Typing tool
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Typing tool
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Complete norovirus genomes
| KC576915 | GII.4 | |
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| GII.P39 |
ORF1: 1..5072
ORF2: 5053..6672
ORF3: 6672..7064
LOCUS KC576915 7064 bp ss-RNA linear VRL 07-FEB-2014
DEFINITION Norovirus Hu/GII.4/KL45/1978/MYS, partial genome.
ACCESSION KC576915
VERSION KC576915.1
DBLINK BioProject: PRJNA70471
KEYWORDS .
SOURCE Norovirus Hu/GII.4/KL45/1978/MYS
ORGANISM Norovirus Hu/GII.4/KL45/1978/MYS
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7064)
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., Kim,M., Bok,K.,
Sosnovtsev,S.V., Wentworth,D.E. and Green,K.Y.
TITLE Direct Submission
JOURNAL Submitted (01-FEB-2013) 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-Assembly-Data-START##
Current Finishing Status :: Finished
Assembly Method :: clc_ref_assemble_long v. 3.22.55705
Genome Coverage :: 431.8x
Sequencing Technology :: Sanger; Illumina; 454
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7064
/organism="Norovirus Hu/GII.4/KL45/1978/MYS"
/mol_type="genomic RNA"
/strain="Hu/GII.4/KL45/1978/MYS"
/host="Homo sapiens; sex: M"
/db_xref="taxon:1292148"
/country="Malaysia: Kuala Lumpur"
/collection_date="23-Mar-1978"
/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.4"
gene <1..5072
/gene="POL"
CDS <1..5072
/gene="POL"
/note="genome polyprotein"
/codon_start=3
/product="putative nonstructural polyprotein"
/protein_id="AGE99611.1"
/translation="AAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKHPPPREIPQ
RPPRPPTPELIKKVPPPPPNGEEEPVVSYNVKDGVSGLPELSTVRQPDENNTAFSVPP
LNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLS
LFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRT
TGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNILNIL
ASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVM
GGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEASELAM
VRSIEDAVLDLEAIENNHLTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGT
INALLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLARELAKKIATTLTG
DQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIE
NKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKAKRDFPGQPD
MWKNAFSPDFSHIKLMLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDE
YELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGGQLKGVRTMPELKQALKNI
SIKKCQIVYGGSTYTLESDGKGSVRVDKVQSATVQTNNELAGALHHLRCARIRYYVKC
VQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQLEDTGEATSKDGCPKPKDEEEFV
VSSDDIKAEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQD
RDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNP
DDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVI
PQGTQEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIKRP
TGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRG
NDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPKLSTK
TKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKQPKPSVL
EAAKRTIINVLEQTIDPPQKWTFAQACASLDKTTSSGHPHHIRKNECWNGDSFTGKLA
DQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAF
GGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAILAA
ALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCTSQWNSIAHWL
LTLCALSEVTDLSPDIVQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPD
KTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMI
PHSQRPTQLMSLLGEAALHGPTFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRFSD
LSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..962
/gene="POL"
/product="putative protein p48"
mat_peptide 963..2060
/gene="POL"
/product="NTPase"
/note="p41"
mat_peptide 2061..2597
/gene="POL"
/product="protein p22"
mat_peptide 2598..2996
/gene="POL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 2997..3539
/gene="POL"
/product="3C-like protease"
/note="3CLpro; calcivirin"
mat_peptide 3540..5069
/gene="POL"
/product="RNA-directed RNA polymerase"
gene 5053..6672
/gene="VP1"
CDS 5053..6672
/gene="VP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AGE99612.1"
/translation="MKMASSDANPSDGSSANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNIIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLSPDLNPYLSHLSRMYNGYAGG
FEVQVILAGNAFTAGKIVFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQANDSTLKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPVLTVEEMTNSRFPIPLERLFTGPSTAFVVQPQNGRCTTDGVLLGTT
QLSAVNICNFRGEVNHIAGTHDYTMRLTSQNWNNYDPTEEIPAPLGTPDFVGRIQGVL
TQTTRSDGSTRSHKATVSTGSVHFTPKLGSVQFTTDTTNDLNAGQNTKFTPVGVEQTS
GDHQSEPQQWTLPNYSGTPNHNVHLAPAVAPTFPGEQLLFFRSTLPGCGGYPNMNLDC
LLPQEWVLHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHRSGFITVAHSGSHDLVI
PPNGYFRFDSWVNQFYTLAPMGNGSGRRRVV"
gene 6672..>7064
/gene="VP2"
CDS 6672..>7064
/gene="VP2"
/note="minor capsid protein"
/codon_start=1
/product="putative capsid protein VP2"
/protein_id="AGE99613.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIDATHKLQQGLMQIKQAVLLEGGFSAADAARGAIN
APMTKALDWSGTRYWAPEARVTTYNAGHF"
ORIGIN
1 ctgccgctgt tgctaacagc aacaacgaca ccgcaaaatc ttcaagtgac ggagtgcttt
61 ctagcatggc tgtcactttt aaacgagccc tcggggcgcg gcctaaacat ccgcccccga
121 gggagatacc acaaagacct ccacgaccgc ccactccgga gttgatcaag aaagtccctc
181 cccccccacc taacggggaa gaggaaccag tggtctctta taacgtcaag gatggcgttt
241 ctgggttgcc tgagctttcc actgtcaggc aaccagatga gaacaacacg gcatttagtg
301 tccctccact caaccaaagg gagaacaggg atgccaagga accactaact ggaacaatcc
361 tggagatgtg ggatggggag atctatcatt atggcttgta tgtggaacga ggcctggtgc
421 ttggcgtgca caaaccgccg gcagccatta gcctcgctaa ggtcgaatta acaccactct
481 ctttgttctg gagacctgtc tacactcccc agtacctcat ctccccagac accctcagga
541 gattgcatgg tgaatccttc ccttatacag cctttgacaa caactgttat gccttttgtt
601 gctgggtttt ggacctgaac gattcatggt tgagcaggag gatgatacag aggacaactg
661 gcttcttcag gccttaccag gattggaaca gaaaacctct tcccaccatg gatgattcca
721 aattaaagaa agtggccaac atattcctgt gtgctttgtc ttcactattc actagaccta
781 tcaaggacat aataggaaag ctaagacctc ttaatatcct caacatttta gcttcatgtg
841 attggacctt tgcaggtata gtggaatccc taatcctctt ggcagaactc tttggagttt
901 tctggacacc cccagatgtg tctgcgatga ttgccccctt actgggtgac tacgaactgc
961 aggggcctga ggacctcgca gtagagctag tgccagtggt aatgggggga ataggtttgg
1021 tgctagggtt caccaaagag aagattggga agatgttgtc atctgccgca tccacactga
1081 gggcctgtaa ggatcttggc gcatatgggc tggagatttt aaaactagtc atgaaatggt
1141 tcttcccaaa gaaagaggag gcgagtgaat tggccatggt gagatccatc gaggacgcag
1201 tgttggacct cgaagcaatt gaaaacaacc atttgaccac cctgctcaag gacaaggaca
1261 gcctggcaac ttacatgaga actcttgacc ttgaggaaga gaaagccagg aaactttcaa
1321 ccaagtccgc ctcacctgac atcgtgggta caatcaacgc tctcctggcg aggatcgcgg
1381 ctgcccgctc cctggtgcat cgggcaaaag aagaactttc cagcaggcca agacccgttg
1441 tcgtgatgat atcaggaaaa ccagggatag ggaagactca ccttgccaga gagctggcta
1501 agaagatcgc aaccaccctt acgggagacc agagggtggg cctcatccca cgcaatggtg
1561 ttgaccattg ggacgcgtac aagggagaga gggtcgtcct ttgggacgac tacggtatga
1621 gtaaccccat ccacgatgcc ctcaggttgc aggagcttgc tgacacttgc cccctaacac
1681 tgaattgtga caggattgag aacaaaggta aagtttttga cagtgatgct ataattatca
1741 ccaccaacct ggccaaccca gcgccactgg actatgtcaa ttttgaggca tgctcgaggc
1801 gcatcgattt cctcgtgtac gccgaagccc ctgatgttga gaaggcgaag cgtgacttcc
1861 caggccaacc cgacatgtgg aagaatgcct ttagccctga cttctctcac ataaagctaa
1921 tgctggcccc gcagggtggt tttgataaga atggcaacac cccacatggg aagggtgtca
1981 tgaagaccct caccaccggt tccctcatcg cccgtgcttc aggactcctc catgagaggc
2041 tggatgagta cgagttgcaa ggcccagccc tcacaacctt caactttgac cgaaacaaag
2101 tgctcgcttt caggcagctt gccgctgaaa acaagtacgg gttgatggac acgatgagag
2161 ttggagggca actcaagggc gtcagaacca tgccagagct caaacaagca ctcaagaata
2221 tctcaattaa gaagtgtcag atagtgtatg gtggcagcac ctacacgctt gaatctgatg
2281 gtaagggtag tgtgagggtt gacaaagttc agagtgccac cgtgcaaacc aacaatgaac
2341 tagccggcgc cctgcatcat ctcaggtgcg ctaggatcag gtactatgtt aagtgtgtcc
2401 aggaagccct gtattccatc attcaaattg caggggctgc atttgtcacc acgcgcattg
2461 tcaagcgcat gaacatacag gatctatggt ccaaaccaca actggaggac acgggagaag
2521 ccactagcaa agacggatgc ccaaaaccca aagatgaaga ggagtttgtt gtctcatccg
2581 acgacatcaa ggctgagggc aagaaaggga agaacaagtc tggtcgcggc aagaaacaca
2641 cagccttctc gagtaaaggt ctcagtgatg aagagtacga tgagtacaaa agaattaggg
2701 aggaaagaaa cggcaagtac tctatagagg agtatctcca agacagagac aagtactatg
2761 aggaggttgc catcgccagg gcgactgaag aggacttctg cgaagaggaa gaggccaaga
2821 tccggcagag gatctttaga ccaacaagga aacaacgcaa ggaggagagg gcttctctcg
2881 gtctagtcac aggctctgag atcaggaaaa ggaacccaga tgacttcaaa cccaagggaa
2941 agttgtgggc cgatgacgac agaagtgtcg attacaacga gaagctcagc tttgaagccc
3001 caccaagcat ctggtcaagg atagtcaact ttggttcggg ctggggtttc tgggtttctc
3061 ccagtctgtt cataacgtca actcatgtta taccccaggg cacacaggag ttctttggag
3121 tgtccatcaa gcaaatccag atacacaaat caggcgagtt ctgtcgcctg cggttcccaa
3181 aaccaatcag gactgatgtg acgggtatga tcctagagga gggtgccccc gaaggcactg
3241 tggccacact actcatcaag agaccaactg gcgagctcat gcctttagca gccagaatgg
3301 gcactcatgc aaccatgaaa attcaaggtc gcactgttgg aggccaaatg ggtatgctcc
3361 taacagggtc caacgccaaa agtatggacc tgggcaccac acctggcgac tgcggttgtc
3421 cctacattta caagagaggg aacgactacg tggtcatcgg ggttcacacg gctgctgccc
3481 gaggggggaa cactgtcata tgtgctaccc aggggagtga aggtgaggcc acacttgagg
3541 gcggtgacaa caaaggcacc tactgtggtg ctccaatcct aggtccagga agtgccccaa
3601 aactcagcac taaaaccaaa ttctggaggt cgtccacagc accactccca cctggcacct
3661 atgaaccagc atacctcggt ggtaaggacc ctagagtcaa gggtggtcct tcactacaac
3721 aagttatgag ggaccagttg aagccattca cggaaccaag gggcaaacaa ccaaagccaa
3781 gtgtgttgga agctgccaag agaactatta ttaatgtcct tgaacaaaca atagacccac
3841 ctcaaaaatg gacatttgca caagcttgcg cgtcccttga caagaccacc tccagtggtc
3901 atccacacca catacggaag aatgaatgct ggaatgggga ttcctttaca ggcaagttgg
3961 cagatcaggc ctcaaaggcc aacttgatgt ttgaggaggg aaagaacatg actccagttt
4021 acacaggtgc ccttaaggat gagttggtca aaactgacaa gatatatggt aagatcaaga
4081 agagactact ctgggggtcg gacctggcaa ccatgatccg gtgtgcccgg gcattcgggg
4141 gcctaatgga tgagctcaag gcccactgtg tcacgcttcc tgtcagagtt ggaatgaaca
4201 tgaatgagga tggccccatc atctttgaaa agcactctag gtatagatat cactatgatg
4261 cagactactc tagatgggat tcaacacaac aaagagctat attggctgca gccctagaaa
4321 tcatggttaa attctcccca gagccacact tggcccaggt agttgcagaa gacctcctgt
4381 cccctagcgt gatggacgtg ggtgatttta agatttcaat caacgagggt ctcccctctg
4441 gggtgccctg cacttcacaa tggaactcta tcgcccactg gctcctcacc ctctgtgctc
4501 tttctgaggt tacggatctt tcccctgaca tcgttcaggc caattctctc ttctccttct
4561 atggtgatga tgagattgtg agtacagata taaaattgga cccagaaaaa ttgacggcaa
4621 agctgaagga atacggactg aagccaaccc gccctgacaa gactgaaggg cctctgatca
4681 tctctgagga tttaaatggt ttgaccttcc tgcgtaggac cgtgacccgt gatccagctg
4741 gttggtttgg taaattggaa caaagctcaa tactcaggca gatgtactgg accaggggcc
4801 ccaaccatga ggacccatct gaaacaatga taccacattc ccaaaggccc acgcagctga
4861 tgtctttgct gggtgaggct gcattgcacg gcccaacatt ctacagcaag atcagtaaac
4921 tagtcatcac agagttgaag gaaggtggca tggattttta cgtgcccaga caagagccga
4981 tgttcagatg gatgagattc tcggacctga gcacgtggga gggcgatcgc aatctggctc
5041 ccagttttgt gaatgaagat ggcgtcgagt gacgccaacc catctgatgg gtcctcagcc
5101 aacctcgtcc cagaggtcaa caatgaggtt atggctttgg aacctgttgt tggtgctgct
5161 atagcagcac ctgtggcagg tcaacaaaat ataattgacc cctggattag aaataatttt
5221 gtgcaagccc ctggtggaga gttcacagtg tcccctagaa acgctccagg tgaaatactg
5281 tggagcgcgc ctctgagccc tgatttgaac ccctatctct ctcacttatc tagaatgtac
5341 aatggttatg caggtggttt tgaagtgcag gtgattcttg cggggaatgc gttcaccgcg
5401 ggaaagatcg tgtttgctgc tgtcccaccc aattttccaa ctgaaggtct gagtcccagt
5461 caagtcacaa tgtttcctca cataatcgtg gatgttaggc aattggaacc tgtgctgatc
5521 cccttaccag atgttagaaa taacttctac cattataatc aagcaaatga ttccaccctg
5581 aagttgatag ctatgttata cacaccactc agggctaaca atgccgggga tgatgttttc
5641 actgtctctt gtcgagtcct tacaagacca tctcctgact ttgattttat tttcctggtc
5701 ccacccacag tcgaatcaag aaccaaacca ttcactgtcc cagtacttac tgttgaagag
5761 atgactaatt caagatttcc tatccctcta gaaagattat ttacaggccc cagcactgct
5821 tttgttgttc agccccaaaa tggcagatgc acaactgatg gcgtccttct tggcaccact
5881 cagttgtcgg ctgtcaatat ctgtaacttc agaggggaag tcaatcacat tgccggtact
5941 cacgattaca ccatgaggct aacttctcag aattggaaca actatgaccc aacagaagag
6001 attccagccc ctcttgggac cccagacttt gtagggagga ttcaaggtgt gctcactcag
6061 accaccagaa gtgatggctc gacccgctcc cacaaggcca cagtgagcac ggggagtgtt
6121 cacttcactc caaaattggg cagtgttcag ttcaccaccg acacaaccaa tgatcttaat
6181 gctgggcaaa acacaaaatt caccccggtc ggtgtcgagc aaaccagcgg cgaccaccaa
6241 agtgagcctc aacaatggac actcccaaat tactcaggta ctccaaatca taatgtgcat
6301 ttggcccccg ctgttgcgcc cactttcccg ggtgaacagc tgcttttctt taggtccact
6361 ctacctgggt gtggcgggta ccctaatatg aatctggact gcttgctccc ccaagagtgg
6421 gttttgcact tctaccaaga agctgcccca gcacaatctg atgtggcctt gctgaggttt
6481 gttaacccag acacaggaag agtgttgttt gaatgtaagc tccatagatc aggcttcatc
6541 acagtggccc actctggttc acatgacttg gttattcccc ctaatggtta tttcagattt
6601 gattcctggg ttaatcagtt ttacactctc gcccccatgg gaaatgggtc ggggcgtaga
6661 cgggtggtat aatggctgga gctttcttcg ctggattggc atctgatgtc ctcggttctg
6721 gtcttggttc tctaatcaat gctggagctg gggccataaa ccaaaaggtg gaatttgaga
6781 ataatagaaa attacaacaa gcttcctttc aatttagcag taatttgcaa caggcttctt
6841 ttcaacatga caaagaaatg ctccaggctc aaattgatgc tacccacaaa ttgcaacaag
6901 gtttaatgca gatcaaacag gcagtgctcc tagagggtgg gttttccgcg gcagacgccg
6961 ctcgcggggc gatcaatgcg cccatgacaa aagccctgga ttggagtgga actaggtact
7021 gggctcccga ggccagagtc acaacataca atgcaggcca cttt
//