LOCUS AJ623289 6895 bp DNA linear VRL 15-APR-2005 DEFINITION Avian endogenous retrovirus EAV-HP partial proviral genome, clone EAV-15I. ACCESSION AJ623289 VERSION AJ623289.1 KEYWORDS env gene; envelope glycoprotein; gag gene; gag polyprotein; pol; gene; reverse transcriptase/integrase. SOURCE Avian endogenous retrovirus EAV-HP ORGANISM Avian endogenous retrovirus EAV-HP Viruses; Retro-transcribing viruses; Retroviridae. REFERENCE 1 AUTHORS Sacco,M.A., Howes,K., Smith,L.P. and Nair,V.K. TITLE Assessing the roles of endogenous retrovirus EAV-HP in avian leukosis virus subgroup J emergence and tolerance JOURNAL J. Virol. 78 (19), 10525-10535 (2004) PUBMED 15367619 REFERENCE 2 (bases 1 to 6895) AUTHORS Sacco,M.A. TITLE Direct Submission JOURNAL Submitted (01-FEB-2004) Sacco M.A., Immunology and Pathology, Institute for Animal Health, Compton, Berkshire, RG20 7NN, UNITED KINGDOM FEATURES Location/Qualifiers source 1..6895 /mol_type="genomic DNA" /db_xref="taxon:93465" /clone="EAV-15I" /proviral /organism="Avian endogenous retrovirus EAV-HP" /host="Gallus gallus" repeat_region <1..194 /rpt_type=long_terminal_repeat regulatory 24..31 /regulatory_class="TATA_box" primer_bind 195..212 /note="tRNA-phe" gene order(344..361,4975..6666) /gene="env" CDS join(344..361,4975..6666) /db_xref="GOA:Q6A2B5" /db_xref="InterPro:IPR005166" /db_xref="InterPro:IPR018154" /db_xref="UniProtKB/TrEMBL:Q6A2B5" /codon_start=1 /protein_id="CAF25154.1" /gene="env" /translation="MDQVIKEMFLGRPKTDSGEKPQQPAGGKKRKQKDTHPLLPSRGY FFFQMILVCVVIISVVPGVGGVHLLQQPGNVWVTWANKTGRTDFCLSLQSATSPFHTC LIGIPQYPLNTFKGYVTNVTACDNNTDLASQTACLIKALNTTLPWDPQELDILGSQMI KNGTTRTCVTFGSVCYKENNRSRVCHNFDGNFNGTGGAEAELRDFIAKWKSDDLLIRP YVNQSWTMVSPINVESFSISRRYCGFTSNETRYYRGDLSNWCSSKRGKWSAGYSNGTK CSSNTTGCGGNCTTEWNYYAYGFTFGKQPEVLWNNGTAKALPPGIFLICGDRAWQGIP RNALGGPCYLGQLTMLSPNFTTWITYGPNITGHHRSRRSLSRLSPDCGDELQLWSVTA RIFASFFAPGIAAAQALKEIERLACWSVKQANLTSLILNAMLEDTSSIRHAVLQNRAA IDFLLLAQGHGCQDVEGMCCFNLSDHSESIHKALQAMKEHTEKIRVEDDPIGDWFTRT FGDLGRWLAKGVKTLLFALLVIACLLAIIPCVIKCFQDCLSRTMNQFMDERIKYHRIR EQL" /product="envelope glycoprotein" gene 344..2386 /gene="gag" CDS 344..2386 /db_xref="GOA:Q6A2B4" /db_xref="InterPro:IPR000721" /db_xref="InterPro:IPR001878" /db_xref="InterPro:IPR001969" /db_xref="InterPro:IPR001995" /db_xref="InterPro:IPR004028" /db_xref="InterPro:IPR008916" /db_xref="InterPro:IPR008919" /db_xref="InterPro:IPR009007" /db_xref="InterPro:IPR010999" /db_xref="InterPro:IPR012344" /db_xref="InterPro:IPR013084" /db_xref="InterPro:IPR018061" /db_xref="InterPro:IPR021109" /db_xref="UniProtKB/TrEMBL:Q6A2B4" /codon_start=1 /protein_id="CAF25155.1" /gene="gag" /translation="MDQVIKVLVQFCKDYCGKSTPSRKEIATVLSLLNELGELDSPRH ILDSNRWDLLTSALCQRAMASQKATELKTWGLMLGALKAAREEDKLGAVMNGEGAPGS GSLEFCRTGAPTGAPTGAPTGAQTTANKTATEREEDCEKEDCEKDNEESQRLGGGATT PTAPPNSIALSPPPPYPKQPLYPSLATTSEQGAGPSPKGKGEGRLKLTDWGQIKEEVA QKGLAATYTLPVVVSEEGGPIWVPLDPKGVARMIEAVEKKGLKSPLTMNALEALTASG PMLPYDIENLMRMVLKPVQYTLWREEWHTKLKQMLITAQGDQRNPIYGSDIQRLTGNA PGLLTPQAQVCQLRPGELIATTDAAIDAFRKLARSAEPTTPWTEIAQGPTEPFQEFAD RLIKAVEGSDLPRAVHGPVILDCLYQKSSEGVQGILRAAPGRLQTPGEAIKYVLDKQK ACPSVAGEVAAAVAGVMMACREADHRSADRQLGPCFKCGQLGHIRAQCRMGTGGGVTC QQCGRKGHAAPQCRARRPPSQGNNNGRQSEHGDIIFRPMQAPDLSLPMAALSLSTHER PLVKATISCTNLPPDFQGPRSIFVTALIDSGADVTVVAETEWPSSWPAEASQSIMGVG GATPSRRSTNEVQVVVINRDGSLEKPALLTPLVARVPGTLLGRDFLRQIGARITNL" /product="gag polyprotein" gene 2386..4962 /gene="pol" CDS 2386..4962 /db_xref="GOA:Q6A2B3" /db_xref="InterPro:IPR000477" /db_xref="InterPro:IPR001037" /db_xref="InterPro:IPR001584" /db_xref="InterPro:IPR002156" /db_xref="InterPro:IPR003308" /db_xref="InterPro:IPR012337" /db_xref="InterPro:IPR017856" /db_xref="UniProtKB/TrEMBL:Q6A2B3" /codon_start=1 /protein_id="CAF25156.1" /gene="pol" /translation="MGATVCQLSAQYAIPLRWKPDTRPVWVDQWPLPKEKLDALQTLV ARELRLGHIEPSLSRWNTPVFVIQKKSGAFRLLHDLRAVNSQLIPFGVVQQGAPVLSA VPEEWEVTAIDLKDCFFSIPLAEQDREAFAFTVPVSNNQRPTQRYQWRVLPQGMACSP TICQMVVGKILGPLHHTSEASECIILHYMDDLLLAAPTLARLQDLETCVISLLTKAGF TVSSEKIQRGSGVQFLGYKFDEGTVRPTGVNITPRIRTLWDVQKLVGALQWIRGALGI PPRLMQPFYDQLKGSDPREPRTFTPDMSEAWDEIVTSCLHTALSRYNCKKELEVAVCK CDSGATGLLGQDLGAKPQPLWWNYSVQPVHAFTSWLEVLAKLICKCRLSAVRIFGQEP SVIYLPRSFRDTSPLPEPILLALVGSSATVTFTDSLSIFELARPMQLSLRCRVQASPV DGPTLFTDASSSTGQGAVVWGRGSCWKSVIFQDVTASVQILEVRAVALALRLWPTIPC NIVTDSAFAAKLLLSMGQEGISSTEAAMVLEDSLCTRTAPVAVMHVRSHSEVPGFFSE GNAAADRAAGTHVFTLKTARELHSTLHIGARALSRTCGIPLTAARDVVQACPHCNSAP AIGSGVNPRGVGPLQIWQTDFTWEDRFSPRRWLAVTVDTASTALVATQHAKANSTSAQ AHWAVAIAILGLPAQIKTDNGSCFTSRSTQEWLSRWGIQHVTGIPGNSQGQAIVERAN RLLKDKIRVLGEGEGYKDKIPVGRQPEILARALYALNHFERGDAKRTPVEKHWQPKIL EEGPLVKVKTNIGVWEPGWRILVWGRGYAAVKHAESGRVVWVPARKVKPDLSKEDDNV EH" /product="reverse transcriptase/integrase" misc_feature 6701..6711 /note="polypurine tract" repeat_region 6712..>6895 /rpt_type=long_terminal_repeat regulatory 6881..6886 /regulatory_class="polyA_signal_sequence" ORIGIN 1 ttcgtgattg gaggaaacac ttgtatttaa acacgtagcc tatagcaata aacgccattt 61 gcctcactta ctcctggggt ctgggtgagc atctggcccc gacctggtaa agggtcggtt 121 tcgcccagca gtaagcccta catgtggaca gaggacgaac accggacgag cgaacggaga 181 ctacatgcaa caagtggtga ccccgacgtg atctgtctgc tgagggtggc tgcccggcgt 241 gcccgtgacg cggagaagag cctgtgaggt ggcggcaggt cgcgcacgga agacgtattg 301 cggttaagag cctgcgaggt ggcggcaggt cgcatacgta acaatggacc aagtcattaa 361 ggtacttgtg cagttttgta aggactactg tggaaaatct actccttccc ggaaggagat 421 cgcgacagtt ttgtcgctgt taaatgagct gggggagctg gactctcccc gccacatttt 481 ggattcgaat aggtgggact tgctcacctc ggcgctatgc cagcgcgcca tggccagtca 541 gaaggctacg gaacttaaaa cgtggggact gatgttagga gcccttaagg cggccaggga 601 agaggacaaa cttggcgcgg tcatgaacgg ggagggagct ccggggagcg ggtctttgga 661 gttttgcagg accggcgctc cgaccggcgc tccgaccggc gctccgaccg gcgctcagac 721 gacagcgaat aaaacggcga cggagagaga ggaagactgc gagaaggaag actgcgagaa 781 ggacaacgaa gagtcgcaga ggctcggggg gggcgcaacg acgccgacgg cccctcctaa 841 ttctattgcg ctgtcgccgc ccccgcccta ccctaagcag ccgctatatc cttccttggc 901 aacgacatcg gagcaggggg cgggaccatc cccaaaagga aagggggagg ggagacttaa 961 gcttactgac tgggggcaga tcaaagagga agtggcacag aaaggcctgg cggcaactta 1021 tacactccca gttgttgtct cggaggaggg aggcccaatc tgggtcccgt tggacccaaa 1081 gggggtagca aggatgattg aggcagtaga aaagaaaggg ctgaagtcgc cattgacgat 1141 gaatgccctt gaggccctca cagcatcggg cccaatgctg ccttatgata ttgaaaattt 1201 aatgcgcatg gtgttgaaac cagtgcagta tacgctctgg agagaggagt ggcataccaa 1261 attaaaacaa atgctgatta cggcgcaggg tgatcaaaga aaccccatat atgggtccga 1321 tatacagaga ttaacgggca atgcaccagg tctgctgacc cctcaagcac aagtttgtca 1381 acttagacca ggagagttga tagcaactac ggacgctgca atagacgcgt tccgaaagct 1441 tgcaaggagc gctgagccca ctactccgtg gacagagatc gcgcaaggcc ccacagagcc 1501 gtttcaggag tttgcagaca gattaattaa ggcagtggaa ggctccgatc tgcccagagc 1561 ggttcacggt cccgtcatcc tggattgctt gtatcagaag tccagtgaag gggtgcaggg 1621 gattttgcga gcggcgccgg ggaggctcca aacccctggt gaggccatca agtatgtcct 1681 agataagcaa aaggcctgtc cgtctgtggc aggggaggta gctgcggcgg tagcaggagt 1741 gatgatggcc tgtagggagg cggatcatcg tagtgcggac cgacagttag gaccttgctt 1801 taaatgtggc cagttgggcc atattagggc ccaatgcaga atgggcacgg gtggaggtgt 1861 aacatgtcag cagtgtgggc ggaagggtca tgcagcaccg caatgcaggg cccgtaggcc 1921 tccaagccag ggaaataaca acgggagaca gtccgagcac ggtgacatca tttttcgacc 1981 tatgcaggcc cctgacctaa gtttacccat ggcggcgctg tctctaagta cccatgagcg 2041 ccctctggtg aaagccacta tttcttgcac caacctcccg ccggattttc aaggccctcg 2101 atctatcttt gtcactgctc tcatagattc cggtgccgac gttactgtgg tcgcggaaac 2161 agaatggcca tcctcgtggc ccgcggaggc ctcgcagtct attatggggg ttggaggggc 2221 gaccccctca cgccggtcta ccaatgaggt acaagtggtt gtgattaaca gggatggctc 2281 cttagagaaa ccggcgttgc ttacaccatt ggtggcgcgt gtccccggaa ctcttctggg 2341 gcgggatttc ttgcgacaaa taggcgctcg cattacaaat ttataatggg ggccacggtc 2401 tgccaattgt cagcgcaata tgctatccct ttgcgctgga aaccggacac ccgtcctgta 2461 tgggtggacc agtggccctt accgaaagag aaacttgatg ctttgcaaac tttagtagcc 2521 cgggagcttc gcctgggtca catagagcct tcgcttagta gatggaacac tccggtgttt 2581 gtaattcaga agaaatcagg ggcttttcgc ttgctgcatg acttgcgcgc tgtcaattct 2641 caacttatac cctttggtgt ggtgcaacag ggagcacctg tgttatctgc ggtgccagag 2701 gaatgggaag taacggccat tgacttgaag gattgttttt tctcaatacc tctagctgag 2761 caggatagag aagctttcgc ttttacagtc cctgtctcta ataatcaaag gccaactcag 2821 aggtaccaat ggcgagtttt accacagggc atggcctgct cccccaccat ttgtcaaatg 2881 gtggtgggta aaattcttgg cccattgcac cacacctcag aggcaagtga atgcattata 2941 ctgcattata tggatgatct gttgctagcc gctccaactt tagcacgact ccaggatctg 3001 gagacctgtg tgatttcgct gttaaccaaa gcaggtttca ctgtctcctc cgaaaaaatt 3061 cagaggggat cgggggtaca atttctagga tataagtttg atgaaggaac ggtacgtccg 3121 actggtgtaa acatcacacc tcgaattagg acactgtggg acgtccaaaa gctagtggga 3181 gctctccagt ggataagggg agcattggga attccccccc ggctgatgca acctttctat 3241 gaccagctga aggggtctga cccccgcgag cctcgtacct ttacccccga tatgtcggaa 3301 gcttgggatg agatagtgac ctcctgcctc cataccgcct tgtctcgata caattgtaag 3361 aaggagttag aggtcgcagt ctgtaagtgt gacagcggtg ctacaggttt actgggacaa 3421 gatctcggag ctaaaccaca gcccttgtgg tggaactact cagtacaacc agtgcacgcc 3481 tttacttcct ggctggaagt cttggctaag cttatctgca aatgccgcct ctctgcggtc 3541 agaatttttg gccaagaacc ctctgtcatt tacctcccca gatcctttcg tgacacatcg 3601 ccgttgcctg agcctattct tctagcgctt gtaggatcta gtgctactgt tacattcaca 3661 gattctttgt ctatcttcga gctcgcgaga ccgatgcaac tatcgttgcg ctgtcgggtc 3721 caagcctcac ctgtggatgg acccacgcta tttacggatg cgtcctcctc aacagggcag 3781 ggtgcagtgg tctggggtcg cggcagttgt tggaagtctg ttattttcca ggacgtgacg 3841 gctagtgtcc agatactaga agtccgtgct gtggcactgg ctttgcgttt gtggccgact 3901 atcccatgta atatagtcac cgactccgcc tttgcagcga agcttttgct atctatgggg 3961 caagaaggaa tctctagcac agaagcggca atggtgctag aggactccct gtgtactcgc 4021 actgcccctg tcgctgtgat gcatgttagg agccactcgg aggttccagg attcttctcc 4081 gaagggaatg cagcagcaga tcgagcagcg ggaacccacg tttttacact caaaacagcg 4141 agagagctgc actccacgct tcatatagga gcccgagcac tatcccgcac ctgtggtatc 4201 cccctcacgg cggccagaga cgttgtgcag gcttgccctc actgcaattc cgccccagct 4261 ataggttcgg gagtcaaccc ccgaggggta ggaccactgc aaatatggca aacggatttc 4321 acctgggagg atcgcttttc acccaggcgg tggctcgcag tcactgtaga cacagcctct 4381 accgcattag tcgcgacaca acacgccaaa gccaactcca cgtcagccca ggcacattgg 4441 gccgtcgcca tcgctattct aggccttccc gcccaaatta agacggacaa tggttcgtgt 4501 ttcacatccc gctccactca ggagtggttg agcagatggg gcatacagca tgtgacaggt 4561 atccccggca actcacaagg ccaggctatc gttgaacggg caaatcgcct cctcaaagac 4621 aaaattcgtg tccttgggga gggggaagga tataaggata agatacctgt aggtaggcag 4681 ccggagattt tagcacgagc cctgtatgct ctgaatcact tcgaaagagg agatgctaaa 4741 aggacaccag tcgaaaaaca ttggcaaccc aaaatcctag aggaaggccc tttggtgaaa 4801 gttaagacga acatcggggt ctgggaaccg ggatggagaa tattggtgtg gggaagagga 4861 tatgctgccg tgaagcatgc ggaatcggga agggttgtat gggtcccggc tcggaaggtt 4921 aaacctgacc tgtcaaagga ggacgataac gtggaacact gagctttctt acaggaaatg 4981 ttcctgggca gaccgaaaac ggactcggga gaaaaacccc agcagcccgc aggcggcaag 5041 aaaaggaagc agaaggacac tcatccattg ctgccatcga gaggttactt cttctttcaa 5101 atgatacttg tgtgcgtggt tattatttcc gttgtcccag gggtgggggg agttcatctg 5161 ttgcaacaac caggaaacgt gtgggtcacc tgggcaaata agacgggccg aacagatttt 5221 tgccttagtc tacagtcagc gacctcacca ttccacacct gcttgatagg cattccacag 5281 tatcctctga acacctttaa gggatatgtc actaatgtta ctgcttgcga taacaacacc 5341 gatttagcca gccaaacagc atgcttgata aaggctctaa atacaaccct cccttgggac 5401 ccccaagaat tggatatttt agggtcccag atgatcaaga acggaacaac acgtacgtgt 5461 gttacctttg gttcggtgtg ctataaagag aacaatcgca gtagagtctg tcacaatttt 5521 gatgggaatt ttaatgggac tggtggggcg gaagcagaat tgcgtgactt catagcaaaa 5581 tggaaaagtg atgaccttct tataaggccc tatgtcaacc aatcatggac gatggtaagt 5641 ccaataaacg tagagagttt ttcaataagt cgtagatatt gtggattcac cagtaacgag 5701 actcgttact atagagggga cctttctaat tggtgtagtt caaaaagggg aaaatggtca 5761 gcggggtaca gcaacgggac aaaatgttcc agcaacacga cgggttgcgg tggtaattgc 5821 acaacggaat ggaattatta tgcatatggg tttaccttcg ggaaacagcc agaggtgttg 5881 tggaacaatg ggactgctaa ggcactccca ccaggtattt tcttgatttg tggggacagg 5941 gcttggcaag gcatcccgcg taatgccttg ggagggccct gttatctagg acaattgact 6001 atgctctctc ctaactttac cacctggata acatatgggc cgaacattac gggtcaccac 6061 cgtagcaggc gctcgctgag tcgtctctcg cctgactgcg gtgatgagct acagctatgg 6121 agtgtgacag cccggatatt tgcttctttc tttgctcctg gtatagcagc agcacaggcc 6181 ttaaaggaga tcgagcgatt ggcatgttgg tcggttaagc aagcgaattt aacatcatta 6241 atattgaatg cgatgctgga ggatacgagc agcatccggc acgcagtgtt gcagaatcga 6301 gcagccatcg atttcttact cctggcgcag ggacacgggt gtcaagacgt ggaagggatg 6361 tgttgcttca atctcagcga tcatagtgag tccattcaca aggcgctcca agccatgaag 6421 gaacatacag agaagatacg ggtggaagat gatcccatag gggattggtt tacgcgcacg 6481 tttggtgatc taggaaggtg gctcgcgaaa ggtgttaaga cgctactgtt tgccttgctt 6541 gtcatagcct gtctattagc tatcattcca tgtgtaatca agtgctttca ggattgtcta 6601 tcgagaacaa tgaatcagtt tatggatgaa cgcataaaat atcatagaat tagggagcag 6661 ctgtaggttc cgaacgcgat gtgacgggag ctatcggcat agggaggggg agatgttgta 6721 ggcgtagcga gggaaacgag gtgtgttgta ggcgtagcga gggaaacgag gtgtgacgcg 6781 tgcaggttcc tatgccacct gtgtgttatg ccacttgtgt gtgccaagtg taacttcgtg 6841 attggaggaa acacttgtat ttaaacacgt agcctatagc aataaacgcc atttg //