Single cell type - RBMS3 - The Human Protein Atlas

RBMS3

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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.	RBMS3
Gene descriptionⁱ Full gene name according to HGNC.	RNA binding motif single stranded interacting protein 3
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.	8

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.	Neurons - Synaptic function (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 (Microglial cells, Inhibitory neurons, Astrocytes, Oligodendrocyte precursor 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.	0.67
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.	Cell type enhanced (Fibroblast)
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.	Immune cell enriched (plasmacytoid DC)
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 (Microglial cells, Inhibitory neurons, Astrocytes, Oligodendrocyte precursor 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: Cell type enhanced (Fibroblast)

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: Immune cell enriched (plasmacytoid DC)
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

RBMS3 is part of cluster 65 Neurons - Synaptic function with confidenceⁱ 1
250 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.
FAM110B	Family with sequence similarity 110 member B	0.8174	65
PDGFD	Platelet derived growth factor D	0.8136	65
PTPRM	Protein tyrosine phosphatase receptor type M	0.7956	65
ALK	ALK receptor tyrosine kinase	0.7840	65
KCNAB1	Potassium voltage-gated channel subfamily A regulatory beta subunit 1	0.7770	65
MYO16	Myosin XVI	0.7768	65
ADAMTSL3	ADAMTS like 3	0.7702	65
EPHA3	EPH receptor A3	0.7550	65
SGCZ	Sarcoglycan zeta	0.7449	65
CTXND1	Cortexin domain containing 1	0.7440	65
TACR1	Tachykinin receptor 1	0.7424	65
PTCHD4	Patched domain containing 4	0.7367	65
FGF13	Fibroblast growth factor 13	0.7355	65
GAD2	Glutamate decarboxylase 2	0.7344	65
SLC6A1	Solute carrier family 6 member 1	0.7286	65

IMMUNE CELLS

RBMS3 is part of cluster 13 Non-specific - Mitochondria with confidenceⁱ 0.99
458 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.
ALG1L2	ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferase like 2	1.0000	13
RIOX2	Ribosomal oxygenase 2	1.0000	13
VASH2	Vasohibin 2	1.0000	13
ZGRF1	Zinc finger GRF-type containing 1	1.0000	13
WNT10A	Wnt family member 10A	1.0000	13
PLS3	Plastin 3	1.0000	13
COX16	Cytochrome c oxidase assembly factor COX16	1.0000	13
POMC	Proopiomelanocortin	0.9762	13
HS3ST3B1	Heparan sulfate-glucosamine 3-sulfotransferase 3B1	0.9762	13
ALG5	ALG5 dolichyl-phosphate beta-glucosyltransferase	0.9762	13
STMN1	Stathmin 1	0.9762	13
RWDD2A	RWD domain containing 2A	0.9762	13
DCPS	Decapping enzyme, scavenger	0.9762	13
USP46	Ubiquitin specific peptidase 46	0.9762	13
CDC6	Cell division cycle 6	0.9762	13

Adipocytes	96.5 nTPM
Adipose tissue	143.9 nTPM
Breast	49.1 nTPM

Alveolar cells type 1	110.7 nTPM
Lung	110.7 nTPM

Alveolar cells type 2	25.7 nTPM
Lung	25.7 nTPM

B-cells	1.1 nTPM
Lung	6.7 nTPM
Thymus	2.9 nTPM
Salivary gland	2.0 nTPM
Skin	1.7 nTPM
Adipose tissue	0.8 nTPM
Lymph node	0.3 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Basal keratinocytes	4.6 nTPM
Tongue	6.4 nTPM
Skin	2.9 nTPM

Ciliated cells	7.8 nTPM
Lung	15.9 nTPM
Bronchus	7.0 nTPM
Fallopian tube	5.6 nTPM
Endometrium	2.5 nTPM

Club cells	17.6 nTPM
Lung	33.8 nTPM
Bronchus	10.4 nTPM
Prostate	8.4 nTPM

Endothelial cells	59.5 nTPM
Prostate	101.3 nTPM
Vascular	96.7 nTPM
Salivary gland	89.0 nTPM
Skeletal muscle	84.3 nTPM
Liver	80.6 nTPM
Heart muscle	72.7 nTPM
Breast	71.2 nTPM
Testis	65.3 nTPM
Thymus	63.0 nTPM
Esophagus	58.9 nTPM
Tongue	53.0 nTPM
Ovary	52.8 nTPM
Fallopian tube	49.9 nTPM
Lung	42.3 nTPM
Endometrium	38.0 nTPM
Skin	27.2 nTPM
Placenta	16.5 nTPM
Pancreas	7.8 nTPM

Enteroendocrine cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	109.5 nTPM
Adipose tissue	213.3 nTPM
Vascular	180.7 nTPM
Salivary gland	179.9 nTPM
Esophagus	163.6 nTPM
Skeletal muscle	146.7 nTPM
Breast	114.1 nTPM
Liver	112.7 nTPM
Heart muscle	112.4 nTPM
Skin	102.3 nTPM
Fallopian tube	101.1 nTPM
Thymus	82.7 nTPM
Lung	73.9 nTPM
Prostate	73.9 nTPM
Stomach	54.8 nTPM
Placenta	31.1 nTPM
Pancreas	9.7 nTPM

Granulocytes	1.5 nTPM
Fallopian tube	3.1 nTPM
Lung	1.5 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.1 nTPM
Colon	0.2 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Lymphatic endothelial cells	50.8 nTPM
Fallopian tube	58.0 nTPM
Ovary	43.6 nTPM

Macrophages	4.9 nTPM
Prostate	16.1 nTPM
Thymus	15.0 nTPM
Vascular	11.7 nTPM
Skeletal muscle	10.0 nTPM
Testis	9.3 nTPM
Salivary gland	6.0 nTPM
Skin	4.5 nTPM
Esophagus	3.9 nTPM
Spleen	3.0 nTPM
Tongue	3.0 nTPM
Fallopian tube	2.7 nTPM
Stomach	2.6 nTPM
Bone marrow	2.0 nTPM
Breast	1.5 nTPM
Endometrium	1.2 nTPM
Lung	0.9 nTPM
Adipose tissue	0.7 nTPM
Kidney	0.0 nTPM
Pancreas	0.0 nTPM

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

Astrocytes	314.0 nTPM
Brain	314.0 nTPM

Bipolar cells	2.1 nTPM
Eye	2.1 nTPM

Cholangiocytes	34.3 nTPM
Liver	34.3 nTPM

Cytotrophoblasts	15.2 nTPM
Placenta	15.2 nTPM

Plasma cells	2.6 nTPM
Fallopian tube	10.6 nTPM
Esophagus	5.2 nTPM
Salivary gland	3.1 nTPM
Thymus	2.0 nTPM
Liver	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Schwann cells	38.9 nTPM
Esophagus	59.9 nTPM
Vascular	56.4 nTPM
Adipose tissue	0.4 nTPM

Serous glandular cells	17.0 nTPM
Salivary gland	25.1 nTPM
Tongue	8.8 nTPM

Smooth muscle cells	81.3 nTPM
Adipose tissue	156.5 nTPM
Liver	139.7 nTPM
Skeletal muscle	131.8 nTPM
Esophagus	127.3 nTPM
Vascular	115.1 nTPM
Tongue	97.6 nTPM
Prostate	75.4 nTPM
Salivary gland	67.3 nTPM
Ovary	66.1 nTPM
Breast	60.0 nTPM
Placenta	59.5 nTPM
Skin	57.5 nTPM
Thymus	43.0 nTPM
Endometrium	41.1 nTPM
Lung	34.1 nTPM
Fallopian tube	29.1 nTPM

T-cells	2.2 nTPM
Salivary gland	6.3 nTPM
Skin	6.0 nTPM
Skeletal muscle	6.0 nTPM
Vascular	5.2 nTPM
Lymph node	4.5 nTPM
Prostate	3.3 nTPM
Thymus	2.8 nTPM
Esophagus	2.4 nTPM
Lung	1.9 nTPM
Liver	1.8 nTPM
Fallopian tube	1.4 nTPM
Endometrium	1.3 nTPM
Kidney	0.9 nTPM
PBMC	0.9 nTPM
Breast	0.7 nTPM
Tongue	0.6 nTPM
Adipose tissue	0.4 nTPM
Spleen	0.2 nTPM
Bone marrow	0.1 nTPM
Stomach	0.1 nTPM
Colon	0.0 nTPM

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

Amygdala excitatory	276.5 nTPM
Thalamus	691.5 nTPM
Basal ganglia	329.6 nTPM
Hippocampus	185.7 nTPM
Amygdala	164.7 nTPM
Hypothalamus	150.4 nTPM
Cerebral cortex	137.2 nTPM

Astrocyte	1771.0 nTPM
Amygdala	3200.7 nTPM
Basal ganglia	2082.1 nTPM
Hippocampus	1936.0 nTPM
Hypothalamus	1914.9 nTPM
Thalamus	1789.5 nTPM
Midbrain	1776.0 nTPM
Cerebral cortex	1734.4 nTPM
Pons	1455.5 nTPM
Spinal cord	1410.7 nTPM
Medulla oblongata	1309.5 nTPM
Cerebellum	871.9 nTPM

Bergmann glia	734.3 nTPM
Pons	759.6 nTPM
Cerebellum	748.6 nTPM
Medulla oblongata	694.7 nTPM

Central nervous system macrophage	44.3 nTPM
Amygdala	81.4 nTPM
Cerebral cortex	78.1 nTPM
Thalamus	67.9 nTPM
Hippocampus	62.7 nTPM
Hypothalamus	46.1 nTPM
Spinal cord	33.0 nTPM
Pons	25.9 nTPM
Basal ganglia	24.3 nTPM
Cerebellum	23.7 nTPM
Midbrain	23.3 nTPM
Medulla oblongata	21.1 nTPM

Cerebellar inhibitory	204.8 nTPM
Pons	409.0 nTPM
Medulla oblongata	281.2 nTPM
Midbrain	188.8 nTPM
Cerebellum	109.5 nTPM
Spinal cord	35.7 nTPM

Cge interneuron	1502.8 nTPM
Thalamus	2234.9 nTPM
Amygdala	1555.4 nTPM
Hypothalamus	1481.3 nTPM
Hippocampus	1479.4 nTPM
Midbrain	1436.5 nTPM
Basal ganglia	1258.7 nTPM
Cerebral cortex	1073.6 nTPM

Choroid plexus epithelial cell	483.0 nTPM
Medulla oblongata	737.0 nTPM
Basal ganglia	598.0 nTPM
Hippocampus	413.2 nTPM
Thalamus	183.6 nTPM

Committed oligodendrocyte precursor	971.1 nTPM
Spinal cord	1471.7 nTPM
Midbrain	1391.9 nTPM
Hippocampus	1245.9 nTPM
Cerebellum	1222.5 nTPM
Amygdala	969.8 nTPM
Pons	921.6 nTPM
Cerebral cortex	920.9 nTPM
Medulla oblongata	750.1 nTPM
Basal ganglia	740.8 nTPM
Hypothalamus	592.7 nTPM
Thalamus	454.5 nTPM

Deep-layer corticothalamic and 6b	159.8 nTPM
Hypothalamus	264.6 nTPM
Amygdala	193.1 nTPM
Hippocampus	149.3 nTPM
Midbrain	139.8 nTPM
Cerebral cortex	110.2 nTPM
Basal ganglia	101.6 nTPM

Deep-layer intratelencephalic	105.8 nTPM
Amygdala	131.9 nTPM
Hypothalamus	123.1 nTPM
Hippocampus	104.0 nTPM
Cerebral cortex	85.1 nTPM
Basal ganglia	84.8 nTPM

Deep-layer near-projecting	169.6 nTPM
Cerebral cortex	237.3 nTPM
Amygdala	205.2 nTPM
Hippocampus	150.9 nTPM
Basal ganglia	132.0 nTPM
Hypothalamus	122.6 nTPM

Eccentric medium spiny neuron	618.9 nTPM
Amygdala	1119.2 nTPM
Hippocampus	911.9 nTPM
Cerebral cortex	699.2 nTPM
Thalamus	472.0 nTPM
Basal ganglia	275.2 nTPM
Hypothalamus	235.6 nTPM

Endothelial cell	2460.9 nTPM
Hypothalamus	3611.5 nTPM
Basal ganglia	3347.1 nTPM
Amygdala	2774.3 nTPM
Spinal cord	2426.7 nTPM
Hippocampus	2423.2 nTPM
Cerebral cortex	2258.7 nTPM
Cerebellum	2223.1 nTPM
Midbrain	2211.5 nTPM
Medulla oblongata	1937.3 nTPM
Thalamus	1935.6 nTPM
Pons	1921.2 nTPM

Ependymal cell	88.9 nTPM
Amygdala	255.4 nTPM
Midbrain	99.0 nTPM
Thalamus	91.1 nTPM
Hypothalamus	88.3 nTPM
Basal ganglia	73.5 nTPM
Pons	50.7 nTPM
Hippocampus	50.2 nTPM
Medulla oblongata	48.1 nTPM
Spinal cord	44.1 nTPM