Typing tool
|
Complete norovirus genomes
KC962462 | GII.4 Sydney | ||
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GII.P4 Yerseke |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS KC962462 7570 bp RNA linear VRL 21-APR-2015 DEFINITION Norovirus GII strain GII/Hu/ZAF/2011/GII.P4_GII.4/Empangeni/8491, partial genome. ACCESSION KC962462 VERSION KC962462.3 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7570) AUTHORS Mans,J., Murray,T.Y. and Taylor,M.B. TITLE Novel norovirus recombinants detected in South Africa JOURNAL Virol. J. 11, 168 (2014) PUBMED 25228444 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 7570) 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 7570) AUTHORS Mans,J. TITLE Direct Submission JOURNAL Submitted (25-JUL-2014) Department of Medical Virology, University of Pretoria, Bophelo Road, Pretoria, Gauteng 0001, South Africa REMARK Sequence update by submitter REFERENCE 4 (bases 1 to 7570) 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 KC962462.2. FEATURES Location/Qualifiers source 1..7570 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="GII/Hu/ZAF/2011/GII.P4_GII.4/Empangeni/8491" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="South Africa" /collection_date="Nov-2011" /collected_by="T.Y. Murray" /identified_by="T.Y. Murray" /note="genotype: GII.P4_New_Orleans_2009/GII.4_Sydney_2012" 5'UTR <1..4 gene 5..5104 /gene="POL" CDS 5..5104 /gene="POL" /codon_start=1 /product="polyprotein" /protein_id="AKE07102.1" /translation="MKMASNDASAAAVANSNNNTAKSSSDGVLSSMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKSIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LARVELAPLSLYWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIMGK LKPLNILNILASCDWTFAGIVESLILLAELFGIFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELALVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVMMISGKPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDVEK AKRDFPGQPDMWKNAFSSDFSHMKLALAPQGGFDKNGNTPHGKGVMKALTTGSLIARA SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLVDTMKVGRQLKDVKTM PELKQALKSVSIKKCQIVYSGSTYTLESDGKGSVKVDRIQSASVQTNNELTGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVENTEETTNKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVSLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHIRKNDGW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL GTMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYAYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQTNSLFSFYGDDEIVSTDIKLDPEKLTAKLR 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="AKE07103.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTESLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTIDGVLLGTT QLSPVNICTFRGDVTHIAGTHNYTMNLATQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTKTDGSTRGHKATVCIGSADFAPKLGRVQFETDTNNDLETNQNTKFTPVGVIQNG ETAHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGSHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAT" gene 6707..7513 /gene="VP2" CDS 6707..7513 /gene="VP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AKE07104.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGILPGRANLRDTVPARGSSSTSS KSSIATSLYSNQTATTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" 3'UTR 7514..7570 ORIGIN 1 gtgaatgaag atggcctcta acgacgcttc cgctgccgct gttgctaaca gcaacaacaa 61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agcctccccc gagggaaata ccacaaagac ccccacgacc 181 acccactcca gaactggtta aaagtattcc cccccctccg cccaacggag aggatgaaat 241 agtggtttct tatagtgtca aagatggtgt ttccggtttg cctgaccttt ccaccgtcag 301 gcaaccagaa gaatctaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag 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 ataatgggga 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 tctaaactgt gacaggattg agaacaaagg 1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact 1801 tgactatgtc aactttgaag catgctcgag gcgcatcgac ttcctcgtgt atgcagatgc 1861 ccctgacgtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc 1921 cttcagttct gacttctcac acatgaagct ggcattggcc ccacaaggtg gcttcgacaa 1981 gaacgggaac accccacacg gaaagggcgt catgaaggct ctcaccacag gctcccttat 2041 tgcccgggca tctgggttgc tccatgagag attagatgaa tttgaactac aaggcccaac 2101 tctcaccacc ttcaattttg atcgcaacaa agtacttgcc tttagacaac ttgctgctga 2161 gaacaaatat ggactagtgg acacaatgaa agttgggaga cagctcaagg atgtcaaaac 2221 catgccagaa ctcaaacaag cactcaagag tgtctcaatc aagaagtgcc agatagtgta 2281 tagtggttcc acctacacac ttgagtctga tggcaagggc agtgtgaaag ttgacagaat 2341 ccagagcgcg 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 tgaggaggtg 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 aaaggcccac 3301 tggggagctc atgcccctag cagctagaat ggggacccat gcaactatga agatccaagg 3361 gcgtactgtt ggaggccaga tgggcatgct tctgacagga tccaacgcca aaagcatgga 3421 tctgggtact acaccaggtg attgtggctg tccctacatc tataagagag gtaatgacta 3481 tgtagtcatt ggagtccaca cagctgccgc tcgtggggga 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 cacatacgga aaaatgatgg 3961 ttggaacggg gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacctgat 4021 gtttgaggaa gggaagaaca tgaccccagt ctacacagct gcgcttaaag atgaattggt 4081 caaaactgac aaaatttatg 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 ttcccctagc gtggtggacg tgggcgactt 4441 cacaatatcg atcaacgagg gtcttccctc tggggtgcct tgcacctccc aatggaattc 4501 catcgcccac tggctactca ctctctgtgc gctctctgaa gtcacaaatt tgtcccctga 4561 caccatacag acaaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga 4621 tataaaattg gacccagaga aattgacagc aaagctcagg gaatatgggt taaaaccaac 4681 ccgccctgat aaaactgaag gaccccttgt catctccgaa gacttgaatg gcctaacttt 4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc 4801 aatactcagg caaatgtact 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 agaaacaatt ttgtacaagc ccctggtgga gagtttacag 5281 tgtcccctag gaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa 5341 acccctacct atcccacttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtgatcct tgcggggaac gcgttcaccg ccgggaagat catatttgca gcagtcccac 5461 caaatttccc aactgaaagc ttgagcccca gtcaggtcac tatgttcccc catataatag 5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aacaatttct 5581 accattataa tcaatcaaat gaccccacta tcaagttgat agcaatgttg tacacaccac 5641 ttagggctaa taatgctggg gacgatgtct tcacagtttc ttgccgagtt ctcacgaggc 5701 catcccccga ttttgacttc atatttttag tgccacccac agttgagtca agaactaaac 5761 cattctctgt cccaatttta actgttgagg agatgaccaa ttcaagattc cccattcctt 5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt 5881 gcacgattga cggcgtgctc ctaggtacta cccaactgtc tcctgtcaac atctgcacct 5941 tcagagggga tgtcactcat attgcaggta ctcacaacta cacaatgaat ttggccactc 6001 aaaattggaa cagttatgac ccaacagaag aaatcccagc ccctctagga actccagatt 6061 tcgtggggaa gattcaaggt gtactcaccc aaaccacaaa gacagatggc tcgacacgcg 6121 gccacaaagc tacagtgtgc attgggagcg ccgactttgc tccaaaattg ggtagagttc 6181 aatttgaaac tgacacaaac aatgatcttg aaactaacca aaacacaaag ttcaccccag 6241 tcggtgtcat ccagaatggt gaaactgccc acaggaatga accccaacag tgggtgctcc 6301 cgagttactc aggcagaaat actcccaatg tgcatttggc ccccgctgta gcccccactt 6361 ttccgggtga acaacttctc ttcttcagat ccactatgcc cggatgcagc gggtatccca 6421 acatggattt ggactgcctg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ccccagcaca 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 ctggagcctt 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 ctgagacaga tgcagcccgt ggggcgatca acgcccccat 7021 gacaaaggct ttggactgga gcgggacaag gtactgggct cctgatgcta ggactacaac 7081 atacaatgca ggccgctttt ccacccctca accatcgggg atactgccgg gaagagctaa 7141 tcttagggat actgtccccg ctcggggttc ctccagcaca tcttctaaat cttctattgc 7201 tacttctttg tattcaaatc aaactgctac aacgagactt ggttctacag ctggttctgg 7261 taccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa 7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaagttt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga 7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt cttttcttta gagtctttga 7561 aaaaaaaaaa //