This gene encodes a member of the semaphorin family of soluble and transmembrane proteins. Semaphorins are involved in numerous functions, including axon guidance, morphogenesis, carcinogenesis, and immunomodulation. The encoded protein is a single-pass type I membrane protein containing an immunoglobulin-like C2-type domain, a PSI domain and a sema domain. It inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. It is an activator of T-cell-mediated immunity and suppresses vascular endothelial growth factor (VEGF)-mediated endothelial cell migration and proliferation in vitro and angiogenesis in vivo. Mutations in this gene are associated with retinal degenerative diseases including retinitis pigmentosa type 35 (RP35) and cone-rod dystrophy type 10 (CORD10). Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
Transcription factors with Perturb-seq knockdown data for SEMA4A. 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 = SEMA4A 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 SEMA4A, 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 |
|---|---|---|---|---|
| chr1:155,856,932–155,857,529 | 292.9 kb | Distal (>10kb) Multiome | 639 | |
| chr1:155,859,095–155,860,745 | 289.6 kb | Distal (>10kb) Multiome | 632 | |
| chr1:155,910,686–155,911,579 | 238.8 kb | Distal (>10kb) Multiome | 691 | |
| chr1:155,934,107–155,934,787 | 215.7 kb | Distal (>10kb) Multiome | 872 | |
| chr1:155,977,296–155,979,264 | 171.5 kb | Distal (>10kb) Multiome | 698 | |
| chr1:156,020,469–156,021,128 | 129.3 kb | Distal (>10kb) Multiome | 558 | |
| chr1:156,052,923–156,055,358 | 95.3 kb | Distal (>10kb) Multiome | 1053 | |
| chr1:156,060,806–156,061,738 | 88.9 kb | Distal (>10kb) Multiome | 318 | |
| chr1:156,076,488–156,077,355 | 73.2 kb | Distal (>10kb) Multiome | 246 | |
| chr1:156,081,942–156,083,586 | 67.6 kb | Distal (>10kb) Multiome | 670 | |
| chr1:156,105,879–156,107,316 | 43.6 kb | Distal (>10kb) Multiome | 663 | |
| chr1:156,114,184–156,115,669 | 35.6 kb | Distal (>10kb) Multiome | 824 | |
| chr1:156,123,520–156,124,091 | 26.4 kb | Distal (>10kb) Multiome | 679 | |
| chr1:156,129,945–156,130,610 | 19.8 kb | Distal (>10kb) Multiome | 733 | |
| chr1:156,141,261–156,141,644 | 8.6 kb | Proximal (<10kb) | 322 | |
| chr1:156,146,058–156,146,760 | 3.4 kb | Proximal (<10kb) | 429 | |
| chr1:156,149,593–156,150,242 | 197 bp | At TSS Multiome | 194 | |
| chr1:156,160,602–156,161,218 | 10.9 kb | Distal (>10kb) Multiome | 218 | |
| chr1:156,161,342–156,161,661 | 116 bp | At TSS | 243 | |
| chr1:156,181,487–156,182,119 | 31.7 kb | Distal (>10kb) Multiome | 145 | |
| chr1:156,193,531–156,194,375 | 43.7 kb | Distal (>10kb) Multiome | 751 | |
| chr1:156,212,611–156,213,686 | 62.9 kb | Distal (>10kb) Multiome HiCAR | 893 | |
| chr1:156,245,413–156,246,269 | 95.6 kb | Distal (>10kb) Multiome | 380 | |
| chr1:156,282,165–156,283,323 | 132.6 kb | Distal (>10kb) Multiome | 973 | |
| chr1:156,291,233–156,291,857 | 141.3 kb | Distal (>10kb) Multiome | 518 | |
| chr1:156,337,825–156,339,056 | 188.3 kb | Distal (>10kb) Multiome | 836 | |
| chr1:156,356,873–156,357,393 | 206.9 kb | Distal (>10kb) Multiome | 506 | |
| chr1:156,368,893–156,369,552 | 219.0 kb | Distal (>10kb) Multiome | 529 | |
| chr1:156,420,712–156,422,291 | 271.6 kb | Distal (>10kb) Multiome | 569 | |
| chr1:156,456,348–156,457,982 | 306.5 kb | Distal (>10kb) Multiome | 1033 |
Genomic view of the SEMA4A 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.