Basic Information
VIS ID
TVIS30006182
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
56580649/56186865 (Hg38)
End
56580649/56186865 (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/1849551; hsa-let-7i/Downstream/1007639;
Nearest TSS
ENST00000382841/Upstream/1642; ENST00000447747/Downstream/2526;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/57364, chr12-CpG: 76/Downstream/2059
Upstream sequence
tcaggtaccattaaggaaactctacaaggtaggtttactaatcccatctagagatgaaggaaccaagactcatgaatgttgcccaagatcacagagccat
Downstream sequence
ccaatggcaaagccaggatttgaacacaagcctgcacaaatccaaatctcaagtccccttttaaccatgccatgAGAGACCTGTGGACTGATCCCAGGTA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate