Typing tool
|
Complete norovirus genomes
KF712497 | GII.4 Den Haag | ||
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GII.P4 New Orleans |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7509LOCUS KF712497 7509 bp ss-RNA linear VRL 26-OCT-2013 DEFINITION Norovirus Hu/GII.4/NIHIC27.2/2012/USA, complete genome. ACCESSION KF712497 VERSION KF712497.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII.4/NIHIC27.2/2012/USA ORGANISM Norovirus Hu/GII.4/NIHIC27.2/2012/USA Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7509) 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., Kim,M., Bok,K., Sosnovtsev,S.V., Wentworth,D.E. and Green,K.Y. TITLE Direct Submission JOURNAL Submitted (29-SEP-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 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 :: 200.3x Sequencing Technology :: Sanger; Illumina ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7509 /organism="Norovirus Hu/GII.4/NIHIC27.2/2012/USA" /mol_type="genomic RNA" /strain="Hu/GII.4/NIHIC27.2/2012/USA" /host="Homo sapiens" /db_xref="taxon:1406800" /country="USA: Maryland" /collection_date="06-Apr-2012" /PCR_primers="fwd_name: 1_Forward, fwd_seq: gtgaatgawgatggcgt, rev_name: 1_Reverse, rev_seq: ttggttgagagyttyctg" /PCR_primers="fwd_name: 2_Forward, fwd_seq: ccgcaaaatcttcaagtg, rev_name: 2_Reverse, rev_seq: cwacaggtcttggtctgctrga" /PCR_primers="fwd_name: 3_Forward, fwd_seq: tcaaccaartctgcttcacctg, rev_name: 3_Reverse, rev_seq: ratcctttgccggatcttgg" /PCR_primers="fwd_name: 4_Forward, fwd_seq: ggcaagaagcacacagcctt, rev_name: 4_Reverse, rev_seq: crrctctytgttgtgttgaatccc" /PCR_primers="fwd_name: 5_Forward, fwd_seq: tggyaagatcaagaagaggc, rev_name: 5_Reverse, rev_seq: acaacaaargcacygctrgg" /PCR_primers="fwd_name: 6_Forward, fwd_seq: gagrccrtccccygattttg, rev_name: 6_Reverse, rev_seq: atcaatyttgtcttttcaca" /note="genotype: GII.4" gene 1..5100 /gene="POL" /locus_tag="H649_46749gpPOL" CDS 1..5100 /gene="POL" /locus_tag="H649_46749gpPOL" /note="genome polyprotein" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AGX85903.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGRGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPQLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLR EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 1..990 /gene="POL" /locus_tag="H649_46749gpPOL" /product="protein p48" mat_peptide 991..2088 /gene="POL" /locus_tag="H649_46749gpPOL" /product="NTPase" /note="p41" mat_peptide 2089..2625 /gene="POL" /locus_tag="H649_46749gpPOL" /product="protein p22" mat_peptide 2626..3024 /gene="POL" /locus_tag="H649_46749gpPOL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3025..3567 /gene="POL" /locus_tag="H649_46749gpPOL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3568..5097 /gene="POL" /locus_tag="H649_46749gpPOL" /product="RNA-directed RNA polymerase" primer_bind 1..13 gene 5081..6703 /gene="VP1" /locus_tag="H649_46749gpVP1" CDS 5081..6703 /gene="VP1" /locus_tag="H649_46749gpVP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AGX85904.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRSNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWSNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSADFTPKLGSIQFATDTENDFETHQNTRFTPVGVIQDG GTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPNFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6703..7509 /gene="VP2" /locus_tag="H649_46749gpVP2" CDS 6703..7509 /gene="VP2" /locus_tag="H649_46749gpVP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AGX85905.1" /translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQRIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQELMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRINPRTPIPARGSPSISS NVSTANSIHSNQTASTRLGSTAGSGTDVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKDVLDSWTGAFNTRRQPLFAHIRRRGESRV" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc 61 gcaaaatctt caagtgacgg agtgctttct agcatggctg tcacttttaa acgagccctc 121 ggggcgcggc ctaaacagcc tcccccgagg gaaaaacccc aaagaccccc acgaccacct 181 actccagaac tggttaaaaa tattccccct cccccaccca acggagagga tgaaatagtg 241 gtttcttata gtgtcaaaga tggtgtttcc ggcttgcctg acctttccac cgtcaggcaa 301 ccggaagaat ccaacacggc cttcagtgtc cctccactca atcagaggga gaatagagat 361 gctaaggagc cactcactgg aacaattctg gaaatgtggg acggggaaat ctaccattac 421 ggcctgtatg tggagcgagg tcttgtacta ggtgtgcaca aaccgccagc tgccatcagc 481 ctcgctaagg ttgagctagc accactctcc ttgtactgga gacctgtgta cactcctcag 541 tacctcatct ctccagacac actcaagaaa ttgtccggag aaacgttccc ctacacagcc 601 tttgacaaca actgttatgc cttttgttgc tgggtcctgg acctaaatga ctcgtggctg 661 agcaggagaa tgatccagag gacaactggt ttcttcaggc cctaccaaga ctggaatagg 721 aaaccccttc ccactatgga tgactccaaa ataaagaagg tagctaacat atttctgtgt 781 gctctgtcct cgctattcac cagacccata aaagatataa tagggaagat aaggcctctt 841 aacatcctca acatcttagc ctcatgtgac tggacctttg cgggcatagt ggagtccctg 901 atactcttgg cagaactctt tggagttttc tggacacccc cagatgtgtc tgcgatgatt 961 gcccccttac ttggtgacta cgagctacaa ggacctgagg accttgcggt ggagctcgtc 1021 cccgtggtga tggggggaat tggtttggtg ctaggattca ccaaagagaa gattgggaaa 1081 atgttgtcat ctgctgcgtc caccttgaga gcttgcaaag accttggtgc atatgggcta 1141 gagatcctaa agttagtcat gaagtggttc ttcccgaaga aggaggaggc aaatgagctg 1201 gctatagtga ggtccatcga ggatgcagtc ctggatctcg aggcaattga aaacaatcat 1261 atgaccacct tactcaaaga taaagacagt ctggcaacct acatgagaac acttgacctt 1321 gaagaggaga aagccaggaa actctcaacc aagtctgcct cacccgacat cgtgggcaca 1381 atcaacgctc tcctggcgag aatcgccgcc gcacgttctc tggtgcatcg agcgaaggag 1441 gagctttcca gcagaccaag acctgtggtg ttgatgatat caggcaggcc aggaataggg 1501 aagacccacc tcgctaggga agtggctaag agaatcgcag cctcccttac aggagaccag 1561 cgtgtgggcc tcatcccacg caatggcgtc gaccattggg atgcgtacaa gggggagagg 1621 gtcgtcctat gggacgatta tggaatgagc aaccctattc acgacgccct caggctgcaa 1681 gaactcgctg acacttgccc cctcactcta aactgtgaca ggattgaaaa taaaggaaag 1741 gtctttgaca gcgatgtcat cattatcact actaatctgg ccaacccagc accactggac 1801 tatgtcaact ttgaagcatg ctcgaggcgc attgacttcc tcgtgtatgc agaagcccct 1861 gatgtcgaaa aggcgaagcg tgacttccca ggccaacctg acatgtggaa gaatgctttc 1921 agttctgatt tctcacacat aaaactagca ctggccccac agggtggttt cgacaagaac 1981 gggaacaccc cacacggaag gggcgtcatg aagactctca ccactggttc ccttattgcc 2041 cgggcatcag ggctactcca tgagaggtta gatgaatttg aactgcaggg cccagctctc 2101 accaccttca acttcgatcg caataaagtg cttgccttta gacagcttgc tgctgaaaat 2161 aaatatggat tgatggacac aatgagggtt gggaaacagc tcaaggatgt cagaaccatg 2221 ccagaactca aacaagcact caagaatgtc tcaatcaaga agtgtcaaat agtgtatagt 2281 ggttgcacct acatgcttga gtctgatggc aagggcaatg tgaaagttga caggatccaa 2341 agcgccgccg tgcagaccaa caatgagctg gctggtgccc tgcaccactt aaggtgtgcc 2401 agaataagat actatgtcaa gtgtgtccag gaagccctgt attccatcat ccaaattgct 2461 ggggctgcat ttgtcaccac gcgcattgcc aagcgcatga acatacaaga cctatggtcc 2521 aagccacaag tggaaaacac agaggagacc accagcaagg acgggtgccc aaaacctaag 2581 gatgatgagg agtttgtcat ttcatccgac gacatcaaaa ctgagggcaa gaaagggaag 2641 aacaagactg gccgtggcaa gaagcacaca gcattttcaa gtaaaggcct cagtgatgaa 2701 gagtacgatg aatacaagag gattagagaa gaaagaaatg gcaagtactc tatagaagag 2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gactgaggaa 2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tctttaggcc aacaaggaaa 2881 caacgcaagg aggaaagagc ctccctcggt ttggtcacag gctctgaaat taggaaaaga 2941 aacccagatg acttcaaacc caaggggaaa ttgtgggctg acgatgacag gagtgtggac 3001 tacaatgaga aactcagttt tgaggcccca ccaagcattt ggtcgagaat agtcaacttt 3061 ggttcaggct ggggattctg ggtctccccc agtctgttca taacatcaac ccatgttata 3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaatacaggt acacaagtca 3181 ggcgagttct gtcgcttgag attccctaaa ccaatcagga ctgatgtgac gggcatgatc 3241 ttagaagaag gcgcacctga gggcaccgtg gtcacactac tcatcaaaag gcccactggg 3301 gaactcatgc ccctagcagc taggatgggg acccatgcga ccatgaagat ccaagggcgc 3361 actgttgggg gccagatggg catgcttctg acaggatcca acgccaagag tatggacctg 3421 ggtactacac caggtgattg tggctgcccc tatatctaca agagaggtaa tgactatgtg 3481 gtcattggag tccacacggc tgccgcacgt ggggggaaca ctgtcatatg tgccacccag 3541 gggagtgaag gagaggctac acttgagggt ggtgacaaca agggaacata ctgtggtgca 3601 ccaatcctag gcccagggag tgccccaaca cttagcacca agaccaaatt ctggagatcg 3661 tccacagcat cactcccacc tggcacctat gaaccagcct atcttggtgg caaggaccct 3721 agagtcaagg gtggcccttc actgcagcaa gtcatgaggg aacagttgaa gccattcaca 3781 gagcccaggg gcaagccacc aaaaccaagt gtattagaag ctgccaagaa gaccatcatc 3841 aatgtccttg agcaaacaat tgatccacct gagaagtggt cgttcgcaca agcttgcgcg 3901 tcccttgaca agaccacttc cagtggtcat ccgcatcaca tgcggaaaaa cgactgctgg 3961 aatggggagt ccttcacagg caagctggca gaccaggctt ccaaggccaa cctgatgttt 4021 gaagaaggga agaacatgac cccagtctac acagctgcgc tcaaggatga gttagttaaa 4081 actgacaaaa tttatggtaa gatcaagaag aggcttcttt ggggctcgga cttggcgacc 4141 atgatccggt gtgctcgagc attcggaggc ctaatggatg aactcaaagc gcactgtgtc 4201 acactcccca ttagagttgg catgaatatg aatgaggatg gccccatcat cttcgagagg 4261 cattccaggt acacgtacca ctatgatgct gattactctc ggtgggattc aacacaacag 4321 agagccgtat tggcagcagc tctagaaatc atggttaaat tctccccaga accacaattg 4381 gctcaggtag ttgcggaaga ccttctttct cctagcgtgg tggacgtggg cgacttcaca 4441 atatcaatca atgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc 4501 gcccactggc ttctcactct ctgtgcgctc tctgaagtca caaacctgtc tcctgacacc 4561 atacaggcta attccctctt ctctttttat ggtgatgatg aaattgttag cacagacata 4621 aaattggacc cagagaaatt gacaacaaag ctcagagaat atgggttaaa accaacccgc 4681 cctgacaaaa ctgaaggacc ccttgtcatc tctgaagacc tgaatggcct aacttttctg 4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagttcaata 4801 ctcaggcaaa tgtactggac taggggtccc aaccacggag acccatctga aacaatgatc 4861 ccacactccc aaagacccat acaattgatg tccctactgg gggaggccgc tctccacggc 4921 ccagcatttt acagtaaaat cagcaaattg gtcattgcag agcttaaaga aggtggtatg 4981 gatttttacg tgcccagaca agagcctatg ttcagatgga tgagattctc agatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga 5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat 5161 ggctttggag cccgttgtcg gtgccgctat tgcggcgcct gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagaa gtaactttgt acaagcccct ggtggagagt tcacagtgtc 5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atctgaatcc 5341 ctacctatct catttggcca gaatgtataa tggttatgca ggtggttttg aagtgcaggt 5401 gatcctcgcg gggaacgcgt tcaccgcggg aaaaatcata tttgcagcag ttccaccaaa 5461 ttttccaact gaaggcttga gtcccagcca agttactatg ttcccccaca taatagtaga 5521 tgttaggcaa ttggaacctg tgttgatccc cttacctgat gttaggaata acttctatca 5581 ctataaccag tcaaatgatt ctaccattaa attgatagca atgctgtaca caccactcag 5641 agccaataat gccggggatg atgtcttcac ggtctcttgt cgagtcctca cgaggccatc 5701 ccctgatttt gacttcatat ttctggtgcc acctacagtt gagtcaagaa ctaagccatt 5761 tactgtccca atcttgactg ttgaagaaat gaccaattca agattcccca ttcctttgga 5821 gaaattgttc acgggtccca gcagtgcctt tgttgttcaa ccacaaaatg gcagatgcac 5881 aactgatggc gtgctcttag gcaccaccca actgtctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccacattg cgggttcccg taattacaca atgaatttgg cctctctaaa 6001 ttggagcaat tacgacccaa cagaagagat tccagcccct ctgggaactc cagatttcgt 6061 gggaaagatc caaggtgtgc tcactcaaac cacaaaggga gatggctcga cccggggcca 6121 taaagctaca gtttacactg ggagtgccga cttcactcca aagctgggca gtattcaatt 6181 tgctactgat acagaaaatg actttgaaac tcaccaaaac acaagattca ccccagtcgg 6241 tgtcattcag gatggtggca ccacccaccg aaatgaaccc caacaatggg tgctcccaag 6301 ttactcaggt agaaatgtcc ataatgtaca cctagcccct gctgtagccc ccaattttcc 6361 aggtgaacag ctccttttct tcaggtccac tatgcccgga tgtagcggat atcccaacat 6421 ggatttggat tgcctactcc cccaggagtg ggtgcaacac ttttaccaag aggcagctcc 6481 agcacaatct gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcttgtt 6541 tgagtgcaaa ctccataaat caggctatgt cacagtggct cataccggcc aacatgattt 6601 ggtcattccc cccaatggtt attttaggtt tgattcctgg gttaatcagt tctacacact 6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcttta taatggctgg agctttcttt 6721 gctggattgg catctgatgt ccttagctct ggacttggtt ccctaatcaa tgctggggct 6781 ggggctatca accaaaggat tgattttgaa aataatagaa aattgcagca agcttccttt 6841 cagtttagta gtaatctaca acaagcttcc tttcaacatg ataaagagat gctccaagca 6901 caaattgagg ctactaaaaa gttgcaacag gaactgatga aagtcaaaca ggcaatgctc 6961 ttagaaggtg gattctctga aacagatgca gcccgtgggg caatcaacgc ccccatgaca 7021 aaggctttgg actggagtgg aacaaggtac tgggcccctg atgctaggac tacaacatac 7081 aatgcaggcc gcttttctac ccctcaacct tcgggggcac tgccaggaag aatcaacccc 7141 aggactccta tccccgcccg gggctcccca agcatatctt ccaatgtttc tactgctaat 7201 tctatacatt caaatcaaac tgcttcaacg agacttggtt ctacagctgg ttctggcacc 7261 gatgtctcga gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga 7321 aatttatcac ctttcatgag gggggctcac aacatatcgt ttgtcacccc accatctagc 7381 agatcctcca gccaaggcac agtctcaacc gtgcctaaag atgttttgga ctcctggact 7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaggcg aggggagtca 7501 cgggtgtaa //