Basic Information
VIS ID
TVIS30005028
Fusion event
HIV-SNX12 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
chrX
Cytoband
q13.1
Reference genome
GRCh37/hg19
Start
70282644/71062794 (Hg38)
End
70282644/71062794 (Hg38)
Orient
+
Location type
Intronic
Target gene
SNX12
miRNAs that regulate target gene
hsa-mir-130b-3p ; hsa-mir-124-3p ; hsa-mir-34a-5p ; hsa-mir-16-5p ; hsa-mir-1229-3p ; hsa-mir-328-3p ; hsa-mir-24-3p ; hsa-let-7b-5p ; hsa-mir-4632-5p ; hsa-mir-4436b-3p ; hsa-mir-6735-5p ; hsa-mir-6879-5p ; hsa-mir-7843-5p ; hsa-mir-6883-5p ; hsa-mir-6785-5p ; hsa-mir-4728-5p ; hsa-mir-149-3p ; hsa-mir-210-5p ; hsa-mir-4749-3p ; hsa-mir-3616-3p ; hsa-mir-548p ; hsa-mir-548x-3p ; hsa-mir-548j-3p ; hsa-mir-548aq-3p ; hsa-mir-548am-3p ; hsa-mir-548aj-3p ; hsa-mir-548ah-3p ; hsa-mir-548ae-3p
Nearest miRNA
hsa-let-7f-2/Upstream/1039871; hsa-mir-105-1/Downstream/3155583;
Nearest TSS
ENST00000429181/Upstream/131669; ENST00000466874/Downstream/137;
Nearest CpG islands
None/Target, chrX-CpG: 62/Upstream/9389, chrX-CpG: 24/Downstream/32852
Upstream sequence
caaaaggtatccccccgatctaaaatactgagatttgatggataagaatgtgttcaccctcttcattcccttcaagactttatagactgtggttgtatgc
Downstream sequence
ccactcagcctATGCAGAGCTCCTCCTCCAAAGATGCCACACAGAGAACAAAGCCATACCTTGCTATCTCTCTCCAGCTCATTTTTCAGCCACTCAAAGT
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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