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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
  • LIM Domain-Binding Protein 1 3 4
  • Nuclear LIM Interactor 3 4
  • CLIM-2 3 4
  • CLIM2 3 4
  • LDB-1 3 4
  • 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. Gene Ontology (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

Additional gene information for LDB1 Gene

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

Genomics for LDB1 Gene

GeneHancer (GH) Regulatory Elements for LDB1 Gene

Promoters and enhancers for LDB1 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
GH10J102111 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 623.6 +2.7 2719 11.6 HDGF ZFX ZNF652 CC2D1A SP1 CTCF ELF3 CBFA2T2 ZNF148 NKRF LDB1 HPS6 PPRC1 NFKB2 NOLC1 BORCS7 C10orf95 KCNIP2-AS1 KCNIP2 PSD
GH10J101828 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 91.9 +289.7 289671 4.8 MTA3 SP1 ZFX ZNF148 MLLT1 GTF2F1 ZNF687 ZSCAN21 MCM2 MAFK PPRC1 LDB1 GBF1 LZTS2 MRPL43 HPS6 NOLC1 SUFU ENSG00000272572 SLF2
GH10J101692 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 23.7 +425.7 425664 4 HDGF ELF3 ZFX NKRF POLR2A MLLT1 ZNF121 GTF2F1 ZNF687 ZSCAN21 FBXW4 PPRC1 GBF1 MRPL43 LDB1 ENSG00000272572 HPS6 OGA TWNK SLF2
GH10J101814 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 21.7 +303.3 303252 6.4 CC2D1A SP1 ELF3 SIX5 ZNF148 NKRF POLR2A MLLT1 ZNF121 CEBPG OGA KCNIP2-AS1 PPRC1 HPS6 LDB1 GBF1 MRPL43 TWNK SUFU NPM3
GH10J101224 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 20.7 +892.5 892499 6.5 SP1 ZSCAN21 ZBTB7A SP7 ZNF548 PRDM1 ZNF680 GLIS2 PKNOX1 ZBTB8A LBX1-AS1 LBX1 GC10M101227 PHBP9 PPRC1 LDB1 CHUK ENSG00000272572 ARMH3 HPS6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LDB1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LDB1 gene promoter:
  • AP-2alpha
  • CREB
  • deltaCREB
  • E47
  • Pax-5

Genomic Locations for LDB1 Gene

Genomic Locations for LDB1 Gene
chr10:102,106,558-102,120,453
(GRCh38/hg38)
Size:
13,896 bases
Orientation:
Minus strand
chr10:103,867,317-103,880,210
(GRCh37/hg19)
Size:
12,894 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

Gene Families for LDB1 Gene

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

Protein Domains for LDB1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LDB1 Gene

GenScript: Design optimal peptide antigens:
  • Nuclear LIM interactor (LDB1_HUMAN)
  • Nuclear LIM interactor (Q9Y4X6_HUMAN)

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

Function for LDB1 Gene

Molecular function for LDB1 Gene

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).
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)

Phenotypes From GWAS Catalog for LDB1 Gene

Gene Ontology (GO) - Molecular Function for LDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001102 RNA polymerase II activating transcription factor binding IBA,IPI 16314316
GO:0001158 enhancer sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA --
GO:0003712 transcription coregulator activity 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:
  • Ldb1 Ldb1<tm1.1Gsv>
  • Ldb1 Ldb1<tm1Lmgd>

Animal Model Products

CRISPR Products

miRNA for LDB1 Gene

miRTarBase miRNAs that target LDB1

Clone Products

  • Applied Biological Materials (abm): Clones for LDB1 - Now 50% OFF >
  • * LDB1 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * LDB1 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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

Subcellular locations from the

Human Protein Atlas (HPA)

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,IBA --
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex IDA 16314316
GO:0031252 cell leading edge IEA,ISS --
genes like me logo Genes that share ontologies with LDB1: view

Pathways & Interactions for LDB1 Gene

PathCards logo

SuperPathways 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

SIGNOR curated interactions for LDB1 Gene

Activates:

Gene Ontology (GO) - Biological Process for LDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IBA 21873635
GO:0000972 transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ISS,IEA --
GO:0001702 gastrulation with mouth forming second IEA --
GO:0001942 hair follicle development IEA --
GO:0006351 transcription, DNA-templated NAS 12792813
genes like me logo Genes that share ontologies with LDB1: view

Drugs & Compounds for LDB1 Gene

No Compound Related Data Available

Transcripts for LDB1 Gene

mRNA/cDNA for LDB1 Gene

Unigene Clusters for LDB1 Gene

LIM domain binding 1:
Representative Sequences:

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for LDB1 - Now 50% OFF >
  • * LDB1 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * LDB1 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

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 CGAP 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, 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.

Evidence on tissue expression from TISSUES for LDB1 Gene

  • Nervous system(4.6)
  • Muscle(4.4)
  • Intestine(2.1)
  • Kidney(2)
genes like me logo Genes that share expression patterns with LDB1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 35 34
  • 99.91 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LDB1 35
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LDB1 35
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LDB1 35 34
  • 96.43 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LDB1 35 34
  • 95.8 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ldb1 34
  • 94.31 (n)
mouse
(Mus musculus)
Mammalia Ldb1 17 35 34
  • 94.22 (n)
chicken
(Gallus gallus)
Aves LDB1 35 34
  • 88.65 (n)
OneToOne
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 35 36
  • 39 (a)
OneToOne
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)
Aminode:
Evolutionary constrained regions (ECRs) for LDB1: view image

Paralogs for LDB1 Gene

Paralogs for LDB1 Gene

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

  • LDB1_HUMAN
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 Variation AA Info Type
rs990101456 A colorectal cancer sample 102,109,138(-) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1000022469 -- 102,114,448(-) T/G 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant
rs1000151858 -- 102,111,942(-) T/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000206814 -- 102,120,436(-) CCCCCC/CCCCCCC 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000435263 -- 102,118,944(-) T/G genic_upstream_transcript_variant, intron_variant

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)

Additional Variant Information for LDB1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for LDB1 Gene

Additional Disease Information for LDB1

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

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 23 58
  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) 2 3 4 58
  3. Regulation of estrogen-dependent transcription by the LIM cofactors CLIM and RLIM in breast cancer. (PMID: 19117995) Johnsen SA … Bach I (Cancer research 2009) 3 4 58
  4. Assembly of the oncogenic DNA-binding complex LMO2-Ldb1-TAL1-E12. (PMID: 17910069) Ryan DP … Matthews JM (Proteins 2008) 3 23 58
  5. Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes. (PMID: 18583962) Bhati M … Matthews JM (The EMBO journal 2008) 3 23 58

Products for LDB1 Gene

Sources for LDB1 Gene

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