Single cell type - RBM42 - 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.	RBM42
Gene descriptionⁱ Full gene name according to HGNC.	RNA binding motif protein 42
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.	6

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	Syncytiotrophoblasts - Pregnancy hormone signaling (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 (Syncytiotrophoblasts)
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 (Syncytiotrophoblasts)

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

RBM42 is part of cluster 18 Syncytiotrophoblasts - Pregnancy hormone signaling with confidenceⁱ 1
186 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
SLC19A3	Solute carrier family 19 member 3	0.7271	18
DDX28	DEAD-box helicase 28	0.7226	18
SLC22A11	Solute carrier family 22 member 11	0.6994	18
CLTA	Clathrin light chain A	0.6991	10
CDO1	Cysteine dioxygenase type 1	0.6965	47
RASA1	RAS p21 protein activator 1	0.6943	18
CALHM4	Calcium homeostasis modulator family member 4	0.6884	18
ERVW-1	Endogenous retrovirus group W member 1, envelope	0.6830	18
SLC13A4	Solute carrier family 13 member 4	0.6786	18
SLC52A1	Solute carrier family 52 member 1	0.6723	18
NFE2L3	Nuclear factor, erythroid 2 like 3	0.6690	18
MLLT1	MLLT1 super elongation complex subunit	0.6617	18
P2RY6	Pyrimidinergic receptor P2Y6	0.6543	18
TINAGL1	Tubulointerstitial nephritis antigen like 1	0.6536	47
SLC19A1	Solute carrier family 19 member 1	0.6496	18

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	56.5 nTPM
Breast	61.2 nTPM
Adipose tissue	51.9 nTPM

Alveolar cells type 1	38.5 nTPM
Lung	38.5 nTPM

Alveolar cells type 2	24.6 nTPM
Lung	24.6 nTPM

Astrocytes	4.6 nTPM
Brain	4.6 nTPM

B-cells	38.4 nTPM
Liver	68.0 nTPM
Stomach	53.1 nTPM
Lymph node	44.8 nTPM
PBMC	41.4 nTPM
Spleen	38.7 nTPM
Bone marrow	36.8 nTPM
Breast	32.1 nTPM
Colon	27.1 nTPM
Kidney	23.8 nTPM
Adipose tissue	18.0 nTPM

Dendritic cells	47.0 nTPM
PBMC	55.8 nTPM
Breast	45.6 nTPM
Adipose tissue	39.7 nTPM

Endothelial cells	50.9 nTPM
Pancreas	92.6 nTPM
Placenta	77.9 nTPM
Testis	57.5 nTPM
Liver	55.9 nTPM
Ovary	54.3 nTPM
Skeletal muscle	54.1 nTPM
Lung	53.0 nTPM
Breast	52.1 nTPM
Skin	51.1 nTPM
Esophagus	41.3 nTPM
Prostate	40.1 nTPM
Eye	38.8 nTPM
Endometrium	31.8 nTPM
Heart muscle	11.8 nTPM

Fibroblasts	47.0 nTPM
Placenta	100.7 nTPM
Adipose tissue	56.1 nTPM
Ovary	54.3 nTPM
Esophagus	53.5 nTPM
Skin	51.9 nTPM
Breast	47.5 nTPM
Skeletal muscle	40.3 nTPM
Prostate	39.0 nTPM
Stomach	34.1 nTPM
Lung	26.8 nTPM
Heart muscle	13.0 nTPM

Intestinal goblet cells	56.4 nTPM
Colon	77.2 nTPM
Rectum	47.0 nTPM
Small intestine	45.1 nTPM

Macrophages	40.9 nTPM
Pancreas	61.2 nTPM
Kidney	54.4 nTPM
Bone marrow	53.7 nTPM
Stomach	49.8 nTPM
Breast	46.6 nTPM
Esophagus	42.5 nTPM
Testis	42.4 nTPM
Adipose tissue	41.7 nTPM
Endometrium	40.3 nTPM
Ovary	36.6 nTPM
Lung	36.0 nTPM
Prostate	34.4 nTPM
Spleen	31.1 nTPM
Skeletal muscle	28.6 nTPM
PBMC	13.6 nTPM

Paneth cells	48.9 nTPM
Colon	52.6 nTPM
Small intestine	48.8 nTPM
Rectum	45.1 nTPM

Plasma cells	43.7 nTPM
Stomach	59.5 nTPM
Spleen	53.6 nTPM
Bone marrow	42.9 nTPM
Esophagus	36.9 nTPM
Adipose tissue	25.8 nTPM

Respiratory ciliated cells	44.5 nTPM
Bronchus	59.8 nTPM
Lung	29.1 nTPM

Smooth muscle cells	92.4 nTPM
Bronchus	417.9 nTPM
Pancreas	129.9 nTPM
Ovary	70.9 nTPM
Skin	66.2 nTPM
Breast	65.7 nTPM
Esophagus	60.4 nTPM
Skeletal muscle	59.2 nTPM
Adipose tissue	45.5 nTPM
Prostate	44.4 nTPM
Endometrium	40.4 nTPM
Heart muscle	16.1 nTPM

T-cells	44.9 nTPM
Kidney	66.4 nTPM
Esophagus	65.5 nTPM
Skin	58.5 nTPM
Stomach	53.5 nTPM
Prostate	52.1 nTPM
Colon	49.9 nTPM
Liver	47.8 nTPM
Bone marrow	45.2 nTPM
Spleen	43.4 nTPM
Lymph node	40.1 nTPM
Ovary	40.0 nTPM
Breast	40.0 nTPM
PBMC	38.8 nTPM
Endometrium	34.5 nTPM
Lung	33.4 nTPM
Adipose tissue	28.5 nTPM
Skeletal muscle	25.9 nTPM

Basal respiratory cells	94.3 nTPM
Bronchus	94.3 nTPM

Basal squamous epithelial cells	43.9 nTPM
Esophagus	43.9 nTPM

Collecting duct cells	53.3 nTPM
Kidney	53.3 nTPM

Cone photoreceptor cells	12.5 nTPM
Eye	12.5 nTPM

Undifferentiated cells	64.7 nTPM
Colon	89.1 nTPM
Small intestine	55.6 nTPM
Rectum	49.4 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