Basic Information
VIS ID
TVIS30006363
Fusion event
HIV-PCDH17 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
chr13
Cytoband
q21.1
Reference genome
GRCh37/hg19
Start
58255856/57681722 (Hg38)
End
58255856/57681722 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA13B ; FRA13C
Target gene
PCDH17
miRNAs that regulate target gene
hsa-mir-6830-3p ; hsa-mir-6875-3p ; hsa-mir-6833-3p ; hsa-mir-4768-5p ; hsa-mir-6873-3p ; hsa-mir-6817-3p ; hsa-mir-7110-3p ; hsa-mir-4659b-3p ; hsa-mir-4659a-3p ; hsa-mir-4279 ; hsa-mir-942-5p ; hsa-mir-6870-3p ; hsa-mir-660-3p ; hsa-mir-5193 ; hsa-mir-6891-3p ; hsa-mir-6072 ; hsa-mir-4793-5p ; hsa-mir-5196-3p ; hsa-mir-570-5p ; hsa-mir-548ba ; hsa-mir-548ai ; hsa-mir-548ag ; hsa-mir-548m ; hsa-mir-3140-3p ; hsa-mir-452-3p ; hsa-mir-6854-5p
Nearest miRNA
hsa-mir-1297/Upstream/2507174; hsa-mir-1267/Downstream/3518076;
Nearest TSS
ENST00000623511/Upstream/46709; ENST00000615202/Downstream/484105;
Nearest CpG islands
None/Target, chr13-CpG: 551/Upstream/46926, chr13-CpG: 52/Downstream/2481804
Nearest cancer related gene
PCDH17(TSG, No orient, 0)
Upstream sequence
CACATTAACACCATTTAAAAATAATTTAATTTCTATATACTCCTAAAACCACCCTTATATATGAGGCTTAGCTTATTAATATATAGCCACTGGTGAAAAC
Downstream sequence
AAGATATAATGAGACAATTCTAAATATATGGTCTATCTCCCCATTCAGTGCCTCTCAGTGCCAAATGGTACTTCTGCTAATTATGAGCAATAAATAAGAT
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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