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. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2015]
Transcription factors with Perturb-seq knockdown data for EPHA4. 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 = EPHA4 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 EPHA4, 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 |
|---|---|---|---|---|
| chr2:219,642,343–219,643,046 | 1929.6 kb | Distal (>10kb) Multiome HiCAR | 686 | |
| chr2:219,916,235–219,917,518 | 1655.3 kb | Distal (>10kb) Multiome HiCAR | 79 | |
| chr2:221,388,384–221,389,191 | 183.5 kb | Distal (>10kb) Multiome | 51 | |
| chr2:221,478,281–221,479,565 | 93.5 kb | Distal (>10kb) Multiome | 273 | |
| chr2:221,495,289–221,496,920 | 76.2 kb | Distal (>10kb) Multiome | 112 | |
| chr2:221,569,397–221,570,767 | 1.5 kb | Proximal (<10kb) | 188 | |
| chr2:221,571,229–221,574,291 | 60 bp | At TSS Multiome | 755 | |
| chr2:221,576,514–221,576,980 | 4.2 kb | Proximal (<10kb) | 103 | |
| chr2:221,792,838–221,793,893 | 221.0 kb | Distal (>10kb) Multiome | 163 | |
| chr2:221,931,292–221,931,996 | 359.2 kb | Distal (>10kb) Multiome HiCAR | 67 |
Genomic view of the EPHA4 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.