Basic Information
VIS ID
TVIS30000859
Fusion event
HIV-PDCD11 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
2016
PubMed ID
26912621
Virus Sequence
Virus name
HIV
Reference genome
K03455.1
Host Sequence
Chromosome
chr10
Cytoband
q24.33
Reference genome
GRCh37/hg19
Start
105195598/103435841 (Hg38)
End
105195598/103435841 (Hg38)
Orient
-
Location type
Intronic
Fragile sites / regions
FRA10D ; FRA10A ; FRA10B
Target gene
PDCD11
miRNAs that regulate target gene
hsa-mir-98-5p ; hsa-let-7b-5p ; hsa-mir-320b ; hsa-mir-361-3p ; hsa-mir-615-3p ; hsa-mir-17-3p ; hsa-let-7e-5p ; hsa-mir-4286 ; hsa-mir-335-3p ; hsa-mir-4793-5p ; hsa-mir-5196-3p ; hsa-mir-6873-5p ; hsa-mir-216a-5p ; hsa-mir-548c-3p
Nearest miRNA
hsa-mir-107/Upstream/41440; hsa-mir-202/Downstream/612248;
Nearest TSS
ENST00000439456/Upstream/1848; ENST00000478543/Downstream/8472;
Nearest CpG islands
None/Target, chr10-CpG: 68/Upstream/39114, chr10-CpG: 31/Downstream/16352
Upstream sequence
acctcaggtgatctgcccatcctggcctcccaaagtggtgggattacaggcatgagccacggtgcctggccCTTTTGCATATATTTGGATACTAATGCAG
Downstream sequence
GTATGTTTGGTAAATAAATTCCTAGAAGTGAAATTGATGGGTTACATACCCtccaaaatgactgtgctaatttatgtccccattaacagtaaatatgact
Reference
Sunshine, S., et al. HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing Assay. J Virol,2016, 90(9): 4511-4519.
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