Single cell type - CPNE3 - 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.	CPNE3
Gene descriptionⁱ Full gene name according to HGNC.	Copine 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	8

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	Macrophages - 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	Low cell type specificity
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	Cell line enhanced (SK-BR-3)
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: Low cell type specificity

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

CPNE3 is part of cluster 41 Macrophages - Immune response with confidenceⁱ 1
307 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
RAB7B	RAB7B, member RAS oncogene family	0.7148	41
XCR1	X-C motif chemokine receptor 1	0.6783	41
PPP1R3G	Protein phosphatase 1 regulatory subunit 3G	0.6654	41
CLEC9A	C-type lectin domain containing 9A	0.6638	41
CPVL	Carboxypeptidase vitellogenic like	0.6487	41
GPR157	G protein-coupled receptor 157	0.6442	41
GPR31	G protein-coupled receptor 31	0.6388	41
WDFY4	WDFY family member 4	0.5919	41
LORICRIN	Loricrin cornified envelope precursor protein	0.5918	41
NFE2L2	Nuclear factor, erythroid 2 like 2	0.5841	41
CXCL9	C-X-C motif chemokine ligand 9	0.5801	41
CCDC6	Coiled-coil domain containing 6	0.5772	41
HLA-DQA2	Major histocompatibility complex, class II, DQ alpha 2	0.5723	41
ANKRD20A3P	Ankyrin repeat domain 20 family member A3, pseudogene	0.5691	41
C1orf54	Chromosome 1 open reading frame 54	0.5525	41

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	84.1 nTPM
Breast	86.8 nTPM
Adipose tissue	81.4 nTPM

Alveolar cells type 1	137.8 nTPM
Lung	137.8 nTPM

Alveolar cells type 2	103.9 nTPM
Lung	103.9 nTPM

Astrocytes	23.2 nTPM
Brain	23.2 nTPM

B-cells	52.0 nTPM
Adipose tissue	77.7 nTPM
PBMC	60.0 nTPM
Colon	55.9 nTPM
Lymph node	54.1 nTPM
Stomach	54.0 nTPM
Breast	46.8 nTPM
Spleen	46.1 nTPM
Bone marrow	45.8 nTPM
Liver	41.2 nTPM
Kidney	38.1 nTPM

Dendritic cells	85.4 nTPM
PBMC	135.5 nTPM
Adipose tissue	61.1 nTPM
Breast	59.4 nTPM

Endothelial cells	66.3 nTPM
Esophagus	93.6 nTPM
Breast	91.2 nTPM
Skeletal muscle	87.4 nTPM
Liver	81.7 nTPM
Testis	79.4 nTPM
Skin	70.4 nTPM
Lung	59.3 nTPM
Eye	59.1 nTPM
Heart muscle	58.6 nTPM
Prostate	58.4 nTPM
Endometrium	56.0 nTPM
Pancreas	50.2 nTPM
Ovary	48.9 nTPM
Placenta	34.7 nTPM

Fibroblasts	92.6 nTPM
Adipose tissue	153.0 nTPM
Esophagus	130.9 nTPM
Skeletal muscle	123.3 nTPM
Breast	112.7 nTPM
Heart muscle	107.5 nTPM
Lung	102.7 nTPM
Skin	78.4 nTPM
Prostate	71.8 nTPM
Stomach	60.9 nTPM
Placenta	42.7 nTPM
Ovary	34.8 nTPM

Intestinal goblet cells	55.3 nTPM
Rectum	72.0 nTPM
Colon	52.1 nTPM
Small intestine	41.9 nTPM

Macrophages	64.0 nTPM
Adipose tissue	120.9 nTPM
Stomach	93.7 nTPM
Spleen	89.2 nTPM
Kidney	86.2 nTPM
Endometrium	77.9 nTPM
Skeletal muscle	76.8 nTPM
Bone marrow	67.5 nTPM
Lung	56.9 nTPM
Breast	53.0 nTPM
Ovary	51.9 nTPM
Esophagus	51.9 nTPM
Prostate	51.6 nTPM
Testis	50.6 nTPM
Pancreas	17.8 nTPM
PBMC	13.6 nTPM

Paneth cells	51.7 nTPM
Rectum	69.2 nTPM
Small intestine	56.3 nTPM
Colon	29.6 nTPM

Plasma cells	49.4 nTPM
Bone marrow	56.0 nTPM
Esophagus	55.5 nTPM
Stomach	53.6 nTPM
Spleen	50.4 nTPM
Adipose tissue	31.6 nTPM

Respiratory ciliated cells	78.8 nTPM
Lung	84.5 nTPM
Bronchus	73.0 nTPM

Smooth muscle cells	77.4 nTPM
Esophagus	134.9 nTPM
Skeletal muscle	100.3 nTPM
Adipose tissue	96.6 nTPM
Breast	87.8 nTPM
Heart muscle	77.6 nTPM
Bronchus	74.1 nTPM
Prostate	71.0 nTPM
Endometrium	62.1 nTPM
Skin	58.2 nTPM
Ovary	51.2 nTPM
Pancreas	37.4 nTPM

T-cells	55.2 nTPM
Skeletal muscle	75.9 nTPM
PBMC	72.5 nTPM
Kidney	65.8 nTPM
Esophagus	65.5 nTPM
Adipose tissue	64.6 nTPM
Bone marrow	62.4 nTPM
Stomach	60.3 nTPM
Spleen	58.2 nTPM
Skin	53.4 nTPM
Lymph node	51.8 nTPM
Breast	51.0 nTPM
Lung	50.1 nTPM
Endometrium	46.6 nTPM
Colon	44.7 nTPM
Liver	43.1 nTPM
Prostate	37.9 nTPM
Ovary	35.6 nTPM

Basal keratinocytes	81.8 nTPM
Skin	81.8 nTPM

Basal prostatic cells	110.6 nTPM
Prostate	110.6 nTPM

Basal respiratory cells	111.8 nTPM
Bronchus	111.8 nTPM

Basal squamous epithelial cells	96.2 nTPM
Esophagus	96.2 nTPM

Undifferentiated cells	75.1 nTPM
Colon	83.3 nTPM
Rectum	77.0 nTPM
Small intestine	65.0 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