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RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue/cell line enriched, group enriched, tissue/cell line enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for The Cancer Genome Atlas (TCGA) data from cancer tissues and internally generated Human Protein Atlas (HPA) data from normal tissues and cell lines.
TCGA (cancer tissue):
Expressed in all
HPA (cell line):
Expressed in all
HPA (normal tissue):
Expressed in all
Protein evidencei
Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.
Evidence at protein level
Protein expression normal tissuei
A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation.
"Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile.
Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.
Antibody staining mainly consistent with RNA expression data.
Reliability score - normal tissuesi
Reliability score (score description), divided into Enhanced, Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between antibody staining pattern, available RNA-Seq and gene/protein characterization data, as well as similarity between independent antibodies targeting the same protein.
Kaplan-Meier plots for all cancers where high expression of this gene has significant (p<0.001) association with patient survival are shown in this summary. Whether the prognosis is favourable or unfavourable is indicated in brackets. Each Kaplan-Meier plot is clickable and redirects to a detailed page that includes individual expression and survival data for patients with the selected cancer.
RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).
TCGA dataseti
RNA-seq data in 17 cancer types are reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA). RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. To access cancer specific RNA and prognostic data, click on the cancer name. The cancer types are color-coded according to which type of normal organ the cancer originates from.
Antibody staining in 20 different cancers is summarized by a selection of four standard cancer tissue samples representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional fifth image can be added as a complement. The assay and annotation is described here. Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.
For each cancer, color-coded bars indicate the percentage of patients (maximum 12 patients) with high and medium protein expression level. The cancer types are color-coded according to which type of normal organ the cancer originates from. Low or not detected protein expression results in a white bar. Mouse-over function shows details about expression level and normal tissue of origin. The images and annotations can be accessed by clicking on the cancer name or protein expression bar. If more than one antibody is analyzed, the tabs at the top of the staining summary section can be used to toggle between the different antibodies.
Cancer tissues displayed weak to moderate cytoplasmic staining. Rare case of cervical cancer was strongly positive. A majority of carcinoid and lymphoma cases were negative.
GENE INFORMATIONi
Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
Gene name
RPS3 (HGNC Symbol)
Synonyms
FLJ26283, FLJ27450, MGC87870, S3
Description
Ribosomal protein S3 (HGNC Symbol)
Entrez gene summary
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]
The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.
At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.
Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more).
The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more).
If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.
Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.
The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.
The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.
The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Enzymes ENZYME proteins Lyases Ribosomal proteins Predicted intracellular proteins Plasma proteins Cancer-related genes Candidate cancer biomarkers Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000184 [nuclear-transcribed mRNA catabolic process, nonsense-mediated decay] GO:0003677 [DNA binding] GO:0003684 [damaged DNA binding] GO:0003723 [RNA binding] GO:0003729 [mRNA binding] GO:0003735 [structural constituent of ribosome] GO:0003906 [DNA-(apurinic or apyrimidinic site) lyase activity] GO:0004520 [endodeoxyribonuclease activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005730 [nucleolus] GO:0005737 [cytoplasm] GO:0005739 [mitochondrion] GO:0005743 [mitochondrial inner membrane] GO:0005759 [mitochondrial matrix] GO:0005783 [endoplasmic reticulum] GO:0005819 [spindle] GO:0005829 [cytosol] GO:0005840 [ribosome] GO:0005844 [polysome] GO:0005856 [cytoskeleton] GO:0005886 [plasma membrane] GO:0005925 [focal adhesion] GO:0006281 [DNA repair] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006364 [rRNA processing] GO:0006412 [translation] GO:0006413 [translational initiation] GO:0006417 [regulation of translation] GO:0006614 [SRP-dependent cotranslational protein targeting to membrane] GO:0006915 [apoptotic process] GO:0006974 [cellular response to DNA damage stimulus] GO:0006979 [response to oxidative stress] GO:0007049 [cell cycle] GO:0007059 [chromosome segregation] GO:0007067 [mitotic nuclear division] GO:0008017 [microtubule binding] GO:0008134 [transcription factor binding] GO:0010628 [positive regulation of gene expression] GO:0015631 [tubulin binding] GO:0015935 [small ribosomal subunit] GO:0016020 [membrane] GO:0016829 [lyase activity] GO:0017148 [negative regulation of translation] GO:0019083 [viral transcription] GO:0019899 [enzyme binding] GO:0019900 [kinase binding] GO:0019901 [protein kinase binding] GO:0022627 [cytosolic small ribosomal subunit] GO:0030529 [intracellular ribonucleoprotein complex] GO:0030544 [Hsp70 protein binding] GO:0031012 [extracellular matrix] GO:0031116 [positive regulation of microtubule polymerization] GO:0031397 [negative regulation of protein ubiquitination] GO:0032079 [positive regulation of endodeoxyribonuclease activity] GO:0032183 [SUMO binding] GO:0032357 [oxidized purine DNA binding] GO:0032358 [oxidized pyrimidine DNA binding] GO:0032587 [ruffle membrane] GO:0042769 [DNA damage response, detection of DNA damage] GO:0042981 [regulation of apoptotic process] GO:0043507 [positive regulation of JUN kinase activity] GO:0044390 [ubiquitin-like protein conjugating enzyme binding] GO:0045738 [negative regulation of DNA repair] GO:0045739 [positive regulation of DNA repair] GO:0051018 [protein kinase A binding] GO:0051225 [spindle assembly] GO:0051301 [cell division] GO:0051536 [iron-sulfur cluster binding] GO:0051879 [Hsp90 protein binding] GO:0061481 [response to TNF agonist] GO:0070062 [extracellular exosome] GO:0070181 [small ribosomal subunit rRNA binding] GO:0070301 [cellular response to hydrogen peroxide] GO:0072686 [mitotic spindle] GO:0097100 [supercoiled DNA binding] GO:1901224 [positive regulation of NIK/NF-kappaB signaling] GO:1902231 [positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage] GO:1902546 [positive regulation of DNA N-glycosylase activity] GO:1905053 [positive regulation of base-excision repair] GO:2001235 [positive regulation of apoptotic signaling pathway] GO:2001272 [positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis]
Enzymes ENZYME proteins Lyases Ribosomal proteins Predicted intracellular proteins Plasma proteins Cancer-related genes Candidate cancer biomarkers Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000184 [nuclear-transcribed mRNA catabolic process, nonsense-mediated decay] GO:0003677 [DNA binding] GO:0003684 [damaged DNA binding] GO:0003723 [RNA binding] GO:0003729 [mRNA binding] GO:0003735 [structural constituent of ribosome] GO:0003906 [DNA-(apurinic or apyrimidinic site) lyase activity] GO:0004520 [endodeoxyribonuclease activity] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005730 [nucleolus] GO:0005737 [cytoplasm] GO:0005739 [mitochondrion] GO:0005743 [mitochondrial inner membrane] GO:0005759 [mitochondrial matrix] GO:0005783 [endoplasmic reticulum] GO:0005819 [spindle] GO:0005829 [cytosol] GO:0005840 [ribosome] GO:0005844 [polysome] GO:0005856 [cytoskeleton] GO:0005886 [plasma membrane] GO:0005925 [focal adhesion] GO:0006281 [DNA repair] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006364 [rRNA processing] GO:0006412 [translation] GO:0006413 [translational initiation] GO:0006417 [regulation of translation] GO:0006614 [SRP-dependent cotranslational protein targeting to membrane] GO:0006915 [apoptotic process] GO:0006974 [cellular response to DNA damage stimulus] GO:0006979 [response to oxidative stress] GO:0007049 [cell cycle] GO:0007059 [chromosome segregation] GO:0007067 [mitotic nuclear division] GO:0008017 [microtubule binding] GO:0008134 [transcription factor binding] GO:0010628 [positive regulation of gene expression] GO:0015631 [tubulin binding] GO:0015935 [small ribosomal subunit] GO:0016020 [membrane] GO:0016829 [lyase activity] GO:0017148 [negative regulation of translation] GO:0019083 [viral transcription] GO:0019899 [enzyme binding] GO:0019900 [kinase binding] GO:0019901 [protein kinase binding] GO:0022627 [cytosolic small ribosomal subunit] GO:0030529 [intracellular ribonucleoprotein complex] GO:0030544 [Hsp70 protein binding] GO:0031012 [extracellular matrix] GO:0031116 [positive regulation of microtubule polymerization] GO:0031397 [negative regulation of protein ubiquitination] GO:0032079 [positive regulation of endodeoxyribonuclease activity] GO:0032183 [SUMO binding] GO:0032357 [oxidized purine DNA binding] GO:0032358 [oxidized pyrimidine DNA binding] GO:0032587 [ruffle membrane] GO:0042769 [DNA damage response, detection of DNA damage] GO:0042981 [regulation of apoptotic process] GO:0043507 [positive regulation of JUN kinase activity] GO:0044390 [ubiquitin-like protein conjugating enzyme binding] GO:0045738 [negative regulation of DNA repair] GO:0045739 [positive regulation of DNA repair] GO:0051018 [protein kinase A binding] GO:0051225 [spindle assembly] GO:0051301 [cell division] GO:0051536 [iron-sulfur cluster binding] GO:0051879 [Hsp90 protein binding] GO:0061481 [response to TNF agonist] GO:0070062 [extracellular exosome] GO:0070181 [small ribosomal subunit rRNA binding] GO:0070301 [cellular response to hydrogen peroxide] GO:0072686 [mitotic spindle] GO:0097100 [supercoiled DNA binding] GO:1901224 [positive regulation of NIK/NF-kappaB signaling] GO:1902231 [positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage] GO:1902546 [positive regulation of DNA N-glycosylase activity] GO:1905053 [positive regulation of base-excision repair] GO:2001235 [positive regulation of apoptotic signaling pathway] GO:2001272 [positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis]
The Human Protein Atlas project is funded
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