Basic Information
VIS ID
TVIS30010879
Fusion event
HIV-DEPDC1B 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
q12.1
Reference genome
GRCh37/hg19
Start
59935703/60639876 (Hg38)
End
59935703/60639876 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA5H
Target gene
DEPDC1B
miRNAs that regulate target gene
hsa-mir-361-5p ; hsa-mir-4282 ; hsa-mir-143-5p ; hsa-mir-3944-5p ; hsa-mir-107 ; hsa-mir-103a-3p ; hsa-mir-95-5p ; hsa-mir-455-5p ; hsa-mir-4703-5p ; hsa-mir-3942-5p ; hsa-mir-641 ; hsa-mir-3617-5p ; hsa-mir-548f-3p ; hsa-mir-548e-3p ; hsa-mir-548az-3p ; hsa-mir-548ar-3p ; hsa-mir-548a-3p ; hsa-mir-548x-3p ; hsa-mir-548j-3p ; hsa-mir-548aq-3p ; hsa-mir-548am-3p ; hsa-mir-548aj-3p ; hsa-mir-548ah-3p ; hsa-mir-548ae-3p ; hsa-mir-548z ; hsa-mir-548h-3p ; hsa-mir-548d-3p ; hsa-mir-548bb-3p ; hsa-mir-548ac
Nearest miRNA
hsa-mir-10397/Upstream/936173; hsa-mir-103a-1/Downstream/11529591;
Nearest TSS
ENST00000502646/Upstream/11185; ENST00000457499/Downstream/8271;
Nearest CpG islands
None/Target, chr5-CpG: 87/Upstream/746195, chr5-CpG: 87/Downstream/59671
Upstream sequence
CGTCCCATGAGGAACAGTGTAGCCAGCCTTCTCTATTTCCATTACAGCATGGAAGAAAGGACCACATCCTCATTGCCTAGCTCTGGCTCAGCAGAAGACT
Downstream sequence
AAACAACTGTACCCAAATAGACCTCTACCCCCAGAGGATCAAAAGCAGCAGCCAAGATAAATTGAAAGGAAATTCTTCCTACAGAATCTCTATAACTAAA
Reference
Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.
Curate