In all eukaryotes, the cell cycle is governed by cyclin-dependent protein kinases (CDKs), whose activities are regulated by cyclins and CDK inhibitors in a diverse array of mechanisms that involve the control of phosphorylation and dephosphorylation of Ser, Thr or Tyr residues. Cyclins are molecules that possess a consensus domain called the 'cyclin box.' In mammalian cells, 9 cyclin species have been identified, and they are referred to as cyclins A through I. Cyclin G is a direct transcriptional target of the p53 tumor suppressor gene product and thus functions downstream of p53. GAK is an association partner of cyclin G and CDK5. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Transcription factors with Perturb-seq knockdown data for GAK. 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 = GAK 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 GAK, 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 |
|---|---|---|---|---|
| chr4:663,207–664,324 | 268.6 kb | Distal (>10kb) Multiome | 298 | |
| chr4:673,501–675,336 | 258.0 kb | Distal (>10kb) Multiome | 920 | |
| chr4:680,919–681,550 | 251.0 kb | Distal (>10kb) Multiome | 275 | |
| chr4:688,280–689,636 | 243.1 kb | Distal (>10kb) Multiome | 218 | |
| chr4:705,313–706,398 | 226.7 kb | Distal (>10kb) Multiome | 613 | |
| chr4:781,187–782,732 | 150.4 kb | Distal (>10kb) Multiome | 893 | |
| chr4:825,232–826,278 | 106.6 kb | Distal (>10kb) Multiome | 317 | |
| chr4:826,462–827,691 | 105.4 kb | Distal (>10kb) Multiome | 180 | |
| chr4:931,599–932,710 | 5 bp | At TSS Multiome | 818 | |
| chr4:945,351–946,054 | 13.2 kb | Distal (>10kb) Multiome | 73 | |
| chr4:972,792–974,408 | 41.2 kb | Distal (>10kb) Multiome | 437 | |
| chr4:986,645–987,589 | 54.8 kb | Distal (>10kb) Multiome | 723 | |
| chr4:1,002,360–1,003,561 | 70.8 kb | Distal (>10kb) Multiome | 176 | |
| chr4:1,008,768–1,012,870 | 79.1 kb | Distal (>10kb) Multiome | 793 | |
| chr4:1,113,486–1,113,937 | 181.3 kb | Distal (>10kb) Multiome | 183 | |
| chr4:1,167,206–1,167,987 | 235.2 kb | Distal (>10kb) Multiome | 553 |
Genomic view of the GAK 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.