Basic Information
VIS ID
TVIS30008681
Fusion event
HIV-RAPGEF2 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
chr4
Cytoband
q32.1
Reference genome
GRCh37/hg19
Start
160266120/159344968 (Hg38)
End
160266120/159344968 (Hg38)
Orient
+
Location type
Intronic
Target gene
RAPGEF2
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-155-5p ; hsa-mir-1-3p ; hsa-mir-615-3p ; hsa-mir-149-5p ; hsa-mir-29b-2-5p ; hsa-mir-10a-5p ; hsa-mir-10b-5p ; hsa-mir-339-5p ; hsa-mir-659-3p ; hsa-mir-3620-3p ; hsa-mir-5002-5p ; hsa-mir-6748-3p ; hsa-mir-19a-3p ; hsa-mir-19b-3p ; hsa-mir-8066 ; hsa-mir-4720-5p ; hsa-mir-335-3p ; hsa-mir-3942-3p ; hsa-mir-7152-3p
Nearest miRNA
hsa-mir-12113/Upstream/216074; hsa-mir-1305/Downstream/3748606;
Nearest TSS
ENST00000502981/Upstream/1674; ENST00000510253/Downstream/248;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/240985, chr4-CpG: 71/Downstream/3821341
Upstream sequence
TTTCCTAGTTGGAACTGAACAGGTGCCAAACataaatttttatatgtatattatgtgtaattttctttaaatttttaaaatCTGTATTATTCTATATTCC
Downstream sequence
TGTGTAACAGTTTACTCACTGGAATGAGGCATGTGACCTTTTGAACATAGACTATTAATATCAGTCTTGGCACATTTTAAATAGATAAAGTACTCCCATG
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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