Typing tool
|
Complete norovirus genomes
KM198580 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 62..5080 ORF2: 5061..6683 ORF3: 6683..7423LOCUS KM198580 7423 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/10223/2009/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198580 VERSION KM198580.1 KEYWORDS . SOURCE Norovirus Hu/GII/10223/2009/VNM ORGANISM Norovirus Hu/GII/10223/2009/VNM Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7423) 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 7423) 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..7423 /organism="Norovirus Hu/GII/10223/2009/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/10223/2009/VNM" /host="Homo sapiens" /db_xref="taxon:1526964" /country="Viet Nam" /collection_date="06-Nov-2009" /note="genotype: GII" CDS 62..5080 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02868.1" /translation="MFSNMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKIPPP PPNGEDEAVVSYSAKDGVSGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT LKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT MDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK VLAFRQLAAENKYGLIDTMKVGRQLKDVKTMPELKQALKNISIKKCQIVYSGCTYTLE SDGKGNVKVDKIQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV TTRIIKRVNIQDLWSKPQVENTEEATNKDGCSKPKDDEEFVISSDDIKTEGKKGKNKT GRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYSIEEYLQDRDKYYEEVAIARATEED FCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSV DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGTHATM KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMT PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR VGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQV VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE DGVE" CDS 5061..6683 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02869.1" /translation="MKMASNDANPTDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6683..>7423 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02870.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRINPRTPTPARGSSSTSS NASTATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTG" ORIGIN 1 cgcttccgct gccgctgttg ctaacagcaa caacgacacc gcaaaatctt caagtgacaa 61 aatgttttct aacatggctg tcacttttaa acgagccctc ggggcgcggc ctaaacagcc 121 ccccccgagg gaaataccac aaagaccccc acgaccacct accccagaac tggtcaaaaa 181 gatcccccct cccccgccca acggagagga tgaagcagtg gtttcttata gtgccaaaga 241 tggcgtttcc ggtttacctg agctttccac cgtcaggcaa ccggaagaaa ccaatacggc 301 cttcagtgtc cctccactca accagaggga gaatagagat gctaaggaac cactgactgg 361 aacaattctg gaaatgtggg atggagaaat ctaccattat ggcctgtatg ttgagcgagg 421 tcttgtgctg ggtgtgcaca aaccaccagc tgccataagc ctcgccaagg tcgaactaac 481 accactctcc ttgttctgga gacctgtgta caccccccag tacctcatct ctccagacac 541 cctcaagaaa ttgcacggag aaacgtttcc ctacacagcc tttgacaaca attgctacgc 601 cttttgttgt tgggtcctgg atctaaatga ctcgtggctg agtaggagaa tgatccagag 661 aacaactggc ttcttcagac cctaccaaga ctggaatagg aaacccctcc ccactatgga 721 tgattccaaa ttaaagaagg tagctaacat attcctgtgc gccctgtctt cgctattcac 781 caggcccata aaagacataa taggaaagct aagacctctc aacatcatca acatcctggc 841 ttcatgtgat tggactttcg caggcatagt ggagtctttg atactcttgg cagagctctt 901 tggagtcttc tggacacccc cagatgtgtc tgcgatgatt gcccccttac tcggtgactt 961 cgagttacaa ggacctgagg accttgtagt ggagctcgtc cctgtagtaa tggggggaat 1021 tggtttggtg ctgggattca ccaaagagaa gattgggaaa atgttgtcat ctgctgcatc 1081 caccttgaga gcttgtaaag atcttggtgc atatgggcta gagatcctaa agttagtcat 1141 gaagtggttc ttcccgaaga aagaggaggc aaatgaactg gctatggtga gatccatcga 1201 ggatgcagta ctggaccttg aggcaattga aaacaaccat atgaccacct tgctcaaaga 1261 caaagacagc ctagcaacct acatgagaac ccttgacctc gaggaagaga aagccagaaa 1321 actctcaacc aagtctgctt cacctgacat cgtgggcaca atcaacgccc ttctggcgag 1381 aatcgccgct gcacgctccc tggtgcaccg agcgaaggag gagctttcca gcagaccaag 1441 acctgtagtc ttgatgatat caggcagacc agggatagga aaaacccacc ttgctaggga 1501 agtggctaag agaatcgcag cctccctcac aggagaccag cgtgtaggcc tcatcccacg 1561 caatggcgtc gatcactggg atgcgtacaa gggggagagg gtcgtcctat gggacgacta 1621 tgggatgagc aaccccatcc acgacgccct taggctgcaa gaactcgctg acacttgccc 1681 ccttactcta aattgtgaca ggattgagaa caaaggaaag gtctttgaca gcgatgtcat 1741 cattatcacc actaatctgg ccaacccagc accactggac tatgtcaact ttgaagcgtg 1801 ctcgaggcgc attgatttcc tcgtgtatgc agaagccccc gaggtcgaaa aggcgaagcg 1861 tgacttcccg ggccaacctg acatgtggaa aaacgctttt agttctgatt tctcacacat 1921 aaaattggca ctggctccac aaggtggctt tgataagaac gggaacaccc cacacgggaa 1981 gggcgtcatg aagactctca ccactggctc cctcattgcc cgggcatcag ggctgctcca 2041 tgagagattg gatgagtttg aactacaggg cccagctctt accaccttca actttgaccg 2101 caacaaagtg cttgccttca gacagcttgc tgctgaaaac aaatatgggt tgatagacac 2161 aatgaaagtt gggaggcagc tcaaggatgt caaaaccatg ccagaactta aacaagcact 2221 caaaaacatc tcaatcaaga agtgccagat tgtgtatagt ggttgcacct acacacttga 2281 gtctgatggc aagggcaatg tgaaagttga caaaatccag agcacctccg tacagaccaa 2341 caatgagctt gctggcgccc tgcatcatct gaggtgcgcc agaatcaggt actatgtcaa 2401 gtgtgtccag gaggccctgt attctatcat ccagattgct ggggccgcat ttgtcaccac 2461 gcgcattatc aagcgtgtga acattcaaga cttatggtcc aagccacaag tggaaaacac 2521 agaggaggcc accaacaagg acgggtgctc aaaacccaaa gatgacgagg agttcgtcat 2581 ttcatctgac gacattaaaa ctgagggtaa gaaagggaag aacaagactg gccgtggcaa 2641 gaagcacaca gccttttcaa gtaaaggtct cagtgatgaa gagtatgatg agtacaagag 2701 aattagagag gaaaggaatg gcaggtattc catagaagag taccttcagg acagggacaa 2761 atactatgag gaggtggcca ttgccagggc gaccgaggaa gacttctgtg aagaggagga 2821 ggccaagatc cggcagagga tctttagacc aacaaggaaa caacgcaagg aagaaagagc 2881 ttctctcggt ttagtcacag gttctgagat taggaaaaga aacccagatg acttcaagcc 2941 taagggaaaa ctgtgggctg acgatgacag aagtgtggac tacaatgaga aactcagttt 3001 tgaggcccca ccaagcatct ggtcaaggat agtcaacttt ggttcaggtt ggggcttctg 3061 ggtctcccct agcctgttca taacatcaac ccacgtcata ccccagggcg caaaggagtt 3121 ctttggagtt cccatcaaac aaattcaggt acacaagtca ggcgaatttt gtcgcttgag 3181 gttcccaaaa ccaatcagga ctgacgtgac tggcatgatc ttggaagaag gtgcgcccga 3241 aggcaccgtg gtcacactac tcatcaaaag gtctactgga gaactcatgc ccctagcagc 3301 tagaatgggg acccatgcaa ccatgaaaat tcaagggcgc accgttggag gacagatggg 3361 catgcttctg acaggatcca acgccaaaag catggatcta ggcaccacac caggtgattg 3421 cggctgtccc tacatctaca agagaggaaa tgactatgtg gtcattggag ttcatacggc 3481 tgccgctcgt gggggaaaca ctgtcatatg tgccacccag gggggcgagg gggaagctac 3541 acttgagggt ggtgacagta agggaacata ctgtggtgca ccaatcctag gcccagggag 3601 tgccccaaaa cttagcacca aaaccaaatt ctggagatca tccacagcac cactcccacc 3661 tggcacctat gaaccagcat accttggtgg caaggacccc agagtcaagg gtggcccttc 3721 gttgcagcaa gtcatgaggg accagctgaa accatttaca gagcccaggg gtaagccgcc 3781 aaagccaagt gtgttagaag ctgccaagaa aaccatcatc aatgtcctcg aacaaacaat 3841 tgacccacct gagaagtggt cgttcgcaca agcttgcgcc tcccttgata agaccacttc 3901 tagcggccac ccgcaccata tgcggaaaaa cgactgctgg aatggggagt ccttcacagg 3961 caagctggca gaccaggctt ctaaggctaa cctgatgttt gaagaaggga agaacatgac 4021 cccagtctac acaggtgcac ttaaggatga attagtcaaa actgacaaaa tttatggtaa 4081 gatcaagaag aggcttctct ggggctcgga tttagcaacc atgatccggt gtgctcgagc 4141 attcggaggc ctaatggatg aacttaaggc acactgtgtc acacttccta ttagagttgg 4201 tatgaatatg aatgaggatg gccccatcat cttcgagaag cattccaggt acagatacca 4261 ctatgatgct gattactctc ggtgggattc aacacaacag agagccgtgc tggcagctgc 4321 tctagaaatc atggttaaat tctcctcaga accacatttg gctcaggtag tcgcagaaga 4381 tcttctttcc cctagcgtgg tggatgtggg tgacttcaca atatcaatca acgagggcct 4441 tccctctggg gtgccctgca cctcccaatg gaactccatc gcccactggc ttctcactct 4501 ttgtgcactc tccgaagtca caaatttgtc cccagacatc atacaggcta attctctctt 4561 ctccttctat ggtgatgatg aaattgttag tacagacata aaattggacc cagagaagtt 4621 gacagcaaag cttaaggaat atgggttgaa accaacccgc cctgacaaaa ctgaaggacc 4681 tctcgttatt tctgaagact tagatggttt gactttcctg cggagaactg tgacccgcga 4741 cccagctggt tggtttggaa aactggagca gagctcaata ctcaggcaaa tgtactggac 4801 taggggcccc aaccatgaag atccatctga atcaatgatt ccacactctc aaagacccat 4861 acaattgatg tccttactgg gagaggccgc actccacggc ccaacattct acagtaaaat 4921 cagcaaatta gtcattgcag agcttaaaga aggtggtatg gatttttacg tgcccaggca 4981 agagccaatg ttcagatgga tgagattctc agatctgagc acgtgggagg gcgatcgcaa 5041 tctggctccc agttttgtga atgaagatgg cgtcgaatga cgccaaccca actgatgggt 5101 ccgcagccaa cctcgtccca gaggtcagca atgaggttat ggctttggag cccgttgtcg 5161 gtgccgctat tgcggcgcct gtagcgggcc aacaaaatgt aattgacccc tggattagaa 5221 acaattttgt acaagcccct ggtggagagt tcacagtatc ccctagaaac gctccaggtg 5281 aaatactatg gagcgcgccc ttaggccctg atctgaaccc ctacctatcc catttggcca 5341 gaatgtataa tggttatgca ggtggttttg aagtgcaggt gatcctcgcg gggaacgcgt 5401 tcaccgccgg gaaaattata tttgcagcag tcccaccaaa ttttccaact gaaggcctga 5461 gtcccagcca ggtcactatg ttcccccaca taatagtaga tgttaggcaa ttagaacctg 5521 tgttgatccc cttacctgat gttaggaata acttctatca ctataatcaa acaaatgatt 5581 ctaccattaa attgatagca atgctgtata caccacttag ggccaataat gctggggaag 5641 atgtcttcac agtctcttgt cgagtcctca ctaggccgtc ccctgatttt gattttatat 5701 ttttggtgcc acccacagtt gagtcaagaa ctaaaccatt tactgtccca atcttaaccg 5761 ttgaagaaat gaccaattca agattcccca ttcctttgga aaagttgttc acgggtccca 5821 gcggtgcctt tgttgtccaa ccacaaaatg gcaggtgcac gactgatggc gtgctcttag 5881 gcactaccca actgtctcct gtcaacatct gcaccttcag aggggatgtc acccacattg 5941 caggttctcg taattacaca atgaatttgg catctctaaa ttggaacaat tatgacccaa 6001 cagaagaaat tccagcccct ctgggaactc cagatttcgt gggaaagatc caaggtgtgc 6061 tcacccaaac cacaaaagga gatggctcga cccgtggcca taaagctaca gtttacactg 6121 ggagtgcccc ctttacccca aagctgggca gtgttcaatt cagtactgac acagaaaatg 6181 attttgaaac tcaccaaaac acaaaattca ccccagtcgg tgtcatccag gatggtggta 6241 ccacccaccg aaatgaaccc caacaatggg tgctcccaag ttattcaggt agagatgttc 6301 ataatgtaca cctagcccct gctgtggccc ccacttttcc gggtgaacaa cttcttttct 6361 tcaggtccac tatgcccgga tgcagcgggt atcccaacat ggatttggat tgcctactcc 6421 cccaggagtg ggtgcagcac ttctaccaag aggcagctcc agcacaatct gatgtggctc 6481 tattgagatt tgtgaatcca gacacgggta gggtcctgtt tgagtgcaaa cttcataaat 6541 caggctatgt cacagtggct cacaccggtc agcatgattt ggtcatcccc cccaatggct 6601 attttaggtt tgattcctgg gttaatcagt tctacacgct tgcccccatg ggaaacggaa 6661 cggggcgtag gcgcgcctta taatggctgg agctttcttt gctggattgg catctgatgt 6721 ccttggctct ggacttggtt ccctaatcaa tgctggggct ggggccatca accaaaagat 6781 tgattttgaa aataatagaa aactgcagca agcttccttc cagtttagca gtaatctaca 6841 acaggcttcc tttcaacacg ataaagagat gctccaagca caaattgagg ccactaaaaa 6901 gttgcaacag gagatgatga aagtcaaaca ggcaatgctc ctagaaggtg gattctctga 6961 aacagatgca gcccgtgggg caatcaacgc ccccatgaca aaggttttgg actggagcgg 7021 aacaaggtac tgggcccctg acgctaggac cacaacatac aatgcaggcc gcttttccac 7081 ccctcaacct tcggggacgc tgccaggaag aatcaatccc agaactccta cccccgctcg 7141 gggctcctcc agcacatctt ctaatgcttc tactgctact tctatatatt caaatcaaac 7201 tgtttcaacg agacttggtt ctacagctgg ttctggtacc aatgtctcga gtctcccgtc 7261 aactgcaagg actaggagct gggttgagga tcaaaacaga aatttgtcac ctttcatgag 7321 gggggctcat aacatatcgt ttgtcacccc accatctagc agatcctcta gccaaggcac 7381 agtctcaacc gtgcctaaag aagttttgga ctcctggact ggc //