This gene belongs to the ephrin receptor subfamily of the protein-tyrosine kinase family. EPH and EPH-related receptors have been implicated in mediating developmental events, particularly in the nervous system. Receptors in the EPH subfamily typically have a single kinase domain and an extracellular region containing a Cys-rich domain and 2 fibronectin type III repeats. The ephrin receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. This gene encodes a protein that binds ephrin-A ligands. Two alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for EPHA3. 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 = EPHA3 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 EPHA3, 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 |
|---|---|---|---|---|
| chr3:88,912,027–88,913,357 | 195.0 kb | Distal (>10kb) Multiome | 204 | |
| chr3:89,098,804–89,099,278 | 8.3 kb | Proximal (<10kb) | 141 | |
| chr3:89,107,260–89,107,984 | 63 bp | At TSS Multiome | 460 | |
| chr3:89,113,978–89,115,168 | 7.1 kb | Proximal (<10kb) Multiome | 475 | |
| chr3:89,117,432–89,117,900 | 9.8 kb | Proximal (<10kb) | 43 | |
| chr3:89,371,250–89,371,812 | 263.9 kb | Distal (>10kb) Multiome | 57 | |
| chr3:90,082,956–90,084,705 | 975.7 kb | Distal (>10kb) Multiome HiCAR | 83 | |
| chr3:90,085,223–90,086,763 | 978.8 kb | Distal (>10kb) Multiome HiCAR | 213 |
Genomic view of the EPHA3 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.