Repbase Reports

2003, Volume 3, Issue 7
July 31, 2003
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 132

Gypsy3-I_TP

Gypsy3-I_TP is an internal portion of the Gypsy3_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; RNAseH; intergrase; Gypsy3_TP; Gypsy3-LTR_TP; Gypsy3-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:
Gypsy3_TP, a family of gypsy-like LTR retrotransposons from diatom Thalassiosira pseudonana.
Journal:
Repbase Reports 3:(7) p. 132 (2003)
Abstract:
Gypsy3_TP is a young family of gypsy-like LTR retrotransposons. Gypsy3-I_TP, an internal portion of Gypsy3_TP is flanked by 100% identical Gypsy3-LTR_TP LTRs. The consensus sequence encodes the 368-aa gag-like Gypsy3_TP1p protein (pos. 421-1524) and 1239-aa Gypsy3_TP2p polyprotein (pos. 1528-5244) composed of the protease, reverse transcriptase, ribonuclease H, and integrase domains. Gypsy3_TP is characterized by 5-bp target site duplications. There is no tRNA-like primer binding site in Gypsy3_TP. Instead, this retrotransposon uses self-priming by the 12-bp CTTTGAATTCAAAC palindrome present at the very 5'-end of its internal portion. Gypsy3_TP1p: MVLDDMFKKKNLLQQWNVNNAEAMRIIELGETPENESALLDLRANKAAAINEAFNLVDRTLDGAAKETWR ECKQRACDKEWKDAQDAVQPARGKTWESLAIARRFFSLTVMVKDAAEQQKNYHENYVKQPRGMKVRDFVT RNHHLNAYYPYLLCMADTDGAPDDMPREDTKLTEMRLSQVVLRAQTQQVQDGWYAIHGSKIPTDVNQLRD ELDPINVQVQRRLKQDQLNRKNQDSVHGSSSDKKNGTARFMSGGEGKKTDTGRIPRKPKGNGNKGDEQKR HRNLCAQFGGNHSTHNTSVCRRWTKEGKQQAGWKQQRPNGNGKRDFAASLEKQEKEIHALKKLLKKKHKK RKRAYQYASDSSSDEESK Gypsy3_TP2p: DNGLSASVCLTDVERHTSSALLNESIGSKVSPKNNYYTTSSNSKSKSITNTNRPMKGTPTNLNVVDKATL IQMNPDDSESTSMNTKATAVLAVPISAKNAAKYSDPRRMGGKVVKLWRVLLDSGSDGDIVFIQKGSNYVS TKRRISSQRWRTSSGTFHTDKVGDVDILLPEYSNSKYISVKADVVEYDGTRGDQKPTYDLILGVNTMREL GIVLDFDTLKITIDKITLPMRDISSLQRTKDCAKIYENSFFLNYFDTAYEPNSTKEMTNRAVEILDAKYE KADLQKIVDEYCSHLTKDQQIQLLRVLEEFEELFDGTLGDWKTSPVQFELKQDAKPYHGKAFPVPFIHKE TLMKEVQRLVDLGVLIPQNDSEWGAPTFIIPKKNGTVRFISDFRELNKRIKRKPFPIPKISTVLQELQGF TYATALDLNMGYYTIRLDPDASKLCTIILPWGKYSYARLPMGVAGSPDLFQSKMSALMANLEYVRTYLDD LLILSKGTFDDHLEKMVEVFERLREAGLRVNAAKSTFATDEIEYLGYILSRAGIKPQPEKVQAILAINPP KNVKELRKFLGIVQYYRDLWEKRSAMSAPLTDLVGECGVTKTTKQKGTVKAPWYWDEKHQQAFENVKAMI ARDVVLAYPNFKEEFVIYTDASKRQLGAVITQNNRPIAFFSRKLSEAQSKYSVTELELLAMVECLKEFKG MLWGQKITIHTDHVNLMRDALGLSSDRVYRWRLLLEEYAPKIVYIKGEVNTVADAISRLEYNPEINPDRK CFYSDKTKKYLFFGESAVSTDHRCMAITKLLVDYTNVSNEKSNTSHINDVFANRSEEEEYYPLTVSEIAE SQQNDTGLQEDLRKSKRHLALRVIEGTEVIVYKGNRLYIPKDLRKRAVVWYHHALQHPGHTRQEETMSAT MYWSGIRTDIRKHVKSCVNCQKNKNSSQQYGKLPEKEPATIPWEWLCCDLIGPYTLKGLDGTVVDFMCLT MIDPATGWFEVVELPLTDVVSEKGDVSEKFDKTSARISRLINQCWLSRYPRPRYVIYDNGSEFKLHFERL FDDFGVKRKPTTIRNPQANAILERIHGVLGNMMRTASLDMAETVTEDAVEYFLTDASWAIRSSHHTVLKA SPGAAIFGRDMLFNIPFIADWEQIGLRRQARIIKDNKRHNKDRIDFDYTVGQKVLLRQDGINRKAAEKFT GPYEITQVHTNGTVRIQRGTVSERLNIRRIKPFFEKDGEIMQTIKQRKR
Derived:
[1] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

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