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    Lmo4 LIM domain only 4 [ Mus musculus (house mouse) ]

    Gene ID: 16911, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Lmo4provided by MGI
    Official Full Name
    LIM domain only 4provided by MGI
    Primary source
    MGI:MGI:109360
    See related
    Ensembl:ENSMUSG00000028266 AllianceGenome:MGI:109360
    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
    Crp3; Etohi4; A730077C12Rik
    Summary
    Enables DNA-binding transcription factor binding activity and transcription corepressor activity. Involved in several processes, including negative regulation of transcription by RNA polymerase II; nervous system development; and positive regulation of kinase activity. Acts upstream of or within several processes, including cell differentiation in spinal cord; thymus development; and ventricular septum development. Located in cell leading edge and nucleus. Part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; integumental system; and sensory organ. Used to study anencephaly. Orthologous to human LMO4 (LIM domain only 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in CNS E18 (RPKM 58.7), cortex adult (RPKM 56.2) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Lmo4 in Genome Data Viewer
    Location:
    3 H2; 3 68.61 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (143894291..143911016, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (144188530..144205255, complement)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 34078 Neighboring gene predicted gene, 34162 Neighboring gene STARR-seq mESC enhancer starr_09175 Neighboring gene STARR-positive B cell enhancer ABC_E1027 Neighboring gene predicted gene, 46828 Neighboring gene STARR-positive B cell enhancer mm9_chr3:143905070-143905370 Neighboring gene predicted gene, 34434

    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. Lmo4 in the basolateral complex of the amygdala modulates fear learning. Maiya R, et al. PLoS One, 2012. PMID 22509321, Free PMC Article
    2. [Gene expression of transcription regulator LMO 4 in tooth morphogenesis]. Zhang L, et al. Zhonghua Kou Qiang Yi Xue Za Zhi, 2005 Sep. PMID 16255927
    3. Loss of the LIM domain protein Lmo4 in the mammary gland during pregnancy impedes lobuloalveolar development. Sum EY, et al. Oncogene, 2005 Jul 14. PMID 15856027
    4. LMO4 mRNA stability is regulated by extracellular ATP in F11 cells. Chen HH, et al. Biochem Biophys Res Commun, 2007 May 25. PMID 17418808
    5. LIM domain only 4 protein promotes granulocyte colony-stimulating factor-induced signaling in neurons. Gomez-Smith M, et al. Cell Mol Life Sci, 2010 Mar. PMID 19997957, Free PMC Article

    See all (167) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Lmo4 synergizes with Fezf2 to promote direct in vivo reprogramming of upper layer cortical neurons and cortical glia towards deep-layer neuron identities.
      Title: Lmo4 synergizes with Fezf2 to promote direct in vivo reprogramming of upper layer cortical neurons and cortical glia towards deep-layer neuron identities.
    2. Lmo4 Deficiency Enhances Susceptibility to Cisplatin-Induced Cochlear Apoptosis and Hearing Loss.
      Title: Lmo4 Deficiency Enhances Susceptibility to Cisplatin-Induced Cochlear Apoptosis and Hearing Loss.
    3. Differential regulation of alcohol consumption and reward by the transcriptional cofactor LMO4.
      Title: Differential regulation of alcohol consumption and reward by the transcriptional cofactor LMO4.
    4. Lmo4-resistin signaling contributes to adipose tissue-liver crosstalk upon weight cycling.
      Title: Lmo4-resistin signaling contributes to adipose tissue-liver crosstalk upon weight cycling.
    5. Findings indicate that the YEATS domain-containing protein 4 (Yeats4)-LIM domain transcription factor LMO4 (Lmo4) axis is required for Innate lymphoid cells (ILCs) lineage commitment.
      Title: Yeats4 drives ILC lineage commitment via activation of Lmo4 transcription.
    6. we provide genetic evidence that a transcription factor, Lmx1a, interacts with its negative regulator, Lmo4, to pattern various vestibular and auditory components of the mammalian inner ear.
      Title: Reciprocal Negative Regulation Between Lmx1a and Lmo4 Is Required for Inner Ear Formation.
    7. Multiple roles of Lmo4 during retinal development.
      Title: Lmo4 and Other LIM domain only factors are necessary and sufficient for multiple retinal cell type development.
    8. These results reveal a novel, LMO4-dependent transcriptional program within the basolateral amygdala that is essential to cue-reward learning.
      Title: A Selective Role for Lmo4 in Cue-Reward Learning.
    9. activation of SLK by haptotactic signals requires its recruitment to the leading edge by LMO4 in a Src-dependent manner.
      Title: Recruitment and activation of SLK at the leading edge of migrating cells requires Src family kinase activity and the LIM-only protein 4.
    10. Thus, our study reveals an essential requirement for LMO4 to modulate central insulin signaling.
      Title: LMO4 is required to maintain hypothalamic insulin signaling.
    Submit: New GeneRIF Correction See all GeneRIFs (40)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Gene trapped (1) 
    • Targeted (10)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in motor neuron axon guidance IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of protein-containing complex assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of protein-containing complex assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within neural tube closure IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neural tube closure IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of cell activation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of cell fate specification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within spinal cord association neuron differentiation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in spinal cord motor neuron cell fate specification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within spinal cord motor neuron differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within thymus development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within ventral spinal cord interneuron differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within ventricular septum development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cell leading edge IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    LIM domain transcription factor LMO4
    Names
    LIM domain only protein 4
    LMO-4
    breast tumor autoantigen
    ethanol induced 4

    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_001161769.1 → NP_001155241.1  LIM domain transcription factor LMO4

      See identical proteins and their annotated locations for NP_001155241.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC123883, AK138278, BY267947
      Consensus CDS
      CCDS51085.1
      UniProtKB/Swiss-Prot
      P61969
      UniProtKB/TrEMBL
      A0A0G2JDX9, Q542S1
      Related
      ENSMUSP00000113513.2, ENSMUST00000121796.8
      Conserved Domains (2) summary
      cd09386
      Location:23 → 77
      LIM1_LMO4; The first LIM domain of LMO4 (LIM domain only protein 4)
      cd09387
      Location:87 → 141
      LIM2_LMO4; The second LIM domain of LMO4 (LIM domain only protein 4)

    2. NM_001161770.1 → NP_001155242.1  LIM domain transcription factor LMO4

      See identical proteins and their annotated locations for NP_001155242.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC123883, AK138278
      Consensus CDS
      CCDS51085.1
      UniProtKB/Swiss-Prot
      P61969
      UniProtKB/TrEMBL
      A0A0G2JDX9, Q542S1
      Related
      ENSMUSP00000113865.2, ENSMUST00000121112.6
      Conserved Domains (2) summary
      cd09386
      Location:23 → 77
      LIM1_LMO4; The first LIM domain of LMO4 (LIM domain only protein 4)
      cd09387
      Location:87 → 141
      LIM2_LMO4; The second LIM domain of LMO4 (LIM domain only protein 4)

    3. NM_010723.3 → NP_034853.1  LIM domain transcription factor LMO4

      See identical proteins and their annotated locations for NP_034853.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC123883, AK080534
      Consensus CDS
      CCDS51085.1
      UniProtKB/Swiss-Prot
      P61969
      UniProtKB/TrEMBL
      A0A0G2JDX9, Q542S1
      Related
      ENSMUSP00000113840.2, ENSMUST00000120539.8
      Conserved Domains (2) summary
      cd09386
      Location:23 → 77
      LIM1_LMO4; The first LIM domain of LMO4 (LIM domain only protein 4)
      cd09387
      Location:87 → 141
      LIM2_LMO4; The second LIM domain of LMO4 (LIM domain only protein 4)

    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_000069.7 Reference GRCm39 C57BL/6J

      Range
      143894291..143911016 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P61969.1 GenPept UniProtKB/Swiss-Prot:P61969

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