Repbase Reports

2001, Volume 1, Issue 4
April 30, 2001
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 4

ATCOPIA94_I

Internal region of the ATCOPIA94 copia-like LTR-retrotransposon.

Submitted:
30-Apr-2001
Accepted:
30-Apr-2001
Key Words:
LTR-retrotransposon; COPIA superfamily; internal region; copia-like polyprotein; reverse transcriptase; the ATCOPIA94 family; ATCOPIA94LTR; ATCOPIA94_I
Source:
Arabidopsis thaliana
Organism:
Arabidopsis thaliana
Taxonomy:
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; Rosidae; Capparales; Brassicaceae; Arabidopsis
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Internal portion of the ATCOPIA94 copia-like LTR-retrotransposon.
Journal:
Repbase Reports 1:(4) p.4 (2001)
Abstract:
ATCOPIA94_I is an internal region of the ATCOPIA94 copia-like endogenous retrovirus. ATCOPIA94 forms a separate family of copia-like retroviruses present in the A. thaliana genome since members of other families are less than 75% identical to ATCOPIA94_I. ATCOPIA94_I encodes remnants of the ATCOPIA94p copia-like polyprotein. The ORF which encodes ATCOPIA94p is damaged by one frame shift induced by a 5-bp deletion at position 3264 (masked by XXXX in the 1436-aa ATCOPIA94p sequence). Such a low damage indicates that ATCOPIA94 has been retrotransposed recently. ATCOPIA94 is inserted exactly between two hypothetical genes that are 86% identical to each other. ATCOPIA94p: IPSPLNAHYSLEDIVSYYYSKASDHPGHVISHPLLRGDNYEEWAINLETALASRKKFGFLDGRISKPEED SSDFDDWKSINALLVSWIKMTIEPNLRSNISHKPVARDLWEHIKKHFCVSNGPRVQQLRKELSNCRQDGL SIETYYGKLTKLWDNMDACRPRIVCTCGKCICDCLAVLETLREHDKVHDFLMGLDESAYGTVRSSLLIQE PLPSLEYVYLKVTQDEDSRSHKQVSDSRPDGMVFAAQHASRVRPGERSSSTTVCTNCGRTGHMAESCFQI LGFPEWWGDRPRNQNGRGCGTKSNGSGRGGGVVARDNVAQGASSSEVVHANVAITDADRAAVLNLTDEQW ISVKRAINATKGNSDEQLSGKSSSTSWILDTGATNHLTCRRDILENVRKSTSTPIILADNRIVMGDMVGS VTLNKHLKLHNVFYIEDLGFDLISVTQLMEENDCVMQLSVPFCVLQDRTTRTLIGVGKPSGGLVYFRSTE VAVAVKGVPKQSLELWHQRLGHPSLKVVESLPDFVFSSHKDFSNKACDVCIRAKQTSSSFPISNNKTTEI FEMIHCDIWGPYCEPSSSGARYFLTIVDDYSRGTWLYLMKNKSDTQTKLRDFIALVDRQFGKKVRVLRSD NGGEFLSLTSYFLASGIVHETSCVGTPQQNGRVERKHRHLLNVARAIMFQGSLPIQFWGECALNAAYLIN RTPSMVLNGKTPYKVLFGKRPSYDHLRTIGCLCYIHNQDHHGDKFASRSRKCVFVGYPYAKKGWRVYDLE KEIFCVSRDVVFDEGIFPFHNDLNPLPLTLDTTSSLTPFYSDDDDDDNGPTTCSVSVPPVPVIPLRVAPI SLADSGSKVDLPNDDLVLPDSASTTPLPTDPKPTRERRQPAYLADYETTFLCGSSSTPYPISDVLTDARF SSAHKAFLTAITLAHEPATYAEAFADPKWRDATKEEIDALVLNHTWDIEDLPLGKVAIGSKWVFKVKHXX XXTVERYKTRLVALGNRQKEGIDFDETFAPVAKMTSVRIFLSIVAARNWEVHQMDVHNAFLHGDLEEEVY MKLPPGYFAQHKGKVCRLRKSLYGLKQAPRCWFAKFATALKNYGFQQSYSDYSLFSFNRDGVSLYVLVYV DDLIVTGNSTTAISEFKQYLDSCFHMKDLGLLKYFLGIEVARSPDGIYLCQRKYVLDILQDTFLLGAQPS GFPIEQNHTLASATGSFLTDLASYRRLVGRLVYLNVTRQDLAYSVRVLTQFMQKPREEHWTAALRVVRYL KGTPGQGVLLRANSDLHIYGWCDSDFSGCPRSRRSLTGWFVQLGQSPVLWRTKKQKVVSMSSAEAEYRAM SLTARELVWLQALLEDLAVFLSRPMTLYCDSTAAIHIAANPVFYERTKHIERDCHFVREKVQNGTIATVH VSTTTQLADIFTKALGSREFDVFRDKLGIEDLHAPT
Derived:
Positions 32279 36916 Accession No AC022354 GenBank (rel. 124.0)
Download Sequence - Format:
IG, EMBL, FASTA
References:
  1. Kapitonov,V.V. and Jurka,J.
    Internal portion of the ATCOPIA94 copia-like LTR-retrotransposon.
    Direct submission (December 05, 2001)

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