Basic Information
VIS ID
TVIS30008951
Fusion event
HIV-SQSTM1 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
chr5
Cytoband
q35.3
Reference genome
GRCh37/hg19
Start
179236321/179809321 (Hg38)
End
179236321/179809321 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA5G
Target gene
SQSTM1
miRNAs that regulate target gene
hsa-mir-16-5p ; hsa-mir-335-5p ; hsa-mir-7-5p ; hsa-mir-877-5p ; hsa-mir-423-5p ; hsa-mir-484 ; hsa-mir-646 ; hsa-mir-548e-5p ; hsa-mir-1252-3p ; hsa-mir-3925-5p ; hsa-mir-3978 ; hsa-mir-4712-3p ; hsa-mir-5093 ; hsa-mir-8069 ; hsa-mir-8075 ; hsa-mir-17-5p ; hsa-mir-20a-5p ; hsa-mir-93-5p ; hsa-mir-106b-5p ; hsa-mir-20b-5p ; hsa-mir-519d-3p ; hsa-mir-146a-5p ; hsa-mir-146b-5p ; hsa-mir-7153-5p ; hsa-mir-7161-3p ; hsa-mir-218-5p ; hsa-mir-5087
Nearest miRNA
hsa-mir-10397/Upstream/10975; hsa-mir-340/Downstream/205982;
Nearest TSS
ENST00000502646/Upstream/1997; ENST00000512234/Downstream/2294;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/1726, chr5-CpG: 89/Downstream/7224
Nearest cancer related gene
SQSTM1(OG, No orient, 0)
Upstream sequence
catctcggctcactgcaacctcagcctcccaggttcaagcgattctcctgcctcagcctcccgagtagctgggattataggcgcccgccaccacgcctgg
Downstream sequence
ctaatttttttttttttttttttttttttttttgagacagagtctcgctatgtcgcccaggctggagtgcgatggcagaatctcggcttactgcaacttc
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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