Typing tool
|
Complete norovirus genomes
KC175390 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 3..5102 ORF2: 5083..6705 ORF3: 6705..7511LOCUS KC175390 7511 bp ss-RNA linear VRL 13-MAR-2013 DEFINITION Norovirus Hu/Norwalk/20014/2009/VNM, complete genome. ACCESSION KC175390 VERSION KC175390.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/Norwalk/20014/2009/VNM ORGANISM Norovirus Hu/Norwalk/20014/2009/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-OCT-2012) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA COMMENT Genome sequence lacks part of non-coding region. ##Assembly-Data-START## Assembly Method :: clc_ref_assemble_long v. 3.22.55705 Coverage :: 329.9x Sequencing Technology :: Illumina; 454 ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7511 /organism="Norovirus Hu/Norwalk/20014/2009/VNM" /mol_type="genomic RNA" /strain="Hu/Norwalk/20014/2009/VNM" /host="Homo sapiens; sex: M" /db_xref="taxon:1261243" /country="Viet Nam: Ho Chi Minh City" /collection_date="14-May-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="AFX81264.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSNMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRSTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVKTM PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRIQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRVVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT 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; calicivirin" 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="AFX81265.1" /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="AFX81266.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRINPRTPTPARGSSSTSS 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 ccggattgcc tgagctttcc accgtcaggc 301 aaccggaaga aaccaatacg gccttcagtg tccctccact caaccagagg gagaatagag 361 atgctaagga accactgact ggaacaattc tggaaatgtg ggatggagaa atctaccatt 421 atggcctgta tgttgagcga ggtcttgtgc tgggtgtgca caaaccacca gctgccataa 481 gcctcgccaa ggtcgaacta acaccactct ccttgttctg gagacctgtg tacactcccc 541 agtacctcat ctctccagac actctcaaga aattacacgg agaaacgttt ccctacacag 601 cctttgacaa caattgctat gccttttgtt gttgggtcct ggatctaaat gactcgtggc 661 tgagtaggag aatgatccag agatcaactg gcttcttcag accctaccaa gattggaata 721 gaaaacccct 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 aaatgttgtc atccgctgca 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 gaaggccagg aaactctcaa ccaagtctgc 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 gcatcgactt 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 cgaactacag ggcccagctc 2101 ttaccacctt caactttgac cgcaacaaag tgcttgcctt cagacagctt gctgctgaaa 2161 acaaatatgg gttgatagac acaatgaaag ttgggaggca gctcaaggat gtcaaaacca 2221 tgccagaact taaacaagca ctcaagaaca tctcaatcaa gaagtgccag attgtgtata 2281 gtggttgcac ctacacgctt gaatctgatg 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 ctaccaacaa ggacgggtgc ccaaaaccca 2581 aagatgatga ggagttcgtc atttcatctg acgacattaa aactgagggt aagaaaggga 2641 agaacaagac tggccgtggc aagaagcaca cagccttctc aagtaaaggt ctcagtgatg 2701 aagagtatga tgagtacaag agaattagag aggaaaggaa tggcaagtat tccatagaag 2761 agtaccttca ggacagggac aaatactatg aggaggtggc cattgccagg gcgaccgagg 2821 aagacttctg tgaagaggag gaggccaaga tccggcaaag gatcttcaga ccaacaagga 2881 aacaacgcaa ggaagaaaga gcttctctcg gtttagtcac aggttctgag attaggaaaa 2941 gaaacccaga agacttcaag cctaagggaa aactatgggc tgacgatgac agaagtgtgg 3001 actacaatga gaaactcagt tttgaggccc caccaagcat ctggtcaagg atagtcaact 3061 ttggttcggg ttggggcttc tgggtctccc ctagcctgtt cataacatca acccacgtca 3121 taccccaggg cgcaaaggag ttctttggag tccccatcaa acaaattcag gtacacaagt 3181 caggcgaatt ctgtcgcttg aggttcccaa aaccaatcag gactgacgtg actggcatga 3241 tcttggaaga aggtgcgccc gaaggcaccg tggtcacgct 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 agtccacacg gctgccgctc gtgggggaaa cactgtcata tgtgccaccc 3541 aggggggcga gggggaagct acacttgaag gtggtgacag taagggaaca tactgtggtg 3601 caccaatcct aggcccaggg agtgccccaa aacttagcac caaaaccaaa ttctggagat 3661 catccacagc accactccca cctggcacct atgaaccagc ctaccttggt 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 ggaatgggga gtccttcaca ggcaagctgg cagaccaggc ttccaaggct aacctgatgt 4021 ttgaagaagg gaagaacatg accccagtct acacaggtgc acttaaggat gaattagtca 4081 aaaccgacaa 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 agagagtcgt gctggcagcc 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 ttctccttct atggtgatga cgaaattgtt agtacagaca 4621 taaaattgga cccagagaag ttgacagcaa agctcaagga 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 aacccgttgt 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 ggaaaaatta 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 atgctgggga agatgtcttc acagtctctt gtcgagtcct cactaggccg 5701 tcccctgatt ttgattttat atttttggtg ccacccacag ttgagtcaag aactaaacca 5761 tttactgtcc caatcttaac cgttgaagaa atgaccaatt caagattccc cattcctttg 5821 gaaaagttgt tcacgggtcc cagcggtgcc tttgttgtcc aaccacaaaa tggcagatgc 5881 acgactgatg gcgtgctctt aggcaccacc caactgtctc ctgtcaacat ctgcaccttc 5941 agaggggatg tcacccacat tgcaggttct cgtaattaca caatgaattt ggcatctcta 6001 aattggaaca attatgaccc aacagaagaa attccagccc ctctgggaac tccagatttc 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 accatgcccg gatgcagcgg gtatcccaac 6421 atggatttgg attgcctact cccccaggag tgggtgcagc acttctacca agaggcagct 6481 ccagcacaat ctgatgtggc tctactgaga tttgtgaatc cagacacggg tagggtcctg 6541 tttgagtgca aacttcataa atcaggttat gtcacagtgg ctcacaccgg tcagcatgat 6601 ttggtcatcc cccccaatgg ctattttagg tttgattcct gggttaatca attttacaca 6661 cttgccccca tgggaaacgg aacggggcgt aggcgcgctt tatgatggct ggagctttct 6721 ttgctggatt ggcatctgat gtccttggct ctggacttgg ctccctgatc aacgctgggg 6781 ctggggctat 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 actacaacat 7081 acaatgcagg ccgcttttcc acccctcaac cttcgggggc gttgccagga agaatcaacc 7141 ccaggactcc tacccccgct cggggctcct ccagcacatc ttctaatgct tctactgcta 7201 cttctataca ttcaaatcaa accgtttcaa 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 //