This gene encodes a calcium-binding protein belonging to the penta-EF-hand protein family. Calcium binding is important for homodimerization and for conformational changes required for binding to other protein partners. This gene product participates in T cell receptor-, Fas-, and glucocorticoid-induced programmed cell death. In mice deficient for this gene product, however, apoptosis was not blocked suggesting this gene product is functionally redundant. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is also located on the short arm of chromosome 5. [provided by RefSeq, May 2012]
Transcription factors with Perturb-seq knockdown data for PDCD6. 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 = PDCD6 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 PDCD6, 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 |
|---|---|---|---|---|
| chr5:52,897–54,263 | 217.9 kb | Distal (>10kb) Multiome | 379 | |
| chr5:91,673–92,358 | 179.6 kb | Distal (>10kb) Multiome | 279 | |
| chr5:188,610–189,107 | 82.9 kb | Distal (>10kb) Multiome | 472 | |
| chr5:217,613–219,286 | 53.4 kb | Distal (>10kb) Multiome | 692 | |
| chr5:271,018–272,107 | 169 bp | At TSS Multiome | 866 | |
| chr5:320,742–322,619 | 49.9 kb | Distal (>10kb) Multiome | 441 | |
| chr5:472,056–474,135 | 201.5 kb | Distal (>10kb) Multiome | 964 | |
| chr5:523,794–524,758 | 252.6 kb | Distal (>10kb) Multiome | 106 | |
| chr5:1,633,700–1,634,325 | 1362.4 kb | Distal (>10kb) Multiome HiCAR | 745 |
Genomic view of the PDCD6 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.