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PDLIM7 Gene

protein-coding   GIFtS: 58
GCID: GC05M176912

PDZ And LIM Domain 7 (Enigma)

  See PDLIM7-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
PDZ And LIM Domain 7 (Enigma)1 2     LMP32
Protein Enigma2 3     LIM Domain Protein2
LMP2 3     Lim Mineralization Protein 32
ENIGMA3 5     PDZ And LIM Domain Protein 72
1110003B01Rik2     LIM Mineralization Protein3
LMP12     

External Ids:    HGNC: 229581   Entrez Gene: 92602   Ensembl: ENSG000001969237   OMIM: 6059035   UniProtKB: Q9NR123   

Export aliases for PDLIM7 gene to outside databases

Previous GC identifers: GC00U914366 GC05M177024 GC05M176843 GC05M171830


(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 PDLIM7 Gene:
The protein encoded by this gene is representative of a family of proteins composed of conserved PDZ and LIM
domains. LIM domains are proposed to function in protein-protein recognition in a variety of contexts including
gene transcription and development and in cytoskeletal interaction. The LIM domains of this protein bind to
protein kinases, whereas the PDZ domain binds to actin filaments. The gene product is involved in the assembly of
an actin filament-associated complex essential for transmission of ret/ptc2 mitogenic signaling. The biological
function is likely to be that of an adapter, with the PDZ domain localizing the LIM-binding proteins to actin
filaments of both skeletal muscle and nonmuscle tissues. Alternative splicing of this gene results in multiple
transcript variants. (provided by RefSeq, Jul 2008)

GeneCards Summary for PDLIM7 Gene:
PDLIM7 (PDZ and LIM domain 7 (enigma)) is a protein-coding gene. Diseases associated with PDLIM7 include pleural empyema, and nasopharynx carcinoma. An important paralog of this gene is LIMS1.

UniProtKB/Swiss-Prot: PDLI7_HUMAN, Q9NR12
Function: May function as a scaffold on which the coordinated assembly of proteins can occur. May play a role as
an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle
and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation, direct bone
formation (e.g. embryonic flat bones mandible and cranium), and endochondral bone formation (e.g. embryonic long
bone development). Plays a role during fracture repair. Involved in BMP6 signaling pathway (By similarity)

Gene Wiki entry for PDLIM7 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_000005.9  NT_023133.14  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the PDLIM7 gene promoter:
         E2F-3a   E2F-1   E2F   AP-1   E2F-2   IRF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPDLIM7 promoter sequence
   Search Chromatin IP Primers for PDLIM7

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PDLIM7


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

Entrez Gene cytogenetic band: 5q35.3   Ensembl cytogenetic band:  5q35.3   HGNC cytogenetic band: 5q35.3

PDLIM7 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PDLIM7 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M176912:  view genomic region     (about GC identifiers)

Start:
176,910,395 bp from pter      End:
176,924,607 bp from pter
Size:
14,213 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: PDLI7_HUMAN, Q9NR12 (See protein sequence)
Recommended Name: PDZ and LIM domain protein 7  
Size: 457 amino acids; 49845 Da
Subunit: Binds via its LIM zinc-binding 3 domain (LIM 3) to endocytic codes of INSR, but not with those of IGF1R,
LDLR, TFRC, or EGFR. Interacts with various PKC isoforms through the LIM zinc-binding domains. Binds to RET in a
phosphorylation-independent manner via its LIM zinc-binding domain 2 (LIM 2). Probably part of a complex with SHC
and the RET dimer. Interacts with TPM2. Interacts with TBX4 and TBX5 (By similarity)
Sequence caution: Sequence=AAC37565.1; Type=Frameshift; Positions=103, 128, 161, 183, 195, 245;
1 PDB 3D structure from and Proteopedia for PDLIM7:
2Q3G (3D)    
Secondary accessions: Q14250 Q5XG82 Q6NVZ5 Q96C91 Q9BXB8 Q9BXB9
Alternative splicing: 6 isoforms:  Q9NR12-1   Q9NR12-2   Q9NR12-3   Q9NR12-4   Q9NR12-5   Q9NR12-6   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PDLIM7: NX_Q9NR12

Explore proteomics data for PDLIM7 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See PDLIM7 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_005442.2  NP_976227.1  NP_998801.1  

    ENSEMBL proteins: 
     ENSP00000431236   ENSP00000352964   ENSP00000348099   ENSP00000439157   ENSP00000377182  
     ENSP00000426213   ENSP00000347776   ENSP00000377177   ENSP00000424850   ENSP00000422363  
     ENSP00000421664   ENSP00000349030  

    PDLIM7 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for PDLIM7

     
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    antibodies-online proteins for PDLIM7 (5 products) 

     
    antibodies-online peptides for PDLIM7

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    antibodies-online antibodies for PDLIM7 (61 products) 

    PDLIM7 Assay Products:

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    antibodies-online kits for PDLIM7 (23 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR001478 PDZ
     IPR001781 Znf_LIM

    Graphical View of Domain Structure for InterPro Entry Q9NR12

    ProtoNet protein and cluster: Q9NR12

    2 Blocks protein domains:
    IPB001478 PDZ/DHR/GLGF domain
    IPB001781 Zn-binding protein


    UniProtKB/Swiss-Prot: PDLI7_HUMAN, Q9NR12
    Domain: The LIM zinc-binding 2 (LIM 2) domain interacts with TBX4 (By similarity)
    Domain: The LIM zinc-binding 3 (LIM 3) domain provides the structural basis for recognition of tyrosine-containing
    tight turn structures. This domain is necessary and sufficient for interaction with TBX5 (By similarity)
    Domain: Anchored to cell periphery via its N-terminal PDZ domain
    Similarity: Contains 3 LIM zinc-binding domains
    Similarity: Contains 1 PDZ (DHR) domain


    Find genes that share domains with PDLIM7           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: PDLI7_HUMAN, Q9NR12
    Function: May function as a scaffold on which the coordinated assembly of proteins can occur. May play a role as
    an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle
    and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation, direct bone
    formation (e.g. embryonic flat bones mandible and cranium), and endochondral bone formation (e.g. embryonic long
    bone development). Plays a role during fracture repair. Involved in BMP6 signaling pathway (By similarity)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI16713569
    GO:0008270zinc ion binding IEA--
         
    Find genes that share ontologies with PDLIM7           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for PDLIM7

    miRNA
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    miRTarBase miRNAs that target PDLIM7:
    hsa-mir-24-3p (MIRT030427), hsa-mir-124-3p (MIRT002914), hsa-mir-30a-5p (MIRT028432), hsa-mir-132-3p (MIRT045848), hsa-mir-1 (MIRT001351)

    Block miRNA regulation of human, mouse, rat PDLIM7 using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate PDLIM7:
    hsa-miR-644 hsa-miR-3065-3p
    SwitchGear 3'UTR luciferase reporter plasmidPDLIM7 3' UTR sequence
    Inhib. RNA
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    Addgene plasmids for PDLIM7 

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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
    PDLI7_HUMAN, Q9NR12: Cytoplasm (By similarity). Cytoplasm, cytoskeleton (By similarity). Note=Colocalizes with
    RET to the cell periphery and in some cytoskeletal components. Colocalizes with TPM2 near the Z line in muscle.
    Colocalizes with TBX4 and TBX5 to actin filaments (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton4
    cytosol3
    nucleus3
    extracellular1
    plasma membrane1

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001725stress fiber IEA--
    GO:0001726ruffle IEA--
    GO:0005634nucleus IDA--
    GO:0005737cytoplasm IEA--
    GO:0005925focal adhesion IDA--

    Find genes that share ontologies with PDLIM7           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 PDLIM7 About    
    See pathways by source

    SuperPathContained pathways About
    1Development EGFR signaling pathway
    Development GDNF family signaling0.45
    GDNF-Family Ligands and Receptor Interactions0.41
    2Signaling events regulated by Ret tyrosine kinase
    Signaling events regulated by Ret tyrosine kinase
    3EBV LMP1 signaling
    EBV LMP1 signaling

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for PDLIM7
        GDNF-Family Ligands and Receptor Interactions

    1 GeneGo (Thomson Reuters) Pathway for PDLIM7
        Development GDNF family signaling

    2 BioSystems Pathways for PDLIM7
        EBV LMP1 signaling
    Signaling events regulated by Ret tyrosine kinase


        Pathway & Disease-focused RT2 Profiler PCR Array including PDLIM7: 
              Lymphoma in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for PDLIM7

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for PDLIM7 (Q9NR121, 2, 3 ENSP000003480994) via UniProtKB, MINT, STRING, and/or I2D (see all 876)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PCBP1Q153652, 3, ENSP000003055564MINT-2866295 MINT-7947479 I2D: score=3 STRING: ENSP00000305556
    BSGP356132, 3, ENSP000003337694MINT-67881 I2D: score=5 STRING: ENSP00000333769
    C20orf195Q9BVV22, 3, ENSP000003591154MINT-68104 I2D: score=5 STRING: ENSP00000359115
    PAK7Q9P2862, 3, ENSP000003229574MINT-66298 I2D: score=4 STRING: ENSP00000322957
    PRKD2Q9BZL62, 3MINT-61756 I2D: score=2 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001503ossification IEA--
    GO:0006898receptor-mediated endocytosis TAS7929196
    GO:0007275multicellular organismal development IEA--
    GO:0030036actin cytoskeleton organization IEA--
    GO:0030154cell differentiation IEA--

    Find genes that share ontologies with PDLIM7           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
      Browse compounds at ApexBio 

    Browse Tocris compounds for PDLIM7 (PDLI7)



    (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 PDLIM7 gene (4 alternative transcripts): 
    NM_005451.4  NM_203352.2  NM_213636.2  NM_203353.1  

    Unigene Cluster for PDLIM7:

    PDZ and LIM domain 7 (enigma)
    Hs.533040  [show with all ESTs]
    Unigene Representative Sequence: AK096826
    17 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000493815 ENST00000359895 ENST00000355841 ENST00000486828(uc003mha.1 uc003mhb.1 uc003mhc.1 uc003mhd.1 uc003mhe.1)
    ENST00000504380 ENST00000505746 ENST00000393551(uc003mhf.3) ENST00000505074
    ENST00000355572(uc003mhg.1) ENST00000393546 ENST00000506161 ENST00000504318
    ENST00000503346 ENST00000503827 ENST00000463411 ENST00000506537 ENST00000356618

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    hsa-miR-644 hsa-miR-3065-3p
    SwitchGear 3'UTR luciferase reporter plasmidPDLIM7 3' UTR sequence
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      QuantiFast Probe-based Assays in human, mouse, rat PDLIM7

    Additional mRNA sequence: 

    AF265209.1 AF345904.1 AF345905.1 AK096826.1 BC001093.2 BC007648.1 BC014521.2 BC023629.2 
    BC084575.1 DQ291143.1 

    24 DOTS entries:

    DT.85105616  DT.91896419  DT.120862389  DT.92443476  DT.102839668  DT.91854702  DT.100894868  DT.120862440 
    DT.91714237  DT.97854788  DT.100030242  DT.97854787  DT.100811139  DT.100811141  DT.100727135  DT.97813779 
    DT.120862455  DT.95085177  DT.95085210  DT.120862462  DT.100811148  DT.86856066  DT.92443473  DT.121623182 

    Selected AceView cDNA sequences (see all 403):

    AW978360 AI973049 AA295228 AI740557 AW206786 BI198984 CB048966 BF477752 
    BF003106 BM700981 BQ690105 BM708868 BQ923519 F27712 AI868905 AI658775 
    BE858022 BG750171 BQ936363 BQ929859 AI817730 BM695955 AW118632 BF434968 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for PDLIM7 (see all 13)    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b · 5c · 5d ^ 6a · 6b · 6c ^ 7a · 7b · 7c · 7d ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^
    SP1:              -     -                                   -     -     -     -     -           -                             -                             -   
    SP2:              -     -                                   -     -     -     -     -           -                             -     -                       -   
    SP3:              -     -                 -     -     -     -     -     -     -                 -                                                           -   
    SP4:              -     -                                   -     -     -     -     -           -                             -     -     -                     
    SP5:              -     -                                   -     -     -     -     -           -                                                               

    ExUns: 12a · 12b ^ 13 ^ 14
    SP1:  -                     
    SP2:  -                     
    SP3:  -                     
    SP4:                        
    SP5:                        


    ECgene alternative splicing isoforms for PDLIM7

    (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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    PDLIM7 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGTGAGCCCC
    PDLIM7 Expression
    About this image


    PDLIM7 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Blood (Cardiovascular System)    fully expand to see all 2 entries
             Granulocytes Peripheral Blood
     
     Spleen (Hematopoietic System)
             Conventional Dendritic Cells I Spleen
     
     Skeletal Muscle (Muscoskeletal System)
    PDLIM7 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PDLIM7 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.533040

    UniProtKB/Swiss-Prot: PDLI7_HUMAN, Q9NR12
    Tissue specificity: Isoform 1 and isoform 2 are expressed ubiquitously, however, isoform 2 predominates in
    skeletal muscle, isoform 1 is more abundant in lung, spleen, leukocytes and fetal liver

        Pathway & Disease-focused RT2 Profiler PCR Array including PDLIM7: 
              Lymphoma in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PDLIM7

    (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 animals.

    Orthologs for PDLIM7 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pdlim71 , 5 PDZ and LIM domain 71, 5 88.4(n)1
    93.87(a)1
      13 (30.06 cM)5
    673991  NM_001114088.21  NP_001107560.11 
     554957955 
    chicken
    (Gallus gallus)
    Aves PDLIM71 PDZ and LIM domain 7 (enigma) 75.28(n)
    75.12(a)
      416362  NM_001005345.1  NP_001005345.2 
    lizard
    (Anolis carolinensis)
    Reptilia PDLIM76
    PDZ and LIM domain 7 (enigma)
    77(a)
    1 ↔ 1
    2(145657233-145711291)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.157172 Transcribed sequence with weak similarity to protein more 79.81(n)    AL848905.2 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc659072 hypothetical protein MGC65907 76.79(n)   393813  BC061704.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Zasp526
    Z band alternatively spliced PDZ-motif protein 52
    7(a)
    1 → many
    2R(11650070-11704509)
    worm
    (Caenorhabditis elegans)
    Secernentea alp-16
    Protein ALP-1, isoform d
    11(a)
    1 → many
    IV(8852500-8862487) WBGene00001132


    ENSEMBL Gene Tree for PDLIM7 (if available)
    TreeFam Gene Tree for PDLIM7 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PDLIM7 gene
    LIMS12  LIMS3L2  FHL32  FHL52  LDB32  LPXN2  FHL12  ENSG000002572072  
    LIMS32  TGFB1I12  PDLIM52  PXN2  LIMS22  FHL22  
    10 SIMAP similar genes for PDLIM7 using alignment to 6 protein entries:     PDLI7_HUMAN (see all proteins):
    PDLIM3    PDLIM5    SYNPO2    PDLIM2    SLC9A3R1    SNTG1
    USH1C    MAGI1    SCRIB    GRIP1

    Find genes that share paralogs with PDLIM7           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for PDLIM7
    PGOHUM00000249601


    (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 PDLIM7 (see all 473)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0361934
    A breast cancer sample4--see VAR_0361932 K N mis40--------
    rs605832451,2
    C--171834285(+) TTTTT-/TTTTT 
            
    GCTGT
    2 -- int11Minor allele frequency- TTTTT:0.00NA 2
    rs1428662991,2
    --176909903(+) GCTCGC/TGCGCA 2 -- ds50010--------
    rs3354271,2
    C--176909905(-) ACTGCG/ACGCGA 2 -- ds50014Minor allele frequency- A:0.14NA EA 244
    rs1449417021,2
    --176910023(+) AATTTC/TTGTAT 2 -- ds50010--------
    rs1483052471,2
    --176910072(+) GTCTCC/GAACTC 2 -- ds50010--------
    rs1155775871,2
    C,F--176910083(+) CTGACC/TTCAAG 2 -- ds50011Minor allele frequency- T:0.05NA 120
    rs562068441,2
    C--176910206(+) CTCCCC/TTCATG 2 -- ds50010--------
    rs285248831,2
    C--176910399(+) ACACAG/ACTGGG 2 -- ut31 ese33Minor allele frequency- A:0.19NA WA 122
    rs1875977921,2
    --176910404(+) GCTGGA/GTACAG 2 -- ut310--------

    HapMap Linkage Disequilibrium report for PDLIM7 (176910395 - 176924607 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for PDLIM7:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv883179CNV Loss21882294
    dgv6379n71CNV Loss21882294
    nsv883180CNV Loss21882294
    nsv883177CNV Loss21882294
    dgv6383n71CNV Loss21882294
    dgv6381n71CNV Loss21882294
    nsv883164CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PDLIM7
    DNA2.0 Custom Variant and Variant Library Synthesis for PDLIM7

    (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: 605903    OMIM disorders: --

    2 diseases for PDLIM7:    
    About MalaCards
    pleural empyema    nasopharynx carcinoma

    4 diseases from the University of Copenhagen DISEASES database for PDLIM7:
    Nasopharynx carcinoma     Lymphoma     Infectious mononucleosis     Pleural empyema

    Find genes that share disorders with PDLIM7           About GenesLikeMe


    Export disorders for PDLIM7 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 PDLIM7 gene, integrated from 10 sources (see all 63):
    (articles sorted by number of sources associating them with PDLIM7)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Overexpressed LIM mineralization proteins do not require LIM domains to induce bone. (PubMed id 11874232)1, 2, 3 Liu Y.... Titus L. (J. Bone Miner. Res. 2002)
    2. 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)
    3. The PDZ domain of the LIM protein enigma binds to beta-tropomyosin. (PubMed id 10359609)1, 2 Guy P.M.... Gill G.N. (Mol. Biol. Cell 1999)
    4. Shc and Enigma are both required for mitogenic signaling by Ret/ptc2. (PubMed id 9528800)1, 2 Durick K.... Taylor S.S. (Mol. Cell. Biol. 1998)
    5. Protein-protein interaction of zinc finger LIM domains with protein kinase C. (PubMed id 8940095)1, 2 Kuroda S.... Kikkawa U. (J. Biol. Chem. 1996)
    6. LIM domain recognition of a tyrosine-containing tight turn. (PubMed id 7929196)1, 2 Wu R.-Y. and Gill G.N. (J. Biol. Chem. 1994)
    7. Modeling and analysis of molecularinteraction between Smurf1-WW2 domain and various isoforms of LIM mineralization protein. (PubMed id 17510966)1, 9 Sangadala S....Reddy B.V. (Proteins 2007)
    8. Poly(ADP-ribose) polymerase-1 modulates Nrf2-dependent transcription. (PubMed id 24140708)1 Wu T....Zhang D.D. (amp 2014)
    9. Characterization of a unique motif in LIM mineralization protein-1 that interacts with jun activation-domain-binding protein 1. (PubMed id 24078030)1 Sangadala S....Boden S.D. (Mol. Cell. Biochem. 2014)
    10. Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions. (PubMed id 24255178)1 Couzens A.L....Gingras A.C. (Sci Signal 2013)

    (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: 9260 HGNC: 22958 AceView: PDLIM7 Ensembl:ENSG00000196923 euGenes: HUgn9260
    ECgene: PDLIM7 H-InvDB: PDLIM7

    (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 PDLIM7 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 PDLIM7 gene:
    Search GeneIP for patents involving PDLIM7

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



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