Typing tool
|
Complete norovirus genomes
KM198575 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7443LOCUS KM198575 7443 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/20069/2009/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198575 VERSION KM198575.1 KEYWORDS . SOURCE Norovirus Hu/GII/20069/2009/VNM ORGANISM Norovirus Hu/GII/20069/2009/VNM Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7443) 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 7443) 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..7443 /organism="Norovirus Hu/GII/20069/2009/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/20069/2009/VNM" /host="Homo sapiens" /db_xref="taxon:1526975" /country="Viet Nam" /collection_date="16-Jul-2009" /note="genotype: GII" CDS 1..5100 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02853.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSNMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVKTM PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRIQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRNKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRVVLAAALEIMVKFSSEPHLAQIVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" CDS 5081..6703 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02854.1" /translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6703..>7443 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02855.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRINPRTPTPARGSSSTSS NASTATSIHSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTG" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacact 61 gcaaaatctt caagtgacaa aatgttttct aacatggctg tcacttttaa acgagccctc 121 ggggcgcggc ctaaacagcc ccccccgagg gaaataccac aaagaccccc acgaccacct 181 actccagaac tggtcaaaaa gatccctcct cccccgccca acggagagga tgaagtagtg 241 gtttcttata gtgccaaaga tggcgtttcc ggtttgcctg agctttccac cgtcaggcaa 301 ccggaagaaa ccaatacggc attcagtgtc cctccactca accagaggga gaatagagat 361 gctaaggaac cactaactgg aacaattctg gaaatgtggg atggagaaat ctaccactat 421 ggcctgtatg ttgagcgagg tcttgtgctg ggtgtgcaca aaccaccagc tgccataagc 481 ctcgccaagg tcgaactaac accactctcc ttgttctgga gacctgtgta cactccccag 541 tacctcatct ctccagacac tctcaagaaa ttgcacggag aaacgtttcc ctacacagcc 601 tttgacaaca attgctatgc cttttgttgt tgggtcctgg atctaaatga ctcgtggctg 661 agtaggagaa tgatccagag aacaactggc ttcttcagac cctaccaaga ctggaatagg 721 aaacccctcc ccactatgga tgattccaaa ttaaagaagg tagctaacat attcctgtgc 781 gccctgtctt cgctattcac caggcccata aaagacataa taggaaagct aagacctctc 841 aacatcatca acatcctggc ttcatgtgat tggactttcg caggcatagt ggagtccttg 901 atactcttgg cagagctctt tggagtcttc tggacacccc cagatgtgtc tgcgatgatt 961 gcccccttac tcggtgattt cgagttacaa ggacctgagg accttgtagt ggagctcgtc 1021 cctgtagtaa tggggggaat tggtttggtg ctgggattca ccaaagagaa gattgggaaa 1081 atgttgtcat ctgctgcatc caccttgaga gcttgtaaag atcttggtgc atatgggcta 1141 gagatcctaa aattagtcat gaagtggttt ttcccgaaga aagaggaggc aaatgaactg 1201 gctatggtga gatccatcga ggatgcagta ctggaccttg aggcaattga aaacaaccat 1261 atgaccacct tgctcaaaga caaagacagc ctggcaacct acatgagaac tcttgacctc 1321 gaggaggaga aagccagaaa actctcaacc aagtctgctt cacctgacat cgtgggcaca 1381 atcaacgccc ttctggcgag aatcgccgct gcacgctccc tggtgcaccg agcgaaggag 1441 gagctttcca gcagaccaag acctgtagtc ttgatgatat caggcagacc agggatagga 1501 aaaacccacc ttgctaggga agtggctaag agaatcgcag cctccctcac aggagaccag 1561 cgtgtaggcc tcatcccacg caatggcgtc gatcactggg atgcgtacaa gggggagagg 1621 gtcgtcctat gggacgacta tggaatgagc aaccccattc acgacgccct taggctgcaa 1681 gaactcgctg acacttgccc ccttactcta aattgtgaca gaattgagaa taaaggaaag 1741 gtctttgaca gcgatgtcat cattatcacc actaatctgg ccaacccagc accactggac 1801 tatgtcaact ttgaagcgtg ctcgaggcgc atcgatttcc tcgtgtatgc agaagccccc 1861 gaggtcgaaa aggcgaagcg tgacttcccg ggccaacctg acatgtggaa aaacgctttt 1921 agttctgatt tctcacacat aaaattggca ctggctccac aaggtggctt tgataagaac 1981 gggaacactc cacacgggaa gggcgtcatg aagactctca ccactggctc ccttattgcc 2041 cgggcatcag ggctgctcca tgagagattg gatgagtttg aactacaggg cccagctctt 2101 accaccttca actttgaccg caacaaagtg cttgccttta gacagcttgc tgctgaaaac 2161 aaatatgggt tgatagacac aatgaaagtt gggaggcagc tcaaggatgt caaaaccatg 2221 ccagaactta aacaagcact caagaacatc tcaatcaaga agtgccagat tgtgtatagt 2281 ggttgcacct acacacttga atctgatggc aagggcaatg tgaaagttga cagaatccag 2341 agcacctccg tacagaccaa caatgagctg gctggcgccc tgcatcatct gaggtgcgcc 2401 agaatcaggt actatgtcaa gtgtgtccag gaggccctgt attctatcat ccagattgct 2461 ggggctgcat ttgtcaccac gcgcatcatc aagcgtgtga acattcaaga cttatggtcc 2521 aagccacaag tggaaaacac agaggaggct accaacaagg acgggtgccc aaaacccaaa 2581 gatgatgagg agttcgtcat ttcatctgac gacattaaaa ctgagggtaa gaaagggaag 2641 aacaagactg gccgtggcaa gaagcataca gccttctcaa gtaaaggtct cagtgatgaa 2701 gagtatgatg agtacaagag aattagagag gaaaggaatg gcaagtattc catagaagag 2761 taccttcagg acaggaacaa atactatgag gaggtggcca ttgccagggc gaccgaggaa 2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tcttcagacc aacaaggaaa 2881 caacgcaagg aagaaagagc ttctctcggt ttagtcacag gttctgagat taggaaaaga 2941 aacccagaag acttcaagcc taagggaaaa ctatgggctg acgatgacag aagtgtggac 3001 tacaatgaga aactcagttt tgaggcccca ccaagcatct ggtcaaggat agtcaacttt 3061 ggttcaggtt ggggcttttg ggtctcccct agcctgttca taacatcaac ccacgtcata 3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaattcaggt acacaagtca 3181 ggcgaattct gtcgcttgag gttcccaaaa ccaatcagga ctgacgtgac tggcatgatc 3241 ttggaagaag gtgcgcccga aggcaccgtg gtcacactac tcatcaaaag gtctactgga 3301 gaactcatgc ccctagcagc tagaatgggg acccatgcaa ccatgaaaat tcaagggcgc 3361 accgttggag gtcagatggg catgcttctg acaggatcca acgccaagag catggatcta 3421 ggcaccacac caggtgattg cggctgtccc tacatctaca agagaggaaa tgactatgtg 3481 gtcattggag tccacacggc tgccgctcgt gggggaaaca ctgtcatatg tgccacccag 3541 gggggcgagg gggaagctac acttgaaggt ggtgacagta agggaacata ctgtggtgca 3601 ccaatcctag gcccagggag tgccccaaaa cttagcacca aaaccaaatt ctggagatca 3661 tccacagcac cactcccacc tggcacctat gaaccagcct accttggtgg caaggacccc 3721 agagtcaagg gtggcccttc attgcagcaa gtcatgaggg accagctgaa accatttaca 3781 gagcccaggg gtaagccacc aaagccaagt gtgttagaag ctgccaagaa aaccatcatc 3841 aatgtccttg aacaaacaat tgacccacct gagaagtggt cgttcgcaca agcttgcgcc 3901 tcccttgaca agaccacttc tagcggccat ccgcaccata tgcggaaaaa cgactgctgg 3961 aatggggagt ccttcacagg caagctggca gaccaggctt ccaaggctaa cctgatgttt 4021 gaagaaggga aaaacatgac cccagtctac acaggtgcac ttaaggatga attagtcaaa 4081 actgacaaaa tttatggtaa gatcaaaaag aggcttctct ggggctcgga tttagcaacc 4141 atgatccggt gtgctcgagc attcggaggc ctaatggatg aactcaaagc acactgtgtc 4201 acacttccta ttagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaag 4261 cattccaggt acagatacca ctatgatgct gattactctc ggtgggattc aacacaacag 4321 agagtcgtgc tggcagctgc cctagaaatc atggttaaat tctcctcaga accacatttg 4381 gctcagatag tcgcagaaga tcttctttcc cctagcgtgg tggatgtggg tgacttcaca 4441 atatcaatca acgagggcct tccctctggg gtgccctgca catcccaatg gaactccatc 4501 gcccactggc ttctcactct ttgtgcactc tccgaagtca caaatttgtc cccagacatc 4561 atacaggcta attctctctt ctccttctat ggtgatgatg aaattgttag tacagacata 4621 aaattggacc cagagaagtt gacagcaaag cttaaggaat atgggttgaa accaacccgc 4681 cctgacaaaa ctgaaggacc tctcgttatt tctgaagact tagatggttt gactttcctg 4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagctcaata 4801 ctcaggcaaa tgtactggac taggggcccc aaccatgaag atccatctga atcaatgatt 4861 ccacactctc aaagacccat acaattgatg tccttactgg gagaggccgc actccacggc 4921 ccaacattct acagtaaaat cagcaaatta gtcattgcag agcttaaaga aggtggtatg 4981 gatttttacg tgcccaggca agagccaatg ttcagatgga tgagattctc agatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga 5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcagca atgaggttat 5161 ggctttggag cccgttgtcg gtgccgctat tgcggcgcct gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagaa acaattttgt acaagcccct ggtggagagt tcacagtatc 5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atctgaatcc 5341 ctacctatct catttggcca gaatgtataa tggttatgca ggtggctttg aagtgcaggt 5401 gatccttgcg gggaacgcgt tcaccgccgg aaaaattata tttgcagcag tcccaccaaa 5461 ctttccaact gaaggcctga gtcccagcca ggtcactatg ttcccccaca taatagtaga 5521 tgttaggcaa ttggaacctg tgttgatccc cttacctgat gttaggaata atttctatca 5581 ttataatcag acaaatgatt ctaccattaa attgatagca atgctgtata caccacttag 5641 ggccaataat gctggggaag atgtcttcac agtctcttgt cgagtcctca ctaggccgtc 5701 ccctgatttt gattttatat ttttggtgcc gcccacagtt gagtcaagaa ctaaaccatt 5761 tactgtccca atcttaaccg ttgaagaaat gaccaattca agatttccca ttcctttgga 5821 aaagttgttc acgggtccca gcggtgcctt tgttgtccaa ccacaaaatg gcaggtgcac 5881 gactgatggc gtgctcttag gtaccaccca actgtctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccacattg caggatctcg taattacaca atgaatttgg catctctaaa 6001 ttggaacaat tatgacccaa cagaagaaat tccagcccct ctgggaactc cagatttcgt 6061 gggaaagatc caaggtgtgc tcactcaaac cacaaaagga gatggctcga cccgtggcca 6121 taaagctaca gtttacactg ggagtgcccc ctttactcca aaactgggca gtgttcaatt 6181 cagtactgac acagaaaatg attttgaaac tcaccaaaac acaaaattca ccccagtcgg 6241 tgtcatccag gatggtggca ccacccaccg aaatgaaccc caacaatggg tgctcccaag 6301 ttattcaggt agagatgttc ataatgtaca cctagcccct gctgtagccc ccacttttcc 6361 gggtgaacaa cttcttttct tcaggtccac tatgcccgga tgtagcgggt atcccaacat 6421 ggatttggat tgcctactcc cccaggagtg ggtgcagcac ttctaccaag aggcagctcc 6481 agcacagtct gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcctgtt 6541 tgagtgcaaa cttcataaat caggctatgt cacagtggcc cacaccggtc agcatgattt 6601 ggtcatcccc cccaatggct attttaggtt tgattcctgg gttaatcagt tctacacact 6661 tgcccccatg ggaaacggaa cggggcgtag gcgcgcttta taatggctgg agctttcttt 6721 gctggactgg catctgatgt ccttggctct ggacttggtt ccctaatcaa tgctggggct 6781 ggggctatca accaaaagat tgattttgaa aataatagaa aattgcagca agcttccttc 6841 cagtttagca gtaatcttca acaggcttcc tttcaacacg ataaagagat gctccaagca 6901 caaatcgagg ccactaaaaa gttgcaacag gaaatgatga aagtcaaaca ggcaatgctc 6961 ctagaaggtg gattctctga aacagatgca gcccgtgggg caatcaacgc ccccatgaca 7021 aaagttttgg actggagcgg aacaaggtac tgggcccctg atgctaggac tacaacatac 7081 aatgcaggcc gcttttccac ccctcaacct tcggggacgc tgccaggaag aatcaatccc 7141 aggactccta cccccgctcg gggctcctcc agtacatctt ctaatgcttc tactgctact 7201 tctatacatt caaatcaaac tgtttcaacg agacttggtt ctacagctgg ttctggtacc 7261 aatgtctcga gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga 7321 aatttgtcac ctttcatgag gggggctcat aacatatcgt ttgtcacccc accatctagc 7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aagttttgga ctcctggact 7441 ggc //