Basic Information
VIS ID
TVIS30013811
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
41421427/41562174 (Hg38)
End
41421427/41562174 (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/1724561; hsa-let-7f-2/Downstream/4183983;
Nearest TSS
ENST00000429181/Upstream/5939; ENST00000620846/Downstream/708;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/87301, chrX-CpG: 143/Downstream/360679
Upstream sequence
taaacaaatttaataaatgcagaaggcttagaactgttcttggcacataccaagcaccatgacagtgttggctgctatCGTTATCtaccagatatgatac
Downstream sequence
gaaggttgtcaattttccaagagttgtgacatgataatatctacacaacagcaaattctgttaaagataatttaatcttttggttggcatttcagcatct
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate