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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. Diseases associated with LDB2 include Retinal Detachment and Artery Disease. Among its related pathways are Ectoderm Differentiation. 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

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

Genomics for LDB2 Gene

Regulatory Elements for LDB2 Gene

Enhancers for LDB2 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
GH04G016843 1 Ensembl ENCODE 11.1 +53.3 53345 3.1 CTCF TFAP4 FOXA2 ZNF384 CHD7 RAD21 YY1 FOS ZNF652 GMEB2 LDB2 GC04P016874 GC04M016735
GH04G016917 0.6 ENCODE dbSUPER 12.6 -20.0 -20033 1.9 CHD7 LDB2 GC04M016908 GC04P016943
GH04G016892 1.2 Ensembl ENCODE dbSUPER 6.1 +2.7 2749 7.1 MXI1 MAX RBBP5 RAD21 YY1 HDAC2 POLR2A SMARCA4 SMC3 POU5F1 LDB2 MED28 GC04P016883
GH04G016967 0.7 ENCODE 10.3 -69.2 -69232 1.2 SOX5 SOX13 FOXA2 NFIA HLF RARA TBX3 CEBPA TCF7 HNF4A LDB2 GC04P016966 GC04M016989
GH04G016890 0.8 FANTOM5 Ensembl ENCODE 9 +7.9 7932 1.1 LDB2 GC04P016883
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LDB2 on UCSC Golden Path with GeneCards custom track

Promoters for LDB2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000166357 1208 2800 MXI1 MAX RBBP5 RAD21 YY1 HDAC2 POLR2A SMARCA4 POU5F1 SMC3

Genomic Location for LDB2 Gene

Chromosome:
4
Start:
16,501,534 bp from pter
End:
16,898,809 bp from pter
Size:
397,276 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).

    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

Protein Domains for LDB2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LDB2 Gene

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

No data available for Gene Families for LDB2 Gene

Function for LDB2 Gene

Molecular function for LDB2 Gene

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

Gene Ontology (GO) - Molecular Function for LDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003712 transcription cofactor activity TAS 9880598
GO:0005515 protein binding IPI 15231748
GO:0019899 enzyme binding IEA --
GO:0030274 LIM domain binding ISS,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

Inhibitory RNA Products

Flow Cytometry 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

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

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 ISS,IEA --
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:0001942 hair follicle development IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter IEA --
GO:0010669 epithelial structure maintenance IEA --
GO:0030334 regulation of cell migration IEA,ISS --
GO:0035019 somatic stem cell population maintenance IEA --
genes like me logo Genes that share ontologies with LDB2: view

No data available for SIGNOR curated interactions for LDB2 Gene

Transcripts for LDB2 Gene

Unigene Clusters for LDB2 Gene

LIM domain binding 2:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry 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
LDB2
ECgene alternative splicing isoforms for
LDB2

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, PaxDb, and MOPED for LDB2 Gene



Protein tissue co-expression partners for LDB2 Gene

NURSA nuclear receptor signaling pathways regulating expression of LDB2 Gene:

LDB2

SOURCE GeneReport for Unigene cluster for LDB2 Gene:

Hs.714330

Evidence on tissue expression from TISSUES for LDB2 Gene

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

Primer Products

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 34 35
  • 99.37 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LDB2 35
  • 98 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LDB2 35
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LDB2 34 35
  • 94.44 (n)
rat
(Rattus norvegicus)
Mammalia Ldb2 34
  • 93.83 (n)
cow
(Bos Taurus)
Mammalia LDB2 34 35
  • 93.6 (n)
mouse
(Mus musculus)
Mammalia Ldb2 34 16 35
  • 92.76 (n)
chicken
(Gallus gallus)
Aves LDB2 34 35
  • 87.42 (n)
lizard
(Anolis carolinensis)
Reptilia LDB2 35
  • 95 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ldb2 34
  • 82.39 (n)
zebrafish
(Danio rerio)
Actinopterygii ldb2a 34 35
  • 77.81 (n)
ldb2b 35
  • 67 (a)
OneToMany
ldb2 34
fruit fly
(Drosophila melanogaster)
Insecta Chi 36 34
  • 66.26 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004691 34
  • 65.93 (n)
worm
(Caenorhabditis elegans)
Secernentea ldb-1 34 35
  • 49.52 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 53 (a)
OneToMany
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

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

Paralogs for LDB2 Gene

Paralogs for LDB2 Gene

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

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 Sequence Context AA Info Type
rs1000005978 -- 16,775,610(+) TCCCT(A/G)TTCTC intron-variant
rs1000025497 -- 16,622,522(+) AGAAG(A/G)ACAAC intron-variant
rs1000031377 -- 16,883,963(+) AAAAA(A/T)AGCTC intron-variant
rs1000031502 -- 16,858,330(+) AATGC(A/G)AGGAA intron-variant
rs1000032669 -- 16,581,158(+) TGCTC(G/T)ACCCA 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)

Relevant External Links for LDB2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LDB2

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

Disorders for LDB2 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
retinal detachment
artery disease
  • arteriopathic disease
- elite association - COSMIC cancer census association via MalaCards
Search LDB2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LDB2

Genetic Association Database (GAD)
LDB2
Human Genome Epidemiology (HuGE) Navigator
LDB2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LDB2
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.-A. (Nat. Biotechnol. 1998) 2 3 4 64
  2. Cloning and chromosomal localization of two novel human genes encoding LIM-domain binding factors CLIM1 and CLIM2/LDB1/NLI. (PMID: 9799849) Semina E.V. … Murray J.C. (Mamm. Genome 1998) 3 4 22 64
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Lhx9: a novel LIM-homeodomain gene expressed in the developing forebrain. (PMID: 9880598) RActaux S. … Besson M.J. (J. Neurosci. 1999) 2 3 64

Products for LDB2 Gene

Sources for LDB2 Gene

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