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Aliases for LDB1 Gene

Aliases for LDB1 Gene

  • LIM Domain Binding 1 2 3 5
  • Carboxyl-Terminal LIM Domain-Binding Protein 2 3 4
  • Carboxy Terminal LIM Domain Protein 2 2 3
  • LIM Domain-Binding Factor CLIM2 3 4
  • Nuclear LIM Interactor 3 4
  • CLIM-2 3 4
  • CLIM2 3 4
  • LDB-1 3 4
  • LIM Domain-Binding Protein 1 3
  • LIM Domain-Binding Factor-1 3
  • HLdb1 4
  • NLI 3

External Ids for LDB1 Gene

Previous GeneCards Identifiers for LDB1 Gene

  • GC10M102760
  • GC10M103100
  • GC10M103997
  • GC10M103531
  • GC10M103857
  • GC10M097499

Summaries for LDB1 Gene

GeneCards Summary for LDB1 Gene

LDB1 (LIM Domain Binding 1) is a Protein Coding gene. Among its related pathways are Transcriptional misregulation in cancer. GO annotations related to this gene include protein homodimerization activity and enzyme binding. An important paralog of this gene is LDB2.

UniProtKB/Swiss-Prot for LDB1 Gene

  • Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors. May regulate the transcriptional activity of LIM-containing proteins by determining specific partner interactions. Plays a role in the development of interneurons and motor neurons in cooperation with LHX3 and ISL1. Acts synergistically with LHX1/LIM1 in axis formation and activation of gene expression. Acts with LMO2 in the regulation of red blood cell development, maintaining erythroid precursors in an immature state (By similarity).

Gene Wiki entry for LDB1 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LDB1 Gene

Genomics for LDB1 Gene

Regulatory Elements for LDB1 Gene

Enhancers for LDB1 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
GH10F101828 1.4 FANTOM5 ENCODE 48.1 +289.5 289470 4.4 HDGF PKNOX1 CREB3L1 ARID4B SIN3A ZNF2 ZNF302 ZNF416 ZNF143 ZNF207 LDB1 PPRC1 GBF1 ENSG00000272572 ARL3 HPS6 SUFU MGEA5 SFXN2 KCNIP2
GH10F102111 1.5 FANTOM5 ENCODE 23.7 +2.7 2720 11.6 HDGF PKNOX1 WRNIP1 ARID4B SIN3A FEZF1 ZNF2 YY1 CBX5 ZNF207 LDB1 HPS6 PPRC1 NOLC1 BORCS7 NFKB2 C10orf95 KCNIP2-AS1 KCNIP2 PSD
GH10F102772 1.4 FANTOM5 ENCODE 20.9 -658.1 -658146 11.7 PKNOX1 ZFP64 SIN3A YY1 ZNF121 GLIS2 FOS ZNF263 ZNF202 REST PDCD11 SFXN2 TAF5 ARL3 PPRC1 GBF1 LDB1 AS3MT INA BORCS7
GH10F101937 1.5 FANTOM5 Ensembl ENCODE 16 +180.5 180493 5.7 PKNOX1 SIN3A YBX1 ZNF121 KLF7 FOS ZNF263 SP3 MAFF GLIS1 HPS6 LDB1 GBF1 PPRC1 KCNIP2 NFKB2 NPM3 WBP1L ENSG00000222430 ENSG00000274742
GH10F102064 1.1 ENCODE 20.8 +54.8 54807 2.5 HDGF ARID4B SIN3A ZNF2 YY1 ZNF416 ZNF143 ZNF207 ZNF263 SP3 HPS6 LDB1 PPRC1 GBF1 SUFU KCNIP2 GC10P102070
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LDB1 on UCSC Golden Path with GeneCards custom track

Promoters for LDB1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000360706 153 2601 ATF1 PKNOX1 ARID4B SIN3A FEZF1 ZNF2 ETS1 GLIS2 FOS KDM4B

Genomic Location for LDB1 Gene

Chromosome:
10
Start:
102,106,558 bp from pter
End:
102,120,453 bp from pter
Size:
13,896 bases
Orientation:
Minus strand

Genomic View for LDB1 Gene

Genes around LDB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LDB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LDB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LDB1 Gene

Proteins for LDB1 Gene

  • Protein details for LDB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86U70-LDB1_HUMAN
    Recommended name:
    LIM domain-binding protein 1
    Protein Accession:
    Q86U70
    Secondary Accessions:
    • B4DUC4
    • O75479
    • O96010
    • Q1EQX1
    • Q9UGM4

    Protein attributes for LDB1 Gene

    Size:
    411 amino acids
    Molecular mass:
    46533 Da
    Quaternary structure:
    • Forms homodimers and heterodimers. Interacts with and activates LHX1/LIM1. Interacts with the LIM domains of ISL1 and LMO2. Can assemble in a complex with LMO2 and TAL1/SCL but does not interact with TAL1/SCL directly. Strongly interacts with the LIM2 domain of LMX1A and more weakly with the LIM1 domain. Homodimerization is not required for, and does not effect, LMX1A-binding. Component of a nuclear TAL-1 complex composed at least of CBFA2T3, LDB1, TAL1 and TCF3. Interacts with LHX6 and LHX9. At neuronal promoters, forms a complex with LHX3 involved in the specification of interneurons, in motor neurons, it is displaced by ISL1 to form a ternary complex in which ISL1 contacts both LHX3 and LDB1 (By similarity). Interacts with ESR1. Interacts with SLK; leading to negatively regulate SLK kinase activity (By similarity).
    Miscellaneous:
    • Acts as a negative coregulator of ESR1-mediated transcription in breast cancer cells.
    SequenceCaution:
    • Sequence=CAB45409.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LDB1 Gene

    Alternative splice isoforms for LDB1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LDB1 Gene

Post-translational modifications for LDB1 Gene

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

Other Protein References for LDB1 Gene

No data available for DME Specific Peptides for LDB1 Gene

Domains & Families for LDB1 Gene

Protein Domains for LDB1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LDB1 Gene

Graphical View of Domain Structure for InterPro Entry

Q86U70

UniProtKB/Swiss-Prot:

LDB1_HUMAN :
  • The dimerization domain is located in the N-terminus.
  • Belongs to the LDB family.
Domain:
  • The dimerization domain is located in the N-terminus.
Family:
  • Belongs to the LDB family.
genes like me logo Genes that share domains with LDB1: view

No data available for Gene Families for LDB1 Gene

Function for LDB1 Gene

Molecular function for LDB1 Gene

GENATLAS Biochemistry:
LIM domain binding 1,predominantly expressed in heart,placenta,lung,liver,skeletal muscle,pancreas,with two alternative transcripts,involved in developmental processes,heterodimerizing with LMO1 in T cell acute leukemia with translocation t(11;14)(p15;q11)
UniProtKB/Swiss-Prot Function:
Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors. May regulate the transcriptional activity of LIM-containing proteins by determining specific partner interactions. Plays a role in the development of interneurons and motor neurons in cooperation with LHX3 and ISL1. Acts synergistically with LHX1/LIM1 in axis formation and activation of gene expression. Acts with LMO2 in the regulation of red blood cell development, maintaining erythroid precursors in an immature state (By similarity).

Gene Ontology (GO) - Molecular Function for LDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000989 transcription factor activity, transcription factor binding IEA --
GO:0001102 RNA polymerase II activating transcription factor binding IPI 16314316
GO:0001158 enhancer sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
genes like me logo Genes that share ontologies with LDB1: view
genes like me logo Genes that share phenotypes with LDB1: view

Animal Models for LDB1 Gene

MGI Knock Outs for LDB1:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LDB1 Gene

Localization for LDB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LDB1 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 LDB1 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for LDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IDA 20855495
GO:0005634 nucleus ISS --
GO:0005667 transcription factor complex IDA 16314316
GO:0031252 cell leading edge IEA,ISS --
GO:0043234 protein complex IEA,ISS --
genes like me logo Genes that share ontologies with LDB1: view

Pathways & Interactions for LDB1 Gene

genes like me logo Genes that share pathways with LDB1: view

Pathways by source for LDB1 Gene

1 KEGG pathway for LDB1 Gene

Gene Ontology (GO) - Biological Process for LDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000972 transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery IEA,ISS --
GO:0001702 gastrulation with mouth forming second IEA --
GO:0001942 hair follicle development IEA --
GO:0006351 transcription, DNA-templated NAS 12792813
GO:0006355 regulation of transcription, DNA-templated NAS 12792813
genes like me logo Genes that share ontologies with LDB1: view

No data available for SIGNOR curated interactions for LDB1 Gene

Transcripts for LDB1 Gene

Unigene Clusters for LDB1 Gene

LIM domain binding 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LDB1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b
SP1: - - -
SP2: - - -
SP3: - -
SP4:
SP5: -
SP6:

Relevant External Links for LDB1 Gene

GeneLoc Exon Structure for
LDB1
ECgene alternative splicing isoforms for
LDB1

Expression for LDB1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LDB1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LDB1 Gene

This gene is overexpressed in Fetal Brain (15.5), Pancreatic juice (15.1), Testis (10.8), and Fetal ovary (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LDB1 Gene



Protein tissue co-expression partners for LDB1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LDB1 Gene:

LDB1

SOURCE GeneReport for Unigene cluster for LDB1 Gene:

Hs.454418

mRNA Expression by UniProt/SwissProt for LDB1 Gene:

Q86U70-LDB1_HUMAN
Tissue specificity: Expressed in a wide range of adult tissues including brain, heart, skeletal muscle, colon, thymus, spleen, kidney, liver, small intestine, lung and peripheral blood leukocytes.
genes like me logo Genes that share expression patterns with LDB1: view

Primer Products

No data available for mRNA differential expression in normal tissues for LDB1 Gene

Orthologs for LDB1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LDB1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LDB1 34 35
  • 99.91 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LDB1 35
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LDB1 35
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LDB1 34 35
  • 96.43 (n)
cow
(Bos Taurus)
Mammalia LDB1 34 35
  • 95.8 (n)
rat
(Rattus norvegicus)
Mammalia Ldb1 34
  • 94.31 (n)
mouse
(Mus musculus)
Mammalia Ldb1 34 16 35
  • 94.22 (n)
chicken
(Gallus gallus)
Aves LDB1 34 35
  • 88.65 (n)
lizard
(Anolis carolinensis)
Reptilia LDB1 35
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ldb1 34
  • 82.93 (n)
Str.5983 34
African clawed frog
(Xenopus laevis)
Amphibia chi-prov 34
zebrafish
(Danio rerio)
Actinopterygii ldb1a 35
  • 93 (a)
OneToOne
ldb1b 34
  • 82.8 (n)
ldb1 34
fruit fly
(Drosophila melanogaster)
Insecta Chi 36 35
  • 61 (a)
worm
(Caenorhabditis elegans)
Secernentea ldb-1 35
  • 20 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 51 (a)
OneToMany
Species where no ortholog for LDB1 was found in the sources mined by GeneCards:
  • 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)
  • 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 LDB1 Gene

ENSEMBL:
Gene Tree for LDB1 (if available)
TreeFam:
Gene Tree for LDB1 (if available)

Paralogs for LDB1 Gene

Paralogs for LDB1 Gene

(1) SIMAP similar genes for LDB1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with LDB1: view

Variants for LDB1 Gene

Sequence variations from dbSNP and Humsavar for LDB1 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
VAR_036366 A colorectal cancer sample
rs1046399 -- 102,107,634(-) CCCTC(C/T)TCCCT intron-variant, utr-variant-3-prime
rs1109463 -- 102,114,681(+) ggggg(C/G)cgcgg intron-variant, utr-variant-5-prime
rs1109464 -- 102,114,262(+) CCCTT(C/T)AGGGA intron-variant
rs111361687 -- 102,118,806(+) GCTGG(G/T)AGAAA intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for LDB1 Gene

Variant ID Type Subtype PubMed ID
nsv1069961 CNV deletion 25765185
nsv1143514 CNV deletion 24896259

Variation tolerance for LDB1 Gene

Residual Variation Intolerance Score: 17.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.80; 16.82% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LDB1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LDB1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LDB1 Gene

Disorders for LDB1 Gene

Relevant External Links for LDB1

Genetic Association Database (GAD)
LDB1
Human Genome Epidemiology (HuGE) Navigator
LDB1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LDB1

No disorders were found for LDB1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LDB1 Gene

Publications for LDB1 Gene

  1. Genomic structure and chromosomal localization of the mouse LIM domain-binding protein 1 gene, Ldb1. (PMID: 9503020) Yamashita T. … Westphal H. (Genomics 1998) 2 3 22 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) 2 3 4 64
  3. Regulation of estrogen-dependent transcription by the LIM cofactors CLIM and RLIM in breast cancer. (PMID: 19117995) Johnsen S.A. … Bach I. (Cancer Res. 2009) 3 4 64
  4. Assembly of the oncogenic DNA-binding complex LMO2-Ldb1-TAL1-E12. (PMID: 17910069) Ryan D.P. … Matthews J.M. (Proteins 2008) 3 22 64
  5. Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes. (PMID: 18583962) Bhati M. … Matthews J.M. (EMBO J. 2008) 3 22 64

Products for LDB1 Gene

Sources for LDB1 Gene

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