The protein encoded by this gene recognizes the sequence CCTTGAG along with other members of the HMG-box class DNA-binding proteins. It acts during chondrocyte differentiation and, with steroidogenic factor 1, regulates transcription of the anti-Muellerian hormone (AMH) gene. Deficiencies lead to the skeletal malformation syndrome campomelic dysplasia, frequently with sex reversal. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for SOX9. 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 = SOX9 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 SOX9, 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 |
|---|---|---|---|---|
| chr17:71,828,085–71,828,747 | 292.6 kb | Distal (>10kb) Multiome | 271 | |
| chr17:72,029,625–72,030,981 | 90.5 kb | Distal (>10kb) Multiome | 532 | |
| chr17:72,115,645–72,116,949 | 4.1 kb | Proximal (<10kb) | 205 | |
| chr17:72,117,747–72,118,875 | 2.1 kb | Proximal (<10kb) | 345 | |
| chr17:72,119,715–72,122,319 | 137 bp | At TSS Multiome | 897 | |
| chr17:72,122,581–72,123,172 | 1.6 kb | Proximal (<10kb) | 397 | |
| chr17:72,123,273–72,124,425 | 2.3 kb | Proximal (<10kb) | 510 | |
| chr17:72,150,786–72,151,388 | 30.2 kb | Distal (>10kb) Multiome | 204 |
Genomic view of the SOX9 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.