Typing tool
|
Complete norovirus genomes
MH218600 | GII.3 | ||
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GII.P21 |
ORF1: 5..5104 ORF2: 5085..6731 ORF3: 6731..7495LOCUS MH218600 7548 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_129_16_03_2015, complete genome. ACCESSION MH218600 VERSION MH218600.1 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_129_16_03_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="16-Mar-2015" /note="genotype: GII.P21_GII.3" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17458.1" /translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARP KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLE ENSTAFSVPPLSQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGVGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEERNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARA SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGALHHLR CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQVEDLEEINSEEGC PKPKNDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPNVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW NGDSFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFRISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTKGP 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="AWR17459.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP LGTPDFRGKVFGVASQRNPDATTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDQNQP TRFTPVGVGVDREADFEQWALPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" gene 6731..7495 /gene="ORF3" CDS 6731..7495 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17460.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA SFNHDKEMLNAQIEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSMSGGFTHQSVHRSTPNFKTNQAPKPTPSSGSSVRSDSTQITSLSS HSSGSSRSSGSTVVSSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG TVSTVPKNILDSWTSAFNTRRQPLFAHLRRRGESNA" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaaa gcaacaacga 61 caacgcaaaa tcttcaagtg acggagtatt atctaatatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agccgccccc gagtgacaaa ccaccaaaac ccccaagacc 181 acccacacca gagttggtta aggcaattcc ccctccccca cccaacgggg aggacgaacc 241 aatcatttct tacaacgtca aagggggtgt ttctggtttg cctgaactct caactgtcac 301 ccaactggaa gagaactcta cagcattcag tgttccccct cttagtcaga gggagaacaa 361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggacggag aaatctacca 421 ttatggctta tacgtagaac gggggttagt gctcggtgta cacaaaccac cagcagccat 481 cagccttgct aaagttgagc tgaccccctt gtctttgtat tggagaccag tgtacacccc 541 acagtacctc atttcccctg acactctcag aaagttgcat ggggagacgt ttccttatac 601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga acgattcatg 661 gctgaacaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggattggaa 721 caggaaaccc ctccccacga tggatgactc caaagtgaaa aaggtggcca atgttgtcct 781 atgcgctctc tcatcattgt tcacaagacc aattaaggac attattggga aattaaaacc 841 cctaaacatt ctcaacatct tagccacatg tgactggact tttgcaggca tagtagaatc 901 cctgatcctt ttggctgaac tttttggagt tttctggaca cccccagatg tgtctgcgat 961 gatcgctccc ttactgggtg attatgaact acagggaccc gaggacctcg ctgtggaact 1021 cgtacccgta gtaatgggag gggtaggttt ggtgctggga ttcaccaaag agaaaatcgg 1081 caagatgctt tcttctgctg cttcaaccct gagagcatgt aaagatctcg gtgcatatgg 1141 gttggagatc ctcaaattgg ttatgaaatg gtttttccca aagaaagaag agagaaacga 1201 attggcaatg gtgagatcca tcgaggatgc agtgctagac cttgaagcca ttgaaaacaa 1261 ccacatgaca gctctactca aggataaaga tagccttgca acctacatga gaactcttga 1321 catggaggag gagaaggcga gaaaactttc caccaagtct gcctctccgg atattgtggg 1381 cacgataaat gccctactgt caaggattgc agctgcccgg tctctagtgc acagggctaa 1441 ggaggagctg tcaagtagac cccgaccggt cgttgtaatg atttcaggga aaccgggtat 1501 agggaaaacc catctagcta gagaattggc aaagaagatc gcctccacac tcacaggtga 1561 ccagagggtg ggcctaatcc cacgcaacgg ggtcgaccac tgggatgcat acaaaggtga 1621 aagagtcgtt ctctgggacg actacgggat gagcagccct gtccacgacg ccctcagact 1681 tcaggagctc gctgacacct gtcctctcac actcaactgt gacaggattg agaacaaagg 1741 taaagttttt gatagtgacg tcataataat aaccaccaat ttggccaacc cagcaccact 1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttcctcgtct atgctgatgc 1861 tcctgaagtt gagaaggcta agcgggactt cccaggccaa ccagacatgt ggaaagacac 1921 cttcaaaccc gacttctcac acataaaatt ggcattagcc ccgcaaggag gttttgacaa 1981 gaatggtaac actcctcatg ggaagggagt catgaagacc ctcactgcca gttccctcgt 2041 tgcccgagca tcagggctcc tccacgagag attagacgag tatgagctgc agggcccaac 2101 tcccacaaca ttcaacttcg accgcaacaa ggtgcttgct tttaggcagc ttgctgctga 2161 aaacaagtac ggtcttgttg acacaatgag ggtcgggtca caactcaaga atgttaaaac 2221 tatgactgaa ctcaagcagg ccctcaagaa catctcagtc aagaaatgtc agcttgtgta 2281 cggtgggggc acatacacac ttgaatctga tggcaaaggt aatgtgcatg tcgaaaaggt 2341 gaacaacacc agtgtgcaaa ctaacaacga gctctccggg gctttgcacc atctcaggtg 2401 tgctagaatc aggtactatg ttaagtgtgt tcaggaagct ctctactcca tcttacaaat 2461 tgccggggct gcattcatca ccacgcgcat tgcaaagcgc acaaacatac aaaacctctg 2521 gtccaaacca caagtggaag atctagagga aattaacagc gaggagggtt gtccaaaacc 2581 taaaaatgat gaagaatttg ttgtctcctc tgatgacatc aagactgagg gtaagaaagg 2641 aaagaacaag actggccgtg gtaagaagca cacagccttt tccagcaaag gactcagtga 2701 tgaggagtac gatgagtata agagaatcag ggaagaaaga aatggtaagt actccataga 2761 ggaataccta caggatagag acaaatacta tgaagaggtg gccatagcca gggcaactga 2821 ggaagatttc tgtgaagaag aggaggccaa aatccggcag aggatattca gaccaacaag 2881 gaaacaacgc aaagaggaaa gagcttctct tggtttggtt acaggctctg agatcaggaa 2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gctgatgatg acaggagtgt 3001 tgactacaat gagaaactta gtttcgaggc tccaccaagc atttggtcac gaatagtcaa 3061 ctttggctcg gggtggggct tttgggtctc gcccagcctc ttcataacat cgacccatgt 3121 cattccccaa ggcgcgcagg agttctttgg agtgcccatc aaacaaatac aaattcacaa 3181 atctggtgag ttctgccggc ttaggttccc gaaaccaatc aggacagatg ttacaggcat 3241 gatcttggag gaaggtgccc cagaaggcac tgttgccaca cttctcatca agagaccaac 3301 tggggaactc atgcccttgg cagccaggat gggcacccac gctaccatga aaattcaggg 3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agagcatgga 3421 tttgggcaca actcctggcg attgtggttg cccctatatc tacaagagag ggaacgacta 3481 cgtggtcatt ggagttcaca ctgccgccgc tcgtggagga aacaccgtca tctgtgcaac 3541 ccaaggaaac gagggtgagg ccatgctaga aggtggtgac aataagggaa cttactgtgg 3601 agcaccaata ttaggccctg ggaatgcccc caaactcagc accaaaacca agttctggag 3661 gtcttccacc acccccctgc cacccggaac ctatgagcca gcttatctgg gtggtaagga 3721 ccccagagtg aaaggtggcc cctcactaca acaggttatg agagaccaac taaaaccatt 3781 cactgagccc agaggcaaac cacccaaacc aaatgtgcta gaagctgcca agaagactat 3841 aatcaatgtg cttgaacaaa caatagaccc acctcaaaaa tggacatacg cacaagcgtg 3901 tgcatcacta gataagacca cttccagcgg tcaccctcac catatgcgga agaacgattg 3961 ctggaatggg gactctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat 4021 gtttgaggaa ggaaagaaca tgactccagt atacacagga gctctgaaag atgagctagt 4081 caagactgac aagatttatg 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 cctggcccag gtggttgcag aagacctttt gtcccccagt gtaatggatg tgggtgattt 4441 taggatatca atcaacgagg gattaccctc tggtgttcct tgcacttcac aatggaactc 4501 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga 4561 catcatccag gcgaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga 4621 catcaaatta gacccagaga aattgacagc aaagctgagg gaatacgggc ttaaaccaac 4681 ccgccctgac aaaacagagg gacccttaat tatctctgaa gatttgaatg gcctgacctt 4741 cttgcggaga acagtgaccc gcgacccggc cggatggttt ggcaaactgg accaaagttc 4801 aatactcaga cagatgtact ggaccaaggg gccaaaccat gaagacccct ttgaaacaat 4861 gataccacac tcccagagac ccatacaatt gatgtcatta cttggtgaag ctgcattgca 4921 cggtccatca ttctacagta aaatcagcaa attggtcatc tcagaactga aagagggtgg 4981 aatggatttt tatgtgccca gacaagaacc aatgttcagg tggatgagat tctcagattt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 atgacgccgc tccatctaat gatggtgccg ccggcctcgt cccagagatc aacaatgagg 5161 caatggcgct agagccagtg gcgggtgcag cgatagcagc acccctcact ggccagcaga 5221 atataattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gagttcacag 5281 tgtcccccag aaattcccct ggtgaagttc ttcttaattt ggaattgggc ccagaaataa 5341 atccctactt ggcccatctt gctagaatgt ataatggtta tgcaggtgga tttgaagtgc 5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gctattcccc 5461 ccaatttccc aattgataat ctaagtgcgg cacagatcac aatgtgccca catgtgattg 5521 tggatgtcag gcagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aataacttct 5581 ttcattataa tcaagggtct gattcaagat tacgcttaat tgcaatgtta tacacacctc 5641 ttagggcaaa caattctggg gatgatgttt ttactgtgtc ttgtagagtg ctgactagac 5701 ctagtcctga tttctcattc aatttccttg tgccacctac tgtggagtca aagacaaaac 5761 ccttttctct ccctatcctg actatctctg aaatgtccaa ttctaggttc ccagtaccaa 5821 ttgattctct gcacaccagt cctactgaga atattgttgt tcaatgccaa aatgggcgcg 5881 tcacccttga tggtgagttg atgggcacca cccaactctt gcctagccaa atctgtgctt 5941 tcaggggcgt tctcaccaga tcaacaagca gggccagtga ccaggccgat acagcaaccc 6001 ctagattgtt taattattat tggcatatac aattggataa tctaaatgga accccttatg 6061 atcctgcaga agatatacca ggccccctag ggacaccaga ttttcgtggc aaagtctttg 6121 gcgtggccag ccaaagaaat cctgatgcca cgactagggc acatgaagca aagatagaca 6181 ccacatctgg ccgcttcacc ccaaagctag gctcattaga gatatccact gaatctagtg 6241 actttgacca aaaccaacca acaagattca ccccagttgg cgttggagtt gaccgtgagg 6301 cagactttga acaatgggcc ctacccgatt acgctggtca gttcacacac aacatgaact 6361 tagccccagc tgttgctccc aacttccccg gtgagcagct ccttttcttc cgctcacatt 6421 tgccatcttc tggtgggcga tccaacggga ttctagactg cctggtcccc caagaatggg 6481 tacagcactt ctaccaagag tcagccccct ctcagtctca agtggctctg gttagatatg 6541 ttaaccctga cactggtaga gtgttatttg aggccaagct acacaaatta ggtttcatga 6601 ctatagccaa gaatggtgat tctccaataa ctgttcctcc aaatgggtat tttaggtttg 6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa 6721 ggattcaata atggctggag cttttatagc aggattggct ggtgacatgc tcacaaatac 6781 tgtaggatct ttagttaatg caggagctaa tgctattaat cagacaattg attttgaaaa 6841 taataaatat ttgcaaaatg cttcttttaa tcatgataag gagatgttga atgcacaaat 6901 tgaggcaaca aagaagttac aggctgacat gattgctatc aagcaagggg tcttgaccgc 6961 tggcggcttc tcccctactg atgcagcccg tggggcaatt aatgccccca tgacaaaagt 7021 cctagattgg aatggaacga gatactgggc accaggtgcc acctctacaa cctcgatgtc 7081 gggtggcttt acacatcaat ctgtgcacag atccacacca aattttaaaa cgaaccaggc 7141 tcccaaaccc acacccagca gtgggtcttc agtgaggtca gactcaaccc aaatcactag 7201 cctgagctca cactcgtccg ggtcgtctcg atccagcggg tctacagttg tcagctcaat 7261 accatcctct aacaggacta gggactgggt caaccaacaa aattttaatt tggaaccaca 7321 catgcctgga tctcttagga cagcttttgt cactccacca tctagtacag cctctagctc 7381 aggcacagtc tcaactgtgc ccaaaaatat tttggactcc tggacatctg cgtttaacac 7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg cttagtgaaa 7501 agattatttt aaatttggtt taaaattagg tttaatttgg aatctttt //