LOCUS AJ623292 5136 bp DNA linear VRL 14-NOV-2006 DEFINITION Avian endogenous retrovirus EAV-HP partial proviral genome, clone EAV-6-3. ACCESSION AJ623292 VERSION AJ623292.1 KEYWORDS env pseudogene; gag pseudogene; pol pseudogene. 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 5136) 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..5136 /mol_type="genomic DNA" /db_xref="taxon:93465" /clone="EAV-6-3" /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 205..627 /pseudo /gene="gag" CDS 205..627 /pseudo /codon_start=1 /gene="gag" gene 627..3203 /gene="pol" CDS 627..3203 /db_xref="GOA:Q6A2B1" /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:Q6A2B1" /codon_start=1 /protein_id="CAF25164.1" /gene="pol" /translation="MGATVCQLSAQYAIPLRWKPDTRPVWVDQWPLPKEKLDALQTLV ARELRLGHIEPSLSRWNTPVFVIQKKSGAFRLLHDLRAVNSQLIPFGVVQQGAPVLSA VPEEWEVTAIDLKDCFFSIPLAEQDREAFAFTVPVSNNQRPTQRYQWRVLPQGMACSP TICQMVVGKILGPLHHTSEASECIILHYMDDLLLAAPTLARLQDLETCVISLLTKAGF TVSSEKIQRGSGVQFLGYKFDEGTVRPTGVNITPRIRTLWDVQKLVGALQWIRGALGI PPRLMQPFYDQLKGSDPREPRTFTPDMSEAWDEIVTSCLHTALSQYNCKKELEVAVCK CDSGATGLLGQDLGAKPQPLWWNYSVQPVHAFTSWLEVLAKLICKCRLSAVRIFGQEP SVIYLPRSFRDTSPLPEPILLALVGSSATVTFTDSLSIFELARPMQLSLHCRVQASPV DGPTLFTDASSSTGQGAVVWGRGSCWKSVIFQDVTASVQILEVRAVALALRLWPTIPC NIVTDSAFAAKLLLSMGQEGISSTEAAMVLEDSLCTRTAPVAVMHVRSHSEVPGFFSE GNAAADRAAGTHVFTLKTARELHSTLHIGARALSRTCGIPLTAARDVVQACPHCNSAP AIGSGVNPRGVGPLQIWQTDFTWEDRFSPRRWLAVTVDTASTALVATQHAKANSTSAQ AHWAVAIAILGLPAQIKTDNGSCFTSRSTQEWLSRWGIQHVTGIPGNSQGQAIVERAN RLLKDKIRVLGEGEGYKDKIPVGRQPEILARALYALNHFERGDAKRTPVEKHWQPKIL EEGPLVKVKTNIGVWEPGWRILVWGRGYAAVKHAESGRVVWVPARKVKPDLSKEDDNV EH" /product="pseudo" gene 3216..4907 /pseudo /gene="ENV" CDS 3216..4907 /pseudo /codon_start=1 /gene="ENV" exon 3216..4907 /pseudo /number=2 /gene="ENV" misc_feature 4942..4952 /note="polypurine tract" repeat_region 4953..5136 /rpt_type=long_terminal_repeat regulatory 5122..5127 /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 atttttcgac ctatgcaggc ccctgaccta 241 agtttaccca tggcggcgct gtctctaagt acccatgagc gccctctggt gaaagccact 301 atttcttgca ccaacctccc gccggatttt caaggccctc gatctatctt tgtcactgct 361 ctcatagatt ccggcgccga cgttactgtg gtcgcggaaa cagaatggcc atcctcgtgg 421 cccgcggagg cctcgcagtc tattatgggg gttggagggg cgaccccctc acgccggtct 481 accaatgagg tacaagtggt tgtgattaac agggatggct ccttagagaa accggcgttg 541 cttacaccat tggtggcgcg tgtccccgga actcttctgg ggcgggattt cttgcgacag 601 ataggcgctc gcattacaaa tttataatgg gggccacggt ctgccaattg tcagcgcaat 661 atgctatccc tttgcgctgg aaaccggata cccgtcctgt atgggtggac cagtggccct 721 taccgaaaga gaaacttgat gctttgcaaa ctttagtagc ccgggagctt cgcctgggtc 781 acatagagcc ttcgcttagt agatggaaca ctccggtgtt tgtaattcag aagaaatcag 841 gggcttttcg cttgctgcat gacttgcgcg ctgtcaattc tcaacttata ccctttggtg 901 tggtgcaaca gggagcacct gtgttatctg cggtgccgga ggaatgggaa gtaacggcca 961 ttgacttgaa ggattgtttt ttctcaatac ctctagctga gcaggataga gaagctttcg 1021 cttttacagt ccctgtctct aataatcaaa ggccaactca gaggtaccaa tggcgagttt 1081 taccacaggg catggcctgc tcccccacca tttgtcaaat ggtggtgggt aaaattcttg 1141 gcccattgca ccacacctca gaggcaagtg aatgcattat actgcattat atggatgatc 1201 tgttgctagc cgctccaact ttagcacgac tccaggatct ggagacctgt gtgatttcgc 1261 tgttaaccaa agcaggtttc actgtctcct ccgaaaaaat tcagagggga tcgggggtac 1321 aatttctagg atataagttt gatgaaggaa cggtacgtcc gactggtgta aacatcacac 1381 ctcgaattag gacactgtgg gacgtccaaa agctagtggg agctctccag tggataaggg 1441 gagcattggg aattcccccc cggctgatgc aacctttcta tgaccagctg aaggggtctg 1501 acccccgcga gcctcgtacc tttacccccg atatgtcgga agcttgggat gagatagtga 1561 cctcctgcct ccataccgcc ttgtctcaat acaattgtaa gaaggagtta gaggtcgcag 1621 tctgtaagtg tgacagcggt gctacaggtt tactgggaca agatctcgga gctaaaccac 1681 agcccttgtg gtggaactac tcagtacaac cagtgcacgc ctttacttcc tggctggaag 1741 tcttggctaa gcttatctgc aaatgccgcc tctctgccgt cagaattttt ggccaagaac 1801 cctctgtcat ttacctcccc agatcctttc gtgacacatc gccgttgcct gagcctattc 1861 ttctagcgct tgtaggatct agtgctactg ttacattcac agattctttg tctatcttcg 1921 agctcgcgag accgatgcaa ctatcgttgc actgtcgggt ccaagcctca cctgtggatg 1981 gacccacgct atttacggat gcgtcctcct caacagggca gggtgcagtg gtctggggtc 2041 gcggcagttg ttggaagtct gttattttcc aggacgtgac ggctagtgtc cagatactag 2101 aagtccgtgc tgtggcactg gctttgcgtt tgtggccgac tatcccatgt aatatagtca 2161 ccgactccgc ctttgcagcg aagcttttgc tatctatggg gcaagaagga atctctagca 2221 cagaagcggc aatggtgcta gaggactccc tgtgtactcg cactgcccct gtcgctgtga 2281 tgcatgttag gagccactcg gaggttccag gattcttctc cgaagggaat gcagcagcag 2341 atcgagcagc gggaacccac gtttttacac tcaaaacagc gagagagctg cactccacgc 2401 ttcatatagg agcccgagca ctatcccgca cctgtggtat ccccctcacg gcggccagag 2461 acgttgtgca ggcttgccct cactgcaatt ccgccccagc tataggttcg ggagtcaacc 2521 cccgaggggt aggaccactg caaatatggc aaacggattt cacctgggag gatcgctttt 2581 cacccaggcg gtggctcgca gtcactgtag acacagcctc taccgcatta gtcgcgacac 2641 aacacgccaa agccaactcc acgtcagccc aggcacattg ggccgtcgcc atcgctattc 2701 taggccttcc cgcccaaatt aagacggaca atggttcgtg tttcacatcc cgctccactc 2761 aggagtggtt gagcagatgg ggcatacagc atgtgacagg tatccccggc aactcacaag 2821 gccaggctat cgttgaacgg gcaaatcgcc tcctcaaaga caaaattcgt gtccttgggg 2881 agggggaagg atataaggat aagatacctg taggtaggca gccggagatt ttagcacgag 2941 ccctgtatgc tctgaatcac ttcgaaagag gagatgctaa aaggacacca gtcgaaaaac 3001 attggcaacc caaaatccta gaggaaggcc ctttggtgaa agttaagacg aacatcgggg 3061 tctgggaacc gggatggaga atattggtgt ggggaagagg atatgctgcc gtgaagcatg 3121 cggaatcggg aagggttgta tgggtcccgg ctcggaaggt taaacctgac ctgtcaaagg 3181 aggacgataa cgtggaacac tgagctttct tacaggaaat gttcctgggc agaccgaaaa 3241 cggactcggg agaaaaaccc cagcagcccg caggcggcaa gaaaaggaag cagaaggaca 3301 ctcatccatt gctgccatcg agaggttact tcctctttca aatgatactt gtgtgcgtgg 3361 ttattatttc cgttgtccca ggggtggggg gagttcatct gttgcaacaa ccaggaaacg 3421 tgtgggtcac ctgggcaaat aagacgggcc gaacagattt ttgccttagt ctacagtcag 3481 cgacctcacc attccgcacc tgcttgatag gcattccaca gtatcctctg aacaccttta 3541 agggatatgt cactaatgtt actgcttgcg ataacaacac cgatttagcc agccaaacag 3601 catgcttgat aaaggctcta aatacaaccc tcccttggga cccccaagaa ttagatattt 3661 tagggtccca gatgatcaag aacggaacaa cacgtacgtg tgttaccttt ggttcggtgt 3721 gctataaaga gaacaatcgt agtagagtct gtcacaattt tgatgggaat tttaatggga 3781 ctggtggggc ggaagcagaa ttgcgtgact tcatagcaaa atggaaaagt gatgaccttc 3841 ttataaggcc ctatgtcaac caatcatgga cgatggtaag tccaataaac gtagagagtt 3901 tttcaataag ccgtagatat tgtggattca ccagtaacga gactcgttac tatagagggg 3961 acctttctaa ttggtgtagt tcaaaaaggg gaaaatggtc agcggggtac agcaacggga 4021 caaaatgttc cagcaacacg acgggttgcg gtggtaattg cacaacggaa tggaattatt 4081 atgcatatgg gtttaccttc gggaaacagc cagaggtgtt gtggaacaat gggactgcta 4141 aggcactccc tccaggtatt ttcttgattt gtggggacag ggcttggcaa ggtatcccac 4201 gtaatgcctt gggagggccc tgttatctag gacaattgac tatgctctct cctaacttta 4261 ccacctggat agcgtatggg ccgaacatta caggtcacca ccgtagcagg cgctcgctga 4321 gtcatctctc gcctgactgc ggtgatgagc tacagctatg gagtgtgaca gcccggatat 4381 ttgcttcttt ctttgctcct ggtatagcag cagcacaggc cttaaaggag atcgaacgat 4441 tggcatgttg gtcggttaag caagcgaatt taacatcatt aatattgaat gcgatgctgg 4501 aggacacgag cagcatccgg cacgcagtgt tgcagaatcg agcagccatc gatttcttac 4561 tcctggcgca gggacacggg tgtcaagacg tggaagggat gtgttgcttc aatctcagcg 4621 atcatagtga gtccattcac aaggtgctcc aagccatgaa ggaacatacg gagaagatac 4681 gggtggaaga tgatcccata ggggactggt ttacgcgcac gtttggtgat ctaggaaggt 4741 ggctcgcgaa aggtgttaag acgctactgt ttgccttgct tgtcatagcc tgtctattag 4801 ctatcattcc atgtataatc aagtgctttc aggattgtct gtcgagaaca atgaatcagt 4861 ttatggatga acgcataaaa tatcatagaa ttagggagca gctgtaggtt ccgaacgcga 4921 tgtgacggga gctatcggca tagggagggg gagatgttgt atgcgtagcg agggaaacga 4981 ggtgtgttgt aggcgtagcg agggaaacga ggtgtgacgc gtgcaggttc ctatgccacc 5041 tgtgtgttat gccacctgtg tgtgccaagt gtaacttcgt gattggagga aacacttgta 5101 tttaaacacg tagcctatag caataaacgc catttg //