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Ldb2 LIM domain binding 2 [ Mus musculus (house mouse) ]

Gene ID: 16826, updated on 21-Apr-2024

Summary

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Official Symbol
Ldb2provided by MGI
Official Full Name
LIM domain binding 2provided by MGI
Primary source
MGI:MGI:894670
See related
Ensembl:ENSMUSG00000039706 AllianceGenome:MGI:894670
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Ldb3; CLIM1; CLP-36
Summary
Enables LIM domain binding activity and enzyme binding activity. Involved in regulation of cell migration and regulation of kinase activity. Acts upstream of or within several processes, including epithelial structure maintenance; hair follicle development; and somatic stem cell population maintenance. Located in cell leading edge. Part of transcription regulator complex. Is expressed in several structures, including brain; branchial arch; eye; genitourinary system; and limb. Orthologous to human LDB2 (LIM domain binding 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in lung adult (RPKM 18.1), limb E14.5 (RPKM 9.7) and 21 other tissues See more
Orthologs
human all
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Genomic context

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Location:
5 B3; 5 24.24 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (44593292..44957466, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (44435955..44799759, complement)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 36017 Neighboring gene predicted gene 5865 Neighboring gene predicted gene, 40297 Neighboring gene predicted gene, 36076 Neighboring gene RIKEN cDNA 4930431F12 gene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. CLP36 promotes p53 deficient sarcoma progression through suppression of atrophin-1 interacting protein-4 (AIP-4)-dependent degradation of YAP1. Lu Y, et al. Theranostics, 2022. PMID 35836803, Free PMC Article
  2. Autophagy protects cardiomyocytes from the myocardial ischaemia-reperfusion injury through the clearance of CLP36. Li S, et al. Open Biol, 2016 Aug. PMID 27512143, Free PMC Article
  3. Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study. Hägg S, et al. PLoS Genet, 2009 Dec. PMID 19997623, Free PMC Article
  4. Characterization of interaction between CLP36 and palladin. Maeda M, et al. FEBS J, 2009 May. PMID 19366376
  5. Proteasomal selection of multiprotein complexes recruited by LIM homeodomain transcription factors. Güngör C, et al. Proc Natl Acad Sci U S A, 2007 Sep 18. PMID 17848518, Free PMC Article

See all (77) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CLP36 promotes p53 deficient sarcoma progression through suppression of atrophin-1 interacting protein-4 (AIP-4)-dependent degradation of YAP1.
    Title: CLP36 promotes p53 deficient sarcoma progression through suppression of atrophin-1 interacting protein-4 (AIP-4)-dependent degradation of YAP1.
  2. Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia.
    Title: Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia.
  3. Animals lacking both Ldb1 and Ldb2 uncover the requirement for Ldb2 during corticospinal motor neuron differentiation
    Title: Compensatory Actions of Ldb Adaptor Proteins During Corticospinal Motor Neuron Differentiation.
  4. Results show that CLP36 is accumulated in Atg7-deficient cardiomyocytes, and suggest that autophagy may protect cardiomyocytes from the ischemia-reperfusion injury through the clearance of CLP36.
    Title: Autophagy protects cardiomyocytes from the myocardial ischaemia-reperfusion injury through the clearance of CLP36.
  5. An intricate regulatory network exists that is mediated by Ldb1 and Ldb2, and promotes retinal progenitor cells proliferation and multipotency; it also controls specification of mammalian retina cells.
    Title: The stage-dependent roles of Ldb1 and functional redundancy with Ldb2 in mammalian retinogenesis.
  6. CLIM interacts with estrogen receptor alpha at the H19 locus, potentially explaining the higher expression of H19 in female than male corneas.
    Title: Cofactors of LIM Domains Associate with Estrogen Receptor α to Regulate the Expression of Noncoding RNA H19 and Corneal Epithelial Progenitor Cell Function.
  7. In Ldlr(-/-)Apob(100/100) mice, loss of Ldb2 increased atherosclerotic lesion size approximately 2-fold and decreased plaque stability.
    Title: Lim domain binding 2: a key driver of transendothelial migration of leukocytes and atherosclerosis.
  8. Isl1 and the Ldb co-regulators of transcription are essential early determinants of mouse limb development
    Title: Isl1 and Ldb co-regulators of transcription are essential early determinants of mouse limb development.
  9. Data show an inhibitory function of CLP-36 in GPVI immunoreceptor tyrosine-based activation motif signaling and as a key regulator of arterial thrombosis.
    Title: CLP36 is a negative regulator of glycoprotein VI signaling in platelets.
  10. The transcription co-factor LIM domain binding 2 (LDB2) was identified as a potential high-hierarchy regulator of the atherosclerosis-module.
    Title: Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (2) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables LIM domain binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of cellular component biogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within epithelial structure maintenance IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within hair follicle development IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within positive regulation of cellular component biogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within somatic stem cell population maintenance IGI
Inferred from Genetic Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in cell leading edge IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  
part_of transcription regulator complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription regulator complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
LIM domain-binding protein 2
Names
LIM domain-binding factor CLIM1
carboxyl-terminal LIM domain-binding protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001077398.2 → NP_001070866.1  LIM domain-binding protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001070866.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site and contains an alternate exon in the 3' coding region, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK146860, BB679977, BY068608
    Consensus CDS
    CCDS80278.1
    UniProtKB/Swiss-Prot
    O55203
    Related
    ENSMUSP00000143775.2, ENSMUST00000199256.5
    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  2. NM_001286348.1 → NP_001273277.1  LIM domain-binding protein 2 isoform 3

    See identical proteins and their annotated locations for NP_001273277.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate exon in the 3' coding region and differs in the 3' UTR, compared to variant 1. It encodes isoform 3, which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK147160, BB679977, BC079611, BY068608
    Consensus CDS
    CCDS80276.1
    UniProtKB/Swiss-Prot
    O55203
    Related
    ENSMUSP00000142442.2, ENSMUST00000199534.5
    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  3. NM_001347349.1 → NP_001334278.1  LIM domain-binding protein 2 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC102487, AC111033, AC129607
    Consensus CDS
    CCDS84878.1
    UniProtKB/TrEMBL
    A0A0G2JFS7
    Related
    ENSMUSP00000143289.2, ENSMUST00000199261.2
    Conserved Domains (2) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein
    pfam17916
    Location:296 → 324
    LID; LIM interaction domain (LID)

  4. NM_001359070.1 → NP_001345999.1  LIM domain-binding protein 2 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses two alternate in-frame splice junctions in the 3' coding sequence compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC102487, AC111033, AC129607
    Conserved Domains (2) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein
    pfam17916
    Location:295 → 323
    LID; LIM interaction domain (LID)

  5. NM_001359071.1 → NP_001346000.1  LIM domain-binding protein 2 isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate 3' splice junction compared to variant 1. The resulting isoform (6) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC102487, AC111033, AC129607
    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  6. NM_010698.4 → NP_034828.3  LIM domain-binding protein 2 isoform 1

    See identical proteins and their annotated locations for NP_034828.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK146860, BB679977, BC079611, BY068608
    Consensus CDS
    CCDS19271.1
    UniProtKB/Swiss-Prot
    O55203, O55205, Q3UHY1, Q6AXE6
    Related
    ENSMUSP00000067737.6, ENSMUST00000070748.10
    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    44593292..44957466 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036164828.1 → XP_036020721.1  LIM domain-binding protein 2 isoform X10

    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  2. XM_036164830.1 → XP_036020723.1  LIM domain-binding protein 2 isoform X11

    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  3. XM_017320689.3 → XP_017176178.1  LIM domain-binding protein 2 isoform X9

    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  4. XM_036164827.1 → XP_036020720.1  LIM domain-binding protein 2 isoform X5

    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  5. XM_030254170.2 → XP_030110030.1  LIM domain-binding protein 2 isoform X6

    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  6. XM_036164825.1 → XP_036020718.1  LIM domain-binding protein 2 isoform X3

    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  7. XM_030254171.2 → XP_030110031.1  LIM domain-binding protein 2 isoform X8

    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  8. XM_006503752.4 → XP_006503815.1  LIM domain-binding protein 2 isoform X1

    Conserved Domains (2) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein
    pfam17916
    Location:297 → 325
    LID; LIM interaction domain (LID)

  9. XM_006503758.5 → XP_006503821.1  LIM domain-binding protein 2 isoform X7

    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  10. XM_036164826.1 → XP_036020719.1  LIM domain-binding protein 2 isoform X4

    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  11. XM_006503754.5 → XP_006503817.1  LIM domain-binding protein 2 isoform X2

    See identical proteins and their annotated locations for XP_006503817.1

    UniProtKB/Swiss-Prot
    O55203
    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O55203.2 GenPept UniProtKB/Swiss-Prot:O55203

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