Basic Information
VIS ID
TVIS30000553
Fusion event
HIV-PCDH9 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
chr13
Cytoband
q21.32
Reference genome
GRCh37/hg19
Start
67395941/66821809 (Hg38)
End
67395941/66821809 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA13B
Target gene
PCDH9
miRNAs that regulate target gene
hsa-mir-155-5p ; hsa-mir-188-5p ; hsa-mir-127-5p ; hsa-mir-4635 ; hsa-mir-7843-3p ; hsa-mir-4735-3p ; hsa-mir-1264 ; hsa-mir-18b-5p ; hsa-mir-18a-5p ; hsa-mir-570-5p ; hsa-mir-548ba ; hsa-mir-548ai ; hsa-mir-548ag ; hsa-mir-548m
Nearest miRNA
hsa-mir-1297/Upstream/603485; hsa-mir-1267/Downstream/10876203;
Nearest TSS
ENST00000623511/Upstream/515500; ENST00000611609/Downstream/3360;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/2977263, chr13-CpG: 92/Downstream/408567
Nearest cancer related gene
PCDH9(TSG, No orient, 0)
Upstream sequence
TTAATTGTTTCATACGAAATCATTATTCTTATGCAAGGATTCCTGTGGTTCATTCAATTCCCCATGTGCCTTCATACCATAACTGGAAATAATTAGCAAC
Downstream sequence
ATGTCTGGAAGATTTAGCTAAGAAACATGTTAATTTTGCCTGGAGACAGTTCTTTTATCCTGCACATTCATTTTCACAAATTTCTTACTGAGTTTCTCAA
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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