Typing tool
|
Complete norovirus genomes
KC409301 | GII.4 New Orleans | ||
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GII.P4 New Orleans |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7513LOCUS KC409301 7535 bp ss-RNA linear VRL 21-FEB-2013 DEFINITION Norovirus Hu/GII/20469/2010/VNM, complete genome. ACCESSION KC409301 VERSION KC409301.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII/20469/2010/VNM ORGANISM Norovirus Hu/GII/20469/2010/VNM Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7535) AUTHORS Madupu,R., Halpin,R.A., Ransier,A., Fedorova,N., Tsitrin,T., McLellan,M., Stockwell,T., Amedeo,P., Appalla,L., Bishop,B., Edworthy,P., Gupta,N., Hoover,J., Katzel,D., Li,K., Schobel,S., Shrivastava,S., Thovarai,V., Wang,S., My,P.V., Campbell,J., Farrar,J., Vinh,H., Hoang,N.V., Wentworth,D.E. and Baker,S. TITLE Direct Submission JOURNAL Submitted (17-DEC-2012) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA COMMENT This work was supported by the National Institute of Allergy and Infectious Diseases (NIAID), Genome Sequencing Centers for Infectious Diseases (GSCID) program. The genome sequence was generated using overlapping PCR amplicons spanning the genome. The amplicons were pooled by sample and then barcoded and sequenced using Next Generation Sequencing platforms. The consensus sequences of the internal PCR primer hybridization sites were manually verified using reads from amplicons that spanned across the sites. ##Genome-Assembly-Data-START## Current Finishing Status :: Finished Assembly Method :: clc_ref_assemble_long v. 3.22.55705 Genome Coverage :: 421.9x Sequencing Technology :: Illumina; 454 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7535 /organism="Norovirus Hu/GII/20469/2010/VNM" /mol_type="genomic RNA" /strain="Hu/GII/20469/2010/VNM" /host="Homo sapiens; sex: F" /db_xref="taxon:1291872" /country="Viet Nam: Ho Chi Minh City" /collection_date="11-Mar-2010" /PCR_primers="fwd_name: Ampl_1_Forward, fwd_seq: gtgaatgawgatggcgt, rev_name: Ampl_1_Reverse, rev_seq: ttggttgagagyttyctg" /PCR_primers="fwd_name: Ampl_2_Forward, fwd_seq: ccgcaaaatcttcaagtg, rev_name: Ampl_2_Reverse, rev_seq: cwacaggtcttggtctgctrga" /PCR_primers="fwd_name: Ampl_3_Forward, fwd_seq: tcaaccaartctgcttcacctg, rev_name: Ampl_3_Reverse, rev_seq: ratcctttgccggatcttgg" /PCR_primers="fwd_name: Ampl_4_Forward, fwd_seq: ggcaagaagcacacagcctt, rev_name: Ampl_4_Reverse, rev_seq: crrctctytgttgtgttgaatccc" /PCR_primers="fwd_name: Ampl_5_Forward, fwd_seq: tggyaagatcaagaagaggc, rev_name: Ampl_5_Reverse, rev_seq: acaacaaargcacygctrgg" /PCR_primers="fwd_name: Ampl_6_Forward, fwd_seq: gagrccrtccccygattttg, rev_name: Ampl_6_Reverse, rev_seq: atcaatyttgtcttttcaca" /note="genotype: II" gene 5..5104 /gene="POL" CDS 5..5104 /gene="POL" /note="genome polyprotein" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AGE89621.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPNLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LARVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYQLQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM PELKQALKNVSIKECQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGGAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 5..994 /gene="POL" /product="protein p48" mat_peptide 995..2092 /gene="POL" /product="NTPase" /note="p41" mat_peptide 2093..2629 /gene="POL" /product="protein p22" mat_peptide 2630..3028 /gene="POL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3029..3571 /gene="POL" /product="3C-like protease" /note="3CLpro; calcivirin" mat_peptide 3572..5101 /gene="POL" /product="RNA-directed RNA polymerase" gene 5085..6707 /gene="VP1" CDS 5085..6707 /gene="VP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AGE89622.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIPGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6707..7513 /gene="VP2" CDS 6707..7513 /gene="VP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AGE89623.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRATVPARGSSSTFS NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SYVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga 61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agcctccccc gagggaaaaa ccacaaagac ccccacgacc 181 acctactcca gaactggtta aaaatattcc ccctccccca cccaacggag aggatgaaat 241 agtggtttct tatagtgtca aagatggtgt ttccggcttg cctaaccttt ccaccgtcag 301 gcaaccggaa gaatctaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag 361 agatgctaag gaaccactta ctggaacaat tctggaaatg tgggacgggg aaatctacca 421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccac cagctgccat 481 cagcctcgct agggttgagc tagcaccact ctccttgtac tggagacctg tgtacactcc 541 tcagtacctc atctctccag acactctcaa gaaattatcc ggagaaacgt tcccctacac 601 agcctttgac aacaactgtt atgccttttg ctgctgggtc ctggacctaa atgactcgtg 661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa 721 taggaaaccc cttcccacta tggatgactc caaaataaag aaggtagcta acatattcct 781 gtgtgctctg tcctcgctgt tcaccagacc cataaaagac ataataggga agataaggcc 841 tcttaacatc ctcaacatct tagcctcatg tgattggact tttgcaggta tagtggagtc 901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gattgccccc ttacttggtg actaccagct gcaaggacct gaggaccttg cagttgagct 1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg 1081 gaaaatgttg tcatctgctg cgtctacctt gagagcttgt aaagaccttg gtgcatatgg 1141 gctagagatc ctaaagttgg tcatgaagtg gttcttcccg aagaaggaag aggcaaatga 1201 gctggctata gtgaggtcta tcgaggatgc agtcctggac ctcgaggcaa ttgaaaacaa 1261 ccatatgacc accttgctca aagacaaaga cagtctggca acctatatga gaacacttga 1321 ccttgaggag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg 1381 cacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc accgagcgaa 1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat 1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga 1561 ccagcgtgtg ggcctcatcc cacgcaatgg cgtcgaccat tgggatgcgt acaaggggga 1621 gagggtcgtc ctatgggacg attatggaat gagcaaccct attcacgatg ccctcaggct 1681 gcaagaactc gctgacactt gccccctcac tctaaactgt gacaggatcg aaaataaagg 1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcgccact 1801 ggactatgtc aactttgaag catgctcgag gcgcatcgac ttcctcgtgt atgcagaagc 1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc 1921 tttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa 1981 gaacgggaac accccacacg gaaagggcgt tatgaagact ctcaccactg gctcccttat 2041 tgcccgggca tcagggctac tccatgagag gttagatgaa tttgaactgc agggcccagc 2101 tctcaccacc ttcaatttcg atcgcaataa ggtgcttgcc tttagacagc ttgctgctga 2161 aaataaatat ggattgatgg acacaatgag agttgggaaa cagctcaagg atgtcagaac 2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aaggagtgcc aaatagtgta 2281 tagtggttgc acctacatac ttgagtctga tggcaagggc aatgtgaaag ttgacagaat 2341 ccaaagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc atttgaggtg 2401 cgccagaatc agatactatg tcaagtgtgt ccaggaggcc ctgtattcca tcattcaaat 2461 tgctggggct gcatttgtca ccacgcgcat tgtcaagcgc atgaacatac aagacctatg 2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggacgggt gcccaaaacc 2581 taaggacgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gtaagaaagg 2641 gaagaacaag actggtcgcg gcaagaagca cacagcattt tcaagcaaag gcctcagtga 2701 tgaagagtac gatgagtaca agaggattag agaagaaagg aatggcaagt actccataga 2761 agagtacctt caggacaggg acaaatacta tgaggaggtg gccattgcca gggcgactga 2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacaag 2881 gaaacaacgc aaggaggaaa gagtctctct cggtctggtc acaggctctg aaattaggaa 2941 aagaaaccca gatgacttca aacccaaagg gaaattgtgg gctgacgatg acaggagtgt 3001 ggactacaat gagaaactca gttttgaggc cccaccaagt atctggtcga gaatagtcaa 3061 ctttggttca ggctggggat tttgggtctc ccccagtctg ttcataacat caacccatgt 3121 cataccccag ggcgcaaaag agttctttgg agtccccatc aaacaaatac aggtacacaa 3181 gtcaggcgag ttctgtcgct tgagattccc aaaaccaatc aggactgatg tgacgggcat 3241 gatcttagaa gaaggcgcac ctgagggcac tgtggtcaca ctactcatca aaaggtccac 3301 tggggaactc atgcccctag cagctaggat ggggacccat gcgactatga agatccaagg 3361 gcgcactgtt ggaggccaga tgggcatgct tctgacagga tccaacgcca agagcatgga 3421 cctgggtact acaccaggtg attgtggctg cccctatatc tacaagagag gtaatgacta 3481 tgtggtcatt ggggtccaca cggctgccgc acgtgggggg aacactgtca tatgtgccac 3541 ccaggggagt gaaggagagg ctacacttga aggtggtgac aacaagggga catactgtgg 3601 tgcaccaatc ctaggcccag ggggtgcccc aacacttagc accaagacca aattctggag 3661 atcgtccaca gcaccactcc cacctggcac ctatgaacca gcctatcttg gtggcaagga 3721 ccctagggtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaagccatt 3781 cacagagccc aggggcaagc caccaaaacc aagtgtgtta gaagctgcca agaagaccat 3841 catcaacgtc cttgagcaaa caattgatcc acctgagaaa tggtcgttcg cacaagcttg 3901 cgcgtccctt gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg 3961 ctggaacggg gagtccttta caggcaagct ggcagaccag gcttccaagg ccaacctgat 4021 gtttgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttagt 4081 taaaactgac aaaatttatg gtaagatcaa gaagaggcta ctctggggct cggacttggc 4141 gaccatgatc cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcacactg 4201 tgtcacactt cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga 4261 gaggcattcc aggtacacat atcattatga tgctgattac tctcgatggg attcaacaca 4321 acagagagcc gtgttggcag cagctctaga aatcatggtt aaattctccc cagaaccaca 4381 cttggctcag gtagtcgcgg aggaccttct ttctcctagc gtggtggacg tgggcgactt 4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc 4501 catcgcccac tggcttctca ctctttgtgc gctctctgaa gtcacaaacc tgtcccctga 4561 taccatacag gctaactccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga 4621 cataaaattg gacccagaaa aattgacagc aaagctcaga gaatatgggt taaaaccaac 4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gacctgaatg gcctaacttt 4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc 4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat 4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca 4921 cggcccagca ttttacagca aaatcagcaa attggtcatt gcagagctaa aagaaggtgg 4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtccacag ccaaccttgt cccagaggtc aacaatgagg 5161 ttatggcttt ggagcccgta gttggtgccg ccattgcggc acctgtagcg ggccaacaaa 5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag 5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatttga 5341 atccctacct ttcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc 5401 aggtaatcct cgcggggaac gcgttcaccg ccggaaaaat catatttgca gcagtcccac 5461 caaatttccc aactgaaggt ttgagcccca gccaggtcac tatgttcccc cacataatag 5521 tagatgttag gcaattggaa cctgtgttga ttcccttacc cgatgttagg aataatttct 5581 accattataa tcaatcaaat gaccccacca tcaaattgat agcaatgttg tacacaccac 5641 ttagggctaa caatgccggg gacgatgtct tcacagtttc ttgtcgagtt ctcacgagac 5701 catcccccga ttttgatttt atatttttgg tgccacccac agttgaatca agaactaaac 5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaaggttc cccattcctt 5821 tggaaaagtt gttcacgggc cccagtagtg cctttgttgt tcaaccacaa aacggcaggt 5881 gcacgactga tggcgtgctc ctaggtacta cccaactgtc tcccgtcaac atctgcacct 5941 tcagagggga cgtcacccat attccaggca gtcgtaacta cacaatgaat ttggcctccc 6001 aaaattggaa cagttacgat ccaacagaag aaatcccagc ccccctggga actccagatt 6061 tcgtggggaa gattcagggt gtgctcaccc aaaccacaag gacaaatggc tcgacccgcg 6121 gccacaaagc tacagtgtac actgggagcg ccgacttttc tccaaaactg ggtagagttc 6181 aatttgccac tgacacagac aatgattttg aaactaacca aaacacaaag ttcaccccag 6241 tcggtgttat ccaggatggt agtaccaccc cccgaaatga accccaacaa tgggtgctcc 6301 caagttactc aggcagaaac attcataatg tgcacctggc ccccgctgta gcccccactt 6361 tcccgggcga gcagctcctc ttcttcagat ctactatgcc cggatgcagc gggtacccca 6421 acatggactt ggactgtctg ctcccccagg aatgggtgca atatttctac caggaggcag 6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccggacaca ggtagggttt 6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggcacacact ggccaacatg 6601 atttagttat cccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca 6661 cacttgcccc catgggaaat gggacggggc gtagacgtgc attataatgg ctggagcttt 6721 ctttgctgga ttggcatctg acgtccttgg ctctggactt ggttccctaa tcaatgctgg 6781 ggctggggcc atcaatcaaa aagttgaatt tgaaaataat agaaaattgc aacaagcttc 6841 cttccaattt agtagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca 6901 agcacaaatt gaggccacca aaaagttgca acaggaaatg atgagagtta aacaagcaat 6961 gctcctagag ggtggattct ctgagacaga tgcagcccgt ggggcgatca acgcccccat 7021 gacaaaaact ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac 7081 atataatgca ggccgctttt ccacccccca accctcgggg gcactaccag gaagagctaa 7141 tcttagggct actgtccccg cccggggttc ctccagcacg ttctctaact cttctattgc 7201 tacttctgtg tattcaaatc aaaccacctc aacgagactt ggttctacag ctggttctgg 7261 caccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa 7321 taggaatttg tcacctttca tgaggggggc ccataacatc tcgtatgtca ccccaccatc 7381 tagcagatcc tctagccaag gcacagtctc aaccgtgccc aaagaagttt tggactcctg 7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgca agcgagggga 7501 gtcacgggtg taatgtgaaa agacaaaatt gataa //