Typing tool
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Complete norovirus genomes
KM198564 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 38..5056 ORF2: 5037..6659 ORF3: 6659..7399LOCUS KM198564 7399 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/C2H-44/2011/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198564 VERSION KM198564.1 KEYWORDS . SOURCE Norovirus Hu/GII/C2H-44/2011/VNM ORGANISM Norovirus Hu/GII/C2H-44/2011/VNM Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7399) 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 7399) 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..7399 /organism="Norovirus Hu/GII/C2H-44/2011/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/C2H-44/2011/VNM" /host="Homo sapiens" /db_xref="taxon:1527018" /country="Viet Nam" /collection_date="31-Oct-2011" /note="genotype: GII" CDS 38..5056 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02820.1" /translation="MFSSMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKVPPP PPNGEDEVVVSYSAKDGISGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT LKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT TDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK VLAFRQLAAENKYGLMDTMRVGRQLKDVKTMPELKQALKSISIKKCQIVYSGCTYTLE SDGKGNVKVDRVQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV TTRIIKRVNIQNLWSKPQVENTEEATNKDGCPKPKDDEEFVITSDDIKTEGKKGKNKT GRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARATEED FCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSV DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIKRSTGELMPLAARMGTHATM KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKSMT PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR VGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQV VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE DGVE" CDS 5037..6659 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02821.1" /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFIVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGGAPFTPKLGSVQFSTDTENDFEAHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6659..>7399 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02822.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGSLPGRINPRTPTPARASSSTSS NASTVTSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTKSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTG" ORIGIN 1 cagcaacaac gacaccgcaa catcttcaag tgacaaaatg ttttctagca tggctgtcac 61 ttttaaacga gccctcgggg cgcggcctaa acagcctccc ccgagggaaa taccgcaaag 121 gcccccacga ccacctactc cagaactggt caaaaaggtc cctcctcccc cgcccaacgg 181 agaggatgaa gtggtggttt cttatagtgc caaagatggc atttctggtc tacctgagct 241 ttccaccgtc agacaaccag aagaaaccaa tacggccttc agtgtccctc cactcaatca 301 gagggagaat agggatgcta aggaaccact gactgggaca attctggaaa tgtgggatgg 361 agaaatctat cattatggcc tgtatgttga acgaggtctt gtgctgggtg tgcacaaacc 421 accagctgcc attagcctcg ccaaggtcga attaacacca ctctccttgt tctggagacc 481 tgtgtacacc ccacagtacc tcatctctcc agacactctc aagaaattac acggagaaac 541 atttccctac acagcctttg acaacaactg ctatgccttt tgctgctggg tcctggatct 601 aaacgactcg tggctgagta ggaggatgat ccagagaaca actggcttct tcagacccta 661 ccaagattgg aataggaaac ccctccctac tacggatgat tccaaattaa agaaggtagc 721 taacatattc ctgtgcaccc tgtcttcgct attcaccagg cccataaaag acataatagg 781 aaagttaagg cctctcaaca tcatcaacat cctagcttca tgtgactgga ctttcgcagg 841 catcgtggaa tccttgatac tcttggcaga gctctttgga gtcttctgga cacccccaga 901 tgtgtctgcg atgattgccc ccttactcgg tgatttcgag ttacaaggac ctgaggacct 961 tgtagtggag ctcgtccctg tggtaatggg gggaattggc ttggtgctgg gattcaccaa 1021 agagaagatt ggaaaaatgt tgtcatctgc tgcatccacc ctaagagctt gtaaagatct 1081 cggtgcatat gggctagaga tcctaaagct agtcatgaag tggttcttcc cgaagaaaga 1141 ggaggcaaat gaactggcta tggtgagatc catcgaggat gcagtactgg accttgaggc 1201 aattgaaaac aaccatatga ccaccttgct caaagataaa gacagcctgg caacctacat 1261 gagaaccctt gacctcgagg aagagaaagc cagaaaactc tcaaccaagt ctgcgtcacc 1321 tgacatcgtg ggcacaatca acgcccttct ggcgagaatc gccgctgcac gctccctggt 1381 gcaccgagcg aaggaggagc tttccagcag accaagacct gtggtcttga tgatatcagg 1441 tagaccaggg atagggaaga cccaccttgc tagggaagtg gccaagagaa tcgcagcatc 1501 cctcacagga gaccagcgcg taggtctcat cccacgcaat ggcgtcgatc actgggatgc 1561 gtacaagggg gagagggtcg tcctatggga cgactatgga atgagcaatc ccatccacga 1621 cgccctcagg ctgcaagaac tcgccgacac ttgccccctc actctaaatt gtgacagaat 1681 tgagaataaa ggaaaggtct ttgacagtga tgtcatcatt atcactacta atctggccaa 1741 cccagcacca ctggactatg tcaactttga agcgtgctcg aggcgcatcg atttcctcgt 1801 gtacgcagaa gcccccgagg tcgaaaaggc gaagcgtgac ttcccaggcc aacctgacat 1861 gtggaaaaac gcctttagtt ctgatttctc acacataaaa ctggcactgg ctccacaagg 1921 tggcttcgat aagaacggga acaccccaca tgggaagggc gtcatgaaga ctctcaccac 1981 tggctccctt attgcccggg catcagggct gctccatgag agattggatg agtttgaact 2041 acagggccca gctctcacca ccttcaactt tgaccgcaac aaagtgcttg ccttcaggca 2101 gcttgctgct gaaaacaaat acgggttgat ggacacaatg agagttggga ggcagctcaa 2161 ggatgtcaaa accatgccag aacttaaaca agcactcaag agcatctcaa tcaagaagtg 2221 tcagattgtg tacagtggtt gcacctacac acttgagtct gatggcaagg gcaatgtgaa 2281 ggttgacaga gttcagagca cctccgtgca gaccaacaat gagctggctg gcgccctgca 2341 ccatctgagg tgcgccagaa tcaggtacta tgttaagtgt gtccaggagg ccctgtattc 2401 tatcattcag attgctggag ctgcattcgt caccacgcgc atcatcaagc gtgtgaacat 2461 tcaaaactta tggtccaagc cacaagtgga aaacacagag gaagccacca acaaggatgg 2521 gtgcccaaaa cccaaagatg atgaggagtt cgtcatcaca tctgacgaca ttaaaactga 2581 gggtaagaaa ggaaagaaca agactggccg tggcaagaag cacacagcct tctcaagtaa 2641 aggtctcagt gatgaagagt atgatgagta caagagaatt agagaggaaa ggaatggcaa 2701 gtactccata gaagagtacc ttcaggacag ggacaaatac tatgaagagg tggccattgc 2761 cagggcgacc gaggaagact tctgtgaaga ggaggaggcc aagatccggc aaaggatctt 2821 cagaccaaca aggaaacaac gcaaggaaga aagagcttcc ctcggtttag tcacaggttc 2881 tgaaattagg aaaagaaacc cagatgattt caagcccaag gggaaactat gggctgacga 2941 tgacagaagt gtggactaca atgagaaact cagttttgag gctccgccaa gcatctggtc 3001 aaggatagtc aactttggct caggttgggg cttctgggtc tcccccagcc tgttcataac 3061 atcaacccac gtcatacccc agggcgcaaa ggagttcttt ggagtcccca tcaaacaaat 3121 tcaggtgcac aagtcaggcg aattctgtcg cttgaggttc ccaaaaccaa tcaggactga 3181 tgtaactggc atgatcttgg aagaaggcgc gcctgaaggc accgtggcca cactactcat 3241 caaaaggtct actggagaac tcatgcccct agcagccaga atggggaccc atgcaaccat 3301 gaagattcaa gggcgcactg ttggaggtca gatgggcatg cttctgacag gatccaacgc 3361 caaaagcatg gatctaggca ccacaccagg tgattgcggt tgtccctaca tctacaagag 3421 agggaatgac tatgtggtca ttggagtcca cacggctgcc gctcgtgggg gaaacactgt 3481 tatatgtgcc acccaggggg gtgaggggga agctacactt gaaggtggtg acagtaaggg 3541 aacgtactgc ggtgcgccaa tcctaggccc agggagcgct ccaaaactta gtaccaaaac 3601 caaattctgg agatcatcca cagcaccact cccacctggc acctatgagc cagcctacct 3661 tggtggcaag gaccccagag tcaagggtgg cccctcgctg cagcaagtca tgagagacca 3721 gctgaaacca ttcacagagc ccaggggtaa gccaccaaag ccaagtgtgt tggaagctgc 3781 caagaaaacc atcatcaatg ttcttgaaca aacaattgac ccacctgaga agtggtcgtt 3841 cgcacaggct tgcgcgtccc ttgacaagac cacttctagc ggccatccgc atcacatgcg 3901 gaaaaacgac tgctggaacg gggagtcctt cacaggcaag ctggcagacc aggcttccaa 3961 ggccaacctg atgtttgaag aagggaagag catgacccca gtttacacag gagcgctcaa 4021 ggacgagttg gtcaaaactg ataaaattta tggcaagatc aagaagaggc ttctctgggg 4081 ctcggattta gcaaccatga tccggtgtgc tcgagcattc ggaggcctaa tggatgaact 4141 caaagcacac tgtgtcacac ttcctatcag agttggtatg aatatgaatg aggatggccc 4201 catcatcttc gagaagcact ccaggtacag gtaccactat gatgctgatt actcccgatg 4261 ggattcaaca caacagagag ccgtgctggc agctgctcta gaaattatgg ttaaattctc 4321 ctcagaacca catttggctc aggtggtcgc agaagacctt ctttctccta gcgtggtgga 4381 tgtgggtgac ttcacaatat caatcaatga gggtcttccc tctggggtgc cctgcacttc 4441 tcaatggaac tccatcgccc actggcttct cactctatgt gcactctccg aagttacaaa 4501 tttgtcccca gacatcatac aggctaattc tctcttctcc ttctatggtg atgatgaaat 4561 tgttagtaca gacataaaac tagacccaga gaagttgaca gcaaagctta aggaatatgg 4621 gttaaaacca acccgccctg acaaaactga aggacctctt gttatttctg aagacttaga 4681 tggtttgact ttcctgcgga gaactgtgac ccgcgaccca gctggttggt ttggaaaact 4741 ggagcagagc tcaatactca ggcaaatgta ctggactagg ggtcccaacc atgaagatcc 4801 atctgaatca atgattccac actctcaaag acccatacaa ttgatgtccc tgctgggaga 4861 ggccgcactc cacggcccaa cattctatag taaaatcagc aaattagtca ttgcagagct 4921 aaaagaaggt ggtatggatt tttacgtgcc caggcaagag ccaatgttca gatggatgag 4981 attctcagat ctgagcacgt gggagggcga tcgcaatctg gctcccagct ttgtgaatga 5041 agatggcgtc gaatgacgcc aacccatctg atgggtccgc agccaacctc gtcccagagg 5101 tcaacaatga ggttatggct ttggagcccg ttgtcggtgc cgctattgcg gcgcctgtag 5161 cgggccaaca aaatgtaatt gacccctgga ttaggaataa ttttgtacaa gcccctggtg 5221 gagaattcac agtatcccct agaaacgctc caggtgaaat actatggagc gcgcccttag 5281 gccctgatct gaatccctac ctatcccatt tggccagaat gtataatggt tatgcaggtg 5341 gctttgaagt gcaggtgatc ctcgcgggga acgcgttcac cgccgggaaa attatatttg 5401 cagcagttcc accaaatttt ccaactgaag gcttgagccc cagccaggtt actatgttcc 5461 cccacataat agtagatgtt aggcaactgg aacctgtgtt gatcccctta cctgatgtta 5521 ggaataactt ctatcattat aatcagtcaa atgattctac cattaaattg atagcaatgc 5581 tgtacacacc acttagagct aataatgctg gggaagatgt cttcacagtc tcttgtcgag 5641 tccttacgag gccatcccct gactttgatt ttatattttt ggtgccaccc acagttgagt 5701 caagaactaa accatttact gtcccaatct taactgttga agaaatgacc aattcaagat 5761 tccccatccc tttggaaaag ttgttcacgg gccccagcgg tgcctttatt gttcaaccac 5821 aaaatggtag atgcacgact gatggcgtgc tcttaggcac cacccaactg tctcctgtca 5881 acatctgcac cttcagaggg gatgtcaccc acattgcagg ttctcgcaat tacacgatga 5941 atttggcttc tctaaattgg aataattatg acccaacaga agaaattcca gcccctctgg 6001 gaactccaga tttcgtggga aagatccaag gtgtgctcac tcaaaccaca aagggagatg 6061 gctcgacccg tggccataaa gcaacagttt acactggggg tgcccccttt actccaaagc 6121 tgggcagtgt tcaattcagt actgacacag aaaatgattt tgaagctcac caaaacacaa 6181 aattcacccc agtcggtgtc atccaggatg gtggcaccac ccaccgaaat gaaccccaac 6241 aatgggtgct cccaagttat tcaggtagag atgtccacaa tgtacacctg gcccctgctg 6301 tagcccccac ttttccgggt gaacaacttc ttttcttcag gtccactatg cccggatgca 6361 gtgggtatcc caacatggat ttggattgcc tactccctca ggagtgggtg cagcacttct 6421 accaagaggc agctccagca caatctgatg tggctctatt gagatttgtg aatccagaca 6481 cgggtagggt cctgtttgag tgcaaacttc ataaatcagg ctatgtcaca gtggctcaca 6541 ccggccagca tgatttggtc atccccccta atggctattt taggtttgac tcctgggtta 6601 accaattcta cacacttgcc cccatgggaa atggaacggg gcgtagacgt gctttataat 6661 ggctggggct ttctttgctg gattggcatc tgatgtcctt ggctctgggc ttggctccct 6721 aatcaatgct ggggctgggg ctatcaacca aaagattgat tttgaaaata acagaaaatt 6781 gcagcaagct tccttccagt ttagcagtaa tctacaacag gcctcctttc aacatgacaa 6841 agagatgctc caagcacaaa tcgaggccac taaaaagttg caacaggaaa tgatgagagt 6901 caaacaggca atgctcttag aaggtgggtt ctctgaaaca gatgcagctc gcggggcaat 6961 caacgccccc atgacaaagg ttttggactg gagtggaaca aggtactggg cccctgatgc 7021 caggactaca acatacaatg caggccgctt ttccaccccc caaccctcgg ggtcattgcc 7081 aggaagaatc aatcccagga ctcctactcc cgctcgggcc tcctctagta catcctctaa 7141 tgcttctact gttacttcta tatattcaaa tcaaactgtt tcaacgagac ttggttctac 7201 agctggctct ggcaccaatg tctcgagtct cccgtcaact gcaaggacta agagttgggt 7261 tgaggatcaa aacagaaatt tgtcaccttt catgaggggg gctcacaaca tatcgtttgt 7321 caccccacca tctagcagat cctctagcca aggcacagtc tcaaccgtgc ctaaagaagt 7381 tttggactcc tggactggc //