Single cell type - RBM4B - The Human Protein Atlas

RBM4B

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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.	RBM4B
Gene descriptionⁱ Full gene name according to HGNC.	RNA binding motif protein 4B
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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	5

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.	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.	Cell type enhanced (Rod photoreceptor cells)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.38
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	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.	Low immune cell specificity
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Cell type enhanced (Rod photoreceptor cells)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Low cell type specificity

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Low immune cell specificity
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

RBM4B is part of cluster 55 Non-specific - Transcription with confidenceⁱ 1
709 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
ZNF16	Zinc finger protein 16	0.4579	55
PIGU	Phosphatidylinositol glycan anchor biosynthesis class U	0.4420	39
ANAPC2	Anaphase promoting complex subunit 2	0.4160	15
TSEN34	TRNA splicing endonuclease subunit 34	0.4130	6
DMAP1	DNA methyltransferase 1 associated protein 1	0.4096	24
ATAT1	Alpha tubulin acetyltransferase 1	0.4089	10
RALGPS2	Ral GEF with PH domain and SH3 binding motif 2	0.4049	73
TAF1A	TATA-box binding protein associated factor, RNA polymerase I subunit A	0.4025	49
ZFP82	ZFP82 zinc finger protein	0.3974	55
L3MBTL1	L3MBTL histone methyl-lysine binding protein 1	0.3971	55
FANCL	FA complementation group L	0.3955	51
CLEC17A	C-type lectin domain containing 17A	0.3954	73
MED6	Mediator complex subunit 6	0.3926	55
PRPF40B	Pre-mRNA processing factor 40 homolog B	0.3897	31
ATF6B	Activating transcription factor 6 beta	0.3871	55

IMMUNE CELLS

RBM4B is part of cluster 42 Non-specific - Vesicular transport with confidenceⁱ 0.99
519 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
PIGH	Phosphatidylinositol glycan anchor biosynthesis class H	0.9048	42
PRDM4	PR/SET domain 4	0.9048	42
PRKAB1	Protein kinase AMP-activated non-catalytic subunit beta 1	0.9048	42
GFM2	GTP dependent ribosome recycling factor mitochondrial 2	0.8810	42
ARMH3	Armadillo like helical domain containing 3	0.8571	42
PTPN1	Protein tyrosine phosphatase non-receptor type 1	0.8571	32
MICU2	Mitochondrial calcium uptake 2	0.8571	42
CASP3	Caspase 3	0.8571	42
PDHA1	Pyruvate dehydrogenase E1 subunit alpha 1	0.8571	42
ELL2	Elongation factor for RNA polymerase II 2	0.8571	22
PHTF2	Putative homeodomain transcription factor 2	0.8333	42
MEA1	Male-enhanced antigen 1	0.8333	42
ACVR1B	Activin A receptor type 1B	0.8333	42
ISG20L2	Interferon stimulated exonuclease gene 20 like 2	0.8333	42
IDNK	IDNK gluconokinase	0.8333	32

Adipocytes	8.1 nTPM
Breast	11.0 nTPM
Adipose tissue	5.1 nTPM

Alveolar cells type 1	2.9 nTPM
Lung	2.9 nTPM

Alveolar cells type 2	4.0 nTPM
Lung	4.0 nTPM

Astrocytes	14.6 nTPM
Brain	14.6 nTPM

B-cells	25.2 nTPM
PBMC	46.2 nTPM
Stomach	34.2 nTPM
Spleen	32.9 nTPM
Lymph node	30.3 nTPM
Esophagus	29.5 nTPM
Liver	29.0 nTPM
Bone marrow	28.4 nTPM
Kidney	20.8 nTPM
Lung	17.4 nTPM
Thymus	17.1 nTPM
Adipose tissue	15.6 nTPM
Salivary gland	14.0 nTPM
Skin	11.9 nTPM

Ciliated cells	15.9 nTPM
Bronchus	21.4 nTPM
Lung	19.6 nTPM
Fallopian tube	11.6 nTPM
Endometrium	11.1 nTPM

Club cells	12.7 nTPM
Bronchus	21.1 nTPM
Lung	9.0 nTPM
Prostate	7.9 nTPM

Endothelial cells	9.0 nTPM
Ovary	20.9 nTPM
Placenta	13.6 nTPM
Pancreas	12.9 nTPM
Testis	12.2 nTPM
Endometrium	10.9 nTPM
Breast	10.5 nTPM
Esophagus	10.0 nTPM
Heart muscle	9.7 nTPM
Fallopian tube	8.3 nTPM
Prostate	8.0 nTPM
Thymus	7.1 nTPM
Skeletal muscle	6.9 nTPM
Skin	6.0 nTPM
Salivary gland	5.7 nTPM
Tongue	5.4 nTPM
Lung	5.2 nTPM
Vascular	4.1 nTPM
Liver	3.8 nTPM

Enteroendocrine cells	10.8 nTPM
Rectum	15.1 nTPM
Colon	10.4 nTPM
Small intestine	6.9 nTPM

Fibroblasts	12.0 nTPM
Placenta	25.3 nTPM
Heart muscle	20.2 nTPM
Breast	19.1 nTPM
Prostate	17.8 nTPM
Esophagus	17.0 nTPM
Fallopian tube	13.8 nTPM
Pancreas	13.3 nTPM
Skin	10.0 nTPM
Skeletal muscle	8.9 nTPM
Thymus	8.6 nTPM
Adipose tissue	8.0 nTPM
Liver	7.1 nTPM
Salivary gland	6.0 nTPM
Vascular	5.9 nTPM
Stomach	5.8 nTPM
Lung	5.3 nTPM

Granulocytes	7.5 nTPM
Fallopian tube	10.0 nTPM
Lung	7.6 nTPM
Tongue	4.9 nTPM

Intestinal goblet cells	13.1 nTPM
Small intestine	17.9 nTPM
Colon	14.5 nTPM
Rectum	6.9 nTPM

Lymphatic endothelial cells	8.4 nTPM
Ovary	10.9 nTPM
Fallopian tube	5.9 nTPM

Macrophages	7.3 nTPM
Pancreas	14.4 nTPM
Breast	12.9 nTPM
Kidney	11.5 nTPM
Bone marrow	10.1 nTPM
Skeletal muscle	8.8 nTPM
Lung	7.9 nTPM
Esophagus	7.7 nTPM
Stomach	7.7 nTPM
Adipose tissue	7.0 nTPM
Testis	6.8 nTPM
Skin	6.7 nTPM
Endometrium	6.1 nTPM
Spleen	6.0 nTPM
Fallopian tube	5.4 nTPM
Prostate	4.6 nTPM
Salivary gland	4.3 nTPM
Vascular	4.0 nTPM
Thymus	3.7 nTPM
Tongue	2.6 nTPM

Paneth cells	10.5 nTPM
Small intestine	20.7 nTPM
Rectum	7.0 nTPM
Colon	3.6 nTPM

Basal prostatic cells	8.7 nTPM
Prostate	8.7 nTPM

Basal squamous epithelial cells	17.5 nTPM
Esophagus	17.5 nTPM

Bipolar cells	35.5 nTPM
Eye	35.5 nTPM

Cholangiocytes	11.4 nTPM
Liver	11.4 nTPM

Plasma cells	13.0 nTPM
Spleen	20.9 nTPM
Stomach	16.8 nTPM
Thymus	12.4 nTPM
Bone marrow	12.1 nTPM
Fallopian tube	11.6 nTPM
Salivary gland	10.7 nTPM
Esophagus	10.4 nTPM
Liver	9.0 nTPM

Schwann cells	13.8 nTPM
Esophagus	24.0 nTPM
Adipose tissue	9.0 nTPM
Vascular	8.4 nTPM

Serous glandular cells	4.9 nTPM
Salivary gland	5.3 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	10.7 nTPM
Placenta	23.6 nTPM
Ovary	19.0 nTPM
Liver	14.4 nTPM
Esophagus	14.4 nTPM
Endometrium	13.9 nTPM
Breast	12.8 nTPM
Fallopian tube	12.0 nTPM
Skin	10.9 nTPM
Skeletal muscle	9.4 nTPM
Adipose tissue	9.1 nTPM
Thymus	7.4 nTPM
Prostate	6.7 nTPM
Salivary gland	6.5 nTPM
Vascular	5.1 nTPM
Tongue	4.2 nTPM
Lung	2.4 nTPM

T-cells	14.7 nTPM
Colon	28.3 nTPM
Esophagus	21.9 nTPM
Stomach	19.8 nTPM
Fallopian tube	19.5 nTPM
Breast	17.7 nTPM
Bone marrow	15.9 nTPM
Spleen	15.9 nTPM
Liver	14.9 nTPM
Skeletal muscle	14.7 nTPM
Kidney	14.2 nTPM
Adipose tissue	14.1 nTPM
Prostate	13.9 nTPM
Lymph node	13.5 nTPM
PBMC	13.4 nTPM
Thymus	11.7 nTPM
Lung	11.6 nTPM
Endometrium	11.0 nTPM
Salivary gland	10.1 nTPM
Tongue	9.6 nTPM
Skin	9.5 nTPM
Vascular	6.8 nTPM

Undifferentiated cells	12.5 nTPM
Small intestine	14.8 nTPM
Colon	12.8 nTPM
Rectum	9.7 nTPM

Amygdala excitatory	33.0 nTPM
Thalamus	51.7 nTPM
Cerebral cortex	42.0 nTPM
Hippocampus	34.6 nTPM
Amygdala	29.5 nTPM
Basal ganglia	28.9 nTPM
Hypothalamus	11.2 nTPM

Astrocyte	34.5 nTPM
Hypothalamus	47.6 nTPM
Cerebral cortex	41.1 nTPM
Hippocampus	38.3 nTPM
Basal ganglia	36.0 nTPM
Medulla oblongata	35.1 nTPM
Thalamus	33.9 nTPM
Midbrain	31.5 nTPM
Pons	30.9 nTPM
Amygdala	30.7 nTPM
Spinal cord	29.7 nTPM
Cerebellum	25.1 nTPM

Bergmann glia	58.8 nTPM
Medulla oblongata	66.1 nTPM
Cerebellum	61.5 nTPM
Pons	48.9 nTPM

Central nervous system macrophage	39.1 nTPM
Basal ganglia	48.2 nTPM
Hypothalamus	45.5 nTPM
Medulla oblongata	43.0 nTPM
Cerebellum	40.0 nTPM
Pons	39.9 nTPM
Cerebral cortex	39.6 nTPM
Thalamus	39.6 nTPM
Midbrain	35.8 nTPM
Hippocampus	35.5 nTPM
Amygdala	32.6 nTPM
Spinal cord	30.3 nTPM

Cerebellar inhibitory	41.5 nTPM
Medulla oblongata	50.3 nTPM
Spinal cord	41.2 nTPM
Pons	41.0 nTPM
Cerebellum	39.4 nTPM
Midbrain	35.5 nTPM

Cge interneuron	42.9 nTPM
Cerebral cortex	49.5 nTPM
Hippocampus	47.2 nTPM
Basal ganglia	46.2 nTPM
Midbrain	45.7 nTPM
Amygdala	43.8 nTPM
Thalamus	41.6 nTPM
Hypothalamus	26.4 nTPM

Choroid plexus epithelial cell	39.9 nTPM
Hippocampus	63.8 nTPM
Medulla oblongata	47.5 nTPM
Thalamus	24.7 nTPM
Basal ganglia	23.7 nTPM

Committed oligodendrocyte precursor	35.1 nTPM
Cerebral cortex	50.0 nTPM
Midbrain	47.0 nTPM
Hypothalamus	40.3 nTPM
Cerebellum	36.5 nTPM
Pons	36.3 nTPM
Basal ganglia	35.6 nTPM
Hippocampus	34.4 nTPM
Medulla oblongata	33.6 nTPM
Thalamus	32.9 nTPM
Amygdala	25.4 nTPM
Spinal cord	14.7 nTPM

Deep-layer corticothalamic and 6b	33.6 nTPM
Basal ganglia	45.7 nTPM
Midbrain	37.7 nTPM
Cerebral cortex	37.4 nTPM
Hippocampus	36.7 nTPM
Amygdala	34.5 nTPM
Hypothalamus	9.5 nTPM

Deep-layer intratelencephalic	34.5 nTPM
Basal ganglia	45.4 nTPM
Hippocampus	41.2 nTPM
Cerebral cortex	37.6 nTPM
Amygdala	37.2 nTPM
Hypothalamus	11.3 nTPM

Deep-layer near-projecting	44.2 nTPM
Hippocampus	65.0 nTPM
Basal ganglia	50.4 nTPM
Amygdala	47.8 nTPM
Cerebral cortex	44.1 nTPM
Hypothalamus	13.5 nTPM

Eccentric medium spiny neuron	35.5 nTPM
Cerebral cortex	43.3 nTPM
Basal ganglia	40.0 nTPM
Amygdala	39.6 nTPM
Hippocampus	31.1 nTPM
Hypothalamus	30.9 nTPM
Thalamus	28.0 nTPM

Endothelial cell	25.3 nTPM
Pons	36.8 nTPM
Hippocampus	32.7 nTPM
Thalamus	31.1 nTPM
Midbrain	29.3 nTPM
Cerebral cortex	28.8 nTPM
Cerebellum	27.1 nTPM
Medulla oblongata	24.6 nTPM
Basal ganglia	22.4 nTPM
Spinal cord	19.0 nTPM
Hypothalamus	14.9 nTPM
Amygdala	11.2 nTPM

Ependymal cell	52.9 nTPM
Medulla oblongata	67.6 nTPM
Midbrain	59.7 nTPM
Pons	55.0 nTPM
Thalamus	52.2 nTPM
Hippocampus	51.8 nTPM
Hypothalamus	51.8 nTPM
Spinal cord	47.9 nTPM
Amygdala	46.6 nTPM
Basal ganglia	43.8 nTPM