Basic Information
VIS ID
TVIS30005690
Fusion event
HIV-SLK 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
chr10
Cytoband
q25.1
Reference genome
GRCh37/hg19
Start
105760933/104001175 (Hg38)
End
105760933/104001175 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA10D ; FRA10A ; FRA10B
Target gene
SLK
miRNAs that regulate target gene
hsa-mir-21-5p ; hsa-mir-615-3p ; hsa-mir-484 ; hsa-let-7c-5p ; hsa-mir-20a-5p ; hsa-mir-106b-5p ; hsa-mir-519d-3p ; hsa-mir-93-5p ; hsa-mir-20b-5p ; hsa-mir-17-5p
Nearest miRNA
hsa-mir-107/Upstream/606774; hsa-mir-202/Downstream/46914;
Nearest TSS
ENST00000439456/Upstream/33974; ENST00000474260/Downstream/7023;
Nearest CpG islands
None/Target, chr10-CpG: 68/Upstream/33507, chr10-CpG: 46/Downstream/120516
Upstream sequence
aaaaaaaaaaaGTAATAATGTAGTGACCTGACATTTGCtttaaatttcaattaaaattttttattaCGAAGTTTTCAAACACACAGAAAGTACATGTACC
Downstream sequence
TACTACCCAGATATAACAATTCTTATCATTTTTGATAAATTTGCTTCAGATTCTtaaaaatgtacagatccagttgcaggtagtccctgcttttgctcaa
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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