Typing tool
|
Complete norovirus genomes
KC409316 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 3..5102 ORF2: 5083..6705 ORF3: 6705..7511LOCUS KC409316 7511 bp ss-RNA linear VRL 13-MAR-2013 DEFINITION Norovirus Hu/GII/30212/2009/VNM, complete genome. ACCESSION KC409316 VERSION KC409316.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII/30212/2009/VNM ORGANISM Norovirus Hu/GII/30212/2009/VNM Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7511) 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 sequence lacks part of non-coding region. ##Genome-Assembly-Data-START## Current Finishing Status :: Finished Assembly Method :: clc_ref_assemble_long v. 3.22.55705 Genome Coverage :: 220.1x Sequencing Technology :: Illumina; 454 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7511 /organism="Norovirus Hu/GII/30212/2009/VNM" /mol_type="genomic RNA" /strain="Hu/GII/30212/2009/VNM" /host="Homo sapiens; sex: F" /db_xref="taxon:1291887" /country="Viet Nam: Ho Chi Minh City" /collection_date="05-Oct-2009" /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 3..5102 /gene="POL" CDS 3..5102 /gene="POL" /note="genome polyprotein" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AGE89666.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSNMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGRMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVKTM PDLKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRIQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG RYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 3..992 /gene="POL" /product="protein p48" mat_peptide 993..2090 /gene="POL" /product="NTPase" /note="p41" mat_peptide 2091..2627 /gene="POL" /product="protein p22" mat_peptide 2628..3026 /gene="POL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3027..3569 /gene="POL" /product="3C-like protease" /note="3CLpro; calcivirin" mat_peptide 3570..5099 /gene="POL" /product="RNA-directed RNA polymerase" gene 5083..6705 /gene="VP1" CDS 5083..6705 /gene="VP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AGE89667.1" /translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6705..7511 /gene="VP2" CDS 6705..7511 /gene="VP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AGE89668.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRINPRTPTPARGSSNTSS NASTATSIHSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV" ORIGIN 1 gaatgaagat ggcgtctaac gacgcttccg ctgccgctgt tgctaacagc aacaacgaca 61 ccgcaaaatc ttcaagtgac aaaatgttct ctaacatggc tgtcactttt aaacgggccc 121 tcggggcgcg gcctaaacag ccccccccga gggaaatacc acaaagaccc ccacgaccac 181 ctaccccaga actggtcaaa aagatccctc ctcccccgcc caacggagag gacgaagtag 241 tggtttctta tagtgccaaa gatggcgttt ccggtttacc tgagctttcc accgtcaggc 301 aaccggaaga aaccaatacg gccttcagtg tccctccact taaccagagg gagaatagag 361 atgctaagga accactgact ggaacaattc tggaaatgtg ggatggagaa atctaccatt 421 atggcctgta tgttgagcga ggtcttgtgc tgggtgtgca caaaccacca gctgccataa 481 gcctcgccaa ggtcgaacta acaccactct ccttgttctg gagacctgtg tatactcccc 541 agtacctcat ctctccagac actctcaaga aattacacgg agaaacgttt ccctacacag 601 cctttgacaa caattgctat gccttttgtt gttgggtcct ggatctaaat gactcgtggc 661 tgagtaggag aatgatccag agaacaactg gcttcttcag accctaccaa gactggaata 721 ggaaacccct ccccactatg gatgattcca aattaaagaa ggtagctaac atattcctgt 781 gcgccctgtc ttcgctattc accaggccca taaaagacat aataggaaag ctaagacctc 841 tcaacatcat caacatcctg gcttcatgtg attggacttt cgcaggcata gtggagtcct 901 tgatactctt ggcagagctc tttggagtct tctggacacc cccagatgtg tctgcgatga 961 ttgccccctt actcggtgat ttcgagttac aaggacctga ggaccttgta gtggagctcg 1021 tccctgtagt aatgggggga attggtttgg tgctgggatt caccaaagag aagattggga 1081 gaatgttgtc atcagctgca tccaccttga gagcttgtaa agatcttggt gcatatgggc 1141 tagagatcct aaagttagtc atgaagtggt tcttcccgaa gaaagaggag gcaaatgaac 1201 tggctatggt gagatccatc gaggatgcag tactggacct tgaggcaatt gaaaacaacc 1261 atatgaccac cttgctcaaa gacaaagaca gcctggcaac ctacatgaga acccttgacc 1321 tcgaggaaga gaaagccaga aaactctcaa ccaagtctgc ttcacctgac atcgtgggta 1381 caatcaacgc ccttctggcg agaatcgccg ctgcacgctc cctggtgcac cgagcgaagg 1441 aggagctttc cagcagacca agacctgtag tcttgatgat atcaggcaga ccggggatag 1501 gaaaaactca ccttgctagg gaagtggcta agagaatcgc agcctccctc acaggagacc 1561 agcgtgtagg cctcatccca cgcaatggcg tcgatcactg ggatgcgtac aagggggaga 1621 gggtcgtcct atgggacgac tatggaatga gcaaccccat tcacgacgcc cttaggctgc 1681 aagaactcgc tgacacttgc ccccttactc taaattgtga caggattgag aataaaggaa 1741 aggtctttga cagcgatgtc atcattatca ccactaatct ggccaaccca gcaccactgg 1801 actatgtcaa ctttgaagcg tgctcgaggc gcatcgattt cctcgtgtat gcagaagccc 1861 ccgaggtcga aaaggcgaag cgtgacttcc cgggccaacc tgacatgtgg aaaaacgctt 1921 ttagttctga tttctcacac ataaaattgg cactggctcc acaaggtggc tttgataaga 1981 acgggaacac cccacacggg aagggcgtca tgaagactct caccactggc tccctcattg 2041 cccgggcatc agggctgctc catgagagat tggatgagtt tgaactacag ggcccagctc 2101 ttaccacctt caactttgac cgcaacaaag tgcttgcctt cagacagctt gctgctgaaa 2161 acaaatatgg gttgatagac acaatgaaag ttgggaggca gctcaaggat gtcaaaacca 2221 tgccagatct taaacaagca ctcaaaaaca tctcaatcaa gaagtgccag attgtgtata 2281 gtggttgcac ctacacactt gagtctgatg gcaagggcaa tgtgaaagtt gacagaatcc 2341 agagcacctc cgtacagacc aacaatgagc tggctggcgc cctgcatcat ctgaggtgcg 2401 ccagaatcag gtactatgtc aagtgtgtcc aggaggccct gtattctatc atccagattg 2461 ctggggctgc atttgtcacc acgcgcatca tcaagcgtgt gaacattcaa gacttatggt 2521 ccaagccaca agtggaaaac acagaggagg ccaccaacaa ggacgggtgc ccaaaaccca 2581 aagatgatga ggagttcgtc atttcatctg acgacattaa aactgagggt aagaaaggga 2641 agaacaagac tggccgtggc aagaagcata cagccttttc aagtaaaggt ctcagtgatg 2701 aagagtatga tgagtacaag agaattagag aggaaaggaa tggcaggtat tccatagaag 2761 agtacctcca ggacagggac aaatactatg aggaggtggc cattgccagg gcgaccgagg 2821 aagacttctg tgaagaggag gaggccaaga tccggcaaag gatctttaga ccaacaagga 2881 aacaacgcaa ggaagaaaga gcttctctcg gtttagtcac aggttctgag attaggaaaa 2941 gaaacccaga tgacttcaag cctaagggaa aactgtgggc tgacgatgac agaagtgtgg 3001 actacaatga gaaactcagt tttgaggccc caccaagcat ctggtcaagg atagtcaact 3061 ttggttcagg ttggggcttc tgggtctccc ctagcctgtt cataacatca acccacgtca 3121 taccccaggg cgcaaaggag ttctttggag tccccatcaa acaaattcag gtacacaagt 3181 cgggcgagtt ttgtcgcttg aggttcccaa aaccaatcag gactgacgtg actggcatga 3241 tcttggaaga aggtgcgccc gaaggcaccg tggtcacact gctcatcaaa aggtctactg 3301 gagaactcat gcccctagca gctagaatgg ggacccatgc aaccatgaaa attcaagggc 3361 gcaccgttgg aggtcagatg ggcatgcttc tgacaggatc caacgccaaa agcatggatc 3421 taggcaccac accaggtgat tgcggctgtc cctacatcta caagagagga aatgactatg 3481 tggtcattgg agtccatacg gctgccgctc gtgggggaaa cactgtcata tgtgccaccc 3541 aggggggcga gggggaagct acacttgaag gtggtgacag taagggaaca tactgtggtg 3601 caccaatcct aggcccaggg agtgccccaa agcttagcac caaaaccaaa ttctggagat 3661 catccacagc accactccca cctggcacct atgaaccagc ataccttggt ggcaaggacc 3721 ccagagtcaa gggtggccct tcgttgcagc aagtcatgag ggaccagctg aaaccattta 3781 cagagcccag gggtaagcca ccaaagccaa gtgtgttaga agctgccaag aaaaccatca 3841 tcaatgtcct tgaacaaaca attgacccac ctgagaagtg gtcgttcgca caagcttgcg 3901 cctcccttga caagaccact tctagcggcc atccgcacca tatgcggaaa aacgactgct 3961 ggaacgggga gtccttcaca ggcaagctgg cagaccaggc ttccaaggct aacctgatgt 4021 ttgaagaagg gaagaacatg accccagtct acacaggtgc acttaaggat gaattagtca 4081 aaactgacaa aatttatggt aagatcaaga agaggcttct ctggggctcg gatttagcaa 4141 ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg 4201 tcacacttcc tattagagtt ggtatgaata tgaatgagga tggccccatc atcttcgaga 4261 agcattccag gtacagatac cactatgatg ctgattactc tcggtgggat tcaacacaac 4321 agagagccgt gctggcagct gctctagaaa tcatggttaa attctcctca gaaccacatt 4381 tggctcaggt agtcgcagaa gatcttcttt cccctagcgt ggtggatgtg ggtgacttca 4441 caatatcaat caacgagggc cttccctctg gggtgccctg cacctcccaa tggaactcca 4501 tcgcccactg gcttctcact ctttgtgcac tctccgaagt cacaaatttg tccccagaca 4561 tcatacaggc taattctctc ttctcctttt atggtgatga tgaaattgtt agtacagaca 4621 taaaattgga cccagagaag ctgacagcaa agcttaagga atatgggttg aaaccaaccc 4681 gccctgacaa aactgaagga cctctcgtta tttctgaaga cttagatggt ttgactttcc 4741 tgcggagaac tgtgacccgc gacccagctg gttggtttgg aaaactggag cagagctcaa 4801 tactcaggca aatgtactgg actaggggcc ccaaccatga agatccatct gaatcaatga 4861 ttccacactc tcaaagaccc atacaattga tgtccttact gggagaggcc gcactccacg 4921 gcccaacatt ctacagtaaa atcagcaaat tagtcattgc agagttaaaa gaaggtggta 4981 tggattttta cgtgcccagg caagagccaa tgttcagatg gatgagattc tcagatctga 5041 gcacgtggga gggcgatcgc aatctggctc ccagttttgt gaatgaagat ggcgtcgaat 5101 gacgccaacc catctgatgg gtccgcagcc aacctcgtcc cagaggtcag caatgaggtt 5161 atggctttgg agcccgttgt cggtgccgct attgcggcgc ctgtagcggg ccaacaaaat 5221 gtaattgacc cctggattag aaacaatttt gtacaagccc ctggtggaga gttcacagta 5281 tcccctagaa acgctccagg tgaaatacta tggagcgcgc ccttaggccc tgatctgaat 5341 ccctacctat ctcatttggc cagaatgtat aatggttatg caggtggttt tgaagtgcag 5401 gtgatcctcg cggggaacgc gttcaccgcc ggaaaaatca tatttgcagc agtcccacca 5461 aattttccaa ctgaaggcct gagtcccagc caggtcacca tgttccccca cataatagta 5521 gatgttaggc aattggaacc tgtgttgatc cccttacctg atgttaggaa taatttctat 5581 cattataatc agacaaatga ttctaccatt aaattgatag caatgctgta tacaccactt 5641 agggccaata acgctgggga agatgtcttc acagtctctt gtcgagtcct cactaggccg 5701 tcccctgatt ttgattttat atttttggtg ccacccacag ttgagtcaag aactaaacca 5761 tttactgtcc caatcttaac cgttgaagaa atgaccaatt caagattccc cattcctttg 5821 gaaaagttgt tcacgggtcc cagcggtgct tttgttgtcc aaccacaaaa tggcaggtgc 5881 acgactgatg gcgtgctctt aggcaccacc caactgtctc ccgtcaacat ctgcaccttc 5941 agaggggatg tcacccacat tgcaggttct cgtaattaca caatgaattt ggcatctcta 6001 aattggaaca attacgaccc aacagaagaa attccagccc ctctgggaac tccagatttt 6061 gtgggaaaga tccaaggtgt gctcactcaa accacaaaag gagatggctc gacccgtggc 6121 cataaagcta cagtttacac tgggagtgcc ccctttactc caaagctggg cagtgttcaa 6181 ttcagtactg acacagaaaa tgattttgaa actcaccaaa acacaaaatt caccccagtc 6241 ggtgtcatcc aggatggtgg caccacccac cgaaatgaac cccaacaatg ggtgctccca 6301 agttattcag gtagagatgt tcataatgta cacctagccc ctgctgtagc ccccactttt 6361 ccgggtgaac aacttctttt cttcaggtcc actatgcccg gatgcagcgg gtatcccaac 6421 atggatttgg attgcctact cccccaggag tgggtgcagc acttctacca agaggcagct 6481 ccagcacaat ctgatgtggc tctattgaga tttgtgaatc cagacacggg tagggtcctg 6541 tttgagtgca aacttcataa atcaggctat gtcacagtgg ctcacaccgg tcagcatgat 6601 ttggtcatcc cccccaatgg ctattttagg tttgattcct gggttaatca gttctacacg 6661 cttgccccca tgggaaacgg aacggggcgt aggcgcgcct tataatggct ggagctttct 6721 ttgctggatt ggcatctgat gtccttggct ctggacttgg ttccctaatc aatgctgggg 6781 ctggggccat caaccaaaag attgattttg aaaataatag aaaattgcag caagcttcct 6841 tccagtttag cagtaatcta caacaggctt cctttcaaca cgataaagag atgctccaag 6901 cacaaattga ggccactaaa aagttgcaac aggaaatgat gaaagtcaag caggcaatgc 6961 tcctagaagg tggattctct gaaacagatg cagcccgtgg ggcaatcaac gcccccatga 7021 caaaggtttt ggactggagc ggaacaaggt actgggcccc tgatgctagg accacaacat 7081 acaatgcagg ccgcttttcc acccctcaac cttcggggac gctgccagga agaatcaatc 7141 ccaggactcc tacccccgct cggggctcct ccaacacatc ttctaatgct tccactgcta 7201 cttctataca ttcaaatcaa actgtttcaa cgagacttgg ttctacagct ggttctggta 7261 ccaatgtctc gagtctcccg tcaactgcaa ggactaggag ttgggttgag gatcaaaaca 7321 gaaatttgtc acctttcatg aggggggctc ataacatatc gtttgtcacc ccaccatcta 7381 gcagatcctc tagccaaggc acagtctcaa ccgtgcctaa agaagttttg gactcctgga 7441 ctggcgcttt caacacgcgc aggcagcctc tcttcgctca cattcgtagg cgaggggagt 7501 cacgggtgta a //