Repbase Reports

2001, Volume 1, Issue 4
April 30, 2001
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 6

ATCOPIA95_I

Internal portion of the ATCOPIA95 copia-like LTR-retrotransposon - a consensus sequence.

Submitted:
30-Apr-2001
Accepted:
30-Apr-2001
Key Words:
LTR-retrotransposon; COPIA superfamily; ATCOPIA95 family; RIRE-1 group; internal region; pol; reverse transcriptase; ATCOPIA95LTR; ATCOPIA95_I
Source:
consensus
Organism:
Arabidopsis thaliana
Taxonomy:
Eukaryota; Viridiplantae; Charophyta/Embryophyta group; Embryophyta; Tracheophyta; euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; Rosidae; Capparales; Brassicaceae; Arabidopsis
[1] Authors:
Kapitonov,V.V. and Jurka,J.
Title:
Internal portion of the ATCOPIA95 copia-like LTR-retrotransposon.
Journal:
Repbase Reports 1:(4) p.6 (2001)
Abstract:
ATCOPIA95_I is a consensus sequence of an internal region of ATCOPIA95 copia-like retroelement flanked by ~8% divergent LTRs, ATCOPIA95LTR, and 5 bp-long TDSs. ATCOPIA95 is one of ~100 families of copia-like LTR-retrotransposons, which were active in the A. thaliana genome during last 20 Myrs. The consensus sequence has been reconstructed based on five copies present in the genome. These copies are ~95% identical to the consensus sequence. ATCOPIA95_I encodes ATCOPIA95p, a 1368-aa copia-like polyprotein. The ATCOPIA95p ORFs in all ATCOPIA95_I copies present in the genome are damaged by false stop codons. There are no stop codons in the corresponding ORF in the consensus sequence. ATCOPIA95p: MTEINTNSKIVGNTTVVETPDEVALRLAKELEKTQITDSGMDNVRRNLFGNGSTNTTIPPSASQGMMPDL FDGKSGFKTWQEKMRYYLVSINMERYLTEDPPIVPQGTTYVYTVGGMDTWAQGDYCCKGLILNRLVNDLF DLYSKAKSSKTLWLTLENKYKTDESGMQRFSTAKFLNFKMVDSKPIMEQVEALQRISQEIELEGMSICNV FKTNCLIEKLPPGWSDFKNYLNFKRKAMTFDDLVRRLMIEGNNRGAHAGAQNQGHDVNVAEHKAKLKGKG KGFSIPQKNLKVSSTTNFKKSNPERKFKGKCHHCGKIGHKADVCKSKAKDVKSQANLTEEDMVAVVTECN MVDDNQVEWYYDTGATTHICTDRTMFSTYVKNKSNEQLFMGNTAMSKIEGKGKVVLKLTSGRELTLQNVK HVPDMRKNLISGTVLSNNGFAVNFESDKLVLKKHGVYLGKGFVKGGLVKMSVMTVFPKNVASASVVEMNE NPIAYLVESFTTWHERLGHVNYKTMRKMQNMNLIPKFKTNQEKCEVCVQAKLTKTPSPRVERTTEPLGLI HTDLCDLKYVQTRGGKKYFVTFIDDCTRYCYVYLLHSKDEALVKFKEFTLEVENQLQRTIKIVRSDRGGE YNEPFNAFCREKGIIHQTTAPYSPESNGVAERKNRTLKEMMNALLQESGLAQNMWGEALLTTNYILNRIP HKVTAKSPHELWKGTVPSYKYLKVWGCLAKVAVPPPKKVTIGPKTVDCIFIGYAHNSSAYRFLVYKSDIP DIHENTVMESRNASFFEDIFPCRKTQKRTREQRDAATSEAEDNTLGTITVEETEQEPEEQPRRSKRARKE KSFGDDFLMAFLAENVPRTYSEAMSTPDAPYWKEAVNTEIDSILQHHTYEIADLPQGSKPLGSKWIFTIK RKTNGDIDRYKARLVVQGFRQKEGLDFFDTYSPVTRITSIRMLIGIAALRDLEIHQMDVKTAFLNGDLEE EIYMKQPEGFVIPGQEHKVCKLVKSLYGLKQAPKQWHEKFDSVMMSNGFTINECDKCIYFKITPTGYILL CLYVDDMLILGSNTDIINQTKNMLKRYFEMKDMGLADVILGIKIIRTDEGLTLSQTHYAEKILDRFKHYS NGTAKTPVDPQLHLTKNSGEPVQQVEYARVIGSLMYLTNSTRPDLAHSVNVLSRYTSNPGHKHWKAITRV LNYLRYTKDHGLHYGKEPAVLEGYSDANWIADSKNSKSTSGYIFTLGGAAVSWKSSKQTVAAKSTMESEF IALDTTAAEAEWLRNFLEDIPMWGKPVPAIRVHCDSQSAIGMAQSTLYNGKSRHIRRRHKTIRQLISTGV ITIDYIKSADNLADPFTKGLNRDQVARSSRGMGLKPTT ATCOPIA95 is much closer to the rice RIRE1 copia-like retrotransposons than to different arabidopsis copia-like families. Internal portions of retrotransposons from other copia families in the A. thaliana genome are less than 75% identical to ATCOPIA95_I. At the same time, the B. napa genome harbors a young copia-like retrotransposon (AL245480, positions 39393 35143) whose 4.2-kb internal portion is 77% identical to ATCOPIA95_I. Presumably, ATCOPIA95-like copia-like elements have invaded B. napa and A. thaliana independently (transmitted from other species).
Derived:
[1] (Consensus)
Download Sequence - Format:
IG, EMBL, FASTA
References:
  1. Kapitonov,V.V. and Jurka,J.
    Internal portion of the ATCOPIA95 copia-like LTR-retrotransposon.
    Direct submission (December 05, 2001)

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