Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| KC409263 | GII.4 Den Haag | |
|
|---|---|---|---|
| GII.P4 Den Haag |
ORF1: 3..5102
ORF2: 5083..6705
ORF3: 6705..7511
LOCUS KC409263 7511 bp ss-RNA linear VRL 13-MAR-2013
DEFINITION Norovirus Hu/GII/20173/2009/VNM, complete genome.
ACCESSION KC409263
VERSION KC409263.1
DBLINK BioProject: PRJNA70471
KEYWORDS .
SOURCE Norovirus Hu/GII/20173/2009/VNM
ORGANISM Norovirus Hu/GII/20173/2009/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-DEC-2012) J. Craig Venter Institute, 9704 Medical
Center Drive, Rockville, MD 20850, USA
COMMENT This work was supported by the National Institute of Allergy and
Infectious Diseases (NIAID), Genome Sequencing Centers for
Infectious Diseases (GSCID) program.
The genome sequence was generated using overlapping PCR amplicons
spanning the genome. The amplicons were pooled by sample and then
barcoded and sequenced using Next Generation Sequencing platforms.
The consensus sequences of the internal PCR primer hybridization
sites were manually verified using reads from amplicons that
spanned across the sites.
Genome sequence lacks part of non-coding region.
##Genome-Assembly-Data-START##
Current Finishing Status :: Finished
Assembly Method :: clc_ref_assemble_long v. 3.22.55705
Genome Coverage :: 361.1x
Sequencing Technology :: Illumina; 454
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7511
/organism="Norovirus Hu/GII/20173/2009/VNM"
/mol_type="genomic RNA"
/strain="Hu/GII/20173/2009/VNM"
/host="Homo sapiens; sex: F"
/db_xref="taxon:1291834"
/geo_loc_name="Viet Nam: Ho Chi Minh City"
/collection_date="24-Sep-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="AGE89507.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSSMAVTFKRALGARP
KQPPPREIPQRPPRPPTPELVKKVPPPPPNGEDEVVVSYSAKDGISGLPELSTVRQPE
ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTTDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGRQLKDVKTM
PELKQALKSISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC
PKPKDDEEFVITSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG
PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKSMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
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; calcivirin"
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="AGE89508.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRDYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFEAHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
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="AGE89509.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGSLPGRINPRAPTPARASSSISS
NASTVTSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 gaatgaagat ggcgtctaac gacgcttccg ctgccgctgt tgctaacagc aacaacgaca
61 ccgcaaaatc ttcaagtgac aaaatgtttt ctagcatggc tgtcactttt aaacgagccc
121 tcggggcgcg gcctaaacag cctcccccga gggaaatacc gcaaagaccc ccacgaccac
181 ctactccaga actggtcaaa aaggtccctc ctcccccgcc caacggagag gatgaagtag
241 tggtttctta tagtgccaaa gatggcattt ctggtctacc tgagctttcc accgtcagac
301 aaccagaaga aaccaatacg gccttcagtg tccctccact caatcagagg gagaataggg
361 atgctaagga accactgact ggaacaattc tggaaatgtg ggatggggaa atctatcatt
421 atggcctgta tgttgaacga ggtcttgtgc tgggtgtgca caaaccacca gctgccatta
481 gcctcgccaa ggtcgaacta acaccactct ccttgttctg gagacctgtg tacaccccac
541 agtacctcat ctctccagac actctcaaga aattacacgg agaaacattt ccctacacag
601 cctttgacaa caactgctat gccttttgtt gctgggtcct ggatctaaac gactcgtggc
661 tgagtaggag aatgatccag agaacaactg gcttcttcag accctaccaa gattggaata
721 ggaaacccct ccctactacg gatgattcca aattaaagaa ggtagctaac atattcctgt
781 gcaccctgtc ttcgctattc accaggccca taaaagacat aataggaaag ttaaggcctc
841 tcaacatcat caacatcctg gcttcatgtg actggacttt cgcaggcatc gtggagtcct
901 tgatactctt ggcagagctc tttggagtct tctggacacc cccagatgtg tctgcgatga
961 ttgccccctt actcggtgat ttcgagttac aaggacctga ggaccttgta gtggagctcg
1021 tccctgtggt aatgggggga attggtttgg tgctgggatt caccaaagag aagattggaa
1081 aaatgttgtc atctgctgca tccaccttga gagcttgtaa agatctcggt gcatatgggc
1141 tagagatcct aaagttagtc atgaagtggt tcttcccgaa gaaagaggag gcaaatgaac
1201 tggctatggt gagatccatc gaggatgcag tactggacct tgaggcaatt gaaaacaacc
1261 atatgaccac cttgctcaaa gataaagaca gcctggcaac ctacatgaga acccttgacc
1321 tcgaggaaga gaaagccaga aaactctcaa ccaagtctgc ttcacctgac atcgtgggca
1381 caatcaacgc ccttctggcg agaatcgccg ctgcacgctc cctggtgcac cgagcgaagg
1441 aggagctttc cagcagacca agacctgtgg tcttgatgat atcaggtaga ccagggatag
1501 ggaagaccca ccttgctagg gaagtggcta agagaatcgc agcctccctc acaggagacc
1561 agcgcgtagg cctcatccca cgcaatggcg tcgatcactg ggatgcgtac aagggggaga
1621 gggtcgtcct atgggacgac tatggaatga gcaatcccat ccacgacgcc ctcaggctgc
1681 aagaactcgc tgacacttgc cccctcactc taaattgtga caggattgag aataaaggaa
1741 aggtctttga cagcgatgtc atcattatca ctaccaatct ggccaaccca gcaccactgg
1801 actatgtcaa ctttgaagcg tgctcgaggc gcatcgattt cctcgtgtac gcagaagccc
1861 ccgaggtcga aaaggcgaag cgtgacttcc cgggccaacc tgacatgtgg aaaaacgctt
1921 ttagttctga tttctcacac ataaaattgg cactggctcc acaaggtggc ttcgataaga
1981 acgggaacac cccacatggg aagggcgtca tgaagactct caccactggc tcccttattg
2041 cccgggcatc agggctgctc catgagagat tggatgagtt tgaactacag ggcccagctc
2101 tcaccacctt caactttgac cgcaacaaag tgcttgcctt caggcagctt gctgctgaaa
2161 acaaatacgg gttgatggac acaatgagag ttgggaggca gctcaaggat gtcaaaacca
2221 tgccagaact taaacaagca ctcaagagca tctcaatcaa gaagtgtcag attgtgtaca
2281 gtggttgcac ctacacactt gagtctgatg gcaagggcaa tgtgaaggtt gacagagttc
2341 agagcacctc cgtacagacc aacaatgagc tggctggcgc cctgcaccat ctgaggtgcg
2401 ccagaatcag gtactatgtt aagtgtgtcc aggaggccct gtattctatc attcagattg
2461 ctggggctgc attcgtcacc acgcgcatca tcaagcgtgt gaacattcaa gacttatggt
2521 ccaagccaca agtggaaaac acagaggaag ccaccaacaa ggacgggtgc ccaaaaccca
2581 aagatgatga ggagttcgtc attacatctg acgacattaa aactgagggt aagaaaggaa
2641 agaacaagac tggccgtggt 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 gtttagtcac aggttctgaa attaggaaaa
2941 gaaacccaga tgacttcaag cccaagggga aactatgggc tgacgatgac agaagtgtgg
3001 actacaatga gaaactcagt tttgaggctc cgccaagcat ctggtcaagg atagtcaact
3061 ttggctcagg ttggggcttc tgggtctccc ccagcctatt cataacatca acccacgtca
3121 taccccaggg cgcaaaggag ttctttggag tccccatcaa acaaattcag gtgcacaagt
3181 caggcgaatt ctgtcgcttg aggttcccaa aaccaatcag gactgatgtg actggcatga
3241 tcttggaaga aggcgcgcct gaaggcaccg tggccacact actcatcaaa aggtctactg
3301 gagaactcat gcccctagca gccagaatgg ggacccacgc aaccatgaag attcaagggc
3361 gcactgttgg aggtcagatg ggcatgcttc tgacaggatc caacgccaaa agcatggatc
3421 taggcaccac accaggtgat tgcggctgtc cctacatcta caagagagga aatgactatg
3481 tggtcattgg agtccacacg gctgccgctc gtgggggaaa cactgtcata tgtgccaccc
3541 aggggggtga gggggaagct acacttgaag gtggtgacag taagggaacg tactgcggtg
3601 cgccaatcct aggcccaggg agcgccccaa aacttagcac caaaaccaaa ttctggagat
3661 cgtccacagc accactccca cctggcacct atgagccagc ctaccttggt ggcaaggacc
3721 ccagagtcaa gggtggcccc tcgctgcagc aagtcatgag agaccagctg aaaccattca
3781 cagagcccag gggtaagcca ccaaagccaa gtgtgttaga agctgccaag aaaaccatca
3841 tcaatgttct tgaacaaaca attgacccac ctgagaagtg gtcgttcgca caggcttgcg
3901 cgtcccttga caagaccact tctagcggcc atccgcacca catgcggaaa aacgactgct
3961 ggaacgggga gtccttcaca ggcaagctgg cggaccaggc ttccaaggcc aacctgatgt
4021 ttgaagaagg gaagagcatg accccagttt acacaggtgc gctcaaggat gagttagtca
4081 aaactgacaa aatttatggc aagatcaaga agaggcttct ctggggctcg gatttagcaa
4141 ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg
4201 tcacacttcc tatcagagtt ggtatgaata tgaatgagga tggccccatc atcttcgaga
4261 agcactccag gtacaggtac cactatgatg ctgattactc tcggtgggat tcaacacaac
4321 agagagccgt gctggcagct gctctagaaa ttatggttaa attctcctca gaaccacatt
4381 tggctcaggt ggtcgcagaa gaccttcttt ctcctagcgt ggtggatgtg ggtgacttca
4441 caatatcaat caatgagggt cttccctctg gggtgccctg cacttcccaa tggaactcca
4501 tcgcccactg gcttctcact ctatgtgcac tctccgaagt tacaaatttg tccccagaca
4561 tcatacaggc taattctctc ttctccttct atggtgatga tgaaattgtt agtacagaca
4621 taaaactaga cccagagaag ttgacagcaa agcttaagga gtatgggtta aaaccaaccc
4681 gccctgacaa aactgaagga cctcttgtta tttctgaaga cttagatggt ttgactttcc
4741 tgcggagaac tgtgacccgc gacccagctg gttggtttgg aaaactggag cagagctcaa
4801 tactcaggca aatgtactgg actaggggcc ccaaccatga agatccatct gaatcaatga
4861 tcccacactc tcaaagaccc atacaattga tgtccctgct gggagaggcc gcactccacg
4921 gcccaacatt ctatagtaaa atcagcaaat tagtcattgc agagctaaaa gaaggtggta
4981 tggattttta cgtgcccagg caagagccaa tgttcagatg gatgagattc tcagatctga
5041 gcacgtggga gggcgatcgc aatctggctc ccagctttgt gaatgaagat ggcgtcgaat
5101 gacgccaacc catctgatgg gtccgcagcc aacctcgtcc cagaggtcaa caatgaggtt
5161 atggctttgg agcccgttgt cggtgccgct attgcggcgc ctgtagcggg ccaacaaaat
5221 gtaattgacc cctggattag gaataatttt gtacaagccc ctggtggaga attcacagta
5281 tcccctagaa acgctccagg tgaaatacta tggagcgcgc ccttaggccc tgatctgaat
5341 ccctacctat ctcatttggc cagaatgtat aatggttatg caggtggctt tgaagtgcag
5401 gtgatcctcg cggggaacgc gttcaccgcc ggaaaaatta tatttgcagc agttccacca
5461 aattttccaa ctgaaggctt gagccccagc caggttacta tgttccccca cataatagta
5521 gatgttaggc aactggagcc tgtgttgatc cccttacctg atgttaggaa taacttctat
5581 cattataatc agtcaaatga ttctaccatt aaactgatag caatgctgta cacaccactt
5641 agggctaata atgctgggga agatgtcttc acagtctctt gtcgagtcct cacgaggcca
5701 tcccctgatt ttgattttat atttttggtg ccacctacag ttgagtcaag aactaaacca
5761 tttactgtcc caatcttaac tgttgaagaa atgaccaatt caagattccc catccctttg
5821 gaaaagttgt tcacgggccc cagcggtgcc tttgttgttc aaccacaaaa tggtagatgc
5881 acgactgatg gcgtgctctt aggcaccacc caactgtctc ctgtcaacat ctgcaccttc
5941 agaggggatg tcacccacat tgcaggttct cgcgattaca cgatgaattt ggcttctcta
6001 aattggaata attatgaccc aacagaagaa attccagccc ctctgggaac tccagatttc
6061 gtgggaaaga tccaaggtgt gctcactcaa accacaaagg gagatggctc gacccgtggc
6121 cataaagcta cagtttacac tgggagtgcc ccctttactc caaagctggg cagtgtccaa
6181 ttcagtactg acacagaaaa tgattttgaa gctcaccaaa acacaaaatt caccccagtc
6241 ggtgtcatcc aggatggtgg caccacccac cgaaatgaac cccaacaatg ggtgctccca
6301 agttattcag gtagagatgt ccacaatgta cacctggccc ctgctgtagc ccccactttt
6361 ccgggtgaac aacttctttt cttcaggtcc actatgcccg gatgcagtgg gtatcccaac
6421 atggatttgg attgcctact cccccaggag tgggtgcagc acttctacca agaggcagct
6481 ccagcacaat ctgatgtggc tctattgaga tttgtgaatc cagacacggg tagggtcctg
6541 tttgagtgca aacttcataa atcaggctat gtcacagtgg ctcacaccgg ccagcatgat
6601 ttggtcatcc cccccaatgg ctattttagg tttgattcct gggttaatca attctacaca
6661 cttgccccca tgggaaatgg aacggggcgt agacgtgctt tataatggct ggggctttct
6721 ttgctggatt ggcatctgat gtccttggct ctggacttgg ctccctaatc aatgctgggg
6781 ctggggctat taaccaaaag attgattttg aaaataacag aaaattgcag caagcttcct
6841 tccagtttag cagtaatcta caacaggcct cctttcaaca tgacaaagag atgctccaag
6901 cacaaattga ggccactaaa aagttgcaac aggaaatgat gaaagtcaaa caggcaatgc
6961 tcttagaagg tgggttctct gaaacagatg cagctcgtgg ggcaatcaac gcccccatga
7021 caaaggtttt ggactggagc ggaacaaggt actgggcccc tgatgctagg actacaacat
7081 acaatgcagg ccgcttttcc acccctcaac cctcggggtc attgccagga agaatcaatc
7141 ccagggctcc tacccccgct cgggcctcct ccagtatatc ctctaatgct tctactgtta
7201 cttctatata ttcaaatcaa actgtttcaa cgagacttgg ttctacagct ggctctggca
7261 ccaatgtctc gagtctcccg tcaactgcaa ggactaggag ttgggttgag gatcaaaaca
7321 gaaatttgtc acctttcatg aggggggctc acaacatatc gtttgtcacc ccaccatcta
7381 gcagatcctc tagccaaggc acagtctcaa ccgtgcctaa agaagttttg gactcctgga
7441 ctggcgcttt caacacgcgc aggcagcctc tcttcgctca cattcgtagg cgaggggagt
7501 cacgggtgta a
//