Repbase Reports

2004, Volume 4, Issue 1
January 31, 2004
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 23

Gypsy1-I_GA

Internal portion of Gypsy1_GA retrotransposon.

Submitted:
31-Jan-2004
Accepted:
31-Jan-2004
Key Words:
LTR; Gypsy retrotransposon; Tf1 group; gag; protease; 5-bp TSD; reverse transcripatase; RNase H; chromodomain; Gypsy1-LTR_GA; Gypsy1-I_GA
Source:
Gasterosteus aculeatus (three spined stickleback)
Organism:
Gasterosteus aculeatus
Taxonomy:
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Gasterosteiformes; Gasterosteidae; Gasterosteus
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Gypsy1_GA, a self-primed Gypsy LTR retrotransposon from the fish Gasterosteus aculeatus.
Journal:
Repbase Reports 4:(1) p. 23 (2004)
Abstract:
Gypsy1-I_GA is an internal portion of a young Gypsy1_GA LTR retrotransposon. The internal sequence is flanked by identical Gypsy1-LTR_SR long terminal repeats. Gypsy1_GA belongs to the Tf1 group of self-primed Gypsy LTR retrotransposons. Its reverse transcription is primed by a heteroduplex formed between a 11-bp portion of PBS (Gypsy1-I_GA, pos. 3-12) and the 10-bp 5' end of the Gypsy1_GA mRNA (Gypsy1-LTR_GA, pos. 214-223). Gypsy1_GA encodes a 1462-aa Gypsy1_GAp polyprotein (Gypsy1-I_GA, pos. 20-4381 and Gypsy1-LTR_GA, pos. 1-22) composed of the gag (pos.125-220), protease (pos.340-450), reverse transcriptase (pos.580-750), RNase H (pos.820-950), integrase (pos.1089-1241) and chromo domains (pos.1380-1442). Gypsy1_GAp: MDSADSGSGLTVLPTPLLQQTEEQFNAVHLGMQGMSERQESLHSQVTFLTSQVQRLMDRLDTFATPITVP APASLPAASPPVVPPRLARPERFSGDSGDCRPFLVQCGLHFELNAPSFQTERSKVAYVISHLSGRAERWA TAEWSRNSRICSSVQLFTETLSKIFNTTNPGREAARALMGFRQGNRRVSDYAIEFRTLAADSGWNEESLF DAFLYGLAEPIKDLLINRELPEDVDSLIALVVKIDKRLQDRGRSRPEYSAPVQRGQSTSAQQSSDGAEEP MQLGRTKLSPEERQRRVREGRCLYCGQRGHYLSNCPVRDQAAARYTLVSHTTVSSVRPSMQAKLITPSQT VTYPFLVDSGADENFMDWRLAKRLNLKLIPLPKQLEAHALDGRLLCKITHRTDPIQMIISERHSEALSFY LFDSPSHPLILGFPWLSKHNPHMNWVTGEITSWDKDCSVTCIHAVSISKISHSSDVSSTKCLELPVSRSA VVSPRTASSDADFPDLSRVPPCYLDLKEVFNKTRAISLPPHRPYDCAIDLLPGTSPPRGRLYSLSSPEVK TMTEYIDSSLAAGLIRPSSSPAGAGFFFVSKKDKTLRPCIDYRGLNEITIKNRYPLPLISSAFELLRNAK IFTKLDLRNAYHLVRIREGDEWKTAFNTPSGHYEYLVMPFGLSNAPAVFQALVNDVLRDMLNQYVFVYLD DILIFSPDEDTHVKHVHQVLQRLLTHQLFVKAEKCEFHVSSVAFLGFIVSQDNIQMDPAKVSAVTEWATP ASRKHLQRFLGFANFYRRFIRNFSTIASPLHKLTSSNIKFQWSLPAERAFQELKERFTTAPILTLPDPNL QFVVEVDASDVGVGAILSQRSEVDRKLHPCAFLSRKLSPAERNYDVGNRELLAIKVALEEWRHWLEGAEQ PFLVLTDHKNLEYIRSAKRLNSRQARWALFFNRFNFSLSYRPGSKNTKADALSRLFDPGSAPRSPSTILP PSCVVGAVTWAIEQRVRQANVNGQVPDGCPPNRLFVSIPLRPQVIHWAHTSRVSCHPGIRRTLFVVKQRF WWPSMEREVREYVTACPVCARNKSSRRPPSGLLQPLPVPHRPWSDISLDFVTGLPPSKGNTTVLTVVDRF SKMVHFIPLPKLPSAKGTADAVLLHVFRIHGFPKDVVSDRGPQFVSQFWKAFCSLLGATVSLSSGYHPQS NGQAERMNQELETGLRCLVSQNPTTWSNHLIWVEYAHNTLPSASTGLSPFQCAYGYQPPLFPDLEREVNV PSAQRFVHRCRRIWKGVREVLLRSSVRTKGAADRRRTLAPTYRTGNRVWLSTRDIPLRVESRKLAPRFIG PFPISRVINPAAVRLQLPSSMRVHPTFHVSRIKPALESPLVPPTKPPPPPRIVDGGPVYTVKRLLAVRRR GRGRQYLVDWKGYGPEERKWVSTKNIVDPNLILDFHRLHPDRPETSSAVPRRGGTVMSSPEY The Gypsy1_GAp is 46% identical to the the Gypsy1_STp encoded by the frog Tf1-like element Gypsy1_ST. At the same time, Gypsy1_STp is 46% identical to the polyprotein encoded by another frog element, Gypsy2_ST element. Also, these proteins are over 40% identical to to proteins encoded by Tf1-like elements in fungi. Most likely, the fish and frog retrotransposons were transferred horizontally into the vertebrate genomes.
Derived:
Positions 44416 48798 Accession No AC146545 GenBank
Download Sequence - Format:
IG, EMBL, FASTA
References:

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