Single cell type - RCSD1 - 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.	RCSD1
Gene descriptionⁱ Full gene name according to HGNC.	RCSD domain containing 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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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	B-cells - Immune response (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 (B-cells, NK-cells, Kupffer cells, monocytes, T-cells, Macrophages, Sertoli cells, Microglial 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	Cell line enhanced (Daudi, HDLM-2, REH, RPMI-8226, THP-1, U-266/70, U-698)
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 some
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 (B-cells, NK-cells, Kupffer cells, monocytes, T-cells, Macrophages, Sertoli cells, Microglial 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

RCSD1 is part of cluster 57 B-cells - Immune response with confidenceⁱ 1
204 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
CD37	CD37 molecule	0.8576	57
FCMR	Fc fragment of IgM receptor	0.8323	57
IGLV3-12	Immunoglobulin lambda variable 3-12	0.8132	57
PTPN6	Protein tyrosine phosphatase non-receptor type 6	0.8109	57
FCER2	Fc fragment of IgE receptor II	0.7948	57
CD79B	CD79b molecule	0.7933	57
CNR2	Cannabinoid receptor 2	0.7874	57
CSK	C-terminal Src kinase	0.7822	57
POU2F2	POU class 2 homeobox 2	0.7817	57
MS4A1	Membrane spanning 4-domains A1	0.7743	57
BTLA	B and T lymphocyte associated	0.7729	57
FCRL3	Fc receptor like 3	0.7720	57
TLR10	Toll like receptor 10	0.7717	57
FCRLA	Fc receptor like A	0.7702	57
CD72	CD72 molecule	0.7675	57

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	18.7 nTPM
Breast	25.4 nTPM
Adipose tissue	12.0 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	6.7 nTPM
Lung	6.7 nTPM

Astrocytes	0.3 nTPM
Brain	0.3 nTPM

Basal keratinocytes	1.1 nTPM
Skin	1.1 nTPM

B-cells	258.0 nTPM
Bone marrow	462.7 nTPM
Stomach	454.6 nTPM
Lymph node	381.5 nTPM
Spleen	348.5 nTPM
PBMC	295.5 nTPM
Adipose tissue	190.5 nTPM
Kidney	147.5 nTPM
Colon	126.2 nTPM
Liver	88.2 nTPM
Breast	84.3 nTPM

Dendritic cells	73.9 nTPM
PBMC	91.6 nTPM
Breast	78.4 nTPM
Adipose tissue	51.6 nTPM

Endothelial cells	18.8 nTPM
Eye	78.5 nTPM
Heart muscle	37.5 nTPM
Skeletal muscle	28.0 nTPM
Ovary	22.3 nTPM
Lung	21.8 nTPM
Pancreas	19.3 nTPM
Breast	14.3 nTPM
Esophagus	11.0 nTPM
Skin	8.2 nTPM
Placenta	8.0 nTPM
Endometrium	5.6 nTPM
Liver	3.7 nTPM
Testis	3.0 nTPM
Prostate	2.1 nTPM

Fibroblasts	12.4 nTPM
Stomach	65.3 nTPM
Heart muscle	29.3 nTPM
Lung	10.1 nTPM
Prostate	7.0 nTPM
Esophagus	7.0 nTPM
Placenta	5.2 nTPM
Skeletal muscle	4.4 nTPM
Breast	2.8 nTPM
Skin	2.7 nTPM
Ovary	2.5 nTPM
Adipose tissue	0.2 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Macrophages	80.7 nTPM
Bone marrow	141.2 nTPM
Stomach	114.3 nTPM
Ovary	105.8 nTPM
Spleen	103.7 nTPM
Testis	99.9 nTPM
Esophagus	92.8 nTPM
Skeletal muscle	91.9 nTPM
Kidney	89.2 nTPM
Breast	86.4 nTPM
Adipose tissue	76.1 nTPM
Endometrium	57.4 nTPM
Prostate	57.3 nTPM
Pancreas	56.2 nTPM
Lung	25.2 nTPM
PBMC	13.6 nTPM

Paneth cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Plasma cells	55.1 nTPM
Bone marrow	82.4 nTPM
Stomach	64.1 nTPM
Spleen	63.7 nTPM
Adipose tissue	40.7 nTPM
Esophagus	24.6 nTPM

Respiratory ciliated cells	0.0 nTPM
Lung	0.0 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	39.7 nTPM
Esophagus	96.1 nTPM
Heart muscle	77.6 nTPM
Endometrium	52.3 nTPM
Adipose tissue	46.2 nTPM
Skeletal muscle	41.1 nTPM
Breast	37.5 nTPM
Ovary	36.6 nTPM
Skin	25.1 nTPM
Prostate	24.1 nTPM
Pancreas	0.6 nTPM
Bronchus	0.0 nTPM

Collecting duct cells	1.8 nTPM
Kidney	1.8 nTPM

Cytotrophoblasts	0.5 nTPM
Placenta	0.5 nTPM

Early spermatids	0.8 nTPM
Testis	0.8 nTPM

Excitatory neurons	4.2 nTPM
Brain	4.2 nTPM

T-cells	97.2 nTPM
PBMC	178.2 nTPM
Bone marrow	168.6 nTPM
Ovary	146.8 nTPM
Liver	140.5 nTPM
Lymph node	139.4 nTPM
Spleen	99.6 nTPM
Esophagus	98.3 nTPM
Kidney	90.3 nTPM
Skeletal muscle	87.3 nTPM
Stomach	84.7 nTPM
Breast	80.5 nTPM
Lung	68.4 nTPM
Prostate	66.3 nTPM
Skin	56.1 nTPM
Adipose tissue	53.2 nTPM
Endometrium	51.6 nTPM
Colon	42.7 nTPM

Undifferentiated cells	0.1 nTPM
Colon	0.3 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 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