This gene encodes a member of the CDC2-like (or LAMMER) family of dual specificity protein kinases. In the nucleus, the encoded protein phosphorylates serine/arginine-rich proteins involved in pre-mRNA processing, releasing them into the nucleoplasm. The choice of splice sites during pre-mRNA processing may be regulated by the concentration of transacting factors, including serine/arginine rich proteins. Therefore, the encoded protein may play an indirect role in governing splice site selection. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]
Transcription factors with Perturb-seq knockdown data for CLK1. 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 = CLK1 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 CLK1, 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 |
|---|---|---|---|---|
| chr2:200,585,716–200,586,842 | 278.6 kb | Distal (>10kb) Multiome | 627 | |
| chr2:200,648,397–200,649,297 | 215.9 kb | Distal (>10kb) Multiome | 229 | |
| chr2:200,713,048–200,713,472 | 151.4 kb | Distal (>10kb) Multiome | 763 | |
| chr2:200,736,302–200,737,549 | 127.7 kb | Distal (>10kb) Multiome | 210 | |
| chr2:200,810,854–200,812,782 | 53.1 kb | Distal (>10kb) Multiome | 1048 | |
| chr2:200,863,766–200,865,261 | 36 bp | At TSS Multiome | 1111 | |
| chr2:200,869,001–200,869,309 | 4.7 kb | Proximal (<10kb) | 40 | |
| chr2:200,888,532–200,889,950 | 24.7 kb | Distal (>10kb) Multiome | 1108 | |
| chr2:200,962,915–200,964,242 | 98.9 kb | Distal (>10kb) Multiome | 1021 | |
| chr2:201,071,202–201,072,338 | 207.1 kb | Distal (>10kb) Multiome | 993 | |
| chr2:201,090,426–201,091,071 | 226.1 kb | Distal (>10kb) Multiome | 68 | |
| chr2:201,116,279–201,117,190 | 252.0 kb | Distal (>10kb) Multiome | 907 | |
| chr2:201,118,264–201,119,153 | 254.0 kb | Distal (>10kb) Multiome | 863 | |
| chr2:201,125,205–201,126,756 | 261.7 kb | Distal (>10kb) Multiome | 696 | |
| chr2:201,157,926–201,158,657 | 293.7 kb | Distal (>10kb) Multiome | 540 |
Genomic view of the CLK1 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.