VISDB - VIS Detail

Basic Information

VIS ID

TVIS30009342

Fusion event

HIV-PTPN12 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

chr7

Cytoband

q11.23

Reference genome

GRCh37/hg19

Start

77254938/77625621 (Hg38)

End

77254938/77625621 (Hg38)

Orient

+

Location type

Intronic

Target gene

PTPN12

miRNAs that regulate target gene

hsa-mir-200b-3p ; hsa-mir-124-3p ; hsa-mir-194-5p ; hsa-mir-375 ; hsa-mir-599 ; hsa-mir-576-5p ; hsa-mir-607 ; hsa-mir-3156-3p ; hsa-mir-4666a-5p ; hsa-mir-6740-3p ; hsa-mir-4301 ; hsa-mir-494-3p

Nearest miRNA

hsa-mir-10525/Upstream/1710352; hsa-mir-10399/Downstream/14578394;

Nearest TSS

ENST00000635602/Upstream/18693; ENST00000407343/Downstream/1535;

Nearest CpG islands

None/Target, chr7-CpG: 39/Upstream/87601, chr7-CpG: 104/Downstream/70472

Nearest cancer related gene

PTPN12(TSG, No orient, 0)

Upstream sequence

tcactctcactctcactcgcgctctctctctcgctctctctctctttttttttttttttttttttttggagacagtcttgctctgtcgcccagactggag

Downstream sequence

tgcagtggcgtgatctcaactcactgccatctccacctcctgggctcaagcaattctcctgcctcagcctcccaagtatctgggactgcaggtgtgtgcc

Reference

Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.