Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in cell differentiation; negative regulation of chondrocyte differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including intestinal epithelial cell development; middle ear morphogenesis; and skeletal system development. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for NKX3-2. 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 = NKX3-2 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 NKX3-2, 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 |
|---|---|---|---|---|
| chr4:13,534,108–13,535,093 | 9.4 kb | Proximal (<10kb) | 79 | |
| chr4:13,535,571–13,536,360 | 8.1 kb | Proximal (<10kb) | 70 | |
| chr4:13,539,011–13,539,477 | 5.0 kb | Proximal (<10kb) | 44 | |
| chr4:13,540,992–13,542,953 | 1.6 kb | Proximal (<10kb) | 321 | |
| chr4:13,543,269–13,545,468 | at TSS | At TSS | 614 | |
| chr4:13,546,533–13,548,322 | 2.0 kb | Proximal (<10kb) | 466 | |
| chr4:13,548,795–13,549,621 | 4.3 kb | Proximal (<10kb) | 388 |
Genomic view of the NKX3-2 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.