Single cell type - EFR3A - 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.	EFR3A
Gene descriptionⁱ Full gene name according to HGNC.	EFR3 homolog A
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.	5

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	Bipolar cells - Visual perception (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 (Bipolar 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	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 (Bipolar 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

EFR3A is part of cluster 56 Bipolar cells - Visual perception with confidenceⁱ 1
199 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
GPR61	G protein-coupled receptor 61	0.8078	56
SLC23A2	Solute carrier family 23 member 2	0.7936	56
LRTM1	Leucine rich repeats and transmembrane domains 1	0.7476	56
LINGO3	Leucine rich repeat and Ig domain containing 3	0.7447	56
GABRR1	Gamma-aminobutyric acid type A receptor subunit rho1	0.7384	56
SMIM18	Small integral membrane protein 18	0.7372	56
GPR179	G protein-coupled receptor 179	0.7259	56
CALY	Calcyon neuron specific vesicular protein	0.7239	56
SLC25A22	Solute carrier family 25 member 22	0.7188	56
CLSTN3	Calsyntenin 3	0.7183	56
CAMK2B	Calcium/calmodulin dependent protein kinase II beta	0.7168	56
FEZF2	FEZ family zinc finger 2	0.7155	56
NYX	Nyctalopin	0.7127	56
MC4R	Melanocortin 4 receptor	0.7042	56
ANKRD34A	Ankyrin repeat domain 34A	0.7037	56

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	32.6 nTPM
Adipose tissue	34.9 nTPM
Breast	30.3 nTPM

Alveolar cells type 1	41.7 nTPM
Lung	41.7 nTPM

Alveolar cells type 2	42.8 nTPM
Lung	42.8 nTPM

Astrocytes	90.8 nTPM
Brain	90.8 nTPM

B-cells	40.7 nTPM
Spleen	60.9 nTPM
Bone marrow	58.9 nTPM
Stomach	54.0 nTPM
Lymph node	50.6 nTPM
Colon	46.4 nTPM
Adipose tissue	45.2 nTPM
PBMC	27.1 nTPM
Kidney	23.8 nTPM
Liver	22.8 nTPM
Breast	17.3 nTPM

Dendritic cells	34.1 nTPM
Adipose tissue	53.5 nTPM
Breast	28.8 nTPM
PBMC	20.0 nTPM

Endothelial cells	29.1 nTPM
Heart muscle	41.9 nTPM
Ovary	39.2 nTPM
Esophagus	38.2 nTPM
Prostate	35.2 nTPM
Endometrium	33.0 nTPM
Eye	31.6 nTPM
Testis	31.2 nTPM
Breast	28.5 nTPM
Skeletal muscle	28.0 nTPM
Liver	22.9 nTPM
Lung	21.8 nTPM
Skin	19.7 nTPM
Pancreas	19.3 nTPM
Placenta	16.5 nTPM

Fibroblasts	34.4 nTPM
Esophagus	55.6 nTPM
Prostate	40.1 nTPM
Heart muscle	37.7 nTPM
Skeletal muscle	37.2 nTPM
Lung	35.7 nTPM
Stomach	35.6 nTPM
Ovary	31.6 nTPM
Adipose tissue	31.6 nTPM
Skin	30.8 nTPM
Breast	26.4 nTPM
Placenta	16.4 nTPM

Intestinal goblet cells	18.7 nTPM
Small intestine	26.4 nTPM
Colon	18.6 nTPM
Rectum	11.1 nTPM

Macrophages	52.9 nTPM
Bone marrow	90.0 nTPM
Spleen	79.9 nTPM
Stomach	76.2 nTPM
Esophagus	75.5 nTPM
Ovary	73.0 nTPM
Kidney	61.3 nTPM
Lung	56.0 nTPM
Adipose tissue	55.2 nTPM
Skeletal muscle	54.6 nTPM
Testis	50.0 nTPM
Prostate	37.9 nTPM
Breast	31.1 nTPM
Pancreas	28.0 nTPM
Endometrium	25.3 nTPM
PBMC	0.0 nTPM

Paneth cells	36.0 nTPM
Small intestine	56.3 nTPM
Colon	36.2 nTPM
Rectum	15.7 nTPM

Plasma cells	32.6 nTPM
Adipose tissue	47.1 nTPM
Spleen	46.9 nTPM
Stomach	34.7 nTPM
Bone marrow	28.0 nTPM
Esophagus	6.1 nTPM

Respiratory ciliated cells	27.7 nTPM
Bronchus	39.4 nTPM
Lung	16.0 nTPM

Smooth muscle cells	41.4 nTPM
Esophagus	63.6 nTPM
Heart muscle	57.1 nTPM
Skeletal muscle	54.7 nTPM
Adipose tissue	47.9 nTPM
Prostate	45.4 nTPM
Endometrium	37.7 nTPM
Pancreas	37.4 nTPM
Breast	36.1 nTPM
Skin	26.5 nTPM
Ovary	25.1 nTPM
Bronchus	24.5 nTPM

T-cells	37.3 nTPM
Spleen	73.8 nTPM
Stomach	69.2 nTPM
Bone marrow	63.6 nTPM
Adipose tissue	53.2 nTPM
Lymph node	42.5 nTPM
Skeletal muscle	39.6 nTPM
Colon	38.5 nTPM
PBMC	33.9 nTPM
Kidney	32.2 nTPM
Breast	28.2 nTPM
Endometrium	26.2 nTPM
Esophagus	26.2 nTPM
Liver	24.1 nTPM
Ovary	22.3 nTPM
Lung	21.3 nTPM
Skin	20.2 nTPM
Prostate	19.0 nTPM

Basal keratinocytes	21.2 nTPM
Skin	21.2 nTPM

Basal respiratory cells	29.5 nTPM
Bronchus	29.5 nTPM

Basal squamous epithelial cells	25.0 nTPM
Esophagus	25.0 nTPM

Cholangiocytes	28.6 nTPM
Liver	28.6 nTPM

Undifferentiated cells	17.0 nTPM
Small intestine	22.0 nTPM
Colon	18.1 nTPM
Rectum	10.8 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