IRX3 is a member of the Iroquois homeobox gene family (see IRX1; MIM 606197) and plays a role in an early step of neural development (Bellefroid et al., 1998 [PubMed 9427753]). Members of this family appear to play multiple roles during pattern formation of vertebrate embryos (Lewis et al., 1999 [PubMed 10370142]).[supplied by OMIM, Aug 2009]
Transcription factors with Perturb-seq knockdown data for IRX3. 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 = IRX3 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 IRX3, 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 |
|---|---|---|---|---|
| chr16:54,055,139–54,055,634 | 231.3 kb | Distal (>10kb) Multiome | 40 | |
| chr16:54,062,266–54,063,051 | 224.2 kb | Distal (>10kb) Multiome | 157 | |
| chr16:54,193,529–54,194,737 | 92.9 kb | Distal (>10kb) Multiome | 513 | |
| chr16:54,199,531–54,200,186 | 87.0 kb | Distal (>10kb) Multiome | 43 | |
| chr16:54,207,934–54,208,931 | 78.5 kb | Distal (>10kb) Multiome | 181 | |
| chr16:54,211,232–54,211,931 | 75.2 kb | Distal (>10kb) Multiome | 25 | |
| chr16:54,281,564–54,282,249 | 4.5 kb | Proximal (<10kb) | 131 | |
| chr16:54,282,317–54,283,163 | 4.3 kb | Proximal (<10kb) Multiome | 207 | |
| chr16:54,283,950–54,287,988 | 150 bp | At TSS Multiome | 857 | |
| chr16:54,289,334–54,289,776 | 2.5 kb | Proximal (<10kb) | 105 | |
| chr16:54,291,177–54,291,532 | 4.4 kb | Proximal (<10kb) | 69 | |
| chr16:54,291,618–54,292,104 | 4.8 kb | Proximal (<10kb) | 56 | |
| chr16:54,292,246–54,292,560 | 5.5 kb | Proximal (<10kb) | 32 | |
| chr16:54,370,455–54,371,426 | 84.1 kb | Distal (>10kb) Multiome | 203 | |
| chr16:54,927,769–54,931,725 | 642.4 kb | Distal (>10kb) Multiome HiCAR | 746 |
Genomic view of the IRX3 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.