Cell atlas - UBE3D - The Human Protein Atlas

GENERAL INFORMATIONⁱ General description of the gene and encoded protein(s) using information from HGNC and Ensembl, as well as predictions made as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Gene name according to HGNC.	UBE3D
Gene description	Ubiquitin protein ligase E3D
Protein classⁱ Protein class(es) of the gene product according to selected gene lists. List of protein classes.	Enzymes
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 transcribed from this 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.
Summaryⁱ Show complete data for human cells assay. The location(s) are highlighted in the illustration on the right.	Localized to the rods & rings.
RNA cell specificityⁱ 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 NX values in all analyzed cell lines. Read more	Low cell line specificity
RNA cell distributionⁱ Classification of genes according to distribution of their RNA expression among the cell lines within the HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected 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
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 Rods & Rings (approved)

DATA RELIABILITYⁱ Reliability score for the manual annotation of subcellular localization of the protein(s) and antibodies used for this assay. Read more
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. Read more	Approved
Antibodiesⁱ Antibodies used for this assay.	HPA027231
	SHOW MORE

ASSAYSⁱ

RNA expression

Human cells

RNA EXPRESSION OVERVIEWⁱ

RNA cell line 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 NX values in all analyzed cell lines.

Read more
: Low cell line specificity

Organ

Origin

Category

Expression

Alphabetical

Cell lines ordered by organ of phenotypic resemblance.

HUMAN CELLSⁱ

Summaryⁱ

Localized to the rods & rings.

Main locationⁱ

Rods & Rings (approved)


	Toggle channelsⁱ 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.	Cell line RNA Expression (NX)ⁱ Information about the gene expression level in the cell line using normalised RNA sequence data. Genes with a value above 1 NX are considered to be expressed. The HPA RNA-seq data is described more in detail in Assays & Annotation.	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.
	HPA027231	HEK 293	16.5	Rods & Rings
	HPA027231	RH-30	8.5	Rods & Rings