Single cell type - COMMD3 - 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.	COMMD3
Gene descriptionⁱ Full gene name according to HGNC.	COMM domain containing 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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	5

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	Early spermatids - Spermatogenesis (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 (Early spermatids)
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 (HDLM-2, U-937)
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 (Early spermatids)

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

COMMD3 is part of cluster 29 Early spermatids - Spermatogenesis with confidenceⁱ 1
337 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
PCMT1	Protein-L-isoaspartate (D-aspartate) O-methyltransferase	0.6507	29
TBC1D3I	TBC1 domain family member 3I	0.6444	29
C12orf73	Chromosome 12 open reading frame 73	0.6356	29
C12orf60	Chromosome 12 open reading frame 60	0.6335	29
SUN5	Sad1 and UNC84 domain containing 5	0.6324	29
SAXO1	Stabilizer of axonemal microtubules 1	0.6204	29
SPATA31D4	SPATA31 subfamily D member 4	0.6186	29
SPACA4	Sperm acrosome associated 4	0.6158	29
ERICH2	Glutamate rich 2	0.6154	29
FAM209B	Family with sequence similarity 209 member B	0.6151	29
TBC1D3C	TBC1 domain family member 3C	0.6137	29
TRIML1	Tripartite motif family like 1	0.6128	29
SPATA31D3	SPATA31 subfamily D member 3	0.6124	29
TBC1D3B	TBC1 domain family member 3B	0.6113	29
ERGIC2	ERGIC and golgi 2	0.6068	29

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	37.6 nTPM
Breast	47.1 nTPM
Adipose tissue	28.1 nTPM

Alveolar cells type 1	41.7 nTPM
Lung	41.7 nTPM

Alveolar cells type 2	31.7 nTPM
Lung	31.7 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	59.0 nTPM
Breast	128.4 nTPM
Liver	117.9 nTPM
PBMC	92.7 nTPM
Kidney	76.1 nTPM
Bone marrow	49.1 nTPM
Adipose tissue	36.6 nTPM
Colon	28.7 nTPM
Spleen	26.3 nTPM
Lymph node	19.8 nTPM
Stomach	14.5 nTPM

Dendritic cells	55.2 nTPM
PBMC	75.7 nTPM
Breast	54.6 nTPM
Adipose tissue	35.4 nTPM

Endothelial cells	37.9 nTPM
Placenta	72.7 nTPM
Pancreas	61.8 nTPM
Heart muscle	53.9 nTPM
Ovary	53.0 nTPM
Liver	45.8 nTPM
Testis	40.3 nTPM
Breast	39.2 nTPM
Eye	31.6 nTPM
Skin	30.8 nTPM
Endometrium	29.4 nTPM
Skeletal muscle	25.8 nTPM
Prostate	19.0 nTPM
Lung	18.7 nTPM
Esophagus	8.8 nTPM

Fibroblasts	42.6 nTPM
Heart muscle	81.1 nTPM
Adipose tissue	62.2 nTPM
Breast	59.8 nTPM
Placenta	51.5 nTPM
Skin	45.2 nTPM
Skeletal muscle	44.7 nTPM
Ovary	42.3 nTPM
Lung	27.9 nTPM
Prostate	22.8 nTPM
Esophagus	16.7 nTPM
Stomach	14.9 nTPM

Intestinal goblet cells	43.4 nTPM
Small intestine	44.9 nTPM
Colon	44.3 nTPM
Rectum	41.0 nTPM

Macrophages	47.6 nTPM
Kidney	83.2 nTPM
Breast	76.7 nTPM
Ovary	70.9 nTPM
Pancreas	68.9 nTPM
Testis	62.7 nTPM
Prostate	52.7 nTPM
Endometrium	47.9 nTPM
Lung	42.0 nTPM
PBMC	40.9 nTPM
Adipose tissue	37.3 nTPM
Spleen	35.3 nTPM
Skeletal muscle	35.2 nTPM
Bone marrow	28.7 nTPM
Stomach	17.6 nTPM
Esophagus	14.2 nTPM

Paneth cells	36.7 nTPM
Rectum	49.5 nTPM
Small intestine	37.6 nTPM
Colon	23.1 nTPM

Plasma cells	63.2 nTPM
Stomach	73.0 nTPM
Bone marrow	67.6 nTPM
Adipose tissue	61.9 nTPM
Spleen	58.2 nTPM
Esophagus	55.5 nTPM

Respiratory ciliated cells	72.1 nTPM
Bronchus	104.9 nTPM
Lung	39.4 nTPM

Smooth muscle cells	66.6 nTPM
Bronchus	279.7 nTPM
Pancreas	87.3 nTPM
Ovary	60.5 nTPM
Heart muscle	55.9 nTPM
Breast	54.8 nTPM
Skin	48.8 nTPM
Skeletal muscle	39.0 nTPM
Adipose tissue	36.5 nTPM
Endometrium	30.2 nTPM
Prostate	29.1 nTPM
Esophagus	10.9 nTPM

T-cells	34.7 nTPM
Kidney	74.0 nTPM
PBMC	54.9 nTPM
Prostate	52.1 nTPM
Liver	45.6 nTPM
Ovary	40.0 nTPM
Breast	38.4 nTPM
Adipose tissue	38.1 nTPM
Skin	36.4 nTPM
Colon	35.1 nTPM
Lung	33.4 nTPM
Bone marrow	29.6 nTPM
Skeletal muscle	28.3 nTPM
Endometrium	25.9 nTPM
Spleen	18.7 nTPM
Lymph node	13.3 nTPM
Esophagus	13.1 nTPM
Stomach	12.8 nTPM

Basal keratinocytes	38.2 nTPM
Skin	38.2 nTPM

Basal prostatic cells	48.4 nTPM
Prostate	48.4 nTPM

Basal respiratory cells	148.4 nTPM
Bronchus	148.4 nTPM

Basal squamous epithelial cells	18.2 nTPM
Esophagus	18.2 nTPM

Undifferentiated cells	40.7 nTPM
Small intestine	56.8 nTPM
Rectum	37.3 nTPM
Colon	27.9 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