Typing tool
|
Complete norovirus genomes
KC175386 | GII.4 New Orleans | ||
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GII.P4 New Orleans |
ORF1: 3..5102 ORF2: 5083..6705 ORF3: 6705..7511LOCUS KC175386 7511 bp ss-RNA linear VRL 13-MAR-2013 DEFINITION Norovirus Hu/Norwalk/10378/2010/VNM, complete genome. ACCESSION KC175386 VERSION KC175386.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/Norwalk/10378/2010/VNM ORGANISM Norovirus Hu/Norwalk/10378/2010/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 :: 291.1x Sequencing Technology :: Illumina; 454 ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7511 /organism="Norovirus Hu/Norwalk/10378/2010/VNM" /mol_type="genomic RNA" /strain="Hu/Norwalk/10378/2010/VNM" /host="Homo sapiens; sex: M" /db_xref="taxon:1261239" /country="Viet Nam: Ho Chi Minh City" /collection_date="23-Mar-2010" /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="AFX81252.1" /translation="MKMASNDASAAAVANSNDDTAKSSSDGVLSSMAVTFKRALGARP KQPPPREKPQRPPRPPTPELVKNVPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LARVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE 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="AFX81253.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHISGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6705..7511 /gene="VP2" CDS 6705..7511 /gene="VP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AFX81254.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQTVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKTLDWTGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRATVPARGSSSTFS NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gaatgaagat ggcgtctaac gacgcttccg ctgccgctgt tgctaacagc aacgacgaca 61 ccgcaaaatc ttcaagtgac ggagtgcttt ctagcatggc tgtcactttt aaacgagccc 121 tcggggcgcg gcctaaacag cctcccccga gggaaaaacc acaaagaccc ccacgaccac 181 ctactccaga actggttaaa aacgttcccc ctcccccacc caacggagag gatgaaatag 241 tggtttctta tagtgtcaaa gatggtgttt ccggcttgcc tgacctttcc accgtcaggc 301 aaccggaaga atctaacacg gccttcagtg tccctccact caatcagagg gagaatagag 361 atgctaagga accacttact gggacaattc tggaaatgtg ggacggggaa atctaccatt 421 atggcctgta tgtggagcga ggtcttgtac taggtgtgca caaaccacca gctgccatca 481 gcctcgctag ggttgagcta gcaccactct ccttgtactg gagacctgtg tacactcctc 541 agtacctcat ctctccagac actctcaaga aattatccgg agaaacgttc ccctacacag 601 cctttgacaa caactgttat gccttttgtt gctgggtcct ggacctaaat gactcgtggc 661 tgagcagaag aatgatccag aggacaactg gtttcttcag gccctaccaa gactggaata 721 ggaaacccct tcccactatg gatgactcca aaataaagaa ggtagctaac atattcctgt 781 gtgctctgtc ctcgctgttc accagaccca taaaagatat aatagggaag ataaggcctc 841 ttaacatcct caacatctta gcctcatgtg attggacttt tgcaggtata gtggagtccc 901 tgatactctt ggcagaactc tttggagttt tctggacacc cccagatgtg tctgcgatga 961 ttgccccctt acttggtgac tacgagctac aaggacctga ggaccttgca gttgagctcg 1021 tccccgtggt gatgggggga attggtttgg tgctaggatt caccaaagag aagattggga 1081 aaatgttgtc atctgctgcg tctaccttga gagcttgtaa agaccttggt gcatatgggc 1141 tagagatcct aaagttggtc atgaagtggt tcttcccgaa gaaggaagag gcaaatgagc 1201 tggctatagt gaggtctatc gaggatgcag tcctggacct cgaggcaatt gaaaacaacc 1261 atatgaccac cttgctcaaa gacaaagaca gtctggcaac ctatatgaga acacttgacc 1321 ttgaggagga gaaagccagg aaactctcaa ccaagtctgc ctcacccgac atcgtgggca 1381 caatcaacgc cctcctggcg agaatcgctg ccgcacgttc tctggtgcac cgagcgaagg 1441 aggagctttc cagcagacca agacctgtgg tgttgatgat atcaggcagg ccaggaatag 1501 ggaagaccca cctcgctagg gaagtggcta agagaatcgc agcctccctt acaggagacc 1561 agcgtgtggg cctcatccca cgcaatggcg tcgaccattg ggacgcgtac aagggggaga 1621 gggtcgtcct atgggacgat tatggaatga gcaaccctat tcacgatgcc ctcaggctgc 1681 aagaactcgc tgacacttgc cccctcactc taaactgtga caggatcgaa aataaaggaa 1741 aggtctttga cagcgatgtc atcattatca ccactaatct ggccaaccca gcgccactgg 1801 actatgtcaa ctttgaagca tgctcgaggc gcatcgactt cctcgtgtat gcagaagccc 1861 ctgaagtcga aaaggcgaag cgtgacttcc caggccagcc tgacatgtgg aagaacgctt 1921 tcagtcctga tttctcacac ataaaactag cactggcccc acagggtggt ttcgacaaga 1981 acgggaacac cccacacgga aagggcgtta tgaagactct caccactggc tcccttattg 2041 cccgggcatc agggctactc catgagaggt tggatgaatt tgaactgcag ggcccagctc 2101 tcaccacctt caatttcgat cgcaataagg tgcttgcctt tagacagctt gctgctgaaa 2161 ataaatatgg attgatggac acaatgagag ttgggaaaca gctcaaggat gtcagaacca 2221 tgccagaact caaacaagca ctcaagaatg tctcaatcaa gaagtgccaa atagtgtata 2281 gtggttgcac ctacatactt gagtctgatg gcaagggcaa tgtgaaagtt gacagaatcc 2341 aaagcgccgc cgtgcagacc aacaatgagc tggctggtgc cctgcaccat ttgaggtgcg 2401 ccagaatcag atactatgtc aagtgtgtcc aggaggccct gtattccatc attcaaattg 2461 ctggggctgc atttgtcacc acgcgcattg ccaagcgcat gaacatacaa gacctatggt 2521 ccaagccaca agtggaaaac acagaggaga ctaccagcaa ggacgggtgc ccaaaaccta 2581 aggacgatga ggagtttgtc atttcatccg acgacatcaa aactgagggt aagaaaggga 2641 agaacaagac tggccgcggc aagaagcaca cagcattttc aagcaaaggc ctcagtgatg 2701 aagagtacga tgagtacaag aggattagag aagaaaggaa tggcaagtac tccatagaag 2761 agtaccttca ggacagggac aaatactatg aggaggtggc cattgccagg gcgactgagg 2821 aagacttctg tgaagaggag gaggccaaga tccggcaaag gatctttagg ccaacaagga 2881 aacaacgcaa ggaggaaaga gcctctctcg gtctggtcac aggctctgaa attaggaaaa 2941 gaaacccaga tgacttcaaa cccaaaggga aattgtgggc tgacgatgac aggagtgtgg 3001 actacaatga gaaactcagt tttgaggccc caccaagcat ctggtcgaga atagtcaact 3061 ttggttcagg ctggggattt tgggtctccc ccagtctgtt cataacatca acccatgtca 3121 taccccaggg cgcaaaggag ttctttggag tccccatcaa acaaatacag gtacacaagt 3181 caggcgagtt ctgtcgcttg agattcccaa aaccaatcag gactgatgtg acgggcatga 3241 tcttagaaga aggcgcacct gagggcactg tggtcacact actcatcaaa aggtccactg 3301 gggaactcat gcccctagca gctagaatgg gaacccatgc gaccatgaag atccaagggc 3361 gcactgttgg aggccagatg ggcatgcttc tgacaggatc caacgccaag agcatggacc 3421 tgggtactac accaggtgat tgtggctgcc cctatatcta caagagaggt aatgactatg 3481 tggtcattgg ggtccacacg gctgccgcac gtggggggaa cactgtcata tgtgccaccc 3541 aggggagtga aggagaggct acacttgaag gtggtgacaa caaggggaca tactgtggtg 3601 caccaatcct aggcccaggg agtgccccaa cacttagcac caagaccaaa ttctggagat 3661 cgtccacagc atcactccca cctggcacct atgaaccagc ctatcttggt ggcaaggacc 3721 ctagggtcaa gggaggccct tcactgcagc aagtcatgag ggaacagttg aagccattca 3781 cagagcccag gggcaagcca ccaaaaccaa gtgtattaga agctgccaag aagaccatca 3841 tcaatgtcct tgagcaaaca attgatccac ctgagaaatg gtcgttcgca caagcttgcg 3901 cgtcccttga caagaccact tccagtggtc atccgcacca catgcggaaa aacgactgct 3961 ggaacgggga gtccttcaca ggcaagctgg cagaccaggc ttccaaggcc aacctgatgt 4021 ttgaagaagg gaagaacatg accccagtct acacagctgc gctcaaggat gagttggtca 4081 aaactgacaa aatttatggt aagatcaaga agaggcttct ctggggctcg gacttggcga 4141 ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg 4201 tcacacttcc cattagagtt ggcatgaata tgaatgagga tggccccatc atcttcgaga 4261 ggcattccag gtacacatat cactatgatg ctgattactc tcgatgggat tcaacacaac 4321 agagagccgt gttggcagca gctctagaaa tcatggttaa attctcccca gaaccacact 4381 tggctcagat agtcgcggag gaccttcttt ctcctagcgt ggtggacgtg ggcgacttca 4441 caatatcaat caacgagggt cttccctctg gggtgccctg cacctcccaa tggaactcca 4501 tcgcccactg gcttctcact ctctgcgcgc tctctgaagt cacaaacctg tcccctgata 4561 ccatacaggc taactccctc ttctcttttt atggtgatga tgaaattgtt agtacagaca 4621 taaaattgga cccagaaaaa ttgacagcaa agctcagaga atatgggtta aaaccaaccc 4681 gccctgacaa aactgaagga ccccttgtca tctctgaaga cctgaatggc ctaactttcc 4741 tgcggagaac tgtgacccgc gacccagctg gttggtttgg aaaactggag cagagttcaa 4801 tactcaggca aatgtactgg actaggggtc ccaaccatgg agacccatct gaaacaatga 4861 ttccacactc ccaaagaccc atacaattga tgtccctact gggggaggcc gctctccacg 4921 gcccagcatt ttacagcaaa atcagcaaat tggtcattgc agagctaaaa gaaggtggca 4981 tggattttta cgtgcccaga caagagccaa tgttcagatg gatgagattc tcagatctga 5041 gcacgtggga gggcgatcgc aatctggctc ccagttttgt gaatgaagat ggcgtcgagt 5101 gacgccaacc catctgatgg gtccacagcc aaccttgtcc cagaggtcaa taatgaggtt 5161 atggctttgg agcccgtagt tggtgccgcc attgcggcac ctgtagcggg ccaacaaaat 5221 gtaattgacc cctggattag aaacaatttt gtacaagccc ctggtggaga gtttacagta 5281 tcccctagaa acgctccagg tgaaatacta tggagcgcgc ccttaggccc tgatttgaat 5341 ccctaccttt cccatttggc cagaatgtac aatggttatg caggtggttt tgaagtgcag 5401 gtaatcctcg cggggaacgc gttcaccgcc gggaaaatca tatttgcagc agtcccacca 5461 aatttcccaa ctgaaggttt gagccccagc caggtcacta tgttccccca cataatagta 5521 gatgttaggc aattggaacc tgtgttgatt cccttacccg atgttaggaa taatttctac 5581 cattataatc aatcaaatga ccccaccatc aaattgatag caatgttgta cacaccactt 5641 agggctaata atgccgggga cgatgtcttc acagtttctt gtcgagttct cacgagacca 5701 tcccccgatt ttgatttcat atttttggtg ccacccacag ttgaatcaag aactaaacca 5761 ttctctgtcc cagttttaac tgttgaggag atgaccaatt caaggttccc cattcctttg 5821 gaaaagttgt tcacgggccc cagtagtgcc tttgttgttc aaccacaaaa cggcaggtgc 5881 acgactgatg gcgtgctcct aggtactacc caactgtctc ccgtcaacat ctgcaccttc 5941 agaggggacg tcacccatat ttcaggcagt cgtaactaca caatgaattt ggcctcccaa 6001 aattggaaca gttacgatcc aacagaagaa atcccagccc ctctaggaac tccagatttc 6061 gtggggaaga ttcaaggtgt gctcacccaa accacaagga caaatggctc gacccgcggc 6121 cacaaagcta cagtgtacac tgggagcgcc gacttttctc caaaactggg tagagttcaa 6181 tttgccactg acacagacaa tgattttgaa actaaccaaa acacaaagtt caccccagtc 6241 ggtgttatcc aggatggtag taccaccccc cgaaatgaac cccaacaatg ggtactccca 6301 agttactcag gcagaaacat tcataatgtg cacctggccc ccgctgtagc ccccactttc 6361 ccgggcgagc agctcctctt cttcagatct actatgcccg gatgcagcgg gtaccccaac 6421 atggacttgg actgtctgct cccccaggaa tgggtgcaat atttctacca ggaggcagcc 6481 ccagcacaat ctgatgtggc tctgctaaga tttgtgaatc cggacacagg tagggttttg 6541 tttgagtgta agcttcataa atcaggctat gttacagtgg ctcacactgg ccaacatgat 6601 ttggttatcc cccccaatgg ttattttaga tttgattcct gggtcaacca gttctacaca 6661 cttgccccca tgggaaatgg gacggggcgt agacgtgcat tataatggct ggagctttct 6721 ttgctggatt ggcatctgac gtccttggct ctggacttgg ttccctaatc aatgctgggg 6781 ctggggccat caatcaaaca gttgaatttg aaaataacag aaaattgcaa caagcttcct 6841 tccaatttag tagtaatcta caacaggctt cctttcaaca tgacaaagag atgctccaag 6901 cacaaattga ggccaccaaa aagttgcaac aggaaatgat gagagttaaa caagcaatgc 6961 tcctagaggg tggattctct gagacagatg cagcccgtgg ggcaatcaac gcccccatga 7021 caaaaacttt ggactggacc gggacaagat actgggctcc cgatgctagg actacaacat 7081 ataatgcagg ccgcttttcc accccccaac cctcgggggc actaccagga agagctaatc 7141 ttagggctac tgtccccgcc cggggttcct ccagcacgtt ctctaactct tctattgcca 7201 cttctgtgta ttcaaatcaa accacctcaa cgagacttgg ttctacagct ggttctggta 7261 ccagtgtctc gagcctcccg tcaactgcaa ggactaggag ctgggttgag gatcaaaata 7321 ggaatttgtc acctttcatg aggggggccc ataacatctc gtttgtcacc ccaccatcta 7381 gcagatcctc tagccaaggc acagtctcaa ccgtgcccaa agaagttttg gactcctgga 7441 ctggcgcttt caacacgcgc aggcagcctc tcttcgctca cattcgcaag cgaggggagt 7501 cacgggtgta a //