This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PCDH1. 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 = PCDH1 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 PCDH1, 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 |
|---|---|---|---|---|
| chr5:141,617,831–141,619,550 | 259.3 kb | Distal (>10kb) Multiome | 1037 | |
| chr5:141,636,256–141,638,491 | 241.5 kb | Distal (>10kb) Multiome | 852 | |
| chr5:141,650,837–141,651,870 | 227.0 kb | Distal (>10kb) Multiome | 438 | |
| chr5:141,680,751–141,681,516 | 197.4 kb | Distal (>10kb) Multiome | 257 | |
| chr5:141,681,692–141,682,621 | 196.2 kb | Distal (>10kb) Multiome | 554 | |
| chr5:141,692,108–141,692,560 | 186.1 kb | Distal (>10kb) Multiome HiCAR | 498 | |
| chr5:141,702,181–141,702,796 | 176.0 kb | Distal (>10kb) Multiome | 351 | |
| chr5:141,795,082–141,795,688 | 83.1 kb | Distal (>10kb) Multiome | 25 | |
| chr5:141,811,578–141,812,181 | 66.5 kb | Distal (>10kb) Multiome HiCAR | 243 | |
| chr5:141,816,277–141,817,287 | 61.6 kb | Distal (>10kb) Multiome HiCAR | 210 | |
| chr5:141,838,853–141,839,539 | 39.1 kb | Distal (>10kb) Multiome | 185 | |
| chr5:141,845,184–141,846,305 | 32.7 kb | Distal (>10kb) Multiome | 188 | |
| chr5:141,848,609–141,851,214 | 29.0 kb | Distal (>10kb) Multiome | 892 | |
| chr5:141,858,059–141,858,606 | 20.1 kb | Distal (>10kb) Multiome | 80 | |
| chr5:141,871,968–141,872,193 | 6.2 kb | Proximal (<10kb) | 6 | |
| chr5:141,875,925–141,877,406 | 2.1 kb | Proximal (<10kb) Multiome | 506 | |
| chr5:141,877,575–141,879,487 | 49 bp | At TSS Multiome | 693 | |
| chr5:141,883,297–141,883,712 | 4.9 kb | Proximal (<10kb) | 267 | |
| chr5:141,923,268–141,924,400 | 45.5 kb | Distal (>10kb) Multiome | 922 | |
| chr5:141,968,679–141,969,625 | 90.7 kb | Distal (>10kb) Multiome | 966 | |
| chr5:142,012,158–142,013,413 | 134.6 kb | Distal (>10kb) Multiome | 665 | |
| chr5:142,083,687–142,084,682 | 205.7 kb | Distal (>10kb) Multiome | 113 | |
| chr5:142,108,404–142,109,356 | 230.4 kb | Distal (>10kb) Multiome | 759 | |
| chr5:142,169,261–142,169,978 | 291.1 kb | Distal (>10kb) Multiome | 405 | |
| chr5:142,175,265–142,176,514 | 297.4 kb | Distal (>10kb) Multiome | 230 |
Genomic view of the PCDH1 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.