Typing tool
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Complete norovirus genomes
MF140677 | GII.6 | ||
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GII.P7 |
ORF1: 1..5063 ORF2: 5044..6687 ORF3: 6687..7463LOCUS MF140677 7480 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2013/GII.P7-GII.6/Rotterdam/E1300312_p5_d204 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140677 VERSION MF140677.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7480) 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 7480) 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..7480 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2013/GII.P7- GII.6/Rotterdam/E1300312_p5_d204" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="12-Dec-2013" /note="genotype: GII.P7-GII.6" CDS <1..5063 /codon_start=3 /product="ORF1" /protein_id="ATN23727.1" /translation="FGSQKSANDSTNTTPSNKEEAGAFSNIKVGFKKMLGAVPKGTKT PSSAQHCPTVKIGDKTLTVPPEPPNGEDVVQYDAKSETVHGLPDLTTVQNEHENTPYS VPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSGGKALGVHKPPAAISLATIELT PISLYWRPVYTPSYLVCPDTLKGLAGEKFPYTAFSNNCYNFCCWVLELNDTWLSRRSI SRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFTKPIKDLLGKLKPLNLL HLLASCDWTFAGVVETVILMAELFNIFWTPPDVSNFISSLVGDFELQGPEDLAVELVP VVMGGVGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMKWFFPKKEEKAE METLRAIEDAVLDMEAIGNNHLTTLLKDKDSLSAYMKTLDLEEEKARKLSTKSSSPDI VGTINAILARIAAARSLLHKAKEEMFSRARPVVVMISGKPGIGKTYMARHLAKGVANT MSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGNPIKDALTLQELADTCPVTLNCD RIENKGKMFDSDVIVITTNLVNPAPLDYVNFEACSRRIDFLVYAESPEIEKVKRDFPG QPDMWKDHFKSDFSHIKLTLAPQGGFDKNGNTPHGRGTMRSLTQGSLIARVAGLVHER KDEFQLQGNDLQTYNFDTNRVSAFRRLAADNKYGIMETMRVGAALKNVKTLEDLKVAL RDVKFNECQIIYRSSKYRISSNGKGSVSIDKVGDQVSQTASEVGSAILRLRQARARYY VSCFQDLIYTLIQVAGASFVVSRISKRFCWERWVKPTETQETNESEKEVVQGGWEIEP KDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDR YYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTGSDIRKRRPDDF QPKGKLWADDTRNVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNLLITTTHVLPKG IKELFGVELKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTVCSILVKRPTGE MIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCGCPYIYKRGNDI VVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPGKAPKLSAKTKF WRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRGKPPRPAILEEA KKTVMNVLEQTIDPAKPWTYSQACASLDKTTSSGSPHHVRKNDHWNGESFTGPLADQA SKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGTMIRCARAFGGL MDSMKASCIALPCRVGMNVNEDGPIIFDKHSKYKYHYDADYSRWDSTQQRCILSAAME VMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQWNSIAHWILTL SAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREYGLVPTRPDKTE GPLVITEDLTGLTFLRRSIVRDPAGWFGKLDQDSILRQLYWTRGPNHENPYESMVPHN QRATQLMALLGEAALHGPQFYKKVSKMVINEIKSGGLEFYVPRHEAMFRWMRFSDLST WEGDRNLAPEGVNEDGVE" CDS 5044..6687 /codon_start=1 /product="ORF2" /protein_id="ATN23728.1" /translation="MKMASNDAAPSNDGAANLVPEVNNEVMALEPVAGASIAAPVVGQ QNIIDPWIRENFVQAPQGEFTVSSRNTTGEVLLNLELGPELNPYLRHLSRMYNGYAGG MQVQVILAGNAFAAGKIIFAAVPPHFPVENISAAQITMFPHVVIDVRQLEPVLLPLPD IRNRFFHYNQENTSRMRLVAMLYTPLRANSGEDMFTVSCRVLTRPAPDFEFTFLVPPT VESKTKPFTLPILTLGELSNSRFPAPIDMLYINPSETIVVRSQNGRCLLDGTLQGTTQ LAPTQICSFRGTLVRQESRSADSVDSARRAMNHPLYVQLRNLDGTSYDPTDEVPAVLG AIDFKGTVFGIASQRDTKGSVGATRAHEVTINTRDAKYSPKLGSVLMHSESTDFTSDQ PIRFTPIGMGEENDWSQWDLPDYSGALTLNMHLAPAVAPAFPGERILFFRSVVPAAGG YGKGEIDCLIPQEWIQHFYQEAAPIQSAVALIRYVNPDTGRSLFEAKLHREGFITVAS SGDNPIVVPSNGYFRFEAWVNQFYTLTPMGAGQGRKRAQ" CDS 6687..7463 /codon_start=1 /product="ORF3" /protein_id="ATN23729.1" /translation="MAGAFLAGLAGDAITNGVGSLINAGANAINQKVEYDFNKQLQLA SFQHDKEMLQSQVLATKQLQQEMMNIKQGVLTAGGFSPTDAARGAVNAPMTKILDWNG TRYFAPNSMKTTSYSGQLSSNPVHKQSTLPRPSPSKTNVSSGSSSVYSSLSSASSQST HSTVLTAGSGSSRTAPSSSTASTLSRTSDWVRGQNERLSPFMNGALQTTFVTPPSSRA SSYGSVSTVPKAVLDSWTPMFNTNRQPLFTHIRRRGESQI" ORIGIN 1 ccttcggcag ccaaaaatct gccaatgaca gtactaacac caccccttct aataaagaag 61 aggctggtgc attctccaac attaaagttg gttttaagaa gatgctgggt gccgttccca 121 aggggaccaa aacacccagt agtgctcagc actgccccac agtcaagatc ggggacaaaa 181 cattaacagt tccacccgag cccccaaatg gtgaggacgt tgtgcagtat gatgcgaagt 241 cagaaactgt gcatgggcta ccagacttga cgacggtgca gaatgagcac gaaaacacac 301 cgtactctgt ccccccattg agtgaaagag aacacagacc agccactgaa ccgcttcctg 361 gcacaatact ggagatgtgg gatggtgaat tttatcacta ctccgtgtat gtcagtggcg 421 gcaaagccct aggagttcac aaaccccctg cagcaataag cctcgcaact atagagctca 481 cgcccatatc tctttactgg aggcccgttt acacccccag ctacttagtc tgcccagaca 541 cgctgaaagg cctcgctggt gagaagtttc cctacacagc tttcagtaac aactgttaca 601 acttttgttg ctgggtgctt gagctcaacg atacgtggct tagcaggaga agcatctcca 661 gaaccaccgg tttcttcaaa ccataccagt cttggaacag gaaacccctt ccaaccgttg 721 atgatggaaa gattaagaag gtggccaacg caatcctctg tgcgcttgga tcactgttta 781 caaaaccaat caaagaccta ttgggaaagc tcaaaccact aaatttgctg cacctgctcg 841 catcatgtga ttggacgttt gcgggtgtag tagagacagt catcctaatg gcggaacttt 901 tcaacatctt ttggacaccg ccagatgttt ccaacttcat atcctccttg gtgggcgact 961 ttgaactgca agggcctgag gacctggctg tggagcttgt ccccgtggtc atgggtggcg 1021 tagggatggt tctcggcttc actgctgaga agataggccg tatgctgtct tccgccgcat 1081 caacgctgcg agcatgcaaa gacctgggga attacgccct tgacatacta aagctggtta 1141 tgaagtggtt cttcccaaag aaagaagaga aggccgagat ggaaacttta agggcaattg 1201 aggacgccgt cctggacatg gaagctatag ggaacaatca tcttacaacc ctcctcaagg 1261 acaaggatag cctctcggcc tacatgaaga ctctggacct ggaagaagaa aaggcaagga 1321 agctgtccac caagtcatcc tcgccagaca ttgtcggcac tatcaatgcc atactggcca 1381 gaatagctgc tgccagatcc ctcctacaca aggctaaaga agaaatgttt agtagggcca 1441 ggcccgtggt tgttatgatt tcgggcaaac ctggcattgg caaaacttac atggcaagac 1501 acctagctaa gggcgtcgcc aacaccatga gtggcgacca aagagttggg ctcgttccgc 1561 gcaacggggt cgaccattgg gacgcctaca ggggggagag ggtggtcttg tgggatgact 1621 atggcatggg gaaccctatc aaggatgctc taacactaca agaattggcc gacacttgtc 1681 cagtcactct aaactgtgat aggattgaaa acaaagggaa gatgttcgac agtgatgtca 1741 ttgtaatcac gaccaattta gtcaacccag cgcccctcga ttatgtaaac ttcgaggcgt 1801 gctccaggag gattgacttt ctggtctatg cagagtcacc agagattgag aaagttaaga 1861 gagacttccc tggccaacct gacatgtgga aagaccattt caaatcagac ttctcccaca 1921 taaagctgac tctggctccc cagggcggat tcgacaagaa tggcaacacc ccacatggta 1981 ggggcaccat gcgatccctg acccaggggt ccctgatcgc aagggtcgcg ggtcttgttc 2041 atgagaggaa agatgagttc cagctccaag ggaacgacct ccaaacatac aactttgaca 2101 ccaacagggt ctccgcattt aggagactag ccgcagacaa caaatatggg atcatggaaa 2161 caatgagagt gggtgcggcg cttaagaatg tcaagacctt ggaagatcta aaggttgccc 2221 tgagggatgt gaagttcaac gagtgtcaga taatttacag gagctccaaa tatcgaatct 2281 cttccaatgg caaaggctct gtctctattg ataaagttgg ggatcaagtg tcccagactg 2341 caagtgaagt gggttcagca atccttagac tcaggcaggc aagggccaga tactatgtca 2401 gctgcttcca agatctcatc tacactttga tacaggttgc cggagcatca ttcgttgtta 2461 gcagaatctc caagaggttc tgttgggaga ggtgggtcaa accaaccgag acccaggaaa 2521 cgaatgaatc cgagaaggaa gtagtccaag gtggatggga gattgaaccc aaggacacag 2581 aaccagaagg caagaagggc aagaacaaga aaggaagagg caagaaacac acggctttct 2641 ccagcaaagg cctgagtgat gaggagtatg acgagtacaa gagaatcagg gaagagagga 2701 acggaaagta ctccattgag gaatacctgc aagaccggga tcgctactat gaggaagtgg 2761 cagttgcccg ggcgacagag gaggactttt gtgaggaaga ggaggccaag ataagacaaa 2821 gaatcttccg ccccacaaag aaacagagga aggaagaaag gggggtgctt ggtttggtca 2881 ccggctcaga catcaggaag aggagaccag acgatttcca accaaagggc aaactgtggg 2941 cagacgacac cagaaatgtg gactataacg agagacttga ctttgaggct cccccgagcg 3001 tctggtcgag aatagttcca ttgggcactg gatggggctt ctgggtttcg tccaatctcc 3061 tgatcacaac aacacacgtc ctgcctaagg ggatcaagga actttttgga gttgaactca 3121 aacagatcca aattcataag tctggagaat tttgcaggtt caggttccca agaccaatta 3181 ggccagatgt cacagggctc gtgctggagg aaggcgctcc agaaggcacc gtctgttcca 3241 tactcgtgaa gagacctaca ggtgaaatga tccccctagc agtgaggatg ggcacacatg 3301 cgtccatgaa gatacagggt aggaccgtcg gtggccagat gggaatgctt ctcacaggag 3361 caaacgcgaa gaacatggat cttggcaccg gccctggtga ctgcggttgt ccttacatct 3421 acaaacgtgg caacgacata gttgtcgcgg gtgtccacac cgcagcagcc cgggggggca 3481 acactgtcat atgtgccacc cagggacaag atggggaggc agtccttgag ggaaatgagg 3541 accttggcac ttactgcggt gccccaattc tgggcccagg caaagcaccc aaactcagtg 3601 cgaagaccaa gttctggcgc tcatcaccag acgctttgcc accaggcacc tatgagcctg 3661 cctatctggg gggtaaggac cccagagtgg agaaaggacc atctctgcaa caagtcatga 3721 gggatcagct aaaacctttc acagaaccca ggggtaaacc tcctagacct gcaatcttag 3781 aagaagccaa aaagacagtt atgaatgtac tagaacaaac cattgatcct gctaaaccat 3841 ggacctattc ccaagcatgt gcttcactgg acaagaccac ttccagtggt agcccccacc 3901 atgtcaggaa aaatgaccat tggaatggag aatctttcac tggccccctt gcagaccaag 3961 catccaaagc caacctcatg tatgaacagg ccaaacatgt gcagcccgta tacacggccg 4021 cgctcaaaga cgagcttgtt aagactgata agatctacaa aaagataaag aagagactct 4081 tgtgggggtc ggaccttggc acgatgatca ggtgcgccag ggcttttggt ggtctcatgg 4141 atagcatgaa ggcaagttgc atagccctcc catgtagagt ggggatgaac gtgaatgagg 4201 atggtcctat catatttgac aagcactcta agtacaagta ccactatgat gctgactatt 4261 ctagatggga ttccacccag caaaggtgca ttctctcggc cgctatggaa gtgatggtgc 4321 ggttttctgc cgagccagag ctggcgcaag tggttgcaga ggatctacta gcacccagcc 4381 aactagacgt tggcgatttt gtcatctcag tccaggaggg tctgccatca ggggtcccgt 4441 gcacatcaca gtggaactca atagcacatt ggatcctaac cttgagtgca atggcagaag 4501 tgtcaggtct ctcaccagat gttgtccaag cccactcttg tttttccttt tacggcgatg 4561 atgagatcgt cagcactgac atcaaccttg accccatgaa gttgacacag aaactcagag 4621 aatatggtct ggtccccacc cgacctgaca aaactgaagg tccccttgta atcactgaag 4681 acctcaccgg cctgacgttc ttgcgtaggt caattgtgag agatccagct gggtggtttg 4741 gaaaattgga ccaagactca atcctcaggc agttatactg gacaaggggc cccaatcatg 4801 agaatccata cgagagcatg gtccctcata accagcgggc aacacagctc atggcccttc 4861 taggtgaggc tgcactgcat ggccctcagt tttacaagaa agttagcaaa atggtcatca 4921 atgaaattaa aagtggtggt ctggaatttt atgtgcccag acatgaggcc atgttcagat 4981 ggatgagatt ctctgacctc agcacatggg agggcgatcg caatcttgct cccgaaggtg 5041 tgaatgaaga tggcgtcgaa tgacgctgct ccatcgaatg atggtgctgc caacctcgta 5101 ccagaggtca acaatgaggt tatggcactt gaaccggtgg cgggagcctc aattgcagct 5161 cctgtcgtcg gccaacaaaa tataattgac ccctggatta gagaaaattt tgttcaggca 5221 ccacagggtg agttcactgt ttcatcaagg aacacaaccg gtgaggtact tctgaatctt 5281 gaattaggcc ctgagctcaa cccttatctg agacatttgt cccgcatgta caacggttat 5341 gctggtggta tgcaggttca ggtgatccta gctgggaatg cgttcgcagc tggtaaaatc 5401 atctttgccg ccgtcccacc acatttccct gtagaaaata ttagtgcagc ccaaatcaca 5461 atgttccccc atgtagttat tgatgtaaga cagcttgagc cagtgctttt acccctccct 5521 gacataagga ataggttctt tcattacaat caggaaaaca cttccagaat gagacttgtg 5581 gctatgttgt acacacccct tagagcaaat tctggtgagg atatgtttac ggtgtcttgc 5641 agagtcctga cccgtccagc ccctgacttt gagttcacgt ttctggtgcc gccaactgta 5701 gaatcaaaga ctaagccctt cacactccca attctaactc ttggagaact atctaattct 5761 agattccctg ccccaataga catgctgtac ataaatccca gtgagacaat tgtggtgagg 5821 tcacaaaatg gccggtgtct tctggacgga acacttcaag ggaccaccca gctggcgccc 5881 acccaaattt gctccttcag gggcacgctg gttcgccagg agtcgaggtc tgcagattca 5941 gtagactcag ctagacgagc aatgaaccat cctctctacg ttcagctgag gaacctcgat 6001 gggacatcat atgatccaac agatgaggtg ccagcggttc tgggtgccat agattttaaa 6061 ggaactgtgt ttgggatcgc tagtcaaagg gacaccaaag gctctgtagg agcgacccgc 6121 gcccatgaag tgacaataaa caccagagat gctaaatact ctccaaaact tggctctgtg 6181 ttgatgcatt ctgaatctac tgattttaca agtgaccagc ccatccgctt tactcctatt 6241 ggtatggggg aggaaaatga ttggagccaa tgggatttgc ctgattattc tggtgccctc 6301 accctcaaca tgcacctagc ccccgcagtt gcccctgctt tccctggtga gcgcattctc 6361 ttctttagat cagtggtgcc agctgctggt ggttatggaa aaggtgaaat agattgtctc 6421 atcccacagg aatggattca gcatttctac caggaggccg ccccaataca atccgcggtg 6481 gcccttatta gatatgttaa tcctgacact gggagaagcc tctttgaggc aaagctacat 6541 agagaagggt tcatcactgt ggcaagttct ggagacaacc ccatagttgt gccctcaaat 6601 ggctacttca gatttgaggc ttgggttaat caattctaca cactcacccc catgggagct 6661 ggacaggggc gcaaaagagc ccagtaatgg caggagcttt cttagctgga ttggcaggtg 6721 acgccataac aaatggtgtc gggtccctga tcaacgctgg ggccaatgca atcaaccaaa 6781 aggtagagta tgacttcaat aaacaactcc aattggcatc ctttcaacat gacaaagaga 6841 tgttgcagtc acaagttctg gccactaaac agctccaaca ggagatgatg aacataaagc 6901 aaggggtctt gaccgctggc ggcttttccc ctacagatgc tgcaagaggc gctgtgaacg 6961 cgccgatgac aaaaattctg gattggaatg gaacgaggta ttttgcccca aacagtatga 7021 agacaaccag ttattcaggc cagctctcca gtaaccctgt acataagcaa tccacactac 7081 cccgtcccag cccttcaaaa actaatgtta gtagtggttc ttctagtgtg tatagttctt 7141 tatcttctgc ttcctcacaa tcaactcatt caacggtttt gactgcggga tccgggtcgt 7201 ctaggacagc tccctcctcc tcaacagctt ccaccttgtc tagaactagt gattgggtaa 7261 gaggacaaaa tgagaggctc agcccgttta tgaatggtgc tctccaaaca acttttgtca 7321 caccaccatc gagcagggct tcatcatatg ggtcggtctc aaccgtcccc aaagctgttt 7381 tggactcctg gactcctatg ttcaatacca ataggcagcc tctcttcact cacattcgta 7441 ggcgagggga gtcacagatt tagtgaaaag attgattagg //