Typing tool
|
Complete norovirus genomes
JX289821 | GII.4 Sydney | ||
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GII.P12 |
ORF1: 5..5104 ORF2: 5085..6704 ORF3: 6704..7169LOCUS JX289821 7169 bp ss-RNA linear VRL 15-NOV-2012 DEFINITION Norovirus Hu/GII.4/MD120-12/1987/USA, partial genome. ACCESSION JX289821 VERSION JX289821.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII.4/MD120-12/1987/USA ORGANISM Norovirus Hu/GII.4/MD120-12/1987/USA Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7169) AUTHORS Madupu,R., Halpin,R., Ransier,A., Fedorova,N., Tsitrin,T., McLellan,M., Stockwell,T., Amedeo,P., Appalla,L., Bishop,B., Edworthy,P., Gupta,N., Hoover,J., Katzel,D., Li,K., Schobel,S., Shrivastava,S., Thovarai,V., Wang,S., Kim,M., Bok,K., Sosnovtsev,S.V., Wentworth,D.E. and Green,K.Y. TITLE Direct Submission JOURNAL Submitted (05-JUL-2012) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA COMMENT ##Assembly-Data-START## Assembly Method :: clc_ref_assemble_long v. 3.20.50819 Coverage :: 47.8x Sequencing Technology :: Sanger; Illumina; 454 ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7169 /organism="Norovirus Hu/GII.4/MD120-12/1987/USA" /mol_type="genomic RNA" /strain="Hu/GII.4/MD120-12/1987/USA" /host="Homo sapiens" /db_xref="taxon:1208059" /country="USA: Maryland" /collection_date="12-Jan-1987" /note="genotype: GII.4" gene 5..5104 /gene="POL" CDS 5..5104 /gene="POL" /note="genome polyprotein" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AFS33551.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAITFKRALGARP KQPPPREILQRPPRPPTPELVKKIPPPPPNGEDELVVSYSVKDGVSGLPELSTVRQPD EANTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKRLHGESFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTVDDSKLKKVANLFLCALSSLFTRPIKDIIGK LRPLNILNILASCDWTFAGIVESLILMAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTSLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK AKRDFPGQPDMWKNAFSPDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEYELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVRTM PELKQALKNISIKRCQIVYSGCTYTLESDGKGSVKVDRVQSATVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVEDTEETINKDGC PKPKDDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNERLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRENDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWSFTQACASLDKTTSSGHPHHIRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFERHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFKISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLTISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 5..994 /gene="POL" /product="protein p48" mat_peptide 995..2092 /gene="POL" /product="NTPase" /note="p41" mat_peptide 2093..2629 /gene="POL" /product="protein p22" mat_peptide 2630..3028 /gene="POL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3029..3571 /gene="POL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3572..5101 /gene="POL" /product="RNA-directed RNA polymerase" gene 5085..6704 /gene="VP1" CDS 5085..6704 /gene="VP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AFS33552.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNIIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLSRMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSHDSTLKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMSNSRFPIPLEKLYTGPSSAFVVQPQNGRCTTDGVLLGTT QLSAVNICNFRGDVTHIVGSHDYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGLL TQTTRADGSTRAHKATVSTGSVHFTPKLGSVQFTTDTNNDFQTGQNTKFTPVGVIQDG DHHQNEPQQWVLPNYSGRTGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDC LLPQEWVLHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGPYDLVI PPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6704..>7169 /gene="VP2" CDS 6704..>7169 /gene="VP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AFS33553.1" /translation="MAGSFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATQKLQQDLMKVKQAVLLEGGFSTTDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRTNPRITVPARGP" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga 61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctatcactt ttaaacgagc 121 cctcggggcg cggcctaaac agcctccccc gagggaaata ctacaaagac ccccacgacc 181 acctacccca gaactggtta aaaagatccc ccctcccccg cccaacgggg aggatgaact 241 agtggtttct tatagtgtca aagatggcgt ttccggtctg cctgagcttt ccactgtcag 301 gcaaccggat gaagccaata cggccttcag tgttccccca ctcaatcaga gggagaatag 361 ggatgccaag gagccactaa ctggaacaat tctggaaatg tgggatggag agatctatca 421 ttacggccta tatgtggagc gaggtcttgt acttggtgtg cacaaaccac cagctgccat 481 cagcctcgcc aaggtcgaac taacaccact ctccttgttc tggagacctg tatacactcc 541 ccagtatctc atctccccag acactctcaa gagattgcac ggagaatcgt tcccctatac 601 agccttcgac aacaattgct atgccttctg ttgctgggtc ttagacctaa acgactcgtg 661 gctgagtagg agaatgatcc agagaacaac tggtttcttt agaccctatc aagactggaa 721 taggaaaccc ctccctactg tggatgactc caaattaaag aaggtagcta atttattcct 781 gtgtgctcta tcttcactat tcaccaggcc catcaaagac ataataggga aactaagacc 841 tctcaacatc ctcaacatct tggcctcatg tgattggact ttcgcaggca tagtggagtc 901 cttgatactc atggcagagc tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gattgccccc ttgctaggtg attacgagtt acaagggcct gaggaccttg cagtggaact 1021 cgttcctata gtgatggggg gaattggttt ggtgctagga tttaccaaag agaagattgg 1081 gaagatgttg tcatctgctg catccacctt aagagcttgt aaagatcttg gtgcatacgg 1141 gctggaaatc ctaaaattag tcatgaagtg gttcttccca aagaaagagg aagcaaatga 1201 gctggctatg gtgagatcca tcgaggatgc ggtgctggac ctcgaggcaa ttgaaaacaa 1261 ccatatgacc agcctgctca aagacaaaga cagtctggca acctacatga gaacccttga 1321 ccttgaggag gagaaagcca ggaagctctc aaccaagtct gcttcacctg atatcgtggg 1381 tacaatcaac gcccttctgg caagaatcgc tgctgcacgt tccctggtgc atcgagcgaa 1441 ggaggagctt tccagcagac caagacccgt tgtcgtgatg atatcaggca gaccagggat 1501 agggaagacc caccttgcca gggaactggc caagagaatc gcagcctccc tcacaggaga 1561 ccagcgtgta ggtctcatcc cacgcaatgg cgtcgaccac tgggacgcat acaaggggga 1621 gagggtcgtc ctatgggacg actatggaat gagtaatccc atccatgatg ccctcaggtt 1681 acaagaactc gctgacactt gccccctcac tctaaactgt gacaggattg agaacaaagg 1741 aaaggtcttt gacagtgatg ccataatcat caccactaat ctggccaacc cagcaccact 1801 ggactacgtc aactttgagg catgctcgag gcgcatcgat ttcctcgtgt atgcagatgc 1861 ccctgaagtc gagaaggcga aacgtgattt tccaggccaa cctgacatgt ggaagaacgc 1921 tttcagtcct gatttctcgc acataaaact aacgctggct ccacagggtg gcttcgacaa 1981 gaatggaaac accccacatg ggaagggcgt catgaagact ctcaccactg gctccctcat 2041 tgcccgggca tcagggctac tccatgagag gttagatgag tatgagctac agggcccaac 2101 tctcaccact ttcaactttg atcgcaacaa ggtgcttgct tttaggcagc ttgctgctga 2161 aaacaaatac gggctgatgg acacaatgaa agttggaaga cagctcaagg atgtcagaac 2221 catgccagag cttaaacaag cactcaagaa tatctcaatc aagaggtgcc agatagtgta 2281 cagtggttgc acctatacac ttgagtctga tggcaagggc agtgtgaaag ttgacagagt 2341 tcagagcgcc accgtgcaga ccaataacga gctggccggc gccctacacc atctaaggtg 2401 cgccagaatt aggtactatg tcaagtgtgt ccaggaggcc ctatattcca tcatccaaat 2461 tgctggagct gcatttgtca ccacgcgcat cgtcaagcgc atgaacatac aagacctctg 2521 gtccaagcca caagtggaag acacagagga gactatcaac aaggacgggt gcccaaaacc 2581 caaagatgat gaggagttcg tcgtctcatc tgacgacatc aaaactgagg gcaagaaagg 2641 gaagaacaag actggccgtg gcaagaagca cacagccttc tcaagcaaag gtctcagtga 2701 tgaagagtac gatgagtaca agagaatcag agaagaaaga aacggcaagt actccataga 2761 agagtacctt caggacaggg acaagtacta tgaggaggtg gccattgcca gggcgaccga 2821 agaggacttc tgtgaagagg aggaggccaa gattcggcag aggattttca ggccaacaag 2881 gaaacaacgc aaggaggaga gggcctctct cggtttagtc acaggctctg aaatcaggaa 2941 gaggaaccca gatgatttca agcccaaggg aaaactgtgg gctgatgatg acaggagtgt 3001 agactacaat gagagactca gttttgaggc cccaccaagc atctggtcga ggatagtcaa 3061 ctttggttca ggttggggct tctgggtttc tcccagcctg ttcataacat caactcatgt 3121 cataccccag ggcgcacagg agttctttgg agtccccatc aagcaaattc agatacacaa 3181 atcgggcgaa ttctgtcgct tgaggttccc aaaaccaatc aggactgatg tgacgggcat 3241 gatcttagaa gaaggtgcgc ccgaaggtac cgtggccaca ctactcatca agaggcctac 3301 tggagaactt atgcccttag cagccagaat ggggacccat gcaaccatga aaattcaagg 3361 gcgcactgtt ggaggtcaaa tgggcatgct tctgacagga tccaacgcca aaagcatgga 3421 tctaggcacc acaccaggtg actgcggctg cccctacatc tacaagaggg agaatgacta 3481 cgtggttatt ggagtccaca cggctgcagc tcgtgggggg aacactgtca tatgtgccac 3541 ccaggggagt gagggagagg ctacacttga aggcggtgac agtaagggaa cctactgtgg 3601 tgcaccaatc ctaggcccag gaagtgcccc aaaactcagc accaagacta aattctggag 3661 atcatctaca acaccactcc cacctggcac ctatgaacca gcctaccttg gtggtaagga 3721 ccccagagtc aagggtggcc cttcattgca acaagtcatg agggatcagc tgaaaccatt 3781 tacagagccc aggggcaaac caccaaagcc aagtgtgttg gaggctgcca agaaaaccat 3841 catcaatgtc cttgaacaaa caattgatcc acctcagaag tggtcattca cgcaagcttg 3901 cgcgtccctc gacaagacta cttccagtgg ccatccgcac cacatacgga aaaacgactg 3961 ctggaacggg gaatccttca caggcaagtt ggcagaccag gcttccaagg ccaacctgat 4021 gttcgaagag gggaagaaca tgaccccggt ctacacaggt gcgcttaagg atgagttggt 4081 caaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggacttagc 4141 gaccatgatc cggtgcgctc gggcattcgg aggcctaatg gatgaactca aagcacactg 4201 tgttacactt cctgtcagag ttggtatgaa tatgaatgag gatggcccca tcatcttcga 4261 gaggcattcc aggtataaat atcactatga tgctgattac tctcggtggg attcaacgca 4321 acagagagcc gtattagcag cagccctaga aatcatggtt aaattctccc cagaaccaca 4381 tctggcccag atagttgcag aagaccttct ctctcctagt gtgatggatg tgggtgactt 4441 caaaatatca atcaatgagg gtctcccctc tggggtgccc tgcacctccc aatggaattc 4501 catcgcccac tggctcctca ctctctgtgc actctctgaa gtcacaaact tgtcccctga 4561 tatcatacag gctaattccc tcttctcctt ttatggcgat gatgaaattg tcagtacaga 4621 tataaagttg gacccagaga aattgacagc aaaactcaag gaatacgggt tgaaaccaac 4681 ccgccctgac aaaactgaag gaccccttac tatctctgaa gacttgaatg gtctgacctt 4741 cctgcggaga actgtgaccc gcgacccagc tggctggttt ggaaaattgg aacagagttc 4801 aatacttagg caaatgtact ggactagggg ccccaaccat gaagacccat ctgaaacaat 4861 gataccacac tcccaaagac ccatacaatt aatgtcccta ctgggcgagg ccgcactcca 4921 cggcccagca ttctacagca aaattagcaa gctagtcatt gcagagctga aggaaggtgg 4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg 5161 ttatggctct ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa 5221 atataattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagtttacag 5281 tgtcccctag aaacgctcca ggtgagatac tatggagcgc gcccttgggc cctgatttga 5341 acccctatct ttctcatttg tccagaatgt acaatggtta tgcaggcggt ttcgaagtgc 5401 aagtaatcct cgcggggaac gcgttcaccg ccgggaaagt tatatttgca gcagttccac 5461 caaactttcc aactgaaggc ttaagcccca gccaggttac tatgttcccc catataattg 5521 tagatgttag gcaattggaa cctgtgttga tccccctacc tgatgttagg aataatttct 5581 atcattacaa tcaatcacat gattctaccc ttaagttgat agcaatgttg tatacaccac 5641 tcagggctaa taatgccggg gacgatgtct tcacagtctc ttgtcgagtt ctcacgaggc 5701 catcccccga ttttgatttc atattcttgg tgccacccac agttgaatca agaactaaac 5761 cattcaccgt cccaatctta actgttgagg aaatgtccaa ttcaagattc cccattcctt 5821 tggaaaagtt gtacacgggt cctagcagtg cttttgttgt ccaaccacaa aatggcagat 5881 gcacgactga tggcgtgctc ttaggtacta cccagctgtc agctgtcaac atctgtaact 5941 ttagggggga tgtcacccat attgtgggca gccatgatta tacaatgaat ctggcttccc 6001 aaaattggag caattatgac ccaacagaag aaatcccagc ccccctggga acaccagatt 6061 ttgtggggaa gatccaaggc ctgctcaccc agaccacaag agcggatggc tcgacccgtg 6121 cccacaaagc tacagtgagc actgggagtg tccacttcac tccaaagctg ggtagtgttc 6181 aattcaccac tgacacaaac aatgatttcc aaactggcca aaacacgaaa ttcaccccag 6241 ttggcgtcat ccaggacggt gatcaccatc agaatgagcc ccaacaatgg gtactcccaa 6301 attactcagg tagaactggt cataatgtgc acctggcccc tgccgttgcc cccacttttc 6361 cgggtgagca actccttttc tttagatcca ctatgcccgg atgtagcggg tatcccaaca 6421 tgaatttgga ttgcctactc ccccaggaat gggtgctgca cttctaccag gaagcagctc 6481 cagcacaatc cgatgtggct ctgctgagat ttgtgaatcc agacacaggt agggttctgt 6541 ttgagtgcaa gctccataaa tcaggctata tcacagtggc tcacactggc ccgtatgact 6601 tggttatccc ccccaatggt tattttagat ttgattcctg ggtcaaccag ttctacacac 6661 ttgcccccat gggaaatgga acggggcgca ggcgtgcatt ataatggctg gatctttctt 6721 tgctggattg gcatctgatg tcctcggctc tggacttggt tctctaatca atgctggagc 6781 tggggccatc aaccaaaaag ttgaatttga aaataacaga aaattgcaac aagcttcctt 6841 ccaatttagt agcaatctac aacaggcttc cttccaacat gataaagaga tgctccaagc 6901 acaaattgag gctactcaaa aattgcaaca ggatctgatg aaggttaaac aggcagtgct 6961 cctagagggt ggattttcca caacagatgc agcccgtggg gcaatcaacg cccccatgac 7021 aaaggctctg gactggagcg gaacaaggta ctgggcccct gatgccagga ccacaacata 7081 caatgcaggc cgcttttcca cccctcagcc ttcgggggca ttgccaggaa gaactaatcc 7141 taggattacc gtccccgctc ggggccccc //