Typing tool
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Typing tool
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Complete norovirus genomes
| JX846928 | GII.4 New Orleans | |
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| GII.P4 New Orleans |
ORF1: 1..5068
ORF2: 5049..6671
ORF3: 6671..7477
LOCUS JX846928 7497 bp ss-RNA linear VRL 24-OCT-2013
DEFINITION Norovirus Hu/GII.4/NIHIC9/2011/USA, partial genome.
ACCESSION JX846928
VERSION JX846928.1
DBLINK BioProject: PRJNA70471
KEYWORDS .
SOURCE Norovirus Hu/GII.4/NIHIC9/2011/USA
ORGANISM Norovirus Hu/GII.4/NIHIC9/2011/USA
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7497)
AUTHORS Madupu,R., Halpin,R., Ransier,A., Fedorova,N., Stockwell,T.,
Amedeo,P., Bishop,B., Edworthy,P., Gupta,N., 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 (31-JUL-2012) J. Craig Venter Institute, 9704 Medical
Center Drive, Rockville, MD 20850, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: clc_ref_assemble_long v. 3.22.55705
Coverage :: 105.2x
Sequencing Technology :: Sanger; Illumina; 454
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7497
/organism="Norovirus Hu/GII.4/NIHIC9/2011/USA"
/mol_type="genomic RNA"
/strain="Hu/GII.4/NIHIC9/2011/USA"
/host="Homo sapiens"
/db_xref="taxon:1260942"
/geo_loc_name="USA: Maryland"
/collection_date="14-Jun-2011"
/note="genotype: GII.4"
gene <1..5068
/gene="POL"
CDS <1..5068
/gene="POL"
/note="genome polyprotein"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="AFX71667.1"
/translation="AVANSNNDIAKSSSDGVLSSMAVTFKRALGARPKQPPPREKPQR
PPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNTAFSVPPL
NQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAVSLAKVELAPLSL
YWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTT
GFFRPYQDWNRKPLPTGDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNILNILA
SCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMG
GIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEKNELAIV
RSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTI
NALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGD
QRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIEN
KGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDM
WKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEF
ELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTMPELKQALKNVS
IKKCQIVYSGCTYTLESDGKGNVKVDKIQSATVQINNELAGALHHLRSARIRYYVKCV
QEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETVSKDGCPKPKDDEEFVI
SSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDR
DKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPD
DFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIP
QGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRPT
GELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGN
DYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPTLSTKT
KFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPKPSVLE
AAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLAD
QASKANLMFEEGKNMTPVYTAALKDELVKTDKIYSKIKKRLLWGSDLATMIRCARAFG
GLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRAVLAAA
LEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLL
TLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKVDPEKLTAKLREYGLKPTRPDK
TEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIP
HSQRPIQLMSLLGEAALHGPAFYRKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDL
STWEGDRNLAPSFVNEDGVE"
mat_peptide <1..958
/gene="POL"
/product="protein p48"
mat_peptide 959..2056
/gene="POL"
/product="NTPase"
/note="p41"
mat_peptide 2057..2593
/gene="POL"
/product="protein p22"
mat_peptide 2594..2992
/gene="POL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 2993..3535
/gene="POL"
/product="3C-like protease"
/note="3CLpro; calicivirin"
mat_peptide 3536..5065
/gene="POL"
/product="RNA-directed RNA polymerase"
gene 5049..6671
/gene="VP1"
CDS 5049..6671
/gene="VP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AFX71668.1"
/translation="MKMASSDASPSDGSTANLVPEVNNEVMALEPVAGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQLNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHISGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG
NTTPRNEPQQWVLPSYSGRNIQNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6671..7477
/gene="VP2"
CDS 6671..7477
/gene="VP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AFX71669.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGVINQKVDFENNRKLQQA
SFQFSSNQQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGASPGRANLRATVPARGSSSTSS
NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTMSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 cgctgttgct aacagcaaca acgacatcgc aaaatcttca agtgacggag tgctttctag
61 catggctgtc acttttaaac gagccctcgg ggcgcggcct aaacagcctc ccccgaggga
121 aaaaccacaa agacccccac gaccacctac tccagaactg gtcaaaaata ttccccctcc
181 cccacccaac ggagaggatg aaatagtggt ctcttatagt gtcaaggatg gtgtttccgg
241 cttgcctgac ctttccaccg tcaggcaacc ggaagaatcc aacacggcct tcagtgtccc
301 tccactcaac cagagggaga atagagatgc taaggagcca cttactggaa caattctgga
361 aatgtgggac ggggaaatct accattatgg cctgtatgtg gagcgaggtc ttgtactagg
421 tgtgcacaaa ccaccagctg ccgtcagcct cgctaaggtt gagctagcac cactctcctt
481 gtactggaga cctgtgtaca ctcctcagta ccttatctct ccagacactc tcaagaaatt
541 atccggagaa acgttcccct acacagcctt tgacaacaac tgttatgcct tttgttgctg
601 ggtcctggac ctaaatgact cgtggctgag caggagaatg atccagagaa caactggttt
661 cttcaggccc taccaagact ggaataggaa accccttccc actggggatg attccaaaat
721 aaagaaggta gctaacatat tcctgtgtgc tctgtcctcg ctgttcacca gacccataaa
781 agatataata gggaagataa ggcctcttaa catcctcaac atcttagcct catgtgattg
841 gacttttgca ggcatagtgg agtccctgat actcttggca gaactctttg gagttttctg
901 gacaccccca gatgtgtctg cgatgattgc ccccttactc ggtgactacg agctacaagg
961 acctgaggac cttgcagtgg agctcgtccc cgtggtgatg gggggaattg gtttggtgct
1021 aggattcacc aaagagaaga ttgggaaaat gttgtcatct gctgcgtcca ccttgagagc
1081 ttgtaaagac cttggtgcat atgggctaga gatcctaaag ttggttatga agtggttctt
1141 cccgaagaag gaggagaaaa atgagctggc tatagtgagg tctatcgagg atgcagtcct
1201 agatctcgag gcaattgaaa acaaccatat gaccaccttg ctcaaagaca aagacagtct
1261 ggcaacctat atgagaacac ttgaccttga ggaggagaaa gccaggaaac tctcaaccaa
1321 gtctgcctca cccgacatcg taggcacaat caacgccctc ctggcgagaa tcgctgccgc
1381 acgttctctg gtgcatcgag cgaaggagga gctttccagc agaccaagac ctgtggtgct
1441 gatgatatca ggcaggccag gaatagggaa gacccacctc gctagggaag tggctaagag
1501 aatcgcagcc tcccttacag gagaccagcg tgtgggcctc atcccacgca atggcgtcga
1561 ccactgggat gcgtacaagg gggaaagggt cgtcctatgg gacgattatg gaatgagcaa
1621 ccctattcac gatgccctca ggctgcaaga actcgctgac acttgccccc tcactctaaa
1681 ctgtgacagg attgaaaata aaggaaaggt ctttgacagc gatgtcatca ttatcaccac
1741 caatctggcc aacccagcac cactggacta tgtcaacttt gaagcatgct cgagacgcat
1801 cgacttcctc gtgtatgcag aagcccctga agtcgaaaag gcgaaacgtg acttcccagg
1861 ccagcctgac atgtggaaga acgctttcag tcctgatttc tcacacataa aactagcact
1921 ggccccacag ggtggtttcg acaagaacgg gaacaccccg cacggaaagg gcgtcatgaa
1981 gactctcacc actggctccc ttattgcccg ggcatcaggg ctactccatg agaggttaga
2041 tgaatttgaa ctacagggcc cagctctcac caccttcaat ttcgatcgca ataaagtgct
2101 tgcctttaga cagcttgctg ctgaaaataa atatggactg atggacacaa tgagggttgg
2161 gaaacagctc aaggatgtca gaaccatgcc agaactcaaa caagcactca agaatgtctc
2221 aatcaagaag tgccaaatag tgtatagtgg ttgcacctac acacttgagt ctgatggcaa
2281 gggcaatgtg aaggttgaca aaatccaaag cgccaccgtg cagatcaaca atgagctggc
2341 tggtgcccta caccatttga ggagcgccag aatcagatac tatgtcaagt gtgtccagga
2401 ggccctgtat tccatcattc aaattgctgg ggctgcattt gtcaccacgc gcattgccaa
2461 gcgcatgaac atacaaaacc tatggtccaa gccacaagtg gaagacacag aggagactgt
2521 cagcaaggac gggtgcccaa aacctaagga tgatgaggag tttgtcattt catccgacga
2581 catcaaaact gagggtaaga aagggaagaa caagactggc cgcggcaaga agcacacagc
2641 attttcaagc aaaggcctca gtgatgaaga gtacgatgag tacaagagga ttagagaaga
2701 aaggaatggc aagtactcca tagaagagta ccttcaggac agggacaaat actatgagga
2761 ggtggccatt gccagggcga ctgaggaaga cttctgtgaa gaggaggagg ccaagatccg
2821 gcaaaggatc tttaggccaa caaggaaaca acgcaaggag gaaagagcct ctctcggtct
2881 ggtcacaggt tctgaaatta ggaaaagaaa cccagatgac ttcaaaccca aggggaaact
2941 gtgggctgac gatgacagga atgtggacta caatgagaaa ctcagttttg aggccccacc
3001 aagcatctgg tcgagaatag tcaactttgg ttcaggctgg ggattctggg tctcccccag
3061 tctgtttata acatcaaccc atgtcatacc ccagggcgca aaggagttct ttggagtccc
3121 catcaaacaa atacaggtac acaagtcagg cgagttctgt cgcttgagat tcccaaaacc
3181 aattaggact gatgtgacgg gcatgatctt agaagaaggc gcacctgagg gcaccgtggt
3241 cacactactc ataaaaaggc ccactgggga actcatgccc ctagcagcta ggatggggac
3301 ccatgcgacc atgaagatcc aagggcgcac tgttggaggc cagatgggca tgcttctgac
3361 aggatccaac gccaagagca tggacctggg tactacacca ggtgattgtg gctgccccta
3421 tatctacaag agaggtaatg actatgtggt cattggagtc cacacggctg ccgcgcgtgg
3481 ggggaacact gtcatatgtg ccacccaggg gagtgaggga gaggctacac ttgaaggtgg
3541 tgacaacaag gggacatact gtggtgcacc aatcctaggc ccagggagtg ccccaacact
3601 tagcaccaag accaaattct ggagatcgtc cacagcatca ctcccacctg gcacctatga
3661 accagcctac cttggtggca aggaccctag agtcaagggt ggcccttcac tgcagcaagt
3721 catgagggaa cagttgaagc cattcacaga gccaaggggc aagccaccaa aaccaagtgt
3781 gttagaagct gccaagaaga ccatcatcaa tgtccttgag caaacaattg atccacctga
3841 gaagtggtcg ttcgcacaag cttgcgcgtc ccttgacaag accacttcca gtggtcatcc
3901 gcaccacatg cggaaaaacg actgctggaa cggggagtcc ttcacaggca agttggcaga
3961 ccaggcttcc aaggccaacc tgatgtttga agaagggaag aacatgaccc cagtctacac
4021 ggctgcgctc aaggatgaat tagttaaaac tgacaaaatt tatagtaaga tcaagaagag
4081 gcttctctgg ggctcggact tggcgaccat gatccggtgt gcccgagcat tcggaggcct
4141 aatggatgaa ctcaaagcac actgtgtcac gcttcccatt agagttggca tgaatatgaa
4201 tgaggatggc cccatcatct tcgagaggca ttccaggtac acgtatcact atgatgctga
4261 ttactctcga tgggattcaa cacaacagag agctgtgttg gcagcagctc tcgaaatcat
4321 ggttaaattc tccccagaac cacatttggc tcaggtagtc gcggaagacc tcctttctcc
4381 tagcgtggtg gacgtgggcg acttcacaat atcaatcaac gagggtcttc cctctggggt
4441 gccctgcacc tcccagtgga actccatcgc ccactggctt ctcactctct gcgcgctctc
4501 cgaagtcaca aacctatccc ctgataccat acaggccaac tctctcttct ctttttatgg
4561 tgatgatgaa attgttagca cagacataaa agtggaccca gagaaattga cagcaaagct
4621 cagagaatat gggttaaaac caacccgccc tgacaaaact gaaggacccc ttgtcatctc
4681 tgaagacctg aatggcctaa ctttcctgcg gagaactgtg acccgtgacc cagctggttg
4741 gtttggaaaa ctggagcaga gttcaatact caggcaaatg tactggacta ggggtcccaa
4801 ccatgaagac ccatctgaaa caatgattcc acactcccaa agacccatac aattgatgtc
4861 cctactgggg gaggccgctc tccacggccc agccttttac agaaaaatca gcaagttggt
4921 cattgcagag ttaaaagaag gtggcatgga tttttacgtg cccagacaag agccaatgtt
4981 cagatggatg agattctcag atctgagcac gtgggagggc gatcgcaatc tggctcccag
5041 ttttgtgaat gaagatggcg tcgagtgacg ccagcccatc tgatgggtcc acagccaacc
5101 tcgtcccaga ggtcaacaat gaggttatgg ctttggagcc cgtagctggt gccgccattg
5161 cggcacctgt agcgggccaa caaaatgtaa ttgacccctg gattagaaac aattttgtac
5221 aagcccctgg tggagagttt acagtatccc ctagaaacgc tccaggtgaa atactatgga
5281 gcgcgccctt aggccctgat ctgaatccct acctttccca tttggccaga atgtacaatg
5341 gttatgcagg tggttttgaa gtgcaggtaa tcctcgcggg gaacgcgttc accgccggga
5401 aaatcatatt tgcagcagtc ccaccaaatt tcccaactga aggtttgagc cccagccagg
5461 tcactatgtt cccccatata atagtagatg ttaggcaatt ggaacctgtg ttgatcccct
5521 tacccgatgt taggaataac ttctaccatt acaatcaatt aaatgacccc accatcaaat
5581 tgatagcaat gttgtacaca ccacttaggg ctaataatgc tggggacgat gtcttcacag
5641 tttcttgtcg agttcttacg agaccatccc ccgattttga tttcatattt ttggtgccac
5701 ccacagttga atcaagaact aaaccattct ctgtcccagt tttaactgtt gaggaaatga
5761 ccaattcaag gttccccatt cctttggaaa agttgttcac gggccccagt agtgccttcg
5821 ttgttcaacc acaaaatggc aggtgcacga ctgatggcgt gctcctaggt actacccaac
5881 tgtcccctgt caacatctgc accttcagag gggatgtcac ccatatttca ggcagtcgta
5941 actacacaat gaatttggcc tcccaaaatt ggaatagtta cgatccaaca gaagaaatcc
6001 cagcccctct aggaactcca gatttcgtgg ggaagattca aggtgtgctc acccaaacca
6061 caaggacaaa tggctcgacc cgcggccaca aagctacagt ttacactggg agcgccgact
6121 tttctccaaa actgggtaga gttcaatttg ccactgacac agacaatgat tttgaaacta
6181 accaaaacac aaagttcacc ccagtcggtg ttatccaaga tggtaacacc accccccgaa
6241 atgaacccca acaatgggtg ctcccaagtt actcaggcag aaacattcaa aatgtgcacc
6301 tggcccccgc tgtagccccc actttcccgg gcgagcagct cctcttcttc agatctacta
6361 tgcccggatg cagcgggtac cccaacatgg acttggactg tctgctcccc caggaatggg
6421 tgcagtactt ctaccaggaa gcagccccag cacaatctga tgtggctctg ttaagatttg
6481 tgaatccaga cacaggtagg gttttgtttg agtgtaagct tcataaatca ggctatgtta
6541 cagtggctca cactggccaa catgatttgg ttatcccccc caatggttat tttagatttg
6601 attcctgggt caaccagttc tacacacttg cccccatggg aaatgggacg gggcgtagac
6661 gtgcattata atggctggag ctttctttgc tggattggca tctgacgtcc ttggctctgg
6721 acttggttcc ctaatcaatg ctggggctgg ggtcatcaac caaaaagttg attttgaaaa
6781 taacagaaaa ttgcaacaag cttccttcca gtttagcagc aatcaacaac aggcttcctt
6841 ccaacatgac aaagagatgc tccaagcaca aattgaggcc accaaaaagt tgcaacagga
6901 aatgatgaga gttaaacaag caatgctcct agagggtgga ttctctgaga cagatgcggc
6961 ccgtggggca atcaacgccc ccatgacaaa agctctggac tggagcggga caaggtactg
7021 ggctcccgat gctaggacta caacatacaa tgcaggccgc ttttccaccc ctcaaccctc
7081 gggggcatca ccaggaagag ctaatcttag ggctaccgtc cccgcccggg gttcctccag
7141 cacgtcttct aactcttcta ttgctacttc tgtgtattca aatcaaacca cctcaacgag
7201 acttggttct acagctggtt ctggtaccag tgtctcgagc ctcccgtcaa ctgcaaggac
7261 catgagctgg gttgaggatc aaaataggaa tttgtcacct ttcatgaggg gggcccacaa
7321 catctcgttt gtcaccccac catctagcag atcctctagc caaggcacag tctcaaccgt
7381 gcccaaagaa gttttggact cctggactgg cgctttcaac acgcgcaggc agcctctctt
7441 cgctcacatt cgcaagcgag gggagtcacg ggtgtaatgt gaaaagacaa aattgat
//