Typing tool
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Complete norovirus genomes
KY442320 | GII.3 | ||
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GII.P41 |
ORF1: 5..5110 ORF2: 5091..6737 ORF3: 6737..7501LOCUS KY442320 7527 bp RNA linear VRL 14-AUG-2017 DEFINITION Norovirus GII.3 strain Hu/US/1972/GII.Pg_GII.3/ShippensburgC2, complete genome. ACCESSION KY442320 VERSION KY442320.1 KEYWORDS . SOURCE Norovirus GII.3 ORGANISM Norovirus GII.3 Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7527) AUTHORS Johnson,J.A., Parra,G.I., Levenson,E.A. and Green,K.Y. TITLE A large outbreak of acute gastroenteritis in Shippensburg, Pennsylvania, 1972 revisited: evidence for common source exposure to a recombinant GII.Pg/GII.3 norovirus JOURNAL Epidemiol. Infect. 145 (8), 1591-1596 (2017) PUBMED 28294087 REFERENCE 2 (bases 1 to 7527) AUTHORS Johnson,J.A., Parra,G.I., Levenson,E.A. and Green,K.Y. TITLE Direct Submission JOURNAL Submitted (10-JAN-2017) LID/NIAID, NIH, 50 South Drive-MSC8026, Bethesda, MD 20892, USA COMMENT ##Assembly-Data-START## Assembly Method :: SAMtools v. 1.3 Assembly Name :: Shippensburg norovirus Coverage :: 3,367 median depth Sequencing Technology :: Generated consensus from Ion Torrent NGS data; IonTorrent; Sanger dideoxy sequencing ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7527 /organism="Norovirus GII.3" /mol_type="genomic RNA" /strain="Hu/US/1972/GII.Pg_GII.3/ShippensburgC2" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:490041" /country="USA" /collection_date="1972" gene 5..5110 /gene="ORF1" CDS 5..5110 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="ARA95793.1" /translation="MKMASNDASAAAAATSNNDNAKSSSDGVLTSMAVTFKRALGARP KQPSPRETTQKQKPPRPPTPELVKKIPPPPPNGEDELVVSYSVKDGVSGLPELSTVSQ PNEANTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAA ISLAKVELTPLSLYWRPVYTPQYLIAPDTLRKLHGESFPYTAFDNNCYAFCCWVLDLN DSWLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKMANIILCALSSLFTRPIKDII GKLRPLNILNILASCDWTFAGVVESLILMAELFGVFWTPPDVSAMIAPLLSDYELQGP EDIAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF FPKKDEANELAMVRSIEDAVLDLEAIENNHMTSLLKDKDSLATYMRTLDLEEEKARRL STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAR ELAKKIAATLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELAD TCPLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDV EKAKRDFPGQPDMWKDAFRSDFSHIKLMLAPQGGFDKNGNTPHGKGIMKTLTSGSLIA RASGLLHERLDEYELQGPTPTTFNFDQNKVFAFRQLAAENKYGLMDTMRVGSQLKGVK TVSELKQALKNIAIKRCQIVYGGLTYSLESDGKGNVKVERVQSTTVQTNNELSGALHH LKCARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSRPQVEDAEEVINRD GCPKPKDDEEFVISSEDIKAEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREER NGKYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLG LVTGSEIRRRNPDDFKPKGKLWADDDRSVDYNERLSFEAPPSIWSRIVNFGSGWGFWV SPSLFITSTHVIPQGSQEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAP EGTVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTP GDCGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGNEGEAILEGGDNKGTYCGAPI LGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFT EPRGKPPNPSVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNE CWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGS DLATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYKYHYDADYSR WDSTQQRAVLAAALEIMVKFSSEPHLAQIVAEDLLSPSVMDVGDFKISITEGLPSGVP CTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAK LKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTR GPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVIAELKEGGMDFYVPR QEPMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" gene 5091..6737 /gene="ORF2" CDS 5091..6737 /gene="ORF2" /codon_start=1 /product="major capsid protein VP1" /protein_id="ARA95794.1" /translation="MKMASNDATPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSARNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKVIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPINLPMPD VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFTLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT QLLPSQICALRGTLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPAP LGTPDFRGKVFGVASQRNPDSTTRAHEAKVDTTSGRFAPKLGSLEISTESSDFDSNQP TRFTPVGIGVDNEADFQQWSLPDYSGQFTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG GRSNGILDCLVPQEWVQHFYQESAPAQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" gene 6737..7501 /gene="ORF3" CDS 6737..7501 /gene="ORF3" /codon_start=1 /product="minor capsid protein VP2" /protein_id="ARA95795.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNSGASAINQKVDFENNKYLQNA SFAHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWSG TRYWAPNATSTTSMSGGFTSQTVHRTAPNFKTNQAPKSTPSSGSSVRSNSTQLTSLSS HSSGSSRSSGSTVVSSLPSSNRTRDWVNQQNLNLEPHMPGSLRTAFVTPPSSTASSSG TVSTVPKSVLDSWTSAFNTRRQPLFAHLRRRGESNV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgctacca gcaacaacga 61 caacgcaaaa tcttcaagtg acggagtact aactagtatg gctgtcactt ttaaacgggc 121 cctcggggcc cggcctaaac agccgtcccc gagggaaaca acacaaaaac aaaagccccc 181 acgaccgccc actccggagt tggtcaaaaa gatcccgcct cccccaccaa acggggagga 241 cgaactagtg gtctcctata gtgttaaaga cggcgtctcc ggtttgcccg aactttctac 301 cgtcagtcag ccgaacgagg ccaacacagc attcagtgtc cccccactca atcagaggga 361 gaacagggac gctaaagagc cactaactgg caccattctg gaaatgtggg acggggagat 421 ctaccattat ggcctgtacg tggaacgggg cctggtgctc ggagtacaca aaccaccagc 481 ggctatcagt cttgccaagg ttgagttgac accactgtct ctatactgga gaccagtgta 541 caccccccag taccttatag ctccagacac tctcagaaag ctacatggag agtcatttcc 601 ttacacggcc tttgacaaca actgttatgc cttctgttgc tgggtcctag acctgaacga 661 ctcttggctt agcaggagaa tgatacagag aacaactggc tttttcaggc cctaccagga 721 ctggaacaga aagcccctcc ctaccatgga tgactccaaa ttgaaaaaga tggccaatat 781 aatcctgtgt gctttgtcat cactgttcac caggcccatc aaggatataa ttggaaaatt 841 aagaccttta aacatcctta acatattggc ttcctgcgat tggacttttg caggcgtagt 901 ggaatcctta atcctcatgg cagagctctt tggagttttc tggacacccc cagatgtgtc 961 tgcgatgatc gcccccttac taagtgacta tgagctacag ggacctgaag acattgctgt 1021 agaactcgta ccagtagtga tgggggggat aggcttggtt ctaggtttca ccaaagaaaa 1081 gattggcaaa atgctatcat ctgctgcgtc cacgcttaga gcgtgtaaag accttggagc 1141 atacggattg gaaattctaa aactggtcat gaaatggttc ttcccgaaga aagatgaggc 1201 aaacgaactt gcaatggtga gatccattga ggacgcagtg ttggacctag aagcaattga 1261 aaacaaccac atgacttctt tgctcaaaga caaggacagc ctggcaacct acatgagaac 1321 cctagatctt gaagaggaga aggccaggag actctccaca aaatctgcct cacctgacat 1381 cgtaggcaca atcaacgccc tgctagcaag gatcgcggcc gctcgttccc tggtgcatcg 1441 ggcaaaagag gagctttcta gcagaccaag gcccgttgtt gtgatgatat caggtaagcc 1501 aggaatagga aagacccacc ttgctagaga attggcaaag aagatcgcag ccaccctcac 1561 aggagatcag agggtgggcc tcgtcccacg taacggcgtc gaccactggg atgcatacaa 1621 aggtgaaaga gttgtccttt gggatgacta tgggatgagc aaccccattc acgacgccct 1681 taggctgcaa gaacttgctg acacttgccc cctaacacta aactgtgata gaattgagaa 1741 caagggaaaa gtctttgaca gtgatgctat aattattaca actaatctgg ccaacccagc 1801 accactggac tatgttaact ttgaagcatg ctcaaggcgt attgacttcc tcgtgtatgc 1861 tgatgcccct gatgttgaga aggcaaagcg cgacttccca gggcagcctg acatgtggaa 1921 ggatgccttt agatctgact tctcacatat aaagctgatg ttggctcctc agggtggttt 1981 tgataagaac ggcaacactc cacatgggaa gggtatcatg aaaaccctta catctggctc 2041 tctcattgct cgtgcgtcag ggctcctcca tgaaagactg gacgaatacg agttgcaagg 2101 cccaacaccc acaacattca acttcgacca gaataaggtt tttgctttca ggcaactcgc 2161 tgctgaaaat aaatacgggc tgatggacac tatgagagtg ggaagtcagc tcaagggtgt 2221 caaaaccgtg tcagagctca agcaggcgct caagaacatc gcaatcaaaa gatgccagat 2281 agtctacggt ggtctcacat actcacttga atctgatggc aaaggcaatg tgaaggttga 2341 gagagtgcag agtacaactg tacaaaccaa caatgagcta tctggcgctc tacaccatct 2401 caagtgcgcc aggatcaggt actatgttaa gtgtgtccag gaggccctgt attctatcat 2461 ccagattgct ggggctgcat ttgtcaccac gcgcattgca aaacgcatga acatacaaaa 2521 tctttggtct aggccacagg tagaggatgc agaagaggtc atcaatagag acgggtgtcc 2581 aaaaccaaaa gatgatgagg agtttgtcat ctcatctgaa gacatcaaag ctgagggcaa 2641 gaaaggaaag aacaagtccg gtcgtggcaa gaaacacaca gccttctcaa gcaagggtct 2701 cagtgatgag gagtacgatg aatacaaaag aattagggaa gaaaggaatg gtaagtactc 2761 tatagaagaa tacctccagg acagagacaa gtattatgaa gaggtggcca tagccagggc 2821 tactgaagag gacttctgtg aagaagagga agccaagatc cgacagagga tttttagacc 2881 aacgaggaaa caacgtaaag aggagagggc ttctcttggc ctggtcacag gctcagaaat 2941 cagaaggagg aacccagatg acttcaaacc caagggaaaa ttgtgggctg atgacgacag 3001 aagtgtcgat tacaacgaaa gacttagttt tgaagctccc ccaagcattt ggtcgagaat 3061 agtcaacttt ggttcaggtt ggggtttctg ggtttcacct agtctgttca taacatccac 3121 tcatgtcata cctcaaggat cacaggagtt cttcggggtt tccattaagc aaatccaaat 3181 ccacaaatcg ggtgagttct gccgcctaag attcccaaaa ccaatcagaa ctgatgtgac 3241 aggcatgatc ttggaagaag gggcccctga aggaacagtg gccacactac tcataaagag 3301 accaactggg gaactcatgc cactggcagc taggatgggc acccatgcaa ccatgaagat 3361 ccagggtcgc actgttgggg gccagatggg aatgctcttg acaggatcta atgctaagag 3421 catggatctg ggcaccacac caggtgactg tgggtgtccc tacatctaca aaagaggaaa 3481 tgactacata gtcattggag tccacacggc cgctgctcgc ggagggaata ctgtcatctg 3541 tgcaacccag ggaaacgagg gtgaggccat acttgaaggt ggtgataaca aaggcaccta 3601 ctgcggtgcc ccaatcctag gcccaggaag tgcccccaag ctcagcacca agaccaaatt 3661 ctggaggtcc tcaacagcac cactcccacc tggaacatat gagccagcct accttggagg 3721 taaggacccc agagttaaag gtggcccctc actacaacaa gtaatgagag accaattaaa 3781 accattcaca gagcccaggg gcaaaccacc aaacccgagt gtgctagagg ctgccaaaaa 3841 gaccatcatc aatgtcctcg aacagacaat agacccaccc caaaaatggt cgtttgcgca 3901 agcttgcgca tctcttgata agaccacctc tagtggccat ccgcaccaca tgcggaagaa 3961 tgaatgctgg aacggagagt ccttcacagg gaaattggca gaccaagcct caaaagccaa 4021 cctaatgttt gaggaaggga aaaacatgac cccagtctac acaggtgccc tcaaggatga 4081 gctagttaaa actgataaaa tatatggtaa aattaagaag aggctcctct ggggatcgga 4141 tctggcaacc atgatccgtt gtgctcgagc attcggaggg ctaatggatg aactcaaggc 4201 tcactgtgtc acactcccta ttagagttgg aatgaacatg aatgaggatg gccctattat 4261 ctttgagaaa cactctagat acaaatacca ttatgatgca gactactctc ggtgggattc 4321 aacacagcag agagctgtac tggctgcagc cctagaaatc atggtcaaat tttcttcaga 4381 accacaccta gcccagatag tcgcagaaga ccttctgtct cccagtgtga tggacgtggg 4441 cgacttcaaa atatcaatca ctgaaggact cccttctggg gtgccttgca cctcacaatg 4501 gaattctatt gcccattggc tcctcacact ctgtgcactc tccgaggtga caaacttatc 4561 ccctgatatt atccaagcca attctctttt ctctttctat ggtgatgatg aaattgtgag 4621 tacagatatt aaattggatc cagaaaaact gacagctaaa ctgaaagagt atgggctaaa 4681 accaacacgc cctgataaga ctgaagggcc tctggtcatc tctgaggacc tgaatggtct 4741 gaccttcctg cggaggactg tgacccgcga tccagctggt tggtttggaa aattggaaca 4801 gagttcaata cttagacaaa tgtattggac caggggtcca aatcatgagg acccctctga 4861 aacaatgata ccacattccc agagacctat acagctaatg tccctgctag gtgaagctgc 4921 actgcatggc ccatcattct acagcaagat cagcaagcta gtcattgcag agttgaagga 4981 aggtggcatg gatttttacg tgcctagaca agagccaatg tttcggtgga tgaggttctc 5041 agacttgagc acgtgggagg gcgatcgcaa tctggctccc agtttcgtga atgaagatgg 5101 cgtcgaatga cgccactcca tctaacgatg gtgccgccgg cctcgtccca gagatcaaca 5161 atgaggcaat ggcgctagag ccagtggcag gtgcagcaat agcagcaccc ctcactggcc 5221 agcaaaatat aattgatccc tggattatga ataattttgt gcaagcacct ggtggtgagt 5281 ttacagtgtc agctaggaac tcccctggtg aagtacttct taatttagaa ttaggtccag 5341 aaataaaccc ctatttggct caccttgcta ggatgtacaa tggttatgca ggtgggtttg 5401 aagtgcaggt agtcctggct ggaaatgcgt ttacagcagg aaaggtgatc tttgcagcta 5461 taccccccaa ttttccaatt gacaatctga gcgcagcaca gattacaatg tgcccgcatg 5521 tgatcgtgga tgtcaggcaa ttggaaccaa tcaaccttcc gatgcctgat gtccgtaata 5581 atttctttca ttataatcaa gggtctgatt cgaggttacg cttaattgca atgttataca 5641 cacctcttag ggcaaataat tcaggagatg atgttttcac tgtgtcttgt agagtattaa 5701 ctaggcctag ccctgatttc tcattcaatt ttcttgttcc acccactgtg gaatcaaaga 5761 caaagccttt caccctcccc attttgacta tctctgaaat gtctaattcc aggtttccag 5821 tgccaattga ctctctgcac accagcccga ctgagaatat tgttgtccag tgccaaaatg 5881 ggcgcgtcac ccttgacggt gagttaatgg gcaccaccca actcttgccg agtcaaatat 5941 gtgctctcag gggcacgctc accagatcaa caagcagggc cagtgaccaa gccgacacgg 6001 caacccctag gctgttcaat tattattggc acatacaatt ggataatcta aatggaaccc 6061 cctacgaccc tgcagaagac ataccagccc ctttgggaac accagacttc cggggcaagg 6121 tctttggcgt agctagccag agaaaccctg acagcacaac aagagcacat gaagcaaaag 6181 tggacacaac atctggtcgc ttcgccccga aattgggttc cctagaaata tccactgaat 6241 ccagtgactt tgactcaaat caaccaacaa ggttcacccc agttggcatt ggggttgaca 6301 atgaggcaga ttttcagcaa tggtccttac ctgactactc cggtcagttc actcataaca 6361 tgaacttagc cccagctgtc gcccccaatt tccctggtga gcagcttctt ttcttccgct 6421 cacagttgcc atcttctggt gggcggtcta acgggattct agactgcctg gttccccagg 6481 aatgggttca acacttctac caggaatcag cccctgccca aacacaggtg gccctggtta 6541 ggtatgttaa ccctgacact ggtagagtgc tatttgaggc caagctacac aaattgggct 6601 tcatgactat agctaagaat ggtgactctc caataactgt ccctccaaat gggtacttta 6661 ggtttgaatc ttgggtgaac cccttttata cacttgcccc catgggaact ggaaatgggc 6721 gtagaaggat tcaataatgg ctggagcttt tatagcagga ttggctggtg acatgctcac 6781 aaatactgta ggatctttag ttaattcagg ggctagtgcc atcaatcaaa aagttgattt 6841 tgaaaataat aaatatttac aaaatgcatc ttttgctcat gataaggaga tgttaaatgc 6901 acaaattgag gcaacaaaga ggctacaggc tgacatgatt gctatcaaac aaggggtctt 6961 gaccgctggc ggcttctccc ccactgatgc agcccgtggg gcaattaatg cccccatgac 7021 aaaagttttg gattggagtg gaacgaggta ctgggcacca aacgccacct ccacaacctc 7081 aatgtcaggt ggcttcacaa gccaaactgt gcacagaacc gcaccaaatt ttaaaacgaa 7141 ccaggccccc aagtccacac ccagcagtgg gtcttcagtg aggtcaaatt caacccaact 7201 cactagcttg agctcacact cctccgggtc gtctcgatcc agcgggtcta cggttgtcag 7261 ctcattgcca tcttccaaca ggactaggga ttgggtcaat caacagaatc tcaatttgga 7321 accacacatg cctggatctc ttaggacagc ttttgtcact ccaccatcta gtacagcctc 7381 tagttcaggc acggtctcaa ccgtgcccaa aagtgttttg gactcctgga catctgcgtt 7441 taatacgcgc agacaaccgc tattcgcaca ccttcgtaga aggggggagt caaatgttta 7501 gtgaaaagat tattttaaat ttaattt //