RPS3
ribosomal protein S3 | FLJ26283, FLJ27450, MGC87870, S3, uS3

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]

Member of: DE-1 DE-1.1 Developmental clusters: GC3
Biological processes 97 terms
DNA N-glycosylase activity (GO:0019104)DNA N-glycosylase activity (GO:0019104)DNA binding (GO:0003677)DNA damage response (GO:0006974)DNA endonuclease activity (GO:0004520)DNA repair (GO:0006281)DNA-(apurinic or apyrimidinic site) endonuclease activity (GO:0003906)DNA-(apurinic or apyrimidinic site) endonuclease activity (GO:0003906)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription factor binding (GO:0140297)Hsp70 protein binding (GO:0030544)Hsp90 protein binding (GO:0051879)NF-kappaB complex (GO:0071159)RNA binding (GO:0003723)RNA binding (GO:0003723)RNA binding (GO:0003723)base-excision repair (GO:0006284)cellular response to hydrogen peroxide (GO:0070301)cellular response to reactive oxygen species (GO:0034614)chromosome segregation (GO:0007059)class I DNA-(apurinic or apyrimidinic site) endonuclease activity (GO:0140078)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasmic translation (GO:0002181)cytoplasmic translation (GO:0002181)cytoplasmic translational initiation (GO:0002183)cytosol (GO:0005829)cytosol (GO:0005829)cytosolic ribosome (GO:0022626)cytosolic ribosome (GO:0022626)cytosolic small ribosomal subunit (GO:0022627)cytosolic small ribosomal subunit (GO:0022627)cytosolic small ribosomal subunit (GO:0022627)cytosolic small ribosomal subunit (GO:0022627)damaged DNA binding (GO:0003684)endoplasmic reticulum (GO:0005783)enzyme binding (GO:0019899)extracellular exosome (GO:0070062)focal adhesion (GO:0005925)iron-sulfur cluster binding (GO:0051536)kinase binding (GO:0019900)mRNA binding (GO:0003729)membrane (GO:0016020)microtubule binding (GO:0008017)mitochondrial inner membrane (GO:0005743)mitochondrial inner membrane (GO:0005743)mitochondrial matrix (GO:0005759)mitotic spindle (GO:0072686)negative regulation of DNA repair (GO:0045738)negative regulation of protein ubiquitination (GO:0031397)negative regulation of translation (GO:0017148)nucleolus (GO:0005730)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)oxidized purine DNA binding (GO:0032357)oxidized pyrimidine DNA binding (GO:0032358)plasma membrane (GO:0005886)positive regulation of DNA repair (GO:0045739)positive regulation of DNA-templated transcription initiation (GO:2000144)positive regulation of apoptotic signaling pathway (GO:2001235)positive regulation of apoptotic signaling pathway (GO:2001235)positive regulation of base-excision repair (GO:1905053)positive regulation of gene expression (GO:0010628)positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)positive regulation of microtubule polymerization (GO:0031116)positive regulation of non-canonical NF-kappaB signal transduction (GO:1901224)positive regulation of transcription by RNA polymerase II (GO:0045944)postsynaptic density (GO:0014069)postsynaptic density (GO:0014069)protein binding (GO:0005515)protein kinase A binding (GO:0051018)protein kinase binding (GO:0019901)regulation of apoptotic process (GO:0042981)response to TNF agonist (GO:0061481)ribonucleoprotein complex (GO:1990904)ribosome (GO:0005840)ruffle membrane (GO:0032587)small ribosomal subunit (GO:0015935)small ribosomal subunit rRNA binding (GO:0070181)spindle (GO:0005819)spindle assembly (GO:0051225)structural constituent of ribosome (GO:0003735)structural constituent of ribosome (GO:0003735)structural constituent of ribosome (GO:0003735)structural constituent of ribosome (GO:0003735)structural constituent of ribosome (GO:0003735)supercoiled DNA binding (GO:0097100)synapse (GO:0045202)translation (GO:0006412)tubulin binding (GO:0015631)ubiquitin-like protein conjugating enzyme binding (GO:0044390)
Expression (TPM)
RPS3 — as a Regulated Gene

TFs regulating RPS3 0 TFs

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.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to RPS3

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

Genome Browser

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.

chr11:75,230,428 – 75,679,059
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq