Single cell type - TMCC3 - 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.	TMCC3
Gene descriptionⁱ Full gene name according to HGNC.	Transmembrane and coiled-coil domain family 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Transporters
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,Membrane
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

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	Intestinal epithelial cells - Unknown function (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 (Oligodendrocytes, Distal enterocytes, Urothelial cells, Adipocytes, Microglial cells, Paneth 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	Immune cell enhanced (neutrophil, eosinophil)
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 many
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 (HUVEC TERT2, Karpas-707, 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 many
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 (Oligodendrocytes, Distal enterocytes, Urothelial cells, Adipocytes, Microglial cells, Paneth 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

TMCC3 is part of cluster 53 Intestinal epithelial cells - Unknown function with confidenceⁱ 1
611 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
CLCA4	Chloride channel accessory 4	0.8038	53
CEACAM1	CEA cell adhesion molecule 1	0.8003	53
AQP8	Aquaporin 8	0.7697	53
CEACAM7	CEA cell adhesion molecule 7	0.7582	53
TRIM31	Tripartite motif containing 31	0.7533	53
TICAM1	Toll like receptor adaptor molecule 1	0.7505	53
MYO15B	Myosin XVB	0.7476	53
MIER3	MIER family member 3	0.7442	53
MS4A12	Membrane spanning 4-domains A12	0.7343	53
TRPM6	Transient receptor potential cation channel subfamily M member 6	0.7330	53
SIRT6	Sirtuin 6	0.7329	53
RSAD2	Radical S-adenosyl methionine domain containing 2	0.7303	53
CLDN23	Claudin 23	0.7303	53
CD177	CD177 molecule	0.7267	53
CA4	Carbonic anhydrase 4	0.7238	53

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

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	2.7 nTPM
Lung	2.7 nTPM

Astrocytes	2.9 nTPM
Brain	2.9 nTPM

B-cells	5.7 nTPM
Colon	8.0 nTPM
Adipose tissue	7.5 nTPM
PBMC	7.1 nTPM
Stomach	6.4 nTPM
Spleen	6.2 nTPM
Liver	6.0 nTPM
Breast	5.3 nTPM
Kidney	4.8 nTPM
Lymph node	3.2 nTPM
Bone marrow	2.5 nTPM

Basal keratinocytes	20.6 nTPM
Skin	20.6 nTPM

Dendritic cells	16.3 nTPM
Adipose tissue	36.1 nTPM
Breast	8.8 nTPM
PBMC	4.0 nTPM

Endothelial cells	31.9 nTPM
Testis	80.0 nTPM
Eye	63.1 nTPM
Endometrium	55.8 nTPM
Placenta	36.9 nTPM
Breast	34.5 nTPM
Esophagus	30.0 nTPM
Liver	28.4 nTPM
Ovary	27.7 nTPM
Prostate	25.7 nTPM
Skeletal muscle	21.2 nTPM
Heart muscle	13.8 nTPM
Skin	11.6 nTPM
Lung	9.3 nTPM
Pancreas	7.7 nTPM

Fibroblasts	4.8 nTPM
Ovary	8.3 nTPM
Lung	7.8 nTPM
Placenta	7.8 nTPM
Stomach	7.4 nTPM
Adipose tissue	5.7 nTPM
Skeletal muscle	5.0 nTPM
Breast	3.5 nTPM
Esophagus	2.7 nTPM
Skin	2.4 nTPM
Prostate	1.0 nTPM
Heart muscle	0.8 nTPM

Intestinal goblet cells	13.0 nTPM
Colon	17.9 nTPM
Rectum	15.8 nTPM
Small intestine	5.4 nTPM

Macrophages	20.3 nTPM
Adipose tissue	61.3 nTPM
Stomach	49.8 nTPM
Prostate	32.0 nTPM
Testis	29.7 nTPM
Spleen	27.9 nTPM
Skeletal muscle	24.0 nTPM
Kidney	13.7 nTPM
Pancreas	12.8 nTPM
Breast	12.5 nTPM
Esophagus	11.0 nTPM
Ovary	10.9 nTPM
Bone marrow	7.5 nTPM
Lung	6.4 nTPM
Endometrium	5.1 nTPM
PBMC	0.0 nTPM

Paneth cells	70.1 nTPM
Colon	174.5 nTPM
Rectum	20.8 nTPM
Small intestine	15.0 nTPM

Plasma cells	7.8 nTPM
Adipose tissue	29.1 nTPM
Stomach	4.4 nTPM
Spleen	3.7 nTPM
Bone marrow	1.7 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	3.0 nTPM
Bronchus	5.9 nTPM
Lung	0.0 nTPM

Smooth muscle cells	6.1 nTPM
Esophagus	21.7 nTPM
Prostate	7.2 nTPM
Adipose tissue	7.0 nTPM
Breast	7.0 nTPM
Ovary	5.1 nTPM
Endometrium	4.8 nTPM
Skeletal muscle	4.6 nTPM
Skin	3.8 nTPM
Bronchus	2.8 nTPM
Heart muscle	2.4 nTPM
Pancreas	0.1 nTPM

T-cells	7.7 nTPM
Colon	34.7 nTPM
Adipose tissue	15.6 nTPM
Esophagus	13.1 nTPM
Stomach	11.1 nTPM
Skeletal muscle	10.5 nTPM
Kidney	7.5 nTPM
Spleen	6.9 nTPM
Liver	6.4 nTPM
Endometrium	5.1 nTPM
Prostate	4.7 nTPM
Bone marrow	4.2 nTPM
Lung	3.0 nTPM
Skin	2.3 nTPM
Ovary	2.2 nTPM
Breast	2.2 nTPM
PBMC	1.5 nTPM
Lymph node	0.2 nTPM

Cholangiocytes	4.3 nTPM
Liver	4.3 nTPM

Collecting duct cells	7.3 nTPM
Kidney	7.3 nTPM

Cytotrophoblasts	16.0 nTPM
Placenta	16.0 nTPM

Early spermatids	5.8 nTPM
Testis	5.8 nTPM

Undifferentiated cells	8.2 nTPM
Colon	11.0 nTPM
Rectum	8.5 nTPM
Small intestine	5.2 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