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 only in the cytoplasm. When translation ends, it interacts with the protein that is a functional homolog of yeast Upf2p to trigger mRNA decapping. Use of multiple polyadenylation sites has been noted for this gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Transcription factors with Perturb-seq knockdown data for UPF1. 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 = UPF1 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 UPF1, 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 |
|---|---|---|---|---|
| chr19:18,543,118–18,544,249 | 288.3 kb | Distal (>10kb) Multiome | 574 | |
| chr19:18,557,570–18,558,196 | 274.2 kb | Distal (>10kb) Multiome | 738 | |
| chr19:18,571,234–18,572,258 | 260.2 kb | Distal (>10kb) Multiome | 972 | |
| chr19:18,588,272–18,591,023 | 241.3 kb | Distal (>10kb) Multiome | 1174 | |
| chr19:18,593,729–18,595,402 | 237.5 kb | Distal (>10kb) Multiome | 464 | |
| chr19:18,611,391–18,612,134 | 220.2 kb | Distal (>10kb) Multiome | 340 | |
| chr19:18,635,894–18,637,555 | 195.3 kb | Distal (>10kb) Multiome | 617 | |
| chr19:18,682,925–18,684,360 | 148.3 kb | Distal (>10kb) Multiome | 701 | |
| chr19:18,785,146–18,785,600 | 46.6 kb | Distal (>10kb) Multiome | 247 | |
| chr19:18,831,386–18,833,070 | 84 bp | At TSS Multiome | 833 | |
| chr19:18,870,063–18,870,526 | 38.5 kb | Distal (>10kb) Multiome | 148 | |
| chr19:18,895,036–18,896,591 | 64.2 kb | Distal (>10kb) Multiome | 554 | |
| chr19:18,918,971–18,919,972 | 87.6 kb | Distal (>10kb) Multiome | 828 | |
| chr19:18,932,038–18,933,012 | 100.6 kb | Distal (>10kb) Multiome | 312 | |
| chr19:18,940,835–18,941,417 | 109.3 kb | Distal (>10kb) Multiome | 336 | |
| chr19:19,017,061–19,017,561 | 185.3 kb | Distal (>10kb) Multiome | 21 | |
| chr19:19,032,820–19,034,059 | 201.7 kb | Distal (>10kb) Multiome | 944 | |
| chr19:19,063,253–19,064,386 | 231.8 kb | Distal (>10kb) Multiome | 781 | |
| chr19:19,105,310–19,106,514 | 273.8 kb | Distal (>10kb) Multiome | 447 | |
| chr19:19,110,429–19,110,857 | 278.7 kb | Distal (>10kb) Multiome | 131 | |
| chr19:19,119,998–19,121,362 | 288.6 kb | Distal (>10kb) Multiome | 304 |
Genomic view of the UPF1 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.