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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA3-8_Mad repbase; DNA; EDCOT; 875 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative non-autonomous Harbinger family DNA transposon from DE apple. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Murbi_MT repbase; DNA; EDCOT; 524 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 non-autonomous DNA transposon from Medicago DE truncatula. XX KW DNA transposon; Transposable Element; Nonautonomous; LTR; KW retroposon; repeat; Interspersed; 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. Flanked on both the termini by CC conserved 8-9 bp TSDs. 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 GYVIT1_LTR repbase; DNA; EDCOT; 1902 BP. XX AC AM448663; XX DT 25-APR-2007 (Rel. 12.04, Created) DT 25-APR-2007 (Rel. 12.04, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon - long terminal repeat (LTR). XX KW Gypsy; LTR Retrotransposon; Transposable Element; 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 are 96% identical to each other and show no similarity to CC 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 PIGY-I_PS repbase; DNA; EDCOT; 9248 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 LTR retrotransposon PIGY-1 (internal). XX KW LTR Retrotransposon; Transposable Element; envelope; Metaviridae; KW PIGY-1; PIGY-LTR_PS; 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 GYPMET_I repbase; DNA; EDCOT; 7285 BP. XX AC AC161863; XX DT 09-NOV-2006 (Rel. 11.11, Created) DT 05-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE Internal region of GYPMET retroposon, from Medicago truncatula. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW Interspersed repeat; LTR retroposon; Medicago; 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 "GYPMET: 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, while the LTR CC sequence shows closest resemblance to Gypsy. Contains conserved CC integrase domain. XX FH Key Location/Qualifiers FT CDS 2015..2992 FT /product="GYPMET_I_1p" FT /translation="MPSSVLDNEIPHSLLFPKDPLYSVPLRVFGSACFVHD FT LSPGRDKLSPRAVKCVFWGYSRVQKGYRCYCPSTHRFYVYADVTFFEDTPF FT FTTPSTSDSTSHSTSQVLPIPLFEPFVPTQRLPQSLTRPGFRRYGATYERR FT HVTIPESAPTDFDNIVQETTPTISDDSSSILILSPNVDPPDPIIDLPIALR FT KDNRSTSNPHPIYNFLSYHRLSPLHHAFVSAISTVSIPKTVKEALSHLGWR FT QAMIDEMNTLESSSTWKLVPIPHGKSKVGCRWVFAIKVGPDGHVDRLIARL FT VAKGYTQIYNSCKNGICSCFLINGFYEPLAFVST" 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 DNA3-4_Mad repbase; DNA; EDCOT; 442 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE non-autonomous Harbinger family DNA transposon from apple. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 TNT1_I repbase; DNA; EDCOT; 4114 BP. XX AC X13777; XX DT 12-SEP-2002 (Rel. 7.08, Created) DT 12-SEP-2002 (Rel. 7.08, Last updated, Version 1) XX DE Nicotiana tabacum retrotransposon TNT1_I, internal region. XX KW LTR Retrotransposon; Transposable Element; reverse transcriptase; KW endonuclease; protease; internal region; 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 "Characterisation 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 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 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. 15.1, 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-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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 TOPIE1_LE_LTR repbase; DNA; EDCOT; 1065 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 TOPIE1_LE_LTR, long DE terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Long terminal repeat; KW retrotransposon; 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; 322 A; 228 C; 132 G; 383 T; 0 other; tgatattcta cacgacctaa taatttactg attttaactt tccacctaag tgtgaaacag 60 gttgactaat gtgttccagc aaagcagtta agatagtaag taaaagcaca ttatttttac 120 gtggaaagac ctagctcaaa aggtgtaaaa accacgacct gtacccttac aagatttaac 180 tccaacttca ctaaatcaat tacgagcctc cacaaaagat agattacaaa ctttgcaacc 240 taccttaact tcaagttatg aatttgaatt acaactcttg taatcctagg aactaactct 300 aattctaacc ttcaacacaa acctcccaag gtatgtgttc ctaacacttc gaattatcac 360 aaccctaaga caatactcct agttcagttt ataactcact gaactaagat tacatcaaga 420 ctcattcaca aagaaaaact cctaacacat aaactctgta aaggattaga ttcttcgatg 480 tgttccttca gttcgctggt agcacttacg aagtgaattt ctcaatcgct tttttactca 540 gtaagtgcac aagtattctg aacgacttcg cttctattta agcacattta tcatagagtt 600 attgttcact tcaaactcct tattgacttg tactctcttg acttagagtt ttacttcaag 660 taagactcct tctttaattt aaacttctaa cttttttaga cttcttcttc aaattacatt 720 cgttgattct tttgtattgt agtcgaactc taacacttca attcagcagt aacttgaaga 780 gttctatttt aagtgagact ttttcttcaa ttaaaattgt ttgtctcttt agtctccttc 840 ttcaaatcaa actcatcaat tctttctctt caattcatca gatgtttatt tccgtggggt 900 ttctgacgaa gttaacatta tccattcttt tatttctgca cttttgtctt tattcatttt 960 agaagctttc tcgaattcaa cagctcgtga cagtgcacct ttgtaccatg ttgactgacg 1020 tgtttcttct ttctttgtca atcatcaaaa ctgcataaat tccaa 1065 // ID SHALINE4_MT repbase; DNA; EDCOT; 2282 BP. XX AC . XX DT 21-DEC-2006 (Rel. 11.12, Created) DT 09-JAN-2007 (Rel. 11.12, Last updated, Version 1) 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 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 LTR 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-72_Mad-LTR repbase; DNA; EDCOT; 260 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 L1-10_Mad repbase; DNA; EDCOT; 5437 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 HAT-1N_Mad repbase; DNA; EDCOT; 951 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-1_Mad; 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 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 PSAT19 repbase; DNA; EDCOT; 659 BP. XX AC AF155749; XX DT 08-NOV-2002 (Rel. 4.3, Created) DT 08-NOV-2002 (Rel. 4.3, Last updated, Version 1) XX DE Pisum sativum dispersed repetitive DNA, PSAT19. XX KW Repetitive sequence; dispersed; PSAT19. 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA3-2_Mad repbase; DNA; EDCOT; 819 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HARB-N3_Mad repbase; DNA; EDCOT; 617 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 DNA9-5_Mad repbase; DNA; EDCOT; 667 BP. XX AC . XX DT 13-OCT-2010 (Rel. 15.1, Created) DT 13-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW 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 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 CAULIV-1B_Mad repbase; DNA; EDCOT; 7676 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Caulimovirus-like sequence. XX KW Caulimoviridae; Integrated Virus; 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 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 Ogre-LE1_I repbase; DNA; EDCOT; 12262 BP. XX AC AC171735; 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-LE1; 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..3882,3886..5538,5807..7351,7355..7789, FT 7825..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 YLHASYPVYNVQPTHFTPPPTQTPNYRNRPSYERRPTKTYTPLAEPIAQLY FT ERLKQAGYVSPIPALPVDVRAKWYDPNKVCAYHSGMKGHTTEVCRALKDKV FT QMLIDTKTIQLKDPTPNVANNPLPNHQVNMVEAGDVWDWEESIWAVETEEA FT MPTTAQAPLIVQGLAPFEVEVAAPRPPFAVYKASSPTQCDTHAVPWDYNKR FT ETNVEETDVATGVTRSERIYTSENLVQGSSSKSKAPIVELEDQSIWKKVKA FT KEYSVIEQLSKTPSQISILELLQSSETHRDALLKILGEAYVPSNITHGEVS FT QMVGQVFEAYKISFHKDELPIEGTTHNKALYISVQYQDKVINKALVDAGSG FT LNICPLSTLTRLGVDSAKIQTWKMNVRAFDGSQRGTIGEITLDMLIGPVTF FT PIAFQILDIPSSYNLLLGRPWIHMAGAVPSTLHQCLKFEWDYEEVVVHGEK FT GHPVYTIEGRENMDGEMYHTVELVGNIELQPWFSQKIIDMMAWFGFELGKG FT LGAKLQGIVEPIQPVRHSTTFGLGYKYTTEEWLDWRPPRDGYYYPLKKPIP FT PLYQSFFPSMYCFQMRTYEIFKSLSIKFFSPFFCLVFNFYYFFFLTSKIHY FT KNVESEIVAYNETAQLNLNDLEEVEDNEVPEELIKRVEEFEEKPNPNLVET FT EVVNLGNAEVIQETRVSIHMTKEDKKEYTEFLIENKDIFAWSYADMTGLST FT AIVAHRLPTDPACPPVKQKLRKYKPEMSLKIKEEVSKQLDVGILQVTEYPT FT WLANVVPVPKKDGKVRVCVDYRDLNKASPKDNFPLPNIHILIDNCAKHETQ FT SFVDCFAGYHQIEMHKDDAEKTAFITPWGVYNYKVMPFGLKNAGATYMRAM FT TTLFHDMIHKEIEVYVDDVIIKSKESLNHLEDLRKFFARLRKYNLKLNPAK FT CVFGVPAGKLLGFIVSRRGIELDPSKIKAIRDLPPPKSKKEVMSFLGRLNY FT ISRFIAQSTVICEPIFKLLKKDAAVKWTSECQQAFDKIKDYLSNPPVLVPP FT ESGRPLLLYILVLDNAFSCILGQHDETGRKEQAIYYMSKKFTSCEARYSLL FT ERTCCALTWVAKLRHYLSSHTTYLISRMDPLKYIFQKPMPTGKLAKWQILL FT SEFDIVYVTQKAVKTQALADHMAENPVDDDYRPLKTYFPDEEVAFVGEDIS FT EEYDGWRMFFDGAKNLNGCGIGAVLISPTGQHYPVSAKLRFLCSKIWPNTK FT PAYEMIIIGDSDLLIHQVRGDWATKNRKLLPYLECVRRLCKRFVKTEFRHV FT PRVQNEFADALATLSSMIRHPDHNYIDPIHIHIHEQPAYCFHVEEEPDGKP FT WYDDIRRYLKSGEYTEDATSVQKRTIRRLATQFFLSGEILYRRTPDLGLLK FT CVEAREARRLVEEIHAGTCGPHMNGFTLAKKILRSGYYWLTMETDCIRYAQ FT KCHQCQTHADMIRVPPNELHVTSSPWPFAAWGMDVIGPIEPTASNGHRFIL FT VAIDYFTKWVEATSHKSVTKKVVDDFVKNNIICRFGIPESIITDNGTNLNS FT DLMRSMCEKFKISHRNSTAYRPQMNGAVEAANKNIKRILRKMIDNHKHWQE FT KLPFALLGYRTTIRTSTGATPYFLVYGTEAVIPAEVEIPSLRIIQEAKLSD FT ADWIRGRAENLALIDGRRINAICHGQLYQNRMARAFNKKVKPRHFSPGQLV FT LKRIFPNQDEAKGKFSPNWQGPYIVSRVLTGGALILAEMDGEVWPKPINSD FT SVKKYYV" 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-N11_Mad repbase; DNA; EDCOT; 1473 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 MuDR-N1_Mad repbase; DNA; EDCOT; 544 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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" 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" 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 L1-15_Mad repbase; DNA; EDCOT; 3799 BP. XX AC . XX DT 07-OCT-2010 (Rel. 15.1, Created) DT 07-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 LTR-6_Mad repbase; DNA; EDCOT; 2364 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-69_Mad-I repbase; DNA; EDCOT; 4558 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Ogre-PT2_I repbase; DNA; EDCOT; 12216 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_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: 6319..6556: 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 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-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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-N13_Mad repbase; DNA; EDCOT; 511 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.1, 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-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 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-85_Mad-LTR repbase; DNA; EDCOT; 388 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-4N1_Mad repbase; DNA; EDCOT; 1680 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW HAT-4_Mad; 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 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 TE-1_Mad repbase; DNA; EDCOT; 2915 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative transposons from the apple genome. XX KW Transposable Element; Nonautonomous; 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 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 PIGY-LTR_PS repbase; DNA; EDCOT; 2653 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 LTR retrotransposon PIGY-1 (Long Terminal Repeat). XX KW LTR Retrotransposon; Transposable Element; Long terminal repeat; KW Metaviridae; PIGY-1; 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 LycEPRV_I repbase; DNA; EDCOT; 7521 BP. XX AC AC171732; XX DT 16-MAR-2006 (Rel. 11.03, Created) DT 19-APR-2006 (Rel. 11.03, Last updated, Version 1) XX DE Endogenous virus from Lycopersicon esculentum (internal portion). XX KW Endogenous Retrovirus; Transposable Element; Interspersed repeat; KW LycEPRV_LTR; 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 DR EMBL/GenBank/DDBJ; AC171732; Positions 86129 93649. XX CC LTRs are ~97% identical. No LTRs have been reported previously CC for CC 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA8-8B_Mad repbase; DNA; EDCOT; 1146 BP. XX AC . XX DT 18-OCT-2010 (Rel. 15.1, Created) DT 18-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 COPIA3-I_LC repbase; DNA; EDCOT; 7511 BP. XX AC . XX DT 09-SEP-2005 (Rel. 10.09, Created) DT 16-SEP-2005 (Rel. 10.09, Last updated, Version 1) 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 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 1-7511 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Ogre-MT4_I repbase; DNA; EDCOT; 12091 BP. XX AC AC145061; 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-MT4; 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: 6054..6356: 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-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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, 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-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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 RTE-1B_Mad repbase; DNA; EDCOT; 7630 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE RTE retrotransposons from the apple genome, consensus. XX KW RTE; Non-LTR Retrotransposon; Transposable Element; 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 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 PSL repbase; DNA; EDCOT; 9932 BP. XX AC AF009516; XX DT 28-AUG-1998 (Rel. 3.07, Created) DT 28-AUG-1998 (Rel. 3.07, Last updated, Version 1) XX DE DNA transposon PSL. XX KW DNA transposon; Transposable Element; 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 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 HAT-N8_Mad repbase; DNA; EDCOT; 532 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-N7_Mad repbase; DNA; EDCOT; 347 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, 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-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 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-27_Mad-LTR repbase; DNA; EDCOT; 473 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; KW 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 DR [1] (Consensus) XX CC TSD is 9-bp long. TIRs (Pos. 5-45 and 642-682) is 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 SINE-4_Mad repbase; DNA; EDCOT; 212 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative SINEs from the apple genome. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Nonautonomous; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 L1-8_Mad repbase; DNA; EDCOT; 3879 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 EGLN1_SM repbase; DNA; EDCOT; 405 BP. XX AC AB016142; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Solanum melongena LINE retrotransposon EGLN1_SM, endonuclease DE region. XX KW L1; Non-LTR Retrotransposon; Transposable Element; endonuclease; KW LINE; long interspersed nuclear element; 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 TAM3_AM repbase; DNA; EDCOT; 3629 BP. XX AC X55078; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 25-MAR-1997 (Rel. 2.02, Last updated, Version 2) XX DE Antirrhinum majus Tam3 gene for Tam3-transposase. XX KW transposable element; AMTAM3TN; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-6_Mad repbase; DNA; EDCOT; 3483 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 U_LTR_MT repbase; DNA; EDCOT; 2966 BP. XX AC . XX DT 13-JUN-2006 (Rel. 11.06, Created) DT 13-JUN-2006 (Rel. 11.06, Last updated, Version 1) XX DE Putative long terminal repeat from Medicago truncatula - DE consensus. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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; 1155 A; 683 C; 325 G; 797 T; 6 other; tgtaacgccc tatttctatt aaagtgataa aacacgcgaa taatataaat attcaagaaa 60 tagacgccac gtcatcaaca aaaaccaaat caacatgcat atataaaaat tctcaacagt 120 cgcagcggat ataaaccata cacctcaaaa gtatacatgt catgatatca aaatacatca 180 tcataaaaat tctccaaatc ccgacaaatg ggtaaatctc cacaacataa ataaatccag 240 aataaacaat ctagaataat cataagacag acatcctaga tcagagccta ccctaagact 300 ctaaggaaac gataacggag atagctcccg atatccaagc aactcaccaa aagcaactaa 360 tcctgcactt cgtctaccca tccatacaga caggtaggtg gtcaaaacca ctaggggggt 420 aagctttaca tcaatcataa tcaacataaa caatttgaac ataaatgaat caaatcaagt 480 atcaattaat taaacataag caattaattt ccatatacac attcatrcaa caattccaaa 540 tatcacaatt aagcattcat caaacacact tatcatcaac attcatcatt cacatgcaac 600 aaataagact catgccaata tgatatgcgc ctaatcccaa cacatatatg catgtggtac 660 caaataacat caaggtcgtc acccatgatg caacaaaaac atcatatgta agatttcaca 720 cccgtcttac attatcaccg atgtaaaaga gtacacctcc ttttacaatt ctcatcaaga 780 ctcaacatga ctatgatgca tggacataca agcaaagact cgayaatgca aaatcacctc 840 ataaatatat caacaacaat rtaaaggwtm acctccaatt atattgatca acctcaacaa 900 caattgcatt atcaagtatt tacgtccaca caatcaatca agtcataatt caattaagag 960 tcatcaycaa attatcatca taatatatca acatcaattg atatatatac attaatcaac 1020 atcaactata taatatagtt caaccactcc aaatatttct cacattccaa gtaaagagaa 1080 aatacaacac cttatgataa acatcatatt caacacctaa caattcattc acatatcttc 1140 atttaatcat ataaagctag tcacgaaaga tttataaggt aattggcttt aaagaatcgt 1200 tttcgacaaa gtccgtatca agtggcaaaa cggccaacat tgataatttt caaaacaagg 1260 taacttattc aagtttgaaa actcacaaat caatcttaat caatcatgta gtcatgagct 1320 taagccactt acgaactatt aaacattagt tcaaagatta gcctaagttc gtatgagaaa 1380 accccaagtt cacatattcc acaatcccac ccgaaaatca agtttgacat gattaagaca 1440 tttaaccaac tttacaagcc ttgcctaagt ccacatggac tgtagaccaa acttgtaatc 1500 ccttttagtt cacaaaagtt catttccgac aaaatccgaa attatcaaaa gttcaagttt 1560 caacccaatt agaaaatccc aagtttgaat gagtaaatca tgttccagta ggtttaggag 1620 tacaaacaga gattaaacaa gttgaaagaa gtgttttaca aagctcggat tggcccccta 1680 aagcccggaa cgaaaatcaa aagttgctga aactgggctt gttcgcttaa gcgaccaggt 1740 tccataagct tacagtagct gttcgcttgc tgttcgctta ccggttcgct taagcgaccg 1800 agttccagaa cctactgtga ttgttcgctt acgcgttcgc ttaagcgaac agtcatcagt 1860 tctgcagaaa aactttcggg tttcaaccct ttttcaccca aaattcccaa ttttgatctc 1920 ccaatgccca aatatgtttc caaagtttgt ttacaggtct tagcacttaa aagggctctc 1980 aagaacacat caaacatgaa aacaaatgtc atttaaacat aattcaccaa atcaacccat 2040 tttcacaaaa ccaacaacaa caacttattt cacatcacaa actcatgatt tatgaacacc 2100 caagctatga atcatcaaca acaatatctc ttaacaacaa caacatcaat taaacatgat 2160 tctcatcaca aatcaacaac aacatagcac aattcaacaa ttagagcaca attcacaata 2220 tatcattttc acatactatg aacatgcaat ttcaccaaca acaattcaat tatcaccaat 2280 ttcatgtact caaacatatc atcataacaa gagcacgaat ttcaacaact aagagcaaaa 2340 taatcactta ttcaattaag cacttaagca tacaattagg gaaaaattac aactaagtga 2400 ttatgattga aatctaaccc ccttacctca ataagcaata atcctagcaa aagcttcaat 2460 ttagctccta gaatctctat cacctcttgg gtcttcaagc tttctccctt ctaacccttt 2520 tcctcttctc ttgaactttc tctctctacc tctctcaaaa ttcttatgaa atgaaatgaa 2580 aacctatttt tctctaaaga caagagttta tataggctcc tctcaaatgg gcttaaccct 2640 aatgccttag tgggcttaac tcactcattc actaattcta aaatgtttct actcacttaa 2700 cggtaaaata ataacaacga tcacttaccg gctcacaact aattaccaca ctagtaactt 2760 agtaaaataa tggttctcac ttgaaacact aaaaataatc ctcaccatga atttactaaa 2820 ttacccttac tcacaaaatg actaaattac ccttctaaca cgaaaaccca taaaaatgca 2880 cccaatgata aataatcaca cacaagcaca tataaacaca tattaaaaca attaaaaata 2940 attctagcga aaatcgggct gttaca 2966 // ID Ogre-PT1_I repbase; DNA; EDCOT; 13364 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 LTR-retrotransposon of Ogre superfamily. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; Ogre-PT1; 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:.6202..6439: 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..7595,7599..8921,8925..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 QAMSAPKTEKEVRSFLGRLNYIARFISQLTVTCEPIFRLLKKNPGVWDEDC FT QEAFDKIKQYLQKPPLLVPPVPRKPLILYLTVTESAMGYVLGQHDESGRKE FT QAIYYLSKKFTECESRYSMIEKLCCGLVWSAKRLRQYMLYYTTWLISKIDP FT LKYIFEKPYMSNRLARWQVLLAEYDIIYKTRKSVKGSAIADHLADNAVEDY FT EPLNFDFPDEDVLVIESDWWTMYFDGAVNVSGNGAGAVIISPEGKQYPISI FT KLQFSCTNNTAEYEACIHGLEAALELKIRKLGVYGDSMLIICQTKGEWQTK FT DEKLKPYQEYLSKLAENFKEIEFNHLGRDKNQFADALATLASMATIDCGIR FT VHPIGIDIRSSPTHCCLVEEEVDGSPWYTDIKRFIQYREYPSEVSKTDKKT FT LRRMVMEYFIDGEILYKRSFDGTLLRCLDRSEANKALCEVHEGICTTHANG FT HMMARQIQRAGYFWLTMEKDCIFVRKCHKCQVYSDKINAPPVPLFNMVSPW FT PFAMWGIDVIGPINPKASNGHRFILVAIDYFTKWVEACSYAHVTQKVVKRF FT IERDLICRYGLPERIVTDNAKNFNGKMIVELCTKWKIKHSNSSPYRPKMNG FT AVEAANKNIKKIVQKMVVTYKDWQEWLPYALHAYRTAIRTSTGATPYSLVY FT GMEAVMPLEVEIPSLRVLMESELEEAKWAEKGQIRYDQ" 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 M2_VM repbase; DNA; EDCOT; 757 BP. XX AC AJ391759; XX DT 08-NOV-2002 (Rel. 4.3, Created) DT 08-NOV-2002 (Rel. 4.3, Last updated, Version 1) XX DE Vicia melanops repetitive DNA sequence, M2_VM. XX KW 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 DR Genbank; AJ391759; Positions 1 757. XX SQ Sequence 757 BP; 202 A; 166 C; 156 G; 233 T; 0 other; tcgaacgctt tctggcaatc ttctgtccat acaacccctt gattctttcg gagaagtttg 60 aagatcggcc cacaagtagc agtcatttga gagatgaatc tggagatgta gttcaatcgt 120 ccaagaaaac ccctcacttg cttttctgtt tttggtgcag gcatttcttg aatagccttg 180 actttgtcag ggtctacttc aaaacctctt tggctgacaa tgaatcctag gagttttcct 240 gatctcaccc caaaagtgca cttgttagga ttcaagcgaa gttgatatat ccttagtcgt 300 tgaaataact tcaaaaggta ttcaacatgt tcctcttctg tgctggactt ggctatcatg 360 tcgtccacat acacttcaat ctctttatgc atcatgtcat gaaagagagt agtcatcgct 420 ctttgataag tcgcgcttgc gttctttaat ccaaacgaca ttactttgta gcaaaaggtg 480 ccccacggtg tgatgaaaga tgttttctcc atgtcttcgg gagccatctt aatctgatta 540 taaccggaga aaccatccat gaaggagaaa acattgaact tagcggtgtt atcaaccaag 600 gtgtcaatat gcggtaaggg aaaataatcc tttggactcg ctttgtttaa gtcatggtag 660 tcaacacaca ttcggacctt tccatctttc tttggaacag gcactatgtt ggctaaccac 720 tgacggtatt cggaagtgac gaggaaacct gcatcga 757 // 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Ogre-MT3_I repbase; DNA; EDCOT; 11878 BP. XX AC AC151524; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 03-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_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: 6026..6311: putative intron. 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; 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 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-85_Mad-I repbase; DNA; EDCOT; 4318 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, 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-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 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 CALYPSHAN_I_MT repbase; DNA; EDCOT; 11739 BP. XX AC CT573400; XX DT 25-JAN-2007 (Rel. 12.01, Created) DT 25-JAN-2007 (Rel. 12.01, Last updated, Version 1) XX DE Internal region sequence of LTR retroposon, CALYPSHAN_MT, from DE Medicago truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW ORF; Interspersed; aspertyl peptidase; CALYPSHAN_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 1-11739 RA Shankar R. and Jurka J.; RT "CALYPSHAN_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 3-3 (2007). XX DR EMBL/GenBank/DDBJ; CT573400; Positions 58822 70560. XX CC The internal region shows characteristic features of a Gypsy-like CC LTR retroposon with arrangement of domains in a pattern of CC gag-protease-RT polymerase-RNAse-Integrase. CC Two ORFs are present. In general the element is present in the CC genome with high copy number but most of them are incomplete or CC interrupted with just ~10 intact copies. The copy number, size of CC internal region and LTRs indicate that this element can belong to CC CALYPSO group of Gypsy-like retroposons. XX FH Key Location/Qualifiers FT CDS 6344..9814 FT /product="GYPSHAN2_I_MT_2p" FT /translation="MCRLNISEPVEHSNPMLPPNFEVPVYEAMIEEDEEIP FT DEIKWMLEQERKTIQPHQEEIEIINLGTEEDKKEIKIGALLETSVKERVIE FT LLREYADIFAWSYKDMPGLDPDVVEHRLPLKPECPPVKQKLRRSNPEMALK FT IKEEVRKQIDAGFLVTSEYPQWLANIVLVPKKDGKVRMCVDYRDLNKASPK FT DNFPLPHIDVLVDNTAKCKVFSFMDGFSGYNQIKMAPEDREKTSFITPWGA FT FCYLVMPFGLINAGATYQRGMTKIFHDMIHKEIEVYVDDMIVKSGTEEEHV FT EYLLKMFQRLRKYKLRLNPNKCTFSVRSGKLLGFIVSQKGIEVDPDKVRAI FT REMPAPKTEKQVRGFLGRLNYISRFISHMTATCGPIFKLLRKDQGVKWNDD FT CQKAFDRIKEYLLEPPILVPPVDGRPLIMYLTVLEDSMGCVLGQQDETGKK FT EHAIYYLSKKFTDCESRYSVLEKTCCALAWAAKRLRHYMINHTTWLISKMD FT PIKYIFEKPALTGRIARWQMLLSEYDIMYRTQKAIKGSILADHLAHQPVED FT YQPIKFDFPDEEVMYLKAKDCDEPVFGEGPDPESEWGLIFDGAVNVYGSGI FT GAVLITPKGTHIPLTARIRFDCTNNIAEYEACIMGIEEAIDLRIKKIVIYG FT DSALVINQIKGEWETRHPGLIPYRDYARRLLTFFNKVELHHVPRDENQMAD FT ALATLSSMIKVNGHNTVPVINVQFLDRPAYVFAAEAVEDDKPWYHDIQVFL FT QTQKYPPGISNKDKKTLRKLSSRFFLNGDVLYKRNFDGVLLRCVNEHEAEE FT LMHEIHEGSFGTHSCGHAMAKKILRAGYYWITMHADCYNHAKRCHKCQIYA FT DKIHIPPSMLNVVSSPWPFSMWGIDMIGRIEPKASNGHRFILVAIDYFTKW FT VEAASYANVTKQVVVKFIKNNIISRYGVPNRIITDNGTNLNNNMMKELCDD FT FKIQHHNSSPYRPQMNGAVEAANKNIKKIIQKMVVTYKDWHEMLPYALYGY FT RTSVRTSTGATPFSLVYGMEAVLPVEVEIPSLRVLMEAELSEAEWCQSRYD FT QLNLIEEKRMAALCHGQLYQSRMKQAFDKRVHPREFKEGDLVVKCIKSFQP FT DPRGKWTPNYEGPYVVKRAFSGGALILTNMDGEELPRPVNSDAVKKYFV" FT CDS join(2437..3369,3373..6051) FT /product="GYPSHAN2_I_MT_1p" FT /translation="MHHTAFIKGVKTKSHTLLISASERSKVARRIQYKPAR FT IHNTRAHIKKRMLAAEQENAQLREELVNLKGEMERMSIIMETLMAEREQAA FT ISDSAPVVVVTAAPDGLPRPTPTTATAIGLTQPLMTDFSSGNMATMGNSGF FT RPIGPHGQFSTPQYSMPLGYPWGMPLTASGGFRPSATEMPFAHGQQTSPPF FT QTDQLFPHAAMTQAGPSVHVEPQQEEQVYHSDSVMGDDKAVNWEERFGALE FT KEMSNMRGKEAVVQSIYDLCLVPDVDIPPKFKVPVFEKYQGDSCLQNHLTM FT YITKMIAYKNNVPLLIHCFDSLTGPAHTWFMGLKGITTFEQLADAFMQQYK FT YKTYLAPSRKELQSLTQKDKESFKEYAQRFIQKASQIRPPLDERELSEMFY FT ETLSPCYSEKMIVCASQKFTDLVETGIRIEEWTRKGVGASGSSAGSSSSGN FT KKFGNGYPKRNAQEVGMVAHGGSQPVYPNQSYVANITPQMTAPQNPNYQPP FT RPQGPSLYYPPLYQQPYNPQQLSQPPYYPQQPYYPQQPYQQRPHYPPQQQP FT RPQAPYNQQNQKQQFDPIPMTYGALLPSLLAQNRVHTLPPPRIPDPLPRWY FT RPELHCVFHQGAAGHDVERCYALKKEVQKLLDSKELTFADPDHVAQNNPLP FT PHGPAVNMIQDCQEDACIIYARDIKTPLVPIHVKMCEMALFSHDHEACHVC FT SVNPRGCMQVQEDVQGLLDKKELVVTKEIKSKSVCVVTPVFRDRRPLVINP FT NSAKPAVTPLVICVPKPAPPSSQKAVPYKYEGTILEPGNETTSSSVVDNIA FT DSSRILRSGRVLPAVVQKSTGVSVEETVKERNTGKGRVREHPKEVDYEDAD FT EILKLIKRSEYRVVDQLLQTPAKISILSLLSSSGAHRDALKKVLDQAFVDY FT DVTLGQFESIVGNVTACNSLSFSDEDLPAEGKKHNQALLISVLCRTDSLSN FT VLIDTGSALNVMPKSTLDQLTYSEALLRPSKVTVRAFDGTRRAVYGEIDLP FT ISVGPHEFQVTFQVMEIQASFSCLLGRPWIHDAGAVTSTLHQKLKFVSHGK FT LITVSGESAFLISNLSAFSVIGGSSSDGSSFQGFSAEGSVSKIGTCMASLK FT DAQRVIQEGKTEGCGQLVELPENKRKEGIGFLNSRSGMFDPTEGSFRSAGF FT IHDSPGINALTDDTPEGVAPVFVTPGGTCCNWIAVDIPSVIPLSK" XX SQ Sequence 11739 BP; 3404 A; 2508 C; 2528 G; 3299 T; 0 other; gaaatggcga cttcactggg gatttagatc ctacgcgggt taaacccacc ttactttctt 60 tattttgtgc tttattattt gtttatactt tgtaaatatt ttgcttacat gattacttta 120 ttacgtgagt ggtgagataa gctctacacc cgagcttgag ggaaacttaa gataggacgg 180 tggtataatc atagttccat gccaagagta ctcttcggta ttggcacatg tgataacccc 240 actcaacgga gggatcttgg aagtatatgt tgtcaacgtg agtactcatg tttggcatgc 300 tattttcaag taacctttga agttgaggac ctttagtcac ctttaaccca tcttggcctt 360 ttaggaacgt agtgcggtgg ctaatcgaga gtactcttga attagttgat acgcgatact 420 acacccaaac gagactttcc gacgaatata attggaatgg gagtactccc gtcacccgat 480 aaatattcgg aagtggttaa agactttggg aacttggtag aacccttgtt acaagtgcaa 540 tctaaaaacc ttagtcctca ccaaatggcg ttgttaccct ttgactccaa catatgaatt 600 taaactcatc atgcatacat gcatccatcc ataaatattt ttttccattc atcatttttt 660 tgaaggactt ataaaagctt tgttgtaaac attgtagata tgaggaacct taggcagtat 720 agtttcagga agccagatct cttgagtttg aggaagctag ggaagaaagt ggtttgtacg 780 gacgatttct acaagcaaca tggaaatttg atgggtgttg ttaagacaga tatcgacgaa 840 gggcttctca acgcttttgt tcagttctat gacccgggct accattgctt tacttttcaa 900 gattaccaga tcctccccac cttggaggag tactcttgtt ggattaatct accagtgttg 960 gacaaagtac ctttcagtgg cctcgaggaa attcccaagc actcaaccat tgccgcagcc 1020 ctctatctcg aaacggacga agtgaaagca catctcatca ctaagggaaa acttttgggt 1080 ttctccaccg atttccttta cgaaaggacc acattctttg acaaaatggg ggttgcctat 1140 gcttttaact ccatccttgc cttgcttatt tatggcctcg tactcttccc tagcctcgac 1200 aactttgtgg acattaaggc cattcaaatt ttcttgtcaa ggaaccccgt tcctacctta 1260 ttaggtgata cttatctctc catccatagg cgtacccagg ctggtcgtgg aactatcctt 1320 tgttgtgcac aattgctata tcgatggatc acctcgcact taccccgaac tcctcgcttc 1380 accaccaatc cagaaaacct tctttggtca aaaagactca tgtccctgac tccaaccgag 1440 gtagtgtggt acgatcgggt ttatgacaaa ggaactatta ttgacagttg tgggaaattt 1500 gccaatgtac cacttcttgg tatagaagga ggaattagct acaatcctac gcttgccaga 1560 cgtcagttcg gatatcccat ggaagggaag ccgctcagca tctatctaga gaatgtgtat 1620 tacctcaaca tagatgacag taaaggcatg aaagagcagg ttgtgcgagc ttggcacacc 1680 attcgtagaa gagacaagag ccagttagga aggaagacag gagccgttca tgaatcatat 1740 actcagtggg tgatagatag agctgttcaa attgggatgc cttacaagat atcaagattt 1800 gtatctgcaa tcactccagc accaccccta cctatgacct ttgacaccga gaaggaatac 1860 caagagcgtt tagttgaggc ggaacgtgaa atacataagt ggaaagggga gtatcagaaa 1920 aaggatcagg agtatgaggc tgtgatggcc ctactagagc aagaagccta tgatagccac 1980 aagaaagatg tgataatcgc ccagctgaaa aagagtatca gagagaaaga tgccgcgctt 2040 gatcaaattc ccgggcggaa gaagaagcgc atggatctct ttgatgggcc gcattctgat 2100 tttgaggagt agctcggttc agaggcttga gagtctttca gtttgttttt gatgtttttg 2160 tgtagttacg gagtctatcc cttggctttg ttgttagaaa gggaattatc tcgttttatt 2220 ttgaaagtct atcccttggc tttgttgtta gaaagggaat tatcttgttt tactttgaaa 2280 gtttatccct tggctttgtt gttagaaagg gaattatctt gtaatcaact ttgtttttaa 2340 tgttttgttt aggttgatat gtttacaaaa ttgcttttat aggtcctttg ataaaatata 2400 aaaaaatctg cacatttttt ttgcatatag catatcatgc atcatactgc attcataaaa 2460 ggcgtcaaaa ccaagtctca tactctcctc atttctgcct cagagagaag caaagtggcc 2520 cggcgtattc agtacaagcc cgctcgcatt cacaacactc gagcccatat caagaagagg 2580 atgttagcgg cagaacagga aaacgctcag cttagagagg agctggttaa cctcaaggga 2640 gagatggaaa gaatgtcaat tataatggaa actttgatgg ctgaaagaga gcaagcagca 2700 atctccgact cagctcctgt tgtggttgtc acagctgcac ctgatggtct cccgcgacca 2760 actcctacta ctgctacagc tatcggcctc acccagcctt tgatgactga tttttcttct 2820 ggtaatatgg caactatggg taactcaggc ttccgtccta ttggccccca tggtcaattt 2880 tccactcctc agtattccat gcctctaggg tacccatggg gcatgccact tacagccagt 2940 gggggttttc gtccaagtgc tactgaaatg cctttcgctc atggtcaaca gacttcacca 3000 ccttttcaga cggaccagct atttcctcat gctgctatga ctcaagcagg acccagtgtg 3060 catgttgagc cacaacagga agaacaggtc tatcattctg acagtgtaat gggggacgac 3120 aaggcagtta actgggaaga gagattcggt gctttggaaa aagagatgag taacatgcgc 3180 ggtaaagagg ctgttgttca gagtatatac gatctttgct tggtaccaga tgtggatata 3240 ccccccaaat tcaaggtgcc ggtgtttgag aagtatcaag gggactcgtg tctacaaaat 3300 catctaacta tgtatattac gaagatgata gcttacaaaa acaatgtacc gttgctcatt 3360 cactgcttct aggacagttt gaccggtcct gcacacactt ggtttatggg tttgaagggc 3420 attactacgt tcgaacagtt ggctgacgct ttcatgcaac aatacaaata caaaacatat 3480 ctggcgccta gtcgcaaaga gttgcaatcc ttgacccaga aggataaaga gtcattcaaa 3540 gagtatgcac aacgcttcat ccaaaaggcc tcccagattc gtccgccctt ggacgagaga 3600 gaattatccg agatgttcta tgagactttg agcccttgtt attcagaaaa aatgattgtc 3660 tgtgcatcac agaagttcac tgatctggta gagacaggga tacgtatcga ggagtggact 3720 cgtaagggag ttggtgcttc aggaagttct gcaggaagtt catctagtgg taacaagaag 3780 tttggtaatg gttacccaaa gaggaatgct caagaagtcg gcatggtggc ccatggcggt 3840 tctcaaccag tgtacccaaa ccagtcttat gttgccaaca tcaccccaca aatgaccgct 3900 cctcagaacc caaactatca accaccaaga cctcaagggc cttcattata ttatccccca 3960 ctatatcaac aaccatataa cccacaacaa ctctctcaac caccctacta tcctcaacaa 4020 ccctactacc ctcaacaacc ataccaacaa aggccacact acccaccaca acaacaaccc 4080 cgtcctcaag ctccctacaa ccagcaaaat caaaaacaac aatttgaccc cataccaatg 4140 acttatggag cattattgcc ttccttgctc gcgcaaaacc gagttcacac attaccacct 4200 cctcgcattc cagatcctct cccacgctgg taccgccctg aacttcattg tgtttttcat 4260 caaggggcag cgggtcacga tgtggaacgc tgttatgccc tcaagaaaga ggtccaaaaa 4320 ttgctcgata gcaaagagtt gactttcgcc gaccctgatc atgttgccca gaacaatcct 4380 ctgccgcctc atgggcctgc tgttaatatg attcaggact gtcaagaaga tgcttgcatt 4440 atctacgcac gcgacatcaa gacccctttg gtaccgatac atgtgaaaat gtgcgagatg 4500 gctctcttca gtcacgatca tgaagcttgt catgtatgtt cggtgaatcc tcgtgggtgc 4560 atgcaagtcc aagaggatgt gcaagggctc ctagataaaa aggaacttgt ggttacaaag 4620 gaaatcaaga gcaaaagtgt ttgtgttgtc accccagtat tcagagatag gaggccactt 4680 gtgataaacc ctaacagtgc aaaacccgct gtcactcctt tggtaatctg tgtgcctaag 4740 cctgcacctc cttcctctca gaaagccgtg ccttacaagt acgagggcac aattttagaa 4800 cctggaaatg aaacgacatc atcctctgtt gtggacaaca ttgccgatag tagtcggatt 4860 ttaagaagcg gccgcgttct tcctgctgtg gttcagaaga gcactggtgt ttcggttgag 4920 gaaacagtaa aggagcggaa cacaggtaaa ggtagagtta gagagcatcc caaagaggtc 4980 gactatgagg atgctgatga aatcctaaag ctgatcaaga gaagtgaata cagggttgtg 5040 gaccaattgt tacaaacccc tgcgaagatt tccattttgt ctctgttatc aagctctggt 5100 gctcatcgag atgccctgaa gaaagttctc gaccaagctt ttgtggatta tgatgtgaca 5160 ttgggccagt ttgaaagtat tgtgggaaat gtgactgcat gtaacagcct gagtttcagt 5220 gatgaagacc tcccggcgga ggggaaaaag cacaatcaag ctttactcat ttccgtactt 5280 tgcagaacag actccctatc caatgttctg attgacaccg gctctgctct taatgtgatg 5340 cccaaatcaa ccttggatca actgacgtat tccgaggctc tcttgaggcc aagtaaggtg 5400 acggtgaggg catttgacgg gaccagaaga gcagtatatg gtgagataga tttgcccatc 5460 tcagtcggcc cccatgagtt tcaggttact tttcaggtca tggaaatcca ggcatctttc 5520 agctgtttac ttggcagacc atggattcat gacgctgggg cagtaacatc cactctccac 5580 cagaagctga agtttgtaag tcatggaaag ctcattactg tgagtggcga gtcagccttt 5640 ttgatcagca atttgtccgc tttctctgtc attggtggta gtagttcaga tgggtcgtca 5700 ttccaagggt tctctgctga aggaagcgta agtaagattg ggacttgtat ggcttcgttg 5760 aaggacgcac agagggtaat ccaggagggc aaaaccgaag gatgtggtca gctagtggag 5820 ttaccggaaa acaagcgcaa ggaagggatt ggttttctta acagtaggtc tgggatgttt 5880 gaccctaccg aaggctcttt tcgcagtgcc ggattcatcc atgattcgcc agggatcaat 5940 gcacttactg atgatacacc ggaaggagtg gcacctgttt ttgtgacacc aggaggaact 6000 tgctgcaact ggattgccgt agacattcct tctgtgatac ccctttctaa gtaatatgtt 6060 tgtcttgtct tttgtttttt acttttaaag aaaactcctt tcgtttttgc ccaagacgaa 6120 agtgaaatca tgtagggctt tgtctttgct tacagtattt tttattatga atgaaaatcg 6180 ccgtttctgt cacggcattt atttattttt tttttatata tatattctgt gcattttctg 6240 aaaaaaatgg taatagaaaa atccgaaaaa atcattctct tttttctttt aaaattttca 6300 aaatcaaagg tctgcattta ctcattaaaa tcaatcatga atcatgtgca gactgaacat 6360 aagcgagccc gttgaacaca gtaaccccat gcttcctccc aactttgaag tcccggttta 6420 cgaggctatg atagaggagg atgaggagat tcctgatgag attaaatgga tgttggaaca 6480 agaaagaaag acaattcagc ctcatcagga agagatagaa atcatcaatc tgggtactga 6540 ggaagacaag aaagaaatta agatcggggc attgttggag acatctgtta aggaaagagt 6600 aattgagctt ctcagagaat atgctgatat atttgcatgg tcatacaagg acatgccggg 6660 tctagaccct gatgtcgtgg aacacagatt gcctttgaag cctgaatgtc ctccggtaaa 6720 gcagaaattg agaagatcta atcccgagat ggccctcaag atcaaagagg aagtacgcaa 6780 gcagattgat gcaggtttcc tggtcacgtc agagtatcct cagtggttag ccaacatagt 6840 gctcgttcca aagaaagatg gcaaagttag aatgtgtgtc gattaccggg atttgaacaa 6900 ggctagtccg aaggataatt tccctttacc tcacattgat gtattggttg ataacactgc 6960 taaatgcaag gtattctcct tcatggacgg tttttccggg tataatcaga taaagatggc 7020 tccagaagat agagaaaaga cgtccttcat cacgccttgg ggtgcttttt gttatttggt 7080 gatgccattt gggttgataa acgctggtgc cacttaccag agaggcatga ccaaaatatt 7140 ccatgacatg attcacaaag aaattgaagt ctacgtagat gatatgattg tcaagtctgg 7200 cacagaagaa gaacatgttg agtatttgtt gaagatgttt cagcggttga gaaagtacaa 7260 actccggttg aatcctaaca aatgtacctt cagtgtcaga tctggtaaac tcctaggctt 7320 tatcgtcagt caaaagggta ttgaagttga tcccgacaag gtcagagcca tcagagaaat 7380 gcctgctcca aagacagaga aacaagtcag aggttttctt ggtagactga attatatctc 7440 cagatttatc tctcacatga ctgccacatg tggaccaatt ttcaagttac tccgcaagga 7500 tcaaggggtg aagtggaatg atgattgtca gaaagctttt gaccgaatca aagaatatct 7560 gttagaacct ccgattcttg ttcctccagt tgacggaaga cctttgatca tgtatctaac 7620 agtactggaa gattccatgg gctgtgtgtt aggtcaacaa gatgaaaccg gaaagaaaga 7680 gcatgctatc tactatttga gtaagaagtt cactgattgt gagtctcgat attctgtact 7740 tgagaaaact tgttgtgctt tggcctgggc cgccaagcgt ctccgtcatt atatgattaa 7800 tcatacaact tggttgatat ccaagatgga tccaatcaag tacatatttg agaagccagc 7860 tttaactgga aggatcgctc gctggcaaat gttattgtcc gagtatgata tcatgtatcg 7920 cacccagaaa gcaatcaaag gcagcatctt ggcagaccat ttggcccatc aaccggttga 7980 agactaccaa ccaatcaagt ttgacttccc agatgaagag gtcatgtatc taaaagcgaa 8040 agattgtgat gaaccagtgt tcggtgaagg tcctgatcct gaatccgaat ggggtttgat 8100 atttgatgga gccgttaatg tctatggtag tggaattggt gcagttctca ttacccctaa 8160 gggtactcac atccctctta ctgcaaggat tcgatttgat tgtacaaata acattgcaga 8220 atacgaagct tgcatcatgg gtatcgaaga agccatcgac ttgaggatca agaaaattgt 8280 catctatgga gattcagctc tcgtgattaa ccagatcaaa ggagaatggg aaactcgcca 8340 tcctggtttg attccctaca gagattatgc aagacgattg ctgactttct tcaacaaagt 8400 agagttacac catgtgcccc gtgatgagaa tcaaatggcg gatgctttag ctactctatc 8460 ctcaatgatc aaagtgaatg gtcacaatac tgtgccggta atcaatgttc aattcctcga 8520 tcggcctgct tatgtgtttg cagctgaagc agttgaggat gacaaaccat ggtatcatga 8580 tatccaagtc ttccttcaga ctcaaaaata cccgcctggg atatccaaca aagacaagaa 8640 gaccttgaga aagttgtcaa gccgtttctt cctcaacgga gatgttttgt ataagagaaa 8700 ctttgatggg gtcctactca gatgtgtgaa tgagcatgaa gcagaagagt tgatgcatga 8760 gatacatgaa ggctctttcg gaactcactc atgtgggcac gccatggcaa agaagatatt 8820 gagggctggg tattactgga taacaatgca tgcggattgc tacaaccatg ccaagagatg 8880 tcacaaatgt cagatctatg ctgacaagat tcatatacca ccatctatgc tcaatgtcgt 8940 ctcttccccg tggcctttct ctatgtgggg cattgacatg attggtcgga ttgaaccaaa 9000 agcctccaat gggcatcgct tcatactagt ggccatcgat tatttcacca agtgggttga 9060 agcagcatct tatgccaatg tgaccaagca ggtagtggtc aaatttatca agaacaacat 9120 catcagccgc tacggtgttc ccaacagaat catcacagac aatggcacaa atttgaataa 9180 caatatgatg aaagagttgt gcgatgactt caagattcaa catcacaatt cttctcccta 9240 caggccacag atgaatgggg cagttgaagc tgcaaacaag aacatcaaga agatcataca 9300 gaagatggta gttacttaca aggactggca tgaaatgtta ccttatgctt tgtatggata 9360 tcgtacctca gtgcgaacct caacaggggc aacccctttc tctttggtat atggtatgga 9420 ggctgtacta ccagtagaag tggagattcc ttctttaaga gtcttgatgg aagctgaatt 9480 gtctgaagca gaatggtgcc agagtaggta cgaccagttg aatttgattg aggagaaacg 9540 catggccgct ttgtgtcatg gacagctata tcagtcaagg atgaaacaag ctttcgataa 9600 aagagtccat cctcgtgaat tcaaggaagg agatcttgtg gtcaaatgta tcaaatcctt 9660 ccaacccgat cctaggggca aatggacgcc aaactatgaa ggtccctacg tggtgaagag 9720 ggctttctct ggtggtgctt taattcttac aaatatggat ggagaggagt tacctcgtcc 9780 tgtgaattct gatgcagtca agaaatactt tgtctaaata tatataaagg aacagctcgg 9840 taggtcgaaa acccgaaagg gcggcttaaa ccaaaaatga gcgtcttggt ggatcgaaaa 9900 cccgaaaggg cgatccaggc aaaaattaga gacaaaaaaa aaaataaaaa aaaaaaaaaa 9960 aaaaaatcct gatagatcga aaacccgcaa gggtgaccta tgcaaaaact aaggatcaag 10020 acaagtaact gcatcagatg aagcatcacc cgcccgagac accctggttg tcataagttc 10080 tctaatatcg aagcatccaa gccgtggaat tcaaagtcgt taagaagcat agcggttatt 10140 gtgttcaatg tacctatctc atataattac catattccaa tttttgtaat ctgtggtgcc 10200 atgcctttgg ccggttacca tttctattaa atcaatttga gcttgtgcct ctttgttgga 10260 attcttgttt attctatgtg caaaaaaaat ctttcttcca tttttagtac taatacttga 10320 agcaaaaact tgaaaatctt tctaaaattt tttatgtgtt aaaaaaaaaa aagagacaaa 10380 aaaaagacaa acatattatc ttaaaaaaaa catgtatcat ataagtatgt gtcaacagtc 10440 ggttcgaaac gagcaggttc aataaagaag aaatagtcat tgcaaaaaaa aaaaaaaaaa 10500 aaaaaaaaag agcgccctag tggatcgaaa atccgaaagg atgatccagg caaaagttag 10560 ggatttcaaa aaaaatatat atacaaaaag gcaatgacta ttcaagcatg gaaatacggt 10620 gttgcattgg tgaaatggcg acttctaccc cggtctgtga gagctgtacc ccaacgatgg 10680 ttgattcatt ccccgtgact ttgtccccaa tgaaggtttc gagtgttcgt ccagtgatgc 10740 cgggccattc tccttgtaga cctgcccagt cctgcctcaa caatcttacc attatgtcgt 10800 catatgagtc tcatacatac tcattcattc atgcatacat agcacgcata taagtatcat 10860 tcatacatag ttgcattttt accctatgac ttattgcaat atccttagat atcaccccca 10920 gcatgtctaa ctccaaaatg tcatcaaatc aaacatgtgg caggtctcac cggtaatcag 10980 tctatacaat ttcccttggt cttcagacaa gttccttgtt cccctcaact ttatctttat 11040 caagtcactc ccttgatacc aaactttaca atgtcttcac ttttaccgtg tgtttgctat 11100 cccacaatgt tagcaaatcc tatcggtcca tcatgtcttt actttcgcca ctcgtcggca 11160 atcaatcatg tttttacttt cgtcactcgt cggcaattaa tcatgtcttt acattcgcca 11220 ctcgtcggca atcaatcatg tttttacttt cgccacttgt cggctaaatc atgtctttac 11280 tttcggccga tcatgttttt actttcgcca cttgtcggct aaatcatgtc tttactttcg 11340 ccactcgtcg gccaatcatg tctttacttt cgtcactcgt cggcaatcaa tcatgtcttt 11400 acattcgcca ctcgtcggca atcaaccatg tttttacttt cgccactcgt cggccaatca 11460 tgtctttact ttcgccttga aacaatgtca tttatactta cccatcattt ctttccccag 11520 tgatccctat ccatttgtct cccagtcagt ctctgcatca tcttttacct tcatacttac 11580 atcatattta gtcgtattgt cacattcatc agcatcacac ttctgacgtt tcaaatggtc 11640 caaaattggc gtttttatat atttaagtct ctccgaccct ttggtttaaa aagttctctt 11700 ttaaaacctt tgtgatgaag aaacttaaat aggggcatc 11739 // 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-N14_Mad repbase; DNA; EDCOT; 886 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.1, 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-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 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 L1-11_Mad repbase; DNA; EDCOT; 5843 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 MuDR-3_Mad repbase; DNA; EDCOT; 4304 BP. XX AC . XX DT 06-OCT-2010 (Rel. 15.1, Created) DT 06-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; 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 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 AFROSINE repbase; DNA; EDCOT; 160 BP. XX AC . XX DT 19-DEC-2003 (Rel. 8.11, Created) DT 20-JUL-2005 (Rel. 8.11, Last updated, Version 2) XX DE SINE elements from African endemic mammals - a consensus DE sequence. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; AFROSINE. XX OS Proboscidea OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; OC asterids; lamiids; Lamiales; Martyniaceae. XX RN [1] RA Nikaido M., Nishihara H., Hukumoto Y. and Okada N.; RT "Ancient SINEs from African Endemic Mammals."; RL Mol. Biol. Evol 20(4), 522-527 (2003). XX RN [2] RA Nikaido M., Nishihara H., Hukumoto Y. and Okada N.; RT "Direct Submission to GenBank."; RL Direct Submission to Genbank (08-NOV-2002)Masato Nikaido, Tokyo RL Institute of Technology, Graduated school of Bioscience of RL Biotechnology; 4259 Nagatsuta-cho Midori-ku, Yokohama, Kanagawa RL 2268501, Japan (E-mail:mnikaido@bio.titech.ac.jp, RL Tel:81459245742, Fax:81459245835). XX RN [3] RA Kohany O. and Jurka J.; RT "AFROSINE consensus."; RL Direct Submission to Repbase Update (30-NOV-2003). XX DR [3] (Consensus) XX CC Average similarity to consensus 92%. XX SQ Sequence 160 BP; 41 A; 38 C; 42 G; 38 T; 1 other; tgctaaccaa aaggtcggca gttcgaaacc accagctgct ccaygggaga aagatgtggc 60 agtctgcttc cgtaaagatt tacagccttg gaaaccctat ggggcagttc tactctgtcc 120 tatagggtca ctatgagtcg gaattgactc catggcagtg 160 // 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. 15.1, 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-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 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 Copia3-VV_LTR repbase; DNA; EDCOT; 192 BP. XX AC AM448401; 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; Copia3-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 1-192 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 1-192 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 680-680 (2007). XX DR Genbank; AM448401; Positions 30716 30525. XX SQ Sequence 192 BP; 64 A; 18 C; 35 G; 73 T; 2 other; tgccaaagtt aggactttaa tttaggaata aaaaaaggag agatcattta ggatatttcc 60 ttatgattta gtttcctaat tttaggagag aattaagcta gattgatttt ttcttattca 120 gtcatttgtg tatatatatg tgtatggtgt gtaccgatwa awatatcaat aaaggagttc 180 agaaattctt ca 192 // 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW 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 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 EnSpm-1_Mad repbase; DNA; EDCOT; 4174 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous EnSpm elements, consensus. XX KW EnSpm; DNA transposon; Transposable Element; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-3A_Mad repbase; DNA; EDCOT; 4397 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 TDC1 repbase; DNA; EDCOT; 5251 BP. XX AC AB001569; XX DT 28-AUG-1998 (Rel. 3.07, Created) DT 16-AUG-2005 (Rel. 3.07, Last updated, Version 2) XX DE DNA transposon TDC1. XX KW DNA transposon; Transposable Element; 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-3_Mad repbase; DNA; EDCOT; 3809 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 BRENSPM1 repbase; DNA; EDCOT; 2112 BP. XX AC AB022082; XX DT 00-0000 (Rel. 4, Created) DT 00-0000 (Rel. 4, Last updated, Version 1) XX DE A portion of En/Spm-like DNA transposon. XX KW DNA transposon; transposase; En/Spm superfamily; BRENSPM1. 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 "Genomic organization of the S locus. Identification and RT characterization of genes in slg/srk region of s(9) haplotype of RT brassica campestris."; RL Genetics 153, 391-400 (1999). 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 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. 15.1, 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-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 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 COPIA2-I_LC repbase; DNA; EDCOT; 10324 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 retrotranposon - internal DE consensus sequence. XX KW 5 bp TSDs; COPIA1-I_LC; COPIA2-I_LC; copia-like retrotransposon; KW gag-pol; integrase. 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 1-6864 RA Gentles A. and Jurka J.; RT "COPIA2_LC: L. corniculatus copia-type LTR retrotransposon."; RL Repbase Reports 5(2), 33-33 (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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 TOPSCOTCH_LP_I repbase; DNA; EDCOT; 4616 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_I, DE internal region. XX KW LTR Retrotransposon; Transposable Element; internal region; KW 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 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 DNA6-1_Mad repbase; DNA; EDCOT; 686 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 SHALINE5_MT repbase; DNA; EDCOT; 7373 BP. XX AC . XX DT 21-DEC-2006 (Rel. 11.12, Created) DT 03-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; retroposon; KW LINE; repeat; ORF; Interspersed; 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. 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 MUDRAVI2 repbase; DNA; EDCOT; 11143 BP. XX AC . XX DT 12-SEP-2007 (Rel. 12.09, Created) DT 02-OCT-2007 (Rel. 12.09, Last updated, Version 1) XX DE DNA transposon from grapevine. XX KW MuDR; DNA transposon; Transposable Element; 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 1-11143 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 3863..6487 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 11143 BP; 3568 A; 1705 C; 1812 G; 4013 T; 45 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 gttanttaaa catagtacat gataaataag gtaaataacc tttttcccat 1260 ttacttatct cttattagac tggaattttt tagattcaac aattttatac ttcaacwttt 1320 aaaatatggt aattaaataa cccttcttac cattaaatag tttagacaat gagcgacaaa 1380 tctataacca gatgttttct ctcaagtcct tttttttata aytatcttat gtcttactct 1440 tgtccctttg attattaggg gtcacaatct ctcaacctct ccttccatta agttaattaa 1500 ttgttacttt ttttattcat taaagaagtc ttagttttcc aactatgaaa tgattaaata 1560 agaacccagc aatgtctttt tgtttgtgct cttaagttaa tatgtgtttg tgttggattg 1620 tttggtgcca agtgacttga ccccaatata gaaataagaa aaaaaaatat atataatttt 1680 tttgaaaaaa actcttatga tataataaaa aaatggttct cgtrtttata atatcattaa 1740 tgatttaaga taaaaaaaaa ttgatttata aaacaattaa ttgattcttt gatatttaag 1800 aaagtaatcc aaaaatctta tttttatata tatatatatt ttgtagagaa atatagattt 1860 atcttatatt ttttaaaaat tattttaatt tttttttaaa tttaagagag tatttttttt 1920 atatcttaat ttttttctta aaataatatt tattatgatt ttctatttta caaaaagaag 1980 gaaatatgtc caaatgtgta cctaagtaat gccttttcaa cgactctttg ataagtttac 2040 tacacrtgtt gaattatttc catgatggga cttttgagaa atttaaaacc catatgtats 2100 aatgcaatga acttgtttgt ttttgtgggt caaagttagt tgtagtgtga aagytgyaag 2160 mgatgaaaag gatttttgta tgaacatgac atgatatgag tgttggtatg aaattcttat 2220 atggtactct tattttgctt taaagcagtc atttgacttt aattaattta tttatatttt 2280 caactttctt aaaagataag grttaatttc attcgtttty ttagaagttt tggttaagca 2340 ctttccttat tgrtttaaaa tttgatcaaa tatctccctt atttttctca tttgttattt 2400 tcagtcacct tatctcttat taaaaaatag attattttta gttacctctc ctcctattta 2460 atgaaatttc aatcaatgag gataaagtgt atttagcmaa atcttggggg gatgtgagtg 2520 ttaaccttga aagataatta kattattttk attttgtcta gtgtatgttt ataaaaawat 2580 ttargaataa gaaacaaagr ataaatatag kacaaaarwa taawaatcaa aaygaagttc 2640 tcawtaaaat atttttgtty tatgyaaatt ktttaattaa awattmtata gattttsctt 2700 ytaytttttg tattcaaats tkmatataga wyatgagatc aaacccactt aaaattkgty 2760 ttataaaaaa tcaaacaaat atttgtgtat tttcattata agatctatta gaaggtagtt 2820 aaagataaat taagtttaat tgtgaataat tgatcaaagg aattaagatt cataatttga 2880 gattttaatg gatttaaatt taaagtaaaa ttaaatatca gtttagatga aattttaagg 2940 tcttcaacct aacttgataa attatagatc ttattgattt tttaatgtcg aaattgattt 3000 ctagtgaatt cgaaatccga gtattttttt tcattaatat attttgttct attttttatt 3060 aatttcattt tttcattaat caaatatcga cttttatgtt ggcatcaatt ttattaaaat 3120 taaaattaat attcaataga tttataaatt aaaattaaat ttaatattaa tttataaatg 3180 attttttccc tatatttaaa attaatatta aatagattta taaaatgttt atttgtttgc 3240 atttttaata ttcaaataat gtttatatat atatatatat atatatatat atatatatat 3300 atatatatat tatatttaat gatttttttt tataattgtg tatttgatat tttattaata 3360 tatttttctg tggtgggtta cttttatttg attttgagtt tttaattttt ttttttaatt 3420 ttatttttaa tcaaatatca agtgattcat grataataac ataattattt aaattatata 3480 ttatttaata cttgataata ttcaatttta ttttaatata tgatatttta ttaaaaaaaa 3540 tttggtggat tattttttat ttaattttaa gattattgta attgtttaac tcaaaattta 3600 ttgatttata acccactatc taagttttaa attaaaattc tataaaacat ttatctatga 3660 ttatatttgt atcatagata actatttaaa taaaaaaaat ttattattat taagtgattt 3720 atatttttcc ctcctaatgt gtaagaaggt gttttattat ataattgtgt attcacatgt 3780 taaaagatta tatgcaattt ctcttgctat tattttcatt aattattaaa ccatttgata 3840 ttgtattttt tgtaggtaaa tcatgtctga atctattgtt cctgtgattt gcttttgtaa 3900 aggaaaaatg ttgaggacag aaacagatgt aaagtatatt ggggatsaag ctgtaattgt 3960 gcctttggat gtgcctgtta gttcaaccta tgaacacttg ttatctatga tatactcgag 4020 aactggcatt gacaaaaaac aatttcaatt agtcctcaac tgtaggtatc ctttaaaaag 4080 ggaaaatagg ttccaacctt gtccaatatg ggatgataat agtttatctc aaatgttgaa 4140 attggttaac acatttggaa tggacgaaat tgaattgtat attgaacaag tgccagtaca 4200 accacgggtg agagggcaat tattgggtaa cttcacacaa ttattactcg gacaaaatga 4260 taatgttgag gaatttgagt atggttgtgg acctagtagt gccccagttg caatgactta 4320 tgagtgtaga gcagatgaag atgaagatga aaaagaatgt gaatcccaag aaggtgatga 4380 tcaaagtgag agagcagaag atgttcaaca tgatggcgat ggggtgttcg aatttattga 4440 tgaggaaaac aataatgtta atgttgtttc atctttctta gctcttcacg aagcaatgga 4500 aagtgaacaa gggagatatg tctctgtgga tggggaaggt tgtgatatgt caaataaccc 4560 agatcctgag gacccaatag agttttcccc tgttcagtat cactcggcac catcattgca 4620 gtttgaaaat gtagaaaaca ttggtaatgc cgtttcaagt gactggaccc catgggggaa 4680 cactaatatt ggaaactcag gtggagagtt catggttggc caagttttta attcaaaagc 4740 agatttacaa catgctgcga agttgtactc tattagtgca caccaagagt acgttgttgt 4800 ttcgtcaact acaaagttgt tagtcttaag atgcaagaag gctaagcaat ctcaatgtcc 4860 atggaaactc cgtgctatgg ttgtaaaagg tacaacttca tttgcaatca ataaatacaa 4920 tggtccgcac aaatgtgtaa atccttgctt gaatcgggac catcaacaat tagattccaa 4980 cttgattgct gctcatatcc aaggaatgat taaggcacaa ttcacattgt cagtggctgc 5040 tattcaagca agtattgtgg agaaattcgg ataccaaata tcatacaaga aggcatctaa 5100 agcgaagctt aaagctctta caaacttatt tggtgatttt tataagtcat atgcagagct 5160 gccacatttt ttcattgcct tagagcaggc aaatccagga tgtgttgtaa tttcaaaaac 5220 atttcctggt attatggaga atacagagat atttcagcga gttttttgga catttcatcc 5280 atctattgaa ggattcaagc attgtcggcc tgtactcagt attgatggta cacatttgta 5340 tgggaagtat aaaggcactt taatgattgc tatgggttgt gatggaaata atcagttatt 5400 cccattggct tttgccctaa cagagggtga gaatattgat agttggggat ggtttttgac 5460 atgtattaga accagagtaa ctcataggag gggactttgt gttatatcag atcgacatcc 5520 aggcattatg gctgcaatga gcgatgttca tcttggttgg tctgagccat acgcatatca 5580 tagggtttgt atgcgtcatc ttgccagtaa ttttatgact cgattcaagg ataaaatatt 5640 gaaaaatctg atgtgcagag cagccttagc aaccaagatt gaaaaattca ataaacatat 5700 gaacacaatt gggaggatta atgcagccgc acaacaatgg ttggaagcaa tcccttttga 5760 gaaatgggcg ctctctcatg acggaggtcg aaggtatggc atcatgacta caaacatgtc 5820 ggaggtgttc aatagtgtgc ttaaaggggc tcgtagctta cccataactg ctttggttca 5880 attgacattt tttcggctaa atagttactt tgttgtgaga agggaacaag gtgctaatcg 5940 acttgcttca aatgaggaat acactccata tgtcgatgct aagattaagg caaatgtggt 6000 taaggcggga tctcatgaga ttgttttata tgatcacatc caaggacaat tccatgtgaa 6060 gactaataag ggtactaaga gtagctcaac tcgtggtcga acatatcgca tcaacttaca 6120 ggagtatgca tgcacatgtg gtaaaacact catatatgga ttcccatgta gccatattct 6180 agcagcatgt cattttcgtt cagttgattt tagaccactt gttcaacact actacagtac 6240 acaatcgtac tataatactt gggcaccctt gttccatccc attttcaatg tatatgagtg 6300 gcctccttat gatggtccga ttatcgtgcc ttctgagtcg atgaaacgtg catcaagtgg 6360 acgacctaaa tcaagtcgtt tgcataatga aatggatgtt agagagggca agacttctat 6420 tacatgtggg ttatgcaaac aaagtggcca caatcgtcgt tcttgtcaaa acagtaatag 6480 aattgattag accatgtgat gtatgcatgt aattttcttg gatattgtga tgtaagctac 6540 tatgatacta cctttatgca attattggct ttggtttgat tataaatatt gatgttattt 6600 gcataatcag gttatttgta tttggaataa tgtccatatt ataggggaaa ctttgtcaaa 6660 attttgaaat tttctattaa aaatgttaac aaaatgctca attgtatttg tatctctaat 6720 tttaatttag actagtatga cttgtttatt ggtcataaat gaattgatgt acttaaattt 6780 atcaaattga tatatactta atatagggaa aactccataa atttttaaaa cttttccatt 6840 agaaatattt ttttttttaa aacaataagt attgtttatt tatcttcaca attttgttac 6900 agatatggag tatagaggac atagttctga tccagatcca ttagatacgt ctgttttggt 6960 tctacaggat agacacaggt ctcatttagt tgactctggc caggtatgta tatgaaaaca 7020 cataatatct ctttaaataa tggaaaaaat ttgcagttta ttatctaaat gatttatttg 7080 tatttttaca gcttgcttca gtcttgactt gtcgacaaca tatatctagg tttatgcggg 7140 agtgggagat ggatcctcgt cttcgacctt atattattcg atctggattt tatggtgtat 7200 accgtattgg acacattaca ctagattggg gattgatcac tagtctagtt gagagatggc 7260 gtcctgagac acacacattt cacttacctg ttggggagat gaccattact ttacaggatg 7320 ttgctgtcat attaggactt cgtattcatg ggcttcccat cactggcaca tgtgacatag 7380 attggtcact gctatgttat gaacttttag gagtgactcc ccctacatct gagattaaag 7440 gatcagcgat atcgacacga tggctatgtc accagttctc tcatccacca gttgatttag 7500 atgatgccac attagagcgg tatgcacgag ctttcatatt aggactcata ggttcaacgc 7560 tatttacaga caagaagggt acccacatcc atatgtgtta tctcccacta cttagagact 7620 tgactcagac atctatgtat agttggggca gtgcagtatt agcacaccta tatagggagt 7680 tgtgtcgagc gagtttggat ggtgccaccg atattgctgg atgtgtcaca ctattacagg 7740 tataattaat tattcacatt agattaaaat ttctagttgc ttcaagttta taatttaagt 7800 aaaattttaa tgttacattt ttttccagtt gtggtcttgg gagagactcc acgtgggtcg 7860 acccgatttt ggtcgaccac cagcccctcc agcagcccag catttagagc atgatgcagc 7920 cgatgattta ccagctgagc agttagacca gggattacag gatgaggcat tgttacacga 7980 gggtttacca gctgatccgt taggatgtag gtggagagta cctttatcat gggctcaaaa 8040 cccatcacgt gtgttgacat tttatcgaga ccaattagat gcacagaccc atgaccaggt 8100 acatataaga tgtaatgtgc tattgttaac catataaacc ttaactcagt attaatgtca 8160 aatgttgatt ttaacaggtt ttatgggagc cttacatggg agacttagtt gcccatcttc 8220 cggcgatatc tctagcagac caggagattt ggcggacgat gtcacctctt atttgctttg 8280 acattgtcga gtggcatcga ccggagcgag tgctgcgaca gtttggcctc caacaaggga 8340 tacctccatc ttgttccata gagctagacc tccattccgt ggataggcga ggacgacata 8400 agtatgattg gggagcattc catgcacagt atattacctt atggggtagt cgtgaggagc 8460 gtattgcgac ggcaccacct atggtgggtg ttatgcagtt tcatgatcca tatatggagt 8520 ggtaccgacg tattacacga cgtttgatca caccccctct ccatagagat cagatgaggt 8580 atcatagtac agcagcagct actcagttat tggtaagatt ttttaattta taaatggttt 8640 attaaattat aattaattaa aaatcatttt tgtttgttta acttttttta ttttttttta 8700 ttttatttag atcactggta tggttgagat tgctagtcga tctgctgggc ctacttcagg 8760 tgcattaggc gacattcatc ggattgctat tgatattttg catgttattg gagaggagca 8820 tcgcatacat tcactccgtc agtcgcctac atcatcatac ccatccatga gcccacctgt 8880 gtcagccact acagttagga tgcagcctat tcgaggccga gggagaggta gtagacgaga 8940 tgatgggcga gctggtcgac agcctcgacg atctatgcat ccacctgaga ccatgttagc 9000 accatccaca tcatctaccc catttgcacc tgaggcttcc acacttcccc cttcacccct 9060 accatcacct tcacctagac cttctccctt agagcatgtc gtatcagata ccactctacc 9120 atcacctgta tttcctacca cagaggccac tatacctgat gtcactatac cagagactac 9180 cccactatct actaatctac catcacctct accttctctc gaggagacca ctacaccaca 9240 tgtcacctca ccatcatcac ttatatctcc tctcctcgag cccactatat cagatgttat 9300 tgcaccagct accattacag cagatgtcat tcttccatct cctatatcac ctcttctaga 9360 tgctaccata tcagatatca ctgtacctga gatcgcccca ccatctacca ctttaccatc 9420 acctacacct cttcccatag agactaccat gcatcatacc cttacacatg ttacacagtt 9480 agatgtatgt ccacctagga gacgtcgtgg tccacgtaga cgtcgagtct tgcctccatc 9540 agctccatct caacctatac atactgagac atggcagatt gcacagatag attccacaaa 9600 gatgtctctt tatcataggc gtccgcagag aaagaggaag accccatcat gtggcactca 9660 ttgaggactg ttttttagtt tttgtgttta ttttcatttg cattatattg ttaacttttt 9720 ttttttatta tgaacaaatt attatatatt taaatgaaaa tatgataaat tttaaactta 9780 aattgaactt atatatatat atatatatat atatatatat atataccact tacatatagc 9840 aatctgacaa tctaaaaaat tggttttagg tttaaattta aactaattat atttataact 9900 aattagttac aacaacacta tattgatata gaaaaaataa tgcattaaaa aaaatttaca 9960 atctaaacct ccaatcaaaa taatttttaa aaaattgaac attcacatga tttaaaattt 10020 gaacttaaaa aattggtttt aggtttaaat ttaaagttat gatcaccaac tactattttg 10080 actatttaaa aaaaaaaatc aaaaatcatg attaccaatt acagttttgt gatgtgaata 10140 cccacatgaa taagacacac atcacattga aaattatttt gagaataaaa ttattttatg 10200 aattttttgt tttaaagaaa tcatttttgc ccaaaactcc cattagtacc caataagaaa 10260 catttttctt attctcaatg aatttacaaa aatattccaa aagcattttc atctatttac 10320 caaaacaatt aaactaaata gtgaattgat tggaaaaaca aaggtatttt ctttctacaa 10380 ttctatattt taagaagtgg aaaaacaaat tcttttaggt tggcatttta agtttaacat 10440 tttaagcctt tccattccat tttgatccca ttttgaaagg agaaaaatgg aaaaaaaaaa 10500 attatttttg ttgtatttaa gtaattttcc aattatttac ccacttgaag tcatattata 10560 ttttgtacaa atgcataatt ggctttaatt tttgcacaaa gttacaaaat aatataatat 10620 tcttcattat gagggtataa aatagtatat ttataactaa ttatatttat attgagtata 10680 gtgccaaata ttttaataaa attatcaaaa tatattttta tatcaaatta aagacatcaa 10740 ttatttaatt tcatatatta ctattcttta aataatgaga tcaattaaag ttaaatattt 10800 ttattacacc actcacatat ttttaatcaa tataaaatca aaataatata atatttttat 10860 ttaaaaaaat taaagttaaa tatatatata tatatatata tatatataat taaagttaaa 10920 gccgtagttg gtgactacgg ctttgactat ttttaaaaat agtcaaagtc gtagtcacca 10980 actacggttt taaattttta aaaaataaaa ccgtagttac caactacggt tttatgacat 11040 ggcaatctac gtggcgcaaa cacattagat tggacattat tttgaaaatg ggggtacttt 11100 atggattttt tttttttaaa tgtagtattt tgggtcaaag ctc 11143 // 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 COPIA2-I_LC repbase; DNA; EDCOT; 10324 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 - 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 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 1-10324 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 DNA3-7_Mad repbase; DNA; EDCOT; 1144 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative non-autonomous Harbinger family DNA transposon from DE apple. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Harbinger1_MT repbase; DNA; EDCOT; 470 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 Harbinger like non-autonomous transposon from Medicago DE truncatula. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW transposon; non-autonomous; Inverted repeats; 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 "Harbinger1_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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Helitron-2_Mad repbase; DNA; EDCOT; 4037 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Helitron family DNA transposons from the apple genome. XX KW Helitron; DNA transposon; Transposable Element; 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 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 SINE-5_Mad repbase; DNA; EDCOT; 165 BP. XX AC . XX DT 08-OCT-2010 (Rel. 15.1, Created) DT 08-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE SINEs from the apple genome. XX KW SINE2/tRNA; SINE; Non-LTR Retrotransposon; Transposable Element; KW 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 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 PSAT28 repbase; DNA; EDCOT; 195 BP. XX AC AF155765; XX DT 08-NOV-2002 (Rel. 4.3, Created) DT 08-NOV-2002 (Rel. 4.3, Last updated, Version 1) XX DE Pisum sativum dispersed repetitive DNA, PSAT28. XX KW Repetitive sequence; dispersed; PSAT28. 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 Copia3-VV_I repbase; DNA; EDCOT; 5188 BP. XX AC AM448401; 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; Copia3-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 1-5188 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 1-5188 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 679-679 (2007). XX DR Genbank; AM448401; Positions 35904 30717. XX CC Positions [2288-2797] - Integrase core CC 'TTAT' target site duplication CC LTRs are 97% similar to each other. XX FH Key Location/Qualifiers FT CDS join(626..1816,1820..3646) FT /product="Copia3-VV_I_1p" FT /translation="MTKYGMASSQVSSVTSPESGGRSEIPNLGGNDSSPIL FT ITGHKLNGHNYLQWSQSVLLFICGKGKDEYLTGEAVMPETTEPGFRKWKIE FT NSMIMSWLINSMNNDIGENFLLFGTAKDIWDAAKETYSSSENTSELFQVES FT ALHDFRQGEQSVTQYYNTLTRYWQQLDLFETHSWKCSDDAATYRQIVEQKR FT LFKFFLGLNRELDDVRGRIMGIKPLPSLREAFSEVRREESRKKVMMGSKEQ FT PAPTLDASALAARSFNSSGGDRQKRDRPWCDYCKKPGHYKETCWKLHGKPA FT DWKPKPRVDRDGRAHVAANSESTSVPEPSPFNKEQMEMLQKLLSQVGSGST FT TGVAFTANRGGMRPWIVDTGASDHMTGDAAILQNYKPSNGHSSVHIADGSK FT SKIGTGSIKLTKDLYLDSVLHVPNLDCNLLSISKLARDLQCVTKFYPNLCV FT FQDLKSGKMIGSAELCSGLYLLSCGQFSNQVSQASCVQSQSMSESFNSVSN FT SKVNKDSEIIMLHYRLGHPSFVYLAKLFPKLFINKNPASYHCEICQFAKHT FT RTVYPQIPYKPSTVFSLVHSDVWGPSRIKNISGTRWFVTFVDDHTRVTWVF FT LMKEKSEVGHIFQTFNLMVQNQFNSKIQVLKSDNAKEYFTSSLSTYLQNHG FT IIHISSCVDTPQQNGVAERKNRHLLEVARCLMFSSNVPNYFWGEAILTATY FT LINRMPSRVLTFQSPRQLFLKQFPHTHAASSDLPLKVFGCTAFVHVYPQNR FT SKFAPRANKCIFLGYSPTKKGYKCYSPTNKRFYTTMDVSFFEHVFFYPKSH FT VQGESMNEHQVWESFLEGVPSFHSESPNPSQFAPTELSTPMPPSVQPAQHT FT NVPSPVTIQSPMPIQPIAPQLANENLQVYIRRRKRQELEHGSQSTCGQYID FT SNSSLPEENIGEDRDGEVLIPSIDDSTLPIALRKGVRRCTDHPIGNYVTYE FT GLSPSYRAFATSLDDTQVPNTIQEALKISEWKKAVQDEIERGRFWGLGQFT FT " XX SQ Sequence 5188 BP; 1489 A; 1150 C; 1143 G; 1398 T; 8 other; tggtatcaga gccagttttc tgaaacccta atcccttctg gccacctctt attcaggcca 60 tcactcattc cggccaaatc tctctggcca tatctcaatc cgatcgtctc tatatctctc 120 tctctctcat tccggtcatc agtccctgtt ctcagagcca agggagaaaa cgctttccga 180 tcagtcgaat cgtcgtcaga aaacactcac cgccggcaaa attttccggc gaacttttcc 240 ggcgaacttt ccggcgacgg ttttttttct acaccgcaag gagcgcctgg aggagatcty 300 caatttgtcc caaagcaccg gaaccagaaa cccatccacg cgccgcccac gcgcgttttt 360 ccgtccgrcg actgcatctc acgcgccggc gcgtgagggc gcgtgagcca ctttccggcg 420 acgcgcttcc tcctccaggc tcgcctgacg ccgaccagcc acccttcctw cctgtttgtg 480 caatccaagc cctgcacgtg cctcttttgg ggttcttttg cttccgcggg ccctctgatc 540 agattttccg gcgtcctccg gctatttttt ctcaactcca gtccctgcac gtgccttggg 600 aagtgttctt ctacctttcc ggtccatgac aaaatacgga atggcatcat cacaagtatc 660 cagcgtcacg tcaccagaat cagggggcag atctgaaatt ccaaaccttg gtggcaatga 720 ttcctctcct attctcatca caggacacaa attaaatggc cataactatt tacagtggtc 780 acaatctgtg ttgctgttca tttgcggtaa aggaaaggat gagtacctca ctggagaagc 840 agtcatgcca gaaactacag aaccgggttt caggaagtgg aagattgaaa acagcatgat 900 catgtcatgg cttatcaatt ccatgaacaa tgacataggc gaaaatttct tgctgtttgg 960 gactgcaaag gacatatggg atgcagccaa agaaacttac tcaagttctg aaaatacttc 1020 agaactgttt caggttgaat cagctctaca tgacttccgc caaggagagc agtcagttac 1080 tcagtattac aacacactca caaggtattg gcagcaactt gacttatttg agactcactc 1140 atggaaatgt tcggatgatg cagcaacata caggcaaatt gtggaacaaa agagactgtt 1200 caagttcttc ctaggactaa acagggaatt ggatgatgtt agaggccgaa tcatgggcat 1260 taaacccctg ccaagtctca gggaggcttt ttcagaggtt aggcgtgaag aaagtagaaa 1320 gaaagtgatg atgggatcaa aagagcaacc tgccccaaca ttggatgcct ctgcccttgc 1380 tgctcggtca tttaatagta gtggtggaga tcgtcagaaa cgggataggc cttggtgtga 1440 ttattgtaag aaaccaggcc attataagga gacttgctgg aagcttcatg gcaaaccggc 1500 tgattggaaa ccaaagccac gggttgacag agatggcaga gcacacgtgg ctgccaactc 1560 tgagagcaca tctgttcccg agccgagtcc attcaacaaa gagcaaatgg agatgctaca 1620 gaaattatta agccaagttg gcagtggcag tactaccggt gtagccttca ctgctaatcg 1680 aggaggaatg aggccgtgga tagtagacac aggtgcttct gatcacatga caggagatgc 1740 tgccattctt caaaattaca agccaagtaa tggtcattca tccgtccata ttgctgatgg 1800 ttcaaagtca aaaattgycg ggacaggttc tataaaactt actaaagact tatatcttga 1860 ctctgtcctc catgttccaa acttggattg taatcttttg tccattagca aattggctcg 1920 tgatctccaa tgtgttacta aattctatcc aaacttgtgt gtttttcagg acttgaaatc 1980 ggggaagatg attggcagtg ctgaactgtg ttccgggctc tacctccttt catgtggcca 2040 attctcaaac caagtctctc aagcaagttg cgtacagtct cagagtatgt cagagtcttt 2100 caattctgtg tcaaattcta aggtcaataa agatagtgag attataatgt tacactatcg 2160 ccttggtcat cctagctttg tttaccttgc gaaattgttt cccaaattat ttatcaataa 2220 aaatccagca tcttatcact gtgaaatttg tcagtttgca aagcatactc gaacagtata 2280 tcctcaaatc ccatacaaac cttcaactgt tttctctcta gtacatagtg atgtgtgggg 2340 tccctcccgg ataaaaaata tttctggcac tcgatggttt gtgacattcg ttgatgatca 2400 tactcgggta acatgggttt tccttatgaa agaaaagtca gaggtcgggc acatttttca 2460 aaccttcaat cttatggttc aaaatcaatt caattccaaa atacaagtcc tcaagtcaga 2520 taatgcaaag gaatacttta ctagtagtct cagtacttat cttcaaaatc atggcattat 2580 ccacataagt tcttgcgttg acaccccaca acaaaatggg gtggctgaac gcaagaatag 2640 acatctcttg gaggttgccc ggtgccttat gttttcctct aatgttccaa actatttctg 2700 gggggaagct attctcacag ctacctattt gattaaccgt atgccatcca gagtgcttac 2760 ctttcaatcc ccacgtcaac ttttcttaaa acagtttcct cacacccatg ccgcctcttc 2820 tgatttacca ctcaaagtat ttggttgcac agcattcgtt catgtgtatc ctcaaaatcg 2880 tagcaaattt gctcctcgag caaataagtg catttttcta gggtattctc caaccaaaaa 2940 agggtacaaa tgctattctc caaccaacaa aagattttac accaccatgg acgtctcttt 3000 ctttgaacat gtcttcttct atcccaaatc tcatgttcag ggggagagca tgaatgaaca 3060 tcaagtttgg gagtcttttc ttgagggtgt accttctttt cactcagagt caccaaatcc 3120 ttcccaattc gcgcccactg agttgtccac acccatgccg ccatcagttc agccagccca 3180 gcacacaaat gttccttctc ccgtgaccat ccagtctccc atgcctattc aacctatagc 3240 cccacaactt gctaatgaga acttacaagt ttacatcagg aggaggaaaa gacaggaatt 3300 agagcacgga tcacagtcaa catgtggcca atatattgac tccaattcaa gtcttcctga 3360 agagaacata ggtgaggata gggatggaga ggtgttaatt cccagcattg atgattctac 3420 tttgccaatt gcattgagga agggtgttag gagatgtaca gatcatccaa ttgggaatta 3480 tgttacgtat gaagggttat caccatctta cagagcattt gctacttctc ttgatgatac 3540 tcaggttccc aacacaatac aagaggcatt aaaaatttca gaatggaaga aggcagtaca 3600 agatgagatt gagagaggaa gattctgggg ccttgggcag tttacttaaa gagcagtgaa 3660 gttaaggtgt ttgaggggtt acatcctagg gaatcatgca cttgagaaga atgggacgtg 3720 gactatcaca gatttgccgg ttgggaagag gcctgtgggg tgcaagtgga ttttcaccat 3780 aaaatacaaa gcagatggat cagtcgaaag attcaaggct cgtttggtag ctagagggtt 3840 tacacaatcc tatgggatag actatcagga aacttttgct cctgttgcaa aactgaacac 3900 tatcaggatc cttctctcat tggctgtcaa tcaagattgg tgcttgcaac aactggacat 3960 aaaaaatgcg tttctaaatg gggacctrga agaggaagtc tacatggaaa taccacctgg 4020 tttcgaagaa agtatggcaa agaatcaggt ttgcaaactc caaaaatcct tgtacggcct 4080 taaacaatct cctcgagcct ggtttgatag attcacaaaa gcagtcctga agctgggcta 4140 caaacaaggt caggctgatc atactctatt tgtcaagaag tctcatgccg ggaaattggc 4200 catattgata gtctatgtcg atgatattat tctatctggg aatgatatgg gggagttaca 4260 gaatttgaag aaatatttgt cagaagagtt tgaagttaaa gaccttggaa atttgaaata 4320 tttccttggt atggaagtgg ctagatcaag gaagggaatc gtagtctctc aaagaaaata 4380 catactcgat cttcttaagg agaccggtat gcttggatgc aaaccaattg atactcctat 4440 ggatagtcag aagaaayttg gtatcgagaa agaaagtaca cckgtagaca gggggagata 4500 tcagcggctt gtcgggcgct tgatttatct ctcacacact cggccagata ttggctttgc 4560 agtgagtgct gtaagtcaat tcatgcacag ccccactgag gaacacatgg aagcagtcta 4620 caggattctt agatatttaa aaatgacacc agggaaaggc ctattcttca gaaagacaga 4680 gaaccgtgac actgaagtat actcagatgc ggattgggca ggaaacatca ttgacaggcg 4740 gtccacttct ggatattgtt cttttgtctg gggaaatctt gttacctgga ggagtaagaa 4800 gcaatcagtt gtagccagaa gtagtgcaga agctgagtac agagctcttg cacagggaat 4860 ctgtgaaggg atttggataa aaagggttct tagtaaattg ggacaaacga gttcatctcc 4920 aattctgatg atgtgtgata atcaggcarc tataagcata gcaaagaacc ccgtgcatca 4980 tgacaggacc aagcatgttg agattgacag acactttatc acagagaagg tgactagtga 5040 gacggtcaaa ttgaactatg ttcctaccaa gcaccaaacc gcagacatcc tcaccaaagc 5100 tttacctagg cctaacttcg aagacttaac ttgcaagctg ggattatatg atatatattc 5160 tccagcttga gggggagtgt tgaaataa 5188 // 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HARB-N4_Mad repbase; DNA; EDCOT; 361 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 TST1 repbase; DNA; EDCOT; 5060 BP. XX AC X52287; X52387; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 11-NOV-1996 (Rel. 1.1, 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; 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 1-5060 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 1-5060 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 1-5060 RA Camirand A., St-Pierre B., Marineau C. and Brisson N.; RT "Occurence 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 5060. XX SQ Sequence 5060 BP; 1625 A; 862 C; 1055 G; 1518 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 tttcatggta tcagagcgga 300 ccatttcccc taatatcata tggataaaac agcctttcac agagacgatc tttctgaaac 360 atcaacagga acgtcctgca aaaaatctga tgacacaagg aggcaatgct tctcacatgc 420 ccttccagtt aacttctcat cgattaaatg ggaagaacta tctggaatgg gcacagtccg 480 taaagcttgc aatcgatggc cgtggaaagc tgggacatct gaccggagag acaaagaagc 540 cgggagttgg agagatcaga gaattcactc gtgattgctt ggttaataaa ttctatggaa 600 ctagtcatag gtaaatctta tctctttttg cccactgcca aggatgcatg ggaagccgtt 660 agggagtcat attctgattt agaaaatgcc tctcaaattt tggagttaaa aattgaacta 720 tggcaagcta agcagggtga gaatgaagtc actacttatt ataatgaaat ggtgtccttg 780 tggcaggagt tagaccagtg ttacaatgat gaatgggagt gttctatgga tagtgtgaaa 840 gccaaaaaaa aggaagaaaa tgagagagtt tacctttttt tagcaagatt aaaccgagag 900 tttgacaagg tcaggtcgcg aatcctagga aaaaatcctc tgccccttcg tgaaactttt 960 tctgaaatta ggacagagga aactgggagg aaagttatgt taaaacctga tttaaatgtt 1020 gaactaaaac ctgttataga ctcttcagct cttgtaacag tgaagaatga agaggacaaa 1080 aagaaaaagc cattgtgtga tcattgcaaa aaatattggc acacccgtga aacgtgttgg 1140 aagattcatg ggaaaccact aaactggaag aacaagggag ttgatgatca tggctttcaa 1200 tctcaaaatg gtcaggccct ccaaacaact tattttgatc aggggcaaca accttctcca 1260 gaaacgtctc tatttacaag ggaacaattg gaaattctgc acaaactcct tcaatctcca 1320 caatttcgtg caaatgcacc aaaatcttct aatccttctt gttcttttgc tgaaactgta 1380 tcatctgtat cgtctgcttt tcttagtgtc aattccaacc aaatagattc ttggatcata 1440 gattcaagag ctagtgacca catgactggg agtttccgtt ttttctctac ttacactcct 1500 tgtgcaggga acagtaaaat caagatagct gatggttcct tctctgcaat tgctggaaaa 1560 ggaactatta aacttatcac catctcttgt acttcatgat actcttcatg ttccaaagct 1620 ctcttgtaat ctagtttctt tccgtaaatt aacccgttct cttaattgtc gtgttatttt 1680 ttattccgat ttgtgtgaat ttcaggaaaa ggtctcgggg aagatgattg gcagtgctag 1740 agaatcagga ggtctttatt ttcttgacaa cgggaacaac tcactacagc tgaatcctat 1800 ttttttaaac tctacttttg ttttgaataa agtcatgctt tggcactatg ggcttggaca 1860 tccaagtttt tattatttaa gacatttgtt acctcagtta tttagaaata aaaatccatc 1920 cttattccaa tgtgaatttt gtgaaatggc taagcatcat gtagatactt cttttccttc 1980 tcaaagatat caggcttcaa aaccttttac aatgattcat agtgatgttt ggggaccgtc 2040 tagaatttca acaatgtttg gaaaacggtg gtttgtaact tttattgacg atcatactag 2100 attgagttgg gtttttttat tgaagggcaa atctgaggtt aaaaatgtgt ttgagacttt 2160 ccatgtcatg gtggaaacac agttcaatga gaaaatcaag atttttcgga gtgacaatgg 2220 ccgtgaattt tttaatgaac aattaggaag ttttttcaga aaaactgggg tagtacacca 2280 aagctcttgt ccagatacac ctcaacaaaa tggtatcgcc gaaagaaaga atagacatct 2340 tttagaggca acgagagctt taatgtttac tagtaaagtt ccacaacacc tttggggaga 2400 ggctctcttg actgccactt accttattaa tagaatgcca tctcgccctc ttgaatttaa 2460 gacacctttt aaagttttca gagaaagttt tcctagttct aggttaacta cagatctacc 2520 tctgagagtt tttggttgta caacatttgt tcatgttcat aatcgtagta aacttgaacc 2580 gcgggctaag aagtgtattt ttgtagggta tgccccaagt caaaagggat ataagtgtta 2640 tgatccacat gctaggaaga taattgtcac aatggaccta actttctttg agtcgcaact 2700 ctattttact actcatcttc agggggagta tcatttaggt gaagattcat tttttgtgat 2760 attgaggaaa ctagatatca agcaaatgag gagcctaata ttacaaataa atactgatgt 2820 gagagatgta ggggaagata taaataagtg tgatccaaga gatgataagg accaaagtga 2880 cttaatgata aaaactcaga aattcaaacc tgaacctgta gcgccttcaa atgacaaaaa 2940 taaaaatggg aatagagaac aaaaaacaga aatgcaggtg tattcgagaa ggaaccgaac 3000 tcaagaaaaa aggaccgaag attctcaaca ctgccaaaaa tcagtcccac aagaccttac 3060 tgtaattcaa ggtactcttc caactgattc tatttctaat tccttagatc tagatctacc 3120 tattgcgaaa cgcaaaggtg ttagaaatac ttctaaatat cctatttcta tgtttgtgtc 3180 ctacaaaaag ttgtctccta gttattcagc ctttacttca caactctcta gtgtggagat 3240 tccaacaaat gtgcaggatg ctctacaagt tcccgagtgg aaggaggcta ttttggagga 3300 attgcgagct cttgaaaaaa atgagacatg ggagttagtg gatttacccg agggaaagaa 3360 accagtgggt tgtaaatggg tgttcaccac caaattcaaa tcagacggat ccttggaaag 3420 gtataaggcc cacctagtag ttaaggatca cacagacata tcgatgcatg actatctcga 3480 gacgtttgct ccagtagcta agctaaactc aattagagtt ctgttgacaa tcgcagtaaa 3540 tctcgactgg tctctttagc aattggatat gaagaatgtt ttcttgaacg ggcacctaga 3600 ggaagaagtc tatatggatc ccccaccagg ttttgaaggg aagtacaagt caaaaatatg 3660 caggcttaga agatctcttt atggtctaaa acaatctcca agggcttggt tcgaaaggtt 3720 tactcaattt gtgaaaaggc aagggtatgt gcaaggacaa gcagatcaca caatgtttac 3780 tcgacattca ctagaaggaa aaacaaccgt tcttatagtg tatgttgacg atatcatcct 3840 cacaggagat gatgtggttg agataaaaaa tctaaaggaa cgtcttgcct cagaatttga 3900 gataaaggac ttaggcccgc taaagtactt tcttggcatg gaggttgcac gatcgaagaa 3960 aggaattata gtgtcacaaa ggaagtatgt tcttgatctg ttaaaagaaa caggaatgag 4020 tggttgtaga ccaactgaaa ctccaattga tccaaatctg aagtttgtaa aggaaggaaa 4080 attgattgat aagggtcaat atcagagatt ggtaggcaag ttgatttact tgtcacatac 4140 tagacctgat atttcctttg ctgtgagcct agtcattcag ttcatgcatt atccacgaga 4200 agaacaccaa gaagctgtgt atcgaatcct aaggtatcta aagagttcac ctgggaaagg 4260 gttgttcttc aagaagaatg agcaaagaag tcttgaggct tatacggatg cagattgggc 4320 tggttcatct attgatagga ggtctacatc tggatattgt acatttgttt ggggaaattt 4380 ggtgacatgg agaagtaaga agcaaaatgt ggtggctcga agtagtgctg aggctgagta 4440 tcgatccatg gctctcggaa tttgtgaaat attgtggctc aagagatttt tggaagaact 4500 aagaagacct gtgagttttc caatgaagtt gtattgtgac aataaggctg ccataagcat 4560 tgctcataat ccagttcaac atgatagaac aaagcatgtt gaagtgacag acacatcatt 4620 aaaaagaaga ttgaagatgg aagtgtgtgc attccttttg ttccaacaac agaacaagtt 4680 gcaaatattt tcacaaaagg tcttttcaga actacttttg agtcctttgt tagcaagtta 4740 ggcatgtttg ctatttacat gccgacttga gggggagtgt tgaatgagta ggcagattta 4800 gtcattatct gctccaccat tgagctggca gatttgatta taatttgctc cacaaataaa 4860 gctggcagat ttgagaatct gccctgtaaa tatgggatta gaatatatta ttctaggaaa 4920 atagtttaga ggaaatccct taattcaagg atttcctaag aattagggat tgattagttt 4980 atttggtctt tacttgttct cttataaata ctgtacaaac actacgaata aaatatactt 5040 ttgcagtatc taaacattca 5060 // 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. 15.1, Last updated, Version 1) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DEM1_LTR repbase; DNA; EDCOT; 2773 BP. XX AC AJ291492; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Malus domestica retrotransposon DEM1_LTR, long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Long terminal repeat; KW retrotransposon; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA9-3B_Mad repbase; DNA; EDCOT; 964 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-3_Mad; KW 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 TTO1_NT repbase; DNA; EDCOT; 5300 BP. XX AC D83003; XX DT 04-MAR-1998 (Rel. 3.02, Created) DT 09-APR-2007 (Rel. 3.02, 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; 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 1-5300 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 1-5300 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 1-5300 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 5300. XX SQ Sequence 5300 BP; 1623 A; 944 C; 1315 G; 1418 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 aacaagtggt atcagagctt tggttagagt 600 actattcata cgtacgagta ctattcatcc atacgggcac tattcatatc cacggttact 660 attcaccgtc ggattttttt tttagattgc aaaagtctgt caaattctga tctaaatgga 720 ggcgaggaca agcaagatgg tcaacctgaa tggcacaaat tatcacttat ggagaaacaa 780 gatgaaggat ctcctgttcg tgacaaagat gcacctgccg gtgttcagtt ctcagaaacc 840 tgaagataag tcagacgagg actgggaatt tgagcacaac caagtgtgcg gctacatacg 900 gcaatttgtt gaagacaatg tgtacaacca catttctggt gtgacacatg caaggtcgtt 960 atgggacaag ctcgaagagt tgtatgcctc taaaacaggt aacaacaaat tattttactt 1020 gacaaaatta atgcaagtaa aatatgtaga agggacaact gtggcagatc accttaatga 1080 aatacaaggg attgtcgacc agttgtcggg aatgggcata aagttcgatg acgaggtact 1140 tgctcttatg gtgctggcaa cactcccaga gtcatgggaa accttgaagg tttcaatcac 1200 caattctgca cccaacggtg tggtaaacat ggagacagtc aagagtggca ttctgaatga 1260 agaaatgaga cgccgatcac aaggaacatc ttcttcacag tcagaggtgt tggctgttac 1320 gaccaggggg agaagtcaaa ataagagcca gagtaacaga gataagagca gaggtaaatc 1380 caacaaattt gcaaatgttg agtgccatta ctgcaaaaag aaggggcata tcaaaagatt 1440 ttgccgacag ttccagaatg accagaagaa gaacaaaggc aaaaaggtga agcccgaaga 1500 aagcagtgat gatgaaacga actcctttgg tgagttcaac gttgtctacg atgacgacat 1560 tatcaatctg acaacccaag agatgacctg ggtgattgat agtggggcta ccattcatgc 1620 gacgccacgg agagaactct tctcatctta cacacttgga gactttggtc gtgtaaagat 1680 gggaaatgcc aatttctcaa cagttgtagg caaaggtgat gtttgcctag agaccatgaa 1740 tgggatgaag ctacttttaa gagatgtcag gcatgttcca gatatgcgcc tgaatctgat 1800 ctccgtagac aagctcgatg aggaaggtta ctgcaatacc ttccataatg gccaatggaa 1860 gctcacgaag ggctcattga tggtggcgcg gggcacgaag cagtcaaagt tgtacgtgac 1920 ccaggcgagc atctcccaac aagttataaa tgttgcggag aatgatagca atatcaagtt 1980 gtggcataga cgtcttggcc acatgagtga gaagtcaatg gcgcgtttgg taaagaagaa 2040 cgccttacca ggtctaaacc agatccagtt gaagaagtgt gctgactgtt tagctgggaa 2100 acaaaacaga gtttcgttca aaagattccc tccttccaga aggcaaaatg tgttggatct 2160 ggtacactca gatgtatgtg ggcctttcaa gaagtccctc ggtggtgccc gatatttcgt 2220 gacctttatt gatgatcatt cacgaaagac atgggtatac acgctgaaga ccaaggatca 2280 agtgtttcaa gttttcaaac agtttctgac cttggtggaa agagagactg gtaagaagtt 2340 gaagtgcatc cggacagaca atggcggtga ataccagggt caatttgatg cttactgtaa 2400 agagcatggt attcgacatc agttcacacc tcctaaaact ccccagttga atggcttggc 2460 tgagaggatg aacagaactt tgatcgagag aaccagatgt ttactctctc attcaaagtt 2520 accaaaggct ttctggggtg aagctctagt tacagcagcc tatgtgctga accattcacc 2580 ctgtgtccct cttcagtaca aggctccaga aaagatttgg ttaggaagag atatctctta 2640 tgatcaatta cgggtatttg gctgcaaagc ctatgtccat gttccgaaag atgaaaggag 2700 caaacttgat gtcaagacaa gggagtgtgt attcatcggc tatggtcaag acatgcttgg 2760 ctataagttc tatgatccgg tggaaaagaa gctcgtcagg agtcgagatg tcgtgttcgt 2820 tgaggaccaa acaattgaag acattgacaa agtagagaag tccactgatg attctgctga 2880 gtttgagttg cctccaacag tggtgccgag acaagttgga gatgatgttc aggataatca 2940 acctgaagcc cctggtcttc ctaatgaaga tgaactagca gatactgaag gtaacgagga 3000 caatggtgat gatgatgcag acgaggagga tcaacctcaa ccaccaatcc tcaataaccc 3060 tccttatcac acaagatctg gaagagttgt gcaacagtct accagatatt ctccacatga 3120 gtatgtgtta ctcactgacg ggggagaacc cgacagcttt gaagaagcta ttgatgatga 3180 acataaggag aagtggatag aagccatgca agacgagata aaatccttgc atgagaacaa 3240 gacgtttgag ctggtgaagt tgccgaaagg caagagagct ttgaagaata agtgggtgtt 3300 caagatgaag catgatgaac acaattccct tccgagattc aaagcaagat tggtcgtcaa 3360 aggtttcaat caaaggaaag gcattgactt tgatgaaata ttctcaccag ttgtgaaaat 3420 gacctcaata cgcacggtgc tgggattagc agcaagcctc aacctggagg ttgaacagat 3480 ggatgtaaaa actgccttcc tacatggtga tttggaagag gagatataca tggagcaacc 3540 agacggtttc cagcaaaagg ggaaagagga ctacgtttgt agattgagga aaagcctcta 3600 tggcttaaaa caggcaccaa ggcagtggta caagaagttc gagtcggtga tggggcaaca 3660 cggctacaag aagacaactt cagaccattg tgtgttcgct cagaagtttt ctgacgatga 3720 tttcatcatc ctattgctct atgtagatga tatgttgatt gttggccgga atgtttccag 3780 aattaatagc ttaaaagaac agctaagcaa gttcttcgcc atgaaagact tggggccagc 3840 aaaacagatc cttgggatga ggattatgcg agaccgagaa gccaagaagt tatggttgtc 3900 tcaggagaag tacatcgaga aggtacttca acggttcaac atggagaaaa ctaaagcagt 3960 tagctgtcct cttgctaacc actttagatt gagcaccaag caaagcccgt caacagatga 4020 tgagagaaga aagatggagc ggattccata tgcttcagca gtaggaagtt tgatgtatgc 4080 catggtttgt acacggccag atatcgctca cgctgtagga gtggtaagta gatttctttc 4140 taatccaggt aaggaacatt gggatgctgt taagtggatt ctcaggtatc ttcgaggaac 4200 ctccaaacta tgcttatgtt ttggagaaga caaccctgtg ttggttggct atactgatgc 4260 agatatggcc ggagatgttg attctagaaa atcaacttca ggatacttga ttaacttttc 4320 agggggagct gtgtcatggc aatcaaagtt gcaaaaatgt gttgcattat caactactga 4380 agctgaattc atcgcagcaa cggaggcttg caaagaattg atatggatga agaagttctt 4440 aactgaactt ggattttcgc aagacggtta tcagttattt tgtgatagtc aaagtgctat 4500 ccaccttgcg aagaatgcct cattccattc cagatccaaa catattgatg tgagatataa 4560 ttggatcagg gatgtgttgg agaagaagat gttgcggctt gaaaagatcc atacagacga 4620 aaatggatcg gacatgttga ccaagacttt accgaaaggg aagtttgagt tctgtagaga 4680 agctgcaggg atagtggatc caccatatag ttggaagggg gagaattgtt agtttttcca 4740 acaattatgg tgatgtatgg gagaggtaag caatgatgca actctcctta gtgagataag 4800 caatgatgca atgagtggta ggtgagatga gaatattgca aattgatcct tcttggtagg 4860 tgagatttgc acttttggtc cctatctcaa aactataaat acccccttcc atttcattgt 4920 ataacacacc aaaaaatata tcaaaactca agaagaaaga gtttgagagg gagagagata 4980 tagttccttt aggaatgttt cctaacaggg gagtgacaaa atagtgagta gaaatactag 5040 tcgggtattt ttcgggaaac acttttgtgt gcgccactat tttgggtaga gctcaggaat 5100 tgttgtacct ccaaattatt gaggaagtct ctctttgtat gcctgctaaa tgttttagtg 5160 gaagttggtg tcggatttgt ggacgtagcc taaacgtttt aggtgaacca cgttaaatat 5220 tgtgtcattt atttttggtt tcgttgatca tttattttat tccgctgtgc agtagtgttt 5280 agtgccaccg gatcctaaca 5300 // 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HARB-2B_Mad repbase; DNA; EDCOT; 4588 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; 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 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 HAT-4N2_Mad repbase; DNA; EDCOT; 1856 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 COPIA3-LTR_LC repbase; DNA; EDCOT; 871 BP. XX AC . XX DT 09-SEP-2005 (Rel. 10.09, Created) DT 09-SEP-2005 (Rel. 10.09, Last updated, Version 1) 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 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 1-871 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 EnSpm-5_VV repbase; DNA; EDCOT; 21507 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-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 OS 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]. 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; 7575 A; 2964 C; 3486 G; 7482 T; 0 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 agagttttga cccaaaatag 1680 tccattgaaa attttttttt tcataaaata aacttatttc caaaataata ctcaatctaa 1740 tgtgtctgta tcacataagt tgtcatgcca taaaattgta attggtgact acagttttat 1800 ttttctaaaa tggttagaaa ccgtagtcac caaccacagt tttaacttta agtttaaagc 1860 cgcaattagt gactacggtt ttgaattctt ttaaaaatga tcaaaaccat agtcaccaac 1920 tacgacttta acttatatat atatatatat tattatcttg tttcatttaa aatatttaac 1980 tttaattttt ttaaataaaa attatattat tttgatttta aataaactta tctcattatt 2040 taaaaaatta ttagtatatg aaattaaata attgatattt ttaatatggt ataaatttgt 2100 tatattttat tttattaaaa caattgacac tatatctaat ataaatttaa ttaattaatt 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 MEGY-I_MT repbase; DNA; EDCOT; 6550 BP. XX AC AC146683; XX DT 09-JUN-2005 (Rel. 10.05, Created) DT 09-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE Medicago truncatula LTR retrotransposon MEGY-1 (internal). XX KW LTR Retrotransposon; Transposable Element; Interspersed repeat; KW Metaviridae; 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 CC 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-71_Mad-I repbase; DNA; EDCOT; 4522 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 COPIA2-LTR_LC repbase; DNA; EDCOT; 571 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 retrotranposon - LTR consensus DE sequence. XX KW COPIA1-LTR_LC; COPIA2-LTR_LC; 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 1-571 RA Gentles A. and Jurka J.; RT "COPIA2_LC: L. corniculatus copia-type LTR retrotransposon."; RL Repbase Reports 5(2), 34-34 (2005). XX DR [1] (Consensus) XX SQ Sequence 571 BP; 165 A; 107 C; 108 G; 190 T; 1 other; tgccctccaa cggtagcatt tcccatgcaa cgctcaaccc taatccttgg agtatatata 60 gaggctgaag attgaaagaa gcggctagaa gcattcacac acgcgcaaga catattcaaa 120 atcttctaag ctttctttca tctgaaattc attgtgttta ctattagctt tttagaagca 180 aatctcttgt aaacaattct ttgataaaca gtttgtttag ttcctttagg agatcaaggt 240 tgatcggatc ctagagaaga ctaagagagt gaatcttagt gtgagctaag tcagtgtaat 300 tgttagtcac ttgtaggttt caagtgcagt tgtaactctt acctgattag tggattgcct 360 tcattctaag aaggaagaaa tcaccttaac gggtggactg gagtagcttg agtgatttat 420 caagtgaacc aggataaaat ccttgtgtgc ttttctatct cttatcttta gcacttaagt 480 tctcgaaaga tttgtcaaaa tctttaaggt ggaagtttta thctgaaaac gttattcaaa 540 cccccccttt ctaccgtttt tcataccttc a 571 // 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 MuDR-4N_Mad repbase; DNA; EDCOT; 1114 BP. XX AC . XX DT 07-OCT-2010 (Rel. 15.1, Created) DT 07-OCT-2010 (Rel. 15.1, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HERA repbase; DNA; EDCOT; 4737 BP. XX AC . XX DT 18-DEC-2006 (Rel. 11.12, Created) DT 18-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE A putative non-autonomous helitron, from Medicago truncatula. XX KW Helitron; DNA transposon; Transposable Element; Nonautonomous; KW transposon; DNA; repeat; Interspersed; HERA. 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 1-4737 RA Shankar R. and Jurka J.; RT "HERA: A putative non-autonomous helitron from barrel medic."; RL Direct Submission to Repbase Update (18-DEC-2006). XX DR [1] (Consensus) XX CC The region encodes for helicase and recombinase. XX FH Key Location/Qualifiers FT CDS 3819..4184 FT /product="HERA_1p" FT /translation="MVEEGGTYQLEGRVISGSNIGEKVFIPRLSLTPSDNR FT IPFKFKRRQFPISVSFAMTINKSQGQSLEHVGVYLPSPIFSHGQLYVAISQ FT VTSRGGLKILINDDDDDDIDVASNVVYREVFRNV" XX SQ Sequence 4737 BP; 1422 A; 930 C; 641 G; 1739 T; 5 other; tattggtaaa tctattgtca ttttcttttt agcatcacaa tatcttctta tatattaaag 60 ttaacacaga agcatatttt agccctaatt ttaacctaaa tttattgcat aaatttacta 120 ttttaaccct gatgctaaat tcctttgttt aaccttattg aatttccccc ttctcaattt 180 ctcgatacat cttatcttat atattaaagt taacacagaa gcatatttta gccctaattt 240 taacctaaat ctattgcata aatttactat tttaactctg atgctaaatt cctttgttta 300 accttattga attttccccc ttctcaattt ctcgatacat cttcttatat attaaagtta 360 acacagaagc atattttagc cctaatttta acctaaacta attgcataaa tttactattt 420 taaccctgat actaaatctt cttatatatt aaagttaaca caaaagcata ttttagcyct 480 aattttaacc taaacctatt kcataaattt tctatttaac cctgatgcta aattcctttg 540 tttaacctta ttgaattttc ccccttctca atttctcgat acttattcct aaacaaagct 600 ttgttgccct aattttaacc taatatttta acytaatatt ttagcaactt ttccctcctt 660 caaaacctaa ccatatttcc taattcccct cctccaaacc ctaaccatga tttcctaact 720 tcactcctcc taaaacctat ctaattgatt tycataaacc atatctccta actcccctcc 780 tccaaaccct caccaatata ttttaatcct ttctcctaaa ccgaaatctc tttctaaaac 840 catacctttc tcttaaaccg aaatttctta atcaacatgg cttccagaaa cattcagact 900 ttgctgtcat accactgcct cactgataac catatcttca ttccactctg gtttatacta 960 aatatataga cttttgctct tattcctcgc tgttgtaaag tataaatcat tctttcaatc 1020 ccttttaatc ttttgtaggt ccgttggtga aaaaccctct ttccgatctt gacaaagcaa 1080 tcaacaagct gagactgaaa tacagatcat atatcgttga atatgacatt gatgttgtat 1140 gtgttttttg cgaaatatac ctattcgggt gcagtatgct tgccaaacat gtttggcggt 1200 gattttggag atcaaattgg gcgctatgca atattgactg atcctaagtc caacaagttt 1260 gaagtattgg tcgacagagt aaacggagca tttttttctc acaaagggat ggaaagcgat 1320 tcgtgacttt tacggaatcg atcttggtgc ctggattacc ttggtttttg ttggtgacgg 1380 acagtttgat atacagttga ctgataggtt tcacaagagt atcccctacc cggtttttga 1440 tccccctatg catttccttc ttgacaagat gaatttgcaa gcaactttcg atgactatct 1500 ccccccaata acatctcttc tcgcttatcg tcacaatatc actgacatgg ttcttgattt 1560 cgttaactga gtatgatgtt actaaaggtt gcatggtatg atacactttt cgtgtccacc 1620 ttaacttctt ttattccttt tccgtttagt tgatataagt tacatggatt tctaattttg 1680 cagattctac tttacaccgg caatgttccg cagatgcttg atacactcaa gacaactgtg 1740 aatattatcg acgattgcgg taacttatgg gtgtgtgagc taacttttgc aacttttcct 1800 tatgaacact tcaagatagg acggcgttgg aataggtttg tggaagctcg caggctccgt 1860 gaaggtgtga agatcagagg gggtgctccg atggttgggt cacatgatac catctacctt 1920 gatgttattt acaattagtc catgtttaga taaattgtgc aacacctttc cactttgaat 1980 tttaagtttt agtttcttaa gagttttgga agcatctatt tttttgtctt tgaatttagc 2040 aaatgtccct tgaatttcat aaataattta gccttgcttg ctttggtttt tgatttatat 2100 atttgtgttt gtgctcctca aactatttag taacgtgaat tttgtaacaa gggaaactta 2160 tatgtgtgtg tatgtttttg tgttgctgaa tcaatttagt agcattgctg tgttattgaa 2220 gcattttagt agcatagctt ttagtaacat tattagtaac aattactacc ttttggtgac 2280 acttttagta acattattac taacaattac taatcctaat ctctaaaata tgttttgggt 2340 ggaatcaaac taaaatccta atcctaattt ctctcattca agtaactaag aaatttcatc 2400 cacatctcta aagtaacttt ttggtggaaa caaactaaaa tccttatttc tctcattcaa 2460 ataattacgg gatttcattc acatctctaa aatatgtttt gggtggaaac aaactaaaaa 2520 tcctaattcc tctcattcaa gtaactacta aagatttcat ccacatctct aaaatatttt 2580 ttaggtggaa acaaactaaa atcctaatcc taatttctct cattcaagta accaagagat 2640 ttcatccaca tctctaaagt aactttttgg tggaaacaaa ctaaaatcct tatttctctc 2700 attcaaataa gtaagagatt tcatccacat ctctaaaata tgttttgggt ggaaacaaac 2760 taaattccta atcctaattt ctctcattca agtaactaag agatttcatc cacatctcta 2820 aagtaacttt ttggtggaaa caaactaaaa tccttatttc tctcattcaa ataattaggg 2880 gatttcatcc acatctctaa aatatgtttt gggtggaaay aaactaaaaa tcctaattcc 2940 tctcattcaa gtaactacta aagatttcat ccacatctct aaaatatgtt ttgggtggaa 3000 acaaattaaa atcctaatcc taatttctct cattcaagta agtaagagat ttaatccaca 3060 tctctaaaat atgttttggc gagtcaacta tggtaattct taagtcaaac acactgcccc 3120 atcaaaaata ttaatttcat attattcata ttaatcttta tccaaaaatg ttgggcattt 3180 cctaatttta ttccacttca actacatccc tttgttctgc gccccttccc tatttacatg 3240 ccaattctta agtaaaacaa agtgccccat caacaatatt aatttcattt tattcatatt 3300 aatctttatc ctaaaatgtt ggccacttcc taattttgtt ccactatttt gtgcttatcc 3360 tgataactaa tactctttat tgctcaaccg acatatccta ctcacacgta ttgcaccttt 3420 ttcctataaa tatatcataa cctattagcc aaaccatctc aatctaaata agcatcctct 3480 ttcttggaaa ggaaaaaaca agccaatgat gtctgccaaa tacactccaa tctcagctgt 3540 ttctggagga agaaggaatc tcaagatgtg tgtgcgagtt gctcacattt ggttgattcg 3600 agagaagaag gtccccacta gcatcatttt catgaacatg ttactggtcg atgaaaaggt 3660 ttctatatgt ttgcactctt agctttaaaa ttaaactaat gtcatcgttg ttttttagtt 3720 atgtaattta accagctgtt taatgttgtt gttttcgtca atagggtgga cgtattcacg 3780 ccacagctag aaaagatttg gtggcaaagt tcaggtccat ggttgaagaa gggggtacat 3840 atcagctcga aggacgggta atatctggtt ctaatatcgg tgagaaggtg tttattccaa 3900 ggttatcgct aacaccatct gataatagaa ttcctttcaa atttaaacga aggcagtttc 3960 cgatatctgt ctcatttgca atgactatta acaagagtca gggtcagtcg ctagaacatg 4020 ttggtgtcta cctaccgtct cctatttttt cacatggaca attgtacgtc gcaatatcac 4080 aggttacttc gaggggtggt ttaaaaatat tgattaatga cgacgacgac gatgatatcg 4140 atgttgcatc aaatgtggtc tacagagaag ttttccgtaa tgtgtaggac ttttttgtgt 4200 actgttcatt ttcttactta ttgaaactat ttgcatgtca acgaacttca atttcccttt 4260 caaaattata tgttatttta aagtaacagg aactacgtac tagaattatg gaacaataac 4320 aaagtctttg gtattgacat tttgctttga ttcacgacaa tttttagatt cacgcgaact 4380 acagtgtctt atttttcagt gaatattatc ttttttaaat gacacgtgcg ttagcacggg 4440 tcaatggtct agttaaagtt aacacaaaag catattttaa ccctaatttt aacctaaatc 4500 tattgcataa attactattt taatcctgat gctaaattcc tttgtttaac cttattgaat 4560 tttccccctt ctcaatttct cgatacatct tcttatcttc ttatatatta aagttaacac 4620 ataagcatat tttagtccta attttaacct aaacctattg cataaattta ctattttaac 4680 cctgatgcta aattcctaac cttatatttt cctcaatttc tcgaatcttc atatata 4737 // 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, 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-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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA8-7_Mad repbase; DNA; EDCOT; 783 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 LycEPRV_LTR repbase; DNA; EDCOT; 185 BP. XX AC AC171732; XX DT 16-MAR-2006 (Rel. 11.03, Created) DT 12-APR-2006 (Rel. 11.03, Last updated, Version 1) XX DE Long terminal repeat of an endogenous retrovirus from DE Lycopersicon esculentum. XX KW Endogenous Retrovirus; Transposable Element; 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 LTR-2_Mad repbase; DNA; EDCOT; 2029 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Ogre-MT3_I repbase; DNA; EDCOT; 11878 BP. XX AC AC151524; 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-MT3; 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: 6026..6311: 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 HAT-10_Mad repbase; DNA; EDCOT; 6710 BP. XX AC . XX DT 20-OCT-2010 (Rel. 15.1, Created) DT 20-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 TreLTRRT2 repbase; DNA; EDCOT; 6103 BP. XX AC . XX DT 03-DEC-2010 (Rel. 15.12, Created) DT 03-DEC-2010 (Rel. 15.12, Last updated, Version 1) XX DE LTR retrotransposon of unknown class from CLUSTALW alignment of DE two, full-length elements from T. repens L Genbank Accessions DE GU443965 positions 104389-112569 and GU443966 positions DE 61716-69898. XX KW LTR Retrotransposon; Transposable Element; 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 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. XX FH Key Location/Qualifiers FT CDS 120..3752 FT /product="TreLTRRT2_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_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 LTR-5_Mad repbase; DNA; EDCOT; 3192 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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" 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" 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 L1-1_Mad repbase; DNA; EDCOT; 6675 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 SINE-3_Mad repbase; DNA; EDCOT; 797 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative SINEs from the apple genome. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Nonautonomous; 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 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 HAT-N10_Mad repbase; DNA; EDCOT; 4909 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, 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-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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-3_Mad repbase; DNA; EDCOT; 3472 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 HAT-N12_Mad repbase; DNA; EDCOT; 1215 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.1, 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-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 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 GmGYPSY11_I repbase; DNA; EDCOT; 5176 BP. XX AC . XX DT 06-JUL-2009 (Rel. 14.07, Created) DT 06-JUL-2009 (Rel. 14.07, Last updated, Version 1) XX DE Gypsy-like retrotransposon from Glycine max, internal region. XX KW LTR Retrotransposon; Transposable Element; consensus; Medicago; KW soybean; Gypshan4; 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Ogre-LE1_I repbase; DNA; EDCOT; 12262 BP. XX AC AC171735; 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-LE1; 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 from 7723 to 7762. 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Ogre-PT2_I repbase; DNA; EDCOT; 12216 BP. XX AC AC182676; 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-PT2; 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: 6319..6556: 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 join(686..1708,1712..2677) FT /product="Ogre-PT2_ORF1" FT /translation="MKRILGHSQNIDEAAFFGKYGRLLEIAKIGVLNPAIK FT ALINFWDPDYRCFSFGNVDLCPTIEEYGMLMEFPKHLHQVYFPLRNDKVIP FT ELSKLLKIPHLSRFLEKNGSGLKWKFLEVELEKKKEQYALVLERDRLIALG FT IYGLVLFPSLKGVISLEAAAAFVEYENTHVNPTTAILAETLLTLNHFRKTG FT KGAVRCCTQLLYIWMVSHVETKKPIFNNFWWFNQKPLKIVEEEELGILGDQ FT GWMKKLQELPSSNFSWKAPWVKSVDVIVSCGQKCWVPLIGITGYVSYAPAL FT VIRQLGGIQHIPRTVGLAEFSGFFKDQSAREVLETIKQDWSQLTLIQKEES FT LRDPSSSEGYEKWRNLTLIATPKKPCSEDGPSRIEERSLKRKKVSNEEDLM FT EQIERLQIELGKSKGDKAALERMMMEGDKSRVFLNEQLESKDAKIGMLELQ FT LSKGKAVIEESEKERGRLILDLMQSSSELEALKADFDGYQENVEYNQDKFL FT HVKAELLDRIEKHDELNKKYMMIESRLAELQEFERKGNEEEVVKADLAAKK FT IEIRILKVKFDKEREKVKQLTNRLEVSEKHKEQIDTNNNTLNRNNMVLIEK FT MAKVDEQMDEAAIHARIIRANARRVGRDIFRYRQSLAETDAFLEKIENRGL FT AFLPVARDMDEEED" FT CDS join(3020..3760,3764..6319,6558..7703,7707..9575, FT 9579..10004) FT /product="Ogre-PT2_ORF2+3" FT /note="gag-pol." FT /translation="MENEERAHIESHYQTELESVKNEVSRLTDLLEQLLRA FT KNGEGTSARQLEGAPAVHIPQASQNQGANSANEQQFVPITPILPPHTPVTV FT DLTTEGVPDNRSPSLIDQDKLFALEERLRAVEGNDWFDPMRAAEVCLVPNI FT VVPKDFRIPEFIKYTGLECPNTHLRSYCNKMAEVIRDDKMLIYFFQDSLAG FT SALSWYMRLDSIRIKSWRDLVEAFLKQYKFNMEIAPDRTSLMAMEKRSQES FT VRAYAQWRDEAMHVQPPLIETEMVSLFANTFKAPYYEHLMGSSSQHFYDAV FT RIAERIEQGIKAGRIAMPVEKKGFIGRKREGDVNNLEDGYKGKKVDSHNPQ FT VPTSQFSRINFNQSFSPNRTNNQSNYQNHYQRPHTRYPSEQLPPLPMPLKD FT MYAKLLSIGHIAPIPTLPLQPPFPIWYKPELTCEYHAGNPGHGIETCYAFK FT KRLLELIKIGWVSFEDKPNVNSNPLPKHASSSSGIGMIEVGNQCKVLKVSM FT EKMYYLLVRSGFLEANMEGHSEGGSYCEFHGRDGHYIEDCIEFCEKIAKMF FT KMGQLRIEPMENGGEVSMMEGQMEMTGVCRVQQTANGPPRLILVKPSYTKG FT NHNAMPYNYGYASNVQAPLPLFQTEISGLTRSGRCFTSEELRKEKGKEVVD FT LDKALEVNKPVTEEESNEFLKLIKHSEYCIVDQLKKTPARISLMSLILSSE FT PHRNALQKVLNKAYVPQDIEHKTMEHLVGRIHATNYLYFTADELDAEGTGH FT NKPLYITVRCKDCLIGKVLIDNGSALNVLPKHMLEEMPIDESHIKPSTMMA FT RAYDGSPRPIIGTLEVELYVGPQMFLVTLQVMDIHPSYSMLLGRPWIHAAG FT AVASSLHQCLKYIMNGMLVTVKAEETVSMIKNVAVPFIEAGDCKGNNIHAF FT EIVNTDWVPENTVLRRPRISEAARMASLCFLNRGIPFQYNFIIRIPEGVNL FT ARMKSAAQKFGLGYQPNQKDYRWAAGWRRARRMARIKGREPDEEKLEIPPL FT CVSFPKAAYIMQHDKEAESLDQELSNMSINTLGENKVEEDDMKTVARKGDE FT ALPQLTVYTIEEVSAKTFVRKLAQDEKFQNWVTQEAPVVFKMNPESGSPTT FT SHIFSIKNKWPNLNEHVIAMEEEEWDESNISEFTRLVEQQEQTWKPIAEEL FT ETINVGSDQLKKELKIGTLVTSEQRTKMIALLQEYADVFAWSYEDMPGLDT FT NIVVHKIPLEEGCKPVKQKLRRAHPDVWIKVKVELEKQWDAGFLEVVRYPQ FT WVSNIVVVPKKEGKIRVCVDFRNLNKASPKDDFPLPHIDVLVDNAARSSTY FT SFMDGFSGYNQIKMAPEDKTKTTFVTPWGTFCYKVMPFGLKNAGVTYQRAM FT VTLFHDMMHKEIEVYVDDMIAKSKRGEDHVEVLRKLFERLRKYELRLNPAK FT CSFGVKSGKLLGFVVSDRGIEVDPDKVRAIQAMSSPKTEKEVRGFLGRINY FT IARFIAQLTTTCEPIFLLRKKNPGTWNEECEEAFNKIKHYLQNPPLLVPPV FT SGKPLVLYLTVTEAAMGCVLGQHDETGRKERAIYYLSKKFTECESRYTEIE FT RLCCALVWAAKRLRHYMLYYTTWLISKVDPLRYICNKPFLSSRIARWQVLL FT AEYDIVYMTRKAVKGSAIADHLADNAVEDYEPLDFDFPDEDILSIEKEEEN FT TDWWTMFFDGAVNVYGNGAGAVIISPDKKQYPVSVKLHFECTNNTAEYEAC FT ILGLEATLELKIKKLDVYGDSMLIICQVKGEWQTKEEKLRSYQEYLSMLAK FT EFEEIRFTHLGREGNHFADALATLAAMTTIDLKCKVQPVHIDIRNDPAHCC FT LVEGEIDGQPWYYDIKNLVQNQEYPVGASKTDKKTLRRLATDFYLDGEILY FT KRSFDGTLLRCLNEADARKALREVHEGICSTHASGHMIARKIQRAGYFWMT FT LEKDCIDYVRKCHKCQVYSDKVNMPPAPLFNLISPWPFAMWGIDVIGPVNP FT KASNGHRFILVAIDYFTKWVEANSYAHVTQKVVKRFIEKDLICRYGPPEKI FT VTDNAQNFNGKMIVELCTKWKIKHSNSSPYRPKMNGAVEAANKNIKKIIQK FT MVVTYRDWHEMLSFALHAYRTTVRTSTTTPYSLVYGMEAVMPLEVEIPSLR FT VLIDSELEEAEWAKVRYEQLNLISEKRMAAICHHQLYQKRMAKAYDKKVRP FT RLFQEGDLVLKKILSLPGDDQSKWAPNYEGPYIVKKAFSGGALKLARMDGE FT DLARPVNSDSVKRYYA" 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 BAMHI_VF repbase; DNA; EDCOT; 250 BP. XX AC M16852; XX DT 11-NOV-1996 (Rel. 2.2, Created) DT 25-MAR-1997 (Rel. 3, Last updated, Version 2) XX DE Broad bean (V.faba) BamHI repetitive element, clone 6. XX KW BamHI repetitive sequence; VFBAMHI; BAMHI_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 1-250 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-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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-79_Mad-LTR repbase; DNA; EDCOT; 201 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA9-11_Mad repbase; DNA; EDCOT; 1309 BP. XX AC . XX DT 20-OCT-2010 (Rel. 15.1, Created) DT 20-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; DNA9-10_Mad; KW 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 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-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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA9-10_Mad repbase; DNA; EDCOT; 154 BP. XX AC . XX DT 20-OCT-2010 (Rel. 15.1, Created) DT 20-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 DNA9-8_Mad repbase; DNA; EDCOT; 398 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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-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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 GYVIT1_I repbase; DNA; EDCOT; 7441 BP. XX AC AM448663; XX DT 25-APR-2007 (Rel. 12.04, Created) DT 25-APR-2007 (Rel. 12.04, Last updated, Version 1) XX DE Gypsy-type LTR retrotransposon - internal sequence. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; GYVIT1_LTR; 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 1-7441 RA Jurka J.; RT "GYVIT1: Gypsy-type element from Vitis vinifera."; RL Repbase Reports 7(4), 142-142 (2007). XX DR EMBL/GenBank/DDBJ; AM448663; Positions 10973 3533. 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..2025 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 GESSQVKDVKALITLRSGKKIEQPTPKPHVEKEEEIKKXKEMEDKXSEISE FT EKKESDSTIKAIPEKEXLKEEMLKKSTSPPFPQALHGKKGG" FT CDS 2009..2929 FT /product="GYVIT1_I_2p" FT /translation="MGKRGVRNAAEILEVLRQVKVNIPLLDMIKQVPTYAK FT FLKDLCTIKRGLTVNKKAFLTEQVSAILQCKSPLKYKDPGSPTISVMIGGK FT VVEKALLDLGASVNLLPYSVYKQLGLGELKPTAITLSLADRSVKIPRGVIE FT DVLVQVDNFYYPVDFVVLDTXPTVKEANLVPIILGRPFLATSNAIINCRNG FT LMQLTFGNMTLDLNIFYMSKKQITPEEEEGPEELCIIDTLVEEHCNQHMQD FT KLXESLVDIEEGFSESPIGLATLQSWXKIEGILPLFNEEXEAAVEKEIPKL FT NLNSAFTCGAEIXIX" FT CDS 4832..5854 FT /product="GYVIT1_I_3p" FT /translation="MEHLLAPRDFFYPRVVTDFYQTMTTKEVRNPTLIHFI FT IDGRHGILGARHIAEALQIPFEPTQFDNFKAWTNPTELEMVRTLTRGAANR FT SHLLRGELPPVMFLIDAFLRHNIYPLQHWTQRRGVLLEALYKMSEGFFFGP FT HHLIMAALLYFEEKVHKKKLQRADCIPLLFPRLLCQVLEHLGYPSEPQQER FT KRICREPFTLDKWNNMTAYKIDQPGQPQPAARRASPRHPPXGITLATPAIP FT RASPXAPAPSQPSTSAEPRMAIPISEYRELCRALETLTASQSNLAQELAAI FT KACQEQMLASQAQQAAILRQLQVHFDLPQAVEPSTEDSTRATLSAFRVS" XX SQ Sequence 7441 BP; 2232 A; 1442 C; 1578 G; 2080 T; 109 other; aatggcgccg ttgccgggga atgagtgtca agttcattgt gataccattt ttgagcactt 60 gtgattttca tcacaagttg gtaaagtttc tttcacttta ctaattttca ttctctcttt 120 gtttatttac aatctaagtt tatcttttta aaatttagtc tagtttaatt ttgytgttgt 180 agccctgttt ttcttgttgt cctctgtttt tgttgtcctc trtttttcat tatttaagtt 240 gyagctgaat actagttgtg tatgcccaag tggatacgag acagtggagg aaggcttgtt 300 aagtgtgata cacctcagaa aggagaattt gaagtaatct tgaatatcat ggaggctgca 360 cctgaagatc agcatagtca ccaaggtcgt caagacaatc tcaatgaatt cagatcaatg 420 agggaccgta tgcatccacc tcgtatgagt gcaccatcat gtatagtgcc ccctacagag 480 cagctagtga tcagaccata tcttgttcca cttctaccaa ctttccatgg gatggaaagt 540 gagaatccgt atgcacacat caaggaattt gaagatgttt gtaatacatt ccaagaggga 600 ggagcttcaa ttgacttgat gaggcttaag ttatttcctt ttactttaaa ggataaggcc 660 aaaatttggc ttaattcttt aaggcctagg agtatccgct cttggactga tttacaagct 720 gagttcctca agaaattttt tcctactcat agaacaaatg gcttgaaaag gcaaatttca 780 aacttctcag ctaaagagaa tgagaaattc tatgagtgtt gggaaagata catggaagct 840 ataaatgctt gtcctcacca tggctttgat acttggctac tggtgagtta tttttatgat 900 ggtatgtcct cctcaatgaa gcaactcctc gagacaatgt gtggaggaga tttcatgagc 960 aaaaatccag aggaagctat ggatttcttg agctatgtag ctgatgtttc aaggggatgg 1020 gatgaaccaa ctaaaggaga agtgggaaag atgaagtctc agttgaatgc ttataatgca 1080 aaagctggga tgtataattt gaaagaagat gatgacatga aagcaaagtt ggcagctatg 1140 acaagaagat tggaggagct ggagctgaaa agaatgcatg aagtgcaagc tgttgctgaa 1200 gcaccagtgc aagtgaagct gtgtcccaat tgtcaatcat ttgaacattt ggtggaggag 1260 tgccctgcaa tttcagctga aagggaaatg tatagagatc aagcaaatgt tgttggacaa 1320 ttcaggccca ataacaatgc tctttatgga aatacctaca attcaagttg gaggaatcat 1380 ccaaatttct catggaaggc cagagcaact caataccaac agccggatcc accatctcag 1440 caatcttcaa gtattgaaca aataatagct aatctcagca aggtagtggg agattttgtg 1500 ggaaagcaag aagccaccaa tgctcgagtg gatcaaagaa tggacagagt ggatcaaaga 1560 atggacagaa tggagagtat gttgaacaaa agaatggatg gaatgcaaaa tgatatgaat 1620 caaaaatttg ataacatcca atattcaatc tccaggctta caaatttgaa tacactgcaa 1680 gaaaagggaa gatttccttc tcaacctaac caaaatccca aaggtgtcca tgaagtggaa 1740 agccttgagg gagaatcatc acaggtgaaa gatgtsaarg cyttgatcac tctaaggagt 1800 ggtaagaaaa ttgagcagcc aacacctaag ccacatgttg agaaagaaga agagataaag 1860 aaakggaagg aaatggaaga taaagrsagt gagatcagtg aagaaaagaa ggaatctgat 1920 tcaacaatca aagcaattcc agagaaagag yttytgaagg aagaaatgct gaagaaatca 1980 acttctccac cttttcctca agcattacat gggaaaaagg ggggttagaa atgcagctga 2040 aatcctagaa gtattgaggc aagtgaaagt taatattcca ctgctggata tgatcaaaca 2100 agttccaacg tatgcaaaat tcctaaagga cttgtgtact atcaaaagag ggttgactgt 2160 aaacaagaaa gccttcttga ctgagcaagt aagtgcaatc ttacagtgta agtctccttt 2220 gaagtacaaa gaccctggaa gtcctaccat ttcagtcatg attggaggaa aggtagtgga 2280 gaaagccttg ctagacttgg gagcaagtgt gaatttgctt ccatactctg tctacaagca 2340 actrggactt ggagagttga agccaacagc aatcacttta tctttggcag atagatcagt 2400 gaaaattcca agaggagtaa ttgaggatgt attggttcaa gtagataatt tctactatcc 2460 tgtagatttt gttgttcttg atactratcc aactgtaaag gaagctaatt tagttcctat 2520 catccttgga aggccatttc ttgcwacttc aaatgcaatc atyaaytgta gaaatgggct 2580 tatgcaactc acttttggta ayatgacmct ggatctcaat attttctata tgtctaaaaa 2640 gcaaatcact cctgargaag aagaaggwcc agaagagyta tgtatwattg atactttggt 2700 ggaggagcac tgcaatcagc atatgcaaga caagttgart gaaagtcttg tggatattga 2760 ggaaggtttt tctgaatctc ctattgggct tgctactcta caaagttgga raaagataga 2820 aggaattcta cctytgttca atgaagaaga kgaggcagct gttgaaaaag aaattccaaa 2880 actcaatctg aattctgcct ttacctgtgg agctgaaata yacatayctt gaagaaaata 2940 atcaatgtcc tgtcgtaatm tcttcatctc aaacccaaag tctcaagtga gaggatgcaa 3000 gcttcaaatg ggatccgggc aaactgaatc aggagcaaat tttttgatgg acttagtctt 3060 tttaaagact agctagtcca tatcttttta ttttgttaat ttcttgtttt aattttgata 3120 tcaatgctta tatcaattcc aaagttgcaa aacagaggat gaagaagtgg catgatcaac 3180 tcatctccaa cwaggaattt caggaagggc aaaaagttct gatgtatgac acaagactcc 3240 atatctttcc tgggaagctc aagtcaaggt ggattggtcc atttgttatt caccgagtat 3300 attccaatgg agtggtggac ttattgaatt ccaatggcaa ggacagcttt agagtcaatg 3360 gatatcgtct taagccgttc atggagtcat tcaaatcaga aaaggaggca atyaacctcc 3420 ttgaacctca aaaagcytaa gkgaaawggg tttgctgggc gtggtcttta ccacagtcca 3480 aaatttttgt aaattttgta aattttcaag ttgtttccat acttttgatc ttagtttttg 3540 atyttaaatc atgtttttag gtgtgtttta atcgttttat atgatcccag gtggaagaaa 3600 tttcaagggg attgaaaaga aaaaaaatcg ggycgaaatt ggagcygaaa cagagcaaaa 3660 acaggggaaa aacagagctc tgcgaaattt cgcagggtra agraaacttc tgcgaaatkk 3720 gmwttttgyt gccaamccry tccgcagcac trtagaagcc tctgcgagtg trtttcgcaa 3780 ttgcgaaagt ggwtttggca cacgagtgcc acttcgcagm acagtrrcat caatttcgca 3840 gctgcgaaac kcrttgcgaa rtgrwaaagc stgatttcgc accaaaagtc cywttccgca 3900 grgyatttcg caattgcgaa agtggwtttg gcacacgagt gccacttcgc agcacagtga 3960 catcaatttc gcagctgcga aactcactgc gaagttgctg cgaaaatggc aagttgctgc 4020 gaaattggcg ttttgttgcg gaacttaaac tgacccctgg gcttccgttt ttcctattta 4080 taccggtcaa aaatgctgcg aaaagggttt caaaaatcag agagccattc tcgcagcccc 4140 ttcatcttct tcgccaagcc acgccgtccg wwyctccggt cgtcttctyc gcttagcaac 4200 gccggccaaa gatcgatakc ycmaaaatgg cacgaacgcg aggrgcaaar tcttcatcyc 4260 cttcgaaccg caaaaggagt ctgcgaaagg agccaagtyc aggctctgtt ccagaacctg 4320 ctccamagcc ttcgccgtcg agaccacaac cttctccagt gaagccggcg ccaccaaagc 4380 cgccggcaag gcgatattta acmagrtcag gyggtcagcc attgaagaag aarcccaggg 4440 ttgagagctc tgaaccaatt gatttgactg agcaatcccc tgagmaatcc ccaaatcctt 4500 caccggttca aactccagta tttcgccgta tctgacaccg gttccctcgc caattccctc 4560 acctgaagca actccaatty catcgccggt accatctccg gcaccccaag aaaaagctca 4620 ggagcctcca gcgccaattc cagagcccca aattgcagct gaagcacctc tggaagaagt 4680 gatccgaagg ccattgctcc cccagccccc aatcgaagga aacttggatt gtcgaacacg 4740 ggcattccat tctgaattga gcttcgaytt agcagcattc agagtgaggc cagagcttgc 4800 ccaatccttc cagctgctga ggagatatca tatggagcat ctgctagctc caagggattt 4860 tttctatccc cgggtagtca cggacttcta ccagaccatg acaaccaaag aagtaagaaa 4920 tccaactctg atccatttca taattgatgg aaggcatggt attttgggag caagacacat 4980 tgctgaagct ctgcaaattc cttttgagcc aacccaattc gacaatttta aagcttggac 5040 aaatccaact gagttagaga tggttcgcac actaaccagr ggagctgcaa atcggtcaca 5100 cctgttgagg ggggagctac ctccagtgat gtttttgatt gatgcctttt tgaggcataa 5160 tatctatccc ctgcagcatt ggacccaaag aaggggagtt ctcttggaag ctctatacaa 5220 gatgtctgaa ggattcttct ttgggcctca tcatctgatc atggcagccc ttctatactt 5280 tgaggaaaag gttcacaaga agaagcttca aagagcagat tgcattccac tcctcttccc 5340 amggctgcta tgccaagttt tggagcatct cggatacccc tctgagcctc agcaggaaag 5400 aaagagaata tgccgtgagc catttaccct tgataaatgg aataatatga cggcctacaa 5460 aattgatcag cctgggcagc ctcagccagc agcaaggaga gcctccccaa gacatccacc 5520 traaggtatt acacttgcta ctcctgccat ccctcgagct tcaccarctg cacctgctcc 5580 atcacagcca tccacatcag ctgagccgag gatggccatc cctatatccg aatatcgaga 5640 gctgtgccgt gcattggaga ctcttacagc ttcccagagc aatcttgctc aggagttggc 5700 agccatcaaa gcatgccagg agcagatgtt agcctctcag gctcaacaag ctgccatcct 5760 aaggcagctt caagtccatt tcgatctgcc acaagctgta gagccytcca ctgaagactc 5820 caccagagcc acactctcag ccttcagagt ctcawgctcc agagcccgaa gccycagctg 5880 atccacctac tgrrgaggca gatccttctg cctagcacta tcaccccact tatcagacat 5940 tatatatata tttgcttgtt tatgttttta tgcatgtttg ttttgtttta gttgaaatga 6000 aatcccagta ttttggtact atatatggga ttccttgtgt tacttgtctt tagcattgta 6060 atcaaatgaa ctcaaagtaa tacaagttga atatttcttg ttaaaartta gcattaagtt 6120 ctccttattt ccttttctca catattctat tctttttgaa acatrtggtt ttccccaatc 6180 aatattcgaa tttgatakca gcatggaggt accacttcct ccyttttatt acagtcactc 6240 aaatcacatt gaggacaatg ctcagttcgg ttggggggta tgaggaagga agtattctaa 6300 acctttttgg tattgcaatt atattggtta attagttgta gtttttactt tttactctag 6360 tgttactcta ttctccatga attttgagga aaaattttca aattaaacca agagaaattg 6420 aamtgttgct ttttcacttg acttagagta tggattatgc ttactaaagt rgttcaattg 6480 ttgaaacttc tactgwaatt gaattgagtt cttcyacttt aagctatcca cacactgtgc 6540 acattagttt ccgattataa satgaaaagc tatttccctc ttgacttagt atawttttgr 6600 gacttggtat atttgacctc atttgataaa aattgaaaca ccctgcaaaa ggccaatgag 6660 cctttgaaat aaagaaagtt gtttgcttgc cttgaaaccc gagcaaggtc tgaggggtat 6720 atggtgaaar yctttaaagc ctggtgccct aarccttaat tggttgggag wcaccgacct 6780 caatgctcgt tacaagggtg aataggtaga gttagcatat ggtagatgct tgggtattag 6840 aaaattcatt cttaaaagtc cggggaaaaa tccgaggagt tagtggttga aagatcctta 6900 aaacttggtg ccctaaacct taattggttg ggagtcatcg atggaccccc attacatgga 6960 caagtcagaa agagtacccc ataaagctac cttaaaaaaa aaaataaaaa aaaaaaaaaa 7020 aaaaaaaaga tgaaagtgtg ttcttttctt attgattttg gtcaggttgc taaagtgttg 7080 aaaagagtta ggttgggggg tgagattagt agcatattat tctcggaacc taaggaacca 7140 atacacatag atttttgtgg aagattgaag tttagttctt agaaagtaga aatgatttta 7200 aaacttcagt ttgcataatg cactcccttg attgacagtg tttagcataa gtgttatgac 7260 tcttgttgag atttgggttt gtatttcttt aatgattcat gtgagaaata gatcatcatg 7320 ccacttaaga attattttcc ttttagcatg atgttgtaaa ttktagatta gtttgctatt 7380 tatttttwat tttctctcct atattgctaa gggatctagc aatgatgtcg gttgggggga 7440 g 7441 // 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. 15.1, Last updated, Version 1) XX DE Non-autonomous EnSpm elements, consensus. XX KW EnSpm; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; KW 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 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 Helitron-N1_Mad repbase; DNA; EDCOT; 713 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous Helitron elements, consensus. XX KW Helitron; DNA transposon; Transposable Element; 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 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-44_Mad-I repbase; DNA; EDCOT; 5564 BP. XX AC . XX DT 22-OCT-2010 (Rel. 15.1, Created) DT 22-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 hAT-N3_Mad repbase; DNA; EDCOT; 660 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 HAT-N6_Mad repbase; DNA; EDCOT; 1215 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, 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-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 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 L1-7_Mad repbase; DNA; EDCOT; 5985 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 HARB-1N1_Mad repbase; DNA; EDCOT; 833 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 Ogre-PT3_I repbase; DNA; EDCOT; 11092 BP. XX AC AC149300; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 03-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_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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; 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 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 HAT-7N1_Mad repbase; DNA; EDCOT; 1035 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, 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-7_Mad; HAT-7N1_Mad; 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 1-1035 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 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 HARB-2_Mad repbase; DNA; EDCOT; 4243 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 TOTO1_LP_I repbase; DNA; EDCOT; 3529 BP. XX AC AF220602; XX DT 08-NOV-2002 (Rel. 4.3, Created) DT 08-NOV-2002 (Rel. 4.3, Last updated, Version 1) XX DE Lycopersicon pimpinellifolium retrotransposon TOTO1_LP_I, DE internal region. XX KW LTR retrotransposon; internal region; 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; 1169 A; 868 C; 513 G; 979 T; 0 other; aatctccccc ttggcttgaa tttctaacaa aataaatttg tccaccttct tcatttaatc 60 ttcaacaact tgcttctcct ctccataatc tcctttgcaa aatctatgtc tcaacacaga 120 gaacctctct gaaacaattt ctcaaacaaa atcttcaata ctgtcaaaaa ggttgcggct 180 agaactgcat ccgtcaagat gaacacctct ttctaacctg gttcaatcat cgtttatcga 240 accataaaac ctgacttcat cattgaatct ggctctgata ccactttgtt gggaaagaca 300 aggcactaac aaagaacgcc tgacaggata acagcggaag aatacccaag tctatacttt 360 cccttctcga tttgaaccaa gagaagacaa acaaccacaa gcaatataat agtaaggcag 420 caattaattc aatcaaacaa atataacaag agaataataa accaatcaca caagacacca 480 agatttacgt ggaaaaccct tcgatgtgaa gagtaaaaaa ccacgggacc aaaagctcca 540 ctataatcac caagtgtttc aatattgttc tccaaaattg gccacaaaca agtgccaaac 600 aacgagcaac aacaaaataa gattgcacca aatctagaga attaaaggag caaaatcacc 660 aatttcgcag ctattgttta cgacagcaaa actgaagctg caggccacca aatccaactc 720 tgttagttcc taatcaaata ttgagatgaa gataatatgc tgtccaaaaa tcagctcaat 780 cagacaagaa atgaagcgcg aatcgcaatt tgaagttggc tgttagggct gaattttgac 840 tgcgaaaatt gctctctctc tctttttttg gttgttgaaa aactctctgt gtatttgaaa 900 ataagaccta aataggctta tatttgcctc ataagaatgg gcctatgggc aaaaaatggg 960 ttggtccaaa ttgggctttt atttatccac ataagaaggg aaaaagaccc ataacccaac 1020 aattctcccc ctcacgacta tgtggaggag accgccatcc cggcgaccat gcaacaatct 1080 tcaaacttcc ctcttggcaa agctttagtc atcatatcag aaccattatc atttgtatga 1140 atctttccaa gctcaagcaa cttagaatcc aacacatctc gaatccaatg gtatctcaca 1200 tcaatgtgtt tagactgacc atggaacgta gaattcttgc caagatgtat agcactttga 1260 ctgtcacaat aaagcacata cctctcttga gcacaaccaa gttcccccaa gaatctcttc 1320 atccaaagca attctttaca agcttcaacg acagcaataa gctcagcttc tgtagtagat 1380 agagcaacac atttttgcaa cctagattgc caagacacag ctccccctgc aaaagtaacc 1440 aagtaccctg aagtagactt gcgagtatca acatcaccag ccatgtctga atcagtataa 1500 ccacaaagaa taggcttccc tgtaccaaaa cacaaactca gactagaagt gccacagaga 1560 tatctcataa cccacttcac agcattccaa tgttctcttc ccggattaga aagaaaacgg 1620 ctaacaactc caacagcgtg agcaatatcc ggtcttgtac aaaccatcgc atacatcaaa 1680 ctaccaacag ctgaagcata aggaactttc ttcatatctt ccttctcatc atcactagaa 1740 ggacactgtt tcgtgctcaa tttgaagtgc atagctaaag gtgtactgac aaccttagct 1800 ttgtccatgc tgaatctgcg aagtactttc tgaatgtact tctcttgtga taataccaat 1860 ttcttggcct ttctatcacg gacaatctgc atgccaagaa tctgccttgc tggtcctaag 1920 tctttcatag caaaagactt actcaactct tgcttcaact tccgaatcct gcaagtatta 1980 tgaccaacaa caagcatgtc atcaacataa agcaacacaa taataaagtc accatcagag 2040 aatttttgca caaaaacaca atggtctgaa gaagtctttt tgaagccctg ctgactcata 2100 aaagaaccaa acttcctgta ccactgcctg ggagcttgtt tcaaaccata caagctcttc 2160 ttcaatttgc aaacataatt ctctttaccc ttgacttcaa aaccttccgg ttgctccata 2220 taaatttctt catcgaagtc accatggagg aaagcagttt aacatccatt tgctcaacct 2280 ctaaatctag acttgcagcc aagcctagaa ccacacgaat ggatgacatc ttcataactg 2340 gagataatat ctcatcaaaa tcaactcccc ttttctgatt aaatcccttg acaactaatc 2400 tagctttgta ccgtggaact ggattaccat cttcatgttt cacccgaaaa acccacctgt 2460 ttttcaaagc ttttctgtct ttaggtaact taaccaaatc aaaggtatga ttatcatgca 2520 aggatttaat ctcatcttcc atagcatcaa accacctttc tttttcttca ctttccatgg 2580 cctcatcaag actctcaggt tctcccccat cagtcaagag tacatactca ttgggagaat 2640 aacgagatga aggaattctc tctctactag atcgtctgag agaactctct ggagcatcta 2700 taattggttg ttggacaacc acatcatctt gcactggagc atcaacaaca tcatgccggt 2760 cattctgaac atgatcacca tcttcattat caacttgatt ttcatcatta tgaagatttt 2820 cttccggtgc aatagtcaaa ggaactggat caacatcaac taagctctca ctactctgaa 2880 aatcagcctt gtcagctttg tcaaaatctt caattgtttg gtcttcaaaa aacacaacat 2940 cacggcttct aacaagtttc ttctcaacag gatcatagaa acgatagcca aattcatctt 3000 gaccataacc aatgaagata cactgcctag ttttaacatc caactttgac ctttcatcct 3060 taggaacatg tacaaaggct ttacacccat ttcggacagc tggtcaagaa caccctgaaa 3120 atcattaata tgatcacaaa taggagtgcc ctctttatac atgatattca ttaattgttt 3180 caataggaac aacttgttgt tgccactctt cgaaacataa agtgtctcga gcttgtccca 3240 caaacttttg gcatgtgtct cattcacaat atgatttcta acattacctt caacccattg 3300 tctaatatag ccacaaacct gcagatgctc aaattcccat tcttcatcat tcaaagactg 3360 agacttatta gaagcaaaca caggtaaatg catcttcttg acaaatagaa gatctttcat 3420 cttgcctttc caaatatgat agttactacc atttaaacac accattttgc tcatatttgc 3480 ctccatcatt caaaacgaca atcaacaata accaatgctc tgataccac 3529 // 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 L1-1_PTr repbase; DNA; EDCOT; 2389 BP. XX AC . XX DT 04-DEC-2009 (Rel. 15.02, Created) DT 04-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 L1-1_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 1-2389 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 266..2200 FT /product="L1-1_PTr_1p" FT /translation="MKGYHKSTGPARCAMKVDLMKAYDSVRWDFVDAMLIK FT MGFPRTVIDWIMVCVTSCQFSINVNGELAGYFQGGRGLRQGDPLSPYLFVL FT CMEILSGLFCKMSANQEFKFHWRCKKDKISHLCFADDLMIFSNGDVNSIRM FT IRTVLTKFQDLSGLYPNPNKSDIFLSGVLNAEREQIIHILGFREGELPMKY FT LGVPLLSSRLKAIYCKGLVDRITSKVRHWTCRTLSYAGRVQLINSVLFSIQ FT VYWASLFLLPGQVIKNVEQIMKSFLWSGSDMRTTGAKVAWDQVCLPKKEGG FT LGIKRITEWNKIALLKHIWNLCNDSDGSIWSTWIRSNLLRGRNFWTIKTPQ FT NCSWAWGKILKLRSLAWPKMKYIIGDGMTTSLWFDNWHPHSPLADSYGERF FT IYDSGMAKNAKVNVLIQNSEWKTPTTQAIGWHPIIEAIPSNSNPKMGQKDE FT IVWLDSPNHRFSVKVAWEQLRRHRQMVEWHDIVWFKNAVPRHSFLLWMAVQ FT QKLTTQDKLHRFGIHGPNRCSLCLRNNEDHNHLFFECSYTKAIWWDVCDRC FT DIPRMTKGWDEWIRWATVSWHGKSFVNFSRKLSFAATVYHVWQERNARIFA FT GMSRTPNLVLNQIECIIRDKLDLMRNVVPTNENKRIQRAWRVNTIDS" XX SQ Sequence 2389 BP; 677 A; 448 C; 545 G; 719 T; 0 other; ggggaagatg taacaacgct gttatccttc tttcagactc gtagaatgct tagaaatgtg 60 caatccattc ccttattcta agttgctaat cctacaggtt gacagatttt cgtcctatat 120 cttgctgcaa tacagtgtac aaatgcatcg ctaagattct agctgggaga atcaaagttg 180 ttttgccatc cttagtggtc catatcagac tgcttttatc tcaggacgga gaatcagtga 240 taacattctt ttgtctcagg aactaatgaa aggctatcat aaatctacgg gacctgctcg 300 ttgtgctatg aaagttgatc tgatgaaggc ttatgactcg gtgcggtggg atttcgttga 360 cgctatgtta ataaaaatgg gattccctag aacagtcatt gattggatca tggtttgtgt 420 tacatcatgt caattctcta tcaacgtcaa tggtgagctt gcaggttact ttcaaggggg 480 aagagggctg agacaagggg atccattgtc cccatatttg tttgtcctat gtatggaaat 540 cctttcgggg ctattctgca agatgagtgc caaccaagaa ttcaagttcc actggagatg 600 caagaaggac aaaatttctc atctttgttt tgctgatgac ttgatgattt ttagcaacgg 660 ggatgtaaac tcaattcgta tgatcagaac tgtgctcaca aagtttcaag atctatcagg 720 tctgtatcca aatccaaaca aaagtgacat cttcttgagc ggtgtgttaa atgctgagag 780 ggaacaaatt attcatattc ttgggtttag agagggggag ctccctatga aatatttggg 840 agtacctctt ctctcgtcca gactaaaggc tatttattgt aagggcctcg tggatcgaat 900 cacctctaaa gttcgacatt ggacttgtag aacactctcg tatgcaggac gggtacaact 960 gattaattca gtcttatttt ccatacaggt ctattgggca tctctctttc tcttacctgg 1020 gcaagtaatt aaaaatgtgg agcaaattat gaaatccttt ctttggtcag gttcagatat 1080 gagaactact ggggctaaag tggcttggga tcaggtatgt cttccaaaaa aggagggggg 1140 gctaggaata aaaaggataa cagaatggaa caagattgct ttgttgaaac acatttggaa 1200 cctgtgcaat gactcagatg gctcaatatg gtctacttgg atcagatcca atctgttgcg 1260 aggtaggaat ttctggacaa tcaagacgcc acagaattgc tcttgggctt ggggaaagat 1320 tctaaagctc agatccttag catggccgaa gatgaagtac atcataggag atggaatgac 1380 aacctctcta tggtttgata attggcatcc tcacagccca ctcgcggatt cttacgggga 1440 aagattcatc tatgattcag gtatggccaa gaacgcgaag gtgaatgtgc taattcagaa 1500 ctcagaatgg aaaactccta ccacccaagc tattggctgg caccccatta tagaagctat 1560 tccttccaat tctaatccta agatggggca aaaggatgag atagtttggt tggattcgcc 1620 aaatcacaga ttctcggtca aagtagcttg ggaacaacta agacgtcatc gtcagatggt 1680 tgaatggcat gacattgtgt ggttcaagaa tgctgttcca agacattcat ttcttctatg 1740 gatggctgtc caacagaaac tcacaactca agataaactt catcggtttg gtatacatgg 1800 tcccaataga tgctcactct gtctccgcaa caatgaggat cacaaccact tgttctttga 1860 atgctcctat actaaagcga tctggtggga tgtttgtgac agatgcgaca ttccaagaat 1920 gacaaaaggc tgggatgaat ggattcgatg ggccactgtc tcttggcatg gcaagagttt 1980 cgtcaatttt tctcgtaaac tgagttttgc agctacagtg tatcatgtat ggcaagaacg 2040 gaatgcaagg atctttgctg gaatgtctag aactccgaat ttggtcctta atcaaatcga 2100 atgtatcatt cgtgataagc ttgatttgat gaggaatgtc gtaccaacaa atgaaaacaa 2160 aaggatccaa cgagcttgga gggtgaatac catagattct taatctgtta gttagctggt 2220 tgtattggtt tccctaacga atctagtgag gtttcagttt tacggtcggt ggctagcctg 2280 tagccatctg ttgttttatg tttctgttat cattgtaaat ctggggtatg ccccttataa 2340 tgtttgtatc ttcttctttt aatacatacg tcaacttacc aaaaaaaaa 2389 // 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-91_Mad-LTR repbase; DNA; EDCOT; 428 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 TGM5_GM repbase; DNA; EDCOT; 1002 BP. XX AC X13528; XX DT 11-NOV-1996 (Rel. 1.1, Created) DT 25-MAR-1997 (Rel. 2.02, Last updated, Version 2) XX DE Soybean Tgm5 transposable element. XX KW transposon; unidentified reading frame; Tgm transposon; KW zinc finger protein; GMTGM5; 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 RASH3_MT repbase; DNA; EDCOT; 1320 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 DNA transposon; Transposable Element; Nonautonomous; repeat; KW non-autonomous; Interspersed; RASH3_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 1-1320 RA Shankar R. and Jurka J.; RT "RASH3_MT: Putative non-autonomous DNA transposon from Barrel RT Medic."; RL Repbase Reports 6(11), 599-599 (2006). XX DR [1] (Consensus) XX CC Present in moderate copy numbers, the sequence is very well CC conserved. XX SQ Sequence 1320 BP; 416 A; 202 C; 223 G; 478 T; 1 other; gagatcaaaa ttgtcggtga aattttattg gagactaaaa ccaaaagttt gaatatttat 60 agggatccaa aacatagtta acctccatgt cattttatgt cattttatac ttatcagcca 120 cttcaacatc taattttacc aaacacttca attttaataa accatctttt cagctataag 180 ctatcagtta taagacatca actataagct agtttttcag atttcaacta gcttatagct 240 tatttttacc aaacacaccc cacatacgtt cataaatttt gttccattcc aaaacctaga 300 acacacataa cgtgcaattt cttcttcatt cttcttccca tcttgattgt tcaattctct 360 cgttccagaa ttgccgtcgt ttccaattat cgtgagaatc gttgtcgtcc ttttgattcc 420 agacattgtg agaatcggtg ttgtttccat aatcacatca ggtatcgtga cttgtcgact 480 actatcgtga cttgattgca accgtttcac acttataatg cgacagtggt gactttcaac 540 tttggcatga attccaatga tgcttccatt tttatttggg ttttgagttt gattgagttg 600 tttgagatta tataaaattg tattttatca cacatatttt gcgtttgatt aagataaatg 660 gatcttcaat gcgttgatta ttaattttat ttttggtaca atattgatta ttaaatttac 720 ttttggaatt tgttttattc aaatcattat attgtgttgt tatgttgttt ttgttcctgg 780 tgaattttgt gttgccgaaa tgaacatttg ttgagattgt gaacacggtg tgaggtcggt 840 taaagctatg gaagagaaga caaagtgaaa taaataaata ataaataatg ctaatacaaa 900 catgaatttc ataaggtgag cgttaattcg tggatatagc ttttggaaac aatggcgatc 960 tcacgatgtc tggaatcaaa cggacggcaa cgattctcac gataattgga aacggcggca 1020 attctggaac gagagaattg aacaatcaag atgrgaagaa aaatgaagag gaatgaagaa 1080 gaaattgcac gttatgtgtg ttctaggttt tggaatggaa caaaatttat gaacgtatat 1140 gatgggttga atttgatgtg aaattttaat tgttacaagc cctatagtgt aaattaatta 1200 agattgtata cctaaatata attaaataaa aattaaaggg ttaaatatgt ttttggtccc 1260 tataaatata ccaacttttc gttttagtcc ctctaaaatt ctccttcaac ttttagtccc 1320 // 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 L1-12_Mad repbase; DNA; EDCOT; 6081 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 TN10MRNA_NA repbase; DNA; EDCOT; 1332 BP. XX AC AF542545; AF542545.1; GI:29468501; VERSION; XX DT 08-JUL-2003 (Rel. 8.06, Created) DT 08-JUL-2003 (Rel. 8.06, Last updated, Version 1) XX DE Nicotiana attenuata transposon TN10 transposase mRNA, complete DE cds. XX KW TN10; TN10MRNA_NA. XX OS Nicotiana attenuata 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 1-1332 RA Hui D. and Li H.; RT "Microarray Analysis of Insect-Induced Changes in Transcript RT Accumulation."; RL Unpublished. XX RN [2] RP 1-1332 RA Hui D. and Li H.; RT "Direct Submission to GenBank."; RL Direct Submission to Genbank (04-SEP-2002)Department of RL Bioorganics, Max-Planck-Institute for Chemical Ecology, RL Winzerlaer Str. 10, Jena 07745, Germany. XX DR Genbank; AF542545; Positions 1 1332. XX SQ Sequence 1332 BP; 404 A; 316 C; 270 G; 342 T; 0 other; gtactgatga atcccctaat gattttggta aaaatcatta agttaaggtg gatacacatc 60 ttgtcatatg atcaaatggt ttcgcgaaaa atcaataatc agacaacaag atgtgcgaac 120 tcgatatttt acacgactct ctttaccaat tctgccccga attacactta aaacgactca 180 acagcttaac gttggcttgc cacgcattac ttgactgtaa aactctcact cttaccgaac 240 ttggccgtaa cctgccaacc aaagcgagaa caaaacataa catcaaacga atcgaccgat 300 tgttaggtaa tcgtcacctc cacaaagagc gactcgctgt ataccgttgg catgctagct 360 ttatctgttc gggcaatacg atgcccattg tacttgttga ctggtctgat attcgtgagc 420 aaaaacgact tatggtattg cgagcttcag tcgcactaca cggtcgttct gttactcttt 480 atgagaaagc gttcccgctt tcagagcaat gttcaaagaa agctcatgac caatttctag 540 ccgaccttgc gagcattcta ccgagtaaca ccacaccgct cattgtcagt gatgctggct 600 ttaaagtgcc atggtataaa tccgttgaga agctgggttg gtactggtta agtcgagtaa 660 gaggaaaagt acaatatgca gacctaggag cggaaaactg gaaacctatc agcaacttac 720 atgatatgtc atctagtcac tcaaagactt taggctataa gaggctgact aaaagcaatc 780 caatctcatg ccaaattcta ttgtataaat ctcgctctaa aggccgaaaa aatcagcgct 840 cgacacggac tcattgtcac cacccgtcac ctaaaatcta ctcagcgtcg gcaaaggagc 900 catgggttct agcaactaac ttacctgttg aaattcgaac acccaaacaa cttgttaata 960 tctattcgaa gcgaatgcag attgaagaaa ccttccgaga cttgaaaagt cctgcctacg 1020 gactaggcct acgccatagc cgaacgagca gctcagagcg ttttgatatc atgctgctaa 1080 tcgccctgat gcttcaacta acatgttggc ttgcgggcgt tcatgctcag aaacaaggtt 1140 gggacaagca cttccaggct aacacagtca gaaatcgaaa cgtactctca acagttcgct 1200 taggcatgga agttttgcgg cattctggct acacaataac aagggaagac ttactcgtgg 1260 ctgcaaccct actagctcaa aatttattca cacatggtta cgctttgggg aaattatgag 1320 gggatctctc ag 1332 // 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 DNA9-9_Mad repbase; DNA; EDCOT; 171 BP. XX AC . XX DT 15-OCT-2010 (Rel. 15.1, Created) DT 15-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 LTR-9_Mad repbase; DNA; EDCOT; 2371 BP. XX AC . XX DT 20-OCT-2010 (Rel. 15.1, Created) DT 20-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 LTR-1_Mad repbase; DNA; EDCOT; 3448 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 MuDR-5_Mad repbase; DNA; EDCOT; 3881 BP. XX AC . XX DT 15-OCT-2010 (Rel. 15.1, Created) DT 15-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; 8-bp TSD; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 EGLN2_SM repbase; DNA; EDCOT; 410 BP. XX AC AB016143; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Solanum melongena LINE retrotransposon EGLN2_SM, endonuclease DE region. XX KW L1; Non-LTR Retrotransposon; Transposable Element; endonuclease; KW LINE; long interspersed nuclear element; 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 DNA8-6_Mad repbase; DNA; EDCOT; 1941 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 L1-2_Mad repbase; DNA; EDCOT; 6555 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 TNA1_NA repbase; DNA; EDCOT; 1863 BP. XX AC Z35426; XX DT 04-MAR-1998 (Rel. 3.02, Created) DT 04-MAR-1998 (Rel. 3.02, Last updated, Version 1) XX DE Nicotiana alata retrotransposon Tna1-2 integrase motif. XX KW Non-LTR Retrotransposon; Transposable Element; retrotransposon; KW Tna1-2; integrase motif; NATPINTR; 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 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-74_Mad-LTR repbase; DNA; EDCOT; 216 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-7_Mad repbase; DNA; EDCOT; 5020 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 HAT-9_Mad repbase; DNA; EDCOT; 5108 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; 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 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 HARB-1_Mad repbase; DNA; EDCOT; 2818 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; 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 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-42_Mad-I repbase; DNA; EDCOT; 11574 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; 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 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(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" 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" 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 SINE-2_Mad repbase; DNA; EDCOT; 208 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative SINEs from the apple genome. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; KW Nonautonomous; 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 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-58_Mad-LTR repbase; DNA; EDCOT; 612 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-70_Mad-I repbase; DNA; EDCOT; 4862 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, 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-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 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 MtPH-A6-4-Ia repbase; DNA; EDCOT; 4699 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-A6-4-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 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 LTR-4_Mad repbase; DNA; EDCOT; 1905 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; 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 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 DNA9-1_Mad repbase; DNA; EDCOT; 181 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 HAT-3N2_Mad repbase; DNA; EDCOT; 710 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-94_Mad-I repbase; DNA; EDCOT; 4805 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 MuDR-4_Mad repbase; DNA; EDCOT; 4222 BP. XX AC . XX DT 07-OCT-2010 (Rel. 15.1, Created) DT 07-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; 8-bp TSD; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; 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 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 DNA9-4_Mad repbase; DNA; EDCOT; 1025 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DEM1_I repbase; DNA; EDCOT; 3790 BP. XX AC AJ291492; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Malus domestica retrotransposon DEM1_I, internal region. XX KW LTR Retrotransposon; Transposable Element; internal region; KW internal portion; 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 ENSPM_MT repbase; DNA; EDCOT; 8153 BP. XX AC . XX DT 31-JUL-2005 (Rel. 10.07, Created) DT 04-AUG-2005 (Rel. 10.07, Last updated, Version 1) XX DE M.truncatula ENSPM type DNA transposon - consensus. XX KW EnSpm; DNA transposon; Transposable Element; autonomous; KW 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 6277..3638 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 WMVDQKEMRSAHVHVLINCAEVKPYLE" XX SQ Sequence 8153 BP; 2590 A; 1681 C; 1315 G; 2458 T; 109 other; cactacaagg aacattgcct tttgccaggg gcaaaatccc tgtcaaaagg acaaaatccc 60 tggcaaacgg gacatttgtg agggaaaaaa cgaggggcag atggcctggc aaaagcgctc 120 atcgcaaaca ctttgccagg ggctacaccc ctggcagaaa aacraggggt tgaacccctg 180 gcaaatcgcg ccactttctc cctggctgaa cccctggcat ggtccgtcac ttttgtctgc 240 agactgcacc tctgaccctg actgactgac ggcttgacga cggctctgac cgaagtgaca 300 acagcaaaaa acgagggaca tgcgaggggt ttaacccctg gcaaatgtcc ttattttttt 360 taaaaaaata ttattttatg aaaacgaatt tttttaatta attaataaaa tatatttaaa 420 ttaatttaaa aatcgatttt ttttaattaa aaaatatata tttaaaaaaa ttaatttttt 480 ttaaaacaca attaaatgca tataaataaa gtttaatcac acaaacacta ataagtctaa 540 ttaaaatgca tgaaatagaa agtgtactta ataatattac aaaccgtgca ggaaaataaa 600 tattgtgcca ggaagtatgg aaaacctccc aaaatcatac aaaccataac ataatagtaa 660 agaaaacaca caacaagcat cataagcatc aatcatccat ctcgaggtcg tcatcatcat 720 cctcttcgcc ctcaccatac acttcatagg ggtcttccgc atcatcatca cacactagag 780 gagccctcac actctctcgg cttccactat gctgcccacc accttgctca ttcatattcc 840 agccttgctc ttgcctaaat gtgtccaact gagagtctag gaattctcgt tgcttcctaa 900 ccacctcatg gatcagctcc tgttgggttt gcatatgggc agcaagctgt tcttgagtca 960 acctagtgat cagatcccgg atttctggag tgagctcagg ttgccgagaa gaaccctccc 1020 cagcattaag ggtcaacttt agagtggtag caacaccctt gcggwagttt ccagctaagt 1080 ttcctgcacc gtacaatcgc cccttcttct tctcaccagc aactttcgtc catgcacgaa 1140 gtgtgagagc ttcatcaaca gagcatccac gggagagcgc ctctgatagc tgacgatcat 1200 actcctccta aaataaataa gaataaaata gttaaagata aataaacatt aacawaaaat 1260 tataaccact aattaataaa attaattaaa atacacttat gtaacaatta cctggcatat 1320 cttggagcga tcatcaacat actggcctga tcgatatgtg tgggtcttct tgtggagctc 1380 atttatgtat ggctccctac ctagcttctt tgcctaattg acaagaaaca caattattra 1440 gtagttagta aaacattaaa ctatatttaa ccacaaaata tttaaaaaca tacattctat 1500 aaaattaatt aacagagtta ttatttttaa ttaccagtcg acgggcatgc tctgctgtgc 1560 ttatgcagcc tcccgtgtgg atgcatcccc ctttctctga tgctctgttc ttctttgcct 1620 tctctgattt cgtcttaaac tctggactcc cccaatagtc caccaactgc ctcataagtg 1680 gctccccgat ccagtagggc ctctttccag cagtctcgtg acgaagtcgg acatgtcgca 1740 acatgtcgga gaggcgggca gaagctctaa tgtgaaagtt cctccttatc tgagcatagt 1800 acttggggtt ccaggcacac ttcatctgca tatttgttaa catattttag gaaattagta 1860 aattataaca tatgtgcaga taagttaaaa tatattatga tatgtattaa tgttacctca 1920 aaaagaccaa accatgcatc cttttcatca tctgggatat caccataagt cttccaaaat 1980 ccatgatacc ttccctggat gatgtctcta atggcactgg cggctggctt gcagggcatg 2040 aaactacaaa caatgaaaac tcatatagtt aaacattaca taaatttata acaatataca 2100 tattgaacaa aaatacataa agacttacga gttcccgcta ggcacaatga tgtaacgctc 2160 ttgttcatct tgcggataat ctgccatctc ctcatcatca tcatcagcac cctgttgggg 2220 ttgggattgg ggttggggtt ggggcggggg ttgttgatgt tggggtggtg ggggttgttg 2280 atgttgaggg atcataaagc cggtctgccc atgaggtaat gatggtggag gaggcaactg 2340 gtaacctgta gggaggataa aaccaacagg tgcaacaaca ccagaccctc cagcgggtgc 2400 acaggcacta gcttgggatg acccagtcga tccytggcta gaagaagagg gtggtctggg 2460 aaagggagtc artgtggcaa gtgtggctgg atccgcaatg tgtgttgtga accgcctcct 2520 ggkgtccttg ctcttgcctt tctctttttg tttcggaggc attgtgaatc tgttaaataa 2580 caaaaaaagt tatattgtaa aggactcaaa tatatataca tcattaaaca agcgatatct 2640 tcattcaaac acaaatgtat tcaagattac aataaattca aattcaatca ttacaagggt 2700 ggataacaat atacttcaag tgttgttatc agatgcatag ttatattcat ctacatcacc 2760 atcatcaact tgattgtctt gstggtcccc ttcattatta tcatcaacaa cgtcttcatt 2820 ctcatcttca acttcattac gcatctccaa aatagaagga tcaacctgat ccccttcaac 2880 ctgagagtct tgccaacttg taacttgatc tacttcaatt atctcattta catgtgtcat 2940 atcatcggct tggtaagcaa cttcttcgtt tsgttcttca gtctcratgc ggcccctcgg 3000 ttttgttttg attgcaacag accaaccycg tttgcgtggt agagttgggg gataaggaac 3060 atagtacact tgcctaacat tatgtgccat gataaacggg tcatattctt tatatttttt 3120 gtcgactcga atgtcaacag tgttgcataa tttattaatt ttagtccatc taggcgaggg 3180 atcaaaccag tcacaataaa acaacaccac tttattgtca ttatatgaaa gctcataaat 3240 gtgtttgatc acgccataga aatcatcttc acctccatct gtaactcctt ttacataaac 3300 accactatta atagtctttt tgccttccgt ccaagagtgg gtatgaaatt tatatccatt 3360 cacgaagtag gtgtgaaatt cattggcaca ttgtaaagga ccctgagata attgccgtaa 3420 acggatgact tcatcagttg gctcggcatt atacactctt tgtttaaacc aagctggaaa 3480 atattcatgt atcgaaccaa ctgtcgatcc ttcaccaaac tccgcataaa aagcaataaa 3540 ttccctaaaa aacaataaat tcaatacgaa gttgttaacc gcgttaaaac ttattgttgt 3600 atgractagt aaaaatgggt aggaatagat ttacttactc aaggtatggt ttaacttccg 3660 cacaattaat caaaacatga acatgagcag accgcatctc tttctgatct accatccaat 3720 attgaagcac cttgcccgcg tgtcgaccat saagattgaa tacggataag gttgayggat 3780 cccgtamatc gttaacctga acttcatttc ttgtatttga tggagtaagt agacgatcaa 3840 cgaaataatg gccgataaag tatgtggttt ccttggcggt gtaaatagca acaattgatc 3900 cttccacttt ggccagattt ttaactgctc gttttgagtc acccatgaat ctttcaaaag 3960 ggtacatcca cctatattga acaggtccgc caagtatagc ttcatatgcc agatgcacag 4020 gaagatgttc catagagtca aagaaacctg gtggaaaaat ttgctccaac tgacagataa 4080 tgattggcat attcttctcc attttctcaa gttcatcaac tctcaaggtt gaagcgcaca 4140 aatttttaaa aaattgacta atctcaataa gtggatctag cacatgtttg ggcaatgaac 4200 taaatgcaat tgggataaag ttctccatga aaatgtgaga gtcatgactt ttcatcccat 4260 gcaaccttcc cgtgttgaca tcggcacacc tgcctatgtt agaagaatat ccatcgggca 4320 ttctcaaatc cttcaaccat tgacacacta atttcgcttc ttgggcagat aggttgtagt 4380 tggctttcgg tttcaacaay ttcccattcg gttgaggttt caactccaaa tcctttctyt 4440 tgcaatatat ttgtaagtct tttctagcct tctcattgtc ttttgttttg cctttgacat 4500 ccatcactgt gttaaatatg ttgtcaaaga cattcttctc aatgtgcatt acatcaagat 4560 tatgtctgag caagttatct ttccaatatg ggaggtccca aaatatactc cttttagtcc 4620 agtggtggtc tactccgtat cttggtattg ggacagctcg accataatca gtgacttttg 4680 gataatcaca aactcttgtc cacacttctt ctgatgtaat cttaggtgga ggaccaacaa 4740 aaactctctc atccttcttg aaaccattct taagtcttct aaacgggtga ttatgaggca 4800 agaacggacg atgacagtca aaccacgaac tcttccctcc actttccaaa gtaaatgcct 4860 ttgtattttc catacaatgt ggacatgcaa atctaccatg agtactccaa ccggacaaca 4920 tgccataagc gggaaaatca ttaattgtcc acatcaaagc tgctctcaac ttgaaatttt 4980 gttttctaga aatatcatat gtcaattctc caacccacaa cctcttcaaa tcatcaatta 5040 amggttgtag aaacacgtct atgcctgctt tagggttatc tggtcctggt acaatacaac 5100 tcaaaaacaa gtatggtttt gtcatgcaca tttcaggagg gagattatac ggggttacaa 5160 tgattggcca acaagaatat ggttttgccg aggattggac atatggctga aaaccgtcag 5220 agcataatcc aagtctcaca ttccgtggat ctgctgcaaa atcaggatgt actcgatcaa 5280 agtgtttcca cgcttcaccg tcagaaggat gtcgcatcac tccggraatt ccatttgaat 5340 gatgccacgt catttgacta gcagttttca tcgatgcaaa yagtctttgt aatcttggta 5400 ttatcggcaa gtaaaacatt gacttaaccg caactcgttt ctgcttgcta ataccgtacc 5460 tcgggctttg acaaaattta cattcctcca atgstccatc atttatccca aactcattgt 5520 cataraacaa catgcatcca tttctacaac aatcaatctt tttaactgat aatcccaact 5580 tcatcaccaa cctcttcgca gcatgataat tcattggcag attatctttg aacggagtma 5640 cggccttcaa catcttcgta atatcatcca taccatcatc aggattaaga tagttcgact 5700 tatgagataa aagccacaca cacatagata gcttagagtg cgaagaccct tcatacaaag 5760 gtgtattact ttcactcaac aatcggtaaa atctttgcgc cttctcattc gggggttgtt 5820 cctcttcatc atcttcaaca tcttcaccgt aagacaattc cacccctaaa gcrtccgcaa 5880 ccatatcatc catcatgttg aattgwtctg tgttgacatc ttcattgtat tccacatttg 5940 tttccacatt tgttccacca tggctagtag aagcttgtgc attgacccct rccccaaaat 6000 tctgaaacat ttcaccatta tatgtccaaa cccaataatt aggcataaaa ccaacttttt 6060 ttaggtgttt cttcacatct ccaggatcgg taattatatg tctgcaccta cattttagac 6120 acggacatct aattcctccc tcatctctac agatttcttg ctcccatgcc catgaaataa 6180 atccgtcaac tccttcgaca aattgcggtt ttagtccagt tcttcccgga aacgtcctat 6240 cgtacatcca acgacgataa tattcataat actccatctt ctacacgttc cgcaacttca 6300 ttgacgtatt ccacgtcaaa aataaattat tactcaacgg agataactaa cattatgcgr 6360 aaaaaaaatc ccgctcaaac aataaaatat aagtttacgc gcaaacaaat taaattttta 6420 tctcgcaaat taaacatata ataattaatt aktaaataat tgtaacatag ttttaatttt 6480 catcgataaa caactttctt gtactatact atttttgagt ccctcctttt taaacaatat 6540 ccattattat attatattgt tttattttat aaaaataata attataacat tttagacacg 6600 gaaatcaaac atattttaat ttattaaaaa aaattagatt ttttaacaaa gttttaattt 6660 wwawaaaaaa aactgatttt taatacacta ttttaataaa ttgttttcca agaaattttt 6720 agtatagtat tttttatgaa gcatttttat tttccwacgc tttgattagt tttaatttat 6780 taaaataata attataattt maatatarma acagattttt aaatatawaa acagatttta 6840 atttattaaa aaacagcatt atgtttaaaa atctgttttt ataatttaga aactagtttt 6900 aatatggcat taactaaact aaaatatatt tataaaaact agttattaaa atttaaaaat 6960 aaawaaattt ttaataacag atttagttta aaacaaacaa tttaactaca gcatgcatat 7020 atttttttta acattctact acaacatrca tatattwcat tttatcamaa aaaaaaaaaa 7080 aaaaacagca tgcawatmtt tcatttaatt aaaattaaaa caacatgcat atatttcatt 7140 tgatcacaaa aaataaaata tgcatatata tatataattc attttatcac aacaaaaaca 7200 tgcatttcat tttatcacaa taaaaaatgg atatatttta aaaattgcca acattgatgc 7260 ataataatat taacaaacaa aaaaaattat catgatataa tttttttttc ttcagatttt 7320 cggaaaaaaa aaataccaaa caatyagcat atwttayata caacacatca tcaacatgta 7380 tatcagytat aktgttatga gaaaaaaawa tcactaacat gttgaagctt tmcwayagaa 7440 atctgcaatg caatccaaaa acarcaagag ttgragcaaa acctaacacc aggaggcrga 7500 taaataacac agctgcaaat aacaaasaaa ataaataasa ttaataagtr ktaaaattta 7560 ayatcatgat aaaacatata asaaatraak wattttttta ccaaakaatw gaagwttgaa 7620 gaatgttttg tatgaaggta ttgwgtttta agagaaggar aargtttcat ttgcacatga 7680 tcaaaccggt gctaccctta tataggaaag ggaaaaaacc agggcctttg ccacggcacg 7740 tccctcggaa aaatcggtca aatcctactt aggtaggcgc araagtaggc gcagaacgks 7800 ttgatattwg csacggaway tagcaawatc cgaggggttc cgcccctggc aggcckgcag 7860 crctyarctt ttgscaggcc cttgtcaact cagctgggaa aacgcaggga wtcytttggt 7920 tttcgcaaay csargggstk ttccctggct ttwtccstcg gttwttkctg acaagsacag 7980 attyccacag mttttcaaat ttcaawctgg cgcctwawca waaccgaggg atttttgwca 8040 aaaagcgagg ggcaaatccc tgkcttttkt gccascggtt ktccctggca aatttgccag 8100 gggtttcaaa cccttgtcaa aatccctggc aaarggymat twttcttgta gtg 8153 // 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-8C_Mad repbase; DNA; EDCOT; 4866 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 L1-3_Mad repbase; DNA; EDCOT; 6384 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 RTIP1_I repbase; DNA; EDCOT; 10281 BP. XX AC AB000394; XX DT 08-NOV-2002 (Rel. 4.3, Created) DT 08-NOV-2002 (Rel. 4.3, Last updated, Version 1) XX DE Ipomoea purpurea retrotransposon RTIP1_I, internal region. XX KW LTR retrotransposon; internal region; RTIP1_I. 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 Helitron-1_Mad repbase; DNA; EDCOT; 7323 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Helitron family DNA transposons from the apple genome. XX KW Helitron; DNA transposon; Transposable Element; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 TNT1_LTR repbase; DNA; EDCOT; 610 BP. XX AC X13777; XX DT 12-SEP-2002 (Rel. 7.08, Created) DT 12-SEP-2002 (Rel. 7.08, Last updated, Version 1) XX DE Nicotiana tabacum retrotransposon TNT1_LTR, long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Long terminal repeat; KW retrotransposon; 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 "Characterisation 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA3-6_Mad repbase; DNA; EDCOT; 1057 BP. XX AC . XX DT 11-OCT-2010 (Rel. 15.1, Created) DT 11-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative non-autonomous Harbinger family DNA transposon from DE apple. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 SIRE1_INT repbase; DNA; EDCOT; 7258 BP. XX AC AY205610; XX DT 09-JUL-2004 (Rel. 9.06, Created) DT 09-JUL-2004 (Rel. 9.06, Last updated, Version 1) XX DE Glycine max cultivar Williams 82 SIRE1-8 retroelement: internal DE sequence. XX KW LTR Retrotransposon; Transposable Element; SIRE1; 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-89_Mad-I repbase; DNA; EDCOT; 4073 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 L1-6_Mad repbase; DNA; EDCOT; 4832 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HARB-N5_Mad repbase; DNA; EDCOT; 697 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-4_Mad repbase; DNA; EDCOT; 5449 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 SHALINE14_MT repbase; DNA; EDCOT; 4346 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 element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; retroposon; KW repeat; ORF; Interspersed; Poly-A; 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 A. 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 EGLN3_SM repbase; DNA; EDCOT; 410 BP. XX AC AB016144; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 08-NOV-2002 (Rel. 7.1, Last updated, Version 1) XX DE Solanum melongena LINE retrotransposon EGLN3_SM, endonuclease DE region. XX KW L1; Non-LTR Retrotransposon; Transposable Element; endonuclease; KW LINE; long interspersed nuclear element; 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 RAM9B_LTR repbase; DNA; EDCOT; 2753 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 Long terminal region of RAM9B retroposon from Medicago DE truncatula. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; LTR; KW Interspersed repeat; retroposon; 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 1-2753 RA Shankar R. and Jurka J.; RT "RAM9B: A LTR retroposon from Barrel Medic."; RL Repbase Reports 6(11), 595-595 (2006). XX DR [1] (Consensus) XX SQ Sequence 2753 BP; 768 A; 405 C; 641 G; 936 T; 3 other; tgtaacgccc actttcgttt aatcgtttat ttaatcgagt ttaggcgatt atattataat 60 tatataatat atgcatgatt ttggtatgtt ttgatgattt attttcgtga taagttatga 120 gttttggagg atttgataag gatatgagaa ttattttatt gttaaataaa ataaagattt 180 gaaaataata taaaatattt agttgagggc tgttttgata ttttagatag ttttggggga 240 gaaagtgaga taagataagt aattaagaag agatataaat aggagataga cctagtattt 300 tagaaactca ttgtacgtac gaaaactttt ggagaaaagg gagaaaaagc ttagagagga 360 gcaagagcat agagagggct gcgattttct tcataacaag gtaagggtga gactaataat 420 tcaataatgt taattgttgt aattctgatg attaattgac aagagttagg attgatttag 480 agaagttttg gaattaggtc aaaaccctaa aaattgatga tcaaacggta aaacttgttt 540 agattgatgt agaaaccgtc ctttaacctt agaatatgtt taggatgaat tctggaatca 600 aaattaggct tagaaccatg ttatttgatg gatttttgtg aaaaacggta gtctgcccgt 660 gcctatgttc atcgctcgcc acggcgagck atgatcctcg cctcgcgagt gatgaacatt 720 catcgctcgc cacgcgagcc ctttcccttc gcctcgcgag ttgtttggtg cagctcgcca 780 tggcgagcaa cccttcctcg ccatcgcgag cttaggcaga gtgcatgtca tattttgtgt 840 ttcgaccttt ttagttggac cttggatgcc tttgagtrcc tgaacatacc tagtattgat 900 taggaatgaa tgtaggatca gattgaaccc agaacaacct tagtttggga gttgagtggt 960 actcgccatg gcgagtaaga actctcgcct cgcgagcaca accagaatgt agttgcttga 1020 gtgtttgtgc gatctgtgtc gcacgtgttg atcaagagtg aacccctaat tggtaatgag 1080 acctaatgat gacgtttaat gcagtctgta aagctgttta agatatgttg atattaattg 1140 aacatgaatt aatgtattgt atattcatgc aagatatgaa agtttaatta tgatgcaatt 1200 gatgtgctat tgatataatg atatcatctt gttatgtgac ttgtttatgc tgcttccgtt 1260 atttaactaa gtgcattgca tatagtatga atgagttgaa gtttagctcc aaattattgg 1320 atgcatgtgt gataatgttg attacgatgt tttgttgata agagtccatg cattagcata 1380 tcattgagct tagtcctcac cacgaatatt aggagctttg tcctccgcac gttttatagg 1440 agctttgtcc tccgcacgat taaagtatat taatacttat gatgacgatt ggtaccacat 1500 gcatataagg agtctaagat gcattgtcac attgtcatga ttaagatgcc ttgttgataa 1560 tgattgaata tgtgattacg tgataagtgt ttattgatta tgttatgttg ttcatgatga 1620 attggatata tgattacgtg ataactgttt agcaattatg caaagttaat aatggaatga 1680 ttatgatgtt aatttatgat tcgcaattac attgattaat gttattttgt tatgaaatct 1740 caccccttct gcttgaaaat gttgcccttc gtatgggtaa cttgcaggtg atcgtgctta 1800 gtgtgcagtt tgctttcgtg agttggcctt gccttcactg tgtcgtctag gtcgctctga 1860 tacgtaacgg gatggggtta tatgctataa catgcttcat tctcttacgt gaactaatat 1920 gttattttta ttatgttatt gattaactct gatttgaaat attttggttg gggcctgcgt 1980 gccaaaacga ttttatgatt tatgattata attttccgct gcaatgttta agatattttg 2040 tgaaggttaa attattattt aactgttttt ggattacgtt tctatgtgat atcccgttgt 2100 tatgrtgttt actctgataa atgtttaaga aatttttata ttgggaaaac ggggtgttac 2160 aattggtatc agagcaggtt gatccgtccg gtcaattaga gagtcgtgtc gagtcttagt 2220 aatatttata ttactatctt atgttgttgt tgctactttt gtagaatatc agaaatggct 2280 ggaagaaacg atgctgcgtt agctgctgct ctacaagctg ttgcccaagc tgtgggacaa 2340 caacctaacg tgaatgctgg tgcaaatgct gaagctagga tgttggagac gttcatgaag 2400 aagaaccctc cgactttcaa aggacgttat gaccctgatg gagcccagac gtggcttaag 2460 gagattgaga ggattttccg agttatgcag tgcactgaag atcagaaggt gcggtttggt 2520 actcatcagc tggccgagga agctgatgac tggtgggttg ctattctgcc taccctcgag 2580 caggaaggag ctgtggtgac ttgggctgtt ttcaggagag agttcctgag aagatacttt 2640 ccggaagatg ttcgcgggaa gaaagagatc gaattccttg agctgaagca aggaaatatg 2700 tccgtgacag agcatgctgc caagttcgtg gagctgtcta agttctatcc gca 2753 // 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA9-3C_Mad repbase; DNA; EDCOT; 792 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative transposons from the apple genome. XX KW Transposable Element; Nonautonomous; 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 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 HAT-N1_Mad repbase; DNA; EDCOT; 813 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 TreLTRRT2-LTR repbase; DNA; EDCOT; 1055 BP. XX AC . XX DT 03-DEC-2010 (Rel. 15.12, Created) DT 03-DEC-2010 (Rel. 15.12, Last updated, Version 1) XX DE LTR from retrotransposon of unknown class from CLUSTALW alignment DE of two, full-length elements from T. repens L Genbank Accessions DE GU443965 positions 104389-112569 and GU443966 positions DE 61716-69898. XX KW LTR Retrotransposon; Transposable Element; 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 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 RAM9B_LTR repbase; DNA; EDCOT; 2659 BP. XX AC . XX DT 22-NOV-2006 (Rel. 11.11, Created) DT 19-JAN-2007 (Rel. 11.11, Last updated, Version 2) XX DE Long terminal region of RAM9B retroposon from Medicago DE truncatula. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; LTR; KW Interspersed repeat; retroposon; 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA8-8_Mad repbase; DNA; EDCOT; 1215 BP. XX AC . XX DT 18-OCT-2010 (Rel. 15.1, Created) DT 18-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 MuDR-1_Mad repbase; DNA; EDCOT; 2638 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; 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 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 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. 15.1, 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-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 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-79_Mad-I repbase; DNA; EDCOT; 3569 BP. XX AC . XX DT 25-SEP-2010 (Rel. 15.1, Created) DT 25-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA9-7_Mad repbase; DNA; EDCOT; 392 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 TOTO1_LP_I repbase; DNA; EDCOT; 3529 BP. XX AC AF220602; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 16-AUG-2004 (Rel. 9.07, Last updated, Version 2) XX DE Lycopersicon pimpinellifolium retrotransposon TOTO1_LP_I, DE internal region. XX KW LTR Retrotransposon; Transposable Element; internal region; KW 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 TE-4_Mad repbase; DNA; EDCOT; 621 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative transposons from the apple genome. XX KW Transposable Element; Nonautonomous; 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 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 MuDr-5N1_Mad repbase; DNA; EDCOT; 148 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 L1-9_Mad repbase; DNA; EDCOT; 6579 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 SHALINE16_MT repbase; DNA; EDCOT; 5758 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 element from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; retroposon; KW repeat; ORF; Interspersed; Poly-A tail; 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 in it's 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 ATLANTYS_LC_I repbase; DNA; EDCOT; 12848 BP. XX AC . XX DT 20-SEP-2005 (Rel. 10.09, Created) DT 30-SEP-2005 (Rel. 10.09, Last updated, Version 1) 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 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 1-12848 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 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" 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" 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 GYPSY-I_MT repbase; DNA; EDCOT; 14109 BP. XX AC AC144893; XX DT 09-JUL-2004 (Rel. 9.06, Created) DT 09-JUL-2004 (Rel. 9.06, Last updated, Version 1) XX DE Medicago truncatula Gypsy-like LTR retroelement (internal). XX KW GYPSY-I_MT; gypsy; LTR 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 1-14109 RA Jurka J.; RT "Medicago truncatula Gypsy-like LTR retroelement."; RL Repbase Reports 4(6), 147-147 (2004). XX DR GenBank; AC144893; Positions 102552 88444. XX SQ Sequence 14109 BP; 4062 A; 3033 C; 3008 G; 4006 T; 0 other; aaaaccgtca agaacattca agtttttttc caaagatttt cctccattaa aagtttcaac 60 caaaacttca ggtaaaactc attttcttct cttagaaagt attaatcacg gtttaaacct 120 gtagaagaaa aatcacgcaa gcagcagatc taaaaatttc cagaattcaa agataagact 180 gtaaccgtaa acacaaaacc tagatccata aggatctaag tgttgaaagc aaaaacaagc 240 actagagagg caataaacga cgaaacgatg tagatccgta aagatctaaa cgttttcttt 300 caaaaaagat caaaatcagt ttcaaaaccg tacgaagttt tttcccgatc tacgtcgttt 360 caagattcgt ttgtaaaaac cagtgccaaa atcatactta gaataagaag acgaatcgtt 420 tgatgtagaa gttttgaagt tctggaaatt taggtcaccg gaggtgctta ggcgcgccgg 480 agaagatgaa gcttccggcg gaccttcaag gtctccgccg tggcttcatc ctcaccggcg 540 gtgagggttt agagagagat gagagaagag agaagagtta gagagagaaa ggatttgcaa 600 aaatgaaata aaccggtact cttctgttta tataagccag cgaaccggac cggttcaatc 660 cggtccattc ccctttgatt cctggccgtt tgatctaggg ttttatgatc ctggatcaat 720 cgtgtggctc ctgtgcatcc ggaccttgta gttttgggct ttgggttggg ctcagttttc 780 tttcacgttt ttttgctttt tttgctattt gcactgtttt tctttgctat ttgaaccaat 840 gtcttgatta aaaatcttga taaatttcct agaaaatcca tgcttacttc ttgacatttt 900 cttgatgttt tacggtgttt ttgcacgctg gaattggcaa aattcttgta tgattaatcc 960 atggcatttt aattttttct tggattattt cttatgatta ttttgtcaat tctatcattg 1020 atttgtgaat acgtgataaa tgccatttga catgttaatg agaggtgctc atgcctacaa 1080 tcttatgttt actttgctgt tttagattga ttcatgaaac cttgattgta tgagcaatgt 1140 atgcatattc taaaagaggg taataagatg ataattctat ctcaaaattg gtatgaagct 1200 aagcttgttt gtttctaatg atcctatgtt tatagcttga gataaaagaa actattttca 1260 aacttgctat agcatgagaa ttagaagcta caaatgcctt gggtttcata tcaaaatttt 1320 aggttttatt accattttat tactatcttt atggcatttt atgcgttctt gcctcttgct 1380 actctttatg ctttatttca ctaacaagtt tatttccatg tttcatgcat ctcatttagc 1440 attccctcca ctttttttag cctagcattt attttttgca agttttaatt catttggtaa 1500 tgtaatttgt tatcattggt ttgtagcttg gcaaaggggc catagaatgt atttaggcaa 1560 tttttgtaat atggactatg gacactatga cgcaccgaca cgcacacact caccttagat 1620 gtatgcatag gattgtatgg ttaaataagc gtttaggttt taaacactta gagaaaatcc 1680 atcttttttt caaaaaaaaa caattgaact tcacttcaaa aattttcata ataaatatga 1740 agtcaacact tcattttttt ttcttttctt ttttcttaag aaaaattcaa ttcaccttaa 1800 tcatttagac tttcttttta atcactaatc aaacctcact ttttttgcta aatctaatgc 1860 ccttgaggcc tctcatctct attcttcaaa atctcttttc aaacttaaaa tcaaccaata 1920 aaaacaaaaa ccatctttga gcaagaacta cgccggtttt gatcccgtaa aacggtacgt 1980 aggcaatgag tcaaaactca tccaagccga aataaaaatc aaattctact tcttctcacc 2040 cccattctta actaatcaca ctttcttttt tacaaataat caataaaatt aaagcgtaga 2100 aataaactta ggaaagcggt tcttatggaa taccataatc gctccgggtg cctaacacct 2160 tcccgtagcg aaaatgaccc ccgaattcgg aaactcaagg gtttttctcc ttttaccctt 2220 cccaagaaaa aagagagata tcaacggtcg aaaggttcaa gtccaattaa tggcttggca 2280 cccaaaaacc atgataacag aaatggcgac ttcactgggg attcttttta gcgggtcgcg 2340 cctagttttc tttagtttat atttacgctt tgttttattg cttacatatg tgaatacttg 2400 tttattttca tttgacgtgt ggggtgagaa tatcaaaagt cctatacccg ggctgagtga 2460 acttatgttt aggtagagat ataatcgaca attcgatccg ggggttgcct cgtgtattgg 2520 attatgcgat caatctcaca tagctgaggc attttgaaag tgatattgtc ggcgtgtgtt 2580 gtcatgctta ggcacttcac tttcaattgt tcgacgaagc tatgaaccgt agttaccaaa 2640 cccatcctag cctttttagg acgtagtgcg gtggctaaat tgagtgttgt ctcaaacttt 2700 agtcgtcacg cgatactaca ctcaaactag accttctcac aaataatcat ggaacgggtg 2760 tcgtcctgta ctaccatgat atatgtgaga gaggttgcag tttgggaact gtgttagaac 2820 cttggttact actatccaaa gcattagttc accggacgcc gtgtccatcc gtagccccgt 2880 tactttgaaa ctcaacccac ttttaaacaa cacaatcatg catacatgca ttcatgcata 2940 aacatttttc atgcattcat cgaagggttt aaacaaatga gaatttttgt aaataatcac 3000 aggtatgaag aagactaagt gctacaagtt caaggaagtg gatttggtta gtttgagaga 3060 gttggcactc aaggtcaaga gtcaaacagg gttccgactc cgatatgggg gattgcttac 3120 tttgctccga accgatgtgg aagagaagct agtgcacact ctagtgcagt tttatgatcc 3180 gagcttccgt tgcttcactt tcccggactt ccagttggtt cctactctcg aggcttactc 3240 caatctagtg ggtctgccta tagccgagaa gacgcctttc accggtcccg ggacttctct 3300 tactcctctg gttattgcta aggatctcta cctcaagact tccgacgtct ccaaccatct 3360 tattaccaaa tctcacatcc gggggttcac ttcgaagtat cttcttgatc aggctaatct 3420 cggtactact cgtcaggata cactcgaggc tattcttgct ttgcttatct acgggctcat 3480 tctcttcccg aacctcgacg acttcgtgga catgaatgct atcgagatct ttcattccaa 3540 gaacccggtt cctactttgc tagcggatac ctaccacgcc atccatgaca ggactctcaa 3600 gggccgtggg tatattcttt gctgcatatc tctcttgtat aggtggttta tttcgcacct 3660 tccgagttcc ttccatgaca actcggaaaa ctggtcctac tcgcagcgga ttatggccct 3720 cactcctaat gaggtcgtct ggctcactcc ggccgctcag gtgaaggaaa tcattatggg 3780 ttgcggagac tttctcaatg tacctcttct tggtacccgt ggaggaatca actacaaccc 3840 cgagcttgct atgagacagt ttggtttccc tatgaagtcg aagcccatca atcttgctac 3900 atctccagag ttcttcttct acacgaatgc tcctaccgga caaaggaaag ctttcgtgga 3960 tgcttggtcc aaggttcgaa ggaaaagtgt gaagcatcta ggtgtgagat ccggtgtcgc 4020 tcatgaggcc tatactcagt gggtgataga tcgagctgag gagattggta tgccttatcc 4080 agctatgaga tacgtgtctt catccactcc gtctatgcct ctacctctac ttcccgcgac 4140 tcaggatatg tatcaggagc atctagctat ggagagtcgt gagaagcaaa tgtggaaagc 4200 tcggtacaat caagctgaga atctaatcat gactctggat ggtagagatg agcagaagac 4260 tcatgagaat ctgatgttga agaaagaact agctaaggcc cggagggaat tggaagagaa 4320 agacgagctg cttatgaggg attccaagag agccagagga cgacgagact tctttgccag 4380 atactgtggt tcagattccg agtccgatga tgctccgact acttcctatg cttgagggct 4440 tcatttgttt atcttgttga aatttcaaag tcttcctttt gaaaatgcta tgtagttttg 4500 attatttgca agatttctat tttgtttaaa aatccttcgg tggaaaaaag aagtcttttg 4560 cattcgcatt tgcgtatcat gcatcatatg catcatgcat tggtcacaaa ggcttccaag 4620 tgctcactct ctcctggttt ctctgcttca gtgtgaaaag tggctcgtgc tcagaaggtc 4680 tacgaacctg atagaatcga tcgaaccaga gagtacagaa gaaggaaaag ggctatggaa 4740 gaagagaacg ctcagcttcg caccgaatta gccactctaa gggaggaatt ggctaaagct 4800 aatgacgtca tgactgctct gctagctgct caagagcaat cagctacagc tatccctaca 4860 accacagctg caccggtgac tacaagcgtg ctcccaacca cttctgcgga cactcgcttt 4920 gctatgccag tggggtttcc gtatgggctt ccaccgttct tcactcccag tactgcagcg 4980 ggcacttcga gcactgctaa caatgttctg atctctgcaa caaatgctgc ctccatcaat 5040 gctactttgc cacaaacaac agcggctgtc actgagcctc ttgtgcatac cctgccccaa 5100 ggtgttaaca tcaacacaca gcacggaagt atccccgtaa ccaagaccat ggaagagatg 5160 atggaggaac ttgctaaaga actccgtcat gagatcaagg ccaatcgagg gaatgcggac 5220 tttttcaaaa ctcaagatct ttgcttagtg tcaaaagtgg atgttcctaa aaagttcaaa 5280 attccggatt tcgaccggta caacgggcta acttgccctc aaaaccacat catcaaatac 5340 gtccgaaaga tgggcaatta caaagacaat gattccctta tgatccactg ttttcaggat 5400 agtttgatgg aggatgccgc tgagtggtat actagtttga gcaagaatga catccatacc 5460 tttgatgaat tagccgctgc tttcaagagc cactacgggt ttaacactcg attgaagccg 5520 aatagggagt ttctcaggtc cctatctcaa aaaaaggagg aaagtttccg tgaatatgcg 5580 caaaggtgga gaggggcagc tgcccgtatc actcctgctt tagatgaaga agaaatgacc 5640 cagacattct taaaaacctt gaagaaagat tatgttgaga ggatgatcat cgctgccccg 5700 aacaactttt cggagatggt cactatggga acccgtcttg aggaagcagt cagggatgga 5760 atcattgtgt ttgagaaagc tgaatcttct acgagtgcat cgaagaggta tggtaatgga 5820 caccacaaga agaaagaaac ggaagtgggg atgatgtcag ctggagccgg tcaatccatg 5880 gctactgttg cacctatcaa tgcagctcaa atgcctccgt catacccata tatgccgtat 5940 tctcagcatc ctttcttccc gccattttat catcagtacc ctctgccgcc gggtcaacct 6000 caagtgcccg tcaatgcaat tgcccaacag atgaaacaac agttgccggt tcaacaacaa 6060 caacaacaac aacagcagca gcaatatacc agaccaactt ttcctcctat accaatgttg 6120 tatgcagaac ttcttccaac tctactccag agagggcatt gtacaactag acagggcaag 6180 ccaccacctg atccgttgcc tccaaggttc aggtctgatc tcaaatgtga ctttcatcaa 6240 ggtgccttag gtcatgatgt cgaggggtgt tatgctttga agtatatcgt gaagaaactc 6300 attgatcaag ggaagctgac ttttgagaat aatgttccac atgtcctcga caatccgcta 6360 ccaaatcatg ccgctgtgaa tatgatcgaa gtgtgtgagg aagctcctag acttgatgtc 6420 cgcaatgtcg caactcctct ggtgcctctg cacatcaagc tgtgcaaagc ttctctgttc 6480 agccatgatc atgccaagtg tctaggatgc ctccgtgatc ctttgggttg ccatgctgtt 6540 caagacgaca tccaaagctt gatggatgat aatcttctga ctgtcagtga tgtttgcgtg 6600 gtcgtgccag tttttcacga tccgcctgtc aagagtgtac ctttgaagaa gtgtgctgag 6660 cctttggtga taaggttgcc aggaccaatt ccttatgttt cggacaaggc agtgccatac 6720 aagtacaatg ctactatgat agaaaatgga gtagaggtgc ctctagcctc ctttgccaca 6780 gtaagcaata ttgccgaagg gacttctgca gcactaagaa gcgggaaggt tcgtccgcca 6840 ttatttcaga agaaggtagc tacgccaatc actccacaag ttgaagaagc aactccaacc 6900 gtcgtttcac ccattgctac agatatgaat cagccaggca agtctataga ggattcgaat 6960 ttagatgaga ttctgagaat aataaagagg agcgactaca agatcgttga tcaattgctg 7020 cagactcctt cgaagatatc tgtattgtca ttgctcttga gctccgaggc tcacaggaat 7080 accttgttga aagtgctgga gcaggcttat gttgaccacg aagttacggt agatcgtttc 7140 ggtggcatag tgggaaatat tactgcttgt aacaacctct ggtttagtga agaagagttg 7200 ccggaagtgg gaaagagtca caatctggct ttgcacatct cggtgaattg taaatcagac 7260 atgatatcaa atgtgttggt ggataccggt tcctctctca atgtaatgcc caagacgact 7320 ctagaccagt tgagctacca tgggaccccg ttgaggagaa gtactttctt ggtcaaagct 7380 tttgatggat ctcgaaagaa tgtgctggga gagatagact tgccgataac cattggccct 7440 gagaatttct tggttacttt ccaagtgatg gacattaatg catcctacag ttgcctgctg 7500 ggaagaccgt ggatacacga tgcaggtgcg gttacttcca ccttacatca gaagttgaaa 7560 tttgtgaaga atggaaagct cgttaccatt catggtgaag aggcatactt agtcagccag 7620 ctgtcttcct tttcttgtat tgaagcaggg tctgctgaag ggactgcttt ccaaggattg 7680 accattgaag gtgcggagcc taagaaagct ggggctgcta tggcttcatt gaaagatgct 7740 cagaaggtta tccaggaagg tcagactgcc ggatggggca aggtgataca gctctgtgag 7800 aacaagcgta aagaaggtct cgggttctcc ccgtcgtcaa gggtttcctc aggagtcttc 7860 cacagtgctg ggtttgttaa tgctgtctct gaagaagcaa ctggatctgg tctcaggcct 7920 gcatttgtta caccaggagg cattgcgaga gattgggatg ccattgacat tccttcaatc 7980 atgcatgtgt ccgagtaatg tgtcttgttg ctttagcgct ttgttttcaa aaataacaat 8040 catctcgctc tgcccaaagc gagagtgata ttttctgtaa gggcatgttt gtttcggcat 8100 tgccgttgat taataaaatt ttgtcgtttc ttccacgact actttttttt agtgcttttt 8160 ttcccttgga aacaatggta atgccagaaa aaaccaaaac atctgtattt tcttattaat 8220 ttcaaaaaaa tctgcatgaa aaaaaaaact cttcctaaaa tcatccaatc attatatgca 8280 ggttgaacca taataaaccc gttgaacaca gtaatcttac ggttcctcca agttttgatt 8340 tccctgtgta tgaagccgaa gatgaggaag gtgatgacat accgtatgag atcactcggt 8400 tacttgagca agaaaagaaa gccattcagt ctcaccaaga agagattgag cttatcaaca 8460 taggtaccga ggaaaacaag cgagaaatca agattggtgc tactctagag gaaggggtta 8520 aacagaagat catccaactc ctccgggaat atccggatat ttttgcatgg tcctatgaag 8580 atatgccagg tctagatcct atgattgtgg agcatcggat ccccaccaag cctgaatgtc 8640 ctcccgtcag gcagaaattg agaaggactc atcctgatat ggctctcaag attaagagcg 8700 aggttcaaaa gcaaattgat gcgggtttcc tcatgacagt tgagtaccct gaatgggttg 8760 ctaatattgt gcccgtgcca aagaaggatg gtaaagtccg gatgtgtgtt gacttcagag 8820 acctgaacaa agccagtcca aaagacaact ttccattacc tcatattgat gtgcttgttg 8880 ataatactgc tcaatctaag gtgttctcct tcatggacgg tttttccggc tataatcaga 8940 tcaaaatgtc tcctgaagat agagaaaaga catcttttat cactccatgg ggtactttct 9000 gctacaaagt gatgccgttc ggcctaatca atgctggtgc tacctaccaa aggggaatga 9060 ccactctgtt tcatgacatg attcacaaag aagttgaggt atatgtggat gacatgattg 9120 tgaagtcagc agatgaggag cagcatgttg aatatttaac aaagatgttt gaaaggttga 9180 gaaaatacaa gctgcgattg aatcccaaca aatgtacatt cggcgtcaga tccggcaagt 9240 tattaggctt cattgtcagc caaaagggca ttgaagtcga tcctgataaa gtccgggcca 9300 tccgagaaat gccagctcca cagacagaga agcaagtcag aggtttcctg ggacgcttga 9360 attacatctc ccgattcata tctcatatga ctgcaacctg cgggccgatc ttcaagctac 9420 ttagaaagaa ccagcctgtt gtatggaatg atgaatgcca agaagctttt gatagcatca 9480 agaattacct gctggaacca cctatccttg tcccacccgt ggaaggaagg cctttgatta 9540 tgtatttggc agtatttgat gaatccatgg gatgcgtact tggtcaacaa gatgaaaccg 9600 gaaagaaaga acatgctatc tactatctaa gcaagaagtt caccgattgt gaaactcggt 9660 atacaatgct tgagaagact tgttgtgctt tagcttgggc tgccaaacgc ctgcgtcatt 9720 acttggtgaa tcatacaact tggttgatat ccagaatgga tccgataaag tatatcttcg 9780 agaaagctgc tgtcactggg aagattgcac gctggcagat gcttttgtct gaatatgata 9840 ttgtgttcaa agctcaaaag gcaatcaaag gtagcattct tgccgatcat cttgcttacc 9900 aacctcttga tgactatcaa ccaattgaat tcgacttccc cgatgaagag atcatgtatt 9960 tgaaatccaa agactgcgaa gaaccgttga ttgatgaagg tccagatccc aatagcaagt 10020 ggggtttagt ctttgatggt gctgtcaatg cttatggtaa aggaatcggg gcagtcattg 10080 tatccccgca gaggcatcac attcctttta ccgccagaat tctgttcgaa tgtaccaaca 10140 atatggctga gtatgaagca tgtatctttg ggatcgagga agcaattgac atgagaatca 10200 aacacctcga catctatgga gattccgcgc tcgtcatcaa tcagataaag ggtgaatggg 10260 agacccacca tgctaagttg attccttatc gtgattatgc gagacgtttg ctgacatatt 10320 ttacaaaggt tgagctgcac catattcctc gtgatgagaa ccaaatggct gatgctcttg 10380 ctactctatc ctccatgttt cgagtaaacc attggaatga tgtgccaata atcaaagtgc 10440 aacgccttga aagaccttca catgtgtttg ctattgggga tgtgatcgat caggctggtg 10500 aaaatgtggt tgactataaa ccctggtact acgacatcaa acagttctta ctaagccgtg 10560 agtatccgcc gggtgcttcc aaacaagata agaagaccct gagaagattg gccagtagat 10620 tccggttaga tggagatatt ctgtacaaga gaaactatga catggtattg ttaaggtgtg 10680 ttgatgaaca tgaagcagag cagttaatgc atgatgtaca tgatggtacc ttcgggaccc 10740 atgctacagg gcatactatg tcaaggaagt tgttacgagc aggttactac tggatgacta 10800 tggagcatga ttgctaccag cacgccagaa agtgccacaa atgtcaaatc tatgctgata 10860 agattcatgt gcctccgcac gctctcaatg ttatgtcatc cccatggccg ttctcaatgt 10920 ggggcatcga catgattgga agaattgaac cgaaggcttc aaatggtcat cgtttcatct 10980 tagtggcaat tgactacttt accaaatggg ttgaagcagc atcttatacc aatgtgacca 11040 agcaagtggt agctaagttc atcaagaaca acatcatctg tcgatatggt gttcccagca 11100 agattattac cgacaatggt accaacctga acaacaatgt ggtgcaagct ctttgtgaag 11160 aattcaaaat tgagcatcat aactcttctc cttatagacc tcagatgaat ggcgcagttg 11220 aggccgccaa caagaatatc aagagaattg tccagaagat ggtaaccact tacaaggact 11280 ggcatgagat gttaccctat gctctgcatg gctaccgtac tactgtgcgc agttcaaccg 11340 gggcaacccc tttctctctt gtatatggta tggaagcggt tcttcctttg gaagtggaga 11400 tcccatctct ccgtgtgatc atggaagcaa agttatctga ggctgaatgg tgccagagcc 11460 ggtatgacca gttgaatttg attgaggaaa aacgtatgga tgccatggct cgtggacatt 11520 catatcaagc aagaatgaag actgcctttg ataagaaagt tcatcctcga gaattcaagg 11580 taggggaact tgtattgaaa aggaggataa gccagcaacc cgacccaagg ggcaagtgga 11640 cgcctaacta tgaaggtcct tatgttgtca agaaggcctt ctccggtggt gctttaattc 11700 ttacacacat ggatggtgta gaacttccaa atccagtgaa tgctgatata gtcaagaaat 11760 actttgccta gaaatatgaa aagaacagcg tggtaggtcg aaaacccgaa agggcggcct 11820 aggcaaaaat gcgcttcccg gtggatcgaa aacccgaaag ggcggtccag gcaaaaataa 11880 gggacaaaaa aaaaacaaat atgaaaagct cgctgagatt gtaaacaact caggcaagaa 11940 tgagcgtctc gatgagccga aaacccggaa gggcggttca tacaaaaatg agattgaaac 12000 aaaaggcaag taactatatc tggctaacca ccgtccccct tggggcatct gcagctgtta 12060 atgactatct tcatcaaaag ctcctacact tgcgaattca aagtttccag gaaatgtaat 12120 gattactgtg ttcaatgtac caccaaccaa taaaattacc attttccaag ctttgtgaat 12180 ccgtggagtc acgccttcgg ctgaccacca ctcttataca tcaaattgag cctgtgcttt 12240 tgtttaaaac tctattttct tctattttca aagctatata caaatcattt tccttctatt 12300 ttgataatga caatgcttga aacaaacatt ttgaaaattg aaaacctttt gtctattttg 12360 aaaagcaaac ctgagcaaca gggtactttc aaatgaaaca tgcatgagcg agagtatgtt 12420 gatgtctatt tcaatatatg ttacaagcag gttctcctcc aggatagtct gtggtcaatg 12480 gcaagaatga aaaaacagaa tgaaaatgca tgaaaataaa tgagctcgct aagttgaaaa 12540 cccgaaaggg cggcttaggc aaaaatgagc accccgctgg attgacaacc cgaaagggca 12600 gttcaggcaa aaatggggca ttgaaaagaa tttatttccc cggtggatcg aaaacccgaa 12660 agggcgatcc aggcaaaaat gggatgcaaa aaatgaatga atgaaattaa gaatataaca 12720 tgcaaaaagc attgaccaca gatgcaatgt ctacaacgta cccagcactg aaatgcccag 12780 cacaacggcg ttttccccag taaagtcttc caagattcta tctccagcaa gttgcatacc 12840 tgcctgccct cagccttggc tccgatacgt ctcccaacga cgtcatctcc aaaaaggatt 12900 tccaagaatg tgtaatatag cacgagccac tacgtgccca atgatctgat gtcttgtctt 12960 ccccgtgaag tcgtgcctac aaaatgccaa cagtcatgca ttacaagcat tcatacatgt 13020 ataatcatgc atattacgta cccatgcata ttaatgaatc tgttatatca tccatgcata 13080 ttgcatttcc aatgtcaaca tcagtctcaa ttcaatactc atgtcaggtt ctctgtcaaa 13140 accttgtgag ccaataatat cggtcaattt ctacctttca aatcaaatcg acgtcaagtc 13200 aatctcaatc tacattttgc caacaaacca atccccagtg aatatgtttc tgtttggtca 13260 agtggctagt tcaagtccaa gaacagcttg tacctatcaa tttgcttatg ttatcggtcg 13320 agtgcccagc tcaatccaag agcagctcgt acctgtcaat atgtttccgt ttggtcaagt 13380 ggctagctcg atccaagagc agcttgtacc tgtctatctg tttctgtccg gtggagtaac 13440 cagttcgcat ccaagaacaa gctcgcacct gtctatttgc cttgctttca gtcgagtaac 13500 tagttcgaat ccctaagaac aactcgtacc tgccaatttt acatgttttc agtcgagtca 13560 ccagttcgaa tccgtaagaa caactcgtac ttgccaattt tctctttttc ccagtcgggt 13620 caccagttcg aatccataag aacaactcgc actttccaat atccccaagt gagttaccag 13680 ttcgaatcca taagaacaac tcatgtttgt ccagtaacct ctatcccctg tgaagtgacc 13740 agttcgaatc cataagaaca actcgcagtt gtctgtttgt ttcatccccg gtcaagtggc 13800 tagtttgaat ccaagaacag cttgtacctg tccaacttgt ttctagtttc ccgttactct 13860 gctattcact atctttgtca atgtccacca atcccgcaat ggatacgaca tattttgtta 13920 attccaatcc ccatgaggtc ttgcattcat aatccaaatg atgcatggca tgcatattat 13980 ttgaaaatgg gtaggcgtat ttttacgtcc aaacacagtg caaatgctaa tatttaagta 14040 tcttcgtcct gtcaagccaa agactccgtc tcttgactct ccagacaaag aaacttaaat 14100 aggggcagc 14109 // 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. 15.1, 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-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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 CAULIV-2_Mad repbase; DNA; EDCOT; 8427 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Caulimovirus-like sequence. XX KW Caulimoviridae; Integrated Virus; 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 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-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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 L1-13_Mad repbase; DNA; EDCOT; 5437 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 L1-14_Mad repbase; DNA; EDCOT; 5978 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Piggy_MT repbase; DNA; EDCOT; 47 BP. XX AC . XX DT 17-NOV-2006 (Rel. 11.11, Created) DT 13-DEC-2006 (Rel. 11.11, Last updated, Version 1) XX DE A putative non-autonomous DNA retroposon with only TIRs. XX KW piggyBac; DNA transposon; Transposable Element; Nonautonomous; KW Interspersed repeat; TIR; TSD; Piggy_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 1-47 RA Shankar R. and Jurka J.; RT "Piggy_MT: A putative DNA transposon only with TIRs, from Barrel RT Medic."; RL Direct Submission to Repbase Update (17-NOV-2006). XX DR [1] (Consensus) XX CC The sequence is flanked on both sides by 4 bp TSDs (TTTT). CC Completely self complementary and contains only terminal inverted CC repeats (TIRs) of the transposon. XX SQ Sequence 47 BP; 3 A; 6 C; 14 G; 15 T; 9 other; ccccgttttg actgggtttg ggtatgggta tgggtbcntn udtmrrw 47 // 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW 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 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 HARB-N2_Mad repbase; DNA; EDCOT; 420 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 Ogre-PT1_I repbase; DNA; EDCOT; 13364 BP. XX AC AC149300; 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-PT1; 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:.6202..6439: putative intron. CC Note: ORF2+3 (gag-pol) is disrupted by two mutations generating CC stop codons at 7596..7598 and 8922..8924. 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 DNA3-1_Mad repbase; DNA; EDCOT; 429 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Helitron-3_Mad repbase; DNA; EDCOT; 6510 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Helitron family DNA transposons from the apple genome. XX KW Helitron; DNA transposon; Transposable Element; 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 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 MITRAV repbase; DNA; EDCOT; 372 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 putative non-autonomous miniature DNA transposon from Medicago DE truncatula. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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. 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 hAT-N2_Mad repbase; DNA; EDCOT; 973 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 Copia25-VV_I repbase; DNA; EDCOT; 5033 BP. XX AC . XX DT 31-AUG-2007 (Rel. 12.09, Created) DT 01-OCT-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; 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 Obukhanych T. and Jurka J.; RT "Copia25-VV."; RL Repbase Reports 7(9), 782-782 (2007). XX DR [1] (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. XX FH Key Location/Qualifiers FT CDS 878..5023 FT /product="Copia25-VV_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 TE-7-1_VV repbase; DNA; EDCOT; 1460 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 TE-7-1_VV, unclassified transposable element - a consensus DE sequence. XX KW Transposable Element; Nonautonomous; Mila; 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 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 TLP1 repbase; DNA; EDCOT; 666 BP. XX AC . XX DT 02-MAY-2002 (Rel. 7.04, Created) DT 02-MAY-2002 (Rel. 7.04, Last updated, Version 1) XX DE Putative non-autonomous DNA transposon - a consensus. XX KW DNA transposon; Transposable Element; 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] 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 1-666 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 666 BP; 233 A; 100 C; 98 G; 219 T; 16 other; tatacataaa tatgaccttt aacttggctt caaatkacat ttatgacctc caactttgag 60 tgtgcacaag tagacactta aacttgtata aaattgaaca aatagacaca tgagtcctac 120 atgacataat acgtcccacg tagggtccta catgtattat gtcatgtagg acatgtgtgt 180 ctatttgttc aactgttata caatttaagt gtctacttgt gcacactcaa agttgaaggg 240 cataaatgta atttgaagcc aagttaaggg tcatatttat gtattatgcc tttntatnta 300 anattnttaa aatwttctyg attnanactn acntttagat anaatnnagn atatatatat 360 attattanat aataggcata atacataaat atgaccttta acttgacttc aaattataat 420 tatgacctcc aactttgatt atgcacaagt agacacttaa acttgtataa aatttgaaca 480 aatagacaca tgagtcctac atgacataat acacgtagga caccacgtag gacaaaaaat 540 gtcatgtagg acatgtgtgt ctatttgttc aacttttata caagtttaag tgtctacttg 600 tgcacactca aagttgaagg gcataaatgt aatttgaagc caagttaaag gacatattta 660 tgtatt 666 // ID GYPSY2-I_MT repbase; DNA; EDCOT; 4619 BP. XX AC . XX DT 31-JUL-2005 (Rel. 10.07, Created) DT 04-AUG-2005 (Rel. 10.07, Last updated, Version 1) XX DE Internal consensus of M. truncatula gypsy element. XX KW Gypsy; LTR Retrotransposon; Transposable Element; 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; 1430 A; 802 C; 957 G; 1423 T; 7 other; gatgccccta tttaagtttc ttcgtccgga gatttgaaga tgaaatcttt gatttgacga 60 gtcgaagaga cttaaataca aaagtacacc atttttgacc taagatgtta tgaatgcatg 120 tgatgcaatt atgaatgcag gacgacaaag atgatttgac tggaatgaga aacaataacg 180 ggatacccaa attckttgaa gaaaaaggga tccgactccg ctaggggaat atagtttcac 240 tggggaaaat gattgtctac tatcgtattg atagctgaac aaagacgatt gatattttta 300 cctaactatc gatgagatag cttaacaaag gtaagaatga aagaaaaacc atcgtctaac 360 tatcgttgaa atgatagctt aacaaagaca aatgatactt ttacctaact atcgatgaga 420 tagcttaaca aaggtaagaa tgagagaaaa accatcgtct aactatcgtt gaaatgatag 480 cttaacaaag acaaatgata cttttaccta actatcgatg agatagctta acaaaggtaa 540 gaatgagaga aaaatcatcg tctaactatc gttgaaatga tagcttaaca aagacaaatg 600 atacttttac ctaactatcg atgagatagc ttaacaaagg taagaatgag agaaaaacca 660 tcgtcgatga gatagcttaa caaaggtaag aatgaaagaa aaaccatcgt ctaactaccg 720 ttgaaatgat agcttaacaa agacaaatga tacttttacc taactatcga tgagatagct 780 taacaaaggt aagaatgaga gaaaaaccat cgtctaacta ccgttgaaat gatagcttaa 840 caaagacaaa tgatactttt acctaactat cgatgagata gcttaacaaa ggtaagaatg 900 aaagaaaaac catcgtctaa ctatcgttga aatgatagct taacaaagac aaatgatact 960 tttacctaac tatcgatgag atagcttaac aaaggtaaga atgaaaggac aacttggtca 1020 gtcacactgg ggatgacact attgagagtt gaaattgaag tttgattagt gtcatgacta 1080 gcacggcttc acgccgggga tgacactttg acaataagaa ggtaaatgga agaggcttat 1140 ttgtagaaac ttgcggcttg acacaatggt aagttaagac tgaactgaag agacacgacc 1200 gaatcgagat tctggacgac tgatgcaatt atgtgtgaat tgatgttgtg catatgatgt 1260 gtacgtataa acgtatgaat atgtgaaaat attgatgaat gcatgattgt atgaatgtat 1320 gaatgtgtga ctgtgtgaat gtatgactgc atgactgtat atgacatgtg actcgatgaa 1380 ccgagacaag acaggtaaga tgggagacgg actgacatcg cagtacaaac actcggcaaa 1440 cttccttgga gatgatacta ttgtgaacaa atcgagccgt tgacggtgta agaacctggc 1500 acaaggtagc aactgatgcc tcctgggggt aaagcccatt gttgataaaa agtttggaag 1560 aagtcgccat ttgtaaaccg gcacagagtg tccttccatt ggtatgcttc agcagtcatg 1620 cttttttttt tatagaaaaa tccctaactt ttgcctggac cgccctttcg ggttttcagt 1680 ccaccgggaa tatattcttt tttgtgcccc taatttttgc ctggaccgcc ctttcgggtt 1740 ttcagtccac cgggacgctc tcttttgcct aagccgcctt ttcaggtttt caacttagcg 1800 agctttgatt tttttttttg tatttctttt ttttttttgt attttttgac tgtgacagca 1860 tcttgctcaa agtagaggtc ctttccatag tgcttagcca tgtttctctt ccggagtgta 1920 accgttctcg aggcgaatgt tgatgtacgc ttcacctact cacgagttca aagagagtgt 1980 gtttgttgtt cacacttttc aaaagatgta aaacaagttt ttgtattttt gaaaattttt 2040 gctttaagta ttgccatcaa aaatagaaga aattatgcaa atagaataaa tgagagttcc 2100 aaataaatgg gcacaggctc aaattttgat gaattgagtg gtgacctgcc aagggcatgg 2160 ctccacggat tttttgaaaa tttttggaaa aatggtaaat gtaatgggaa gggtacattg 2220 aacacaaata accgctattc tccctaacaa ctttgaatgc ccctgttccg agtctttgat 2280 ctgcagatgc ttcgaatcgg aggtcttttg atagctggat gccccaagtg gattgtgccc 2340 gaccggatgc agttactttg tcttttgatc cttaactttt gcatagatcg ccctttcggg 2400 ttttcaatct atcaggataa tcatttttgt tcatgtctct aacttttgcc tggaccgccc 2460 ttttgggttt tcagtccacc gagacgctca tttttgccta agccgccttt tcaggtttgc 2520 gacttatcga gcttttatat tttgacagag tatttcttga ctgcaccggc attcatagga 2580 agtgcaagtt tgtcaccatc catagttgta aaagtcattg cacatgagcc ttcatagtta 2640 ggcgtccact tgcccctgga gtctggttgg aaagatagta cctttttggg cacaaagtct 2700 ctttcttgaa tttcacgggg acgaaccttc ttgttggaag tttgtttcaa cctcttttga 2760 catggttgta caaggtcgtc atgcatttta agttcaatca agcttggatt tcggcagaac 2820 tcctattgtc gggacttcga cctccacggg aagcatgacc ttcatgttgt atacttgagg 2880 gaaagagggg gttgcccctg ttgaagtgtg tactgaagta caatactcat gaagtgcaaa 2940 tggtagcatc tcgtgccagt ctttgtaaat gaaagccatc ttctggacaa tcttctttga 3000 tattttgttt gcagctttga cggctaagat gccccagtat gcgagagatc ttgtcgggag 3060 tctcttcatt cttgtcttct tcagcttcgg atacaaggaa ctcaaagttg gaagagagta 3120 catggttatt gtgttcaacg ggtttattaa tgcatgattt atttattgat tttgacaagt 3180 aagtacaagt tatgattatg cagatatttg agaatgatta ttgaaagatt ttttgggttt 3240 tttgtattac catttttcca gaaaaaagca caaaatgaaa acaaagtcgg gatcaaaacg 3300 acctttttat taatgatgac aattcttaaa gcaaaaagcc ctacaccagt tcactttcat 3360 ctcgggcggg acgaaaggat gttttttttg aaaagagaaa agcaacaaac ataacattat 3420 ttgaacaaat aagtggtgga aggaaccaaa tacttcttta gcaatgctgg gagtcaatag 3480 tgttgttacc tcttcacgaa tgctcgtgga tttcttgttc aaactgatat gttctttctt 3540 tttgtttgca cgagtgttgt aagtgcgagt tggctttgga cgaggacagt tgggacacyt 3600 ttgagatgga ttgaccttta gtagaaaaga cacagtgtaa gactcagact tgaaattatg 3660 aatgcaaaat gatgcatgct atgcttatgc aaaaatagac acattttttt tgaaggactt 3720 gtcaaagtaa ttgtaaactt gataaggaac attgttttat ttgaaaattg tgaagatgtt 3780 gcaattggtt cccttttcaa aagtaagaac gaaaccaagg aaaaaagttc ttaacaaaag 3840 ctaaagctta gttaagattt ttgaagttgt atttcttggt gttccttctt acaaggtcca 3900 tatctttgat gtttacaara acttatctaa gtccttcgat attagtgaga aaaatttttt 3960 atgaatgaat gcatgtatgc atgattatgc taaagaacgt ggaatgcatg gtgaggttaa 4020 gtccacaatg ttggagtcaa gggtaacaac gccatttggt aaggactatg gtttcaaatt 4080 gtacctgtat cacgggttct accaagttcc caaagtcatt aaccacttcc gaatatttat 4140 cgggtkacgg gactactccc gttccaatta acattcgtag gaaagtctcg tttgagtgta 4200 gtatcgcgta tcaactaatt caagactact cttgattagc caccgcacta cgtcctaaaa 4260 ggccaagatg ggttaaaggt ractaaaggt cctcaacttc gacggtcact tgaaaatart 4320 agtgccaaac atgactactc aygttgacaa catattactt ccaagatccc tccgttgagt 4380 ggggttatac cacatgtacc aatacccaag agttgactct tggaatggca ctatgattat 4440 accaccgtcc tatcttaaat ttctctcaag cccgggtgta ggacttatct caccactcac 4500 gtttagaaag aaggaagaag aaggaagaac atatatacaa gtatttccat cttttatttt 4560 tttttttttt tttaagcaag ttatagcaca aagaattaaa taaagccaag ttaggctca 4619 // 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. 15.1, 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-7_Mad; HAT-7N1_Mad; 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 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 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. 15.1, 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-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 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 Ogre-SD1_I repbase; DNA; EDCOT; 13767 BP. XX AC AC146506; 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-SD1; 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); 7234..7394: putative intron. 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 TDC1 repbase; DNA; EDCOT; 5251 BP. XX AC AB001569; XX DT 28-AUG-1998 (Rel. 3.07, Created) DT 28-AUG-1998 (Rel. 3.07, Last updated, Version 1) XX DE DNA transposon TDC1. XX KW DNA transposon; Transposable Element; 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 "Direct submission."; RL Direct Submission to EMBL/GenBank/DDBJ (04-MAR-1997). Yoshihiro RL Ozeki, Tokyo University of Agriculture and Technology, Department RL of Biotechnology; 2-24-16 Naka-cho, Koganei, Tokyo 184, Japan RL (E-mail:ozeky@cc.tuat.ac.jp, Tel:423-88-7239, Fax:423-88-7239). XX DR GenBank; AB001569; Positions 5254 4. 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 TOTO1_LP_LTR repbase; DNA; EDCOT; 456 BP. XX AC AF220602; XX DT 08-NOV-2002 (Rel. 4.3, Created) DT 08-NOV-2002 (Rel. 4.3, Last updated, Version 1) XX DE Lycopersicon pimpinellifolium retrotransposon TOTO1_LP_LTR, long DE terminal repeat. XX KW Long terminal repeat; retrotransposon; 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; 188 A; 93 C; 75 G; 100 T; 0 other; tgttaggacc gaaaataagc aggtgtaaac gcggaagcta gcaaagcaaa cctcaaaaga 60 ccacgagtaa gaagacaacg agaaatatac caaaagacac aaagatttaa cgtggttcga 120 tctatcgacc tacgtctaca aaggagatga gcaatccatt ataaatatga gagtacaaaa 180 tacaaagaga aacaatctca actaattctc tcagaataca tgggaggttc acacaagtga 240 taacgtatca agcttgtgac ccataaattc tcccctaaac aaaactctca aagcccttaa 300 gactacattg tgaatgctga ttaagttcga aggaacatac ctctatttat agagtcctaa 360 accttttcct acgagaaaag gattagtcaa tccaaaacct tttcctaaaa gaaaaaccta 420 tttatggtaa gaaatcaggg caaataaaac ccaaca 456 // 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-2N_Mad repbase; DNA; EDCOT; 1090 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 LCCOPIA1_LTR repbase; DNA; EDCOT; 255 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 LTR consensus. XX KW Copia; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; LTR-retrotransposon; integrase; gag-pol; KW LCCOPIA1_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 1-255 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA9-12_Mad repbase; DNA; EDCOT; 214 BP. XX AC . XX DT 21-OCT-2010 (Rel. 15.1, Created) DT 21-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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-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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 TOPIE1_LE_I repbase; DNA; EDCOT; 3201 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 TOPIE1_LE_I, internal DE region. XX KW LTR Retrotransposon; Transposable Element; internal region; KW 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 SQ Sequence 3201 BP; 979 A; 619 C; 439 G; 1163 T; 1 other; aaaatttccc ctttttgatg atgacaaacc tcttttcttt gtgcattcaa acagttttat 60 ttgtagacac tgaagcataa aatactaaca tgaaacaagt tagtcgatgg attataaaca 120 ctgcacaact cttatcttcc cccttttggc atcattgaaa agttatgtca atcctataat 180 atacaagcta gattgatcag ttaaacaatt catgctcact gactatcacc aagacaatca 240 gataacgact tcatgcaaca taataatgta ttatagagag caagaacatg agtcattaaa 300 gcaatcaata attaatccat caaactacca gataatgttt tatataagat caaagtcata 360 ctgaatgaag caaaaacgac tgagcactaa taaaaaaaac aaatagttga catgagtaga 420 aaaaaacata gggactaaca ttggaagtga agcaaataat ggaacaagtg gagatagtag 480 tgtcaacaat ctttatcaag aacaatcttt agagcttaaa gtcatatctg attttttttc 540 cataagcaat atgaccaacc tccagtaaaa caatcttatt agtgaaatta ttacttcaac 600 cttttcattg gagtagcagt tttcctcatt gacgcatata ggtcaacatg gttcatctac 660 tcaataattt tttttctata tttgtttttt gaaaaaccat gcatgaattg gaattgagtg 720 ttcctcaaaa cttacaatgg aaatcatgtt atctttgttt ttttcatgct agctctaaga 780 taatggcatc ttgttgacac ttttgatttc tagatgagag ttcaaggtgg aatagagaaa 840 aaaatgtgtt ttaggagttg attcttcctg ataactgaaa ttgagaaact gtcttcttta 900 agcttgcaaa aataatacaa gaagacaaag tgagagagaa caatttgaaa gaatgagact 960 cttgcacttg gacggttaat ttttttctat attagagcaa ttaatacatg anacatgagt 1020 cctcaacttt ttcactttat acaatattaa cctccatcaa tatataacat acctgataag 1080 agcaattttg tgaccatcat tacttgtttt taccatttct ctgcacaatc taatacaaaa 1140 ttagattaaa ataagtaaaa gatctgaagt tgggacacac aactgaatgt gtaagactta 1200 attgaataac attttagctc ataaagttag gagaataatt attctagcca atcattcagg 1260 ggagttcatg caatctcaat catccccaag tctaacttat tcttttcata atgctcctta 1320 cttagtgtca caattcatca attgtcgttt gaaaaagaac aaggtgagcc aacaagcaca 1380 aacttttgta gtcaaatcag ttttaagatt cattgttccc cctataaata tgtccttagt 1440 ttgttcaaca aatgaaatat gtggtacaac gtgtttcaat tcactcttat cagtttcact 1500 ttaatcctca ccttgttttt gcttccccct tacacatgca ttacctcctt ttttttcttt 1560 ttttttaaat gacacattcc cccttttgcg aagtgagcga aagtaacttt tatttatctt 1620 catttatatc tcttacgcaa gcaatattta tgaatttcat cacttgcttc ctttctactt 1680 cacctgcaaa ataacttaga ggttagtctt aggaacccac acaagcttgg gtcctttctt 1740 atgatcaaaa gggtgaatca aatttcttca gttacactca tttttacttt tccttattca 1800 gtaattttca tccttaaaat ttcagacttt agatctaggt tagatgactc aagtttttca 1860 acatgtttct tcagacaatt attttgttta tcagttacaa ttttgtcatc tttgagatcc 1920 atgtactcaa attttttatc tgcaaaggct ttaaacaact tatctctttc acatgttaat 1980 tcttcaaggt catcaattaa cctatttatt aatccaatta atctactttt agaaaatgag 2040 tgcagttttt ctttaacatc agtgatacta acctcagaat tttcatcatc tttagcgtct 2100 gaatcgccca gagctaagaa tgttgtttca tcaatttcat catcagattc tccatctctt 2160 gaaccccaag aagctaccat tgcatattcc tcctttttct ttgaattcct ttccttttcc 2220 atcctttctt tcctccaatt agcttcccat tgcgggcagt tcttaacatg atgacccatt 2280 ttttcacact tgtagcatcc attttgagat ttatcattta tccacttctt ttgattggtt 2340 ttcttctttt cattttcctt ctccttcctg agatacttct tatatccttt tgctagaagt 2400 gacattttat cctcatcata ctcaatatct tcaccatcag acacttttag ggctaatgct 2460 ttttcgctaa gcatttcccc cttctttaag tcatccatat tcatctcata agttctgaga 2520 ttttccacaa gttgatcaaa tgtcatgatg agatgtcttt agcttctctt atggcagtta 2580 cttttacatc tcatttgttt ttaggaagga tccttagaac cttgtcaaca tgttcttcag 2640 tagtgaggat ttttcccagt gatgacaact cgtttaccaa cttagtgagt ctagtaatca 2700 tttttgacat aggctcacct taatcatttt gaatgtttca tattcagtga atagcatgtc 2760 tactatgaat ttccacactt gacttgttcc ttcataagca tcaaccaatg catcccagat 2820 ttgtttagca gtagtatagt ttgaaattct gttgtactca tctggtccaa gaccacaaac 2880 aagaatgttt ttgttcttag catttttcct gagagctgat aaatcttccg tggtgaagtc 2940 aatcttaacc ttttgtaatt taagtccttc gacaatcttc attgcaatag tgggtcctat 3000 atttatccta tccataattc ataatattct gcttgaataa atcctccatg tgtgctttcc 3060 actagccaaa gtgagaccca ttgaacattg ggagtctaac agtttactgt ctttcgctgt 3120 gaccaatagg tggtacagaa ttcatctcga tcttttatct taggtgttaa cctgtaaaag 3180 acaacctggt ttgataccaa t 3201 // 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 MEGY-LTR_MT repbase; DNA; EDCOT; 1279 BP. XX AC AC146683; XX DT 09-JUN-2005 (Rel. 10.05, Created) DT 09-JUN-2005 (Rel. 10.05, Last updated, Version 1) XX DE Medicago truncatula LTR retrotransposon MEGY-1 (LTR). XX KW LTR Retrotransposon; Transposable Element; Interspersed repeat; KW Long terminal repeat; Metaviridae; 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 Ogre-VP1_I repbase; DNA; EDCOT; 12174 BP. XX AC AY936172; 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; gag-pol; Ty3/gypsy-like; LTRs; intron; KW plant retrotransposon; Ogre superfamily; Ogre-VP1; 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: 7057..7373: putative intron; CC 10326: frameshift mutation (insertion of 1 bp). 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 hAT-N5_Mad repbase; DNA; EDCOT; 1684 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA9-3_Mad repbase; DNA; EDCOT; 995 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 Piggy1_MT repbase; DNA; EDCOT; 2228 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 Mariner like non autonomous DNA transposon from Medicago DE truncatula. XX KW DNA transposon; Transposable Element; Nonautonomous; mariner; KW Inverted repeats; 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 1-2228 RA Shankar R. and Jurka J.; RT "Piggy1_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 codes of a transposon like peptide sharing CC similarity with a bacterial transposase. Flanked by 2 bp TSD CC (TA). XX FH Key Location/Qualifiers FT CDS 325..543 FT /product="Piggy1_MT_1p" FT /translation="MSLNSSFTFIKFLPFQNPERENKNISFFQISSSLFFH FT IDQFLFLFHSSSHFDCSILSFQIAAISNYRENCRCF" XX SQ Sequence 2228 BP; 816 A; 317 C; 290 G; 805 T; 0 other; ccctctcttg tttagagggt aatttaccct ctcatgatat caaccaatca aaatgtaata 60 tacataggta acattaaatg tcaaataaat gagtagattt tttctaaaaa taaaagagtt 120 aatcttaatt tttttttttt tgaaggagag ttaatcttaa tcataaggta acttttaata 180 cttttaattt ttatttaatt tttttttttg aaacaacaaa tgatttaatt ttttttattt 240 ttatattaag gtgttcaatc ttaattaatt tacactacaa gacttataac aaataaaatt 300 ttacatcaaa tttctttcat ctggatgtcc ttaaattcat catttacatt cataaaattt 360 cttccattcc agaaccccga acgtgagaac aaaaacatct ccttctttca aatttcttct 420 tctttattct tccatattga tcaatttttg tttctttttc attcttcttc ccattttgat 480 tgttcaattt tgtcgttcca aattgccgca atttccaatt atcgtgagaa ttgtcgttgt 540 ttctagaacc gcgtcaggta tcgtgactta ttttttttta tttaagcagc caacctaata 600 aaatctgtta acacgcatag acctgtctca ctatcagcaa aagcctttaa gtccaaacaa 660 aagaacaaaa gcctcatcac ataaccattt cagcagcaac caaaaaaatg ctagcaaact 720 cccacaacat cacagcggca acacctgcta gcagccctca aagtacaacg gatgatttac 780 tcaattgtta taattaacta cctcacaacc aagaaaaatc aaatcaaaaa gaaaaatcaa 840 gtcatcatac ctgacgttgt actggaaata acggcaattc tcacgatatt tgaaatcaaa 900 cgaacgatga cgattctcac gaaaattgaa aaatgcggca gttgggaacg acaaaattga 960 acaatcaaaa tgggaagaag aaattttatg aatataactg ataaatttaa ggacattcag 1020 atgaaagaaa tttgatgtga aattttaatt gttctaagcc agtcctgtag tgtaaattaa 1080 ttaagattga acacctaaat ataattaagg caatattaca ttatgggtcc tttatcttat 1140 ttatttgtaa cactttggtc ctttgtcttt attttttccc gtttaggtcc tttatctctc 1200 ttaaaagcac atatacatct tttttcgcat tttttttatt aaaaaataca taattttatt 1260 tttaaaaata tatttttatt aaaactgaaa aaaaaatcca aaaatatgat gaagatgttc 1320 atcatcttca tcttcttcct ttgaatcttc atcatcttct ttaaataaat aaaaaattct 1380 actaaaatat atctccaaat atcgtgaatt aatgttatat tcacctcaaa tcttctttta 1440 aacacaaaaa tcaaaacctt aatttcacaa atgttgcaag gcggatggtg gaggcttagt 1500 cactggcgga agggttaggc tttacgaaag ttaagattgt tctggaaaca acaaaattga 1560 tgtgcaaagc tgctatcaat tttggggtta tttttatgtc gggcttgaat attgagttag 1620 aaaataataa taataataat aatatacagc gtgacaattt atataactat tttttttttt 1680 tgtgatgaaa ctaaatctct ttctctatag ggttttgatt tttgtgttta aaagaagatt 1740 tgaggtgaat ataacattaa ttcatgatat ttggagatat atttgtgtag aaattttttt 1800 gattcaatga agatgatgaa gattcaaagg aagaagatga agatgatgaa catcttcatc 1860 atatttctgg atttgtttca tttttaataa aaatatattt taaaaaataa aattatgtat 1920 tttttttaat aaaaaaaatg agaaaaatga tgtatatgtg cttttataag agataaaaga 1980 cctaagcgga aaaaaataaa gataaaggac ccaagtgtaa caaataaata agataaagga 2040 tctctaatgt aatcatgtct ataattaaat aaaaattaaa agtattaaaa gttaccttat 2100 gattataatt gattcttttt ttagaaaaaa aattgactca tttatgacat ttaatgttgt 2160 caatgtatat ttacattttg attggttgat atcatgagag ggtaaaatac cctctaaata 2220 agagaggg 2228 // 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-8N1_Mad repbase; DNA; EDCOT; 807 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, 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-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 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 L1-4_Mad repbase; DNA; EDCOT; 6391 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Copia; LTR Retrotransposon; Transposable Element; KW 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 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 SIRE1 repbase; DNA; EDCOT; 2389 BP. XX AC U22103; XX DT 11-NOV-1996 (Rel. 2.2, Created) DT 11-NOV-1996 (Rel. 2.2, Last updated, Version 1) XX DE Glycine max partial SIRE-1 sequence gag-protease polyprotein DE mRNA, complete cds and pol protein mRNA, partial cds. XX KW gag; pol; retrovirus-like element; SIRE1. 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 1-2389 RA Bi Y. and Laten M.H.; RT "Sequence analysis of a cDNA from the soybean retrovirus-like RT element, SIRE-1."; RL Unpublished. XX RN [2] RP 1-2389 RA Laten M.H.; RT "Direct Submission."; RL Direct Submission to Repbase Update (02-MAR-1995)Howard M. Laten, RL Loyola University of Chicago, Biology, 6525 N. Sheridan Rd., RL Chicago, IL 60626, USA. XX DR GenBank; U22103; Positions 1 2389. XX CC SIRE1 (AC U22103) replaces previous, shorter, SIRE1 (AC L06326). XX SQ Sequence 2389 BP; 802 A; 452 C; 587 G; 548 T; 0 other; tccggtccct ggcttggtag cccccagatg taggtgaggt tgcaccgaac tgggttaaca 60 attctcttgt gttagttact tgtttaatct gttcatacag tcaaacataa tctgcatgtt 120 ctgaagcgtg atgtcgtgac atccggtacg acatctgtca ttggtatcag aatttcaatt 180 ggtatcagag caggcactcg aattcactga gtgagatcta gggagataaa ttctgatgaa 240 catggagaaa gaaggaggac cagtgaacag accaccaatt ctggatggaa ccaactatga 300 atactggaaa gcaaggatgg tggccttcct caaatcactg gatagcagaa cctggaaagc 360 tgtcatcaaa gactgggaac atcccaagat gctggacaca gaaggaaagc ccactgatgg 420 attgaagcca gaagaagact ggactaaaga agaagacgaa ttggcacttg gaaactccaa 480 agctttgaat gctctattca atggagttga caagaatatc ttcagactga tcaacacatg 540 cacagtggcc aaggatgcat gggagatcct gaaaaccact catgaaggaa cctccaaagt 600 gaagatgtcc agattgcaac tattggccac aaaattcgaa aatctgaaga tgaaggagga 660 agagtgtatt catgactttc acatgaacat tcttgaaatt gccaatgctt gcactgcctt 720 gggagaaaga atgactgatg aaaagctggt gagaaagatc ctcagatcct tgcctaagag 780 atttgacatg aaagtcactg caatagagga ggcccaagac atttgcaacc tgagagtaga 840 tgaactcatt ggttcccttc aaacctttga gctaggactc tcggatagga ctgaaaagaa 900 gagcaagaat ctggcgttcg tgtccaatga tgaaggagaa gaagatgagt atgacctgga 960 tacagatgaa ggtctgacta atgcagttgt gctccttgga aaacagttca acaaagtgct 1020 gaacagaatg gacaggaggc agaaaccaca tgtccggaac atccctttcg acatcaggaa 1080 aggtagtgaa taccagaaaa ggtcagatga aaagcccagt cacagcaaag gatttcaatg 1140 ccatgggtgt gaaggctatg gacacatcaa agctgaatgt cccactcatc tcaagaagca 1200 gaggaaagga ctttctgtat gtcggtctga tgatacagag agtgaacaag aaagtgattc 1260 tgacagagat gtgaatgcac tcactgggag atttgaatct gctgaagatt caagtgatac 1320 agacagtgaa atcacttttg atgagcttgc tacatcctat agagaactat gcatcaaaag 1380 tgagaagatt cttcagcaag aagcacaact gaagaaggtc attgcaaatc tggaggctga 1440 gaaggaggca catgaagagg agatctctga gcttaaagga gaagttggtt ttctgaactc 1500 taaactggaa aacatgacaa aatcaataaa gatgctgaat aaaggctcag atatgcttga 1560 tgaggtgcta cagcttggga agaatgttgg aaaccagaga ggacttgggt ttaatcataa 1620 atctgctggc agaataacca tgacagaatt tgttcctgcc aaaatcagca ctggagccac 1680 gatgtcacaa catcggtctc gacatcatgg aacgcagcag aaaaagagta aaagaaagaa 1740 gtggaggtgt cactactgtg gcaagtatgg tcacataaag cccttttgct atcatctaca 1800 tggccatcca catcatggaa ctcaaagtag cagcagcaga aggaagatga tgtgggttcc 1860 aaaacacaag attgtcagtc ttgttgttca tacttcactt agagcatcag ctaaggaaga 1920 ttggtaccta gatagcggct gttccagaca catgacagga gtcaaagaat ttctggtgaa 1980 cattgaaccc tgctccacta gctatgtgac atttggagat ggctctaaag gaaagatcac 2040 tggaatggga aagctagtcc atgatggact tcgttatgtc aaggaataag atcgggctgc 2100 acaatgcaca aggcaagata aaatgtcaaa tgaagaattg aagctgcagg atccatgatg 2160 tcggatacaa tgtccaggac atcctgcccg aaaatactgg agttgctgca caatgcacaa 2220 ggcaagataa aagaagtgaa gctgcaggat ccacgatgtc ggatacgatg tccaggacat 2280 ctggcccgaa aatactggac acataaatct gttatatctt taacagatta ttgtgcagtt 2340 agcaacaggt tagacgatct atctttagga acgaactctt ctagttccg 2389 // 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA3-3_Mad repbase; DNA; EDCOT; 374 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative non-autonomous Harbinger family DNA transposon from DE apple. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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-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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 GYPSY-LTR_MT repbase; DNA; EDCOT; 1197 BP. XX AC AC144893; XX DT 09-JUL-2004 (Rel. 9.06, Created) DT 09-JUL-2004 (Rel. 9.06, Last updated, Version 1) XX DE Medicago truncatula Gypsy-like LTR-retroelement (Long Terminal DE Repeat). XX KW GYPSY-I_MT; GYPSY-LTR_MT; gypsy; LTR 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 1-1197 RA Jurka J.; RT "Medicago truncatula Gypsy-like LTR retroelement."; RL Repbase Reports 4(6), 148-148 (2004). XX DR Genbank; AC144893; Positions 88443 87247. XX SQ Sequence 1197 BP; 354 A; 239 C; 181 G; 423 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 atcatca 1197 // 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-64_Mad-I repbase; DNA; EDCOT; 4238 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 MtPH-M-I-Ia repbase; DNA; EDCOT; 5140 BP. XX AC AC144478; XX DT 14-APR-2008 (Rel. 13.04, Created) DT 14-APR-2008 (Rel. 13.04, Last updated, Version 1) XX DE Harbinger-type element (MtMaster). XX KW Harbinger; DNA transposon; Transposable Element; MtPH-M-I-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 FH Key Location/Qualifiers FT CDS join(1086..1520,1524..2141) FT /product="MtPH-M-I-Ia_1p" FT /translation="MDSLKRKVSANPPSTNNEGQSSKASWRDIKATEYFVK FT ACLDQVTKGQRNGTCFTKKGWQGIVSQFHEQSGLNYDKVQLKNRYDSLRKE FT WKVWYNLFGKVTGLGWNFEKNTVDASDEWWEKKELVCESQIFCLGYFYVYI FT YHSFICVMNMQENPQYAKFRDKGLPFAHQLTTLFKDVVANGEHAWAPSSGV FT LPNENLGNDDIDVGLDDAEGSGDSEDASIGAATGFGNINLNTSQGAVSQSS FT GQKRKRVIGAEQKGKKKATPSTSIAEAVNVIAETCKSRNEAISNASIGEVM FT AEIQTMEAVTSDLEFHTMCCNLMMFKPAREMFVSLRGFEERRLIWLKFASF FT NPTLFMRP" FT CDS join(3308..4150,4154..4660) FT /product="MtPH-M-I-Ia_2p" FT /translation="MVCLYIVIYTHVHFIKMNFWKEQLEHNTQEEEDDDTF FT EESYILAALLGEYATKYLCKEPCRTSELTGHAWVQEILQGNPTRCYEMFRM FT EKHIFHKLCHELVEHDLKSSKHMGVEEMVAMFLVVVGHGVGNRMIQERFQH FT SGETVSRHFHRVLHACLKLSFKYIKPEDPMFCECHAKIKNDQRYWPFFKNA FT IGVIDGTHVSCVVSASEQPRFIGRKGYPTQNIMAVCDWNMCFTFVLAGWEG FT TAHDARVFDKALTTANLNFPHPPQGMLYIALLYMINLLYQLIYFHILIINL FT FLGKYYLVDSGYPTPIGYIGPYRCERYHLPEFRRSSGFENHNEVFNYYHSS FT LRCTIERTFGVWKNRFAILRSMPKFKYETQVHIVVATMAIHNFIRRSAEMD FT VDFNLYEDENTVIHHDDDHRSTNLNQSQSFNVASSSEMDHARNSIRDQIIA FT YKLNN" 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 DNA9-2_Mad repbase; DNA; EDCOT; 477 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 Ogre-MT4_I repbase; DNA; EDCOT; 12091 BP. XX AC AC145061; XX DT 20-MAR-2007 (Rel. 12.03, Created) DT 03-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_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: 6054..6356: putative intron. 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 DNA8-3_Mad repbase; DNA; EDCOT; 1063 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 BNINTMO repbase; DNA; EDCOT; 632 BP. XX AC X99804; XX DT 30-MAY-2000 (Rel. 5.04, Created) DT 30-MAY-2000 (Rel. 5.04, Last updated, Version 1) XX DE B.napus DNA fragment with retrotransposon intergrase motif. XX KW Non-LTR Retrotransposon; Transposable Element; integrase; KW retrotransposon; 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 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 RTE-1_Mad repbase; DNA; EDCOT; 8343 BP. XX AC . XX DT 27-SEP-2010 (Rel. 15.1, Created) DT 27-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE RTE retrotransposons from the apple genome. XX KW RTE; Non-LTR Retrotransposon; Transposable Element; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW 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 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 HAT-8_Mad repbase; DNA; EDCOT; 4667 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 MuDR-2_Mad repbase; DNA; EDCOT; 4021 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; 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 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 HAT-3N1_Mad repbase; DNA; EDCOT; 413 BP. XX AC . XX DT 12-OCT-2010 (Rel. 15.1, Created) DT 12-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 HAT-8B_Mad repbase; DNA; EDCOT; 3449 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; HAT-8_Mad; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 LTR-8_Mad repbase; DNA; EDCOT; 2322 BP. XX AC . XX DT 15-OCT-2010 (Rel. 15.1, Created) DT 15-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 TE-2_Mad repbase; DNA; EDCOT; 175 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative transposons from the apple genome. XX KW Transposable Element; Nonautonomous; 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 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 SIRE1_LTR repbase; DNA; EDCOT; 999 BP. XX AC AY205610; XX DT 09-JUL-2004 (Rel. 9.06, Created) DT 09-JUL-2004 (Rel. 9.06, Last updated, Version 1) XX DE Glycine max cultivar Williams 82 SIRE1-8 retroelement: long DE terminal repeat. XX KW LTR Retrotransposon; Transposable Element; SIRE1; 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 TOTO1_LP_LTR repbase; DNA; EDCOT; 456 BP. XX AC AF220602; XX DT 08-NOV-2002 (Rel. 7.1, Created) DT 16-AUG-2004 (Rel. 9.07, Last updated, Version 2) XX DE Lycopersicon pimpinellifolium retrotransposon TOTO1_LP_LTR, long DE terminal repeat. XX KW LTR Retrotransposon; Transposable Element; Long terminal repeat; KW retrotransposon; 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 SHALINE2_MT repbase; DNA; EDCOT; 7617 BP. XX AC . XX DT 19-DEC-2006 (Rel. 11.12, Created) DT 19-DEC-2006 (Rel. 11.12, Last updated, Version 1) XX DE A LINE from Medicago truncatula. XX KW L1; Non-LTR Retrotransposon; Transposable Element; Nonautonomous; KW retroposon; LINE; repeat; Interspersed; 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 putative non-autonomous LINE element from barrel RT 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 GYPMET_LTR repbase; DNA; EDCOT; 2753 BP. XX AC AC161863; XX DT 09-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 Interspersed repeat; LTR retroposon; Medicago; 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 "GYPMET: 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 and the internal region is closest to Copia type. 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 EnSpm-3_Mad repbase; DNA; EDCOT; 2304 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous EnSpm elements, consensus. XX KW EnSpm; DNA transposon; Transposable Element; 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 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 DNA3-9_Mad repbase; DNA; EDCOT; 2569 BP. XX AC . XX DT 21-OCT-2010 (Rel. 15.1, Created) DT 21-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous Harbinger family DNA transposon from apple. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 HAT-N9_Mad repbase; DNA; EDCOT; 989 BP. XX AC . XX DT 05-OCT-2010 (Rel. 15.1, Created) DT 05-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT-type DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 SINE_LC repbase; DNA; EDCOT; 141 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 Lotus corniculatus var. japonicus SINE element. XX KW SINE; Non-LTR Retrotransposon; Transposable Element; SINE element; KW SINE_LC. 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 1-141 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 L1-5_Mad repbase; DNA; EDCOT; 6062 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE L1-type non-LTR retrotransposon - consensus. XX KW L1; Non-LTR Retrotransposon; Transposable Element; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-60_Mad-LTR repbase; DNA; EDCOT; 268 BP. XX AC . XX DT 22-SEP-2010 (Rel. 15.1, Created) DT 22-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 EnSpm-2_Mad repbase; DNA; EDCOT; 7584 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous EnSpm elements, consensus. XX KW EnSpm; DNA transposon; Transposable Element; 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 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 TABARE repbase; DNA; EDCOT; 7981 BP. XX AC AJ238747; XX DT 16-MAR-2006 (Rel. 11.03, Created) DT 16-MAR-2006 (Rel. 11.03, Last updated, Version 1) XX DE Nicotiana tabacum pararetrovirus-like sequence, ORF1, ORF2, ORF3, DE ORF4. XX KW Endogenous Retrovirus; Transposable Element; 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 EMBL/GenBank/DDBJ; AJ238747; Positions 1 7981. XX CC Distantly-related to Gypsy-like elements. 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-1N2_Mad repbase; DNA; EDCOT; 1030 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HAT-5_Mad repbase; DNA; EDCOT; 3641 BP. XX AC . XX DT 01-OCT-2010 (Rel. 15.1, Created) DT 01-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 Copia14-VV_I repbase; DNA; EDCOT; 4747 BP. XX AC AM483491; 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 Interspersed repeat; LG_I; Copia14-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 1-4747 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 1-4747 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 724-724 (2007). XX DR Genbank; AM483491; Positions 2707 7453. XX CC Positions [1982-2482] - Integrase core CC 'ATTA' target site duplication CC LTRs are 93% similar to each other. XX FH Key Location/Qualifiers FT CDS 1043..2647 FT /product="Copia14-VV_I_1p" FT /translation="MEDLVNQRLKIVTTRTTYGALIVRRARHTRERCWKLH FT GKPPSREWGQKGEQPSNNGQAHVTTVQQNGATPQEIGSLNQEEVERMRSLI FT CNLDKPAGTGSLAYSGKFPFSIGLNVSDITFANSWVIDSGATGHMTHSPNI FT FSTYFSCSSNRKIATADGSLTTVAGIGDVKISPSLILKNVLHVPRLTMNLI FT SIQKLTQDLHCNVVFYHSHCVFQDEDSGRMIGHARERDGLYYLKAPSQSNI FT TKGKSSHSFVSEDFSFNKEKVWLHHRRLGHPSFRVIKILFPSLFKGLDVEH FT FHCEVCELAKHKRVSFPISNKRSFIPFYLIHSDIWGPSPIPNITGAKWFVS FT FIDDCTRVTWIFLLKHKFDVSTVLPNFCSMIKTQFGVNIKRFRSDNAKDYF FT NQVLTPYFQREGIIHESSCVNTPQQNGVAERKNGHLLNSTRSFMFQKNVPK FT SFWGEAVLTTAHLINRLPSRILGFKSPMDILSTFYPNLHTTNNLVPRIFGC FT VAFVHVHNQNRGKLDPRALKCVFLGYSSTQKGYKCYHPP" XX SQ Sequence 4747 BP; 1479 A; 896 C; 992 G; 1377 T; 3 other; tggtatcaga gctgaattag gatccttgga atttattttg tttcagcttt cattgctgaa 60 tacagtgccc aatttttctt ctgtttttga aactcaaaac cgagcatttg tttcctctcc 120 tggaattttc attttcttct tggccttcat tgccattcat ttgccttctt ttttttgcct 180 tcattgtcaa tctgatctct tggctttcaa cgttgtctat tgttgaccca cgtgctttgc 240 ctgaatcacc tagaaattac tgtttttttt ccttaaaaaa tgtcagagat tgcagaaaca 300 accactacaa tctaatcaga ggagattatt cgaccccaac attccggaga attgcaaaat 360 atctaggctg catataggct ggatggaaaa aattatctga aatggtccca acttgtttgc 420 atcgtgttga aagggaaagg gaagatcagc catctcatgg gtacagggcc gaaactagga 480 gatcctcatt ttgaagcatg ggatgaagaa gactccatga ttatggcatg gttgtggaat 540 tctatgattc ttgaaatcag tgacacatgc atgttcctag ctactgccaa ggacatttgg 600 aatgcaatcc aacagacgta ctctaaggcg agagatgcag cccaagtata cgaggtcaag 660 gtgaaaaatg ttgctgctaa acagggagat aaaactgtta ctgagtatgc taatcaattg 720 aaatctttat ggcaagaact tgatcattat agggtaataa agaccaagtg tcccgaagat 780 gctgctattc tcaaggattt catagaacaa gatcgagtct atgattttct tgttggactc 840 aatccagaat ttgaccaagt gcgaatccag attcttggca agcaagaagt ttcgtgcttt 900 aatgaggtgg tggcattaat tcgaagagag gaaagcagaa gatgcctgat gcttaatcca 960 cagaacacgg acagctcggc tatggtggct ggtagtggta acaattcagc cacaaatatg 1020 gaaagagtac tagtttctgg caatggaaga tctagtcaac caaagactca aaatcgtgac 1080 tacaaggaca acttatggtg cacttattgt aagaagggca cgccatacgc gtgagcggtg 1140 ctggaaacta catggaaaac caccaagtcg agagtgggga cagaagggag aacaaccaag 1200 taataatggt caagcccatg ttacaacagt acaacagaat ggagcaacac cgcaagagat 1260 aggcagtctt aatcaagaag aagttgagag gatgaggtct cttatttgca accttgacaa 1320 accagcaggt actggttcat tggcgtattc aggtaagttt ccattctcta ttggattaaa 1380 tgtctcggat ataacctttg ccaactcctg ggtcattgac tcaggtgcta ccggccatat 1440 gactcattca ccaaacattt tttccacata tttctcatgt tcaagcaata gaaaaatagc 1500 cacagccgat ggctccttga ccaccgtagc aggtatagga gatgtcaaaa taagcccatc 1560 actgatatta aaaaatgttc ttcatgtccc taggttaacc atgaacctca tttctatcca 1620 aaaactcact caagatttac attgcaatgt ggttttttat catagtcatt gtgtatttca 1680 ggaygaggat tcggggagga tgattggaca tgctagagaa cgggatggac tctactatct 1740 caaagcacca agtcaatcaa acattaccaa aggcaaatca tctcattctt ttgtctcaga 1800 agatttttca ttcaataaag aaaaagtttg gcttcatcat cgccgacttg gacatccatc 1860 atttagggtt attaaaattc tgtttccttc tttatttaaa ggtctagacg tcgaacattt 1920 tcattgtgaa gtgtgtgaac ttgctaaaca caaacgtgtg tcttttccaa ttagcaataa 1980 aagaagtttt attccttttt atctcataca cagtgacatt tggggtcctt ctcctattcc 2040 taacattact ggggctaaat ggtttgtttc attcattgat gattgtactc gagtcacttg 2100 gatttttttg ctcaaacata aatttgatgt cagtactgtc cttccaaatt tttgttctat 2160 gattaagact caatttggag tcaatatcaa aagatttagg tcggataatg ctaaggatta 2220 tttcaatcaa gtcctaactc catactttca gagggaagga ataatacatg agtcatcttg 2280 tgtcaacact ccacagcaaa acggagtggc agaaagaaaa aacggtcacc ttcttaactc 2340 aacccgatcc ttcatgtttc agaaaaatgt gcctaaatcc ttttggggag aagcagttct 2400 tacaactgct catctcataa atagattgcc ttctaggatc ttgggattca aaagtccaat 2460 ggacatactt tcaacattct atccaaacct acacactaca aacaatcttg ttcctaggat 2520 atttgggtgt gtggcatttg tccatgttca taatcaaaac agggggaagt tagatccacg 2580 ggcattaaaa tgtgtttttt tgggttattc ttcaactcag aaagggtata agtgttacca 2640 tcctccatga aaaagattct atgtctcagt agatgttact ttccatgaac aagaatctta 2700 tttcactatt tcttatcttc agggggaraa tttggtactg gaagataagg atatggggga 2760 ttttttattc cttgatctgc catcactccc cttgtcaaaa caatctcgtc ccactgatcc 2820 tttattraaa ccttacctaa attgcccaat cagcctgaaa cctgtgcctg aaaatccaaa 2880 atctgcccct gaagaatgtg agatttgaca aagtgttttc gaggaagaag acaggtgtcc 2940 ctgaatctgt gcaagtccaa gacttcaacc caaattctga gaatgaggta acaatttcta 3000 atccttcatt gcaatctaaa tctcatgtga acaatgatga ccaggacctc cctattgttg 3060 ttaggaaagg gattagagaa tgcacaaatc aacctttata ccctcttaca cacttcctat 3120 cctttaaaaa attttcacca tctcatagag ccttccttgt tagcctaaac actatttcta 3180 tccctaccac cgtatccgag gctttaaccg atgaaaaatg gaaacaagct atgaatgtgg 3240 agatggaggc attagaaaaa aacaaaactt gggagttggt aaaattgccg acaggaaaga 3300 aacccgtggg gtgtaaatgg gtttatactg tgaaatatag agcagatgga tcaatagaaa 3360 gatacaaggc tagattggtt gccaagggtt atgctcaaac ctatgggatt gattaccaag 3420 aaacttttgc tccagtcgca aagatgaaca ctgttagagt cttgttgtca ttaacagcta 3480 attacaattg ggatttgcag caatttgatg tcaagaatgc ttttttgcat ggagaactag 3540 aggaagaaat ttatatggag gtcccgccag gttatgacaa taatttagct gctcatattg 3600 tatgtaaatt aaaaaaggcc ttgtacggac ttaagcaatc accacgagca tggtttggaa 3660 gatttgcaag agtgataata accatgggat ataggcaaag tcaaggagat catatgttgt 3720 tcattaaaca ctcatcttcg aggagactca cagctctctt ggtgtatgtc gatgacataa 3780 tagtgacagg aaacgatgac aaggagagac aggttctaaa tcaatgtttg gctaaggaat 3840 ttgagatcaa ggcattaggg aggttgaaat atttcttggt attgaggtgg ctcactctaa 3900 gcaaggcatt tttatctccc aacagaagta tgttacagat cttctcaaag aaactggcaa 3960 gaccgcatgc aaaccagcaa gtactccaat agatccgaat cttagactcg aagaggcaga 4020 aaatgatgct acagtagata aagaaatgta tcaacgcttg gtgggaaggc tcatttatct 4080 atctcataca cgactagata tagcatatgt agtgagtgtg attagtcaat tcatgcataa 4140 gtccaaagga agctcatctg caggtagctt atcgagtgtt acaatatctc aaagggacac 4200 caggtaaagg tattctgttc aaaaggaatg gtgggttagt acttgaggca tacacagatg 4260 ctgactatgc cggctcaact attgacagaa ggtcaacttc tggatattgc acctttcttg 4320 gtggaaatct cgtgacatgg atgagtaaga aacagaatgt ggtagcgcgg tctagtgcgg 4380 aggcagaatt ccaagcaatg gctcagggtg tgtgtgaact tctatggttg aatatcgttt 4440 tagaagactt aaagattgaa tgggatggcc caatgagact ctattgtgat aataaatctg 4500 caatcagcat agctcacaac ccggtacagc atgatcgaac gaagcacatt gaaattgaca 4560 gacacttcat caaagagaag ttggataatg gatggatatg tacaccttat gtgtctacac 4620 atggtcaact tgccgatata cttaccaaag ggctaagtag ttcagtgttt caaagctttg 4680 tatccaagct gggaatggtg aatacctatt caccagcttg agggggagtg tgggaaaacg 4740 tgaatta 4747 // 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 CAULIV-1_Mad repbase; DNA; EDCOT; 7907 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE Caulimovirus-like sequence. XX KW Caulimoviridae; Integrated Virus; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 HARB-N1_Mad repbase; DNA; EDCOT; 785 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Harbinger family DNA transposons from the apple genome. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 CALYPSHAN_LTR_MT repbase; DNA; EDCOT; 1930 BP. XX AC CT573400; 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, CALYPSHAN_MT, from Medicago truncatula. XX KW Gypsy; LTR Retrotransposon; Transposable Element; LTR; retroposon; KW repeat; Interspersed; terminal; CALYPSHAN_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 1-1930 RA Shankar R. and Jurka J.; RT "CALYPSHAN_MT: LTR retroposon from barrel medic."; RL Repbase Reports 7(1), 4-4 (2007). XX DR [1] (Consensus) XX SQ Sequence 1930 BP; 641 A; 365 C; 254 G; 670 T; 0 other; tgtcataccc caattttaga ccgtttaaaa tctcttgtcc gtattttaaa tttggtcaca 60 ttcccattta ttcgttgtct ttttaccatt taaagttcgt gtttcttgtc tttagtcatt 120 caaaaagttt tatttttacg ttaaatcaac gttcgcattt cacaacaatt taaaaccgtc 180 tcactttcat ttttacgacg catagtcttt ttttaatcgt aacgatcacg tcaaaaaaga 240 gaaggcctaa tcgcatttta aaaggcgttt tttttattaa tcattgcaaa caaaatttcg 300 gcagggagga tactttgaag tacctcatgt cagatttcga agggactttt tattttcttt 360 tttaggctag tttgtttatt attattattt tttttattta ttttattttt tattttttat 420 tttttatttt tttttagaaa aaacaaagaa atgaaagtca ctcacgtgac tttcttcctt 480 cttttttctt ttctttttta tttttttatt tttttatttt attcattttg ttttttttta 540 tttatttatt tatctttttg tcaaatcttt ttctccaagt ctcagctgca ggggcatttt 600 tggtcatttg tttgtaccag agccaaccct agtttgtcac tataaaaaca ctgtcaatca 660 ttgggaaatg ggccagaaat cactgttcac gtcagaaaaa tcagcagcaa ttcacaaaca 720 ctcattttct acttttccaa ccctttttca gatcaaacac taaaaattac aaagaaataa 780 catgaacata tgaagaaagt tcatagattc aaaaatccag caacacaaaa ctaaaacaaa 840 aaaaacctca aatcaatcca tacacacaaa tcatcatcca aacagatatg aaacaaagag 900 aaacgaaccg gagcagaaaa ccagaaccga accggaacaa gaaaagcttg cgccgaaccg 960 gaacaaaaaa acctgcgccg aaccggaaaa gggaggaaca accgaaccgt agcaagggaa 1020 aacaagagaa ccggaccgga aaagctagga aaggaggaga ccggaaaaag agcatgcaca 1080 tttaatttta tcattatttt attttgtcat tgacttagta tgtataaata gggaattgat 1140 gtaattttat ttcttgcatt ttattttggc ttaaaggcct tagggttgta tttaggaatt 1200 gatgtaataa tgtaggtaac acaagcaccg acacatgcac cgacactacc acattttatt 1260 taccgctttc cgttaatttt ttacgacgtt acgttagtgt tcaccgttag tttagaaaaa 1320 aatcattttc acaaaaaaat caaataagtc aaattcaaaa atcttttttc ttagcaacat 1380 tttctcttta ttttcttaat caaattttta atcaatttta attcaacttc aatcattttc 1440 aaaatttaaa atcaatcaac ctcactcatt tcttttatct catgccttga ggcctctttc 1500 tcttcttaaa accattttca aaaaaatctt aaaatcaacc taacccacca aagaaatttt 1560 tgaggtgaac tacattggtt ttgatccctt tctttaaggg tatgtaggca taggattttt 1620 atccttccaa atcaaataaa aataaccaaa aaacatactt cttctccctc cattctttca 1680 cttaaacatt aggcaataat ttttcaaata aacaagtagc ttagcacaag ataatctagg 1740 taagaggttc ctatggaata ccatagacgc ttaggatgct agcaccttcc cttcgcgtaa 1800 ccaacccccg aatccaaagt ctcgaaaggg tttttactca ttttttccct tcccaagaat 1860 aaaaatcgag agttcaaaga tcgacgattc aaatcaatta atggtttgac atccgaaaat 1920 cgcgagcaca 1930 // 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Copia14-VV_LTR repbase; DNA; EDCOT; 268 BP. XX AC AM483491; 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; KW Interspersed repeat; LG_I; Copia14-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 1-268 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 i), W265-W268 (2007). XX RN [2] RP 1-268 RA Kohany O. and Jurka J.; RT "LTR retrotransposons from grapevine."; RL Repbase Reports 7(8), 725-725 (2007). XX DR Genbank; AM483491; Positions 2439 2706. XX SQ Sequence 268 BP; 75 A; 34 C; 49 G; 110 T; 0 other; tggttgtaaa ttaatggctt gtgttttgtt gtgtatagta aattatgcta gtttaggaca 60 gtttgtttgt aacagccaga attcctagaa ttaggttaat ttagttagtt tcctattttg 120 tttatcccat aaatcatggg atttgatata gcctagtaat tagtttcctt ttctatagct 180 aagacttttc tgtataaagc tagtgtagtt ttctgagaag gaaggagaat aaaattattc 240 cacaattctg ctctctcaat ttacgtca 268 // 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 MuDR-N2_Mad repbase; DNA; EDCOT; 1293 BP. XX AC . XX DT 21-OCT-2010 (Rel. 15.1, Created) DT 21-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE MuDR-type DNA transposons from the apple genome. XX KW MuDR; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 TE-3_Mad repbase; DNA; EDCOT; 1535 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Putative transposons from the apple genome. XX KW Transposable Element; Nonautonomous; 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 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 DNA-3_Mad repbase; DNA; EDCOT; 137 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, 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-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 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 LTR-3_Mad repbase; DNA; EDCOT; 3217 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: long terminal repeat. XX KW LTR Retrotransposon; Transposable Element; 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 Kojima K.K. and Jurka J.; RT "LTR retrotransposons from the apple genome."; RL Repbase Reports 10(10), 1786-1786 (2010). XX DR [1] (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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-95_Mad-I repbase; DNA; EDCOT; 2059 BP. XX AC . XX DT 19-OCT-2010 (Rel. 15.1, Created) DT 19-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Copia; LTR Retrotransposon; Transposable Element; Nonautonomous; KW 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 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 GYPSY2-LTR_MT repbase; DNA; EDCOT; 1619 BP. XX AC . XX DT 31-JUL-2005 (Rel. 10.07, Created) DT 04-AUG-2005 (Rel. 10.07, Last updated, Version 1) XX DE LTR consensus of M. truncatula gypsy element. XX KW Gypsy; LTR Retrotransposon; Transposable Element; KW Interspersed repeat; 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; 644 A; 171 C; 291 G; 511 T; 2 other; tgtcgcgtca tttttcggag atcaaggcta tttgattagc ttttgactca ctaatttatt 60 tcacgactga acatttaatt ttttaagaaa aaggggaaaa agttcaaact accccatttt 120 gaaaagattt agggttcggg ggttagttac ataaagggaa ggtattagca ccctatatgt 180 tcgtagtact ctacgagaac ctcttgattt tatttaatta atgtgctata acttgcttgc 240 ttattttkaa aaagaartta gaattaaagt gaaaaaaata aagacctaat tatctacatt 300 ttttattgat ttgaaaggac gattgtcctc tgcctacgta cccgtgaggg atcaaaacct 360 cgtagttcgg ggtagaaaat gacgtttgat tggtttttgt gttttttatt agttttgaaa 420 aaggttttaa aatgaaaagc caagtggcaa ataagtattt gtttgtgttt tttaatatta 480 aaaaaagaga cttaaagtaa aattaaattg attgaagttt gattaagaaa agaaaataaa 540 aatgcggtca cttgatttgg atcaaggttt atttatgaaa atatttttgt gattttgatt 600 atttgcatgt tttttgttgt ttttttggaa tattaaataa aaattaaact aacggagcaa 660 taaaaataaa agcgcgtgga tttttgtagt gacgttggat caccacaaaa tccctaatct 720 aatttttttg catttttgga tatatctaag gcggtaaaga aataaaatga cacaaacaaa 780 tacccacaca cttttctcat ttatatttac attggaccta aatacattct aattgctgga 840 aaataaataa caataattaa aatgctaaat agaaattaaa aaaatgcaaa aatgctaaaa 900 agaaataaaa tgcaagaaaa taaaagaaat tgacaaccga aggggcaaaa attactgaag 960 ggacttttcc gaagggactt attccgaagg gacagaaaaa agagggagaa gaaaagaata 1020 gctcgtcaac acaagctaaa gagggagaag agagaaaagt tctttgacta ctcaagagaa 1080 cttttggtgt gtgaaattgt gtggaatgag ggctctattt ataggtcagg agtttgatga 1140 aaaaaggaaa attggtttaa tggaaatgat ggacaattat gtgaattttg aaaaaggaat 1200 gttaaagttg acactttgat ttgaattttt ttttagacct tgggcatttt atttttggac 1260 ctattgacac tttgtttttt tggacactaa ttaattaaaa agaaataaaa taaaaataaa 1320 ataaatctaa tacgaaataa aaataaaaac aaattaaact aaattatgta aagaaaaata 1380 aaattaaaag atggaaatta aaaattatta aatataaaaa aagtaactta tcttaaaatt 1440 aaaattaata aaagatggaa ataaaataaa aaagagaaaa gagggtccga ctcggaatca 1500 aaaaaatgag gtattttaaa atacctccct gccgaatttt tttactgaaa agtcagagat 1560 cgatcagagt taagtgacat gtgtcagtgg gaccttaggt caaaaattgg ggtatgaca 1619 // 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA3-5_Mad repbase; DNA; EDCOT; 2540 BP. XX AC . XX DT 30-SEP-2010 (Rel. 15.1, Created) DT 30-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous DNA transposon from apple. XX KW Harbinger; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 HAT-1_Mad repbase; DNA; EDCOT; 3634 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 RAM9B_I repbase; DNA; EDCOT; 3894 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 Internal region sequence of RAM9B LTR retroposon, from Medicago DE truncatula. XX KW LTR Retrotransposon; Transposable Element; Nonautonomous; LTR; KW Interspersed repeat; retroposon; internal region; 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 DNA7-1_Mad repbase; DNA; EDCOT; 180 BP. XX AC . XX DT 04-OCT-2010 (Rel. 15.1, Created) DT 04-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 DNA9-6_Mad repbase; DNA; EDCOT; 399 BP. XX AC . XX DT 14-OCT-2010 (Rel. 15.1, Created) DT 14-OCT-2010 (Rel. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; 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 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 HAT-2_Mad repbase; DNA; EDCOT; 3491 BP. XX AC . XX DT 29-SEP-2010 (Rel. 15.1, Created) DT 29-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-66_Mad-LTR repbase; DNA; EDCOT; 795 BP. XX AC . XX DT 24-SEP-2010 (Rel. 15.1, Created) DT 24-SEP-2010 (Rel. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 SORE1_GM repbase; DNA; EDCOT; 431 BP. XX AC AB033271; XX DT 08-NOV-2002 (Rel. 4.3, Created) DT 08-NOV-2002 (Rel. 4.3, Last updated, Version 1) XX DE Glycine max gypsy-type retrotransposon SORE1_GM, partial DE sequence. XX KW retrotransposon; GYPSY superfamily; reverse transcriptase; KW partial sequence; SORE1_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 1-431 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 hAT-N4_Mad repbase; DNA; EDCOT; 911 BP. XX AC . XX DT 28-SEP-2010 (Rel. 15.1, Created) DT 28-SEP-2010 (Rel. 15.1, Last updated, Version 1) XX DE Non-autonomous hAT elements, consensus. XX KW hAT; DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version 1) XX DE DNA transposons from the apple genome. XX KW DNA transposon; Transposable Element; Nonautonomous; KW 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 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 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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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-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. 15.09, Last updated, Version 1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 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. 15.1, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 Copia25-VV_LTR repbase; DNA; EDCOT; 169 BP. XX AC . XX DT 31-AUG-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; 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 Obukhanych T. and Jurka J.; RT "Copia25-VV."; RL Repbase Reports 7(9), 783-783 (2007). XX DR [1] (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 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. 15.1, Last updated, Version 1) XX DE LTR retrotransposon from the apple genome: internal portion. XX KW Gypsy; LTR Retrotransposon; Transposable Element; 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 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 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. 15.09, Last updated, Version -1) 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 OS Malus x domestica OC Eukaryota; Viridiplantae; 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 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 //