Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family, and is highly expressed in nociceptive neurons of dorsal root ganglia and trigeminal ganglia. It mediates brain-derived neurotrophic factor-evoked membrane depolarization and is a major effector of peripheral inflammatory pain hypersensitivity. Mutations in this gene have been associated with hereditary sensory and autonomic neuropathy type VII and familial episodic pain syndrome-3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2017]
Transcription factors with Perturb-seq knockdown data for SCN11A. 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 = SCN11A 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 SCN11A, 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 |
|---|---|---|---|---|
| chr3:39,051,625–39,052,625 | 138 bp | At TSS Multiome | 881 | |
| chr3:39,106,596–39,108,201 | 55.7 kb | Distal (>10kb) Multiome | 754 | |
| chr3:39,150,367–39,155,021 | 99.1 kb | Distal (>10kb) Multiome | 1014 | |
| chr3:39,177,458–39,178,406 | 126.0 kb | Distal (>10kb) Multiome | 531 | |
| chr3:39,180,469–39,181,324 | 129.0 kb | Distal (>10kb) Multiome | 541 | |
| chr3:39,288,216–39,288,885 | 236.6 kb | Distal (>10kb) Multiome | 463 |
Genomic view of the SCN11A 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.