Basic Information
VIS ID
TVIS30016310
Fusion event
HIV-RAPGEF6 integration
Validated
Yes
Detection method
LM PCR
Data source
Curated
Sample type
PBMC
Disease
HIV-infected disease (HID)
Quality evaluation
Good
Reported year
2014
PubMed ID
24968937
Virus Sequence
Virus name
HIV
Reference genome
Not given
Host Sequence
Chromosome
chr5
Cytoband
q31.1
Reference genome
GRCh37/hg19
Start
130826440/131490747 (Hg38)
End
130826299/131490747 (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/2093600; hsa-mir-103a-1/Downstream/727102;
Nearest TSS
ENST00000502646/Upstream/17827; ENST00000446275/Downstream/17410;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/226034, chr5-CpG: 85/Downstream/143975
Upstream sequence
tctgagggaaaagtcactgtgggaaaaaaatgttacgctctattgaacacaagtatcttcaggaaggcaagaacatataatactgtatcacccatctgtt
Downstream sequence
ccttaaaaaagtactaaaagaagtaccaaagacaactgtgaaatgagttgaaataatggggatatacagtgcaaatgaaataaaagtgatcaatgaaatc
Target sequence
caacattaagttgatgtgataactttctgtgactttagtattctgagggaaaagtcactgtgggaaaaaaatgttacgctctattgaacacaagtatcttcaggaaggcaagaacatataatactgtatcacccatctgtt
Reference
Maldarelli, F., et al. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science,2014, 345(6193): 179-183.
Curate