Basic Information
VIS ID
TVIS30009256
Fusion event
HIV-HDAC9 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
chr7
Cytoband
p21.1
Reference genome
GRCh37/hg19
Start
18881330/18841707 (Hg38)
End
18881330/18841707 (Hg38)
Orient
-
Location type
Intronic
Target gene
HDAC9
miRNAs that regulate target gene
hsa-mir-342-3p ; hsa-mir-8485 ; hsa-mir-29a-5p
Nearest miRNA
hsa-mir-1302-6/Upstream/714398; hsa-mir-10399/Downstream/863651;
Nearest TSS
ENST00000635602/Upstream/5798; ENST00000496026/Downstream/9693;
Nearest CpG islands
None/Target, chr7-CpG: 39/Upstream/754321, chr7-CpG: 34/Downstream/264542
Upstream sequence
gtactttGTTGGTCCCAAACCATACAGGAACTGTAGTCCCTGTGTCAAGAGTATGGGATAACAAAACAATCATATAGCGAAAAATTCTTTGCAATGCATT
Downstream sequence
TTAGTCTATTTAACTTTGGCTTGGACATCTAAACTGGTAAGTGCCCCAAAATTGAAAATTTAGACTTTCACTACCCTTGATATCTCCAAGCCACTTCTCC
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
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