This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PCDHB2. 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 = PCDHB2 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 PCDHB2, 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 |
|---|---|---|---|---|
| chr5:140,925,961–140,927,592 | 168.1 kb | Distal (>10kb) Multiome | 419 | |
| chr5:140,965,919–140,967,712 | 128.0 kb | Distal (>10kb) Multiome | 368 | |
| chr5:141,001,892–141,002,584 | 92.3 kb | Distal (>10kb) Multiome | 246 | |
| chr5:141,003,899–141,004,593 | 90.3 kb | Distal (>10kb) Multiome | 331 | |
| chr5:141,039,880–141,041,470 | 53.4 kb | Distal (>10kb) Multiome | 682 | |
| chr5:141,094,443–141,094,942 | 77 bp | At TSS Multiome | 336 | |
| chr5:141,320,208–141,321,296 | 226.1 kb | Distal (>10kb) Multiome | 954 | |
| chr5:141,557,658–141,558,135 | 463.3 kb | Distal (>10kb) Multiome HiCAR | 373 |
Genomic view of the PCDHB2 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.