Basic Information
VIS ID
TVIS30002545
Fusion event
HIV-SMPD3 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
q22.1
Reference genome
GRCh37/hg19
Start
68469514/68435611 (Hg38)
End
68469514/68435611 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA16B
Target gene
SMPD3
miRNAs that regulate target gene
hsa-mir-26b-5p
Nearest miRNA
hsa-mir-1225/Upstream/202112; hsa-mir-11401/Downstream/1130197;
Nearest TSS
ENST00000527434/Upstream/63353; ENST00000619354/Downstream/12831;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/63241, chr16-CpG: 155/Downstream/11350
Upstream sequence
TCCCCCGTATCCCCTAACACAGAGGTGCCAGTTCTGCCGAGGGCCACAGACAGGAAGGGCTGGGGCCTGGGAAAGGCACGGTGGGGGCTGGCTGGGGTGG
Downstream sequence
GAGGGACATCCTGCCAGGGCCCAAGTTCTCCAGAGGGAGACACAGGCCAAGAAGGGCCTCATCTTCTGGGGGGCCTGAGGGGCAGGAGTGGGACTGGCCT
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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