CC ****************************************************************
CC                                                                *
CC   REPBASE UPDATE                                               *
CC   (C) 1997-1999  Genetic Information Research Institute        *
CC   All rights reserved                                          *
CC                                                                *
CC   A REFERENCE COLLECTION OF ZEBRA FISH REPETITIVE SEQUENCES    *
CC   RELEASE 4.0.0; OCTOBER 1999                                  *
CC                                                                *
CC   This release was supported in part by U.S.                   *
CC   Department of Energy grant DE-FG0395ER62139                  *
CC   and by N.I.H. grant 1P41LM06252-01.                          *
CC                                                                *
CC ****************************************************************
XX
ID   BRSATI    repbase; DNA; ZEB; 186 BP.
CC   BRSATI DNA
XX
AC   M89944;
XX
DT   22-DEC-1995 (Rel. 2.0, Created)
DT   22-DEC-1995 (Rel. 2.0, Last updated, Version 1)
XX
DE   Zebrafish satellite type I DNA.
XX
KW   Repetitive DNA; satellite type I; BRSATI.
XX
OS   Brachydanio rerio
CC   Brachydanio rerio (strain Oregon AB) (library: lambda ZAP) DNA.
OC   Eukaryota; Animalia; Chordata; Vertebrata; Osteichthyes;
OC   Actinopterygii; Cypriniformes; Cyprinoidei; Cyprinidae.
XX
RN   [1]
RP   1-186
RC   [1]  (bases 1 to 190)
RA   Ekker M., Fritz A., Westerfield M.;
RT   "Identification of two families of satellite-like repetitive DNA
RT   sequences from the sebrafish (Brachydanio rerio)";
RL   Genomics 13, 1169-1173 (1992)
XX
DR   GENBANK; M89944; 77.0.
CC   Positions       1     186  Accession No M89944        GenBank (rel. 77.0)
XX
SQ   Sequence 186 BP; 56 A; 36 C; 30 G; 64 T; 0 other;
     gatccagcca taaaatgcat cattcttttt tgttttagac aacatttcat gcactgttaa        60
     acatgttaaa gcaagttgca agtgaaaatc tatgtctctg actgagtttg cattactgtg       120
     atttgacctc tctgctggct gagataagct cattttcaac gtccaattca gaatgtaata       180
     aaacct                                                                  186
//
ID   DANA      repbase; DNA; ZEB; 394 BP.
CC   DANA DNA
XX
AC   L42295;
XX
DT   22-DEC-1995 (Rel. 2.0, Created)
DT   22-DEC-1995 (Rel. 2.0, Last updated, Version 1)
XX
DE   Danio rerio (clone DANA-m1) DANA retroposon.
XX
KW   SINE; microsatellite; retroposon; repetitive element.
XX
OS   Danio rerio
CC   Danio rerio (clone: DANA-m1) (clone library: Jay White & Martin
CC   Petkovich's) 0-24h, mixed DNA.
OC   Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata;
OC   Vertebrata; Actinopterygii; Neopterygii; Teleostei; Euteleostei;
OC   Ostariophysi; Cypriniformes; Cyprinoidea; Cyprinidae; Rasborinae;
OC   Danio.
XX
RN   [1]
RP   1-394
RC   [1]  (bases 1 to 394)
RA   Izsvak Z., Ivics Z., Garcia-Estefania D., Fahrenkrug S.C.,
RA   Hackett P.B.;
RT   "DANA elements: a family of composite, tRNA-derived short
RT   interspersed DNA elements associated with mutational activities in
RT   zebrafish (Danio rerio)";
RL   Proc. Natl. Acad. Sci. U.S.A. 93 (3), 1077-1081 (1996)
RX   MEDLINE; 96165521.
XX
CC     misc_signal     1..64
CC                     /note="tRNA-related region"
CC     misc_signal     11..22
CC                     /note="Pol III promoter A box; putative"
CC     misc_feature    55..64
CC                     /note="Pol III promoter B box; putative"
CC     repeat_region   231..250
CC                     /note="TG dinucleotide"
CC                     /rpt_family="microsatellite"
CC     polyA_signal    368..373
CC                     /note="putative"
CC
CC   	DNA is the first SINE isolated from zebrafish (Danio rerio) exhibiting
CC   all the hallmarks of these tRNA-derived elements. DANA is unique in
CC   its clearly defined substructure of distinct cassettes. In contrast to
CC   generic SINE elements, DANA appears to have been assembled by
CC   insertions of short sequences into a progenitor, tRNA-derived element.
CC   Once associated with each other, these subunits were amplified as a
CC   new transposable element with such a remarkable success that
CC   DANA-related sequences comprise approximately 10% of the modern
CC   zebrafish genome. At least some of the sequences comprised by the
CC   full-length element were capable of movement, forming a new group of
CC   mobile, composite transposons, one of which caused an insertional
CC   mutation in the zebrafish no tail gene. Being present only in the
CC   genus Danio, and estimated to be as old as the genus itself, DANA may
CC   have played a role in Danio speciation by massive amplification and
CC   genome-wide dispersion. There are extensive DNA polymorphisms between
CC   zebrafish populations and strains detected by PCR amplification using
CC   primers specific to DANA, suggesting that the DANA element will be
CC   useful as a molecular tool for genetic and phylogenetic analyses.
XX
DR   GENBANK; L42295; 94.0.
CC   Positions       1     394  Accession No L42295        GenBank (rel. 94.0)
XX
SQ   Sequence 394 BP; 90 A; 81 C; 119 G; 104 T; 0 other;
     ggcgacgcag tggcgcagtg ggaagtgctg tcgcctcaca gcaagaagct cgctggttcg        60
     agcctcggtt aacaaggttt gaacgagcct cgctcagttg gcgtttctgt gtggagtttg       120
     catgttctcc ctgcgttcca tgggtttcct ccgggtgctc cgttccccca cagtcctaag       180
     gcatgtggta caggtgaatt gggtaggcta aattgtccgt agtgtatgag tgtgtgtgaa       240
     tgtgtgtgtg gatgtttccc agcgatgggt tgcggctgga aggcgatccg ctaaaactaa       300
     aaaaaaaact tgattaaaaa cttgctggat aagttggcgg ttcattccgc tgtggtgacc       360
     ctggattaat aaagggacta agccaaaaag aaaa                                   394
//
ID   DRSATII   repbase; DNA; ZEB; 173 BP.
CC   DRSATII DNA
XX
AC   ;
XX
DT   11-AUG-1999 (Rel. 3.1, Created)
DT   11-AUG-1999 (Rel. 3.1, Last updated, Version 1)
XX
DE   Zebrafish satellite type II DNA  - consensus.
XX
KW   repeat region; satellite type II; DRSATII.
XX
OS   Danio rerio (consensus)
CC   consensus
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Actinopterygii;
OC   Neopterygii; Teleostei; Euteleostei; Ostariophysi; Cypriniformes;
OC   Cyprinoidea; Cyprinidae; Rasborinae; Danio.
XX
RN   [1]
RP   1-173
RC   [1]
RA   Ekker M., Fritz A., Westerfield M.;
RT   "Identification of two families of satellite-like repetitive DNA
RT   sequences from the sebrafish (Brachydanio rerio)";
RL   Genomics 13, 1169-1173 (1992)
RX   MEDLINE; 92372011.
XX
RN   [2]
RP   1-173
RC   [2]  (bases 1 to 173)
RA   Jurka J.
RT   ;
RL   Direct submission (August, 1999)
XX
CC   [2] Consensus
XX
SQ   Sequence 173 BP; 61 A; 33 C; 17 G; 58 T; 4 other;
     aagcttcaaa tccaaattac aaatttacac tggattttgt atcccttcaa tgcttgtaaa        60
     gcatctattt gacatctatt tgwmwtctat ttgacatcca cacattgatg cctctttgac       120
     cachaaagaa accacacaaa aagtatcata atatataaag tttaattatt tga              173
//
ID   TZF28     repbase; DNA; ZEB; 1613 BP.
CC   TZF28 DNA
XX
AC   U51227;
XX
DT   10-APR-1997 (Rel. 3.0, Created)
DT   10-APR-1997 (Rel. 3.0, Last updated, Version 1)
XX
DE   Danio rerio transposon Tzf.28.
XX
KW   DNA transposon; TZF28.
XX
OS   Danio rerio (zebrafish)
CC   zebrafish.
OC   Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata;
OC   Vertebrata; Actinopterygii; Neopterygii; Teleostei; Euteleostei;
OC   Ostariophysi; Cypriniformes; Cyprinoidea; Cyprinidae; Rasborinae;
OC   Danio.
XX
RN   [1]
RP   1-1613
RC   [1]  (bases 1 to 1613)
RA   Lam W.L., Lee T.S., Gilbert W.;
RT   "Active Transposition in Zebrafish";
RL   Unpublished
XX
RN   [2]
RP   1-1613
RC   [2]  (bases 1 to 1613)
RA   Lam W.L., Lee T.S., Gilbert W.;
RT   "Direct Submission";
RL   Submitted (13-MAR-1996) Wan L. Lam, Molecular and Cellular Biology,
RL   Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
XX
DR   GENBANK; U51227; 97.0.
CC   Positions       1    1613  Accession No U51227        GenBank (rel. 97.0)
XX
SQ   Sequence 1613 BP; 531 A; 305 C; 337 G; 440 T; 0 other;
     tacagtgtat ccgcaaagta ttcatagcgc ttcacttttt ccacattttt tatgttacag        60
     ccttattcca attccaaaat ggattaaatt aatttatttc atcaacattc tacccacaat       120
     accccataat gacaatgtga aaaaaatttt tttttttaat tattgcataa aaaaaaaaaa       180
     gctgaaaaat cacatgtaca taagtattca cagcttttgc agtgaagcta aattgagctc       240
     aggtacgttc tgtttcaagt gttcattctt gaaatgtttc agacaggtta attggaattt       300
     cacctgtggt aaattaagtt gatttggaca tgatttgaaa aggcatacac ctgtctatat       360
     aaggtcccag ggttgacagt gcatgtcaaa gcacaaacca aacatgaaga caaaggaatt       420
     gtctgcagac ctccgataca ggattgtcgt caaggcacaa ggctggggaa ggttacagaa       480
     aaaatttctg ctgctctgaa agttccaatg agcacagcga cctccatcat ccatgtggaa       540
     gatgtttgga accaccagga ctcttactag agctggccag ccatctaagc taagtgatca       600
     ggagagaagg gccttagtta gggaggtgat caataactca atggtcactc tgtctagctc       660
     cagccatctt ctatggagag aggagaacct tacagaagga caaccatctg tgcagcaatc       720
     caccaatcag gcctgtatgg tagattagcc agtgttaacc actcctcgtc tggaatttgc       780
     aaaaaggcat ctgaaggatt ctcacaccat aagaaacaaa attctctggt ctgatgagac       840
     taaaattgaa ctctttagag tgaatgccag gcgttacttt tggagaattc aggcaccgct       900
     catcaccagg ctaacaccat cactacagtg aagcatggtg gtggcatgca tcaagctgtg       960
     gggatgtttt ttcagcagca tgaaatggaa gactagtcag aatagaggga agatgaatga      1020
     agcaatgtac agagacatcc tgaagtgaaa accttcttca gagtaatctt gatttcagac      1080
     tggggtgacg gtttatcttc cagcaggaca atgaccgaaa gcacactgcc aaaatatcag      1140
     tggagtggct tcacaacaac tcgatgaata ccttaagtga accagccaga gcccagacct      1200
     aaatcctttt gaatatctct gaagagatgt aaaatggctg tacaccgtcg cttcccatcc      1260
     aacctgatag agtttgagag gtactgcaaa gaggaatggg cacaaattct caatgacagg      1320
     tgagccaagc tgtggcatga tattcaaaaa gagttgaggc tgtagttgct gccaaagatg      1380
     catcaacaaa gtattgagca aagactgtac atttttatat gaacgtgatt ttttgaccct      1440
     tttaatttta ataaatttga aacaatttca aaaaatgttt tttcacattg gcattatggg      1500
     caactgtgtg tagaatgttg aggaaataaa tgaaattaat ccgtttttga ataaggtaaa      1560
     aaggtggaaa aaaatgaggt agaattatga tatcactttc ccgatgcact gca             1613
//
