Typing tool
|
Complete norovirus genomes
KC960616 | GII.4 New Orleans | ||
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GII.P4 New Orleans |
ORF1: 1..5070 ORF2: 5051..6673 ORF3: 6673..7479LOCUS KC960616 7499 bp ss-RNA linear VRL 30-APR-2013 DEFINITION Norovirus Hu/GII.4/20406/2010/VNM, partial genome. ACCESSION KC960616 VERSION KC960616.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII.4/20406/2010/VNM ORGANISM Norovirus Hu/GII.4/20406/2010/VNM Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7499) 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 (18-APR-2013) 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-Assembly-Data-START## Current Finishing Status :: Finished Assembly Method :: clc_ref_assemble_long v. 3.22.55705 Genome Coverage :: 388.5x Sequencing Technology :: Sanger; Illumina; 454 ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7499 /organism="Norovirus Hu/GII.4/20406/2010/VNM" /mol_type="genomic RNA" /strain="Hu/GII.4/20406/2010/VNM" /host="Homo sapiens; sex: F; age: 20M" /db_xref="taxon:1325537" /country="Viet Nam: Ho Chi Minh City" /collection_date="24-Jan-2010" /PCR_primers="fwd_name: 1F-1298R_Forward, fwd_seq: gtgaatgawgatggcgt, rev_name: 1F-1298R_Reverse, rev_seq: ccagrctrtctttrtctt" /PCR_primers="fwd_name: 762F-1472R_Forward, fwd_seq: ccgcaaaatcttcaagtg, rev_name: 762F-1472R_Reverse, rev_seq: cwacaggtcttggtctgctrga" /PCR_primers="fwd_name: 1348F-2866R_Forward, fwd_seq: tcaaccaartctgcttcacctg, rev_name: 1348F-2866R_Reverse, rev_seq: ratcctttgccggatcttgg" /PCR_primers="fwd_name: 2659F-4331R_Forward, fwd_seq: ggcaagaagcacacagcctt, rev_name: 2659F-4331R_Reverse, rev_seq: crrctctytgttgtgttgaatccc" /PCR_primers="fwd_name: 4098F-5860R_Forward, fwd_seq: tggyaagatcaagaagaggc, rev_name: 4098F-5860R_Reverse, rev_seq: acaacaaargcacygctrgg" /PCR_primers="fwd_name: 5695F-7550R_Forward, fwd_seq: gagrccrtccccygattttg, rev_name: 5695F-7550R_Reverse, rev_seq: atcaatyttgtcttttcaca" /note="genotype: II.4" gene <1..5070 /gene="POL" /locus_tag="H649_36414gpPOL" CDS <1..5070 /gene="POL" /locus_tag="H649_36414gpPOL" /note="genome polyprotein" /codon_start=1 /product="putative nonstructural polyprotein" /protein_id="AGK36313.1" /translation="AAVANSNNDTAKSSSDGVLSSVAVTFKRALGARPKQPPPREKPQ RPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNTAFSVPP LNQRENRDAKEPLTGTVLEMWDGEIYHYGLYVERGLVLGVHKPPAAISLARVELAPLS LYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRT TGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNILNIL ASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVM GGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAI VRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGT INALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTG DQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIE NKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPD MWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDE FELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELKQALKNV SIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARIRYYVKC VQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPKGDEEFV ISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQD RDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNP DDFKPKGKLWADDDRGVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVI PQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRS TGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRG NDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPTLSTK TKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPKPSVL EAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLA DQSSKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAF GGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRAVLAA ALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWL LTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKPTRPD KTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPSETMI PHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSD LSTWEGDRNLAPSFVNEDGVE" mat_peptide <1..960 /gene="POL" /locus_tag="H649_36414gpPOL" /product="putative protein p48" mat_peptide 961..2058 /gene="POL" /locus_tag="H649_36414gpPOL" /product="NTPase" /note="p41" mat_peptide 2059..2595 /gene="POL" /locus_tag="H649_36414gpPOL" /product="protein p22" mat_peptide 2596..2994 /gene="POL" /locus_tag="H649_36414gpPOL" /product="viral genome-linked protein" /note="VPg" mat_peptide 2995..3537 /gene="POL" /locus_tag="H649_36414gpPOL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3538..5067 /gene="POL" /locus_tag="H649_36414gpPOL" /product="RNA-directed RNA polymerase" gene 5051..6673 /gene="VP1" /locus_tag="H649_36414gpVP1" CDS 5051..6673 /gene="VP1" /locus_tag="H649_36414gpVP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AGK36314.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIPGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6673..7479 /gene="VP2" /locus_tag="H649_36414gpVP2" CDS 6673..7479 /gene="VP2" /locus_tag="H649_36414gpVP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AGK36315.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRATVPARGSSSTSS NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gccgctgttg ctaacagcaa caacgacacc gcaaaatctt caagtgacgg agtgctttct 61 agcgtggctg tcacttttaa acgagccctc ggggcgcggc ctaaacagcc tcccccgagg 121 gaaaaaccac aaagaccccc acgaccacct actccagaac tggttaaaaa tattccccct 181 cccccaccca acggagagga tgaaatagtg gtttcttata gtgtcaaaga tggtgtttcc 241 ggcttgcctg acctttccac cgtcaggcaa ccggaagaat ctaacacggc cttcagtgtc 301 cctccactca atcagaggga gaatagagat gctaaggaac cacttactgg aacagttctg 361 gaaatgtggg acggggaaat ctaccattat ggcctgtatg tggagcgagg tcttgtacta 421 ggtgtgcaca aaccaccagc tgccatcagc ctcgctaggg ttgagctagc accactctcc 481 ttgtactgga gacctgtgta cactcctcag tacctcatct ctccagacac tctcaagaaa 541 ttatccggag aaacgttccc ctacacagcc tttgacaaca actgttatgc cttttgttgc 601 tgggtcctgg acctaaatga ctcgtggctg agcaggagaa tgatccagag aacaactggt 661 ttcttcaggc cctaccaaga ctggaatagg aaaccccttc ccactatgga tgactccaaa 721 ataaagaagg tagctaacat attcctgtgt gctctgtcct cgctgttcac cagacccata 781 aaagatataa tagggaagat aaggcctctt aacatcctca acatcttagc ctcatgtgat 841 tggacttttg caggtatagt ggagtccctg atactcttgg cagaactctt tggagttttc 901 tggacacccc cagatgtgtc tgcgatgatt gcccccttac ttggtgacta cgagctacaa 961 ggacctgagg accttgcagt tgagctcgtc cccgtggtga tggggggaat tggtttggtg 1021 ctaggattca ccaaagagaa gattgggaaa atgttgtcat ctgctgcgtc taccttgaga 1081 gcttgtaaag acctcggtgc atatgggcta gagatcctaa agttggtcat gaagtggttc 1141 ttcccgaaga aggaagaggc aaatgagctg gctatagtga ggtctatcga ggatgcagtc 1201 ctggacctcg aggcaattga aaacaaccat atgaccacct tgctcaaaga caaagacagt 1261 ctggcaacct atatgagaac acttgacctt gaggaggaga aagccaggaa actctcaacc 1321 aagtctgcct cacccgacat cgtgggcaca atcaacgccc tcctggcgag aatcgctgcc 1381 gcacgttctc tggtgcaccg agcgaaggag gagctttcca gcagaccaag acctgtggtg 1441 ttgatgatat caggcaggcc aggaataggg aagacccacc tcgctaggga agtggctaag 1501 agaatcgcag cctcccttac aggagaccag cgtgtgggcc tcatcccacg caatggcgtc 1561 gaccattggg atgcgtacaa gggggagagg gtcgtcctat gggacgatta tggaatgagc 1621 aaccccattc acgatgccct taggctgcaa gaactcgctg acacttgccc cctcactcta 1681 aactgtgaca ggatcgaaaa taaaggaaag gtctttgaca gcgatgtcat cattatcacc 1741 actaatctgg ccaacccagc gccactggac tatgtcaact ttgaagcatg ctcgaggcgc 1801 atcgacttcc tcgtgtatgc agaagcccct gaagtcgaaa aggcgaagcg tgacttccca 1861 ggccagcctg acatgtggaa gaacgctttc agttctgatt tctcacacat aaaactagca 1921 ctggccccac agggtggttt cgacaagaac gggaacaccc cacacggaaa gggcgttatg 1981 aagactctca ccactggctc ccttattgcc cgggcatcag ggctactcca tgagaggcta 2041 gatgagtttg aactgcaggg cccagctctc accaccttca atttcgatcg caataaggtg 2101 cttgccttta gacagcttgc tgctgaaaat aaatatggat tgatggacac aatgagagtt 2161 gggaaacagc tcaaggatgt caaaaccatg ccagaactca aacaagcact caagaatgtc 2221 tcaatcaaga agtgccaaat agtgtatagt ggttgcacct acatacttga gtctgatggc 2281 aagggcaatg tgaaagttga cagaatccaa agcgccgccg tgcagaccaa caatgagctg 2341 gctggtgccc tgcaccattt gaggtgcgcc agaatcagat actatgtcaa gtgtgtccag 2401 gaggccctgt attccatcat tcaaatcgct ggggctgcat ttgtcaccac gcgcattgcc 2461 aagcgcatga acatacaaga cctatggtcc aagccacaag tggaaaacac agaggagact 2521 accagcaagg acgggtgccc aaaacctaag ggcgatgagg agtttgtcat ttcatccgac 2581 gacatcaaaa ctgagggtaa gaaagggaag aacaagactg gccgcggcaa gaagcacaca 2641 gcattttcaa gcaaaggcct cagtgatgaa gagtacgatg agtacaagag gattagagaa 2701 gaaaggaatg gcaagtactc tatagaagag taccttcagg acagggacaa atactatgag 2761 gaggtggcca ttgccagggc gactgaggaa gacttctgtg aagaggagga ggccaagatc 2821 cggcaaagga tctttaggcc aacaaggaaa caacgcaagg aggaaagagc ctctctcggt 2881 ctggtcacag gctctgaaat taggaaaaga aacccagatg acttcaaacc caaagggaaa 2941 ttgtgggctg acgatgacag gggtgtggac tacaatgaga aactcagttt tgaggcccca 3001 ccaagcatct ggtcgagaat agtcaacttt ggttcaggct ggggattttg ggtctccccc 3061 agtctgttca taacatcaac ccatgtcata ccccagggcg caaaggagtt ctttggagtc 3121 cccatcaaac aaatacagat acacaagtca ggcgagttct gtcgcttgag attcccaaaa 3181 ccaatcagga ctgatgtgac gggcatgatc ttagaagaag gcgcacctga gggcaccgtg 3241 gtcacactac tcatcaaaag gtccactggg gaactcatgc ccctagcagc taggatgggg 3301 acccatgcga ccatgaagat ccaagggcgc actgttggag gccagatggg catgcttctg 3361 acagggtcca acgccaagag catggacctg ggtactacac caggtgattg tggttgcccc 3421 tatatctaca agagaggtaa tgactatgtg gtcattgggg tccacacggc tgccgcacgt 3481 ggggggaaca ctgtcatatg tgccacccag gggagtgaag gagaagctac acttgaaggc 3541 ggtgacaaca aggggacata ctgtggtgca ccaatcctag gcccagggag tgccccaaca 3601 cttagcacca agaccaaatt ctggaggtcg tccacagcat cactcccacc tggcacctat 3661 gaaccagcct atcttggtgg caaggaccct agggtcaagg gtggcccttc actgcagcaa 3721 gtcatgaggg aacagttgaa gccattcaca gagcccaggg gcaagccacc aaaaccaagt 3781 gtattagaag ctgccaagaa gaccatcatc aatgtccttg agcaaacaat tgatccacct 3841 gagaaatggt cgttcgcgca agcttgcgcg tcccttgaca agaccacttc cagtggtcat 3901 ccgcaccaca tgcggaaaaa cgactgctgg aacggggagt ccttcacagg caagctggca 3961 gaccagtctt ccaaggccaa cctgatgttt gaagaaggga agaacatgac cccagtctac 4021 acagctgcgc tcaaggatga gttagttaaa actgacaaaa tttatggtaa gatcaagaag 4081 aggcttctct ggggctcgga cttggcgacc atgatccggt gtgctcgagc attcggaggc 4141 ctaatggatg aactcaaagc acactgtgtc acacttccca ttagagttgg catgaatatg 4201 aatgaggatg gccccatcat cttcgagagg cattccaggt acacatatca ctatgatgct 4261 gattactctc gatgggattc aacacaacag agagccgtgt tggcagcagc tctagaaatc 4321 atggttaaat tctccccaga accacacttg gctcaggtag tcgcggagga ccttctttct 4381 cctagcgtgg tggacgtggg cgacttcaca atatcaatca acgagggtct tccctctggg 4441 gtgccctgca cctcccaatg gaactccatc gcccactggc ttctcactct ctgtgcgctc 4501 tctgaagtca caaacctgtc ccctgatacc atacaggcta actccctctt ctctttttat 4561 ggtgatgatg aaattgtaag cacagacata aaattggacc cggaaaaatt gacagcaaag 4621 ctcagagaat atgggttaaa accaacccgc cctgacaaaa ctgaaggacc ccttgtcatc 4681 tctgaagacc tgaatggcct aacttttctg cggagaactg tgacccgcga cccagctggt 4741 tggtttggaa aactggagca gagttcaata ctcaggcaaa tgtactggac taggggtccc 4801 aaccatggag acccatctga aacaatgatt ccacactccc aaagacccat acaattgatg 4861 tccctactgg gggaggccgc tctccacggc ccagcatttt acagcaaaat cagcaaattg 4921 gtcattgcag agctaaaaga aggtggcatg gatttttacg tgcccagaca agagccaatg 4981 ttcagatgga tgagattctc agatctgagc acgtgggagg gcgatcgcaa tctggctccc 5041 agtttcgtga atgaagatgg cgtcgagtga cgccaaccca tctgatgggt ccacagccaa 5101 ccttgtccca gaggtcaaca atgaggttat ggctttggag cccgtagttg gtgccgccat 5161 tgcggcacct gtagcgggcc aacaaaatgt aattgacccc tggattagaa acaattttgt 5221 acaagcccct ggtggagagt ttacagtgtc ccctagaaac gctccaggtg aaatactatg 5281 gagcgcgccc ttaggccctg atttgaatcc ctacctttcc catttggcca gaatgtacaa 5341 tggttatgca ggtggttttg aagtgcaggt aatcctcgcg gggaacgcgt tcaccgccgg 5401 gaaaatcata tttgcagcag ttccaccaaa tttcccaact gaaggtttga gccccagcca 5461 ggtcactatg ttcccccaca taatagtaga tgttaggcaa ttggaacctg tgttgattcc 5521 cttacccgat gttaggaata atttctacca ttataatcaa tcaaacgacc ccaccatcaa 5581 attgatagca atgttgtaca caccacttag ggctaataat gccggggacg atgtcttcac 5641 agtttcttgt cgagttctca cgagaccatc ccccgatttt gatttcatat ttttggtgcc 5701 acccacagtt gaatcaagaa ctaaaccatt ctctgtccca gttttaactg ttgaggagat 5761 gaccaattca aggttcccca ttcctttgga aaagttgttc acgggcccca gtagtgcctt 5821 tgttgttcaa ccacaaaacg gcaggtgcac gactgatggc gtgctcctag gtactaccca 5881 actgtctccc gtcaacatct gcaccttcag aggggacgtc acccatattc caggcagtcg 5941 taactacaca atgaatttgg cctcccaaaa ttggaacagt tacgacccaa cagaagaaat 6001 cccagcccct ctaggaactc cagatttcgt ggggaagatt caaggtgtgc tcacccaaac 6061 cacaaggaca aatggctcga cccgcggcca caaagctaca gtgtacactg ggagcgccga 6121 cttttctcca aaactgggta gagttcaatt tgccactgac acagacaatg attttgaaac 6181 taaccaaaac acaaagttca ccccagtcgg tgttatccag gatggtagta ccaccccccg 6241 aaatgaaccc caacaatggg tgctcccaag ttactcaggc agaaacattc ataatgtgca 6301 cctggccccc gctgtagccc ccactttccc gggcgagcag ctcctcttct tcagatctac 6361 tatgcccgga tgcagcgggt accccaacat ggacttggac tgtctgctcc cccaggaatg 6421 ggtgcaatat ttctaccagg aggcagcccc agcacaatct gatgtggctc tgctaagatt 6481 tgtgaatccg gacacaggta gggttttgtt tgagtgtaag cttcataaat caggctatgt 6541 tacagtggct cacactggcc aacatgattt ggttatcccc cccaatggtt attttagatt 6601 tgattcctgg gtcaaccagt tctacacact tgcccccatg ggaaatggga cggggcgtag 6661 acgtgcatta taatggctgg agctttcttt gctggattgg catctgacgt ccttggctct 6721 ggacttggtt ccctaatcaa tgctggggct ggggccatca accaaaaagt tgaatttgaa 6781 aataacagaa aattgcaaca agcttccttc caatttagta gcaatctaca acaggcttcc 6841 tttcaacatg acaaagagat gctccaagca caaattgagg ccaccaaaaa gttgcaacag 6901 gaaatgatga gagttaaaca agcaatgctc ctagagggtg gattctctga gacagatgca 6961 gcccgtgggg caatcaacgc ccccatgaca aaaactttgg actggagcgg gacaaggtac 7021 tgggctcccg atgctaggac aacaacatat aatgcaggcc gcttttccac cccccaaccc 7081 tcgggggcac taccaggaag agctaatctt agggctactg tccccgcccg gggttcctcc 7141 agcacgtcct ctaactcttc tattgctact tctgtgtatt caaatcaaac cacctcaacg 7201 agacttggtt ctacagctgg ttctggtacc agtgtctcga gcctcccgtc aactgcaagg 7261 actaggagct gggttgagga tcaaaatagg aatttgtcac ctttcatgag gggggcccat 7321 aacatctcgt ttgtcacccc accatctagc agatcctcta gccaaggcac agtctcaacc 7381 gtgcccaaag aagttttgga ctcctggact ggcgctttca acacgcgcag gcagcctctc 7441 ttcgctcaca ttcgcaagcg aggggagtca cgggtgtaat gtgaaaagac aaaattgat //