The removal of introns from nuclear pre-mRNAs occurs on complexes called spliceosomes, which are made up of 4 small nuclear ribonucleoprotein (snRNP) particles and an undefined number of transiently associated splicing factors. This gene product is one of several proteins that associate with U4 and U6 snRNPs. Mutations in this gene are associated with retinitis pigmentosa-18. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PRPF3. 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 = PRPF3 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 PRPF3, 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 |
|---|---|---|---|---|
| chr1:150,066,903–150,067,886 | 253.9 kb | Distal (>10kb) Multiome | 986 | |
| chr1:150,149,493–150,150,439 | 171.4 kb | Distal (>10kb) Multiome | 448 | |
| chr1:150,162,838–150,163,636 | 158.2 kb | Distal (>10kb) Multiome | 550 | |
| chr1:150,213,532–150,214,095 | 107.8 kb | Distal (>10kb) Multiome | 441 | |
| chr1:150,234,435–150,235,519 | 86.8 kb | Distal (>10kb) Multiome | 725 | |
| chr1:150,235,635–150,236,696 | 85.3 kb | Distal (>10kb) Multiome | 905 | |
| chr1:150,255,443–150,256,199 | 65.8 kb | Distal (>10kb) Multiome | 441 | |
| chr1:150,256,563–150,257,324 | 64.5 kb | Distal (>10kb) Multiome | 223 | |
| chr1:150,257,589–150,258,594 | 63.4 kb | Distal (>10kb) Multiome | 233 | |
| chr1:150,259,728–150,260,778 | 61.4 kb | Distal (>10kb) Multiome | 362 | |
| chr1:150,268,574–150,269,453 | 52.4 kb | Distal (>10kb) Multiome | 785 | |
| chr1:150,281,629–150,283,038 | 39.1 kb | Distal (>10kb) Multiome | 503 | |
| chr1:150,293,680–150,294,144 | 27.7 kb | Distal (>10kb) Multiome | 755 | |
| chr1:150,313,761–150,314,506 | 7.4 kb | Proximal (<10kb) Multiome | 108 | |
| chr1:150,321,137–150,321,825 | 23 bp | At TSS Multiome | 806 | |
| chr1:150,363,368–150,364,980 | 42.5 kb | Distal (>10kb) Multiome | 971 | |
| chr1:150,487,154–150,487,710 | 165.8 kb | Distal (>10kb) Multiome | 929 | |
| chr1:150,515,085–150,516,227 | 194.1 kb | Distal (>10kb) Multiome | 781 | |
| chr1:150,548,849–150,549,823 | 227.7 kb | Distal (>10kb) Multiome | 620 | |
| chr1:150,560,828–150,562,623 | 239.8 kb | Distal (>10kb) Multiome | 897 | |
| chr1:150,578,554–150,580,300 | 258.1 kb | Distal (>10kb) Multiome | 990 |
Genomic view of the PRPF3 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.