Typing tool
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Typing tool
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Complete norovirus genomes
| KF712494 | GII.4 New Orleans | |
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| GII.P4 Hunter |
ORF1: 1..4585
ORF2: 4566..6185
ORF3: 6185..6991
LOCUS KF712494 6991 bp ss-RNA linear VRL 26-OCT-2013
DEFINITION Norovirus Hu/GII.4/NIHIC1.7/2012/USA, partial genome.
ACCESSION KF712494
VERSION KF712494.1
DBLINK BioProject: PRJNA70471
KEYWORDS STANDARD_DRAFT.
SOURCE Norovirus Hu/GII.4/NIHIC1.7/2012/USA
ORGANISM Norovirus Hu/GII.4/NIHIC1.7/2012/USA
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 6991)
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 :: Standard Draft
Assembly Method :: clc_ref_assemble_long v. 3.22.55705
Genome Coverage :: 155.2x
Sequencing Technology :: Sanger; Illumina
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..6991
/organism="Norovirus Hu/GII.4/NIHIC1.7/2012/USA"
/mol_type="genomic RNA"
/strain="Hu/GII.4/NIHIC1.7/2012/USA"
/host="Homo sapiens"
/db_xref="taxon:1406810"
/country="USA: Maryland"
/collection_date="27-Apr-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..4585
/gene="POL"
/locus_tag="H649_46726gpPOL"
CDS <1..4585
/gene="POL"
/locus_tag="H649_46726gpPOL"
/note="genome polyprotein"
/codon_start=2
/product="putative nonstructural polyprotein"
/protein_id="AGX85894.1"
/translation="WRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLN
DSWLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDII
GKLRPLNILNILASCDWSFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLAVKWF
FPKKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKSSLAAYMKTLDLEEEKARKL
STKSASPDIVGTVNALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTYLAR
EVAKRIAASLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELAD
TCPLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLAYAEAPEV
EKAKRDFPGQPDMWKNAFSPDFTHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
RASGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVR
TMPELKQALKNISIKKCQIVYSGSTYTLESDGKGNVKVDRVQSASVQTNNELAGALHH
LRTARMRYYVRCVQEALYSIIQIAGAAFVTTRIVKRMNIQSLWSKPQVENTEETTSRD
GCPKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREER
NGKYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLG
LVTGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWV
SPSLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRADVTGMILEEGAP
EGTVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTP
GDCGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPI
LGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFT
EPRGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKND
CWNGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGS
DLATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSR
WDSTQQRAVLAVALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVP
CTSQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAK
LREYGLKPTRPDKTEGPLAISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTR
GSNHEDPSETMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPR
QEPMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..475
/gene="POL"
/locus_tag="H649_46726gpPOL"
/product="putative protein p48"
mat_peptide 476..1573
/gene="POL"
/locus_tag="H649_46726gpPOL"
/product="NTPase"
/note="p41"
mat_peptide 1574..2110
/gene="POL"
/locus_tag="H649_46726gpPOL"
/product="protein p22"
mat_peptide 2111..2509
/gene="POL"
/locus_tag="H649_46726gpPOL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 2510..3052
/gene="POL"
/locus_tag="H649_46726gpPOL"
/product="3C-like protease"
/note="3CLpro; calicivirin"
mat_peptide 3053..4582
/gene="POL"
/locus_tag="H649_46726gpPOL"
/product="RNA-directed RNA polymerase"
gene 4566..6185
/gene="VP1"
/locus_tag="H649_46726gpVP1"
CDS 4566..6185
/gene="VP1"
/locus_tag="H649_46726gpVP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AGX85895.1"
/translation="MKMASSDANPSDGSTANLVPEANNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEVLWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFAAGKIIFAAVPPNFPTEGLSPSQVTMFPHLIIDVRQLEPVMIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNVGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESKTNPFSVPILTIEEMTNSRFPIPLEKLFTGPSSALVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITKTHSYQMNLAAQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGNGSTRAHKATVYTGSTEFTPKLGRIQLVTDTDNDLETNQNTKFTPVGVIQDG
DTHQNEPQQWVLPSYLGRNNHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDC
LLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGHHDLFI
PPNGYFRFDSWVSPFYTLAPMGNGTGRRRAL"
gene 6185..6991
/gene="VP2"
/locus_tag="H649_46726gpVP2"
CDS 6185..6991
/gene="VP2"
/locus_tag="H649_46726gpVP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AGX85896.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQD
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPGARTTTYNAGYFSTPQHSGALPGRANLRAAVPARGSSRVSS
NSSTATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLNSQTGAFNTRRQPLFAHIRRRGESRA"
ORIGIN
1 ctggagacct gtgtacactc ctcagtacct catttctcca gacactctca agaaattaca
61 cggagaaaca tttccctaca cagcctttga caacaattgc tatgcctttt gttgctgggt
121 cctggattta aacgactcgt ggctgagtag gagaatgatc cagagaacaa ctggcttctt
181 cagaccctac caagattgga ataggaaacc cctccccact atggatgact ccaaattaaa
241 gaaggtggct aacatattcc tgtgtgcatt gtcttcgcta ttcaccaggc ctataaaaga
301 tataataggg aagctaaggc ctcttaacat ccttaacatc ttggcttcat gtgattggtc
361 ttttgcaggc atagtggagt ccttgatact cttggcagaa ctctttggag ttttctggac
421 acccccagat gtgtctgcga tgattgcccc cttactcggt gactacgaac tgcagggacc
481 tgaggacctt gcagtggagc tcgtccctgt agtgatgggg ggaattggtt tggtgctagg
541 attcaccaaa gagaagattg gaaaaatgtt gtcatctgct gcatccaccc tgagagcttg
601 taaagatctt ggtgcatatg ggctagagat cctaaagttg gctgtgaagt ggttcttccc
661 gaagaaagag gaagcaaatg aactggctat agtgagatcc atcgaggatg cagtcctgga
721 tctcgaagca attgaaaaca accatatgac caccttgctc aaagacaaaa gcagtctggc
781 agcctacatg aaaacccttg accttgagga ggagaaagcc aggaaactct caaccaagtc
841 tgcttcacct gacattgtgg gcacagtcaa cgcccttctg gcgagaatcg ctgctgcacg
901 ttctctggtg catcgagcga aggaggaact ttctagcaga ccaagacctg tagtgttgat
961 gatatcaggc agaccaggaa tagggaagac ctaccttgcc agagaagtgg ctaagagaat
1021 cgcagcctcc cttacaggag accagcgtgt aggcctcgtc ccacgcaatg gcgtcgacca
1081 ctgggatgcg tacaaggggg agagggtcgt tctatgggac gactatggaa tgagcaatcc
1141 tatccaagat gccctcagat tgcaagaact cgctgacact tgtcccctca ccctgaactg
1201 tgacaggatt gagaacaaag gaaaggtctt tgacagcgat gtcatcatta tcaccactaa
1261 cctggctaac ccagcaccac tggactatgt caacttcgaa gcatgctcga ggcgcatcga
1321 cttcctcgcg tatgcagaag cccctgaggt cgaaaaggcg aagcgtgact tcccaggcca
1381 acccgatatg tggaagaacg ccttcagtcc tgatttcaca cacataaaac taacattggc
1441 tccacagggt ggtttcgaca agaacgggaa caccccacac gggaagggcg tcatgaagac
1501 tctcaccacc ggctccctca ttgcccgggc atcagggcta ctccatgaga ggctagatga
1561 atttgaacta cagggcccaa ctctcaccac tttcaacttt gatcgcaata aagtgcttgc
1621 ctttagacaa cttgctgctg aaaacaaata tgggttgatg gacacaatga aagttgggag
1681 gcagctcaag gatgtcagaa caatgccaga gctcaagcaa gcactcaaga atatttcaat
1741 caagaagtgc cagatagtgt acagtggtag cacctacaca cttgagtctg atggcaaggg
1801 taatgtgaag gttgacagag tccaaagcgc ctccgtgcag accaacaatg agctggctgg
1861 cgccctacac catctaagga cagccagaat gagatactat gtcaggtgtg tccaggaggc
1921 cctgtattcc atcatccaga ttgctggggc tgcatttgtc accacgcgca tcgtcaagcg
1981 catgaacata caaagcctat ggtctaaacc acaagtggaa aacacagagg agactaccag
2041 cagggacggg tgtccaaaac ccaaagatga tgaggagttc gtcatttcat ccgacgacat
2101 caagactgaa ggcaagaaag ggaaaaacaa gactggccgc ggtaagaagc acacagcctt
2161 ctcaagcaaa ggtctcagtg atgaagagta cgatgagtac aagaggatta gagaagaaag
2221 gaatggtaag tactccatag aagagtacct tcaagacagg gacaaatact atgaggaggt
2281 ggccattgcc agggcgactg aggaagactt ctgtgaagag gaggaggcca agatccggca
2341 aaggatcttc aggccaacaa ggaaacaacg caaggaggaa agagcttctc tcggtttagt
2401 cacaggttct gaaattagga aaagaaatcc agatgatttc aaacccaagg ggaaattgtg
2461 ggctgacgat gacagaagtg tggactacaa tgagaaactc agttttgaag ccccaccaag
2521 catctggtcg aggatagtca actttggttc aggttgggga ttctgggttt cccccagttt
2581 gttcataaca tcaacccatg tcatacccca gggagcaaag gagttctttg gagtccccat
2641 caaacaaatt caggtacata agtcaggcga attctgtcgc ttgagattcc caaaaccaat
2701 cagggctgat gtgacgggca tgatcttaga agaaggtgca cccgagggca ccgtggttac
2761 actactcatc aaaaggtcca ctggggaact catgccccta gcagctagga tggggaccca
2821 tgcaaccatg aaaatccaag gacgcactgt tggaggtcaa atgggcatgc ttctgacagg
2881 atccaacgcc aaaagcatgg acctgggtac cacaccaggt gattgtggct gtccctacat
2941 ctacaagaga ggaaatgact atgtagtcat tggagtccac acggctgccg ctcgtggggg
3001 caacactgtc atctgtgcca cccaggggag tgagggagag gctacacttg aaggtggtga
3061 caacaaaggg acatactgtg gtgcaccaat cctaggccca gggagtgccc caaaacttag
3121 caccaagacc aaattctgga gatcgtccac agcaccactc ccacctggca cctatgaacc
3181 agcctatctt ggtggtaagg atcccagagt caagggtggg ccttcactac agcaggtcat
3241 gagggatcag ctgaagccat tcacagagcc caggggcaag ccaccaaagc caagtgtgtt
3301 ggaagctgct aagaaaacca tcatcaatgt ccttgagcaa acaattgatc cacctgagaa
3361 atggtcgttc gcacaagctt gcgcgtcact tgataagacc acctccagtg gtcacccgca
3421 tcacatgcgg aaaaacgact gctggaacgg ggagtccttc acaggcaagc tggcagacca
3481 ggcttccaag gccaacctga tgtttgaaga ggggaagaac atgacgccag tctatacagc
3541 tgcgcttaag gatgaattag ttaaaactga caagatttat ggtaagatca agaaaaggct
3601 tctctggggc tcggatttgg cgaccatgat ccggtgtgct cgagcattcg gaggcctaat
3661 ggatgaactc aaagcgcact gtgtcacact tcccatcaga gttggtatga atatgaatga
3721 ggatggcccc atcatcttcg agaggcactc caggtacacg taccactatg atgctgatta
3781 ctctcgatgg gattcaacac aacagagagc cgtgttggca gtagctctag aaattatggt
3841 taagttctcc ccagaaccac atttggccca ggtagtcgca gaagaccttc tttcccctag
3901 cgtggtggac gtgggtgact ttacaatatc aattaacgag ggtcttccct ctggagtgcc
3961 ctgcacctcc caatggaact ccatagccca ctggcttctc accctctgtg cgctctctga
4021 agttacaaac ttgtctcctg acaccataca agctaattcc ctcttctctt tttatggtga
4081 tgatgaaatt gttagcacag acataaaatt ggacccagaa aagttgacag caaagctcag
4141 ggaatatggg ttaaaaccaa cccgccccga caaaactgaa ggaccccttg ccatctctga
4201 agacttggat ggcctgactt tcttgcgaag aactgtgacc cgcgacccag ctggttggtt
4261 tggaaaactg gagcagagct caatactcag gcaaatgtac tggactaggg gttccaacca
4321 tgaagaccca tctgaaacaa tgattccaca ctcccaaagg cccatacaac tgatgtccct
4381 actgggggag gccgcactcc acggcccaac attctacagc aaaatcagca agttagtcat
4441 tgcagagcta aaagaaggtg gcatggattt ttacgtgccc agacaagagc caatgttcag
4501 atggatgaga ttctcagatc tgagcacgtg ggagggcgat cgcaatctgg ctcccagttt
4561 tgtgaatgaa gatggcgtcg agtgacgcca acccatctga tgggtccaca gccaacctcg
4621 tcccagaggc caacaatgag gttatggctt tggagcccgt tgttggtgcc gccattgcgg
4681 cgcctgtagc gggccaacaa aatgtaattg acccctggat tagaaacaat tttgtgcaag
4741 cccctggtgg agaatttaca gtatccccta gaaacgctcc aggtgaagta ctatggagcg
4801 cgcccttagg ccctgatttg aatccctacc tttctcattt ggccagaatg tacaatggtt
4861 atgcaggtgg ttttgaagtg caggtaatcc tcgcggggaa cgcgttcgcc gccggaaaaa
4921 tcatattcgc agcagtccca ccaaatttcc caactgaagg cttgagcccc agccaggtca
4981 ctatgttccc ccacttaata atagatgtta ggcaactgga acctgtgatg atccccttac
5041 ccgatgttag gaataatttc tatcattaca atcaatcaaa tgatcccacc atcaaattga
5101 tagcaatgtt gtatacacct cttagggcta ataatgttgg tgacgatgtc ttcacagttt
5161 cttgtcgggt actcacgaga ccatcccccg attttgattt catatttcta gtgccaccca
5221 cagttgaatc aaaaaccaac ccattctctg ttccaatttt aactattgag gagatgacca
5281 attcaagatt ccccattcct ttggaaaagc tgttcacggg ccccagcagt gcccttgttg
5341 ttcaaccaca aaacggcagg tgcacgactg atggcgtgct cctaggtacc acccaactgt
5401 ctcctgtcaa catctgcacc ttcagagggg atgtcaccca tattacaaaa actcatagct
5461 accaaatgaa tttggctgct caaaattgga acagttatga cccaacagaa gaaatcccag
5521 cccccctagg aactccagat ttcgtgggaa agatccaagg tgtgctcacc caaaccacga
5581 agggaaatgg ctcaacccgt gcccacaaag ctacagtgta cactgggagc accgaattca
5641 ctccaaaact gggtagaatc caacttgtca ctgacacaga caacgatctt gaaactaacc
5701 aaaacacaaa gttcacccca gtcggtgtca tccaggatgg tgatacccac caaaatgaac
5761 cccaacaatg ggtactccca agttacttag gtagaaataa tcacaatgtg cacctggccc
5821 ccgctgtagc ccccactttt ccgggcgagc aacttctctt cttcagatcc actatgcccg
5881 gatgcagcgg gtaccccaac atgaatttgg actgtctgct tccccaggaa tgggtgcaat
5941 atttctatca agaggcagcc ccagcacaat ctgatgtggc tttgctaaga tttgtgaatc
6001 cagatacagg tagggttttg tttgagtgca agcttcataa atcaggttat gtcacagtgg
6061 ctcacaccgg ccaccatgat ttgtttatcc cccccaatgg ttatttcaga tttgattcct
6121 gggtcagccc cttctacaca cttgccccca tgggaaatgg aacggggcgt agacgtgcat
6181 tataatggct ggagctttct ttgctggatt ggcatctgac gtccttggat ccggacttgg
6241 ttctctgatc aatgccgggg ctggggccat caaccaaaaa gttgaatttg aaaacaacag
6301 aaaattgcaa caagattcct tccaatttag tagcaatctg caacaggctt cctttcaaca
6361 tgataaagag atgctccaag cacaaattga ggccaccaaa aagttgcaac aggaaatgat
6421 gagagttaaa caggcaatgc tcctagaggg tgggttctct gagacagatg cagcccgtgg
6481 ggcaatcaac gcccccatga caaaggtttt ggactggagt gggacaaggt actgggctcc
6541 cggtgctagg actacaacat acaatgcagg ctacttttcc actccccaac actcgggggc
6601 actgccagga agagctaatc ttagggctgc tgtccccgct cggggctcct ctagagtatc
6661 ttctaattct tctactgcta cctctgtgta ttcaaatcaa actgcttcaa cgagacttgg
6721 ttctacagct ggttctggta ccagtgtctc gagcctcccg tcaactgcaa ggactaggag
6781 ttgggttgag gatcaaaata ggaatttgtc acctttcatg aggggggccc acaacatatc
6841 gtttgtcacc ccaccatcta gcagatcctc tagccaaggc acagtctcaa ccgtgcccaa
6901 agaagttttg aactcccaga ctggcgcttt caatacgcgc aggcagcctc tctttgctca
6961 cattcgtagg cgaggggagt cacgggcgta a
//