Single cell type - RBM43 - The Human Protein Atlas

RBM43

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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.	RBM43
Gene descriptionⁱ Full gene name according to HGNC.	RNA binding motif protein 43
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.	2

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.	Ovarian stromal cells - 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 (Ovarian stromal 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.	0.47
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 (Ovarian stromal 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

RBM43 is part of cluster 6 Ovarian stromal cells - Transcription with confidenceⁱ 1
188 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.
ZNF66	Zinc finger protein 66	0.6703	6
TULP3	TUB like protein 3	0.6136	6
HP1BP3	Heterochromatin protein 1 binding protein 3	0.5698	55
TMSB15B	Thymosin beta 15B	0.5489	6
ZNF765	Zinc finger protein 765	0.5440	6
SCN7A	Sodium voltage-gated channel alpha subunit 7	0.5421	26
ZNF665	Zinc finger protein 665	0.5386	55
ENSG00000285218	Novel protein	0.5291	6
TMSB15B	Thymosin beta 15B	0.5283	6
COLEC11	Collectin subfamily member 11	0.5164	6
PCDHGA3	Protocadherin gamma subfamily A, 3	0.5144	26
NR5A1	Nuclear receptor subfamily 5 group A member 1	0.5137	6
ZFP90	ZFP90 zinc finger protein	0.5101	7
ZNF431	Zinc finger protein 431	0.5064	6
LHX9	LIM homeobox 9	0.5005	6

IMMUNE CELLS

RBM43 is part of cluster 43 Non-specific - Transcription & Translation with confidenceⁱ 0.5
433 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.
RPRD2	Regulation of nuclear pre-mRNA domain containing 2	1.0000	43
SFI1	SFI1 centrin binding protein	0.9762	43
ASTN2	Astrotactin 2	0.9524	39
PRAF2	PRA1 domain family member 2	0.9524	43
TRBJ2-4	T cell receptor beta joining 2-4	0.9524	39
TRBJ2-3	T cell receptor beta joining 2-3	0.9524	43
IPP	Intracisternal A particle-promoted polypeptide	0.9524	43
ZSCAN26	Zinc finger and SCAN domain containing 26	0.9524	43
THAP2	THAP domain containing 2	0.9524	43
VIRMA	Vir like m6A methyltransferase associated	0.9524	24
ATG14	Autophagy related 14	0.9524	43
PTBP2	Polypyrimidine tract binding protein 2	0.9524	43
DCAF17	DDB1 and CUL4 associated factor 17	0.9524	43
GNPNAT1	Glucosamine-phosphate N-acetyltransferase 1	0.9524	43
MSMO1	Methylsterol monooxygenase 1	0.9286	43

Adipocytes	27.6 nTPM
Adipose tissue	32.8 nTPM
Breast	22.3 nTPM

Alveolar cells type 1	6.5 nTPM
Lung	6.5 nTPM

Alveolar cells type 2	7.9 nTPM
Lung	7.9 nTPM

Astrocytes	2.8 nTPM
Brain	2.8 nTPM

B-cells	9.8 nTPM
Kidney	20.8 nTPM
Bone marrow	17.6 nTPM
Salivary gland	14.7 nTPM
PBMC	13.9 nTPM
Lymph node	12.9 nTPM
Skin	10.2 nTPM
Adipose tissue	9.9 nTPM
Liver	9.7 nTPM
Thymus	7.9 nTPM
Spleen	4.8 nTPM
Stomach	4.2 nTPM
Lung	1.3 nTPM
Esophagus	0.0 nTPM

Ciliated cells	29.4 nTPM
Endometrium	35.2 nTPM
Lung	34.2 nTPM
Fallopian tube	34.2 nTPM
Bronchus	13.9 nTPM

Club cells	8.0 nTPM
Prostate	12.9 nTPM
Lung	7.2 nTPM
Bronchus	4.0 nTPM

Endothelial cells	18.3 nTPM
Ovary	33.2 nTPM
Prostate	32.8 nTPM
Vascular	30.2 nTPM
Testis	26.6 nTPM
Esophagus	24.5 nTPM
Salivary gland	21.6 nTPM
Heart muscle	21.2 nTPM
Tongue	18.6 nTPM
Endometrium	16.7 nTPM
Skeletal muscle	16.7 nTPM
Breast	16.7 nTPM
Liver	13.9 nTPM
Skin	12.7 nTPM
Lung	11.3 nTPM
Thymus	11.1 nTPM
Placenta	10.8 nTPM
Fallopian tube	7.6 nTPM
Pancreas	2.6 nTPM

Enteroendocrine cells	4.9 nTPM
Rectum	8.4 nTPM
Small intestine	3.4 nTPM
Colon	2.7 nTPM

Fibroblasts	22.4 nTPM
Adipose tissue	42.5 nTPM
Esophagus	39.8 nTPM
Breast	34.0 nTPM
Vascular	29.3 nTPM
Prostate	29.0 nTPM
Salivary gland	27.2 nTPM
Skeletal muscle	26.6 nTPM
Heart muscle	21.5 nTPM
Liver	20.2 nTPM
Stomach	20.2 nTPM
Fallopian tube	16.6 nTPM
Skin	14.6 nTPM
Lung	12.8 nTPM
Thymus	11.9 nTPM
Placenta	7.0 nTPM
Pancreas	5.3 nTPM

Granulocytes	18.4 nTPM
Lung	28.7 nTPM
Tongue	14.6 nTPM
Fallopian tube	11.9 nTPM

Intestinal goblet cells	7.7 nTPM
Small intestine	11.3 nTPM
Rectum	7.9 nTPM
Colon	3.9 nTPM

Lymphatic endothelial cells	15.6 nTPM
Ovary	21.8 nTPM
Fallopian tube	9.4 nTPM

Macrophages	8.6 nTPM
Prostate	13.7 nTPM
Spleen	13.0 nTPM
Vascular	12.2 nTPM
Kidney	11.5 nTPM
Bone marrow	11.1 nTPM
Stomach	10.3 nTPM
Lung	10.1 nTPM
Testis	9.3 nTPM
Adipose tissue	9.0 nTPM
Salivary gland	8.1 nTPM
Skeletal muscle	7.9 nTPM
Fallopian tube	7.8 nTPM
Esophagus	7.7 nTPM
Breast	7.4 nTPM
Skin	6.7 nTPM
Endometrium	6.1 nTPM
Thymus	6.0 nTPM
Tongue	5.1 nTPM
Pancreas	0.0 nTPM

Paneth cells	5.2 nTPM
Small intestine	10.4 nTPM
Rectum	5.1 nTPM
Colon	0.0 nTPM

Basal prostatic cells	13.2 nTPM
Prostate	13.2 nTPM

Basal respiratory cells	5.5 nTPM
Bronchus	5.5 nTPM

Basal squamous epithelial cells	5.8 nTPM
Esophagus	5.8 nTPM

Bipolar cells	5.6 nTPM
Eye	5.6 nTPM

Plasma cells	4.8 nTPM
Fallopian tube	7.1 nTPM
Salivary gland	5.8 nTPM
Stomach	5.4 nTPM
Thymus	5.3 nTPM
Esophagus	5.2 nTPM
Spleen	3.6 nTPM
Liver	3.0 nTPM
Bone marrow	3.0 nTPM

Schwann cells	38.6 nTPM
Vascular	62.7 nTPM
Esophagus	47.9 nTPM
Adipose tissue	5.1 nTPM

Serous glandular cells	5.9 nTPM
Salivary gland	7.3 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	19.2 nTPM
Adipose tissue	40.5 nTPM
Ovary	33.1 nTPM
Lung	28.2 nTPM
Vascular	27.9 nTPM
Liver	24.2 nTPM
Tongue	22.8 nTPM
Prostate	18.9 nTPM
Esophagus	16.8 nTPM
Skeletal muscle	16.1 nTPM
Breast	15.3 nTPM
Placenta	13.1 nTPM
Salivary gland	12.7 nTPM
Fallopian tube	12.0 nTPM
Endometrium	11.7 nTPM
Thymus	8.4 nTPM
Skin	6.3 nTPM

T-cells	14.9 nTPM
PBMC	31.6 nTPM
Salivary gland	24.6 nTPM
Bone marrow	22.9 nTPM
Lymph node	21.9 nTPM
Vascular	20.1 nTPM
Adipose tissue	18.2 nTPM
Esophagus	17.0 nTPM
Fallopian tube	16.9 nTPM
Liver	15.5 nTPM
Lung	14.7 nTPM
Skeletal muscle	13.2 nTPM
Spleen	13.2 nTPM
Kidney	12.4 nTPM
Prostate	12.1 nTPM
Thymus	12.1 nTPM
Endometrium	10.0 nTPM
Tongue	9.3 nTPM
Skin	8.8 nTPM
Breast	8.3 nTPM
Stomach	7.8 nTPM
Colon	2.9 nTPM

Undifferentiated cells	4.6 nTPM
Small intestine	5.3 nTPM
Rectum	5.1 nTPM
Colon	3.4 nTPM

Amygdala excitatory	2.2 nTPM
Hypothalamus	3.4 nTPM
Hippocampus	2.6 nTPM
Cerebral cortex	2.4 nTPM
Amygdala	2.3 nTPM
Basal ganglia	2.2 nTPM
Thalamus	0.5 nTPM

Astrocyte	7.3 nTPM
Basal ganglia	9.2 nTPM
Thalamus	8.9 nTPM
Midbrain	8.6 nTPM
Amygdala	8.2 nTPM
Cerebral cortex	7.8 nTPM
Pons	7.8 nTPM
Hippocampus	7.4 nTPM
Hypothalamus	6.6 nTPM
Medulla oblongata	6.4 nTPM
Cerebellum	5.3 nTPM
Spinal cord	4.3 nTPM

Bergmann glia	7.9 nTPM
Pons	12.9 nTPM
Cerebellum	8.6 nTPM
Medulla oblongata	2.1 nTPM

Central nervous system macrophage	10.9 nTPM
Basal ganglia	12.6 nTPM
Amygdala	12.3 nTPM
Thalamus	12.3 nTPM
Midbrain	11.5 nTPM
Hippocampus	11.2 nTPM
Cerebral cortex	10.9 nTPM
Medulla oblongata	10.5 nTPM
Pons	10.3 nTPM
Spinal cord	10.3 nTPM
Cerebellum	9.0 nTPM
Hypothalamus	8.4 nTPM

Cerebellar inhibitory	8.3 nTPM
Spinal cord	13.7 nTPM
Midbrain	9.3 nTPM
Medulla oblongata	7.2 nTPM
Cerebellum	7.0 nTPM
Pons	4.1 nTPM

Cge interneuron	2.4 nTPM
Basal ganglia	2.7 nTPM
Thalamus	2.7 nTPM
Cerebral cortex	2.6 nTPM
Hippocampus	2.5 nTPM
Midbrain	2.3 nTPM
Amygdala	1.9 nTPM
Hypothalamus	1.8 nTPM

Choroid plexus epithelial cell	6.3 nTPM
Basal ganglia	9.9 nTPM
Hippocampus	8.3 nTPM
Medulla oblongata	6.8 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	7.8 nTPM
Spinal cord	22.1 nTPM
Pons	10.6 nTPM
Medulla oblongata	10.3 nTPM
Basal ganglia	7.1 nTPM
Cerebral cortex	6.3 nTPM
Hippocampus	6.0 nTPM
Midbrain	5.9 nTPM
Hypothalamus	5.5 nTPM
Amygdala	5.1 nTPM
Cerebellum	4.8 nTPM
Thalamus	2.0 nTPM

Deep-layer corticothalamic and 6b	0.8 nTPM
Basal ganglia	1.7 nTPM
Hypothalamus	1.2 nTPM
Cerebral cortex	0.9 nTPM
Hippocampus	0.8 nTPM
Amygdala	0.5 nTPM
Midbrain	0.0 nTPM

Deep-layer intratelencephalic	1.3 nTPM
Basal ganglia	1.8 nTPM
Amygdala	1.7 nTPM
Cerebral cortex	1.3 nTPM
Hippocampus	1.2 nTPM
Hypothalamus	0.6 nTPM

Deep-layer near-projecting	0.1 nTPM
Basal ganglia	0.2 nTPM
Cerebral cortex	0.2 nTPM
Hypothalamus	0.2 nTPM
Amygdala	0.0 nTPM
Hippocampus	0.0 nTPM

Eccentric medium spiny neuron	3.0 nTPM
Hippocampus	4.6 nTPM
Hypothalamus	3.8 nTPM
Amygdala	3.5 nTPM
Cerebral cortex	2.8 nTPM
Basal ganglia	1.9 nTPM
Thalamus	1.5 nTPM

Endothelial cell	15.1 nTPM
Thalamus	22.0 nTPM
Hippocampus	19.6 nTPM
Medulla oblongata	19.5 nTPM
Hypothalamus	14.9 nTPM
Amygdala	14.5 nTPM
Cerebellum	13.9 nTPM
Pons	13.7 nTPM
Midbrain	13.2 nTPM
Cerebral cortex	12.8 nTPM
Basal ganglia	12.1 nTPM
Spinal cord	10.4 nTPM

Ependymal cell	18.3 nTPM
Spinal cord	32.6 nTPM
Thalamus	21.9 nTPM
Hippocampus	17.9 nTPM
Amygdala	17.1 nTPM
Hypothalamus	17.0 nTPM
Midbrain	16.5 nTPM
Medulla oblongata	14.3 nTPM
Basal ganglia	14.2 nTPM
Pons	13.0 nTPM