Repbase Reports

2002, Volume 2, Issue 10
October 31, 2002
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 4

DOC5_DM

DOC5_DM is a non-LTR retrotransposon - a partial consensus.

Submitted:
31-Oct-2002
Accepted:
31-Oct-2002
Key Words:
Non-LTR retrotransposon; ORF1; ORF2; JOCKEY clade; reverse transcriptase; Porto-1; DOC5_DM
Source:
consensus
Organism:
Drosophila melanogaster
Taxonomy:
Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta; Pterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila
[2] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
DOC5_DM, a family of Jockey-like non-LTR retrotransposons from D. melanogaster.
Journal:
Repbase Reports 2:(10) p. 4 (2002)
Abstract:
DOC5_DM belongs to the JOCKEY clade of non-LTR retrotransposons. DOC5_DM is a separate family. Members of this family are ~94% identical to the DOC5_DM consensus sequence. Therefore, this family was active a few million years ago. A portion od DOC5_DM (positions 4578-4089) was described previously as the Porto-1 repeat [1]. DOC5_DM is less than 70% identical to reported retrotransposons. The sequence is incomplete, There are ~30 copies of DOC5_DM present in the sequenced portion of the D. melanogaster genome. The amount of sequence data is not enough for a complete reconstruction of the ORF2 protein encoded by DOC5_DM. ORF2 in the consensus sequence is corrupted by mutations accumulated in DOC5_DM elements during their immobile vacation in the genome. ORF1p (positions 211-1947): MSASDAQNQKRELQAKQNKNNSYLSFTHISNYTNNYQSLHPQSDGRARSCSPALERPNNYSQHRSAECAP NSSARTPTTTSAIPINTHSTLPLTAVTLSALPLWTLPLSATSETNTTTVATIATTTTVFYVSMPICSSSA NIKTPSSIPASTKINKTQSSLPNQQNLKLYRDNQSPNSSKDLLNNNKKQRNKAQTATQKTLKKYWLAEPH SSNRFELLAQDDEDENQTDNGTNATINTQMQIEHKSAKPPPIYVQNVENIYALTTALNSLEETRYELKAL SSNEIKIQPLETTHYHNILRLLKDKSTKYYTFRPKDQRGFKVILRNVHHATDKDDIINELAQQGHEVINL HNIQRYDSKQPLPLFSIELKMKDNNKDIYKIEHLLHCKVIFEPPRPKRTLPQCTNCQKYGHTKNYCTKDP TCVKCAGKHSSSSCTINTRSDRTSIKCALCSENHTANYKGCMVYKALQIQKYPTLRKKEIPVTETTHQTT QHSTTNNVVSLKTPALSYAEVLNKNQVTSHQTNSTPQPTIVPDIQPASTQLSQTAQNDFDELKQMMKQLI AQMTNMMNIFTLLLFKLDK C-end of ORF2p (positions 2937-4427): NRLQYYLSKLETTLSTNYSLWKATKKFTNSTIHKPPIKRNNNTWARSNKEKADTIYNDNAELPRQITNLN CAIKTITKAEIKSHIKQIKNKKAPGYDLIGGKILKELPDAIITYIRNLFNGILRLQYFPITWKVGQIKAI PKPNKNANTVSSYRPISLLPVLSKVFEKVLFEKLLFNRIEPILKQKNIIPPHQFGFRKQHSTVQQVHRVI NKITDDFDKKKFCYAVYLDIAKAFDKVWHKGLLHKLRNILPYNLYTILQSYITDRYFYIKYDNECSDIMP VSAGVPQGSVLGPILYLIYTSDIPAPTTPGSMIATFADDTVLMSSSACEKTAASTLQQIMTQTVSWFERW GIEINKDKTQQVIYTKRQPKNFAIKINDNQILLHPYAKYLGLTIDSKLTWKQHILNKRNEIKNKFRQLNW LIGKHSKLELHNKIAIYKAIIKPIWTYGIELWGTASKSHLQLIQRTQSKMLRIITKAEWYIRNEDIHNDL NIETVNETIKKKQQKTHKSTT
Derived:
[2] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:
  1. Coelho,P.A., Nurminsky,D., Hartl,D. and Sunkel,C.E.
    Identification of Porto-1, a new repeated sequence that localizes close to the centromere of chromosome 2 of Drosophila melanogaster
    Chromosoma 105 (4), 211-222 (1996)

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