LOCUS NC_028970 7270 bp RNA linear VRL 13-AUG-2018
DEFINITION Avisivirus Pf-CHK1/AsV, complete genome.
ACCESSION NC_028970
VERSION NC_028970.1
DBLINK BioProject: PRJNA485481
KEYWORDS RefSeq.
SOURCE Avisivirus Pf-CHK1/AsV
ORGANISM Avisivirus Pf-CHK1/AsV
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Picornaviridae; Paavivirinae; Avisivirus.
REFERENCE 1 (bases 1 to 7270)
AUTHORS Boros,A., Pankovics,P., Adonyi,A., Fenyvesi,H., Day,J.M.,
Phan,T.G., Delwart,E. and Reuter,G.
TITLE A diarrheic chicken simultaneously co-infected with multiple
picornaviruses: Complete genome analysis of avian picornaviruses
representing up to six genera
JOURNAL Virology 489, 63-74 (2015)
PUBMED 26707271
REMARK Publication Status: Available-Online prior to print
REFERENCE 2 (bases 1 to 7270)
CONSRTM NCBI Genome Project
TITLE Direct Submission
JOURNAL Submitted (05-JAN-2016) National Center for Biotechnology
Information, NIH, Bethesda, MD 20894, USA
REFERENCE 3 (bases 1 to 7270)
AUTHORS Boros,A., Reuter,G. and Adonyi,A.
TITLE Direct Submission
JOURNAL Submitted (06-OCT-2015) Regional Laboratory of Virology, ANTSZ,
Baranya County Institute of State Public Health Service, Szabadsag
u. 7, Pecs H-7623, Hungary
COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final
NCBI review. The reference sequence is identical to KT880669.
##Assembly-Data-START##
Sequencing Technology :: Sanger dideoxy sequencing
##Assembly-Data-END##
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..7270
/organism="Avisivirus Pf-CHK1/AsV"
/mol_type="genomic RNA"
/strain="Pf-CHK1/AsV"
/isolation_source="cloacal sample"
/host="Gallus gallus domesticus (domestic chicken)"
/db_xref="taxon:1766559"
/country="Hungary"
/collection_date="2013"
5'UTR 1..561
gene 562..7002
/locus_tag="AVT86_gp1"
/db_xref="GeneID:26641536"
CDS 562..7002
/locus_tag="AVT86_gp1"
/codon_start=1
/product="polyprotein"
/protein_id="YP_009215118.1"
/db_xref="GeneID:26641536"
/translation="MEQVGAAIAAVSEAAASLAENPVQEIIEGVGNLATTVSTNALVQ
TSNPTVETGLPDSTNIISDDYLSCACTVDSDTMNVEKTILFGTDDWSSNHTFGTCISR
YDVPNAFLDSNSCPAYGQSSYFRYLRCGFRFQITTNPPPGAGGSLILAYVPPGFQFRV
QPKGQTITGFDSEAVLTLPHVIVDIRSSTHSALTIPYVNHKNYFNYAYQQDFRGTVVV
FVLGQYTVGSGTSSTVGVSVFGEMLEADFQCPRPYQSQGQNRRRIRRRKAPPPPSNPP
VGRHVNIGPAPGAVVAANSVLNVTTADSLAIGNEGTAVDCTTAGASSAIPDVKELASD
WQILHQESRSWAALTAGARVWSGNFAPYEVGNIGALMDKFMYWRGSFEVQLVVYGSSL
TSGRIQLSFYPGMPNNNSRTLQDMRNAFYSTGDISATPTRLTIPFTNDSWRRRCDQQY
GSFYIHIVNRVCVNASASPTMSFVLFVRLGPDFQLFCPRYGDYHIEGPIVEKTPEESE
EGETYSGQPHVFLNFDCVEVPIHGASHTLVRNLFGRLWLQEHTVSPSSGTHVVNLEVP
NESHAAILQCFAYFSGEIILSIRNGGDTTVIAAHTYVPEEQHDPTNEFSIMSLGAVVI
PPLEIKTIRVPFYSPSPLRMIRRHNTFEPTFGYLYLCSPSTTNVTVYMGLANPNLFFK
LPCPRYTTNTRSRSARSAPRFFREDDDHYNILLGGDIEENPGPVVVCGPSKGGKTRLL
CAMAGHPIVPNFPGPHVANMLGEEFTEIPEDMKLPLNKKILVVLGEDNDANANYIQWL
SEEYPSWNHRAVVFCWPGCQLTGNNFRICRNPIAVSALLAQSLPYNTRGTQLVYQDRG
LYRHYGVLLDNKVFHLDSQDILKSGLKGSAVVSVDDPLEWVPCSATDLAGSLDLANSG
TIEIDFNINSNCETWAKGVIGDLSPTQSDRLKKVLVVAAAAGFLYCLPHDQSGFMDGV
TKCLINLFSKQVKSAMIRMAIKFVCRLVCYLILYCHSPNILNTGVLTTLLLMDVFELE
VDEGLDKLAHALIEGDFKGLGKFLKKRTGRDCDDFEPGDDHRPIFRAEGPDDLPKTFN
SWSLMAKNVEWWITKFADFCKWLKEKVFPENHEDQIEQVEKLKDTLALTICQADKHLV
AMRTDRDYATSYEANIYHQNLMVKLVDLNAKDWGPDFRELSIKLGQVLQRMQAVNFES
SNMNGLRAEPVGIWISGGPGCGKSFLAQILIKHLRLAHGFSTYNHPTGSEHMDGYTGQ
EVHYIDDMGQIREEEDMKLLCQLISSQPFIVPKAELLSKGTQYRAKIVIATTNRTSFD
TMVLSDTGALQRRFPIRLKIRAHSFYTKADGTLDVALAMERKAFEDGSCWEINVGNDS
RPCWQTLNWEVLTDEIDRMVATRSSIASLFNQGARCDLESDEVELIPETGPGSVNPKT
MDKVKNWLNSLLTDALSWWERNKQWLLLVSALSTLASLAIGAIPAYRAIQNQLYHGEP
SAKPKDRVKRDFKPEGPNFHSLKDRMVEIGTSHSTGLLLCDKKVLTFGHNTDCGFITH
KDQTFKVTSETYISVSGCDQDLKILEVETPYQFKNCSHKIYSGNYKGDGNLIFLRNNQ
LIIKDVFRIREKQGIGTIDGTYTHSAYAYSARTGSGSCGGILVGYVSGNPIILGMHVA
GNGDTGIAARLYPCFAQGVTMHKWKQEQMFDTNYHQPRRSKFSPSCFFDTGAQEPAIL
SNRDPRNPGIEDITKHNADKLTGNVFDPPEDAFALAKSRLIGSMSVHVEPEGQATFEE
AVSSELLPIDWGTSPGDKYRGKTKAELVDDKKFRADVYNLVKRFNGDPDREPVDVYFT
CYLKDELRPKEKARACKTRVISAANWDYTIATRMVAGPILRQLYAWGREFGFGPGLNP
YSHFDDLYDKILPFVICLDFKGFDGSLSSDLMFEAAQVIACFSTKPEAIMASAELTIG
STERVSDEVWYNYGGMPSGSPWTTTLNTICNLLMCYTYLLDMGHCWSDTYVVAYGDDV
VISANIKHNLEGIENWFKTKFGATVTSSDKQSKITWTTKNNMEFLKRRPKELEFLPKI
VGALDLDNMLQHLEWTKGHIQDQLNSFYLELALHGREKYEEIRAKLAPRAPQLVHPTY
ACARATITPMVAIL"
misc_feature 877..1317
/locus_tag="AVT86_gp1"
/note="Picornavirus capsid protein domain_like.
Picornaviruses are non-enveloped plus-strand ssRNA animal
viruses with icosahedral capsids composed of 60 copies
each of 4 virus encoded proteins; alignment includes
picornaviridae, like poliovirus, hepatitis A...; Region:
rhv_like; cd00205"
/db_xref="CDD:119412"
misc_feature order(877..879,952..954,958..960,964..966,1012..1014,
1102..1104,1171..1173,1195..1197,1279..1281)
/locus_tag="AVT86_gp1"
/note="drug-binding pocket [chemical binding]; other site"
/db_xref="CDD:119412"
misc_feature 1627..2031
/locus_tag="AVT86_gp1"
/note="Picornavirus capsid protein domain_like.
Picornaviruses are non-enveloped plus-strand ssRNA animal
viruses with icosahedral capsids composed of 60 copies
each of 4 virus encoded proteins; alignment includes
picornaviridae, like poliovirus, hepatitis A...; Region:
rhv_like; cd00205"
/db_xref="CDD:119412"
misc_feature order(1702..1704,1708..1710,1714..1716,1762..1764,
1816..1818,1891..1893,1909..1911,1990..1992)
/locus_tag="AVT86_gp1"
/note="drug-binding pocket [chemical binding]; other site"
/db_xref="CDD:119412"
misc_feature <2272..2631
/locus_tag="AVT86_gp1"
/note="Picornavirus capsid protein domain_like.
Picornaviruses are non-enveloped plus-strand ssRNA animal
viruses with icosahedral capsids composed of 60 copies
each of 4 virus encoded proteins; alignment includes
picornaviridae, like poliovirus, hepatitis A...; Region:
rhv_like; cl13999"
/db_xref="CDD:417456"
misc_feature order(2311..2313,2317..2319,2323..2325,2365..2367,
2425..2427,2488..2490,2524..2526,2575..2577)
/locus_tag="AVT86_gp1"
/note="drug-binding pocket [chemical binding]; other site"
/db_xref="CDD:119412"
misc_feature 4210..4506
/locus_tag="AVT86_gp1"
/note="RNA helicase; Region: RNA_helicase; pfam00910"
/db_xref="CDD:425942"
misc_feature 4222..4245
/locus_tag="AVT86_gp1"
/note="Walker A motif; other site"
/db_xref="CDD:99707"
misc_feature order(4225..4248,4504..4506)
/locus_tag="AVT86_gp1"
/note="ATP binding site [chemical binding]; other site"
/db_xref="CDD:99707"
misc_feature 4558..4560
/locus_tag="AVT86_gp1"
/note="arginine finger; other site"
/db_xref="CDD:99707"
misc_feature 5083..5574
/locus_tag="AVT86_gp1"
/note="3C cysteine protease (picornain 3C); Region:
Peptidase_C3; pfam00548"
/db_xref="CDD:278947"
misc_feature 5908..6996
/locus_tag="AVT86_gp1"
/note="catalytic core domain of RNA-dependent RNA
polymerase (RdRp) in the genus Avisivirus of
positive-sense single-stranded RNA [(+)ssRNA] viruses,
within the family Picornaviridae; Region: Avisivirus_RdRp;
cd23231"
/db_xref="CDD:438081"
misc_feature order(5929..5934,5941..5943,5950..5955,5989..5991,
6091..6093,6097..6099,6148..6150,6154..6156,6184..6186,
6217..6219,6247..6258,6487..6507,6595..6606,6745..6753,
6817..6819,6841..6843,6850..6855,6859..6867,6874..6876)
/locus_tag="AVT86_gp1"
/note="putative RNA binding site [nucleotide binding];
other site"
/db_xref="CDD:438081"
misc_feature 6088..6153
/locus_tag="AVT86_gp1"
/note="conserved polymerase motif F; other site"
/db_xref="CDD:438081"
misc_feature 6301..6345
/locus_tag="AVT86_gp1"
/note="conserved polymerase motif A; other site"
/db_xref="CDD:438081"
misc_feature 6481..6552
/locus_tag="AVT86_gp1"
/note="conserved polymerase motif B; other site"
/db_xref="CDD:438081"
misc_feature 6580..6624
/locus_tag="AVT86_gp1"
/note="conserved polymerase motif C; other site"
/db_xref="CDD:438081"
3'UTR 7003..7270
ORIGIN
1 cattcccctt tccccagcca tgggttaaat ggcccctcac caggttcggt gctgtctagg
61 cttccagtaa agaagtcaac cgagcattga acaaaacctc agtgggtatg gtagttaacc
121 ccgtccactg gacaactttg tcctcttaaa agtggatcaa tccaccccaa ctccccccct
181 agccacctga gccatggtgg atagcagtga cgaaactagg gaccccaata cctctagtgc
241 caagagaatt cccccctcgc gagaggtgct cttgggcccg aaaggctagt tggcagggtg
301 aagtgaagga agctgctagc gtggcaacct taagcgtagc ccgaagctga ccttagaggt
361 taaccctagt ggaccactgg atgaagctgt ggaggtggtg gataggaaag ttggccactt
421 gtgagtagat gcccagaagg cataaggctg atctggggcc agtgactata ccgttccggt
481 aaacctggta taaaaaccat gaaagcaagt gggtttaaaa tttcttctaa ttccttcatt
541 tcagtagtga taactggcag aatggagcag gttggtgccg ctatcgctgc tgtttcagag
601 gctgcagcca gtctggctga aaacccagtg caagagataa ttgaaggtgt tgggaatctg
661 gctacaacgg tgagcacaaa tgcgttggta cagacatcca atccgactgt tgagactggt
721 ttgccagact caactaatat tatttcagat gattacttga gctgtgcttg tactgttgac
781 tctgacacca tgaatgtaga gaagactatt ctatttggaa ctgatgactg gtcatctaat
841 cacacctttg gaacttgtat ttcgaggtat gacgttccaa atgcatttct agattcaaat
901 tcatgcccag cttatggaca atcaagctat ttcaggtacc tcaggtgcgg atttcgcttc
961 caaatcacaa ccaatcctcc tccaggtgct ggaggtagcc tgatcctggc ctatgtccct
1021 cctggtttcc agttccgagt tcaaccaaag ggtcagacga taacaggctt tgactctgaa
1081 gctgttctaa cacttcccca tgttattgtt gacattcgat caagcacgca tagtgctttg
1141 actatacctt atgtcaacca caagaactac ttcaactatg cttaccagca agattttcgg
1201 ggcactgttg ttgtctttgt gttagggcag tacacagttg gatctggaac ctcctcaaca
1261 gtgggtgtct ctgtctttgg tgaaatgctt gaagcagatt tccagtgccc cagaccctac
1321 cagtctcaag gccaaaacag gcggagaata cgtaggagga aggccccacc acccccttca
1381 aatccaccag tggggagaca tgttaacatt ggcccagcac cgggggctgt tgttgctgca
1441 aactctgtcc taaatgtcac cactgctgat tcactagcca ttggaaacga ggggacagct
1501 gttgactgta caacggctgg agcatcttct gcgatacctg atgtcaaaga attggcatct
1561 gactggcaga tcctccacca agaatcacgt tcatgggcag ctttgactgc tggagcccgt
1621 gtgtggagtg gaaactttgc accctatgaa gtcgggaaca ttggagcctt gatggacaag
1681 ttcatgtatt ggaggggatc tttcgaagtc caactggtgg tttatgggtc ctctctgaca
1741 tctgggcgaa tacagttgag cttctaccct gggatgccta ataataattc ccgcaccctg
1801 caggacatga gaaatgcctt ctactcgact ggagacatta gcgccactcc aacaaggcta
1861 acaattccat ttactaatga cagttggagg cgcaggtgtg accaacagta tggttccttc
1921 tacatccaca ttgtcaaccg tgtgtgtgtg aacgcatcag cgagtcccac tatgtcattt
1981 gttctctttg tgagattggg accagacttc caactcttct gcccccggta tggggactac
2041 cacattgagg gacccattgt tgagaagacc ccagaagaat ctgaggaggg tgagacctat
2101 agtgggcaac cacatgtctt cctcaatttt gactgtgttg aagttccaat acatggggcc
2161 agtcacactc tagttaggaa tttatttggc agactttggt tgcaagagca tactgtgtca
2221 ccatcttcag gaacccatgt tgtaaatctt gaggttccaa atgaatcaca tgcagccata
2281 cttcaatgct ttgcatattt tagtggggag ataattcttt caattagaaa tggaggagac
2341 accacagtca ttgctgcaca tacttatgtt cctgaagaac aacatgatcc cactaatgag
2401 ttttccatca tgtctttggg agctgtagta atcccaccgt tggaaattaa gacaattaga
2461 gtcccctttt acagtcccag tccattaagg atgattcgta gacacaacac ttttgaacca
2521 acatttggtt atctctattt gtgttcaccc agcacaacaa atgtcacagt ttacatgggc
2581 cttgcaaatc caaatctctt cttcaagttg ccgtgcccac ggtacaccac taacacacgt
2641 tccaggtcag cccgatctgc gccacgattc ttcagggaag atgacgatca ttacaacatc
2701 cttcttggtg gtgacattga agagaaccca ggccctgttg tagtgtgtgg accatcaaaa
2761 gggggtaaga cacgccttct ctgtgcaatg gctggacacc ccattgttcc aaattttcca
2821 ggaccacatg tagccaatat gcttggggag gaattcactg agatcccaga agatatgaag
2881 ttgcctctca acaagaagat tctggttgtc cttggtgagg acaatgatgc caatgcaaat
2941 tacattcaat ggctaagtga ggagtaccca tcctggaacc atcgggcagt ggtattctgt
3001 tggcctggct gccaattaac tgggaacaat tttagaatct gcaggaatcc aattgcagtt
3061 tctgcactct tggctcaatc actcccttat aacaccaggg gtacacaatt ggtttatcaa
3121 gatcgtggcc tttataggca ttatggggtc ctcttagaca ataaggtgtt ccaccttgat
3181 tcacaagaca tcctcaagtc aggactgaaa gggagtgctg tggtcagtgt tgacgaccct
3241 cttgaatggg taccctgtag tgccacagat cttgctggct ctcttgatct tgccaatagt
3301 gggacaatag aaattgactt taatatcaat agcaattgtg agacatgggc caaaggagta
3361 attggggatt tgtcaccgac acaatcagac agactcaaaa aggttcttgt tgtggcagca
3421 gctgctggat ttttgtattg cctaccacat gatcaatctg gttttatgga tggggtgact
3481 aaatgtctta ttaatctctt ttcaaaacaa gttaagtctg caatgattag aatggcaatc
3541 aagtttgttt gcagactagt ctgctacctc attctctact gccatagtcc aaacattctc
3601 aatactggag tcctaacaac tctcctcctt atggatgtct ttgaattgga agttgatgag
3661 ggccttgata aattggcaca tgctctcatt gagggagact ttaaggggct tggcaaattc
3721 cttaagaaaa gaactggaag ggactgtgat gactttgagc caggtgatga ccaccgccct
3781 atttttagag ctgagggccc agacgacctt ccaaaaacct ttaactcctg gagcctaatg
3841 gcaaagaatg ttgaatggtg gatcaccaaa tttgctgatt tctgcaaatg gctcaaggaa
3901 aaagtcttcc ctgagaacca tgaggaccaa attgaacagg ttgaaaaatt aaaggacacc
3961 cttgctctca caatctgcca agcagacaaa cacctggtcg caatgagaac tgatagagat
4021 tatgccacta gctatgaggc caacatttac catcaaaatt tgatggttaa gctagttgac
4081 ctcaatgcca aagattgggg accagacttc agggagttat caattaaatt gggccaagtc
4141 ctccaaagga tgcaggctgt aaattttgaa tccagcaaca tgaatggtct acgtgcagaa
4201 ccagttggga tttggattag tggtggtcct ggatgcggaa aaagtttcct ggcccaaatt
4261 ttgataaaac acctcagatt ggcgcatggt ttcagtacct acaatcaccc cactggaagc
4321 gagcatatgg atggctacac tggccaggag gtccactata ttgatgacat gggtcaaatc
4381 cgagaggagg aggacatgaa acttctgtgt caattgatct cctcacaacc attcattgtc
4441 ccgaaggcag agctcctctc aaagggcaca caatatcgtg ccaaaattgt gatagcaaca
4501 acaaatagga ccagctttga caccatggtt ctaagtgaca caggggctct tcagaggaga
4561 tttccaatta ggcttaaaat tagggcacat tcattttata ctaaagctga tggcaccctt
4621 gatgtggccc tagctatgga gaggaaggcc ttcgaggatg ggtcatgttg ggaaataaat
4681 gttggaaatg actcccgccc atgttggcag actctgaact gggaagtcct tacagatgag
4741 atagatcgaa tggttgcaac taggagctcg attgcatctc tttttaatca gggagctcgt
4801 tgtgaccttg agtctgatga ggttgaatta attccagaga ctggcccagg cagtgttaac
4861 cccaaaacca tggataaagt gaagaattgg ttaaattcac ttcttactga cgccctatct
4921 tggtgggaga gaaacaagca gtggctcctc ttggtgtctg cactcagtac acttgcttca
4981 ttagccattg gagcgattcc agcctacaga gctattcaaa accaacttta ccatggtgaa
5041 ccaagtgcaa aaccaaaaga ccgggtaaag cgtgacttta agccagaagg cccaaatttt
5101 cattcactta aagatagaat ggttgaaatt ggtacatcac actcaactgg gcttctcctt
5161 tgtgacaaga aagttctaac atttggccat aacacagact gtggtttcat tacccataaa
5221 gaccaaacat ttaaggtcac ttctgaaacc tacatatcag tgagtggctg tgaccaagat
5281 cttaaaattc ttgaggttga aaccccttac cagttcaaga attgtagcca taaaatttac
5341 tcaggtaatt ataagggtga tggaaatttg attttcctca ggaacaacca actcatcatt
5401 aaagatgtgt tccggattag ggagaagcag ggaattggca ctattgatgg aacctacact
5461 cacagtgctt atgcctattc agctagaaca ggctctggat catgtggtgg aattctggtt
5521 ggatatgtta gtggaaatcc aatcatcctc ggtatgcacg ttgcaggaaa tggggatact
5581 ggtattgctg cccgtctcta tccatgcttt gctcaaggag tcactatgca caagtggaag
5641 caggagcaga tgtttgacac caactaccac cagccacgca ggtcaaagtt ttctccatct
5701 tgtttctttg acactggagc tcaggagcca gctattctgt caaatcgcga ccctcgcaac
5761 cctggcattg aagatattac taaacacaat gctgacaaat tgactgggaa cgtctttgat
5821 ccaccagaag acgcctttgc cctagcaaag tcaaggctta ttggttcaat gtctgtacat
5881 gttgaaccag aggggcaggc aacctttgag gaagccgtga gttctgagct cctccccatt
5941 gactggggta catcccctgg agacaagtat aggggcaaga caaaagctga gttagttgat
6001 gacaagaagt ttagggctga tgtctacaat ttggttaaac gcttcaatgg ggatccagat
6061 cgtgaaccag ttgatgtcta cttcacttgt tatcttaagg acgagcttcg ccccaaagag
6121 aaagcaaggg cttgcaagac aagagtgatt tcagctgcaa attgggatta tacaattgcc
6181 actagaatgg ttgcaggacc aatcttgcgt caactctatg cttggggtcg tgaatttggt
6241 tttggtccag gactcaatcc ttactcccac tttgatgacc tctatgacaa gattttaccc
6301 tttgtcatat gtctggattt caaaggattc gatggctcat tgtcatctga tctgatgttt
6361 gaggctgcac aggtcattgc atgtttttca acaaaacctg aggctattat ggctagtgca
6421 gaattaacta ttggatcaac tgagcgcgta tctgatgagg tctggtacaa ctatggtggg
6481 atgccctctg gctcaccttg gactactacg ctgaacacaa tctgcaatct cctaatgtgc
6541 tacacttatc ttcttgacat gggccactgc tggtcagata cctatgtcgt ggcatatggg
6601 gatgatgttg tcatttcagc aaatataaag cacaatcttg agggcattga gaattggttc
6661 aaaactaaat ttggtgcaac tgtgacatct agtgataagc agtcaaaaat cacctggacc
6721 accaaaaata atatggaatt cctcaaacgc agaccaaaag aattggaatt cctacccaaa
6781 atcgttggag ctctagattt ggataatatg cttcaacacc ttgagtggac caagggccac
6841 attcaggacc agctgaactc attctaccta gaattggcac tgcatggtag ggaaaaatat
6901 gaggaaatca gagctaaatt ggccccccga gctcctcaac tggttcatcc aacatatgct
6961 tgtgcaagag cgactattac accaatggtc gccatactgt aatctctagc tcacgagggt
7021 aaactgagta gccgtggtct cggctatata aatgaccatt tcaggcagca ccctagctca
7081 cgggttgaaa ctgagtagcc gtggtctcgg ctatataaat gaccagagta gtttaggtaa
7141 gttcttttgt ctttctatca tcttcttttc cacagggcaa gagatccctt ttcaactctc
7201 cggtatttgg cacccgtagt gcccctaatt tgactttctg ttgtttatag aattaggacc
7261 aatcaaaatc
//
