;ID ATCOPIA94_I DNA ; ATH ; 4638 BP ;XX ;DE Internal region of the ATCOPIA94 copia-like LTR-retrotransposon. ;XX ;AC AC022354 ;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; internal region; ;KW copia-like polyprotein; reverse transcriptase; the ATCOPIA94 ;KW family; ATCOPIA94LTR; ATCOPIA94_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 4638) ;RA Kapitonov,V.V. and Jurka,J. ;RT Internal portion of the ATCOPIA94 copia-like LTR-retrotransposon. ;RL Repbase Reports 1:(4) p. 4 (2001) ;XX ;CC ATCOPIA94_I is an internal region of the ATCOPIA94 copia-like ;CC endogenous retrovirus. ;CC ATCOPIA94 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 ATCOPIA94_I. ;CC ATCOPIA94_I encodes remnants of the ATCOPIA94p copia-like ;CC polyprotein. The ORF which encodes ATCOPIA94p is damaged by ;CC one frame shift induced by a 5-bp deletion at position 3264 ;CC (masked by XXXX in the 1436-aa ATCOPIA94p sequence). ;CC Such a low damage indicates that ATCOPIA94 has been retrotransposed ;CC recently. ;CC ATCOPIA94 is inserted exactly between two hypothetical genes ;CC that are 86% identical to each other. ;CC ATCOPIA94p: ;CC IPSPLNAHYSLEDIVSYYYSKASDHPGHVISHPLLRGDNYEEWAINLETALASRKKFGFLDGRISKPEED ;CC SSDFDDWKSINALLVSWIKMTIEPNLRSNISHKPVARDLWEHIKKHFCVSNGPRVQQLRKELSNCRQDGL ;CC SIETYYGKLTKLWDNMDACRPRIVCTCGKCICDCLAVLETLREHDKVHDFLMGLDESAYGTVRSSLLIQE ;CC PLPSLEYVYLKVTQDEDSRSHKQVSDSRPDGMVFAAQHASRVRPGERSSSTTVCTNCGRTGHMAESCFQI ;CC LGFPEWWGDRPRNQNGRGCGTKSNGSGRGGGVVARDNVAQGASSSEVVHANVAITDADRAAVLNLTDEQW ;CC ISVKRAINATKGNSDEQLSGKSSSTSWILDTGATNHLTCRRDILENVRKSTSTPIILADNRIVMGDMVGS ;CC VTLNKHLKLHNVFYIEDLGFDLISVTQLMEENDCVMQLSVPFCVLQDRTTRTLIGVGKPSGGLVYFRSTE ;CC VAVAVKGVPKQSLELWHQRLGHPSLKVVESLPDFVFSSHKDFSNKACDVCIRAKQTSSSFPISNNKTTEI ;CC FEMIHCDIWGPYCEPSSSGARYFLTIVDDYSRGTWLYLMKNKSDTQTKLRDFIALVDRQFGKKVRVLRSD ;CC NGGEFLSLTSYFLASGIVHETSCVGTPQQNGRVERKHRHLLNVARAIMFQGSLPIQFWGECALNAAYLIN ;CC RTPSMVLNGKTPYKVLFGKRPSYDHLRTIGCLCYIHNQDHHGDKFASRSRKCVFVGYPYAKKGWRVYDLE ;CC KEIFCVSRDVVFDEGIFPFHNDLNPLPLTLDTTSSLTPFYSDDDDDDNGPTTCSVSVPPVPVIPLRVAPI ;CC SLADSGSKVDLPNDDLVLPDSASTTPLPTDPKPTRERRQPAYLADYETTFLCGSSSTPYPISDVLTDARF ;CC SSAHKAFLTAITLAHEPATYAEAFADPKWRDATKEEIDALVLNHTWDIEDLPLGKVAIGSKWVFKVKHXX ;CC XXTVERYKTRLVALGNRQKEGIDFDETFAPVAKMTSVRIFLSIVAARNWEVHQMDVHNAFLHGDLEEEVY ;CC MKLPPGYFAQHKGKVCRLRKSLYGLKQAPRCWFAKFATALKNYGFQQSYSDYSLFSFNRDGVSLYVLVYV ;CC DDLIVTGNSTTAISEFKQYLDSCFHMKDLGLLKYFLGIEVARSPDGIYLCQRKYVLDILQDTFLLGAQPS ;CC GFPIEQNHTLASATGSFLTDLASYRRLVGRLVYLNVTRQDLAYSVRVLTQFMQKPREEHWTAALRVVRYL ;CC KGTPGQGVLLRANSDLHIYGWCDSDFSGCPRSRRSLTGWFVQLGQSPVLWRTKKQKVVSMSSAEAEYRAM ;CC SLTARELVWLQALLEDLAVFLSRPMTLYCDSTAAIHIAANPVFYERTKHIERDCHFVREKVQNGTIATVH ;CC VSTTTQLADIFTKALGSREFDVFRDKLGIEDLHAPT ;XX ;DR Positions 32279 36916 Accession No AC022354 GenBank (rel. 124.0) ;XX ;SQ Sequence 4638 BP; 1184 A; 921 C; 1041 G; 1492 T; 0 other; ATCOPIA94_I tggtgtttaattgttgaatttctgttttgttgtttcattctttattgatctctgaattactgtatgaccc agtgtttttaattcgtagtttaaatcgtttatttctttgcatttttatatacaattatgaaaacaaaaca aatatcatttatgctttacataaaaacgagtctcacaaatctttagagcatcagacgtggttcttatgaa tcgaccgcatatttattgtcttacgattaattgtatcatgttactactccagcaattaattagtatcata tctggtttcagaacaagaaaacataattttaaaactttaatctgaattccatccccattaaacgcacatt actcacttgaagatattgtgtcatattattattcaaaagcaagtgatcatccgggacatgtcatctccca tccacttctccgaggtgataactatgaagaatgggctatcaacttggagactgctcttgcctcgagaaag aagtttggttttctcgatggtcgaatttcgaagccagaagaagactcttccgactttgatgattggaaat caatcaacgccctcttggtctcatggatcaagatgacaatcgaaccgaatctgcgctccaacatctcaca caaacctgttgcgcgtgacttgtgggaacatatcaagaaacatttttgcgtttcgaacggtcctcgtgta caacaactacgcaaggagttatcgaattgtcgtcaggatggtctctcgattgagacatactacggcaaac taacaaagttgtgggacaacatggatgcttgtcgaccacgtattgtgtgtacttgtggaaagtgcatatg tgattgtcttgccgtgttggagacgctaagggaacacgacaaggttcatgattttctcatgggacttgat gaatcagcctatggcactgtccgctcgtctcttttgattcaagaacctttaccaagtcttgagtatgtat accttaaggtgactcaagatgaggattctcgctctcacaagcaagtcagtgactctcgacccgacgggat ggtgtttgcagcacaacacgcgtctcgtgtacgacccggggaaagatcttcttcgacaaccgtgtgtacc aactgtgggagaactggtcacatggcagaaagctgttttcagattcttgggtttccagaatggtggggag ataggcctcgtaatcaaaacggacgtggttgtggtactaaatccaatggatctggacgtggcggtggagt tgttgcacgagataatgttgctcagggagcatcgtcatcagaagttgttcatgccaatgttgctatcaca gatgccgatcgtgcggctgtgctcaatctcaccgacgaacagtggataagtgtcaaacgggccataaatg caactaaaggaaactccgatgagcaactctctggtaagtcttcctctacttcgtggattttggatacagg tgcgacaaatcatttgacatgccgccgtgatatacttgaaaatgttagaaaatcgacttcgactccaatt attcttgctgataatcggattgtgatgggtgacatggttggttctgtgacattgaataaacacttgaagt tacacaatgtgttttatattgaagatttgggttttgatttgatctctgttactcagttgatggaggagaa tgattgtgtaatgcagttgagtgttccattttgtgttcttcaggaccgcactacgaggacgctgattgga gtaggtaagccctctggagggttggtctattttcgaagcacggaggttgctgttgcggtgaagggtgttc caaaacaatctttggagttgtggcatcaacgcttagggcatccgtctttgaaagtagtcgagtctttacc ggattttgttttttctagtcataaggatttttcgaataaggcgtgtgacgtttgtatccgcgctaagcaa actagttcttcttttccgataagcaataataagactactgagatttttgagatgattcattgtgatattt ggggtccttactgtgaaccttcttcttctggagcacgatatttcttgacaattgttgacgattactctcg tggtacttggctttatcttatgaagaataaaagtgacactcaaacaaagcttcgtgattttattgctttg gttgataggcaatttggcaagaaagttcgtgttctaagaagtgataatggtggtgaattcttgtcactca catcttattttcttgcatctggtattgtccatgaaacgagttgtgtgggtactcctcagcaaaacggtcg cgttgagcgtaaacaccgtcatctcttgaatgttgcacgagcaattatgtttcaaggatctcttcctatt cagttttggggagagtgtgcgttgaatgcggcttaccttattaatcggactccttcgatggttcttaatg gaaagactccatacaaggttctctttgggaaacgtccttcttatgatcatcttcgaaccattggttgttt atgctatatacataatcaagatcatcatggagataagtttgctagtcgcagccgcaaatgtgtttttgtt ggatatccatatgctaagaagggttggcgtgtgtatgatctcgagaaagaaattttttgtgtgtcacgag acgtggtctttgatgaagggatttttccatttcataatgatttgaatccgcttccactcactttggatac cacgtcttcactcacacctttctattccgacgatgatgatgatgacaatggtccaacgacatgctccgtc tcggttccaccggttcctgttatcccacttcgtgttgcaccaatatctttagcagattccggttcgaaag ttgatttgcctaatgatgatttggttctaccagattctgcttctactactccactaccaacggatccaaa acctactcgtgaacgacgtcaacctgcttaccttgccgattacgaaacgacgtttctatgtggttcatca tcgactccgtatccgattagtgatgtcctcactgatgctcgtttttcatcagctcacaaagcttttctta cagctattacattagctcatgaaccggcaacttatgcagaagcttttgcagacccaaaatggcgtgatgc cacgaaagaagagattgatgctcttgtcttgaatcacacatgggatattgaagatttaccactaggaaaa gttgcgattggttccaagtgggtcttcaaggttaagcatcgctaggacagtggaacggtacaagactcgg ttagttgctttaggaaaccgacagaaagagggcattgattttgatgagacatttgctccggttgcgaaaa tgacttcggttcgtatatttttatcgattgtggctgctcggaattgggaggtgcaccaaatggatgttca taatgcgttcttacatggtgatctcgaagaagaggtctacatgaagttaccgccaggatactttgcccaa cacaaaggtaaagtgtgtcgtcttcgaaagtcattgtatggcttgaaacaagctccacgatgttggtttg caaaatttgcaacagcacttaaaaattatggttttcaacaatcatattccgattactctttgttttcatt caaccgtgatggtgtgtctttatacgttttggtctacgttgatgacttgattgttactggaaactccact acggcgataagtgagtttaagcagtatcttgattcatgctttcacatgaaggatcttggtcttttgaagt atttcttgggtatcgaggttgctagaagccccgatggtatttacttatgtcaacggaagtatgttcttga tattcttcaagacacgtttcttcttggagcacaaccatcaggttttcccattgagcaaaaccatactctt gcttctgctaccggttcgtttctaacagatctagcatcttatcgtcgtcttgttggtcggctcgtttatc ttaatgtcactagacaggaccttgcatactcggttcgtgttctcactcaattcatgcagaaaccacgtga agaacattggacagcggcactacgtgttgttcgttatctcaaaggaactccgggacaaggtgttctctta cgagctaattctgatcttcacatatacgggtggtgtgactctgatttctctggctgccctcgttcgcgtc gctctttaacagggtggtttgttcagctcggtcaatctccagtattatggcgaactaagaaacaaaaggt tgttagtatgtcttcagctgaggccgaatatcgtgctatgtcacttactgcacgagagttggtttggttg caagctttgcttgaagatcttgctgtgtttctctctcgcccaatgacgttgtattgtgatagtacagcag ctatccatattgcggccaatccagttttctacgaacgtacgaagcatatcgaacgagactgtcattttgt tcgcgaaaaagttcagaatggtactattgccacagttcatgtttcaacgactactcagcttgcggacatt ttcactaaggcattgggaagtcgggagtttgatgtttttcgggacaagttgggcattgaggatctccatg ctccaacttgagggaggg1