Basic Information
VIS ID
TVIS30002060
Fusion event
HIV-SMARCC2 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
chr12
Cytoband
q13.2
Reference genome
GRCh37/hg19
Start
56562185/56168401 (Hg38)
End
56562185/56168401 (Hg38)
Orient
-
Location type
Intronic
Target gene
SMARCC2
miRNAs that regulate target gene
hsa-mir-34a-5p ; hsa-mir-615-3p ; hsa-mir-92b-3p ; hsa-mir-320a ; hsa-mir-186-5p ; hsa-let-7b-5p ; hsa-mir-5682 ; hsa-mir-585-5p ; hsa-mir-6748-3p ; hsa-mir-6890-3p ; hsa-mir-126-5p ; hsa-mir-7109-3p ; hsa-mir-214-5p
Nearest miRNA
hsa-mir-1244-3/Upstream/1831087; hsa-let-7i/Downstream/1026103;
Nearest TSS
ENST00000382841/Upstream/6620; ENST00000447747/Downstream/6312;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/38900, chr12-CpG: 76/Downstream/20523
Upstream sequence
GTCACAACCCATGGTGAAAGGGCTTGACTTTTTTgtgctgggattataggcgtgagccaccgtgtcttttttcttttttctttttttttttttgggacag
Downstream sequence
tctcactctgttgcccaggctggagtacagtggcatgatctcagctcactgtaacctctacctcctgggttcaagcaattctcgtgcctttgcctcccca
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate