Cell type atlas - COPA - The Human Protein Atlas

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COPA

SUMMARY

TISSUE

CELL TYPE

PATHOLOGY

BRAIN

BLOOD

CELL

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.	COPA
Gene descriptionⁱ Full gene name according to HGNC.	Coatomer protein complex subunit alpha
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes 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,Secreted
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.
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Low cell type specificity
Blood cell specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Low cell type specificity
Blood cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines.	Low cell line specificity
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines.	Detected in all
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data. Read more	Protein predicted to be secreted

SINGLE CELL TYPESⁱ A summary of single cell RNA (NX) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types Group Expression Alphabetical RNA single cell type specificity: Low cell type specificity

SINGLE CELL TISSUESⁱ Single cell RNA in cell types from tissue are shown separately for each analyzed tissue. For easier navigation across tissues, use the grey browser on the left side of the window. Barchart shows pTPM levels in each cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ RNA expression data (NX) of tissue culture cell lines.The analyzed cell lines are divided into 16 color-coded groups according to the organ they were obtained from. Detailed information about a specific cell line is revealed by hovering over the corresponding bar in the chart. The chart is clickable and redirects to more Cell Atlas data. Read more
Organ Expression Alphabetical

Alveolar cells type 1	72 NX
Lung	72 NX

Alveolar cells type 2	41 NX
Lung	41 NX

B-cells	52 NX
Colon	66 NX
Liver	52 NX
Kidney	13 NX

Basal glandular cells	30 NX
Prostate	30 NX

Basal keratinocytes	25 NX
Skin	25 NX

Bipolar cells	50 NX
Eye	50 NX

Cardiomyocytes	41 NX
Heart muscle	41 NX

Cholangiocytes	48 NX
Liver	48 NX

Ciliated cells	54 NX
Lung	54 NX

Club cells	42 NX
Lung	42 NX

Collecting duct cells	38 NX
Kidney	38 NX

Cone photoreceptor cells	77 NX
Eye	77 NX

Cytotrophoblasts	34 NX
Placenta	34 NX

Distal tubular cells	12 NX
Kidney	12 NX

Ductal cells	45 NX
Pancreas	45 NX

Early spermatids	11 NX
Testis	11 NX

Endothelial cells	42 NX
Prostate	58 NX
Eye	56 NX
Heart muscle	46 NX
Liver	45 NX
Lung	44 NX
Testis	42 NX
Placenta	38 NX
Pancreas	32 NX
Skin	29 NX

Enterocytes	70 NX
Small intestine	89 NX
Rectum	68 NX
Colon	54 NX

Erythroid cells	0 NX
Liver	0 NX

Exocrine glandular cells	43 NX
Pancreas	43 NX

Extravillous trophoblasts	55 NX
Placenta	55 NX

Fibroblasts	50 NX
Prostate	67 NX
Lung	61 NX
Placenta	56 NX
Heart muscle	48 NX
Skin	46 NX

Glandular cells	56 NX
Prostate	56 NX

Granulocytes	44 NX
Lung	51 NX
Colon	37 NX

Hepatocytes	65 NX
Liver	65 NX

Hofbauer cells	46 NX
Placenta	46 NX

Horizontal cells	43 NX
Eye	43 NX

Intestinal endocrine cells	53 NX
Rectum	66 NX
Colon	41 NX

Ito cells	53 NX
Liver	53 NX

Kupffer cells	85 NX
Liver	85 NX

Late spermatids	5 NX
Testis	5 NX

Leydig cells	66 NX
Testis	66 NX

Macrophages	62 NX
Prostate	80 NX
Lung	69 NX
Kidney	67 NX
Testis	60 NX
Pancreas	54 NX
Skin	45 NX

Melanocytes	25 NX
Skin	25 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	32 NX
Pancreas	32 NX

Mucus-secreting cells	79 NX
Rectum	84 NX
Small intestine	76 NX
Colon	64 NX

Muller glia cells	38 NX
Eye	38 NX

Pancreatic endocrine cells	46 NX
Pancreas	46 NX

Paneth cells	46 NX
Rectum	57 NX
Small intestine	46 NX
Colon	29 NX

Peritubular cells	53 NX
Testis	53 NX

Proximal tubular cells	39 NX
Kidney	39 NX

Rod photoreceptor cells	48 NX
Eye	48 NX

Sertoli cells	39 NX
Testis	39 NX

Smooth muscle cells	52 NX
Pancreas	72 NX
Heart muscle	53 NX
Prostate	52 NX
Skin	31 NX

Spermatocytes	38 NX
Testis	38 NX

Spermatogonia	24 NX
Testis	24 NX

Suprabasal keratinocytes	28 NX
Skin	28 NX

Syncytiotrophoblasts	58 NX
Placenta	58 NX

T-cells	42 NX
Prostate	61 NX
Skin	52 NX
Colon	52 NX
Lung	49 NX
Liver	39 NX
Kidney	19 NX

Undifferentiated cells	60 NX
Rectum	67 NX
Small intestine	60 NX
Colon	45 NX

Urothelial cells	44 NX
Prostate	44 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.