Typing tool
|
Complete norovirus genomes
OQ940069 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS OQ940069 7560 bp RNA linear VRL 31-JUL-2023 DEFINITION Norovirus GII isolate SH20-212, complete genome. ACCESSION OQ940069 VERSION OQ940069.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7560) AUTHORS Ao,Y. TITLE Emergence of recombinant GII.4 Sydney[P16] norovirus in Shanghai, China JOURNAL Unpublished REFERENCE 2 (bases 1 to 7560) AUTHORS Ao,Y. TITLE Direct Submission JOURNAL Submitted (08-MAY-2023) Department of Clinical Laboratory, Children's hospital of Fudan University, 399 wanyuan road, Minhang district, Shanghai, Shanghai 201102, China COMMENT ##Assembly-Data-START## Assembly Method :: DNAStar v. v. 11.1 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7560 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="SH20-212" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="China" /collection_date="10-Nov-2020" /note="genotype: GII.4 Sydney[P16]" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="WGV43876.1" /translation="MKMASNDATVAVACNNNNDKERSSGEGLFTNMSSTLKKALGARP KQPAPRDESQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA ISMARVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP EDLAIELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSIQTNNELAGALHH LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSRPQLDQNESETREE APKSEDDEFVISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV TGSEIRRRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP SLFITSTHVIPAGITEAFGVPTKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVRGGPSLQQVMRDQLKPFTEP RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHARKNEFW NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT SQWNSITHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide 5..1000 /gene="ORF1" /product="p48" mat_peptide 1001..2098 /gene="ORF1" /product="NTPase" mat_peptide 2099..2629 /gene="ORF1" /product="p22" mat_peptide 2630..3028 /gene="ORF1" /product="VPg" mat_peptide 3029..3571 /gene="ORF1" /product="Pro" mat_peptide 3572..5101 /gene="ORF1" /product="RdRp" gene 5085..6707 /gene="ORF2" CDS 5085..6707 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="WGV43877.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV" gene 6707..7513 /gene="ORF3" CDS 6707..7513 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="WGV43878.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARITTYNSGHFSTPQPSGALPGRANLRDAVPARGPSTKSS NSSAATSVYSNQTTSTRLGSAAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga 61 caaggaaaga tcttcaggtg aaggcttatt cacaaatatg tcttccactt taaagaaagc 121 cctcggggct aggcccaaac agcctgcccc gagagatgaa tcacaaaagc ccccaagacc 181 accaactccc gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga 241 agaaccagtc attaggtatg aagttaagag tgggatctct ggcctgcccg agctcacaac 301 agttccccaa ccggacgtgg ccaacacagc atttagtgtt ccaccactga gcttgagaga 361 aaacagggag gccaaggaac cgctaacagg ggcaatacta gagatgtggg atggagagat 421 ataccactat ggcctgtacg tggagaaggg cttagtgttg ggtgtgcaca aaccacctgc 481 agctataagc atggcaagag tggagttggc gccgctgtca ttgtactggc gtgtggtgta 541 cactccccaa tacctcatct cccctgaaac tctcaggagg ctcaacggag aggcgtttcc 601 ttacaccgct ttcgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga 661 ctcatggctt agcaggagga tggtgcaaag aacaacgggc ttcttcaggc cttaccaaga 721 gtggaataga aaacccttgc ctactatgga tgactccaaa ataaagaagg tagcaaatat 781 attcctatgt tcactgtcca cattattcac cagacccata aaagacctca taggaaaaat 841 caaaccacta aacatattga acatcttggc aacgtgtgac tggacgtttg ccggaatagt 901 ggagtctctg atattgcttg ccgagctctt cggagttttc tggacacccc cagatgtgtc 961 tgctatgatc gctcccttac tcggtgacta cgagttacaa gggccagaag acctcgccat 1021 tgaactcgta cctgtggtaa tgggagggat tggtttggtg ttgggattca ccaaagagaa 1081 aatcggcaaa atgttgtcct cagcagcatc aacactcagg gcttgtaaag atcttggtgc 1141 ctatggctta gagatactca aactggtcat gaagtggttc ttcccaaaga aagaggaggc 1201 caatgagcta gccatggtga gggccataga ggatgccgtg ctagatcttg aggcaataga 1261 gaataaccac atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac 1321 actggacatg gaggaggaga aagccagaag gttatccaca aaatctgcat cccccgacat 1381 agttgggaca atcaacgccc tgctggctcg aatagcagcc gccaggtcat tagtccacag 1441 ggccaaggaa gagctgtcta gcaggataag accagtggtt gtaatgatat ctggcaaacc 1501 aggaataggc aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac 1561 aggggaccaa agagtcggac tcataccaag aaacggtgtg gaccactggg atgcatacaa 1621 aggtgagaga gtcgtgctgt gggacgacta cggcatgagt aaccccattc atgatgctct 1681 ccgcatacaa gaattggctg atacgtgtcc ccttacctta aattgtgaca gaattgaaaa 1741 taagggaaaa gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaacccagc 1801 cccacttgat tatgtcaact tcgaggcctg ttctaggaga attgatttcc tggtgtacgc 1861 tgaggcacca gaagtagaaa aggcaaaacg ggattttcct ggtcagccag atatgtggaa 1921 ggacgccttc aagccggact tttcacacat caagctacag cttgcacccc agggcggctt 1981 tgacaagaat ggcaataccc cacatgggaa aggagtgatg aagaccctca ctaccggttc 2041 tctgattgcc cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg 2101 tcccacaatc accactttca atttcgaccg gaatagaatc acagcattca gacaattggc 2161 tgcagaaaac aagtatggac tggtggacac catgaaagtt ggcaatcaac taaaaggagt 2221 gaaaaccatg gaagaactca aacaggcaat cagaaatgtg accatcaaga ggtgccggat 2281 catctacggt ggttccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga 2341 aaaggtcaag aacacctcta tacaaaccaa caacgagttg gccggggccc tgcaccatct 2401 taaacatgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat 2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga 2521 actctggtcg aggccacaat tagatcaaaa tgaatcagag actagggaag aggcccccaa 2581 gtcagaagat gacgagttcg tcatatcttc taaggatatc aaggaggaag ggaagaaggg 2641 caaaaacaaa actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga 2701 tgaggagtat gacgagtaca agaggataag agaagagaga aacgggaagt actctataga 2761 ggaatatctt caagacagag acaggtatta tgaggagctc gccattgcca aggccacgga 2821 agaagacttc tgtgaagagg aggaaatcaa aatccgtcag agaattttcc gtcccaccag 2881 gaaacaaaga aaagaagaga gggccacatt agggctggta acaggttcag aaatcagaag 2941 aagaaaccct gatgatttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt 3001 tgactacaat gagaaactgg actttgaggc ccccccaagt atatggtcta gaattgtgag 3061 ctttggttct ggctggggct tctgggtatc accaagcctg ttcataacat caacccatgt 3121 tatccctgca ggcataacag aagcatttgg agtccccacc aaacaaattc agattcacaa 3181 atcaggtgaa ttttgtcgat tcagattccc aaaaccaatt agaccagatg tgacaggaat 3241 gatcttggaa gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac 3301 cggagagctc atgcctcttg cagccagaat gggaacacac gcaaccatga agattcaagg 3361 ccgcatggtt ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga 3421 tttgggaaca actcctggtg actgtggctg cccttacatc tataaaaggg gcaatgacta 3481 tatagtcatt ggggtacaca ctgcagcagc ccgtggtgga aacaccgtta tctgtgccac 3541 acagggaagt gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg 3601 ggcacccatt ctaggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag 3661 gtcatcgaac acgccccttc caccagggac atatgagcct gcctacctcg gtggccgtga 3721 cccgcgtgtt aggggtgggc cctccttaca gcaggtaatg agagaccagt tgaagccatt 3781 cactgaaccc aggggcaaac ctccaagacc aagtgttttg gaggcagcca aacagaccat 3841 tatcaatgtc ctcgaacaaa ccctggatcc tccacaaaaa tggacatacg cacaggcgtg 3901 tgcctcactt gacaaaacca cctccagcgg gcatccacac cacgcccgaa agaatgaatt 3961 ctggaatggt gagaccttca ctggtaaatt ggcagaccaa gcatcaaaag caaacctaat 4021 gtttgaggaa gggaaacaca tgacaccagt gtatacagca gcactcaagg acgagctagt 4081 caagactgag aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc 4141 caccatgatc cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg 4201 catatcactc ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga 4261 gaaacattcc agatacaaat atcactatga tgcagactac tctcgctggg attcaacaca 4321 acagagggca gtattagcag cagccttgga aatcatggtc agattttctg cagaaccaca 4381 attggcacaa atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt 4441 taaaatcaca ataaatgaag ggctcccatc tggtgtgcca tgcacttctc aatggaactc 4501 cataacacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga 4561 cattatacaa gcaaattcta tgttctcatt ttacggtgat gacgagattg tcagcaccga 4621 cataaaattg gaccctgaac agttgaccgc caagttgaag gagtacggcc tgaaaccaac 4681 tcgcccagac aagaccgagg gacccctgat catcagtgaa gatttgaacg gactcacttt 4741 cctccgaagg acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc 4801 aattttgagg cagatgtact ggactagagg gccaaatcat gaagacccca atgagacaat 4861 gataccccat tctcagagac ccatacagct catggcactg cttggtgaag cctctcttca 4921 cggaccctct ttctacagta gaatcagtaa attggtcata actgaactta aagaaggtgg 4981 gatggacttt tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt 5041 gagcacgtgg gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg 5161 ttatggcttt ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtggg gagttcacag 5281 tatcccctag aaatgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa 5341 atccctacct atcccattta gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtaattct cgcggggaac gcgttcaccg ccgggaagat tatatttgca gcagtcccac 5461 caaattttcc aactgaaggt ttaagcccta gccaggtcac tatgttcccc cacataatag 5521 tagatgttag acaattggaa cctgtgctga tccccttacc cgatgtcagg aataatttct 5581 atcattacaa tcagtcaaat gattccacta ttaagttgat agcaatgttg tacacaccac 5641 ttagggctaa taatgctggg gatgatgttt tcacagtttc gtgccgagtt ctcacgagac 5701 catcccccga ttttgatttc atatttttag taccacccac agttgaatca agaactaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccatccctt 5821 tggaaaagtt gtttacaggc cccagcagtg catttgtcgt tcaaccacaa aacggcagat 5881 gcacaactga tggcgtgctt ctaggcacca cccaactttc tcctgtcaac atctgtacct 5941 tcagggggga tgtcactcac atcacaggta gtcacaacta cactatgaat ttggcttctc 6001 aaaattggaa caactatgac ccaacagaag aaatcccagc ccctctagga actccagatt 6061 ttgtggggaa gattcaaggt atgctcaccc agaccacaag gacagatggt tcaacacgcg 6121 gtcacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc 6181 aatttgaaac tgacacaaac catgattttg aagccaatca aaacacaaag ttcaccccag 6241 tcggtgtcat tcaagatggt agcaccaccc atcgaaacga accccagcag tgggtgctcc 6301 caagttactc aggcagaaat actcacaatg tacatttggc ccccgctgta gcccccacct 6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag 6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgagtg caagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg 6601 atttggttat cccccccaat ggttacttta ggtttgattc ctgggtcaac cagttctaca 6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt 6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg 6781 ggctggggcc atcaaccaaa agattgagtt tgaaaataac agaaaattgc aacaagcatc 6841 ctttcaattt agcagcaatt tgcaacaggc ttcctttcaa catgataaag agatgctcca 6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgagagtta agcaggcaat 6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat 7021 gacaaaggct ttggactgga gcgggacaag gtactgggct ccagatgcta gaattacaac 7081 atacaattca ggccactttt ccacccctca accatcgggg gcgctgccag gaagagctaa 7141 tcttagggat gctgtccctg ctcggggacc ctccaccaaa tcttctaact cttctgctgc 7201 cacttctgtg tactcaaatc aaactacttc aacgagactt ggttctgcag ctggttctgg 7261 aaccagtgtc tcgagcctcc cgtcgactgc aaggactagg agctgggttg aggatcaaaa 7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcatttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaaattt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga 7501 gtcacgggtg taaagtgaaa agacaaaaca gattatcttt ctttttcttt agtgtctttt //