Typing tool
|
Complete norovirus genomes
MN960578 | GII.17 | ||
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GII.P17 |
ORF1: 1..5099 ORF2: 5080..6702 ORF3: 6702..7481LOCUS MN960578 7500 bp RNA linear VRL 15-MAR-2020 DEFINITION Norovirus GII isolate SCD1042 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MN960578 VERSION MN960578.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7500) AUTHORS Zhang,Z., Wang,D., Liu,D. and Zhang,Z. TITLE Whole Genome Analysis for Co-Infected Different Genotypes of Human Norovirus JOURNAL Unpublished REFERENCE 2 (bases 1 to 7500) AUTHORS Zhang,Z., Wang,D., Liu,D. and Zhang,Z. TITLE Direct Submission JOURNAL Submitted (21-JAN-2020) School of Agriculture & Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd. Minhang Dist, Shanghai 200240, China COMMENT ##Assembly-Data-START## Assembly Method :: CLC workbentch v. 2018 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7500 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="SCD1042" /isolation_source="anal swab" /host="Homo sapiens" /db_xref="taxon:122929" /country="China: Shanghai" /collection_date="18-Feb-2018" /note="genotype: GII.17[P17]" gene <1..5099 /gene="ORF1" CDS <1..5099 /gene="ORF1" /codon_start=3 /product="nonstructural polyprotein" /protein_id="QHJ14088.1" /translation="SNDASAAVAGKNNNNDKEKSSSDSLFANMSVTFKKALGARSKQP PPGETKQIQKPPRPPTPELVKRIPPPPPNGEDEPGIVYKVGEGVSGLPDLTTVVQPDA QNTAYSVPPLSQREVGEAKEPLPGSILEMWDGEIYHYGLYVERGNVLGVHKPPAAISL AKIEITPLSLYWRVVYTPQYLIDPGTLKNLSGETFPYTAFDNNCYAFCCWVLDLNDSW LSRRMIQRTTGFFKPYQDWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDIIGNL RPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYEMQGPEDL AVELVPVVMGGVGLVLGFTKEKIGKMLSSAATTLRACKDLGSYGLEILKLVMKWFFPK KEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTK SASPDIVGTINALLARIAAARSLVHKAKEELSSRQRPVVVMISGRPGIGKTHLARELA KKVASTLSGDQRIGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELADTCP LTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDIEKA KRDFPGQPDMWKDHFRPDFSHIKLQLAPQGGFDKNGNTPHGKGVVKSLTIGSLIARAS GLLHERMDEFELQGSDLPTFNFDRNKVAAFRQLAAENKYGLMDTLRVGNQLKNVKTLD ELKQAIKNISIKKCQIVYNGCTYTMESDGRGKVVVEKVQNATVQTNNELVGALHHLRS ARIRYYVKCFQEAIYSLLQIAGAAFVTSRIVRRMNVSNLWSKPPIEEGDEPEDRGGCP KPRDEDDLTIDSRDIKVEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT GSEIRKRNPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFWVSPS LFITSTHVIPKGITEAFGVPINQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGAPEGT VVSILIKRTTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDC GCPYIYKRGNDFVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGP GNAPKLSTKTKFWRSSNAPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR GKPPNPNVLESAKKTIINVLEQTIDPPQKWSYAQACASLDKTTSSGYPHHVRKNDYWS GESFTGKLADQASKANLMYEEGKHMQPVYTAALKDELVKTDKIYGKIKKRLLWGSDLS TMIRCARAFGGLMDEFKANCITLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDS TQQRAVLEAALEIMVRFSAEPQLAQIVAEDLLSPSVVDVGDFKIAINEGLPSGVPCTS QWNSIAHWLLTLCALSEVTGLGPDIIQANSMYSFYGDDEIVSTDIKLDPEKLTAKLKE YGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQLYWTRGPN HEDPSETMIPHAQRPVQLMALLGESSLHGPSFYSKVSKLVISELKEGGMDFYVPRQES MFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide <1..989 /gene="ORF1" /product="p48" mat_peptide 990..2087 /gene="ORF1" /product="NTPase" mat_peptide 2088..2624 /gene="ORF1" /product="p22" mat_peptide 2625..3023 /gene="ORF1" /product="VPg" mat_peptide 3024..3566 /gene="ORF1" /product="Pro" mat_peptide 3567..5096 /gene="ORF1" /product="RdRp" gene 5080..6702 /gene="ORF2" CDS 5080..6702 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QHJ14089.1" /translation="MKMASNDAAPSNDGAAGLVPEGNNETLPLEPVAGAAIAAPVTGQ NNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHLIVDVRTLEPIMIPLPD VRNTFFHYSNQPNSRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFTYLVPP SVESKTKPFSLPILTLSELTNSRFPVPIDSLFTAQNNVLQVQCQNGRCTLDGELQGTT QLLPSGICAFRGRVTAQINQRDRWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGVVFGM VSQRNVGSDAPGSTRAQQAWVSTYSPQFVPKLGSVNLRISDNDDFQFQPTKFTPVGVN DDDDGHPFRQWELPNYSGELTLNMNLAPPVAPNFPGEQLLFFRSFVPCSGGYNQGIID CLIPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVAHSGDYPLV VPANGHFRFDSWVNQFYSLAPMGTGNGRRRAQ" gene 6702..7481 /gene="ORF3" CDS 6702..7481 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QHJ14090.1" /translation="MAGAFIAGLAGDMLTSSVGSLVNAGANAINQKIDFENNKQLQSA SFQHDKEMLQAQVRATKQLQSEMIALKQGVLAAGGFSPTDAARGSIGAPMTKVLDWSG TRYWAPNSTKTTGYSGQFTSSPVHMSSPNAPQSKPAKPRSLAPSSSSSSVYSTYTQST HLTSGSSSNASSASTKLTNLSSGSSQNRTAEWVNQQRSLSPFMSGALNISHVTPPSSR ASSSGTVSTVPKEVLDSWTSAFNTHRQPLFAHLRVRGESRV" ORIGIN 1 cgtctaacga cgcttccgct gccgttgctg gcaaaaacaa caacaacgac aaggaaaaat 61 cttcaagtga cagcctgttt gctaacatgt ctgtcacctt taagaaagcc ctcggggcgc 121 ggtctaaaca accgcccccg ggagaaacaa aacaaataca aaaaccacca aggccaccga 181 caccggaatt ggtgaagaga atacctccac ccccacccaa tggcgaggat gaaccaggga 241 tagtgtacaa ggtgggagag ggtgtgtctg ggctgcccga cctgacaact gtggtacaac 301 ctgacgcaca aaacacagct tatagtgttc ccccacttag ccagagagaa gtcggcgaag 361 ctaaagaacc gctgcctggc tccattctgg aaatgtggga tggtgagatc taccactatg 421 ggctgtatgt tgagcggggg aatgtgctcg gagtacacaa accacccgct gcaataagcc 481 ttgccaaaat tgaaataaca ccgctgtctc tctactggag agtggtctac actccccagt 541 atttgataga tccaggaact cttaagaact tgagtggaga gactttccca tacacggcct 601 ttgacaacaa ctgttatgcc ttctgttgtt gggtcctaga cctcaacgac tcctggctta 661 gcaggagaat gatccaaaga acaactggat tcttcaaacc ttaccaggat tggaacagaa 721 aacccttacc aaccatggat gaaccgaaaa tcaagaaggc cgcgaatgct gtcctatgcg 781 ctctctcctc actcttcact aggcccatta aggacatcat tggaaatctt agaccactga 841 acattcttaa tatactggca acctgcgatt ggacttttgc aggcatagtg gaatccttga 901 tccttcttgc tgaactcttt ggggtgttct ggacaccccc agatgtgtct gcgatgattg 961 ctcccttact cggtgactac gagatgcaag gccccgaaga cctggccgtg gaacttgtgc 1021 ccgtggtgat gggaggagta ggtttggtgt taggattcac caaagaaaag atcggcaaga 1081 tgctttcatc agctgcgacc acacttaggg cctgcaagga tctaggatct tatggattgg 1141 agatactcaa attggtcatg aagtggttct tccccaagaa ggaggaggct aacgaactag 1201 ccatggtgag agccattgag gatgcagtcc tggatttgga ggcaatagaa aacaatcaca 1261 tgaccaccct tctcaaggac aaagacagcc tggccacata catgaggact cttgacttgg 1321 aagaagagaa agcaaggaaa ctgtcaacca aatcggcgtc acctgacatc gtgggtacaa 1381 taaacgcatt attggctagg atagcagccg ccaggtcact ggtccacaag gctaaggagg 1441 agctctcgag cagacagaga cctgttgttg taatgatatc aggtagacca ggtataggaa 1501 agacccatct ggccagagag ctagccaaga aagttgcgtc aacactgtca ggcgaccaaa 1561 ggattggact ggtacctaga aatggcgtcg accattggga cgcctacaag ggagaaaggg 1621 tggttctgtg ggatgattat ggtatgagca accctataca ggacgcactg aggctccaag 1681 aattggctga cacctgtcct ctgaccctaa attgtgatag gattgaaaac aaaggaaaag 1741 tgttcgacag tgatgccata attataacaa ccaaccttgc aaacccagca ccactagact 1801 atgtcaactt tgaggcctgc tctagacgca tagacttctt ggtgtatgca gacgcacctg 1861 acattgagaa ggctaagcgt gacttccctg gccaaccaga tatgtggaaa gaccatttca 1921 gaccagactt ctcacacatt aaacttcagc tggcaccaca gggaggtttt gacaaaaatg 1981 gcaacacccc acatggtaaa ggtgtggtga agtccctgac gattggttct ctgatcgcca 2041 gggcctccgg cttgctccac gagagaatgg atgaattcga gctccaaggc tctgacctgc 2101 caaccttcaa ttttgaccgc aacaaagtcg ccgccttcag acaattagca gctgaaaaca 2161 aatatggtct tatggacaca ctgagggtcg gcaaccaact gaaaaatgtt aagaccctgg 2221 atgagctgaa gcaggccata aagaacatca gtatcaagaa gtgtcagata gtgtataatg 2281 gatgcaccta taccatggaa tctgatggga ggggcaaggt tgtggttgaa aaggtacaaa 2341 acgcaacagt tcaaaccaac aatgaacttg taggggcgct ccaccacctg agatctgcaa 2401 ggataagata ctatgttaaa tgtttccaag aagccattta ctctctactc caaattgctg 2461 gtgcagcctt cgtcacctca cgcatcgtga ggcgcatgaa cgtgtcaaac ctctggtcga 2521 agccacccat cgaggaaggt gatgagcctg aagacagagg aggatgcccc aagcccaggg 2581 atgaagatga cctcactatt gactctagag acatcaaagt ggaagggaag aagggcaaga 2641 acaagtctgg ccggggcaag aaacacacag ccttctcttc caagggcctc agtgatgaag 2701 agtacgatga gtacaaaaga atcagagagg agaggaatgg taaatactca atagaggaat 2761 acctccaaga tagggacaga tactatgaag agcttgccat tgctaaggcc actgaggagg 2821 acttctgtga ggaggaggag atcaaaatcc gccagagaat cttccgaccc accaggaagc 2881 agcggaaaga ggagagggcc acgcttgggc ttgtcacagg atcggaaatc agaaagagga 2941 atccagatga ctttaaacca aaaggaaaat tgtgggctga tgacaacagg agcgtggatt 3001 acaatgagag gatagatttt gaggctcccc cgagtgtttg gtctaggata gtcaactttg 3061 gcacaggctg gggattctgg gtttctccaa gtctctttat aacttcaaca cacgtcatac 3121 caaaaggaat cactgaggcc tttggagtgc ccataaacca aatccaaatt cacaaatctg 3181 gagaattttg ccgcttgcgg tttccaaagc caattagacc agacgtgagt gggatgatct 3241 tggaagaggg cgcccctgaa ggcactgttg tgtctattct catcaaaagg acaacagggg 3301 agctaatgcc tcttgcagtc agaatgggga ctcatgccac aatgaaaatc caaggtagaa 3361 cggtgggtgg tcagatgggt atgcttctca ctggctcaaa tgctaaaagc atggacctag 3421 gcacaacacc aggtgactgc ggatgtccat acatatacaa aaggggcaat gactttgtgg 3481 tcattggggt gcacactgca gcggctcgtg gaggcaacac ggtcatatgt gccacacagg 3541 gaagtgaagg tgaagccact cttgaaggag gtgataacaa gggtacatat tgtggagctc 3601 ccattttggg acctggcaat gcaccaaaac tgagcacaaa gacgaaattc tggagatcct 3661 ctaacgcacc gcttccccca ggtacttatg aaccagcata ccttggtgga agagacccgc 3721 gcgtgaaggg aggcccatct ctgcaacaag ttatgagaga ccaacttaaa ccttttacag 3781 agcccagagg gaagccacca aacccaaatg tcttagagtc agcaaagaag actatcatca 3841 atgttctgga acaaaccatt gacccccctc aaaagtggtc atatgcccaa gcttgtgcat 3901 ccctcgacaa gacaacctcc agtggatacc cgcaccacgt ccggaagaat gactattgga 3961 gtggtgaatc cttcacagga aagcttgcag atcaggcttc aaaagcaaat ctcatgtatg 4021 aggaaggcaa gcacatgcaa ccagtttaca ccgcagcact caaagacgag ctcgtgaaaa 4081 ctgacaaaat ttatggcaaa atcaagaaaa gactcctgtg gggttctgac ctctccacaa 4141 tgattcgatg cgccagagca tttggtggtc tcatggatga attcaaagca aattgtatta 4201 cactccctgt cagagttggt atgaatatga atgaagatgg tcccataata tttgagaaac 4261 actccaggta taggtaccac tatgatgctg attactcccg ttgggactcc acacaacagc 4321 gggcagtgct ggaagcggca cttgaaatca tggtgagatt ttctgctgaa ccacagctgg 4381 cacaaatagt ggcagaggac ctgctgtcac caagtgtggt tgatgtgggc gatttcaaaa 4441 tcgctatcaa tgaaggccta ccatctggcg tgccttgcac ctcacaatgg aattctattg 4501 cccactggtt gcttaccttg tgtgcccttt ctgaagtgac aggattaggt cctgacatca 4561 tacaagctaa ctccatgtac tctttctatg gtgatgatga gattgtgagc acagacataa 4621 aattggaccc agagaaattg accgcaaagc tcaaagagta tggccttaaa cccactcggc 4681 ccgacaaaac tgaggggccg ttggtgatta gtgaggacct aaacgggttg actttcctcc 4741 gccgaacagt cacccgtgat ccagcaggtt ggtttggaaa gttggaccaa aactccatcc 4801 tcaggcagtt gtactggaca agaggaccca accatgaaga ccccagtgag accatgatac 4861 cacacgcaca aagacctgtg cagctcatgg cactactagg agaatcctcc ctacatggac 4921 cctcatttta cagcaaggtt agcaaattag tcatatctga acttaaagag ggaggaatgg 4981 atttttatgt gcccagacaa gagtcaatgt tcagatggat gaggttctca gatctaagca 5041 catgggaggg cgatcgcaat ctggctccca gttttgtgaa tgaagatggc gtcgaatgac 5101 gccgctccat ctaatgatgg tgctgctggt ctcgtaccag agggcaacaa cgagaccctt 5161 cccctagaac cagttgcggg cgcagctata gccgcacccg tcactggcca aaataacata 5221 attgacccct ggattagaac aaattttgtg caagcaccaa atggagagtt cacagtatca 5281 cccagaaact ctcctggaga aattttatta aacttagagt tgggtcctga tttgaaccct 5341 tatttggctc atttgtcaag gatgtacaat gggtatgctg gtggagtgga agttcaggtt 5401 ctcctggcag ggaacgcgtt cactgccgga aagatcctct tcgccgctgt cccgccaaat 5461 ttcccagtgg aattcttaag cccagcccag atcacaatgc tcccacattt aatagtagat 5521 gttaggactc ttgaaccaat tatgatccca ctccctgatg ttaggaatac attcttccat 5581 tatagtaacc agccgaacag ccgcatgaga ttagtggcta tgctctatac cccacttagg 5641 tctaatggct caggtgatga tgtctttact gtctcttgca gggttttgac taggcctact 5701 cctgattttg agttcactta tctagtgcca ccttctgttg aatctaaaac taagcctttt 5761 tccttgccta ttttaaccct ttctgagctt acaaattcga ggttcccagt tcccatcgat 5821 tcgcttttca ccgcccagaa taacgtgttg caggtgcagt gtcaaaatgg caggtgtaca 5881 cttgatggtg agttacaagg cacaacccag ttgctcccat ctggcatctg tgcattcaga 5941 ggacgggtga cagcacaaat taaccaacgt gacaggtggc acatgcaact gcaaaacctc 6001 aatggtacaa catatgaccc aactgatgat gtgccagccc cgctgggtac acctgacttc 6061 aagggcgtcg tgtttgggat ggttagccaa agaaatgtgg gtagtgatgc gcctggctca 6121 accagagccc aacaggcgtg ggtttcaacc tatagccccc aatttgtccc caaattaggt 6181 tctgtcaatc ttagaattag tgataatgat gatttccaat tccaaccgac aaaattcaca 6241 ccagtgggcg tcaatgatga cgatgatggc cacccgttca gacaatggga actaccaaac 6301 tattcagggg agcttacctt gaatatgaat cttgcccccc cagttgctcc aaattttcct 6361 ggtgaacaat tgttattctt cagatctttc gtgccatgct caggaggtta caaccaaggt 6421 attatagatt gtcttattcc ccaagaatgg atccaacact tctatcagga atcagcaccc 6481 tcccagtcag acgtggccct aatcaggtat gtcaaccccg atacgggacg tacactgttt 6541 gaagcaaaat tgcacagatc tggttatatt actgtggctc actctggaga ctatcctctt 6601 gttgttccgg ctaatggaca ctttagattt gattcttggg taaatcagtt ttactcactc 6661 gccccaatgg gaactgggaa tgggcgtagg agggctcagt aatggctggg gctttcattg 6721 cagggttggc aggcgacatg ctcacgtcat ctgtgggctc ccttgtgaac gcaggggcaa 6781 acgccatcaa tcaaaagata gactttgaaa acaacaaaca actccagtct gcttcctttc 6841 agcatgataa agagatgctc caagcgcagg tgagggcaac caagcagctg caatctgaaa 6901 tgatagccct aaaacagggg gttttggccg caggcggctt ttcccccact gatgcagcaa 6961 ggggatccat tggtgccccc atgacaaagg tgcttgactg gtctggcact cgatactggg 7021 cgcccaattc cacaaagaca actggctatt cgggacaatt cacctcttca cctgtgcata 7081 tgtctagccc aaatgctcca caatcaaaac ctgcaaagcc taggtctcta gctccttcct 7141 cttcttctag cagtgtctat agtacgtata ctcaatctac tcatttgaca tctggctctt 7201 ctagtaatgc ttcttctgcc tccacaaaat tgacaaattt aagctctggc tcctctcaaa 7261 acagaacagc agagtgggta aatcaacaga gaagtcttag ccctttcatg agtggcgcac 7321 ttaacatctc acatgtcacg ccaccctcaa gtagggcttc cagttctggg acggtctcga 7381 ccgtgcccaa ggaagttttg gactcctgga cgtctgcgtt taacacacac agacagccgc 7441 tcttcgcgca cctcagagtg aggggggagt cacgtgttta gtgaaaagaa ataattggcc //