;ID ATLINE1_5 DNA ; ATH ; 6835 BP ;XX ;DE ATLINE1_5, non-LTR retrotransposon - a fossil. ;XX ;AC AC007047 ;XX ;DT 30-NOV-2001 (Rel. 6.3, Created) ;DT 30-NOV-2001 (Rel. 6.3, Last updated, Version 1) ;XX ;KW non-LTR retrotransposon; L1 superfamily; poly(A) tail; ORF1; ORF2; ;KW reverse transcriptase; ATLINE1_5. ;XX ;OS thale cress ;XX ;OC Arabidopsis thaliana ;OC Eukaryota; Plantae; Embryobionta; Magnoliophyta; Magnoliopsida; ;OC Dilleniidae; Capparales; Brassicaceae. ;XX ;RN [1] (bases 1 to 6835) ;RA Kapitonov,V. and Jurka,J. ;RT ATLINE1_5, a non-LTR retrotransposon. ;RL Repbase Reports 1:(3) p. 34 (2001) ;XX ;CC ATLINE1_5 is a non-LTR retrotransposon. Its individual copies are ;CC ~88% identical to each other. There are only 3 copies of ;CC ATLINE1_5 present in the genome. ATLINE1_5 belongs to the L1 ;CC superfamily of non-LTR retrotransposons, its copies are flanked ;CC by ~15-bp target site duplications. ;CC Two proteins, ATLINE1_5p1 and ATLINE1_5p2, are encoded by ORF1 ;CC (position 431-2546) and ORF2 (position 2691-6710), respectively. ;CC Both ORFs are saturated by several false stop codons. ;CC Stop codons at positions 1019 and 5675 are replaced by R in the ;CC corresponding protein sequences, based on their comparison with ;CC other homologous proteins. ;CC ATLINE1_5p1 (771 aa): ;CC MSKRMRPSWYRDSPPKQLPYAFVPEEDDDVVILPQVDNSALLGRLQLSLVGRMFHQGGRSTEALLSFLPN ;CC IWDVEGRVRGVSLGDSRFQFFFESETDLQKVLNKRPCHFSKWSFALERWKSHIGISFPDTMTFWIKTEGI ;CC PTEFWEEEVLRNFGASIGAVRRVDSSKGRLQISVKADVPFRFNKNAQLPNGEVVKVKLFYEKLFGWCTYC ;CC RRICHELDQCPLLDENQRVALMAEDQRHSHLDGSVDGRS*SLSLSQGGTVVPRNGPGERVVSLPEGPQI* ;CC KSNPSYGPNRLAANNPPLSKSSSRFGGSRSRRHPHPPSSRRLPTDRAPPPNRASGSVRRSSPPEGRKRRY ;CC GVSFSQEKIVEKPSKGNQDLARVVPSSSLPPSTIPGELRSSPHLSDSQITISDPLLAPSRAKQRTSSPAY ;CC VRERPFRLNLSKKHSASEKGKGKVGDPPMSLGDTTPGSSPSAKKSLNFDLDPSSKITTTPSSVNHVVQVP ;CC SPPGKRLSWYEMKVEEDEANARALGAGPDTILAAKFSQVVSFASPVVDVPALPDRQSHSPPLSGGSPQAE ;CC WDKNLNPLSEALNLDWTAEDEAAYHALEPPFTTGEEDVAGKNTLRIESHVSSLERLETQSSISLASTQRP ;CC TPSKVLEGATENGGDVENRDQLLSLDGLLSLEIDFVSTLGGPKKGVKKKRAETHSRKGNTTSGKVQSSLG ;CC LLVNLASKKIQNVKGRSPSKRLLLKGGASKSRAAKRPSSAPRSSIFPSSKVKSPGSIGGSVGSMEPPDTN ;CC P ;CC ATLINE1_5p2 contains the reverse transcriptase and endonuclease ;CC domains. ;CC ATLINE1_5p2 (1402 aa): ;CC MSKDVLRVSVSCSKVGLPSQELLNVRLRLLVQASSRHPKSNLRGLLVARWGPWNPPTLTHEDLSVEDMCR ;CC MYSPGFLFLSETKNDLLYLQNMQVSLGFDCLQTVDPIGNSGGLALLYSNEFPVTVVFLNDQLIDIETIID ;CC GNRVCITFVYGDPNVQYRELVWERLTRIGIIRSDPWFMIGDFNEITGNHEKKGGKSWSESSFLPFRCMIE ;CC NCGMIEIPSHDNLFSWVGRRSCGVTGRRVRKVIKARLDRAMANEEWHNIFSHSNVEYVKLWGSDHRPLLG ;CC SIQNSPQRNFKQFSFDKRWFGKSGFKESVYEGWNLSSHDGDFFSQKVKSCRKSISTWKKASSTNSEKKIV ;CC DLQDQIDRAQEDEAISAEDLLALKWKLCDAYREEEIFWRQKSRELWYKSGDNNTNFFHAITKQRRAKNKI ;CC IGLLNQDGLWIDNEVGIENLEVDYFKDLVTTSNPQDFHSAIRDVPVIISEEINKNLTKDISPAEVKRALF ;CC SLNPDKAPGPDGMTSFFYQKFWDLTGPDLVIIVQNFLSSGAFDKQLNETNICLIPKVDRPRKMVEFRPIS ;CC LCNVSYKVISKVLSFRLKKLLPDLISETQSAFVAGRLITDNILIAQENFHALRNNPACRKKFMAIKTDMS ;CC KAYDRVEWCFLQALMLKMGFSQKWVDLITFCISSVTYKVLVNGSPRGFIKPSRGIRQGDPISPFLFILCT ;CC EALVASLKDAEWHGRIQGLQISRASPSTSHLLFADDSLFFCRADPVQGQEIIKILRTYGEASGQQLNSAK ;CC SSILFGHDVENTIRNNIKVAIGIHKDGGMGSYLGLPEKIHGSKVQVFSFVRDRLQKRLNTWTAKFLSKGD ;CC KEVLIKSVAQALPTYVMSCFLLPKAIRSKLSNAIANVWWKTNENSNGIHWIAWDTLCKPHSEGGIGFRTL ;CC EEFNLALLAKQLWRLIRFPNSLLSRILRGRYFRFSDPLHIGASFRPSYGWRSIMAAKPLLLLGLRRTIGS ;CC GMLTRVWEDPWIPSIPARPAKSILDTRDPHLYVNDLIDQNTQSWKIDRLTSLIDPVDIPLILGIRPSRTY ;CC LSDGYSWPYTKSGNYSVKSGYWAARDLSRPICDPPSQGPGVTALQAQVWKLKTTRKLKHFAWQCISGCLS ;CC TCQRLAYRHMGTDKSCPRCGASEESINHLLFHCPPSRQIWALSPIPSSGSLFPRNSLFYNFDFFLWRGRE ;CC FDIEEDVIALFPWIIWYIWKSRNRFIFENVREPPPETLALALQEAAAWKQAMLIDEDHVDAPPPPSFAEA ;CC PPAELVECQFDASWHAEDSLSGFGWVFVRHDVVLHLGLKSERRSLSPLHAEFDSLLWAMESLISIGMTTG ;CC AFASDCANLISILDNQDEWPSFAAEIVSYRSLVCLFSSFSIRFVPRSFNFRADCLAKKARVRNCIFSHAV ;CC GS ;CC There are no elements in the genome that are more than 81% identical ;CC to ATLINE1_5. Given the well preserved ORF1 and ORF2, ATLINE1_5 is ;CC a relatively young retrotransposon, which is represented just by ;CC one copy in the genome. ;XX ;DR Positions 83766 90600 Accession No AC007047 GenBank (rel. 124.0) ;XX ;SQ Sequence 6835 BP; 1730 A; 1564 C; 1534 G; 2007 T; 0 other; ATLINE1_5 atttggtgacagatgctaaaaaaactctctcatgcactcttctcgaggtgtctgaaattggcaatgtttg tcaaaaaaagtagatcttgacttcttcttttagctattttgagaaacttttcttacccttccatgaactt tgcagtcctcgagccttgtaatggagggtttagcgtcttcttatatgtatacttgcatcaactttctgtg atagacagttctctcctatcacaagcgaaattttttcagtctttgcttctctctgttgtggtcacgaaca gctcgtttcttgtccgaaggaattaagcttttactgaacttttcctgcttgagcagtgtggtgttctttc gttctctatctcttaagcctcttcctcatgactcccttatctctcgttctatttccatgtctaagagaat gagaccaagttggtacagggattctcccccaaaacagctcccgtatgcctttgtgccggaagaagatgat gacgttgtcatccttcctcaagttgacaattcggctctcctaggtcgtcttcaacttagcttggttggta gaatgtttcatcaaggtggtcggagtactgaagctttgctctcttttctcccaaatatatgggatgtcga agggagggtccggggagtttctcttggagattcccggttccaattcttctttgaatctgagactgatctt cagaaggtccttaataagagaccttgccacttcagtaagtggtcctttgcgctggaaagatggaagtccc acattggcatttccttccctgatacgatgaccttctggatcaaaactgaaggaatccctactgaattctg ggaggaggaagtgctgagaaattttggtgcttccattggagcagttaggcgagttgactcttcaaaagga agactccaaatctctgttaaggcagacgtccctttcaggtttaataagaatgctcaactcccaaatggtg aagtagttaaagtaaaactattttatgaaaagctcttttgatggtgtacctactgtcgccggatctgtca cgaacttgaccagtgtcccctcctcgatgaaaatcagcgagtggctctaatggcagaggatcagagacat agtcatctcgacggatcagttgatggtcgttcctagtctctctctctcagtcaaggaggaacagtggttc ctcgtaacggccctggtgagcgggttgtgtctctccctgaaggtcctcaaatctgaaagtccaatccgtc ttacggacccaatcgtttggcggcgaacaatcctcccctgtccaagtcttcttcccgctttggtggctct cgctcccggcgccatcctcatcctccttcctctcgacgtctgcctacggaccgggctccaccgcctaacc gggcttctggctctgtacgacgctcgtctccccctgaaggtcgtaagcgacgttatggtgtctctttctc tcaggagaagattgtggaaaagccatctaaaggaaatcaggacctggcgcgtgtagttccctcctcctcg ctcccaccttccaccatccctggtgagctgcgatcctcacctcacctctctgactcgcagataacaatct cggaccccctcctggctccctcaagagcaaaacagagaacctcttccccggcttatgtcagggaaagacc tttccgcctaaacctatctaagaagcactctgcttcagaaaaaggaaagggcaaagtgggggatcctccc atgtctctcggagacacgactccggggtctagcccctctgccaagaaatctcttaatttcgatctagatc cttcatcgaagatcacaactaccccaagttctgtaaatcatgttgtgcaagtcccttccccacctggtaa gcgtctgagctggtacgagatgaaggtggaagaagatgaagccaatgcccgggctttaggtgcaggaccg gacacgatattagcggcgaagttttctcaggtcgtctcctttgcaagcccagttgttgatgtccctgctc tccctgaccggcaatcccactctcctcccctctctggtggctcccctcaagccgaatgggataagaacct caatcctctctcggaggcgcttaacctagactggacggccgaggatgaggctgcctatcacgctctggaa cctccgttcaccacgggggaagaagatgtggcaggaaaaaacactctgagaattgagtcccatgtttctt ctctagaacgtttggagacgcagtcgtcgatctccctcgcttccacgcagcgtccgactccgtccaaagt tcttgaaggagcgactgagaacggcggtgatgtggagaacagagatcagcttctgtccctagatgggctt ctctctttggaaatagattttgtttctactctcggtgggccaaaaaagggagtaaaaaagaagagggccg aaacccattctcgcaagggtaatactacttctggtaaagtccagtcctctttgggccttttggtgaatct agcttcaaaaaagatacaaaatgtcaaaggacgttctccgagtaagcgtctcttgctcaaaggtggggct tccaagtcaagagctgctaaacgtccgtcttcggctcctcgttcaagcatcttcccgtcatccaaagtca aatctccggggtctattggtggctcggtggggtccatggaaccccccgacactaacccatgaggatctta gcgtggaggacatgtgtcgcatgtattctccgggttttctttttttatcggaaactaaaaatgatctttt gtatcttcagaatatgcaagtatctctaggctttgattgtctccaaactgttgaccctataggtaacagt ggtggattagctctattgtactctaatgaatttccggttacggttgtttttcttaatgatcagcttattg atattgagactattattgatggtaaccgtgtttgtattacttttgtttatggcgacccgaatgtccaata tcgggaactagtttgggaacggttgacccgtattggtattattcgttcagatccatggttcatgatagga gatttcaatgaaatcaccgggaaccatgagaaaaagggaggcaaaagttggtccgaatcttctttccttc ctttccgatgtatgatcgaaaattgcgggatgattgaaattccatcccatgacaatcttttctcatgggt gggacgacggagttgtggagttacgggacgacgggtccggaaagtcattaaagctcggttggatagggct atggccaatgaggaatggcataatattttttcccactcgaatgtggagtatgttaaattatggggatcag atcaccgccctctccttggttcaatacaaaacagtccccaacgtaattttaagcagttttcttttgataa acgatggtttgggaaatcgggctttaaagaatctgtgtacgaagggtggaacctatcttcccatgatggt gattttttttcacaaaaagtgaaaagttgtagaaaatctatttctacttggaagaaagctagttcaacta attcagagaaaaaaattgtggacttgcaagatcagattgatcgagctcaagaagatgaggccatctctgc agaggacctcctagccctgaaatggaaactctgtgatgcgtatagagaagaggaaattttttggcgccaa aagagtagggaattgtggtacaagtccggtgataataacacaaatttttttcatgcgataactaagcaga gaagagcgaaaaacaagattattggcttattgaatcaagacggtctgtggattgataacgaggtgggaat tgaaaatctagaagtggattatttcaaggatttagtcaccacctcaaatccacaagatttccattccgcc attcgggatgtgccagtgataatttcagaagaaataaacaaaaatctcacaaaagatatttccccggcag aagtcaaacgcgcccttttttctctcaacccagataaagctccaggtccagatggaatgacaagtttttt ctatcaaaagttttgggatttgacgggccctgatttagttataatagtccaaaactttctttcttcaggt gcttttgacaagcagttgaatgagacaaacatttgcttgatccctaaggtagaccgacctaggaaaatgg tggagtttcgccctattagtctgtgtaatgtgagctacaaagttatctcaaaagttcttagcttccggct aaagaaactacttccggacttgatatccgagacgcaatctgcctttgtggcaggtcgcctaattacagat aatattctaattgcacaagaaaactttcatgctctccggaataacccggcttgcagaaaaaagtttatgg ctattaagacagatatgagcaaagcttatgaccgggttgaatggtgttttcttcaagcgcttatgttgaa aatgggtttttcccaaaaatgggttgacttaataaccttttgtatctcttcggtcacttataaagtcctt gtaaatggttccccgagaggctttattaaaccatcaagaggtatccgtcaaggagacccaatctcccctt tcctcttcatcttgtgcacagaggctttggtagcaagcctcaaagatgcggagtggcacggccggattca aggcctacaaatctctcgtgcgagcccttcaacctctcacctattgttcgcggatgacagtcttttcttc tgtagagcggatcctgtccaagggcaggaaattattaaaattcttcggacatacggggaggcctcgggtc agcagttaaactctgctaagtcttccattttgtttggacatgatgtggaaaatactattcgtaacaacat taaagtagctattgggatccataaggatggcggtatgggttcatatctgggcttaccagagaagatccat ggttcaaaagttcaagtcttctcttttgtaagagatcgtcttcaaaaacgcttgaatacttggacggcta aattcttgtcaaaaggcgacaaagaagtacttataaagtctgtagctcaggcccttccgacatacgtcat gtcgtgcttccttctcccaaaagcaattcgctccaagctaagtaatgccattgccaatgtttggtggaaa accaatgaaaacagtaacggtattcattggatagcttgggataccctttgtaaaccccattcggaggggg ggataggctttagaacacttgaagagtttaacttagctctgttagctaaacaattatggcggctgattcg atttccgaattctcttctcagtagaatcttacgtggaagatatttccgttttagtgatccactccatatt ggtgcttcgtttagaccctcttatggatggagaagtattatggcggcgaaaccccttcttcttttgggcc tccgtcggaccataggttctggaatgttgactcgcgtctgggaagatccttggatcccctcaattcctgc aaggccagctaagagcatccttgatacaagagatccccatctttatgtaaacgacctgattgatcaaaac actcaatcgtggaagatcgaccgtcttacatccttgatagaccccgttgacattccacttatattaggaa tttgaccaagtcggacctacttgagtgatggatatagctggccgtatactaaatctggtaattactctgt taagtccggatattgggccgcgagagatctttctcgtcctatttgtgaccccccttctcagggaccaggt gttacggcacttcaggcacaagtatggaagcttaaaactacacgaaagcttaagcatttcgcgtggcaat gtatttcagggtgtctttctacctgtcaacgtctagcttacagacatatgggtaccgataagagttgccc ccgttgcggtgcttcggaggagtcgattaaccatttactctttcattgtccaccttctcgacaaatatgg gcactctcgcctattccttcctcagggagtcttttccctagaaattctctcttttataacttcgattttt ttctttggcgtggccgggaattcgatatagaagaagatgttattgctctctttccatggattatttggta tatctggaaaagtagaaaccgctttatatttgaaaacgtcagggaaccccctcctgaaactctcgcattg gccctccaagaagctgctgcttggaaacaagccatgctaattgacgaggatcatgtagatgctccccctc cgcctagcttcgcggaagcccccccagctgagctcgttgagtgtcaatttgatgcgtcctggcacgctga agactctctaagtggctttggttgggtgttcgtcagacatgatgttgtcttacacctgggtctcaagagt gagcgtcggagtttatcaccgctccatgctgaatttgactccttgttatgggcgatggaatcactgatct ctattggtatgacgactggtgcctttgcttcggattgcgcaaatctgatctctatcctggataatcaaga tgagtggccatccttcgctgcggagattgtctcatatcgatctttagtctgtttattctcgtcttttagt attcgctttgttcctcgtagttttaactttcgagctgattgtctagctaaaaaagctcgagtccgcaatt gtattttttctcatgcagtcggttcctgaatggctctccgtagaggagagcctcttcctgacatcttaac gagaatggtgtttgatgaaaaatctaaaaataaaaaataaaaaaa1