Typing tool
|
Complete norovirus genomes
MH218598 | GII.3 | ||
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GII.P21 |
ORF1: 5..5104 ORF2: 5085..6731 ORF3: 6731..7495LOCUS MH218598 7548 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_127-3_24_03_2015, complete genome. ACCESSION MH218598 VERSION MH218598.1 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_127-3_24_03_2015" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="24-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="AWR17452.1" /translation="MKMASNDASAAAAANSNNDNAKSSSDGVLSNMAVSLKRALGARS KQPPPKDKPSRPPRPPTPELVKSIPPPPPNGEDEPIISYNAEKGVSGLPELTTVTQLE ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRATGFFRPYQDWNRKPLPTMDDSKVKKVANIVLCALSALFTRPIKDIIGK LKPLNVLNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEKSELAMVRSIEDAVLDLEAIENNHITALLKDKDSLATYMRTLDMEEEKARKLST KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL AKKIASSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK AKRDFPGQPDMWKDTFKPDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTASSLVARA SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM TELKQALNNIKVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTNVQTNNELSGALHHLK CARIRYYVKCVQEALYSILQIAGAAFITTRIARRTNIQNLWSKPQVENLEETNNEEGC PKPKNDEEFVISSNDITTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKNMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAMLEGGDNKGTYCGAPILG PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKRTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW NGETFTGKLADQASKANLMYEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTIKLK EYGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTKGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE 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="AWR17453.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNNFFHYNQGSDPRLRLIAMLYTPLRANSSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKVKSFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGST QLLPSQICAFRGTLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPCP LGIPDFQGKVFGVASQRNPDTTTRAHEAKIDTKSGRFAPKLGSLEISTESGDFDQNKP TRFTPVGVGVDHEADFQQWALPDYAGQFTHNMHLAPAVAPNFPGEQLLFFRSQLPSSG GRSNGILDCLVPQEWVQHFYQESAPSQSLVALVRYVNPDTGRVLFEAKLHKLGFMTIA KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRNQ" gene 6731..7495 /gene="ORF3" CDS 6731..7495 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17454.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNV SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSMSGGFTNQIVHRSTPNLKTGQAPKPAPSSGSSVKSNSTQVTSLSS HSSGSSRSSGSTVVSSIPSTNRTRDWVNQQNLNLEPYMPGSLRTAFVTPPSSTASSSG TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNA" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaca gcaacaacga 61 caacgcaaaa tcttcaagtg acggcgtact ttctaatatg gccgtctctc ttaaacgggc 121 cctcggggcg cggtctaaac agccgccccc gaaggacaaa ccatcaaggc ccccaagacc 181 acccacacca gaattggtta aatcaatccc ccctccccca cccaacgggg aggacgaacc 241 aatcatttct tacaacgctg aaaagggtgt ctctggtttg cctgaactca caactgtcac 301 ccaactggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacag 361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggatgggg agatctacca 421 ttatggctta tacgtggaac gagggttagt gctaggtgta cacaaaccac cagcagccat 481 cagccttgct aaggttgagc tgaccccttt gtctttgtat tggagaccag tgtacacccc 541 acaatatctc atctcccctg acactctcag aaagttgcat ggggagacgt tcccttatac 601 agcctttgac aacaactgtt atgccttctg ctgttgggta cttgacttga acgactcatg 661 gctgagcaga aggatgatac aaagggcaac aggattcttc cgaccctacc aggactggaa 721 caggaaaccc ctccccacga tggatgactc caaagtgaaa aaggtggcca atattgtcct 781 ctgtgccctc tcagcattgt ttacaagacc aattaaggac attattggga agttgaaacc 841 cctaaacgtc ctcaacatcc tagccacatg tgattggact tttgcaggca tagtagaatc 901 cctgatcctt ttggctgaac tgtttggagt tttctggaca cccccagatg tgtctgcaat 961 gattgctccc ttactgggtg attacgagct gcagggaccc gaggacctcg ctgtggaact 1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg 1081 caaaatgctt tcatcagctg cctcaaccct tagggcatgc aaagatctcg gtgcatatgg 1141 gttggagatc ctcaagttgg tcatgaaatg gtttttccca aagaaagaag agaaaagcga 1201 actggcaatg gtgagatcca ttgaggatgc agtgctagat cttgaggcca ttgagaacaa 1261 ccatataaca gctctactca aggacaaaga cagccttgca acctacatga ggactcttga 1321 catggaggag gagaaggcga ggaaactttc caccaagtct gcctcgccgg acattgtggg 1381 cacaataaat gccttactat caaggattgc agctgcccga tctctagtgc acagggccaa 1441 ggaggagctg tcaagcaggc cccgaccggt cgttgtgatg atttcaggga gaccaggtat 1501 agggaaaacc catttagcta gagagttggc aaagaagatc gcctcctcac tcacaggtga 1561 ccagagggtg ggtcttatcc cacgcaacgg agttgaccac tgggatgcat acaaaggtga 1621 aagagttgtt ctctgggacg actacgggat gagcaaccct atccacgacg ccctcagact 1681 tcaggagctc gctgatacct gtcctcttac actcaactgt gacaggattg agaacaaagg 1741 caaagtcttt gacagtgacg ccataataat aaccaccaat ttagccaacc cagcgccact 1801 ggattacgtc aactttgaag cctgctcaag acgcatagac ttcctcgtct atgctgatgc 1861 ccctgaggtt gagaaggcta aacgggactt tccaggccaa ccagacatgt ggaaagacac 1921 cttcaaacct gatttctcac acataaaact gacattagct ccgcaaggag gttttgataa 1981 gaatggtaac actcctcatg ggaagggtgt catgaagacc ctcactgcca gttccctcgt 2041 tgcccgagca tcagggcttc tccacgagag attagacgaa tatgagctgc agggcccaac 2101 ccccacaaca ttcaacttcg accgcaataa ggtgcttgct tttaggcaac ttgctgctga 2161 aaacaagtac ggtcttgttg acacaatgag agtcggatca cagctcaaga atgtcaagac 2221 catgacggaa cttaagcagg ctctcaataa catcaaagtc aagaagtgtc agcttgtgta 2281 tggtggtggc acgtacacac ttgaatctga tggcaaaggc aatgtgcatg tcgagaaggt 2341 gaacaacacc aatgtgcaaa ctaacaacga gctctccgga gctttgcacc atctcaagtg 2401 tgccagaatc aggtactatg ttaagtgtgt ccaggaagct ctctactcca tcttgcaaat 2461 tgccggggct gcattcatca ctacgcgcat tgcaaggcgc acaaacatac aaaacctctg 2521 gtccaaacca caagtagaaa atctggagga gactaacaac gaggagggct gtccaaaacc 2581 taaaaatgat gaagagtttg tcatctcctc taatgacatc acaaccgagg gcaagaaagg 2641 aaagaacaag actggccgtg gcaagaaaca cacagccttt tccagcaaag ggctcagtga 2701 tgaggagtac gatgagtata aaagaatcag agaagagaga aatggcaagt actccataga 2761 ggaataccta caggacagag acaaatacta tgaggaggtg gccatagcca gggcaactga 2821 ggaagacttc tgtgaagaag aggaggcaaa aatccggcaa aggatattta gaccaacaag 2881 gaaacaacgc aaagaggaaa gggcctctct tggtttggtt acaggttctg agatcaggaa 2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gccgatgatg acaggagtgt 3001 tgattacaat gagaaactta gttttgaggc tccaccaagc atttggtcac gaatagtcaa 3061 ctttggctca gggtggggtt tttgggtctc gcccagcctc ttcataacat caacccatgt 3121 cattccccaa ggcgcacagg agttctttgg agtgcccatc aaacaaatac aaattcacaa 3181 atcaggtgag ttctgccgac tcaggttccc aaaaccaatc aggacagatg tcacaggtat 3241 gatcttggag gaaggtgctc cagaaggcac cgttgccaca cttctcatca agagaccaac 3301 tggggaactc atgcccttgg cagccagaat gggcacccac gcgaccatga aaatccaggg 3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaatgcta agaatatgga 3421 cctgggcaca actcctggcg attgtggctg tccctatatc tacaagagag ggaatgacta 3481 cgtggtcatt ggagtccaca ctgctgccgc tcgtggagga aacactgtca tctgtgcaac 3541 ccaaggaagc gagggtgagg ccatgttaga aggtggtgac aacaagggaa cttattgtgg 3601 agcaccaata ttaggtcctg gaaatgcacc caaactcagc accaaaacca aattctggag 3661 gtcttccacc acccctttgc ctcccgggac ctatgagcca gcttatctgg gcggcaagga 3721 tcctagagta aaaggtggcc cctcactgca acaggttatg agggaccaac taaaaccatt 3781 cactgagccc agaggtaaac cacccaaacc aagcgtgcta gaagctgcca agagaactat 3841 aatcaatgtg cttgaacaaa caatagaccc accccaaaaa tggacatacg cacaggcgtg 3901 tgcatcacta gacaagacca cttctagcgg ccaccctcac cacatgcgga agaacgattg 3961 ctggaatggg gagaccttca caggaaaact ggcagaccaa gcatcaaagg ctaacctaat 4021 gtatgaggaa ggaaagaaca tgaccccagt ttacacagga gctctaaaag atgagctagt 4081 caagactgat aagatctatg gcaaaatcaa gaagagactc ctgtggggtt cagacctatc 4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgaactca aggcccattg 4201 cgtcacgcta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga 4261 gaaacattcc agatataaat atcattatga tgcagattac tctcgctggg actcaacaca 4321 acaaagagcg gtgctggctg cagccctgga aataatggtc aaattctcac cagaacccca 4381 tctggcccag gtggttgcag aggacctctt gtcccccagt gtaatggatg tgggtgattt 4441 caagatatca atcaacgagg gattaccctc tggtgttccc tgcacctcac aatggaactc 4501 cattgcccac tggctcctca cactatgtgc actgtctgaa gtaacagacc tgtcccctga 4561 catcatccag gcaaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga 4621 catcaaacta gacccagaga aactaacaat aaaattgaag gaatacgggc tgaaaccaac 4681 ccgccctgac aaaacagaag gacccttaat tatctctgaa gacttggatg gcctgacctt 4741 cttacgtaga acggtgaccc gtgatccggc cgggtggttt ggcaaactgg accaaagttc 4801 aatactcagg cagatgtact ggaccaaggg accaaaccat ggggacccct ctgaaacaat 4861 gataccacac tcccaaagac ccatacaact gatgtcattg ttgggtgaag ctgcattgca 4921 tggtccatcg ttctacagca aaatcagtaa attggtcatc tcagaattga aagagggtgg 4981 aatggatttt tacgtgccca gacaagagcc aatgttcagg tggatgagat tctcagactt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 atgacgccgc tccatctaat gatggtgccg ccggcctcgt cccagagatc aacaatgagg 5161 caatggcgct agagccagtg gcgggtgcag cgatagcagc gcccctcact ggtcagcaaa 5221 atataattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gaatttacag 5281 tgtcccctag aaattcccct ggtgaagttc ttctaaattt ggaattgggc ccagaaataa 5341 acccctattt ggcccatctt gccagaatgt ataatggtta tgcaggtgga tttgaagtgc 5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gctattcccc 5461 ccaactttcc aattgacaac ctaagtgcgg cacagatcac aatgtgtcca catgtgattg 5521 tggatgtcag gcagctggaa ccagtcaacc tcccgatgcc tgacgttcgc aacaacttct 5581 ttcattacaa tcaagggtct gatccgagat tgcgcctaat tgcaatgctg tatacacctc 5641 ttagggcaaa cagttctgga gatgatgttt ttactgtgtc ttgcagagtg ctaactagac 5701 ctagccctga tttttcattt aatttccttg tgccacctac tgtggagtca aaggtaaaat 5761 cattttcact ccctattctg actatctctg aaatgtccaa ttctaggttc ccagtaccaa 5821 ttgattctct gcacactagt cccactgaga atattgttgt ccagtgtcag aatgggcgcg 5881 ttacccttga tggtgagttg atgggctcca cccaactctt acctagccaa atttgtgctt 5941 tcaggggcac gctcaccaga tcaacaagca gggccagtga ccaggccgac acagcaaccc 6001 ccagattgtt taattattat tggcatatac aattggataa tctaaatgga actccttatg 6061 accctgcaga agatatacca tgccccttag ggataccaga tttccagggc aaagtctttg 6121 gcgtggccag ccagagaaat cctgacacca caactagggc acatgaagca aagatagaca 6181 caaaatctgg ccgtttcgcc ccaaaactag gttcattaga gatttccact gagtctggtg 6241 attttgatca aaacaaacca acaagattca ccccagttgg tgttggggtt gaccatgagg 6301 cagactttca acaatgggct ctccccgact atgctggtca gttcacccac aatatgcact 6361 tagccccagc tgttgctccc aacttccctg gtgagcagct ccttttcttc cgctcacagt 6421 tgccatcctc tggtgggcga tccaacggga tcctggactg cctggtcccc caagaatggg 6481 tacagcattt ctaccaagaa tcagccccct cccaatctct agtggccctg gttaggtatg 6541 tcaaccctga cactggcaga gtgttattcg aggccaagtt gcacaaatta ggtttcatga 6601 ctatagccaa gaatggtgat tctccaataa ctgtccctcc aaatggatac tttaggtttg 6661 aatcttgggt gaaccccttt tatacacttg cccccatggg aacagggaat gggcgtagaa 6721 ggaatcaata atggctggag cttttatagc aggattggct ggtgatatgc tcacaaacac 6781 tgtaggatct ttagttaatg caggggctaa tgctattaat cagacaattg attttgaaaa 6841 taataaatat ttgcagaatg tttcttttaa tcatgataag gagatgttaa atgcacaaat 6901 tgaggcaaca aagaggttac aggctgacat gattgctatc aaacaagggg ttttgaccgc 6961 tggcggcttc tcccctactg atgcagcccg cggggcaatt aatgccccca tgacaaaagt 7021 cctagattgg aacgggacga gatactgggc accaggcgcc acctccacaa cctcgatgtc 7081 gggtggcttc acaaatcaaa tcgtgcacag gtccacacca aatcttaaaa caggccaggc 7141 tcccaaaccc gcacccagca gtgggtcttc agtgaagtca aattcaaccc aagtcaccag 7201 cctgagttca cactcgtccg ggtcgtctcg atccagcggg tctacagttg tcagctcaat 7261 accatccact aacaggacta gggactgggt caaccaacaa aatctcaatt tggaaccata 7321 tatgcctgga tctcttagga cagcttttgt cactccacca tctagtacag cctctagctc 7381 aggcacagtc tcaactgtgc ccaaaaatgt tttggactcc tggacatctg cgtttaacac 7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg cttagtgaaa 7501 agattatttt aaatttgatt taaaattagg tttaatctgg aatctttt //