Typing tool
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Typing tool
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Complete norovirus genomes
| KM198521 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 70..5088
ORF2: 5069..6691
ORF3: 6691..7431
LOCUS KM198521 7431 bp RNA linear VRL 13-NOV-2014
DEFINITION Norovirus Hu/GII/10176/2009/VNM nonstructural polyprotein and
capsid protein VP1 genes, complete cds; and capsid protein VP2
gene, partial cds.
ACCESSION KM198521
VERSION KM198521.1
KEYWORDS .
SOURCE Norovirus Hu/GII/10176/2009/VNM
ORGANISM Norovirus Hu/GII/10176/2009/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7431)
AUTHORS Cotten,M., Petrova,V., Phan,M.V., Rabaa,M.A., Watson,S.J.,
Ong,S.H., Kellam,P. and Baker,S.
TITLE Deep sequencing of norovirus genomes defines evolutionary patterns
in an urban tropical setting
JOURNAL J. Virol. 88 (19), 11056-11069 (2014)
PUBMED 25056894
REFERENCE 2 (bases 1 to 7431)
AUTHORS Cotten,M.L., Petrova,V., Phan,M.V.T., Rabaa,M.A., Watson,S.J.,
Kellam,P. and Baker,S.
TITLE Direct Submission
JOURNAL Submitted (13-JUL-2014) Virus Genomics, The Wellcome Trust Sanger
Institute, Hinxton CB10 1SA, United Kingdom
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. 2.4.0
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7431
/organism="Norovirus Hu/GII/10176/2009/VNM"
/mol_type="genomic RNA"
/isolate="Hu/GII/10176/2009/VNM"
/host="Homo sapiens"
/db_xref="taxon:1526956"
/country="Viet Nam"
/collection_date="14-Sep-2009"
/note="genotype: GII"
CDS 70..5088
/note="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AII02691.1"
/translation="MFSNMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKIPPP
PPNGEDEVVVSYSAKDGVSGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI
LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT
LKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT
MDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL
AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM
LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN
HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR
AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA
YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL
ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL
APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK
VLAFRQLAAENKYGLIDTMKVGRQLKDVKTMPDLKQALKNISIKKCQIVYSGCTYTLE
SDGKGNVKVDRIQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV
TTRIIKRVNIQDLWSKPQVENTEEATNKDGCPKPKDDEEFVISSDDIKTEGKKGKNKT
GRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYSIEEYLQDRDKYYEEVAIARATEED
FCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSV
DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV
HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGTHATM
KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN
TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE
PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP
PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMT
PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR
VGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQV
VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII
QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF
LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA
LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE
DGVE"
CDS 5069..6691
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AII02692.1"
/translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICAFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6691..>7431
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AII02693.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRINPRTPTPARGSSSTSS
NASTATSIHSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWAG"
ORIGIN
1 tttaacgacg cttccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca
61 agtgacaaaa tgttctctaa catggctgtc acttttaaac gagccctcgg ggcgcggcct
121 aaacagcccc ccccgaggga aataccacaa agacccccac gaccacctac cccagaactg
181 gtcaaaaaga tccctcctcc cccgcccaac ggagaggacg aagtagtggt ttcttatagt
241 gccaaagatg gcgtttccgg tttacctgag ctttccaccg tcaggcaacc ggaagaaacc
301 aatacggcct tcagtgtccc tccacttaac cagagggaga atagagatgc taaggaacca
361 ctgactggaa caattctgga aatgtgggat ggagaaatct accattatgg cctgtatgtt
421 gagcgaggtc ttgtgctggg tgtgcacaaa ccaccagctg ccataagcct cgccaaggtc
481 gaactaacac cactctcctt gttctggaga cctgtgtaca ctccccagta cctcatctct
541 ccagacactc tcaagaaatt acacggagaa acgtttccct acacagcctt tgacaacaat
601 tgctatgcct tttgttgttg ggtcttggat ctaaatgact cgtggctgag taggagaatg
661 atccagagaa caactggctt cttcagaccc taccaagact ggaataggaa acccctcccc
721 actatggatg attccaaatt aaagaaggta gctaacatat tcctgtgcgc cctgtcttcg
781 ctattcacca ggcccataaa agacataata ggaaagctaa gacctctcaa catcatcaat
841 atcctggctt catgtgattg gactttcgca ggcatagtgg agtccttgat actcttggca
901 gagctctttg gagtcttctg gacaccccca gatgtgtctg cgatgattgc ccccttactc
961 ggtgatttcg agttacaagg acctgaggac cttgtagtgg agctcgtccc tgtagtaatg
1021 gggggaattg gtttggtgct gggattcacc aaagagaaga ttgggaaaat gttgtcatca
1081 gctgcatcca ccttgagagc ttgtaaagat cttggtgcat atgggctaga gatcctaaag
1141 ttagtcatga agtggttctt cccgaagaaa gaggaggcaa atgaactggc tatggtgaga
1201 tccatcgagg atgcagtact ggaccttgag gcaattgaaa acaaccatat gaccaccttg
1261 ctcaaagaca aagacagcct ggcaacctac atgagaaccc ttgacctcga ggaagagaaa
1321 gccagaaaac tctcaaccaa gtctgcttca cctgacatcg tgggtacaat caacgccctt
1381 ctggcgagaa tcgccgctgc acgctccctg gtgcaccgag cgaaggagga gctttccagc
1441 agaccaagac ctgtagtctt gatgatatca ggcagaccgg ggataggaaa aactcacctt
1501 gctagggaag tggctaagag aatcgcagcc tccctcacag gagaccagcg tgtaggcctc
1561 atcccacgca atggcgtcga tcactgggat gcgtacaagg gggagagggt cgtcctatgg
1621 gacgactatg gaatgagcaa ccccattcac gacgccctta ggctgcaaga actcgctgac
1681 acttgccccc ttactctaaa ttgtgacagg attgagaata aaggaaaggt ctttgacagc
1741 gatgtcatca ttatcaccac taatctggcc aacccagcac cactggacta tgtcaacttt
1801 gaagcgtgct cgaggcgcat cgatttcctc gtgtatgcag aagcccccga ggtcgaaaag
1861 gcgaagcgtg acttcccggg ccaacctgac atgtggaaaa acgcttttag ttctgatttc
1921 tcacacataa aattggcact ggctccacaa ggtggctttg ataagaacgg gaacacccca
1981 cacgggaagg gcgtcatgaa gactctcacc actggctccc tcattgcccg ggcatcaggg
2041 ctgctccatg agagattgga tgagtttgaa ctacagggcc cagctcttac caccttcaac
2101 tttgaccgca acaaagtgct tgccttcaga cagcttgctg ctgaaaacaa atatgggttg
2161 atagacacaa tgaaagttgg gaggcagctc aaggatgtca aaaccatgcc agatcttaaa
2221 caagcactca aaaacatctc aatcaagaag tgccagattg tgtatagtgg ttgcacctac
2281 acacttgagt ctgatggcaa gggcaatgtg aaagttgaca gaatccagag cacctccgta
2341 cagaccaaca atgagctggc tggcgccctg catcatctga ggtgcgccag aatcaggtac
2401 tatgtcaagt gtgtccagga ggccctgtat tctatcatcc agattgctgg ggctgcattt
2461 gtcaccacgc gcatcatcaa gcgtgtgaac attcaagact tatggtccaa gccacaagtg
2521 gaaaacacag aggaggccac caacaaggac gggtgcccaa aacccaaaga tgatgaggag
2581 ttcgtcattt catctgacga cattaaaact gagggtaaga aagggaagaa caagactggc
2641 cgtggcaaga agcatacagc cttttcaagt aaaggtctca gtgatgaaga gtatgatgag
2701 tacaagagaa ttagagagga aaggaatggc aggtattcca tagaagagta cctccaggac
2761 agggacaaat actatgagga ggtggccatt gccagggcga ccgaggaaga cttctgtgaa
2821 gaggaggagg ccaagatccg gcaaaggatc tttagaccaa caaggaaaca acgcaaggaa
2881 gaaagagctt ctctcggttt agtcacaggt tctgagatta ggaaaagaaa cccagatgac
2941 ttcaagccta agggaaaact gtgggctgac gatgacagaa gtgtggacta caatgagaaa
3001 ctcagttttg aggccccacc aagcatctgg tcaaggatag tcaactttgg ttcaggttgg
3061 ggcttctggg tctcccctag cctgttcata acatcaaccc acgtcatacc ccagggcgca
3121 aaggagttct ttggagtccc catcaaacaa attcaggtac acaagtcagg cgaattttgt
3181 cgcttgaggt tcccaaaacc aatcaggact gacgtgactg gcatgatctt ggaagaaggt
3241 gcgcccgaag gcaccgtggt cacactactc atcaaaaggt ctactggaga actcatgccc
3301 ctagcagcta gaatggggac ccatgcaacc atgaaaattc aagggcgcac cgttggaggt
3361 cagatgggca tgcttctgac aggatccaac gccaaaagca tggatctagg caccacacca
3421 ggtgattgcg gctgtcccta catctacaag agaggaaatg actatgtggt cattggagtc
3481 catacggctg ccgctcgtgg gggaaacact gtcatatgtg ccacccaggg gggcgagggg
3541 gaagctacac ttgaaggtgg tgacagtaag ggaacatact gtggtgcacc aatcctaggc
3601 ccagggagtg ccccaaagct tagcaccaaa accaaattct ggagatcatc cacagcacca
3661 ctcccacctg gcacctatga accagcatac cttggtggca aggaccccag agtcaagggt
3721 ggcccttcgt tgcagcaagt catgagggac cagctgaaac catttacaga gcccaggggt
3781 aagccaccaa agccaagtgt gttagaagct gccaagaaaa ccatcatcaa tgtccttgaa
3841 caaacaattg acccacctga gaagtggtcg ttcgcacaag cttgcgcctc ccttgacaag
3901 accacttcta gcggccatcc gcaccatatg cggaaaaacg actgctggaa cggggagtcc
3961 ttcacaggca agctggcaga ccaggcttcc aaggctaacc tgatgtttga agaagggaag
4021 aacatgaccc cagtctacac aggtgcactt aaggatgaat tagtcaaaac tgacaaaatt
4081 tatggtaaga tcaagaagag gcttctctgg ggctcggatt tagcaaccat gatccggtgt
4141 gctcgagcat tcggaggcct aatggatgaa ctcaaagcac actgtgtcac acttcctatt
4201 agagttggta tgaatatgaa tgaggatggc cccatcatct tcgagaagca ttccaggtac
4261 agataccact atgatgctga ttactctcgg tgggattcaa cacaacagag agccgtgctg
4321 gcagctgctc tagaaatcat ggttaaattc tcctcagaac cacatttggc tcaggtagtc
4381 gcagaagatc ttctttcccc tagcgtggtg gatgtgggtg acttcacaat atcaatcaac
4441 gagggccttc cctctggggt gccctgcacc tcccaatgga actccatcgc ccactggctt
4501 ctcactcttt gtgcactctc cgaagtcaca aatttgtccc cagacatcat acaggctaat
4561 tctctcttct ccttctatgg tgatgatgaa attgttagta cagacataaa attggaccca
4621 gagaagttga cagcaaagct taaggaatat gggttgaaac caacccgccc tgacaaaact
4681 gaaggacctc tcgttatttc tgaagactta gatggtttga ctttcctgcg gagaactgtg
4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gctcaatact caggcaaatg
4801 tactggacta ggggccccaa ccatgaagat ccatctgaat caatgattcc acactctcaa
4861 agacccatac aattgatgtc cttactggga gaggccgcac tccacggccc aacattctac
4921 agtaaaatca gcaaattagt cattgcagag ctaaaagaag gtggtatgga tttttacgtg
4981 cccaggcaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgaatgacg ccaacccatc
5101 tgatgggtcc gcagccaacc tcgtcccaga ggtcagcaat gaggttatgg ctttggagcc
5161 cgttgtcggt gccgctattg cggcgcctgt agcgggccaa caaaatgtaa ttgacccctg
5221 gattagaaac aattttgtac aagcccctgg tggagagttc acagtatccc ctagaaacgc
5281 tccaggtgaa atactatgga gcgcgccctt aggccctgat ctgaatccct acctatctca
5341 tttggccaga atgtataatg gttatgcagg tggttttgaa gtgcaggtga tcctcgcggg
5401 gaacgcgttc accgccggaa aaattatatt tgcagcagtc ccaccaaatt ttccaactga
5461 aggcctgagt cccagccagg tcactatgtt cccccacata atagtagatg ttaggcaatt
5521 ggaacctgtg ttgatcccct tacctgatgt taggaataat ttctatcatt ataatcagac
5581 aaatgattct accattaaat tgatagcaat gctgtataca ccacttaggg ccaataacgc
5641 tggggaagat gtcttcacag tctcttgtcg agtcctcact aggccgtccc ctgattttga
5701 ttttatattt ttggtgccac ccacagttga gtcaagaact aaaccattta ctgtcccaat
5761 cttaaccgtt gaagaaatga ccaattcaag attccccatt cctttggaaa agttgttcac
5821 gggtcccagc ggtgcttttg ttgtccaacc acaaaatggc aggtgcacga ctgatggcgt
5881 gctcttaggc accacccaac tgtctcccgt caacatctgc gccttcagag gggatgtcac
5941 ccacattgca ggttctcgta attacacaat gaatttggca tctctaaatt ggaacaatta
6001 tgacccaaca gaagaaattc cagcccctct gggaactcca gatttcgtgg gaaagatcca
6061 aggtgtgctc actcaaacca caaaaggaga tggctcgacc cgtggccata aagctacagt
6121 ttacactggg agtgccccct ttactccaaa gctgggcagt gttcaattca gtactgacac
6181 agaaaatgat tttgaaactc accaaaacac aaaattcacc ccagtcggtg tcatccagga
6241 tggtggcacc acccaccgaa atgaacccca acaatgggtg ctcccaagtt attcaggtag
6301 agatgttcat aatgtacacc tagcccctgc tgtagccccc acttttccgg gtgaacaact
6361 tcttttcttc aggtccacta tgcccggatg cagcgggtat cccaacatgg atttggattg
6421 cctactcccc caggagtggg tgcagcactt ctaccaagag gcagctccag cacaatctga
6481 tgtggctcta ttgagatttg tgaatccaga cacgggtagg gtcctgtttg agtgcaaact
6541 tcataaatca ggctatgtca cagtggctca caccggtcag catgatttgg tcatcccccc
6601 caatggctat tttaggtttg attcctgggt taatcagttc tacacgcttg cccccatggg
6661 aaacggaacg gggcgtaggc gcgccttata atggctggag ctttctttgc tggattggca
6721 tctgatgtcc ttggctctgg acttggttcc ctaatcaatg ctggggctgg ggccatcaac
6781 caaaagattg attttgaaaa taatagaaaa ttgcagcaag cttccttcca gtttagcagt
6841 aatctacaac aggcttcctt tcaacacgat aaagagatgc tccaagcaca aattgaggcc
6901 actaagaagt tgcaacagga aatgatgaaa gtcaagcagg caatgctcct agaaggtgga
6961 ttctctgaaa cagatgcagc ccgtggggca atcaacgccc ccatgacaaa ggttttggac
7021 tggagcggaa caaggtactg ggcccctgat gctaggacca caacatacaa tgcaggccgc
7081 ttttccaccc ctcaaccttc ggggacgctg ccaggaagaa tcaatcccag gactcctacc
7141 cccgctcggg gctcctccag cacatcttct aatgcttcca ctgctacttc tatacattca
7201 aatcaaactg tttcaacgag acttggttct acagctggtt ctggtaccaa tgtctcgagt
7261 ctcccgtcaa ctgcaaggac taggagttgg gttgaggatc aaaacagaaa tttgtcacct
7321 ttcatgaggg gggctcataa catatcgttt gtcaccccac catctagcag atcctctagc
7381 caaggcacag tctcaaccgt gcctaaagaa gttttggact cctgggctgg c
//