Basic Information
VIS ID
TVIS30003243
Fusion event
HIV-HDAC4 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
chr2
Cytoband
q37.3
Reference genome
GRCh37/hg19
Start
240279879/239358184 (Hg38)
End
240279879/239358184 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA2J
Target gene
HDAC4
miRNAs that regulate target gene
hsa-mir-29b-3p ; hsa-mir-140-5p ; hsa-mir-1-3p ; hsa-mir-22-3p ; hsa-mir-30c-5p ; hsa-mir-302b-3p ; hsa-mir-9-5p ; hsa-mir-206 ; hsa-mir-3149 ; hsa-mir-587 ; hsa-mir-4686 ; hsa-mir-513c-3p ; hsa-mir-513a-3p ; hsa-mir-3606-3p ; hsa-mir-4282 ; hsa-mir-19b-3p ; hsa-mir-19a-3p ; hsa-mir-381-3p ; hsa-mir-125a-5p ; hsa-mir-675-5p
Nearest miRNA
hsa-mir-10b/Upstream/6380; hsa-mir-149/Downstream/584831;
Nearest TSS
ENST00000437798/Upstream/48972; ENST00000428471/Downstream/42765;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/82883, chr2-CpG: 263/Downstream/41899
Upstream sequence
TCGTGGGCCTGAatccatcagagcagccgggctgtgacactcactgtcatgatgtttgcctagtggtgacatccaaatcacctcctttttgctgcactta
Downstream sequence
ttacttagaattccaaggcaaggatgagctttcactgctccatcttcccagtgactcagtaatctgcttccgttcgtgtggactcacagatagttacgtt
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate