Single cell type - TOR3A - 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.	TOR3A
Gene descriptionⁱ Full gene name according to HGNC.	Torsin family 3 member A
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. Read more	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. Read more	Plasma cells - Humoral 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. Read more	Cell type enhanced (Plasma cells, Langerhans cells)
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. Read more	Low immune cell specificity
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Cell line enhanced (U-266/70, U-266/84)
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in all
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Cell type enhanced (Plasma cells, Langerhans cells)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

TOR3A is part of cluster 55 Plasma cells - Humoral immune response with confidenceⁱ 1
379 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
BFSP2	Beaded filament structural protein 2	0.6728	55
IGLV8-61	Immunoglobulin lambda variable 8-61	0.6523	55
IGHG2	Immunoglobulin heavy constant gamma 2 (G2m marker)	0.6481	55
MIXL1	Mix paired-like homeobox	0.6474	55
IGKV2D-29	Immunoglobulin kappa variable 2D-29	0.6452	55
MZB1	Marginal zone B and B1 cell specific protein	0.6450	55
IGLV1-36	Immunoglobulin lambda variable 1-36	0.6441	55
SLAMF7	SLAM family member 7	0.6330	55
IGLC7	Immunoglobulin lambda constant 7	0.6327	55
IGKV6D-41	Immunoglobulin kappa variable 6D-41 (non-functional)	0.6326	55
IGHV3-53	Immunoglobulin heavy variable 3-53	0.6297	55
IGHV3-35	Immunoglobulin heavy variable 3-35 (non-functional)	0.6243	55
IGKV1D-16	Immunoglobulin kappa variable 1D-16	0.6239	55
POU2AF1	POU class 2 homeobox associating factor 1	0.6236	55
IGLC3	Immunoglobulin lambda constant 3 (Kern-Oz+ marker)	0.6220	55

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	24.8 nTPM
Adipose tissue	25.2 nTPM
Breast	24.4 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	11.7 nTPM
Lung	11.7 nTPM

Astrocytes	4.9 nTPM
Brain	4.9 nTPM

B-cells	65.2 nTPM
Liver	157.7 nTPM
Breast	95.0 nTPM
Adipose tissue	72.7 nTPM
Stomach	66.8 nTPM
Colon	60.7 nTPM
Lymph node	60.4 nTPM
PBMC	42.8 nTPM
Spleen	39.8 nTPM
Bone marrow	31.9 nTPM
Kidney	23.8 nTPM

Dendritic cells	32.5 nTPM
PBMC	51.8 nTPM
Breast	29.2 nTPM
Adipose tissue	16.5 nTPM

Endothelial cells	19.3 nTPM
Skin	41.7 nTPM
Ovary	27.9 nTPM
Skeletal muscle	23.3 nTPM
Prostate	22.6 nTPM
Esophagus	21.7 nTPM
Placenta	20.5 nTPM
Endometrium	19.3 nTPM
Breast	19.1 nTPM
Lung	15.6 nTPM
Liver	14.7 nTPM
Eye	14.6 nTPM
Heart muscle	13.6 nTPM
Testis	11.2 nTPM
Pancreas	3.9 nTPM

Fibroblasts	19.8 nTPM
Ovary	28.6 nTPM
Placenta	28.2 nTPM
Adipose tissue	23.7 nTPM
Breast	22.3 nTPM
Prostate	21.8 nTPM
Skin	20.1 nTPM
Skeletal muscle	19.4 nTPM
Lung	16.8 nTPM
Esophagus	15.3 nTPM
Stomach	13.4 nTPM
Heart muscle	8.3 nTPM

Intestinal goblet cells	18.9 nTPM
Small intestine	22.2 nTPM
Rectum	18.1 nTPM
Colon	16.5 nTPM

Macrophages	36.4 nTPM
Endometrium	73.1 nTPM
Breast	71.6 nTPM
Prostate	66.4 nTPM
Adipose tissue	54.1 nTPM
Spleen	36.3 nTPM
Esophagus	34.6 nTPM
Skeletal muscle	33.7 nTPM
Stomach	32.2 nTPM
Kidney	29.5 nTPM
Testis	27.8 nTPM
Ovary	23.8 nTPM
Pancreas	23.0 nTPM
Lung	20.5 nTPM
Bone marrow	18.8 nTPM
PBMC	0.0 nTPM

Paneth cells	17.9 nTPM
Rectum	28.7 nTPM
Small intestine	15.0 nTPM
Colon	9.9 nTPM

Plasma cells	153.7 nTPM
Stomach	210.4 nTPM
Esophagus	178.6 nTPM
Spleen	164.6 nTPM
Bone marrow	146.6 nTPM
Adipose tissue	68.3 nTPM

Respiratory ciliated cells	13.4 nTPM
Bronchus	15.1 nTPM
Lung	11.7 nTPM

Smooth muscle cells	17.3 nTPM
Ovary	33.2 nTPM
Pancreas	26.2 nTPM
Skeletal muscle	21.0 nTPM
Prostate	20.9 nTPM
Esophagus	20.1 nTPM
Breast	19.3 nTPM
Adipose tissue	15.1 nTPM
Endometrium	15.0 nTPM
Skin	10.1 nTPM
Heart muscle	6.1 nTPM
Bronchus	3.6 nTPM

T-cells	24.8 nTPM
Esophagus	45.9 nTPM
Ovary	37.8 nTPM
Breast	30.8 nTPM
Liver	29.9 nTPM
Kidney	27.4 nTPM
Skeletal muscle	26.6 nTPM
Stomach	25.7 nTPM
Colon	25.6 nTPM
Prostate	23.6 nTPM
Bone marrow	23.2 nTPM
Spleen	20.8 nTPM
Lymph node	19.7 nTPM
Skin	18.8 nTPM
PBMC	18.2 nTPM
Adipose tissue	17.5 nTPM
Lung	16.7 nTPM
Endometrium	13.3 nTPM

Basal keratinocytes	17.0 nTPM
Skin	17.0 nTPM

Basal prostatic cells	14.0 nTPM
Prostate	14.0 nTPM

Basal respiratory cells	19.2 nTPM
Bronchus	19.2 nTPM

Basal squamous epithelial cells	10.8 nTPM
Esophagus	10.8 nTPM

Undifferentiated cells	27.0 nTPM
Small intestine	28.7 nTPM
Rectum	28.0 nTPM
Colon	24.1 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC