Typing tool
|
Complete norovirus genomes
MT238672 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5096 ORF2: 5077..6699 ORF3: 6699..7505LOCUS MT238672 7568 bp RNA linear VRL 01-MAY-2020 DEFINITION Norovirus GII isolate 259-3 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MT238672 VERSION MT238672.1 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 7568) 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..7568 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="259-3" /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..5096 /gene="ORF1" CDS <1..5096 /gene="ORF1" /codon_start=3 /product="nonstructural polyprotein" /protein_id="QIQ09403.1" /translation="MASNDATVAVACNNNNDKEKSSGEGLFTNMSFTLKKALGARPKQ PAPRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPD VANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAIS MARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDS WLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGK IKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREV ARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTC PLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTM EELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLK HARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAP KSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY SIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTG SEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSL FITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPRPIRPDVTGMILEEGAPEGTV ATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCG CPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGYDKGTYCGAPILGPG GAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRG KPPRPSVLEAAKQTVINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNG ETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDLST MIRCARSFGGLMDEMKAHCISLPVRVGMNVNEDGPIIFEKHSRYKYHYDADYSRWDST QQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQ WNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEY GLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNH EDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPM FRWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide <1..992 /gene="ORF1" /product="p48" mat_peptide 993..2090 /gene="ORF1" /product="NTPase" mat_peptide 2091..2621 /gene="ORF1" /product="p22" mat_peptide 2622..3020 /gene="ORF1" /product="VPg" mat_peptide 3021..3563 /gene="ORF1" /product="Pro" mat_peptide 3564..5093 /gene="ORF1" /product="RdRp" gene 5077..6699 /gene="ORF2" CDS 5077..6699 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QIQ09404.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6699..7505 /gene="ORF3" CDS 6699..7505 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QIQ09405.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 agatggcgtc taacgacgct accgttgccg ttgcttgcaa caacaacaac gacaaggaaa 61 aatcttcagg tgaaggctta ttcacaaata tgtctttcac cttaaagaaa gccctcgggg 121 ctaggcccaa acagcctgcc ccgagagacg aaccacaaaa gcccccaaga ccaccaaccc 181 ccgagttggt caagaggata ccccctcctc cacctaatgg cgaaggagaa gaagaaccag 241 tcattaggta tgaggttaag agtgggatct ctggcctgcc cgagctcaca acagtccccc 301 aaccggacgt ggccaacaca gcattcagtg ttccaccact gagcttgaga gaaaacaggg 361 aggccaagga accgctaaca ggggcaatat tagagatgtg ggatggagag atataccact 421 atggcctgta cgtggagaaa ggcttagtgt tgggtgtgca caaaccacct gcagccataa 481 gcatggcaag agtggagctg acgccgctgt cattgtactg gcgtgtggtg tacactcccc 541 aatacctcat ctcccctgaa actctcagga ggctcaacgg agaggcgttc ccttacaccg 601 ccttcgacaa caactgctac gccttttgct gctgggtgtt agacctcaat gactcatggc 661 ttagcaggag gatggtgcaa agaacaacgg gcttcttcag accttaccaa gagtggaaca 721 gaaagcccct gcctaccatg gatgactcca aaattaagaa ggtagcaaat atattcctat 781 gttcattgtc cacattattc accagaccca taaaagacct catagggaaa attaaaccat 841 taaacatatt gaacatcctg gcaacgtgtg actggacgtt tgccggaata gtggagtctc 901 tgatattact tgctgaactc ttcggagttt tctggacgcc cccagatgtg tctgctatga 961 tcgctccctt actcggggac tacgagttgc aagggccaga agacctcgcc gttgaactcg 1021 tacctgtggt aatgggaggg attggtttgg tgttgggatt caccaaagag aaaattggca 1081 aaatgttgtc ctcagcagca tcaacactca gggcttgcaa agatcttggt gcctatggct 1141 tagagatact caagttggtc atgaagtggt tcttcccaaa gaaagaggag gccaatgagc 1201 tagccatggt gagggccata gaggatgccg tgctagatct tgaggcaata gaaaataacc 1261 acatgacaac cctgttgaaa gacaaagaca gcttagcaac atacatgaaa acactggaca 1321 tggaggagga gaaagccaga aggttgtcca caaaatctgc atcccctgac atagttggga 1381 caatcaacgc cctgctggct cgaatagcag cggccaggtc attagtccac agggccaagg 1441 aagagctatc tagcaggata aggccagtag ttgttatgat atctggcaaa ccaggaatag 1501 gcaaaactca tctggccagg gaggtggcaa gaaaggtggc atccactctc acaggggacc 1561 aaagagtcgg actcatacca agaaacggtg tggaccattg ggatgcatac aaaggtgaga 1621 gagtcgtgct gtgggacgac tatggcatga gtaaccccat ccatgatgct cttcgcatac 1681 aagaattggc tgatacgtgt ccccttacct taaattgtga cagaattgaa aataagggaa 1741 aagtttttga cagtgaagtc ataataatta caacaaacct tgccaatcca gccccacttg 1801 attatgtcaa ctttgaggcc tgttccagga gaattgattt cctggtgtac gctgaggcac 1861 cagaagtaga aaaggcaaaa cgggactttc ctggtcagcc agatatgtgg aaggacgcct 1921 tcaagccgga cttttcacac atcaagctac agcttgcacc tcagggcggc tttgacaaga 1981 atggcaacac cccacatggg aaaggagtga tgaagaccct cactaccggt tctctgattg 2041 cccgtgcatc aggcctacta catgagagga tggatgaatt tgaactccaa ggtcccacaa 2101 tcaccacctt caatttcgac cgaaacagaa tcacagcatt cagacaattg gctgcagaaa 2161 acaagtatgg attggtggat accatgaaag ttggcaatca attaaaagga gtgaaaacca 2221 tggaagaact caaacaagca atcagaaatg tgaccatcaa gaggtgccgg atcatctacg 2281 gtggctccac gtatgacctt gaatctgatg gcaagggcaa agttttggtg gaaaaggtca 2341 agaacacctc tgtacagacc aacaacgagt tggccggggc cctgcaccat ctcaaacacg 2401 cccgaatcag gtactatgtc aaatgtgtgc aagaagcagt ctattccatc atacaaattg 2461 ccggcgctgc gtttgtcacc acgcgcattg cacgccgcat gaacatacaa gaactctggt 2521 cgaagccaca attagatcaa aatgaatcag agactaagga agaggccccc aaatcagaag 2581 atgacgagtt catcatatct tctaaggaca tcaaggagga aggaaagaag ggcaaaaaca 2641 aaactggccg tggcaagaaa cacactgcat tctccagcaa gggcttgagc gatgaggagt 2701 atgacgagta caagaggata agagaagaga gaaatgggaa gtactctata gaggagtatc 2761 ttcaagacag agacaggtac tatgaggagc tcgccattgc caaggccacg gaagaagact 2821 tctgtgaaga ggaggagata aaaatccgtc agagaatttt ccgtcccacc aggaaacaaa 2881 gaaaggaaga gagggccaca ttaggactgg taacaggttc agaaatcaga aaaagaaacc 2941 ctgatgactt caaacccaaa gggaagctgt gggccgatga caacagaagt gttgactata 3001 atgagaaact ggactttgag gcccccccaa gcatatggtc taggattgtg agctttggtt 3061 ctggctgggg cttctgggta tcaccaagcc tgttcataac atcaactcat gtaatccccg 3121 caggcataac agaagcattt ggagtcccca tcaaacaaat tcagatccac aaatcaggtg 3181 aattttgccg attcagattc ccaagaccaa ttagaccaga cgtgacagga atgatcttgg 3241 aagaaggtgc gcctgaaggc accgtggcaa ctgtgctcat caaacgcccc accggagagc 3301 tcatgcctct tgcagccaga atgggaacac acgcaaccat gaaaattcaa ggccgcatgg 3361 ttggcggaca gatgggtatg ttgctcactg gatcaaatgc taaaggaatg gatttgggaa 3421 caactcctgg tgactgtggc tgtccttaca tctacaaaag gggcaatgac tatatagtca 3481 ttggggtgca cactgcagca gcccgtggtg gaaacaccgt catctgtgcc acacagggaa 3541 gtgagggtga ggcaactctt gagggtggat atgacaaagg aacatactgt ggggcaccca 3601 ttctaggccc tgggggtgca ccaaagttga gcaccaaaac caaattttgg aggtcatcga 3661 acacgcccct cccaccaggg acatatgagc ctgcctacct cggtggccgt gatccgcgtg 3721 ttaagggtgg gccctccttg cagcaggtaa tgagagacca gttgaagcca ttcactgaac 3781 ccaggggcaa acctccaaga ccaagtgtat tggaagcagc caaacaaacc gttatcaatg 3841 tcctcgaaca aaccctggat cctccacaaa aatggacata cgcacaggcg tgtgcctcac 3901 ttgacaaaac cacttccagc gggcatcctc atcacgtccg aaagaatgaa ttctggaatg 3961 gtgagacctt caccggcaaa ttggcagacc aagcatcaaa agcaaaccta atgtttgagg 4021 aagggaaaca catgacacca gtgtatacag cagcactcaa ggacgagcta gtcaagactg 4081 agaaaatcta tagaaagatc aagaagagac tgctctgggg ctctgacttg tccaccatga 4141 tccggtgcgc taggtcattt ggtgggctca tggacgagat gaaggcacac tgcatatcac 4201 tcccagtacg agttggcatg aatgtgaatg aagatggccc aataatattt gagaaacatt 4261 ccagatacaa ataccactat gacgcagact actctcgttg ggattcaaca caacagaggg 4321 cagtactagc agcagccttg gaaatcatgg tcagattctc tgcagaacca caattggcac 4381 aaatagtcgc tgaggatctt ctggccccta gcgtagtaga tgtaggagac tttaaaatca 4441 ctataaatga agggctccca tctggtgtgc catgcacctc ccaatggaac tccatcgcac 4501 actggctgct aactctctgt gccttgtctg aagtcaccaa actgtcccct gacattatac 4561 aagcaaattc catgttctca ttttacggtg atgacgagat tgtcagcacc gacataaaat 4621 tggaccctga acagttaacc gccaagttga aggagtatgg cctgaaacca acccgcccag 4681 acaagaccga gggacccctg atcatcagtg aagatttgaa cggactcact ttcctccgaa 4741 ggacggtgac tcgtgaccca gctggctggt ttggaaaact ggaccaaagt tcaattttga 4801 ggcagatgta ctggactaga ggaccaaatc acgaagatcc caatgagaca atgatacccc 4861 attctcaaag acccatacag ctcatggcac tgcttggtga agcctctctt cacggaccct 4921 ctttctacag tagaatcagt aaattggtca taactgaact caaagaaggt gggatggact 4981 tttacgtgcc aaggcaggaa cccatgttca ggtggatgag gttttctgac ttgagcacgt 5041 gggagggcga tcgcaatctg gctcccaatt ttgtgaatga agatggcgtc gagtgacgcc 5101 aacccatctg atgggtccgc agccaacctc gtaccagagg tcaacaatga ggttatggct 5161 ttggagcccg ttgtcggtgc cgctattgcg gcacctgtag cgggccaaca aaatgtaatt 5221 gacccctgga ttagaaataa ttttgtacaa gcccctggtg gggagtttac agtatccccc 5281 agaaacgctc caggtgaaat actatggagc gcgcccctag gccctgacct aaatccctac 5341 ctatcccatt tggccagaat gtacaatggt tatgcaggtg gttttgaagt gcaggtaatt 5401 ctcgcgggga acgcgttcac cgccgggaag atcatatttg cagcagtccc accaaatttt 5461 ccaactgaag gcttaagtcc tagccaggtc actatgttcc cccatataat agtagatgtt 5521 agacagttag aacctgtgct gattccttta cccgatgtta ggaataattt ctatcattac 5581 aatcagtcaa atgactccac tattaagttg atagcaatgt tgtacacacc acttagggct 5641 aataatgctg gggatgatgt tttcacagtt tcgtgccgag ttctcacgag accatccccc 5701 gattttgatt tcatattttt agtgccaccc acagttgagt caagaactaa accattctct 5761 gtcccagttt taactgttga ggagatgacc aattcaagat tccccatccc tttggaaaag 5821 ctgttcacag gccccagcag tgcctttgtt gttcaaccac aaaacggcag gtgcacaact 5881 gatggcgtgc tcctaggcac cacccaactt tctcctgtca acatctgcac cttcagaggg 5941 gatgtcaccc acatcacagg tagtcgcaac tacacaatga atttggcttc tcaaaattgg 6001 aacaactatg acccaacaga agaaatccca gcccctctag gaactccaga ttttgtgggg 6061 aagattcaag gcatgctcac ccaaaccaca aggacagatg gttcaacacg cggccacaaa 6121 gctacagtgt acactgggag cgccgacttt gctccaaaac tgggtagagt tcaatttgaa 6181 actgacacag accatgattt tgaagctaat caaaacacaa agttcacccc agtcggtgtc 6241 atccaagatg gtagcaccac ccatcgaaac gaaccccaac agtgggtgct cccaagttac 6301 tcaggcagaa atactcacaa tgtacatctg gcccccgctg tagcccccac ctttccgggt 6361 gagcaacttc tcttcttcag atccaccatg cccggatgca gcgggtaccc caacatggat 6421 ttggactgtc tgctccccca ggaatgggtg cagtacttct atcaagaggc agccccagca 6481 caatctgatg tggctctgct aagatttgtg aatccagaca caggtagggt tttgtttgag 6541 tgcaagcttc acaaatcagg ctatgttaca gtggctcaca ctggccaaca tgatttggtt 6601 atccccccca atggctactt tagatttgat tcctgggtca accagttcta tacgcttgcc 6661 cccatgggaa atggaacggg gcgtagacgt gtagtataat ggctggagct ttctttgctg 6721 gattggcatc tgatgtcctt ggctctggac ttggttccct catcaatgct ggggctgggg 6781 ccatcaacca aaaagttgag tttgaaaata acagaaaatt gcaacaagca tccttccaat 6841 ttagcagcaa tctgcaacag gcttcctttc aacatgataa agagatgctc caagcacaaa 6901 ttgaggccac taaaaagcta caacaggaaa tgatgaaagt taagcaggca atgctcctag 6961 agggtgggtt ctctgagaca gatgcagccc gcggggcaat taacgccccc atgacaaaag 7021 ctttggactg gagtgggaca aggtactggg ctcccgatgc taggactaca acatacaatg 7081 caggccgctt ttccacccct caaccatcgg gggcactgcc aggaagagct aatcttaggg 7141 atgctgtccc tgctcgggga ccctccaaca aatcttctaa ctcttctact gccacctctg 7201 tgtattcaaa tcaaactatt tcaacgagac ttggttctac agctggttct ggaaccagtg 7261 tctcgagcct cccgtcaact gcaaggacta ggagctgggt tgaggatcaa aataggaatt 7321 tgtcaccttt catgaggggg gcccacaaca tatcatttgt caccccacca tctagcagat 7381 cctctagcca aggcacagtc tcaaccgtgc ctaaagagat tttggactcc tggactggcg 7441 ctttcaacac gcgcaggcag cctctcttcg ctcacattcg taagcgaggg gagtcacggg 7501 tgtaatgtga aaagacaaaa ttgattattt ttctttttct ttagtgtctt ttaaaaaaaa 7561 aaaaaaaa //