Single cell type - RNF213 - The Human Protein Atlas

RNF213

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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.	RNF213
Gene descriptionⁱ Full gene name according to HGNC.	Ring finger protein 213
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Enzymes Human disease related genes Potential drug targets
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.	Membrane, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4

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.	NK-cells - Adaptive immune response (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 (NK-cells, Alveolar cells type 1, Exocrine glandular 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.	0.33
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 (Leukocyte, Central nervous system macrophage)
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 (NK-cells, Alveolar cells type 1, Exocrine glandular 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 (Leukocyte, Central nervous system macrophage)

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

RNF213 is part of cluster 19 NK-cells - Adaptive immune response with confidenceⁱ 1
266 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.
IL32	Interleukin 32	0.6167	45
APOL6	Apolipoprotein L6	0.5962	78
UNC5CL	Unc-5 family C-terminal like	0.5925	38
ITGAL	Integrin subunit alpha L	0.5543	19
CC2D1B	Coiled-coil and C2 domain containing 1B	0.5535	33
TC2N	Tandem C2 domains, nuclear	0.5419	78
IL12RB1	Interleukin 12 receptor subunit beta 1	0.5416	19
TRBC1	T cell receptor beta constant 1	0.5320	19
STK10	Serine/threonine kinase 10	0.5277	19
CD8B	CD8b molecule	0.5274	19
DUOXA2	Dual oxidase maturation factor 2	0.5254	45
ADAR	Adenosine deaminase RNA specific	0.5250	58
SH2D1A	SH2 domain containing 1A	0.5248	19
HCST	Hematopoietic cell signal transducer	0.5225	19
RTP4	Receptor transporter protein 4	0.5219	14

IMMUNE CELLS

RNF213 is part of cluster 35 Neutrophils - Protein binding with confidenceⁱ 0.69
504 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.
SYTL4	Synaptotagmin like 4	0.9762	35
AGO2	Argonaute RISC catalytic component 2	0.9524	35
ENSG00000289282	Novel protein	0.9524	35
MBD6	Methyl-CpG binding domain protein 6	0.9524	35
CCNJL	Cyclin J like	0.9524	35
AOC2	Amine oxidase copper containing 2	0.9524	35
DOK4	Docking protein 4	0.9524	35
MPL	MPL proto-oncogene, thrombopoietin receptor	0.9524	35
MADCAM1	Mucosal vascular addressin cell adhesion molecule 1	0.9524	35
RLF	RLF zinc finger	0.9286	35
TPD52L1	TPD52 like 1	0.9286	20
PSD4	Pleckstrin and Sec7 domain containing 4	0.9286	24
ATG2A	Autophagy related 2A	0.9286	35
ALOX12	Arachidonate 12-lipoxygenase, 12S type	0.9286	35
GABARAPL1	GABA type A receptor associated protein like 1	0.9286	35

Adipocytes	76.6 nTPM
Breast	87.8 nTPM
Adipose tissue	65.4 nTPM

Alveolar cells type 1	328.2 nTPM
Lung	328.2 nTPM

Alveolar cells type 2	87.9 nTPM
Lung	87.9 nTPM

Astrocytes	53.9 nTPM
Brain	53.9 nTPM

B-cells	76.7 nTPM
Salivary gland	110.6 nTPM
Thymus	104.7 nTPM
Lung	103.3 nTPM
Adipose tissue	97.9 nTPM
PBMC	83.1 nTPM
Bone marrow	82.8 nTPM
Liver	82.1 nTPM
Lymph node	69.0 nTPM
Spleen	65.9 nTPM
Kidney	62.4 nTPM
Esophagus	53.1 nTPM
Stomach	53.1 nTPM
Skin	28.8 nTPM

Ciliated cells	58.4 nTPM
Bronchus	90.1 nTPM
Endometrium	53.2 nTPM
Lung	49.4 nTPM
Fallopian tube	40.7 nTPM

Club cells	66.2 nTPM
Prostate	70.3 nTPM
Lung	66.4 nTPM
Bronchus	61.8 nTPM

Dendritic cells	120.3 nTPM
PBMC	129.5 nTPM
Adipose tissue	111.2 nTPM

Endothelial cells	89.3 nTPM
Heart muscle	169.1 nTPM
Ovary	130.9 nTPM
Vascular	119.2 nTPM
Skeletal muscle	113.3 nTPM
Salivary gland	112.9 nTPM
Testis	98.6 nTPM
Thymus	97.1 nTPM
Tongue	86.4 nTPM
Lung	84.5 nTPM
Endometrium	81.6 nTPM
Skin	74.8 nTPM
Esophagus	73.4 nTPM
Liver	70.5 nTPM
Breast	65.9 nTPM
Pancreas	64.6 nTPM
Prostate	61.9 nTPM
Placenta	56.2 nTPM
Fallopian tube	47.4 nTPM

Enteroendocrine cells	48.8 nTPM
Small intestine	79.0 nTPM
Rectum	38.6 nTPM
Colon	28.8 nTPM

Fibroblasts	53.2 nTPM
Liver	93.7 nTPM
Vascular	76.8 nTPM
Salivary gland	73.6 nTPM
Skeletal muscle	70.7 nTPM
Thymus	62.1 nTPM
Esophagus	57.6 nTPM
Skin	55.9 nTPM
Breast	54.8 nTPM
Adipose tissue	51.9 nTPM
Lung	50.2 nTPM
Heart muscle	48.1 nTPM
Pancreas	42.0 nTPM
Prostate	37.0 nTPM
Stomach	36.0 nTPM
Fallopian tube	32.6 nTPM
Placenta	7.6 nTPM

Granulocytes	48.4 nTPM
Lung	59.5 nTPM
Fallopian tube	51.7 nTPM
Tongue	34.0 nTPM

Intestinal goblet cells	63.5 nTPM
Small intestine	118.6 nTPM
Rectum	41.6 nTPM
Colon	30.3 nTPM

Lymphatic endothelial cells	122.7 nTPM
Ovary	196.4 nTPM
Fallopian tube	49.1 nTPM

Macrophages	140.5 nTPM
Lung	211.0 nTPM
Thymus	197.5 nTPM
Fallopian tube	186.6 nTPM
Vascular	185.7 nTPM
Salivary gland	183.1 nTPM
Spleen	177.4 nTPM
Skeletal muscle	176.0 nTPM
Bone marrow	147.0 nTPM
Stomach	131.2 nTPM
Kidney	124.8 nTPM
Prostate	122.7 nTPM
Breast	122.5 nTPM
Esophagus	122.0 nTPM
Tongue	119.1 nTPM
Testis	112.2 nTPM
Endometrium	104.5 nTPM
Adipose tissue	98.0 nTPM
Pancreas	78.1 nTPM
Skin	69.1 nTPM

Basal keratinocytes	39.7 nTPM
Tongue	46.2 nTPM
Skin	33.2 nTPM

Basal prostatic cells	44.0 nTPM
Prostate	44.0 nTPM

Basal respiratory cells	37.8 nTPM
Bronchus	37.8 nTPM

Basal squamous epithelial cells	40.3 nTPM
Esophagus	40.3 nTPM

Paneth cells	51.1 nTPM
Small intestine	82.9 nTPM
Colon	36.2 nTPM
Rectum	34.2 nTPM

Plasma cells	123.5 nTPM
Bone marrow	250.7 nTPM
Thymus	185.8 nTPM
Spleen	171.5 nTPM
Liver	136.2 nTPM
Salivary gland	89.5 nTPM
Stomach	74.1 nTPM
Fallopian tube	49.2 nTPM
Esophagus	31.2 nTPM

Schwann cells	76.4 nTPM
Vascular	130.1 nTPM
Esophagus	83.9 nTPM
Adipose tissue	15.2 nTPM

Serous glandular cells	46.9 nTPM
Salivary gland	58.3 nTPM
Tongue	35.4 nTPM

Smooth muscle cells	54.6 nTPM
Liver	83.6 nTPM
Vascular	80.5 nTPM
Thymus	68.7 nTPM
Salivary gland	67.5 nTPM
Lung	61.1 nTPM
Skeletal muscle	58.4 nTPM
Tongue	57.8 nTPM
Endometrium	54.0 nTPM
Breast	52.0 nTPM
Adipose tissue	51.9 nTPM
Skin	50.4 nTPM
Esophagus	49.3 nTPM
Ovary	48.5 nTPM
Prostate	34.1 nTPM
Placenta	32.3 nTPM
Fallopian tube	23.7 nTPM

Suprabasal keratinocytes	35.7 nTPM
Tongue	36.6 nTPM
Skin	34.8 nTPM

T-cells	209.9 nTPM
Skeletal muscle	314.2 nTPM
Bone marrow	290.7 nTPM
Tongue	279.3 nTPM
Adipose tissue	270.9 nTPM
PBMC	257.3 nTPM
Lung	250.5 nTPM
Endometrium	249.4 nTPM
Vascular	223.1 nTPM
Liver	218.2 nTPM
Breast	215.1 nTPM
Spleen	211.6 nTPM
Fallopian tube	203.1 nTPM
Esophagus	192.3 nTPM
Kidney	180.0 nTPM
Salivary gland	179.9 nTPM
Thymus	175.4 nTPM
Stomach	159.2 nTPM
Lymph node	157.6 nTPM
Skin	152.1 nTPM
Colon	120.9 nTPM
Prostate	107.2 nTPM

Undifferentiated cells	31.3 nTPM
Small intestine	43.7 nTPM
Rectum	27.4 nTPM
Colon	22.7 nTPM

Amygdala excitatory	29.4 nTPM
Thalamus	43.1 nTPM
Cerebral cortex	41.4 nTPM
Hippocampus	32.5 nTPM
Amygdala	24.3 nTPM
Basal ganglia	23.0 nTPM
Hypothalamus	12.3 nTPM

Astrocyte	164.3 nTPM
Cerebellum	213.2 nTPM
Midbrain	194.4 nTPM
Pons	194.2 nTPM
Thalamus	189.4 nTPM
Spinal cord	158.1 nTPM
Medulla oblongata	157.2 nTPM
Amygdala	154.7 nTPM
Hypothalamus	140.5 nTPM
Basal ganglia	140.2 nTPM
Hippocampus	140.2 nTPM
Cerebral cortex	124.9 nTPM

Bergmann glia	140.8 nTPM
Cerebellum	152.3 nTPM
Medulla oblongata	136.4 nTPM
Pons	133.8 nTPM

Central nervous system macrophage	373.0 nTPM
Amygdala	526.0 nTPM
Midbrain	420.7 nTPM
Thalamus	398.2 nTPM
Cerebral cortex	375.7 nTPM
Hippocampus	371.8 nTPM
Pons	362.0 nTPM
Basal ganglia	358.7 nTPM
Cerebellum	346.6 nTPM
Hypothalamus	326.6 nTPM
Spinal cord	320.0 nTPM
Medulla oblongata	296.8 nTPM

Cerebellar inhibitory	28.5 nTPM
Medulla oblongata	37.9 nTPM
Pons	30.2 nTPM
Cerebellum	26.4 nTPM
Midbrain	25.8 nTPM
Spinal cord	22.0 nTPM

Cge interneuron	16.5 nTPM
Cerebral cortex	20.9 nTPM
Hippocampus	18.0 nTPM
Basal ganglia	16.9 nTPM
Thalamus	16.4 nTPM
Amygdala	15.6 nTPM
Midbrain	15.5 nTPM
Hypothalamus	12.4 nTPM

Choroid plexus epithelial cell	56.4 nTPM
Hippocampus	58.2 nTPM
Basal ganglia	57.9 nTPM
Thalamus	57.5 nTPM
Medulla oblongata	52.0 nTPM

Committed oligodendrocyte precursor	58.1 nTPM
Thalamus	91.0 nTPM
Hypothalamus	81.9 nTPM
Hippocampus	69.8 nTPM
Amygdala	68.2 nTPM
Cerebral cortex	65.2 nTPM
Basal ganglia	52.6 nTPM
Spinal cord	51.5 nTPM
Cerebellum	49.2 nTPM
Midbrain	48.7 nTPM
Pons	44.3 nTPM
Medulla oblongata	16.8 nTPM

Deep-layer corticothalamic and 6b	34.2 nTPM
Cerebral cortex	43.6 nTPM
Hippocampus	40.1 nTPM
Midbrain	38.8 nTPM
Basal ganglia	34.1 nTPM
Amygdala	29.9 nTPM
Hypothalamus	18.7 nTPM

Deep-layer intratelencephalic	30.2 nTPM
Cerebral cortex	36.8 nTPM
Basal ganglia	34.3 nTPM
Hippocampus	32.9 nTPM
Amygdala	27.1 nTPM
Hypothalamus	19.8 nTPM

Deep-layer near-projecting	42.3 nTPM
Cerebral cortex	55.7 nTPM
Amygdala	48.5 nTPM
Basal ganglia	46.8 nTPM
Hippocampus	44.9 nTPM
Hypothalamus	15.4 nTPM

Eccentric medium spiny neuron	29.3 nTPM
Basal ganglia	41.5 nTPM
Cerebral cortex	33.1 nTPM
Hypothalamus	26.8 nTPM
Thalamus	26.2 nTPM
Amygdala	24.4 nTPM
Hippocampus	23.6 nTPM