Basic Information
VIS ID
TVIS30004066
Fusion event
HIV-CSMD1 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
chr8
Cytoband
p23.2
Reference genome
GRCh37/hg19
Start
3779019/3921497 (Hg38)
End
3779019/3921497 (Hg38)
Orient
-
Location type
Intronic
Target gene
CSMD1
miRNAs that regulate target gene
hsa-mir-297 ; hsa-mir-3924 ; hsa-mir-190a-3p ; hsa-mir-4789-5p ; hsa-mir-567 ; hsa-mir-5011-5p ; hsa-mir-4704-5p ; hsa-mir-5583-3p ; hsa-mir-4517 ; hsa-mir-1277-5p ; hsa-mir-338-5p ; hsa-let-7c-3p ; hsa-mir-10b-5p
Nearest miRNA
hsa-mir-3674/Upstream/1844857; hsa-mir-10400/Downstream/2700627;
Nearest TSS
ENST00000518652/Upstream/213001; ENST00000522905/Downstream/110603;
Nearest CpG islands
None/Target, chr8-CpG: 109/Upstream/899071, chr8-CpG: 256/Downstream/1069949
Nearest cancer related gene
CSMD1(TSG, No orient, 0)
Upstream sequence
tattatctaacttgtattattttctttcttctattaactttgagcttggtttgttcttttcctagttcagtgaggtgtaaagttaggttgcttatataaa
Downstream sequence
atactttttatttttttcatgtaggccatcatttctgtaaacttccctcttagaaccacttttgcttcatctattttggtgtgcttggtttccattttca
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate