LOCUS NC_001699 5130 bp DNA circular VRL 13-AUG-2018
DEFINITION JC polyomavirus, complete genome.
ACCESSION NC_001699
VERSION NC_001699.1
DBLINK BioProject: PRJNA485481
KEYWORDS RefSeq.
SOURCE JC polyomavirus (JCPyV)
ORGANISM JC polyomavirus
Viruses; Monodnaviria; Shotokuvirae; Cossaviricota;
Papovaviricetes; Sepolyvirales; Polyomaviridae; Betapolyomavirus;
Betapolyomavirus secuhominis.
REFERENCE 1 (sites)
AUTHORS Miyamura,T., Furuno,A. and Yoshiike,K.
TITLE DNA rearrangement in the control region for early transcription in
a human polyomavirus JC host range mutant capable of growing in
human embryonic kidney cells
JOURNAL J. Virol. 54 (3), 750-756 (1985)
PUBMED 2987529
REFERENCE 2 (sites)
AUTHORS Martin,J.D., King,D.M., Slauch,J.M. and Frisque,R.J.
TITLE Differences in regulatory sequences of naturally occurring JC virus
variants
JOURNAL J. Virol. 53 (1), 306-311 (1985)
PUBMED 2981353
REFERENCE 3 (sites)
AUTHORS Kenney,S., Natarajan,V., Strike,D., Khoury,G. and Salzman,N.P.
TITLE JC virus enhancer-promoter active in human brain cells
JOURNAL Science 226 (4680), 1337-1339 (1984)
PUBMED 6095453
REFERENCE 4 (bases 1 to 5130)
AUTHORS Frisque,R.J., Bream,G.L. and Cannella,M.T.
TITLE Human polyomavirus JC virus genome
JOURNAL J. Virol. 51 (2), 458-469 (1984)
PUBMED 6086957
REFERENCE 5 (bases 1 to 283; 4684 to 5130)
AUTHORS Frisque,R.J.
TITLE Nucleotide sequence of the region encompassing the JC virus origin
of DNA replication
JOURNAL J. Virol. 46 (1), 170-176 (1983)
PUBMED 6298454
REFERENCE 6 (bases 1 to 64; 4250 to 5130)
AUTHORS Miyamura,T., Jikuya,H., Soeda,E. and Yoshiike,K.
TITLE Genomic structure of human polyoma virus JC: nucleotide sequence of
the region containing replication origin and small-T-antigen gene
JOURNAL J. Virol. 45 (1), 73-79 (1983)
PUBMED 6296460
REFERENCE 7 (bases 1 to 5130)
CONSRTM NCBI Genome Project
TITLE Direct Submission
JOURNAL Submitted (01-AUG-2000) National Center for Biotechnology
Information, NIH, Bethesda, MD 20894, USA
COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final
NCBI review. The reference sequence is identical to J02226.
[5] sites; sequence analysis of regulatory variants. [6] sites;
mutational rearrangement in early control region;. [4] sites;
enhancer-promoter sequence.
Draft entry and computer-readable sequence for [2] kindly provided
by R.J.Frisque, 22-JAN-1987.
JCV is a polyomavirus more closely related to SV40 and BKV than to
polyoma (PY). It can apparently cause the human disease
progressive multifocal leukoencephalopathy and it can be highly
oncogenic in primates. It grows well only in human fetal glial
cells.
The E strand, having the polarity of the late mRNAs, is shown as it
is reported in its entirety by [3]. That reference is also the
primary source for the annotation herein, most of which is inferred
by analogy with SV40 and BKV. The map units are calculated by
JC + 3408
mu = ------------- x 100,
5130
where, as with other polyoma viruses, the single EcoRI site (at
base 1722 ) is taken as 0.00%.
The mRNA start and end points are no more than putative: a possible
promoter element ('TATA') for early mRNA initiation is found at
base 22 on the comp strand, and similar elements for late mRNA
initiation are found at bases 15 and 117.
As with BKV and SV40 (but not PY) the JC virus does not appear to
encode a middle t-antigen; rather it appears to induce a host-cell
specific middle t-antigen in transformed cells [3]. The Mad-1
strain of JCV is severely restricted in its growth in vitro.
References [5], [6] and [4] show that mutations in the noncoding,
regulatory region of the genome can affect host cell range. On the
basis of seven independent isolates, [5] proposes that an enhancer
segment (bases 12 to 207 below) is hypervariable. [6] has sequenced
a fragment of an isolate (see separate entry) which has adapted to
growth on originally nonpermissive human embryonic kidney cells;
this form has an insertion of around 800 bp in the noncoding region
near the origin of replication, yet can replicate DNA and direct
large t-antigen synthesis in HEK cells. [4] specifically studies
the enhancer region from bases 57 to 109 below, which is embedded
in the first 98 bp tandem repeat; this sequence is shown to be
homologous to an 82 bp rat brain-specific transcription factor.
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..5130
/organism="JC polyomavirus"
/mol_type="genomic DNA"
/strain="Mad1"
/db_xref="taxon:10632"
rep_origin join(5118..5130,1..12)
/note="origin of replication (both ends putative); 66.67%
[3]; putative"
rep_origin 1..12
/note="putative"
repeat_region 11..109
/note="first 98 bp tandem repeat 5' 66.65%"
repeat_region 110..207
/note="second 98 bp tandem repeat 5' 68.58%"
prim_transcript 163..2594
/note="late mRNA [3]"
gene 277..492
/locus_tag="Jvgp1"
/db_xref="GeneID:1489519"
CDS 277..492
/locus_tag="Jvgp1"
/note="agnoprotein"
/codon_start=1
/product="hypothetical protein"
/protein_id="NP_043508.1"
/db_xref="GeneID:1489519"
/translation="MVLRQLSRKASVKVSKTWSGTKKRAQRILIFLLEFLLDFCTGED
SVDGKKRQRHSGLTEQTYSALPEPKAT"
misc_feature 277..480
/locus_tag="Jvgp1"
/note="agnoprotein; Provisional; Region: PHA02621"
/db_xref="CDD:177440"
intron 493..1426
/note="late mRNA intron (mVP1 transcript)"
intron 493..521
/note="late mRNA intron (mVP1/mVP2 transcripts) [3]"
gene 526..1560
/locus_tag="Jvgp2"
/db_xref="GeneID:1489522"
CDS 526..1560
/locus_tag="Jvgp2"
/note="VP2 capsid protein"
/codon_start=1
/product="hypothetical protein"
/protein_id="NP_043509.1"
/db_xref="GeneID:1489522"
/translation="MGAALALLGDLVATVSEAAAATGFSVAEIAAGEAAATIEVEIAS
LATVEGITSTSEAIAAIGLTPETYAVITGAPGAVAGFAALVQTVTGGSAIAQLGYRFF
ADWDHKVSTVGLFQQPAMALQLFNPEDYYDILFPGVNAFVNNIHYLDPRHWGPSLFST
ISQAFWNLVRDDLPALTSQEIQRRTQKLFVESLARFLEETTWAIVNSPANLYNYISDY
YSRLSPVRPSMVRQVAQREGTYISFGHSYTQSIDDADSIQEVTQRLDLKTPNVQSGEF
IERSIAPGGANQRSAPQWMLPLLLGLYGTVTPALEAYEDGPNKKKRRKEGPRASSKTS
YKRRSRSSRS"
misc_feature 526..1533
/locus_tag="Jvgp2"
/note="VP3; Provisional; Region: PHA02620"
/db_xref="CDD:177439"
gene 883..1560
/locus_tag="Jvgp3"
/db_xref="GeneID:1489520"
CDS 883..1560
/locus_tag="Jvgp3"
/note="VP3 capsid protein"
/codon_start=1
/product="hypothetical protein"
/protein_id="NP_043510.1"
/db_xref="GeneID:1489520"
/translation="MALQLFNPEDYYDILFPGVNAFVNNIHYLDPRHWGPSLFSTISQ
AFWNLVRDDLPALTSQEIQRRTQKLFVESLARFLEETTWAIVNSPANLYNYISDYYSR
LSPVRPSMVRQVAQREGTYISFGHSYTQSIDDADSIQEVTQRLDLKTPNVQSGEFIER
SIAPGGANQRSAPQWMLPLLLGLYGTVTPALEAYEDGPNKKKRRKEGPRASSKTSYKR
RSRSSRS"
misc_feature <883..1533
/locus_tag="Jvgp3"
/note="VP3; Provisional; Region: PHA02620"
/db_xref="CDD:177439"
gene 1469..2533
/locus_tag="Jvgp4"
/db_xref="GeneID:1489518"
CDS 1469..2533
/locus_tag="Jvgp4"
/note="VP1 capsid protein"
/codon_start=1
/product="hypothetical protein"
/protein_id="NP_043511.1"
/db_xref="GeneID:1489518"
/translation="MAPTKRKGERKDPVQVPKLLIRGGVEVLEVKTGVDSITEVECFL
TPEMGDPDEHLRGFSKSISISDTFESDSPNRDMLPCYSVARIPLPNLNEDLTCGNILM
WEAVTLKTEVIGVTSLMNVHSNGQATHDNGAGKPVQGTSFHFFSVGGEALELQGVLFN
YRTKYPDGTIFPKNATVQSQVMNTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLT
GGENVPPVLHITNTATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLS
RYFKVQLRKRRVKNPYPISFLLTDLINRRTPRVDGQPMYGMDAQVEEVRVFEGTEELP
GDPDMMRYVDKYGQLQTKML"
misc_feature 1472..2530
/locus_tag="Jvgp4"
/note="Major capsid protein VP1; Provisional; Region:
PHA02614"
/db_xref="CDD:222910"
prim_transcript complement(2527..5115)
/note="early mRNA (3' end +/- 8bp) [3]"
regulatory complement(2548..2553)
/regulatory_class="polyA_signal_sequence"
/note="early mRNA polyadenyation signal on comp strand;
16.10% [3]"
regulatory 2568..2573
/regulatory_class="polyA_signal_sequence"
/note="late mRNA polyadenyation signal; 16.49% [3]"
gene complement(2603..5013)
/locus_tag="Jvgp5"
/db_xref="GeneID:1489517"
CDS complement(join(2603..4426,4771..5013))
/locus_tag="Jvgp5"
/note="large t-antigen"
/codon_start=1
/product="hypothetical protein"
/protein_id="NP_043512.1"
/db_xref="GeneID:1489517"
/translation="MDKVLNREESMELMDLLGLDRSAWGNIPVMRKAYLKKCKELHPD
KGGDEDKMKRMNFLYKKMEQGVKVAHQPDFGTWNSSEVPTYGTDEWESWWNTFNEKWD
EDLFCHEEMFASDDENTGSQHSTPPKKKKKVEDPKDFPVDLHAFLSQAVFSNRTVASF
AVYTTKEKAQILYKKLMEKYSVTFISRHGFGGHNILFFLTPHRHRVSAINNYCQKLCT
FSFLICKGVNKEYLFYSALCRQPYAVVEESIQGGLKEHDFNPEEPEETKQVSWKLVTQ
YALETKCEDVFLLMGMYLDFQENPQQCKKCEKKDQPNHFNHHEKHYYNAQIFADSKNQ
KSICQQAVDTVAAKQRVDSIHMTREEMLVERFNFLLDKMDLIFGAHGNAVLEQYMAGV
AWIHCLLPQMDTVIYDFLKCIVLNIPKKRYWLFKGPIDSGKTTLAAALLDLCGGKSLN
VNMPLERLNFELGVGIDQFMVVFEDVKGTGAESRDLPSGHGISNLDCLRDYLDGSVKV
NLERKHQNKRTQVFPPGIVTMNEYSVPRTLQARFVRQIDFRPKAYLRKSLSCSEYLLE
KRILQSGMTLLLLLIWFRPVADFAAAIHERIVQWKERLDLEISMYTFSTMKANVGMGR
PILDFPREEDSEAEDSGHGSSTESQSQCFSQVSEASGADTQENCTFHICKGFQCFKKP
KTPPPK"
misc_feature complement(join(2762..4426,4771..5013))
/locus_tag="Jvgp5"
/note="large T antigen; Provisional; Region: PHA02624"
/db_xref="CDD:222912"
exon complement(<2603..4426)
/locus_tag="Jvgp5"
/note="large t-antigen"
/number=2
intron complement(4427..4770)
/locus_tag="Jvgp5"
/note="large t-antigen intron [3]"
intron complement(4427..4493)
/locus_tag="Jvgp5"
/note="small t-antigen intron [3] [3]"
gene complement(4495..5013)
/locus_tag="Jvgp6"
/db_xref="GeneID:1489521"
CDS complement(4495..5013)
/locus_tag="Jvgp6"
/note="small t-antigen"
/codon_start=1
/product="hypothetical protein"
/protein_id="NP_043513.1"
/db_xref="GeneID:1489521"
/translation="MDKVLNREESMELMDLLGLDRSAWGNIPVMRKAYLKKCKELHPD
KGGDEDKMKRMNFLYKKMEQGVKVAHQPDFGTWNSSEVGCDFPPNSDTLYCKEWPNCA
TNPSVHCPCLMCMLKLRHRNRKFLRSSPLVWIDCYCFDCFRQWFGCDLTQEALHCWEK
VLGDTPYRDLKL"
misc_feature complement(4561..4995)
/locus_tag="Jvgp6"
/note="Small T antigen; Reviewed; Region: PHA03102"
/db_xref="CDD:222986"
repeat_region 5074..5090
/note="17 bp palindrome; 65.34%"
rep_origin 5118..5130
/note="putative"
ORIGIN
1 gcctcggcct cctgtatata taaaaaaaag ggaagggatg gctgccagcc aagcatgagc
61 tcatacctag ggagccaacc agctaacagc cagtaaacaa agcacaaggc tgtatatata
121 aaaaaaaggg aagggatggc tgccagccaa gcatgagctc atacctaggg agccaaccag
181 ctaacagcca gtaaacaaag cacaagggga agtggaaagc agccaaggga acatgttttg
241 cgagccagag ctgttttggc ttgtcaccag ctggccatgg ttcttcgcca gctgtcacgt
301 aaggcttctg tgaaagttag taaaacctgg agtggaacta aaaaaagagc tcaaaggatt
361 ttaatttttt tgttagaatt tttgctggac ttttgcacag gtgaagacag tgtagacggg
421 aaaaaaagac agagacacag tggtttgact gagcagacat acagtgcttt gcctgaacca
481 aaagctacat aggtaagtaa tgtttttttt tgtgttttca ggttcatggg tgccgcactt
541 gcacttttgg gggacctagt tgctactgtt tctgaggctg ctgctgccac aggattttca
601 gtagctgaaa ttgctgctgg agaggctgct gctactatag aagttgaaat tgcatccctt
661 gctactgtag aggggattac aagtacctct gaggctatag ctgctatagg ccttactcct
721 gaaacatatg ctgtaataac tggagctccg ggggctgtag ctgggtttgc tgcattggtt
781 caaactgtaa ctggtggtag tgctattgct cagttgggat atagattttt tgctgactgg
841 gatcataaag tttcaacagt tgggcttttt cagcagccag ctatggcttt acaattattt
901 aatccagaag actactatga tattttattt cctggagtga atgcctttgt taacaatatt
961 cactatttag atcctagaca ttggggcccg tccttgttct ccacaatctc ccaggctttt
1021 tggaatcttg ttagagatga tttgccagcc ttaacctctc aggaaattca gagaagaacc
1081 caaaaactat ttgttgaaag tttagcaagg tttttggaag aaactacttg ggcaatagtt
1141 aattcaccag ctaacttata taattatatt tcagactatt attctagatt gtctccagtt
1201 aggccctcta tggtaaggca agttgcccaa agggagggaa cctatatttc ttttggccac
1261 tcatacaccc aaagtataga tgatgcagac agcattcaag aagttaccca aaggctagat
1321 ttaaaaaccc caaatgtgca atctggtgaa tttatagaaa gaagtattgc accaggaggt
1381 gcaaatcaaa gatctgctcc tcaatggatg ttgcctttac ttttagggtt gtacgggact
1441 gtaacacctg ctcttgaagc atatgaagat ggccccaaca aaaagaaaag gagaaaggaa
1501 ggaccccgtg caagttccaa aacttcttat aagaggagga gtagaagttc tagaagttaa
1561 aactggggtt gactcaatta cagaggtaga atgcttttta actccagaaa tgggtgaccc
1621 agatgagcat cttaggggtt ttagtaagtc aatatctata tcagatacat ttgaaagtga
1681 ctccccaaat agggacatgc ttccttgtta cagtgtggcc agaattccac tacccaatct
1741 aaatgaggat ctaacctgtg gaaatatact catgtgggag gctgtgacct taaaaactga
1801 ggttataggg gtgacaagtt tgatgaatgt gcactctaat gggcaagcaa ctcatgacaa
1861 tggtgcaggg aagccagtgc agggcaccag ctttcatttt ttttctgttg ggggggaggc
1921 tttagaatta cagggggtgc tttttaatta cagaacaaag tacccagatg gaacaatttt
1981 tccaaagaat gccacagtgc aatctcaagt catgaacaca gagcacaagg cgtacctaga
2041 taagaacaaa gcatatcctg ttgaatgttg ggttcctgat cccaccagaa atgaaaacac
2101 aagatatttt gggacactaa caggaggaga aaatgttcct ccagttcttc atataacaaa
2161 cactgccaca acagtgttgc ttgatgaatt tggtgttggg ccactttgca aaggtgacaa
2221 cttatacttg tcagctgttg atgtctgtgg catgtttaca aacaggtctg gttcccagca
2281 gtggagagga ctctccagat attttaaggt gcagctaagg aaaaggaggg ttaaaaaccc
2341 ctacccaatt tctttccttc ttactgattt aattaacaga aggactccta gagttgatgg
2401 gcagcctatg tatggcatgg atgctcaagt agaggaggtt agagtttttg agggaacaga
2461 ggagcttcca ggggacccag acatgatgag atacgttgac aaatatggac agttgcagac
2521 aaaaatgctg taatcaaaag cctttattgt aatatgcagt acattttaat aaagtataac
2581 cagctttact taacagttgc agttattttg ggggaggggt ctttggtttt ttgaaacatt
2641 gaaagccttt acagatgtga aaagtgcagt tttcctgtgt gtctgcacca gaggcttctg
2701 agacctggga aaagcattgt gattgtgatt cagtgcttga tccatgtcca gagtcttctg
2761 cttcagaatc ttcctctcta ggaaagtcaa gaatgggtct ccccatacca acattagctt
2821 tcatagtaga aaatgtatac atgcttattt ctaaatccag cctttctttc cactgcacaa
2881 tcctctcatg aatggcagct gcaaagtcag caactggcct aaaccagatt aaaagcaaaa
2941 gcaaagtcat accactttgc aaaatccttt tttctagcaa atactcagag cagcttagtg
3001 attttctcag gtaggccttt ggtctaaaat ctatctgcct tacaaatctg gcctgtaaag
3061 ttctaggcac tgaatattca ttcatggtta caattccagg tggaaacacc tgtgttcttt
3121 tgttttggtg ttttctctct aaattaactt ttacacttcc atctaagtaa tctcttaagc
3181 aatcaaggtt gcttatgcca tgccctgaag gtaaatccct tgactctgca ccagtgcctt
3241 ttacatcctc aaatacaacc ataaactgat ctatacccac tcctaattca aagtttaatc
3301 tttctaatgg catattaaca tttaatgact ttcccccaca gagatcaagt aaagctgcag
3361 ctaaagtagt tttgccactg tctattggcc ccttgaatag ccagtacctt ttttttggaa
3421 tgtttaatac aatgcatttt agaaagtcat aaataacagt gtccatttga ggcagcaagc
3481 aatgaatcca ggccacccca gccatatatt gctctaaaac agcattgcca tgtgccccaa
3541 aaattaagtc cattttatca agcaagaaat taaacctttc aactaacatt tcttctctgg
3601 tcatgtggat gctgtcaacc ctttgtttgg ctgctacagt atcaacagcc tgctggcaaa
3661 tgcttttttg atttttgcta tctgcaaaaa tttgggcatt ataatagtgt ttttcatgat
3721 ggttaaagtg atttggctga tccttttttt cacatttttt gcattgctgt gggttttcct
3781 gaaagtctaa gtacatgccc ataagcaaaa aaacatcctc acacttggtt tccaaggcat
3841 actgtgtaac taatttccat gaaacctgct tagtttcttc tggttcttct gggttaaagt
3901 catgctcctt aaggcccccc tgaatacttt cttccactac tgcatatggc tgtctacaca
3961 gggcactata aaacaagtat tccttattca cacctttaca aattaaaaaa ctaaaggtac
4021 atagtttttg acagtagtta ttaattgctg acactctatg tctatgtggt gttaagaaaa
4081 acaaaatatt atgaccccca aaaccatgtc tacttataaa agttacagaa tatttttcca
4141 taagtttctt atataaaatt tgagcttttt ctttagtggt atacacagca aaagaagcaa
4201 cagttctatt actaaacaca gcttgactga ggaatgcatg cagatctaca ggaaagtctt
4261 tagggtcttc tacctttttt ttctttttag gtggggtaga gtgttgggat cctgtgtttt
4321 catcatcact ggcaaacatt tcttcatggc aaaacaggtc ttcatcccac ttctcattaa
4381 atgtattcca ccaggattcc cattcatctg ttccataggt tggcacctaa aaaaaaacaa
4441 ttaagtttat tgtaaaaaac aaaatgccct gcaaaagaaa aatagtggtt taccttaaag
4501 ctttagatcc ctgtaggggg tgtctccaag aactttctcc cagcaatgaa gagcttcttg
4561 ggttaagtca cacccaaacc attgtctgaa gcaatcaaag caatagcaat ctatccacac
4621 aagtgggctg cttcttaaaa attttctgtt tctatgcctt aattttagca tgcacattaa
4681 acaggggcaa tgcactgaag gattagtggc acagttaggc cattccttgc aataaagggt
4741 atcagaatta ggaggaaaat cacaaccaac ctctgaacta ttccatgtac caaaatcagg
4801 ctgatgagca acttttacac cttgttccat ttttttatat aaaaaattca ttctcttcat
4861 cttgtcttcg tccccacctt tatcagggtg gagttctttg cattttttca gataagcttt
4921 tctcatgaca ggaatgttcc cccatgcaga cctatcaagg cctaataaat ccataagctc
4981 catggattcc tccctattca gcactttgtc cattttagct ttttgcagca aaaaattact
5041 gcaaaaaagg gaaaaacaag ggaatttccc tggcctccta aaaagcctcc acgcccttac
5101 tacttctgag taagcttgga ggcggaggcg
//
