Repbase Reports

2004, Volume 4, Issue 9
September 30, 2004
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 225

GYPSY1-I_CB

GYPSY1-I_CB is an internal portion of the GYPSY1_CB LTR retrotransposon - a cosensus.

Submitted:
00-Sep-2004
Accepted:
30-Sep-2004
Key Words:
LTR; Gypsy clade; mag lineage; 5bp TSDs; GYPSY1-LTR_CB; Cb000423; gag; protease; reverse transcriptase; RNase-H; integrase; GYPSY1-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:
GYPSY1_CB - a young family of autonomous LTR retrotransposons.
Journal:
Repbase Reports 4:(9) p.225 (2004)
Abstract:
The consensus sequence was reconstructed from the Ensemble genome annotation. Copies are 99% identical to the consensus. Flanked by 5bp-long target duplications. GYPSY1-I_CB is related to GYPSY21-I_AG, GYPSY3-I_AG, and GYPSY18-I_AG. The 5' LTR (24bp) and the internal part encodes a 1390aa long gap-pol polyprotein. LTRs are listed as GYPSY1-LTR_CB. GYPSY1-I_CB_ORF: N-24nt - 4147 (1390 aa) MPPPGDTTTGDQATELADLTKQIGLLVNIFAKLAQASANAPLTTTPTSGHNLLVESISKRIPIFTYDPDD DQTFDTWYARYEDVLTKDGESLEEGEKSRVILSKLSSKEYSHFTNRILPKLPNELNFAELISKLRETFKS TSSIFRKRQDFLRTEYFGGAIEEYTGQVLRKFTSSEFKKMTDDQVCCMVWINGLRDNTYSDIRTKALQVM EAKPECTLLELEQNIKRLLDVRADSKSVCKLEPKSSEINAISTKETKRDKPQKAPPSPCYKCGGNHWAKE CQKQVTCHLCKKDGHIAKFCRTKKRETDQKGKNNRIKSVMVRSASTFEPSRIYRIVTINGTKIQMQMDTG ADVTLISTKDWNRLGRPQLQAPTIQVKSANHQPIKVRGSFQCNFVINGNVASGQAHVAETGTLLGTDWIS KDPTLWKTLNQQICAVSSDVGSACDYLDNTREQLKSNLEKEFNNVFQPGLGKCTKTKASILLKPGAQPVF RKARPVPFAALTTVSEELERLQQSGVISPVDHSEWAAPIVLVKKKNGSIRMCSDFSTGLNDSIQQHQHPL PTADDIFATLNGGKYFSQIDLAEAYLQIEIDEQAKQMLCINTHRGLFSYNRLPFGVKSAPGCFQQVMDAM ITGLDGAAAYLDDIIITGSTIEEHNSRLKSVFKRIDDYGFRVKLEKCTFLMPRITFLGFCIDKDGRRPDP EKVTAIQQMPEPKNDSQVRSFLGLIQFYGTFIKELFKFRPPLDALTKKDAEFKWTSECQSSFDNIKQMLQ SDLLLTHYDPKLPIIVAADACQYGIGAVISHRFPDGSEKAIYHISKALTAPQRNYSQIEKEAFGLITAVT KFHKFIHGRHFTLKTDHKPLLSIFGEKKGIPIYSANRLQRWATILLNYDFTIEYVNTHDFGQADALSRLI SEQIQQKECEDRVIAQVEMDVITNLVNTCEQLPVTAEMVKDYSKKDTLLAEVYEYTTSGSWPNNIDKSSQ IVFFHNRRDQLSIVSDCLMFNDRIVIPVSLRARVLKMLHRAHTGMVRMKQLARTLVYWPSIDKDIENIVR SCDQCAAVSKNPIKNTLCSWPISTKPWQRVHVDYAGPVEGTYYLVVVDSFSKWPEIVPTTSITSAATINI LRKMFAQFGDPETLVTDNGTQFTSAQFHDFCKDRGIQHTRSPPFHPQSNGQAERFVDTLKRALGKLKGEG NTDASLYLFLQSYRSSPCTASPNGSSPAENFIGRKIRTFLDQLLPTDQLPNSHDTEMEKQFNNQHGARCR NFNVGDKVYVKDYRSINTTTWIPGTIQRRIGRTMYRVTVENNNFWIRHTNQLRRRDTPTSFDVPLDTMDT MDAIDWTPLSTTLPDRSPPTPAPILPGSPTAPSPKPIRKSTRTVKPPPKFVMKPNKKSYH
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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