggcggc gcgtgtgtgt cacgcgccac 660 ccacggcgag tgggttcgcg caatattaaa ttaattatta aaaaaaaaat taattttgca 720 ttgccgcttt gggcggcgcg tgggccgtgt ttttgggaca cggctggcga gtgaatcatt 780 gtggttcact gacctacgta agtgtatatt taggtttggt attagagacg tttttaattt 840 actaaaatta aggaaacgtt cttaattaac ctttaaaaaa tatccaacac atgccaagat 900 tttaggaaaa tcaaaaagag ataatgtcga tcaaatttgc tcatgttgat tgagcatttt 960 aaattagaaa ggaatattct ttaggagaat atttaaaaaa gattacctaa ttaataaaaa 1020 ataatgaaat tagactgggg ttcactaatg gtcacctctt atttgatgtg gtgtctagga 1080 aaaatcttta aggagacact tcgggtgtca aagaggttcg gtttttaaaa gcttcgcact 1140 gccacccctc ccggatttga cctggccgca cttacggagg cccacatgtc gagcccattg 1200 tctaaaaacc ctaatcgttg tgcactcaat tggatgttgc atgaaaaatg gataagctta 1260 aaacataata atgtttaaat tagatttatt tcgaaaataa ttagaaaata tgatcttgac 1320 tcttagaatt gaatggtaat tacgagcgac ttagcggatt tttcaatttc aacctaggag 1380 aaaaagtgaa atattttcta atgagttttt gaaataaata aatgtaagat gtgtaattaa 1440 taatgtcaaa attatttcac ccttgtagaa agaaatggct gccaaaaatg ttgttgctga 1500 tttgaccaaa ggagaaaagc tggttggaac caactatgat atttggcata ggaagatcca 1560 atatcttctc aatgaacaag agctcttgga gcctttggag gcttcggtgg atgagcctga 1620 tcttgagaga gatggaacca ctgcggctca gcatacggct agagtaaggt cttatgaatc 1680 ttggttcaag aaagatcgaa gtgcgcgctt tactatgtta agcagcatgc atgatgatct 1740 tattggtgag tatgaagggt actcgaccgc caaggagatg tgggaccagc tgaaatttgc 1800 ttttggtgga acctcaacta ctaggctgag aagtctagtg ttgaagtttg aggtttacag 1860 gatggatcct aagcactctg tatctgaaca tcttaggaag atgtccagca tgatacgaga 1920 tttgaaagct gctgggagta tcctcaccga tgaacagcaa gtccaagctg tgattaggtc 1980 cctcccagac tcgtgggatg cccttaaaca gatcatgacg cacaatgatc agattaagaa 2040 ctttcatgac atctcgcgtc atgttgaact ggaaggtgag cgtcgagtgg cgacccagag 2100 tactgccctt ttgactcaag gtgggtccaa aaagggtaac cagttcaaag gaaagggtaa 2160 gaccaagtct gagaaaaagg atgcaaagct tgctcctaat tctaataaga tcaaggccca 2220 cagaggtaaa cgtggcaaga aagacgaatc caagtcaacg tgctttaact gtaaaaagaa 2280 gggacacttc gctcgtaatt gcactgagcc gaatagaaag gtaatcccta accctaaatc 2340 tgtcattgtt tgtgtatgtt cgcatataca tgttgctcac acgtccgaca attggattgt 2400 agacacagga gcaaccaagc atgtgacgcg agataaaagg gggttcgaaa aattatcaac 2460 gctttccagc aaagtcacac tgggtgtacg tgggtgaagg aagtcgtaca gaagctttgg 2520 gagttggttc gtatcgactt caactaagca ctgggtgtca actacttctg catgatgtct 2580 tgcacgcccc tggaatgcaa tttaatttac tttcagttac tgcactttta tatgaaggat 2640 attgttttta cttaagcccg tctagacttg tgatctattt ggatcaagtt gaaattggat 2700 atggttcaat aaagaacgat tttgtttgct tggatttgat tgattcttgt tcttctactt 2760 ctttagtaac tgttattaaa catgttaatt ctgaaacatg gcatgctaga ctagggcata 2820 tagggcaaga tagaatgaca aggttagtta gagaaggcct gttggggtca ctcactaatg 2880 tcaatctgcc tgtatgtgag ccttgtttag ctggcaaagc agttagaaag ccttttggaa 2940 aggctgttcg agctactcaa ccgttagagt taatccactc tgacatctgt ggaccaatga 3000 gtgtgaaggc ccgtcatggc gcctcttatt ttctgacttt gattgacgat tacacgcgat 3060 atggttatgt gtacttgatc gctcatcgct atgaagcttt agattgtttc aaatgcttcg 3120 tagctgaggt tgagaataaa aaagggaaga ctgtaaaagc tcttcgcact gatcgtggac 3180 gcgagtattt gtctgaccaa ttcaaggttt tttgtgaaag taaggggata cgcagacaac 3240 tttatgttcc ttacacgcca caacaaaatg gtgttgctga aaggagaaac agaactttat 3300 tagacatggt caggtctatg atggcgcagg aaatctcccc atatctttct ggggtgatgc 3360 attattgact gcgacgtata tacttaaccg tgtgccttca aagatggttc cctcaacccc 3420 atacgaactt tggaatgatg taaaacccaa tctgggtaat ttgcgtcctt ggggttgtgc 3480 tggatttgtt cataatcaat cacataagtt tggaaagttg ggtcctagag caaataaaca 3540 tatctttata agatattgtg aaaactcgaa aggttatgtg atgtatggtg aacatccaga 3600 tggagggaga accgagattg attcacgtga tgtggaattc atagagaatg acttcccaaa 3660 acttggcgat actgtcaaaa accttgatct ccatgagttg gagaaagatg aagaactcgt 3720 aacatcttca agcgaatgag gggaattaat ttccaatccg atggtcgctg aatatgatgt 3780 aggaggactt gatccgagtg ggagtacaca acccagtggg agtaatgtat ccataaacac 3840 tcaagagaat acgcccaatg atgggagcgt accctctgaa attcaaggtc acacagttcg 3900 aagaagcaag agaggccaca ttcccaaacg tcattttgag gttgatgggg aggcctacat 3960 ttgcatacct tcagaggaag acgaaccttc ttcttacaaa gaagcgttgt cttcaacggc 4020 caaagaaaag tggataactg caatggagga agagatgagc tccatggaca aaaatactgt 4080 ttgggagtta gttgaccttc cgcctgggcg taaaaccatt ggaaacaagt gggttttaaa 4140 aatcaaacgc aaggcggatg gttcaattga caaatataag gcacgccttg tggcgaaagg 4200 atacactcag caattgggtg tagactatga agagacattc tcccctgtgg tgaggtttgc 4260 ctctattcgc ctcattttag ctattgttgc tcaactagat ttggaacttt accaaatgga 4320 tgttaagaca gcatttctca atggagaact agacgaggag atatacatgg atcaacctct 4380 aggcttcgag gccaagggac aagagcgcaa agtttgccgc ctaaaacgtt ccatatatgg 4440 cctcaagcaa gcgtctagac agtggaacat tagattccat aattcaatca cttcatttgg 4500 ttttgagatg attgaggaag accactgtgt gtatcttaag aaatctggga aaagtattct 4560 catactttct ctgtatgttg acgacatcct aatagcggga aatgacaaaa cctccataga 4620 aaccacgaaa gcgtggttgt catcccattt tgagatgaca gatatgggtg aagcacatta 4680 tgtgcttgga gttaagatca cgagagatcg ctcaaggaaa cttctaagtt tgtctcaaga 4740 gacttacatt aagaaggtac ttgaacgatt taagatggag aactccaaac ccatagacac 4800 tcatatggaa agaggcgcga tattgtcctt agaacagtgt ccaaagacta agaaagagaa 4860 agaacaaatg gcaaacgtcc cctatgcctc tgcggtagga agtctgatgt acgcgatgct 4920 ttgcacgcgt ccggacattt gccatgccgt gggcatggta agccgctatc aaagtaatcc 4980 tggacaagct cactggcaag ccgtcaagag gattatgaga tacctgcaag gaacaaaaga 5040 tttagcccta tgttaccaag gaggggatct gaagttgaga ggatatagtg atgcagactg 5100 ggcaagcgat agagatgaac gcaagtccac ctcaggttat gcttttgtcc ttggaggtgg 5160 aattgtttct tggtgtagca agaagcaaac ttgtattgct ctgtccacaa tggagtcaga 5220 atatgttgcc cttggatcag ctgttcaaga agctgtttgg cttaggaggt ttctacgaca 5280 gatgggagtt acggcttatg ctcaagaagc tgtacttgtc tactgtgata gtacttcggc 5340 cttagcatac actaaagatc ctaagtatca tggcaaatct aagcacatag atacacgata 5400 tcatttcttt aggaacaagg ttaccaaggg tgaagtagtg ttgaaacata tctcgaccag 5460 caatatgctc gctgatccca tgactaaacc cataattaga aactcgtttc tgactcatgt 5520 aaagaatatg ggtttatgta gggtttgatg tgtttttctt tgtatttgac attattattg 5580 aataaaaagg cattgaagtt tttcatttca tatttattta tttttgaaat gattgtttac 5640 acatctttac gagtgtcacc aagctagaat ccgtttttca cacgaacgat tcgccctggc 5700 gctgagatag cgagtaggat gagacatttg tgtcctcaac gcattggact gcgagaccgg 5760 acacgtgtat gttgaacgta ccaatatgca caaggtaaac gtcgccttag aaatgtctaa 5820 gatgagactt aacagaagtc gaacatgaga tttgtttcat gttgaagctt gtaaagccgg 5880 atatgagtat ctaggtgggc gccgagaagg cgactaggct agaagactca ggttaggcgc 5940 ttgtgtagcg actagactaa gatccgtatg gtgtatgtcc aatggacatg tgacacactc 6000 attgaaatga ggatacacca tagcatacaa atcatactgt atgtgctata accgaccgat 6060 agtgggagtg atgaattgat ccctgcttca atcactgtgt gaaccacaag gaatctatac 6120 gattccaccc ttatgccctt tgaactaaag tctatgttag aaagatgagg tttaatgatc 6180 gctactttag cacgtttatc taagacggtc aagttagcta ctgtcccaag aggcgtgtct 6240 aggcaagcag ttaaatcaaa ttagactgac atgagagctt aaggaagaca gttcgaagaa 6300 aacaccatgt catgtgattc attagctgcg cggcgtcttt tgatatttgt tatcaaacat 6360 aagacatgga tacatgatac ttgtgagaca tgacattgtt ttttatttca taacgaggga 6420 taaagaatgt caagtctggt gtgtgacgaa cagtctgggg cataaagcga tgaacttccg 6480 agtgatgcac tgttgttagt ttagtgatag cttaa 6515 // ID HAT-3_Mad repbase; DNA; EDCOT; 3472 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-3_Mad. XX NM HAT-3_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3472 RA Bao W. and Jurka J.; RT "hAT-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1612-1612 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC TIR is 13-bp long. XX FH Key Location/Qualifiers FT CDS 889..3327 FT /product="HAT-3_Mad_1p" FT /translation="MERYYKRKSSSISSDNHIPNSSSPNLDSSNPIPNSSP FT PIPSSSNPIGGNSTPQQNELKVDLDNLERDPGKRIPMKDYPPDIRDEVRRA FT YILMEPFRAKDHDFPFTLHSNKKRRFVDNWLKEFHWLEYSISKDAAFCFYC FT YLFKVNFEQSGSDVFTEVGFQNWKHARACFEKHVGMVGSFHNKAVEAAGNL FT MNQKTHIETVVVKQSEEARMAYRTCLNASIDCTKFLLRQGLSFRGHDESDT FT SNNRGNYLELLQFLADHDEKIKAVVLDKAPGNLKLIAPSIQKDLVHSCSIE FT TIKTIISDMKNARFFSLLVDEARDVSIKEQMAVVLRYVDKNGKVIERFVGV FT QHVPDTTSNTLKESIDAFIHFNELSFSNLRGQGYDGASNMKGEFNGLKTKI FT LNDQPCAFYVHCFAHQLQLALVAVAKDNVDVNTFFLLANNVVNNIGASCKR FT RDALREMQQKELMKALENDSLMTGRGLNQETSLKRAGATRWNSHYGTLISL FT ITMFSSVVNVLEMIVDDNTNDSVAEANRLLKDIQSFEFVFLLFLMKSILGI FT TNDLSQALQKDDQEIVNAMALVNTCKEQLLYMRNDEGFDLLVDKVLSFCVQ FT HHIEVINMDETYVAHGRSRRNTHKKTNRHRYKVELFFVVIDSQLTELNDRF FT NETSTELLICLASLSPNDSFAAFDKEKLLRLAQLYPQDFTKQDLLALEDQL FT DIYIHSMRSRSDFSQLQSISDLAKKMVEKRLHRVFQYVYLLIELALVLPVA FT TASVERAFSAMNIIKSPLRNRMGDQWLNDSLVVYIEKDVFSCIDNETIMTR FT FQSMRSRRGQI" XX SQ Sequence 3472 BP; 1016 A; 608 C; 708 G; 1140 T; 0 other; caggggcgga tctattaagg gaccagggtg gtcccgggac cacccgaagc tcggaaaaat 60 ggctgtgagg atcttcaagg accacccatg ttagtgatgc tgcacaagtg atgcgcagca 120 tgtgattgca caagtgatgc tgcacaatga cttggccaaa acgacgtcgt tttgagccaa 180 gtcattaaaa aaatttaaaa cctcactcac gtgagaacct tcacacgata gagcactcag 240 ctccttcaca cgatagagca atcagaacct tcactttacc aataatacct aatcgtctgc 300 cgctcggccc gctcctgttc cttacggcat cgatcaactc tctgttgcac tctagtttct 360 gttcaccgtt gcaccgacgg gcggggcgac gacatctctg gtgaaaatct gtaacccttc 420 tgcatttttt ctccgtgtaa agctctggtc cggaggctag ccgctggtcc tcttcttctt 480 ggtcgaagag gtttgtactc tctttgactc tgtccattaa ataattttgc catccactat 540 ctgatattaa attatttgtg gtgttcgata tttaaataat tttaccatcc actatttgat 600 ttatttgtgg tgttagatat tttgtttaag aagtattttt atttttaatg tttggtggtg 660 aatctggtga tgaattaaac ttttaatgtt tctttgaagt gatggcagtc tatttgtggc 720 atgcatctct ttgtctttgg cattcataat attagaatcc cacgggcacg gacctaatta 780 taaatttata aatgaatctg atttctcgtt tttcatataa tatttttttt agtttcatca 840 attgatatag atttttttta ttaattgata tgtgtagaaa ttagaagtat ggaacgatat 900 tacaagcgaa aatcatcatc gattagttcg gacaatcata ttccaaatag ttcatctcca 960 aacttggata gttccaatcc tattccgaac agttcccctc caattccaag tagttctaat 1020 ccaattgggg gtaattccac tccacaacaa aatgagttaa aagttgattt ggataatctt 1080 gagagagacc ccggaaagag aattccaatg aaggattatc ctccagatat tcgagatgag 1140 gtccgaagag catatatatt gatggagcct tttagagcta aagatcatga ttttccattc 1200 actttgcatt cgaataaaaa gcgacggttc gttgataatt ggttgaagga atttcattgg 1260 ttggaatata gtatatctaa agatgctgca ttttgctttt attgctatct attcaaagtc 1320 aactttgaac aatcaggcag tgacgtcttt actgaggtag gctttcaaaa ttggaagcac 1380 gcaagagcct gttttgaaaa acatgtggga atggttggta gctttcacaa taaagctgtt 1440 gaagctgctg gtaatctaat gaatcaaaag acacatattg aaacagttgt ggtcaaacag 1500 tcagaagaag ctcgtatggc ttatcgcact tgcttgaatg cgtcaattga ttgcactaag 1560 tttttgttgc gacaaggtct ttcatttcgt ggtcatgatg aaagtgacac ttcaaacaat 1620 agaggtaact atttggagct cttgcaattc cttgcggatc atgatgagaa aataaaggcc 1680 gttgtgttag ataaagctcc gggaaatctc aagctaatag ctccttcaat tcaaaaagat 1740 cttgttcatt catgttctat tgaaaccatt aaaactatca taagtgatat gaagaatgct 1800 aggttctttt ctctattggt tgatgaggca cgtgatgttt ctataaagga gcaaatggcg 1860 gtggttttgc gttatgtgga caaaaatggg aaagtcattg aaaggtttgt aggagttcaa 1920 catgttcccg acaccacttc aaacacatta aaggagtcta ttgatgcctt cattcatttc 1980 aatgagttga gcttctccaa tttacgaggg caaggttacg atggtgctag taatatgaaa 2040 ggtgagttca atggactcaa gacaaagatt ttgaatgatc aaccttgtgc attctatgtt 2100 cattgctttg ctcatcaact ccaattagct cttgttgccg tagcaaagga taatgttgat 2160 gttaacacat tcttcctatt ggctaataat gtggtaaata atattggagc ttcatgtaag 2220 cgtcgtgatg cacttagaga gatgcaacaa aaagaactta tgaaagctct tgaaaatgat 2280 tctcttatga cgggacgagg cttaaatcaa gaaactagtc tcaaacgtgc cggagctaca 2340 agatggaatt cacattatgg tactttgatt agtttgatta ctatgttctc atccgtggtc 2400 aatgtgcttg aaatgattgt tgatgataat accaatgata gtgtggccga agcaaatagg 2460 ttattgaaag acatacaatc ttttgagttt gtgtttctcc tatttttgat gaaatctata 2520 ttgggaatca cgaatgattt atcacaagca ttacaaaagg atgatcaaga gattgtgaat 2580 gcaatggctt tagtcaacac atgtaaagaa caactactct acatgaggaa tgatgagggg 2640 tttgaccttt tggttgacaa agtattgtca ttttgtgtcc aacatcatat tgaggttatt 2700 aacatggatg agacatatgt agctcatggg aggtcgcgcc gtaataccca caaaaagacc 2760 aaccgtcatc gttacaaagt ggagctcttt tttgttgtca ttgattccca acttacagag 2820 ttaaatgatc gcttcaatga aacaagtacc gaattgctca tttgtttggc tagtttgagt 2880 ccaaatgatt cttttgcagc ttttgacaaa gaaaagctac ttcgccttgc tcaattgtac 2940 cctcaagatt ttacgaagca agacctattg gcacttgaag atcaactcga tatttatatt 3000 cattctatgc gttcgagaag tgacttttct cagttgcaaa gcattagtga tcttgctaag 3060 aaaatggtgg aaaaaaggtt gcatcgagta tttcaatatg tgtatttact tattgaattg 3120 gctttggttt tacctgttgc aactgcttca gtggagagag cattttccgc catgaatatc 3180 attaagagtc cactccgcaa cagaatgggg gatcaatggt taaatgatag cttagttgtt 3240 tacattgaga aagatgtttt ttcttgtatt gacaatgaaa ctatcatgac acgttttcaa 3300 agtatgagat cccgtcgtgg acaaatttag tatttctagc ttgtttagca caaagattat 3360 gaatgaaaat tgtagtttgc catttatttg ttcaatgata ttttcgtctt gttttttttt 3420 tggagctttt atattgggac caccctaagt taaaatcctg gatccgccac tg 3472 // ID Copia-4_SL-I repbase; DNA; EDCOT; 4101 BP. XX AC AC243415; XX DT 22-JAN-2011 (Rel. 16.02, Created) DT 22-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the tomato genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-4_SL_; KW Copia-4_SL-LTR; Copia-4_SL-I. XX OS Solanum lycopersicum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-4101 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the tomato genome."; RL Direct Submission to RU (22-JAN-2011). XX DR Genome; AC243415; Positions 39787 43887. XX CC Positions [1483-1992] - Integrase core CC 'GAAAC' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 1036..2010 FT /product="Copia-4_SL-I_1p" FT /translation="MGNQSSASIVGIGDIRVQTNVGCYLTLRDVRHIPDLR FT LNLLSANVLDEEGYKHTFGEGKWKLSKGSLTVARGKLCCTLYKTHLKVCSG FT ELNAIEEKTSPNLWHRRLGHVSEKGIKLLAGKSLIPADVTISLDPCDHCLA FT GKQHRVSFLRTSTRKKVRLELVYSDVCGPIEVESLGGNKYFVTFIDDATRR FT TWVYMMKHKSEVFGIFKKFHAMVERETDCKLKRLRTDNGGEYTSNEFKAYC FT SRYGIRHERTEPSTPQHNGVAERMNRTIIEKVRCMLRMSNLPKSFWGETAG FT TAVYLINRAPSVPLEFDIPERVWFGKDPSLILT" FT CDS 2037..4052 FT /product="Copia-4_SL-I_2p" FT /translation="MHVPKEHRLKLDFKTSPCVFVGYGDEEFGYRLYDPAK FT QKVVRSRDVVFYEHEMGFHLLGADKTYYSNFSHDVIDMPMPHVSTSDDQLT FT GDAPEDGHEIAHEHDHIEEVQPDVVVPQPDDEAVDVQHGESSNQGEKSSPQ FT VEEPTLRKSTRVRQPSRLYPSSEYILITDEGEPESLQEVLSHSDKDHWLKA FT MQEEMDSLKKNETYDLVKPPKGKKVLKNRWLFKNKKVDNKLVKWKARLVVK FT GCHQKKGIDFDEIFAPVVKMTSIRMILGLAACLNLELEQLDVKTAFLHGDL FT HEEIYMEQPEGFEVKGKENFVCKLKKSLYGLKQAPRQWYHKFDSFMSSNEY FT KRTTADPCVYFRKFSEGNFIILCLYVDDMLIVGQDVEKDLGPAKQILGMEI FT ARDRKAGKLWLSQEKYIERVLERFNMKNAKQVNTPLAAHFKLSKRCCPTTE FT KEKESMSHIPYFSAVGSLMYAMVCTRPDIAHAVGLVSRYLANPSKVHWEAV FT KWILRYLRGTSNLSLCFGGGEPILEGFTDADMAGDLDNRKSTSGYLFKFAG FT GAISWQSKLQKCVALSTTEAEYIAAVEASKEMLWLKRFLQELGLKQSEYVV FT FCDSQSAMDLSKNSMYHARTKHIDVRYHWLRVVIEEQLMKLKKIHTNKNGA FT DMLTKVVPRSKLEFCSKLAGMSS" XX SQ Sequence 4101 BP; 1227 A; 662 C; 1034 G; 1178 T; 0 other; attggtatca gagctgagtg ttaaaccata gacatgaagc atggaaataa ctctatggtt 60 aaactgacat caaccaatta ttccatttgg cgtccgatga tggaagattt gctatattgc 120 aaggatttgt ttgatccaat tgatgtggat aaaacaaaga aagatgacca gcccactaag 180 ccagagaaga tgacagaaaa agaatgggaa aagctgaaga gaaagacctt ggggacaatc 240 agacagtgga ttgatattag catattcaat catgtatccc aggagactga gccgcttgag 300 ctatggagaa aattggaggg tctttatgag aggaagaccg ctcataacaa ggcctcgttg 360 attaagaggc ttgttaatct caagttgaag ccagggaagt ctgtttctga gcatcttagc 420 gactttcaag atattattaa caagttgact gttatgaaaa ttgtccttga tgatgagttg 480 caggctttat tcctcttgag ttctttgcca gacagttggg aaactttggt tgtgtccatc 540 agcaactcag ctccagatgg tacgctttca ttggatgtca tcaaagagag catgttcaat 600 gaagagctta gaagaaagga gatgggtgtt gatatttcgc aggcacttgt ggtagagaat 660 agaggaagaa gcaagagtag aggtcccaaa gggcgtggca agtcaaagta taggtcaaag 720 tccaaggatg ggagaaaacc tacgatatgc cactattgta gcaagcctgg ccacattcaa 780 aagttttgct acaagttgaa aagagaccag caaaataaga aaaatgacca tcataaagag 840 ggtgatgaca agaatacagc tgctacaact tctagttctg atgatcgtgt ttctttgata 900 tgtgctactg gataatgttg tcatgttgat agttctgaca ctgaatggct tattgataca 960 ggagcttcct atcattgtgt tcctaataag gagtacttta ttgactaccg agctggagat 1020 tttggtagtg tgaagatggg gaaccagagc tcagcaagta ttgttggcat tggagatatt 1080 cgagtccaaa ccaatgtagg gtgctatttg acgttgagag atgttcgcca cattccagat 1140 ttacgcctca atttattgtc tgctaacgta cttgatgaag agggttacaa gcacactttt 1200 ggtgagggta aatggaaatt gtctaagggt tccttgactg ttgctcgtgg caagctttgt 1260 tgcaccttgt ataagacaca tttgaaagtg tgtagtggtg agttgaatgc tattgaggag 1320 aaaacatctc ctaacttatg gcaccgaaga ttggggcatg ttagtgagaa gggtataaag 1380 ttgttggccg gtaagtctct tattcctgct gatgttacta tttcacttga cccttgtgat 1440 cattgtttag caggaaagca acacagagtt tcttttctga ggacatctac aagaaagaaa 1500 gtgaggttag agttggttta ctctgatgtg tgtggtccca tagaagtgga atcacttggt 1560 ggtaacaaat actttgttac ttttattgat gatgctactc ggagaacttg ggtttatatg 1620 atgaagcaca aaagtgaggt gttcggtatc ttcaagaagt ttcatgcaat ggttgaaagg 1680 gagacagatt gcaaactgaa gcgtcttcga actgataatg gaggtgaata cacttcaaat 1740 gagtttaaag catattgctc aagatatggc attcgacatg agagaacaga accgagtacc 1800 ccacaacaca atggcgttgc cgagaggatg aacagaacca ttattgagaa agtgagatgc 1860 atgcttagaa tgtccaatct tcctaagtca ttttggggtg aaacagctgg aactgctgtg 1920 tatttgataa atagagcacc atcagttcct ttggagtttg atattcccga gagagtttgg 1980 tttgggaaag acccctctct tattctcact tgagggtgtt tggatgcaag gcttttatgc 2040 atgtgccgaa ggaacataga ttgaagcttg atttcaagac ttctccttgt gtgtttgttg 2100 gatatggtga tgaagagttt ggttacagac tttatgatcc agcaaagcaa aaagttgtga 2160 gaagtagaga tgttgtcttt tatgagcacg agatgggttt tcatctcttg ggtgctgata 2220 agacttatta ttctaatttc tctcatgatg ttattgatat gcccatgcct catgtttcta 2280 cttcagatga tcaattaaca ggtgatgctc cagaggatgg tcatgaaatt gctcatgaac 2340 atgaccatat tgaagaggta caacctgatg ttgttgtacc acaacctgat gatgaagctg 2400 tagatgttca acatggagag tcttccaatc agggggagaa atccagccca caggtagaag 2460 agccaacact tagaaaatcg accagagttc gtcaaccttc aagactttat ccaagttcag 2520 aatacatcct aatcactgat gagggggagc ctgaaagcct tcaagaggtc ttgtcacact 2580 cagacaaaga ccattggctc aaggctatgc aagaggagat ggattctttg aagaagaatg 2640 aaacctatga cttggtgaag cctccaaaag ggaagaaagt cttgaagaac aggtggttgt 2700 ttaagaacaa gaaagttgac aacaagctag tgaagtggaa ggcaagatta gtggtgaagg 2760 gatgccatca gaaaaaaggc atcgacttcg atgagatttt tgcaccggtg gtgaagatga 2820 cttccattcg tatgattttg ggactagctg cctgtttgaa tcttgaactt gaacaacttg 2880 atgttaaaac tgctttctta catggtgatt tgcatgagga gatttacatg gagcagccgg 2940 aaggatttga agttaaggga aaagagaatt ttgtttgcaa gttgaaaaag agtctctatg 3000 gactcaaaca agcaccaagg caatggtatc acaagtttga ttccttcatg agtagtaatg 3060 agtacaagcg gactactgca gatccttgtg tgtattttag aaaattctct gaaggtaact 3120 tcattatcct ttgcttgtat gttgatgata tgttgattgt gggacaagat gttgagaaag 3180 atttgggtcc tgcgaagcaa attcttggta tggaaattgc tcgtgataga aaagctggta 3240 agctttggtt gtcacaagaa aagtatattg aacgggtgct tgaaaggttc aatatgaaga 3300 atgccaagca agttaataca ccacttgcag cccatttcaa gttgagcaag cgttgttgtc 3360 ctacaaccga gaaagaaaag gaaagtatgt ctcatattcc ttacttctct gctgttggtt 3420 cattgatgta tgccatggtg tgtacaagac cggatatagc acatgctgtt ggattggtta 3480 gcagatactt ggcaaatccg agcaaggttc attgggaagc tgtaaagtgg atcttaagat 3540 atttgcgagg cacatcaaat ctgagtttgt gttttggagg tggtgagcct attcttgagg 3600 gatttacgga tgctgacatg gctggagatc ttgataaccg gaagtctacc tcgggttact 3660 tgttcaaatt tgcaggggga gccatttcat ggcaatccaa gctacagaag tgtgtagcgt 3720 tgtctacaac cgaggcagaa tatatagcag cagtggaagc aagcaaagaa atgctttggt 3780 taaagcgttt ccttcaagag ttaggtttga agcaaagcga gtatgttgtg ttttgtgata 3840 gtcaaagtgc tatggacttg agcaaaaaca gcatgtacca tgctcgcaca aagcatattg 3900 atgtgagata tcattggttg cgtgttgtca ttgaagagca actaatgaag ttgaagaaga 3960 ttcacaccaa caagaatggt gctgatatgt tgacaaaggt ggtccctcga agcaagcttg 4020 aattttgttc caagcttgca ggtatgtctt cttgatgacc ttttatgttt ggtctccccg 4080 aactgggctg gagggggaga t 4101 // ID LINE1B_MT repbase; DNA; EDCOT; 2782 BP. XX AC AC135415; XX DT 22-MAY-2006 (Rel. 11.05, Created) DT 22-MAY-2006 (Rel. 11.05, Last updated, Version 1) XX DE L1-type element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; LINE1B_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-2782 RA Jurka J.; RT "LINE1B_MT: L1 element from barrel medic."; RL Repbase Reports 6(5), 247-247 (2006). XX DR EMBL/GenBank/DDBJ; AC135415; Positions 16551 13770. XX CC This is a relatively young sequence. It can be 5' truncated. XX FH Key Location/Qualifiers FT CDS 306..2726 FT /product="LINE1B_MT_1p" FT /translation="MNRMRGRTGYFVIKVDLAKAYDMLNWDFIWRTLKEIG FT FPDVLIDLIMHGVTSVETNVKWNGARTEYFRPQRGIRQGDPISPYLFVLCM FT DKLSHLITHEVNQGRWKALRAGRRGPVISHLMFADDLLLYGEATTSQMKCV FT TDTLKTFCDLSGQQVSQEKTSMLFSKNVHRGVRQQLLLLCGFKETSFLGKY FT LGVPLLGRAPKRADFQYVIDQVNGKLAAWKTNQLSFAGRVTLAKSVIEAVP FT IYPMMTNIIPKACIDEIHKIQRQFISGDNENNKRYHAVSWETVSKPKVFGG FT LGLRRLNVMNKACIMKLGWSIYSGSTSLWAEVMRGKYQRSDILAELFIAKP FT SDSSLWKALVKLWPALERNIFWSIGDGKSVGAWSQMWIEERLCVSELEIDI FT PQQCKEMKVADLVDFNGNWNFELLNQWLPYDVVQRIMTIAVPDENDGNDKQ FT MWSGSSNGKFTIASAYHMLSKFDNDAQDEIWLKLWKIRAPERIKHFMWMLY FT HGRLLTNLRKHKMGIGNPMCRFCHDEIESEIHVLRDCPKATALWLCVVDNA FT ARTSFFEGDLSNWINFNLFTNVYWNHNVEWRDFWATACHAIWNWRNKETHN FT DNYQRPLHAKNIIMSYVNDYHNAIAKSVIVTSQLRHLEEVGWKEPPIGWVK FT INTDGACKDGSIAGCGGLIRGSQGEWLAGFSKFLGKCDAFIAELWGVLEGL FT RCAKRMGFTAVELNVDSLVVVNIITSGKESNARGRSLVQKIRKLLQMEWEV FT KVKHSYREANRCADALANIGCIMENGMMFYESCPTQINHLLAADQAGVTFP FT RLIKM" XX SQ Sequence 2782 BP; 825 A; 394 C; 713 G; 850 T; 0 other; aatcttggga tgttgtagga aagaatattt gtgagtttgt tagagatgtg tggagagagc 60 ctgacaaaat aagcacggtt aacaaaacag atatttgctt gattccgaag attaatcaac 120 cggaatttgt gagtcaattt cgtccgatat cgctttgcaa cactatttat aagatagtga 180 gtaaggttgt tgttgggagg cttaaagaat atattcctca tattgtgtca ccgcatcaga 240 ctggttttgt tccgggacgt agtatccatg agaatatcgt tgtggctcaa gagttggcac 300 atagcatgaa tcggatgaga ggaagaacag gttattttgt tatcaaagtt gatttagcaa 360 aagcatacga catgcttaac tgggatttta tttggaggac tttgaaggag attggttttc 420 cggatgtttt gattgattta atcatgcatg gtgttacaag tgttgaaaca aatgttaaat 480 ggaacggagc gaggacggag tatttcagac ctcaacgagg tattagacaa ggggatccca 540 tctctcctta tttatttgtt ttatgcatgg acaaattgtc tcatcttatc actcatgaag 600 ttaaccaagg tcgttggaaa gcacttcgag ctggaagaag gggtcccgtg atatcccatc 660 taatgtttgc tgatgatctt ttactatatg gtgaagcaac tacatctcag atgaaatgtg 720 ttactgatac tttgaagact ttttgtgact tgtctgggca acaagtgagt caagagaaga 780 caagtatgct tttttccaaa aatgtgcatc gaggagtacg acagcagctg ctgcttttat 840 gtggcttcaa ggaaacaagt tttttaggga aatatttagg tgtgccgttg cttggaagag 900 caccaaaacg agcagatttt caatatgtta ttgatcaagt gaatggtaag cttgcggcgt 960 ggaaaactaa tcaactctcg tttgctggga gagtgacact agctaagagt gttattgaag 1020 ctgttccaat atatcccatg atgactaata ttattcctaa ggcatgtatt gacgaaattc 1080 ataaaatcca acgacaattc atatcgggtg acaacgagaa caacaagaga tatcatgctg 1140 ttagttggga aacagtgtca aaaccaaaag tctttggtgg tctaggctta aggagactca 1200 acgtaatgaa taaggcgtgc ataatgaaac tgggttggag tatatattct ggatcaactt 1260 ctctttgggc tgaggttatg aggggtaaat atcagcgaag tgatattctt gctgagttat 1320 ttatagcaaa accgtcggat tcaagcctct ggaaggcttt agtaaagtta tggcctgcat 1380 tagagcgaaa tattttttgg tcgataggcg atggtaaaag tgttggagcc tggagtcaaa 1440 tgtggattga ggagaggctt tgtgtgtccg agttagaaat tgatattccg caacagtgta 1500 aagagatgaa ggttgcagat ctggttgatt ttaatggtaa ttggaatttt gaattgttga 1560 atcaatggtt gccttatgat gttgttcaga ggatcatgac cattgcggtg ccggatgaga 1620 atgatggaaa tgacaagcaa atgtggtcgg gttcttctaa tggaaaattc acaattgcat 1680 cagcttatca tatgctgtca aaatttgaca atgatgcaca agatgagatt tggttaaagt 1740 tgtggaagat tagagcacct gaacgtataa agcattttat gtggatgctc taccatggaa 1800 gattgttaac aaatttgagg aagcataaga tggggattgg taatcctatg tgtaggttct 1860 gtcatgatga gattgagtct gaaattcatg ttttgaggga ctgtccaaaa gccacggcac 1920 tttggttgtg tgtagtggac aatgctgcaa gaacaagttt ctttgaaggt gatttatcta 1980 attggattaa ttttaatttg tttactaatg tctattggaa tcacaatgtg gagtggagag 2040 acttttgggc cactgcttgt cacgctatat ggaattggag aaacaaggaa actcataatg 2100 ataactacca aagaccttta catgctaaaa atattattat gagttatgtt aatgattatc 2160 ataatgcaat agcaaagtct gttattgtga catctcagct gagacatttg gaggaagtgg 2220 gatggaagga accaccgatt gggtgggtca agatcaatac tgacggagcg tgtaaggatg 2280 gtagtatcgc ggggtgtgga ggacttatcc gaggttcgca aggcgagtgg ttagcggggt 2340 tctccaaatt tttagggaag tgtgatgctt ttattgcaga gctatgggga gttttggaag 2400 gtctccggtg tgcgaaacgt atggggttca ctgcagtaga attaaatgtg gattctctgg 2460 tggttgtgaa tattattacg agtgggaagg aaagcaatgc gaggggtagg agtcttgttc 2520 aaaaaattag aaaacttctt caaatggaat gggaagtgaa ggttaaacac tcgtatcgtg 2580 aagcaaatag gtgcgctgat gcgttagcta atattggatg tatcatggag aatgggatga 2640 tgttttatga gtcgtgtccg actcaaatta accatttgtt agctgctgat caagcggggg 2700 ttacttttcc gcgcttgatt aagatgtaat ttctttttcc gggcttcggc cctccctttc 2760 atcaaaaaaa aaaaaaaaaa aa 2782 // ID DNA-3-2B_PTr repbase; DNA; EDCOT; 1100 BP. XX AC . XX DT 10-DEC-2009 (Rel. 15.02, Created) DT 10-DEC-2009 (Rel. 15.02, Last updated, Version 1) XX DE Non-autonomous DNA transposon - consensus. XX KW DNA transposon; Transposable Element; Nonautonomous; TSD 3-bp; KW DNA-3-2B_PTr. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-1100 RA Bao W. and Jurka J.; RT "Non-autonomous DNA transposons from black cottonwood."; RL Repbase Reports 10(2), 192-192 (2010). XX DR [1] (Consensus) XX SQ Sequence 1100 BP; 324 A; 268 C; 178 G; 330 T; 0 other; ctaagtgcgt gtttggcgct gcggctgcgt ttacagaaaa acatcgttgt catgtgtttg 60 gttacggtct aaacacaatt ttctgtttgt gggacccatc atcatctgcg tttaaaccgc 120 aagataacca aaagcaactt caagctgctt tttgtgctga gttgcaaact ttataaacag 180 aggccgcaag aagaagagca gaaacagagc aggaatagga acagtggaga gcagctccct 240 ctcaccaccg gcctccgccg tttccaccgc cagccactgc tcttcctctt ccccttctcc 300 ttctcctttg tcttctgcat tctccactgt tcacgttgca tgtgaacagt ggagagcagc 360 tcaccaccgg cctccgccgt ttccaccgcc agccactgct cttcctcttc cccttcccct 420 tctccttctt cttctgcatt ctccactgtt cacgtgaaca gtggagagcg tctccactgt 480 tcatggccgg accgggtccg gcccaaacct aaatgcattg gaccgggtcc gacccagtaa 540 aataaaaaaa tccaaaaaaa tttctcagat attgtgtttt atttgaaaaa ctagtgttta 600 acattattca atgacactac ataattatat tagaaggaga tcgcatgatg acgtagcatt 660 tgcagaattt gatcgcaatc ccaattttgt tcctgatgat attttacctg atgttgttgc 720 acgctcagga agccatggaa actgtagtcc ttgtcggatg gatttcgtac gtgatggaat 780 tgcaaatagt ttaatggaac aataaaaaat actttatata aagtattgtt tatttcatga 840 tgtaatagca gtagttaaat ctacaatatt tcaattaaaa accatcaata ttaatatatg 900 tcttttttag ttattttata acctcaattt gaaaagcatt cttaaccaaa cacattaaac 960 tactttttgt tcaacctcaa tttcaaccac agttttaacc aaacatatat ttttccaaac 1020 caacctcaac taaaagtact ttttataaaa caactttttc aaaccacaac cacaacagct 1080 accacaatac caaacacaca 1100 // ID Copia-35_Mad-LTR repbase; DNA; EDCOT; 304 BP. XX AC ACYM01061940; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-35_Mad-I; KW Copia-35_Mad-LTR; Copia-35_Mad_. XX NM Copia-35_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-304 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1385-1385 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01061940; Positions 5952 5649. XX SQ Sequence 304 BP; 71 A; 49 C; 54 G; 130 T; 0 other; tgataagtct ggttgttctc ttcgttatag gactcaacca cttagtttgt tttggtttta 60 aataaattcc tattatctag gaagacttgt tctacgtaga ctatttcctc atgcacgtta 120 ccactttccg agtagtgtgg atcgtgggct gtttttaggg ttttgttact tctgtaaggc 180 tatataatag ccaaactttc ctttcaataa agaagtcatt catccagatt gtttgagtta 240 tttgcagtat tactttgagt tatttgcagt attactcttt gtatatttgt tcttgttctt 300 aaca 304 // ID Copia-18_Mad-LTR repbase; DNA; EDCOT; 488 BP. XX AC ACYM01115884; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-18_Mad-I; KW Copia-18_Mad-LTR; Copia-18_Mad_. XX NM Copia-18_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-488 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1363-1363 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01115884; Positions 2689 2202. XX SQ Sequence 488 BP; 144 A; 90 C; 92 G; 162 T; 0 other; tgttgagaat taagctgcct actagcatta agatcaatct gcagatgtta atcctgcaga 60 tcaaatcgag aggaacctga gaatcaagag atgaacaact tccaatttta gaaaggagcc 120 gttgagtttg atttgtaacg gctagtttct tttacattgt tagaaagttc acagctggta 180 tttttgtttt atttagtagt actatgcatt ctcatccccg tccaggtgga tggatgatat 240 cctccaaagc ccttagtggc cggagaagtg tactagatcc ctaaaatgta ggatttggtt 300 ttgactaggt agaggggcat atagcctttg taattttcat ttttcttgga tatcagaaat 360 atactgactc ttcctctccc tcttattctc tctcgaaaag cacaagatcc attgaaacaa 420 tctgtaaaaa gtttcaatct ttactaagat tattaaatct atcaggatgc ctggtaccat 480 ttcaaaca 488 // ID Gypsy-29_Mad-I repbase; DNA; EDCOT; 8139 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-29_Mad-I. XX NM Gypsy-29_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-8139 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1752-1752 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS join(107..697,701..6112) FT /product="Gypsy-29_Mad-I_1p" FT /translation="MGSEGSHSTQNDTPLAPSVRQRRKERKKFALQAKVEE FT LEAQNNKIAMKNEVLQEQYEKLFEMLHEARHTQSHEPVAPVDVNHHLGAPQ FT HGGSPVFDMDIPDEERATHQCVDQHETSLNPAASTRSRRSGGRHLLAEGVE FT GSKAVYRDCRDFLRQRRENPIHISSKINDPRVSERLGPLPRPRPAANLGKE FT RQCPRGTRYRGLEVFRQTRPRSQYGESKEKPHALDQTSLLPRGDGDLRKKV FT PVVHDSTQDPLVLQLLEEVNKLKAERQAEIPDWNQPRPGPLTRRILDTPLQ FT AKTKQKLGLQLYTGREDPIEHLNLFESTMAYRMHTDEERCLLFPSTLSGGA FT LNWYCRLPPETVDSFEELRKLFVSQHIFQTDRLHSADDLYTIRQKPDESLR FT EYAGRFSHEYSRCAEADDKTALKAFTAGLRDCFFKYMINANTWKTYSEVMA FT QAYNHASAEARTYQGKPPTATPYQQVGSGSQIQPSEKTSTFQTAAAPPPAL FT LNTLPSQQTYQSQGKRKDFHPHQSHFSKRSKGHYRDNQGYRHDNPRPQAVN FT TVGQARVRTAPTPRYEAYTPLNATCVAIYPSIAHLIPKPKPRHPDYKPTKN FT TGTFCCYHEHNGHDGEKCITLRDHIEALAREGKIDQFLLHPPRGNRNQRQV FT NVIYSISGGTPISKSSNRAMKNSERALRSGHQVFHVEDIRGGKYQKPNWDP FT ICFYPEEERGIIYPHNDPLIVEAHIANFEVRRILVDTGASVNIMFAEAFRA FT LNVAEHLLDRSISPLISFSGDIVQPLGSIHLPLTIGTGPYTATITTNFLVV FT DCPTAYNVIFGRTXINDLKAMVSTHMLLMKFPTPYGNGYIRGDQLSARSCY FT NTSVKQQHLPVPKETLSIHDQVIKTSPDEANLDLHGGNSQPDDPRDDSFTQ FT QAQPAEELEKVSISKDYPDRMVKIGTTLSPPIRLALISFLQENTEVFAWSY FT EDMPGISPDIICHRLSIDPKTKPVRQKRRSYDAERYEAMKAEVEKLKGIGF FT VREVNYPTWVANVVLVKKNPTKESLLLQKVLWRMCVDYTDLNKGCPKDSFP FT LPLIDRLIDSTAGCELLSFMDAYSGYNQILMNPPDQEHTAFTTDRGLYCYK FT VMPFGLKNAGATYQRLVNSMFAEQIGKSMEVYVDDMLVKSKHADQHITNLS FT ETFTILKRYRMRLNPNKCAFGVGSGKFLGFMISQRGIEANPEKIKAILDMK FT EPVTSKDIQSLTGKVAALTRFISKATDRCAPFFKALKGSKKYITWTDECAE FT AFKNLKDYMSKAXLLSKPEVGDTLIIYLSVSASAVSSVLIRNDGNVERPVY FT YASKALQDAETRYSNIEKLALALVMSARKLRPYFQAHSIIVLTNHPLRQIL FT QSPDTSGRMIKWAIALGEFDISYQPKPAEKGQAVADFIADFTYPVDIVSTP FT KEVVSLPSEAQKIEPTAPAWSLYVDGSSNQQGCGAGLVLTTPDKVAMEYAL FT RFKFKASNNEAEYEALLAGLRLAKHLGVKRIDIFSDSQLVVNQVTNNFDAK FT DSSMAAYLAQTQLLLKHFHYQITQIPRAANSHADALARLASAVEDKIGRKI FT QVELLAAPSTMAAEVCNLQQGDSWITPIYRFLAHGTLPNDKVQAKQIRYKA FT TRYLIINDQLYKRGFNLPYLRCLTPAEAETVLREIHEGVCGDHAGSRSLAH FT KAFRQGYYWPTLHQDAIRISRSCDKCQRYATIPHSPPEPLTPMISPWPFAQ FT WGLDLIGPMPAGKGKVRYAIVAVDYFTKWAEVEPLATITEAKIEDFVWKNI FT LCRFGIPNAIVTDNGRQFDNNKFRMFCSKFNINLCFASPAHPQSNGQVEAI FT NKIIKRTLKTSLDKAKGCWPEFVPQVLWSYRTSYRTSTGETPFSLAFGTEA FT VVPVELEQATFRVQNYVQSENDKQLTLNLDLVEEHRNQAHLRNVAYKQRIS FT NYYDSRVKPRSFKVGDWVLKKRLLCDRVPSEGTLSPNWDGPFEVVGISRPG FT SYKLRSSDGKTLGHPWNADHLKYYYK" XX SQ Sequence 8139 BP; 2444 A; 2137 C; 1694 G; 1861 T; 3 other; tttggcgccg tctgtgggaa cgacacttat tcctactctc ttcagctttg tcaagctggt 60 ttccatcgtt cgtacactct cttttgacca ggcatccctc tccaacatgg ggagcgaagg 120 aagccacagc acacagaacg acacccccct tgcgcctagt gtgaggcagc gaaggaagga 180 acgaaagaag tttgctcttc aagctaaagt cgaagagctg gaggctcaga acaacaagat 240 agcaatgaag aatgaggtcc tccaggagca gtatgagaag ctcttcgaga tgctccacga 300 ggctaggcat actcaatcac acgagcccgt tgcccctgtg gacgtcaacc atcacctggg 360 tgccccccaa cacggagggt caccggtctt cgacatggat atccctgatg aggagcgagc 420 tactcatcaa tgcgttgatc aacatgagac ttctctcaac ccagctgctt cgacccgaag 480 caggagaagt ggagggagac acctccttgc agagggggtg gaaggatcga aagccgttta 540 tcgtgactgt cgagacttcc tgaggcaacg tcgagagaat cccatccaca taagctcaaa 600 gatcaatgac ccaagggttt ctgaaagact cggtccccta ccacgaccca ggccagctgc 660 caatctaggg aaggaacgac aatgtcctag aggaacatga aggtataggg gactcgaggt 720 attccgacag acacgcccta gaagccagta cggcgagtcc aaggaaaaac cacatgccct 780 tgatcaaact tccctacttc caagaggtga tggagactta cgaaagaaag tcccagtggt 840 acatgactcc actcaggacc cccttgtcct acagctcctt gaggaagtaa acaagttgaa 900 ggccgaacgt caggccgaga tacctgactg gaaccaaccc aggcccggcc ctctcacaag 960 gaggatcctt gacacccctc ttcaagcaaa gacaaaacaa aagcttggct tacaactcta 1020 tactggaagg gaggacccaa ttgaacacct taacctcttt gagtccacca tggcataccg 1080 gatgcacact gacgaagaac gatgtcttct cttcccctcc accctctctg gcggagctct 1140 aaactggtat tgccgtcttc cacctgagac agtagattca tttgaggagc tgaggaaact 1200 gtttgtctct caacacatct tccagaccga tcgcttgcac tctgcagatg acttgtacac 1260 tattcgccag aagccagacg agtcactacg tgagtatgcc ggtcgcttca gccatgagta 1320 ttctcgttgc gctgaggcag atgacaagac cgccctcaag gccttcacgg caggcctacg 1380 tgattgtttc ttcaagtaca tgatcaatgc caacacttgg aagacttact ctgaggtgat 1440 ggcacaggct tacaaccatg cctccgccga ggcaaggaca tatcaaggga aaccccctac 1500 ggccacccct tatcaacaag tggggagtgg aagccagatc caaccaagtg agaagacctc 1560 gaccttccaa acggcagctg cacctccccc tgccttactt aatactttgc caagtcaaca 1620 gacatatcaa tctcagggca agaggaaaga tttccatcct caccagtctc attttagtaa 1680 gaggagtaag ggacactatc gcgataacca agggtatcgc catgataatc cccgacccca 1740 ggcagtcaac acagtgggtc aagcacgtgt caggacagcc cctaccccga ggtatgaggc 1800 atacacacct ttgaacgcca catgcgtggc catttacccc agcatagcac acttgatacc 1860 gaagccaaag ccgaggcacc cggattacaa gcccacgaag aacacgggca cgttttgctg 1920 ctaccacgag cataacggcc atgacggcga gaagtgtatc acccttcgtg atcatattga 1980 agctttggca cgtgaaggaa aaattgatca attcctcctt caccctccaa ggggtaaccg 2040 taaccaacgc caggtgaatg tgatatattc cataagtggt ggcacaccca tatctaaatc 2100 ttccaacagg gccatgaaaa atagtgaacg agctttaagg tctggccacc aagtgtttca 2160 cgtggaagac atcaggggag gcaagtatca aaagcctaac tgggatccaa tatgtttcta 2220 ccctgaggaa gaaagaggta tcatctaccc tcacaacgac ccactgatcg tggaggctca 2280 catagccaac tttgaagtgc gacggatcct ggtagacacg ggggcttcgg tcaatatcat 2340 gtttgctgaa gctttcaggg cacttaatgt agctgaacac ttgctcgatc gctcgatttc 2400 ccctctgata agcttctccg gtgatatcgt gcaacctttg gggagcatac acttacctct 2460 caccattggt acaggccctt acacagctac cattaccact aacttcctgg tggttgactg 2520 cccaacggca tacaatgtca tcttcgggcg cacakgcatc aatgatctca aggccatggt 2580 atccacacat atgttgttga tgaagtttcc aaccccttat ggcaatggtt acatcagagg 2640 agatcaactt agtgcacgat catgttacaa cacttcggtc aagcaacaac acctgcctgt 2700 gcccaaggaa accctctcta tacatgacca agtcataaag accagcccag acgaagccaa 2760 cttggatctt catggtggca acagtcaacc cgacgatcct cgagatgact ctttcaccca 2820 gcaagcacaa cccgctgaag agttggagaa ggtctctatc tcaaaagact atccggatcg 2880 catggtgaag attggcacca ccttgtcacc acccattcgg ttggcattga tctctttttt 2940 gcaagagaac accgaggtct tcgcctggtc atacgaggac atgccaggca tctctcccga 3000 tatcatctgt catcgcttga gtattgaccc caagaccaag ccagtgagac agaagcgaag 3060 atcttatgac gctgaacggt acgaggcaat gaaggcagaa gttgaaaaac tcaaaggcat 3120 aggcttcgtc cgtgaagtca attatccaac gtgggtagca aatgttgtcc ttgttaagaa 3180 gaatccgacc aaggaaagtc tcctgctcca aaaggtcttg tggagaatgt gtgtcgacta 3240 caccgaccta aacaaaggat gcccgaagga tagctttcct cttcctctca ttgacagact 3300 tatagactct acggcagggt gtgaactctt gagcttcatg gatgcttact cagggtacaa 3360 ccaaatcctc atgaaccctc cggaccaaga acacacagcc ttcactactg acaggggact 3420 atattgctat aaagtcatgc ccttcggcct aaagaatgca ggagcgactt atcagagact 3480 agtcaattca atgttcgccg aacagattgg gaagagcatg gaagtttacg ttgatgatat 3540 gctagtcaag agcaaacatg ctgaccaaca catcaccaac ctatctgaaa ccttcaccat 3600 tctgaagagg tatcgaatga ggttgaaccc caacaaatgt gccttcggcg taggctctgg 3660 caaattcttg ggcttcatga twagccaacg aggcattgag gctaaccccg agaagatcaa 3720 agcaatcctc gacatgaagg aaccggtaac ttcaaaagac atccagagcc ttactggcaa 3780 ggtggcagcc ttaaccaggt tcatctctaa ggccacagac agatgtgctc ctttcttcaa 3840 agcacttaag ggaagtaaga agtacattac atggactgat gaatgtgctg aggcattcaa 3900 gaacctcaaa gactacatga gtaaagcccm tttgctctcc aaacctgagg ttggtgacac 3960 tctcattatc tatctgtcgg tatcggcttc agcagtaagt tccgttctca ttcgaaatga 4020 tggtaatgtc gaacggcctg tctactacgc tagcaaggcc ttacaagatg cggagacacg 4080 atactccaac attgagaaat tggctctagc attggtcatg tctgctcgaa aacttcgccc 4140 ttacttccaa gcacactcca tcatcgtgct taccaatcat cctcttcgac agatactcca 4200 aagtcctgac acttccgggc gaatgatcaa atgggcgata gcattgggtg agtttgacat 4260 ctcctaccaa ccaaagccag ctgagaaggg ccaagcagtg gcagacttca tcgccgactt 4320 cacatatcct gttgacattg tttctacgcc taaagaagtg gtttcattac cctcggaagc 4380 tcagaaaata gaaccaacag ccccagcatg gagtctatat gttgatggct cgtccaacca 4440 acagggttgt ggagcaggac tagtccttac gacccctgac aaagtggcga tggagtatgc 4500 tcttcgtttc aaattcaagg cgtcgaacaa tgaggccgaa tatgaagccc tcctagcagg 4560 cttacgtttg gccaaacacc ttggggttaa acgaattgat atcttcagtg actcccaatt 4620 ggtggttaac caggtcacca acaactttga cgctaaggat agctccatgg cagcatatct 4680 ggcacaaaca caattgttgc tcaagcactt ccactaccag atcacccaaa ttcctcgagc 4740 ggcaaacagt catgcagatg ctttggctcg cctcgcctca gcggtggaag acaagattgg 4800 gagaaaaatt caggtcgaat tgttggcagc accaagcacc atggctgcgg aagtgtgcaa 4860 cttacaacaa ggggatagtt ggattacccc gatttataga ttccttgctc atggcaccct 4920 tccaaatgac aaagtccaag ctaagcagat tcgatacaag gctacccgtt acttgatcat 4980 taatgaccaa ctctacaagc ggggttttaa cctaccatac ctaagatgcc ttacgcccgc 5040 agaggcggaa actgtccttc gggaaataca tgaaggagtc tgcggagatc atgctggatc 5100 tcgatcccta gcacacaagg cttttcgcca aggatattac tggccaacac tccaccaaga 5160 tgccatcaga atatcccgct catgtgataa gtgtcaacgc tacgcaacta ttcctcactc 5220 ccctcccgag ccgctcactc ctatgatcag cccttggccc ttcgcccaat ggggacttga 5280 tttgatcggc ccaatgcctg cagggaaggg caaggttcgc tatgcaatcg ttgcagttga 5340 ctacttcaca aagtgggccg aagtagaacc cttggcaacc attactgagg caaaaataga 5400 agacttcgta tggaagaaca tcctttgcag attcggcatt cccaatgcga tagtcactga 5460 caacgggcga cagttcgaca acaataagtt caggatgttc tgctctaagt tcaacatcaa 5520 cttatgtttt gcctccccag ctcatcccca gtctaatgga caagttgaag ccatcaacaa 5580 aataatcaag cgaactttga aaaccagctt ggacaaggct aaaggttgtt ggccagaatt 5640 tgtaccccaa gttctttggt cataccgcac ttcgtatcgg acatcaacag gagaaacccc 5700 attctcactt gcctttggta cagaggcagt tgtcccagtt gagcttgagc aagcaacgtt 5760 ccgagtccag aactacgtgc aaagcgaaaa tgacaaacaa cttaccctca acttagatct 5820 agtcgaggaa cacagaaacc aggctcactt gaggaatgtc gcctacaagc agcgcatctc 5880 caactactat gactcaaggg tcaaacctcg ttctttcaaa gtgggggact gggtattgaa 5940 gaaaagatta ctctgcgaca gagtcccgag tgaaggaaca cttagtccaa actgggatgg 6000 accgtttgaa gttgttggca tcagtcgccc tggctcctac aagcttagaa gctccgatgg 6060 caagaccctt ggccatccat ggaacgctga tcacttgaag tactattaca agtaaactca 6120 cattgtacaa gtgttaagct tcagccgttc ggcatcctat gtaacgaaga ctatttggca 6180 tgaattcaat aaagaggtga tttagacaac tcgatcctaa tcctcttaca ttcctagcaa 6240 tgaaacactc gggttcaaag cttcaacatg aatgcttcca acatgaaaca aagtctaagt 6300 atatgtcaac aagactatac aaataaacga acagcttcac agtatattcg ttcaatcata 6360 cattccaaca cattcataca taagccaact gtgctttgaa agggttcaac atactttgtg 6420 tcattcgaca cttgctacaa tgtgcctaga caccttgccc ttattctcac caaccaggtg 6480 atgaaatgtg aagaaggaac tcatcttcat gccaccaacc aggtgatgaa atgtacaacc 6540 cgtactctcc ttcatgccac caaccaggtg atgaaatgta caacccgtac tctaatatca 6600 tttggcaact tgccactcat gccaccaacc aggtgaagaa ggaactcatc ttcatgccac 6660 caaccaggtg atgaaatgta caacccgtac tctaatatca tttggcaact tgccactcat 6720 gccaccaacc aggtgaagaa ggaactcatc ttcgtgccac caaccaggtg atgaaatgtg 6780 atgaaaggtg atgaaggaac tcaccttcgt accaccaacc aagtgatgaa agcaactcac 6840 cattcattcc accaaccaga agacgagtgg tacaacttgt acatgtgaac tcctagcatt 6900 cacaaataat aaaaaaccct caagctttac aactcaacta ggggagcact tatgcccaac 6960 aagagttata gtcaccaaca aagtcttatt gcaagccaac aacggcttca gtgcatggca 7020 tacgaagatc aagctcttca gccctcttgc atctgcttca gacatttctc ctctgtaaca 7080 atgcaaacac tacaactcgt agaaagcttc acacactctt gatcaagact gttcgaagca 7140 aattcaattt atatggttca tccaaacctt cgactactac aaggtgtggc ttgcatcaca 7200 atctcttgct caacagtgtg gaagcaaaat ttgtatatgt tgtctctccc acattttcaa 7260 atttctagtt ttcccaaaaa aaaaaaaaag gaaattggga aattcaacag cttcaacaaa 7320 tggagggcaa ctacaattct caaaagcttc acacactctt gatcaagata gtgtgaagca 7380 aaatcaattc atggtaccca acaaagcttc aacctcaaag cttcacctac aaagcttcaa 7440 cacaaaagct tcaccacaaa agcttcaaca aatggagggc aactacaatt ctcaaaagct 7500 tcacacactc ttgatcaaga tagtgtgaag caaaatcaat tcatggtacc caacaaaagc 7560 ttcacctcca aagcttcaac acaaaagctt cacctacaaa gcttcaactc caaagcttca 7620 cctacaaagc ttcaacacaa aagcttcacc tacaaaagct tcacctacta atagtgtgaa 7680 gcaaaatcaa ttcatggtac ccaacaaagc ttcaacctca aagcttcacc tacaaagctt 7740 caacaccaaa gcttcaccta caaagcttca aatatatatt ttttaaaata aaaaattcaa 7800 aaattcggaa attcgaaaat tcaaaaaaat tcaaaaaaaa aaaaaaaaaa attgcctagg 7860 cctcctcttc tttgggccta acaactttca taacaaatat atatgaagga ggagttttgg 7920 gctaccactt agaaaggaaa atggtgaagt tttgttactt tggaaacttg gctactagca 7980 agacacctca ttcgtcaact ccctcgaccg gagacttggg ggactcctac catatgctac 8040 tacaccttgg tactcggaag tctcacgacc actcagtgac ttggattttt caagtctcca 8100 accgagaagt tttcctcact cgggaaatta agggagcac 8139 // ID COPIA-LTR_MT repbase; DNA; EDCOT; 1242 BP. XX AC . XX DT 07-DEC-2004 (Rel. 9.11, Created) DT 07-DEC-2004 (Rel. 9.11, Last updated, Version 1) XX DE Medicago truncatula COPIA_MT copia-like retrotransposon, LTR DE sequence - a consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; COPIA-LTR_MT; KW LTR sequence; copia-like retrotransposon. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-1242 RA Gentles A. and Jurka J.; RT "Copia-like retrotransposon COPIA_MT."; RL Repbase Reports 4(11), 288-288 (2004). XX DR [1] (Consensus) XX SQ Sequence 1242 BP; 399 A; 220 C; 239 G; 384 T; 0 other; tgttggaaca aaatgtgttt cacaatgaac cttattaagt tttgatgata acaaggtatt 60 aaaaattgtc aattggttat tactaataat tgttcaagtg tacaggacca aaggctactc 120 aagttatttc aataggtctt ggaagaacaa tggaaagaaa aagaaattct gagcatctga 180 agaaaactgc tcctgaagct gaagtgctcc tgaagagatg acgtcatcag aagcagaagg 240 tcatcagaag caaaagtttt catcagaagc aatatcttca ccagaagcta cgtttgatcc 300 tttaatcaaa ctgaagattc aaagtagctg attctcaatt cagtcttatc aaagaagaac 360 gaagaattga aagggaggta tcaacggata tatggatagc actgagcact tgtctctcat 420 taatagagtt gacaaagtac aagtgtacaa ccactacctc cactactctg ttttctgtct 480 acgctacaag acaaaacaac agccatgcct gcagaatttg tacactcaag atgggaatga 540 atttgaagct tattcttcaa aggactacac ccaaatcagg caaaggatca ctggtggata 600 atcaaaggat ttcaaacgac tctttagacg tgctgattat ctcaacgtct ctttcacgcc 660 tctatataaa ggagtgaaga cttgaagatt aaagatagag atacataagt tcaaaagcgc 720 caaaactctg tcaatttgat tctacaaagc acactgaatt tctgcactga tttgatacat 780 cttagaaatt caaagtctag agtcttttct gtattgtatt gtgaacacca ctgattgtat 840 atcaagtgtt caattcaaac tcaattctct gtatttttgt ttgattagaa gtctcttgcc 900 tgcgtgcttg agcattagaa gtctcttgct tagtgcttga gcattggaag actcttgcgt 960 gtgtgcttga gcattttttt gtgaagtctc atacttagaa agtattgagc agttgtaatc 1020 tttgtgatta tagtgaaatc tccttggaag tgcaaggggg actggactac ttccgtgttg 1080 tggaaggaac caggataact gcttgtgtct ttgtctttct tttctctgct ctgttctttt 1140 ccgctgcaat ctgactctga tcatttcatc agaagcaatc aaactgcttc tgaagtttta 1200 tcagaagaag tattttttaa gagaaaaaga aaacacaatt ca 1242 // ID COP6_I_MT repbase; DNA; EDCOT; 4120 BP. XX AC . XX DT 28-DEC-2006 (Rel. 11.12, Created) DT 28-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE Internal regions sequence of COP6_MT LTR retroposon from Medicago DE truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW internal region; Interspersed; repeat; terminal; COP6_I_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-4120 RA Shankar R. and Jurka J.; RT "COP6_MT: A copia type LTR retroposon from barrel medic."; RL Repbase Reports 6(12), 611-611 (2006). XX DR [1] (Consensus) XX CC The internal region shows a single ORF having LTR reverse CC transcriptase polyprotein with high conservation for catalytic CC domains. On both termini the sequence is flanked by LTRs. The CC element exists with few complete copies in the Medicago genome. XX FH Key Location/Qualifiers FT CDS join(50..1330,1334..2719) FT /product="COP6_I_MT_1p" FT /translation="MASAANNNKNDLPSSVSVKLDRNNYPLWKSLVLPVVR FT GCKLDGYMLGTKKCPEEFITSSDSSKSNNPAFEEWQANDQRLLGWMLNSMA FT TEMATQLLHCETSKQLWDEAQSLAGAHTRSQIIYLKSEFHSIRKGEMKMED FT YLIKMKNLADKLKLAGNPISNSDLIIQTLNGLDSEYNPIVVKLSDHTTLSW FT VDLQAQLLTFESRIEQLNNLTNLNLNATANVANKFDHRDNRFNSNNNWRGS FT NFRGWRGGRGRGRSSKAPCQVCGKTNHTAINCFHRFDKNYSRSNYSADSDK FT QGSHNAFIASQNSVEDYDWYFDSGASNHVTHQTNKFQDLTEHHGKNSLVVG FT NGDKLEIVATCSSKLKSLNLDDVLYVPNITKNLLSVSKLAADNNIFVEFDK FT NCCFVKEKLTGKVILKGLLKNGLYQLSGTKGNPAFVSVKESWHRRLGHPNN FT KVLDKVLKSCNVKVPPSDNFRFCEACQYGKMHLLPFKSSSSHAQEPLELVH FT TDVWGPAPIMSSSGFKYYVHFIDDFSRFTWIYPLKLKSETVQAFTQFKNLT FT ENQFNKRIKVIQCDGGGEYKPVQKLAIDAGIQFRMSCPYTSQQNGRAERKH FT RHIAEFGLTLLAQAQMPLHYWWEAFFTAVYLINRLPSQVTQNESPYSLIFH FT KEPDYKLLKPFGCACYPCLKPYNQHKLQFHTTRCVFLGYSNSHKGYKCLNS FT HGRTFISRHVIFNEDLFPFHEGFLNTRSPLKTTINNPSTSFPLCSAGNSIN FT DASIPIIEEENQDETNEEDSQGVTSDTEQTDNGSSEGDTTHEETPDIVQQQ FT NVGESSLDTNTSNAIHTRSKSGIHKPKLPYIGITETYKDTVEPTNVKEALT FT RTLWKEAMQKEFQALMSNKTWILVPYQDQENIVDSK" XX SQ Sequence 4120 BP; 1384 A; 866 C; 786 G; 1084 T; 0 other; ttggcatcag agctcttaag ctgaaaagct cttgatccat cagaaaaaca tggcttccgc 60 tgccaacaac aacaaaaatg acctaccatc atctgtatct gtcaagctgg acagaaacaa 120 ttatccccta tggaaatctc tagttctacc agtggtcaga ggatgcaagc tcgatggata 180 tatgttggga acgaaaaagt gtcctgaaga attcattacc tcttcggact caagcaagag 240 caacaaccct gcctttgaag aatggcaagc caatgatcaa cgcctccttg ggtggatgct 300 caactcgatg gctactgaaa tggcaactca gctgctgcat tgtgagacct ccaaacagct 360 ttgggatgag gctcaaagtc tggctggagc acacacaagg tctcaaatca tttatctcaa 420 gtctgaattt cacagcatca gaaaagggga aatgaaaatg gaagactatc taatcaaaat 480 gaagaacctt gctgacaaac tcaaacttgc cggcaatccg atttcaaatt ctgatctgat 540 cattcaaact cttaatggtt tggattccga atataatcct atagttgtaa aattgtccga 600 tcataccaca ctcagctggg tggatttaca agctcaatta ctaacttttg aaagtagaat 660 tgagcaactg aataacctca ctaatctgaa tttgaatgca acagcaaatg ttgcaaacaa 720 atttgatcac cgagacaaca ggttcaattc caacaacaat tggagaggtt ccaacttcag 780 aggttggaga ggaggcagag gaagaggcag gtcatccaaa gcaccatgcc aagtctgtgg 840 caagactaat cacactgcaa taaattgctt tcacaggttt gacaaaaact actcaagatc 900 caattattca gcagacagtg acaagcaagg atctcacaat gccttcatag cctctcagaa 960 ctcagtcgaa gactatgact ggtactttga tagcggtgca agcaatcatg taacacatca 1020 aactaacaag ttccaagact tgactgagca ccatggtaag aattctctgg ttgttggtaa 1080 tggtgataaa ttagagattg tggccacatg ttcttcaaaa cttaagtcac tcaatttaga 1140 tgatgtctta tatgtaccta acattaccaa aaatctatta agtgtttcaa aattggctgc 1200 tgacaacaac atatttgttg agtttgataa aaattgttgc tttgtgaagg aaaaattgac 1260 agggaaggta atactaaaag ggctacttaa aaatggatta taccagctct caggcaccaa 1320 aggaaaccca taagcttttg tatctgtcaa ggaaagctgg cataggagac ttggtcatcc 1380 taataataag gtcttagaca aagtcttgaa aagttgtaat gtcaaagtac cacctagtga 1440 taattttcgt ttttgcgagg catgccaata tggcaaaatg caccttttac cttttaagtc 1500 ttcttcttct cacgcccagg aaccacttga gttggtccac actgatgtat ggggtcctgc 1560 accaataatg tcttcctctg gttttaaata ctatgtgcac tttattgatg atttcagtag 1620 gtttacctgg atttatccct tgaaactaaa gtctgaaact gtgcaggctt ttactcaatt 1680 taaaaaccta actgaaaacc agttcaataa aagaatcaaa gtaattcaat gtgatggtgg 1740 tggtgaatac aaacctgtgc agaaacttgc aatagatgct ggtatacaat ttagaatgtc 1800 atgcccatat acctctcaac aaaatggaag agccgagagg aaacacagac atatagctga 1860 atttggctta accttacttg cacaagctca aatgccctta cattattggt gggaagcctt 1920 ctttactgca gtatacctca ttaacagact gccatcccaa gttactcaaa atgagagtcc 1980 ctattcactc atatttcata aagaacctga ctataagttg ctaaaaccat ttggttgtgc 2040 gtgttaccct tgcctcaaac cgtataacca acacaagcta caattccaca caaccaggtg 2100 tgtgttcttg ggatatagca actcccacaa aggttacaaa tgtctcaact ctcatggaag 2160 gactttcata tcaagacatg tcatctttaa tgaagacctt tttccattcc atgaggggtt 2220 tctcaataca agaagtcctt tgaaaacaac aattaacaat ccatctactt cttttccttt 2280 gtgcagtgca ggtaattcta tcaatgatgc tagcattcca atcattgaag aagaaaatca 2340 agatgagaca aacgaagaag actctcaagg tgttactagt gacacagaac aaactgacaa 2400 tggttcatca gaaggtgaca ccactcatga agagacacca gacatagttc agcagcaaaa 2460 tgtgggtgaa tcaagcttgg acacaaatac aagtaatgca atacacacaa ggagtaagtc 2520 aggcattcac aagccgaagc taccttacat tggaatcact gagacttaca aagacacagt 2580 ggaacctaca aatgtcaagg aagctctcac aagaacctta tggaaagaag caatgcaaaa 2640 ggagtttcaa gctctcatgt ccaacaagac gtggatacta gtcccttacc aagatcaaga 2700 aaacatagtt gactcaaaat gagtcttcaa gaccaactac aagtcagatg gttccataga 2760 aaggaggaaa gccagactag ttgcaaaggg gtttcaacaa acagctggaa tcgactatga 2820 agaaacattt agtcctgtag tcaaagctag cacagtcaga gtcatcctct caattgcagt 2880 acacctcaat tgggaagtta ggcaactaga catcaacaat gcgttcctaa atggatacct 2940 caaagaaacc gtattcatgc atcagccaga aggatttgtt gatcctacca agcctaatca 3000 catatgcaaa ctatctaaag caatttatgg gctgaagcag gcaccgagag cttggtttga 3060 tagtctcaaa actgcattgt taaattgggg ctttcaaaac acaaaaagtg atccttctct 3120 ttttctttta aaaggtaaag atcatatcac atttctcctt atatatgtgg atgacataat 3180 agtcacaggc agcagcaaca atttccttca agctttcatc aaacaactta atgatgtctt 3240 ctctctcaaa gatttgggtc gtttacacta ctttctgggc atagaagtac aaagagatgc 3300 aagtggaatg taccttaaac aatccaaata catcggtgac ttgctgaaga aattcaagat 3360 ggaaaatgcc tcaccatgtc caacaccgat gataacagga agacatttca cagttgaggg 3420 ggagaaattg aaagatccaa ctgtgttcag acaagccata ggagggctgc aatatttaac 3480 tcacacaaga cctgacatag ccttttctgt taataaactc agtcaataca tgagttcacc 3540 taccactgac cattggcaag gtataaaaag aatcttgaga tatctccaag gcaccatcaa 3600 ttattgcctg cacatcaagc catccactga cttggatata acaggttttt ctgatgcaga 3660 ctgggccact agtattgatg acagaaaatc catggctggt caatgtgtgt tccttggtga 3720 aacactcatc tcttggtcct caagaaaaca aaaagtagta tcaagatcaa gcacagagtc 3780 agagtacaga gcactagctg acctagctgc tgagatagca tggattcgtt cactactttt 3840 tgaactgaaa ctcccattgc caaggaagcc catactatgg tgtgataact tgagtgccaa 3900 ggcactagct tctaatccag tattgcatgc tcgttctaag catattgaaa ttgatgttca 3960 ttacatcaga gaccaagtac tacaaaataa ggttgttgtg gcttatgttc ctacaacgga 4020 tcaaattgca gattgtctca ccaagccatt aagtcacaca cgtttcagtc aactaagaga 4080 caaacttggt gtgattcact caccaccagt ttgaaggggg 4120 // ID Copia-45_Mad-LTR repbase; DNA; EDCOT; 117 BP. XX AC ACYM01043826; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 0) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-45_Mad-I; KW Copia-45_Mad-LTR; Copia-45_Mad_. XX NM Copia-45_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-117 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1395-1395 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01043826; Positions 763 647. XX SQ Sequence 117 BP; 24 A; 44 C; 11 G; 37 T; 1 other; tggcttctca atcttcctct cccattccct ttcctaatgt ctccaatttt ctcacgatca 60 aacttgatcg taccaactac cctctctggc aagcccaaat gctacytctc ctccgca 117 // ID Copia-38_Mad-I repbase; DNA; EDCOT; 3975 BP. XX AC ACYM01018656; XX DT 19-SEP-2010 (Rel. 15.09, Created) DT 19-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-38_Mad-I; KW Copia-38_Mad-LTR; Copia-38_Mad_. XX NM Copia-38_Mad-I. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-3975 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(9), 1308-1308 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR Genome; ACYM01018656; Positions 6043 2069. XX CC Positions [1255-1755] - Integrase core CC LTRs are 100% similar to each other. XX FH Key Location/Qualifiers FT CDS 1096..3357 FT /product="Copia-38_Mad-I_1p" FT /translation="MWHAHLGHPSTAIFQVLANKYHIAISGTLSSNKKCHI FT CPLGKACRLLFSSRMSMAPSPLDVLHLDVWGPAPVVSNFGYKYYLSIVDDY FT SRFVWLFPLVRKSDVMTTFVTFKRIIENRLNSTIKVLQTDGGGEFTSLAFR FT HFLRDHGITHQLSCPHMPQQNGIVERKHRHVTEIGLCLLAQSHLPQTFWVE FT AFTTAAFLINRLPLHNLGNVSPYEKLFAKVPDYRFLKTFGCTCFPHSVPYN FT KHKLMPKSIPCVFIGYDNNYKGYRCLDVASGKMYISRNVQFDELTFPYKDR FT RTDSPHHKQSHQPLFLEPLMHAAAPVFPCHILPTVSDPPPPHSPPTAIAAP FT IPTSPAAPFQSSASTTASSPQPVPSPDSTPPRKFGSINALTYDSPRHPLPH FT GLTTALEDPMFIEPTSYTQTSKFPHWQQAMKEEHDALLHNHTWSLVPATPH FT MNIVGCKWVFRVKHKADGSIDHHKACLVAKRFNQQVGVDYDETFSPVVKPG FT TICTILALAVSQHWSLQQLDVRNAFLNGILHEEVYMKQPPGFVDSNHSQYV FT CRLHKAIYGLKQAPRAWFQRLASFLLNQGFSHSKSDASLFIYHSSTYSLYV FT LVYVDDLIVIGSNNDVIHRFIDTICTSFASRKLGDLHFFLGMEVTRRGRQL FT SLAQSRYASDLLQKFQMDQCKPSPIPFLSSLRLSAHDGDPISDPDVYRSMV FT GGLQYLTLTRPDISFAVNQVCQYMHNPKSTHLQAVKRIYRYIKGTVEQGLL FT FRS" XX SQ Sequence 3975 BP; 949 A; 1098 C; 674 G; 1216 T; 38 other; nnnnnnnnnn nnnnnnnggt atcatccttt ctcacaagct aacgcttccc aacgttcgat 60 cctctatacg ccctcaccac cccaaccctc cactgcctcc tttgattcct ctctttcttc 120 acccatggct gcatataatg cttccctccc caccaccttc aacatctccc acaccatcaa 180 tactcccatg gaccgaaata attatctcag ttagcgatct caatttttcg acattcttga 240 aattcatggt ctggaagatg tcgtgaccac caataccaaa cctcccaaaa agcttgatga 300 tggatctctt aatccaaatt attctcagga caaacttgtc ctcagttgga tcaagtctac 360 ttgctcaccc tatatccgct ctatactgct tccttgcgcc tacgttttcg atgcttggtc 420 tcttctggaa aagcgtttgt ctcctgtctc caagacttac atccgcaccc aaccgtcaag 480 ccaactggaa tcctcatcgg cctaacccca gtccatcgca cgacactcga ccacctcttc 540 ttccaacccc gtcgctgcta cctaagccac ccacatttga atatgatggc tactgtcaac 600 tttgcgaaga atatggtcac aaagcccgcc agtgtcccac tcgaggaaat tttgcctacc 660 tagcgactgc ggactctccc tcgccaacac cttgggtggt tgattccggc gccacaaatc 720 acatgaccaa taatccttcc gctctcacac aaatcccaac catacacagg taccgatact 780 attgttgtgg gcaacgacca tcacttgcct atatctcatg tcggtaaatc ctccatctct 840 agtttacatg gacctatgtt gctaaagatg tgttatatgt cccagctatt aagaagaact 900 tattatccct tcgtcgtttt tgttatgaca atcactcttt ttttttagat tgatgatcgt 960 tcttttcgtg tgaaggacaa gaaaacgggc caacttcttc tgattgggca taactatggc 1020 gaactttact atattagagc tgctcctcac gttactccaa agcttgtgtt ttatggcgaa 1080 cggacgatta gcgatatgtg gcatgctcac ttgggtcacc catccactgc tatatttcaa 1140 gttttggcaa ataagtacca tatcgccatt agtggtacac tttcatctaa taaaaaatgt 1200 catatttgtc cactaggcaa ggcatgtcgc cttctgtttt cttctcggat gtccatggct 1260 ccatctcctt tagacgtctt acatcttgat gtatggggcc ccgctcctgt tgtgtctaat 1320 tttggctaca agtactattt atctatagtg gatgattatt caagatttgt gtggttgttc 1380 cctcttgttc gtaagtccga tgtcatgact acctttgtta ctttcaaacg aataattgaa 1440 aatcgtttga atagcactat taaagtatta caaacggatg gtggtggtga attcactagc 1500 cttgcatttc ggcattttct tcgtgatcat ggcataacac accaactctc ttgcccacat 1560 atgccacaac aaaacggtat agttgagcgc aaacatcgcc atgttaccga aataggacta 1620 tgtctccttg ctcaatctca tctcccacaa actttttggg tggaggcctt cacaaccgcc 1680 gcatttctta taaatcggtt gcctcttcat aatcttggga atgtttctcc ttatgaaaaa 1740 ctatttgcca aagttccaga ttaccgattt ctaaagacgt ttgggtgcac atgctttccc 1800 cactcggttc cttacaacaa acataagtta atgcccaagt ccatcccatg tgtcttcatt 1860 ggttacgaca acaactacaa aggctaccgt tgtctcgatg ttgcttctgg taagatgtat 1920 atttctcgca atgtacaatt tgatgaactc acctttccgt ataaagatcg caggacagat 1980 tctcctcatc acaagcagtc ccatcaacca ttatttttgg agccactaat gcatgccgca 2040 gcacctgtgt ttccctgcca cattctacca actgtttctg atcctccacc gcctcactct 2100 ccacccacgg ctattgcagc gcctatacca acttcacctg cagcaccttt tcaatcatct 2160 gcatccacca ctgcttcttc accgcaacct gtcccttctc cagattctac tcctccacgc 2220 aagttcggga gcatcaatgc cctcacttat gactcgccta gacatccact tcctcatggt 2280 ttaaccactg cccttgaaga tcctatgttc attgagccta ctagctatac tcaaacgtct 2340 aagttcccgc attggcagca agcgatgaaa gaggaacatg atgcacttct tcataatcac 2400 acatggtctc ttgttcctgc tactcctcat atgaatattg tgggatgcaa atgggtattt 2460 cgtgttaaac acaaggccga cggctccatt gaccaccaca aggcttgtct cgtcgccaag 2520 aggttcaatc aacaagttgg ggttgactac gatgagacct ttagtccggt tgttaaacca 2580 ggtactattt gtaccattct tgccttagca gtctcacaac attggtcatt gcagcaactt 2640 gacgtccgta atgctttctt gaatggtatt cttcacgagg aagtttatat gaaacaacct 2700 cctggctttg ttgattccaa ccactctcag tatgtttgtc gccttcacaa ggctatttat 2760 ggcctcaaac aagcacctcg ggcttggttc cagcgtttag cctcattcct gcttaatcaa 2820 ggcttttccc atagcaaatc agatgcatcc ctgtttattt accattcctc tacatactca 2880 ctctatgttc tggtatacgt tgatgatctc attgtcatag gttctaacaa tgatgttatt 2940 cacaggttca ttgatacaat atgtaccagc tttgctagcc gcaagctagg tgacctccat 3000 ttttttcttg gaatggaagt cactcgacga ggccgccaac tatctctcgc tcaaagccgt 3060 tatgcctctg atttattaca gaaatttcaa atggaccagt gcaagcccag ccctatacca 3120 ttcctctcct ccttgcgttt gtctgctcat gatggtgatc ctatctcgga tcctgatgtc 3180 tatcggagca tggttggtgg acttcagtac ctgaccctca cccgccccga catttccttt 3240 gccgttaatc aagtttgtca gtacatgcac aaccccaaat caactcatct tcaggccgty 3300 aaacgcatct accgctacat caaagggact gttgaacaag gtcttttatt tcgttcgyct 3360 ccagacttct ctmttcaggg cttttctgat gctgactggg ccggttccat tgatgatcgt 3420 cgctcaacaa gtggtgcttg catttttctt ggtcccaacc tccttacatr gaccsccaaa 3480 aagcaatcca cwgtgtctcg ttctagttcy gaagctgaat aycgtgytct tgccaccaca 3540 gccgctgaaa ttcgttggtt ttgctatcty ttccgtgaac taggcattcc gcttcgtact 3600 cyaccttgca ttttcgtcga caatgtctct gcycttcaca tggcmgccaa cccagttttt 3660 catgcrcgta ctcgtcacat agagattgac taccactttg ttcgagagct tctcacccak 3720 ggtgtccttc aaactcgrca catctcctct catcatcaaa tcgctgatat cttcaccaaa 3780 ggactttcac gcgatcgatt mtctttcctt gcttccaagc tcaatctaca ctttgttccg 3840 tttcgcttra ggggggatga caagagtatt gaatccacca caaatctctc caccacatct 3900 gctgtcwaam cgtratccca ccattctctc tatattgttt tatgtaaata atcaagagtt 3960 attagttacc tttta 3975 // ID L1-5_Mad repbase; DNA; EDCOT; 6062 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-5_Mad. XX NM L1-5_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-6062 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1809-1809 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 302..1876 FT /product="L1-5_Mad_1p" FT /translation="LAMAGGSPKEDLEELGTRFGTNLILSEKEQGGVCIER FT KDVEGALLGFQYTLIAEVLTAKAVKGDVFVDCFMSLWRGREGVSIREIGDR FT RFLARFAGKRDLQRVVEADLPWMFKNDLVLVADRTEKGLNRWTPLSLGVFW FT VQLHNVPVLSMTQAVAETIGSLMGEVRSVDKTGSRDCIGRFLRVKIGFNVR FT EPLMRGTFVTFPDDGKIWIDFKYESLPNYCLICGKLGHPTRICKETLDERT FT DPGDCTKTRNEAFAFRGLDAVSDLRGNPLGAGPRSRASSGSNGGRSGSERW FT NDELGGGRRSGRSSTASGMGCQPQKFASRSQSGSECTAPLEEEVIDTATSP FT SKPRWSSNKMGHRDNVLAGKIRRQRLAEEEARSARELAFDAGLIGPGGAVA FT AGAEHVVLNDHYEQEGRVDTVSMTLNGGSTFDLNLVPGVGEDGDSVSASRR FT EASDGRGCVSGCDLATDDDPFELEAIIEAVMNENKGKKRSAREVEYDEVNP FT CVEPKRSKLSRKSYVEAEETSREGSPKSK" FT CDS join(1876..4074,3621..6032) FT /product="L1-5_Mad_2p" FT /translation="MRLLTWNCQGIGGDLTVDNLLEQNRLHTPDIVVLLET FT KNKSSRYGYLKKRLDLEYMHAVEPRSIGGGLCVFWRDASQVTLVKSEDFVI FT EVKIWDEHKKCHWYLFAIYASTDEKKRRDQWGYLSRRLGNNRGKTLLIGDF FT NDILCNDEKEGGNYRPTSSMRDFREFVAQNELMDLGFVGYPFTWRNNQEAK FT PIQQRLDRGLATMGWQDLYPENTIRHVVLEGSDHALLFLSTEKVKAWRGRK FT FSYDARWSKTEECRQLVVEEWRDKHGGSHAFRFCEKLKALRHRLKXWYRGR FT GRNSKKVIEQLKEEIRAAYMSTDFASXVVKMKERELRAAHRNEEAYWRVKS FT RAQWLKEGDKNSKFFHAQTLKRRRFNQIKGLEDVNGVWQEDEAAISSIATS FT YFAELFKSSSPGQIDEIGECLAPRVSAEDNLALTAAVTEEEIKTAVFQIPP FT IRAPGPDGYSGCFYQDHWDTVGKDVIKIVKAFWHSGTILRKLNHTNLVLIP FT KVKCPKNMTQYRPIALCNVIYKVIAKVLTNRLKMVMPKVICDNQSAFVAGK FT QIQDNILVVHELLHSLLHQKKGDQTGMAIKLDMAKAYDRVEWVFLLSMMAK FT LGFAPLFCNWIKECISTASFSILVNGNPTGLVLPERGLRQGDPLSPYLFLL FT CTEGLPCSLGEGWSGVPSTGSVCRXMGPRSRTCFLRMTRCYSVMRVWRRRE FT ASWRCCGHMPVALAKLLICPKARFSSARRPRTGGVRPRGVGVPLIHDGEIG FT VRSPXLQLDQGVHFHXLFQHPSKWEPDWACPAGARAATRRPPISLSLPALY FT GRSSMLIRRGMERGALHGFSVSANGTPISHLFFADDSVLFGHASVEEARGI FT VEVLRTYARGSGQAVNLSKSSIFFGSKTSNRVRRKIGRTMGIQCKXGFGRY FT LGLQSDFGHSKRVVFEEVRDRLESRLAGWAEQFLSQAGKEVLVKAVAMAMP FT NYAMSCFKLPIGVCRDLEKAIRNFWWRGSEQRKGVHWISWERLMKQKRVGG FT LGFRDIQCFNLAFLAKIGWRLIQNPGSLLATVLKEKYYPGKXFTEAGKGRN FT TSWGWKGIFDARKVLLQGLRWRVGDGACINIREDPWFPRPSTFKVXPLVSL FT XATXVSELIDSGSSSWKXDLILASFHRDDVGPILSIPLSKTGCRDRMVWHH FT NANGVYSVRSGYGVAMNLMENGALGKKGRGSASDKPKNCYAWNLIWKLKVP FT NKIKIFIWRCCNNALAVRRNLKRRHMRVDNVCGVCGAMDESETHLFFRCHL FT SHLFWFSSPLQLNSFELAGADFLSSWELFWARVKGRDNAEEIMQEFAFGLW FT RLWKNRNEVVFNGVHRQPLELLEAWXRNISEFRDATLCEPAGKQPGCRPMI FT APLDRGACRWEKPAFGVLKVNTDASWCKTTLRTGVGWVCRDFAGLLHGAGG FT SGAXLCHSAAAGEAAAIRTALLACIDYGYDNVVIESDAKVIIQMIRHEXDH FT DFSLECILGDIEVLARRLRSVSFSYVPREGNVAAHSVAKFVFKEGREFGWD FT CIGPEFLFNILAQDVNLSIRI" XX SQ Sequence 6062 BP; 1424 A; 1238 C; 1927 G; 1450 T; 23 other; gtgcctcgaa aggaggagtg cggtgctccg tcgacgagcg cgtcctgtag tcggatcgtc 60 gtccgagatc tgaccggcta gtccctcctt ctcgaagctc tggttgcgaa tccggggact 120 tggctcggct gtcgcgatta gctggggaaa ckgcgagcga agtagctcct ctggcggctc 180 gtgggcggcc tgcccaggtg aggagatctg gatctggtgg agatctgaga gkagaaaagg 240 tacctgtggc tggcgctcgt ggtggtggcc actgggggtg agtggggtgc ggctcttctg 300 actggccatg gctgggggaa gtccgaagga ggacctagag gagttgggga cacgatttgg 360 gaccaacctc atcctgtctg agaaagaaca gggaggcgtg tgcattgaga gaaaggatgt 420 cgaaggtgct ctattagggt ttcagtacac cctgattgca gaagttctca ctgctaaggc 480 ggtgaaagga gatgtgttcg ttgactgctt tatgtccctc tggcgcggac gtgagggggt 540 ctcgattagg gagattggag atcggagatt cctcgctcgt tttgcgggga aaagggatct 600 gcaacgggtg gttgaggcsg acctgccttg gatgttcaaa aatgaccttg tattggtggc 660 ggatcgaacg gagaaggggc tgaaccgatg gacccctctc tccctggggg tgttctgggt 720 ccagctgcat aacgtcccgg tgctcagtat gacccaagcg gtagctgaaa caataggtag 780 tttgatgggt gaggttcgat cggtggacaa aactgggagc cgagactgca ttggacgatt 840 cctccgggtg aaaattggct tcaatgttcg cgaaccccta atgagaggga cctttgtgac 900 ctttcccgac gacggcaaga tctggattga tttcaagtat gaatcgcttc ctaactactg 960 tctcatttgt ggaaagctgg gacaccctac taggatttgc aaggaaackc tggatgaaag 1020 aacagaccca ggggattgca ccaagacgag gaatgaggca tttgcgttcc gtgggttaga 1080 tgcagtgtcg gacctgagag gcaatccgct gggagctgga cccaggagca gggcatcctc 1140 tgggtcaaat ggtggacgga gtggatcgga gcggtggaac gatgaactgg gtggtggtag 1200 acgctccggg cggtcctcga cggcgtcagg aatgggatgt caaccccaga aatttgctag 1260 cagatctcag agcggcagtg agtgcaccgc gccgttggag gaggaggtta ttgacactgc 1320 aacatcgcca agcaagccca ggtggtcgtc taacaaaatg ggacacagag acaacgtgct 1380 tgctgggaaa atccgacgtc aacggctagc tgaagaagag gcgaggtctg cgagagaact 1440 ggctttcgat gcaggcttaa ttgggccggg gggtgcggtg gcagcgggag cggaacacgt 1500 ggtactcaac gaccattacg agcaggaggg acgggtggat acggtcagca tgactctgaa 1560 tggaggctct acttttgatc ttaaccttgt gcctggcgtt ggtgaggatg gggacagtgt 1620 gagtgctagt cggagggaag ctagtgatgg tcgggggtgc gtgagtgggt gtgacttggc 1680 tacggatgat gatccttttg agctggaagc tatcattgaa gccgtgatga acgagaataa 1740 aggcaaaaag agaagtgcca gagaggtgga gtatgatgag gttaacccct gtgtggaacc 1800 taaaagatct aagctaagta ggaagtcata tgttgaggcg gaggagacca gccgtgaggg 1860 gtctcccaag tccaaatgag gctacttact tggaactgtc agggtatcgg gggtgacctg 1920 acagttgaca atctgctgga gcagaatcgg ctccacaccc ctgacattgt ggttttgctg 1980 gaaaccaaga ataaaagcag tcggtatggg tatctcaaga aacgtttgga tttggagtac 2040 atgcacgcag tggaacctag gagcattggg ggaggcctct gtgttttctg gcgggatgct 2100 tcccaggtta ctctggtgaa gtctgaggac tttgttattg aagttaaaat ttgggatgag 2160 cacaagaagt gtcactggta tttgtttgca atctacgcaa gcactgatga gaagaaacgg 2220 cgggaccaat gggggtatct gagcaggcgg cttgggaaca acaggggaaa gactcttctc 2280 atcggggact ttaatgacat tctgtgtaat gatgagaaag aggggggcaa ctacagaccg 2340 acgtctagta tgcgwgactt tagagagttt gtggctcaaa atgagctcat ggacctgggt 2400 tttgttggct atccgtttac gtggcggaac aaccaggagg cgaagcctat tcagcagcgc 2460 ctggacaggg gattggctac watgggatgg caggaccttt accctgagaa cacaatcagg 2520 cacgtggtac tggaagggtc tgaccatgct ctgttatttt tgtccacgga gaaagtgaaa 2580 gcgtggaggg ggaggaaatt ctcttatgat gcacgatgga gcaaaacgga ggagtgtcgg 2640 caactggtgg tagaggaatg gagagataaa catggggggt cacacgcctt tcgcttttgt 2700 gaaaaactga aagccctaag gcacaggctt aaggawtggt atcgggggag aggaaggaac 2760 tcaaagaaag tcatcgagca gctgaaagag gagattagag cggcttatat gtctactgac 2820 tttgcctcgg akgtggttaa gatgaaggag agagagctca gggccgccca tcgaaacgaa 2880 gaagcttact ggagggtgaa gtcgcgtgcc caatggttaa aggaaggtga taaaaattct 2940 aagttcttcc atgctcaaac cctcaaaaga aggaggttca accaaatcaa ggggttggag 3000 gacgtgaatg gagtgtggca ggaggacgaa gcagcgatat cttcaattgc tacctcttat 3060 tttgcggagt tatttaagtc gagcagccct gggcaaatcg atgagattgg ggaatgcctg 3120 gcaccacgtg tgtctgctga ggacaacctt gccttgacgg cagcggtgac tgaggaggaa 3180 atcaaaacgg ctgtcttcca aatccctcca attagggccc cgggtccgga cgggtactct 3240 ggatgctttt accaggatca ttgggatact gtgggcaagg atgtgatcaa gatagtcaaa 3300 gccttctggc attctggtac tattctgagg aaacttaatc atactaacct tgtgcttatc 3360 cctaaggtca agtgcccgaa gaacatgacg caataccggc ctattgcact atgtaatgta 3420 atctacaaag tcattgccaa ggttctcact aaccggctaa agatggtgat gccaaaggtg 3480 atttgtgaca accaatctgc ctttgtggcg gggaaacaaa ttcaggataa cattttggtg 3540 gtgcacgagc tcctacactc actgcttcat caaaaaaaag gtgaccagac tggcatggct 3600 attaagctcg acatggctaa ggcgtacgac cgcgtggagt gggtgttcct cttatccatg 3660 atggcgaaat tggggttcgc tcccctwttt tgcaactgga tcaaggagtg catttccack 3720 gcctctttca gcatcctagt aaatgggaac ccgactgggc ttgtcctgcc ggagcgaggg 3780 ctgcgacaag gagaccccct atctccctat ctcttcctgc tctgtacgga aggtcttcca 3840 tgctcattag gagagggatg gagcggggtg ccctccacgg gttcagtgtg tcggcwaatg 3900 ggaccccgat ctcgcacctg ttttttgcgg atgactcggt gttattcggt catgcgagtg 3960 tggaggaggc gagaggcatc gtggaggtgt tgcggacata tgcccgtggc tctggccaag 4020 ctgttaatct gtccaaaagc tcgattttct tcggctcgaa gacctcgaac agggtgagga 4080 ggaagattgg ccggaccatg ggaatccaat gtaagwctgg gtttggtagg tatcttgggc 4140 tgcaatctga ttttggccac tctaaaagag tggtttttga agaggtgcgg gacaggcttg 4200 aatctcggct ggcgggttgg gctgagcaat ttctatctca agcaggaaag gaagtcctag 4260 tcaaggcagt ggccatggcg atgccaaact atgccatgag ctgttttaaa ctacccattg 4320 gggtatgtag agacctggag aaagctatcc ggaatttctg gtggagaggg agcgagcaga 4380 gaaagggggt ccactggatc tcatgggagc ggttaatgaa gcaaaaacga gtcggcgggc 4440 tgggctttag ggatatccag tgttttaacc tggcgttcct tgccaagatt gggtggcggc 4500 tgatccagaa cccggggtct ttgctcgcta ctgttctgaa ggaaaaatac tatcctggga 4560 agwgctttac tgaggcggga aagggtagga acacgtcgtg gggttggaag ggcatttttg 4620 atgcccgaaa ggtgctccta caaggcctgc ggtggcgggt mggggacggg gcmtgcatca 4680 acattaggga ggacccgtgg tttcctaggc cctctacgtt taaagttawg cctttggtaa 4740 gcttgcawgc tactwtggta agcgagttaa ttgattcggg gtccagctct tggaaamgtg 4800 atctgatcct ggcaagcttt caccgggatg atgtgggacc gatcttaagc attcccttaa 4860 gcaagactgg gtgccgggac cggatggtgt ggcaccacaa tgcgaatggg gtttattcgg 4920 ttcgatcggg gtacggagtg gctatgaacc tcatggaaaa tggcgctttg gggaagaaag 4980 gccgtgggtc tgccagcgac aaaccaaaga actgctatgc ttggaacctg atctggaagt 5040 tgaaggtacc caacaaaatt aaaattttta tctggcgttg ttgtaacaat gctctggctg 5100 ttcgacgtaa cctgaagcgg agacatatga gagtggacaa cgtctgtgga gtttgtggtg 5160 ctatggatga gtcggaaact catctcttct tccgatgtca ccttagccac ctgttctggt 5220 tctcctctcc gcttcagttg aattcctttg agctggcagg ggcagacttc ctatctagct 5280 gggagttgtt ctgggctcgg gttaagggga gggacaacgc ggaggagatc atgcaggagt 5340 ttgcctttgg gttatggaga ctgtggaaaa acagaaacga ggtggttttt aatggggtgc 5400 accggcagcc cttggagctt ttggaggctt ggagmaggaa catctctgaa ttcagagacg 5460 ctacactctg cgagcctgcg ggaaagcagc ctgggtgccg accgatgatt gctcccctgg 5520 accgtggggc ttgtagatgg gagaagccgg cgttcggggt cctcaaggtc aacactgacg 5580 cctcgtggtg caagaccacc ctccgcacgg gggtgggctg ggtctgccgc gactttgctg 5640 gactgcttca tggtgcaggg ggctctggag ctgmgctgtg tcactccgcg gctgctgggg 5700 aagctgctgc aatcaggacc gccctcttgg cttgcattga ctacgggtat gataatgttg 5760 ttattgaatc tgatgccaaa gtgattattc agatgattag gcatgaamtg gatcatgatt 5820 tcagtcttga atgtattctt ggtgatattg aggttctagc gcgtaggttg aggtcagttt 5880 cgttctctta cgtgcctagg gagggcaatg ttgctgctca ctcggttgct aagtttgttt 5940 tcaaggaggg tcgkgaattt gggtgggact gtattgggcc tgaatttttg tttaatatcc 6000 tagcccagga tgtaaacctt tctattcgta tctaatatat ttctatcttc ggggaaaaaa 6060 aa 6062 // ID L1-13_Mad repbase; DNA; EDCOT; 5437 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; L1-13_Mad. XX NM L1-13_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-5437 RA Bao W. and Jurka J.; RT "Non-LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1817-1817 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX FH Key Location/Qualifiers FT CDS 1768..5436 FT /product="L1-13_Mad_2p" FT /translation="MNNFINFLNRGNLLSLNASGVPFTWTNCHTDHTVVFE FT RLDRVVANPLWLNMFPNYHLHNYPIFXSDHSPILLSLNSSEEKNNYFSFKF FT EAMWLNHPQFKMFVQNSWHCDPTINPKDKFRVCAGKFKFLVCKWNKDTFGN FT LKEKKKELLNEIDELQKQIMSNNSVDLMMEKSLRDELNHVLLCEEIMWAQR FT AKTNWLQLGDKNTKFFQTVATIRKKMNEITKVKDENGFWWSVGQGLEQVFV FT HDFKKRFSCDSPPSGADLSNLADIIQPCVSNHHNESLLSLVTDEEIWDAVS FT SIGALKALGPDGLSVAFFHGCWDQIRDSVSCLVKDFFQNGSSLRLINHTNI FT ALVPKIDNPETVSNYRPISLCNVSYKIITKIIIKRLKPLLDLCISQNQGAF FT APGRAIQDNILIAHEMFAGFNRMKGRTGAMGVKLDLEKAYDYLNWDYIRYV FT LLRFGFDNRWVELVMECITSPSFSVLINGRPHGYFYPKRGIRQGDPLSPYI FT FIICMEPLIRHLNTLTNNPKSHIGILSSPRGFKISNLVFADDCLLFAKATP FT RGARNILQILNMFSKAAGQQINFHKSSLYFSKNTTSPTRIDIVNILHIQHK FT TTIGKYLGIHNIVFWKDQVNGNELLKRVKRKLAGWKASTLSRAGRLTLINS FT NLTGMPNHVMSCFKCPDKIVNKLNKECRDFFWGRDKKIFPVAWDSVCAPKK FT MGGLGVRRLDHFNNACLAKLGWKVMTEEDNWWVKLVKSKYLRKENFLDNKI FT RQNHSFAWKGILKSRDVILKGMRWRVGNGKDILFWSHNWVFPYPLFHLLPN FT IDNQNINWDLKVNEFIDNYCWDRRKLSQVVSNEIVRKICNITIPLQDSKDV FT LVWGPNTNGKFSVKSATWIXKGTLTQSTKHKLINKMWKLNIPPKVKMFAWL FT FIRDRLQTRKRLSHIVINSDKMCPFCNSVDEDQMHLFFNCGVTKLIWDLCS FT IKPGNFTNANFDSAVDWLNSLKHVDKEVPSDLSLCLLLCWQIWNDRNNMVF FT RNVLPIPARSKLLAISMGERYLKANGKGLRRNTDDTSTIVKWHPPDKSFVK FT LNFDGSVAGDKAAAGFVLRNHNGQIIGGGALNLDGATISEVEARALREGLL FT FAQRKGYTKIMVEGDSKLVIQSVLDRGATPWNLVPIIEDIKWTATNFDCID FT WKHIYREANFVADAFARHGLLITDCHIWDHCIPSFALHALQFDSVRNSCTR FT GFFPLIYFSCLQK" FT CDS join(3..1292,1283..1669) FT /product="L1-13_Mad_1p" FT /translation="EXXRRIGXSILVRIXLWPLFLAXICILVKVDRLINGF FT KVNWRTDNCWYLVXFCDLANGSXVNALFNDKCXWAEXIHAIYNPNCSFXSN FT WVVXXISPLANYQWWVLGSGAQRQIIRVATXXGXLRSPHXXLTTSLKLGFW FT ARNDLGANEEFGLAVIQLNGASQSRGCGFLXLNCSIPCKYMGFVAYLMFNK FT FGEHEIEAYVRVHVLCGLSGEQVKMQGAEVVKIFGSDDEGLMQEPDIVKIR FT FNFHWMLKVMVGILVHDQGVSSVNCSSSGXIXSISNLFIFRQNEGRWIVIS FT SINXIDSMFGDDESFIMPCXNNLVCDYKSVNFDFXDVTNDLALYLVVDMSN FT VXSEEAEXRENTRNXVXAFXKAEVGSVSAGPKTGMMSPKKRVCEXDAVKXG FT PSGGDPRATVRMLSPRKRIRXEIAIKEEFSYLEELDRIRLMKCLAWNCRGI FT RRKEFPSNFNFICSLAKLDLFCLMEIKVVVHKVPRNFYSKYFDNIFCCDPI FT GRSGGLCLCWNSTKVFVSIISSSPRYIHCSVKDLVTNLEQLVTFIYAFPQK FT HCSVTCGRRSSS" XX SQ Sequence 5437 BP; 1513 A; 813 C; 1247 G; 1821 T; 43 other; tggagckcwg acggcgcata gggcsgagta tcctggtgcg aattcsgctm tggcccctgt 60 ttctwgctst aatttgcatt ttagttaaag tagataggct aatcaatggg ttcaaagtta 120 attggagaac agataattgc tggtatttag ttsggttttg cgatttagct aatggctcta 180 scgtaaatgc tttgttcaat gataagtgtk ggtgggctga akgtattcat gcaatttaca 240 atccaaattg cagcttcktg tctaactggg ttgtmkttas katttctcct ctagctaatt 300 atcaatggtg ggtcttgggg agtggagccc agaggcaaat matcagggtt gcaacgawtt 360 gsggggkgct gaggagcccc catgwgkctc ttactaccag tttaaaactg ggattttggg 420 cacgcaacga tttgggtgcc aatgaagaat tcgggttggc tgtgattcaa ttaaatggtg 480 cctcacaaag ccgtggttgc gggtttctag akcttaattg ctcaatccct tgcaaatata 540 tggggtttgt agcttatctg atgttcaata aatttgggga acatgagata gaagcctatg 600 tgagagttca tgtgctatgc gggctatctg gggaacaagt aaagatgcag ggcgctgaag 660 tagtgaagat ctttgggagc gatgacgaag gtttgatgca ggaacctgac attgtgaaaa 720 taagattcaa ttttcattgg atgcttaagg taatggtggg gattctsgta catgaccagg 780 gggtaagctc tgtgaattgt agctcmtctg ggwttatawa ttctatctct aatcttttta 840 tctttagaca aaacgagggt agatggatag ttatctctag tattaattwt attgactcta 900 tgtttggtga tgatgagtcc tttatcatgc catgtsacaa taatcttgtt tgtgattata 960 aaagtgttaa ttttgatttc kttgatgtta cgaatgatct tgctttatac ctggttgtwg 1020 atatgtcaaa tgtgaawagt gaggaggctg aawctaggga gaacactaga aacwtggttt 1080 mtgcttttcw taaagcagag gttggctctg tgagtgcagg gcccaaaaca ggaatgatga 1140 gtccaaagaa aagagtwtgt gaggwggatg ctgttaaagm tgggcctagt ggtggtgacc 1200 ctcgtgccac tgttaggatg ctgagtccga gaaagagaat mcgakaggaa attgcaatta 1260 aggaagagtt tagttatctt gaagaattag attgatgaag tgtcttgcat ggaactgtag 1320 gggtattagg agaaaggaat ttcctagtaa ttttaatttt atatgtagtt tagctaaatt 1380 ggaccttttt tgcttgatgg agattaaggt ggttgttcat aaggtcccta ggaactttta 1440 ttccaagtat tttgacaata ttttttgctg tgatccaatt ggccgatctg ggggcctctg 1500 cttatgttgg aatagtacta aggtttttgt tagtataatt tcttcctctc cgagatatat 1560 ccattgttct gtgaaggact tagttactaa tttagagcaa ttagttactt tcatttatgc 1620 ctttccccaa aaacattgca gtgtgacctg tgggaggagg tcctcaagtt agatccaatt 1680 catagtcctt ggtgcttagt tggagatttt aacaatattg ttgatctttc agagaaggtt 1740 ggaggtaatc aaacccatac cacggacatg aacaatttta tcaattttct taatcgtggc 1800 aaccttttgt ctttaaatgc gtctggagtt ccttttactt ggactaattg tcatacggat 1860 catacggttg ttttcgagag attggatagg gtggtggcta accctttatg gttaaatatg 1920 ttccctaatt atcatttgca taactatcct atttttkgtt ctgatcatag tcctatttta 1980 ttatctctaa attctagtga ggagaagaat aactacttct cgtttaaatt tgaggctatg 2040 tggcttaatc atcctcagtt taaaatgttt gtgcaaaatt cttggcattg tgaccctact 2100 attaatccta aagataaatt cagagtgtgt gctggtaagt ttaaatttct agtttgtaaa 2160 tggaacaagg acacttttgg caatttaaag gagaaaaaga aagaattgtt aaatgaaatt 2220 gatgagcttc aaaagcaaat tatgagtaac aactctgttg atttgatgat ggaaaaatct 2280 cttcgagatg aattgaatca tgtgttactt tgtgaagaaa ttatgtgggc ccagagagct 2340 aaaactaatt ggctgcaact tggggataag aatactaaat tctttcaaac tgtggctact 2400 attcgtaaga aaatgaatga aattacaaaa gtcaaagatg agaatggttt ttggtggtct 2460 gttggtcagg gccttgaaca ggtttttgtg cacgatttta aaaagcgctt ttcctgtgac 2520 agtcctccct cgggtgctga cctaagtaat ttagcggata tcattcaacc ttgtgtttct 2580 aatcatcata atgaaagttt gttgtctctt gttacagatg aggaaatttg ggatgctgtg 2640 agtagtattg gagctcttaa agccctgggt cctgatggtt tgagtgtggc cttttttcat 2700 ggttgctggg accaaattag ggactctgtt tcctgtttgg tcaaagattt tttccaaaat 2760 ggttccagct taagactcat aaatcatact aacatcgctt tagttcctaa aatagataat 2820 ccggaaactg ttagtaacta taggcctatt agtttgtgta atgttagtta taaaattatc 2880 acaaagatca tcattaagcg actaaaacct ctgttagatc tttgcatctc tcaaaatcaa 2940 ggtgcttttg ctccgggtag agccattcag gataatattc ttattgctca cgaaatgttt 3000 gctggtttca ataggatgaa aggaagaact ggagctatgg gtgtcaagct ggatctggaa 3060 aaggcatatg attacttaaa ctgggattac attcggtatg ttcttcttag atttggtttt 3120 gataatcgtt gggttgaatt agttatggaa tgtattactt ctccttcctt ctctgtgctt 3180 ataaatgggc gacctcatgg ttatttttat ccgaagcggg gaattagaca aggggacccc 3240 ttgtcccctt atattttcat catttgtatg gaaccgttaa ttagacacct caatacccta 3300 acaaataatc cgaagtctca tattggtatt ttgtcctcac ctagaggatt taaaatctca 3360 aatctagtgt ttgctgatga ctgtctcctg tttgctaagg ccacaccgag gggtgcgagg 3420 aatattcttc aaatccttaa tatgttttct aaagcggcgg gccaacaaat aaactttcat 3480 aagtcgtcct tgtatttttc caagaatacc acttctccaa ctagaattga tattgttaat 3540 attttacata ttcaacataa aactactatt ggtaagtatc taggaattca taatattgtt 3600 ttctggaaag accaagttaa tggtaatgag ttacttaaga gggttaagcg aaaattagct 3660 ggttggaaag caagcactct ttcgagagcg gggaggctta ctttaattaa ctctaatcta 3720 acgggtatgc ctaatcatgt tatgtcttgc tttaagtgtc ctgacaagat tgtcaataag 3780 cttaataaag agtgtaggga ttttttctgg ggtagggaca agaaaatctt cccagtggct 3840 tgggattcgg tctgtgctcc taagaaaatg ggaggtttgg gagttagaag actagatcat 3900 tttaataatg cttgtctcgc taagttgggt tggaaggtaa tgactgagga ggataactgg 3960 tgggtgaagt tagtaaaaag taagtatctt agaaaggaaa attttctaga taataaaatt 4020 agacaaaatc attcttttgc ttggaaaggt atcttgaaaa gtagggatgt tattcttaag 4080 ggtatgagat ggagagtggg taatggtaag gacattttgt tctggtccca caattgggtt 4140 tttccttacc cgttgttcca tctcttaccc aatattgaca accaaaacat taattgggac 4200 ttgaaagtta atgaatttat tgataattat tgttgggata ggagaaagct ttcgcaagtg 4260 gttagtaatg aaattgtgag gaaaatttgt aatattacaa ttcccttgca ggattccaaa 4320 gatgtgctag tttggggtcc aaatacaaat ggtaagttct ctgttaaatc agctacttgg 4380 atccakaaag ggacgttgac tcaatctaca aagcataagt taattaataa gatgtggaaa 4440 cttaatattc ctcctaaagt taagatgttt gcgtggttgt tcattcgtga tagacttcaa 4500 actagaaaaa gattaagtca tattgtaatt aatagtgata agatgtgtcc tttttgtaat 4560 tccgtagacg aggaccaaat gcatttattt tttaattgtg gtgtcactaa attgatttgg 4620 gacctttgtt caattaagcc gggcaatttc actaatgcta acttcgactc ggcagtagac 4680 tggctaaatt ctttaaagca tgttgataag gaagttccta gtgatttgag cttgtgtttg 4740 ctcctttgtt ggcaaatttg gaatgaccgt aataatatgg tgttcagaaa tgttttgccc 4800 atcccggcaa gatctaagtt attggctata tctatgggtg agcgatatct taaagccaat 4860 ggtaaaggtt tgagaagaaa tactgatgat acttccacaa ttgttaaatg gcatccgccg 4920 gataagagtt ttgttaagtt aaattttgat ggttcggtgg ctggggacaa ggcggcggcg 4980 ggatttgtct taaggaatca taatgggcag attattggag gtggagcttt aaatctggat 5040 ggtgccacta tttctgaagt ggaggctagg gctctcagag agggccttct ttttgctcag 5100 aggaagggct atacaaagat tatggttgaa ggtgactcta agttggtcat tcagtcagtg 5160 ttggaccggg gtgcgacgcc atggaatctg gttcctatta ttgaagatat caagtggacg 5220 gcgaccaatt ttgattgcat tgactggaaa catatttata gagaggctaa ctttgtggcg 5280 gatgccttcg ctcgccatgg ccttcttatt actgattgtc atatttggga tcattgtatt 5340 ccttcatttg ctcttcatgc tcttcagttt gattctgtaa ggaacagttg tactcgtggg 5400 tttttccctt taatatattt ttcttgttta caaaaaa 5437 // ID Copia12-PTR_LTR repbase; DNA; EDCOT; 233 BP. XX AC LG_III; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia12-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-233 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-233 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 197-197 (2007). XX DR Genome; LG_III; Positions 6461637 6461869. XX SQ Sequence 233 BP; 75 A; 46 C; 39 G; 73 T; 0 other; tgttagcgtg agccattaga agttacaagg aaataaaaca ccagttgtat caacttccta 60 gttgcagttg tatatatcga ctccctagtt ttcaggcttc aatctaggag aggctgttat 120 gtaaaagtag attagttaaa acacatctct aaactccttc ccctgtatct ctatatatat 180 accgtgagtc aattaataaa gcaagttagt ctgcttctcc agaaaatctg aca 233 // ID SHACOP21_LTR_MT repbase; DNA; EDCOT; 232 BP. XX AC AC161106; XX DT 29-JAN-2007 (Rel. 12.01, Created) DT 29-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE LTR of LTR retroposon, SHACOP21_MT, from Medicago truncatula. XX KW Copia; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW terminal; Interspersed; repeat; SHACOP21_LTR_MT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-232 RA Shankar R. and Jurka J.; RT "SHACOP21_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 68-68 (2007). XX DR EMBL/GenBank/DDBJ; AC161106; Positions 34921 35152. XX SQ Sequence 232 BP; 70 A; 42 C; 27 G; 93 T; 0 other; tgttaaatga taatttgtaa ttttccatat tcctaggttc cttaatgtat cagtaagttc 60 cagagaatgt catttaatat tcctaggtgc attcacttat ttactagaac tttctatgta 120 tcaatataac tagaggttct atgtattgac aaggcactac aatgaaaaga aacattactt 180 tcaatctata actttcacgt tttctgttcc ttttattcct ctttctccaa ca 232 // ID TNT1_LTR repbase; DNA; EDCOT; 610 BP. XX AC X13777; XX DT 12-SEP-2002 (Rel. 7.08, Created) DT 09-APR-2007 (Rel. 12.05, Last updated, Version 2) XX DE Nicotiana tabacum retrotransposon TNT1_LTR, long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Long terminal repeat; retrotransposon; TNT1_LTR. XX NM TNT1_LTR. XX OS Nicotiana tabacum OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; OC Nicotianeae; Nicotiana. XX RN [1] RA Grandbastien A.M., Spielmann A. and Caboche M.; RT "Tnt1, a mobile retroviral-like transposable element of tobacco RT isolated by plant cell genetics."; RL Nature 337(6205), 376-380 (1989). XX RN [2] RA Casacuberta M.J. and Grandbastien A.M.; RT "Characterization of LTR sequences involved in the protoplast RT specific expression of the tobacco Tnt1 retrotransposon."; RL Nucleic Acids Res 21(9), 2087-2093 (1993). XX RN [3] RA Vernhettes S., Grandbastien A.M. and Casacuberta M.J.; RT "The evolutionary analysis of the Tnt1 retrotransposon in RT Nicotiana species reveals the high variability of its regulatory RT sequences."; RL Mol. Biol. Evol 15(7), 827-836 (1998). XX RN [4] RA Melayah D., Bonnivard E., Chalhoub B., Audeon C. RA and Grandbastien A.M.; RT "The mobility of the tobacco Tnt1 retrotransposon correlates with RT its transcriptional activation by fungal factors."; RL Plant J 28(2), 159-168 (2001). XX DR Genbank; X13777; Positions 1 610. XX SQ Sequence 610 BP; 163 A; 89 C; 140 G; 218 T; 0 other; tgatgatgtc catctcattg aagaagtatt aggcatgtgc ctaataagag ttttctttgg 60 tttggtagcc aaccttgttg acttggtttg gttggtagcc aaccttgttg aatccttgtt 120 ggattggtag ccaactttgt tgaattgtga aaaatgtgtg taaattgtca aatattgtag 180 gctttagagg gtgaagcttt ggctataaaa ggagagcttc aactctcatt tcttcacacc 240 aacaaagaga gaaagaaaga gtgaggtttc acagacaagg tataagaaaa tagtctgtga 300 ggaaaataga gagtgagcga tattgtagtg aggtgggaat atcaaaagag ggttatttct 360 tttgagtgtt gtagtggtct ttggagtatt tacctccgac ctacaaagtg taaaattcct 420 tactatagtg atatcagttg ctcctctcgg ggtcgtggtt ttttttccct tattcagaag 480 ggttttccac gtaaaaatct tggtgtcatt gttactcttt tattcttgtt aattaccgta 540 tctcggtgct acattattat tccgctttat taccgtgaat attattttgg taaggggttt 600 attcccaaca 610 // ID Gypsy-32_Mad-LTR repbase; DNA; EDCOT; 366 BP. XX AC . XX DT 08-OCT-2010 (Rel. 15.1, Created) DT 08-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW Gypsy-32_Mad-LTR. XX NM Gypsy-32_Mad-LTR. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-366 RA Bao W. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1759-1759 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX SQ Sequence 366 BP; 100 A; 90 C; 70 G; 106 T; 0 other; tgtttgtacc atacttaggg cctccgtatt tagatctcgt ataaatactc gggggactca 60 aatgtaatta tgtaataaat gaaggggcaa atatgtaata agtgaggagc ccttattcta 120 taaaaggacc cctcactctc ctcattaagg gaggccaatt cttaggcctg actctcaccc 180 tcagaagcct cactctcaca ttcagaggct ctctccctca caatcctctc agagaaatac 240 aatatcagtg tggacgtagc ccaaacattg gggtgaacca cgatacatct tgtgttattt 300 actttcttgc agattcacgg tcggatttac gttgttccaa gacccctccg gttttgtgca 360 tcaaca 366 // ID TOTO1_LP_I repbase; DNA; EDCOT; 3529 BP. XX AC AF220602; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 09-APR-2007 (Rel. 9.07, Last updated, Version 3) XX DE Lycopersicon pimpinellifolium retrotransposon TOTO1_LP_I, DE internal region. XX KW Copia; LTR Retrotransposon; Transposable Element; internal region; KW TOTO1_LP_I; internal portion. XX NM TOTO1_LP_I. XX OS Solanum pimpinellifolium OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; OC Solanum; Lycopersicon. XX RN [1] RP 1-3529 RA Lavelle T.D., Oldroyd E.G., Dalhbeck D., Staskawicz J.B. RA and Michelmore W.R.; RT "Direct submission."; RL Direct Submission to Genbank (04-JAN-2000). XX DR Genbank; AF220602; Positions 37858 41386. XX SQ Sequence 3529 BP; 979 A; 513 C; 868 G; 1169 T; 0 other; gtggtatcag agcattggtt attgttgatt gtcgttttga atgatggagg caaatatgag 60 caaaatggtg tgtttaaatg gtagtaacta tcatatttgg aaaggcaaga tgaaagatct 120 tctatttgtc aagaagatgc atttacctgt gtttgcttct aataagtctc agtctttgaa 180 tgatgaagaa tgggaatttg agcatctgca ggtttgtggc tatattagac aatgggttga 240 aggtaatgtt agaaatcata ttgtgaatga gacacatgcc aaaagtttgt gggacaagct 300 cgagacactt tatgtttcga agagtggcaa caacaagttg ttcctattga aacaattaat 360 gaatatcatg tataaagagg gcactcctat ttgtgatcat attaatgatt ttcagggtgt 420 tcttgaccag ctgtccgaaa tgggtgtaaa gcctttgtac atgttcctaa ggatgaaagg 480 tcaaagttgg atgttaaaac taggcagtgt atcttcattg gttatggtca agatgaattt 540 ggctatcgtt tctatgatcc tgttgagaag aaacttgtta gaagccgtga tgttgtgttt 600 tttgaagacc aaacaattga agattttgac aaagctgaca aggctgattt tcagagtagt 660 gagagcttag ttgatgttga tccagttcct ttgactattg caccggaaga aaatcttcat 720 aatgatgaaa atcaagttga taatgaagat ggtgatcatg ttcagaatga ccggcatgat 780 gttgttgatg ctccagtgca agatgatgtg gttgtccaac aaccaattat agatgctcca 840 gagagttctc tcagacgatc tagtagagag agaattcctt catctcgtta ttctcccaat 900 gagtatgtac tcttgactga tgggggagaa cctgagagtc ttgatgaggc catggaaagt 960 gaagaaaaag aaaggtggtt tgatgctatg gaagatgaga ttaaatcctt gcatgataat 1020 catacctttg atttggttaa gttacctaaa gacagaaaag ctttgaaaaa caggtgggtt 1080 tttcgggtga aacatgaaga tggtaatcca gttccacggt acaaagctag attagttgtc 1140 aagggattta atcagaaaag gggagttgat tttgatgaga tattatctcc agttatgaag 1200 atgtcatcca ttcgtgtggt tctaggcttg gctgcaagtc tagatttaga ggttgagcaa 1260 atggatgtta aactgctttc ctccatggtg acttcgatga agaaatttat atggagcaac 1320 cggaaggttt tgaagtcaag ggtaaagaga attatgtttg caaattgaag aagagcttgt 1380 atggtttgaa acaagctccc aggcagtggt acaggaagtt tggttctttt atgagtcagc 1440 agggcttcaa aaagacttct tcagaccatt gtgtttttgt gcaaaaattc tctgatggtg 1500 actttattat tgtgttgctt tatgttgatg acatgcttgt tgttggtcat aatacttgca 1560 ggattcggaa gttgaagcaa gagttgagta agtcttttgc tatgaaagac ttaggaccag 1620 caaggcagat tcttggcatg cagattgtcc gtgatagaaa ggccaagaaa ttggtattat 1680 cacaagagaa gtacattcag aaagtacttc gcagattcag catggacaaa gctaaggttg 1740 tcagtacacc tttagctatg cacttcaaat tgagcacgaa acagtgtcct tctagtgatg 1800 atgagaagga agatatgaag aaagttcctt atgcttcagc tgttggtagt ttgatgtatg 1860 cgatggtttg tacaagaccg gatattgctc acgctgttgg agttgttagc cgttttcttt 1920 ctaatccggg aagagaacat tggaatgctg tgaagtgggt tatgagatat ctctgtggca 1980 cttctagtct gagtttgtgt tttggtacag ggaagcctat tctttgtggt tatactgatt 2040 cagacatggc tggtgatgtt gatactcgca agtctacttc agggtacttg gttacttttg 2100 cagggggagc tgtgtcttgg caatctaggt tgcaaaaatg tgttgctcta tctactacag 2160 aagctgagct tattgctgtc gttgaagctt gtaaagaatt gctttggatg aagagattct 2220 tgggggaact tggttgtgct caagagaggt atgtgcttta ttgtgacagt caaagtgcta 2280 tacatcttgg caagaattct acgttccatg gtcagtctaa acacattgat gtgagatacc 2340 attggattcg agatgtgttg gattctaagt tgcttgagct tggaaagatt catacaaatg 2400 ataatggttc tgatatgatg actaaagctt tgccaagagg gaagtttgaa gattgttgca 2460 tggtcgccgg gatggcggtc tcctccacat agtcgtgagg gggagaattg ttgggttatg 2520 ggtctttttc ccttcttatg tggataaata aaagcccaat ttggaccaac ccattttttg 2580 cccataggcc cattcttatg aggcaaatat aagcctattt aggtcttatt ttcaaataca 2640 cagagagttt ttcaacaacc aaaaaaagag agagagagca attttcgcag tcaaaattca 2700 gccctaacag ccaacttcaa attgcgattc gcgcttcatt tcttgtctga ttgagctgat 2760 ttttggacag catattatct tcatctcaat atttgattag gaactaacag agttggattt 2820 ggtggcctgc agcttcagtt ttgctgtcgt aaacaatagc tgcgaaattg gtgattttgc 2880 tcctttaatt ctctagattt ggtgcaatct tattttgttg ttgctcgttg tttggcactt 2940 gtttgtggcc aattttggag aacaatattg aaacacttgg tgattatagt ggagcttttg 3000 gtcccgtggt tttttactct tcacatcgaa gggttttcca cgtaaatctt ggtgtcttgt 3060 gtgattggtt tattattctc ttgttatatt tgtttgattg aattaattgc tgccttacta 3120 ttatattgct tgtggttgtt tgtcttctct tggttcaaat cgagaaggga aagtatagac 3180 ttgggtattc ttccgctgtt atcctgtcag gcgttctttg ttagtgcctt gtctttccca 3240 acaaagtggt atcagagcca gattcaatga tgaagtcagg ttttatggtt cgataaacga 3300 tgattgaacc aggttagaaa gaggtgttca tcttgacgga tgcagttcta gccgcaacct 3360 ttttgacagt attgaagatt ttgtttgaga aattgtttca gagaggttct ctgtgttgag 3420 acatagattt tgcaaaggag attatggaga ggagaagcaa gttgttgaag attaaatgaa 3480 gaaggtggac aaatttattt tgttagaaat tcaagccaag ggggagatt 3529 // ID RAHAT repbase; DNA; EDCOT; 3506 BP. XX AC AC135103; XX DT 15-DEC-2006 (Rel. 11.12, Created) DT 05-JAN-2007 (Rel. 11.12, Last updated, Version 1) XX DE A putative DNA transposon from Medicago truncatula. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; RAHAT. XX OS Medicago truncatula OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; OC Medicago. XX RN [1] RP 1-3506 RA Shankar R. and Jurka J.; RT "RAHAT: A hAT like putative novel DNA transposon from barrel RT medic."; RL Repbase Reports 6(12), 638-638 (2006). XX DR EMBL/GenBank/DDBJ; AC135103; Positions 50082 53587. XX CC The sequence is present in multiple copies. It looks close to HAT CC transposon. Contains hAT dimerization domain and transposase. XX FH Key Location/Qualifiers FT CDS 889..3354 FT /product="RAHAT_1p" FT /translation="MKFQRIDSIFKRKAVDIQKDEVIISSSEPEQVHENPR FT IEENESRPSKINRVDPDDIENSLERDPGKCIPIYQYPPNQKDAIRRAYLKW FT GPYQSNLENYPMSGIGKAQRRFQNSWFSLFSSWLEYSPSEDAAYCLQCYLF FT SNKPSGRLGSEVFISTGFRSWRKVRNGENCSFLKHIGKDPRSPHNNAMKAC FT QDFLNQDGHLRNVIEVQSSSQILNNRLCLKTSIDTVRWLTIQACAFRGHRE FT GNKSRNQGNFLELLKLLASYNDEVAKVVLKNAPEKCNYTSHQIQKEILQIL FT SSRVRKHIREEIGDSKFCIVVDEARDESKKKQMALVLRFVDKAGLIQERFF FT DVARVNDTASLTLKEAVCGILSRHNLDVSNIRGQGYDGASNMRGEWNGLQA FT LFMKDCPYAYYVHCFAHRLQLALVTASREVASIHKFFEKLTFVVNVVGSST FT KRHDELQAAQAKEIENLLETGEIVTGKGKNQVGTVKRDGDTRWGSHFNSIC FT SLISMYEATCTVLKIIAKDAKKFAQRADADSSYNHLKSFDFIFILHLMKEI FT MGTTDLLCQALQKQSQDVVNAVILVRSTKALIQDLRENGWDKLFANVVSFC FT EKHDIEVPDLNDCHSTTRFGRSRLEENQVTIEHYFRVEFLFTTIDKQLQEL FT NSRFSEQAMDLLTLSCALSPEDGYKAFDINTICTLVEKYYPMDFSDQEKIN FT LPFHLKHFLFEARESSTLKNLSTIQELCSCLAAAVPANGQPKKHLLLDRLL FT RLVMTLPVSTATTERSFSAMKIIKSKLRNKMEHGFLANSMSVYIERDISEC FT ISSESIIDDFKSLRKRKVRL" XX SQ Sequence 3506 BP; 1033 A; 624 C; 671 G; 1178 T; 0 other; cagtggcgga tccagggggt ggcaaggggg agccacagcc accccatttt ttttgtgaaa 60 ttacgaagat gcccttgctt attaataata ttttccaact gatatttcat ttggtcagca 120 tatttttctc tcttcagaac aaaaaaacgt gacttctctt gttcagaaca aacacacgcg 180 acttctcttc ttcttctcca aattccatcg ctgatcactc catccaattc caaactcttc 240 ttcttccgcg gccgccactg ctccagtcgc aaccgccgct gcaaccgcct ccttctcgcc 300 actgcgtcac tgcgaccacc ttcttctcca aattccaatc gctgatcact ccatccaaac 360 tcttcttctt ccgcggccgc cactgctcga atcgcaaccg ccgctgcaac cacctccttc 420 tccaatctcc atgactccat ccatcttctc tgttgtctaa agtctccaca aaccctaatt 480 cttgtaaatt gcaaggtaat aagaaattga atctattttc cttcaaatat gattattctc 540 tgatgattac atgttcttga atgctcttta actgcttgtt ggttttgaaa aagtatagct 600 ttttgttgat tttatttaag ttatctgtta gttgtgataa cttgttctat attttcgttg 660 gttttaatca cttttagtta cctctgattg ttcaatttat tggttttttc aagtgttggt 720 tcactttgag ttcaattatc aattttagag actctgttag ttgtgattct gttaaaatag 780 actttggaat attatgttcc cttaatccct ttgatctgtt tcaaactatt gttgattgta 840 atcttattgt tggtttgatt cttgctgtta acaggtggaa aagttaagat gaagtttcaa 900 agaatcgatt ctattttcaa gaggaaggcc gttgatattc aaaaagatga agttataatt 960 tcttcatccg aacctgaaca agttcatgag aatccaagaa tcgaagaaaa tgagtcccgt 1020 ccttcaaaga ttaatagagt tgatccggat gacattgaaa attctttaga aagggatcca 1080 ggaaaatgta ttccaattta ccaatatcca ccaaatcaaa aggatgcaat acgaagagcc 1140 tatctaaaat ggggtcctta tcaatcaaac ttagaaaact atcccatgtc cggtatcggg 1200 aaagcacaaa ggaggtttca aaacagttgg tttagcttgt tttcttcgtg gctagaatat 1260 tcgccgtcgg aagatgctgc ctattgctta caatgttatc tatttagcaa caaaccaagt 1320 ggacgtctcg gatcagaagt attcatttct actggcttta gaagttggag gaaagttagg 1380 aatggagaga attgttcctt tcttaaacat atagggaagg atcctcgctc accacacaac 1440 aatgcaatga aagcttgcca agacttcttg aatcaagatg ggcatcttag gaatgttatt 1500 gaagtgcaaa gttcgagtca aattctgaat aatcgactat gtctcaagac ttcaattgac 1560 actgttcgtt ggttaacaat tcaagcttgt gcttttaggg gtcaccgtga aggaaacaaa 1620 tcgagaaatc aaggtaattt tcttgaattg ttaaaacttt tagcatccta caatgatgaa 1680 gttgcaaaag ttgtgttgaa aaatgctcca gaaaaatgca attatacttc acatcaaatc 1740 caaaaagaga tattgcaaat tctttctagt agggtgagaa aacatattcg tgaagaaatt 1800 ggtgattcta aattttgtat cgtcgttgat gaagctcgtg atgagtcaaa aaagaaacaa 1860 atggctcttg tgttaaggtt tgttgataaa gctggtttga tacaagagag attttttgat 1920 gtggcacgtg ttaatgacac tgcttcctta actcttaagg aagcagtatg tggtatactt 1980 tctcgacata accttgatgt ttctaacatt cgtggtcaag ggtatgacgg tgctagcaat 2040 atgagaggag aatggaatgg tttacaagca ctttttatga aagattgtcc ttatgcttac 2100 tatgtccact gttttgctca tcggttgcaa cttgctttag ttactgcatc aagagaagtt 2160 gcatcaattc ataaattctt tgagaagctg acttttgttg tcaatgttgt tggttcttct 2220 actaagcgcc atgatgagtt acaagctgcc caagcaaaag aaatcgaaaa tttgttagag 2280 actggggaga ttgtaactgg taaaggtaaa aaccaagttg gaactgtgaa aagagatgga 2340 gatactcgtt ggggatcaca tttcaactct atttgtagct tgataagtat gtatgaagca 2400 acttgtacag ttttgaaaat cattgcaaaa gatgcaaaaa aatttgccca acgtgcggat 2460 gctgatagtt cttacaatca cctaaagtct tttgatttta tatttatctt gcatttgatg 2520 aaagaaatta tggggacaac agatttgctt tgtcaagcct tgcaaaaaca atctcaggat 2580 gttgttaacg ctgtaatttt ggttcgttca acaaaagctc ttattcaaga tttgagagaa 2640 aatggttggg ataagttgtt tgccaatgtc gtgtcttttt gtgaaaaaca tgatattgag 2700 gttcctgacc tcaatgattg tcattcaaca acaagatttg ggcgttctcg ccttgaagag 2760 aatcaggtaa caatagaaca ttatttcaga gttgaatttc tttttactac cattgacaaa 2820 caattgcaag agttgaatag cagatttagt gagcaagcaa tggatttgtt gactttaagt 2880 tgtgctttgt ctccggagga tggatataaa gcttttgaca ttaacactat atgtactctt 2940 gttgaaaaat attatcccat ggattttagt gaccaggaga agattaattt gccatttcat 3000 cttaaacatt tcctttttga ggctcgtgaa tcatcaactt tgaaaaattt atcaactatt 3060 caagaattat gctcatgttt ggctgctgcc gttcctgcca atggacaacc caaaaaacac 3120 ttgttgcttg ataggttgtt gcgtcttgtt atgactcttc cggtttctac agccacaact 3180 gaaagatctt tttcagcaat gaaaattatc aaatctaagt tgagaaacaa gatggaacat 3240 gggtttttag caaatagcat gtcagtttac atcgaaaggg atattagtga gtgtattagt 3300 tctgaatcaa ttattgatga tttcaagtca ctccgaaagc gtaaagtgcg tctttaggta 3360 tgtaatgatc gactttatat attatgtagt ttaaattttg aatgattggt ttttggttta 3420 ttttaatgat ttatatatta tattttagtt tattttgatg gcgggatgac ggccacccca 3480 aacatttttg tctggctccg ccactg 3506 // ID MuDR-9_VV repbase; DNA; EDCOT; 10453 BP. XX AC . XX DT 11-JUL-2008 (Rel. 13.07, Created) DT 11-JUL-2008 (Rel. 13.07, Last updated, Version 1) XX DE MuDR-9_VV, an autonomous DNA transposon - a consensus sequence. XX KW MuDR; DNA transposon; Transposable Element; mutator; TIR; KW Mutavine-9; MuDR-9_VV. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-10453 RA Benjak A., Forneck A. and Casacuberta J.M.; RT "Genome-wide analysis of the cut-and-paste transposons of RT grapevine. PlosONE: submitted."; RL Repbase Reports 8(7), 769-769 (2008). XX DR [1] (Consensus) XX CC MuDR-9_VV (Mutavine-9 in [1]) consensus is an autonomous element. CC Its individual copies are >90% identical to the consensus CC sequence. MuDR-9_VV contains 78 bp-long TIRs which are 80% CC identical. XX FH Key Location/Qualifiers FT CDS join(1634..1887,1977..3141,3247..3864) FT /product="MuDR-9_VV_Transposase" FT /note="MUDRA transposase." FT /translation="MYIGQGMSYADFVSKACERLDINSNGYTFHYTLEFDP FT SALQQLDDDEDMHMMLSHSYDYARIYVLKRTRRVEVEGGIVNVQNDYCHNS FT TEETHNSVASCQANNESNLGLSQGFMSRCAETEVRPHDLSLCPQPIIGSGH FT SFPNADEFRNALYTMSLVGRFQYKFKKNSPKRISVCCLVDGCPWRITANSV FT GTTKILKVNIFIDVHNHCADVECSSQPSMRGRRGARVIEQVIRATPQYLPR FT QICKDFRSRYGVSLSYKQAWTYKEMAKERIYGLPENSYMLLPWLCQRLVDI FT NPGTIAECTRQDGHFWQLFIAHSFSIQGFLMGCRPVIAIDSTHLSGPYRGS FT LFSATTYDADDGMFPIAFGVVSSENYEDWLWFLQKLKGILQDKEVVIISDR FT HQAILRSVSQLFGVENHAYCYRHVKENFSSYVTKHSMKGKKCKMDALLLLD FT SVAYARLDDDYVVAMEKLKTYNSDLAKWEERHYTIFNLVMTHMDKFAHLAC FT DHMGTTENWKAPIGPKTEEKLLENIIKSGSFPVYPYVGGVFKVFNMKVYVD FT VNLRERTCTCKAWQMVGIPCEHACAAIRQMKQDVYEYVDSYFKLPMQELIY FT SGHFNSIPNHNMPTVDADGCVRDAQGRLYPSLKPPCSKRPPGRPRHRRIES FT QFSSKRLTFCSRCQVAGHNRASCKNPLPVP" XX SQ Sequence 10453 BP; 3717 A; 1551 C; 1624 G; 3534 T; 27 other; gggagaatta cccttaaggg taggctgggg aaagatatga ctgatgaggg taggtaaagt 60 tgataattat tgtaaagggt agggtaaaat tatgataatt cctccaaagg ccttattttg 120 tttaaatgac aatactaccc ttaataagtg aaaagcaaca gcaaagtgaa aagcaacaga 180 aaataaaaaa gagttttctt caacctacct ggagtttgtc ggtgttgtag aagaaaaaag 240 ggaaaggaaa aaggtccagc acttcaggtc attatctgca actgtttaca caaaacttgt 300 ttttttttgt gtgaatctag caagaaatcc attaaaggtc ggtttttttt tttaatacaa 360 aaaaaaccgt cagtttatgg aaaaataaat aaataattta aaaatcagat tgaatgaagg 420 aaaagttaat aattttaaca atgtagctgt aagatattag atctgaaata ttgaatgagg 480 ttttgagaaa gaaattacat tttttttaaa tgttatttaa atttattatt ttgaattttt 540 tttatattat tttggtcata ttgaagatgt gtttttattt ttaatttatt ttatgggtgg 600 gttgtttgac atgattatta ttgatttcca ttgaaaaggt ttgcacttta gttttgttgt 660 taagactttt tgacatgatt gaagaaaaaa tgttctcagt tgtttcatgc ttgtttggga 720 ccactttgtt tatgtattta tgaagatatt tggattgtca ttgaaaactg aaatcccctt 780 tgtacgagac cactttgtct tttattatga atttgttaaa gagttaagat cactatattt 840 twtwtawaaa tttgttacct ttttgtataa gtattatttt ggtatgatga gtcgaatgcc 900 tartartttg aaggttgtgt aaaagaacca ttayttcagt tataaagtat aagtataata 960 caaatgcaat atagttacaa tgaaaaaaca ttaacattac gatacattac aatataccaa 1020 aatgacaaaa tattgaatta ttttttactg aactagcatt tctaggctat catgttgtat 1080 tcctatcata aagcatcatt gcaaaccaaa atgataaaaa gataacaaaa atacactatt 1140 gtaatttcaa tatatgaagt tgttgatgat aatccaatga tggataaaaa aaaacgataa 1200 aattaatttt ttttatataa aaatatagag gtataataaa aatacactat aattacaata 1260 caaatacaat aacattacga tacattacga taaggtaaag ttttgaaaat ttcaaatttc 1320 ttatgaaact gggcaattgt gggttctttg gcatatccct aacatgtcta atatacaaca 1380 aatattgtta tttattatat aaaatatgtc tcaatttatt ataattttca tttttttatt 1440 ttgtatttgt tgaaaatttt ccttaattgt aatattgtga aatagattga tttgattgtc 1500 ggtgaaagaa gatgtacttc taaattggta aatggacttg gaaaattcca tttatggtta 1560 ccttcatgaa ggagtggaga ttgtacctaa ggaggataaa taaatacaat acaagggtga 1620 gcaacaaaaa aacatgtaca ttggacaagg gatgtcatat gctgattttg tttcaaaggc 1680 atgtgaacgg ttggatatta attcaaatgg atatacattt cattacaccc ttgagtttga 1740 tccatctgca cttcaacagt tggatgatga tgaggacatg catatgatgt tatcccatag 1800 ttatgattat gctcgtattt atgtattaaa acggactcga agagtagaag ttgaaggagg 1860 tatagtcaat gtgcaaaatg attattggta agtgatatat cttgtattag ttgtcattaa 1920 ttccatgatg caaggtgctt ataatattaa ttaactgagt gtgctataaa atgcagtcat 1980 aatagtacgg aggagacaca caattcagtt gcatcatgtc aagcaaacaa tgagtctaat 2040 ttaggacttt ctcaaggctt catgtccaga tgtgcagaaa ctgaagttag gccacatgat 2100 ttaagtcttt gtcctcaacc tattattggg agtgggcata gttttcctaa tgcagatgaa 2160 tttagaaatg cattatatac gatgtcatta gttggtagat ttcaatacaa attcaaaaag 2220 aactctccaa agcgaatatc tgtgtgttgt ttagtggatg ggtgcccttg gagaataact 2280 gctaattcag taggcacaac caaaattttg aaggttaaca tcttcattga tgtacacaat 2340 cattgtgcag atgttgagtg ttcaagccaa ccttcaatgc ggggaaggag aggtgctcgt 2400 gtcatagagc aagtaataag ggcaacccct cagtatttgc cccgtcaaat ttgcaaagat 2460 ttcaggagtc ggtatggtgt ttcattgagt tataagcaag cttggacata caaagaaatg 2520 gcaaaagaga gaatatatgg tcttccagaa aactcatata tgttgttgcc atggttatgt 2580 cagagattgg tagacattaa tccagggacg attgctgaat gtaccagaca agatgggcat 2640 ttttggcaat tgttcattgc acattctttt tcaattcaag ggtttttaat gggttgtcga 2700 cctgttattg caattgactc aactcatttg agtggaccgt ataggggctc cttattttct 2760 gcaacaactt atgatgctga tgatggcatg ttcccaattg catttggtgt tgtaagttca 2820 gaaaactatg aggattggct atggtttttg cagaaattga agggcatact tcaagataaa 2880 gaggtagtca taatatcaga taggcatcaa gcaatccttc gtagtgtttc tcaacttttt 2940 ggagtagaaa atcatgcata ttgctatcgt catgtgaaag agaattttag tagctatgtg 3000 acgaaacata gtatgaaggg aaaaaaatgt aaaatggatg cattgttgct acttgatagt 3060 gttgcgtatg ctaggttgga tgatgattat gttgtagcca tggaaaaatt aaagacatat 3120 aacagtgacc tagcgaagtg ggttgaagag aacagtccac aacattgggc aatgtcaaag 3180 tttgccaaaa aacgatggga taagatgaca actaatcttg ctgaatcatt caatgcttgg 3240 ctgaaggagg aacgtcatta cacaattttc aacttagtaa tgacacatat ggataagttt 3300 gctcatctag catgtgatca tatgggtact acagaaaatt ggaaagctcc aattggccca 3360 aagaccgagg aaaagttgtt ggaaaacatt ataaagagtg ggtcatttcc tgtatatccc 3420 tatgttggtg gtgtgtttaa ggtattcaat atgaaagtat atgtagacgt gaatttgaga 3480 gagcgtacat gtacttgtaa ggcttggcaa atggtcggaa taccttgtga gcatgcatgt 3540 gcagcaatac gccagatgaa acaagatgtt tatgaatatg ttgactcata tttcaagctt 3600 ccaatgcaag agttgatata ttctggacac ttcaattcaa ttccaaatca caatatgcct 3660 acagttgatg ctgatggatg tgttcgtgat gctcaaggtc gcttatatcc ttcacttaaa 3720 cctccatgct caaaacgacc acctggaagg cctcgacacc gtcgaataga gtctcaattt 3780 agttcaaaaa ggcttacctt ctgttcacga tgtcaagttg caggccataa tcgagcttca 3840 tgcaaaaatc cattacccgt tccatgattt tagtgttatg cttgtatggt ggcatgctac 3900 tttttatctt attttgattg tgatgatatg tgtggtttat gaaattagaa tttgtaagaa 3960 tttgttttgg aamttactta tttacttgat tgtcatgaca aagatgtttg tattacatat 4020 gtcacttagt tagacttatg atcttatcat tatttaaggt ggtttgtaac catgttttta 4080 tttttattaa ctttgtacat gttcrttaca tttgtttaac ttttttttcc attgaaatac 4140 aggttatatc atgacatctt caagtgcttc atttagaaat acaagaggta atactagaaa 4200 caatgaatat ctactttatc ataactgaat gtgtaaatgt tcaccaagac agagggcaat 4260 tgttagaatt tccgaatcaa aggataaccc aaataggtta tattattgtt gtcaatatgc 4320 aaatactaga gatgactatc atttctttaa atgggcattc cccgaaagat ttggtgataa 4380 caacacctac caagaactag aaaaggttgt tcaaagaaga atgtatggag tggatgaaga 4440 ttttaaacat atttgaacaa gaattgagtt catgcagaaa gtaattttag taggactact 4500 tttatttttt gttctatgtt tgaaaattgt ttaatcatac acttacttca tgtctattat 4560 gttttggatt atacatgtaa tgcttaattt tattgtactg tgatctattt gtatttgkag 4620 ttatttgtaa taggttaatt atctccatca tgtggatttg tgttagattt ttaattgtaa 4680 tagttcacag ttttcactac atttttatta catttacaac ataaattcrc taacattatc 4740 ttaaaaaaca ctaatcatat gataaattac aacataaact aacaatgcga tattttgact 4800 aaataaagtc caatttgttg ggttgattac caatttctta tatataatgg ttcaacaaat 4860 gtgaagctac ttaaaagcaa cagagaaaag ttgattgaaa agtttggtcg ccatattcac 4920 ctgttttttg aaagatttat gtttgtaatt tttcacgacg attggtataa tgtctttcaa 4980 aggcaaatac caagacataa tactgaagga aaatcatatc cttcttacca agtatgtctt 5040 aaaataattt tttttgtaac ctcaaattag aaatgtcttt ttagctttga taatgagctt 5100 ttgtattttt tttttttaaa ttgcaacgat ytgaaaatat tatagaatag agtatttata 5160 aacttatttt tgtgtagaaa taaattatac aaatatgtca aattaaaatt ttattttatt 5220 aaattaaaat ctatttatta ttttttctat ttttttctaa tttttttttg gttcaaatga 5280 actcaaaatg gtagctttta ccatgtcaag gttgaaatgt taggaaggta tatgacgatg 5340 gtaaaatagg caatcatcat tttccacttg caaaaaaaat cataaaatag gcaatggtca 5400 tttcaatatc tatatcattc atcagactag taaatttgga attagaactc cattagactg 5460 taaaaaaaat caactactat aaaccaacaa aagaacaaaa aaaataagaa aatcataata 5520 gaacttccat ttccaaacta ttgcttgtat gaactattat ccacctgcca accataattt 5580 caaaatgtga cttcatcatg cttacaatgt tatagaccaa acaaactcct agaatgactt 5640 ttctcaactt atataatctt aaataaatct tatttcagaa acaacatagc ctaattatct 5700 aatgaaacaa catcactcat ccatagattg gtagacattt tccttgactt cattttctgg 5760 agacattatc agttgtgtta ggagtttttc cctgtacttt atgaccttgt cttatacaaa 5820 agagtatata atagaatatt aacgaaaatt cacgaacata aaaaataaaa aatattttat 5880 tcaacacaat ataatacatt tgcaattgta gaaaaaatcc atcgttactc cataattgca 5940 taaacttgat tacaaatatg ccacaatcca tcctgtaaat agtaattaag gaaattataa 6000 gtaaattgtg catcaaatta gtaaatttat aacctcattt tctttccata gttaaagagg 6060 aatacaaatc ttgcaactta cggattcaat tgttggacaa cttcgggaac aacgaattca 6120 aattctatca tgtccattga tggtcttttt tcttgaatcc taatgacagt tgacaaaacg 6180 ttcaccttaa cacaatataa aattataaat atgaacatct ttaaaaaata atgacaacaa 6240 ttcacataag taattagact ataactatat ttaccagttt ctcagtgaag rcatycatcc 6300 gctttttcct tccgtcaatt aatgaatcca acaactcgat tctttttgca tgaatattca 6360 aaatgtttaa gtaccaatga tttttcttgc atattggtat gaacaactaa aatgaacaaa 6420 aaaagaaaaa aacaatgatt ttatcaaatt agttgtgttc atgtattttc tacacaatac 6480 ttaaaaatat ccaactacaa atgactttca ttaaactaaa taaaacccgt tcatatgtgt 6540 gcaaccgagt attttttaaa tatttccata aattgtcaca tatgtatttt ggagataatg 6600 tacccctctt cttttccaca tcagactgta ataaaaaaaa aatacaaaac atacattaga 6660 gtaaaacaat ctacgtaaaa caagaaaacc aatctataat tcttacaata tatcttaccg 6720 caaagtttgg agataagaga tgcttcctat tttctttatt cataccattc aaaattcaac 6780 aatgcatggt tacaaccttc atgtaaatta atgaaaatta gatatatagt tttagattaa 6840 ttttacccta acttcacata actaaatatg aataccttat tgtcaaccaa tttgtcgggt 6900 cccgagcatt tgaagtcaaa ccttgtcaag aagaaatcgt acatggaaca taatatttgg 6960 ctacacatta ataattaaga tgttagaaat taaaactaat tatttcaaat ggctatttta 7020 attgtatttg tttatactaa attaagttta accttacctt tcatcacgtg tatcgtccaa 7080 ttcatatgcc aaaacttgct ttgctacaga tgaagacgct gaaaatttga ttgacgattg 7140 taccacatat ggtgattata gggcaatagc atgtcgacgt agccgatatg aacgtaatgg 7200 aggatgtcca gtctggtaag gaataatagc attcgtttga acttcatctt caactatatg 7260 tatagaaaat aagagaaaat aaaattcatt aacgaaaata acaygcacaa gaaakactag 7320 ccattattat gtactcatta ttattttgat attaaaamat aaaratrmag aaagtatact 7380 rctatgttgc gctattggtt gtgaggtcga tgggcctgca ttatcttcac catgagcaaa 7440 acgatcattt agtggtgatc cataagctaa tttcagaatg cataacaacc aaaattaatt 7500 tttccaaaaa aaacattata gaacattcgc aattaaatta aaagtaatac aaattataat 7560 gactagtgct ataaaaaccg tactaccatg tggtggtgat gggaaagaat cattgatatc 7620 aggttgatta tgactttcgc tttgatgaga agataatgag gttttatttg tattatgccg 7680 ctttgctagt ttatcaattg ttcttctcat tgttcgaagc aattggtgaa tctgtctctc 7740 cgctgcatta tattctacta taatttccta caaaatggta caaagtgtaa aagatgtata 7800 ttattatgca tagcatgttt ggtttactct ttaaataaaa gaatagatgt agaaggttct 7860 cacatcacta gtctcttctt caacttcatt tactggatta acagggtctt catgcgcatc 7920 ttcccccctt tcatcttctt gaacctacaa taataaaaag aatatataat ttttttaaaa 7980 ctatttttca aatatgaaaa taaaagaaaa tgttgaaaga aaattttgtc ccttacatca 8040 gctagtccaa agtcgccata atcctgcaaa tttgcatgca ccattttctt catcaagtca 8100 tcactccacg ctgcacatat tgggatggta catggcacca acatggttgg aatgtagaat 8160 ttatttacat aaaaaaagtt gatacacaaa tattccacac atcaatacgt tatttagaaa 8220 agacttgtta aaacatagaa aatgatatgg aaaccttcag catttaataa aaaaaggtat 8280 ctacctgcaa aaaaataagg caacctataa accatgagcc tttacccaat tgaaaatgtc 8340 taattccaac aaccaatgtg caagtacaaa ttggccccaa ttaacattga tgtcaaagtc 8400 tccagcaagc aaagtatacc acaacgcatg actaccatct aactttgatg ttgaagcaag 8460 taatatagca catgagaaga agataaacaa tttttttgaa ctcgcccatg tcttccattg 8520 aaataagcct atctctaaga tctgataggt tttccatcct attattccta ttggtaggtg 8580 aaagtaggag cctcctacca atatatggaa tacccataat ttcccttaca tcagaacaag 8640 taattggaaa ttgtctttct tgtcctatgt ctaacctaca gtgggctata ttgaaatgat 8700 ttattatcca tctgcataag ctatgcctta tctctatgaa agagagctaa agcaatccac 8760 caaagccaat atgttgaatt atactctttt tttcatcact tagatcatca agtagatgtc 8820 taagtttttt tgtggagcat cgactattta ttttgacctc ttgtagaagt aaataaacga 8880 tattataaaa taaaaattta tatagtaaaa ttaaacaaca atgtcaaaca ttaatatagt 8940 caaaataaaa taatactaat taaaagaatg ttcaaacctg gttgtattgt attgtttttt 9000 gccttttatc catgtattat actccacact gcactataga atttatatca aataatcaat 9060 tgtcataatt aaatgtataa tgaatcaagt aatgttgtaa tatgttatac ttctagtgya 9120 attgtattgt aaatgtaggg catttgtatt gtaycyttat ttattttggt gtaactacta 9180 ttattgatcc caaatatagt tacatacatt ctactgtaaa cacactgagc cattgtatta 9240 gtggataaca aatttaagtt gtttgatggt aatccaatat gtacatattg ttaatgctca 9300 tcatggctaa ccttttaaac cgtatataat ttataaaaac taggtacaac atatatgcat 9360 tatacttaca atacaaatac actaacgtta caatatatta caatataatt taatttattt 9420 atgtttattt tttcatatgt tatgtcccct gaccatccaa tatgatgtat gacagctccc 9480 aagaatatat attaaatccg aaagaattga aatgtagaaa aagatatgat actttgtttg 9540 cattaaaaaa atgatgtcca atattcccta agacaatatt ggaaacacaa tcctaaagaa 9600 taatacaaat tacataaaac atctaaaata taacatattt gagaaactaa tactaaaaac 9660 tagaaaagaa aataagattc taagtttttt ttccattctt ctcattcatt tttcaatgac 9720 cacctacaac aaataatgaa aataactaca acaacttcaa taagaggcca gattggtttt 9780 ccccaaataa ccaatttaaa taacgcaatc aaacttcatt catactctat ttttccattt 9840 ctcttgcaaa tcgaagaaca taacaccgca ataatccagt tgttcagtga ataggtaccc 9900 catataaacc ctagaaacta aaatcgtacg atgaaaaaat ttaaacgaac gaaccctaga 9960 aactaaaatc atatgatgaa aaaatttaaa tgaaccctag aaattaaaat ctaagatttc 10020 tcatatttaa atgaaaaaaa aatcacctct ttcagatacg atgaaaaaaa ratgcsgttg 10080 aagacrtcgt cgaagccaca atattcaaaa tggagacacg ccaacaatga tgyagaaagg 10140 aaatcttcaa cggagtcatc attggaacaa tggaactgta catgtctaca caagatttag 10200 tatctcacac aatatgatac caccgtgaaa acacccagat gatgcgaaaa gggaaggttt 10260 caaagggaag acattggaat gacagtcttc tccctttttt ttcaattctt ttattcttta 10320 aaaattataa ttttagaatt taatccaggg taaattagtc taataaaaat gttaggcctt 10380 tagaagaatt atcaaatcta cccacccttc tcggtaattt tttttcttag cctaccctta 10440 agggtaattc tcc 10453 // ID Copia-37_VV-LTR repbase; DNA; EDCOT; 340 BP. XX AC chr1; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-37_VV_; KW Copia-37_VV-I; Copia-37_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-340 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr1; Positions 263914 263575. XX SQ Sequence 340 BP; 91 A; 52 C; 65 G; 132 T; 0 other; tgttgagagt tatgccttag tagctgctga gggaaaggct gaaatcgtca accacatgca 60 attgaagtca acaagattac tagaatgctg aagctatttt tatgtttctg tttttgctgt 120 tgctattttt atgttttttg cttttaagtt aaattctgat gctattttgt aggaggtagt 180 tgtttgttca acaagtagct taatttgatg ctttttttga ggtcatatct gttacacaat 240 ctgtataaat tcagccttat gataaataaa aaaatcagat cagtagtagc acatctctgt 300 tctcagttgc ttggtgtgat aacctcccct gtttccaaca 340 // ID Copia-42_VV-LTR repbase; DNA; EDCOT; 274 BP. XX AC chr11; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia-42_VV_; KW Copia-42_VV-I; Copia-42_VV-LTR. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-274 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr11; Positions 7897924 7898197. XX SQ Sequence 274 BP; 83 A; 30 C; 50 G; 111 T; 0 other; tgtaaaatta taggaagatt taatttgatg atttgtcagc aatgttaagg gctaagattg 60 aggatatcta cagctaacaa atcatttttt cttatcccat gattttatgg gatttggtaa 120 tctgttacca aatccatttc tgttttaggt agttttgact tttttttttg ataagttgta 180 aatatcccta aaatagatga gtattatcat ctatatgtaa aggggaatgt aatcagtatt 240 atgaatggtg gaatgttgag tttttccttc caca 274 // ID Copia7-PTR_LTR repbase; DNA; EDCOT; 177 BP. XX AC LG_I; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; Copia7-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-177 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-177 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 291-291 (2007). XX DR Genome; LG_I; Positions 26420867 26421043. XX SQ Sequence 177 BP; 61 A; 24 C; 29 G; 63 T; 0 other; tgagggaaag aatcccgaat aattagatga tacgatgtaa tcaatgggat tgaatgttta 60 tctcctataa taactcctag aatatctcct agtatagtgg atctaattgt atatatatgt 120 tgtacatatg ctgttcttgt ttatcacgaa atatacagag aatcaattat atttcca 177 // ID Gypsy12-VV_LTR repbase; DNA; EDCOT; 1646 BP. XX AC AM431879; XX DT 16-AUG-2007 (Rel. 12.08, Created) DT 16-AUG-2007 (Rel. 12.08, Last updated, Version 1) XX DE LTR retrotransposon from grapevine: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy12-VV_LTR; KW Interspersed repeat; LG_I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-1646 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-1646 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 705-705 (2007). XX DR Genbank; AM431879; Positions 4029 2384. XX SQ Sequence 1646 BP; 493 A; 304 C; 296 G; 546 T; 7 other; tgattactac tcaaaacatg ctattttgta gcttgtaatt agctctttta aacacccttg 60 agtagtaatt attacctttt aacccaatta acatgttagg gacccttgca atcgtttcta 120 acaattgtgt taagttttgg tgctttttga tagctttatg ctcaccaaag caatttaaga 180 atgagggaga gctatttata gttcatggaa aagcttttga aagcttaaat ttatgaagaa 240 atcaagctat ggagcctcat aatcctttgc cttagtcgtt caaagtatac aaggtagaaa 300 caatggagaa gaggaaaaca ggggacacag ctgcagtctt tcattgcact tttggagcac 360 tttccgaagt ccatttttta cattctatat accatttcaa agctcagaaa gtcaagaatc 420 caacggttca aaccatgtac aatttggagc tgaaatgaga aagatatggc attcggaaga 480 caactgcatc aagctgaggg acaatttcgc acgatggaaa tcaaggtgcg aattcctcag 540 tccactgtgc gaaaatttcg cacacctcaa atcaaagtrc gaaattggaa ctccagcgtg 600 cgaaaattgg atatttttgc cgactctttt tcttctgata tttttgtgtc taaatttcca 660 ttttctcctt gtattcaacc actcatgtaa ttccttagct aggaagtatc caaggaaggg 720 taaaattacc ttcctatata aattctcttg taatcactga aaatgsatct ttcggggarc 780 tttctccagg agaccaamtt atgtaaattt gwtacttagt gaaatacaga gatcttyttt 840 tgctttyttt tttctctctt ctattttcta ttttcttgca agccaaacac cctctgagga 900 tgttttccca gaggatgaga ggctaaacat ttagtttctt ggagtaaagg aagctaggtg 960 aaaagtccag attaaaacat ggaaagtttc cgtgcattaa attcaggtag ttggagtcca 1020 taaatggttt ttaaagccaa ggttttgcct taaatccctt cgaatcactt tgactggcca 1080 atacatggta agcttaaggt ctctgtggat gcttattgct agatccatat cagtccatta 1140 gttatcatgt atgagccatt ggaaagtgat tcaaggtgat agcctatagt gtcttaagcc 1200 attaatggac cttgaccacc atctctagtg actttttatg gattaaaact tcattgtcaa 1260 acctataccg gttcgggaaa taactatagg ttaaatcccc aatgcgagga gaaaaatccg 1320 gaattttcca ctttgcatct ggaacttgaa cctagcaacc tttagctccg agagactttc 1380 tttcttccac tttttactta gttctatgtg agtttagttt aaatcaccac ttttaaaaca 1440 attttatttt cttttaaatt tcaagtttgt gctaaaggaa atcatcagaa tcaatttcta 1500 atttagagtc tgtcactgat agagtgaaaa cccatccctg agttcgaccc tagaactgct 1560 atactatagt agctttgcta cgctagtata aggtcatagg ttttataaat gtttttgatt 1620 aaaagacccg gttgggcatc gaatca 1646 // ID EnSpm-2_Mad repbase; DNA; EDCOT; 7584 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE Autonomous EnSpm elements, consensus. XX KW EnSpm; DNA transposon; Transposable Element; EnSpm-2_Mad. XX NM EnSpm-2_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-7584 RA Kojima K.K. and Jurka J.; RT "EnSpm-type DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1602-1602 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC >92% identical to consensus. Incomplete 3'-terminus. XX FH Key Location/Qualifiers FT CDS join(1464..3731,3735..4130,4390..5115) FT /product="EnSpm-2_Mad_1p" FT /note="transposase." FT /translation="MDKSWLTIPRNXEAYTAGINLFLDQAVANGVGPDKFR FT CPCKRCCNRYTFVRNTIVEHLILYDMDKDYKNAWWRHHGEQNIGEQNVAIG FT EEETGDEVTGMHDFLNDVFVQPLTEEGVGPSTEPPIGEGRPEEVETFFRLL FT EEADQDLWPGCKEFKKLEAVVRLYQIKCLAGMPDEIFTTLLELIKRMLPEG FT DCLPESCYKAKKLINDLGLTYVKIDACPNDCMIYWKDTSDLTVCSVCGESR FT YKITNAEDSSRKKIAAKVMWYFPLKPRLQRFFMSKHTAEHMRWHATECPKD FT EFMRHPSDSPAWKHLDNLYPDFASEIRNVRLGLASDGFNPFGKMRNDHSTW FT PVVLSVYNLPPWMCMKQPNLLLSLLIPGPRSPGKEIDVYMRPLIDELNELW FT EVGTPTYDAYSNQSFTMKAAVLWTISDFPAYGMLSGWSTHGYKACPHCMHD FT KESIYLPASRKICYMGHRRFLEDNHRFRRQTTTFNGRREHRSAPRQWTGLQ FT CLEELSTLRFTFGKPKKDASVGQRRKRTSSSTSSNSQWKKKSIFYELPYWR FT HLLIRHNLDVMHIEKNICDSVVGTLLDIEKSKDGLAARADLEVLNIRRSQH FT PRREGNRTFLPPALFTLKREEKTAFCKVLSTIRVPDGYSSNLSRCVHVNER FT KIHGLKSHDCHVLMQQLLPLAIRPVLPKAVTMVLLELSAIFRQLCSKKESE FT EGFKQLNSRIALTLCQLEKIFPPAFFDIMVHLPVHLADEAALAGPVQYRWM FT YPIERLINFYKFFTIVVITLIYNYNNLCFVYNCRYLQTLKRYVRNKGRPEG FT SIAEAYLVDECLSFCSMYLRDVESRRTRRGRNEDGIGRGVSGGLSIFDSKG FT CYMGSGENVELDLNVLDQCHRYILNNCDEVNPFRRLSCQLLSSYLLQMNSR FT CHANDTLISQDLRWLANYPSRVVSRYKSHIVHGFRFRIKSVDDKHKNQNCG FT VFVPANVPGAIGQVNCYGRVVDMFEVKYCGPAEAGDRGRAVMLFKCEWVNS FT ESPRGMKTDQYGFTMVNFNRLGFKEDPFILASQALQAFYVEDTIEKDWHVV FT VRTQPRDLFDVLEDSDAIDDYAIPNLDDRILDXENFHTRVGVEETPFHESL FT PLPTQFASHANADDDXTDDDME" XX SQ Sequence 7584 BP; 2251 A; 1155 C; 1616 G; 2559 T; 3 other; cactactaca aaatggtctt atagtgtcag tgggtggtgt cggtttaatc taatatagtg 60 gcggacaaga cagttgcgac actaactgaa catgacgtcg gatttactgt cgcttataag 120 cgtcataaaa tactggtgtc gcttttaaac cgacgtaaac atacatttta atatttttaa 180 atactggtgt cgcttttaaa ccgacgtaaa catacatttt aatattttta ataccggtgt 240 cgcttttaaa ccgacgtaaa catacattta atatttttaa acactggtgt cgcttttaag 300 cgacataaag taggagagct tttcaatcag tgttgcaaaa gcttccttat ttcgagccac 360 atcaggctca cgtcggtttg aaccgacgca aacttggcct atttcgaggc cgcttgctac 420 gactgtcaag actgtcaggg acacgtcggt tttaaccgac gcaaacttgt ccttatttcg 480 acgccacaca aacttgtcct tattgttttt aaatatttta aagcctgcgt cggttctgag 540 cgacatagat tttagttttt taaaatattt taaaacctgg tgtcggttgt aagcgacaga 600 ataatggtct ttatatactt tcccccgtgt tttcttcttc ctctcttgca tttttcttat 660 tcgttcttcc aatttacaaa ccctcccgtg ttctctcttg cacctttctt atttgttctt 720 cctaacttca tttgttcctt cttcacaaca gtaagttttt cttgcttcta atatttttat 780 tttctccact tatgtttaat ttttatttac aatttatttt tgtagggaat ttatttgagc 840 tggttgagta cataaagatt tgatcgacga cggaattctt ccataattca ggtttctatc 900 actaaattct ttaattttta aattgtataa tacacaagtt tatttattta aaagttctaa 960 tttaagtact tagataaatt tatactattt ttgttaaatt aataaatatt tagtcgaatt 1020 aattaatttt gtcacttgaa ttgttatgag aaaatggaaa tgaataatat ttataagcat 1080 ttatgttaaa ttgacaatat taaatataac ataaacttat aatatttagt aatataagaa 1140 tatattatgt taaattaatt tgttttgcac tctaattgtt attttaattt gtttttgttg 1200 ttattttgat aactttgata acttttggtt gttatttact agaatggatt agatgagcat 1260 aattttgata actttttgtt gttattttaa tttgttttta ctataatagg tgttgaaaat 1320 taaaagattg caatcgtgat agagttcgag ggttgaaaga tagaaattga aaattctaat 1380 agttatgcct acatgatagg gattgaaaga ttgtaggcat cttagtgtca acgtaatatt 1440 ttgccctcgt aaagtggtaa aacatggaca agagttggtt gacgatacct cgaaatttkg 1500 aagcgtatac agctggaatt aatttgtttt tggatcaagc agttgcaaat ggtgttggcc 1560 ctgataagtt tagatgtcct tgcaaaagat gttgtaatcg atatactttt gttaggaaca 1620 ctattgttga acatctcata ttgtatgata tggataaaga ttataaaaac gcttggtggc 1680 gacatcatgg cgagcaaaac attggagagc aaaatgtggc aattggagaa gaagaaacag 1740 gagatgaggt gactggtatg catgattttc ttaatgatgt atttgtccaa ccattaacag 1800 aagaaggtgt tgggccgtct actgaacccc ctattgggga agggcgtcca gaagaggtgg 1860 agactttttt taggttgctt gaagaggcag atcaagattt gtggccaggg tgtaaggagt 1920 ttaagaaatt ggaagcagtt gtaagactgt atcagatcaa gtgtttagcg ggaatgccag 1980 acgagatctt caccacttta ctggagttaa ttaaaagaat gttgcctgaa ggggattgtt 2040 tgcctgaatc ctgttataag gcaaaaaaac ttataaatga cttgggtctg acgtatgtga 2100 aaattgatgc atgtcccaat gattgcatga tctattggaa agatacttcg gatttgaccg 2160 tgtgctcggt ttgtggtgaa tcaagatata aaattaccaa cgcagaggat agctcgagaa 2220 aaaagatcgc agctaaggtt atgtggtatt ttcctttaaa accacgattg caacgatttt 2280 ttatgtcgaa gcatacggct gaacatatga ggtggcacgc aactgaatgt cctaaggatg 2340 agtttatgag acatccttca gattctccag catggaagca tttggataat ttatatccgg 2400 attttgcgtc agaaattcga aatgtccgat tagggttggc cagtgatgga tttaatcctt 2460 ttgggaaaat gaggaatgac catagcacat ggcctgtggt gctttctgtt tacaatttgc 2520 cgccttggat gtgcatgaag caaccaaatt tgttgttgtc tctattaata ccaggaccgc 2580 gcagtcctgg taaagagatt gatgtataca tgcgtccact gattgacgag ttgaatgagt 2640 tgtgggaggt gggcactccc acttatgatg cgtattccaa ccaaagtttt acgatgaagg 2700 ctgccgtctt atggactata agtgattttc cggcttatgg aatgttgtca ggatggagta 2760 cacatggcta taaagcctgt ccacattgca tgcatgataa agaatctatt tacttgccgg 2820 cgagtcgtaa gatttgttat atggggcatc gacgctttct tgaagataat cataggtttc 2880 gaaggcaaac cacaactttt aatggtcgtc gagagcatcg tagtgcacca aggcagtgga 2940 ctggtttaca atgtctcgaa gaactttcta cattgagatt tacttttgga aaaccaaaga 3000 aagatgcttc agttgggcaa cgcagaaaaa gaacttcgag cagtacaagt agtaacagtc 3060 agtggaagaa gaaatctatt ttttatgaac taccttattg gaggcatctg ttgattagac 3120 acaatcttga tgttatgcat atcgagaaga atatatgtga cagtgtggtg ggaacattgc 3180 tagatataga aaagtctaaa gatggattgg ctgcacgtgc agatcttgaa gtcttgaaca 3240 taagacgtag tcaacaccca cgtagagaag gaaatagaac atttctacct ccagcattgt 3300 tcacgttgaa aagagaagaa aaaactgcgt tttgcaaagt gttgtctact attcgggtcc 3360 ccgatggata ttcatcaaat ttatcgcgat gtgtgcacgt gaatgaacga aaaatacatg 3420 ggttgaaaag tcacgattgc catgttttaa tgcagcagtt actcccgctt gcaatacgcc 3480 cggttttgcc taaagctgtt actatggtat tattagagtt gagtgcaatt ttcagacagt 3540 tgtgtagtaa gaaggagtct gaggaaggat tcaagcaact gaattcaaga attgccttga 3600 cattatgtca acttgaaaaa atattccctc ctgcattttt tgatataatg gtgcaccttc 3660 cagttcactt ggcagatgaa gcagctcttg cagggcctgt tcaatataga tggatgtatc 3720 caattgaacg gtaattaata aatttttata aattttttac aattgtagtc ataactttaa 3780 tttataatta taataatttg tgtttcgttt ataattgtag gtatttgcaa acgttgaagc 3840 gctatgttcg taataagggt cgtcctgaag gttctattgc tgaagcatat ttggtggatg 3900 agtgcttgtc cttctgttcc atgtatctta gagatgtcga gtctcgtcgc acccgtagag 3960 gccgaaatga agatggtatt ggacgtggag tgtctggtgg gttatcaatt tttgactcca 4020 aaggatgtta tatgggttca ggagaaaatg tggagctcga tctaaatgtt cttgatcagt 4080 gccatagata cattctaaat aattgtgatg aagttaaccc atttagaagg taagaacgtt 4140 taatcatacg tcttaatgtt ttattggttt tcttaacttt gaaaaattaa ttatctaaat 4200 ttggacataa ttgcctaggc aacatgagga attcttgaaa actaaacatc gtcgagaaag 4260 gttaactatg cgacaaatta aggagctaag caagaaagaa tttccagaat ggttcaagca 4320 acatgtgagt tgatacaaca atcacattat ttatttattt ttttgcattt taattataac 4380 atgttatagt tatcatgtca acttttatct tcatacttat tacagatgaa ttcaagatgt 4440 catgctaatg acacgttgat atctcaagac ttgcgttggc tagctaatta tcctagcagg 4500 gttgtgagta gatataaaag tcacattgtt catgggttca gatttcgtat aaaatctgtg 4560 gatgataagc ataagaatca aaattgtggt gtctttgtac ctgcaaatgt tcctggtgca 4620 attgggcaag tgaattgtta tggcagagtt gtagatatgt tcgaggttaa atattgtggt 4680 cctgctgagg caggagatag gggtcgagct gtgatgttat ttaagtgcga atgggttaat 4740 agtgaaagtc cacgaggaat gaagaccgat caatatggat ttactatggt gaacttcaat 4800 cgattgggat ttaaagagga tcctttcata ttagcatcac aagcattaca agcattttac 4860 gtggaggaca caattgaaaa agattggcac gtagttgttc gaacgcagcc gagggatttg 4920 tttgacgtat tagaggatag tgatgcaatt gatgattatg ccataccaaa tttggatgat 4980 cggatacttg acmatgaaaa tttccataca agggttggcg tggaagagac tccttttcat 5040 gaatcattac cgttgcctac ccagttcgct agtcatgcca atgccgacga cgacmcgaca 5100 gatgatgaca tggaataaat atattaatta ttttatgtgt tttaagtatt aattagacaa 5160 tatttcgttt tctattacgt atatggttta agttcaattt tatttattaa aatcttaaaa 5220 tgttatatga gataacaaaa aaaaaaaaaa ctcgatattt attttttatg ggttaaactt 5280 tttttttttt tttaaactat tttcctgtcg cttttaggcg acggcatggg tgagatagtg 5340 tcggctaaaa ccgacgtgaa gtggacttgg gaagaccact ttcaattagt cacttcgtaa 5400 gtaaagtggg tcggaaagtg gttgtttgat ttaatgtggc agtaaagtgt gtcagttgta 5460 gtgtcggttt aaaccgacac taaatataac taaaccgacg caacggccac atcattaaag 5520 cttgtcagac aatagtgtcg gttttaagcg acaccaagat taactaaagc gacgccatgt 5580 aaatttcaaa taactatgtc agaaagttgt tgtctgatta gatgcagcag taaatgtgtc 5640 agtgatggtg tcggtttaaa ccgacaccaa gtttagttaa agcgacgctg gtttattaaa 5700 ttttgtcaga agtgtgtgga ggcagtaaat gtgtcagtgg tggtgtcggt ttaaaccgac 5760 accaagttaa gctaaagcga cgctggttca ttaaattttg tcagaagtgc tggatttaat 5820 tgtagcagta aatgtgtcag tgatggtgtc ggtttgaacc gacaccaagt gtagctaaac 5880 cgacgcaacg ttcggttcat taaattttgt cagaaagtag gtgggtttaa ttttatcagt 5940 aaatgtatca gtggtattgt cggtttaaac cgacactatg actcagttat ttcgacgcca 6000 gcgggtttta aagcgacgtc agtggtttaa tgtcggtttt aaccgacgcc aacttagcat 6060 ccatatttaa ccccttcttt cccccccccc ccatttcgcc cgcgctttct tttcttccca 6120 aaattcagtc tgtccatctc cctcccaatt tcgtccgttt ttccacttct tctctcattt 6180 cactttttag ttttttactt cttgcaaatt gttttgctat ggatcatttt gaagatgaac 6240 atgctgacga accccatttc gaagaggaag aagtcgaagg ttgttcattt ttaatttatt 6300 atggttttta gtttcagttt ttttgttttg gtccatggtt tttaattgtt ttttctttgt 6360 ttataaggaa caactcaacg aggacgggga ccctcgattc ccaactggaa ggaacaagtt 6420 tgttgttttg atgcgtcggg aaaatgcatt agtgaaaatt ctagtgcatt ttcaaaacat 6480 gtagcggcag aggtaagaga ttctagacat atgccgttgg tgagtgattg gcgtcaaatc 6540 aaggaagatc gcagagaagc tttttggaat agaataaagg tagaattatt tttttgttac 6600 tagaagagag tataataagt caatgtttgt agtaataatt aatttgcttg atttttttta 6660 tgcgtacagg aaactattat ttttcaagaa gaggatatgg cgaaaatgcc aatgatccgg 6720 cacatgacac ttcatattgc ggagcatgcg cataaggagt atagaaataa attaaaaaaa 6780 aatattatac tgataaacca gttgaggagc accggaaaac tcctcctaat gtggatcctc 6840 aacagtgggc tgaattggtc tcctactgga acaaagaaaa aacgaaggta aactttttat 6900 tatttatttt attaaagttt gtaatgtgtt taataaatta ttttttttta ggagattgct 6960 gcaaaaaata agtataatcg gcggttgaaa acgatgaacc acacaactgg tgcaaagtct 7020 tttgcaagag ttcgggcaga acttgtaagg gttgttcatt ttcaagaatt gtagatattt 7080 ttaaatttaa tatattattg gtagaaattt atttataatt tgatggttgg tgaaaattgt 7140 tctttttttt ttgttgactt ataattatag cggaaaaagc atgggaagga ggcggatcct 7200 gtttcgtttt ttcgtcactg tcatactcga aaggatcgca cttggattga tgaaacgtcg 7260 gagcgcactg gggtaattga ttttttcttt gtagtatatc attgttatta aattttatta 7320 tctatagttg aattcttatt tttaaaattt ttattgcaag gcaactatgg aggggaatat 7380 tcaaactatg attgagtctg ggcatgaaga tggtgatgag cttaggaccc gggtttatgt 7440 ggagacgatg ggtcctgagc gtcataatag agtacgaggg tatggacatg gggtgactcc 7500 ggatatggtg tcgtatgcat cttcctcaac ttcttctaat tcttccagaa gatcatccaa 7560 gagttcagtg gcagtgttgt tgac 7584 // ID Gypsy16-PTR_I repbase; DNA; EDCOT; 4419 BP. XX AC scaffold_465; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy16-PTR_I; KW Interspersed repeat; internal portion. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-4419 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-4419 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 310-310 (2007). XX DR Genome; scaffold_465; Positions 45917 41499. XX CC Positions [3311-3805] - Integrase core CC 'TTTCC' target site duplication CC LTRs are 98% similar to each other. XX FH Key Location/Qualifiers FT CDS 23..4417 FT /product="Gypsy16-PTR_I_1p" FT /translation="MTTNKERIENLEAALGGLQDNFNKMELGVTDKLQQLE FT AAISRISEVLLPRQEPNSSNVQERSGQAFGARSRDTTDGGRSMFSSKLAKL FT EFPKYFGTDPTEWLTRVDQFFEYQGTLEAQKVSLASFHLESEANQWWQWLR FT KAYHEDKKEVSWEIFVEELWARFGPTDCEDFDESLSKIRQTGSLREYQKEF FT ERLGNRVQGWTPKALVGTFMGGLKPEIADGIRMFKPKSLKEAISLARMRDE FT QMIRQEKPHRPLYRTSDNSDRPFKHTDVSNRPFTRSVGVSSPFKTQSASPM FT KRLTWSEMQQRRAQGLCFNCDERFVLGHKCKGPQLLLLESSYEDDEIDNEE FT PEISLHALTGWSTARTMRVSAKVGHHELIVLIDSGSTHNFINERVAEILHL FT PVVPTEPFAVKVANGVPLRCQGRFDNVHVLLQGIPFTLTLYSLPLIGLDMV FT LGVQWLEQLGTVGCDWKRMTMKFSWMNQHHQLEGIGNQPIQPIQVQALSKE FT LKQGNSIFAVCLQPAGEETPQMNRPDMQQLLQEFADIHQEPQQLPPQREID FT HHITLKEGTEPINVRPYRYAYFQKAEIEKQVHDMLKLGLIRSSTSPFSSPV FT LLVKKKDGTWRFCTDYRALNAATIKDRFPIPTVDDMLDELYGAAFFTKLDL FT RSGYHQVRVNPLDIHKTAFRTHNGHYEYLVMPFGLCNAPSTFQAVMNSIFR FT PYLRKFVLVFFDDILIYSPNWTMHIEHVKTAFEILRHHQFFIKLNKCVFGQ FT QEVEYLSHIVTSQGVKADKGKIQSMLNWPCPTNVSELRGFLGLTGYYRKFV FT RNYGIIARPLTNLLKKGLFRWTEEADAAFLALKQAMTSTPTLAMPNFNEPF FT VIETDASGTGIGAVLTQHGRPIAFMSRALGVTKLSWSTYAKEMLAIVQAIR FT LWRPYLLGRKFFIHTDHCSLKYLMEQRIVTPEQQKWVSKLVGYDYEITYKP FT GKENSAADALSRVIGSPSLNALFVPQASLWQTLKEEANQHPYMIRIGKLAT FT ANPGAPYKWLNGLVCYNNRVVIPPNSTLVQLLLQEFHDSPSGGHSGVLRTY FT KRMAQQFYWPSMHRVVQQYVASCTVCQKNKADTLSPAGLLQPLPVPCQIWD FT DITMDFIEGLPPSNGKSTIFVVVDRLSKSAHFLALAHPYTAKMVAEKFVEG FT IVKLHGMPKSIISDRDPIFISHFWREFFKMSGTKLHMSSAYHPQTDDQSEV FT VNRCVEQYLRCFVSQQPRKWCSFLAWAEFWYNTTFHSSIGMSPFQALYGRP FT PPSIPNYQIGASSVHEVDQTMISRTSLLRQLKINLQAAINRMKQGADSKRR FT DVNFQVGDLVFLKLHPYRQQSLFRRPAQKLASRFYGPYKVEEKVGKVAYKL FT QLPTDARIHPVFHVSLLKKQVGESTVTSAELPPITDDGEFVLKPIAVLETR FT WVRKGSTFVEELLVQWEHLSKEDATWENAQELRDKFLSFNLEDKVLIQDRG FT " XX SQ Sequence 4419 BP; 1207 A; 927 C; 1033 G; 1252 T; 0 other; ttggtatcag agctttcaca ctatgactac caataaagag aggatcgaga atttagaagc 60 agctcttggg ggacttcaag acaatttcaa caagatggaa ctgggtgtta ctgacaaatt 120 acaacagcta gaggctgcta ttagcagaat ttctgaagta ctgcttccaa ggcaagagcc 180 gaactctagc aatgtccaag aacgcagtgg acaagccttt ggtgcgcgat ctcgtgacac 240 cacagacggt ggccgctcaa tgttctcctc caaattggct aagctcgaat ttcccaagta 300 ttttggtact gacccaactg aatggctcac gcgtgttgat caattttttg aataccaggg 360 cactttggaa gcacaaaaag tgtctttggc ttcttttcat ttggaaagcg aagcaaatca 420 atggtggcag tggttacgca aggcttatca tgaggacaaa aaggaggtat catgggagat 480 ttttgtggaa gaattatggg ctcgttttgg tcccacggat tgcgaagatt ttgatgagtc 540 tttatcaaaa ataaggcaaa cgggatcctt acgggagtat cagaaagaat ttgagaggct 600 gggaaacaga gtgcaagggt ggactccgaa ggctttggtg ggtactttta tgggtggtct 660 caagcctgaa attgctgatg gaattcggat gtttaagcca aagtccttga aagaagccat 720 cagtttggca cggatgagag atgagcagat gattcgtcaa gagaaaccac atcgaccact 780 ctacagaacc tctgataatt ctgatcgacc attcaagcac actgacgtct ctaatcgtcc 840 attcaccagg tctgttggcg tctcttcacc ttttaaaacc cagtctgcat cacctatgaa 900 gcgattaaca tggtctgaga tgcaacaaag gcgtgctcaa ggcctttgct ttaattgtga 960 tgaaaggttt gtattggggc acaaatgtaa ggggccgcag ctgttattgc ttgaaagcag 1020 ttatgaagat gatgagattg ataatgagga acctgaaatt tcactccatg ctctcacggg 1080 gtggtcaaca gctagaacca tgagagtctc ggccaaagtg ggacatcatg aattgattgt 1140 gcttattgac agtgggtcaa cccacaattt catcaatgaa cgggtagctg aaatattgca 1200 tttaccggtg gtgcccactg aaccctttgc tgtgaaagtg gctaacggag ttccgctaag 1260 gtgtcagggg agatttgaca atgtgcacgt cttattgcaa ggtattccat ttaccttaac 1320 tctttattcg ttaccactaa ttgggttgga tatggtgttg ggagtccagt ggctagaaca 1380 gttgggaacg gtgggttgtg attggaagag gatgacgatg aagttttcat ggatgaatca 1440 gcatcatcaa ttggaaggaa ttggcaatca accaattcag ccgatacagg ttcaagcact 1500 gtcgaaggag ctgaagcagg gcaattctat ttttgctgtg tgtctacagc cggctgggga 1560 agaaacacca cagatgaacc gacctgatat gcaacaattg ttacaagaat ttgcggacat 1620 tcatcaagaa ccacaacagc tccctcccca aagagaaata gaccaccaca tcaccctcaa 1680 agaaggaact gagcccatca atgtccggcc atacaggtat gcctattttc aaaaagctga 1740 gattgaaaag caagttcatg acatgttaaa attggggcta attagatcta gcacaagtcc 1800 attttcttct cctgtgttgt tagttaaaaa aaaagatggc acttggcgat tttgtaccga 1860 ttatagagcc ctaaatgctg caacaataaa agatagattt cctattccaa ctgtcgatga 1920 catgcttgat gaattatatg gggctgcttt ctttactaaa cttgatttac gttctgggta 1980 tcaccaagtc cgggtcaatc ctttagatat ccacaaaact gcctttcgca cacacaatgg 2040 tcattatgag tatttagtta tgccgtttgg gttatgtaat gctccttcca catttcaggc 2100 tgtcatgaat tccatatttc gtccttacct tcgcaaattt gtattagttt tctttgatga 2160 tattctaatc tatagcccca attggaccat gcatattgaa catgttaaaa cagcttttga 2220 aatattaagg catcatcagt ttttcatcaa attgaataag tgtgtgtttg ggcaacaaga 2280 ggtggagtat ttgagtcaca ttgtgacgtc ccaaggtgtg aaggccgaca agggcaaaat 2340 tcaatctatg cttaattggc cctgcccaac taatgtttct gaattgcgag ggttcttagg 2400 ccttacaggt tactaccgga agtttgttcg caattatgga atcattgccc gaccactcac 2460 aaaccttttg aagaaggggc tatttcggtg gacagaggag gcagatgcgg cattccttgc 2520 cttgaagcaa gcgatgactt caactcctac gcttgctatg cctaatttta atgaaccttt 2580 tgtcattgaa actgatgctt caggtactgg tattggggcg gtgttaactc agcacgggag 2640 acccattgca ttcatgagcc gagcattggg ggtcactaaa ctgtcatggt ccacatatgc 2700 caaagaaatg cttgccattg ttcaagctat tcggttgtgg cgtccgtact tgctgggcag 2760 gaaatttttc atacacactg atcattgcag cctcaagtac ttgatggagc agcgcattgt 2820 caccccagaa cagcagaaat gggtgtccaa attagtaggg tatgactacg aaatcactta 2880 taagccggga aaggagaatt ctgccgctga tgccttatca agagtaattg gcagccctag 2940 ccttaatgca ctatttgttc ctcaagcatc tttgtggcag actctcaagg aggaagccaa 3000 ccagcatcct tacatgatcc gtattggcaa acttgctact gccaatccgg gagctcccta 3060 taaatggttg aatggtttgg tgtgttacaa taaccgagta gtcattcccc ctaattcaac 3120 tcttgtccag cttctattac aggaattcca tgattcacct tctggaggtc attcgggggt 3180 gttacgcaca tacaaaagaa tggcgcaaca attttattgg ccatccatgc atagagtggt 3240 tcagcaatat gttgcttctt gcacggtttg ccaaaagaat aaggctgata ctttatctcc 3300 agccgggctt ctacaaccgc tgccagttcc ttgtcaaatc tgggacgata ttaccatgga 3360 tttcattgaa gggttaccac cttctaatgg taaaagcacc atttttgtgg tcgtggaccg 3420 tttaagcaaa tctgctcatt ttttggcttt agcacatcct tacacggcca aaatggttgc 3480 tgagaaattt gtggagggga ttgtcaagct tcatggcatg ccgaagtcca ttattagtga 3540 ccgggatcct atcttcatca gtcatttttg gcgtgaattc ttcaagatgt cagggacaaa 3600 gctgcacatg agttccgctt atcatcccca aaccgacgat caatcggagg tggttaacag 3660 gtgtgttgag cagtatcttc gatgttttgt ttctcaacaa cctcgaaagt ggtgttcttt 3720 tcttgcatgg gctgaatttt ggtacaacac cacattccat tcctctatcg ggatgtctcc 3780 ttttcaagct ctctatggcc gaccaccacc gagcatcccg aattatcaga ttggggcctc 3840 ttcagtgcac gaggtggatc agactatgat ttctcgtact tctcttttac gtcagctcaa 3900 aattaatctg caggctgcaa ttaatcgaat gaagcagggg gctgattcca aaagacggga 3960 cgtgaacttc caagtggggg atttagtctt tctcaaacta catccttatc gccaacaatc 4020 tctgtttcgg agaccagctc agaagttggc cagtcgtttt tatggtcctt ataaggttga 4080 ggaaaaggtg ggaaaggttg cttacaagct tcagcttcct acagatgctc gaatacaccc 4140 tgtttttcat gtttcacttc tcaagaagca agttggagag tccacggtca ccagcgcaga 4200 actgcctccc attactgatg atggtgagtt tgttttaaaa cctattgctg tgttggaaac 4260 ccgatgggtg cggaaagggt ctacttttgt tgaggaactc cttgtccaat gggaacactt 4320 gtcaaaggag gatgctacgt gggaaaatgc acaggagctg cgtgacaagt ttctgtcctt 4380 caaccttgag gacaaggttc taattcaaga caggggcaa 4419 // ID DNA9-4_Mad repbase; DNA; EDCOT; 1025 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.11, Last updated, Version 2) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-4_Mad. XX NM DNA9-4_Mad. XX OS Malus x domestica OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Rosales; Rosaceae; Spiraeoideae; Pyrodae; Pyreae; OC Malus. XX RN [1] RP 1-1025 RA Kojima K.K. and Jurka J.; RT "DNA transposons from the apple genome."; RL Repbase Reports 10(10), 1485-1485 (2010). XX RN [2] RA Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., RA Kalyanaraman A., Fontana P., Bhatnagar S.K. et al.; RT "The genome of the domesticated apple (Malus x domestica RT Borkh)."; RL Nat Genet 42(10), 833-839 (2010). XX DR [1] (Consensus) XX CC ~84% identical to the consensus. 9-bp TSDs. 394-bp TIRs. XX FH Key Location/Qualifiers FT CDS 256..717 FT /product="DNA9-4_Mad_1p" FT /note="membrane-associated zinc metalloprotease, FT N-terminal portion." FT /translation="MIINLSASPPSSSFSLIKLSNSKSPISDFPSKPKTHH FT PKPPSSSICCSFSSPDLGFHCKDRFFIENGRCPHGKRFKFRTCAIPGFDSG FT NFESAQSVLEAAAVLTAIIVVHESGHFVAAYLQGIHVSKWKKMEVLGGGFW FT VLMENQRWVIWNWIT" XX SQ Sequence 1025 BP; 287 A; 212 C; 219 G; 307 T; 0 other; ggcctaatcg gataaacggt cctcgtggtg ataaggtaat cggaagatag ccctcgtggt 60 aaaaaaatta ggatttaaac cctcgtggta gagtccgtta gcaaatttag tccaaaatta 120 atttttccgt tacttgtccg ttaaatacag ggataaaaat gtattttaac gtgtacgcct 180 tcttcttcct ccctctgcgt ttcatctgtt tatatcttaa aacaacccct accagaaaac 240 cacagaaaat aaaccatgat cattaatctc tcagcttctc caccctcctc ttctttctct 300 ctcatcaagt tatccaattc caaatcaccc atctctgatt ttccatcaaa acccaaaacc 360 caccacccaa aacctccatc ttcttccatt tgctgctcat tttcttcacc agaccttggt 420 tttcactgca aggatcgatt tttcattgaa aatggcaggt gcccacatgg gaaaaggttc 480 aagtttagga cttgcgcgat tcctgggttc gactctggca acttcgaaag tgctcagtcg 540 gttttggagg cggctgccgt gttaacggcc ataattgttg tccatgagag cggtcacttc 600 gttgcagctt atctccaagg catccatgta agcaaatgga agaagatgga ggttttgggt 660 ggtgggtttt gggttttgat ggaaaatcag agatgggtga tttggaattg gataacttga 720 tgagagagaa agaagaggag ggtggagaag ctgagagatt aatgatcatg gtttattttc 780 tgtggttttc tggtaggggg ttgttttaag atataaacag atgaaacgca gagggaggaa 840 gaagaaggcg tacacgttaa aatacatttt tatccctgta tttaacggac aagtaacgga 900 aaaatcaatt ttggactaaa tttgctaacg gactctacca cgagggttta aatcctaatt 960 tttttaccac gagggctatc ttccgattac cttatcacca cgaggaccgt ttatccgatt 1020 aggcc 1025 // ID ATLANTYS_LC_LTR repbase; DNA; EDCOT; 787 BP. XX AC . XX DT 20-SEP-2005 (Rel. 10.09, Created) DT 20-SEP-2005 (Rel. 10.09, Last updated, Version 1) XX DE ATLANTYS-like retroelement from Lotus japonicus - LTR consensus. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Atlantys; KW ATLANTYS_LC_LTR. XX OS Lotus japonicus OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus. XX RN [1] RP 1-787 RA Gentles A. and Jurka J.; RT "An ATLANTYS-like LTR retrotransposon of the legume Lotus RT japonicus."; RL Repbase Reports 5(9), 236-236 (2005). XX DR [1] (Consensus) XX CC LTR sequence corresponding to ATLANTYS_LC_I. XX SQ Sequence 787 BP; 251 A; 170 C; 147 G; 194 T; 25 other; tgttggccca atattttggc ccaagaaaga aaaacgcatt cagcccaaaa cwctcraggw 60 agtcgaattc tgactaaaga aaggaaragg aarwtgcacc aagttaatgg ggcrgcmaaa 120 ytcgacaaca acaattactr ctaaacacag gcacatgtaa cacgtgccac attgaccaag 180 tcaaattcyc cccacgatgg tcgaaaacrt ggccaggaaa cggttgragc agttgaagca 240 cacgatctcc accaccatgc ryrgaacttc cggagcaagc atcagatcgt gggagaaacc 300 agacccacta acctawccam taaggaagaa aaccgtcaag gacacgcrgr rcacgaarct 360 ctataaatag gagaatccaa ttcagaaagg rggttcccaa ctcaaactct gaaaaattca 420 ccagaaagct ctaatgtccg catcaatgag actcaaggag caaaacgtga tgatggagga 480 gtatgttgca gaaccaacac tttagtttcc ctgcatttca gyttgttgat ttccagttct 540 tttgtgtagt ttgtttgtcg aaatctgcag ttcatgtagt tttcatgtta ttttagtttg 600 tttgactgtt ttgtaatcga ctcrtattca ataaaatcca gtttcatctg agttgcttgt 660 tgttgtcgaa aacacattca ttcacacaca acactttggc aaagcgtttt ctcaaaagga 720 ccctgaaatc taaacttcct ttagtcgaac taagaggata tttgtttacc aaaaatccgt 780 gtaaaca 787 // ID Gypsy8-PTR_LTR repbase; DNA; EDCOT; 367 BP. XX AC scaffold_1123; XX DT 22-JUN-2007 (Rel. 12.06, Created) DT 22-JUN-2007 (Rel. 12.06, Last updated, Version 1) XX DE LTR retrotransposon from Populus trichocarpa: long terminal DE repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy8-PTR_LTR; KW Interspersed repeat. XX OS Populus trichocarpa OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus. XX RN [1] RP 1-367 RA Xu Z. and Wang H.; RT "LTR_FINDER: an efficient tool for the prediction of full-length RT LTR retrotransposons."; RL Nucleic Acids Res 35(Web Server issue), W265-W268 (2007). XX RN [2] RP 1-367 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from Populus trichocarpa."; RL Repbase Reports 7(6), 341-341 (2007). XX DR Genome; scaffold_1123; Positions 5623 5257. XX SQ Sequence 367 BP; 99 A; 76 C; 65 G; 127 T; 0 other; tgatatgtgc aacagaccct tcaccatgca accacgacat gcacacagac caccttcgcc 60 atgcaaccac gacatgcacc acgttcgtgg atcatgggct gacatgtcac agttagttag 120 ttttaagtga tgcaaataat tagtggggtt agtgccctgc ttttcgttat atgcagaatg 180 tgtgtgggaa tcatgcaccg attatttctg ctattatttc catttcattg tatcagttgt 240 ttttactcat tcattagttg gctataaaaa agtcatctga agtgtaagga aaggatatga 300 attaattatg caaaactctc ttctctgttt ctcattctgt caattcttct tcttttctta 360 aattaca 367 // ID Gypsy-25_VV-I repbase; DNA; EDCOT; 10896 BP. XX AC chr12; XX DT 20-JAN-2011 (Rel. 16.02, Created) DT 27-JAN-2011 (Rel. 16.02, Last updated, Version -1) XX DE LTR retrotransposon from the common grape vine: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Gypsy-25_VV_; KW Gypsy-25_VV-LTR; Gypsy-25_VV-I. XX OS Vitis vinifera OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC rosids; Vitales; Vitaceae; Vitis. XX RN [1] RP 1-10896 RA Jurka J. and Kohany O.; RT "LTR retrotransposons from the common grape vine."; RL Direct Submission to RU (20-JAN-2011). XX DR Genome; chr12; Positions 10088365 10099260. XX CC Positions [8306-8761] - Reverse transcriptase CC Positions [9776-10051] - Integrase core CC 'CACAG' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS 602..1510 FT /product="Gypsy-25_VV-I_1p" FT /translation="MVKVMSRGSRRRFTVESKAYELVIDEVGGKLRGCIWE FT RCKGLSSWIRFGDASLSSLLVGVESCCRDRDDSNWSLAWEEEGRKYRLERR FT TNEAGRFILCSVRDLEAKRFCLIFPEGKRLSRGWNILAEKLREVGVAPFRG FT VKDPLSLEVLKKEKEPDQRTYADVAKLKLGRLGDKVWLEAGRRVKPSRLEQ FT LGRCLVGSWDKVENHPPALDFLKNWVVHAWLLKGKLDIAVIGGGLILFEFE FT LISEAERVLARGKRKVLGSVLLMERWHPEVGCFSNGAFASEVWVKVVGLQW FT QSCNGLESRGV" FT CDS 8105..9295 FT /product="Gypsy-25_VV-I_4p" FT /translation="MRNVQHAIDFIPDASLPNLPAYRMNPTEHAELKRQVD FT ELLTKDFIRESLSPCGVPALLTPKKNESWRMCVDSRAINIITIKYRFPIPR FT LDDMLDMMVGSVIFSKIDLRSGYHQIRIRPRDEWKTSFKTKDGLYEWLVMP FT FGLTNAPSTFMRVMTQVLKPFIGRFVVVYFDDILIYSRSCEDHEEHLKQVM FT HTLRAEKFYINLKKCTFMSLSVVFLGFVVSSKGVETDLEKIKAIVDWPVPT FT NIHEVRSFHGMTTFYRRFIRNFSSIMAPIIECMKAGLFIWTKAANKAFEEI FT KSKMVNPPILRLPDFEKVFEVACDASHVGIEAVFSQEGHLVAFFSEKLNGA FT KKKYSTYDLEFYAVVQAIRHWQHYLSYKEFVLYSDHEALRYLNSQKKLNSR FT PAK" FT CDS join(2945..4786,4790..6574) FT /product="Gypsy-25_VV-I_2p" FT /translation="MKIKILSWNVRGVNDRNKRSSIKALIRSHKVDLVCLQ FT ETKMSQMSLGVVRSLGVGRFLDWGVLNARGAAEGVLVFWDKRVLELEGMEV FT GLFSISCRFKNYEDGFYWVFSRVYGPTLKRYRELFWEELGAIRGLWSDPWC FT IGGDFNSIRFPNESRKGGRLSSSMRRFSEVIDDLDLRDLPLQGGPFTWSGG FT LNNQAMTRIDRFLVSEDWEGHFKGAVQCTLPRPVSDHFPILLDGGGVRRGP FT VPFRFENMWLKEEGFKDLLKGWWQSLSFNGLFSFILAKKLKALKAILKSWN FT KDVFGQVGVNKKVALDKVNFWDGQEKLRPLSLEELEARKVAKGDFEKWALM FT EEVSWRQKSREVWLREGDRNTGFFHKMANSHRRRNCLSKIKVDGIWLTEEQ FT EIKRGVVKAFKDQLTDPGDWHPSMEGLDFNRIGDEDAARLEEVFSEEEVLK FT ALSDLNGDKAPGPDNFPLRFWQFCWDVVKKEIMGFLLEFHERGRFVRSLNS FT TFLVLIPKKAGAEDLRDFRPINLVGGLYKLLAKVLANRLKKVVGKVVSSAQ FT NAFVEGRQILDAALIANEAIDSLLKRNESGVLCKLDLEKAYDHINWNFLLF FT VLQSMGFGEKWTRWISCISTATFSVLINGTPEGYFNSSRGLRQGDPLSPYL FT FVIGMEALSRLIHRAMGGGFLLGCRVNGRGGNGALVSHLLFADDTLVFCEA FT SEDQMVHLSWLLMWFEAISGLRINLDKNEISPVGRVENLALEAGCKVGKLP FT SSYLGIPLGANHKSVVVWDGVEERFRKRLALWKRQFISKGGRITLIRSTLS FT SMLIYLMSLLRMPRVVSLRLEKIQRDFLWGGGALERKPHLVNWDTVCMDKR FT KGGLGVRRLSILNRALLCKCFAIERENFWRHVISRKFGEEEGGWSSREVRE FT SYGVGFWKEIRKEGALMQNKVAFLVGNGRRVKFWKDIWWGNLALCNSFPSL FT YAFASSKEAWVEEFWDTLGGEGAWSPRFSKPFNDWEVEEVERLLLTIRGAR FT LSPLMEDRMMWKVNSNGIFSVKSLYNDLSSRRAGLFPHGLIWNPSVPSKVS FT FFAWEASWGKVLTMDQLKKRGWAIANRCFLCCEEEESIDHILIHCSKARAL FT WELLLALFGVCWVLPSSARETLIEWRGFMLGKKHSMVWKAAPLCLFWAVWM FT ERNRIAFDNEDFSVHRLKNSFVCNLWVWTKTIVNEGPLTLPSFFYWLGAR" XX SQ Sequence 10896 BP; 3118 A; 1730 C; 2951 G; 3097 T; 0 other; attttggtat cagagccaaa gttcttggct tgaaagcata tgcaattaag gagcggagca 60 acttatgcaa gcatgagttc caaaaaaact tctagcaatc tagatgccgc tacaatacac 120 ttggaggaaa tttcagccac acaacaatcc catcaagatg ctatagtaca actaaatagc 180 aaacttgatg agatcatgaa tttattagaa aatagtcaag aaaaacgacc aattgaagag 240 gagattgcaa gtcatcaatt tagacaatcg ccaaatcaat cacacgaaga acaagacaat 300 tttatgatgg ggactcaaag aaaggccaga ctttttgagc tagatgatga tgtgactaaa 360 aaggtatgtc ttgaagtttc tgaattttat ggaaaactaa atccaacagc ttttcttgat 420 tggattatgt caatggaaga ttactttgat tggtatgcaa tgcccgaaaa tagaaaagtt 480 tgttttgtga aggcaaaggt gaaaggagca gcacgtctat ggtggcataa tattgagaga 540 gcttgtgaca aaccctcaaa taagctgcat agtgatggag aaaaggttct gtttttagac 600 gatggtgaag gttatgtcta gaggaagtag aagacggttt actgtggaat ccaaagctta 660 tgaacttgtg attgatgaag taggaggaaa gctgagagga tgtatttggg agagatgtaa 720 agggttatca tcttggatca gatttggaga tgcaagtctc agtagtttgt tggtaggagt 780 ggagtcctgc tgtagagata gagatgatag taactggtcc ctcgcatggg aggaggaggg 840 aaggaagtat agattggagc gtcgtacaaa tgaggcgggt agattcattc tctgttctgt 900 tcgtgatttg gaggcaaaaa ggttttgctt aatttttcca gaaggaaaga ggctatctag 960 aggatggaat atcttggctg agaagctgag agaggttggg gtagctccat ttagaggagt 1020 aaaggaccct ctttctcttg aggtgctgaa gaaggaaaag gagcctgatc aaaggacata 1080 tgcggatgta gcaaaactga aattggggag acttggggat aaggtttggc tggaagcggg 1140 aaggagggtg aagcctagta gattagagca gctgggtcgt tgcttagtgg gtagttggga 1200 taaggtggag aaccatcccc ctgcgttgga ttttctgaaa aactgggttg tccacgcttg 1260 gctcctcaaa ggcaagctgg acatagctgt aattggaggt gggctaatac tctttgagtt 1320 cgaattgatt agtgaggccg agcgtgttct tgctagaggg aagagaaagg ttctaggcag 1380 tgtattattg atggaaagat ggcacccgga ggtggggtgc tttagcaatg gtgcttttgc 1440 tagcgaggta tgggtgaaag tggtaggtct tcaatggcag agctgcaatg ggctagaatc 1500 gagaggtgtt taagttgata ggagatggtt gtggtgggtt cattgctgtg gataacaaga 1560 cagattcaat ggcagagctg caatgggcta gaatgttggt gaaatcggcg ggcaggaaca 1620 caccttcctc tgtccagatt gtggatgaga tggggtgctt ctcagtccag ctgtggtggg 1680 aatccccacc ttggttctct caggtggtgc cggcgggaag tggccttggg aaaggggatg 1740 tagtggttgt agaagttaca gggagtgggt ctcgtaatga gtgtagagga ggcgtgctgg 1800 tgaaggttgg acagccaaag gagcagaggg gagtaactga gccgccctgt ggtagttctt 1860 caaaaggggc tttaggctat ccatatgagt tggctgaaag agggcttgga gaggaggtaa 1920 ctgatggaga agacagctgc gggatcagaa gtcgaggtgg agggaaatta gcaaacctgg 1980 gaggttttaa atctgggcca gcagcttgtg tttttgggac cgattgggag gcccaagtca 2040 ggagcgggct tggagaggat ggtattaagt caaactatgt gggagcccaa atatttgggc 2100 cagattgtga gcccaggccc atcacgttaa aaggatgggt aatgggctgc gaggataggc 2160 ccttcctcat aaaggggtcg attgcgggct gtgaaggaag ggccgacatg ggttttgagc 2220 ctgagttggg agggataaaa ggaaataggg cttctccttg tgccgaggtc ggggggatgg 2280 agattaaggc tacgatggaa gcttcgggtg gccaagttaa ggaggacggg gggatcgcgt 2340 gcttcctagg aggagattag agggattctg agtctctaat ggcgaaggcg agagcgcgaa 2400 tgactgaaga agcgttgtca gctgaagcgt ccaggtacga gcccgttacc gatgttcttg 2460 ggggggatcg ggacttcttc tcttcttcta ctctttctgg gtgcgatcgg gctatggtgg 2520 tggggggtgt taggggtacg gtagtcattg acgaagatgt tgggtatcaa gctccgttgt 2580 gtgccgtgtt gattgatggt agtccgtggg agacgagtac agagggggga aagaacaggg 2640 gtttcaggtc aaaggagagt gaggatctgg aggaagaaga ggactagggt agcggttggg 2700 atgacagtag cttggctaag ttcagtaaga ctttgggatt ctcgacagtt ggcgttgaag 2760 gggaagtcct taaattactg ttaaggctga aatcaaggag ggatcaaggc aagaagaaag 2820 gaattgcagg gatgactagg tttgataggg aagtgaaaaa atcggaatgg tcgattaatt 2880 atgaaggaga aagcaggaag aaaggctcgg atagaagaaa tggggataga gctctgtgtc 2940 ttaaatgaaa attaaaatcc tatcttggaa tgtccggggg gtgaatgata gaaataagag 3000 aagttcaatt aaggccttaa tcagatccca taaagtggat ttggtatgcc tgcaagagac 3060 taaaatgtct cagatgtctt taggggtggt gagaagtctt ggagtgggga gatttttaga 3120 ttggggagta ctgaatgcga ggggggcagc tgaaggggtg ctggtttttt gggacaaaag 3180 agtgttggag ctggaaggga tggaggtggg ccttttctcc atctcctgcc ggttcaagaa 3240 ctatgaagat ggattttatt gggttttttc aagagtgtat ggccctacct taaagagata 3300 tagagagctg ttttgggaag agctaggggc catccgcgga ctctggagcg atccttggtg 3360 tatcggaggt gacttcaatt caatcagatt tccaaatgag agtagaaaag ggggaagatt 3420 gtcttcttca atgagaagat tttcggaagt gattgacgac ttggatttga gggatcttcc 3480 ccttcagggg ggtccattca cctggagtgg aggactgaac aatcaagcta tgaccaggat 3540 agaccgtttc ttggtgtcgg aggattggga gggtcacttt aagggggcgg tgcagtgtac 3600 tcttcctagg cctgtgtccg accacttccc tattctattg gatgggggag gggttagaag 3660 aggtcctgtt cctttccgtt ttgaaaatat gtggcttaag gaggagggat ttaaggatct 3720 gttgaagggg tggtggcaga gtctaagctt taatggtttg tttagtttca tccttgctaa 3780 gaagttgaag gctttgaagg ctattctaaa gtcgtggaat aaggatgttt ttgggcaggt 3840 gggtgtcaat aagaaagtgg ccctggacaa ggtgaatttc tgggatggtc aggagaagct 3900 tcgcccctta tcattggagg aattggaagc tagaaaggta gcaaaggggg acttcgaaaa 3960 atgggctcta atggaggagg tttcttggag acaaaaatca agagaagttt ggctaaggga 4020 gggtgataga aacacaggtt tttttcataa aatggctaac tcccatagaa ggagaaactg 4080 cctgtccaag attaaagttg acggtatatg gttaacagag gagcaggaga taaagagagg 4140 ggtggttaaa gctttcaagg accaattgac tgacccgggg gactggcacc cttctatgga 4200 aggtctggac tttaatagaa ttggagatga ggatgcagct agattggagg aggttttttc 4260 agaggaagag gtcctcaagg ctctttcaga tctgaatggg gacaaggctc cgggtccaga 4320 caacttcccc cttaggtttt ggcaattttg ctgggatgtt gtcaaaaaag agatcatggg 4380 ttttttgtta gaatttcatg agcgcggcag atttgttagg agcttaaatt cgaccttcct 4440 ggtcctaatc ccaaaaaaag ctggcgccga ggaccttaga gacttcagac cgatcaattt 4500 ggtgggcgga ttgtataaac tgttggcaaa agtgttagcc aacaggctta agaaggtagt 4560 gggcaaagtg gtgtcctcag ctcaaaacgc ttttgttgaa ggaagacaga ttctcgatgc 4620 tgcccttatt gccaatgagg caatagattc tttgttgaaa cgaaacgaga gtggggtgtt 4680 atgtaaattg gacttagaga aggcatacga tcacataaac tggaattttt tgttgtttgt 4740 attgcaaagc atgggatttg gggagaagtg gactaggtgg atctcctagt gcatctctac 4800 agcaacgttt tcagtattga tcaatggcac cccggaaggc tacttcaaca gttcaagggg 4860 gctgcgtcag ggggaccccc tatcccctta cctttttgtg ataggaatgg aggcccttag 4920 taggctgatc catagagcaa tggggggagg gttcctatta ggctgtaggg ttaatggaag 4980 gggtgggaat ggggctttgg tatctcattt gctgtttgcc gacgacacgt tagtgttttg 5040 tgaagcttct gaagatcaga tggtccactt aagctggttg ttgatgtggt ttgaagccat 5100 atcaggtttg agaatcaact tggacaaaaa cgaaatttcg ccggttggta gagtggagaa 5160 tttggctctt gaggctggct gtaaagtggg caagctgcct tcttcttatt tggggatccc 5220 tttgggggcg aatcacaagt ctgtggttgt ttgggatggg gtggaagaga gatttcggaa 5280 acggctggcc ttgtggaaga gacaatttat ttccaaagga gggagaatta ctctaattcg 5340 gagtacattg tcaagtatgc tcatatactt gatgtcttta cttcgaatgc caagagtggt 5400 tagtctaagg ttggagaaaa ttcaaaggga tttcttgtgg ggagggggtg ctttggagag 5460 gaagcctcac ttagttaatt gggataccgt ttgcatggat aaaaggaagg ggggtttggg 5520 agttagacgc ctttccatcc ttaatagggc ccttctttgc aagtgttttg cgattgaaag 5580 ggagaacttt tggaggcacg tcattagtag gaagttcggg gaggaagaag ggggttggag 5640 ttctagagaa gttagggaga gttatggagt aggattttgg aaggaaataa ggaaggaagg 5700 tgcccttatg caaaataaag tcgctttttt agtggggaat ggtagaaggg taaaattttg 5760 gaaagatata tggtggggaa acctcgcctt atgcaattct tttccctcct tgtatgcttt 5820 tgcctcctct aaggaggcct gggtagagga gttttgggac actttgggag gggaaggggc 5880 ttggagtcct agattttcta agcccttcaa tgattgggag gtggaagagg tggagaggct 5940 tcttttgaca atccgaggtg caaggcttag tcctcttatg gaagatagaa tgatgtggaa 6000 ggtgaattcg aatgggattt tttcagttaa atcactctat aatgatctat cttcaagaag 6060 agctggtctt ttccctcatg gtttgatttg gaaccctagt gtgccttcca aagtgagttt 6120 ctttgcttgg gaggcttctt ggggtaaggt gcttactatg gatcagctta aaaagagggg 6180 gtgggctatt gctaacagat gttttctgtg ctgtgaggaa gaggagtcaa ttgatcatat 6240 tcttatacat tgctccaagg caagagcttt atgggaatta ttgctcgccc tctttggagt 6300 gtgttgggtc ctcccatctt cggctagaga gacccttatt gaatggaggg gctttatgtt 6360 gggcaagaag catagtatgg tgtggaaggc agccccgtta tgcctttttt gggcggtttg 6420 gatggaaaga aacaggattg ctttcgataa tgaggacttt tcggttcata ggttgaaaaa 6480 ttcttttgtt tgtaatcttt gggtgtggac aaaaacaatt gtaaatgaag gtcctcttac 6540 tttacctagt tttttttatt ggctaggcgc tagatgaggg tcgggtttgt tttttctctt 6600 cttttgtgtg tgccttaagg ggccttttgt atactccctg tatgctattg ggctttcctc 6660 ttggtgccct tttctaatat atttctgctt ttgcctatca aaaaaaaaat aatattaaga 6720 atcaagttca tagaactagc caaccaccta ttgacacatg ggacaagatg aagttgaaga 6780 tgaaggagca ctttctccca actgattatg aacaacttat gcatacaaaa ttgttttccc 6840 ttaaataagg taccaagtcc gttgaagaat atacagaaga attccatgaa ttgagcattc 6900 gaaatcaagt gtgggaaagt gatgctcaac ttgcagccca ctataaagct ggacttcgaa 6960 tggagattca acttgagatg atagttgcac acacttatac cgtagatgac gtttatcaac 7020 tagccctcaa aatagaagaa ggcctcaaat ttcgggtttc caagcgtcca agttcacaaa 7080 ttgggagcac tttctccaac aggacagcaa gcaaaccttt aagcacatca aacttcagaa 7140 cttctaatca tgtgactggt gggggcaaca ctcaacaaac ttcgaatgtg gctcataaga 7200 atggtaataa gggtaaaaat tcaatgagta ttggagatag aaaagtagat gtgactcctt 7260 tatgctttaa gtgtggtggg catggtcatt atgctgtggt atgcccaacc aaaggtttac 7320 acttttgtgt tgaagaaccg gaatttgaat tggaaagtta cctaaaggaa gaagagacct 7380 acaatgaaaa tgaagttagt gaagaatgtg actactatga tggtatgacg gaaggacata 7440 gtcttgtaat acgaccttta ttaactgtcc caaaagtaaa aggagaagaa gattggcgac 7500 gtactagcat tttccaaaca catatttctt gccaagggag attatgcacc atgatcattg 7560 atggaggtag cagtttgaac atagcttcac aagaacttgt tgagaagcta aaccttaaaa 7620 cagagagaca tccaaatcca ttcagagtag catgagttaa tgacacctct atctcgataa 7680 gttttcgctg cttagtaaca ttcctttttg gtaaggactt tgaagagttc gtatagtgta 7740 aggtcttacc cattaaagta agtcatattt tacttggaag accttggctc tttgatagaa 7800 gagtttaaca tgacggctat gaaaatacat atgctctcat acacaacgaa tgtaagaaga 7860 tccttcgtcc aatgaaagaa gtccctccaa ttaagaagtc aaaagaggat gcacaaccaa 7920 aaaaggtact tactatgtgt caatttgaaa atgagagcaa ggaaactaaa gttatttttg 7980 ctttaatggc tcggaatgtg gaagaattta aagaacaaga taaggaatat ccagcaaacg 8040 tacgtaaaat ccttgatgac ttttctgact tatggcctac agagttacct aatcaacccc 8100 tcctatgcgt aacgtacaac atgccattga ttttattccc gatgcatcat taccaaattt 8160 accagcctac agaatgaatc caacagagca tgctgaattg aaaaggcaag ttgatgaatt 8220 acttactaaa gactttattc gtgaaagcct aagtccttgt ggagttcctg ccctactaac 8280 accaaagaag aatgaatcat ggcggatgtg tgtggatagt cgtgcaatca acataatcac 8340 aatcaagtat cgatttccaa ttccaagact tgatgacatg ctagatatga tggttggatc 8400 agtaatcttc tcaaagattg atctaagaag tggatatcat caaatacgta ttagaccaag 8460 agatgaatgg aagacatctt tcaaaactaa ggatggattg tatgagtggt tagtcatgcc 8520 gtttggacta accaatgctc caagtacctt catgcgggtt atgacgcagg tattaaaacc 8580 ttttattgga cggtttgttg ttgtctattt tgatgatatt cttatctata gtcgatcttg 8640 tgaagatcat gaggaacact tgaagcaagt aatgcacact cttagggctg aaaaatttta 8700 cattaatttg aaaaaatgta ctttcatgag ccttagtgtt gtatttcttg gctttgttgt 8760 gtcttctaag ggtgttgaaa cagatctgga gaagattaaa gctattgttg attggccagt 8820 accaacaaat atccatgagg tgcgaagctt ccatggaatg actacatttt atagacgatt 8880 tattcgaaat ttcagctcta ttatggcccc aattatcgaa tgcatgaaag ctggtttatt 8940 tatttggact aaggcggcca acaaggcatt tgaagaaatc aaatccaaga tggtgaaccc 9000 tcctatccta cgtctaccag actttgagaa agtatttgag gtggcctgtg atgcttccca 9060 tgtgggaatt gaagcagttt ttagccaaga gggacatctt gtggctttct ttagtgagaa 9120 actcaatggg gcaaagaaaa aatactccac atatgatctt gaattttatg cggtggtgca 9180 agcaattagg cattggcaac attatctcag ttacaaggaa tttgttttgt attcagatca 9240 tgaagccttg cgatatctta attctcaaaa gaagcttaac tctcgacctg caaaatgaag 9300 tagttttctt cagctgttta cctttaattt aaagcattgt gcaggaattg aaaataaagt 9360 agttgatgcc cttagtagga agacccttct cctagtaaac atgccaacca ctacaattgg 9420 aattgaagaa ttaaagcatt ggtatgataa tgatgctgat tttggagatg tttattcctc 9480 tcttttgagt ggttcaaaag caacatgtat tgatttgcag attttagaag ggtacttgtt 9540 ttataaaaat cgtttatgct taccagggac ttctctacat gatcatgtca catgggaact 9600 ttatggaggc ggaatgggtg gacattttga acgagataag accattgctt tggtggaata 9660 tcgcttcttt tggcctagtt taaagaagga tgtttggaag gttatcaaac aatgtcgagc 9720 atgtcaagta ggaaaagggt caaagcaaaa tacggggtta tatacgccat taccaattcc 9780 atccaaacct tgggaagact tgagcatgga ttttgtactt ggattaccaa ggacacaacg 9840 gggctttgat tctatatttg ttgtggttga tagattttcc aaaatggcac attttatccc 9900 atgtaagaag gcttcggatg cttcttatgt tgctgcctta ttctttaaag aagtagttcg 9960 attgcatgga ttaccacaat ccattgtttt ttattgtgat gtcaagttta taagctattt 10020 ttggaaaacc ttgtgggcca agctaggtac ttaattaaaa ttttcaagtt cttttcatcc 10080 tcaaactgat ggacaaatag aagttgtcaa tcgcagtctt ggtaatcttt tgagatgcat 10140 tgtgagagat cagttgagaa attgggataa tgtcttacca caagccgaat ttgctttcaa 10200 tagctccact aatcgtacta ctgggtactc accttttgaa gtggcatatg ggttgaaacc 10260 taagcaacct gttgatctta taccattacc tacttttgtc cgcaccagcc aagatggtga 10320 tgcatttgca cgtcatatac gagatataca tgaaaaggta cgagaaaaaa tcaaaatcag 10380 caatgaaaac tataaagagg cagcagatgc acatcgaaga tatattcagt ttcaagaagg 10440 tgatctagtg attgtccgtt tacgactaga aaaatttcat ccgagcacat atcaaaagct 10500 tcaagctaag aaagcgggtc cattttggga actaaagcgg ttgggtgaga atgcttattt 10560 gttagagctc tcttcaaact tgcattttag tccaatattt aatgtggaag atttgtatat 10620 ctaccatggt catcacaacg atgtaagtga agagttggat cttcaattac cacctactct 10680 tagcccacgt cctgagattg agtatattct tgatgatcaa cttgtgtcta ctcgacaagg 10740 tggataccaa aattttttgg tgaaatggcg aggcaaacca cattcttaga atacatggat 10800 tacgacaacg gattttcaga agattaatcc cgatctcgat gaattgtatc aagcatctaa 10860 ctcgtcggag ccgagttctt tcaagccggg gagaat 10896 //