Typing tool
|
Complete norovirus genomes
KF712493 | GII.4 New Orleans | ||
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GII.P4 Hunter |
ORF1: 1..5099 ORF2: 5080..6699 ORF3: 6699..7505LOCUS KF712493 7505 bp ss-RNA linear VRL 26-OCT-2013 DEFINITION Norovirus Hu/GII.4/NIHIC1.10/2012/USA, partial genome. ACCESSION KF712493 VERSION KF712493.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII.4/NIHIC1.10/2012/USA ORGANISM Norovirus Hu/GII.4/NIHIC1.10/2012/USA Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7505) 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-Assembly-Data-START## Current Finishing Status :: Finished Assembly Method :: clc_ref_assemble_long v. 3.22.55705 Genome Coverage :: 199.0x Sequencing Technology :: Sanger; Illumina ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7505 /organism="Norovirus Hu/GII.4/NIHIC1.10/2012/USA" /mol_type="genomic RNA" /strain="Hu/GII.4/NIHIC1.10/2012/USA" /host="Homo sapiens" /db_xref="taxon:1406812" /country="USA: Maryland" /collection_date="28-Aug-2012" /PCR_primers="fwd_name: 1_Forward, fwd_seq: gtgaatgawgatggcgt, rev_name: 1_Reverse, rev_seq: ccagrctrtctttrtctt" /PCR_primers="fwd_name: 2_Forward, fwd_seq: ygactcgtggctgagyagga, rev_name: 2_Reverse, rev_seq: gytgggccctgyagttcawa" /PCR_primers="fwd_name: 3_Forward, fwd_seq: tcaaccaartctgcttcacctg, rev_name: 3_Reverse, rev_seq: aagtcytcctcrgtcgccct" /PCR_primers="fwd_name: 4_Forward, fwd_seq: gggaaraacaagrctggycg, rev_name: 4_Reverse, rev_seq: crrctctytgttgtgttgaatccc" /PCR_primers="fwd_name: 5_Forward, fwd_seq: tggyaagatcaagaagaggc, rev_name: 5_Reverse, rev_seq: atcagtcgtgcayctgccrt" /PCR_primers="fwd_name: 6_Forward, fwd_seq: cagtytcttgtcgrgtyctca, rev_name: 6_Reverse, rev_seq: atcaatyttgtcttttcaca" /note="genotype: GII.4" gene <1..5099 /gene="POL" /locus_tag="H649_46728gpPOL" CDS <1..5099 /gene="POL" /locus_tag="H649_46728gpPOL" /note="genome polyprotein" /codon_start=3 /product="putative nonstructural polyprotein" /protein_id="AGX85891.1" /translation="KMASNDASAAAVANSNNDTVKSSSDGVLSSMAVTFKRALGARPK QPPPREIPQRPPRPPTPELIKNIPPPPPNGEDDIVVSYSVKDGISGLPDLSTVRQPEE SNTAFSIPPLNQRESREAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISL ARVELTPLSLYWRPVYTPQYLISPDALKRLHGETFPYTAFDNNCYAFCCWVLDLNDSW LSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKL RPLNILNILASCDWSFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL AVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLAVKWFFPK KEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKSSLAAYMKTLDLEEEKARKLSTK SASPDIVGTVNALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTYLAREVA KRIAASLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELADTCP LTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLAYAEAPEVEKA KRDFPGQPDMWKNAFSPDFTHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS GLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVRTMP ELKQALKNISIKKCQIVYSGSTYTLESDGKGNVKVDRVQSASVQTNNELAGALHHLRT ARMRYYVRCVQEALYSIIQIAGAAFVTTRIVKRMNIQSLWSKPQVENTEETTSRDGCP KPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK YSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVT GSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPS LFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRADVTGMILEEGAPEGT VVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDC GCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGP GSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPR GKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWN GESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLA TMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDS TQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTS QWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLRE YGLKPTRPDKTEGPLAISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGSN HEDPSETMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQEP MFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide <1..989 /gene="POL" /locus_tag="H649_46728gpPOL" /product="putative protein p48" mat_peptide 990..2087 /gene="POL" /locus_tag="H649_46728gpPOL" /product="NTPase" /note="p41" mat_peptide 2088..2624 /gene="POL" /locus_tag="H649_46728gpPOL" /product="protein p22" mat_peptide 2625..3023 /gene="POL" /locus_tag="H649_46728gpPOL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3024..3566 /gene="POL" /locus_tag="H649_46728gpPOL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3567..5096 /gene="POL" /locus_tag="H649_46728gpPOL" /product="RNA-directed RNA polymerase" primer_bind 1..13 gene 5080..6699 /gene="VP1" /locus_tag="H649_46728gpVP1" CDS 5080..6699 /gene="VP1" /locus_tag="H649_46728gpVP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AGX85892.1" /translation="MKMASSDANPSDGSTANLVPEANNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEVLWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFAAGKIIFAAVPPNFPTEGLSPSQVTMFPHLIVDVRQLEPVMIPLPD IRNNFYHYNQSNDPTIKLIAMLYTPLRANNVGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESKTNPFSVPILTIEEMTNSRFPIPLEKLFTGPSSALVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHTTKTHTYQMNLAAQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGNGSTRAHKATVYTGGVEFTPKLGRIQLFTDTDNDLEANQNTKFTPVGVIQDG DTHQNEPQQWVLPSYSGRNNHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDC LLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGHHDLFI PPNGYFRFDSWVSPFYTLAPMGNGTGRRRAL" gene 6699..7505 /gene="VP2" /locus_tag="H649_46728gpVP2" CDS 6699..7505 /gene="VP2" /locus_tag="H649_46728gpVP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AGX85893.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQD SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPGARTTTYNAGYFSTPQHSGALPGRANLRAAVPARGSSRVSS NSSTATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLNSQTGVFNTRRQPLFAHIRRRGESRA" ORIGIN 1 tgaagatggc gtctaacgac gcttccgctg ccgctgttgc taacagcaac aacgacaccg 61 ttaaatcttc aagtgacgga gtgctttcta gcatggctgt cactttcaaa cgagccctcg 121 gggcgcggcc taaacagcct cccccgaggg aaataccaca aagacccccg cgaccaccca 181 ctccagaact gatcaaaaat atcccccctc ccccacccaa tggagaggat gatatagtgg 241 tttcttatag cgtcaaagat ggtatctctg gtttacctga tctttccacc gtcaggcaac 301 cggaagaatc taatacggcc ttcagtatcc ctccactcaa tcagagggag agtagagaag 361 ctaaggaacc actgactgga acaattttgg aaatgtggga tggagaaatc tatcattatg 421 gcctgtacgt agagcgaggt cttgtactag gtgtgcacaa accaccagct gccatcagtc 481 tcgctagggt cgaactaaca ccactttcct tgtactggag acctgtgtac actccccagt 541 acctcatctc tccagacgct ctcaagagac tacacggaga gacgttcccc tacacagcct 601 ttgacaacaa ctgctatgcc ttttgttgtt gggtcctgga cctaaacgac tcgtggctga 661 gtaggagaat gatccagaga acaactggct tcttcagacc ctaccaagat tggaatagga 721 aacccctccc cactatggat gactccaaat taaagaaggt ggctaacata ttcctgtgtg 781 cattgtcttc gctattcacc aggcctataa aagatataat agggaagcta aggcctctta 841 acatccttaa catcttggct tcatgtgatt ggtcttttgc aggcatagtg gagtccttga 901 tactcttggc agaactcttt ggagttttct ggacgccccc agatgtgtct gcgatgattg 961 cccccttact cggtgactac gaactgcagg gacctgagga ccttgcagtg gagctcgtcc 1021 ctgtagtgat ggggggaatt ggtttggtgc taggattcac caaagagaag attggaaaaa 1081 tgttgtcatc tgctgcatcc accctgagag cttgtaaaga tcttggtgca tatgggctag 1141 agatcctaaa gttggctgtg aagtggttct tcccgaagaa agaggaagca aatgaactgg 1201 ctatagtgag atccatcgag gatgcagtcc tggatctcga agcaattgaa aacaaccata 1261 tgaccacctt gctcaaagac aaaagcagtc tggcagccta catgaaaacc cttgaccttg 1321 aggaggagaa agccaggaaa ctctcaacca agtctgcttc acctgacatt gtgggcacag 1381 tcaacgccct tctggcgaga atcgctgctg cacgttctct ggtgcatcga gcgaaggagg 1441 aactttctag cagaccaaga cctgtagtgt tgatgatatc aggcagacca ggaataggga 1501 agacctacct tgccagagaa gtggctaaga gaatcgcagc ctcccttaca ggagaccagc 1561 gtgtaggcct cgtcccacgc aatggcgtcg accactggga tgcgtacaag ggggagaggg 1621 tcgttctatg ggatgactat ggaatgagca atcccatcca agatgccctc agattgcaag 1681 aactcgctga cacttgtccc ctcaccctga actgtgacag gattgagaac aaaggaaagg 1741 tctttgacag cgatgtcatc attatcacca ctaacctggc taacccagca ccactggact 1801 atgtcaactt cgaagcatgc tcgaggcgca tcgacttcct cgcgtatgca gaagcccctg 1861 aggtcgaaaa ggcgaagcgt gacttcccag gccaacccga tatgtggaag aacgccttca 1921 gtcctgattt cacacacata aaactaacat tggctccaca gggtggtttc gacaagaacg 1981 ggaacacccc acacgggaag ggcgtcatga agactctcac caccggctcc ctcattgccc 2041 gggcatcagg gctactccat gagaggctag atgaatttga actacagggc ccaactctca 2101 ccactttcaa ctttgaccgc aataaagtgc ttgcctttag acaacttgct gctgaaaaca 2161 aatatgggtt gatggacaca atgaaagttg ggaggcagct caaggatgtc agaacaatgc 2221 cagagctcaa gcaagcactc aagaatattt caatcaagaa gtgccagata gtgtacagtg 2281 gtagcaccta cacacttgag tctgatggca agggtaatgt gaaggttgac agagtccaaa 2341 gcgcctccgt gcagaccaac aatgagctgg ctggcgccct acaccatcta aggacagcca 2401 gaatgagata ctatgtcagg tgtgtccagg aggccctgta ttccatcatc cagattgctg 2461 gggctgcatt tgtcaccacg cgcatcgtca agcgcatgaa catacaaagc ctatggtcta 2521 aaccacaagt ggaaaacaca gaggagacta ccagcaggga cgggtgtcca aaacccaaag 2581 atgatgagga gttcgtcatt tcatccgacg acatcaagac tgaaggcaag aaagggaaaa 2641 acaagactgg ccgcggtaag aagcacacag ccttctcaag caaaggtctc agtgatgaag 2701 agtacgatga gtacaagagg attagagaag aaaggaatgg taagtactcc atagaagagt 2761 accttcaaga cagggacaaa tactatgagg aggtggccat tgccagggcg accgaggaag 2821 acttctgtga agaggaggag gccaagatcc ggcaaaggat cttcaggcca acaaggaaac 2881 aacgcaagga ggaaagagct tctctcggtt tagtcacagg ttctgaaatt aggaaaagaa 2941 atccagatga tttcaaaccc aaggggaaat tgtgggctga cgatgacaga agtgtggact 3001 acaatgagaa actcagtttt gaagccccac caagcatctg gtcgaggata gtcaactttg 3061 gttcaggttg gggattctgg gtttccccca gtttgttcat aacatcaacc catgtcatac 3121 cccagggagc aaaggagttc tttggagtcc ccatcaaaca aattcaggta cataagtcag 3181 gcgaattctg tcgcttgaga ttcccaaaac caatcagggc tgatgtgacg ggcatgatct 3241 tagaagaagg tgcacccgag ggcaccgtgg ttacactact catcaaaagg tccactgggg 3301 aactcatgcc cctagcagct aggatgggga cccatgcaac catgaaaatc caaggacgca 3361 ctgttggagg tcaaatgggc atgcttctga caggatccaa cgccaaaagc atggacctgg 3421 gtaccacacc aggtgattgt ggctgtccct acatctacaa gagaggaaat gactatgtag 3481 tcattggagt ccacacggct gccgctcgtg ggggcaacac tgtcatctgt gccacccagg 3541 ggagtgaggg agaggctaca cttgaaggtg gtgacaacaa agggacatac tgtggtgcac 3601 caatcctagg cccagggagt gccccaaaac ttagcaccaa gaccaaattc tggagatcgt 3661 ccacagcacc actcccacct ggcacctatg aaccagccta tcttggtggt aaggatccca 3721 gagtcaaggg tgggccttca ctacagcagg tcatgaggga tcagctgaag ccattcacag 3781 agcccagggg caagccacca aagccaagtg tgttggaagc tgctaagaaa accatcatca 3841 atgtccttga gcaaacaatt gatccacctg agaaatggtc gttcgcacaa gcttgcgcgt 3901 cacttgataa gaccacctcc agtggtcacc cgcaccacat gcggaaaaac gactgctgga 3961 acggggagtc cttcacaggc aagctggcag accaggcttc caaggccaac ctgatgtttg 4021 aagaggggaa gaacatgacg ccagtctata cagctgcgct taaggatgaa ttagttaaaa 4081 ctgacaagat ttatggtaag atcaagaaaa ggcttctctg gggctcggat ttggcgacca 4141 tgatccggtg tgctcgagca ttcggaggcc taatggatga actcaaagcg cactgtgtca 4201 cacttcccat cagagttggt atgaatatga atgaggatgg ccccatcatc ttcgagaggc 4261 actccaggta cacgtaccac tatgatgctg attactctcg atgggattca acacaacaga 4321 gagccgtgtt ggcagcagct ctagaaatta tggttaagtt ctccccagaa ccacatttgg 4381 cccaggtagt cgcagaagac cttctttccc ctagcgtggt ggacgtgggt gactttacaa 4441 tatcaattaa cgagggtctt ccctctggag tgccctgcac ctcccaatgg aactccatag 4501 cccactggct tctcaccctc tgtgcgctct ctgaagttac aaacttgtct cctgacacca 4561 tacaagctaa ttccctcttc tctttttatg gtgatgatga aattgttagc acagacataa 4621 aattggaccc agaaaagttg acagcaaagc tcagggaata tgggttaaaa ccaacccgcc 4681 ccgacaaaac tgaaggaccc cttgccatct ctgaagactt ggatggcctg actttcttgc 4741 gaagaactgt gacccgcgac ccagctggtt ggtttggaaa actggagcag agctcaatac 4801 tcaggcaaat gtactggact aggggttcca accatgaaga cccatctgaa acaatgattc 4861 cacactccca aaggcccata caactgatgt ccctactggg ggaggccgca ctccacggcc 4921 caacattcta cagcaaaatc agcaagttag tcattgcaga gctaaaagaa ggtggcatgg 4981 atttttacgt gcccagacaa gagccaatgt tcagatggat gagattctca gatctgagca 5041 cgtgggaggg cgatcgcaat ctggctccca gttttgtgaa tgaagatggc gtcgagtgac 5101 gccaacccat ctgatgggtc cacagccaac ctcgtcccag aggccaacaa tgaggttatg 5161 gctttggagc ccgttgttgg tgccgccatt gcggcgcctg tagcgggcca acaaaatgta 5221 attgacccct ggattagaaa caattttgtg caagcccctg gtggagagtt tacagtatcc 5281 cctagaaacg ctccaggtga agtactatgg agcgcgccct taggccctga tttgaatccc 5341 tacctttccc atttggccag aatgtacaat ggttatgcag gtggttttga agtgcaggta 5401 atcctcgcgg ggaacgcgtt cgccgccgga aaaatcatat tcgcagcagt cccaccaaat 5461 ttcccaactg aaggcttgag ccccagccag gtcactatgt tcccccactt aatagtagat 5521 gttaggcaac tggaacctgt gatgatcccc ttacccgata ttaggaataa tttctatcat 5581 tataatcaat caaatgatcc caccatcaaa ttgatagcaa tgttgtatac acctcttagg 5641 gctaataatg ttggtgacga tgtcttcaca gtttcttgtc gggtactcac gagaccatcc 5701 cccgattttg atttcatatt tctagtgcca cccacagttg aatcaaaaac caacccattc 5761 tctgttccaa ttctaactat tgaggagatg accaattcaa gattccccat tcctttggaa 5821 aagctgttca cgggccccag cagtgccctt gttgttcaac cacaaaacgg caggtgcacg 5881 actgatggcg tgctcctggg taccacccaa ctgtctcctg tcaacatctg caccttcaga 5941 ggggatgtca cccatactac aaaaactcat acctaccaaa tgaatttggc tgctcaaaat 6001 tggaacagtt atgacccaac agaagaaatc ccagcccccc taggaactcc agatttcgtg 6061 ggaaagatcc aaggtgtgct cacccaaacc acgaagggaa atggctcaac ccgtgcccac 6121 aaagctacag tgtacactgg gggcgtcgag ttcactccaa aactgggtag aatccaactt 6181 ttcactgaca cagacaacga tcttgaagct aaccaaaaca caaagttcac cccagtcggt 6241 gtcatccagg atggtgatac ccaccaaaat gaaccccaac aatgggtact cccaagttac 6301 tcaggtagaa ataatcacaa tgtgcacctg gcccccgctg tagcccccac ttttccgggc 6361 gagcaacttc tcttcttcag atccactatg cccggatgca gcgggtaccc caacatgaat 6421 ttggactgtc tgcttcccca ggaatgggtg caatatttct atcaagaggc agccccagca 6481 caatctgatg tggctttgct aagatttgtg aatccagata caggtagggt tttgtttgag 6541 tgcaagcttc ataaatcagg ttatgtcaca gtggctcaca ccggccacca tgatttgttt 6601 atccccccta atggttattt cagatttgat tcctgggtca gccccttcta cacacttgcc 6661 cccatgggaa atggaacggg gcgtagacgt gcattataat ggctggagct ttctttgctg 6721 gattggcatc tgacgtcctt ggatccggac ttggttctct gatcaatgcc ggggctgggg 6781 ccatcaacca aaaagttgaa tttgaaaaca acagaaaatt gcaacaagat tccttccaat 6841 ttagtagcaa tctgcaacag gcttcctttc aacatgataa agagatgctc caagcacaaa 6901 ttgaggccac caaaaagttg caacaggaaa tgatgagagt taaacaggca atgctcctag 6961 agggtgggtt ctctgagaca gatgcagccc gtggggcaat caacgccccc atgacaaagg 7021 ttttggactg gagtgggaca aggtactggg ctcccggtgc taggactaca acatacaatg 7081 caggctactt ttccactccc caacactcgg gggcactgcc aggaagagct aatcttaggg 7141 ctgctgtccc cgctcggggc tcctctagag tatcttctaa ttcttctact gctacctctg 7201 tgtattcaaa tcaaactgct tcaacgagac ttggttctac agctggttct ggtaccagtg 7261 tctcgagcct cccgtcaact gcaaggacta ggagttgggt tgaggatcaa aataggaatt 7321 tgtcaccttt catgaggggg gcccacaaca tatcgtttgt caccccacca tctagcagat 7381 cctctagtca aggcacagtc tcaaccgtgc ccaaagaagt tttgaactcc cagactggcg 7441 ttttcaatac gcgcaggcag cctctctttg ctcacattcg taggcgaggg gagtcacggg 7501 cgtaa //