Repbase Reports

2002, Volume 2, Issue 11
November 30, 2002
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 3

DOC6_DM

DOC6_DM is a non-LTR retrotransposon - a consensus.

Submitted:
00- - 0
Accepted:
30-Nov-2002
Key Words:
Non-LTR retrotransposon; ORF1; ORF2; JOCKEY clade; reverse transcriptase; endonuclease; Strider; DOC6_DM
Source:
Drosophila melanogaster
Organism:
Drosophila melanogaster
Taxonomy:
Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta; Pterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
[3] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
DOC6_DM, a family of Jockey-like non-LTR retrotransposons from D. melanogaster.
Journal:
Repbase Reports 2:(11) p.3 (2002)
Abstract:
DOC6_DM belongs to the JOCKEY clade of non-LTR retrotransposons. DOC6_DM is a separate family. Members of this family are over 99% identical to the DOC6_DM consensus sequence. Therefore, this family was active very recently. A portion of DOC6_DM (positions 1482-4089) was described previously as the Strider non-LTR retrotransposon [1-2]. DOC6_DM is less than 70% identical to reported retrotransposons. There are 10 copies of DOC6_DM present in the sequenced portion of the D. melanogaster genome. DOC6_DM encodes the 389-aa DOC6_DM-ORF1p (positions 178-1327) and the 884-aa DOC6_DM-ORF2p (positions 1328-3979) proteins most similar to the ORF1 and ORF2 protein, respectively, encoded by DOC-like non-LTR retrotransposons from the JOCKEY clade. DOC6_DM-ORF1p: MRTKRNKPLVERQNERGSKQFTNYFRPLQTLDDDNDDKPIETDTLDEIIIKPPPITLIKQNTKFVHELMA KIKTDDYFIKTISIGIKIFLPNMDCFNAACNQLKEHNCEFYTYDTRSNKPYKAILSGLDKLPIETVKSML QNLGLQCTEVKIVEKKTKSDHELLLYIVYFVNKSITVKELRKNFMYVNHTKVRWEYKVKLQNKITQCYNC QLFGHGSNNCSVKTSCAHCAGSHQTAVCMDVNNKKCANCKGDHPSTELTCPCRISYLNLLSKRSSQRIGR NNLEAHGMRNSKQHIAPSALFGNQPQISLPTQTKRVQQLNFGSYSNALTNIHTLPNPKANITNETNLFSC EEINSLLSELITRFNECSNKGEQFQVISQLAIKYVYTNK DOC6_DM-ORF2p: MFTQTNNFIDNLNIMAWNARAVRNKRIELIKFLENNHIHIALINETWLTHSDRFNIPEYTIYRNDRKESR GGGVAIAVSNTLIHEQIPCIKSHVIENVGIQINTDSNSSLKIYSIYFAGNTSKCIPSSCDLSWDHNHLKS LYRSDLLKISQINGNFLICGDFNSRHRAWKCTRANGWGKILNELSDLGKFSILYPTQPTYIPHNHKAKAS TLDLCLTNIPNQLANPAVMQELSSDHLPVVIKYSTNFMRNVKTYPILGRANWALFKRIINERLMVEEVVV NCSQISTLDIDNLIGSFTRVINYAFLKAVPHKPIHHSKLTLPVHITELFKTRNIIQRQWFRSRHPLLKSR CDHLNYIIRKELFIYNNAKWNNKLQKLDKCSKPFWNITKAIKKRKQIVPCLSKADEIYASGKEKANILAD VFQLKHNLTHSYSNQNTIDQVKISLQSIAETPNNIAEICRVTYPEVFSIVKALHTRKSPGIDGIPNISLK NLPTSAINHIVNIANHCLQAGYFPRDWKIAKIVPILKPGKPPDNPESYRPISLLSGLSKILEKLIKLRLV KFLDIHNTLPTVQYGFRNGLNTILPTLKLRNYIKESIQSKQSVGLVTLDIEAAFDTVWHDGLLHKLKMIG TPIYLIKIVQNFLTHRYFSVNLNSSQSARRILNAGVPQGSVLGPTLFNIFTHDIPQATNCVLSLFADDAA VYSAGFSYSEINQSMQSYLNELDIYYKKWKIKINPNKTNAIFFTKRRKPRYLPDRQLRILDSPIQWVDNI RYLGIIFDKKLTFKYHINNTIMKVNKIICTLYPLINRKSKLSISNKIIIFKTIFNPILMYGSPVWGRCAQ THIKKLQICQNKLLKLIMNLPYYTNTKYLHIKAGVQKVQQKIQY Copies of DOC6_DM are flanked by ~15-bp target site duplications. The 3' poly(A) tails of DOC6_DN elements are formed of the (TTAAA), (TTAA) or (TAAA) microsatellites that follow the 3' AATAAA polyadenylation signal. The tail is not included in the consensus sequence.
Derived:
[3] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:
  1. Kronmiller,B.A., Svirskas,R., Carlson,J., Patel,S.P., Wan,K., Pacleb,J., Champe,M., Kaminker,J., Rubin,G. and Celniker,S.E.
    Drosophila melanogaster transposon strider.
    Unpublished
  2. Kronmiller,B.A., Svirskas,R., Carlson,J., Patel,S.P., Wan,K., Pacleb,J., Champe,M., Kaminker,J., Rubin,G. and Celniker,S.E.
    Direct submission to GenBank.
    Direct Submission to Genbank (2001) Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA

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