The protein encoded by this gene belongs to the dual specificity protein phosphatase family. It was identified as a cyclin-dependent kinase inhibitor, and has been shown to interact with, and dephosphorylate CDK2 kinase, thus prevent the activation of CDK2 kinase. This gene was reported to be deleted, mutated, or overexpressed in several kinds of cancers. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]
Transcription factors with Perturb-seq knockdown data for CDKN3. 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 = CDKN3 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 CDKN3, 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 |
|---|---|---|---|---|
| chr14:54,187,126–54,188,017 | 209.4 kb | Distal (>10kb) Multiome | 54 | |
| chr14:54,291,237–54,292,121 | 105.4 kb | Distal (>10kb) Multiome | 321 | |
| chr14:54,361,880–54,362,724 | 34.7 kb | Distal (>10kb) Multiome | 146 | |
| chr14:54,366,777–54,367,506 | 30.0 kb | Distal (>10kb) Multiome | 393 | |
| chr14:54,392,880–54,394,206 | 2.8 kb | Proximal (<10kb) | 67 | |
| chr14:54,396,464–54,397,605 | 118 bp | At TSS Multiome | 808 | |
| chr14:54,440,764–54,441,825 | 44.3 kb | Distal (>10kb) Multiome | 860 | |
| chr14:54,472,369–54,472,855 | 75.6 kb | Distal (>10kb) Multiome | 154 | |
| chr14:54,488,387–54,489,472 | 92.0 kb | Distal (>10kb) Multiome | 922 | |
| chr14:54,509,366–54,510,519 | 112.8 kb | Distal (>10kb) Multiome | 801 | |
| chr14:54,564,898–54,567,596 | 168.3 kb | Distal (>10kb) Multiome | 963 | |
| chr14:54,567,716–54,568,327 | 171.1 kb | Distal (>10kb) Multiome | 296 |
Genomic view of the CDKN3 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.