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 studi... See more...

Aliases for LDB2 Gene

Aliases for LDB2 Gene

  • LIM Domain Binding 2 2 3 5
  • CLIM1 2 3 4
  • Carboxyl-Terminal LIM Domain-Binding Protein 1 3 4
  • LIM Domain-Binding Factor CLIM1 3 4
  • LIM Domain-Binding Protein 2 3 4
  • LDB-2 3 4
  • LDB1 2 3
  • LIM Domain-Binding Factor-2 3
  • LIM Binding Domain 2 3
  • CLIM-1 4
  • LDB2 5

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. Diseases associated with LDB2 include Retinal Detachment and Nail-Patella Syndrome. Among its related pathways are Ectoderm Differentiation. Gene Ontology (GO) annotations related to this gene include enzyme binding and obsolete transcription factor activity, transcription factor binding. An important paralog of this gene is LDB1.

UniProtKB/Swiss-Prot Summary for LDB2 Gene

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

Gene Wiki entry for LDB2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LDB2 Gene

Genomics for LDB2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LDB2 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
GH04J016892 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 606 +2.2 2164 8.3 POLR2A RAD21 YY1 CTCF MAFK SIN3A MAX SMARCA4 TAF1 SP1 LDB2 LOC107986188 lnc-TAPT1-6 MED28 lnc-QDPR-5 TAPT1
GH04J016843 Enhancer 1 Ensembl ENCODE CraniofacialAtlas 11.1 +53.1 53061 3.7 KDM1A POLR2A RXRB SP1 CEBPA CEBPB FOXA2 USF1 FOS YY1 LDB2 piR-50437-490 piR-48759-223 lnc-TAPT1-6 TAPT1
GH04J016969 Enhancer 0.8 Ensembl ENCODE 10.3 -71.1 -71149 1.1 RXRB CEBPA SOX13 TCF7 CEBPB FOXA2 FOSL2 SMAD4 HOMEZ HNF4A LDB2 RF00994-721 lnc-CLRN2-5 QDPR
GH04J016917 Enhancer 0.6 Ensembl ENCODE dbSUPER 12.6 -20.0 -20033 1.9 NANOG LDB2 MG828668-079 QDPR
GH04J016827 Enhancer 0.6 Ensembl 11 +70.6 70608 3.6 POLR2A SP1 YY1 ZBTB33 JUND NR2F2 HNF4A RXRA ATF2 FOXA1 LDB2 piR-48759-223 piR-50437-490 lnc-TAPT1-6 TAPT1
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LDB2

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

Genomic Locations for LDB2 Gene

Genomic Locations for LDB2 Gene
chr4:16,501,534-16,898,809
(GRCh38/hg38)
Size:
397,276 bases
Orientation:
Minus strand
chr4:16,503,164-16,900,432
(GRCh37/hg19)
Size:
397,269 bases
Orientation:
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:
    O43679-LDB2_HUMAN
    Recommended name:
    LIM domain-binding protein 2
    Protein Accession:
    O43679
    Secondary Accessions:
    • O60619
    • O75480

    Protein attributes for LDB2 Gene

    Size:
    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).
    Miscellaneous:
    • [Isoform 2]: Lacks LIM-binding domain.

    Alternative splice isoforms for LDB2 Gene

    UniProtKB/Swiss-Prot:

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

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

Protein Domains for LDB2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LDB2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ52487, highly similar to LIM domain-binding protein 2 (B7Z2D3_HUMAN)
  • LIM domain-binding factor CLIM1 (LDB2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O43679

UniProtKB/Swiss-Prot:

LDB2_HUMAN :
  • Belongs to the LDB family.
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:0001102 RNA polymerase II activating transcription factor binding IBA 21873635
GO:0003712 transcription coregulator activity IEA --
GO:0005515 protein binding IPI 15231748
GO:0019899 enzyme binding IEA --
GO:0030274 LIM domain binding IEA,ISS --
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LDB2

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

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 LDB2 gene
Compartment Confidence
nucleus 5
plasma membrane 4
cytosol 3
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleoplasm (3)
  • Plasma membrane (1)
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:0005654 nucleoplasm IDA --
GO:0005667 transcription factor complex IEA,IBA 21873635
GO:0005730 nucleolus IDA --
GO:0005886 plasma membrane IDA --
genes like me logo Genes that share ontologies with LDB2: view

Pathways & Interactions for LDB2 Gene

PathCards logo

SuperPathways 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 21873635
GO:0001942 hair follicle development IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IBA --
GO:0007399 nervous system development IBA 21873635
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

mRNA/cDNA for LDB2 Gene

4 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
16 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LDB2

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
LDB2

Expression for LDB2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LDB2

SOURCE GeneReport for Unigene cluster for LDB2 Gene:

Hs.714330

Evidence on tissue expression from TISSUES for LDB2 Gene

  • Nervous system(5)
  • Lung(4.5)
  • Heart(2.5)
  • Spleen(2.5)
  • Muscle(2.4)
  • Bone marrow(2.4)
  • Kidney(2.3)
  • Blood(2.3)
  • Liver(2.3)
  • Thyroid gland(2.1)
  • Skin(2)
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
Chimpanzee
(Pan troglodytes)
Mammalia LDB2 30 31
  • 99.37 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LDB2 31
  • 98 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LDB2 31
  • 97 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia LDB2 30 31
  • 94.44 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ldb2 30
  • 93.83 (n)
Cow
(Bos Taurus)
Mammalia LDB2 30 31
  • 93.6 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ldb2 30 17 31
  • 92.76 (n)
OneToOne
Chicken
(Gallus gallus)
Aves LDB2 30 31
  • 87.42 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LDB2 31
  • 95 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ldb2 30
  • 82.39 (n)
Zebrafish
(Danio rerio)
Actinopterygii ldb2a 30 31
  • 77.81 (n)
OneToMany
ldb2b 31
  • 67 (a)
OneToMany
ldb2 30
Fruit Fly
(Drosophila melanogaster)
Insecta Chi 30 32
  • 66.26 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004691 30
  • 65.93 (n)
Worm
(Caenorhabditis elegans)
Secernentea ldb-1 30 31
  • 49.52 (n)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 53 (a)
OneToMany
Species where no ortholog for LDB2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for LDB2 (if available)
TreeFam:
Gene Tree for LDB2 (if available)
Aminode:
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:

  • LDB2_HUMAN
  • B7Z2D3_HUMAN
  • D6RAT1_HUMAN
  • E7EX95_HUMAN
  • E9PFI4_HUMAN
  • E9PGU0_HUMAN
  • G5E9Y7_HUMAN
  • H0YA09_HUMAN
  • Q4W5E7_HUMAN
genes like me logo Genes that share paralogs with LDB2: view

Variants for LDB2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LDB2 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
784036 Benign: not provided 16,759,189(-) T/C NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for LDB2 Gene

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
LDB2

SNP Genotyping and Copy Number Assay Products

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

Disorders for LDB2 Gene

MalaCards: The human disease database

(7) MalaCards diseases for LDB2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
retinal detachment
  • retinal detachments
nail-patella syndrome
  • nps
spherocytosis, type 2
  • sph2
spherocytosis, type 4
  • sph4
spherocytosis, type 3
  • hs3
- elite association - COSMIC cancer census association via MalaCards
Search LDB2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LDB2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with LDB2: view

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

Publications for LDB2 Gene

  1. Selection system for genes encoding nuclear-targeted proteins. (PMID: 9853615) Ueki N … Muramatsu M (Nature biotechnology 1998) 2 3 4
  2. 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 23
  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 41
  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
  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

Products for LDB2 Gene

Sources for LDB2 Gene