Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| KM198580 | GII.4 Den Haag | |
|
|---|---|---|---|
| GII.P4 Den Haag |
ORF1: 62..5080
ORF2: 5061..6683
ORF3: 6683..7423
LOCUS KM198580 7423 bp RNA linear VRL 13-NOV-2014
DEFINITION Norovirus Hu/GII/10223/2009/VNM nonstructural polyprotein and
capsid protein VP1 genes, complete cds; and capsid protein VP2
gene, partial cds.
ACCESSION KM198580
VERSION KM198580.1
KEYWORDS .
SOURCE Norovirus Hu/GII/10223/2009/VNM
ORGANISM Norovirus Hu/GII/10223/2009/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7423)
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 7423)
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..7423
/organism="Norovirus Hu/GII/10223/2009/VNM"
/mol_type="genomic RNA"
/isolate="Hu/GII/10223/2009/VNM"
/host="Homo sapiens"
/db_xref="taxon:1526964"
/geo_loc_name="Viet Nam"
/collection_date="06-Nov-2009"
/note="genotype: GII"
CDS 62..5080
/note="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AII02868.1"
/translation="MFSNMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKIPPP
PPNGEDEAVVSYSAKDGVSGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI
LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT
LKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT
MDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL
AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM
LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN
HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR
AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA
YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL
ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL
APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK
VLAFRQLAAENKYGLIDTMKVGRQLKDVKTMPELKQALKNISIKKCQIVYSGCTYTLE
SDGKGNVKVDKIQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV
TTRIIKRVNIQDLWSKPQVENTEEATNKDGCSKPKDDEEFVISSDDIKTEGKKGKNKT
GRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYSIEEYLQDRDKYYEEVAIARATEED
FCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSV
DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV
HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGTHATM
KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN
TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE
PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP
PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMT
PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR
VGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQV
VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII
QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF
LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA
LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE
DGVE"
CDS 5061..6683
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AII02869.1"
/translation="MKMASNDANPTDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6683..>7423
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AII02870.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRINPRTPTPARGSSSTSS
NASTATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTG"
ORIGIN
1 cgcttccgct gccgctgttg ctaacagcaa caacgacacc gcaaaatctt caagtgacaa
61 aatgttttct aacatggctg tcacttttaa acgagccctc ggggcgcggc ctaaacagcc
121 ccccccgagg gaaataccac aaagaccccc acgaccacct accccagaac tggtcaaaaa
181 gatcccccct cccccgccca acggagagga tgaagcagtg gtttcttata gtgccaaaga
241 tggcgtttcc ggtttacctg agctttccac cgtcaggcaa ccggaagaaa ccaatacggc
301 cttcagtgtc cctccactca accagaggga gaatagagat gctaaggaac cactgactgg
361 aacaattctg gaaatgtggg atggagaaat ctaccattat ggcctgtatg ttgagcgagg
421 tcttgtgctg ggtgtgcaca aaccaccagc tgccataagc ctcgccaagg tcgaactaac
481 accactctcc ttgttctgga gacctgtgta caccccccag tacctcatct ctccagacac
541 cctcaagaaa ttgcacggag aaacgtttcc ctacacagcc tttgacaaca attgctacgc
601 cttttgttgt tgggtcctgg atctaaatga ctcgtggctg agtaggagaa tgatccagag
661 aacaactggc ttcttcagac cctaccaaga ctggaatagg aaacccctcc ccactatgga
721 tgattccaaa ttaaagaagg tagctaacat attcctgtgc gccctgtctt cgctattcac
781 caggcccata aaagacataa taggaaagct aagacctctc aacatcatca acatcctggc
841 ttcatgtgat tggactttcg caggcatagt ggagtctttg atactcttgg cagagctctt
901 tggagtcttc tggacacccc cagatgtgtc tgcgatgatt gcccccttac tcggtgactt
961 cgagttacaa ggacctgagg accttgtagt ggagctcgtc cctgtagtaa tggggggaat
1021 tggtttggtg ctgggattca ccaaagagaa gattgggaaa atgttgtcat ctgctgcatc
1081 caccttgaga gcttgtaaag atcttggtgc atatgggcta gagatcctaa agttagtcat
1141 gaagtggttc ttcccgaaga aagaggaggc aaatgaactg gctatggtga gatccatcga
1201 ggatgcagta ctggaccttg aggcaattga aaacaaccat atgaccacct tgctcaaaga
1261 caaagacagc ctagcaacct acatgagaac ccttgacctc gaggaagaga aagccagaaa
1321 actctcaacc aagtctgctt cacctgacat cgtgggcaca atcaacgccc ttctggcgag
1381 aatcgccgct gcacgctccc tggtgcaccg agcgaaggag gagctttcca gcagaccaag
1441 acctgtagtc ttgatgatat caggcagacc agggatagga aaaacccacc ttgctaggga
1501 agtggctaag agaatcgcag cctccctcac aggagaccag cgtgtaggcc tcatcccacg
1561 caatggcgtc gatcactggg atgcgtacaa gggggagagg gtcgtcctat gggacgacta
1621 tgggatgagc aaccccatcc acgacgccct taggctgcaa gaactcgctg acacttgccc
1681 ccttactcta aattgtgaca ggattgagaa caaaggaaag gtctttgaca gcgatgtcat
1741 cattatcacc actaatctgg ccaacccagc accactggac tatgtcaact ttgaagcgtg
1801 ctcgaggcgc attgatttcc tcgtgtatgc agaagccccc gaggtcgaaa aggcgaagcg
1861 tgacttcccg ggccaacctg acatgtggaa aaacgctttt agttctgatt tctcacacat
1921 aaaattggca ctggctccac aaggtggctt tgataagaac gggaacaccc cacacgggaa
1981 gggcgtcatg aagactctca ccactggctc cctcattgcc cgggcatcag ggctgctcca
2041 tgagagattg gatgagtttg aactacaggg cccagctctt accaccttca actttgaccg
2101 caacaaagtg cttgccttca gacagcttgc tgctgaaaac aaatatgggt tgatagacac
2161 aatgaaagtt gggaggcagc tcaaggatgt caaaaccatg ccagaactta aacaagcact
2221 caaaaacatc tcaatcaaga agtgccagat tgtgtatagt ggttgcacct acacacttga
2281 gtctgatggc aagggcaatg tgaaagttga caaaatccag agcacctccg tacagaccaa
2341 caatgagctt gctggcgccc tgcatcatct gaggtgcgcc agaatcaggt actatgtcaa
2401 gtgtgtccag gaggccctgt attctatcat ccagattgct ggggccgcat ttgtcaccac
2461 gcgcattatc aagcgtgtga acattcaaga cttatggtcc aagccacaag tggaaaacac
2521 agaggaggcc accaacaagg acgggtgctc aaaacccaaa gatgacgagg agttcgtcat
2581 ttcatctgac gacattaaaa ctgagggtaa gaaagggaag aacaagactg gccgtggcaa
2641 gaagcacaca gccttttcaa gtaaaggtct cagtgatgaa gagtatgatg agtacaagag
2701 aattagagag gaaaggaatg gcaggtattc catagaagag taccttcagg acagggacaa
2761 atactatgag gaggtggcca ttgccagggc gaccgaggaa gacttctgtg aagaggagga
2821 ggccaagatc cggcagagga tctttagacc aacaaggaaa caacgcaagg aagaaagagc
2881 ttctctcggt ttagtcacag gttctgagat taggaaaaga aacccagatg acttcaagcc
2941 taagggaaaa ctgtgggctg acgatgacag aagtgtggac tacaatgaga aactcagttt
3001 tgaggcccca ccaagcatct ggtcaaggat agtcaacttt ggttcaggtt ggggcttctg
3061 ggtctcccct agcctgttca taacatcaac ccacgtcata ccccagggcg caaaggagtt
3121 ctttggagtt cccatcaaac aaattcaggt acacaagtca ggcgaatttt gtcgcttgag
3181 gttcccaaaa ccaatcagga ctgacgtgac tggcatgatc ttggaagaag gtgcgcccga
3241 aggcaccgtg gtcacactac tcatcaaaag gtctactgga gaactcatgc ccctagcagc
3301 tagaatgggg acccatgcaa ccatgaaaat tcaagggcgc accgttggag gacagatggg
3361 catgcttctg acaggatcca acgccaaaag catggatcta ggcaccacac caggtgattg
3421 cggctgtccc tacatctaca agagaggaaa tgactatgtg gtcattggag ttcatacggc
3481 tgccgctcgt gggggaaaca ctgtcatatg tgccacccag gggggcgagg gggaagctac
3541 acttgagggt ggtgacagta agggaacata ctgtggtgca ccaatcctag gcccagggag
3601 tgccccaaaa cttagcacca aaaccaaatt ctggagatca tccacagcac cactcccacc
3661 tggcacctat gaaccagcat accttggtgg caaggacccc agagtcaagg gtggcccttc
3721 gttgcagcaa gtcatgaggg accagctgaa accatttaca gagcccaggg gtaagccgcc
3781 aaagccaagt gtgttagaag ctgccaagaa aaccatcatc aatgtcctcg aacaaacaat
3841 tgacccacct gagaagtggt cgttcgcaca agcttgcgcc tcccttgata agaccacttc
3901 tagcggccac ccgcaccata tgcggaaaaa cgactgctgg aatggggagt ccttcacagg
3961 caagctggca gaccaggctt ctaaggctaa cctgatgttt gaagaaggga agaacatgac
4021 cccagtctac acaggtgcac ttaaggatga attagtcaaa actgacaaaa tttatggtaa
4081 gatcaagaag aggcttctct ggggctcgga tttagcaacc atgatccggt gtgctcgagc
4141 attcggaggc ctaatggatg aacttaaggc acactgtgtc acacttccta ttagagttgg
4201 tatgaatatg aatgaggatg gccccatcat cttcgagaag cattccaggt acagatacca
4261 ctatgatgct gattactctc ggtgggattc aacacaacag agagccgtgc tggcagctgc
4321 tctagaaatc atggttaaat tctcctcaga accacatttg gctcaggtag tcgcagaaga
4381 tcttctttcc cctagcgtgg tggatgtggg tgacttcaca atatcaatca acgagggcct
4441 tccctctggg gtgccctgca cctcccaatg gaactccatc gcccactggc ttctcactct
4501 ttgtgcactc tccgaagtca caaatttgtc cccagacatc atacaggcta attctctctt
4561 ctccttctat ggtgatgatg aaattgttag tacagacata aaattggacc cagagaagtt
4621 gacagcaaag cttaaggaat atgggttgaa accaacccgc cctgacaaaa ctgaaggacc
4681 tctcgttatt tctgaagact tagatggttt gactttcctg cggagaactg tgacccgcga
4741 cccagctggt tggtttggaa aactggagca gagctcaata ctcaggcaaa tgtactggac
4801 taggggcccc aaccatgaag atccatctga atcaatgatt ccacactctc aaagacccat
4861 acaattgatg tccttactgg gagaggccgc actccacggc ccaacattct acagtaaaat
4921 cagcaaatta gtcattgcag agcttaaaga aggtggtatg gatttttacg tgcccaggca
4981 agagccaatg ttcagatgga tgagattctc agatctgagc acgtgggagg gcgatcgcaa
5041 tctggctccc agttttgtga atgaagatgg cgtcgaatga cgccaaccca actgatgggt
5101 ccgcagccaa cctcgtccca gaggtcagca atgaggttat ggctttggag cccgttgtcg
5161 gtgccgctat tgcggcgcct gtagcgggcc aacaaaatgt aattgacccc tggattagaa
5221 acaattttgt acaagcccct ggtggagagt tcacagtatc ccctagaaac gctccaggtg
5281 aaatactatg gagcgcgccc ttaggccctg atctgaaccc ctacctatcc catttggcca
5341 gaatgtataa tggttatgca ggtggttttg aagtgcaggt gatcctcgcg gggaacgcgt
5401 tcaccgccgg gaaaattata tttgcagcag tcccaccaaa ttttccaact gaaggcctga
5461 gtcccagcca ggtcactatg ttcccccaca taatagtaga tgttaggcaa ttagaacctg
5521 tgttgatccc cttacctgat gttaggaata acttctatca ctataatcaa acaaatgatt
5581 ctaccattaa attgatagca atgctgtata caccacttag ggccaataat gctggggaag
5641 atgtcttcac agtctcttgt cgagtcctca ctaggccgtc ccctgatttt gattttatat
5701 ttttggtgcc acccacagtt gagtcaagaa ctaaaccatt tactgtccca atcttaaccg
5761 ttgaagaaat gaccaattca agattcccca ttcctttgga aaagttgttc acgggtccca
5821 gcggtgcctt tgttgtccaa ccacaaaatg gcaggtgcac gactgatggc gtgctcttag
5881 gcactaccca actgtctcct gtcaacatct gcaccttcag aggggatgtc acccacattg
5941 caggttctcg taattacaca atgaatttgg catctctaaa ttggaacaat tatgacccaa
6001 cagaagaaat tccagcccct ctgggaactc cagatttcgt gggaaagatc caaggtgtgc
6061 tcacccaaac cacaaaagga gatggctcga cccgtggcca taaagctaca gtttacactg
6121 ggagtgcccc ctttacccca aagctgggca gtgttcaatt cagtactgac acagaaaatg
6181 attttgaaac tcaccaaaac acaaaattca ccccagtcgg tgtcatccag gatggtggta
6241 ccacccaccg aaatgaaccc caacaatggg tgctcccaag ttattcaggt agagatgttc
6301 ataatgtaca cctagcccct gctgtggccc ccacttttcc gggtgaacaa cttcttttct
6361 tcaggtccac tatgcccgga tgcagcgggt atcccaacat ggatttggat tgcctactcc
6421 cccaggagtg ggtgcagcac ttctaccaag aggcagctcc agcacaatct gatgtggctc
6481 tattgagatt tgtgaatcca gacacgggta gggtcctgtt tgagtgcaaa cttcataaat
6541 caggctatgt cacagtggct cacaccggtc agcatgattt ggtcatcccc cccaatggct
6601 attttaggtt tgattcctgg gttaatcagt tctacacgct tgcccccatg ggaaacggaa
6661 cggggcgtag gcgcgcctta taatggctgg agctttcttt gctggattgg catctgatgt
6721 ccttggctct ggacttggtt ccctaatcaa tgctggggct ggggccatca accaaaagat
6781 tgattttgaa aataatagaa aactgcagca agcttccttc cagtttagca gtaatctaca
6841 acaggcttcc tttcaacacg ataaagagat gctccaagca caaattgagg ccactaaaaa
6901 gttgcaacag gagatgatga aagtcaaaca ggcaatgctc ctagaaggtg gattctctga
6961 aacagatgca gcccgtgggg caatcaacgc ccccatgaca aaggttttgg actggagcgg
7021 aacaaggtac tgggcccctg acgctaggac cacaacatac aatgcaggcc gcttttccac
7081 ccctcaacct tcggggacgc tgccaggaag aatcaatccc agaactccta cccccgctcg
7141 gggctcctcc agcacatctt ctaatgcttc tactgctact tctatatatt caaatcaaac
7201 tgtttcaacg agacttggtt ctacagctgg ttctggtacc aatgtctcga gtctcccgtc
7261 aactgcaagg actaggagct gggttgagga tcaaaacaga aatttgtcac ctttcatgag
7321 gggggctcat aacatatcgt ttgtcacccc accatctagc agatcctcta gccaaggcac
7381 agtctcaacc gtgcctaaag aagttttgga ctcctggact ggc
//