Single cell type - RAPGEF3 - 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.	RAPGEF3
Gene descriptionⁱ Full gene name according to HGNC.	Rap guanine nucleotide exchange factor 3
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	Adipocytes & Endothelial cells - Angiogenesis (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 (Astrocytes, Adipocytes, Collecting duct cells, Endothelial cells, Oligodendrocytes)
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 (EFO-21, HUVEC TERT2, NB-4, RPTEC TERT1, TIME)
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 (Astrocytes, Adipocytes, Collecting duct cells, Endothelial cells, Oligodendrocytes)

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

RAPGEF3 is part of cluster 14 Adipocytes & Endothelial cells - Angiogenesis with confidenceⁱ 1
354 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
AQP1	Aquaporin 1 (Colton blood group)	0.7778	14
HIF3A	Hypoxia inducible factor 3 subunit alpha	0.7587	14
VWF	Von Willebrand factor	0.7449	14
BTNL9	Butyrophilin like 9	0.7405	14
ARHGEF15	Rho guanine nucleotide exchange factor 15	0.7393	14
USHBP1	USH1 protein network component harmonin binding protein 1	0.7375	14
EMCN	Endomucin	0.7256	14
MMRN2	Multimerin 2	0.7133	14
CYYR1	Cysteine and tyrosine rich 1	0.7076	14
NOTCH4	Notch receptor 4	0.7009	14
F8	Coagulation factor VIII	0.6999	14
TPO	Thyroid peroxidase	0.6918	14
C1QTNF9	C1q and TNF related 9	0.6850	14
SHANK3	SH3 and multiple ankyrin repeat domains 3	0.6791	14
HSPA12B	Heat shock protein family A (Hsp70) member 12B	0.6756	14

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

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	11.7 nTPM
Lung	11.7 nTPM

B-cells	0.7 nTPM
Breast	5.3 nTPM
Liver	1.3 nTPM
Lymph node	0.6 nTPM
Spleen	0.3 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Basal keratinocytes	2.7 nTPM
Skin	2.7 nTPM

Basal prostatic cells	5.8 nTPM
Prostate	5.8 nTPM

Adipocytes	130.6 nTPM
Adipose tissue	144.5 nTPM
Breast	116.7 nTPM

Dendritic cells	1.4 nTPM
Breast	4.0 nTPM
Adipose tissue	0.1 nTPM
PBMC	0.0 nTPM

Endothelial cells	53.0 nTPM
Heart muscle	157.9 nTPM
Skeletal muscle	124.6 nTPM
Esophagus	85.9 nTPM
Breast	80.8 nTPM
Testis	65.8 nTPM
Ovary	39.2 nTPM
Skin	36.5 nTPM
Lung	34.3 nTPM
Prostate	30.1 nTPM
Pancreas	23.1 nTPM
Eye	19.4 nTPM
Endometrium	17.3 nTPM
Liver	13.7 nTPM
Placenta	13.7 nTPM

Fibroblasts	6.3 nTPM
Ovary	17.6 nTPM
Heart muscle	16.3 nTPM
Esophagus	6.8 nTPM
Stomach	6.0 nTPM
Skin	5.9 nTPM
Skeletal muscle	5.4 nTPM
Breast	3.9 nTPM
Prostate	3.6 nTPM
Lung	2.2 nTPM
Placenta	1.3 nTPM
Adipose tissue	0.9 nTPM

Intestinal goblet cells	6.6 nTPM
Colon	11.4 nTPM
Small intestine	5.0 nTPM
Rectum	3.4 nTPM

Macrophages	1.5 nTPM
Skeletal muscle	4.9 nTPM
Esophagus	4.8 nTPM
Breast	2.8 nTPM
Prostate	2.2 nTPM
Lung	1.7 nTPM
Testis	1.7 nTPM
Endometrium	1.7 nTPM
Kidney	1.5 nTPM
Adipose tissue	0.8 nTPM
Ovary	0.3 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	6.3 nTPM
Small intestine	15.0 nTPM
Colon	3.3 nTPM
Rectum	0.6 nTPM

Plasma cells	4.4 nTPM
Esophagus	12.3 nTPM
Stomach	7.4 nTPM
Adipose tissue	1.9 nTPM
Spleen	0.7 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	1.9 nTPM
Lung	2.9 nTPM
Bronchus	0.9 nTPM

Smooth muscle cells	5.1 nTPM
Heart muscle	13.5 nTPM
Adipose tissue	10.8 nTPM
Breast	8.6 nTPM
Skeletal muscle	7.5 nTPM
Esophagus	6.2 nTPM
Skin	3.2 nTPM
Ovary	1.8 nTPM
Prostate	1.5 nTPM
Endometrium	1.3 nTPM
Bronchus	1.0 nTPM
Pancreas	0.7 nTPM

Astrocytes	143.0 nTPM
Brain	143.0 nTPM

Cytotrophoblasts	0.2 nTPM
Placenta	0.2 nTPM

Distal tubular cells	7.9 nTPM
Kidney	7.9 nTPM

Early spermatids	1.6 nTPM
Testis	1.6 nTPM

T-cells	1.3 nTPM
Esophagus	6.6 nTPM
Lung	4.5 nTPM
Breast	4.5 nTPM
Kidney	2.7 nTPM
Skin	1.4 nTPM
Endometrium	1.1 nTPM
Liver	0.6 nTPM
Colon	0.5 nTPM
Skeletal muscle	0.5 nTPM
Adipose tissue	0.2 nTPM
Stomach	0.1 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Ovary	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Undifferentiated cells	0.8 nTPM
Colon	1.5 nTPM
Rectum	0.7 nTPM
Small intestine	0.3 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