Typing tool
|
Complete norovirus genomes
KM198543 | GII.4 New Orleans | ||
---|---|---|---|
GII.P4 New Orleans |
ORF1: 82..5088 ORF2: 5069..6691 ORF3: 6691..7431LOCUS KM198543 7431 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/20357/2009/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198543 VERSION KM198543.1 KEYWORDS . SOURCE Norovirus Hu/GII/20357/2009/VNM ORGANISM Norovirus Hu/GII/20357/2009/VNM Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7431) 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 7431) 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..7431 /organism="Norovirus Hu/GII/20357/2009/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/20357/2009/VNM" /host="Homo sapiens" /db_xref="taxon:1291863" /country="Viet Nam" /collection_date="30-Dec-2009" /note="genotype: GII" CDS 82..5088 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02757.1" /translation="MAVTFKRALGARPKQPPPREKPQRPPRPPTPELVKNIPPPPPNG EDEIVVSYSVKDGVSGLPDLSTVRQPEESNTAFSVPPLNQRENRDAKEPLTGTILEMW DGEIYHYGLYVDRGLVLGVHKPPAAISLARVELAPLSLYWRPVYTPQYLISPDTLKKL SGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPTMDDS KIKKVANIFLCALSSLFTRPIKDIIGKIRPLNILNILASCDWTFAGIVESLILLAELF GVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSA ASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAIVRSIEDAVLDLEAIENNHMTT LLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHRAKEE LSSRPRPVVLMISGRPGIGKTYLAREVAKRIAASLTGDQRVGLIPRNGVDHWDAYKGE RVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNLANPA PLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLALAPQG GFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNKVLAF RQLAAENKYGLMDTMRVGKQLKDVRTMPELKQALKNVSIKKCQLVYSGCTYILESDGK GNVKVDRIQSAAVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFVTTRI AKRMNIQDLWSKPQVENTEETTSKDGCPKPKDDEEFVISSDDIKAEGKKGKNKTGRGK KHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARATEEDFCEE EEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSVDYNE KLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQVHKSG EFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGTHATMKIQG RTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGNTVIC ATQGSEGEATLEGGDNKGTYCGAPILGPGSAPTLSTKTKFWRSSTASLPPGTYEPAYL GGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPEKW SFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYT AALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIRVGMN MNEDGPIIFERHSRYTYHYDADYSRWDSTQQRAVLAAALEIMVKFSPEPHLAQVVAED LLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDTIQANS LFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKPTRPDKTEGPLVISEDLNGLTFLRRT VTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPSETMIPHSQRPIQLMSLLGEAALHGP AFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE " CDS 5069..6691 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02758.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIPGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6691..>7431 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02759.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRATVPARGSSSTSS NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTG" ORIGIN 1 cctaacgacg cttccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca 61 agtgacggag tgctttctag catggctgtc acttttaaac gagccctcgg ggcgcggcct 121 aaacagcctc ccccgaggga aaaaccacaa agacccccac gaccacctac tccagaactg 181 gttaaaaata ttccccctcc cccacccaac ggagaggatg aaatagtggt ttcttatagt 241 gttaaagatg gtgtttccgg cttgcctgac ctttccaccg tcaggcaacc ggaagaatct 301 aacacggcct tcagtgtccc tccactcaac cagagggaga atagagatgc taaggaacca 361 cttactggaa cgattctgga aatgtgggac ggggaaatct accattatgg cctgtatgtg 421 gatcgaggtc ttgtactggg tgtgcacaaa ccaccagctg ccatcagcct cgctagggtt 481 gagctagcac cactctcctt gtactggaga cctgtgtaca ctcctcagta cctcatctct 541 ccagacactc tcaagaaatt atccggagaa acgttcccct acacagcctt tgacaacaac 601 tgttatgcct tttgctgctg ggtcctggac ctaaatgact cgtggctgag caggagaatg 661 atccagagaa caactggttt cttcaggccc taccaagact ggaataggaa accccttccc 721 actatggatg actccaaaat aaagaaggta gctaacatat tcctgtgtgc tctgtcctcg 781 ctgttcacca gacccataaa agatataata gggaagataa ggcctcttaa catcctcaac 841 atcttagcct catgtgattg gacttttgca ggtatagtgg agtccctgat actcttggca 901 gaactctttg gagttttctg gacaccccca gatgtgtctg cgatgattgc ccccttactt 961 ggtgactacg agctacaagg acctgaggac cttgcagttg agctcgtccc cgtagtgatg 1021 gggggaattg gtttggtgct aggattcacc aaagagaaga ttgggaaaat gttgtcatct 1081 gctgcgtcca ccttgagagc ttgtaaagac cttggtgcat atgggctaga gatcctaaag 1141 ttggtcatga agtggttctt cccgaagaag gaagaggcaa atgagctggc tatagtgagg 1201 tctatcgagg atgcagtcct ggatctcgag gcaattgaaa acaaccatat gaccaccttg 1261 ctcaaagaca aagacagtct ggcaacctat atgagaacac ttgaccttga ggaggagaaa 1321 gccaggaaac tctcaaccaa gtctgcctca cccgacatcg tgggcacaat caacgccctc 1381 ctggcgagaa tcgctgccgc acgttctctg gtgcaccgag cgaaggagga gctttccagc 1441 agaccaagac ctgtggtgtt gatgatatca ggcaggccag gaatagggaa gacatacctc 1501 gctagggaag tggctaagag aatcgcagcc tcccttacag gagaccagcg tgtgggcctc 1561 atcccacgca atggcgtcga ccattgggat gcgtacaagg gggagagggt cgtcctatgg 1621 gacgattatg gaatgagcaa ccctattcac gacgccctca ggctgcaaga actcgctgac 1681 acttgccccc tcactctaaa ctgtgacagg atcgaaaaca aaggaaaggt ctttgacagc 1741 gacgtcatca ttatcaccac taatctggcc aacccagcgc cactggacta tgtcaacttt 1801 gaagcatgct cgaggcgcat cgacttcctc gtgtatgcag aagcccctga agtcgaaaag 1861 gcgaagcgtg acttcccagg ccagcctgac atgtggaaga acgctttcag ttctgatttc 1921 tcacacataa aactagcact ggccccacag ggtggtttcg acaagaacgg gaacacccca 1981 cacggaaagg gcgttatgaa gactctcacc actggctccc ttattgcccg ggcatcaggg 2041 ctactccatg agaggttaga tgaatttgaa ctgcagggcc cagctctcac caccttcaat 2101 ttcgatcgca ataaggtgct tgcctttaga cagcttgctg ctgaaaataa atatggattg 2161 atggacacaa tgagagttgg gaaacagctc aaggatgtca gaaccatgcc agaactcaaa 2221 caagcactca agaatgtctc aatcaagaag tgccaattag tgtatagtgg ttgcacctac 2281 atacttgagt ctgatggcaa gggcaatgtg aaagtcgaca gaatccaaag cgccgccgtg 2341 cagaccaaca atgagctggc tggtgccctg caccatttga ggtgcgccag aatcagatac 2401 tatgtcaagt gtgtccagga ggccctgtat tccatcattc aaatcgctgg ggctgcattt 2461 gtcaccacgc gcattgccaa gcgcatgaac atacaagacc tatggtccaa gccacaagtg 2521 gaaaacacag aggagactac cagcaaggac gggtgcccaa aacctaagga cgatgaggag 2581 tttgtcattt catccgacga catcaaagct gagggtaaga aagggaagaa caagactggc 2641 cgcggcaaga agcacacagc attttcaagc aaaggcctca gtgatgaaga gtacgatgag 2701 tacaagagga ttagagaaga aaggaatggc aagtactcca tagaagagta ccttcaggac 2761 agggacaaat actatgagga ggtggccatt gccagggcga ctgaggaaga cttctgtgaa 2821 gaggaggagg ccaagatccg gcaaaggatc tttaggccaa caaggaaaca acgcaaggag 2881 gaaagagcct ctctcggtct ggtcacaggc tctgaaatta ggaaaagaaa cccagatgac 2941 ttcaaaccca aagggaaatt gtgggctgac gatgacagga gtgtagacta caatgagaaa 3001 ctcagttttg aggccccacc aagcatctgg tcgagaatag tcaactttgg ttcaggctgg 3061 ggattttggg tctcccccag tctgttcata acatcaaccc atgtcatacc ccagggcgca 3121 aaggagttct ttggagtccc catcaaacaa atacaggtac acaagtcggg cgagttctgt 3181 cgcttgagat tcccaaaacc aatcaggact gatgtgacgg gcatgatctt agaagaaggc 3241 gcacctgagg gcaccgtggt cacactactc atcaaaaggt ccactgggga actcatgccc 3301 ctagcagcta ggatggggac ccatgcgacc atgaagatcc aagggcgcac tgttggaggc 3361 cagatgggca tgcttctgac aggatccaac gccaagagca tggacctggg tactacacca 3421 ggtgattgtg gctgccccta tatctacaag agaggtaatg actatgtggt cattggggtc 3481 cacacggctg ccgcacgtgg ggggaacact gtcatatgtg ccacccaggg gagtgaagga 3541 gaggctacac ttgaaggtgg tgacaacaag gggacatact gtggtgcacc aatcctaggc 3601 ccagggagtg ccccaacact tagcaccaag accaaattct ggagatcgtc cacagcatca 3661 ctcccacctg gcacctatga accagcctat cttggtggca aggaccctag ggtcaagggt 3721 ggtccttcac tgcagcaagt catgagggaa cagttgaagc cattcacaga gcccaggggc 3781 aagccaccaa aaccaagtgt attagaagct gccaagaaga ccatcatcaa tgtccttgag 3841 caaacaattg atccacctga gaaatggtcg ttcgcacaag cttgcgcgtc ccttgacaag 3901 accacttcca gtggtcatcc gcaccacatg cggaaaaacg actgctggaa cggggagtcc 3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgtttga agaagggaag 4021 aacatgaccc cagtctacac agctgcgctc aaggatgagt tagttaaaac tgacaaaatt 4081 tatggtaaga ttaagaagag gcttctctgg ggctcggact tggcgaccat gatccggtgt 4141 gctcgagcat tcggaggcct aatggatgaa ctcaaagcac actgtgtcac acttcctatt 4201 agagttggca tgaatatgaa tgaggatggc cccatcatct tcgagaggca ttccaggtac 4261 acatatcact atgatgctga ttactctcga tgggattcaa cacaacagag agccgtgttg 4321 gcagcagctc tagaaatcat ggttaaattc tccccagaac cacacttggc tcaggtagtc 4381 gcggaggacc ttctttctcc tagcgtggtg gacgtgggcg acttcacaat atcaatcaac 4441 gagggtcttc cctctggggt gccctgcacc tcccaatgga actccatcgc ccactggctt 4501 ctcactctct gtgcgctctc tgaagtcaca aacctgtccc ctgataccat acaggctaac 4561 tccctcttct ctttttatgg tgatgatgaa attgttagca cagacataaa attggaccca 4621 gaaaaattga cagcaaagct cagagaatat gggttaaaac caacccgccc tgacaaaact 4681 gaaggacccc ttgtcatctc tgaagacctg aatggcctaa ctttcctgcg gagaactgtg 4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gttcaatact caggcaaatg 4801 tactggacta ggggtcccaa ccatggagac ccatctgaaa caatgattcc acactcccaa 4861 agacccatac aattgatgtc cctactgggg gaggccgctc tccacggccc agcattttac 4921 agcaaaatca gcaaattggt cattgcagag ctaaaagaag gtggcatgga tttttacgtg 4981 cccagacaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc 5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgagtgacg ccaacccatc 5101 tgatgggtcc acagccaacc ttgtcccaga ggtcaacaat gaggttatgg ctttggagcc 5161 cgtagttggt gccgctattg cggcacctgt agcgggccaa caaaatgtaa ttgacccctg 5221 gattagaaac aattttgtac aagcccctgg tggagagttt acagtatccc ctagaaacgc 5281 tccaggtgaa atactatgga gcgcgccctt aggccctgat ttgaatccct acctttccca 5341 tttggccaga atgtacaatg gttatgcagg tggttttgaa gtgcaggtaa tcctcgcggg 5401 gaacgcgttc accgccggga aaatcatatt tgcagcagtc ccaccaaatt tcccaactga 5461 aggtttgagc cccagccagg tcactatgtt cccccacata atagtagatg ttaggcaatt 5521 ggaacctgtg ttgattccct tacccgatgt taggaataat ttctaccatt ataatcaatc 5581 aaatgacccc accatcaaat tgatagcaat gttgtacaca ccacttaggg ctaataatgc 5641 cggggacgat gtcttcacag tttcttgtcg agttctcacg agaccatccc ccgattttga 5701 tttcatattt ttggtgccac ctacagtcga atcaagaact aaaccattct ctgtcccagt 5761 tttaactgtt gaggagatga ccaattcaag gttccccatt cctttggaaa agttgttcac 5821 gggccccagt agtgcctttg ttgttcaacc acaaaacggc aggtgcacga ctgatggcgt 5881 gctcctaggt actacccaac tgtctcccgt caacatctgc accttcagag gggatgtcac 5941 ccatattcca ggcagtcgta actacacaat gaatttggcc tcccaaaatt ggaacagtta 6001 cgatccaaca gaagaaatcc cagcccctct aggaactcca gatttcgtgg ggaagattca 6061 aggtgtgctc acccaaacca caaggacaaa tggctcgacc cgcggccaca aagctacagt 6121 gtacactggg agcgccgact tttctccaaa actgggtaga gttcaatttg ccactgacac 6181 agacaatgat tttgaaacta accaaaacac aaagttcacc ccagtcggtg ttatccagga 6241 tggtagtacc accccccgaa atgaacccca acaatgggtg ctcccaagtt actcaggcag 6301 aaacattcac aatgtgcacc tggcccccgc tgtagccccc actttcccgg gcgagcagct 6361 cctcttcttc agatctacta tgcccggatg cagcgggtac cccaacatgg acttggactg 6421 tctgctcccc caggaatggg tgcagtattt ctaccaggag gcagccccag cacaatctga 6481 tgtggctctg ctaagatttg tgaatccgga cacaggtagg gttttgtttg agtgtaagct 6541 tcataaatca ggctatgtta cagtggctca cactggccaa catgatttgg ttatcccccc 6601 caatggttat tttagatttg attcctgggt caaccagttc tacacacttg cccccatggg 6661 aaatgggacg gggcgcagac gtgcattata atggctggag ctttctttgc tggattggca 6721 tctgacgtcc ttggctctgg acttggttcc ctaatcaatg ctggggctgg ggccatcaac 6781 caaaaagttg aatttgaaaa taacagaaaa ttgcaacaag cttccttcca atttagtagc 6841 aatctacaac aggcttcctt tcaacatgac aaagaaatgc tccaagcaca aattgaggcc 6901 accaaaaagt tgcaacagga aatgatgaga gttaaacagg caatgctcct agagggtgga 6961 ttctctgaga cagatgcagc ccgtggggca atcaacgccc ccatgacaaa aactttggac 7021 tggagcggga caaggtactg ggctcccgat gctaggacta caacatataa tgcaggccgc 7081 ttttccaccc cccaaccctc gggggcacta ccaggaagag ctaatcttag ggctactgtc 7141 cccgcccggg gttcctccag cacgtcctct aactcttcta ttgctacttc tgtgtattca 7201 aatcaaacca cctcaacgag acttggttct acagctggtt ctggtaccag tgtctcgagc 7261 ctcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaaataggaa tttgtcacct 7321 ttcatgaggg gggcccataa catctcgttt gtcaccccac catctagcag atcctctagc 7381 caaggcacag tctcaaccgt gcccaaagaa gttttggact cctggactgg c //