Repbase Reports

2003, Volume 3, Issue 7
July 31, 2003
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 128

Gypsy1-I_TP

Gypsy1-I_TP is an internal portion of the Gypsy1_TP LTR retrotransposon - a consensus sequence.

Submitted:
31-Jul-2003
Accepted:
31-Jul-2003
Key Words:
LTR retrotransposon; Gypsy clade; 4-bp TSD; gag; protease; reverse transcriptase; intergrase; Gypsy1_TP; Gypsy1-LTR_TP; Gypsy1-I_TP
Source:
consensus
Organism:
Thalassiosira pseudonana
Taxonomy:
Eukaryota; stramenopiles; Bacillariophyta; Coscinodiscophyceae; Thalassiosirophycidae; Thalassiosirales; Thalassiosiraceae; Thalassiosira
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Gypsy1_TP, a family of gypsy-like LTR retrotransposons from diatom Thalassiosira pseudonana.
Journal:
Repbase Reports 3:(7) p. 128 (2003)
Abstract:
Gypsy1_TP is a young family of gypsy-like LTR retrotransposons. Gypsy1-I_TP, an internal portion of Gypsy1_TP is flanked by 100% identical Gypsy1-LTR_TP LTRs. The consensus sequence encodes the 334-aa gag-like Gypsy1_TP1p protein (pos. 47-1048) and 1164-aa polyprotein (pos. 1052-4543) composed of the protease, reverse transcriptase, and integrase domains. Gypsy1_TP is characterized by 4-bp target site duplications. There is no tRNA-like primer binding site in Gypsy1_TP. Instead, this retrotransposon uses self-priming by the 12-bp CTGTAATTACAA palindrome present at the very 5'-end of its internal portion. Gypsy1_TP1p: MSSSMNNPCVGYERGYTNADVNTAPTRKFIKYITDEDGNRDRKEAIIRMDDGTKTVEYAQRVTVRDVEYA ATELEWSDNECYKHFPSVLEGYASTVWEEVLEELKDEDKAKANSFKSIAIPRFYKKLGGDDRKQGDTILY YLEHKWKKPMSKTPQQHYHRMVELLQIAEKLNKSQPTPNXENKKLLFFHAMPLEWQTAYKSMGRSLDDED LLGRVLPFMTSMHEKELKLQAAKKKVSFKANEKRNEQEKKRPATQQSNSNKRTTADGQKYGGTKQCLKHP GHKHTWNECFDNPKGTNYKPKTDNKSGKPAKKSTDSGDAKINDEVSSDSLFSNE Gypsy1_TP2p: GFQRQSEILYSGTQKPDSEVESKLKLKSNCTDDAKLEYGIHTSSSSILDDNTIEVFDMEEERTEYDGMPI PKIATTVDPNRYTPVTILMCDTIATLQSRKMFKVLFDSGSTRTLIKRDCLPTNAKAKALRESKTFKTLAG ELKTTEVVTMRDIKLPEFSRNRTIDSQKALVFNSPCRYDVILGADFLTKSGINLNYAKSELQWYGVSVPM KDPLALTDEDYQAMIDVHLTEEDDEVHDDWFDAYVVAPIKDAKYEAVDVDDVVKQQTHLTDEQRNDLNQL LKKYTRLFSGKLGLYPHRKVHIDLIEGAEAKHCKPYPVPHIHYETFKKELEHLVRLGVLIKQGTSEWASP SFIIPKKDGTVRWVSDQRQLNKVIKRKVYPLPVITDILKRRTGYAFFTKLDLSMQYFTFELDEESADLCT IITPFGKYKYNRLPMGLKCSPDIAQEAMENVLHGIDDTEVYLDDIGVFSKTWQDHLKVLEKVLNALEVNG FTVNPLKCEWAVKETDWLGYWLTPTGLKPWKKKIDGILKMQPPKNLKELRGFIGAVNYYRDMWPKRAQTL KPLTDKSGAKKFEWTQEMNKAYEAMRSMIVAETLLTYPNHNKPFDIYTDASDYQMGACIMQEGKPVAHWS RKLTGAQRNYTTMEKELLSIVEVLREFRGMLLGAELRVHTDHKNLTYHKLNTQRVLRWRCFIEEYSPKLI YIKGEKNVIADTYSRLERNDTIDVSKTPPQINDEIDEMSYLYEDSELLECYLEIPECYLIMPEMTEGAPG QSPLVYQWIREHQEACQELQQMKTKFPNQYREKQFPDNVRLIVHVKHGDNPDTQWKIALSRSMLQPTIKW YHEMLGHPGSKRLCLSLQARYYHPQLRSFVDKYTCEACKKYKLDGRGYGLLNERDINIAPWDEVAIDLIG PWTIEINNQKYEFNDLTCIDPVSNLVELIRIDKKTAKHVRRKFEQAWLARYPLPKRCIHDNGGEFTGYEF QTLLSRLNIKDVPTTSRNPQSNAICERMHQTVGNILRTLLHTTPPTDVDNATELIDEALSTAMHAMRTTV ATALGSSPGALVFARDMFLDIPLIAEWQTIASRREQIVNESLRRQNAKRRSYDYVVGQNVYKKVVDPSKL GRRVDGPYTVRQVHTNGNITIELRQGVTERINIRRVIPADEEPQ
Derived:
[1] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

© 2001-2020 - Genetic Information Research Institute