This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. 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 binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome X. Two splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for UPF3B. 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 = UPF3B 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 UPF3B, 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 |
|---|---|---|---|---|
| chrX:119,573,862–119,575,243 | 278.5 kb | Distal (>10kb) Multiome | 734 | |
| chrX:119,605,775–119,606,635 | 246.6 kb | Distal (>10kb) Multiome | 518 | |
| chrX:119,692,568–119,693,792 | 159.7 kb | Distal (>10kb) Multiome | 595 | |
| chrX:119,757,760–119,759,432 | 94.7 kb | Distal (>10kb) Multiome | 507 | |
| chrX:119,791,353–119,792,197 | 61.2 kb | Distal (>10kb) Multiome | 699 | |
| chrX:119,852,659–119,853,400 | 112 bp | At TSS Multiome | 612 | |
| chrX:119,871,438–119,872,306 | 18.9 kb | Distal (>10kb) Multiome | 720 | |
| chrX:119,943,211–119,943,921 | 90.7 kb | Distal (>10kb) Multiome | 763 |
Genomic view of the UPF3B 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.