This gene encodes a regulator of CDK5 (cyclin-dependent kinase 5) activity. The protein encoded by this gene is localized to the centrosome and Golgi complex, interacts with CDK5R1 and pericentrin (PCNT), plays a role in centriole engagement and microtubule nucleation, and has been linked to primary microcephaly and Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
Transcription factors with Perturb-seq knockdown data for CDK5RAP2. 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 = CDK5RAP2 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 CDK5RAP2, 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 |
|---|---|---|---|---|
| chr9:120,324,863–120,325,581 | 254.9 kb | Distal (>10kb) Multiome | 158 | |
| chr9:120,348,743–120,349,526 | 231.1 kb | Distal (>10kb) Multiome | 233 | |
| chr9:120,439,246–120,439,443 | 1.8 kb | Proximal (<10kb) | 54 | |
| chr9:120,528,894–120,529,093 | 7.3 kb | Proximal (<10kb) | 23 | |
| chr9:120,531,729–120,531,995 | 4.4 kb | Proximal (<10kb) | 82 | |
| chr9:120,533,982–120,535,010 | 45.7 kb | Distal (>10kb) Multiome | 82 | |
| chr9:120,535,185–120,535,479 | 957 bp | At TSS | 9 | |
| chr9:120,579,589–120,580,675 | 47 bp | At TSS Multiome | 900 | |
| chr9:120,713,676–120,715,795 | 134.4 kb | Distal (>10kb) Multiome | 761 | |
| chr9:120,730,681–120,731,453 | 150.8 kb | Distal (>10kb) Multiome | 456 | |
| chr9:120,792,955–120,793,917 | 213.3 kb | Distal (>10kb) Multiome | 991 | |
| chr9:120,842,458–120,843,456 | 262.9 kb | Distal (>10kb) Multiome | 838 | |
| chr9:120,868,216–120,869,551 | 288.7 kb | Distal (>10kb) Multiome | 643 | |
| chr9:120,873,261–120,874,043 | 293.5 kb | Distal (>10kb) Multiome | 247 | |
| chr9:120,875,854–120,877,760 | 296.1 kb | Distal (>10kb) Multiome | 982 |
Genomic view of the CDK5RAP2 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.