This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PCDHGB6. 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 = PCDHGB6 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 PCDHGB6, 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 |
|---|---|---|---|---|
| chr5:141,320,208–141,321,296 | 87.3 kb | Distal (>10kb) Multiome | 954 | |
| chr5:141,407,865–141,408,477 | 33 bp | At TSS Multiome | 109 | |
| chr5:141,412,882–141,413,082 | 4.9 kb | Proximal (<10kb) | 122 | |
| chr5:141,417,522–141,418,139 | 9.7 kb | Proximal (<10kb) Multiome | 106 | |
| chr5:141,475,524–141,476,908 | 67.9 kb | Distal (>10kb) Multiome | 402 | |
| chr5:141,484,493–141,485,507 | 76.9 kb | Distal (>10kb) Multiome | 189 | |
| chr5:141,508,593–141,509,337 | 101.0 kb | Distal (>10kb) Multiome | 242 | |
| chr5:141,512,198–141,512,900 | 104.5 kb | Distal (>10kb) Multiome | 300 | |
| chr5:141,513,616–141,515,069 | 106.6 kb | Distal (>10kb) Multiome | 392 | |
| chr5:141,524,502–141,525,311 | 116.9 kb | Distal (>10kb) Multiome | 605 | |
| chr5:141,557,658–141,558,135 | 149.9 kb | Distal (>10kb) Multiome | 373 | |
| chr5:141,560,663–141,561,120 | 152.9 kb | Distal (>10kb) Multiome | 327 | |
| chr5:141,617,831–141,619,550 | 211.1 kb | Distal (>10kb) Multiome | 1037 | |
| chr5:141,636,256–141,638,491 | 228.9 kb | Distal (>10kb) Multiome | 852 | |
| chr5:141,650,837–141,651,870 | 243.4 kb | Distal (>10kb) Multiome | 438 | |
| chr5:141,680,751–141,681,516 | 273.0 kb | Distal (>10kb) Multiome | 257 | |
| chr5:141,681,692–141,682,621 | 274.2 kb | Distal (>10kb) Multiome | 554 | |
| chr5:141,692,108–141,692,560 | 284.3 kb | Distal (>10kb) Multiome | 498 | |
| chr5:141,702,181–141,702,796 | 294.4 kb | Distal (>10kb) Multiome | 351 |
Genomic view of the PCDHGB6 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.