Single cell type - SYNPO2 - 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.	SYNPO2
Gene descriptionⁱ Full gene name according to HGNC.	Synaptopodin 2
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.	7

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	Smooth muscle cells - ECM organization (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 (Smooth muscle cells, Excitatory neurons, Cardiomyocytes, Sertoli cells, Endometrial stromal cells, Peritubular cells, Skeletal myocytes)
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	Cell line enhanced (fHDF/TERT166, LHCN-M2, SH-SY5Y)
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 some
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 (Smooth muscle cells, Excitatory neurons, Cardiomyocytes, Sertoli cells, Endometrial stromal cells, Peritubular cells, Skeletal myocytes)

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

SYNPO2 is part of cluster 48 Smooth muscle cells - ECM organization with confidenceⁱ 1
270 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
ARHGEF25	Rho guanine nucleotide exchange factor 25	0.7398	48
TPM2	Tropomyosin 2	0.7066	48
EDNRA	Endothelin receptor type A	0.7002	48
ITGA7	Integrin subunit alpha 7	0.6888	48
CCDC3	Coiled-coil domain containing 3	0.6886	48
CAP2	Cyclase associated actin cytoskeleton regulatory protein 2	0.6764	8
MYOCD	Myocardin	0.6561	48
ARHGEF17	Rho guanine nucleotide exchange factor 17	0.6524	48
ABCC9	ATP binding cassette subfamily C member 9	0.6524	48
SCN4B	Sodium voltage-gated channel beta subunit 4	0.6472	48
DNAJB5	DnaJ heat shock protein family (Hsp40) member B5	0.6452	37
DMPK	DM1 protein kinase	0.6278	48
SMARCD3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	0.6212	48
RERGL	RERG like	0.6204	48
FAM162B	Family with sequence similarity 162 member B	0.6190	48

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	25.5 nTPM
Breast	40.9 nTPM
Adipose tissue	10.1 nTPM

Alveolar cells type 1	3.2 nTPM
Lung	3.2 nTPM

Alveolar cells type 2	1.1 nTPM
Lung	1.1 nTPM

Astrocytes	42.7 nTPM
Brain	42.7 nTPM

B-cells	1.1 nTPM
Lymph node	2.1 nTPM
Spleen	2.1 nTPM
Liver	2.0 nTPM
Colon	1.6 nTPM
Breast	1.3 nTPM
Stomach	0.9 nTPM
Bone marrow	0.8 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM

Dendritic cells	0.5 nTPM
Breast	1.5 nTPM
Adipose tissue	0.2 nTPM
PBMC	0.0 nTPM

Endothelial cells	11.3 nTPM
Breast	41.2 nTPM
Skin	20.1 nTPM
Heart muscle	18.4 nTPM
Eye	17.8 nTPM
Prostate	16.2 nTPM
Endometrium	13.2 nTPM
Skeletal muscle	8.9 nTPM
Esophagus	8.3 nTPM
Testis	7.7 nTPM
Liver	4.6 nTPM
Ovary	1.0 nTPM
Placenta	0.6 nTPM
Lung	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	41.5 nTPM
Heart muscle	92.4 nTPM
Ovary	84.5 nTPM
Esophagus	57.3 nTPM
Prostate	38.5 nTPM
Placenta	36.5 nTPM
Stomach	34.1 nTPM
Breast	30.8 nTPM
Adipose tissue	29.6 nTPM
Skeletal muscle	23.0 nTPM
Skin	22.2 nTPM
Lung	7.8 nTPM

Intestinal goblet cells	0.2 nTPM
Small intestine	0.4 nTPM
Rectum	0.2 nTPM
Colon	0.0 nTPM

Macrophages	3.8 nTPM
Esophagus	23.6 nTPM
Skeletal muscle	8.1 nTPM
Prostate	6.9 nTPM
Endometrium	4.4 nTPM
Breast	4.0 nTPM
Testis	2.9 nTPM
Adipose tissue	2.7 nTPM
Spleen	2.1 nTPM
Kidney	0.8 nTPM
Lung	0.8 nTPM
Ovary	0.6 nTPM
PBMC	0.0 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	0.4 nTPM
Rectum	1.2 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	0.8 nTPM
Bone marrow	1.7 nTPM
Spleen	1.3 nTPM
Adipose tissue	0.6 nTPM
Stomach	0.5 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	2.5 nTPM
Lung	4.4 nTPM
Bronchus	0.5 nTPM

Smooth muscle cells	206.1 nTPM
Esophagus	379.9 nTPM
Skin	353.7 nTPM
Prostate	341.1 nTPM
Endometrium	288.9 nTPM
Heart muscle	247.8 nTPM
Breast	233.4 nTPM
Adipose tissue	225.7 nTPM
Skeletal muscle	168.8 nTPM
Ovary	26.2 nTPM
Pancreas	1.0 nTPM
Bronchus	0.0 nTPM

T-cells	2.6 nTPM
Skin	10.5 nTPM
Endometrium	9.0 nTPM
Esophagus	6.6 nTPM
Spleen	3.6 nTPM
Lymph node	3.5 nTPM
Bone marrow	3.0 nTPM
Skeletal muscle	2.0 nTPM
Stomach	1.9 nTPM
Lung	1.5 nTPM
Liver	1.1 nTPM
Breast	1.1 nTPM
Colon	0.5 nTPM
Adipose tissue	0.2 nTPM
PBMC	0.1 nTPM
Kidney	0.0 nTPM
Prostate	0.0 nTPM
Ovary	0.0 nTPM

Basal keratinocytes	13.5 nTPM
Skin	13.5 nTPM

Basal prostatic cells	17.9 nTPM
Prostate	17.9 nTPM

Basal respiratory cells	3.7 nTPM
Bronchus	3.7 nTPM

Basal squamous epithelial cells	46.1 nTPM
Esophagus	46.1 nTPM

Undifferentiated cells	0.2 nTPM
Colon	0.4 nTPM
Small intestine	0.2 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