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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 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 artery disease. Among its related pathways are Transcriptional misregulation in cancer. 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 Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LDB2 Gene

Genomics for LDB2 Gene

Regulatory Elements for LDB2 Gene

Promoters for LDB2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around LDB2 on UCSC Golden Path with GeneCards custom track

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

Proteomics data for LDB2 Gene at MOPED

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.
genes like me logo Genes that share phenotypes with LDB2: view

Animal Models for LDB2 Gene

MGI Knock Outs for LDB2:

Animal Model Products

miRNA for LDB2 Gene

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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
Jensen Localization Image for LDB2 Gene COMPARTMENTS Subcellular localization image for LDB2 gene
Compartment Confidence
nucleus 5
cytosol 3

No data available for Gene Ontology (GO) - Cellular Components for LDB2 Gene

Pathways & Interactions for LDB2 Gene

genes like me logo Genes that share pathways with LDB2: view

Pathways by source for LDB2 Gene

1 KEGG 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:0010669 epithelial structure maintenance IEA --
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

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:

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 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



SOURCE GeneReport for Unigene cluster for LDB2 Gene Hs.714330

genes like me logo Genes that share expression patterns with LDB2: view

Protein tissue co-expression partners for LDB2 Gene

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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
cow
(Bos Taurus)
Mammalia LDB2 35
  • 93.6 (n)
  • 98.65 (a)
LDB2 36
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LDB2 35
  • 94.44 (n)
  • 97.04 (a)
LDB2 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ldb2 35
  • 92.76 (n)
  • 97.59 (a)
Ldb2 16
Ldb2 36
  • 98 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LDB2 35
  • 99.37 (n)
  • 99.73 (a)
LDB2 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ldb2 35
  • 93.83 (n)
  • 98.39 (a)
oppossum
(Monodelphis domestica)
Mammalia LDB2 36
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LDB2 36
  • 98 (a)
OneToOne
chicken
(Gallus gallus)
Aves LDB2 35
  • 87.42 (n)
  • 97.3 (a)
LDB2 36
  • 88 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LDB2 36
  • 95 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ldb2 35
  • 82.39 (n)
  • 93.3 (a)
zebrafish
(Danio rerio)
Actinopterygii ldb2 35
ldb2a 35
  • 77.81 (n)
  • 88.59 (a)
ldb2a 36
  • 73 (a)
OneToMany
ldb2b 36
  • 67 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Chi 37
  • 62 (a)
Chi 35
  • 66.26 (n)
  • 69.42 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004691 35
  • 65.93 (n)
  • 74.53 (a)
worm
(Caenorhabditis elegans)
Secernentea ldb-1 35
  • 49.52 (n)
  • 40.58 (a)
ldb-1 36
  • 19 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 53 (a)
OneToMany
Species with no ortholog for LDB2:
  • 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
rs49969 -- 16,830,189(+) ccaaa(C/T)ctcat intron-variant
rs108720 -- 16,762,921(-) CTCAC(A/G)TATGT intron-variant
rs114429 -- 16,841,157(-) TTTTT(C/T)TACAG intron-variant
rs114430 -- 16,841,057(-) AATTT(C/T)ACAGG intron-variant
rs123043 -- 16,822,277(-) CAATG(G/T)TCTAT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv527861 CNV Gain 19592680
nsv4247 CNV Insertion 18451855
nsv4248 CNV Loss 18451855
esv2661262 CNV Deletion 23128226
esv2727231 CNV Deletion 23290073
nsv4249 CNV Insertion 18451855
esv2595356 CNV Deletion 19546169
esv2727232 CNV Deletion 23290073
esv1978042 CNV Deletion 18987734
esv2671328 CNV Deletion 23128226
esv4963 CNV Deletion 18987735
nsv291652 CNV Loss 16902084
esv1009687 CNV Deletion 20482838
esv1074354 CNV Deletion 17803354
esv2727233 CNV Deletion 23290073
nsv470018 CNV Gain 18288195
nsv292768 CNV Loss 16902084
nsv293129 CNV Loss 16902084

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

HapMap Linkage Disequilibrium report
LDB2

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

Disorders for LDB2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LDB2 Gene - From: GeneCards

Disorder Aliases PubMed IDs
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 67
  2. Lhx9: a novel LIM-homeodomain gene expressed in the developing forebrain. (PMID: 9880598) RActaux S. … Besson M.J. (J. Neurosci. 1999) 2 3
  3. 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 23
  4. Lim domain binding 2: a key driver of transendothelial migration of leukocytes and atherosclerosis. (PMID: 24925974) Shang M.M. … BjAPrkegren J.L. (Arterioscler. Thromb. Vasc. Biol. 2014) 3
  5. Generalization of Variants Identified by Genome-Wide Association Studies for Electrocardiographic Traits in African Americans. (PMID: 23534349) Jeff J.M. … Crawford D.C. (Ann. Hum. Genet. 2013) 3

Products for LDB2 Gene

Sources for LDB2 Gene

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