Typing tool
|
Complete norovirus genomes
KP784698 | GII.4 New Orleans | ||
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GII.P4 New Orleans |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS KP784698 7570 bp RNA linear VRL 22-NOV-2016 DEFINITION Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/Johannesburg/BW, complete genome. ACCESSION KP784698 VERSION KP784698.1 KEYWORDS . SOURCE Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/Johannesburg/BW ORGANISM Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/Johannesburg/BW Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7570) AUTHORS Botha,J.C., Mans,J. and Taylor,M.B. TITLE Comparative analysis of South African norovirus GII.4 strains identifies minor recombinant variants JOURNAL Unpublished REFERENCE 2 (bases 1 to 7570) AUTHORS Botha,J.C., Mans,J. and Taylor,M.B. TITLE Direct Submission JOURNAL Submitted (13-FEB-2015) Medical Virology, University of Pretoria, Pretoria, Gauteng, South Africa COMMENT ##Assembly-Data-START## Assembly Method :: Sequencher v. 4.10.1 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7570 /organism="Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/Johannesburg/BW" /mol_type="genomic RNA" /isolate="GII/Hu/ZAF/2012/GII.P4_GII.4/Johannesburg/BW" /host="Homo sapiens" /db_xref="taxon:1777889" /country="South Africa" /collection_date="2012" /note="genotype: GII.P4_GII.4_New_Orleans_2009" 5'UTR 1..4 gene 5..5104 /gene="POL" CDS 5..5104 /gene="POL" /codon_start=1 /product="polyprotein" /protein_id="ALX87362.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDGIVVSYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAVVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEELAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGRIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 5..994 /gene="POL" /product="protein p48" mat_peptide 995..2092 /gene="POL" /product="NTPase" mat_peptide 2093..2629 /gene="POL" /product="protein p22" mat_peptide 2630..3028 /gene="POL" /product="VPg" mat_peptide 3029..3571 /gene="POL" /product="3C-like protease" mat_peptide 3572..5101 /gene="POL" /product="RNA dependent RNA polymerase" gene 5084..6707 /gene="VP1" CDS 5085..6707 /gene="VP1" /note="major capsid protein" /codon_start=1 /product="capsid protein VP1" /protein_id="ALX87363.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHISGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFTPKLGRVQFATDTDNDFVTNQNTKFTPVGVIQDG STTPRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6705..7513 /gene="VP2" CDS 6707..7513 /gene="VP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="ALX87364.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEYENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARATTYNAGRFSTPQPSGALPGRANLRATVPARGSSSTSS NPSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNKNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA" 3'UTR 7514..7570 ORIGIN 1 gtgaatgaag atggcctcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga 61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agcctccccc gagggaaaaa ccacaaagac ccccacgacc 181 acctactcca gaactggtta aaaatattcc ccctccccca cccaacggag aggatggaat 241 agtggtttct tatagtgtta aagatggtgt ttccggcttg cctgaccttt ccaccgtcag 301 gcagccagaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag 361 agatgctaag gagccactca ctggaacaat tttggaaatg tgggacgggg aaatctacca 421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccgc cagctgccat 481 cagcctcgct aaggttgagc tagcaccact ctccttgtac tggagacctg tgtacactcc 541 tcagtacctc atctctccag acactctcaa gaaattgtcc ggagaaacgt tcccctacac 601 agcctttgac aacaactgtt atgccttttg ttgctgggtc ctggacctaa atgactcgtg 661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa 721 taggaaaccc cttcccacta tggatgactc caaaataaag aaggtagcta acatatttct 781 gtgtgctttg tcctcgctat tcactagacc cataaaagat ataataggga agataaggcc 841 tcttaacatc ctcaacatct tagcctcatg tgattggacc tttgcgggca tagtggagtc 901 cctaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gattgccccc ttacttggtg actacgagct acaaggacct gaggaccttg cagtggagct 1021 cgtccccgtg gtgatggggg gaattggttt ggtgttagga ttcaccaaag aaaagattgg 1081 gaaaatgttg tcatctgctg cgtccactct gagagcttgc aaagaccttg gtgcatatgg 1141 gctagagatc ctaaagttag tcatgaagtg gttcttcccg aagaaggagg aggcaaatga 1201 gctggctata gtgaggtcca tcgaggatgc agtcctggat ctcgaggcaa ttgaaaacaa 1261 tcatatgacc accctgctca aagataaaga cagtctggca acctacatga gaacacttga 1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg 1381 cacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa 1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat 1501 agggaagacc cacctcgcta gggaagtggc aaagagaatc gcagcctccc ttacaggaga 1561 ccagcgtgtg ggactcatcc cacgcaatgg cgtcgaccat tgggatgcgt acaaggggga 1621 gagggtcgtc ctgtgggacg attatggaat gagcaaccct attcacgatg ccctcaggct 1681 gcaagaactc gctgacactt gccccctcac tctgaactgt gacaggattg aaaataaagg 1741 aaaggtcttt gacagcgatg tcatcattat taccactaat ctggccaacc cagcaccact 1801 ggactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtgt atgcagaagc 1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc 1921 tttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa 1981 gaacgggaac accccacacg ggaagggcgt catgaagact ctcaccactg gctcccttat 2041 tgcccgggca tcagggctac tccatgagag gttagatgag tttgaactgc agggcccagc 2101 tctcaccacc ttcaatttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga 2161 aaacaaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcagaac 2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgtc aaatagtgta 2281 tagtggttgc acctacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacagaat 2341 ccaaagcgcc gtcgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg 2401 cgccagaatc agatactatg tcaagtgtgt ccaggaagcc ctgtactcca tcatccaaat 2461 tgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aagacctatg 2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggacggat gcccaaaacc 2581 taaggatgat gaggaatttg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg 2641 gaagaacaag actggccgtg gcaagaagca cacagcattt tcaagcaaag gcctcagtga 2701 tgaagagtac gatgaataca agaggattag agaggaaagg aatggcaagt actctataga 2761 agagtacctt caggacaggg acaaatacta tgaggagttg gccattgcca gggcgactga 2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacaag 2881 gaaacaacgc aaggaagaaa gagtctctct cggtctggtc acaggctctg aaattaggaa 2941 aagaaaccca gatgacttca aacccaaggg gaaattgtgg gctgatgatg acaggagtgt 3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atttggtcga gaatagtcaa 3061 ctttggttca ggctggggat tctgggtctc ccccagtctg ttcataacat caacccatgt 3121 tataccccag ggcgcaaagg aattctttgg agtccccatc aaacaaatac aggtgcataa 3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggcat 3241 gatcttagaa gaaggcgcac ctgagggcac cgtggtcacg ctactcatca aaaggtccac 3301 cggggaactt atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg 3361 gcgcactgtt gggggccaga tgggcatgct tctgacagga tctaacgcca agagcatgga 3421 cttgggtact acaccaggtg actgtggctg cccctatatc tacaagagag gtaatgacta 3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac 3541 ccaggggagt gagggagagg ctacacttga gggtggtgac aacaagggga catactgtgg 3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag 3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcctatcttg gtggcaagga 3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacaat tgaagccatt 3781 cacagagccc aggggcaagc caccaaaacc aagtgtatta gaagctgcca agaagaccat 3841 cattaatgtc cttgagcaaa caattgatcc acctgaaaaa tggtcgttcg cacaagcttg 3901 cgcgtccctt gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg 3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacctgat 4021 gtttgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttagt 4081 taagactgac aaaatttatg gtaggatcaa gaagaggctt ctctggggct cggacttggc 4141 gaccatgatc cggtgtgctc gagcgttcgg aggcctaatg gatgaactca aagcgcactg 4201 tgtcacactt cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga 4261 gaggcattcc aggtacacgt accactatga tgctgattac tctcgatggg attcaacaca 4321 acagagagcc gtgttggcag cagctctaga aatcatggtt aaattctccc cagaaccaca 4381 tttggctcag gtagtcgcgg aagaccttct ttctcctagc gtggtggacg tgggcgactt 4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc 4501 catcgcccac tggcttctca ctctctgtgc gctctctgaa gtcacaaacc tgtctcctga 4561 taccatacag gccaattccc tcttctcttt ctatggtgat gatgaaattg ttagcacaga 4621 cataaaattg gacccagaga agttaacagc aaagctcaga gagtatgggt taaaaccaac 4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gatctgaatg gcctaacttt 4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc 4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat 4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca 4921 cggcccagca ttttacagca aaatcagcaa attggtcatt gcagagctaa aagaaggtgg 4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccacag ccaacctcgt cccagaggtc aacaatgagg 5161 ttatggcttt ggagcccgta gttggtgccg ctattgcggc acctgtagcg ggccagcaaa 5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag 5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatttga 5341 atccctacct ttcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtaatcct cgcggggaat gcgttcaccg ccgggaaaat catatttgca gcagtcccac 5461 caaatttccc aactgaaggt ttgagcccca gccaagtcac tatgttcccc cacataatag 5521 tagatgttag gcaattggaa cctgtgttga ttcccttacc cgatgttagg aataatttct 5581 accattataa ccagtcaaat gactccacca tcaaactgat agcaatgttg tacacaccac 5641 ttagggctaa caatgctggg gacgatgtct tcacagtttc ttgtcgagtt ctcacgagac 5701 catcccccga ttttgatttt atatttttgg tgccacccac agtcgaatca agaactaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaaggttc cccattcctt 5821 tggaaaaatt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt 5881 gcacgactga tggcgtgctc ctaggtacta cccaactgtc tcctgtcaac atctgcacct 5941 tcagagggga tgtcacccac atttcaggca gtcgtaacta cacaatgaat ttggcctccc 6001 aaaattggaa cagttacgat ccaacagaag aaatcccagc ccccctagga actccagatt 6061 tcgtggggaa gattcaaggt gtactcaccc agaccacaag gacagatggc tcaacccgcg 6121 gccacaaagc tacagtgtac actgggagcg ccgactttac tccaaaactg ggtagggttc 6181 aatttgccac tgacacagac aatgattttg taactaatca aaacacaaag ttcaccccag 6241 tcggtgttat ccaggatggt agtactaccc cccgaaatga accccaacaa tgggtgctcc 6301 caagttactc aggcagaaac actcataatg tgcacctggc ccccgctgta gcccccactt 6361 tcccgggcga gcagctcctc ttcttcagat ctaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtatttctac caggaggcag 6481 ccccagcaca atctgatgtg gcactattaa gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggctcatact ggccaacatg 6601 atttagttat cccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca 6661 cacttgcccc catgggaaat gggacggggc gtagacgtgc attgtaatgg ctggagcctt 6721 ctttgctgga ttggcatctg acgtccttgg ctctggactt ggttccctaa tcaatgctgg 6781 ggctggggcc atcaaccaaa aagttgaata tgaaaacaac agaaaattgc aacaagcttc 6841 cttccaattt agtagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca 6901 agcacaaatt gaggccacca aaaagttgca acaggaaatg atgagagtta aacaagcaat 6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgt ggggcaatca acgcccccat 7021 gacaaaagct ttggactgga gcggaacaag gtactgggct cccgatgcca gggctacaac 7081 atacaatgca ggccgctttt ccacccccca accctcgggg gcactaccag gaagagctaa 7141 tcttagggct actgtccccg cccggggttc ctctagcacg tcttctaacc cttctattgc 7201 tacttctgtg tattcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg 7261 taccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa 7321 taagaatttg tcacctttca tgaggggggc ccacaacatc tcgtttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgccc aaagaagttt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgca agcgagggga 7501 gtcacgggcg taatgtgaaa agacaaaatt gatcatcttt cttttctttt gtgtctttta 7561 aaaaaaaaaa //