This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PCDHA4. 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 = PCDHA4 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 PCDHA4, 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 |
|---|---|---|---|---|
| chr5:140,546,917–140,548,500 | 259.4 kb | Distal (>10kb) Multiome | 784 | |
| chr5:140,556,971–140,557,959 | 249.5 kb | Distal (>10kb) Multiome | 886 | |
| chr5:140,564,055–140,565,123 | 242.4 kb | Distal (>10kb) Multiome | 827 | |
| chr5:140,639,043–140,640,146 | 167.6 kb | Distal (>10kb) Multiome | 898 | |
| chr5:140,647,175–140,648,159 | 159.3 kb | Distal (>10kb) Multiome | 863 | |
| chr5:140,664,368–140,665,161 | 142.3 kb | Distal (>10kb) Multiome | 856 | |
| chr5:140,673,200–140,673,759 | 133.5 kb | Distal (>10kb) Multiome | 144 | |
| chr5:140,691,053–140,691,933 | 115.5 kb | Distal (>10kb) Multiome | 924 | |
| chr5:140,699,981–140,700,742 | 106.7 kb | Distal (>10kb) Multiome | 607 | |
| chr5:140,710,433–140,711,671 | 96.0 kb | Distal (>10kb) Multiome | 856 | |
| chr5:140,718,340–140,718,978 | 88.4 kb | Distal (>10kb) Multiome | 763 | |
| chr5:140,725,570–140,726,438 | 81.1 kb | Distal (>10kb) Multiome | 719 | |
| chr5:140,806,893–140,807,333 | at TSS | At TSS | 86 | |
| chr5:140,807,526–140,807,927 | 490 bp | At TSS | 39 | |
| chr5:140,925,961–140,927,592 | 119.5 kb | Distal (>10kb) Multiome | 419 | |
| chr5:140,965,919–140,967,712 | 159.6 kb | Distal (>10kb) Multiome | 368 | |
| chr5:141,001,892–141,002,584 | 195.3 kb | Distal (>10kb) Multiome | 246 | |
| chr5:141,003,899–141,004,593 | 197.3 kb | Distal (>10kb) Multiome | 331 | |
| chr5:141,039,880–141,041,470 | 234.1 kb | Distal (>10kb) Multiome HiCAR | 682 | |
| chr5:141,094,443–141,094,942 | 287.6 kb | Distal (>10kb) Multiome | 336 |
Genomic view of the PCDHA4 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.