Basic Information
VIS ID
TVIS30002786
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
61874774/63797414 (Hg38)
End
61874774/63797414 (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/853102; hsa-mir-1250/Downstream/703360;
Nearest TSS
ENST00000595228/Upstream/4883; ENST00000577978/Downstream/2737;
Nearest CpG islands
None/Target, chr17-CpG: 26/Upstream/22712, chr17-CpG: 56/Downstream/29952
Upstream sequence
gcactccagcctgggcaacgagagcgaaactccatctcaaaaaaaaaaaaaaaaaagaaTTGCCTATGAAAAATGTAAAAACTACACACATTTAACTCAC
Downstream sequence
TCCAGCCCCAAGGATTCTGATTTAGTAGATGTAGAAcagaattttcagccttgagactactgtcatttggcgctggataattatttgttgtggggctttc
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate