Repbase Reports

2005, Volume 5, Issue 1
January 31, 2005
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 11

Gypsy-19-I_DR

An internal portion of the Gypsy-19_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-19_DR; Gypsy-19-LTR_DR; Gypsy-19-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-19_DR, a family of LTR retrotransposons from zebrafish
Journal:
Repbase Reports 5:(1) p.11 (2005)
Abstract:
Gypsy-19-I_DR is an internal portion of the Gypsy-19_DR LTR retrotransposon that belongs to the Gypsy superfamily. Its long terminal repeat is deposited in Repbase as Gypsy-19-LTR_DR. The genome contains one copy of Gypsy-19-I_DR that is flanked by 2% diverged LTRs. The internal portion contains two ORFs encoding gypsy-like gag and pol proteins. The first ORF contains one frame shift and encodes the 601-aa Gypsy-19_DR1p gag (pos. 94-1892). The second ORF encodes the 1566-aa Gypsy-19_DR2p pol protein (pos. 1847-6544) composed of the protease, reverse transcriptase, and integrase domains. Gypsy-19_DR1p: MEIVKRENIEIQNSVIVSGLTLSALDEELEDYLKRYGSVKSNLLIDNPESEYHHNTIVEFDCDT AMSNLEPSLPMDIQSTQDSNAVFHVRSLGSVYASAASSSLTEGYLESLVAIAQSSGKPLQDVLQ MELQKMNALKLPASDSPRPDTPVQMFQNLKTLSRKAHQISHPPYYSISNNASTADTISLNLPTS ALNPPGIQRVVLEHVVKTSDAVSSSNAAYRLKAFSGRSPRQNTEPDFETWRASIDFLINDQSLS DSHKTRKILDSLLPPASDVVRHVGPDVSPTKCLELLESVYGSVEDADELLVKFISTLQNQGEKP SAYLHRLHVMLSATIRRGGVTEAERKGYLLKQFCRGCWDNNLISDLQLERRKAAPPSFAELIVL IRTAEDKLLLKEERMKKHLGINKHVSVPVKFRTATHQQSVYYADAIDEPRVENNHESLRQKSAK PKSKSDQSELDALKKEVAKLQAKISSMMADPIRENKKKASSDANEFNQLKKQVAELQAHLVPVV QGRCFEKSPASKNFPVRHRPNVMGPEMHKEERPTWNSTNRPRPGYCFQCGEDGHLAVHCKNAPN PQRVEEKRRELRDRQAAWDLQNSLN Gypsy-19_DR2p: AEGQTSCMGSTEFFKLRSVSVVGRTETGGNKQCPKKHSYKQNVNSTSKLPARLVGTRCTASIQI EGKVVSCLLDTGSQVTTIPMSYYKKHLSRHPMKSVEHLLEVEGANGQSVPYLGYVELNLKFPKE FLGVEVEIPTLALIVPDLTTVPQILIGTNSLDVLYTNYTEGETSACKSNFYGYQAVINVLERRN QQASIETVGSVRLKGKQEIIPAGCVVVLEGVMQLKNPLFKKVVSVESPMSSHLPGGLLVANSLH TLPARQRVAQLSILVKNETQTDLIIPSRAIIAEAHAVERIVEREISKKSAENEKMELNEQKIPI DFGNSPLSPEWKKRITSVLNSMPDVFALNDLDYGHTDKVKHRIKLNDETPFKHRARPIHPQDVD AVRKHLQELLEAGIIRESESPFSSPIVIVRKKNNSVRLCIDFRKLNSQTIKDAYALPNLEEAFS VLTGSRWFSVLDLKSGYYQIEMEEADKQKTAFVCPLGFWEFNRMPQGITNAPSTFQRLMERCMG DLNRKEVLVFIDDLIVFSETLEEHETRLMQVLKRLKEFGLKLSPEKCKFCQTSVKYLGHIVSQH GVETDPSKVEALKTWPRPNNLKELRSFLGFSGYYRRFVQDYSKIVKPLNDLTAGYPPLQKHCNK KRDETKQYFNPKEQFEERWTLECQQAFDTVIEKLTSAPVLGFADPKLPYVLHTDASTTGLGAAL YQEQDGQKRVIAFASRGLTKSEAKYPAHKLEFLALKWAVTAKFNDYLYGADFTVVTDSNPLTYV LTSAKLDATSYRWLSSLSTFNFKIQYRAGNRNQDADGLSRRPQEAMPDDLETTKERERIRQFAY HHLTDASSAVVSSEAIKAICERHEVCQSNSHTDSLYQPVTLVESLAVGEKVLPQSFQQEETCRS GEIFLLSEQDLRERQRADPEIGIIIKHLEHEEKPCLKTIPSHLALWLREWNRLVMKNGVLFRKR NEQGSESYQLALPVNLRDVVIKELHDEMGHLGIERTLDLVRSRFFWPKMSLTIEQKVKTCERCI RRKTPPEKAAPLVNIKTSRPLELVCMDFLSIEPDQSNIKDILVITDHFTKYAVAVPTRNQKAQT VAKTLWDNFLVHYGFPEKLHSDQGPDFESRTIKELCRVAGISKTRTTPYHPRGNPVERFNRTLL QMLGTLNTKEKSNWKDFVKPLVHAYNCTRNDVTGFSPYELMFGRQPRLPIDLAFGLPVSSQPES HSKYVQSLKNRLEESYMVATKNASKVAARNKTRYDQRVVSSTLDVGDRVLVRNVRLRGKHKLAD KWESDVYVVVKKAVELPVYTVKPEGKDGPLRTLHRDLLLPCGFLLMDKPKEPLDKEVPVKPRTR ASSAKELEKCESQSEHSEDDDLSESYAPERTLEIETRIVSNTNPVACIRNRQTKNLPSVETAIE PSTECPIQHEPINDNLPEPVERNIPYLPEAEDQDLLCESERENVEELINHQSTENEINYISSQK DHTPCQSPLIDQDEMPQPEKTQRRSQRSHEPPKRLQYPQLGNPLSMVIQSLLSGLSTAFTNSLE ENLEQFNSVPTIVTVQPQMQRDLHAFRRGE
Derived:
Positions 7939002 7932459 Accession No chr13 Zebrafish.v4
Download Sequence - Format:
IG, EMBL, FASTA
References:

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