This gene encodes a subunit of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and a 12S RNA unit, forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence-independent manner and may anchor the U2 snRNP to the pre-mRNA. The protein encoded by this gene contains a PHD-finger-like domain that is flanked by highly basic N- and C-termini. This protein belongs to the PHD-finger superfamily and may act as a chromatin-associated protein. This gene has several pseudogenes on different chromosomes. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PHF5A. 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 = PHF5A 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 PHF5A, 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 |
|---|---|---|---|---|
| chr22:41,197,028–41,198,019 | 271.1 kb | Distal (>10kb) Multiome | 640 | |
| chr22:41,204,902–41,205,619 | 263.4 kb | Distal (>10kb) Multiome | 640 | |
| chr22:41,237,372–41,238,796 | 230.8 kb | Distal (>10kb) Multiome | 302 | |
| chr22:41,285,539–41,286,833 | 182.3 kb | Distal (>10kb) Multiome | 879 | |
| chr22:41,301,155–41,301,870 | 167.2 kb | Distal (>10kb) Multiome | 658 | |
| chr22:41,380,458–41,382,737 | 87.0 kb | Distal (>10kb) Multiome | 925 | |
| chr22:41,413,486–41,414,305 | 54.8 kb | Distal (>10kb) Multiome | 832 | |
| chr22:41,444,084–41,445,743 | 24.1 kb | Distal (>10kb) Multiome | 607 | |
| chr22:41,446,165–41,449,007 | 21.8 kb | Distal (>10kb) Multiome | 1188 | |
| chr22:41,468,341–41,469,602 | 242 bp | At TSS Multiome | 920 | |
| chr22:41,512,659–41,513,151 | 44.3 kb | Distal (>10kb) Multiome | 354 | |
| chr22:41,543,855–41,544,782 | 75.9 kb | Distal (>10kb) Multiome | 755 | |
| chr22:41,589,188–41,590,530 | 121.3 kb | Distal (>10kb) Multiome | 758 | |
| chr22:41,620,173–41,622,049 | 152.4 kb | Distal (>10kb) Multiome | 880 | |
| chr22:41,666,496–41,667,405 | 198.2 kb | Distal (>10kb) Multiome | 725 | |
| chr22:41,697,169–41,697,792 | 228.7 kb | Distal (>10kb) Multiome | 464 |
Genomic view of the PHF5A 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.