SYNPO protein expression summary - The Human Protein Atlas

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HUMAN PROTEIN ATLAS SUMMARYⁱ 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.
Proteinⁱ Full gene name according to HGNC.	Synaptopodin
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	SYNPO (KIAA1029)
Tissue specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Group enriched (heart muscle, placenta, skeletal muscle)
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 enriched (Cardiomyocytes)
Blood specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed blood cell 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	Group enriched (naive B-cell, memory B-cell)
Brain specificityⁱ The regional specificity category is based on mRNA expression levels in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression profile is based on a combination of data from GTEX and FANTOM5. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low human brain regional specificity
Cancer prognostic summary	Prognostic marker in renal cancer (unfavorable)
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
Subcellular summaryⁱ The main location is characterized by presence in all tested cell lines and/or increased intensity compared to other locations. Additional locations are characterized by either a markedly lower staining intensity than the main location, or that it is only observed in a subset of the cell lines.	Located in Nucleoplasm, Actin filaments, Cytosol
Protein function (UniProt)ⁱ Useful information about the protein provided by UniProt.	Actin-associated protein that may play a role in modulating actin-based shape and motility of dendritic spines and renal podocyte foot processes. Seems to be essential for the formation of spine apparatuses in spines of telencephalic neurons, which is involved in synaptic plasticity (By similarity).... show less
Molecular function (UniProt)ⁱ Keywords assigned by UniProt to proteins due to their particular molecular function.	Actin-binding
Gene summary (Entrez)ⁱ Useful information about the gene from Entrez	Synaptopodin is an actin-associated protein that may play a role in actin-based cell shape and motility. The name synaptopodin derives from the protein's associations with postsynaptic densities and dendritic spines and with renal podocytes (Mundel et al., 1997).[supplied by OMIM, Mar 2008]... show less

TISSUE ATLASⁱ Summary of data presented in the Tissue Atlas and representative images of protein expression (left) and mRNA expression (right). The images are clickable and will redirect to more Tissue Atlas data. The Tissue Atlas contains information regarding the expression profiles of protein-coding genes in normal human tissue, both on the mRNA and protein level. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry. Read more

Tissue specificity (RNA)ⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: tissue enriched, group enriched, tissue enhanced, low tissue specificity and not detected. Read more	Group enriched (heart muscle, placenta, skeletal muscle)
Tissue distribution (RNA)ⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on a combination of data from HPA, GTEX and FANTOM5. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in many
Protein expressionⁱ A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation. "Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile. Read more	Cytoplasmic expression in several tissues, including glomeruli in kidney, skeletal and heart muscle, and the CNS.

SINGLE CELL TYPE ATLASⁱ Summary of data presented in the Cell Type Atlas and an interactive image showing mRNA expression in cell type groups e.g. epithelial cells and germ cells. The image is clickable and will redirect to more Cell Type Atlas data. The Cell Type Atlas contains information about single cell type RNA expression based on scRNAseq of human tissues. The data also covers transcriptomics analysis of human blood and cultured cell lines. Read more

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 enriched (Cardiomyocytes)
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.	Cell line enhanced (BEWO, EFO-21, HUVEC TERT2, TIME, U-87 MG)

PATHOLOGY ATLASⁱ Summary of data presented in the Pathology Atlas , with representative images of protein expression in cancer (left) and correlation between mRNA expression and patient survival (right). Images are clickable and redirect to pages with more Pathology Atlas data. The Pathology Atlas contains mRNA and protein expression data from 17 different forms of human cancer, as well as correlation analysis of mRNA expression and patient survival. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry. Read more
	Renal cancer p<0.001
Prognostic summary	Prognostic marker in renal cancer (unfavorable)
Cancer specificity (RNA)ⁱ Specificity of RNA expression in 17 cancer types is categorized as either cancer enriched, group enriched, cancer enhanced, low cancer specificity and not detected. Read more	Low cancer specificity
Cancer distribution (RNA)ⁱ Distribution of RNA expression in 17 cancer types is categorized as either detected in single, detected in some, detected in many, detected in all, or not detected. Read more	Detected in all

BRAIN ATLASⁱ Summary of data presented in the Brain Atlas and a representative image of mRNA expression in the human brain. The image is clickable and will redirect to more Brain Atlas data. The Brain Atlas explores the protein expression in the mammalian brain by visualization and integration of data from three mammalian species (human, pig and mouse). Transcriptomics data combined with affinity-based protein in situ localization down to single cell level is available in a brain-centric sub atlas of the Human Protein Atlas. Read more

Human regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression profile is based on a combination of data from GTEX and FANTOM5. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity
Pig regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression profile is based on a combination of data from GTEX and FANTOM5. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Low region specificity
Mouse regional specificityⁱ The regional specificity category is based on mRNA expression levels in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression profile is based on a combination of data from GTEX and FANTOM5. The specificity categories include: regionally enriched, group enriched, regionally enhanced, low regional specificity and not detected. The classification rules are the same used for the tissue specificity category. Read more	Group enriched (amygdala, basal ganglia, cerebral cortex, hippocampal formation, olfactory region)

BLOOD ATLASⁱ Summary of data presented in the Blood Atlas and a representative image of mRNA expression in immune cells in the blood. The image is clickable and will redirect to more Blood Atlas data. The Blood Atlas contains single cell type RNA information covering various immune cells in the blood, e.g. B-cells and granulocytes. Analysis of the human secretome (including annotation of the genes predicted to be actively secreted to human blood) and proteins detected in human blood are also presented. Read more

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	Group enriched (naive B-cell, memory B-cell)
Detected in blood by immunoassayⁱ The blood-based immunoassay category applies to actively secreted proteins and is based on plasma or serum protein concentrations established with enzyme-linked immunosorbent assays, compiled from a literature search. The categories include: detected and not detected, where detection refers to a concentration found in the literature search. Read more	No (not applicable)
Detected in blood by mass spectrometryⁱ Detection or not of the gene in blood, based on spectral count estimations from a publicly available mass spectrometry-based plasma proteomics data set obtained from the PeptideAtlas.	No

CELL ATLASⁱ Summary of data presented in the Cell Atlas and a representative image of subcellular localization. The Cell Atlas provides RNA expression data derived from RNA sequencing of a large panel of cell lines and protein localization data derived from antibody-based profiling by immunofluorescence confocal microscopy, using a subset of cell lines selected based on RNA expression. Read more

Main locationⁱ Main subcellular location(s) and reliability score(s) for the encoded protein(s) in human cells. The main location(s) may be characterized by presence in all tested cell lines and/or ihigher staining intensity compared to the potential additional location(s). If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively. Read more	Localized to the Nucleoplasm, Cytosol
Additional locationⁱ Additonal subcellular location(s) for the encoded protein(s) in human cells. The additional location(s) may not be present i all cell lines and may have lower staining intensity compared to the main location(s). If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively. Read more	In addition localized to the Actin filaments
Cell cycle dependencyⁱ Cell-cycle dependance of single-cell varations in RNA and/or protein expression as observed in an additional assay for characterizing single-cell varations. "NA" indicates a lack of such data. Read more	NA

GENE INFORMATIONⁱ Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
Gene name	SYNPO (HGNC Symbol)
Synonyms	KIAA1029
Description	Synaptopodin (HGNC Symbol)
Chromosome	5
Cytoband	q33.1
Chromosome location (bp)	150601080 - 150659220
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	4
Protein evidence	Evidence at protein level (all genes)
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more
Ensembl	ENSG00000171992 (version 92.38)
Entrez gene	11346
UniProt	Q8N3V7 (UniProt - Evidence at protein level)
neXtProt	NX_Q8N3V7
Antibodypedia	SYNPO antibodies

PROTEIN BROWSERⁱ

SYNPO-201

SYNPO-202

SYNPO-204

SYNPO-205

PROTEIN INFORMATIONⁱ The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database. The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein. The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class. The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Splice variant	UniProt	Protein class	Gene ontology	Length & mass	Signal peptide (predicted)	Transmembrane regions (predicted)
SYNPO-201 ENSP00000302139 ENST00000307662	Q8N3V7 [Direct mapping] Synaptopodin Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Peptideatlas) Show all	GO:0003779 [actin binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005737 [cytoplasm] GO:0005856 [cytoskeleton] GO:0005886 [plasma membrane] GO:0005923 [bicellular tight junction] GO:0014069 [postsynaptic density] GO:0015629 [actin cytoskeleton] GO:0016020 [membrane] GO:0030018 [Z disc] GO:0030054 [cell junction] GO:0032233 [positive regulation of actin filament bundle assembly] GO:0042995 [cell projection] GO:0043197 [dendritic spine] GO:0043204 [perikaryon] GO:0045202 [synapse] GO:0045211 [postsynaptic membrane] GO:0098886 [modification of dendritic spine] Show all	903 aa 96.4 kDa	No	0
SYNPO-202 ENSP00000377789 ENST00000394243	Q8N3V7 [Direct mapping] Synaptopodin Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Peptideatlas) Show all	GO:0003779 [actin binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005737 [cytoplasm] GO:0005856 [cytoskeleton] GO:0005886 [plasma membrane] GO:0005923 [bicellular tight junction] GO:0008542 [visual learning] GO:0014069 [postsynaptic density] GO:0015629 [actin cytoskeleton] GO:0016020 [membrane] GO:0030018 [Z disc] GO:0030054 [cell junction] GO:0032233 [positive regulation of actin filament bundle assembly] GO:0042995 [cell projection] GO:0043197 [dendritic spine] GO:0043204 [perikaryon] GO:0045202 [synapse] GO:0045211 [postsynaptic membrane] GO:0048169 [regulation of long-term neuronal synaptic plasticity] GO:0097444 [spine apparatus] GO:0098886 [modification of dendritic spine] GO:1905355 [spine apparatus assembly] Show all	929 aa 99.5 kDa	No	0
SYNPO-204 ENSP00000429268 ENST00000519664	Q8N3V7 [Direct mapping] Synaptopodin Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Peptideatlas) Show all	GO:0003779 [actin binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005737 [cytoplasm] GO:0005856 [cytoskeleton] GO:0005886 [plasma membrane] GO:0005923 [bicellular tight junction] GO:0014069 [postsynaptic density] GO:0015629 [actin cytoskeleton] GO:0016020 [membrane] GO:0030018 [Z disc] GO:0030054 [cell junction] GO:0032233 [positive regulation of actin filament bundle assembly] GO:0042995 [cell projection] GO:0043197 [dendritic spine] GO:0043204 [perikaryon] GO:0045202 [synapse] GO:0045211 [postsynaptic membrane] GO:0098886 [modification of dendritic spine] Show all	685 aa 73.7 kDa	No	0
SYNPO-205 ENSP00000428378 ENST00000522122	Q8N3V7 [Direct mapping] Synaptopodin Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Peptideatlas) Show all	GO:0003779 [actin binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005737 [cytoplasm] GO:0005856 [cytoskeleton] GO:0005886 [plasma membrane] GO:0005923 [bicellular tight junction] GO:0014069 [postsynaptic density] GO:0015629 [actin cytoskeleton] GO:0016020 [membrane] GO:0030018 [Z disc] GO:0030054 [cell junction] GO:0032233 [positive regulation of actin filament bundle assembly] GO:0042995 [cell projection] GO:0043197 [dendritic spine] GO:0043204 [perikaryon] GO:0045202 [synapse] GO:0045211 [postsynaptic membrane] GO:0098886 [modification of dendritic spine] Show all	929 aa 99.5 kDa	No	0

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The Human Protein Atlas project is funded
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