Basic Information
VIS ID
TVIS30013698
Fusion event
HIV-PTPRD 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
chr9
Cytoband
p23
Reference genome
GRCh37/hg19
Start
9179056/9179056 (Hg38)
End
9179056/9179056 (Hg38)
Orient
+
Location type
Intronic
Target gene
PTPRD
miRNAs that regulate target gene
hsa-mir-429 ; hsa-mir-200a-3p ; hsa-mir-200c-3p ; hsa-mir-141-3p ; hsa-mir-1-3p ; hsa-mir-200b-3p ; hsa-mir-190a-3p ; hsa-mir-5011-5p ; hsa-mir-374b-3p ; hsa-mir-3924 ; hsa-mir-340-5p ; hsa-mir-4524b-5p ; hsa-mir-4791 ; hsa-mir-4524a-5p ; hsa-mir-3201 ; hsa-mir-891b ; hsa-mir-1246 ; hsa-mir-8076 ; hsa-mir-3163 ; hsa-mir-646 ; hsa-mir-5583-3p ; hsa-mir-503-5p ; hsa-mir-424-5p ; hsa-mir-15a-5p ; hsa-mir-497-5p ; hsa-mir-6838-5p ; hsa-mir-15b-5p ; hsa-mir-16-5p ; hsa-mir-195-5p ; hsa-mir-135a-5p
Nearest miRNA
hsa-mir-101-2/Upstream/3171152; hsa-let-7a-1/Downstream/9394250;
Nearest TSS
ENST00000422679/Upstream/242977; ENST00000449531/Downstream/620367;
Nearest CpG islands
None/Target, chr9-CpG: 64/Upstream/320348, chr9-CpG: 76/Downstream/1433579
Nearest cancer related gene
PTPRD(TSG, No orient, 0)
Upstream sequence
ACCTGAATATGTTCCTGCTACGTGTAATGCTAATTACTTCTTTACTAAAAGTAACTAAAAACAGGCTCACTTAATGGTATGCCTTAGTTAGAAGATCTGG
Downstream sequence
TTTATGTCTCCAAACTAGTGCTACTCAGAACTTCACAAACAATTCTTAAAATCAACTAAAGAAACCTTAGTATTTCTGATTTTCTTAATTGTTGAAACTC
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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