Single cell type - COPZ2 - 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.	COPZ2
Gene descriptionⁱ Full gene name according to HGNC.	COPI coat complex subunit zeta 2
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.	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 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	Fibroblasts - ECM organization (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 (Fibroblasts, Endometrial stromal cells, Leydig cells, Basal keratinocytes, Smooth muscle 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	Not detected in immune cells
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	Not detected
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 (ASC diff, ASC TERT1, BJ, BJ hTERT+, fHDF/TERT166)
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 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

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 (Fibroblasts, Endometrial stromal cells, Leydig cells, Basal keratinocytes, Smooth muscle 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

COPZ2 is part of cluster 33 Fibroblasts - ECM organization with confidenceⁱ 1
171 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
CD248	CD248 molecule	0.8096	50
COL6A1	Collagen type VI alpha 1 chain	0.7979	33
COL1A2	Collagen type I alpha 2 chain	0.7907	33
COL6A2	Collagen type VI alpha 2 chain	0.7854	33
TMEM119	Transmembrane protein 119	0.7785	33
COL1A1	Collagen type I alpha 1 chain	0.7655	33
RCN3	Reticulocalbin 3	0.7568	33
ISM1	Isthmin 1	0.7480	50
LUM	Lumican	0.7405	33
OLFML3	Olfactomedin like 3	0.7366	33
TWIST1	Twist family bHLH transcription factor 1	0.7359	50
AEBP1	AE binding protein 1	0.7314	50
GPC3	Glypican 3	0.7301	33
OGN	Osteoglycin	0.7265	33
PLAC9	Placenta associated 9	0.7209	50

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	31.6 nTPM
Breast	42.8 nTPM
Adipose tissue	20.3 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	2.2 nTPM
Lung	2.2 nTPM

Astrocytes	8.1 nTPM
Brain	8.1 nTPM

B-cells	2.6 nTPM
Breast	20.0 nTPM
Liver	3.7 nTPM
Adipose tissue	1.5 nTPM
Stomach	0.5 nTPM
Spleen	0.3 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM

Dendritic cells	7.5 nTPM
Breast	13.9 nTPM
Adipose tissue	8.6 nTPM
PBMC	0.0 nTPM

Endothelial cells	15.6 nTPM
Skin	34.1 nTPM
Breast	32.1 nTPM
Liver	22.0 nTPM
Heart muscle	20.7 nTPM
Eye	20.3 nTPM
Ovary	17.9 nTPM
Skeletal muscle	17.5 nTPM
Prostate	16.3 nTPM
Esophagus	14.5 nTPM
Endometrium	8.7 nTPM
Testis	8.3 nTPM
Placenta	6.2 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	77.7 nTPM
Adipose tissue	178.0 nTPM
Breast	147.6 nTPM
Skin	129.5 nTPM
Placenta	112.5 nTPM
Skeletal muscle	85.8 nTPM
Esophagus	51.9 nTPM
Ovary	48.9 nTPM
Heart muscle	48.3 nTPM
Prostate	24.4 nTPM
Stomach	22.3 nTPM
Lung	5.6 nTPM

Intestinal goblet cells	2.3 nTPM
Rectum	3.8 nTPM
Colon	2.9 nTPM
Small intestine	0.4 nTPM

Macrophages	3.4 nTPM
Skeletal muscle	8.7 nTPM
Breast	8.1 nTPM
Ovary	7.5 nTPM
Endometrium	6.5 nTPM
Kidney	5.3 nTPM
Prostate	3.4 nTPM
Adipose tissue	3.3 nTPM
Esophagus	3.1 nTPM
Testis	1.7 nTPM
Lung	1.4 nTPM
Bone marrow	1.2 nTPM
Spleen	1.0 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Plasma cells	3.5 nTPM
Adipose tissue	6.4 nTPM
Esophagus	6.1 nTPM
Stomach	4.5 nTPM
Spleen	0.3 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	0.6 nTPM
Bronchus	1.3 nTPM
Lung	0.0 nTPM

Smooth muscle cells	49.2 nTPM
Pancreas	113.2 nTPM
Bronchus	102.6 nTPM
Breast	73.2 nTPM
Adipose tissue	57.0 nTPM
Prostate	41.8 nTPM
Esophagus	38.8 nTPM
Skin	35.2 nTPM
Skeletal muscle	26.7 nTPM
Endometrium	25.4 nTPM
Heart muscle	15.8 nTPM
Ovary	11.5 nTPM

T-cells	3.7 nTPM
Ovary	11.1 nTPM
Prostate	9.5 nTPM
Skin	8.8 nTPM
Skeletal muscle	7.7 nTPM
Endometrium	6.6 nTPM
Kidney	6.2 nTPM
Liver	4.3 nTPM
Breast	3.9 nTPM
Adipose tissue	1.6 nTPM
Bone marrow	1.4 nTPM
PBMC	1.2 nTPM
Colon	0.5 nTPM
Stomach	0.4 nTPM
Spleen	0.3 nTPM
Lung	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM

Collecting duct cells	7.3 nTPM
Kidney	7.3 nTPM

Distal tubular cells	11.7 nTPM
Kidney	11.7 nTPM

Early spermatids	7.0 nTPM
Testis	7.0 nTPM

Exocrine glandular cells	5.1 nTPM
Pancreas	5.1 nTPM

Undifferentiated cells	0.4 nTPM
Rectum	0.7 nTPM
Colon	0.3 nTPM
Small intestine	0.2 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