This gene encodes a protein which contains three CUT domains and a homeodomain; both domains are DNA-binding motifs. A similar gene, whose gene product possesses different DNA-binding activities, is located on chromosome on chromosome 7. Two pseudogenes of this gene have been identified on chromosomes 10 and 4. [provided by RefSeq, Jan 2013]
Transcription factors with Perturb-seq knockdown data for CUX2. 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 = CUX2 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 CUX2, 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 |
|---|---|---|---|---|
| chr12:110,742,238–110,743,370 | 291.2 kb | Distal (>10kb) Multiome | 801 | |
| chr12:110,772,664–110,773,461 | 261.1 kb | Distal (>10kb) Multiome | 88 | |
| chr12:110,846,588–110,847,239 | 187.3 kb | Distal (>10kb) Multiome | 371 | |
| chr12:110,860,936–110,861,527 | 172.9 kb | Distal (>10kb) Multiome | 127 | |
| chr12:110,936,931–110,937,646 | 96.9 kb | Distal (>10kb) Multiome | 373 | |
| chr12:111,024,263–111,024,472 | 9.7 kb | Proximal (<10kb) | 198 | |
| chr12:111,033,333–111,033,515 | 648 bp | At TSS | 156 | |
| chr12:111,033,748–111,035,142 | 652 bp | At TSS Multiome | 235 |
Genomic view of the CUX2 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.