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Typing tool
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Complete norovirus genomes
MK616560 | GII.12 | ![]() |
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GII.P16 |
ORF1: 1..5037 ORF2: 5018..6625 ORF3: 6625..7404LOCUS MK616560 7439 bp RNA linear VRL 17-MAR-2019 DEFINITION Norovirus GII isolate CA-RGDS-1019 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MK616560 VERSION MK616560.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7439) 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and Wadford,D.A. TITLE Norovirus GII.P16-GII.12 genomes from gastroenteritis outbreaks, California, 2018 JOURNAL Unpublished REFERENCE 2 (bases 1 to 7439) AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and Wadford,D.A. TITLE Direct Submission JOURNAL Submitted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..7439 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="CA-RGDS-1019" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /geo_loc_name="USA: CA" /collection_date="Aug-2018" /note="genotype: GII.P16-GII.12" gene <1..5037 /gene="ORF1" CDS <1..5037 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QBL14287.1" /translation="KSSGEGLFTNMSSTLKKALGARPKQPAPRDKPQKPPRPPTPELV KRIPPPPPNGEEEEEPVIRYEVKSGVSGLPELTTVPQPDVANTAFSVPPLSLRENREA KEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMAKVELTPLSLYWRVVYTP QYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWFSRRMVQRTTGFFRPYQE WNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNILATCDWTFAG IVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGF TKEKIGRMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAIEDAVL DLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTINALLARIA AARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLTGDQRVGLIPR NGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGKVFDSE VIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKAKRDFPGQPDMWKDAFKSD FSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQGPTIT TFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKRCRIIY GGSTYDLESDGKGKVLVEKVKNASVQTNNELAGALHHLKHARIRYYVKCVQEAVYSII QIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKPEDDEFVISCKDIKEEGK KGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYEELAIA KATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKPKGKLWA DDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPTGITEAFGVP IKQVQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMPLAARM GTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYIVIGVHTA AARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWRSSNTPL PPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQTIINVL EQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFWNGETFTGKLADQASKANLMFE EGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDEMKAHC ISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMVRFSAE PQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTK LSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGPLIISED LNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRPIQLMA LLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLA PNFVNEDGVE" mat_peptide <1..933 /gene="ORF1" /product="p48" mat_peptide 934..2031 /gene="ORF1" /product="NTPase" mat_peptide 2032..2562 /gene="ORF1" /product="p22" mat_peptide 2563..2961 /gene="ORF1" /product="VPg" mat_peptide 2962..3504 /gene="ORF1" /product="Pro" mat_peptide 3505..5034 /gene="ORF1" /product="RdRp" gene 5018..6625 /gene="ORF2" CDS 5018..6625 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QBL14288.1" /translation="MKMASNDAVPSNDGAAGLVPEVNNETMALEPVAGASIAAPLTGQ NNVIDPWIRLNFVQAPNGEFTVSPRNSPGEVLLNLELGPELNPYLAHLSRMYNGYAGG VEVQVLLAGNAFTAGKLVFAAVPPHFPLENISPGQITMFPHVIIDVRTLEPVLLPLPD VRNNFFHYNQQNEPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFNYLVPP TVESKTKPFTLPVLTIGELTNSRFPVPIDELYTSPNESLVVQPQNGRCALDGELQGTT QLLPTAICSFRGRINQKVSGENHVWNMQVTNINGTPFDPTEDVPAPLGTPDFSGKLFG VLSQRDHDNACRSHDAVIATDSTKFTPKLGAVQIGTWEQDDVHINQPTKFTPVGLFEN EGFNQWTLPNYSGALTLNMGLAPPVAPTFPGEQILFFRSHIPLKGGVADPVIDCLLPQ EWIQHLYQESAPSQTDVALIRFTNPDTGRVLFEAKLHRSGYITVANTGSRPIVVPANG YFRFDSWVNQFYSLAPMGTGNGRRRMQ" gene 6625..7404 /gene="ORF3" CDS 6625..7404 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QBL14289.1" /translation="MAGAFIAGLAGDIVTNSIGSLVNAGANAINQKVDFENNKQLQQA SFNHDKEMLQAQIQATKQLQADMIAIRQGVLTAGGFSPTDAARGAVNAPMTQVLDWNG TRHWAPGAAKTTAFSGGFTSASHARTVDLTKKTSATPAPMPVSRPSSIASTVSTRSTL ISGSSDSPSSARSSSSVSSQPTSSSSRTSEWVRSQNRALEPYMNGALRTAYVTPPSSR ASSNGTVSTVPKEVLDSWSSAFNTHRQPLFAHLRRRGESQA" ORIGIN 1 aaatcttcag gtgaaggctt attcacaaat atgtcttcca ccttaaagaa agccctcggg 61 gctaggccca aacagcctgc cccgagagac aaaccacaaa agcccccaag accaccaact 121 cccgagttgg tcaagaggat accccctcct ccacctaacg gcgaagaaga agaagaacca 181 gtcattaggt atgaggttaa gagtggggtc tctggcctgc ccgagctcac aacagtcccc 241 caaccggacg tggccaacac agcattcagt gttccaccac tgagcttgag agaaaacagg 301 gaagccaagg aaccgctgac aggggcaata ttagagatgt gggatggaga gatataccac 361 tacggcctgt acgtggagaa aggcttagtg ttgggtgtac acaaaccacc tgcagccata 421 agcatggcaa aagtggagct gacgccgctg tcattgtatt ggcgtgtggt gtacactccc 481 caatacctca tctcccctga aactctcagg aggctcaacg gagaggcatt cccttacacc 541 gcctttgaca acaactgcta tgccttttgc tgctgggtat tagacctcaa tgactcatgg 601 tttagcagga gaatggtgca aagaacaacg ggcttcttca gaccttacca agagtggaac 661 agaaaacccc tgcctaccat ggacgactcc aaaattaaga aggtagcaaa tatattccta 721 tgttcattgt ccacattgtt cactagaccc ataaaagacc tcataggaaa aattaaacca 781 ttaaacatat tgaatatcct ggcaacgtgt gactggacgt ttgccggaat agtggagtct 841 ctaatactac ttgctgaact cttcggagtt ttctggacac ccccagatgt gtctgctatg 901 atcgctccct tacttgggga ttacgagttg caagggccag aagacctcgc cgtcgaactc 961 gtacctgtgg tgatgggtgg gattggtttg gtgttgggat tcaccaaaga gaaaattggc 1021 agaatgttgt cctcggcagc atcaacactc agggcttgca aagaccttgg tgcctatggc 1081 ttagagatac tcaaattagt catgaagtgg ttcttcccaa agaaagagga ggccaatgag 1141 ctagccatgg tgagggccat agaggacgct gtactagatc ttgaggcaat agaaaataac 1201 cacatgacaa ccctgttgaa agacaaagac agcttagcaa catacatgaa aacactggac 1261 atggaggagg agaaagccag aaggttgtcc acaaaatctg catcccctga catagttggg 1321 acaatcaacg ccctgctggc tcgaatagca gcggccaggt cattagtcca cagggccaag 1381 gaagagctat ctagcaggat cagaccagta gttgttatga tatctggcaa accaggaata 1441 ggcaaaactc atctggccag ggaagtggca agaaaggtgg catccactct cacaggggat 1501 caaagagtcg gactcatacc aagaaacggt gtggaccatt gggatgcata caaaggtgag 1561 agagtcgtgc tgtgggacga ctatggcatg agtaacccca ttcatgatgc tcttcgcata 1621 caagaattgg ctgatacgtg tcccctcacc ttaaattgtg acagaattga aaataaagga 1681 aaagtttttg acagtgaagt cataataatc acaacaaacc ttgccaatcc agccccgctt 1741 gattatgtca actttgaggc ctgttccagg agaattgatt tcctggtgta cgctgaggca 1801 ccagatgtgg aaaaggcaaa acgggacttt cctggtcagc cagatatgtg gaaggacgcc 1861 ttcaaatcgg acttttcaca catcaagcta cagcttgcac ctcagggcgg ctttgacaaa 1921 aacggcaaca ccccacatgg gaaaggggtg atgaagaccc tcactaccgg ttctttgatt 1981 gcccgtgcat caggcctact gcatgagagg atggatgaat ttgaactcca aggtcctaca 2041 atcaccacct tcaatttcga ccggaacaga atcacagcat tcagacaatt ggctgcagaa 2101 aacaagtatg gactggtgga caccatgaaa gtcggcaatc aattaaaagg agtgaaaacc 2161 atggaagagc tcaaacaagc aatcaggaat gtgaccatca agaggtgccg gatcatctac 2221 ggtggctcca catatgacct tgaatctgat ggcaagggca aagttttggt ggaaaaggtc 2281 aagaacgcct ctgtacagac caacaacgag ttggccgggg ccctgcacca tctcaaacac 2341 gcccgaatca ggtactatgt caagtgtgtg caagaagcag tctattctat catacaaatt 2401 gccggcgctg cgtttgtcac cacgcgcatt gcacgccgca tgaacataca agaactctgg 2461 tcgaagccac aattggatca aaatgaatca gagactaagg aagaggcccc caagccagaa 2521 gatgacgagt tcgtcatatc ttgtaaggac atcaaggagg aaggaaagaa gggcaaaaat 2581 aaaactggcc gtggcaagaa acacactgca ttctccagca agggcttgag cgatgaggag 2641 tatgacgagt acaagaggat aagagaagag agaaatggga agtactctat agaggaatac 2701 cttcaagaca gagacaggta ctatgaagaa ctcgccattg ccaaggccac ggaagaagac 2761 ttctgtgaag aggaggagat aaaaatccgt cagagaattt tccgtcctac caggaaacaa 2821 aggaaggaag agagggccac attagggcta gtaacaggtt cagaaatcag aaaaagaaat 2881 cctgatgact tcaaacccaa agggaagctg tgggccgatg acaacagaag tgttgactac 2941 aatgagaagc tggattttga ggccccccca agcatatggt ctaggattgt gagctttggt 3001 tctggctggg gcttctgggt atcaccaagc ctgttcataa catcaactca tgtaatcccc 3061 acaggcataa cagaagcgtt tggagtcccc atcaaacaag ttcaaatcca caaatcaggt 3121 gaattttgcc gattcagatt cccaaagcca attagaccag atgtgacagg aatgatcttg 3181 gaagaaggtg cgcctgaggg caccgtggca actgtgctca tcaaacgccc caccggagag 3241 ctcatgcctc ttgcagccag aatgggaaca cacgcaacca tgaaaattca aggccgcatg 3301 gttggcggac agatgggcat gttgctcact ggatcaaatg ctaaaggaat ggatttggga 3361 acaactcctg gagactgtgg ctgtccttac atctataaaa ggggcaatga ctatatagtc 3421 attggggtgc acactgcagc agcccgtggt ggaaacaccg tcatctgtgc cacacaggga 3481 agtgagggtg aggcaactct tgagggtgga gatgacaaag gaacatattg tggggcaccc 3541 atcctaggcc ctgggggtgc accaaaattg agcaccaaaa ccaaattttg gaggtcatcg 3601 aacacgcccc ttccaccagg gacatatgag cctgcctacc tcggcggtcg tgacccgcgt 3661 gttaagggtg ggccctcctt gcagcaggta atgagagacc agttgaagcc attcactgaa 3721 cccaggggca aacctccaag accaagtgta ttggaagcag ccaaacaaac catcatcaat 3781 gtcctcgagc aaaccctgga ccctccacaa aaatggacat acgcacaggc gtgtgcctca 3841 cttgacaaaa caacctctag cggtcacccc tatcacgttc gaaagaatga attctggaat 3901 ggtgagacct tcactggtaa attggcagac caagcatcaa aagcaaacct aatgtttgag 3961 gaagggaaac acatgacacc agtgtataca gcagcactca aggacgagct agtcaagact 4021 gagaaaatct atggaaaaat caagaagaga ctgctctggg gctctgattt gtccaccatg 4081 atccggtgtg ctaggtcatt tggtgggctc atggacgaga tgaaggcaca ctgcatatca 4141 ctcccagtcc gagttggcat gaatatgaat gaagatggcc caataatatt tgagaaacat 4201 tctagataca aatatcacta tgatgcagac tactctcgtt gggattcaac acaacagagg 4261 gcagtactgg cagcagcctt ggaaatcatg gtcagattct ctgcagaacc acaattggca 4321 caaatagtcg ctgaggacct actggcccct agtgtagtag atgtaggaga ctttaaaatc 4381 acaataaatg aggggctccc ctctggtgtg ccatgcactt ctcaatggaa ctccatcgca 4441 cactggttgc taactctctg tgccttgtct gaagtcacta agctgtcacc tgacattata 4501 caggcaaatt ccatgttctc attttacggt gatgacgaga ttgtcagcac cgacataaaa 4561 ttggaccccg aacagttaac cgccaaattg aaggagtacg gtctaaaacc aacccgccca 4621 gacaaaaccg agggacccct gatcatcagt gaagatttga acggactcac tttcctccga 4681 aggacggtga ctcgtgaccc agctggctgg tttggaaaac tggaccaaag ctcaattttg 4741 aggcagatgt actggactag aggaccaaat catgaagacc ccaatgagac aatgataccc 4801 cattctcaaa ggcccataca gctcatggca ctgcttggtg aagcctctct tcacggaccc 4861 tctttctaca gtaaaatcag taaattggtc ataactgaac tcaaagaagg tgggatggac 4921 ttttacgtgc caaggcagga acccatgttc aggtggatga ggttttctga cctgagcacg 4981 tgggagggcg atcgcaatct ggctcccaat tttgtgaatg aagatggcgt cgaatgacgc 5041 cgttccatct aatgatggtg cagccggtct cgtaccagag gtcaacaatg agaccatggc 5101 acttgaaccg gtggctgggg cttcgatagc cgccccactc accggccaaa ataatgttat 5161 agacccctgg attagattaa attttgtgca ggcccctaat ggagagttta cagtctcacc 5221 ccgcaactcg cctggggaag tcctactcaa tttggaatta ggtcccgaat tgaatccata 5281 tttggcacac ctttctagaa tgtataatgg ttatgcaggt ggagttgagg tacaagtgct 5341 actggctggg aacgcgttca cggctggaaa attggtattt gctgcagttc cccctcattt 5401 tccattagag aatataagcc ctggtcaaat aaccatgttc cctcatgtaa ttattgatgt 5461 taggactttg gaaccagttt tattgcctct accagatgtc agaaataact tcttccatta 5521 caaccagcaa aatgagccga ggatgaggct tgttgcaatg ctttataccc ctcttagatc 5581 taatggttct ggtgatgatg tgttcaccgt ctcctgtagg gtgctcactc gaccctctcc 5641 tgattttgat tttaattatt tggtgccccc aacagttgaa tctaaaacaa aaccattcac 5701 actccctgtc ttgaccattg gggagttaac caattccagg ttccctgtgc ccatagatga 5761 actctacact agccccaatg agagtttggt ggttcaaccc cagaatggga ggtgcgcgct 5821 ggatggggag ttgcagggca ccacccagct ccttcccacg gcgatttgct cgttcagggg 5881 tcggatcaat cagaaagtga gtggagagaa tcatgtttgg aacatgcaag tcaccaacat 5941 taacggaacc ccttttgatc caacagagga tgttccagcc cctctgggca cgccagactt 6001 ttctggcaag ctctttggtg tcctaagcca gagggaccat gataatgcct gcaggagtca 6061 tgatgcagtg attgcaactg attctaccaa atttacccca aaattgggtg ctgtacaaat 6121 tggcacatgg gaacaagatg atgtacacat caaccaaccc accaagttta ctccagttgg 6181 attgtttgag aatgaaggtt ttaatcaatg gacacttcct aattattctg gagctttaac 6241 actcaatatg gggttggccc cccctgtggc ccccacattc cctggtgagc aaattctctt 6301 cttcaggtcc cacattcccc ttaaaggagg tgttgcagac ccagttattg attgtcttct 6361 accccaagag tggatccagc acctttatca ggagtcagcc ccttcacaaa cagatgtggc 6421 actgattaga ttcacaaatc cagacacagg gcgtgtccta tttgaagcaa aattgcacag 6481 gagtggttac atcacagtgg ccaacactgg tagcagacca attgtggtgc cagctaatgg 6541 ttatttcagg tttgactctt gggttaatca gttttactct cttgccccca tgggaactgg 6601 gaatgggcgc agaaggatgc agtaatggct ggagctttca tagcagggct tgccggtgac 6661 atagtcacca acagcattgg ctcactcgtg aacgctgggg ccaatgcaat aaaccagaaa 6721 gtagactttg aaaacaacaa gcaactacaa caggcatctt ttaaccatga caaagagatg 6781 ttgcaagctc aaattcaggc caccaaacaa ctacaggctg atatgattgc gatcagacaa 6841 ggggtgttga ccgcaggcgg cttctcccct actgatgcag caagaggtgc agtcaacgcg 6901 cccatgactc aagtcttgga ttggaatggg accagacatt gggcccccgg agccgcgaaa 6961 acaactgctt tctccggtgg gtttaccagt gcctctcatg ccaggaccgt tgacctgacc 7021 aagaagacat cagccacacc agcccctatg cctgtttcta ggcccagttc tattgcttcc 7081 actgtttcta ctcgctctac tttgattagt gggtcctctg attctccttc ttcagctagg 7141 agctcttcta gtgtttcttc ccaacccact tcctcatcct cccgaactag tgagtgggta 7201 cgcagtcaaa atagggcgct ggagccttat atgaatgggg cgctgcgtac agcctacgtg 7261 acgcctccat ccagtagggc ttctagcaat ggcacagtct caaccgtgcc aaaagaggtt 7321 ttggactcct ggtcgtctgc gtttaataca cacagacagc cgctgtttgc tcatctccgt 7381 cggagagggg agtcacaagc ttagtgaaaa gatggtcttt tctttctttc ctttgaaaa //