Repbase Reports

2004, Volume 4, Issue 9
September 30, 2004
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 229

GYPSY3-I_CB

Caenorhabditis briggsae family of LTR retrotransposons - a consensus.

Submitted:
00-Sep-2004
Accepted:
30-Sep-2004
Key Words:
LTR; Gypsy clade; 4bp TSDs; GYPSY3-LTR_CB; gag; AP protease; reverse transcriptase; RNase-H; integrase; GYPSY3-I_CB
Source:
consensus
Organism:
Caenorhabditis briggsae
Taxonomy:
Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Pseudocoelomata; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
[1] Authors:
Pavlicek,A. and Jurka,J.
Title:
GYPSY3_CB - a family of LTR retrotransposons.
Journal:
Repbase Reports 4:(9) p.229 (2004)
Abstract:
There is only one copy of GYPSY3_CB internal sequence in the genome. It contains fragments of gap and pol ORFs. This internal sequence was probably autonomous, all other elements contains just 5' fragments. LTRs are listed as GYPSY3-LTR_CB. GYPSY3-I_CB is related to CER1, CER2-I_CE, CER3-I_CE elements from C. elegans and Saci-2_INT from Schistosoma mansoni. GYPSY3-I_CB_ORF: 716-1277 (187 aa) gag fragment MDDLLESPTSSNGMEKSTLLQNPNESLVNELLNWEMPVPVQKETVSDDVEMKEVEDRKKAEKAEKAGGAE RVEEGVATEAEKSTKVRMVWEKQCCAEEDEEARKEALANLMKYAKGSLIHLEGILKPLDKRIEKKNGMIE LKNSEIVEMKRINAILENEILDLQIDGNRLESPRRPDSTKVKKVTEE GYPSY3-I_CB_ORF: 1307-1964 (219 aa) gag fragment MDIHALEDMKEIFRKTESIKKQKATLDELVNATETEKNWLQAQLTKQRQQWNEDKLKMRMLEERVRQYEE EDKWKVGNSQSNSYSRIGKNKESTDENSAKNGFQTQGDAFPSGPSTRRRMPMEDKCHMQGECGNSEELGE RRERPRTMMEGVNLSYGAHGDESGREYEEEVKQGYYQSVWGQGRQTHHQGEQGEGWKMVLAHKRYRSLPY SRLKERIPA GYPSY3-I_CB_ORF: 4158-5424 (422 aa) pol fragment MSPRVQWLAPSVCQANSEGKALENLFNSSSTPLELKKGDVIAVGELEGFDVVGDKAEHMEDEALDEYINS LGFHEQENAISINEISVTGNDRLKVICEQLKKGEVTPEEERVWKVVEEFQDTFAIDDCELGKAEVVQCEI ELKEGTEPIRQRPRPIPLAIRPEIKEMIRKMLKQGVIRESRSPWSCPVVLVKKKDGTVRMCIDYRRVNKV VKNNAHPLPHIESTLQSLVGKKIYSTLDCLAGYWQIPLAEGSKQITAFAIGSELFEWNVLPFGLVTSRAV FQATMEMVVEDLLGKCAYVYVDDLLVASETLEQHAEDLREILLRLRKSGMRLKAKKCHIARMEVEYLGHM TTPGGVKTEYLKVERMLNYERPTDKKGVHSFIGLFGHYRRFIWNFAAMACPLTPLTSSKREWVWGEEQET AF GYPSY3-I_CB_ORF: 5487-6687 (400 aa) pol fragment MTGENPFLIYTDASKKGVGAVLAQLGEDGEQHPILFMSKALTPAETRYHVTDLEALAILQALKRFKAIIY GAQIIVFTDHKPLMYLLKGSPLSDRLLRWSLEFMEYNMKVVYVAGKANAVADALSRGGCLKLEIDDAETT DLIGSLEVEEGEESNELEVAKWFDWLKEEEGWREVIQLLESGVSVGKVKVEGQKKKILVQNYMIIGGRLK NIEMEEKNRLVVPERERLKLVTQAHSGPLSGHFGTDKVWKQLKKEFYWPTMRAFIEKFIKGCTKCLCVND RPRLTAPLHPYETTSPLEIVACDLIDVGLSTLGNRYILTMIDLFTKIATAVPIQDKCAETVMRAFIERWA LGECRIPEMLLTDQGKEFANDHFKKFTQMMGIEHVMTKGYNSRANGAVDR GYPSY3-I_CB_ORF: 6700-7189 (163 aa) pol fragment MHIIAKKAAVPMEWDAQVPFAVYAYNTTLHGTTRESPLFLMTGKDPKGPLQMAGVDADGISYVDIDEYKH LMTQELLKIHKMARKNAEWERGRNKHLFDEKLKTEMRKYPQPGSRVLIEIPSEKLGARCPKLVNKWRGPY RVISCSENSATVTPILGKDKEKK GYPSY3-I_CB_ORF: 7482-8388 (302 aa) pol fragment MKAKKDVAPEATSDVSGRPHQDRAEQLQWEQEAMLLSQGPHPDFNGLPDYEACMRLSRCPSMMLVATTLP GWKDAFDFQRAQFLQKHFRSDLFKPKLFHCVRLPGVAEKEVPLSQKVFQINSKQEYVDAEGPKEIRKAKS VLMVVPFTTEETEIESWNRYIQKVDSKVEIWLVPSPRMDLNAGRIVTFGNLLSQMQRGDGGPLHVFSPDD QNKEHPLWSIAFNKNFRDYWRNVKAIADAKKLRWPGFHVDDKVDRKPEDAATASTSSSSRKIDRPTSSNC PRYQLYITTTMQKAGKGRYQHQ
Derived:
[1] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

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