Basic Information
VIS ID
TVIS30008881
Fusion event
HIV-DDX46 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
134159636/134823946 (Hg38)
End
134159636/134823946 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA5C
Target gene
DDX46
miRNAs that regulate target gene
hsa-mir-93-5p ; hsa-mir-21-5p ; hsa-mir-423-3p ; hsa-mir-99a-5p ; hsa-mir-138-2-3p ; hsa-mir-4482-3p ; hsa-mir-7159-3p
Nearest miRNA
hsa-mir-10397/Upstream/598094; hsa-mir-103a-1/Downstream/979039;
Nearest TSS
ENST00000502646/Upstream/5030; ENST00000506332/Downstream/1867;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/64865, chr5-CpG: 78/Downstream/21847
Upstream sequence
GGCAATAAAACCTTTGGTGTACATGGAGTCAGGATTTTATTTTCTGCTTGAATACATGGGTATCATTTAAGCAAAATTAATATTTTAACTGCTTGCCTTA
Downstream sequence
TAAAGAGGTAAGTGAGAGACATGATTATTTGCTTTGAAAAAGAATTCTTTTCGTAATTCATTTATTAATTTAAATGCAGTGTTTGCTTAGTATGGTATAA
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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