This gene encodes a member of the DHH protein superfamily of phosphoesterases. This protein has been found to function as both a nucleotide phosphodiesterase and an exopolyphosphatase. This protein is believed to stimulate cancer progression and metastases through the induction of cell motility. A pseuodgene has been identified on chromosome 13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Transcription factors with Perturb-seq knockdown data for PRUNE1. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = PRUNE1 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of PRUNE1, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr1:150,487,154–150,487,710 | 521.1 kb | Distal (>10kb) Multiome HiCAR | 929 | |
| chr1:150,875,863–150,877,222 | 131.7 kb | Distal (>10kb) Multiome | 912 | |
| chr1:150,925,543–150,926,754 | 82.1 kb | Distal (>10kb) Multiome | 813 | |
| chr1:150,973,876–150,975,458 | 33.6 kb | Distal (>10kb) Multiome | 590 | |
| chr1:150,979,331–150,979,990 | 28.9 kb | Distal (>10kb) Multiome | 562 | |
| chr1:150,981,212–150,981,672 | 27.0 kb | Distal (>10kb) Multiome | 379 | |
| chr1:151,006,389–151,007,024 | 1.6 kb | Proximal (<10kb) Multiome | 496 | |
| chr1:151,008,116–151,008,852 | 19 bp | At TSS Multiome | 763 | |
| chr1:151,008,955–151,009,142 | 536 bp | At TSS | 320 | |
| chr1:151,024,599–151,024,843 | at TSS | At TSS | 261 | |
| chr1:151,047,405–151,048,764 | 40.2 kb | Distal (>10kb) Multiome | 714 | |
| chr1:151,059,187–151,059,842 | 51.2 kb | Distal (>10kb) Multiome | 821 | |
| chr1:151,060,204–151,060,723 | 52.1 kb | Distal (>10kb) Multiome | 346 | |
| chr1:151,070,369–151,071,463 | 62.7 kb | Distal (>10kb) Multiome | 835 | |
| chr1:151,131,105–151,132,256 | 123.0 kb | Distal (>10kb) Multiome | 247 | |
| chr1:151,145,115–151,147,333 | 138.4 kb | Distal (>10kb) Multiome | 709 | |
| chr1:151,165,133–151,166,350 | 157.5 kb | Distal (>10kb) Multiome | 940 | |
| chr1:151,189,687–151,190,378 | 181.7 kb | Distal (>10kb) Multiome | 875 | |
| chr1:151,198,185–151,199,073 | 190.1 kb | Distal (>10kb) Multiome | 721 | |
| chr1:151,254,421–151,255,083 | 246.3 kb | Distal (>10kb) Multiome | 770 | |
| chr1:151,281,008–151,283,557 | 272.9 kb | Distal (>10kb) Multiome | 1121 |
Genomic view of the PRUNE1 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.