Typing tool
|
Complete norovirus genomes
KC409256 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 3..5102 ORF2: 5083..6705 ORF3: 6705..7511LOCUS KC409256 7511 bp ss-RNA linear VRL 13-MAR-2013 DEFINITION Norovirus Hu/GII/20156/2009/VNM, complete genome. ACCESSION KC409256 VERSION KC409256.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII/20156/2009/VNM ORGANISM Norovirus Hu/GII/20156/2009/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 :: 232.2x Sequencing Technology :: Illumina; 454 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7511 /organism="Norovirus Hu/GII/20156/2009/VNM" /mol_type="genomic RNA" /strain="Hu/GII/20156/2009/VNM" /host="Homo sapiens; sex: F" /db_xref="taxon:1291827" /country="Viet Nam: Ho Chi Minh City" /collection_date="17-Sep-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="AGE89486.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSSMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKKVPPPPPNGEDEVVVSYSAKDGISGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLNRRMIQRTTGFFRPYQDWNRKPLPTTDDSKLKKVANIFLCTLSSLFTRPIKDIIGK LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGRQLKDVKTM PELKQALKSISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC PKPKDDEEFVITSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVATLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGRLADQASKANLMFEEGKSMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL 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="AGE89487.1" /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFEAHQNTKFTPVGVIQDG 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="AGE89488.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSAPQPSGSLPGRINPRAPTPARVSSSTSS NASTVTSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV" ORIGIN 1 gaatgaagat ggcgtctaac gacgcttccg ctgccgctgt tgctaacagc aacaacgaca 61 ccgcaaaatc ttcaagtgac aaaatgtttt ctagcatggc tgtcactttt aaacgagccc 121 tcggggcgcg gcctaaacag cctcccccga gggaaatacc gcaaagaccc ccacgaccac 181 ctactccaga actggtcaaa aaggtccctc ctcccccgcc caacggagag gatgaagtag 241 tggtttctta tagtgccaaa gatggcattt ccggtctacc tgagctttcc accgtcagac 301 aaccagaaga aaccaatacg gccttcagtg tccctccact caatcagagg gagaataggg 361 atgctaagga accactgact ggaacaattc tggaaatgtg ggatggagaa atctatcatt 421 atggcctgta tgttgaacga ggtcttgtgc tgggtgtgca caaaccacca gctgccatta 481 gcctcgccaa ggtcgaacta acaccactct ccttgttctg gagacctgtg tacaccccac 541 agtacctcat ctctccagac actctcaaga aattacacgg agaaacattt ccctacacag 601 cctttgacaa caactgctat gccttctgtt gctgggtcct ggatctaaac gactcgtggc 661 tgaataggag aatgatccag agaacaactg gcttcttcag accctaccaa gactggaata 721 ggaaacccct ccctactacg gatgattcca aattaaagaa ggtagctaac atattcctgt 781 gcaccctgtc ttcgctattc accaggccca taaaagacat aatagggaag ttaaggcctc 841 tcaacatcat caacatcctg gcttcatgtg attggacttt cgcaggcatc gtggagtcct 901 tgatactctt ggcagagctc tttggagtct tctggacacc cccagatgtg tctgcgatga 961 ttgccccctt actcggtgat ttcgagttac aaggacctga ggaccttgta gtggagctcg 1021 tccctgtggt aatgggggga attggtttgg tgctgggatt caccaaagag aagattggaa 1081 aaatgttgtc atctgctgca tccaccttga gagcttgtaa agatctcggt gcatatgggc 1141 tagagatcct aaagttagtc atgaagtggt tcttcccgaa gaaagaggag gcaaatgaac 1201 tggctatggt gagatccatc gaggatgcag tactggacct tgaggcaatt gaaaacaacc 1261 atatgaccac cttgctcaaa gataaagaca gcctggcaac ctacatgaga acccttgacc 1321 tcgaggaaga gaaagccaga aaactctcaa ccaagtctgc ttcacctgac atcgtgggca 1381 caatcaacgc ccttctggcg agaatcgccg ctgcacgctc cctggtgcac cgagcgaagg 1441 aggagctttc cagcagacca agacctgtgg tcttgatgat atcaggtaga ccagggatag 1501 ggaagaccca ccttgctagg gaagtggcta agagaatcgc agcctccctc acaggagacc 1561 agcgcgtagg cctcatccca cgcaatggcg tcgatcactg ggatgcgtac aagggggaga 1621 gggtcgtcct atgggacgac tatggaatga gcaatcccat ccacgacgcc ctcaggctgc 1681 aagaactcgc tgacacttgc cccctcactc taaattgtga caggattgag aataaaggaa 1741 aggtctttga cagcgatgtc atcattatca ctactaatct ggccaaccca gcaccactgg 1801 actatgtcaa ctttgaagcg tgctcgaggc gcatcgattt cctcgtgtac gcagaagccc 1861 ccgaggtcga aaaggcgaag cgtgacttcc cgggccaacc tgacatgtgg aaaaacgctt 1921 ttagttctga tttctcacac ataaaattgg cactggctcc acaaggtggc ttcgataaga 1981 acgggaacac cccacacggg aagggcgtca tgaagactct caccactggc tcccttattg 2041 cccgggcatc agggctgctc catgagagat tggatgagtt tgaactacag ggcccagctc 2101 tcaccacctt caactttgac cgcaacaaag tgcttgcctt caggcagctt gctgctgaaa 2161 acaaatacgg gttgatggac acaatgagag ttgggaggca gctcaaggat gtcaaaacca 2221 tgccagaact taaacaagca ctcaagagca tctcaatcaa gaagtgtcag attgtgtaca 2281 gtggttgcac ctacacactt gagtctgatg gcaagggcaa tgtgaaggtt gacagagttc 2341 agagcacctc cgtacagacc aacaatgagc tggctggcgc cctgcaccat ctgaggtgcg 2401 ccagaatcag gtactatgtt aagtgtgtcc aggaggccct gtattctatc attcagattg 2461 ctggggctgc atttgtcacc acgcgcatca tcaagcgtgt gaacattcaa gacttatggt 2521 ccaagccaca agtggaaaac acagaggaag ccaccaacaa ggacgggtgc ccaaaaccca 2581 aagatgatga ggagttcgtc attacatctg acgacattaa aactgagggt aagaaaggaa 2641 agaacaagac tggccgtggt aagaagcaca cagccttctc aagtaaaggt ctcagtgatg 2701 aagagtatga tgagtacaag agaattagag aggaaaggaa tggcaaatac tccatagaag 2761 agtaccttca ggacagggac aaatactatg aggaggtggc cattgccagg gcgaccgagg 2821 aagacttctg tgaagaggag gaggccaaga tccggcaaag gatcttcaga ccaacaagga 2881 aacaacgcaa ggaagaaaga gcttctctcg gtttagtcac aggttctgaa attaggaaaa 2941 gaaacccaga tgacttcaag cccaagggga aactatgggc tgacgatgac agaagtgtgg 3001 actacaatga gaaactcagt tttgaggctc cgccaagcat ctggtcaagg atagtcaact 3061 ttggctcagg ttggggcttc tgggtctccc ccagcctatt cataacatca acccacgtca 3121 taccccaggg cgcaaaggag ttctttggag tccccatcaa acaaattcag gtgcacaagt 3181 caggcgaatt ctgtcgcttg aggttcccaa aaccaatcag gactgatgtg actggcatga 3241 tcttggaaga aggcgcgcct gaaggcaccg tggccacact actcatcaaa aggtctactg 3301 gagaactcat gcccctagca gccagaatgg ggacccatgc aaccatgaag attcaagggc 3361 gcactgttgg aggtcagatg ggcatgcttc tgacaggatc caacgccaaa agcatggatc 3421 taggcaccac accaggtgat tgcggctgtc cctacatcta caagagagga aatgactatg 3481 tggtcattgg agtccacacg gctgccgctc gtgggggaaa cactgtcata tgtgccaccc 3541 aggggggtga gggggaagct acacttgaag gtggtgacag taagggaacg tactgtggtg 3601 cgccaatcct aggcccaggg agcgccccaa aacttagcac caaaaccaaa ttctggagat 3661 catccacagc accactccca cctggcacct atgagccagc ctaccttggt ggcaaggacc 3721 ccagggtcaa gggtggcccc tcgctgcagc aagtcatgag agaccagctg aaaccattca 3781 cagagcccag gggtaagcca ccaaagccaa gtgtgttaga agctgccaag aaaaccatca 3841 tcaatgttct tgaacaaaca attgacccac ctgagaagtg gtcgttcgca caggcttgcg 3901 cgtcccttga caagaccact tctagcggcc atccgcacca catgcggaaa aacgactgct 3961 ggaacgggga gtccttcaca ggcaggctgg cagaccaggc ttccaaggcc aacctgatgt 4021 ttgaagaagg gaagagcatg accccagttt acacaggtgc gctcaaggat gagttagtca 4081 aaactgacaa aatttatggc aagatcaaga agaggcttct ctggggctcg gatttagcaa 4141 ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg 4201 tcacacttcc tatcagagtt ggtatgaata tgaatgagga tggccccatc atcttcgaga 4261 agcactccag gtacaggtac cactatgatg ctgattactc tcggtgggat tcaacacaac 4321 agagagccgt gctggcagct gctctagaaa ttatggttaa attctcctca gaaccacatt 4381 tggctcaggt ggtcgcagaa gaccttcttt ctcctagcgt ggtggatgtg ggtgacttca 4441 caatatcaat caatgagggt cttccctctg gggtgccctg cacttcccaa tggaactcca 4501 tcgcccactg gcttctcact ctatgtgcac tctccgaagt tacaaatttg tccccagaca 4561 tcatacaggc taattctctc ttctccttct atggtgatga tgaaattgtt agtacagaca 4621 taaaactaga cccagagaag ttgacagcaa agcttaagga atatgggtta aaaccaaccc 4681 gccctgataa aactgaagga cctcttgtta tttctgaaga cttagatggt ttgactttcc 4741 tgcggagaac tgtgacccgc gacccagctg gttggtttgg aaaactggag cagagctcaa 4801 tactcaggca aatgtactgg accaggggcc ccaaccatga agatccatct gaatcaatga 4861 ttccacactc tcaaagaccc atacaattga tgtccctact gggagaggcc gcactccacg 4921 gcccaacatt ctatagtaaa atcagcaaat tagtcattgc agagctaaaa gaaggtggta 4981 tggattttta cgtgcccagg caagagccaa tgttcagatg gatgagattc tcagatctga 5041 gcacgtggga gggagatcgc aatctggctc ccagctttgt gaatgaagat ggcgtcgaat 5101 gacgccaacc catctgatgg gtccgcagcc aacctcgtcc cagaggtcaa caatgaggtt 5161 atggctttgg agcccgttgt cggtgccgct attgcggcgc ctgtagcggg ccaacaaaat 5221 gtaattgacc cctggattag gaataatttt gtacaagccc ctggtggaga gttcacagta 5281 tcccctagaa acgctccagg tgaaatacta tggagcgcgc ccttaggccc tgatctgaat 5341 ccctacctat ctcatttggc cagaatgtat aatggttatg caggtggctt tgaagtgcag 5401 gtgatcctcg cggggaacgc gttcaccgcc ggaaaaatta tatttgcagc agttccacca 5461 aattttccaa ctgaaggctt gagccccagc caggttacta tgttccccca cataatagta 5521 gatgttaggc aactggaacc tgtgttgatc cccttacctg atgttaggaa taacttctat 5581 cattataatc agtcaaatga ttctaccatt aagttgatag caatgctgta cacaccactt 5641 agggctaata atgctgggga agatgtcttc acagtctctt gtcgagtcct cacgaggcca 5701 tcccctgatt ttgattttat atttttggtg ccacctacag ttgagtcaag aactaaacca 5761 tttactgtcc caatcttaac tgttgaagaa atgaccaatt caagattccc catccctttg 5821 gaaaagttgt tcacgggccc cagcggtgcc tttgttgttc aaccacaaaa tggtaggtgc 5881 acgactgatg gcgtgctctt aggcaccacc caactgtctc ctgtcaacat ctgcaccttc 5941 agaggggatg tcacccacat tgcaggttct cgcaattaca cgatgaattt ggcttctcta 6001 aattggaaca attatgaccc aacagaagaa attccagccc ctctgggaac tccagatttc 6061 gtgggaaaga tccaaggtgt gctcactcaa accacaaagg gagatggctc gacccgtggc 6121 cataaagcta cagtttacac tgggagtgcc ccctttactc caaagctggg cagtgtccaa 6181 ttcagcactg atacagaaaa tgattttgaa gctcaccaaa acacaaaatt caccccagtc 6241 ggtgtcatcc aggatggtgg caccacccac cgaaatgaac cccaacaatg ggtgctccca 6301 agctattcag gtagagatgt ccacaatgta cacctggccc ctgctgtagc ccccactttt 6361 ccgggtgaac aacttctttt cttcaggtcc actatgcccg gatgcagtgg gtatcccaac 6421 atggatttgg attgcctact cccccaggag tgggtgcagc acttctacca agaggcagct 6481 ccagcacaat ctgatgtggc tctattgaga tttgtgaatc cagacacggg tagggtcctg 6541 tttgagtgca aacttcataa atcaggctat gtcacagtgg ctcacactgg ccagcatgat 6601 ttggtcatcc cccccaatgg ctattttagg tttgattcct gggttaatca attctacaca 6661 cttgccccca tgggaaatgg aacggggcgt agacgtgctt tataatggct ggggctttct 6721 ttgctggatt ggcatctgat gtccttggct ctggacttgg ctccctaatc aatgctgggg 6781 ctggggctat caaccaaaag attgattttg aaaataacag aaaattgcag caagcttcct 6841 tccagtttag cagtaatcta caacaggcct cctttcaaca tgacaaagag atgctccaag 6901 cacaaattga ggccactaaa aagttgcaac aggaaatgat gaaagtcaaa caggcaatgc 6961 tcttagaagg tgggttctct gaaacagatg cagctcgtgg ggcaatcaac gcccccatga 7021 caaaggtttt ggactggagc ggaacaaggt actgggcccc tgatgctagg actacaacat 7081 acaatgcagg ccgcttttcc gcccctcaac cctcggggtc attgccagga agaatcaatc 7141 ccagggctcc tacccccgct cgggtctcct ccagtacatc ctctaatgct tctactgtta 7201 cttctatata ttcaaatcaa actgtttcaa cgagacttgg ttctacagct ggctctggca 7261 ccaatgtctc gagtctcccg tcaactgcaa ggactaggag ttgggttgag gatcaaaaca 7321 gaaatttgtc acctttcatg aggggggctc acaacatatc gtttgtcacc ccaccatcta 7381 gcagatcctc tagccaaggc acagtctcaa ccgtgcctaa agaagttttg gactcctgga 7441 ctggcgcttt caacacgcgc aggcagcctc tcttcgctca cattcgtagg cgaggggagt 7501 cacgggtgta a //