Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| KC517369 | GII.4 Den Haag | |
|
|---|---|---|---|
| GII.P4 Den Haag |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS KC517369 7509 bp RNA linear VRL 02-APR-2015
DEFINITION Norovirus Hu/GII-4/Taoyuan/CGMH59/2012/TW ORF1, VP1, and VP2 genes,
complete cds.
ACCESSION KC517369
VERSION KC517369.1
KEYWORDS .
SOURCE Norovirus Hu/GII-4/Taoyuan/CGMH59/2012/TW
ORGANISM Norovirus Hu/GII-4/Taoyuan/CGMH59/2012/TW
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7509)
AUTHORS Chen,S.Y., Feng,Y., Chao,H.C., Lai,M.W., Huang,W.L., Lin,C.Y.,
Tsai,C.N., Chen,C.L. and Chiu,C.H.
TITLE Emergence in Taiwan of Novel Norovirus GII.4 Variants Causing Acute
Gastroenteritis and Intestinal Hemorrhage in Children
JOURNAL J. Med. Microbiol. (2015) In press
PUBMED 25752853
REMARK Publication Status: Available-Online prior to print
REFERENCE 2 (bases 1 to 7509)
AUTHORS Tsai,C.N., Lin,C.Y., Huang,W.L., Chen,Z.S., Chen,S.Y. and Chiu,C.H.
TITLE Direct Submission
JOURNAL Submitted (23-JAN-2013) Chang Gung University, Graduate Institute
of Clinical Medical Sciences, No. 259, Wenhua 1st Rd., Guishan
Township, Taoyuan County 333, Taiwan (R.O.C.)
COMMENT ##Assembly-Data-START##
Assembly Method :: Vector NTI v. 10
Sequencing Technology :: Sanger dideoxy sequencing
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7509
/organism="Norovirus Hu/GII-4/Taoyuan/CGMH59/2012/TW"
/mol_type="genomic RNA"
/isolate="Hu/GII-4/Taoyuan/CGMH59/2012/TW"
/isolation_source="feces"
/host="Homo sapiens"
/db_xref="taxon:1325213"
/geo_loc_name="Taiwan"
/collection_date="23-Apr-2012"
/note="genotype: GII.4"
CDS 1..5100
/codon_start=1
/product="ORF1"
/protein_id="AGK25907.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSSMAVTFKRALGARP
KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELSTVRQPE
ETSTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMMRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTM
PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSIQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEDATNKDGC
PKPKDIEEFVISSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGTEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVAGMILEEGAPEG
TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDGKGTYCGAPILG
PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYPRWD
STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLRPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5081..6703
/note="viral capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AGK25908.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFATVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFETDTENDFETHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRNVPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6703..7509
/note="minor capsid protein"
/codon_start=1
/product="VP2"
/protein_id="AGK25909.1"
/translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDREMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAVN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRVNPRTPTPARGSPNTSS
NASTATSLYLNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc
61 gcaaaatctt caagtgacaa aatgttttct agcatggctg tcacttttaa acgagccctc
121 ggggcgcggc ccaaacagcc ccccccgagg gaaataccac aaagaccccc acgaccacct
181 accccagaac tggtcaaaaa gatccctcct cccccgccca acggagagga tgaattagtg
241 gtttcttaca gtgccaaaga tggcgtttcc ggtttacctg agctctccac cgtcaggcaa
301 ccggaagaaa ctagtacggc cttcagtgtc cctccactca atcagaggga gaatagggat
361 gctaaggaac cactgactgg aacaattctg gaaatgtggg atggagagat ctaccattat
421 ggcctgtatg ttgagcgagg tcttgtgctg ggtgtgcaca aaccaccagc tgctattagc
481 ctcgccaagg tcgaactaac accactctcc ttgttctgga gacctgtgta cactcctcag
541 tacctcatct ctccagacac tctcaagaaa ttacacggag aaacattccc ctacacagcc
601 ttcgacaaca attgctatgc cttttgttgc tgggtcctgg atctaaacga ctcgtggctg
661 aacaggagaa tgatccagag aacaactggc ttcttcagac cttaccaaga ttggaatagg
721 aaacctctcc ccactatgga tgattccaaa ttaaagaagg tggctaatat attcctgtgc
781 accctgtctt cgctattcac caggcccata aaagacataa tagggaagtt aagacccctc
841 aacatcatca acatcctggc ttcatgtgat tggaccttcg caggcatagt ggagtccttg
901 atactcttgg cagagctctt tggagtcttc tggacacccc cagatgtgtc tgcgatgatt
961 gcccccttac tcggtgactt cgagttacaa ggacctgagg accttgtagt ggagctcgtc
1021 cctgtagtaa tggggggaat tggtttggtg ctagggttca ccaaagagaa aattggaaaa
1081 atgttgtcat ctgctgcatc taccttgaga gcttgtaaag atcttggtgc atatgggcta
1141 gagatcctaa agttagtcat gaagtggttc ttcccgaaga aagaagaagc aaatgaactg
1201 gctatgatga gatccatcga ggatgcagta ctggatcttg aagcaattga aaacaaccac
1261 atgaccacct tgctcaaaga caaagacagc ctggcaacct atatgagaac ccttgacctc
1321 gaggaagaaa aagccagaaa actctcaacc aaatctgctt cacctgacat cgtgggcaca
1381 atcaacgccc ttctggcgag aatcgccgct gcacgctcct tggtgcaccg agcgaaggag
1441 gagctctcca gcagaccaag acctgtagtc ttgatgatat caggcagacc aggaataggg
1501 aagacccacc ttgctaggga agtggctaag agaatcgcag cctccctcac aggagaccag
1561 cgtgtgggcc tcatcccacg caatggcgtc gaccactggg atgcgtataa gggggagagg
1621 gtcgtcctat gggacgacta cggaatgagc aatcccatcc acgacgccct caggctgcaa
1681 gaactcgctg acacctgccc cctcactcta aattgtgaca ggattgagaa taaagggaag
1741 gtctttgaca gcgatgtcat tatcatcact actaacctgg ccaacccagc accactggac
1801 tatgttaact ttgaggcgtg ctcgaggcgc attgatttcc tcgtgtatgc agaagccccc
1861 gaggtcgaaa aggcgaagcg tgacttcccg ggtcaacctg acatgtggaa aaacgctttt
1921 agttctgatt tctcacacat aaaactggca ttggctccac aaggtggctt tgataagaac
1981 gggaacaccc cacacgggaa gggcgtcatg aagaccctca ccactggctc cctcatcgcc
2041 cgggcatcag ggctactcca tgagagattg gatgagtttg aactacaggg cccagctctt
2101 accaccttca actttgaccg caacaaagtg cttgccttca ggcagcttgc tgctgaaaac
2161 aaatacgggt tgatggacac aatgaaagtt gggaggcagc tcaaggatgt caaaaccatg
2221 ccagaactta aacaagcact caagaatatc tcaatcaaga agtgccagat tgtgtatagt
2281 ggttgcacct acacacttga gtctgatggt aagggcaatg tgaaagttga cagagttcag
2341 agtacttcta ttcagaccaa caatgagctg gctggcgccc tgcatcacct aaggtgcgcc
2401 agaatcaggt actatgtcaa gtgtgttcag gaggccctgt attctatcat ccagattgct
2461 ggggctgcgt ttgtcaccac gcgcatcatc aagcgtgtga acattcaaga cttatggtcc
2521 aagccacaag tggaaaacac agaggatgcc accaacaagg acgggtgtcc aaaacccaaa
2581 gatattgagg agttcgtcat ttcatctgac gacattaaaa ctgagggtaa gaaagggaag
2641 aacaaatctg gccgtggcaa gaagcacacg gccttctcaa gtaaaggtct cagtgatgaa
2701 gagtatgatg agtacaagag aattagagag gaaaggaatg gcaagtactc catagaagag
2761 tacctacagg acagggacag atactatgag gaggtggcca ttgccagggc gaccgaggaa
2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tcttcagacc aacaaggaag
2881 caacgcaagg aagaaagggc ttctctcggt ttagtcacag gcactgaaat taggaaaagg
2941 aacccagaag acttcaagcc taaggggaaa ctatgggctg acgatgacag aagtgtggac
3001 tacaatgaaa aactcagctt tgaggcccca ccaagcattt ggtcaaggat agtcaacttt
3061 ggctcaggtt ggggcttctg ggtctccccc agcctgttca taacatcaac ccacgtcata
3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaattcaggt gcacaagtca
3181 ggcgaattct gtcgcttgag gttcccaaaa ccaatcagga ctgatgtggc tggcatgatc
3241 ttggaagaag gtgcgcccga aggcaccgtg gttacactac tcatcaaaag gtctactgga
3301 gaactcatgc ccctagcagc tagaatgggg acccatgcaa ccatgaagat tcaggggcgc
3361 actgttggag gtcagatggg catgcttctg acaggatcca acgccaaaag catggatcta
3421 ggcaccacac caggtgactg cggctgcccc tacatctaca agagagggaa tgactatgtt
3481 gtcattgggg tccacacggc tgccgctcgt gggggaaaca ctgtcatttg tgccacccaa
3541 gggggtgagg gggaagctac acttgaaggt ggtgacggta agggaacata ctgtggtgca
3601 ccaatcctag gcccagggag tgccccaaaa cttagcacca aaaccaaatt ctggagatca
3661 tccacagcac cactcccacc tggcacctat gaaccagcct acctaggtgg caaggatccc
3721 agggtcaagg gtggcccctc gttgcagcaa gtcatgaggg accagctgaa accatttaca
3781 gagcccaggg gtaagccacc aaagccaagt gtgttagaag ctgccaagaa aaccatcatc
3841 aatgtccttg aacaaacaat tgacccacct gagaagtggt cgttcgcaca agcttgcgcg
3901 tcccttgaca agaccacttc tagcggccat ccgcaccaca tgcggaaaaa cgactgctgg
3961 aacggggaat ccttcacggg caagctggca gaccaggctt ccaaagccaa cctgatgttt
4021 gaagagggga agaacatgac cccagtctac acaggtgcac ttaaggatga gttagtcaaa
4081 actgacaaaa tttatggtaa gatcaagaag aggcttctct ggggctcgga tttagcaacc
4141 atgatccggt gcgctcgagc attcggaggc ctaatggatg aactcaaagc acactgtgtc
4201 acacttccta tcagagttgg tatgaacatg aatgaggatg gtcccatcat cttcgagaag
4261 cattccaggt acagatacca ctatgatgct gattaccctc ggtgggattc aacacagcag
4321 agagccgtgt tggcagctgc tctagaaatc atggttaaat tctcctcaga accacatttg
4381 gctcaggtgg tagcagaaga cctcctttct cctagcgtgg tggatgtggg tgacttcaca
4441 atatcaatca acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc
4501 gcccactggc ttctcactct ctgtgcactc tccgaagtca caaatttgtc cccagacatc
4561 atacaggcta attctctctt ctccttctat ggtgatgatg aaattgttag tacagacata
4621 aaattagacc cagagaaatt gacagcaaag cttaaggaat acggattgag accaactcgc
4681 cctgataaaa ctgaaggacc tcttgttatc tctgaagact tagatggttt gaccttcctg
4741 cggagaaccg tgacccgcga cccagctggt tggtttggaa aactggagca gagctcaata
4801 ctcaggcaaa tgtactggac taggggcccc aaccatgaag atccatctga atcaatgatt
4861 ccacactctc aaagacccat acaattgatg tccttactgg gagaggccgc actccacggc
4921 ccaacattct acagcaaaat cagcaaatta gtcattgcag agctaaaaga aggtggtatg
4981 gatttttacg tgcccaggca agagccaatg ttcagatgga tgagattctc agatctgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat
5161 ggctttggag cccgttgtcg gtgccgctat tgcggcgcct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggagagt tcacagtatc
5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atctgaatcc
5341 ctacctatct catttggcca gaatgtataa tggttatgca ggtggttttg aagtgcaggt
5401 gattctcgcg gggaacgcgt tcaccgccgg aaaaattata tttgcaacag tcccaccaaa
5461 ttttccaact gaaggcttga gtcccagtca ggtcaccatg ttcccccata taatagtgga
5521 tgttaggcaa ttggaacctg tgttgatccc cttacctgat gttaggaata atttctacca
5581 ctataatcag tcaaatgatt ctaccattaa attgatagca atgctgtata caccacttag
5641 ggctaataat gctggggaag atgtcttcac agtctcttgt cgagttctca cgaggccatc
5701 ccctgacttt gatttcatat ttttggtgcc acctacagtt gagtcaagaa ctaagccatt
5761 tactgtccca atcctaactg ttgaagaaat gaccaactca aggttcccca ttcctttgga
5821 gaagttgttc acgggtccca gcagtgcctt tgttgttcaa ccacaaaatg gcagatgcac
5881 aactgatggc gtgctcttag gcaccaccca gctgtctcct gttaacatct gcaccttcag
5941 aggggatgtc acccacattg caggttctcg taattacaca atgaatttgg cttctctaaa
6001 ttggaacaac tatgacccaa cagaagaaat tccagcccct ctaggaactc cagatttcgt
6061 gggaaagatc caaggtgtgc tcactcaaac cacaaaggga gatggctcga cccgtggcca
6121 taaagctaca gtttacactg ggagtgcccc cttcactcca aagctgggca gtgtccaatt
6181 cgaaactgac acagaaaatg attttgaaac ccaccaaaac acaaaattca ccccagtcgg
6241 tgtcatccag gatggtggca ccacccaccg aaatgaacct caacaatggg tgctcccaag
6301 ttattcaggt agaaatgtcc ctaatgtaca cctagcccct gctgtagccc ccacttttcc
6361 gggtgaacaa ctccttttct ttaggtccac tatgcccgga tgcagcgggt atcccaacat
6421 ggacttggac tgcctgctac cccaggagtg ggtgcagcac ttctaccaag aggcagctcc
6481 agcacaatct gatgtggcgc tattgagatt tgtgaatcca gacacgggta gggtcctgtt
6541 tgagtgcaaa cttcataaat caggctatgt cacagtggcc cacaccggtc agcatgattt
6601 ggtcatcccc cccaatggtt attttaggtt tgattcctgg gttaaccaat tctacacgct
6661 tgcccccatg ggaaacggaa cggggcgtag acgtgctttg taatggctgg agctttcttt
6721 gctggattgg catctgatgt ccttagctct ggacttggtt ccctaatcaa tgctggggct
6781 ggggctatca accaaaagat tgattttgaa aataatagaa aattgcagca agcttccttc
6841 cagtttagca gtaatctaca acaggcttcc tttcaacatg acagagagat gcttcaagca
6901 caaattgagg ccactaaaaa gttgcaacag gaaatgatga aagtcaaaca ggcaatgctc
6961 ttagaaggtg gattctctga aacagatgca gcccgtgggg cagtcaacgc ccctatgaca
7021 aaggttttgg actggagcgg aacgaggtac tgggcccctg atgctaggac tacaacatac
7081 aatgcaggcc gtttttccac ccctcaacct tcaggggcat tgccaggaag agtcaatccc
7141 aggactccca cccccgctcg gggctccccc aacacatctt ctaatgcttc tactgctact
7201 tctttgtatt taaatcaaac tgtttcaacg agacttggtt cgacagctgg ttctggcacc
7261 aatgtctcga gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaagcaga
7321 aatttgtcac ctttcatgag gggggctcac aacatatcgt tcgtcacccc accatctagt
7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aagttttgga ctcctggact
7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaggcg gggggagtca
7501 cgggtgtaa
//