This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. Paired box transcription factors are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. This gene encodes the B-cell lineage specific activator protein that is expressed at early, but not late stages of B-cell differentiation. Its expression has also been detected in developing CNS and testis and so the encoded protein may also play a role in neural development and spermatogenesis. This gene is located at 9p13, which is involved in t(9;14)(p13;q32) translocations recurring in small lymphocytic lymphomas of the plasmacytoid subtype, and in derived large-cell lymphomas. This translocation brings the potent E-mu enhancer of the IgH gene into close proximity of the PAX5 promoter, suggesting that the deregulation of transcription of this gene contributes to the pathogenesis of these lymphomas. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
Transcription factors with Perturb-seq knockdown data for PAX5. 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 = PAX5 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 PAX5, 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 |
|---|---|---|---|---|
| chr9:36,765,822–36,766,468 | 260.4 kb | Distal (>10kb) Multiome | 470 | |
| chr9:37,025,271–37,025,777 | 797 bp | At TSS | 94 | |
| chr9:37,026,066–37,028,063 | 1.2 kb | Proximal (<10kb) Multiome | 872 | |
| chr9:37,034,136–37,035,908 | 8.0 kb | Proximal (<10kb) Multiome | 387 | |
| chr9:37,036,528–37,038,168 | 11.2 kb | Distal (>10kb) Multiome | 340 | |
| chr9:37,079,324–37,080,475 | 53.2 kb | Distal (>10kb) Multiome | 1035 | |
| chr9:37,119,886–37,121,225 | 93.8 kb | Distal (>10kb) Multiome | 1074 |
Genomic view of the PAX5 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.