Basic Information
VIS ID
TVIS30006166
Fusion event
HIV-NCKAP1L 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
chr12
Cytoband
q13.2
Reference genome
GRCh37/hg19
Start
54897144/54503360 (Hg38)
End
54897144/54503360 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA12A
Target gene
NCKAP1L
miRNAs that regulate target gene
hsa-mir-6739-3p ; hsa-mir-6875-3p ; hsa-mir-3692-3p ; hsa-mir-4677-5p ; hsa-mir-7156-5p ; hsa-mir-4273 ; hsa-mir-22-5p ; hsa-mir-2116-5p ; hsa-mir-4445-5p ; hsa-mir-6839-5p ; hsa-mir-378j ; hsa-mir-4308 ; hsa-mir-140-3p ; hsa-mir-5685 ; hsa-mir-4690-3p ; hsa-mir-6779-3p
Nearest miRNA
hsa-mir-1244-3/Upstream/166046; hsa-let-7i/Downstream/2691144;
Nearest TSS
ENST00000382841/Upstream/4576; ENST00000548916/Downstream/6513;
Nearest CpG islands
None/Target, chr12-CpG: 104/Upstream/83953, chr12-CpG: 66/Downstream/84789
Upstream sequence
tTTATTTGAATTTTAAATAATGAGCATGtattatttttataaacataaaaaataaaaattaatatgatgtttttgaaagaaaaattgataaggtattatt
Downstream sequence
aaaattttaaaaattaatGTCGTAATTTTACATTTAGAAATTTGTCATAAGGAAACAGAATTGTTTCATGGGGAAATAAAAAaaggaaacaaatgcaaag
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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