Basic Information
VIS ID
TVIS30012365
Fusion event
HIV-DDX42 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
chr17
Cytoband
q23.3
Reference genome
GRCh37/hg19
Start
61882254/63804894 (Hg38)
End
61882254/63804894 (Hg38)
Orient
+
Location type
Intronic
Target gene
DDX42
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-615-3p ; hsa-mir-345-5p ; hsa-mir-186-5p ; hsa-mir-10a-5p ; hsa-mir-99a-5p ; hsa-mir-6867-3p ; hsa-mir-670-5p ; hsa-mir-4685-3p ; hsa-mir-4287 ; hsa-mir-7113-3p ; hsa-mir-4469 ; hsa-mir-6734-3p ; hsa-mir-5088-3p ; hsa-mir-6752-3p ; hsa-mir-1324
Nearest miRNA
hsa-mir-10226/Upstream/860582; hsa-mir-1250/Downstream/695880;
Nearest TSS
ENST00000595228/Upstream/4717; ENST00000581477/Downstream/614;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/30192, chr17-CpG: 56/Downstream/22472
Upstream sequence
gccaggatcgcaccactgcactacagcctgggtgacagagcgaaactgtctcaaccaataaaagaaGTAGGTTGGTGTTTATATTGAAAATAGGAACAGA
Downstream sequence
AAACAAACTAGCTATACTTTTTAGGATCTAAGCTGAGAATAAATTAATTTTTTTGCTTTCTCTAGCTGGAATGGCTTTACTTGTGTAAAATTTGGAAAAG
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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