LMO4 Gene (Protein Coding)

LIM Domain Only 4

GC01P087329
GIFtS:
39
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] See more...

Aliases for LMO4 Gene

Aliases for LMO4 Gene

  • LIM Domain Only 4 2 3 5
  • LIM Domain Transcription Factor LMO4 3 4
  • LIM Domain Only Protein 4 3 4
  • Breast Tumor Autoantigen 3 4
  • LMO-4 3 4
  • LIM-Only 4 Protein 3
  • LMO4 5

External Ids for LMO4 Gene

Previous GeneCards Identifiers for LMO4 Gene

  • GC01P088293
  • GC01P086963
  • GC01P087086
  • GC01P087216
  • GC01P087506
  • GC01P087566
  • GC01P087794
  • GC01P085907

Summaries for LMO4 Gene

Entrez Gene Summary for LMO4 Gene

  • 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]

GeneCards Summary for LMO4 Gene

LMO4 (LIM Domain Only 4) is a Protein Coding gene. Diseases associated with LMO4 include Precursor T-Cell Acute Lymphoblastic Leukemia and Attention Deficit-Hyperactivity Disorder. Among its related pathways are Neuroscience and IL-6 signaling pathway. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and enhancer sequence-specific DNA binding. An important paralog of this gene is LMX1B.

UniProtKB/Swiss-Prot Summary for LMO4 Gene

Gene Wiki entry for LMO4 Gene

Additional gene information for LMO4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LMO4 Gene

Genomics for LMO4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for LMO4 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01J087327 Promoter/Enhancer 3.3 VISTA UCNEbase EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +3.2 3221 10.2 SP1 HNRNPL CREB1 CTCF TEAD4 PRDM10 ZNF629 IKZF1 KDM1A ZNF692 LMO4 ODF2L lnc-SELENOF-12 lnc-HS2ST1-1
GH01J087131 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 4.4 -196.8 -196752 1.7 BRCA1 GATAD2A CTCF BACH1 LARP7 ZNF143 ZIC2 PATZ1 REST RAD21 LINC01140 LMO4 lnc-SELENOF-9 lnc-SELENOF-10 ENSG00000267561
GH01J087294 Enhancer 0.6 Ensembl CraniofacialAtlas 11.9 -32.6 -32579 4.2 NR2F1 SPI1 EBF1 SMARCA4 KLF1 ZNF24 LMO4 lnc-SELENOF-11 FJ601684-024 ENSG00000267561
GH01J087287 Enhancer 0.5 Ensembl 11.9 -41.5 -41536 0.7 SIX5 ZNF143 USF2 USF1 HCFC1 THAP11 FOS RAD51 NFYC LMO4 lnc-SELENOF-11 FJ601684-024 LINC02801 ENSG00000267561
GH01J087293 Enhancer 0.4 UCNEbase 11.9 -35.2 -35161 0.2 CTCF LMO4 lnc-SELENOF-11 FJ601684-024 LINC02801 ENSG00000267561
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LMO4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LMO4

Top Transcription factor binding sites by QIAGEN in the LMO4 gene promoter:
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AP-2gamma
  • Oct-B1
  • oct-B2
  • oct-B3
  • POU2F1a
  • SRY
  • STAT3

Genomic Locations for LMO4 Gene

Genomic Locations for LMO4 Gene
chr1:87,328,880-87,348,923
(GRCh38/hg38)
Size:
20,044 bases
Orientation:
Plus strand
chr1:87,794,151-87,814,606
(GRCh37/hg19)
Size:
20,456 bases
Orientation:
Plus strand

Genomic View for LMO4 Gene

Genes around LMO4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LMO4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LMO4 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for LMO4 Gene

Proteins for LMO4 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for LMO4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P61968-LMO4_HUMAN
    Recommended name:
    LIM domain transcription factor LMO4
    Protein Accession:
    P61968
    Secondary Accessions:
    • D3DT23
    • O00158
    • O88894

    Protein attributes for LMO4 Gene

    Size:
    165 amino acids
    Molecular mass:
    17994 Da
    Quaternary structure:
    • Interacts strongly with LDBS. Interacts with DEAF1; LMO4 blocks export from nucleus. Interacts with CLIM1 and CLIM2. Interacts (via the LIM zinc-binding domain 1) with RBBP8. Interacts with BRCA1 (via the BRCT domains); the interaction represses BRCA1 transcriptional activity (By similarity).

    Three dimensional structures from OCA and Proteopedia for LMO4 Gene

neXtProt entry for LMO4 Gene

Protein Expression for LMO4 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for LMO4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LMO4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LMO4 Gene

Domains & Families for LMO4 Gene

Gene Families for LMO4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LMO4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LMO4 Gene

GenScript: Design optimal peptide antigens:
  • LIM domain only protein 4 (LMO4_HUMAN)
genes like me logo Genes that share domains with LMO4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LMO4 Gene

Function for LMO4 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for LMO4 Gene

UniProtKB/Swiss-Prot Function:
Probable transcriptional factor.

Phenotypes From GWAS Catalog for LMO4 Gene

Gene Ontology (GO) - Molecular Function for LMO4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000987 proximal promoter sequence-specific DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity TAS 10209267
GO:0005515 protein binding IPI 15231748
GO:0008134 transcription factor binding ISS --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LMO4: view
genes like me logo Genes that share phenotypes with LMO4: view

Animal Models for LMO4 Gene

MGI Knock Outs for LMO4:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LMO4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for LMO4 Gene

Localization for LMO4 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LMO4 gene
Compartment Confidence
nucleus 4
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Midbody ring (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LMO4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005667 transcription factor complex ISS --
GO:0031252 cell leading edge ISS --
genes like me logo Genes that share ontologies with LMO4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for LMO4 Gene

Pathways & Interactions for LMO4 Gene

genes like me logo Genes that share pathways with LMO4: view

Pathways by source for LMO4 Gene

1 BioSystems pathway for LMO4 Gene
1 Cell Signaling Technology pathway for LMO4 Gene

Gene Ontology (GO) - Biological Process for LMO4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001843 neural tube closure ISS --
GO:0003281 ventricular septum development IEA --
GO:0006366 transcription by RNA polymerase II ISS --
GO:0021514 ventral spinal cord interneuron differentiation IEA --
GO:0021522 spinal cord motor neuron differentiation IEA --
genes like me logo Genes that share ontologies with LMO4: view

No data available for SIGNOR curated interactions for LMO4 Gene

Drugs & Compounds for LMO4 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for LMO4 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for LMO4 Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LMO4

Alternative Splicing Database (ASD) splice patterns (SP) for LMO4 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c
SP1: - - - -
SP2: -
SP3: - - -
SP4: - -
SP5:

Relevant External Links for LMO4 Gene

GeneLoc Exon Structure for
LMO4

Expression for LMO4 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LMO4 Gene

mRNA expression in normal human tissues for LMO4 Gene
mRNA expression by GTEx for LMO4 GenemRNA expression by BioGPS for LMO4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LMO4 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x5.2), Brain - Anterior cingulate cortex (BA24) (x4.6), and Brain - Cortex (x4.3).

Protein differential expression in normal tissues from HIPED for LMO4 Gene

This gene is overexpressed in Testis (23.0), Ovary (18.4), NK cells (14.8), and Fetal heart (12.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LMO4 Gene



Protein tissue co-expression partners for LMO4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LMO4

SOURCE GeneReport for Unigene cluster for LMO4 Gene:

Hs.436792

Evidence on tissue expression from TISSUES for LMO4 Gene

  • Nervous system(4.9)
  • Lung(4.5)
  • Eye(4.4)
genes like me logo Genes that share expression patterns with LMO4: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LMO4 Gene

Orthologs for LMO4 Gene

This gene was present in the common ancestor of animals.

Orthologs for LMO4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia LMO4 30 31
  • 99.8 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia LMO4 31
  • 99 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia LMO4 31
  • 99 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia LMO4 30 31
  • 97.58 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia LMO4 30 31
  • 97.17 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Lmo4 30
  • 96.16 (n)
Mouse
(Mus musculus)
 Mammalia Lmo4 30 17 31
  • 95.76 (n)
 OneToOne
Chicken
(Gallus gallus)
 Aves LMO4 30 31
  • 92.53 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia LMO4 31
  • 99 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia lmo4.1 30
  • 86.67 (n)
Str.145 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.24588 30
Zebrafish
(Danio rerio)
 Actinopterygii lmo4b 30 31
  • 81.41 (n)
 OneToOne
Dr.19236 30
Fruit Fly
(Drosophila melanogaster)
 Insecta CG5708 30 31 32
  • 56.94 (n)
 OneToOne
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 45 (a)
 OneToOne
Species where no ortholog for LMO4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for LMO4 Gene

ENSEMBL:
Gene Tree for LMO4 (if available)
TreeFam:
Gene Tree for LMO4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LMO4: view image

Paralogs for LMO4 Gene

Paralogs for LMO4 Gene

(17) SIMAP similar genes for LMO4 Gene using alignment to 1 proteins:

  • LMO4_HUMAN
genes like me logo Genes that share paralogs with LMO4: view

Variants for LMO4 Gene

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  1. SNP Genotyping and Copy Number Assay

Additional dbSNP identifiers (rs#s) for LMO4 Gene

Structural Variations from Database of Genomic Variants (DGV) for LMO4 Gene

Variant ID Type Subtype PubMed ID
esv24748 CNV gain 19812545
nsv1077471 CNV deletion 25765185

Variation tolerance for LMO4 Gene

Residual Variation Intolerance Score: 39.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.28; 6.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LMO4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LMO4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LMO4 Gene

Disorders for LMO4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LMO4 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
precursor t-cell acute lymphoblastic leukemia
  • precursor t-cell acute lymphoblastic leukemia/lymphoma
attention deficit-hyperactivity disorder
  • adhd
- elite association - COSMIC cancer census association via MalaCards
Search LMO4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LMO4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with LMO4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LMO4 Gene

Publications for LMO4 Gene

  1. Case-control study of six genes asymmetrically expressed in the two cerebral hemispheres: association of BAIAP2 with attention-deficit/hyperactivity disorder. (PMID: 19733838) Ribasés M … Cormand B (Biological psychiatry 2009) 3 23 41
  2. Molecular cloning of LMO41, a new human LIM domain gene. (PMID: 10209267) Racevskis J … Ruan H (Biochimica et biophysica acta 1999) 3 4 23
  3. Evaluating new candidate SNPs as low penetrance risk factors in sporadic breast cancer: a two-stage Spanish case-control study. (PMID: 18950845) Vega A … Carracedo A (Gynecologic oncology 2009) 3 41
  4. Genome-wide association scan identifies candidate polymorphisms associated with differential response to anti-TNF treatment in rheumatoid arthritis. (PMID: 18615156) Liu C … Gregersen PK (Molecular medicine (Cambridge, Mass.) 2008) 3 41
  5. LIM only 4 is overexpressed in late stage pancreas cancer. (PMID: 19099607) Yu J … Tanaka M (Molecular cancer 2008) 3 23

ExternalLinks

View latest publications for LMO4 gene in Mastermind

Products for LMO4 Gene

Sources for LMO4 Gene