Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit, where it forms part of the domain where translation is initiated. The protein belongs to the S3P family of ribosomal proteins. Studies of the mouse and rat proteins have demonstrated that the protein has an extraribosomal role as an endonuclease involved in the repair of UV-induced DNA damage. The protein appears to be located in both the cytoplasm and nucleus but not in the nucleolus. Higher levels of expression of this gene in colon adenocarcinomas and adenomatous polyps compared to adjacent normal colonic mucosa have been observed. This gene is co-transcribed with the small nucleolar RNA genes U15A and U15B, which are located in its first and fifth introns, respectively. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]
Transcription factors with Perturb-seq knockdown data for RPS3. 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 = RPS3 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 RPS3, 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 |
|---|---|---|---|---|
| chr11:75,240,428–75,242,358 | 157.8 kb | Distal (>10kb) Multiome | 618 | |
| chr11:75,331,054–75,332,820 | 67.4 kb | Distal (>10kb) Multiome | 273 | |
| chr11:75,343,281–75,343,976 | 55.8 kb | Distal (>10kb) Multiome | 375 | |
| chr11:75,351,219–75,352,738 | 47.3 kb | Distal (>10kb) Multiome | 868 | |
| chr11:75,388,579–75,389,156 | 10.7 kb | Distal (>10kb) Multiome | 323 | |
| chr11:75,393,988–75,394,501 | 5.0 kb | Proximal (<10kb) | 73 | |
| chr11:75,399,325–75,400,051 | 16 bp | At TSS Multiome | 982 | |
| chr11:75,400,888–75,401,057 | 1.4 kb | Proximal (<10kb) | 58 | |
| chr11:75,425,349–75,425,850 | 26.2 kb | Distal (>10kb) Multiome | 134 | |
| chr11:75,427,839–75,428,742 | 28.9 kb | Distal (>10kb) Multiome | 209 | |
| chr11:75,429,695–75,430,823 | 30.7 kb | Distal (>10kb) Multiome | 340 | |
| chr11:75,524,766–75,526,517 | 126.5 kb | Distal (>10kb) Multiome | 663 | |
| chr11:75,547,627–75,548,081 | 148.3 kb | Distal (>10kb) Multiome | 241 | |
| chr11:75,554,271–75,554,862 | 155.1 kb | Distal (>10kb) Multiome | 441 | |
| chr11:75,559,107–75,559,968 | 160.0 kb | Distal (>10kb) Multiome | 262 | |
| chr11:75,561,674–75,564,448 | 162.7 kb | Distal (>10kb) Multiome | 813 | |
| chr11:75,582,925–75,584,268 | 184.4 kb | Distal (>10kb) Multiome | 489 | |
| chr11:75,667,242–75,669,059 | 268.1 kb | Distal (>10kb) Multiome | 328 |
Genomic view of the RPS3 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.