This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin loop and a C-terminal basic domain. This gene is expressed by the endothelial cells where it was found to act in an autocrine fashion to induce apoptosis, inhibit cell proliferation and survival, and function as an anti-tumorigenic agent. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
Transcription factors with Perturb-seq knockdown data for SEMA3F. 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 = SEMA3F 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 SEMA3F, 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 |
|---|---|---|---|---|
| chr3:49,856,099–49,857,163 | 298.4 kb | Distal (>10kb) Multiome | 664 | |
| chr3:49,869,590–49,870,249 | 285.1 kb | Distal (>10kb) Multiome | 251 | |
| chr3:49,903,411–49,904,277 | 251.1 kb | Distal (>10kb) Multiome | 415 | |
| chr3:49,929,290–49,930,212 | 225.3 kb | Distal (>10kb) Multiome | 799 | |
| chr3:49,939,635–49,940,747 | 215.0 kb | Distal (>10kb) Multiome | 949 | |
| chr3:50,088,748–50,089,596 | 66.1 kb | Distal (>10kb) Multiome | 677 | |
| chr3:50,121,279–50,122,037 | 33.3 kb | Distal (>10kb) Multiome HiCAR | 364 | |
| chr3:50,138,509–50,140,035 | 15.7 kb | Distal (>10kb) Multiome HiCAR | 198 | |
| chr3:50,154,437–50,155,741 | 28 bp | At TSS Multiome | 450 | |
| chr3:50,155,742–50,156,220 | 698 bp | At TSS | 164 | |
| chr3:50,157,218–50,157,451 | 2.2 kb | Proximal (<10kb) | 112 | |
| chr3:50,160,572–50,161,312 | 5.5 kb | Proximal (<10kb) | 121 | |
| chr3:50,204,913–50,205,545 | 50.2 kb | Distal (>10kb) Multiome | 367 | |
| chr3:50,205,645–50,206,357 | 51.2 kb | Distal (>10kb) Multiome | 347 | |
| chr3:50,226,120–50,228,328 | 71.2 kb | Distal (>10kb) Multiome | 915 | |
| chr3:50,235,551–50,236,824 | 81.0 kb | Distal (>10kb) Multiome | 632 | |
| chr3:50,240,985–50,241,805 | 86.2 kb | Distal (>10kb) Multiome | 137 | |
| chr3:50,245,721–50,247,161 | 91.3 kb | Distal (>10kb) Multiome | 671 | |
| chr3:50,259,568–50,260,922 | 105.2 kb | Distal (>10kb) Multiome HiCAR | 869 | |
| chr3:50,264,309–50,265,446 | 109.8 kb | Distal (>10kb) Multiome HiCAR | 568 | |
| chr3:50,275,163–50,276,639 | 121.4 kb | Distal (>10kb) Multiome | 151 | |
| chr3:50,291,628–50,292,796 | 137.5 kb | Distal (>10kb) Multiome | 855 | |
| chr3:50,298,495–50,300,110 | 144.5 kb | Distal (>10kb) Multiome | 872 | |
| chr3:50,303,363–50,303,840 | 148.6 kb | Distal (>10kb) Multiome | 484 | |
| chr3:50,320,603–50,322,739 | 166.5 kb | Distal (>10kb) Multiome | 816 | |
| chr3:50,324,456–50,325,020 | 169.7 kb | Distal (>10kb) Multiome | 392 | |
| chr3:50,327,933–50,328,581 | 173.2 kb | Distal (>10kb) Multiome | 697 | |
| chr3:50,336,856–50,338,227 | 182.5 kb | Distal (>10kb) Multiome | 952 | |
| chr3:50,340,624–50,341,322 | 185.9 kb | Distal (>10kb) Multiome | 345 | |
| chr3:50,345,443–50,346,042 | 190.7 kb | Distal (>10kb) Multiome | 209 | |
| chr3:50,350,496–50,351,298 | 195.9 kb | Distal (>10kb) Multiome | 902 | |
| chr3:50,358,889–50,360,012 | 204.6 kb | Distal (>10kb) Multiome | 796 | |
| chr3:50,364,552–50,365,867 | 210.2 kb | Distal (>10kb) Multiome | 331 | |
| chr3:50,435,932–50,436,533 | 281.2 kb | Distal (>10kb) Multiome | 248 |
Genomic view of the SEMA3F 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.