ID DQ365814; SV 1; linear; genomic DNA; STD; VRL; 7704 BP. XX AC DQ365814; XX DT 31-JAN-2007 (Rel. 90, Created) DT 31-JAN-2007 (Rel. 90, Last updated, Version 1) XX DE Avian leukosis virus strain MQNCSU, complete genome. XX KW . XX OS Avian leukosis virus OC Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae; OC Alpharetrovirus. XX RN [1] RP 1-7704 RA Chesters P.M., Howes K., Nair V.; RT "Isolation and Characterization of an Avian Leukosis Virus from Chicken RT Macropohage Cell Line MQ-NCSU"; RL Unpublished. XX RN [2] RP 1-7704 RA Chesters P.M., Howes K., Nair V.; RT ; RL Submitted (16-JAN-2006) to the INSDC. RL Department of Viral Oncogenesis, Institute for Animal Health, High Street, RL Compton, Newbury, Berkshire RG20 7NN, UK XX DR RFAM; RF00214; Retro_dr1. DR RFAM; RF00467; RSV_PBS. DR RFAM; RF01417; RSV_RNA. XX FH Key Location/Qualifiers FH FT source 1..7704 FT /organism="Avian leukosis virus" FT /strain="MQNCSU" FT /mol_type="genomic DNA" FT /country="USA" FT /note="subgroup: A" FT /db_xref="taxon:11864" FT LTR 1..314 FT /note="5' LTR" FT repeat_region 1..213 FT /rpt_type=DIRECT FT /note="U3" FT 5'UTR 214..592 FT repeat_region 214..234 FT /rpt_type=DIRECT FT /note="R" FT repeat_region 235..314 FT /rpt_type=DIRECT FT /note="U5" FT gene 593..7105 FT /gene="env" FT CDS join(593..610,5300..7105) FT /codon_start=1 FT /gene="env" FT /product="envelope polyprotein" FT /db_xref="GOA:A2SXN7" FT /db_xref="InterPro:IPR005166" FT /db_xref="InterPro:IPR018154" FT /db_xref="UniProtKB/TrEMBL:A2SXN7" FT /protein_id="ABC94884.1" FT /translation="MEAVIKAFLTGYPGETSKKDSKKKPPATSKKDPEKTPLLPTRVNY FT ILIIGVLVLCEVTGVRADVHLLEQPGNLWITWANRTGQTDFCLSTQSATSPFQTCLIGI FT PSPISEGDFKGYASDTNCATSETDRLVSSADFTGGPDNSTTLTYRKVSCLLLKLNVSMW FT DEPPELQLLGSQSLPNITNITQISGVTGGCVGFRPKGVPWYLGWSRQEATRFLLRRPSF FT SNSSKPFTVVTADRHNLFTGSEYCGAYGYRFWNIYNCSQVGQQYRCGNARRPRPGHPET FT QCTRRGGKWVNQSQKINETEPFSFTVTCTASNLGNVSGCCGKAGMILPGIWVDSTQDSF FT TKPKALPPAIFLICGDRAWQGIPSRPVGGPCYLGKLTMLAPNHTDILKVLANSSRTGIR FT RKRNTSHLDDTCSDEVRLWGPTARIFASILAPGVAAAQALREIERLACWSVKQANLTTS FT LLGDLLDDVTSIRHAVLQNRAAIDFLLLAHGHGCEDVAGMCCFNLSDHSESIQKKFQLM FT KEHVNKIGVDSDPIGSWLRGIFGGIGEWAVHLLKGLLLGLVVILLLVVCLPCLLQFVSN FT SIRKMINNSISYHTEYKKLQKACGQPESRIV" FT mat_peptide 5474..6493 FT /gene="env" FT /product="gp85 (SU) domain" FT mat_peptide 6494..7102 FT /gene="env" FT /product="gp37 (TM) domain" FT gene 593..2707 FT /gene="gag" FT CDS 593..2707 FT /codon_start=1 FT /gene="gag" FT /product="gag polyprotein" FT /db_xref="GOA:A2SXN8" FT /db_xref="InterPro:IPR000721" FT /db_xref="InterPro:IPR001878" FT /db_xref="InterPro:IPR001969" FT /db_xref="InterPro:IPR001995" FT /db_xref="InterPro:IPR004028" FT /db_xref="InterPro:IPR008916" FT /db_xref="InterPro:IPR008919" FT /db_xref="InterPro:IPR009007" FT /db_xref="InterPro:IPR010999" FT /db_xref="InterPro:IPR012344" FT /db_xref="InterPro:IPR013084" FT /db_xref="InterPro:IPR018061" FT /db_xref="InterPro:IPR021109" FT /db_xref="UniProtKB/TrEMBL:A2SXN8" FT /protein_id="ABC94885.1" FT /translation="MEAVIKVISSACKTYCGKTSPSKKEIGAMLSLLQKEGLLMSPSDL FT YSPGSWDPITAALSQRAMVLGKSGESKTWGLVLGALKAAREEQVTSEQAKFWLGLGGGR FT VSPPGPECIEKPATERRIDKGEEVGETTVQRDAKMAKMAPEETTTPKTVGTSCYHCGTA FT VGCNCAAASAPPPPYVGSGLYPSLAGVGEQQGQGGDTPRGAEQPRAEPGHAGLAPGPAL FT TDWARIREELASTGPPVVAMPVVIKTEGPAWTPLEPKLITRLADTVRTKGLRSPITMAE FT VEALMSSPLLPHDVTNLMRVILGPAPYALWMDAWGVQLQTVIAAATRDPRHPANGQGRG FT ERTNLDRLKGLADGMVGNPQGQAALLRPGELVAITASALQAFREVARLAEPAGPWADIT FT QGPSESFVDFANRLIKAVEGSDLPPSARAPVIIDCFRQKSQPDIQQLIRAAPSTLTTPG FT EIIKYVLDRQKTAPLTDQGIAAAMSSAIQPLVMAVVNRERDGQTGSGGRARGLCYTCGS FT PGHYQAQCPKKRKSGNSRERCQLCDGMGHNAKQCRKRDGNQGQRPGRGLSSGPWPGPEP FT PAVSLAMTMEHKDRPLVRVILTNTGSHPVKQRSVYITALLDSGADITIISEEDWPTDWP FT VVDTANPQIHGIGGGIPMRKSRDMIELGVINRDGSLERPLLLFPAVAMVRGSILGRDCL FT QGLGLRLTNL" FT mat_peptide 836..1132 FT /gene="gag" FT /product="p2" FT mat_peptide 1133..1318 FT /gene="gag" FT /product="p10" FT mat_peptide 2066..2332 FT /gene="gag" FT /product="nucleocapsid protein NCp12" FT mat_peptide 2333..2704 FT /gene="gag" FT /product="protease PR p15" FT gene <2725..5412 FT /gene="pol" FT CDS <2725..5412 FT /codon_start=1 FT /gene="pol" FT /product="polymerase polyprotein" FT /db_xref="GOA:A2SXN9" FT /db_xref="InterPro:IPR000477" FT /db_xref="InterPro:IPR001037" FT /db_xref="InterPro:IPR001584" FT /db_xref="InterPro:IPR002156" FT /db_xref="InterPro:IPR003308" FT /db_xref="InterPro:IPR012337" FT /db_xref="InterPro:IPR017856" FT /db_xref="UniProtKB/TrEMBL:A2SXN9" FT /protein_id="ABC94886.1" FT /translation="TVALHLAIPLKWKPDHTPVWIDQWPLPEGKLVALTQLVEKELQLG FT HIEPSLSCWNTPVFVIRKASGSYRLLHDLRAVNAKLVPFGAVQQGAPVLSALPHGWPLM FT VLDLKDCFFSIPLAEQDREAFAFTLPSVNNQAPARRFQWKVLPQGMTCSPTICQLVVGQ FT VLEPLRLKHPSLRMLHYMDDLLLAASSHDGLEAAGEEVISTLERAGFTISPDKIQKEPG FT VQYLGYKLGSTYVAPVGLVAEPRIATLWDVQKLVGSLQWLRPALGIPPRLMGPFYEQLR FT GSDPNEAREWNLDMKMAWREIVQLSTTAALERWDPALPLEGAVARCEQGAIGVLGQELS FT THPRPCLWLFSTQPTKAFTAWLEVLTLLITKLRASAVRTFGKEVDILLLPACFREDLPL FT PEGILLALRGFAGKIRSSDTPSIFDIARPLHVSLKVRVTDHPVPGPTVFTDASSSTHKG FT VVVWREGPRWEIKEIADLGASVQQLEARAVAMALLLWPTAPTNVVTDSAFVARMLLKMG FT QEGVPSTAAAFILEDALSQRSAMAAVLHVRSHSEVPGFFTEGNDVADSQATFQAYPLRE FT AKDLHTTLHIGPRALSKACNISMQQAREVVQTCPHCNSAPALEAGVNPRGLGPLQIWQT FT DFTLEPRMAPRSWLAVTVDTASSAIVVTQHGRVTSVAAQHHWATAIAVLGRPKAIKTDN FT GSCFTSKSTREWLARWGIAHTTGIPGNSQGQAMVERANRLLKDKIRVLAEGDGFMKRIP FT TSKQGELLAKAMYALNHFERGENTKTPIQKHWRPTVLTEGPPVKIRIETGEWEKGWNVL FT VWGRGYAAVKNRDTDKVIWVPSRKVKPDITQQDEVTKKDEASPLFAGISDWIPWGDKQE FT GLQEEAASNKQEGPGEDTLAANES" FT mat_peptide 2725..5409 FT /gene="pol" FT /product="reverse transcriptase beta subunit" FT mat_peptide 2725..4440 FT /gene="pol" FT /product="reverse transcriptase alpha subunit" FT mat_peptide 4411..5409 FT /gene="pol" FT /product="integrase IN p32" FT 3'UTR 7106..7605 FT misc_feature 7255..7395 FT /note="E or XSR element" FT LTR 7391..7704 FT /note="3' LTR" FT repeat_region 7391..7605 FT /rpt_type=DIRECT FT /note="U3" FT repeat_region 7606..7626 FT /rpt_type=DIRECT FT /note="R" FT repeat_region 7627..7704 FT /rpt_type=DIRECT FT /note="U5" XX SQ Sequence 7704 BP; 1880 A; 1856 C; 2207 G; 1761 T; 0 other; tgtagtctta cacaataatg ttatgtaacg atgaaacagc aatatgcctt ataaggagag 60 aaagggtacc gtgcatgatg attggtggaa gtaaggtggt acgatcgtgc cttattagga 120 aggtaacaga cgggtcttac acggattgga cgatctcctt gattccgcat agtagaaatg 180 ttgtatttaa gtagctagct tgatacaata aacgccattt taccatccac cacattggtg 240 tgcacctggg tagatggccg gaccgtcgat tccctgacga ctacgagcac ctgtatgaag 300 cagaaggctt catttggtga ccccgacgtg atcgttaggg aatagtggtc ggccacagac 360 ggcgtggcga tcctgtcctc atccgtctcg cttattcggg gagcggacga tgaccctagg 420 agagggggct gcggcttagg agggcagaag ctgagtggcg tcggagggag ctctactgca 480 gggagccaac ataccctacc gagccctcag agagtcgttg gaagacggga aggaagcccg 540 acgactgagc ggtccacccc agacgcggtt ctggtcgccc ggaggatcaa gtatggaagc 600 cgtcataaag gtgatttcgt ccgcgtgcaa aacctattgc ggaaaaacct ctccttctaa 660 gaaggaaata ggggccatgt tgtccctctt acaaaaggaa gggttgctta tgtctccctc 720 agacttatac tccccggggt cctgggatcc cattaccgcg gcgctctccc agcgagctat 780 ggtacttggg aaatcgggag agtcaaaaac ctggggattg gttttgggag cattgaaggc 840 ggctcgagag gaacaggtta catctgagca agcgaagttt tggttgggat tagggggagg 900 gagggtctct cccccaggtc cggagtgcat cgagaaacca gcaacggagc ggcgaatcga 960 caagggggag gaagtgggag aaacaactgt gcagcgagat gcgaagatgg cgaagatggc 1020 gccggaggaa acgaccacgc ctaaaaccgt tggcacatcc tgttatcatt gcggaacagc 1080 cgttggctgt aattgcgcag cagcctcggc tcctcctcct ccttatgtgg ggagtggttt 1140 gtatccttcc ctggcggggg tgggagagca gcagggccag gggggtgaca cacctcgggg 1200 ggcggaacag ccaagggcgg agccagggca cgcgggtctg gcccctgggc cggccctgac 1260 tgactgggca aggatcaggg aggagcttgc gagtacaggt ccgcccgtgg tggccatgcc 1320 tgtagtgatt aagacagagg gacccgcctg gacccctctg gagccaaaat tgatcacaag 1380 actggctgat acggtcagga ccaagggctt acgatccccg attactatgg cagaagtgga 1440 agcgcttatg tcctccccgc tgctgccgca tgacgtcacg aatctaatga gagttatttt 1500 aggacctgcc ccatatgcct tatggatgga cgcttgggga gtccaactac agacggttat 1560 agcggcagcc actcgcgacc cccgacaccc agcgaatggt caagggcggg gggaacggac 1620 taacttggat cgcttaaagg gcttggcgga tgggatggtt ggtaatccac agggtcaggc 1680 tgcattatta agaccggggg aattggtcgc tatcacggca tcggctctcc aggcgtttag 1740 agaagttgcc cggctggcgg aacctgcagg tccatgggcg gacatcacgc agggaccatc 1800 tgagtccttt gttgatttcg ccaatcggct tataaaggcg gttgaggggt cagatctccc 1860 gccttccgcg cgggctccgg tgatcattga ctgctttagg cagaagtcac agccagatat 1920 ccagcagctt atacgggcag caccttccac gctgaccacc ccaggagaga taatcaaata 1980 tgtgttagac aggcagaaga ccgcccctct tacggatcaa ggcatagctg cggccatgtc 2040 gtctgctatt cagcccttag ttatggcagt agtcaataga gagagggatg gacaaactgg 2100 gtcgggtggt cgtgcccgag ggctctgcta cacttgtgga tccccgggac attatcaggc 2160 gcagtgcccg aaaaaacgaa agtcaggaaa cagccgtgag cgatgtcagt tgtgtgacgg 2220 gatggggcac aatgctaaac agtgtaggaa gcgggatggc aaccagggtc aacgcccggg 2280 aagaggtctc tcttcggggc cgtggcccgg ccctgagccg cctgccgtct cgttagcgat 2340 gacaatggaa cataaagatc gccccttggt tagggtcatt ctgactaaca ctgggagcca 2400 tccggtcaaa cagcgttcgg tgtatatcac cgcgctgttg gactccggag cggacatcac 2460 tattatttcg gaggaggatt ggcctactga ttggccggtg gtggacaccg cgaacccaca 2520 gatccatggc ataggagggg gaattcccat gcgaaaatct cgtgacatga tagagttggg 2580 ggttattaac cgagacgggt ccttggagcg acccctgctc ctcttccccg cagtggctat 2640 ggttagaggg agtatcctgg gaagagactg tctgcagggc ctagggctgc gcttgacaaa 2700 tttataggga gggccactgt tcttactgtt gcgctacatc tggccattcc gctcaaatgg 2760 aagccggacc acacgcctgt gtggattgac cagtggcccc ttcctgaagg taaacttgta 2820 gcgctaacgc aattagtgga aaaagaatta cagttaggac atatagaacc ttcacttagt 2880 tgttggaaca cacctgtctt cgtgatccgg aaggcttccg ggtcttaccg cttattgcat 2940 gatctgcgcg ctgttaatgc caagcttgtt ccctttgggg ccgtccaaca gggggcgcca 3000 gttctctctg cgctcccgca tggctggccc ctaatggtcc tagaccttaa ggattgcttc 3060 ttctctattc ctcttgcgga acaagatcgc gaagcttttg cattcacgct cccctctgtg 3120 aataaccagg cccccgctcg aagatttcaa tggaaggtct taccccaggg gatgacctgt 3180 tctcccacta tctgccagct ggtagtgggt caggtacttg agcccttgcg actcaagcac 3240 ccatctctgc gcatgttgca ttatatggac gatcttttgc tagccgcctc aagtcatgat 3300 gggttggaag cggcagggga ggaggttatc agtacattgg aaagagccgg gttcaccatt 3360 tcgcctgata agatccagaa ggagcccggc gttcaatatc ttgggtataa gttaggcagt 3420 acatatgtag cacccgtagg cttggtagca gaacccagga tagccactct gtgggatgtt 3480 caaaagttgg tagggtcact tcagtggctt cgcccagcgt taggaatccc gccaagactg 3540 atgggccctt tttatgagca gttacgaggg tcagatccta acgaagcgag ggaatggaat 3600 ctggacatga aaatggcctg gagagagatt gtacagctta gtaccactgc tgccctggaa 3660 cgatgggacc ctgccctgcc tctggaggga gcggtcgcca ggtgtgaaca gggggcaata 3720 ggggtcctgg gacaggaact gtccacacac ccaaggccat gtttgtggtt attctccacc 3780 caacccacca aggcgtttac tgcttggtta gaagtgctca cccttttgat tactaagcta 3840 cgcgcttcgg cagtgcgaac ctttggcaag gaggttgata tcctcctgtt gcctgcatgc 3900 tttcgggagg accttccgct cccggagggg atcctgttag cacttagggg gtttgcagga 3960 aaaatcagga gtagtgacac gccatctatt tttgacattg cgcgtccact gcatgtttct 4020 ctgaaagtga gggttaccga ccaccctgtg ccgggaccca ctgtctttac cgacgcctcc 4080 tcaagcaccc ataagggggt ggtagtctgg agggagggcc caaggtggga gataaaagaa 4140 atagctgatt tgggggcaag tgtacaacaa ctggaggcac gcgctgtggc catggcactt 4200 ctgctgtggc cgacagcgcc cactaatgta gtgactgact ctgcgtttgt tgcgagaatg 4260 ttactcaaga tgggacagga gggagtcccg tctacagcgg cggcttttat tttagaggat 4320 gcgttaagcc aaaggtcagc catggccgcc gttctccacg tgcggagtca ttctgaagtg 4380 ccagggtttt tcacagaagg aaatgatgtg gcagacagcc aagccacctt tcaagcatat 4440 cccttgagag aggctaaaga tcttcatact actctccata ttggaccccg cgcgctatcc 4500 aaagcgtgta atatatctat gcagcaggct agggaggttg ttcagacctg cccgcattgc 4560 aattcagccc ctgcgttgga ggccggggta aaccctaggg gtttgggacc cctacagata 4620 tggcagacag actttacgct tgagcctagg atggcccccc gttcctggct cgctgttact 4680 gtggataccg cctcatcagc gatagtcgta actcagcatg gccgtgtcac atcagttgct 4740 gcacaacatc attgggccac ggccatcgcc gttctgggaa gaccaaaggc cataaaaaca 4800 gataacgggt cctgcttcac gtctaaatcc acgcgagagt ggctcgcgag atgggggata 4860 gcacacacca ccgggattcc gggtaattcc cagggtcaag ctatggtaga gcgggccaac 4920 cggctcctga aagataagat ccgcgtgctc gcggaggggg acggctttat gaaaagaatc 4980 cccaccagca aacaggggga actactagcc aaggcaatgt atgccctcaa tcactttgag 5040 cgtggtgaaa acacaaaaac accgatacaa aaacactgga gacctaccgt tcttacagaa 5100 ggacccccgg ttaaaatacg aatagagaca ggggagtggg agaaaggatg gaatgtgctg 5160 gtctggggac gaggttatgc cgctgtgaaa aacagggaca ctgataaggt tatttgggta 5220 ccctctcgaa aagttaaacc ggacattacc caacaggatg aggtgactaa gaaagatgag 5280 gcgagccctc tttttgcagg catttctgac tggataccct ggggagacaa gcaagaagga 5340 ctccaagaag aagccgccag caacaagcaa gaaggacccg gagaagacac ccttgctgcc 5400 aacgagagtt aactatattc tcatcattgg tgtcctggtc ctgtgtgagg ttacgggggt 5460 aagagctgat gttcacttac tcgagcagcc ggggaacctt tggattacat gggccaaccg 5520 tacaggccaa acggatttct gcctttctac acagtcagcc acctcccctt ttcaaacatg 5580 tttgataggt atcccgtccc ctatttctga gggtgatttt aagggatatg cttctgatac 5640 aaattgcgcc acctcggaaa ctgaccggtt agtctcgtca gctgacttta ctggcggtcc 5700 tgacaacagc accaccctca cttatcggaa ggtctcatgc ttattattaa agctcaatgt 5760 ttctatgtgg gatgagccac ctgaactaca gctgttaggt tcccagtctc tccctaacat 5820 tactaatatt actcagatct ccggtgtaac cgggggatgc gtaggcttca ggccaaaagg 5880 ggttccttgg tatctgggtt ggtctagaca ggaagccacg cggtttctcc ttagacgccc 5940 ctctttctct aactcctcga aaccgtttac agtggtgaca gcggataggc acaatctttt 6000 cacggggagt gagtactgcg gtgcatatgg ctacagattt tggaacatat ataactgctc 6060 acaggtgggg cagcagtacc gctgtggcaa tgcacgccgc ccccgcccgg gtcatcctga 6120 aacccagtgt acaaggagag gaggcaaatg ggttaatcaa tcacagaaaa ttaatgagac 6180 agagccgttc agctttacgg taacctgtac agctagtaat ttgggtaatg tcagtgggtg 6240 ttgcggaaaa gcaggcatga ttctcccggg aatctgggtc gacagcacac aagatagttt 6300 caccaaacca aaagcgctac cacccgcaat tttcctcatt tgtggggatc gcgcatggca 6360 aggaattccc agtcgtccgg tagggggccc ctgctattta ggcaagctta ccatgttagc 6420 acctaaccat acagatattc tcaaggtgct tgccaattca tcgcggacag gtataagacg 6480 taaacgaaac acctcacacc tggatgatac atgctcagat gaagtacggc tttggggtcc 6540 tacagcaaga atctttgcat ctatcttagc cccgggggta gcagctgcac aagccttaag 6600 agaaatcgag agactagcct gttggtccgt taaacaggct aacttaacta catcactcct 6660 cggggactta ttggatgatg tcacgagtat tcgtcacgcg gtcctgcaga accgagcggc 6720 tattgacttc ttgctcctag ctcacggcca tggctgtgag gacgttgccg gaatgtgttg 6780 tttcaatctg agtgatcaca gtgagtctat acagaagaag ttccagctaa tgaaggaaca 6840 tgtcaataag atcggcgtag acagcgaccc aatcggaagt tggctgcgag ggatattcgg 6900 aggaatagga gagtgggccg ttcatttgct gaaaggactg cttttggggc ttgtagttat 6960 tttgttgtta gtagtgtgcc tgccgtgcct tttgcaattt gtgtccaata gcatccgaaa 7020 gatgattaat aattccatca gctaccacac ggaatataag aagctgcaaa aggcctgtgg 7080 gcagcctgaa agcagaatag tataaggcag tacatgggtg gtgatatagc gcttgcgagt 7140 cgggctgtaa cggggcatgg cttaactaag gggactatgg catgtatagg cgtaaagcgg 7200 ggcttcggtt gtacgcggtt aggagtcccc ctaggatata gtaggcacgc ttttgcataa 7260 cttccttgtt ttgcccttag actattcaag ttgcctctgt ggattagggc tggagacagc 7320 tcggatggtc tgatggccag ataaggtggg caagaaaact atgaaatacg cttttgcata 7380 gggaggggga aatgtagtct tacacaataa tgttatgtaa cgatgaaaca gcaatatgcc 7440 ttataaggag agaaagggta ccgtgcatga tgattggtgg aagtaaggtg gtacgatcgt 7500 gccttattag gaaggtaaca gacgggtctt acacggattg gacgatctcc ttgattccgc 7560 atagtagaaa tgttgtattt aagtagctag cttgatacaa taaacgccat tttaccatcc 7620 accacattgg tgtgcacctg ggtagatggc cggaccgtcg attccctgac gactacgagc 7680 acctgtatga agcagaaggc ttca 7704 //