Basic Information
VIS ID
TVIS30005058
Fusion event
HIV-TNFRSF9 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
chr1
Cytoband
p36.23
Reference genome
GRCh37/hg19
Start
7976382/7916322 (Hg38)
End
7976382/7916322 (Hg38)
Orient
-
Location type
UTR3
Fragile sites / regions
FRA1A
Target gene
TNFRSF9
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-98-5p ; hsa-mir-1277-5p ; hsa-mir-190a-3p ; hsa-mir-5011-5p ; hsa-mir-524-5p ; hsa-mir-520d-5p ; hsa-mir-374a-3p ; hsa-mir-3140-3p ; hsa-mir-4267 ; hsa-mir-4733-3p ; hsa-mir-1226-3p ; hsa-mir-1305 ; hsa-mir-607 ; hsa-mir-3671 ; hsa-mir-627-3p ; hsa-mir-4762-5p ; hsa-mir-203a-3p ; hsa-mir-3613-3p
Nearest miRNA
hsa-mir-12136/Upstream/1486426; hsa-mir-101-1/Downstream/950180;
Nearest TSS
ENST00000473358/Upstream/62810; ENST00000460192/Downstream/18778;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/88906, chr1-CpG: 31/Downstream/26026
Upstream sequence
TTTTAATCATAGAAATTTACATTTATTTCTATTAAACCTAATTATGGAACTTTCTAAATTAAACCCAGAAGGGGATCATTTTATTCTGTCTCAATGTTCC
Downstream sequence
TTCCTTATTAATTGTCATTTAGGGGGAGCAATGACTCACATGCCAAGTTCCTGTGTTTTTCATTTATAGCTTTTGCACATGATACCAGAATAGGCTATGA
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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