The protein encoded by this gene is a member of the homeodomain family of DNA binding proteins. It may regulate gene expression, morphogenesis, and differentiation and it may also play a role in the cell cycle progession. Several alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Feb 2011]
Transcription factors with Perturb-seq knockdown data for CUX1. 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 = CUX1 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 CUX1, 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 |
|---|---|---|---|---|
| chr7:101,602,457–101,603,098 | 213.3 kb | Distal (>10kb) Multiome | 367 | |
| chr7:101,688,200–101,688,846 | 127.5 kb | Distal (>10kb) Multiome HiCAR | 537 | |
| chr7:101,733,762–101,734,227 | 82.0 kb | Distal (>10kb) Multiome | 351 | |
| chr7:101,743,251–101,744,281 | 72.2 kb | Distal (>10kb) Multiome | 560 | |
| chr7:101,814,010–101,814,588 | 1.4 kb | Proximal (<10kb) | 666 | |
| chr7:101,815,030–101,816,851 | 171 bp | At TSS Multiome | 762 | |
| chr7:101,817,355–101,817,891 | 1.4 kb | Proximal (<10kb) | 390 | |
| chr7:101,936,102–101,937,458 | 121.0 kb | Distal (>10kb) Multiome | 278 |
Genomic view of the CUX1 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.