Typing tool
|
Complete norovirus genomes
KM198562 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7443LOCUS KM198562 7443 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/C2H-55/2011/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198562 VERSION KM198562.1 KEYWORDS . SOURCE Norovirus Hu/GII/C2H-55/2011/VNM ORGANISM Norovirus Hu/GII/C2H-55/2011/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/C2H-55/2011/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/C2H-55/2011/VNM" /host="Homo sapiens" /db_xref="taxon:1527024" /country="Viet Nam" /collection_date="25-Nov-2011" /note="genotype: GII" CDS 1..5100 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02814.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSNMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKKVPPPPPNGEDEVVVSYSAKDGISGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTTDDSKLKKVANIFLCTLSSLFTRPIKDIIGK LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPAPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGRQLKDVKTM PELKQALKSISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQNLWSKPQVENTEEATNKDGC PKPTDDEEFVITSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKSMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" CDS 5081..6703 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02815.1" /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFIVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRDYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFEAHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6703..>7443 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02816.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSSLQQASFQHDKEMLQAQVEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQTSGSLPGRINPRAPTPARASSGTSS NASTVNSIYSNQTVSTRLGSTAGSVTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTG" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc 61 gcaaaatctt caagtgacaa aatgttttct aacatggctg tcacttttaa acgagccctc 121 ggggcgcggc ctaaacagcc tcccccgagg gaaataccgc aaagaccccc acgaccacct 181 actccagaat tggtcaaaaa ggtccctcct cccccgccca acggagagga tgaagtggtg 241 gtttcttata gtgccaaaga tggcatttct ggtctacctg agctttccac cgtcagacaa 301 ccagaagaaa ccaatacggc cttcagtgtc cctccactca atcagaggga gaatagggat 361 gctaaggaac cactgactgg aacaattctg gaaatgtggg atggagaaat ctatcattat 421 ggcctgtatg ttgaacgagg tcttgtgctg ggtgtgcaca aaccaccagc tgccattagc 481 ctcgccaagg tcgaactaac accactctcc ttgttctgga gacctgtgta caccccacag 541 tacctcatct ctccagacac tctcaagaaa ttacacggag aaacatttcc ctacacagcc 601 tttgacaaca actgctatgc cttttgttgc tgggtcctgg atctaaacga ctcgtggctg 661 agtaggagaa tgatccagag aacaactggc ttcttcagac cctaccaaga ttggaatagg 721 aaacccctcc ctactacgga tgattccaaa ttaaagaagg tagctaacat attcctgtgc 781 accctgtctt cgctattcac caggcccata aaagacataa taggaaagtt aaggcctctc 841 aacatcatca acatcctagc ttcatgtgac tggactttcg caggcatcgt ggaatctttg 901 atactcttgg cagagctctt tggagtcttc tggacacccc cagatgtgtc tgcgatgatt 961 gcccccttac tcggtgattt cgagttacaa ggacctgagg accttgtagt ggagctcgtc 1021 cctgtggtaa tggggggaat tggtttggtg ctgggattca ccaaagagaa gattggaaaa 1081 atgttgtcat ctgctgcgtc caccttgaga gcttgtaaag atctcggtgc atatgggcta 1141 gagatcctaa agctagtcat gaagtggttc ttcccgaaga aagaggaggc aaatgaactg 1201 gctatggtga gatccatcga ggatgcagta ctggaccttg aggcaattga aaacaaccat 1261 atgaccacct tgctcaaaga taaagacagc ctggcaacct acatgagaac ccttgacctc 1321 gaggaagaga aagccagaaa actctcaacc aagtctgctt cacctgacat cgtgggcaca 1381 atcaacgccc ttctggcgag aatcgccgct gcacgctccc tggtgcaccg agcgaaggag 1441 gagctttcca gcagaccaag acctgtggtc ttgatgatat caggtagacc agggataggg 1501 aagacccacc ttgctaggga agtggctaag agaatcgcag cctccctcac aggggaccag 1561 cgcgtaggcc tcatcccacg caatggcgtc gatcactggg atgcgtacaa gggggagagg 1621 gtcgtcctat gggacgacta tggaatgagc aatcccatcc acgacgccct caggctgcaa 1681 gaactcgctg acacttgccc cctcactcta aattgtgaca ggattgagaa taaaggaaag 1741 gtctttgaca gtgatgtcat cattatcact actaatctgg ccaacccagc accactggac 1801 tatgtcaact ttgaagcgtg ctcgaggcgc atcgatttcc tcgtgtacgc agaagccccc 1861 gaggtcgaaa aggcgaagcg tgacttcccg ggccaacctg acatgtggaa aaacgctttt 1921 agttctgatt tctcacacat aaaactggca ctggctccac aaggtggctt cgataagaac 1981 gggaacaccc cacatgggaa gggcgtcatg aagactctca ccactggctc ccttattgcc 2041 cgggcatcag ggctgctcca tgagagattg gatgagtttg aactacaggg cccagctccc 2101 accaccttca actttgaccg caacaaagtg cttgccttca ggcagcttgc tgctgaaaac 2161 aaatacgggt tagtggacac aatgagagtt gggaggcagc tcaaggatgt caaaaccatg 2221 ccagaactta aacaagcact caagagcatc tcaatcaaga agtgtcagat tgtgtacagt 2281 ggttgcacct acacacttga gtctgatggc aagggcaatg tgaaggttga cagagttcag 2341 agcacctccg tgcagaccaa caatgagctg gctggcgccc tgcaccatct gagatgcgcc 2401 agaatcagat actatgttaa gtgtgtccag gaggccctgt attctatcat ccaaattgct 2461 ggagctgcat tcgtcaccac gcgcatcatc aagcgtgtga acattcaaaa cttatggtcc 2521 aaaccacaag tggaaaacac agaggaagcc accaacaagg atgggtgccc aaaacccaca 2581 gatgatgagg agttcgtcat tacatctgac gacattaaaa ctgagggtaa gaaaggaaag 2641 aacaagactg gccgtggtaa gaagcacaca gccttctcaa gtaaaggtct cagtgatgaa 2701 gagtatgatg agtacaagag aattagagag gaaaggaatg gcaagtactc catagaagag 2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gaccgaggaa 2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tctttagacc aacaaggaaa 2881 caacgcaagg aagaaagagc ttctctcggt ttagtcacag gttctgaaat taggaaaaga 2941 aacccagatg atttcaagcc caaggggaaa ctatgggctg acgatgacag aagtgtggac 3001 tacaatgaga agctcagttt tgaggctccg ccaagcatct ggtcaaggat agtcaacttt 3061 ggctcaggtt ggggcttctg ggtctccccc agcctattca taacatcaac ccacgtcata 3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaattcaggt gcacaagtca 3181 ggcgaattct gtcgcttgag gttcccaaaa ccaatcagga ctgatgtgac tggcatgatc 3241 ttggaagaag gcgcgcctga aggcaccgtg gccacactac tcatcaaaag gtctactgga 3301 gaactcatgc ccctagcagc cagaatgggg acccatgcaa ccatgaagat tcaagggcgc 3361 actgttggag gtcagatggg catgcttctg acagggtcca acgccaaaag catggaccta 3421 ggcaccacac caggtgattg cggctgtccc tacatctaca agagagggaa tgactatgtg 3481 gtcattggag ttcacacggc tgccgctcgt gggggaaaca ctgttatatg tgccacccag 3541 gggggtgagg gggaagctac acttgaaggt ggtgacagta agggaacgta ctgcggtgcg 3601 ccaatcctag gcccagggag cgccccaaaa cttagcacca aaaccaaatt ctggagatca 3661 tccacagcac cactcccacc tggcacctat gagccagcct accttggtgg caaggacccc 3721 agagtcaagg gtggcccctc gctgcagcaa gtcatgagag accagctgaa accattcaca 3781 gagcccaggg gtaagccacc aaagccaagt gtgttggaag ctgccaagaa aaccatcatc 3841 aatgttcttg aacaaacaat tgacccacct gagaagtggt cgttcgcaca ggcttgcgcg 3901 tcccttgaca agaccacttc tagcggccat ccgcaccaca tgcggaaaaa cgactgctgg 3961 aacggggagt ccttcacagg caagctggca gaccaggctt ccaaggccaa cctgatgttt 4021 gaagaaggga agagcatgac cccagtctac acaggtgcgc tcaaggatga gttggtcaaa 4081 actgataaaa tttatggcaa gatcaagaag aggcttctct ggggctcgga tttagcaacc 4141 atgattcggt gtgctcgagc attcggaggc ctaatggatg aactcaaagc acactgtgtc 4201 acacttccta tcagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaag 4261 cactccaggt ataggtacca ctatgatgct gattactctc gatgggattc aacacaacag 4321 agagccgtgc tggcagctgc tctagaaatt atggttaaat tctcctcaga accacatttg 4381 gctcaggtgg tcgcagaaga ccttctttct cctagcgtgg tggatgtggg tgacttcaca 4441 atatcaatca atgagggtct tccctctggg gtgccctgca cttcccaatg gaactccatc 4501 gcccactggc ttctcactct atgtgcactc tccgaagtta caaatttgtc cccagacatc 4561 atacaggcta actctctctt ctccttctat ggtgatgatg aaattgttag tacagacata 4621 aaactagacc cagagaagtt gacagcaaag cttaaggaat acgggttaaa accaacccgc 4681 cctgacaaaa ctgaaggacc tcttgttatt tctgaagact tggatggttt gactttcctg 4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagctcaata 4801 ctcaggcaaa tgtactggac taggggcccc aaccatgaag atccatctga atcaatgatt 4861 ccacactctc aaagacccat acaattgatg tccctgctgg gagaggccgc actccacggc 4921 ccaacattct atagtaaaat cagcaaatta gtcattgcag agctaaaaga aggtggtatg 4981 gatttttacg tgcccaggca agagccaatg ttcagatgga tgagattctc agatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agctttgtga atgaagatgg cgtcgaatga 5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat 5161 ggctttggag cccgttgtcg gtgccgctat tgcggcgcct gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagga ataattttgt acaagcccct ggtggagaat tcacagtatc 5281 ccctagaaac gctccaggtg agatactatg gagcgcgccc ttaggccctg atctgaatcc 5341 ctacctatcc catttggcca gaatgtataa tggttatgca ggtggctttg aagtgcaggt 5401 gatcctcgcg gggaacgcgt tcaccgccgg aaaaattata tttgcagcag ttccaccaaa 5461 ttttccaact gaaggcttga gccccagcca ggttactatg ttcccccata taatagtaga 5521 tgttaggcaa ctggaacctg tgttgatccc cttacctgat gttaggaata acttctatca 5581 ttataatcag tcaaatgatt ccaccattaa attgatagca atgctgtaca caccacttag 5641 ggctaataat gctggggaag atgtcttcac agtctcttgt cgagttctca cgaggccatc 5701 ccctgatttt gattttatat ttttggtgcc acccacagtt gagtcaagaa ctaaaccatt 5761 tactgtccca atcttaactg ttgaagaaat gaccaattca agattcccca tccctttgga 5821 aaagttgttc acgggcccca gcggtgcctt tattgttcaa ccacaaaatg gtaggtgcac 5881 gactgatggc gtgctcttag gcaccaccca actgtctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccacattg caggttctcg cgattacacg atgaatttgg cttctctaaa 6001 ttggaataat tatgacccaa cagaagaaat tccagcccct ctgggaactc cagatttcgt 6061 gggaaagatc caaggtgtgc tcactcaaac cacaaaggga gatggctcga cccgtggcca 6121 caaagcaaca gtttacactg ggagtgcccc cttcactcca aagctgggca gtgttcaatt 6181 cagtactgac acagaaaatg attttgaagc tcaccaaaac acaaaattca ccccagtcgg 6241 tgtcatccag gatggtggta ccacccaccg aaatgaaccc cagcaatggg tgctcccaag 6301 ttattcaggt agagatgtcc acaatgtaca cctggcccct gctgtagccc ccacttttcc 6361 gggtgaacaa cttctcttct tcaggtccac tatgcccgga tgcagtgggt atcctaacat 6421 ggatttggat tgcctactcc ctcaggagtg ggtgcagcac ttctaccaag aggcagctcc 6481 agcacaatct gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcctgtt 6541 tgagtgcaaa cttcataaat caggttatgt cacagtggct cacaccggcc agcatgattt 6601 ggtcatcccc cctaatggct attttaggtt tgattcctgg gttaaccaat tctacacact 6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcttta taatggctgg ggctttcttt 6721 gctggattgg catctgatgt ccttggctct ggacttggct ccctaatcaa tgctggggct 6781 ggggctatca accagaagat tgattttgaa aataacagaa aattgcagca agcttccttc 6841 cagtttagca gtagtctaca acaggcctcc tttcaacatg acaaagagat gctccaagca 6901 caagttgagg ccactaaaaa gttgcaacag gaaatgatga gagtcaaaca ggcaatgctc 6961 ttagaaggtg ggttttctga aacagatgca gctcgtgggg caatcaacgc ccccatgaca 7021 aaagttttgg attggagtgg aacaaggtac tgggcccctg atgccaggac tacaacatac 7081 aatgcaggcc gcttttccac cccccaaacc tcggggtcat tgccaggaag aatcaatccc 7141 agggctccta cccccgctcg ggcctcttct ggtacatcct ctaatgcttc tactgttaat 7201 tctatatatt caaatcaaac tgtttcaacg aggcttggtt ctacagctgg ctctgtcacc 7261 aatgtctcga gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga 7321 aatttgtcgc ctttcatgag gggggctcac aacatatcgt ttgtcacccc accatctagc 7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aagttttgga ctcctggact 7441 ggc //