Typing tool
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Complete norovirus genomes
KM198576 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 70..5088 ORF2: 5069..6691 ORF3: 6691..7431LOCUS KM198576 7431 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/C2H-43/2011/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198576 VERSION KM198576.1 KEYWORDS . SOURCE Norovirus Hu/GII/C2H-43/2011/VNM ORGANISM Norovirus Hu/GII/C2H-43/2011/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/C2H-43/2011/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/C2H-43/2011/VNM" /host="Homo sapiens" /db_xref="taxon:1527017" /country="Viet Nam" /collection_date="14-Oct-2011" /note="genotype: GII" CDS 70..5088 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02856.1" /translation="MFSSMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKVPPP PPNGEDEVVVSYSAKDGISGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT LKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT TDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK VLAFRQLAAENKYGLMDTMRVGRQLKDVKTMPELKQALKSISIKKCQIVYSGCTYTLE SDGKGNVKVDRVQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV TTRIIKRVNIQNLWSKPQMENTEEATNKDGCPKPKDDEEFVITSDDIKTEGKKGKNKT GRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARATEED FCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSV DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIKRSTGELMPLAARMGTHATM KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKSMT PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR VGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQV VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE DGVE" CDS 5069..6691 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02857.1" /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFIVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFEAHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKPGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6691..>7431 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02858.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGPLPGRINPRTPTPARASSSTSS NASTITSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTKSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTG" ORIGIN 1 tctaacgtcg cttccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca 61 agtgacaaaa tgttttctag catggctgtc acttttaaac gagccctcgg ggcgcggcct 121 aaacagcctc ccccgaggga aataccgcaa agacccccac gaccacctac tccagaacta 181 gtcaaaaagg tccctcctcc cccgcccaac ggagaggatg aagtggtggt ttcttatagt 241 gccaaagatg gcatttctgg tctacctgag ctttccaccg tcagacaacc agaagaaacc 301 aatacggcct tcagtgtccc tccactcaat cagagggaga atagggatgc taaggaacca 361 ctgactggga caattctgga aatgtgggat ggagaaatct atcattatgg cctgtatgtt 421 gaacgaggtc ttgtgctggg tgtgcacaaa ccaccagctg ccattagcct cgccaaggtc 481 gaactaacac cactctcctt gttctggaga cctgtgtaca ccccacagta cctcatctct 541 ccagacactc tcaagaaatt acacggagaa acatttccct acacagcctt tgacaacaac 601 tgctatgcct tttgttgctg ggtcctggat ctaaacgact cgtggctgag taggagaatg 661 atccagagaa caactggctt cttcagaccc taccaagatt ggaataggaa acccctccct 721 actacggatg attccaaatt aaagaaggta gctaacatat tcctgtgcac cctgtcttcg 781 ctattcacca ggcccataaa agacataata ggaaagttaa ggcccctcaa catcatcaac 841 atcctagctt catgtgactg gactttcgca ggcatcgtgg aatccttgat actcttggca 901 gagctctttg gagtcttctg gacaccccca gatgtgtctg cgatgattgc ccccttactc 961 ggtgatttcg agttacaagg acctgaggac cttgtagtgg agctcgtccc tgtggtaatg 1021 gggggaattg gtttggtgct gggattcacc aaagagaaga ttggaaaaat gttgtcatct 1081 gctgcgtcca ccttgagagc ttgtaaagat cttggtgcat atgggctaga gatcctaaag 1141 ctagtcatga agtggttctt cccgaagaaa gaggaggcaa atgaactggc tatggtgaga 1201 tccatcgagg atgcagtact ggaccttgag gcaattgaaa acaaccacat gaccaccttg 1261 ctcaaagata aagacagcct ggcaacctac atgagaaccc ttgacctcga ggaagagaaa 1321 gccagaaaac tctcaaccaa gtctgcttca cctgacatcg tgggcacaat caacgccctt 1381 ctggcgagaa tcgccgctgc acgctccctg gtgcaccgag cgaaggagga gctttccagc 1441 agaccaagac ctgtggtctt gatgatatca ggtagaccag ggatagggaa gacccacctt 1501 gctagggaag tggctaagag gatcgcagcc tccctcacag gagaccagcg cgtaggcctc 1561 atcccacgca atggcgtcga tcactgggat gcgtacaagg gggagagggt cgtcctatgg 1621 gacgactatg gaatgagcaa tcccatccac gacgccctca ggctgcaaga actcgccgac 1681 acttgccccc tcactctaaa ttgtgacagg attgagaata aaggaaaggt ctttgacagt 1741 gatgtcatca ttatcactac taatctggcc aacccagcac cactggacta tgtcaacttt 1801 gaagcgtgct cgaggcgcat cgatttcctc gtgtacgcag aagcccccga ggtcgaaaag 1861 gcgaagcgtg acttcccggg ccaacctgac atgtggaaaa acgcttttag ttctgatttc 1921 tcacacataa aactggcact ggctccacaa ggtggcttcg ataagaacgg gaacacccca 1981 catgggaagg gcgtcatgaa gactctcacc actggctccc ttattgcccg ggcatcaggg 2041 ctgctccatg agaggttgga tgagtttgaa ctacagggcc cagctctcac caccttcaac 2101 tttgaccgca acaaagtgct tgccttcagg caactcgctg ctgaaaacaa atacgggttg 2161 atggacacaa tgagagttgg gaggcagctc aaggatgtca aaaccatgcc agaacttaaa 2221 caagcactca agagcatctc aatcaagaag tgtcagattg tgtacagtgg ttgcacctac 2281 acacttgagt ctgatggcaa gggcaatgtg aaggttgaca gagttcagag cacctccgtg 2341 cagaccaaca atgagctggc tggcgccctg caccatctga ggtgcgccag aatcaggtac 2401 tatgttaagt gcgtccagga ggccctgtat tctatcattc agattgctgg agctgcattc 2461 gtcaccacgc gcatcatcaa gcgtgtgaac attcaaaact tatggtccaa gccacaaatg 2521 gaaaatacag aggaagccac caacaaggat gggtgcccaa aacccaaaga tgatgaggag 2581 ttcgtcatca catctgacga cattaaaact gagggtaaga aaggaaagaa caagactggc 2641 cgtggtaaga agcacacagc cttctcaagt aaaggtctca gtgatgaaga gtatgatgag 2701 tacaagagaa ttagagagga aaggaatggc aagtactcca tagaagagta ccttcaggac 2761 agggacaaat actacgagga ggtggccatt gccagggcga ccgaggaaga cttctgtgaa 2821 gaggaggagg ccaagatccg gcaaaggatc ttcagaccaa caaggaaaca acgcaaggaa 2881 gaaagagctt ctctcggttt agtcacaggt tctgaaatta ggaaaagaaa cccagatgat 2941 ttcaagccca aggggaaact atgggctgac gatgacagaa gtgttgacta caatgagaaa 3001 ctcagttttg aggctccgcc aagcatctgg tcaaggatag tcaactttgg ctcaggttgg 3061 ggcttctggg tctcccccag cctgttcata acatcaaccc acgtcatacc ccagggcgca 3121 aaggagttct ttggagtccc catcaaacaa attcaggtgc acaagtcagg cgaattctgt 3181 cgcttgaggt tcccaaaacc aatcaggact gatgtgactg gcatgatctt ggaagaaggc 3241 gcgcctgaag gcaccgtggc cacactactc atcaaaaggt ctactggaga actcatgccc 3301 ctagcagcca gaatggggac ccatgcaacc atgaaaattc aagggcgcac tgttggaggt 3361 cagatgggca tgcttctgac aggatccaac gccaaaagca tggatctagg caccacacca 3421 ggtgattgcg gctgtcccta catctacaag agagggaatg actatgtggt cattggagtc 3481 cacacggctg ccgctcgtgg gggaaacact gttatatgtg ccacccaggg gggtgagggg 3541 gaagctacac ttgaaggtgg tgacagcaag ggaacgtact gcggtgcgcc aatcctaggc 3601 ccagggagcg ccccaaaact tagtaccaaa accaaattct ggaggtcatc cacagcacca 3661 ctcccacctg gcacctatga gccagcctac cttggtggca aggaccccag agtcaagggt 3721 ggcccctcgc tgcagcaagt catgagagac cagctgaaac cattcacaga gcccaggggt 3781 aagccaccaa agccaagtgt gttggaagct gccaagaaaa ccatcatcaa tgttcttgaa 3841 caaacaattg acccacctga gaagtggtcg ttcgcacagg cttgcgcgtc ccttgacaag 3901 accacttcta gcggccatcc gcatcacatg cggaaaaacg actgctggaa cggggagtcc 3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgtttga agaagggaag 4021 agcatgaccc cagtttacac aggtgcgctc aaggacgagt tggtcaaaac tgataaaatt 4081 tatggcaaga taaagaagag gcttctctgg ggctcggatt tagcaaccat gatccggtgt 4141 gctcgagcat tcggaggcct aatggatgaa ctcaaagcac actgtgtcac acttcctatc 4201 agagttggta tgaatatgaa tgaggatggc cccatcatct tcgagaagca ctccaggtac 4261 aggtaccact atgatgctga ttactctcga tgggattcaa cacaacagag agccgtgctg 4321 gcagctgctc tagaaattat ggttaaattc tcctcagaac cacatttggc tcaggtggtc 4381 gcagaagacc ttctttctcc tagcgtggtg gatgtgggtg acttcacaat atcaatcaat 4441 gagggtcttc cctctggggt gccctgcact tctcaatgga actccatcgc ccactggctt 4501 ctcactctat gtgcactctc cgaagttaca aatttgtccc cagacatcat acaggctaat 4561 tctctcttct ccttctatgg tgatgatgaa attgttagta cagacataaa actagaccca 4621 gagaagttga cagcaaagct taaggaatat gggttaaaac caacccgccc tgacaaaact 4681 gaaggacctc ttgttatttc tgaagactta gatggtttga ctttcctgcg gagaactgtg 4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gctcaatact caggcaaatg 4801 tactggacta ggggccccaa ccatgaagat ccatctgaat caatgattcc acactctcaa 4861 agacccatac aattgatgtc cctgctggga gaggccgcac tccacggccc aacattctat 4921 agtaaaatta gcaaattagt cattgcagag ctaaaagaag gtggtatgga tttttacgtg 4981 cccaggcaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc 5041 gatcgcaatc tggctcccag ctttgtgaat gaagatggcg tcgaatgacg ccaacccatc 5101 tgatgggtcc gcagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctttggagcc 5161 cgttgtcggt gccgctattg cggcgcctgt agcgggccaa caaaatgtaa ttgacccctg 5221 gattaggaat aattttgtac aagcccctgg tggagaattc acagtatccc ctagaaacgc 5281 tccaggtgaa atactatgga gcgcgccctt aggccctgat ctgaatccct acctatccca 5341 tttggccaga atgtataatg gctatgcagg tggctttgaa gtgcaggtga tcctcgcggg 5401 gaacgcgttc accgccggaa aaattatatt tgcagcagtt ccaccaaatt ttccaactga 5461 aggcttgagc cccagccagg ttactatgtt cccccacata atagtagatg ttaggcaact 5521 ggaacctgtg ttgatcccct tacctgatgt taggaataac ttctatcatt ataatcagtc 5581 aaatgattct accattaaat tgatagcaat gctgtacaca ccacttaggg ctaataatgc 5641 tggggaagat gtcttcacag tctcttgtcg agtcctcacg aggccatccc ctgattttga 5701 ttttatattt ttggtgccac ccacagttga gtcaagaact aaaccattta ctgtcccaat 5761 cttaactgtt gaagaaatga ccaattcaag attccccatc cctttggaaa agttgttcac 5821 gggccccagc ggtgccttca ttgttcaacc acaaaatggt agatgcacga ccgatggcgt 5881 gctcttaggc accacccaac tgtctcctgt caacatctgc accttcagag gggatgtcac 5941 ccacattgca ggttctcgca attacacgat gaatttggct tctctaaatt ggaataatta 6001 tgacccaaca gaagaaattc cagcccctct gggaactcca gatttcgtgg gaaagatcca 6061 aggtgtgctc actcaaacca caaagggaga tggctcgacc cgtggccata aagcaacagt 6121 ttacactggg agtgccccct ttactccaaa gctgggcagt gttcaattca gtactgacac 6181 agaaaatgat tttgaagctc accaaaacac aaaattcacc ccagtcggtg tcatccagga 6241 tggtggcacc acccaccgaa atgaacccca acaatgggtg ctcccaagtt attcaggtag 6301 agatgtccac aatgtacacc tggcccctgc tgtagccccc acttttccgg gtgaacaact 6361 tcttttcttc aggtccacta tgcccggatg cagtgggtat cccaacatgg atttggattg 6421 cctactccct caggagtggg tgcagcactt ctaccaagag gcagctccag cacaatctga 6481 tgtggctcta ttgagatttg tgaatccaga cacgggtagg gtcctgtttg agtgcaaact 6541 tcataaacca ggctatgtca cagtggctca caccggccag catgatttgg tcatcccccc 6601 taatggctat tttaggtttg attcctgggt taaccaattc tacacacttg cccccatggg 6661 aaatggaacg gggcgtagac gtgctttata atggctgggg ctttctttgc tggattggca 6721 tctgatgtcc ttggctctgg acttggctcc ctaatcaatg ctggggctgg ggctatcaac 6781 caaaagattg attttgaaaa taacagaaaa ttgcagcaag cttccttcca gtttagcagt 6841 aatctacaac aggcctcctt tcaacatgac aaagagatgc tccaagcaca aattgaggcc 6901 actaaaaagt tgcaacagga aatgatgaga gtcaaacagg caatgctctt agaaggtggg 6961 ttctctgaaa cagatgcagc tcgtggggca atcaacgccc ccatgacaaa ggttttggac 7021 tggagtggaa caaggtactg ggcccctgat gccaggacta caacatacaa tgcaggccgc 7081 ttttccaccc cccaaccctc ggggccattg ccaggaagaa tcaatcccag gactcctact 7141 cccgctcggg cctcctccag tacatcctct aatgcttcta ctattacttc tatatattca 7201 aatcaaactg tttcaacgag acttggttct acagctggct ctggcaccaa tgtctcgagt 7261 ctcccgtcaa ctgcaaggac taagagttgg gttgaggatc aaaacagaaa tttgtcacct 7321 ttcatgaggg gggctcacaa catatcattt gtcaccccac catctagcag atcctctagc 7381 caaggcacag tctcaaccgt gcctaaagaa gttttggact cctggactgg c //