Typing tool
|
Complete norovirus genomes
MT238671 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS MT238671 7579 bp RNA linear VRL 01-MAY-2020 DEFINITION Norovirus GII isolate 259-2, complete genome. ACCESSION MT238671 VERSION MT238671.1 DBLINK BioProject: PRJNA604000 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7579) AUTHORS Yang,Z., Williams-Hill,D., Wolfe,J., Silva,A.J., Hirneisen,K., Ruelle,S., Kulka,M. and Hellberg,R. TITLE Direct Submission JOURNAL Submitted (24-MAR-2020) Molecular Virology Team/Devision of Molecular Biology, OARSA/CFSAN/FDA, 8301 Muirkirk Rd., Laurel, MD 20708, USA COMMENT ##Assembly-Data-START## Assembly Method :: CLC Genomics Workbench v. 11 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7579 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="259-2" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="17-Dec-2018" /note="genotype: GII.P16-GII.4" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QIQ09400.1" /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSFTLKKALGARP KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQ PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPRPIRPDVTGMILEEGAPEG TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGYDKGTYCGAPILG PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPSVLEAAKQTVINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDL STMIRCARSFGGLMDEMKAHCISLPVRVGMNVNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK 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="QIQ09401.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6707..7513 /gene="ORF3" CDS 6707..7513 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QIQ09402.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga 61 caaggaaaaa tcttcaggtg aaggcttatt cacaaatatg tctttcacct taaagaaagc 121 cctcggggct aggcccaaac agcctgcccc gagagacgaa ccacaaaagc ccccaagacc 181 accaaccccc gagttggtca agaggatacc ccctcctcca cctaatggcg aaggagaaga 241 agaaccagtc attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac 301 agtcccccaa ccggacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga 361 aaacagggag gccaaggaac cgctaacagg ggcaatatta gagatgtggg atggagagat 421 ataccactat ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc 481 agccataagc atggcaagag tggagctgac gccgctgtca ttgtactggc gtgtggtgta 541 cactccccaa tacctcatct cccctgaaac tctcaggagg ctcaacggag aggcgttccc 601 ttacaccgcc ttcgacaaca actgctacgc cttttgctgc tgggtgttag acctcaatga 661 ctcatggctt agcaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga 721 gtggaacaga aagcccctgc ctaccatgga tgactccaaa attaagaagg tagcaaatat 781 attcctatgt tcattgtcca cattattcac cagacccata aaagacctca tagggaaaat 841 taaaccatta aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt 901 ggagtctctg atattacttg ctgaactctt cggagttttc tggacgcccc cagatgtgtc 961 tgctatgatc gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt 1021 tgaactcgta cctgtggtaa tgggagggat tggtttggtg ttgggattca ccaaagagaa 1081 aattggcaaa atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc 1141 ctatggctta gagatactca agttggtcat gaagtggttc ttcccaaaga aagaggaggc 1201 caatgagcta gccatggtga gggccataga ggatgccgtg ctagatcttg aggcaataga 1261 aaataaccac atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac 1321 actggacatg gaggaggaga aagccagaag gttgtccaca aaatctgcat cccctgacat 1381 agttgggaca atcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag 1441 ggccaaggaa gagctatcta gcaggataag gccagtagtt gttatgatat ctggcaaacc 1501 aggaataggc aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac 1561 aggggaccaa agagtcggac tcataccaag aaacggtgtg gaccattggg atgcatacaa 1621 aggtgagaga gtcgtgctgt gggacgacta tggcatgagt aaccccatcc atgatgctct 1681 tcgcatacaa gaattggctg atacgtgtcc ccttacctta aattgtgaca gaattgaaaa 1741 taagggaaaa gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaatccagc 1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc 1861 tgaggcacca gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa 1921 ggacgccttc aagccggact tttcacacat caagctacag cttgcacctc agggcggctt 1981 tgacaagaat ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc 2041 tctgattgcc cgtgcatcag gcctactaca tgagaggatg gatgaatttg aactccaagg 2101 tcccacaatc accaccttca atttcgaccg aaacagaatc acagcattca gacaattggc 2161 tgcagaaaac aagtatggat tggtggatac catgaaagtt ggcaatcaat taaaaggagt 2221 gaaaaccatg gaagaactca aacaagcaat cagaaatgtg accatcaaga ggtgccggat 2281 catctacggt ggctccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga 2341 aaaggtcaag aacacctctg tacagaccaa caacgagttg gccggggccc tgcaccatct 2401 caaacacgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat 2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga 2521 actctggtcg aagccacaat tagatcaaaa tgaatcagag actaaggaag aggcccccaa 2581 atcagaagat gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg 2641 caaaaacaaa actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga 2701 tgaggagtat gacgagtaca agaggataag agaagagaga aatgggaagt actctataga 2761 ggagtatctt caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga 2821 agaagacttc tgtgaagagg aggagataaa aatccgtcag agaattttcc gtcccaccag 2881 gaaacaaaga aaggaagaga gggccacatt aggactggta acaggttcag aaatcagaaa 2941 aagaaaccct gatgacttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt 3001 tgactataat gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag 3061 ctttggttct ggctggggct tctgggtatc accaagcctg ttcataacat caactcatgt 3121 aatccccgca ggcataacag aagcatttgg agtccccatc aaacaaattc agatccacaa 3181 atcaggtgaa ttttgccgat tcagattccc aagaccaatt agaccagacg tgacaggaat 3241 gatcttggaa gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac 3301 cggagagctc atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg 3361 ccgcatggtt ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga 3421 tttgggaaca actcctggtg actgtggctg tccttacatc tacaaaaggg gcaatgacta 3481 tatagtcatt ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac 3541 acagggaagt gagggtgagg caactcttga gggtggatat gacaaaggaa catactgtgg 3601 ggcacccatt ctaggccctg ggggtgcacc aaagttgagc accaaaacca aattttggag 3661 gtcatcgaac acgcccctcc caccagggac atatgagcct gcctacctcg gtggccgtga 3721 tccgcgtgtt aagggtgggc cctccttgca gcaggtaatg agagaccagt tgaagccatt 3781 cactgaaccc aggggcaaac ctccaagacc aagtgtattg gaagcagcca aacaaaccgt 3841 tatcaatgtc ctcgaacaaa ccctggatcc tccacaaaaa tggacatacg cacaggcgtg 3901 tgcctcactt gacaaaacca cttccagcgg gcatcctcat cacgtccgaa agaatgaatt 3961 ctggaatggt gagaccttca ccggcaaatt ggcagaccaa gcatcaaaag caaacctaat 4021 gtttgaggaa gggaaacaca tgacaccagt gtatacagca gcactcaagg acgagctagt 4081 caagactgag aaaatctata gaaagatcaa gaagagactg ctctggggct ctgacttgtc 4141 caccatgatc cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg 4201 catatcactc ccagtacgag ttggcatgaa tgtgaatgaa gatggcccaa taatatttga 4261 gaaacattcc agatacaaat accactatga cgcagactac tctcgttggg attcaacaca 4321 acagagggca gtactagcag cagccttgga aatcatggtc agattctctg cagaaccaca 4381 attggcacaa atagtcgctg aggatcttct ggcccctagc gtagtagatg taggagactt 4441 taaaatcact ataaatgaag ggctcccatc tggtgtgcca tgcacctccc aatggaactc 4501 catcgcacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga 4561 cattatacaa gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga 4621 cataaaattg gaccctgaac agttaaccgc caagttgaag gagtatggcc tgaaaccaac 4681 ccgcccagac aagaccgagg gacccctgat catcagtgaa gatttgaacg gactcacttt 4741 cctccgaagg acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc 4801 aattttgagg cagatgtact ggactagagg accaaatcac gaagatccca atgagacaat 4861 gataccccat tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca 4921 cggaccctct ttctacagta gaatcagtaa attggtcata actgaactca 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 gtcggtgccg ctattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtggg gagtttacag 5281 tatcccccag aaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa 5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtaattct cgcggggaac gcgttcaccg ccgggaagat catatttgca gcagtcccac 5461 caaattttcc aactgaaggc ttaagtccta gccaggtcac tatgttcccc catataatag 5521 tagatgttag acagttagaa cctgtgctga ttcctttacc cgatgttagg aataatttct 5581 atcattacaa tcagtcaaat gactccacta ttaagttgat agcaatgttg tacacaccac 5641 ttagggctaa taatgctggg gatgatgttt tcacagtttc gtgccgagtt ctcacgagac 5701 catcccccga ttttgatttc atatttttag tgccacccac agttgagtca agaactaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccatccctt 5821 tggaaaagct gttcacaggc cccagcagtg cctttgttgt tcaaccacaa aacggcaggt 5881 gcacaactga tggcgtgctc ctaggcacca cccaactttc tcctgtcaac atctgcacct 5941 tcagagggga tgtcacccac atcacaggta gtcgcaacta cacaatgaat ttggcttctc 6001 aaaattggaa caactatgac ccaacagaag aaatcccagc ccctctagga actccagatt 6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag gacagatggt tcaacacgcg 6121 gccacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc 6181 aatttgaaac tgacacagac catgattttg aagctaatca aaacacaaag ttcaccccag 6241 tcggtgtcat ccaagatggt agcaccaccc atcgaaacga accccaacag tgggtgctcc 6301 caagttactc aggcagaaat actcacaatg tacatctggc ccccgctgta gcccccacct 6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctat caagaggcag 6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt 6541 tgtttgagtg caagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg 6601 atttggttat cccccccaat ggctacttta gatttgattc ctgggtcaac cagttctata 6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt 6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctca tcaatgctgg 6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc 6841 cttccaattt agcagcaatc tgcaacaggc ttcctttcaa catgataaag agatgctcca 6901 agcacaaatt gaggccacta aaaagctaca acaggaaatg atgaaagtta agcaggcaat 6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat 7021 gacaaaagct ttggactgga gtgggacaag gtactgggct cccgatgcta ggactacaac 7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa 7141 tcttagggat gctgtccctg ctcggggacc ctccaacaaa tcttctaact cttctactgc 7201 cacctctgtg tattcaaatc aaactatttc aacgagactt ggttctacag ctggttctgg 7261 aaccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa 7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcatttgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga 7501 gtcacgggtg taatgtgaaa agacaaaatt gattattttt ctttttcttt agtgtctttt 7561 aaaaaaaaaa aaaaaaaaa //