Typing tool
|
Complete norovirus genomes
KM198484 | GII.3 | ||
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GII.P21 |
ORF1: 1..5100 ORF2: 5081..6727 ORF3: 6727..7425LOCUS KM198484 7425 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/30212/2009/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198484 VERSION KM198484.1 KEYWORDS . SOURCE Norovirus Hu/GII/30212/2009/VNM ORGANISM Norovirus Hu/GII/30212/2009/VNM Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7425) AUTHORS Cotten,M., Petrova,V., Phan,M.V., Rabaa,M.A., Watson,S.J., Ong,S.H., Kellam,P. and Baker,S. TITLE Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting JOURNAL J. Virol. 88 (19), 11056-11069 (2014) PUBMED 25056894 REFERENCE 2 (bases 1 to 7425) AUTHORS Cotten,M.L., Petrova,V., Phan,M.V.T., Rabaa,M.A., Watson,S.J., Kellam,P. and Baker,S. TITLE Direct Submission JOURNAL Submitted (13-JUL-2014) Virus Genomics, The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. 2.4.0 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7425 /organism="Norovirus Hu/GII/30212/2009/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/30212/2009/VNM" /host="Homo sapiens" /db_xref="taxon:1291887" /country="Viet Nam" /collection_date="06-Oct-2009" /note="genotype: GII" CDS 1..5100 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02580.1" /translation="MKMASNDASAAAAANSNNDNAKSSSDGVFSNMAVTFKRALGARS KQPPPRDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKEGVSGLPELSTVTQPE ESSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLYWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGVGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL AKKIASSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARA SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGALHHLR CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRMNIQNLWSKPQAEDLEETSNEEGC PKPKNDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNERLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPYHMRKNDCW NGETFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGTIKKRLLWGSDL STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLK EYGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP NHEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" CDS 5081..6727 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02581.1" /translation="MKMASNDAAPSNDGAAGLVPEINSEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVLLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT QLLPSQICAFRGMLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP LGTPDFRGKVFGVASQRNPDATTRAHEAKIDTTSGRFTPKLGSLEISTESGDFDQNQP TRFTPVGIGVDHEADFQQWTLPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG GRSNGILDCLVPQEWVQHFYQESAPSQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA KSGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" CDS 6727..>7425 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02582.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSMSGGFINQTVHRSTPNFKTNQAPKPTPSSGSSVRSNSTQITSLSS HSSGSSRSSGSTVVSSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG TVSTVPKNVLDSWTG" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgctgctg ccaacagcaa caacgacaac 61 gcaaaatctt caagtgacgg agtattttct aatatggctg tcacttttaa acgagccctc 121 ggggcgcggt ctaaacagcc gcccccgagg gacaaaccac caaaaccccc aagaccaccc 181 acaccagagt tggttaaagc aatcccccct cccccaccca acggggagga cgaaccaatc 241 atttcttaca acgtcaaaga gggggtttct ggtctgcctg aactctcaac tgtcacccaa 301 ccggaagaga gctctacagc attcagcgtt ccccctctta gccagaggga gaacagagat 361 gcaaaggaac cattgactgg aaccatcctg gagatgtggg acggggagat ctaccattat 421 ggcttatatg tggaacgagg gttagtgcta ggtgtacaca aaccaccagc agccatcagc 481 cttgctaagg ttgagctgac ccccttgtct ttgtattgga gaccagtgta caccccacag 541 tacctcattt cccctgacac tctcaaaaag ttgcatgggg agacattccc ttatacagcc 601 tttgataaca actgttatgc cttctgctgt tgggtacttg acttgaacga ttcatggctg 661 agtagaagga tgatacagag gacaacaggc ttcttccgac cctaccagga ctggaacagg 721 aaacccctcc ccacgatgga tgactccaaa gtgaaaaagg tggctaatgt tgtcctctgt 781 gctctctcgt cattgtttac aagaccaatt aaggacatta ttgggaagtt gaaaccccta 841 aacatcctca acatcctagc cacatgtgat tggacttttg caggcatagt agaatccctg 901 atccttttgg ctgaactgtt tggagttttc tggacacccc cagatgtgtc tgcaatgatc 961 gctcccttac tgggtgatta tgagctgcag ggacccgagg acctcgctgt ggaactcgta 1021 cccgtagtaa tgggaggggt aggtttggtg ctgggattca ccaaagagaa aatcggcaaa 1081 atgctttcat ctgctgcttc aaccctgagg gcatgcaaag atctcggtgc atatgggttg 1141 gagatcctca agttggtcat gaagtggttt ttcccaaaga aagaagagaa aaacgaattg 1201 gcaatggtga gatccatcga ggatgcagtg ctagatcttg aggccattga gaacaaccac 1261 atgacagctc tactcaagga taaagacagc cttgcaacct acatgaggac tcttgacatg 1321 gaggaggaga aggcgaggaa actttccacc aagtctgcct cgccggatat tgtgggcacg 1381 ataaacgccc tactgtcaag gattgcagct gcccggtctc tagtgcacag ggctaaggag 1441 gaactgtcaa gcaggccccg accggtcgtt gtgatgattt cagggagacc aggcataggg 1501 aaaacccacc tagctagaga gctggcaaag aagatcgcct cctcactcac aggtgaccag 1561 agggtgggtc ttatcccacg caacggggtc gaccactggg atgcatacaa aggtgaaagg 1621 gtcgttctct gggacgacta cgggatgagc aaccctatcc acgacgccct cagactccag 1681 gagctcgctg atacctgtcc tcttacactt aactgtgaca ggattgagaa caaaggcaaa 1741 gtctttgaca gtgacgccat aataataacc accaatctgg ccaacccagc gccactggat 1801 tacgtcaact ttgaagcctg ctcaagacgc atagacttcc tcgtctatgc tgatgcccct 1861 gaagttgaga aggctaaacg ggacttccca ggccaaccag acatgtggaa agacaccttt 1921 aaacctgact tctcacacat aaaactggca ttagccccgc aaggaggttt tgacaagaat 1981 ggtaacactc ctcatgggaa gggtgtcatg aagaccctca ctgccagttc cctcgttgcc 2041 cgagcatcgg ggctcctcca cgagagatta gacgaatacg agctgcaggg cccaactccc 2101 acaacattca acttcgaccg caacaaggtg cttgctttta ggcagcttgc tgctgaaaac 2161 aagtacggcc ttgttgacac aatgagggtc ggatcacagc tcaagaatgt caaaactatg 2221 acagaactca agcaggctct taagaacatc tcagtcaaga aatgtcagct tgtgtatggt 2281 gggggcacgt acacactcga atctgatggc aaaggcaatg tgcatgtcga gaaggtgaac 2341 aacaccagtg tgcaaactaa caacgagctc tccggggctt tgcaccatct caggtgtgcc 2401 agaatcaggt actatgttaa gtgtgtccag gaagctctct actccatctt gcaaattgct 2461 ggggctgcat tcattaccac gcgcattgca aagcgcatga acatacaaaa cctctggtcc 2521 aaaccacagg cagaagatct ggaggagact agcaatgagg agggttgtcc aaaacctaaa 2581 aatgatgagg agtttgtcat ctcctctgat gacatcaaaa ctgagggcaa gaaaggaaag 2641 aataagaccg gccgtggcaa gaagcacaca gccttttcca gcaaaggact cagtgatgag 2701 gagtacgatg aatataaaag aatcagggaa gaaagaaatg gcaagtactc catagaggaa 2761 tacctacagg atagagacaa gtactatgag gaggtggcca tagccagggc aactgaggaa 2821 gacttctgtg aagaagagga ggcaaaaatc cggcaaagga tatttagacc aacaaggaaa 2881 caacgcaaag aggaaagggc ctctcttggt ttggttacag gttctgagat caggaagaga 2941 aacccagatg acttcaagcc caaagggaaa ctgtgggccg atgatgacag gagtgttgac 3001 tacaatgaga gacttagttt cgaggctcca ccaagcattt ggtcacgaat agtcaacttt 3061 ggctcagggt ggggcttttg ggtctcgccc agcctcttca taacatcaac ccatgtcatt 3121 ccccaaggcg cacaggagtt ctttggagtg cccatcaaac aaatacaaat tcacaagtca 3181 ggtgagttct gccggcttag gttcccaaaa ccaatcagga cagatgtcac aggcatgatc 3241 ctggaggaag gtgctccaga aggcactgtt gccacacttc tcatcaagag accaactggg 3301 gaactcatgc ccttggcagc cagaatgggc acccacgcga ccatgaaaat tcagggtcgc 3361 actgttggtg gacagatggg catgttactc acagggtcta acgctaagag tatggacctg 3421 ggtacaactc ctggcgattg tggttgtccc tatatctaca agagggggaa cgactacgtg 3481 gtcattgggg ttcacactgc cgccgctcgt ggaggaaaca ccgtcatctg tgcaactcaa 3541 ggaaacgagg gtgaggccat gttagaaggt ggtgacaaca agggaactta ctgtggagca 3601 ccaatattgg gccctggaaa tgcccccaaa ctcagcacca aaaccaaatt ttggagatct 3661 tccaccaccc ccctgccacc cggaacctat gagccagctt atctgggtgg caaggaccct 3721 agagtgaaag gtggcccctc actgcaacag gttatgaggg accaactaaa accattcact 3781 gagcccagag gcaaaccacc caaaccaagt gtgctagaag ccgccaagaa gactataatc 3841 aatgtgcttg aacaaacaat agacccacct cagaaatgga catacgcaca ggcgtgtgca 3901 tcactagaca agaccacttc cagcggccac ccttaccaca tgcggaagaa cgattgctgg 3961 aatggggaga ctttcacagg aaaactggca gaccaagcat caaaggctaa cctaatgttt 4021 gaggaaggaa agaacatgac cccagtatac acaggagctc tgaaagatga gctagtcaag 4081 actgataaga tctatggaac aatcaagaag agactcctgt ggggttcaga cctatcaacc 4141 atgatacggt gtgcacgagc cttcggtggg ctaatggacg aactcaaggc ccattgcgtc 4201 acactaccag tcagggttgg tatgaacatg aatgaggatg gacccataat ctttgagaaa 4261 cattccagat acaaatacca ttatgatgca gactactccc gttgggattc aacacaacaa 4321 agagcagtgt tggctgcagc cctggagata atggtcaaat tctcaccaga accccatctg 4381 gcccaagtgg ttgcagaaga cctcttatcc cccagtgtga tggatgtggg tgacttcaag 4441 atatcaatca acgaggggtt accctctggt gttccctgca cctcacaatg gaactccatt 4501 gcccactggc tcctcacact atgtgcactg tctgaagtca cagacctgtc tcctgacatc 4561 atccaggcaa attccctgtt ctccttttat ggtgatgatg aaatagtgag cacagatatc 4621 aaactggacc cagaaaaatt aacaacaaaa ttgaaggaat acgggctaaa accaacccgt 4681 cctgacaaaa cagaaggacc cttaatcatc tctgaagatt tggatggcct gaccttctta 4741 cggagaacgg tgacccgtga tccggccggg tggtttggca aactggacca aagttcaata 4801 ctcaggcaga tgtactggac caggggacca aaccatgagg accccttcga aacaatgata 4861 ccacactccc aaagacccat acaactgatg tcattattgg gtgaagccgc gttgcatggt 4921 ccatcattct acagtaaaat cagcaaattg gtcatctcag aattgaaaga gggtggaatg 4981 gatttttacg tgcccagaca agaaccaatg ttcaggtgga tgagattctc agatttgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga 5101 cgccgctcca tctaatgatg gtgccgccgg cctcgtccca gagatcaaca gtgaggcaat 5161 ggcgctagag ccagtggcgg gtgcagcgat agcagcaccc ctcactggtc agcaaaatat 5221 aattgatccc tggattatga ataattttgt gcaagcacct ggtggtgagt tcacagtatc 5281 ccctagaaat tcccctggtg aagttcttct caatttggaa ttgggtccag aaataaatcc 5341 ctacttggcc catcttgcta gaatgtataa tggttatgca ggtggatttg aagtgcaggt 5401 gctcctagct ggaaatgcgt ttacagcagg aaagataatc tttgcagcta ttccccctaa 5461 ttttccaatt gataatctaa gtgcagcaca gatcacaatg tgtccacatg tgattgtgga 5521 tgttagacag ctggaaccag tcaacctccc gatgcctgac gttcgcaaca actttttcca 5581 ttacaatcag gggtctgatt cgagattgcg cctaattgca atgctatata cacctcttag 5641 ggcaaataac tctggggatg atgttttcac tgtgtcttgc agagtgctaa ctagacctag 5701 tcctgacttc tcatttaatt tccttgtgcc acccactgtg gagtcaaaga caaaaccctt 5761 ttccctcccc attctgacta tctctgaaat gtccaattct aggttcccag taccaattga 5821 ttctctgcac accagcccta ctgagaacat tgttgtccag tgccagaatg gacgcgtcac 5881 ccttgatggt gagttgatgg gcaccaccca acttttacct agccaaatct gtgctttcag 5941 gggcatgctc accagatcaa caagcagggc cagtgaccag gccgatacag caacccctag 6001 attgtttaat tattattggc atatacaatt ggataaccta aatggaactc cttatgaccc 6061 tgcagaagat ataccaggcc ccctagggac accagatttc cggggcaaag tctttggcgt 6121 ggccagccag agaaatcctg atgccacgac tagggcacat gaagcaaaga tagacacaac 6181 atctggccgc ttcaccccaa aattaggctc actagagatt tccactgagt ctggagattt 6241 tgatcaaaac caaccaacaa gattcacccc agttggcatt ggggttgacc atgaggcaga 6301 ttttcaacaa tggactcttc ccgactatgc tggccagttc acccacaaca tgaacttagc 6361 cccagctgtt gctcccaact tccctggtga gcagctcctt ttcttccgct cacagttgcc 6421 atcttctggt gggcggtcca acgggattct agactgcctg gtcccccaag aatgggtaca 6481 gcacttctac caagaatcag ccccctccca aactcaagtg gccctggtta ggtatgtcaa 6541 ccctgacact ggtagagtgt tatttgaggc caagctgcac aaattaggtt tcatgactat 6601 agccaagagt ggtgactctc caataactgt ccccccaaat ggatacttta ggtttgaatc 6661 ttgggtgaac cccttttata cacttgcccc catgggaact gggaatgggc gtagaaggat 6721 tcaataatgg ctggagcttt tatagcagga ttggctggtg acatgctcac aaatactgta 6781 ggatctttag ttaacgcagg ggctaatgcc attaatcaaa caattgattt tgaaaataat 6841 aaatatttgc aaaatgcctc ttttaatcat gataaggaga tgttgaatgc acaaattgag 6901 gcaacaaaga ggttacaggc tgacatgatt gctatcaaac aaggggtttt gaccgctggc 6961 ggcttctccc ctactgatgc agcccgcggg gcaattaatg cccccatgac aaaagtccta 7021 gattggaatg gaacgagata ctgggcgcca ggtgccacct ccacaacctc gatgtcgggt 7081 ggcttcataa atcaaactgt gcacagatcc acaccaaatt ttaaaacgaa ccaggccccc 7141 aaacccacac ccagcagtgg gtcttcagtg aggtcaaatt caacccaaat cactagcctg 7201 agctcacact cgtccgggtc gtctcgatcc agcgggtcta cagttgtcag ctcaataccg 7261 tcctctaaca ggactaggga ctgggttaac caacaaaatt ttaatttgga accacacatg 7321 cctggatctc ttaggacagc ttttgtcact ccaccatcta gtacagcctc tagctcaggc 7381 acagtctcaa ctgtgcccaa aaatgttttg gactcctgga ctggc //