This gene encodes a protein belonging to the serine/threonine type protein kinase family. This protein is a nuclear dual-specificity kinase that regulates the intranuclear distribution of the serine/arginine-rich (SR) family of splicing factors. Two transcript variants encoding different isoforms have been found for this gene. Related pseudogenes are located on chromosomes 1 and 9. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for CLK3. 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 = CLK3 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 CLK3, 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 |
|---|---|---|---|---|
| chr15:74,354,072–74,354,610 | 244.2 kb | Distal (>10kb) Multiome | 15 | |
| chr15:74,365,599–74,366,233 | 232.6 kb | Distal (>10kb) Multiome HiCAR | 441 | |
| chr15:74,373,469–74,375,034 | 224.1 kb | Distal (>10kb) Multiome HiCAR | 745 | |
| chr15:74,433,053–74,434,500 | 164.6 kb | Distal (>10kb) Multiome | 695 | |
| chr15:74,460,798–74,461,761 | 137.3 kb | Distal (>10kb) Multiome | 925 | |
| chr15:74,531,382–74,531,884 | 66.9 kb | Distal (>10kb) Multiome | 217 | |
| chr15:74,540,389–74,542,119 | 57.4 kb | Distal (>10kb) Multiome | 838 | |
| chr15:74,588,521–74,588,900 | 9.6 kb | Proximal (<10kb) | 175 | |
| chr15:74,598,102–74,598,966 | 36 bp | At TSS Multiome | 689 | |
| chr15:74,614,343–74,616,348 | 17.3 kb | Distal (>10kb) Multiome | 1019 | |
| chr15:74,621,115–74,621,412 | 5.3 kb | Proximal (<10kb) | 421 | |
| chr15:74,695,758–74,696,387 | 97.6 kb | Distal (>10kb) Multiome | 775 | |
| chr15:74,720,336–74,720,840 | 122.1 kb | Distal (>10kb) Multiome | 16 | |
| chr15:74,725,773–74,726,537 | 127.7 kb | Distal (>10kb) Multiome | 607 | |
| chr15:74,759,107–74,760,837 | 161.9 kb | Distal (>10kb) Multiome HiCAR | 637 | |
| chr15:74,761,837–74,762,260 | 163.6 kb | Distal (>10kb) Multiome HiCAR | 34 | |
| chr15:74,770,975–74,771,578 | 172.8 kb | Distal (>10kb) Multiome HiCAR | 485 | |
| chr15:74,781,439–74,783,648 | 183.6 kb | Distal (>10kb) Multiome HiCAR | 679 | |
| chr15:74,842,412–74,843,723 | 244.5 kb | Distal (>10kb) Multiome | 879 | |
| chr15:74,872,771–74,874,092 | 274.8 kb | Distal (>10kb) Multiome | 758 | |
| chr15:74,889,894–74,890,629 | 291.6 kb | Distal (>10kb) Multiome | 816 | |
| chr15:74,905,926–74,907,376 | 308.3 kb | Distal (>10kb) Multiome | 743 |
Genomic view of the CLK3 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.