VISDB - VIS Detail

Basic Information

VIS ID

TVIS30003461

Fusion event

HIV-PPARG 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

chr3

Cytoband

p25.2

Reference genome

GRCh37/hg19

Start

12414705/12373206 (Hg38)

End

12414705/12373206 (Hg38)

Orient

+

Location type

Intronic

Target gene

PPARG

miRNAs that regulate target gene

hsa-mir-20b-5p ; hsa-mir-27b-3p ; hsa-mir-138-5p ; hsa-mir-130a-3p ; hsa-mir-130b-3p ; hsa-mir-20a-5p ; hsa-mir-1-3p ; hsa-mir-215-5p ; hsa-mir-192-5p ; hsa-mir-27a-3p ; hsa-mir-218-5p

Nearest miRNA

hsa-mir-12127/Upstream/1978644; hsa-let-7g/Downstream/3123033;

Nearest TSS

ENST00000440867/Upstream/21637; ENST00000396999/Downstream/6500;

Nearest CpG islands

None/Target, chr3-CpG: 148/Upstream/84372, chr3-CpG: 61/Downstream/111044

Nearest cancer related gene

PPARG(OG, No orient, 0)

Upstream sequence

TCAACTTACAGCTTGGCAGAAACAGTAGCTTATGTTTTCTAGAGACAAAATTAGAAGCAGGCTTTCTGGACCCATCTCTAAGTCAAAATAAAATAAAATG

Downstream sequence

TCTAGGGAACCACTGTGCCTCCCAGTAACTATGGTCCATGGAATAATATTGTTTAGGTCAAGGTGTCCCAGAGTAAAAGGGAAGGGAGAAGGGCAGGGGG

Reference

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