U2 auxiliary factor (U2AF), comprised of a large and a small subunit, is a non-snRNP protein required for the binding of U2 snRNP to the pre-mRNA branch site. This gene encodes the U2AF large subunit which contains a sequence-specific RNA-binding region with 3 RNA recognition motifs and an Arg/Ser-rich domain necessary for splicing. The large subunit binds to the polypyrimidine tract of introns early during spliceosome assembly. Multiple transcript variants have been detected for this gene, but the full-length natures of only two have been determined to date. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for U2AF2. 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 = U2AF2 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 U2AF2, 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 |
|---|---|---|---|---|
| chr19:55,369,099–55,370,447 | 285.0 kb | Distal (>10kb) Multiome | 383 | |
| chr19:55,383,539–55,384,553 | 271.1 kb | Distal (>10kb) Multiome | 374 | |
| chr19:55,384,697–55,386,560 | 269.3 kb | Distal (>10kb) Multiome | 903 | |
| chr19:55,406,950–55,408,675 | 247.0 kb | Distal (>10kb) Multiome | 965 | |
| chr19:55,452,738–55,453,308 | 201.9 kb | Distal (>10kb) Multiome | 339 | |
| chr19:55,460,784–55,462,230 | 193.2 kb | Distal (>10kb) Multiome | 947 | |
| chr19:55,476,048–55,477,307 | 178.3 kb | Distal (>10kb) Multiome | 1007 | |
| chr19:55,484,846–55,485,682 | 169.9 kb | Distal (>10kb) Multiome | 594 | |
| chr19:55,503,638–55,504,310 | 151.0 kb | Distal (>10kb) Multiome | 710 | |
| chr19:55,516,768–55,517,459 | 137.9 kb | Distal (>10kb) Multiome | 583 | |
| chr19:55,536,923–55,537,366 | 117.8 kb | Distal (>10kb) Multiome | 180 | |
| chr19:55,549,822–55,550,343 | 105.0 kb | Distal (>10kb) Multiome | 396 | |
| chr19:55,580,080–55,581,090 | 74.2 kb | Distal (>10kb) Multiome | 718 | |
| chr19:55,585,644–55,586,314 | 69.2 kb | Distal (>10kb) Multiome | 370 | |
| chr19:55,586,698–55,587,594 | 67.7 kb | Distal (>10kb) Multiome | 463 | |
| chr19:55,598,551–55,600,991 | 54.6 kb | Distal (>10kb) Multiome | 1018 | |
| chr19:55,604,520–55,606,690 | 49.7 kb | Distal (>10kb) Multiome | 820 | |
| chr19:55,623,637–55,625,055 | 30.5 kb | Distal (>10kb) Multiome | 650 | |
| chr19:55,640,091–55,641,769 | 14.0 kb | Distal (>10kb) Multiome | 821 | |
| chr19:55,642,197–55,644,356 | 11.5 kb | Distal (>10kb) Multiome | 884 | |
| chr19:55,647,711–55,648,342 | 6.9 kb | Proximal (<10kb) Multiome | 671 | |
| chr19:55,652,138–55,653,078 | 2.6 kb | Proximal (<10kb) Multiome | 105 | |
| chr19:55,653,199–55,656,056 | 356 bp | At TSS Multiome | 1123 | |
| chr19:55,674,767–55,675,613 | 20.1 kb | Distal (>10kb) Multiome | 765 |
Genomic view of the U2AF2 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.