Basic Information
VIS ID
TVIS30013337
Fusion event
HIV-CDC42SE2 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
chr5
Cytoband
q31.1
Reference genome
GRCh37/hg19
Start
130688793/131353100 (Hg38)
End
130688793/131353100 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA5C
Target gene
CDC42SE2
miRNAs that regulate target gene
hsa-mir-421 ; hsa-mir-15a-5p ; hsa-mir-16-5p ; hsa-mir-103a-3p ; hsa-mir-107 ; hsa-mir-15b-5p ; hsa-mir-195-5p ; hsa-mir-424-5p ; hsa-mir-497-5p ; hsa-mir-545-3p ; hsa-mir-4524a-5p ; hsa-mir-4641 ; hsa-mir-4690-3p ; hsa-mir-4524b-5p ; hsa-mir-5685 ; hsa-mir-6838-5p ; hsa-mir-5680 ; hsa-mir-885-3p ; hsa-mir-203a-3p ; hsa-mir-646 ; hsa-mir-503-5p
Nearest miRNA
hsa-mir-10397/Upstream/1955953; hsa-mir-103a-1/Downstream/864749;
Nearest TSS
ENST00000502646/Upstream/89000; ENST00000506929/Downstream/32506;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/88387, chr5-CpG: 85/Downstream/281622
Upstream sequence
ctggtgcccaggctttactgcagtggcgcgtcttggtgtactgcagcctcgacttcctgggctctagtgatcctccaaactcagccttccaagtagctga
Downstream sequence
taccacaagtgcttgccaccacacccagctaatttttaaaatgtttttgtagttacggaattctgtcatgttgtctaggttggtctcgaactcctggtct
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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