This gene encodes a member of the Clp1 family. The encoded protein is a multifunctional kinase which is a component of the tRNA splicing endonuclease complex and a component of the pre-mRNA cleavage complex II. This protein is implicated in tRNA, mRNA, and siRNA maturation. Mutations in this gene are associated with pontocerebellar hypoplasia type 10 (PCH10). Alternatively splice transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]
Transcription factors with Perturb-seq knockdown data for CLP1. 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 = CLP1 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 CLP1, 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 |
|---|---|---|---|---|
| chr11:57,426,113–57,427,448 | 230.7 kb | Distal (>10kb) Multiome | 451 | |
| chr11:57,457,029–57,457,825 | 200.3 kb | Distal (>10kb) Multiome | 458 | |
| chr11:57,460,127–57,461,576 | 197.2 kb | Distal (>10kb) Multiome | 418 | |
| chr11:57,480,236–57,481,014 | 177.2 kb | Distal (>10kb) Multiome | 300 | |
| chr11:57,482,336–57,483,518 | 174.6 kb | Distal (>10kb) Multiome | 338 | |
| chr11:57,493,430–57,494,126 | 164.1 kb | Distal (>10kb) Multiome | 521 | |
| chr11:57,499,261–57,500,331 | 158.0 kb | Distal (>10kb) Multiome | 548 | |
| chr11:57,514,003–57,516,118 | 143.3 kb | Distal (>10kb) Multiome | 833 | |
| chr11:57,530,326–57,531,572 | 126.8 kb | Distal (>10kb) Multiome | 824 | |
| chr11:57,567,377–57,568,664 | 89.6 kb | Distal (>10kb) Multiome | 665 | |
| chr11:57,597,419–57,598,821 | 59.7 kb | Distal (>10kb) Multiome | 359 | |
| chr11:57,637,508–57,640,656 | 19.6 kb | Distal (>10kb) Multiome | 699 | |
| chr11:57,644,541–57,645,304 | 12.8 kb | Distal (>10kb) Multiome | 237 | |
| chr11:57,646,682–57,652,802 | 7.9 kb | Proximal (<10kb) Multiome | 580 | |
| chr11:57,653,349–57,654,303 | 3.4 kb | Proximal (<10kb) | 37 | |
| chr11:57,656,843–57,658,231 | 148 bp | At TSS Multiome | 827 | |
| chr11:57,662,964–57,663,154 | 5.2 kb | Proximal (<10kb) | 66 | |
| chr11:57,666,634–57,668,805 | 10.0 kb | Distal (>10kb) Multiome | 958 | |
| chr11:57,711,417–57,713,054 | 54.5 kb | Distal (>10kb) Multiome | 857 | |
| chr11:57,740,872–57,742,140 | 83.7 kb | Distal (>10kb) Multiome | 973 | |
| chr11:57,761,276–57,762,144 | 104.0 kb | Distal (>10kb) Multiome | 612 | |
| chr11:57,778,066–57,779,000 | 121.0 kb | Distal (>10kb) Multiome | 688 | |
| chr11:57,780,962–57,781,951 | 123.9 kb | Distal (>10kb) Multiome | 317 | |
| chr11:57,800,273–57,801,159 | 143.0 kb | Distal (>10kb) Multiome | 547 | |
| chr11:57,902,618–57,904,039 | 245.5 kb | Distal (>10kb) Multiome | 362 |
Genomic view of the CLP1 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.