Semaphorins are a large family of conserved secreted and membrane associated proteins which possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Based on sequence and structural similarities, semaphorins are put into eight classes: invertebrates contain classes 1 and 2, viruses have class V, and vertebrates contain classes 3-7. Semaphorins serve as axon guidance ligands via multimeric receptor complexes, some (if not all) containing plexin proteins. This gene encodes a class 4 semaphorin. This gene encodes a class 3 semaphorin. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]
Transcription factors with Perturb-seq knockdown data for SEMA3E. 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 = SEMA3E 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 SEMA3E, 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 |
|---|---|---|---|---|
| chr7:83,459,268–83,460,284 | 189.3 kb | Distal (>10kb) Multiome | 175 | |
| chr7:83,640,990–83,641,688 | at TSS | At TSS | 119 | |
| chr7:83,644,950–83,645,242 | 3.5 kb | Proximal (<10kb) | 18 | |
| chr7:83,648,424–83,649,394 | 38 bp | At TSS Multiome | 416 | |
| chr7:83,649,690–83,649,977 | 8.3 kb | Proximal (<10kb) | 41 | |
| chr7:83,652,908–83,653,242 | 3.8 kb | Proximal (<10kb) | 13 | |
| chr7:83,656,062–83,656,228 | 6.9 kb | Proximal (<10kb) | 68 | |
| chr7:83,666,258–83,667,242 | 17.6 kb | Distal (>10kb) Multiome | 80 | |
| chr7:83,684,857–83,685,509 | 36.0 kb | Distal (>10kb) Multiome | 278 |
Genomic view of the SEMA3E 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.