Basic Information
VIS ID
TVIS30009218
Fusion event
HIV-PRKN 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
chr6
Cytoband
q26
Reference genome
GRCh37/hg19
Start
162949932/162528900 (Hg38)
End
162949932/162528900 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA6E
Target gene
PRKN
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-26b-5p ; hsa-mir-3187-3p ; hsa-mir-1303 ; hsa-mir-4435 ; hsa-mir-588 ; hsa-mir-4701-5p ; hsa-mir-548s ; hsa-mir-193b-5p ; hsa-mir-4755-3p ; hsa-mir-483-5p ; hsa-mir-19a-3p ; hsa-mir-19b-3p ; hsa-mir-181a-5p
Nearest miRNA
hsa-mir-10398/Upstream/3764147; hsa-mir-1913/Downstream/3980454;
Nearest TSS
ENST00000381078/Upstream/253514; ENST00000544266/Downstream/198232;
Nearest CpG islands
None/Target, chr6-CpG: 120/Upstream/882243, chr6-CpG: 75/Downstream/198444
Nearest cancer related gene
PRKN(TSG, No orient, 0)
Upstream sequence
TTaaaacaaaacaaaacaaaacaaaacaaaaACCTAGAAGAGAGTAACAGCACCATACTCAGCTTTCTCAGCtttttacttatttattttttttggagac
Downstream sequence
ggagtcttgatgtgtcgcccaggctggagtgcagtggcgtgatctcggctcactgcaacctccacctcctgggttcaagcaattctagtgccttagcctc
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate