Single cell type - UBR4 - The Human Protein Atlas

UBR4

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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.	UBR4
Gene descriptionⁱ Full gene name according to HGNC.	Ubiquitin protein ligase E3 component n-recognin 4
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes Metabolic proteins
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.	6

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.	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.	0.34
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.	Immune cell enhanced (basophil)
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: Immune cell enhanced (basophil)
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

UBR4 is part of cluster 49 Non-specific - Transcription with confidenceⁱ 1
378 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.
AFTPH	Aftiphilin	0.5270	55
RBM19	RNA binding motif protein 19	0.5210	49
TNKS2	Tankyrase 2	0.5166	55
EDC4	Enhancer of mRNA decapping 4	0.5023	49
SRCAP	Snf2 related CREBBP activator protein	0.5000	49
SPEN	Spen family transcriptional repressor	0.4968	37
EIF3C	Eukaryotic translation initiation factor 3 subunit C	0.4880	49
ACOT6	Acyl-CoA thioesterase 6	0.4839	56
ABCC1	ATP binding cassette subfamily C member 1	0.4795	78
RPP14	Ribonuclease P/MRP subunit p14	0.4713	49
API5	Apoptosis inhibitor 5	0.4699	49
ATG9A	Autophagy related 9A	0.4670	49
NUP205	Nucleoporin 205	0.4642	49
WDR83OS	WD repeat domain 83 opposite strand	0.4539	49
ZGPAT	Zinc finger CCCH-type and G-patch domain containing	0.4470	49

IMMUNE CELLS

UBR4 is part of cluster 38 Monocytes & Neutrophils - Degranulation with confidenceⁱ 0.97
501 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.
NBPF14	NBPF member 14	0.9762	38
CDHR4	Cadherin related family member 4	0.9762	38
FFAR4	Free fatty acid receptor 4	0.9762	38
FURIN	Furin, paired basic amino acid cleaving enzyme	0.9524	38
CLEC9A	C-type lectin domain containing 9A	0.9524	38
CACNB4	Calcium voltage-gated channel auxiliary subunit beta 4	0.9524	38
TLR6	Toll like receptor 6	0.9524	38
OLR1	Oxidized low density lipoprotein receptor 1	0.9524	38
SERTAD3	SERTA domain containing 3	0.9524	38
ACOT11	Acyl-CoA thioesterase 11	0.9524	38
GRN	Granulin precursor	0.9524	38
PRCP	Prolylcarboxypeptidase	0.9524	38
CNPY3	Canopy FGF signaling regulator 3	0.9524	38
TRPM4	Transient receptor potential cation channel subfamily M member 4	0.9524	38
PLAU	Plasminogen activator, urokinase	0.9524	38

Adipocytes	12.3 nTPM
Adipose tissue	14.6 nTPM
Breast	9.9 nTPM

Alveolar cells type 1	26.3 nTPM
Lung	26.3 nTPM

Alveolar cells type 2	18.8 nTPM
Lung	18.8 nTPM

Astrocytes	81.1 nTPM
Brain	81.1 nTPM

B-cells	24.0 nTPM
Thymus	47.8 nTPM
Spleen	36.9 nTPM
Bone marrow	35.1 nTPM
Lymph node	34.3 nTPM
Salivary gland	32.1 nTPM
Stomach	31.2 nTPM
Adipose tissue	23.0 nTPM
Esophagus	17.7 nTPM
Liver	14.5 nTPM
Lung	12.1 nTPM
Kidney	10.4 nTPM
Skin	10.2 nTPM
PBMC	6.2 nTPM

Ciliated cells	17.4 nTPM
Endometrium	20.6 nTPM
Fallopian tube	20.4 nTPM
Lung	17.0 nTPM
Bronchus	11.5 nTPM

Club cells	13.1 nTPM
Prostate	18.7 nTPM
Lung	11.4 nTPM
Bronchus	9.1 nTPM

Dendritic cells	26.3 nTPM
Adipose tissue	38.1 nTPM
PBMC	14.4 nTPM

Endothelial cells	17.8 nTPM
Thymus	41.2 nTPM
Esophagus	31.4 nTPM
Vascular	29.8 nTPM
Salivary gland	26.5 nTPM
Lung	23.3 nTPM
Skeletal muscle	19.5 nTPM
Heart muscle	18.4 nTPM
Endometrium	17.2 nTPM
Tongue	17.2 nTPM
Fallopian tube	14.8 nTPM
Prostate	14.0 nTPM
Ovary	13.4 nTPM
Testis	12.2 nTPM
Skin	12.2 nTPM
Liver	11.3 nTPM
Placenta	9.7 nTPM
Breast	6.2 nTPM
Pancreas	2.6 nTPM

Enteroendocrine cells	7.5 nTPM
Small intestine	10.3 nTPM
Colon	7.3 nTPM
Rectum	5.0 nTPM

Fibroblasts	18.8 nTPM
Esophagus	48.9 nTPM
Thymus	36.0 nTPM
Stomach	28.8 nTPM
Vascular	27.9 nTPM
Salivary gland	26.1 nTPM
Skeletal muscle	20.0 nTPM
Fallopian tube	16.8 nTPM
Skin	16.4 nTPM
Liver	15.4 nTPM
Lung	14.6 nTPM
Prostate	11.2 nTPM
Adipose tissue	10.6 nTPM
Breast	7.7 nTPM
Placenta	7.1 nTPM
Pancreas	6.9 nTPM
Heart muscle	6.0 nTPM

Granulocytes	34.1 nTPM
Tongue	38.8 nTPM
Fallopian tube	35.2 nTPM
Lung	28.2 nTPM

Intestinal goblet cells	11.0 nTPM
Small intestine	17.3 nTPM
Rectum	9.5 nTPM
Colon	6.2 nTPM

Lymphatic endothelial cells	13.2 nTPM
Fallopian tube	15.5 nTPM
Ovary	10.9 nTPM

Macrophages	30.6 nTPM
Stomach	100.3 nTPM
Thymus	51.3 nTPM
Spleen	45.1 nTPM
Bone marrow	36.5 nTPM
Esophagus	34.7 nTPM
Vascular	34.2 nTPM
Salivary gland	33.8 nTPM
Skeletal muscle	33.3 nTPM
Adipose tissue	31.4 nTPM
Fallopian tube	30.5 nTPM
Tongue	25.2 nTPM
Lung	21.8 nTPM
Prostate	19.7 nTPM
Kidney	19.5 nTPM
Testis	16.7 nTPM
Skin	16.7 nTPM
Endometrium	14.8 nTPM
Breast	9.8 nTPM
Pancreas	6.2 nTPM

Basal prostatic cells	20.2 nTPM
Prostate	20.2 nTPM

Basal respiratory cells	8.8 nTPM
Bronchus	8.8 nTPM

Bipolar cells	31.7 nTPM
Eye	31.7 nTPM

Distal enterocytes	12.4 nTPM
Colon	14.3 nTPM
Rectum	10.5 nTPM

Paneth cells	6.6 nTPM
Colon	14.5 nTPM
Rectum	5.3 nTPM
Small intestine	0.0 nTPM

Plasma cells	21.8 nTPM
Thymus	39.4 nTPM
Salivary gland	25.5 nTPM
Spleen	25.3 nTPM
Stomach	25.1 nTPM
Bone marrow	21.1 nTPM
Fallopian tube	20.9 nTPM
Esophagus	10.4 nTPM
Liver	7.0 nTPM

Schwann cells	27.8 nTPM
Esophagus	35.9 nTPM
Vascular	26.1 nTPM
Adipose tissue	21.5 nTPM

Serous glandular cells	18.9 nTPM
Salivary gland	28.9 nTPM
Tongue	8.8 nTPM

Smooth muscle cells	21.1 nTPM
Thymus	46.5 nTPM
Vascular	32.4 nTPM
Esophagus	30.0 nTPM
Salivary gland	29.5 nTPM
Lung	28.2 nTPM
Skeletal muscle	25.2 nTPM
Tongue	23.4 nTPM
Fallopian tube	17.7 nTPM
Endometrium	17.6 nTPM
Prostate	17.6 nTPM
Adipose tissue	16.9 nTPM
Skin	12.9 nTPM
Liver	12.3 nTPM
Ovary	10.5 nTPM
Breast	10.4 nTPM
Placenta	7.1 nTPM

Suprabasal keratinocytes	63.6 nTPM
Skin	106.6 nTPM
Tongue	20.6 nTPM

T-cells	26.5 nTPM
Thymus	44.0 nTPM
Esophagus	43.8 nTPM
Tongue	39.0 nTPM
Salivary gland	38.1 nTPM
Bone marrow	38.0 nTPM
Spleen	36.4 nTPM
Lymph node	35.3 nTPM
Stomach	33.5 nTPM
Skeletal muscle	29.9 nTPM
Vascular	29.3 nTPM
Adipose tissue	27.8 nTPM
Endometrium	25.9 nTPM
Fallopian tube	25.4 nTPM
Prostate	20.6 nTPM
Breast	19.9 nTPM
Skin	16.1 nTPM
Lung	15.0 nTPM
PBMC	13.4 nTPM
Colon	9.7 nTPM
Liver	8.0 nTPM
Kidney	7.1 nTPM

Undifferentiated cells	6.4 nTPM
Small intestine	6.9 nTPM
Rectum	6.5 nTPM
Colon	5.9 nTPM

Amygdala excitatory	101.2 nTPM
Amygdala	114.4 nTPM
Hippocampus	109.0 nTPM
Hypothalamus	107.8 nTPM
Cerebral cortex	99.0 nTPM
Thalamus	88.5 nTPM
Basal ganglia	88.3 nTPM

Astrocyte	151.1 nTPM
Amygdala	182.0 nTPM
Midbrain	172.3 nTPM
Cerebellum	172.2 nTPM
Thalamus	169.3 nTPM
Pons	161.5 nTPM
Hippocampus	152.7 nTPM
Cerebral cortex	143.9 nTPM
Basal ganglia	133.3 nTPM
Spinal cord	130.2 nTPM
Hypothalamus	124.6 nTPM
Medulla oblongata	119.7 nTPM

Bergmann glia	98.1 nTPM
Cerebellum	110.6 nTPM
Pons	96.4 nTPM
Medulla oblongata	87.4 nTPM

Central nervous system macrophage	90.5 nTPM
Amygdala	116.3 nTPM
Hypothalamus	97.9 nTPM
Midbrain	95.3 nTPM
Hippocampus	94.0 nTPM
Thalamus	91.2 nTPM
Cerebellum	89.5 nTPM
Pons	88.5 nTPM
Spinal cord	83.9 nTPM
Basal ganglia	82.7 nTPM
Cerebral cortex	81.4 nTPM
Medulla oblongata	75.2 nTPM

Cerebellar inhibitory	94.8 nTPM
Spinal cord	118.2 nTPM
Cerebellum	93.8 nTPM
Midbrain	90.5 nTPM
Medulla oblongata	86.9 nTPM
Pons	84.5 nTPM

Cge interneuron	91.8 nTPM
Hypothalamus	102.6 nTPM
Amygdala	97.5 nTPM
Thalamus	92.3 nTPM
Midbrain	91.2 nTPM
Hippocampus	89.3 nTPM
Cerebral cortex	86.1 nTPM
Basal ganglia	83.3 nTPM

Choroid plexus epithelial cell	74.3 nTPM
Basal ganglia	118.5 nTPM
Medulla oblongata	85.2 nTPM
Thalamus	52.1 nTPM
Hippocampus	41.6 nTPM

Committed oligodendrocyte precursor	83.1 nTPM
Spinal cord	114.1 nTPM
Thalamus	93.9 nTPM
Pons	93.8 nTPM
Amygdala	93.0 nTPM
Hippocampus	92.6 nTPM
Midbrain	79.8 nTPM
Cerebral cortex	77.9 nTPM
Hypothalamus	77.8 nTPM
Basal ganglia	75.6 nTPM
Cerebellum	61.8 nTPM
Medulla oblongata	54.2 nTPM

Deep-layer corticothalamic and 6b	87.3 nTPM
Hippocampus	106.6 nTPM
Hypothalamus	103.4 nTPM
Amygdala	101.9 nTPM
Cerebral cortex	80.6 nTPM
Basal ganglia	73.5 nTPM
Midbrain	57.7 nTPM

Deep-layer intratelencephalic	108.4 nTPM
Hypothalamus	120.5 nTPM
Hippocampus	119.5 nTPM
Amygdala	111.2 nTPM
Cerebral cortex	100.1 nTPM
Basal ganglia	90.7 nTPM

Deep-layer near-projecting	80.9 nTPM
Amygdala	95.3 nTPM
Hypothalamus	91.6 nTPM
Cerebral cortex	83.2 nTPM
Basal ganglia	76.4 nTPM
Hippocampus	57.9 nTPM

Eccentric medium spiny neuron	83.1 nTPM
Hypothalamus	93.0 nTPM
Hippocampus	92.0 nTPM
Amygdala	81.9 nTPM
Thalamus	80.2 nTPM
Cerebral cortex	79.9 nTPM
Basal ganglia	71.8 nTPM