Cell type atlas - CST3 - The Human Protein Atlas

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CST3

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.	CST3
Gene descriptionⁱ Full gene name according to HGNC.	Cystatin C
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes 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	Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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	Cell type enhanced (Macrophages, Kupffer cells)
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	Group enriched (myeloid DC, intermediate monocyte, classical monocyte, plasmacytoid DC, non-classical monocyte)
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 many
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.	Cell line enhanced (ASC diff, ASC TERT1)
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 many
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: Cell type enhanced (Macrophages, Kupffer cells)

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	107 NX
Lung	107 NX

Alveolar cells type 2	165 NX
Lung	165 NX

B-cells	122 NX
Colon	205 NX
Liver	122 NX
Kidney	94 NX

Basal glandular cells	459 NX
Prostate	459 NX

Basal keratinocytes	838 NX
Skin	838 NX

Bipolar cells	35 NX
Eye	35 NX

Cardiomyocytes	213 NX
Heart muscle	213 NX

Cholangiocytes	1646 NX
Liver	1646 NX

Ciliated cells	66 NX
Lung	66 NX

Club cells	135 NX
Lung	135 NX

Collecting duct cells	609 NX
Kidney	609 NX

Cone photoreceptor cells	28 NX
Eye	28 NX

Cytotrophoblasts	430 NX
Placenta	430 NX

Distal tubular cells	352 NX
Kidney	352 NX

Ductal cells	407 NX
Pancreas	407 NX

Early spermatids	35 NX
Testis	35 NX

Endothelial cells	721 NX
Skin	1567 NX
Eye	1002 NX
Placenta	938 NX
Testis	759 NX
Prostate	721 NX
Liver	414 NX
Pancreas	236 NX
Heart muscle	153 NX
Lung	82 NX

Enterocytes	2161 NX
Small intestine	3308 NX
Rectum	1911 NX
Colon	1542 NX

Erythroid cells	23 NX
Liver	23 NX

Exocrine glandular cells	693 NX
Pancreas	693 NX

Extravillous trophoblasts	270 NX
Placenta	270 NX

Fibroblasts	1052 NX
Skin	2935 NX
Prostate	2552 NX
Placenta	787 NX
Heart muscle	588 NX
Lung	243 NX

Glandular cells	865 NX
Prostate	865 NX

Granulocytes	358 NX
Colon	505 NX
Lung	212 NX

Hepatocytes	2073 NX
Liver	2073 NX

Hofbauer cells	1660 NX
Placenta	1660 NX

Horizontal cells	46 NX
Eye	46 NX

Intestinal endocrine cells	848 NX
Rectum	934 NX
Colon	761 NX

Ito cells	529 NX
Liver	529 NX

Kupffer cells	3434 NX
Liver	3434 NX

Late spermatids	96 NX
Testis	96 NX

Leydig cells	1975 NX
Testis	1975 NX

Macrophages	4110 NX
Skin	20456 NX
Kidney	5642 NX
Prostate	4958 NX
Testis	3263 NX
Pancreas	1074 NX
Lung	794 NX

Melanocytes	1483 NX
Skin	1483 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	256 NX
Pancreas	256 NX

Mucus-secreting cells	1276 NX
Rectum	1538 NX
Colon	1318 NX
Small intestine	988 NX

Muller glia cells	131 NX
Eye	131 NX

Pancreatic endocrine cells	997 NX
Pancreas	997 NX

Paneth cells	2367 NX
Colon	2652 NX
Small intestine	2367 NX
Rectum	1320 NX

Peritubular cells	1683 NX
Testis	1683 NX

Proximal tubular cells	940 NX
Kidney	940 NX

Rod photoreceptor cells	35 NX
Eye	35 NX

Sertoli cells	2160 NX
Testis	2160 NX

Smooth muscle cells	728 NX
Prostate	1713 NX
Skin	996 NX
Pancreas	494 NX
Heart muscle	276 NX

Spermatocytes	83 NX
Testis	83 NX

Spermatogonia	461 NX
Testis	461 NX

Suprabasal keratinocytes	719 NX
Skin	719 NX

Syncytiotrophoblasts	392 NX
Placenta	392 NX

T-cells	90 NX
Skin	512 NX
Prostate	135 NX
Lung	109 NX
Kidney	91 NX
Liver	64 NX
Colon	61 NX

Undifferentiated cells	866 NX
Rectum	1188 NX
Colon	778 NX
Small intestine	686 NX

Urothelial cells	802 NX
Prostate	802 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

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