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PDXP Gene

protein-coding   GIFtS: 56
GCID: GC22P038054

Pyridoxal (Pyridoxine, Vitamin B6) Phosphatase

  See 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
Pyridoxal (Pyridoxine, Vitamin B6) Phosphatase1 2     dJ37E16.52
CIN2 3     Pyridoxal Phosphate Phosphatase2
PLP2 3     Chronophin3
PLP Phosphatase2 3     EC 3.1.3.33
EC 3.1.3.743 8     PLPP3
chronophin2     EC 3.1.38

External Ids:    HGNC: 302591   Entrez Gene: 570262   Ensembl: ENSG000002413607   OMIM: 6092465   UniProtKB: Q96GD03   

Export aliases for PDXP gene to outside databases

Previous GC identifers: GC00U914367 GC22P036299 GC22P036379 GC22P021021


(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 PDXP Gene:
Pyridoxal 5-prime-phosphate (PLP) is the active form of vitamin B6 that acts as a coenzyme in maintaining
biochemical homeostasis. The preferred degradation route from PLP to 4-pyridoxic acid involves the
dephosphorylation of PLP by PDXP (Jang et al., 2003 (PubMed 14522954)).(supplied by OMIM, Mar 2008)

GeneCards Summary for PDXP Gene:
PDXP (pyridoxal (pyridoxine, vitamin B6) phosphatase) is a protein-coding gene. Diseases associated with PDXP include hypopyon ulcer, and hypopyon. GO annotations related to this gene include phosphoserine phosphatase activity and phosphoprotein phosphatase activity. An important paralog of this gene is PGP.

UniProtKB/Swiss-Prot: PLPP_HUMAN, Q96GD0
Function: Protein serine phosphatase that dephosphorylates 'Ser-3' in cofilin and probably also dephosphorylates
phospho-serine residues in DSTN. Regulates cofilin-dependent actin cytoskeleton reorganization. Required for
normal progress through mitosis and normal cytokinesis. Does not dephosphorylate phospho-threonines in LIMK1.
Does not dephosphorylate peptides containing phospho-tyrosine. Pyridoxal phosphate phosphatase. Has some activity
towards pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PMP) and pyridoxine 5'-phosphate (PNP), with a
highest activity with PLP followed by PNP




(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:
NC_000022.11  NC_018933.2  NT_011520.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the PDXP gene promoter:
         NF-1   NF-1/L   AP-1   p53   ATF-2   GATA-2   YY1   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPDXP promoter sequence
   Search Chromatin IP Primers for PDXP

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


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

Entrez Gene cytogenetic band: 22q12.3   Ensembl cytogenetic band:  22q13.1   HGNC cytogenetic band: 22q12.3

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

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P038054:  view genomic region     (about GC identifiers)

Start:
38,054,734 bp from pter      End:
38,062,941 bp from pter
Size:
8,208 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: PLPP_HUMAN, Q96GD0 (See protein sequence)
Recommended Name: Pyridoxal phosphate phosphatase  
Size: 296 amino acids; 31698 Da
Cofactor: Divalent ions. Magnesium is the most effective
Subunit: Homodimer
6 PDB 3D structures from and Proteopedia for PDXP:
2CFR (3D)        2CFS (3D)        2CFT (3D)        2OYC (3D)        2P27 (3D)        2P69 (3D)    
Secondary accessions: Q9UGY2

Explore the universe of human proteins at neXtProt for PDXP: NX_Q96GD0

Explore proteomics data for PDXP at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • 3 DME Specific Peptides for PDXP (Q96GD0)
     LTLTGVS  EACAHLRDP  LFDCDGVLW 


    See PDXP Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_064711.1  
    ENSEMBL proteins: 
     ENSP00000215904   ENSP00000385336  

    PDXP Human Recombinant Protein 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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    4 InterPro protein domains:
     IPR023214 HAD-like_dom
     IPR006357 HAD-SF_hydro_IIA
     IPR006349 PGP_euk
     IPR023215 NPhePase-like_dom

    Graphical View of Domain Structure for InterPro Entry Q96GD0

    ProtoNet protein and cluster: Q96GD0

    UniProtKB/Swiss-Prot: PLPP_HUMAN, Q96GD0
    Similarity: Belongs to the HAD-like hydrolase superfamily


    PDXP for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PLPP_HUMAN, Q96GD0
    Function: Protein serine phosphatase that dephosphorylates 'Ser-3' in cofilin and probably also dephosphorylates
    phospho-serine residues in DSTN. Regulates cofilin-dependent actin cytoskeleton reorganization. Required for
    normal progress through mitosis and normal cytokinesis. Does not dephosphorylate phospho-threonines in LIMK1.
    Does not dephosphorylate peptides containing phospho-tyrosine. Pyridoxal phosphate phosphatase. Has some activity
    towards pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PMP) and pyridoxine 5'-phosphate (PNP), with a
    highest activity with PLP followed by PNP
    Catalytic activity: Pyridoxal 5'-phosphate + H(2)O = pyridoxal + phosphate
    Catalytic activity: O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate
    Enzyme regulation: Inhibited by NaF, Zn(2+), Ca(2+), Mn(2+) and EDTA

         Enzyme Numbers (IUBMB): EC 3.1.3.741 2 EC 3.1.32 EC 3.1.3.31

         Gene Ontology (GO): Selected molecular function terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000287magnesium ion binding ISS--
    GO:0004647phosphoserine phosphatase activity IEA--
    GO:0004721phosphoprotein phosphatase activity IDA15580268
    GO:0005515protein binding IPI17500066
    GO:0016791phosphatase activity ----
         
    PDXP for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for PDXP:
     Increased G2M DNA content  Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PDXP
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    miRNA
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    miRTarBase miRNAs that target PDXP:
    hsa-mir-25-3p (MIRT050278), hsa-mir-324-5p (MIRT043152), hsa-mir-331-3p (MIRT043505)

    Block miRNA regulation of human, mouse, rat PDXP using miScript Target Protectors
    5 qRT-PCR Assays for microRNAs that regulate PDXP:
    hsa-miR-141 hsa-miR-1281 hsa-miR-3121-3p hsa-miR-200a hsa-miR-30b*
    SwitchGear 3'UTR luciferase reporter plasmidPDXP 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat PDXP

    Gene Editing
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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
    PLPP_HUMAN, Q96GD0: Cytoplasm, cytosol. Cytoplasm, cytoskeleton. Cell projection, ruffle membrane; Peripheral
    membrane protein; Cytoplasmic side. Cell projection, lamellipodium membrane; Peripheral membrane protein;
    Cytoplasmic side. Cell membrane; Peripheral membrane protein; Cytoplasmic side. Note=Colocalizes with the actin
    cytoskeleton in membrane ruffles and lamellipodia. Diffusely distributed throughout the cytosol during
    pro-metaphase and metaphase. Detected at the dynamic cell poles during telophase. Detected at the cleavage furrow
    and contractile ring during cytokinesis. Transiently detected at the plasma membrane in late stages of
    cytokinesis. Detected at the midbody
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton5
    cytosol5
    plasma membrane5
    extracellular1
    mitochondrion1
    nucleus1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol IDA15580268
    GO:0005886colocalizes with plasma membrane IDA15580268
    GO:0015629colocalizes with actin cytoskeleton IDA15580268
    GO:0030027colocalizes with lamellipodium IDA15580268
    GO:0030496colocalizes with midbody IDA15580268

    PDXP for ontologies           About GeneDecksing


    (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 PDXP About    
    See pathways by source

    SuperPathContained pathways About
    1Metabolism
    Metabolic pathways0.38
    2Vitamin B6 metabolism
    Vitamin B6 metabolism
    3Phosphatases
    Phosphatases
    4Cytoskeletal Signaling
    Cytoskeletal Signaling

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    2 Cell Signaling Technology (CST) Pathways for PDXP
        Phosphatases
    Cytoskeletal Signaling


    2 Kegg Pathways  (Kegg details for PDXP):
        Vitamin B6 metabolism
    Metabolic pathways


    PDXP for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PDXP
    Interactions:

        GeneGlobe Interaction Network for PDXP

    STRING Interaction Network Preview (showing 5 interactants - click image to see 15)

    Selected Interacting proteins for PDXP (Q96GD01, 3 ENSP000002159044) via UniProtKB, MINT, STRING, and/or I2D (see all 17)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DDA1Q9BW613I2D: score=1 
    AOX1ENSP000003638324STRING: ENSP00000363832
    PNPOENSP000002255734STRING: ENSP00000225573
    PDXKENSP000002915654STRING: ENSP00000291565
    PHOSPHO2ENSP000003527824STRING: ENSP00000352782
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006470protein dephosphorylation IDA15580268
    GO:0007088regulation of mitosis IMP15580268
    GO:0008152metabolic process ----
    GO:0030836positive regulation of actin filament depolymerization IMP15580268
    GO:0031247actin rod assembly IMP19000834

    PDXP for ontologies           About GeneDecksing



    (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 Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PDXP (PLPP)

    9 HMDB Compounds for PDXP    About this table
    CompoundSynonyms CAS #PubMed Ids
    MagnesiumMagnesium (see all 2)7439-95-4--
    PhosphateNFB Orthophosphate (see all 13)14265-44-2--
    Pyridoxal3-Hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxaldehyde (see all 3)66-72-8--
    Pyridoxal 5'-phosphateApolon B6 (see all 27)54-47-7--
    Pyridoxamine2-methyl-4-aminomethyl-5-hydroxymethyl-3-Pyridinol (see all 5)85-87-0--
    Pyridoxamine 5'-phosphatePyridoxamine 5'-phosphate (see all 2)529-96-4--
    Pyridoxine2-Methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine (see all 16)65-23-6--
    Pyridoxine 5'-phosphate5-Hydroxy-4-(hydroxymethyl)-6-methyl-3-pyridylmethyl dihydrogen phosphate (see all 11)447-05-2--
    WaterDihydrogen oxide (see all 2)7732-18-5--

    1 DrugBank Compound for PDXP    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Pyridoxal PhosphateCodecarboxylase (see all 9)54-47-7targetcofactor17531224 16336786 14522954 16336194 11000053

    Selected Novoseek inferred chemical compound relationships for PDXP gene (see all 15)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    pyridoxine 5-phosphate 93 3 14522954 (1), 7625842 (1), 8053678 (1)
    pyridoxal 91 24 15452547 (6), 14522954 (2), 8053678 (2), 11000053 (2) (see all 11)
    pyridoxal 5-phosphate 90.4 82 9166745 (7), 10052942 (6), 14522954 (5), 17116355 (5) (see all 18)
    dehydroalanine 79.1 1 10052942 (1)
    vitamin b6 76.9 4 17482557 (2), 7814235 (1), 14522954 (1)
    cystathionine 54.7 1 11000053 (1)
    hydroxylamine 39.9 2 10052942 (2)
    pyridine 36.4 2 12460116 (1)
    serine 35.5 3 10052942 (1), 15580268 (1), 8679597 (1)
    aspartate 34.2 4 7814235 (1), 12460116 (1)



    PDXP for compounds           About GeneDecksing



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for PDXP gene: 
    NM_020315.4  

    Unigene Cluster for PDXP:

    Pyridoxal (pyridoxine, vitamin B6) phosphatase
    Hs.632762  [show with all ESTs]
    Unigene Representative Sequence: BC064922
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000215904(uc003atm.1) ENST00000403251
    miRNA
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    5 qRT-PCR Assays for microRNAs that regulate PDXP:
    hsa-miR-141 hsa-miR-1281 hsa-miR-3121-3p hsa-miR-200a hsa-miR-30b*
    SwitchGear 3'UTR luciferase reporter plasmidPDXP 3' UTR sequence
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    Additional mRNA sequence: 

    AK057265.1 AY125047.1 BC000320.2 BC009756.2 BC012832.2 BC018844.2 BC064922.1 

    12 DOTS entries:

    DT.448479  DT.100766554  DT.100856284  DT.100870723  DT.86821142  DT.100865256  DT.100768181  DT.100856666 
    DT.100867924  DT.120664730  DT.100645371  DT.100757530 

    Selected AceView cDNA sequences (see all 335):

    CR456576 CR617992 NM_020315 BM552420 CR618685 CR617653 BE552177 BC008282 
    AK126873 BM909859 BQ018954 BQ051565 CR593618 BM695047 AA563645 BX387308 
    BC018844 AL157480 BF221496 CR615223 BQ923764 AK126556 BX465098 BM826513 

    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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    PDXP expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTACCCGTAC
    PDXP Expression
    About this image


    PDXP expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebral Cortex
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Metencephalon
    PDXP Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PDXP Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.632762

    UniProtKB/Swiss-Prot: PLPP_HUMAN, Q96GD0
    Tissue specificity: Ubiquitous. Highly expressed in all the regions of central nerve system except the spinal
    cord. Also expressed at high level in liver and testis. In fetus, it is weakly expressed in all organs except
    brain

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PDXP

    (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 eukaryotes.

    Orthologs for PDXP gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pdxp1 , 5 pyridoxal (pyridoxine, vitamin B6) phosphatase1, 5 89.84(n)1
    92.47(a)1
      15 (37.70 cM)5
    570281  NM_020271.31  NP_064667.21 
     789139195 
    chicken
    (Gallus gallus)
    Aves LOC7712071 pyridoxal phosphate phosphatase-like 76(n)
    74.06(a)
      771207  XM_003640384.2  XP_003640432.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1944091 zgc:194409 64.58(n)
    56.1(a)
      561030  NM_001128705.1  NP_001122177.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG55676
    CG324876
    (see all 8)
    --
    32(a)
    27(a)
    (see all 8)
    many ↔ many
    many ↔ many
    (see all 8)
    3L(17834640-17836644)
    3L(3016150-3017256)
    worm
    (Caenorhabditis elegans)
    Secernentea K09H11.76
    F44E7.26
    (see all 5)
    Protein F44E7.2 (F44E7.2) mRNA, complete cds
    (see all 5)
    29(a)
    27(a)
    (see all 5)
    many ↔ many
    many ↔ many
    (see all 5)
    V(5752463-5753532) WBGene00019604
    V(5770455-5771767) WBGene00018424
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes PHO136
    Alkaline phosphatase specific for p-nitrophenyl ph...
    28(a)
    1 → many
    IV(32296-33234) YDL236W
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G367901 AT5G36790 44.28(n)
    37.69(a)
      833646  NM_001203499.1  NP_001190428.1 
    rice
    (Oryza sativa)
    Liliopsida Os04g04908001 Os04g0490800 48.13(n)
    37.69(a)
      4336245  NM_001059702.1  NP_001053167.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PDXP gene
    PGP2  
    2 SIMAP similar genes for PDXP using alignment to 2 protein entries:     PLPP_HUMAN (see all proteins):
    SH3BP1    PGP

    PDXP for paralogs           About GeneDecksing



    (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 PDXP (see all 250)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1169486471,2
    F--38052839(+) AAAAAA/TAATTT 1 -- us2k11Minor allele frequency- T:0.22NA 120
    rs763286031,2
    --38052840(+) AAAAAA/TATTTT 1 -- us2k12Minor allele frequency- T:0.22NA 122
    rs104276361,2
    C,A--38052841(+) AAAAAA/TTTTTA 1 -- us2k14Minor allele frequency- T:0.21WA NA EA 244
    rs2019235061,2
    --38053002(+) AAAAC-/AAAAAA 1 -- us2k10--------
    rs1151040361,2
    --38053062(+) GCCATA/GTAACC 1 -- us2k10--------
    rs1389551981,2
    --38053071(+) CCTAGA/GCTCAT 1 -- us2k10--------
    rs597832861,2
    C--38053154(+) CTGAAC/GGTGAA 1 -- us2k10--------
    rs1131189341,2
    --38053205(+) TGTTTT/ATTTTT 1 -- us2k11Minor allele frequency- A:0.00CSA 1
    rs2004710461,2
    --38053205(+) TGTTT-/ATTTTT 1 -- us2k10--------
    rs104277541,2
    C,F--38053258(+) TTGGCG/ACGATC 1 -- us2k14Minor allele frequency- A:0.38WA NA CSA 8

    HapMap Linkage Disequilibrium report for PDXP (38054734 - 38062941 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for PDXP:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv26329CNV Loss19812545
    nsv829203CNV Loss20364138
    nsv834191CNV Loss17160897
    nsv471197CNV Loss18288195
    nsv915035CNV Loss21882294
    dgv4964n71CNV Loss21882294
    nsv915038CNV Loss21882294
    dgv4965n71CNV Loss21882294
    dgv1406e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PDXP
    DNA2.0 Custom Variant and Variant Library Synthesis for PDXP

    (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: 609246    OMIM disorders: --

    10 diseases for PDXP:    
    About MalaCards
    hypopyon ulcer    hypopyon    laurence-moon syndrome    autoimmune hepatitis
    down syndrome    pneumonia    tuberculosis    hepatitis
    cerebritis    neuronitis

    2 diseases from the University of Copenhagen DISEASES database for PDXP:
    Laurence-Moon syndrome     Kidney failure

    PDXP for disorders           About GeneDecksing

    3 Novoseek inferred disease relationships for PDXP gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    neurological disorders 42.6 1 15452547 (1)
    inflammation 0 1 11000053 (1)
    cancer 0 3 15452547 (3)


    Export disorders for PDXP 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 PDXP gene, integrated from 10 sources (see all 44):
    (articles sorted by number of sources associating them with PDXP)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human pyridoxal phosphatase. Molecular cloning, functional expression, and tissue distribution. (PubMed id 14522954)1, 2, 3, 7, 9 Jang Y.M.... Kwon O.-S. (J. Biol. Chem. 2003)
    2. Chronophin, a novel HAD-type serine protein phosphatase, regulates cofilin-dependent actin dynamics. (PubMed id 15580268)1, 2, 9 Gohla A.... Bokoch G.M. (Nat. Cell Biol. 2005)
    3. Identification of an essential cysteine residue in pyridoxal phosphatase from human erythrocytes. (PubMed id 8132548)1, 2, 9 Gao G.-J. and Fonda M.L. (J. Biol. Chem. 1994)
    4. Human brain pyridoxal-5'-phosphate phosphatase: production and characterization of monoclonal antibodies. (PubMed id 16336786)1, 7, 9 Kim D.W....Choi S.Y. (J. Biochem. Mol. Biol. 2005)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    6. The DNA sequence of human chromosome 22. (PubMed id 10591208)1, 2 Dunham I.... Wright H. (Nature 1999)
    7. Chronophin mediates an ATP-sensing mechanism for cofilin dephosphorylation and neuronal cofilin-actin rod formation. (PubMed id 19000834)1, 9 Huang T.Y....Bokoch G.M. (Dev. Cell 2008)
    8. Human brain pyridoxal-5'-phosphate phosphatase (PLPP):protein transduction of PEP-1-PLPP into PC12 cells. (PubMed id 18510874)1, 9 Lee Y.P....Choi S.Y. (BMB Rep 2008)
    9. Increased homocyst(e)ine associated with smoking, chronic inflammation, and aging may reflect acute-phase induction of pyridoxal phosphatase activity. (PubMed id 11000053)7, 9 McCarty M.F. (Med. Hypotheses 2000)
    10. Time course of changes in pyridoxal 5'-phosphate (vitamin B6 active form) and its neuroprotection in experimental ischemic damage. (PubMed id 17531224)7, 9 Hwang I.K....Won M.H. (Exp. Neurol. 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: 57026 HGNC: 30259 AceView: SH3BP1 Ensembl:ENSG00000241360 euGenes: HUgn57026
    ECgene: PDXP Kegg: 57026 H-InvDB: PDXP

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for PDXP Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for PDXP gene:
    Search GeneIP for patents involving PDXP

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



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