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PDLIM1 Gene

protein-coding   GIFtS: 59
GCID: GC10M096997

PDZ And LIM Domain 1

(Previous name: PDZ and LIM domain 1 (elfin))
(Previous symbol: CLIM1)
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(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 11 2     CLP-362
CLIM11 2 3 5     HEL-S-1122
CLP362 3 5     Epididymis Secretory Protein Li 1122
Carboxyl Terminal LIM Domain Protein 11 2     hCLIM12
elfin1 2     PDZ And LIM Domain Protein 12
LIM Domain Protein CLP-362 3     Elfin3
PDZ And LIM Domain 1 (Elfin)1     C-Terminal LIM Domain Protein 13

External Ids:    HGNC: 20671   Entrez Gene: 91242   Ensembl: ENSG000001074387   OMIM: 6059005   UniProtKB: O001513   

Export aliases for PDLIM1 gene to outside databases

Previous GC identifers: GC10M095890 GC10M096230 GC10M097128 GC10M096661 GC10M096987 GC10M090624


(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 PDLIM1 Gene:
This gene encodes a member of the enigma protein family. The protein contains two protein interacting domains, a
PDZ domain at the amino terminal end and one to three LIM domains at the carboxyl terminal. It is a cytoplasmic
protein associated with the cytoskeleton. The protein may function as an adapter to bring other LIM-interacting
proteins to the cytoskeleton. Pseudogenes associated with this gene are located on chromosomes 3, 14 and 17.
(provided by RefSeq, Oct 2012)

GeneCards Summary for PDLIM1 Gene:
PDLIM1 (PDZ and LIM domain 1) is a protein-coding gene. Diseases associated with PDLIM1 include hyperacusis, and scimitar syndrome. GO annotations related to this gene include transcription coactivator activity. An important paralog of this gene is PDLIM4.

UniProtKB/Swiss-Prot: PDLI1_HUMAN, O00151
Function: Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the
cytoskeleton

Gene Wiki entry for PDLIM1 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:
NC_000010.11  NC_018921.2  NT_030059.14  
Regulatory elements:
   Regulatory transcription factor binding sites in the PDLIM1 gene promoter:
         STAT1   STAT4   STAT1beta   FOXD1   STAT5A   STAT1alpha   C/EBPalpha   Egr-2   STAT2   STAT3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPDLIM1 promoter sequence
   Search Chromatin IP Primers for PDLIM1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PDLIM1


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

Entrez Gene cytogenetic band: 10q23.1   Ensembl cytogenetic band:  10q24.1   HGNC cytogenetic band: 10q23.1

PDLIM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PDLIM1 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M096997:  view genomic region     (about GC identifiers)

Start:
96,997,329 bp from pter      End:
97,050,781 bp from pter
Size:
53,453 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, 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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: PDLI1_HUMAN, O00151 (See protein sequence)
Recommended Name: PDZ and LIM domain protein 1  
Size: 329 amino acids; 36072 Da
Subunit: Interacts with alpha-actinins 1, 2 and 4
2 PDB 3D structures from and Proteopedia for PDLIM1:
1X62 (3D)        2PKT (3D)    
Secondary accessions: B2RBS6 Q5VZH5 Q9BPZ9

Explore the universe of human proteins at neXtProt for PDLIM1: NX_O00151

Explore proteomics data for PDLIM1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys22
  • Modification sites at PhosphoSitePlus

  • See PDLIM1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_066272.1  
    ENSEMBL proteins: 
     ENSP00000360305  

    PDLIM1 Human Recombinant Protein Products:

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    Novus Biologicals PDLIM1 Proteins
    Novus Biologicals PDLIM1 Lysates
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for PDLIM1

    PDLIM1 Antibody Products:

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    LSBio Antibodies in human, mouse, rat for PDLIM1

    PDLIM1 Assay Products:

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    Cloud-Clone Corp. ELISAs for PDLIM1
    Cloud-Clone Corp. CLIAs for PDLIM1


    (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:
     IPR028537 PDLIM1
     IPR006643 ZASP
     IPR001478 PDZ
     IPR001781 Znf_LIM

    Graphical View of Domain Structure for InterPro Entry O00151

    ProtoNet protein and cluster: O00151

    3 Blocks protein domains:
    IPB001478 PDZ/DHR/GLGF domain
    IPB001781 Zn-binding protein
    IPB006643 ZASP


    UniProtKB/Swiss-Prot: PDLI1_HUMAN, O00151
    Similarity: Contains 1 LIM zinc-binding domain
    Similarity: Contains 1 PDZ (DHR) domain


    PDLIM1 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: PDLI1_HUMAN, O00151
    Function: Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the
    cytoskeleton

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003713transcription coactivator activity IEA--
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
         
    PDLIM1 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for PDLIM1:
     Downregulation of NF-kappaB pa  Downregulation of NF-kappaB pa 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PDLIM1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for PDLIM1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for PDLIM1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for PDLIM1

    miRNA
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    miRTarBase miRNAs that target PDLIM1:
    hsa-mir-26b-5p (MIRT029619), hsa-mir-504-5p (MIRT041081), hsa-mir-92a-3p (MIRT049434), hsa-mir-320a (MIRT044643)

    Block miRNA regulation of human, mouse, rat PDLIM1 using miScript Target Protectors
    Search for qRT-PCR Assays for microRNAs that regulate PDLIM1
    SwitchGear 3'UTR luciferase reporter plasmidPDLIM1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat PDLIM1

    Gene Editing
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    GenScript: all cDNA clones in your preferred vector: PDLIM1 (NM_020992)
    Sino Biological Human cDNA Clone for PDLIM1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PDLIM1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PDLIM1

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for PDLIM1 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PDLIM1


    (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
    PDLI1_HUMAN, O00151: Cytoplasm (By similarity). Cytoplasm, cytoskeleton (By similarity). Note=Associates with the
    actin stress fibers (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol3
    cytoskeleton2
    nucleus2
    mitochondrion1
    plasma membrane1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005667transcription factor complex IEA--
    GO:0005737cytoplasm IEA--
    GO:0005856cytoskeleton IEA--

    PDLIM1 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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        Pathway & Disease-focused RT2 Profiler PCR Array including PDLIM1: 
              Oxidative Stress in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for PDLIM1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 16)

    Selected Interacting proteins for PDLIM1 (O001512, 3 ENSP000003603054) via UniProtKB, MINT, STRING, and/or I2D (see all 23)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ACTN4O437072, 3, ENSP000002526994MINT-68435 I2D: score=7 STRING: ENSP00000252699
    MAPK6Q166592, 3MINT-8261604 I2D: score=2 
    RPS6KA5O755822, 3MINT-8269648 I2D: score=2 
    VIMP086702, 3, ENSP000002242374MINT-67503 I2D: score=5 STRING: ENSP00000224237
    SUPT4H1P632722, 3, ENSP000002255044MINT-8272399 I2D: score=2 STRING: ENSP00000225504
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001666response to hypoxia IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--
    GO:0006979response to oxidative stress TAS8522188

    PDLIM1 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 PDLIM1 (PDLI1)

    1 Novoseek inferred chemical compound relationship for PDLIM1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    calcium 5.81 2 2329796 (1), 12599114 (1)



    PDLIM1 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,
    Conferences by KenesGroup, 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 PDLIM1 gene: 
    NM_020992.3  

    Unigene Cluster for PDLIM1:

    PDZ and LIM domain 1
    Hs.368525  [show with all ESTs]
    Unigene Representative Sequence: AK091847
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000329399(uc001kkh.3) ENST00000492511 ENST00000477757 ENST00000490391
    ENST00000493949

    miRNA
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    Block miRNA regulation of human, mouse, rat PDLIM1 using miScript Target Protectors
    Search for qRT-PCR Assays for microRNAs that regulate PDLIM1
    SwitchGear 3'UTR luciferase reporter plasmidPDLIM1 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for PDLIM1
    Predesigned siRNA for gene silencing in human, mouse, rat PDLIM1
    Clone
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    GenScript: all cDNA clones in your preferred vector: PDLIM1 (NM_020992)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PDLIM1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PDLIM1
    Primer
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    OriGene qPCR primer pairs and template standards for PDLIM1
    OriGene qSTAR qPCR primer pairs in human, mouse for PDLIM1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat PDLIM1
      QuantiTect SYBR Green Assays in human, mouse, rat PDLIM1
      QuantiFast Probe-based Assays in human, mouse, rat PDLIM1

    Additional mRNA sequence: 

    AJ310549.1 AK091847.1 AK314792.1 BC000915.2 BC018755.1 U90878.1 

    20 DOTS entries:

    DT.448694  DT.100030819  DT.100887789  DT.100887791  DT.100030821  DT.121217697  DT.100887795  DT.100887785 
    DT.100887806  DT.121217657  DT.100035146  DT.100689814  DT.100801669  DT.100887804  DT.101955574  DT.120776564 
    DT.87016421  DT.95236934  DT.95373757  DT.87016420 

    Selected AceView cDNA sequences (see all 667):

    CB123683 CB217102 BQ644844 BG289758 CA407466 BU186564 BM820429 CR620933 
    BX401636 BQ548934 N92107 BM845158 BI517315 CR593176 BU162556 CR623245 
    BM552279 CR617851 AA303236 BM977430 BM914088 CR597094 BP352351 CR619278 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for PDLIM1 (see all 8)    About this scheme

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


    ECgene alternative splicing isoforms for PDLIM1

    (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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    PDLIM1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCCGGGAGCG
    PDLIM1 Expression
    About this image


    PDLIM1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 15) fully expand
     
     Kidney (Urinary System)    fully expand to see all 2 entries
             Renal Collecting Duct System
     
     Peripheral Nervous System (Nervous System)
             Schwann Precursor Cells Peripheral Nerve Domain
     
     Brain (Nervous System)
             Myelinating Oligodendrocyte Cells Forebrain White Matter
     
     Colon (Gastrointestinal Tract)
     
     Uterus (Reproductive System)
    PDLIM1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PDLIM1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.368525

    UniProtKB/Swiss-Prot: PDLI1_HUMAN, O00151
    Tissue specificity: Strongly expressed in the heart and skeletal muscle, moderately expressed in the spleen, small
    intestine, colon, placenta, and lung. A lower level expression is seen in liver, thymus, kidney, prostate and
    pancreas and is not found in the brain, testis, ovary, and peripheral blood leukocytes

        Pathway & Disease-focused RT2 Profiler PCR Array including PDLIM1: 
              Oxidative Stress in human mouse rat

    Primer
    Products:
    OriGene qPCR primer pairs and template standards for PDLIM1
    OriGene qSTAR qPCR primer pairs in human, mouse for PDLIM1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat PDLIM1
    QuantiTect SYBR Green Assays in human, mouse, rat PDLIM1
    QuantiFast Probe-based Assays in human, mouse, rat PDLIM1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PDLIM1

    (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 PDLIM1 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pdlim11 , 5 PDZ and LIM domain 1 (elfin)1, 5 87.38(n)1
    89.85(a)1
      19 (34.24 cM)5
    541321  NM_016861.41  NP_058557.21 
     402211735 
    chicken
    (Gallus gallus)
    Aves PDLIM11 PDZ and LIM domain 1 73.5(n)
    78.9(a)
      428948  XM_426503.4  XP_426503.4 
    lizard
    (Anolis carolinensis)
    Reptilia PDLIM16
    PDZ and LIM domain 1
    73(a)
    1 ↔ 1
    GL343297.1(1553617-1582710)
    African clawed frog
    (Xenopus laevis)
    Amphibia BC041514.12   -- 77.93(n)    BC041514.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.233762 Transcribed sequence with weak similarity to protein more 74.65(n)    CK027259.1 


    ENSEMBL Gene Tree for PDLIM1 (if available)
    TreeFam Gene Tree for PDLIM1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PDLIM1 gene
    PDLIM42  PDLIM22  PDLIM32  
    3 SIMAP similar genes for PDLIM1 using alignment to 1 protein entry:     PDLI1_HUMAN:
    PDLIM4    PDLIM3    PDLIM2

    PDLIM1 for paralogs           About GeneDecksing


    4 Pseudogenes.org Pseudogenes for PDLIM1
    PGOHUM00000248164 PGOHUM00000236979 PGOHUM00000236993 PGOHUM00000238114


    (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 PDLIM1 (see all 1153)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs455746361,2
    C,F--96996877(-) ACCTCG/ATGATC 1 -- ds50015Minor allele frequency- A:0.01NS 188
    rs455386321,2
    C,F--96996892(-) GGTCTT/CGATCT 1 -- ds50015Minor allele frequency- C:0.01NS 188
    rs456104331,2
    C,F--96996900(-) GCCAGC/GATGGT 1 -- ds50015Minor allele frequency- G:0.01NS 188
    rs454830971,2
    C,F--96996911(-) TCACCA/GCATTA 1 -- ds50016Minor allele frequency- G:0.05NS NA 190
    rs454658951,2
    C,F--96996920(-) GACGGG/AGTTTC 1 -- ds50016Minor allele frequency- A:0.01NS CSA 190
    rs455955351,2
    C,F--96996922(-) GAGACG/AGGGTT 1 -- ds50015Minor allele frequency- A:0.02NS 188
    rs127639391,2
    C,F--96996940(+) aatacA/Gaaaaa 1 -- ds50019Minor allele frequency- G:0.06NS NA 196
    rs1451385101,2
    C--96996968(+) GCAGGC/TGCCTG 1 -- ds50010--------
    rs1841109341,2
    --96997021(+) AACCCA/GGGAGG 1 -- ds50010--------
    rs1869243351,2
    --96997079(+) CGACAC/TAGCGA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for PDLIM1 (96997329 - 97050781 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for PDLIM1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv22688CNV Gain+Loss19812545

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PDLIM1
    DNA2.0 Custom Variant and Variant Library Synthesis for PDLIM1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 605900    OMIM disorders: --

    Selected diseases for PDLIM1 (see all 28):    
    About MalaCards
    hyperacusis    scimitar syndrome    johanson-blizzard syndrome    donohue syndrome
    faces syndrome    pulmonary valve stenosis    supravalvular aortic stenosis    dental enamel hypoplasia
    strabismus    mitral valve prolapse    acanthosis nigricans    hypertrichosis
    hypercalcemia    chronic granulomatous disease    aortic valve stenosis    williams-beuren syndrome
    craniosynostosis    otitis media    protein s deficiency    attention deficit hyperactivity disorder

    5 diseases from the University of Copenhagen DISEASES database for PDLIM1:
    Aortic valve stenosis     Williams-Beuren syndrome     Donohue Syndrome     Intellectual disability
    Hypercalcemia

    PDLIM1 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    10 Novoseek inferred disease relationships for PDLIM1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    aortic stenosis supravalvular 93.4 11 1824530 (1), 7503839 (1), 9285033 (1), 8766044 (1) (see all 10)
    williams syndrome 93.3 19 8138341 (3), 13677282 (2), 2033166 (2), 14635404 (1) (see all 15)
    hypercalcemia 68.7 9 15303821 (1), 9285033 (1), 13677282 (1), 2033166 (1) (see all 9)
    mental retardation 65.9 12 13677282 (2), 1824530 (1), 7503839 (1), 8527335 (1) (see all 11)
    developmental delay 55.1 2 14636357 (1), 2329796 (1)
    heart defects congenital 42.3 3 17625998 (1), 14636357 (1), 12599114 (1)
    mitral valve prolapse 41.3 1 8351994 (1)
    aortic stenosis 40.8 3 1488232 (1), 8469630 (1), 8620979 (1)
    mitral regurgitation 35.7 2 8351994 (1), 2038171 (1)
    strabismus 31.6 1 7503839 (1)

    Genetic Association Database (GAD): PDLIM1
    Human Genome Epidemiology (HuGE) Navigator: PDLIM1 (4 documents)

    Export disorders for PDLIM1 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 PDLIM1 gene, integrated from 10 sources (see all 83):
    (articles sorted by number of sources associating them with PDLIM1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Interaction of hCLIM1, an enigma family protein, with alpha-actinin 2. (PubMed id 10861853)1, 2, 3, 9 Kotaka M.... Waye M.M.Y. (J. Cell. Biochem. 2000)
    2. Human CLP-36, a PDZ-domain and LIM-domain protein, binds to alpha- actinin-1 and associates with actin filaments and stress fibers in activated platelets and endothelial cells. (PubMed id 11110697)1, 2, 9 Bauer K.... Siess W. (Blood 2000)
    3. CLP-36 PDZ-LIM protein associates with nonmuscle alpha-actinin-1 and alpha-actinin-4. (PubMed id 10753915)1, 2, 9 Vallenius T.... Makela T.P. (J. Biol. Chem. 2000)
    4. Characterization of the human 36-kDa carboxyl terminal LIM domain protein (hCLIM1). (PubMed id 10022510)1, 2, 9 Kotaka M.... Waye M.M.Y. (J. Cell. Biochem. 1999)
    5. Refined genomic localization and ethnic differences observed for the IBD5 association with Crohn's disease. (PubMed id 17213842)1, 4 Silverberg M.S....Daly M.J. (Eur. J. Hum. Genet. 2007)
    6. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PubMed id 16385451)1, 4 Grupe A....Goate A. (Am. J. Hum. Genet. 2006)
    7. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PubMed id 15592455)1, 2 Rush J.... Comb M.J. (Nat. Biotechnol. 2005)
    8. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)1, 2 Deloukas P.... Rogers J. (Nature 2004)
    9. Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry. (PubMed id 15144186)1, 2 Brill L.M....Peters E.C. (Anal. Chem. 2004)
    10. 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)

    (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: 9124 HGNC: 2067 AceView: PDLIM1 Ensembl:ENSG00000107438 euGenes: HUgn9124
    ECgene: PDLIM1 H-InvDB: PDLIM1

    (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 PDLIM1 Pharmacogenomics, SNPs, Pathways
    NIEHS-SNPshttp://egp.gs.washington.edu/data/pdlim1/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PDLIM1 gene:
    Search GeneIP for patents involving PDLIM1

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



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