Repbase Reports |
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| 2001, Volume 1, Issue 3 |
| March 31, 2001 |
| Copyright © 2001-2016 - Genetic Information Research Institute |
| ISSN# 1534-830X |
| Page 4 |
ATCOPIA78_I |
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Internal portion of the ATCOPIA78 copia-like LTR-retrotransposon - a consensus sequence. |
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Submitted: 31-Mar-2001 |
Accepted: 31-Mar-2001 |
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Key Words: LTR-retrotransposon; COPIA superfamily; ATCOPIA78 family; internal region; pol; reverse transcriptase; ATCOPIA78LTR; ATCOPIA78_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 ATCOPIA78 copia-like LTR-retrotransposon. |
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Journal: Repbase Reports 1:(3) p. 4 (2001) |
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Abstract: ATCOPIA78_I is a consensus sequence of an internal region of ATCOPIA78 copia-like retroelement flanked by ~1% divergent LTRs, ATCOPIA78LTR, and 5 bp-long target-site duplicates. ATCOPIA78 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 eight copies present in the genome. These copies are ~99.4% identical to the consensus sequence. ATCOPIA78_I encodes ATCOPIA78p, a 1352-aa copia-like polyprotein. ATCOPIA78p: MASNNVPFQVPVLTKSNYDNWSLRMKAILGAHDVWEIVEKGFIEPENEGSLSQTQKDGLRDSRKRDKKAL CLIYQGLDEDTFEKVVEATSAKEAWEKLRTSYKGADQVKKVRLQTLRGEFEALQMKEGELVSDYFSRVLT VTNNLKRNGEKLDDVRIMEKVLRSLDLKFEHIVTVIEETKDLEAMTIEQLLGSLQAYEEKKKKKEDIVEQ VLNMQITKEENGQSYQRRGGGQVRGRGRGGYGNGRGWRPHEDNTNQRGENSSRGRGKGHPKSRYDKSSVK CYNCGKFGHYASECKAPSNKKFEEKANYVEEKIQEEDMLLMASYKKDEQEENHKWYLDSGASNHMCGRKS MFAELDESVRGNVALGDESKMEVKGKGNILIRLKNGDHQFISNVYYIPSMKTNILSLGQLLEKGYDIRLK DNNLSIRDQESNLITKVPMSKNRMFVLNIRNDIAQCLKMCYKEESWLWHLRFGHLNFGGLELLSRKEMVR GLPCINHPNQVCEGCLLGKQFKMSFPKESSSRAQKPLELIHTDVCGPIKPKSLGKSNYFLLFIDDFSRKT WVYFLKEKSEVFEIFKKFKAHVEKESGLVIKTMRSDRGGEFTSKEFLKYCEDNGIRRQLTVPRSPQQNGV AERKNRTILEMARSMLKSKRLPKELWAEAVACAVYLLNRSPTKSVSGKTPQEAWSGRKPGVSHLRVFGSI AHAHVPDEKRSKLDDKSEKYIFIGYDNNSKGYKLYNPDTKKTIISRNIVFDEEGEWDWNSNEEDYNFFPH FEEDEPEPTREEPPSEEPTTPPTSPTSSQIEESSSERTPRFRSIQELYEVTENQENLTLFCLFAECEPMD FQEAIEKKTWRNAMDEEIKSIQKNDTWELTSLPNGHKAIGVKWVYKAKKNSKGEVERYKARLVAKGYSQR AGIDYDEVFAPVARLETVRLIISLAAQNKWKIHQMDVKSAFLNGDLEEEVYIEQPQGYIVKGEEDKVLRL KKALYGLKQAPRAWNTRIDKYFKEKDFIKCPYEHALYIKIQKEDILIACLYVDDLIFTGNNPSMFEEFKK EMTKEFEMTDIGLMSYYLGIEVKQEDNGIFITQEGYAKEVLKKFKMDDSNPVCTPMECGIKLSKKEEGEG VDPTTFKSLVGSLRYLTCTRPDILYAVGVVSRYMEHPTTTHFKAAKRILRYIKGTVNFGLHYSTTSDYKL VGYSDSDWGGDVDDRKSTSGFVFYIGDTAFTWMSKKQPIVTLSTCEAEYVAATSCVCHAIWLRNLLKELS LPQEEPTKIFVDNKSAIALAKNPVFHDRSKHIDTRYHYIRECVSKKDVQLEYVKTHDQVADIFTKPLKRE DFIKMRSLLGVAKSSLRGGVES It's possible that some copies of ATCOPIA78 are still active retrotransposons.
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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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