Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| KM198515 | GII.4 Den Haag | |
|
|---|---|---|---|
| GII.P4 Den Haag |
ORF1: 70..5088
ORF2: 5069..6691
ORF3: 6691..7431
LOCUS KM198515 7431 bp RNA linear VRL 13-NOV-2014
DEFINITION Norovirus Hu/GII/C2H-31/2011/VNM nonstructural polyprotein and
capsid protein VP1 genes, complete cds; and capsid protein VP2
gene, partial cds.
ACCESSION KM198515
VERSION KM198515.1
KEYWORDS .
SOURCE Norovirus Hu/GII/C2H-31/2011/VNM
ORGANISM Norovirus Hu/GII/C2H-31/2011/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/C2H-31/2011/VNM"
/mol_type="genomic RNA"
/isolate="Hu/GII/C2H-31/2011/VNM"
/host="Homo sapiens"
/db_xref="taxon:1527014"
/country="Viet Nam"
/collection_date="28-Sep-2011"
/note="genotype: GII"
CDS 70..5088
/note="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AII02673.1"
/translation="MFSSMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKVPPP
PPNGEDEVVVSYSAKDGISGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI
LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT
LKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT
TDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL
AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM
LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN
HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR
AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA
YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL
ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL
APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK
VLAFRQLAAENKYGLMDTMRVGRQLKDVKTMPELKQALKSISIKKCQIVYSGCTYTLE
SDGKGNVKVDRVQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV
TTRIIKRVNIQNLWSKPQVENTEEATNKDGCPKPKDDEEFVITSDDIKTEGKKGKNKT
GRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARATEED
FCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSV
DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV
HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIKRSTGELMPLAARMGTHATM
KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN
TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE
PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP
PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKSMT
PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR
VGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQV
VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII
QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF
LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA
LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE
DGVE"
CDS 5069..6691
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AII02674.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFIVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFEAHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6691..>7431
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AII02675.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGSLPGRINPRTPTPARASSSTSS
NASTVTSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTKSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTG"
ORIGIN
1 tcgaacgacg cttccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca
61 agtgacaaaa tgttttctag catggctgtc acttttaaac gagccctcgg ggcgcggcct
121 aaacagcctc ccccgaggga aataccgcaa aggcccccac gaccacctac tccagaactg
181 gtcaaaaagg tccctcctcc cccgcccaac ggagaggatg aagtggtggt ttcttacagt
241 gccaaagatg gcatttctgg tctacctgag ctttccaccg tcagacaacc agaagaaacc
301 aatacggcct tcagtgtccc tccactcaat cagagggaga atagggatgc taaggaacca
361 ctgactggga caattctgga aatgtgggat ggagaaatct atcattatgg cctgtatgtt
421 gaacgaggtc ttgtgctggg tgtgcacaaa ccaccagctg ccattagcct cgccaaggtc
481 gaactaacac cactctcctt gttctggaga cctgtgtaca ccccacagta cctcatctct
541 ccagacactc tcaagaaatt acacggagaa acatttccct acacagcctt tgacaacaac
601 tgctatgcct tttgttgctg ggtcctggat ctaaacgact cgtggctgag taggaggatg
661 atccagagaa caactggctt cttcagaccc taccaagatt ggaataggaa acccctccct
721 actacggatg attccaaatt aaagaaggta gctaacatat tcctgtgcac cctgtcttcg
781 ctattcacca ggcccataaa agacataata ggaaagttaa ggcctctcaa catcatcaac
841 atcctagctt catgtgactg gactttcgca ggcatcgtgg aatccttgat actcttggca
901 gagctctttg gagtcttctg gacaccccca gatgtgtctg cgatgattgc ccccttactc
961 ggtgatttcg agttacaagg acctgaggac cttgtagtgg agctcgtccc tgtggtaatg
1021 gggggaattg gtttggttct gggattcacc aaagagaaga ttggaaaaat gttgtcatct
1081 gctgcatcca ccctaagagc ttgtaaagat ctcggtgcat atgggctaga gatcctaaag
1141 ctagtcatga agtggttctt cccgaagaaa gaggaggcaa atgaactggc tatggtgaga
1201 tccatcgagg atgcagtact ggaccttgag gcaattgaaa acaaccatat gaccaccttg
1261 ctcaaagata aagacagcct ggcaacctac atgagaaccc ttgacctcga ggaagagaaa
1321 gccagaaaac tctcaaccaa gtctgcgtca cctgacatcg tgggcacaat caacgccctt
1381 ctggcgagaa tcgccgctgc acgctccctg gtgcaccgag cgaaggagga gctttccagc
1441 agaccaagac ctgtggtctt gatgatatca ggcagaccag ggatagggaa gacccacctt
1501 gctagggaag tggccaagag aatcgcagca tccctcacag gagaccagcg cgtaggcctc
1561 atcccacgca atggcgtcga tcactgggat gcgtacaagg gggagagggt cgtcctatgg
1621 gacgactatg gaatgagcaa tcccatccac gacgccctca ggctgcaaga actcgccgac
1681 acttgccccc tcactctaaa ttgtgacaga attgagaata aaggaaaggt ctttgacagt
1741 gatgtcatca ttatcactac taatctggcc aacccagcac cactggacta tgtcaacttt
1801 gaagcgtgct cgaggcgcat cgatttcctc gtgtacgcag aagcccccga ggtcgaaaag
1861 gcgaagcgtg acttcccggg ccaacctgac atgtggaaaa acgcctttag ttctgatttc
1921 tcacacataa aactggcact ggctccacaa ggtggcttcg ataagaacgg gaacacccca
1981 catgggaagg gcgtcatgaa gactctcacc actggctccc ttattgcccg ggcatcaggg
2041 ctgctccatg agagattgga tgagtttgaa ctacagggcc cagctctcac caccttcaac
2101 tttgaccgca acaaagtgct tgccttcagg cagcttgctg ctgaaaacaa atacgggttg
2161 atggacacaa tgagagttgg gaggcagctc aaggatgtca aaaccatgcc agaacttaaa
2221 caagcactca agagcatctc aatcaagaag tgtcagattg tgtacagtgg ttgcacctac
2281 acacttgagt ctgatggcaa gggcaatgtg aaggttgaca gagttcagag cacctccgtg
2341 cagaccaaca atgagctggc tggcgccctg caccatctga ggtgcgccag aatcaggtac
2401 tatgttaagt gtgtccagga ggccctgtat tctatcattc agattgctgg agctgcattc
2461 gtcaccacgc gcatcatcaa gcgtgtgaac attcaaaact tatggtccaa gccacaagtg
2521 gaaaacacag aggaagccac caacaaggat gggtgcccaa aacccaaaga tgatgaggag
2581 ttcgtcatca catctgacga cattaaaact gagggtaaga aaggaaagaa caagactggc
2641 cgtggtaaga agcacacagc cttctcaagt aaaggtctca gtgatgaaga gtatgatgag
2701 tacaagagaa ttagagagga aaggaatggc aagtactcca tagaagagta ccttcaggac
2761 agggacaaat actatgagga ggtggccatt gccagggcga ccgaggaaga cttctgtgaa
2821 gaggaggagg ccaagatccg gcaaaggatc ttcagaccaa caaggaaaca acgcaaggaa
2881 gaaagagctt ctctcggttt agtcacaggt tctgaaatta ggaaaagaaa cccagatgat
2941 ttcaagccca aggggaaact atgggctgac gatgacagaa gtgtggacta caatgagaaa
3001 ctcagttttg aggctccgcc aagtatctgg tcaaggatag tcaactttgg ctcaggttgg
3061 ggcttctggg tctcccccag cctgttcata acatcaaccc acgtcatacc ccagggcgca
3121 aaggagttct ttggagtccc catcaaacaa attcaggtgc acaagtcagg cgaattctgt
3181 cgcttgaggt tcccaaaacc aatcaggact gatgtaactg gcatgatctt ggaagaaggc
3241 gcgcctgaag gcaccgtggc cacactactc atcaaaaggt ctactggaga actcatgccc
3301 ctagcagcca gaatggggac ccatgcaacc atgaaaattc aagggcgcac tgttggaggt
3361 cagatgggca tgcttctgac aggatccaac gccaaaagca tggatctagg caccacacca
3421 ggtgattgcg gctgtcccta catctacaag agagggaatg actatgtggt cattggagtc
3481 cacacggctg ccgctcgtgg gggaaacact gttatatgtg ccacccaggg gggtgagggg
3541 gaagctacac ttgaaggtgg tgacagtaag ggaacgtact gcggtgcgcc aatcctaggc
3601 ccagggagcg ccccaaaact tagtaccaaa accaaattct ggagatcatc cacagcacca
3661 ctcccacctg gcacctatga gccagcctac cttggtggca aggaccccag agtcaagggt
3721 ggcccctcgc tgcagcaagt catgagagac cagctgaaac cattcacaga gcccaggggt
3781 aagccaccaa agccaagtgt gttggaagct gccaagaaaa ccatcatcaa tgttcttgaa
3841 caaacaattg acccacctga gaagtggtcg ttcgcacagg cttgcgcgtc ccttgacaag
3901 accacttcta gcggccatcc gcatcacatg cggaaaaacg actgctggaa cggggagtcc
3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgtttga agaagggaag
4021 agcatgaccc cagtttacac aggtgcgctc aaggacgagt tggtcaaaac tgataaaatt
4081 tatggcaaga tcaagaagag gcttctctgg ggctcggatt tagcaaccat gatccggtgt
4141 gctcgagcat tcggaggcct aatggatgaa ctcaaagcac actgtgtcac acttcccatc
4201 agagttggta tgaatatgaa tgaggatggc cccatcatct tcgagaagca ctccaggtac
4261 aggtaccact atgacgctga ttactctcga tgggattcaa cacaacagag agccgtgctg
4321 gcagctgctc tagaaattat ggttaaattc tcctcagaac cacatttggc tcaggtggtc
4381 gcagaagacc ttctttctcc tagcgtggtg gatgtgggtg acttcacaat atcaatcaat
4441 gagggtcttc cctctggggt gccctgcact tctcaatgga actccatcgc ccactggctt
4501 ctcactctat gtgcactctc cgaagttaca aatttgtccc cagacatcat acaggctaat
4561 tctctcttct ccttctatgg tgatgatgaa attgttagta cagacataaa actagaccca
4621 gagaagttga cagcaaagct taaggaatat gggttaaaac caacccgccc tgacaaaact
4681 gaaggacctc ttgttatttc tgaagactta gatggtttga ctttcctgcg gagaactgtg
4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gctcaatact caggcaaatg
4801 tactggacta ggggtcccaa ccatgaagat ccatctgaat caatgattcc acactctcaa
4861 agacccatac aattgatgtc cctgctggga gaggccgcac tccacggccc aacattctat
4921 agtaaaatca gcaaattagt cattgcagag ctaaaagaag gtggtatgga tttttacgtg
4981 cccaggcaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ctttgtgaat gaagatggcg tcgaatgacg ccaacccatc
5101 tgatgggtcc gcagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctttggagcc
5161 cgttgtcggt gccgctattg cggcacctgt agcgggccaa caaaatgtaa ttgacccctg
5221 gattaggaat aattttgtac aagcccctgg tggagaattc acagtatccc ctagaaacgc
5281 tccaggtgaa atactatgga gcgcgccctt aggccctgat ctgaatccct acctatccca
5341 tttggccaga atgtataatg gttatgcagg tggctttgaa gtgcaggtga tcctcgcggg
5401 gaacgcgttc accgccggga aaattatatt tgcagcagtt ccaccaaatt ttccaactga
5461 aggcttgagc cccagccagg ttactatgtt cccccacata atagtagatg ttaggcaact
5521 ggaacctgtg ttgatcccct tacctgatgt taggaataac ttctatcatt ataatcagtc
5581 aaatgattct accattaaat tgatagcaat gctgtacaca ccacttagag ctaataatgc
5641 tggggaagat gtcttcacag tctcttgtcg agtcctcacg aggccatccc ctgactttga
5701 ttttatattt ttggtgccac ccacagttga gtcaagaact aaaccattta ctgtcccaat
5761 cttaactgtt gaagaaatga ccaattcaag attccccatc cctttggaaa agttgttcac
5821 gggccccagc ggtgccttta ttgttcaacc acaaaatggt agatgcacga ctgatggcgt
5881 gctcttaggc accacccaac tgtctcctgt caacatctgc accttcagag gggatgtcac
5941 ccacattgca ggttctcgca attacacgat gaatttggct tctctaaatt ggaataatta
6001 tgacccaaca gaagaaattc cagcccctct gggaactcca gatttcgtgg gaaagatcca
6061 aggtgtgctc actcaaacca caaagggaga tggctcgacc cgtggccata aagcaacagt
6121 ttacactggg agtgccccct ttactccaaa gctgggcagt gttcaattca gtactgacac
6181 agaaaatgat tttgaagctc accaaaacac aaaattcacc ccagtcggtg tcatccagga
6241 tggtggcacc acccaccgaa atgaacccca acaatgggtg ctcccaagtt attcaggtag
6301 agatgtccac aatgtacacc tggcccctgc tgtagccccc acttttccgg gtgaacaact
6361 tcttttcttc aggtccacta tgcccggatg cagtgggtat cccaacatgg atttggattg
6421 cctactccct caggagtggg tgcagcactt ctaccaagag gcagctccag cacaatctga
6481 tgtggctcta ttgagatttg tgaatccaga cacgggtagg gtcctgtttg agtgcaaact
6541 tcataaatca ggctatgtca cagtggctca caccggccag catgatttgg tcatcccccc
6601 taatggctat tttaggtttg actcctgggt taaccaattc tacacacttg cccccatggg
6661 aaatggaacg gggcgtagac gtgctttata atggctgggg ctttctttgc tggattggcg
6721 tctgatgtcc ttggctctgg acttggctcc ctaatcaatg ctggggctgg ggctattaac
6781 caaaagattg attttgaaaa taacagaaaa ttgcagcaag cttccttcca gtttagcagt
6841 aatctacaac aggcctcctt tcaacatgac aaagagatgc tccaagcaca aatcgaggcc
6901 actaaaaagt tgcaacagga aatgatgaga gtcaaacagg caatgctctt agaaggtggg
6961 ttctctgaaa cagatgcagc tcgtggggca atcaacgccc ccatgacaaa ggttttggac
7021 tggagtggaa caaggtactg ggcccctgat gccaggacta caacatacaa tgcaggccgc
7081 ttttccaccc cccaaccctc ggggtcattg ccaggaagaa tcaatcccag gactcctact
7141 cccgctcggg cctcctccag tacatcctct aatgcttcta ctgttacttc tatatattca
7201 aatcaaactg tttcaacgag acttggttct acagctggct ctggcaccaa tgtctcgagt
7261 ctcccgtcaa ctgcaaggac taagagttgg gttgaggatc aaaacagaaa tttgtcacct
7321 ttcatgaggg gggctcacaa catatcgttt gtcaccccac catctagcag atcctctagc
7381 caaggcacag tctcaaccgt gcctaaagaa gttttggact cctggactgg c
//