This gene encodes a member of the bicoid subfamily of homeodomain-containing transcription factors. The encoded protein acts as a transcription factor and plays a role in brain, craniofacial, and sensory organ development. The encoded protein also influences the proliferation and differentiation of dopaminergic neuronal progenitor cells during mitosis. Mutations in this gene cause syndromic microphthalmia 5 (MCOPS5) and combined pituitary hormone deficiency 6 (CPHD6). This gene is also suspected of having an oncogenic role in medulloblastoma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Pseudogenes of this gene are known to exist on chromosomes two and nine. [provided by RefSeq, Jul 2012]
Transcription factors with Perturb-seq knockdown data for OTX2. 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 = OTX2 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 OTX2, 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 |
|---|---|---|---|---|
| chr14:56,552,658–56,553,598 | 252.8 kb | Distal (>10kb) Multiome | 60 | |
| chr14:56,579,396–56,580,264 | 226.0 kb | Distal (>10kb) Multiome | 723 | |
| chr14:56,657,366–56,658,170 | 147.9 kb | Distal (>10kb) Multiome | 55 | |
| chr14:56,659,300–56,659,979 | 146.0 kb | Distal (>10kb) Multiome HiCAR | 126 | |
| chr14:56,795,799–56,797,370 | 8.3 kb | Proximal (<10kb) | 78 | |
| chr14:56,797,476–56,799,717 | 6.7 kb | Proximal (<10kb) Multiome | 305 | |
| chr14:56,804,880–56,806,970 | 141 bp | At TSS Multiome | 343 | |
| chr14:56,808,566–56,809,371 | 2.9 kb | Proximal (<10kb) | 138 | |
| chr14:56,810,408–56,810,605 | 4.7 kb | Proximal (<10kb) | 43 | |
| chr14:56,811,355–56,811,797 | 5.7 kb | Proximal (<10kb) | 46 | |
| chr14:56,811,966–56,812,705 | 6.3 kb | Proximal (<10kb) | 105 | |
| chr14:56,846,930–56,847,795 | 41.7 kb | Distal (>10kb) Multiome | 173 | |
| chr14:56,855,868–56,856,570 | 50.5 kb | Distal (>10kb) Multiome | 256 | |
| chr14:56,858,307–56,858,852 | 53.0 kb | Distal (>10kb) Multiome | 104 | |
| chr14:56,998,512–56,999,273 | 193.2 kb | Distal (>10kb) Multiome HiCAR | 139 | |
| chr14:57,049,791–57,050,396 | 244.4 kb | Distal (>10kb) Multiome HiCAR | 43 |
Genomic view of the OTX2 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.