This gene encodes paired box protein Pax-6, one of many human homologs of the Drosophila melanogaster gene prd. In addition to a conserved paired box domain, a hallmark feature of this gene family, the encoded protein also contains a homeobox domain. Both domains are known to bind DNA and function as regulators of gene transcription. Activity of this protein is key in the development of neural tissues, particularly the eye. This gene is regulated by multiple enhancers located up to hundreds of kilobases distant from this locus. Mutations in this gene or in the enhancer regions can cause ocular disorders such as aniridia and Peter's anomaly. Use of alternate promoters and alternative splicing results in multiple transcript variants encoding different isoforms. Interestingly, inclusion of a particular alternate coding exon has been shown to increase the length of the paired box domain and alter its DNA binding specificity. Consequently, isoforms that carry the shorter paired box domain regulate a different set of genes compared to the isoforms carrying the longer paired box domain. [provided by RefSeq, Mar 2019]
Transcription factors with Perturb-seq knockdown data for PAX6. 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 = PAX6 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 PAX6, 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 |
|---|---|---|---|---|
| chr11:31,797,814–31,799,520 | 5.9 kb | Proximal (<10kb) | 221 | |
| chr11:31,799,658–31,800,256 | 5.2 kb | Proximal (<10kb) | 54 | |
| chr11:31,802,527–31,803,248 | 2.2 kb | Proximal (<10kb) | 61 | |
| chr11:31,803,398–31,803,696 | 1.8 kb | Proximal (<10kb) | 41 | |
| chr11:31,804,516–31,806,498 | at TSS | At TSS | 220 | |
| chr11:31,807,374–31,808,054 | 1.9 kb | Proximal (<10kb) | 35 | |
| chr11:31,809,858–31,815,212 | 4.4 kb | Proximal (<10kb) | 719 | |
| chr11:31,815,345–31,815,712 | 9.9 kb | Proximal (<10kb) | 78 | |
| chr11:31,815,841–31,816,162 | 8.2 kb | Proximal (<10kb) | 176 | |
| chr11:31,816,322–31,818,635 | 8.7 kb | Proximal (<10kb) | 399 | |
| chr11:31,818,793–31,819,408 | 7.5 kb | Proximal (<10kb) | 43 | |
| chr11:31,819,537–31,820,941 | 8.2 kb | Proximal (<10kb) | 197 | |
| chr11:31,822,793–31,823,338 | 7.8 kb | Proximal (<10kb) | 55 | |
| chr11:31,823,464–31,824,163 | 8.5 kb | Proximal (<10kb) | 97 | |
| chr11:31,824,867–31,825,385 | 9.9 kb | Proximal (<10kb) | 49 | |
| chr11:31,825,773–31,826,408 | 7.8 kb | Proximal (<10kb) | 114 | |
| chr11:31,826,787–31,827,506 | 8.8 kb | Proximal (<10kb) | 133 |
Genomic view of the PAX6 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.