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Aliases for PDLIM5 Gene

Aliases for PDLIM5 Gene

  • PDZ And LIM Domain 5 2 3 5
  • Enigma-Like PDZ And LIM Domains Protein 3 4
  • Enigma Homolog 3 4
  • ENH 3 4
  • Enigma-Like LIM Domain Protein 3
  • PDZ And LIM Domain Protein 5 3
  • Enh1 3
  • LIM 3
  • L9 3

External Ids for PDLIM5 Gene

Previous GeneCards Identifiers for PDLIM5 Gene

  • GC04P095731
  • GC04P095592
  • GC04P095373
  • GC04P091110

Summaries for PDLIM5 Gene

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 Nephrogenic Adenofibroma and Nail-Patella Syndrome. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. GO annotations related to this gene include actin binding and protein kinase C binding. An important paralog of this gene is LDB3.

UniProtKB/Swiss-Prot for PDLIM5 Gene

  • 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

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDLIM5 Gene

Genomics for PDLIM5 Gene

Regulatory Elements for PDLIM5 Gene

Enhancers for PDLIM5 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04G094515 1.7 FANTOM5 Ensembl ENCODE dbSUPER 17.5 +65.0 65049 3.2 PKNOX1 INSM2 FEZF1 ZNF121 SCRT2 CREM EGR2 CEBPB ZNF398 ZNF843 PDLIM5 PIR44106
GH04G094484 1.4 Ensembl ENCODE dbSUPER 18.6 +36.6 36639 7.9 FOXA2 TCF12 ZNF121 ELK1 GATA2 FOS REST ZNF592 MAFF SMARCA4 PDLIM5 PIR44106
GH04G094546 1.8 FANTOM5 Ensembl ENCODE dbSUPER 13.9 +97.8 97799 5.8 PKNOX1 FOXA2 ATF1 ARNT E2F7 TCF12 GATA2 FOS SP5 NCOA1 PDLIM5 HPGDS PIR44106
GH04G094523 1.2 Ensembl ENCODE dbSUPER 16.1 +71.7 71695 1.1 JUN MAFG CEBPB ZNF623 ZNF592 FOSL1 JUND PRDM6 ATF3 SMARCA4 PDLIM5 PIR44106
GH04G094531 1.5 Ensembl ENCODE dbSUPER 12 +83.3 83312 7.5 HDGF PKNOX1 ARNT YY1 TCF12 ZNF121 ZNF766 GATA2 NCOA1 SMARCB1 PDLIM5 PIR44106
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PDLIM5 on UCSC Golden Path with GeneCards custom track

Promoters for PDLIM5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000170798 1143 3601 HDGF HNRNPUL1 PKNOX1 ARNT WRNIP1 ARID4B SIN3A FEZF1 ZNF2 YY1

Transcription factor binding sites by QIAGEN in the PDLIM5 gene promoter:

Genomic Location for PDLIM5 Gene

Chromosome:
4
Start:
94,451,857 bp from pter
End:
94,668,227 bp from pter
Size:
216,371 bases
Orientation:
Plus strand

Genomic View for PDLIM5 Gene

Genes around PDLIM5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDLIM5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDLIM5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDLIM5 Gene

Proteins for PDLIM5 Gene

  • Protein details for PDLIM5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96HC4-PDLI5_HUMAN
    Recommended name:
    PDZ and LIM domain protein 5
    Protein Accession:
    Q96HC4
    Secondary Accessions:
    • A8K6F9
    • D6RB78
    • E9PBF5
    • O60705
    • Q56VN4
    • Q5UW38
    • Q8WVK0

    Protein attributes for PDLIM5 Gene

    Size:
    596 amino acids
    Molecular mass:
    63945 Da
    Quaternary structure:
    • 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).

    Three dimensional structures from OCA and Proteopedia for PDLIM5 Gene

    Alternative splice isoforms for PDLIM5 Gene

neXtProt entry for PDLIM5 Gene

Post-translational modifications for PDLIM5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PDLIM5 Gene

Domains & Families for PDLIM5 Gene

Gene Families for PDLIM5 Gene

Protein Domains for PDLIM5 Gene

Suggested Antigen Peptide Sequences for PDLIM5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PDLIM5: view

No data available for UniProtKB/Swiss-Prot for PDLIM5 Gene

Function for PDLIM5 Gene

Molecular function for PDLIM5 Gene

UniProtKB/Swiss-Prot 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) - Molecular Function for PDLIM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding ISS --
GO:0005080 protein kinase C binding IEA,ISS --
GO:0005515 protein binding IPI 25416956
GO:0008270 zinc ion binding IEA --
GO:0042805 actinin binding IEA,ISS --
genes like me logo Genes that share ontologies with PDLIM5: view
genes like me logo Genes that share phenotypes with PDLIM5: view

Animal Models for PDLIM5 Gene

MGI Knock Outs for PDLIM5:

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PDLIM5 Gene

Localization for PDLIM5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDLIM5 Gene

Cell junction, synapse, postsynaptic cell membrane, postsynaptic density. Cell junction, synapse, synaptosome. Cytoplasm. Note=Detected both at presynaptic and postsynaptic sites. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDLIM5 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
plasma membrane 4
nucleus 4
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for PDLIM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol ISS,IEA --
GO:0005886 plasma membrane IEA --
GO:0005913 cell-cell adherens junction IDA 25468996
GO:0014069 postsynaptic density ISS --
genes like me logo Genes that share ontologies with PDLIM5: view

Pathways & Interactions for PDLIM5 Gene

genes like me logo Genes that share pathways with PDLIM5: view

Pathways by source for PDLIM5 Gene

Gene Ontology (GO) - Biological Process for PDLIM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0051963 regulation of synapse assembly IEA,ISS --
GO:0061001 regulation of dendritic spine morphogenesis ISS,IEA --
GO:0061049 cell growth involved in cardiac muscle cell development ISS,IEA --
GO:0098609 cell-cell adhesion IEA --
genes like me logo Genes that share ontologies with PDLIM5: view

No data available for SIGNOR curated interactions for PDLIM5 Gene

Drugs & Compounds for PDLIM5 Gene

(7) Drugs for PDLIM5 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PDLIM5: view

Transcripts for PDLIM5 Gene

Unigene Clusters for PDLIM5 Gene

PDZ and LIM domain 5:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDLIM5 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
SP1: -
SP2: -
SP3: - -
SP4: - -
SP5:
SP6: - - -

Relevant External Links for PDLIM5 Gene

GeneLoc Exon Structure for
PDLIM5
ECgene alternative splicing isoforms for
PDLIM5

Expression for PDLIM5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDLIM5 Gene

mRNA differential expression in normal tissues according to GTEx for PDLIM5 Gene

This gene is overexpressed in Heart - Left Ventricle (x7.6), Muscle - Skeletal (x7.4), and Heart - Atrial Appendage (x4.3).

Protein differential expression in normal tissues from HIPED for PDLIM5 Gene

This gene is overexpressed in Bone marrow stromal cell (22.6), Heart (9.7), and Uterus (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDLIM5 Gene



Protein tissue co-expression partners for PDLIM5 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDLIM5 Gene:

PDLIM5

SOURCE GeneReport for Unigene cluster for PDLIM5 Gene:

Hs.480311

mRNA Expression by UniProt/SwissProt for PDLIM5 Gene:

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

Evidence on tissue expression from TISSUES for PDLIM5 Gene

  • Heart(4.8)
  • Blood(4.5)
  • Liver(4.5)
  • Muscle(4.5)
  • Nervous system(4.4)
  • Skin(4.3)
  • Kidney(2.9)
  • Lung(2.6)
  • Intestine(2.2)
genes like me logo Genes that share expression patterns with PDLIM5: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDLIM5 Gene

Orthologs for PDLIM5 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDLIM5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDLIM5 34 35
  • 99.44 (n)
dog
(Canis familiaris)
Mammalia PDLIM5 34 35
  • 92 (n)
rat
(Rattus norvegicus)
Mammalia Pdlim5 34
  • 86.35 (n)
mouse
(Mus musculus)
Mammalia Pdlim5 34 16 35
  • 86.24 (n)
cow
(Bos Taurus)
Mammalia PDLIM5 35
  • 86 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PDLIM5 35
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDLIM5 35
  • 63 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDLIM5 34 35
  • 75.18 (n)
lizard
(Anolis carolinensis)
Reptilia PDLIM5 35
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdlim5 34
  • 70.18 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2356 34
zebrafish
(Danio rerio)
Actinopterygii pdlim5a 34 35
  • 62.09 (n)
pdlim5b 35
  • 46 (a)
OneToMany
zgc56116 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7740 34
fruit fly
(Drosophila melanogaster)
Insecta Zasp52 35
  • 9 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea alp-1 35
  • 12 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 36 (a)
ManyToMany
-- 35
  • 34 (a)
ManyToMany
Species where no ortholog for PDLIM5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PDLIM5 Gene

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

Paralogs for PDLIM5 Gene

Variants for PDLIM5 Gene

Sequence variations from dbSNP and Humsavar for PDLIM5 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs10000208 -- 94,545,944(+) GAAAT(A/G)TGTCT intron-variant
rs1000021794 -- 94,633,949(+) CAGAG(C/G)GAACA intron-variant
rs1000024591 -- 94,473,592(+) ATACT(C/T)CTCAA intron-variant
rs1000028354 -- 94,569,667(+) TGAGA(A/G)AATGA intron-variant
rs1000035588 -- 94,588,329(+) GAGGC(C/T)GAGGC intron-variant, downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for PDLIM5 Gene

Variant ID Type Subtype PubMed ID
dgv2855n106 CNV deletion 24896259
esv1135092 CNV deletion 17803354
esv2304226 CNV deletion 18987734
esv2451649 CNV deletion 19546169
esv2492606 CNV deletion 19546169
esv2727990 CNV deletion 23290073
esv3310128 CNV mobile element insertion 20981092
esv3326324 CNV insertion 20981092
esv3349257 CNV insertion 20981092
esv3422122 CNV insertion 20981092
esv3449928 CNV insertion 20981092
esv3564279 CNV deletion 23714750
esv4831 CNV loss 18987735
esv6075 CNV loss 19470904
esv991897 CNV deletion 20482838
nsv1074199 CNV deletion 25765185
nsv1141989 OTHER inversion 24896259
nsv477201 CNV novel sequence insertion 20440878
nsv594901 CNV gain 21841781
nsv956329 CNV deletion 24416366

Variation tolerance for PDLIM5 Gene

Residual Variation Intolerance Score: 47.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.21; 52.23% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDLIM5 Gene

Human Gene Mutation Database (HGMD)
PDLIM5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDLIM5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDLIM5 Gene

Disorders for PDLIM5 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PDLIM5 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
nephrogenic adenofibroma
  • metanephric adenofibroma
nail-patella syndrome
  • fong disease
bipolar disorder
  • bipolar depression
schizophrenia
  • schizophrenia 12
left ventricular noncompaction
  • left ventricular hypertrabeculation
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for PDLIM5

Genetic Association Database (GAD)
PDLIM5
Human Genome Epidemiology (HuGE) Navigator
PDLIM5
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDLIM5
genes like me logo Genes that share disorders with PDLIM5: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDLIM5 Gene

Publications for PDLIM5 Gene

  1. Gene expression and association analyses of LIM (PDLIM5) in bipolar disorder and schizophrenia. (PMID: 16044170) Kato T. … Yoshikawa T. (Mol. Psychiatry 2005) 3 4 22 46 64
  2. Positive association between the PDLIM5 gene and bipolar disorder in the Chinese Han population. (PMID: 19448850) Zhao T. … Yu L. (J Psychiatry Neurosci 2009) 3 22 46 64
  3. A major single nucleotide polymorphism of the PDLIM5 gene associated with recurrent major depressive disorder. (PMID: 18197271) Liu Z. … Li W. (J Psychiatry Neurosci 2008) 3 22 46 64
  4. The PDLIM5 gene and lithium prophylaxis: an association and gene expression analysis in Sardinian patients with bipolar disorder. (PMID: 18456508) Squassina A. … Zompo M.D. (Pharmacol. Res. 2008) 3 22 46 64
  5. PDLIM5 and susceptibility to bipolar disorder: a family-based association study and meta-analysis. (PMID: 18496208) Shi J. … Liu C. (Psychiatr. Genet. 2008) 3 22 46 64

Products for PDLIM5 Gene

Sources for PDLIM5 Gene

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