Basic Information
VIS ID
TVIS30005089
Fusion event
HIV-VPS13D 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
chr1
Cytoband
p36.22
Reference genome
GRCh37/hg19
Start
12469206/12409153 (Hg38)
End
12469206/12409153 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA1A
Target gene
VPS13D
miRNAs that regulate target gene
hsa-mir-132-3p ; hsa-mir-128-3p ; hsa-mir-7-5p ; hsa-mir-342-5p ; hsa-mir-10a-3p ; hsa-let-7e-5p ; hsa-mir-8485 ; hsa-mir-6868-3p ; hsa-mir-6881-3p ; hsa-mir-6780a-3p ; hsa-mir-7111-3p ; hsa-mir-9-3p ; hsa-mir-7106-3p ; hsa-mir-20a-3p ; hsa-mir-6728-3p ; hsa-mir-6817-3p ; hsa-mir-4685-3p ; hsa-mir-4287 ; hsa-mir-3667-3p ; hsa-mir-6769b-3p ; hsa-mir-6734-3p ; hsa-mir-4723-3p ; hsa-mir-3183 ; hsa-mir-5088-3p ; hsa-mir-4429 ; hsa-mir-320d ; hsa-mir-320c ; hsa-mir-320b ; hsa-mir-320a
Nearest miRNA
hsa-mir-12136/Upstream/217380; hsa-mir-101-1/Downstream/169804;
Nearest TSS
ENST00000473358/Upstream/1899; ENST00000481484/Downstream/685;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/178011, chr1-CpG: 18/Downstream/131168
Upstream sequence
CAGCTTTTTGTCTTTTTACTTTGCTTTTGGCGTGTGTGTGTGTGTGTTTGTGTTTAATTATACAAGAGCTGTTTATTTTTATGTTGTCAAATTTATTAGT
Downstream sequence
CTTTTGCTGTTTTGAATCTAATTTTTTTTTGAAAActacatgttcagagaaattctctagtaacaaactgtagaaatgatccctgaaagcatagtcttGA
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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