Typing tool
|
Complete norovirus genomes
KC175357 | GII.4 Den Haag | ||
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GII.P4 Den Haag |
ORF1: 3..5102 ORF2: 5083..6705 ORF3: 6705..7511LOCUS KC175357 7511 bp ss-RNA linear VRL 13-MAR-2013 DEFINITION Norovirus Hu/Norwalk/10148/2009/VNM, complete genome. ACCESSION KC175357 VERSION KC175357.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/Norwalk/10148/2009/VNM ORGANISM Norovirus Hu/Norwalk/10148/2009/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 :: 367.0x Sequencing Technology :: Illumina; 454 ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7511 /organism="Norovirus Hu/Norwalk/10148/2009/VNM" /mol_type="genomic RNA" /strain="Hu/Norwalk/10148/2009/VNM" /host="Homo sapiens; sex: M" /db_xref="taxon:1261210" /country="Viet Nam: Ho Chi Minh City" /collection_date="10-Aug-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="AFX81165.1" /translation="MKMASNDAFAAAVANSNNDTAKSSSDKMFSSMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDIEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRVAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTM PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC PKPKDNEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGRDPRVKDGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQIYWTRGP 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="AFX81166.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRNVPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD 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="AFX81167.1" /translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYSAGRFSTPQPSGALPGRTNPRAPIPARGSPSTSS GASTATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV" ORIGIN 1 gaatgaagat ggcgtctaac gacgctttcg ctgccgctgt tgctaacagc aacaacgaca 61 ccgcaaaatc ttcaagtgac aaaatgtttt ctagcatggc tgtcactttt aaacgagccc 121 tcggggcgcg gcctaaacag ccccccccga gggaaatacc acaaagaccc ccacgaccac 181 ctactccaga actggtcaaa aagatccctc ctcccccgcc caacggagag gatgaagtag 241 tggtctctta cagtgccaaa gatggcgttt ccggcttacc tgagctttcc accgtcaggc 301 aaccggaaga aaccaatacg gccttcagtg tccctccact caaccagagg gagaataggg 361 atgctaagga accactgact ggaacaattc tggagatgtg ggacggagaa atctaccatt 421 atggcctgta tgttgagcga ggtcttgtgc tgggtgtgca caaaccacca gctgccatta 481 gcctcgccaa ggtcgaatta acaccactct ccttgttctg gagacctgtg tacactcctc 541 agtacctcat ctctccagac actctcaaga aattacacgg agaaacattt ccctacacag 601 ccttcgacaa caattgctat gccttttgct gctgggtcct ggatctaaac gactcgtggc 661 tgagtaggag aatgatccag agaacaactg gcttcttcag accctaccaa gattggaata 721 ggaaacccct ccccactatg gatgattcca aattaaagaa ggtagctaac atattcctgt 781 gcaccctgtc ttcgctattc acaaggccca taaaagacat aatagggaag ttaaggcctc 841 tcaacatcat caacatcctg gcttcatgtg attggacttt cgcaggcata gtggagtcct 901 tgatactctt ggcagagctc tttggagtct tctggacacc cccagatgtg tctgcgatga 961 ttgccccctt actcggtgat ttcgagttac aaggacctga ggaccttgta gtggagctcg 1021 tccctgtagt aatgggggga attggcttgg tgctaggatt caccaaagag aagattggaa 1081 aaatgttgtc atctgctgca tccaccttga gagcttgtaa agatcttggt gcgtatgggc 1141 tagagatcct aaagttagtc atgaagtggt tcttcccgaa gaaagaggaa gcaaatgaac 1201 tggctatggt gagatccatc gaggatgcag tgctggatct tgaggcaatt gaaaacaacc 1261 atatgaccac cttgctcaaa gacaaagaca gcctggcaac ctatatgaga acccttgaca 1321 tcgaggaaga gaaagccaga aaactctcaa ccaagtccgc ttcacctgac atcgtgggta 1381 caatcaacgc ccttctggcg agaatcgccg ctgcacgctc cctggtgcac cgagcgaagg 1441 aggagctttc cagcagacca agacctgtag tcttgatgat atcaggcaga ccaggaatag 1501 gtaagaccca ccttgccagg gaagtggcta agagagtcgc agcctccctc acaggagacc 1561 agcgtgtagg cctcatccca cgcaatggcg tcgatcactg ggatgcgtac aagggggaga 1621 gggtcgtcct atgggacgac tatggaatga gtaatcccat ccacgacgcc ctcaggctgc 1681 aagaactcgc tgacacttgc cccctcactc taaattgtga caggattgag aataaaggaa 1741 aggtctttga cagcgatgtc atcatcatca ctactaacct ggccaaccca gcaccactgg 1801 attatgtcaa ctttgaagcg tgctcgaggc gcatcgattt cctcgtgtat gcagaagccc 1861 ccgaggtcga aaaggcaaag cgtgacttcc cgggccaacc cgacatgtgg aaaaacgctt 1921 ttagttctga tttctcacac ataaaattgg cactggctcc gcaaggtggc tttgacaaga 1981 acgggaacac cccacacggg aagggcgtca tgaagactct caccactggc tccctcattg 2041 cccgggcatc agggctgctc catgagagat tggatgagtt tgaactacag ggcccagccc 2101 ttaccacctt caattttgat cgcaacaaag tgcttgcctt caggcagctt gctgctgaaa 2161 acaaatacgg gttgatggac acaatgaaag ttgggaggca gctcaaggat gtcaaaacca 2221 tgccagaact taaacaagca ctcaagaata tctcaatcaa gaagtgccag attgtgtata 2281 gtggttgcac ctacacactt gagtctgatg gcaagggcaa tgtgaaagtt gacagagttc 2341 agagcacctc cgttcagacc aacaatgagc tggctggcgc cctgcaccat ctaaggtgcg 2401 ccagaatcag gtactatgtc aagtgtgttc aggaggccct gtattctatc atccagattg 2461 ctggggctgc atttgtcacc acgcgcatca tcaagcgtgt gaatattcaa gacttgtggt 2521 ccaagccaca agtggaaaac acagaggagg ccaccaacaa ggacgggtgc ccaaaaccca 2581 aagataatga ggagttcgtc atttcatctg acgacattaa aactgagggt aagaaaggga 2641 agaacaagac tggccgtggc aagaagcaca cagccttctc aagtaaaggt ctcagtgatg 2701 aagagtatga tgagtacaag agaattagag aggaaaggaa tggcaagtac tccatagaag 2761 agtaccttca ggacagggac aaatactatg aggaggtggc cattgccagg gcgaccgagg 2821 aagacttctg tgaagaggag gaggccaaga tccggcaaag gatcttcaga ccaacaagga 2881 aacaacgcaa ggaagaaaga gcttctctcg gtttggtcac aggttctgaa atcaggaaaa 2941 ggaacccaga agacttcaag cccaagggga aactatgggc tgacgatgac agaagtgtgg 3001 actacaatga aaaactcagc tttgaggccc caccaagcat ctggtcaagg atagtcaact 3061 ttggctcagg ttggggcttc tgggtctcac ccagcctgtt cataacatca acccacgtca 3121 taccccaggg cgcgaaggag ttctttggag tccccatcaa gcaaattcag gtacacaagt 3181 caggcgaatt ctgtcgcttg aggttcccaa aaccaatcag gactgatgtg actggcatga 3241 tcttggaaga aggtgcgccc gaaggcaccg tggtcacact actcatcaaa aggtctactg 3301 gagaactcat gcccctagcg gctagaatgg ggacccatgc aaccatgaaa atccaagggc 3361 gcactgttgg aggtcagatg ggcatgcttc tgacagggtc caacgccaaa agcatggatc 3421 taggcaccac accaggtgat tgcggctgtc cctacatcta caagagagga aatgactatg 3481 tggtcattgg agtccacacg gctgccgctc gtgggggaaa cactgtcata tgtgccaccc 3541 aagggggtga gggggaagct acacttgaag gtggtgacag taagggaaca tactgtggtg 3601 caccaatcct aggcccaggg agtgccccaa aacttagtac caaaaccaaa ttctggagat 3661 catccacagc accactccca cctggcacct atgagccagc ctaccttggt ggcagggacc 3721 ccagagtcaa ggatggcccc tcgttgcagc aagtcatgag ggaccagctg aaaccattta 3781 cagagcctag gggcaaaccg ccaaagccaa gtgtgttaga agctgccaag aaaaccatca 3841 tcaatgtcct tgaacaaaca attgacccac ctgagaagtg gtcgttcgca caagcttgcg 3901 cgtcccttga caagaccact tctagcggcc atccgcacca catgcggaaa aacgactgct 3961 ggaacgggga gtccttcaca ggcaaattgg cagaccaggc ttccaaggcc aacctgatgt 4021 ttgaagaagg gaagaacatg accccagtct acacaggtgc acttaaggat gaattagtca 4081 aaactgacaa aatttatggt aagatcaaga agaggcttct ctggggctcg gatttggcaa 4141 ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg 4201 tcacacttcc tatcagagtt ggtatgaata tgaatgagga tggccccatc atcttcgaga 4261 agcattccag gtacagatac cactatgatg ctgattactc tcggtgggat tcaacacaac 4321 agagagccgt gctggcagct gctctagaaa tcatggttaa attctcctca gaaccacatt 4381 tggctcaggt agtagcagaa gaccttcttt ctcctagcgt ggtggacgtg ggtgacttca 4441 caatttcaat caacgagggt cttccctctg gggtgccctg cacctcccag tggaactcca 4501 tcgcccactg gcttcttact ctctgtgcac tctccgaagt tacaaatttg tccccagaca 4561 tcatacaggc taattctctc ttctccttct atggtgatga tgaaattgtt agtacagaca 4621 taaaattaga cccagagaag ttgacagcaa agcttaaaga atacgggttg aaaccaaccc 4681 gccctgataa aactgaagga cctcttgtta tttctgaaga cttagatggt ttgactttcc 4741 tgcggagaac tgtgacccgc gacccagctg gttggtttgg aaaactggag cagagctcaa 4801 tactcaggca aatatactgg actaggggcc ccaaccatga agatccatct gaatcaatga 4861 ttccacactc tcaaagaccc atacaattga tgtctttact gggagaggcc gcactccacg 4921 gcccaacatt ctatagtaaa atcagtaaat tagtcattgc agagctaaaa gaaggtggta 4981 tggattttta cgtgcccagg caagagccaa tgttcagatg gatgagattc tcagatctga 5041 gcacgtggga gggcgatcgc aatctggctc ccagttttgt gaatgaagat ggcgtcgagt 5101 gacgccaacc catctgatgg gtccgcagcc aacctcgtcc cagaggtcaa caatgaggtt 5161 atggctttgg agcccgttgt cggtgccgct attgcggcgc ctgtagcggg ccaacaaaat 5221 gtaattgacc cctggattag aaataatttt gtacaagccc ctggtggaga gttcacagta 5281 tcccctagaa acgctccagg tgaaatacta tggagcgcgc ccttaggccc tgatctgaat 5341 ccctatctat ctcatttggc cagaatgtat aatggttatg caggtggttt tgaagtgcag 5401 gtgatcctcg cggggaacgc gttcaccgcc ggaaaaatta tatttgcagc agtcccacca 5461 aattttccaa ctgaaggctt gagtcccagc caggtcacta tgttccccca cataatagtg 5521 gatgttaggc aattggaacc tgtgttgatc cccttacctg atgttaggaa taacttctat 5581 cactataacc agtcaaatga ttctaccatt aaactgatag caatgctgta tacaccactt 5641 agggctaata atgctgggga agatgtcttc acagtctctt gtcgagttct cacgaggcca 5701 tcccctgatt ttgattttat atttttggtg ccacctacag ttgagtcaag aactaaacca 5761 tttactgtcc caatcttaac tgttgaagaa atgactaatt caaggttccc cattcctttg 5821 gaaaaactgt tcacgggtcc cagcagcgcc tttgttgttc aaccacaaaa tggcagatgc 5881 acgactgatg gcgtgctctt aggcaccacc caactgtctc ctgtcaacat ctgcaccttc 5941 agaggggatg tcacccacat tgcaggttct cgtaattaca caatgaattt ggcttctcta 6001 aactggaaca attatgaccc aacagaagaa attccagccc ctctaggaac tccagatttc 6061 gtgggaaaga tccaaggtgt gctcactcaa accacaaagg gagatggttc gacccgtggc 6121 cataaagcca cagtttacac tgggagtgcc cccttcactc caaagctggg cagtgttcaa 6181 ttcagcaccg acacagaaaa tgattttgaa actcaccaaa acacaaaatt caccccagtc 6241 ggcgtcatcc aggatggtgg caccacccac cgaaatgaac ctcaacaatg ggtgctccca 6301 agttattcag gtagaaatgt ccctaatgta cacctagccc ctgctgtagc ccccactttt 6361 ccgggtgaac aacttctctt ctttaggtcc actatgcccg gatgcagcgg gtatcccaac 6421 atggatttgg attgcctact cccccaggag tgggtgcagc acttctacca agaggcagct 6481 ccagcacaat ctgatgtggc tctattaaga tttgtgaatc cagacacggg tagggtcctg 6541 tttgagtgca aacttcataa atcaggctat gtcacagtgg ctcacaccgg ccagcatgat 6601 ttggtcatcc cccccaatgg ttattttagg tttgattcct gggttaatca attctacaca 6661 cttgccccca tgggaaatgg aacggggcgt agacgtgctt tataatggct ggagctttct 6721 ttgctggatt ggcatctgat gtccttagct ctggacttgg ttccctaatc aatgctgggg 6781 ctggggctat caaccaaaag attgattttg aaaataacag aaaattgcag caagcttcct 6841 tccaatttag tagtaatcta caacaggctt cctttcaaca tgataaggag atgctccaag 6901 cacaaattga ggccactaaa aagttacaac aggaaatgat gaaagtcaaa caggcaatgc 6961 tcttagaagg tggattctct gaaacagatg cagcccgtgg ggcaatcaat gcccctatga 7021 caaaggcttt ggactggagc ggaacaaggt actgggcccc tgatgctagg actacaacat 7081 atagtgcagg ccgtttttct acccctcaac cttcgggggc actgccagga agaaccaatc 7141 ccagggcccc tatccccgcc cggggctccc ccagcacatc ttctggtgct tctactgcta 7201 cttctatata ttcaaatcaa actgtttcaa cgagacttgg ttctacagct ggttctggca 7261 ccaatgtctc gagtctcccg tcaactgcaa ggactaggag ttgggttgag gatcaaaaca 7321 gaaatctgtc accttttatg aggggggctc acaacatatc gtttgtcacc ccaccatcta 7381 gcaggtcctc tagccaaggc acagtctcaa ccgtgcctaa agaagttttg gactcctgga 7441 ctggcgcttt caatacgcgc aggcagcctc tcttcgctca cattcgtagg cgaggggagt 7501 cacgggtgta a //