Single cell type - SMIM3 - 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.	SMIM3
Gene descriptionⁱ Full gene name according to HGNC.	Small integral membrane protein 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	Membrane
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. Read more	Myeloid cells - Hemostasis (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 (Sertoli cells, granulocytes, Basal prostatic cells, Basal squamous epithelial cells, Macrophages, Smooth muscle 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 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 (ASC diff, ASC TERT1, LHCN-M2, U-87 MG)
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 (Sertoli cells, granulocytes, Basal prostatic cells, Basal squamous epithelial cells, Macrophages, Smooth muscle 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

SMIM3 is part of cluster 51 Myeloid cells - Hemostasis with confidenceⁱ 1
155 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
KCNE5	Potassium voltage-gated channel subfamily E regulatory subunit 5	0.6921	65
PARVB	Parvin beta	0.6352	51
PTCRA	Pre T cell antigen receptor alpha	0.6042	51
ARHGAP6	Rho GTPase activating protein 6	0.5729	51
CARD19	Caspase recruitment domain family member 19	0.5424	51
LGALS12	Galectin 12	0.5361	51
F13A1	Coagulation factor XIII A chain	0.5303	4
TLN1	Talin 1	0.5300	51
CORO1C	Coronin 1C	0.5276	65
PTPN18	Protein tyrosine phosphatase non-receptor type 18	0.5256	51
FERMT3	Fermitin family member 3	0.5255	51
KCNK17	Potassium two pore domain channel subfamily K member 17	0.5124	65
GNA15	G protein subunit alpha 15	0.5092	65
MFSD1	Major facilitator superfamily domain containing 1	0.5005	4
SMIM41	Small integral membrane protein 41	0.4988	65

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	53.7 nTPM
Adipose tissue	68.4 nTPM
Breast	39.0 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	8.6 nTPM
Lung	8.6 nTPM

Astrocytes	2.6 nTPM
Brain	2.6 nTPM

B-cells	3.2 nTPM
Colon	17.6 nTPM
Adipose tissue	4.5 nTPM
Stomach	3.2 nTPM
PBMC	2.8 nTPM
Breast	2.6 nTPM
Liver	0.9 nTPM
Lymph node	0.4 nTPM
Spleen	0.3 nTPM
Kidney	0.0 nTPM
Bone marrow	0.0 nTPM

Dendritic cells	22.8 nTPM
PBMC	35.8 nTPM
Adipose tissue	24.3 nTPM
Breast	8.4 nTPM

Endothelial cells	25.4 nTPM
Eye	108.4 nTPM
Skeletal muscle	58.5 nTPM
Endometrium	44.7 nTPM
Prostate	42.4 nTPM
Placenta	40.4 nTPM
Breast	20.1 nTPM
Testis	10.9 nTPM
Heart muscle	8.5 nTPM
Liver	8.2 nTPM
Esophagus	7.6 nTPM
Lung	3.1 nTPM
Ovary	2.5 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM

Fibroblasts	53.5 nTPM
Adipose tissue	153.0 nTPM
Prostate	132.1 nTPM
Esophagus	72.4 nTPM
Skeletal muscle	59.6 nTPM
Placenta	54.0 nTPM
Stomach	47.5 nTPM
Heart muscle	22.3 nTPM
Breast	21.6 nTPM
Lung	20.1 nTPM
Ovary	5.9 nTPM
Skin	0.0 nTPM

Intestinal goblet cells	36.8 nTPM
Colon	40.0 nTPM
Small intestine	35.2 nTPM
Rectum	35.1 nTPM

Macrophages	79.3 nTPM
PBMC	504.7 nTPM
Adipose tissue	124.9 nTPM
Prostate	111.2 nTPM
Ovary	95.6 nTPM
Pancreas	76.5 nTPM
Skeletal muscle	50.2 nTPM
Stomach	49.8 nTPM
Endometrium	36.2 nTPM
Spleen	30.0 nTPM
Esophagus	29.9 nTPM
Kidney	20.4 nTPM
Bone marrow	16.3 nTPM
Breast	15.8 nTPM
Lung	14.1 nTPM
Testis	13.4 nTPM

Paneth cells	1.1 nTPM
Rectum	3.4 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	3.5 nTPM
Adipose tissue	8.4 nTPM
Esophagus	6.1 nTPM
Stomach	3.1 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Respiratory ciliated cells	0.0 nTPM
Lung	0.0 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	77.2 nTPM
Adipose tissue	218.8 nTPM
Skeletal muscle	204.4 nTPM
Prostate	148.4 nTPM
Heart muscle	85.8 nTPM
Pancreas	73.1 nTPM
Esophagus	51.2 nTPM
Breast	42.9 nTPM
Ovary	16.5 nTPM
Endometrium	8.1 nTPM
Skin	0.0 nTPM
Bronchus	0.0 nTPM

T-cells	28.8 nTPM
Prostate	123.0 nTPM
Stomach	96.2 nTPM
Esophagus	52.4 nTPM
Colon	50.8 nTPM
Adipose tissue	41.2 nTPM
Skeletal muscle	22.9 nTPM
Breast	19.9 nTPM
Endometrium	13.7 nTPM
Lymph node	13.1 nTPM
Kidney	10.9 nTPM
Lung	10.6 nTPM
Spleen	8.9 nTPM
PBMC	8.1 nTPM
Liver	6.9 nTPM
Ovary	6.7 nTPM
Bone marrow	5.0 nTPM
Skin	0.0 nTPM

Cholangiocytes	7.2 nTPM
Liver	7.2 nTPM

Collecting duct cells	7.3 nTPM
Kidney	7.3 nTPM

Early spermatids	0.8 nTPM
Testis	0.8 nTPM

Endometrial stromal cells	11.1 nTPM
Endometrium	11.1 nTPM

Undifferentiated cells	7.4 nTPM
Small intestine	10.8 nTPM
Rectum	5.8 nTPM
Colon	5.6 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