EFNB3
ephrin B3 | LERK-8, EPLG8

EFNB3, a member of the ephrin gene family, is important in brain development as well as in its maintenance. Moreover, since levels of EFNB3 expression were particularly high in several forebrain subregions compared to other brain subregions, it may play a pivotal role in forebrain function. The EPH and EPH-related receptors comprise the largest subfamily of receptor protein-tyrosine kinases and have been implicated in mediating developmental events, particularly in the nervous system. EPH Receptors typically have a single kinase domain and an extracellular region containing a Cys-rich domain and 2 fibronectin type III repeats. The ephrin ligands and receptors have been named by the Eph Nomenclature Committee (1997). 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 similarly divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. [provided by RefSeq, Jul 2008]

Biological processes 25 terms
Expression (TPM)
EFNB3 — as a Regulated Gene

TFs regulating EFNB3 0 TFs

Transcription factors with Perturb-seq knockdown data for EFNB3. 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 = EFNB3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to EFNB3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of EFNB3, 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
chr17:7,435,167–7,437,681 268.1 kb Distal (>10kb) Multiome 828
chr17:7,437,892–7,438,555 266.9 kb Distal (>10kb) Multiome 224
chr17:7,440,048–7,441,211 264.5 kb Distal (>10kb) Multiome 487
chr17:7,444,968–7,446,142 259.6 kb Distal (>10kb) Multiome 632
chr17:7,455,450–7,456,019 249.5 kb Distal (>10kb) Multiome 414
chr17:7,478,839–7,480,126 225.7 kb Distal (>10kb) Multiome 574
chr17:7,483,139–7,485,576 220.7 kb Distal (>10kb) Multiome 1156
chr17:7,548,693–7,549,285 156.2 kb Distal (>10kb) Multiome 387
chr17:7,560,249–7,562,536 143.3 kb Distal (>10kb) Multiome 759
chr17:7,572,039–7,574,418 131.3 kb Distal (>10kb) Multiome 1071
chr17:7,579,018–7,579,876 125.7 kb Distal (>10kb) Multiome 844
chr17:7,583,063–7,584,547 121.4 kb Distal (>10kb) Multiome 921
chr17:7,588,871–7,590,534 115.0 kb Distal (>10kb) Multiome 319
chr17:7,614,065–7,615,780 90.1 kb Distal (>10kb) Multiome 708
chr17:7,627,090–7,628,247 77.4 kb Distal (>10kb) Multiome 712
chr17:7,650,010–7,652,127 54.4 kb Distal (>10kb) Multiome 467
chr17:7,685,876–7,686,907 18.9 kb Distal (>10kb) Multiome 765
chr17:7,687,214–7,687,777 17.7 kb Distal (>10kb) Multiome 710
chr17:7,687,867–7,688,863 16.9 kb Distal (>10kb) Multiome 700
chr17:7,703,383–7,703,975 1.5 kb Proximal (<10kb) Multiome 141
chr17:7,704,799–7,705,590 67 bp At TSS Multiome 325
chr17:7,716,832–7,717,983 12.2 kb Distal (>10kb) Multiome 759
chr17:7,833,417–7,837,960 130.4 kb Distal (>10kb) Multiome 1160
chr17:7,841,438–7,843,228 137.0 kb Distal (>10kb) Multiome 861
chr17:7,843,355–7,844,130 138.4 kb Distal (>10kb) Multiome 614
chr17:7,844,349–7,845,186 139.7 kb Distal (>10kb) Multiome 617
chr17:7,851,538–7,852,239 146.7 kb Distal (>10kb) Multiome 531
chr17:7,856,600–7,858,747 152.3 kb Distal (>10kb) Multiome 942
chr17:7,885,205–7,885,734 180.1 kb Distal (>10kb) Multiome 371
chr17:7,887,616–7,888,198 182.6 kb Distal (>10kb) Multiome 581
chr17:7,915,430–7,916,499 210.7 kb Distal (>10kb) Multiome 869
chr17:7,922,863–7,923,421 217.8 kb Distal (>10kb) Multiome 205
chr17:7,929,559–7,930,172 224.6 kb Distal (>10kb) Multiome 106
chr17:7,931,533–7,932,876 226.9 kb Distal (>10kb) Multiome 767
chr17:7,971,685–7,972,375 266.7 kb Distal (>10kb) Multiome 45
chr17:7,989,908–7,990,676 285.1 kb Distal (>10kb) Multiome 652

Genome Browser

Genomic view of the EFNB3 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.

chr17:7,425,167 – 8,000,676
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq