Typing tool
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Typing tool
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Complete norovirus genomes
| MN960578 | GII.17 | |
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| GII.P17 |
ORF1: 1..5099
ORF2: 5080..6702
ORF3: 6702..7481
LOCUS MN960578 7500 bp RNA linear VRL 15-MAR-2020
DEFINITION Norovirus GII isolate SCD1042 nonstructural polyprotein (ORF1)
gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete
cds.
ACCESSION MN960578
VERSION MN960578.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7500)
AUTHORS Zhang,Z., Wang,D., Liu,D. and Zhang,Z.
TITLE Whole Genome Analysis for Co-Infected Different Genotypes of Human
Norovirus
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7500)
AUTHORS Zhang,Z., Wang,D., Liu,D. and Zhang,Z.
TITLE Direct Submission
JOURNAL Submitted (21-JAN-2020) School of Agriculture & Biology, Shanghai
Jiao Tong University, 800 Dongchuan Rd. Minhang Dist, Shanghai
200240, China
COMMENT ##Assembly-Data-START##
Assembly Method :: CLC workbentch v. 2018
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7500
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="SCD1042"
/isolation_source="anal swab"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="China: Shanghai"
/collection_date="18-Feb-2018"
/note="genotype: GII.17[P17]"
gene <1..5099
/gene="ORF1"
CDS <1..5099
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="QHJ14088.1"
/translation="SNDASAAVAGKNNNNDKEKSSSDSLFANMSVTFKKALGARSKQP
PPGETKQIQKPPRPPTPELVKRIPPPPPNGEDEPGIVYKVGEGVSGLPDLTTVVQPDA
QNTAYSVPPLSQREVGEAKEPLPGSILEMWDGEIYHYGLYVERGNVLGVHKPPAAISL
AKIEITPLSLYWRVVYTPQYLIDPGTLKNLSGETFPYTAFDNNCYAFCCWVLDLNDSW
LSRRMIQRTTGFFKPYQDWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDIIGNL
RPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYEMQGPEDL
AVELVPVVMGGVGLVLGFTKEKIGKMLSSAATTLRACKDLGSYGLEILKLVMKWFFPK
KEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTK
SASPDIVGTINALLARIAAARSLVHKAKEELSSRQRPVVVMISGRPGIGKTHLARELA
KKVASTLSGDQRIGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELADTCP
LTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDIEKA
KRDFPGQPDMWKDHFRPDFSHIKLQLAPQGGFDKNGNTPHGKGVVKSLTIGSLIARAS
GLLHERMDEFELQGSDLPTFNFDRNKVAAFRQLAAENKYGLMDTLRVGNQLKNVKTLD
ELKQAIKNISIKKCQIVYNGCTYTMESDGRGKVVVEKVQNATVQTNNELVGALHHLRS
ARIRYYVKCFQEAIYSLLQIAGAAFVTSRIVRRMNVSNLWSKPPIEEGDEPEDRGGCP
KPRDEDDLTIDSRDIKVEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
GSEIRKRNPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFWVSPS
LFITSTHVIPKGITEAFGVPINQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGAPEGT
VVSILIKRTTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDC
GCPYIYKRGNDFVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGP
GNAPKLSTKTKFWRSSNAPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPNPNVLESAKKTIINVLEQTIDPPQKWSYAQACASLDKTTSSGYPHHVRKNDYWS
GESFTGKLADQASKANLMYEEGKHMQPVYTAALKDELVKTDKIYGKIKKRLLWGSDLS
TMIRCARAFGGLMDEFKANCITLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDS
TQQRAVLEAALEIMVRFSAEPQLAQIVAEDLLSPSVVDVGDFKIAINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTGLGPDIIQANSMYSFYGDDEIVSTDIKLDPEKLTAKLKE
YGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQLYWTRGPN
HEDPSETMIPHAQRPVQLMALLGESSLHGPSFYSKVSKLVISELKEGGMDFYVPRQES
MFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..989
/gene="ORF1"
/product="p48"
mat_peptide 990..2087
/gene="ORF1"
/product="NTPase"
mat_peptide 2088..2624
/gene="ORF1"
/product="p22"
mat_peptide 2625..3023
/gene="ORF1"
/product="VPg"
mat_peptide 3024..3566
/gene="ORF1"
/product="Pro"
mat_peptide 3567..5096
/gene="ORF1"
/product="RdRp"
gene 5080..6702
/gene="ORF2"
CDS 5080..6702
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QHJ14089.1"
/translation="MKMASNDAAPSNDGAAGLVPEGNNETLPLEPVAGAAIAAPVTGQ
NNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHLIVDVRTLEPIMIPLPD
VRNTFFHYSNQPNSRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFTYLVPP
SVESKTKPFSLPILTLSELTNSRFPVPIDSLFTAQNNVLQVQCQNGRCTLDGELQGTT
QLLPSGICAFRGRVTAQINQRDRWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGVVFGM
VSQRNVGSDAPGSTRAQQAWVSTYSPQFVPKLGSVNLRISDNDDFQFQPTKFTPVGVN
DDDDGHPFRQWELPNYSGELTLNMNLAPPVAPNFPGEQLLFFRSFVPCSGGYNQGIID
CLIPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVAHSGDYPLV
VPANGHFRFDSWVNQFYSLAPMGTGNGRRRAQ"
gene 6702..7481
/gene="ORF3"
CDS 6702..7481
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QHJ14090.1"
/translation="MAGAFIAGLAGDMLTSSVGSLVNAGANAINQKIDFENNKQLQSA
SFQHDKEMLQAQVRATKQLQSEMIALKQGVLAAGGFSPTDAARGSIGAPMTKVLDWSG
TRYWAPNSTKTTGYSGQFTSSPVHMSSPNAPQSKPAKPRSLAPSSSSSSVYSTYTQST
HLTSGSSSNASSASTKLTNLSSGSSQNRTAEWVNQQRSLSPFMSGALNISHVTPPSSR
ASSSGTVSTVPKEVLDSWTSAFNTHRQPLFAHLRVRGESRV"
ORIGIN
1 cgtctaacga cgcttccgct gccgttgctg gcaaaaacaa caacaacgac aaggaaaaat
61 cttcaagtga cagcctgttt gctaacatgt ctgtcacctt taagaaagcc ctcggggcgc
121 ggtctaaaca accgcccccg ggagaaacaa aacaaataca aaaaccacca aggccaccga
181 caccggaatt ggtgaagaga atacctccac ccccacccaa tggcgaggat gaaccaggga
241 tagtgtacaa ggtgggagag ggtgtgtctg ggctgcccga cctgacaact gtggtacaac
301 ctgacgcaca aaacacagct tatagtgttc ccccacttag ccagagagaa gtcggcgaag
361 ctaaagaacc gctgcctggc tccattctgg aaatgtggga tggtgagatc taccactatg
421 ggctgtatgt tgagcggggg aatgtgctcg gagtacacaa accacccgct gcaataagcc
481 ttgccaaaat tgaaataaca ccgctgtctc tctactggag agtggtctac actccccagt
541 atttgataga tccaggaact cttaagaact tgagtggaga gactttccca tacacggcct
601 ttgacaacaa ctgttatgcc ttctgttgtt gggtcctaga cctcaacgac tcctggctta
661 gcaggagaat gatccaaaga acaactggat tcttcaaacc ttaccaggat tggaacagaa
721 aacccttacc aaccatggat gaaccgaaaa tcaagaaggc cgcgaatgct gtcctatgcg
781 ctctctcctc actcttcact aggcccatta aggacatcat tggaaatctt agaccactga
841 acattcttaa tatactggca acctgcgatt ggacttttgc aggcatagtg gaatccttga
901 tccttcttgc tgaactcttt ggggtgttct ggacaccccc agatgtgtct gcgatgattg
961 ctcccttact cggtgactac gagatgcaag gccccgaaga cctggccgtg gaacttgtgc
1021 ccgtggtgat gggaggagta ggtttggtgt taggattcac caaagaaaag atcggcaaga
1081 tgctttcatc agctgcgacc acacttaggg cctgcaagga tctaggatct tatggattgg
1141 agatactcaa attggtcatg aagtggttct tccccaagaa ggaggaggct aacgaactag
1201 ccatggtgag agccattgag gatgcagtcc tggatttgga ggcaatagaa aacaatcaca
1261 tgaccaccct tctcaaggac aaagacagcc tggccacata catgaggact cttgacttgg
1321 aagaagagaa agcaaggaaa ctgtcaacca aatcggcgtc acctgacatc gtgggtacaa
1381 taaacgcatt attggctagg atagcagccg ccaggtcact ggtccacaag gctaaggagg
1441 agctctcgag cagacagaga cctgttgttg taatgatatc aggtagacca ggtataggaa
1501 agacccatct ggccagagag ctagccaaga aagttgcgtc aacactgtca ggcgaccaaa
1561 ggattggact ggtacctaga aatggcgtcg accattggga cgcctacaag ggagaaaggg
1621 tggttctgtg ggatgattat ggtatgagca accctataca ggacgcactg aggctccaag
1681 aattggctga cacctgtcct ctgaccctaa attgtgatag gattgaaaac aaaggaaaag
1741 tgttcgacag tgatgccata attataacaa ccaaccttgc aaacccagca ccactagact
1801 atgtcaactt tgaggcctgc tctagacgca tagacttctt ggtgtatgca gacgcacctg
1861 acattgagaa ggctaagcgt gacttccctg gccaaccaga tatgtggaaa gaccatttca
1921 gaccagactt ctcacacatt aaacttcagc tggcaccaca gggaggtttt gacaaaaatg
1981 gcaacacccc acatggtaaa ggtgtggtga agtccctgac gattggttct ctgatcgcca
2041 gggcctccgg cttgctccac gagagaatgg atgaattcga gctccaaggc tctgacctgc
2101 caaccttcaa ttttgaccgc aacaaagtcg ccgccttcag acaattagca gctgaaaaca
2161 aatatggtct tatggacaca ctgagggtcg gcaaccaact gaaaaatgtt aagaccctgg
2221 atgagctgaa gcaggccata aagaacatca gtatcaagaa gtgtcagata gtgtataatg
2281 gatgcaccta taccatggaa tctgatggga ggggcaaggt tgtggttgaa aaggtacaaa
2341 acgcaacagt tcaaaccaac aatgaacttg taggggcgct ccaccacctg agatctgcaa
2401 ggataagata ctatgttaaa tgtttccaag aagccattta ctctctactc caaattgctg
2461 gtgcagcctt cgtcacctca cgcatcgtga ggcgcatgaa cgtgtcaaac ctctggtcga
2521 agccacccat cgaggaaggt gatgagcctg aagacagagg aggatgcccc aagcccaggg
2581 atgaagatga cctcactatt gactctagag acatcaaagt ggaagggaag aagggcaaga
2641 acaagtctgg ccggggcaag aaacacacag ccttctcttc caagggcctc agtgatgaag
2701 agtacgatga gtacaaaaga atcagagagg agaggaatgg taaatactca atagaggaat
2761 acctccaaga tagggacaga tactatgaag agcttgccat tgctaaggcc actgaggagg
2821 acttctgtga ggaggaggag atcaaaatcc gccagagaat cttccgaccc accaggaagc
2881 agcggaaaga ggagagggcc acgcttgggc ttgtcacagg atcggaaatc agaaagagga
2941 atccagatga ctttaaacca aaaggaaaat tgtgggctga tgacaacagg agcgtggatt
3001 acaatgagag gatagatttt gaggctcccc cgagtgtttg gtctaggata gtcaactttg
3061 gcacaggctg gggattctgg gtttctccaa gtctctttat aacttcaaca cacgtcatac
3121 caaaaggaat cactgaggcc tttggagtgc ccataaacca aatccaaatt cacaaatctg
3181 gagaattttg ccgcttgcgg tttccaaagc caattagacc agacgtgagt gggatgatct
3241 tggaagaggg cgcccctgaa ggcactgttg tgtctattct catcaaaagg acaacagggg
3301 agctaatgcc tcttgcagtc agaatgggga ctcatgccac aatgaaaatc caaggtagaa
3361 cggtgggtgg tcagatgggt atgcttctca ctggctcaaa tgctaaaagc atggacctag
3421 gcacaacacc aggtgactgc ggatgtccat acatatacaa aaggggcaat gactttgtgg
3481 tcattggggt gcacactgca gcggctcgtg gaggcaacac ggtcatatgt gccacacagg
3541 gaagtgaagg tgaagccact cttgaaggag gtgataacaa gggtacatat tgtggagctc
3601 ccattttggg acctggcaat gcaccaaaac tgagcacaaa gacgaaattc tggagatcct
3661 ctaacgcacc gcttccccca ggtacttatg aaccagcata ccttggtgga agagacccgc
3721 gcgtgaaggg aggcccatct ctgcaacaag ttatgagaga ccaacttaaa ccttttacag
3781 agcccagagg gaagccacca aacccaaatg tcttagagtc agcaaagaag actatcatca
3841 atgttctgga acaaaccatt gacccccctc aaaagtggtc atatgcccaa gcttgtgcat
3901 ccctcgacaa gacaacctcc agtggatacc cgcaccacgt ccggaagaat gactattgga
3961 gtggtgaatc cttcacagga aagcttgcag atcaggcttc aaaagcaaat ctcatgtatg
4021 aggaaggcaa gcacatgcaa ccagtttaca ccgcagcact caaagacgag ctcgtgaaaa
4081 ctgacaaaat ttatggcaaa atcaagaaaa gactcctgtg gggttctgac ctctccacaa
4141 tgattcgatg cgccagagca tttggtggtc tcatggatga attcaaagca aattgtatta
4201 cactccctgt cagagttggt atgaatatga atgaagatgg tcccataata tttgagaaac
4261 actccaggta taggtaccac tatgatgctg attactcccg ttgggactcc acacaacagc
4321 gggcagtgct ggaagcggca cttgaaatca tggtgagatt ttctgctgaa ccacagctgg
4381 cacaaatagt ggcagaggac ctgctgtcac caagtgtggt tgatgtgggc gatttcaaaa
4441 tcgctatcaa tgaaggccta ccatctggcg tgccttgcac ctcacaatgg aattctattg
4501 cccactggtt gcttaccttg tgtgcccttt ctgaagtgac aggattaggt cctgacatca
4561 tacaagctaa ctccatgtac tctttctatg gtgatgatga gattgtgagc acagacataa
4621 aattggaccc agagaaattg accgcaaagc tcaaagagta tggccttaaa cccactcggc
4681 ccgacaaaac tgaggggccg ttggtgatta gtgaggacct aaacgggttg actttcctcc
4741 gccgaacagt cacccgtgat ccagcaggtt ggtttggaaa gttggaccaa aactccatcc
4801 tcaggcagtt gtactggaca agaggaccca accatgaaga ccccagtgag accatgatac
4861 cacacgcaca aagacctgtg cagctcatgg cactactagg agaatcctcc ctacatggac
4921 cctcatttta cagcaaggtt agcaaattag tcatatctga acttaaagag ggaggaatgg
4981 atttttatgt gcccagacaa gagtcaatgt tcagatggat gaggttctca gatctaagca
5041 catgggaggg cgatcgcaat ctggctccca gttttgtgaa tgaagatggc gtcgaatgac
5101 gccgctccat ctaatgatgg tgctgctggt ctcgtaccag agggcaacaa cgagaccctt
5161 cccctagaac cagttgcggg cgcagctata gccgcacccg tcactggcca aaataacata
5221 attgacccct ggattagaac aaattttgtg caagcaccaa atggagagtt cacagtatca
5281 cccagaaact ctcctggaga aattttatta aacttagagt tgggtcctga tttgaaccct
5341 tatttggctc atttgtcaag gatgtacaat gggtatgctg gtggagtgga agttcaggtt
5401 ctcctggcag ggaacgcgtt cactgccgga aagatcctct tcgccgctgt cccgccaaat
5461 ttcccagtgg aattcttaag cccagcccag atcacaatgc tcccacattt aatagtagat
5521 gttaggactc ttgaaccaat tatgatccca ctccctgatg ttaggaatac attcttccat
5581 tatagtaacc agccgaacag ccgcatgaga ttagtggcta tgctctatac cccacttagg
5641 tctaatggct caggtgatga tgtctttact gtctcttgca gggttttgac taggcctact
5701 cctgattttg agttcactta tctagtgcca ccttctgttg aatctaaaac taagcctttt
5761 tccttgccta ttttaaccct ttctgagctt acaaattcga ggttcccagt tcccatcgat
5821 tcgcttttca ccgcccagaa taacgtgttg caggtgcagt gtcaaaatgg caggtgtaca
5881 cttgatggtg agttacaagg cacaacccag ttgctcccat ctggcatctg tgcattcaga
5941 ggacgggtga cagcacaaat taaccaacgt gacaggtggc acatgcaact gcaaaacctc
6001 aatggtacaa catatgaccc aactgatgat gtgccagccc cgctgggtac acctgacttc
6061 aagggcgtcg tgtttgggat ggttagccaa agaaatgtgg gtagtgatgc gcctggctca
6121 accagagccc aacaggcgtg ggtttcaacc tatagccccc aatttgtccc caaattaggt
6181 tctgtcaatc ttagaattag tgataatgat gatttccaat tccaaccgac aaaattcaca
6241 ccagtgggcg tcaatgatga cgatgatggc cacccgttca gacaatggga actaccaaac
6301 tattcagggg agcttacctt gaatatgaat cttgcccccc cagttgctcc aaattttcct
6361 ggtgaacaat tgttattctt cagatctttc gtgccatgct caggaggtta caaccaaggt
6421 attatagatt gtcttattcc ccaagaatgg atccaacact tctatcagga atcagcaccc
6481 tcccagtcag acgtggccct aatcaggtat gtcaaccccg atacgggacg tacactgttt
6541 gaagcaaaat tgcacagatc tggttatatt actgtggctc actctggaga ctatcctctt
6601 gttgttccgg ctaatggaca ctttagattt gattcttggg taaatcagtt ttactcactc
6661 gccccaatgg gaactgggaa tgggcgtagg agggctcagt aatggctggg gctttcattg
6721 cagggttggc aggcgacatg ctcacgtcat ctgtgggctc ccttgtgaac gcaggggcaa
6781 acgccatcaa tcaaaagata gactttgaaa acaacaaaca actccagtct gcttcctttc
6841 agcatgataa agagatgctc caagcgcagg tgagggcaac caagcagctg caatctgaaa
6901 tgatagccct aaaacagggg gttttggccg caggcggctt ttcccccact gatgcagcaa
6961 ggggatccat tggtgccccc atgacaaagg tgcttgactg gtctggcact cgatactggg
7021 cgcccaattc cacaaagaca actggctatt cgggacaatt cacctcttca cctgtgcata
7081 tgtctagccc aaatgctcca caatcaaaac ctgcaaagcc taggtctcta gctccttcct
7141 cttcttctag cagtgtctat agtacgtata ctcaatctac tcatttgaca tctggctctt
7201 ctagtaatgc ttcttctgcc tccacaaaat tgacaaattt aagctctggc tcctctcaaa
7261 acagaacagc agagtgggta aatcaacaga gaagtcttag ccctttcatg agtggcgcac
7321 ttaacatctc acatgtcacg ccaccctcaa gtagggcttc cagttctggg acggtctcga
7381 ccgtgcccaa ggaagttttg gactcctgga cgtctgcgtt taacacacac agacagccgc
7441 tcttcgcgca cctcagagtg aggggggagt cacgtgttta gtgaaaagaa ataattggcc
//