Single cell type - PSMA3 - The Human Protein Atlas

PSMA3

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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.	PSMA3
Gene descriptionⁱ Full gene name according to HGNC.	Proteasome 20S subunit alpha 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Enzymes Plasma 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.	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.	Non-specific - Mixed 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.	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.	0.25
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

PSMA3 is part of cluster 15 Non-specific - Mixed function with confidenceⁱ 1
295 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.
PSMB1	Proteasome 20S subunit beta 1	0.7957	15
PSMB2	Proteasome 20S subunit beta 2	0.7834	15
PSMA5	Proteasome 20S subunit alpha 5	0.7751	15
PSMB3	Proteasome 20S subunit beta 3	0.7705	15
PSMB6	Proteasome 20S subunit beta 6	0.7187	15
EMG1	EMG1 N1-specific pseudouridine methyltransferase	0.7138	15
PSMC2	Proteasome 26S subunit, ATPase 2	0.6766	15
MAGOH	Mago homolog, exon junction complex subunit	0.6722	15
TXNDC9	Thioredoxin domain containing 9	0.6694	15
PSMB5	Proteasome 20S subunit beta 5	0.6657	15
PSMC4	Proteasome 26S subunit, ATPase 4	0.6556	15
MRPL15	Mitochondrial ribosomal protein L15	0.6357	15
EIF3I	Eukaryotic translation initiation factor 3 subunit I	0.6341	15
PSMD11	Proteasome 26S subunit, non-ATPase 11	0.6339	15
PSMD4	Proteasome 26S subunit ubiquitin receptor, non-ATPase 4	0.6285	15

IMMUNE CELLS

PSMA3 is part of cluster 13 Non-specific - Mitochondria with confidenceⁱ 0.62
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.
TRAM1	Translocation associated membrane protein 1	0.9762	13
ATP2A1	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1	0.9762	13
PSMD14	Proteasome 26S subunit, non-ATPase 14	0.9762	13
ENSG00000273047	Novel transcript, LIME1-SLC2A4RG readthrough	0.9524	13
BCCIP	BRCA2 and CDKN1A interacting protein	0.9524	13
ANKRD39	Ankyrin repeat domain 39	0.9286	13
CDV3	CDV3 homolog	0.9286	5
CHORDC1	Cysteine and histidine rich domain containing 1	0.9286	9
PMS2	PMS1 homolog 2, mismatch repair system component	0.9048	13
PAXIP1	PAX interacting protein 1	0.9048	13
HIKESHI	Heat shock protein nuclear import factor hikeshi	0.9048	13
EBP	EBP cholestenol delta-isomerase	0.9048	5
NICN1	Nicolin 1, tubulin polyglutamylase complex subunit	0.9048	5
TMEM50B	Transmembrane protein 50B	0.9048	5
TMX1	Thioredoxin related transmembrane protein 1	0.9048	13

Adipocytes	121.9 nTPM
Breast	128.6 nTPM
Adipose tissue	115.3 nTPM

Alveolar cells type 1	202.7 nTPM
Lung	202.7 nTPM

Alveolar cells type 2	204.9 nTPM
Lung	204.9 nTPM

Astrocytes	20.7 nTPM
Brain	20.7 nTPM

B-cells	68.5 nTPM
Skin	94.9 nTPM
Lymph node	78.7 nTPM
PBMC	78.5 nTPM
Spleen	74.4 nTPM
Adipose tissue	73.7 nTPM
Kidney	72.8 nTPM
Stomach	71.7 nTPM
Lung	71.1 nTPM
Liver	67.6 nTPM
Salivary gland	67.2 nTPM
Bone marrow	55.9 nTPM
Thymus	54.1 nTPM
Esophagus	29.5 nTPM

Ciliated cells	127.5 nTPM
Bronchus	175.9 nTPM
Endometrium	129.7 nTPM
Fallopian tube	105.9 nTPM
Lung	98.5 nTPM

Club cells	132.9 nTPM
Bronchus	230.7 nTPM
Lung	107.0 nTPM
Prostate	60.9 nTPM

Dendritic cells	102.5 nTPM
PBMC	104.3 nTPM
Adipose tissue	100.6 nTPM

Endothelial cells	119.6 nTPM
Pancreas	261.1 nTPM
Heart muscle	203.5 nTPM
Skeletal muscle	172.5 nTPM
Fallopian tube	153.9 nTPM
Placenta	152.7 nTPM
Lung	148.9 nTPM
Testis	109.6 nTPM
Skin	106.5 nTPM
Tongue	106.3 nTPM
Endometrium	102.8 nTPM
Thymus	101.4 nTPM
Breast	95.8 nTPM
Ovary	90.8 nTPM
Esophagus	82.8 nTPM
Salivary gland	77.1 nTPM
Prostate	72.6 nTPM
Vascular	63.0 nTPM
Liver	51.6 nTPM

Enteroendocrine cells	71.0 nTPM
Colon	122.8 nTPM
Small intestine	54.9 nTPM
Rectum	35.2 nTPM

Fibroblasts	108.1 nTPM
Pancreas	222.0 nTPM
Lung	173.4 nTPM
Heart muscle	130.9 nTPM
Placenta	130.0 nTPM
Fallopian tube	125.9 nTPM
Thymus	104.8 nTPM
Skeletal muscle	103.7 nTPM
Breast	103.5 nTPM
Adipose tissue	100.7 nTPM
Stomach	89.3 nTPM
Liver	78.3 nTPM
Skin	78.0 nTPM
Prostate	76.6 nTPM
Salivary gland	75.6 nTPM
Vascular	73.9 nTPM
Esophagus	62.6 nTPM

Granulocytes	97.5 nTPM
Fallopian tube	128.2 nTPM
Lung	86.7 nTPM
Tongue	77.6 nTPM

Intestinal goblet cells	84.5 nTPM
Colon	153.0 nTPM
Small intestine	52.4 nTPM
Rectum	48.1 nTPM

Lymphatic endothelial cells	82.8 nTPM
Fallopian tube	94.7 nTPM
Ovary	70.9 nTPM

Macrophages	86.5 nTPM
Pancreas	185.0 nTPM
Lung	158.4 nTPM
Kidney	131.0 nTPM
Endometrium	102.7 nTPM
Breast	101.3 nTPM
Spleen	83.2 nTPM
Testis	82.5 nTPM
Thymus	78.1 nTPM
Adipose tissue	76.9 nTPM
Bone marrow	76.0 nTPM
Stomach	74.6 nTPM
Fallopian tube	73.5 nTPM
Prostate	71.3 nTPM
Skeletal muscle	67.3 nTPM
Tongue	60.6 nTPM
Skin	60.2 nTPM
Vascular	55.7 nTPM
Esophagus	55.2 nTPM
Salivary gland	49.8 nTPM

Basal keratinocytes	141.5 nTPM
Tongue	162.8 nTPM
Skin	120.1 nTPM

Basal prostatic cells	94.1 nTPM
Prostate	94.1 nTPM

Basal respiratory cells	415.1 nTPM
Bronchus	415.1 nTPM

Basal squamous epithelial cells	80.4 nTPM
Esophagus	80.4 nTPM

Paneth cells	85.5 nTPM
Small intestine	107.1 nTPM
Colon	76.0 nTPM
Rectum	73.6 nTPM

Plasma cells	150.8 nTPM
Thymus	229.0 nTPM
Liver	213.3 nTPM
Spleen	197.5 nTPM
Bone marrow	140.4 nTPM
Stomach	131.1 nTPM
Fallopian tube	130.3 nTPM
Salivary gland	107.4 nTPM
Esophagus	57.2 nTPM

Schwann cells	63.8 nTPM
Adipose tissue	130.4 nTPM
Vascular	61.1 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	97.7 nTPM
Tongue	119.3 nTPM
Salivary gland	76.1 nTPM

Smooth muscle cells	92.9 nTPM
Placenta	146.3 nTPM
Skeletal muscle	141.8 nTPM
Lung	131.7 nTPM
Fallopian tube	121.0 nTPM
Breast	102.9 nTPM
Ovary	99.9 nTPM
Endometrium	93.2 nTPM
Thymus	91.9 nTPM
Liver	75.6 nTPM
Adipose tissue	75.3 nTPM
Skin	75.2 nTPM
Prostate	74.2 nTPM
Vascular	74.0 nTPM
Tongue	73.3 nTPM
Esophagus	57.7 nTPM
Salivary gland	53.0 nTPM

Suprabasal keratinocytes	140.7 nTPM
Tongue	177.5 nTPM
Skin	104.0 nTPM

T-cells	85.7 nTPM
Kidney	143.6 nTPM
Breast	114.0 nTPM
Fallopian tube	109.9 nTPM
Liver	106.5 nTPM
Adipose tissue	103.8 nTPM
Endometrium	97.5 nTPM
Spleen	91.3 nTPM
Lymph node	86.8 nTPM
Stomach	85.5 nTPM
Prostate	84.9 nTPM
Lung	82.2 nTPM
Skin	82.0 nTPM
Bone marrow	80.9 nTPM
Skeletal muscle	76.4 nTPM
Tongue	75.9 nTPM
PBMC	74.6 nTPM
Thymus	67.9 nTPM
Esophagus	65.7 nTPM
Salivary gland	61.8 nTPM
Colon	59.5 nTPM
Vascular	48.2 nTPM

Undifferentiated cells	125.1 nTPM
Colon	197.5 nTPM
Small intestine	106.2 nTPM
Rectum	71.5 nTPM

Amygdala excitatory	32.8 nTPM
Thalamus	41.7 nTPM
Basal ganglia	36.9 nTPM
Cerebral cortex	34.5 nTPM
Hippocampus	32.2 nTPM
Amygdala	29.3 nTPM
Hypothalamus	22.2 nTPM

Astrocyte	45.3 nTPM
Hypothalamus	61.0 nTPM
Basal ganglia	51.8 nTPM
Medulla oblongata	49.6 nTPM
Cerebral cortex	47.2 nTPM
Thalamus	45.4 nTPM
Amygdala	44.8 nTPM
Pons	43.2 nTPM
Midbrain	42.5 nTPM
Spinal cord	40.6 nTPM
Hippocampus	40.4 nTPM
Cerebellum	31.7 nTPM

Bergmann glia	76.1 nTPM
Medulla oblongata	85.2 nTPM
Pons	80.6 nTPM
Cerebellum	62.6 nTPM

Central nervous system macrophage	60.7 nTPM
Hypothalamus	77.6 nTPM
Basal ganglia	70.3 nTPM
Medulla oblongata	67.8 nTPM
Thalamus	67.8 nTPM
Pons	62.6 nTPM
Cerebellum	59.0 nTPM
Midbrain	57.8 nTPM
Cerebral cortex	52.0 nTPM
Hippocampus	51.7 nTPM
Amygdala	50.3 nTPM
Spinal cord	50.3 nTPM

Cerebellar inhibitory	52.1 nTPM
Medulla oblongata	59.3 nTPM
Pons	53.9 nTPM
Spinal cord	52.2 nTPM
Cerebellum	48.0 nTPM
Midbrain	47.0 nTPM

Cge interneuron	39.8 nTPM
Thalamus	46.6 nTPM
Basal ganglia	44.1 nTPM
Midbrain	43.8 nTPM
Cerebral cortex	41.3 nTPM
Hippocampus	39.6 nTPM
Amygdala	38.0 nTPM
Hypothalamus	25.3 nTPM

Choroid plexus epithelial cell	38.0 nTPM
Medulla oblongata	50.6 nTPM
Thalamus	38.4 nTPM
Hippocampus	33.3 nTPM
Basal ganglia	29.7 nTPM

Committed oligodendrocyte precursor	41.3 nTPM
Cerebellum	55.5 nTPM
Medulla oblongata	55.5 nTPM
Midbrain	49.6 nTPM
Spinal cord	47.8 nTPM
Pons	45.2 nTPM
Cerebral cortex	45.0 nTPM
Basal ganglia	34.5 nTPM
Amygdala	32.1 nTPM
Hippocampus	31.8 nTPM
Thalamus	29.9 nTPM
Hypothalamus	27.3 nTPM

Deep-layer corticothalamic and 6b	32.2 nTPM
Basal ganglia	42.4 nTPM
Cerebral cortex	35.7 nTPM
Hippocampus	35.3 nTPM
Amygdala	32.8 nTPM
Midbrain	26.6 nTPM
Hypothalamus	20.2 nTPM

Deep-layer intratelencephalic	34.9 nTPM
Basal ganglia	42.4 nTPM
Cerebral cortex	37.2 nTPM
Amygdala	35.8 nTPM
Hippocampus	34.7 nTPM
Hypothalamus	24.6 nTPM

Deep-layer near-projecting	44.5 nTPM
Hippocampus	57.9 nTPM
Basal ganglia	47.0 nTPM
Amygdala	46.0 nTPM
Cerebral cortex	45.6 nTPM
Hypothalamus	26.1 nTPM

Eccentric medium spiny neuron	37.4 nTPM
Basal ganglia	41.6 nTPM
Amygdala	39.1 nTPM
Cerebral cortex	38.9 nTPM
Thalamus	35.7 nTPM
Hypothalamus	35.4 nTPM
Hippocampus	33.6 nTPM