Repbase Reports

2005, Volume 5, Issue 1
January 31, 2005
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 15

Gypsy-21-I_DR

An internal portion of the Gypsy-21_DR LTR retrotransposon - a consensus sequence.

Submitted:
00-Jan-2005
Accepted:
31-Jan-2005
Key Words:
LTR retrotransposon; endogenous retrovirus; Gypsy superfamily; gag; protease; reverse transcriptase; integrase; Gypsy-21_DR; Gypsy-21-LTR_DR; Gypsy-21-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-21_DR, a family of LTR retrotransposons from zebrafish
Journal:
Repbase Reports 5:(1) p.15 (2005)
Abstract:
Gypsy-21-I_DR is an internal portion of the Gypsy-21_DR LTR retrotransposon that belongs to the Gypsy superfamily. Its long terminal repeat is deposited in Repbase as Gypsy-21-LTR_DR. The consensus sequence was reconstructed based on multiple alignment of five proviral copies (they are less than 1% divergent from the consensus sequence). Gypsy-21_DR retrotransposons are characterized by 4-bp target site duplications. The internal portion contains two ORFs encoding the 562-aa Gypsy-21_DR1p gag (pos. 86-1771) and 1585-aa Gypsy-21_DR2p pol proteins (pos. 1672-6426) composed of the protease, reverse transcriptase, and integrase domains. The second protein, including the protease domain, does not start from Met. Presumably, the gag-pol fusion protein is formed originally due to a ribosomal frame shift. Gypsy-21_DR1p: MEIIEQENIKVPNSLIVSGTTDTESDIDLTEHLGKYGCINRIVRIDSPGSPHHKNVIVEYESGS AVKILEPQLPFIFENPHQADIQYEIKALSSIYVETVTTSATKGYMEKLKSIAKLSGRRFEDLLQ EELSKCREPVAQADDDTTDVASDLRSGIPQVNPAQGSQEMPMGAAFVPLVGTNVPNVNPPEIQR VVVEHIVKSEEATSHMHAPLKLRFFSGRSPRPANEVDYEIWHNSVELMLQDPAVSDLVRSRKII DSLLPPASDIVRTLGLHATPRAYLDLLDSAFGTVEDGDELFAKFLSTMQNAGEKPSQFLQRLQV ALAQAIRRGGVPSSEADRHLVRQFCRGCWDDALISELQLEQKKANPPSFSELLLLLRTAEDKIS TKELRMRKHLGASKLRTSSYSVCASSDEVVSTQTIVSDLKKQIAELQNQVEGLTKAKKQAQCAP EGRVCDLQKQVVGLKGQIVEAKPSKSAKTQSATRMNKTQSVQTNLSEVVSSVPLKQLSKPKPWY CFHCGEDSHIASTCDRDANPALVAAKRKLLKERQSSWEAQMGSSHRTPLK Gypsy-21_DR2p: CKSCLGSCQKKAFKRAAVVLGGTNGVIPSHSFKIESAPVVGQTGAEKCSRRPKNSKFCNHHASS RSKPFILPKGLVGAKCTAEVSIAGQKCSVLFDTGSQVTTVSQTYYEQNLSHLEIKPLEHLEVEA ANGQFVPYLGYVEIDVVFPKEFLGAEITLTTLALVTADTSSNVQSPVLIGTNTLDLAYEAQFDS EVAQPSHVLPYGFKVVMNVLRHRFKLKTNSMIGLVRAQGTKPEVVPAGQTLVLEGSINSRELSS DKWVLMEAPLQSSLPGGLLCASSLVTLSQRSFQKIPVILKNETEHDILVPAKSVIAELYSLQSV NVKEPATESNSQGKELPPYTLDFGDSPIPNEWKERISQKLCAMSDVFALHDLDFGKTDKVTHRI RLHDQTPFKQRARPIHPQDFDAVRKHLQELLDAGVIRESESPFSSPIVVVRKKNGDVRLCVDYR KLNLQTIKDAYALPNLEETFSALTGSRWFSVLDLKSGYYQIEVEESDKHKTAFVCPLGFWEFNR MPQGVTNAPSTFQRLMERCMSDVHLKEVVVFLDDLIVFSDTLEEHERRLLRVLHRLREFGLKLS LEKCRFFQTSVKYLGHIVSSSGVETDPDKVAALKTWPVPKNLKELRSFLGFSGYYRRFIRDYAA IVKPLNDLTSGYPPHRKSSKVRERRDYHNPKEPFGSRWSANCQKAFEAIIEALTTAPVLGFADP KLPYVLHTDASTVGLGAALYQEQEGQLKVIAYASRGLSRSEARYPAHKLEFLALKWAVTEKFYD YLYGNQFTVVTDSNPLTYVLTSAKLDSTSYRWLSALSAFSFKLQYRAGKQNIDADSLSRLPHGA LKNDVASQKEQERIRQFALNHLFDDVQTMSPEVIQAICDKHIVYCKSVDCGVTPMTLVESLAIH VDAIPGSFDHDENNFGCPVVPTFGENDLKEKQRSDPIIREVIVQLETGETIPPLVRKELPMLSL LMRELSKLELQNGILYRRRHDGDTITYQLVLPESLRSMVLTCLHDDMGHLGVDRTLDLVRSRFY WPKMLVDIERKIRTCPRCVCRKSLPDHAAPLVNIQVTRPLELVCMDFLSIEPDSRNTKDVLVIT DFFTKYAVAVPTCNQKSRTVAKALWENFIVHYGIPEKLHSDQGADFESKTIKELCELMGIHKIR TTPYHPRGNPVERFNRTLLNMLGTLKKCDKVHWSSFVKPLVHAYNCTKHDSTGFSPYELMFGRQ PRLPIDLAFDVPLNREEYKTHSQFVHDLKCRLKKTYDLAMKSTAKVGERNKARFDKHVVESVLD IGDRVLVKNVHLRGKQKLADKWESLVYVVVKRAGDLPVYTVKPEGKEGPLRTLHRDLLLPCDLL QLPEEVLALPSTRKRPPTRKNPCNKVQDQVDFDSDDDDSSLELMHSDLLIPTNITFTEVYEAGT GPQTEVPSIPIVQDTVGHISTENLPVSADSPIECLPEIENFQIDNAPTLNVLPVDDPDVVESDE NLPAEVPVNLGDQQIPVEETVKVSEHETETKKHENDGNVIRKSDRVRQKPRIFTYPELGNPLVS IVQSLFQSLSTAVTDSIIENNSFTKAADAVVTQPVSFMHRDVHRVNGGGA
Derived:
[1] (consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

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