This gene encodes the delta subunit of rod-specific photoreceptor phosphodiesterase (PDE), a key enzyme in the phototransduction cascade. A similar protein in cow functions in solubilizing membrane-bound PDE. In addition to its role in the PDE complex, the encoded protein is thought to bind to prenyl groups of proteins to target them to subcellular organelles called cilia. Mutations in this gene are associated with Joubert syndrome-22. Alternative splicing results in multiple splice variants. [provided by RefSeq, Mar 2014]
Transcription factors with Perturb-seq knockdown data for PDE6D. 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 = PDE6D 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 PDE6D, 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 |
|---|---|---|---|---|
| chr2:231,482,645–231,483,215 | 298.3 kb | Distal (>10kb) Multiome | 450 | |
| chr2:231,483,468–231,484,163 | 297.4 kb | Distal (>10kb) Multiome | 197 | |
| chr2:231,514,074–231,514,984 | 266.8 kb | Distal (>10kb) Multiome | 731 | |
| chr2:231,530,197–231,530,963 | 250.8 kb | Distal (>10kb) Multiome | 395 | |
| chr2:231,557,621–231,558,377 | 223.2 kb | Distal (>10kb) Multiome | 215 | |
| chr2:231,601,487–231,602,111 | 179.5 kb | Distal (>10kb) Multiome | 239 | |
| chr2:231,604,056–231,605,408 | 176.5 kb | Distal (>10kb) Multiome | 677 | |
| chr2:231,611,822–231,613,019 | 168.6 kb | Distal (>10kb) Multiome | 673 | |
| chr2:231,613,128–231,615,041 | 167.1 kb | Distal (>10kb) Multiome | 956 | |
| chr2:231,621,037–231,621,485 | 159.8 kb | Distal (>10kb) Multiome | 189 | |
| chr2:231,661,829–231,663,079 | 118.9 kb | Distal (>10kb) Multiome | 645 | |
| chr2:231,666,093–231,667,175 | 114.7 kb | Distal (>10kb) Multiome | 778 | |
| chr2:231,672,732–231,673,910 | 107.9 kb | Distal (>10kb) Multiome | 570 | |
| chr2:231,674,697–231,675,325 | 106.2 kb | Distal (>10kb) Multiome | 455 | |
| chr2:231,679,801–231,681,869 | 100.1 kb | Distal (>10kb) Multiome | 959 | |
| chr2:231,687,250–231,687,863 | 93.8 kb | Distal (>10kb) Multiome | 640 | |
| chr2:231,706,062–231,711,186 | 72.9 kb | Distal (>10kb) Multiome | 1322 | |
| chr2:231,713,567–231,715,698 | 66.0 kb | Distal (>10kb) Multiome HiCAR | 974 | |
| chr2:231,780,179–231,780,344 | 918 bp | At TSS | 196 | |
| chr2:231,780,605–231,781,892 | 172 bp | At TSS Multiome | 832 | |
| chr2:231,786,115–231,787,127 | 5.2 kb | Proximal (<10kb) Multiome | 1074 | |
| chr2:231,924,925–231,927,159 | 144.0 kb | Distal (>10kb) Multiome | 655 | |
| chr2:231,961,157–231,962,183 | 180.4 kb | Distal (>10kb) Multiome | 981 |
Genomic view of the PDE6D 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.