Typing tool
|
Complete norovirus genomes
MH218587 | GII.3 | ||
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GII.P21 |
ORF1: 5..5104 ORF2: 5085..6731 ORF3: 6731..7495LOCUS MH218587 7548 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_117_01_11_2014, complete genome. ACCESSION MH218587 VERSION MH218587.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7548) AUTHORS Brown,J.R., Roy,S., Shah,D., Williams,C.A., Williams,R., Dunn,H., Hartley,J., Harris,K. and Breuer,J. TITLE Norovirus transmission dynamics in a paediatric hospital using full genome sequences JOURNAL Clin. Infect. Dis. (2018) In press PUBMED 29800111 REMARK Publication Status: Available-Online prior to print REFERENCE 2 (bases 1 to 7548) AUTHORS Brown,J.R., Roy,S., Shah,D., Williams,C.A., Williams,R., Dunn,H., Hartley,J., Harris,K. and Breuer,J. TITLE Direct Submission JOURNAL Submitted (17-APR-2018) Division of Infection and Immunity, University College London, 90 Gower St, London, London WC1E 6BT, United Kingdom COMMENT ##Assembly-Data-START## Assembly Method :: CLC Genomics Workbench v. 10.1 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7548 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="NORO_117_01_11_2014" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="01-Nov-2014" /note="genotype: GII.P21_GII.3" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17419.1" /translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARP KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLE ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKIELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTAGSLVARA SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM TELKQALKNISVKKCQLVYGGGTYTLESDGRGNVHVEKVNNTSVQTNNELSGVLHHLR CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEDLEETNNEEGC PKPKSDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSGKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAQEFYGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLIVSEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP NHEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 5..994 /gene="ORF1" /product="p48" mat_peptide 995..2092 /gene="ORF1" /product="NTPase" mat_peptide 2093..2629 /gene="ORF1" /product="p22" mat_peptide 2630..3028 /gene="ORF1" /product="VPg" mat_peptide 3029..3571 /gene="ORF1" /product="Pro" mat_peptide 3572..5101 /gene="ORF1" /product="RdRp" gene 5085..6731 /gene="ORF2" CDS 5085..6731 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWR17420.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP LGTPDFRGKVFGVASQRNPDATTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDQNQP TRFTPVGIGVDHEADFQQWTLPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" gene 6731..7495 /gene="ORF3" CDS 6731..7495 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17421.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA SFNHDKEMLNAQIEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaaa gcaacaacga 61 caacgcaaaa tcttcaagtg acggagtatt atctaatatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agccgccccc gagtgacaaa ccaccaaaac ccccaaggcc 181 acccacacca gagttggtta aggcaattcc cccaccccca cccaacgggg aagatgaacc 241 aatcatttct tacaacgtca aagggggtgt ttctggtttg cctgagctct caactgtcac 301 ccaactggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacag 361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggacgggg agatctacca 421 ttatggcttg tacgtagaac gagggttagt gctcggcgtg cacaaaccac cagcagcaat 481 cagccttgct aagattgagc tgaccccctt gtctttgtat tggagaccag tgtacacccc 541 acagtacctc atttcccctg acactctcag aaagttgcat ggggagacat tcccttatac 601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga acgattcatg 661 gctgaacaga aggatgatac agaggacaac aggcttcttc cgaccctatc aggattggaa 721 caggaaaccc ctccccacga tggatgattc caaagtgaaa aaggtggcca atgttgtcct 781 atgtgctctc tcatcattgt tcacaagacc aattaaggac atcattggga agttaaaacc 841 cctaaacatt ctcaatatct tagccacatg tgattggact tttgcaggca tagtagaatc 901 cctgatcctt ttggctgaac tttttggagt tttctggaca cccccagatg tgtctgcgat 961 gatcgctccc ttactgggtg attatgaact acagggaccc gaggacctcg ctgtggaact 1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg 1081 caagatgctt tcttctgctg cttcaaccct gagggcatgt aaagatctcg gtgcatatgg 1141 gttggagatc ctcaaattgg ttatgaaatg gtttttccca aagaaagaag agaaaaacga 1201 attggcaatg gtgagatcca tcgaggatgc agtgctagac cttgaagcca ttgagaacaa 1261 ccatatgaca gctctactca aggataaaga cagccttgca acctacatga ggactcttga 1321 catggaggag gagaaggcga gaaaactttc caccaagtct gcctctccgg atattgtggg 1381 tacgataaat gccctactgt caaggattgc agctgcccgg tctctagtgc acagggctaa 1441 ggaagagctg tcaagcaggc cccgaccggt cgttgtaatg atttcaggga aaccgggtat 1501 agggaaaacc catctagcta gagagttggc gaagaagatc gcctccacac tcacgggtga 1561 ccagagggtg ggtcttatcc cacgtaacgg ggtcgaccac tgggatgcat acaaaggtga 1621 aagagtcgtt ctctgggacg actacgggat gagcagccct gtccacgacg ccctcagact 1681 ccaggagctc gctgacacct gtcctctcac actcaactgc gacaggattg agaacaaagg 1741 taaagtcttt gacagtgacg tcataataat aaccaccaat ttggccaacc cagcgccact 1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttcctcgtct atgctgatgc 1861 tcccgaagtt gagaaggcta agcgggactt cccaggccaa ccagacatgt ggaaagacac 1921 cttcaaacct gacttctcac acataaaatt ggcattagcc ccgcaaggag gttttgacaa 1981 gaatggtaac actcctcatg ggaagggagt catgaagacc ctcactgccg gttccctcgt 2041 tgcccgagca tcagggctcc tccacgagag attggacgag tatgagctgc agggcccaac 2101 tcccacaaca ttcaacttcg accgcaacaa ggtgcttgct tttaggcagc ttgctgctga 2161 aaacaagtac ggtctagttg acacaatgag ggtcgggtca caactcaaga atgtcaaaac 2221 tatgacagaa ctcaaacagg ccctcaagaa catctcagtc aagaaatgtc agcttgtgta 2281 cggtgggggc acatacacac tcgaatctga tggcagaggc aatgtgcatg tcgaaaaggt 2341 gaacaacacc agtgtgcaaa ctaacaacga gctctccggg gttttgcacc atctcaggtg 2401 tgctagaatc aggtactatg ttaagtgtgt tcaggaagct ctctactcca tcttacaaat 2461 tgccggggct gcattcatca ccacgcgcat tgctaagcgc acgaacatac aaaacctctg 2521 gtccaaacca caagcagaag atctagagga gactaacaac gaggagggtt gtccaaaacc 2581 taaaagtgat gaagaatttg tcgtctcctc tgatgacatc aaaactgagg gtaagaaagg 2641 aaagaacaag actggccgtg gtaagaagca cacggccttt tccggcaaag gactcagtga 2701 tgaggagtac gatgagtata agagaatcag ggaagagaga aatggtaagt actccataga 2761 ggaataccta caggacagag acaaatacta tgaggaggtg gccatagcca gggcaactga 2821 ggaagatttc tgtgaagaag aggaggccaa aatccggcag aggatattca gaccaacaag 2881 gaaacaacgc aaagaggaaa gagcttctct tggtttggtt acaggttctg agatcaggaa 2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gccgatgatg acaggagtgt 3001 cgactacaat gagaaactta gtttcgaggc tccaccaagt atttggtcac gaatagtcaa 3061 ctttggctca gggtggggct tttgggtctc gcccagcctc ttcataacat caacccatgt 3121 cattccccag ggcgcgcagg agttctatgg agtgcccatc aaacaaatac aaattcacaa 3181 gtcaggtgag ttctgccggc ttaggttccc aaaaccaatc aggacagatg ttacaggtat 3241 gatcttggag gaaggtgctc cagaaggcac tgttgccaca cttctcatca agagaccaac 3301 tggggaactc atgcccttgg cagccaggat gggcacccac gccaccatga gaattcaggg 3361 tcgcactgtt ggtggacaga tgggtatgct actcacaggg tctaacgcta agagcatgga 3421 tttgggcaca actcctggcg attgtggctg tccctacatc tacaagagag ggaacgacta 3481 cgtggtcatt ggagttcaca ctgccgccgc gcgtggagga aacaccgtca tctgtgcaac 3541 ccaaggaaac gagggtgagg ccatgctaga gggtggtgat aacaagggaa cttattgtgg 3601 agcaccaata ttaggccctg gaaatgcccc caaactcagc accaaaacca aattctggag 3661 gtcttccacc acccccctgc cacccggaac ctatgagcca gcctatctgg gtggcaagga 3721 ccctagagtg aaaggtggcc cctcactgca acaggtaatg agagaccaac taaaaccatt 3781 cactgagccc agaggcaaac cacccaaacc aagtgtgcta gaagctgcca agaagactat 3841 aatcaatgtg cttgaacaaa caatagaccc acctcaaaaa tggacatacg cacaagcgtg 3901 tgcatcacta gacaagacta cttccagcgg tcaccctcac cacatgcgga agaacgattg 3961 ctggaatggg gaatctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat 4021 gtttgaggaa ggaaagaaca tgactccagt atacacagga gctctgaaag atgagctagt 4081 caaaactgac aagatctatg gggtagtcaa gaagaggctc ctgtggggtt cagacctatc 4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgagctca aggcccattg 4201 cgtcacacta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga 4261 gaaacactcc agatacaaat atcattatga tgcagattac tcccgctggg actcaacaca 4321 acaaagagca gtgctagccg cagccctgga aataatggtc aaattctcac cagaacccca 4381 tctggcccaa gtggttgcag aagacctttt gtcccccagt gtgatggatg tgggtgattt 4441 caagatatca atcaacgagg gattgccctc tggtgtccct tgcacttcac aatggaactc 4501 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga 4561 catcatccag gcgaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga 4621 catcaaatta gatccagaga aattgacagc aaaactgagg gaatacgggc ttaaaccaac 4681 ccgccctgac aaaacggagg gacccttaat tgtctctgaa gatttgaatg gcctgacctt 4741 cctgcggaga acagtgaccc gcgacccggc cggatggttt ggcaaactgg accaaagttc 4801 aatactcagg cagatgtact ggaccagggg gccaaaccat gaagacccct ttgaaacaat 4861 gataccacac tcccaaagac ccatacaact gatgtcattg cttggtgaag ctgcattgca 4921 tggtccatca ttctacagta aaatcagcaa attggtcatc tcggaactga aagagggtgg 4981 aatggatttc tacgtgccca gacaagaacc aatgttcagg tggatgagat tctcagattt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttc gtgaatgaag atggcgtcga 5101 atgacgccgc tccatctaat gatggtgccg ccggcctcgt cccagagatc aacaatgagg 5161 caatggcgct agagccagtg gcgggtgcag cgatagcagc acccctcact ggtcagcaaa 5221 atataattga tccctggatt atgaataatt ttgtacaagc acctggtggt gaatttacag 5281 tgtcccccag aaattcccct ggtgaagtcc ttcttaattt ggaattgggc ccagaaataa 5341 atccctattt ggcccatctt gctagaatgt ataatggtta tgcaggtgga tttgaagtgc 5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gccatccccc 5461 ccaattttcc aattgacaat ttaagtgcag cacagatcac aatgtgccca catgtgattg 5521 tggatgtcag acagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aataacttct 5581 ttcattataa tcaagggtct gattcgaggt tacgcctaat tgcaatgcta tacacacctc 5641 ttagggcaaa caattctggg gatgatgtct ttactgtgtc ttgtagagtg ctaactagac 5701 ctagtcctga tttctcattt aatttccttg tgccacccac tgtggagtca aagacaaaac 5761 ccttttccct ccctatcctg actatctctg aaatgtccaa ttctaggttc ccagtaccaa 5821 ttgattccct acacaccagt cctactgaga atattgttgt tcagtgccaa aatgggcgcg 5881 tcacccttga tggtgagctg atgggcacca cccaactctt gcctagccaa atctgtgctt 5941 tcaggggcgt tctcactaga tcaacaagca gggccagtga ccaggccgac acagcaaccc 6001 ctagattgtt taattattat tggcatatac aattggataa tctaaatgga accccttatg 6061 atcctgcaga agacatacca ggccccctag ggacaccaga cttccgtggc aaagtctttg 6121 gcgtggccag ccagagaaat cctgatgcca cgactagggc acatgaagca aagatagaca 6181 ccacatctgg ccgcttcacc ccaaagctag gctcattaga gatatccact gaatctagtg 6241 attttgatca aaaccaacca acaagattca ccccagttgg cattggagtt gaccatgagg 6301 cagactttca gcaatggacc ctacccgact acgctggtca gttcacacac aacatgaact 6361 tagccccagc tgttgctccc aacttccctg gtgagcagct ccttttcttc cgctcacatt 6421 tgccatcttc tggtgggcga tccaacggga ttctagactg cctggttccc caagaatggg 6481 tacagcactt ctaccaagag tcagccccct ctcagtctca agtggccctg gttaggtatg 6541 ttaatcctga cactggtaga gtgttatttg aggccaagct acacaaatta ggtttcatga 6601 ctatagccaa gaatggtgat tctccaataa ctgtccctcc aaatggatac tttaggtttg 6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa 6721 ggattcaata atggctggag cttttatagc aggattggct ggtgatatgc taacaaatac 6781 tgtaggatct ttagttaatg caggagctaa tgctattaat caaacaattg attttgaaaa 6841 taataaatat ttgcaaaatg cttcttttaa tcatgataag gagatgttaa atgcgcaaat 6901 tgaggcaaca aagaagttac aggctgacat gattgctatc aaacaagggg ttttgaccgc 6961 tggcggcttc tctcctactg atgcagcccg tggggcaatt aatgccccca tgacaaaagt 7021 cctagattgg aatggaacga gatactgggc accaggtgcc acctccacaa cttcgatgtc 7081 gggtggcttt acacatcaaa ctgtgcacag atccacacca aattttaaaa cgaaccaggc 7141 ccccaaatcc acacccagca gtgggtcttc agtgaggtca aactcaaccc aaatcactag 7201 cctgagctca cactcgtccg ggtcgtctcg atccagcggg tctacagtca tcagctcaat 7261 accatcctct aacaggacta gggactgggt caaccaacaa aattttaatt tggaaccaca 7321 catgcctggg tctcttagga cagcttttgt cactccacca tctagtacgg cctctagctc 7381 aggcacagtc tcaactgtgc ccaaaaatgt tttggactcc tggacatctg cgtttaacac 7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa 7501 agattatttt aaatttggtt taaaattagg tttaatttgg aatctttt //