Typing tool
|
Complete norovirus genomes
MF140689 | GII.3 | ||
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GII.P21 |
ORF1: 1..5088 ORF2: 5069..6718 ORF3: 6718..7479LOCUS MF140689 7531 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2012/GII.P21-GII.3/Rotterdam/E1300327_p7_d637 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140689 VERSION MF140689.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7531) AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E., Verjans,G.M.G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T., Cotten,M.L. and Koopmans,M.P.G. TITLE Whole genome next generation sequencing to study within-host evolution of chronic norovirus infection among immunocompromised patients JOURNAL J. Infect. Dis. (2017) In press PUBMED 29029115 REMARK Publication Status: Available-Online prior to print REFERENCE 2 (bases 1 to 7531) AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E., Verjans,G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T., Cotten,M.L. and Koopmans,M.P.G. TITLE Direct Submission JOURNAL Submitted (19-MAY-2017) Centre for infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven, Utrecht 3721 MA, Netherlands COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. 3.9.0 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7531 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2012/GII.P21- GII.3/Rotterdam/E1300327_p7_d637" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="20-Nov-2012" /note="genotype: GII.P21-GII.3" CDS <1..5088 /codon_start=1 /product="ORF1" /protein_id="ATN23763.1" /translation="SNDASAAAAANSNNDNAKSSSDGVLSNMAVTFKRALGARSKQPP PRDIPPKPPRPPTPELVKAIPPPPPNGEDEPTISYNVKEGVSGLPELSTVTQLEENST AFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAVSLAKI ELTPLSLYWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSR RMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGKLKPL NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE KNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLSTKSAS PDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKI ASSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL NCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEKAKRD FPGQPDMWKDTFKPDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTASSLVARASGLL HERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTMTELK QALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGALHHLKCARI RYYVKCVQEALYSILQIAGAAFITTRITKRMNIQNLWSKPQAEDLEETNNEEGCPKPK NDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE IRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI TSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVAT LLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP YIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILGHGNA PKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKP PKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCWNGET FTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGTIKKRLLWGSDLSTMI RCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQ RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCTSQWN SIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGL KPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHED PFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQEPMFR WMRFSDLSTWEGDRNLAPCFVNEDGVE" CDS 5069..6718 /codon_start=1 /product="ORF2" /protein_id="ATN23764.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTDNIVVQCQNGRVTLDGELMGTT QLLPSQICAFRGVLTRSTSRASDQADTAAPRLFNYYWHIKLDNLNGTPYDPAEDMPGP LGTPDFLGKVFGVASQRDPDTTTRAHEAKIDTSSGRFAPKLGSLEISTESADFNPNKP TRFTPVGIGVDQAEGDFQQWTLPDYAGAITHNMNLAPAVAPNFPGEQLLFFRSHLPSS GGRSDGILDCLVPQEWVQHFYQESAPSQSQVALIRYINPDNGRVLFEAKLHKLGFITI AKNGNSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" CDS 6718..7479 /codon_start=1 /product="ORF3" /protein_id="ATN23765.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKHLQNA SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSMSGGFTNQTVHRSTPNFKTNQAPRPAPSSGSSVRSNSTQITSLSS HSSGSSRSSGSTVVSSISTNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSSASSSGT VSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV" ORIGIN 1 tctaacgacg cttccgctgc cgctgctgcc aacagcaaca acgacaacgc aaaatcttca 61 agtgacggag tattatctaa tatggctgtc acttttaaac gagccctcgg ggcgcggtct 121 aaacagccgc ccccgaggga cataccacca aaacccccaa gaccacccac accagagttg 181 gttaaggcaa tcccccctcc cccacccaac ggggaggacg aaccaaccat ttcttataac 241 gtcaaagaag gtgtttctgg tttgcctgaa ctctcaactg tcacccaact agaggagaac 301 tctacagcgt tcagtgttcc ccctcttagt cagagggaga acagggatgc taaggaacca 361 ctgactggaa ccatcctgga gatgtgggac ggggagatct accattatgg cttatacgtg 421 gaacgagggt tagtgctcgg tgtacacaaa ccaccggcag ccgtcagtct tgctaagatt 481 gagctgaccc ccttgtcttt gtattggaga ccagtgtaca ccccacagta cctcatttcc 541 cctgacactc tcaaaaagtt gcatggggag acgttccctt atacagcctt tgataacaac 601 tgttatgcct tctgctgttg ggtacttgac ttgaacgatt catggctgag cagaaggatg 661 atacagagga caacaggctt cttccgaccc taccaggact ggaacaggaa acccctcccc 721 acgatggatg attccaaagt gaaaaaggtg gccaatgttg tcctttgtgc tctctcatca 781 ttgttcacaa gaccaattaa ggacattatt gggaagttga aacccctaaa catccttaac 841 atcctagcca catgtgattg gacttttgca ggcatagtgg aatccctgat ccttttggct 901 gaactgtttg gagttttctg gacaccccca gatgtgtctg caatgatcgc tcccttactg 961 ggtgattatg agctacaggg acccgaggac ctcgctgtgg aactcgtacc cgtagtaatg 1021 ggagggatag gtttggtgct gggattcacc aaagagaaaa ttggaaaaat gctttcatct 1081 gctgcttcaa ccctgagggc atgcaaagat ctcggtgcat atgggttgga gatcctcaag 1141 ttggtcatga aatggttttt cccaaagaaa gaagagaaaa acgaattggc aatggtgaga 1201 tccatcgagg atgcagtgct agatcttgag gccattgaga acaaccatat gacagctcta 1261 ctcaaggata aagacagcct tgcaacctac atgaggactc ttgacatgga ggaggagaaa 1321 gcgaggaaac tttccaccaa gtctgcctcg ccggatatcg tgggcacgat aaacgcccta 1381 ctgtcaagaa ttgctgctgc ccggtctcta gtgcacaggg ctaaggagga gctgtcaagc 1441 aggccccgac cagtcgttgt gatgatttca gggagaccag gtattgggaa aacccaccta 1501 gctagagagt tggcaaagaa gatcgcctcc tcactcacag gtgaccagag ggtgggtctt 1561 atcccacgca acggggtcga ccactgggat gcatacaaag gtgaaagagt cgttctctgg 1621 gacgactacg ggatgagcaa ccccattcac gacgccctca gactccagga gctcgctgac 1681 acctgtcctc tcacactcaa ctgtgacagg attgagaata aaggcaaagt ctttgacagt 1741 gacgccataa taataaccac caatttggcc aacccagcgc cactggatta cgttaacttt 1801 gaagcttgct caagacgcat agatttcctc gtctatgctg atgcccctga agttgagaag 1861 gccaaacggg acttcccagg ccaaccagac atgtggaaag acacctttaa acctgacttc 1921 tctcacataa aactgacatt agccccgcaa ggaggttttg acaagaatgg taacactcct 1981 catgggaagg gtgtcatgaa gaccctcaca gccagttctc tcgttgcccg agcatcaggt 2041 ctccttcacg agagattgga cgaatatgaa ctgcagggcc caacccccac aacattcaac 2101 ttcgaccgca acaaggtgct tgcttttagg cagcttgctg ctgaaaacaa atacggtctt 2161 gttgacacaa tgagggtcgg atcacagctc aagaatgtta aaaccatgac agaactcaag 2221 caggctctca agaacatctc agtcaagaaa tgtcagcttg tgtatggtgg gggcacgtac 2281 acacttgaat ctgatggcaa aggcaatgtg cacgtcgaga aggtgaacaa cactagtgtg 2341 caaactaaca acgagctctc cggggctttg caccatctca agtgtgccag aattaggtac 2401 tatgttaagt gtgtccagga agctctctac tccatcctgc aaattgccgg ggctgcattc 2461 atcaccacgc gcatcacaaa gcgcatgaac atacaaaacc tctggtccaa accacaagca 2521 gaagatctgg aggagaccaa caacgaggag ggctgtccaa aacctaaaaa tgatgaggaa 2581 tttgttatct cctctgatga catcaaaacc gagggcaaga aaggaaagaa caagactggc 2641 cgtggtaaga agcacacagc cttttccagc aaaggactca gtgatgagga gtacgatgag 2701 tacaagagaa tcagggaaga gagaaatggc aagtactcca tagaggaata cctacaggac 2761 agagacaaat actatgagga ggtggccata gccagggcaa ctgaagagga cttctgtgaa 2821 gaagaggagg ctaaaatccg gcagaggata ttcagaccaa caaggaaaca acgcaaagag 2881 gaaagggcct ctcttggttt ggttacaggt tctgagatca ggaagagaaa cccagatgac 2941 ttcaagccca aagggaaact atgggccgat gatgacagga atgttgacta caatgagaaa 3001 cttagtttcg aggctccacc aagcatttgg tcacgaatag tcaactttgg ctcagggtgg 3061 ggcttttggg tctcgcccag cctcttcata acatcaaccc atgtcattcc ccaaggcgca 3121 caggagttct ttggagtgcc catcaaacaa atacaaatcc acaagtcagg tgagttctgc 3181 cggcttaggt tcccaaaacc aatcagaacg gatgtcacag gcatgatctt ggaggaaggt 3241 gctccagaag gcactgttgc cacacttctc atcaagagac caactggaga actcatgccc 3301 ttggcagcca gaatgggcac ccacgcaacc atgaaaattc agggtcgcac tgttggtgga 3361 cagatgggca tgctactcac agggtccaac gctaagagca tggatttggg cacaactcct 3421 ggcgattgtg gttgtcccta catctacaag agagggaacg actacgtggt cattggagtt 3481 cacactgccg ccgctcgtgg aggaaacacc gtcatctgtg caacccaagg aaacgagggg 3541 gaggccatgc tagaaggtgg tgacaacaag ggaacttact gtggagcacc aatattaggc 3601 catggaaatg cccccaaact cagcaccaaa accaaattct ggaggtcttc caccaccccc 3661 ttgccacctg gaacctatga gccagcctat ctgggtggca aggaccccag agtgaaaggt 3721 ggcccctcac tgcaacaggt tatgagggac caactaaaac cattcactga gcccagaggc 3781 aaaccaccca aaccaagtgt gctagaagcc gccaagaaga ctataatcaa tgtgcttgaa 3841 caaacaatag acccacctca aaaatggaca tacgcgcagg cgtgtgcatc actagacaag 3901 accacctcca gcggccaccc tcaccacatg cggaagaacg attgttggaa tggggagact 3961 ttcacaggaa aattggcaga ccaagcatca aaggctaacc taatgtttga ggaagggaag 4021 aacatgaccc cagtatacac aggagctctg aaagacgagc tagtcaagac tgataagatc 4081 tatggaacaa tcaagaagag actcctgtgg ggttcagacc tatcaactat gatacggtgt 4141 gcacgagcct tcggtgggct aatggacgag ctcaaggccc actgcgtcac actaccagtc 4201 agggttggta tgaacatgaa tgaggatgga cccataatat ttgagaaaca ttccagatat 4261 aaatatcatt atgatgcaga ttactcccgc tgggactcaa cacaacaaag agcagtgctg 4321 gctgcagccc tggaaataat ggtcaaattc tcaccagaac cccatctggc ccaagtagtt 4381 gcagaagacc tcttgtcccc cagtgtgatg gatgtgggtg atttcaagat atcaatcaac 4441 gagggattac cctctggcgt cccttgcacc tcacaatgga actccattgc ccactggctc 4501 ctcacactat gtgcactgtc tgaagtcaca gacctatccc ctgacatcat ccaggcaaat 4561 tccctgttct ccttttatgg tgatgatgaa atagtgagca cagacatcaa attggaccca 4621 gagaaattga cagcaaaatt gaaggaatac gggctgaaac caacccgtcc tgataaaaca 4681 gaaggaccct taatcatctc tgaagatttg gatggcctga ccttcttacg gagaacggta 4741 acccgtgatc cggccgggtg gtttggcaaa ctggaccaaa gctcaatact caggcagatg 4801 tactggacca ggggaccaaa ccatgaggac ccctttgaaa cgatgatacc acactcccaa 4861 agacccatac aactgatgtc attattgggt gaagctgcat tgcatggtcc atcattctac 4921 agcaaaatca gcaaactagt catctcagaa ttgaaagagg gtggaatgga cttttacgtg 4981 cccagacaag aaccaatgtt caggtggatg agattctcag atttgagcac gtgggagggc 5041 gatcgcaatc tggctccctg ttttgtgaat gaagatggcg tcgaatgacg ccgctccatc 5101 taatgatggt gccgccggcc tcgtcccaga gatcaacaat gaggcaatgg cgctagagcc 5161 agtggcgggt gcagcgatag cagcacccct cactggtcag caaaatataa ttgatccctg 5221 gattatgaac aattttgtgc aagcacctgg tggtgagttc acagtgtccc ctagaaattc 5281 ccctggtgaa gttcttctta atttggagtt ggggcctgaa ataaatcctt atttggccca 5341 tcttgctaga atgtataatg gttatgcagg tggatttgaa gtgcaggtgg tcctagctgg 5401 aaatgcgttt acagcaggaa agataatctt tgcagctatt ccccccaatt ttccaattga 5461 caatctaagt gcagcacaga tcacaatgtg tccacatgtg attgtggacg tcagacagtt 5521 ggaaccagtc aacctcccga tgcctgatgt tcgcaacaac ttctttcatt acaatcaagg 5581 gtctgattcg agattgcgcc taattgcaat gctgtataca cctcttagag caaataattc 5641 tggggatgat gtcttcactg tgtcctgcag agtgctaact agacctagtc ctgacttctc 5701 atttaatttc cttgtgccac ctactgtgga gtcaaagaca aaaccctttt ccctccctat 5761 tctgaccatc tctgaaatgt ccaattctag gttcccagta ccaattgatt ctctgcacac 5821 tagccctact gataatattg ttgtccagtg ccagaatggg cgcgtcaccc ttgacggtga 5881 gttgatgggc accacccaac tcttgcctag ccaaatctgt gctttcaggg gcgtactcac 5941 cagatcaaca agcagggcca gtgaccaggc cgatacagca gcccctaggt tgtttaatta 6001 ttattggcac ataaaattgg ataatctaaa tggaactccc tatgatcctg cagaagacat 6061 gccaggcccc ctgggaacac cagatttcct gggcaaagtc tttggcgtgg ccagccagag 6121 agatcctgat accacgacta gggcacatga agcaaagata gacacatcat ctggccgttt 6181 cgccccaaaa ctaggctcac tagagatatc cactgaatct gctgatttca atccaaacaa 6241 accaacaaga ttcaccccag ttggcattgg ggttgaccag gctgagggag actttcaaca 6301 atggactcta cccgactatg ctggcgcgat cacccacaac atgaacttgg ccccagctgt 6361 cgctcccaac ttccctggtg agcagctcct cttcttccgc tcacatttgc catcttctgg 6421 tgggcgatcc gacgggattc tagactgcct ggtcccccaa gagtgggtac agcacttcta 6481 ccaagaatca gccccctctc aatctcaagt ggctctgatt aggtacatca accctgataa 6541 tggtagagta ttatttgagg ccaagctgca caaattaggt ttcataacta tagctaagaa 6601 tggtaattct ccaataactg tccccccaaa tggatacttt aggtttgaat cttgggtgaa 6661 ccccttttat acacttgccc ccatgggaac tgggaatggg cgtagaagga ttcaataatg 6721 gctggagctt ttatagcagg attggctggt gatatgctca caaatactgt aggatcttta 6781 gttaatgcag gggctaatgc cattaatcaa acaattgatt ttgaaaataa taaacatttg 6841 caaaatgctt cttttaatca tgataaggag atgttgaatg cacaaattga ggcaacaaaa 6901 agattacagg ctgacatgat tgctatcaaa caaggggttt tgaccgctgg cggcttttcc 6961 cctactgatg cagcccgtgg ggcaattaat gcccccatga caaaagtcct agattggaat 7021 ggaacgagat actgggcacc aggtgccacc tccacaacct cgatgtcggg tggcttcaca 7081 aatcaaactg tgcacagatc cacaccaaat tttaaaacga accaggctcc cagacccgca 7141 cccagcagtg ggtcttcagt aaggtcaaat tcaacccaaa tcactagcct gagctcacac 7201 tcgtccgggt cgtctcgatc cagcgggtcc acagttgtca gctcaatatc cactaacagg 7261 actagggact gggtcaacca acaaaatttt aatttggaac cacacatgcc tggatctctt 7321 aggacagctt ttgtcactcc accatctagt tcagcctcta gctcaggcac agtctcaact 7381 gtgcccaaga atgttttgga ctcctggaca tctgcgttta acacgcgcag acagccgcta 7441 ttcgcacacc ttcgcagaag gggggagtca aatgtttagt gaaaagatta tttttaaatt 7501 tgatttaaaa ttacatttaa tttggcatct t //