Typing tool
|
Complete norovirus genomes
KF712500 | GII.4 New Orleans | ||
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GII.P4 Hunter |
ORF1: 1..5097 ORF2: 5078..6694 ORF3: 6694..7500LOCUS KF712500 7500 bp ss-RNA linear VRL 26-OCT-2013 DEFINITION Norovirus Hu/GII.4/NIHIC1.14/2012/USA, partial genome. ACCESSION KF712500 VERSION KF712500.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII.4/NIHIC1.14/2012/USA ORGANISM Norovirus Hu/GII.4/NIHIC1.14/2012/USA Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7500) 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 :: 198.7x Sequencing Technology :: Sanger; Illumina ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7500 /organism="Norovirus Hu/GII.4/NIHIC1.14/2012/USA" /mol_type="genomic RNA" /strain="Hu/GII.4/NIHIC1.14/2012/USA" /host="Homo sapiens" /db_xref="taxon:1406808" /country="USA: Maryland" /collection_date="21-Oct-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..5097 /gene="POL" /locus_tag="H649_46731gpPOL" CDS <1..5097 /gene="POL" /locus_tag="H649_46731gpPOL" /note="genome polyprotein" /codon_start=1 /product="putative nonstructural polyprotein" /protein_id="AGX85912.1" /translation="KMASNDASAAAVADSNNDTVKSSSDGVLSSMAVTFKRALGARPK QPPPREIPQRPPRPPTPELIKNIPPPPPNGEDDVVVSYSVKDGISGLPDLSTVRQPEE SNTAFSIPPLNQRESREAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISL ARVELTPLSLYWRPVYTPQYLISPDALKRLHGETFPYTAFDNNCYAFCCWVLDLNDSW LSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKL RPLNILNILASCDWSFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL AVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLAVKWFFPK KEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKSSLAAYMKTLDLEEEKARKLSTK SASPDIVGTVNALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTYLAREVA KRIAASLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELADTCP LTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLAYAEAPEVEKA KRDFPGQPDMWKNAFSPDFTHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS GLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVRTMP ELKQALKNISIKKCQIVYSGSTYTLESDGKGNVKVDRVQSASVQTNNELAGALHHLRT ARMRYYVRCVQEALYSIIQIAGAAFVTTRIVKRMNIQSLWSKPQVENTEETTSRDGCP KPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK YSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVT GSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPS LFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRADVTGMILEEGAPEGT VVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDC GCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGP GSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR GKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWN GESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLA TMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDS TQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTS QWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLRE YGLKPTRPDKTEGPLAISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGSN HEDPSETMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQEP MFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide <1..987 /gene="POL" /locus_tag="H649_46731gpPOL" /product="putative protein p48" mat_peptide 988..2085 /gene="POL" /locus_tag="H649_46731gpPOL" /product="NTPase" /note="p41" mat_peptide 2086..2622 /gene="POL" /locus_tag="H649_46731gpPOL" /product="protein p22" mat_peptide 2623..3021 /gene="POL" /locus_tag="H649_46731gpPOL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3022..3564 /gene="POL" /locus_tag="H649_46731gpPOL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3565..5094 /gene="POL" /locus_tag="H649_46731gpPOL" /product="RNA-directed RNA polymerase" gene 5078..6694 /gene="VP1" /locus_tag="H649_46731gpVP1" CDS 5078..6694 /gene="VP1" /locus_tag="H649_46731gpVP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AGX85913.1" /translation="MKMASSDANPSDGSTANLVPEANNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEVLWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFAAGKIIFAAVPPNFSTEGLSPSQVTMFPHLIVDVRQLEPVMIPLPD IRNNFYHYNQSNDPTIKLIAMLYTPLRANNVGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESKTNPFSVPILTIEEMTNSRFPIPLEKLFTGPSSALVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHTTKTHTYQMNLAAQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTKENGSTRAHKATVYTGTVEFTPKLGRIQLFTDTDNDLEANQNTKFTPVGVIQDG DHQNEPQQWVLPSYSGRNNHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCL LPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGHHDLVIP PNGYFRFDSWVSPFYTLAPMGNGTGRRRAL" gene 6694..7500 /gene="VP2" /locus_tag="H649_46731gpVP2" CDS 6694..7500 /gene="VP2" /locus_tag="H649_46731gpVP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AGX85914.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQD SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPGARTTTYNAGYFSTPQHSGALPGRANLRAVVPARGSSRVSS NSSTATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLNSQTGVFNTRRQPLFAHIRRRGESRA" ORIGIN 1 aagatggcgt ctaacgacgc ttccgctgcc gctgttgctg acagcaacaa cgacaccgtt 61 aaatcttcaa gtgacggagt gctttctagc atggctgtca ctttcaaacg agccctcggg 121 gcgcggccta aacagcctcc cccgagggaa ataccacaaa gacccccgcg accacccact 181 ccagaactga tcaaaaatat cccccctccc ccacccaatg gagaggatga tgtagtggtt 241 tcttatagcg tcaaagatgg tatctctggt ttacctgatc tttccaccgt caggcaaccg 301 gaagaatcta atacggcctt cagtatccct ccactcaatc agagggagag tagagaagct 361 aaggaaccac tgactggaac aattttggaa atgtgggatg gagaaatcta tcattatggc 421 ctgtacgtag agcgaggtct tgtactaggt gtgcacaaac caccagctgc catcagtctc 481 gctagggtcg aactaacacc actttccttg tactggagac ctgtgtacac tccccagtac 541 ctcatctctc cagacgctct caagagacta cacggagaga cgttccccta cacagccttt 601 gacaacaact gctatgcctt ttgttgttgg gtcctggacc taaacgactc gtggctgagt 661 aggagaatga tccagagaac aactggcttc ttcagaccct accaagattg gaataggaaa 721 cccctcccca ctatggatga ctccaaatta aagaaggtgg ctaacatatt cctgtgtgca 781 ttgtcttcgc tattcaccag gcctataaaa gatataatag ggaagctaag gcctcttaac 841 atccttaaca tcttggcttc atgtgattgg tcttttgcag gcatagtgga gtccttgata 901 ctcttggcag aactctttgg agttttctgg acgcccccag atgtgtctgc gatgattgcc 961 cccttactcg gtgactacga actgcaggga cctgaggacc ttgcagtgga gctcgtccct 1021 gtagtgatgg ggggaattgg tttggtgcta ggattcacca aagagaagat tggaaaaatg 1081 ttgtcatctg ctgcatccac cctgagagct tgtaaagatc ttggtgcata tgggctagag 1141 atcctaaagt tggctgtgaa gtggttcttc ccgaagaaag aggaagcaaa tgaactggct 1201 atagtgagat ccatcgagga tgcagtcctg gatctcgaag caattgaaaa caaccatatg 1261 accaccttgc tcaaagacaa aagcagtctg gcagcctaca tgaaaaccct tgaccttgag 1321 gaggagaaag ccaggaaact ctcaaccaag tctgcttcac ctgacattgt gggcacagtc 1381 aacgcccttc tggcgagaat cgctgctgca cgttctctgg tgcatcgagc gaaggaggaa 1441 ctttctagca gaccaagacc tgtagtgttg atgatatcag gcagaccagg aatagggaag 1501 acctaccttg ccagagaagt ggctaagaga atcgcagcct cccttacagg agaccagcgt 1561 gtaggcctcg tcccacgcaa tggcgtcgac cactgggatg cgtacaaggg ggagagggtc 1621 gttctatggg atgactatgg aatgagcaat cccatccaag atgccctcag attgcaagaa 1681 ctcgctgaca cttgtcccct caccctgaac tgtgacagga ttgagaacaa aggaaaggtc 1741 tttgacagcg atgtcatcat tatcaccact aacctggcta acccagcacc actggactat 1801 gtcaacttcg aagcatgctc gaggcgcatc gacttcctcg cgtatgcaga agcccctgag 1861 gtcgaaaagg cgaagcgtga cttcccaggc caacccgata tgtggaagaa cgccttcagt 1921 cctgatttca cacacataaa actaacattg gctccacagg gtggtttcga caagaacggg 1981 aacaccccac acgggaaggg cgtcatgaag actctcacca ccggctccct cattgcccgg 2041 gcatcagggc tactccatga gaggctagat gaatttgaac tacagggccc aactctcacc 2101 actttcaact ttgaccgcaa taaagtgctt gcctttagac aacttgctgc tgaaaacaaa 2161 tatgggttga tggacacaat gaaagttggg aggcagctca aggatgtcag aacaatgcca 2221 gagctcaagc aagcactcaa gaatatttca atcaagaagt gccagatagt gtacagtggt 2281 agcacctaca cacttgagtc tgatggcaag ggtaatgtga aggttgacag agtccaaagc 2341 gcctccgtgc agaccaacaa tgagctggct ggcgccctac accatctaag gacagccaga 2401 atgagatact atgtcaggtg tgtccaggag gccctgtatt ccatcatcca gattgctggg 2461 gctgcatttg tcaccacgcg catcgtcaag cgcatgaaca tacaaagcct atggtctaaa 2521 ccacaagtgg aaaacacaga ggagactacc agcagggacg ggtgtccaaa acccaaagat 2581 gatgaggagt tcgtcatttc atccgacgac atcaagactg aaggcaagaa agggaaaaac 2641 aagactggcc gcggtaagaa gcacacagcc ttctcaagca aaggtctcag tgatgaagag 2701 tacgatgagt acaagaggat tagagaagaa aggaatggta agtactccat agaagagtac 2761 cttcaagaca gggacaaata ctatgaggag gtggccattg ccagggcgac tgaggaagac 2821 ttctgtgaag aggaggaggc caagatccgg caaaggatct tcaggccaac aaggaaacaa 2881 cgcaaggagg aaagagcttc tctcggttta gtcacaggtt ctgaaattag gaaaagaaat 2941 ccagatgatt tcaaacccaa ggggaaattg tgggctgacg atgacagaag tgtggactac 3001 aatgagaaac tcagttttga agccccacca agcatctggt cgaggatagt caactttggt 3061 tcaggttggg gattctgggt ttcccccagt ttgttcataa catcaaccca tgtcataccc 3121 cagggagcaa aggagttctt tggagtcccc atcaaacaaa ttcaggtaca taagtcaggc 3181 gaattctgtc gcttgagatt cccaaaacca atcagggctg atgtgacggg catgatctta 3241 gaagaaggtg cacccgaggg caccgtggtt acactactca tcaaaaggtc cactggggaa 3301 ctcatgcccc tagcagctag gatggggacc catgcaacca tgaaaatcca aggacgcact 3361 gttggaggtc aaatgggcat gcttctgaca ggatccaacg ccaaaagcat ggacctgggt 3421 accacaccag gtgattgtgg ctgtccctac atctacaaga gaggaaatga ctatgtagtc 3481 attggagtcc acacggctgc cgctcgtggg ggcaacactg tcatctgtgc cacccagggg 3541 agtgagggag aggctacact tgaaggtggt gacaacaaag ggacatactg tggtgcacca 3601 atcctaggcc cagggagtgc cccaaaactt agcaccaaga ccaaattctg gagatcgtcc 3661 acagcaccac tcccacctgg cacctatgaa ccagcctatc ttggtggtag ggatcccaga 3721 gtcaagggtg ggccttcact acagcaggtc atgagggatc agctgaagcc attcacagag 3781 cccaggggca agccaccaaa gccaagtgtg ttggaagctg ctaagaaaac catcatcaat 3841 gtccttgagc aaacaattga tccacctgag aaatggtcgt tcgcacaagc ttgcgcgtca 3901 cttgataaga ccacctccag tggtcacccg caccacatgc ggaaaaacga ctgctggaac 3961 ggggagtcct tcacaggcaa gctggcagac caggcttcca aggccaacct gatgtttgaa 4021 gaggggaaga acatgacgcc agtctataca gctgcgctta aggatgaatt agttaaaact 4081 gacaagattt atggtaagat caagaaaagg cttctctggg gctcggattt ggcgaccatg 4141 atccggtgtg ctcgagcatt cggaggccta atggatgaac tcaaagcgca ctgtgtcaca 4201 cttcccatca gagttggtat gaatatgaat gaggatggcc ccatcatctt cgagaggcac 4261 tccaggtaca cgtaccacta tgatgctgat tactctcgat gggattcaac acaacagaga 4321 gccgtgttgg cagcagctct agaaattatg gttaagttct ccccagaacc acatttggcc 4381 caggtagtcg cagaagacct tctttcccct agcgtggtgg acgtgggtga ctttacaata 4441 tcaattaacg agggtcttcc ctctggagtg ccctgcacct cccaatggaa ctccatagcc 4501 cactggcttc tcaccctctg tgcgctctct gaagttacaa acttgtctcc tgacaccata 4561 caagctaatt ccctcttctc tttttatggt gatgatgaaa ttgttagcac agacataaaa 4621 ttggacccag aaaagttgac agcaaagctc agggaatatg ggttaaaacc aacccgcccc 4681 gacaaaactg aaggacccct tgccatctct gaagacttgg atggcctgac tttcttgcga 4741 agaactgtga cccgcgaccc agctggttgg tttggaaaac tggagcagag ctcaatactc 4801 aggcaaatgt actggactag gggttccaac catgaagacc catctgaaac aatgattcca 4861 cactcccaaa ggcccataca actgatgtcc ctactggggg aggccgcact ccacggccca 4921 acattctaca gcaaaatcag caagttagtc attgcagagc taaaagaagg tggcatggat 4981 ttttacgtgc ccagacaaga gccaatgttc agatggatga gattctcaga tctgagcacg 5041 tgggagggcg atcgcaatct ggctcccagt tttgtgaatg aagatggcgt cgagtgacgc 5101 caacccatct gatgggtcca cagccaacct cgtcccagag gccaacaatg aggttatggc 5161 tttggagccc gttgttggtg ccgccattgc ggcgcctgta gcgggccaac aaaatgtaat 5221 tgacccctgg attagaaaca attttgtgca agcccctggt ggagagttta cagtatcccc 5281 tagaaacgct ccaggtgaag tactatggag cgcgccctta ggccctgatt tgaatcccta 5341 cctttcccat ttggccagaa tgtacaatgg ttatgcaggt ggttttgaag tgcaggtaat 5401 cctcgcgggg aacgcgttcg ccgccggaaa aatcatattc gcagcagtcc caccaaattt 5461 ctcaactgaa ggcttgagcc ccagccaggt cactatgttc ccccacttaa tagtagatgt 5521 taggcaactg gaacctgtga tgatcccctt acccgatatt aggaataatt tctatcatta 5581 caatcaatca aatgatccca ccatcaaatt gatagcaatg ttgtatacac ctcttagggc 5641 taataatgtt ggtgacgatg tcttcacagt ttcttgtcgg gtactcacga gaccatcccc 5701 cgattttgat ttcatatttc tagtgccacc cacagttgaa tcaaaaacca acccattctc 5761 tgttccaatt ctaactattg aggagatgac caattcaaga ttccccattc ctttggaaaa 5821 gctgttcacg ggccccagca gtgcccttgt tgttcaacca caaaacggca ggtgcacgac 5881 tgatggcgtg ctcctgggta ccacccaact gtctcctgtc aacatctgca ccttcagagg 5941 ggatgtcacc catactacaa aaactcatac ctaccaaatg aatttggctg ctcaaaattg 6001 gaacagttat gacccaacag aagaaatccc agccccccta ggaactccag atttcgtggg 6061 aaagatccaa ggtgtgctca cccaaaccac gaaggaaaat ggctcaaccc gtgcccacaa 6121 agctacagtg tacactggga ccgtcgagtt cactccaaaa ctgggtagaa tccaactttt 6181 cactgacaca gacaacgatc ttgaagctaa ccaaaacaca aagttcaccc cagtcggtgt 6241 catccaggat ggtgaccacc aaaatgaacc ccaacaatgg gtactcccaa gttactcagg 6301 tagaaataat cacaatgtgc acctggcccc cgctgtagcc cccacttttc cgggcgagca 6361 acttctcttc ttcagatcca ctatgcccgg atgcagcggg taccccaaca tgaatttgga 6421 ctgtctgctt ccccaggaat gggtgcaata tttctatcaa gaggcagccc cagcacaatc 6481 tgatgtggct ttgctaagat ttgtgaatcc agatacaggt agggttttgt ttgagtgcaa 6541 gcttcataaa tcaggttatg tcacagtggc tcacaccggc caccatgatt tggttatccc 6601 ccctaatggt tatttcagat ttgattcctg ggtcagcccc ttctacacac ttgcccccat 6661 gggaaatgga acggggcgta gacgtgcatt ataatggctg gagctttctt tgctggattg 6721 gcatctgacg tccttggatc cggacttggt tctctgatca atgccggggc tggggccatc 6781 aaccaaaaag ttgaatttga aaacaacaga aaattgcaac aagattcctt ccaatttagt 6841 agcaatctgc aacaggcttc ctttcaacat gataaagaga tgctccaagc acaaattgag 6901 gccaccaaaa agttgcaaca ggaaatgatg agagttaaac aggcaatgct cctagagggt 6961 gggttctctg agacagatgc agcccgtggg gcaatcaacg cccccatgac aaaggttttg 7021 gactggagtg ggacaaggta ctgggctccc ggtgctagga ctacaacata caatgcaggc 7081 tacttttcca ctccccaaca ctcgggggca ctgccaggaa gagctaatct tagggctgtt 7141 gtccccgctc ggggctcctc tagagtatct tctaattctt ctactgctac ctctgtgtat 7201 tcaaatcaaa ctgcttcaac gagacttggt tctacagctg gttctggtac cagtgtctcg 7261 agcctcccgt caactgcaag gactaggagt tgggttgagg atcaaaatag gaatttgtca 7321 cctttcatga ggggggccca caacatatcg tttgtcaccc caccatctag cagatcctct 7381 agtcaaggca cagtctcaac cgtgcccaaa gaagttttga actcccagac tggcgttttc 7441 aatacgcgca ggcagcctct ctttgctcac attcgtaggc gaggggagtc acgggcgtaa //