This gene encodes one of four subunits of the splicing factor 3B. The protein encoded by this gene cross-links to a region in the pre-mRNA immediately upstream of the branchpoint sequence in pre-mRNA in the prespliceosomal complex A. It also may be involved in the assembly of the B, C and E spliceosomal complexes. In addition to RNA-binding activity, this protein interacts directly and highly specifically with subunit 2 of the splicing factor 3B. This protein contains two N-terminal RNA-recognition motifs (RRMs), consistent with the observation that it binds directly to pre-mRNA. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for SF3B4. 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 = SF3B4 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 SF3B4, 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 |
|---|---|---|---|---|
| chr1:149,636,175–149,637,106 | 291.3 kb | Distal (>10kb) Multiome | 687 | |
| chr1:149,812,136–149,812,633 | 115.4 kb | Distal (>10kb) Multiome | 190 | |
| chr1:149,885,029–149,889,131 | 39.5 kb | Distal (>10kb) Multiome | 1126 | |
| chr1:149,899,425–149,900,227 | 28.1 kb | Distal (>10kb) Multiome | 650 | |
| chr1:149,917,583–149,918,019 | 9.8 kb | Proximal (<10kb) | 232 | |
| chr1:149,927,507–149,928,019 | 122 bp | At TSS Multiome | 744 | |
| chr1:149,928,151–149,928,438 | 348 bp | At TSS | 486 | |
| chr1:150,010,143–150,011,088 | 82.9 kb | Distal (>10kb) Multiome | 961 | |
| chr1:150,066,903–150,067,886 | 139.8 kb | Distal (>10kb) Multiome | 986 | |
| chr1:150,149,493–150,150,439 | 222.3 kb | Distal (>10kb) Multiome | 448 | |
| chr1:150,162,838–150,163,636 | 235.5 kb | Distal (>10kb) Multiome HiCAR | 550 | |
| chr1:150,213,532–150,214,095 | 285.9 kb | Distal (>10kb) Multiome | 441 |
Genomic view of the SF3B4 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.