Basic Information
VIS ID
TVIS30005682
Fusion event
HIV-GBF1 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
chr10
Cytoband
q24.32
Reference genome
GRCh37/hg19
Start
104043849/102284092 (Hg38)
End
104043849/102284092 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA10D ; FRA10A ; FRA10B
Target gene
GBF1
miRNAs that regulate target gene
hsa-mir-193b-3p ; hsa-mir-7-5p ; hsa-let-7f-5p ; hsa-let-7b-5p ; hsa-let-7a-5p ; hsa-mir-17-5p ; hsa-mir-20a-5p ; hsa-mir-93-5p ; hsa-mir-106b-5p ; hsa-mir-20b-5p ; hsa-mir-519d-3p ; hsa-mir-485-5p ; hsa-mir-377-3p ; hsa-mir-485-3p
Nearest miRNA
hsa-mir-107/Upstream/682595; hsa-mir-1307/Downstream/152420;
Nearest TSS
ENST00000439456/Upstream/38560; ENST00000476019/Downstream/75007;
Nearest CpG islands
None/Target, chr10-CpG: 68/Upstream/38257, chr10-CpG: 146/Downstream/109880
Upstream sequence
TCCACTGACATTTCTGCAACCAGTTTTGGTGAGTGGAAAGCAACTAGGTAAGTTTCACTTTTTGCAAGAATCCCAAGTGACCCTTTGCACTATGGACTGA
Downstream sequence
GGTACCTGCTTGTCTCTACAAAAACTATAGAGGAGACACGACAGGCTTTAACTGGAAATTGTTCATGGTTTCTTAGAAGGGAAGCTCATATCCTGTTAAA
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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