The protein encoded by this gene is part of a heteromeric complex that binds U4, U5, and U6 small nuclear RNAs and is involved in pre-mRNA splicing. The encoded protein also is a mitotic checkpoint protein and a regulator of chemoresistance in human ovarian cancer. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2016]
Transcription factors with Perturb-seq knockdown data for PRPF4. 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 = PRPF4 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 PRPF4, 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 |
|---|---|---|---|---|
| chr9:113,011,893–113,012,348 | 263.5 kb | Distal (>10kb) Multiome | 444 | |
| chr9:113,056,219–113,057,065 | 218.9 kb | Distal (>10kb) Multiome | 732 | |
| chr9:113,150,622–113,151,556 | 124.6 kb | Distal (>10kb) Multiome | 705 | |
| chr9:113,220,980–113,222,241 | 54.2 kb | Distal (>10kb) Multiome | 819 | |
| chr9:113,274,507–113,274,713 | 943 bp | At TSS | 207 | |
| chr9:113,274,845–113,275,974 | 112 bp | At TSS Multiome | 852 | |
| chr9:113,331,229–113,332,031 | 56.1 kb | Distal (>10kb) Multiome | 69 | |
| chr9:113,339,770–113,340,691 | 64.6 kb | Distal (>10kb) Multiome | 941 | |
| chr9:113,349,409–113,349,994 | 74.0 kb | Distal (>10kb) Multiome | 358 | |
| chr9:113,376,590–113,377,575 | 101.4 kb | Distal (>10kb) Multiome | 710 | |
| chr9:113,400,912–113,402,007 | 125.7 kb | Distal (>10kb) Multiome HiCAR | 859 | |
| chr9:113,409,973–113,410,921 | 134.9 kb | Distal (>10kb) Multiome | 997 | |
| chr9:113,463,361–113,464,008 | 188.0 kb | Distal (>10kb) Multiome | 526 | |
| chr9:113,541,084–113,541,543 | 265.7 kb | Distal (>10kb) Multiome | 160 | |
| chr9:113,591,435–113,592,161 | 316.1 kb | Distal (>10kb) Multiome HiCAR | 345 | |
| chr9:113,593,578–113,594,410 | 318.4 kb | Distal (>10kb) Multiome HiCAR | 433 |
Genomic view of the PRPF4 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.