This gene was first identified by the similarity of its product to the Aspergillus nidulans SUDD protein. This gene is now recognized as a member of the right open reading frame (RIO) kinase gene family. This gene encodes a serine/threonine kinase that localizes to the cytoplasm and plays a role in the processing of the pre-40 S ribosomal subunit. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2017]
Transcription factors with Perturb-seq knockdown data for RIOK3. 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 = RIOK3 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 RIOK3, 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 |
|---|---|---|---|---|
| chr18:23,259,654–23,260,831 | 193.1 kb | Distal (>10kb) Multiome | 655 | |
| chr18:23,437,346–23,438,074 | 15.4 kb | Distal (>10kb) Multiome | 628 | |
| chr18:23,452,793–23,453,775 | 97 bp | At TSS Multiome | 796 | |
| chr18:23,502,975–23,503,998 | 50.1 kb | Distal (>10kb) Multiome | 907 | |
| chr18:23,586,020–23,587,174 | 133.4 kb | Distal (>10kb) Multiome | 908 | |
| chr18:23,609,370–23,609,991 | 156.4 kb | Distal (>10kb) Multiome | 79 | |
| chr18:23,618,918–23,619,643 | 166.0 kb | Distal (>10kb) Multiome | 295 | |
| chr18:23,662,307–23,663,058 | 209.5 kb | Distal (>10kb) Multiome | 349 | |
| chr18:23,689,205–23,690,311 | 236.2 kb | Distal (>10kb) Multiome | 469 | |
| chr18:23,721,611–23,722,408 | 268.8 kb | Distal (>10kb) Multiome | 82 |
Genomic view of the RIOK3 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.