PAX2 encodes paired box gene 2, one of many human homologues of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcriptional supression by the tumor suppressor gene WT1. Mutations within PAX2 have been shown to result in optic nerve colobomas and renal hypoplasia. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Transcription factors with Perturb-seq knockdown data for PAX2. 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 = PAX2 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 PAX2, 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 |
|---|---|---|---|---|
| chr10:100,739,174–100,740,373 | 5.2 kb | Proximal (<10kb) | 205 | |
| chr10:100,741,019–100,741,214 | 4.4 kb | Proximal (<10kb) | 46 | |
| chr10:100,741,435–100,742,741 | 2.8 kb | Proximal (<10kb) | 105 | |
| chr10:100,743,670–100,744,309 | 1.3 kb | Proximal (<10kb) | 280 | |
| chr10:100,744,447–100,746,357 | at TSS | At TSS | 379 | |
| chr10:100,747,830–100,748,384 | 2.2 kb | Proximal (<10kb) | 89 |
Genomic view of the PAX2 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.