Basic Information
VIS ID
TVIS30008942
Fusion event
HIV-FAM193B 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
176976082/177549081 (Hg38)
End
176976082/177549081 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA5G
Target gene
FAM193B
miRNAs that regulate target gene
hsa-mir-93-3p ; hsa-mir-1291 ; hsa-mir-181c-3p ; hsa-mir-328-3p ; hsa-mir-4530 ; hsa-mir-4640-5p ; hsa-mir-4690-3p ; hsa-mir-4726-5p ; hsa-mir-5685 ; hsa-mir-624-5p ; hsa-mir-6775-3p ; hsa-mir-6779-3p ; hsa-mir-6851-3p
Nearest miRNA
hsa-mir-10397/Upstream/919581; hsa-mir-1229/Downstream/2249197;
Nearest TSS
ENST00000502646/Upstream/9730; ENST00000606358/Downstream/4185;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/17565, chr5-CpG: 105/Downstream/4707
Upstream sequence
ctttctaccaccttgtcctctggagaacttctacacaaccttgaagactcagctctgagaagcattctctgacccATCTTCCTCTAGGTTATGTCTTGGG
Downstream sequence
CAACCCTGACACCAAATATCTACAATACTCAGAGCTACCACTtgtgttaagcataccgcacttgttggaccctaacattaaccatgtaagactggattgt
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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