Typing tool
|
Complete norovirus genomes
MH218732 | GII.3 | ||
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GII.P21 |
ORF1: 5..5104 ORF2: 5085..6731 ORF3: 6731..7495LOCUS MH218732 7548 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_93_03_12_2014, complete genome. ACCESSION MH218732 VERSION MH218732.1 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_93_03_12_2014" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="03-Dec-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="AWR17854.1" /translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARP KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLE ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKIELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLNRRMIQRTTGFFRPYQDWNKKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVLMISGKPGIGKTHLAREL AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTAGSLVARA SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLR CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEDLEETNNEEGC PKPKNDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEETKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRIVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATIKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPQRWTYAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL STMIRCARAFGGLMDELKAHCTTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP NHEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKVSRLVISELKEGGMDFYVPRQE 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="AWR17855.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP LGTPDFRGKVFGVASQRNPDATTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDQNQP TRFTPVGIGVDHEADFQQWTLPDYAGQLTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG GRSDGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" gene 6731..7495 /gene="ORF3" CDS 6731..7495 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17856.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANVINQTIDFENNKYLQNA SFNHDKEMLNAQIEATKKLQANMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS HSSGSSRSSGSTIINSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaaa gcaacaacga 61 caacgcaaaa tcttcaagtg acggagtatt atccaatatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agccgccccc gagtgacaaa ccaccaaaac ccccaagacc 181 acccacacca gagttggtta aggcaattcc ccctccccca cccaacgggg aagacgaacc 241 aatcatttct tacaacgtca aagggggtgt ttctggttta cctgagctct caactgttac 301 ccaactggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacag 361 agatgcaaag gaaccattga ctggaactat cctggagatg tgggacgggg agatctacca 421 ttatggctta tacgtagaac gagggttagt gctcggtgtg cacaaaccac cagcagcaat 481 cagccttgct aagattgagc tgaccccctt gtctttgtat tggaggccag tgtacacccc 541 acagtacctc atttcccctg acactctcag aaagttgcat ggggagacat tcccttatac 601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga acgactcatg 661 gctgaacaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggattggaa 721 caagaaaccc ctccccacga tggatgactc caaagtgaaa aaagtggcca atgttgtcct 781 atgtgctctc tcatcactgt tcacaagacc aattaaggac attattggga agttaaaacc 841 cctaaacatt ctcaacatct tagccacatg tgattggact tttgcaggca tagtagaatc 901 cctgatcctc ttggctgaac tttttggagt tttctggaca cccccagatg tgtctgcgat 961 gatcgctccc ttactgggtg attacgaact acagggaccc gaggacctcg ctgtggaact 1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg 1081 caagatgctt tcttctgctg cttcaaccct gagggcatgt aaagatctcg gcgcatatgg 1141 gttggagatt ctcaaattgg ttatgaaatg gtttttccca aagaaagaag agaaaaacga 1201 attggcaatg gtgagatcca tcgaggatgc agtgctagac cttgaagcca ttgagaacaa 1261 ccatatgaca gctctactca aggataaaga cagccttgca acctacatga ggactcttga 1321 catggaggag gagaaggcga gaaaactttc caccaagtct gcctccccgg atattgtggg 1381 tacgataaat gccctactgt caaggattgc agctgcccgg tctctagtgc acagggctaa 1441 ggaagagctg tcaagcaggc cccgaccggt tgttttaatg atttcaggga aaccgggtat 1501 agggaaaacc catctagcta gagagttggc aaagaagatc gcctccacac tcacaggtga 1561 ccagagagtg ggtcttatcc cacgtaacgg ggtcgaccac tgggatgcat acaaaggtga 1621 aagagtcgtt ctctgggacg actacgggat gagcagccct gtccacgacg ccctcagact 1681 ccaggagctc gctgacacct gtcctctcac actcaattgt gacaggattg agaacaaagg 1741 taaagtcttt gacagtgacg tcataataat aaccaccaat ttggccaacc cagcgccact 1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttcctcgtct atgctgatgc 1861 tcccgaagtt gagaaggcta agcgggactt cccaggccaa ccagacatgt ggaaagacac 1921 cttcaaaccc gacttctcac acataaaatt ggcattagcc ccgcaaggag gttttgacaa 1981 gaatggtaat actcctcatg ggaagggagt catgaaaacc ctcactgccg gttccctcgt 2041 tgcccgagca tcagggctcc tccacgagag attagacgag tatgagctgc agggcccaac 2101 tcccacaaca ttcaacttcg accgcaataa ggtgcttgct tttaggcagc ttgctgctga 2161 aaacaagtac ggtctagttg acacaatgag ggtcgggtca caactcaaga atgtcaaaac 2221 tatgacagaa ctcaaacagg ccctcaagaa catctcagtc aagaaatgtc agcttgtgta 2281 cggtgggggc acatacacac tcgaatctga tggcaagggc aatgtgcatg tcgagaaggt 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 taaaaatgat gaagaatttg tcgtctcctc tgatgacatc aaaactgagg gtaagaaagg 2641 aaagaacaag actggccgtg gtaagaagca cacagccttt tccagcaaag gactcagtga 2701 tgaggagtac gatgagtata agagaatcag ggaagagaga aatggtaagt actccataga 2761 ggaataccta caggacagag acaaatacta tgaggaggtg gccatagcca gggcaactga 2821 agaagatttc tgtgaagaag aggagaccaa aatccggcag aggatattca ggccaacaag 2881 gaaacaacgc aaagaggaaa gagcttctct tggtttggtt acaggttctg agatcaggaa 2941 gagaaaccca gatgacttta agcccaaagg gaaactatgg gctgatgatg acaggattgt 3001 tgactacaat gagaaactta gtttcgaggc cccaccaagc atctggtcac gaatagtcaa 3061 ctttggctca gggtggggct tttgggtctc gcccagcctc ttcataacat caacccatgt 3121 cattccccaa ggcgcgcagg agttctttgg ggtgcccatc aaacaaatac aaattcacaa 3181 gtcaggtgag ttctgccggc ttaggttccc aaaaccaatc aggacagatg ttacaggcat 3241 gatcttggag gaaggtgctc cagaaggcac tgttgccaca cttctcatca agagaccaac 3301 tggggaactc atgcccttgg cagccaggat gggcacccac gctaccataa aaattcaggg 3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agagcatgga 3421 tttgggcaca actcctggcg attgtggttg tccctacatc tacaagagag ggaacgacta 3481 cgtggtcatt ggagttcaca ctgccgccgc tcgtggagga aacaccgtca tctgtgcaac 3541 ccaaggaaac gagggtgagg ccatgctaga gggtggtgat aacaagggaa cttattgtgg 3601 agcaccaata ttaggccctg gaagtgcccc caaactcagc accaaaacca aattctggag 3661 gtcttccacc acccccctgc cacccggaac ctatgagcca gcctatctgg gtggcaagga 3721 ccctagagtg aaaggtggcc cctcactgca acaggtaatg agagaccaac taaaaccatt 3781 cactgaaccc agaggcaaac cacccaaacc aagtgtgcta gaagctgcca agaagactat 3841 aatcaatgtg cttgaacaaa caatagaccc acctcaaaga tggacatacg cgcaagcgtg 3901 tgcatcacta gacaagacca cttccagcgg tcaccctcac cacatgcgga agaacgattg 3961 ctggaatggg gaatctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat 4021 gtttgaggaa ggaaagaaca tgaccccagt atacacagga gctctgaaag atgagctagt 4081 caagactgac aagatctatg gggtagtcaa gaagaggctc ctgtggggtt cagacctatc 4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgagctca aggcccattg 4201 caccacacta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga 4261 gaaacactcc agatacaaat accattatga tgcagattac tcccgctggg actcaacaca 4321 acaaagagca gtgctagccg cagccctgga aataatggtc aaattctcac cagaacccca 4381 tctggcccaa gtggttgcag aagacctttt gtcccccagt gtgatggatg taggtgattt 4441 caagatatca atcaacgagg gattgccctc tggtgtccct tgcacttcac aatggaactc 4501 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga 4561 catcatccag gcgaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga 4621 catcaaatta gacccagaga aattgacagc aaaactgagg gaatacggac ttaaacctac 4681 ccgccctgac aaaacagagg gacccttaat tatctctgaa gatcttaatg gcctgacctt 4741 cctgcggaga acagtgaccc gcgacccggc cggatggttt ggcaaactgg accaaagttc 4801 aatactcagg cagatgtact ggaccagggg gccaaaccat gaagacccct ttgaaacaat 4861 gataccacac tcccaaagac ccatacaact gatgtcacta cttggtgaag ctgcattgca 4921 tggtccatca ttctacagta aagtcagcag attggtcatt tcggaactga aagagggtgg 4981 aatggatttt tacgtgccca gacaagaacc aatgttcagg tggatgagat tctcagattt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 atgacgccgc tccatctaat gatggtgccg ccggcctcgt cccagagatc aacaatgagg 5161 caatggcgct agaaccagtg gcgggtgcag cgatagcagc acccctcact ggtcagcaaa 5221 atataattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gagtttacag 5281 tgtcccccag aaattcccct ggtgaagtcc ttctcaattt ggaactgggc ccagaaataa 5341 atccctattt ggcccatctt gctagaatgt acaatggtta tgcaggtgga tttgaagtgc 5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gccatccccc 5461 ccaattttcc aattgataat ttaagtgcag cacagatcac aatgtgccca catgtgattg 5521 tggatgtcag acagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aataacttct 5581 tccattataa tcaagggtct gattcgaggt tacgcctaat tgcaatgcta tacacacctc 5641 ttagggcaaa caattctggg gatgatgttt ttactgtgtc ttgtagagtg ctaactagac 5701 ctagtcctga tttctcattc aattttcttg 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 tctcaccaga tcaacaagca gagccagtga tcaggccgat acagcaaccc 6001 ctagattgtt taattattat tggcatatac aattggataa tctaaatgga accccttatg 6061 atcctgcaga agatatacca 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 acagtggacc ctacccgact acgctggtca gctcacacat aacatgaact 6361 tagccccagc tgttgctccc aacttccctg gtgagcagct ccttttcttc cgctcacatt 6421 tgccatcttc tggtgggcga tccgacggga ttctagactg cctggttccc caagaatggg 6481 tacagcactt ctaccaagag tcagccccct ctcagtctca agtggccctg gttaggtatg 6541 ttaatcctga cactggtaga gtgttatttg aggccaagct acacaaatta ggttttatga 6601 ctatagccaa gaatggtgat tctccaataa ctgtccctcc aaatggatat tttaggtttg 6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa 6721 ggattcaata atggctggag cttttatagc aggattggct ggtgacatgc ttacaaatac 6781 tgtaggatct ttagttaacg caggagctaa tgttatcaat caaacaattg attttgaaaa 6841 taataaatat ttgcaaaatg cttcttttaa ccatgataag gagatgttga atgcacaaat 6901 tgaggcaaca aagaagttac aggctaacat gattgctatc aaacaagggg ttttgaccgc 6961 tggcggcttc tcccctactg atgcagcccg tggggcaatt aatgccccca tgacaaaagt 7021 cctggattgg aatggaacga gatactgggc accaggtgcc acctccacaa cctcgatgtc 7081 gggtggcttt acacatcaaa ctgtgcacag atccacacca aattttaaaa cgaaccaggc 7141 ccccaaatcc acacccagca gtgggtcttc agtgaggtcg aactcaaccc aaatcactag 7201 cctgagctca cactcgtccg ggtcgtctcg atccagcggg tctacaatta tcaactcaat 7261 accatcctct aacaggacta gggactgggt caaccaacaa aacttcaatt tggaaccaca 7321 catgcctgga tctcttagga cagcttttgt cactccacca tctagtacag cctctagctc 7381 aggcacagtc tcaactgtgc ccaaaaatgt tttggactcc tggacatctg cgtttaacac 7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa 7501 agattatttt aaatttggtt taaaattagg tttaatttgg aatctttt //