Basic Information
VIS ID
TVIS30010578
Fusion event
HIV-SAFB 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
chr19
Cytoband
p13.3
Reference genome
GRCh37/hg19
Start
5646017/5646006 (Hg38)
End
5646017/5646006 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA19B
Target gene
SAFB
miRNAs that regulate target gene
hsa-mir-26b-5p ; hsa-mir-1229-3p ; hsa-mir-331-5p ; hsa-mir-92a-3p ; hsa-let-7c-5p ; hsa-let-7b-5p
Nearest miRNA
hsa-mir-1227/Upstream/713266; hsa-let-7e/Downstream/743632;
Nearest TSS
ENST00000633603/Upstream/4155; ENST00000592707/Downstream/2849;
Nearest CpG islands
None/Target, chr19-CpG: 112/Upstream/22305, chr19-CpG: 100/Downstream/34416
Nearest cancer related gene
SAFB(TSG, No orient, 0)
Upstream sequence
TCTGAAATTGCCCAGATTTCATTTAATGACTGTATCATCCTACCTGTTTCATTGGCATCTCTGTAAATATTAAATCTTAGATGAGAACAGATGAGTTGAG
Downstream sequence
AATTTCCAGGTATGATTTTTATATTTGTGGGTCTTGAGTTTCCTTTTTTTTTCCAGCCTACATAGATACAAATTGTTAGAACACACTTACCTAGGTAGCT
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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