Repbase Reports

2004, Volume 4, Issue 9
September 30, 2004
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 233

GYPSY5-I_CB

Caenorhabditis briggsae family of LTR retrotransposons - a consensus.

Submitted:
00-Sep-2004
Accepted:
30-Sep-2004
Key Words:
LTR; Gypsy clade; 5bp TSDs; GYPSY5-LTR_CB; Cb000288; GYPSY5-I_CB
Source:
consensus
Organism:
Caenorhabditis briggsae
Taxonomy:
Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Pseudocoelomata; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
[2] Authors:
Pavlicek,A. and Jurka,J.
Title:
GYPSY5_CB - a family of autonomous LTR retrotransposons.
Journal:
Repbase Reports 4:(9) p.233 (2004)
Abstract:
The consensus sequence was reconstructed from the Ensemble genome annotation. The internal part contains two putative ORFs and thus the family was probably autonomous. Flanked by 5bp target duplications. Related to GYPSY6-I_CB, GYPSY1-I_CB, GYPSY21-I_AG, and GYPSY18-I_AG. LTRs are listed as GYPSY5-LTR_CB. GYPSY5-I_CB_ORF: 37-2320 (761 aa) MADLTQQLASLITAFGQFVQNPASSPTSVPSNVSTRTSQLVESISTRIPNFSYDPDEEKTFDGWWNRYED IITKDGSSLTEDAKVRFVLSKLDSKEYYHFSNRVLPATPNSLKFTDLISKLSDTFKSTSSIFRKRQEFLR MEYDGSSIEEYTVLVLRRFTSSEFKKMTDDQTCCMVWINGLRDSSYIDIRTKALQIMESKPTTTLLELEK EIKRLLDIREDSKSVCRVQQPAEVNAINRKSSTDKSQKSQKPPPSPCFKCSGNHWARECQKKVTCLNCQK SGHIAKFCRTKVKGNECPKGKIKSVIIGSATNSQVNRIYRTVIINGKKLKMQMDTGADITMISIKDWKLL GRPELQSPTIQVKSANHQPIAVKGFFKCHFKLNGTSASGMAHVAETGTLLGTDWISKDPHFWRMLNANQV SKVSSDVGSACDYLDNMREGLKAELNKQFSDVFKPELGRCTKTKASLVLKPNAQPVFRKARPVPFAAVST VSEEIERLQKAGVISPVDHSDWAAPIVLVKKKNGSLRMCADFSTGLNDAIQLHQHPLPTADDIFATLNGG KYFSQIDLAEAYFQLKLDEQAKSMLCINTHKGLFRYNRLAFGVKSAPGSFQQVMDSMITGLDGTAAYLDD IIISGSTIEEHNKRLMALMKRINDYGFRIRLEKCTFLMERITFLGFVIDANGRRPDPEKIAAIDQMPPPT NDSQVRSFLGFIQFYGSLSRSCSSFVHHWMPLQRRMSNSNGLLNVNFHSTASSRFFVPICC GYPSY5-I_CB_ORF: 3154-4141 (329 aa) MNVLLFLKIQQKNTLCSWPIPTAPWQRVHCDYAGPVNGRYYLVIVDAFSKWPEVIPTTSITSTATINILR RIFAQFGDPETLVTDNGTQFTSSQFQSFCKDRGISHLRSPPFHPQSNGQAERFVDTLKRGLGKLKGEENT DTALYVFLQNYRSTPCSSSPDGSTPAENFIGRKIRTFLDQLLPNDQLLVSHDTEMEKQFNKQHGARRRSF IADEKVYVKNFSSINTTTWIPGIIQRHIGRTLYRVLVKDTVWIRHANQLRRRDNPIYIDVPLNLMDQIDV TPTPAPALTSSTAPPSPVPTPPTPMPRKSTRITRQPQRLVVQPSQKSYN
Derived:
[2] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:
  1. Stein,L.D., Bao,Z., Blasiar,D., Blumenthal,T., Brent,M.R., Chen,N., Chinwalla,A., Clarke,L., Clee,C., Coghlan,A., Coulson,A., D'Eustachio,P., Fitch,D.H., Fulton,L.A., Fulton,R.E., Griffiths-Jones,S., Harris,T.W., Hillier,L.W., Kamath,R., Kuwabara,P.E., Mardis,E.R., Marra,M.A., Miner,T.L., Minx,P., Mullikin,J.C., Plumb,R.W., Rogers,J., Schein,J.E., Sohrmann,M., Spieth,J., Stajich,J.E., Wei,C., Willey,D., Wilson,R.K., Durbin,R. and Waterston,R.H.
    The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics.
    PLoS Biol. 1(2), 166-192 (2003)

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