Typing tool
|
Complete norovirus genomes
KM198506 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 70..5088 ORF2: 5069..6691 ORF3: 6691..7431LOCUS KM198506 7431 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/10199/2009/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198506 VERSION KM198506.1 KEYWORDS . SOURCE Norovirus Hu/GII/10199/2009/VNM ORGANISM Norovirus Hu/GII/10199/2009/VNM Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7431) AUTHORS Cotten,M., Petrova,V., Phan,M.V., Rabaa,M.A., Watson,S.J., Ong,S.H., Kellam,P. and Baker,S. TITLE Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting JOURNAL J. Virol. 88 (19), 11056-11069 (2014) PUBMED 25056894 REFERENCE 2 (bases 1 to 7431) AUTHORS Cotten,M.L., Petrova,V., Phan,M.V.T., Rabaa,M.A., Watson,S.J., Kellam,P. and Baker,S. TITLE Direct Submission JOURNAL Submitted (13-JUL-2014) Virus Genomics, The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. 2.4.0 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7431 /organism="Norovirus Hu/GII/10199/2009/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/10199/2009/VNM" /host="Homo sapiens" /db_xref="taxon:1526962" /country="Viet Nam" /collection_date="20-Oct-2009" /note="genotype: GII" CDS 70..5088 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02646.1" /translation="MFSNMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKIPPP PPNGEDEAVVSYSAKDGVSGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT LKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT MDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK VLAFRQLAAENKYGLIDTMKVGRQLKDVKTMPELKQALKNISIKKCQIVYSGCTYTLE SDGKGNVKVDRIQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV TTRIIKRVNIQDLWSKPQVENTEEATNKDGCPKPKDDEEFVISSDDIKTEGKKGKNKT GRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYSIEEYLQDRDKYYEEVAIARATEED FCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSV DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGTHATM KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMT PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR VGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQV VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE DGVE" CDS 5069..6691 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02647.1" /translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG GTTHRNEPQQWALPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6691..>7431 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02648.1" /translation="MAGAFFAGLASDVLGSGLSSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAVN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRINPRTPTPARGSSSTSS NASTATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTG" ORIGIN 1 tctaacgtcg cttccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca 61 agtgacaaaa tgttttctaa catggctgtc acttttaaac gagccctcgg ggcgcggcct 121 aaacagcccc ccccgaggga aataccacaa agacccccac gaccacctac cccagaactg 181 gtcaaaaaga tcccccctcc cccgcccaac ggagaggatg aagcagtggt ttcttatagt 241 gccaaagatg gcgtttccgg tttacctgag ctttccaccg tcaggcaacc ggaagaaacc 301 aatacggcct tcagtgtccc tccactcaac cagagggaga atagagatgc taaggaacca 361 ctgactggaa caattctgga aatgtgggat ggagaaatct accattatgg cctgtatgtt 421 gagcgaggtc ttgtgctggg tgtgcacaaa ccaccagctg ccataagcct cgccaaggtc 481 gaactaacac cactctcctt gttctggaga cctgtgtaca ccccccagta cctcatctct 541 ccagacaccc tcaagaaatt gcacggagaa acgtttccct acacagcctt tgacaacaat 601 tgctatgcct tttgttgttg ggtcctggat ctaaatgact cgtggctgag taggagaatg 661 atccagagaa caactggctt cttcagaccc taccaagact ggaataggaa acccctcccc 721 actatggatg attccaaatt aaagaaggta gctaacatat tcctgtgcgc cctgtcttcg 781 ctattcacca ggcccataaa agacataata ggaaagctaa gacctctcaa catcatcaac 841 atcctggctt catgtgattg gactttcgca ggcatagtgg agtctttgat actcttggca 901 gagctctttg gagtcttctg gacaccccca gatgtgtctg cgatgattgc ccccttactc 961 ggtgatttcg agttacaagg acctgaggac cttgtagtgg agctcgtccc tgtagtaatg 1021 gggggaattg gtttggtgct gggattcacc aaagagaaga ttgggaaaat gttgtcatct 1081 gctgcatcca ccttgagagc ttgtaaagat cttggtgcat atgggctaga gatcctaaag 1141 ttagtcatga agtggttctt cccgaagaaa gaggaggcaa atgaactggc tatggtgaga 1201 tccatcgagg atgcggtact ggaccttgag gcaattgaaa acaaccatat gaccaccttg 1261 ctcaaagaca aagacagcct agcaacctac atgagaaccc ttgacctcga ggaagagaaa 1321 gccagaaaac tctcaaccaa gtctgcttca cctgacatcg tgggtacaat caacgccctt 1381 ctggcgagaa tcgccgctgc acgctccctg gtgcaccgag cgaaggagga gctttccagc 1441 agaccaaggc ccgtagtctt gatgatatca ggcagaccag ggataggaaa aacccacctt 1501 gctagggaag tggctaagag aatcgcagcc tccctcacag gagaccagcg tgtaggcctc 1561 atcccacgca atggcgtcga tcactgggat gcgtacaagg gggagagggt cgtcctatgg 1621 gacgactatg gaatgagcaa ccccattcac gacgccctta ggctgcaaga actcgctgac 1681 acttgccccc ttactctaaa ttgtgacagg attgagaaca aaggaaaggt ctttgacagc 1741 gatgtcatca ttatcaccac taatctggcc aacccagcac cactggacta tgtcaacttt 1801 gaagcgtgct cgaggcgcat cgatttcctc gtgtatgcag aagcccccga ggtcgaaaag 1861 gcgaagcgtg acttcccggg ccaacctgac atgtggaaaa acgcttttag ttctgatttc 1921 tcacacataa aattggcact ggctccacaa ggtggctttg ataagaacgg aaacacccca 1981 cacgggaagg gcgtcatgaa gactctcacc actggctccc tcattgcccg ggcatcaggg 2041 ctgctccatg agagattgga tgagtttgaa ctacagggcc cagctcttac caccttcaac 2101 tttgaccgca acaaagtgct tgccttcaga cagcttgcag ctgaaaacaa atatgggttg 2161 atagacacaa tgaaagttgg gaggcagctc aaggatgtca aaaccatgcc agaacttaaa 2221 caagcactca aaaacatctc aatcaagaag tgccagattg tgtatagtgg ttgcacctac 2281 acacttgagt ctgatggcaa gggcaatgtg aaagttgaca gaatccagag cacctccgta 2341 cagaccaaca atgagcttgc tggcgccctg catcatctga ggtgcgccag aatcaggtac 2401 tatgtcaagt gtgtccagga ggccctgtat tctatcatcc agattgctgg ggccgcattt 2461 gtcaccacgc gcattatcaa gcgtgtgaac attcaagact tatggtccaa gccacaagtg 2521 gaaaacacag aggaggccac caacaaggac gggtgcccaa aacccaaaga tgatgaggag 2581 ttcgtcattt catctgacga cattaaaact gagggtaaga aagggaagaa caagactggc 2641 cgtggcaaga agcatacagc cttttcaagt aaaggtctca gtgatgaaga gtatgatgag 2701 tacaagagaa ttagagagga aaggaatggc aggtattcca tagaagagta ccttcaggac 2761 agggacaaat actatgagga ggtggccatt gccagggcga ccgaggaaga cttctgtgaa 2821 gaggaggagg ccaagatccg gcagaggatc tttagaccaa caaggaaaca acgcaaggaa 2881 gaaagagctt ctctcggttt agtcacaggt tctgagatta ggaaaagaaa cccagatgac 2941 ttcaagccta agggaaaact gtgggctgac gatgacagaa gtgtggacta caatgagaaa 3001 ctcagttttg aggccccacc aagcatctgg tcaaggatag tcaactttgg ttcaggttgg 3061 ggcttctggg tctcccctag cctgttcata acatcaaccc acgtcatacc ccagggcgca 3121 aaggagttct ttggagttcc catcaaacaa attcaggtac acaagtcagg cgaattttgt 3181 cgcttgaggt tcccaaaacc aatcaggact gacgtgactg gcatgatctt ggaagaaggt 3241 gcgcccgaag gcaccgtggt cacactactc atcaaaaggt ctactggaga actcatgccc 3301 ctagcagcta gaatggggac ccatgcaacc atgaaaattc aagggcgcac cgttggagga 3361 cagatgggca tgcttctgac aggatccaac gccaaaagca tggatctagg caccacacca 3421 ggtgattgcg gctgtcccta catctacaag agaggaaatg actatgtggt cattggagtt 3481 catacggctg ccgctcgtgg gggaaacact gtcatatgtg ccacccaagg gggcgagggg 3541 gaagctacac ttgaaggtgg tgacagtaag ggaacatact gtggtgcacc aatcctaggc 3601 ccagggagtg ccccaaaact tagcaccaaa accaaattct ggagatcatc cacagcacca 3661 ctcccacctg gcacctatga accagcatac cttggtggca aggaccccag agtcaagggt 3721 ggcccttcgt tgcagcaagt catgagggac cagctgaaac catttacaga gcccaggggt 3781 aagccaccaa agccaagtgt gttagaagct gccaagaaaa ccatcatcaa tgtccttgaa 3841 caaacaattg acccacctga gaagtggtcg ttcgcacaag cttgtgcctc ccttgacaag 3901 accacttcta gcggccatcc gcaccatatg cggaaaaacg actgctggaa tggggagtcc 3961 ttcacaggca agctggcaga ccaggcttct aaggccaacc tgatgtttga agaagggaag 4021 aacatgaccc cagtctacac aggtgcactt aaggatgaat tagtcaaaac tgacaaaatt 4081 tatggtaaga tcaagaagag gcttctctgg ggctcggatt tagcaaccat gatccggtgt 4141 gctcgagcat tcggaggcct aatggatgaa cttaaagcac actgtgtcac acttcctatt 4201 agagttggta tgaatatgaa tgaggatggc cccatcatct tcgagaagca ttccaggtac 4261 agataccact atgatgctga ttactctcgg tgggattcaa cacaacagag agccgtgctg 4321 gcagctgctc tagaaatcat ggttaaattc tcctcagaac cacatttggc tcaggtagtc 4381 gcagaagatc ttctttcccc tagcgtggtg gatgtgggtg acttcacaat atcaatcaac 4441 gagggccttc cctctggggt gccctgcacc tcccaatgga actccatcgc ccactggctt 4501 ctcactcttt gtgcactctc cgaagtcaca aatttgtccc cagacatcat acaggctaat 4561 tctctcttct ccttctatgg tgatgatgaa attgttagta cagacataaa attggaccca 4621 gagaagttga cagcaaagct taaggaatat gggttgaaac caacccgccc tgacaaaact 4681 gaaggacctc tcgttatttc tgaagactta gatggtttga ctttcctgcg gagaactgtg 4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gctcaatact caggcaaatg 4801 tactggacta ggggccccaa ccatgaagat ccatctgaat caatgattcc acactctcaa 4861 agacccatac aattgatgtc cttactggga gaggccgcac tccacggccc aacattctac 4921 agtaaaatca gcaaattagt cattgcagag ctaaaagaag gtggtatgga tttttacgtg 4981 cccaggcaag agccaatgtt caggtggatg agattctcag atctgagcac gtgggagggc 5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgaatgacg ccaacccatc 5101 tgatgggtcc gcagccaacc tcgtcccaga ggtcagcaat gaggttatgg ctttggagcc 5161 cgttgtcggt gccgctattg cggcgcctgt agcgggccaa caaaatgtaa ttgacccctg 5221 gattagaaac aattttgtac aagcccctgg tggagagttc acagtatccc ctagaaacgc 5281 tccaggtgaa atactatgga gcgcgccctt aggccctgat ctgaatccct atctatccca 5341 tttggccaga atgtataatg gttatgcagg tggttttgaa gtgcaggtga tcctcgcggg 5401 gaacgcgttc accgccggaa aaattatatt tgcagcagtc ccaccaaatt ttccaactga 5461 aggcctgagt cccagccagg tcactatgtt cccccacata atagtagatg ttaggcaatt 5521 ggaacctgtg ttgatcccct tacctgatgt taggaataac ttctatcatt ataatcaaac 5581 aaatgattct accattaaat tgatagcaat gctgtataca ccacttaggg ccaataatgc 5641 tggggaagat gtcttcacag tctcttgtcg agtcctcact aggccgtccc ctgattttga 5701 ttttatattt ttggtgccac ccacagttga gtcaagaact aaaccattta ctgtcccaat 5761 cttaaccgtt gaagaaatga ccaattcaag attccccatt cctttggaaa agttgttcac 5821 gggtcccagc ggtgcctttg ttgtccaacc acaaaatggc aggtgcacga ctgatggcgt 5881 gctcttaggc accacccaac tgtctcctgt caacatctgc accttcagag gggatgtcac 5941 ccacattgca ggttctcgta attacacaat gaatttggca tctctaaatt ggaacaatta 6001 tgacccaaca gaagaaattc cagcccctct gggaactcca gatttcgtgg gaaagatcca 6061 aggtgtgctc actcaaacca caaaaggaga tggctcgacc cgtggccata aagctacagt 6121 ttacactggg agtgccccct ttactccaaa gctgggcagt gttcaattca gtactgacac 6181 agaaaatgat tttgaaactc accaaaacac aaaattcacc ccagtcggtg tcatccagga 6241 tggtggcacc acccaccgaa atgaacccca acaatgggcg ctcccaagtt attcaggtag 6301 agatgttcat aatgtacacc tagcccctgc tgtggccccc acttttccgg gtgaacaact 6361 tcttttcttc aggtccacta tgcccggatg cagcgggtat cccaacatgg atttggattg 6421 cctactcccc caggagtggg tgcagcactt ctaccaagag gcagctccag cacaatctga 6481 tgtggctcta ttgagatttg tgaatccaga cacgggtagg gtcctgtttg agtgcaaact 6541 tcataaatca ggctatgtca cagtggctca caccggtcag catgatttgg tcatcccccc 6601 caatggctat tttaggtttg attcctgggt taatcagttc tacacgcttg cccccatggg 6661 aaacggaacg gggcgtaggc gcgccttata atggctggag ctttctttgc tggattggca 6721 tctgatgtcc ttggctctgg acttagttcc ctaatcaatg ctggggctgg ggccatcaac 6781 caaaagattg attttgaaaa taatagaaaa ttgcagcaag cttccttcca gtttagcagt 6841 aatctacaac aggcttcctt tcaacacgat aaagagatgc tccaagcaca aattgaggcc 6901 actaaaaagt tgcaacagga gatgatgaaa gtcaaacagg caatgctcct agaaggtgga 6961 ttctctgaaa cagatgcagc ccgtggggca gtcaacgccc ccatgacaaa ggttttggac 7021 tggagcggaa caaggtactg ggcccctgat gctaggacca caacatacaa tgcaggccgc 7081 ttttccaccc ctcaaccttc ggggacgctg ccaggaagaa tcaatcccag gactcctacc 7141 cccgctcggg gctcctccag cacatcttct aatgcttcta ctgctacttc tatatattca 7201 aatcaaactg tttcaacgag acttggttct acagctggtt ctggcaccaa tgtctcgagt 7261 ctcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaaacagaaa tttgtcacct 7321 ttcatgaggg gggctcataa catatcgttt gtcaccccac catctagcag atcctctagc 7381 caaggcacag tctcaaccgt gcctaaagaa gttttggact cctggactgg c //