Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| KM198532 | GII.4 Den Haag | |
|
|---|---|---|---|
| GII.P4 Den Haag |
ORF1: 71..5089
ORF2: 5070..6692
ORF3: 6692..7432
LOCUS KM198532 7432 bp RNA linear VRL 13-NOV-2014
DEFINITION Norovirus Hu/GII/10108/2009/VNM nonstructural polyprotein and
capsid protein VP1 genes, complete cds; and capsid protein VP2
gene, partial cds.
ACCESSION KM198532
VERSION KM198532.1
KEYWORDS .
SOURCE Norovirus Hu/GII/10108/2009/VNM
ORGANISM Norovirus Hu/GII/10108/2009/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7432)
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 7432)
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..7432
/organism="Norovirus Hu/GII/10108/2009/VNM"
/mol_type="genomic RNA"
/isolate="Hu/GII/10108/2009/VNM"
/host="Homo sapiens"
/db_xref="taxon:1526941"
/country="Viet Nam"
/collection_date="02-Jul-2009"
/note="genotype: GII"
CDS 71..5089
/note="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AII02724.1"
/translation="MFSNMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKIPPP
PPNGEDEAVVSYSAKDGVSGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI
LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT
LKKLHGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT
MDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL
AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM
LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN
HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR
AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA
YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL
ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL
APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK
VLAFRQLAAENKYGLIDTMKVGRQLKDVKTMPELKQALKNISIKKCQIVYSGCTYTLE
SDGKGNVKVDRIQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV
TTRIIKRVNIQDLWSKPQVENTEEATNKDGCPKPKDDEEFVISSDDIKTEGKKGKNKT
GRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYSIEEYLQDRDKYYEEVAIARATEED
FCEEEEARIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSV
DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV
HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGTHATM
KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN
TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE
PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP
PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMT
PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR
VGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQV
VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII
QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF
LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA
LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE
DGVE"
CDS 5070..6692
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AII02725.1"
/translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPVPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6692..>7432
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AII02726.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRINPRTPTPARGSSSTSS
NASTATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTG"
ORIGIN
1 tctaacggac gcttccgctg ccgctgttgc taacagcaac aacgacaccg caaaatcttc
61 aagtgacaaa atgttttcta acatggctgt cacttttaaa cgagccctcg gggcgcggcc
121 taaacagccc cccccgaggg aaataccaca aagaccccca cgaccaccta ctccagaact
181 ggtcaaaaag atccctcctc ccccgcccaa cggagaggat gaagcagtgg tttcttatag
241 tgccaaagat ggcgtttccg gtttacctga gctttccacc gtcaggcaac cggaagaaac
301 caatacggcc ttcagtgtcc ctccactcaa ccagagggag aatagagatg ctaaggaacc
361 actgactgga acaattctgg aaatgtggga tggagaaatc taccattatg gcctgtatgt
421 tgagcgaggt cttgtgctgg gtgtgcacaa accaccagct gccataagcc tcgccaaggt
481 cgaactaaca ccactctcct tgttctggag acctgtgtac actccccagt acctcatctc
541 tccagacacc ctcaagaaat tgcacggaga agcgtttccc tacacagcct ttgacaacaa
601 ttgctatgcc ttttgttgtt gggtcctgga tctaaatgac tcgtggctga gtaggagaat
661 gatccagaga acaactggct tcttcagacc ctaccaagac tggaatagga aacccctccc
721 cactatggat gattccaaat taaagaaggt agctaacata ttcctgtgcg ccctgtcttc
781 gctattcacc aggcccataa aagacataat aggaaagcta agacctctca acatcatcaa
841 catcctggct tcatgtgatt ggactttcgc aggcatagtg gagtctttga tactcttggc
901 agagctcttt ggagtcttct ggacaccccc agatgtgtct gcgatgattg cccccttact
961 cggtgatttc gagttacaag gacctgagga ccttgtagtg gagctcgtcc ctgtagtaat
1021 ggggggaatt ggtttggtgc tgggattcac caaagagaag attgggaaaa tgttgtcatc
1081 tgctgcatcc accttgagag cttgtaaaga tcttggtgca tatgggctag agatcctaaa
1141 gttagtcatg aagtggttct tcccgaagaa agaggaggca aatgaactgg ctatggtgag
1201 atccatcgag gatgcagtac tggaccttga ggcaattgaa aacaaccata tgaccacctt
1261 gctcaaagac aaagacagcc tggcaaccta catgagaacc cttgacctcg aggaagagaa
1321 agccagaaaa ctctcaacca agtctgcttc acctgacatc gtgggtacaa tcaacgccct
1381 tctggcgaga atcgccgctg cgcgctccct ggtgcaccga gcgaaggagg agctttccag
1441 cagaccaaga cctgtagtct tgatgatatc aggcagacca gggataggaa aaacccacct
1501 tgctagggaa gtggctaaga gaatcgcagc ctccctcaca ggagaccagc gtgtaggcct
1561 catcccacgc aatggcgtcg atcactggga tgcgtacaag ggggagaggg tcgtcctatg
1621 ggacgactat ggaatgagca accccattca cgacgccctt aggctgcaag aactcgctga
1681 cacttgcccc cttactctaa attgtgacag gattgagaac aaaggaaagg tctttgacag
1741 cgatgtcatc attatcacca ctaatctggc caacccagca ccactggact atgtcaactt
1801 tgaagcgtgc tcgaggcgca tcgatttcct cgtgtatgca gaagcccccg aggtcgaaaa
1861 ggcgaagcgt gacttcccgg gccaacctga catgtggaaa aacgctttta gttctgattt
1921 ctcacacata aaattggcac tggctccaca aggtggcttt gataagaacg ggaacacccc
1981 acacgggaag ggcgtcatga agactctcac cactggctcc ctcattgccc gggcatcagg
2041 gctgctccat gagagattgg atgagtttga actacagggc ccagctctta ccaccttcaa
2101 ctttgaccgc aacaaagtgc ttgccttcag acagcttgca gctgaaaaca aatatgggtt
2161 gatagacaca atgaaagttg ggaggcagct caaggatgtc aaaaccatgc cagaacttaa
2221 acaagcactc aaaaacatct caatcaagaa gtgccagatt gtgtatagtg gttgcaccta
2281 cacacttgag tctgatggca agggcaatgt gaaagttgac agaatccaga gcacctccgt
2341 acagaccaac aatgagcttg ctggcgccct gcatcatctg aggtgcgcca gaatcaggta
2401 ctatgtcaag tgtgtccagg aggccctgta ttctatcatc cagattgctg gggccgcatt
2461 tgtcaccacg cgcattatca agcgtgtgaa cattcaagac ttatggtcca agccacaagt
2521 ggaaaacaca gaggaggcca ccaacaagga cgggtgccca aaacccaaag atgatgagga
2581 gttcgtcatt tcatctgacg acattaaaac tgagggtaag aaagggaaga acaagactgg
2641 ccgtggcaag aagcacacag ccttttcaag taaaggtctc agtgatgaag agtatgatga
2701 gtacaagaga attagagagg aaaggaatgg caggtattcc atagaagagt accttcagga
2761 cagggacaaa tactatgagg aggtggccat tgccagggcg accgaggaag acttctgtga
2821 agaggaggag gccaggatcc ggcaaaggat ctttagacca acaaggaaac aacgcaagga
2881 agaaagagct tctctcggtt tagtcacagg ttctgagatt aggaaaagaa acccagatga
2941 cttcaagcct aagggaaaac tgtgggctga cgatgacaga agtgtggatt acaatgagaa
3001 actcagtttt gaggccccac caagcatctg gtcaaggata gtcaactttg gttcaggttg
3061 gggcttctgg gtctccccta gcctgttcat aacatcaacc cacgtcatac cccagggcgc
3121 aaaggagttc tttggagttc ccatcaagca aattcaggtg cacaagtcag gcgaattttg
3181 tcgcttgagg ttcccaaaac caatcaggac tgacgtgact ggcatgatct tggaagaagg
3241 tgcgcccgaa ggcaccgtgg tcacactact catcaaaagg tctactggag aactcatgcc
3301 cctagcagct agaatgggga cccatgcaac catgaaaatt caagggcgca ccgttggagg
3361 ccagatgggc atgcttctga caggatccaa cgccaaaagc atggatctag gcaccacacc
3421 aggtgattgc ggctgtccct acatctacaa gagaggaaat gactatgtgg tcattggagt
3481 ccatacggct gccgctcgtg ggggaaacac tgtcatatgt gccacccagg ggggcgaggg
3541 ggaagctaca cttgaaggtg gtgacagtaa gggaacatac tgtggtgcac caatcctagg
3601 cccagggagt gccccaaaac ttagcaccaa aaccaaattc tggagatcat ccacagcacc
3661 actcccacct ggcacctatg aaccagcata ccttggtggc aaggacccca gagtcaaggg
3721 tggcccttcg ttgcagcaag tcatgaggga ccagctgaaa ccatttacag agcccagggg
3781 taagccacca aagccaagtg tgttagaagc tgccaagaaa accatcatca atgtccttga
3841 acaaacaatt gacccacctg agaagtggtc gttcgcacaa gcttgcgcct cccttgacaa
3901 gaccacttct agcggccatc cgcaccatat gcggaaaaac gactgctgga atggggagtc
3961 cttcacaggc aagctggcag accaggcttc taaggctaac ctgatgtttg aagaagggaa
4021 gaacatgacc ccagtctaca caggtgcact taaggatgaa ttagtcaaaa ctgacaaaat
4081 ttatggtaag atcaagaaga ggcttctctg gggctcggat ttagcaacca tgatccggtg
4141 tgctcgagca ttcggaggcc taatggatga acttaaagca cactgtgtca cacttcctat
4201 tagagttggt atgaatatga atgaggatgg ccccatcatc ttcgagaagc attccaggta
4261 cagataccac tatgatgctg attactctcg gtgggattca acacaacaga gagccgtgct
4321 ggcagctgct ctagaaatca tggttaaatt ctcctcagaa ccacatttgg ctcaggtagt
4381 cgcagaagat cttctttccc ctagcgtggt ggatgtgggt gacttcacaa tatcaatcaa
4441 cgagggcctt ccctctgggg tgccctgcac ctcccaatgg aactccatcg cccactggct
4501 tctcactctt tgtgcactct ccgaagtcac aaatttgtcc ccagacatca tacaggctaa
4561 ttctctcttc tccttctatg gtgatgatga aattgttagt acagacataa aattggaccc
4621 agagaagttg acagcaaagc ttaaggaata tgggttgaaa ccaacccgcc ctgacaaaac
4681 tgaaggacct ctcgttattt ctgaagactt agatggtttg actttcctgc ggagaactgt
4741 gacccgcgac ccagctggtt ggtttggaaa actggagcag agctcaatac tcaggcaaat
4801 gtactggact aggggcccca accatgaaga tccatctgaa tcaatgattc cacactctca
4861 aagacccata caattgatgt ccttactggg agaggccgca ctccacggcc caacattcta
4921 cagtaaaatc agcaaattag tcattgcaga gctaaaagaa ggtggtatgg atttttacgt
4981 gcccaggcaa gagccaatgt tcagatggat gagattctca gatctgagca cgtgggaggg
5041 cgatcgcaat ctggctccca gttttgtgaa tgaagatggc gtcgaatgac gccaacccat
5101 ctgatgggtc cgcagccaac ctcgtcccag aggtcagcaa tgaggttatg gctttggagc
5161 ccgttgtcgg tgccgctatt gcggcgcctg tagcgggcca acaaaatgta attgacccct
5221 ggattagaaa caattttgta caagcccctg gtggagagtt cacagtatcc cctagaaacg
5281 ctccaggtga aatactatgg agcgcgccct taggccctga tctgaacccc tacctatccc
5341 atttggccag aatgtataat ggttatgcag gtggttttga agtgcaggtg atcctcgcgg
5401 ggaacgcgtt caccgccgga aaaattatat ttgcagcagt cccaccaaat tttccaactg
5461 aaggcctgag tcccagccag gtcactatgt tcccccacat aatagtagat gttaggcaat
5521 tggaacctgt gttgatcccc ttacctgatg ttaggaataa cttctatcat tataatcaaa
5581 caaatgattc taccattaaa ttgatagcaa tgctgtatac accacttagg gccaataatg
5641 ctggggaaga tgtcttcaca gtctcttgtc gagtcctcac taggccgtcc cctgattttg
5701 attttatatt tttggtgcca cccacagttg agtcaagaac taaaccattt actgtcccaa
5761 tcttaaccgt tgaagaaatg accaattcaa gattccccgt tcctttggaa aagttgttca
5821 cgggtcccag cggtgccttt gttgtccaac cacaaaatgg caggtgcacg actgatggcg
5881 tgctcttagg caccacccaa ctgtctcctg tcaacatctg caccttcaga ggggatgtca
5941 cccacattgc aggttctcgt aattacacaa tgaatttggc atctctaaat tggaacaatt
6001 atgacccaac agaagaaatt ccagcccctc tgggaactcc agatttcgtg ggaaagatcc
6061 aaggtgtgct cactcaaacc acaaaaggag atggctcgac ccgtggccat aaagctacag
6121 tttacactgg gagtgccccc tttactccaa agctgggcag tgttcaattc agtactgaca
6181 cagaaaatga ttttgaaact caccaaaaca caaaattcac cccagtcggt gtcatccagg
6241 atggtggcac tacccaccga aatgaacccc aacaatgggt gctcccaagt tattcaggta
6301 gagatgtcca taatgtacac ctagcccctg ctgtagcccc cacttttccg ggtgaacaac
6361 ttcttttctt caggtccact atgcccggat gcagcgggta tcccaacatg gatttggatt
6421 gcctactccc ccaggagtgg gtgcagcact tctaccaaga ggcagctcca gcacaatctg
6481 atgtggctct attgagattt gtgaatccag acacgggtag ggtcctgttt gagtgcaaac
6541 ttcataaatc aggctatgtc acagtggctc acaccggtca gcatgatttg gtcatccccc
6601 ccaatggcta ttttaggttt gattcctggg ttaatcagtt ctacacgctt gcccccatgg
6661 gaaacggaac ggggcgtcgg cgcgccttat aatggctgga gctttctttg ctggattggc
6721 atctgatgtc cttggctctg gacttggttc cctaatcaat gctggggctg gggccatcaa
6781 ccaaaagatt gattttgaga ataatagaaa attgcagcaa gcttccttcc agtttagcag
6841 taatctacaa caggcttcct ttcaacacga taaagagatg ctccaagcac aaattgaggc
6901 cactaaaaag ttgcaacagg aaatgatgaa agtcaaacag gcaatgctcc tagaaggtgg
6961 attctctgaa acagatgcag cccgtggggc aatcaacgcc cccatgacaa aggttttgga
7021 ctggagcgga acaaggtact gggcccctga tgctaggacc acaacataca atgcaggccg
7081 cttttccacc cctcagcctt cggggacgct gccaggaaga atcaatccca ggactcctac
7141 ccccgctcgg ggctcctcca gcacatcttc taatgcttct actgctactt ctatatattc
7201 aaatcaaact gtttcaacga gacttggttc tacagctggt tctggtacca atgtctcgag
7261 tctcccgtca actgcaagga ctaggagctg ggttgaggat caaaacagaa atttgtcacc
7321 tttcatgagg ggggctcata acatatcgtt tgtcacccca ccatctagca gatcctctag
7381 ccaaggcaca gtctcaaccg tgcctaaaga agttttggac tcctggactg gc
//