Ephrin receptors and their ligands, the ephrins, mediate numerous developmental processes, particularly in the nervous system. Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. The Eph family of receptors are divided into two groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. Ephrin receptors make up the largest subgroup of the receptor tyrosine kinase (RTK) family. This gene encodes a receptor for ephrin-B family members. [provided by RefSeq, Mar 2010]
Transcription factors with Perturb-seq knockdown data for EPHB3. 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 = EPHB3 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 EPHB3, 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 |
|---|---|---|---|---|
| chr3:184,260,815–184,262,571 | 300.1 kb | Distal (>10kb) Multiome | 511 | |
| chr3:184,298,591–184,299,718 | 262.7 kb | Distal (>10kb) Multiome | 768 | |
| chr3:184,314,169–184,315,514 | 247.2 kb | Distal (>10kb) Multiome | 761 | |
| chr3:184,335,265–184,337,276 | 225.8 kb | Distal (>10kb) Multiome | 796 | |
| chr3:184,361,172–184,363,709 | 198.6 kb | Distal (>10kb) Multiome | 1034 | |
| chr3:184,379,849–184,380,935 | 181.6 kb | Distal (>10kb) Multiome | 242 | |
| chr3:184,513,458–184,514,228 | 47.9 kb | Distal (>10kb) Multiome | 391 | |
| chr3:184,525,317–184,526,423 | 35.7 kb | Distal (>10kb) Multiome | 281 | |
| chr3:184,558,752–184,559,234 | 2.9 kb | Proximal (<10kb) Multiome | 58 | |
| chr3:184,561,059–184,562,613 | 182 bp | At TSS Multiome | 671 | |
| chr3:184,563,867–184,564,294 | 2.1 kb | Proximal (<10kb) | 49 | |
| chr3:184,568,694–184,569,481 | 6.9 kb | Proximal (<10kb) | 342 | |
| chr3:184,570,404–184,570,842 | 8.6 kb | Proximal (<10kb) | 83 | |
| chr3:184,583,141–184,585,336 | 23.0 kb | Distal (>10kb) Multiome | 270 | |
| chr3:184,601,537–184,603,254 | 40.5 kb | Distal (>10kb) Multiome | 179 | |
| chr3:184,603,592–184,605,089 | 42.8 kb | Distal (>10kb) Multiome | 321 | |
| chr3:184,629,636–184,630,157 | 68.1 kb | Distal (>10kb) Multiome | 71 | |
| chr3:184,642,851–184,643,762 | 81.4 kb | Distal (>10kb) Multiome | 135 | |
| chr3:184,645,190–184,645,870 | 83.8 kb | Distal (>10kb) Multiome | 234 | |
| chr3:184,711,525–184,712,457 | 150.3 kb | Distal (>10kb) Multiome HiCAR | 896 | |
| chr3:184,750,804–184,752,976 | 190.8 kb | Distal (>10kb) Multiome HiCAR | 252 | |
| chr3:184,777,796–184,778,258 | 216.2 kb | Distal (>10kb) Multiome HiCAR | 220 | |
| chr3:184,795,215–184,795,741 | 233.7 kb | Distal (>10kb) Multiome HiCAR | 80 | |
| chr3:184,796,565–184,797,275 | 235.1 kb | Distal (>10kb) Multiome HiCAR | 149 | |
| chr3:184,811,949–184,812,608 | 250.4 kb | Distal (>10kb) Multiome HiCAR | 663 |
Genomic view of the EPHB3 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.