Single cell type - COPZ1 - The Human Protein Atlas

COPZ1

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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.	COPZ1
Gene descriptionⁱ Full gene name according to HGNC.	COPI coat complex subunit zeta 1
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	11

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.	Plasma cells - Protein processing (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.	Low cell type specificity
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.27
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	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.	Low immune cell specificity
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Low cell type specificity

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Low cell type specificity

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Low immune cell specificity
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

COPZ1 is part of cluster 77 Plasma cells - Protein processing with confidenceⁱ 1
324 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
B4GALT7	Beta-1,4-galactosyltransferase 7	0.6248	77
PARK7	Parkinsonism associated deglycase	0.6221	39
OSTC	Oligosaccharyltransferase complex non-catalytic subunit	0.6160	77
MCTS1	MCTS1 re-initiation and release factor	0.6087	77
TMED9	Transmembrane p24 trafficking protein 9	0.6013	77
SEC13	SEC13 homolog, nuclear pore and COPII coat complex component	0.5891	77
TMEM167A	Transmembrane protein 167A	0.5828	29
ARL1	ADP ribosylation factor like GTPase 1	0.5807	77
MYDGF	Myeloid derived growth factor	0.5806	77
BET1	Bet1 golgi vesicular membrane trafficking protein	0.5799	50
SSR3	Signal sequence receptor subunit 3	0.5659	77
TMED10	Transmembrane p24 trafficking protein 10	0.5652	77
SEC61B	SEC61 translocon subunit beta	0.5638	77
SSR2	Signal sequence receptor subunit 2	0.5578	77
EXOSC1	Exosome component 1	0.5523	15

IMMUNE CELLS

COPZ1 is part of cluster 10 Non-specific - Membrane trafficking with confidenceⁱ 0.95
408 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
TBC1D9B	TBC1 domain family member 9B	1.0000	10
LILRB4	Leukocyte immunoglobulin like receptor B4	1.0000	10
KIRREL3	Kirre like nephrin family adhesion molecule 3	0.9762	10
ENSG00000283761	Novel protein	0.9762	10
ENSG00000271810	Novel protein, PPM1J-RHOC readthrough	0.9762	10
ENSG00000267001	Novel protein	0.9762	10
SFT2D2	SFT2 domain containing 2	0.9762	10
CLN8	CLN8 transmembrane ER and ERGIC protein	0.9762	10
ARPP21	CAMP regulated phosphoprotein 21	0.9762	44
GPRC5C	G protein-coupled receptor class C group 5 member C	0.9762	44
UCHL3	Ubiquitin C-terminal hydrolase L3	0.9762	44
SLC1A5	Solute carrier family 1 member 5	0.9762	10
MYDGF	Myeloid derived growth factor	0.9762	44
HERPUD1	Homocysteine inducible ER protein with ubiquitin like domain 1	0.9524	13
SCARB2	Scavenger receptor class B member 2	0.9524	10

Adipocytes	51.4 nTPM
Breast	60.5 nTPM
Adipose tissue	42.3 nTPM

Alveolar cells type 1	96.1 nTPM
Lung	96.1 nTPM

Alveolar cells type 2	131.1 nTPM
Lung	131.1 nTPM

Astrocytes	14.6 nTPM
Brain	14.6 nTPM

B-cells	51.1 nTPM
Lung	95.2 nTPM
PBMC	70.8 nTPM
Skin	52.5 nTPM
Bone marrow	48.9 nTPM
Liver	48.3 nTPM
Spleen	47.5 nTPM
Esophagus	47.2 nTPM
Kidney	46.8 nTPM
Stomach	46.0 nTPM
Salivary gland	43.2 nTPM
Adipose tissue	41.2 nTPM
Thymus	40.2 nTPM
Lymph node	36.5 nTPM

Ciliated cells	77.6 nTPM
Bronchus	89.4 nTPM
Lung	86.4 nTPM
Fallopian tube	70.1 nTPM
Endometrium	64.4 nTPM

Club cells	93.7 nTPM
Bronchus	130.1 nTPM
Prostate	80.8 nTPM
Lung	70.2 nTPM

Dendritic cells	73.1 nTPM
PBMC	100.7 nTPM
Adipose tissue	45.4 nTPM

Endothelial cells	53.8 nTPM
Placenta	107.9 nTPM
Breast	82.6 nTPM
Pancreas	80.1 nTPM
Lung	60.2 nTPM
Ovary	54.7 nTPM
Testis	54.3 nTPM
Prostate	53.8 nTPM
Endometrium	52.2 nTPM
Tongue	47.4 nTPM
Esophagus	46.6 nTPM
Fallopian tube	45.6 nTPM
Liver	44.1 nTPM
Vascular	42.1 nTPM
Heart muscle	40.8 nTPM
Skeletal muscle	40.8 nTPM
Skin	39.9 nTPM
Salivary gland	38.2 nTPM
Thymus	37.6 nTPM

Enteroendocrine cells	76.9 nTPM
Colon	104.8 nTPM
Small intestine	82.4 nTPM
Rectum	43.6 nTPM

Fibroblasts	71.8 nTPM
Pancreas	151.6 nTPM
Placenta	144.8 nTPM
Lung	85.0 nTPM
Adipose tissue	84.6 nTPM
Breast	81.5 nTPM
Prostate	66.0 nTPM
Fallopian tube	64.5 nTPM
Esophagus	63.3 nTPM
Liver	56.9 nTPM
Thymus	56.6 nTPM
Vascular	56.3 nTPM
Stomach	53.3 nTPM
Skeletal muscle	52.4 nTPM
Salivary gland	51.2 nTPM
Skin	43.1 nTPM
Heart muscle	37.1 nTPM

Granulocytes	56.5 nTPM
Lung	71.6 nTPM
Fallopian tube	68.8 nTPM
Tongue	29.1 nTPM

Intestinal goblet cells	124.5 nTPM
Colon	172.2 nTPM
Small intestine	106.2 nTPM
Rectum	94.9 nTPM

Lymphatic endothelial cells	56.8 nTPM
Fallopian tube	70.0 nTPM
Ovary	43.6 nTPM

Macrophages	71.6 nTPM
Pancreas	141.8 nTPM
Kidney	122.1 nTPM
Lung	118.0 nTPM
Stomach	92.6 nTPM
Prostate	75.7 nTPM
Bone marrow	68.9 nTPM
Endometrium	67.0 nTPM
Thymus	65.7 nTPM
Breast	65.1 nTPM
Spleen	64.2 nTPM
Testis	60.8 nTPM
Vascular	58.1 nTPM
Fallopian tube	57.5 nTPM
Adipose tissue	54.3 nTPM
Esophagus	53.9 nTPM
Tongue	53.8 nTPM
Skeletal muscle	53.6 nTPM
Salivary gland	46.3 nTPM
Skin	40.1 nTPM

Basal keratinocytes	44.7 nTPM
Tongue	65.2 nTPM
Skin	24.2 nTPM

Basal prostatic cells	115.1 nTPM
Prostate	115.1 nTPM

Basal respiratory cells	133.5 nTPM
Bronchus	133.5 nTPM

Basal squamous epithelial cells	43.0 nTPM
Esophagus	43.0 nTPM

Paneth cells	77.3 nTPM
Small intestine	103.6 nTPM
Rectum	66.8 nTPM
Colon	61.5 nTPM

Plasma cells	144.6 nTPM
Stomach	181.8 nTPM
Liver	167.2 nTPM
Bone marrow	161.6 nTPM
Spleen	152.5 nTPM
Thymus	151.4 nTPM
Fallopian tube	135.1 nTPM
Esophagus	104.0 nTPM
Salivary gland	103.0 nTPM

Schwann cells	38.3 nTPM
Adipose tissue	68.3 nTPM
Vascular	34.5 nTPM
Esophagus	12.0 nTPM

Serous glandular cells	122.3 nTPM
Salivary gland	151.8 nTPM
Tongue	92.8 nTPM

Smooth muscle cells	52.5 nTPM
Placenta	158.8 nTPM
Prostate	62.0 nTPM
Salivary gland	59.4 nTPM
Ovary	57.9 nTPM
Fallopian tube	56.6 nTPM
Lung	55.3 nTPM
Liver	50.1 nTPM
Endometrium	48.1 nTPM
Breast	45.3 nTPM
Thymus	42.5 nTPM
Vascular	42.3 nTPM
Tongue	37.4 nTPM
Esophagus	34.8 nTPM
Adipose tissue	34.5 nTPM
Skeletal muscle	28.2 nTPM
Skin	27.0 nTPM

Suprabasal keratinocytes	76.9 nTPM
Tongue	119.9 nTPM
Skin	33.9 nTPM

T-cells	54.7 nTPM
Kidney	127.7 nTPM
Liver	80.0 nTPM
Colon	72.1 nTPM
PBMC	68.6 nTPM
Lung	66.9 nTPM
Prostate	66.5 nTPM
Bone marrow	64.6 nTPM
Breast	59.6 nTPM
Spleen	50.3 nTPM
Fallopian tube	48.5 nTPM
Stomach	48.0 nTPM
Skeletal muscle	44.6 nTPM
Salivary gland	43.8 nTPM
Thymus	41.7 nTPM
Skin	41.0 nTPM
Endometrium	40.4 nTPM
Tongue	40.2 nTPM
Lymph node	39.4 nTPM
Vascular	37.8 nTPM
Esophagus	36.5 nTPM
Adipose tissue	31.0 nTPM

Undifferentiated cells	89.3 nTPM
Colon	113.4 nTPM
Small intestine	93.4 nTPM
Rectum	60.9 nTPM

Amygdala excitatory	13.8 nTPM
Thalamus	18.1 nTPM
Basal ganglia	16.5 nTPM
Hippocampus	14.7 nTPM
Cerebral cortex	12.6 nTPM
Amygdala	11.5 nTPM
Hypothalamus	9.5 nTPM

Astrocyte	14.1 nTPM
Cerebellum	15.9 nTPM
Cerebral cortex	15.6 nTPM
Medulla oblongata	15.4 nTPM
Hippocampus	15.2 nTPM
Midbrain	15.1 nTPM
Pons	14.9 nTPM
Spinal cord	14.3 nTPM
Thalamus	13.1 nTPM
Basal ganglia	13.0 nTPM
Amygdala	12.2 nTPM
Hypothalamus	10.6 nTPM

Bergmann glia	19.1 nTPM
Medulla oblongata	27.7 nTPM
Cerebellum	15.1 nTPM
Pons	14.4 nTPM

Central nervous system macrophage	11.0 nTPM
Cerebral cortex	13.5 nTPM
Medulla oblongata	12.6 nTPM
Pons	12.4 nTPM
Hippocampus	11.6 nTPM
Thalamus	11.5 nTPM
Midbrain	11.2 nTPM
Basal ganglia	10.6 nTPM
Spinal cord	10.6 nTPM
Cerebellum	9.8 nTPM
Amygdala	9.1 nTPM
Hypothalamus	8.0 nTPM

Cerebellar inhibitory	17.6 nTPM
Pons	21.4 nTPM
Midbrain	21.2 nTPM
Medulla oblongata	20.4 nTPM
Cerebellum	19.4 nTPM
Spinal cord	5.5 nTPM

Cge interneuron	20.8 nTPM
Thalamus	26.8 nTPM
Midbrain	22.5 nTPM
Cerebral cortex	21.7 nTPM
Basal ganglia	20.5 nTPM
Hippocampus	20.5 nTPM
Amygdala	18.6 nTPM
Hypothalamus	14.8 nTPM

Choroid plexus epithelial cell	17.2 nTPM
Medulla oblongata	30.0 nTPM
Basal ganglia	27.9 nTPM
Hippocampus	5.5 nTPM
Thalamus	5.5 nTPM

Committed oligodendrocyte precursor	21.0 nTPM
Medulla oblongata	31.0 nTPM
Pons	28.3 nTPM
Spinal cord	25.8 nTPM
Midbrain	25.2 nTPM
Hippocampus	21.2 nTPM
Cerebellum	20.6 nTPM
Basal ganglia	19.2 nTPM
Cerebral cortex	18.4 nTPM
Thalamus	17.8 nTPM
Hypothalamus	12.3 nTPM
Amygdala	11.8 nTPM

Deep-layer corticothalamic and 6b	13.3 nTPM
Basal ganglia	15.6 nTPM
Cerebral cortex	14.6 nTPM
Midbrain	14.4 nTPM
Hippocampus	12.3 nTPM
Amygdala	12.1 nTPM
Hypothalamus	11.0 nTPM

Deep-layer intratelencephalic	12.6 nTPM
Cerebral cortex	14.9 nTPM
Basal ganglia	14.3 nTPM
Hippocampus	13.2 nTPM
Amygdala	11.2 nTPM
Hypothalamus	9.4 nTPM

Deep-layer near-projecting	14.2 nTPM
Cerebral cortex	16.2 nTPM
Basal ganglia	16.0 nTPM
Hippocampus	14.6 nTPM
Amygdala	14.1 nTPM
Hypothalamus	10.1 nTPM

Eccentric medium spiny neuron	17.3 nTPM
Hypothalamus	18.9 nTPM
Basal ganglia	18.5 nTPM
Hippocampus	18.2 nTPM
Thalamus	17.6 nTPM
Cerebral cortex	16.5 nTPM
Amygdala	14.0 nTPM