Typing tool
|
Complete norovirus genomes
MH218725 | GI.3 | ||
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GI.P3 |
ORF1: 5..5404 ORF2: 5388..7025 ORF3: 7025..7672LOCUS MH218725 7745 bp RNA linear VRL 11-JUN-2018 DEFINITION Norovirus GI isolate NORO_84_04_11_2014, complete genome. ACCESSION MH218725 VERSION MH218725.1 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_84_04_11_2014" /host="Homo sapiens" /db_xref="taxon:122928" /country="United Kingdom" /collection_date="04-Nov-2014" /note="genotype: GI.P3_GI.3" gene 5..5404 /gene="ORF1" CDS 5..5404 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWR17833.1" /translation="MMMASNDAIAVADVSNNNANTNNDNIGSRLMARIRGRMGPQRGE TTTKITDANMALNLLRRSQTPSPSRQESPPKSQRDRPPRTASEVKKVLGWDVEPEHQE STAKAWCDLTQEEKEEIMRNNEKLFDAGGITPSTLPSTFERADPVDSPIEQQPVTWSA SGGVDIGVNDLTTVSGPFWNMCPLPPLDARNNGPAKEPLIGDMIEFYEGHIFHYAIYI GQGKTIGVHSPQAAFSIPRITIHPLVAWWRVCYVPTNQQRLTYDQLKELENEPWPYAS ITNNCYEFCCRVMALDDTWLERRLVSTGKFNHPTQDWSQDTPDFHQDSKLEMVRDAVL SAINGLVSQPFKNILSKIKPLNVLNLLSNCDWTFMGVVELIVLLAELFDVFWTPPDIS SFIASLLPEFHLQGPEDLARDLVPLILGGIGLAIGFTRDKVTKVMKSAVDGLRSATQL GQYGLEIFSIIKKYFFGGDQTEKTLRGIEDAVIDMEVLSSTNVTQLVKDKKLARTYMN VLDNEEEKARKLSVRSADPHIVTSVNNLISRISMARSALAKAQAEMTSRPRPVVIMMC GPPGIGKTKAAEHLAGRLANEIRPGGKVGLVPRESIDHWDGYHGEDVLLWDDYGMSKI TEDCNKLQAIADTAPLSLNCDRIENKGMQFSSDAIIITTNAPGPAPVDFVNLGPVCRR VDFLVYCSAPEIEQMRRTHPGDANAIKDLYKRDYSHLKMELAPQGGFDSQGNTPFGKG IMKPTTLNRLLIQATALAMERQDEFQLQGAVYNFDEDRVSAFTSLARANGLGLLSMAT LGKRLRSVKSMEGLRNALVGYKIGECDIIWNTRVYSIKSDGSTVTIKEKQTPTSPQYQ AISTATLALSRLRAARALAYASCLQSAVLSILQVAGSALVVSRAVKRMFGTRTEQPML EGKHKEHNCRVHRAEAAGHGPIGHDGVIERYGLCESEQEEEGEQTVELPTANKEGKNK GKTKKGRGRKSNFNAFSRRGLSDEEYEEYKKIREEKSGNYSIQEYLEDRQRYEEELAE VQAGGDGGIGETEAEIRHRVFYKSKSGMRKQRQEERRQLGLVSGSEIRKRKPIDWTPP KNDWSEDTRTVNYDEHISFEAPPSIWSRVVKFGSGWGFWVSSTVFITTTHVIPPGAKE VFGEDLSNVAIHRVGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCTIMIKRDSGELLP LAVRMGAVASMKIQGKLMHGQSGMLLTGANAKGMDLGTIPGDCGAPYVHKRGNDWVVC GVHAAATKSGNTVVCAIQGGDGEATLEGGGQNKGHYAGHPILRYGNGPSLSTKTKFWK STPQPLPPGTYEPAYLGGRDPRVEGGPSLQQVLRDQLKPFAEPRGRLPEAGLLEAAVE TVTNAIEQVMDTPVAWSYSDACMSLDKTTSSGHPHHKKKNDDWNGNSFVRELGDQAAH ANSMYELGKSMKPVYTAALKDELVKPDKVYTKIKKRLLWGADLGTVIRAARAFGPFCE 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="AWR17834.1" /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="AWR17835.1" /translation="MAQAILGAIAATAAGSAVGAGIQAGTEAALQHQRFQQDLTLQKN SFIHDKEMMGLQVEASTALLQNSLGTRYNMLTKAGMTSADAARMVVGAPATRVVDWNG TRIAAPMSTATTLRSGGFMTVPTVYRGSKNKQSIGGGFSNVNYDPSVSSSRTSQWVSS QNLMRSTLEPFHPGALRTTWVTPPGSTSTSTISTVSTVPKFFNTERLPLFANRGK" ORIGIN 1 gtgaatgatg atggcgtcta acgacgctat tgccgttgct gatgtcagca ataacaatgc 61 taacaccaac aatgataaca ttggatcccg cctcatggcg aggatccgtg ggcgcatggg 121 cccacaacgt ggtgaaacaa ccacaaaaat aacagacgcc aatatggcgc ttaatctgct 181 acgccggtca caaacacctt ccccatcccg gcaagagagc cctcctaaga gccagagaga 241 ccgaccccct cggactgctt ctgaggtgaa gaaagtgttg gggtgggatg ttgaaccaga 301 acaccaggaa agcacggcca aggcatggtg cgacctcacg caagaagaga aggaggagat 361 aatgcgcaat aatgaaaagc tcttcgatgc tgggggaatc accccatcaa ctttgcctag 421 cacgtttgaa agggccgacc cagttgatag ccccattgaa cagcaacctg tgacatggtc 481 tgctagtggt ggggtcgata ttggtgtcaa tgatttgacc accgtcagtg gcccattttg 541 gaatatgtgc cccctcccgc cactggatgc tcggaataat ggccccgcta aggagcccct 601 cataggagat atgatagagt tctatgaggg tcatatattc cattatgcca tctatattgg 661 acaaggtaag accattgggg tccactcacc gcaagcagct ttctccatac caaggataac 721 catccatcct ctggtagcct ggtggcgcgt gtgctacgtt ccaactaacc agcagcgcct 781 cacttatgac cagctcaaag agttggagaa tgagccatgg ccctacgctt ccattacaaa 841 caattgctat gagttttgct gcagagtgat ggcacttgac gacacatggc ttgagaggag 901 gttagtcagc actggaaaat tcaatcaccc cacacaagat tggtcacagg ataccccgga 961 ttttcaccag gactcgaaac ttgagatggt aagagatgcc gtgctatcag ctattaatgg 1021 ccttgtgtca cagcccttta aaaacatttt gtcaaagatc aaaccattaa acgttctcaa 1081 tctcttgtca aattgtgatt ggaccttcat gggggttgtg gaactgattg tgctcctagc 1141 ggagttgttt gatgtgttct ggaccccacc agacatctca agtttcattg cctcactact 1201 acctgaattt cacctgcagg gcccagaaga cctagctagg gacttggtcc ctctcatcct 1261 aggtggcata ggcctggcta ttggctttac aagagacaaa gtgacgaaag tgatgaagag 1321 tgccgtcgat gggttgagat cggcgacaca gctcgggcag tacggactgg aaatattctc 1381 aatcatcaag aaatatttct ttggtgggga tcaaacggaa aagaccttgc ggggtattga 1441 ggatgcagtg atagacatgg aggtgttatc tagcaccaat gtgacacaat tggttaaaga 1501 taagaaattg gccagaacct acatgaatgt gctagacaat gaagaggaaa aagcaaggaa 1561 actttcagtc cgtagtgctg atccgcacat agtgacctca gtcaacaatc tgatatcacg 1621 aatatctatg gcaagatcag ccttggccaa agcccaggct gagatgacat ctcgcccacg 1681 ccctgtggtc ataatgatgt gtggcccccc cggcatcgga aaaaccaagg ccgccgaaca 1741 cctggctggc cgattggcaa acgagattag accaggaggt aaggttggac ttgtgccccg 1801 ggaatccata gatcactggg acggatacca tggcgaggat gtcctactat gggatgacta 1861 tggcatgtca aagataacag aggactgtaa taagctacaa gccatagctg acactgcacc 1921 cctatcactt aattgtgaca ggatagagaa caaaggcatg caattctcct cagatgcaat 1981 aatcataacc accaatgccc ctggcccggc cccggtggac tttgttaacc taggccctgt 2041 gtgcaggcga gtagactttt tagtttactg ttctgcccct gaaattgagc aaatgagaag 2101 gacccaccct ggtgatgcca atgccatcaa agacctatac aaaagggact actcacactt 2161 aaaaatggaa ttggccccac aaggtggttt tgatagtcag ggtaacacac catttgggaa 2221 gggcatcatg aaacccacga ccctcaatag gctactcatt caggcaacag cattagctat 2281 ggagcggcaa gacgagttcc agctccaagg ggctgtctac aactttgatg aagacagggt 2341 gtccgccttc acaagcctgg cccgagctaa cggcttgggg cttttaagca tggcaacatt 2401 gggtaaaagg ctcagaagtg tcaaatctat ggagggcctg cgtaacgcat tggtgggcta 2461 caaaatagga gagtgtgata taatctggaa cactagagtg tattcaatta aaagtgatgg 2521 tagtactgtc acaatcaagg aaaaacaaac cccaacttca ccccaatacc aagccattag 2581 cacagccact cttgcactct ctaggttgcg ggccgctaga gctctcgcgt acgcctcctg 2641 cctgcagagt gcagtgctgt caatacttca agtagctggc tctgccctgg tggtgagcag 2701 agccgttaag cgcatgtttg gcacgcgcac tgaacaacct atgttggaag gcaagcacaa 2761 agaacacaac tgtagagtgc accgcgcaga ggcagctggc catggtccta ttgggcacga 2821 tggagtcatc gaacgctatg gcctctgtga gagtgagcaa 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 aaagcaacgc caagaagaac ggcgtcagtt gggtctcgtt agcggttctg agatccgcaa 3241 acgcaagccc atagactgga ccccccctaa gaatgattgg tcagaagaca ccaggactgt 3301 caactatgat gaacacatta gctttgaagc ccctccctca atttggagta gggtggtgaa 3361 gtttggcagt ggttggggtt tttgggtgag ctcaacagta ttcataacca cgacccatgt 3421 cataccacct ggggccaaag aagtctttgg tgaagacctc agtaatgtgg ccatccatag 3481 agttggtgag ttcacccagt tccgtttctc caaaaagatg agacctgacc tcaccggtat 3541 ggttttagaa gaaggttgcc cagagggaac agtgtgcacc ataatgatca agagagattc 3601 tggtgagttg ctgccgctcg ctgttcggat gggggcagtg gcatcaatga agatccaagg 3661 caaacttatg catgggcaat caggaatgtt actcaccggt gctaatgcca aaggcatgga 3721 ccttgggact atacccggtg attgtggggc accctatgtc cacaagaggg gaaatgactg 3781 ggtggtctgt ggagtgcatg cagccgccac aaaatcaggc aacactgtgg tgtgcgccat 3841 acaaggtggc gatggtgaag ccactctaga aggcggcggt caaaacaagg gccactatgc 3901 agggcatccg atactaaggt atgggaatgg cccttcacta tcaaccaaaa caaaattttg 3961 gaaatcaacc ccccagcctt tgcctcctgg tacatatgag ccagcttacc ttggaggtag 4021 agaccccaga gttgaggggg gcccatcctt acagcaggtg ttaagggacc agttgaaacc 4081 atttgccgaa ccccgtggca gattacccga agcgggctta ttggaagctg cagttgaaac 4141 ggtcaccaat gctattgaac aggtcatgga cacaccggtg gcatggagct atagtgatgc 4201 ttgcatgtca ctagataaga caaccagttc cggccacccc catcacaaga agaaaaatga 4261 tgattggaat gggaattcat ttgtgagaga attgggtgac caggcggcac acgctaacag 4321 catgtatgag cttggtaagt ccatgaaacc tgtgtataca gcagccctaa aggatgagct 4381 agtcaaacca gataaggtgt acacaaaaat caaaaagaga ctgctttggg gcgcggacct 4441 cggtaccgtc attcgcgctg ccagagcatt tggaccattc tgtgaggcca taaaacccca 4501 tgtaattaag ttgcctatca aggtgggtat gaatgccata gaggatggcc ccttgattta 4561 tgctgagcac tccaaatata aatttcatta tgatgctgac tatacagctt gggactcaac 4621 acaaaacagg gaaatcatga tggagtcttt caatattatg tgcaagctta cagccaatcc 4681 ctccttggcc gcagtggtgg cacaggatct actctcccca tctgaaatgg atgttggtga 4741 ctatgtaatc agtgtcaaag atggtttacc atctggcttt ccatgcactt cacaggtgaa 4801 cagtatcaac cactggatac taaccctgtg tgcactgtca gaagtcactg gcttgtcccc 4861 agatgtgata cagtcacaat cctacttctc attttatggt gatgatgaaa tagtctcaac 4921 agatatagaa tttgacccaa ttagattgac acaaatactg aaggaatatg gtttgaagcc 4981 tacaagacct gacaaaactg atggcccaat tattattaga caacaggttg atggcctggt 5041 cttcctccgg cgcaccattt ctaaggatgc cattggatac cagggacgac tcgaccgtaa 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 ggttccatga 5341 tctaagtttg tggacaggag accgcgatct cctgcccgat 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 tattttgttt gatttacaat 5641 taggccccca ccttaaccct ttcttatctc atttggccca aatgtataat ggctgggttg 5701 gcaatatgaa agtgaaggtt ttattggctg gtaatgcttt cacggctggt aaaataatta 5761 ttagttgcat acctcctggc tttgccgcac aaaatatttc tattgcccag gccaccatgt 5821 tcccccatgt catagctgat gttagggttt tggaacccat tgaggtgcca ttggaagatg 5881 tgaggaatgt gctcttccac aacaatgaca acacgccaac tatgcggttg gtgtgcatgc 5941 tatacacccc cttgcgggcc agtggtagct cgtctggaac tgaccccttt gtgattgctg 6001 ggcgtgtttt gacatgccca agtcctgatt ttagcttttt gtttttggtc ccccccaatg 6061 tagagcaaaa gactaaacct ttcagtgtcc caaaccttcc attgaatact ctttcaaatt 6121 cgagagtccc ttctttaatc aaatcaatga tggtgtccag ggaccatggg cagatggttc 6181 agtttcaaaa tggtagggtc accctagatg ggcagctgca aggcaccaca cccacatcag 6241 ctagtcagct gtgcaaaatc aggggcagtg tcttccatgc caatggtggg aatgggtaca 6301 acttaacaga actggatggg agcccatacc acgcatttga aagccccgca ccaataggtt 6361 ttccagatct aggtgaatgt gattggcaca tggaggcttc tcctaccacc caatttaaca 6421 ctggagatgt tataaaacaa attaatgtta aacaagagtc agcatttgcc ccccaccttg 6481 gcaccgtaca ggtagacggc ctgagtgatg tgagtgtcaa caccaacatg atagctaaat 6541 taggatgggt gtctcccgtc agtgatggac acaaagggga tgtcgacccg tgggtcattc 6601 cacgctatgg ttcaactctg actgaggccg cccaattagc ccccccaata tatcccccag 6661 gctttggtga ggccattgtg tttttcatgt cagactttcc cattgcccat ggcaccaatg 6721 gcttgagtgt gccttgcact ataccccaag aatttgtcac ccattttgtc aatgaacagg 6781 cccctactag aggggaagca gccttgctac actatctgga ccctgatact aatagaaatc 6841 ttggtgagtt taaattatac cctgatggct tcatgacatg tgtgcctaac tccagtggca 6901 ctggtccaca aactcttcca atcaatggtg tctttgtctt tgtgtcctgg gtttctagat 6961 tttatcaatt aaagcctgtg ggaacagccg gcccggctcg taggcttggg attaggagat 7021 cataatggct caagccatac ttggagccat agcagcaaca gcagccggta gtgctgttgg 7081 tgctggtata caagctggaa ccgaagctgc cctacagcat caaagatttc agcaagatct 7141 gaccttacaa aagaattcct ttattcatga taaagagatg atgggcctac aggtagaggc 7201 ttcaactgca ctcctccaaa acagcttggg tacgaggtac aatatgttga ccaaagcagg 7261 gatgacatcc gcagacgcgg cacgtatggt agtgggggca cccgcgactc gtgtcgttga 7321 ctggaacggg actaggatcg ccgcacccat gtcaactgcg acgacactta ggtctggcgg 7381 tttcatgacc gtaccaactg tttatagggg tagtaagaat aaacaatcaa ttggtggtgg 7441 tttttctaat gtaaattatg atccctcagt ctcctcttcc cgcacttctc aatgggtctc 7501 ttctcaaaat ttaatgcgtt ccactctgga accgtttcat ccaggtgctc tgagaaccac 7561 atgggtcacc ccacctgggt caacttctac ttctacaatt tctacagttt ctactgtgcc 7621 aaaattcttt aatacagaaa ggttaccctt attcgcaaac aggggtaagt gattttgtaa 7681 tatgaattag tgggcatcat attcaatttg gaatcaatta gatatttaga ttggcagatg 7741 atgtt //