Repbase Reports

2004, Volume 4, Issue 12
December 31, 2004
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 319

Gypsy13-I_DR

An internal portions of the Gypsy13_DR LTR retrotransposon - a consensus sequence.

Submitted:
00-Dec-2004
Accepted:
31-Dec-2004
Key Words:
LTR retrotransposon; endogenous retrovirus; Gypsy superfamily; gag; reverse transcriptase; integrase; Gypsy13_DR; Gypsy13-LTR_DR; Gypsy13-I_DR
Source:
Danio rerio
Organism:
Danio rerio
Taxonomy:
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Danio
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Gypsy13_DR, an LTR retrotransposon from zebrafish
Journal:
Repbase Reports 4:(12) p.319 (2004)
Abstract:
Gypsy13-I_DR is an internal portion of the Gypsy13_DR LTR retrotransposon that belongs to the Gypsy superfamily. Its long terminal repeat is deposited in Repbase as Gypsy13-LTR_DR. Gypsy13_DR is characterized by 4-bp target site duplications. The internal portion encodes two proteins: the 556-aa gag Gypsy13_DR1p (pos. 95-1755) and 1577-aa polyprotein (pos. 1756-6486, conceptual translation) composed of the protease, reverse transcriptase, and integrase domains. PBS is identical to that in Gypsy9_DR. Some internal portions are flanked by 100% identical LTRs. PBS is complementary Arg-tRNA. Gypsy13-I_DR1p: MDIIEAEGIKIPNSVIISGLTQDKSDDELFDFLKQYGSFAKTVFISDKDSEFYQSVILEYTSGQ ALHSLEPQLPYTHQLSSDPSVTYHVRALSSVFTQYKGTSVTKSYLEGLKEVAKLSGTDFEIVLS QMLSQMTAELTPTSADTEADDEDLDEPQAQVCPEESFTPAPVKISQPDDSLSQHTSAKPNKPPL LTSSEVLNPPEVQKLVIEHVVRTGEVATQGLMQQRLRVFSGKCPRPGSEVDYDTWRSSVELMLK DSTLSDLNVSRKIVDSLLPPAADVIKHLSSEAPSSAYLQLLDSAFGVVEDGDELLAKFMNTLQD AGEKPSTYLYRLQTALRVTIKRGGVSPEEADRHLLKQFCRGCWDNDLITDLQLERRRNNPPSFG QLLLMLRTEEDKHTAKVTRMKQHLGSSKPRAVMHSQRTWVSSEVEQGEVSNMVSLAAETKEIKR QIAKLQSQLASLVPAHKTQKKASQQAVVNKQDKKKSDTANQLTRTPVSQRQKDRPRPWYCFTCG EDCHIASSCTSEPNPTLVNAKRKLLREKQLLWDSQNANSNPDLN Gypsy13-I_DR2p: FKLESVLVVGQTGAELESQCPNTNHVFEKSQVSKVQSTSLPKGLIGAMSIAEVTIANEKCSCLL DTGSQVTTVPKSFYEQHLSGYPIKSIDDILEVEGANGLSVPYEGYIEMGITFPEELLGVSVEIP TVALVVPDVKAHNQSMVLIGTNTLDVLYKKYLSADPPKFQPCSYGYKVVLKTLEIRWRQNTSGV LGHVRLRSRAPKVLMAGQTVVVGGSVSNPCRIDQTILVEHSPDSSLPGGVFVKRCLLNQPENQM NSIPVVLTNETNHNITIPPRCVIAELHAVDSLQSLSKTSNSNGEGDFTLNFGDSPLPQVWKERI SKKLREIPEVFSHHDLDFGHTQKVKHSIKLHDETPFKQRARPIHPQDIEAVRRHLQDLLASGVI RESESPFSSPIVVVRKKNGDVRLCIDYRKLNIQTVRDAYALPNLEETFSALTGSKWFSVLDLKS GYYQIEVDEADKPKTAFVCPLGFWEFNRMPQGVTNAPSTFQRLMEKCMGDINLKEVLVFLDDLI VFSDTLEEHETRLLNVLFRLKEYGLKLSLEKCKFFQTSVRYLGHIVSEHGVETDPEKVQALKTW PVPKNLKELRSFLGFGGYYRRFIKDYSKIVKPLNDLTSGYPPLRKGAKKCNKGSQYHNPKESFG DRWTPSCEEAFRTLIEKLTSAPILGFADPKLPYFLHTDASTKGLGAALYQEQDGQMRAIAFASR GLSHSESRYPAHKLEFLALKWAVTEKFNDYLYGNHFTVITDSNPLTYILTTAKLDATSYRWLSA LSTFSFKLQYRAGKQNVDADSLSRRPQEPIPETAWSSKEQERIHQFVQHHHHDAADIVSAPNDV VHAICEKHLINQDAASGVALVGSLALRPDAIPDEYGEDCNLDGLPVMPYLPHEIGEKQRADSVL REVIFHLELGEKPSPTVRKEIPTFPLFLKEWNRLELRDGILYRRRQENNLLTYQLVLPEELRPL VMSSLHDDMGHLGIERTVDLIRSRFYWPKMAADVERKVKECSRCVRRKAQPQKAAPLVNFHATR PLQLVCMDFLSLEPDRSNTKDILVITDFFTKYAVAYPTPNQKAKTVAKCLWENFVTHYGFPERL HSDQGPDFESHVIRELCEVSGIKKSRTTPYHPQGNPVERFNRTLLGMLGTLEEKDKAHWKDFVK PLVHAYNCTKHEVTGFTPYELMFGRQPRLPVDLAFGLPHHGKSDVIPHSEYVKQLKSHLKESYL LASQGMLKTAEKNKTRFDKSVTHSSLEVGDRVLVRNVRLRGKHKLADKWESEVYVVVKKAGDLP VYTVHPENSESPLRTLHRDLLLPCGYLPLSNSSNPSPPKMSRPRTRQNPGFQQPEEDCSFLSPE DEDYEWYGDNHQNVEPLQFSTVYDVPQPVKGKSVSLADESAGQNLGKDGTQCKEGTQNDNLPVT PPVDNLPDDLPANDPPVYNAPVHSSVDNPSDDVLEVCETTETPGKDQPETDNSKDLPTQRESKV EEANDSENSVSCEREEQQSEQEIPSLRRSARERDKPERLTYFQLGNPLSHVVQSLFQGLSTALV NSLNSVEDLGDSPITSDIPANIVTTQPLRACKGTCIVSRGEA
Derived:
[1] (consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

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