Repbase Reports

2005, Volume 5, Issue 1
January 31, 2005
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 9

Gypsy-18-I_DR

An internal portion of the Gypsy-18_DR LTR retrotransposon - a fossilized sequence.

Submitted:
00-Jan-2005
Accepted:
31-Jan-2005
Key Words:
LTR retrotransposon; endogenous retrovirus; Gypsy superfamily; gag; protease; reverse transcriptase; integrase; Gypsy-18_DR; Gypsy-18-LTR_DR; Gypsy-18-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:
Gypsy-18_DR, a family of LTR retrotransposons from zebrafish
Journal:
Repbase Reports 5:(1) p.9 (2005)
Abstract:
Gypsy-18-I_DR is an internal portion of the Gypsy-18_DR LTR retrotransposon that belongs to the Gypsy superfamily. Its long terminal repeat is deposited in Repbase as Gypsy-18-LTR_DR. The genome contains one copy of Gypsy-18-I_DR that is flanked by identical LTRs. The internal portion contains two ORFs encoding gypsy-like gag and pol proteins. The first ORF encodes the 612-aa Gypsy-18_DR1p gag (pos. 225- 2060). The second ORF encodes the 1578-aa Gypsy-18_DR2p pol protein (pos. 2021-6754) composed of the protease, reverse transcriptase, and integrase domains. This retrotransposon can be still active. Gypsy-18_DR1p: MEIVKRENVNVQNAVIVSGLTLSDIDQDLEAYLIKYGSIKQNLVIDDPNSEHHHSAIVEFSHDS AMQNLKPSLPMSIKSTLDDNVVFHVRSLASVYTPAASSDVTEDYLMNLQAIAHDSGKTLQEVLK SELQKISMLTFPESRASEQVLEKEQPMYDSSMHMTEPENPAKVSTPSQSPHQSRIPDASVDENM SLNIPTSALSPPGVQRVIMEHVIRTSDTVSAPHVSLRLKAFSGRIPRPSHEPDFDTWSATVDFL LNDKSLSDSQKTGKILDSLLPPASDVVKHIGPYALPSECLKLLESVYGSVEDGDELFAKFIGAL QNQGEKPSSYLHRLHVMLSTAIRRGGVTEAERDRCLLKQFCRGCWDNSLIIDLQLERKRATPPP FAELVILIRTAEDKQSLKEERMKKHLGLNKQTSVPFKLRTATNQQFAYCSEMPDESHKVESCQL SAKQKSAKPSSKAENSEIENLKKEITKLQTQITMMKTEPGPKEKSSPSVDGISELRRDIAELQA HLVPRFQREYQEQSPTLRAFPAKHRPRLTGTEVTTTQRPSEQLYSRPRPGYCFHCGGDGHIAVN CENEPNPRKVEEKRRELRERQAKWDLQNSPNLQHLN Gypsy-18_DR2p: MGPPELSQLAAFKLKSVSITGRTEARKEKCPKKKEHLLHQRTYKSPCYQLPTGLVGTRCTTKIQ IEGREVNCLLDTGSQVTTIPKSYYDQYLQQHPIKSLQHLLEVEGANGQAIPYLGYVELNLKFPQ DFLGVEAEVPTLALIVPDLTTIPQILIGTNSLDVLYTYCTQGNKRILKSHCHGYQSVINILEKR RQQASGAAVGPVKLKGNQQEVVPAGSTVVLEGLVQVKGPLFEKWVSVEPATTPFLPGGILVASC LHSLPSRQRIVQLPVVLRNDSHTDIVIPPKAVIAEAHAVQRVEKEFSKVDADSEEADSILPKVP VDFGDSPLPPEWKERITSMLNSMPDVFALHDLDYGHTDQVKHRIKLSDETPFKHRARPIHPQDV DAVRKHLQELLEAGVIRESESPFSSPIVVVRKKNNSVRLCIDFRKLNSQTIKDAYALPNLEEAF SVLTGSKWFSVLDLKSGYYQIEMEESDKQKTAFVCPLGFWEFNRMPQGITNAPSTFQRLMERCM GDLNRKEVLVFIDDLIVFSSTLEEHETRLKQVLKRLREFGLKLSPEKCKFCQTSVKYLGHIVSQ HGVETDPAKVEALKTWPTPKNLKELRSFLGFSGYYRRFVQDFSKIVKPLNDLTAGYPPLQKENR KKMVESKKQYFNPREPFGGRWTQECQHAFNTVIAKLTSAPVLGFANPKLPYVLHTDASTTGLGA ALYQDQDGQMRVIAFASRGLTRSESKYPAHKLEFLALKWAVTTKFNDYLYGAEFTVITDSNPLT YLLTSAKLDATSYRWLSSLSTFIFKIRYRAGSRNQDADGLSRRPQTEIPDDLETQKERERIRQF THQHLTNEQSMLVSEEEVRAICERHQIVQSGDDPDHLHPSVTLVESITVNVDALPQAFQQDDAY QITEIPQLSEENLRKRQREDPEIGIVVKQIKSKEKPCFKTILPELIPWFREWSRLELRNGVLFR RKQEHGDSSYQLALPADLRDMVLTELHDKMGHMGVERTLDLVRSRFFWPKMSAAVEKKIKTCER CVRRKSLPEKAAPLVNIRTNRPLELVCMDFLSLEPDQSNTKDILVMTDHFTKYAIAVPTRNQKA QTVAKCLWDNFLVHYGFPEKLHSDQGADFESRTIKELCKVAGISKTRTTPYHPRGNPVERFNRT LLQMLGTLNNKEKSRWKDYVKPLVHAYNCTKSDVTGFTPYELMFGRQPRLPIDLAFGLPVDGQT ESHSKYVQDLKSRLEESYKVATENANKVAGRNKKRYDKHVVNSTIEVGDRVLVKNVRLKGKHKL ADKWETEVYVVTKKAGDLPVYTVKPERKDGPLRTLHRDLLLPCGFLSASAPDTPVERKVMQKPR TRAQCAEESENLSEHSESEYDPVDYYDPERFTIDTRILPTSGLEPSSSSKHTVNLPVAKPGMKK GEERLVSITLVDEENLPDVETSRPAETDRHVLELPLESNLPDLSEIQVLDENIVDESEKEMAQI ADQEKPDNCVGSSESSDRKDERGTNLTQREIGTSREFQETQREGTETESLRRSRRQGEPPHRLN YPQLGNPFCSVIQSLFSSLSTAITNSLEDSNPSRRYSPVENI
Derived:
Positions 4020218 4027018 Accession No chr10 Zebrafish.v4
Download Sequence - Format:
IG, EMBL, FASTA
References:

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