ID B1_Rn repbase; DNA; ROD; 148 BP. CC B1_Rn DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus B1 Alu-like SINE element. XX KW SINE element; Alu-like repetitive sequence; rat-specific SINE element; KW B1_Rn. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-148 RC [1] RA Quentin Y.A.; RT "Successive waves of fixation of B1 variants in rodent lineage history"; RL J.Mol.Evol. 28:299-305 (1989) XX RN [2] RP 1-148 RC [2] RA Quentin Y.A.; RT "A master sequence related to a free left Alu monomer (FLAM) at RT the origin of the B1 family in rodent genomes."; RL Nucleic Acids Res. 22, 2222-2227 (1994) XX RN [3] RP 1-148 RC [3] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC B1_Rn is a rat specific SINE element that appears to be CC extinct. The mouse equivalent B1_Mm has continued to CC proliferate in that lineage. Average similarity to consensus CC of these rat elements is around 82%, and youngest copies are CC still 6-7% diverged from consensus. There are around 44,000 CC copies in the rat genome. Rodent B1 elements seem to have CC derived from a 7SL RNA gene, as did primate Alus. XX CC [3] (consensus) XX SQ Sequence 148 BP; 39 A; 40 C; 47 G; 22 T; 0 other; agccgggcgg tggtggcgca cgcctttaat cccagcactc gggaggcaga ggcaggcgga 60 tctctgagtt cgaggccagc ctggtctaca gagtgagttc caggacagcc agggctacac 120 agagaaaccc tgtctcgaaa aaacaaaa 148 // ID B2_Rat1 repbase; DNA; ROD; 188 BP. CC B2_Rat1 DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus B2 SINE element. XX KW SINE element; B2 repetitive sequence; B2_Rat1. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-188 RC [1] RA Bains W., Temple-Smith K.; RT "Similarity and Divergence among Rodent Repetitive DNA Sequences"; RL J Mol Evol 28, 191-199 (1989) XX RN [2] RP 1-188 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC Rat-specific B2 SINE element that has an unknown tRNA-like CC internal region followed by a unique 120 bp sequence. Average CC 91% similarity to consensus. There are around 12000 copies in CC the rat genome. XX CC [2] (consensus) XX SQ Sequence 188 BP; 58 A; 41 C; 42 G; 47 T; 0 other; ggggctggag agatggctca gcggttaaga gcaccgactg ctcttccaga ggtcctgagt 60 tcaattccca gcaaccacat ggtggctcac aaccatctgt aatgggatct gatgccctct 120 tctggtgtgt ctgaagacag ctacagtgta ctcatatata ataaataaat aaatctttaa 180 aaaaaaaa 188 // ID B2_Rat2 repbase; DNA; ROD; 188 BP. CC B2_Rat2 DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus B2 SINE element. XX KW SINE element; B2 repetitive sequence; B2_Rat2. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-188 RC [1] RA Bains W., Temple-Smith K.; RT "Similarity and Divergence among Rodent Repetitive DNA Sequences"; RL J Mol Evol 28, 191-199 (1989) XX RN [2] RP 1-188 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC Rat-specific B2 SINE element that has an unknown tRNA-like CC internal region followed by a unique 120 bp sequence. Average CC similarity to consensus 93%. There are around 30000 copies in CC the rat genome. XX CC [2] (consensus) XX SQ Sequence 188 BP; 60 A; 38 C; 41 G; 49 T; 0 other; ggggctggag agatggctca gtggttaaga gcactgactg ctcttccaga ggtcctgagt 60 tcaaatccca gcaaccacat ggtggctcac aaccatctgt aatgagatct gatgccctct 120 tctggtgtgt ctgaagacag ctacagtgta cttatatata ataaataaat aaatctttaa 180 aaaaaaaa 188 // ID B2_Rat3 repbase; DNA; ROD; 188 BP. CC B2_Rat3 DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus B2 SINE element. XX KW SINE element; B2 repetitive sequence; B2_Rat3. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-188 RC [1] RA Bains W., Temple-Smith K.; RT "Similarity and Divergence among Rodent Repetitive DNA Sequences"; RL J Mol Evol 28, 191-199 (1989) XX RN [2] RP 1-188 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC Rat-specific B2 SINE element that has an unknown tRNA-like CC internal region followed by a unique 120 bp sequence. Average CC 90% similarity to consensus. There are around 10000 copies in CC the rat genome. XX CC [2] (consensus) XX SQ Sequence 188 BP; 59 A; 41 C; 43 G; 45 T; 0 other; ggggctggag agatggctca gcggttaaga gcactgactg ctcttccaga ggtcctgagt 60 tcaattccca gcaaccacat ggtggctcac aaccatctgt aatgggatcc gatgccctct 120 tctggtgtgt ctgaagacag cgacagtgta ctcatataaa ataaataaat aaatctttaa 180 aaaaaaaa 188 // ID B2_Rat4 repbase; DNA; ROD; 188 BP. CC B2_Rat4 DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus B2 SINE element. XX KW SINE element; B2 repetitive sequence; B2_Rat4. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-188 RC [1] RA Bains W., Temple-Smith K.; RT "Similarity and Divergence among Rodent Repetitive DNA Sequences"; RL J Mol Evol 28, 191-199 (1989) XX RN [2] RP 1-188 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC Rat-specific B2 SINE element that has an unknown tRNA-like CC internal region followed by a unique 120 bp sequence. Average CC 91% similarity to consensus. There are around 38000 copies in CC the rat genome. XX CC [2] (consensus) XX SQ Sequence 188 BP; 58 A; 43 C; 42 G; 45 T; 0 other; ggggctggag agatggctca gcggttaaga gcactgactg ctcttccaga ggtcctgagt 60 tcaattccca gcaaccacat ggtggctcac aaccatctgt aatgggatcc gatgccctct 120 tctggtgtgt ctgaagacag ctacagtgta ctcacataca taaaataaat aaatctttaa 180 aaaaaaaa 188 // ID B2_Rn repbase; DNA; ROD; 189 BP. CC B2_Rn DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus B2 SINE element. XX KW SINE element; B2 repetitive sequence; B2_Rn. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-189 RC [1] RA Bains W., Temple-Smith K.; RT "Similarity and Divergence among Rodent Repetitive DNA Sequences"; RL J Mol Evol 28, 191-199 (1989) XX RN [2] RP 1-189 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC Rat-specific B2 SINE element that has an unknown tRNA-like CC internal region followed by a unique 120 bp sequence. Average CC similarity to consensus 96%. XX CC [2] (consensus) XX SQ Sequence 189 BP; 62 A; 40 C; 40 G; 47 T; 0 other; ggggctggag agatggctca gcggttaaga gcacccgact gctcttccag aggtcatgag 60 ttcaattccc agcaaccaca tggtggctca caaccatctg taaagagatc tgatgccctc 120 ttctggtgta tctgaagaca gctacagtgt acttatatat aataaataaa taaatcttta 180 aaaaaaaaa 189 // ID B2_Rn1 repbase; DNA; ROD; 189 BP. CC B2_Rn1 DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus B2 SINE element. XX KW SINE element; B2 repetitive sequence; B2_Rn1. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-189 RC [1] RA Bains W., Temple-Smith K.; RT "Similarity and Divergence among Rodent Repetitive DNA Sequences"; RL J Mol Evol 28, 191-199 (1989) XX RN [2] RP 1-189 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC Rat-specific B2 SINE element that has an unknown tRNA-like CC internal region followed by a unique 120 bp sequence. Average CC 95% similarity to consensus. XX CC [2] (consensus) XX SQ Sequence 189 BP; 60 A; 42 C; 41 G; 46 T; 0 other; ggggctggag agatggctca gcggttaaga gcacccgact gctcttccag aggtcctgag 60 ttcaattccc agcaaccaca tggtggctca caaccatctg taaagagatc cgatgccctc 120 ttctggtgta tctgaagaca gctacagtgt acttatatat aataaatgaa taaatcttta 180 aaaaaaaaa 189 // ID B2_Rn2 repbase; DNA; ROD; 188 BP. CC B2_Rn2 DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus B2 SINE element. XX KW SINE element; B2 repetitive sequence; B2_Rn2. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-188 RC [1] RA Bains W., Temple-Smith K.; RT "Similarity and Divergence among Rodent Repetitive DNA Sequences"; RL J Mol Evol 28, 191-199 (1989) XX RN [2] RP 1-188 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC Rat-specific B2 SINE element that has an unknown tRNA-like CC internal region followed by a unique 120 bp sequence. Average CC 94% similarity to consensus. XX CC [2] (consensus) XX SQ Sequence 188 BP; 59 A; 40 C; 42 G; 47 T; 0 other; ggggctggag agatggctca gcggttaaga gcactgactg ctcttccaga ggtcctgagt 60 tcaattccca gcaaccacat ggtggctcac aaccatctgt aaagagatcc gatgccctct 120 tctggtgtgt ctgaagacag ctacagtgta cttatatata ataaatgaat aaatctttaa 180 aaaaaaaa 188 // ID B2_RnY repbase; DNA; ROD; 191 BP. CC B2_RnY DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus B2 SINE element. XX KW SINE element; rodent B2 repetitive sequence; B2_RnY. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-191 RC [1] RA Bains W., Temple-Smith K.; RT "Similarity and Divergence among Rodent Repetitive DNA Sequences"; RL J Mol Evol 28, 191-199 (1989) XX RN [2] RP 1-191 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC Rat-specific B2 SINE element that has an unknown tRNA-like CC internal region followed by a unique 120 bp sequence. Average CC similarity to consensus 90%. XX CC [2] (consensus) XX SQ Sequence 191 BP; 62 A; 40 C; 41 G; 48 T; 0 other; ggggctggag agatggctca gcggttaaga gcacccgact gctcttccag aggttatgag 60 ttcaattccc agcaaccaca tggtggctca caaccatctg taaagagatc cgatgccctc 120 ttctggtgta tctgaagaca gctacagtgt gtacttatat ataataaata aataaatctt 180 taaaaaaaaa a 191 // ID ID4_Rn repbase; DNA; ROD; 83 BP. CC ID4_Rn DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus ID4 SINE element element. XX KW SINE element; ID4 repetitive sequence; ID4_Rn. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-83 RC [1] RA Smit A.F.A.; RT "Structure and evolution of mammalian interspersed repeats"; RL Ph.D. thesis (USC 1995) XX RN [2] RP 1-83 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC ID4_Rn is a rat ID element that occurs roughly 20000 times in CC the rat genome, and is equally frequent to the highly similar CC ID4b_Rn. Average similarity to the consensus is 75%. XX CC [2] (consensus) XX SQ Sequence 83 BP; 19 A; 21 C; 28 G; 14 T; 1 other; ggggctgggg atgtagctca gtggtagagt gcntgcctag catgcgcgag gccctgggtt 60 caatccccag caccgcaaaa aaa 83 // ID ID4b_Rn repbase; DNA; ROD; 83 BP. CC ID4b_Rn DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus ID4 SINE element. XX KW ID4 repetitive sequence; SINE element; ID4b_Rn. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-83 RC [1] RA Smit A.F.A.; RT "Structure and evolution of mammalian interspersed repeats"; RL Ph.D. thesis (USC 1995) XX RN [2] RP 1-83 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC ID4b_Rn is a rat ID element with roughly 20000 copies in the CC rat genome, and is equally frequent to the highly similar CC ID4_Rn. Average similarity to the consensus is 73%. XX CC [2] (consensus) XX SQ Sequence 83 BP; 18 A; 22 C; 29 G; 14 T; 0 other; ggggctgggg atgtagctca gtggtagagc gcttgcctag catgcgcgag gccctgggtt 60 cgatccccag caccgcaaaa aaa 83 // ID ID_Rn1 repbase; DNA; ROD; 96 BP. CC ID_Rn1 DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus ID SINE element. XX KW SINE element; ID repetitive sequence; ID_Rn1. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-96 RC [1] RA Martignetti J.A., Brosius J.; RT "Neural BC1 RNA as an evolutionary marker: guinea pig remains a RT rodent"; RL Proc. Natl. Acad. Sci. U.S.A. 90 (20), 9698-9702 (1993) XX RN [2] RP 1-96 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC ID_Rn1 is a rat-specific ID SINE element composed of a CC tRNA-like internal promoter region. Older copies of ID CC elements match an Ala-tRNA, and may have derived from this. ID CC elements have proliferated in rat since the rat-mouse CC speciation, with some 160,000 copies generated. They appear to CC be almost extinct in the mouse lineage. ID_Rn1 is younger CC than, but closely related to ID_Rn2. XX CC [2] (consensus) XX SQ Sequence 96 BP; 31 A; 20 C; 29 G; 16 T; 0 other; ggggttgggg atttagctca gtggtagagc gcttgcctag caagcgcaag gccctgggtt 60 cggtccccag ctccgaaaaa aagaaaaaaa aaaaaa 96 // ID ID_Rn2 repbase; DNA; ROD; 96 BP. CC ID_Rn2 DNA XX AC ; XX DT 22-OCT-2004 (Rel. 1.00, Created) DT 22-OCT-2004 (Rel. 1.00, Last updated, Version 1) XX DE Rattus norvegicus ID sine element. XX KW SINE element; ID repetitive sequence; ID_Rn2. XX OS Rattus norvegicus CC Rattus norvegicus OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; OC Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-96 RC [1] RA Martignetti J.A., Brosius J.; RT "Neural BC1 RNA as an evolutionary marker: guinea pig remains a RT rodent"; RL Proc. Natl. Acad. Sci. U.S.A. 90 (20), 9698-9702 (1993) XX RN [2] RP 1-96 RC [2] RA Rat Genome Sequencing Consortium; RT "Genome sequence of the Brown Norway rat yields insights into RT mammalian evolution."; RL Nature 428, 493-521 (2004) XX CC ID_Rn2 is a rat-specific ID SINE element composed of a CC tRNA-like internal promoter region. Older copies of ID CC elements match an Ala-tRNA, and may have derived from this. ID CC elements have proliferated in rat since the rat-mouse CC speciation, with some 160,000 copies generated. They appear to CC be almost extinct in the mouse lineage. ID_Rn2 is older than, CC but closely related to ID_Rn1. XX CC [2] (consensus) XX SQ Sequence 96 BP; 31 A; 20 C; 29 G; 16 T; 0 other; ggggttgggg atttagctca gtggtagagc gcttgcctag caagcgcaag gccctgggtt 60 cggtccccag ctccgaaaaa aagaaaaaaa aaaaaa 96 //