Single cell type - SPCS2 - 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.	SPCS2
Gene descriptionⁱ Full gene name according to HGNC.	Signal peptidase complex subunit 2
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Metabolic proteins 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,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	6

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Plasma cells - Humoral immune response (mainly)
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 (Plasma cells)
Immune 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 immune cell specificity
Immune 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. Read more	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. Read more	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

SINGLE CELL TYPESⁱ A summary of single cell RNA (nTPM) 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 (Plasma cells)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

SPCS2 is part of cluster 55 Plasma cells - Humoral immune response with confidenceⁱ 0.93
379 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
ALG5	ALG5 dolichyl-phosphate beta-glucosyltransferase	0.7806	55
LMAN2	Lectin, mannose binding 2	0.7666	55
LMAN1	Lectin, mannose binding 1	0.7477	55
TMED10	Transmembrane p24 trafficking protein 10	0.7061	55
PDIA6	Protein disulfide isomerase family A member 6	0.6992	55
DDOST	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase non-catalytic subunit	0.6940	55
HSP90B1	Heat shock protein 90 beta family member 1	0.6595	55
TMEM258	Transmembrane protein 258	0.6551	55
DERL2	Derlin 2	0.6368	26
OSTC	Oligosaccharyltransferase complex non-catalytic subunit	0.6277	55
DAD1	Defender against cell death 1	0.6167	55
SSR3	Signal sequence receptor subunit 3	0.6147	55
PDIA4	Protein disulfide isomerase family A member 4	0.6128	55
SPCS3	Signal peptidase complex subunit 3	0.6061	55
HM13	Histocompatibility minor 13	0.6047	55

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated 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 Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	192.3 nTPM
Breast	226.7 nTPM
Adipose tissue	158.0 nTPM

Alveolar cells type 1	86.6 nTPM
Lung	86.6 nTPM

Alveolar cells type 2	143.6 nTPM
Lung	143.6 nTPM

Astrocytes	40.5 nTPM
Brain	40.5 nTPM

B-cells	323.2 nTPM
Liver	1068.8 nTPM
Breast	708.8 nTPM
PBMC	259.8 nTPM
Kidney	223.8 nTPM
Stomach	204.4 nTPM
Spleen	183.4 nTPM
Lymph node	160.2 nTPM
Bone marrow	155.3 nTPM
Colon	135.8 nTPM
Adipose tissue	131.8 nTPM

Basal squamous epithelial cells	129.7 nTPM
Esophagus	129.7 nTPM

Dendritic cells	233.5 nTPM
PBMC	255.1 nTPM
Breast	241.3 nTPM
Adipose tissue	204.0 nTPM

Endothelial cells	181.4 nTPM
Pancreas	266.4 nTPM
Prostate	264.8 nTPM
Skin	226.8 nTPM
Placenta	224.6 nTPM
Breast	196.3 nTPM
Eye	182.1 nTPM
Liver	177.9 nTPM
Ovary	167.1 nTPM
Lung	165.3 nTPM
Testis	150.8 nTPM
Endometrium	149.4 nTPM
Skeletal muscle	147.7 nTPM
Esophagus	132.4 nTPM
Heart muscle	88.6 nTPM

Enteroendocrine cells	125.4 nTPM
Colon	163.4 nTPM
Rectum	87.4 nTPM

Erythroid cells	191.5 nTPM
Liver	272.8 nTPM
Bone marrow	110.1 nTPM

Fibroblasts	239.4 nTPM
Prostate	484.8 nTPM
Skin	330.0 nTPM
Adipose tissue	289.3 nTPM
Breast	277.4 nTPM
Placenta	258.2 nTPM
Esophagus	207.1 nTPM
Stomach	197.5 nTPM
Lung	174.3 nTPM
Skeletal muscle	156.9 nTPM
Ovary	140.2 nTPM
Heart muscle	117.1 nTPM

Intestinal goblet cells	255.1 nTPM
Colon	470.2 nTPM
Small intestine	149.1 nTPM
Rectum	145.9 nTPM

Macrophages	159.7 nTPM
Pancreas	347.1 nTPM
Kidney	229.9 nTPM
Endometrium	204.0 nTPM
Prostate	199.5 nTPM
Breast	175.2 nTPM
Adipose tissue	162.0 nTPM
Ovary	160.3 nTPM
Lung	142.6 nTPM
Testis	141.7 nTPM
Spleen	122.4 nTPM
Esophagus	121.2 nTPM
Bone marrow	121.2 nTPM
Stomach	111.3 nTPM
Skeletal muscle	101.7 nTPM
PBMC	54.6 nTPM

Paneth cells	140.0 nTPM
Colon	154.8 nTPM
Small intestine	138.9 nTPM
Rectum	126.4 nTPM

Plasma cells	933.5 nTPM
Stomach	1423.4 nTPM
Esophagus	1127.2 nTPM
Spleen	902.2 nTPM
Bone marrow	776.2 nTPM
Adipose tissue	438.6 nTPM

Cholangiocytes	214.4 nTPM
Liver	214.4 nTPM

Collecting duct cells	239.1 nTPM
Kidney	239.1 nTPM

Cone photoreceptor cells	52.1 nTPM
Eye	52.1 nTPM

Cytotrophoblasts	330.8 nTPM
Placenta	330.8 nTPM

Respiratory ciliated cells	231.1 nTPM
Bronchus	347.0 nTPM
Lung	115.2 nTPM

Smooth muscle cells	253.6 nTPM
Bronchus	764.8 nTPM
Pancreas	344.3 nTPM
Prostate	225.4 nTPM
Skin	210.6 nTPM
Breast	203.7 nTPM
Ovary	187.2 nTPM
Esophagus	178.3 nTPM
Adipose tissue	174.4 nTPM
Endometrium	170.5 nTPM
Heart muscle	167.5 nTPM
Skeletal muscle	162.8 nTPM

T-cells	204.6 nTPM
Prostate	374.0 nTPM
Kidney	297.7 nTPM
Ovary	287.0 nTPM
Skin	265.7 nTPM
Lung	227.8 nTPM
Colon	209.6 nTPM
Liver	207.7 nTPM
Breast	204.2 nTPM
Stomach	201.5 nTPM
Adipose tissue	187.1 nTPM
PBMC	179.3 nTPM
Endometrium	167.0 nTPM
Skeletal muscle	164.2 nTPM
Spleen	157.7 nTPM
Bone marrow	143.2 nTPM
Lymph node	119.5 nTPM
Esophagus	85.2 nTPM

Undifferentiated cells	189.5 nTPM
Colon	288.9 nTPM
Small intestine	152.5 nTPM
Rectum	126.9 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC