Subcellular - DDX21 - 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.	DDX21
Gene descriptionⁱ Full gene name according to HGNC.	DExD-box helicase 21
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes Plasma proteins
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. Read more	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. Read more	Localized to the Nucleoli rim (enhanced), Mitotic chromosome (enhanced)
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. Read more	In addition localized to the Nucleoplasm (enhanced)
Single-cell variationⁱ Single-cell variations of protein expression or distribution observed within single images in human cells. Variation in protein expression levels can be observed as varaiations in the intensity of the immunofluorescent signal, while spatial variations can be observed asvariations in subcellular distribution of the protein. Read more	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. Read more	Variation in protein expression correlates with the cell-cycle. Transcript variation is not correlated to the cell cycle.
siRNAⁱ Validation score for the subcellular location(s) of the encoded proteins(s) according to siRNA validation. Read more	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). 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. Read more	Enhanced
Antibodiesⁱ Antibodies used for this assay. Click on an antibody for more information.	HPA036592 , HPA036593
	SHOW MORE

ASSAYSⁱ

RNA expression

Human cells

Custom data

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 nucleoli rim & mitotic chromosome. In addition localized to the nucleoplasm.

Main locationⁱ

Nucleoli rim (enhanced), Mitotic chromosome (enhanced)

Additional locationⁱ

Nucleoplasm (enhanced)


	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. Read more	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 asvariations in subcellular distribution of the protein. Read more	Cell cycle dependent variationⁱ Cell-cycle dependance of observed single-cell varations in RNA and/or protein expression as observed in an additional assay for characterizing single-cell varations.
HPA036592	A-431	194.4	Nucleoplasm	Intensity
HPA036592	A-431	194.4	Nucleoli rim
HPA036592	U-251MG	142.8	Nucleoplasm
HPA036592	U-251MG	142.8	Nucleoli rim
HPA036592	U2OS	97.1	Nucleoplasm
			Nucleoli rim
			Mitotic chromosome	Intensity	Intensity
HPA036593	A-431	194.4	Nucleoli rim
HPA036593	U-251MG	142.8	Nucleoplasm	Intensity
HPA036593	U-251MG	142.8	Nucleoli rim
HPA036593	U2OS	97.1	Nucleoli rim
HPA036593	U2OS	97.1	Mitotic chromosome	Intensity	Intensity

CUSTOM DATAⁱ


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

Thumbnailⁱ Minatures of all available images. The checkboxes can be used to select which three images to compare in the window above. All images are also 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.	Assayⁱ Depending on the type of custom data the assay can be an immunofluorescent image, an immunofluorescent image stack, siRNA validation data or a time-lapse movie.	Descriptionⁱ Description of the assay used to generate the displayed custom data.
	HPA036592	HEK293	Tagged protein image	Endogenously mNG-tagged Hek293T cell lines were generated using a high-throughput CRISPR/Cas9 mediated approach in collaboration with the OpenCell team at the Chan Zuckerberg Biohub. The cells were seeded and immunostained. The specificity of the antibody was validated by co-localization with mNG-tagged protein.
	HPA036593	HEK293	Tagged protein image	Endogenously mNG-tagged Hek293T cell lines were generated using a high-throughput CRISPR/Cas9 mediated approach in collaboration with the OpenCell team at the Chan Zuckerberg Biohub. The cells were seeded and immunostained. The specificity of the antibody was validated by co-localization with mNG-tagged protein.

SINGLE CELL VARIATIONⁱ

Summaryⁱ

Variation in protein expression correlates with the cell-cycle. Transcript variation is not correlated to the cell cycle.

Protein expression
peak phaseⁱ

Intensity variationⁱ

Mitotic chromosome, Nucleoplasm

Protein expression across cell cycleⁱ

HPA036592: U-2 OS FUCCI	HPA036592: 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

HPA036593

siRNA validationⁱ

Enhanced: Significant downregulation > 25% by one siRNA.

Analysis performed inⁱ

Nuclear region of segmented cells in 10x-images

siRNA 2ⁱ

RFIⁱ

43%

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

Thumbnail 10xⁱ Minatures of all available images acquired with a 10x objective after siRNA downregulation. The checkboxes can be used to select which three images to compare in the window above. All images are also 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.	Thumbnail 40xⁱ Minatures of all available images acquired with a 40x objective after siRNA downregulation. The checkboxes can be used to select which three images to compare in the window above. All images are also 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.	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.
		HPA036593	siRNA 2	U2OS
		HPA036593	scrambled	U2OS