Typing tool
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Typing tool
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Complete norovirus genomes
| MK641589 | GII.14 | |
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| GII.P7 |
ORF1: 5..5098
ORF2: 5079..6689
ORF3: 6689..7483
LOCUS MK641589 7529 bp RNA linear VRL 23-MAR-2019
DEFINITION Norovirus GII isolate CA-RGDS-1023, complete genome.
ACCESSION MK641589
VERSION MK641589.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7529)
AUTHORS Pan,C.-Y., Huynh,T., Newsum,M., Fitzpatrick,K., Castro,C.J.,
Ng,T.F., Marine,R.L. and Wadford,D.A.
TITLE Norovirus GII.P7-GII.14 genome from a school outbreak, Arizona 2018
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7529)
AUTHORS Pan,C.-Y., Huynh,T., Newsum,M., Fitzpatrick,K., Castro,C.J.,
Ng,T.F., Marine,R.L. and Wadford,D.A.
TITLE Direct Submission
JOURNAL Submitted (15-MAR-2019) 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..7529
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="CA-RGDS-1023"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA: AZ"
/collection_date="Feb-2018"
/note="genotype: GII.P7-GII.14"
gene 5..5098
/gene="ORF1"
CDS 5..5098
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QBM30993.1"
/translation="MKMASNDATAALGSQKSVNDSNIATPSNKEEVGTFSNIKVGFKK
MLGAVPKGTKAPSSDQHCPTVKIRPKTLTIPPEPPNGEDTVQFDAKSETVIGLPDLTT
VQNEHENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSDGKALGVHKPP
AAISLATIELTPISLYWRPVYTPNYLVSPDTLKGLAGEKFPYTAFSNNCYNFCCWVLE
LNDTWLNRRCISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKD
LLGKLKPLNLLHLLASCDWTFAGIVETVILMAELFNVFWTPPDVSNFIASLIGDFELQ
GPEDLAVELVPVVMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMK
WFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKAR
KLSTKSSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHM
ARHLAKSIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGSPVKDALTLQEL
ADTCPVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESP
EIEKVKRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSL
TARVAGLVHERKDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGAALKS
VKTLEDLKVALRDVKFNECEIIYKNSKYRVSSNGKGSVSIDKVEDNASQTVNEVHSAL
LRLRQARARYYISCFQDLVYTLIQVAGASFVVSRISRRFCWERWVKPTETQEVNESEK
EAAQGRWEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKY
SIEEYLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTRKQRKEERGVLGLVTG
SDIRKRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNL
LITTTHVLPKGIRELFGVEIKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTV
CSVLVKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCG
CPYIYKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPG
KAPKLSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRG
RLPRPAILEEAKKTVMNVLEQTIDPAKPWSYSQACASLDKTTSSGSPHHVKKNDHWNG
ESFTGPLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGT
MIRCARAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDST
QQRCILSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQ
WNSIAHWILTLSAMAEVSGLSPDVIQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREY
GLVPTRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNH
ENPYESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAM
FRWMRFSDLSTWEGDRNLAPEGVNEDGVE"
mat_peptide 5..1006
/gene="ORF1"
/product="p48"
mat_peptide 1007..2104
/gene="ORF1"
/product="NTPase"
mat_peptide 2105..2623
/gene="ORF1"
/product="p22"
mat_peptide 2624..3022
/gene="ORF1"
/product="VPg"
mat_peptide 3023..3565
/gene="ORF1"
/product="Pro"
mat_peptide 3566..5095
/gene="ORF1"
/product="RdRp"
gene 5079..6689
/gene="ORF2"
CDS 5079..6689
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QBM30994.1"
/translation="MKMASNDATPSDDGAAGLVPEINNEVMALEPVAGASLAAPVVGQ
QNIIDPWIRNNFVQAPAGEFTVSPRNSPGELLLDLELGPELNPYLAHLARMYNGHAGG
MEVQIVLAGNAFTAGKILFAAIPPSFPYENLSPAQLTMCPHVIVDVRQLEPVLLPMPD
IRNVFYHYNQNNSPKLRLVAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFQFTFLVPP
TVESKTKNFTLPVLRVSEMTNSRFPVVLDQMYTSRNENIIVQPQNGRCTTDGELLGTT
ILQSVSICNFKGTMQAKLNEEPRYQLQLTNLDGSPIDPTDDMPAPLGTPDFQAMLYGV
ASQRSSRDNATRAHDAQVDTAGDTFAPKIGQVRFKSSSNDFDLHDPTKFTPIGVNVDD
QHPFRQWSLPNYGGHLALNNHLAPAVTPLFPGEQILFFRSYIPSAGGHTDGAMDCLLP
QEWIEHFYQEAAPSQSDIALVRFINPDTGRVLFEAKLHKQGFLTIAASGDHPIVMPTN
GYFRFEAWVNPFYTLAPVGTGSGRRRIQ"
gene 6689..7483
/gene="ORF3"
CDS 6689..7483
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QBM30995.1"
/translation="MAGAFLAGLAGDVVASSLGSLVGAGANAINQKVEYDFNRQLQEA
SFRHDKDMLKAQVAATAGLQQAMIDIKREALTAGGFSPADAARGAVKAPMTQILDWNG
SRYWAPNSMKTTGYSGTFTSQGIRSSPHLSNQTPSAVKPTRPLPSISSSSSVYSSPST
APSQSTQSTTLSAGTGSSRPNTVSTKTSTLSRTSDWVRGQNEMLGPFMSGALQTAYVT
PPSSKASSQGTVSTVPKAVLDSWTPMFNTHRQPLFAHLRRRGESQI"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgctac cgctgccctt ggcagtcaaa aatctgtcaa
61 tgacagtaat atagccaccc cttctaacaa agaagaggtt ggtacattct ccaacattaa
121 agttggattc aagaaaatgc tgggtgccgt acccaaaggt accaaggcac ccagcagtga
181 tcagcattgc cccacagtta agatcaggcc taaaacattg acaatccccc ccgaaccccc
241 aaatggtgaa gacaccgtac aatttgatgc aaagtcagaa actgtaattg ggctaccgga
301 cttgacaacg gtgcaaaacg aacacgaaaa tactccatac actgtccccc cattaagtga
361 gagggagcac agaccggcca ctgaaccact tcctggcaca atattggaga tgtgggatgg
421 tgagttttac cattactccg tgtacgtcag cgatggtaaa gctctagggg tccacaaacc
481 accggcggct ataagtctcg cgacgataga actcaccccc atatcacttt actggagacc
541 cgtctacacc cccaactact tggtctcccc agacacatta aaaggcctcg ctggtgaaaa
601 gttcccctac acggccttca gcaacaactg ttacaacttc tgttgttggg tgcttgagct
661 caacgacacg tggcttaaca gaagatgcat ctccagaact accggcttct ttaaaccata
721 ccagtcttgg aataggaaac ccctcccaac tgttgatgat ggaaagatca aaaaggtggc
781 caacgcgatc ctctgtgcac tcggctcgct gttttcaaaa ccaatcaaag atctattagg
841 taaactcaaa ccattgaatc tactacactt gcttgcgtcc tgtgattgga cgtttgcggg
901 tatagtagag acagtcatct taatggcgga gcttttcaat gtgttctgga ccccgccaga
961 tgtctctaat tttatagcct ccctgatagg tgattttgaa ttgcaaggtc ctgaagactt
1021 ggctgtggag ctcgttcccg tggttatggg tggcataggg atggttctcg gcttcaccgc
1081 tgagaagata ggccgcatgc tgtcgtccgc ggcatcaaca ctacgggcgt gcaaagactt
1141 agggaactat gcccttgaca tactcaaatt ggtcatgaaa tggttcttcc caaagaagga
1201 agagaaagct gagatggaga ccttgagggc gattgaagat gctgtccttg acatggaagc
1261 tatagggaat aaccatctca caacccttct caaggacaaa gacagcctca cggctttcat
1321 gaaaaccctg gatctagaag aggagaaagc aaggaaactg tccactaaat catcttcacc
1381 ggacatagtc ggcaccatta acgccatact agctaggata gctgctgcta gatccctact
1441 acataaggcc aaagaggaaa tgtttagcag aatcagacca gtagttgtca tgatctcagg
1501 cagacctggc attggaaaaa ctcatatggc aagacacttg gctaagagca tcgccaacac
1561 catgagtggc gaccaaaggg tcggactcgt cccacgcaac ggtgtcgatc actgggatgc
1621 ctacagagga gagagagtag tcttgtggga tgactacggc atggggagcc ctgtcaaaga
1681 cgccctgaca ctgcaagaat tggccgacac atgtccagtc actttaaatt gtgataggat
1741 tgagaataag gggaagatgt ttgatagtga tgtcatcata atcacgacca acttagtcaa
1801 ccccgcgccc ctcgactatg tgaacttcga ggcgtgttcc aggagagttg atttcctggt
1861 ttatgcagag tcaccagaaa ttgaaaaggt caagagagat ttccccggcc agcctgacat
1921 gtggaaagac cattttaagc cagacttctc ccacattaag ctgactctag ccccccaggg
1981 tggatttgac aagaatggta acaccccaca tggcaagggc accatgcggt ccctaaccca
2041 ggggtcccta accgcgagag ttgcaggcct tgtccatgaa aggaaggacg agttccagct
2101 ccaaggaaat gaccttcaaa catacaattt tgacaccaac agagtctccg catttagaaa
2161 attggccgca gacaacaagt atgggatcat ggagacgatg agagttggcg cagcgctcaa
2221 gagcgtgaag accttggaag atcttaaagt tgcattgagg gatgtaaaat tcaatgagtg
2281 tgaaataatt tacaagaatt ctaagtaccg agtctcttcc aacggtaaag gctcagtctc
2341 tattgacaaa gttgaagaca atgcttccca gacagtgaac gaggtgcatt cagccctcct
2401 cagactcagg caggcgaggg ccagatacta catcagctgc ttccaagacc tcgtctacac
2461 tctcatacag gttgccgggg catcatttgt tgttagtagg atctccagga ggttctgctg
2521 ggaaaggtgg gtcaaaccga ccgagaccca ggaggtgaat gagtccgaaa aggaagcggc
2581 ccaaggcaga tgggaaattg agcccaagga cacagaacca gaaggcaaga agggtaagaa
2641 caagaaagga aggggcaaga aacacacagc cttctctagc aaaggtctga gtgatgaaga
2701 gtatgatgag ttcaagagga tcagggaaga aagaaatgga aagtactcca ttgaggaata
2761 cctgcaggac cgagaccgct attatgaaga agtagcagtt gctcgagcga cagaggagga
2821 cttctgtgaa gaggaagagg ccaagataag acaaagaatt ttccgcccga caaggaagca
2881 gaggaaggag gaaaggggcg tactcggctt ggtcaccggc tcagacatca ggaagaggag
2941 accagacgat tttcaaccaa aaggcaatct atgggctgat gacaccagaa gtgtggacta
3001 caatgagagg cttgattttg aagcaccccc gagtgtctgg tcaagaatag tcccactagg
3061 cactggttgg gggttttggg tgtcatccaa ccttctgatc acaacaacac acgtcctgcc
3121 taaagggatt agggaacttt ttggagttga aatcaaacaa atccaaattc ataagtctgg
3181 agagttttgc aggtttagat tcccaagacc tatcaggcca gatgtcacag gactcgtgct
3241 ggaggagggc gccccagagg gcactgtctg ttctgtgctc gtgaaaagac ccacaggtga
3301 aatgatcccc cttgcagtga ggatgggcac acacgcatcc atgaaaatac agggtaggac
3361 cgttggtggc cagatgggaa tgctcctcac aggagcaaac gcaaagaaca tggatcttgg
3421 caccggccct ggtgactgcg gttgccccta tatctataag cgtggcaacg acatcgttgt
3481 tgcgggcgtc cacaccgcag cagcccgggg aggcaacact gtgatatgtg ctacccaggg
3541 gcaagatggg gaagcagtcc ttgagggaaa tgaggacctt ggcacctact gtggtgcccc
3601 aattctgggc cctggtaagg cgcctaaact cagcacgaag accaagtttt ggcgctcatc
3661 accagatgcc ctgccacctg gcacatatga acctgcttac ctaggaggca aagaccctag
3721 agtggaaaaa ggtccctccc tgcagcaagt catgagagat cagctgaagc ccttcacaga
3781 acccagaggc agactaccta gacctgcaat tttagaggaa gccaaaaaga cagtaatgaa
3841 tgttctagag caaaccattg accccgccaa gccatggtcc tattcgcagg catgtgcctc
3901 attggacaaa accacttcaa gtggtagccc ccatcacgtt aagaaaaatg accactggaa
3961 tggagagtcc ttcactggtc ctcttgcaga ccaggcttcc aaagccaacc tcatgtatga
4021 gcaggctaaa catgtgcagc ccgtgtatac ggctgcgctg aaagatgagc ttgttaagac
4081 tgacaagatc tacaagaaga taaagaagag gcttctatgg gggtcagacc ttggcacaat
4141 gatcaggtgc gccagggctt ttggcggtct catggacagc atgaaggcaa gttgtatagc
4201 tcttccttgt agggtaggaa tgaacatgaa tgaagatggc cccatcatat ttgacaaaca
4261 ctctaagtac aggtaccact atgatgctga ctattctagg tgggactcaa cccaacaaag
4321 gtgtatcctc tctgccgcta tggaagtgat ggtgcggttt tctgctgagc cagaattggc
4381 acaagtggtt gcagaggacc ttttggcacc tagccagctt gatgttggcg actttgtcat
4441 ctcagtccag gagggcctgc catcaggagt cccatgcaca tcgcaatgga attcaatagc
4501 acactggata ctcactttga gtgcgatggc agaagtgtca ggcctctcac cagatgttat
4561 ccaagctcac tcttgttttt cattttatgg ggatgatgag atcgtcagca ctgacatcaa
4621 ccttgacccc atgaagttaa cacaaaaact tagggagtat ggcctggttc ccacccggcc
4681 tgacaaaact gaaggtcccc tcgtcataac tgaagacctc accggcctga cgttccttcg
4741 taggtcgatt gctcgggacc cagctggctg gtttggaaaa ctagaccaag attcaatcct
4801 caggcaactg tactggacga gggggcctaa ccatgagaac ccgtacgaga gcatggtccc
4861 tcattctcag cgggctacac aactcatggc ccttcttggt gaggcctcac tgcatggtcc
4921 tcagttttac aagaaagtta gcaaaatggt catcaatgaa attaagagtg gtggtctgga
4981 gttttacgtg cccagacaag aggccatgtt cagatggatg aggttctctg acctcagcac
5041 gtgggagggc gatcgcaatc ttgctcccga aggtgtgaat gaagatggcg tcgaatgacg
5101 ctactccatc tgatgatggt gcagccggcc tcgtaccaga gatcaacaat gaggttatgg
5161 ctcttgaacc cgtcgctggg gcctcccttg cagcccctgt agtcggtcaa cagaatataa
5221 ttgatccctg gattagaaac aattttgtac aagcccctgc tggtgaattt acagtttccc
5281 ctagaaactc tcctggagaa ctcctacttg atttggaatt gggtcctgaa cttaacccct
5341 atcttgcaca tttggccagg atgtacaatg ggcacgcagg aggaatggaa gtgcagatag
5401 tactggctgg gaatgcgttc acagctggta agatcctatt tgccgccatc ccacctagct
5461 tcccttatga aaatttgtca cccgcccaat tgactatgtg cccccatgtg atagtggatg
5521 tgaggcaatt ggaaccagtg ctcttgccaa tgccagatat aagaaatgtt ttctatcatt
5581 ataatcagaa caacagtccc aaacttaggc ttgtggctat gctttacact cctctgaggg
5641 ctaataattc aggtgatgat gtgttcacgg tgtcttgtcg cgttctaacg cgaccttctc
5701 cagatttcca gttcactttc ctggtcccac ctacagttga gtctaaaact aagaacttca
5761 cccttcccgt tctcagagtc tcagagatga caaactcaag gttccccgtt gttttggacc
5821 aaatgtacac aagcaggaat gaaaacatca ttgtccaacc ccaaaacggc agatgcacaa
5881 ctgatggtga gctgcttggt accactatct tacaatctgt gtctatttgc aatttcaaag
5941 gaacaatgca ggcgaagctg aatgaagagc cacgatacca attgcaactc accaacttgg
6001 atgggtcacc catagatcca acagatgata tgcctgcccc tcttggcaca ccagacttcc
6061 aggccatgtt atatggcgtt gcaagccaac gctcttccag agacaatgcc accagggcac
6121 atgatgcaca ggttgacact gcgggtgaca cattcgcccc gaagattggc caggttcgat
6181 ttaaatcaag ctccaatgat tttgacctac atgaccctac aaaattcaca cctattggtg
6241 tcaatgtgga tgaccagcac ccttttagac agtggtccct gccaaactac ggtggtcacc
6301 ttgccctgaa caatcattta gccccagctg tgacgccgct cttccctggc gagcaaatct
6361 tgttctttag gtcatacatt ccaagcgccg gaggccatac agacggtgct atggactgtt
6421 tgctgcccca agagtggata gagcacttct accaggaggc ggctccttcc caatctgaca
6481 tcgcactggt aaggttcatc aaccctgaca caggaagagt gctctttgaa gctaaattgc
6541 ataaacaagg tttcctcaca attgcagcat ctggagacca ccctattgtg atgcccacca
6601 atggttactt taggtttgaa gcttgggtta atcctttcta tactctcgcc cccgtgggaa
6661 ctgggtctgg gcgcaggagg attcaataat ggctggagct ttccttgcag gtttggcagg
6721 tgacgttgtg gcttccagct tgggctcact cgtgggtgct ggagccaacg ccatcaatca
6781 gaaagtggag tatgacttca acaggcaact ccaggaggca tcttttagac atgacaagga
6841 tatgctcaaa gcccaggttg cagcaacagc aggccttcaa caggccatga tagacatcaa
6901 gcgggaggca ttgactgcag gcggcttttc ccccgctgat gctgcaagag gtgcagtcaa
6961 agcgcctatg acgcagatcc ttgattggaa tggttctaga tattgggctc ctaactccat
7021 gaagacaact ggctattcag gtacatttac ttctcaaggc attagaagtt cccctcatct
7081 gtctaatcaa accccaagtg ctgttaaacc tactagacct ttaccatcta tatctagttc
7141 ttctagtgtg tatagttctc cctctactgc cccttcacaa tcaacacaat caacaacgct
7201 gtctgcaggg acagggtcct ccagacctaa cactgtgtcc acaaagacct ccacattgtc
7261 gaggacaagt gattgggtca gaggccaaaa tgagatgctt ggcccgttca tgagtggtgc
7321 actccaaact gcttatgtca caccaccatc gagcaaggcc tcatcacaag ggacggtctc
7381 gaccgtaccc aaggctgttt tggactcctg gactcccatg tttaacaccc acaggcagcc
7441 tctcttcgcc cacttgcgta ggcgagggga gtcacagatt tagtgaaaag gatgattagg
7501 gttccttcct tcccccttct tattctttt
//