Typing tool
|
Complete norovirus genomes
KM198498 | GII.6 | ||
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GII.P7 |
ORF1: 1..5094 ORF2: 5075..6727 ORF3: 6727..7440LOCUS KM198498 7440 bp RNA linear VRL 13-NOV-2014 DEFINITION Norovirus Hu/GII/20088/2009/VNM nonstructural polyprotein and capsid protein VP1 genes, complete cds; and capsid protein VP2 gene, partial cds. ACCESSION KM198498 VERSION KM198498.1 KEYWORDS . SOURCE Norovirus Hu/GII/20088/2009/VNM ORGANISM Norovirus Hu/GII/20088/2009/VNM Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7440) AUTHORS Cotten,M., Petrova,V., Phan,M.V., Rabaa,M.A., Watson,S.J., Ong,S.H., Kellam,P. and Baker,S. TITLE Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting JOURNAL J. Virol. 88 (19), 11056-11069 (2014) PUBMED 25056894 REFERENCE 2 (bases 1 to 7440) AUTHORS Cotten,M.L., Petrova,V., Phan,M.V.T., Rabaa,M.A., Watson,S.J., Kellam,P. and Baker,S. TITLE Direct Submission JOURNAL Submitted (13-JUL-2014) Virus Genomics, The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. 2.4.0 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7440 /organism="Norovirus Hu/GII/20088/2009/VNM" /mol_type="genomic RNA" /isolate="Hu/GII/20088/2009/VNM" /host="Homo sapiens" /db_xref="taxon:1526976" /country="Viet Nam" /collection_date="28-Jul-2009" /note="genotype: GII" CDS 1..5094 /note="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AII02622.1" /translation="MKMASNDATAALGSQNSVNDSINTTPSNKEEAGAFSNIKVGFKK MLGAVPKGTKAPSSDQHCPIVKIGPKTLTVPPEPPNGEDIVQFDAKSETVIGLPDLTT VQNEHENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSGGKALGVHKPP AAISLATIELTPISLYWRPVYTPNYLVCPDTLKGLAGEKFPYTAFSNNCYNFCCWVLE LNDTWLSRRSISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKD LLGKLKPLNLLHLLASCDWTFAGIVETVILMAELFNVFWTPPDVSNFIASLIGDFELQ GPEDLAVELVPVVMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMK WFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKAR KLSTKSSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHM ARHLAKNIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGNPVKDALTLQEL ADTCPVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRIDFLVYAESP EIEKVKRDFPGQPDMWKDYFKQDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSL TARVAGLVHERKDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGAALKN VKTLEDLKVALRDVKFNECEIIYRNSKYRVSSNGKGSVSVDKVEDHTSQTANEVGSAL LRLRQARARYYVSCFQDLVYTLIQVAGASFVVNRISKRFCWERWVKPTETQEASEPEK EVAQGRWEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKY SIEEYLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTRKQRKEERGVLGLVTG SDIRKRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNL LITTTHVLPKGVKELFGVEVKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTV CSILIKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCG CPYIYKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNENLGTYCGAPILGPG KAPKLSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRG KPPRPAVLEEAKKTVMNVLEQTIDPAKPWTYSQACASLDKTTSSGSPHHVRKNDHWNG ESFTGPLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGT MIRCARAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDST QQRSILSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQ WNSIAHWILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPIKLTQKLREY GLVPTRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNH ENPYESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAM FRWMRFSDLSTWEGDRNLAPEGVNEDGVE" CDS 5075..6727 /note="ORF2" /codon_start=1 /product="capsid protein VP1" /protein_id="AII02623.1" /translation="MKMASNDATPSNDGAANLVPEANNEVMALEPVVGASIAAPVVGQ QNIIDPWIRENFVQAPQGEFTVSPRNSPGEMLLNLELGPELNPYLSHLSRMYNGYAGG MQVQVVLAGNAFTAGKIIFAAVPPHFPVDNISAAQITMCPHVIVDVRQLEPVLLPLPD IRNRFFHYNQENTPRMRLVAMLYTPLRANSGEDVFTVSCRVLTRPAPDFEFTFLVPPT VESKTKPFTLPILTLGELSNSRFPAAIDMLYTDPNESIVVQPQNGRCTLDGTLQGTTQ LVPTQICAFRGTLISQTARAADSTDFPQRARNHPLHVQVKNLDGTQYDPTDDIPAVLG AIDFKGTVFGVASQRDVSGTQEQGHYATRAHEAHIDTTDPKYAPKLGTILIKSESTDF NTNQPIRFTPVGMGDNNWRQWELPDYSGSLTLNMNLAPAVSPSFPGERILFFRSIVPS AGGYGSGYIDCLIPQEWVQHFYQEAAPSQSAVALVRYVNPDTGRNIFEAKLHREGFLT VANSGNNPIVVPPNGYFRFEAWVNQFYTLAPMGSGQGRRRAQ" CDS 6727..>7440 /note="ORF3" /codon_start=1 /product="capsid protein VP2" /protein_id="AII02624.1" /translation="MAGAFFAGLAGDVVSNGIGSLINAGANAVNQKVEYDFNKQLQMA SFKHDKEMLQSQVLATKQLQQEMMNIKQGMLTAGGFSPADAARGAVNAPMTKILDWNG TRYWAPNSMKTTSYSGQFSSSPVHRSPAPLQHTAPPKSKLQSDSASVYSSPSTVSSQS THSTVLSAGTGSSRSTPTSTATSTLSRTSDWVRGQNERLSPFMDGALQTTFVTPPSSK ASSNGTVSTVPKAVLDSWTG" ORIGIN 1 atgaagatgg cgtctaacga cgctaccgct gcccttggca gtcaaaactc tgtcaatgac 61 agtatcaaca ccaccccttc aaacaaagaa gaggctggtg cattctccaa catcaaagtt 121 ggatttaaga aaatgctggg tgccgtacct aagggcacca aagcacccag cagtgaccag 181 cactgtccaa tagttaagat tgggcccaaa acactaacag tcccccctga acccccaaat 241 ggtgaagaca ttgtacagtt tgatgcaaaa tcggaaactg taattgggct accggacttg 301 acaacagtgc aaaatgaaca tgaaaacacc ccatacactg tccctccact gagtgagagg 361 gaacatagac cagccactga gccacttcct ggcacaatat tggagatgtg ggatggtgaa 421 ttctaccact actccgtgta cgtcagcggc ggcaaagctc tgggggttca caaacctccg 481 gcagctataa gcctcgcgac gatagagctc acccccatat ccctatattg gaggcccgtt 541 tacaccccca actacctggt ctgcccagac acactgaaag gtctcgctgg tgaaaagttc 601 ccctacacgg ccttcagcaa caattgctac aacttctgtt gctgggtgct tgagctcaat 661 gacacgtggc ttagcagaag aagcatctcc agaaccaccg gcttcttcaa accgtaccag 721 tcttggaaca ggaaacctct cccaaccgtt gacgatggaa agatcaaaaa ggtggccaac 781 gcgatcctct gtgcactcgg ttcgctgttc tcaaagccaa tcaaggacct gttaggcaag 841 ctcaaaccat tgaacttact gcacctgctc gcgtcgtgtg attggacgtt cgcaggtata 901 gtggagacag tcatcttaat ggcagaactt ttcaacgtct tttggacccc gccagacgtc 961 tctaatttta tagcctccct gataggtgat tttgagttgc agggacctga ggacttggcg 1021 gtagagcttg ttcctgtggt catgggtggt ataggaatgg ttctcggctt cacagctgag 1081 aagataggtc gcatgctgtc gtccgctgcg tcaacactgc gggcgtgtaa agacttaggg 1141 aactatgccc ttgacatact taaattggtt atgaaatggt tcttcccaaa gaaagaggag 1201 aaagccgaga tggaaacctt gagggcgatt gaggatgccg tcctagatat ggaggccata 1261 ggtaacaatc acctcacgac cctcctcaag gataaagaca gtctcacggc cttcatgaag 1321 accttggatc tagaagaaga gaaggcaagg aagctatcca ccaaatcatc ctcgccggac 1381 atcgtcggca ccatcaatgc catactggct aggatagctg ccgctagatc cctcctgcac 1441 aaagccaaag aagagatgtt cagcaggatc agaccagtgg ttgttatgat ctcaggcaga 1501 cctggcattg gcaaaaccca tatggcaaga catttggcta aaaacatcgc caacaccatg 1561 agtggtgacc aaagagtcgg gctcgttccg cgcaacgggg ttgaccactg ggacgcttac 1621 agaggagaga gagtggtctt gtgggatgat tatggaatgg ggaaccctgt caaagatgct 1681 ttaacactac aagagctagc tgacacatgc ccagtcactc taaactgtga taggatcgag 1741 aacaagggaa aaatgttcga cagtgatgtc attataatca cgaccaatct agtcaaccct 1801 gcacctctcg attatgtgaa cttcgaggcg tgctctagaa gaattgattt cttggtctat 1861 gcagagtcac cagaaattga gaaggttaag agagatttcc ctggccaacc tgacatgtgg 1921 aaagactatt tcaaacaaga cttttcccat ataaagctaa ccctagcccc ccaaggcgga 1981 ttcgacaaga atggtaacac cccgcatggt aagggcacca tgcgatccct cacccagggg 2041 tccctgactg caagagttgc aggccttgtt catgagagaa aggatgagtt ccagctacaa 2101 gggaatgacc tccagacata caactttgac accaacaggg tctctgcgtt caggaaactg 2161 gctgcagaca acaagtatgg gatcatggaa acaatgagag tgggtgcagc gctcaaaaat 2221 gtcaaaactt tggaggatct gaaggtcgcc ttgagagatg taaagttcaa tgagtgtgag 2281 ataatttaca ggaattctaa gtaccgagtc tcttccaacg gcaagggctc tgtttctgtt 2341 gacaaagttg aggatcacac gtctcagact gcaaatgaag tgggctcagc actcctcaga 2401 cttaggcaag caagggctag atattatgtc agctgcttcc aagacctcgt ctacaccctc 2461 atacaggttg ctggggcatc attcgttgtc aacagaatct ccaaaaggtt ctgctgggaa 2521 agatgggtta aaccaaccga aacccaagaa gcgagtgagc ccgaaaagga agtagctcaa 2581 ggtagatggg agatagagcc caaggacaca gaaccagaag gcaagaaggg taagaacaag 2641 aaagggagag gcaagaaaca cacagccttc tccagcaaag gcctaagtga tgaagagtat 2701 gatgagttta agagaatcag agaagagagg aacggaaaat actccattga ggaatacctg 2761 caagaccggg accgctacta tgaagaagtg gcagttgccc gagcaacaga agaggacttt 2821 tgtgaagaag aagaagccaa gataagacaa agaatcttcc gcccgacaag gaagcaaaga 2881 aaggaggaaa ggggggtact tggcttagtc actggctcag atatcaggaa gaggaggcca 2941 gacgattttc aaccaaaagg caacctgtgg gcagatgaca ctaggagtgt ggattacaat 3001 gagagacttg actttgaggc tcccccaagc gtctggtcaa gaatagtccc attgggcact 3061 ggttggggct tctgggtttc atcaaacctc ctgatcacaa caacacacgt tctgcccaag 3121 ggggtcaagg aactctttgg ggtcgaagtc aaacagattc aaatccacaa gtctggagag 3181 ttttgcaggt ttaggttccc aagaccaatc aggccagatg tcacaggact cgtgttggag 3241 gaaggtgctc ctgaaggtac tgtctgttct atactcataa agaggcctac aggtgagatg 3301 atccccctag cagtgaggat gggcacgcat gcatccatga aaatacaggg taggaccgtc 3361 ggtggtcaga tgggaatgct tctcacaggg gcaaatgcaa agaacatgga tcttggcacc 3421 ggtcctggtg actgcggttg cccttacatc tataagcgcg gcaacgacat agttgtcgcg 3481 ggtgtccaca ccgcagcagc ccgggggggc aacactgtta tttgtgccac tcaaggacaa 3541 gacggagagg cagtccttga gggaaatgaa aaccttggca cctactgtgg tgctccaatt 3601 ctaggccctg gcaaagcgcc taaactcagc acgaaaacca aattttggcg atcatcacca 3661 gatgccctac ctcctggtac gtatgaacct gcttatctgg ggggtaagga tcccagagtg 3721 gaaaaggggc cctccctaca gcaagttatg agagaccagc tgaaaccatt cacagagccc 3781 aggggcaaac cacctagacc agcggttttg gaggaggcta aaaagacagt gatgaatgtt 3841 ctagaacaga ctattgaccc tgctaaacca tggacctact cacaagcatg tgcttcactg 3901 gacaagacca cttctagtgg aagcccccac catgttagga aaaatgacca ctggaatggg 3961 gagtctttta ctggtcccct cgcggaccaa gcatccaaag ccaacctcat gtatgaacag 4021 gcaaaacatg tgcagcccgt gtatacggcc gcgctcaaag atgagcttgt taagactgat 4081 aagatctaca agaaaataaa gaagaggctt ctatgggggt cagaccttgg tacaatgatc 4141 aggtgtgcca gggcttttgg cggccttatg gacagcatga aagcaagttg tatagccctt 4201 ccatgcaggg tggggatgaa catgaatgag gatggcccta tcatatttga caaacactcc 4261 aagtataggt accactatga tgctgactac tctaggtggg actcaaccca gcaaaggagc 4321 attctttccg ccgccatgga ggtgatggtg agattctctg ctgaaccaga attagcacaa 4381 gtggtcgcag aggacctctt ggcgcctagc cagctagatg ttggcgattt tgtcatctca 4441 gtccaggagg gcctgccatc aggagtccca tgtacatcac aatggaattc aatagcgcac 4501 tggattctaa ctctgagcgc aatggcagaa gtgtcaggtc tctcaccaga cgttgtccaa 4561 gcccattcct gtttttcatt ttatggcgac gatgagattg tcagcactga catcaacctt 4621 gaccccataa aattgacaca aaaactcagg gagtatggtc tggtccccac ccggcctgat 4681 aagactgaag gccccctcgt tataactgaa gacctcaccg gcctgacatt cctgcgtagg 4741 tcgattgcac gggatccagc tggatggttt ggaaaattgg accaagactc aatcctcagg 4801 caattgtact ggacaagggg gcccaatcat gaaaacccat acgagagcat ggttccccac 4861 tcccagcgag ctacccagct catggccctt cttggtgagg cttcattgca tggtccccag 4921 ttttacaaga aagtcagcaa gatggtcatc aatgagatta agagtggtgg tctggagttt 4981 tatgtgccca gacaagaggc catgtttagg tggatgagat tctctgacct cagcacatgg 5041 gagggcgatc gcaatcttgc tcccgagggt gtgaatgaag atggcgtcga atgacgccac 5101 tccatcaaat gatggtgctg ccaacctcgt accagaggcc aacaatgagg ttatggcact 5161 tgaaccggtg gtgggagctt caatcgcagc tcctgttgtc ggtcagcaaa atataattga 5221 cccctggatt agagaaaatt ttgtccaagc accacagggc gagtttactg tttcaccaag 5281 gaattcgccc ggtgagatgc ttcttaatct tgaattgggc ccagaactta acccctattt 5341 gagtcatttg tcccgcatgt acaatgggta tgctggtggc atgcaggttc aggtggtcct 5401 agctgggaat gcgttcacag ctgggaagat catctttgcc gctgtgccac cacacttccc 5461 tgtggataat attagtgcag cccagataac tatgtgtcct catgtgattg tcgatgtgag 5521 acagcttgaa ccagtgcttc tgcctctccc cgatataagg aacaggttct tccattacaa 5581 tcaggaaaac accccccgga tgagactcgt ggccatgctc tacacgcctc taagggctaa 5641 ttctggagag gacgtgttca ctgtgtcctg tagggttctg actcgccccg ctccagattt 5701 tgaatttaca tttttagttc caccaactgt tgaatcaaaa acaaaaccct tcactttacc 5761 tattctaacc cttggtgagt tgtctaattc ccgttttcct gctgccatag atatgcttta 5821 tactgatccc aatgaatcaa tagttgttca gccccaaaat ggtagatgca cccttgatgg 5881 cacattgcaa ggcacaacac aattagttcc aacacagatt tgtgccttta gaggtacctt 5941 gatcagccag accgcgagag cggccgattc aacggatttc ccccagagag cccgtaatca 6001 cccgttacat gtccaggtca agaacctaga tggcacacag tatgacccaa cagatgacat 6061 ccctgcagtc ctgggggcta ttgatttcaa aggcacagtg ttcggagtgg caagtcagag 6121 ggacgtctct ggaacacaag aacagggcca ttatgccacc cgggcccatg aagcacacat 6181 tgacacaact gacccaaagt atgcacctaa attaggcaca attctcatca aatctgaatc 6241 tactgatttc aacacaaatc agcccattag gttcactcca gtgggcatgg gtgataacaa 6301 ttggagacag tgggaactgc ctgactattc tggtagtttg actctaaata tgaaccttgc 6361 ccccgctgtt tccccatcct tccctggtga acgaatcctt ttcttcaggt ctatagtacc 6421 atcagctgga ggctatgggt ctggctatat agactgtctc ataccccagg aatgggtgca 6481 acacttctac caggaggcag caccttcaca atctgccgtt gcactggtta ggtatgtcaa 6541 ccccgacact gggcgtaaca tctttgaggc caaattgcat agagaagggt tcctcaccgt 6601 ggctaattct ggaaataatc ctattgtggt tccccctaat ggttatttta gatttgaggc 6661 ttgggttaat caattttaca cacttgcccc catgggatct ggacaggggc gtagaagggc 6721 tcagtaatgg ctggagcctt cttcgcaggg ttagcaggtg atgtcgtgtc gaacggcatc 6781 ggttccctca tcaatgcagg tgctaatgca gtcaaccaaa aggttgagta tgattttaat 6841 aagcaacttc agatggcatc atttaaacat gataaggaga tgttacaatc acaggtgttg 6901 gcaaccaaac aactgcagca ggaaatgatg aacataaagc aggggatgtt gaccgctggc 6961 ggcttttccc ctgcggacgc tgctagaggg gctgttaacg ctccaatgac aaaaatactg 7021 gactggaatg gcacaagata ttgggcaccc aacagcatga aaaccacaag ctattcagga 7081 cagttctcta gtagccccgt ccacaggtct cctgctcccc tccagcacac tgccccacca 7141 aaaagtaagt tgcaaagtga ttctgctagt gtgtatagct ccccttccac tgtttcttca 7201 caatcaaccc attcaacagt gttgtctgca ggaaccgggt cgtccagatc cacccccacg 7261 tccacagcaa cctccaccct gtctaggacc agcgactggg ttagaggaca aaatgagagg 7321 cttagcccgt ttatggatgg tgctctccaa actacttttg tcacaccacc atcgagcaaa 7381 gcttcatcaa atgggacagt ctcgaccgtg cccaaagctg ttttggactc ctggactggc //