Basic Information
VIS ID
TVIS30008191
Fusion event
HIV-SGSM3 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
chr22
Cytoband
q13.1
Reference genome
GRCh37/hg19
Start
40781849/40385845 (Hg38)
End
40781849/40385845 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA22A
Target gene
SGSM3
miRNAs that regulate target gene
hsa-mir-124-3p ; hsa-let-7e-5p ; hsa-mir-19b-3p
Nearest miRNA
hsa-mir-1286/Upstream/2396992; hsa-let-7a-3/Downstream/428038;
Nearest TSS
ENST00000624155/Upstream/15206; ENST00000481028/Downstream/2372;
Nearest CpG islands
None/Target, chr22-CpG: 279/Upstream/14816, chr22-CpG: 22/Downstream/32967
Upstream sequence
CAACTAGAGATGAATGAAGGTTGCTGAGCAACCGTGAAGATAAATAGCATGTGGCTTGTTCCCTAACTTTGTCCAGGAGGAACATGAGCAGAAAGAGCAG
Downstream sequence
AGGAACAACttttttttttcttgaagaccgggtctcactctggttgcccaggctggagtgcagtggtgcaacctcagcccactgcagcgtcgacctcccg
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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