Basic Information
VIS ID
TVIS30008871
Fusion event
HIV-RAPGEF6 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
q31.1
Reference genome
GRCh37/hg19
Start
130809250/131473557 (Hg38)
End
130809250/131473557 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA5C
Target gene
RAPGEF6
miRNAs that regulate target gene
hsa-mir-21-5p ; hsa-mir-940 ; hsa-mir-629-3p ; hsa-mir-6867-3p ; hsa-mir-4713-5p ; hsa-mir-6881-3p ; hsa-mir-188-3p ; hsa-mir-4268 ; hsa-mir-130b-5p ; hsa-mir-2116-3p ; hsa-mir-532-3p ; hsa-mir-150-5p ; hsa-mir-766-3p ; hsa-mir-877-3p ; hsa-mir-4267 ; hsa-mir-6736-3p ; hsa-mir-4698 ; hsa-mir-19b-3p ; hsa-mir-19a-3p
Nearest miRNA
hsa-mir-10397/Upstream/2076410; hsa-mir-103a-1/Downstream/744292;
Nearest TSS
ENST00000502646/Upstream/637; ENST00000446275/Downstream/34600;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/208844, chr5-CpG: 85/Downstream/161165
Upstream sequence
CTGTCACTTAGGTTTTAGATACCCCCAAATTTTAGCTTACTTTTAAGCAAAACAGTCCTATAAAAACATAAGATAGCAGTGAAAAAAATTTCCATCAACA
Downstream sequence
TCAATAACCAAAAACTACTTCTAAGGGTTGTACTTACATTAAAACCAATGCTCTGTTACTATTAATTCTTGTCTATATTTTATCAAATGCAGCATTCTGC
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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