Basic Information
VIS ID
TVIS30008616
Fusion event
HIV-RAP1GDS1 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
q23
Reference genome
GRCh37/hg19
Start
99279370/98358219 (Hg38)
End
99279370/98358219 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA4E
Target gene
RAP1GDS1
miRNAs that regulate target gene
hsa-mir-3688-5p ; hsa-mir-7847-3p ; hsa-mir-6739-5p ; hsa-mir-6733-5p ; hsa-mir-3153 ; hsa-mir-4668-5p ; hsa-mir-6851-5p ; hsa-mir-4470 ; hsa-mir-3689d ; hsa-mir-6134 ; hsa-mir-4797-3p ; hsa-mir-4264 ; hsa-mir-194-3p ; hsa-mir-5693 ; hsa-mir-6865-5p ; hsa-mir-6815-5p ; hsa-mir-4796-3p ; hsa-mir-676-5p
Nearest miRNA
hsa-mir-12113/Upstream/11057636; hsa-mir-1243/Downstream/639168;
Nearest TSS
ENST00000502981/Upstream/5706; ENST00000514139/Downstream/20883;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/96171, chr4-CpG: 97/Downstream/299772
Upstream sequence
ttatgataaaaaggaatattttagttctttaatcaaacaacttttgagacaaaatagtaggagggacttatcaggatgtcattaattccctagatgattc
Downstream sequence
tgtgcacatacctagttacaatatgtaaggatatttactggcattatagtgtacctagtgacggttctacaaaagttgcccagatgttttccatgtgatt
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate