Typing tool
|
Complete norovirus genomes
KJ685405 | GII.4 New Orleans | ||
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GII.P4 New Orleans |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7509LOCUS KJ685405 7509 bp ss-RNA linear VRL 28-JAN-2015 DEFINITION Norovirus Hu/GII/BG1C0282/2011/BGD, complete genome. ACCESSION KJ685405 VERSION KJ685405.1 DBLINK BioProject: PRJNA242747 KEYWORDS . SOURCE Norovirus Hu/GII/BG1C0282/2011/BGD ORGANISM Norovirus Hu/GII/BG1C0282/2011/BGD Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7509) AUTHORS Das,S.R., Halpin,R.A., Mohan,M., Fedorova,N., Tsitrin,T., Puri,V., Stockwell,T., Amedeo,P., Bishop,B., Gupta,N., Hoover,J., Katzel,D., Schobel,S., Shrivastava,S., Ahmed,T., Haque,R., Knobler,S., Miller,M., Wentworth,D.E. and Nelson,M. TITLE Direct Submission JOURNAL Submitted (03-APR-2014) 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 sequence lacks part of non-coding region. ##Genome-Assembly-Data-START## Current Finishing Status :: Finished Assembly Method :: clc_ref_assemble_long v. 3.22.55705 Genome Coverage :: 197.8x Sequencing Technology :: Ion Torrent ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7509 /organism="Norovirus Hu/GII/BG1C0282/2011/BGD" /mol_type="genomic RNA" /strain="Hu/GII/BG1C0282/2011/BGD" /host="Homo sapiens; sex: M; age: 179D" /db_xref="taxon:1486692" /country="Bangladesh: Dhaka" /collection_date="26-Aug-2011" /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: GII" gene 1..5100 /gene="POL" /locus_tag="DC54_49771gpPOL" CDS 1..5100 /gene="POL" /locus_tag="DC54_49771gpPOL" /note="genome polyprotein" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AHX22024.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP KQSPPREKPQRPPRPPTPELVKNMPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHRPPAAIS LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM PELKQALKNVSIKKCQIVYSGCTYSLESDGKGNVRVDRIQSAAVQTNNELTGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDEFKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 1..990 /gene="POL" /locus_tag="DC54_49771gpPOL" /product="protein p48" mat_peptide 991..2088 /gene="POL" /locus_tag="DC54_49771gpPOL" /product="NTPase" /note="p41" mat_peptide 2089..2625 /gene="POL" /locus_tag="DC54_49771gpPOL" /product="protein p22" mat_peptide 2626..3024 /gene="POL" /locus_tag="DC54_49771gpPOL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3025..3567 /gene="POL" /locus_tag="DC54_49771gpPOL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3568..5097 /gene="POL" /locus_tag="DC54_49771gpPOL" /product="RNA-directed RNA polymerase" gene 5081..6703 /gene="VP1" /locus_tag="DC54_49771gpVP1" CDS 5081..6703 /gene="VP1" /locus_tag="DC54_49771gpVP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AHX22025.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQTILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQTNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHISGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6703..7509 /gene="VP2" /locus_tag="DC54_49771gpVP2" CDS 6703..7509 /gene="VP2" /locus_tag="DC54_49771gpVP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AHX22026.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQVMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRVTAPARGSSSTSS NSSIATSVYSSQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc 61 gcaaaatctt caagtgacgg agtgctttct agcatggctg tcacttttaa acgagccctc 121 ggggcgcggc ctaaacagtc tcccccgagg gaaaaaccac agagaccccc acgaccaccc 181 actccagaac tggttaaaaa tatgccccct cccccaccca acggagagga tgaaatagtg 241 gtttcttata gtgtcaaaga tggtgtttcc ggcttgcctg acctttccac cgtcaggcaa 301 ccggaagaat ctaacacggc ctttagtgtc cctccactca atcagaggga aaatagagat 361 gctaaggagc cacttactgg aacaattctg gaaatgtggg atggggaaat ttaccattat 421 ggcctgtatg tggagcgagg ccttgtacta ggtgtgcaca gaccaccagc tgccatcagc 481 ctcgctaagg ttgagctagc accactctcc ttgtactgga ggcctgtgta cacccctcag 541 tacctcatct ctccagacac tctcaagaaa ttatctggag aaacgttccc ctacacagcc 601 tttgacaaca actgttatgc cttttgttgc tgggtcctgg acctaaatga ctcgtggctg 661 agcaggagaa tgatccaaag aacaactggt ttcttcaggc cctaccagga ctggaatagg 721 aaacccctcc ccactatgga tgactctaaa ataaagaagg tagctaacat attcctgtgt 781 gccctgtcct cgctgttcac cagacccata aaagatataa tagggaagat aaggcctctt 841 aacatcctca acatcttagc ctcatgtgat tggacttttg caggcatagt ggaatccctg 901 atactcttgg cagaactctt cggagttttc tggacacccc cagatgtgtc tgcgatgatt 961 gcccccttac ttggtgacta cgagctacaa ggacctgagg accttgcagt ggagctcgtc 1021 cccgtggtga tggggggaat tggtttggtg ctaggattca ccaaagagaa gattggaaaa 1081 atgttgtcat ctgctgcgtc caccttgaga gcctgtaaag accttggtgc atatgggctg 1141 gagatcctaa agttggtcat gaagtggttc ttcccgaaga aggaggaggc aaatgagctg 1201 gccatagtga ggtctatcga ggatgcagtc ctggatctcg aggcaattga aaacaaccat 1261 atgaccacct tgctcaaaga caaagacagt ctggcaacct atatgagaac acttgacctt 1321 gaggaggaga aagccaggaa actttcaacc aagtctgcct cacccgacat cgtgggcaca 1381 atcaacgccc tcctggcgag aatcgctgcc gcacgatctc tggtgcatcg agcgaaggag 1441 gagctttcca gcagaccaag acctgtggtg ttgatgatat caggcaggcc aggaataggg 1501 aagacccacc tcgctaggga agtggctaag agaatcgcag cctcccttac aggagaccag 1561 cgtgtgggcc tcatcccacg caatggcgtc gaccattggg atgcatacaa gggggagagg 1621 gtcgtcctat gggacgatta tggaatgagc aaccctattc acgatgccct caggcttcaa 1681 gaactcgctg acacttgccc cctcactcta aactgtgaca ggattgaaaa taaagggaag 1741 gtctttgaca gcgatgtcat cattatcacc actaatctgg ccaacccagc accactggac 1801 tatgtcaact ttgaagcatg ctcgaggcgc atcgacttcc tcgtgtatgc agaagcccct 1861 gaagtcgaaa aggcgaagcg tgacttccca ggccagcctg acatgtggaa gaacgctttc 1921 agttctgact tctcacacat aaaactagca ctggccccgc agggtggctt cgacaagaac 1981 gggaacaccc cacacggaaa gggcgtcatg aagactctca ccactggctc ccttattgcc 2041 cgggcatcag ggctactcca tgagaggtta gatgaatttg aactacaggg cccagctctc 2101 accaccttca atttcgatcg caataaagta cttgccttta ggcagcttgc tgctgaaaat 2161 aagtatggat tgatggacac aatgagagtt gggaaacagc tcaaggatgt cagaaccatg 2221 ccagaactca aacaagcact caagaatgtc tcaatcaaga agtgccaaat agtgtacagt 2281 ggttgcacct attcacttga atctgatggc aagggcaatg tgagagttga cagaatccaa 2341 agcgccgccg tgcagaccaa caatgagctg actggtgccc tgcaccattt gaggtgcgcc 2401 agaatcagat actatgtcaa gtgtgtccag gaggccctgt attccatcat tcaaattgct 2461 ggggctgcat ttgtcaccac gcgcattgcc aagcgcatga acatacaaga cctatggtcc 2521 aagccacaag tggaaaacac agaggagact accagcaagg acgggtgccc aaaacctaaa 2581 gatgatgagg agtttgtcat ttcatctgac gacatcaaaa ctgagggtaa gaaagggaag 2641 aacaaaactg gccgcggcaa gaaacacaca gcattctcaa gcaaaggcct cagtgatgaa 2701 gagtacgacg agtacaagag aattagagaa gaaaggaatg gcaagtactc catagaagag 2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gactgaggaa 2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tctttaggcc aacaagaaaa 2881 caacgcaagg aggaaagggc ctctcttggt ctggtcacag gctctgaaat taggaaaaga 2941 aacccagacg acttcaaacc caaggggaaa ttgtgggctg acgatgacag gagcgtggac 3001 tacaatgaga aactcagttt tgaggcccca ccaagcatct ggtcgagaat agtcaacttt 3061 ggttcaggct ggggattttg ggtctccccc agtctgttca taacatcaac ccatgtcata 3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaatacaggt gcacaagtca 3181 ggcgagttct gtcgcttgag attcccaaaa ccaatcagga ctgatgtgac gggcatgatc 3241 ttagaagaag gcgcacctga gggcaccgta gtcacactac tcatcaaaag gtccaccggg 3301 gaactcatgc ccctagcagc taggatggga acccatgcga ccatgaagat ccaagggcgc 3361 actgttggag gccagatggg catgctcctg acaggatcca acgccaagag catggacctg 3421 ggtactacac caggtgattg tggctgcccc tatatctaca agagaggtaa tgactatgtg 3481 gtcattggag tccacacggc tgccgcacgt gggggaaaca ctgtcatatg cgccacccag 3541 ggaagtgaag gagaggctac acttgaaggt ggcgacaaca aggggacata ctgtggtgca 3601 ccaatcctag gcccaggtag tgccccaaca cttagcacca agaccaaatt ctggagatcg 3661 tccacagcat cactcccacc tggcacctat gaaccagctt atcttggtgg caaggatcct 3721 agagtcaagg gtggcccttc actgcagcaa gtcatgaggg aacagttgaa gccattcaca 3781 gagcccaggg gcaagccacc aaaaccaagt gtattagaag ctgccaagaa gaccatcatc 3841 aatgtccttg agcaaacaat tgatccacct gagaaatggt cgttcgcaca agcttgcgcg 3901 tcccttgaca aaaccacttc cagtggtcat ccgcaccaca tgcggaaaaa cgactgctgg 3961 aacggggagt ccttcacagg caagctggcg gaccaggctt ccaaggccaa cctgatgttt 4021 gaagaaggga agaacatgac cccagtctac acagctgcac tcaaggacga gttagttaaa 4081 actgataaaa tttatggtaa gatcaagaag aggctcctct ggggctcgga cctggcaacc 4141 atgatccggt gtgctcgagc gttcggaggc ctaatggatg aattcaaagc acactgtgtc 4201 acactcccca ttagagttgg catgaatatg aatgaggatg gccccatcat cttcgagagg 4261 cattccaggt atacatatca ctatgatgct gattactctc gatgggattc aacacaacag 4321 agggccgtgt tggcagcagc tctagaaatc atggtcaaat tctccccaga accacatttg 4381 gctcaagtag tcgcggaaga cctcctttct cctagcgtgg tggacgtggg cgacttcaca 4441 atatcaatca acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc 4501 gcccactggc ttctcactct ctgtgcgctc tctgaagtca caaacctgtc ccctgatacc 4561 atacaggcta actccctctt ctctttttat ggtgatgatg aaattgttag cacagacata 4621 aaactggacc cagagaagtt gacagcaaag ctcagagaat atgggttaaa gccaacccgc 4681 cctgacaaaa ctgaaggacc ccttgtcatc tctgaagacc tgaatggcct aactttcctg 4741 cgaagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagttcaata 4801 ctcaggcaaa tgtactggac tagaggtccc aatcatggag acccatctga aacaatgatt 4861 ccacactccc aaagacccat acaattgatg tccctactgg gggaggccgc tctccacggc 4921 ccagcatttt acagcaaaat cagcaaattg gtcattgcag agctaaaaga aggcggcatg 4981 gatttttacg tgcccagaca ggagccaatg ttcagatgga tgagattctc agatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga 5101 cgccaaccca tctgatgggt ccacagccaa cctcgtccca gaggtcaaca atgaggttat 5161 ggctttggag cccgtggttg gtgccgcaat tgcggcacct gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagaa acaattttgt acaagcccct ggtggagagt tcacagtatc 5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atttgaatcc 5341 ctacctttcc catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcagac 5401 aatcctcgcg gggaacgcgt tcaccgccgg gaaaatcata tttgcagcag tcccaccaaa 5461 tttcccaact gaaggtttga gccccagcca ggttactatg ttcccccaca taatagtaga 5521 tgttaggcaa ttggaacctg tgttgattcc cttacccgat gttagaaata atttctacca 5581 ttacaaccaa acaaatgacc ccaccatcaa attgatagca atgttgtaca caccacttag 5641 ggctaataat gccggggacg atgtcttcac agtctcttgt cgagttctca caagaccatc 5701 ccccgatttt gatttcatat ttttggtgcc acccacagtt gaatcaagaa ctaaaccatt 5761 ctctgtcccg gttttgactg ttgaggagat gaccaattca aggttcccca ttcctttgga 5821 gaaattgttc acgggcccca gtagtgcctt tgttgttcaa ccacaaaacg gcaggtgcac 5881 gactgatggc gtgctcctag gtactaccca actgtctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccacattt caggcagtcg taactacaca atgaatttgg cctcccaaaa 6001 ttggaacagt tacgatccaa cagaagaaat cccagcccct ctaggaactc cagatttcgt 6061 ggggaagatt caaggtgtgc tcacccaaac cacaaggaca gatggctcga cccgcggcca 6121 caaagctaca gtgtacactg ggagcgccga cttttctcca aaactgggta gagttcaatt 6181 tgccactgat acagacaatg attttgaaac taaccaaaat acaaagttca ccccagtcgg 6241 tgttatccag gatggtggta ctacccaccg aaatgaaccc caacaatggg tgctcccaag 6301 ttactcaggc agaaacactc ataatgtgca cctggccccc gctgtagccc ccactttccc 6361 gggcgagcag ctcctctttt tcagatctac tatgcccgga tgcagcgggt accccaacat 6421 ggatttggac tgtctgctcc cccaggaatg ggtgcagtat ttttaccagg aggcagcccc 6481 agcacaatct gatgtggctc tgttaagatt tgtgaatcca gatacaggta gggtcctgtt 6541 tgagtgtaaa cttcataaat caggctatgt tacagtggct cacactggcc aacatgattt 6601 ggttatcccc cccaatggtt attttagatt tgactcctgg gtcaaccagt tctatacact 6661 tgcccccatg ggaaatggga cggggcgtag acgtgcatta taatggctgg agctttcttt 6721 gctggattgg catctgacgt ccttggctct ggacttggtt ccctaatcaa tgctggggct 6781 ggggctatca accaaaaggt tgaatttgaa aacaacagaa aactgcaaca agcttccttc 6841 caatttagca gcaatctaca acaggcttcc tttcaacatg acaaagagat gcttcaagca 6901 caaattgagg ccaccaaaaa gttgcaacag gaaatgatga gagtcaaaca agtaatgctc 6961 ctagagggtg gattctctga gacagatgca gcccgtgggg caatcaacgc ccccatgaca 7021 aaagctttgg actggagcgg gacaaggtac tgggctcccg atgctaggac tacaacatat 7081 aatgcaggcc gcttttccac ccctcaaccc tcgggggcac tgccaggaag agctaatctt 7141 agggttactg cccccgcccg gggttcctcc agcacgtctt ctaactcttc tattgctact 7201 tctgtgtatt caagtcaaac cacttcaacg agacttggtt ctacagctgg ttctggtacc 7261 agtgtctcga gtctcccttc aactgcaagg actaggagct gggttgagga tcaaaatagg 7321 aatttatcac ctttcatgag gggggcccac aacatctcgt tcgtcacccc accatctagc 7381 agatcctcta gccaaggcac agtctcaacc gtgcccaaag aagttttgga ctcctggact 7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcata ttcgcaagcg aggggagtca 7501 cgggtgtaa //