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Aliases for LDB2 Gene

Aliases for LDB2 Gene

  • LIM Domain Binding 2 2 3 5
  • Carboxyl-Terminal LIM Domain-Binding Protein 1 3 4
  • LIM Domain-Binding Factor CLIM1 3 4
  • CLIM1 3 4
  • LDB-2 3 4
  • LIM Domain-Binding Protein 2 3
  • LIM Domain-Binding Factor-2 3
  • LIM Binding Domain 2 3
  • CLIM-1 4
  • LDB1 3

External Ids for LDB2 Gene

Previous GeneCards Identifiers for LDB2 Gene

  • GC04M016318
  • GC04M016191
  • GC04M016254
  • GC04M016179
  • GC04M015852

Summaries for LDB2 Gene

Entrez Gene Summary for LDB2 Gene

  • The protein encoded by this gene belongs to the LIM-domain binding family. Members of this family are characterized by a conserved nuclear localization sequence, an amino-terminal homodimerization domain and a carboxy-terminal LIM interaction domain. These proteins function as adapter molecules to allow assembly of transcriptional regulatory complexes. Genetic association studies suggest functions for this gene in rhegmatogenous retinal detachment and coronary artery disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

GeneCards Summary for LDB2 Gene

LDB2 (LIM Domain Binding 2) is a Protein Coding gene. Among its related pathways are Ectoderm Differentiation. Gene Ontology (GO) annotations related to this gene include enzyme binding and transcription factor activity, transcription factor binding. An important paralog of this gene is LDB1.

UniProtKB/Swiss-Prot for LDB2 Gene

  • Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors.

Gene Wiki entry for LDB2 Gene

Additional gene information for LDB2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LDB2 Gene

Genomics for LDB2 Gene

GeneHancer (GH) Regulatory Elements for LDB2 Gene

Promoters and enhancers for LDB2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J016892 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 656.1 +2.7 2749 7.1 MXI1 MAX SIN3A RAD21 YY1 SP1 POLR2A POU5F1 LDB2 MED28 GC04P016883
GH04J016843 Enhancer 0.9 Ensembl ENCODE 11.1 +53.3 53345 3.1 TFAP4 USF1 FOXA2 ZNF384 RAD21 YY1 POLR2A FOS GMEB2 SP5 LDB2 GC04P016874 GC04M016735
GH04J016890 Enhancer 0.7 FANTOM5 Ensembl ENCODE 9 +7.9 7931 1.1 LDB2 GC04P016883
GH04J016917 Enhancer 0.5 ENCODE dbSUPER 12.6 -20.0 -20033 1.9 NANOG LDB2 GC04M016908 GC04P016943
GH04J016969 Enhancer 0.6 ENCODE 10.3 -71.2 -71161 1.1 SOX5 SOX13 FOXA2 RXRA SAP130 RARA SKI SP1 CEBPA TCF7 LDB2 GC04P016966 GC04M016989
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LDB2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LDB2 gene promoter:
  • Pax-4a
  • AML1a
  • NCX
  • GATA-2
  • GATA-1
  • GATA-3
  • POU3F2 (N-Oct-5b)
  • POU3F2 (N-Oct-5a)
  • POU3F2

Genomic Locations for LDB2 Gene

Genomic Locations for LDB2 Gene
397,276 bases
Minus strand
397,269 bases
Minus strand

Genomic View for LDB2 Gene

Genes around LDB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LDB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LDB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LDB2 Gene

Proteins for LDB2 Gene

  • Protein details for LDB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    LIM domain-binding protein 2
    Protein Accession:
    Secondary Accessions:
    • O60619
    • O75480

    Protein attributes for LDB2 Gene

    373 amino acids
    Molecular mass:
    42793 Da
    Quaternary structure:
    • Interacts with LHX9 (By similarity). Interacts with SLK; leading to negatively regulate SLK kinase activity (By similarity).

    Alternative splice isoforms for LDB2 Gene


neXtProt entry for LDB2 Gene

Post-translational modifications for LDB2 Gene

  • Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LDB2 Gene

Domains & Families for LDB2 Gene

Gene Families for LDB2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LDB2 Gene


Suggested Antigen Peptide Sequences for LDB2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the LDB family.
  • Belongs to the LDB family.
genes like me logo Genes that share domains with LDB2: view

Function for LDB2 Gene

Molecular function for LDB2 Gene

UniProtKB/Swiss-Prot Function:
Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors.
GENATLAS Biochemistry:
LIM domain binding 2,involved in developmental processes

Phenotypes From GWAS Catalog for LDB2 Gene

Gene Ontology (GO) - Molecular Function for LDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000989 transcription factor activity, transcription factor binding IBA --
GO:0001102 RNA polymerase II activating transcription factor binding IBA --
GO:0003712 transcription coregulator activity TAS 9880598
GO:0005515 protein binding IPI 11882901
GO:0019899 enzyme binding IEA --
genes like me logo Genes that share ontologies with LDB2: view
genes like me logo Genes that share phenotypes with LDB2: view

Animal Models for LDB2 Gene

MGI Knock Outs for LDB2:

Animal Model Products

  • Taconic Biosciences Mouse Models for LDB2

miRNA for LDB2 Gene

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LDB2 Gene

Localization for LDB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LDB2 Gene

Subcellular locations from

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 LDB2 gene
Compartment Confidence
nucleus 5
plasma membrane 4
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleus (3)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 9853615
GO:0005667 transcription factor complex IEA --
GO:0005730 nucleolus IDA --
GO:0005886 plasma membrane IDA --
GO:0031252 cell leading edge IEA,ISS --
genes like me logo Genes that share ontologies with LDB2: view

Pathways & Interactions for LDB2 Gene

SuperPathway Contained pathways
1 Ectoderm Differentiation
genes like me logo Genes that share pathways with LDB2: view

Pathways by source for LDB2 Gene

1 BioSystems pathway for LDB2 Gene

Gene Ontology (GO) - Biological Process for LDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IBA --
GO:0001942 hair follicle development IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IBA --
GO:0010669 epithelial structure maintenance IEA --
genes like me logo Genes that share ontologies with LDB2: view

No data available for SIGNOR curated interactions for LDB2 Gene

Drugs & Compounds for LDB2 Gene

No Compound Related Data Available

Transcripts for LDB2 Gene

Unigene Clusters for LDB2 Gene

LIM domain binding 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LDB2 Gene

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

Relevant External Links for LDB2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LDB2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LDB2 Gene

Protein differential expression in normal tissues from HIPED for LDB2 Gene

This gene is overexpressed in Fetal testis (66.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LDB2 Gene

Protein tissue co-expression partners for LDB2 Gene

NURSA nuclear receptor signaling pathways regulating expression of LDB2 Gene:


SOURCE GeneReport for Unigene cluster for LDB2 Gene:


Evidence on tissue expression from TISSUES for LDB2 Gene

  • Nervous system(5)
  • Lung(4.4)
genes like me logo Genes that share expression patterns with LDB2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LDB2 Gene

Orthologs for LDB2 Gene

This gene was present in the common ancestor of animals.

Orthologs for LDB2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LDB2 34 33
  • 99.37 (n)
(Ornithorhynchus anatinus)
Mammalia LDB2 34
  • 98 (a)
(Monodelphis domestica)
Mammalia LDB2 34
  • 97 (a)
(Canis familiaris)
Mammalia LDB2 34 33
  • 94.44 (n)
(Rattus norvegicus)
Mammalia Ldb2 33
  • 93.83 (n)
(Bos Taurus)
Mammalia LDB2 34 33
  • 93.6 (n)
(Mus musculus)
Mammalia Ldb2 16 34 33
  • 92.76 (n)
(Gallus gallus)
Aves LDB2 34 33
  • 87.42 (n)
(Anolis carolinensis)
Reptilia LDB2 34
  • 95 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ldb2 33
  • 82.39 (n)
(Danio rerio)
Actinopterygii ldb2a 34 33
  • 77.81 (n)
ldb2b 34
  • 67 (a)
ldb2 33
fruit fly
(Drosophila melanogaster)
Insecta Chi 35 33
  • 66.26 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004691 33
  • 65.93 (n)
(Caenorhabditis elegans)
Secernentea ldb-1 34 33
  • 49.52 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
Species where no ortholog for LDB2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 LDB2 Gene

Gene Tree for LDB2 (if available)
Gene Tree for LDB2 (if available)
Evolutionary constrained regions (ECRs) for LDB2: view image

Paralogs for LDB2 Gene

Paralogs for LDB2 Gene

(1) SIMAP similar genes for LDB2 Gene using alignment to 9 proteins:

  • B7Z2D3_HUMAN
  • E7EX95_HUMAN
  • G5E9Y7_HUMAN
  • H0YA09_HUMAN
  • Q4W5E7_HUMAN
genes like me logo Genes that share paralogs with LDB2: view

Variants for LDB2 Gene

Sequence variations from dbSNP and Humsavar for LDB2 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000005978 -- 16,775,610(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000025497 -- 16,622,522(-) A/G genic_downstream_transcript_variant, intron_variant
rs1000031377 -- 16,883,963(-) T/A genic_upstream_transcript_variant, intron_variant
rs1000031502 -- 16,858,330(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000032669 -- 16,581,158(-) T/G genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LDB2 Gene

Variant ID Type Subtype PubMed ID
esv1009687 CNV deletion 20482838
esv1074354 CNV deletion 17803354
esv1978042 CNV deletion 18987734
esv2595356 CNV deletion 19546169
esv2661262 CNV deletion 23128226
esv2671328 CNV deletion 23128226
esv2727231 CNV deletion 23290073
esv2727232 CNV deletion 23290073
esv2727233 CNV deletion 23290073
esv3599761 CNV loss 21293372
esv3599762 CNV loss 21293372
esv3599766 CNV loss 21293372
esv4963 CNV loss 18987735
nsv1074157 CNV deletion 25765185
nsv1114490 CNV deletion 24896259
nsv1114491 CNV deletion 24896259
nsv1121624 CNV deletion 24896259
nsv1143282 CNV deletion 24896259
nsv1147879 CNV deletion 26484159
nsv291652 CNV deletion 16902084
nsv292768 CNV deletion 16902084
nsv293129 CNV deletion 16902084
nsv4247 CNV insertion 18451855
nsv4248 CNV deletion 18451855
nsv4249 CNV insertion 18451855
nsv470018 CNV gain 18288195
nsv527861 CNV gain 19592680
nsv593780 CNV loss 21841781
nsv954409 CNV deletion 24416366

Variation tolerance for LDB2 Gene

Residual Variation Intolerance Score: 14.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.35; 7.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LDB2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LDB2 Gene

Disorders for LDB2 Gene

Additional Disease Information for LDB2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for LDB2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LDB2 Gene

Publications for LDB2 Gene

  1. Cloning and chromosomal localization of two novel human genes encoding LIM-domain binding factors CLIM1 and CLIM2/LDB1/NLI. (PMID: 9799849) Semina EV … Murray JC (Mammalian genome : official journal of the International Mammalian Genome Society 1998) 3 4 22 58
  2. Selection system for genes encoding nuclear-targeted proteins. (PMID: 9853615) Ueki N … Muramatsu M (Nature biotechnology 1998) 2 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Lhx9: a novel LIM-homeodomain gene expressed in the developing forebrain. (PMID: 9880598) Rétaux S … Besson MJ (The Journal of neuroscience : the official journal of the Society for Neuroscience 1999) 2 3 58

Products for LDB2 Gene

Sources for LDB2 Gene

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