Typing tool
|
Complete norovirus genomes
MF140684 | GII.3 | ||
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GII.P21 |
ORF1: 1..5083 ORF2: 5064..6713 ORF3: 6713..7474LOCUS MF140684 7489 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2011/GII.P21-GII.3/Rotterdam/E1300322_p7_d0 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140684 VERSION MF140684.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7489) 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 7489) 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..7489 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2011/GII.P21- GII.3/Rotterdam/E1300322_p7_d0" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="22-Feb-2011" /note="genotype: GII.P21-GII.3" CDS <1..5083 /codon_start=2 /product="ORF1" /protein_id="ATN23748.1" /translation="DASAAAAANSNNDNAKSSSDGVLSNMAVTFKRALGARSKQPPPR DKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKEGVSGLPELSTVTQLEENSTAF SVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVDRGLVLGVHKPPAAISLAKVEL TPLSLYWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRM IQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGKLKPLNI LNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEKN ELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLSTKSASPD IVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKIAS SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC DRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEKAKRDFP GQPDMWKDTFKPDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTASSLVARASGLLHE RLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTMTELKQA LKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGALHHLKCARIRY YVKCVQEALYSILQIAGAAFITTRITKRMNIQNLWSKPQAEDLEETNNEEGCPKPKND EEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIR KRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITS THVIPQGAQEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLL IKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI YKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILGPGNAPK LSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPK PSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCWNGETFT GKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGTIKKRLLWGSDLSTMIRC ARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA VLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCTSQWNSI AHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLKEYGLKP TRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPF ETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQEPMFRWM RFSDLSTWEGDRNLAPCFVNEDGVE" CDS 5064..6713 /codon_start=1 /product="ORF2" /protein_id="ATN23749.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT QLLPSQICAFRGVLTRSTSRASDQADTAAPRLFNYYWHIQLDNLNGTPYDPAEDIPGP LGTPDFLGKVFGVASQRDPDTTTRAHEAKIDTSSGRFAPKLGSLEISTESADFNPNKP TRFTPVGIGVDQAEGDFQQWTLPDYAGKITHNMNLAPAVAPNFPGEQLLFFRSHLPSS GGRSDGILDCLVPQEWVQHFYQESAPSQSQVALIRYINPDTGRVLFEAKLHKLGFITI AKNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ" CDS 6713..7474 /codon_start=1 /product="ORF3" /protein_id="ATN23750.1" /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG TRYWAPGATSTTSMSGGFTNQTVHRSTPNFKTNQAPRPTPSSGSSARSNSTQITSLSS HSSGSSRSSGSTVVSSISSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSSASSSGT VSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV" ORIGIN 1 cgacgcttcc gctgccgctg ctgccaacag caacaacgac aacgcaaaat cttcaagtga 61 cggagtatta tctaatatgg ctgtcacttt taaacgagcc ctcggggcgc ggtctaaaca 121 gccgcccccg agggacaaac caccaaaacc cccaagacca cccacaccag agttggttaa 181 ggcaatcccc cctcccccac ccaacgggga ggacgaacca atcatttctt ataacgtcaa 241 agagggtgtt tctggtttgc ctgaactctc aactgtcacc caactagagg agaactctac 301 agcgttcagt gttccccctc ttagtcagag ggagaacaga gatgcaaagg aaccattgac 361 tggaaccatc ctggagatgt gggacgggga gatctaccat tatggcttat acgtggaccg 421 agggttagtg ctcggtgtac acaaaccacc agcagccatc agtcttgcta aggttgagct 481 gacccccttg tctttgtatt ggagaccagt gtacacccca cagtacctca tttcccctga 541 cactctcaaa aagttgcatg gggagacgtt cccttataca gcctttgata acaactgtta 601 tgccttctgc tgttgggtac ttgacttgaa cgattcatgg ctgagcagaa ggatgataca 661 gaggacaaca ggcttcttcc gaccctacca ggactggaac aggaaacccc tccccacgat 721 ggatgattcc aaagtgaaaa aggtggccaa tgttgtcctt tgtgctctct catcattgtt 781 cacaagacca attaaggaca ttattgggaa gttgaaaccc ctaaacatcc ttaacatcct 841 agccacatgt gattggactt ttgcaggcat agtagaatcc ctgatccttt tggctgaact 901 gtttggagtt ttctggacac ccccagatgt gtctgcaatg atcgctccct tactgggtga 961 ttatgagcta cagggacccg aggacctcgc tgtggaactc gtacccgtag taatgggagg 1021 gataggtttg gtgctgggat tcaccaaaga gaaaattgga aaaatgcttt catctgctgc 1081 ttcaaccctg agggcatgca aagatctcgg tgcatatggg ttggagatcc tcaagttggt 1141 catgaaatgg tttttcccaa agaaagaaga gaaaaacgaa ttggcaatgg tgagatccat 1201 cgaggatgca gtgctagatc ttgaggccat tgagaacaac catatgacag ctctactcaa 1261 ggataaagac agccttgcaa cctacatgag gactcttgac atggaggagg agaaagcgag 1321 gaaactttcc accaagtctg cctcgccgga tattgtgggc acgataaacg ccctactgtc 1381 aaggattgct gctgcccggt ctctagtgca cagggctaag gaggagctgt caagcaggcc 1441 ccgaccggtc gttgtgatga tttcagggag accaggtatt gggaaaaccc acctagctag 1501 agagttggca aagaagatcg cctcctcact cacaggtgac cagagggtgg gtcttatccc 1561 acgcaacggg gtcgaccact gggatgcata caaaggtgaa agagtcgttc tctgggacga 1621 ctacgggatg agcaacccca tccacgacgc cctcagactc caggagctcg ctgacacctg 1681 tcctctcaca ctcaactgtg acaggattga gaataaaggc aaagtctttg acagtgacgc 1741 cataataata accaccaatt tggccaaccc agcgccactg gattacgtta actttgaagc 1801 ttgctcaaga cgcatagatt tcctcgtcta tgctgatgcc cctgaagttg agaaggccaa 1861 acgggacttc ccaggccaac cagacatgtg gaaagacacc tttaaacctg acttctctca 1921 cataaaactg acattagccc cgcaaggagg ttttgacaag aatggtaaca ctcctcatgg 1981 gaagggtgtc atgaagaccc tcactgccag ttccctcgtt gcccgagcat caggtctcct 2041 ccacgagaga ttagacgaat atgaactgca gggcccaaca cccacaacat tcaacttcga 2101 ccgcaacaag gtgcttgctt ttaggcagct tgctgctgaa aacaaatacg gtcttgttga 2161 cacaatgagg gtcggatcac agctcaagaa tgtcaaaact atgacagaac tcaagcaggc 2221 tctcaagaac atctcagtca agaaatgtca gcttgtgtat ggtgggggca cgtacacact 2281 tgaatctgat ggcaaaggca atgtgcacgt cgagaaggtg aacaacacta gtgtgcaaac 2341 taacaacgag ctctccgggg ctttgcacca tctcaagtgt gccagaatta ggtactatgt 2401 taagtgtgtc caggaagctc tctactccat cctgcaaatt gccggggctg cattcattac 2461 cacgcgcatc acaaagcgca tgaacataca aaacctctgg tccaaaccac aagcagaaga 2521 tctggaggag accaacaacg aggagggctg tccaaaacct aaaaatgatg aggaatttgt 2581 tatctcctct gatgacatca aaaccgaggg caagaaagga aagaacaaga ctggccgtgg 2641 taagaagcac acagcctttt ccagcaaagg actcagtgat gaggagtacg atgagtacaa 2701 gagaatcagg gaagagagaa atggcaagta ctccatagag gaatacctac aggacagaga 2761 caaatactat gaggaggtgg ccatagccag ggcaactgag gaagacttct gtgaagaaga 2821 ggaggctaaa atccggcaga ggatattcag accaacaagg aaacaacgca aagaggaaag 2881 ggcctctctt ggtttggtta caggttctga gatcaggaag agaaacccag atgacttcaa 2941 gcccaaaggg aaactatggg ccgatgatga caggaatgtt gactacaatg agaaacttag 3001 tttcgaggct ccaccaagca tttggtcacg aatagtcaac tttggctcag ggtggggctt 3061 ttgggtctcg cccagcctct tcataacatc aacccatgtc attccccaag gcgcacagga 3121 gttctttgga gtgtccatca aacaaataca aatccacaag tcaggtgagt tctgccggct 3181 taggttccca aaaccaatca gaacggatgt cacaggcatg atcttggagg aaggtgctcc 3241 agaaggcact gttgccacac ttctcatcaa gagaccaact ggggaactca tgcccttggc 3301 agccagaatg ggcacccacg cgaccatgaa aattcagggt cgcactgttg gtggacagat 3361 gggcatgcta ctcacagggt ccaacgctaa gagcatggat ttaggcacaa ctcctggcga 3421 ttgtggttgt ccctatatct acaagagagg gaacgactac gtggtcattg gagttcacac 3481 tgccgccgct cgtggaggaa acaccgtcat ctgtgcaacc caaggaaacg agggggaggc 3541 catgctagaa ggtggtgaca acaagggaac ttactgtgga gcaccaatat taggccctgg 3601 aaatgccccc aaactcagca ccaaaaccaa attctggagg tcttccacca cccccctgcc 3661 acctggaacc tatgagccag cctatctggg tggcaaggac cccagagtga aaggtggccc 3721 ctcactgcaa caggttatga gggaccaact aaaaccattc actgagccca gaggcaaacc 3781 acccaaacca agtgtgctag aagccgccaa gaagactata atcaatgtgc ttgaacaaac 3841 aatagaccca cctcaaaaat ggacatacgc gcaggcgtgt gcatcactag acaagaccac 3901 ctccagcggc caccctcacc acatgcggaa gaacgattgt tggaatgggg agactttcac 3961 aggaaaattg gcagaccaag catcaaaggc taacctaatg tttgaggaag gaaagaacat 4021 gaccccagta tacacaggag ctctgaaaga cgagctagtc aagactgata agatctatgg 4081 aacaatcaag aagagactcc tgtggggttc agacctatca actatgatac ggtgtgcacg 4141 agccttcggt gggctaatgg acgagctcaa ggcccactgc gtcacactac cagtcagggt 4201 tggtatgaac atgaatgagg atggacccat aatatttgag aaacattcca gatataaata 4261 tcattatgat gcagattact cccgctggga ctcaacacaa caaagagcag tgctggctgc 4321 agccctggaa ataatggtca aattctcacc agaaccccat ctggcccaag tagttgcaga 4381 agacctcttg tcccccagtg tgatggatgt gggtgatttc aagatatcaa tcaacgaggg 4441 attaccctct ggcgtccctt gcacctcaca atggaactcc attgcccact ggctcctcac 4501 actatgtgca ctgtctgaag tcacagacct atcccctgac atcatccagg caaattccct 4561 gttctccttt tatggtgatg atgaaatagt gagcacagac atcaaattgg acccagagaa 4621 attgacaaca aaattgaagg aatacgggct gaaaccaacc cgtcctgata aaacagaagg 4681 acccttaatc atctctgaag atttggatgg cctgaccttc ttacggagaa cggtaacccg 4741 tgatccggcc gggtggtttg gcaaactgga ccaaagctca atactcaggc agatgtactg 4801 gaccagggga ccaaaccatg aggacccctt tgaaacgatg ataccacact cccaaagacc 4861 catacaactg atgtcattat tgggtgaagc tgcattgcat ggtccatcat tctacagtaa 4921 aatcagcaaa ctagtcatct cagaattgaa agagggtgga atggactttt acgtgcccag 4981 acaagaacca atgttcaggt ggatgagatt ctcagatttg agcacgtggg agggcgatcg 5041 caatctggct ccctgttttg tgaatgaaga tggcgtcgaa tgacgccgct ccatctaatg 5101 atggtgccgc cggcctcgtc ccagagatca acaatgaggc aatggcgcta gagccagtgg 5161 cgggtgcagc gatagcagca cccctcactg gtcagcaaaa tataattgat ccctggatta 5221 tgaacaattt tgtgcaagca cctggtggtg agttcacagt gtcccctaga aattcccctg 5281 gtgaagttct tcttaatttg gagttggggc ctgaaataaa tccttatttg gcccatcttg 5341 ctagaatgta taatggttat gcaggtggat ttgaagtgca ggtggtccta gctggaaatg 5401 cgtttacagc aggaaagata atctttgcag ctattccccc caattttcca attgacaatc 5461 taagtgcagc acagatcaca atgtgtccac atgtgattgt ggacgtcaga cagttggaac 5521 cagtcaacct cccgatgcct gacgttcgca acaacttctt tcattacaat caagggtctg 5581 attcgagatt gcgcctaatt gcaatgctgt atacacctct tagggcaaat aattctgggg 5641 atgatgtttt cactgtgtcc tgcagagtgc taactagacc tagtcctgac ttctcattta 5701 atttccttgt gccacctact gtggagtcaa agacaaaacc cttttccctc cctattctga 5761 ccatctctga aatgtccaat tctaggttcc cagtgccaat tgattctctg cacactagcc 5821 ctactgaaaa tattgttgtc cagtgccaga atgggcgcgt cacccttgac ggtgagttga 5881 tgggcaccac ccaactctta cctagccaaa tttgtgcttt caggggcgtg ctcaccagat 5941 caacaagcag ggccagtgac caggccgata cagcagcccc taggttgttt aattattatt 6001 ggcatataca attggacaat ctaaatggaa ctccttatga tcctgcagaa gacataccag 6061 gccccctggg aacaccagat ttcctgggca aagtctttgg cgtggccagc cagagagatc 6121 ctgataccac gactagggca catgaagcaa agatagacac atcatctggc cgtttcgccc 6181 caaaactagg ctcactagag atatccactg agtctgctga tttcaatcca aacaaaccaa 6241 caagattcac cccagttggc attggggttg accaggctga gggagacttt caacaatgga 6301 ctctacccga ctatgctggc aagatcaccc acaacatgaa cttggcccca gctgttgctc 6361 ccaacttccc tggtgagcag ctcctcttct tccgctcaca tttgccatct tctggtgggc 6421 gatccgacgg gattctagac tgcctggtcc cccaagagtg ggtacagcac ttctaccaag 6481 aatcagcccc ctctcaatct caagtggctc tgattaggta catcaaccct gatactggta 6541 gagtattatt tgaggccaag ctgcacaaat taggtttcat aactatagct aagaatggtg 6601 attctccaat aactgtcccc ccaaatggat actttaggtt tgaatcttgg gtgaacccct 6661 tttatacact tgcccccatg ggaactggga atgggcgtag aaggattcaa taatggctgg 6721 agcttttata gcaggattgg ctggtgatat gctcacaaat actgtaggat ctttagttaa 6781 tgcaggggct aatgccatta atcaaacaat tgattttgaa aataataaat atttgcaaaa 6841 tgcttctttt aatcatgata aggagatgtt gaatgcacaa attgaggcaa caaagagatt 6901 acaggctgac atgattgcta tcaaacaagg ggttttgacc gctggcggct tttcccctac 6961 tgatgcagcc cgtggggcaa ttaatgcccc catgacaaaa gtcctagatt ggaatggaac 7021 gagatactgg gcaccaggtg ccacctccac aacctcgatg tcgggtggct tcacaaatca 7081 aactgtgcac agatccacac caaattttaa aacgaaccag gctcccagac ccacacccag 7141 cagtgggtct tcagcgaggt caaattcaac ccaaatcact agcctgagct cacactcgtc 7201 cgggtcgtct cgatccagcg ggtctacagt tgtcagctca atatcctcta acaggactag 7261 ggactgggtc aaccaacaaa attttaattt ggaaccacac atgcctggat ctcttaggac 7321 agcttttgtc actccaccat ctagttcagc ctctagctca ggcacagtct caactgtgcc 7381 caagaatgtt ttggactcct ggacatctgc gtttaacacg cgcagacagc cgctattcgc 7441 acaccttcgc agaagggggg agtcaaatgt ttagtgaaaa gattatttt //