Typing tool
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Complete norovirus genomes
KM198558 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7443LOCUS KM198558 7443 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/30257/2009/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198558 VERSION KM198558.1 KEYWORDS . SOURCE Norovirus Hu/GII/30257/2009/VNM ORGANISM Norovirus Hu/GII/30257/2009/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/30257/2009/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/30257/2009/VNM" /host="Homo sapiens" /db_xref="taxon:1291808" /country="Viet Nam" /collection_date="30-Oct-2009" /note="genotype: GII" CDS 1..5100 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02802.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSNMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEAVVSYSAKDGVSGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVKTM PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRIQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC PKPEDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG RYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPERWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" CDS 5081..6703 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02803.1" /translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQTNDPTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRDYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTRGDGSTRGHKATVYTGSAPFAPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6703..>7443 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02804.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIS APMTKVLDWSGTRYWAPDARTTTYNSGRFSTPQPSGTLPGRINPRTPTPARGSSSTSS NASTATSIHLNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWAG" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc 61 gcaaaatctt caagtgacaa aatgttttct aacatggctg tcacttttaa acgagccctc 121 ggggcgcggc ctaaacagcc ccccccgagg gaaataccac aaagaccccc acgaccacct 181 actccagaac tggtcaaaaa gatccctcct cccccgccca acggagagga tgaagcagtg 241 gtttcttata gtgccaaaga tggcgtttcc ggtttacctg agctttccac cgtcaggcaa 301 ccggaagaaa ccaatacggc cttcagtgtc cctccactca accagaggga gaatagagat 361 gctaaggaac ctctgactgg aacaattctg gaaatgtggg atggagaaat ctaccattat 421 ggcctgtatg ttgagcgagg tcttgtgctg ggtgtgcaca aaccaccagc tgccataagc 481 ctcgccaagg tcgaactaac accactctcc ttgttctgga gacctgtgta cactccccag 541 tacctcatct ctccagacac tctcaagaaa ttacacggag aaacgtttcc ctacacagcc 601 tttgacaaca attgctatgc cttttgttgt tgggtcctgg atctaaatga ctcgtggctg 661 agtaggagaa tgatccagag aacaactggc ttctttagac cctaccaaga ctggaatagg 721 aaacccctcc ccactatgga tgattccaag ttaaagaagg tagctaacat attcctgtgc 781 gccctgtctt cgctattcac caggcccata aaagacataa taggaaagct aagacctctc 841 aacatcatca acatcctggc ttcatgtgat tggactttcg caggcatagt ggagtctttg 901 atactcttgg cagagctctt tggagtcttc tggacacccc cagatgtgtc tgcgatgatt 961 gcccccttac tcggtgattt cgagttacaa ggacctgagg accttgtagt ggagctcgtc 1021 cctgtagtaa tggggggaat tggtttggtg ttgggattca ccaaagagaa gattgggaaa 1081 atgttgtcat ctgctgcatc caccttgaga gcttgtaaag atcttggtgc atatgggcta 1141 gagatcctaa agttagtcat gaagtggttc ttcccgaaga aagaggaggc aaatgaactg 1201 gctatggtga gatccatcga ggatgcagta ctggaccttg aggcaattga aaacaaccat 1261 atgaccacct tgctcaaaga caaagacagc ctggcaacct acatgagaac ccttgacctc 1321 gaggaagaga aagccagaaa actctcaacc aagtctgctt cacctgacat cgtgggcaca 1381 attaacgccc 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 ggattgagaa 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 gggaacaccc cacacgggaa gggcgtcatg aagactctca ccactggctc cctcattgcc 2041 cgggcatcag ggctgctcca tgagagattg gatgagtttg aactacaggg cccagctctc 2101 accaccttca actttgatcg caacaaagta cttgccttca gacagcttgc agctgaaaac 2161 aaatatgggt tgatagacac aatgaaagtt gggaggcagc tcaaggatgt caaaaccatg 2221 ccagaactta aacaagcact caaaaacatc tcaatcaaga agtgccagat tgtgtatagt 2281 ggttgcacct acacacttga gtctgatggc aagggcaatg tgaaagttga cagaatccag 2341 agcacctccg tacagaccaa caatgagctt gctggcgccc tgcatcatct gaggtgcgcc 2401 agaatcagat actatgtcaa gtgtgtccag gaggccctat attctatcat ccagattgct 2461 ggggccgcat ttgtcaccac gcgcattatc aagcgtgtga acattcaaga cttatggtcc 2521 aagccacaag tggaaaacac agaggaggcc accaacaagg acgggtgccc aaaacccgaa 2581 gatgatgagg agttcgtcat ttcatctgac gacattaaaa ctgagggtaa gaaagggaag 2641 aacaagactg gccgtggcaa gaagcataca gccttttcaa gtaaaggtct cagtgatgaa 2701 gagtatgatg agtacaagag aattagagag gaaaggaatg gcaggtattc catagaagag 2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gaccgaggaa 2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tctttagacc aacaaggaaa 2881 caacgcaagg aagaaagagc ttctctcggt ttagtcacag gttctgagat taggaaaaga 2941 aacccagatg acttcaagcc taagggaaaa ctgtgggctg acgatgacag aagtgtggac 3001 tacaatgaga aactcagttt tgaggcccca ccaagcatct ggtcaaggat agtcaacttt 3061 ggttcaggtt ggggcttctg ggtctcacct agcctgttca taacatcaac ccacgtcata 3121 ccccagggcg caaaggagtt ctttggagtt cccatcaaac aaattcaggt acacaagtca 3181 ggcgaatttt gtcgcttgag gttcccaaaa ccaatcagga ctgacgtgac tggcatgatc 3241 ttggaagaag gtgcgcccga aggcaccgtg gtcacactac tcatcaaaag gtctactgga 3301 gaactcatgc ccctagcagc tagaatgggg acccatgcaa ccatgaaaat tcaagggcgc 3361 accgttggag gtcagatggg catgcttctg acaggatcca acgccaaaag catggatcta 3421 ggcaccacac caggtgattg cggctgtccc tacatctaca agagaggaaa tgactatgtg 3481 gtcattggag tccatacggc tgccgctcgt gggggaaaca ctgtcatatg tgccacccag 3541 gggggcgagg gggaagctac acttgaaggt ggtgacagta agggaacata ctgtggtgca 3601 ccaatcctag gcccagggag tgccccaaaa cttagcacca aaaccaaatt ctggagatca 3661 tccacagcac cactcccacc tggcacctat gaaccagcat accttggtgg caaggacccc 3721 agagtaaagg gtggcccttc gttgcagcaa gtcatgaggg accagctgaa accattcaca 3781 gagcccaggg gtaagccacc aaagccaagt gtgttagaag ctgccaagaa aaccatcatc 3841 aatgtccttg aacaaacaat tgacccacct gagaggtggt cgttcgcaca agcttgcgcc 3901 tcccttgaca agaccacttc tagcggccat ccgcaccata tgcggaaaaa cgactgctgg 3961 aatggggagt ccttcacagg caagctggca gaccaggctt ctaaggctaa cctgatgttt 4021 gaagaaggga agaacatgac cccagtctac acaggtgcac ttaaggatga attagtcaaa 4081 actgacaaaa tttatggtaa gatcaagaag aggcttctct ggggctcgga tttagcaacc 4141 atgatccggt gtgctcgagc attcggaggc ctaatggatg aactcaaagc acactgtgtc 4201 acacttccca ttagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaag 4261 cattccaggt acagatacca ctatgatgct gattactctc ggtgggattc aacacaacag 4321 agagccgtgc tggcagctgc tctagaaatc atggttaaat tctcctcaga accacatttg 4381 gctcaggtag tcgcagaaga tcttctttcc cctagcgtgg tggatgtggg tgatttcaca 4441 atatcaatca acgagggcct tccctctggg gtgccctgca cctcccaatg gaactccatc 4501 gcccactggc ttctcactct ttgtgcactc tccgaagtca caaatttatc 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 agctaaaaga 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 ggtggttttg aagtgcaggt 5401 gatcctcgcg gggaacgcgt tcaccgccgg aaaaattata tttgcagcag tcccaccaaa 5461 ttttccaact gaaggcctga gtcccagcca agtcactatg ttcccccaca taatagtaga 5521 tgttaggcaa ttggaacctg tgttgatccc cttacctgat gttaggaata acttctatca 5581 ttataatcag acaaatgatc ctaccattaa attgatagca atgctgtata caccacttag 5641 ggccaataat gctggggaag atgtcttcac agtctcttgt cgagtcctca ctaggccgtc 5701 ccctgatttt gattttatat ttttggtgcc acccacagtt gagtcaagaa ctaaaccatt 5761 tactgtccca atcttaaccg ttgaagaaat gaccaattca agattcccca tccctttgga 5821 aaagttgttc acgggtccca gcggtgcctt tgttgtccaa ccacaaaatg gcaggtgcac 5881 gactgatggc gtgctcttag gcaccaccca actgtctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccacattg caggttctcg tgattacaca atgaatttgg catctctaaa 6001 ttggaacaat tatgacccaa cagaagaaat tccagcccct ctgggaactc cagatttcgt 6061 gggaaagatc caaggtgtgc tcactcaaac cacaagagga gatggctcga cccgtggcca 6121 taaagctaca gtttacactg ggagtgcccc ctttgctcca 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 tgcagcgggt atcccaacat 6421 ggatttggat tgcctactcc cccaggagtg ggtgcagcac ttctaccaag aggcagctcc 6481 agcacaatct gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcctgtt 6541 cgagtgcaaa cttcataaat caggctatgt cacagtggct cacaccggtc agcatgattt 6601 ggtcatcccc cctaatggct attttaggtt tgattcttgg gtcaatcagt tctacacgct 6661 tgcccccatg ggaaacggaa cggggcgtag gcgcgcctta taatggctgg agctttcttt 6721 gctggattgg catctgatgt ccttggctct ggacttggtt ccctaatcaa tgctggggct 6781 ggggccatca accaaaagat tgattttgaa aataatagaa aattgcagca agcttccttc 6841 cagtttagca gtaatctaca acaggcttcc tttcaacacg ataaagagat gcttcaagca 6901 caaattgagg ccactaaaaa gttgcaacag gaaatgatga aagtcaaaca ggcaatgctc 6961 ctagaaggtg gattctctga aacagatgca gcccgtgggg caatcagcgc ccccatgaca 7021 aaggttttgg actggagcgg aacaaggtac tgggcccctg atgctaggac cacaacatac 7081 aattcaggcc gcttttccac cccccaacct tcggggacgc tgccaggaag aatcaatccc 7141 aggactccta cccccgctcg gggctcctct agcacatctt ctaatgcttc tactgctact 7201 tctatacatt taaatcaaac tgtttcaacg agacttggtt ctacagctgg ttctggcacc 7261 aatgtctcga gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga 7321 aatttgtcac ctttcatgag gggggctcat aacatatcgt ttgtcacccc accatctagc 7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aaattttgga ctcctgggct 7441 ggc //