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

Gene ID: 8543, updated on 10-Dec-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
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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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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
    UniProtKB/TrEMBL
    A8K963

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
    UniProtKB/TrEMBL
    A8K963
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P61968.1 GenPept UniProtKB/Swiss-Prot:P61968

Gene LinkOut

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