;ID ATCOPIA95_I DNA ; ATH ; 5139 BP ;XX ;DE Internal portion of the ATCOPIA95 copia-like LTR-retrotransposon ;DE - a consensus sequence. ;XX ;AC . ;XX ;DT 27-DEC-2001 (Rel. 6.3, Created) ;DT 27-DEC-2001 (Rel. 6.3, Last updated, Version 1) ;XX ;KW LTR-retrotransposon; COPIA superfamily; ATCOPIA95 family; RIRE-1 ;KW group; internal region; pol; reverse transcriptase; ATCOPIA95LTR; ;KW ATCOPIA95_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 5139) ;RA Kapitonov,V.V. and Jurka,J. ;RT Internal portion of the ATCOPIA95 copia-like LTR-retrotransposon. ;RL Repbase Reports 1:(4) p. 6 (2001) ;XX ;CC ATCOPIA95_I is a consensus sequence of an internal region of ;CC ATCOPIA95 copia-like retroelement flanked by ~8% divergent LTRs, ;CC ATCOPIA95LTR, and 5 bp-long TDSs. ;CC ATCOPIA95 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 five ;CC copies present in the genome. ;CC These copies are ~95% identical to the consensus sequence. ;CC ATCOPIA95_I encodes ATCOPIA95p, a 1368-aa copia-like polyprotein. ;CC The ATCOPIA95p ORFs in all ATCOPIA95_I copies present in the genome ;CC are damaged by false stop codons. There are no stop codons ;CC in the corresponding ORF in the consensus sequence. ;CC ATCOPIA95p: ;CC MTEINTNSKIVGNTTVVETPDEVALRLAKELEKTQITDSGMDNVRRNLFGNGSTNTTIPPSASQGMMPDL ;CC FDGKSGFKTWQEKMRYYLVSINMERYLTEDPPIVPQGTTYVYTVGGMDTWAQGDYCCKGLILNRLVNDLF ;CC DLYSKAKSSKTLWLTLENKYKTDESGMQRFSTAKFLNFKMVDSKPIMEQVEALQRISQEIELEGMSICNV ;CC FKTNCLIEKLPPGWSDFKNYLNFKRKAMTFDDLVRRLMIEGNNRGAHAGAQNQGHDVNVAEHKAKLKGKG ;CC KGFSIPQKNLKVSSTTNFKKSNPERKFKGKCHHCGKIGHKADVCKSKAKDVKSQANLTEEDMVAVVTECN ;CC MVDDNQVEWYYDTGATTHICTDRTMFSTYVKNKSNEQLFMGNTAMSKIEGKGKVVLKLTSGRELTLQNVK ;CC HVPDMRKNLISGTVLSNNGFAVNFESDKLVLKKHGVYLGKGFVKGGLVKMSVMTVFPKNVASASVVEMNE ;CC NPIAYLVESFTTWHERLGHVNYKTMRKMQNMNLIPKFKTNQEKCEVCVQAKLTKTPSPRVERTTEPLGLI ;CC HTDLCDLKYVQTRGGKKYFVTFIDDCTRYCYVYLLHSKDEALVKFKEFTLEVENQLQRTIKIVRSDRGGE ;CC YNEPFNAFCREKGIIHQTTAPYSPESNGVAERKNRTLKEMMNALLQESGLAQNMWGEALLTTNYILNRIP ;CC HKVTAKSPHELWKGTVPSYKYLKVWGCLAKVAVPPPKKVTIGPKTVDCIFIGYAHNSSAYRFLVYKSDIP ;CC DIHENTVMESRNASFFEDIFPCRKTQKRTREQRDAATSEAEDNTLGTITVEETEQEPEEQPRRSKRARKE ;CC KSFGDDFLMAFLAENVPRTYSEAMSTPDAPYWKEAVNTEIDSILQHHTYEIADLPQGSKPLGSKWIFTIK ;CC RKTNGDIDRYKARLVVQGFRQKEGLDFFDTYSPVTRITSIRMLIGIAALRDLEIHQMDVKTAFLNGDLEE ;CC EIYMKQPEGFVIPGQEHKVCKLVKSLYGLKQAPKQWHEKFDSVMMSNGFTINECDKCIYFKITPTGYILL ;CC CLYVDDMLILGSNTDIINQTKNMLKRYFEMKDMGLADVILGIKIIRTDEGLTLSQTHYAEKILDRFKHYS ;CC NGTAKTPVDPQLHLTKNSGEPVQQVEYARVIGSLMYLTNSTRPDLAHSVNVLSRYTSNPGHKHWKAITRV ;CC LNYLRYTKDHGLHYGKEPAVLEGYSDANWIADSKNSKSTSGYIFTLGGAAVSWKSSKQTVAAKSTMESEF ;CC IALDTTAAEAEWLRNFLEDIPMWGKPVPAIRVHCDSQSAIGMAQSTLYNGKSRHIRRRHKTIRQLISTGV ;CC ITIDYIKSADNLADPFTKGLNRDQVARSSRGMGLKPTT ;CC ATCOPIA95 is much closer to the rice RIRE1 copia-like retrotransposons ;CC than to different arabidopsis copia-like families. ;CC Internal portions of retrotransposons from other copia families ;CC in the A. thaliana genome are less than 75% identical to ATCOPIA95_I. ;CC At the same time, the B. napa genome harbors a young copia-like ;CC retrotransposon (AL245480, positions 39393 35143) whose 4.2-kb ;CC internal portion is 77% identical to ATCOPIA95_I. Presumably, ;CC ATCOPIA95-like copia-like elements have invaded B. napa and ;CC A. thaliana independently (transmitted from other species). ;XX ;DR [1] (Consensus) ;XX ;SQ Sequence 5139 BP; 1674 A; 985 C; 1109 G; 1371 T; 0 other; ATCOPIA95_I atcttaattcaataaatccgcttttagcttatcgctctagacggattgagaatttttcgaattttttaaa acgatttcaaaatcttctaaaaattgtttctgctatcatctttgggtgcttacgcggaaggtttatagaa gaacgttattacttctttctttctcctctttctaaactgcttcgcaaacgctacgtagcgattgttgtgg acagtttcttatataaacttctctagtttccacgaacgctcatacttgagtgagtttgtgaaacgcgaaa caagtttctgcgaacgcttcttaagcgagtttgcaaaactaattcggtgtaatttagttacctgaatttt ttggttaatatactaatcagatctgtttttctgtgaacagaatgactgagatcaacaccaacagcaagat cgttggcaacaccacagttgttgagaccccggatgaggtagctttgcgccttgcgaaagagcttgaaaag acacagatcaccgattctggtatggataatgtgcgccgaaatctgttcggtaatggttcaaccaacacta ccataccaccctctgcttcccaagggatgatgccagacttgtttgatggcaaatccgggttcaaaacgtg gcaagaaaagatgcgctactatttggtcagcataaacatggaaaggtacctcacagaggatccaccaata gttccgcaaggtaccacatatgtgtatacggttggaggtatggatacctgggctcaaggtgactattgtt gcaaaggtctgatcctgaaccgcttggtgaacgatctgtttgacctctacagcaaggccaagtcttccaa aacactgtggctaactttagagaacaagtacaagactgatgagtctggaatgcaaagattctcaactgcg aagtttctgaatttcaagatggtggactccaaaccaatcatggaacaggtggaggctcttcaacgtatct ctcaagagatagagttggaagggatgtcgatctgcaacgtcttcaagacgaattgcttgatcgagaagct accaccgggctggtcagatttcaagaattaccttaacttcaaacgtaaggcaatgacttttgatgatctc gtccgaaggttgatgattgaaggcaacaatcgtggggctcacgcgggtgctcagaatcaagggcatgatg ttaatgtagctgagcataaggccaagctgaaaggcaagggaaaagggttctctattcctcagaagaactt gaaggtttcatcgacaacaaacttcaagaagagcaatcctgagcggaagttcaaaggaaagtgtcatcat tgtggaaagattggacacaaggctgatgtttgcaagagcaaagccaaggatgtcaagagccaggcaaacc taactgaagaggatatggttgcagtggtcactgaatgtaacatggtggacgacaaccaagtggagtggta ctacgacactggtgcaaccacacacatctgcacagataggaccatgttctccacctatgtgaagaacaag tcaaacgaacaactcttcatgggcaacacggcgatgtctaagattgaaggtaagggcaaagtggttctga agctgacttcgggacgtgagcttactctgcaaaacgtgaagcatgtacctgacatgcggaagaatctcat ctctggaacggtgctaagcaacaatggctttgccgttaactttgagtctgataagctagttcttaagaaa catggggtgtatctgggaaagggttttgttaagggtggactggtcaaaatgtctgtaatgacagtctttc cgaaaaatgtagcttctgcttctgttgttgaaatgaatgaaaatcctattgcttacttggttgagtcgtt tactacttggcatgaacgtttaggacatgtcaattataaaacaatgcgaaaaatgcaaaacatgaattta attccgaaattcaaaactaaccaagaaaaatgtgaagtatgcgtacaggcaaaactcactaaaactccct caccacgagttgaaagaacaactgaacctctaggtttaattcacacagacttatgtgatttaaaatatgt gcaaactagaggtggtaagaaatactttgttaccttcatagatgattgcacaagatattgttatgtatat ctattgcatagcaaagatgaagctctggtaaaattcaaagaatttacactcgaagtagaaaatcaacttc agagaactataaaaatagttcgaagtgatagaggaggagaatataatgagccattcaatgcattttgcag agaaaaaggcattatacaccaaacaactgctccctattcaccagaatctaacggagttgcggaacgaaag aatcgaactctgaaagaaatgatgaatgcactgttgcaggaatctgggttagcccagaacatgtgggggg aagctttgcttaccactaactacatcctcaataggataccacataaggtgactgcaaagtcaccacatga actttggaaaggtacagtaccctcgtacaaatacctaaaagtgtgggggtgtctagcaaaagtggctgta ccacctcccaaaaaggtcacaattgggcctaagaccgtagactgtatcttcatcggatatgcgcacaaca gcagtgcttatcgatttcttgtttataaatcggatattccagatatccatgaaaatacagttatggaatc aagaaatgcatcgttttttgaagatatttttccttgtaggaaaactcaaaaacgaactcgtgaacaacga gatgcagcaacctcggaagctgaggacaatactttgggtactattactgttgaagaaacagaacaggaac ctgaagaacaacctaggcggagcaaaagagctcgcaaagagaaatctttcggtgatgatttcttgatggc gtttttagctgaaaacgtaccaagaacttattcagaagccatgtctacccctgatgcaccttattggaag gaagcagtcaatactgaaatagactctatcttgcaacatcatacttacgagatagcagatctaccccaag gttctaaaccattggggagtaaatggattttcactattaaaaggaaaacgaatggtgatattgataggta caaggctaggcttgtggtacaaggatttcgacaaaaagaaggtttagatttctttgatacctattctccg gtaacgagaataacttcaatcaggatgctcataggcattgcagccttacgagatcttgaaatacatcaaa tggatgtaaaaacagctttcttaaatggagatttggaagaggaaatctacatgaaacaacctgaagggtt tgttatcccaggacaagaacacaaagtgtgtaaacttgtgaagtcactatacggactcaaacaggctcct aagcagtggcatgagaagtttgacagtgttatgatgtctaatggttttaccattaatgaatgtgacaaat gcatatatttcaaaattactccaacagggtacattttgttatgtttatatgtagacgatatgctcatctt ggggagcaacacagatatcataaatcaaactaaaaacatgctcaaaagatattttgaaatgaaagacatg ggtctagcagatgttattttgggtataaaaatcatcagaactgatgaaggccttaccttgtctcaaaccc actatgctgagaagatacttgatcgtttcaagcattactctaatgggactgcaaaaactccagtagatcc tcaacttcacttgaccaaaaactctggtgaacctgtgcaacaggtggaatatgcaagagtaattggcagt ttaatgtacttgacaaacagtacaagaccggatttagcgcactctgtaaatgtacttagtcgctacacaa gcaatccaggacataagcattggaaggctataactagagttttgaactacctacgttataccaaagatca tggcttgcactatggtaaagaacccgcagttttggaaggttacagtgatgccaactggatcgcagattcc aaaaactctaaatccacaagtggatacatctttacacttggaggtgcagcagtatcctggaaatctagca aacaaactgtggcagccaaatcaactatggaatcggaattcatagcattggatacaactgcagcggaagc cgaatggctccgtaatttcttggaagacattccaatgtgggggaaacctgtgcctgcaatacgtgtacac tgtgatagccaatcagctataggcatggcacaaagtaccctatataatggtaaatctcgtcacatcagac gacgacataaaaccattcgacaacttatctcaactggagtaatcacgatcgattacatcaagtcagctga caacctagcggatccatttacaaaaggtttgaatcgagatcaagttgcaagatcatcaagaggaatgggt ttaaagcctaccacctaagaggaagtttgatggtaaccccacctacaaagattggagatcccatgacata ggttcaaagggacaactaaatcaaactaaatctgttataagcactgagagactgttgtctcttcctagtt cctaaaatgatgtacagtgcttcctgtatgtgtaaaggttaagcatttgcttttaatgatttgaacctag ctttgtaagatatgtgaagtacttacaggatacttttttaaatacaagcagctagtaaatcaccttgtga gtgtgaaatggggccgtttctaggagaatatgtgaggctatactctccaagttcactcatgattaaccag gcatgttcaaggccacaatgaacacaaacagagaacctcgttctacgagaaaatgaagttgtgttatacc tgctgtctaagtttgcatcaaactccggatggttcaagacatcatgttcaccatctggccgagtaaactc gacaggtactaacaatgagtaggttcaaagctgaaaaacgccaccaactcagatacagttagttttcgtt tatactctcgaaggtctgtctagtctagctagttgggtcagtccttaggattagtaaagtcgtcatatgt ttagacttatttctattcatgtgggggat1