Typing tool
|
Complete norovirus genomes
MF140647 | GII.7 | ||
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GII.P7 |
ORF1: 1..5080 ORF2: 5061..6683 ORF3: 6683..7456LOCUS MF140647 7525 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2013/GII.P7-GII.7/Rotterdam/E1300275_p12_d54 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140647 VERSION MF140647.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7525) 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 7525) 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..7525 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2013/GII.P7- GII.7/Rotterdam/E1300275_p12_d54" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="17-Sep-2013" /note="genotype: GII.P7-GII.7" CDS <1..5080 /codon_start=2 /product="ORF1" /protein_id="ATN23637.1" /translation="NDATAAFGSQNSVNDSDNATPSNKEEVGAFSNIKVGFKKMLGAV PKGTKAPSSGQHCPTVKVGSKTLTIPPEPPNGEDTVQFNAKSETIVGLPDLTTVQNEH ENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSDGRALGVHKPPAAISL ATIELTPISLYWRPVYTPNYLVSPDTLKGLAGEKFPYTAFSNNCYNFCCWVLELNDTW LNRRCISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKDLLGKL KPLNLLHLLASCDWTFAGIVETVILMAELFNVFWTPPDVSNFIASLIGDFELQGPEDL AMELVPVVMGGVGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMKWFFPK KEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKARKLSTK SSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHMARHLA KSIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGSPVKDALTLQELADTCP VTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESPEIEKV KRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSLTARVA GLVHERRDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGATLKNVKTLE DLKIALRDVKFNECEIIYKNSKYRVSSNGKGSVSVDKVEDNASQTVNEVQSAILRLRQ ARARYYISCFQDLVYTLMQVAGASFVVNRISRRFCWERWVKPAETQEVNESEKEVAQG RWEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKYSIEEY LQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTGSDIRK RRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNLLITTT HVLPKGVKELFGVEIKQIQVHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTVCSILI KRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCGCPYIY KRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPGKAPKL STKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLRPFTEPRGKPPRP AVLEEAKKTVMNVLEQTIDPAKPWSYSQACASLDKTTSSGSPHHVKKNDHWNGETFTG PLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGTMIRCA RAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDSTQQRNI LSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQWNSIA HWILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREYGLVPT RPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNHENPYE SMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAMFRWMR FSDLSTWEGDRNLAPEGVNEDGVE" CDS 5061..6683 /codon_start=1 /product="ORF2" /protein_id="ATN23638.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEVMPLEPVAGASLATPVAGQ HNIIDPWIRNNFVQAPAGEFTVSPRNSPGEILLDLELGPELNPYLAHLARMYNGHAGG MEVQIVLAGNAFTAGKIIFAAIPPGFPYENLSPSQITMCPHVIIDVRQLEPVLLPMPD IRNNFFHYNQGNDPKLRLIAMLYTPLRANNSGDDVFTVSCRVLTKPSPDFEFTFLVPP TVESKTKQFSLPILKISEMTNSRFPVPVEMMYTARNENQVVQPQNGRVTLDGELLGTT PLLAVNICKFKGEVIAKNGDVSSYRMDMEITNTDGTPIDPTEDTPGPIGSPDFQGVLF GVASQRNKNEQNPPTRAHEANINTGGDQYAPKLAQVKFFSESQDFEVHQPTVFTPVGV AGDPSHPFRQWVLPRYGGHLTNNTHLAPAVAPLFPGEQILFFRSQIPSSGGYESGNMD CLVPQEWVQHFYQEAATAQSEVALIRFINPDTGRVLFEAKLHKQGFITVAHTGDNPIV MPPNGYFRFEAWVNQFYSLAPVGTGNGRRRIQ" CDS 6683..7456 /codon_start=1 /product="ORF3" /protein_id="ATN23639.1" /translation="MASAFFANLAGGVASNGISSLINAGANAINQKVEFDYNKQLQNA SFSHDKEMLQAQIEATKRLQQEMIDIKQGVLTAAGFSPTDAARGSVGAPMTKLVDWSG TRYWAPGAMRTTGYSGTFTHLPPVQSASYVNNQNRQSPKVDPPPPSSSGSSVSSVKTQ STTLSGTSRVGSSSHLTLSTRPSTRTSDWVRSQNERLSPFMNGALQTTYVTPPSSRAS SVSTVSTVPKEVLDSWTPMFNTHRQPLFAHLRRRGESQI" ORIGIN 1 taacgacgct actgctgcct ttggcagtca aaactctgtc aatgacagtg acaacgccac 61 cccttctaat aaagaagagg ttggtgcatt ctccaacatc aaagttggat tcaagaaaat 121 gctgggtgcc gttcccaagg gcaccaaagc acccagcagt ggtcaacatt gccccacagt 181 taaggttggg tctaaaacat taacaatccc ccctgagccc ccgaatggtg aagacaccgt 241 acagtttaat gcaaagtcag aaactatagt tgggttgccg gacttgacaa cggtgcaaaa 301 tgaacatgaa aacaccccat acactgtccc tccattaagt gagagggagc acaggccggc 361 caccgaacca cttcctggca caatattaga gatgtgggat ggtgagtttt accattattc 421 cgtgtacgtc agcgacggca gagctctggg agtccacaaa ccaccggcgg ctataagcct 481 cgcgacgata gagctcaccc ccatatcact ttactggagg cccgtttata cccccaatta 541 cttggtctcc ccggacacat taaaaggtct cgctggtgag aagttcccct atacggcctt 601 cagtaacaac tgttataact tctgttgctg ggtgcttgag ctcaacgaca cgtggcttaa 661 cagaagatgc atttccagaa ccaccggctt cttcaagcca taccagtctt ggaacagaaa 721 acctctccca accgttgatg atggaaagat taagaaagtg gccaatgcaa tcctctgtgc 781 actcggctca ctgttctcaa aaccaatcaa agacctgtta ggcaaactca agccattgaa 841 tctactacac ttgcttgcgt cttgtgattg gacgtttgcg ggtatagtgg agacagtcat 901 cttgatggcg gagcttttca atgtcttctg gaccccccca gatgtctcta attttatagc 961 ctccctaata ggtgattttg aattgcaagg gcctgaggac ctggctatgg agctcgtccc 1021 cgtggtcatg ggcggcgtag ggatggttct cggttttacc gccgagaaga taggccgcat 1081 gctatcgtcc gctgcatcaa cactgcgggc gtgcaaagac ctagggaact atgcccttga 1141 catactcaaa ttggtcatga agtggttctt cccgaagaag gaagagaaag ctgagatgga 1201 aaccttgagg gcgattgagg atgccgtcct ggatatggaa gccataggga acaaccacct 1261 cacaaccctt cttaaggaca aagatagcct cacggctttc atgaagaccc tggatctgga 1321 agaggagaag gcaaggaaac tgtccactaa atcatcttca ccggacatag tcggcaccat 1381 caatgccata ctagctagga tagctgctgc tagatccctt ctacataagg ccaaagagga 1441 gatgttcagc aggatcaggc cagtggttgt tatgatatca ggcaggcctg gcattggaaa 1501 aacccacatg gcgagacatt tggctaagag catcgccaac accatgagtg gcgaccaaag 1561 agtcgggctc gttccgcgca acggcgtcga tcactgggat gcctacaggg gagagagggt 1621 ggtcttgtgg gatgactacg gcatggggag ccctgttaag gacgctctaa cactgcaaga 1681 gctggccgac acatgcccag tcactttaaa ttgtgacagg attgagaata aggggaagat 1741 gtttgacagt gatgtcatca taatcacgac caacctagtc aaccccgcgc ccctcgacta 1801 tgtgaacttc gaggcgtgtt ctaggagagt tgacttcctg gtctatgcag agtcaccaga 1861 aattgaaaag gtcaagagag acttcccagg ccagcctgac atgtggaaag accattttaa 1921 accagacttc tcccacatca agctgactct agccccccag ggtgggtttg acaaaaatgg 1981 caacacccca cacggtaagg gaaccatgcg gtccctaacc caggggtccc tgactgcgag 2041 agttgcaggc cttgtccatg agaggagaga tgaattccag ctccaaggaa atgacctcca 2101 aacatacaac tttgacacca acagagtctc cgcattcagg aaattggctg cagataacaa 2161 gtatgggatc atggagacga tgagagtggg tgcgacactc aagaatgtga agaccctgga 2221 agatcttaaa attgcattga gggatgtaaa attcaatgag tgtgaaataa tctacaagaa 2281 ctctaagtat cgagtctctt ccaacggtaa aggctcagtt tctgttgaca aagttgaaga 2341 caatgcatcc cagactgtaa acgaggtaca atccgcaatt ctcaggctca ggcaagcgag 2401 ggccagatat tacatcagct gcttccaaga cctcgtctat actctcatgc aggttgccgg 2461 agcatcattc gtagtcaaca ggatctccag aaggttctgc tgggaaaggt gggtcaaacc 2521 ggccgagacc caggaggtga atgagtccga aaaggaagtg gcacaaggca gatgggaaat 2581 tgagcccaag gatacagaac cagaaggcaa gaaaggtaag aacaagaaag gaagaggtaa 2641 gaaacacaca gctttctcta gcaaaggcct gagtgatgaa gagtatgacg agttcaagag 2701 aattagggaa gaaaggaacg gaaagtactc cattgaggaa tacctgcaag accgggaccg 2761 ctactatgaa gaagtggcag ttgcccgggc gacagaggag gacttctgtg aagaggaaga 2821 ggccaagata agacaaagga ttttccgccc gacaaagaaa cagaggaagg aggagagggg 2881 tgtgcttggc ttagtcaccg gctcagacat caggaagagg agaccagatg acttccaacc 2941 aaaaggcaac ctgtgggcag atgacaccag aagtgtggac tacaatgaga ggcttgattt 3001 tgaagcgccc ccgagtgttt ggtcaagaat agttccatta ggcactggtt ggggattctg 3061 ggtttcatcc aaccttctga tcacaacaac acacgtcctg cctaaagggg ttaaggagct 3121 ctttggagtt gaaatcaaac aaatccaagt tcacaagtct ggagagtttt gcaggttcag 3181 attcccaaga cctatcaggc cagatgtcac aggactcgtg ttggaggaag gcgccccaga 3241 aggcactgtc tgttctatac tcataaaaag gcccacaggt gagatgatcc ccttagcagt 3301 gaggatgggc acacatgcat ccatgaaaat acagggcaga accgttggtg gccagatggg 3361 aatgcttctc acaggagcga acgcgaagaa catggacctc ggcactggtc ctggtgactg 3421 cggttgccct tacatctaca aacgtggcaa cgacattgtt gtcgcgggtg ttcacaccgc 3481 agcagccaga ggaggcaaca ctgttatatg tgccacccaa gggcaagatg gggaagcagt 3541 ccttgaggga aatgaggacc ttggcaccta ttgtggcgcc ccaattctgg gccctggcaa 3601 ggcgcctaaa ctcagcacga agactaagtt ctggcgttca tcaccagatg ccttgccacc 3661 tggcacatat gagcctgctt acctaggagg caaagaccct agagtggaaa aaggtccttc 3721 ccttcaacaa gtcatgaggg accagttgag acccttcaca gaacccaggg gcaaaccacc 3781 tagacctgca gtcttggagg aagccaaaaa gacagtgatg aatgttctag aacaaaccat 3841 tgaccccgcc aagccatggt cctattcgca ggcgtgtgcc tcattggaca aaaccacctc 3901 cagtggtagt ccccatcatg ttaagaaaaa tgaccactgg aatggggaga ccttcactgg 3961 tccacttgca gatcaggcat ctaaagccaa tctcatgtat gagcaggcta aacatgtgca 4021 gcccgtgtat acggccgcgc tcaaagatga gcttgttaag actgacaaga tctacaagaa 4081 aataaagaag aggctcctat gggggtcgga ccttggcaca atgatcaggt gcgccagggc 4141 ctttggtggt ctcatggaca gcatgaaggc aagttgtata gctcttcctt gcagggtagg 4201 gatgaacatg aatgaagatg gccctattat atttgacaaa cattctaagt acaggtacca 4261 ctatgatgct gactattcta ggtgggactc aacccaacaa aggaacattc tttctgccgc 4321 tatggaagtg atggtgcggt tctctgctga accagaattg gcacaagtgg ttgcagagga 4381 ccttttagca cctagccagc ttgatgttgg cgattttgtc atctcagtcc aggagggtct 4441 gccatcagga gtcccatgca catcacaatg gaattcaata gcacactgga tcctaacttt 4501 gagtgcaatg gcagaagtgt caggtctctc accagatgtt gtccaagccc actcttgttt 4561 ttccttttat ggggacgatg agatcgtcag tactgacatc aatcttgacc ccatgaagtt 4621 gacacagaaa ctcagggagt atggtctggt tcccacccgg cctgataaaa ctgaaggtcc 4681 cctcgtcata actgaagacc tcaccggcct gacgttcctc cgtaggtcga ttgctcggga 4741 cccagctggt tggtttggaa agctggacca agactcaatc cttaggcagc tgtactggac 4801 aagggggcct aaccatgaga acccgtacga gagcatggtt cctcattctc agcgggccac 4861 acaactcatg gcccttcttg gtgaggcctc actacatggc ccccagtttt ataagaaagt 4921 tagcaagatg gtcatcaatg agattaagag tggtggtctg gagttttatg tgcccagaca 4981 agaggccatg ttcaggtgga tgagattctc tgacctcagc acatgggagg gcgatcgcaa 5041 tcttgctccc gaaggtgtga atgaagatgg cgtcgaatga cgcagctcca tctaatgatg 5101 gtgcagcagg cctcgtacca gagatcaaca atgaggtcat gccccttgag cccgtagctg 5161 gtgcatcgct ggcgacacca gttgccgggc aacataatat aattgatccc tggataagaa 5221 ataattttgt acaagctcct gcaggtgagt ttacagtttc ccctagaaat tcccctggtg 5281 aaattttgct cgatttggag ttgggaccag aactaaaccc ctatctcgct catctggccc 5341 gtatgtataa tgggcacgct ggtggcatgg aagtgcaaat tgtgttagct gggaatgcgt 5401 tcacagctgg caagatcata tttgctgcca tccctccagg gttcccatat gaaaacttgt 5461 caccttcaca aatcacaatg tgccctcatg ttataattga tgttagacaa ttagaaccag 5521 ttctattacc tatgccagat attagaaaca acttcttcca ttacaatcag ggcaatgacc 5581 caaaattgag attgatagct atgctctaca cccctttaag ggctaataat tctggtgatg 5641 atgtgttcac agtttcttgt agggtcctca ctaaaccgtc acctgatttt gaattcacat 5701 ttttggtccc ccctacggtt gaatctaaaa ccaaacagtt ctcactgccc atcctcaaaa 5761 tatcagagat gaccaactca agattcccag tgccagtgga aatgatgtac acagccagga 5821 atgagaacca agttgtccag ccacagaatg gtagggtcac acttgatggc gagctactag 5881 gcaccacacc cttgttggct gtcaacatct gcaaattcaa gggggaggtt atagctaaga 5941 atggagatgt gagttcctat aggatggaca tggaaattac caacactgat ggcaccccaa 6001 ttgaccccac agaagataca cctggtccca ttggttcacc tgactttcaa ggtgtactct 6061 ttggcgttgc cagccaacgc aacaagaatg agcaaaaccc ccccacgaga gcccatgaag 6121 ccaacattaa cactggtgga gaccaatacg cccccaaatt ggcccaagtg aaattcttct 6181 cagagtccca ggatttcgag gtgcaccagc ccacagtttt caccccagtt ggtgtggcag 6241 gcgacccctc ccatcctttc agacagtggg tcctgcctcg atacggtgga catctcacca 6301 acaacaccca cctggctcca gcagtggccc ccctattccc aggtgagcag atcctattct 6361 ttagatcaca aatacccagc tcaggcggct atgaatcggg taacatggac tgccttgtcc 6421 cccaagaatg ggtccaacac ttctatcaag aagctgccac agctcagtct gaggtggcac 6481 tcataaggtt catcaaccca gacactggca gagtcctctt tgaggccaag ctgcacaagc 6541 aaggctttat aactgtggct cacactggtg ataacccaat tgtcatgcca ccaaatgggt 6601 actttagatt tgaagcttgg gttaatcagt tttactcact cgcccccgtg ggaactggga 6661 atgggcgcag gaggatccaa taatggccag tgctttcttt gcaaatttgg caggaggcgt 6721 tgcctccaat ggaattagtt cactcataaa tgctggggct aatgctatta accaaaaagt 6781 tgagtttgat tataataaac aactccaaaa tgcatccttc tcccatgata aggaaatgct 6841 ccaagcccaa attgaagcca ccaaacgtct gcaacaagag atgattgaca taaaacaagg 6901 ggtgctgaca gctgcgggat tctctcctac ggatgccgcg aggggttctg tcggcgcacc 6961 aatgacaaaa ttagttgatt ggagtggcac tagatattgg gcgcctggtg ccatgaggac 7021 aacaggctat tcaggaactt ttactcactt gccccctgtg cagtctgctt catatgttaa 7081 taatcagaat agacaatctc ctaaagtaga tccccctcct ccttcttcga gtggttcttc 7141 tgtttcttct gttaaaacac aatcgactac cctctcaggc acttcaaggg tgggctcctc 7201 atcccattta accctgtcaa ccaggccgag cacaaggaca tctgattggg tgcgcagcca 7261 gaatgaaagg ttgagtccct tcatgaatgg agcgttgcaa acaacatatg taacgccacc 7321 atccagtagg gcgtcaagtg tcagcacagt ctcgaccgtg ccgaaagagg ttttggactc 7381 ctggacgcct atgtttaaca ctcacaggca gccactcttc gcccatctgc gtaggcgagg 7441 ggagtcacag atttagtgaa aagattggtt aggaaagttg attagtttgc tcttcttttc 7501 cactattcct ttaattcttt ctttt //