Repbase Reports |
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| 2003, Volume 3, Issue 1 |
| January 31, 2003 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 1 |
DIRS1_DR |
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DIRS1_DR is a DIRS-like LTR retrotransposon - a consensus. |
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Submitted: 31-Jan-2003 |
Accepted: 31-Jan-2003 |
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Key Words: LTR retrotransposon; gypsy; endogenous retrovirus; DIRS superfamily; reverse transcriptase RNase H; phage integrase; DIRS1; DIRS1_DR |
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Source: consensus |
Organism: Danio rerio |
Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Ostariophysi; Cypriniformes; Cyprinoidea; Cyprinidae; Rasborinae; Danio |
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| [2] |
Authors: Kapitonov,V.V. and Jurka,J. |
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Title: DIRS1_DR, a family of DIRS-like endogenous retroviruses in zebrafish. |
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Journal: Repbase Reports 3:(1) p. 1 (2003) |
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Abstract: DIRS1_DR is a family of DIRS1-like retrotransposons. These elements are related to gypsy-like LTR retrotransposons and endogenous retroviruses. There are ~100 copies of DIRS1a_DR in the genome, they are ~0.3% divergent from the consensus sequence. Therefore, this family retrotransposed in the zebrafish genome very recently. The unusual structure of DIRS1_DR is depicted in the next figure. GTTCCCCTTCGGTTGGGGAACTTCAGTGCCATGAATGGGAGGATTCGGATCAGAAGCCGCTTATCTGGAG <====== ======> <--------------------------------------------- AGTATTGAACGGGCCAATGAATGAAATTAATTGGCAGCGTAAGCTTGCGCAGGTGTGCGACATCTGCAAT ---------------------------------------------------------------------- TATCTCAGCATATAAGCACACCTGAAGCCAGCAGACGCCATCCTTTTCGCTTCAGATCCTTTCTGAGTGA ----------------------------------------------- ...................................................................... ...................................................................... GGTGCAGTCATTATGGCGCTTTCCATATTCTCCCATTCATGGCACTGAAGTTCCCCAACCGAAGGGGAAC <====== ======> <~~ GTTCGAGGTTACAGAAGTAACCCTTCGTTCCCCGAGGAGGGGAACGGAAGTGCCATATTCCGTCGCCATA ~~~~~~~~~~~~~~~~~~~~~~~~~~<====== ======> ATGACTGTCCCTTAGCTGTTTGAAAGTCTCTTCAGCTT AAAAGGATGGCGTCTGCTGGCTTCAGGTGTGCTTATATGCTGAGATAATTGCAGATGTCGCACACCTGCG ---------------------------------------------------------------------- CAAGCTTACGCTGCCAATTAATTTCATTCATTGGCCCGTTCAATACTCTCCAGATAAGCGGCTTCTGATC ---------------------------------------------------------------------- CGAATCCTCCCATTCATGGCACTTCCGTTCCCCTCCTCGGGGAACgaagggttacttctgtaacctcgaacgtt ----------------------> <====== ======>~~~~~~~~~~~~~~~~~~~~~~~~~~~~> Fig.1 Termini of DIRS1_DR. The 163-bp sub-terminal inverted repeats are underlined by a single line. DIRS1_DR encodes three ORFs. ORF1 (positions 414-1632) codes for the gag-like protein. ORF2 (positions 1633-2597) codes for reverse transcriptase and RNase H. ORF3 (positions 2598-5129) codes for the phage integrase. ORF1p: MALRLCVSGCGGFLSPDDGHDHCIACLGVQHVNAVLAGGSCRHCDAMTVAQLRSRLTFARERATPVASCS KKAAGARADLRVSAGANPPPTGSRTSRSSRRSIQASGGESDPSNQMVALTLADTGDQMSSAASEGGLSLS DEDPDPLAPSGQVSAVKSDPEADMLAVLSRAASAVGLEMVYPPAPRPDRLDGCYVEDQKAKPSKPLVPFF PEVHSRLTQSWRAPFSARAASASALTALDGGAARGYEAIPSVERAIAVNLCPRGASTWRGLPRLPSKACR LSASLGARAYKAAGQAASALHAMATYQRYQAQALAELHEGGSNPSLLHELRTATDYALRTTKSAACALGR TMSTLVVQERHLWLNLADMRDVDKVRFLDSPISQAGLFGDTVGEFTQEFKAVKEQSDAMGNVIYRRGRKP APPAEPSTSAVPRRGRPPTSAAPPPPAPPAKRARRSPRKQAAPPAQGAVKSGKRTAKRP ORF2p: MRWAMSSIGVAVSPLRPPSHPPPLFLAEGARQRVLPRPRLRLRPSGRGVHLESRQPLLPRAPLSPVNGPR SVPETGHPEKRKLALSPLEGGAPITTVLFSATKTSVKEHFFPSPDVTARVLPVRDALPSGSQTLRASPVA HERWGDGLPSLSPPAPSPESGCGARANRSPPAFPRDPRASRISTPTPRCPTAGTSAIVAMTPLARALPAW LARASPSRWLIRTIRLGYAIQFAKRPPKFTGVYFSRVNPLSAPVLREEIAALLAKGAIEPVPPAEMESGF YSPYFIVPKKSGGSRPILDLRVLNRCLHKLPFRMLTQRRILQCVRPRDWFAAIDLKDAYFHVSILPRHRQ FLRFAFEGRAWQYKVLPFGLSLSPRVFTKLAEGALAPLRLAGIRILSYLDDWLILAHSREQLIMHRDEVL RHLRLLGLQVNREKSKLAPVQRISFLGMELDSITMVAHLSEERARLLLNCLRELDSKLVVPLKFFQRLLG HMASAAAVTPLGLLHMRPLQHWLHDRVPRRAWHAGTHRVSVTALCRRALSPWNDPSFLQAGVPLGQASSH VVVSTDASNTGWGAVCRGHAAAGLWKGAQLHWHINRLELLAVFLALHRFLPVLERQHVLVRTDSTAAAAY INRMGGMRSRRMSQLARRLLLWSHPRLKSLRAIHVPGTLNRAADALSRQLLRPGEWRLHPESVQLIWARF GEAQIDLFASPENAHCQLFFSLTEGSLGTDALAHSWPRGMRKYAFPPVSLLAQFLCKVREDEEQVLLVAP LWPNRTWISELSLLATALPWRIPLREDLLSQGQGTIWHPRPDLWNLHVWSLDARKT ORF3p: MRSSSGLVCSHRPEGRVFPCLHSSTPPPISAVCVRGSSVAVQGPPLRALSVSAGLHQTRGGCPSAPSARG HSHTQLSRRLADFSPLAGAIDYAQGRGASASPPTGASGQPRKEQTRPRAEDFFSRDGAGLDHHGSAPLRG TRSPVAELSEGARQQTSGPTEVLSEAPGAYGIRSRRHAARVAPYETTSALASRSGPQTRMARGHTPGLGY CAVSPRPQPLERPLVPTGRCASRTGVQPCCCFNRRFQHGLGGRVSRACGCGPLEGCPAALAYQSPRAVGS VPRSPPLFTGAGAATRAGQDGQYGGGGVYQPHGGYALSPHVSARPPSAPLESPAAEIAARHSRPRHAQSC SRCALTTAVTPWRMETPPRVCSADMGAIRGGPDRSVCFPRERSLPVVFFPDRGLSRHGCTGPQLASGHAQ VCVSPSEPARAVSVQGQGGRGTGSASCAPLAQPDLDIRALTPRDGPPLADPFERGPTLSGTGHHLAPSPR SLEPPRVVPRREEDLGNLPTAVVNTITQARAPSTRRAYALKWSLFTEWCVSRREDPRNCQISVVLSFLQE KLDSRLSPSTLKVYVAAISAYHSAVAGGTVGKHNLVIQFLRGARRINPSRPPLMPSWDLALVLTSLRSDP FEPLESVSLRFLSLKTALLVALASIKRVGDLEAFSVSDSCLEFGPDYSHVILRPRPGYVPKVPTTPFRDQ VVNLQALPPEEADPALSLLCPVRALRIYVDRTQNFRSSEQLFVCYGGRQQGSAVSKQRLSHWIVDAISLA YSSRGQPCPPGVRAHSTRSVASSWARARGASLTDICRAAGWATPNTFARFYNLRVEPVSSRVLGNPLVIE ETTR
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Derived: [2] (Consensus) |
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Download Sequence - Format: IG, EMBL, FASTA |
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References: |
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