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PDX1 Gene

protein-coding   GIFtS: 63
GCID: GC13P028494

Pancreatic And Duodenal Homeobox 1

(Previous names: insulin promoter factor 1, homeodomain transcription factor)
(Previous symbol: IPF1)
  See PDX1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Pancreatic And Duodenal Homeobox 11 2     IPF-12 3
IPF11 2 3 5     IUF-12 3
Insulin Promoter Factor 1, Homeodomain Transcription Factor1 2     PDX-12 3
Somatostatin Transcription Factor 11 2     STF-12 3
Glucose-Sensitive Factor2 3     MODY42 5
Insulin Upstream Factor 12 3     IUF12
Islet/Duodenum Homeobox-12 3     Pancreas/Duodenum Homeobox Protein 12
Somatostatin-Transactivating Factor 12 3     Pancreatic-Duodenal Homeobox Factor 12
GSF2 3     STF13
IDX-12 3     Insulin Promoter Factor 13

External Ids:    HGNC: 61071   Entrez Gene: 36512   Ensembl: ENSG000001395157   OMIM: 6007335   UniProtKB: P529453   

Export aliases for PDX1 gene to outside databases

Previous GC identifers: GC11P036490 GC11P035616 GC13P027393 GC13P009314


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PDX1 Gene:
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 (NIDDM), as well as maturity onset diabetes of the young type 4 (MODY4).
(provided by RefSeq, Jul 2008)

GeneCards Summary for PDX1 Gene:
PDX1 (pancreatic and duodenal homeobox 1) is a protein-coding gene. Diseases associated with PDX1 include pdx1-related permanent neonatal diabetes mellitus, and maturity-onset diabetes of the young, type 4. GO annotations related to this gene include chromatin binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is GSX1.

UniProtKB/Swiss-Prot: PDX1_HUMAN, P52945
Function: Activates insulin, somatostatin, glucokinase, islet amyloid polypeptide and glucose transporter type 2
gene transcription. Particularly involved in glucose-dependent regulation of insulin gene transcription. As part
of a PDX1:PBX1b:MEIS2b complex in pancreatic acinar cells is involved in the transcriptional activation of the
ELA1 enhancer; the complex binds to the enhancer B element and cooperates with the transcription factor 1 complex
(PTF1) bound to the enhancer A element. Binds preferentially the DNA motif 5'-[CT]TAAT[TG]-3'. During
development, specifies the early pancreatic epithelium, permitting its proliferation, branching and subsequent
differentiation. At adult stage, required for maintaining the hormone-producing phenotype of the beta-cell

Gene Wiki entry for PDX1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000013.10  NC_018924.2  NT_024524.15  
Regulatory elements:
   Regulatory transcription factor binding sites in the PDX1 gene promoter:
         RORalpha1   HEN1   NRSF form 1   Egr-1   p300   AP-4   NRSF form 2   E47   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPDX1 promoter sequence
   Search Chromatin IP Primers for PDX1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PDX1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 13q12.1   Ensembl cytogenetic band:  13q12.2   HGNC cytogenetic band: 13q12.1

PDX1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PDX1 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13P028494:  view genomic region     (about GC identifiers)

Start:
28,494,157 bp from pter      End:
28,500,451 bp from pter
Size:
6,295 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: PDX1_HUMAN, P52945 (See protein sequence)
Recommended Name: Pancreas/duodenum homeobox protein 1  
Size: 283 amino acids; 30771 Da
Subunit: Interacts with the basic helix-loop-helix domains of TCF3(E47) and NEUROD1 and with HMG-I(Y). Interacts
with SPOP (By similarity). Interacts with the methyltransferase SETD7. Part of a PDX1:PBX1b:MEIS2b complex
Miscellaneous: According to PubMed:16141209, it may be methylated by SETD7 in vitro. However, the relevance of
methylation is unsure in vivo
Secondary accessions: O60594 Q5VYW2

Explore the universe of human proteins at neXtProt for PDX1: NX_P52945

Explore proteomics data for PDX1 at MOPED

Post-translational modifications: 

  • Phosphorylated by the SAPK2 pathway at high intracellular glucose concentration. Phosphorylated by HIPK2 on
    Ser-268 upon glucose accumulation. This phoyphorylation mediates subnuclear localization shifting.
    Phosphorylation by PASK may lead to translocation into the cytosol (By similarity)1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See PDX1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_000200.1  
    ENSEMBL proteins: 
     ENSP00000370421  
    Reactome Protein details: P52945

    PDX1 Human Recombinant Protein Products:

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    Browse Sino Biological Cell Lysates
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    Browse Proteins at Cloud-Clone Corp.

     
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    antibodies-online proteins for PDX1 (7 products) 

     
    antibodies-online peptides for PDX1

    PDX1 Antibody Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    HOXL: Homeoboxes / ANTP class : HOXL subclass

    5 InterPro protein domains:
     IPR020479 Homeobox_metazoa
     IPR017995 Homeobox_antennapedia
     IPR017970 Homeobox_CS
     IPR001356 Homeobox_dom
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry P52945

    ProtoNet protein and cluster: P52945

    2 Blocks protein domains:
    IPB000047 Lambda and other repressor helix-turn-helix signature
    IPB001827 Homeobox protein


    UniProtKB/Swiss-Prot: PDX1_HUMAN, P52945
    Domain: The Antp-type hexapeptide mediates heterodimerization with PBX on a regulatory element of the somatostatin
    promoter (By similarity)
    Domain: The homeodomain, which contains the nuclear localization signal, not only mediates DNA-binding, but also
    acts as a protein-protein interaction domain for TCF3(E47), NEUROD1 and HMG-I(Y) (By similarity)
    Similarity: Belongs to the Antp homeobox family. IPF1/XlHbox-8 subfamily
    Similarity: Contains 1 homeobox DNA-binding domain


    Find genes that share domains with PDX1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PDX1_HUMAN, P52945
    Function: Activates insulin, somatostatin, glucokinase, islet amyloid polypeptide and glucose transporter type 2
    gene transcription. Particularly involved in glucose-dependent regulation of insulin gene transcription. As part
    of a PDX1:PBX1b:MEIS2b complex in pancreatic acinar cells is involved in the transcriptional activation of the
    ELA1 enhancer; the complex binds to the enhancer B element and cooperates with the transcription factor 1 complex
    (PTF1) bound to the enhancer A element. Binds preferentially the DNA motif 5'-[CT]TAAT[TG]-3'. During
    development, specifies the early pancreatic epithelium, permitting its proliferation, branching and subsequent
    differentiation. At adult stage, required for maintaining the hormone-producing phenotype of the beta-cell

         Genatlas biochemistry entry for PDX1:
    lipoyl-containing protein (protein X),subunit of the pyruvate dehydrogenase complex,tightly associated with E2 and
    binding E3 subunit

         Summary: 
    During embryonic development, PDX1 as signaling molecule is secreted from the following cells:
                
    Lateral Plate Mesoderm: Angioblasts (Embryonic Capillary Plexus)

    It affects the following cells:
    Pancreas: Pancreatic Progenitor Cells (Dorsal Pancreatic Bud)
    Gut Tube: Dorsal Foregut Endoderm Cells (Dorsal Foregut Endoderm)

         Gene Ontology (GO): Selected molecular function terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001046core promoter sequence-specific DNA binding IEA--
    GO:0003677DNA binding ----
    GO:0003682chromatin binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity TAS17941991
    GO:0005515protein binding ----
         
    Find genes that share ontologies with PDX1           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for PDX1:
     Decreased viability with pacli  Synthetic lethal with Ras 

         13 MGI mutant phenotypes (inferred from 10 alleles(MGI details for Pdx1):
     cellular  digestive/alimentary  endocrine/exocrine gland  growth/size/body  homeostasis/metabolism 
     immune system  integument  liver/biliary system  mortality/aging  muscle 
     no phenotypic analysis  normal  renal/urinary system 

    Find genes that share phenotypes with PDX1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for PDX1: Pdx1tm1Ted Pdx1tm1Cvw Pdx1tm3Cvw

       genOway: Develop your customized and physiologically relevant rodent model for PDX1

    Transcription Factor Targeting: 
    Targeting motifs: HOMER Transcription Factor Regulatory Elements motif viewer 
                                          Consensus sequence:  TCATCAATCA 

    miRNA
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    1 qRT-PCR Assays for microRNA that regulate PDX1:
    hsa-miR-629*
    SwitchGear 3'UTR luciferase reporter plasmidPDX1 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PDX1_HUMAN, P52945: Nucleus. Cytoplasm, cytosol (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    endoplasmic reticulum1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm ----
    GO:0005829cytosol IEA--

    Find genes that share ontologies with PDX1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for PDX1 About   (see all 8)  
    See pathways by source

    SuperPathContained pathways About
    1Type II diabetes mellitus
    Type II diabetes mellitus0.38
    Type II diabetes mellitus0.35
    Anti-diabetic Drug Potassium Channel Inhibitors Pathway, Pharmacodynamics0.38
    2Regulation of beta-cell development
    Regulation of beta-cell development0.64
    Maturity onset diabetes of the young0.61
    Regulation of gene expression in beta cells0.64
    Regulation of gene expression in early pancreatic precursor cells0.00
    3L1CAM interactions
    Developmental Biology0.63
    4Insulin secretion
    Insulin secretion0.36
    5GABA signaling in brain
    GABA signaling in brain0.32


    Find genes that share SuperPaths with PDX1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for PDX1
        MODY (Maturity-Onset Diabetes of Young)

    1 Cell Signaling Technology (CST) Pathway for PDX1
        Glucose / Energy Metabolism

    2 BioSystems Pathways for PDX1
        Type II diabetes mellitus
    FOXA2 and FOXA3 transcription factor networks

    2 Reactome Pathways for PDX1
        Regulation of gene expression in beta cells
    Regulation of gene expression in early pancreatic precursor cells

    1 PharmGKB Pathway for PDX1
        Anti-diabetic Drug Potassium Channel Inhibitors Pathway, Pharmacodynamics

    3 Kegg Pathways  (Kegg details for PDX1):
        Insulin secretion
    Type II diabetes mellitus
    Maturity onset diabetes of the young

        Pathway & Disease-focused RT2 Profiler PCR Arrays including PDX1: 
              Insulin Resistance in human mouse rat
              Embryonic Stem Cells in human mouse rat
              Diabetes in human mouse rat
              Stem Cells in human mouse rat
              Homeobox (HOX) Genes in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for PDX1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 22)

    Selected Interacting proteins for PDX1 (P529452, 3 ENSP000003704214) via UniProtKB, MINT, STRING, and/or I2D (see all 27)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PASKQ96RG22, 3, ENSP000002340404MINT-8145315 I2D: score=1 STRING: ENSP00000234040
    MAFAQ8NHW33, ENSP000003283644I2D: score=2 STRING: ENSP00000328364
    NEUROD1Q135623, ENSP000002951084I2D: score=1 STRING: ENSP00000295108
    PRKDCP785273, ENSP000003134204I2D: score=1 STRING: ENSP00000313420
    XRCC6P129563, ENSP000003522574I2D: score=1 STRING: ENSP00000352257
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 50):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
    GO:0001889liver development IEA--
    GO:0003309type B pancreatic cell differentiation ISS--
    GO:0006006glucose metabolic process IEA--
    GO:0006091generation of precursor metabolites and energy TAS8954967

    Find genes that share ontologies with PDX1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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      Browse compounds at ApexBio 

    Browse Tocris compounds for PDX1

    Selected Novoseek inferred chemical compound relationships for PDX1 gene (see all 31)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    c-peptide 68.2 11 19757377 (1), 16630561 (1), 17612586 (1), 16186387 (1) (see all 8)
    preproinsulin 68.2 12 11319727 (2), 14563207 (2), 15935394 (2), 16213778 (1) (see all 5)
    glucose 68 169 11574405 (7), 10426567 (6), 7980425 (6), 9252422 (5) (see all 71)
    i-app 54.8 8 10748090 (4), 8922372 (2), 17426693 (1), 11118882 (1)
    nicotinamide 51 2 18060872 (2)
    incretin 50.5 1 12323111 (1)
    proglucagon 37.2 2 16213778 (1)
    sulfonylurea 34.6 2 16339272 (1), 18708284 (1)
    streptozotocin 33.7 2 17426693 (1)
    lactacystin 31.9 1 12488243 (1)



    Find genes that share compounds with PDX1           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PDX1 gene: 
    NM_000209.3  

    Unigene Cluster for PDX1:

    Pancreatic and duodenal homeobox 1
    Hs.32938  [show with all ESTs]
    Unigene Representative Sequence: NM_000209
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000381033(uc001urt.2)
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    Additional mRNA sequence: 

    U30329.1 U35632.1 X99894.1 

    2 DOTS entries:

    DT.97763786  DT.97835837 

    Selected AceView cDNA sequences (see all 26):

    BV183905 CB068470 CA849020 CA843531 U30329 BM504017 CA848737 U35632 
    CA777063 BM352781 X99894 NM_000209 CA777186 CB177387 CA843291 BI715297 
    CA867458 CA776904 CB177388 CA771381 BM510164 CA776782 BI714743 CB069243 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PDX1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PDX1 Expression
    About this image


    PDX1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Pancreas (Endocrine System)    fully expand to see all 44 entries
             Delta Cells Islets of Langerhans
             Islets of Langerhans
             Posterior foregut endoderm-like cells
             pancreas ; exocrine glandular cells   
     
     Gut Tube (Gastrointestinal Tract)    fully expand to see all 4 entries
             Pre-Pancreatic Foregut Endoderm Cells Prepancreatic Ventral Foregut Endoderm
             Anterior foregut progenitor cells
     
     Blood (Hematopoietic System)    fully expand to see all 2 entries
             Peripheral blood-derived hematopoietic stem cells
     
     NULL (Uncategorized)    fully expand to see all 3 entries
             Definitive endoderm-like cells
     
     Endoderm (Gastrulation Derivatives)    fully expand to see all 3 entries
             Definitive endoderm-like cells
    PDX1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PDX1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.32938

    UniProtKB/Swiss-Prot: PDX1_HUMAN, P52945
    Tissue specificity: Duodenum and pancreas (Langerhans islet beta cells and small subsets of endocrine
    non-beta-cells, at low levels in acinar cells)

        Pathway & Disease-focused RT2 Profiler PCR Arrays including PDX1: 
              Insulin Resistance in human mouse rat
              Embryonic Stem Cells in human mouse rat
              Diabetes in human mouse rat
              Stem Cells in human mouse rat
              Homeobox (HOX) Genes in human mouse rat

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for PDX1 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pdx11 , 5 pancreatic and duodenal homeobox 11, 5 83.51(n)1
    87.99(a)1
      5 (86.84 cM)5
    186091  NM_008814.31  NP_032840.11 
     1472699595 
    chicken
    (Gallus gallus)
    Aves PDX11 pancreatic and duodenal homeobox 1 79.09(n)
    77.73(a)
      771348  XM_001234635.2  XP_001234636.2 
    lizard
    (Anolis carolinensis)
    Reptilia PDX16
    pancreatic and duodenal homeobox 1
    68(a)
    1 ↔ 1
    GL343306.1(1494109-1527270)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia pdx11 pancreatic and duodenal homeobox 1 68.91(n)
    69.06(a)
      100490648  XM_002934019.2  XP_002934065.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ipf12 insulin promoter factor 1, homeodomain transcription factor less 76.49(n)   30721  AF036325.1 


    ENSEMBL Gene Tree for PDX1 (if available)
    TreeFam Gene Tree for PDX1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PDX1 gene
    GSX12  HOXA32  MEOX12  EVX22  HOXA12  HOXB12  HOXB32  HOXD12  
    HOXA22  GSX22  EVX12  HOXB22  MEOX22  HOXD32  
    2 SIMAP similar genes for PDX1 using alignment to 1 protein entry:     PDX1_HUMAN:
    HOXC6    HOXB4

    Find genes that share paralogs with PDX1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PDX1 (see all 199)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0093104
    Maturity-onset diabetes of the young 4 (MODY4)4--see VAR_0093102 Q L mis40--------
    VAR_0093094
    Maturity-onset diabetes of the young 4 (MODY4)4--see VAR_0093092 C R mis40--------
    VAR_0093124
    Maturity-onset diabetes of the young 4 (MODY4)4--see VAR_0093122 R H mis40--------
    rs803566611,2
    Cpathogenic19452707(+) AAGGAG/TTTCCT 2 E D mis10--------
    rs803566621,2
    Cpathogenic19452747(+) GGGTGA/GAGCTG 2 K E mis10--------
    rs285094411,2
    Cprobable-non-pathogenic19448666(+) GCCCTA/GGGCGC 2 L syn1 ese30--------
    rs754989351,2
    C,Fprobable-non-pathogenic19452758(+) GCTGTC/TATGTT 2 V syn11Minor allele frequency- T:0.00NA 4544
    rs1939223581,2
    Cprobable-pathogenic19452940(+) GCCGCC/TGCCCC 2 P L mis10--------
    rs1939223511,2
    Cunknown19448487(+) GTGCCC/TAATCC 1 -- ut510--------
    rs1929020981,2
    Cunknown19448601(+) GCCCCA/CCTGCG 2 T P mis10--------

    HapMap Linkage Disequilibrium report for PDX1 (28494157 - 28500451 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for PDX1: --
    Human Gene Mutation Database (HGMD): PDX1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PDX1
    DNA2.0 Custom Variant and Variant Library Synthesis for PDX1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 600733   
    OMIM disorders: 260370  606392  125853  
    UniProtKB/Swiss-Prot: PDX1_HUMAN, P52945
  • Pancreatic agenesis, congenital (PAGEN) [MIM:260370]: Autosomal recessive disorder is characterized by
    absence or hypoplasia of pancreas, leading to early-onset insulin-dependent diabetes mellitus. This was found in
    a frameshift mutation that produces a truncated protein and results in a second initiation that produces a second
    protein that act as a dominant negative mutant. Note=The disease is caused by mutations affecting the gene
    represented in this entry
  • Diabetes mellitus, non-insulin-dependent (NIDDM) [MIM:125853]: A multifactorial disorder of glucose
    homeostasis caused by a lack of sensitivity to the body's own insulin. Affected individuals usually have an obese
    body habitus and manifestations of a metabolic syndrome characterized by diabetes, insulin resistance,
    hypertension and hypertriglyceridemia. The disease results in long-term complications that affect the eyes,
    kidneys, nerves, and blood vessels. Note=Disease susceptibility is associated with variations affecting the gene
    represented in this entry
  • Maturity-onset diabetes of the young 4 (MODY4) [MIM:606392]: A form of diabetes that is characterized by
    an autosomal dominant mode of inheritance, onset in childhood or early adulthood (usually before 25 years of
    age), a primary defect in insulin secretion and frequent insulin-independence at the beginning of the disease.
    Note=The disease is caused by mutations affecting the gene represented in this entry

  • 16 diseases for PDX1:    
    About MalaCards
    pdx1-related permanent neonatal diabetes mellitus    maturity-onset diabetes of the young, type 4    lacticacidemia due to pdx1 deficiency    pancreatic gastrinoma
    pancreatic agenesis    maturity-onset diabetes of the young    maturity-onset diabetes of the young, type 1    permanent neonatal diabetes mellitus
    neonatal diabetes mellitus    monogenic diabetes    diabetes mellitus    glucose intolerance
    exocrine pancreatic insufficiency    hyperglycemia    pancreatic cancer    type 2 diabetes mellitus

    3 diseases from the University of Copenhagen DISEASES database for PDX1:
    maturity-onset diabetes of the young     Diabetes mellitus     Hyperglycemia

    Find genes that share disorders with PDX1           About GenesLikeMe

    Selected Novoseek inferred disease relationships for PDX1 gene (see all 24)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    neonatal diabetes mellitus 77.8 3 19496967 (2)
    niddm 74.2 38 10720084 (3), 11078452 (2), 9887471 (2), 15754742 (2) (see all 25)
    insulinoma 67.2 14 18219478 (2), 10940482 (1), 15144884 (1), 15743769 (1) (see all 10)
    hyperglycemia 66.1 6 18086901 (1), 19393272 (1), 19656489 (1), 19817786 (1) (see all 5)
    pancreas exocrine 55.2 3 20009086 (2), 11246871 (1)
    diabetes mellitus 50.5 14 18406800 (2), 9326926 (1), 15144884 (1), 9628281 (1) (see all 9)
    glucose intolerance 39.1 1 17003335 (1)
    pancreatic cancer 38.7 35 17552012 (7), 12947327 (6), 18665085 (4), 17161985 (2) (see all 7)
    metaplasia 32.2 10 16938521 (6), 14960508 (1), 18400571 (1)
    glucagonoma 32.1 3 15862113 (1), 10580420 (1)

    GeneTests: PDX1
    GeneReviews: PDX1
    Genetic Association Database (GAD): PDX1
    Human Genome Epidemiology (HuGE) Navigator: PDX1 (24 documents)

    Export disorders for PDX1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PDX1 gene, integrated from 10 sources (see all 429):
    (articles sorted by number of sources associating them with PDX1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Localization of human homeodomain transcription factor insulin promoter factor 1 (IPF1) to chromosome band 13q12.1. (PubMed id 7590740)1, 2, 3 Stoffel M....Bell G.I. (Genomics 1995)
    2. The p38/reactivating kinase mitogen-activated protein kinase cascade mediates the activation of the transcription factor insulin upstream factor 1 and insulin gene transcription by high glucose in pancreatic beta-cells. (PubMed id 9252422)1, 2, 9 Macfarlane W.M.... Docherty K. (J. Biol. Chem. 1997)
    3. Defective mutations in the insulin promoter factor-1 (IPF-1) gene in late-onset type 2 diabetes mellitus. (PubMed id 10545531)1, 2, 9 Hani E.H.... Froguel P. (J. Clin. Invest. 1999)
    4. Isolation, characterization, and chromosomal mapping of the human insulin promoter factor 1 (IPF-1) gene. (PubMed id 8635654)1, 2, 9 Inoue H.... Permutt M.A. (Diabetes 1996)
    5. Missense mutations in the insulin promoter factor-1 gene predispose to type 2 diabetes. (PubMed id 10545530)1, 2, 9 Macfarlane W.M.... Hattersley A.T. (J. Clin. Invest. 1999)
    6. A-beta-subtype of ketosis-prone diabetes is not predominantly a monogenic diabetic syndrome. (PubMed id 19228875)1, 4, 9 Haaland W.C....Metzker M.L. (Diabetes Care 2009)
    7. Assessment of genetic risk for myocardial infarction. (PubMed id 16894468)1, 4, 9 Yamada Y....Nozawa Y. (Thromb. Haemost. 2006)
    8. Role of a proline insertion in the insulin promoter factor 1 (IPF1) gene in African Americans with type 2 diabetes. (PubMed id 17003361)1, 4, 9 Elbein S.C....Kao W.H. (Diabetes 2006)
    9. Pdx-1 links histone H3-Lys-4 methylation to RNA polymerase II elongation during activation of insulin transcription. (PubMed id 16141209)1, 2, 9 Francis J.... Mirmira R.G. (J. Biol. Chem. 2005)
    10. Association of gene polymorphisms with myocardial infarction in individuals with or without conventional coronary risk factors. (PubMed id 17143557)1, 4, 9 Nishihama K....Nozawa Y. (Int. J. Mol. Med. 2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 3651 HGNC: 6107 AceView: IPF1 Ensembl:ENSG00000139515 euGenes: HUgn3651
    ECgene: PDX1 Kegg: 3651 H-InvDB: PDX1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PDX1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for PDX1 Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=PDX1[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PDX1 gene:
    Search GeneIP for patents involving PDX1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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