PDX1 protein expression summary - The Human Protein Atlas

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PDX1

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GENERAL INFORMATIONⁱ 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.
Gene nameⁱ Gene name according to HGNC.	PDX1 (IDX-1, IPF1, MODY4, PDX-1, STF-1)
Gene description	Pancreatic and duodenal homeobox 1
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 transcribed from this gene as defined by Ensembl.	1
Protein evidenceⁱ 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
	SHOW MORE

TISSUE ATLASⁱ

RNA 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 (gallbladder, intestine, pancreas)
RNA tissue distributionⁱ 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 some
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	Selective nuclear expression in islets of Langerhans and intercalated ducts in pancreas, as well as in duodenum and small intestine.

CELL ATLASⁱ

Main locationⁱ The main location is characterized by presence in all tested cell lines and/or increased intensity compared to other locations. It is highlighted in the illustration to the right. 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.	Localized to the Nucleoplasm
Summaryⁱ Show complete data for human cells assay. The location(s) are highlighted in the illustration on the right.	Localized to the nucleoplasm.
RNA cell specificityⁱ The cell lines in the Human Protein Atlas have been analyzed by RNA-seq to estimate the transcript abundance of each protein-coding gene. The RNA-seq data was then used to classify all genes according to their cell line-specific expression into one of six different categories, defined based on the total set of all NX values in all analyzed cell lines. Read more	Cell line enhanced (AN3-CA, CACO-2, CAPAN-2, HDLM-2, HEK93, HeLa)
RNA cell distributionⁱ Classification of genes according to distribution of their RNA expression among the cell lines within the HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in some

PATHOLOGY ATLASⁱ

Cancer expression 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	Group enriched (colorectal cancer, liver cancer, pancreatic cancer, stomach cancer)
Cancer expression 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 many
Prognostic summary	Gene product is not prognostic

BRAIN ATLAS

	Human brain	Pig brain	Mouse brain
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	Not detected	Low region specificity	Not detected
Regional distributionⁱ The regional distribution category is based on mRNA expression detected above cut off or not in the analyzed brain samples, grouped into 10 main brain regions and calculated for the three different species. The human brain expression is based on a combination of data from GTEX and FANTOM5. The distribution categories include: detected in all, detected in many, detected in some, detected in single and not detected. The classification rules are the same used for the tissue distribution category. Read more	Not detected	Detected in many	Not detected

BLOOD ATLAS

RNA blood cell type 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
RNA blood cell type 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
Blood-based 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	Not analysed since only proteins predicted to be actively secreted to blood is analysed here
Mass spectrometry:ⁱ 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.	Not detected

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	PDX1 (HGNC Symbol)
Synonyms	IDX-1, IPF1, MODY4, PDX-1, STF-1
Description	Pancreatic and duodenal homeobox 1 (HGNC Symbol)
Entrez gene summary	The protein encoded by this gene is a transcriptional activator of several genes, including insulin, somatostatin, glucokinase, islet amyloid polypeptide, and glucose transporter type 2. The encoded nuclear protein is involved in the early development of the pancreas and plays a major role in glucose-dependent regulation of insulin gene expression. Defects in this gene are a cause of pancreatic agenesis, which can lead to early-onset insulin-dependent diabetes mellitus (IDDM), as well as maturity onset diabetes of the young type 4 (MODY4). [provided by RefSeq, Aug 2017]
Chromosome	13
Cytoband	q12.2
Chromosome location (bp)	27920020 - 27926231
Protein evidence	Evidence at protein level (all genes)
Protein classⁱ Protein class(es) of the gene product according to selected gene lists. List of protein classes.	Disease related genes Predicted intracellular proteins Transcription factors
Ensembl	ENSG00000139515 (version 92.38)
Entrez gene	3651
UniProt	P52945 (UniProt - Evidence at protein level)
neXtProt	NX_P52945
Antibodypedia	PDX1 antibodies

PROTEIN BROWSERⁱ

PDX1-201

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)
PDX1-201 ENSP00000370421 ENST00000381033	P52945 [Direct mapping] Pancreas/duodenum homeobox protein 1 Show all	Predicted intracellular proteins Intracellular proteins predicted by MDM and MDSEC Transcription factors Helix-turn-helix domains Disease related genes Mapped to neXtProt neXtProt - Evidence at protein level Protein evidence (Peptideatlas) Show all	GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] GO:0000978 [RNA polymerase II proximal promoter sequence-specific DNA binding] GO:0000981 [RNA polymerase II transcription factor activity, sequence-specific DNA binding] GO:0001889 [liver development] GO:0003309 [type B pancreatic cell differentiation] GO:0003677 [DNA binding] GO:0003682 [chromatin binding] GO:0003700 [DNA binding transcription factor activity] GO:0005622 [intracellular] GO:0005634 [nucleus] GO:0005654 [nucleoplasm] GO:0005737 [cytoplasm] GO:0005829 [cytosol] GO:0006006 [glucose metabolic process] GO:0006091 [generation of precursor metabolites and energy] GO:0006351 [transcription, DNA-templated] GO:0006355 [regulation of transcription, DNA-templated] GO:0006357 [regulation of transcription from RNA polymerase II promoter] GO:0006366 [transcription from RNA polymerase II promoter] GO:0007263 [nitric oxide mediated signal transduction] GO:0007275 [multicellular organism development] GO:0008284 [positive regulation of cell proliferation] GO:0008285 [negative regulation of cell proliferation] GO:0009887 [animal organ morphogenesis] GO:0016331 [morphogenesis of embryonic epithelium] GO:0016607 [nuclear speck] GO:0030073 [insulin secretion] GO:0030154 [cell differentiation] GO:0031016 [pancreas development] GO:0031017 [exocrine pancreas development] GO:0031018 [endocrine pancreas development] GO:0035774 [positive regulation of insulin secretion involved in cellular response to glucose stimulus] GO:0042127 [regulation of cell proliferation] GO:0042593 [glucose homeostasis] GO:0043565 [sequence-specific DNA binding] GO:0045893 [positive regulation of transcription, DNA-templated] GO:0045944 [positive regulation of transcription from RNA polymerase II promoter] GO:0048565 [digestive tract development] GO:0051594 [detection of glucose] GO:1902236 [negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway] GO:2000675 [negative regulation of type B pancreatic cell apoptotic process] Show all	283 aa 30.8 kDa	No	0

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The Human Protein Atlas

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