Repbase Reports |
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| 2001, Volume 1, Issue 4 |
| April 30, 2001 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 6 |
ATCOPIA95_I |
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Internal portion of the ATCOPIA95 copia-like LTR-retrotransposon - a consensus sequence. |
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Submitted: 30-Apr-2001 |
Accepted: 30-Apr-2001 |
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Key Words: LTR-retrotransposon; COPIA superfamily; ATCOPIA95 family; RIRE-1 group; internal region; pol; reverse transcriptase; ATCOPIA95LTR; ATCOPIA95_I |
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Source: consensus |
Organism: Arabidopsis thaliana |
Taxonomy: Eukaryota; Viridiplantae; Charophyta/Embryophyta group; Embryophyta; Tracheophyta; euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; Rosidae; Capparales; Brassicaceae; Arabidopsis |
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| [1] |
Authors: Kapitonov,V.V. and Jurka,J. |
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Title: Internal portion of the ATCOPIA95 copia-like LTR-retrotransposon. |
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Journal: Repbase Reports 1:(4) p.6 (2001) |
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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).
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Derived: [1] (Consensus) |
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Download Sequence - Format: IG, EMBL, FASTA |
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References:
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