Single cell type - OTUD3 - 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.	OTUD3
Gene descriptionⁱ Full gene name according to HGNC.	OTU deubiquitinase 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Enzymes
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.	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. Read more	Non-specific - Cell cycle regulation (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	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. Read more	Not detected in immune cells
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	Not detected
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	Low cell line specificity
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: Low cell type specificity

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

OTUD3 is part of cluster 12 Non-specific - Cell cycle regulation with confidenceⁱ 1
294 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
ARHGEF28	Rho guanine nucleotide exchange factor 28	0.4765	40
ZNF318	Zinc finger protein 318	0.4726	13
ZNF214	Zinc finger protein 214	0.4560	49
CCKBR	Cholecystokinin B receptor	0.4436	40
ALOX12B	Arachidonate 12-lipoxygenase, 12R type	0.4390	62
DNAH14	Dynein axonemal heavy chain 14	0.4360	21
GPR63	G protein-coupled receptor 63	0.4303	21
SLC9A5	Solute carrier family 9 member A5	0.4273	13
XRCC2	X-ray repair cross complementing 2	0.4265	12
SETD6	SET domain containing 6, protein lysine methyltransferase	0.4233	20
CFAP74	Cilia and flagella associated protein 74	0.4208	49
AKAP8L	A-kinase anchoring protein 8 like	0.4188	6
SLC25A14	Solute carrier family 25 member 14	0.4084	49
ORC6	Origin recognition complex subunit 6	0.4064	12
PPP4R4	Protein phosphatase 4 regulatory subunit 4	0.4001	21

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	5.0 nTPM
Breast	5.3 nTPM
Adipose tissue	4.7 nTPM

Alveolar cells type 1	16.0 nTPM
Lung	16.0 nTPM

Alveolar cells type 2	7.5 nTPM
Lung	7.5 nTPM

Astrocytes	11.4 nTPM
Brain	11.4 nTPM

B-cells	5.6 nTPM
Stomach	10.5 nTPM
Adipose tissue	7.5 nTPM
Bone marrow	7.4 nTPM
Lymph node	6.9 nTPM
Spleen	4.9 nTPM
Kidney	4.8 nTPM
Liver	4.6 nTPM
PBMC	4.3 nTPM
Breast	4.0 nTPM
Colon	1.6 nTPM

Dendritic cells	6.5 nTPM
Adipose tissue	12.0 nTPM
Breast	7.6 nTPM
PBMC	0.0 nTPM

Endothelial cells	5.1 nTPM
Heart muscle	11.2 nTPM
Liver	8.2 nTPM
Endometrium	6.7 nTPM
Prostate	6.4 nTPM
Breast	6.4 nTPM
Skeletal muscle	6.1 nTPM
Skin	5.3 nTPM
Ovary	4.6 nTPM
Esophagus	4.6 nTPM
Placenta	3.4 nTPM
Lung	3.1 nTPM
Testis	2.7 nTPM
Eye	2.4 nTPM
Pancreas	0.0 nTPM

Fibroblasts	7.0 nTPM
Breast	11.7 nTPM
Skeletal muscle	11.1 nTPM
Prostate	11.0 nTPM
Lung	6.7 nTPM
Skin	6.7 nTPM
Adipose tissue	6.4 nTPM
Esophagus	6.0 nTPM
Stomach	6.0 nTPM
Heart muscle	3.9 nTPM
Ovary	3.9 nTPM
Placenta	3.7 nTPM

Intestinal goblet cells	7.0 nTPM
Small intestine	7.9 nTPM
Colon	7.2 nTPM
Rectum	5.8 nTPM

Macrophages	5.2 nTPM
PBMC	13.6 nTPM
Bone marrow	10.0 nTPM
Endometrium	8.2 nTPM
Adipose tissue	6.9 nTPM
Breast	6.3 nTPM
Skeletal muscle	6.1 nTPM
Stomach	5.9 nTPM
Kidney	3.8 nTPM
Lung	3.8 nTPM
Prostate	3.4 nTPM
Esophagus	3.1 nTPM
Pancreas	2.5 nTPM
Ovary	2.5 nTPM
Testis	1.2 nTPM
Spleen	1.0 nTPM

Paneth cells	6.7 nTPM
Colon	9.9 nTPM
Rectum	6.5 nTPM
Small intestine	3.7 nTPM

Plasma cells	8.6 nTPM
Esophagus	12.3 nTPM
Adipose tissue	12.2 nTPM
Stomach	7.9 nTPM
Spleen	5.9 nTPM
Bone marrow	5.0 nTPM

Respiratory ciliated cells	9.7 nTPM
Lung	11.7 nTPM
Bronchus	7.6 nTPM

Smooth muscle cells	6.1 nTPM
Prostate	12.9 nTPM
Endometrium	8.0 nTPM
Esophagus	7.8 nTPM
Skeletal muscle	7.5 nTPM
Ovary	6.9 nTPM
Breast	6.9 nTPM
Adipose tissue	6.8 nTPM
Skin	4.5 nTPM
Pancreas	4.1 nTPM
Heart muscle	1.2 nTPM
Bronchus	0.9 nTPM

T-cells	7.0 nTPM
Adipose tissue	11.8 nTPM
Ovary	11.1 nTPM
Breast	10.3 nTPM
Lymph node	10.1 nTPM
Endometrium	9.8 nTPM
Skeletal muscle	9.7 nTPM
Colon	7.6 nTPM
Esophagus	6.6 nTPM
Spleen	6.5 nTPM
Stomach	6.2 nTPM
PBMC	5.6 nTPM
Skin	5.5 nTPM
Bone marrow	4.9 nTPM
Prostate	4.7 nTPM
Lung	3.0 nTPM
Liver	2.9 nTPM
Kidney	2.0 nTPM

Basal keratinocytes	14.1 nTPM
Skin	14.1 nTPM

Collecting duct cells	9.2 nTPM
Kidney	9.2 nTPM

Cone photoreceptor cells	16.7 nTPM
Eye	16.7 nTPM

Excitatory neurons	32.6 nTPM
Brain	32.6 nTPM

Undifferentiated cells	7.0 nTPM
Colon	7.3 nTPM
Rectum	7.0 nTPM
Small intestine	6.7 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