;ID ATCOPIA90_I DNA ; ATH ; 4887 BP ;XX ;DE Internal region of the ATCOPIA90 copia-like LTR-retrotransposon. ;XX ;AC AC069326 ;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; internal region; ;KW copia-like polyprotein; reverse transcriptase; the ATCOPIA90 ;KW family; ATCOPIA90LTR; ATCOPIA90_I. ;XX ;OS Arabidopsis thaliana ;XX ;OC Arabidopsis thaliana ;OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; ;OC euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; ;OC Rosidae; Capparales; Brassicaceae; Arabidopsis. ;XX ;RN [1] (bases 1 to 4887) ;RA Kapitonov,V.V. and Jurka,J. ;RT Internal portion of the ATCOPIA90 copia-like LTR-retrotransposon. ;RL Repbase Reports 1:(3) p. 24 (2001) ;XX ;CC ATCOPIA90_I is an internal region of the ATCOPIA90 copia-like ;CC endogenous retrovirus flanked by the 99% identical ATCOPIA90LTR ;CC long terminal repeats and a 5-bp target-site duplication (GAAGC). ;CC ATCOPIA90 forms a separate family of copia-like retroviruses ;CC present in the A. thaliana genome since members of other families ;CC are less than 75% identical to ATCOPIA90_I. ;CC ATCOPIA90_I (positions 442-4878) encodes remnants of the 1479-aa ;CC ATCOPIA90p copia-like polyprotein. The ORF which encodes ;CC ATCOPIA90p is damaged by two false stop codons at positions ;CC 2503-2505 and 3457-3459 (marked by Xs in the ATCOPIA90p sequence). ;CC ATCOPIA90p: ;CC MALNVRNKLGFIDGTILKPNETHKDFGSWSRCNDMVATWLMNSVSKKIGQSLLFISTAEGIWKNLMSRFK ;CC QDDAPRVYEIEQRLSVIQQGSMDVSAYYTELVTLWEEYRNHVELPVCTCGKCECNAAALWEKLQQRSRVT ;CC KFLMGLNESYEATRRHILMLKQIPTIEDAFNMVTQDERQKNIKPVSKIDNVVFNTSDNNQLSYYDGSVQN ;CC QNQNVYQGPLDNNVYAAMQNQYIPRAPRPVCTYCGQTGHVIQKCFKKHGYPPGYIPGFKSNGGYQNQPTR ;CC PFTPFFNQNLDPRAQFSNSRPTTQHAANMMNGNQQAISAPNVDVSQMNKEQMQSLLQQLNSQVQLSENQV ;CC PIPLVASVTQNGVMDSQSFSGSVSFPSTSLRFENNKLTFQHQCLSSLSNQIPQGSWIIDTGATSHVCSDL ;CC TLFNDIVTVTGVTVSLPNATRVEIAHTGTIHLSSSLILHDVLHVPSFKFNLIFVSSLLKHSNASAHFFPD ;CC FCYIHESIQNLMIGKGVLLHNLYILELDSPHPATHSSLSAPHFSGSLMVDGHLWHQRLGHPSSDKLKLLS ;CC GTLSMPKNSSLVESHCPVCPLAKQKRLSFESHNHMSSSPFDLIHLDVWGPFKRESVEGYKYFLTIVNDHT ;CC RVTWIYMLRNKSDVSKCFPVFLKYVSTQYNAILKRIRTDNAPELAFTDILEQSGITHXFSCPYTPQQNSV ;CC VERKHQHLLNVARSLMFQSNLPLAYWSDCILTSVFLINRIPSKVLNNLTPYEMLTKKAPDYSFLKSFGCL ;CC CYVSTLQKDRHKFSPRADKCVFLGYSSGYKGYKVLHLDSNIVSVSRNVIFHEKDFPFKTATHSIPASDIF ;CC DKCVLPASTPFDIDSPSHIHHDASDIHTPALHTTPHSSVTDHSQEAVTSDTTTVSLPTVRPKRTSKAPGY ;CC LSDYHCALIQTSSPPEKVTTTPYHISSFLSYDQFSPDYQSFICNISIETEPKIFKQAIISEKWTAAMGVE ;CC LGSMELNKTWSVVSLPQGKNVVGCKXVFTIKYNADGSIERYKARLVAKGFIQQEGVDYFDTFSPVAKLAS ;CC VKLLLDLTAKKGWSTSQMDISSAFLHSDLEEEIYMSLPEGYTPPDGVPLPPNAVCRLHKSIYGLKQASRQ ;CC WYKCLSAVLLDDGFIQSYADNMLFVKVTGTSIVALLVYVDDILIVSNDDEAVRSVKAVLGKHFKTKDLGE ;CC AKFFLGLEIARNADGISVSQRKYCLDMLADSGLLGCKPKSVPVDPKVPLTKETGTLLENARPYREIIGRL ;CC LYLCITRPDITYAVNRLSQFLSCPTDVHLQAAYQILKYLKNNPGQGLFYSSQPDICLNGFADADWGTCLD ;CC TRRSTSGMCVFLGHSLITWKSKKQDIVSSSSTEAEYRSMAVTTKELLWLSQMLKDLHIQVDSSAKLFCDN ;CC KSATYIAINPVFHERTKHVEIDCHITRDQVKNGFLKVLHVATENQLADIMTKPLHPGPFYSLLSRLSVSS ;CC LFNPSDDSA ;XX ;DR Positions 30244 25358 Accession No AC069326 GenBank (rel. 124.0) ;XX ;SQ Sequence 4887 BP; 1423 A; 966 C; 907 G; 1591 T; 0 other; ATCOPIA90_I tggtatcagagcaaaaataagctctttgttttctcattccttcccgggaaagtgaccaagaaaattcaca aatcctatcatcttcttccacaaattctccgattgatcttcacatatcttcgattaatcaccatcttcat cgattacatccattttctttcacaaattcatccatttctcagatcaacgaactcatcaaaatcgattcgt tgtttcattcatttccgccaaaatcaaagtcactttctttgggaatcttcttccgctactcaagatcttc ttcgttttctctgattctttcgattctttgattctatgatgactactgatcaatacgataaccattactt tcttcacaactccgatcacgcaggcttagttcttgtgtcagatcgacttacgactggagctgactttcac tcttggcgatgatcggtgcgaatggcactcaatgtccgcaataagcttgggttcatagatggtacaattc ttaaacccaatgaaactcataaagattttggatcgtggtcccgttgcaatgatatggtagccacatggct catgaattctgtttccaagaagattggacaaagcttgttattcatttccactgctgaaggcatttggaag aatctgatgtcaagatttaaacaagatgatgctcctcgggtgtatgagattgagcaacgtttgagtgtta tacaacaaggttctatggatgttagtgcatattatacagaattggtaaccttatgggaagaatatcgtaa tcatgtggaacttcctgtgtgtacttgtggtaaatgcgagtgtaatgcagctgctctttgggagaaattg caacagagaagcagagtcactaagttcttgatgggtctcaatgaatcctatgaagctactcgcagacata tcctaatgttgaagcaaattccaaccattgaagatgcgttcaatatggtgactcaggacgagcgtcagaa gaatatcaaaccagtgtctaagattgacaatgtggtgtttaatacttcagataacaatcagttgagttac tatgatggtagtgtacagaatcagaatcagaatgtctatcaaggtcctcttgacaataatgtctatgctg caatgcagaatcaatatataccaagagcaccaaggccagtttgtacttactgtggtcagactggtcatgt aatccagaagtgtttcaagaaacatggataccctccgggttatatcccagggtttaagagtaatggagga tatcagaatcaacctacaagaccatttactccatttttcaatcagaatctagatccaagagcgcagttct ctaactctagacctacaactcaacatgctgcaaacatgatgaatggaaatcaacaggctatatcagcacc aaatgtggatgtaagccagatgaacaaggaacaaatgcagtcattgttacaacagctaaattctcaagtt cagctttcagagaatcaagttcctattccattagtagcgtctgttacacagaatggtgtaatggattctc aatctttttcgggtagtgtctcttttccatctacttcactacgttttgaaaataataaactcacatttca acatcagtgtctatcatctctttctaaccaaattcctcagggtagttggataattgacactggagcaaca agtcatgtttgctctgatttgactctattcaatgacattgtcacagtgactggtgttacagtttctttgc ctaatgccactagagtggaaattgcacacactggcactatacatttatcatcatctcttatattgcacga tgttttacatgttccatcattcaaattcaatcttatatttgttagtagtctattaaaacatagtaatgca tcagctcatttctttcctgatttttgctatatccacgagtctattcagaacttgatgattggtaaaggag ttcttctgcataatctttacattctagagcttgattcaccacatcctgctactcattcatcattgtctgc acctcatttctctggatccttgatggtagatggacatctatggcaccagcgcctcggacacccatcttct gacaagttaaagttgttgtctggtacactttctatgcctaagaatagttctttagtcgagtctcattgtc ctgtgtgtcctctagctaaacaaaaacggttaagtttcgagtctcataatcacatgtcttcgtctccatt tgatttgattcatttagatgtctggggtccatttaaacgagagtctgtagaagggtataaatacttcctt accattgttaatgatcatactcgtgtaacctggatttacatgttaaggaataaaagtgatgtttcaaaat gttttcctgtttttcttaaatatgttagtactcagtataatgccattttgaaaagaataagaactgataa tgcaccagaactagcttttactgatattcttgaacaatctggaattacacattaattttcttgcccttat actccacaacagaattctgttgtggaacgcaaacatcagcatttgttgaatgtagctaggtctttgatgt ttcaatctaatcttcctttagcatattggagtgattgcatattaacatctgtcttcctgataaatagaat tccatcaaaagttttgaacaatttaactccttatgagatgttaacaaagaaagcacctgattactctttt ctaaaatcgtttggttgtttgtgttatgtgtctactttacagaaagataggcataagttcagtcctagag cagataaatgtgtctttttaggctactcatctggatataaaggttacaaagttttacatttagactcgaa cattgtatctgtctctaggaatgtcattttccatgaaaaagattttccattcaaaactgcaacacattcc atccctgcatctgatatatttgataaatgtgttcttcctgcttctactccttttgacattgattcgccat ctcacattcatcatgatgcatctgacattcatacacctgcattacacacaacaccacactctagtgtcac agatcattcacaggaagctgtaacttcagacacgaccacagtttcattgcctacagtcagaccaaagcga acttctaaagctccaggctacttatctgactatcactgtgctctcatacaaacatcatcaccaccagaaa aggtcacaactactccttatcatatttcctcttttctttcatatgaccaattttcaccagactatcaatc cttcatatgcaatatttcgatagagacagaaccgaaaatttttaagcaagctattatctctgagaaatgg actgctgctatgggtgtggaacttgggtctatggaacttaacaaaacatggagtgttgtttctttacctc agggtaagaatgtagtaggctgcaaatgagtttttactattaagtataatgctgatggctctatagaaag atataaggccagattagtagcaaaggggtttatacaacaagaaggagttgattattttgatactttctct cctgtggcaaaattggccagtgttaaacttttgcttgatctaacagctaagaaaggttggagtacttctc agatggatatctctagtgcttttttacacagtgacttggaggaagagatctatatgagtttaccagaggg gtacacgccaccagatggagttccattgcctcctaatgctgtttgcagactgcacaaatccatttatgga ttaaaacaagcttcacgccagtggtataaatgtttatcagctgttcttcttgatgatggattcattcagt cctatgctgataatatgctattcgtcaaagtcactggtacgtctattgttgctctacttgtttatgtaga tgacattttgatagtgagcaatgatgatgaggctgtgagatccgttaaagctgttctagggaaacacttt aaaaccaaggatttaggtgaggcaaaattcttcttaggacttgagattgctagaaatgcagatggtatct ctgttagtcaaaggaagtattgtttggatatgctagctgattcaggactattgggttgcaaaccaaaatc tgtacctgtggatcctaaagtccctttaaccaaggaaactggtactcttttggagaatgcaaggccttac cgtgagataattgggaggttattgtatttgtgcattactaggcctgatatcacctatgcagtgaatcggc tgagccagtttttatcttgtcccactgatgttcacctacaagcagcgtatcagattctgaagtatcttaa gaacaatccgggtcagggtttgttttattcttctcaaccagatatatgcttaaatggcttcgctgatgca gactggggtacctgccttgatacaagacgatctacttctggtatgtgtgtttttcttggacattcactga ttacatggaagtcaaagaagcaggacattgtaagcagcagtagtacagaagctgagtatcgatccatggc tgtgactacaaaagaacttctatggttgagtcagatgcttaaggatcttcatatacaggttgattcatca gctaaactgttttgtgacaataagtctgcaacttatattgcgattaatcctgtatttcacgagagaacga aacatgtcgaaattgattgtcacatcacacgagatcaagtgaagaatggcttcttgaaggttctacatgt agctacagaaaatcaattagcagacatcatgacaaagcctcttcatcctggtccattctattctctcctt agtcgactatcggtttcaagcctctttaatccttcagatgattcggcttgagggggg1