Cell type atlas - SDC1 - The Human Protein Atlas

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SDC1

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.	SDC1
Gene descriptionⁱ Full gene name according to HGNC.	Syndecan 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes CD markers Plasma proteins Transporters
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,Membrane,Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4

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 (Hepatocytes, Urothelial cells, Cholangiocytes)
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	Cell type enriched (memory B-cell)
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 single
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 (HBEC3-KT, hTCEpi, U-251 MG, U-266/70, U-266/84)
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 (Hepatocytes, Urothelial cells, Cholangiocytes)

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	86 NX
Lung	86 NX

Alveolar cells type 2	91 NX
Lung	91 NX

B-cells	3 NX
Liver	58 NX
Kidney	5 NX
Colon	2 NX

Basal glandular cells	136 NX
Prostate	136 NX

Basal keratinocytes	101 NX
Skin	101 NX

Bipolar cells	0 NX
Eye	0 NX

Cardiomyocytes	1 NX
Heart muscle	1 NX

Cholangiocytes	298 NX
Liver	298 NX

Ciliated cells	3 NX
Lung	3 NX

Club cells	64 NX
Lung	64 NX

Collecting duct cells	40 NX
Kidney	40 NX

Cone photoreceptor cells	0 NX
Eye	0 NX

Cytotrophoblasts	2 NX
Placenta	2 NX

Distal tubular cells	27 NX
Kidney	27 NX

Ductal cells	55 NX
Pancreas	55 NX

Early spermatids	0 NX
Testis	0 NX

Endothelial cells	1 NX
Skin	11 NX
Prostate	11 NX
Liver	5 NX
Pancreas	4 NX
Heart muscle	1 NX
Placenta	1 NX
Testis	1 NX
Lung	0 NX
Eye	0 NX

Enterocytes	103 NX
Rectum	165 NX
Small intestine	99 NX
Colon	74 NX

Erythroid cells	23 NX
Liver	23 NX

Exocrine glandular cells	19 NX
Pancreas	19 NX

Extravillous trophoblasts	43 NX
Placenta	43 NX

Fibroblasts	10 NX
Skin	12 NX
Placenta	11 NX
Prostate	10 NX
Lung	3 NX
Heart muscle	0 NX

Glandular cells	42 NX
Prostate	42 NX

Granulocytes	6 NX
Lung	12 NX
Colon	0 NX

Hepatocytes	520 NX
Liver	520 NX

Hofbauer cells	2 NX
Placenta	2 NX

Horizontal cells	21 NX
Eye	21 NX

Intestinal endocrine cells	10 NX
Rectum	14 NX
Colon	7 NX

Ito cells	7 NX
Liver	7 NX

Kupffer cells	10 NX
Liver	10 NX

Late spermatids	0 NX
Testis	0 NX

Leydig cells	1 NX
Testis	1 NX

Macrophages	5 NX
Prostate	13 NX
Skin	8 NX
Kidney	6 NX
Lung	6 NX
Pancreas	2 NX
Testis	1 NX

Melanocytes	20 NX
Skin	20 NX

Mixed cell types	NX
Pancreas	NX

Mixed immune cells	NX
Heart muscle	NX

Monocytes	1 NX
Pancreas	1 NX

Mucus-secreting cells	72 NX
Rectum	82 NX
Colon	56 NX
Small intestine	48 NX

Muller glia cells	0 NX
Eye	0 NX

Pancreatic endocrine cells	67 NX
Pancreas	67 NX

Paneth cells	74 NX
Rectum	78 NX
Small intestine	74 NX
Colon	60 NX

Peritubular cells	1 NX
Testis	1 NX

Proximal tubular cells	68 NX
Kidney	68 NX

Rod photoreceptor cells	0 NX
Eye	0 NX

Sertoli cells	0 NX
Testis	0 NX

Smooth muscle cells	7 NX
Pancreas	38 NX
Prostate	16 NX
Heart muscle	6 NX
Skin	5 NX

Spermatocytes	1 NX
Testis	1 NX

Spermatogonia	13 NX
Testis	13 NX

Suprabasal keratinocytes	200 NX
Skin	200 NX

Syncytiotrophoblasts	210 NX
Placenta	210 NX

T-cells	4 NX
Prostate	22 NX
Lung	16 NX
Liver	5 NX
Colon	4 NX
Skin	4 NX
Kidney	3 NX

Undifferentiated cells	67 NX
Colon	95 NX
Rectum	70 NX
Small intestine	63 NX

Urothelial cells	356 NX
Prostate	356 NX

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

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