This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein is located in the perinuclear area. It interacts with translation release factors and the proteins that are functional homologs of yeast Upf1p and Upf3p. Two splice variants have been found for this gene; both variants encode the same protein. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for UPF2. 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 = UPF2 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 UPF2, 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 |
|---|---|---|---|---|
| chr10:11,741,667–11,743,276 | 300.4 kb | Distal (>10kb) Multiome | 482 | |
| chr10:11,799,285–11,799,933 | 243.3 kb | Distal (>10kb) Multiome | 102 | |
| chr10:11,823,198–11,824,010 | 219.4 kb | Distal (>10kb) Multiome | 551 | |
| chr10:11,869,855–11,870,414 | 172.6 kb | Distal (>10kb) Multiome | 105 | |
| chr10:11,874,348–11,875,590 | 167.9 kb | Distal (>10kb) Multiome | 672 | |
| chr10:11,913,209–11,913,675 | 129.3 kb | Distal (>10kb) Multiome | 34 | |
| chr10:12,041,862–12,043,685 | 318 bp | At TSS Multiome | 849 | |
| chr10:12,063,340–12,063,818 | 20.8 kb | Distal (>10kb) Multiome | 219 | |
| chr10:12,068,387–12,069,409 | 26.0 kb | Distal (>10kb) Multiome | 831 | |
| chr10:12,129,046–12,130,594 | 86.7 kb | Distal (>10kb) Multiome | 734 | |
| chr10:12,195,567–12,196,550 | 153.3 kb | Distal (>10kb) Multiome | 929 | |
| chr10:12,264,254–12,264,720 | 221.6 kb | Distal (>10kb) Multiome | 542 |
Genomic view of the UPF2 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.