Basic Information
VIS ID
TVIS30009702
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
20726505/20726506 (Hg38)
End
20726505/20726506 (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/10318; hsa-let-7a-1/Downstream/785609;
Nearest TSS
ENST00000422679/Upstream/155; ENST00000603492/Downstream/62828;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/41869, chr9-CpG: 34/Downstream/304933
Upstream sequence
CCCCATTTCTTGTCTTAATGTGCTTGGTAAGAAGGTTATACTCTGGATAAACCAGGCTAGCACTTGATTTGTATGCCTTTTGTGCTCTCAGACAGGGAAG
Downstream sequence
GGACCTGCATTCGAGGTATTTGGGAATATAAAGTGTATTAAAGTGTATTTTCTGAGACTTCTAAAGTCTACCTTTTAATGAAATTTAGCATAGGATATTA
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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