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PDGFD Gene

protein-coding   GIFtS: 65
GCID: GC11M103777

Platelet Derived Growth Factor D

  See PDGFD-related disease
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
Platelet Derived Growth Factor D1 2     Spinal Cord-Derived Growth Factor B2 3
IEGF2 3 5     PDGF-D2 3
SCDGFB2 3 5     SCDGF-B2 3
Spinal Cord Derived Growth Factor B1 2     Platelet-Derived Growth Factor D2
Iris-Expressed Growth Factor2 3     Spinal Cord-Derived Growth Factor-B2

External Ids:    HGNC: 306201   Entrez Gene: 803102   Ensembl: ENSG000001709627   OMIM: 6096735   UniProtKB: Q9GZP03   

Export aliases for PDGFD gene to outside databases

Previous GC identifers: GC11M103315 GC11M103283 GC11M099706


(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 PDGFD Gene:
The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of
this family are mitogenic factors for cells of mesenchymal origin and are characterized by a core motif of eight
cysteines, seven of which are found in this factor. This gene product only forms homodimers and, therefore, does
not dimerize with the other three family members. It differs from alpha and beta members of this family in having
an unusual N-terminal domain, the CUB domain. Two splice variants have been identified for this gene. (provided
by RefSeq, Jul 2008)

GeneCards Summary for PDGFD Gene:
PDGFD (platelet derived growth factor D) is a protein-coding gene. Diseases associated with PDGFD include mesangial proliferative glomerulonephritis. GO annotations related to this gene include growth factor activity and platelet-derived growth factor receptor binding. An important paralog of this gene is PDGFC.

UniProtKB/Swiss-Prot: PDGFD_HUMAN, Q9GZP0
Function: Growth factor that plays an essential role in the regulation of embryonic development, cell
proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Plays an
important role in wound healing. Induces macrophage recruitment, increased interstitial pressure, and blood
vessel maturation during angiogenesis. Can initiate events that lead to a mesangial proliferative
glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix (By
similarity)

summary for PDGFD Gene:
Platelet-derived growth factor receptors (PDGFRs) are catalytic receptors that have intracellular tyrosine
kinase activity. They have roles in the regulation of many biological processes including embryonic
development, angiogenesis, cell proliferation and differentiation, and contribute to the pathophysiology of
some diseases, including cancer. There are two isoforms of the PDGFR receptor; PDGFRalpha and PDGFRbeta,
which can form homo- or heterodimers. The endogenous PDGFR ligands are PDGF-A, -B, -C and -D, which induce
receptor dimerization and transphosphorylation at specific tyrosine residues upon binding. This activates
the intracellular kinase activity, initiating intracellular signaling through the MAPK, PI 3-K and PKCgamma
pathways.

Gene Wiki entry for PDGFD 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_000011.9  NC_018922.2  NT_033899.9  
Regulatory elements:
   Regulatory transcription factor binding sites in the PDGFD gene promoter:
         TBP   NF-1   NF-1/L   Nkx2-5   MEF-2A   AREB6   aMEF-2   Msx-1   MRF-2   En-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPDGFD promoter sequence
   Search Chromatin IP Primers for PDGFD

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


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

Entrez Gene cytogenetic band: 11q22.3   Ensembl cytogenetic band:  11q22.3   HGNC cytogenetic band: 11q22.3

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

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M103777:  view genomic region     (about GC identifiers)

Start:
103,777,914 bp from pter      End:
104,035,107 bp from pter
Size:
257,194 bases      Orientation:
minus 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: PDGFD_HUMAN, Q9GZP0 (See protein sequence)
Recommended Name: Platelet-derived growth factor D precursor  
Size: 370 amino acids; 42848 Da
Subunit: Homodimer; disulfide-linked. Interacts with PDGFRB homodimers, and with heterodimers formed by PDGFRA and
PDGFRB
Developmental stage: Not detectable in the earliest stages of glomerulogenesis, and not detected in the
metanephric blastema or surrounding cortical interstitial cells. In later stages of glomerulogenesis, localized
to epithelial cells transitioning from the early developing nephrons of the comma- and S-shaped stages to the
visceral epithelial cells of differentiated glomeruli. In the developing pelvis, expressed at the basement
membrane of immature collecting ducts and by presumptive fibroblastic cells in the interstitium
Secondary accessions: A8K9T6 Q9BWV5
Alternative splicing: 2 isoforms:  Q9GZP0-1   Q9GZP0-2   

Explore the universe of human proteins at neXtProt for PDGFD: NX_Q9GZP0

Explore proteomics data for PDGFD at MOPED

Post-translational modifications: 

  • Activated by proteolytic cleavage. Proteolytic removal of the N-terminal CUB domain releasing the core domain is
    necessary for unmasking the receptor-binding epitopes of the core domain. Cleavage after Arg-247 or Arg-249 by
    urokinase plasminogen activator gives rise to the active form1
  • Ubiquitination2 at Lys160
  • Glycosylation2 at Asn276
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins (2 alternative transcripts): 
    NP_079484.1  NP_149126.1  

    ENSEMBL proteins: 
     ENSP00000376865   ENSP00000302193   ENSP00000432909  
    Reactome Protein details: Q9GZP0

    PDGFD Human Recombinant Protein Products:

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    Sino Biological Recombinant Protein for PDGFD
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    ProSpec Recombinant Protein for PDGFD
    Cloud-Clone Corp. Proteins for PDGFD

     
    Search eBioscience for Proteins for PDGFD 

     
    antibodies-online proteins for PDGFD (8 products) 

     
    antibodies-online peptides for PDGFD

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    antibodies-online antibodies for PDGFD (38 products) 

    PDGFD Assay Products:

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    Cloud-Clone Corp. ELISAs for PDGFD
    Cloud-Clone Corp. CLIAs for PDGFD
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    antibodies-online kits for PDGFD (32 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR027123 PDGFC/D
     IPR000859 CUB_dom
     IPR000072 PDGF/VEGF_dom

    Graphical View of Domain Structure for InterPro Entry Q9GZP0

    ProtoNet protein and cluster: Q9GZP0

    2 Blocks protein domains:
    IPB000072 Platelet-derived growth factor (PDGF)
    IPB000859 CUB domain


    UniProtKB/Swiss-Prot: PDGFD_HUMAN, Q9GZP0
    Similarity: Belongs to the PDGF/VEGF growth factor family
    Similarity: Contains 1 CUB domain


    Find genes that share domains with PDGFD           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: PDGFD_HUMAN, Q9GZP0
    Function: Growth factor that plays an essential role in the regulation of embryonic development, cell
    proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Plays an
    important role in wound healing. Induces macrophage recruitment, increased interstitial pressure, and blood
    vessel maturation during angiogenesis. Can initiate events that lead to a mesangial proliferative
    glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix (By
    similarity)

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005161platelet-derived growth factor receptor binding IEA--
    GO:0008083growth factor activity IEA--
         
    Find genes that share ontologies with PDGFD           About GenesLikeMe


    Phenotypes:
         1 MGI phenotypic allele for Pdgfd (no phenotypes)

    Find genes that share phenotypes with PDGFD           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Pdgfdtm1Lex for PDGFD

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

    miRNA
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    miRTarBase miRNAs that target PDGFD:
    hsa-mir-21-5p (MIRT030746)

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    Selected qRT-PCR Assays for microRNAs that regulate PDGFD (see all 14):
    hsa-miR-2052 hsa-miR-203 hsa-miR-3132 hsa-miR-495 hsa-miR-7-2* hsa-miR-545 hsa-miR-33a hsa-miR-7-1*
    SwitchGear 3'UTR luciferase reporter plasmidPDGFD 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat PDGFD

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    GenScript: all cDNA clones in your preferred vector (see all 2): PDGFD (NM_033135)
    Sino Biological Human cDNA Clone for PDGFD
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PDGFD
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    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PDGFD


    (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
    PDGFD_HUMAN, Q9GZP0: Secreted. Note=Released by platelets upon wounding
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    endoplasmic reticulum4
    golgi apparatus4
    plasma membrane2
    cytoskeleton1
    endosome1
    lysosome1
    mitochondrion1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000139Golgi membrane TAS--
    GO:0005576extracellular region TAS--
    GO:0005788endoplasmic reticulum lumen TAS--
    GO:0016020membrane ----

    Find genes that share ontologies with PDGFD           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 PDGFD About   (see all 10)  
    See pathways by source

    SuperPathContained pathways About
    1Focal adhesion
    Focal adhesion0.65
    Focal Adhesion0.65
    2Glioma
    Melanoma0.43
    Prostate cancer0.39
    3Ras signaling pathway
    Rap1 signaling pathway0.36
    Ras signaling pathway0.36
    4Signaling by FGFR
    Signaling by PDGF0.87
    5Signaling by GPCR
    Signal Transduction0.58


    Find genes that share SuperPaths with PDGFD           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for PDGFD (see all 59)
        Nuclear Receptor Activation by Vitamin-A
    Paxillin Interactions
    Telomerase Components in Cell Signaling
    Mitochondrial Apoptosis
    Molecular Mechanisms of Cancer

    2 GeneGo (Thomson Reuters) Pathways for PDGFD
        Cytoskeleton remodeling Role of PDGFs in cell migration
    Development PDGF signaling via MAPK cascades

    1 BioSystems Pathway for PDGFD
        Focal Adhesion


    1 Reactome Pathway for PDGFD
        Signaling by PDGF


    Selected Kegg Pathways  (Kegg details for PDGFD) (see all 8):
        Ras signaling pathway
    Rap1 signaling pathway
    PI3K-Akt signaling pathway
    Focal adhesion
    Gap junction

        Pathway & Disease-focused RT2 Profiler PCR Array including PDGFD: 
              Angiogenic Growth Factors in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for PDGFD

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

    Selected Interacting proteins for PDGFD (Q9GZP03 ENSP000003768654) via UniProtKB, MINT, STRING, and/or I2D (see all 15)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PDGFRBP096193, ENSP000002617994I2D: score=1 STRING: ENSP00000261799
    PDGFRAENSP000002572904STRING: ENSP00000257290
    PLATENSP000002208094STRING: ENSP00000220809
    PLAUENSP000003618504STRING: ENSP00000361850
    PLAURENSP000003393284STRING: ENSP00000339328
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--
    GO:0048008platelet-derived growth factor receptor signaling pathway IEA--
    GO:0050730regulation of peptidyl-tyrosine phosphorylation IEA--
    GO:0051781positive regulation of cell division IEA--
    GO:0071230cellular response to amino acid stimulus IEA--

    Find genes that share ontologies with PDGFD           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 Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
    Selected ApexBio Compounds for PDGFD (see all 14)     About this table
    CompoundAction CAS #
    Amuvatinib (MP-470, HPK 56)Multi-kinase inhibitor, inhibits PDGFR, c-Kit, and Flt3[850879-09-3]
    Crenolanib (CP-868596)Potent and selective PDGFR-beta inhibitor[670220-88-9]
    Flumatinib mesylatemulti-kinase inhibitor for c-Abl, PDGFRbeta and c-Kit[895519-91-2]
    Imatinib Mesylate (STI571)Multi-target kinase inhibitor of abl, c-kit, and PDGFR[220127-57-1]
    Masitinib (AB1010)tyrosine kinase, c-Kit, PDGFR, FGFR3, the FAK pathway inhibitor[790299-79-5]
    MK-2461potent inhibitor of Met, Ron, Flt1, Flt 3, PDGFRbeta, and Mer with IC50 of 2.5 nM, 7 nM, 10 nM, 22 nM, 22 nM and 24 nM, respectively[917879-39-1]
    Nintedanib (BIBF 1120)Multi-target kinase inhibitor, inhibits VEGFR, PDGFR, and FGFR[928326-83-4]
    Pazopanib (GW-786034)Multi-target kinase inhibitor, inhibits VEGFR, PDGFR, and FGFR[635702-64-6]
    Ponatinib (AP24534)pan-BCR-ABL inhibitor[943319-70-8]
    RegorafenibMulti-kinase inhibitor, inhibits VEGFR, PDGFR, FGFR, mutant kit, RET, and Raf-1[755037-03-7]

    Compounds for PDGFD available from Tocris Bioscience    About this table
    CompoundAction CAS #
    SU 6668 PDGFR, VEGFR and FGFR inhibitor [252916-29-3]
    Sunitinib malate Potent VEGFR, PDGFRbeta and KIT inhibitor [341031-54-7]
    DMPQ dihydrochloride Potent, selective inhibitor of PDGFRbeta [137206-97-4]
    SU 16fPotent and selective PDGFRbeta inhibitor[251356-45-3]



    (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 PDGFD gene (2 alternative transcripts): 
    NM_025208.4  NM_033135.3  

    Unigene Cluster for PDGFD:

    Platelet derived growth factor D
    Hs.352298  [show with all ESTs]
    Unigene Representative Sequence: BC030645
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000393158 ENST00000302251(uc001php.3 uc001phq.3) ENST00000529268

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    hsa-miR-2052 hsa-miR-203 hsa-miR-3132 hsa-miR-495 hsa-miR-7-2* hsa-miR-545 hsa-miR-33a hsa-miR-7-1*
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    Additional mRNA sequence: 

    AB033832.1 AF113216.1 AF335584.1 AF336376.1 AK292801.1 AY027517.1 AY027518.1 AY359116.1 
    BC030645.2 

    4 DOTS entries:

    DT.211370  DT.100033675  DT.99932823  DT.120725526 

    Selected AceView cDNA sequences (see all 94):

    AA620733 NM_025208 AA448806 NM_033135 AI631061 BM667348 BM710630 BP872435 
    AI005125 AW271765 AI962915 AA808265 AA620703 BU431765 BQ182229 BQ003700 
    AA488996 AF113216 AA620856 BC030645 AA778655 BQ575044 AI079299 BE018544 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for PDGFD    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b
    SP1:                                                      
    SP2:        -                                             


    ECgene alternative splicing isoforms for PDGFD

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


    PDGFD expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 12) fully expand
     
     Blood (Cardiovascular System)    fully expand to see all 2 entries
             Natural Killer Cells Peripheral Blood
     
     Neural Crest (Gastrulation Derivatives)
             PureStem 7SMOO32, NCr-fac & Meso Progenitor
     
     Bone (Muscoskeletal System)
             HyStem+BMP4-induced SM30 cells
     
     Gonad
             Primordial germ cell-like cells
     
     Kidney (Urinary System)
             Ureteric Bud Cells Ureteric Bud
    PDGFD Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PDGFD Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.352298

    UniProtKB/Swiss-Prot: PDGFD_HUMAN, Q9GZP0
    Tissue specificity: Expressed at high levels in the heart, pancreas, adrenal gland and ovary and at low levels in
    placenta, liver, kidney, prostate, testis, small intestine, spleen and colon. In the kidney, expressed by the
    visceral epithelial cells of the glomeruli. A widespread expression is also seen in the medial smooth muscle
    cells of arteries and arterioles, as well as in smooth muscle cells of vasa rectae in the medullary area.
    Expressed in the adventitial connective tissue surrounding the suprarenal artery. In chronic obstructive
    nephropathy, a persistent expression is seen in glomerular visceral epithelial cells and vascular smooth muscle
    cells, as well as de novo expression by periglomerular interstitial cells and by some neointimal cells of
    atherosclerotic vessels. Expression in normal prostate is seen preferentially in the mesenchyme of the gland
    while expression is increased and more profuse in prostate carcinoma. Expressed in many ovarian, lung, renal and
    brain cancer-derived cell lines

        Pathway & Disease-focused RT2 Profiler PCR Array including PDGFD: 
              Angiogenic Growth Factors 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 PDGFD gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pdgfd1 , 5 platelet-derived growth factor, D polypeptide1, 5 85.86(n)1
    85.14(a)1
      9 (2.46 cM)5
    717851  NM_027924.21  NP_082200.11 
     61686125 
    chicken
    (Gallus gallus)
    Aves PDGFD1 platelet derived growth factor D 79.14(n)
    81.15(a)
      418978  NM_001277811.1  NP_001264740.1 
    lizard
    (Anolis carolinensis)
    Reptilia PDGFD6
    platelet derived growth factor D
    58(a)
    1 ↔ 1
    3(191399725-191598474)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004920601 platelet-derived growth factor D-like 70.42(n)
    71.7(a)
      100492060  XM_002934934.2  XP_002934980.2 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1005357181 platelet-derived growth factor D-like 66.15(n)
    69.37(a)
      100535718  XM_003200098.2  XP_003200146.2 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PDGFD gene
    PDGFC2  
    3 SIMAP similar genes for PDGFD using alignment to 2 protein entries:     PDGFD_HUMAN (see all proteins):
    PDGFC    MASP1    NRP2

    Find genes that share paralogs with PDGFD           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 PDGFD (see all 5471)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0364184
    A colorectal cancer sample4--see VAR_0364182 D Y mis40--------
    rs106066951,2
    C--103689079(+) ttttt-/T/TTTT
            
    gagac
    2 -- int11NA 2
    rs8382431,2
    C,F,H--103777445(+) TTGGGG/AAACAA 2 -- ds50015Minor allele frequency- A:0.01NS NA 792
    rs1389287001,2
    C--103777453(+) CAAAG-/TGTTGTTC 2 -- ds50010--------
    rs1870402391,2
    C--103777453(+) CAAAGG/TGTTGT 2 -- ds50010--------
    rs1894590721,2
    C--103777461(+) TGTTCC/TTTCGG 2 -- ds50010--------
    rs1815159291,2
    --103777484(+) GAAGCC/TTTCAG 2 -- ds50010--------
    rs1852556141,2
    --103777598(+) AGTGCA/CGTGGC 2 -- ds50010--------
    rs1138757821,2
    C,F--103777611(+) GATCTC/TGGCTT 2 -- ds50011Minor allele frequency- T:0.50NA 2
    rs1900147421,2
    --103777615(+) TCGGCC/TTACTG 2 -- ds50010--------

    HapMap Linkage Disequilibrium report for PDGFD (103777914 - 104027914 bp, first 250kb of PDGFD)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PDGFD (see all 30):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2676733CNV Deletion23128226
    esv2745011CNV Deletion23290073
    esv3736CNV Deletion18987735
    esv3147CNV Deletion18987735
    esv2671461CNV Deletion23128226
    esv2666036CNV Deletion23128226
    esv1417082CNV Deletion17803354
    esv991768CNV Deletion20482838
    esv2597532CNV Deletion19546169
    esv2205640CNV Deletion18987734

    Human Gene Mutation Database (HGMD): PDGFD
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PDGFD
    DNA2.0 Custom Variant and Variant Library Synthesis for PDGFD

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 609673    OMIM disorders: --

    1 disease for PDGFD:    
    About MalaCards
    mesangial proliferative glomerulonephritis


    Find genes that share disorders with PDGFD           About GenesLikeMe

    Genetic Association Database (GAD): PDGFD
    Human Genome Epidemiology (HuGE) Navigator: PDGFD (6 documents)

    Export disorders for PDGFD 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 PDGFD gene, integrated from 10 sources (see all 50):
    (articles sorted by number of sources associating them with PDGFD)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning of SCDGF-B, a novel growth factor homologous to SCDGF/PDGF-C/fallotein. (PubMed id 11162582)1, 2, 3, 9 Hamada T.... Miyata Y. (Biochem. Biophys. Res. Commun. 2001)
    2. Platelet-derived growth factor D: tumorigenicity in mice and dysregulated expression in human cancer. (PubMed id 11980634)1, 2, 3 LaRochelle W.J....Lichenstein H.S. (Cancer Res. 2002)
    3. Platelet-derived growth factor-D expression in developing and mature human kidneys. (PubMed id 12427128)1, 2, 9 Changsirikulchai S.... Alpers C.E. (Kidney Int. 2002)
    4. Chromosomal location, exon structure, and vascular expression patterns of the human PDGFC and PDGFC genes. (PubMed id 11342471)1, 2, 9 Uutela M.... Alitalo K. (Circulation 2001)
    5. Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. (PubMed id 21347282)1, 4 Lettre G....Boerwinkle E. (PLoS Genet. 2011)
    6. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    7. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    8. Association of platelet-derived growth factor-D gene polymorphism with ischemic stroke in a Chinese case-control study. (PubMed id 18600092)1, 4 Han S.H....Nie S.F. (amp 2008)
    9. Platelet-derived growth factor D is activated by urokinase plasminogen activator in prostate carcinoma cells. (PubMed id 15988036)1, 2 Ustach C.V. and Kim H.-R.C. (Mol. Cell. Biol. 2005)
    10. PDGF-D induces macrophage recruitment, increased interstitial pressure, and blood vessel maturation during angiogenesis. (PubMed id 15271796)1, 2 Uutela M.... Alitalo K. (Blood 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    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: 80310 HGNC: 30620 AceView: PDGFD Ensembl:ENSG00000170962 euGenes: HUgn80310
    ECgene: PDGFD Kegg: 80310 H-InvDB: PDGFD

    (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 PDGFD Pharmacogenomics, SNPs, Pathways

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

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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