Single cell type - COPS7B - 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.	COPS7B
Gene descriptionⁱ Full gene name according to HGNC.	COP9 signalosome subunit 7B
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.	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. Read more	Spermatogonia & Spermatocytes - 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	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	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: 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

COPS7B is part of cluster 20 Spermatogonia & Spermatocytes - Spermatogenesis with confidenceⁱ 1
181 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
RFPL4AL1	Ret finger protein like 4A like 1	0.6179	20
DCAF4L1	DDB1 and CUL4 associated factor 4 like 1	0.6101	20
KRTAP20-4	Keratin associated protein 20-4	0.5896	20
DCAF4L2	DDB1 and CUL4 associated factor 4 like 2	0.5848	20
TKTL1	Transketolase like 1	0.5747	20
FOXR1	Forkhead box R1	0.5725	20
GAGE13	G antigen 13	0.5724	20
DMRT1	Doublesex and mab-3 related transcription factor 1	0.5709	20
TFDP3	Transcription factor Dp family member 3	0.5691	20
MAGEA12	MAGE family member A12	0.5673	20
GAGE2A	G antigen 2A	0.5656	20
YY2	YY2 transcription factor	0.5651	20
RHOXF2	Rhox homeobox family member 2	0.5647	20
PAGE2	PAGE family member 2	0.5645	20
DDX53	DEAD-box helicase 53	0.5643	23

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	10.6 nTPM
Breast	13.8 nTPM
Adipose tissue	7.5 nTPM

Alveolar cells type 1	16.0 nTPM
Lung	16.0 nTPM

Alveolar cells type 2	11.3 nTPM
Lung	11.3 nTPM

Astrocytes	28.1 nTPM
Brain	28.1 nTPM

B-cells	17.1 nTPM
Lymph node	26.8 nTPM
Bone marrow	22.1 nTPM
PBMC	20.0 nTPM
Breast	20.0 nTPM
Spleen	18.3 nTPM
Liver	16.7 nTPM
Stomach	13.2 nTPM
Adipose tissue	13.0 nTPM
Colon	11.2 nTPM
Kidney	9.5 nTPM

Dendritic cells	19.7 nTPM
Breast	30.3 nTPM
Adipose tissue	16.8 nTPM
PBMC	12.0 nTPM

Endothelial cells	11.1 nTPM
Testis	20.1 nTPM
Liver	17.4 nTPM
Placenta	15.9 nTPM
Ovary	15.5 nTPM
Esophagus	12.9 nTPM
Breast	12.9 nTPM
Skin	12.3 nTPM
Eye	12.2 nTPM
Endometrium	12.2 nTPM
Skeletal muscle	8.6 nTPM
Prostate	6.1 nTPM
Heart muscle	5.5 nTPM
Lung	3.1 nTPM
Pancreas	0.0 nTPM

Fibroblasts	12.3 nTPM
Ovary	18.7 nTPM
Placenta	18.5 nTPM
Breast	18.0 nTPM
Esophagus	11.9 nTPM
Stomach	11.9 nTPM
Skin	10.9 nTPM
Adipose tissue	10.8 nTPM
Prostate	9.8 nTPM
Lung	8.9 nTPM
Skeletal muscle	8.7 nTPM
Heart muscle	7.7 nTPM

Intestinal goblet cells	15.7 nTPM
Small intestine	17.2 nTPM
Rectum	15.1 nTPM
Colon	15.0 nTPM

Macrophages	10.1 nTPM
Breast	20.1 nTPM
PBMC	13.6 nTPM
Testis	12.2 nTPM
Stomach	11.7 nTPM
Prostate	11.5 nTPM
Esophagus	11.0 nTPM
Ovary	10.3 nTPM
Pancreas	10.2 nTPM
Adipose tissue	9.9 nTPM
Endometrium	8.2 nTPM
Lung	7.9 nTPM
Kidney	7.6 nTPM
Bone marrow	7.5 nTPM
Skeletal muscle	6.8 nTPM
Spleen	3.1 nTPM

Paneth cells	9.5 nTPM
Rectum	14.4 nTPM
Small intestine	7.5 nTPM
Colon	6.5 nTPM

Plasma cells	13.5 nTPM
Spleen	21.5 nTPM
Bone marrow	19.8 nTPM
Adipose tissue	10.3 nTPM
Stomach	9.6 nTPM
Esophagus	6.1 nTPM

Respiratory ciliated cells	11.4 nTPM
Bronchus	21.3 nTPM
Lung	1.5 nTPM

Smooth muscle cells	13.5 nTPM
Pancreas	25.5 nTPM
Bronchus	17.8 nTPM
Breast	16.8 nTPM
Ovary	16.3 nTPM
Esophagus	14.0 nTPM
Skin	12.9 nTPM
Endometrium	12.7 nTPM
Adipose tissue	11.2 nTPM
Skeletal muscle	7.9 nTPM
Prostate	6.9 nTPM
Heart muscle	6.1 nTPM

T-cells	16.5 nTPM
PBMC	28.0 nTPM
Breast	27.5 nTPM
Esophagus	26.2 nTPM
Lymph node	22.6 nTPM
Ovary	20.1 nTPM
Liver	19.1 nTPM
Colon	18.5 nTPM
Kidney	17.8 nTPM
Bone marrow	16.9 nTPM
Skeletal muscle	13.9 nTPM
Spleen	13.1 nTPM
Endometrium	13.0 nTPM
Adipose tissue	12.9 nTPM
Skin	12.4 nTPM
Stomach	12.1 nTPM
Lung	6.1 nTPM
Prostate	0.0 nTPM

Basal respiratory cells	24.0 nTPM
Bronchus	24.0 nTPM

Basal squamous epithelial cells	18.2 nTPM
Esophagus	18.2 nTPM

Cholangiocytes	10.0 nTPM
Liver	10.0 nTPM

Cone photoreceptor cells	10.4 nTPM
Eye	10.4 nTPM

Undifferentiated cells	14.3 nTPM
Small intestine	16.4 nTPM
Colon	14.8 nTPM
Rectum	11.7 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