NC_001408 Avian leukosis virus LOCUS NC_001408 7286 bp ss-RNA linear VRL 12-JAN-2004 DEFINITION Avian leukosis virus, complete genome. ACCESSION NC_001408 VERSION NC_001408.1 GI:9626201 KEYWORDS . SOURCE Avian leukosis virus ORGANISM Avian leukosis virus Viruses; Retroid viruses; Retroviridae; Alpharetrovirus. REFERENCE 1 (bases 1 to 7286) AUTHORS Bieth,E. and Darlix,J.L. TITLE Complete nucleotide sequence of a highly infectious avian leukosis virus JOURNAL Nucleic Acids Res. 20 (2), 367 (1992) MEDLINE 92158628 PUBMED 1311072 COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence was derived from M37980. Draft entry and computer-readable sequence for [Unpublished (1990)] kindly submitted by E.Bieth, 24-AUG-1990. CRBGC du CNRS 118 route de Narbonne 31062 Toulouse Cedex France. FEATURES Location/Qualifiers source 1..7286 /organism="Avian leukosis virus" /mol_type="genomic RNA" /db_xref="taxon:11864" 5'UTR 1..371 misc_feature 1..21 /note="5' terminal redundancy" misc_feature 1 /note="CAP site" RBS 10..41 misc_feature 22..101 /note="U5 region" repeat_unit 91..101 /note="5'imperfect repeat" /rpt_type=terminal misc_feature 102..371 /note="leader sequence" protein_bind 102..120 /bound_moiety="primer" misc_feature 210..270 /note="dimer promoting sequence" misc_feature 218..248 /note="encapsidation element" RBS 331..371 gene 372..6872 /gene="env" /locus_tag="ALVgp01" /db_xref="GeneID:1491907" CDS join(372..388,5069..6872) /gene="env" /locus_tag="ALVgp01" /codon_start=1 /product="envelope protein" /protein_id="NP_040548.1" /db_xref="GI:9626203" /db_xref="GeneID:1491907" /translation="MEAVIKAFLTGYPGKTSKKDSKEKPLATSKKDPEKTPLLPTRVN YILIIGVLVLCEVTGVRADVHLLEQPGNLWITWANRTGQTDFCLSTQSATSPFQTCLI GIPSPISEGDFKGYVSDNCTTLGTDRLVSSADFTGGPDNSTTLTYRKVSCLLLKLNVS MWDEPHELQLLGSQSLPNITNIAQISGITGGCVGFRPQGVPWYLGWSRQEATRFLLRH PSFSKSTEPFTVVTADRHNLFMGSEYCGAYGYRFWNMYNCSQVGRQYRCGNARSPRPG LPEIQCTRRGGKWVNQSQEINESEPFSFTVNCTASSLGNASGCCGKAGTILPGKWVDS TQGSFTKPKALPPAIFLICGDRAWQGIPSRPVGGPCYLGKLTMLAPKHTDILKVLVNS SRTGIRRKRSTSHLDDTCSDEVQLWGPTARIFASILAPGVARAQALREIERLACWSVK QANLTTSFLGDLLDDVTSIRHAVLQNRAAIDFLLLAHGHGCEDVAGMCCFNLSDHSES IQKKFQLMKEHVNKIGVDSDPIGSWLRGLFGGIGEWAVHLLKGLLLGLVVILLLVVCL PCLLQIVCGNIRKMINNSISYHTEYKKLQKACGQPESRIV" gene 372..2474 /gene="MAp19" /locus_tag="ALVgp02" /db_xref="GeneID:1491902" misc_feature 372..2474 /gene="MAp19" /locus_tag="ALVgp02" /note="3' imperfect repeat; matrix protein" gene 372..1029 /gene="trans-acting factor" /locus_tag="ALVgp03" /db_xref="GeneID:1491911" CDS join(372..387,674..1029) /gene="trans-acting factor" /locus_tag="ALVgp03" /codon_start=1 /product="trans-acting factor" /protein_id="NP_040549.1" /db_xref="GI:9626202" /db_xref="GeneID:1491911" /translation="MEAVIREGGSLPQVRSASRNQQRSGESTKGRKWEKQLRSEMRRW RRRKWPHLKPLAHPAISAEQLLAVIAPQPRPLLLLMWGVVCILPWRGWESSRARGVTH LGGRNSQGRSQGTRVWPLGRP" protein_bind 423..440 /gene="trans-acting factor" /locus_tag="ALVgp03" /bound_moiety="nucleocapsid" protein_bind 502..511 /gene="trans-acting factor" /locus_tag="ALVgp03" /bound_moiety="nucleocapsid" misc_feature 512..540 /gene="trans-acting factor" /locus_tag="ALVgp03" /note="dimer linkage structure" misc_feature 536..556 /gene="trans-acting factor" /locus_tag="ALVgp03" /note="dimer linkage structure" misc_feature 701..792 /gene="trans-acting factor" /locus_tag="ALVgp03" /note="negative splicing regulator" protein_bind 805..818 /gene="trans-acting factor" /locus_tag="ALVgp03" /bound_moiety="nucleocapsid" misc_feature 817..876 /gene="trans-acting factor" /locus_tag="ALVgp03" /note="enhancer domain" gene 837..902 /gene="p2" /locus_tag="ALVgp04" /db_xref="GeneID:1491909" protein_bind 880..897 /gene="p2" /locus_tag="ALVgp04" /bound_moiety="nucleocapsid" gene 903..1088 /gene="p10" /locus_tag="ALVgp05" /db_xref="GeneID:1491908" gene 1836..2102 /gene="NCp12" /locus_tag="ALVgp06" /db_xref="GeneID:1491903" misc_feature 1836..2102 /gene="NCp12" /locus_tag="ALVgp06" /note="nucleocapsid protein" protein_bind 1941..1948 /gene="NCp12" /locus_tag="ALVgp06" /bound_moiety="nucleocapsid" gene 2103..2474 /gene="PRp15" /locus_tag="ALVgp07" /db_xref="GeneID:1491904" misc_feature 2103..2474 /gene="PRp15" /locus_tag="ALVgp07" /note="neutral protease large subunit" protein_bind 2388..2400 /gene="PRp15" /locus_tag="ALVgp07" /bound_moiety="nucleocapsid" gene <2495..5182 /gene="pol" /locus_tag="ALVgp08" /db_xref="GeneID:1491910" CDS <2495..5182 /gene="pol" /locus_tag="ALVgp08" /codon_start=1 /product="polymerase" /protein_id="NP_040550.1" /db_xref="GI:9626204" /db_xref="GeneID:1491910" /translation="TVALHLAIPLKWKPDHTPVWIDQWPLPEGKLVALTQLVEKELQL GHIEPSLSCWNTPVFVIRKASGSYRLLHDLRAVNAKLVPFGAVQQGAPVLSALPRGWP LMVLDLKDCFFSIPLAEQDREAFAFTLPSVNNQAPARRFQWKVLPQGMTCSPTICQLV VGQVLEPLRLKHPSLRMLHYMDDLLLAASSHDGLEAAGEEVISTLERAGFTISPDKIQ REPGVQYLGYKLGSTYVAPVGLVAEPRIATLWDVQKLVGSLQWLRPALGIPPRLMGPF YEQLRGSDPNEAREWNLDMKMAWREIVQLSTTAALERWDPALPLEGAVARCEQGAIGV LGQGLSTHPRPCLWLFSTQPTKAFTAWLEVLTLLITKLRASAVRTFGKEVDILLLPAC FREDLPLPEGILLALRGFAGKIRSSDTPSIFDIARPLHVSLKVRVTDHPVPGPTAFTD ASSSTHKGVVVWREGPRWEIKEIADLGASVQQLEARAVAMALLLWPTTPTNVVTDSAF VAKMLLKMGQEGVPSTAAAFILEDALSQRSAMAAVLHVRSHSEVPGFFTEGNDVADSQ ATFQAYPLREAKDLHTALHIGPRALSKACNISMQQAREVVQTCPHCNSAPALEAGVNP RGLGPLQIWQTDFTLEPRMAPRSWLAVTVDTASSAIVVTQHGRVTSVAAQHHWATAIA VLGRPKAIKTDNGSCFTSKSTREWLARWGIAHTTGIPGNSQGQAMVERANRLLKDKIR VLAEGDGFMKRIPTSKQGELLAKAMYALNHFERGENTKTPIQKHWRPTVLTEGPPVKI RIETGEWEKGWNVLVWGRGYAAVKNRDTDKVIWVPSRKVKPDVTQKDEVTKKDEASPL FAGISDWIPWEDEQEGLQGETASNKQERPGEDTLAANES" misc_feature 2495..5179 /gene="pol" /locus_tag="ALVgp08" /note="reverse transcriptase beta-subunit" misc_feature 2495..4210 /gene="pol" /locus_tag="ALVgp08" /note="reverse transcriptase alpha-subunit" protein_bind 2950..2964 /gene="pol" /locus_tag="ALVgp08" /bound_moiety="nucleocapsid" gene 4211..5179 /gene="INp32" /locus_tag="ALVgp09" /db_xref="GeneID:1491901" misc_feature 4211..5179 /gene="INp32" /locus_tag="ALVgp09" /note="integrase" protein_bind 4747..4758 /gene="INp32" /locus_tag="ALVgp09" /bound_moiety="nucleocapsid" gene 5244..6260 /gene="SU" /locus_tag="ALVgp10" /db_xref="GeneID:1491905" misc_feature 5244..6260 /gene="SU" /locus_tag="ALVgp10" /note="surface protein" protein_bind 5712..5727 /gene="SU" /locus_tag="ALVgp10" /bound_moiety="nucleocapsid" protein_bind 6187..6201 /gene="SU" /locus_tag="ALVgp10" /bound_moiety="nucleocapsid" gene 6261..6869 /gene="TM" /locus_tag="ALVgp11" /db_xref="GeneID:1491906" misc_feature 6261..6869 /gene="TM" /locus_tag="ALVgp11" /note="transmembrane protein" protein_bind 6414..6425 /gene="TM" /locus_tag="ALVgp11" /bound_moiety="nucleocapsid" repeat_unit 7037..7047 /note="3'imperfect repeat" /rpt_type=terminal ORIGIN 1 gccatttgac cattcaccac attggtgtgc acctgggttg atggccggac cgttgattcc 61 ctgacgacta cgagcacctg catgaagcag aaggcttcat ttggtgaccc cgacgtgata 121 gttagggaat agtggtcggc cacagacggc gtggcgatcc tgtctccatc cgtctcgtct 181 atcgggaggc gagttcgatg accctggtgg agggggctgc ggcttaggga ggcagaagct 241 gagtaccgtc ggagggagct ccagggcccg gagcgactga cccctgccga gaactcagag 301 ggtcgtcgga agacggagag tgagcccgac gaccacccca ggcacgtctt tggtcggcct 361 gcggatcaag catggaagcc gtcattaagg tgatttcgtc cgcgtgtaaa acctattgcg 421 ggaaaatctc tccttctaag aaggaaatag gggccatgtt gtccctgtta caaaaggaag 481 ggttgcttat gtctccctca gatttatatt ccccggggtc ctgggatccc atcactgcgg 541 cgctctccca gcgggcaatg gtacttggga aatcgggaga gttaaaaacc tggggattgg 601 ttttgggggc attgaaggcg gctcgagagg aacaggttac atctgagcaa gcaaagtttt 661 ggttgggatt agggggaggg agggtctctc ccccaggtcc ggagtgcatc gagaaaccag 721 caacggagcg gcgaatcgac aaaggggagg aagtgggaga aacaactgcg cagcgagatg 781 cgaagatggc gccggagaaa atggccacac ctaaaaccgt tggcacatcc tgctatcagt 841 gcggaacagc tactggctgt aattgcgcca cagcctcggc ccctcctcct ccttatgtgg 901 ggagtggttt gtatccttcc ctggcggggg tgggagagca gcagggccag gggggtgaca 961 caccttgggg ggcggaacag ccaagggcgg agccagggca cgcgggtctg gcccctgggc 1021 cggccctgac tgactgggca aggatcaggg aggagcttgc gagtacaggt ccgcccgtgg 1081 tggccatgcc tgtagtgatt aagacagagg gacccgcctg gacccctctg gagccaaaat 1141 tgatcacaag actggctgat acggtcagga ccaagggctt acgatccccg atcactatgg 1201 cagaagtgga agcgctcatg tcctccccgt tgctgccgca tgacgtcacg aatctaatga 1261 gagtgatttt aggacctgcc ccatatgcct tatggatgga cgcttgggga gtccaactcc 1321 agacggttat agcggcagcc actcgcgacc cccgacaccc agcgaacggt caagggcggg 1381 gggaacggac taacttggat cgattaaagg gcttagctga tgggatggtg ggcaacccac 1441 agggtcaggc cgcattatta agaccggggg aattggttgc tattacggcg tcggctctcc 1501 aggcgtttag agaagttgcc cggctggcgg aacctgcagg tccatgggcg gacatcacgc 1561 agggaccatc tgagtccttt gttgattttg ccaatcggct tataaaggcg gttgaggggt 1621 cagatctccc gccttccgcg cgggctccgg tgatcattga ctgctttagg cagaagtcac 1681 agccagatat tcagcagctt atacgggcag caccctccac gctgaccacc ccaggagaga 1741 taatcaaata tgtgctagac aggcagaaga ttgcccctct tacggatcaa ggcatagccg 1801 cggccatgtc gtctgctatc cagcccttag ttatggcagt agtcaataga gagagggatg 1861 gacaaactgg gtcgggtggt cgtgcccgag ggctctgcta cacttgtgga tccccgggac 1921 attatcaggc gcagtgcccg aaaaaacgaa agtcaggaaa cagccgtgag cgatgtcagc 1981 tgtgtgacgg gatgggacac aacgctaaac agtgcagaag gcgggatggc aaccagggcc 2041 aacgcccagg aaaaggcctc tcttcggggt cgtggcccgt ctctgagcag cctgccgtct 2101 cgttagcgat gacaatggaa cataaagatc gccccttggt tagggtcatt ctgactaaca 2161 ctgggagtca tccggtcaaa cagcgttcgg tgtatatcac cgcgctgttg gactctggag 2221 cggacatcac tattatttca gaggaggact ggcccaccga ttggccagtg atggaggccg 2281 cgaacccgca gatccatggg ataggagggg gaattcccat gcgaaaatcc cgggatatga 2341 tagaggtggg ggttattaac cgagacgggt ctttggagcg acccctgctc ctcttccccg 2401 cagtagctat ggttagaggg agtatcctag gaagagattg tctgcagggc ctagggctcc 2461 gcttgacaaa tttataggga gggccactgt tcttactgtt gcgctacatc tggctattcc 2521 gctcaaatgg aagccagacc acacgcctgt gtggattgac cagtggcccc ttcctgaagg 2581 taaacttgta gcgctaacgc aattagtgga aaaagaatta cagttaggac atatagaacc 2641 ttcacttagt tgttggaaca cacctgtctt tgtgatccgg aaggcttccg ggtcttatcg 2701 cttattgcat gacttgcgcg ctgttaacgc caagcttgtt ccttttgggg ccgtccaaca 2761 gggggcgcca gttctctccg cgctcccgcg tggctggccc ctgatggtcc tagacctcaa 2821 ggattgcttc ttttctattc ctcttgcgga acaagatcgc gaagcttttg catttacgct 2881 cccctctgtg aataaccagg cccccgctcg aagattccaa tggaaggtct tgccccaagg 2941 gatgacctgt tctcccacta tctgtcagtt ggtggtgggt caggtacttg agcccttgcg 3001 actcaagcac ccatctctgc gcatgttgca ttatatggat gatcttttgc tagccgcctc 3061 aagtcatgat gggttggaag cggcagggga ggaggttatc agtacattgg aaagagccgg 3121 gttcaccatt tcgcctgata agatccagag ggaacccgga gtacaatatc ttgggtacaa 3181 gttaggcagt acgtatgtag cacccgtagg cctggtagca gaacccagga tagccacctt 3241 gtgggatgtt caaaagctgg tggggtcact tcagtggctt cgcccagcgt taggaatccc 3301 gccacgactg atgggcccct tctatgagca gttacgaggg tcagatccta acgaggcgag 3361 ggaatggaat ctagacatga aaatggcctg gagagagatc gtacagctta gcaccactgc 3421 tgccttggaa cgatgggacc ctgccctgcc tttggaggga gcggtcgcta ggtgtgaaca 3481 gggggcaata ggggtcctgg gacagggact gtccacacac ccaaggccat gtttgtggtt 3541 attctccacc caacccacca aggcgtttac tgcttggtta gaagtgctca cccttttgat 3601 tactaagcta cgcgcttcgg cagtgcgaac ctttggcaag gaggttgata tcctcctgtt 3661 gcctgcatgc tttcgggagg accttccgct cccggagggg atcctgttag cccttagggg 3721 gtttgcagga aaaatcagga gtagtgacac gccatctatt tttgacattg cgcgtccact 3781 gcatgtttct ctgaaagtga gggtcaccga ccaccctgta ccgggaccca ctgcctttac 3841 cgacgcctcc tcaagcaccc ataaaggggt ggtagtctgg agggagggcc caaggtggga 3901 gataaaagaa atagctgatt tgggggcaag tgtacaacaa ctggaagcac gcgctgtggc 3961 catggcactt ctgctgtggc cgacaacgcc cactaatgta gtgactgact ccgcgtttgt 4021 cgcgaaaatg ttactcaaga tgggacagga gggagtcccg tctacagcgg cggcttttat 4081 tttagaggat gcgttaagcc aaaggtcagc catggccgcc gttctccacg tgcggagtca 4141 ttctgaagtg ccagggtttt tcacagaagg aaatgacgtg gcagatagcc aagccacctt 4201 tcaagcgtat cccttgagag aggctaaaga tcttcatact gctctccata ttggaccccg 4261 cgcgctatcc aaagcgtgta atatatctat gcagcaggct agggaggttg ttcagacctg 4321 cccgcattgt aattcagccc ctgcgttgga ggccggggta aaccctaggg gtttgggacc 4381 cctacagata tggcagacag actttacgct tgagcctaga atggcccccc gttcctggct 4441 cgctgttact gtggataccg cctcatcggc gatagtcgta actcagcatg gccgtgtcac 4501 atcggttgct gcacaacatc attgggccac ggctatcgcc gttttgggaa gaccaaaggc 4561 cataaaaaca gataatgggt cctgtttcac gtctaaatcc acgcgagagt ggctcgcgag 4621 atgggggata gcacacacca ccgggattcc gggtaattcc cagggtcaag ctatggtaga 4681 gcgggccaac cggctcctga aagataagat ccgtgtgctt gcggaggggg acggctttat 4741 gaaaagaatc cccaccagca aacaggggga actactagcc aaggcaatgt atgccctcaa 4801 tcactttgag cgcggtgaaa acacaaaaac accgattcaa aaacactgga gacctaccgt 4861 tcttacagaa ggacccccgg ttaaaatacg aatagagaca ggggagtggg aaaaaggatg 4921 gaatgtgctg gtctggggac gaggttatgc agctgtgaaa aacagggaca ctgataaggt 4981 tatttgggta ccctctcgga aagttaaacc ggatgtcacc caaaaggatg aggtgactaa 5041 gaaagatgag gcgagccctc tttttgcagg catttctgac tggataccct gggaagacga 5101 gcaagaagga ctccaaggag aaaccgctag caacaagcaa gaaagacccg gagaagacac 5161 ccttgctgcc aacgagagtt aattatattc tcattattgg tgtcctggtc ttgtgtgagg 5221 ttacgggggt aagagctgat gtccacttac tcgagcagcc agggaacctt tggattacat 5281 gggccaaccg tacaggccaa acggattttt gcctctctac acagtcagcc acctcccctt 5341 ttcaaacatg tttgataggt atcccgtccc ctatttccga aggtgatttt aagggatacg 5401 tctctgataa ttgcaccacc ttgggaactg atcggttagt ctcgtcagcc gactttactg 5461 gcggacctga caacagtacc accctcactt atcggaaggt ctcatgcttg ttgttaaagc 5521 tgaatgtctc tatgtgggat gagccacatg aactacagct gttaggttcc cagtctctcc 5581 ctaacattac taatattgct cagatttccg gtataaccgg gggatgcgta ggtttcagac 5641 cacaaggggt tccttggtat ctaggttggt ctagacagga ggccacgcgg tttctcctta 5701 gacacccctc tttctctaaa tccacggaac cgtttacggt ggtgacagcg gataggcaca 5761 atctttttat ggggagtgag tactgcggtg catatggcta cagattttgg aacatgtata 5821 actgctcaca ggtggggcgg cagtaccgct gtggtaatgc gcgcagcccc cgcccgggtc 5881 ttcctgaaat ccagtgtaca aggagaggag gcaaatgggt taatcaatca caggaaatta 5941 atgagtcgga gccgttcagc tttacggtga actgtacagc tagtagtttg ggtaatgcca 6001 gtgggtgttg cggaaaagca ggcacgattc tcccgggaaa gtgggtcgac agcacacaag 6061 gtagtttcac caaaccaaaa gcgctaccac ccgcaatttt cctcatttgt ggggatcgcg 6121 catggcaagg aattcccagt cgtccggtag ggggcccctg ctatttaggc aagcttacca 6181 tgttagcacc taagcataca gatattctca aggtgcttgt caattcatcg cggacaggta 6241 taagacgtaa acgaagcacc tcacacctgg atgatacatg ctcagatgaa gtgcagcttt 6301 ggggtcctac agcaagaatc tttgcatcta tcttagcccc gggggtagca cgtgcgcaag 6361 ccttaagaga aattgagaga ctagcctgtt ggtccgttaa acaggctaac ttgacaacat 6421 cattcctcgg ggacttattg gatgatgtca cgagtattcg acacgcggtc ctgcagaacc 6481 gagcggctat tgacttcttg cttctggctc acggccatgg ctgtgaggac gttgccggaa 6541 tgtgttgttt caatctgagt gatcacagtg agtctataca gaagaagttc cagctaatga 6601 aggaacatgt caataagatc ggcgtggaca gcgacccaat cggaagttgg ctgcgaggat 6661 tattcggggg aataggggaa tgggccgttc atttgctgaa aggactgctt ttggggcttg 6721 tagttatttt gttgctagta gtgtgcctgc cttgcctttt gcaaatcgta tgcggtaaca 6781 tcagaaagat gattaataac tccatcagct accacacgga atataagaag ctgcaaaagg 6841 cctgtgggca gcctgaaagc agaatagtat aaggcagtac atgggtggtg gtatagcgct 6901 tgcgagtcgg gttgtaacgg ggcatggctt aactaagggg actatggcat gtataggcgc 6961 aaagcggggc ttcggttgta cgcggttagg agtcccctca ggatatagta gtttcgcttt 7021 tgcataggga gggggaaatg tagtcttatg caatactctt gtagtcttgc aacatggtaa 7081 cgatgagtta gcaacatgcc ttacaaggag agaaaaagca ccgtgcatgc cgattggtgg 7141 aagtaaggtg gtacgatcgt gccttattag gaaggcaaca gacgggtctg acatggattg 7201 gacgaaccac tgaattccgc attgcagaga tattgtattt aagtgcctag ctcgatacaa 7261 taaacgccat ttgaccattc accaca //