Typing tool
|
Complete norovirus genomes
MH218729 | GI.3 | ||
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GI.P3 |
ORF1: 5..5404 ORF2: 5388..7025 ORF3: 7025..7672LOCUS MH218729 7745 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GI isolate NORO_90_22_06_2015, complete genome. ACCESSION MH218729 VERSION MH218729.1 KEYWORDS . SOURCE Norovirus GI ORGANISM Norovirus GI Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7745) 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 7745) 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..7745 /organism="Norovirus GI" /mol_type="genomic RNA" /isolate="NORO_90_22_06_2015" /host="Homo sapiens" /db_xref="taxon:122928" /country="United Kingdom" /collection_date="22-Jun-2015" /note="genotype: GI.P3_GI.3" gene 5..5404 /gene="ORF1" CDS 5..5404 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17845.1" /translation="MMMASNDAIAVADVSNNNANTNNDNIGSRLMARIRGRMGPQRGE TTTKITDANMALNLLRRSQTPSPSRQESPPKSQRDRPPRTASEVKKVLGWDVEPEHQE STAKAWCDLTQEEKEEIMRNNEKLFDAGGITPSTLPSTFERADPVDSPIEQQPVTWSA SSGVDIGVNDLTTVSGPFWNMCPLPPLDARNNGPAKEPLIGDMIEFYEGHIFHYAIYI GQGKTIGVHSPQAAFSIPRITIHPLVAWWRVCYVPTNQQRLTYDQLKELENEPWPYAS ITNNCYEFCCRVMALDDTWLERRLVSTGKFNHPTQDWSQDTPDFHQDSKLEMVRDAVL SAINGLVSQPFKNILSKIKPLNVLNLLSNCDWTFMGIVELIVLLAELFDVFWTPPDIS SFIASLLPEFHLQGPEDLARDLVPLILGGIGLAIGFTRDKVTKVMKSAVDGLRSATQL GQYGLEIFSIIKKYFFGGDQTEKTLRGIEDAVIDMEVLSSTNVTQLVKDKKLARTYMN VLDNEEEKARKLSVRSADPHIVTSVNNLISRISMARSALAKAQAEMTSRPRPVVIMMC GPPGIGKTKAAEHLAGRLASEIRPGGKVGLVPRESIDHWDGYHGEDVLLWDDYGMSKI TEDCNKLQAIADTAPLSLNCDRIENKGMQFSSDAIIITTNAPGPAPVDFVNLGPVCRR VDFLVYCSAPEIEQMRRTHPGDANAIKDLYKRDYSHLKMELAPQGGFDSQGNTPFGKG IMKPTTLNRLLIQATALAMERQDEFQLQGAVYNFDEDRVSAFTSLARANGLGLLSMAT LGKRLRSVKSMEGLRNALVGYKIGECDIIWNTRVYSIKSDGSTVTIKEKQTPTSPQYQ AISIATLALSRLRAARALAYASCLQSAVLSILQVAGSALVVSRAVKRMFGTRTEQPML EGKHKEHNCRVHRAEAAGHGPIGHDGVIERYGLCESEQEEEGEQTVELPTANKEGKNK GKTKKGRGRKSNFNAFSRRGLSDEEYEEYKKIREEKSGNYSIQEYLEDRQRYEEELAE VQAGGDGGIGETEAEIRHRVFYKSKSGMRKQRQEERRQLGLVSGSEIRKRKPIDWTPP KNDWSEDTRTVNYDEHISFEAPPSIWSRVVKFGSGWGFWVSSTVFITTTHVIPPGAKE VFGEDLSNVAIHRVGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCTIMIKRDSGELLP LAVRMGAVASMKIQGKLMHGQSGMLLTGANAKGMDLGTIPGDCGAPYVHKRGNDWVVC GVHAAATKSGNTVVCAIQGGDGEATLEGGGQNKGHYAGHPILRYGNGPSLSTKTKFWK STPQPLPPGTYEPAYLGGRDPRVEGGPSLQQVLRDQLKPFAEPRGRLPEAGLLEAAVE TVTNAIEQVMDTPVAWSYSDACMSLDKTTSSGHPHHKKKNDDWNGNSFVRELGDQAAH ANSMYELGKPMKPVYTAALKDELVKPDKVYTKIKKRLLWGADLGTVIRAARAFGPFCE AIKPHVIKLPIKVGMNAIEDGPLIYAEHSKYKFHYDADYTAWDSTQNREIMMESFNIM CKLTANPSLAAVVAQDLLSPSEMDVGDYVISVKDGLPSGFPCTSQVNSINHWILTLCA LSEVTGLSPDVIQSQSYFSFYGDDEIVSTDIEFDPIRLTQILKEYGLKPTRPDKTDGP IIIRQQVDGLVFLRRTISKDAIGYQGRLDRNSIERQLWWTRGPNHEDPFETLVPHSQR KVQLISLLGEAALHGEKFYRKIAGRVIQEVKEGGLEIYIPGWQAMFRWMRFHDLSLWT GDRDLLPDYVNDDGV" mat_peptide 5..1219 /gene="ORF1" /product="p48" mat_peptide 1220..2308 /gene="ORF1" /product="NTPase" mat_peptide 2309..2908 /gene="ORF1" /product="p22" mat_peptide 2909..3328 /gene="ORF1" /product="VPg" mat_peptide 3329..3871 /gene="ORF1" /product="Pro" mat_peptide 3872..5401 /gene="ORF1" /product="RdRp" gene 5388..7025 /gene="ORF2" CDS 5388..7025 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWR17846.1" /translation="MMMASKDAPTNMDGTSGAGQLVPEANTAEPISMEPVAGAATAAA TAGQVNMIDPWIMNNYVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLSHLAQMYNG WVGNMKVKVLLAGNAFTAGKIIISCIPPGFAAQNISIAQATMFPHVIADVRVLEPIEV PLEDVRNVLFHNNDNTPTMRLVCMLYTPLRASGSSSGTDPFVIAGRVLTCPSPDFSFL FLVPPNVEQKTKPFSVPNLPLNTLSNSRVPSLIKSMMVSRDHGQMVQFQNGRVTLDGQ LQGTTPTSASQLCKIRGSVFHANGGNGYNLTELDGSPYHAFESPAPIGFPDLGECDWH MEASPTTQFNTGDVIKQINVKQESAFAPHLGTVQVDGLSDVSVNTNMIAKLGWVSPVS DGHKGDVDPWVIPRYGSTLTEAAQLAPPIYPPGFGEAIVFFMSDFPIAHGTNGLSVPC TIPQEFVTHFVNEQAPTRGEAALLHYLDPDTNRNLGEFKLYPDGFMTCVPNSSGTGPQ TLPINGVFVFVSWVSRFYQLKPVGTAGPARRLGIRRS" gene 7025..7672 /gene="ORF3" CDS 7025..7672 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWR17847.1" /translation="MAQAILGAIAATAAGSAVGAGIQAGTEAALQHQRFQQDLTLQKN SFIHDKEMMGLQVEASTVLLQNSLGTRYNMLTKAGMTSADAARMVVGAPATRVVDWNG TRIAAPMSTATTLRSGGFMTVPTVYRGSKNKQSIGGGFSNVNYDPSVSSSRTSQWVSS QNSMRSTLEPFHPGALRTTWVTPPGSTSTSTISTVSTVPKFFNTERLPLFANRGK" ORIGIN 1 gtgaatgatg atggcgtcta acgacgctat tgccgttgct gatgtcagca ataacaatgc 61 taacaccaac aatgataaca ttggatcccg cctcatggca aggatccgtg ggcgcatggg 121 cccacaacgt ggtgaaacaa ccacaaaaat aacagacgcc aatatggcgc ttaatctgct 181 acgccggtca caaacacctt ccccatcccg gcaagagagc cctcctaaga gccagagaga 241 ccgcccccct cgtactgctt ctgaggtgaa gaaagtgttg gggtgggatg ttgaaccaga 301 acaccaggaa agcacggcta aggcatggtg cgacctcacg caagaagaga aggaggagat 361 aatgcgcaat aatgaaaaac tcttcgatgc tgggggaatc accccatcaa ctttgcctag 421 cacgtttgaa agggccgacc cagttgatag ccccattgaa cagcaacctg tgacatggtc 481 tgctagtagt ggggtcgata ttggtgtcaa tgatttgacc accgtcagtg gcccattttg 541 gaatatgtgc cccctcccgc cactggatgc tcggaataat ggccccgcta aggaacccct 601 cataggagat atgatagagt tctatgaggg tcatatattc cattatgcca tctatattgg 661 acaaggtaag accattgggg tccactcacc acaagcagct ttctccatac caaggataac 721 catccatcct ctggtagcct ggtggcgcgt gtgctacgtc ccaactaacc agcagcgcct 781 cacttatgac cagctcaaag agttggagaa tgagccatgg ccctacgctt ccattacaaa 841 caattgctat gagttttgct gcagagtgat ggcacttgac gatacatggc ttgagaggag 901 gttagtcagc actggaaaat tcaatcaccc cacacaagat tggtcacagg ataccccgga 961 ttttcaccag gactcgaaac ttgagatggt aagagatgcc gtgctatcag ctattaatgg 1021 ccttgtgtca cagcccttta aaaacatttt gtcaaagatc aaaccattaa acgttctcaa 1081 tctcttgtca aattgcgatt ggaccttcat ggggattgtg gaactgattg tgctcctagc 1141 ggagttgttt gatgtgttct ggaccccacc agacatctca agtttcattg cctcactact 1201 acctgaattt cacctgcagg gcccagaaga cctagctagg gacttggtcc ctctcatcct 1261 aggtggcata ggcctggcca ttggctttac aagagacaaa gtgacgaaag tgatgaagag 1321 tgccgtcgat gggttgagat cggcgacaca gctcgggcag tacggactgg aaatattctc 1381 aatcatcaag aaatatttct ttggtgggga ccaaacggaa aagaccttgc ggggtattga 1441 ggatgcagtg atagacatgg aggtgttatc tagcaccaat gtgacacaat tggttaaaga 1501 taagaaattg gccagaacct acatgaatgt gctagacaat gaagaggaaa aagcaaggaa 1561 actctcagtc cgtagtgctg atccgcacat agtgacctca gtcaacaatc tgatatcacg 1621 aatatccatg gcaagatcag ccttggccaa agcccaggct gagatgacat ctcgcccacg 1681 ccctgtggtc ataatgatgt gtggcccccc cggcatcgga aaaaccaagg ccgccgaaca 1741 cctggctggc cgattggcaa gcgagattag accagggggt aaggttggac ttgtgccccg 1801 ggaatccata gatcactggg acggatacca tggcgaggat gtcctactat gggatgacta 1861 tggcatgtca aagataacag aggactgtaa taagctacaa gccatagctg acactgcacc 1921 cctatcactt aattgtgaca ggatagagaa caaaggtatg caattctcct cagatgcaat 1981 aatcataacc accaatgccc ctggcccggc cccggtggac tttgtcaacc taggccctgt 2041 gtgcaggcga gtggactttt tagtttactg ttctgcccct gaaattgagc aaatgagaag 2101 gacccatcct ggtgatgcca atgccatcaa ggacttatac aaaagggact actcacactt 2161 aaaaatggaa ttggccccac aaggtggttt tgatagtcag ggtaacacac catttgggaa 2221 gggcatcatg aaacctacga ccctcaatag gctactcatt caggcaacag cattagctat 2281 ggagcggcaa gacgagttcc agctccaagg ggctgtctac aacttcgatg aagacagggt 2341 gtccgccttc acaagcctgg cccgagctaa cggcttgggg cttttaagta tggcaacatt 2401 gggtaaaagg ctcagaagtg tcaaatctat ggagggcctg cgcaacgcat tggtaggcta 2461 caaaatagga gagtgtgata taatctggaa cactagagtg tattcaatta aaagtgatgg 2521 tagtactgtc acaatcaagg aaaaacaaac cccaacttca ccccaatacc aagccattag 2581 catagccact cttgcactct ctaggttgcg ggccgctaga gctctcgcgt acgcctcctg 2641 cctacagagt gcagtgctgt caatacttca agtagctggc tctgccctgg tggtgagcag 2701 agccgttaag cgcatgtttg gcacgcgcac tgaacaacct atgttggaag gcaagcacaa 2761 agaacacaac tgtagagtgc accgcgcaga ggcagctggc catggtccta ttgggcacga 2821 tggagtcatc gaacgctatg gcctctgtga gagtgaacaa gaagaagaag gcgagcaaac 2881 agttgagcta cccactgcca ataaagaagg caaaaacaag ggcaagacca aaaagggccg 2941 tggacgaaaa tccaatttta atgctttctc aagacgaggc ctcagtgatg aagagtatga 3001 agaatacaag aagatcagag aagaaaagag tggcaattac agcatccagg agtacctcga 3061 ggaccgccaa cgatatgagg aagaacttgc tgaagtgcag gctggtgggg atggtggaat 3121 tggtgagact gaagcagaga ttcgccatcg ggttttctat aaatcaaaat ccggcatgag 3181 aaagcagcgc caagaagaac ggcgtcagtt gggtctcgtt agcggttctg agatccgcaa 3241 acgcaagccc atagactgga ccccccctaa gaatgattgg tcagaagaca ccaggactgt 3301 caactatgat gaacacatta gctttgaagc ccctccctca atttggagta gggtggtgaa 3361 gtttggcagt ggttggggtt tttgggtgag ctcaacagtg ttcataacca cgacccatgt 3421 cataccacct ggggccaaag aagtctttgg tgaagacctc agtaatgtgg caatccatag 3481 agttggtgaa ttcacccagt tccgtttctc caaaaagatg aggcctgacc tcaccggtat 3541 ggttttagaa gaaggttgcc cagagggaac agtgtgcacc ataatgatca agagagattc 3601 tggtgagttg ctgccgctcg ccgttcggat gggggcagtg gcatcaatga agatccaagg 3661 caaacttatg catgggcaat cagggatgtt gctcaccggt gctaatgcca aaggcatgga 3721 ccttgggact atacccggtg attgtggggc accctatgtc cacaagaggg gaaatgactg 3781 ggtggtctgt ggggtacatg cagccgccac aaaatcaggc aacactgtgg tgtgcgccat 3841 acaaggtggc gatggtgaag ccactctaga aggcggcggt caaaacaagg gccactatgc 3901 agggcatccg atactaaggt atgggaatgg cccttcacta tcaaccaaaa caaaattttg 3961 gaaatcaacc ccccagcctt tgcctcctgg tacatatgag ccagcttacc ttggaggcag 4021 agaccccaga gttgaggggg gcccatcctt acagcaggta ttaagggacc agttaaaacc 4081 atttgccgag ccccgtggca gattacccga agcgggcttg ttggaagctg cagttgaaac 4141 agtcaccaat gctattgaac aggtcatgga cacaccggtg gcatggagct atagtgatgc 4201 ttgcatgtca ctagataaga caaccagttc cggccacccc catcacaaga agaaaaatga 4261 tgattggaat gggaattcat ttgtgagaga attgggtgac caggcggcac acgctaacag 4321 catgtatgag cttggtaagc ccatgaaacc tgtgtataca gcagccctaa aggatgagct 4381 agtcaaacca gataaagtgt acacaaaaat caaaaagaga ctgctttggg gcgcggacct 4441 cggtaccgtc attcgcgctg ccagagcatt tggaccattt tgtgaggcca taaaacccca 4501 tgtaattaag ttgcctatta aggtgggcat gaatgccata gaggatggcc ccttgattta 4561 tgctgagcac tccaagtata aatttcatta tgatgctgac tatacagctt gggactcaac 4621 acaaaacaga gaaatcatga tggaatcttt caacattatg tgcaagctta cagccaatcc 4681 ctccttggcc gcagtggtgg cacaggatct actctcccca tctgaaatgg atgttggtga 4741 ctatgtgatc agtgtcaaag atggtttgcc atctggcttt ccatgcactt cacaggtgaa 4801 cagtatcaac cactggatac tgaccctgtg tgcactgtca gaagtcactg gcttgtcccc 4861 agatgtgata cagtcacagt cctacttctc attttatggt gatgatgaaa tagtctcaac 4921 agatatagaa tttgacccaa ttagattgac acaaatattg aaggaatatg gtttgaagcc 4981 tacaagacct gacaaaactg atggcccaat tattattaga caacaggttg atggcctggt 5041 cttcctccgg cgcaccattt ctaaggatgc cattggatac cagggacgac ttgaccgtaa 5101 ctctattgaa aggcagcttt ggtggactcg tggaccaaac catgaggacc catttgagac 5161 actggtccca cattcacaga gaaaggtcca attaatatcc ttgctaggtg aagcagcact 5221 ccacggtgaa aagttctaca ggaagatagc tggtagggtc attcaagaag tcaaagaggg 5281 agggcttgaa atctacattc ctggttggca ggccatgttc cgctggatgc gattccatga 5341 tctaagtttg tggacaggag accgcgatct cttgcccgat tatgtaaatg atgatggcgt 5401 ctaaggacgc cccaacaaac atggatggca ccagtggtgc cggccagctg gtaccagagg 5461 caaacacagc tgagcctata tcaatggagc ccgtggctgg ggcagcaaca gctgccgcaa 5521 ctgctggcca agttaatatg attgacccct ggataatgaa caattatgta caagcccccc 5581 aaggtgaatt taccatatcg cctaataaca caccaggtga cattttgttt gatttacaat 5641 taggccccca ccttaaccct ttcttatctc atttggccca aatgtataat ggctgggttg 5701 gcaatatgaa agtgaaggtt ctattggctg gtaatgcttt cacggctggt aaaataatca 5761 ttagttgcat accccctggc tttgccgcac aaaatatttc tattgcccag gccaccatgt 5821 tcccccatgt tatagctgat gttagggttt tggagcccat tgaggtgcca ttggaagatg 5881 tgaggaatgt gctcttccac aacaatgata acacgccaac tatgcggttg gtgtgcatgc 5941 tatacacccc cttgcgggcc agtggtagtt cgtctggaac tgaccccttt gtgattgctg 6001 ggcgtgtttt gacatgccca agtcctgatt ttagcttttt gtttttggtc ccccccaatg 6061 tagagcaaaa gactaaacct tttagtgtcc caaaccttcc attgaatacc ctttcaaatt 6121 cgagagtccc ttctctaatc aaatcaatga tggtgtctag ggaccatggg cagatggttc 6181 agtttcaaaa tggtagggtc accctagatg ggcagctgca aggcaccaca cccacatcag 6241 ctagtcagct gtgcaaaatc agaggcagtg tctttcatgc caatggtggg aatgggtaca 6301 acttaacaga actggatggg agcccatacc acgcatttga gagccccgcg ccaatagggt 6361 ttccagatct aggtgaatgt gattggcaca tggaggcttc tcctaccacc caatttaata 6421 ctggagatgt tataaaacaa attaatgtta aacaagagtc agcatttgcc ccccaccttg 6481 gcaccgtaca ggtagacggc ctgagtgatg tgagtgtcaa caccaacatg atagctaaat 6541 taggatgggt gtctcccgtc agtgatggac acaaagggga tgtcgacccg tgggtcattc 6601 cacgctatgg ttcaaccctg actgaggccg cccaattagc ccccccaata tatcccccag 6661 gctttggtga ggccattgtg tttttcatgt cagattttcc cattgcccat ggcaccaatg 6721 gcttgagtgt gccctgcact ataccccaag aatttgtcac ccattttgtc aatgaacagg 6781 cccccactag aggggaagca gccttgctac actatctgga ccctgatact aatagaaatc 6841 ttggtgagtt taaattatat cctgatggct tcatgacttg tgtgcctaat tccagtggca 6901 ctggcccaca aactcttcca atcaatggtg tctttgtctt tgtgtcctgg gtttctagat 6961 tttatcaatt aaagcctgtg ggaacagccg gcccggctcg taggcttggg attaggagat 7021 cataatggct caagctatac ttggagccat agcagcaaca gcagccggta gtgctgttgg 7081 tgctggtata caggctggaa ccgaagctgc cctacagcat caaagatttc agcaagattt 7141 gaccttacaa aagaattcct ttattcatga taaagagatg atgggcctac aggtagaggc 7201 ttcaactgta ctcctccaaa acagcttggg tacgaggtac aatatgttga ccaaagcagg 7261 gatgacatcc gcagacgcgg cacgtatggt agtgggggca cccgcgactc gtgtcgttga 7321 ctggaacggg actaggatcg ccgcacccat gtcaactgcg acgacactta ggtctggtgg 7381 tttcatgacc gtaccaactg tttatagggg tagtaaaaat aaacaatcaa ttggtggtgg 7441 tttttctaat gtaaattatg atccctcagt ctcctcttcc cgcacttctc aatgggtctc 7501 ttctcaaaat tcaatgcgtt ccactctgga accatttcat ccaggtgctc tgagaaccac 7561 gtgggtcacc ccacctgggt caacttctac ttctacaatt tctacagttt ctactgtgcc 7621 aaaattcttt aatacagaaa ggttaccctt attcgcaaac aggggtaagt gattttgtaa 7681 tatgaattag tgggcatcat attcaatttg gaatcaatta gatatttaga ttggcagatg 7741 atgtt //