This gene encodes a nuclear receptor that may be a negative regulator of the Wnt/beta-catenin signaling pathway. The encoded protein localizes to the nuclear membrane and has been implicated in the nuclear trafficking of the transcription repressors REST/NRSF and REST4. Mutations in this gene have been linked to progressive myoclonus epilepsy. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 3. [provided by RefSeq, Sep 2009]
Transcription factors with Perturb-seq knockdown data for PRICKLE1. 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 = PRICKLE1 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 PRICKLE1, 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 |
|---|---|---|---|---|
| chr12:42,237,254–42,239,022 | 245.5 kb | Distal (>10kb) Multiome | 833 | |
| chr12:42,325,595–42,326,457 | 157.0 kb | Distal (>10kb) Multiome | 748 | |
| chr12:42,481,470–42,481,669 | 1.4 kb | Proximal (<10kb) | 30 | |
| chr12:42,482,483–42,484,824 | 1.0 kb | Proximal (<10kb) Multiome | 761 | |
| chr12:42,485,748–42,486,391 | 2.7 kb | Proximal (<10kb) | 112 | |
| chr12:42,588,923–42,590,912 | 106.7 kb | Distal (>10kb) Multiome | 540 | |
| chr12:42,596,117–42,596,474 | 6.4 kb | Proximal (<10kb) | 13 | |
| chr12:42,756,801–42,757,785 | 274.1 kb | Distal (>10kb) Multiome | 310 | |
| chr12:42,780,540–42,781,256 | 297.8 kb | Distal (>10kb) Multiome HiCAR | 117 | |
| chr12:42,801,079–42,802,243 | 318.4 kb | Distal (>10kb) Multiome HiCAR | 104 | |
| chr12:42,807,084–42,808,043 | 324.5 kb | Distal (>10kb) Multiome HiCAR | 145 | |
| chr12:42,921,773–42,922,952 | 439.2 kb | Distal (>10kb) Multiome HiCAR | 314 |
Genomic view of the PRICKLE1 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.