This gene encodes a member of the bicoid sub-family of homeodomain-containing transcription factors. The encoded protein acts as a transcription factor and may play a role in brain and sensory organ development. A similar protein in mouse is required for proper brain and sensory organ development and can cause epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
Transcription factors with Perturb-seq knockdown data for OTX1. 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 = OTX1 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 OTX1, 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 |
|---|---|---|---|---|
| chr2:63,043,630–63,045,334 | 5.4 kb | Proximal (<10kb) | 458 | |
| chr2:63,047,309–63,049,101 | 1.6 kb | Proximal (<10kb) | 304 | |
| chr2:63,049,346–63,049,706 | 1.0 kb | Proximal (<10kb) | 247 | |
| chr2:63,049,767–63,052,378 | at TSS | At TSS | 881 | |
| chr2:63,053,825–63,054,680 | 3.1 kb | Proximal (<10kb) | 227 | |
| chr2:63,054,998–63,056,049 | 4.3 kb | Proximal (<10kb) | 159 | |
| chr2:63,056,639–63,057,039 | 5.9 kb | Proximal (<10kb) | 82 | |
| chr2:63,058,008–63,060,072 | 7.3 kb | Proximal (<10kb) | 391 |
Genomic view of the OTX1 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.