LOCUS JN389518 7636 bp DNA linear VRL 21-DEC-2011 DEFINITION Avian leukosis virus strain sdau1002, complete genome. ACCESSION JN389518 VERSION JN389518.1 KEYWORDS . SOURCE Avian leukosis virus ORGANISM Avian leukosis virus Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; Alpharetrovirus. REFERENCE 1 (bases 1 to 7636) AUTHORS Qu,Y. TITLE Sequence analysis for the complete proviral genome of subgroup J Avian Leukosis virus associated with Haemangiomas,leiomyosarcoma and myeloma in layer flocks JOURNAL Unpublished REFERENCE 2 (bases 1 to 7636) AUTHORS Qu,Y. TITLE Direct Submission JOURNAL Submitted (22-JUL-2011) College of Animal Science and Veterinary Medicine, Shandong Agriculture University, Daizong Road No.61, Taian, Shandong 271018, China FEATURES Location/Qualifiers source 1..7636 /mol_type="genomic DNA" /country="China" /collection_date="2010" /host="layer chicken" /note="subgroup: J" /PCR_primers="fwd_seq: tgtagtgttatgcaatgcaatactcttatgtaacg, fwd_seq: agggagtatcctgggaagag, fwd_seq: ggagaagacacccttgctgcc, rev_seq: ttgagcggaatagccagatgtag, rev_seq: acaacggaaataataaccacgc, rev_seq: tgaagccatccgcttcatgc" /db_xref="taxon:11864" /strain="sdau1002" /proviral /organism="Avian leukosis virus" repeat_region 1..325 /rpt_type=long_terminal_repeat /note="5'" repeat_region 1..224 /rpt_type=direct /note="U3" 5'UTR 225..603 repeat_region 225..245 /rpt_type=direct /note="R" repeat_region 246..325 /rpt_type=direct /note="U5" gene 603..6992 /gene="env" CDS join(603..620,5475..6992) /codon_start=1 /protein_id="AEW29034.1" /gene="env" /translation="MEAVIKGVHLLQQPGNVWVTWANKTGQTDFCLSLQSATSPFRTC LIGIPQYPLSAFKGYVTNVTACDNDADLASQTACLIQALNTTLPWDPQELDILGSQMI KNGTNRTCVTFGSVCYKENNGSTVCHIFDGNFNGTGGAEAELRDFIEKWKGDDHLIRP YVNQSWTMVSPINTESFSVSSRYCGFTSNETRYYRGNLSDWCNSKGGEWSAGYKNGTQ CSSNTAGCGGNCTAEWNYYAYGFTFENKTEVLWNNGTAKALPPGIFLICGDRAWQGIP SNALGGPCYLGQLTMLSPNFTTWMTYGPNITGHHRSRRSMSHLSSDCSDEVQLWSATA RIFASFFAPGVAAAQALREIERLACWSVKQANLTSLVLNAMLEDMNSIRHAVLQNRAA IDFLLLAQGHGCQDVEGMCCFNLSDHSESIHKTLQAMKEHTEKIRVEDDPIGDWFTRT FGSFGGWLAKGVKTLLFALLVIVCLLAIIPCIIKCLQDCLLRTMYQFMDERIRYHRIR EQL" /product="envelope protein" /note="env protein" mat_peptide 5475..6398 /gene="env" /product="gp85 (SU) domain" mat_peptide 6399..6989 /gene="env" /product="gp37 (TM) domain" gene 603..2708 /gene="gag" CDS 603..2708 /codon_start=1 /protein_id="AEW29035.1" /gene="gag" /translation="MEAVIKVISSACKTYCGKTSPSKKEIGAMLSLLQGEGLLMSPSD LYSPGSWDPITAALSQRAMVLGKSGELKTWGLILGALKAAREEQATSEQAKFWLGLGG GRVSPPGPECIEKPATERRIDKGEEVGETTVQRDAKMAPEETATPKTVGTSCYHCGTA IGCNCATASAPPPPYVGSGLYPSLAGVGEQQGQEGDTPRGAEQPRAEPGHAGQAPGPA LTDWARIREELASTGPPVVAMPVVIKTEGPAWTPLEPKLITRLADTVRTKGLRSPITM AEVEALMSSPLLPHDVTNLMRVILGPAPYALWMDAWGVQLQTVIAAATRDPRHPANGQ GRGERTNLDRLKGLADGMVGNPQGQAALLRPGELVAITASALQAFREVARLAEPVGPW ADITQGPSESFVDFANRLIKAVEGSDLPSSARAPVIIDCFRQKSQPDIQQLIRAAPST LTTPGEIIKYVLDRQKTAPLTDRGIAAAMSSAIQPLVMAVVNRERDGQTGSGGRARGL CYTCGSPGHYQAQCPKKRKSGNSRERCQLCDGMGHNAKQCRRRDGSQGQRPGRGLSSG PWPGPDQPAVSLAMTMEHKDRPLVRVILTNTGSHPVKQRSVYITALLDSGADITIISE EDWPTDWPVVDTANPQIHGIGGGIPMRKSRDMIEVGVINRDGSLERPLLLFPAVAMVR GSILGRDCLQGLGLRLTNL" /product="gag protein" gene <2726..5347 /gene="pol" CDS <2726..5347 /codon_start=1 /protein_id="AEW29036.1" /gene="pol" /translation="TAALHLAIPLKWKPDHTPVWIDQWPLPEGKLVALTQLVEEELQL GHIEPSLSCWNTPVFVIRKASGSYRLLHDLRAVNAKLVPFGAVQQGAPVLSALPRGWP LMVLDLKDCFFSIPLAEQDREAFAFTLPSMNNQAPARRFQWKVLPQGMTCSPTICQLV VGQVLEPLRLKHPSLCMLHYMDDLLLAASSHDGLEAAGEEVISTLERAGFTISPDKVQ REPGVQYLGYKLGSTYVAPVGLVAEPRIATLWDVQKLVGSLQWLRPALGIPPRLMGPF YEQLRGSDPNEAREWNLDMKMAWREIVQLSTTAALERWDPALPLEGAVARCEQGAIGV LGQGLSTHPRPCLWLFSTQPTKAFTAWLEVLTLLITKLRASAVRTFGKEVDILLLPAC FREDLPLPEGILLALKGFAGKIRSSDTPSIFDIARPLHVSLKVRVTDHPVPGPTVFTD ASSSTHKGVVVWREGPRWEIKEIADLGASVQQLEARAVAMALLLWPTTPTNVVTDSAF VAKMLLKMGQEGVPSTAAAFILEDALSQRSAMAAVLHVRSHSEVPGFFTEGNDVADSQ ATFQAYPLREAKDLHTALHIGPRALSKACNISMQQAREVVQTCPHCNSAPALEAGVNP RGLGPLQIWQTDFTLEPRMAPRSWLAVTVDTASSAIVVTQHGRVTSVAAQHHWATAIA VLGRPKAIKTDNGSCFTSKSTREWLARWGIAHTTGIPGNSQGQAMVERANRLLKDKIR VLAEGDGFMKRIPTGKQGELLAKAMYALNHFERGENTKTPIQKHWRPTVLTEGPPVKI RIETGEWEKGWNVLVWGRGYAAVKNRDTDKIIWVPSRKVKPDITQKDEVTKKDEASPL FAGISDWAPWKGEQEGL" /product="polymerase protein" /note="pol protein" 3'UTR 6993..7534 misc_feature 7153..7298 /note="E or XSR element" repeat_region 7312..7636 /rpt_type=long_terminal_repeat /note="3'" repeat_region 7312..7535 /rpt_type=direct /note="U3" repeat_region 7536..7556 /rpt_type=direct /note="R" repeat_region 7557..7636 /rpt_type=direct /note="U5" ORIGIN 1 tgtagtctta tgcaatactc ttatgtaacg atgaaacagc aatatgcctt ataaggagaa 61 agaaggcact gtacccgttg attggtggaa gtaaggtggt acggtcatgg tatgatcgtg 121 ccttattagg aaggcaacag acgggtcaga catggattgg acgatctcct tagttccgcg 181 ttgcaaagaa attgtattta agtgcctagc ttgatacaat aaacgccatt ttacctccca 241 ccacattggt gtgcacctgg gttgatggcc ggaccgtcga ttccctgacg attacgaaca 301 cctgcatgaa gcggaaggct tcatttggtg accccgacgt gatcgttagg gaatagtggt 361 cggccaccgg cggcgtggcg atcctgccct catccgtccc gcttaacggg gagcgggcga 421 tgaccctggt agagggggct gcggcttagg agggcagaag ctgagtggcg tcggagggag 481 ctctactgca gggagcccac ataccctacc gagcactcag agggtcgttg gaagacggga 541 aggaagcccg acgactgagc agtccacccc aggcgtgatt ctggtcgccc tgtggatcaa 601 gcatggaagc cgtcataaag gtgatttcgt ccgcgtgtaa aacctattgc gggaaaacct 661 ctccttctaa gaaggaaata ggggccatgt tgtccctgtt acaaggggag gggttgctta 721 tgtctccctc agacttatat tccccggggt cctgggatcc cattaccgcg gcgctctccc 781 agcgggctat ggtgcttggg aaatcgggag agttaaaaac ctggggattg attttggggg 841 cattgaaggc ggctcgagag gaacaggcta catctgagca agcaaagttt tggttgggat 901 tagggggagg gagggtctct cccccaggtc cggagtgcat cgagaaacca gcaacggagc 961 ggcgaatcga caagggggag gaagtgggag aaacaactgt gcagcgagat gcgaagatgg 1021 cgccggagga aacggccaca cctaaaaccg ttggcacatc ctgctatcat tgcggaacag 1081 ctattggctg taattgcgcc acagcctcgg ctcctcctcc tccttatgtg ggaagtggtt 1141 tgtatccttc cctggcgggg gtgggagagc agcagggcca ggagggtgac acacctcggg 1201 gggcggaaca gccaagggcg gagccagggc acgcgggtca ggcccctggg ccggccctga 1261 ctgactgggc aaggatcagg gaggagcttg cgagtacagg tccgcccgtg gtggccatgc 1321 ctgtagtgat taagacagag ggacccgcct ggacccctct ggagccaaaa ttgatcacaa 1381 gactggccga tacggtcagg accaagggct tacgatcccc gatcactatg gcagaagtgg 1441 aagcacttat gtcctccccg ctgctgccgc atgacgtcac gaatctaatg agagttattt 1501 taggacctgc cccatacgcc ttatggatgg acgcttgggg agtccaacta cagacggtta 1561 tagcggcagc cactcgcgac ccccgacatc cagcgaatgg tcaagggcga ggggaacgga 1621 ctaatttgga tcgcttaaag ggcttggctg atgggatggt gggcaacccg cagggtcagg 1681 ccgcattatt gagaccgggg gaattggttg ctatcacagc atcggctctc caggcgttta 1741 gagaggttgc tcggctggcg gaacctgtgg gcccatgggc ggatatcaca cagggaccat 1801 ctgagtcctt tgttgatttc gctaatcgtc ttataaaggc ggttgaaggg tcagatcttc 1861 catcttccgc gcgggctccg gtgatcattg actgctttag gcagaagtca cagccagata 1921 tccagcagct tatacgggca gcaccctcca cgctgaccac cccaggagag ataatcaaat 1981 atgtgctaga caggcagaag actgcccctc ttacggatcg aggcatagcc gcggccatgt 2041 catctgctat tcagccctta gttatggcag tagtcaatag agagagggat ggacaaactg 2101 ggtcgggtgg tcgtgcccga gggctctgct acacttgtgg atccccggga cattatcagg 2161 cgcagtgccc gaaaaaacga aagtcaggga acagccgtga gcgatgccag ttgtgtgacg 2221 ggatgggaca caacgctaaa caatgtagaa ggcgggatgg cagtcagggc caacgcccag 2281 gaagaggcct ctcttcgggg ccgtggcccg gccctgacca gcctgccgtc tcgttagcga 2341 tgacaatgga acataaagat cgccccttgg ttagggtcat tctgactaac actgggagtc 2401 atccagtcaa acagcgttcg gtgtatatca ccgcgctgtt ggactctgga gcggacatca 2461 ctattatctc ggaggaggat tggcctacgg attggccggt ggtggacacc gcgaacccgc 2521 agatccatgg cataggaggg ggaatcccca tgcgaaaatc tcgtgacatg atagaggtgg 2581 gggttattaa ccgagacggg tctttggagc gacccctgct cctcttcccc gcagtagcta 2641 tggttagagg gagtatcctg ggaagagatt gtctgcaggg cctagggctc cgcttgacaa 2701 atttataggg agggccactg ttcttactgc tgcgctacat ctggctattc cgctcaaatg 2761 gaagccagac cacacgcccg tgtggattga ccagtggccc cttcctgagg gtaaacttgt 2821 agcgctaacg caattagtgg aagaagaatt acagttagga catatagaac cttcacttag 2881 ttgttggaac acacctgtct ttgtgatccg gaaggcttcc gggtcttatc gcttattgca 2941 tgacttgcgc gctgttaacg ccaagcttgt tccttttggg gccgtccaac agggggcgcc 3001 agttctctcc gcgctcccgc gtggctggcc cctgatggtc ctagacctca aggattgctt 3061 cttttctatt cctcttgcgg aacaagatcg cgaagctttt gcatttacgc tcccctctat 3121 gaataaccag gcccccgctc gaagattcca atggaaggtc ttgccccaag ggatgacctg 3181 ttctcccact atctgtcagt tggtagtggg tcaggtactt gagcccttgc gactcaagca 3241 cccatctctg tgcatgttgc attatatgga tgatcttttg ctagccgcct caagtcatga 3301 tgggttggaa gcagcagggg aggaggttat cagtacattg gaaagagccg ggttcaccat 3361 ttcgcctgat aaggtccaga gggagcctgg agtacaatat cttgggtata agttaggaag 3421 tacgtatgta gcacccgtag gcctggtagc agaacccagg atagccacct tgtgggatgt 3481 tcaaaagctg gtggggtcac ttcagtggct tcgtccagca ttaggaatcc caccacgact 3541 gatgggcccc ttttatgagc agttgcgagg gtcagatcct aacgaggcga gggaatggaa 3601 tctagacatg aaaatggcct ggagagagat cgtacagctc agtaccactg ctgccttgga 3661 acgatgggac cctgccctgc ctctggaagg agcggtcgct agatgtgaac agggggcaat 3721 aggggtcctg ggacagggac tgtccacaca cccaaggccg tgtttgtggt tattctccac 3781 ccaacccacc aaggcgttta ctgcttggtt agaagtgctc acccttttga ttactaagct 3841 acgtgcttcg gcagtgcgaa cctttggcaa ggaggttgat atcctcctgc tgcctgcatg 3901 ctttcgggag gaccttccgc tcccggaggg gatcctgtta gcccttaagg ggtttgcagg 3961 aaaaatcagg agtagtgaca cgccatctat ttttgacatt gcgcgtccac tgcatgtttc 4021 tctgaaagtg agggttaccg accaccctgt accaggaccc actgtcttta ccgacgcctc 4081 ctcaagcacc cataaggggg tggtagtctg gagggagggc ccaaggtggg agataaaaga 4141 aatagctgat ttgggggcaa gtgtacaaca actggaagca cgcgctgtgg ccatggcact 4201 tctgctgtgg ccgacaacgc ccactaatgt agtgactgac tccgcgtttg ttgcgaaaat 4261 gttactcaag atgggtcagg agggagtccc gtctacagcg gcggctttta ttttagagga 4321 tgcgttaagc caaaggtcag ccatggccgc cgttctccac gtgcggagtc attctgaagt 4381 gccagggttt ttcacagaag gaaatgacgt ggcagatagc caagccacct ttcaagcgta 4441 tcccttgaga gaggctaaag atcttcatac tgctctccat attggacccc gcgcgctatc 4501 caaagcgtgt aatatatcta tgcagcaggc tagggaggtt gttcagacct gcccgcattg 4561 taattcagcc cctgcgttgg aggccggggt aaaccctagg ggtttgggac ccctacagat 4621 atggcagaca gactttacgc ttgagcctag aatggccccc cgttcctggc tcgctgttac 4681 tgtggatacc gcctcgtcgg cgatagtcgt aactcagcat ggccgtgtca catcggttgc 4741 tgcgcaacat cattgggcca cggctatcgc cgttttggga agaccaaagg ccataaaaac 4801 agataacggg tcttgcttca cgtctaaatc cacgcgagag tggctcgcga gatgggggat 4861 agcacacacc accgggattc cgggtaattc ccagggtcaa gctatggtag agcgggccaa 4921 ccggctcctg aaggataaga tccgtgtgct tgcggagggg gacggcttta tgaaaagaat 4981 ccccaccggc aaacaggggg aactactagc caaggcaatg tatgccctca atcactttga 5041 gcgtggtgag aacacaaaaa caccgataca aaaacactgg agacctaccg ttcttacaga 5101 aggacccccg gttaaaatac gaatagagac aggggagtgg gaaaaaggat ggaacgtgct 5161 agtctgggga cgaggttatg ccgctgtgaa aaacagggac actgataaga ttatttgggt 5221 accctctcga aaagttaaac cggacatcac ccaaaaggat gaggtgacta agaaggatga 5281 ggcgagccct ctctttgcag gcatttctga ctgggcaccc tggaaaggtg agcaagaagg 5341 actctaagaa gaagccgcca gcaacaagca agaaagaccc ggagaaggca cccttgctgc 5401 cgtcgagagg ttatttcttc tttcaaatga tacttgtgtg cgtggttatt atttctgttg 5461 tcccaggggt ggggggagtt catctgttgc aacaaccagg aaacgtgtgg gtcacctggg 5521 caaataagac gggccaaaca gatttttgcc ttagtctaca gtcagcgacc tcgccattcc 5581 gcacctgctt gataggcatt ccacagtatc ctctgagcgc ctttaaggga tatgtcacta 5641 atgttactgc ttgcgataac gatgccgatt tagccagcca aacagcatgc ttgatacagg 5701 ctctaaatac aaccctccct tgggaccccc aagaattgga tattttaggg tcccagatga 5761 tcaagaacgg aacaaaccgt acgtgtgtta cctttggttc ggtgtgctat aaagagaaca 5821 atggcagtac agtctgccac atttttgatg ggaattttaa tgggactggt ggggcggaag 5881 cagaattgcg tgacttcata gaaaaatgga aaggtgatga ccatcttata aggccctatg 5941 tcaaccaatc atggacgatg gtaagtccaa taaacacaga gagtttttca gtaagtagta 6001 gatattgtgg attcaccagc aacgagactc gttattatag agggaacctt tctgattggt 6061 gtaattcaaa agggggagaa tggtcagcgg ggtacaagaa cgggacacaa tgttccagca 6121 acacggcggg ttgcggtggt aattgcacag cggaatggaa ttattatgca tatgggttta 6181 ccttcgagaa taagacagag gtattgtgga ataatgggac tgctaaggca ctccccccag 6241 gtattttctt gatttgtggg gacagggctt ggcaaggcat cccgagtaac gccttgggag 6301 ggccctgtta tctaggacaa ttgactatgc tctctcctaa ctttaccacc tggatgacgt 6361 atgggccgaa cattacgggt caccaccgta gcaggcgctc gatgagtcat ctctcgtctg 6421 actgcagtga cgaggtacag ctatggagtg cgacagcccg gatatttgcc tctttctttg 6481 ctcctggtgt agctgcagca caggccttaa gggagattga acgcttggca tgttggtcgg 6541 ttaagcaagc aaatttaaca tcattagtat tgaatgcgat gctggaggac atgaacagca 6601 tccggcacgc ggtgttgcag aatcgagcag ccatcgattt cttactcctg gcgcagggac 6661 acgggtgtca agacgtagaa gggatgtgtt gcttcaatct cagcgatcac agtgagtcca 6721 ttcacaagac gctccaagcc atgaaggaac atacagagaa gatacgggtg gaagacgatc 6781 ccatagggga ttggtttacg cgcacgtttg gtagttttgg agggtggctc gcgaaaggtg 6841 ttaagacgct actgtttgca ttgcttgtca tagtctgtct attagctatc attccatgta 6901 taatcaagtg cctccaggac tgtctattga gaacaatgta tcagttcatg gatgaacgca 6961 taagatatca tagaattagg gagcaactgt aggttccgaa cgcgatgtga cgggaggctg 7021 cgagggatat tcgggggaat aggagaatgc gaatcgggct gtaacggggc aaggcttgac 7081 tgaggggact ataacatgta taggcgctga gcggggcttc ggttgtacgc ggataggaat 7141 cccctcagga caattctgct tgaaatgtga tggcaccttc ctgttttgcc cttagactat 7201 tcaagttgcc tctgtggatt aggactggag acagctcgga tggtctgatg gccaaataga 7261 gcaagctaga taggtagctg cgaaatacgc ttttgcatag ggagggggaa atgtagtctt 7321 atgcaatact cttatgtaac gatgaaacag caatatgcct tataaggaga aagaaggcac 7381 tgtacccgtt gattggtgga agtaaggtgg tacggtcatg gtatgatcgt gccttattag 7441 gaaggcaaca gacgggtcag acatggattg gacgatctcc ttagttccgc gttgcaaaga 7501 aattgtattt aagtgcctag cttgatacaa taaacgccat tttacctccc accacattgg 7561 tgtgcacctg ggttgatggc cggaccgtcg attccctgac gattacgaac acctgcatga 7621 agcggaaggc ttcatt //