Repbase Reports

2004, Volume 4, Issue 9
September 30, 2004
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 227

GYPSY2-I_CB

Caenorhabditis briggsae family of LTR retrotransposons - a consensus.

Submitted:
00-Sep-2004
Accepted:
30-Sep-2004
Key Words:
LTR; Gypsy clade; CER; 4bp TSDs; Cb000348; gag; AP protease; reverse transcriptase; RNase-H; integrase; GYPSY2-LTR_CB; GYPSY2-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:
GYPSY2_CB - a family of autonomous LTR retrotransposons.
Journal:
Repbase Reports 4:(9) p.227 (2004)
Abstract:
Individual GYPSY2-I_CB copies are 97% identical to the consensus. GYPSY2-I_CB is similar to CER3-I_CE and CER2-I_CE from C. elegans. The LTRs are listed as GYPSY2-LTR_CB and flanked by 4bp target duplications. The consensus is taken from the single elements with long ORFs found in the genome. GYPSY2-I_CB_ORF: 442-1993 (517 aa) gag-like MTEQIIFEVATAMNTVASVKQCVVSDLQSVHQKIQEIASLSIDRLEAVEDRVAENTDRINTLFANRADNS GTPSTHNSAQTSHPPSRRASPTPPNEILGSSINVLGLKIGSRIPIFSGAPAENFSTFVRSFMDHVKAVNP ALEESSVRAVFLTYLTEFARDKAEELLEKHPSYTCQQLVEEMRKTFEDPNRAEMERQQLRQCSQRTDESV DDFCTRVRKLALSAHAGNSRDFIQEKAKEAFIDGLLFNLKFLVKGESPTNFQEAQNSAMKFELLLKEAAR SNTIAPQGLAVIPAPAPAQNSPWSKPKRECFYCGIPGHFARECRRKIADQAKGIFQKTNKVSNLRSQTRS FPQRNPVDNHQIFSNNPGVQAIQPVVSTIHAQMEAMQTELEVRQNQINALIKRNDELTTNPGNHQVPNRR VSCLRWSQTYLLILITFMSLFTQVAAISPLVCMPHTPQSYLRLPAPLDCSRATGHEPHPVTQKELTIFRP NTIAYEANGTLCKIVKRITKYSVNFSE GYPSY2-I_CB_ORF: 2052-3102 (350 aa) pol? MKKFLHCSHGDLVPFNGIYKTLNDHILTWPSAPFSAFLGTQTAESTNCVMMPTRVMTRFGKETPESPAGS MVGCRFSSGFCNTREGAAFQWTPNPKQECKYLELRTMKGFMTKNIWVSTEKEFAISFDQNNTRLLDCGRK LVISDQGYGIALPNRNKRSNSVDELTNFVTSNQLAAQLLAVEEVVLETTAAWFAGNFMSWCSSFNAVAAA TRAAVASNPTLAARQMLKKENIFAKYIGNDVLSLQVCSPVPQDSYEFVPFTKTCYSKPALRVRLPKNTSI VTFVDLTTRVITNRAHPVDCSLVTSFQYVSNKTLYSLNPFTLELKTDTNFQTMTIPSRSWICYSRTSNLP GYPSY2-I_CB_ORF: 3366-6717 (1117 aa) pol-like MILVSNVLTPYLPFRQPAQPQFERPQSPDGQVCDYVTLTERLRSPRINALAHPTEYFSAVVPLKANGINC WALIDTGASFTVAGQGILHLLGIPRLQEPLSYMAVGLGNNEVKMAGSAVVKFQIGSHVLFQNTHFTTGQC TPGGPRDYDFIIGNDAHYMVTDVELPSEPAQRISESTTLQMIQDFRNETTKWMTIDTPITSVPNGKRNPN VATLSRFDCDRIFALYIVKESAGGNLHLNPAHRELVSYDRPDLYTVHLTRHSEDILNPGPPNPANYYIGD LLVVLSLKRRPGAKLNEIKRDFVDILDMNKCHFWQVNKFALVQRKVEKDQPLWKMDDLKEPIDPRRKLKM PWKAECIGYNQNQVVEAKIALFKELHPQDQKCTAADILVPVLEPASTLRSLLPGDARHAVITATNVQPPI VPLKPTVTAVRVLPGKFRKYISIAPNAFKGAESDPDYDLGGKALLWTARFGLAATLAIANKGRDTTTYST TITESETTGRRSTVTFTIRRPSTAAPVSSWTRSTAFKMDISPGGTCDLEVESATLINTQLTIRAKFTFES QSRINEKNLLNQNAVVWQQLDDNLHQLRTFPEPEDWLKVPVDSPSGNVLIALTGGPEIDGIMPWDKTDVV DFAGSAVKLSEEQSYYANTLAKTKIAGVIANAPPGVGKTLMVAGAAIHAIRETNDLRSIQTLTGMTNVSV LPMVKTLRTLDPETRYPPVRLISESHREHLDPALRTEIDYPILWIKVFKDLLHRIDPSTAVATIRENPDL MSAIQHLHAKKIDPEEFAHHFIRKAVAKGPNSDRNTTPKAELFRKLYNPRIVVGTVASVLESFKTPDWTW LRENVSAIQVDEASQLPLYALAALALMFQRARLALVGDIHQLPPFEDSDLPKDIAAFAISRVLQEAIKRR TLPIIDLTVGRRCPPQVTRMYNELFYNQRLTSLWSPEKEAELRAFTAALKFGNDFPIQILDLQSSHTQSG TSLTNIEEAKAAVRIARTIQTRVGTNDIGILCFYKAQAGEVAALLGDAPFYVGTIDGSQGHEFQAVIILT TRTSSFRDSEFIEDCRRINVAISRTKRICCIIVDRPKVTTNGTWSRLIRRIPHEAKSNFSVMTARWL
Derived:
[1] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:

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