Basic Information
VIS ID
TVIS30005521
Fusion event
HIV-EFCAB2 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
chr1
Cytoband
q44
Reference genome
GRCh37/hg19
Start
245202703/245039401 (Hg38)
End
245202703/245039401 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA1I
Target gene
EFCAB2
miRNAs that regulate target gene
hsa-mir-574-5p ; hsa-mir-6867-5p ; hsa-mir-4711-3p ; hsa-mir-431-5p ; hsa-mir-3976
Nearest miRNA
hsa-mir-101-1/Upstream/1693146; hsa-mir-3124/Downstream/2162566;
Nearest TSS
ENST00000473358/Upstream/22159; ENST00000427529/Downstream/44055;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/67992, chr1-CpG: 323/Downstream/113844
Upstream sequence
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagccaagtgtggtggcacagtgcttccagctgctcaggaggttgaggtggttggattgcttgaacccag
Downstream sequence
gagctcgaggctgcagtgagctatgatggcatcactgcacttcagagtgcaacagagtgagacgctgcctcttaaaaaaaaaaaaaaagagtttgtgtat
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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