Typing tool
|
Complete norovirus genomes
MT238667 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5090 ORF2: 5071..6693 ORF3: 6693..7499LOCUS MT238667 7540 bp RNA linear VRL 01-MAY-2020 DEFINITION Norovirus GII isolate 782-1 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MT238667 VERSION MT238667.1 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 7540) 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..7540 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="782-1" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="17-Dec-2018" /note="genotype: GII.P16-GII.4" gene <1..5090 /gene="ORF1" CDS <1..5090 /gene="ORF1" /codon_start=3 /product="nonstructural polyprotein" /protein_id="QIQ09388.1" /translation="SNDATVAVACNNNNDKEKSSGEGLFTNMSFTLKKALGARPKQPA PRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPDVA NTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMA RVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWL SRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIK PLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLA VELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKK EEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKS ASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVAR KVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPL TLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAK RDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASG LLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEE LKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHA RIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKS EDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI EEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSE IRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFI TSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPRPIRPDVTGMILEEGAPEGTVAT VLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCP YIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGYDKGTYCGAPILGPGGA PKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKP PRPSVLEAAKQTVINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGET FTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDLSTMI RCARSFGGLMDEMKAHCISLPVRVGMNVNEDGPIIFEKHSRYKYHYDADYSRWDSTQQ RAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWN SIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGL KPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHED PNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFR WMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide <1..986 /gene="ORF1" /product="p48" mat_peptide 987..2084 /gene="ORF1" /product="NTPase" mat_peptide 2085..2615 /gene="ORF1" /product="p22" mat_peptide 2616..3014 /gene="ORF1" /product="VPg" mat_peptide 3015..3557 /gene="ORF1" /product="Pro" mat_peptide 3558..5087 /gene="ORF1" /product="RdRp" gene 5071..6693 /gene="ORF2" CDS 5071..6693 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QIQ09389.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6693..7499 /gene="ORF3" CDS 6693..7499 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QIQ09390.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 cgtctaacga cgctaccgtt gccgttgctt gcaacaacaa caacgacaag gaaaaatctt 61 caggtgaagg cttattcaca aatatgtctt tcaccttaaa gaaagccctc ggggctaggc 121 ccaaacagcc tgccccgaga gacgaaccac aaaagccccc aagaccacca acccccgagt 181 tggtcaagag gataccccct cctccaccta atggcgaagg agaagaagaa ccagtcatta 241 ggtatgaggt taagagtggg atctctggcc tgcccgagct cacaacagtc ccccaaccgg 301 acgtggccaa cacagcattc agtgttccac cactgagctt gagagaaaac agggaggcca 361 aggaaccgct aacaggggca atattagaga tgtgggatgg agagatatac cactatggcc 421 tgtacgtgga gaaaggctta gtgttgggtg tgcacaaacc acctgcagcc ataagcatgg 481 caagagtgga gctgacgccg ctgtcattgt actggcgtgt ggtgtacact ccccaatacc 541 tcatctcccc tgaaactctc aggaggctca acggagaggc gttcccttac accgccttcg 601 acaacaactg ctacgccttt tgctgctggg tgttagacct caatgactca tggcttagca 661 ggaggatggt gcaaagaaca acgggcttct tcagacctta ccaagagtgg aacagaaagc 721 ccctgcctac catggatgac tccaaaatta agaaggtagc aaatatattc ctatgttcat 781 tgtccacatt attcaccaga cccataaaag acctcatagg gaaaattaaa ccattaaaca 841 tattgaacat cctggcaacg tgtgactgga cgtttgccgg aatagtggag tctctgatat 901 tacttgctga actcttcgga gttttctgga cgcccccaga tgtgtctgct atgatcgctc 961 ccttactcgg ggactacgag ttgcaagggc cagaagacct cgccgttgaa ctcgtacctg 1021 tggtaatggg agggattggt ttggtgttgg gattcaccaa agagaaaatt ggcaaaatgt 1081 tgtcctcagc agcatcaaca ctcagggctt gcaaagatct tggtgcctat ggcttagaga 1141 tactcaagtt ggtcatgaag tggttcttcc caaagaaaga ggaggccaat gagctagcca 1201 tggtgagggc catagaggat gccgtgctag atcttgaggc aatagaaaat aaccacatga 1261 caaccctgtt gaaagacaaa gacagcttag caacatacat gaaaacactg gacatggagg 1321 aggagaaagc cagaaggttg tccacaaaat ctgcatcccc tgacatagtt gggacaatca 1381 acgccctgct ggctcgaata gcagcggcca ggtcattagt ccacagggcc aaggaagagc 1441 tatctagcag gataaggcca gtagttgtta tgatatctgg caaaccagga ataggcaaaa 1501 ctcatctggc cagggaggtg gcaagaaagg tggcatccac tctcacaggg gaccaaagag 1561 tcggactcat accaagaaac ggtgtggacc attgggatgc atacaaaggt gagagagtcg 1621 tgctgtggga cgactatggc atgagtaacc ccatccatga tgctcttcgc atacaagaat 1681 tggctgatac gtgtcccctt accttaaatt gtgacagaat tgaaaataag ggaaaagttt 1741 ttgacagtga agtcataata attacaacaa accttgccaa tccagcccca cttgattatg 1801 tcaactttga ggcctgttcc aggagaattg atttcctggt gtacgctgag gcaccagaag 1861 tagaaaaggc aaaacgggac tttcctggtc agccagatat gtggaaggac gccttcaagc 1921 cggacttttc acacatcaag ctacagcttg cacctcaggg cggctttgac aagaatggca 1981 acaccccaca tgggaaagga gtgatgaaga ccctcactac cggttctctg attgcccgtg 2041 catcaggcct actacatgag aggatggatg aatttgaact ccaaggtccc acaatcacca 2101 ccttcaattt cgaccgaaac agaatcacag cattcagaca attggctgca gaaaacaagt 2161 atggattggt ggataccatg aaagttggca atcaattaaa aggagtgaaa accatggaag 2221 aactcaaaca agcaatcaga aatgtgacca tcaagaggtg ccggatcatc tacggtggct 2281 ccacgtatga ccttgaatct gatggcaagg gcaaagtttt ggtggaaaag gtcaagaaca 2341 cctctgtaca gaccaacaac gagttggccg gggccctgca ccatctcaaa cacgcccgaa 2401 tcaggtacta tgtcaaatgt gtgcaagaag cagtctattc catcatacaa attgccggcg 2461 ctgcgtttgt caccacgcgc attgcacgcc gcatgaacat acaagaactc tggtcgaagc 2521 cacaattaga tcaaaatgaa tcagagacta aggaagaggc ccccaaatca gaagatgacg 2581 agttcatcat atcttctaag gacatcaagg aggaaggaaa gaagggcaaa aacaaaactg 2641 gccgtggcaa gaaacacact gcattctcca gcaagggctt gagcgatgag gagtatgacg 2701 agtacaagag gataagagaa gagagaaatg ggaagtactc tatagaggag tatcttcaag 2761 acagagacag gtactatgag gagctcgcca ttgccaaggc cacggaagaa gacttctgtg 2821 aagaggagga gataaaaatc cgtcagagaa ttttccgtcc caccaggaaa caaagaaagg 2881 aagagagggc cacattagga ctggtaacag gttcagaaat cagaaaaaga aaccctgatg 2941 acttcaaacc caaagggaag ctgtgggccg atgacaacag aagtgttgac tataatgaga 3001 aactggactt tgaggccccc ccaagcatat ggtctaggat tgtgagcttt ggttctggct 3061 ggggcttctg ggtatcacca agcctgttca taacatcaac tcatgtaatc cccgcaggca 3121 taacagaagc atttggagtc cccatcaaac aaattcagat ccacaaatca ggtgaatttt 3181 gccgattcag attcccaaga ccaattagac cagacgtgac aggaatgatc ttggaagaag 3241 gtgcgcctga aggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga gagctcatgc 3301 ctcttgcagc cagaatggga acacacgcaa ccatgaaaat tcaaggccgc atggttggcg 3361 gacagatggg tatgttgctc actggatcaa atgctaaagg aatggatttg ggaacaactc 3421 ctggtgactg tggctgtcct tacatctaca aaaggggcaa tgactatata gtcattgggg 3481 tgcacactgc agcagcccgt ggtggaaaca ccgtcatctg tgccacacag ggaagtgagg 3541 gtgaggcaac tcttgagggt ggatatgaca aaggaacata ctgtggggca cccattctag 3601 gccctggggg tgcaccaaag ttgagcacca aaaccaaatt ttggaggtca tcgaacacgc 3661 ccctcccacc agggacatat gagcctgcct acctcggtgg ccgtgatccg cgtgttaagg 3721 gtgggccctc cttgcagcag gtaatgagag accagttgaa gccattcact gaacccaggg 3781 gcaaacctcc aagaccaagt gtattggaag cagccaaaca aaccgttatc aatgtcctcg 3841 aacaaaccct ggatcctcca caaaaatgga catacgcaca ggcgtgtgcc tcacttgaca 3901 aaaccacttc cagcgggcat cctcatcacg tccgaaagaa tgaattctgg aatggtgaga 3961 ccttcaccgg caaattggca gaccaagcat caaaagcaaa cctaatgttt gaggaaggga 4021 aacacatgac accagtgtat acagcagcac tcaaggacga gctagtcaag actgagaaaa 4081 tctatagaaa gatcaagaag agactgctct ggggctctga cttgtccacc atgatccggt 4141 gcgctaggtc atttggtggg ctcatggacg agatgaaggc acactgcata tcactcccag 4201 tacgagttgg catgaatgtg aatgaagatg gcccaataat atttgagaaa cattccagat 4261 acaaatacca ctatgacgca gactactctc gttgggattc aacacaacag agggcagtac 4321 tagcagcagc cttggaaatc atggtcagat tctctgcaga accacaattg gcacaaatag 4381 tcgctgagga tcttctggcc cctagcgtag tagatgtagg agactttaaa atcactataa 4441 atgaagggct cccatctggt gtgccatgca cctcccaatg gaactccatc gcacactggc 4501 tgctaactct ctgtgccttg tctgaagtca ccaaactgtc ccctgacatt atacaagcaa 4561 attccatgtt ctcattttac ggtgatgacg agattgtcag caccgacata aaattggacc 4621 ctgaacagtt aaccgccaag ttgaaggagt atggcctgaa accaacccgc ccagacaaga 4681 ccgagggacc cctgatcatc agtgaagatt tgaacggact cactttcctc cgaaggacgg 4741 tgactcgtga cccagctggc tggtttggaa aactggacca aagttcaatt ttgaggcaga 4801 tgtactggac tagaggacca aatcacgaag atcccaatga gacaatgata ccccattctc 4861 aaagacccat acagctcatg gcactgcttg gtgaagcctc tcttcacgga ccctctttct 4921 acagtagaat cagtaaattg gtcataactg aactcaaaga aggtgggatg gacttttacg 4981 tgccaaggca ggaacccatg ttcaggtgga tgaggttttc tgacttgagc acgtgggagg 5041 gcgatcgcaa tctggctccc aattttgtga atgaagatgg cgtcgagtga cgccaaccca 5101 tctgatgggt ccgcagccaa cctcgtacca gaggtcaaca atgaggttat ggctttggag 5161 cccgttgtcg gtgccgctat tgcggcacct gtagcgggcc aacaaaatgt aattgacccc 5221 tggattagaa ataattttgt acaagcccct ggtggggagt ttacagtatc ccccagaaac 5281 gctccaggtg aaatactatg gagcgcgccc ctaggccctg acctaaatcc ctacctatcc 5341 catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt aattctcgcg 5401 gggaacgcgt tcaccgccgg gaagatcata tttgcagcag tcccaccaaa ttttccaact 5461 gaaggcttaa gtcctagcca ggtcactatg ttcccccata taatagtaga tgttagacag 5521 ttagaacctg tgctgattcc tttacccgat gttaggaata atttctatca ttacaatcag 5581 tcaaatgact ccactattaa gttgatagca atgttgtaca caccacttag ggctaataat 5641 gctggggatg atgttttcac agtttcgtgc cgagttctca cgagaccatc ccccgatttt 5701 gatttcatat ttttagtgcc acccacagtt gagtcaagaa ctaaaccatt ctctgtccca 5761 gttttaactg ttgaggagat gaccaattca agattcccca tccctttgga aaagctgttc 5821 acaggcccca gcagtgcctt tgttgttcaa ccacaaaacg gcaggtgcac aactgatggc 5881 gtgctcctag gcaccaccca actttctcct gtcaacatct gcaccttcag aggggatgtc 5941 acccacatca caggtagtcg caactacaca atgaatttgg cttctcaaaa ttggaacaac 6001 tatgacccaa cagaagaaat cccagcccct ctaggaactc cagattttgt ggggaagatt 6061 caaggcatgc tcacccaaac cacaaggaca gatggttcaa cacgcggcca caaagctaca 6121 gtgtacactg ggagcgccga ctttgctcca aaactgggta gagttcaatt tgaaactgac 6181 acagaccatg attttgaagc taatcaaaac acaaagttca ccccagtcgg tgtcatccaa 6241 gatggtagca ccacccatcg aaacgaaccc caacagtggg tgctcccaag ttactcaggc 6301 agaaatactc acaatgtaca tctggccccc gctgtagccc ccacctttcc gggtgagcaa 6361 cttctcttct tcagatccac catgcccgga tgcagcgggt accccaacat ggatttggac 6421 tgtctgctcc cccaggaatg ggtgcagtac ttctatcaag aggcagcccc agcacaatct 6481 gatgtggctc tgctaagatt tgtgaatcca gacacaggta gggttttgtt tgagtgcaag 6541 cttcacaaat caggctatgt tacagtggct cacactggcc aacatgattt ggttatcccc 6601 cccaatggct actttagatt tgattcctgg gtcaaccagt tctatacgct tgcccccatg 6661 ggaaatggaa cggggcgtag acgtgtagta taatggctgg agctttcttt gctggattgg 6721 catctgatgt ccttggctct ggacttggtt ccctcatcaa tgctggggct ggggccatca 6781 accaaaaagt tgagtttgaa aataacagaa aattgcaaca agcatccttc caatttagca 6841 gcaatctgca acaggcttcc tttcaacatg ataaagagat gctccaagca caaattgagg 6901 ccactaaaaa gctacaacag gaaatgatga aagttaagca ggcaatgctc ctagagggtg 6961 ggttctctga gacagatgca gcccgcgggg caattaacgc ccccatgaca aaagctttgg 7021 actggagtgg gacaaggtac tgggctcccg atgctaggac tacaacatac aatgcaggcc 7081 gcttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctt agggatgctg 7141 tccctgctcg gggaccctcc aacaaatctt ctaactcttc tactgccacc tctgtgtatt 7201 caaatcaaac tatttcaacg agacttggtt ctacagctgg ttctggaacc agtgtctcga 7261 gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaaatagg aatttgtcac 7321 ctttcatgag gggggcccac aacatatcat ttgtcacccc accatctagc agatcctcta 7381 gccaaggcac agtctcaacc gtgcctaaag agattttgga ctcctggact ggcgctttca 7441 acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca cgggtgtaat 7501 gtgaaaagac aaaattgatt atttttcttt ttctttagtg //