Repbase Reports

2003, Volume 3, Issue 7
July 31, 2003
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 126

Copia4-I_TP

Copia4-I_TP is an internal portion of the Copia4_TP LTR retrotransposon - a consensus sequence.

Submitted:
31-Jul-2003
Accepted:
31-Jul-2003
Key Words:
LTR retrotransposon; Copia clade; 5-bp TSD; gag; protease; integrase; reverse transcriptase; RNaseH; Copia4_TP; Copia4-LTR_TP; Copia4-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:
Copia4_TP, a family of copia LTR retrotransposons from diatom Thalassiosira pseudonana.
Journal:
Repbase Reports 3:(7) p. 126 (2003)
Abstract:
Copia4_TP is a young family of copia-like LTR retrotransposons. Copia4-I_TP, an internal portion of Copia4_TP is flanked by 99% identical Copia4-LTR_TP LTRs. There is no tRNA-like primer binding site in Copia4_TP. Instead, this retrotransposon uses self-priming by the 12-bp TACTTCGAAGTA palindrome present at the very 5'-end of its internal portion. The internal portion encodes the 328-aa Copia4_TP1p gag (pos. 191-1131) and 1319-aa Copia4_TP2p pol (pos. 1132-5088), respectively. Copia4_TP1p includes RING Zn-finger, 39% identical to a similar motif in gag (NC) encoded by Rous sarcoma avian retrovirus. Copia4_TP2p is composed of the protease, integrase, reverse transcriptase and ribonuclease H domains. Copia4_TP1p: MSGDSRNVQYPKWDGKASTCPRYLDHVESLAVFHDCGDAFDKTTMANCPKKSEFDILMGQSTKTDDDKEK INLYKQNRRMCAILKLGQESDHGLAIVKKSVSVDHPNGLAWKIVKHLTDKYRPNDVAARIQMTNALKKLK FGDANKYYNDVVGVCAKFNVVKSETEMIEIMADAVTDPVYSQMVLRHLESSDADDLEQLCLEMSKLQRIT KTSEHVPEDKKQKEVQLATTDGNSNSGGSFNGICRNCNKKGHKKAQCPEKKSKSYKNDGDSKECAGCGRK GHSESHCWKKHPEKAPKWFKDGSKTESASGVNVEVCLSQLDVTGQDFA Copia4_TP2p: SLFESVGCHWAGFCLGLSDSPQYWQADDDFDAELDVGNVLEAEKPETAAAVTRTQWLADGDSTVEKPERT TAVITNTPWLAGNVSETEKREARAVKNTLWLADGDSTVEKPRAVKNTLWLALEVMYAVVCVIAVTGWLVL DFLKDRVLTVVAGRLDVDVSAAKLETVGSFGMLQDNDTWICDTGATGHSTSNNIGARNAREAVSVSLGNA GQAIKAQSVIDIAGQFVNNDGTSGIRGTLKDVSYHPEFNFNLLSLTKLLTDGWEIRTGNGERIVVVNKVG DVINFDLKIPTARGMLLACRFIRDVEIGAASTSTGLKLNIHKAHRLLGHRSEASTRAIAAMLGWTITRGT LGPCEFCARGKAKQKNTNKNRDESVEKVTVPGELVHLDLSKVTVHEDDGSEFDLNHKYWKILVDAATGKK WSHFTTTKSGMVEPTCEWLNKCKTRGLNVKAIRLDPAGENKKLEKRAQSVEWQSLQPLDFQFTSRDTPQH NSDAETSFPYLAGCSRAMMGAAYIPGGVRGKVVIEALQCATMLDGLVAVTVNGVTATRDEHVFKSNPKWA NHLRTWGEAGVVKEGKRSKTGDRGKTMMFVGYAADRESDSFRMWDSDTNRVVVTRDVIFLKRMFFERPVH ESNYLMDEMSEETRTNVRKEASEGIDGDSDDEDETPPDDRDSDEDESEAGRVDDDDAIATRQSRVGRVCR TPEWLKDYETKLVNSEPGTFAEMRYLCLLAECHNDELFTVMKAYNDMETMFIGAGVGGGFSNTNELKVMN FKQAMASDDADEWNDEIGNEHKRFKKFNAVTVVKRKDLPKGAKVCTTTWAMKKKANGTYRGRLNVCGFEQ VEGMHFFVDSIAAPVTNPNTIRFCLVLLECMPLWISRVLDVEGAFLQGQFVNGEVIYIGVPDGMEKYYGS RDDVVLLLNVPLYGTKQAANCFYTSLRKSASKRNYKRSRADPCLYYIWTDGRLALFATWVDDIIVFGHPQ DVDAIEKNLKEAFVCKSEGELKEYVGSKIDVMRKSNGLATIKITQPVLIQKLEDEFDVSTGKAPGTPARP GEVLSKLHGGELLTSAAATNYRSGTATLMFIMQWSRPDIFNATRGCARHMSAPGTVHNDALYWLIHYVIS TRNRGLVLEPDRVWDGSSKFKFRIGGRADSNYAANEDDRRSVSGGRVRLEGCPVTFRSATQRFVTLSVTE AEGAAGNMVAQDMMYLYRSLTEIGLSVELPMVLEMDNSGAVDLANSYSVGGRTRHVDVRLYYLRELKEEG LLVIKHIPGENNDADIFTKNTDARTFERHIPSFVGKDEYMVGGEEDVKKPRRVRFANGS
Derived:
[1] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

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