Basic Information
VIS ID
TVIS30012817
Fusion event
HIV-PDE6D 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
q37.1
Reference genome
GRCh37/hg19
Start
232630244/231765534 (Hg38)
End
232630244/231765534 (Hg38)
Orient
+
Location type
Intronic
Target gene
PDE6D
miRNAs that regulate target gene
hsa-mir-196a-5p ; hsa-mir-218-5p ; hsa-mir-675-3p ; hsa-mir-6864-3p ; hsa-mir-3672 ; hsa-mir-4747-5p ; hsa-mir-5196-5p ; hsa-mir-4533 ; hsa-mir-5589-5p ; hsa-mir-4731-5p ; hsa-mir-769-5p ; hsa-mir-4646-5p ; hsa-mir-4786-5p ; hsa-mir-204-3p ; hsa-mir-4728-3p ; hsa-mir-8083
Nearest miRNA
hsa-mir-10b/Upstream/52136; hsa-mir-1471/Downstream/126708;
Nearest TSS
ENST00000437798/Upstream/54403; ENST00000479430/Downstream/15729;
Nearest CpG islands
None/Target, chr2-CpG: 135/Upstream/54411, chr2-CpG: 100/Downstream/15069
Upstream sequence
GAATTTAAAAGCCCATTCTGCATTAAGTTTGAATTCATGACTTGACAGAGTACTCATAAATTATATATGGGCATGTGGCTCTGAGTAATTTCCAGGTAAG
Downstream sequence
TATATTTTTCAGGCAAAATGGCTGACTAAGCATATAATGATATATGCTAATGTCTACTATGGCAGACCAGAGCACTATGAGGCAAAGCTTCAAAACCAAG
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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