;ID ATCOPIA78_I DNA ; ATH ; 4077 BP ;XX ;DE Internal portion of the ATCOPIA78 copia-like LTR-retrotransposon ;DE - a consensus sequence. ;XX ;AC . ;XX ;DT 30-NOV-2001 (Rel. 6.3, Created) ;DT 30-NOV-2001 (Rel. 6.3, Last updated, Version 1) ;XX ;KW LTR-retrotransposon; COPIA superfamily; ATCOPIA78 family; internal ;KW region; pol; reverse transcriptase; ATCOPIA78LTR; ATCOPIA78_I. ;XX ;OS consensus ;XX ;OC Arabidopsis thaliana ;OC Eukaryota; Viridiplantae; Charophyta/Embryophyta group; ;OC Embryophyta; Tracheophyta; euphyllophytes; Spermatophyta; ;OC Magnoliophyta; eudicotyledons; Rosidae; Capparales; Brassicaceae; ;OC Arabidopsis. ;XX ;RN [1] (bases 1 to 4077) ;RA Kapitonov,V.V. and Jurka,J. ;RT Internal portion of the ATCOPIA78 copia-like LTR-retrotransposon. ;RL Repbase Reports 1:(3) p. 4 (2001) ;XX ;CC ATCOPIA78_I is a consensus sequence of an internal region of ;CC ATCOPIA78 copia-like retroelement flanked by ~1% divergent LTRs, ;CC ATCOPIA78LTR, and 5 bp-long target-site duplicates. ;CC ATCOPIA78 is one of ~100 families of copia-like LTR-retrotransposons, ;CC which were active in the A. thaliana genome during last 20 Myrs. ;CC The consensus sequence has been reconstructed based on eight ;CC copies present in the genome. ;CC These copies are ~99.4% identical to the consensus sequence. ;CC ATCOPIA78_I encodes ATCOPIA78p, a 1352-aa copia-like polyprotein. ;CC ATCOPIA78p: ;CC MASNNVPFQVPVLTKSNYDNWSLRMKAILGAHDVWEIVEKGFIEPENEGSLSQTQKDGLRDSRKRDKKAL ;CC CLIYQGLDEDTFEKVVEATSAKEAWEKLRTSYKGADQVKKVRLQTLRGEFEALQMKEGELVSDYFSRVLT ;CC VTNNLKRNGEKLDDVRIMEKVLRSLDLKFEHIVTVIEETKDLEAMTIEQLLGSLQAYEEKKKKKEDIVEQ ;CC VLNMQITKEENGQSYQRRGGGQVRGRGRGGYGNGRGWRPHEDNTNQRGENSSRGRGKGHPKSRYDKSSVK ;CC CYNCGKFGHYASECKAPSNKKFEEKANYVEEKIQEEDMLLMASYKKDEQEENHKWYLDSGASNHMCGRKS ;CC MFAELDESVRGNVALGDESKMEVKGKGNILIRLKNGDHQFISNVYYIPSMKTNILSLGQLLEKGYDIRLK ;CC DNNLSIRDQESNLITKVPMSKNRMFVLNIRNDIAQCLKMCYKEESWLWHLRFGHLNFGGLELLSRKEMVR ;CC GLPCINHPNQVCEGCLLGKQFKMSFPKESSSRAQKPLELIHTDVCGPIKPKSLGKSNYFLLFIDDFSRKT ;CC WVYFLKEKSEVFEIFKKFKAHVEKESGLVIKTMRSDRGGEFTSKEFLKYCEDNGIRRQLTVPRSPQQNGV ;CC AERKNRTILEMARSMLKSKRLPKELWAEAVACAVYLLNRSPTKSVSGKTPQEAWSGRKPGVSHLRVFGSI ;CC AHAHVPDEKRSKLDDKSEKYIFIGYDNNSKGYKLYNPDTKKTIISRNIVFDEEGEWDWNSNEEDYNFFPH ;CC FEEDEPEPTREEPPSEEPTTPPTSPTSSQIEESSSERTPRFRSIQELYEVTENQENLTLFCLFAECEPMD ;CC FQEAIEKKTWRNAMDEEIKSIQKNDTWELTSLPNGHKAIGVKWVYKAKKNSKGEVERYKARLVAKGYSQR ;CC AGIDYDEVFAPVARLETVRLIISLAAQNKWKIHQMDVKSAFLNGDLEEEVYIEQPQGYIVKGEEDKVLRL ;CC KKALYGLKQAPRAWNTRIDKYFKEKDFIKCPYEHALYIKIQKEDILIACLYVDDLIFTGNNPSMFEEFKK ;CC EMTKEFEMTDIGLMSYYLGIEVKQEDNGIFITQEGYAKEVLKKFKMDDSNPVCTPMECGIKLSKKEEGEG ;CC VDPTTFKSLVGSLRYLTCTRPDILYAVGVVSRYMEHPTTTHFKAAKRILRYIKGTVNFGLHYSTTSDYKL ;CC VGYSDSDWGGDVDDRKSTSGFVFYIGDTAFTWMSKKQPIVTLSTCEAEYVAATSCVCHAIWLRNLLKELS ;CC LPQEEPTKIFVDNKSAIALAKNPVFHDRSKHIDTRYHYIRECVSKKDVQLEYVKTHDQVADIFTKPLKRE ;CC DFIKMRSLLGVAKSSLRGGVES ;CC ;CC It's possible that some copies of ;CC ATCOPIA78 are still active retrotransposons. ;XX ;DR [1] (Consensus) ;XX ;SQ Sequence 4077 BP; 1464 A; 671 C; 965 G; 977 T; 0 other; ATCOPIA78_I aaagtggtatcagagcttgaagatcctaaagatggcgagtaacaatgttcccttccaagtcccggtgctc acaaagagcaactatgataattggagtctacgaatgaaggctatcctaggagcacatgacgtgtgggaga tagtcgagaaaggtttcattgaaccggagaatgaaggtagtctttctcaaactcaaaaagatggtttgag agactcaagaaagagagacaagaaagctctctgtctaatctatcaaggattagatgaagatacgttcgag aaggtcgttgaagctacgtcggcgaaagaagcatgggagaagcttcgaacctcttacaaaggtgccgatc aagtcaagaaagtacgtcttcaaactctaagaggagaatttgaagcactacaaatgaaggaaggtgaact cgtctccgattacttctcaagagtgttgacggttactaataaccttaaaagaaacggagagaagctagat gatgtgagaatcatggagaaagttcttagatcattggatctaaaatttgagcatattgtcaccgtcattg aagaaacaaaagatttagaagctatgacaatagagcaacttcttgggtcattacaagcttatgaagaaaa gaagaagaagaaagaagatatcgtcgaacaagtcctcaatatgcaaattacaaaagaagaaaacggccaa agttaccaaagaagaggtggtggtcaagtacgaggacgaggtcgtggtggatatggaaatggacgtggtt ggaggccacatgaagacaacacaaaccaaagaggtgaaaactcatcaagaggtcgtgggaaaggacaccc aaaatcaagatacgataaatcaagtgtcaaatgctacaattgtgggaagtttggacattatgcttctgaa tgtaaagctcctagcaacaaaaaatttgaggagaaggccaactacgttgaagaaaaaattcaagaagaag acatgttattaatggctagctacaagaaagatgaacaagaagagaatcataagtggtacctcgatagtgg tgcaagtaatcacatgtgcgggagaaaaagtatgttcgcggagcttgatgaatcggtgagaggaaatgtg gctttaggagatgaatcgaagatggaggtaaaaggtaaaggaaacattctcattcgattgaagaatggag atcatcaatttatttccaacgtttactatattccgagcatgaagacaaacatcttgagccttggacaact cttagagaaaggttatgatattagattaaaagataataacctttcaataagagaccaagaaagcaatctc attaccaaggtgccaatgtcgaaaaatagaatgtttgtcctcaacattcgaaatgacattgcacaatgtc ttaagatgtgttacaaagaggagtcttggctatggcatcttcgattcggacatctaaattttggaggatt ggagttgctttcaaggaaggaaatggtgagagggctaccttgtataaatcatccaaatcaagtgtgtgaa ggatgtctacttggaaagcaattcaaaatgagctttccaaaggagtcaagttcaagagcacaaaaaccgt tggagctaatacacaccgatgtgtgtggtccgatcaagccgaaatcacttggtaaaagtaattacttcct tctctttattgatgatttttcaagaaaaacatgggtatattttttgaaagaaaaatccgaggtgttcgaa attttcaaaaagtttaaagcccatgttgagaaggagagtggtcttgtgatcaaaaccatgagatccgacc gtggaggagaatttacatccaaggagtttcttaagtattgtgaagacaacggcattcgaagacaattaac ggtgccaagatcccctcaacaaaatggtgtagcggaaagaaagaatagaacaattcttgagatggcaagg agcatgctcaaaagtaagagactaccaaaagagttgtgggcggaagcggtcgcgtgtgcggtttatctat taaatcgatctccaacaaaaagtgtctccggaaaaacaccacaagaagcttggagcggaagaaagcccgg tgtttctcatttaagagtctttggaagtattgctcatgctcatgtaccggatgagaagcggagcaaacta gatgacaaaagtgagaagtatatcttcattggttatgataacaactccaaaggctacaagctctataatc ccgatacgaagaagacaattattagtcgaaatatagtgttcgatgaagaaggagaatgggattggaactc aaatgaagaagattataacttctttccacattttgaagaagatgagccggagccaacaagagaggagcca ccaagtgaagagcctactacaccaccaacttcaccaacaagttctcaaatagaagaaagttcgagtgaaa ggactccgcgttttagaagtatacaagagctctatgaggtaaccgaaaatcaagaaaaccttaccttatt ttgtttatttgcggagtgcgaacccatggatttccaagaagccattgaaaagaagacttggagaaatgcc atggatgaagagatcaaatcaatacaaaagaatgacacatgggagttaacttcacttccaaatggacaca aggcaattggcgtgaagtgggtgtataaagcaaagaaaaactctaaaggagaagtggaaagatacaaagc aagattggttgcaaaaggttatagtcaaagagccggaattgactatgacgaggtatttgctcccgttgct cgtctagaaacggttagactaatcatctcactagcggctcaaaacaagtggaagatacatcaaatggatg tcaagtcggccttcttaaatggagatcttgaagaagaagtttacattgagcaaccacaaggctacatagt caaaggtgaagaagacaaagtcttgaggctaaaaaaggcgctttatggattaaaacaagccccaagagct tggaatactcgaattgacaagtatttcaaggagaaagatttcatcaagtgtccatatgagcatgcactct atatcaaaattcaaaaagaagatatattgatcgcatgcttatatgtagatgacttgatattcacgggtaa caatccaagcatgttcgaagaattcaagaaagagatgacgaaggagttcgagatgacggacattggattg atgtcttactatctcggaattgaagtaaaacaagaagacaatggaatattcataactcaagaaggctatg ctaaggaggtacttaagaagttcaagatggatgactcaaatcccgtttgtacaccaatggaatgcggaat caaactatcaaagaaagaagaaggggaaggagtggatccaacaacctttaagagcttggttggaagcttg agatacttaacatgcacaaggcccgatattttatatgcggtcggagttgttagtcgttacatggagcatc caacaacaactcatttcaaagcggcaaaaaggattcttcgctatatcaaaggtaccgtaaactttggctt acattattcaactactagtgattacaagcttgttggatatagcgatagcgattggggtggagacgtagat gaccgaaagagtacaagtggttttgtgttttacattggagacacggctttcacatggatgtcgaagaaac aaccaattgtcactctatccacttgtgaagcggagtatgtagcggctacgtcatgtgtatgccatgctat ttggttaagaaacctcttgaaggagttaagcttaccacaagaggaaccaacgaagatctttgtggacaac aagtcggcaatagctttggcgaagaacccggtcttccatgatcgaagtaaacacattgacacacgctatc actacattagagagtgtgttagcaagaaggacgtgcaattggagtatgtgaagacacatgatcaagtagc cgatatttttaccaagcctctcaagcgtgaagactttatcaagatgaggagtttgcttggagtagcaaaa tcaagtttaagaggggg1