Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| KM198564 | GII.4 Den Haag | |
|
|---|---|---|---|
| GII.P4 Den Haag |
ORF1: 38..5056
ORF2: 5037..6659
ORF3: 6659..7399
LOCUS KM198564 7399 bp RNA linear VRL 13-NOV-2014
DEFINITION Norovirus Hu/GII/C2H-44/2011/VNM nonstructural polyprotein and
capsid protein VP1 genes, complete cds; and capsid protein VP2
gene, partial cds.
ACCESSION KM198564
VERSION KM198564.1
KEYWORDS .
SOURCE Norovirus Hu/GII/C2H-44/2011/VNM
ORGANISM Norovirus Hu/GII/C2H-44/2011/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7399)
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 7399)
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..7399
/organism="Norovirus Hu/GII/C2H-44/2011/VNM"
/mol_type="genomic RNA"
/isolate="Hu/GII/C2H-44/2011/VNM"
/host="Homo sapiens"
/db_xref="taxon:1527018"
/geo_loc_name="Viet Nam"
/collection_date="31-Oct-2011"
/note="genotype: GII"
CDS 38..5056
/note="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AII02820.1"
/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 5037..6659
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AII02821.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFIVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGGAPFTPKLGSVQFSTDTENDFEAHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6659..>7399
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AII02822.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGSLPGRINPRTPTPARASSSTSS
NASTVTSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTKSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTG"
ORIGIN
1 cagcaacaac gacaccgcaa catcttcaag tgacaaaatg ttttctagca tggctgtcac
61 ttttaaacga gccctcgggg cgcggcctaa acagcctccc ccgagggaaa taccgcaaag
121 gcccccacga ccacctactc cagaactggt caaaaaggtc cctcctcccc cgcccaacgg
181 agaggatgaa gtggtggttt cttatagtgc caaagatggc atttctggtc tacctgagct
241 ttccaccgtc agacaaccag aagaaaccaa tacggccttc agtgtccctc cactcaatca
301 gagggagaat agggatgcta aggaaccact gactgggaca attctggaaa tgtgggatgg
361 agaaatctat cattatggcc tgtatgttga acgaggtctt gtgctgggtg tgcacaaacc
421 accagctgcc attagcctcg ccaaggtcga attaacacca ctctccttgt tctggagacc
481 tgtgtacacc ccacagtacc tcatctctcc agacactctc aagaaattac acggagaaac
541 atttccctac acagcctttg acaacaactg ctatgccttt tgctgctggg tcctggatct
601 aaacgactcg tggctgagta ggaggatgat ccagagaaca actggcttct tcagacccta
661 ccaagattgg aataggaaac ccctccctac tacggatgat tccaaattaa agaaggtagc
721 taacatattc ctgtgcaccc tgtcttcgct attcaccagg cccataaaag acataatagg
781 aaagttaagg cctctcaaca tcatcaacat cctagcttca tgtgactgga ctttcgcagg
841 catcgtggaa tccttgatac tcttggcaga gctctttgga gtcttctgga cacccccaga
901 tgtgtctgcg atgattgccc ccttactcgg tgatttcgag ttacaaggac ctgaggacct
961 tgtagtggag ctcgtccctg tggtaatggg gggaattggc ttggtgctgg gattcaccaa
1021 agagaagatt ggaaaaatgt tgtcatctgc tgcatccacc ctaagagctt gtaaagatct
1081 cggtgcatat gggctagaga tcctaaagct agtcatgaag tggttcttcc cgaagaaaga
1141 ggaggcaaat gaactggcta tggtgagatc catcgaggat gcagtactgg accttgaggc
1201 aattgaaaac aaccatatga ccaccttgct caaagataaa gacagcctgg caacctacat
1261 gagaaccctt gacctcgagg aagagaaagc cagaaaactc tcaaccaagt ctgcgtcacc
1321 tgacatcgtg ggcacaatca acgcccttct ggcgagaatc gccgctgcac gctccctggt
1381 gcaccgagcg aaggaggagc tttccagcag accaagacct gtggtcttga tgatatcagg
1441 tagaccaggg atagggaaga cccaccttgc tagggaagtg gccaagagaa tcgcagcatc
1501 cctcacagga gaccagcgcg taggtctcat cccacgcaat ggcgtcgatc actgggatgc
1561 gtacaagggg gagagggtcg tcctatggga cgactatgga atgagcaatc ccatccacga
1621 cgccctcagg ctgcaagaac tcgccgacac ttgccccctc actctaaatt gtgacagaat
1681 tgagaataaa ggaaaggtct ttgacagtga tgtcatcatt atcactacta atctggccaa
1741 cccagcacca ctggactatg tcaactttga agcgtgctcg aggcgcatcg atttcctcgt
1801 gtacgcagaa gcccccgagg tcgaaaaggc gaagcgtgac ttcccaggcc aacctgacat
1861 gtggaaaaac gcctttagtt ctgatttctc acacataaaa ctggcactgg ctccacaagg
1921 tggcttcgat aagaacggga acaccccaca tgggaagggc gtcatgaaga ctctcaccac
1981 tggctccctt attgcccggg catcagggct gctccatgag agattggatg agtttgaact
2041 acagggccca gctctcacca ccttcaactt tgaccgcaac aaagtgcttg ccttcaggca
2101 gcttgctgct gaaaacaaat acgggttgat ggacacaatg agagttggga ggcagctcaa
2161 ggatgtcaaa accatgccag aacttaaaca agcactcaag agcatctcaa tcaagaagtg
2221 tcagattgtg tacagtggtt gcacctacac acttgagtct gatggcaagg gcaatgtgaa
2281 ggttgacaga gttcagagca cctccgtgca gaccaacaat gagctggctg gcgccctgca
2341 ccatctgagg tgcgccagaa tcaggtacta tgttaagtgt gtccaggagg ccctgtattc
2401 tatcattcag attgctggag ctgcattcgt caccacgcgc atcatcaagc gtgtgaacat
2461 tcaaaactta tggtccaagc cacaagtgga aaacacagag gaagccacca acaaggatgg
2521 gtgcccaaaa cccaaagatg atgaggagtt cgtcatcaca tctgacgaca ttaaaactga
2581 gggtaagaaa ggaaagaaca agactggccg tggcaagaag cacacagcct tctcaagtaa
2641 aggtctcagt gatgaagagt atgatgagta caagagaatt agagaggaaa ggaatggcaa
2701 gtactccata gaagagtacc ttcaggacag ggacaaatac tatgaagagg tggccattgc
2761 cagggcgacc gaggaagact tctgtgaaga ggaggaggcc aagatccggc aaaggatctt
2821 cagaccaaca aggaaacaac gcaaggaaga aagagcttcc ctcggtttag tcacaggttc
2881 tgaaattagg aaaagaaacc cagatgattt caagcccaag gggaaactat gggctgacga
2941 tgacagaagt gtggactaca atgagaaact cagttttgag gctccgccaa gcatctggtc
3001 aaggatagtc aactttggct caggttgggg cttctgggtc tcccccagcc tgttcataac
3061 atcaacccac gtcatacccc agggcgcaaa ggagttcttt ggagtcccca tcaaacaaat
3121 tcaggtgcac aagtcaggcg aattctgtcg cttgaggttc ccaaaaccaa tcaggactga
3181 tgtaactggc atgatcttgg aagaaggcgc gcctgaaggc accgtggcca cactactcat
3241 caaaaggtct actggagaac tcatgcccct agcagccaga atggggaccc atgcaaccat
3301 gaagattcaa gggcgcactg ttggaggtca gatgggcatg cttctgacag gatccaacgc
3361 caaaagcatg gatctaggca ccacaccagg tgattgcggt tgtccctaca tctacaagag
3421 agggaatgac tatgtggtca ttggagtcca cacggctgcc gctcgtgggg gaaacactgt
3481 tatatgtgcc acccaggggg gtgaggggga agctacactt gaaggtggtg acagtaaggg
3541 aacgtactgc ggtgcgccaa tcctaggccc agggagcgct ccaaaactta gtaccaaaac
3601 caaattctgg agatcatcca cagcaccact cccacctggc acctatgagc cagcctacct
3661 tggtggcaag gaccccagag tcaagggtgg cccctcgctg cagcaagtca tgagagacca
3721 gctgaaacca ttcacagagc ccaggggtaa gccaccaaag ccaagtgtgt tggaagctgc
3781 caagaaaacc atcatcaatg ttcttgaaca aacaattgac ccacctgaga agtggtcgtt
3841 cgcacaggct tgcgcgtccc ttgacaagac cacttctagc ggccatccgc atcacatgcg
3901 gaaaaacgac tgctggaacg gggagtcctt cacaggcaag ctggcagacc aggcttccaa
3961 ggccaacctg atgtttgaag aagggaagag catgacccca gtttacacag gagcgctcaa
4021 ggacgagttg gtcaaaactg ataaaattta tggcaagatc aagaagaggc ttctctgggg
4081 ctcggattta gcaaccatga tccggtgtgc tcgagcattc ggaggcctaa tggatgaact
4141 caaagcacac tgtgtcacac ttcctatcag agttggtatg aatatgaatg aggatggccc
4201 catcatcttc gagaagcact ccaggtacag gtaccactat gatgctgatt actcccgatg
4261 ggattcaaca caacagagag ccgtgctggc agctgctcta gaaattatgg ttaaattctc
4321 ctcagaacca catttggctc aggtggtcgc agaagacctt ctttctccta gcgtggtgga
4381 tgtgggtgac ttcacaatat caatcaatga gggtcttccc tctggggtgc cctgcacttc
4441 tcaatggaac tccatcgccc actggcttct cactctatgt gcactctccg aagttacaaa
4501 tttgtcccca gacatcatac aggctaattc tctcttctcc ttctatggtg atgatgaaat
4561 tgttagtaca gacataaaac tagacccaga gaagttgaca gcaaagctta aggaatatgg
4621 gttaaaacca acccgccctg acaaaactga aggacctctt gttatttctg aagacttaga
4681 tggtttgact ttcctgcgga gaactgtgac ccgcgaccca gctggttggt ttggaaaact
4741 ggagcagagc tcaatactca ggcaaatgta ctggactagg ggtcccaacc atgaagatcc
4801 atctgaatca atgattccac actctcaaag acccatacaa ttgatgtccc tgctgggaga
4861 ggccgcactc cacggcccaa cattctatag taaaatcagc aaattagtca ttgcagagct
4921 aaaagaaggt ggtatggatt tttacgtgcc caggcaagag ccaatgttca gatggatgag
4981 attctcagat ctgagcacgt gggagggcga tcgcaatctg gctcccagct ttgtgaatga
5041 agatggcgtc gaatgacgcc aacccatctg atgggtccgc agccaacctc gtcccagagg
5101 tcaacaatga ggttatggct ttggagcccg ttgtcggtgc cgctattgcg gcgcctgtag
5161 cgggccaaca aaatgtaatt gacccctgga ttaggaataa ttttgtacaa gcccctggtg
5221 gagaattcac agtatcccct agaaacgctc caggtgaaat actatggagc gcgcccttag
5281 gccctgatct gaatccctac ctatcccatt tggccagaat gtataatggt tatgcaggtg
5341 gctttgaagt gcaggtgatc ctcgcgggga acgcgttcac cgccgggaaa attatatttg
5401 cagcagttcc accaaatttt ccaactgaag gcttgagccc cagccaggtt actatgttcc
5461 cccacataat agtagatgtt aggcaactgg aacctgtgtt gatcccctta cctgatgtta
5521 ggaataactt ctatcattat aatcagtcaa atgattctac cattaaattg atagcaatgc
5581 tgtacacacc acttagagct aataatgctg gggaagatgt cttcacagtc tcttgtcgag
5641 tccttacgag gccatcccct gactttgatt ttatattttt ggtgccaccc acagttgagt
5701 caagaactaa accatttact gtcccaatct taactgttga agaaatgacc aattcaagat
5761 tccccatccc tttggaaaag ttgttcacgg gccccagcgg tgcctttatt gttcaaccac
5821 aaaatggtag atgcacgact gatggcgtgc tcttaggcac cacccaactg tctcctgtca
5881 acatctgcac cttcagaggg gatgtcaccc acattgcagg ttctcgcaat tacacgatga
5941 atttggcttc tctaaattgg aataattatg acccaacaga agaaattcca gcccctctgg
6001 gaactccaga tttcgtggga aagatccaag gtgtgctcac tcaaaccaca aagggagatg
6061 gctcgacccg tggccataaa gcaacagttt acactggggg tgcccccttt actccaaagc
6121 tgggcagtgt tcaattcagt actgacacag aaaatgattt tgaagctcac caaaacacaa
6181 aattcacccc agtcggtgtc atccaggatg gtggcaccac ccaccgaaat gaaccccaac
6241 aatgggtgct cccaagttat tcaggtagag atgtccacaa tgtacacctg gcccctgctg
6301 tagcccccac ttttccgggt gaacaacttc ttttcttcag gtccactatg cccggatgca
6361 gtgggtatcc caacatggat ttggattgcc tactccctca ggagtgggtg cagcacttct
6421 accaagaggc agctccagca caatctgatg tggctctatt gagatttgtg aatccagaca
6481 cgggtagggt cctgtttgag tgcaaacttc ataaatcagg ctatgtcaca gtggctcaca
6541 ccggccagca tgatttggtc atccccccta atggctattt taggtttgac tcctgggtta
6601 accaattcta cacacttgcc cccatgggaa atggaacggg gcgtagacgt gctttataat
6661 ggctggggct ttctttgctg gattggcatc tgatgtcctt ggctctgggc ttggctccct
6721 aatcaatgct ggggctgggg ctatcaacca aaagattgat tttgaaaata acagaaaatt
6781 gcagcaagct tccttccagt ttagcagtaa tctacaacag gcctcctttc aacatgacaa
6841 agagatgctc caagcacaaa tcgaggccac taaaaagttg caacaggaaa tgatgagagt
6901 caaacaggca atgctcttag aaggtgggtt ctctgaaaca gatgcagctc gcggggcaat
6961 caacgccccc atgacaaagg ttttggactg gagtggaaca aggtactggg cccctgatgc
7021 caggactaca acatacaatg caggccgctt ttccaccccc caaccctcgg ggtcattgcc
7081 aggaagaatc aatcccagga ctcctactcc cgctcgggcc tcctctagta catcctctaa
7141 tgcttctact gttacttcta tatattcaaa tcaaactgtt tcaacgagac ttggttctac
7201 agctggctct ggcaccaatg tctcgagtct cccgtcaact gcaaggacta agagttgggt
7261 tgaggatcaa aacagaaatt tgtcaccttt catgaggggg gctcacaaca tatcgtttgt
7321 caccccacca tctagcagat cctctagcca aggcacagtc tcaaccgtgc ctaaagaagt
7381 tttggactcc tggactggc
//