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. The protein belongs to the S25E family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for RPS25. 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 = RPS25 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 RPS25, 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 |
|---|---|---|---|---|
| chr11:118,689,268–118,690,813 | 328.2 kb | Distal (>10kb) Multiome HiCAR | 804 | |
| chr11:118,789,603–118,790,362 | 228.5 kb | Distal (>10kb) Multiome | 293 | |
| chr11:118,790,448–118,793,117 | 225.4 kb | Distal (>10kb) Multiome | 958 | |
| chr11:118,907,074–118,907,685 | 111.0 kb | Distal (>10kb) Multiome | 491 | |
| chr11:118,909,181–118,909,816 | 109.0 kb | Distal (>10kb) Multiome | 326 | |
| chr11:118,909,976–118,911,609 | 107.7 kb | Distal (>10kb) Multiome | 652 | |
| chr11:118,911,717–118,912,963 | 106.1 kb | Distal (>10kb) Multiome | 689 | |
| chr11:118,916,429–118,917,335 | 101.4 kb | Distal (>10kb) Multiome | 355 | |
| chr11:118,917,640–118,918,851 | 99.9 kb | Distal (>10kb) Multiome | 522 | |
| chr11:118,925,703–118,926,356 | 92.3 kb | Distal (>10kb) Multiome | 595 | |
| chr11:118,927,947–118,930,852 | 88.9 kb | Distal (>10kb) Multiome | 892 | |
| chr11:118,997,538–118,998,797 | 20.3 kb | Distal (>10kb) Multiome | 798 | |
| chr11:119,018,081–119,019,265 | 190 bp | At TSS Multiome | 897 | |
| chr11:119,028,269–119,028,679 | 9.9 kb | Proximal (<10kb) | 68 | |
| chr11:119,029,885–119,031,330 | 12.6 kb | Distal (>10kb) Multiome | 876 | |
| chr11:119,056,436–119,057,778 | 38.9 kb | Distal (>10kb) Multiome | 815 | |
| chr11:119,067,446–119,068,100 | 49.4 kb | Distal (>10kb) Multiome | 762 | |
| chr11:119,084,563–119,085,756 | 66.7 kb | Distal (>10kb) Multiome | 846 | |
| chr11:119,093,969–119,096,070 | 77.2 kb | Distal (>10kb) Multiome | 1046 | |
| chr11:119,101,351–119,102,791 | 83.8 kb | Distal (>10kb) Multiome | 871 | |
| chr11:119,106,906–119,107,993 | 89.0 kb | Distal (>10kb) Multiome | 650 | |
| chr11:119,120,857–119,122,037 | 103.1 kb | Distal (>10kb) Multiome | 787 | |
| chr11:119,144,795–119,145,355 | 126.7 kb | Distal (>10kb) Multiome | 230 | |
| chr11:119,148,816–119,149,933 | 131.2 kb | Distal (>10kb) Multiome | 262 | |
| chr11:119,168,601–119,169,645 | 150.6 kb | Distal (>10kb) Multiome | 794 | |
| chr11:119,205,241–119,207,150 | 187.8 kb | Distal (>10kb) Multiome | 695 | |
| chr11:119,315,017–119,315,819 | 297.0 kb | Distal (>10kb) Multiome | 270 | |
| chr11:119,316,693–119,317,760 | 298.9 kb | Distal (>10kb) Multiome | 463 |
Genomic view of the RPS25 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.