Typing tool
|
Complete norovirus genomes
MH218574 | GII.3 | ||
---|---|---|---|
GII.P21 |
ORF1: 5..5104 ORF2: 5085..6731 ORF3: 6731..7495LOCUS MH218574 7548 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GII isolate NORO_104_07_07_2014, complete genome. ACCESSION MH218574 VERSION MH218574.1 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_104_07_07_2014" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom" /collection_date="07-Jul-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="AWR17380.1" /translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARP KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLE ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAVS LAKIELTPLSLYWRPVYTPQYLISPDTLRKLHGEIFPYTAFDNNCYAFCCWVLDLNDS WLNRRMIQRTTGFFRPYQDWNRKPLPTTDDSKVKKVANVVLCALSSLFTRPIKDIIGK LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEE LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTAGSLVARA SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLR CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEDLEETNNEEGC PKPKNDEEFVVSSDDIKTEGRKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP 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="AWR17381.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP LGTPDFRGKVFGVASQRNSDTTTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDQNQP TRFTPVGIGVDHEADFQQWTLPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" gene 6731..7495 /gene="ORF3" CDS 6731..7495 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17382.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV" 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 aagacgaacc 241 aatcatttct tacaacgtca aagggggtgt ttctggtttg cctgagctct caactgtcac 301 ccaactggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacag 361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggacgggg agatctacca 421 ttatggctta tacgtagaac gagggttagt gctcggtgtg cacaaaccac cagcagcagt 481 cagccttgct aagattgagc tgaccccctt gtctttgtat tggagaccag tgtacacccc 541 acagtacctc atttcccctg acactctcag aaagttgcat ggggagatat tcccttatac 601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga atgattcatg 661 gctgaacaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggattggaa 721 caggaaaccc ctccccacga cggatgactc caaagtgaaa aaggtggcca atgttgtcct 781 atgtgctctc tcatcattgt tcacaagacc aattaaggac attattggga agttaaaacc 841 cctaaacatt ctcaacatct tagccacatg tgattggact tttgcaggca tagtagaatc 901 cctgatcctt ttggctgaac tttttggagt tttctggaca cccccagatg tgtctgcgat 961 gatcgctccc ttactgggtg attatgaact acagggaccc gaggaactcg ctgtggaact 1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg 1081 caagatgctt tcttctgctg cttcaaccct gagggcatgt aaagatcttg gtgcatatgg 1141 gttggagatc ctcaaattgg ttatgaaatg gtttttccca aagaaagaag agaaaaacga 1201 attggcaatg gtgagatcca tcgaggatgc agtgctagac cttgaagcca ttgagaacaa 1261 ccatatgaca gctctactta 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 aaagaagatc gcctccacac tcacaggtga 1561 ccagagggtg ggtcttatcc cacgtaacgg ggtcgaccac tgggatgcat acaaaggtga 1621 gagagtcgtt ctctgggacg actatgggat gagcagccct gtccacgacg ccctcagact 1681 ccaggagctc gctgacacct gtcctctcac actcaactgt gacaggattg agaacaaagg 1741 taaagtcttt gacagtgacg tcataataat aaccaccaat ttggccaacc cagcgccact 1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttcctcgtct atgctgatgc 1861 tcccgaagtt gagaaggcta agcgggactt cccaggccag ccagacatgt ggaaagacac 1921 cttcaaaccc gacttctcac acataaaatt ggcattagcc ccgcaaggag gttttgacaa 1981 gaatggtaac actcctcatg ggaagggagt catgaagacc ctcactgctg gttccctcgt 2041 tgcccgagca tcagggctcc tccacgagag attagacgag 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 tggtaaaggc aatgtgcatg tcgaaaaggt 2341 gaacaacacc agtgtgcaaa ctaacaacga gctctccggg gttttgcacc atctcaggtg 2401 tgctagaatc aggtactatg ttaagtgtgt tcaggaagct ctctactcca tcttacaaat 2461 tgccggggct gcattcatca ccacgcgcat tgctaagcgc acgaacatac aaaacctctg 2521 gtccaagcca caagcagaag atctagagga gactaacaac gaggagggtt gtccaaaacc 2581 caaaaatgat gaagaatttg tcgtctcctc tgatgacatc aaaactgagg gtaggaaagg 2641 aaagaacaag actggccgtg gtaagaagca cacagccttt tccagcaaag 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 gctgatgatg acaggagtgt 3001 tgactacaat gagaaactta gtttcgaggc tccaccaagc atttggtcac gaatagtcaa 3061 cttcggctca gggtggggct tttgggtctc gcccagcctc ttcataacat caacccatgt 3121 cattccccaa ggcgcgcagg agttctttgg agtgcccatc aaacaaatac aaattcacaa 3181 gtcaggtgag ttctgccggc ttaggttccc aaaaccaatc aggacagatg ttacgggcat 3241 gattttggag gaaggtgctc cagaaggcac tgttgccaca cttctcatca agagaccaac 3301 tggggaactc atgcccttgg cagccaggat gggcacccac gctaccatga aaattcaggg 3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agagcatgga 3421 tttgggcaca actcctggcg attgtggttg tccctacatc tacaagagag ggaacgacta 3481 cgtggtcatt ggagttcaca ctgccgccgc tcgtggagga aacactgtca 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 tggacatatg cacaagcgtg 3901 tgcatcacta gacaagacca cttccagcgg tcaccctcac catatgcgga agaacgattg 3961 ctggaatggg gaatctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat 4021 gtttgaggaa ggaaagaaca tgactccagt atacacagga gctctgaaag atgagctagt 4081 caagactgac aagatttatg gggtggtcaa gaagaggctc ctgtggggtt cagacctatc 4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgagctca aggcccattg 4201 cgtcacacta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga 4261 gaaacactcc agatacaagt accattatga tgcagattac tcccgctggg actcaacaca 4321 acaaagagca gtgctagccg cagccctgga aataatggtc aaattctcac cagaacctca 4381 tctggcccaa gtggttgcag aagacctttt gtcccccagt gtgatggatg tgggtgattt 4441 caagatatca atcaacgagg gactgccctc tggtgtccct tgcacttcac aatggaactc 4501 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga 4561 catcatccag gcgaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga 4621 catcaaatta gacccagaga aattgacagc aaaactgagg gaatacgggc ttaaaccaac 4681 ccgccctgac aaaacagagg gacccttaat tatctctgaa gatctgaatg gcctgacctt 4741 cctgcggaga acagtgaccc gcgacccggc cggatggttt ggcaaactgg accaaagctc 4801 aatactcagg cagatgtact ggaccagggg gccaaaccat gaagacccct ttgaaacaat 4861 gataccacac tcccagagac ccatacaact gatgtcatta cttggtgaag ctgcattgca 4921 tggtccgtca ttctacagta aaatcagcaa attggtcatt tcggaactga aagagggtgg 4981 aatggatttt tacgtgccca gacaagaacc aatgttcagg tggatgaggt tctcagattt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 atgacgccgc tccatctaac gatggtgccg ccggcctcgt cccagagatc aacaatgagg 5161 caatggcgct agagccagtg gcgggtgcag caatagcagc acccctcact ggtcagcaaa 5221 atataattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gagtttacag 5281 tgtcccccag aaattcccct ggtgaagtcc ttcttaattt ggaactgggc ccagaaataa 5341 atccctattt ggcccatctt gctagaatgt acaatggtta 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 gactcgaggt tacgcctaat tgcaatgcta tacacacctc 5641 ttagggcaaa caattctggg gatgatgttt ttactgtgtc ttgtagagtg ctaactagac 5701 ctagtcctga tttctcattc aatttccttg tgccacccac tgtggagtca aagacaaaac 5761 ccttttccct ccctatcctg actatctctg aaatgtccaa ttctaggttc ccagtaccaa 5821 ttgattccct acacaccagt cccactgaga atattgttgt tcagtgccaa aatgggcgcg 5881 tcacccttga tggtgagctg atgggcacca cccaactctt gcctagccaa atctgtgctt 5941 tcaggggcgt tctcaccaga tcaacaagca gagccagtga ccaggccgat acagcaaccc 6001 ctagattgtt taattattat tggcatatac aattggataa tctaaatgga accccttatg 6061 atcctgcaga agacatacca ggccccctag ggacaccaga tttccgtggc aaagtctttg 6121 gcgtggccag ccagagaaat tctgatacca cgactagggc acatgaagca aagatagaca 6181 ccacatctgg ccgcttcacc ccaaagctag gctcattaga gatatccact gaatctagtg 6241 attttgatca aaaccaacca acaagattca ccccagttgg cattggagtt gaccatgagg 6301 cagactttca acaatggacc ctacccgact acgctggtca gttcacacat aacatgaact 6361 tagccccagc tgttgctccc aacttccctg gtgagcagct ccttttcttc cgctcacatt 6421 tgccatcttc tggtgggcga tccaacggga ttctagactg cctggttccc caagaatggg 6481 tacagcactt ctaccaagag tcagccccct ctcagtctca agtggctctg gttaggtatg 6541 ttaatcctga cactggtaga gtgttatttg aggccaaact acataaacta ggtttcatga 6601 ctatagccaa gaatggtgat tctccaataa ctgtccctcc aaatggatac tttaggtttg 6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa 6721 ggattcaata atggctggag cttttatagc aggattggct ggtgacatgc tcacaaatac 6781 tgtaggatct ttagttaatg caggggctaa tgctattaat caaacaattg attttgaaaa 6841 taataaatat ttgcaaaatg cttcttttaa tcatgataag gagatgttga atgcacaaat 6901 tgaggcaaca aagaggttac aggctgacat gattgctatc aaacaagggg ttttgaccgc 6961 tggcggcttc tcccctactg atgcagcccg tggggcaatt aatgccccca tgacaaaagt 7021 cctagattgg aatggaacga gatactgggc accaggtgcc acctccacaa cctcgatgtc 7081 gggtggcttt acacatcaaa ctgtgcacag atccacacca aattttaaaa cgaaccaggc 7141 ccccaaatcc acacccagca gtgggtcttc agtgaggtca aactcaaccc aaatcactag 7201 cctgagctca cactcgtccg ggtcgtctcg atccagcgga tctacagtta tcagctcaat 7261 accatcctct aacaggacta gggactgggt caaccaacaa aattttaatt 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 //