Typing tool
|
Complete norovirus genomes
KM198490 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 70..5088 ORF2: 5069..6691 ORF3: 6688..7431LOCUS KM198490 7431 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/10002/2009/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198490 VERSION KM198490.1 KEYWORDS . SOURCE Norovirus Hu/GII/10002/2009/VNM ORGANISM Norovirus Hu/GII/10002/2009/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/10002/2009/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/10002/2009/VNM" /host="Homo sapiens" /db_xref="taxon:1175309" /country="Viet Nam" /collection_date="04-May-2009" /note="genotype: GII" CDS 70..5088 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02598.1" /translation="MFSNMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKIPPP PPNGEDEVVVSYSAKDGVSGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT LKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT MDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK VLAFRQLAAENKYGLIDTMKVGRQLKDVKTMPELKQALKNISIKKCQIVYSGCTYTLE SDGKGNVKVDRIQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV ATRIIKRVNIQDLWSKPQVENTEEATNKDGCPKPKDDEEFVISSDDIKTEGKKGKNKT GRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARATEED FCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPEDFKPKGKLWADDDRSV DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGTHATM KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMT PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR VGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRVVLAAALEIMVKFSSEPHLAQV VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE DGVE" CDS 5069..6691 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02599.1" /translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDITHIAGSRDYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKRDGSTRGHKATVYTGSAPFTPKLGSVRFSTDTENDFETHQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6688..>7431 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02600.1" /translation="MMAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQ ASFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAI NAPMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRINPRTPTPARGSSSTS SNASTATSIHSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHN ISFVTPPSSRSSSQGTVSTVPKEVLNSWTG" ORIGIN 1 tctaacgacg cctccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca 61 agtgacaaaa tgttttctaa catggctgtc acttttaaac gagccctcgg ggcgcggcct 121 aaacagcccc ccccgaggga aataccacaa agacccccac gaccacctac tccagaactg 181 gtcaaaaaga tccctcctcc cccgcccaac ggagaggatg aagtagtggt ttcttatagt 241 gccaaagatg gcgtttccgg attacctgag 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 ctccccagta cctcatctct 541 ccagacactc tcaagaaatt acacggagaa 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 agtccttgat 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 atgcagtact ggaccttgag gcaattgaaa acaaccatat gaccaccttg 1261 ctcaaagaca aagacagcct ggcaacctac atgagaaccc ttgacctcga ggaagagaag 1321 gccagaaaac tctcaaccaa gtctgcttca cctgacatcg tgggcacaat caacgccctt 1381 ctggcgagaa tcgccgctgc acgctccctg gtgcaccgag cgaaggagga gctttccagc 1441 agaccaagac ctgtagtctt gatgatatca ggaagaccag 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 attgagaata 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 gaacacccca 1981 cacgggaagg gcgtcatgaa gactctcacc actggctccc tcattgcccg ggcgtcaggg 2041 ctgctccatg agagattgga tgagtttgaa ctacagggcc cagctcttac caccttcaac 2101 tttgaccgca acaaagtgct tgccttcaga cagcttgctg ctgaaaacaa atatgggttg 2161 atagacacaa tgaaagttgg gaggcagctc aaggatgtca aaaccatgcc agaacttaaa 2221 caagcactca agaacatctc aatcaagaag tgccagattg tgtatagtgg ttgcacctac 2281 acgcttgaat ctgatggcaa gggcaatgtg aaagttgaca gaatccagag cacctccgta 2341 cagaccaaca atgagctggc tggcgccctg catcatctga ggtgcgccag aatcaggtac 2401 tatgtcaagt gtgtccagga ggccctgtat tctatcatcc agattgctgg ggctgcattt 2461 gtcgccacgc gcatcatcaa gcgtgtgaac attcaagact tatggtccaa gccacaagtg 2521 gaaaacacag aggaggctac caacaaggac gggtgcccaa aacccaaaga tgatgaggag 2581 ttcgtcattt catctgacga cattaaaact gagggtaaga aagggaagaa caagactggc 2641 cgtggcaaga agcacacagc cttctcaagt aaaggtctca gtgatgaaga gtatgatgag 2701 tacaagagaa ttagagagga aaggaatggc aagtattcca tagaagagta tcttcaggac 2761 agggacaaat actatgagga ggtggccatt gccagggcga ccgaggaaga cttctgtgaa 2821 gaggaggagg ccaagatccg gcaaaggatc ttcagaccaa caaggaaaca acgcaaggaa 2881 gaaagagctt ctctcggttt agtcacaggt tctgagatta ggaaaagaaa cccagaagac 2941 ttcaagccta agggaaaact atgggctgac gatgacagaa gtgtggacta caatgagaaa 3001 ctcagttttg aggccccacc aagcatctgg tcaaggatag tcaactttgg ttcaggttgg 3061 ggcttctggg tctcccctag cctgttcata acatcaaccc acgtcatacc ccagggcgca 3121 aaggagttct ttggagtccc catcaaacaa attcaggtac acaagtcagg cgaattctgt 3181 cgcttgaggt tcccaaaacc aatcaggact gacgtgactg gcatgatctt ggaagaaggt 3241 gcgcccgaag gcaccgtggt cacgctactc atcaaaaggt ctactggaga actcatgccc 3301 ctagcagcta gaatggggac ccatgcaacc atgaaaattc aagggcgcac cgttggaggt 3361 cagatgggca tgcttctgac aggatccaac gccaaaagca tggatctagg caccacacca 3421 ggtgattgcg gctgtcccta catctacaag agaggaaatg actatgtggt cattggagtc 3481 cacacggctg ccgctcgtgg gggaaacact gtcatatgtg ccacccaggg gggcgagggg 3541 gaagctacac ttgaaggtgg tgacagtaag ggaacatact gtggtgcacc aatcctaggc 3601 ccagggagtg ccccaaaact tagcaccaaa accaaattct ggagatcatc cacagcacca 3661 ctcccacctg gcacctatga accagcctac cttggtggca aggaccccag agtcaagggt 3721 ggcccttcgt tgcagcaagt catgagggac cagctgaaac catttacaga gcccaggggt 3781 aagccaccaa agccaagtgt gttggaagct gccaagaaaa ccatcatcaa tgtccttgaa 3841 caaacaattg acccacctga gaagtggtcg ttcgcacaag cttgcgcctc ccttgacaag 3901 accacttcta gcggccatcc gcaccacatg cggaaaaacg actgctggaa tggggagtcc 3961 ttcacaggca agctggcaga ccaggcttcc aaggctaacc tgatgtttga agaagggaag 4021 aacatgaccc cagtctacac aggtgcactt aaggatgaat tagtcaaaac cgacaaaatt 4081 tatggtaaga tcaagaagag gcttctctgg ggctcggatt tagcaaccat gatccggtgt 4141 gctcgagcat tcggaggcct aatggatgaa ctcaaagcac actgtgtcac acttcctatt 4201 agagttggta tgaatatgaa tgaggatggc cctatcatct tcgagaagca ttccaggtac 4261 agataccact atgatgctga ttactctcgg tgggattcaa cacaacagag agtcgtgctg 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 caaggaatat gggttgaaac caacccgccc tgataaaact 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 cagatggatg agattctcag atctgagcac gtgggagggc 5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgaatgacg ccaacccatc 5101 tgatgggtcc gcagccaacc tcgtcccaga ggtcagcaat gaggttatgg ctttggaacc 5161 cgttgtcggt gccgctattg cggcgcctgt agcgggccaa caaaatgtaa ttgacccctg 5221 gattagaaac aattttgtac aagcccctgg tggagagttc acagtatccc ctagaaacgc 5281 tccaggtgaa atactatgga gcgcgccctt aggccctgat ctgaatccct acctatctca 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 taggaataat ttctatcatt ataatcagac 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 agatgcacga ctgatggcgt 5881 gctcttaggc accacccaac tgtctcctgt caacatctgc accttcagag gggatatcac 5941 ccacattgca ggttctcgtg attacacaat gaatttggca tctctaaatt ggaacaatta 6001 tgacccaaca gaagaaattc cagcccctct gggaactcca gatttcgtgg gaaagatcca 6061 aggtgtgctc actcaaacca caaaaagaga tggctcgacc cgtggccata aagctacagt 6121 ttacactggg agtgccccct ttactccaaa gctgggcagt gttcgattca gtactgacac 6181 agaaaatgat tttgaaactc accaaaacac aaaattcacc ccagtcggtg tcatccagga 6241 tggtagcacc acccaccgaa atgaacccca acaatgggtg ctcccaagtt attcaggtag 6301 agatgttcat aatgtacacc tagcccctgc tgtagccccc acttttccgg gtgaacaact 6361 tcttttcttc aggtccacca tgcccggatg cagcgggtat cccaacatgg acttggattg 6421 cctactcccc caggagtggg tgcagcactt ctaccaagag gcagctccag cacaatctga 6481 tgtggctcta ctgagatttg tgaatccaga cacgggtagg gtcctgtttg agtgcaaact 6541 tcataaatca ggttatgtca cagtggctca caccggtcag catgatttgg tcatcccccc 6601 caatggctat tttaggtttg attcttgggt taaccaattc tacacacttg cccccatggg 6661 aaacggaacg gggcgtaggc gcgctttatg atggctggag ctttctttgc tggattggca 6721 tctgatgtcc ttggctctgg acttggctcc ctgatcaatg ctggggctgg ggctatcaac 6781 caaaagattg attttgaaaa taatagaaaa ttgcagcaag cttccttcca gtttagcagt 6841 aatctacaac aggcttcctt tcaacacgat aaagagatgc tccaagcaca aattgaggcc 6901 actaaaaagt tgcaacagga aatgatgaaa gtcaaacagg caatgctcct agaaggtgga 6961 ttctctgaaa cagatgcagc ccgtggggca atcaacgccc ccatgacaaa ggctttggac 7021 tggagcggaa caaggtactg ggcccctgat gctaggacta caacatacaa tgcaggccgc 7081 ttttccaccc ctcaaccttc gggggcgctg ccaggaagaa tcaatcccag gactcctacc 7141 cccgctcggg gctcctccag cacatcttct aatgcttcta ctgctacttc tatacattca 7201 aatcaaaccg tttcaacgag acttggttct acagctggtt ctggtaccaa tgtctcgagt 7261 ctcccgtcaa ctgcaaggac taggagttgg gttgaggatc aaaacagaaa tttgtcacct 7321 ttcatgaggg gggctcataa catatcgttt gtcaccccac catctagcag atcctctagc 7381 caaggcacag tctcaaccgt gcctaaagaa gttttgaact cctggactgg c //