Basic Information
VIS ID
TVIS30009930
Fusion event
HIV-CASK 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
p11.4
Reference genome
GRCh37/hg19
Start
41520262/41661009 (Hg38)
End
41520262/41661009 (Hg38)
Orient
+
Location type
Intronic
Target gene
CASK
miRNAs that regulate target gene
hsa-mir-16-5p ; hsa-mir-203a-3p ; hsa-mir-6838-5p ; hsa-mir-497-5p ; hsa-mir-424-5p ; hsa-mir-195-5p ; hsa-mir-15b-5p ; hsa-mir-15a-5p ; hsa-mir-3908 ; hsa-mir-4724-5p ; hsa-mir-4519 ; hsa-mir-4274 ; hsa-mir-4524b-5p ; hsa-mir-4524a-5p ; hsa-mir-646 ; hsa-mir-503-5p
Nearest miRNA
hsa-mir-1587/Upstream/1823396; hsa-let-7f-2/Downstream/4085148;
Nearest TSS
ENST00000429181/Upstream/70927; ENST00000620846/Downstream/4422;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/186136, chrX-CpG: 143/Downstream/261844
Upstream sequence
ttaaaatttttaaagaaatatttttaagatatgttttaaaaaatCGAGGTTAGCAATAATTGTGAACTGTGCAAAGTTTTTAATAGGATATTTTGGTCAC
Downstream sequence
TGCATATCAACTTCGGTGTTTAGGAAAAAGTATTCTACTACCGTAGGTCCCACAGAATAACAGATTTGCTTGAATACTGTCCTCAGTGAAGTTACTTTTG
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate