This gene encodes a member of the D subfamily of sex determining region y-related transcription factors that are characterized by a conserved DNA-binding domain termed the high mobility group box and by their ability to bind the minor groove of DNA. The encoded protein is a transcriptional activator that is required for normal development of the central nervous system, chondrogenesis and maintenance of cardiac and skeletal muscle cells. The encoded protein interacts with other family members to cooperatively activate gene expression. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]
Transcription factors with Perturb-seq knockdown data for SOX6. 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 = SOX6 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 SOX6, 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 |
|---|---|---|---|---|
| chr11:15,327,601–15,328,237 | 1278.0 kb | Distal (>10kb) Multiome HiCAR | 136 | |
| chr11:15,622,013–15,623,710 | 983.4 kb | Distal (>10kb) Multiome HiCAR | 210 | |
| chr11:15,649,647–15,651,014 | 955.8 kb | Distal (>10kb) Multiome HiCAR | 787 | |
| chr11:15,695,035–15,695,841 | 910.6 kb | Distal (>10kb) Multiome HiCAR | 201 | |
| chr11:16,603,261–16,603,722 | 2.3 kb | Proximal (<10kb) | 56 | |
| chr11:16,603,833–16,608,197 | 1.1 kb | Proximal (<10kb) Multiome | 849 | |
| chr11:16,610,280–16,611,185 | 4.3 kb | Proximal (<10kb) | 141 | |
| chr11:16,611,809–16,612,213 | 5.8 kb | Proximal (<10kb) | 55 | |
| chr11:16,613,116–16,614,766 | 8.0 kb | Proximal (<10kb) Multiome | 562 | |
| chr11:16,737,938–16,739,159 | 132.6 kb | Distal (>10kb) Multiome | 894 | |
| chr11:16,824,772–16,825,501 | 219.2 kb | Distal (>10kb) Multiome | 111 | |
| chr11:16,883,061–16,883,703 | 277.4 kb | Distal (>10kb) Multiome | 186 | |
| chr11:16,956,235–16,957,153 | 350.8 kb | Distal (>10kb) Multiome | 281 | |
| chr11:16,959,532–16,960,122 | 353.9 kb | Distal (>10kb) Multiome | 154 | |
| chr11:17,013,111–17,015,356 | 407.5 kb | Distal (>10kb) Multiome | 708 |
Genomic view of the SOX6 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.