Basic Information
VIS ID
TVIS30008346
Fusion event
HIV-PBRM1 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
chr3
Cytoband
p21.1
Reference genome
GRCh37/hg19
Start
52623357/52589341 (Hg38)
End
52623357/52589341 (Hg38)
Orient
-
Location type
Intronic
Target gene
PBRM1
miRNAs that regulate target gene
hsa-mir-30a-5p ; hsa-mir-155-5p ; hsa-mir-93-5p ; hsa-mir-21-5p ; hsa-mir-1229-3p ; hsa-mir-1226-3p ; hsa-mir-877-3p ; hsa-mir-3686 ; hsa-mir-3607-3p ; hsa-mir-4528 ; hsa-mir-5583-5p ; hsa-mir-3129-3p ; hsa-mir-7844-5p ; hsa-mir-30e-5p ; hsa-mir-30d-5p ; hsa-mir-30b-5p ; hsa-mir-30c-5p ; hsa-mir-181c-5p ; hsa-mir-181d-5p ; hsa-mir-181b-5p ; hsa-mir-181a-5p ; hsa-mir-485-3p
Nearest miRNA
hsa-let-7g/Upstream/295033; hsa-mir-12124/Downstream/257122;
Nearest TSS
ENST00000440867/Upstream/52736; ENST00000468885/Downstream/20120;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/52515, chr3-CpG: 69/Downstream/96146
Nearest cancer related gene
PBRM1(TSG, No orient, 0)
Upstream sequence
ACTCTTTTCAGCTTCTTAGGTAAAAAAATAAATAAATAAAGGAAAAAGGTACTCACCAAAGGGATGCTGAAGTCAGATGTAGGGTTCAAACAACACATAC
Downstream sequence
TAATAATACATTTAATACATTTAATTCCATTTGCAACATGCGAAGGCAGGAATCAGCAATAGTATGATCTTCACATTCCTAATAGCCTCTACTCAAAACT
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate