Basic Information
VIS ID
TVIS30004652
Fusion event
HIV-PRKCA integration
Validated
No
Detection method
QiaQuick PCR and Sequencing
Data source
download(RID)
Sample type
Cell line
Disease
HIV-infected disease (HID)
Quality evaluation
Normal
Reported year
2013
PubMed ID
23953889
Virus Sequence
Virus name
HIV
Reference genome
Not given
Host Sequence
Chromosome
chr17
Cytoband
q24.2
Reference genome
GRCh37/hg19
Start
64319416/66323298 (Hg38)
End
64319416/66323298 (Hg38)
Orient
+
Location type
Intronic
Target gene
PRKCA
miRNAs that regulate target gene
hsa-mir-375 ; hsa-mir-505-3p ; hsa-mir-193b-3p ; hsa-mir-92a-3p ; hsa-mir-17-3p ; hsa-mir-203a-3p ; hsa-mir-218-5p ; hsa-mir-371b-5p ; hsa-mir-6828-5p ; hsa-mir-1976 ; hsa-mir-6747-3p ; hsa-mir-6727-3p ; hsa-mir-4722-3p ; hsa-mir-660-3p ; hsa-mir-5193 ; hsa-mir-5196-3p ; hsa-mir-6821-5p ; hsa-mir-6842-3p ; hsa-mir-647 ; hsa-mir-6514-3p ; hsa-mir-7977 ; hsa-mir-1268b ; hsa-mir-1268a ; hsa-mir-585-3p ; hsa-mir-5787 ; hsa-mir-4505 ; hsa-mir-4430 ; hsa-mir-3652 ; hsa-mir-24-3p ; hsa-mir-4284 ; hsa-mir-6847-3p ; hsa-mir-6811-3p ; hsa-mir-214-5p ; hsa-mir-4486 ; hsa-mir-142-3p ; hsa-mir-150-5p
Nearest miRNA
hsa-mir-10226/Upstream/1501196; hsa-mir-1250/Downstream/463774;
Nearest TSS
ENST00000595228/Upstream/20341; ENST00000307139/Downstream/91675;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/19799, chr17-CpG: 48/Downstream/511670
Nearest cancer related gene
PRKCA(OG, No orient, 0)
Upstream sequence
cacaatcagaattttgctaattgcatgctcccagtgcacgttaccacattcctttgtattttctgcaaattggcagcttgatccagaggttcaaatgatc
Downstream sequence
agactcaggttGATCTGGGTTATTTAGTTTTTAAGATGCCTTTATAACTTCACATGCTTGTTAATTATGGGTCTGTTATTGTGGAAAGAACACCAATGGA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
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