Basic Information
VIS ID
TVIS30002432
Fusion event
HIV-NDE1 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
chr16
Cytoband
p13.11
Reference genome
GRCh37/hg19
Start
15774887/15681030 (Hg38)
End
15774887/15681030 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA16A
Target gene
NDE1
miRNAs that regulate target gene
hsa-mir-124-3p ; hsa-mir-215-5p ; hsa-mir-192-5p ; hsa-mir-30a-5p ; hsa-mir-877-5p ; hsa-mir-744-5p ; hsa-mir-92b-5p ; hsa-mir-423-5p ; hsa-mir-296-3p ; hsa-mir-769-5p ; hsa-mir-652-3p ; hsa-mir-423-3p ; hsa-mir-151a-3p ; hsa-mir-378a-3p ; hsa-mir-181b-5p ; hsa-mir-100-5p ; hsa-mir-99a-5p ; hsa-mir-25-3p ; hsa-mir-3196
Nearest miRNA
hsa-mir-1225/Upstream/37658; hsa-mir-11401/Downstream/619129;
Nearest TSS
ENST00000527434/Upstream/3105; ENST00000574109/Downstream/6397;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/30464, chr16-CpG: 44/Downstream/175952
Upstream sequence
TTTTCCATACAAATATTTCCTTTTTTCTCTTTTGAAAAAAAATTTTTTATACATGTATTTTTCATTTTTAGGTCATCAGTTACATCTTTTTTTAAATACC
Downstream sequence
TTCTAGGTTTGCAGATTTCACTAGGGAAGTCTCCTTGGTTCTTGATTGTTCATGTGTTTTGTGTTTTTTTTGCAATATTTTTTAATTGTTTAATTTTTTT
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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