Single cell type - RNF113A - The Human Protein Atlas

RNF113A

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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.	RNF113A
Gene descriptionⁱ Full gene name according to HGNC.	Ring finger protein 113A
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	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.	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	1

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.	Low cell type specificity
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.	0.32
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: Low cell type specificity

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

RNF113A is part of cluster 19 NK-cells - Adaptive immune response with confidenceⁱ 0.99
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.
TRGC2	T cell receptor gamma constant 2	0.6017	19
IFNG	Interferon gamma	0.5998	19
TBCC	Tubulin folding cofactor C	0.5959	78
APOBEC3G	Apolipoprotein B mRNA editing enzyme catalytic subunit 3G	0.5906	19
TRBC2	T cell receptor beta constant 2	0.5832	78
BTN3A1	Butyrophilin subfamily 3 member A1	0.5794	19
TRBC1	T cell receptor beta constant 1	0.5753	19
PTPN7	Protein tyrosine phosphatase non-receptor type 7	0.5708	19
ANXA2R	Annexin A2 receptor	0.5676	19
SLFN12L	Schlafen family member 12 like	0.5474	19
TRAC	T cell receptor alpha constant	0.5434	19
TBC1D10C	TBC1 domain family member 10C	0.5353	19
CCDC88C	Coiled-coil domain containing 88C	0.5320	19
SLAMF6	SLAM family member 6	0.5257	19
IL2RG	Interleukin 2 receptor subunit gamma	0.5207	19

IMMUNE CELLS

RNF113A is part of cluster 3 Non-specific - Nuclear processes with confidenceⁱ 0.96
471 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.
CCDC167	Coiled-coil domain containing 167	0.9762	3
EMC9	ER membrane protein complex subunit 9	0.9762	12
GDPD5	Glycerophosphodiester phosphodiesterase domain containing 5	0.9762	3
ZCRB1	Zinc finger CCHC-type and RNA binding motif containing 1	0.9762	3
CDKN2C	Cyclin dependent kinase inhibitor 2C	0.9762	3
XAB2	XPA binding protein 2	0.9524	3
ZNF546	Zinc finger protein 546	0.9524	3
C12orf60	Chromosome 12 open reading frame 60	0.9524	3
BBS9	Bardet-Biedl syndrome 9	0.9524	3
HROB	Homologous recombination factor with OB-fold	0.9286	12
DCAF8	DDB1 and CUL4 associated factor 8	0.9286	3
SMAD3	SMAD family member 3	0.9286	3
RNF34	Ring finger protein 34	0.9286	3
PDXDC1	Pyridoxal dependent decarboxylase domain containing 1	0.9286	3
CSRNP2	Cysteine and serine rich nuclear protein 2	0.9048	3

Adipocytes	13.9 nTPM
Breast	19.3 nTPM
Adipose tissue	8.5 nTPM

Alveolar cells type 1	6.3 nTPM
Lung	6.3 nTPM

Alveolar cells type 2	9.9 nTPM
Lung	9.9 nTPM

Astrocytes	2.5 nTPM
Brain	2.5 nTPM

B-cells	38.4 nTPM
Kidney	62.4 nTPM
Lymph node	53.4 nTPM
Adipose tissue	45.3 nTPM
PBMC	41.6 nTPM
Bone marrow	41.0 nTPM
Lung	40.2 nTPM
Liver	38.6 nTPM
Thymus	34.8 nTPM
Spleen	34.2 nTPM
Stomach	31.2 nTPM
Salivary gland	30.6 nTPM
Esophagus	29.5 nTPM
Skin	16.9 nTPM

Ciliated cells	13.0 nTPM
Bronchus	22.1 nTPM
Endometrium	12.8 nTPM
Fallopian tube	9.4 nTPM
Lung	7.5 nTPM

Club cells	15.5 nTPM
Bronchus	22.6 nTPM
Prostate	13.8 nTPM
Lung	9.9 nTPM

Dendritic cells	29.4 nTPM
Adipose tissue	30.0 nTPM
PBMC	28.8 nTPM

Endothelial cells	15.4 nTPM
Pancreas	25.9 nTPM
Liver	25.2 nTPM
Esophagus	22.0 nTPM
Breast	20.2 nTPM
Skin	19.7 nTPM
Fallopian tube	16.1 nTPM
Heart muscle	15.3 nTPM
Ovary	14.8 nTPM
Endometrium	14.3 nTPM
Skeletal muscle	14.2 nTPM
Testis	14.0 nTPM
Prostate	13.7 nTPM
Placenta	13.1 nTPM
Tongue	10.8 nTPM
Thymus	10.6 nTPM
Salivary gland	9.9 nTPM
Lung	9.6 nTPM
Vascular	8.5 nTPM

Enteroendocrine cells	12.8 nTPM
Small intestine	17.2 nTPM
Colon	14.6 nTPM
Rectum	6.7 nTPM

Fibroblasts	13.9 nTPM
Pancreas	22.6 nTPM
Skin	20.8 nTPM
Placenta	18.2 nTPM
Esophagus	16.6 nTPM
Heart muscle	16.0 nTPM
Prostate	15.8 nTPM
Stomach	14.4 nTPM
Liver	13.0 nTPM
Breast	12.6 nTPM
Fallopian tube	12.0 nTPM
Thymus	11.6 nTPM
Adipose tissue	11.1 nTPM
Salivary gland	10.6 nTPM
Lung	9.3 nTPM
Vascular	9.0 nTPM
Skeletal muscle	8.3 nTPM

Granulocytes	24.5 nTPM
Lung	41.3 nTPM
Fallopian tube	22.5 nTPM
Tongue	9.7 nTPM

Intestinal goblet cells	16.3 nTPM
Colon	20.4 nTPM
Small intestine	17.3 nTPM
Rectum	11.1 nTPM

Lymphatic endothelial cells	9.0 nTPM
Fallopian tube	12.5 nTPM
Ovary	5.5 nTPM

Macrophages	15.8 nTPM
Breast	30.4 nTPM
Lung	24.6 nTPM
Endometrium	22.8 nTPM
Esophagus	21.8 nTPM
Pancreas	20.6 nTPM
Prostate	18.6 nTPM
Kidney	17.7 nTPM
Spleen	17.0 nTPM
Salivary gland	16.2 nTPM
Skin	15.6 nTPM
Testis	14.3 nTPM
Adipose tissue	14.2 nTPM
Fallopian tube	12.7 nTPM
Bone marrow	11.1 nTPM
Thymus	11.1 nTPM
Vascular	10.7 nTPM
Tongue	10.3 nTPM
Skeletal muscle	7.5 nTPM
Stomach	2.6 nTPM

Basal prostatic cells	17.9 nTPM
Prostate	17.9 nTPM

Basal squamous epithelial cells	26.1 nTPM
Esophagus	26.1 nTPM

Bipolar cells	12.1 nTPM
Eye	12.1 nTPM

Cholangiocytes	13.4 nTPM
Liver	13.4 nTPM

Paneth cells	16.2 nTPM
Small intestine	27.6 nTPM
Rectum	13.8 nTPM
Colon	7.2 nTPM

Plasma cells	46.9 nTPM
Esophagus	72.8 nTPM
Stomach	63.7 nTPM
Spleen	57.0 nTPM
Bone marrow	49.8 nTPM
Liver	46.1 nTPM
Thymus	36.5 nTPM
Salivary gland	32.2 nTPM
Fallopian tube	17.0 nTPM

Schwann cells	6.5 nTPM
Adipose tissue	16.4 nTPM
Vascular	3.1 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	12.5 nTPM
Salivary gland	16.2 nTPM
Tongue	8.8 nTPM

Smooth muscle cells	15.0 nTPM
Endometrium	21.7 nTPM
Liver	20.0 nTPM
Ovary	19.3 nTPM
Esophagus	19.2 nTPM
Skin	18.8 nTPM
Breast	17.9 nTPM
Placenta	17.6 nTPM
Prostate	17.6 nTPM
Lung	15.3 nTPM
Fallopian tube	13.0 nTPM
Thymus	12.2 nTPM
Tongue	12.0 nTPM
Vascular	10.2 nTPM
Skeletal muscle	9.4 nTPM
Salivary gland	8.1 nTPM
Adipose tissue	7.8 nTPM

Suprabasal keratinocytes	20.1 nTPM
Skin	22.3 nTPM
Tongue	18.0 nTPM

T-cells	48.0 nTPM
Liver	63.5 nTPM
Adipose tissue	60.5 nTPM
Breast	58.6 nTPM
Skin	58.5 nTPM
Prostate	57.0 nTPM
Lymph node	54.6 nTPM
Fallopian tube	54.6 nTPM
Lung	51.7 nTPM
Kidney	51.4 nTPM
Spleen	48.7 nTPM
Thymus	48.1 nTPM
Stomach	46.9 nTPM
PBMC	46.7 nTPM
Esophagus	43.8 nTPM
Endometrium	43.4 nTPM
Salivary gland	41.9 nTPM
Colon	40.0 nTPM
Bone marrow	38.1 nTPM
Tongue	36.8 nTPM
Skeletal muscle	35.2 nTPM
Vascular	27.3 nTPM

Undifferentiated cells	16.2 nTPM
Rectum	17.1 nTPM
Small intestine	16.2 nTPM
Colon	15.3 nTPM

Amygdala excitatory	2.7 nTPM
Hippocampus	3.4 nTPM
Thalamus	3.2 nTPM
Amygdala	2.9 nTPM
Cerebral cortex	2.9 nTPM
Basal ganglia	2.6 nTPM
Hypothalamus	1.3 nTPM

Astrocyte	2.7 nTPM
Basal ganglia	3.8 nTPM
Cerebral cortex	3.4 nTPM
Hippocampus	2.9 nTPM
Medulla oblongata	2.8 nTPM
Pons	2.7 nTPM
Spinal cord	2.7 nTPM
Thalamus	2.5 nTPM
Midbrain	2.4 nTPM
Amygdala	2.3 nTPM
Cerebellum	2.2 nTPM
Hypothalamus	2.1 nTPM

Bergmann glia	6.0 nTPM
Pons	7.2 nTPM
Medulla oblongata	6.4 nTPM
Cerebellum	4.5 nTPM

Central nervous system macrophage	10.0 nTPM
Medulla oblongata	13.3 nTPM
Basal ganglia	12.4 nTPM
Cerebral cortex	11.3 nTPM
Pons	10.9 nTPM
Midbrain	10.6 nTPM
Spinal cord	10.6 nTPM
Hippocampus	10.5 nTPM
Cerebellum	8.8 nTPM
Thalamus	7.7 nTPM
Hypothalamus	7.4 nTPM
Amygdala	6.7 nTPM

Cerebellar inhibitory	6.6 nTPM
Pons	9.1 nTPM
Spinal cord	8.2 nTPM
Medulla oblongata	5.5 nTPM
Midbrain	5.3 nTPM
Cerebellum	4.8 nTPM

Cge interneuron	4.6 nTPM
Thalamus	7.0 nTPM
Hippocampus	5.3 nTPM
Midbrain	4.7 nTPM
Basal ganglia	4.4 nTPM
Amygdala	4.3 nTPM
Cerebral cortex	4.3 nTPM
Hypothalamus	2.3 nTPM

Choroid plexus epithelial cell	2.5 nTPM
Medulla oblongata	3.8 nTPM
Hippocampus	2.8 nTPM
Thalamus	2.7 nTPM
Basal ganglia	0.8 nTPM

Committed oligodendrocyte precursor	5.4 nTPM
Spinal cord	11.0 nTPM
Cerebral cortex	8.9 nTPM
Pons	8.9 nTPM
Midbrain	7.6 nTPM
Hippocampus	6.5 nTPM
Cerebellum	4.8 nTPM
Thalamus	3.4 nTPM
Basal ganglia	2.7 nTPM
Medulla oblongata	2.6 nTPM
Amygdala	2.3 nTPM
Hypothalamus	1.4 nTPM

Deep-layer corticothalamic and 6b	3.4 nTPM
Midbrain	5.5 nTPM
Hippocampus	3.7 nTPM
Basal ganglia	3.6 nTPM
Cerebral cortex	3.4 nTPM
Amygdala	3.2 nTPM
Hypothalamus	0.7 nTPM

Deep-layer intratelencephalic	2.9 nTPM
Hippocampus	4.0 nTPM
Cerebral cortex	3.7 nTPM
Basal ganglia	3.4 nTPM
Amygdala	2.8 nTPM
Hypothalamus	0.8 nTPM

Deep-layer near-projecting	2.8 nTPM
Basal ganglia	4.4 nTPM
Cerebral cortex	3.6 nTPM
Hippocampus	2.9 nTPM
Amygdala	2.3 nTPM
Hypothalamus	0.9 nTPM

Eccentric medium spiny neuron	2.1 nTPM
Basal ganglia	2.5 nTPM
Hypothalamus	2.3 nTPM
Hippocampus	2.1 nTPM
Cerebral cortex	2.0 nTPM
Thalamus	1.9 nTPM
Amygdala	1.8 nTPM