Typing tool
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Typing tool
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Complete norovirus genomes
| KP784691 | GII.4 Farmington Hills | |
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| GII.P4 New Orleans |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS KP784691 7570 bp RNA linear VRL 22-NOV-2016
DEFINITION Norovirus GII/Hu/ZAF/2009/GII.P4_GII.4/Johannesburg/4175, complete
genome.
ACCESSION KP784691
VERSION KP784691.1
KEYWORDS .
SOURCE Norovirus GII/Hu/ZAF/2009/GII.P4_GII.4/Johannesburg/4175
ORGANISM Norovirus GII/Hu/ZAF/2009/GII.P4_GII.4/Johannesburg/4175
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7570)
AUTHORS Botha,J.C., Mans,J. and Taylor,M.B.
TITLE Comparative analysis of South African norovirus GII.4 strains
identifies minor recombinant variants
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7570)
AUTHORS Botha,J.C., Mans,J. and Taylor,M.B.
TITLE Direct Submission
JOURNAL Submitted (13-FEB-2015) Medical Virology, University of Pretoria,
Pretoria, Gauteng, South Africa
COMMENT ##Assembly-Data-START##
Assembly Method :: Sequencher v. 4.10.1
Sequencing Technology :: Sanger dideoxy sequencing
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7570
/organism="Norovirus
GII/Hu/ZAF/2009/GII.P4_GII.4/Johannesburg/4175"
/mol_type="genomic RNA"
/isolate="GII/Hu/ZAF/2009/GII.P4_GII.4/Johannesburg/4175"
/host="Homo sapiens"
/db_xref="taxon:1777882"
/country="South Africa"
/collection_date="2009"
/note="genotype:
GII.P4_New_Orleans_2009/GII.4_Hunter_2004"
5'UTR 1..4
gene 5..5104
/gene="POL"
CDS 5..5104
/gene="POL"
/codon_start=1
/product="polyprotein"
/protein_id="ALX87341.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVRDGVSGLPDLSTVRQPE
ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LARVELTPLSLYWRPVYTPQYLISPDSLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNKKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLIMKWFFP
KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM
PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSASVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTARIVKRMNIQDLWSKPQVENTEETTSKDGC
PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKSMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLR
EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 5..994
/gene="POL"
/product="protein p48"
mat_peptide 995..2092
/gene="POL"
/product="NTPase"
mat_peptide 2093..2629
/gene="POL"
/product="protein p22"
mat_peptide 2630..3028
/gene="POL"
/product="VPg"
mat_peptide 3029..3571
/gene="POL"
/product="3C-like protease"
mat_peptide 3572..5101
/gene="POL"
/product="RNA dependent RNA polymerase"
gene 5084..6707
/gene="VP1"
CDS 5085..6707
/gene="VP1"
/note="major capsid protein"
/codon_start=1
/product="capsid protein VP1"
/protein_id="ALX87342.1"
/translation="MKMASNDATPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRGDGSTRGHKATVSTGDAHFTPKLGSVMFSTDTNNDFETGQNTRFTPVGVVQDG
STTHQNEPQQWVLPSYLGRDSHNVHLAPAVAPSFPGEQLLFFRSTMPGCSGYPNMNMD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6705..7513
/gene="VP2"
CDS 6707..7513
/gene="VP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="ALX87343.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRTNPRATVPARGSSSIPS
NTSTATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
3'UTR 7513..7570
ORIGIN
1 gtgaatgaag atggcctcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
121 cctcggggcg cggcctaaac agcctccccc gagggaaaaa ccacaaagac ccccacgacc
181 acctactcca gaactggtta aaaatattcc ccctcccccg cccaacggag aggatgaaat
241 agtggtttct tatagtgtca gagatggtgt ttccggtttg cctgatcttt ccaccgtcag
301 acaaccggaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag
361 agatgcaaag gagccactta ctggaacaat tctggaaatg tgggatgggg aaatctacca
421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccac cagccgccat
481 cagcctcgct agggttgagc taacaccact ctccttgtac tggagacctg tgtacacccc
541 tcagtacctc atctctccag actctctcaa gaaattacac ggagaaacgt tcccctacac
601 agcctttgac aacaactgtt atgccttttg ttgctgggtc ctggatctaa atgactcgtg
661 gctgagcagg aggatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa
721 taagaaaccc cttcccacta tggatgactc caaattaaag aaggtagcta atatattctt
781 gtgtgctctg tcctcgctgt tcaccagacc cataaaagat ataataggga agataaggcc
841 tcttaacatc ctcaacatct tagcctcatg tgattggact tttgcaggca tagtggagtc
901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
961 gattgccccc ttactcggtg actacgagct acaaggacct gaggaccttg cagtggagct
1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
1081 aaaaatgttg tcatctgctg cgtccacctt gagagcttgt aaagatcttg gtgcatatgg
1141 gctagagatc ctaaagttga tcatgaagtg gttcttcccg aagaaggagg aagcaaatga
1201 gctggctata gtgaggtcta ttgaggatgc agtcctggat ctcgaggcaa ttgaaaacaa
1261 ccatatgacc accttgctca aagacaaaga cagtctggca acctacatga gaacacttga
1321 ccttgaggag gagaaagcca ggaaactttc aaccaagtct gcctcacctg acatcgtggg
1381 cacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc accgagcgaa
1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca gaccaggaat
1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga
1561 ccagcgtgtg ggcctcatcc cacgcaatgg cgtcgaccat tgggatgcgt acaaggggga
1621 gagggtcgtc ctatgggacg attatggaat gagtaaccct attcacgatg ccctcaggct
1681 gcaagaactc gctgacactt gccccctcac tctaaactgt gacaggatag agaataaagg
1741 aaaggtcttt gacagcgatg tcatcatcat caccactaat ctggccaacc cagcaccact
1801 ggactatgtc aactttgaag catgttcgag gcgcatcgac ttcctcgtgt atgcagaagc
1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
1921 cttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa
1981 gaacgggaac accccacacg gaaagggcgt catgaagact ctcaccactg gctcccttat
2041 cgcccgggca tcagggctac tccatgagag gttagatgaa tttgaactac agggcccagc
2101 tctcaccacc ttcaatttcg atcgcaataa agtgcttgcc tttagacaac ttgctgctga
2161 aaataaatat ggattgatgg acacaatgag agttgggaaa cagctcaagg atgttagaac
2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgcc aaatagtgta
2281 tagtggttgc acctacatac ttgagtctga cggcaagggc aatgtgaaag ttgacagaat
2341 ccaaagcgcc tccgtgcaaa ccaacaatga gctggctggc gccctgcacc atttgaggtg
2401 cgccagaatc agatactatg tcaagtgtgt ccaggaggcc ctgtattcca tcattcaaat
2461 tgctggggct gcatttgtca ccgcgcgcat cgtcaagcgc atgaacatac aggacctatg
2521 gtccaagcca caagtggaaa acacagagga gaccaccagc aaggacgggt gcccaaaacc
2581 caaggatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg
2641 gaagaacaag actggccgtg gcaagaagca cacagccttt tcaagcaaag gcctcagtga
2701 tgaagagtac gatgagtaca agaggattag agaagaaagg aatggcaagt actccataga
2761 agagtacctt caggacaggg acaaatacta tgaggaggtg gccattgcca gggcgactga
2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacaag
2881 gaaacaacgc aaggaggaaa gagcttctct cggtctggtc acaggctctg aaattaggaa
2941 aagaaaccca gatgacttca aacccaaggg taaattgtgg gctgacgatg acagaagtgt
3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atctggtcga gaatagtcaa
3061 ctttggttca ggctggggat tctgggtctc ccccagtctg ttcataacat caacccatgt
3121 cataccccag ggtgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
3181 gtcaggcgag ttctgtcgct tgagattccc aaaaccaatc aggactgatg tgacgggcat
3241 gatcttagaa gaaggcgcac ctgagggcac cgtggtcaca ctactcatca aaaggtccac
3301 cggggaactc atgcccctag cagctaggat ggggacccat gcaaccatga agatccaagg
3361 gcgcactgtc ggaggccaga tgggcatgct tctgacagga tccaatgcca agagcatgga
3421 cctgggtact acaccaggtg attgtggctg tccctatatc tacaagagag gcaatgacta
3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac
3541 ccaggggagt gaaggggagg ccacacttga aggtggtgac aacaagggga catactgcgg
3601 tgcaccaatc ctaggaccag ggagtgcccc aacccttagc accaagacca aattctggag
3661 atcgtccaca gcaccgctcc cacctggcac ctatgaacca gcctatcttg gtggcaagga
3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaaaccatt
3781 cacagagcca aggggcaaac caccaaagcc aagtgtatta gaggctgcca agaagaccat
3841 catcaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcattcg cacaagcttg
3901 cgcgtccctt gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg
3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacctgat
4021 gtttgaagaa gggaagagca tgaccccagt ctacacagct gcgctcaagg atgagttagt
4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggtt cggacttggc
4141 gaccatgatc cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcacactg
4201 tgtcacactt cccattagag ttggtatgaa tatgaatgag gatggcccca tcatcttcga
4261 gaggcattcc aggtacacat atcactatga tgctgattac tctcgatggg attcaacaca
4321 acagagagcc gtgctggcag cagctctaga aatcatggtt aaattctccc cagaaccaca
4381 tttggctcag gtagtcgcgg aagaccttct ttctcctagc gtggtggacg tgggcgactt
4441 cacaatatca atcaacgagg gccttccctc tggggtgccc tgcacctccc aatggaattc
4501 catcgcccac tggcttctca ctctctgcgc gctctctgaa gtcacaaact tgtcccctga
4561 taccatacag gctaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
4621 cataaaattg gacccagaga aattaactac aaagctcagg gaatatgggt taaaaccaac
4681 ccgccctgac aaaactgaag gaccccttgt catttctgaa gacttgaatg gcctaacttt
4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagctc
4801 aatactcagg caaatgtact ggactagggg ccccaaccat ggagacccat ctgaaacaat
4861 gattccacac tcccaaagac ccatacaatt gatgtccctg ctgggggagg ctgctctcca
4921 cggcccagca ttttacagca aaatcagcaa attggtcatt gcagagctaa aagaaggtgg
4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 atgacgccac cccatctgat gggtccacag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggcttt ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtggt gagtttacag
5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatttga
5341 acccctacct ttcccattta gccaggatgt acaatggcta cgcaggtggt tttgaagtgc
5401 aggtaatcct cgcggggaat gcgttcaccg ccggaaaaat tatatttgca gcagtcccac
5461 caaacttccc aactgaaggc ttgagcccca gccaggtcac tatgtttccc catataatag
5521 tagatgttag gcaattggaa cctgtgctga tccccttacc tgatgttagg aacaatttct
5581 atcattacaa tcaatcaaat gaccccacca tcaaattgat agcaatgctg tacacaccac
5641 ttagggcaaa caatgctgga gatgatgtct ttacagtctc ttgtcgagtc ctcacgagac
5701 catcccccga ttttgatttc atatttctgg tgccacccac agttgagtca agaactaaac
5761 cattctctgt cccaatttta actgttgaag agatgaccaa ttcaagattc cccatccctt
5821 tggaaaagtt gtttacgggt cccagcagtg cctttgttgt tcaaccacaa aatggcagat
5881 gcacgactga tggcgtgctc ttaggtacta cccaactgtc tcctgtcaac atctgcacct
5941 tcagagggga tgtcacccac attgcaggta cccacaatta cacaatgaat ctggcctccc
6001 aaaattggaa caattatgac ccaacagaag aaatcccagc tcctctggga actccagatt
6061 tcgtgggaaa gatccaaggc gtactcaccc aaaccacaag gggggatggc tcgacccgcg
6121 gtcacaaggc tacagtgagc actggggacg cccacttcac cccaaagctg ggcagtgtta
6181 tgttctccac tgatacaaac aatgactttg aaactggcca aaacacgaga ttcaccccag
6241 tcggtgtcgt ccaggacggt agcaccaccc accaaaatga accccaacaa tgggttctcc
6301 caagctactt aggtagagac agtcacaatg tgcatttagc ccctgccgtg gccccctctt
6361 tcccgggtga gcaacttctt ttcttcaggt ccactatgcc cggatgcagc gggtatccca
6421 acatgaacat ggattgccta ctcccccaag agtgggtgca gcacttctat caagaggcag
6481 ccccagcgca atctgatgtg gctctactga gatttgtgaa tccagacaca ggtagggttc
6541 tgtttgagtg caagcttcat aaatcaggtt atgtcacagt ggcccacact ggccaacatg
6601 atttagttat tccccccaat ggttatttta gatttgattc ttgggtcaac caattctaca
6661 ctcttgcccc catgggaaat ggaacggggc gcagacgagc attataatgg ctggagcttt
6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctaa tcaatgctgg
6781 ggctggggcc atcaaccaaa agattgactt tgaaaataat agaaaattgc aacaagcttc
6841 cttccaattt agcagcaacc tacaacaggc ttcttttcag catgataaag agatgctcca
6901 agcacaaatt gaggccacca aaaagttgca acaggagatg atgaaagtta aacaggcaat
6961 gctcctagag ggcgggttct ctgagacaga tgcagcccgt ggggcaatca acgcccccat
7021 gacaaaggct ttggactgga gcggaacaag gtactgggct cctgatgcta ggactacaac
7081 atacaatgca ggccgctttt ccacccccca accctcaggg gcactgccag gaagaactaa
7141 tcccagggct acagtccccg ctcgtggctc ctccagtata ccttctaaca cttctactgc
7201 tacttctgtg tactcaaatc aaactgcttc aacgagactt ggttctacag ctggttctgg
7261 aactagtgtc tcgagcctcc cgtcaactgc aagaactagg agctgggttg aggatcaaaa
7321 ccggaatttg tcacctttca tgaggggggc ccacaacata tcgttcgtca ccccaccatc
7381 tagcaggtcc tctagccaag gcacagtctc aaccgtgcct aaagaagttt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacatacgta agcgagggga
7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt cttttcttta gtgtctttga
7561 aaaaaaaaaa
//