Basic Information
VIS ID
TVIS30015591
Fusion event
HIV-SMCHD1 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
chr18
Cytoband
p11.32
Reference genome
GRCh37/hg19
Start
2701025/2701027 (Hg38)
End
2701088/2701027 (Hg38)
Orient
+
Location type
Intronic
Target gene
SMCHD1
miRNAs that regulate target gene
hsa-mir-210-3p ; hsa-mir-132-3p ; hsa-mir-128-3p ; hsa-mir-181a-5p ; hsa-mir-877-5p ; hsa-mir-421 ; hsa-mir-149-5p ; hsa-mir-221-3p ; hsa-mir-10b-5p ; hsa-mir-10a-5p ; hsa-mir-100-5p ; hsa-mir-30a-5p ; hsa-mir-18a-5p ; hsa-mir-6768-5p ; hsa-mir-1277-5p ; hsa-mir-4789-5p ; hsa-mir-3941 ; hsa-mir-5011-5p ; hsa-mir-603 ; hsa-mir-362-3p ; hsa-mir-329-3p ; hsa-mir-8485 ; hsa-mir-1264 ; hsa-mir-3184-3p ; hsa-mir-510-3p ; hsa-mir-203a-3p ; hsa-mir-190a-3p
Nearest miRNA
hsa-mir-8078/Upstream/2588688; hsa-mir-1-2/Downstream/1184326;
Nearest TSS
ENST00000575820/Upstream/168; ENST00000577300/Downstream/2667;
Nearest CpG islands
None/Target, chr18-CpG: 67/Upstream/44209, chr18-CpG: 150/Downstream/145540
Nearest cancer related gene
SMCHD1(TSG, No orient, 0)
Upstream sequence
TTAAATATAAAGTTGTGAATATTTGCAAATGTTTTATTTTTAAGTAAAAGAAGACACTAGCAGTGTAGGTTTTTATTGATATTTTGCATCAAAAGACTAT
Downstream sequence
TTTAGTAATGACTAAACCTACCTAGTAAAGACTAGGTTTGGATAGAATTTACATATCTTCATTAGttttttttgtttttttttttttaagacaggagttt
Target sequence
GATGTATAAATTTTTTTATGAGCAGTCAAGTGTTCACATTACTAAAAAATTTAAAGCTAATTT
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