CC ****************************************************************
CC                                                                *
CC   REPBASE UPDATE                                               *
CC   (C) 1997-2004  Genetic Information Research Institute        *
CC   All rights reserved                                          *
CC                                                                *
CC   A REFERENCE COLLECTION OF MOUSE REPETITIVE SUBFAMILIES       *
CC   RELEASE 1.00.1; OCTOBER 2004                                 *
CC                                                                *
CC                                                                *
CC ****************************************************************
XX
ID   B1_Mm     repbase; DNA; MUS; 147 BP.
CC   B1_Mm 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   Mus musculus B1 SINE element, consensus.
XX
KW   SINE element; B1 repetitive sequence; B1_Mm.
XX
OS   Mus musculus
CC   Mus musculus
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
OC   Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi;
OC   Muridae; Murinae; Mus.
XX
RN   [1]
RP   1-147
RC   [1]
RA   Quentin Y.;
RT   "Successive waves of fixation of B1 variants in rodent lineage history";
RL   J.Mol.Evol. 28:299-305(1989)
XX
RN   [2]
RP   1-147
RC   [2] 
RA   Mouse Genome Sequencing Consortium;
RT   "Initial sequencing and comparative analysis of the mouse genome.";
RL   Nature 420 (6915), 520-562 (2002)
XX
CC   B1_Mm is a SINE element which probably originates from a 7SL
CC   RNA gene, similarly to primate Alus. Average similarity to
CC   consensus is 92%, and there are around 40000 genomic copies in
CC   mouse.
XX
CC   [2] (consensus)
XX
SQ   Sequence 147 BP; 40 A; 38 C; 45 G; 24 T; 0 other;
     agccgggcgt ggtggcgcac gcctttaatc ccagcactcg ggaggcagag gcaggcggat        60
     ttctgagttc gaggccagcc tggtctacaa agtgagttcc aggacagcca gggctataca       120
     gagaaaccct gtctcgaaaa aacaaaa                                           147
//
ID   B1_Mus1   repbase; DNA; MUS; 148 BP.
CC   B1_Mus1 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   Mus musculus B1 SINE element, consensus.
XX
KW   SINE element; B1 repetitive sequence; B1_Mus1.
XX
OS   Mus musculus
CC   Mus musculus
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
OC   Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi;
OC   Muridae; Murinae; Mus.
XX
RN   [1]
RP   1-148
RC   [1]
RA   Quentin Y.;
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   Mouse Genome Sequencing Consortium;
RT   "Initial sequencing and comparative analysis of the mouse genome.";
RL   Nature 420 (6915), 520-562 (2002)
XX
CC   B1_Mus1 is a SINE element which probably originates from a 7SL
CC   RNA gene, similarly to primate Alus. Average similarity to
CC   consensus is 90%, and there are around 88000 genomic copies in
CC   mouse.
XX
CC   [2] (consensus)
XX
SQ   Sequence 148 BP; 40 A; 38 C; 46 G; 24 T; 0 other;
     agccgggcag tggtggcgca cgcctttaat cccagcactt gggaggcaga ggcaggcgga        60
     tttctgagtt cgaggccagc ctggtctaca gagtgagttc caggacagcc agggctacac       120
     agagaaaccc tgtctcgaaa aaacaaaa                                          148
//
ID   B2_Mm1a   repbase; DNA; MUS; 193 BP.
CC   B2_Mm1a 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   Mus musculus B2 element.
XX
KW   B2 repetitive sequence; SINE element; B2_Mm1a.
XX
OS   Mus musculus
CC   Mus musculus
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
OC   Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi;
OC   Muridae; Murinae; Mus.
XX
RN   [1]
RP   1-193
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   1-193
RC   [2] 
RA   Mouse Genome Sequencing Consortium;
RT   "Initial sequencing and comparative analysis of the mouse genome.";
RL   Nature 420 (6915), 520-562 (2002)
XX
CC   B2_Mm1a is a mouse B2 SINE element, with a tRNA-derived
CC   promoter region (most probably Ala-tRNA).
XX
CC   [2] (consensus)
XX
SQ   Sequence 193 BP; 64 A; 44 C; 42 G; 43 T; 0 other;
     ggggctggtg agatggctca gtgggtaaga gcacccgact gctcttccga aggtccggag        60
     ttcaaatccc agcaaccaca tggtggctca caaccatccg taacgagatc tgactccctc       120
     ttctggagtg tctgaagaca gctacagtgt acttacatat aataaataaa taaatcttta       180
     aaaaaaaaaa aaa                                                          193
//
ID   B2_Mm1t   repbase; DNA; MUS; 193 BP.
CC   B2_Mm1t 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   Mus musculus B2 SINE element.
XX
KW   B2 repeat element; SINE element; B2_Mm1t.
XX
OS   Mus musculus
CC   Mus musculus
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
OC   Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi;
OC   Muridae; Murinae; Mus.
XX
RN   [1]
RP   1-193
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   1-193
RC   [2] 
RA   Mouse Genome Sequencing Consortium;
RT   "Initial sequencing and comparative analysis of the mouse genome.";
RL   Nature 420 (6915), 520-562 (2002)
XX
CC   Has internal tRNA-derived promoter, most similar to Ala-tRNA.
CC   There are around 350000 genomic B2 copies in mouse.
XX
CC   [2] (consensus)
XX
SQ   Sequence 193 BP; 63 A; 44 C; 43 G; 43 T; 0 other;
     ggggctggtg agatggctca gtgggtaaga gcacccgact gctcttccga aggtccggag        60
     ttcaaatccc agcaaccaca tggtggctca caaccatccg taacgagatc tgacgccctc       120
     ttctggtgtg tctgaagaca gctacagtgt acttacatat aataaataaa taaatcttta       180
     aaaaaaaaaa aaa                                                          193
//
ID   B2_Mm2    repbase; DNA; MUS; 195 BP.
CC   B2_Mm2 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   Mus musculus B2 SINE element.
XX
KW   SINE element; B2 repetitive sequence; B2_Mm2.
XX
OS   Mus musculus
CC   Mus musculus
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
OC   Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi;
OC   Muridae; Murinae; Mus.
XX
RN   [1]
RP   1-195
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   1-195
RC   [2] 
RA   Mouse Genome Sequencing Consortium;
RT   "Initial sequencing and comparative analysis of the mouse genome.";
RL   Nature 420 (6915), 520-562 (2002)
XX
CC   B2 element containing tRNA-like internal promoter, most similar
CC   to Ala-tRNA.
XX
CC   [2] (consensus)
XX
SQ   Sequence 195 BP; 64 A; 42 C; 42 G; 47 T; 0 other;
     ggggctggag agatggctca gcggttaaga gcactgactg ctcttccaga ggtcctgagt        60
     tcaattccca gcaaccacat ggtggctcac aaccatctgt aatgggatct gatgccctct       120
     tctggtgtgt ctgaagacag ctacagtgta ctcacataca taaataaata aataaatctt       180
     taaaaaaaaa aaaaa                                                        195
//
ID   BC1_Mm    repbase; DNA; MUS; 152 BP.
CC   BC1_Mm 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   Mouse neural specific BC1 RNA and ID repetitive sequence.
XX
KW   ID repetitive sequence; developmentally regulated BC1 RNA;
KW   SINE element; BC1_Mm.
XX
OS   Mus musculus
CC   Mus musculus
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
OC   Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi;
OC   Muridae; Murinae; Mus.
XX
RN   [1]
RP   1-152
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   1-152
RC   [2] 
RA   Mouse Genome Sequencing Consortium;
RT   "Initial sequencing and comparative analysis of the mouse genome.";
RL   Nature 420 (6915), 520-562 (2002)
XX
CC   BC1_Mm is a mouse-specific ID SINE element which is closely
CC   related to other rodent BC1 repeats. It appears to be nearly
CC   extinct in mouse, with only a few hundred copies inserted
CC   since speciation from rat.
XX
CC   [2] (consensus)
XX
SQ   Sequence 152 BP; 63 A; 30 C; 35 G; 24 T; 0 other;
     ggggttgggg atttagctca gtggtagagc gcttgcctag caagcgcaag gccctgggtt        60
     cggtcctcag ctctggaaaa aaaaaaaaaa aaaaaaagac aaaataacaa aaagaccaaa       120
     aaaaaacaag gtaactggca cacacaacct tt                                     152
//
