Typing tool
|
Complete norovirus genomes
KC962453 | GII.4 New Orleans | ||
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GII.P4 Yerseke |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7510LOCUS KC962453 7567 bp RNA linear VRL 21-APR-2015 DEFINITION Norovirus GII strain GII/Hu/ZAF/2010/GII.P4_GII.4/Bushbuckridge/5928, partial genome. ACCESSION KC962453 VERSION KC962453.2 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7567) AUTHORS Murray,T.Y., Mans,J. and Taylor,M.B. TITLE Noroviruses detected in paediatric patients with gastroenteritis in South Africa JOURNAL Unpublished REFERENCE 2 (bases 1 to 7567) AUTHORS Murray,T.Y. TITLE Direct Submission JOURNAL Submitted (24-APR-2013) Department of Medical Virology, University of Pretoria, Bophelo Road, Pretoria, Gauteng 0001, South Africa REFERENCE 3 (bases 1 to 7567) AUTHORS Botha,J.C. and Mrray,T. TITLE Direct Submission JOURNAL Submitted (21-APR-2015) Department of Medical Virology, University of Pretoria, Bophelo Road, Pretoria, Gauteng 0001, South Africa REMARK Sequence update by submitter COMMENT On Apr 21, 2015 this sequence version replaced KC962453.1. FEATURES Location/Qualifiers source 1..7567 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="GII/Hu/ZAF/2010/GII.P4_GII.4/Bushbuckridge/5928" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="South Africa" /collection_date="Jul-2010" /collected_by="T.Y. Murray" /identified_by="T.Y. Murray" /note="genotype: GII.P4_Yerseke_2006a/GII.4_Apeldoorn_2007" 5'UTR <1..4 gene 5..5104 /gene="POL" CDS 5..5104 /gene="POL" /codon_start=1 /product="polyprotein" /protein_id="AGX93463.2" /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARS KQPPPREIPQRPPRPPTPELIKNVPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGSILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LARVELAPLSLYWRSVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK LRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAREVEK AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVTKSLTTGSLIARA TGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGRQLKDVRTM PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDKIQSASVQTNNELTGALHHLR CARIRYYVKCIQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVEDTEETTSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSVKEYLQDRDKYYEEVAIARATEEDFCEEGEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRPTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG PGSAPALSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRIKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIVNVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMYEEGKNMTPVFTASLKDELVKTDKIYGKIRKRLLWGSDL ATMIRCARAFGGLMDEFKAHCVTLPIRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFTVSINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDSEKLTAKLR 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="viral genome like protein" /note="VPg" mat_peptide 3029..3571 /gene="POL" /product="3C-like protein" mat_peptide 3572..5101 /gene="POL" /product="RNA dependent RNA polymerase" gene 5085..6707 /gene="VP1" CDS 5085..6707 /gene="VP1" /note="major capsid protein" /codon_start=1 /product="capsid protein VP1" /protein_id="AKE07100.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTISPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSIPVLTIEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCSTDGVLLGTT QLSPVNICTFRGDVTHIAGSHNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRADGSTRGHKATVLTGSANFTPKLGRIQFATDTDNDFETNQNTKFTPVGVIQDG DTAHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMDLD CLLPQEWVQFFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6707..7510 /gene="VP2" CDS 6707..7510 /gene="VP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AKE07101.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGHFSTPQPSGAPLGRANLRAAVPTRGSSSTSS NSSIATSVYSNQTASTRLGSTAGSGASVSSLPSTARTRSWVEDQRNLSPFMRGAHNIS FVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" 3'UTR 7511..7567 ORIGIN 1 gtgaatgaag atggcctcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga 61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc 121 cctcggggcg cggtctaaac agcctccccc gagggaaata ccacagagac ccccacgacc 181 acctactcca gaactgatta agaatgttcc cccccccccg cccaacgggg aggatgaaat 241 agtggtttct tatagtgtca aagatggtgt ttccggtttg cctgaccttt ccaccgtcag 301 gcaaccggaa gaatccaaca cggctttcag tgtccctcca ctcaatcaga gggagaatag 361 agatgctaag gagccactta ccggatcaat tctggaaatg tgggatggag aaatctacca 421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccac cagctgccat 481 cagcctcgct agggttgagc tagcaccact ctccttgtac tggagatctg tgtacactcc 541 tcaatacctc atctccccag acactctcaa gaaattacac ggagaaacgt tcccctacac 601 agcctttgac aacaattgtt atgccttttg ttgctgggtc ctggacctaa atgactcgtg 661 gctgagtagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagattggaa 721 taggaaaccc cttcccacta tggatgactc taaattaaag aaggtagcca acatattctt 781 gtgtgctctg tcttcgctat tcaccaggcc cataaaagac ataataggga agctaaggcc 841 tcttaacatc ctcaacatct tagcctcatg tgattggact tttgcaggca tagtggagtc 901 cctgatactc ttggcagagc tctttggagt cttctggaca cccccagatg tgtctgcgat 961 gatcgctccc ttactcggtg actacgagct gcaaggacct gaggaccttg cagtggagct 1021 cgtccccgta gtgatgggtg ggattggttt ggtgctagga ttcaccaaag agaaaattgg 1081 gaaaatgttg tcatctgctg catccacctt gagagcttgt aaagacctcg gtgcatatgg 1141 gctagagatc ctaaagttgg tcatgaagtg gttcttcccg aagaaggagg aagcaaatga 1201 actggctata gtgagatcta tcgaggatgc agtcttagat ctcgaggcaa ttgaaaacaa 1261 ccatatgacc accttgctca aagacaaaga cagtttggca acctatatga gaacccttga 1321 ccttgaggag gagaaagcca ggaaactctc aaccaagtct gcctcacctg acatcgtggg 1381 cacaatcaac gctcttctgg cgagaatcgc cgctgcacgc tctttggttc atcgagcaaa 1441 ggaggaactt tccagcagac caaggcctgt agtgttgatg atatcaggta gaccaggaat 1501 agggaagacc caccttgcta gggaagtggc taagagaatc gcagcctccc tcacaggaga 1561 ccagcgtgta ggcctcgtcc cacgcaatgg cgttgaccat tgggatgcgt acaaggggga 1621 gagggtcgtc ctttgggacg attatggaat gagcaaccct attcacgatg ccctcaggtt 1681 gcaagaactc gctgacactt gccccctcac tctaaactgt gacaggattg agaataaagg 1741 aaaggtcttt gacagcgatg tcatcatcat caccactaat ctggccaacc cagcaccact 1801 ggactatgtc aactttgaag catgctcgag gcgcatcgac ttcctcgtgt atgcagaagc 1861 ccgtgaagtt gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc 1921 tttcagttct gacttctcac acataaaact aacattggct ccacagggtg gcttcgacaa 1981 gaacgggaac accccacacg gaaagggcgt cacgaagtct ctcaccactg gctcccttat 2041 tgcccgggca accgggttgc tccatgagag gttagatgaa tttgaactac agggcccaac 2101 actcaccacc tttaacttcg atcgcaataa agtgcttgcc tttagacaac tagctgctga 2161 gaacaaatat ggactgatgg acacaatgag agttgggaga cagctcaagg atgtcagaac 2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgcc agatagtgta 2281 tagtggttgc acctacatac ttgagtctga tggcaagggc aatgtgaaag ttgacaaaat 2341 tcagagcgcc tccgtgcaga ctaacaacga gctgaccggt gccctgcacc atttgaggtg 2401 cgccaggatt agatactatg tcaagtgcat ccaggaagcc ctgtattcca tcatccaaat 2461 tgctggagct gcatttgtca ccacgcgcat cgtcaagcgc atgaacatac aagacctgtg 2521 gtctaagcca caagtggaag acacagagga gaccaccagc aaggacgggt gtccaaaacc 2581 caaagatgat gaggagtttg tcatttcatc tgacgacatc aaaactgaag gtaagaaagg 2641 gaagaacaag actggccgcg gcaagaagca cacagccttt tcaagcaaag gcctcagtga 2701 tgaagagtac gatgagtaca agaggattag ggaagaaagg aatggtaagt attccgtaaa 2761 agagtacctt caggacaggg acaaatacta tgaggaggtg gccattgcca gggcaactga 2821 ggaagacttc tgtgaagagg gggaggccaa aatccggcaa aggatcttca ggccaacaag 2881 gaaacaacgc aaggaggaaa gagcttctct cggtctggtt acaggttctg aaattaggaa 2941 aagaaaccca gatgatttca aacccaaggg gaaactgtgg gctgacgatg acagaagtgt 3001 ggactataat gagaaactca gttttgaggc cccaccaagc atctggtcaa ggatagtcaa 3061 ctttggttca ggttggggat tctgggtctc ccccagtctg ttcataacat caacccatgt 3121 tataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaattc aaatacacaa 3181 gtcaggcgag ttctgccgct tgagattccc aaagccaatc aggactgatg tgacgggcat 3241 gatcttagaa gaaggcgcac ctgagggcac tgtagtcaca ctacttatca aaaggcccac 3301 tggggaactc atgcccctag cagttaggat ggggacccat gcaaccatga agatccaagg 3361 gcgcactgtt ggaggccaaa tgggcatgct cctgacaggg tccaacgcca aaagcatgga 3421 cctgggtact acaccaggtg attgtggctg tccctacatc tacaagagag gcaatgacta 3481 tgtggccatt ggagtccaca cggctgctgc tcgtggggga aacaccgtca tatgtgccac 3541 ccaggggagt gaaggagagg ctacacttga gggtggtgac gacaagggga catactgtgg 3601 tgcaccaata ttaggcccag ggagtgcccc agcacttagc accaagacca aattctggag 3661 atcatccaca gcaccactcc cacctggcac ctatgaacca gcctaccttg gtggcaagga 3721 ccctagaatc aagggtggcc cttcactaca gcaagtcatg agggaacagt tgaagccatt 3781 cacagagccc aggggcaagc caccaaagcc aagtgtgtta gaagctgcca agaaaaccat 3841 cgtcaatgtc cttgagcaaa caattgatcc acctgagaag tggtcattcg cacaagcttg 3901 cgcgtccctc gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg 3961 ctggaatggg gagtccttca caggcaagct ggcagaccaa gcttccaaag ccaacctgat 4021 gtatgaagaa gggaagaata tgaccccagt cttcacagct tcgctcaagg atgaactagt 4081 taagactgac aaaatttatg gtaagatcag gaagaggctt ctctggggct cggacttagc 4141 gaccatgatc cggtgcgctc gagctttcgg aggcctaatg gatgaattca aagcacactg 4201 tgtcacactt cccattagag ttggtatgaa tatgaatgag gatggcccca tcatcttcga 4261 gaagcattcc aggtacaaat atcactatga tgctgattac tctcgatggg attcaacaca 4321 acagagagcc gtgttggcag cagctctaga aatcatggtc aaattctccc cagaaccaca 4381 tttggctcag gtagtcgcgg aagaccttct ttctcctagc gtgatggacg tgggcgactt 4441 cacagtatca atcaatgagg gtcttccctc cggggtgccc tgcacctccc aatggaactc 4501 catcgcccat tggcttctca ctctctgtgc gctctctgaa gtcacaaact tgtcccctga 4561 tatcatacag gctaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga 4621 tataaaattg gactcagaga aattgacagc aaagctcagg gaatatgggt taaaaccaac 4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gacttaaatg gcctgacttt 4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc 4801 aatactcagg caaatgtact ggactagggg ccccaaccat ggagacccat ctgaaacaat 4861 gattccacat tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca 4921 cggcccagca ttctacagca aaattagcaa attggtcatt gcagagctaa aagaaggtgg 4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccacag ccaacctcgt cccagaggtc aacaatgagg 5161 ttatggcttt ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagttcacaa 5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatttga 5341 atccctacct ttcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtaatcct tgcggggaat gcgttcaccg ccggaaaagt catatttgca gcagtcccac 5461 caaatttccc aactgaaggc ttgagcccca gccaggtcac tatgtttccc catatagtag 5521 tagatgttag gcaactggag cctgtgttga tccccttacc cgatgttagg aataatttct 5581 accactacaa tcaatcaaat gaccccacca tcaaattgat agcaatgttg tatacaccac 5641 ttagggctaa caatgctggg gacgatgtct tcacagtttc ttgtcgcgtt ctcacgagac 5701 catcccccga ctttgatttc atatttctag tgccacccac agttgaatca agaactaaac 5761 cattctctat cccagtttta actattgagg agatgaccaa ttcaagattc cccattcctc 5821 tggaaaagtt gttcacgggt cccagcagcg cctttgttgt tcaaccacaa aacggcaggt 5881 gctcgactga tggcgtgctc ctaggtacta cccaactgtc tcctgtcaac atctgcacct 5941 tcagagggga tgtcacccac atcgcaggta gccacaacta cacaatgaat ttggcttctc 6001 aaaattggaa cagttatgat ccaacggaag aaatcccagc ccctttagga actccagatt 6061 tcgtgggcaa gattcaaggt gtgctcaccc aaaccacaag ggcagatggc tcgacccgcg 6121 gccacaaagc tacagtactc actgggagcg ccaactttac tccaaagctg ggtagaattc 6181 aatttgccac tgacacagac aatgattttg aaactaacca aaacacaaaa ttcaccccag 6241 tcggtgtcat ccaggatggt gatactgccc accgaaatga accccaacag tgggtgctcc 6301 caagttactc aggtagaaac actcataatg tgcatctggc ccccgctgta gcccccactt 6361 ttccgggtga acaacttctt ttcttcaggt ccaccatacc cggatgcagc gggtacccca 6421 atatggattt ggactgtctg ctcccccagg aatgggtgca gttcttctac caagaggcag 6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgaatg caagcttcat aaatcaggct acattacagt ggcccacaca ggccaacatg 6601 atttggttat cccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca 6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc attataatgg ctggagcttt 6721 ctttgctgga ttggcatctg acgtccttgg ctctggactt ggttccctga tcaatgctgg 6781 ggctggggcc atcaaccaaa aagttgaatt tgaaaataac agaaaattgc aacaagcttc 6841 ctttcaattt agcagcaatt tacaacaggc ttcctttcaa catgataagg agatgctcca 6901 agcacaaatt gaggccacca aaaagttgca acaggaaatg atgaaagtta aacaggcagt 6961 gctcctagag ggtggattct ctgagacaga cgcagcccgt ggggcaatca acgcccccat 7021 gacaaaggct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac 7081 atacaatgca ggccactttt ccacccctca accctcgggg gcaccgctag ggagggctaa 7141 tcttagggct gctgtcccca ctcggggttc ctccagcaca tcttctaact cttctattgc 7201 tacttctgtg tattcaaatc aaactgcttc aacgagactt ggttctacag ctggttctgg 7261 tgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag 7321 gaacttgtca cctttcatga ggggggccca caacatatcg tttgtcaccc caccatctag 7381 cagatcctct agccaaggca cagtctcaac cgtgcctaaa gaagttttgg actcctggac 7441 tggcgctttc aacacgcgca ggcagcctct cttcgctcac attcgtaagc gaggggagtc 7501 acgggtgtaa tgtgaaaaga caaaattgat tatctttctt tttctttact gtcttttaaa 7561 aaaaaaa //