Typing tool
|
Complete norovirus genomes
KM198485 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7443LOCUS KM198485 7443 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/10148/2009/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198485 VERSION KM198485.1 KEYWORDS . SOURCE Norovirus Hu/GII/10148/2009/VNM ORGANISM Norovirus Hu/GII/10148/2009/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/10148/2009/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/10148/2009/VNM" /host="Homo sapiens" /db_xref="taxon:1526950" /country="Viet Nam" /collection_date="11-Aug-2009" /note="genotype: GII" CDS 1..5100 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02583.1" /translation="MKMASNDAFAAAVANSNNDTAKSSSDKMFSSMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDIEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVKTM PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRIQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC PKPKDNEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGRDPRVKDGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQIYWTRGP NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" CDS 5081..6703 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02584.1" /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6703..>7443 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02585.1" /translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRTNPRTPTPARGSPSTSS NASTATSIHSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTG" ORIGIN 1 atgaagatgg cgtctaacga cgctttcgct gccgctgttg ctaacagcaa caacgacacc 61 gcaaaatctt caagtgacaa aatgttttct agcatggctg 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 cttcagcgtc cctccactca accagaggga gaatagagat 361 gctaaggaac cactgactgg 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 acctaaatga 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 tggcttggtg ctaggattca ccaaagagaa gattggaaaa 1081 atgttgtcat ctgctgcatc caccttgaga gcttgtaaag atcttggtgc atatgggcta 1141 gagatcctaa aattagtcat gaagtggttc ttcccgaaga aagaggaagc aaatgaactg 1201 gctatggtga gatccatcga ggatgcagta ctggaccttg aggcaattga aaacaaccat 1261 atgaccacct tgctcaaaga caaagacagc ctggcaacct acatgagaac ccttgacatc 1321 gaggaagaga aagccagaaa actctcaacc aagtccgctt cacctgacat cgtgggcaca 1381 atcaacgccc ttctggcgag aatcgccgct gcacgctccc tggtgcaccg agcgaaggag 1441 gagctttcca gcagaccaag acctgtagtc ttgatgatat caggcagacc aggaatagga 1501 aaaacccacc ttgccaggga agtggctaag agaatcgcag cctccctcac aggagaccag 1561 cgtgtaggcc tcatcccacg caatggcgtc gatcactggg atgcgtacaa gggggagagg 1621 gtcgtcctat gggacgacta tggaatgagc aaccccatcc acgacgccct caggctgcaa 1681 gaactcgctg acacttgccc cctcactcta aattgtgaca ggattgagaa taaaggaaag 1741 gtctttgaca gcgatgtcat catcatcacc actaacctgg ccaacccagc accactggac 1801 tatgtcaact ttgaagcgtg ctcgaggcgc atcgatttcc tcgtgtatgc agaagccccc 1861 gaggtcgaaa aggcaaagcg tgacttcccg ggccaacccg acatgtggaa aaacgctttt 1921 agttctgatt tctcacacat aaaattggca ctggctccac aaggtggctt tgacaagaac 1981 gggaacaccc cacacgggaa gggcgtcatg aagactctca ccactggctc cctcattgcc 2041 cgggcatcag ggctgctcca tgagagattg gatgagtttg aactacaggg cccagccctt 2101 accaccttca actttgaccg caacaaagtg cttgccttca gacagcttgc tgctgaaaac 2161 aaatacgggt tgatagacac aatgaaagtt gggaggcagc tcaaggatgt caaaaccatg 2221 ccagaactta aacaagcact caagaacatc tcaatcaaga agtgccagat tgtgtatagt 2281 ggttgcacct acacacttga atctgatggc aagggcaatg tgaaagttga cagaatccag 2341 agcacctccg tacagaccaa caatgagctg gctggcgccc tgcaccatct aaggtgcgcc 2401 agaatcaggt actatgtcaa gtgtgtccag gaggccctgt attctatcat ccagattgct 2461 ggggctgcat ttgtcaccac gcgcatcatc aagcgtgtga acattcaaga cttatggtcc 2521 aagccacaag tggaaaacac agaggaggcc accaacaagg acgggtgccc aaaacccaaa 2581 gataatgagg agttcgtcat ttcatctgac gacattaaaa ctgagggtaa gaaagggaag 2641 aacaagactg gccgtggcaa gaagcacaca gccttctcaa gtaaaggtct cagtgatgaa 2701 gagtatgatg agtacaagag aattagagag gaaaggaatg gcaagtactc catagaagag 2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gaccgaggaa 2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tcttcagacc aacaaggaaa 2881 caacgcaagg aagaaagagc ttctctcggt ttggtcacag gttctgaaat caggaaaagg 2941 aacccagaag acttcaagcc caaggggaaa ctatgggctg acgatgacag aagtgtggac 3001 tacaatgaaa aactcagctt tgaggcccca ccaagcatct ggtcaaggat agtcaacttt 3061 ggctcaggtt ggggcttctg ggtctcaccc agcctgttca taacatcaac ccacgtcata 3121 ccccagggcg cgaaggagtt ctttggagtc cccatcaagc aaattcaggt acacaagtca 3181 ggcgaattct gtcgcttgag gttcccaaaa ccaatcagga ctgatgtgac tggcatgatc 3241 ttggaagaag gtgcgcccga aggcaccgtg gtcacactac tcatcaaaag gtctactgga 3301 gaactcatgc ccctagcggc tagaatgggg acccatgcaa ccatgaaaat ccaagggcgc 3361 actgttggag gtcagatggg catgcttctg acagggtcca acgccaaaag catggatcta 3421 ggcaccacac caggtgattg cggctgtccc tacatctaca agagaggaaa tgactatgtg 3481 gtcattggag tccacacggc tgccgctcgt gggggaaaca ctgtcatatg tgccacccaa 3541 gggggtgagg gggaagctac acttgaaggt ggtgacagta agggaacata ctgtggtgca 3601 ccaatcctag gcccagggag tgccccaaaa cttagtacca aaaccaaatt ctggagatca 3661 tccacagcac cactcccacc tggcacctat gagccagcct accttggtgg cagggacccc 3721 agagtcaagg atggcccctc gttgcagcaa gtcatgaggg accagctgaa accatttaca 3781 gagcctaggg gcaaaccgcc aaagccaagt gtgttagaag ctgccaagaa aaccatcatc 3841 aatgtccttg aacaaacaat tgacccacct gagaagtggt cgttcgcaca agcttgcgcg 3901 tcccttgaca agaccacttc tagcggccat ccgcaccaca tgcggaaaaa cgactgctgg 3961 aacggggagt ccttcacagg caaattggca gaccaggctt ccaaggccaa cctgatgttt 4021 gaagaaggga agaacatgac cccagtctac acaggtgcac ttaaggatga attagtcaaa 4081 actgacaaaa tttatggtaa gatcaagaag aggcttctct ggggctcgga tttggcaacc 4141 atgatccggt gtgctcgagc attcggaggc ctaatggatg aactcaaagc acactgtgtc 4201 acacttccta tcagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaag 4261 cattccaggt acagatacca ctatgatgct gattactctc ggtgggattc aacacaacag 4321 agagccgtgc tggcagctgc tctagaaatc atggttaaat tctcctcaga accacatttg 4381 gctcaggtag tagcagaaga ccttctttct cctagcgtgg tggacgtggg tgacttcaca 4441 atttcaatca acgagggtct tccctctggg gtgccctgca cctcccagtg gaactccatc 4501 gcccactggc ttcttactct ctgtgcactc tccgaagtta caaatttgtc cccagacatc 4561 atacaggcta attctctctt ctccttctat ggtgatgatg aaattgttag tacagacata 4621 aaattagacc cagagaagtt gacagcaaag cttaaagaat acgggttgaa accaacccgc 4681 cctgataaaa ctgaaggacc tcttgttatt tctgaagact tagatggttt gactttcctg 4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagctcaata 4801 ctcaggcaaa tatactggac taggggcccc aaccatgaag atccatctga atcaatgatt 4861 ccacactctc aaagacccat acaattgatg tctttactgg gagaggccgc actccacggc 4921 ccaacattct atagtaaaat cagtaaatta gtcattgcag agctaaaaga aggtggtatg 4981 gatttttacg tgcccaggca agagccaatg ttcagatgga tgagattctc agatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga 5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat 5161 ggctttggaa 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 ctttccaact gaaggcctga gtcccagcca ggtcactatg ttcccccaca taatagtaga 5521 tgttaggcaa ttggaacctg tgttgatccc cttacctgat gttaggaata acttctatca 5581 ctataaccag acaaatgatt ctaccattaa actgatagca atgctgtata caccacttag 5641 ggccaataat gctggggaag atgtcttcac agtctcttgt cgagtcctca cgaggccatc 5701 ccctgatttt gattttatat ttttggtgcc acccacagtt gagtcaagaa ctaaaccatt 5761 tactgtccca atcttaaccg ttgaagaaat gaccaattca agattcccca ttcctttgga 5821 aaaactgttc acgggtccca gcagcgcctt tgttgtccaa ccacaaaatg gcagatgcac 5881 gactgatggc gtgctcttag gcaccaccca actgtctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccacattg caggttctcg taattacaca atgaatttgg catctctaaa 6001 ctggaacaat tatgacccaa cagaagaaat tccagcccct ctaggaactc cagatttcgt 6061 gggaaagatc caaggtgtgc tcactcaaac cacaaaagga gatggctcga cccgtggcca 6121 taaagccaca gtttacactg ggagtgcccc cttcactcca aagctgggca gtgttcaatt 6181 cagcaccgac acagaaaatg attttgaaac tcaccaaaac acaaaattca ccccagtcgg 6241 cgtcatccag gatggtggca ccacccaccg aaatgaaccc caacaatggg tgctcccaag 6301 ttattcaggt agaaatgtcc ataatgtaca cctagcccct gctgtagccc ccacttttcc 6361 gggtgaacaa cttctcttct tcaggtccac tatgcccgga tgcagcgggt atcccaacat 6421 ggatttggat tgcctactcc cccaggagtg ggtgcagcac ttctaccaag aggcagctcc 6481 agcacaatct gatgtggctc tattaagatt tgtaaatcca gacacgggta gggtcctgtt 6541 tgagtgcaaa cttcataaat caggctatgt cacagtggcc cacaccggcc agcatgattt 6601 ggtcatcccc cccaatggct attttaggtt tgattcctgg gttaatcaat tctacacact 6661 tgcccccatg ggaaacggaa cggggcgtag acgcgcttta taatggctgg agctttcttt 6721 gctggactgg catctgatgt ccttagctct ggacttggtt ccctaatcaa tgctggggct 6781 ggggctatca accaaaagat tgattttgaa aataacagaa aattgcagca agcttccttc 6841 caatttagca gtaatctaca acaggcttcc tttcaacacg ataaagagat gctccaagca 6901 caaatcgagg ccactaaaaa gttacaacag gaaatgatga aagtcaaaca ggcaatgctc 6961 ctagaaggtg gattctctga aacagatgca gcccgtgggg caatcaacgc ccccatgaca 7021 aaagctttgg actggagcgg aacaaggtac tgggcccctg atgctaggac tacaacatac 7081 aatgcaggcc gcttttccac ccctcaacct tcggggacac tgccaggaag aaccaatccc 7141 aggaccccta cccccgcccg gggctccccc agcacatctt ctaatgcttc tactgctact 7201 tctatacatt caaatcaaac tgtttcaacg agacttggtt ctacagctgg ttctggcacc 7261 aatgtctcga gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga 7321 aatctgtcac ctttcatgag gggggctcac aacatatcgt ttgtcacccc accatctagc 7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aagttttgga ctcctggact 7441 ggc //