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PDLIM5 Gene

protein-coding   GIFtS: 59
GCID: GC04P095373

PDZ And LIM Domain 5

  See PDLIM5-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 51 2     ENH12
ENH2 3 5     LIM2
Enigma Homolog2 3     Enigma-Like LIM Domain Protein2
Enigma-Like PDZ And LIM Domains Protein2 3     PDZ And LIM Domain Protein 52

External Ids:    HGNC: 174681   Entrez Gene: 106112   Ensembl: ENSG000001631107   OMIM: 6059045   UniProtKB: Q96HC43   

Export aliases for PDLIM5 gene to outside databases

Previous GC identifers: GC04P095731 GC04P095592 GC04P091110


(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 PDLIM5 Gene:
This gene encodes a member of a family of proteins that possess a 100-amino acid PDZ domain at the N terminus and
one to three LIM domains at the C-terminus. This family member functions as a scaffold protein that tethers
protein kinases to the Z-disk in striated muscles. It is thought to function in cardiomyocyte expansion and in
restraining postsynaptic growth of excitatory synapses. Alternative splicing of this gene results in multiple
transcript variants. (provided by RefSeq, Jan 2012)

GeneCards Summary for PDLIM5 Gene:
PDLIM5 (PDZ and LIM domain 5) is a protein-coding gene. Diseases associated with PDLIM5 include nail-patella syndrome, and barth syndrome. GO annotations related to this gene include actin binding and actinin binding. An important paralog of this gene is LIMS1.

UniProtKB/Swiss-Prot: PDLI5_HUMAN, Q96HC4
Function: May play an important role in the heart development by scaffolding PKC to the Z-disk region. May play a
role in the regulation of cardiomyocyte expansion. Overexpression promotes the development of heart hypertrophy.
Contributes to the regulation of dendritic spine morphogenesis in neurons. May restrain postsynaptic growth of
excitatory synapses (By similarity)

Gene Wiki entry for PDLIM5 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_000004.11  NT_016354.20  NC_018915.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the PDLIM5 gene promoter:
         SRF   SRF (504 AA)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPDLIM5 promoter sequence
   Search Chromatin IP Primers for PDLIM5

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PDLIM5


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

Entrez Gene cytogenetic band: 4q22   Ensembl cytogenetic band:  4q22.3   HGNC cytogenetic band: 4q22

PDLIM5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PDLIM5 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P095373:  view genomic region     (about GC identifiers)

Start:
95,373,037 bp from pter      End:
95,589,377 bp from pter
Size:
216,341 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: PDLI5_HUMAN, Q96HC4 (See protein sequence)
Recommended Name: PDZ and LIM domain protein 5  
Size: 596 amino acids; 63945 Da
Subunit: Interacts with various PKC isoforms through the LIM domains. Interacts (via LIM domains) with SIPA1L1.
Interacts (via PDZ domain) with actin and ACTN1 (By similarity)
2 PDB 3D structures from and Proteopedia for PDLIM5:
2DAR (3D)        2UZC (3D)    
Secondary accessions: A8K6F9 D6RB78 E9PBF5 O60705 Q56VN4 Q5UW38 Q8WVK0
Alternative splicing: 7 isoforms:  Q96HC4-1   Q96HC4-2   Q96HC4-3   Q96HC4-4   Q96HC4-5   Q96HC4-6   Q96HC4-7   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PDLIM5: NX_Q96HC4

Explore proteomics data for PDLIM5 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See PDLIM5 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (9 alternative transcripts): 
    NP_001011513.3  NP_001011515.1  NP_001011516.1  NP_001243354.1  NP_001243355.1  NP_001243356.1  NP_001243357.1  NP_001243358.1  
    NP_006448.4  

    ENSEMBL proteins: 
     ENSP00000352210   ENSP00000321746   ENSP00000426379   ENSP00000424297   ENSP00000423009  
     ENSP00000426804   ENSP00000424360   ENSP00000422833   ENSP00000429577   ENSP00000422528  
     ENSP00000398469   ENSP00000369527   ENSP00000322021   ENSP00000401579   ENSP00000439795  
     ENSP00000442187  

    PDLIM5 Human Recombinant Protein Products:

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    antibodies-online proteins for PDLIM5 (4 products) 

     
    antibodies-online peptides for PDLIM5

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    antibodies-online antibodies for PDLIM5 (43 products) 

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

    Graphical View of Domain Structure for InterPro Entry Q96HC4

    ProtoNet protein and cluster: Q96HC4

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


    UniProtKB/Swiss-Prot: PDLI5_HUMAN, Q96HC4
    Similarity: Contains 3 LIM zinc-binding domains
    Similarity: Contains 1 PDZ (DHR) domain


    Find genes that share domains with PDLIM5           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: PDLI5_HUMAN, Q96HC4
    Function: May play an important role in the heart development by scaffolding PKC to the Z-disk region. May play a
    role in the regulation of cardiomyocyte expansion. Overexpression promotes the development of heart hypertrophy.
    Contributes to the regulation of dendritic spine morphogenesis in neurons. May restrain postsynaptic growth of
    excitatory synapses (By similarity)

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003779actin binding ISS--
    GO:0005080protein kinase C binding ISS--
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
    GO:0042805actinin binding ISS--
         
    Find genes that share ontologies with PDLIM5           About GenesLikeMe


    Phenotypes:
         3 GenomeRNAi human phenotypes for PDLIM5:
     G0/1 arrest  Increased G1 DNA content  Synthetic lethal with imatinib 

         6 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Pdlim5):
     behavior/neurological  cardiovascular system  mortality/aging  muscle  nervous system 
     reproductive system 

    Find genes that share phenotypes with PDLIM5           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Pdlim5tm1.1Chen for PDLIM5

       genOway: Develop your customized and physiologically relevant rodent model for PDLIM5

    miRNA
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    miRTarBase miRNAs that target PDLIM5:
    hsa-mir-16-5p (MIRT032035), hsa-mir-155-5p (MIRT001527), hsa-mir-17-5p (MIRT051014)

    Block miRNA regulation of human, mouse, rat PDLIM5 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate PDLIM5 (see all 49):
    hsa-miR-142-5p hsa-miR-4291 hsa-miR-520e hsa-miR-302d hsa-miR-1321 hsa-miR-106a hsa-miR-513a-5p hsa-miR-486-3p
    SwitchGear 3'UTR luciferase reporter plasmidPDLIM5 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector (see all 4): PDLIM5 (NM_006457)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PDLIM5
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PDLIM5
    Addgene plasmids for PDLIM5 

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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
    PDLI5_HUMAN, Q96HC4: Cell junction, synapse, postsynaptic cell membrane, postsynaptic density (By similarity).
    Cell junction, synapse, synaptosome (By similarity). Cytoplasm (By similarity). Note=Detected both at presynaptic
    and postsynaptic sites (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton4
    cytosol4
    nucleus3
    plasma membrane3
    golgi apparatus1

    Gene Ontology (GO): Selected cellular component terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol ISS--
    GO:0014069postsynaptic density ISS--
    GO:0015629actin cytoskeleton IDA--
    GO:0016020membrane ISS--
    GO:0030018Z disc ----

    Find genes that share ontologies with PDLIM5           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PDLIM5
    Interactions:

        GeneGlobe Interaction Network for PDLIM5

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

    Selected Interacting proteins for PDLIM5 (Q96HC42, 3 ENSP000003217464) via UniProtKB, MINT, STRING, and/or I2D (see all 80)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GFI1BQ5VTD92, 3, ENSP000003447824MINT-2868588 I2D: score=3 STRING: ENSP00000344782
    ENSG00000224994Q9HCM93, ENSP000004119494I2D: score=5 STRING: ENSP00000411949
    ENSG00000232839Q9HCM93, ENSP000003983554I2D: score=5 STRING: ENSP00000398355
    TRIM39Q9HCM93, ENSP000003658444I2D: score=5 STRING: ENSP00000365844
    ENSG00000206495Q9HCM93I2D: score=5 
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0051963regulation of synapse assembly ISS--
    GO:0061001regulation of dendritic spine morphogenesis ISS--

    Find genes that share ontologies with PDLIM5           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 PDLIM5 (PDLI5)

    7 Novoseek inferred chemical compound relationships for PDLIM5 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    zinc 43.7 16 7583761 (2), 7938009 (1), 8595880 (1), 16199866 (1) (see all 14)
    tyrosine 24.3 2 19917054 (1), 16331329 (1)
    threonine 6.18 2 9655398 (1), 8906871 (1)
    calcium 0 5 16044170 (1), 18197271 (1), 16595163 (1)
    histidine 0 1 7583761 (1)
    serine 0 2 9655398 (1), 8906871 (1)
    cysteine 0 2 1966549 (1), 7848918 (1)



    Find genes that share compounds with PDLIM5           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PDLIM5 gene (9 alternative transcripts): 
    NM_001011513.3  NM_001011515.2  NM_001011516.2  NM_001256425.1  NM_001256426.1  NM_001256427.1  NM_001256428.1  NM_001256429.1  
    NM_006457.4  

    Unigene Cluster for PDLIM5:

    PDZ and LIM domain 5
    Hs.480311  [show with all ESTs]
    Unigene Representative Sequence: NM_001256426
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 23):
    ENST00000359265 ENST00000317968(uc003hti.3 uc011cdy.2) ENST00000514830
    ENST00000512274 ENST00000509333 ENST00000503974 ENST00000504489 ENST00000508216
    ENST00000514743 ENST00000511767 ENST00000510099 ENST00000509357 ENST00000513341
    ENST00000508531 ENST00000511586 ENST00000380176 ENST00000506632 ENST00000437932(uc011cdx.1 uc003hth.3 uc003htj.3 uc003htk.3 uc003htl.3)

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    Selected qRT-PCR Assays for microRNAs that regulate PDLIM5 (see all 49):
    hsa-miR-142-5p hsa-miR-4291 hsa-miR-520e hsa-miR-302d hsa-miR-1321 hsa-miR-106a hsa-miR-513a-5p hsa-miR-486-3p
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    Addgene plasmids for PDLIM5 
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      QuantiTect SYBR Green Assays in human, mouse, rat PDLIM5
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    Additional mRNA sequence: 

    AB209531.1 AF061258.1 AK129886.1 AK291624.1 AK291898.1 AK296980.1 AK304125.1 AL049969.1 
    AL832157.1 AL832686.1 AL833151.1 AL833438.1 AL833439.1 AY345240.1 AY598328.1 BC008741.2 
    BC017902.1 BC026029.2 BT007328.1 BX648059.1 NR_046186.1 

    Selected DOTS entries (see all 36):

    DT.100782824  DT.100782822  DT.100000841  DT.312272  DT.95087086  DT.87016811  DT.100793081  DT.87016812 
    DT.218133  DT.95342119  DT.95342122  DT.100782823  DT.100657973  DT.75190383  DT.92450691  DT.121233876 
    DT.75184298  DT.121233927  DT.121234016  DT.100771909  DT.100840029  DT.121234008  DT.75137580  DT.75171881 

    Selected AceView cDNA sequences (see all 536):

    BU618599 AL691773 AL599593 F33877 AA133788 AA192750 AI126537 BF952161 
    BM670741 BI792934 D62621 AI620824 AA887825 BF061001 AA129772 F01813 
    BX501179 BI792992 BF002744 Z39378 BQ026748 BU621920 AI332596 BM843638 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for PDLIM5 (see all 6)    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
    SP1:                                      -                                                                     
    SP2:                                      -                                                                     
    SP3:                                      -     -                                                               
    SP4:                          -           -                                                                     
    SP5:                                                                                                            


    ECgene alternative splicing isoforms for PDLIM5

    (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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    PDLIM5 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTCATTCTGT
    PDLIM5 Expression
    About this image


    PDLIM5 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 16) fully expand
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Cerebral Cortex
     
     Gut Tube (Gastrointestinal Tract)
             Midgut
     
     Neural Tube (Nervous System)
             Diencephalic Ventricular Zone
     
     Eye (Sensory Organs)
             GABAergic Amacrine Cells Inner Nuclear Layer
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
    PDLIM5 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PDLIM5 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.480311

    UniProtKB/Swiss-Prot: PDLI5_HUMAN, Q96HC4
    Tissue specificity: Heart and skeletal muscle specific. Expression is commonly increased in the brain of patients
    with bipolar disorder, schizophrenia, and major depression

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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PDLIM5

    (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 PDLIM5 gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pdlim51 , 5 PDZ and LIM domain 51, 5 86.24(n)1
    89.17(a)1
      3 (66.69 cM)5
    563761  NM_019808.31  NP_062782.21 
     1422395865 
    chicken
    (Gallus gallus)
    Aves PDLIM51 PDZ and LIM domain 5 75.18(n)
    72.74(a)
      422699  NM_001031149.1  NP_001026320.1 
    lizard
    (Anolis carolinensis)
    Reptilia PDLIM56
    PDZ and LIM domain 5
    57(a)
    1 ↔ 1
    5(49000282-49336670)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.23562 Xenopus laevis transcribed sequence with moderate similarity more 83.03(n)    BG730843.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc561162 hypothetical protein MGC56116 76.09(n)   393165  BC045922.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Zasp526
    Z band alternatively spliced PDZ-motif protein 52
    9(a)
    1 → many
    2R(11650070-11704509)
    worm
    (Caenorhabditis elegans)
    Secernentea alp-16
    Protein ALP-1, isoform d
    12(a)
    1 → many
    IV(8852500-8862487) WBGene00001132


    ENSEMBL Gene Tree for PDLIM5 (if available)
    TreeFam Gene Tree for PDLIM5 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PDLIM5 gene
    LIMS12  PDLIM72  LIMS3L2  FHL32  FHL52  LDB32  LPXN2  FHL12  
    ENSG000002572072  LIMS32  TGFB1I12  PXN2  LIMS22  FHL22  
    Selected SIMAP similar genes for PDLIM5 using alignment to 9 protein entries:     PDLI5_HUMAN (see all proteins) (see all similar genes):
    PDLIM2    PDLIM3    LIM    PDLIM7    LIMS1    CRIP1
    PXN    ABLIM3    CRIP2    LHX2    SCRIB    DKFZp686P2249
    LMO3    LHX3    ZYX    AJUBA    LDB3    LHx4

    Find genes that share paralogs with PDLIM5           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 PDLIM5 (see all 4185)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1489398061,2
    C,Funtested195578650(+) CCATTC/TGGAAC 12 R W mis12Minor allele frequency- T:0.00NA EU 5873
    rs1122298991,2
    C--95235932(+) CCCCA-/ACACACA 8 -- int11Minor allele frequency- AC:0.50CSA 2
    rs623219921,2
    C,F--95371072(+) CTACAC/TGACGC 10 -- us2k16Minor allele frequency- T:0.15NA WA CSA EA 364
    rs1486996101,2
    --95371219(+) GCTCAC/TGTAAG 10 -- us2k10--------
    rs1176423591,2
    F--95371290(+) TATTAT/CTATTA 10 -- us2k11Minor allele frequency- C:0.01EA 120
    rs1428672691,2
    C--95371302(+) TACTC-/TTTTTTT 10 -- us2k10--------
    rs1862865571,2
    --95371316(+) TGGTGA/C/TGGAGT 10 -- us2k10--------
    rs623219931,2
    C,F--95371334(+) TGTCGT/CCCAGG 10 -- us2k12Minor allele frequency- C:0.25NA WA 4
    rs1906623601,2
    --95371363(+) GTCTCG/TGCTCA 10 -- us2k10--------
    rs623219941,2
    C--95371494(+) TCGCCT/ATGTTG 10 -- us2k11Minor allele frequency- A:0.00NA 2

    HapMap Linkage Disequilibrium report for PDLIM5 (95373037 - 95589377 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for PDLIM5 (see all 11):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2304226CNV Deletion18987734
    esv2727990CNV Deletion23290073
    esv2492606CNV Deletion19546169
    esv1135092CNV Deletion17803354
    esv991897CNV Deletion20482838
    esv2451649CNV Deletion19546169
    esv4831CNV Deletion18987735
    esv274400CNV Insertion20981092
    esv270916CNV Insertion20981092
    esv273051CNV Insertion20981092

    Human Gene Mutation Database (HGMD): PDLIM5
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PDLIM5
    DNA2.0 Custom Variant and Variant Library Synthesis for PDLIM5

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 605904    OMIM disorders: --

    2 diseases for PDLIM5:    
    About MalaCards
    nail-patella syndrome    barth syndrome

    1 disease from the University of Copenhagen DISEASES database for PDLIM5:
    Mucoepidermoid carcinoma

    Find genes that share disorders with PDLIM5           About GenesLikeMe

    Selected Novoseek inferred disease relationships for PDLIM5 gene (see all 16)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    nail-patella syndrome 56.6 2 17570941 (1), 11978876 (1)
    t-all 48.2 2 8078932 (1)
    bipolar disorder 37.7 26 19448850 (6), 16044170 (5), 15362566 (2), 18496210 (2) (see all 7)
    leukemia t-cell 24.2 1 7957052 (1)
    breast cancer 12.2 10 19117995 (2), 17956604 (1), 20461080 (1), 12571245 (1) (see all 7)
    myopia 11.2 9 17101130 (4), 15949800 (1), 17924678 (1)
    cancer 9.85 6 16314921 (1), 17332327 (1), 19307596 (1), 19917054 (1) (see all 5)
    acute leukemia 7.77 1 9103675 (1)
    major depression 4.42 8 18197271 (2), 16595163 (2), 16044170 (1)
    tumors 1.71 4 19139564 (1), 18957717 (1), 18942711 (1)

    Genetic Association Database (GAD): PDLIM5
    Human Genome Epidemiology (HuGE) Navigator: PDLIM5 (18 documents)

    Export disorders for PDLIM5 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 PDLIM5 gene, integrated from 10 sources (see all 213):
    (articles sorted by number of sources associating them with PDLIM5)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Gene expression and association analyses of LIM (PDLIM5) in bipolar disorder and schizophrenia. (PubMed id 16044170)1, 2, 4, 9 Kato T.... Yoshikawa T. (Mol. Psychiatry 2005)
    2. A polymorphism in the PDLIM5 gene associated with gene expression and Schizophrenia. (PubMed id 16213469)1, 2, 4 Horiuchi Y.... Arinami T. (Biol. Psychiatry 2006)
    3. Cloning and identification of a novel human gene PDLIM5, a homolog of AD-associated neuronal thread protein (AD7c-NTP). (PubMed id 15346770)1, 2, 3 Wu M....Mao Y. (DNA Seq. 2004)
    4. Positive association between the PDLIM5 gene and bipolar disorder in the Chinese Han population. (PubMed id 19448850)1, 4, 9 Zhao T....Yu L. (amp 2009)
    5. A case-control association study of the PDLIM5 gene and bipolar disorder in a Sardinian sample. (PubMed id 18496210)1, 4, 9 Squassina A....Del Zompo M. (Psychiatr. Genet. 2008)
    6. PDLIM5 and susceptibility to bipolar disorder: a family-based association study and meta-analysis. (PubMed id 18496208)1, 4, 9 Shi J....Liu C. (Psychiatr. Genet. 2008)
    7. A major single nucleotide polymorphism of the PDLIM5 gene associated with recurrent major depressive disorder. (PubMed id 18197271)1, 4, 9 Liu Z....Li W. (amp 2008)
    8. The PDLIM5 gene and lithium prophylaxis: an association and gene expression analysis in Sardinian patients with bipolar disorder. (PubMed id 18456508)1, 4, 9 Squassina A....Zompo M.D. (Pharmacol. Res. 2008)
    9. Inherited genetic markers discovered to date are able to identify a significant number of men at considerably elevated risk for prostate cancer. (PubMed id 20878950)1, 4 Sun J....Xu J. (Prostate 2011)
    10. Prostate cancer risk-associated variants reported from genome-wide association studies: meta-analysis and their contribution to genetic Variation. (PubMed id 20564319)1, 4 Kim S.T....Sun J. (Prostate 2010)

    (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: 10611 HGNC: 17468 AceView: LIM Ensembl:ENSG00000163110 euGenes: HUgn10611
    ECgene: PDLIM5 H-InvDB: PDLIM5

    (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 PDLIM5 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for PDLIM5 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PDLIM5 gene:
    Search GeneIP for patents involving PDLIM5

    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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