This intronless gene encodes a member of the SRY-related HMG-box (SOX) family of transcription factors involved in the regulation of embryonic development and in the determination of cell fate. The product of this gene is required for stem-cell maintenance in the central nervous system, and also regulates gene expression in the stomach. Mutations in this gene have been associated with optic nerve hypoplasia and with syndromic microphthalmia, a severe form of structural eye malformation. This gene lies within an intron of another gene called SOX2 overlapping transcript (SOX2OT). [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for SOX2. 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 = SOX2 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 SOX2, 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 |
|---|---|---|---|---|
| chr3:181,694,870–181,696,497 | 16.4 kb | Distal (>10kb) Multiome | 327 | |
| chr3:181,700,134–181,701,495 | 11.2 kb | Distal (>10kb) Multiome | 431 | |
| chr3:181,701,594–181,702,555 | 9.4 kb | Proximal (<10kb) | 283 | |
| chr3:181,704,516–181,705,421 | 7.0 kb | Proximal (<10kb) Multiome | 135 | |
| chr3:181,707,992–181,708,401 | 3.5 kb | Proximal (<10kb) | 140 | |
| chr3:181,709,626–181,710,028 | 1.9 kb | Proximal (<10kb) | 249 | |
| chr3:181,710,172–181,713,363 | 171 bp | At TSS Multiome | 617 | |
| chr3:181,715,499–181,716,222 | 3.6 kb | Proximal (<10kb) | 231 | |
| chr3:181,719,364–181,719,952 | 7.4 kb | Proximal (<10kb) | 89 | |
| chr3:181,725,481–181,728,258 | 14.9 kb | Distal (>10kb) Multiome | 336 | |
| chr3:181,756,093–181,757,255 | 44.9 kb | Distal (>10kb) Multiome | 218 | |
| chr3:181,858,761–181,860,940 | 148.5 kb | Distal (>10kb) Multiome HiCAR | 302 | |
| chr3:181,943,123–181,943,852 | 231.5 kb | Distal (>10kb) Multiome | 135 | |
| chr3:182,139,755–182,140,412 | 428.2 kb | Distal (>10kb) Multiome HiCAR | 141 | |
| chr3:182,180,388–182,181,238 | 468.9 kb | Distal (>10kb) Multiome HiCAR | 222 | |
| chr3:182,284,560–182,285,367 | 573.0 kb | Distal (>10kb) Multiome HiCAR | 259 | |
| chr3:182,682,115–182,683,252 | 970.6 kb | Distal (>10kb) Multiome HiCAR | 512 |
Genomic view of the SOX2 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.