The protein encoded by this gene is an atypical member of the family of growth factor receptor protein tyrosine kinases, differing from other members at a number of conserved residues in the activation and nucleotide binding domains. This gene product belongs to a subfamily whose members do not appear to be regulated by phosphorylation in the activation segment. It has been suggested that mediation of biological activity by recruitment of a signaling-competent auxiliary protein may occur through an as yet uncharacterized mechanism. The encoded protein has a leucine-rich extracellular domain with a WIF-type Wnt binding region, a single transmembrane domain, and an intracellular tyrosine kinase domain. This protein is involved in stimulating Wnt signaling pathways such as the regulation of axon pathfinding. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2012]
Transcription factors with Perturb-seq knockdown data for RYK. 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 = RYK 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 RYK, 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 |
|---|---|---|---|---|
| chr3:133,988,622–133,989,245 | 261.9 kb | Distal (>10kb) Multiome | 246 | |
| chr3:134,028,965–134,030,691 | 220.8 kb | Distal (>10kb) Multiome | 495 | |
| chr3:134,243,196–134,243,591 | 7.3 kb | Proximal (<10kb) | 43 | |
| chr3:134,250,095–134,251,199 | 27 bp | At TSS Multiome | 719 | |
| chr3:134,251,903–134,252,461 | 1.0 kb | Proximal (<10kb) | 214 | |
| chr3:134,308,427–134,308,921 | 57.8 kb | Distal (>10kb) Multiome | 478 | |
| chr3:134,312,827–134,313,997 | 62.6 kb | Distal (>10kb) Multiome | 368 | |
| chr3:134,333,562–134,334,597 | 83.0 kb | Distal (>10kb) Multiome | 224 | |
| chr3:134,363,600–134,365,141 | 113.4 kb | Distal (>10kb) Multiome | 492 | |
| chr3:134,372,925–134,375,830 | 123.8 kb | Distal (>10kb) Multiome | 1010 | |
| chr3:134,406,305–134,407,815 | 156.0 kb | Distal (>10kb) Multiome | 295 | |
| chr3:134,485,113–134,486,743 | 235.2 kb | Distal (>10kb) Multiome | 1009 |
Genomic view of the RYK 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.