The protein encoded by this gene is a cyclin-dependent kinase 2 (CDK2) -associated protein which is thought to negatively regulate CDK2 activity by sequestering monomeric CDK2, and targeting CDK2 for proteolysis. This protein was found to also interact with DNA polymerase alpha/primase and mediate the phosphorylation of the large p180 subunit, which suggests a regulatory role in DNA replication during the S-phase of the cell cycle. This protein also forms a core subunit of the nucleosome remodeling and histone deacetylation (NURD) complex that epigenetically regulates embryonic stem cell differentiation. This gene thus plays a role in both cell-cycle and epigenetic regulation. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2012]
Transcription factors with Perturb-seq knockdown data for CDK2AP1. 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 = CDK2AP1 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 CDK2AP1, 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 |
|---|---|---|---|---|
| chr12:122,974,115–122,975,704 | 297.4 kb | Distal (>10kb) Multiome | 889 | |
| chr12:122,980,138–122,981,155 | 291.7 kb | Distal (>10kb) Multiome | 817 | |
| chr12:123,049,639–123,050,104 | 222.5 kb | Distal (>10kb) Multiome | 45 | |
| chr12:123,150,285–123,151,740 | 121.3 kb | Distal (>10kb) Multiome | 487 | |
| chr12:123,232,511–123,233,923 | 39.2 kb | Distal (>10kb) Multiome | 1073 | |
| chr12:123,269,375–123,269,864 | 2.6 kb | Proximal (<10kb) Multiome | 217 | |
| chr12:123,270,951–123,272,226 | 1.1 kb | Proximal (<10kb) Multiome | 488 | |
| chr12:123,363,804–123,365,980 | 92.8 kb | Distal (>10kb) Multiome | 1015 | |
| chr12:123,383,367–123,384,963 | 111.6 kb | Distal (>10kb) Multiome | 836 | |
| chr12:123,388,500–123,389,409 | 116.5 kb | Distal (>10kb) Multiome | 446 | |
| chr12:123,436,072–123,436,895 | 164.3 kb | Distal (>10kb) Multiome | 742 | |
| chr12:123,458,045–123,458,697 | 186.1 kb | Distal (>10kb) Multiome | 925 | |
| chr12:123,533,444–123,534,540 | 261.7 kb | Distal (>10kb) Multiome | 718 |
Genomic view of the CDK2AP1 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.