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Aliases for PDLIM4 Gene

Aliases for PDLIM4 Gene

  • PDZ And LIM Domain 4 2 3 5
  • Reversion-Induced LIM Protein 3 4
  • LIM Protein RIL 3 4
  • RIL 3 4
  • PDZ And LIM Domain Protein 4 3
  • LIM Domain Protein 3
  • Enigma Homolog 3

External Ids for PDLIM4 Gene

Previous GeneCards Identifiers for PDLIM4 Gene

  • GC00U914365
  • GC05P131670
  • GC05P131621
  • GC05P126785

Summaries for PDLIM4 Gene

Entrez Gene Summary for PDLIM4 Gene

  • This gene encodes a protein which may be involved in bone development. Mutations in this gene are associated with susceptibility to osteoporosis. [provided by RefSeq, Nov 2009]

GeneCards Summary for PDLIM4 Gene

PDLIM4 (PDZ And LIM Domain 4) is a Protein Coding gene. Diseases associated with PDLIM4 include Osteoporosis and Multiple Personality Disorder. An important paralog of this gene is PDLIM3.

Gene Wiki entry for PDLIM4 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDLIM4 Gene

Genomics for PDLIM4 Gene

Regulatory Elements for PDLIM4 Gene

Enhancers for PDLIM4 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
GH05G132257 1.5 FANTOM5 ENCODE dbSUPER 18.2 +2.0 1999 5.3 HDGF ZNF133 SIN3A GLIS2 GATA2 EGR1 SCRT2 FOS RELB IKZF2 P4HA2 MIR3936HG PDLIM4 SLC22A4 SLC22A5 KIF3A GC05M132271
GH05G132300 1.4 Ensembl ENCODE dbSUPER 11.4 +44.0 44047 2.4 ATF1 PKNOX1 NFIB ZBTB40 ZNF335 TCF12 CREM ZBTB11 CEBPB ZEB2 MIR3936HG SLC22A5 PDLIM4 P4HA2 PIR38624
GH05G132317 1.4 Ensembl ENCODE dbSUPER 10.5 +61.1 61087 1.5 TCF12 GLIS2 REST ZNF592 SMARCA4 PBX2 MYNN GLIS1 NR2C1 KDM1A MIR3936HG P4HA2 SLC22A4 PDLIM4 P4HA2-AS1 LOC107987500 SLC22A5 PIR38624
GH05G132384 1.5 Ensembl ENCODE dbSUPER 9.6 +130.0 130027 6.6 HDGF WRNIP1 ARID4B SIN3A ZNF48 ZBTB7B YY1 GLIS2 ELK1 ZNF143 MIR3936HG SLC22A5 RAD50 ENSG00000248648 C5orf56 IRF1 ENSG00000202533 LOC105379175 LOC102723741 SOWAHA
GH05G132070 1.2 FANTOM5 ENCODE 10.4 -186.9 -186888 0.4 ATF1 TCF12 ZNF766 GATA2 EGR1 FOS CREM ZEB2 ELF1 ZNF592 CSF2 IL3 P4HA2 LOC107987500 P4HA2-AS1 PDLIM4 IL5 FNIP1 RAPGEF6 SLC22A4
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PDLIM4 on UCSC Golden Path with GeneCards custom track

Promoters for PDLIM4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000186827 42 1001 HDGF LEF1 EGR1 POLR2A SCRT2 ZSCAN29 SMARCA5 SCRT1 PHF8 SP5

Genomic Location for PDLIM4 Gene

Chromosome:
5
Start:
132,257,658 bp from pter
End:
132,273,454 bp from pter
Size:
15,797 bases
Orientation:
Plus strand

Genomic View for PDLIM4 Gene

Genes around PDLIM4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDLIM4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDLIM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDLIM4 Gene

Proteins for PDLIM4 Gene

  • Protein details for PDLIM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P50479-PDLI4_HUMAN
    Recommended name:
    PDZ and LIM domain protein 4
    Protein Accession:
    P50479
    Secondary Accessions:
    • B2R8U1
    • Q53Y39
    • Q96AT8
    • Q9BTW8
    • Q9Y292

    Protein attributes for PDLIM4 Gene

    Size:
    330 amino acids
    Molecular mass:
    35398 Da
    Quaternary structure:
    • Interacts with the LIM domain with the second and fourth PDZ domains of PTPN13.

    Three dimensional structures from OCA and Proteopedia for PDLIM4 Gene

    Alternative splice isoforms for PDLIM4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDLIM4 Gene

Post-translational modifications for PDLIM4 Gene

  • Phosphorylated on tyrosine residue(s). Can be dephosphorylated by PTPN13 (By similarity).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PDLIM4 Gene

No data available for DME Specific Peptides for PDLIM4 Gene

Domains & Families for PDLIM4 Gene

Gene Families for PDLIM4 Gene

Protein Domains for PDLIM4 Gene

Suggested Antigen Peptide Sequences for PDLIM4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PDLIM4: view

No data available for UniProtKB/Swiss-Prot for PDLIM4 Gene

Function for PDLIM4 Gene

Gene Ontology (GO) - Molecular Function for PDLIM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10826496
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PDLIM4: view

Phenotypes for PDLIM4 Gene

genes like me logo Genes that share phenotypes with PDLIM4: view

Animal Model Products

CRISPR Products

miRNA for PDLIM4 Gene

miRTarBase miRNAs that target PDLIM4

Inhibitory RNA Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDLIM4 Gene

Localization for PDLIM4 Gene

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 PDLIM4 gene
Compartment Confidence
nucleus 3
cytosol 3
cytoskeleton 2
plasma membrane 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for PDLIM4 Gene

Pathways & Interactions for PDLIM4 Gene

SuperPathways for PDLIM4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PDLIM4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for PDLIM4 Gene

Drugs & Compounds for PDLIM4 Gene

No Compound Related Data Available

Transcripts for PDLIM4 Gene

Unigene Clusters for PDLIM4 Gene

PDZ and LIM domain 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDLIM4 Gene

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

Relevant External Links for PDLIM4 Gene

GeneLoc Exon Structure for
PDLIM4
ECgene alternative splicing isoforms for
PDLIM4

Expression for PDLIM4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDLIM4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDLIM4 Gene

This gene is overexpressed in Bone marrow stromal cell (30.1) and Uterus (13.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDLIM4 Gene



Protein tissue co-expression partners for PDLIM4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDLIM4 Gene:

PDLIM4

SOURCE GeneReport for Unigene cluster for PDLIM4 Gene:

Hs.424312

mRNA Expression by UniProt/SwissProt for PDLIM4 Gene:

P50479-PDLI4_HUMAN
Tissue specificity: Isoform 2 is found in brain.

Evidence on tissue expression from TISSUES for PDLIM4 Gene

  • Nervous system(4.5)
  • Bone marrow(4.2)
  • Liver(4.1)
  • Lung(4.1)
genes like me logo Genes that share expression patterns with PDLIM4: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDLIM4 Gene

Orthologs for PDLIM4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDLIM4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDLIM4 34 35
  • 99.49 (n)
cow
(Bos Taurus)
Mammalia PDLIM4 34 35
  • 90.2 (n)
dog
(Canis familiaris)
Mammalia PDLIM4 34 35
  • 88.79 (n)
mouse
(Mus musculus)
Mammalia Pdlim4 34 16 35
  • 86.02 (n)
rat
(Rattus norvegicus)
Mammalia Pdlim4 34
  • 85.01 (n)
oppossum
(Monodelphis domestica)
Mammalia PDLIM4 35
  • 64 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDLIM4 35
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDLIM4 34 35
  • 70.15 (n)
lizard
(Anolis carolinensis)
Reptilia PDLIM4 35
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdlim4 34
  • 62.99 (n)
MGC75597 34
zebrafish
(Danio rerio)
Actinopterygii pdlim4 34 35
  • 60.45 (n)
Species where no ortholog for PDLIM4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for PDLIM4 Gene

ENSEMBL:
Gene Tree for PDLIM4 (if available)
TreeFam:
Gene Tree for PDLIM4 (if available)

Paralogs for PDLIM4 Gene

Paralogs for PDLIM4 Gene

(2) SIMAP similar genes for PDLIM4 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with PDLIM4: view

Variants for PDLIM4 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for PDLIM4 Gene

PDLI4_HUMAN-P50479
Genetic variations in PDLIM4 may be correlated with bone mineral density (BMD). Low BMD is a risk factor for osteoporotic fracture. Osteoporosis is characterized by reduced bone mineral density, disruption of bone microarchitecture, and the alteration of the amount and variety of non-collagenous proteins in bone. Osteoporotic bones are more at risk of fracture.

Sequence variations from dbSNP and Humsavar for PDLIM4 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs1000024773 -- 132,260,914(+) CGCCC(A/G)CAGAA intron-variant
rs1000245579 -- 132,273,875(+) TGCCC(A/T)GAATC downstream-variant-500B
rs1000543047 -- 132,261,215(+) TGGGT(A/G)TCTCC intron-variant
rs1000631200 -- 132,267,155(+) GCCAA(A/G)TGGGG intron-variant
rs1000962280 -- 132,269,648(+) CACAG(G/T)CTCAA intron-variant

Variation tolerance for PDLIM4 Gene

Residual Variation Intolerance Score: 38.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.53; 77.76% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDLIM4 Gene

Human Gene Mutation Database (HGMD)
PDLIM4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDLIM4

No data available for Structural Variations from Database of Genomic Variants (DGV) for PDLIM4 Gene

Disorders for PDLIM4 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PDLIM4 Gene - From: OMIM, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
osteoporosis
  • osteoporosis, postmenopausal, susceptibility
multiple personality disorder
  • dissociative identity disorder
retinitis pigmentosa 60
  • rp60
dissociative disorder
  • dissociative disease
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for PDLIM4

Genetic Association Database (GAD)
PDLIM4
Human Genome Epidemiology (HuGE) Navigator
PDLIM4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDLIM4
genes like me logo Genes that share disorders with PDLIM4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDLIM4 Gene

Publications for PDLIM4 Gene

  1. Association of genetic variation of the RIL gene, encoding a PDZ-LIM domain protein and localized in 5q31.1, with low bone mineral density in adult Japanese women. (PMID: 12908099) Omasu F. … Emi M. (J. Hum. Genet. 2003) 3 4 22 64
  2. The human RIL gene: mapping to human chromosome 5q31.1, genomic organization and alternative transcripts. (PMID: 9573374) Bashirova A.A. … Frolova E.I. (Gene 1998) 2 3 4 64
  3. Genetic association study for RSV bronchiolitis in infancy at the 5q31 cytokine cluster. (PMID: 19131452) Forton J.T. … Hull J. (Thorax 2009) 3 46 64
  4. Reversion-induced LIM interaction with Src reveals a novel Src inactivation cycle. (PMID: 19307596) Zhang Y. … Wu C. (J. Cell Biol. 2009) 3 22 64
  5. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges L.M. … Zmuda J.M. (J. Bone Miner. Res. 2009) 3 46 64

Products for PDLIM4 Gene

Sources for PDLIM4 Gene

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