Single cell type - ELL3 - 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.	ELL3
Gene descriptionⁱ Full gene name according to HGNC.	Elongation factor for RNA polymerase II 3
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.	2

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.	Cell type enhanced (Squamous epithelial cells, Basal squamous epithelial cells, Proximal enterocytes, Gastric mucus-secreting 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.	0.92
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 enriched (Choroid plexus epithelial cell)
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.	Group enriched (naive B-cell, memory B-cell)
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

Cell type enrichment

Single nuclei - Brain

Immune cells

Expression clustering

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 (Squamous epithelial cells, Basal squamous epithelial cells, Proximal enterocytes, Gastric mucus-secreting 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 enriched (Choroid plexus epithelial cell)

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: Group enriched (naive B-cell, memory B-cell)
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

ELL3 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.
EIF4EBP3	Eukaryotic translation initiation factor 4E binding protein 3	0.8181	49
UGT1A7	UDP glucuronosyltransferase family 1 member A7	0.8133	12
LY6G6D	Lymphocyte antigen 6 family member G6D	0.8011	12
NME2	NME/NM23 nucleoside diphosphate kinase 2	0.7590	49
KRTAP3-2	Keratin associated protein 3-2	0.7509	12
KRT33A	Keratin 33A	0.7483	12
RASSF10	Ras association domain family member 10	0.7448	12
ALDOA	Aldolase, fructose-bisphosphate A	0.7300	49
PAM16	Presequence translocase associated motor 16	0.7174	49
SLC9A3	Solute carrier family 9 member A3	0.7094	49
CDK3	Cyclin dependent kinase 3	0.7060	49
UGT1A10	UDP glucuronosyltransferase family 1 member A10	0.7059	12
HTD2	Hydroxyacyl-thioester dehydratase type 2	0.7003	49
ANXA8L1	Annexin A8 like 1	0.6995	12
ZNF296	Zinc finger protein 296	0.6947	73

IMMUNE CELLS

ELL3 is part of cluster 14 Non-specific - Unknown function with confidenceⁱ 1
292 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.
IGLV5-52	Immunoglobulin lambda variable 5-52	1.0000	14
SLC6A16	Solute carrier family 6 member 16	1.0000	14
H2AC13	H2A clustered histone 13	1.0000	14
CC2D2B	Coiled-coil and C2 domain containing 2B	1.0000	14
L3MBTL3	L3MBTL histone methyl-lysine binding protein 3	0.9762	14
SLC24A1	Solute carrier family 24 member 1	0.9762	14
C19orf18	Chromosome 19 open reading frame 18	0.9762	14
AUTS2	Activator of transcription and developmental regulator AUTS2	0.9762	14
STRBP	Spermatid perinuclear RNA binding protein	0.9762	14
BUB1B	BUB1 mitotic checkpoint serine/threonine kinase B	0.9524	14
FBXW8	F-box and WD repeat domain containing 8	0.9524	14
CXXC5	CXXC finger protein 5	0.9524	14
CD38	CD38 molecule	0.9524	14
LAMC1	Laminin subunit gamma 1	0.9524	14
RRAS2	RAS related 2	0.9524	14