Basic Information
VIS ID
TVIS30013798
Fusion event
HIV-SH3KBP1 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
chrX
Cytoband
p22.12
Reference genome
GRCh37/hg19
Start
19708554/19690436 (Hg38)
End
19708554/19690436 (Hg38)
Orient
-
Location type
Intronic
Target gene
SH3KBP1
miRNAs that regulate target gene
hsa-mir-1914-5p ; hsa-mir-5692a ; hsa-mir-218-5p ; hsa-mir-1305 ; hsa-mir-607 ; hsa-mir-4775 ; hsa-mir-590-3p ; hsa-mir-548ah-5p ; hsa-mir-3609 ; hsa-mir-548t-5p ; hsa-mir-548az-5p ; hsa-mir-335-3p ; hsa-mir-19b-3p ; hsa-mir-19a-3p
Nearest miRNA
hsa-mir-3690-1/Upstream/2264482; hsa-let-7f-2/Downstream/326652;
Nearest TSS
ENST00000429181/Upstream/19438; ENST00000424026/Downstream/5265;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/174793, chrX-CpG: 157/Downstream/196473
Upstream sequence
tgtgagccaccacacctggccTCCATCTTCATCTTTGTCTTAGCCTGACAAGTCACTAAATTATCAGAACCTCAACTTTTTAAATAAGGAATTAGGAAAA
Downstream sequence
TGAGAAATTCAATAACAACAGAAAACTCATGGTTATTAATGGTTACAGAAAGAAAATGCAAACTTTCTCCCTCTGAAGATTGTGAGAAATAACTGAAAAT
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate