This gene encodes a regulator of cyclin-dependent kinase 5 activity. This protein has also been reported to modify RNA by adding a methylthio-group and may thus have a dual function as an RNA methylthiotransferase and as an inhibitor of cyclin-dependent kinase 5 activity. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, May 2013]
Transcription factors with Perturb-seq knockdown data for CDK5RAP1. 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 = CDK5RAP1 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 CDK5RAP1, 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 |
|---|---|---|---|---|
| chr20:33,401,239–33,401,685 | at TSS | At TSS | 1045 | |
| chr20:33,443,149–33,444,777 | 42.4 kb | Distal (>10kb) Multiome | 726 | |
| chr20:33,475,400–33,476,091 | 74.2 kb | Distal (>10kb) Multiome | 98 | |
| chr20:33,477,323–33,477,813 | 76.0 kb | Distal (>10kb) Multiome | 124 | |
| chr20:33,489,654–33,490,762 | 88.5 kb | Distal (>10kb) Multiome | 1000 | |
| chr20:33,663,243–33,664,235 | 262.2 kb | Distal (>10kb) Multiome HiCAR | 895 | |
| chr20:33,666,358–33,668,405 | 265.3 kb | Distal (>10kb) Multiome HiCAR | 603 | |
| chr20:33,673,732–33,675,136 | 273.0 kb | Distal (>10kb) Multiome | 826 | |
| chr20:33,685,755–33,686,963 | 285.0 kb | Distal (>10kb) Multiome HiCAR | 830 |
Genomic view of the CDK5RAP1 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.