;ID ATCOPIA42I DNA ; ATH ; 5072 BP ;XX ;DE Internal region of ATCOPIA42 copia-like endogenous retrovirus - ;DE a consensus sequence. ;XX ;AC . ;XX ;DT 31-AUG-2000 (Rel. 5.8, Created) ;DT 31-AUG-2000 (Rel. 5.8, Last updated, Version 1) ;XX ;KW LTR-retrotransposon; endogenous retrovirus; COPIA superfamily; ;KW internal region; pol; env; ATCOPIA42LTR; ATCOPIA42I. ;XX ;OS thale cress ;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 5072) ;RA Kapitonov,V.V. and Jurka,J. ;RL Direct submission (August 2000) ;XX ;RN [2] ;RA Kapitonov,V.V. and Jurka,J. ;RT Molecular paleontology of transposable elements from ;RT Arabidopsis thaliana. ;RL Genetica 107 (1-3), 27-37 (1999) ;XX ;CC ATCOPIA42I is an internal region of the ATCOPIA42 copia-like ;CC endogenous retrovirus flanked by ATCOPIA42LTR; 5-bp target-site ;CC duplication. The consensus sequence was derived from three copies, ;CC they are ~95% identical to the consensus sequence. ;CC Gag and RT portions of a copia-like polyprotein encoded by ATCOPIA42I ;CC are damaged by several false stop-codons. ;CC ATCOPIA42I encodes also env-like protein (position 3492-4687): ;CC MNAIFSGLQRLVQQRSVTPSSNLSEAASEEHPSQSLKAEEEENLNKAMVLYAEPEPTSLRSELPNKENQD ;CC EQAAVSPEPPVIVELPDECESTVVHVHRSETPIQAETRNQTCDQVPPLNNENPQVVQISDASESAQAVDS ;CC TDLSVSSRLLKRKQSAVVERMKRQKTNERKEAAGSSACGEIGLQRLATYHSXCXEEVEDDSVKVCVRGME ;CC YEFSPAKINVLFGLQSVDARAQQMQIAGLMDDEVTSYLTDGQVKVLQSLPMSTFSKNCRKLFKFSCRNWS ;CC PTTSEGYASTDRALLVYQIAHKLAFDFGKMVYEHIMQLALKPEAKFYIPFPSLVYQLLQMQHPVKFHVEK ;CC PEPLVQTKKKTAKKPSTQGVQTGDSTNGSGHRRAMKLAIEVLQTALDAGKCFSVFL ;CC Two false stop-codons in the env are masked ;XX ;DR [1] (Consensus) ;XX ;SQ Sequence 5072 BP; 1536 A; 915 C; 1244 G; 1377 T; 0 other; ATCOPIA42I attggtatcagagcggacacctgataaaagaatttgttaatcttttcaacaggtgagatcttgcgacaag ggatggagaaagcacaacggttcgttgcgatacctaagccactgaagctggatgctgagcattacgggta ttggaaggtgttgatcaggcaatcgattcaaagtatcgacatggatgcatggtttgcagtagaagatggt tggacgcctcctaccacaaaggatgcaaagggagacattgtcttgaaatcaaggactgaatggactccgg atgagaacacaacagccaatcacaactctcaggcactgtctgtgattcttggatctttgccaaggaataa gttcactcaggttcaaggatgcttatcagcaaaggaagcatgggacattctgcaagactcattcgaaggc accaacaatgtgaagcgtactcgtctggacatgcttgcgttagagtttgagaatctgaccatggaagttg aagaatccgtggatgacttcaccggcaaactgagctccatcacacaagaggctgttgtcctaggaaaaac gtacaaggacaagaagatggtgaaaaaatttctcaggagtctgccagacaagcttcagtcacacaagtca gcgattgatgtatctctgaactcagatcaattaaagtctgatcaggtcgttgggatgatgcaggcgtatg atactgattcagtgaacgatgagcatggattctctttggagaaagtcaggattctaattgaggagttgat tctgaaaaggaaggaaaataaggagctcatttctgaaaagggaatcttgatggaaaaagtttctgcactt gaaaaggagcttggtgaagagagaatcaaatcccaaggactggagaaacagctagaagaccaactgagaa acatcaagatgctgagtagggggactaaagacttggataagctcctgactgttggaagaacttcaaacgt tacttggggtcttggatatgatggaacaagttcaaaaggaggaacgcgttttgtcaaagggacaacttca gatgagaaatctgatgatatccaaccagcagaagcacaccgcacggatgcaccttcgaaggctcgaaagg cgttgaccaggagtatgcctactcataactggagacagtcagattatcaggttgatcacaatcatctgag gagcagaagaacaggatgttggtattgcggaagtcagaaacactacagagctgattgttacagcttcctg aatcgtgttacgcaagtcaggcaccacaagcagcaccacaagaacgataagcaagggaatcaagtctaca taaagaaagatgatctttatcgtaatggtggatattcatgtacctcaattaaggttatgaatagagctgt tcttgttaacaactttgctaagtctggttatgtgaaggcaaggacgagatcagaagcaagagttagtcag tcgagtgtcaaacagctgagcagaagaacgaggaattgtttctgtagtgaccaaggacagattacagcta gttgtaacttgtgttacaatcgagtaactaaattgctgaagcgaaacaaatatcacagcgatatttgtat atccaatcgagattggatgaagaaacctaatgtttgccgtcatgttgctgataaacaaggacgtacgacc ctcaaaagtgtgcgaactggtgactgctgttacatgtggaatccatccaatccacattcaaagcagtttg ttcagagaggtgttctgaatccgaagtgcctacatagccaggacttggccactagtagcaaggtgcagca gtctggtaagtgttcgaatcatatcccacatgatgctatgggaaggattcggggggagaaagttaccaag cctgctggtggcggatgaatcaggaactgaatctgatggtgtttgtacatatgtctgtacatatctggag tcaaagttgatgagtctctgtacatatcaggggagttgcagtgcatggataccattacaagagtctgatg cagtgcaagatgctgactggactggatccgtggaagattgctgaagtacaagtggttgatgcttcttcat gggtagcaacatggtctcgaggtagagtaaggagcagaatattgtgtctctatccattgctgaaatagag tactttgctctagggagttgctacactcaaatcatgtggatgaaacaaatggcagctgactatggtatga tctctgattctttactaatttattgtgataatcagagtgcattaaacataggaaataatcttgttcaaca ttcacgcactaagcatattgatattttacaccatttcattcgtgaacttgttgaggcgaaactgatagta gttgatcatgtgagtactgaatatcaactatctgatttgtgtaccaaaatcttggagtttattagcctca gtgatctgagaaagttaattggtgtgcgtgagatctaatctgtttcgtgagatgtgttgatctaagacag gaacaaaaaatgcaagaacaggccatggaaatccaaggatgaatagaagatcaacactctgtgaataaag gtgtgtggaaaatagctgcctgtcatgccgattctgtagtcagccgtaaaacgttgtcgtctaacaggag gtcaaagagctgaggagatcaatttattgtgcaaaccaaactaagggtatctaaagcctaatttggtgtc aagtgaccatcatgcactgatatcagcagttgagaagtcaagtgatgctgctgatatgaaactgacagat caacagggattcaaagtttaaaaaaagaaaagaagaaaaaggagaaccctgttgtatctaaatctgagga agtgtggaaataaaagcagcacactcctgattctttgagcaatctccaaaggaaaattccagctgcctgt tacacgttgagccgatctactggaattgaaggcatgacagtgtgaaagactagccactgtacccagagtt gatctatcaaagatctgagtggttatggtagcttcttgctgagttctgaacaactggttggcacggaaca cggaacagatctcaaaggtataaaaatgttttgaatccaacgtagtgtactcacatgtttcaataacttt ctgggtcactaaactctgttcatgagtgaatggttgttcgctaaatgatttttaatctgaactatgctaa catgtgatgttgatcaatgggatgatatgaatcaatgggattatttgcaagtgtgcactaatgtttttgt ttagtgtttcaggctctaattattttaggtatagcctaagcccatttgttttgaaggcccatgaacaaat taagcccattacttaatgtctaggttggagggaaaaagagttagggtttctcatgtcaaatcaaacctgc ctagggagtcgttaactcgaagacttgtgctcaaagagaatcaagttgaaatctttcttgaagatgaatg cgattttctctggacttcaacggctcgtgcaacaaagatctgtgacaccgtcgtcgaacctgtcagaagc agcctctgaggagcatccatcgcagtctctgaaagctgaagaggaagaaaatctaaacaaagctatggtg ttgtatgctgagcccgaaccaacatctctcagatctgagcttccaaacaaggagaaccaagatgaacagg cagccgtatctccagagccaccggtgattgtggaactgcctgacgagtgtgaatctactgttgttcatgt gcatagatctgagacacccattcaagctgagaccagaaaccagacttgtgaccaagttccaccactcaac aacgagaatcctcaagtggtgcagatctctgatgcgtctgaatccgcacaagctgttgactcaacagatc tgtctgtgtcctcgcgtctgctgaaaaggaaacagtctgctgttgtggagaggatgaaaagacagaagac taacgaaaggaaggaagctgctggttcaagtgcttgtggagaaattggtcttcaacggcttgcgacttat cactcatgatgctaagaagaggtcgaagacgattctgtcaaggtatgtgtgcgaggcatggagtacgaat tctctcctgccaagatcaacgttttgtttggtctgcaatcagttgatgccagagctcaacagatgcaaat tgctggtctgatggatgatgaggtcaccagctatctgactgatggacaagtgaaggttcttcagagtctt ccgatgagcaccttctcgaaaaactgtaggaagctgttcaagttctcgtgcagaaattggtctccaacaa ccagcgagggatatgcaagtacagacagggctttgcttgtgtatcagattgcacacaagttggcttttga ctttgggaagatggtgtatgagcatatcatgcagcttgctttgaaacccgaggcaaagttctacattccg tttccgagtcttgtgtatcaacttcttcagatgcagcatcctgtgaagtttcatgttgagaagccagagc ccttagtccagactaagaagaagactgcaaagaagccatcaacacaaggagtgcaaactggtgactccac taatggttcaggacatcgcagagcaatgaaactggccattgaagttctgcagactgctttagatgcaggt aagtgtttctctgttttcctctgaaatattatatctctaatgatgtttgtgtgatttttgactaagtcat gcacttaagcaggaggagatgtgtctgattctgatgatgatgggggaaattaatttgtgggggagcttga tgtttttaacgtttaaaatctagtttttgacaagcttgtttttatttcacaccatgcttttgtttttgtt ctttttgaactgatgatatgtatcatctgaaaacttgggtctgtaataagttaaacacagctgcttggac gaatcttatcttttgatatgtatgctagaaacgtttctagattttgtcttgttgctgtgtttgggtttcc ttctgtttgactttcaggtcttgtcagggaga1