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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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