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Aliases for LDB3 Gene

Aliases for LDB3 Gene

  • LIM Domain Binding 3 2 3
  • ZASP 3 4 6
  • Cardiomyopathy, Dilated 1C (Autosomal Dominant) 2 3
  • Z-Band Alternatively Spliced PDZ Motif Protein 2 3
  • Z-Band Alternatively Spliced PDZ-Motif Protein 3 4
  • Protein Cypher 3 4
  • CYPHER 3 6
  • CMD1C 3 6
  • LVNC3 3 6
  • MFM4 3 6
  • LIM Domain-Binding Protein 3 3
  • PDZ And LIM Domain 6 3
  • KIAA01613 6
  • KIAA0613 4
  • Cypher 2
  • Oracle 2
  • LDB3Z1 3
  • LDB3Z4 3
  • ORACLE 3
  • PDLIM6 3
  • CMPD3 3

External Ids for LDB3 Gene

Previous Symbols for LDB3 Gene

  • CMD1C

Summaries for LDB3 Gene

Entrez Gene Summary for LDB3 Gene

  • This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. The protein encoded by this gene interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also interacts with all three members of the myozenin family. Mutations in this gene have been associated with myofibrillar myopathy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding different isoforms have been identified; all isoforms have N-terminal PDZ domains while only longer isoforms (1, 2 and 5) have C-terminal LIM domains. [provided by RefSeq, Jan 2010]

GeneCards Summary for LDB3 Gene

LDB3 (LIM Domain Binding 3) is a Protein Coding gene. Diseases associated with LDB3 include myopathy, myofibrillar, 4 and cardiomyopathy, dilated 1c. GO annotations related to this gene include cytoskeletal protein binding and muscle alpha-actinin binding. An important paralog of this gene is LIMS1.

UniProtKB/Swiss-Prot for LDB3 Gene

  • May function as an adapter in striated muscle to couple protein kinase C-mediated signaling via its LIM domains to the cytoskeleton.

Gene Wiki entry for LDB3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LDB3 Gene

Genomics for LDB3 Gene

Genomic Location for LDB3 Gene

86,666,717 bp from pter
86,736,072 bp from pter
69,356 bases
Plus strand

Genomic View for LDB3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LDB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LDB3 Gene

Regulatory Elements for LDB3 Gene

Proteins for LDB3 Gene

  • Protein details for LDB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    LIM domain-binding protein 3
    Protein Accession:
    Secondary Accessions:
    • A2TDB7
    • A6NIV4
    • B4E3K3
    • Q5K6N9
    • Q5K6P0
    • Q5K6P1
    • Q96FH2
    • Q9Y4Z3
    • Q9Y4Z4
    • Q9Y4Z5

    Protein attributes for LDB3 Gene

    727 amino acids
    Molecular mass:
    77135 Da
    Quaternary structure:
    • Interacts via its LIM domains with various PKC isoforms (By similarity). Interacts via its PDZ domain with the ACTN2 C-terminal region. Interacts with MYOZ1, MYOZ2 and MYOZ3.
    • Sequence=BAA31588.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LDB3 Gene

    Alternative splice isoforms for LDB3 Gene

neXtProt entry for LDB3 Gene

Proteomics data for LDB3 Gene at MOPED

Post-translational modifications for LDB3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LDB3 Gene

Domains for LDB3 Gene

Protein Domains for LDB3 Gene

Suggested Antigen Peptide Sequences for LDB3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 3 LIM zinc-binding domains.:
    • O75112
  • Contains 1 PDZ (DHR) domain.:
    • O75112
genes like me logo Genes that share domains with LDB3: view

No data available for Gene Families for LDB3 Gene

Function for LDB3 Gene

Molecular function for LDB3 Gene

UniProtKB/Swiss-Prot Function: May function as an adapter in striated muscle to couple protein kinase C-mediated signaling via its LIM domains to the cytoskeleton.

Gene Ontology (GO) - Molecular Function for LDB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005080 protein kinase C binding IEA --
GO:0005515 protein binding IPI 10427098
GO:0008092 cytoskeletal protein binding IPI 17987659
GO:0008270 zinc ion binding IEA --
GO:0051371 muscle alpha-actinin binding IEA --
genes like me logo Genes that share ontologies with LDB3: view
genes like me logo Genes that share phenotypes with LDB3: view

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for LDB3 Gene

Localization for LDB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LDB3 Gene

Cytoplasm, perinuclear region. Cell projection, pseudopodium. Cytoplasm, cytoskeleton. Cytoplasm, myofibril, sarcomere, Z line. Note=Localized to the cytoplasm around nuclei and pseudopodia of undifferentiated cells and detected throughout the myotubes of differentiated cells. Colocalizes with ACTN2 at the Z-lines.

Subcellular locations from

Jensen Localization Image for LDB3 Gene COMPARTMENTS Subcellular localization image for LDB3 gene
Compartment Confidence
cytoskeleton 5
cytosol 3
nucleus 3
mitochondrion 2

Gene Ontology (GO) - Cellular Components for LDB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005856 cytoskeleton IDA 10427098
GO:0030018 Z disc IDA 10427098
GO:0031143 pseudopodium IEA --
GO:0042995 cell projection --
GO:0048471 perinuclear region of cytoplasm IEA --
genes like me logo Genes that share ontologies with LDB3: view

Pathways for LDB3 Gene

SuperPathways for LDB3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LDB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045214 sarcomere organization IEA --
genes like me logo Genes that share ontologies with LDB3: view

No data available for Pathways by source for LDB3 Gene

Transcripts for LDB3 Gene

Unigene Clusters for LDB3 Gene

LIM domain binding 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LDB3 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b · 3c ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15a · 15b ^
SP2: - -
SP3: - - - -
SP4: - - - - -
SP5: - - - - - - - -
SP7: -
SP11: - - - - -

ExUns: 16

Relevant External Links for LDB3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LDB3 Gene

mRNA expression in normal human tissues for LDB3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LDB3 Gene

This gene is overexpressed in Heart - Left Ventricle (17.3), Muscle - Skeletal (14.6), and Heart - Atrial Appendage (9.7).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for LDB3 Gene

SOURCE GeneReport for Unigene cluster for LDB3 Gene Hs.657271

mRNA Expression by UniProt/SwissProt for LDB3 Gene

Tissue specificity: Expressed primarily in skeletal muscle and to a lesser extent in heart. Also detected in brain and placenta.
genes like me logo Genes that share expressions with LDB3: view

Orthologs for LDB3 Gene

This gene was present in the common ancestor of animals.

Orthologs for LDB3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LDB3 36
  • 100 (a)
(Bos Taurus)
Mammalia LDB3 36
  • 91 (a)
(Canis familiaris)
Mammalia LDB3 35
  • 82.2 (n)
  • 84.09 (a)
LDB3 36
  • 72 (a)
(Mus musculus)
Mammalia Ldb3 35
  • 82.47 (n)
  • 86.53 (a)
Ldb3 16
Ldb3 36
  • 82 (a)
(Monodelphis domestica)
Mammalia LDB3 36
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia LDB3 36
  • 76 (a)
(Gallus gallus)
Aves LDB3 36
  • 60 (a)
LOC101750026 35
  • 78.32 (n)
  • 85.31 (a)
(Anolis carolinensis)
Reptilia LDB3 36
  • 59 (a)
African clawed frog
(Xenopus laevis)
Amphibia ldb3-prov 35
tropical clawed frog
(Silurana tropicalis)
Amphibia MGC75668 35
(Danio rerio)
Actinopterygii ldb3b 36
  • 52 (a)
fruit fly
(Drosophila melanogaster)
Insecta Zasp52 36
  • 11 (a)
(Caenorhabditis elegans)
Secernentea alp-1 36
  • 14 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 35 (a)
-- 36
  • 40 (a)
Species with no ortholog for LDB3:
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 LDB3 Gene

Gene Tree for LDB3 (if available)
Gene Tree for LDB3 (if available)

Paralogs for LDB3 Gene

Selected SIMAP similar genes for LDB3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with LDB3: view

Variants for LDB3 Gene

Sequence variations from dbSNP and Humsavar for LDB3 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type MAF
rs1129720 -- 86,734,559(+) TTATG(G/T)GAATG utr-variant-3-prime
rs1140171 -- 86,687,120(+) GCCCT(A/G)TCGGC synonymous-codon, reference, intron-variant
rs1140172 -- 86,687,146(+) GGTGA(A/C)GGGGC reference, missense, intron-variant
rs1578895 -- 86,686,876(+) CAAGG(A/T)TTTTC intron-variant
rs1806471 -- 86,673,560(-) TCCCC(A/G)TGGTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LDB3 Gene

Variant ID Type Subtype PubMed ID
nsv467411 CNV Loss 19166990
nsv470968 CNV Loss 18288195
dgv116n27 CNV Loss 19166990
dgv793n71 CNV Gain 21882294
nsv524269 CNV Loss 19592680
nsv895836 CNV Loss 21882294
nsv517139 CNV Gain+Loss 19592680
nsv895857 CNV Loss 21882294
nsv520811 CNV Loss 19592680
nsv519805 CNV Loss 19592680

Relevant External Links for LDB3 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LDB3 Gene

Disorders for LDB3 Gene

(2) OMIM Diseases for LDB3 Gene (605906)


  • Cardiomyopathy, dilated 1C (CMD1C) [MIM:601493]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. Cardiomyopathy dilated type 1C is associated with left ventricular non-compaction in some patients. Left ventricular non-compaction is characterized by numerous prominent trabeculations and deep intertrabecular recesses in hypertrophied and hypokinetic segments of the left ventricle. {ECO:0000269 PubMed:14660611, ECO:0000269 PubMed:14662268}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Left ventricular non-compaction 3 (LVNC3) [MIM:601493]: A disease due to an arrest of myocardial morphogenesis. It is characterized by a hypertrophic left ventricle with deep trabeculations and with poor systolic function, with or without associated left ventricular dilation. In some cases, it is associated with other congenital heart anomalies. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Myopathy, myofibrillar, 4 (MFM4) [MIM:609452]: A neuromuscular disorder characterized by distal and proximal muscle weakness with signs of cardiomyopathy and neuropathy. Note=The disease is caused by mutations affecting the gene represented in this entry.

(4) University of Copenhagen DISEASES for LDB3 Gene

(1) Novoseek inferred disease relationships for LDB3 Gene

Disease -log(P) Hits PubMed IDs
myopathy 75.1 4

Relevant External Links for LDB3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with LDB3: view

Publications for LDB3 Gene

  1. ZASP: a new Z-band alternatively spliced PDZ-motif protein. (PMID: 10427098) Faulkner G. … Lanfranchi G. (J. Cell Biol. 1999) 2 3 4
  2. Mutations in Cypher/ZASP in patients with dilated cardiomyopathy and left ventricular non-compaction. (PMID: 14662268) Vatta M. … Towbin J.A. (J. Am. Coll. Cardiol. 2003) 2 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  4. Calsarcin-3, a novel skeletal muscle-specific member of the calsarcin family, interacts with multiple Z-disc proteins. (PMID: 11842093) Frey N. … Olson E.N. (J. Biol. Chem. 2002) 3 4
  5. Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9734811) Ishikawa K. … Ohara O. (DNA Res. 1998) 3 4

Products for LDB3 Gene

Sources for LDB3 Gene

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