Single cell type - POLR2J3 - The Human Protein Atlas

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.	POLR2J3
Gene descriptionⁱ Full gene name according to HGNC.	RNA polymerase II subunit J3
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.	Neurons - Neurotransmission & signaling (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 (Esophageal apical cells, Bergmann glia, Ocular epithelial cells, Oligodendrocytes, Astrocytes, Ependymal 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.	0.94
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 type

Single nuclei - Brain

Immune cells

Expression clustering

SINGLE CELL TYPESⁱ A summary of normalized single cell RNA (nCPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. * Single nuclei Read more
Single cell type groups RNA single cell type group specificity: Cell type enhanced (Apical squamous epithelial cells, Barrier epithelial cells, Glial cells, Ciliated cells)

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

POLR2J3 is part of cluster 98 Neurons - Neurotransmission & signaling with confidenceⁱ 1
318 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.
ST6GALNAC6	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	0.5251	98
RXRB	Retinoid X receptor beta	0.5217	102
PPAN	Peter pan homolog	0.5116	98
ZFTRAF1	Zinc finger TRAF-type containing 1	0.5054	98
FAM83A	Family with sequence similarity 83 member A	0.5027	100
NEURL4	Neuralized E3 ubiquitin protein ligase 4	0.4934	22
WBP1	WW domain binding protein 1	0.4808	98
AMT	Aminomethyltransferase	0.4800	22
PIK3R2	Phosphoinositide-3-kinase regulatory subunit 2	0.4794	22
PANK4	Pantothenate kinase 4 (inactive)	0.4784	98
GTF2H4	General transcription factor IIH subunit 4	0.4742	35
PRSS53	Serine protease 53	0.4664	35
CHMP4A	Charged multivesicular body protein 4A	0.4655	22
KRT24	Keratin 24	0.4609	100
SMN2	Survival of motor neuron 2, centromeric	0.4601	98

IMMUNE CELLS

POLR2J3 is part of cluster 21 Neutrophils - Unknown function with confidenceⁱ 1
492 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.
H3C10	H3 clustered histone 10	0.9762	21
SMIM27	Small integral membrane protein 27	0.9762	21
MYLK	Myosin light chain kinase	0.9762	21
ERVH48-1	Endogenous retrovirus group 48 member 1	0.9762	21
TECPR2	Tectonin beta-propeller repeat containing 2	0.9762	21
FMNL1	Formin like 1	0.9762	21
KLHL21	Kelch like family member 21	0.9762	21
ZMAT2	Zinc finger matrin-type 2	0.9762	21
FFAR2	Free fatty acid receptor 2	0.9524	21
WBP2	WW domain binding protein 2	0.9524	21
TMOD2	Tropomodulin 2	0.9524	21
IFRD1	Interferon related developmental regulator 1	0.9524	21
KBTBD7	Kelch repeat and BTB domain containing 7	0.9524	21
IQCE	IQ motif containing E	0.9524	21
TMEM40	Transmembrane protein 40	0.9524	21