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    LMO4 LIM domain only 4 [ Homo sapiens (human) ]

    Gene ID: 8543, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LMO4provided by HGNC
    Official Full Name
    LIM domain only 4provided by HGNC
    Primary source
    HGNC:HGNC:6644
    See related
    Ensembl:ENSG00000143013 MIM:603129; AllianceGenome:HGNC:6644
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene encodes a cysteine-rich protein that contains two LIM domains but lacks a DNA-binding homeodomain. The encoded protein may play a role as a transcriptional regulator or as an oncogene. [provided by RefSeq, Aug 2008]
    Expression
    Ubiquitous expression in brain (RPKM 22.8), stomach (RPKM 12.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LMO4 in Genome Data Viewer
    Location:
    1p22.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (87328880..87348923)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (87171579..87191625)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (87794563..87814606)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1140 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:87612561-87613060 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:87614396-87615060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:87616858-87617456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:87617457-87618055 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:87666183-87666684 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:87666685-87667184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1043 Neighboring gene long intergenic non-protein coding RNA 2801 Neighboring gene Sharpr-MPRA regulatory region 9281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1045 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:87794473-87795050 Neighboring gene VISTA enhancer hs809 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:87797046-87797684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:87797685-87798323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1049 Neighboring gene VISTA enhancers hs174 and hs322 Neighboring gene long intergenic non-protein coding RNA 1364 Neighboring gene uncharacterized LOC105378833

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. LIM only 4 is overexpressed in late stage pancreas cancer. Yu J, et al. Mol Cancer, 2008 Dec 22. PMID 19099607, Free PMC Article
    2. Repression of Lim only protein 4-activated transcription inhibits proliferation and induces apoptosis of normal mammary epithelial cells and breast cancer cells. Tian Y, et al. Clin Exp Metastasis, 2010 Oct. PMID 20526802
    3. LMO4 expression in squamous cell carcinoma of the anterior tongue. Kwong RA, et al. Histopathology, 2011 Feb. PMID 21362019
    4. Expression of LMO4 and outcome in pancreatic ductal adenocarcinoma. Murphy NC, et al. Br J Cancer, 2008 Feb 12. PMID 18231110, Free PMC Article
    5. Stabilization of a binary protein complex by intein-mediated cyclization. Jeffries CM, et al. Protein Sci, 2006 Nov. PMID 17001033, Free PMC Article

    See all (68) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. IL-6 Up-Regulates Expression of LIM-Domain Only Protein 4 in Psoriatic Keratinocytes through Activation of the MEK/ERK/NF-kappaB Pathway.
      Title: IL-6 Up-Regulates Expression of LIM-Domain Only Protein 4 in Psoriatic Keratinocytes through Activation of the MEK/ERK/NF-κB Pathway.
    2. CircLDLR Promotes Papillary Thyroid Carcinoma Tumorigenicity by Regulating miR-637/LMO4 Axis.
      Title: CircLDLR Promotes Papillary Thyroid Carcinoma Tumorigenicity by Regulating miR-637/LMO4 Axis.
    3. MicroRNA-139-5p Alleviates High Glucose-Triggered Human Retinal Pigment Epithelial Cell Injury by Targeting LIM-Only Factor 4.
      Title: MicroRNA-139-5p Alleviates High Glucose-Triggered Human Retinal Pigment Epithelial Cell Injury by Targeting LIM-Only Factor 4.
    4. Research and Clinical Significance of the Differentially Expressed Genes TP63 and LMO4 in Human Immunodeficiency Virus-Related Penile Squamous Cell Carcinoma.
      Title: Research and Clinical Significance of the Differentially Expressed Genes TP63 and LMO4 in Human Immunodeficiency Virus-Related Penile Squamous Cell Carcinoma.
    5. Long noncoding RNA SNHG1 promotes breast cancer progression by regulation of LMO4.
      Title: Long non‑coding RNA SNHG1 promotes breast cancer progression by regulation of LMO4.
    6. LMO4 appears to mediate IL-23-related responses in psoriatic keratinocytes and is a potential therapeutic target in psoriasis.
      Title: LMO4 Is a Disease-Provocative Transcription Coregulator Activated by IL-23 in Psoriatic Keratinocytes.
    7. Lmo4 participates in the regulation of lung epithelial cell proliferation but is not essential for tumor progression.
      Title: The LIM-domain only protein 4 contributes to lung epithelial cell proliferation but is not essential for tumor progression.
    8. LMO4 appears to form a hub in protein-protein interaction networks, linking numerous pathways within cells.
      Title: The structure of an LIM-only protein 4 (LMO4) and Deformed epidermal autoregulatory factor-1 (DEAF1) complex reveals a common mode of binding to LMO4.
    9. Clim2, in a complex with LMO4, supports mammary stem cells by directly targeting the Fgfr2 promoter in basal cells to increase its expression
      Title: The co-factor of LIM domains (CLIM/LDB/NLI) maintains basal mammary epithelial stem cells and promotes breast tumorigenesis.
    10. Existence of a region in the lateral portion of the mammalian cochlea that is competent to make an organ of Corti is demonstrated in the absence of LMO4 function.
      Title: LMO4 functions as a negative regulator of sensory organ formation in the mammalian cochlea.
    Submit: New GeneRIF Correction See all GeneRIFs (31)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association scan identifies candidate polymorphisms associated with differential response to anti-TNF treatment in rheumatoid arthritis.
    EBI GWAS Catalog
    Identification of nine novel loci associated with white blood cell subtypes in a Japanese population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    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 GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in motor neuron axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of protein-containing complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neural tube closure ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of kinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell activation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell fate specification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in spinal cord association neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spinal cord motor neuron cell fate specification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in thymus development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ventral spinal cord interneuron differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ventricular septum development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell leading edge ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of transcription regulator complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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

    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_001369491.1 → NP_001356420.1  LIM domain transcription factor LMO4

      Status: REVIEWED

      Source sequence(s)
      AC092392
      Consensus CDS
      CCDS713.1
      UniProtKB/Swiss-Prot
      D3DT23, O00158, O88894, P61968
      UniProtKB/TrEMBL
      A8K963
      Related
      ENSP00000359573.1, ENST00000370542.1
      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_006769.4 → NP_006760.1  LIM domain transcription factor LMO4

      See identical proteins and their annotated locations for NP_006760.1

      Status: REVIEWED

      Source sequence(s)
      AC092392, AI962216, BU580860, BU619915, U24576
      Consensus CDS
      CCDS713.1
      UniProtKB/Swiss-Prot
      D3DT23, O00158, O88894, P61968
      UniProtKB/TrEMBL
      A8K963
      Related
      ENSP00000359575.4, ENST00000370544.10
      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_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      87328880..87348923
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047432941.1 → XP_047288897.1  LIM domain transcription factor LMO4 isoform X1

      UniProtKB/Swiss-Prot
      D3DT23, O00158, O88894, P61968

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      87171579..87191625
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339323.1 → XP_054195298.1  LIM domain transcription factor LMO4 isoform X1

      UniProtKB/Swiss-Prot
      D3DT23, O00158, O88894, P61968
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P61968.1 GenPept UniProtKB/Swiss-Prot:P61968

    Gene LinkOut

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

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