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Show complete data for human cells assay. The location(s) are highlighted in the illustration on the right.
Localized to the cytosol & endoplasmic reticulum.
RNA cell categoryi
The cell lines in the Human Protein Atlas have been analyzed by RNA-seq to estimate the transcript abundance of each protein-coding gene. The RNA-seq data was then used to classify all genes according to their cell line-specific expression into one of six different categories, defined based on the total set of all TPM values in all analyzed cell lines.
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
Main locationi
The main location is characterized by presence in all tested cell lines and/or increased intensity compared to other locations. It is highlighted in the illustration to the right. If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively.
Localized to the Endoplasmic reticulum (enhanced), Cytosol (enhanced)
DATA RELIABILITY
Reliability scorei
A reliability score is set for all genes and indicates the level of reliability of the analyzed protein expression pattern based on available protein/RNA/gene characterization data. The reliability of the annotated protein expression data is also scored depending on similarity in immunostaining patterns and consistency with available experimental gene/protein characterization data in the UniProtKB/Swiss-Prot database.
Below is an overview of RNA expression data generated in the HPA project. The analyzed cell lines are divided into 12 color-coded groups according to the organ they were obtained from. By clicking the toolbars in the top right corner it is possible to sort the cell lines in the chart by different criteria: the organ and the origin that the cell line was obtained from, the category of the cell line according to cellosaurus, alphabetically or by descending RNA expression. Detailed information about a specific cell line can be accessed by hovering over the corresponding bar in the chart. The RNA-sequencing results generated in the HPA are reported as number of Transcripts per Kilobase Million (TPM). In the Human Protein Atlas a TPM value of 1.0 is defined as a treshhold for expression of the corresponding protein.
The cell lines in the Human Protein Atlas have been analyzed by RNA-seq to estimate the transcript abundance of each protein-coding gene. The RNA-seq data was then used to classify all genes according to their cell line-specific expression into one of six different categories, defined based on the total set of all TPM values in all analyzed cell lines.
Cell lines sorted after organ of phenotypic resemblance.
Cell lines sorted after biological source for establishment.
Cell lines sorted after the cell line category according to Cellosaurus.
Cell lines sorted on descending RNA expression.
Cell lines sorted alphabetically.
HUMAN CELLSi
The "human cells" section gives an overview about the subcellular location of the protein of interest obtained by indirect immunofluorescence microscopy, an antibody-based protein-visualization technique. The immunofluorescent analysis is carried out in three different cell lines, one of them always being U-2 OS. A selection of immunofluorescent images is displayed below. Three different organelle probes are displayed as different channels in the multicolor images - nucleus stained in blue, microtubules in red and ER in yellow. The antibody staining targeting the protein of interest is shown in green. By using the toggle channel buttons, the different channels can be turned on and off. For the selection of the images to compare, use the checkboxes next to the images at the bottom. Three images can be compared at a time. All images are clickable for an enlarged view. The selected image will appear in large size and miniature images with all other staining results for this gene will be listed at the top left of the image. The selected miniature image has an orange overlay. For cell structure reference, visit the cell dictionary.
Summaryi
Summary of the immunofluorescent analysis in all studied cell lines with all tested antibodies.
Localized to the cytosol & endoplasmic reticulum.
Main locationi
The main location is characterized by presence in all tested cell lines and/or increased intensity compared to other locations.
Three different organelle probes are displayed as different channels in the multicolor images - nucleus stained in blue, microtubules in red and ER in yellow. The antibody staining targeting the protein of interest is shown in green. By using the "toggle channels"-buttons, the different channels can be turned on and off. The intensity toggle shows the pixel intensity range in 16 different colors for the selected channel. The object toggle shows the computational segmentation of the cells used for further analysis in the HPA project. For samples where cell cycle dependency for the protein is suggested according to a correlation assay the predicted cell cycle position of each cell is displayed when using the object toggle.
Low
High
G1
S
G2
M
N/A
Thumbnaili
Representative images for the assay. Three images can be compared at the same time. To change which images to compare, use the checkboxes next to the images below. All images are clickable for an enlarged view. The selected image will appear in large size and miniature images with all other staining results for this gene will be listed at the top left of the image. The selected miniature image has an orange overlay.
Antibodyi
Antibody used for analysis. Clicking the antibody ID links to the antibody validation page.
Cell linei
Cell line used for analysis. Read more about the cell lines in the Human Protein Atlas.
Locationi
Location(s) annotated in the corresponding cell line.
Single-cell variationi
As the images in the Cell Atlas provide single cell resolution, variations in protein expression patterns from cell to cell can be observed. A single-cell variation can either be observed in the intensity of the immunofluorescent signal or in the spatial distribution pattern of the protein. This column contains information about whether and for which of the annotated locations a single-cell variation pattern was manually annotated.
Cell cycle dependent variationi
A likely cause for single-cell variation in the immunofluorescent images is cell cycle dependency. This column contains information about whether the manually observed cell-to-cell variation pattern correlates with cell cycle progression.
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)
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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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