Mutations in the Schizosaccharomyces pombe Rae1 and Saccharomyces cerevisiae Gle2 genes have been shown to result in accumulation of poly(A)-containing mRNA in the nucleus, suggesting that the encoded proteins are involved in RNA export. The protein encoded by this gene is a homolog of yeast Rae1. It contains four WD40 motifs, and has been shown to localize to distinct foci in the nucleoplasm, to the nuclear rim, and to meshwork-like structures throughout the cytoplasm. This gene is thought to be involved in nucleocytoplasmic transport, and in directly or indirectly attaching cytoplasmic mRNPs to the cytoskeleton. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for RAE1. 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 = RAE1 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 RAE1, 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 |
|---|---|---|---|---|
| chr20:57,089,540–57,090,158 | 261.3 kb | Distal (>10kb) Multiome HiCAR | 323 | |
| chr20:57,231,910–57,232,397 | 119.0 kb | Distal (>10kb) Multiome | 241 | |
| chr20:57,263,861–57,265,018 | 86.8 kb | Distal (>10kb) Multiome | 521 | |
| chr20:57,265,156–57,267,217 | 84.6 kb | Distal (>10kb) Multiome | 462 | |
| chr20:57,323,005–57,323,752 | 28.0 kb | Distal (>10kb) Multiome | 226 | |
| chr20:57,350,979–57,351,567 | 38 bp | At TSS Multiome | 833 | |
| chr20:57,389,119–57,389,876 | 38.2 kb | Distal (>10kb) Multiome | 590 | |
| chr20:57,390,113–57,392,016 | 40.1 kb | Distal (>10kb) Multiome | 692 | |
| chr20:57,596,872–57,597,457 | 246.0 kb | Distal (>10kb) Multiome | 473 |
Genomic view of the RAE1 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.