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General description of the gene and encoded protein(s) using information from HGNC and Ensembl, as well as predictions made as well as predictions made by the Human Protein Atlas project.
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.
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.
Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.
Evidence at protein level
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.
Standardized explanatory sentences with additional information required for full understanding of the protein expression profile, based on knowledge-based and secretome-based annotation.
Antibody staining mainly consistent with RNA expression data.
Reliability scorei
A reliability score is manually set for all genes and indicates the level of reliability of the analyzed protein expression pattern based on available RNA-seq data, protein/gene characterization data and immunohistochemical data from one or several antibodies with non-overlapping epitopes. The reliability score is based on the 44 normal tissues analyzed, and if there is available data from more than one antibody, the staining patterns of all antibodies are taken into consideration during evaluation.
The reliability score is divided into Enhanced, Supported, Approved, or Uncertain, and is displayed on both Tissue Atlas and Pathology Atlas.
Below is an overview of RNA and protein expression data generated in the Human Protein Atlas project. Analyzed tissues are divided into color-coded groups according to which functional features they have in common. For each group, a list of included tissues is accessed by clicking on group name, group symbol, RNA bar, or protein bar. Subsequent selection of a particular tissue in this list links to the image data page.
Images of selected tissues give a visual summary of the protein expression profile furthest to the right.
The gray human body provides links to a histology dictionary when clicking on any part of the figure.
RNA expression (TPM)i
RNA expression summary shows the consensus RNA-data based on normalized expression (NX) data from three different sources: internally generated Human Protein Atlas (HPA) RNA-seq data, RNA-seq data from the Genotype-Tissue Expression (GTEx) project and CAGE data from FANTOM5 project. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
Each bar represents the highest expression score found in a particular group of tissues. Protein expression scores are based on a best estimate of the "true" protein expression from a knowledge-based annotation, described more in detail under Assays & annotation. For genes where more than one antibody has been used, a collective score is set displaying the estimated true protein expression.
Protein expression data is shown for each of the 44 tissues. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. Mouse-over function shows protein score for analyzed cell types in a selected tissue. To access image data click on tissue name or bar. Annotation of protein expression is described in detail in Assays & annotation.
For genes with available protein data for which a knowledge-based annotation gave inconclusive results, no protein expression data is displayed in the protein expression data overview. However, all immunohistochemical images are still available and the annotation data can be found under Primary data.
Organ
Expression
Alphabetical
RNA EXPRESSION OVERVIEWi
RNA expression overview shows RNA-data from three different sources, respectively: Internally generated Human Protein Atlas (HPA) RNA-seq data, RNA-seq data from the Genotype-Tissue Expression (GTEx) project and CAGE data from FANTOM5 project, as well as the consensus dataset which is based on a combination of all three sources. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
HPA dataset HPA RNA-seq tissue data is reported as mean pTPM (protein-coding transcripts per million), corresponding to mean values of the different individual samples from each tissue. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
GTEx dataset RNA-seq tissue data generated by the Genotype-Tissue Expression (GTEx) project is reported as mean pTPM (protein-coding transcripts per million), corresponding to mean values of the different individual samples from each tissue. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
FANTOM5 dataset Tissue data for RNA expression obtained through Cap Analysis of Gene Expression (CAGE) generated by the FANTOM5 project are reported as Scaled Tags Per Million. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
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
SRF (HGNC Symbol)
Synonyms
MCM1
Description
Serum response factor (HGNC Symbol)
Entrez gene summary
This gene encodes a ubiquitous nuclear protein that stimulates both cell proliferation and differentiation. It is a member of the MADS (MCM1, Agamous, Deficiens, and SRF) box superfamily of transcription factors. This protein binds to the serum response element (SRE) in the promoter region of target genes. This protein regulates the activity of many immediate-early genes, for example c-fos, and thereby participates in cell cycle regulation, apoptosis, cell growth, and cell differentiation. This gene is the downstream target of many pathways; for example, the mitogen-activated protein kinase pathway (MAPK) that acts through the ternary complex factors (TCFs). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]
The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.
At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.
Below the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more).
The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more).
If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.
Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
SRF-001
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.
SPOCTOPUS predicted secreted proteins Predicted intracellular proteins Transcription factors alpha-Helices exposed by beta-structures Protein evidence (Kim et al 2014)
Show all
GO:0000790 [nuclear chromatin] GO:0000978 [RNA polymerase II core promoter proximal region sequence-specific DNA binding] GO:0000982 [transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding] GO:0000983 [transcription factor activity, RNA polymerase II core promoter sequence-specific] GO:0000987 [core promoter proximal region sequence-specific DNA binding] GO:0001076 [transcription factor activity, RNA polymerase II transcription factor binding] GO:0001077 [transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding] GO:0001228 [transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding] GO:0001569 [branching involved in blood vessel morphogenesis] GO:0001666 [response to hypoxia] GO:0001701 [in utero embryonic development] GO:0001707 [mesoderm formation] GO:0001764 [neuron migration] GO:0001829 [trophectodermal cell differentiation] GO:0001947 [heart looping] GO:0002011 [morphogenesis of an epithelial sheet] GO:0002042 [cell migration involved in sprouting angiogenesis] GO:0002521 [leukocyte differentiation] GO:0003257 [positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation] GO:0003677 [DNA binding] GO:0003682 [chromatin binding] GO:0003700 [transcription factor activity, sequence-specific DNA binding] GO:0003705 [transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding] GO:0005515 [protein binding] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005737 [cytoplasm] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006366 [transcription from RNA polymerase II promoter] GO:0007015 [actin filament organization] GO:0007160 [cell-matrix adhesion] GO:0007275 [multicellular organism development] GO:0007369 [gastrulation] GO:0007507 [heart development] GO:0007616 [long-term memory] GO:0008134 [transcription factor binding] GO:0008285 [negative regulation of cell proliferation] GO:0008306 [associative learning] GO:0009636 [response to toxic substance] GO:0009725 [response to hormone] GO:0010669 [epithelial structure maintenance] GO:0010735 [positive regulation of transcription via serum response element binding] GO:0010736 [serum response element binding] GO:0016337 [single organismal cell-cell adhesion] GO:0021766 [hippocampus development] GO:0022028 [tangential migration from the subventricular zone to the olfactory bulb] GO:0030036 [actin cytoskeleton organization] GO:0030038 [contractile actin filament bundle assembly] GO:0030155 [regulation of cell adhesion] GO:0030168 [platelet activation] GO:0030220 [platelet formation] GO:0030336 [negative regulation of cell migration] GO:0030878 [thyroid gland development] GO:0030900 [forebrain development] GO:0031175 [neuron projection development] GO:0031490 [chromatin DNA binding] GO:0033561 [regulation of water loss via skin] GO:0034097 [response to cytokine] GO:0035855 [megakaryocyte development] GO:0035912 [dorsal aorta morphogenesis] GO:0042789 [mRNA transcription from RNA polymerase II promoter] GO:0042803 [protein homodimerization activity] GO:0042826 [histone deacetylase binding] GO:0043149 [stress fiber assembly] GO:0043565 [sequence-specific DNA binding] GO:0043589 [skin morphogenesis] GO:0045059 [positive thymic T cell selection] GO:0045214 [sarcomere organization] GO:0045597 [positive regulation of cell differentiation] GO:0045773 [positive regulation of axon extension] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0045987 [positive regulation of smooth muscle contraction] GO:0046016 [positive regulation of transcription by glucose] GO:0046716 [muscle cell cellular homeostasis] GO:0046983 [protein dimerization activity] GO:0048538 [thymus development] GO:0048589 [developmental growth] GO:0048666 [neuron development] GO:0048821 [erythrocyte development] GO:0051091 [positive regulation of sequence-specific DNA binding transcription factor activity] GO:0051150 [regulation of smooth muscle cell differentiation] GO:0051491 [positive regulation of filopodium assembly] GO:0055003 [cardiac myofibril assembly] GO:0060055 [angiogenesis involved in wound healing] GO:0060218 [hematopoietic stem cell differentiation] GO:0060261 [positive regulation of transcription initiation from RNA polymerase II promoter] GO:0060292 [long term synaptic depression] GO:0060324 [face development] GO:0060347 [heart trabecula formation] GO:0060425 [lung morphogenesis] GO:0060532 [bronchus cartilage development] GO:0060534 [trachea cartilage development] GO:0060947 [cardiac vascular smooth muscle cell differentiation] GO:0061029 [eyelid development in camera-type eye] GO:0061145 [lung smooth muscle development] GO:0070830 [bicellular tight junction assembly] GO:0070878 [primary miRNA binding] GO:0071333 [cellular response to glucose stimulus] GO:0090009 [primitive streak formation] GO:0090136 [epithelial cell-cell adhesion] GO:0090398 [cellular senescence] GO:1900222 [negative regulation of beta-amyloid clearance] GO:1902894 [negative regulation of pri-miRNA transcription from RNA polymerase II promoter] GO:1902895 [positive regulation of pri-miRNA transcription from RNA polymerase II promoter]
The Human Protein Atlas project is funded
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