Basic Information
VIS ID
TVIS30004160
Fusion event
HIV-FOCAD 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
chr9
Cytoband
p21.3
Reference genome
GRCh37/hg19
Start
20858449/20858450 (Hg38)
End
20858449/20858450 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA9C
Target gene
FOCAD
miRNAs that regulate target gene
hsa-mir-186-5p ; hsa-mir-6083 ; hsa-mir-539-3p ; hsa-mir-485-3p ; hsa-mir-190a-3p ; hsa-mir-487a-3p ; hsa-mir-154-3p ; hsa-mir-3074-3p ; hsa-mir-5011-5p ; hsa-mir-5692c ; hsa-mir-5692b ; hsa-mir-1277-5p ; hsa-mir-5692a
Nearest miRNA
hsa-mir-101-2/Upstream/142262; hsa-let-7a-1/Downstream/653665;
Nearest TSS
ENST00000422679/Upstream/35457; ENST00000604828/Downstream/14357;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/173813, chr9-CpG: 34/Downstream/172989
Upstream sequence
cttctgggttttccaatttattgtcgatagttgctcataatcttctctaatgatcctttgaatttttgtggtattgtattttgtgaatgttttttgtaat
Downstream sequence
gtcccctttttcatctctgattttatttatttgaatgttctctctttttttcttagtctggccaaaggtttgttgattttactcatcttttcaagaaacc
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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