CC * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
CC                                                               *
CC   REPBASE UPDATE                                              *
CC   (C) 1997-2003  Genetic Information Research Institute       *
CC   All rights reserved                                         *
CC                                                               *
CC   A REFERENCE COLLECTION OF VERTEBRATE REPETITIVE ELEMENTS    *
CC   (AN APPENDIX)                                               *
CC                                                               *
CC * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
XX
ID   PSLINE    repbase; DNA; VRT; 388 BP.
CC   PSLINE DNA
XX
AC   D82939;
XX
DT   10-APR-1997 (Rel. 3.0, Created)
DT   10-APR-1997 (Rel. 3.0, Last updated, Version 1)
XX
DE   Platemys spixii CR1-like LINE, partial sequence.
XX
KW   Retrotransposon; CR1-like LINE.
XX
OS   Platemys spixii
CC   Platemys spixii DNA, clone:4-2(Ps).
OC   Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata;
OC   Vertebrata; Testudines; Pleurodira; Chelidae; Platemys.
XX
RN   [1]
RP   1-388
RC   [1]  (bases 1 to 388)
RA   Okada N.;
RT   "Direct Submission";
RL   Submitted (05-JAN-1996) to the DDBJ/EMBL/GenBank databases.
RL   Norihiro Okada, Tokyou Institute of Technology, Faculty of
RL   Bioscience and Biotechnology; 4259 Nagatsuta-cho, Midori-ku,
RL   Yokohama, Kanagawa 227, Japan (E-mail:nokada@bio.titech.ac.jp,
RL   Tel:81-45-923-1136, Fax:81-45-923-1136)
XX
RN   [2]
RP   1-388
RC   [2]  (bases 1 to 388)
RA   Ohshima K., Hamada M., Terai Y., Okada N.;
RT   "The 3' ends of tRNA-derived short interspersed repetitive elements
RT   are derived from the 3' ends of long interspersed repetitive
RT   elements";
RL   Mol. Cell. Biol. 16 (7), 3756-3764 (1996)
RX   MEDLINE; 96251325.
XX
CC   3' end of LINE, CR1 like.
CC   291-351 portion of PSLINE is similar to GRTE9 (116-179).
XX
DR   GENBANK; D82939; 97.0.
CC   Positions       1     388  Accession No D82939        GenBank (rel. 97.0)
XX
SQ   Sequence 388 BP; 101 A; 68 C; 119 G; 100 T; 0 other;
     ctgcagaaga gaaaaatgag gggggatttg atagcagcct ttaactaccc aaaagggggt        60
     tccagggagg atggagctaa gctgttttca gaggtggcag atgacagaac aaggaacaat       120
     ggtctcaagt tgcagtgggc gaggtctagg ttggacatta ggaaaaagtt tttcactagg       180
     agggtggtga agcattggaa taggttacct agggaggtgg tggcatctct accttagagg       240
     ttattaagct gcggcttgac aaaaccctcg ctgggatgat ttagctaggg ttggtcctgc       300
     tttgagcagg gggttggact agatgacctt ctgaggtccc ttccaattct aatattctat       360
     gattctctga catggcatgc cacatccg                                          388
//
ID   REM1_XL   repbase; DNA; VRT; 125 BP.
CC   REM1_XL DNA
XX
AC   X00678;
XX
DT   10-APR-1997 (Rel. 3.0, Created)
DT   10-APR-1997 (Rel. 3.0, Last updated, Version 1)
XX
DE   Xenopus laevis REM 1 sequence (repetitive Eco RI Monomers).
XX
KW   Inverted repeat; repetitive sequence; XLECORI.
XX
OS   Xenopus laevis
CC   clawed frog
OC   Eukaryota; Animalia; Metazoa; Chordata; Vertebrata; Amphibia;
OC   Lissamphibia; Anura; Archeobatrachia; Pipoidea; Pipidae.
XX
RN   [1]
RP   1-125
RC   [1]  (bases 1 to 497)
RA   Hummel S., Meyerhof W., Korge E., Knoechel W.;
RT   "Characterization of highly and moderately repetitive 500 bp Eco RI
RT   fragments from Xenopus laevis DNA";
RL   Nucleic Acids Res. 12, 4921-4938 (1984)
XX
DR   GENBANK; X00678; 77.0.
CC   Positions       1     125  Accession No X00678        GenBank (rel. 77.0)
XX
SQ   Sequence 125 BP; 38 A; 26 C; 20 G; 41 T; 0 other;
     gaattctgca ctgaaatcca tttctcaaaa gagcaaacag atttttttat attcaatttt        60
     gaaatctgac atggggctag acatattgtc aatttcccag ctgccccaag tcatgtaact       120
     tgtgc                                                                   125
//
ID   TOL2_OL   repbase; DNA; VRT; 4681 BP.
CC   TOL2_OL DNA
XX
AC   D84375;
XX
DT   21-APR-1997 (Rel. 3.0, Created)
DT   21-APR-1997 (Rel. 3.0, Last updated, Version 1)
XX
DE   DNA transposon Tol2.
XX
KW   Tol2; DNA transposon.
XX
OS   Oryzias latipes
CC   Oryzias latipes (strain:i4) DNA, clone:Tol2-tyr.
OC   Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata;
OC   Vertebrata; Actinopterygii; Neopterygii; Teleostei; Euteleostei;
OC   Acanthopterygii; Atherinomorpha; Cyprinodontiformes;
OC   Adrianichthyoidei; Adrianichthyidae; Oryziinae; Oryzias.
XX
RN   [1]
RP   1-4681
RC   [1]  (bases 1 to 4681)
RA   Hori H.;
RT   "Direct Submission";
RL   Submitted (10-APR-1996) to the DDBJ/EMBL/GenBank databases. Hiroshi
RL   Hori, Nagoya University, Division of Biological Science; Furo-cho,
RL   Chikusa-ku, Nagoya, Aichi 464-01, Japan
RL   (E-mail:hori@bio.nagoya-u.ac.jp, Tel:052-789-2504,
RL   Fax:052-789-2974)
XX
RN   [2]
RP   1-4681
RC   [2]  (sites)
RA   Koga A., Suzuki M., Inagaki H., Bessho Y., Hori H.;
RT   "Transposable element in fish";
RL   Nature 383 (6595), 30 (1996)
XX
CC   repeat_unit     1..19
CC                   /note="5' terminal inverted repeat"
CC   repeat_unit     4665..4681
CC                   /note="3' terminal inverted repeat"
CC   CDS             320..673
CC                   /note="ORF1"
CC   repeat_unit     1433..1734
CC                   /note="internal inverted repeat"
CC   repeat_unit     1785..2087
CC                   /note="internal inverted repeat"
CC   CDS             2167..3225
CC                   /note="ORF2"
CC   CDS             3323..3631
CC                   /note="ORF3"
CC   CDS             4013..4369
CC                   /note="ORF4"
XX
DR   GENBANK; D84375; 99.0.
CC   Positions       1    4681  Accession No D84375        GenBank (rel. 99.0)
XX
SQ   Sequence 4681 BP; 1401 A; 880 C; 874 G; 1526 T; 0 other;
     cagaggtgta aagtacttga gtaattttac ttgattactg tacttaagta ttatttttgg        60
     ggatttttac tttacttgag tacaattaaa aatcaatact tttactttta cttaattaca       120
     tttttttaga aaaaaaagta ctttttactc cttacaattt tatttacagt caaaaagtac       180
     ttattttttg gagatcactt cattctattt tcccttgcta ttaccaaacc aattgaattg       240
     cgctgatgcc cagtttaatt taaatgttat ttattctgcc tatgaaaatc gttttcacat       300
     tatatgaaat tggtcagaca tgttcattgg tcctttggaa gtgacgtcat gtcacatcta       360
     ttaccacaat gcacagcacc ttgacctgga aattagggaa attataacag tcaatcagtg       420
     gaagaaaatg gaggaagtat gtgattcatc agcagctgcg agcagcacag tccaaaatca       480
     gccacaggat caagagcacc cgtggccgta tcttcgcgaa ttcttttctt taagtggtgt       540
     aaataaagat tcattcaaga tgaaatgtgt cctctgtctc ccgcttaata aagaaatatc       600
     ggccttcaaa agttcgccat caaacctaag gaagcatatt gaggtaagta cattaagtat       660
     tttgttttac tgatagtttt tttttttttt tttttttttt tttttgggtg tgcatgtttt       720
     gacgttgatg gcgcgccttt tatatgtgta gtaggcctat tttcactaat gcatgcgatt       780
     gacaatataa ggctcacgta ataaaatgct aaaatgcatt tgtaattggt aacgttaggt       840
     ccacgggaaa tttggcgcct attgcagctt tgaataatca ttatcattcc gtgctctcat       900
     tgtgtttgaa ttcatgcaaa acacaagaaa accaagcgag aaattttttt ccaaacatgt       960
     tgtattgtca aaacggtaac actttacaat gaggttgatt agttcatgta ttaactaaca      1020
     ttaaataacc atgagcaata catttgttac tgtatctgtt aatctttgtt aacgttagtt      1080
     aatagaaata cagatgttca ttgtttgttc atgttagttc acagtgcatt aactaatgtt      1140
     aacaagatat aagtattagt aaatgttgaa attaacatgt atacgtgcag ttcattatta      1200
     gttcatgtta actaatgtag ttaactaacg aaccttattg taaaagtgtt accatcaaaa      1260
     ctaatgtaat gaaatcaatt caccctgtca tgtcagcctt acagtcctgt gtttttgtca      1320
     atataatcag aaataaaatt aatgtttgat tgtcactaaa tgctactgta tttctaaaat      1380
     caacaagtat ttaacattat aaagtgtgca attggctgca aatgtcagtt ttattaaagg      1440
     gttagttcac ccaaaaatga aaataatgtc attaatgact cgccctcatg tcgttccaag      1500
     cccgtaagac ctccgttcat cttcagaaca cagtttaaga tattttagat ttagtccgag      1560
     agctttctgt gcctccattg agaatgtatg tacggtatac tgtccatgtc cagaaaggta      1620
     ataaaaacat caaagtagtc catgtgacat cagtgggtta gttagaattt tttgaagcat      1680
     cgaatacatt ttggtccaaa aataacaaaa cctacgactt tattcggcat tgtattctct      1740
     tccgggtctg ttgtcaatcc gcgttcacga cttcgcagtg acgctacaat gctgaataaa      1800
     gtcgtaggtt ttgttatttt tggaccaaaa tgtattttcg atgcttcaaa taattctacc      1860
     taacccactg atgtcacatg gactactttg atgtttttat tacctttctg gacatggaca      1920
     gtataccgta catacatttt cagtggaggg acagaaagct ctcggactaa atctaaaata      1980
     tcttaaactg tgttccgaag atgaacggag gtgttacggg cttggaacga catgagggtg      2040
     agtcattaat gacatctttt catttttggg tgaactaacc ctttaatgct gtaatcagag      2100
     agtgtatgtg taattgttac atttattgca tacaatataa atatttattt gttgttttta      2160
     cagagaatgc acccaaatta cctcaaaaac tactctaaat tgacagcaca gaagagaaag      2220
     atcgggacct ccacccatgc ttccagcagt aagcaactga aagttgactc agttttccca      2280
     gtcaaacatg tgtctccagt cactgtgaac aaagctatat taaggtacat cattcaagga      2340
     cttcatcctt tcagcactgt tgatctgcca tcatttaaag agctgattag tacactgcag      2400
     cctggcattt ctgtcattac aaggcctact ttacgctcca agatagctga agctgctctg      2460
     atcatgaaac agaaagtgac tgctgccatg agtgaagttg aatggattgc aaccacaacg      2520
     gattgttgga ctgcacgtag aaagtcattc attggtgtaa ctgctcactg gatcaaccct      2580
     ggaagtcttg aaagacattc cgctgcactt gcctgcaaaa gattaatggg ctctcatact      2640
     tttgaggtac tggccagtgc catgaatgat atccactcag agtatgaaat acgtgacaag      2700
     gttgtttgca caaccacaga cagtggttcc aactttatga aggctttcag agtttttggt      2760
     gtggaaaaca atgatatcga gactgaggca agaaggtgtg aaagtgatga cactgattct      2820
     gaaggctgtg gtgagggaag tgatggtgtg gaattccaag atgcctcacg agtcctggac      2880
     caagacgatg gcttcgaatt ccagctacca aaacatcaaa agtgtgcctg tcacttactt      2940
     aacctagtct caagcgttga tgcccaaaaa gctctctcaa atgaacacta caagaaactc      3000
     tacagatctg tctttggcaa atgccaagct ttatggaata aaagcagccg atcggctcta      3060
     gcagctgaag ctgttgaatc agaaagccgg cttcagcttt taaggccaaa ccaaacgcgg      3120
     tggaattcaa cttttatggc tgttgacaga attcttcaaa tttgcaaaga agcaggagaa      3180
     ggcgcacttc ggaatatatg cacctctctt gaggttccaa tgtaagtgtt tttcccctct      3240
     atcgatgtaa acaaatgtgg gttgtttttg tttaatactc tttgattatg ctgatttctc      3300
     ctgtaggttt aatccagcag aaatgctgtt cttgacagag tgggccaaca caatgcgtcc      3360
     agttgcaaaa gtactcgaca tcttgcaagc ggaaacgaat acacagctgg ggtggctgct      3420
     gcctagtgtc catcagttaa gcttgaaact tcagcgactc caccattctc tcaggtactg      3480
     tgacccactt gtggatgccc tacaacaagg aatccaaaca cgattcaagc atatgtttga      3540
     agatcctgag atcatagcag ctgccatcct tctccctaaa tttcggacct cttggacaaa      3600
     tgatgaaacc atcataaaac gaggtaaatg aatgcaagca acatacactt gacgaattct      3660
     aatctgggca acctttgagc cataccaaaa ttattctttt atttatttat ttttgcactt      3720
     tttaggaatg ttatatccca tctttggctg tgatctcaat atgaatattg atgtaaagta      3780
     ttcttgcagc aggttgtagt tatccctcag tgtttcttga aaccaaactc atatgtatca      3840
     tatgtggttt ggaaatgcag ttagatttta tgctaaaata agggatttgc atgattttag      3900
     atgtagatga ctgcacgtaa atgtagttaa tgacaaaatc cataaaattt gttcccagtc      3960
     agaagcccct caaccaaact tttctttgtg tctgctcact gtgcttgtag gcatggacta      4020
     catcagagtg catctggagc ctttggacca caagaaggaa ttggccaaca gttcatctga      4080
     tgatgaagat tttttcgctt ctttgaaacc gacaacacat gaagccagca aagagttgga      4140
     tggatatctg gcctgtgttt cagacaccag ggagtctctg ctcacgtttc ctgctatttg      4200
     cagcctctct atcaagacta atacacctct tcccgcatcg gctgcctgtg agaggctttt      4260
     cagcactgca ggattgcttt tcagccccaa aagagctagg cttgacacta acaattttga      4320
     gaatcagctt ctactgaagt taaatctgag gttttacaac tttgagtagc gtgtactggc      4380
     attagattgt ctgtcttata gtttgataat taaatacaaa cagttctaaa gcaggataaa      4440
     accttgtatg catttcattt aatgtttttt gagattaaaa gcttaaacaa gaatctctag      4500
     ttttctttct tgcttttact tttacttcct taatactcaa gtacaatttt aatggagtac      4560
     ttttttactt ttactcaagt aagattctag ccagatactt ttacttttaa ttgagtaaaa      4620
     ttttccctaa gtacttgtac tttcacttga gtaaaatttt tgagtacttt ttacacctct      4680
     g                                                                      4681
//
ID   EFG_GG    repbase; RNA; VRT; 1245 BP.
CC   EFG_GG RNA
XX
AC   X08030;
XX
DT   22-DEC-1995 (Rel. 2.0, Created)
DT   26-MAR-1997 (Rel. 3.0, Last updated, Version 2)
XX
DE   Chicken EGF-like repeat.
XX
KW   EGF-like repeat; GGEFG.
XX
OS   Gallus gallus (chicken)
CC   chicken
OC   Eukaryota; Animalia; Metazoa; Chordata; Vertebrata; Aves;
OC   Neornithes; Neognathae; Galliformes; Phasianidae.
XX
RN   [1]
RP   1-1245
RC   [1]  (bases 1 to 1899)
RA   Chiquet-Ehrismann R.;
RT   "Direct Submission";
RL   Submitted (06-JUL-1988) Chiquet-Ehrismann R., Friedrich Miescher
RL   Institut, PO Box 2543, CH-4002 Basel, Switzerland.
XX
RN   [2]
RP   1-1245
RC   [2]  (bases 1 to 1899)
RA   Pearson C.A., Pearson D., Shibahara S., Hofsteenge J.,
RA   Chiquet-Ehrismann R.;
RT   "Tenascin: cDNA cloning and induction by TGF-B";
RL   EMBO J. 7, 2977-2982 (1988)
XX
CC   This is a protein.
XX
DR   GENBANK; X08030; 77.0.
CC   Positions     255    1499  Accession No X08030        GenBank (rel. 77.0)
XX
SQ   Sequence 1245 BP; 223 A; 334 C; 475 G; 213 T; 0 other;
     tgcgtgtgcg agccaggccg gaaaggcccc aactgctccg aaccggcctg cccacgcaac        60
     tgcctcaacc gcggcctctg cgtgcggggc aaatgcatct gcgaggaggg ctttaccggc       120
     gaggactgca gccaggctgc ctgcccgtct gactgcaacg accaaggcaa gtgtgtggat       180
     ggggtgtgcg tctgcttcga gggctacacg ggcccggact gcggcgagga gctctgcccc       240
     cacgggtgtg gcattcacgg gcgctgtgtg ggtggacgct gtgtgtgcca cgagggcttc       300
     actggcgagg actgcaatga gcccctgtgc cccaacaact gtcacaaccg cgggcgctgt       360
     gtggacaacg agtgcgtctg cgatgagggc tacacgggag aggactgcgg cgagctgatt       420
     tgccccaatg actgctttga ccgtgggcgc tgtatcaacg ggacctgctt ctgcgaggag       480
     ggctacactg gagaggactg cggcgagctg acctgcccca acaactgcaa cggcaacggg       540
     cgctgcgaga acgggctgtg tgtgtgccat gagggcttcg tgggggatga ctgcagccag       600
     aagaggtgcc cgaaggactg caataaccgc gggcactgcg tggatgggcg ctgtgtgtgc       660
     catgaggggt acctggggga ggactgtggg gagctgcggt gccccaacga ctgccacaac       720
     cgcgggcgct gcatcaatgg gcagtgtgtg tgtgatgagg gattcattgg ggaggactgt       780
     ggagagctgc ggtgccccaa cgactgccac aaccgcgggc gctgcgtcaa tgggcagtgc       840
     gagtgccacg agggattcat cggggaggac tgcggggagc tgcggtgtcc caacgactgc       900
     aacagccatg ggcgctgtgt caatgggcag tgcgtgtgtg atgaggggta cacaggggag       960
     gactgcgggg agttgcggtg ccccaacgac tgccacaacc gcgggcgctg cgtggaggga      1020
     cgctgtgtgt gtgacaacgg cttcatgggg gaggactgcg gggagctgtc ctgtcccaat      1080
     gactgccacc agcacgggcg ctgcgtcgat gggcgctgcg tgtgccacga gggcttcact      1140
     ggggaagact gccgggaacg gtcctgcccc aatgactgca acaacgtggg ccgctgtgtc      1200
     gagggacggt gtgtctgtga ggaaggttac atggggatcg actgt                      1245
//
ID   INV_GG    repbase; DNA; VRT; 2119 BP.
CC   INV_GG DNA
XX
AC   X02218;
XX
DT   22-DEC-1995 (Rel. 2.0, Created)
DT   26-MAR-1997 (Rel. 3.0, Last updated, Version 2)
XX
DE   Chicken inverted repeat.
XX
KW   Inverted repeat; GGINV.
XX
OS   Gallus gallus (chicken)
CC   chicken
OC   Eukaryota; Animalia; Metazoa; Chordata; Vertebrata; Aves;
OC   Neornithes; Neognathae; Galliformes; Phasianidae.
XX
RN   [1]
RP   1-2119
RC   [1]  (bases 1 to 8384)
RA   Wang S.W., Robins A.J., D'Andrea R., Wells J.R.E.;
RT   "Inverted duplication of histone genes in chicken and disposition of
RT   regulatory sequences";
RL   Nucleic Acids Res. 13, 1369-1387 (1985)
XX
CC   This is a protein
XX
DR   GENBANK; X02218; 77.0.
CC   Positions     639    2757  Accession No X02218        GenBank (rel. 77.0)
XX
SQ   Sequence 2119 BP; 345 A; 770 C; 657 G; 347 T; 0 other;
     ggccccgccc tccagggagg aggaggcagt ggcgctcccg cccccgcctg ggccccgccc        60
     ctggtttcaa tcaggtccga ccatacgcca taacacccgc gcgcgccccg ccacatcctc       120
     actggtgtcg gacgactcag gctctcggca tgtctggcag aggcaagggc gggaaggggc       180
     tcggcaaggg cggcgccaag cgccaccgca aggtgctgcg cgacaatatc cagggcatca       240
     ccaagccggc catccgccgc ctggcgcggc gcggcggcgt caagcgcatc tcggggctca       300
     tctacgagga gacgcgcggc gtgctcaagg tcttcctgga gaacgtcatc cgcgacgccg       360
     tcacctacac cgagcacgcc aagaggaaga cggtcacggc catggacgtg gtctacgcgc       420
     tcaagcgcca gggacgcacc ctctacggct tcggcggtta aactcgtctc cgattccggc       480
     cacccgaact cgtttttagc aacccaaagg ctcttttcag agccgcccac ttggttccaa       540
     caaagagctg tgtcacctcg cctgatgtga cggggctttt tcacttaata gttaggctct       600
     tttatctccc ccagccgtat tttcagctct tcgctttccg tgtccggact gcagagctgt       660
     gtagcacagc tctagcgcct cgcggcgtcc ctccgttccc tcgcaagcgg ctcgctgcct       720
     ccgcttcccc gcagcaggct ctcaccgggc agctttcggg ctccgctcgc tccagggcgc       780
     gctcttgact tctattcccg ttgctagcga ccgggtcagg cacgtgcgac acagtgccca       840
     ggcgcgaatc cagcccctcc cttcggcacc gcgtccggaa aggccaggag aagggggccg       900
     gccccattac tcacagaccg ggggaagggc gaaggagaag caggttctgc cctgacagga       960
     accccccgag gtggggggag aaatggggaa gaggcggcta ttccgcttcc gcccgcccgc      1020
     aggccgcgca cgccgggctg cgcggcaaga ggcggacacc acaacggacc ccgcggtgtc      1080
     cgctcctttt ccccccaact gggcgtttcg cccgccctta cgaaaggcgc gcgcggggcg      1140
     cccacgcggg acgcggatgc gcggctgccg ctcgagaggg ggacggggag cggcttcagc      1200
     gcagcgtttc gggttgcagt caggacaggg cagcgacgcc caggggaaaa ctcggggctt      1260
     cccgaacgaa cacagcgcct ctccggcgga gctgcgaggg ccgcacggac ggaaaacccc      1320
     ccagtgccgc cgtgcgccca gcagtacgga acctcccgca acaacacacc acacaagcac      1380
     tcgtcgagtc accgcattcc gagctctttc tcgagactgt gggtggctct gaaaagagcc      1440
     tttgggtttc acttcgctgc tcggcgcgct tcctcggggc cggcctactt agccttggcc      1500
     ttgtggctgt cggtcttctt gggcagcagc acggcctgga tgttgggcag caccccaccc      1560
     tgcgcgatgg tcaccttgcc cagcagcttg ttgagctcct cgtcgttgcg gatggccagc      1620
     tgcaggtggc gggggatgat gcgcgtcttc ttgttgtcgc gggccgcgtt gcccgccagc      1680
     tccaggatct cggccgtcag gtactccagc acggccgcca ggtacaccgg ggcgccggcg      1740
     cccacccgct ccgcgtagtt gcccttgcgc agcagccggt gcacgcggcc cacggggaac      1800
     tgcagcccgg cccgcgacga gcgcgacttg gccttggcgc gcgccttccc gccctgcttc      1860
     ccgcgccccg acatcgccga tcagtcgctc agaagctcaa ctgccaactc aacagaaatc      1920
     aaaacacgca acagctgccc gcgctcgccc gcgcgccttt atatcccttc cccgttgcgc      1980
     gcccgccggc tcctgatagg cggacgtgtc ctcacgggga acgagcgccc aatggcgtag      2040
     cgaatctcgg cccgaccaat agcgacgggc gcccttcccc gccccgcccc tctctctgct      2100
     cacagcaatg gcggggcgg                                                   2119
//
ID   LFFP2     repbase; DNA; VRT; 298 BP.
CC   LFFP2 DNA
XX
AC   X56096;
XX
DT   22-DEC-1995 (Rel. 2.0, Created)
DT   22-DEC-1995 (Rel. 2.0, Last updated, Version 1)
XX
DE   Lesser black-backed gull (L. fuscus) female specific DNA repeat
DE   P2000-17.
XX
KW   Female-specific repeat sequence.
XX
OS   Larus fuscus
CC   Larus fuscus
OC   Eukaryota; Animalia; Metazoa; Chordata; Vertebrata; Aves;
OC   Neornithes; Neognathae; Charadriiformes; Laridae.
XX
RN   [1]
RP   1-298
RC   [1]  (bases 1 to 298)
RA   Griffiths R., Holland P.W.H.;
RT   "A novel avian W chromosome DNA repeat sequence in the lesser
RT   black-backed gull (Larus fuscus)";
RL   Chromosoma 99, 243-250 (1990)
XX
CC   This is a protein.
XX
DR   GENBANK; X56096; 77.0.
CC   Positions       1     298  Accession No X56096        GenBank (rel. 77.0)
XX
SQ   Sequence 298 BP; 84 A; 90 C; 61 G; 63 T; 0 other;
     gatcaaagca tagataaagt cgaacctgac tcaactccac agactagtct ggttccactg        60
     ccactatctg aaacccccga caatgacacc ttattgagcg gacttaagaa tctgcccctt       120
     gatgatgagc tttgggataa tgcactgtca cgatacactg caagcactga gacattagaa       180
     aacatgaggg atttaaatac acctgccctc ctctccccag cgccagtgtg tgcagtatgc       240
     gctgaaggct cgcccgctgc ggcgctacat ccccaagaac ccctaccagt accagatc         298
//
ID   BRIDGE1_FR repbase; DNA; VRT; 1430 BP.
CC   BRIDGE1_FR DNA
XX
AC   ;
XX
DT   28-JUL-1999 (Rel. 3.1, Created)
DT   28-JUL-1999 (Rel. 3.1, Last updated, Version 1)
XX
DE   BRIDGE1_FR is a non-LTR retrotransposon - an incomplete consensus
DE   sequence.
XX
KW   Non-LTR retrotransposon; LINE; BRIDGE superfamily; ORF1;
KW   reverse transcriptase; BRIDGE1_FR.
XX
OS   Fugu rubripes (consensus)
CC   consensus.
OC   Eukaryota; Metazoa; Chordata; Vertebrata; Actinopterygii;
OC   Neopterygii; Teleostei; Euteleostei; Acanthopterygii; Percomorpha;
OC   Tetraodontiformes; Tetraodontoidei; Tetraodontidae; Fugu.
XX
RN   [1]
RP   1-1430
RC   [1]  (bases 1 to 1430)
RA   Kapitonov V.V., Jurka J.
RT   ;
RL   Direct submission (July, 1999)
XX
CC   BRIDGE1_FR is a non-LTR retrotransposon that belongs to the
CC   BRIDGE superfamily. Its consensus sequence has been recovered
CC   from numerous (~50) GSS sequences. The consensus sequence can
CC   be expanded when additional DNA from the fugu genomae will be
CC   available. BRIDGE1_FR is a young retrotransposon since its 
CC   copies are, on average, 95% identical with the consensus
CC   sequence.  
XX
CC   [1] (Consensus)
XX
SQ   Sequence 1430 BP; 515 A; 239 C; 258 G; 418 T; 0 other;
     ttggcaattt ttaccggggt ttcaatttaa aaaaattttt ttcaaagttt tttggaacct        60
     tccggttgga aacccccctt ttggggggat tccccccccg gaattgggga atttgattgg       120
     aaaagttctg gaaacattta aaaatcattt tatttcagtc aaggaaaatt taaatatttc       180
     attaccagaa ataaaagcat tacaggagct acaacataaa aagaatatag ttattaaacc       240
     agcagacaaa gggtctgcaa ttgtcattct ggaccgggaa caatatattt ttgaagtaga       300
     gcgacaactt aatgacacgg aatattataa aaagttagaa aaaccaattt atttagatac       360
     aattcccatg gtagctacaa ttttagacac attaaagaga aagaaattca tttgcgaaaa       420
     acaaaggaag tatttagttg gggatgtaga acctagggaa aggagattct atattcttcc       480
     caaaattcac aaggagccag aaaagtggac aattccatat gaactgcccc cgggaaggcc       540
     aatcgtctct gactgtggga gcgagacata tttcactgcg gaattcttag atttttacct       600
     gaatccgctg tccacaaaac atcctgcctt tgtcagagac acttatcatt tcatagagat       660
     tataaaaacc ttgaagattc ctgcagattc ctatttcttc tctatggatg tggatagtct       720
     atatactaat atccccattg aatctggcat caactgtatt agaaatatat ttgaaaaata       780
     tcctgacccc aagagaccag atgaagagct cttacaatta ttagaaataa atttgagcag       840
     aaatgatttc atatttaatg gtaaatacta tttacaaacc aaaggaactg ctatgggcaa       900
     aaggtttgcc ccggcatatg cgaatatttt catggcaaac tgggaagaag aggcactatt       960
     gaaatgtaaa cataaaccag ctcactatct acggtattta gatgatgttt ggggaatatg      1020
     gacaggatct gaactacagt ttagggaatt tgttgagacc ttaaattccc acgatccctc      1080
     tattaaactt aaaacagaaa ttaataaaca ttcaattaat tttttagata caacagtttt      1140
     caaagggcca gattttctaa aaactgccaa attggacatt aaagtatatt ttaaaagcac      1200
     tgatacccat gcattgcttc ataaaacaag ttttcatcca aaacatacat ttaaaggcat      1260
     agtaaaatct caaattatta gatttaagcg aatttgcaca agggatgagg aattcaagga      1320
     agcagtaaat gttttattta aggcccttcg taaaagaggg tattccaaac cctttttgaa      1380
     acactgcttt aaatctgttc aaaaaagaaa aaatggggga gatcgtgggg                 1430
//
ID   LINE_FR   repbase; DNA; VRT; 4585 BP.
CC   LINE_FR DNA
XX
AC   AF086712;
XX
DT   20-JUL-1999 (Rel. 3.0, Created)
DT   20-JUL-1999 (Rel. 3.0, Last updated, Version 1)
XX
DE   Fugu rubripes CR1-like LINE retrotransposon - complete cds.
XX
KW   LINE_FR.
XX
OS   Fugu rubripes
CC   Fugu rubripes.
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Actinopterygii;
OC   Neopterygii; Teleostei; Euteleostei; Acanthopterygii; Percomorpha;
OC   Tetraodontiformes; Tetraodontoidei; Tetraodontidae; Fugu.
XX
RN   [1]
RP   1-4585
RC   [1]  (bases 1 to 4585)
RA   Poulter R., Butler M., Ormandy J.;
RT   "A LINE element from the pufferfish (fugu) Fugu rubripes which shows
RT   similarity to the CR1 family of non-LTR retrotransposons";
RL   Gene 227 (2), 169-179 (1999)
RX   MEDLINE; 99148008.
XX
RN   [2]
RP   1-4585
RC   [2]  (bases 1 to 4585)
RA   Poulter R.T.M., Butler M.I., Ormandy J.;
RT   "Direct Submission";
RL   Submitted (24-AUG-1998) Biochemistry, University of Otago,
RL   Cumberland Street, Dunedin, New Zealand
XX
CC   Putative nucleic acid binding protein and reverse transcriptase-like 
CC   protein genes.
XX
DR   GENBANK; AF086712; 110.0.
CC   Positions       1    4585  Accession No AF086712     GenBank (rel. 110.0)
XX
SQ   Sequence 4585 BP; 1202 A; 1083 C; 995 G; 1305 T; 0 other;
     gtattgcgtc acttcctgtc ttctcaatcg ttcgttggtt gcactgtgca tggggtgttg        60
     tattcactta atattgaaca cttggtgtgt tgtattcact taatattgaa cacttggtgt       120
     gttgtattca ctttacttaa aattttgaac acttgggaca ttctagtcac ctgataacaa       180
     cagtgagaaa caacccatat taaacaaata cagggctcca ccgattatca gcgttagcat       240
     ggcctcaccg tctgtttcac ccggtgtctt tgtctgttca gcgtgtgaaa tgtttagtta       300
     ctcctctgcc tcctttagtg aagggaatag gtgcagaaag tgtagtttat ttatggctat       360
     ggaggcgaga cttagcgagc ttgagacgcg gttccgcagc ttggagttag ctggagttgc       420
     gtcaggtagc caggagaagc tagctgctgc ggagccgcct agcgtagcta cagctagcgg       480
     tcccccggca gcagccgagc agccggctag ccagggcggc tgggtgacgg ttcgtaggaa       540
     gcgtagccca aaacaaaggc ccacggtgca ccaccaaccg cttcccgtgg ctaaccgctt       600
     ttccccactc ggcgacacac ccgctgagaa accgaccctg gtaattggcg actctgtttt       660
     gcgctacgtg aagccgactc cagcgaccat agttaagtgc attccggggg ccagagcggg       720
     cgacatagaa gcaaatttac ggctgctggc gagacgtaat cgtaaatttg gtaaagttat       780
     tattcacgtc ggagccaacg acacccggct tcgtcagtcg gaggtcacca aaattaactt       840
     ggagtcggtg tgtaactacg caaaaacgat gtcggactcc gtagcattct ctggtcccct       900
     ccccaatctg gccagcgagg agatgtttag ccgcatgtcg tcgcttcgtc gctggctgtc       960
     acggtggtgc cccgaaaacc aggtggcctt tatagacaat tggagcactt tttggggaaa      1020
     acctggtctg attaggagag acggtgtcca tcccacacgg gatggtgctt ctctcatttc      1080
     tagtaatttg gctaatttta ttagacccaa agtgacctga caatccaggg tccagaccag      1140
     gatgcagagt tgtagtctta cacacctctc tgctgcttcc ttagaaccct catccaccaa      1200
     caataacata tttaacacta tagaggtagt ctctgttcca cggttaaaag ttcaccaagc      1260
     acagagcagg ggagcggtca atcaccataa tcttattaaa attaatacca aagcacaagt      1320
     tggagaaact aatatcacaa ttaagtgtgg actgttaaat attagatctc ttttgtgtaa      1380
     atccctgtta gtgcacgacc tgatagcgga tcatcacatt gatttatttt gtcttactga      1440
     gacctggctt caggaggagg agtatgttag cttaaatgaa tctactcctc ctacccatct      1500
     taattatcat attcctcgtg ttactggtcg aggaggggga gtggcagcaa tctatcactc      1560
     caagttatta attaatccca gaccaaaaca tggcttcagt tcatttgaaa gcctgactct      1620
     tggcatcact catctgaact ggaggacaga aaagccactt ctgtttgtag ttgtatatcg      1680
     gccccctgct gggccacatt cagagttcct gtctgagttc tctgacttct tatctgactt      1740
     ggtccttaga acggacaaag tcattatcat tggagacttt aacatccata tggacgttat      1800
     aaatgacagc tttagaaatg gcttcatttc attacttgag tcagttggtt tcctccagca      1860
     gataaaccaa ccaactcaca gctttaacca caccctagat ctagttctga cttatggtgt      1920
     tgaggtagaa catgtgtcag tgttccctca gaaccccctc ctgtcagacc attctttgat      1980
     cacttttaca tttatgatta aggattcttc tatgctcaga acacagtctt actatagcag      2040
     atgtctttca gataatgctg tagctaagtt taaggaagcg atccctgtgc tgatcccagg      2100
     accaccgtgt gtttccccag ggatcaatca ttacaatctt agccctgctg aggttgactc      2160
     tattgctgaa ggtgcagcaa cctcactgag aatcacgctt gattctgttg cccccctgaa      2220
     aaagaaaata gtaaatcaga ggaggtgtgc cccctggtat aattcacata tcaggaccct      2280
     caagcagaaa gtgcgaagac tggaaaggaa gtggcattct tgtaaaatag acagctacca      2340
     tgtagcctgg aaagactgtc tattagttta caaaaaggcc cttcgcaagg ctagaacagc      2400
     ttatttttct tctttgattg aggaaaataa gagcaacccc aggtttcttt tcagcactgt      2460
     ggccaaatta actaagagtc acagtgtttt agatccacgt atcccttctt cccttagtgg      2520
     tgaagacttc atgagcttct tcactgataa agttctagct atcagagaaa aagctaacca      2580
     ggccatccca acaactggac catcaccaga tgtgctgact gtgggaacat acagggtctc      2640
     caacgagccc ttaaactcct tcagccctat atatttttct gaggcgtcat cgctaattca      2700
     gaaatccaag accaccacgt gtcttttaga tcccatccca acacacctgt tgaaggatgt      2760
     tttaccattg ataggcagtt ctatcctgga ccagatcaat ggttctttag tgtcaggtta      2820
     tgtaccccgg tcctacaagg tggcagtgat taagccgttg cttaaaaaac catcactgga      2880
     tcctgatgtc ttagcaaatt ataggccaat atccaacctt ccttttatct ctaaagttct      2940
     agagaaggtg gtggtgactc agttactgga gcacctgcag aggaacagcc tgtttgagat      3000
     gtttcagtca ggctttagag ctcaccacag cacagaaaca gcacttctta aagtcactaa      3060
     tgatcttctc atagcttccg atcatggact ggtctctatg ctggttctgc tggacctcag      3120
     tgctgctttt gatacagttg atcacagcat cctgttacag agactggaac atgtgattgg      3180
     gattaaaggg acagcactag actggtttag atcatattta tctgatagat accagtttgc      3240
     tcatgtccat ggtgttccct cctcatacag tagggttagc catggagttc ctcaaggttc      3300
     tgtacttgga ccaatcctct tcaccttgta catgcttccc ttagggaaca ttattcggca      3360
     gcatgggata aattttcatt gttatgctga tgacactcag ctttatttat ccatgaaacc      3420
     agaggagaca gagaagttag tgaagctcca gacctgtctt aaagacataa agtcctggat      3480
     gtcttcaaat ttcctcctcc ttaacccagg aaaaactgag gtcatggtgt ttggtcctga      3540
     acctctcagg gatagattag atcacatgat cactctagat ggtatctcat taacatctag      3600
     tctctctgtg aggaatctag gagtaacttt tgatcaaaat ctctccttca actcacacat      3660
     taaattagtc tctagaagtg ccttttttca cttgaggaac atcacaaaga tcaggaaact      3720
     actgacacgg catgatgctg aaaagttagt ccatgcattt gttacttcca ggctggacta      3780
     ttgtaattct ttattatcag ggtgtccaaa caactcttta agaagcctcc aggtgatcca      3840
     aaatgctgca gccagagttc tgacaggtat tgacaaaaga gatcacataa ctcctgtact      3900
     ggcgtctctt cattggctgc ccattaaatt tagaataatt tttaaaactc ttcttctgac      3960
     ctacaaggtc ctcagatgcc tagctccatc ctacctggaa gagctagtga caccttatca      4020
     gcccaataga ccgctccgct ctcagaatgc tggtctactt gtggttccca gagtttctag      4080
     ggttagaatg gggggccgag catttagcta ccaggccccc ctgctatgga accagctccc      4140
     tgtccaggta cgggaggctg actccatcgc tacttttaag atcagactta aaacctacct      4200
     ctttgaaaaa gcttattgtt actaattctg gagttccagt tactatcata gacagacaaa      4260
     taatcatact tagggggtcg tctaatcatt aggttaacat cttagtcatg ctgttatagg      4320
     ccaaggctgc cggggtccag aaacatgatc acctgacagg cctctgtcac cccactgggt      4380
     catggtttcc tctttaccca gccggccatc agcaggaggg tccccctaca tgagcctggt      4440
     cctgctcaag gtttcttcct gttaaagggg agtttttcct tgccactgtt gcttgtctgg      4500
     ggtcaggccc tgggattctg gaaagcgcct tgaaacaatt ttgattgtat aagacgctat      4560
     ataaataaag attgattgat tgatt                                            4585
//
ID   BRIDGE1_FR repbase; DNA; VRT; 4209 BP.
CC   BRIDGE1_FR DNA
XX
AC   ;
XX
DT   28-JUL-1999 (Rel. 3.1, Created)
DT   09-AUG-1999 (Rel. 3.1, Last updated, Version 2)
XX
DE   BRIDGE1_FR is a non-LTR retrotransposon - a consensus
DE   sequence.
XX
KW   Non-LTR retrotransposon; LINE; BRIDGE superfamily; ORF1;
KW   ORF2; ORF3; reverse transcriptase; BRIDGE1_FR.
XX
OS   Fugu rubripes (consensus)
CC   consensus.
OC   Eukaryota; Metazoa; Chordata; Vertebrata; Actinopterygii;
OC   Neopterygii; Teleostei; Euteleostei; Acanthopterygii; Percomorpha;
OC   Tetraodontiformes; Tetraodontoidei; Tetraodontidae; Fugu.
XX
RN   [1]
RP   1-4209
RC   [1]  (bases 2713 to 4135)
RA   Kapitonov V.V., Jurka J.
RT   ;
RL   Direct submission (July, 1999)
XX
RN   [2]
RP   1-4209
RC   [2]  (bases 1 to 4209)
RA   Kapitonov V.V., Jurka J.
RT   ;
RL   Direct submission (August, 1999)
XX
CC   BRIDGE1_FR is a non-LTR retrotransposon that belongs to the
CC   BRIDGE superfamily. Its consensus sequence has been recovered
CC   from numerous (~120) GSS sequences. 
CC   BRIDGE1_FR is a young retrotransposon since its 
CC   copies are, on average, 95% identical with the consensus
CC   sequence. BRIDGE1_FR has three overlaped open reading frames:
CC   ORF1 (position 684-1556), ORF2 (1307-2512 or 1466-2512) and
CC   ORF3 (2455-4206). ORF3 encodes reverse transcriptase similar
CC   to these encoded by the Penelope non-LTR retrotransposon in 
CC   drosophila and BRIDGE2_FR in fugu.
XX
CC   [1] (Consensus)
XX
SQ   Sequence 4209 BP; 515 A; 239 C; 258 G; 418 T; 0 other;
     gggggaattg ggttcccccg cgtggcggcc gtttagaaat agtgttcccc cggggtgcag        60
     ggatttgata cccctaatct taccctaacc ctaaatccta acccaaagat taaatattac       120
     atttgatatc aaactaattt aatttggcat ttagggggtt aaaatggtag ggtgaaaaaa       180
     tgaaaaaaga aaaaacatcg cgtatatagt gttttttaaa aaaaagcgat gccacagcag       240
     acactatata agggactcga gttcgcaaaa agggaccatt tgcttttcaa ccagcgtatg       300
     gaacacatcg tccacagcca atacagcgag ccagcttttg gttatttagt gtgccctacc       360
     tgaagaagac ccataggggg tcgaaacgtc gttttttggc acactcttcc ttagttattt       420
     aatacattta ttgatttttg gttttatttt acttaccttt taagaaaagg gagaaattaa       480
     aagaaaaaaa tacttaccct taaaaaaata aaaaaaaaaa caaaataaac aaaaaaaaca       540
     ttaaaatact tacctttttc ctttcctatt ttttggaaag cgcttttatt tcaaaaaact       600
     ttctaaaata aataactttc ctattttttg gaaagcactt ttagttcaaa aaactttcta       660
     aaataaataa cttaccttga tttatggagc cgggttggac ggaggtgcgc tatggcaggg       720
     gtcgccagcg tgcccatcgt caacaacaag gatttcaggg ttatgggagg tcggttggga       780
     ggaaggaccg tgctttccct gtctcgtatg ggaggcaggg tacattcccc taccctatcc       840
     ggccagtgct tcctccacgg atcgcccatt accctgttcc tcaacagcgt acatatgcag       900
     cagtggttcg gcaagggtac ccgcaagcat cccaaagacg ggtgtttcca agggccagta       960
     ggccgggggt ccaataccaa taccaatacc aaccagctga cccccagttt gggaaactgg      1020
     tacgcaaact acattcagtg atcaaaacag tccaccacct acaaaatgtg gctccaaagg      1080
     aggggaaacc tgaaccccgg atgatttctc ggatggtgga tatcctgaca gatatgatta      1140
     agcctgctgc tcccacacag cgcacaaaag acttgatttc tgggaatgct aaaaattggg      1200
     gttataatac ctacctgatt ttgatggagc actacgaagc aaacctagca gaatatctgg      1260
     atgaagtatc tggcctcctc acgccagaat ggagggcagc ctttgaggtg gctgttcgtt      1320
     gggctcgacg aaacttacct cgtattacac gggacgagat agaccatgcc caggcattgg      1380
     taacagctcg agtggacact atggtcccgg cagtggttca ggtcccgcag cagaccacag      1440
     tcagtacaga cacgagggac ctggcatgtg ggcattcacc acgacagact gttgtcacag      1500
     ctgcaaccca gtgttgtgga cagtgtatag ctcaagtggt tctagggacg agatagaagg      1560
     aagggctgag actccattac agccgacaac caagagagcg gtcgttacta tgactgactc      1620
     tactggccag cattcggact ggcactttga tcccccatac gtagagcctc ctcgggagct      1680
     tagagtggga cgtaagtgcc taaggaagac caaacatttt gtcccaaatg aggacgactt      1740
     actacaggat gacccagaag atttgatggg gagggggaca cccgttggag acgccacact      1800
     cctggaccta agcggtcttt ttgtggaatc tcaaaatgag gaagctgagg tcgggaccgc      1860
     tagacacgag atggttgttc aggctccccg agggccctcc ttatttgagg aggatagctt      1920
     tgaggactcc ttcgaccatt tcgtagaggc gggccctcca atgtttcagg tgttgagaca      1980
     ccctaatacc caaaggaaat tgattgattg ggacttggtg gttagaaaga aatggttgat      2040
     cattggggat tcaaatctct gcagtttccc agattttgcc atcaagaacc tacagattga      2100
     tagttatcca ggggcccact tccgccatgc acaggctctt attgaaaaaa ctgaaccacc      2160
     tttagatttg gtagtggaaa agattgtact gtcctttggg atcaacagta gggggaatag      2220
     ctcgaaggga actacggtaa aaaacgtcca ggctgccctt cgggttgcaa agaaaaaatt      2280
     tccctatgca gagatgtggg ttcctctgct caatttctcg aataatcttc ctgaggagga      2340
     aagggagaac ctccaacttc tcaatcacca cctggagagg aacatgccct tcattcctct      2400
     tctgccggga agattctttc gcacagggac agataatgtt cattggacag ttgaaacagg      2460
     aagggctatg tttcaccatt ggatggagtt tttaaacttc accacccctt gagtctggaa      2520
     cagagaggga tagatggacc acagtcctct cattctcagg aagtggttgt tctagctaaa      2580
     aatttcaaac tttttagacc acaacaggac ctgttaagca aagggttgtc gttcattcct      2640
     tcttggaacg taggcaggga tcaaaaggta cagctccaat tggacattca aaattatcac      2700
     cgtaagatta aattggcaac ttattacaga gattcaacta aaaaactata ttcaaagttt      2760
     attggaacct cagattggac accaccattg ggggaattgc caccggtaat tggagaattg      2820
     attagaaaag atctggaaac atttaaaaat cattttattt cagtcaagga aaatctaaat      2880
     atttcattac cagaaataaa agcattacag gagctacaac ataaaaagaa tatagttatt      2940
     aaaccagcag acaaagggtc tgcaattgtc attctggacc gggaacaata tatttttgaa      3000
     gtagagcgac aacttaatga cacggaatat tataaaaagt tagaaaaacc aatttattta      3060
     gatacaattc ccatggtagc tacaatttta gacacattaa agagaaagaa attcatttgc      3120
     gaaaaacaaa ggaagtattt agttggggat gtagaaccta gggaaaggag attctatatt      3180
     cttcccaaaa ttcacaagga gccagaaaag tggacaattc catatgaact gcccccggga      3240
     aggccaatcg tctctgactg tgggagcgag acatatttca ctgcggaatt cttagatttt      3300
     tacctgaatc cgctgtccac aaaacatcct gcctttgtca gagacactta tcatttcata      3360
     gagattataa aaaccttgaa gattcctgca gattcctatt tcttctctat ggatgtggat      3420
     agtctatata ctaatatccc cattgaatct ggcatcaact gtattagaaa tatatttgaa      3480
     aaatatcctg accccaagag accagatgaa gagctcttac aattattaga aataaatttg      3540
     agcagaaatg atttcatatt taatggtaaa tactatttac aaaccaaagg aactgctatg      3600
     ggcaaaaggt ttgccccggc atatgcgaat attttcatgg caaactggga agaagaggca      3660
     ctattgaaat gtaaacataa accagctcac tatctacggt atttagatga tgtttgggga      3720
     atatggacag gatctgaact acagtttagg gaatttgttg agaccttaaa ttcccacgat      3780
     ccctctatta aacttaaaac agaaattaat aaacattcaa ttaatttttt agatacaaca      3840
     gttttcaaag ggccagattt tctaaaaact gccaaattgg acattaaagt atattttaaa      3900
     agcactgata cccatgcatt gcttcataaa acaagttttc atccaaaaca tacatttaaa      3960
     ggcatagtaa aatctcaaat tattagattt aagcgaattt gcacaaggga tgaggaattc      4020
     aaggaagcag taaatgtttt atttaaggcc cttcgtaaaa gagggtattc caaacccttt      4080
     ttgaaacact gctttaaatc tgttcaaaaa agaaaaaatg ggggagatcg tggggatttg      4140
     atccctctta ttacaacata ttcttcggtt aataaatctc taaacatagg tttgaaaaca      4200
     atttgaaaa                                                              4209
//
ID   BRIDGE2_FR repbase; DNA; VRT; 618 BP.
CC   BRIDGE2_FR DNA
XX
AC   ;
XX
DT   28-JUL-1999 (Rel. 3.1, Created)
DT   28-JUL-1999 (Rel. 3.1, Last updated, Version 1)
XX
DE   BRIDGE2_FR is a non-LTR retrotransposon - an incomplete consensus
DE   sequence.
XX
KW   Non-LTR retrotransposon; LINE; BRIDGE superfamily; ORF1;
KW   reverse transcriptase; BRIDGE2_FR.
XX
OS   Fugu rubripes (consensus)
CC   consensus.
OC   Eukaryota; Metazoa; Chordata; Vertebrata; Actinopterygii;
OC   Neopterygii; Teleostei; Euteleostei; Acanthopterygii; Percomorpha;
OC   Tetraodontiformes; Tetraodontoidei; Tetraodontidae; Fugu.
XX
RN   [1]
RP   1-618
RC   [1]  (bases 1 to 618)
RA   Kapitonov V.V., Jurka J.
RT   ;
RL   Direct submission (July, 1999)
XX
CC   BRIDGE2_FR is a non-LTR retrotransposon that belongs to the
CC   BRIDGE superfamily. Its consensus sequence has been recovered
CC   from numerous GSS sequences. The consensus sequence can
CC   be expanded when additional DNA from the fugu genomae will be
CC   available. BRIDGE2_FR is a young retrotransposon since its 
CC   copies are, on average, 92% identical with the consensus
CC   sequence. BRIDGE1_FR and BRIDGE2_FR are significantly
CC   similar on the protein level only.
XX
CC   [1] (Consensus)
XX
SQ   Sequence 618 BP; 181 A; 157 C; 154 G; 125 T; 1 other;
     atcttacaga aagaacaacc ttaacaccgg cccaaatctg caccatgctg gacctgtgtt        60
     tgaacaccac ctatttccaa tacagagaag gcttctacag gcagaaacat ggctgtgcca       120
     tgggctcacc agtatccccc atagttgcca atctatacat ggagaaggtg gaatcccagg       180
     ccctgacatc cttcacagga actgcgccaa gccactggtt caggtatgtg gatgacacct       240
     gggtcaaaat tcaaacacaa gaattggaag cgttctccga tcacctcaac aaaacagacg       300
     agcatgtaaa attcacccgg gaagaggtaa aaggaaacag tctggccttt ctggactgcg       360
     cagtcaagat cactgaggac agaaatcagt agtcagaaac acagtctgtc agtccatcca       420
     ggtcctcacc atgtggttca cagagagcag accagttggt ggtctccagg gcatcccgca       480
     gacagtccat ggcaccatct gaccatttcc taacagtcct cacagtgact gattgctgct       540
     gaaccacagg tgtgtatgat ggggagggca gmaggagatt atgatcagac ttgcggagcg       600
     gagggagtgc agtggaag                                                     618
//
ID   CR1POL    repbase; DNA; VRT; 2232 BP.
CC   CR1POL DNA
XX
AC   L22152;
XX
DT   10-APR-1997 (Rel. 3.0, Created)
DT   10-APR-1997 (Rel. 3.0, Last updated, Version 1)
XX
DE   Gallus gallus reverse transcriptase gene, 3' end.
XX
KW   POL-like gene; LINE; CR1.
XX
OS   Gallus gallus
CC   Gallus gallus (strain White Leghorn, sub_species domesticus) DNA.
OC   Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata;
OC   Vertebrata; Archosauria; Aves; Neognathae; Galliformes;
OC   Phasianidae; Phasianinae; Gallus.
XX
RN   [1]
RP   1-2232
RC   [1]  (bases 1 to 2232)
RA   Burch J.B.E., Davis D.L., Haas N.B.;
RT   "Chicken repeat 1 elements contain a pol-like open reading frame and
RT   belong to the non-long terminal repeat class of retrotransposons";
RL   Proc. Natl. Acad. Sci. U.S.A. 90, 8199-8203 (1993)
RX   MEDLINE; 93376771.
XX
CC   3' part of LINE element, pol-like region.    
CC   Parts of CR1POL are also listed as CR1_GG and CAM1_GG.
CC   1326-1713 CR1POL is similar to 1-379 CAM1_GG (73%);
CC   1714-2230 CR1POL is similar to 1-501 CR1_GG (73%).
XX
DR   GENBANK; L22152; 97.0.
CC   Positions       1    2232  Accession No L22152        GenBank (rel. 97.0)
XX
SQ   Sequence 2232 BP; 575 A; 484 C; 710 G; 463 T; 0 other;
     tcgagggatg tgggcctggc aaatggtggg gtcaggaccc tgaactttgg aagagagaac        60
     tttaagctgt tcaatggatc gttagccatg atcccctgga atgctgtcat taaagataaa       120
     gatgttgagg agagctggct actcttcaag gatgccctcc tgaaagcaca agaggtctcc       180
     atccctctga ataggaaagt gggcagacga gataggaaac cagcatggct cggcaaggac       240
     ctgctgggca cactgagggt gaagaaaggt gcgtacaagc tctggaaaca agggcgtgtc       300
     acctgggaag agtacaggga tgctgtccgg acttgcagac gtaggatcag gaaagccaag       360
     gcgcaggtag aactgaactt agcgagggat gtgaaaaaca ataagaagac attctacagg       420
     tacattggcc agaaaagaca gaccaaaaca ggtgtacctt ctttagtaaa cttaaaagga       480
     gaactggctt caacggatga agagaaagcg gaggtactga atgagttctt tgcctcagtc       540
     ttcactggag gccaggattc cagtctttct cacgtccctg agccctgcac ccccaagcct       600
     ccaggtgggg accagggggg taaatccccc cccacactaa gggcagagca agtccgagac       660
     cgcctcatga gactggatga gtacaagtct tcagggccgg atggtgtgca tcccagggtt       720
     ctgaaggagc tggctgaggt ggttgctgag ccactctcca tcatatttga gaagtcatgg       780
     ctgtcaggcg aggtcccaga tgactggagg aagggttacg tcactcccat ttacaagaaa       840
     gggagcaagg aggacccagg gaactacagg ccggtgagtc tcacctctgt gcctgggaag       900
     atcatggaac agatcctcct ggatgacatg ctcgatcaca tgaggaatga gcgtgtgatc       960
     cgagacagcc agcacggctt caccagggga aggtcatgct taaccaatct tgtggccttc      1020
     tatgatggag tgacggcgtt ggtggatgag gggaaggcga ccgatgtcat ttacctggac      1080
     ttgaccaagg cctttgacat ggtcccccac cacatcctta tctccaaatt ggagggatgt      1140
     ggatttgatg ggtggaccac tcattggata agaaattggt tgaaaggccg cagacagagg      1200
     gtggtgacca atggctctat gtccaggtgg aggccggtaa tgagcggagt cccccagggg      1260
     tctgtcttgg gaccggtgct ctttaacatc tttatcaatg acattgacga tggaatcgag      1320
     tgcaccctca gcaaatttgc tgacgacacc aaactgagtg gtgcggttga cacggaggaa      1380
     ggaagggatg ccattcagag ggaccttgac agacttgaaa ggtgggcccg ggtgaaccta      1440
     atgaggttca acacggcaaa gtgcagggtt ttgcacttgg gctggaggaa ccccaggcat      1500
     ctatacagac tggaaggagc agtccttgag agcagctctg cagagaagga cctgggggtc      1560
     ctgatggatg acaaacttaa catgagccag cagtgtgctc ttgcagctca gaaagcaaat      1620
     ggtatcctgg gctccatcat gagaggggtg gccagcaggg acagggaggt gattgtccct      1680
     ctctactctg ctcttgtgag gccccatctg gagtactgtg tccaggtatg gaggccccag      1740
     tacaagaaag acagagagct gttggagagg gtccagagga gggccacaaa gatgatcagg      1800
     gggctggagc acctccccta cgaggacagg ctgagggagc tgggcttatt cagcctggag      1860
     aagagaaggc tgcgcggtga cctcattgca gcctttcagt acctgaaggg agcctataaa      1920
     caggaaggga gtaaactctt tgaaagggta gataacagca ggacaagggg gaacggtttt      1980
     aagttgaaag agggaagatt taggttggat gttaggggga agttctttac caggagagtg      2040
     gtgaggtgct ggaacaggct gcccagagag gttgtggatg ctctgtccct ggaggtgttc      2100
     aaggccaggt tggatggggc cctgggcaac ctggtctagt aaatggggat gttggtggcc      2160
     ctgcccagca ggggggttgg agattcgtga tcctcgaggt cccttccaac ccaggccatt      2220
     ctgtgattct gt                                                          2232
//
ID   CR1_GG    repbase; DNA; VRT; 555 BP.
CC   CR1_GG DNA
XX
AC   M17963;
XX
DT   22-DEC-1995 (Rel. 2.0, Created)
DT   26-MAR-1997 (Rel. 3.0, Last updated, Version 2)
XX
DE   Chicken CR1 repetitive sequence.
XX
KW   CR1 repetitive sequence; GGCR1.
XX
OS   Gallus gallus
CC   Chicken (hen) amplified cosmid chicken library DNA, clone CR1 OMb.
OC   Eukaryota; Animalia; Chordata; Vertebrata; Aves; Neornithes;
OC   Neognathae; Galliformes; Phasianidae.
XX
RN   [1]
RP   1-555
RC   [1]  (bases 1 to 555)
RA   Scott M.J., Tsai M.-J., O'Malley B.W.;
RT   "Deoxyribonuclease I sensitivity of the ovomucoid-ovoinhibitor gene
RT   complex in oviduct nuclei and relative location of CR1 repetitive
RT   sequences";
RL   Biochemistry 26, 6831-6840 (1987)
XX
DR   GENBANK; M17963; 77.0.
CC   Positions       1     555  Accession No M17963        GenBank (rel. 77.0)
XX
SQ   Sequence 555 BP; 139 A; 114 C; 179 G; 123 T; 0 other;
     tattgcatcc aggcctgggg cccagcatga gaaagatgtg gaactgttgg agtgggtcca        60
     taggaggcca tgaagacaat cacagggctg gagcacctct cttatgacga aaggctgagg       120
     gagctgggct tgttcagcat caagaaggga aagctgagag gacacctcat tggagtcttc       180
     cagtacttga agggagcttg caagcaggaa ggggaacaaa cttctacatg gtctgaacag       240
     agatagacaa gggggagtgg ctttaagcta aaaagaggga agatttgggt gagatgttgg       300
     gaagaaatac tttactcaga ggttggtgtg acactggcac tgctgcccag agctgtgggt       360
     gccccatccc tgtacatgag ctgaaggcca gattggatgg ggctctgtgc agcctgatct       420
     ggtgggggca gccagcccat ggcaggggtt ggggtagatg ggttgtatgg cccttttcaa       480
     cccaaaccat tcaatgattc tatgattctc agataagcct gcctgcccat atctgagctc       540
     acggtgctcg ctggg                                                        555
//
ID   TC1L_SS   repbase; DNA; VRT; 1555 BP.
CC   TC1L_SS DNA
XX
AC   L12206;
XX
DT   20-JUL-1999 (Rel. 3.0, Created)
DT   20-JUL-1999 (Rel. 3.0, Last updated, Version 1)
XX
DE   Tc1-like DNA transposon (inactive).
XX
KW   pseudogene; transposase; transposon; TC1L_SS.
XX
OS   Salmo salar
CC   Salmo salar adult liver DNA.
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Actinopterygii;
OC   Neopterygii; Teleostei; Euteleostei; Protacanthopterygii;
OC   Salmoniformes; Salmonidae; Salmo.
XX
RN   [1]
RP   1-1555
RC   [1]  (bases 1 to 3243)
RA   Radice A.R., Bugaj B., Fitch D.H.A., Emmons S.W.;
RT   "Ancient origin of the Tc1 transposon family";
RL   Unpublished (1993)
XX
CC   Similar to SSNHEI, and distantly to TC1_XL, TZF28 and TXZ19.
XX
DR   GENBANK; L12206; 110.0.
CC   Positions    1545    3099  Accession No L12206       GenBank (rel. 110.0)
XX
SQ   Sequence 1555 BP; 523 A; 297 C; 334 G; 401 T; 0 other;
     aactatagtt tttggcaagt cggtttggac atctactttg tgcatgacac aagtaatttt        60
     tttcaacaat tgtttacaga cagattattt cacttacaat tcactgtatc acaattccag       120
     tgggtcagaa gtttacatgt actaagttga atgtgcattt aaacagcttg gacaattcca       180
     gaaaatgatg tcatggcttt agaagcctct gataggctaa ttgacataat ttgagtcaat       240
     tggaggtgta cctgtggatg tatgtcaagg cctaccttca aactcagtgc ctctttgatt       300
     gacatcatgg gaaaatcaaa agaaatcagc caagacctca gaaaaaaaat tgtagacctc       360
     cacaagtttg gttcatcctt gggagcaaat tccaaacacc tgaaagtacc acgttcatct       420
     gtacaaacaa tagtacgcaa gtataaacac catgggacct cgcagccatc ataccgctca       480
     ggaagacgcg ttctgtctcc tagagatgaa cgtagtttgg tgtgaaaagt gcaaatcaat       540
     cccagaacaa cagcaaagga tcttgtgaag attctggagg aaacaggtac aaaagtatct       600
     ttatccacag taaaaaggtc ctatatcgac ataacctgag aggccgctca gcaaggaaga       660
     agctactgct ccaaaaccca cataaaaaag ccagactacg gtttgcaact gcacatgggg       720
     acaaagattg tactttttgg agaaatgtcc tctggtctga tgaaacaaaa atagaactgt       780
     ttggccataa tgaccattgt tatgtttgga ggaaaaaggg ggagacttgc aagccgaaga       840
     acaccatcct aaacatgaag cacgggggtg gcagcatcct gttgtggggg tgctttgctg       900
     caggagggac tggtgcactt cacaaaatag atggcatcat gaggaagaaa aatgatgtgg       960
     atatattgaa gcaacatctc aagacatcag tcaggaagtt aaagcttggt cgcaaatggg      1020
     tcttccaaat ggacaatgac cccaagtata cttccaaaga tgtggcaaaa tggcttaagg      1080
     acaacaaagt caaggtattg gagtggccat cacaaagccc tgacctcaat cctatagaac      1140
     atttgtgggc agaactgaaa aagcgtgtgc gagccaggag gcctacaaac ctgattcagt      1200
     tacaccagct ctgtcaggag gaatgggcca aaattcaccc aacttattgt gggaagcttg      1260
     tggaaggcta cctgaaacgt ttgacccaag ttaaacaatt taaaggcaat tctaccaatt      1320
     actagttgag tgtatgtaaa cttcttaccc accgggaatg tgatgaaaga aataaaagct      1380
     gaaataaata attctctcta ctattattct gacatttcac attcttaaaa taaagtggtg      1440
     atcctaactg acctaaaaca gggaattttt actaggatta aatgtcagga attgtgaaaa      1500
     actgagttta aatgtatttg gctaaggtgt atgtaaactt ccactttcaa atgta           1555
//
ID   TOL-TYR   repbase; DNA; VRT; 1855 BP.
CC   TOL-TYR DNA
XX
AC   D42062;
XX
DE   DNA transposon Tol-tyr.
XX
KW   DNA transposon Tol-tyr.
XX
OS   Oryzias latipes
CC   Oryzias latipes DNA.
OC   Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata;
OC   Vertebrata; Actinopterygii; Neopterygii; Teleostei; Euteleostei;
OC   Acanthopterygii; Atherinomorpha; Cyprinodontiformes;
OC   Adrianichthyoidei; Adrianichthyidae; Oryziinae; Oryzias.
XX
RN   [1]
RP   1-1855
RC   [1]  (bases 1 to 1855)
RA   Hori H.
RT   ;
RL   Unpublished (1996)
XX
RN   [2]
RP   1-1855
RC   [2]  (bases 1 to 1855)
RA   Hori H.;
RT   "Direct Submission";
RL   Submitted (08-NOV-1994) to the DDBJ/EMBL/GenBank databases. Hiroshi
RL   Hori, Nagoya University, Division of Biological Science; Furo-cho,
RL   Chikusa-ku, Nagoya, Aichi 464-01, Japan
RL   (E-mail:hori@bio.nagoya-u.ac.jp, Tel:052-789-2504,
RL   Fax:052-789-2974)
XX
DR   GENBANK; D42062; 105.0.
CC   Positions       1    1855  Accession No D42062       GenBank (rel. 105.0)
XX
SQ   Sequence 1855 BP; 534 A; 315 C; 432 G; 574 T; 0 other;
     cagtagcggt tctaggcacg ggccgtccgg gcggtggcct ggggcggaaa actgaagggg        60
     ggcggcaccg gcggctcagc cctttgtaat atattaatat gcaccactat tggtttactt       120
     atgtcacagt ttgtaagttt gtaacagcct gaacctggcc gcgccgccgc cctcgccccg       180
     cagctgcgct ctcctgtctt tgagaagtag acacaaatgt gtgtgaagaa ggagaaggga       240
     gggggcgcgg ggtgagcacg gagcgtcgcc gcgtttgcgc atgcgcaaaa cctggctggc       300
     tcatctttca ggggaggcga cggtcgcggg cttgatgaaa aaaataaaag taaaaactgc       360
     gactgcgccg tcatgtagcg aatcagcgcc cctggctgta gctgcacgcg ctcctgctgg       420
     aaatgtgtga agaggggggg gggggggggg gctgcgggga atcagttcaa ttgtgggacg       480
     cttccaaatt aagtggctag gtggggacaa gggcgggggt ttgaatctac ttcataaaac       540
     ctttttatat tataagtcag tcataaggtg acattctata acctacattt taataaaggt       600
     ataaaaaata tattctgctt tttttgggtt aattttgtgt gaaatgtcca aataaaaaaa       660
     atggcaacac aaaacaatgc tgtcactaag gtgacagttg gttcagtcga cggacttgat       720
     gccttcttcg tgacgtgagg acatttatgc caaacaaacg ccaataaaca tctaaaatat       780
     ggaaaagaaa aggtcaaagc catctggtgc ccaatttaga aagaaaagaa aagaagaaga       840
     ggagaaaaga gataaagaaa agggtaagtc ctcacagctt gatgcatgtt ttttctaaat       900
     tctaatgcta cctgccctac aacaacgttg ccgatgaaaa ctttattttg gtcgatgacc       960
     aacactgaat taggcccaaa tgttgcaaat agcgtcattt tttttttttt ttttagattt      1020
     tattcttaaa aatttgctct gccttaactt gtaacattag ttatgattca tgtgtctgtc      1080
     tgctctgctg taacacaaag gttttgttgg gttttgctgt tgtatactag ctcataatgt      1140
     taaaaaagct gtgatggtta cacagcatgc tggtgctgcc ataagatgct aatggggcaa      1200
     ataatttgag attggtcatt aatttaataa tcatttgtgg cagcctaaac gttttcacaa      1260
     tgtttttttg acatttaact ggggatttag gggttaattt tgagcctgca tatgaagttt      1320
     attttttatt tgttttacaa atgtgggatt atatttttag ccaatagaat ttccataaat      1380
     ctgtaggtag ttttaaaaat gaatatttac catttactgc aactctatgg ggacaaaaca      1440
     taatgtaaca ggtcataact aaaaatgtgc caatcaaagg attgaagacg gaaaacatga      1500
     gttaattttt cttctctgaa gtagagatcg atatagaaca tgacaattta aatttccaat      1560
     tcataaatgt ttttaaaata tttattttat attatttatt taacattgag tttgattcaa      1620
     tattttctta gctaactgta tttttgccat gcttatggtc ttttattttt tgtgttctga      1680
     taacttttat aatgcttttc agaattttga catcttttgt atccacttct taatttcaat      1740
     gacaataaaa catttcagtt gacgaagaca aacaaagttc tgttgtgact atgggggggg      1800
     ggggcgcctg gggatggtct cgcccgggga gtaattcagg gtagaaccgc cactg           1855
//
ID   SINE_HE1  repbase; DNA; VRT; 364 BP.
CC   SINE_HE1 DNA
XX
AC   ;
XX
DT   29-OCT-2001 (Rel. 4.0, Created)
DT   29-OCT-2001 (Rel. 4.0, Last updated, Version 1)
XX
DE   Heterodontus japonicus HE1 SINE - a consensus.
XX
KW   SINE_HE1.
XX
OS   Heterodontus japonicus (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Chondrichthyes;
OC   Elasmobranchii; Galeomorphii; Heterodontoidea; Heterodontiformes;
OC   Heterodontidae; Heterodontus.
XX
RN   [1]
RP   1-364
RC   [1]
RA   Ogiwara I., Miya M., Ohshima K., Okada N.;
RT   "Retropositional parasitism of SINEs on LINEs: identification of
RT   SINEs and LINEs in elasmobranchs";
RL   Mol. Biol. Evol. 16 (9), 1238-1250 (1999)
XX
CC   [1] (Consensus)
XX
SQ   Sequence 364 BP; 83 A; 70 C; 112 G; 93 T; 6 other;
     gagggcggca cagtggcgca gtggttagca ccgcagcctc acagctccag cgacccgggt        60
     tcaattctgg gtactgcctg tgtggagttt gcaagttctc cctgtgtctg cgtgggtttc       120
     ctccgggtgc tccggtttcc tcccacawgc caaaagactt gcaggttgat aggtaaattg       180
     gccattataa nattgycact agtataggta ggtggtaggg aaatataggg acaggtgggg       240
     aatgtggtag saatatggga ttagtgtagg attagtataa atgggtggtt gatggtcggc       300
     acagactcgg tgggccgaag ggcctgnttc agtgctgtat ctctaaacta aactaaacta       360
     awat                                                                    364
//
ID   Merlin1_CI repbase; DNA; VRT; 1791 BP.
CC   Merlin1_CI DNA
XX
AC   ;
XX
DT   16-JUN-2003 (Rel. 4.01, Created)
DT   16-JUN-2003 (Rel. 4.01, Last updated, Version 1)
XX
DE   DNA transposon Merlin1_CI - a consensus.
XX
KW   DNA transposon, Merlin/IS1016 superfamily; 9-bp TSD; Merlin1m_CI;
KW   Merlin1_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-1791
RC   [1]  (bases 1 to 1791)
RA   Feschotte C., Wessler S.R.;
RT   "Merlin1_CI, a family of Merlin/IS1016-like
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(5) p. 93 (2003)
XX
CC   The Merlin1_CI family is one of the founding members of a new 
CC   superfamily of eukaryotic DNA transposons related to the IS1016 
CC   group of bacterial insertion sequences. There are at least 3 copies 
CC   of Merlin1_CI containing large ORFs in the C. intestinalis draft 
CC   genome sequence (WGS assembly 1.0, 116.7 Mb). The sequence below 
CC   is a consensus constructed from these 3 copies. Merlin1_CI has been
CC   recently active because the three copies are ~94-98% similar to the 
CC   consensus. Merlin1_CI are related and have probably provided the 
CC   transposase to a large family of nonautonomous elements (Merlin1m_CI, 
CC   see description in RR). The Merlin1_CI consensus sequence is 1791-bp 
CC   long with 155-bp TIRs (8 mismatches). It contains one predicted gene 
CC   (positions 518-1435), which can encode a 273-aa protein, Merlin1_CIp. 
CC   The C-terminal half of this protein has strong similarity with the 
CC   putative transposases of IS1016 from Haemophilus influenzae (and 
CC   related IS) and with ORFs from a wide range of eukaryotes, including 
CC   other ascidians (annotated transposase, GenBank AAM76104), nematodes, 
CC   flat worms, mosquito (described previosly in the AF293351 GenBank locus
CC   as an IS1016-like insertion), zebrafish, Xenopus and humans. Many of 
CC   these ORFs are clearly parts of transposable elements. 
CC   Multiple alignments reveal that the most conserved domain 
CC   of these proteins contains a putative DDE motif  (D(60)D(36)E in 
CC   Merlin1_CIp). A HTH DNA-binding domain is predicted in the N-terminal 
CC   region of Merlin1_CIp. Thus, this protein is likely to represent the 
CC   Merlin1_CI transposase. Merlin1_CI elements create a 9-bp TSD upon 
CC   insertion, unlike most other members of the Merlin/IS1016, which 
CC   create an 8-bp TSD. There may be other lineages of Merlin transposases 
CC   in Ciona intestinalis. 
CC   
CC   Putative Merlin1_CIp transposase: 
CC   MQKDFEGENSESLPCIRCKSCGTYVSPRKNSFFAFMDNRNRANVKISYKQVMAILINWVQRVPVGTTQQ
CC   NYGFGAHTVTDWYNFCREMCMLGFSKREPMGGPNTIVEIDESLLRGKRKYNRAGIEGPWIFGMCHVTVD
CC   SEGARSTQEVRFFHVLRRDKQTLLPIIQNEVLPSTTIHSDQWAAYTGLDQLGYSHQSVNHSENFIDPQT
CC   GAHTQTIESTWHHMKTTLLRNMRGVEPELLDSYLAELWARKLYRDHAALLEKLFDWIVEAYPIRNI
XX
CC   [1] (Consensus)
XX
SQ   Sequence 1791 BP; 504 A; 380 C; 393 G; 508 T; 6 other;
     ggtaatcctg ccgctggtga ccagtgaaaa ttttggtctc aaaatgttcc ttacgtctct        60
     ctgatactcg ctgtatatat ttaaaaaaaa caaactcggg cgttcgtatc gaaaattaac       120
     tttgaaaatc cgcgaaaaac tgctgcgtca ccgtactcgc ctgtgctgaa caaaatcaac       180
     gaatatatgg ttacattatg acgtcacata gtagttacgt caaaatgatg gaaaatccgt       240
     tctgttacgt cataatacaa ccctaaatat atataccggt ccacgtgttg cgaaactcct       300
     ttttttgctc aaaattttaa cttgtactct ataacgatgg cattttttcc acacatgcaa       360
     gccattattg cggatgcaga caaattacaa ggttacttac tagaaaaaaa tcttatacgg       420
     ggtccatctt cttttgatcg atgcccgaac cgaagttgtc gcaagagtat actcttgttt       480
     ggggtagccg gcggagaccc ctgaacgcag caagctcatg caaaaagatt ttgagggcga       540
     gaactcagaa tctttgccgt gtattcgatg caaatcttgc ggcacgtatg tttccccgag       600
     aaaaaattca ttttttgcct ttatggataa ccggaaccgt gccaatgtta aaatcagcta       660
     taagcaggtt atggccattt taattaactg ggtgcaacgg gtacccgtcg gcacaacgca       720
     acagaactat ggttttggcg cacacacagt tactgattgg tataatttct gtcgagaaat       780
     gtgcatgctg ggatttagca agagagagcc catgggaggt ccaaacacga tcgtggaaat       840
     tgatgagtct cttcttcggg gcaagaggaa gtataaccgt ggcaggttac ttcgtggtga       900
     cgtccgagaa gacgatgtca atgacacgga cgatgaggac ctggtcgcgc atgtatctga       960
     cgcccgcaat tacggttcca ggatcgaagg accatggatt tttgggatgt gtcatgtcac      1020
     cgtcgactcg gaaggggcaa ggtctacaca agaagtgcgt ttttttcacg ttttaaggcg      1080
     tgataaacag accttgctcc caatcattca aaacgaagtc ctccccagta ccaccataca      1140
     ctccgatcaa tgggcagctt acactggatt ggaccagctc gggtattcgc accagtctgt      1200
     caatcacagc gagaacttca ttgatccgca gactggcgca cacacacaga ccattgagtc      1260
     cacgtggcac cacatgaaga cgacactact ccgcaatatg cgaggtgttg agcctgagtt      1320
     actggattcc tatttggcag agctttgggc aagaaagttg taccgcgacc acgccgcatt      1380
     attggagaag ctttttgact ggatcgttga agcttatccg atccgcaata tttaattttt      1440
     ttatttattt tttttatttt gaacagttct ttttagagct acgagccttc gggttcactt      1500
     ttaaacaagt atttatgaaa taagattagt tatttgcgct akttcacgca ataagacaag      1560
     ttttctattg tgacgtcata gttgtattgt gacgttaaaa acbgcctttt acttataggt      1620
     aaacaatatg gcgcatgcaa ttacggtgac gcagcagttt ttcgcagatt ttcaaagtta      1680
     attttcgata cgaacgcccg agtttttttt aaaatataca gcgagtatcw gggagwcgta      1740
     agraayattt tgagaccaaa attttcactg gtcaccagcg gcaggattac c               1791
//
ID   Merlin1m_CI repbase; DNA; VRT; 605 BP.
CC   Merlin1m_CI DNA
XX
AC   ;
XX
DT   16-JUN-2003 (Rel. 4.01, Created)
DT   16-JUN-2003 (Rel. 4.01, Last updated, Version 1)
XX
DE   Nonautonomous DNA transposon Merlin1m_CI - a consensus.
XX
KW   Nonautonomous DNA transposon, Merlin/IS1016 superfamily; 9-bp TSD; 
KW   Merlin1_CI; Merlin1m_CI.
XX
OS   Ciona intestinalis (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona;
OC   Phlebobranchia; Cionidae; Ciona.
XX
RN   [1]
RP   1-605
RC   [1]  (bases 1 to 605)
RA   Feschotte C., Wessler S.R.;
RT   "Merlin1m_CI, a family of nonautonomous Merlin/IS1016-like
RT   DNA transposons from the sea squirt Ciona intestinalis";
RL   Repbase Reports 3:(5) p. 96 (2003)
XX
CC   Merlin1m_CI is a family of nonautonomous elements related to the 
CC   Merlin1_CI family. There are ~250 Merlin_Ci1m elements in the C. 
CC   intestinalis draft genome sequence (WGS assembly 1.0, 116.7 Mb). 
CC   The sequence below is a consensus constructed from 20 copies 
CC   extracted from the database. Elements can be grouped into subfamilies
CC   that range in size from 400 to 700 bp and have 90-99% similarity to 
CC   the consensus. Some subfamilies have recently expanded because 
CC   they are very homogeneous in length and sequence. The Merlin1m_CI 
CC   consensus sequence is 605-bp long with 155-bp TIRs (5 mismatches). 
CC   The TIRs are almost identical to those of the Merlin_Ci1 consensus, 
CC   but the internal 295 bp are of unknown origin. Like Merlin1_CI, 
CC   Merlin1m_CI elements create a 9-bp TSD upon insertion. 
XX
CC   [1] (Consensus)
XX
SQ   Sequence 605 BP; 170 A; 109 C; 132 G; 184 T; 10 other;
     ggtaatactg ccgctggtga ccagtgaaaa ttttggtctc aaaatgttcc ttacgtctcc        60
     ctgatactcg ctgtataatt ttttttwaaa aaactcgggc gttcgtatcg aaaattaact       120
     ttgaaaatgc gcgaaatcgt gctgcgtcac cgtattttcc acacgagccg tcaaaggtta       180
     gattatkacg tcatagaatg cgtattacma cctttgattt cwacgttaca gattacgtaa       240
     tttgttagtt tttttrgatt tagrggttrs gggttaaamg taggggttag ggttgggtta       300
     agggttaggg cttggggttt tccctagcat aaaacagtgc gaaaaacaag attataacgt       360
     gctgtaacgt acgtaatatg tcactactgt gacgtaacat atcgctattg tgacgtaata       420
     aatcgttaac cttacgcaag tcaggcgaat tacggtgacg cagcacgttt tcgcgcattt       480
     tcaaagttaa ttttcgacac gaacgcccga gttttttcwa aaaaaaatta tacagcgggt       540
     atcagggaga cgtaaggaac attttgagac caaaattttc actggtcacc agcggcagta       600
     ttacc                                                                   605
//
