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    Limd1 LIM domains containing 1 [ Mus musculus (house mouse) ]

    Gene ID: 29806, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Limd1provided by MGI
    Official Full Name
    LIM domains containing 1provided by MGI
    Primary source
    MGI:MGI:1352502
    See related
    Ensembl:ENSMUSG00000025239 AllianceGenome:MGI:1352502
    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
    D9Ertd192e
    Summary
    Enables transcription corepressor activity. Involved in negative regulation of canonical Wnt signaling pathway; negative regulation of osteoblast differentiation; and osteoblast development. Located in cytoplasm. Is expressed in several structures, including branchial arch; early conceptus; genitourinary system; hemolymphoid system; and limb. Orthologous to human LIMD1 (LIM domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in large intestine adult (RPKM 22.1), spleen adult (RPKM 19.7) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    9 F4; 9 74.0 cM
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (123306790..123350617)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (123478661..123521552)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene leucyl-tRNA synthetase, mitochondrial Neighboring gene predicted gene, 46137 Neighboring gene STARR-seq mESC enhancer starr_25567 Neighboring gene predicted gene, 40586 Neighboring gene STARR-positive B cell enhancer ABC_E5115 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:123428421-123428574 Neighboring gene STARR-positive B cell enhancer ABC_E717 Neighboring gene nuclear encoded tRNA arginine 2 (anticodon ACG) Neighboring gene SAC1 suppressor of actin mutations 1-like (yeast)

    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. LIMD1 phase separation contributes to cellular mechanics and durotaxis by regulating focal adhesion dynamics in response to force. Wang Y, et al. Dev Cell, 2021 May 3. PMID 33891898
    2. The LIM protein LIMD1 influences osteoblast differentiation and function. Luderer HF, et al. Exp Cell Res, 2008 Sep 10. PMID 18657804, Free PMC Article
    3. The chromosome 3p21.3-encoded gene, LIMD1, is a critical tumor suppressor involved in human lung cancer development. Sharp TV, et al. Proc Natl Acad Sci U S A, 2008 Dec 16. PMID 19060205, Free PMC Article
    4. A novel gene containing LIM domains (LIMD1) is located within the common eliminated region 1 (C3CER1) in 3p21.3. Kiss H, et al. Hum Genet, 1999 Dec. PMID 10647888
    5. TGFβ regulates epithelial-mesenchymal interactions through WNT signaling activity to control muscle development in the soft palate. Iwata J, et al. Development, 2014 Feb. PMID 24496627, Free PMC Article

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LIMD1 phase separation contributes to cellular mechanics and durotaxis by regulating focal adhesion dynamics in response to force.
      Title: LIMD1 phase separation contributes to cellular mechanics and durotaxis by regulating focal adhesion dynamics in response to force.
    2. Limd1 influences not only stress osteoclastogenesis but also osteoblast function and osteoblast progenitor commitment. Together, these data identify Limd1 as a novel regulator of both bone osetoclast and bone osteoblast development and function.
      Title: The LIM protein LIMD1 influences osteoblast differentiation and function.
    3. Limd1 regulates AP-1 activation through an interaction with Traf6 to influence osteoclast development
      Title: The LIM protein, Limd1, regulates AP-1 activation through an interaction with Traf6 to influence osteoclast development.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (1)  1 citation
    • Endonuclease-mediated (3) 

    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription corepressor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription corepressor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within P-body assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cytoskeleton organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in miRNA-mediated gene silencing by inhibition of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within miRNA-mediated post-transcriptional gene silencing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of canonical Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of hippo signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of hippo signaling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of osteoblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in osteoblast development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in phosphorylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cell shape ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulatory ncRNA-mediated gene silencing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to hypoxia IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to hypoxia ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in P-body ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of RISC complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in adherens junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in anchoring junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in focal adhesion 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
    		  

    General protein information

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    Preferred Names
    LIM domain-containing 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_001410486.1 → NP_001397415.1  LIM domain-containing protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC125254, AC132852

    2. NM_013860.3 → NP_038888.2  LIM domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_038888.2

      Status: VALIDATED

      Source sequence(s)
      AC125254, AC132852
      Consensus CDS
      CCDS23660.1
      UniProtKB/Swiss-Prot
      Q8C8G4, Q9CW55, Q9QXD8
      Related
      ENSMUSP00000026269.3, ENSMUST00000026269.4
      Conserved Domains (3) summary
      cd09352
      Location:464 → 517
      LIM1_Ajuba_like; The first LIM domain of Ajuba-like proteins
      cd09355
      Location:529 → 581
      LIM2_Ajuba_like; The second LIM domain of Ajuba-like proteins
      cd09438
      Location:589 → 650
      LIM3_Ajuba_like; The third LIM domain of Ajuba-like proteins

    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_000075.7 Reference GRCm39 C57BL/6J

      Range
      123306790..123350617
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036155046.1 → XP_036010939.1  LIM domain-containing protein 1 isoform X2

      Conserved Domains (2) summary
      PRK04654
      Location:92 → 162
      PRK04654; sec-independent translocase; Provisional
      cl02475
      Location:464 → 495
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

    2. XM_011242977.3 → XP_011241279.1  LIM domain-containing protein 1 isoform X3

      Conserved Domains (1) summary
      PRK04654
      Location:92 → 162
      PRK04654; sec-independent translocase; Provisional
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9QXD8.2 GenPept UniProtKB/Swiss-Prot:Q9QXD8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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