Typing tool
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Typing tool
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Complete norovirus genomes
| KC175402 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 3..5102
ORF2: 5083..6705
ORF3: 6705..7511
LOCUS KC175402 7511 bp ss-RNA linear VRL 13-MAR-2013
DEFINITION Norovirus Hu/Norwalk/20094/2009/VNM, complete genome.
ACCESSION KC175402
VERSION KC175402.1
DBLINK BioProject: PRJNA70471
KEYWORDS .
SOURCE Norovirus Hu/Norwalk/20094/2009/VNM
ORGANISM Norovirus Hu/Norwalk/20094/2009/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7511)
AUTHORS Madupu,R., Halpin,R.A., Ransier,A., Fedorova,N., Tsitrin,T.,
McLellan,M., Stockwell,T., Amedeo,P., Appalla,L., Bishop,B.,
Edworthy,P., Gupta,N., Hoover,J., Katzel,D., Li,K., Schobel,S.,
Shrivastava,S., Thovarai,V., Wang,S., My,P.V., Campbell,J.,
Farrar,J., Vinh,H., Hoang,N.V., Wentworth,D.E. and Baker,S.
TITLE Direct Submission
JOURNAL Submitted (17-OCT-2012) J. Craig Venter Institute, 9704 Medical
Center Drive, Rockville, MD 20850, USA
COMMENT Genome sequence lacks part of non-coding region.
##Assembly-Data-START##
Assembly Method :: clc_ref_assemble_long v. 3.22.55705
Coverage :: 446.3x
Sequencing Technology :: Illumina; 454
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7511
/organism="Norovirus Hu/Norwalk/20094/2009/VNM"
/mol_type="genomic RNA"
/strain="Hu/Norwalk/20094/2009/VNM"
/host="Homo sapiens; sex: M"
/db_xref="taxon:1261255"
/geo_loc_name="Viet Nam: Ho Chi Minh City"
/collection_date="02-Aug-2009"
/PCR_primers="fwd_name: Ampl_1_Forward, fwd_seq:
gtgaatgawgatggcgt, rev_name: Ampl_1_Reverse, rev_seq:
ttggttgagagyttyctg"
/PCR_primers="fwd_name: Ampl_2_Forward, fwd_seq:
ccgcaaaatcttcaagtg, rev_name: Ampl_2_Reverse, rev_seq:
cwacaggtcttggtctgctrga"
/PCR_primers="fwd_name: Ampl_3_Forward, fwd_seq:
tcaaccaartctgcttcacctg, rev_name: Ampl_3_Reverse, rev_seq:
ratcctttgccggatcttgg"
/PCR_primers="fwd_name: Ampl_4_Forward, fwd_seq:
ggcaagaagcacacagcctt, rev_name: Ampl_4_Reverse, rev_seq:
crrctctytgttgtgttgaatccc"
/PCR_primers="fwd_name: Ampl_5_Forward, fwd_seq:
tggyaagatcaagaagaggc, rev_name: Ampl_5_Reverse, rev_seq:
acaacaaargcacygctrgg"
/PCR_primers="fwd_name: Ampl_6_Forward, fwd_seq:
gagrccrtccccygattttg, rev_name: Ampl_6_Reverse, rev_seq:
atcaatyttgtcttttcaca"
/note="genotype: II"
gene 3..5102
/gene="POL"
CDS 3..5102
/gene="POL"
/note="genome polyprotein"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AFX81300.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSSMAVTFKRALGARP
KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE
ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRVAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTM
PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC
PKPKDNEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG
PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGRDPRVKDGPSLHQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQIYWTRGP
NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 3..992
/gene="POL"
/product="protein p48"
mat_peptide 993..2090
/gene="POL"
/product="NTPase"
/note="p41"
mat_peptide 2091..2627
/gene="POL"
/product="protein p22"
mat_peptide 2628..3026
/gene="POL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 3027..3569
/gene="POL"
/product="3C-like protease"
/note="3CLpro; calicivirin"
mat_peptide 3570..5099
/gene="POL"
/product="RNA-directed RNA polymerase"
gene 5083..6705
/gene="VP1"
CDS 5083..6705
/gene="VP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AFX81301.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNVPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6705..7511
/gene="VP2"
CDS 6705..7511
/gene="VP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AFX81302.1"
/translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYSAGRFSTPQPSGALPGRTNPRAPIPARGSPSTSS
GASTATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 gaatgaagat ggcgtctaac gacgcttccg ctgccgctgt tgctaacagc aacaacgaca
61 ccgcaaaatc ttcaagtgac aaaatgtttt ctagcatggc tgtcactttt aaacgagccc
121 tcggggcgcg gcctaaacag ccccccccga gggaaatacc acaaagaccc ccacgaccac
181 ctactccaga actggtcaaa aagatccctc ctcccccgcc caacggagag gatgaagtag
241 tggtctctta cagtgccaaa gatggcgttt ccggcttgcc tgagctttcc accgtcaggc
301 aaccggaaga aaccaatacg gccttcagtg tccctccact caaccagagg gagaataggg
361 atgctaagga accactgact ggaacaattc tggagatgtg ggacggagaa atctaccatt
421 atggcctgta tgttgagcga ggtcttgtgc tgggtgtgca caaaccacca gctgccatta
481 gcctcgccaa ggtcgaatta acaccactct ccttgttctg gagacctgtg tacactcctc
541 agtacctcat ctctccagac actctcaaga aattacacgg agaaacattt ccctacacag
601 ccttcgacaa caattgctat gccttttgct gctgggtcct ggatctaaac gactcgtggc
661 tgagtaggag aatgatccag agaacaactg gcttcttcag accctaccaa gattggaata
721 ggaaacccct ccccactatg gatgattcca aattaaagaa ggtagctaac atattcctgt
781 gcaccctgtc ttcgctattc acaaggccca taaaagacat aatagggaag ttaaggcctc
841 tcaacatcat caacatcctg gcttcatgtg attggacttt cgcaggcata gtggagtcct
901 tgatactctt ggcagagctc tttggagtct tctggacacc cccagatgtg tctgcgatga
961 ttgccccctt actcggtgat ttcgagttac aaggacctga ggaccttgta gtggagctcg
1021 tccctgtagt aatgggggga attggcttgg tgctaggatt caccaaagag aagattggaa
1081 aaatgttgtc atctgctgca tccaccttga gagcttgtaa agatcttggt gcgtatgggc
1141 tagagatcct aaagttagtc atgaagtggt tcttcccgaa gaaagaggaa gcaaatgaac
1201 tggctatggt gagatccatc gaggatgcag tgctggatct tgaggcaatt gaaaacaacc
1261 atatgaccac cttgctcaaa gacaaagaca gcctggcaac ctatatgaga acccttgacc
1321 tcgaggaaga gaaagccaga aaactctcaa ccaagtctgc ttcacctgac atcgtgggta
1381 caatcaacgc ccttctggcg agaatcgccg ctgcacgctc cctggtgcac cgagcgaagg
1441 aggagctttc cagcagacca agacctgtag tcttgatgat atcaggcaga ccaggaatag
1501 gtaagaccca ccttgccagg gaagtggcta agagagtcgc agcctctctc acaggagatc
1561 agcgtgtagg cctcatccca cgcaatggcg tcgatcactg ggatgcgtac aagggggaga
1621 gggtcgtcct atgggacgac tatggaatga gtaatcccat ccacgacgcc ctcaggctgc
1681 aagaactcgc tgacacttgc cccctcactc taaattgtga caggattgag aataaaggaa
1741 aggtctttga cagcgatgtc atcatcatca ctactaacct ggccaaccca gcaccactgg
1801 attatgtcaa ctttgaagcg tgctcgaggc gcatcgattt cctcgtgtat gcagaagccc
1861 ccgaggtcga aaaggcaaag cgtgacttcc cgggccaacc tgacatgtgg aaaaacgctt
1921 ttagttctga cttctcacac ataaaattgg cactggctcc gcaaggtggc tttgacaaga
1981 acgggaacac cccacacggg aagggcgtca tgaagactct caccactggc tccctcattg
2041 cccgggcatc agggctgctc catgagagat tggatgagtt tgaactacag ggcccagccc
2101 ttaccacctt caactttgat cgcaacaaag tgcttgcctt caggcagctt gctgctgaaa
2161 acaaatacgg gttgatggac acaatgaaag ttgggaggca gctcaaggat gtcaaaacca
2221 tgccagaact taaacaagca ctcaagaata tctcaatcaa gaagtgccag attgtgtata
2281 gtggttgcac ctacacactt gagtctgatg gcaagggcaa tgtgaaagtt gacagagttc
2341 agagcacctc cgttcagacc aacaatgagc tggctggcgc cctgcaccat ctaaggtgcg
2401 ccagaatcag gtactatgtc aagtgtgttc aggaggccct gtattctatc atccagattg
2461 ctggggctgc atttgtcacc acgcgcatca tcaagcgtgt gaatattcaa gacttgtggt
2521 ccaagccaca agtggaaaac acagaggagg ccaccaacaa ggacgggtgc ccaaaaccca
2581 aagataatga ggagttcgtc atttcatctg acgacattaa aactgagggt aagaaaggga
2641 agaacaagac tggccgtggc aagaagcaca cagccttctc aagtaaaggt ctcagtgatg
2701 aagagtatga tgagtacaag agaattagag aggaaaggaa tggcaagtac tccatagaag
2761 agtaccttca ggacagggac aaatactatg aggaggtggc cattgccagg gcgaccgagg
2821 aagacttctg tgaagaggag gaggccaaga tccggcaaag gatcttcaga ccaacaagga
2881 aacaacgcaa ggaagaaaga gcttctctcg gtttggtcac aggttctgaa atcaggaaaa
2941 ggaacccaga agacttcaag cccaagggga aactatgggc tgacgatgac agaagtgtgg
3001 actacaatga aaaactcagc tttgaggccc caccaagcat ctggtcaagg atagtcaact
3061 ttggctcagg ttggggcttc tgggtctcac ccagcctgtt tataacatca acccacgtca
3121 taccccaggg cgcgaaggag ttctttggag tccccatcaa gcaaattcag gtacacaagt
3181 caggcgaatt ctgtcgcttg aggttcccaa aaccaatcag gactgatgtg actggcatga
3241 tcttggaaga aggtgcgccc gaaggcaccg tggtcacact actcatcaaa aggtctactg
3301 gagaactcat gcccctagcg gctagaatgg ggacccatgc aaccatgaaa attcaagggc
3361 gcactgttgg aggtcagatg ggcatgcttc tgacagggtc caacgccaaa agcatggatc
3421 taggcaccac accaggtgat tgcggctgtc cctacatcta caagagagga aatgactatg
3481 tggtcattgg agtccacacg gctgccgctc gtgggggaaa cactgtcata tgtgccacac
3541 aagggggtga gggggaagct acacttgaag gtggtgacag taagggaaca tactgtggtg
3601 caccaatcct aggcccaggg agtgccccaa aacttagtac caaaaccaaa ttctggagat
3661 catccacagc accactccca cctggcacct atgagccagc ctaccttggt ggcagggacc
3721 ccagagtcaa ggatggcccc tcgttgcatc aagtcatgag ggaccagctg aaaccattta
3781 cagagcctag gggcaaacca ccaaagccaa gtgtgttaga agctgccaag aagaccatca
3841 tcaatgtcct tgaacaaaca attgacccac ctgagaagtg gtcgttcgca caagcttgcg
3901 cgtcccttga caagaccact tctagcggcc atccgcacca catgcggaaa aacgactgct
3961 ggaacgggga gtccttcaca ggcaaattgg cagaccaggc ttccaaggcc aacctgatgt
4021 ttgaagaagg gaagaacatg accccagtct acacaggtgc acttaaggat gaattagtca
4081 aaactgacaa aatttatggt aagatcaaga agaggcttct ctggggctcg gatttggcaa
4141 ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg
4201 tcacacttcc tatcagagtt ggtatgaata tgaatgagga tggccccatc atcttcgaga
4261 agcattccag gtacagatac cactatgatg ctgattactc tcggtgggat tcaacacaac
4321 agagagccgt gctggcagct gctctagaaa tcatggttaa attctcctca gaaccacatt
4381 tggctcaggt agtagcagaa gaccttcttt ctcctagcgt ggtggacgtg ggtgacttca
4441 caatttcaat caacgagggt cttccctctg gggtgccctg cacctcccaa tggaactcca
4501 tcgcccactg gcttcttact ctctgtgcac tctccgaagt tacaaatttg tccccagaca
4561 ccatacaggc taattctctc ttctccttct atggtgatga tgaaattgtt agtacagaca
4621 taaaattaga cccagagaag ttgacagcaa agcttaaaga atacgggttg aaaccaaccc
4681 gccctgataa aactgaagga cctcttgtta tttctgaaga cttagatggt ttgactttcc
4741 tgcggagaac tgtgacccgc gacccagctg gttggtttgg aaaactggag cagagctcaa
4801 tactcaggca aatatactgg actaggggcc ccaaccatga agatccatct gaatcaatga
4861 ttccacactc tcaaagaccc atacaattga tgtctttact gggagaggcc gcactccacg
4921 gcccaacatt ctacagtaaa atcagcaaat tagtcattgc agagctaaaa gaaggtggta
4981 tggattttta cgtgcccagg caagagccaa tgttcagatg gatgagattc tcagatctga
5041 gcacgtggga gggcgatcgc aatctggctc ccagttttgt gaatgaagat ggcgtcgagt
5101 gacgccaacc catctgatgg gtccgcagcc aacctcgtcc cagaggtcaa caatgaggtt
5161 atggctttgg agcccgttgt cggtgccgct attgcggcgc ctgtagcggg ccaacaaaat
5221 gtaattgacc cctggattag aaataatttt gtacaagccc ctggtggaga gttcacagtg
5281 tcccctagaa acgctccagg tgaaatacta tggagcgcgc ccttaggccc tgacctgaat
5341 ccctacctat ctcatttggc cagaatgtat aatggttatg caggtggttt tgaagtgcag
5401 gtgatcctcg cggggaacgc gttcaccgcc ggaaaaatta tatttgcagc agtcccacca
5461 aattttccaa ctgaaggctt gagtcccagc caggtcacta tgttccccca cataatagtg
5521 gatgttaggc aattggaacc tgtgttgatc cccttacctg atgttaggaa caacttctat
5581 cactataacc agtcaaatga ttctaccatt aaactgatag caatgctgta tacaccactt
5641 agggctaata atgctgggga agatgtcttc acagtctctt gtcgagttct cacgaggcca
5701 tcccctgatt ttgattttat atttttggtg ccacctacag ttgagtcaag aactaaacca
5761 tttactgtcc caatcttaac tgttgaagaa atgaccaatt caaggttccc cattcctttg
5821 gaaaaattgt tcacgggtcc cagcagtgcc tttgttgttc aaccacaaaa tggcagatgc
5881 acgactgatg gcgtgctctt aggcaccacc caactgtctc ctgtcaacat ctgcaccttc
5941 agaggggatg tcacccacat tgcaggttct cgtaattaca caatgaattt ggcttctcta
6001 aactggaaca attatgaccc aacagaagaa attccagctc ctctaggaac tccagatttc
6061 gtgggaaaga tccaaggtgt gctcactcaa accacaaagg gagatggttc gacccgtggc
6121 cataaagcca cagtttacac tgggagtgcc ccctttactc caaagctggg cagtgttcaa
6181 ttcagcaccg acacagaaaa tgattttgaa actcaccaaa acacaaaatt caccccagtc
6241 ggcgtcatcc aggatggtag caccacccac cgaaatgaac ctcaacaatg ggtgctccca
6301 agttattcag gtagaaatgt ccctaatgta cacctagccc ctgctgtagc ccccactttt
6361 ccgggtgaac aacttctctt ctttaggtcc actatgcccg gatgcagcgg gtatcccaac
6421 atggatttgg attgcctact cccccaggag tgggtgcagc acttctacca agaggcagct
6481 ccagcacaat ctgatgtggc tctattaaga tttgtgaatc cagacacggg tagggtcctg
6541 tttgagtgca aacttcataa atcaggctat gtcacagtgg ctcacaccgg ccagcatgat
6601 ttggtcatcc cccccaatgg ttattttagg tttgattcct gggttaatca attctacaca
6661 cttgccccca tgggaaatgg aacggggcgt agacgtgctt tataatggct ggagctttct
6721 ttgctggatt ggcatctgat gtccttagct ctggacttgg ttccctaatc aatgctgggg
6781 ctggggctat caaccaaaag attgattttg aaaataacag aaaactgcag caagcttcct
6841 tccaatttag tagtaatcta caacaggctt cctttcaaca tgataaggag atgctccaag
6901 cacaaattga ggccactaaa aagttacaac aggaaatgat gaaagtcaaa caggcaatgc
6961 tcttagaagg tggattctct gaaacagatg cagcccgtgg ggcaatcaat gcccctatga
7021 caaaggcttt ggactggagc ggaacaaggt actgggcccc tgatgctagg actacaacat
7081 atagtgcagg ccgtttttct acccctcaac cttcgggggc actgccagga agaaccaatc
7141 ccagggcccc tatccccgcc cggggctccc ccagcacatc ttctggtgct tctactgcta
7201 cttctatata ttcaaatcaa actgtttcaa cgagacttgg ttctacagct ggttctggca
7261 ccaatgtctc gagtctcccg tcaactgcaa ggactaggag ttgggttgag gatcaaaaca
7321 ggaatctgtc accttttatg aggggggctc acaacatatc gtttgtcacc ccaccatcta
7381 gcaggtcctc tagccaaggc acagtctcaa ccgtgcctaa agaagttttg gactcctgga
7441 ctggcgcttt caatacgcgc aggcagcctc tcttcgctca cattcgtagg cgaggggagt
7501 cacgggtgta a
//