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Typing tool
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Complete norovirus genomes
MK616558 | GII.12 | ![]() |
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GII.P16 |
ORF1: 1..5052 ORF2: 5033..6640 ORF3: 6640..7419LOCUS MK616558 7466 bp RNA linear VRL 17-MAR-2019 DEFINITION Norovirus GII isolate CA-RGDS-1017 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MK616558 VERSION MK616558.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7466) AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and Wadford,D.A. TITLE Norovirus GII.P16-GII.12 genomes from gastroenteritis outbreaks, California, 2018 JOURNAL Unpublished REFERENCE 2 (bases 1 to 7466) AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and Wadford,D.A. TITLE Direct Submission JOURNAL Submitted (11-MAR-2019) Viral and Rickettsial Disease Laboratory, California Department of Public Health, 850 Marina Bay Parkway, Richmond, CA 94804, USA COMMENT ##Assembly-Data-START## Assembly Method :: Geneious v. R10; SPAdes v. 3.6 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7466 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="CA-RGDS-1017" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /geo_loc_name="USA: CA" /collection_date="Jan-2018" /note="genotype: GII.P16-GII.12" gene <1..5052 /gene="ORF1" CDS <1..5052 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QBL14281.1" /translation="TNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDKPQKPPRPL TPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAFSVPPLSLR ENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMAKVELTPLSLYWR VVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQRTTGFF RPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNILATCD WTFAGIVESLILFAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIG LVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAI EDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTINAL LARIAAARSLVHRAKEELSSRMRPVVVMISGKPGIGKTHLAREVARKVASTLTGDQRV GLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGK VFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKAKRDFPGQPDMWKD AFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQ GPTTTTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKR CRIIYGGSTYDLESDGKGKVLVEKVKNASVQTNNELAGALHHLKHARIRYYVKCVQEA VYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKPEDDEFVISSKDI KEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYE ELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKPK GKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPTGITE AFGVPIKQVQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMP LAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYIVI GVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGDAPKLSTKTKFWRS SNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQT IINVLEQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFWNGETFTGKLADQASKA NLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDE MKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMV RFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTLCAL SEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLREYGLKPTRPDKTEGPL IISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRP IQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEG DRNLAPNFVNEDGVE" mat_peptide <1..948 /gene="ORF1" /product="p48" mat_peptide 949..2046 /gene="ORF1" /product="NTPase" mat_peptide 2047..2577 /gene="ORF1" /product="p22" mat_peptide 2578..2976 /gene="ORF1" /product="VPg" mat_peptide 2977..3519 /gene="ORF1" /product="Pro" mat_peptide 3520..5049 /gene="ORF1" /product="RdRp" gene 5033..6640 /gene="ORF2" CDS 5033..6640 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QBL14282.1" /translation="MKMASNDAAPSNDGAAGLVPEVNNETMALEPVAGASIAAPLTGQ NNVIDPWIRLNFVQAPNGEFTVSPRNSPGEVLLNLELGPELNPYLAHLSRMYNGYAGG VEVQVLLAGNAFTAGKLVFAAVPPHFPLENISPGQITMFPHVIIDVRTLEPVLLPLPD VRNNFFHYNQQNEPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFNYLVPP TVESKTKPFTLPVLTIGELTNSRFPVPIDELYTSPNESLVVQPQNGRCALDGELQGTT QLLPTAICSFRGRINQKVNGENHVWNMQVTNINGTPFDPTEDVPAPLGTPDFSGKLFG VLSQRDHDNACRSHDAVIATDSTKFTPKLGAVQIGTWEQDDVHINQPTKFTPVGLFEN EGFNQWTLPNYSGALTLNMGLAPPVAPTFPGEQILFFRSHIPLKGGVADPVIDCLLPQ EWIQHLYQESAPSQTDVALIRFTNPDTGRVLFEAKLHRSGYITVANTGSRPIVVPANG YFRFDSWVNQFYSLAPMGTGNGRRRMQ" gene 6640..7419 /gene="ORF3" CDS 6640..7419 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QBL14283.1" /translation="MAGAFIAGLAGDIVTNSIGSLVNAGANAINQKVDFENNKQLQQA SFNHDKEMLQAQIQATKQLQADMIAIRQGVLTAGGFSPTDAARGAVNAPMTQVLDWNG TRHWAPGATKTTAFSGGFTSASHARTVDLTKKTSATPAPMPVSRPSSIASTVSTRSTL ISGSSNSPSSASSSSSVSSQPISSSSRTSEWVRSQNRALEPYMNGALRTAYVTPPSSR ASSNGTVSTVPKEVLDSWSSAFNTHRQPLFAHLRRRGESQA" ORIGIN 1 accaacgaca aggaaaaatc ttcaggtgaa ggcttattca caaatatgtc ttccacctta 61 aagaaagccc tcggggctag gcccaaacag cctgccccga gagacaaacc acaaaagccc 121 ccaagaccac taactcccga gttggtcaag aggatacccc ctcctccacc taatggcgaa 181 gaagaagaag aaccagtcat taggtatgag gttaagagtg ggatctctgg cctgcccgag 241 ctcacaacag tcccccaacc ggacgtggcc aacacagcat tcagtgttcc accactgagc 301 ttgagagaaa acagggaagc caaggaaccg ctaacagggg caatattaga gatgtgggat 361 ggagagatat accactacgg cctgtacgtg gagaaaggct tagtgttggg tgtacacaaa 421 ccacctgcag ccataagcat ggcaaaagtg gagctgacgc cgctgtcatt gtattggcgt 481 gtggtgtaca ctccccaata cctcatctcc cctgaaactc tcaggaggct caacggagag 541 gcattccctt acaccgcttt tgacaacaac tgctatgcct tttgctgctg ggtattagac 601 ctcaatgatt catggcttag caggaggatg gtgcaaagaa caacgggctt cttcagacct 661 taccaagagt ggaacagaaa acccctgcct accatggatg actccaaaat taagaaggtg 721 gcaaatatat tcctatgttc attgtccaca ttgttcacta gacccataaa agacctcata 781 ggaaaaatta aaccattaaa catattgaat atcctggcaa cgtgtgactg gacgtttgcc 841 ggaatagtgg agtctctaat attatttgct gaactcttcg gagttttctg gacaccccca 901 gatgtgtctg ctatgatcgc tcccttactt ggggattacg agttgcaagg gccagaagac 961 ctcgccgttg aactcgtacc tgtggtgatg ggagggattg gtttggtgtt gggattcacc 1021 aaagagaaaa ttggcaaaat gttgtcctca gcagcatcaa cactcagggc ttgcaaagac 1081 cttggtgcct atggcttaga gatactcaaa ttggtcatga agtggttctt cccaaagaaa 1141 gaggaggcca atgagctagc catggtgagg gccatagagg acgctgtact agatcttgag 1201 gcaatagaaa ataaccacat gacaaccctg ttgaaagaca aagacagctt agcaacatac 1261 atgaaaacac tggacatgga ggaggagaaa gccagaaggt tgtccacaaa atctgcatcc 1321 cctgacatag ttgggacaat caacgccctg ctggctcgaa tagcagcggc caggtcatta 1381 gttcacaggg ccaaggaaga gctatctagc aggatgagac cagtagttgt tatgatatct 1441 ggcaaaccag gaataggcaa aactcatctg gccagggaag tggcaagaaa ggtggcatcc 1501 actctcacag gggatcaaag agtcggactc ataccaagaa acggtgtgga ccattgggat 1561 gcatacaaag gtgagagagt cgtgctgtgg gacgactatg gcatgagtaa ccccattcat 1621 gatgctcttc gcatacaaga attggctgat acgtgtcccc tcaccttaaa ttgtgacaga 1681 attgaaaata aaggaaaagt ttttgacagt gaagtcataa taatcacaac aaaccttgcc 1741 aatccagccc cgcttgatta tgtcaacttt gaggcctgtt ccaggagaat tgatttcctg 1801 gtgtacgctg aggcaccaga tgtggaaaag gcaaaacggg acttccctgg tcaaccagat 1861 atgtggaagg acgccttcaa accggacttt tcacacatca agctacagct tgcacctcag 1921 ggcggctttg acaaaaacgg caacacccca catgggaaag gggtgatgaa gaccctcact 1981 accggttctc tgattgcccg cgcatcaggc ctactgcatg agaggatgga tgaatttgaa 2041 ctccaaggtc ctacaaccac caccttcaat ttcgaccgga acagaatcac agcattcaga 2101 caattggctg cagaaaacaa gtatggactg gtggacacca tgaaagtcgg caatcaatta 2161 aaaggagtga aaaccatgga agaacttaaa caagcaatca ggaatgtgac catcaagagg 2221 tgccggatca tctacggtgg ctccacatat gaccttgaat ctgatggcaa gggcaaagtt 2281 ttggtggaaa aggtcaagaa cgcctctgta cagaccaaca acgagttggc cggggccctg 2341 caccatctca aacacgcccg aatcaggtac tatgtcaagt gtgtgcaaga agcagtctat 2401 tctatcatac aaattgccgg cgctgcgttt gtcaccacgc gcattgcacg ccgcatgaac 2461 atacaagaac tctggtcgaa gccacaattg gatcaaaatg aatcagagac taaggaagag 2521 gcccccaagc cagaagatga cgagttcgtc atatcttcta aggacatcaa ggaggaagga 2581 aagaagggca aaaataagac tggccgtggc aagaaacaca ctgcattctc cagcaagggc 2641 ttgagcgatg aggagtatga cgagtacaag aggataagag aagagagaaa tgggaagtac 2701 tctatagagg aatatcttca agacagagac aggtactatg aagaactcgc cattgccaag 2761 gccacggaag aagacttctg tgaagaggag gagataaaaa tccgtcagag aattttccgt 2821 cctaccagga aacaaaggaa ggaagagagg gccacattgg ggctagtaac aggttcagaa 2881 atcagaaaaa gaaaccctga tgacttcaaa cccaaaggga agttgtgggc cgatgacaac 2941 agaagtgttg actacaatga gaaactggat tttgaggccc ccccaagcat atggtctagg 3001 attgtgagtt ttggttctgg ctggggcttc tgggtatcac caagcctgtt cataacatca 3061 actcatgtaa tccccacagg cataacagaa gcatttggag tccccatcaa acaagttcaa 3121 atccacaaat caggtgaatt ttgccgattc agattcccaa aaccaattag accagatgtg 3181 acaggaatga tcttggaaga aggtgcgcct gagggcaccg tggcaactgt gctcatcaaa 3241 cgccccaccg gagagctcat gcctcttgca gccagaatgg gaacacacgc aaccatgaaa 3301 attcaaggcc gcatggttgg cggacagatg ggcatgttgc tcactggatc aaatgctaaa 3361 ggaatggatt tgggaacaac tcctggagac tgtggctgtc cttacatcta taaaaggggc 3421 aatgactata tagtcattgg ggtgcacact gcagcagccc gtggtggaaa caccgtcatc 3481 tgtgccacac agggaagtga gggtgaggca actcttgagg gtggagatga caaaggaacg 3541 tactgtgggg cacccatcct aggccctggg gatgcaccaa aattgagcac caaaaccaaa 3601 ttttggaggt cgtcgaacac gccccttcca ccagggacat atgagcctgc ctacctcggc 3661 ggccgtgacc cgcgtgttaa gggtgggccc tccttgcagc aggtaatgag agaccagttg 3721 aagccattca ctgaacccag gggcaaacct ccaagaccaa gtgtattgga agcagccaaa 3781 caaaccatca tcaatgtcct tgagcaaacc ctggaccctc cacaaaaatg gacatacgca 3841 caggcgtgtg cctcacttga caaaaccacc tccagcggtc acccctacca cgttcgaaag 3901 aatgaattct ggaatggtga gaccttcact ggtaaattgg cagaccaagc atcaaaagca 3961 aacctaatgt ttgaggaagg gaagcacatg acaccagtgt atacagcagc actcaaggac 4021 gagctagtca agactgagaa aatctatgga aagatcaaga agagactgct ctggggctct 4081 gatttgtcca ccatgatccg gtgcgctagg tcatttggtg ggctcatgga cgagatgaag 4141 gcacactgca tatcactccc agtccgagtt ggcatgaata tgaatgaaga tggcccaata 4201 atatttgaga aacattccag atacaaatat cactatgatg cagactactc tcgttgggat 4261 tcaacacaac agagggcagt actggcagca gccttggaaa tcatggtcag attctctgca 4321 gaaccacaat tggcacaaat agtcgctgag gacctactgg cccctagtgt agtagatgta 4381 ggagacttta aaattacaat aaatgagggg ctcccctctg gtgtgccatg cacttctcaa 4441 tggaactcca tcgcacactg gctgctaact ctctgtgcct tgtctgaagt cactaagctg 4501 tcacctgaca ttatacaggc aaattccatg ttctcatttt acggtgatga cgagattgtc 4561 agcaccgaca taaaattgga ccccgaacag ttaaccgcca aattgaggga gtacggccta 4621 aaaccaaccc gcccagacaa aaccgaggga cccctgatca tcagtgaaga tttgaacgga 4681 ctcaccttcc tccgaagaac ggtgactcgt gatccagctg gttggtttgg aaaactggac 4741 caaagctcaa ttttgaggca gatgtactgg actagaggac caaatcatga agaccccaat 4801 gagacaatga taccccattc tcaaaggccc atacagctca tggcactgct tggtgaagcc 4861 tctcttcacg gaccctcttt ctacagtaaa atcagtaaat tggtcataac tgaactcaaa 4921 gaaggtggga tggactttta cgtgccaagg caggaaccca tgttcaggtg gatgaggttt 4981 tctgacttga gcacgtggga gggcgatcgc aatctggctc ccaattttgt gaatgaagat 5041 ggcgtcgaat gacgccgctc catctaatga tggtgcagcc ggtctcgtac cagaggtcaa 5101 caatgagacc atggcacttg aaccggtggc tggggcttcg atagccgccc cactcaccgg 5161 ccaaaataat gttatagacc cctggattag attaaatttt gtgcaggccc ctaatggaga 5221 gtttacagtc tcaccccgca actcgcctgg ggaagtccta ctcaatttgg aattaggtcc 5281 cgaattgaat ccatatttgg cacatctttc tagaatgtat aatggttatg caggtggagt 5341 tgaggtacaa gtgctactgg ctgggaacgc gttcacggct ggaaaattgg tatttgctgc 5401 agttccccct cattttccat tagagaatat aagccctggt caaataacca tgttccctca 5461 tgtaattatt gatgttagga ctttggaacc agttttattg cctctaccag atgtcagaaa 5521 taacttcttc cattacaatc agcaaaatga gccgaggatg aggcttgttg caatgcttta 5581 tacccctctt agatctaatg gttctggtga tgatgtgttc accgtctcct gtagggtgct 5641 cactcgaccc tctcctgatt ttgattttaa ttatttggtg cccccaacag ttgaatctaa 5701 aacaaaacca ttcacactcc ctgtcttgac cattggggag ttaaccaatt ccaggttccc 5761 tgtgcccata gatgaactct acactagccc caatgagagt ttggtggttc aaccccagaa 5821 cgggaggtgc gcgctggatg gggagttgca gggcaccacc cagctccttc ccacggcgat 5881 ttgctcgttc aggggtcgaa tcaatcagaa agtgaatgga gagaatcatg tttggaacat 5941 gcaagtcacc aacattaacg gaaccccttt tgatccaaca gaggatgttc cagcccctct 6001 gggcacgcca gacttttctg gcaagctctt tggtgtccta agccagaggg accatgataa 6061 tgcctgcagg agtcatgatg cagtgattgc aactgattct accaaattta ccccaaaatt 6121 gggtgctgta caaattggca catgggaaca agatgatgta cacatcaacc aacccaccaa 6181 gtttactcca gttggattgt ttgagaatga aggttttaat caatggacac ttcctaatta 6241 ttctggagct ttaacactca atatggggtt ggctccccct gtggccccca catttcctgg 6301 tgagcaaatt ctcttcttca ggtcccacat tccccttaaa ggaggtgttg cagacccagt 6361 tattgattgt cttctacccc aagagtggat tcaacacctt tatcaggagt cagccccttc 6421 acaaacagat gtggcactga ttagattcac aaatccagac acagggcgtg tcctatttga 6481 agcaaaattg cacaggagtg gctacatcac agtggccaac actggtagca gaccaattgt 6541 ggtgccagct aatggttatt tcaggtttga ctcttgggtt aatcaatttt actctcttgc 6601 ccccatggga actgggaatg ggcgcagaag gatgcagtaa tggctggagc tttcatagca 6661 gggcttgccg gtgacatagt caccaatagc attggctcac tcgtgaacgc tggggccaat 6721 gcaataaacc agaaagtaga ctttgaaaac aacaagcaac tacaacaggc atctttcaac 6781 catgacaaag agatgttgca agctcaaatt caggccacca aacagctaca ggctgatatg 6841 attgcaatca ggcaaggggt gttgaccgca ggcggcttct cccctactga tgcagcaaga 6901 ggtgcagtca acgcgcccat gactcaagtc ttggattgga atgggaccag acattgggcc 6961 cccggagcca cgaaaacaac tgctttctcc ggtgggttta ccagtgcctc tcatgccagg 7021 accgttgacc tgaccaagaa gacatcagcc acaccagccc ctatgcctgt ttctaggccc 7081 agttctattg cttccactgt ttctactcgc tctactttga ttagtgggtc ctctaattct 7141 ccttcttcag ctagtagctc ttctagtgtt tcttcccaac ccatttcctc atcctcccga 7201 actagtgagt gggtacgcag tcaaaatagg gcgctggagc cttatatgaa tggggcgctg 7261 cgtacagcct acgtgacgcc tccatccagt agggcttcta gcaatggcac agtctcaacc 7321 gtgccaaaag aggttttgga ctcctggtcg tctgcgttca atacacacag acagccgctg 7381 tttgctcatc tccgtcggag aggggagtca caagcttagt gaaaagatgg tcttttcttt 7441 ctttcctttg aaaatatctg tctttt //