This gene encodes a classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium-dependent cell-cell adhesion protein is comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. This gene is located in a gene cluster in a region on the long arm of chromosome 16 that is involved in loss of heterozygosity events in breast and prostate cancer. In addition, aberrant expression of this protein is observed in cervical adenocarcinomas. Mutations in this gene are associated with hypotrichosis with juvenile macular dystrophy and ectodermal dysplasia, ectrodactyly, and macular dystrophy syndrome (EEMS). [provided by RefSeq, Nov 2015]
Transcription factors with Perturb-seq knockdown data for CDH3. 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 = CDH3 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 CDH3, 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 |
|---|---|---|---|---|
| chr16:68,420,400–68,420,906 | 224.7 kb | Distal (>10kb) Multiome | 58 | |
| chr16:68,447,981–68,449,250 | 196.7 kb | Distal (>10kb) Multiome | 795 | |
| chr16:68,520,489–68,521,019 | 124.5 kb | Distal (>10kb) Multiome | 602 | |
| chr16:68,528,418–68,529,128 | 116.6 kb | Distal (>10kb) Multiome | 552 | |
| chr16:68,529,733–68,530,671 | 115.1 kb | Distal (>10kb) Multiome | 831 | |
| chr16:68,538,873–68,540,027 | 106.0 kb | Distal (>10kb) Multiome | 764 | |
| chr16:68,642,503–68,643,044 | 2.6 kb | Proximal (<10kb) Multiome | 288 | |
| chr16:68,644,824–68,646,405 | 29 bp | At TSS Multiome | 442 | |
| chr16:68,736,847–68,738,492 | 91.9 kb | Distal (>10kb) Multiome | 537 | |
| chr16:68,778,480–68,779,271 | 133.7 kb | Distal (>10kb) Multiome | 248 | |
| chr16:68,843,238–68,844,359 | 198.5 kb | Distal (>10kb) Multiome | 918 |
Genomic view of the CDH3 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.