Basic Information
VIS ID
TVIS30003673
Fusion event
HIV-SMARCAD1 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
chr4
Cytoband
q22.3
Reference genome
GRCh37/hg19
Start
95186989/94265838 (Hg38)
End
95186989/94265838 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA4E
Target gene
SMARCAD1
miRNAs that regulate target gene
hsa-mir-196a-5p ; hsa-let-7d-5p ; hsa-mir-320a ; hsa-let-7a-5p ; hsa-let-7b-5p ; hsa-let-7c-5p ; hsa-let-7e-5p ; hsa-let-7f-5p ; hsa-mir-98-5p ; hsa-let-7g-5p ; hsa-let-7i-5p ; hsa-mir-3927-3p ; hsa-mir-4458 ; hsa-mir-4500 ; hsa-mir-6831-5p ; hsa-mir-190a-3p ; hsa-mir-4443 ; hsa-mir-4650-3p ; hsa-mir-5011-5p ; hsa-mir-5692a ; hsa-mir-6515-5p ; hsa-mir-1277-5p ; hsa-mir-524-5p ; hsa-mir-520d-5p ; hsa-mir-6851-5p ; hsa-mir-3689d ; hsa-mir-5002-5p ; hsa-mir-5680 ; hsa-mir-338-5p ; hsa-mir-1251-3p ; hsa-mir-892c-5p ; hsa-mir-5583-5p ; hsa-mir-3129-3p ; hsa-mir-548av-3p ; hsa-mir-548f-3p ; hsa-mir-548e-3p ; hsa-mir-548az-3p ; hsa-mir-548ar-3p ; hsa-mir-548a-3p
Nearest miRNA
hsa-mir-12113/Upstream/6965255; hsa-mir-1243/Downstream/4731549;
Nearest TSS
ENST00000502981/Upstream/1310; ENST00000514232/Downstream/4729;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/57700, chr4-CpG: 88/Downstream/185812
Upstream sequence
accatggaaacaaatggagttcctaaaattagggaataattgaaatgaattatggtatatccatactttgcaatgttacacaactttcaaaatgaGTTAC
Downstream sequence
ATCTGTTCAAAGTATTTCTGATAGGTTAAGATTAGCAGTAGGATCTCATTAAAATTAATTGCCTTAGTTGCTGATTTTATTTACTTCTGATATTTTTCTA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate