This gene encodes a WW-domain containing protein similar to yeast splicing factor PRP40. This protein has been shown to interact with Huntingtin and methyl CpG binding protein 2 (MeCP2). Alternative splicing results in different transcript variants. [provided by RefSeq, Aug 2014]
Transcription factors with Perturb-seq knockdown data for PRPF40B. 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 = PRPF40B 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 PRPF40B, 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 |
|---|---|---|---|---|
| chr12:49,297,237–49,297,902 | 270.6 kb | Distal (>10kb) Multiome | 330 | |
| chr12:49,322,593–49,323,536 | 245.1 kb | Distal (>10kb) Multiome | 647 | |
| chr12:49,336,785–49,337,369 | 231.0 kb | Distal (>10kb) Multiome | 482 | |
| chr12:49,341,800–49,343,265 | 225.6 kb | Distal (>10kb) Multiome HiCAR | 631 | |
| chr12:49,347,124–49,348,156 | 220.4 kb | Distal (>10kb) Multiome HiCAR | 790 | |
| chr12:49,366,450–49,368,011 | 200.9 kb | Distal (>10kb) Multiome HiCAR | 868 | |
| chr12:49,538,551–49,539,219 | 29.3 kb | Distal (>10kb) Multiome | 284 | |
| chr12:49,550,509–49,551,225 | 17.2 kb | Distal (>10kb) Multiome HiCAR | 126 | |
| chr12:49,567,505–49,568,696 | 96 bp | At TSS Multiome | 807 | |
| chr12:49,574,219–49,574,522 | 6.0 kb | Proximal (<10kb) | 13 | |
| chr12:49,622,768–49,624,150 | 55.3 kb | Distal (>10kb) Multiome | 788 | |
| chr12:49,626,898–49,627,168 | 3.3 kb | Proximal (<10kb) | 15 | |
| chr12:49,706,780–49,708,002 | 139.4 kb | Distal (>10kb) Multiome HiCAR | 854 | |
| chr12:49,741,069–49,742,357 | 173.2 kb | Distal (>10kb) Multiome | 980 | |
| chr12:49,827,122–49,829,288 | 260.3 kb | Distal (>10kb) Multiome | 839 | |
| chr12:49,842,401–49,843,296 | 274.8 kb | Distal (>10kb) Multiome | 806 | |
| chr12:49,866,994–49,867,580 | 299.1 kb | Distal (>10kb) Multiome | 334 |
Genomic view of the PRPF40B 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.