Typing tool
|
Complete norovirus genomes
KC409289 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 3..5102 ORF2: 5083..6705 ORF3: 6705..7511LOCUS KC409289 7511 bp ss-RNA linear VRL 13-MAR-2013 DEFINITION Norovirus Hu/GII/20302/2009/VNM, complete genome. ACCESSION KC409289 VERSION KC409289.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII/20302/2009/VNM ORGANISM Norovirus Hu/GII/20302/2009/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 :: 341.1x Sequencing Technology :: Illumina; 454 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7511 /organism="Norovirus Hu/GII/20302/2009/VNM" /mol_type="genomic RNA" /strain="Hu/GII/20302/2009/VNM" /host="Homo sapiens; sex: F" /db_xref="taxon:1291860" /country="Viet Nam: Ho Chi Minh City" /collection_date="30-Nov-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="AGE89585.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSNMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLVDTMKVGRQLKDVKTM PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRIQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG RYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVIGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPERWSFAQACASLDKTTSSGHPHHMRKNDCW 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="AGE89586.1" /translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQTNDPTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEVPAPLGTPDFVGKIQGVL 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="AGE89587.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGMLPGRINPRTPTPARGSSSTSS NASTATSIHSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV" ORIGIN 1 gaatgaagat ggcgtctaac gacgcttccg ctgccgctgt tgctaacagc aacaacgaca 61 ccgcaaaatc ttcaagtgac aaaatgtttt ctaacatggc tgtcactttt aaacgagccc 121 tcggggcgcg gcctaaacag ccccccccga gggaaatacc acaaagaccc ccacgaccac 181 ctactccaga actggtcaaa aagatccctc ctcccccgcc caacggagag gatgaagtag 241 tggtttctta tagtgccaaa gatggcgttt ccggtttacc tgagctttcc accgtcaggc 301 aaccggaaga aaccaatacg gccttcagtg tccctccact caaccagagg gagaatagag 361 atgctaagga accactgact ggaacaattc tggagatgtg ggatggagaa atctaccatt 421 atggcctgta tgttgagcga ggtcttgtgc tgggtgtgca caaaccacca gctgccataa 481 gcctcgccaa ggtcgaatta acaccactct ccctgttctg gagacctgtg tacactcccc 541 agtacctcat ctctccagac actctcaaga aattacacgg agaaacgttt ccctacacag 601 cctttgacaa caattgttat gccttttgtt gttgggtcct ggatctaaat gactcgtggc 661 tgagtaggag aatgatccag agaacaactg gcttctttag accctaccaa gactggaata 721 ggaaacccct ccccactatg gatgattcca aattaaagaa ggtagctaac atattcctgt 781 gcgccctgtc ttcgctattc accagaccca taaaagacat aataggaaag ctaagacctc 841 tcaacatcat caacatcctg gcttcatgtg attggacttt cgcaggcata gtggagtctt 901 tgatactctt ggcagagctc tttggagtct tctggacacc cccagatgtg tctgcgatga 961 ttgccccctt actcggtgat ttcgagttac aaggacctga ggaccttgta gtggagctcg 1021 tccctgtagt aatgggggga attggtttgg tgttgggatt caccaaagag aagattggga 1081 aaatgttgtc atctgctgca tccaccttga gagcttgtaa agatcttggt gcatatgggc 1141 tagagatcct aaagttagtc atgaagtggt tcttcccgaa gaaagaggag gcaaatgaac 1201 tggctatggt gagatccatc gaggatgcag ttctggacct tgaggcaatt gaaaacaacc 1261 atatgaccac cttgctcaaa gacaaagaca gcctggcaac ctacatgaga acccttgacc 1321 tcgaggaaga gaaagccaga aaactctcaa ccaaatctgc ttcacctgac atcgtgggca 1381 caatcaacgc ccttctggcg agaatcgccg ctgcacgctc cctggtgcac cgagcgaagg 1441 aggagctttc cagcagacca agacctgtag tcttgatgat atcaggcaga ccagggatag 1501 gaaaaaccca 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 tcaccacctt caactttgac cgcaacaaag tgcttgcctt caggcagctt gcagctgaaa 2161 acaaatatgg gttagtagac acaatgaaag ttgggaggca gctcaaggat gtcaaaacca 2221 tgccagaact taaacaagca ctcaaaaaca tctcaatcaa gaagtgccag attgtgtata 2281 gtggttgcac ctacacactt gagtctgatg gcaagggcaa tgtgaaagtt gacagaatcc 2341 agagcacctc cgtacagacc aacaatgagc ttgctggcgc cctgcatcat ctgaggtgcg 2401 ccagaatcag gtactatgtc aagtgtgttc aggaggccct gtattctatc atccagattg 2461 ctggggccgc atttgtcacc acgcgcatta ttaagcgtgt 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 agtaccttca 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 cgccaagcat ctggtcaagg atagtcaact 3061 ttggttcagg ttggggcttc tgggtctccc ctagcctgtt cataacatca acccacgtca 3121 taccccaggg cgcaaaggag ttctttggag ttcccatcaa acaaattcag gtacacaagt 3181 caggcgaatt ttgtcgcttg aggttcccaa aaccaatcag gactgacgtg attggcatga 3241 tcttggaaga aggtgcgccc gaaggcaccg tggtcacact actcatcaaa 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 aacttagcac 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 ctgagaggtg gtcgttcgca caagcttgcg 3901 cctcccttga caagaccact tctagcggcc atccgcacca tatgcggaaa aacgactgct 3961 ggaatgggga gtccttcaca ggcaagctgg cagaccaggc ttctaaggct aacctgatgt 4021 ttgaagaagg gaagaacatg accccagtct acacaggtgc gcttaaggat gaattagtca 4081 aaactgacaa aatttatggt aagatcaaga agaggcttct ctggggctcg gatttagcaa 4141 ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg 4201 tcacacttcc cattagagtt ggtatgaata tgaatgagga tggccccatc atcttcgaga 4261 agcattccag gtacagatac cactatgatg ctgattactc tcggtgggat tcaacacaac 4321 agagagccgt gctggcagct gctctagaaa tcatggttaa attctcctca gaaccacatt 4381 tggctcaggt agtcgcagaa gatcttcttt cccctagcgt ggtggatgtg ggtgatttca 4441 caatatcaat caacgagggc cttccctctg gggtgccctg cacctcccaa tggaactcca 4501 tcgcccactg gcttctcact ctttgtgcac tctccgaagt cacaaatttg tccccagaca 4561 tcatacaggc taattctctc ttctccttct atggtgatga tgaaattgtt agtacagaca 4621 taaaattgga cccagagaag ttgacagcaa 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 agagctaaaa 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 cggagccgct attgcggcgc ctgtagcggg ccaacaaaat 5221 gtaattgacc cctggattag aaacaatttt gtacaagccc ctggtggaga gttcacagta 5281 tcccctagaa acgctccagg tgaaatatta tggagcgcgc ccttaggccc tgatctgaat 5341 ccctacctat ctcatttggc cagaatgtat aatggttatg caggtggttt tgaagtgcag 5401 gtgatcctcg cggggaacgc gttcaccgcc ggaaaaatta tatttgcagc agtcccacca 5461 aattttccaa ctgaaggcct gagtcccagc caagtcacta tgttccccca cataatagta 5521 gatgttaggc aattggaacc tgtgttgatc cccttacctg atgttaggaa taacttctat 5581 cattataatc agacaaatga tcctaccatt aaattgatag caatgctgta tacaccactt 5641 agggccaata atgctgggga agatgtcttc acagtctctt gtcgagtcct cactaggccg 5701 tcccctgatt ttgattttat atttttggtg ccacccacag ttgagtcaag aactaaacca 5761 tttactgtcc caatcctaac cgttgaagaa atgaccaatt caagattccc cattcctttg 5821 gaaaagttgt tcacgggtcc cagcggtgcc tttgttgtcc aaccacaaaa tggcaggtgc 5881 acgactgatg gcgtgctctt aggcaccacc caactgtctc ctgtcaacat ctgcaccttc 5941 agaggggatg tcacccacat tgcaggttct cgtaattaca caatgaattt ggcatctcta 6001 aattggaaca attatgaccc aacagaagaa gttccagccc ctctgggaac tccagatttc 6061 gtgggaaaga tccaaggtgt gctcactcaa accacaaaag gagatggctc gacccgtggc 6121 cacaaagcta cagtttacac tgggagtgcc ccctttactc caaagctggg cagtgttcaa 6181 ttcagtactg acacagaaaa tgattttgaa actcaccaaa acacaaaatt caccccagtt 6241 ggtgttatcc aggatggtgg caccacccac cgaaatgaac cccaacaatg ggtgctccca 6301 agctattcag gtagagatgt tcataatgta cacctagccc ctgctgtagc ccccactttt 6361 ccgggtgaac aacttctttt cttcaggtcc actatgcccg gatgcagcgg gtatcccaac 6421 atggatttgg attgcctact cccccaggag tgggtgcagc acttctacca agaggcagct 6481 ccagcgcaat 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 gaaagtcaaa caggcaatgc 6961 tcctagaagg tggattctct gaaacagatg cagcccgtgg ggcaatcaac gcccccatga 7021 caaaggtttt ggactggagc ggaacaaggt actgggcccc tgatgctagg accacaacat 7081 acaatgcagg ccgcttttcc accccccaac cttcggggat gctgccagga agaatcaatc 7141 ccaggactcc tacccccgct cggggctcct ccagcacatc ttctaatgct tctactgcta 7201 cttctataca ttcaaatcaa actgtttcaa cgagacttgg ttctacagct ggttctggta 7261 ccaatgtctc gagtctcccg tcaactgcaa ggactaggag ttgggttgag gatcaaaata 7321 gaaatttgtc acccttcatg aggggggctc ataatatatc gtttgtcacc ccaccatcta 7381 gcagatcctc tagccaaggc acagtctcaa ccgtgcctaa agaagttttg gactcctgga 7441 ctggcgcttt caacacgcgc aggcagcctc tcttcgctca cattcgtagg cgaggggagt 7501 cacgggtgta a //