Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MZ203488 | GI.3 | |
|
|---|---|---|---|
| GI.P13 |
ORF1: 5..5410
ORF2: 5394..7028
ORF3: 7028..7675
LOCUS MZ203488 7675 bp RNA linear VRL 19-MAY-2021
DEFINITION Norovirus GI isolate Hu/US/2012/GI.3[P13]/CA-RGDS-1101
nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
complete cds.
ACCESSION MZ203488
VERSION MZ203488.1
KEYWORDS .
SOURCE Norovirus GI
ORGANISM Norovirus GI
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7675)
AUTHORS Pan,C.-Y., Huynh,T., Padilla,T., Montmayeur,A.M., Chhabra,P.,
Barclay,L., Vinje,J., Wadford,D.A. and Morales,C.
TITLE Direct Submission
JOURNAL Submitted (14-MAY-2021) Viral and Rickettsial Disease Laboratory,
California Department of Public Health, 850 Marina Bay Parkway,
Richmond, CA 94804, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. R10; SPades v. 3.6
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7675
/organism="Norovirus GI"
/mol_type="genomic RNA"
/strain="CA-RGDS-1101"
/isolate="Hu/US/2012/GI.3[P13]/CA-RGDS-1101"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122928"
/country="USA"
/collection_date="01-Aug-2012"
/note="Amplicon sequencing: first 35 nt does represent
primer sequence;
genotype: GI.3[P13]"
gene 5..5410
/gene="ORF1"
CDS 5..5410
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QVI17106.1"
/translation="MMMASNDAIAVADVSNNNANTNNENIGSRLMAKIRGRIGPQRGE
TTTKIKDANMALDLLRRSQTPSPCRQTNDSAPKAQRDRPPRTASEVKRALGWDAEPEH
QESTARAWCDLSKEEKEEIMRNNERLFDAGGVTPSILPSTFERTDSSGATDEQQPVTW
SSSGGVDLGINDLTTVRGPFWNMCPLPPLDARNNGPAKEPLIGDMVEFYEGHIFHYAI
YIGQGKTIGVHSPQAAFSIPRITIHPLVAWWRVCYVPTNQQRLTYEQLKELENEPWPY
ASITNNCYEFCCKVMALDDTWLQRKLVNSGKFNHPTQDWSQDTPDFHQDSKLEMVRDA
VLSAINGLVSQPFKNILSKIKPLNVLSLLSNCDWTFMGVVELVVLLAELFDVFWTPPD
ISSFIASLLPDFHLQGPEDLAKDLVPLILGGIGLAIGFTRDKITKVMKSAVDGLRSAT
QLGQYGLEIFSIIKKYFFGGDQTEKTLRGIEDAVIDMEVLSSTNVTQLVKDKKLAKAY
MNVLDSEEEKARKLSVRSADPHIVTSVNNLISRISMARSALAKAQAEMTSRPRPVVIM
MCGPPGIGKTKAAEHLAGRLAAEIRPGGKVGLVPRESIDHWDGYHGEDVLLWDDYGMS
KITEDCNKLQAIADTAPLSLNCDRIENKGMQFSSDAIIITTNAPGPAPVDFVNLGPVC
RRVDFLVYCSAPEIEQTRRAHPGDTNAIKDLFKKDFSHLKMELAPQGGFDSQGNTPFG
KGVMKTTTLNRLLIQATALAMERQDEFQLQGTVYNFDEDRVAAFTNLARANGLGLISM
ATLGKKLRSVKSMEGLRNALLGYKIGECDIVWNTRVYSVKSDGSNVIIKEKQVPSSPQ
HQAISTATLALSRLRAARALAYASCLQSAVLSILQVAGSALVVSRAVKRMFGTRTEQP
ILEGKHKEHNCRVHRAEAAGHGPIGHDGIIERYGLCESEQEGEDDHTVELPTADKEGK
NKGKTKKGRGRKSNFNAFSRRGLSDEEYEEYKKVREEKGGNYSIQEYLEDRQRYEEEL
AEVQAGGDGGIGETEAEIRHRVFYKSKSGMRKQRQEERRQLGLVSGTEIRKRKPIDWT
PPKNDWSEDTRTVNYDEHISFEAPPSIWSRVVKFGSGWGFWVSSTVFITTTHVIPPGA
KEIFGENLSNIAIHRVGEFTQFRFSKKMRPDLSGMVLEEGCPEGTVCTIMIKRDSGEL
LPLAVRMGAVASMKIQGKLMHGQSGMLLTGANAKGMDLGTIPGDCGAPYIHKRGNDWV
VCGVHAAATKSGNTVVCAIQGGEGEATLEGGDQNKGHYAGHPILRYGNGPSLSTKTKF
WKSNPQPLPPGTYEPAYLGGRDPRVEGGPSLQQVLRDQLKPFAEPRGRLPEAGLLEAA
VETVTNAIEQVMDAPVAWSYSDACMSLDKTTSSGYPHHKRKNDDWNGSSFVRELGDQA
AHANSMYELGKSMKPVYTAALKDELVKPDKVYNKIKKRLLWGADLGTVIRAARAFGPF
CEAIKPHVIKLPIKVGMNAIEDGPLIYAEHSKYKYHFDADYTAWDSTQNREIMMESFN
IMCKLTANPSLAAVVAQDLLSPSEMDVGDYVISVKDGLPSGFPCTSQVNSINHWIYTL
CALSEVTGLAPDVIQSQSYFSFYGDDEIVSTDIEFDSNRLTQVLKEYGLKPTRPDKTD
GPIIVRQQVDGLVFLRRTISKDAIGYQGRLDRNSIERQLWWTRGPNHDDPFETLVPHT
QRKVQLISLLGEAALHGEKFYRKIASRVIQEVKEGGLEIYIPGWQAMFRWMRFHDLSL
WTGDRDLLPDYVNDDGV"
mat_peptide 5..1225
/gene="ORF1"
/product="p48"
mat_peptide 1226..2314
/gene="ORF1"
/product="NTPase"
mat_peptide 2315..2914
/gene="ORF1"
/product="p22"
mat_peptide 2915..3334
/gene="ORF1"
/product="VPg"
mat_peptide 3335..3877
/gene="ORF1"
/product="Pro"
mat_peptide 3878..5407
/gene="ORF1"
/product="RdRp"
gene 5394..7028
/gene="ORF2"
CDS 5394..7028
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QVI17107.1"
/translation="MMMASKDAPTNMDGTSGAGQLVPEANTAEPISMDPVAGAATAVA
TAGQINMIDPWIMSNFVQAPQGEFTVSPNNTPGDVLFDLQLGPQLNPFLAHLAQMYNG
WVGNMRVKVLLAGNAFTAGKIIISCIPPGFTSQNISIAQMTMFPHVIADVRVLEPIEI
PLEDVRNVLFHTNDNRPTMRLVCMLYTPLRANGSSSGTDPFVIAGRVLTCPDSNFSFL
FLVPPNVEQKTRPFSVPNIPLNTLSNSRVPSLIKSMTISRDQNQIIQFQNGRVTLDGQ
LQGTTPTSVSQLCKIRGTTYHATGGNGINLTELNGEPYHAFESPAPIGFPDLGGCDWH
LTATPTQAFNDGAKVVRLSVTQGAAFAPHLGTIHYTTTDTDYNPNTSIICTLDWLSQT
AGQSNVDPWQIPTYGSTLTEAAQLAPPIFPPGFGETLVFFLSDFPISNGKNGLSVPCT
LPQEFVTHFVNEQAPIRGEAALLHYVDPDTHRNLGEFKLYPEGFMTCVPNTSGGGPQT
LPINGVFVFVSWVSRFYQLKPVGTAGAARRLGIRRS"
gene 7028..7675
/gene="ORF3"
CDS 7028..7675
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QVI17108.1"
/translation="MAQAILGAIAATAAGSAVGAGIQAGTEAALQHQRFQQDLTLQSN
TFKHDKEMLAMQVEASTSLLQNSLNTRYNLLTQAGLTSADAARAVAGAPVTRVVDWNG
TRIAAPLSTATTLRSGGFMSIPVMYRGAKTEQQKLTGFSNPNYETGSSVSRTSQWVSS
QNSMRSSVAPFHPDALRTTWVTPPGSSSTSTVSSASSIPRFFNTERLPLFANNKR"
ORIGIN
1 gtgaatgatg atggcgtcta acgacgctat tgccgttgct gatgtcagca ataacaatgc
61 taacaccaac aatgaaaaca ttgggtctcg cctcatggcg aagatccgtg ggcgtatagg
121 cccacaacgt ggtgaaacaa ccacaaaaat taaggatgcc aacatggcgc ttgatctttt
181 acgtcggtca caaacaccat ctccatgtcg gcaaactaat gacagtgccc ccaaagctca
241 aagggaccgc cccccacgga ccgcttcaga ggtaaaaagg gcactgggat gggatgctga
301 accagaacat caagaaagca cggctagggc atggtgtgac ctctctaaag aggagaagga
361 ggagataatg cgtaacaacg agaggctctt tgatgctgga ggtgtcaccc catcaattct
421 gcccagcaca tttgagagga ctgactcaag cggtgccact gacgagcaac aaccagtgac
481 atggtcttct agtggtggag ttgaccttgg catcaatgat ttgaccacag ttcgtggccc
541 gttttggaac atgtgccccc tcccaccact ggatgcccgt aataatggcc ctgccaagga
601 accccttata ggggacatgg tcgagttcta tgaaggccac atattccact atgccattta
661 catcgggcag ggtaaaacca ttggagtcca ctcgccgcag gccgctttct ccatacccag
721 aataactatc cacccactag tggcctggtg gcgcgtgtgt tacgtcccca ctaatcaaca
781 acgcctcacc tacgagcaac ttaaggagtt ggaaaatgaa ccatggccct atgcctcaat
841 caccaacaac tgttatgagt tttgctgtaa agtgatggcg cttgatgata cctggctcca
901 gaggaaattg gtcaatagtg gaaaatttaa ccaccccaca caggactggt cacaggacac
961 cccagatttt catcaagatt caaaacttga aatggtaagg gacgctgttc tgtcagccat
1021 taacggtctt gtatcacaac ctttcaagaa cattctgtca aaaattaaac cattaaatgt
1081 gctcagtctt ttatcaaact gtgattggac tttcatgggc gtcgtggagc tggttgtgct
1141 cctggcagaa ctgtttgatg tgttctggac cccaccggac atttcaagct tcattgcatc
1201 tttactgcca gactttcatc tacaaggtcc agaagaccta gccaaagact tagtccccct
1261 tatattaggt ggtataggtc tggcaattgg tttcacaaga gacaaaataa caaaagtgat
1321 gaagagcgcc gttgatgggc tgcggtcagc aacacagctc ggacaatatg gattggagat
1381 attctcaatc atcaagaaat acttctttgg aggggatcaa acagaaaaga ccctgcgggg
1441 tattgaagat gcggtgatag acatggaagt attgtccagt accaatgtga cacaactagt
1501 caaagataag aagttagcca aagcctacat gaatgtactg gacagtgagg aagaaaaagc
1561 gaggaagctc tcagtccgta gcgctgaccc acacatagtg acctctgtca acaacctgat
1621 atcacgcatc tctatggcaa gatcagctct ggctaaagcc caagctgaga tgacgtcccg
1681 cccacgacca gtggttataa tgatgtgtgg cccccctggt atcggaaaga ctaaggctgc
1741 cgagcaccta gctggccgac tagctgctga aattagacct ggaggcaaag ttggccttgt
1801 acctcgggag tccatagatc attgggatgg atatcatggc gaggatgtct tgctctggga
1861 tgactatggc atgtcaaaga taacagagga ttgtaataaa ttgcaggcta tagccgacac
1921 tgcaccactg tcgcttaatt gtgacagaat agaaaataaa ggcatgcaat tctcttctga
1981 tgcaataatt ataaccacca atgcccctgg cccagcccca gtcgactttg tcaacctagg
2041 ccccgtgtgc aggcgagtgg actttttagt ctactgttct gcacctgaga ttgaacaaac
2101 gcggagggct catccaggtg acactaatgc catcaaggat ctgtttaaaa aggacttctc
2161 acacctaaaa atggaattgg ctccacaggg cggctttgac agtcagggca atacaccttt
2221 tgggaagggt gtcatgaaga ccacaactct caacagactg ctaatacagg ccacagcatt
2281 agccatggaa cgacaagatg aattccaact ccaggggact gtttataact ttgatgagga
2341 cagagtggcc gccttcacca atttggctcg cgctaatggc ctagggctta taagcatggc
2401 aacgttgggt aagaaattaa ggagtgttaa gtccatggaa ggcctgcgca atgcactact
2461 gggatacaag attggagagt gtgatatagt ttggaacacc agggtgtact cagtcaagag
2521 tgacgggagc aatgtcataa ttaaagaaaa gcaggtaccg tcctcacccc aacatcaagc
2581 tatttccaca gccaccctcg cgctctctag actgcgggct gctagagctc ttgcgtatgc
2641 ctcctgtctg caaagtgcgg tgctgtcaat actccaggtg gccggctctg ccttagtggt
2701 gagcagggcc gtaaaacgta tgtttggcac tcgcaccgaa cagcccattc tggagggtaa
2761 gcataaagaa cataactgca gagtacaccg tgcagaggct gccggccacg gccctattgg
2821 tcatgatgga atcattgaac gttatggtct gtgtgagagt gagcaagaag gggaagatga
2881 ccatactgtg gagctgccca ctgctgacaa agaaggtaag aacaaaggca aaaccaagaa
2941 gggccgcggg cggaagtcta atttcaatgc attctctagg cgtggactta gtgatgaaga
3001 atatgaggag tacaagaaag taagagaaga gaagggtggt aactacagca tacaagagta
3061 ccttgaggat cgccagcgtt atgaagaaga actcgctgag gtgcaagctg gcggagatgg
3121 tgggatcggt gaaactgaag cagagatccg ccaccgggtc ttctataaat caaagtctgg
3181 catgagaaaa caacggcaag aggaacgccg ccagttgggc cttgtgagcg gtactgaaat
3241 ccgtaagcgt aagcccatag attggacccc ccccaaaaat gattggtcag aggacactag
3301 aactgttaac tatgatgaac atattagctt tgaagcccct ccttcaattt ggagtagagt
3361 agttaaattt ggcagtggct ggggcttctg ggtaagttca acagtgttca tcactacaac
3421 acatgttata ccacctggtg ctaaggagat ctttggtgag aatcttagca acattgccat
3481 ccacagggtt ggtgagttca cccaattccg tttctctaag aaaatgaggc ctgatctctc
3541 tggtatggtc cttgaagagg ggtgccctga aggcacagtg tgcaccataa tgataaaaag
3601 agactctgga gagctgttgc cgctagccgt tcgtatggga gcagtggcct caatgaagat
3661 tcaagggaaa ctcatgcacg ggcaatcagg aatgttgctc actggtgcta atgccaaggg
3721 catggacctt ggaaccatac ctggggactg tggagcgcct tacatccata agagagggaa
3781 tgactgggtg gtttgcggtg tgcatgcagc agccacgaaa tcaggtaaca ccgtggtgtg
3841 cgccatccag ggtggtgaag gtgaagccac gctagagggt ggcgatcaaa ataagggaca
3901 ctatgcagga cacccaatat taagatatgg aaatggtcct tcactgtcaa ctaaaacaaa
3961 attctggaaa tcaaaccccc agcctctacc ccctggtaca tatgaaccag cctacctcgg
4021 tggcagagac cccagagttg aaggcggtcc atctttgcag caggtgttgc gagaccagct
4081 aaagccattt gctgaacccc gtggcagatt gcccgaagca ggattgctag aagccgcggt
4141 tgaaactgtc accaatgcaa ttgagcaggt catggacgca ccagtagcat ggagttacag
4201 cgacgcctgc atgtccttag ataaaacaac cagttctggc tacccccatc acaaaaggaa
4261 gaatgatgat tggaatggga gttcatttgt gagagaattg ggagatcaag cagcgcatgc
4321 taacagcatg tatgagcttg gtaagtctat gaaaccagtg tatacagcag cacttaagga
4381 tgaactcgtc aaaccagaca aggtgtacaa taaaatcaag aaaagactac tctggggggc
4441 ggatcttggc actgtcatcc gtgccgctag ggcttttggg ccattttgtg aagcaataaa
4501 accccatgtg attaagttac ccattaaagt gggtatgaac gccatagagg atggcccctt
4561 aatttatgca gaacattcca agtataagta tcactttgat gctgactaca cagcatggga
4621 ttcaacacaa aacagggaga tcatgatgga atcctttaac atcatgtgca aacttaccgc
4681 taacccctcc ctagccgcag tggtggcaca ggacctgctc tccccttctg aaatggatgt
4741 cggtgattat gtgatcagtg tcaaagatgg tctaccatct ggttttccat gcacctcaca
4801 agtaaacagc atcaaccatt ggatctacac tttgtgtgcc ctgtcagagg tcactggttt
4861 agctcctgat gtaatacagt cacaatctta cttttcattt tatggtgatg atgaaatagt
4921 ttcaacagat attgaatttg actcaaacag actaacacag gtattaaaag agtatggcct
4981 aaaacccaca agacctgata aaactgacgg cccaatcatt gtaaggcaac aggttgatgg
5041 cttggttttc ctccggcgca ccatctcgaa ggatgccatc gggtaccagg gtcggcttga
5101 ccgtaattcc attgaaagac agctctggtg gacccgggga cccaaccacg atgatccgtt
5161 tgaaacctta gtcccacaca cacagaggaa ggtccaactg atatccttgc tgggtgaagc
5221 tgcactccat ggtgagaaat tctatagaaa gatagccagt agggtgatcc aggaggtcaa
5281 agaaggagga ttggaaattt acatccctgg ttggcaggcc atgttccgct ggatgcgatt
5341 ccatgatttg agcttgtgga caggagaccg cgatctcttg cccgattatg taaatgatga
5401 tggcgtctaa ggacgcccca acaaacatgg atggcaccag tggtgccggt cagctggtac
5461 cagaggcaaa tacagctgaa cctatatcaa tggatccagt ggctggagcc gcaacagcgg
5521 ttgcaactgc tggacaaatt aatatgattg acccctggat aatgagtaat tttgtgcaag
5581 ccccacaagg ggaattcact gtctcaccta ataacacccc tggagatgtt ctgtttgatt
5641 tacaattggg gcctcaacta aatccattcc tcgcccatct agcccagatg tataatggct
5701 gggtaggcaa tatgcgtgtg aaggtgctgc ttgctggcaa cgcttttact gcagggaaaa
5761 taataattag ctgcataccc ccaggtttta cctcccaaaa tatttctatt gcccaaatga
5821 caatgtttcc tcatgtcatc gctgacgtga gggttctgga acctatagaa ataccccttg
5881 aggatgtgag gaatgtgctg tttcatacca atgacaaccg cccaacaatg aggcttgtat
5941 gcatgttgta tactcccttg cgagccaatg gcagttcttc tggcacggac ccttttgtca
6001 tagctggtcg ggttctcacc tgcccagatt caaatttcag tttcctattt ttagtacccc
6061 ctaatgtaga acaaaagact agacctttta gtgttcccaa tatacctctg aatacattgt
6121 caaattcaag ggtgccatca ttgatcaagt ctatgaccat ctctagagat cagaatcaaa
6181 taatccaatt ccaaaatggc agggtcacat tggatggtca gctacagggc accacaccca
6241 catcagtgag ccagttgtgt aaaattagag gcactacata ccacgcaact ggaggtaatg
6301 ggataaattt aacagagttg aatggtgagc cataccatgc ctttgaaagc cccgccccga
6361 tagggtttcc agaccttggt ggttgcgatt ggcatctcac agcaaccccc acgcaggctt
6421 tcaacgatgg agcgaaggtc gtgcgcctgt cagtcaccca gggcgcagcc tttgcaccac
6481 acctgggtac catacattac accactactg atactgatta caaccccaac accagcataa
6541 tttgcacact agattggctg tcccaaactg ctggtcagag taatgttgac ccttggcaga
6601 taccaactta tgggtcgact ttaactgaag ccgctcagtt ggcgcctccc atctttcccc
6661 ctgggtttgg agaaacattg gttttctttc tatcagactt tcctatttcc aatggcaaga
6721 acggactcag tgtaccgtgc actctcccac aggaatttgt cacccatttt gtgaatgaac
6781 aggccccaat cagaggagag gccgccctct tacactatgt tgatcctgac actcatcgta
6841 atcttggaga gtttaaattg tatccagaag gttttatgac ttgtgttcct aatactagtg
6901 gtggtggtcc ccaaactttg cctatcaatg gagtctttgt ctttgtttct tgggtctctc
6961 gcttttacca gttgaagcct gtgggaacag ccggtgcggc tcgtaggctt ggaatcagga
7021 gatcataatg gctcaagcta tcttaggagc aattgcagcc acagccgctg gcagcgcagt
7081 tggggcaggc attcaggctg gcactgaagc tgcactgcaa catcagcgct ttcaacaaga
7141 cttgactcta caaagtaaca catttaaaca tgataaggag atgttggcta tgcaggtgga
7201 ggcttctact tctttattac agaatagctt gaatactcgc tataacttgt tgacccaggc
7261 aggtctgact tctgcagatg ccgccagagc agtggcgggg gcccccgtca ctcgtgtggt
7321 ggactggaat ggcactcgca tcgccgctcc actatcaact gccaccactc tccgctctgg
7381 aggatttatg tctataccgg tcatgtatag gggtgcaaaa acagaacagc agaaattgac
7441 aggcttctca aaccccaatt acgagactgg ttcatctgtg tcgcgcacat cgcaatgggt
7501 ttcctcacaa aactcaatgc ggtctagcgt agcaccattc cacccagatg cactcaggac
7561 aacttgggtc acaccgcctg gttcgtcttc tacatctact gtttcttcag cttcatctat
7621 acctagattc tttaatactg aaagattacc cttgttcgca aacaataaga ggtga
//