Typing tool
|
Complete norovirus genomes
JN400616 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7509LOCUS JN400616 7509 bp RNA linear VRL 19-DEC-2013 DEFINITION Norovirus Hu/GII-4/CGMH18/2008/TW, complete genome. ACCESSION JN400616 VERSION JN400616.1 KEYWORDS . SOURCE Norovirus Hu/GII-4/CGMH18/2008/TW ORGANISM Norovirus Hu/GII-4/CGMH18/2008/TW Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7509) AUTHORS Tsai,C.N., Lin,C.Y., Lin,C.W., Shih,K.C., Chiu,C.H. and Chen,S.Y. TITLE Clinical relevance and genotypes of circulating noroviruses in northern Taiwan, 2006-2011 JOURNAL J. Med. Virol. 86 (2), 335-346 (2014) PUBMED 24009100 REFERENCE 2 (bases 1 to 7509) AUTHORS Tsai,C.-N., Lin,C.-Y., Lin,C.-W., Shih,K.-C., Chi,H.-C., Chao,H.-C., Lai,M.-W., Yu,T.-H., Chen,S.-Y. and Chiu,C.-H. TITLE Direct Submission JOURNAL Submitted (27-JUL-2011) Graduate Institute of clinical medical sciences, 259, Wen-Hwa 1st Rd, Kwei-Shan, Taoyuan, Taiwan FEATURES Location/Qualifiers source 1..7509 /organism="Norovirus Hu/GII-4/CGMH18/2008/TW" /mol_type="genomic RNA" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:1195630" /country="Taiwan" /collection_date="03-Oct-2008" /note="serogroup: GII-4" CDS 1..5100 /note="ORF1; encodes NTPase, 3A, VPg, 3Cpro and 3Dpol" /codon_start=1 /product="non-structural polyprotein" /protein_id="AFN09968.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSNMAVTLKRALGARP KQPPPREITQGPPRPTTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTM PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC PKPKDNEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLI TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPENWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYNKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" gene 5081..6703 /gene="VP1" CDS 5081..6703 /gene="VP1" /note="ORF2" /codon_start=1 /product="major viral capsid protein" /protein_id="AFN09969.1" /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRDVPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6703..7509 /gene="VP2" CDS 6703..7509 /gene="VP2" /note="ORF3" /codon_start=1 /product="minor viral capsid protein" /protein_id="AFN09970.1" /translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGVLPGRANPRTPTPARGSPNTSS NASTATSIYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGGSQH IVCHPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRGGESRV" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc 61 gcaaaatctt caagtgacaa aatgttttct aacatggctg tcactctcaa acgagccctc 121 ggggcgcggc ctaaacagcc ccccccgagg gaaataacac aaggaccccc acgaccaact 181 actccagaac tggtcaaaaa gatccctccc cccccgccca acggagagga cgaagtagtg 241 gtttcttata gtgccaaaga tggtgtttcc ggtttacctg agctttccac cgttaggcaa 301 ccggaagaaa ccaatacggc tttcagtgtc cctcccctca atcagaggga gaatagggat 361 gctaaggaac cactgactgg aacaattctg gaaatgtggg atggagaaat ctaccattat 421 ggcctgtatg ttgagcgagg tcttgtgctg ggtgtgcaca aaccaccagc tgccattagc 481 ctcgccaagg tcgaactaac accactctcc ttgttctgga gacctgtgta cactcctcag 541 tacctcatct ctccagacac tctcaagaaa ttacacggag aaacatttcc ctacacagcc 601 ttcgataaca attgctatgc cttctgttgt tgggtcctgg atctaaacga ctcgtggctg 661 agtaggagaa tgatccagag aacaactggc ttcttcagac cctaccaaga ttggaatagg 721 aaacccctcc ccactatgga tgattccaaa ttaaagaagg tagctaacat attcctgtgc 781 accctgtctt cgctattcac caggcccata aaagacataa tagggaagtt aaggcctctc 841 aacatcatca acatcctggc ttcatgtgat tggactttcg caggcatagt ggagtccttg 901 atactcttgg cagagctctt tggagtcttc tggacacccc cagatgtgtc tgcgatgatt 961 gcccccttac tcggtgattt cgagttacaa gggcctgagg accttgtagt ggagctcgtc 1021 cctgtagtaa tggggggaat tggtttggtg ctaggattca ccaaagagaa gattggaaaa 1081 atgttgtcgt ctgctgcatc taccttaaga gcttgtaaag atcttggtgc gtatgggcta 1141 gagatcctaa agttagtcat gaagtggttc ttcccgaaga aagaggaagc aaatgaactg 1201 gctatggtga gatccatcga ggatgcagtg ctagaccttg aggcaattga aaacaaccat 1261 atgaccacct tgctcaaaga caaagacagc ctggcaacct atatgagaac ccttgacctc 1321 gaggaagaga aagccagaaa actctcaacc aagtctgctt cacctgacat cgtgggcaca 1381 atcaacgccc ttctggcgag aatcgccgct gcacgctccc tggtgcaccg agcgaaggag 1441 gagctttcta gcagaccaag acctgtagtc ttgatgatat caggcagacc aggaataggg 1501 aagacccacc ttgctaggga agtggctaag agaatcgcag cctccctcac aggagaccag 1561 cgtgtaggcc tcatcccacg caatggcgtc gatcactggg atgcgtacaa gggagagagg 1621 gtcgtcctat gggacgacta tggaatgagc aatcccatcc acgacgccct caggctgcaa 1681 gaactcgctg acacttgccc cctcactcta aactgtgaca ggattgagaa taaaggaaag 1741 gtctttgaca gcgatgtcat cattatcact actaacctgg ccaacccagc accactggac 1801 tatgtcaact ttgaagcgtg ctcgaggcgc attgatttcc tcgtgtatgc agaagccccc 1861 gaggtcgaaa aggcgaagcg tgacttccca ggccaacctg acatgtggaa aaacgctttt 1921 agttctgatt tctcacacat aaaattggca ctggctccac aaggtggctt tgataagaac 1981 gggaacaccc cacatgggaa gggcgtcatg aagactctca ccactggctc cctcattgcc 2041 cgggcatcag ggctgctcca tgagagattg gatgagtttg aactacaggg cccagctctt 2101 accaccttca actttgaccg caacaaagtg cttgccttca ggcagcttgc tgctgaaaat 2161 aaatacgggt tgatggacac aatgaaagtt gggaggcagc tcaaggatgt caaaaccatg 2221 ccagaactta aacaagcact caagaatatc tcaatcaaga agtgccagat tgtgtatagt 2281 ggttgcacct acacacttga gtctgatggc aagggcaatg tgaaagttga cagagttcag 2341 agcacctccg ttcagaccaa caatgagctg gctggcgctc tgcaccacct gaggtgcgcc 2401 agaatcaggt actatgtcaa gtgtgttcag gaagccctgt attctatcat ccagattgct 2461 ggggctgcat ttgtcaccac gcgcatcatc aagcgtgtga acattcaaga cttatggtcc 2521 aagccacaag tggaaaacac agaggaggcc accaacaagg acgggtgccc aaaacccaaa 2581 gataatgagg agttcgtcat ttcatctgac gacattaaaa ctgagggtaa gaaagggaag 2641 aacaagactg gccgtggcaa gaagcacaca gccttctcaa gtaaaggtct cagtgatgaa 2701 gagtatgatg agtacaagag aattagagag gaaaggaatg gtaagtactc catagaagag 2761 tatcttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gaccgaggaa 2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tcttcagacc aacaaggaaa 2881 caacgcaagg aagaaagagc ttctctcggt ttaatcacag gttctgaaat taggaaaagg 2941 aacccagacg acttcaagcc taaggggaaa ttatgggctg acgatgacag aagtgtggac 3001 tacaatgaaa aactcagttt tgaggcccca ccaagcatct ggtcaaggat agtcaacttt 3061 ggctcaggtt ggggcttctg ggtctccccc agcctgttta taacatcaac ccacgtcata 3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaattcaggt acacaagtca 3181 ggcgaattct gtcgcttgag gttcccaaaa ccaatcagga ctgatgtgac tggcatgatc 3241 ctggaagaag gcgcgcccga aggcaccgtg gtcactctac tcatcaaaag gtctactgga 3301 gaactcatgc ccttagcagc tagaatgggg acccatgcaa ccatgaaaat tcaagggcgc 3361 actgttggag gtcagatggg catgcttctg acaggatcca acgccaaaag catggatcta 3421 ggcaccacac caggtgattg cggctgtccc tacatctaca agagaggaaa tgactatgtg 3481 gtcattggag tccacacggc tgccgctcgt gggggaaaca ctgtcatatg tgccacccag 3541 gggggtgagg gggaagctac acttgaaggt ggtgacagta agggaacata ctgtggcgca 3601 ccaatcctag gcccagggag tgccccaaaa cttagcacca aaaccaaatt ctggagatca 3661 tccacagcac cactcccacc tggcacctat gaaccagcct accttggtgg caaggacccc 3721 agagtcaagg gtggcccctc gttgcagcaa gttatgaggg accagctgaa accatttaca 3781 gagcctaggg gtaagccacc aaagccaagt gtgttagaag ctgccaagaa aaccatcatc 3841 aatgtccttg aacaaacaat tgacccacct gagaattggt cgttcgcaca agcttgcgcg 3901 tcccttgaca agaccacttc tagcggccat ccacaccaca tgcggaaaaa cgactgctgg 3961 aacggggaat ctttcacagg caagctggcg gaccaggctt ccaaggccaa cctgatgttt 4021 gaagaaggga agaacatgac tccagtctac acaggtgcac ttaaggatga attagtcaaa 4081 actgacaaaa tttatggtaa gatcaagaag aggctactct ggggctcgga tttggcaacc 4141 atgatccggt gtgctcgagc attcggaggc ctaatggatg aactcaaagc acactgtgtc 4201 acactcccta tcagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaag 4261 cattccaggt ataggtacca ctatgatgct gattactctc ggtgggattc aacacagcag 4321 agagccgtac tggcagctgc tctagagatt atggttaaat tctcctcaga accacatttg 4381 gcccaggtag tagcagaaga ccttctttct cctagcgtgg tggacgtggg ggacttcaca 4441 atatcaatca acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc 4501 gcccactggc ttctcactct ctgtgcactc tccgaagtta caaatttgtc cccagacatc 4561 atacaggcta attctctctt ctccttctat ggtgatgatg aaattgttag tacggacata 4621 aaattagacc cagagaagtt gacagcaaag cttaaggaat acgggttgaa accaacccgc 4681 cctgataaaa ctgaaggacc tcttgttatt tctgaagact tagatggctt gaccttcctg 4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagctcaata 4801 ctcaggcaaa tgtactggac taggggccct aaccatgaag atccatctga atcaatgatt 4861 ccacactctc aaagacccat acagttgatg tccttactgg gagaggccgc actccacggc 4921 ccaacattct acaataaaat cagcaaatta gtcattgcag agttaaaaga aggtggtatg 4981 gatttttacg tgcccaggca agagccaatg ttcagatgga tgagattctc agatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga 5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat 5161 ggctttggag cccgttgtcg gtgccgctat tgcggcgcct gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggagagt tcacagtatc 5281 ccctagaaac gctccaggtg aaatactatg gagcgcaccc ttaggccctg atctgaatcc 5341 ctacctatct catttggcca gaatgtataa tggttatgca ggtggttttg aagtgcaggt 5401 gatcctcgcg gggaacgcgt tcaccgccgg aaaaattata tttgcagcag tcccaccaaa 5461 ttttccaact gaaggcttga gccccagcca ggtcactatg ttcccccaca taatagtgga 5521 tgttaggcaa ttggaacctg tgttgatccc cttacctgat gttaggaata acttctatca 5581 ttataatcaa tcaaatgatt ctaccattaa gttgatagca atgctgtata caccacttag 5641 ggctaataat gctggggaag atgtcttcac agtctcttgt cgagtcctca cgaggccatc 5701 ccctgatttt gattttatat ttttggtgcc acctacagtt gagtcaagaa ctaaaccatt 5761 tactgtccca atcttgactg ttgaggaaat gaccaattca agattcccca ttcctttgga 5821 aaagttgttc acgggtccca gcagtgcctt tgttgttcaa ccacaaaatg gcaggtgcac 5881 gactgatggc gtgctcttag gcaccaccca actgtctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccacattg caggttctcg taattacaca atgaatttgg cttctctaaa 6001 ttggaacaat tatgacccaa cagaagaaat tccagcccct ctaggaactc cagatttcgt 6061 gggaaagatc caaggtgtgc tcactcaaac cacaaaggga gatggttcga cccgtggcca 6121 taaagctaca gtttacactg ggagtgcccc ctttactcca aagctgggca gtgttcaatt 6181 cagcactgat acagaaaatg attttgaaac tcaccaaaac acaaaattca ccccagtcgg 6241 tgtcatccag gatggtggca ccacccaccg aaatgaaccc caacaatggg tgctcccaag 6301 ttattcaggt agagatgtcc ctaatgtgca cctagcccct gctgtagccc ccactttccc 6361 gggtgaacaa cttcttttct ttaggtctac tatgcccgga tgcagcgggt atcccaacat 6421 ggatttggat tgcctactcc cccaggagtg ggtgcagcac ttctaccaag aggcagctcc 6481 agcacaatct gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcctgtt 6541 tgagtgcaaa cttcataaat caggctatgt cacagtggct cacaccggcc agcatgattt 6601 ggtcatcccc cccaatggtt attttaggtt tgattcctgg gttaatcaat tctacacact 6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcttta taatggctgg agctttcttt 6721 gctggattgg catctgatgt ccttagctct ggacttggtt ccctaatcaa tgctggggct 6781 ggggctatca accaaaagat tgattttgaa aataacagaa aattgcagca agcttccttc 6841 cagtttagca gtaatctaca acaggcttcc tttcaacatg ataaagaaat gctccaagca 6901 caaattgagg ccactaaaaa gttgcaacag gaaatgatga aagtcaaaca ggcagtgctc 6961 ttagaaggtg ggttctctga aacagatgca gcccgtgggg caatcaacgc ccctatgaca 7021 aaggctctgg actggagcgg aacaaggtac tgggcccctg atgctaggac tacaacatac 7081 aacgcaggcc gtttttccac ccctcaacct tcgggggtac tgccaggaag agccaatccc 7141 aggactccta cccccgctcg gggctccccc aatacatctt ctaacgcttc tactgctact 7201 tctatatatt caaatcaaac tgtttcaacg agacttggtt ctacagctgg ttctggcacc 7261 agtgtctcga gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga 7321 aatttgtcac ctttcatgag ggggggctca caacatatcg tttgtcaccc cccatctagc 7381 agatcctcta gccaaggcac agtttcaacc gtgcctaaag aagttttgga ctcctggact 7441 ggcgctttca acacgcgcag gcagcctctt ttcgctcaca ttcgtagggg aggggagtca 7501 cgggtgtaa //