Subcellular - YARS1 - The Human Protein Atlas

GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	YARS1
Gene descriptionⁱ Full gene name according to HGNC.	Tyrosyl-tRNA synthetase 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Disease related genes Enzymes Human disease related genes Metabolic proteins Plasma proteins Potential drug targets
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Main locationⁱ Main subcellular location(s) and reliability score(s) for the encoded protein(s) in human cells. The main location(s) may be characterized by presence in all tested cell lines and/or ihigher staining intensity compared to the potential additional location(s). 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 Cytosol (supported)
Additional locationⁱ Additonal subcellular location(s) for the encoded protein(s) in human cells. The additional location(s) may not be present i all cell lines and may have lower staining intensity compared to the main location(s). 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.	In addition localized to the Nuclear bodies (supported)
Single-cell variationⁱ Single-cell variations in protein expression levels or distribution observed between cells within the same images of human cells stained by immunocytochemistry.	Single-cell variation in protein expression observed.
Cell cycle dependencyⁱ Cell-cycle dependance of single-cell varations in RNA and/or protein expression as observed in an additional assay for characterizing single-cell varations. "NA" indicates a lack of such data.	Variation in protein and transcript expression do not correlate to the cell-cycle.
siRNAⁱ Validation score for the subcellular location(s) of the encoded proteins(s) according to siRNA validation.	The location(s) are Enhanced based on siRNA mediated gene silencing.
Reliability scoreⁱ Overall gene reliability score for the subcellular location(s) of the encoded protein(s). The score indicates the level of reliability of the annotated protein localization based on agreement with available experimental gene/protein characterization data in the UniProtKB/Swiss-Prot database and presence of antibody validation assays for immunocytochemistry.	Supported
Antibodiesⁱ Antibodies used for this assay. Click on an antibody for more information.	HPA018950 , HPA018954
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ASSAYSⁱ

RNA expression

Human cells

Single cell variation

siRNA

RNA EXPRESSION OVERVIEWⁱ

Organ

Origin

Category

Expression

Alphabetical

Cell lines ordered by organ of phenotypic resemblance.

HUMAN CELLSⁱ

Summaryⁱ

Mainly localized to the cytosol. In addition localized to the nuclear bodies.

Main locationⁱ

Cytosol (supported)

Additional locationⁱ

Nuclear bodies (supported)


	Toggle channelsⁱ Buttons for turning on and off the different channels in the multi-color images. 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

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.	Cell line RNA Expression (nTPM)ⁱ RNA expression level in the cell line based on normalised RNA sequencing data. Genes with a value above 1 NX are considered to be expressed.	Locationⁱ Observed subcellular location(s).	Single-cell variationⁱ Observed single-cell variation(s) in the staining pattern. Variation in protein expression levels can be observed as varaiations in the intensity of the immunofluorescent signal, while spatial variations can be observed as variations in subcellular distribution of the protein.
HPA018950	A-431	156.9	Nuclear bodies	Yes
HPA018950	A-431	156.9	Cytosol	Yes
HPA018950	U-251MG	113.5	Nuclear bodies	Yes
HPA018950	U-251MG	113.5	Cytosol	Yes
HPA018950	U2OS	112.7	Nuclear bodies	Yes
HPA018950	U2OS	112.7	Cytosol	Yes
HPA018954	A-431	156.9	Cytosol
HPA018954	U-251MG	113.5	Cytosol
HPA018954	U2OS	112.7	Cytosol

SINGLE CELL VARIATIONⁱ

Summaryⁱ

Variation in protein and transcript expression do not correlate to the cell-cycle.

Locationⁱ

Nuclear bodies, Cytosol

Protein expression across cell cycleⁱ

HPA018950: U-2 OS FUCCI	HPA018950: U-2 OS FUCCI
Toggle channelsⁱ Buttons for turning on and off the different channels in the multi-color images.

RNA expression across cell cycleⁱ

siRNA VALIDATIONⁱ

Antibodyⁱ

HPA018954

siRNA validationⁱ

Enhanced: Significant downregulation > 25% by both siRNA:s.

Analysis performed inⁱ

Cytoplasmic region of segmented cells in 10x-images

siRNA 1ⁱ

siRNA 2ⁱ

RFIⁱ

49%

44%

p-valueⁱ

< 0.01


	Toggle channelsⁱ Buttons for turning on and off the different channels in the multi-color images. The intensity toggle shows the pixel intensity range in 16 different colors for the selected channel. The antibody and intensity channel toggle can be used to further illustrate the intensity downregulation when comparing images from scrambled and targeting siRNA samples in the images. The object toggle shows the segmentation compartment in which the change in intensity after siRNA downregulation was measured.	Low High

Antibodyⁱ Antibody used for analysis. Clicking the antibody ID links to the antibody validation page.	Sampleⁱ siRNA that was used for the analysis.	Cell lineⁱ Cell line used for analysis. Read more about the cell lines in the Human Protein Atlas.
HPA018954	siRNA 1	U2OS
HPA018954	siRNA 2	U2OS
HPA018954	scrambled	U2OS