Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]
Transcription factors with Perturb-seq knockdown data for SEMA6D. 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 = SEMA6D 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 SEMA6D, 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 |
|---|---|---|---|---|
| chr15:45,704,015–45,705,263 | 1479.6 kb | Distal (>10kb) Multiome HiCAR | 178 | |
| chr15:47,183,926–47,185,405 | 323 bp | At TSS Multiome | 352 | |
| chr15:47,189,160–47,189,664 | 5.1 kb | Proximal (<10kb) | 91 | |
| chr15:47,332,292–47,333,157 | 148.6 kb | Distal (>10kb) Multiome | 161 | |
| chr15:47,716,988–47,718,949 | 533.2 kb | Distal (>10kb) Multiome | 447 | |
| chr15:47,726,475–47,726,953 | 9.1 kb | Proximal (<10kb) | 35 | |
| chr15:47,727,319–47,727,589 | 9.9 kb | Proximal (<10kb) | 24 | |
| chr15:47,735,693–47,736,927 | 552.2 kb | Distal (>10kb) Multiome | 176 | |
| chr15:47,777,992–47,778,863 | 594.3 kb | Distal (>10kb) Multiome | 100 | |
| chr15:47,884,598–47,885,796 | 701.1 kb | Distal (>10kb) Multiome | 168 | |
| chr15:47,932,981–47,934,021 | 749.4 kb | Distal (>10kb) Multiome | 155 | |
| chr15:48,330,845–48,332,487 | 1147.2 kb | Distal (>10kb) Multiome HiCAR | 865 |
Genomic view of the SEMA6D 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.