This gene encodes a protein which belongs to the C2H2-type zinc finger proteins subclass of the Gli family. They are characterized as DNA-binding transcription factors and are mediators of Sonic hedgehog (Shh) signaling. The protein encoded by this gene localizes in the cytoplasm and activates patched Drosophila homolog (PTCH) gene expression. It is also thought to play a role during embryogenesis. Mutations in this gene have been associated with several diseases, including Greig cephalopolysyndactyly syndrome, Pallister-Hall syndrome, preaxial polydactyly type IV, and postaxial polydactyly types A1 and B. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for GLI3. 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 = GLI3 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 GLI3, 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 |
|---|---|---|---|---|
| chr7:41,942,720–41,943,557 | 284.5 kb | Distal (>10kb) Multiome HiCAR | 490 | |
| chr7:41,955,596–41,956,493 | 271.7 kb | Distal (>10kb) Multiome | 347 | |
| chr7:42,090,952–42,092,704 | 135.7 kb | Distal (>10kb) Multiome HiCAR | 476 | |
| chr7:42,192,714–42,193,475 | 34.6 kb | Distal (>10kb) Multiome | 338 | |
| chr7:42,222,264–42,222,533 | 5.2 kb | Proximal (<10kb) | 86 | |
| chr7:42,222,978–42,223,189 | 4.5 kb | Proximal (<10kb) | 55 | |
| chr7:42,224,696–42,224,883 | 2.8 kb | Proximal (<10kb) | 72 | |
| chr7:42,227,611–42,228,873 | 515 bp | At TSS Multiome | 271 | |
| chr7:42,232,291–42,232,550 | 4.6 kb | Proximal (<10kb) | 182 | |
| chr7:42,235,905–42,238,900 | 9.9 kb | Proximal (<10kb) Multiome | 642 | |
| chr7:42,887,741–42,889,424 | 660.7 kb | Distal (>10kb) Multiome HiCAR | 819 |
Genomic view of the GLI3 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.