Single cell type - SH2D3C - 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.	SH2D3C
Gene descriptionⁱ Full gene name according to HGNC.	SH2 domain containing 3C
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.	8

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	Adipocytes & Endothelial cells - Angiogenesis (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 (Adipocytes, Endothelial cells, Hepatic stellate cells, dendritic 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 (HMC-1, HUVEC TERT2, REH, RPMI-8226, TIME)
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 (Adipocytes, Endothelial cells, Hepatic stellate cells, dendritic 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

SH2D3C is part of cluster 14 Adipocytes & Endothelial cells - Angiogenesis with confidenceⁱ 1
354 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
USHBP1	USH1 protein network component harmonin binding protein 1	0.7056	14
APOL3	Apolipoprotein L3	0.6899	14
ARHGEF15	Rho guanine nucleotide exchange factor 15	0.6846	14
VWF	Von Willebrand factor	0.6764	14
SHANK3	SH3 and multiple ankyrin repeat domains 3	0.6620	14
FZD4	Frizzled class receptor 4	0.6568	14
ADCY4	Adenylate cyclase 4	0.6459	14
UACA	Uveal autoantigen with coiled-coil domains and ankyrin repeats	0.6337	14
HSPA12B	Heat shock protein family A (Hsp70) member 12B	0.6267	14
F8	Coagulation factor VIII	0.6125	14
NOTCH4	Notch receptor 4	0.6049	14
BTNL9	Butyrophilin like 9	0.6033	14
PECAM1	Platelet and endothelial cell adhesion molecule 1	0.5966	14
CDH5	Cadherin 5	0.5932	14
EMCN	Endomucin	0.5928	14

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	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	5.8 nTPM
Lung	5.8 nTPM

Astrocytes	0.7 nTPM
Brain	0.7 nTPM

B-cells	15.9 nTPM
Lymph node	27.7 nTPM
PBMC	27.1 nTPM
Kidney	23.8 nTPM
Bone marrow	21.3 nTPM
Spleen	18.3 nTPM
Stomach	12.3 nTPM
Breast	10.7 nTPM
Liver	8.1 nTPM
Adipose tissue	8.1 nTPM
Colon	1.6 nTPM

Basal keratinocytes	1.3 nTPM
Skin	1.3 nTPM

Dendritic cells	29.7 nTPM
PBMC	55.8 nTPM
Breast	24.8 nTPM
Adipose tissue	8.5 nTPM

Endothelial cells	52.2 nTPM
Heart muscle	113.5 nTPM
Skeletal muscle	81.2 nTPM
Ovary	71.8 nTPM
Esophagus	68.0 nTPM
Placenta	66.5 nTPM
Testis	56.8 nTPM
Pancreas	46.4 nTPM
Endometrium	44.1 nTPM
Lung	43.7 nTPM
Breast	41.6 nTPM
Liver	41.2 nTPM
Eye	23.5 nTPM
Skin	18.8 nTPM
Prostate	13.7 nTPM

Fibroblasts	3.1 nTPM
Stomach	10.4 nTPM
Heart muscle	5.2 nTPM
Breast	3.9 nTPM
Placenta	3.5 nTPM
Skeletal muscle	2.7 nTPM
Esophagus	2.1 nTPM
Skin	1.7 nTPM
Adipose tissue	1.5 nTPM
Ovary	1.3 nTPM
Lung	1.2 nTPM
Prostate	0.4 nTPM

Intestinal goblet cells	0.3 nTPM
Small intestine	0.8 nTPM
Colon	0.0 nTPM
Rectum	0.0 nTPM

Macrophages	10.7 nTPM
Kidney	25.7 nTPM
Bone marrow	25.0 nTPM
Stomach	23.5 nTPM
Lung	15.2 nTPM
Endometrium	14.7 nTPM
Testis	11.7 nTPM
Breast	10.6 nTPM
Adipose tissue	8.8 nTPM
Skeletal muscle	8.6 nTPM
Esophagus	7.9 nTPM
Spleen	4.2 nTPM
Ovary	3.0 nTPM
Prostate	1.2 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM

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

Plasma cells	7.6 nTPM
Esophagus	12.3 nTPM
Bone marrow	9.9 nTPM
Stomach	7.4 nTPM
Adipose tissue	5.2 nTPM
Spleen	3.2 nTPM

Respiratory ciliated cells	0.8 nTPM
Lung	1.5 nTPM
Bronchus	0.1 nTPM

Smooth muscle cells	12.5 nTPM
Endometrium	33.7 nTPM
Heart muscle	29.5 nTPM
Ovary	18.1 nTPM
Breast	13.3 nTPM
Adipose tissue	11.4 nTPM
Skeletal muscle	11.1 nTPM
Esophagus	9.3 nTPM
Skin	8.7 nTPM
Bronchus	2.0 nTPM
Prostate	0.4 nTPM
Pancreas	0.1 nTPM

T-cells	15.5 nTPM
Bone marrow	38.1 nTPM
Ovary	24.5 nTPM
Breast	21.1 nTPM
Liver	20.7 nTPM
PBMC	19.1 nTPM
Lung	18.2 nTPM
Endometrium	18.2 nTPM
Spleen	17.3 nTPM
Kidney	15.1 nTPM
Lymph node	14.5 nTPM
Skin	13.8 nTPM
Esophagus	13.1 nTPM
Stomach	12.5 nTPM
Skeletal muscle	10.7 nTPM
Adipose tissue	3.8 nTPM
Colon	2.4 nTPM
Prostate	0.0 nTPM

Cholangiocytes	2.8 nTPM
Liver	2.8 nTPM

Endometrial stromal cells	2.8 nTPM
Endometrium	2.8 nTPM

Excitatory neurons	10.8 nTPM
Brain	10.8 nTPM

Undifferentiated cells	0.1 nTPM
Small intestine	0.2 nTPM
Colon	0.0 nTPM
Rectum	0.0 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