Basic Information
VIS ID
TVIS30015688
Fusion event
HIV-SMARCA4 integration
Validated
Yes
Detection method
LM PCR
Data source
Curated
Sample type
PBMC
Disease
HIV-infected disease (HID)
Quality evaluation
Good
Reported year
2014
PubMed ID
24968937
Virus Sequence
Virus name
HIV
Reference genome
Not given
Host Sequence
Chromosome
chr19
Cytoband
p13.2
Reference genome
GRCh37/hg19
Start
11084562/10973886 (Hg38)
End
11084687/10973886 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA19B
Target gene
SMARCA4
miRNAs that regulate target gene
hsa-mir-21-5p ; hsa-mir-155-5p ; hsa-mir-34a-5p ; hsa-mir-98-5p ; hsa-let-7b-5p ; hsa-mir-342-5p ; hsa-mir-615-3p ; hsa-mir-222-3p ; hsa-mir-16-5p ; hsa-mir-139-5p
Nearest miRNA
hsa-mir-1181/Upstream/144851; hsa-let-7e/Downstream/139588;
Nearest TSS
ENST00000633603/Upstream/12565; ENST00000647011/Downstream/10266;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/12222, chr19-CpG: 22/Downstream/13833
Nearest cancer related gene
SMARCA4(TSG, No orient, 0)
Upstream sequence
tctcgatctcctgaccctcgtgatccacccgccttggcctcccaaagtgctgggattacaggcgtgagccaccgcgcccggccTGGAGGTTTTCTTATAG
Downstream sequence
TCTGCTGCTGAAATGTGTCCGTGAACAAATTTCCCCAAGCCCCAAAAAACACAATAGCAGATATCCTGGGACCAAACTTAAATATAATGCTAGTTTCTCA
Target sequence
ACCACCGAGGGGAACATTTTGTTTTGTAGTTCACGCATAGTAAACGGGGCTGGCTCTGCGGAAGCCATCCTGCCCATTGCTGTTGTTCCGCCCAAGCCTCTGCCATAACCTGACTCCCACGTTGG
Reference
Maldarelli, F., et al. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science,2014, 345(6193): 179-183.
Curate