Basic Information
VIS ID
TVIS30004759
Fusion event
HIV-PNKP 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
chr19
Cytoband
q13.33
Reference genome
GRCh37/hg19
Start
50368220/49864963 (Hg38)
End
50368220/49864963 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA19A
Target gene
PNKP
miRNAs that regulate target gene
hsa-mir-26b-5p
Nearest miRNA
hsa-mir-10395/Upstream/10312; hsa-let-7e/Downstream/23212;
Nearest TSS
ENST00000633603/Upstream/901; ENST00000598789/Downstream/420;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/1934, chr19-CpG: 56/Downstream/2159
Upstream sequence
TGGACATAAAAAATCCTCATCGTAATAGCTCCTACTGAGACAGTCATGGTCATTGCTGAttactgggtggtcactgtgggtaacgcaggagctgacatat
Downstream sequence
atcattctccccactgcttaactgcttacaacgatccctgcatttatcattaggcccatttctcagaaaagtaagtagaggctaaaaagttgagAGCACG
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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