Typing tool
|
Complete norovirus genomes
KP784694 | GII.4 Sydney | ||
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GII.P4 Yerseke |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS KP784694 7570 bp RNA linear VRL 22-NOV-2016 DEFINITION Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/Empangeni/8604, complete genome. ACCESSION KP784694 VERSION KP784694.1 KEYWORDS . SOURCE Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/Empangeni/8604 ORGANISM Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/Empangeni/8604 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TITLE Comparative analysis of South African norovirus GII.4 strains identifies minor recombinant variants JOURNAL Unpublished REFERENCE 2 (bases 1 to 7570) AUTHORS Botha,J.C., Mans,J. and Taylor,M.B. TITLE Direct Submission JOURNAL Submitted (13-FEB-2015) Medical Virology, University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/Empangeni/8604" /mol_type="genomic RNA" /isolate="GII/Hu/ZAF/2012/GII.P4_GII.4/Empangeni/8604" /host="Homo sapiens" /db_xref="taxon:1777887" /country="South Africa" /collection_date="2012" /note="genotype: GII.P4_New_Orleans_2009/GII.4_Sydney_2012" 5'UTR 1..4 gene 5..5105 /gene="POL" CDS 5..5104 /gene="POL" /codon_start=1 /product="polyprotein" /protein_id="ALX87350.1" /translation="MKMASNDASATAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKSIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LARVELAPLSLYWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK LKPLNILNILASCDWTFAGIVESLILLAELFGIFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELALVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVMMISGKPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDVEK AKRDFPGQPDMWKNAFSSDFSHMKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLVDTMKVGRQLKDVKTM PELKQALKNVSIKKCQIVYSGSTYTLESDGKGSVKVDRIQSASVQTNNELTGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVENTEETTNKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVSLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDGW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL GTMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYAYHYDADYSRWD 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="ALX87351.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAADPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSHNYTMNLATQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTKTDGSTRSHKATVYTGSADFAPKLGRVQFETDTNNDFETNQNTKFTPVGVIQNG ETAHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGSHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAT" gene 6705..7513 /gene="VP2" CDS 6707..7513 /gene="VP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="ALX87352.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSEADAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRANLRDTVPARGSSSTSS KSSIATSLYSNQTATTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRSLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA" 3'UTR 7514..7570 ORIGIN 1 gtgaatgaag atggcctcta acgacgcttc cgctaccgct gttgctaaca gcaacaacga 61 taccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agcctccccc gagggaaata ccacaaagac ccccacgacc 181 acccacccca gaactggtta aaagcattcc cccccctccg cccaacggag aggatgaaat 241 agtggtttcc tatagtgtca aagatggtgt ttccggtttg cctgaccttt ccaccgtcag 301 gcaaccggaa gaatctaaca cggccttcag tgtccctcca ctcaatcaga gggaaaatag 361 agatgctaag gagccactta ctggaacaat tctcgaaatg tgggatggag aaatctacca 421 ttatggcctg tatgtggagc gaggtctcgt actaggtgtg cacaaaccac cagctgccat 481 cagcctcgct agggttgagc tggcaccact ctccttgtac tggagacctg tgtacactcc 541 tcagtacctc atctctccag acactctcaa gaaattacac ggagaaacgt tcccctacac 601 agcctttgac aacaattgct atgccttttg ctgctgggtc ctggatctaa atgactcgtg 661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa 721 taggaaaccc cttcccacta tggatgactc caaattaaag aaggtagcta acatattcct 781 gtgtgctctg tcctcgctgt tcaccaggcc cataaaagac ataataggga agctaaagcc 841 tctcaacatc ctcaacatct tagcctcatg tgattggact tttgcaggca tagtggaatc 901 cctgatactc ttggcagagc tctttggaat tttctggacg cccccagatg tgtctgcgat 961 gattgcaccc ttactcggtg actatgagct gcaaggacct gaggaccttg cagtggagct 1021 cgtccccgta gtgatgggtg gaattggttt ggtgctagga tttaccaaag agaagattgg 1081 gaaaatgttg tcatccgctg catccacctt gagagcatgt aaagaccttg gtgcatatgg 1141 gctagagatc ctaaagttgg tcatgaagtg gttcttcccg aaaaaggagg aggcgaatga 1201 actggcttta gtgagatcta tcgaggatgc agtcttggat ctcgaggcaa ttgaaaacaa 1261 ccatatgacc accctgctca aagacaaaga cagtctggca acctatatga gaacccttga 1321 ccttgaggag gagaaagcca ggaaactctc aaccaaatct gcctcacccg acatcgtggg 1381 cacaatcaac gctctcctgg cgagaatcgc tgctgcacgc tctctggtgc atcgagcgaa 1441 ggaggaactt tccagcagac caagacctgt agtaatgatg atatcaggca aaccaggaat 1501 agggaagacc caccttgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga 1561 ccagcgtgta ggcctcatcc cgcgcaatgg cgtcgaccat tgggatgcgt acaaggggga 1621 gagggtcgtc ctttgggacg attatggaat gagcaacccc attcacgatg ccctcaggtt 1681 gcaagagctc gctgacactt gccccctcac tctgaactgt gacaggattg agaacaaagg 1741 aaaggtcttt gacagcgatg tcatcattat caccactaac ctggccaacc cagcaccact 1801 tgactatgtc aactttgaag catgctcgag gcgcatcgac ttcctcgtgt atgcagatgc 1861 ccctgacgtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc 1921 cttcagttct gacttctcac acatgaaact ggcattggcc ccacaaggtg gcttcgacaa 1981 gaacgggaac accccacacg gaaaaggcgt catgaagact ctcaccacag gctcccttat 2041 tgcccgggca tctgggttgc tccatgagag attagatgaa tttgaactac aaggcccaac 2101 actcaccacc ttcaattttg atcgcaacaa agtacttgcc tttagacaac ttgctgctga 2161 gaacaaatat ggattagtgg acacaatgaa agttgggagg cagctcaagg atgtcaaaac 2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgcc agatagtgta 2281 tagtggttcc acctacacac ttgagtctga tggcaaaggt agtgtgaaag ttgacagaat 2341 ccagagcgcc tccgtgcaga ccaacaatga gctgaccggt gccctgcacc atttgaggtg 2401 cgccagaatc agatattatg tcaagtgtgt ccaggaggcc ctgtactcca tcatccaaat 2461 tgctggggct gcatttgtca ccacgcgcat cgtcaagcgc atgaacatac aagacctgtg 2521 gtccaagcca caagtggaaa acacagagga gaccaccaac aaagacgggt gcccaaaacc 2581 caaagatgat gaggagttcg tcatttcatc tgacgacatc aaaactgagg gtaagaaggg 2641 gaagaacaag actggccgcg gcaagaagca cacagccttt tcaagcaaag gcctcagtga 2701 tgaagagtac gatgagtaca agagaattag ggaagaaagg aatggcaagt actccataga 2761 agagtacctc caggacaggg acaaatacta cgaggaggtg gccattgcca gggcgactga 2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa agaatcttca ggccaacaag 2881 gaaacaacgc aaggaggaaa gagcttctct cggtctagtt acaggttctg aaattaggaa 2941 aagaaaccca gatgatttca aacccaaggg gaaattgtgg gctgacgatg acagaagtgt 3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atctggtcga ggatagtcaa 3061 ctttggttcg ggttggggat tttgggtctc ccccagtctg ttcataacat caacccatgt 3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaattc aggtacacaa 3181 atcaggcgag ttctgtcgcc tgagattccc aaaaccaatc aggactgatg tgacgggcat 3241 gatcttggaa gaaggcgcac ctgagggcac cgtggtctca ctactcatca aaaggtccac 3301 tggggagctc atgcccctag cagctagaat ggggacccat gcaactatga agatccaagg 3361 gcgcactgtt ggaggccaga tgggcatgct tctgacagga tccaacgcca aaagcatgga 3421 tctgggtacc acaccaggtg attgtggctg tccctacatc tataagaggg gtaatgacta 3481 tgtagtcatt ggagtccaca cagctgccgc tcgtgggggg aacactgtca tatgtgccac 3541 ccaggggagt gaaggagagg ctacacttga aggaggtgac aacaaaggga catactgtgg 3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag 3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcctatcttg gtggcaagga 3721 ccctagagtc aagggtggcc cttcactaca gcaagtcatg agggaacagt tgaagccatt 3781 cacagagccc aggggcaagc caccaaagcc aagtgtgtta gaagctgcca agaagaccat 3841 catcaatgtc cttgagcaaa caattgatcc gcctgagaaa tggtcattcg cgcaagcttg 3901 cgcgtccctt gacaagacca cttccagcgg tcacccgcac cacatgcgga aaaatgatgg 3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacctgat 4021 gtttgaggaa gggaagaaca tgaccccagt ctacacagct gcgcttaaag atgaattggt 4081 caaaactgac aaaatatatg gtaagatcaa aaagaggctt ctctggggct cggacttggg 4141 aaccatgatc cggtgtgctc gggcattcgg aggcctaatg gatgaactca aagcgcactg 4201 tgtcacactc cccattagag ttggtatgaa tatgaatgag gatggcccca tcatcttcga 4261 gaggcactcc aggtacgcat atcactatga tgctgattac tctcgatggg attcgacaca 4321 acagagagcc gtattggcag cagctctaga aatcatggtt aaattctccc cagaaccaca 4381 tttggctcag gtagtcgcgg aggacctcct atctcctagc gtggtggacg tgggcgactt 4441 cacaatatcg atcaacgagg gtcttccctc tggggtgcct tgcacctccc aatggaattc 4501 catcgcccac tggcttctca ctctctgtgc gctctctgaa gtcacaaatt tgtcccctga 4561 caccatacag gctaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga 4621 tataaaattg gacccagaga aattgacagc aaagctcagg gaatatgggt taaaaccaac 4681 ccgccctgat aaaactgaag gaccccttgt catctccgaa gacttgaatg gcctaacctt 4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc 4801 aatactcagg cagatgtact ggactagggg ccccaaccat ggagacccat ctgaaacaat 4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca 4921 cggcccagca ttctacagca aaatcagcaa gttggttatt gcagagctaa aagaaggtgg 4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagcttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg 5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagtttacag 5281 tgtcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa 5341 acccctacct atcccacttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtgatcct tgcggggaac gcgttcaccg ccgggaagat catatttgca gcagacccac 5461 caaatttccc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catataatag 5521 tagatgttag gcaactagaa cctgtgttga tccccttacc cgatgttagg aacaatttct 5581 accattataa tcaatcaaat gaccccacta tcaagttgat agcaatgttg tacacaccac 5641 ttagggctaa taatgctggg gacgatgtct ttacagtttc ttgccgagtt ctcacgaggc 5701 catcccccga ttttgacttc atatttttag tgccacccac agttgagtca agaactaaac 5761 cattctctgt cccaatttta actgttgagg agatgaccaa ttcaagattc cccattcctt 5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt 5881 gcacgactga cggcgtgctc ctaggtacta cccaactgtc tcctgtcaac atctgcacct 5941 tcagagggga tgtcactcat attgcaggtt ctcacaacta cacaatgaat ttggccactc 6001 aaaattggaa cagttatgac ccaacagaag aaatcccagc ccctctagga actccagatt 6061 tcgtggggaa gattcaaggt gtactcaccc aaaccacaaa gacagatggc tcgacacgca 6121 gccacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaattg ggtagagttc 6181 aatttgaaac tgacacaaac aatgattttg aaaccaacca aaacacaaag ttcaccccag 6241 tcggtgtcat ccagaatggt gaaactgccc acaggaatga accccaacag tgggtgctcc 6301 caagttactc aggcagaaat actcccaatg tgcatttggc ccccgctgta gcccccactt 6361 ttccgggtga acaacttctc ttcttcagat ccactatgcc cggatgcagc gggtatccca 6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ccccagcgca atctgatgtg gctctactaa gatttgtgaa cccagacaca ggtagggttt 6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggctcacact ggttcacatg 6601 atttggttat cccccctaat ggttatttta ggtttgattc ctgggtcaac cagttctaca 6661 cacttgcccc catgggaaat gggacggggc gtagacgtgc aacataatgg ctggagcttt 6721 ctttgctgga ttggcatctg acgtccttgg ctctgggctt ggttctctga tcaatgctgg 6781 ggctggggcc atcaaccaaa aagttgaatt tgaaaataac agaaaattgc aacaagcttc 6841 cttccaattt agcagcaatc tacaacaagc ttcttttcaa catgataaag agatgctcca 6901 agcacaaatt gaggccacca aaaagttgca gcaggaaatg atgaaagtta aacaggcagt 6961 gctcctagag ggtgggttct ctgaggcaga tgcagcccgt ggggcgatca acgcccccat 7021 gacaaaggct ttggactgga gcgggacaag gtactgggct cctgatgcta ggactacaac 7081 atacaatgca ggccgctttt ccacccctca accatcgggg acactgccgg gaagagctaa 7141 tcttagggat actgtccccg ctcggggttc ctctagcaca tcttctaaat cttctattgc 7201 tacttctttg tattcaaatc aaactgccac aacgagactt ggttctacag ctggctctgg 7261 taccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa 7321 taggagtttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaagttt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga 7501 gtcacgggcg taatgtgaaa agacaaaatt gattatcttt cttttcttta gagtcttgaa 7561 aaaaaaaaaa //