Typing tool
|
Complete norovirus genomes
KC175387 | GII.4 New Orleans | ||
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GII.P4 New Orleans |
ORF1: 3..5102 ORF2: 5083..6705 ORF3: 6705..7511LOCUS KC175387 7511 bp ss-RNA linear VRL 13-MAR-2013 DEFINITION Norovirus Hu/Norwalk/10386/2010/VNM, complete genome. ACCESSION KC175387 VERSION KC175387.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/Norwalk/10386/2010/VNM ORGANISM Norovirus Hu/Norwalk/10386/2010/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 :: 351.5x Sequencing Technology :: Illumina; 454 ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7511 /organism="Norovirus Hu/Norwalk/10386/2010/VNM" /mol_type="genomic RNA" /strain="Hu/Norwalk/10386/2010/VNM" /host="Homo sapiens; sex: F" /db_xref="taxon:1261240" /country="Viet Nam: Ho Chi Minh City" /collection_date="24-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="AFX81255.1" /translation="MKMASNDASAAAVANSNNDTAKSPSDGVLSSMAVTFKRALGARP KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LARVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVISSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT 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="AFX81256.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIPGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL 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="AFX81257.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSSLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRATVPARGSSSTSS NSSIATSVYSNQTTSTRLGSTAGSGTSVSSHPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gaatgaagat ggcgtctaac gacgcttccg ctgccgctgt tgctaacagc aacaacgaca 61 ccgcaaaatc tccaagtgac ggagtgcttt ctagcatggc tgtcactttt aaacgagccc 121 tcggggcgcg gcctaaacag cctcccccga gggaaaaacc acaaagaccc ccacgaccac 181 ctactccaga actggttaaa aatattcccc ctcccccacc caacggagag gatgaaatag 241 tggtctctta tagtgtcaaa gatggtgttt ccggcttgcc tgacctttcc accgtcaggc 301 aaccggaaga atctaacacg gccttcagtg tccctccact caatcagagg gagaatagag 361 atgctaagga accacttact ggaacaattc tggaaatgtg ggacggggaa atttaccatt 421 atggcctgta tgtggagcga ggtcttgtac tgggtgtgca caaaccacca gctgccatca 481 gcctcgctag ggttgagcta gcaccactct ccttgtactg gagacctgtg tacactcctc 541 agtacctcat ctctccagac actctcaaga aattatccgg agaaacgttc ccctacacag 601 cctttgacaa caactgttat gccttttgtt gctgggtcct ggacctaaat gactcgtggc 661 tgagcaggag aatgatccag agaacaactg 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 actcggtgac tacgagctac aaggacctga ggaccttgca gttgagctcg 1021 tccccgtggt gatgggggga attggtttgg tgctaggatt taccaaagag aagattggga 1081 aaatgttgtc atctgctgcg tccaccttga gagcttgtaa agaccttggt gcatatggac 1141 tagagatcct aaagttggtc atgaagtggt tcttcccgaa gaaggaagag gcaaatgagc 1201 tggctatagt gaggtctatc gaggatgcag tcctggatct 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 ggatgcgtac aagggggaga 1621 gggtcgtcct atgggacgat tatggaatga gcaaccctat tcacgatgcc ctcaggctgc 1681 aagaactcgc tgacacttgc cccctcactc taaactgtga caggatcgaa aacaaaggaa 1741 aggtctttga cagcgatgtc atcattatca ctactaatct ggccaaccca gcgccactgg 1801 actatgtcaa ctttgaagca tgctcgaggc gcatcgactt cctcgtgtat gcagaagccc 1861 ctgaagtcga aaaggcgaag cgtgacttcc caggccagcc tgacatgtgg aagaacgctt 1921 tcagttctga tttctcacac ataaaactag cactggcccc acagggtggt ttcgacaaga 1981 acgggaacac cccacacgga aagggcgtta tgaagactct caccactggc tcccttattg 2041 cccgggcatc agggctactc catgagaggt tagatgaatt 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 ccagaattag atactatgtc aagtgtgtcc aggaggccct gtactccatc attcaaatcg 2461 ctggggctgc atttgtcacc acgcgcattg ccaagcgcat gaacatacaa gacctatggt 2521 ccaagccaca agtggaaaac acagaggaga ctaccagcaa ggacgggtgc ccaaaaccta 2581 aggacgatga ggagtttgtc atttcatccg acgacatcaa agctgagggt aagaaaggga 2641 agaataagac tggccgcggc aagaagcaca cagcattctc aagcaaaggc ctcagtgatg 2701 aagagtacga tgagtacaag aggattagag aagaaaggaa tggcaagtac tccatagaag 2761 agtaccttca ggacagggat aaatactatg aggaggtggc cattgccagg gcgactgagg 2821 aagacttctg tgaagaggag gaggccaaga tccggcaaag gatctttagg ccaacaagga 2881 aacaacgcaa ggaggaaaga gcctctctcg gtctggtcac aggctctgaa attaggaaaa 2941 gaaacccaga tgacttcaaa cccaaaggga aattgtgggc tgacgatgac aggagtgtag 3001 actacaatga gaaactcagt tttgaggccc caccaagcat ctggtcgaga atagtcaact 3061 ttggttcagg ctggggattt tgggtctccc ccagtctgtt cataacatca acccatgtca 3121 taccccaggg cgcaaaggag ttctttggag tccccatcaa acaaatacag gtacacaagt 3181 cgggcgagtt ctgtcgcttg agattcccaa aaccaatcag gactgatgtg acgggcatga 3241 tcttagaaga aggcgcgcct gagggcaccg tggtcacact actcatcaaa aggtccactg 3301 gggaactcat gcccctagca gctaggatgg ggacccatgc gaccatgaag atccaagggc 3361 gcactgttgg aggccagatg ggcatgcttc tgacaggatc caacgccaag agcatggatc 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 gggtggtcct 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 gagttagtta 4081 aaactgacaa aatttatggt aagatcaaga agaggcttct ctggggctcg gacttggcga 4141 ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg 4201 tcacacttcc tattagagtt ggcatgaata tgaatgagga cggccccatc atcttcgaga 4261 ggcattccag gtacacgtat cactatgatg ctgattactc tcgatgggat tcaacacaac 4321 agagagccgt gttggcagca gctctagaaa tcatggttaa attctcccca gaaccacact 4381 tggctcaggt agtcgcggag gaccttcttt ctcctagcgt ggtggacgtg ggcgacttca 4441 caatatcaat caacgagggt cttccctctg gggtgccctg cacctcccaa tggaactcca 4501 tcgcccactg gcttctcact ctctgtgcgc tctctgaagt cacaaacctg tcccctgata 4561 ccatacaggc taactccctc ttctcttttt atggtgatga tgaaattgtt agcacagaca 4621 taaaattgga cccagaaaaa ttgacagcaa agctcagaga atatgggtta aaaccaaccc 4681 gccctgataa 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 caatgaggtt 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 agaggggatg tcacccatat tccaggcagt 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 ggtgctccca 6301 agttattcag gcagaaacat tcacaatgtg cacctagccc ctgctgtagc ccccactttt 6361 ccgggtgagc agctcctctt cttcagatct actatgcccg gatgcagcgg gtaccccaac 6421 atggacttgg actgtctgct cccccaggaa tgggtgcagt 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 caaccaaaaa gttgaatttg aaaataacag aaaattgcaa caagcttcct 6841 tccaatttag tagcagtcta caacaggctt cctttcaaca tgacaaagag atgctccaag 6901 cacaaattga ggccaccaaa aagttgcaac aggaaatgat gagagttaaa caagcaatgc 6961 tcctagaggg tggattctct gagacagatg cagcccgtgg ggcaatcaac gcccccatga 7021 caaaaacttt ggactggagc gggacaaggt actgggctcc cgatgctagg actacaacat 7081 ataatgcagg ccgcttttcc accccccaac cctcgggggc actaccagga agagctaatc 7141 ttagggctac tgtccccgcc cggggttcct ccagcacgtc ctctaactct tctattgcta 7201 cttctgtgta ttcaaatcaa accacctcaa cgagacttgg ttctacagct ggttctggta 7261 ccagtgtctc gagccacccg 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 //