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Aliases for PDLIM1 Gene

Aliases for PDLIM1 Gene

  • PDZ And LIM Domain 1 2 3 5
  • Elfin 2 3 4
  • Carboxyl Terminal LIM Domain Protein 1 2 3
  • LIM Domain Protein CLP-36 3 4
  • CLIM1 3 4
  • CLP36 3 4
  • Epididymis Secretory Protein Li 112 3
  • C-Terminal LIM Domain Protein 1 4
  • PDZ And LIM Domain 1 (Elfin) 2
  • PDZ And LIM Domain Protein 1 3
  • HEL-S-112 3
  • CLP-36 3
  • HCLIM1 3

External Ids for PDLIM1 Gene

Previous HGNC Symbols for PDLIM1 Gene

  • CLIM1

Previous GeneCards Identifiers for PDLIM1 Gene

  • GC10M095890
  • GC10M096230
  • GC10M097128
  • GC10M096661
  • GC10M096987
  • GC10M096997
  • GC10M090624

Summaries for PDLIM1 Gene

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 Supravalvular Aortic Stenosis and Hyperacusis. Gene Ontology (GO) annotations related to this gene include transcription coactivator activity. An important paralog of this gene is PDLIM3.

UniProtKB/Swiss-Prot for PDLIM1 Gene

  • Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the cytoskeleton (PubMed:10861853). Involved in assembly, disassembly and directioning of stress fibers in fibroblasts. Required for the localization of ACTN1 and PALLD to stress fibers. Required for cell migration and in maintaining cell polarity of fibroblasts (By similarity).

Gene Wiki entry for PDLIM1 Gene

Additional gene information for PDLIM1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDLIM1 Gene

Genomics for PDLIM1 Gene

GeneHancer (GH) Regulatory Elements for PDLIM1 Gene

Promoters and enhancers for PDLIM1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10I095286 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 561.8 -1.1 -1066 11.8 HDGF PKNOX1 SMAD1 ARID4B SIN3A FEZF1 IRF4 ZNF213 ZNF207 ZNF143 PDLIM1 TBC1D12 CYP2C8 ENTPD1 SORBS1 GC10M095392
GH10I095259 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 16.9 +26.6 26614 10.2 SMAD1 FOXA2 ARNT NEUROD1 ZNF766 ZNF213 ZNF143 FOS JUNB ZNF592 PDLIM1 CYP2C8 ACSM6 GC10M095264 GC10M095235
GH10I095182 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE 10.6 +107.5 107539 1.6 ATF1 SIN3A ZNF2 YY1 ETS1 ZNF121 GLIS2 ZNF213 ZNF207 ZNF143 PAWRP1 ZNF518A TCTN3 CCNJ PDLIM1 HELLS ENTPD1-AS1 CYP2C8 ACSM6 SORBS1
GH10I095227 Promoter/Enhancer 1.5 Ensembl ENCODE dbSUPER 10.8 +60.9 60939 5.4 HDAC1 PKNOX1 NFIB SIN3A RFX5 YY1 ETS1 RCOR1 FOS CBFB ENSG00000234026 ACSM6 PDLIM1 CYP2C8 TCTN3
GH10I095234 Enhancer 1.2 Ensembl ENCODE dbSUPER 11.3 +55.2 55159 2.2 PKNOX1 BMI1 BATF KLF5 IRF4 ATF7 ETV6 FOS BCLAF1 IKZF2 GC10M095235 ACSM6 PDLIM1 CYP2C8 TCTN3 ENSG00000234026
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PDLIM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDLIM1 gene promoter:

Genomic Locations for PDLIM1 Gene

Genomic Locations for PDLIM1 Gene
chr10:95,237,568-95,291,148
(GRCh38/hg38)
Size:
53,581 bases
Orientation:
Minus strand
chr10:96,997,329-97,050,781
(GRCh37/hg19)

Genomic View for PDLIM1 Gene

Genes around PDLIM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDLIM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDLIM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDLIM1 Gene

Proteins for PDLIM1 Gene

  • Protein details for PDLIM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O00151-PDLI1_HUMAN
    Recommended name:
    PDZ and LIM domain protein 1
    Protein Accession:
    O00151
    Secondary Accessions:
    • B2RBS6
    • Q5VZH5
    • Q9BPZ9

    Protein attributes for PDLIM1 Gene

    Size:
    329 amino acids
    Molecular mass:
    36072 Da
    Quaternary structure:
    • Interacts with ACTN1, ACTN2 and ACTN4 (PubMed:10861853, PubMed:10753915, PubMed:11110697). Interacts with PDLIM4 (By similarity).

    Three dimensional structures from OCA and Proteopedia for PDLIM1 Gene

neXtProt entry for PDLIM1 Gene

Post-translational modifications for PDLIM1 Gene

Other Protein References for PDLIM1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PDLIM1 Gene

Domains & Families for PDLIM1 Gene

Gene Families for PDLIM1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for PDLIM1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PDLIM1: view

No data available for UniProtKB/Swiss-Prot for PDLIM1 Gene

Function for PDLIM1 Gene

Molecular function for PDLIM1 Gene

UniProtKB/Swiss-Prot Function:
Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the cytoskeleton (PubMed:10861853). Involved in assembly, disassembly and directioning of stress fibers in fibroblasts. Required for the localization of ACTN1 and PALLD to stress fibers. Required for cell migration and in maintaining cell polarity of fibroblasts (By similarity).

Phenotypes From GWAS Catalog for PDLIM1 Gene

Gene Ontology (GO) - Molecular Function for PDLIM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity IEA --
GO:0046872 metal ion binding IEA --
GO:0098641 cadherin binding involved in cell-cell adhesion IDA 25468996
genes like me logo Genes that share ontologies with PDLIM1: view
genes like me logo Genes that share phenotypes with PDLIM1: view

Animal Model Products

miRNA for PDLIM1 Gene

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDLIM1 Gene

Localization for PDLIM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDLIM1 Gene

Cytoplasm. Cytoplasm, cytoskeleton. Cytoplasm, myofibril, sarcomere, Z line. Note=Associates with actin stress fibers. {ECO:0000269 PubMed:11110697}.

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 PDLIM1 gene
Compartment Confidence
cytoskeleton 4
cytosol 3
nucleus 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (3)
  • Cell Junctions (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PDLIM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005667 transcription factor complex IEA --
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA --
GO:0005913 cell-cell adherens junction IDA 25468996
GO:0005925 focal adhesion HDA,IDA 21423176
genes like me logo Genes that share ontologies with PDLIM1: view

Pathways & Interactions for PDLIM1 Gene

SuperPathways for PDLIM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PDLIM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006979 response to oxidative stress TAS 8522188
GO:0098609 cell-cell adhesion IEA --
genes like me logo Genes that share ontologies with PDLIM1: view

No data available for Pathways by source and SIGNOR curated interactions for PDLIM1 Gene

Drugs & Compounds for PDLIM1 Gene

(1) Drugs for PDLIM1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PDLIM1: view

Transcripts for PDLIM1 Gene

Unigene Clusters for PDLIM1 Gene

PDZ and LIM domain 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDLIM1 Gene

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: - - - - - - - -
SP6: -
SP7: - - - - - -
SP8:

Relevant External Links for PDLIM1 Gene

GeneLoc Exon Structure for
PDLIM1
ECgene alternative splicing isoforms for
PDLIM1

Expression for PDLIM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDLIM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDLIM1 Gene

This gene is overexpressed in Muscle - Skeletal (x5.4).

Protein differential expression in normal tissues from HIPED for PDLIM1 Gene

This gene is overexpressed in Platelet (19.2), Bone marrow stromal cell (6.8), and Peripheral blood mononuclear cells (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDLIM1 Gene



Protein tissue co-expression partners for PDLIM1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDLIM1 Gene:

PDLIM1

SOURCE GeneReport for Unigene cluster for PDLIM1 Gene:

Hs.368525

mRNA Expression by UniProt/SwissProt for PDLIM1 Gene:

O00151-PDLI1_HUMAN
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.

Evidence on tissue expression from TISSUES for PDLIM1 Gene

  • Heart(4.6)
  • Pancreas(4.6)
  • Liver(4.5)
  • Blood(4.4)
  • Lung(3.9)
  • Nervous system(3.7)
  • Intestine(3.5)
  • Muscle(3)
  • Kidney(2.3)
  • Skin(2.3)
  • Eye(2.2)
genes like me logo Genes that share expression patterns with PDLIM1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PDLIM1 Gene

Orthologs for PDLIM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDLIM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDLIM1 33 34
  • 99.5 (n)
cow
(Bos Taurus)
Mammalia PDLIM1 33 34
  • 91.16 (n)
dog
(Canis familiaris)
Mammalia PDLIM1 33 34
  • 88.55 (n)
mouse
(Mus musculus)
Mammalia Pdlim1 33 16 34
  • 87.38 (n)
oppossum
(Monodelphis domestica)
Mammalia PDLIM1 34
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdlim1 33
  • 86.44 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PDLIM1 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDLIM1 33 34
  • 73.5 (n)
lizard
(Anolis carolinensis)
Reptilia PDLIM1 34
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdlim1 33
  • 71.08 (n)
MGC76041 33
zebrafish
(Danio rerio)
Actinopterygii pdlim1 33 34
  • 68.03 (n)
Dr.23376 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10330 33
Species where no ortholog for PDLIM1 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)
  • 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 PDLIM1 Gene

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

Paralogs for PDLIM1 Gene

Paralogs for PDLIM1 Gene

(3) SIMAP similar genes for PDLIM1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PDLIM1: view

Variants for PDLIM1 Gene

Sequence variations from dbSNP and Humsavar for PDLIM1 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs1000035864 -- 95,271,695(-) T/C coding_sequence_variant, intron_variant, synonymous_variant
rs1000083911 -- 95,281,062(-) C/T intron_variant
rs1000268790 -- 95,246,991(-) G/T intron_variant
rs1000339445 -- 95,261,283(-) T/C intron_variant
rs1000359280 -- 95,241,049(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PDLIM1 Gene

Variant ID Type Subtype PubMed ID
esv22688 CNV gain+loss 19812545
nsv1069957 CNV deletion 25765185
nsv1110852 OTHER inversion 24896259
nsv1113331 CNV deletion 24896259

Variation tolerance for PDLIM1 Gene

Residual Variation Intolerance Score: 27.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.06; 21.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDLIM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDLIM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDLIM1 Gene

Disorders for PDLIM1 Gene

MalaCards: The human disease database

(13) MalaCards diseases for PDLIM1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
supravalvular aortic stenosis
  • svas
hyperacusis
  • low tolerance to sound
williams-beuren syndrome
  • wbs
idiopathic infantile hypercalcemia
  • autosomal recessive infantile hypercalcemia
strabismus
  • strabismus, susceptibility to
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PDLIM1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PDLIM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDLIM1 Gene

Publications for PDLIM1 Gene

  1. Interaction of hCLIM1, an enigma family protein, with alpha-actinin 2. (PMID: 10861853) Kotaka M … Waye MM (Journal of cellular biochemistry 2000) 2 3 4 22 58
  2. CLP-36 PDZ-LIM protein associates with nonmuscle alpha-actinin-1 and alpha-actinin-4. (PMID: 10753915) Vallenius T … Mäkelä TP (The Journal of biological chemistry 2000) 3 4 22 58
  3. Human CLP36, 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. (PMID: 11110697) Bauer K … Siess W (Blood 2000) 3 4 22 58
  4. Characterization of the human 36-kDa carboxyl terminal LIM domain protein (hCLIM1). (PMID: 10022510) Kotaka M … Waye MM (Journal of cellular biochemistry 1999) 3 4 22 58
  5. Refined genomic localization and ethnic differences observed for the IBD5 association with Crohn's disease. (PMID: 17213842) Silverberg MS … NIDDK IBD Genetics Consortium (European journal of human genetics : EJHG 2007) 3 44 58

Products for PDLIM1 Gene

Sources for PDLIM1 Gene

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