Single cell type - SPCS1 - 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.	SPCS1
Gene descriptionⁱ Full gene name according to HGNC.	Signal peptidase complex subunit 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Metabolic 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	Membrane
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 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	Spermatids - Spermatogenesis (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 (Late spermatids)
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 (Late spermatids)

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

SPCS1 is part of cluster 25 Spermatids - Spermatogenesis with confidenceⁱ 1
458 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
ZNF706	Zinc finger protein 706	0.5711	25
RABAC1	Rab acceptor 1	0.5659	25
NLRP7	NLR family pyrin domain containing 7	0.5632	65
CHID1	Chitinase domain containing 1	0.5432	13
TMEM147	Transmembrane protein 147	0.5334	10
UBL7	Ubiquitin like 7	0.5216	10
TECR	Trans-2,3-enoyl-CoA reductase	0.5158	10
PSMD6	Proteasome 26S subunit, non-ATPase 6	0.4907	10
CREB3	CAMP responsive element binding protein 3	0.4857	25
ALG3	ALG3 alpha-1,3- mannosyltransferase	0.4821	55
OGFOD2	2-oxoglutarate and iron dependent oxygenase domain containing 2	0.4802	25
DPP7	Dipeptidyl peptidase 7	0.4791	25
PTPMT1	Protein tyrosine phosphatase mitochondrial 1	0.4759	25
HIF1AN	Hypoxia inducible factor 1 subunit alpha inhibitor	0.4749	25
PRDX4	Peroxiredoxin 4	0.4684	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	172.5 nTPM
Breast	208.7 nTPM
Adipose tissue	136.3 nTPM

Alveolar cells type 1	64.1 nTPM
Lung	64.1 nTPM

Alveolar cells type 2	104.2 nTPM
Lung	104.2 nTPM

Astrocytes	23.8 nTPM
Brain	23.8 nTPM

B-cells	282.3 nTPM
Breast	738.2 nTPM
Liver	649.8 nTPM
Kidney	261.8 nTPM
PBMC	244.1 nTPM
Stomach	184.0 nTPM
Spleen	172.0 nTPM
Lymph node	145.2 nTPM
Bone marrow	144.7 nTPM
Colon	143.8 nTPM
Adipose tissue	139.3 nTPM

Basal squamous epithelial cells	136.1 nTPM
Esophagus	136.1 nTPM

Dendritic cells	488.1 nTPM
PBMC	1083.9 nTPM
Breast	213.2 nTPM
Adipose tissue	167.2 nTPM

Endothelial cells	157.6 nTPM
Placenta	255.8 nTPM
Pancreas	220.0 nTPM
Skin	192.3 nTPM
Breast	183.9 nTPM
Testis	178.4 nTPM
Eye	163.4 nTPM
Ovary	154.9 nTPM
Prostate	152.6 nTPM
Esophagus	143.9 nTPM
Skeletal muscle	139.0 nTPM
Liver	122.9 nTPM
Endometrium	118.6 nTPM
Heart muscle	93.6 nTPM
Lung	87.4 nTPM

Enteroendocrine cells	167.7 nTPM
Colon	177.7 nTPM
Rectum	157.8 nTPM

Erythroid cells	143.9 nTPM
Bone marrow	148.8 nTPM
Liver	139.0 nTPM

Fibroblasts	181.9 nTPM
Placenta	312.0 nTPM
Breast	220.4 nTPM
Adipose tissue	201.8 nTPM
Ovary	201.6 nTPM
Skin	185.8 nTPM
Heart muscle	170.4 nTPM
Esophagus	162.6 nTPM
Prostate	161.5 nTPM
Stomach	158.9 nTPM
Skeletal muscle	136.1 nTPM
Lung	90.4 nTPM

Intestinal goblet cells	291.3 nTPM
Colon	431.0 nTPM
Rectum	232.1 nTPM
Small intestine	211.0 nTPM

Macrophages	192.5 nTPM
Pancreas	324.1 nTPM
Kidney	316.1 nTPM
Testis	221.4 nTPM
Breast	220.0 nTPM
Endometrium	215.9 nTPM
Stomach	202.2 nTPM
Prostate	193.8 nTPM
Ovary	184.2 nTPM
Bone marrow	178.7 nTPM
Spleen	175.2 nTPM
Adipose tissue	161.9 nTPM
Lung	138.1 nTPM
Esophagus	130.6 nTPM
Skeletal muscle	129.0 nTPM
PBMC	95.5 nTPM

Paneth cells	274.1 nTPM
Small intestine	315.3 nTPM
Colon	273.4 nTPM
Rectum	233.7 nTPM

Plasma cells	888.8 nTPM
Stomach	1763.3 nTPM
Esophagus	1151.7 nTPM
Spleen	660.5 nTPM
Bone marrow	456.5 nTPM
Adipose tissue	412.2 nTPM

Cholangiocytes	221.6 nTPM
Liver	221.6 nTPM

Collecting duct cells	310.8 nTPM
Kidney	310.8 nTPM

Cone photoreceptor cells	118.9 nTPM
Eye	118.9 nTPM

Cytotrophoblasts	373.5 nTPM
Placenta	373.5 nTPM

Respiratory ciliated cells	374.1 nTPM
Bronchus	545.6 nTPM
Lung	202.6 nTPM

Smooth muscle cells	335.5 nTPM
Bronchus	1600.1 nTPM
Pancreas	370.7 nTPM
Heart muscle	245.9 nTPM
Breast	241.2 nTPM
Esophagus	217.1 nTPM
Skeletal muscle	192.9 nTPM
Skin	187.9 nTPM
Adipose tissue	184.1 nTPM
Ovary	178.3 nTPM
Prostate	152.9 nTPM
Endometrium	119.0 nTPM

T-cells	220.8 nTPM
Kidney	339.5 nTPM
Prostate	293.5 nTPM
Skin	290.1 nTPM
PBMC	270.3 nTPM
Stomach	233.5 nTPM
Breast	227.1 nTPM
Ovary	224.7 nTPM
Colon	221.5 nTPM
Lung	211.1 nTPM
Adipose tissue	209.3 nTPM
Liver	206.1 nTPM
Skeletal muscle	202.0 nTPM
Spleen	189.1 nTPM
Lymph node	185.2 nTPM
Bone marrow	182.1 nTPM
Endometrium	144.9 nTPM
Esophagus	124.5 nTPM

Undifferentiated cells	267.7 nTPM
Colon	329.1 nTPM
Small intestine	239.2 nTPM
Rectum	234.9 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