Single cell type - RBM4 - 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.	RBM4
Gene descriptionⁱ Full gene name according to HGNC.	RNA binding motif protein 4
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	Non-specific - Transcription (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

RBM4 is part of cluster 59 Non-specific - Transcription 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
ARMCX5	Armadillo repeat containing X-linked 5	0.6894	59
ANKHD1	Ankyrin repeat and KH domain containing 1	0.6746	59
DIABLO	Diablo IAP-binding mitochondrial protein	0.6702	59
ABHD18	Abhydrolase domain containing 18	0.6684	59
WBP1	WW domain binding protein 1	0.6557	59
METTL17	Methyltransferase like 17	0.6480	59
PRICKLE4	Prickle planar cell polarity protein 4	0.6304	59
RTEL1	Regulator of telomere elongation helicase 1	0.6151	59
OVCA2	OVCA2 serine hydrolase domain containing	0.6117	59
ARPC4-TTLL3	ARPC4-TTLL3 readthrough	0.6079	59
ERVK3-1	Endogenous retrovirus group K3 member 1	0.6050	59
RNASEK	Ribonuclease K	0.6003	59
C11orf98	Chromosome 11 open reading frame 98	0.5918	59
LTB4R2	Leukotriene B4 receptor 2	0.5878	59
ST20-MTHFS	ST20-MTHFS readthrough	0.5876	59

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
Adipose tissue	21.9 nTPM
Breast	17.4 nTPM

Alveolar cells type 1	28.9 nTPM
Lung	28.9 nTPM

Alveolar cells type 2	42.2 nTPM
Lung	42.2 nTPM

Astrocytes	8.1 nTPM
Brain	8.1 nTPM

B-cells	64.0 nTPM
Spleen	104.8 nTPM
Stomach	93.1 nTPM
Colon	84.7 nTPM
Lymph node	81.2 nTPM
PBMC	74.3 nTPM
Bone marrow	55.6 nTPM
Adipose tissue	44.1 nTPM
Kidney	38.1 nTPM
Breast	36.0 nTPM
Liver	28.0 nTPM

Basal squamous epithelial cells	112.7 nTPM
Esophagus	112.7 nTPM

Dendritic cells	48.7 nTPM
Adipose tissue	60.6 nTPM
PBMC	43.8 nTPM
Breast	41.6 nTPM

Endothelial cells	28.5 nTPM
Esophagus	84.3 nTPM
Prostate	48.0 nTPM
Endometrium	30.1 nTPM
Placenta	28.4 nTPM
Skeletal muscle	27.1 nTPM
Eye	25.9 nTPM
Skin	25.9 nTPM
Lung	24.9 nTPM
Ovary	23.0 nTPM
Testis	22.2 nTPM
Breast	19.4 nTPM
Pancreas	19.3 nTPM
Liver	15.6 nTPM
Heart muscle	5.2 nTPM

Fibroblasts	33.6 nTPM
Stomach	68.3 nTPM
Esophagus	60.9 nTPM
Lung	56.9 nTPM
Prostate	42.2 nTPM
Ovary	32.3 nTPM
Placenta	24.5 nTPM
Skeletal muscle	20.9 nTPM
Breast	20.9 nTPM
Adipose tissue	19.3 nTPM
Skin	17.8 nTPM
Heart muscle	5.7 nTPM

Intestinal goblet cells	15.5 nTPM
Colon	17.2 nTPM
Rectum	16.1 nTPM
Small intestine	13.1 nTPM

Macrophages	27.5 nTPM
Stomach	67.4 nTPM
Bone marrow	45.0 nTPM
Spleen	36.3 nTPM
Adipose tissue	31.0 nTPM
Prostate	28.7 nTPM
Esophagus	28.3 nTPM
Endometrium	27.7 nTPM
Lung	24.2 nTPM
Pancreas	23.0 nTPM
Skeletal muscle	23.0 nTPM
Breast	22.6 nTPM
Kidney	20.4 nTPM
Testis	20.3 nTPM
Ovary	13.8 nTPM
PBMC	0.0 nTPM

Paneth cells	23.6 nTPM
Small intestine	37.6 nTPM
Rectum	20.1 nTPM
Colon	13.2 nTPM

Plasma cells	60.2 nTPM
Esophagus	80.1 nTPM
Stomach	64.7 nTPM
Spleen	58.9 nTPM
Adipose tissue	51.0 nTPM
Bone marrow	46.2 nTPM

Respiratory ciliated cells	41.1 nTPM
Lung	45.2 nTPM
Bronchus	37.0 nTPM

Smooth muscle cells	28.3 nTPM
Esophagus	80.6 nTPM
Prostate	39.7 nTPM
Skeletal muscle	35.6 nTPM
Skin	27.9 nTPM
Ovary	27.9 nTPM
Endometrium	26.6 nTPM
Breast	25.1 nTPM
Adipose tissue	19.9 nTPM
Pancreas	12.9 nTPM
Heart muscle	9.9 nTPM
Bronchus	5.6 nTPM

Cholangiocytes	15.7 nTPM
Liver	15.7 nTPM

Collecting duct cells	20.2 nTPM
Kidney	20.2 nTPM

Cone photoreceptor cells	93.8 nTPM
Eye	93.8 nTPM

Cytotrophoblasts	36.2 nTPM
Placenta	36.2 nTPM

T-cells	66.3 nTPM
Spleen	114.1 nTPM
Lymph node	104.0 nTPM
Stomach	100.8 nTPM
Prostate	99.4 nTPM
PBMC	82.4 nTPM
Bone marrow	78.6 nTPM
Colon	75.6 nTPM
Adipose tissue	62.2 nTPM
Liver	54.2 nTPM
Esophagus	52.4 nTPM
Skeletal muscle	50.2 nTPM
Breast	46.1 nTPM
Kidney	45.8 nTPM
Ovary	44.5 nTPM
Skin	43.7 nTPM
Endometrium	43.0 nTPM
Lung	30.4 nTPM

Undifferentiated cells	24.8 nTPM
Colon	31.8 nTPM
Small intestine	23.4 nTPM
Rectum	19.0 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