Typing tool
|
Complete norovirus genomes
MT238666 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5092 ORF2: 5073..6695 ORF3: 6695..7501LOCUS MT238666 7501 bp RNA linear VRL 01-MAY-2020 DEFINITION Norovirus GII isolate 526-1 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MT238666 VERSION MT238666.1 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 7501) 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..7501 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="526-1" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="08-Jan-2016" /note="genotype: GII.P16-GII.4" gene <1..5092 /gene="ORF1" CDS <1..5092 /gene="ORF1" /codon_start=2 /product="nonstructural polyprotein" /protein_id="QIQ09385.1" /translation="ASNDATVAVACNNNNDKEKSSGEGLFINMSSTLKKALGARPKQP APRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDV ANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISM ARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSW LSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKI KPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGEYELQGPEDL AVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPK KEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTK SASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVA RKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCP LTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKA KRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS GLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTME ELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKH ARIRYYVKCVQEAIYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPK SEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYS IEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGS EIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLF ITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVA TVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGC PYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGG APKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGK PPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHARKNEFWNGE TFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTM IRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQ QRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQW NSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYG LKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHE DPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMF RWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide <1..988 /gene="ORF1" /product="p48" mat_peptide 989..2086 /gene="ORF1" /product="NTPase" mat_peptide 2087..2617 /gene="ORF1" /product="p22" mat_peptide 2618..3016 /gene="ORF1" /product="VPg" mat_peptide 3017..3559 /gene="ORF1" /product="Pro" mat_peptide 3560..5089 /gene="ORF1" /product="RdRp" gene 5073..6695 /gene="ORF2" CDS 5073..6695 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QIQ09386.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPIAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6695..7501 /gene="ORF3" CDS 6695..7501 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QIQ09387.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTVTSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 ggcgtctaac gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc 61 ttcaggtgaa ggcttattca taaatatgtc ttccacctta aagaaagccc tcggggctag 121 gcccaaacag cccgccccga gagacgaacc acaaaagccc ccaagaccac caactcccga 181 gttggtcaag aggatacccc ctcctccacc taatggcgaa gaagaagaag aaccagtcat 241 taggtatgag gttaagagtg ggatctctgg cctgcccgag ctcacaacag tcccccaacc 301 ggacgtggcc aacacagcat tcagtgttcc accactgagc ttgagagaaa acagggaggc 361 caaggaaccg ctaacagggg caatattaga gatgtgggat ggagagatat accactatgg 421 cctgtacgtg gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat 481 ggcaagagtg gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca ctccccaata 541 cctcatctcc cctgaaactc tcaggaggct caacggagag gcgttccctt acaccgcctt 601 cgacaacaac tgctatgcct tttgctgctg ggtgttagac ctcaatgact catggcttag 661 caggaggatg gtgcaaagaa caacgggctt cttcagacct taccaagagt ggaacagaaa 721 acccctgcct accatggatg actccaaaat taagaaggta gcaaatatat tcctatgttc 781 attgtccacg ttattcacca gacccataaa agacctcata ggaaaaatta aaccattaaa 841 catattgaac atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg aatctctgat 901 attacttgct gaactcttcg gagttttctg gacaccccca gatgtgtctg ctatgatcgc 961 tcccttactc ggggaatacg agttgcaagg gccagaagac ctcgccgttg aactcgtacc 1021 tgtggtaatg ggagggattg gtttggtgtt gggattcacc aaagagaaaa ttggcaaaat 1081 gttgtcctca gcagcatcaa cactcagggc ttgcaaagat cttggtgcct atggcttaga 1141 gatactcaaa ttggtcatga agtggttctt cccaaagaaa gaggaggcca atgagctagc 1201 catggtgagg gccatagagg atgccgtatt agatcttgag gcaatagaaa ataaccacat 1261 gacaaccctg ttgaaagaca aagacagctt agcaacatac atgaaaacac tggacatgga 1321 ggaggagaaa gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat 1381 caacgccctg ctggctcgaa tagcagcggc caggtcatta gtccacaggg ccaaggaaga 1441 gctatctagc aggataagac cagtagttgt tatgatatct ggcaaaccag gaataggcaa 1501 aactcatctg gccagggagg tggcaagaaa ggtggcatcc actctcacag gggatcaaag 1561 agtcggactc ataccaagaa acggtgtgga ccattgggat gcatacaaag gtgagagagt 1621 cgtgctgtgg gacgactatg gcatgagtaa ccccattcat gatgctcttc gcatacaaga 1681 attggctgat acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata agggaaaagt 1741 ttttgacagt gaagtcataa taattacaac aaaccttgcc aatccagccc cacttgatta 1801 tgtcaacttt gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg aggcaccaga 1861 agtagaaaag gcaaaacggg actttcctgg tcagccagat atgtggaagg acgccttcaa 1921 gccggacttt tcacacatca agctacagct tgcacctcag ggcggctttg acaagaatgg 1981 caacacccca catgggaaag gagtgatgaa gaccctcact accggttctc tgattgcccg 2041 tgcatcaggc ctactgcatg agaggatgga tgaatttgaa ctccaaggtc ccacaatcac 2101 caccttcaat ttcgaccgga acagaatcac agcattcaga caattggctg cagaaaacaa 2161 gtatggattg gtggatacca tgaaagttgg caatcaacta aaaggagtga aaaccatgga 2221 agaactcaaa caagcaatca ggaatgtgac catcaagagg tgccggatca tctacggtgg 2281 ctccacgtac gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa aggtcaagaa 2341 cacctctgta cagaccaaca acgagttggc cggggccctg caccatctca aacacgcccg 2401 aatcaggtac tatgtcaaat gtgtgcaaga agcaatctac tccatcatac aaattgccgg 2461 cgctgcgttt gtcaccacgc gcattgcacg ccgcatgaac atacaagaac tctggtcgaa 2521 gccacaatta gatcaaaatg aatcagagac taaggaagag gcccccaagt cagaagacga 2581 cgagttcatc atatcttcta aggacatcaa ggaggaagga aagaagggca aaaacaaaac 2641 tggccgtggc aagaaacaca ctgcattctc cagcaagggt ttgagcgatg aggagtatga 2701 cgagtacaag aggataagag aagagagaaa tgggaagtac tctatagagg agtatcttca 2761 agatagagac aggtactatg aggagctcgc cattgccaag gccacagaag aagacttctg 2821 tgaagaggag gagatcaaaa tccgtcagag aattttccgt cccaccagga aacaaagaaa 2881 ggaagagagg gccacattag ggctagtaac aggttcagaa atcagaaaaa gaaaccctga 2941 tgacttcaaa cccaaaggga agctgtgggc cgatgacaac agaagtgttg actacaatga 3001 gaaactggac tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg 3061 ctggggcttc tgggtatcac caagcctgtt cataacatca actcatgtaa tccccgcagg 3121 cataacagaa gcgtttggag tccccatcaa acaaattcag atccacaaat caggtgaatt 3181 ttgccgattc agattcccaa aaccaattag accagatgtg acaggaatga tcttggaaga 3241 aggtgcgcct gaaggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat 3301 gcctcttgca gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg 3361 cggacagatg ggtatgttgc tcactggatc aaatgccaaa ggaatggatt tgggaacaac 3421 tcctggtgac tgtggctgtc cttacatcta taagaggggc aatgactaca tagtcattgg 3481 ggtgcacact gcagcagccc gaggtggaaa caccgtcatc tgtgctacac agggaagtga 3541 gggtgaggca actcttgagg gtggagatga caaaggaaca tactgtgggg cacccatttt 3601 aggccctggg ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt catcgaacac 3661 gccccttcca ccagggacat atgagcctgc ctacctcggt ggccgtgatc cgcgtgttaa 3721 gggtgggccc tccttgcagc aggtaatgag agaccagttg aagccattca ctgaacccag 3781 gggcaaacct ccaagaccaa gtgtattgga agcagccaaa caaaccatta tcaatgtcct 3841 cgaacaaacc ctggaccctc cacaaaaatg gacatacgca caggcgtgtg cctcacttga 3901 caaaaccacc tccagcgggc atccccatca cgcccgaaag aatgaattct ggaatggtga 3961 gaccttcact ggtaaattgg cagaccaagc atcaaaagca aacctaatgt ttgaggaagg 4021 gaaacacatg acaccagtgt atacagcagc actcaaggat gagctagtca agactgagaa 4081 aatctatgga aagatcaaga agagactact ctggggctct gacttgtcca ccatgatccg 4141 gtgcgctagg tcatttggtg ggctcatgga cgagatgaag gcacactgca tatcactccc 4201 agtacgagtt ggcatgaata tgaatgaaga tggcccaata atatttgaga aacattccag 4261 atataaatac cactatgatg cagactactc tcgttgggat tcaacacaac agagggcagt 4321 actagcagca gctttggaaa tcatggtcag attctctgca gaaccacaat tggcacaaat 4381 agtcgctgag gatctgctgg cccctagtgt agtagatgta ggagacttta aaatcacaat 4441 aaatgaaggg ctcccatctg gtgtgccatg cacttctcaa tggaactcca tcgcacactg 4501 gctgctaact ctctgtgcct tgtctgaagt caccaaactg tcccctgaca ttatacaagc 4561 aaattccatg ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga 4621 ccctgaacag ttaaccgcca agttgaagga gtacggcctg aaaccaaccc gcccagacaa 4681 gaccgaggga cccctgatca tcagtgaaga tttgaacgga ctcactttcc tccgaaggac 4741 ggtgactcgt gacccagctg gctggtttgg aaaactggac caaagctcaa ttttgagaca 4801 gatgtactgg actagaggac caaatcatga agaccccaat gagacaatga taccccattc 4861 tcaaagaccc atacagctca tggcactgct tggtgaagcc tctcttcacg gaccctcttt 4921 ctacagtaaa atcagtaaat tggtcataac tgaactcaaa gaaggtggga tggactttta 4981 cgtgccaagg caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga 5041 gggcgatcgc aatctggctc ccaattttgt gaatgaagat ggcgtcgagt gacgccaacc 5101 catctgatgg gtccgcagcc aacctcgtac cagaggtcaa caatgaggtt atggctttgg 5161 agcccgttgt tggtgccgct attgcggcac ctatagcggg ccaacaaaat gtaattgacc 5221 cctggattag aaataatttt gtgcaagccc ctggtgggga gtttacagta tcccctagaa 5281 acgctccagg tgaaatacta tggagcgcgc ccctaggccc tgacctaaat ccctacctat 5341 cccatttggc cagaatgtac aatggttatg caggtggttt tgaagtgcag gtaattctcg 5401 cggggaacgc gttcaccgcc gggaagatca tatttgcagc agtcccacca aattttccaa 5461 ctgaaggctt aagtcctagc caagtcacta tgttccccca tataatagta gatgttagac 5521 aattagaacc tgtgctgatt cccttacccg atgttaggaa taatttctat cattataatc 5581 agtcaaatga ctccactatt aagttgatag caatgttgta tacaccactt agggctaata 5641 atgctgggga tgatgttttc acagtttcgt gccgagttct cacgagacca tcccccgatt 5701 ttgatttcat atttttagtg ccacccacag ttgagtcaag aactaaacca ttctctgtcc 5761 cagttttaac tgttgaggag atgaccaatt caagattccc cattcctttg gaaaagttgt 5821 tcacgggccc cagcagtgcc tttgttgttc aaccacaaaa cggcaggtgc acaactgatg 5881 gcgtgctcct aggcaccacc caactgtctc ctgtcaacat ctgcaccttc agaggggatg 5941 tcacccacat cacaggtagt cgcaactaca caatgaattt ggcttctcaa aattggaaca 6001 attatgaccc aacagaagaa atcccagccc ctctaggaac tccagatttt gtggggaaga 6061 ttcaaggcat gctcacccaa accacaagga cagatggttc aacacgcggc cacaaagcta 6121 cagtgtacac tgggagcgcc gactttgctc caaaactggg tagagttcaa tttgaaactg 6181 acacagacca tgattttgaa gctaatcaaa acacaaagtt caccccagtc ggtgtcatcc 6241 aagatggtag caccacccac cgaaacgaac cccaacagtg ggtgctccca agttactcag 6301 gcagaaatac tcacaatgta catctggccc ccgctgtagc ccccaccttt ccgggtgagc 6361 aacttctctt cttcagatcc accatgcccg gatgcagcgg gtaccccaac atggatttgg 6421 actgtctgct cccccaggaa tgggtgcagt acttctacca agaggcagcc ccagcacaat 6481 ctgatgtggc tctgctaaga tttgtgaatc cagacacagg tagggttttg tttgagtgca 6541 agcttcacaa atcaggctat gttacagtgg ctcacactgg ccaacatgat ttggttatcc 6601 ctcccaatgg ttactttagg tttgattcct gggtcaacca gttctacacg cttgccccca 6661 tgggaaatgg aacggggcgt agacgtgtag tataatggct ggagctttct ttgctggatt 6721 ggcatctgat gtccttggct ctggacttgg ttccctcatc aatgctgggg ctggggccat 6781 caaccaaaaa gttgagtttg aaaataacag aaaattacaa caagcatcct tccaatttag 6841 cagcaatctg caacaggctt cctttcaaca tgataaagag atgctccaag cacaaattga 6901 ggccaccaaa aagctacaac aggaaatgat gaaagttaag caggcagtgc tcctagaggg 6961 tgggttctct gagacagatg cagcccgcgg ggcaattaac gcccccatga caaaagcttt 7021 ggattggagc gggacaaggt actgggctcc cgatgctagg actacaacat acaatgcagg 7081 ccgcttttcc acccctcaac catcgggggc actgccagga agagctaatc ttagggatgc 7141 tgtccctgct cggggaccct ccaacaaatc ttctaactct tctactgtca cctctgtgta 7201 ctcaaatcaa actatttcaa cgagacttgg ttctacagct ggttctggaa ccagtgtctc 7261 gagcctcccg tcaactgcaa ggactaggag ctgggttgag gatcaaagta ggaatttgtc 7321 acctttcatg aggggggccc acaacatatc atttgtcacc ccaccatcta gcagatcctc 7381 tagccaaggc acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt 7441 caacacgcgc aggcagcctc tcttcgctca cattcgtaag cgaggggagt cacgggtgta 7501 a //