Single cell type - RCAN3 - 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.	RCAN3
Gene descriptionⁱ Full gene name according to HGNC.	RCAN family member 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.	9

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	Non-specific - Transcription regulation (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 (T-cells, Endometrial ciliated cells, Enteroendocrine 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	Immune cell enhanced (T-reg)
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 many
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 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 (T-cells, Endometrial ciliated cells, Enteroendocrine 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

RCAN3 is part of cluster 24 Non-specific - Transcription regulation with confidenceⁱ 1
415 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
FOXP3	Forkhead box P3	0.8616	24
CD40LG	CD40 ligand	0.8459	24
CD28	CD28 molecule	0.8388	24
CCR4	C-C motif chemokine receptor 4	0.8350	24
ICOS	Inducible T cell costimulator	0.8269	24
PMCH	Pro-melanin concentrating hormone	0.8229	24
CTLA4	Cytotoxic T-lymphocyte associated protein 4	0.8175	24
CCR8	C-C motif chemokine receptor 8	0.8010	24
IL7R	Interleukin 7 receptor	0.7991	24
CCR6	C-C motif chemokine receptor 6	0.7922	24
TNFSF8	TNF superfamily member 8	0.7628	24
SPOCK2	SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2	0.7558	24
PBX4	PBX homeobox 4	0.7416	24
LEPROTL1	Leptin receptor overlapping transcript like 1	0.7362	24
TRAT1	T cell receptor associated transmembrane adaptor 1	0.7351	24

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	19.7 nTPM
Breast	20.2 nTPM
Adipose tissue	19.2 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	13.3 nTPM
Lung	13.3 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	32.4 nTPM
PBMC	55.7 nTPM
Adipose tissue	45.2 nTPM
Lymph node	44.1 nTPM
Stomach	35.9 nTPM
Bone marrow	33.5 nTPM
Kidney	28.5 nTPM
Spleen	27.3 nTPM
Breast	22.8 nTPM
Colon	20.8 nTPM
Liver	10.3 nTPM

Dendritic cells	18.9 nTPM
PBMC	27.9 nTPM
Adipose tissue	19.2 nTPM
Breast	9.5 nTPM

Endothelial cells	8.6 nTPM
Heart muscle	21.7 nTPM
Skeletal muscle	20.2 nTPM
Breast	13.6 nTPM
Esophagus	12.4 nTPM
Skin	12.3 nTPM
Eye	8.1 nTPM
Testis	6.8 nTPM
Liver	6.4 nTPM
Prostate	6.4 nTPM
Ovary	4.1 nTPM
Pancreas	3.9 nTPM
Endometrium	3.4 nTPM
Placenta	0.6 nTPM
Lung	0.0 nTPM

Fibroblasts	6.0 nTPM
Breast	12.5 nTPM
Skin	12.1 nTPM
Placenta	7.9 nTPM
Skeletal muscle	6.6 nTPM
Stomach	6.0 nTPM
Adipose tissue	5.5 nTPM
Esophagus	5.1 nTPM
Prostate	4.3 nTPM
Heart muscle	3.3 nTPM
Ovary	1.7 nTPM
Lung	1.2 nTPM

Intestinal goblet cells	14.4 nTPM
Colon	15.7 nTPM
Rectum	15.3 nTPM
Small intestine	12.1 nTPM

Macrophages	23.0 nTPM
Prostate	43.5 nTPM
PBMC	40.9 nTPM
Breast	40.4 nTPM
Adipose tissue	28.6 nTPM
Esophagus	26.8 nTPM
Endometrium	24.9 nTPM
Spleen	22.8 nTPM
Testis	21.5 nTPM
Skeletal muscle	19.6 nTPM
Stomach	17.6 nTPM
Ovary	17.1 nTPM
Lung	15.0 nTPM
Bone marrow	10.0 nTPM
Kidney	8.3 nTPM
Pancreas	7.7 nTPM

Paneth cells	11.3 nTPM
Small intestine	15.0 nTPM
Rectum	12.4 nTPM
Colon	6.5 nTPM

Plasma cells	22.0 nTPM
Adipose tissue	52.2 nTPM
Esophagus	30.7 nTPM
Stomach	20.9 nTPM
Spleen	4.2 nTPM
Bone marrow	1.7 nTPM

Respiratory ciliated cells	67.7 nTPM
Lung	80.2 nTPM
Bronchus	55.2 nTPM

Smooth muscle cells	10.4 nTPM
Adipose tissue	25.3 nTPM
Skeletal muscle	16.8 nTPM
Breast	14.1 nTPM
Heart muscle	13.6 nTPM
Esophagus	10.9 nTPM
Prostate	9.1 nTPM
Skin	8.4 nTPM
Bronchus	5.7 nTPM
Ovary	3.9 nTPM
Pancreas	3.8 nTPM
Endometrium	3.4 nTPM

T-cells	106.8 nTPM
Adipose tissue	294.9 nTPM
PBMC	216.4 nTPM
Lymph node	167.4 nTPM
Breast	141.7 nTPM
Prostate	127.8 nTPM
Skin	113.3 nTPM
Colon	113.1 nTPM
Skeletal muscle	100.8 nTPM
Spleen	96.3 nTPM
Stomach	83.0 nTPM
Endometrium	77.6 nTPM
Bone marrow	72.0 nTPM
Ovary	55.6 nTPM
Esophagus	45.9 nTPM
Liver	40.5 nTPM
Kidney	38.3 nTPM
Lung	30.4 nTPM

Basal respiratory cells	8.9 nTPM
Bronchus	8.9 nTPM

Basal squamous epithelial cells	11.4 nTPM
Esophagus	11.4 nTPM

Cholangiocytes	25.8 nTPM
Liver	25.8 nTPM

Cone photoreceptor cells	64.6 nTPM
Eye	64.6 nTPM

Undifferentiated cells	12.2 nTPM
Rectum	15.4 nTPM
Colon	11.5 nTPM
Small intestine	9.6 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