SERF1A protein expression summary - The Human Protein Atlas

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SERF1A

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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.	Small EDRK-rich factor 1A
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	SERF1A (4F5, FAM2A, H4F5, SERF1, SMAM1)
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	Low tissue specificity
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	Group enriched (Cardiomyocytes, Rod photoreceptor cells, Cone photoreceptor cells)
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	Low immune cell specificity
Cancer prognostic summary	Gene product is not prognostic
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 (different isoforms)
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 Nuclear bodies
Protein function (UniProt)ⁱ Useful information about the protein provided by UniProt.	Positive regulator of amyloid protein aggregation and proteotoxicity 1, 2, 3. Induces conformational changes in amyloid proteins, such as APP, HTT, and SNCA, driving them into compact formations preceding the formation of aggregates 4, 5, 6.... show less
Gene summary (Entrez)ⁱ Useful information about the gene from Entrez	This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. The duplication region includes both a telomeric and a centromeric copy of this gene. Deletions of this gene, the telomeric copy, often accompany deletions of the neighboring SMN1 gene in spinal muscular atrophy (SMA) patients, and so it is thought that this gene may be a modifier of the SMA phenotype. The function of this protein is not known; however, it bears low-level homology with the RNA-binding domain of matrin-cyclophilin, a protein which colocalizes with small nuclear ribonucleoproteins (snRNPs) and the SMN1 gene product. Alternatively spliced transcripts have been documented but it is unclear whether alternative splicing occurs for both the centromeric and telomeric copies of the gene. [provided by RefSeq, Jul 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	Low tissue specificity
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

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	Group enriched (Cardiomyocytes, Rod photoreceptor cells, Cone photoreceptor cells)
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.	Low cell line specificity

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

Prognostic summary	Gene product is not prognostic
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	Not detected
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	Not detected

No regional specificity can be calculated, but other data exist for this gene

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	Low cell type specificity
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 Nuclear bodies
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	SERF1A (HGNC Symbol)
Synonyms	4F5, FAM2A, H4F5, SERF1, SMAM1
Description	Small EDRK-rich factor 1A (HGNC Symbol)
Chromosome	5
Cytoband	q13.2
Chromosome location (bp)	70900665 - 70918530
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	8
Protein evidence	Evidence at transcript level (all genes)
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more
Ensembl	ENSG00000172058 (version 92.38)
Entrez gene	8293
UniProt	O75920 (UniProt - Evidence at transcript level)
neXtProt	NX_O75920
Antibodypedia	SERF1A antibodies

PROTEIN BROWSERⁱ

SERF1A-201

SERF1A-202

SERF1A-204

SERF1A-205

SERF1A-206

SERF1A-207

SERF1A-208

SERF1A-209

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)
SERF1A-201 ENSP00000321791 ENST00000317633	O75920 [Direct mapping] Small EDRK-rich factor 1 Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Mapped to neXtProt neXtProt - Evidence at transcript level Show all	GO:0003674 [molecular_function] GO:0005575 [cellular_component] GO:0007399 [nervous system development] Show all	62 aa 7.3 kDa	No	0
SERF1A-202 ENSP00000346892 ENST00000354833	O75920 [Direct mapping] Small EDRK-rich factor 1 Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Mapped to neXtProt neXtProt - Evidence at transcript level Show all	GO:0003674 [molecular_function] GO:0005575 [cellular_component] GO:0007399 [nervous system development] Show all	110 aa 12.3 kDa	No	1
SERF1A-204 ENSP00000426322 ENST00000504458	D6RC42 [Direct mapping] Small EDRK-rich factor 1 Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Show all		75 aa 8.4 kDa	No	0
SERF1A-205 ENSP00000428386 ENST00000507348	E5RIQ9 [Direct mapping] Small EDRK-rich factor 1 Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Show all		48 aa 5.7 kDa	No	0
SERF1A-206 ENSP00000429293 ENST00000511162	E5RIX6 [Direct mapping] Small EDRK-rich factor 1 Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Show all		20 aa 2.3 kDa	No	0
SERF1A-207 ENSP00000430582 ENST00000512649	D6RCL9 [Direct mapping] Small EDRK-rich factor 1 Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Show all	GO:0016020 [membrane] GO:0016021 [integral component of membrane] Show all	96 aa 10.7 kDa	No	1
SERF1A-208 ENSP00000429748 ENST00000512868	E5RHJ0 [Direct mapping] Small EDRK-rich factor 1 Show all	Predicted membrane proteins Prediction method-based Membrane proteins predicted by MDM MEMSAT3 predicted membrane proteins MEMSAT-SVM predicted membrane proteins Phobius predicted membrane proteins SCAMPI predicted membrane proteins SPOCTOPUS predicted membrane proteins THUMBUP predicted membrane proteins TMHMM predicted membrane proteins # TM segments-based 1TM proteins predicted by MDM Show all	GO:0016020 [membrane] GO:0016021 [integral component of membrane] Show all	89 aa 9.8 kDa	No	1
SERF1A-209 ENSP00000422339 ENST00000513436	D6RC90 [Direct mapping] Small EDRK-rich factor 1 Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Show all		81 aa 8.8 kDa	No	0

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The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.