This gene encodes a member of the vaccinia-related kinase (VRK) family of serine/threonine protein kinases. In both human and mouse, this gene has substitutions at several residues within the ATP binding motifs that in other kinases have been shown to be required for catalysis. In vitro assays indicate the protein lacks phosphorylation activity. The protein, however, likely retains its substrate binding capability. This gene is widely expressed in human tissues and its protein localizes to the nucleus. Alternative splicing results in multiple transcripts encoding different isoforms. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for VRK3. 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 = VRK3 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 VRK3, 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 |
|---|---|---|---|---|
| chr19:49,746,188–49,746,748 | 278.9 kb | Distal (>10kb) Multiome | 283 | |
| chr19:49,766,231–49,767,440 | 258.7 kb | Distal (>10kb) Multiome | 718 | |
| chr19:49,802,146–49,802,787 | 222.9 kb | Distal (>10kb) Multiome | 200 | |
| chr19:49,805,226–49,805,871 | 219.8 kb | Distal (>10kb) Multiome | 245 | |
| chr19:49,808,201–49,809,746 | 216.5 kb | Distal (>10kb) Multiome | 509 | |
| chr19:49,812,926–49,813,834 | 211.9 kb | Distal (>10kb) Multiome | 650 | |
| chr19:49,817,356–49,818,721 | 207.2 kb | Distal (>10kb) Multiome | 784 | |
| chr19:49,850,394–49,852,067 | 174.5 kb | Distal (>10kb) Multiome | 862 | |
| chr19:49,866,817–49,868,124 | 158.0 kb | Distal (>10kb) Multiome | 874 | |
| chr19:49,869,068–49,870,398 | 155.8 kb | Distal (>10kb) Multiome | 832 | |
| chr19:49,875,842–49,878,576 | 147.7 kb | Distal (>10kb) Multiome | 1153 | |
| chr19:49,889,853–49,891,381 | 134.9 kb | Distal (>10kb) Multiome | 640 | |
| chr19:49,928,884–49,930,473 | 95.5 kb | Distal (>10kb) Multiome | 1141 | |
| chr19:49,987,157–49,987,669 | 38.1 kb | Distal (>10kb) Multiome | 1095 | |
| chr19:50,024,875–50,026,285 | 274 bp | At TSS Multiome | 1137 | |
| chr19:50,147,523–50,148,432 | 122.7 kb | Distal (>10kb) Multiome | 615 | |
| chr19:50,203,034–50,204,072 | 178.1 kb | Distal (>10kb) Multiome | 363 | |
| chr19:50,205,195–50,205,903 | 180.0 kb | Distal (>10kb) Multiome | 364 | |
| chr19:50,311,942–50,312,908 | 286.9 kb | Distal (>10kb) Multiome | 364 | |
| chr19:50,313,900–50,314,529 | 288.8 kb | Distal (>10kb) Multiome | 114 | |
| chr19:50,315,313–50,316,408 | 290.6 kb | Distal (>10kb) Multiome | 363 | |
| chr19:50,325,322–50,326,594 | 300.4 kb | Distal (>10kb) Multiome | 748 |
Genomic view of the VRK3 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.